# 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/Thermoplasma_volcanium_GSS1_uid57751/NC_002689.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/Thermoplasma_volcanium_GSS1_uid57751/NC_002689.PFam32-A
# per-seq hits tabular output:     /oak/stanford/groups/akundaje/marinovg/genomes/Archaea/Euryarchaeota/Thermoplasma_volcanium_GSS1_uid57751/NC_002689.PFam32-A.tblout
# number of worker threads:        20
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       gi|13540832|ref|NP_110520.1|  [L=360]
Description: GTPase [Thermoplasma volcanium GSS1]
Scores for complete 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-25   87.8   0.2      1e-24   86.6   0.2    1.7  1  MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
      1e-23   83.6   0.2      2e-23   82.7   0.2    1.7  1  MMR_HSR1      50S ribosome-binding GTPase
    3.6e-19   68.5   0.0    7.1e-19   67.6   0.0    1.5  1  TGS           TGS domain
    1.5e-15   57.1   0.2    1.2e-14   54.1   0.1    2.2  2  FeoB_N        Ferrous iron transport protein B
    0.00025   21.2   0.7       0.59   10.2   0.0    2.7  2  Dynamin_N     Dynamin family
      0.009   15.9   0.2      0.081   12.8   0.0    2.4  3  RsgA_GTPase   RsgA GTPase
  ------ inclusion threshold ------
      0.015   14.7   0.0      0.032   13.7   0.0    1.5  1  SRPRB         Signal recognition particle receptor beta subun
      0.044   12.8   0.3          3    6.7   0.0    2.8  2  MeaB          Methylmalonyl Co-A mutase-associated GTPase Mea
      0.054   13.0   0.3         13    5.3   0.1    3.3  3  GTP_EFTU      Elongation factor Tu GTP binding domain
      0.055   12.9   0.0         11    5.5   0.0    2.4  2  Arf           ADP-ribosylation factor family
      0.091   13.0   0.2       0.89    9.8   0.0    2.4  2  Roc           Ras of Complex, Roc, domain of DAPkinase
        2.5    8.2   6.7        7.5    6.7   1.9    2.8  2  DUF1192       Protein of unknown function (DUF1192)


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 !   86.6   0.2   6.8e-28     1e-24       2     106 .]     181     284 ..     180     284 .. 0.95

  Alignments for each domain:
  == domain 1  score: 86.6 bits;  conditional E-value: 6.8e-28
                  MMR_HSR1_Xtn   2 gGikitstvkltkldeetvkkilkeykihnaevliredvtvDdlidviegnrvYipclyvlNKiDlisleeldelarepns 82 
                                   gGi++++  +  ++d e +++++ke+k++na+v+ire+v+ Dd+i+++++n vYip+++++NKiD+    +++ l+r  ++
  gi|13540832|ref|NP_110520.1| 181 GGIRVHKPKN-VDIDSEYIRQLMKEFKLVNADVYIREQVNEDDIIEAVQKNYVYIPSIVAVNKIDMNGAFDTSPLTRFGEV 260
                                   9****97755.45****************************************************************99** PP

                  MMR_HSR1_Xtn  83 vviSaekelnldeLkekiweeLnL 106
                                   + +Sa++++++deL e i+++L+L
  gi|13540832|ref|NP_110520.1| 261 FKVSAKNRIGIDELREGIYRSLKL 284
                                   **********************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 !   82.7   0.2   1.3e-26     2e-23       2     100 ..      63     162 ..      62     242 .. 0.93

  Alignments for each domain:
  == domain 1  score: 82.7 bits;  conditional E-value: 1.3e-26
                                   EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSSHHHHHHHHHHHHHHHHC.TSEEEE CS
                      MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgkeielvDtpGliegaseekglgkaflalee.adlill 81 
                                   va+vG pNvGKS+L+n lt+++++v+++++tT++ + g +++kg ei+++D+pG+ie+as + g g+++l+  + adli++
  gi|13540832|ref|NP_110520.1|  63 VALVGFPNVGKSSLLNVLTNSESEVGSYAFTTLKAIPGVMEYKGAEIQILDLPGIIENASYGAGRGREILSTVRsADLIVI 143
                                   9**********************************************************************88868***** PP

                                   EEETTTTCSHHHHHHHHHH CS
                      MMR_HSR1  82 vvdaseeklkpldeeleel 100
                                   v d+++++l+++ +el + 
  gi|13540832|ref|NP_110520.1| 144 VTDVETGGLDKIVKELYNS 162
                                   ***8877787777776554 PP

>> TGS  TGS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.6   0.0   4.8e-22   7.1e-19       2      59 ..     286     357 ..     285     358 .. 0.98

  Alignments for each domain:
  == domain 1  score: 67.6 bits;  conditional E-value: 4.8e-22
                                   EEEE.TTSSEEE......EETTB-HHHHHHHHSTTHHHHEEEEEECS.......EEEETTSBB-SSEEEEEE CS
                           TGS   2 rvyt.PdGkvpd......lprgatveDfAykIhrslakkfiyAlVnG.......qrvgldhvLedgdvveIv 59 
                                   rvy+ +++ v+d      l+ g+tv+D+++kI+rsl+++f+yA++ G       qrvg+d++L d+d+v+I+
  gi|13540832|ref|NP_110520.1| 286 RVYLrNKAGVVDfdkpliLTDGSTVRDVCRKINRSLIDSFRYAIISGknrpigeQRVGIDYPLLDEDIVTII 357
                                   8**********************************************************************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 !   54.1   0.1   8.1e-18   1.2e-14       2      88 ..      62     147 ..      61     155 .. 0.86
   2 ?    0.4   0.0      0.27     4e+02     107     154 ..     235     276 ..     220     278 .. 0.67

  Alignments for each domain:
  == domain 1  score: 54.1 bits;  conditional E-value: 8.1e-18
                                   EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETTEEEEEEE----SSSSSSSHHHHHHHHHHHC.TSSSE CS
                        FeoB_N   2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkgkeveivDlPGiYslsayseeekvardflle.eepdv 81 
                                   tvalvG pnvGk++l+n lt+++++vg ++ +t +   g +++kg e++i+DlPGi   ++ s      r++l + +++d+
  gi|13540832|ref|NP_110520.1|  62 TVALVGFPNVGKSSLLNVLTNSESEVGSYAFTTLKAIPGVMEYKGAEIQILDLPGII--ENASYGAGRGREILSTvRSADL 140
                                   79*****************************************************95..5555556667777764155777 PP

                                   EEEEEEG CS
                        FeoB_N  82 vvnvvda 88 
                                   +v v d 
  gi|13540832|ref|NP_110520.1| 141 IVIVTDV 147
                                   7777775 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.27
                                   SEEEEEETHHHHHHTTEEE-HHHHHHHHTS-EEEEBTTTTBTHHHHHH CS
                        FeoB_N 107 pvvlalnmideaekkgieidlkkLsekLgvpvvktsakkkegieellk 154
                                   p ++a+n+id         d++ L++    +v k+sak++ gi+el++
  gi|13540832|ref|NP_110520.1| 235 PSIVAVNKIDMN----GAFDTSPLTRF--GEVFKVSAKNRIGIDELRE 276
                                   666666666653....34555555543..3688888888888888876 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.2    0.0012       1.7       1      22 [.      63      84 ..      63      98 .. 0.81
   2 !   10.2   0.0    0.0004      0.59     101     140 ..     107     149 ..     100     173 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0012
                                  EEEEEBTTTTHHHHHHHHHTS- CS
                     Dynamin_N  1 iavvGsqSsGKSSvlnaLlged 22
                                  +a+vG  + GKSS+ln L+ ++
  gi|13540832|ref|NP_110520.1| 63 VALVGFPNVGKSSLLNVLTNSE 84
                                  7999**************9887 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0004
                                   -SEEEEE---B-SSSGTTS...HHHHHHHSTTEEEEEEEETTS CS
                     Dynamin_N 101 kgltlvDlPGldsvnkrdq...elvkeyikkadiilavtsanh 140
                                    ++ ++DlPG+++++       + + +++++ad+i+ vt+ ++
  gi|13540832|ref|NP_110520.1| 107 AEIQILDLPGIIENASYGAgrgREILSTVRSADLIVIVTDVET 149
                                   6799*********988777788*****************9876 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.0   5.4e-05     0.081      99     125 ..      60      85 ..      15      96 .. 0.87
   2 ?   -3.5   0.0       5.7   8.5e+03      70      99 ..     133     161 ..     128     166 .. 0.61
   3 ?    0.1   0.0      0.44   6.6e+02      47      96 ..     234     277 ..     208     285 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.4e-05
                                   TSEEEEECSTTSSHHHHHHHHCTT--- CS
                   RsgA_GTPase  99 dktsvlvGqSGvGKStLinallpelel 125
                                   d t++lvG   vGKS+L+n+l+++ e 
  gi|13540832|ref|NP_110520.1|  60 DATVALVGFPNVGKSSLLNVLTNS-ES 85 
                                   57999****************987.44 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 5.7
                                   HHHHHTTSEEEE--TTTHTTHHHHHHHCTT CS
                   RsgA_GTPase  70 eelealgyevllvsaktkegleelkellkd 99 
                                   ++++++++ v++++++t  gl+++ ++l +
  gi|13540832|ref|NP_110520.1| 133 STVRSADLIVIVTDVET-GGLDKIVKELYN 161
                                   56666666777776664.466776666655 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.44
                                   -EEEEEEE-GGG--HHHHHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHH CS
                   RsgA_GTPase  47 iepvivlnKiDlleeeeeleelkeelealgyevllvsaktkegleelkel 96 
                                   i+ ++++nKiD+    +      + l+++g ev++vsak++ g++el+e 
  gi|13540832|ref|NP_110520.1| 234 IPSIVAVNKIDMNGAFD-----TSPLTRFG-EVFKVSAKNRIGIDELREG 277
                                   67788888888876666.....45555563.6788888888888888775 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   2.1e-05     0.032       4      58 ..      61     116 ..      58     122 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.1e-05
                                   -EEEEE-STTSSHHHHHHHHHHSS---B---S.S-EEETTG...GGTT-SEEEETT CS
                         SRPRB   4 pavllvGlsdsGKTslftrLttdsvkktvtSq.essaalkvksekgskltliDfPG 58 
                                    +v lvG  + GK sl++ Lt+ + +    +    +a   v + kg +++++D+PG
  gi|13540832|ref|NP_110520.1|  61 ATVALVGFPNVGKSSLLNVLTNSESEVGSYAFtTLKAIPGVMEYKGAEIQILDLPG 116
                                   5799*****************99665555544366666677888***********9 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0     0.002         3      24      53 ..      56      84 ..      53      96 .. 0.83
   2 ?    2.5   0.1     0.039        58     158     222 ..     224     275 ..     206     294 .. 0.55

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.002
                                  GG-S-SEEEEEEE-TTSSHHHHHHHHHHHH CS
                          MeaB 24 akaGraqvvGltGvPGaGkstlvealglel 53
                                  +k+G a+ v l G+P +Gks l++ l+ + 
  gi|13540832|ref|NP_110520.1| 56 PKSGDAT-VALVGFPNVGKSSLLNVLTNSE 84
                                  6788876.6899***********9998765 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.039
                                   TTT--CCCHHH-SEEEEE---HHHHHHHHHHHHHHHHHCSTTBTTB--EEEEEBCCCTBSHHHHH CS
                          MeaB 158 lqgikkGileiaDiivvnkaDkkeaekaarelraaleleeekekeWrpkvlktsavegeGidelv 222
                                   + +++k  + i  i++vnk D ++a  ++               +   +v k+sa++  Gidel 
  gi|13540832|ref|NP_110520.1| 224 IEAVQKNYVYIPSIVAVNKIDMNGAFDTSP-------------LTRFGEVFKVSAKNRIGIDELR 275
                                   445555555555555555555544433322.............1223345555555555555555 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       0.6     9e+02       6      29 ..      63      86 ..      61      94 .. 0.80
   2 ?    3.1   0.0     0.039        58      63     106 ..     102     150 ..      81     162 .. 0.71
   3 ?    5.3   0.1    0.0086        13     120     135 ..     231     246 ..     212     284 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.6
                                  EEEEESTTSSHHHHHHHHHHHTTS CS
                      GTP_EFTU  6 igiighvDhGKtTLtdrLlyktga 29
                                  ++++g  + GK++L+  L+ + ++
  gi|13540832|ref|NP_110520.1| 63 VALVGFPNVGKSSLLNVLTNSESE 86
                                  677888899******999977655 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.039
                                   EETTCSSEEEEEEEESSSGG...GH....HHHHHHHHT-SEEEEEEETTTB CS
                      GTP_EFTU  63 leketkkylinliDtPGHvd...Fs....kevirglrvlDgavlvvdaveG 106
                                   +  e+k  +i+++D PG ++   +     +e+  ++r +D+ v+v d++ G
  gi|13540832|ref|NP_110520.1| 102 M--EYKGAEIQILDLPGIIEnasYGagrgREILSTVRSADLIVIVTDVETG 150
                                   3..589999999999996552226422225777789999999999999987 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.0086
                                   HTTTEEEEEEESCGST CS
                      GTP_EFTU 120 kegvpiivfiNKmDrl 135
                                    + +p iv++NK+D+ 
  gi|13540832|ref|NP_110520.1| 231 YVYIPSIVAVNKIDMN 246
                                   556889********97 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0    0.0098        15      15      67 ..      61     116 ..      54     122 .. 0.79
   2 ?    5.5   0.0    0.0072        11     115     153 ..     233     271 ..     205     287 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0098
                                   EEEEEEESTTSSHHHHHHHHHHSSCEE...CSSSSSEEEEEEEETTEEEEEEEE-S CS
                           Arf  15 lrilllGLDnaGKtTilkklkleelvt...tvPTigfnveeleiknlkftvwDvGG 67 
                                   + + l+G  n GK+ +l+ l++ e +       T+      +e+k+ ++++ D+ G
  gi|13540832|ref|NP_110520.1|  61 ATVALVGFPNVGKSSLLNVLTNSESEVgsyAFTTLKAIPGVMEYKGAEIQILDLPG 116
                                   567799**************998876544455666666677789999999999876 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0072
                                   TSEEEEEEE-TTSTTSS-HHHHHHHTTGGGSSSSSSEEE CS
                           Arf 115 evallvlaNKqDlpealseeelrellgleelkgkrklei 153
                                    ++ +v  NK+D+++a +++ l++  ++ ++++k+++ i
  gi|13540832|ref|NP_110520.1| 233 YIPSIVAVNKIDMNGAFDTSPLTRFGEVFKVSAKNRIGI 271
                                   567899*************99999988888887776665 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 ?    9.8   0.0    0.0006      0.89       2      25 ..      63      86 ..      62     116 .. 0.81
   2 ?    0.2   0.1      0.55   8.3e+02      92     120 .]     217     245 ..     194     245 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0006
                                  EEEESSTTSSHHHHHHCHCT-CCC CS
                           Roc  2 vvlvGdsgvGKtsllkrfvedkfs 25
                                  v lvG  +vGK+sll+ +++++ +
  gi|13540832|ref|NP_110520.1| 63 VALVGFPNVGKSSLLNVLTNSESE 86
                                  789**************9988765 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.55
                                   HHCHHHHHHHHHHHCSSS-EEEEEE-TTT CS
                           Roc  92 senlkeWlkelkkvagkspvilvgnkiDl 120
                                   + n ++ ++ ++k+   +p i+ +nkiD+
  gi|13540832|ref|NP_110520.1| 217 QVNEDDIIEAVQKNYVYIPSIVAVNKIDM 245
                                   445566788888888899999******96 PP

>> DUF1192  Protein of unknown function (DUF1192)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   1.9     0.005       7.5      25      41 ..       4      20 ..       1      27 [. 0.86
   2 ?    3.3   0.2     0.058        87      28      45 ..      27      44 ..      24      49 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.005
                       DUF1192 25 LeerIalLeaEIaRlea 41
                                  +eerI++ e+EI+R++ 
  gi|13540832|ref|NP_110520.1|  4 IEERIKEIEDEIKRTQY 20
                                  89************975 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.058
                       DUF1192 28 rIalLeaEIaRleaaiak 45
                                   I lL+a IaRl+ + ++
  gi|13540832|ref|NP_110520.1| 27 HIGLLKAKIARLQMEARA 44
                                  6999*******9987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       698  (0.0389313); expected 358.6 (0.02)
Passed bias filter:                      518  (0.0288917); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.59u 0.32s 00:00:00.90 Elapsed: 00:00:00.50
# Mc/sec: 2164.91
//
Query:       gi|13540833|ref|NP_110521.1|  [L=669]
Description: formate dehydrogenase, alpha subunit [Thermoplasma volcanium GSS1]
Scores for complete 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  319.3   0.1      5e-95  319.0   0.1    1.1  1  Molybdopterin    Molybdopterin oxidoreductase
    8.3e-31  106.3   0.0    1.9e-30  105.2   0.0    1.6  1  Molydop_binding  Molydopterin dinucleotide binding domain
    3.2e-14   52.6   1.6    6.2e-14   51.7   1.6    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 !  319.0   0.1   8.4e-99     5e-95       1     431 [.      55     475 ..      55     476 .. 0.95

  Alignments for each domain:
  == domain 1  score: 319.0 bits;  conditional E-value: 8.4e-99
                                   B--S-EEECTTTTTSEEEE--HHHHHHHHHHHHHHHHHHCSGGGEEEEEBTSSCSHHHHHHHHHHHHHTT-EEE-BEECCG CS
                 Molybdopterin   1 RlkyPmvRkqargeGkFvrvsWdeAleliaaslkytikkygpdrvagfssgplmsmeslaslkkllsllggknlsfydwya 81 
                                   Rl+yPm+R   + +G + +v+W eAl++++++lk ++ kyg d+va+ ss + + +e+ ++++k ++ +g    +++d++a
  gi|13540833|ref|NP_110521.1|  55 RLNYPMIR---K-NGILTKVTWNEALDYVSEKLKTIRNKYGADAVAFQSSAKCT-NEENYLMQKIARMFGT---NNIDHCA 127
                                   9*******...6.8********************************76666666.9****9***9999998...8****** PP

                                   GGTTHHHH....CHHCCCCCTTTS-SS-CCGGGG-SEEEEESS-HHHHSHHHHHHHHHHHHTTC-EEEEECSSB-HCGGGC CS
                 Molybdopterin  82 dlppasaq....qtigsdsrsnyessnpledlensdliilwGsNvreerpilnarirkaalkkkakvivigpryaellkfa 158
                                   + +++s++    +tig+  +     + ++++l  ++  +++GsN  e +pi  + ++k  +  +  +iv +pr+++l++ a
  gi|13540833|ref|NP_110521.1| 128 RSCHSSTVagliKTIGTAAA-----TGSIKSLKSTKTYFIIGSNTTEQHPIIGTTVLKGKKS-GSYLIVADPRKTKLASNA 202
                                   ******99988888888655.....667889*********************7777775555.499*************** PP

                                   SEEEEEHTTTHHHHHHHHHHHHHHCCCCTCHHHHHHEECHHHCCCCCCCEECCSHHHHHHCCHHHHHHHHHHHHHHTSSEE CS
                 Molybdopterin 159 dewlaikpgtdaalalamghvilqelkvdkeflrkytygkeetdmpllvtleeetgkkkevvariarelarnaaktagksm 239
                                   d  l  +pgtd+al+++++ vil+e+++d+ef++++t  +++++  ++++ +e t+++++v a+ +r+ a+ +ak ++ s+
  gi|13540833|ref|NP_110521.1| 203 DIFLQFRPGTDVALLNSIMFVILKENLYDEEFIKNRTEDFDKLAAEIEKYPPELTEAITGVDAELVRRAAEIYAKYKP-SA 282
                                   ******************************************************************************.** PP

                                   EEECHHHHTSTTHHHHHHHHHHHHHHCTHCSSTTCEEEEESSCTTHHHCHHHHTCCTTCCCCCCCTT..HHHHHCCCTTTC CS
                 Molybdopterin 240 iivGaglnhrqdgdaiyravinLallvgnvgqpgGgwahlnGqlilagaaekvgalpvllsvkslke..ekikfaaeqpgn 318
                                   i++G+g++++ +g+++++ v nLal++gn+g+ g+g + l+Gq++++g  +++gal+  ++ +  +   + ++f + ++ +
  gi|13540833|ref|NP_110521.1| 283 ILYGMGITQHIHGTENVMSVSNLALMTGNIGKYGAGIFPLRGQNNVQG-SSDMGALAEFYPGYIPVDseGVKRFEDLWKTE 362
                                   ************************************************.*******999999888888899********** PP

                                   STSS--ECGGCHHHHHHTTSSSEEEEESH.HHHHSTTSCCCHCHHHCSSEEEEEESCSSHHHHTSSEEEEBE-CCGSEEEE CS
                 Molybdopterin 319 lgnfprnlfversnllkssgkkvlyllgnnpevdhadenevekalekldlvvvldgrltstalyaDiiLPaatwyEkedly 399
                                   l+++ + +++e+ +++  +++k++yl+g+np+++ a+  evek  e+l+l++v d++lt+ta+ aD++LPaat +Ek++++
  gi|13540833|ref|NP_110521.1| 363 LPKKVGLTLSEMFDAAAAGKVKAIYLMGENPVITEANVAEVEKGIENLELFIVQDIFLTETASLADVVLPAATALEKDGTF 443
                                   ********************************************************************************* PP

                                   E-TTSEEEEEEESSS-STT-BEHHHHHHHHHH CS
                 Molybdopterin 400 tndegrfqhlkqavsppgeaksdwkIlkaLak 431
                                   tn+e+r+q++  + sppgeak+dw+Il+++a 
  gi|13540833|ref|NP_110521.1| 444 TNTERRVQRIVSVKSPPGEAKQDWWILSEIAH 475
                                   ******************************96 PP

>> Molydop_binding  Molydopterin dinucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.2   0.0   3.1e-34   1.9e-30       1     110 [.     558     663 ..     558     664 .. 0.98

  Alignments for each domain:
  == domain 1  score: 105.2 bits;  conditional E-value: 3.1e-34
                                   EEEEEE-BTTBSTTTTTCGCCHHHHCSSS.-EEEEEHHHHHHHT--TT-EEEEEETTEEEEEEEEEESSB-TTEEEEESSH CS
               Molydop_binding   1 lrLitgrsldqlhsqtrtrpvlrlakpep.evveinpedAaalGikdGdlVevesrrGsvevrakvtervrpGvvfmpfgw 80 
                                   ++L+tgr+++++hs+t+tr++  l +++p ++vei+  dA++l+i+dG+ + vesr+G+++++akvt+ ++ G +f+pf++
  gi|13540833|ref|NP_110521.1| 558 FILTTGRNYYHWHSGTMTRRSDILERESPsPYVEISMMDAKQLNIRDGQAIDVESRHGRITLPAKVTDKIPTGIIFVPFHF 638
                                   79******************************************************************************* PP

                                   CC.....S-GHCTS--SCSTTT--CSTT-E CS
               Molydop_binding  81 weagekggnaNaltddatdplsgtpefksv 110
                                    e     + +N l+ d +dp+s++pefk+v
  gi|13540833|ref|NP_110521.1| 639 KE-----ARVNLLVGDNLDPYSKIPEFKVV 663
                                   88.....*********************97 PP

>> Molybdop_Fe4S4  Molybdopterin oxidoreductase Fe4S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.7   1.6     1e-17   6.2e-14       4      52 ..       2      49 ..       1      52 [. 0.94

  Alignments for each domain:
  == domain 1  score: 51.7 bits;  conditional E-value: 1e-17
                                  EEEE-SSBTT--EEEEEEETTEEEEEEE-TTSTTTTT---HHHHTCHHC CS
                Molybdop_Fe4S4  4 vktaCpyCgvgCglevhvkdgkivkvegdpdhpvnegrlCvKGrtller 52
                                  + t+CpyCg+gC+++v+ ++g + +v+g++++ vn+g+lC+KG+++l +
  gi|13540833|ref|NP_110521.1|  2 TLTVCPYCGTGCQINVEYRNGHF-TVHGYNKSIVNQGKLCIKGYQGLSY 49
                                  569********************.9*******************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (669 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       726  (0.0404931); expected 358.6 (0.02)
Passed bias filter:                      655  (0.036533); 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: 0.70u 0.32s 00:00:01.02 Elapsed: 00:00:00.49
# Mc/sec: 4088.50
//
Query:       gi|13540834|ref|NP_110522.1|  [L=306]
Description: ferredoxin subunit of sulfhydrogenase II [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-26   92.1   9.3    3.1e-26   92.1   9.3    2.0  2  Fer4_22   4Fe-4S dicluster domain
      3e-09   37.2  10.4    1.8e-08   34.7   9.4    2.2  2  Fer4_8    4Fe-4S dicluster domain
    9.1e-07   28.9  10.1     0.0023   18.0   0.3    2.7  2  Fer4_10   4Fe-4S dicluster domain
    1.7e-06   28.5  15.8    1.1e-05   25.8  10.8    2.9  3  Fer4_17   4Fe-4S dicluster domain
    5.3e-06   26.6   2.3     0.0026   17.9   0.1    2.3  2  Fer4_18   4Fe-4S dicluster domain
    8.6e-06   25.8   9.8     0.0027   17.8   0.3    2.5  2  Fer4_21   4Fe-4S dicluster domain
    4.1e-05   24.1  13.5      0.012   16.2  17.1    2.7  2  Fer4_7    4Fe-4S dicluster domain
    0.00024   20.8  21.3     0.0021   17.8   3.7    3.1  3  Fer4      4Fe-4S binding domain
     0.0009   19.4  20.1     0.0012   19.0  16.1    2.8  2  Fer4_9    4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.032   14.0   0.1      0.032   14.0   0.1    2.6  2  Fer4_20   Dihydroprymidine dehydrogenase domain II, 4Fe-4S cl
      0.068   13.2   0.0       0.12   12.3   0.0    1.3  1  Prp19     Prp19/Pso4-like
      0.083   13.0  21.6      0.063   13.4   4.3    2.7  2  Fer4_6    4Fe-4S binding domain
       0.21   11.7  22.6       0.17   12.0   3.0    3.2  3  Fer4_2    4Fe-4S binding domain
       0.51   11.4  22.1       0.24   12.4   2.5    3.6  4  Fer4_3    4Fe-4S binding domain
        1.3   10.0  20.7        0.2   12.6   2.4    3.0  3  Fer4_16   4Fe-4S double cluster binding domain
        7.5    7.3  28.2      0.084   13.4   2.7    3.2  2  Fer4_4    4Fe-4S binding domain
        8.3    7.0  16.5        3.6    8.2   6.8    2.8  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I


Domain annotation for each model (and alignments):
>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1       4.6   4.8e+03       8      20 ..     114     126 ..     111     144 .. 0.81
   2 !   92.1   9.3   2.9e-29   3.1e-26       2      96 .]     206     293 ..     205     293 .. 0.97

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 4.6
                       Fer4_22   8 CtlvCptCsCfdv 20 
                                   C  +C+  +C+++
  gi|13540834|ref|NP_110522.1| 114 CEKMCSGGFCTSF 126
                                   8899999999765 PP

  == domain 2  score: 92.1 bits;  conditional E-value: 2.9e-29
                       Fer4_22   2 ClsCgaCtlvCptCsCfdvedetkeeskegervrvwdsClleeftkvaggenvrkekkerlrqrllhklsefkekfgesgC 82 
                                   C+sCgaC++ CptC+C+dv d+ +       r + wdsC+le+ft++a+g nvr+e +erlrqr++hk++++k + g++ C
  gi|13540834|ref|NP_110522.1| 206 CISCGACNYSCPTCYCVDVYDDDD------GRKKEWDSCILEGFTRTAAG-NVRPELSERLRQRFYHKFKYYKLSRGAYLC 279
                                   *********************985......6899****************.****************************** PP

                       Fer4_22  83 vGCgRCieacpvki 96 
                                   +GC+RC++ cpv+i
  gi|13540834|ref|NP_110522.1| 280 TGCNRCVDDCPVDI 293
                                   ***********987 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.59   6.3e+02       9      22 ..     112     135 ..     110     195 .. 0.64
   2 !   34.7   9.4   1.7e-11   1.8e-08       3      65 .]     204     293 ..     202     293 .. 0.74

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.59
                        Fer4_8   9 gaCqsaC..........pvlrrtk 22 
                                   + C+++C          pvl + +
  gi|13540834|ref|NP_110522.1| 112 FVCEKMCsggfctsfggPVLDEYD 135
                                   789999966555555554433333 PP

  == domain 2  score: 34.7 bits;  conditional E-value: 1.7e-11
                        Fer4_8   3 ekCieCgaCqsaCpvlrrtk.khlldargeaae................dvqeeqvlee..................eeal 48 
                                   ++Ci CgaC+ +Cp++ + +  +  d r++  +                         e                   +++
  gi|13540834|ref|NP_110522.1| 204 NYCISCGACNYSCPTCYCVDvYDDDDGRKKEWDscilegftrtaagnvrP--------ElserlrqrfyhkfkyyklSRGA 276
                                   79**************9998556555555555577766666666555541........044444556677899999999** PP

                        Fer4_8  49 wsCttcgaCtevCpvgi 65 
                                   + Ct+c++C++ Cpv+i
  gi|13540834|ref|NP_110522.1| 277 YLCTGCNRCVDDCPVDI 293
                                   **************987 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   4.1   4.7e-05      0.05       6      32 ..     203     226 ..     198     248 .. 0.67
   2 !   18.0   0.3   2.1e-06    0.0023       8      25 ..     278     295 ..     272     306 .] 0.76

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.7e-05
                       Fer4_10   6 ddtCirCgkCvkaCPadltsvgakgea 32 
                                   ++ Ci Cg+C+ +CP++   + +  ++
  gi|13540834|ref|NP_110522.1| 203 ANYCISCGACNYSCPTC---YCVDVYD 226
                                   578************93...3322222 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 2.1e-06
                       Fer4_10   8 tCirCgkCvkaCPadlts 25 
                                    C++C++Cv+ CP+d++ 
  gi|13540834|ref|NP_110522.1| 278 LCTGCNRCVDDCPVDIDI 295
                                   5*************7633 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.4       8.3   8.7e+03       8      13 ..     114     119 ..     112     127 .. 0.70
   2 !   15.3   3.2   2.1e-05     0.023      24      58 ..     178     218 ..     166     221 .. 0.64
   3 !   25.8  10.8   1.1e-08   1.1e-05       2      61 .]     206     294 ..     205     294 .. 0.63

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 8.3
                       Fer4_17   8 ClpeCp 13 
                                   C+++C+
  gi|13540834|ref|NP_110522.1| 114 CEKMCS 119
                                   777775 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 2.1e-05
                       Fer4_17  24 kllraaklglleeaeke......ekaslCieCgeCerkCPq 58 
                                   +l  ++++  +e+ +k       + a+ Ci+Cg C+++CP 
  gi|13540834|ref|NP_110522.1| 178 SLYGRLNVDGIENRMKWssnlwnKFANYCISCGACNYSCPT 218
                                   55555555333332221244554899**************5 PP

  == domain 3  score: 25.8 bits;  conditional E-value: 1.1e-08
                       Fer4_17   2 CiqCgyClpeCpsyea.................ydnepkkllraakl........................glleeaekee 41 
                                   Ci+Cg+C  +Cp++++                 +            l                        +++++ + ++
  gi|13540834|ref|NP_110522.1| 206 CISCGACNYSCPTCYCvdvyddddgrkkewdscI------------LegftrtaagnvrpelserlrqrfyHKFKYYKLSR 274
                                   *************999777544333322222220............02222222233333444444444446777777889 PP

                       Fer4_17  42 kaslCieCgeCerkCPqgld 61 
                                    a lC++C++C+ +CP ++d
  gi|13540834|ref|NP_110522.1| 275 GAYLCTGCNRCVDDCPVDID 294
                                   ****************9987 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.4    0.0023       2.4      50      74 ..     195     219 ..     167     241 .. 0.77
   2 !   17.9   0.1   2.5e-06    0.0026      46      79 ..     264     297 ..     243     302 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0023
                       Fer4_18  50 keerkekgagdcidcescvkvcPtg 74 
                                   + +  +k a+ ci+c++c   cPt 
  gi|13540834|ref|NP_110522.1| 195 SSNLWNKFANYCISCGACNYSCPTC 219
                                   45555677889************95 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 2.5e-06
                       Fer4_18  46 alkekeerkekgagdcidcescvkvcPtgidirk 79 
                                    +k k  + ++ga  c+ c+ cv+ cP++idi++
  gi|13540834|ref|NP_110522.1| 264 YHKFKYYKLSRGAYLCTGCNRCVDDCPVDIDIKE 297
                                   455555666777888*****************97 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   4.0   0.00039      0.41       6      27 ..     204     223 ..     193     239 .. 0.65
   2 !   17.8   0.3   2.6e-06    0.0027      40      54 ..     278     292 ..     265     297 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00039
                       Fer4_21   6 dkCigCgkCliaCedtshqaie 27 
                                   + Ci+Cg C  +C++    +++
  gi|13540834|ref|NP_110522.1| 204 NYCISCGACNYSCPT--CYCVD 223
                                   568888888888873..44554 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 2.6e-06
                       Fer4_21  40 eCvGCnlCssvCPve 54 
                                    C+GCn C++ CPv+
  gi|13540834|ref|NP_110522.1| 278 LCTGCNRCVDDCPVD 292
                                   6*************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 !   14.2   2.6   4.9e-05     0.051      32      50 ..     200     218 ..     111     220 .. 0.64
   2 !   16.2  17.1   1.1e-05     0.012       2      52 .]     206     293 ..     205     293 .. 0.57

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.9e-05
                        Fer4_7  32 eidpekClgCgaCvavCPt 50 
                                   +  +++C++CgaC   CPt
  gi|13540834|ref|NP_110522.1| 200 NKFANYCISCGACNYSCPT 218
                                   5566789999999999997 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 1.1e-05
                        Fer4_7   2 CigCgaCvaaCp.vkaieldeeenek......................gtekv.................eidpekClgCg 42 
                                   Ci CgaC   Cp  +++++ ++++ +                      +   +                    +  C+gC+
  gi|13540834|ref|NP_110522.1| 206 CISCGACNYSCPtCYCVDVYDDDDGRkkewdscilegftrtaagnvrpE---LserlrqrfyhkfkyyklSRGAYLCTGCN 283
                                   ***********97566666554333333444555554444444443330...033334444443332222444567***** PP

                        Fer4_7  43 aCvavCPtga 52 
                                   +Cv+ CP+++
  gi|13540834|ref|NP_110522.1| 284 RCVDDCPVDI 293
                                   *******985 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.8       8.5     9e+03      14      18 ..     114     118 ..     113     119 .. 0.86
   2 !   14.4   2.4   2.4e-05     0.025       6      20 ..     204     218 ..     201     218 .. 0.91
   3 !   17.8   3.7   1.9e-06    0.0021       7      21 ..     278     292 ..     276     293 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 8.5
                                   HHHHS CS
                          Fer4  14 CvevC 18 
                                   C+++C
  gi|13540834|ref|NP_110522.1| 114 CEKMC 118
                                   99999 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 2.4e-05
                                   TTSSS-THHHHHSTT CS
                          Fer4   6 ekCigCGaCvevCPv 20 
                                   + Ci CGaC   CP+
  gi|13540834|ref|NP_110522.1| 204 NYCISCGACNYSCPT 218
                                   67************7 PP

  == domain 3  score: 17.8 bits;  conditional E-value: 1.9e-06
                                   TSSS-THHHHHSTTT CS
                          Fer4   7 kCigCGaCvevCPvg 21 
                                   +C+gC++Cv+ CPv+
  gi|13540834|ref|NP_110522.1| 278 LCTGCNRCVDDCPVD 292
                                   7*************8 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1       1.3   1.4e+03       8      18 ..     114     124 ..     112     136 .. 0.75
   2 !   19.0  16.1   1.1e-06    0.0012       1      49 [.     205     292 ..     205     293 .. 0.96

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 1.3
                        Fer4_9   8 CveaCpagvvv 18 
                                   C+++C  g ++
  gi|13540834|ref|NP_110522.1| 114 CEKMCSGGFCT 124
                                   88899877665 PP

  == domain 2  score: 19.0 bits;  conditional E-value: 1.1e-06
                        Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraase.......................................eaCigCgaC 42 
                                   +C++CgaC ++Cp++ +v+       r ++++                                          C+gC++C
  gi|13540834|ref|NP_110522.1| 205 YCISCGACNYSCPTCYCVDVYDDDDGRKKEWDScilegftrtaagnvrpelserlrqrfyhkfkyyklsrgaYLCTGCNRC 285
                                   6*****************9999999999998889**************************************99******* PP

                        Fer4_9  43 veaCpkg 49 
                                   v+ Cp +
  gi|13540834|ref|NP_110522.1| 286 VDDCPVD 292
                                   *****98 PP

>> Fer4_20  Dihydroprymidine dehydrogenase domain II, 4Fe-4S cluster
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   1.7      0.13   1.3e+02      19      40 ..     201     220 ..     187     226 .. 0.78
   2 ?   14.0   0.1     3e-05     0.032      10      47 ..     265     300 ..     257     305 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.13
                                   HHHTT----TT-HHHHCSTT-- CS
                       Fer4_20  19 eeAsRClqCkkapcvkgCPvei 40 
                                   + A+ C++C    c+ +CP+  
  gi|13540834|ref|NP_110522.1| 201 KFANYCISC--GACNYSCPTCY 220
                                   56999****..78******865 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 3e-05
                                   ----HHHHHHHHTT----TT-HHHHCSTT---HHHHHH CS
                       Fer4_20  10 lglteeealeeAsRClqCkkapcvkgCPveidipefik 47 
                                   ++++  +  + A  C  C  + cv+ CPv+idi+e i+
  gi|13540834|ref|NP_110522.1| 265 HKFKYYKLSRGAYLCTGC--NRCVDDCPVDIDIKEVIT 300
                                   55666667778889****..89************9987 PP

>> Prp19  Prp19/Pso4-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00012      0.12      13      43 ..     232     261 ..     230     262 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00012
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Prp19  13 qnEWDalmletfelrkqleqtrqeLsqaLYq 43 
                                   ++EWD+++le f+ r++  ++r eLs+ L q
  gi|13540834|ref|NP_110522.1| 232 KKEWDSCILEGFT-RTAAGNVRPELSERLRQ 261
                                   58**********6.99***********9977 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   9.4      0.04        43       7      21 ..     204     218 ..     202     224 .. 0.91
   2 ?   13.4   4.3     6e-05     0.063       8      22 ..     278     292 ..     277     294 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.04
                        Fer4_6   7 dkCigCgdCvrvCPe 21 
                                   + Ci+Cg+C   CP+
  gi|13540834|ref|NP_110522.1| 204 NYCISCGACNYSCPT 218
                                   78************7 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 6e-05
                        Fer4_6   8 kCigCgdCvrvCPeg 22 
                                   +C+gC++Cv+ CP +
  gi|13540834|ref|NP_110522.1| 278 LCTGCNRCVDDCPVD 292
                                   7************75 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.5       3.4   3.6e+03       9      18 ..     117     125 ..     112     126 .. 0.62
   2 ?   10.1   5.2   0.00068      0.72      10      22 .]     206     218 ..     203     218 .. 0.92
   3 ?   12.0   3.0   0.00016      0.17       9      21 ..     278     290 ..     272     291 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 3.4
                        Fer4_2   9 rCigCgaCvs 18 
                                   +C g g C+s
  gi|13540834|ref|NP_110522.1| 117 MCSG-GFCTS 125
                                   4555.78876 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00068
                        Fer4_2  10 CigCgaCvsaCPa 22 
                                   Ci+CgaC  +CP+
  gi|13540834|ref|NP_110522.1| 206 CISCGACNYSCPT 218
                                   *******999**7 PP

  == domain 3  score: 12.0 bits;  conditional E-value: 0.00016
                        Fer4_2   9 rCigCgaCvsaCP 21 
                                    C+gC+ Cv+ CP
  gi|13540834|ref|NP_110522.1| 278 LCTGCNRCVDDCP 290
                                   5************ PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.2       4.8   5.1e+03       7      12 ..     114     119 ..     113     122 .. 0.74
   2 ?   12.4   2.5   0.00022      0.24       1      13 [.     206     218 ..     206     219 .. 0.95
   3 ?   -1.0   0.2       4.5   4.8e+03       4      10 ..     219     224 ..     218     224 .. 0.80
   4 ?   10.1   3.5    0.0013       1.3       1      14 [.     279     292 ..     279     293 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 4.8
                        Fer4_3   7 CvevCP 12 
                                   C++ C 
  gi|13540834|ref|NP_110522.1| 114 CEKMCS 119
                                   888885 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00022
                        Fer4_3   1 CtgCgaCvevCPv 13 
                                   C+ CgaC  +CP+
  gi|13540834|ref|NP_110522.1| 206 CISCGACNYSCPT 218
                                   ************6 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 4.5
                        Fer4_3   4 CgaCvev 10 
                                   C+ Cv+v
  gi|13540834|ref|NP_110522.1| 219 CY-CVDV 224
                                   97.*987 PP

  == domain 4  score: 10.1 bits;  conditional E-value: 0.0013
                        Fer4_3   1 CtgCgaCvevCPvg 14 
                                   CtgC++Cv+ CPv+
  gi|13540834|ref|NP_110522.1| 279 CTGCNRCVDDCPVD 292
                                   ************97 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   6.0     0.025        27       2      14 ..     206     218 ..     162     219 .. 0.78
   2 ?    5.8  18.4     0.025        26       2      66 ..     206     291 ..     205     292 .. 0.65
   3 ?   12.6   2.4   0.00019       0.2       2      16 ..     279     293 ..     278     305 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.025
                       Fer4_16   2 CgtCgkCaevCPt 14 
                                   C++Cg+C  +CPt
  gi|13540834|ref|NP_110522.1| 206 CISCGACNYSCPT 218
                                   6666666666665 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.025
                       Fer4_16   2 CgtCgkCaevCPtnaikek......kekeiearecisy..................ntaekkdlaedeekckkqeaitgCd 58 
                                   C++Cg+C  +CPt            ++ke++++    +                  +++  ++++  + ++  ++ +tgC+
  gi|13540834|ref|NP_110522.1| 206 CISCGACNYSCPTCYCVDVyddddgRKKEWDSCI--LEgftrtaagnvrpelserlRQRFYHKFKYYKLSRG-AYLCTGCN 283
                                   *************776644222234555555554..224455555656565554555555666666666665.6889**** PP

                       Fer4_16  59 iCqdvCPa 66 
                                   +C+d CP+
  gi|13540834|ref|NP_110522.1| 284 RCVDDCPV 291
                                   *******7 PP

  == domain 3  score: 12.6 bits;  conditional E-value: 0.00019
                       Fer4_16   2 CgtCgkCaevCPtna 16 
                                   C++C++C++ CP++ 
  gi|13540834|ref|NP_110522.1| 279 CTGCNRCVDDCPVDI 293
                                   ************975 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   8.6      0.01        11       2      16 ..     204     218 ..     203     226 .. 0.91
   2 ?   13.4   2.7     8e-05     0.084       4      16 ..     279     291 ..     273     292 .. 0.91

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.01
                        Fer4_4   2 erCigCgsCvaaCPq 16 
                                   + Ci Cg+C ++CP+
  gi|13540834|ref|NP_110522.1| 204 NYCISCGACNYSCPT 218
                                   68************6 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 8e-05
                        Fer4_4   4 CigCgsCvaaCPq 16 
                                   C+gC +Cv+ CP+
  gi|13540834|ref|NP_110522.1| 279 CTGCNRCVDDCPV 291
                                   ************7 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   6.8    0.0034       3.6       5      23 ..     205     223 ..     203     240 .. 0.82
   2 ?    3.3   2.1      0.12   1.2e+02       6      17 ..     279     290 ..     277     295 .. 0.93

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0034
                       Fer4_13   5 tCiacgaCvelaPdvFeed 23 
                                    Ci+cgaC   +P ++  d
  gi|13540834|ref|NP_110522.1| 205 YCISCGACNYSCPTCYCVD 223
                                   5************999754 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.12
                       Fer4_13   6 CiacgaCvelaP 17 
                                   C++c+ Cv+ +P
  gi|13540834|ref|NP_110522.1| 279 CTGCNRCVDDCP 290
                                   *********999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       806  (0.0449551); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 1990.92
//
Query:       gi|13540835|ref|NP_110523.1|  [L=244]
Description: anaerobic sulfite reduction protein B [Thermoplasma volcanium GSS1]
Scores for complete 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-12   46.4   0.0    7.5e-12   45.9   0.0    1.3  1  NAD_binding_1    Oxidoreductase NAD-binding domain
    3.1e-09   36.5   1.3      6e-09   35.6   1.3    1.5  1  DHODB_Fe-S_bind  Iron-sulfur cluster binding domain of dihydr
     0.0084   16.2   0.0      0.015   15.4   0.0    1.5  1  NAD_binding_6    Ferric reductase NAD binding domain


Domain annotation for each model (and alignments):
>> NAD_binding_1  Oxidoreductase NAD-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.9   0.0   1.3e-15   7.5e-12       2     107 ..      88     185 ..      87     187 .. 0.89

  Alignments for each domain:
  == domain 1  score: 45.9 bits;  conditional E-value: 1.3e-15
                                   EEEGGGGHHHHHHHHHHHHHCTTCSEEEEEEEESSGCGSTTHHHHHHHHHHCTTEEEEEEEESSCTTTSSSEESSHHHHHH CS
                 NAD_binding_1   2 iagGtGiaPvrsvlraileeakdktkvvlvyGnrteedllyreeleelakklpgrlkvvavvsreeagweggkgrvqdall 82 
                                   iagG Gi P++++++ ++   +   k++++yG+r+  d++yr e+e+++++++ r+   + v++ +++w+g  g v++ + 
  gi|13540835|ref|NP_110523.1|  88 IAGGIGIPPIKALIEDMQGH-TSLDKLTVLYGARSPSDIVYRSEIETWKEEMDFRI---T-VDKGDENWRGHVGVVTTLV- 162
                                   9******************8.7779***********************77777663...4.4999*********999988. PP

                                   HHHHHHSSTTEEEEEECSHHHHHHH CS
                 NAD_binding_1  83 eellslkkeethvyvCGppgMikav 107
                                    e+ +   +   ++v Gpp M+k+ 
  gi|13540835|ref|NP_110523.1| 163 PEIKE--YNHGAAFVIGPPVMMKFS 185
                                   77888..799999*********986 PP

>> DHODB_Fe-S_bind  Iron-sulfur cluster binding domain of dihydroorotate dehydrogenase B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.6   1.3     1e-12     6e-09       1      40 [.     204     235 ..     204     237 .. 0.93

  Alignments for each domain:
  == domain 1  score: 35.6 bits;  conditional E-value: 1e-12
                                   ----SSSSSSS-TTEEEETTCTT.CEEETTTT-CEEECCC CS
               DHODB_Fe-S_bind   1 eerMaCGvGaClgCvvktkggdggeykrvCkdGPvFdade 40 
                                   e+rM CG+G+C++C +           ++C+dGP+F++++
  gi|13540835|ref|NP_110523.1| 204 ERRMECGIGVCGHCNIGR--------WYACEDGPIFKYSD 235
                                   89**************99........89********9875 PP

>> NAD_binding_6  Ferric reductase NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   2.6e-06     0.015       1      41 [.      82     117 ..      82     145 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.6e-06
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 NAD_binding_6   1 yenvllvagGiGitpfisilkdllkkskkealktkkikliw 41 
                                   ye+v+ +agGiGi+p+  ++ d+   ++       k++   
  gi|13540835|ref|NP_110523.1|  82 YEHVVAIAGGIGIPPIKALIEDMQGHTS-----LDKLTVLY 117
                                   89******************99977766.....55555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 1511.78
//
Query:       gi|13540836|ref|NP_110524.1|  [L=476]
Description: phosphate ABC transporter permease [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.5e-50  172.4  26.6    1.8e-50  172.1  26.6    1.1  1  Sugar_tr    Sugar (and other) transporter
    4.7e-33  114.6  44.7    5.1e-28   98.0  35.7    2.0  2  MFS_1       Major Facilitator Superfamily
    0.00015   20.7  16.5      0.011   14.6  11.1    2.3  2  MFS_1_like  MFS_1 like family


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 !  172.1  26.6   3.1e-54   1.8e-50       4     449 ..      24     461 ..      21     463 .. 0.87

  Alignments for each domain:
  == domain 1  score: 172.1 bits;  conditional E-value: 3.1e-54
                                   HHHHHHHHHHHHHHCGGGTHHHHHHHHTSTT--SHHHHHH...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHH CS
                      Sugar_tr   4 vaalggllfgYdtgvigafltllkfaknfglsksksskeessvlsglivsiflvGaiiGslfagllgdrfGRkkslliaav 84 
                                   +a +g +   Yd++vig+++++l      g++k ++ +       +++ si l+ ++iG++++g l d +GRk ++ +  +
  gi|13540836|ref|NP_110524.1|  24 IAGMGFFTDAYDLFVIGTVISILP---LAGWDKLNTYDI------SILSSISLLASVIGAVIFGRLLDALGRKRVYGFELM 95 
                                   6667779999*******9999999...789999997555......7*********************************** PP

                                   HHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHH.HTS CS
                      Sugar_tr  85 lfvigavlqaaakgknsvevlivgRvlvGigvGlasvlvPmyisEiApkklRgalvslyqlaitfGilvaaifglgl.nkt 164
                                   l++ ga+ +a+    n +  li+ R+++G+g+G+ ++ +++ + E++ +k Rg+lv++  +   +G + +  ++lgl + +
  gi|13540836|ref|NP_110524.1|  96 LLILGALGSAFVVPVNGINYLIAWRFILGLGIGGDYAGSSTIMTEFSNTKNRGQLVGMVFSLQGVGLIAGPLITLGLlSFI 176
                                   *************99**************************************************************9999 PP

                                   S-.TTHHHHHHHCCHHHHHHHHHHGGGS---HHHH.HHTT-HHHHHHHHHHHHHCHHHHHHH.HHHHHHHHHHHH...... CS
                      Sugar_tr 165 sn.adgwrillglqlvpallllilllflPESPryl.vekgkeeeakevlaklrgeedadrel.aeekdsleaeqeee.kas 241
                                   +n +  wr+l+++ +vpa ++l+++  + E+Pry    kg+ + a ++++k+ g+++++ +  + e++ ++ ++  +   +
  gi|13540836|ref|NP_110524.1| 177 HNlDLVWRVLFFIGAVPAFIVLYGRRAIGETPRYAlRVKGDASSAMQSVEKISGDSKVSVSReDLEMSNIKWTDLFKnRYF 257
                                   99*99*****************************846677777********988866655430233444444433333455 PP

                                   HTTHHHHSH...HHHHHHHHHHHHHHTTHHHHHHHTTTHHHHS.S-THH....HHHHHHHHHHHHHHHHHHHHHHHHS-SH CS
                      Sugar_tr 242 wkellssktvrqrlligvvlqifqqltGinaimyysptifenl.glsks....llvtiivgvvnfvatfvaiflvdrfGRR 317
                                   + +l+++ +      ++++l+++   + i++   +s  i +++ gl+k     +++ ii+ v  f a  +a f+vdr+GR+
  gi|13540836|ref|NP_110524.1| 258 MLSLIGTAG------TWFLLDWAFYGNSIMSHEMLSALIPSSMsGLNKLklstFYTLIIFAVSAFPAYWIATFTVDRIGRK 332
                                   556666655......666666666666666666666666554424444477799*************************** PP

                                   HHHHHHHHHHHHHHHHHH..HHHHTTSS...CHHHHHHHHHHHHHHHTTTTHHHHHHHHHHSHTTTHHHHHHHHHHHHHHH CS
                      Sugar_tr 318 tllllGaagmaicfvilgivalllvakskaasivaivfialfialfalgwgpvpwvlvsElfpqsvRskalaiavavnwla 398
                                   ++ ++G+++m i f ilg   + +  + +  ++ ++v  + + ++ ++g++ + +++++E+fp+++R++++ i+ a   + 
  gi|13540836|ref|NP_110524.1| 333 RMQVIGFLIMGITFGILG--IFRYLMSPTFVTYFLLVYGISY-FFTEFGPNVTTFIYAPEMFPTAIRGLGSGISSAGGKTG 410
                                   ******************..5555555557888888888888.788*********************************** PP

                                   HHHHHHHHHHHHCHHHT-HHHHHHHHHHHHHHHHHHHHS--STT--CCCCG CS
                      Sugar_tr 399 nflisllfpiiteaigggyvflvfaglavlfiifvfffvpetkgrtleeie 449
                                    f+ + l  ii+  +g+g  fl+ ag+ +l+++++++ +pet  r+le+i+
  gi|13540836|ref|NP_110524.1| 411 AFIGTALNVIIFTLYGEGELFLILAGISMLGMLMTLVLLPETSRRKLEDIS 461
                                   ************************************************986 PP

>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.0  35.7   8.5e-32   5.1e-28       4     320 ..      28     380 ..      25     387 .. 0.79
   2 !   22.0   2.3   1.1e-08   6.6e-05     107     186 ..     384     463 ..     380     475 .. 0.88

  Alignments for each domain:
  == domain 1  score: 98.0 bits;  conditional E-value: 8.5e-32
                         MFS_1   4 aaflsalarsilgpalpl.al..aedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllf 81 
                                   ++f  a++ +++g+++++  l   + l+     i++l ++  l+++++++++Grl d +Gr+rv+ + l l++lg+l  +f
  gi|13540836|ref|NP_110524.1|  28 GFFTDAYDLFVIGTVISIlPLagWDKLN--TYDISILSSISLLASVIGAVIFGRLLDALGRKRVYGFELMLLILGALGSAF 106
                                   5666666666666666643332233333..4459*****************************************666668 PP

                         MFS_1  82 a...sslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslg.....Wravf 154
                                   +   +++ +l++ r++ Glg g+ ++++ +++++ ++ ++rg+ +g++ +  ++G i gpl+   l+s +      Wr++f
  gi|13540836|ref|NP_110524.1| 107 VvpvNGINYLIAWRFILGLGIGGDYAGSSTIMTEFSNTKNRGQLVGMVFSLQGVGLIAGPLITLGLLSFIHnldlvWRVLF 187
                                   55779999***********************************************************9999********** PP

                         MFS_1 155 yilaivsllafvlfllllpeepperkrkspkeee........kgtgpaplvp........awkallkdpvl.......... 209
                                   +i a+ ++++ + +   + e+p+   r+++   +        +g+ + +++          w+ l+k++++          
  gi|13540836|ref|NP_110524.1| 188 FIGAVPAFIV-LYGRRAIGETPRYALRVKGDASSamqsvekiSGDSKVSVSRedlemsniKWTDLFKNRYFmlsligtagt 267
                                   *********9.66889999999999999988888999998773333333333666677789********995555444444 PP

                         MFS_1 210 w.illialllfffgfsg........lltllplylqevlglsglllaglllallalvgailallagrlsdrlgrrrrlllal 281
                                   w +l +a++       g        l++l+p+ +    +l+  l++ ++l ++a+ ++++  +a++ +dr+gr+r+ ++++
  gi|13540836|ref|NP_110524.1| 268 WfLLDWAFY-------GnsimshemLSALIPSSMSGLNKLK--LSTFYTLIIFAVSAFPAYWIATFTVDRIGRKRMQVIGF 339
                                   432223333.......1333445559999999544444444..6666666666777777788999999************* PP

                         MFS_1 282 lllllaalglallavtssavllllvlvliGfglgfv..fps 320
                                   l++ +++ +l ++    s++++ ++l+++G+ ++f+   p 
  gi|13540836|ref|NP_110524.1| 340 LIMGITFGILGIFRYLMSPTFVTYFLLVYGISYFFTefGPN 380
                                   *******************************8888864343 PP

  == domain 2  score: 22.0 bits;  conditional E-value: 1.1e-08
                         MFS_1 107 aaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllafvlfllllpeepperkrkspke 186
                                    +++ ++fp   rg++ g+ sag   Ga +g +l  ++ +++g   +f+ila++s+l++++ l+llpe+ +++  + + e
  gi|13540836|ref|NP_110524.1| 384 FIYAPEMFPTAIRGLGSGISSAGGKTGAFIGTALNVIIFTLYGEGELFLILAGISMLGMLMTLVLLPETSRRKLEDISGE 463
                                   67899**************************************999**************98888888887776666655 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 !    9.4   0.2     7e-05      0.42      31      85 ..      54     107 ..      51     176 .. 0.86
   2 !   14.6  11.1   1.9e-06     0.011     264     370 ..     306     414 ..     254     433 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 7e-05
                    MFS_1_like  31 lkaseigiitlilpltsilsppiwgvlaDrfgkrkkvvilslllsavlflsllfi 85 
                                   l+ ++i i+++i  l s++++ i+g l D +g+ k v  + l+l ++  l+  f+
  gi|13540836|ref|NP_110524.1|  54 LNTYDISILSSISLLASVIGAVIFGRLLDALGR-KRVYGFELMLLILGALGSAFV 107
                                   899****************************96.556555555555544444444 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 1.9e-06
                    MFS_1_like 264 slvalgvvaeiplfffaeklleklGhvklliiallayilrfllyaii...enawlvlpievLhgisfgll.w...aaavey 337
                                    ++++ +v+  p +++a   ++++G  ++ +i++l++ ++f +++i+    ++ +v  + + +gis+  + +   ++   y
  gi|13540836|ref|NP_110524.1| 306 YTLIIFAVSAFPAYWIATFTVDRIGRKRMQVIGFLIMGITFGILGIFrylMSPTFVTYFLLVYGISYFFTeFgpnVTTFIY 386
                                   46777899***************************************99999*************9876535111344445 PP

                    MFS_1_like 338 vskiapksleatgqgllsglyfglGralGsliG 370
                                   + +++p  +++ g g+      ++G+  G++iG
  gi|13540836|ref|NP_110524.1| 387 APEMFPTAIRGLGSGIS-----SAGGKTGAFIG 414
                                   56666666666655554.....45555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (476 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       673  (0.037537); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.66u 0.32s 00:00:00.98 Elapsed: 00:00:00.50
# Mc/sec: 2843.34
//
Query:       gi|13540837|ref|NP_110525.1|  [L=135]
Description: hypothetical protein TVN0006 [Thermoplasma volcanium GSS1]
Scores for complete sequence (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   56.8   0.2    2.4e-15   56.2   0.2    1.3  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
  ------ inclusion threshold ------
      0.019   15.0   0.7      0.032   14.2   0.7    1.3  1  DZR             Double zinc ribbon
      0.036   14.4   0.9      0.062   13.6   0.8    1.5  1  C1_2            C1 domain
      0.096   12.6   1.5       0.15   12.0   1.5    1.3  1  C1_1            Phorbol esters/diacylglycerol binding domain 
       0.89    9.3   4.5        1.1    9.0   3.0    2.0  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 !   56.2   0.2   6.7e-19   2.4e-15       1      67 [.      30      98 ..      30     100 .. 0.87

  Alignments for each domain:
  == domain 1  score: 56.2 bits;  conditional E-value: 6.7e-19
                OrfB_Zn_ribbon  1 frklkeqleykakeyGikveevnp...ayTSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNil 67
                                  ++ l  q+ yka ++G + +e  +   ++TS  Cs+C    +   +gr +kC++Cg e+drDvnA+iNi+
  gi|13540837|ref|NP_110525.1| 30 YGMLASQVMYKASWEGLPAIELTRketRNTSRMCSVCDTLARI-GHGRILKCDSCGIEIDRDVNACINIA 98
                                  5678899*********9888765411167***********999.*************************8 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.7     9e-06     0.032       7      46 ..      55      95 ..      53      96 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 9e-06
                           DZR  7 elppdarfCseCgtklkavaa..edrCpsCgekvdpearfCp 46
                                  e+++ +r+Cs C t  +   +    +C+sCg ++d + + C 
  gi|13540837|ref|NP_110525.1| 55 ETRNTSRMCSVCDTLAR-IGHgrILKCDSCGIEIDRDVNACI 95
                                  678899*******9875.5666799**************996 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.8   1.7e-05     0.062       9      43 ..      51      88 ..      47      95 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.7e-05
                          C1_2  9 lskgedssesfnCsaCgrk...idgffYsCseCdfslh 43
                                  l+++e+++ s+ Cs+C++    ++g   +C+ C + ++
  gi|13540837|ref|NP_110525.1| 51 LTRKETRNTSRMCSVCDTLariGHGRILKCDSCGIEID 88
                                  556799999**********99666666******98887 PP

>> C1_1  Phorbol esters/diacylglycerol binding domain (C1 domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   1.5   4.1e-05      0.15       9      44 ..      58      96 ..      53     105 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.1e-05
                                  SS--B-TTT-SB--SSSS-EEEETTT--EE-CC...CCT CS
                          C1_1  9 kqptfCkhCgeflwgkekqglkCswCkllvHkk...Che 44
                                  + +  C+ C+ + + +  ++lkC+ C++ ++ +   C++
  gi|13540837|ref|NP_110525.1| 58 NTSRMCSVCDTLARIGHGRILKCDSCGIEIDRDvnaCIN 96
                                  56789*******95599**********999887777766 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.78   2.8e+03      26      31 ..      36      41 ..      35      41 .. 0.79
   2 ?    9.0   3.0   0.00031       1.1       3      25 ..      63      85 ..      62      87 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.78
                                  ---B-- CS
                DNA_RNApol_7kD 26 RilYKk 31
                                   ++YK+
  gi|13540837|ref|NP_110525.1| 36 QVMYKA 41
                                  69***5 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00031
                                  -SSS--B----SSS----SSS-- CS
                DNA_RNApol_7kD  3 CgeCgaevslkkgdpiRCkeCGh 25
                                  C  C++  ++ +g +++C  CG 
  gi|13540837|ref|NP_110525.1| 63 CSVCDTLARIGHGRILKCDSCGI 85
                                  999*******************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-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 0.30s 00:00:00.72 Elapsed: 00:00:00.47
# Mc/sec: 871.47
//
Query:       gi|13540838|ref|NP_110526.1|  [L=150]
Description: 30S ribosomal protein S19e [Thermoplasma volcanium GSS1]
Scores for complete 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  163.7   0.1      2e-48  163.5   0.1    1.0  1  Ribosomal_S19e  Ribosomal protein S19e
     0.0039   17.0   0.0      0.022   14.6   0.0    2.0  2  RuvB_C          RuvB C-terminal 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 !  163.5   0.1   2.3e-52     2e-48       1     136 [.       3     137 ..       3     138 .. 0.97

  Alignments for each domain:
  == domain 1  score: 163.5 bits;  conditional E-value: 2.3e-52
                                   TSSSHHHHHHHHHS--S---S-SSS-SSSS-SS-S-SS-SSTTTHHHHHHHHHHHTS--TTSGGGGS----SS-SSS---- CS
                Ribosomal_S19e   1 tvkdVpaeelikalaeeLkksgklevPewadlvKtgsakelapededWfyvRaAsilRkvylrgpvGverlrkvYGgkkrr 81 
                                   +vk Vp + li+ ++ +Lk+++k++ P+w+++vKtg++ke++p ++dW yvRaAs+lRk+y++g +G++r++++YGgk +r
  gi|13540838|ref|NP_110526.1|   3 SVKYVPSDMLINYVSGKLKEEKKIKEPNWVKFVKTGVSKEKPPLQDDWIYVRAASMLRKLYINGYLGISRMSSEYGGKVDR 83 
                                   5899***************************************************************************** PP

                                   ---THHHHHHHHHTTSSS--SSS---SS-HHHHHTHHHHH--SS--S--XXXXXX CS
                Ribosomal_S19e  82 gvrpshfvkasgsvirkilqqLeklglvkkekkkgrrltkkGqrlldriaeevak 136
                                   g++++h +++s+s++r ++++Le++glv+k++k gr l+++G++lld+ ++e++k
  gi|13540838|ref|NP_110526.1|  84 GSKRYHAASGSRSITRFLFHELESAGLVQKTQK-GRSLSPQGMSLLDNASKEIIK 137
                                   ****************************88855.******************986 PP

>> RuvB_C  RuvB C-terminal winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.14   1.2e+03      13      31 ..      57      75 ..      53      82 .. 0.79
   2 !   14.6   0.0   2.5e-06     0.022      51      71 ..     108     128 ..     104     129 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.14
                                  HHHHHT.TT--B-HHHHHH CS
                        RuvB_C 13 kllkekfkggpvglktlaa 31
                                  ++l + + +g++g++ +++
  gi|13540838|ref|NP_110526.1| 57 SMLRKLYINGYLGISRMSS 75
                                  5677788999999998876 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 2.5e-06
                                   TTSEEEETTEEEE-HHHHHHH CS
                        RuvB_C  51 eglIertsrGRilTkkglkyl 71 
                                    gl+++t++GR l+++g+++l
  gi|13540838|ref|NP_110526.1| 108 AGLVQKTQKGRSLSPQGMSLL 128
                                   69****************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 936.61
//
Query:       gi|13540839|ref|NP_110527.1|  [L=124]
Description: hypothetical protein TVN0008 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      5e-28   97.6  18.7    5.8e-28   97.4  18.7    1.1  1  dsDNA_bind      Double-stranded DNA-binding domain
  ------ inclusion threshold ------
      0.097   11.9  14.3       0.12   11.6  14.3    1.0  1  Radial_spoke_3  Radial spoke protein 3
       0.19   11.4   9.8       0.28   10.9   9.8    1.3  1  Cwf_Cwc_15      Cwf15/Cwc15 cell cycle control protein
        1.4    9.3   8.1        3.2    8.1   7.7    1.9  1  Mac             Maltose acetyltransferase
        1.6    6.4   5.2        1.8    6.2   5.2    1.0  1  Herpes_UL32     Herpesvirus large structural phosphoprotein U


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 !   97.4  18.7   1.6e-31   5.8e-28       1     107 [.      19     120 ..      19     124 .] 0.90

  Alignments for each domain:
  == domain 1  score: 97.4 bits;  conditional E-value: 1.6e-31
                                   XXXXXXXXXXXXXXXXXXXX...XXXX--SS..S--SSHHHHTTS--HHHHHHHHHHTTT-HHHHHHHHHHHHHHHH--SS CS
                    dsDNA_bind   1 irkarlaelqaqagsssgsggaseqqeqqqeaseeeakqaiLsqiLepeAreRLsrirlvkperaeavenrLiqlaqsGql 81 
                                   ir+++++elq+qa +++      +++e++q++ e++++q+iL+qiL+p+AreRL+++rlv+p+ a++ven+Liqla++G++
  gi|13540839|ref|NP_110527.1|  19 IRRRQMEELQRQAMQRQM-----AEEEEKQREIEKARRQQILRQILDPSARERLNNVRLVRPDLADNVENQLIQLASMGRI 94 
                                   9************98876.....333333444699********************************************** PP

                                   -----HHHHHHHHHHHS---XXXXX. CS
                    dsDNA_bind  82 rskvteeqLkeLLeqvaekkketkiv 107
                                   ++ ++e++++++L++++e+k+e ki+
  gi|13540839|ref|NP_110527.1|  95 NRIIKESDIIDILSKLTENKREPKIE 120
                                   ************************94 PP

>> Radial_spoke_3  Radial spoke protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6  14.3   3.3e-05      0.12     147     257 ..       8     113 ..       5     123 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.3e-05
                Radial_spoke_3 147 lEVleEeELaalreqqrafeelRnaelaevqrLeeqekrlreekerrlkqqkealkkeketaekiaaralakqylaellps 227
                                   +E+ ++eEL+++r++q +  ++++     +qr  ++e++++ e e+ ++qq  ++  +  ++e++ + +l++  la+ +++
  gi|13540839|ref|NP_110527.1|   8 IEMSDDEELEKIRRRQMEELQRQA-----MQRQMAEEEEKQREIEKARRQQILRQILDPSARERLNNVRLVRPDLADNVEN 83 
                                   799**********99977655543.....45555555555556666666677777778899******************** PP

                Radial_spoke_3 228 vlesLedsgyfydpverdveteflpwLmee 257
                                    l +L + g +   ++++   ++l  L+e+
  gi|13540839|ref|NP_110527.1|  84 QLIQLASMGRINRIIKESDIIDILSKLTEN 113
                                   ******999888888755444555555444 PP

>> Cwf_Cwc_15  Cwf15/Cwc15 cell cycle control protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   9.8   7.8e-05      0.28     151     185 ..      14      48 ..      11      71 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 7.8e-05
                                   ----------------------------------- CS
                    Cwf_Cwc_15 151 rELekikreraeekerkerekaeeeekereeeiat 185
                                    ELeki+r ++ee +r++ +++ +ee+e+++ei +
  gi|13540839|ref|NP_110527.1|  14 EELEKIRRRQMEELQRQAMQRQMAEEEEKQREIEK 48 
                                   59****************99999999999888854 PP

>> Mac  Maltose acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   7.7   0.00088       3.2      12      49 ..      12      59 ..       9      67 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00088
                                  TSHHHHHHHHHHHHHHHHHH.TS.........TTT-HHHHHHHHHHHS CS
                           Mac 12 sDpeLvaeRlrarelcrryN.qt.........rpsdkdeRrelLrell 49
                                  +D+eL++ R+r  e ++r   q+         r+ +k++R+++Lr++l
  gi|13540839|ref|NP_110527.1| 12 DDEELEKIRRRQMEELQRQAmQRqmaeeeekqREIEKARRQQILRQIL 59
                                  69*******9986655554424534433333333366669*******9 PP

>> Herpes_UL32  Herpesvirus large structural phosphoprotein UL32
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   5.2   0.00051       1.8     366     441 ..       9      85 ..       2      97 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.00051
                   Herpes_UL32 366 gyldeeekkkerskrvddevvqrekqqlkaweerqqsllrrqrqP.ppptrkpgasrrlfgskadeddddddddeki 441
                                      d+ee+ k r++++++   q  ++q+   ee+q+++ + +rq        p a  rl   +    d  d+ +++ 
  gi|13540839|ref|NP_110527.1|   9 EMSDDEELEKIRRRQMEELQRQAMQRQMAEEEEKQREIEKARRQQiLRQILDPSARERLNNVRLVRPDLADNVENQL 85 
                                   56799***********966667777888889999*9999866655156778999*99**999999999999876654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3139  (0.175079); expected 358.6 (0.02)
Passed bias filter:                     1002  (0.0558871); 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: 0.54u 0.33s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 776.77
//
Query:       gi|13540840|ref|NP_110528.1|  [L=51]
Description: 50S ribosomal protein L39e [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.8e-20   70.7  13.8    6.9e-20   70.4  13.8    1.1  1  Ribosomal_L39  Ribosomal L39 protein
  ------ inclusion threshold ------
       0.54   10.3   4.5       0.56   10.3   4.5    1.1  1  REV            REV protein (anti-repression trans-activator p


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 !   70.4  13.8   7.7e-24   6.9e-20       1      42 []       9      50 ..       9      50 .. 0.98

  Alignments for each domain:
  == domain 1  score: 70.4 bits;  conditional E-value: 7.7e-24
                 Ribosomal_L39  1 kKlrLaKalkqNrpvPaWvrlktdrkvrynpkrRhWRrtkLk 42
                                  +K+rL+K++kqNr+vP Wv+++t rkv++np rR+WRr +Lk
  gi|13540840|ref|NP_110528.1|  9 RKIRLMKKVKQNRRVPGWVMMRTARKVTQNPLRRNWRRGNLK 50
                                  7***************************************98 PP

>> REV  REV protein (anti-repression trans-activator protein)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   4.5   6.2e-05      0.56       9      51 ..       4      46 ..       1      51 [] 0.78

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 6.2e-05
                           REV  9 eeelirklrllkllyqsnPyPqgeGtasarrnrrrrrrerqlr 51
                                  + el rk+rl+k + q    P     + ar+  +   r++++r
  gi|13540840|ref|NP_110528.1|  4 NKELGRKIRLMKKVKQNRRVPGWVMMRTARKVTQNPLRRNWRR 46
                                  679******************9999999998765555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (51 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       341  (0.0190195); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.31s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 327.15
//
Query:       gi|13540841|ref|NP_110529.1|  [L=89]
Description: 50S ribosomal protein L31e [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.7e-06   26.5   0.2    6.4e-06   26.3   0.2    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 !   26.3   0.2   3.6e-10   6.4e-06       3      70 ..       6      76 ..       4      83 .. 0.85

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 3.6e-10
                Ribosomal_L31e  3 vtreytInih.krihgvgfkkraprAlkeikkfamkemg..tpdvridtrLnkavwakgirnvpyrirvrl 70
                                  v++e   ni  +  +  ++k+ra   +  +++++ k+++  t+   id+++++++w+kg +++p ++  ++
  gi|13540841|ref|NP_110529.1|  6 VSKEIIMNIPlREAKLSSRKRRADTSISILRNYVSKKLKvdTSKIWIDPKVSETIWKKGREKPPSKLSLKI 76
                                  778888888525566678999****************997788889******************9987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       402  (0.0224218); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 568.96
//
Query:       gi|13540842|ref|NP_110530.1|  [L=218]
Description: translation initiation factor IF-6 [Thermoplasma volcanium GSS1]
Scores for complete 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-62  209.7   2.8    3.2e-62  209.4   2.8    1.2  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 !  209.4   2.8   1.8e-66   3.2e-62       1     197 []       6     199 ..       6     217 .. 0.98

  Alignments for each domain:
  == domain 1  score: 209.4 bits;  conditional E-value: 1.8e-66
                                   .E-BTTB--HHHH-EE-SSEEEE-TTS-HHHHHHHHHHHT-EEEE--BTTBS-HHHH-EE-SSEEEEETT--HHHHHHHHH CS
                         eIF-6   1 rlsiegsseiGvfarltnkyalvpegveeefvkaieeeLkvevvettiagsrlvGslvvgNsngllvpstvtdeeleklke 81 
                                   ++s+ +ss iG++a++++++a++++ ++e++v++++e+L+v++ +++i gs+l+G++++ Nsng+++p   + + l+ ++ 
  gi|13540842|ref|NP_110530.1|   6 KTSVMRSSFIGIYAKAWDDVAFITKMADEKTVNEFREVLQVDIKRISIDGSTLIGTMIAVNSNGIVLPYGSNIDGLDGIDG 86 
                                   578999**************************************************************9999999999997 PP

                                   HHH---EEE--SS--HHHHEEE-SSEEEE-GGGGG.GHHHHHHHHTSEEEE--BTTBS-TTTSEEE-SSEEEE-TT--HHH CS
                         eIF-6  82 slkleverleekltAlGNvilaNDkvAlvhpdlsketveiiadvLgvevvrgtiagiktvGsaavvtnkgllvhpkateee 162
                                      ++v  l++k++A+GN i+aND++A++h+ +s++++++i+d+Lgve++r++i++i tvGsa+v+t+kg+lv+p+++++e
  gi|13540842|ref|NP_110530.1|  87 ---RNVLYLKDKINAVGNDIIANDHGAIIHKAFSNKARKEIEDTLGVETIRTSIGNILTVGSASVLTSKGMLVNPETDDDE 164
                                   ...5***************************************************************************** PP

                                   HHHHHHHHT-SEEE--BTTTBS-GGGTEEE-SS-E CS
                         eIF-6 163 leeleellkveveagTvNrGsklvgsglvaNdkga 197
                                   le+l++++kv+v+ gT N+Gs +vg+++vaN+kg+
  gi|13540842|ref|NP_110530.1| 165 LEFLKDFFKVSVKSGTANFGSIYVGASIVANSKGI 199
                                   *********************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       409  (0.0228122); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1420.52
//
Query:       gi|13540843|ref|NP_110531.1|  [L=166]
Description: orotate phosphoribosyltransferase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      3e-08   33.3   0.9    5.4e-08   32.5   0.9    1.4  1  Pribosyltran  Phosphoribosyl transferase domain
  ------ inclusion threshold ------
      0.011   15.1   0.0      0.014   14.8   0.0    1.2  1  UPRTase       Uracil phosphoribosyltransferase
      0.043   13.8   0.0       0.06   13.3   0.0    1.4  1  ADH_zinc_N    Zinc-binding dehydrogenase
       0.12   11.8   0.3       0.17   11.3   0.3    1.2  1  DUF5321       Family of unknown function (DUF5321)


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 !   32.5   0.9   1.2e-11   5.4e-08      21     131 ..      43     145 ..      31     152 .. 0.84

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 1.2e-11
                                   EEEEE..--GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE........EE----TTSEEEEE-SEESS CS
                  Pribosyltran  21 eilee..yngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdesrlledpagkkVliVDDildt 99 
                                   ei +e  +  +   ++g + g+vp+  +++  +++p+++vrk++ ++  s  +           ++ +g+ V +++D+++t
  gi|13540843|ref|NP_110531.1|  43 EIASEfsKMIHARKIAGMELGAVPLIVATSLNMGIPYVIVRKERSHGTLSLIVG----------RLNRGEEVDVIEDVVTT 113
                                   444443333445689***************999*99999999998888777775..........689************** PP

                                   SHHHHHHHHHHHCC-BSEEEEEEEEE-HHHHH CS
                  Pribosyltran 100 GgTllaalelLkekgpeevriavlvdkpatee 131
                                   G+++l+a++ L+e g+ +  + ++vd+ ++  
  gi|13540843|ref|NP_110531.1| 114 GNSVLKAINVLRENGVVVKDAYCVVDREEGGA 145
                                   ****************9999999999988766 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   3.2e-06     0.014     123     160 ..     103     138 ..      77     159 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.2e-06
                       UPRTase 123 tvlllDpviaTGgsaaaaiqlLkergvgeekIlvlsvl 160
                                   +v +++ v+ TG+s+ +ai++L+e+gv +++    +v+
  gi|13540843|ref|NP_110531.1| 103 EVDVIEDVVTTGNSVLKAINVLRENGVVVKDAY--CVV 138
                                   5667889********************998644..445 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   1.3e-05      0.06      34      86 ..      76     131 ..      44     154 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.3e-05
                                   TESEEEETTTC.H..HHHHHHHHTTTSSEEEEEESSCSHHHHHHHHHCEEEEEEEE CS
                    ADH_zinc_N  34 Gadevinykea.d..lverikeltggegvdvvfecvGsgatleaalkllkpgGrlv 86 
                                   G  +vi +ke  +  l+  + +l +ge vdv+ ++v +g ++  a+++l+++G +v
  gi|13540843|ref|NP_110531.1|  76 GIPYVIVRKERsHgtLSLIVGRLNRGEEVDVIEDVVTTGNSVLKAINVLRENGVVV 131
                                   55555555332112234444455579****************************98 PP

>> DUF5321  Family of unknown function (DUF5321)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.3   3.8e-05      0.17      83     108 ..      90     116 ..      79     126 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 3.8e-05
                       DUF5321  83 lLreviekvqrGEevdv.eklLGtGde 108
                                   +L  ++ +++rGEevdv e +  tG++
  gi|13540843|ref|NP_110531.1|  90 TLSLIVGRLNRGEEVDViEDVVTTGNS 116
                                   67789***********86889999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       548  (0.030565); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1086.15
//
Query:       gi|13540844|ref|NP_110532.1|  [L=614]
Description: Rad3-related DNA helicase [Thermoplasma volcanium GSS1]
Scores for complete 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  193.3   0.4    1.3e-56  191.3   0.8    1.9  2  HBB           Helical and beta-bridge domain
    9.3e-41  139.4   0.2    1.7e-40  138.5   0.2    1.4  1  DEAD_2        DEAD_2
    4.7e-33  114.8   0.0    1.2e-32  113.4   0.0    1.7  1  Helicase_C_2  Helicase C-terminal domain
    2.2e-10   40.8   0.1    1.4e-09   38.2   0.0    2.4  2  ResIII        Type III restriction enzyme, res subunit
    3.3e-08   33.5   0.0    7.9e-06   25.8   0.0    2.6  2  DEAD          DEAD/DEAH box helicase
     0.0031   17.0   0.0      0.025   14.0   0.0    2.4  2  PhoH          PhoH-like protein
  ------ inclusion threshold ------
      0.049   13.0   0.0      0.082   12.2   0.0    1.3  1  CTP_synth_N   CTP synthase N-terminus


Domain annotation for each model (and alignments):
>> HBB  Helical and beta-bridge domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  191.3   0.8   5.1e-60   1.3e-56       2     190 .]     237     427 ..     236     427 .. 0.99
   2 ?   -2.6   0.0       1.5   3.8e+03      51      71 ..     578     598 ..     576     603 .. 0.85

  Alignments for each domain:
  == domain 1  score: 191.3 bits;  conditional E-value: 5.1e-60
                                   CHCHCCCCHHCCCCCCCH..HHHHHHHHCCCCHHHHSTTTE.CCHCHHHHHCHCHHHCHHHHHHHHHHHHHHHHHHHCCHH CS
                           HBB   2 ikeaketdepklqdeysr..LvegLreaeeereeeyvleee.pilpdeileeavpglirsaehflsllkrlveygkarree 79 
                                   +kea+++++p+l++ +++  ++e++r++ e++ +e+v+e++ +i+++e+ e+++++++ s++++++l ++l+ +g+++++e
  gi|13540844|ref|NP_110532.1| 237 EKEAQSFGDPELDRGVHVtdFIEMIRSTLERTIKERVKEDDvRIRFQEFKEYLMIMNKKSEKSIRDLNNYLYLFGEYVENE 317
                                   79************************************9999*************************************** PP

                                   CCCTCC-SHHHHHHHHHHHHHHHTS.TTTEEEEEE.STT.EECCCCS-TCCHHHHHHHCHCCCCCCTS-SSHHHHHHHHT. CS
                           HBB  80 kieksesPrsflsrlaefllawlssdeedYvrlvskeegesLeavcldPskalrflkerlssllmsgtltpleeysdiiGl 160
                                   k++  ++P s++s+la++l+a++++d+++Y++++sk+e+ +++a+cldPs++l+ lke+ ++++msgtl+p+e+ysd++G+
  gi|13540844|ref|NP_110532.1| 318 KEKAGKVPVSYCSSLAQRLEAMMDEDDAMYAAILSKSESGYIQASCLDPSSILSSLKES-KTIHMSGTLEPFEFYSDVTGF 397
                                   ***********************************************************.********************* PP

                                   ...EEE.S..S.GGHCCCCCCCCCSHTCCC CS
                           HBB 161 eaklkkfpspfpkEnlivlfatdVsTkyke 190
                                   ++++++++++fp En++v++++ VsTky++
  gi|13540844|ref|NP_110532.1| 398 DIPFRRIENVFPIENRFVSYYEGVSTKYDT 427
                                   ***************************985 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.5
                                   HCHHHCHHHHHHHHHHHHHHH CS
                           HBB  51 avpglirsaehflsllkrlve 71 
                                   a+ +l  +a++f++++ +lv+
  gi|13540844|ref|NP_110532.1| 578 ACVILDKRAKQFRRFIPDLVK 598
                                   677888999******999987 PP

>> DEAD_2  DEAD_2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  138.5   0.2   6.6e-44   1.7e-40       1     176 []      56     233 ..      56     233 .. 0.93

  Alignments for each domain:
  == domain 1  score: 138.5 bits;  conditional E-value: 6.6e-44
                                   EEESSHHHHHHHHHHHHHHHHHCHHHS---EEEE--CCCC-SCHHCCCHHC...CCCHHHHHHHHHCCHHCCHTTTTTT-S CS
                        DEAD_2   1 ycsRThsqleqvvkelkklesykkkkekvkvviLgSRknlCineevkkekk...ekavneaCkelkkkkaeekeekCsffe 78 
                                   y +RT+sq eqv++el+ +++ +    k++++++++R nlCi ++  ++ k    ++++++C+++k++++e ++e+C++++
  gi|13540844|ref|NP_110532.1|  56 YLVRTNSQEEQVIRELRTISKNR----KIRALPMQGRINLCILYKTADDLKeatAESLSKFCNSRKRQVMEGHQEACPYYT 132
                                   899****************7555....5***************9998766523366778********************** PP

                                   CCCCHHHHHHHHHHC---CHHHHHHHHHCT--HHHHHHHHHCCTSEEEEEHHHHTSCCCHHHHH...T..GCGCEEEECTC CS
                        DEAD_2  79 nleelkklkkllleevvdiedlvelgeklklCPYylsrelledadiiilpYqyLldekireslk...gislknsivilDEA 156
                                    + ++k++k++l+e++ + e+++e+   ++lCPY + ++ l+dadi+++pY y+l++ +++++    g+s ++ i++lDEA
  gi|13540844|ref|NP_110532.1| 133 IKVRSKETKDFLFENLPTAEEFYEYAFTNNLCPYESIKASLSDADIVVAPYMYFLNKTVADRFLshwGVSREQLIIVLDEA 213
                                   **9*********************************************************99877999************* PP

                                   CCHHHHHHHCC-EEEECHHH CS
                        DEAD_2 157 hNiedvceeaasveiseesl 176
                                   hN+ d+ +++ s++is esl
  gi|13540844|ref|NP_110532.1| 214 HNLPDIGRSLGSFRISIESL 233
                                   ***************98775 PP

>> Helicase_C_2  Helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.4   0.0   4.7e-36   1.2e-32       1     157 [.     440     588 ..     440     599 .. 0.89

  Alignments for each domain:
  == domain 1  score: 113.4 bits;  conditional E-value: 4.7e-36
                  Helicase_C_2   1 llellevvpggvlvffpSyklleevverlkeeleskkieifvee...keesrekvleeykekkkkgaillavcrGklsEGi 78 
                                   + ++++ v+ +++v+fpSy+++++v+    +      +++++e+   ++ ++ +v++++++    g+ llav +G+lsEG+
  gi|13540844|ref|NP_110532.1| 440 IENIVNGVKRNTIVYFPSYAVMDKVIGSGLD------FDFLQEKknlDQTEFYDVVKKFRN---GGKPLLAVSGGRLSEGM 511
                                   5789999*******************96554......455555444455899999****99...9**************** PP

                  Helicase_C_2  79 dfsddllraviivglPfpnpkdpeveakreyldekgkknsgkewylpealravnQaiGRliRhkdDygaivllDeRfak 157
                                   +f++++l++++i g+Pfp p d +++a  +y++ k k ++++++ l +a+ +++Q iGRliR kdD+ga v+lD+R ++
  gi|13540844|ref|NP_110532.1| 512 NFPGRELELILIAGIPFPRP-DATNRALYDYYEMKYK-KGWEYAVLAPAIIKIRQEIGRLIRGKDDHGACVILDKRAKQ 588
                                   ********************.78889999*******9.99999*********************************987 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.2   0.0   5.5e-13   1.4e-09       3     146 ..       3     218 ..       1     240 [. 0.72
   2 ?   -3.0   0.1       2.4   6.1e+03      72     116 ..     283     334 ..     263     348 .. 0.55

  Alignments for each domain:
  == domain 1  score: 38.2 bits;  conditional E-value: 5.5e-13
                                   EE-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHG......... CS
                        ResIII   3 elreyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleef......... 74 
                                   e r+yQ eai+ +++kl   +   + ++++TG+GKT++a+    +++ +g+  k+l lv ++s  eq ++e+         
  gi|13540844|ref|NP_110532.1|   3 EDRSYQNEAIDFIASKLA--NYPGVALEAPTGSGKTMMALLGSLKYAYNGHL-KILYLVRTNSQEEQVIRELrtisknrki 80 
                                   569**************5..777888*************9999999999887.*******************555555555 PP

                                   ..........................GGGTGG....GEEEESSS-B--....................-SEEEEEHHHHHH CS
                        ResIII  75 ..........................kkflseaykeigkkvsgdkkka.............kekdstnkkilvttiqslda 116
                                                             +        + +k+ +++k++              k +++++k++l+++  ++ +
  gi|13540844|ref|NP_110532.1|  81 ralpmqgrinlcilyktaddlkeataE--------SLSKFCNSRKRQVmeghqeacpyytiKVRSKETKDFLFENLPTAEE 153
                                   555555555555555554222222220........2444444444444677777778888877888888888888888777 PP

                                   TH.................................HHHTTT-S..........EEEEETGGGTTS CS
                        ResIII 117 dseee.........................eeeseellrdrfd..........viiiDEaHrlga 146
                                     e +                          +  ++   drf+          +i+ DEaH+l +
  gi|13540844|ref|NP_110532.1| 154 FYEYAftnnlcpyesikaslsdadivvapyMYFLNKTVADRFLshwgvsreqlIIVLDEAHNLPD 218
                                   775558888888877777777788888888444444444444455556666668999****9875 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2.4
                                   HHGGGGTGG....GEEEESSS-B--..............-SEEEEEHHHHHH CS
                        ResIII  72 eefkkflseaykeigkkvsgdkkka.......kekdstnkkilvttiqslda 116
                                   +efk++l   +k+ +k++++ ++         ++++++  k+ v+  +sl +
  gi|13540844|ref|NP_110532.1| 283 QEFKEYLMIMNKKSEKSIRDLNNYLylfgeyvENEKEKAGKVPVSYCSSLAQ 334
                                   4444444444444444443333333555555555555555555555555555 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.0   3.1e-09   7.9e-06       3      79 ..       7      83 ..       5     120 .. 0.81
   2 !    5.0   0.0    0.0072        19      98     138 ..     176     221 ..     156     242 .. 0.64

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 3.1e-09
                                  HHHHHHHHHHTT....CEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEE CS
                                  xxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD  3 iQaeaiplilgg....gdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvl 79
                                  +Q eai+ i ++      v ++a+TGsGKT+++l+  l+  y+     + k+l+++ t +  eq++++l+++ k+ ++r+l
  gi|13540844|ref|NP_110532.1|  7 YQNEAIDFIASKlanyPGVALEAPTGSGKTMMALLGSLKYAYN----GHLKILYLVRTNSQEEQVIRELRTISKNRKIRAL 83
                                  79999999995444446899******************99985....999************************8776554 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0072
                                   CSEEEEEHHHHHH.HH.....HCTSSHCTTEEEEEEETHHHHHHTTT CS
                                   xxxxxxxxxxxxx.xx.....xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD  98 vdivvgtpgrldd.ll.....stgklnlsqvrflVlDEadrlldqgf 138
                                   +divv+    +++  +     s   ++ +q+ ++VlDEa++l d g+
  gi|13540844|ref|NP_110532.1| 176 ADIVVAPYMYFLNkTVadrflSHWGVSREQL-IIVLDEAHNLPDIGR 221
                                   5666655543333233222223333333344.79*******988755 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.0   9.8e-06     0.025      10      63 ..       9      66 ..       4     120 .. 0.82
   2 ?   -0.7   0.0      0.31   7.8e+02     119     131 ..     204     216 ..     155     220 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 9.8e-06
                                  HHHHHHHH....H-SEEEEE--TTSSTTHHHHHHHHHHHHTTS-SEEEEEE-S--TT- CS
                          PhoH 10 keylealk....kndivfaiGpaGtGKtylavalavealkkkkvkriiltrpaveage 63
                                  +e+++ +     ++  v   +p+G+GKt++a+   +++  ++++k + l+r + + ++
  gi|13540844|ref|NP_110532.1|  9 NEAIDFIAsklaNYPGVALEAPTGSGKTMMALLGSLKYAYNGHLKILYLVRTNSQEEQ 66
                                  44444444333377789999*************************9999998877554 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.31
                                   -SEEEEE-SGGG- CS
                          PhoH 119 ndafvilDEAQnt 131
                                   ++ +++lDEA n+
  gi|13540844|ref|NP_110532.1| 204 EQLIIVLDEAHNL 216
                                   4556888888876 PP

>> CTP_synth_N  CTP synthase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   3.2e-05     0.082     180     244 ..      66     130 ..      38     148 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.2e-05
                                   TTTSSB-HHHHHHHHHHHHHHT---SEEEEEESS---HHHHHHHHHHCT--GGGEEEEE--S-GG CS
                   CTP_synth_N 180 kaagelktkptqhsvkelrslGiqpdiivcrsekeleeevkekialfcnvekeavisvkdvesiy 244
                                   +  +el+t + ++ +++l   G  +  i++++ ++l+e++ e +++fcn +k++v++ ++    y
  gi|13540844|ref|NP_110532.1|  66 QVIRELRTISKNRKIRALPMQGRINLCILYKTADDLKEATAESLSKFCNSRKRQVMEGHQEACPY 130
                                   4567999999**********************************************988766544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (614 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       839  (0.0467957); expected 358.6 (0.02)
Passed bias filter:                      600  (0.0334653); 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: 0.73u 0.31s 00:00:01.04 Elapsed: 00:00:00.49
# Mc/sec: 3766.94
//
Query:       gi|13540845|ref|NP_110533.1|  [L=151]
Description: N-terminal acetyltransferase complex, Ard1 subunit [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.5e-17   62.7   0.0    4.4e-17   62.4   0.0    1.1  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    6.1e-15   55.3   0.0      7e-15   55.1   0.0    1.1  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    1.2e-13   51.3   0.0    1.7e-13   50.8   0.0    1.2  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    2.1e-06   28.0   0.0    2.7e-06   27.6   0.0    1.2  1  Acetyltransf_4   Acetyltransferase (GNAT) domain
    3.1e-06   27.1   0.0    4.9e-06   26.4   0.0    1.3  1  FR47             FR47-like protein
      5e-06   27.2   0.0    9.5e-06   26.3   0.0    1.4  1  Acetyltransf_3   Acetyltransferase (GNAT) domain
    0.00013   21.7   0.1    0.00018   21.2   0.1    1.3  1  Acetyltransf_8   Acetyltransferase (GNAT) domain
      0.001   19.2   0.4     0.0018   18.4   0.3    1.5  1  Acetyltransf_6   Acetyltransferase (GNAT) domain
     0.0049   17.0   0.0     0.0082   16.3   0.0    1.4  1  Acetyltransf_CG  GCN5-related N-acetyl-transferase
  ------ inclusion threshold ------
      0.058   13.5   0.0       0.44   10.6   0.0    2.1  2  Acetyltransf_9   Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.4   0.0   2.5e-20   4.4e-17       4     117 .]      21     128 ..      17     128 .. 0.83

  Alignments for each domain:
  == domain 1  score: 62.4 bits;  conditional E-value: 2.5e-20
                                   HHHHHHHHTHHHHHHHHHHHHHHHHHSTTCEEEEEEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHH CS
                Acetyltransf_1   4 lvellvesffppnedaseeefeesfsleaegllvaeedgeliGfisllkipdekggvayieslaVspeyrgkGlGsaLlea 84 
                                   ++++++ s ++ + +a   +    +++ +e++ v+   g ++Gfi ++k+      +a i  +aV++ +r++G+GsaL++a
  gi|13540845|ref|NP_110533.1|  21 VYRIAQTSLTEYYTQALILD---LHREWPESFMVYTVAGSVVGFIVGSKYSR---TEARILLFAVDERFRRMGVGSALMDA 95 
                                   55555555444333333333...34445778999999***************...89************************ PP

                                   HHHHHHHTTESEEEEEEETTEHHHHHHHHHTTE CS
                Acetyltransf_1  85 leerareegikkivlaveedndaairlYeklGF 117
                                    +  +re++   + l+v+ dnd air+Y+k GF
  gi|13540845|ref|NP_110533.1|  96 FLSLCREQNMLSVRLEVRTDNDEAIRFYKKYGF 128
                                   ********99788***************88**9 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.1   0.0   3.9e-18     7e-15      28     109 ..      44     131 ..      10     147 .. 0.84

  Alignments for each domain:
  == domain 1  score: 55.1 bits;  conditional E-value: 3.9e-18
               Acetyltransf_10  28 egealllvaeeggkivGvi...el.rdgshisllfVdpeyrgqGigkaLleaveeeaekdgikl.eltvnasp.yavpfYe 102
                                   e    ++v+++ g++vG+i   ++ r++ +i l++Vd+ +r+ G+g+aL++a ++ +++++    +l+v+ ++ +a++fY+
  gi|13540845|ref|NP_110533.1|  44 EWPESFMVYTVAGSVVGFIvgsKYsRTEARILLFAVDERFRRMGVGSALMDAFLSLCREQNMLSvRLEVRTDNdEAIRFYK 124
                                   44566899999********9877767777*******************************9999***************** PP

               Acetyltransf_10 103 klGFkav 109
                                   k+GF+ +
  gi|13540845|ref|NP_110533.1| 125 KYGFVIT 131
                                   ****966 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.8   0.0   9.7e-17   1.7e-13       5      75 ..      49     129 ..      44     130 .. 0.73

  Alignments for each domain:
  == domain 1  score: 50.8 bits;  conditional E-value: 9.7e-17
                                   EEEEEETTEEEEEEEEEEES...TCTEEEEE-GGGTTSSHHHHHHHH.....TTSEEEEE...EEEETHHHHHHHHHHTTE CS
                Acetyltransf_7   5 vfVaeddgkivGfialslld...aeitrlaVdpeyrgkGiGraLlea.....aekgiile...qlelnaekaikfYeklGF 74 
                                   + V+   g +vGfi+ s ++   a i  +aVd+ +r+ G+G+aL++a     +e+++  +   ++++++++ai+fY+k+GF
  gi|13540845|ref|NP_110533.1|  49 FMVYTVAGSVVGFIVGSKYSrteARILLFAVDERFRRMGVGSALMDAflslcREQNML-SvrlEVRTDNDEAIRFYKKYGF 128
                                   5666666999*****99999876666669*****************756544223322.221234444459********** PP

                                   E CS
                Acetyltransf_7  75 e 75 
                                   +
  gi|13540845|ref|NP_110533.1| 129 V 129
                                   8 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.0   1.5e-09   2.7e-06      51     151 ..      48     145 ..      10     148 .. 0.83

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 1.5e-09
                Acetyltransf_4  51 vflvae.sdrivGyaylgqfkkrakdwkaelsvylaerdnnkeglgrelidaleqvlkeqnienllaeiaspnensiqfhk 130
                                    f+v+  ++ +vG   ++  k+  ++++ +l + ++ +  + +g+g++l+da     +eqn+++   e+  +n+++i f+k
  gi|13540845|ref|NP_110533.1|  48 SFMVYTvAGSVVGFIVGS--KY-SRTEARILLFAVD-ERFRRMGVGSALMDAFLSLCREQNMLSVRLEVRTDNDEAIRFYK 124
                                   5899999999***99998..55.6799999999996.67****************************************** PP

                Acetyltransf_4 131 alGFelvgifkkcikkngrwi 151
                                   + GF +++ + +++ +    +
  gi|13540845|ref|NP_110533.1| 125 KYGFVITAMLPNYYSDSSNAY 145
                                   *******99999988776666 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.0   2.7e-09   4.9e-06      23      78 ..      73     129 ..      57     137 .. 0.87

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 2.7e-09
                                   SEEEEEE-GGG-SSSHHHHHHHHHHHHHHH.S-S-EEEEEETT-HHHHHHHHHHT-E CS
                          FR47  23 elgalqvlpehrrrGlgsrlvkalakeiae.rgktvllvvvasNtpsirlyeklGfe 78 
                                    +    v++ +rr+G gs l  a     +e +   v l v+++N+++ir+y+k Gf 
  gi|13540845|ref|NP_110533.1|  73 RILLFAVDERFRRMGVGSALMDAFLSLCREqNMLSVRLEVRTDNDEAIRFYKKYGFV 129
                                   5677889*********************99445577899****************95 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.0   5.3e-09   9.5e-06       3     137 ..       9     128 ..       9     129 .. 0.84

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 5.3e-09
                Acetyltransf_3   3 lLrplteeDlealfelrsdpevmrylpepltleeaeewlerawaeeseeegygwaivlkdtgviGsvglrdleeedeeael 83 
                                   ++r+++++D+e ++++++   +++y+++ l l+  +ew e++         + +++   ++ v+G++   ++++ +    l
  gi|13540845|ref|NP_110533.1|   9 TIREFSPKDIESVYRIAQ-TSLTEYYTQALILDLHREWPESF---------MVYTV--AGS-VVGFIVGSKYSRTEA-RIL 75 
                                   689***********9777.66788999999999999999954.........45777..455.9****8888887653.556 PP

                Acetyltransf_3  84 gymlapsfwgkGyateavralleyafeelglerlvavidkeNeaSirvleklGf 137
                                    + +++ f++ G+++  + a+l ++ +e+++  ++ ++ ++N   ir ++k Gf
  gi|13540845|ref|NP_110533.1|  76 LFAVDERFRRMGVGSALMDAFLSLC-REQNMLSVRLEVRTDNDEAIRFYKKYGF 128
                                   6777788******************.6777888********************9 PP

>> Acetyltransf_8  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.1   9.9e-08   0.00018      85     139 ..      77     130 ..      14     134 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 9.9e-08
                                   EESSHHHCTTTCHHHHHHHHHHHHHCCTT--EEEE--BTT-HHHHHHHHHTT-EE CS
                Acetyltransf_8  85 ligeaeargkglttallralvhylfadprtrrvvvEPdvrNerairllekaGfek 139
                                   +  ++++r+ g+++al+ a+++++ ++  + +v +E + +N +air+++k Gf+ 
  gi|13540845|ref|NP_110533.1|  77 FAVDERFRRMGVGSALMDAFLSLCREQ-NMLSVRLEVRTDNDEAIRFYKKYGFVI 130
                                   4447899***************99887.899**********************86 PP

>> Acetyltransf_6  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.3     1e-06    0.0018      58     132 ..      34     109 ..      19     125 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1e-06
                Acetyltransf_6  58 lrdllaalaargalr.lyvlrldgrpvAvalglrsgd.rlyywlggydpelaklspgllllweliedaaeeGlrrfd 132
                                    ++l+ +l  r++ + ++v  + g +v++++g ++ +  +  +l ++d++++++++g  l+   +  ++e+ + ++ 
  gi|13540845|ref|NP_110533.1|  34 TQALILDL-HREWPEsFMVYTVAGSVVGFIVGSKYSRtEARILLFAVDERFRRMGVGSALMDAFLSLCREQNMLSVR 109
                                   33333343.34444415556669**********9887367799*******************999999998876665 PP

>> Acetyltransf_CG  GCN5-related N-acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   4.6e-06    0.0082      24      58 ..      71     105 ..      48     111 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 4.6e-06
               Acetyltransf_CG  24 vldfthTeVpeelrGkGiAkkLvkaalddareegl 58 
                                   +  +    V+e++r+ G++++L++a l   re+++
  gi|13540845|ref|NP_110533.1|  71 EARILLFAVDERFRRMGVGSALMDAFLSLCREQNM 105
                                   45555568************************997 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.28   5.1e+02       2      28 ..      10      36 ..       9      63 .. 0.75
   2 ?   10.6   0.0   0.00025      0.44      75     125 ..      73     128 ..      62     131 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.28
                                  EEEE-GGGHHHHHHHHHHHTT----H. CS
                Acetyltransf_9  2 irelteedldevlellkyaFqdeespl 28
                                  ire  ++d++ v+++ +++  +  +++
  gi|13540845|ref|NP_110533.1| 10 IREFSPKDIESVYRIAQTSLTEYYTQA 36
                                  899999999999999999887766665 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00025
                                   EEEEEEE-CCGTTS-HHHHHHHHHHHHHHHTT--EEEE--.....SSHHHHHTTT- CS
                Acetyltransf_9  75 gvtgVavapehrgrgvlskLlaraleemreegqplsllfP.....ssipiYrrfGy 125
                                    +   av+   r+ gv s+L++++l  +re++   + l        +i++Y+++G+
  gi|13540845|ref|NP_110533.1|  73 RILLFAVDERFRRMGVGSALMDAFLSLCREQNMLSVRLEVrtdndEAIRFYKKYGF 128
                                   5667799999********************99888888888777767899999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       567  (0.0316247); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 1000.16
//
Query:       gi|13540846|ref|NP_110534.1|  [L=400]
Description: S-adenosylmethionine synthetase [Thermoplasma volcanium GSS1]
Scores for complete 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-170  566.0   7.7     4e-170  565.9   7.7    1.0  1  AdoMet_Synthase  S-adenosylmethionine synthetase (AdoMet synt
  ------ inclusion threshold ------
      0.035   14.8   2.4        1.4    9.6   0.0    3.6  5  S-AdoMet_synt_N  S-adenosylmethionine synthetase, N-terminal 


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 !  565.9   7.7  4.5e-174    4e-170       1     396 []       3     396 ..       3     396 .. 0.98

  Alignments for each domain:
  == domain 1  score: 565.9 bits;  conditional E-value: 4.5e-174
                                   --EEEEE-TTS-GTTSSEEEEEEE-TTSHHHHHHHHHHHHHHHHHHHHHHHHSS---EEEEEEEEE--EEEEETTEEEEEE CS
               AdoMet_Synthase   1 rnivveelkkkpveeqevEivErKGiGHPDsiaDgiaeavsralskeylekfgailhhniDkvllvaGesepkfgGGevie 81 
                                   rni+veel++ p+ ++evEivErKGiGHPDs+aDgiaeavsr+lsk+yle++g+ilhhn+D+v++v+G+s+pk+gGG v+e
  gi|13540846|ref|NP_110534.1|   3 RNISVEELNQIPTPKKEVEIVERKGIGHPDSVADGIAEAVSRSLSKYYLEHYGRILHHNTDQVEVVGGQSAPKYGGGLVLE 83 
                                   79******************************************************************************* PP

                                   -EEEEEEEEEEEEE.EEE--HHHHHHHHHHHHHHHH-SS--TTTSEEEEEEEEEEEEHHHHHHCH-SS..-BESSSEEEEE CS
               AdoMet_Synthase  82 pieillsgratkevegekipveeialeaakeylkenlraldlekdvivdvklgkgsadLkdvferkkkevplaNDtSfgvg 162
                                   p++illsgrat++v+++++p+++i+++aak+yl++n+++ld++ dv++d ++g+gs dL++v++++k    +aNDtSfgvg
  gi|13540846|ref|NP_110534.1|  84 PTYILLSGRATTKVGNDRVPYKSITIKAAKDYLRNNFSHLDVDADVMIDSRIGQGSVDLVEVYDTSKL---EANDTSFGVG 161
                                   *****************************************************************655...8********* PP

                                   EES--HHHHHHHHHHHHHTSHHHHHH-TTEEEEEEEEEEEETTEEEEEEEEEEEGGG--SHHHHHHHHHHHHHHHHHHHHH CS
               AdoMet_Synthase 163 yaplseleklvleterllnskelkkklpevGeDiKvmglRekkkielTvavalvdrlvkdleeYlevkeeikeeveelakk 243
                                   +aplse+e++vl+ter+ln  +lkkklp+vG DiKvmg+R+k++i+lTva+a+vd+++kd++eY++ k+++k+ v ++a +
  gi|13540846|ref|NP_110534.1| 162 FAPLSETENIVLKTERYLNG-SLKKKLPMVGYDIKVMGFRQKDTINLTVAAAFVDKYIKDADEYFNLKDQLKDLVLDNAVE 241
                                   *******************7.88********************************************************** PP

                                   HSTTSEEEEEE-TT-BGG..GTB--EESSSSGGGTT--EETTSS--TTSSB-TTS----S--TTS-TTT-HHHHHHHHHHH CS
               AdoMet_Synthase 244 ltkerevevevNtaDkke..eesvyltvtGtsaEegDdGsvGRGNRvnGlitpnrpmslEAaaGKNPvsHvGKiYnvlane 322
                                    t+ +ev+v++NtaD  e  +++ yltvtG+s+E+gDdGsvGRGNRvnGlitp+r ms+EAaaGKNPv+HvGK+Ynvlan+
  gi|13540846|ref|NP_110534.1| 242 ETD-KEVKVYINTADIREnsKSVGYLTVTGMSMENGDDGSVGRGNRVNGLITPYRAMSMEAAAGKNPVTHVGKLYNVLANK 321
                                   999.***********887668889********************************************************* PP

                                   HHHHHHHH-.TTEEEEEEEEEE-TTSBTTS-SEEEEEEEESSS---HHSHHHHHHHHHHHHT-HHHHHHHHTTT- CS
               AdoMet_Synthase 323 iakeiveev.egvkevyvrllsqiGkpidePlvasvqvilekgvsleevekeveeiideelekieeiteeliegk 396
                                   ia++iv+e  ++++ev vr++sqiG+pid+P+vasvqvi+e +v+ ++++++++++++++l++++++t++++egk
  gi|13540846|ref|NP_110534.1| 322 IANDIVQEEgNDIAEVLVRIVSQIGRPIDDPHVASVQVIYEGNVDHSKHKNNIRNLVNDRLAHVSDLTMQFVEGK 396
                                   *****9876266************************************************************996 PP

>> S-AdoMet_synt_N  S-adenosylmethionine synthetase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00016       1.4      11      25 ..      28      42 ..      21      70 .. 0.85
   2 ?   -1.1   0.0      0.35   3.1e+03      66      87 ..     182     203 ..     154     218 .. 0.76
   3 ?    2.2   0.1     0.032   2.9e+02      18      43 ..     228     254 ..     226     274 .. 0.81
   4 ?   -1.6   0.0      0.51   4.6e+03      39      75 ..     298     331 ..     292     350 .. 0.58
   5 ?   -2.3   0.1       0.8   7.2e+03      75      75 ..     346     346 ..     309     385 .. 0.59

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00016
               S-AdoMet_synt_N 11 eGHPDkvadqisdai 25
                                   GHPD vad i++a+
  gi|13540846|ref|NP_110534.1| 28 IGHPDSVADGIAEAV 42
                                  6***********997 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.35
               S-AdoMet_synt_N  66 ivrevikeigYekeelgfdakt 87 
                                     ++++  +gY+ + +gf+ k+
  gi|13540846|ref|NP_110534.1| 182 SLKKKLPMVGYDIKVMGFRQKD 203
                                   5677888899998788887654 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.032
               S-AdoMet_synt_N  18 adqisdaildailke.dpkarvacetl 43 
                                    dq+ d +ld+ ++e d++ +v ++t+
  gi|13540846|ref|NP_110534.1| 228 KDQLKDLVLDNAVEEtDKEVKVYINTA 254
                                   59999*****99987588889999886 PP

  == domain 4  score: -1.6 bits;  conditional E-value: 0.51
               S-AdoMet_synt_N  39 acetlvttglvvvageittkakvdiekivrevikeig 75 
                                   ++e+++ ++ v+ +g++ +   v  +ki+ + ++e g
  gi|13540846|ref|NP_110534.1| 298 SMEAAAGKNPVTHVGKLYN---VLANKIANDIVQEEG 331
                                   5666666777766666632...344455555544444 PP

  == domain 5  score: -2.3 bits;  conditional E-value: 0.8
               S-AdoMet_synt_N  75 g 75 
                                   g
  gi|13540846|ref|NP_110534.1| 346 G 346
                                   3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (400 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       639  (0.0356406); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); 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 0.26s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 2738.01
//
Query:       gi|13540847|ref|NP_110535.1|  [L=489]
Description: bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase [Thermoplasma volcanium GSS1]
Scores for complete 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-99  331.1   0.1    7.7e-99  330.9   0.1    1.1  1  AICARFT_IMPCHas  AICARFT/IMPCHase bienzyme
    3.8e-12   46.2   0.0    8.5e-12   45.1   0.0    1.6  1  MGS              MGS-like domain
  ------ inclusion threshold ------
       0.14   12.0   0.0       0.35   10.7   0.0    1.6  1  BING4CT          BING4CT (NUC141) 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 !  330.9   0.1  1.3e-102   7.7e-99       1     296 []     120     423 ..     120     423 .. 0.95

  Alignments for each domain:
  == domain 1  score: 330.9 bits;  conditional E-value: 1.3e-102
                                   HHHTTTT-EEE-SGGGHHHHHHHHHCT.B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCS...E...EEEEEEEEESSSS CS
               AICARFT_IMPCHas   1 AAKNhksVtvvvdpadYeevleelkkgevsletrkklaakaFahtaaYDaaiaeylskqlp...etlklslekkqkLrYGe 78 
                                   AAKN+k+V+v+++p+dY+e +e +++g+ + e rk++a+kaFa++a+YDa i + ls+ ++   e++ + ++k ++LrYGe
  gi|13540847|ref|NP_110535.1| 120 AAKNYKNVLVLSSPDDYTEAAEIISSGKNDAEYRKRMALKAFARMAEYDAIIYNGLSDLFKiekENFFVVGKKGERLRYGE 200
                                   9*******************************************************988776556778888********** PP

                                   STTS-EEEEE-TTSTTHHH-EEEESS---HHHHHHHHHHHHHHCTS..EEEEEEETTEEEEEEEESSHHHHHHHHHCCSHH CS
               AICARFT_IMPCHas  79 NphQkaalyeeeeeeglakaeqlqGkelsynNllDadaalelvkef..aavaivKHanpcGvAvgetlaeAyekAlaaDpv 157
                                   Np+Q++ ly++ ++ g+a+ae+l+GkelsynN+lDad+a++++ ef   +v+++KH++p Gv++++++ +A+++A++aD+ 
  gi|13540847|ref|NP_110535.1| 201 NPDQEGFLYSDGSAYGVANAEKLNGKELSYNNILDADSAFDTALEFdePTVVVMKHNTPSGVSSHNDIVNAFKRAWDADSE 281
                                   *********9999*********************************764788***************************** PP

                                   HHTTEEEEECCEE-HHHHHHHTTS-ECEEEECEE-CCHHHCCTTSSS-EEEE-SS..-...EEEEETTEEEEEE--G..TT CS
               AICARFT_IMPCHas 158 SaFGgiialnrevdaetaeeikkefleviiApsfeeealeilkkkknlrvlelke..e...elrsvsgglLvqerdeakie 233
                                   Sa+G++ia+nr+v  ++a+e+++ f+ev+iAp+++e al+ l+kkknlr+l+++   +   ++rs+s+glLvq+  +++++
  gi|13540847|ref|NP_110535.1| 282 SAYGSVIAVNRKVPLDLAKEMRHLFIEVLIAPEYDEYALSELRKKKNLRILRIPWirDqsmRYRSISNGLLVQTPMASSFK 362
                                   *****************************************************775515669************9976554 PP

                                   CCCSEEECSC---HHHHHHHHHHHHHCCCS-SS-EEEEETTEEEEEE-SSSSHHHHHHHHHHH CS
               AICARFT_IMPCHas 234 eeelkvvtkkkpteeeledllfawkvvkhvkSNaivlakdgqtvgiGaGqmsRvdsarlAvek 296
                                     elk+vt+k +++++++dllfawkvv h +SNaiv+akd++t giGaGq+sRv+s+r+A+e+
  gi|13540847|ref|NP_110535.1| 363 --ELKLVTEKGADSKTIDDLLFAWKVVAHSRSNAIVFAKDKTTTGIGAGQTSRVESVRIAMER 423
                                   ..6*********************************************************986 PP

>> MGS  MGS-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.1   0.0   1.4e-15   8.5e-12       4      94 ..      15     114 ..      12     115 .. 0.89

  Alignments for each domain:
  == domain 1  score: 45.1 bits;  conditional E-value: 1.4e-15
                                   HHHHHHHHTTCEEEEEHHHHHHHHHTT--EEECCCCHSTGSGGTHCH.............HHHHHHHTTSCCEEEEE--TH CS
                           MGS   4 elakklkelgfellATgGTakllkeagipvtevvektgegerlggrv.............eildaikngeidlvintlypf 71 
                                   ++  + k++   ++ATgGTak+l+++g  v++ +e+tg+ + lggrv                 + ++ ++d+++ +lypf
  gi|13540847|ref|NP_110535.1|  15 DFLARVKANIDYIYATGGTAKFLEKNGYTVRDTSEITGFSDLLGGRVktlhpkiyaallyREKNEASDLHFDVLVSNLYPF 95 
                                   5566666666679***************************************99999999778888999999********* PP

                                   HHHHHCHHHHHHHHHHHTTSHEE CS
                           MGS  72 katvakdgykirraaenidIplp 94 
                                   + ++     +  +++enidI+++
  gi|13540847|ref|NP_110535.1|  96 TGNTG----NENEMIENIDIGGV 114
                                   *9985....6799********97 PP

>> BING4CT  BING4CT (NUC141) domain
   #    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       9      40 ..     430     461 ..     425     471 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 5.8e-05
                       BING4CT   9 gskieslrFvpfeDvlgvghskgissiivPGs 40 
                                   gs ++s +F pf D + v+ + gi+ ii PG 
  gi|13540847|ref|NP_110535.1| 430 GSVMASDAFFPFPDSIDVAAKAGIKAIIQPGG 461
                                   56677889**********************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (489 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 3473.71
//
Query:       gi|13540848|ref|NP_110536.1|  [L=251]
Description: enoyl-CoA hydratase [Thermoplasma volcanium GSS1]
Scores for complete 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-54  183.8   0.0    3.9e-54  183.6   0.0    1.0  1  ECH_1     Enoyl-CoA hydratase/isomerase
    5.3e-32  111.6   0.0    9.1e-32  110.9   0.0    1.3  1  ECH_2     Enoyl-CoA hydratase/isomerase
  ------ inclusion threshold ------
      0.066   13.6   0.0       0.12   12.7   0.0    1.4  1  Desmo_N   Viral Desmoplakin N-terminus


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 !  183.6   0.0   6.6e-58   3.9e-54       3     250 ..      14     250 ..      12     251 .] 0.96

  Alignments for each domain:
  == domain 1  score: 183.6 bits;  conditional E-value: 6.6e-58
                                   ETTEEEEEE--CGCTTEE-HHHHHHHHHHHHHHHHSTTECEEEEEEBTSEEEEEB-HHHHHHHHCHHHHHHHCCHHHHHHH CS
                         ECH_1   3 eagvaviklnrPeavNalsaelltEliqalekleddksvravvLtGgdkaFaaGadlkemaeeekakqallkeevlelwtk 83 
                                   ++g+  ++++r + +N l+  +l+E+ +a    +++   ++vvL G++kaF+aGad+++ +  + +++  ++   ++ ++ 
  gi|13540848|ref|NP_110536.1|  14 HEGIRIVTIRRENSLNPLNLDTLEEIEDAV---RES--GKVVVLKGSEKAFSAGADINNFLDMSDRDAFHFSDRGQQVMDS 89 
                                   68999*********************9996...444..899*********************9999999************ PP

                                   HHHSSSEEEEEE-SEEETHHHHHHHHSSEEEEETTTEEE-GGGGGTS--CTTCHHHHHHHHHHHHHHHHHHHT-EEEHHHH CS
                         ECH_1  84 lytvpkpviaavnGaaigGGlelalacDiviaadnasfglnelklGlipgaggtqilarkvGkskAeeilllgkkisaqea 164
                                   +++ + pviaav G+a+gGG+elalacD++i + + ++g +e++lG++pg+ggtq+++ + Gks  ++++++gk i  qea
  gi|13540848|ref|NP_110536.1|  90 ISDYERPVIAAVHGYALGGGFELALACDFRISDVKTKYGFPEVNLGIMPGFGGTQRIIDIAGKSYGMYLVMTGKTIDEQEA 170
                                   ********************************************************************************* PP

                                   HHCTSSSEEESGGGHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTSHHHHHHHHHHHTCSH CS
                         ECH_1 165 lkvGlvdkvvpeeqlleealelaeklaekspaalrqlkealnakledalaeqleaeaklfestfskddikeGlqaflEkrk 245
                                   lk+G+vd v   e+ l+ a+ela++l ek+ +++r +ke +n+    + +e+  +e++ f  tf+++d  eG+ af+Ekrk
  gi|13540848|ref|NP_110536.1| 171 LKHGIVDSV--SEKYLDLAIELAKELSEKPATSIRYIKEVMNR----RDKEGYMMERERFALTFKTEDHLEGIRAFKEKRK 245
                                   ********9..58899************************997....5678899999************************ PP

                                   ----- CS
                         ECH_1 246 pefed 250
                                   + f++
  gi|13540848|ref|NP_110536.1| 246 AVFKG 250
                                   ***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 !  110.9   0.0   1.5e-35   9.1e-32       1     229 [.      17     231 ..      17     248 .. 0.79

  Alignments for each domain:
  == domain 1  score: 110.9 bits;  conditional E-value: 1.5e-35
                                   .EEEEE--GGGTT-B-HHHHHHHHHHHHHHCC-TT-SEEEEEESSSSECE--B--HHHHHHHHCS-THHHHHHHHHHHHHH CS
                         ECH_2   1 vgvitLnrpkalNaLslemvralkealkewekddevklvvlkgagekafCAGgDvralyeaakegkkeeeeffreeYklny 81 
                                   ++++t+ r+++lN L+l+ ++++++a++e     + k+vvlkg +ekaf+AG D++++ +  ++++    +f  +  ++  
  gi|13540848|ref|NP_110536.1|  17 IRIVTIRRENSLNPLNLDTLEEIEDAVRE-----SGKVVVLKG-SEKAFSAGADINNFLDMSDRDAF---HFSDRGQQVMD 88 
                                   5899**********************998.....689******.66*************99999664...499******** PP

                                   HHHC-SS-EEEEE-BEEETHHHHHHTTSSEEEE-TT-EEE--GGGGT----TTHHHHHHCSST.THHHHHHHH---B-HHH CS
                         ECH_2  82 liatypkpvvalmdGivmGgGvGlsvhgsfrvvtertvfAmPEtaIGlfPDvGgsyfLsrlpg.elGlylalTGarlkgad 161
                                    i++y++pv+a ++G+++GgG  l++ + fr+   +t+   PE+++G++P  Gg+  +  + g ++G+yl +TG+++++++
  gi|13540848|ref|NP_110536.1|  89 SISDYERPVIAAVHGYALGGGFELALACDFRISDVKTKYGFPEVNLGIMPGFGGTQRIIDIAGkSYGMYLVMTGKTIDEQE 169
                                   ******************************************************998888766599*************** PP

                                   HHHTTS--EE--GGGHHHHHHHHHTT............--------......----SHHHHHHHHHHHT.-S CS
                         ECH_2 162 alaaglathyvpseklealeeaLaelessd....eeaveevleelaeeaeeeeeeselaekreaidrlfsad 229
                                   al+ g+ + + ++    +l+ +La+  s++     + ++ev+++  +e         +  +re+ + +f+++
  gi|13540848|ref|NP_110536.1| 170 ALKHGIVDSVSEK--YLDLAIELAKELSEKpatsIRYIKEVMNRRDKE-------GYM-MERERFALTFKTE 231
                                   ********98654..455555555543332111144444444443332.......222.2455555555444 PP

>> Desmo_N  Viral Desmoplakin N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0     2e-05      0.12      25      73 ..      32      79 ..      16      93 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2e-05
                       Desmo_N 25 kiktledyeeklreihkvvlilkPslkknsaemdalpllimqflsdlkv 73
                                   + tle+ e+++re  kv ++lk s k  sa  d ++ l m     ++ 
  gi|13540848|ref|NP_110536.1| 32 NLDTLEEIEDAVRESGKV-VVLKGSEKAFSAGADINNFLDMSDRDAFHF 79
                                  4679***********775.679**********99999998766555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       524  (0.0292264); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 1616.70
//
Query:       gi|13540849|ref|NP_110537.1|  [L=278]
Description: hypothetical protein TVN0018 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   1.1e-108  363.0  29.8   1.2e-108  362.8  29.8    1.0  1  SPP            Signal-peptide peptidase, presenilin aspartyl 


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 !  362.8  29.8  6.9e-113  1.2e-108       2     283 .]       2     277 ..       1     277 [. 0.99

  Alignments for each domain:
  == domain 1  score: 362.8 bits;  conditional E-value: 6.9e-113
                           SPP   2 alfvvvqvlalllavplesaelq.atedPtqvlnsvv.yivlllvftlfvlivikkdkkliiskviyvivva.vifyvflv 79 
                                    +fv ++++alllav+++++e++ ++++Pt++l++++ yiv++++f+ fv+i++++ kkl+i+++iy++vva vifyvfl+
  gi|13540849|ref|NP_110537.1|   2 LIFVAASIMALLLAVAVYNSEPSiSHRSPTYGLSYIFvYIVAAFLFS-FVIIYLGRRKKLRIFRIIYSVVVAyVIFYVFLI 81 
                                   689********************9***********************.************************9******** PP

                           SPP  80 llsivlvvaglvnlaslvvaialvvllyaypeWyvidlaGvilavGvsalfGislgvlpavvllialavydaisvyktkhm 160
                                   llsi+l + +++  +s+ +ai++++ll++++eWy++d aG++lavG+++++Gi++gv++av++l+++++yd+i+vyktkhm
  gi|13540849|ref|NP_110537.1|  82 LLSIFLDNLYAILAISVAIAISYFYLLLFKNEWYITDTAGFFLAVGIASIWGITFGVWAAVAFLVVFEIYDYIAVYKTKHM 162
                                   ********************************************************************************* PP

                           SPP 161 ialaegvvdlklPillvvPetlaysfveeafeeaeeaearnvlfiGlGdavlPsilvvsaavfleshilaglelavllala 241
                                   i+la+++vd++lP+l+v+Pe+  +++ + +fe+++e   +n+l+iG+Gd++lPsilvvs+a++++s+il    +++ll+l 
  gi|13540849|ref|NP_110537.1| 163 ISLARYAVDSDLPMLFVIPENRDFTMKNVTFENRGE---GNALMIGFGDIALPSILVVSSALYGISNIL----YFTLLPLG 236
                                   ************************************...888************************999....******** PP

                           SPP 242 GtlvGllvlsilvlrgrpaaGlPllnsGaiaGfligvlaagv 283
                                   G+l+G++vl++  +r+rpa+GlP++n+G+iaGfli++++++v
  gi|13540849|ref|NP_110537.1| 237 GGLIGMAVLYF-CNRDRPAPGLPYINTGTIAGFLIAFVMFKV 277
                                   ***********.**************************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1214  (0.0677115); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); 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):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.47
# Mc/sec: 1775.85
//
Query:       gi|13540850|ref|NP_110538.1|  [L=770]
Description: DNA topoisomerase I [Thermoplasma volcanium GSS1]
Scores for complete 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-116  387.4   0.0     1e-115  387.1   0.0    1.1  1  Topoisom_bac    DNA topoisomerase
    4.8e-15   55.6   0.3    1.7e-14   53.9   0.3    2.0  1  Toprim          Toprim domain
    1.1e-13   50.7  15.6    2.1e-13   49.8   1.7    3.6  3  zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
    0.00076   19.3   2.6       0.01   15.7   0.7    2.5  2  zf-FPG_IleRS    Zinc finger found in FPG and IleRS
    0.00092   19.3   4.5       0.38   11.0   0.6    2.6  2  Auto_anti-p27   Sjogren's syndrome/scleroderma autoantigen 1 
  ------ inclusion threshold ------
      0.051   14.0   0.2       0.12   12.8   0.2    1.7  1  Toprim_4        Toprim domain
        0.1   12.9   0.0       0.34   11.2   0.0    1.9  1  DUF2283         Protein of unknown function (DUF2283)
       0.11   12.0   4.8        3.6    7.1   1.7    3.0  2  zf-ribbon_3     zinc-ribbon domain
       0.12   12.5   1.8        7.7    6.7   0.1    2.6  2  Zn-ribbon_8     Zinc ribbon domain
       0.13   12.4   1.8         19    5.5   0.0    3.0  2  Ribosomal_S27   Ribosomal protein S27a
       0.26   11.0   5.4          4    7.2   0.1    3.3  3  zf-RRN7         Zinc-finger of RNA-polymerase I-specific TFII
       0.69    9.8   4.2          2    8.3   0.1    3.0  2  Rad50_zn_hook   Rad50 zinc hook motif


Domain annotation for each model (and alignments):
>> Topoisom_bac  DNA topoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  387.1   0.0  6.7e-119    1e-115       2     413 .]     156     554 ..     155     554 .. 0.94

  Alignments for each domain:
  == domain 1  score: 387.1 bits;  conditional E-value: 6.7e-119
                  Topoisom_bac   2 inenlvdaaeaRrelDwliGinlsrlltkklkg..kkvlsaGRVqtptLaliveRereienFvpeeyweveatlkkekkek 80 
                                   +n nl+daa+aR+ +D+++G+ l+r++++++ +    +lsaGRVqtptLa++veRereienF+p+++w++++t++ke++++
  gi|13540850|ref|NP_110538.1| 156 VNYNLADAADARESIDLIWGAVLTRFFSLATGRlgRYFLSAGRVQTPTLAIVVEREREIENFKPQTFWTISITFQKEGEFQ 236
                                   689**************************55556689************************************98777664 PP

                  Topoisom_bac  81 ekkkkkkkerikdkeeaeaileklkkkeakvesvekkekkkppplpfdtttLqkeasrklglsakktlsiaqkLYekagli 161
                                       ++ +++++dk+ a++++++++  + +v ++ek e++ ++p+pf+tt++++easr+ g+ + k++sia++LY++ gli
  gi|13540850|ref|NP_110538.1| 237 ----AAYEKKLFDKDVANSVFSSINGRDGTVIKFEKHEESIRRPTPFSTTEFLREASRI-GIMPTKAMSIAESLYTR-GLI 311
                                   ....789999**************6658******************************8.****************7.*** PP

                  Topoisom_bac 162 tYpRTdstrlseeaelkailealakkygkeylefaekllkktkkks..vvknkkveaHeAIrPteelpklkelsddekklY 240
                                   +YpRTd+t++++  +l+++l++++k    +y++++e+ l  +k      +++ ++++H++I+P+ e+pk +el++d++++Y
  gi|13540850|ref|NP_110538.1| 312 SYPRTDNTVYPRAINLRNVLQKFSKS---KYSNYVEEILGWEK--IipSRGRTETTDHPPIYPV-EMPK-EELKGDYARIY 385
                                   *************779*****99995...69999999998766..4457888889*********.7785.8********** PP

                  Topoisom_bac 241 elIvrrflaslmkdakyeettvkleveeeefkasgktilekGfkkvykeekkeeeeeelpelkegeevkvkeveleekkTk 321
                                   +lI rrf+ +l++d + + ++++++v++++f a+g+++++ G+++vy +++ +e    +p+l+ege++  ++  l+e +Tk
  gi|13540850|ref|NP_110538.1| 386 DLILRRFISTLYRDGRKTVKEAEIDVNGYKFLARGSQTTDLGWMAVYGYSSRDEF---MPDLSEGEILHGTNWLLNEDQTK 463
                                   ***********************************************99888754...9********************** PP

                  Topoisom_bac 322 ppkryteasLikamekagiGtpaTraeiieklvergYverkkkslvptelGkalvellekf.kdlvspelTaeleekLdeI 401
                                   pp+ry  asL+k+me+ ++Gt++Tr++ii kl++rg++e +   ++pt lG+a +++++ + +++++p++Ta+le+++d+I
  gi|13540850|ref|NP_110538.1| 464 PPPRYDMASLLKKMEDLNLGTKSTRHDIIGKLIDRGFIEGNP--VRPTGLGIAFIDAVKSVnSSIADPDMTAKLEQDMDKI 542
                                   ***************************************966..**************999899***************** PP

                  Topoisom_bac 402 aegkadakevld 413
                                   ++  ++++ev+d
  gi|13540850|ref|NP_110538.1| 543 ERSLMSKQEVVD 554
                                   *********985 PP

>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.9   0.3   1.1e-17   1.7e-14       2     102 ..       7     140 ..       6     141 .. 0.87

  Alignments for each domain:
  == domain 1  score: 53.9 bits;  conditional E-value: 1.1e-17
                                   EEEESSHHHHHHHHHTHT....................STEEEEEEESSSSEEEHS..........TTEEEEE....ECTT CS
                        Toprim   2 lvivEgpsdaktiakalg....................sgfqavtaslGhildlet..........efkpvye....eied 48 
                                   ++i+E+  + + ia +l+                    ++++  ++++Ghi++ ++          ++k+ ++    ++ +
  gi|13540850|ref|NP_110538.1|   7 VIIAEKVDAGRRIAYFLSngtakarrvkglsyiefesnGKKTLLIPLSGHIVEADFpenfsnwektDLKELIDadivKKVK 87 
                                   79***********************************9999***************8777666666333333366546666 PP

                                   THHHHHHHHHHHHHHSEEEEECSSSHHHHHHHHHHHHHHTHHHTTTEEEEEESS CS
                        Toprim  49 kkkvlkalkelakradeiilatDpDreGeaiawellevlkellenkigrvefse 102
                                   +k++ ++l + + +adeii+atD DreGe i+ e+l+ +ke++e+ + r++fs+
  gi|13540850|ref|NP_110538.1|  88 NKSAYQTLSSFKGKADEIIIATDYDREGELIGVEALDIIKEGQEK-VLRAKFSS 140
                                   6667777*********************************99999.******97 PP

>> zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.1     0.083   1.2e+02       2      13 ..     634     645 ..     633     653 .. 0.81
   2 !   49.8   1.7   1.4e-16   2.1e-13       2      38 ..     672     709 ..     671     710 .. 0.96
   3 !    5.5   2.3    0.0096        14       1      21 [.     717     739 ..     717     754 .. 0.65

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.083
                                   EE-SSS--EEEE CS
                zf-C4_Topoisom   2 ekCPkCggdLvl 13 
                                   + CP Cg +L++
  gi|13540850|ref|NP_110538.1| 634 QLCPVCGLPLIK 645
                                   78*****99875 PP

  == domain 2  score: 49.8 bits;  conditional E-value: 1.4e-16
                                   EE-SSS--EEEEEE-SSS.EEEEESST.T----EEB-G CS
                zf-C4_Topoisom   2 ekCPkCggdLvlkrgkkG.kFvGCsnYPeCkftkklkk 38 
                                   ++CPk gg L+l+++++G +F+GCsnYP+C++t++l++
  gi|13540850|ref|NP_110538.1| 672 GECPKDGGRLILRQSRYGkRFLGCSNYPKCTVTYPLPQ 709
                                   68*********************************997 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.0096
                                   -EE-SSS--EEEE.EE-SSS.EE CS
                zf-C4_Topoisom   1 vekCPkCggdLvl.krgkkG.kF 21 
                                   +ekCP Cg++L++  +gk+  kF
  gi|13540850|ref|NP_110538.1| 717 GEKCPICGAPLLEaVNGKRRwKF 739
                                   68******877642566655555 PP

>> zf-FPG_IleRS  Zinc finger found in FPG and IleRS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0     0.068     1e+02       2      18 ..     634     650 ..     633     655 .. 0.71
   2 !   15.7   0.7   6.8e-06      0.01       1      26 [.     717     742 ..     717     742 .. 0.97

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.068
                                   SB-TTT--BBEEEECTT CS
                  zf-FPG_IleRS   2 epCpRCwryiervgqag 18 
                                   + Cp+C+ ++ ++   g
  gi|13540850|ref|NP_110538.1| 634 QLCPVCGLPLIKIIRRG 650
                                   56999998887776555 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 6.8e-06
                                   TSB-TTT--BBEEEECTTEEEEE-TT CS
                  zf-FPG_IleRS   1 GepCpRCwryiervgqagrstyfCpr 26 
                                   Ge+Cp C+ ++ + + + r   fCp+
  gi|13540850|ref|NP_110538.1| 717 GEKCPICGAPLLEAVNGKRRWKFCPN 742
                                   9************************6 PP

>> Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.2    0.0009       1.3      13      27 ..     631     645 ..     629     658 .. 0.84
   2 !   11.0   0.6   0.00025      0.38      14      37 ..     716     741 ..     716     745 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0009
                 Auto_anti-p27  13 MLaetCpvCgvPLmr 27 
                                   ++++ CpvCg PL +
  gi|13540850|ref|NP_110538.1| 631 LMDQLCPVCGLPLIK 645
                                   7899*********87 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00025
                 Auto_anti-p27  14 LaetCpvCgvPLmrdr..kggkvyCv 37 
                                   ++e Cp Cg+PL++    k+  ++C+
  gi|13540850|ref|NP_110538.1| 716 TGEKCPICGAPLLEAVngKRRWKFCP 741
                                   5899**********876544455776 PP

>> Toprim_4  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.2   8.3e-05      0.12      49      86 ..      97     134 ..      74     137 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 8.3e-05
                      Toprim_4  49 eaekkvkevilaldgDaeGeataerlaellleegvkvt 86 
                                     ++k++e+i+a+d D eGe    ++++ ++e+++kv 
  gi|13540850|ref|NP_110538.1|  97 SFKGKADEIIIATDYDREGELIGVEALDIIKEGQEKVL 134
                                   367788*************9888777776666666665 PP

>> DUF2283  Protein of unknown function (DUF2283)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00022      0.34      29      47 ..     104     124 ..      87     125 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00022
                       DUF2283  29 dii..lDfDedGrlvGIEiLn 47 
                                   +ii   D+D++G+l+G+E L+
  gi|13540850|ref|NP_110538.1| 104 EIIiaTDYDREGELIGVEALD 124
                                   444347************886 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.1      0.02        30      16      26 .]     633     643 ..     627     643 .. 0.86
   2 ?    7.1   1.7    0.0024       3.6       4      12 ..     719     728 ..     716     742 .. 0.64

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.02
                   zf-ribbon_3  16 dnvCpyCGtkl 26 
                                   d+ Cp CG +l
  gi|13540850|ref|NP_110538.1| 633 DQLCPVCGLPL 643
                                   78999999987 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0024
                   zf-ribbon_3   4 rCPnCGa.pl 12 
                                   +CP CGa +l
  gi|13540850|ref|NP_110538.1| 719 KCPICGApLL 728
                                   7999999445 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.1    0.0051       7.7       3      40 .]     607     647 ..     607     647 .. 0.69
   2 ?    4.5   0.3     0.026        39      19      36 ..     709     727 ..     699     731 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0051
                   Zn-ribbon_8   3 iYeYrCee..Cghefevlqsisdaplta.CPeCgsevrrvi 40 
                                   +Y  rCe   C  +f +    s + + + CP Cg ++ ++i
  gi|13540850|ref|NP_110538.1| 607 TYRIRCEVdgCRIDFKIKKNGSISLMDQlCPVCGLPLIKII 647
                                   68888988667777775555555556666*****8887765 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.026
                   Zn-ribbon_8  19 qsis.dapltaCPeCgsev 36 
                                   q+ + ++  ++CP Cg+++
  gi|13540850|ref|NP_110538.1| 709 QKGKiEKTGEKCPICGAPL 727
                                   55565667778*****954 PP

>> Ribosomal_S27  Ribosomal protein S27a
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.013        19       5      25 ..     621     640 ..     620     642 .. 0.96
   2 ?    5.1   0.0     0.018        26       9      26 ..     709     725 ..     704     728 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.013
                                   CCESSSSSEEESS-B-SS-S- CS
                 Ribosomal_S27   5 YkvddsgkverlrkeCpreCG 25 
                                   +k++++g+++   + Cp  CG
  gi|13540850|ref|NP_110538.1| 621 FKIKKNGSISLMDQLCPV-CG 640
                                   89****************.*8 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.018
                                   SSSSEEESS-B-SS-S-T CS
                 Ribosomal_S27   9 dsgkverlrkeCpreCGa 26 
                                   ++gk+e++ ++Cp  CGa
  gi|13540850|ref|NP_110538.1| 709 QKGKIEKTGEKCPI-CGA 725
                                   67************.*97 PP

>> zf-RRN7  Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.1    0.0026         4       2      15 ..     607     621 ..     606     627 .. 0.83
   2 ?    0.0   0.1      0.47     7e+02       7      11 ..     636     640 ..     632     641 .. 0.87
   3 ?    4.2   0.1     0.024        36       3      12 ..     716     725 ..     714     733 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0026
                       zf-RRN7   2 ekgppCgvCgcr.sf 15 
                                   +++++C+v+gcr +f
  gi|13540850|ref|NP_110538.1| 607 TYRIRCEVDGCRiDF 621
                                   799********7465 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.47
                       zf-RRN7   7 CgvCg 11 
                                   C+vCg
  gi|13540850|ref|NP_110538.1| 636 CPVCG 640
                                   ****9 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.024
                       zf-RRN7   3 kgppCgvCgc 12 
                                   +g+ C++Cg+
  gi|13540850|ref|NP_110538.1| 716 TGEKCPICGA 725
                                   699******7 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 ?    0.7   1.0      0.32   4.8e+02      22      28 ..     636     642 ..     633     643 .. 0.81
   2 ?    8.3   0.1    0.0013         2      14      29 ..     712     727 ..     711     730 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.32
                                   -TTT--E CS
                 Rad50_zn_hook  22 CPlCgRe 28 
                                   CP+Cg +
  gi|13540850|ref|NP_110538.1| 636 CPVCGLP 642
                                   ****966 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0013
                                   HHTT-SEE-TTT--EE CS
                 Rad50_zn_hook  14 elkeakgcCPlCgRel 29 
                                   ++++++++CP Cg +l
  gi|13540850|ref|NP_110538.1| 712 KIEKTGEKCPICGAPL 727
                                   5788889******998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (770 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       767  (0.0427799); expected 358.6 (0.02)
Passed bias filter:                      609  (0.0339673); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.75u 0.30s 00:00:01.05 Elapsed: 00:00:00.49
# Mc/sec: 4721.29
//
Query:       gi|13540851|ref|NP_110539.1|  [L=90]
Description: acylphosphatase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-21   77.1   0.0    1.1e-21   77.0   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 !   77.0   0.0   6.2e-26   1.1e-21       2      85 .]       6      88 ..       5      88 .. 0.96

  Alignments for each domain:
  == domain 1  score: 77.0 bits;  conditional E-value: 6.2e-26
               Acylphosphatase  2 rllvtGrVQgvgFRkfvrrlAkelglkGyvrNlsdgsVeivaegeeekvekfleelksgppkarvdeveveeleeeeefkdFe 84
                                  r++ +GrVQg++FR  +  +A elg+kG+++Nl+dgsVe++++ge e++ek+++ + s++p+a+v++ +v  ++++e  +dF+
  gi|13540851|ref|NP_110539.1|  6 RVRFYGRVQGINFRSNTLVKALELGVKGWIKNLPDGSVEALFSGESEQIEKLISYCVSNMPYAEVKRYDVYIEPYTEF-QDFQ 87
                                  67899*****************************************************************98888777.***9 PP

               Acylphosphatase 85 i 85
                                  i
  gi|13540851|ref|NP_110539.1| 88 I 88
                                  8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       338  (0.0188521); 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: 0.51u 0.32s 00:00:00.83 Elapsed: 00:00:00.52
# Mc/sec: 516.44
//
Query:       gi|13540852|ref|NP_110540.1|  [L=492]
Description: permease [Thermoplasma volcanium GSS1]
Scores for complete 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-98  328.8  79.0    6.9e-98  328.7  79.0    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 !  328.7  79.0  3.9e-102   6.9e-98       1     444 [.       3     483 ..       3     489 .. 0.94

  Alignments for each domain:
  == domain 1  score: 328.7 bits;  conditional E-value: 3.9e-102
                        12TM_1   1 nirlsvllqsimftvlglvlvgpsliserasflSslliLlfvlslfitalnslyfassl...dllepLrsLPvkfkdrvla 78 
                                   +++ls++++si+f+ ++lvlv+psl s+ + +lS ++++l ++ lfi+++nsl+f++s+   ++l+pLr LP++++++v+a
  gi|13540852|ref|NP_110540.1|   3 YVNLSYAMTSISFMLFSLVLVVPSLLSHHIFTLSNIVLILYIYVLFINVSNSLLFFVSIsinHILDPLRALPLDLPQNVIA 83 
                                   5899***************************************************************************** PP

                        12TM_1  79 vfllieslsvlaFlv..sillavllvgnltagllglLwailaillGfslvlllfilfGsrisgrkslskallriaglilfl 157
                                   v+++i+++s+++F+v  ++++a+   gn+++ llg +w+ +++llG+ +++llfi f+ ri g++++s+ ++r+ag+++fl
  gi|13540852|ref|NP_110540.1|  84 VSWFIYTGSSSLFAVmpAVFIASAFYGNAYIALLGFIWSLFTMLLGYTIGSLLFIIFSRRILGKRTRSSIIIRNAGRVIFL 164
                                   ****************99*************************************************************** PP

                        12TM_1 158 vlifglyliiqyaanilylvikeipeaykyifP........ffflsIeepffslllsllYtallsfaykyslkrlfkrlee 230
                                   +++f +++ii+y+a++++++++++  +y++++P        f++ s  + f+++ ls+lY++ + f + ++++ +f rl e
  gi|13540852|ref|NP_110540.1| 165 IFVFVIFEIILYNADYVNIIVPNMAFPYSFVIPiinipktlFYADSLLKAFMGFSLSILYLLFIIFSFTKLNSIAFSRLVE 245
                                   *******************************************************************************88 PP

                        12TM_1 231 iakvkgrvktky..kikvrspltamliKDfkillRksqalvlllvPivivlpnvfsivseaqpvl.....ltifiialiiv 304
                                    ++ +gr + +     k r p +++++KD+ +++Rksq+lvll++Pi++v+p+v+s+  + +        l++  ia++ v
  gi|13540852|ref|NP_110540.1| 246 PMRSSGRAEVNLerAEKIRKPYLSFFYKDIWLSSRKSQNLVLLIMPIFFVFPTVMSELLYSPEISvnpisLYNVLIAFVVV 326
                                   8999998774331134678999**********************************99887655559999*********** PP

                        12TM_1 305 lSsvylilllaievsgfsllkaLPlerreillsKlltilliylvvsvvlvllvliykg.snalylliilpspilvvliall 384
                                   +Ss+y+il+l+ie++g+s+l++LP++ ++++ +Kl +++li++++  +++l+ l++k  + ++y++ ++ ++il++ i+l+
  gi|13540852|ref|NP_110540.1| 327 VSSFYSILFLVIEGNGISFLRSLPVSPKNVIAWKLPAPFLIFAAIT-SAMLITLSIKIrMTPIYYFLVFFDTILYFIISLF 406
                                   *******************************************555.566666666666********************** PP

                        12TM_1 385 islnrl......gaetinlpsf.gvlktivlfilslvivgivaipslilsepls......flvslvitl....iial 444
                                   ++++rl       a+tin++sf g+l+++v+f+ s++ivg  + +s+ l++ +       fl++++i++    i a 
  gi|13540852|ref|NP_110540.1| 407 FNVRRLyskipaSADTINFYSFgGQLAFMVTFFYSGLIVGFPDLLSFSLQYTYHlsyglfFLLNTAIGIsvgsILAY 483
                                   **********************9****************************99999***********9975554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (492 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1013  (0.0565006); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.65u 0.32s 00:00:00.97 Elapsed: 00:00:00.49
# Mc/sec: 3045.12
//
Query:       gi|13540853|ref|NP_110541.1|  [L=259]
Description: ABC-type multidrug transport system, ATPase component [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-25   90.6   0.0    4.9e-25   88.6   0.0    1.8  2  ABC_tran      ABC transporter
    1.2e-11   45.0   0.1    4.1e-05   23.6   0.2    2.1  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    0.00023   21.7   0.0    0.00039   21.0   0.0    1.4  1  AAA_23        AAA domain
    0.00093   19.0   0.0     0.0031   17.2   0.0    2.0  1  AAA_30        AAA domain
     0.0011   18.8   0.1     0.0031   17.3   0.0    1.6  2  AAA_15        AAA ATPase domain
     0.0014   18.6   0.2     0.0031   17.5   0.1    1.7  2  ATPase_2      ATPase domain predominantly from Archaea
      0.002   18.0   0.1     0.0037   17.1   0.1    1.4  1  MobB          Molybdopterin guanine dinucleotide synthesis pr
     0.0026   18.0   0.1       0.12   12.6   0.0    2.3  2  AAA_22        AAA domain
     0.0036   17.1   0.1     0.0059   16.4   0.1    1.4  1  CLP1_P        mRNA cleavage and polyadenylation factor CLP1 P
     0.0055   16.4   0.5      0.011   15.5   0.5    1.5  1  AAA_29        P-loop containing region of AAA domain
      0.006   16.7   0.8      0.016   15.3   0.8    1.8  1  DUF87         Helicase HerA, central domain
     0.0085   15.5   0.9      0.027   13.9   0.2    1.9  2  SMC_N         RecF/RecN/SMC N terminal domain
     0.0097   15.7   0.0      0.015   15.1   0.0    1.3  1  ATP_bind_1    Conserved hypothetical ATP binding protein
  ------ inclusion threshold ------
      0.016   15.1   0.1      0.031   14.2   0.1    1.4  1  NACHT         NACHT domain
      0.019   15.0   0.0      0.033   14.2   0.0    1.7  1  AAA_14        AAA domain
      0.021   15.4   0.4      0.052   14.1   0.4    1.9  1  AAA_18        AAA domain
      0.022   14.8   0.0      0.027   14.5   0.0    1.3  1  CbiA          CobQ/CobB/MinD/ParA nucleotide binding domain
      0.023   14.3   0.1      0.048   13.3   0.1    1.4  1  SRP54         SRP54-type protein, GTPase domain
      0.028   14.9   0.1      0.096   13.1   0.0    1.9  2  AAA           ATPase family associated with various cellular 
      0.031   12.9   0.0      0.044   12.4   0.0    1.2  1  AAA_13        AAA domain
      0.032   13.7   0.0      0.066   12.7   0.0    1.5  1  RecA          recA bacterial DNA recombination protein
      0.032   14.6   0.0      0.078   13.3   0.0    1.8  1  AAA_16        AAA ATPase domain
      0.041   14.3   0.1       0.13   12.6   0.1    1.9  1  RNA_helicase  RNA helicase
      0.048   14.0   0.1          1    9.7   0.1    2.1  2  AAA_19        AAA domain
      0.066   13.1   0.6       0.18   11.7   0.1    1.8  2  NTPase_1      NTPase
      0.067   12.8   0.0       0.13   11.9   0.0    1.4  1  PrkA          PrkA serine protein kinase C-terminal domain
      0.073   12.6   0.1       0.12   11.9   0.1    1.4  1  cobW          CobW/HypB/UreG, nucleotide-binding domain
      0.074   12.1   0.1       0.12   11.4   0.1    1.3  1  T2SSE         Type II/IV secretion system protein
       0.15   12.3   0.0       0.24   11.6   0.0    1.4  1  Roc           Ras of Complex, Roc, domain of DAPkinase
        0.2   11.3   0.2       0.31   10.7   0.1    1.5  1  AAA_24        AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.6   0.0   8.1e-28   4.9e-25       1     136 [.      20     163 ..      20     164 .. 0.96
   2 ?   -0.3   0.0       2.4   1.5e+03      40     104 ..     185     252 ..     174     257 .. 0.62

  Alignments for each domain:
  == domain 1  score: 88.6 bits;  conditional E-value: 8.1e-28
                                   EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                      ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren.. 79 
                                   lk v+l++  g++++i+G+nG+GK+tL+k+l  ll++++G++ + g d+++ +  + ++  g++p++p l + +t  e   
  gi|13540853|ref|NP_110541.1|  20 LKGVNLTIPSGSIYGILGPNGSGKTTLMKILVSLLSKKSGRVSVCGLDVDK-DQMKIKEIAGYIPETPVLYESMTPLELfd 99 
                                   799************************************************.777788889**************99999* PP

                                   ...........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                   ...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  80 ...........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                               + ++++++++ +++k+  ++ +     sLS G kq+va+  al+ +pk+l++DE +
  gi|13540853|ref|NP_110541.1| 100 fvgsvrhipvdSYARRLNALIDAFSIKDYLNEFI----GSLSFGNKQKVAIISALVHDPKVLIVDEGM 163
                                   **********999999******************....****************************65 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 2.4
                                   EEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.....HHHTCHHHHHHHSTTGGTTCBGEST CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  40 Geilldgkdlkeqeleslrkeigvlpqepqlfpeltvren.....esdeeiekalsklglkelkdtvvks 104
                                   G+i + ++++ e   e l  ++++l + + + +++ +r+      e ++++e++  kl ++e+  +vvks
  gi|13540853|ref|NP_110541.1| 185 GKIVVFSTHILE-IAENLCDSVAILYEGSIVANGT-IRDLessapENSQNLEDIFLKLTNSEDLGDVVKS 252
                                   555555555555.4555555555555554444444.5555667777777788888888888888887754 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.2   6.8e-08   4.1e-05       2      44 ..      33      61 ..      32     131 .. 0.69
   2 !   19.9   0.0   8.7e-07   0.00052     228     300 ..     127     196 ..      99     199 .. 0.81

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 6.8e-08
                        AAA_21  2 nvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirk 44
                                   ++ GpNgsGK++L+++l  l +              +++ r+
  gi|13540853|ref|NP_110541.1| 33 YGILGPNGSGKTTLMKILVSLLS--------------KKSGRV 61
                                  689***************99964..............333333 PP

  == domain 2  score: 19.9 bits;  conditional E-value: 8.7e-07
                        AAA_21 228 dgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSpl 300
                                   d+ +  + +lS G k+  a+++al  ++   ++l++DE  ngL+P+  r + ++l + +++g  v+++TH  +
  gi|13540853|ref|NP_110541.1| 127 DYLNEFIGSLSFGNKQKVAIISALVHDP---KVLIVDEGMNGLDPRSARIFKDILMDMKNRGKIVVFSTHILE 196
                                   5555557899****************99...9*************88888889997776745555*****765 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   6.5e-07   0.00039      18      49 ..      29      60 ..      12      93 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 6.5e-07
                        AAA_23 18 skgltlItGpNGaGKTTildAiklaLygetpr 49
                                  s  ++ I GpNG+GKTT++  +   L  +++r
  gi|13540853|ref|NP_110541.1| 29 SGSIYGILGPNGSGKTTLMKILVSLLSKKSGR 60
                                  556899*************9998888776655 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   5.2e-06    0.0031      20      52 ..      32      64 ..      22     190 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 5.2e-06
                        AAA_30 20 vavltGpAGtGKttalkalreaweaaggrvigl 52
                                  +  + Gp G+GKtt++k l+ ++ ++ grv ++
  gi|13540853|ref|NP_110541.1| 32 IYGILGPNGSGKTTLMKILVSLLSKKSGRVSVC 64
                                  67799********************97777665 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   5.2e-06    0.0031      28      59 ..      35      74 ..      23      86 .. 0.74
   2 ?   -2.5   0.0       5.2   3.1e+03     327     364 ..     157     193 ..     140     198 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 5.2e-06
                        AAA_15 28 liGkNnsGKSsilealdlFlnnkekkn...........kkvik 59
                                  + G+N+sGK++++++l  +l++k   +           k+ +k
  gi|13540853|ref|NP_110541.1| 35 ILGPNGSGKTTLMKILVSLLSKK---SgrvsvcgldvdKDQMK 74
                                  78*******************88...34456655544433333 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 5.2
                        AAA_15 327 lliEEPEahLHpqaqkvlikllkelandnktQviitTH 364
                                   l+++E  + L p   +++ + l ++ n +k  v+++TH
  gi|13540853|ref|NP_110541.1| 157 LIVDEGMNGLDPRSARIFKDILMDMKNRGK-IVVFSTH 193
                                   555555566667888888888888888888.8888999 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1   5.2e-06    0.0031      20      49 ..      30      59 ..       7      89 .. 0.88
   2 ?   -2.5   0.0       6.7     4e+03      42      56 ..     179     193 ..     170     243 .. 0.62

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 5.2e-06
                      ATPase_2 20 neiyfiYGpegsGKtaLlkeiienledkdk 49
                                   +iy i Gp gsGKt+L+k +++ l++k+ 
  gi|13540853|ref|NP_110541.1| 30 GSIYGILGPNGSGKTTLMKILVSLLSKKSG 59
                                  57999******************9977664 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 6.7
                      ATPase_2  42 enledkdkyviyyia 56 
                                      ++ +k v++ + 
  gi|13540853|ref|NP_110541.1| 179 MDMKNRGKIVVFSTH 193
                                   333444444444444 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 !   17.1   0.1   6.3e-06    0.0037       2      34 ..      33      65 ..      32      77 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 6.3e-06
                          MobB  2 lgivgksgsGKTtLleklipelkarglrvgtiK 34
                                   gi g +gsGKTtL++ l++ l+++  rv++  
  gi|13540853|ref|NP_110541.1| 33 YGILGPNGSGKTTLMKILVSLLSKKSGRVSVCG 65
                                  57999***********************99865 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.0    0.0002      0.12       7      31 ..      32      56 ..      28      84 .. 0.80
   2 ?    3.2   0.0      0.17     1e+02      88     121 ..     152     182 ..     128     198 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.0002
                        AAA_22  7 ilvvtGesGtGKTtllrrlleqlde 31
                                  i  + G+ G+GKTtl++ l++ l +
  gi|13540853|ref|NP_110541.1| 32 IYGILGPNGSGKTTLMKILVSLLSK 56
                                  66689*************9998854 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.17
                        AAA_22  88 aravielliiDEaqh.lr..seealeeLrsllnlsrk 121
                                   +   +++li+DE  + l+  s+++++++  l++   k
  gi|13540853|ref|NP_110541.1| 152 HD--PKVLIVDEGMNgLDprSARIFKDI--LMD--MK 182
                                   33..57******9999988668888888..444..22 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   9.9e-06    0.0059       1      39 [.      37      75 ..      37     128 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 9.9e-06
                        CLP1_P  1 GpkdsGKSTlarlLlNyalrkgrkpvyvDlDvGqseisp 39
                                  Gp+ sGK+Tl+++L+  + +k+ ++ +  lDv + ++ +
  gi|13540853|ref|NP_110541.1| 37 GPNGSGKTTLMKILVSLLSKKSGRVSVCGLDVDKDQMKI 75
                                  899****************99999999888887766555 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.5   1.8e-05     0.011      18      46 ..      26      54 ..      19      62 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.8e-05
                        AAA_29 18 eidlkg.atlltGpsGsGKSTllDAiqalL 46
                                  +i  +g ++ + Gp+GsGK+Tl+  +  lL
  gi|13540853|ref|NP_110541.1| 26 TIP-SGsIYGILGPNGSGKTTLMKILVSLL 54
                                  554.455888************96666666 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.8   2.7e-05     0.016      27      55 ..      34      61 ..      32     200 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.7e-05
                         DUF87 27 AilgsTGsGKSntvavLleellekkgati 55
                                  +ilg  GsGK++++++L++ l  kk++++
  gi|13540853|ref|NP_110541.1| 34 GILGPNGSGKTTLMKILVSLLS-KKSGRV 61
                                  89*******************9.777655 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.2   4.5e-05     0.027      25      53 ..      31      59 ..      19      64 .. 0.83
   2 ?   -0.0   0.0      0.83   4.9e+02     157     196 ..     153     191 ..      66     208 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.5e-05
                                  SEEEEEESTTSSHHHHHHHHHHHCTT.TT CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 25 sftaivGpNGSGKsnlldAilFvLGersa 53
                                  s+  i+GpNGSGK+ l+  +  +L+++s 
  gi|13540853|ref|NP_110541.1| 31 SIYGILGPNGSGKTTLMKILVSLLSKKSG 59
                                  56789************999988887765 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.83
                                   S--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE- CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 157 kpaplyllDeidaaLDeknvkkvaellkeksknaQfivis 196
                                   +p+ + ++De    LD +  +++ ++l   +++  ++v s
  gi|13540853|ref|NP_110541.1| 153 DPK-VLIVDEGMNGLDPRSARIFKDILMDMKNRGKIVVFS 191
                                   343.346788888899999998888888888777777765 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   2.5e-05     0.015       1      38 [.      35      72 ..      35      78 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.5e-05
                    ATP_bind_1  1 vvGpaGsGKttfvgalseilelrgrsvavvNLDPAaee 38
                                  ++Gp GsGKtt+++ l+++l+++  +v v  LD   ++
  gi|13540853|ref|NP_110541.1| 35 ILGPNGSGKTTLMKILVSLLSKKSGRVSVCGLDVDKDQ 72
                                  68*********************999999999976665 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   5.1e-05     0.031       5      27 ..      35      57 ..      32      63 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5.1e-05
                                  EEC-TTTCHHHHHHHHHHHHCTS CS
                         NACHT  5 lqGeaGsGKTtLlqklalawaeg 27
                                  + G++GsGKTtL++ l++++ ++
  gi|13540853|ref|NP_110541.1| 35 ILGPNGSGKTTLMKILVSLLSKK 57
                                  78***************999876 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   5.6e-05     0.033       3      58 ..      31      84 ..      29     200 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5.6e-05
                        AAA_14  3 kilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelile 58
                                   i+ i G+  +GKTtl+k l++ l  k+ ++    ld ++d+++ ++  +  +i e
  gi|13540853|ref|NP_110541.1| 31 SIYGILGPNGSGKTTLMKILVSLLSKKSGRVSVCGLDVDKDQMKIKE--IAGYIPE 84
                                  6899*************999966555555555555555555433322..4555555 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.4   8.7e-05     0.052       3      23 ..      35      56 ..      34     196 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 8.7e-05
                        AAA_18  3 ltGtpGvGKttlakeLskrl.g 23
                                  + G+ G+GKttl k L ++l +
  gi|13540853|ref|NP_110541.1| 35 ILGPNGSGKTTLMKILVSLLsK 56
                                  89**************777622 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 ?   14.5   0.0   4.5e-05     0.027       9      55 ..      40     139 ..      37     254 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.5e-05
                                   TSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH................................... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................................... RF
                          CbiA   9 GvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep................................... 54 
                                   G+GKTtl   L  +l+++  rV +  +D++    + ++   ++i +                                   
  gi|13540853|ref|NP_110541.1|  40 GSGKTTLMKILVSLLSKKSGRVSVCGLDVDKDQMK-IKEIAGYIPEtpvlyesmtplelfdfvgsvrhipvdsyarrlnal 119
                                   9****************999999999999966666.555555554467778888888888888888878777766666666 PP

                                   ...................C CS
                                   ...................x RF
                          CbiA  55 ...................d 55 
                                                      +
  gi|13540853|ref|NP_110541.1| 120 idafsikdylnefigslsfG 139
                                   66666665555555555552 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1     8e-05     0.048       6      39 ..      35      68 ..      31      74 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 8e-05
                                  EEESTTSSHHHHHHHHHHHHHHTTS-EEEEEEST CS
                         SRP54  6 lvGlqGaGKTttlaKLaallkkegkkvllvaaDt 39
                                  ++G++G+GKTt +  L  ll+k+  +v ++ +D+
  gi|13540853|ref|NP_110541.1| 35 ILGPNGSGKTTLMKILVSLLSKKSGRVSVCGLDV 68
                                  79*********************99999999886 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   0.00016     0.096       3      49 ..      35      78 ..      33      92 .. 0.78
   2 ?   -1.2   0.0       4.2   2.5e+03      57      66 ..     151     161 ..     110     199 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00016
                                  EESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHH CS
                           AAA  3 lyGppGtGKTllakavakelgvefleisgsellskyvgesekkirel 49
                                  + Gp G GKT+l+k +++ l+ +  ++s+  l    v + ++ki+e+
  gi|13540853|ref|NP_110541.1| 35 ILGPNGSGKTTLMKILVSLLSKKSGRVSVCGLD---VDKDQMKIKEI 78
                                  57****************998777777776666...55566666555 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 4.2
                                   S.TSEEEEEET CS
                           AAA  57 a.kpsilfiDE 66 
                                     +p++l++DE
  gi|13540853|ref|NP_110541.1| 151 VhDPKVLIVDE 161
                                   23477777777 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   7.4e-05     0.044      21      56 ..      35      69 ..      30      98 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 7.4e-05
                        AAA_13 21 iYGwNGaGKTtLSrllrslelgetepkfangsieit 56
                                  i G NG+GKTtL ++l sl + + + + + + + + 
  gi|13540853|ref|NP_110541.1| 35 ILGPNGSGKTTLMKILVSLLS-KKSGRVSVCGLDVD 69
                                  6689*************9954.44666666666554 PP

>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00011     0.066      50      85 ..      27      62 ..      19      78 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00011
                                  EETTSEEEEEESTTSSHHHHHHHHHHHHHHTT--EE CS
                          RecA 50 lpkGriieiyGpessGkttlalhaiaeaqkkggvaa 85
                                  +p G i  i Gp+ sGkttl   +++   kk+g ++
  gi|13540853|ref|NP_110541.1| 27 IPSGSIYGILGPNGSGKTTLMKILVSLLSKKSGRVS 62
                                  89******************9999999888888765 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   0.00013     0.078      24      76 ..      30      82 ..      19     190 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00013
                        AAA_16 24 pelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqal 76
                                  +++  + G+ G+GK++l++ l   l+k+ g +  +  d  + ++    +a ++
  gi|13540853|ref|NP_110541.1| 30 GSIYGILGPNGSGKTTLMKILVSLLSKKSGRVSVCGLDVDKDQMKIKEIAGYI 82
                                  4677799************9998888887777666666664443333344444 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   0.00022      0.13       3      26 ..      35      58 ..      33      81 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00022
                  RNA_helicase  3 lyGpsgeGKStlakeLakallkkl 26
                                  + Gp+g GK+tl+k L++ l+kk+
  gi|13540853|ref|NP_110541.1| 35 ILGPNGSGKTTLMKILVSLLSKKS 58
                                  68***************9999887 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.1    0.0017         1      12      39 ..      32      59 ..      22      76 .. 0.85
   2 ?    2.3   0.0      0.32   1.9e+02      99     128 ..     150     180 ..     108     190 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0017
                        AAA_19 12 vllvtaGpGtGKTrvlkhivallvelgg 39
                                  +  ++++ G+GKT+++k  v+ll +  g
  gi|13540853|ref|NP_110541.1| 32 IYGILGPNGSGKTTLMKILVSLLSKKSG 59
                                  56799***************99988765 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.32
                        AAA_19  99 klqeeellivDE.fqdvdelqyrLlkallge 128
                                    +++ ++livDE +  +d+   r++k +l +
  gi|13540853|ref|NP_110541.1| 150 LVHDPKVLIVDEgMNGLDPRSARIFKDILMD 180
                                   4556669*****6677899999999988754 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   0.00031      0.18       4      33 ..      35      66 ..      33      78 .. 0.82
   2 ?   -1.0   0.0       2.5   1.5e+03      89     134 ..     147     194 ..     138     214 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00031
                                  EE--TTSSHHHHHHHHHHHH.....GGGEEEE CS
                      NTPase_1  4 iTGppGvGKtTlvkkvlellkss..gvkvgGf 33
                                  i Gp G+GKtTl+k +++ll+++   v+v+G+
  gi|13540853|ref|NP_110541.1| 35 ILGPNGSGKTTLMKILVSLLSKKsgRVSVCGL 66
                                  669*****************887435777776 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 2.5
                                   HHHHHHHH-EEEE--.-STTGGG-.HHHHHHHHHHHTTTSEEEEE--S CS
                      NTPase_1  89 lrkalseadviviDE.iGkmElks.kkfkeaveevLksekpvlavihr 134
                                   ++  ++++ v+++DE    +   s + fk+ + ++ +++k+v++  h 
  gi|13540853|ref|NP_110541.1| 147 ISALVHDPKVLIVDEgMNGLDPRSaRIFKDILMDMKNRGKIVVFSTHI 194
                                   555556677777777322233333033444444444456666655554 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 ?   11.9   0.0   0.00021      0.13      31      76 ..     160     204 ..     136     213 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00021
                          PrkA  31 reGmsGispRyvikilsealssseakeekcinpldvlealeeglke 76 
                                   +eGm+G++pR++ +i++++l++ +++ + ++  +++le  e++++ 
  gi|13540853|ref|NP_110541.1| 160 DEGMNGLDPRSA-RIFKDILMDMKNRGKIVVFSTHILEIAENLCDS 204
                                   8*********97.69******999999**********999999876 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 ?   11.9   0.1   0.00021      0.12       3      26 ..      33      58 ..      31      78 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00021
                                  EEEEESTTCCHHHHHHHHH..CT--S CS
                          cobW  3 tvltGflGsGKTtLlnhll..enrag 26
                                  +++ G+ GsGKTtL++ l+    +++
  gi|13540853|ref|NP_110541.1| 33 YGILGPNGSGKTTLMKILVslLSKKS 58
                                  6799***********99985533333 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1    0.0002      0.12     134     160 ..      35      61 ..       4      65 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0002
                         T2SSE 134 vsGgTgsGKttllyallkeinksderi 160
                                   + G+ gsGKttl+ +l++ + k++ r+
  gi|13540853|ref|NP_110541.1|  35 ILGPNGSGKTTLMKILVSLLSKKSGRV 61 
                                   569******************998887 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 ?   11.6   0.0    0.0004      0.24       4      47 ..      35      78 ..      33     130 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0004
                                  EESSTTSSHHHHHHCHCT-CCC.-EEETTTTEEEEEEECGGSGGC CS
                           Roc  4 lvGdsgvGKtsllkrfvedkfs.ekekstigvdfltkevtkikgv 47
                                  ++G +g+GKt+l+k +v+   + + + s +g+d+ + ++ kik++
  gi|13540853|ref|NP_110541.1| 35 ILGPNGSGKTTLMKILVSLLSKkSGRVSVCGLDVDKDQM-KIKEI 78
                                  79**************99655415578999999988776.66654 PP

>> AAA_24  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      0.31       6      23 ..      34      58 ..      30     161 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00052
                        AAA_24  6 liyGpsgiGKTtlakel.......g 23
                                   i Gp+g+GKTtl+k l        
  gi|13540853|ref|NP_110541.1| 34 GILGPNGSGKTTLMKILvsllskkS 58
                                  699***********99866665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       605  (0.0337442); expected 358.6 (0.02)
Passed bias filter:                      581  (0.0324056); expected 358.6 (0.02)
Passed Vit filter:                       118  (0.00658152); expected 17.9 (0.001)
Passed Fwd filter:                        30  (0.00167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              30  [number of targets reported over threshold]
# CPU time: 0.60u 0.31s 00:00:00.90 Elapsed: 00:00:00.47
# Mc/sec: 1672.78
//
Query:       gi|13540854|ref|NP_110542.1|  [L=326]
Description: hypothetical protein TVN0023 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.3e-22   79.1  14.9    2.8e-12   47.0   0.3    2.5  3  VIT1          VIT family
    9.6e-07   29.3   4.4    2.1e-06   28.2   4.4    1.5  1  Rubrerythrin  Rubrerythrin
  ------ inclusion threshold ------
      0.035   13.9   0.8       0.59    9.9   0.0    2.4  3  COQ7          Ubiquinone biosynthesis protein COQ7
      0.063   13.5   0.2          3    8.0   0.1    2.3  2  Ferritin_2    Ferritin-like domain
       0.49    9.9   5.3        2.1    7.8   0.0    2.5  3  IpaC_SipC     Salmonella-Shigella invasin protein C (IpaC_Sip


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 ?   -3.4   0.0         2   7.2e+03      98     148 ..      37      83 ..      17      87 .. 0.57
   2 !   47.0   0.3   7.9e-16   2.8e-12       2      69 ..     148     214 ..     147     231 .. 0.87
   3 !   38.6   6.3   2.8e-13   9.9e-10     130     214 ..     231     314 ..     210     315 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 2
                          VIT1  98 elaqevaaellknpdallelmlreelgpsaseelasplkaAlssalsfliG 148
                                   +l+ ++ +   ++ + ++e m r++ + s+  +  + +k  +   + +++G
  gi|13540854|ref|NP_110542.1|  37 NLS-KLSEIEREHSEFWKENMKRFGIKYSN--R-YNRFKVTFLLLARYFLG 83 
                                   333.33455555666666666666655443..2.35566666666666666 PP

  == domain 2  score: 47.0 bits;  conditional E-value: 7.9e-16
                          VIT1   2 rdavlGanDGLvspfalvaGlsaaslgssktvllaGlaellAGaiSMgiGeYlsvkserdlekaerkr 69 
                                   +d+++G++DGLv ++a  aGl ++  +++  + l+Gl   ++G  SM iG+Yls kse ++   e+++
  gi|13540854|ref|NP_110542.1| 148 KDVIYGISDGLVEVLAALAGLTSII-ENNIDIALGGLVVGISGTASMTIGAYLSKKSETEYKLVEEEK 214
                                   79********************665.7999****************************9988776555 PP

  == domain 3  score: 38.6 bits;  conditional E-value: 2.8e-13
                          VIT1 130 elasplkaAlssalsfliGgliPllpylfvesvglalvvsiavtllalllfGavkalltgssklvsalrmlliGalAaaaa 210
                                    +a++ ++Al ++ls+++G+++P+lp++f++   lal++si+++ ++  +  a+ al +++++++ a+r   + +lAaa++
  gi|13540854|ref|NP_110542.1| 231 IKAESKTSALYVGLSYILGSAVPILPFVFLH-KYLALILSIILVFIVQGIANAMVALSVNVRVMKMAIRASSLALLAAAIT 310
                                   2245668**********************99.9************************************************ PP

                          VIT1 211 ylig 214
                                   +++g
  gi|13540854|ref|NP_110542.1| 311 FFVG 314
                                   *997 PP

>> Rubrerythrin  Rubrerythrin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2   4.4   5.8e-10   2.1e-06       8     136 ..      13     136 ..      11     137 .. 0.87

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 5.8e-10
                                   HHHHHHHHHHHHHHHCHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTHH.B.SSBBS-------TTGGHHHHHH.. CS
                  Rubrerythrin   8 agEssarrlYkelaekakegypqiaelFeelAeeEreHakilnklleklepelelevkekvreyaeakpkflttaknLe.. 86 
                                   + E +++++Y  l++ +k     ++e + +l+e EreH+++ ++ ++ +  ++          y  +k +fl+ a++    
  gi|13540854|ref|NP_110542.1|  13 RDELTDMNFYSKLSRTIK--DDYLRENLSKLSEIEREHSEFWKENMKRFGIKYS-------NRYNRFKVTFLLLARYFLgn 84 
                                   6799**************..7778***************************999.......56666666666666655555 PP

                                   ..HHHHHHHHHHHCHHHHHHHHHHHTTSHHHHHHHHHHHHHHHHHHHHHHHH CS
                  Rubrerythrin  87 ..eaiegayaeeeemyrfyeelaekegneeakklfkklaeaEkkHeerlrkl 136
                                     +a+ +++ e +++      l++k  +e+ + ++ k+ ++E  Hee+++k+
  gi|13540854|ref|NP_110542.1|  85 flTARLLEHGEISTVSVYSDYLKKKDLDEDFRARLSKILDEEINHEEIFEKA 136
                                   558999999999999877788888899999*******************997 PP

>> COQ7  Ubiquinone biosynthesis protein COQ7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0     0.044   1.6e+02      30      64 ..      30      64 ..      15      78 .. 0.78
   2 ?    9.9   0.0   0.00016      0.59      11      59 ..      93     140 ..      87     167 .. 0.89
   3 ?   -3.6   0.1       2.4   8.5e+03      56      79 ..     292     315 ..     288     316 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.044
                          COQ7 30 kdpelkpllkemleqEkeHlatfeellkerrvrps 64
                                  kd  l++ l++  e E+eH ++++e +k+ +++ s
  gi|13540854|ref|NP_110542.1| 30 KDDYLRENLSKLSEIEREHSEFWKENMKRFGIKYS 64
                                  45567889999999999999999999999888776 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00016
                          COQ7  11 aGElgAvaiYkgqlavlakkdpelkpllkemleqEkeHlatfeellker 59 
                                    GE+  v +Y+  l   +  d+++++ l+++l++E +H ++fe+ +++ 
  gi|13540854|ref|NP_110542.1|  93 HGEISTVSVYSDYLKK-KDLDEDFRARLSKILDEEINHEEIFEKAMEKS 140
                                   5999999999999888.6888899*********************9987 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 2.4
                          COQ7  56 lkerrvrpslllplwkvagfalGa 79 
                                   + +  +r s l  l  +  f++G+
  gi|13540854|ref|NP_110542.1| 292 VMKMAIRASSLALLAAAITFFVGF 315
                                   556678888888888888888886 PP

>> Ferritin_2  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0     0.034   1.2e+02      18      66 ..      10      63 ..       9      88 .. 0.72
   2 ?    8.0   0.1   0.00084         3      19      68 ..     101     145 ..      82     150 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.034
                    Ferritin_2 18 afYtaalegasldd...kalldaevrevaeeiakheeaHveflkaale..Gaaa 66
                                  +fY   l+ +++ +    +  d+  re + ++ + e++H ef+k+  +  G ++
  gi|13540854|ref|NP_110542.1| 10 EFYRDELTDMNFYSklsRTIKDDYLRENLSKLSEIEREHSEFWKENMKrfGIKY 63
                                  5777777766665566566677777999****************9987555444 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00084
                    Ferritin_2  19 fYtaalegaslddkalldaevrevaeeiakheeaHveflkaale.Gaaava 68 
                                    Y+  l+      k+ ld++ r+ + +i ++e++H e++++a e ++ +v+
  gi|13540854|ref|NP_110542.1| 101 VYSDYLK------KKDLDEDFRARLSKILDEEINHEEIFEKAMEkSQDTVE 145
                                   3444444......999**************************987666665 PP

>> IpaC_SipC  Salmonella-Shigella invasin protein C (IpaC_SipC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0      0.79   2.8e+03     162     178 ..      34      50 ..      23      63 .. 0.63
   2 ?    7.8   0.0   0.00058       2.1      21     112 ..      98     189 ..      92     202 .. 0.82
   3 ?    2.0   2.5     0.035   1.2e+02      73     103 ..     274     304 ..     266     310 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.79
                     IpaC_SipC 162 lkknlaklakLkkesae 178
                                   l++nl kl ++++e+ e
  gi|13540854|ref|NP_110542.1|  34 LRENLSKLSEIEREHSE 50 
                                   55555555555555554 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.00058
                     IpaC_SipC  21 rvaalrsalaasvenagkkpdlettandrrtvkleevvqkelkelaaeqtptld.isglssalvallalaavllsal.rqa 99 
                                   +v++  ++l+ +  + ++++ l + + +   ++ ee+ +k +++ + ++++  d i g+s+ lv +la+ a l s + ++ 
  gi|13540854|ref|NP_110542.1|  98 TVSVYSDYLKKKDLDEDFRARLSKILDE--EINHEEIFEKAMEKSQDTVERNKDvIYGISDGLVEVLAALAGLTSIIeNNI 176
                                   6888899999999999999999999985..8999***************99777368**************9999883356 PP

                     IpaC_SipC 100 dlalsgkLslvaf 112
                                   d al+g    ++ 
  gi|13540854|ref|NP_110542.1| 177 DIALGGLVVGISG 189
                                   8888876655555 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.035
                     IpaC_SipC  73 ldisglssalvallalaavllsalrqadlal 103
                                   + + g+ +a+val +++ v+  a+r + lal
  gi|13540854|ref|NP_110542.1| 274 FIVQGIANAMVALSVNVRVMKMAIRASSLAL 304
                                   7799**********************99998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1666  (0.0929221); expected 358.6 (0.02)
Passed bias filter:                      733  (0.0408835); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 2097.80
//
Query:       gi|13540855|ref|NP_110543.1|  [L=449]
Description: 4-aminobutyrate aminotransferase [Thermoplasma volcanium GSS1]
Scores for complete 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-117  392.6   0.0   1.8e-117  392.4   0.0    1.0  1  Aminotran_3    Aminotransferase class-III
     0.0015   17.8   0.0      0.002   17.3   0.0    1.3  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 !  392.4   0.0    2e-121  1.8e-117       3     406 .]      32     445 ..      30     445 .. 0.94

  Alignments for each domain:
  == domain 1  score: 392.4 bits;  conditional E-value: 2e-121
                                   -TTB--SCEEEEEEEBTEEEETTS-EEEESSHHHHTTTT-BT-HHHHHHHHHHHTT-S---TTTCEEHHHHHHHHHHHHHC CS
                   Aminotran_3   3 areednlllvitkaeGvyltdvdgkrylDlvssiavvnlGhahPkvvkavkeqaaklshvsfgaltnepalklaekllkla 83 
                                   ar+ + l++v + ++Gvy++dvdg+ ylD++s+i+v+nlGh +P v++ v+eq++kl+h     + +e ++ +a+ l++++
  gi|13540855|ref|NP_110543.1|  32 ARSTQSLPVVGKLGKGVYVEDVDGNVYLDFASGISVTNLGHLDPYVTQKVEEQLHKLWHFPGTDFYTEMQVLAAKSLIEVT 112
                                   5666677789999************************************************9999999999999******* PP

                                   T-..S.EEEEESSHHHHHHHHHHHHHHHHHHTSHCTT-EEEEETTT---SSHHHHHHSS--TTTTTTCTTB-TSEEEE-TT CS
                   Aminotran_3  84 pkgld.kvflansGseAvetAlKlarkyarekkatektkiiafkgafHGrtlgalsvtgskkkyktlfgpflpevvrlkyp 163
                                   p++++ kvf+ nsG+e+ve+A+K+a++      +t+++++i f gafHGrt+g+ls t+sk++++++f p++p+v ++++p
  gi|13540855|ref|NP_110543.1| 113 PGKFNkKVFFTNSGTESVEAAIKIAKS------YTHRERFIGFIGAFHGRTQGSLSFTASKPIHHKGFFPSMPGVEHVPFP 187
                                   ***9989********************......9*********************************************** PP

                                   BGGGTB-HH....HHHHHHHHHHHHHH......CHTCCCEEEEEE-SCETTTTSEB--CCHHHHHHHHHHHHT-EEEEE-T CS
                   Aminotran_3 164 deevlkene....eeeaalleeleale......kkkkdevaAvivEpiqgegGvvvaspeflaklrelckkhdvllivDEv 234
                                    +++ ++n     e ++ + + +  +e       +  ++va+++ EpiqgegG++v++ +f+++lr+l++k+ + l++DEv
  gi|13540855|ref|NP_110543.1| 188 NPYRNPFNIdgyeEPDELVNRVIDYIEtyllktYVPPEDVAGILAEPIQGEGGYIVPPMNFFKELRKLADKYHIPLLIDEV 268
                                   *******985665444444444444446668777789******************************************** PP

                                   TTTTTTTSSSSGGGGCTS--SEEEE-GGGGTTSS-EEEEEEHHHHTTS-TTSB--TTTT-HHHHHHHHHHHHHHHHTTHHH CS
                   Aminotran_3 235 qtGfGrTGklfAlehagvspDlmtlaKaltgGlplsavlataevmqalapgshgsTfgGnplacavalavleiieeeklle 315
                                   q+GfGrTGk+fA eh+gv+pD++tlaK++++G+p+ a++ ++e m+  ++g h++TfgGn +a a+++a+++ +++ + +e
  gi|13540855|ref|NP_110543.1| 269 QSGFGRTGKFFASEHFGVEPDVITLAKSIASGIPMGAAVMKEE-MNFSENGLHSNTFGGNLIASAACVATIDEMKKLNAVE 348
                                   **************************************99988.56777899***************************** PP

                                   HHHHHHHHHHHHHHHHCTT-TTEEEEEEETTEEEEEEBCCCETTC......HHHHHHHHHCTEE-EEETTTEEEE---TT- CS
                   Aminotran_3 316 naqelgaalkegLeelqkkyevikevRgkGlmiaielkeeaevke......keilkkakekGvlilsaGdnvirllpplii 390
                                   na++ ga++k++L elq+ky+ i++vRg+Glm+ai++++++++ke      ++++++a ++G+++ls+G+++ir++pplii
  gi|13540855|ref|NP_110543.1| 349 NAAKQGAYMKKRLVELQNKYNEIGDVRGLGLMLAIDFVKDRRTKEpnsklrNDVINNAFKNGLILLSTGSSAIRIIPPLII 429
                                   ******************************************9999*****9***************************** PP

                                   -HHHHHHHHHHHHHHH CS
                   Aminotran_3 391 tdeeidelleilkkal 406
                                   t+e++de++e l ka+
  gi|13540855|ref|NP_110543.1| 430 TQEQVDEGIEVLDKAI 445
                                   ************9987 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 !   17.3   0.0   2.3e-07     0.002     168     291 ..     247     364 ..     242     441 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2.3e-07
                                   HHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEEEEEEHHHHHHHHHHHH CS
                 Aminotran_1_2 168 eeleklldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKafGlaGeRvGyilgnaavvsqlrklsr 248
                                   +  ++l +la+ky++ l++De+ +gf  + + +++ +++ve+++      +l+K+ +  G+ +G+++ ++++    + l++
  gi|13540855|ref|NP_110543.1| 247 NFFKELRKLADKYHIPLLIDEVQSGFGRTGKFFASEHFGVEPDVI-----TLAKSIA-SGIPMGAAVMKEEMNFSENGLHS 321
                                   556666777********************9888788*****9855.....99**996.48888999999999999999999 PP

                                   HHTSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                 Aminotran_1_2 249 pflsssllqaavaaalsdallkqseleemrqrlqkrrkelrde 291
                                   +    +l + a+  a+ d+ +k + +e+++++ + + k+l++ 
  gi|13540855|ref|NP_110543.1| 322 NTFGGNLIASAACVATIDEMKKLNAVENAAKQGAYMKKRLVEL 364
                                   9888666666666666666666678888888888888887764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (449 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 3416.08
//
Query:       gi|13540856|ref|NP_110544.1|  [L=170]
Description: hypothetical protein TVN0025 [Thermoplasma volcanium GSS1]
Scores for complete 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-24   83.3   0.1    1.3e-23   82.8   0.1    1.2  1  Hjc        Archaeal holliday junction resolvase (hjc)
  ------ inclusion threshold ------
      0.062   12.9   0.0      0.091   12.3   0.0    1.4  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 !   82.8   0.1   1.5e-27   1.3e-23       2      91 ..       6     123 ..       5     124 .. 0.98

  Alignments for each domain:
  == domain 1  score: 82.8 bits;  conditional E-value: 1.5e-27
                                   HHHHHHHHHHHTT........................-EEEEBSCSSSSSSSS-SEEEEETTEEEEEEEEEESSSEEEE.. CS
                           Hjc   2 yERelvkiLrerg........................favvRsagSggatkplpDviAirgdvvlviEvKsskkeriyl.. 56 
                                   yERe+++iL +r                         f v+R+agS ga     D+iAir+d+++viEvKss   r yl  
  gi|13540856|ref|NP_110544.1|   6 YEREIRDILSGRAqavekyaqrvgengstvrslitspFFVTRAAGSLGA-----DIIAIRHDISMVIEVKSSI--RSYLaf 79 
                                   8************************************************.....*******************..999999 PP

                                   ......EHHHHHHHHHHHHHHTCEEEEEEEE...TTTEEEEEEG CS
                           Hjc  57 ......kkeqvekllefarkaggelllavkl...qgkewkllvv 91 
                                         k++q+e+l e+ ++ag++l++a++l   +g++w+l+ v
  gi|13540856|ref|NP_110544.1|  80 seasgkKQDQAERLSEMVNRAGIFLVYAFRLknaSGDPWRLFTV 123
                                   *******************************99899*****986 PP

>> AHJR-like  REase_AHJR-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0     1e-05     0.091      44      65 ..      53      74 ..      19      98 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1e-05
                     AHJR-like 44 rpDliarkdeeaviiEvksrrs 65
                                    D+ia++ +  ++iEvks++ 
  gi|13540856|ref|NP_110544.1| 53 GADIIAIRHDISMVIEVKSSIR 74
                                  57*****************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       338  (0.0188521); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 1074.54
//
Query:       gi|13540857|ref|NP_110545.1|  [L=258]
Description: arsenite transporting ATPase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.5e-19   70.4   0.1    4.1e-19   68.9   0.1    1.5  1  ArsA_ATPase  Anion-transporting ATPase
    0.00019   21.0   0.6     0.0025   17.3   0.6    2.4  1  ParA         NUBPL iron-transfer P-loop NTPase
    0.00025   21.1   0.0     0.0004   20.4   0.0    1.4  1  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
     0.0094   15.9   0.5      0.025   14.5   0.1    2.0  2  AAA_31       AAA domain
  ------ inclusion threshold ------
      0.019   15.2   0.8       0.72   10.1   0.0    2.4  2  Roc          Ras of Complex, Roc, domain of DAPkinase
      0.036   14.2   0.0      0.085   13.0   0.0    1.6  2  AAA_33       AAA domain
      0.074   12.7   0.2        0.2   11.3   0.2    1.7  2  SRP54        SRP54-type protein, GTPase domain
      0.096   12.4   0.1       0.16   11.7   0.1    1.5  1  AAA_24       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 !   68.9   0.1   1.8e-22   4.1e-19       6     244 ..       5     220 ..       2     227 .. 0.81

  Alignments for each domain:
  == domain 1  score: 68.9 bits;  conditional E-value: 1.8e-22
                                   EEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-STTTHHHHHHTS--BSS-EEETSSEEEEE--HHHHHHHHHCCHHGGGSC CS
                   ArsA_ATPase   6 vgGKGGVGKttvsaatavklsekgkkvllistDPAhslsDsfdqklgkeptkvkeNLsavEidpeveleeakqevqkeeea 86 
                                   + GKGGVGKtt++aa ++ ++e+g  + ++stD  +sl  +f ++        + NL + Ei  ++ +++ +++ +  +  
  gi|13540857|ref|NP_110545.1|   5 FVGKGGVGKTTIAAAYSLICAEHGS-TAIVSTDTMPSLHYIFPEN--------TVNLDVFEISESE-VSKLWKKRYGDQVY 75 
                                   78********************996.6689************993........3599999998774.66666665544444 PP

                                   CH...HHHHHHHHHHHHHTSSTTHHHHHHHHHHHHHHHCSSSSEEEEESBSCCHTCGGGGHHHHHHHHHHHHHHHHHHHHH CS
                   ArsA_ATPase  87 ll...gleeledvlaeelaslPGideilsfeellkyvkeeeydvvvlDtaPTGhtlrllslpevleklleklvklkeklsp 164
                                    +    +++  +++++ +++ PG+ e +   +++ + +++++d++v Dt+    t+ ll l + + + l + +k      +
  gi|13540857|ref|NP_110545.1|  76 DIvsrFFDTGFEIIDHIANA-PGVAEEFMISQIVGMGETKKFDYLVWDTPASSSTMHLLYLEKDFYEHLGRDIKFYF---S 152
                                   33233446788999999999.*******************************************9999996666544...3 PP

                                   HHHHHCCCSHCHHHHHHHHHHHHHHHHHHHHHHHHHHTSTTTEEEEEEEESSHHHHHHHHHHHHHHHHTT-EEEEEEEEE CS
                   ArsA_ATPase 165 lakqlvkllglggvsieealeeleetkeeikkveeiltdpertsfrlVvipEklslkEteRaikeLkkygikvdavivNk 244
                                   ++ ++         +++++le l+e  e  kkv + +   e + f lV++ ++lsl  +    ++Lk++gi+v a i N+
  gi|13540857|ref|NP_110545.1| 153 MKDAF---------KTNKTLEILNEWRELSKKVWNEI---ENSKFYLVSTHDELSLLQSYEIEEDLKRMGISVSARIYNR 220
                                   44444.........45566777777777777555555...55669******************************99997 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.6   1.1e-06    0.0025       9     129 ..       5     133 ..       1     218 [. 0.73

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.1e-06
                          ParA   9 lSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgvee........ekpeqs..ekkliPveakgi.kvmS. 77 
                                     gKGGVGK+t+a+  +l  a++g  ++++ +D + ps+  ++  ++        +   +s  +k +   + +++  ++S 
  gi|13540857|ref|NP_110545.1|   5 FVGKGGVGKTTIAAAYSLICAEHGS-TAIVSTDTM-PSLHYIFPENTvnldvfeiS---ESevSKLWKKRYGDQVyDIVSr 80 
                                   56*************9999998885.789999976.89988887666445444321...1112223444443333133441 PP

                          ParA  78 .igfllesedeavvwrGpmkskaikqllkdvewgelDyLiiDlPPGtgDeqlt 129
                                    +++  e  d+     G   + +i+q++   e ++ DyL+ D+P   + ++l 
  gi|13540857|ref|NP_110545.1|  81 fFDTGFEIIDHIANAPGVAEEFMISQIVGMGETKKFDYLVWDTPASSSTMHLL 133
                                   13333344455555667777789999999999999999999999888888875 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   1.8e-07    0.0004       6      60 ..       7     210 ..       4     243 .. 0.68

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 1.8e-07
                                   SSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCH........HTTEB-HHHH........................ CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxx........................ RF
                          CbiA   6 tkGGvGKTtlaanLaralarrglrVllvDaDpqannlai........leglendiep........................ 54 
                                   +kGGvGKTt+aa+   + a+    ++ v +D++ ++l++        l                                 
  gi|13540857|ref|NP_110545.1|   7 GKGGVGKTTIAAAYSLICAE-HGSTAIVSTDTM-PSLHYifpentvnL--------Dvfeisesevsklwkkrygdqvydi 77 
                                   8******************9.667889999999.77776454444332........0234444557778888888888888 PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                          CbiA  55 ................................................................................. 54 
                                                                                                                    
  gi|13540857|ref|NP_110545.1|  78 vsrffdtgfeiidhianapgvaeefmisqivgmgetkkfdylvwdtpassstmhllylekdfyehlgrdikfyfsmkdafk 158
                                   888888888888888888888888888888888888888888888888888888888888777777777777776666665 PP

                                   ..............................................CCHCCC CS
                                   ..............................................xxxxxx RF
                          CbiA  55 ..............................................dlkrll 60 
                                                                                 dlkr++
  gi|13540857|ref|NP_110545.1| 159 tnktleilnewrelskkvwneienskfylvsthdelsllqsyeieeDLKRMG 210
                                   5555555555555555555555555555555555444444444444444444 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.1   1.1e-05     0.025       9      81 ..       7      74 ..       1     136 [. 0.58
   2 ?   -2.4   0.0       1.8     4e+03      82      97 ..     179     194 ..     149     210 .. 0.49

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.1e-05
                        AAA_31  9 qKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQanattglgiekneiektlyevlieeknikeaiiktkvenl 81
                                   KGGvGKTT + + +   a+ g    +v  D+  ++     + +n+++ +++e+  +e++++++ +k+  +++
  gi|13540857|ref|NP_110545.1|  7 GKGGVGKTTIAAAYSLICAEHGSTA-IVSTDTMPSLHY--IFPENTVNLDVFEI--SESEVSKLWKKRYGDQV 74
                                  6***************999999765.456665554444..33455555556555..45666666665554444 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.8
                        AAA_31  82 dlipssidLaeaeiel 97 
                                   ++  s+  L++ ++el
  gi|13540857|ref|NP_110545.1| 179 EIENSKFYLVSTHDEL 194
                                   2223333333333333 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00032      0.72       4      39 ..       5      40 ..       4      78 .. 0.70
   2 ?    3.7   0.2     0.032        71      46      78 ..     106     141 ..      76     194 .. 0.51

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00032
                                  EESSTTSSHHHHHHCHCT-CCC-EEETTTTEEEEEE CS
                           Roc  4 lvGdsgvGKtsllkrfvedkfsekekstigvdfltk 39
                                  +vG++gvGKt+++  +     ++ ++++++ d++ +
  gi|13540857|ref|NP_110545.1|  5 FVGKGGVGKTTIAAAYSLICAEHGSTAIVSTDTMPS 40
                                  79************9997777777777777776553 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.032
                                   GCTTBTTTTCEEEEEEEE-SG.GCTTT..T-HHHHC CS
                           Roc  46 gvendkkvkkvklniWDtaGq.erfrs..lhplylr 78 
                                   ++    ++kk+ + +WDt      ++   l++ +++
  gi|13540857|ref|NP_110545.1| 106 QIVGMGETKKFDYLVWDTPASsSTMHLlyLEKDFYE 141
                                   33334456789999***9654044443224455553 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   3.8e-05     0.085       4      61 ..       5      80 ..       3     116 .. 0.75
   2 ?   -2.0   0.0       1.6   3.5e+03      34      34 ..     173     173 ..     128     227 .. 0.57

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.8e-05
                        AAA_33  4 lvGlpGsGKstlaerl...lkklg.avllssdt............lrrrlfg..tdqqsktdytrvldrlyqilne 61
                                  +vG  G+GK+t a  +   ++++g + ++s+dt            +   +f+  + + sk + +r  d++y+i+++
  gi|13540857|ref|NP_110545.1|  5 FVGKGGVGKTTIAAAYsliCAEHGsTAIVSTDTmpslhyifpentVNLDVFEisESEVSKLWKKRYGDQVYDIVSR 80
                                  89*************988888999999******6666655555442223333433333455666666666666655 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.6
                        AAA_33  34 r 34 
                                   +
  gi|13540857|ref|NP_110545.1| 173 S 173
                                   1 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.2   8.9e-05       0.2       5      39 ..       4      37 ..       1      39 [. 0.82
   2 ?   -2.0   0.0         1   2.3e+03      71      92 ..     103     124 ..      89     162 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 8.9e-05
                                  EEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEEST CS
                         SRP54  5 llvGlqGaGKTttlaKLaallkkegkkvllvaaDt 39
                                  ++vG  G+GKTt +a  + ++  e+ ++++v++Dt
  gi|13540857|ref|NP_110545.1|  4 AFVGKGGVGKTTIAAAYSLICA-EHGSTAIVSTDT 37
                                  69**********9999986655.566789999998 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1
                                   HHHHHHHHHHHTTSSEEEEEE- CS
                         SRP54  71 vakeavekakeekidvvlvDTa 92 
                                   ++++ v + + +k+d+++ DT 
  gi|13540857|ref|NP_110545.1| 103 MISQIVGMGETKKFDYLVWDTP 124
                                   5566667777888888888885 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1     7e-05      0.16       8      73 ..       6     123 ..       4     176 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 7e-05
                        AAA_24   8 yGpsgiGKTtlakel......gpkplfidtek..Glksldadkfpdieswedfldevvel..................... 59 
                                   +G+ g+GKTt+a+ +        +++++ t+   +l+ + + + +++  +e   +ev +l                     
  gi|13540857|ref|NP_110545.1|   6 VGKGGVGKTTIAAAYslicaeHGSTAIVSTDTmpSLHYIFPENTVNLDVFEISESEVSKLwkkrygdqvydivsrffdtgf 86 
                                   79*************777777666666666655555555555555555444444444444444455555556666677777 PP

                        AAA_24  60 .......................aaeladyktlviDt 73 
                                                            e ++++ lv+Dt
  gi|13540857|ref|NP_110545.1|  87 eiidhianapgvaeefmisqivgMGETKKFDYLVWDT 123
                                   7777777777777777777777777777777777777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       831  (0.0463495); expected 358.6 (0.02)
Passed bias filter:                      617  (0.0344135); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.62u 0.32s 00:00:00.94 Elapsed: 00:00:00.50
# Mc/sec: 1546.02
//
Query:       gi|13540858|ref|NP_110546.1|  [L=378]
Description: cell division protein FtsZ [Thermoplasma volcanium GSS1]
Scores for complete 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  131.9   0.2    6.8e-38  130.8   0.2    1.5  1  Tubulin         Tubulin/FtsZ family, GTPase domain
      5e-20   71.6   0.3    1.4e-19   70.1   0.3    1.8  1  FtsZ_C          FtsZ family, C-terminal domain
  ------ inclusion threshold ------
       0.19   11.6   2.5       0.26   11.2   0.3    2.3  3  NAD_binding_10  NAD(P)H-binding
        1.1    8.4   6.2        0.4    9.8   0.3    2.2  2  Tubulin_2       Tubulin like


Domain annotation for each model (and alignments):
>> Tubulin  Tubulin/FtsZ family, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.8   0.2   1.5e-41   6.8e-38       1     194 [.      45     203 ..      45     206 .. 0.97

  Alignments for each domain:
  == domain 1  score: 130.8 bits;  conditional E-value: 1.5e-41
                                   EEEEEEEHHHHHHHHHHHHH...HHHCH....HHHT.....TTEEEEE....EEESBHHHHHTS-GS......EEEE--CC CS
                       Tubulin   1 eiivigvGqcGnqignelwellakehgiqsdgdslesfFsesgkveyiprsvaidtdpqvlneikagselfnpnklllgke 81 
                                   +i+v+g+G++G++++++l+e    e g+             +g +++i    a++td+++l+ ik +      +kll+g  
  gi|13540858|ref|NP_110546.1|  45 KIKVVGCGGGGSNTVSRLYE----E-GL-------------KG-ADLI----ALNTDASHLKTIKVA------KKLLIGYR 96 
                                   699*****************....8.99.............88.8888....***************......******** PP

                                   CCTTC--TT-HHHHHHHHHHTHHHHHHHHTT-SE.SEEEEEEETTSSHHHHHHHHHHHHHHHTSTTSEEEEEEEE--GG.G CS
                       Tubulin  82 gagnngaggypevgkeaaeeileeirkevekcdslqgffitaslgGGTGSGlgpvilevlkeeypkalvvtvvvlPsefse 162
                                    ++++g g++p+vg+eaa e    i+k+v+++d    +f+ta+lgGGTG+G +pv+++++ke   +a+v++vv+lP++  e
  gi|13540858|ref|NP_110546.1|  97 TTRGLGTGADPKVGEEAAAEEIVSIKKMVQNTDI---VFVTAGLGGGTGTGSAPVVAKAAKEA--GAIVISVVTLPFDS-E 171
                                   **********************************...**************************..************98.* PP

                                   -HHHHHHHHHHHHHHHHT-SEEEEEEHHHHHC CS
                       Tubulin 163 vvvepynailalkelieesdavividNdaLlk 194
                                   +  ++ na+ +l++l + sd++i i+N++Ll 
  gi|13540858|ref|NP_110546.1| 172 GPMRMDNAVIGLENLAQFSDTLIAIPNQRLLS 203
                                   *****************************985 PP

>> FtsZ_C  FtsZ family, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.1   0.3   3.2e-23   1.4e-19       1      94 [.     253     347 ..     253     348 .. 0.97

  Alignments for each domain:
  == domain 1  score: 70.1 bits;  conditional E-value: 3.2e-23
                                   EEEEEEEEEE.ESTTHHHHHHHHHHTSGGGT--GGG-SEEEEEEEE-TT--HHHHHHHHHHHHHHS-TTSEEEEEEEE-TT CS
                        FtsZ_C   1 GvAmmgvGea.sgedraeeaaeaaisspLLdvdlsgAkgvlvnitggsdltlkEveevaetireevdeeanvivGavidee 80 
                                   GvAm+g+G++ +g dr ++a e+a++  L+dvd+s Ak  +++i + +d+t++Ev +++++i++++  ++++i+G ++d++
  gi|13540858|ref|NP_110546.1| 253 GVAMIGMGQSkKGGDRIMTALEEALKPRLIDVDISTAKDCIFKIIAPPDITVSEVGKAMSEIKKRITAKSRIIWGLTVDKN 333
                                   99******872579******************************************************************* PP

                                   --SEEEEEEEEES- CS
                        FtsZ_C  81 ledeirvtvvatgl 94 
                                   l++ ++v + +tg+
  gi|13540858|ref|NP_110546.1| 334 LDQDVKVLIFMTGV 347
                                   *************8 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       1.4   6.4e+03       5      36 ..      53      86 ..      51      91 .. 0.74
   2 ?   11.2   0.3   5.8e-05      0.26      49      97 ..     116     165 ..     108     184 .. 0.80
   3 ?   -1.2   0.1      0.35   1.6e+03      74     102 ..     262     290 ..     214     322 .. 0.74

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 1.4
                                  HHHHHHHHHHHHC-..T-EEEEEETTHHHCHHHH CS
                NAD_binding_10  5 kvGrllvkellarg..ghevtalvRnpeklaele 36
                                  + G+  v++l ++g  g ++ al  ++++l+ ++
  gi|13540858|ref|NP_110546.1| 53 GGGSNTVSRLYEEGlkGADLIALNTDASHLKTIK 86
                                  5578888888888888888888888888887664 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 5.8e-05
                                   T-CCHHHHHHTT-SEEEES---TCCHHHH.HHHHHHHHHHCT--EEEEEE CS
                NAD_binding_10  49 tdvedlaealkgadaVvsalggggkdeeg.aknivdaakeagvkRfvlvs 97 
                                   ++  ++++ ++++d+V++++g gg++ +g a  +++aakeag   + +v+
  gi|13540858|ref|NP_110546.1| 116 EEIVSIKKMVQNTDIVFVTAGLGGGTGTGsAPVVAKAAKEAGAIVISVVT 165
                                   5667899*************8877755665888999*****986665554 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.35
                                   HHHHHHHHHHHHHHCT--EEEEEEETTTT CS
                NAD_binding_10  74 deegaknivdaakeagvkRfvlvsaigvg 102
                                    ++g ++i++a++ea   R++ v    ++
  gi|13540858|ref|NP_110546.1| 262 SKKGGDRIMTALEEALKPRLIDVDISTAK 290
                                   34566777777777777777766655555 PP

>> Tubulin_2  Tubulin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   1.1     0.043   1.9e+02       2      18 ..      48      64 ..      48      69 .. 0.91
   2 ?    9.8   0.3   8.9e-05       0.4     154     174 ..     127     147 ..      83     163 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.043
                     Tubulin_2  2 viGLGGtGgkvlaelrr 18
                                  v+G+GG G++++++l +
  gi|13540858|ref|NP_110546.1| 48 VVGCGGGGSNTVSRLYE 64
                                  79***********9975 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 8.9e-05
                     Tubulin_2 154 eglnvfVvgSLaGGTGSGifl 174
                                   +   vfV  +L GGTG G++ 
  gi|13540858|ref|NP_110546.1| 127 NTDIVFVTAGLGGGTGTGSAP 147
                                   33579*************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (378 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       541  (0.0301746); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); 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: 0.60u 0.31s 00:00:00.90 Elapsed: 00:00:00.51
# Mc/sec: 2244.94
//
Query:       gi|13540859|ref|NP_110547.1|  [L=226]
Description: orotidine 5'-phosphate decarboxylase [Thermoplasma volcanium GSS1]
Scores for complete 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-32  110.4   0.0    1.2e-31  110.1   0.0    1.1  1  OMPdecase  Orotidine 5'-phosphate decarboxylase / HUMPS famil


Domain annotation for each model (and alignments):
>> OMPdecase  Orotidine 5'-phosphate decarboxylase / HUMPS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.1   0.0   6.6e-36   1.2e-31       2     223 ..      11     207 ..      10     209 .. 0.86

  Alignments for each domain:
  == domain 1  score: 110.1 bits;  conditional E-value: 6.6e-36
                                   EEEEEE-SSSHHHHHHHHHHHGGGSSEEEEEHHHHHHHTHH.HHTHHHHHHHHHTSEEEEEEEE-S-HHHHHHHHHSTCHH CS
                     OMPdecase   2 nLclalDvatarelleladkvgpsivvlKthydlvegwgfegtgaklaalarkhgflifeDrKfaDIGntvekqatagsar 82 
                                   ++++alDv+++++++++a+ + + +  +K++++lv   +      +++ ++ + g ++++D+K+aDI++t +++ +     
  gi|13540859|ref|NP_110547.1|  11 RIIVALDVKEKKKAIDIAESLSDIVFAFKINWPLVLYSS-----PEVIGEISQYG-KVICDFKVADIPYTNSLITE---RV 82 
                                   789************************************.....**********9.9******************9...67 PP

                                   HHTTESEEEEEGTGHHHHHHHHHHHHHHTTS.EEEEEESTSSGGHHHHHHHSHHHHHHHHHHHHHHHTTESEEECCCHTH. CS
                     OMPdecase  83 ikewadivtvhavaGkasvkalaeaaekwgnrgllilaqmsskgnlmlqekgytqacveaarehkaedfvmGfvaqetln. 162
                                    +++a+ ++ h ++G++s+k++++aa+ +   +++ ++ ms++g+ m  +       + ++ + + e++v Gfva +++  
  gi|13540859|ref|NP_110547.1|  83 RDLGAWGIISHSFLGEESLKSVVNAAKGM---HVFSVVAMSHPGSDMINS------NAMQLMKLSIECGVYGFVAPANKId 154
                                   8*************************888...6***************99......5555566666699*********995 PP

                                   HHHHH..TTCSCEEEHHHTTEEEEECTTCCGGGHHHHHHHTTCSEEEESHHHHTSSSHHHHHH CS
                     OMPdecase 163 ateed..addfihltpgigleqggdgkgqqyntpekligiagadiiivGRgIlkagdpveeae 223
                                   +++ +  a d +++ pgig+         q  +p  ++  +g+d++ivGR+++++++p+ e+ 
  gi|13540859|ref|NP_110547.1| 155 DLRMIrsATDRVIISPGIGA---------QGGDPYTAVL-NGSDYLIVGRSVYESDKPELEVS 207
                                   33333455566666666665.........4444555555.79****************98876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1550.88
//
Query:       gi|13540860|ref|NP_110548.1|  [L=230]
Description: secreted serine protease (ClpP class) [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.9e-44  151.3   0.1    2.4e-44  151.0   0.1    1.1  1  Peptidase_S49  Peptidase family S49
    6.6e-10   39.2   0.8    9.8e-07   28.8   0.1    2.1  2  CLP_protease   Clp protease
  ------ inclusion threshold ------
      0.014   15.4   0.2      0.024   14.6   0.2    1.4  1  DUF2118        Uncharacterized protein conserved in archaea (
      0.096   12.9   0.4        0.4   10.9   0.1    2.0  2  DUF2543        Protein of unknown function (DUF2543)
      0.096   12.5   0.0       0.22   11.3   0.0    1.6  1  DUF126         Aconitase X swivel domain
       0.11   12.4   0.6        8.5    6.4   0.0    2.6  2  KH_7           KH domain


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 !  151.0   0.1   8.2e-48   2.4e-44       3     151 ..      60     208 ..      58     211 .. 0.98

  Alignments for each domain:
  == domain 1  score: 151.0 bits;  conditional E-value: 8.2e-48
                                   HHTT--EEEEEEEEEETHHHHHHTTSSEEEE-TT-EEE---EEEEEEE-HHHHHHTT-EEEEEESSTTCCCCCTTSS--HH CS
                 Peptidase_S49   3 kkakkPvvasaenvaaSggYylasaadkivanpstivgsiGvitqllnlenlldklgvevqvvkaGeyksavslrreltee 83 
                                    ++kkPv+ +a ++ aSg+Y++asa+ ki+a  ++++gsiGvi   +n+++l++k+gv+v v k+G+yk++ s+++e +ee
  gi|13540860|ref|NP_110548.1|  60 IRKKKPVYSLALGICASGAYWIASASTKIYAIDTSLIGSIGVISIRPNVKKLMEKIGVDVMVYKSGKYKDMTSPFSEPNEE 140
                                   579****************************************************************************** PP

                                   HHHHHHHHHHHHHHHHHHHHHHHHTS-HHHHHCHHCCHEEEHHHHHHTTSSSEETSHHHHHHHHHHHC CS
                 Peptidase_S49  84 ereilqrlldetyqqFvqtVaknRnlsveqvdkiAegrvltgqqAlklgLvdelgtvddavaeleela 151
                                   e++ +qrlld+++++F+ +Va+ R++++e++d+iA+g v++++ A ++gL+d++ ++dd+v+ l +++
  gi|13540860|ref|NP_110548.1| 141 EKSVYQRLLDDIFEKFKRSVAEDRGIPSEKIDEIANGMVYSAKMAADNGLIDRIANYDDLVSDLTKEV 208
                                   **************************************************************999986 PP

>> CLP_protease  Clp protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   0.1   3.3e-10   9.8e-07      19      99 ..       6      88 ..       3      96 .. 0.91
   2 !    9.0   0.0   0.00041       1.2     129     180 ..     146     196 ..     135     198 .. 0.87

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 3.3e-10
                                  EEEES-BSHHHHHHHHHHHHHHHHH-SSS-EEEEEEE--B-HHHHHHHHHHHHHS..SS-EEEEEEEEEETHHHHHHHTS-TT CS
                  CLP_protease 19 iflgseiddevankiiaqLllLeaedpdkdillyinspGGsvtaglaIydtmqyi..kpdvsticlGlaaSmgslllaagekg 99
                                  i + + i+  +++ +   L ++e ++++  + l+ ns GG+  ++  I+d+++ i  k +v+ ++lG+ aS +  +++a +k 
  gi|13540860|ref|NP_110548.1|  6 INIEGTINYGLYKYLYPALKAAEGKKSIAGLILVFNSGGGDAASSQLIHDLVKKIrkKKPVYSLALGICASGAYWIASASTKI 88
                                  78899999999********************************************877889999***************9986 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00041
                                   HHHHHHHHHHHHHHHHHHHTS-HHHHHHHHCSTEEEEHHHHHHHTSSSEE-S CS
                  CLP_protease 129 aeellkikerlneilakhtgqslekiekdldrdtflsaeeAveyGLidevie 180
                                    + l+ i e+ ++ +a+  g + eki + + + ++ sa+ A + GLid++ +
  gi|13540860|ref|NP_110548.1| 146 QRLLDDIFEKFKRSVAEDRGIPSEKIDE-IANGMVYSAKMAADNGLIDRIAN 196
                                   56678888999999************86.78899***************976 PP

>> DUF2118  Uncharacterized protein conserved in archaea (DUF2118)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.2     8e-06     0.024      16      63 ..     116     163 ..     107     174 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 8e-06
                       DUF2118  16 evevileeeeevekfadkveekklkgkvvYeelldeivdvleekvtrd 63 
                                   +v v++ + ++ ++++ + +e+  ++k vY++lld+i+++ ++ v +d
  gi|13540860|ref|NP_110548.1| 116 GVDVMVYKSGKYKDMTSPFSEPNEEEKSVYQRLLDDIFEKFKRSVAED 163
                                   6789999*********************************99988765 PP

>> DUF2543  Protein of unknown function (DUF2543)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00013       0.4      47      73 ..     150     176 ..     127     182 .. 0.87
   2 ?   -0.5   0.0      0.48   1.4e+03      62      74 ..     185     197 ..     178     202 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00013
                       DUF2543  47 eeiseeaqkemareagideqrideiae 73 
                                   ++i e+ ++ +a++ gi+ ++ideia+
  gi|13540860|ref|NP_110548.1| 150 DDIFEKFKRSVAEDRGIPSEKIDEIAN 176
                                   5799999*******************8 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.48
                       DUF2543  62 gideqrideiaef 74 
                                   + d+  id ia++
  gi|13540860|ref|NP_110548.1| 185 AADNGLIDRIANY 197
                                   4566779999998 PP

>> DUF126  Aconitase X swivel domain
   #    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      23      52 ..      30      59 ..      25      66 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 7.5e-05
                                  T-B-TTSEEEES--S--SS-TTHHHHHHHH CS
                        DUF126 23 gqsiagkiLvlpsgkGStvgsyvllelakn 52
                                   +siag iLv++sg G  ++s+ +++l+k+
  gi|13540860|ref|NP_110548.1| 30 KKSIAGLILVFNSGGGDAASSQLIHDLVKK 59
                                  589**********************99886 PP

>> KH_7  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.1     0.025        75      44      58 ..      49      63 ..      46      66 .. 0.88
   2 ?    6.4   0.0    0.0028       8.5      40      62 ..     193     215 ..     190     216 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.025
                          KH_7 44 ngdlirklAkelrkR 58
                                  +++li  l+k++rk+
  gi|13540860|ref|NP_110548.1| 49 SSQLIHDLVKKIRKK 63
                                  689**********97 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0028
                          KH_7  40 lfaengdlirklAkelrkRiviR 62 
                                    +a+ +dl++ l ke+ kR+ ++
  gi|13540860|ref|NP_110548.1| 193 RIANYDDLVSDLTKEVGKRLKVK 215
                                   57899***************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       629  (0.0350828); expected 358.6 (0.02)
Passed bias filter:                      551  (0.0307323); 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: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 1650.27
//
Query:       gi|13540861|ref|NP_110549.1|  [L=310]
Description: cobalamin biosynthesis protein [Thermoplasma volcanium GSS1]
Scores for complete 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-82  274.9   0.1    7.8e-82  274.6   0.1    1.1  1  CobD_Cbib  CobD/Cbib protein


Domain annotation for each model (and alignments):
>> CobD_Cbib  CobD/Cbib protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  274.6   0.1   4.3e-86   7.8e-82       1     274 [.      11     285 ..      11     287 .. 0.90

  Alignments for each domain:
  == domain 1  score: 274.6 bits;  conditional E-value: 4.3e-86
                     CobD_Cbib   1 lllAlllDlllgdprrllhPvvligklisalekrlrkakkerlaGvllalllvllallvalllllla.laallglvleall 80 
                                   l+ Al +D+++g+p++++hPvv+ g+++sa+e ++rk  ++ +aG+l+ +++++l+++ ++l+++l+ +  ++++v+++++
  gi|13540861|ref|NP_110549.1|  11 LIGALSIDIIFGEPKEYIHPVVFSGRVASAIEGYFRKFDNRFRAGILFSIAVIVLTAIPYFLAVYLSsFILVVYVVVSMVI 91 
                                   688********************************99889999****************99999977422233779***** PP

                     CobD_Cbib  81 lkltlalrsLleevrkvakal.kgdleaaReavsmiVgRdtseldeeeiarAavEsvaENlsDgvvaPlfyflllglpgal 160
                                   lk+t++++s+ e+++ + ++l kg++ +aR ++smiV+Rdts+l+e+ei++Aa+Es+aE l+Dg++ Plf+f+++glpga+
  gi|13540861|ref|NP_110549.1|  92 LKTTFSITSMGEHIKLITDSLkKGNIMEARMHLSMIVRRDTSRLNENEISSAAIESIAEGLVDGYITPLFFFVFFGLPGAF 172
                                   *********************559********************************************************* PP

                     CobD_Cbib 161 aykavnTlDsmvGYkneryedfGwaaArlDDllnyiPARltalllala.......aalriarrdarkhpSpNsgwpeaalA 234
                                   + +++nTlDsm GYk+++  +fG+++A +D+++nyiPAR++ +++ ++       +    +rr+ r+ +S N+gwp+a +A
  gi|13540861|ref|NP_110549.1| 173 IARIINTLDSMYGYKDRKNFEFGRFSAFMDTVINYIPARISWFFITFSsdilnyrSKAIPVRRYIRRFDSVNAGWPIASMA 253
                                   ***********************************************65555554335568999***************** PP

                     CobD_Cbib 235 galgvrLggpnvY.lgkleekptlgdkkrpleaedieralr 274
                                    al++rL+++++Y  ++            ++ ++die++++
  gi|13540861|ref|NP_110549.1| 254 SALNLRLEKKGHYiVNDDGY---------QPGVADIEKSMK 285
                                   *************5442222.........235566666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1041  (0.0580624); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.33s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 1914.47
//
Query:       gi|13540862|ref|NP_110550.1|  [L=468]
Description: cobyric acid synthase [Thermoplasma volcanium GSS1]
Scores for complete 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-37  127.0   0.2    1.2e-36  126.1   0.1    1.5  2  GATase_3    CobB/CobQ-like glutamine amidotransferase domain
    7.3e-18   64.9   0.0    1.3e-17   64.1   0.0    1.3  1  CbiA        CobQ/CobB/MinD/ParA nucleotide binding domain
    3.6e-14   53.1   0.0    3.2e-13   50.0   0.0    2.0  1  AAA_26      AAA domain
     0.0015   17.9   0.0     0.0023   17.3   0.0    1.3  1  VirC1       VirC1 protein
     0.0063   16.4   0.0      0.079   12.8   0.0    2.4  2  MobB        Molybdopterin guanine dinucleotide synthesis prot
  ------ inclusion threshold ------
      0.023   14.6   0.6        0.2   11.5   0.6    2.2  1  AAA_31      AAA domain
      0.029   13.6   0.2      0.083   12.2   0.1    1.7  2  DUF1611     Domain of unknown function (DUF1611_C) P-loop dom
       0.11   12.2   0.1        0.2   11.4   0.1    1.6  1  PRK         Phosphoribulokinase / Uridine kinase family
       0.11   12.1   0.1        6.2    6.4   0.1    2.2  2  SRP54       SRP54-type protein, GTPase domain
       0.14   12.1   0.0       0.24   11.3   0.0    1.3  1  APS_kinase  Adenylylsulphate kinase
       0.15   11.8   0.0       0.25   11.1   0.0    1.3  1  GATase      Glutamine amidotransferase class-I


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 ?   -3.5   0.0       3.9   6.4e+03      30      49 ..     115     134 ..     101     147 .. 0.68
   2 !  126.1   0.1   7.7e-40   1.2e-36       1     195 [.     246     422 ..     246     423 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 3.9
                      GATase_3  30 vplkdeslgedadlvilpGg 49 
                                   v+ + e+l+e++d++i  G 
  gi|13540862|ref|NP_110550.1| 115 VKESIERLPEKYDVIIAEGA 134
                                   33366888899999987654 PP

  == domain 2  score: 126.1 bits;  conditional E-value: 7.7e-40
                      GATase_3   1 kiavirlpaisnytdldpLeaepevrvrfvplkdeslgedadlvilpGgkdtiqdlallresgldeaikeaaeaggpvlgi 81 
                                   +i+vir+p ++ny+d+dpL   ++   ++ + + ++l ++a l+ilpG+k++ +dl++ +++g++e++ e    ++ +lgi
  gi|13540862|ref|NP_110550.1| 246 EICVIRYPFMENYSDVDPLVLSGKGFTFVTEKNINAL-DNAKLIILPGSKNVPADLEYVKNTGIAEKLSERR-GKALILGI 324
                                   69*****************999976666666555555.66******************************65.6999**** PP

                      GATase_3  82 CGGlqmLGeeiedpegvegeageveglglLdietefekekltgqvegevelaaegeevkGyEiHsGrtilkekakpllkvk 162
                                   CGG+q+LG++i   +g+     +++ l +L+++te+++ek+t++++ +   a+ +    GyEiH+G++i+ +++kp+    
  gi|13540862|ref|NP_110550.1| 325 CGGYQILGSRID-YYGK-----SMSCLSFLKCHTEYREEKTTRSIRFK--FAEGKYWSDGYEIHYGEVIN-DGEKPMNLT- 395
                                   **********75.6899.....********************999998..444448889*******8885.556665555. PP

                      GATase_3 163 vggnng.ekdGavkksedgnvlGtYlHglfdnrn 195
                                        + + +G++  sedg+v+Gt +H ++ n++
  gi|13540862|ref|NP_110550.1| 396 -----ElGYEGCI--SEDGTVFGTNIHNILGNSD 422
                                   .....4499****..89************99986 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.1   0.0   7.9e-21   1.3e-17       3     118 ..       6     228 ..       4     233 .. 0.95

  Alignments for each domain:
  == domain 1  score: 64.1 bits;  conditional E-value: 7.9e-21
                                   EEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH............................. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................. RF
                          CbiA   3 iastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep............................. 54 
                                   + +t++G+GKTt++ +L+r+l+r+g+ V++++a +++ n+ i    e +i++                             
  gi|13540862|ref|NP_110550.1|   6 VLGTSSGAGKTTVSMALCRILSRQGYSVAPFKAMNMSLNSVI-VEGEYEIARaqwlqaiaaktdpsrymnplllkpegdgt 85 
                                   889*********************************999985.44444555567*************************** PP

                                   ...............................................................................CC CS
                                   ...............................................................................xx RF
                          CbiA  55 ...............................................................................dl 56 
                                                                                                                  d+
  gi|13540862|ref|NP_110550.1|  86 sqlivlgksigkkgikeyydylrskgkgivkesierlpekydviiaegagspaeinlldsdiansfvssiygtpailvgDI 166
                                   ********************************************************************************* PP

                                   HCCCHHHHHHCHCHHHH.....EEEEEEEEESS...-TTCHHHHHHHHHHCTS-EEEEEE--CCH CS
                                   xxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          CbiA  57 krllellealgkkkall...lkiagvvlnrvdgeneetllkealeelkqrygvpvlgviprdeav 118
                                   +r +++++++++++ l     +++ +++n+ +g+    +l+ ++e+l+  + ++v+g++p+ +++
  gi|13540862|ref|NP_110550.1| 167 DR-GGVFASIYGTLMLMpnsELVKWIIINKMRGD--VSMLNPGIERLENLISRKVIGILPYQSGF 228
                                   **.**********988899***************..***********9989**********9875 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.0   0.0   1.9e-16   3.2e-13       3     192 ..       4     226 ..       2     228 .. 0.78

  Alignments for each domain:
  == domain 1  score: 50.0 bits;  conditional E-value: 1.9e-16
                        AAA_26   3 ifvtgtdtgvGKTvvslgLvralkrkgvkvgyfKPiqtgie........ededselikellgldqtyelpeplalsaplsp 75 
                                   i v gt+ g+GKT+vs++L+r+l+r+g++v+ fK ++  ++        e  ++++++ ++  ++++ +++pl+l+ +   
  gi|13540862|ref|NP_110550.1|   4 IQVLGTSSGAGKTTVSMALCRILSRQGYSVAPFKAMNMSLNsvivegeyEIARAQWLQAIAAKTDPSRYMNPLLLKPEGDG 84 
                                   6799*******************************9888887776544334499999******************966433 PP

                        AAA_26  76 elaarqegedidlekiv..................kelekdadivvVEGagglgvpiteellnadiaknl.....gapvil 133
                                   + +    g++i  + i                   ++l++++d+++ EGag+       +ll+ dia +      g p il
  gi|13540862|ref|NP_110550.1|  85 TSQLIVLGKSIGKKGIKeyydylrskgkgivkesiERLPEKYDVIIAEGAGSPA---EINLLDSDIANSFvssiyGTPAIL 162
                                   3222222444443333366689999999*****99***************9755...555555555555555556****** PP

                        AAA_26 134 Vargglg.tinqllltiealrqknvrvlGvilNkvrnpe.....nvetlekksgipvlGvvPylp 192
                                   V+ +++g  ++ ++ t+  l  +   v+ +i+Nk+r +       +e le+ ++ +v+G++Py++
  gi|13540862|ref|NP_110550.1| 163 VGDIDRGgVFASIYGTLM-LMPNSELVKWIIINKMRGDVsmlnpGIERLENLISRKVIGILPYQS 226
                                   ******725566666666.5555677999******9994555679*****************985 PP

>> VirC1  VirC1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   1.4e-06    0.0023       1      39 [.       1      39 [.       1      61 [. 0.91

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.4e-06
                         VirC1  1 mklitfcslkGGaGkttalmglcsalasdgkrvalfead 39
                                  mk+i +     GaGktt  m+lc  l  +g  va f+a 
  gi|13540862|ref|NP_110550.1|  1 MKMIQVLGTSSGAGKTTVSMALCRILSRQGYSVAPFKAM 39
                                  88899999999************************9985 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 !   12.8   0.0   4.9e-05     0.079       2      36 ..       4      39 ..       3      50 .. 0.85
   2 ?    0.4   0.0      0.35   5.7e+02      81      98 ..     115     133 ..      99     140 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.9e-05
                          MobB  2 lgivgk.sgsGKTtLleklipelkarglrvgtiKha 36
                                  +++ g+ sg+GKTt    l ++l+++g++v+  K  
  gi|13540862|ref|NP_110550.1|  4 IQVLGTsSGAGKTTVSMALCRILSRQGYSVAPFKAM 39
                                  566665489*********************998865 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.35
                          MobB  81 leellarl.sevDlvlvEG 98 
                                   ++e ++rl +++D++++EG
  gi|13540862|ref|NP_110550.1| 115 VKESIERLpEKYDVIIAEG 133
                                   67889999778*******9 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.6   0.00012       0.2       1      36 [.       1      36 [.       1     147 [. 0.60

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00012
                        AAA_31  1 gkvIaianqKGGvGKTTtsvnlaaalaklgkkvLlv 36
                                  +k+I +     G GKTT s++l+  l+++g+ v   
  gi|13540862|ref|NP_110550.1|  1 MKMIQVLGTSSGAGKTTVSMALCRILSRQGYSVAPF 36
                                  68999999999*******************998644 PP

>> DUF1611  Domain of unknown function (DUF1611_C) P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   5.1e-05     0.083      13      45 ..       2      34 ..       1      46 [. 0.90
   2 ?   -2.0   0.0       1.1   1.9e+03      73      98 ..     113     136 ..     111     137 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 5.1e-05
                       DUF1611 13 krvlvvGTdcavGKrttaleleealeerGlkaa 45
                                  k + v+GT++ +GK t +++l + l ++G+ +a
  gi|13540862|ref|NP_110550.1|  2 KMIQVLGTSSGAGKTTVSMALCRILSRQGYSVA 34
                                  7899*************************9876 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.1
                       DUF1611  73 GaveglvkkaaeeeepdlilveGQgs 98 
                                   G v + ++++ e +  d+i+ eG gs
  gi|13540862|ref|NP_110550.1| 113 GIVKESIERLPE-KY-DVIIAEGAGS 136
                                   667788888886.55.9******998 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00012       0.2       4      48 ..       7      52 ..       3     134 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00012
                           PRK  4 vagsSGaGkttvarklekifgrekvkaaei.egdsflrldraekdl 48
                                  ++ sSGaGkttv+ +l  i+ r++   a    +   l+ +++e ++
  gi|13540862|ref|NP_110550.1|  7 LGTSSGAGKTTVSMALCRILSRQGYSVAPFkAMNMSLNSVIVEGEY 52
                                  4579*****************9887744432233334444444444 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.1    0.0038       6.2       6      33 ..       6      34 ..       1      39 [. 0.83
   2 ?    3.4   0.0     0.031        50      46      94 ..      86     136 ..      83     166 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0038
                                  EEES.TTSSHHHHHHHHHHHHHHTTS-EE CS
                         SRP54  6 lvGl.qGaGKTttlaKLaallkkegkkvl 33
                                  ++G+  GaGKTt    L ++l+++g++v+
  gi|13540862|ref|NP_110550.1|  6 VLGTsSGAGKTTVSMALCRILSRQGYSVA 34
                                  555427*******************9986 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.031
                                   HHHHHHHHHTTEEEEE...SSTTSCHHHHHHHHHHHHHHTTSSEEEEEE--S CS
                         SRP54  46 eQLktlaeklgvpvik...kkeeadpaavakeavekakeekidvvlvDTaGr 94 
                                    QL +l++++g + ik    +  ++   ++ke++e+  e k+dv++   aG 
  gi|13540862|ref|NP_110550.1|  86 SQLIVLGKSIGKKGIKeyyDYLRSKGKGIVKESIERLPE-KYDVIIAEGAGS 136
                                   6888888887766666443667778999*******9998.89********96 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00015      0.24       8      34 ..       8      34 ..       2      45 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00015
                                  ESSTTSSHHHHHHHHHHHHHHTT--EE CS
                    APS_kinase  8 tGlsgsGKstianalekkLvekgisvy 34
                                     sg+GK+t+++al + L ++g+sv 
  gi|13540862|ref|NP_110550.1|  8 GTSSGAGKTTVSMALCRILSRQGYSVA 34
                                  4569*******************9986 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00015      0.25      36      86 ..     278     333 ..     267     383 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00015
                                   HHHTHHSTSEEEEEEESSCTT...TTTHHHHHHHHCT..STS-EEEETHHHHHHHH CS
                        GATase  36 ilellknpdgilvsgGpgspg...vegkieaikeare..nkiPiLGICLGmQllai 86 
                                   ++++l+n++ i+++g  + p+   + +   +++++ e   k  iLGIC G Q+l+ 
  gi|13540862|ref|NP_110550.1| 278 NINALDNAKLIILPGSKNVPAdleYVKNTGIAEKLSErrGKALILGICGGYQILGS 333
                                   2235889999999999888889885555666666666444778**********975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (468 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       459  (0.025601); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); 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: 0.64u 0.34s 00:00:00.98 Elapsed: 00:00:00.50
# Mc/sec: 2815.38
//
Query:       gi|13540863|ref|NP_110551.1|  [L=790]
Description: valyl-tRNA synthetase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   1.4e-116  390.2   0.3   2.9e-115  385.8   0.3    2.0  1  tRNA-synt_1    tRNA synthetases class I (I, L, M and V)
    2.6e-33  115.1   1.1    4.2e-33  114.5   1.1    1.3  1  Anticodon_1    Anticodon-binding domain of tRNA
    5.6e-23   81.3   7.2    5.8e-12   45.1   0.0    4.3  5  tRNA-synt_1g   tRNA synthetases class I (M)
    1.8e-08   34.1   0.0     0.0027   17.1   0.0    2.7  2  tRNA-synt_1e   tRNA synthetases class I (C) catalytic domain
    4.5e-07   29.6   0.0    8.2e-06   25.5   0.0    2.8  4  tRNA-synt_1_2  Leucyl-tRNA synthetase, Domain 2
  ------ inclusion threshold ------
      0.013   15.5   2.0       0.36   10.9   0.2    2.7  3  DZR            Double zinc ribbon
      0.049   13.1   6.5        5.5    6.5   0.3    3.6  3  zf-ribbon_3    zinc-ribbon domain
       0.12   12.5   1.7        3.2    7.8   0.1    3.0  3  HypA           Hydrogenase/urease nickel incorporation, metal
       0.17   12.0   3.9         19    5.4   0.1    3.7  3  zf-ACC         Acetyl-coA carboxylase zinc finger domain
       0.36   11.0   2.7        6.1    7.0   0.3    2.9  3  Zn-ribbon_8    Zinc ribbon domain
        4.5    6.9   8.4         19    4.9   0.3    3.9  4  zf_UBZ         Ubiquitin-Binding Zinc Finger


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 !  385.8   0.3  1.8e-118  2.9e-115       1     601 [.      11     559 ..      11     560 .. 0.96

  Alignments for each domain:
  == domain 1  score: 385.8 bits;  conditional E-value: 1.8e-118
                   tRNA-synt_1   1 klyekWeeedvfkkelekekekkefilvdgPPyvtGslHiGhalaktlkdivirykrmkGkevlyvpGwDhaGlaieakve 81 
                                   k+++ We++d++      ++++k f++  +PP v G++H+Gh++  +  d++ rykrm+G++v +  G+D  Gla+e  ve
  gi|13540863|ref|NP_110551.1|  11 KWLKYWEDNDIYTFI--PSEREKVFTIDTPPPTVSGKMHMGHSFSYSHIDFIARYKRMRGYHVFFPWGFDDNGLATERYVE 89 
                                   5899********999..6677899********************************************************* PP

                   tRNA-synt_1  82 kklgakekkerkklgreefrekvrewkaeyaeeirkqvkrlGvsvDfdreylTldkeleeavkevfvrladkgliyrgkkl 162
                                   k+ g+k      +  +e+f++ +re+ + + +   + +kr+G+s+ f++ y+T ++e  +  + +f  l++k  +yr   +
  gi|13540863|ref|NP_110551.1|  90 KETGIKPT----DGNVEHFINLCREFSQASEKALIEGWKRMGMSCYFKDYYVTSSPESVKISQSMFLDLVKKNRVYRDLAP 166
                                   ***99996....999****************************************************************** PP

                   tRNA-synt_1 163 vnwstklktalselEveykdkkdalihvafpladkeevklviaTTtPeTllgdtavavnpeldyvitkeklilaeallksl 243
                                      ++++kt++s++E++ +  k+ l++++f++++++   l iaT +Pe l + +a+ vn e                    
  gi|13540863|ref|NP_110551.1| 167 TIRCPTCKTSISQIEMKDEMLKSKLVYINFDVEGSK---LTIATSRPELLGSCVALFVNNE-------------------- 224
                                   ********************************9875...69********************.................... PP

                   tRNA-synt_1 244 vkkesekkiledergkeLegkevelplvnrkipiiaddyvdkeaGtGvVkiaPahdedDyevgkkynlevinildedgtlt 324
                                              der+k+++g+e++ pl + k+pi+ d+ +dk++GtG+  +    d++D  + kky l++   +d+dg+++
  gi|13540863|ref|NP_110551.1| 225 -----------DERYKNIIGREATVPLFGHKVPIMGDESIDKDFGTGAEMVCTFGDQNDLDLWKKYSLPLRISIDKDGKMN 294
                                   ...........9************************************9999999************************** PP

                   tRNA-synt_1 325 eeaaefeglkvfdarkkvveelkekglllkaekiehsvpfcerskkpiiyrateqWfvrvkeladaalkavekvqfvpksk 405
                                   e+a+  +gl+++d rkk++e lk +g  +k+e+i+hsv + er ++p++  + +qWf+r  +l+++ +++ + v+++p+  
  gi|13540863|ref|NP_110551.1| 295 ENAGPLNGLSINDGRKKIIELLKSEGFVVKEEDIKHSVNTHERCGTPVEIFIEKQWFIRYLDLKKDFIDSGRAVKWIPDYM 375
                                   ********************************************************************************* PP

                   tRNA-synt_1 406 ekryaswleniq.dWciSRqrwWGhriplfvsketeevvvreelkelvagreeeeaekkalekeakdklkkekgelekded 485
                                   ++ry++w++  + dWciSRqr++G++ p+++ ++ +++v+ ++++  v  r +  +++ +         k++  +l  + d
  gi|13540863|ref|NP_110551.1| 376 RTRYENWVNGLKwDWCISRQRYYGVPFPVWYCSDCGNTVFADDKDLPVDPRLQPPSKRCD---------KCGSSNLVPERD 447
                                   *********9866***************************88888888877777776666.........5688999***** PP

                   tRNA-synt_1 486 vlDvWFsSgswpfstlgypeedteelkkffpadmlleGlDiirgWvarlillslaltgsePfkevlvhglvrdeeGrKmSK 566
                                   v+D+W  S+++p+  l     +   ++k++p d+  +G Dii +W  + i  s    +  P+ +++++g v d  G KmSK
  gi|13540863|ref|NP_110551.1| 448 VMDTWATSSLTPRIALS----HFGLFDKYYPEDLRGQGHDIISFWAFTTIARSKIHDNTIPWLTLMISGNVFDMYGEKMSK 524
                                   ************99888....345699**************************999999********************** PP

                   tRNA-synt_1 567 slgNvidpldvikkygadalRltlilsdvgrdinl 601
                                   s+gN++d   + +kygadalR++  + ++g+di++
  gi|13540863|ref|NP_110551.1| 525 SKGNIVDIYAITDKYGADALRFWASTVSQGEDIRV 559
                                   *************************9999**9987 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 !  114.5   1.1   2.6e-36   4.2e-33       2     151 ..     602     751 ..     601     752 .. 0.89

  Alignments for each domain:
  == domain 1  score: 114.5 bits;  conditional E-value: 2.6e-36
                   Anticodon_1   2 rwilselnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedk....raaqevllevletllrlla 78 
                                    wil+e +k+vk vt+++++y+ +ka sal  ffwn++cd+yle++k + + ++++++    +++ ++  +v++ ++++ a
  gi|13540863|ref|NP_110551.1| 602 LWILTEESKVVKLVTDSMDNYEVSKARSALDVFFWNTFCDNYLEMIKAIVQAANEKNDlgtvDETIYTASKVMRDVVKMYA 682
                                   5*************************************************9999888899966688*************** PP

                   Anticodon_1  79 PfmPfitEelwqreeeel.gkkesimlaewpekaeelekeleeeevellkeivkairklrselkikpsselkvv 151
                                   P+mPfitEe++q+ e  + gkk+s++   wp ++ e  ++   +ev ++ +i+  ir+++s+ k++  ++++++
  gi|13540863|ref|NP_110551.1| 683 PIMPFITEEIYQSIE--IeGKKKSVHIDCWPMENREYVEA---SEVRYVTSIIDKIRAAKSNAKVSVGTPVRKA 751
                                   ***********8633..44899*********744333333...58*********************99998875 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 ?   -1.2   0.2       0.4   6.5e+02     267     288 ..       7      25 ..       3      29 .. 0.75
   2 !   45.1   0.0   3.6e-15   5.8e-12       3     131 ..      35     178 ..      33     189 .. 0.82
   3 !    7.7   0.0   0.00079       1.3     172     238 ..     338     403 ..     318     415 .. 0.73
   4 !   29.3   0.1   2.2e-10   3.6e-07     289     373 ..     481     566 ..     469     580 .. 0.83
   5 ?   -1.8   0.0      0.61   9.9e+02     324     390 ..     699     770 ..     693     771 .. 0.70

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.4
                                   TTSGGGG.G--S......EEEE CS
                  tRNA-synt_1g 267 geeekwkeyWakdkevelvhfi 288
                                   + e+kw +yW +  + +++ fi
  gi|13540863|ref|NP_110551.1|   7 QMEKKWLKYW-E--DNDIYTFI 25 
                                   5689******.3..56677777 PP

  == domain 2  score: 45.1 bits;  conditional E-value: 3.6e-15
                                   EEE--B--SS---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHHT.TS-HHH........HHHHHHHHH CS
                  tRNA-synt_1g   3 vttalpYangklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkAeke.gvtpee........lvekvheei 74 
                                   + t+ p ++gk+H+Gh  ++   D +aRykr+rg++v+f  g D  G ++e   eke g++p +        l+++++++ 
  gi|13540863|ref|NP_110551.1|  35 IDTPPPTVSGKMHMGHSFSYSHIDFIARYKRMRGYHVFFPWGFDDNGLATERYVEKEtGIKPTDgnvehfinLCREFSQAS 115
                                   77888999******************************************9988764499997443444444777777766 PP

                                   HHH....HHHTT--..-SEEEETTSHHHHHHHHHHHHHHHHTT-EEEEEEEEEEETTTTEEE- CS
                  tRNA-synt_1g  75 kel....fkklnis..fdkygrttseehkelvqeifkklkekgliyekeieqlycpkderflp 131
                                   ++     +k++++s  f +y+ t+s e  +++q++f  l +k+ +y+     + cp++++ ++
  gi|13540863|ref|NP_110551.1| 116 EKAliegWKRMGMScyFKDYYVTSSPESVKISQSMFLDLVKKNRVYRDLAPTIRCPTCKTSIS 178
                                   65422226776554439**************************************99998765 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.00079
                                   .....EEE.EEEEEE-GGGGHHHHHHHH.HH-TT..SHHHHHHHH.HHHHT----EE-ESS-SSS-EET CS
                  tRNA-synt_1g 172 sgskpevketehlffklskfekklkewieeeeke..leenvkkivkewlkegLkdlaisrdldwGipvP 238
                                   +g+  e+  ++++f +  +++k+   +i++ ++    ++ +++  ++w++    d++isr+  +G+p+P
  gi|13540863|ref|NP_110551.1| 338 CGTPVEIFIEKQWFIRYLDLKKD---FIDSGRAVkwIPDYMRTRYENWVNGLKWDWCISRQRYYGVPFP 403
                                   55555666677777777666654...55444433447888899999**998555*************99 PP

  == domain 4  score: 29.3 bits;  conditional E-value: 2.2e-10
                                   EGGGHHHHHTHH..HHHHHHTT----S-EEEE--EEE--------------HHHHHHHH-HHHHHHHHHHHS-TTS-EEE- CS
                  tRNA-synt_1g 289 gkdiikFHtifw..PaillgaelklpkkvvaheyltvegkKlSkSrgvvvkakealerldadllRYylaaeapekkDldfs 367
                                   g dii F +      + ++++ +  ++ +++ + + + g+K+SkS+g++v++  +++++ ad+lR++ a++ ++ +D+  +
  gi|13540863|ref|NP_110551.1| 481 GHDIISFWAFTTiaRSKIHDNTIPWLTLMISGNVFDMYGEKMSKSKGNIVDIYAITDKYGADALRFW-ASTVSQGEDIRVK 560
                                   778888876543003444558888889999999********************************98.566788999*999 PP

                                   HHHHHH CS
                  tRNA-synt_1g 368 wedfve 373
                                   ++dfv+
  gi|13540863|ref|NP_110551.1| 561 EQDFVR 566
                                   999987 PP

  == domain 5  score: -1.8 bits;  conditional E-value: 0.61
                                   --------------HHHHHHHH-HHHHHHHHHH...HS-TTS-EEE-H....HHHHHHHHHHCCCHHHHHHHHH CS
                  tRNA-synt_1g 324 egkKlSkSrgvvvkakealerldadllRYylaa...eapekkDldfsw....edfvervNseLadklgnlvnRv 390
                                   egkK  kS ++  ++ e  e+++a  +RY+ +     + +k++++ s     +++  + N+ +a+k+ ++++R+
  gi|13540863|ref|NP_110551.1| 699 EGKK--KSVHIDCWPMENREYVEASEVRYVTSIidkIRAAKSNAKVSVgtpvRKALIKCNASIAEKYRDMLSRM 770
                                   5555..78888899999999999999999865532345666777776511114555678999999999999997 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 !   13.9   0.0   1.5e-05     0.025      10      50 ..      33      73 ..      24      81 .. 0.85
   2 !   17.1   0.0   1.7e-06    0.0027     226     294 ..     493     562 ..     474     568 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.5e-05
                                  EEEEEEEEBTTS--BHHHHHHHHHHHHHHHHHHHTT-EEEE CS
                  tRNA-synt_1e 10 vtlYvCGptvydashlGhaRslvafDilrrilqalgYdvqf 50
                                   t+ +  ptv  ++h+Gh+ s+  +D ++r+ +++gY+v f
  gi|13540863|ref|NP_110551.1| 33 FTIDTPPPTVSGKMHMGHSFSYSHIDFIARYKRMRGYHVFF 73
                                  55666679*******************************88 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 1.7e-06
                                   HHHHHHHSS.S--EEEEEEE--EEETTBE--TTTT---BHHHHHTTS-HHHHHHHHHSS-TTS-EEE-HH CS
                  tRNA-synt_1e 226 laqseaafd.kqlvkyflhnghlkiegekmsksLknfitikdvlkkfdprqlRllllsahyrsqldfkee 294
                                   +a+s+   +  ++    +  ++  + gekmsks +n++ i ++  k+ + +lR+   ++   + +  ke+
  gi|13540863|ref|NP_110551.1| 493 IARSKIHDNtIPWLTLMISGNVFDMYGEKMSKSKGNIVDIYAITDKYGADALRFWASTVSQGEDIRVKEQ 562
                                   5666665555677777777888899*****************************9888777666666665 PP

>> tRNA-synt_1_2  Leucyl-tRNA synthetase, Domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.0       5.3   8.6e+03      52      74 ..      95     117 ..      83     128 .. 0.75
   2 ?    0.4   0.0      0.25   4.1e+02       7      42 ..     189     222 ..     187     231 .. 0.78
   3 !   25.5   0.0     5e-09   8.2e-06      86     146 ..     233     293 ..     221     317 .. 0.87
   4 ?   -4.0   0.0       5.5   8.9e+03     128     158 ..     639     670 ..     638     676 .. 0.61

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 5.3
                 tRNA-synt_1_2  52 aekkkelaafieevkkksesere 74 
                                   + ++ ++++fi+ +++ s+++++
  gi|13540863|ref|NP_110551.1|  95 KPTDGNVEHFINLCREFSQASEK 117
                                   56777899999999988877654 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.25
                 tRNA-synt_1_2   7 seGleiefkveeseeklevfttrpdtlfGvtfvala 42 
                                   s+ + i+f+ve+s+  l++ t+rp+ l +   + + 
  gi|13540863|ref|NP_110551.1| 189 SKLVYINFDVEGSK--LTIATSRPELLGSCVALFVN 222
                                   6667899***9975..*********99876665555 PP

  == domain 3  score: 25.5 bits;  conditional E-value: 5e-09
                 tRNA-synt_1_2  86 glkaihPitgekipiwvanyvlmeygtgavmavPahdqrDfeFakkynlpikqvikpedee 146
                                   g +a+ P+ g+k+pi   + +  ++gtga m +   dq+D++ +kky lp++  i ++++ 
  gi|13540863|ref|NP_110551.1| 233 GREATVPLFGHKVPIMGDESIDKDFGTGAEMVCTFGDQNDLDLWKKYSLPLRISIDKDGKM 293
                                   778999**********************************************999976654 PP

  == domain 4  score: -4.0 bits;  conditional E-value: 5.5
                 tRNA-synt_1_2 128 Fakkynlpikqvikpedeekklee.seeayte 158
                                   F ++y   ik +++ ++e+++l +  e++yt+
  gi|13540863|ref|NP_110551.1| 639 FCDNYLEMIKAIVQAANEKNDLGTvDETIYTA 670
                                   66667677888888888776666413444444 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0     0.058        94      28      39 ..     167     178 ..     142     183 .. 0.77
   2 ?   -3.9   0.0       9.3   1.5e+04      17      22 ..     337     342 ..     333     343 .. 0.73
   3 ?   10.9   0.2   0.00022      0.36      14      37 ..     406     440 ..     403     447 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.058
                           DZR  28 edrCpsCgekvd 39 
                                    +rCp C+++++
  gi|13540863|ref|NP_110551.1| 167 TIRCPTCKTSIS 178
                                   578888888754 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 9.3
                           DZR  17 eCgtkl 22 
                                   +Cgt++
  gi|13540863|ref|NP_110551.1| 337 RCGTPV 342
                                   688776 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 0.00022
                           DZR  14 fCseCgtklkavaa...........edrCpsCgek 37 
                                   +Cs+Cg+++ a  +           ++rC++Cg++
  gi|13540863|ref|NP_110551.1| 406 YCSDCGNTVFADDKdlpvdprlqppSKRCDKCGSS 440
                                   8*******976555999999999*9********98 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.3    0.0034       5.5       2      12 ..     167     177 ..     166     179 .. 0.82
   2 ?    2.1   0.1     0.086   1.4e+02       4      11 ..     406     414 ..     405     420 .. 0.73
   3 ?    5.8   0.1    0.0056       9.1       3      16 ..     432     447 ..     430     449 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0034
                   zf-ribbon_3   2 tvrCPnCGapl 12 
                                   t+rCP C++ +
  gi|13540863|ref|NP_110551.1| 167 TIRCPTCKTSI 177
                                   89*****9954 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.086
                   zf-ribbon_3   4 rCPnCGa.p 11 
                                   +C+ CG+ +
  gi|13540863|ref|NP_110551.1| 406 YCSDCGNtV 414
                                   79****977 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.0056
                   zf-ribbon_3   3 vrCPnCGa.p.lssdd 16 
                                   +rC +CG+ + + ++d
  gi|13540863|ref|NP_110551.1| 432 KRCDKCGSsNlVPERD 447
                                   79******98666665 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0      0.11   1.7e+02      86     105 ..     167     186 ..     130     192 .. 0.75
   2 ?    7.8   0.1     0.002       3.2      71      97 ..     405     442 ..     398     447 .. 0.83
   3 ?   -1.5   0.1       1.5   2.4e+03      11      74 ..     647     710 ..     639     746 .. 0.65

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.11
                                   HHS-TTTSSS-EEEEESSSE CS
                          HypA  86 alrCpkCgsadveivsGeel 105
                                   ++rCp+C+++  +i   +e+
  gi|13540863|ref|NP_110551.1| 167 TIRCPTCKTSISQIEMKDEM 186
                                   34888888877776665555 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.002
                                   EEETTTS-EEECHHHHH...........S-TTTSSS-E CS
                          HypA  71 vrCreCgkefeleekal...........rCpkCgsadv 97 
                                    +C++Cg+++  ++k+l           rC kCgs+++
  gi|13540863|ref|NP_110551.1| 405 WYCSDCGNTVFADDKDLpvdprlqppskRCDKCGSSNL 442
                                   68*****9999776545678999***********9876 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 1.5
                                   HHHHHHHHCCTT..EEEEEEEEEETTCT--HHHHHHHHHHHH..CC.TTTT-EEEEEEE--EEEET CS
                          HypA  11 vevveeeakeaaarkvtkvkvevGelsgvepeaLefafella..egtvlegaeLeieevpvkvrCr 74 
                                   ++++ ++a+  + +   +v  ++ + s+v  ++++++  ++    +++ ++ e+e ++++v++ C 
  gi|13540863|ref|NP_110551.1| 647 IKAIVQAAN--EKNDLGTVDETIYTASKVMRDVVKMYAPIMPfiTEEIYQSIEIEGKKKSVHIDCW 710
                                   344444443..3346666666777777777777777666653225556666777777777777775 PP

>> zf-ACC  Acetyl-coA carboxylase zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.1     0.012        19       2      18 ..     168     184 ..     168     186 .. 0.87
   2 ?    3.8   0.0     0.038        62       3      15 ..     406     418 ..     405     418 .. 0.86
   3 ?    1.6   0.2      0.18   2.9e+02       3      10 ..     433     440 ..     432     445 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.012
                        zf-ACC   2 tKCpsCgemlykkeLer 18 
                                   ++Cp C++++ + e+ +
  gi|13540863|ref|NP_110551.1| 168 IRCPTCKTSISQIEMKD 184
                                   79********9999887 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.038
                        zf-ACC   3 KCpsCgemlykke 15 
                                    C  Cg+++++ +
  gi|13540863|ref|NP_110551.1| 406 YCSDCGNTVFADD 418
                                   6********9876 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.18
                        zf-ACC   3 KCpsCgem 10 
                                   +C++Cg++
  gi|13540863|ref|NP_110551.1| 433 RCDKCGSS 440
                                   6*****86 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0     0.086   1.4e+02      25      34 ..     165     175 ..     158     180 .. 0.70
   2 ?   -3.7   0.0       8.3   1.4e+04      10      17 ..     337     344 ..     336     346 .. 0.68
   3 ?    7.0   0.3    0.0038       6.1       8      36 ..     407     442 ..     404     443 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.086
                   Zn-ribbon_8  25 plta.CPeCgs 34 
                                   ++t  CP+C+ 
  gi|13540863|ref|NP_110551.1| 165 APTIrCPTCKT 175
                                   44555****86 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 8.3
                   Zn-ribbon_8  10 eCghefev 17 
                                   +Cg+  e+
  gi|13540863|ref|NP_110551.1| 337 RCGTPVEI 344
                                   68888776 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.0038
                   Zn-ribbon_8   8 CeeCghefe......vlqsisdapltaCPeCgs.ev 36 
                                   C +Cg++        ++ +  ++p + C +Cgs ++
  gi|13540863|ref|NP_110551.1| 407 CSDCGNTVFaddkdlPVDPRLQPPSKRCDKCGSsNL 442
                                   999998877788888666655788888*****9775 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.3     0.012        19       2      17 ..     167     182 ..     166     185 .. 0.84
   2 ?   -1.7   0.0       1.4   2.3e+03       6      16 ..     336     347 ..     336     349 .. 0.77
   3 ?    1.9   0.0       0.1   1.7e+02       3      16 ..     405     418 ..     404     420 .. 0.77
   4 ?    2.6   0.1     0.066   1.1e+02       4      17 ..     433     446 ..     431     447 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.012
                        zf_UBZ   2 tylCerCgkeipesel 17 
                                   t+ C+ C+++i++ e+
  gi|13540863|ref|NP_110551.1| 167 TIRCPTCKTSISQIEM 182
                                   678********98755 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.4
                        zf_UBZ   6 erCgkeipes.e 16 
                                   erCg+++++  e
  gi|13540863|ref|NP_110551.1| 336 ERCGTPVEIFiE 347
                                   79***9988655 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.1
                        zf_UBZ   3 ylCerCgkeipese 16 
                                   + C++Cg ++  ++
  gi|13540863|ref|NP_110551.1| 405 WYCSDCGNTVFADD 418
                                   57*****9886655 PP

  == domain 4  score: 2.6 bits;  conditional E-value: 0.066
                        zf_UBZ   4 lCerCgkeipesel 17 
                                    C++Cg++ +++e+
  gi|13540863|ref|NP_110551.1| 433 RCDKCGSSNLVPER 446
                                   6*****99777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (790 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       753  (0.041999); expected 358.6 (0.02)
Passed bias filter:                      621  (0.0346366); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.79u 0.33s 00:00:01.12 Elapsed: 00:00:00.53
# Mc/sec: 4474.58
//
Query:       gi|13540864|ref|NP_110552.1|  [L=540]
Description: CTP synthetase [Thermoplasma volcanium GSS1]
Scores for complete 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-118  392.8   1.5   9.3e-118  392.3   1.5    1.2  1  CTP_synth_N    CTP synthase N-terminus
    3.9e-51  173.5   0.0    7.3e-51  172.7   0.0    1.5  1  GATase         Glutamine amidotransferase class-I
    3.6e-07   30.2   0.0    5.2e-05   23.1   0.0    2.5  2  Peptidase_C26  Peptidase C26
     0.0016   18.5   0.0     0.0042   17.2   0.0    1.8  2  CbiA           CobQ/CobB/MinD/ParA nucleotide binding domain
  ------ inclusion threshold ------
      0.033   13.2   0.2      0.054   12.5   0.2    1.3  1  MeaB           Methylmalonyl Co-A mutase-associated GTPase Me
      0.048   13.3   0.0      0.091   12.3   0.0    1.4  1  Peptidase_C47  Staphopain peptidase C47


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 !  392.3   1.5  3.1e-121  9.3e-118       1     260 [.       2     259 ..       2     262 .. 0.98

  Alignments for each domain:
  == domain 1  score: 392.3 bits;  conditional E-value: 3.1e-121
                                   EEEEEEE--STTTTHHHHHHHHHHHHHCTT--EEEEEEE-SSSSSSTT--CCCC--EEE-TT--EEETHHHHHHHHHT--- CS
                   CTP_synth_N   1 kyilvtGGvvSglGkGiiaaslgallksrglkvtlikiDPYlnvdagtlsplehGEvfvlddGaetDlDlGnYeRfldikl 81 
                                   +yi+vtGGv+SglGkG i++s+g++lk +g+kv+++kiDPY+n+dagt++p++hGEvfvlddG+e+DlDlGnYeRf+di+l
  gi|13540864|ref|NP_110552.1|   2 QYIVVTGGVISGLGKGTITSSIGHILKDSGFKVSSVKIDPYINYDAGTMNPYQHGEVFVLDDGSEVDLDLGNYERFMDINL 82 
                                   69******************************************************************************* PP

                                   -GGGEEEHHHHHHHHHHHHHTTTTTT----CCCHHHHHHHHHHHHHH.HCT-SEEEEEE-S-TTSGGGHHHHHHHHHHHHH CS
                   CTP_synth_N  82 tkennittGkiyksviekerrGdylGktvqviphvtdeikeriekvakkveadvviveigGtvgdieslpfleairqlkle 162
                                   + +nnittGk+y +vieker+GdylGktvq+iph+tdeik+ri++va++++ad+v++e+gGtvgdies+pflea+rqlk e
  gi|13540864|ref|NP_110552.1|  83 SWKNNITTGKVYLEVIEKERHGDYLGKTVQIIPHITDEIKRRIRDVATSSKADFVLIEVGGTVGDIESMPFLEAVRQLKRE 163
                                   ************************************************99****************************988 PP

                                   H-TTTEEEEEEEE--B-TTTSSB-HHHHHHHHHHHHHHT---SEEEEEESS---HHHHHHHHHHCT--GGGEEEEE--S-G CS
                   CTP_synth_N 163 lgkenvllihvtlvpvlkaagelktkptqhsvkelrslGiqpdiivcrsekeleeevkekialfcnvekeavisvkdvesi 243
                                     ++nv++ hvtlvp +  ++e+ktkptqhsvk+lr++Giqpdii++rs+++l ee+k++i+lf++v++  +isv dve++
  gi|13540864|ref|NP_110552.1| 164 --ENNVIFAHVTLVPEIGPTEEQKTKPTQHSVKALREIGIQPDIIFARSKNRLLEETKKRISLFTDVPEGGIISVYDVENV 242
                                   ..59***************************************************************************** PP

                                   GGHHHHHHHCTHHHHHH CS
                   CTP_synth_N 244 yevpllleeqglaelil 260
                                   y +p ++ ++g+ +++ 
  gi|13540864|ref|NP_110552.1| 243 YLLPEVMVNEGFISYLS 259
                                   **********9998876 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  172.7   0.0   2.4e-54   7.3e-51       2     188 ..     297     518 ..     296     520 .. 0.94

  Alignments for each domain:
  == domain 1  score: 172.7 bits;  conditional E-value: 2.4e-54
                                   EEESSTSTHHHHHHHHHHTT-EEEEEETTSHHHHHHH.THHSTSEEEEEEESSCTTTTTHHHHHHHHCTSTS-EEEETHHH CS
                        GATase   2 liDnydsvtenlvhalvelgvkvevvpidasaeeile.llknpdgilvsgGpgspgvegkieaikearenkiPiLGICLGm 81 
                                   l D+y s +e+  h   ++g+ v++++ d+++ + ++ +l+++d+il++gG+g++gvegki+a+++a+en+iP+LGICLG+
  gi|13540864|ref|NP_110552.1| 297 LHDAYISHKEAFSHVTGNTGIAVDIKWLDSEKVKDDQsMLSDVDAILIPGGFGYRGVEGKIAATRFALENHIPFLGICLGF 377
                                   68****************************999998878****************************************** PP

                                   HHHHHHTTTEEE.......................EEECEEEEEEEEEEEETTT........CGGTTTTSEEEEEEEEEEE CS
                        GATase  82 Qllaiefgrkvv.......................kekekehhggtmrlgddet........allyglknevierhrHrye 131
                                   Q+++ie++r+++                       ++k  +++ggtmrlg+++         +++yg+ ++++erhrHrye
  gi|13540864|ref|NP_110552.1| 378 QVAVIEIARDIIglqnanstefdpatkypvidilpEQKGIKDLGGTMRLGSKKVlikdgtlaKRIYGT-DTIYERHRHRYE 457
                                   *********8888888888888888888888****9999************888*************9.************ PP

                                   EESG...CHHHTTEEEEEEEETTEEEEEEEEETT.T.EEEESSBTTSTTSTTHHHHHHHHHH CS
                        GATase 132 vnpk...elepaglevtakseddeelmeiiekkn.p.fvgvQFHPEststpegpellfnfli 188
                                   vnp+    +e+ag+++++++ed+  +mei ekk    f+++Q+H E++s+p +p+ +   l+
  gi|13540864|ref|NP_110552.1| 458 VNPNyisIIEKAGFVFSGTDEDG-IRMEILEKKGdEsFIATQYHSEFKSRPLNPSRVHLHLV 518
                                   ******8899**********888.8********9978****************999887766 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0      0.01        30      22      67 ..     299     347 ..     288     352 .. 0.75
   2 !   23.1   0.0   1.7e-08   5.2e-05      95     216 .]     357     502 ..     353     502 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.01
                 Peptidase_C26  22 esyla.asyveavekagglpvllpiee..deedvkaildkldgllltGg 67 
                                   ++y++ ++ ++ v++  g++v +   +  + +d +++l+ +d++l++Gg
  gi|13540864|ref|NP_110552.1| 299 DAYIShKEAFSHVTGNTGIAVDIKWLDseKVKDDQSMLSDVDAILIPGG 347
                                   445441445788999999999997764235567789************9 PP

  == domain 2  score: 23.1 bits;  conditional E-value: 1.7e-08
                 Peptidase_C26  95 laLiraalergvPilgiCrGlqllnvalGGtlyqdieeqsgltdhrehe...............q.....saashavkvek 155
                                   +a  r ale+++P lgiC+G+q+  + +  ++    +++s++ d    +               +        s++v ++ 
  gi|13540864|ref|NP_110552.1| 357 IAATRFALENHIPFLGICLGFQVAVIEIARDIIGLQNANSTEFDPA--TkypvidilpeqkgikDlggtmRLGSKKVLIKD 435
                                   56678899**************998877766654333322333222..2346788888876665155556888******** PP

                 Peptidase_C26 156 gsllaellgseeievnslHhqaike......laeelrveAvaeDgv.iEaieseeakafvlgvQwHPE 216
                                   g+l ++++g+++i     H+  ++          ++  + ++eDg+ +E +e +  ++ +++ Q+H E
  gi|13540864|ref|NP_110552.1| 436 GTLAKRIYGTDTIYERHRHRYEVNPnyisiiEKAGFVFSGTDEDGIrMEILEKKG-DESFIATQYHSE 502
                                   *********99999999***999999999877889**********8799999999.55999*****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 !   17.2   0.0   1.4e-06    0.0042       8      55 ..      12     147 ..       4     319 .. 0.74
   2 ?   -2.5   0.0       1.7   5.1e+03     104     120 ..     403     419 ..     385     425 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.4e-06
                                   TTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH.................................. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.................................. RF
                          CbiA   8 GGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep.................................. 54 
                                   +G GK t++ +++ +l++ g++V  v+ Dp  n +a   g+ n  +                                   
  gi|13540864|ref|NP_110552.1|  12 SGLGKGTITSSIGHILKDSGFKVSSVKIDPYINYDA---GTMNPYQHgevfvlddgsevdldlgnyerfmdinlswknnit 89 
                                   99*****************************99988...666665556777777777777777888888888888888777 PP

                                   .........................................................C CS
                                   .........................................................x RF
                          CbiA  55 .........................................................d 55 
                                                                                            d
  gi|13540864|ref|NP_110552.1|  90 tgkvyleviekerhgdylgktvqiiphitdeikrrirdvatsskadfvlievggtvgD 147
                                   7777777777777777777766666665555555555555555555555555555552 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.7
                                   CTS-EEEEEE--CCHCC CS
                                   xxxxxxxxxxxxxxxxx RF
                          CbiA 104 ygvpvlgviprdeavae 120
                                   ++ pv++++p+ +++ +
  gi|13540864|ref|NP_110552.1| 403 TKYPVIDILPEQKGIKD 419
                                   3899******9998865 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 ?   12.5   0.2   1.8e-05     0.054      34      75 ..       6      49 ..       1      51 [. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.8e-05
                                  EEE..-TTSSHHHHHHHHHHHHHCTT--EEEEEE---------- CS
                          MeaB 34 ltG..vPGaGkstlvealglelrrrGkrvavlavDPsspftGGs 75
                                  +tG  + G Gk t+++ +g  l++ G +v+ + +DP  ++  G+
  gi|13540864|ref|NP_110552.1|  6 VTGgvISGLGKGTITSSIGHILKDSGFKVSSVKIDPYINYDAGT 49
                                  6664568*****************************98888776 PP

>> Peptidase_C47  Staphopain peptidase C47
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0     3e-05     0.091      72     160 ..     257     347 ..     234     351 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3e-05
                 Peptidase_C47  72 efGksqGrdiqylervtsyeevdqltknnkGiavlgkrvessng..ihaGhalavvGnakvdngqeviiiwnpwdnelmiq 150
                                   +  k  G++i+y++   +y e  +  k+ + ia++gk v+ ++    h      v Gn+ +  + + +      d++ m+ 
  gi|13540864|ref|NP_110552.1| 257 YLSKLSGKEIKYRDSWKAYTENIKHPKDRVKIAIVGKYVDLHDAyiSHKEAFSHVTGNTGIAVDIKWLDSEKVKDDQSMLS 337
                                   346889*********************************87665213444445699****999999988888899999999 PP

                 Peptidase_C47 151 daksnlipvs 160
                                   d ++ lip  
  gi|13540864|ref|NP_110552.1| 338 DVDAILIPGG 347
                                   9988888755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (540 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:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 4110.57
//
Query:       gi|13540865|ref|NP_110553.1|  [L=109]
Description: sterol carrier protein [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.3e-08   33.0   0.5    6.8e-08   32.9   0.5    1.1  1  SCP2          SCP-2 sterol transfer family
     0.0005   20.3   0.0    0.00066   19.9   0.0    1.2  1  Alkyl_sulf_C  Alkyl sulfatase C-terminal
  ------ inclusion threshold ------
       0.27   11.5   2.4        0.7   10.2   0.5    2.4  2  SPACA7        Sperm acrosome-associated protein 7


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 !   32.9   0.5   1.1e-11   6.8e-08       6      91 ..      17      99 ..       5     109 .] 0.84

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 1.1e-11
                                  HHHHHHHHHHHHCCH-EEEEEEECTC.TEEEEEETTSTEEESSCTTBS-SEEEEEEHHHHHHHHCTSS-HHHHHHTTSSEEEC CS
                          SCP2  6 erlkdpekkealkklagvlrfdltdlkgsltldlkegqldvaakdegkadvtlslsledllelaegklnpqkafmqgkLkieG 88
                                  +  +dp+++e+lk+++  + ++  ++  ++++ l +  l+ +++++ +adv + +s+e + ++++++++p +a++++++ki+ 
  gi|13540865|ref|NP_110553.1| 17 Q--DDPKYREKLKDVKKSVNLEFDGK-DNYHFYLENAHLSDVEEGKIDADVNVMVSSEVFSKILSKEIDPLTAYLTKQIKIKA 96
                                  3..378***********888888888.44777778878999999999**********************************97 PP

                                  -HH CS
                          SCP2 89 Die 91
                                   ++
  gi|13540865|ref|NP_110553.1| 97 SLM 99
                                  665 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 !   19.9   0.0   1.1e-07   0.00066      27     101 ..      24      95 ..      18     105 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 1.1e-07
                                   HHHTT-EEEEEEEETTTTEEEEEEEETTEEEE.ECT---TTSSEEEEE-HHHHHHHHTTSS-HHHHHHTTTEEEE CS
                  Alkyl_sulf_C  27 pkaadkdltinlvvtDvdekyllrlsngvLthtrkaaqaddadltvtltreqLvalllgkatlgkevaagklkie 101
                                   +k++d + ++nl + D +++y+  l+n+ L    ++ +  dad+ v ++ e + ++l+++  + ++  ++++ki+
  gi|13540865|ref|NP_110553.1|  24 EKLKDVKKSVNLEF-DGKDNYHFYLENAHLSD-VEEGK-IDADVNVMVSSEVFSKILSKEIDPLTAYLTKQIKIK 95 
                                   57788899999999.7789*************.44344.8********************999999999999996 PP

>> SPACA7  Sperm acrosome-associated protein 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.5   0.00012       0.7      65      99 ..      29      63 ..       2      71 .. 0.80
   2 ?    1.2   0.1     0.071   4.3e+02      29      43 ..      70      83 ..      64     109 .] 0.64

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00012
                        SPACA7 65 akidenyQkeasenYhellenlqfspgtedkiknd 99
                                   k + n   ++ +nYh  len + s   e ki  d
  gi|13540865|ref|NP_110553.1| 29 VKKSVNLEFDGKDNYHFYLENAHLSDVEEGKIDAD 63
                                  3567788899***************9999999877 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.071
                        SPACA7 29 aevldEiLvqeiLdp 43
                                  +ev+  iL +ei dp
  gi|13540865|ref|NP_110553.1| 70 SEVFSKILSKEI-DP 83
                                  678888888887.33 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       795  (0.0443416); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 748.56
//
Query:       gi|13540866|ref|NP_110554.1|  [L=1081]
Description: DNA polymerase II large subunit [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
          0 1116.4   0.0          0 1112.6   0.0    2.3  2  PolC_DP2        DNA polymerase II large subunit DP2
    0.00011   22.2   2.6        0.3   11.1   0.1    2.6  2  HypA            Hydrogenase/urease nickel incorporation, meta
     0.0098   15.9   5.5          1    9.4   0.5    2.4  2  DZR             Double zinc ribbon
  ------ inclusion threshold ------
      0.019   15.1  11.4       0.67   10.1   4.4    2.7  2  Zn-ribbon_8     Zinc ribbon domain
       0.18   11.6  14.3        1.9    8.3   1.3    2.5  2  Rubredoxin_2    Rubredoxin metal binding domain
       0.34   10.8  10.5       0.36   10.7   3.2    2.5  2  DUF35_N         Rubredoxin-like zinc ribbon domain (DUF35_N)
       0.38   10.9   4.1        2.4    8.4   0.3    2.3  2  zf-UBR          Putative zinc finger in N-recognin (UBR box)
       0.39   10.7   2.6        8.7    6.4   0.1    2.3  2  zinc-ribbons_6  zinc-ribbons
        1.4    7.6   3.9       0.65    8.7   0.5    1.9  2  NRDD            Anaerobic ribonucleoside-triphosphate reducta
        2.7    8.0  11.7        1.7    8.7   0.1    3.8  4  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
          6    6.9  13.3        4.1    7.4   0.4    3.3  3  Zn_ribbon_SprT  SprT-like zinc ribbon domain


Domain annotation for each model (and alignments):
>> PolC_DP2  DNA polymerase II large subunit DP2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1112.6   0.0         0         0       2     864 .]      11     826 ..      10     826 .. 0.96
   2 ?   -3.0   0.1      0.72   1.2e+03     631     653 ..     993    1018 ..     989    1059 .. 0.45

  Alignments for each domain:
  == domain 1  score: 1112.6 bits;  conditional E-value: 0
                      PolC_DP2   2 YfeklekeleeayeiaekarskgldpkeevEiplAkdladRvekllgikgvaerirelekelsreevalkiakeiaegkvg 82 
                                   Y +k+++e++e++++a++ar+ g+d++++vEiplA+d+a+R+e+l+gi+g+a++ir+l+k++sreev+l++++++a+    
  gi|13540866|ref|NP_110554.1|  11 YRKKISDEVRECFDLASQARELGMDVTDKVEIPLASDMAERIEALIGISGIADQIRDLSKKMSREEVSLEMSRRVANIFK- 90 
                                   99************************************************************************997654. PP

                      PolC_DP2  83 eaeskeeavdkavrtalalltegvvaAPleGiakvkikknddgteylkvyyaGPiRsaGGtaqalsvLvaDyvrkklgldr 163
                                     ++k+ea+dka+r++la+lteg+++APleGia+v i+kn dg++y+ ++yaGPiR+aGGtaqalsvL++D+vr++lg+ r
  gi|13540866|ref|NP_110554.1|  91 --DNKKEALDKAIRVGLAILTEGILVAPLEGIADVYIGKNADGSDYVGISYAGPIRGAGGTAQALSVLIGDVVRRELGITR 169
                                   ..6799*************************************************************************** PP

                      PolC_DP2 164 ykpreeeieRyveEielYervaslqyspsdeeirlivknipveidGeatedeevsgyrdlervetnrvRGGmllvlaeGia 244
                                   y p+eeeieRy+eEie+Y+r+++lqy p+++ei+l+vkn pv+idGe +e+eevsg+rd+ rv+tnr+RGGm+lvl+eG++
  gi|13540866|ref|NP_110554.1| 170 YIPTEEEIERYIEEIESYDRIKHLQYLPTPDEIKLVVKNSPVCIDGEGSEEEEVSGHRDMARVKTNRIRGGMCLVLCEGLV 250
                                   ********************************************************************************* PP

                      PolC_DP2 245 lkakKikkkvkklklegWewleelikaekeekkeeeeekkevkpkekylrdliaGRpvlshpsrkGGfRLrYGRsrntgla 325
                                   +ka+Ki+k++++++le+W +l+++  +     ++++ +k    +++k+l+d++aGRpv+shpsr+GGfRLrYGRsr +gla
  gi|13540866|ref|NP_110554.1| 251 QKARKILKYTSSMHLEEWSFLSSISGK-----SDDKGSK----KSDKFLKDIVAGRPVFSHPSRPGGFRLRYGRSRVSGLA 322
                                   **********************98777.....4444444....789*********************************** PP

                      PolC_DP2 326 tagihPatmelldeflavGtqlkverPgKaaavvpvdsiegPtvklknGdvvriddveealeikkeveeildlGeiLvayG 406
                                   +a+++Patm+++ +f+a+G+q+kve PgKaaav+p+d+i+gPtv l+nGd+v+i+++e+a+e+ +ev ei d GeiL+ayG
  gi|13540866|ref|NP_110554.1| 323 AASLNPATMYIMGKFIAIGSQIKVELPGKAAAVTPCDTIDGPTVLLRNGDHVKINNIEKAKELYDEVVEITDAGEILIAYG 403
                                   ********************************************************************************* PP

                      PolC_DP2 407 eflennhpLvpasyveewwiqelekaaakkeaeekpsaeealelseeldvpLhPkytylwhdisveelekLaeavaekkkl 487
                                   +flenn +L +as+++eww+q l +        +++++ +a+els+++++pLhP++ y+whdis eele+L +av++ + l
  gi|13540866|ref|NP_110554.1| 404 DFLENNYNLPTASFTKEWWMQYLPDGLDG----NEVDQFRAVELSRQYNIPLHPDFDYYWHDISFEELEYLISAVENGR-L 479
                                   **********************9955554....4689***************************************999.7 PP

                      PolC_DP2 488 eeeklvleleeevkeiLekllvehkvkeekivieealallkslgldleeekleke....eekdalelvnelsglevrekap 564
                                   +++++ ++++    e+L kl+v++k +++ +v++++++ll slg+d+ e+k+++     +++++le+vn lsg++++ +ap
  gi|13540866|ref|NP_110554.1| 480 SDNSFLIPYSA--SEVLIKLGVQFKRSGNFLVLNQYYPLLVSLGYDVFEDKIKRVkpyqRKSSVLETVNYLSGITIKPRAP 558
                                   77999999965..59******************************998888866667766669****************** PP

                      PolC_DP2 565 trigaRmGRPeKskeRkmkpavhvLfpigeaggkrrsvkeaak.kkgeieveiarrkCkkCgketlearCeeCgekteekl 644
                                   tr+g+R+GRPeK+ +Rkmkp+vh+Lfp++++g++rrs+ +a k + g+ ++e+  ++C++Cg e+ + +C++Cg++ ++  
  gi|13540866|ref|NP_110554.1| 559 TRVGSRLGRPEKAGDRKMKPMVHSLFPVESYGEARRSILNANKkTDGTYKAEVFFYRCTSCGYESPSPTCPKCGSRSKP-- 637
                                   *******************************************668999***************************999.. PP

                      PolC_DP2 645 vCkkceeeveeekcekcekeakavkkkkidlkellekaleklgereekleelkgvkgltskekipEpleKgilRakhdvsv 725
                                                          +k+ +idl+ +l+ka ++lg++ ++l+e+kgvk+l+skek++Ep+eKgilRa h++sv
  gi|13540866|ref|NP_110554.1| 638 ---------------------IGTKNSEIDLSVILRKAEDRLGIKLDELKEFKGVKKLMSKEKVAEPIEKGILRAIHGISV 697
                                   .....................4677899***************************************************** PP

                      PolC_DP2 726 fkdgtvRyDmtdlplthfrpkeigvsveklrelGYteDieGkplesedqivelkvqDivlsedaaeyllkvakfvDdlLek 806
                                   +kdgt+R+Dm+d+p+thfr keig+s ekl elGY          + +++ e+ +qD++++++aa+yl+ v+kf+DdlL++
  gi|13540866|ref|NP_110554.1| 698 NKDGTCRFDMSDIPITHFRYKEIGISKEKLSELGY----------EVKDVNEIFPQDVIIPRKAAKYLFDVSKFIDDLLVR 768
                                   ***********************************..........457899****************************** PP

                      PolC_DP2 807 lyglerfYnvekkedLiGklviglaPHtsagvlgRiiGftkasvgyahPyfHaakRRn 864
                                   +ygl++fY+++++edL+G+lviglaPHts+gv+gRiiGf+++++ yahP+fHaakRRn
  gi|13540866|ref|NP_110554.1| 769 YYGLPPFYSLKSEEDLVGHLVIGLAPHTSGGVVGRIIGFSDVNAFYAHPFFHAAKRRN 826
                                   *********************************************************9 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 0.72
                      PolC_DP2  631 arCeeCgektee...klvCkkceeev 653 
                                    +rC++C++k +    + +C+kc++++
  gi|13540866|ref|NP_110554.1|  993 FRCTKCNAKYRRiplSGRCMKCGSDS 1018
                                    34444444333211123344443322 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.2   0.00031       0.5      71      97 ..     614     636 ..     597     649 .. 0.80
   2 !   11.1   0.1   0.00019       0.3      69     106 ..     991    1028 ..     987    1033 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00031
                                   EEETTTS-EEECHHHHHS-TTTSSS-E CS
                          HypA  71 vrCreCgkefeleekalrCpkCgsadv 97 
                                   +rC++Cg+e  +     +CpkCgs++ 
  gi|13540866|ref|NP_110554.1| 614 YRCTSCGYESPSP----TCPKCGSRSK 636
                                   69*****998865....8*****9865 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00019
                                    -EEEETTTS-EEECHHHHHS-TTTSSS-EEEEESSSEE CS
                          HypA   69 vkvrCreCgkefeleekalrCpkCgsadveivsGeell 106 
                                     ++rC++C+++++    + rC kCgs +++++  ++  
  gi|13540866|ref|NP_110554.1|  991 QEFRCTKCNAKYRRIPLSGRCMKCGSDSLTLTIHKGSV 1028
                                    579*********96644689******998877655555 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.5    0.0014       2.3      29      49 .]     614     632 ..     591     639 .. 0.71
   2 !    9.4   0.5   0.00063         1      14      37 ..     994    1017 ..     988    1022 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0014
                           DZR  29 drCpsCgekvdpearfCpeCG 49 
                                   +rC sCg++ ++   +Cp+CG
  gi|13540866|ref|NP_110554.1| 614 YRCTSCGYESPSP--TCPKCG 632
                                   5666666664443..466665 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00063
                           DZR   14 fCseCgtklkavaaedrCpsCgek 37  
                                     C +C++k ++ + + rC++Cg++
  gi|13540866|ref|NP_110554.1|  994 RCTKCNAKYRRIPLSGRCMKCGSD 1017
                                    6*********9999*******986 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   4.4   0.00041      0.67       6      35 ..     614     634 ..     611     637 .. 0.80
   2 ?    8.3   0.6    0.0015       2.5       5      35 ..     992    1018 ..     992    1021 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00041
                   Zn-ribbon_8   6 YrCeeCghefevlqsisdapltaCPeCgse 35 
                                   YrC++Cg  +e       +p ++CP+Cgs+
  gi|13540866|ref|NP_110554.1| 614 YRCTSCG--YE-------SPSPTCPKCGSR 634
                                   *******..55.......45889*****96 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0015
                   Zn-ribbon_8    5 eYrCeeCghefevlqsisdaplta.CPeCgs.e 35  
                                    e+rC++C+ ++ ++       l   C +Cgs  
  gi|13540866|ref|NP_110554.1|  992 EFRCTKCNAKYRRIP------LSGrCMKCGSdS 1018
                                    8*******9999775......4455*****944 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   5.7    0.0015       2.5       1      22 [.     614     633 ..     614     633 .. 0.92
   2 ?    8.3   1.3    0.0011       1.9       1      22 [.     993    1016 ..     993    1018 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0015
                  Rubredoxin_2   1 YvCsqCGfesakwfGrCpsCgs 22 
                                   Y+C +CG+es++    Cp Cgs
  gi|13540866|ref|NP_110554.1| 614 YRCTSCGYESPSP--TCPKCGS 633
                                   9***********9..5999996 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0011
                  Rubredoxin_2    1 YvCsqCGfesak..wfGrCpsCgs 22  
                                    ++C +C++++++  + GrC  Cgs
  gi|13540866|ref|NP_110554.1|  993 FRCTKCNAKYRRipLSGRCMKCGS 1016
                                    8*********995569******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 ?   10.7   3.2   0.00022      0.36      10      34 ..     612     634 ..     610     636 .. 0.89
   2 ?    3.7   0.7     0.034        56      13      36 ..     997    1019 ..     991    1020 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00022
                       DUF35_N  10 vgqrCpdCGtvqfPPravCphCgsd 34 
                                    + rC++CG     P + Cp+Cgs+
  gi|13540866|ref|NP_110554.1| 612 FFYRCTSCGYES--PSPTCPKCGSR 634
                                   567********7..*********98 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.034
                       DUF35_N   13 rCpdCGtvqfPPr.avCphCgsddl 36  
                                    +C +  +++  P    C +Cgsd+l
  gi|13540866|ref|NP_110554.1|  997 KCNA--KYRRIPLsGRCMKCGSDSL 1019
                                    4444..6666677799*******98 PP

>> zf-UBR  Putative zinc finger in N-recognin (UBR box)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.3    0.0015       2.4       7      34 ..     608     635 ..     602     648 .. 0.84
   2 ?    3.4   0.3     0.055        90      13      32 ..     993    1016 ..     985    1029 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0015
                        zf-UBR   7 kkgevvyrCltCsldetsviCeeCfkas 34 
                                   k++ ++yrC +C+ ++ s  C +C  +s
  gi|13540866|ref|NP_110554.1| 608 KAEVFFYRCTSCGYESPSPTCPKCGSRS 635
                                   566799*********999******8766 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.055
                        zf-UBR   13 yrCltCsld....etsviCeeCfk 32  
                                    +rC +C+ +    + s+ C++C  
  gi|13540866|ref|NP_110554.1|  993 FRCTKCNAKyrriPLSGRCMKCGS 1016
                                    89******9999988999999965 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   0.4     0.035        58      16      38 ..     613     634 ..     599     638 .. 0.81
   2 ?    6.4   0.1    0.0053       8.7      15      37 ..     991    1016 ..     978    1026 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.035
                                   EEE-TTT--EEEEEEE-SSS-S- CS
                zinc-ribbons_6  16 qyhCeaCqedlkkealCpeCeqe 38 
                                    y+C +C  +    ++Cp+C+++
  gi|13540866|ref|NP_110554.1| 613 FYRCTSCGYES-PSPTCPKCGSR 634
                                   589****9885.5799****975 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0053
                                    SEEE-TTT--EEEEEEE...-SSS-S CS
                zinc-ribbons_6   15 eqyhCeaCqedlkkeal...CpeCeq 37  
                                    ++++C +C++++++ +l   C +C++
  gi|13540866|ref|NP_110554.1|  991 QEFRCTKCNAKYRRIPLsgrCMKCGS 1016
                                    67899999998777654222666654 PP

>> NRDD  Anaerobic ribonucleoside-triphosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.5    0.0004      0.65     507     530 ..     613     636 ..     589     643 .. 0.84
   2 ?   -1.1   0.2      0.37   6.1e+02     509     529 ..     994    1018 ..     982    1039 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0004
                                   EEEETT.--EESSSB-TTT--BE. CS
                          NRDD 507 idvCnecgykgeiekCpkCgseee 530
                                   + +C +cgy+    +CpkCgs+++
  gi|13540866|ref|NP_110554.1| 613 FYRCTSCGYESPSPTCPKCGSRSK 636
                                   669******999999*****9875 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.37
                                    EETT.--EESS....SB-TTT--BE CS
                          NRDD  509 vCnecgykgei....ekCpkCgsee 529 
                                    +C +c+ k  +     +C kCgs++
  gi|13540866|ref|NP_110554.1|  994 RCTKCNAKYRRiplsGRCMKCGSDS 1018
                                    68888884444478877*****765 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 ?   -2.8   0.0         4   6.4e+03       1      12 [.     172     183 ..     172     184 .. 0.88
   2 ?    1.8   0.2      0.15   2.4e+02      35      45 ..     611     621 ..     600     622 .. 0.78
   3 ?    8.7   0.1     0.001       1.7      19      33 ..     626     641 ..     623     653 .. 0.85
   4 ?    2.4   1.5     0.093   1.5e+02      13      44 ..     987    1015 ..     985    1020 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 4
                 Zn_Tnp_IS1595   1 pdEeearalLea 12 
                                   p+Eee+++++e+
  gi|13540866|ref|NP_110554.1| 172 PTEEEIERYIEE 183
                                   69*******997 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.15
                 Zn_Tnp_IS1595  35 rglfqCkeCrk 45 
                                    + ++C +C++
  gi|13540866|ref|NP_110554.1| 611 VFFYRCTSCGY 621
                                   589******98 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.001
                 Zn_Tnp_IS1595  19 fvCPhCgsr.kayrik 33 
                                   ++CP+Cgsr k++ +k
  gi|13540866|ref|NP_110554.1| 626 PTCPKCGSRsKPIGTK 641
                                   89*******9988776 PP

  == domain 4  score: 2.4 bits;  conditional E-value: 0.093
                 Zn_Tnp_IS1595   13 lrWpngfvCPhCgsr.kayriktrglfqCkeCr 44  
                                    +++ + f+C +C  + + + +++    +C +C+
  gi|13540866|ref|NP_110554.1|  987 RFFSQEFRCTKCNAKyRRIPLSG----RCMKCG 1015
                                    56788899999998888888888....666665 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.4    0.0025       4.1       3      14 ..     612     623 ..     610     626 .. 0.82
   2 ?    1.1   0.2      0.24   3.9e+02       6      15 ..     627     636 ..     627     639 .. 0.81
   3 ?    4.7   2.1     0.017        28       6      31 ..     994    1015 ..     992    1022 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0025
                Zn_ribbon_SprT   3 yvYrCtgCgrey 14 
                                   + YrCt+Cg e+
  gi|13540866|ref|NP_110554.1| 612 FFYRCTSCGYES 623
                                   56*******776 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.24
                Zn_ribbon_SprT   6 rCtgCgreyt 15 
                                   +C+ Cg++++
  gi|13540866|ref|NP_110554.1| 627 TCPKCGSRSK 636
                                   59***98876 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.017
                Zn_ribbon_SprT    6 rCtgCgreythhlsirrhnYrCrrCk 31  
                                    rCt C  +y ++  + r    C +C+
  gi|13540866|ref|NP_110554.1|  994 RCTKCNAKYRRIPLSGR----CMKCG 1015
                                    8**************99....88887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1081 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       910  (0.0507558); expected 358.6 (0.02)
Passed bias filter:                      815  (0.0454571); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.96u 0.34s 00:00:01.30 Elapsed: 00:00:00.51
# Mc/sec: 6404.07
//
Query:       gi|13540867|ref|NP_110555.1|  [L=257]
Description: GTPase [Thermoplasma volcanium GSS1]
Scores for complete 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-53  179.8   0.0    8.7e-53  179.6   0.0    1.0  1  ATP_bind_1    Conserved hypothetical ATP binding protein
    0.00035   20.4   0.0      0.011   15.6   0.0    2.2  2  CLP1_P        mRNA cleavage and polyadenylation factor CLP1 P
    0.00073   19.5   0.4     0.0051   16.8   0.0    2.3  2  MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
      0.001   19.6   0.0     0.0092   16.5   0.0    2.1  2  AAA_18        AAA domain
     0.0013   18.5   0.0     0.0022   17.8   0.0    1.4  1  AAA_24        AAA domain
     0.0018   17.8   0.1      0.081   12.4   0.1    2.7  2  GTP_EFTU      Elongation factor Tu GTP binding domain
     0.0033   17.7   0.0     0.0063   16.8   0.0    1.4  1  AAA_22        AAA domain
     0.0039   17.1   0.0        1.9    8.4   0.0    2.9  3  RsgA_GTPase   RsgA GTPase
     0.0042   17.1   0.0     0.0076   16.3   0.0    1.5  1  CbiA          CobQ/CobB/MinD/ParA nucleotide binding domain
  ------ inclusion threshold ------
      0.013   15.1   1.0       0.98    9.0   0.1    2.8  3  cobW          CobW/HypB/UreG, nucleotide-binding domain
      0.013   15.2   0.1      0.043   13.5   0.0    1.7  2  AAA_30        AAA domain
      0.016   14.2   0.0      0.033   13.2   0.0    1.4  1  MeaB          Methylmalonyl Co-A mutase-associated GTPase Mea
      0.017   14.9   0.2       0.53   10.0   0.1    2.8  3  PduV-EutP     Ethanolamine utilisation - propanediol utilisat
      0.023   14.6   0.0          2    8.2   0.0    2.7  2  dNK           Deoxynucleoside kinase
      0.032   13.4   0.0       0.18   10.9   0.0    2.0  2  ArsA_ATPase   Anion-transporting ATPase
      0.033   13.1   0.0       0.44    9.4   0.0    2.2  2  AAA_PrkA      PrkA AAA domain
      0.034   13.9   0.0      0.065   13.0   0.0    1.5  1  NOG1          Nucleolar GTP-binding protein 1 (NOG1)
      0.042   13.8   0.1        0.4   10.6   0.0    2.3  3  NTPase_1      NTPase
      0.044   13.5   0.0        0.4   10.4   0.0    2.2  2  PRK           Phosphoribulokinase / Uridine kinase family
      0.047   14.1   0.0       0.18   12.2   0.0    1.9  2  RNA_helicase  RNA helicase
      0.054   13.4   0.0        0.1   12.5   0.0    1.3  1  APS_kinase    Adenylylsulphate kinase
      0.079   13.2   0.2       0.18   12.1   0.1    1.5  2  Phage_TAC_8   Phage tail assembly chaperone protein Gp14 ()A1
       0.09   12.0   0.0       0.13   11.6   0.0    1.1  1  V-ATPase_H_N  V-ATPase subunit H
       0.11   12.8   0.0       0.15   12.4   0.0    1.4  1  AAA_16        AAA ATPase domain
       0.15   11.8   0.1        0.3   10.9   0.1    1.5  1  AAA_29        P-loop containing region of AAA domain


Domain annotation for each model (and alignments):
>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  179.6   0.0   1.2e-55   8.7e-53       1     234 [.       7     241 ..       7     247 .. 0.96

  Alignments for each domain:
  == domain 1  score: 179.6 bits;  conditional E-value: 1.2e-55
                    ATP_bind_1   1 vvGpaGsGKttfvgalseilelrgrsvavvNLDPAaeelpYeaavdirelitledvmedlglgpngalvvaleflresldw 81 
                                   v+GpaG GK+tf gal e+l+  + + a++NLDP+a+ lpYe++ dire+i+le +m d++lgpng+ +va++++ +  d+
  gi|13540867|ref|NP_110555.1|   7 VTGPAGTGKSTFSGALKEWLQRMEFDAAIINLDPGADYLPYEPDFDIREYISLEGIMSDYNLGPNGSQIVAADMIINFTDK 87 
                                   89***********************************************************************988888** PP

                    ATP_bind_1  82 ldeelekeeddyllfDtPGQielfthseslakiveeLesefalvvvyLvDsqrltdptkfisgllsalsamlrlelPhvvv 162
                                   ++e  ++ +d yl++DtPGQielft++ s  +iv++++   + ++ y++D++ +t p+ fi + ++  s+  r   P+  v
  gi|13540867|ref|NP_110555.1|  88 IKEFTDELQDYYLVVDTPGQIELFTFRTSSTEIVDRIS-GEKSMIAYIADAPLATYPSGFIAQKMLYASVFSRFFKPMMFV 167
                                   *999977799****************************.699999************************************ PP

                    ATP_bind_1 163 lnkfDllkek.lekeleffedvealslllekee.ekykklaeaiaelleefalvlrflplssekeesiedllsl 234
                                   lnk+Dl++++  e   ++  d++ l+++  +e+ +  k+ + ++ e+++e +++++++p+ss++  ++ed++s 
  gi|13540867|ref|NP_110555.1| 168 LNKIDLVSDEdVETVKKWERDPDLLNEAFIDEKgNIEKDYFLNLLEAFKESNIMTKVYPVSSRDSFGFEDIYSN 241
                                   ********99999999*********99988888688889999***************************99876 PP

>> CLP1_P  mRNA cleavage and polyadenylation factor CLP1 P-loop
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.5e-05     0.011       1      34 [.       9      42 ..       9      48 .. 0.95
   2 ?    2.7   0.0      0.14        98      96     117 ..      90     111 ..      70     126 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.5e-05
                        CLP1_P  1 GpkdsGKSTlarlLlNyalrkgrkpvyvDlDvGq 34
                                  Gp  +GKST++  L +++ r++   ++++lD+G 
  gi|13540867|ref|NP_110555.1|  9 GPAGTGKSTFSGALKEWLQRMEFDAAIINLDPGA 42
                                  899*****************************95 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.14
                        CLP1_P  96 eenkkakasgliIntpGwvkgl 117
                                   e  ++ +++ l+++tpG ++ +
  gi|13540867|ref|NP_110555.1|  90 EFTDELQDYYLVVDTPGQIELF 111
                                   33456799*********99865 PP

>> MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   7.1e-06    0.0051      52      79 ..     158     185 ..     150     205 .. 0.87
   2 ?   -0.2   0.0       1.4     1e+03      75      99 ..     217     241 ..     206     244 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 7.1e-06
                  MMR_HSR1_Xtn  52 nrvYipclyvlNKiDlisleeldelare 79 
                                   +r ++p+++vlNKiDl+s+e+++++++ 
  gi|13540867|ref|NP_110555.1| 158 SRFFKPMMFVLNKIDLVSDEDVETVKKW 185
                                   57899******************99984 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.4
                  MMR_HSR1_Xtn  75 elarepnsvviSaekelnldeLkek 99 
                                   e + + ++ ++S+++ ++++++ ++
  gi|13540867|ref|NP_110555.1| 217 ESNIMTKVYPVSSRDSFGFEDIYSN 241
                                   3344578999********9998766 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   1.3e-05    0.0092       3      38 ..       7      63 ..       6     127 .. 0.71
   2 ?    0.9   0.0      0.86   6.2e+02      33      69 ..     185     220 ..     150     239 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.3e-05
                        AAA_18  3 ltGtpGvGKttlakeLskrl.gf....................gvnlrdvakengll 38
                                  +tG++G+GK+t++ +L++ l  +                     + +r++++ +g+ 
  gi|13540867|ref|NP_110555.1|  7 VTGPAGTGKSTFSGALKEWLqRMefdaaiinldpgadylpyepDFDIREYISLEGIM 63
                                  8***************88764446566666666666666666655555555555544 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.86
                        AAA_18  33 kenglllevdpealdeskrldedkldklldaleenss 69 
                                   +e+++ l ++++ +de+  +++d+  +ll+a++e++ 
  gi|13540867|ref|NP_110555.1| 185 WERDPDLLNEAF-IDEKGNIEKDYFLNLLEAFKESNI 220
                                   344444444444.889999999999999999999864 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0     3e-06    0.0022       6      78 ..       6     109 ..       4     133 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 3e-06
                        AAA_24   6 liyGpsgiGKTtlakel.......gpkplfidtekGlksldadkfpdie.........................swedfld 54 
                                    ++Gp+g+GK+t+   l       + ++++i+++ G++ l      di+                          +++f d
  gi|13540867|ref|NP_110555.1|   6 YVTGPAGTGKSTFSGALkewlqrmEFDAAIINLDPGADYLPYEPDFDIReyislegimsdynlgpngsqivaadMIINFTD 86 
                                   689***********999999999999**************9999999999**99999999999999999999999999999 PP

                        AAA_24  55 evvelaaeladyktlviDtidele 78 
                                   +++e+ +el+dy  lv+Dt +++e
  gi|13540867|ref|NP_110555.1|  87 KIKEFTDELQDY-YLVVDTPGQIE 109
                                   99999****999.68889977765 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 ?    1.6   0.0      0.24   1.7e+02       6      25 ..       5      24 ..       2      45 .. 0.84
   2 !   12.4   0.1   0.00011     0.081      72     186 ..      99     240 ..      80     247 .. 0.61

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.24
                                  EEEEESTTSSHHHHHHHHHH CS
                      GTP_EFTU  6 igiighvDhGKtTLtdrLly 25
                                  + + g   +GK+T++++L +
  gi|13540867|ref|NP_110555.1|  5 LYVTGPAGTGKSTFSGALKE 24
                                  56889999********9965 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00011
                                   EEEEEESSSGGGHHHHHHHHHT-S......EEEE.EEETT......TBSTHHHHHHHHHHHHTTTEEEEEEESCGSTHHHH CS
                      GTP_EFTU  72 inliDtPGHvdFskevirglrvlD......gavl.vvdav......eGvepqteevlrlalkegvpiivfiNKmDrlkael 139
                                   + ++DtPG ++     + +++++D       ++  + d +      +G  +q    + + ++   p+++++NK+D + +e 
  gi|13540867|ref|NP_110555.1|  99 YLVVDTPGQIELFTFRTSSTEIVDrisgekSMIAyIAD-AplatypSGFIAQKMLYASVFSRFFKPMMFVLNKIDLVSDED 178
                                   55667777776333344444444422211112220222.135555567777777777788888889***********4444 PP

                                   HHHHHHHHHHHHHH................HHHHHHHHHTTTTTEEEEEEBTTTTBTHHHHHH CS
                      GTP_EFTU 140 keiveevkqklsrk................eeklekygekgekevpvvfgSalkgegvktlle 186
                                    e+v++ +++ +                   + le+++e++   ++v+++S+ + +g++++ +
  gi|13540867|ref|NP_110555.1| 179 VETVKKWERDPDLLneafidekgniekdyfLNLLEAFKESN-IMTKVYPVSSRDSFGFEDIYS 240
                                   44444444433111334555566666666666666666665.589999999999999987765 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   8.8e-06    0.0063       7      33 ..       4      30 ..       3      58 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 8.8e-06
                        AAA_22  7 ilvvtGesGtGKTtllrrlleqldeea 33
                                   l+vtG++GtGK+t    l+e+l++ +
  gi|13540867|ref|NP_110555.1|  4 TLYVTGPAGTGKSTFSGALKEWLQRME 30
                                  589********************8654 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0      0.03        22     102     121 ..       5      24 ..       3      35 .. 0.83
   2 ?   -0.5   0.0       1.4     1e+03     151     161 ..      97     107 ..      87     112 .. 0.78
   3 !    8.4   0.0    0.0026       1.9      48      72 ..     163     186 ..     142     221 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.03
                                   EEEECSTTSSHHHHHHHHCT CS
                   RsgA_GTPase 102 svlvGqSGvGKStLinallp 121
                                     + G+ G GKSt+  al++
  gi|13540867|ref|NP_110555.1|   5 LYVTGPAGTGKSTFSGALKE 24 
                                   5689*********9988875 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.4
                                   TTEEEESS-SS CS
                   RsgA_GTPase 151 egglliDtPGf 161
                                   +  l++DtPG 
  gi|13540867|ref|NP_110555.1|  97 DYYLVVDTPGQ 107
                                   45689****95 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.0026
                                   EEEEEEE-GGG--HHHHHHHHHHHH CS
                   RsgA_GTPase  48 epvivlnKiDlleeeeeleelkeel 72 
                                   +++ vlnKiDl+++e+ +e++k+  
  gi|13540867|ref|NP_110555.1| 163 PMMFVLNKIDLVSDED-VETVKKWE 186
                                   46789**********9.66655543 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   1.1e-05    0.0076       8      86 ..      11     173 ..       5     205 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.1e-05
                                   TTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCH..HTTEB-HHHH................................ CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxx................................ RF
                          CbiA   8 GGvGKTtlaanLaralarrglrVllvDaDpqannlai..leglendiep................................ 54 
                                    G+GK+t++ +L   l+r +++ + + +Dp a  l +   +  +++i                                  
  gi|13540867|ref|NP_110555.1|  11 AGTGKSTFSGALKEWLQRMEFDAAIINLDPGADYLPYepDFDIREYISLegimsdynlgpngsqivaadmiinftdkikef 91 
                                   69*****************************99999666333333333377777777799999999999999999888888 PP

                                   .....................................................CCHCCCHHHHHHCHCHHHH..EEEEEEE CS
                                   .....................................................xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          CbiA  55 .....................................................dlkrllellealgkkkalllkiagvvln 82 
                                                                                        + +  + l +++  ++   +k++++vln
  gi|13540867|ref|NP_110555.1|  92 tdelqdyylvvdtpgqielftfrtssteivdrisgeksmiayiadaplatypsGFIAQKMLYASVFSRF---FKPMMFVLN 169
                                   888888888888888888888888888888888866666666666666655554444333333333332...777888888 PP

                                   EESS CS
                                   xxxx RF
                          CbiA  83 rvdg 86 
                                   ++d 
  gi|13540867|ref|NP_110555.1| 170 KIDL 173
                                   8764 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0     0.081        58       3      20 ..       5      22 ..       4      42 .. 0.67
   2 ?   -0.4   0.1         1   7.2e+02     137     157 ..      73      92 ..      71     108 .. 0.74
   3 ?    9.0   0.1    0.0014      0.98     143     167 ..     164     187 ..      99     195 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.081
                                  EEEEESTTCCHHHHHHHH CS
                          cobW  3 tvltGflGsGKTtLlnhl 20
                                  + +tG+ G+GK+t+  +l
  gi|13540867|ref|NP_110555.1|  5 LYVTGPAGTGKSTFSGAL 22
                                  579*********974444 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1
                                   HHHHTSSEEEEE-HHHHCHC. CS
                          cobW 137 dqlaaadllvlnKtDlldeea 157
                                   +q+ aad+ ++n tD ++e +
  gi|13540867|ref|NP_110555.1|  73 SQIVAADM-IINFTDKIKEFT 92 
                                   68889996.568899888763 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.0014
                                   SEEEEE-HHHHCHC..HHHHHHHHH CS
                          cobW 143 dllvlnKtDlldeeallekleerlr 167
                                    ++vlnK+Dl+++e ++e+++++ r
  gi|13540867|ref|NP_110555.1| 164 MMFVLNKIDLVSDE-DVETVKKWER 187
                                   589**********9.4577777655 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     6e-05     0.043      22      45 ..       6      29 ..       3      41 .. 0.85
   2 ?   -1.4   0.0       2.2   1.6e+03      92     116 ..     195     219 ..     168     227 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6e-05
                        AAA_30 22 vltGpAGtGKttalkalreaweaa 45
                                   +tGpAGtGK+t  +al+e +++ 
  gi|13540867|ref|NP_110555.1|  6 YVTGPAGTGKSTFSGALKEWLQRM 29
                                  689**************9988765 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.2
                        AAA_30  92 livDEagmvdtkqlaallkaaekag 116
                                     +DE g +  + + +ll+a ++++
  gi|13540867|ref|NP_110555.1| 195 AFIDEKGNIEKDYFLNLLEAFKESN 219
                                   4699999999999999999988765 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   4.5e-05     0.033      33      70 ..       6      43 ..       2      45 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.5e-05
                                  EEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE----- CS
                          MeaB 33 GltGvPGaGkstlvealglelrrrGkrvavlavDPssp 70
                                   +tG  G+Gkst+  al + l+r     a++ +DP++ 
  gi|13540867|ref|NP_110555.1|  6 YVTGPAGTGKSTFSGALKEWLQRMEFDAAIINLDPGAD 43
                                  58*********************************986 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.38   2.7e+02       6      23 ..       7      24 ..       3      41 .. 0.80
   2 ?   10.0   0.1   0.00074      0.53      38     114 ..      99     185 ..      87     189 .. 0.62
   3 ?   -1.9   0.0       3.6   2.6e+03     120     138 ..     221     239 ..     192     243 .. 0.69

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.38
                     PduV-EutP  6 liGkvgsGKttLtqalkg 23
                                  + G+ g+GK t + alk+
  gi|13540867|ref|NP_110555.1|  7 VTGPAGTGKSTFSGALKE 24
                                  6799*********99997 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00074
                     PduV-EutP  38 deviDtPGe...ylenrklysalivtsaeadvialvqda.........teeesvfppgfasvfnkeviGiitkidlaedee 106
                                     v+DtPG+   +    +  + +  +s e ++ia + da          +++ +++  f+  f k+++ ++ kidl+ ++e
  gi|13540867|ref|NP_110555.1|  99 YLVVDTPGQielFTFRTSSTEIVDRISGEKSMIAYIADAplatypsgfIAQKMLYASVFS-RFFKPMMFVLNKIDLV-SDE 177
                                   557888886332233333444455677777888777775222111111344444555554.4669************.889 PP

                     PduV-EutP 107 nieaveel 114
                                   ++e+v+++
  gi|13540867|ref|NP_110555.1| 178 DVETVKKW 185
                                   99999987 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 3.6
                     PduV-EutP 120 aekifevsavekegieell 138
                                   ++k++ vs+ ++ g+e++ 
  gi|13540867|ref|NP_110555.1| 221 MTKVYPVSSRDSFGFEDIY 239
                                   4677777777777777765 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.0    0.0027         2       2      82 ..       6     123 ..       5     135 .. 0.74
   2 ?    3.2   0.0     0.097        69     148     176 ..     199     228 ..     190     246 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0027
                                   EEEESTTSSHHHHHHHHHCCSTCEEEE-......HHHHCCSSSS.............................HHHHHHHH CS
                           dNK   2 vveGnIgaGKstlvklLskklgvkvfeE......pvdkwtnvqk.............................nlLekfYk 47 
                                    v G+ g GKst+   L++ l+   f        p +++ + +                               ++ +f +
  gi|13540867|ref|NP_110555.1|   6 YVTGPAGTGKSTFSGALKEWLQRMEFDAaiinldPGADYLPYEPdfdireyislegimsdynlgpngsqivaaDMIINFTD 86 
                                   589**************9988743333323334455555444447777777777778888888888888888888888888 PP

                                   SHHHHHHHHHHHHHHHHHHHHHCHH..SSS-EEEEES CS
                           dNK  48 dpsrwsfalqtyvllsrlkqqleal..atkqvvvleR 82 
                                   ++++++ +lq+y+l+  +  q e +  +t+++++++R
  gi|13540867|ref|NP_110555.1|  87 KIKEFTDELQDYYLVVDTPGQIELFtfRTSSTEIVDR 123
                                   8888999999888888887777776678888888888 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.097
                                   CT.TS-HHHHHHHHHHHHHHHTSGGCS-EE CS
                           dNK 148 ek.kieldYlekLhekyeewlkklnevpvl 176
                                   ek +ie+dY+ +L e ++e+ + ++  pv 
  gi|13540867|ref|NP_110555.1| 199 EKgNIEKDYFLNLLEAFKESNIMTKVYPVS 228
                                   5559***************99998888876 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00025      0.18       4      40 ..       5      41 ..       3      45 .. 0.93
   2 ?   -0.6   0.0      0.82   5.9e+02     255     281 ..     195     221 ..     149     242 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00025
                                  EEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-STT CS
                   ArsA_ATPase  4 ilvgGKGGVGKttvsaatavklsekgkkvllistDPA 40
                                  + v+G  G GK+t s a+  +l +++ +  +i +DP 
  gi|13540867|ref|NP_110555.1|  5 LYVTGPAGTGKSTFSGALKEWLQRMEFDAAIINLDPG 41
                                  6799********************************5 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.82
                                   HHHHHHHHHHHHHHHHHHHHTTTSEEE CS
                   ArsA_ATPase 255 eflearkkiqkkylkeieelfedlevv 281
                                    f++++ +i+k y  ++ e f++ +++
  gi|13540867|ref|NP_110555.1| 195 AFIDEKGNIEKDYFLNLLEAFKESNIM 221
                                   566666677777777777777666554 PP

>> AAA_PrkA  PrkA AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0   0.00061      0.44      91     115 ..       5      29 ..       3      48 .. 0.86
   2 ?    1.1   0.1       0.2   1.5e+02      49      77 ..     218     246 ..     182     252 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00061
                      AAA_PrkA  91 lyllGPvggGksslverlkklleaa 115
                                   ly+ GP g+Gks++  +lk+ l+ +
  gi|13540867|ref|NP_110555.1|   5 LYVTGPAGTGKSTFSGALKEWLQRM 29 
                                   9*******************99987 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.2
                      AAA_PrkA  49 snetikkypafeedffGleetiekiveyf 77 
                                   sn   k yp+ ++d fG+e+  +++  +f
  gi|13540867|ref|NP_110555.1| 218 SNIMTKVYPVSSRDSFGFEDIYSNMSMFF 246
                                   45566888888888888888877776666 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 ?   13.0   0.0     9e-05     0.065      29      58 .]     144     172 ..     127     172 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 9e-05
                          NOG1  29 ysleeQlsLleeikelfankpvivvlnKiD 58 
                                     +  Q  L+ ++ ++f  kp++ vlnKiD
  gi|13540867|ref|NP_110555.1| 144 SGFIAQKMLYASVFSRFF-KPMMFVLNKID 172
                                   5566899**********9.9*********9 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00055       0.4       2      27 ..       5      30 ..       4      34 .. 0.86
   2 ?   -0.0   0.0         1   7.2e+02      98     129 ..      99     131 ..      63     141 .. 0.56
   3 ?   -2.2   0.0       4.7   3.4e+03      99     109 ..     195     205 ..     170     231 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00055
                                  EEEE--TTSSHHHHHHHHHHHH...G CS
                      NTPase_1  2 vfiTGppGvGKtTlvkkvlellkssg 27
                                  +++TGp G+GK+T+   + e l++ +
  gi|13540867|ref|NP_110555.1|  5 LYVTGPAGTGKSTFSGALKEWLQRME 30
                                  68************999999888765 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 1
                                   EEEE---STTGGG-.HHHHHHHHHHHTTTSEEE CS
                      NTPase_1  98 viviDEiGkmElks.kkfkeaveevLksekpvl 129
                                    +v+D  G++El++ ++ ++++ + ++ ek ++
  gi|13540867|ref|NP_110555.1|  99 YLVVDTPGQIELFTfRTSSTEIVDRISGEKSMI 131
                                   445555666665541233334444444444444 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 4.7
                                   EEE---STTGG CS
                      NTPase_1  99 iviDEiGkmEl 109
                                     iDE G++E 
  gi|13540867|ref|NP_110555.1| 195 AFIDEKGNIEK 205
                                   36888888885 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00055       0.4       4      36 ..       7      39 ..       4      56 .. 0.88
   2 ?    0.2   0.0      0.75   5.4e+02     133     151 ..     170     188 ..     152     191 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00055
                           PRK  4 vagsSGaGkttvarklekifgrekvkaaeiegd 36
                                  v+g+ G Gk+t++ +l++ ++r +  aa i++d
  gi|13540867|ref|NP_110555.1|  7 VTGPAGTGKSTFSGALKEWLQRMEFDAAIINLD 39
                                  8***********************999999876 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.75
                           PRK 133 kiyvdisidlelarklqRD 151
                                   ki ++ ++d+e  +k +RD
  gi|13540867|ref|NP_110555.1| 170 KIDLVSDEDVETVKKWERD 188
                                   7889**************9 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00025      0.18       1      27 [.       5      30 ..       5      47 .. 0.73
   2 ?   -1.5   0.0       4.6   3.3e+03      27      54 ..     103     131 ..      83     155 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00025
                  RNA_helicase  1 iwlyGpsgeGKStlakeLakallkklk 27
                                  ++++Gp+g+GKSt++    k++l++++
  gi|13540867|ref|NP_110555.1|  5 LYVTGPAGTGKSTFSGA-LKEWLQRME 30
                                  699************99.555555653 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 4.6
                  RNA_helicase  27 klkkkdsvys.rnpeddfwdgYtgqevvv 54 
                                   +++ + ++++ r+++++++d  +g++ ++
  gi|13540867|ref|NP_110555.1| 103 DTPGQIELFTfRTSSTEIVDRISGEKSMI 131
                                   44555555566888888888888777665 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00014       0.1       4      35 ..       4      35 ..       2      41 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00014
                                  EEEEESSTTSSHHHHHHHHHHHHHHTT--EEE CS
                    APS_kinase  4 vvwltGlsgsGKstianalekkLvekgisvyl 35
                                  ++++tG +g+GKst + al++ L+++   + +
  gi|13540867|ref|NP_110555.1|  4 TLYVTGPAGTGKSTFSGALKEWLQRMEFDAAI 35
                                  79**********************99866554 PP

>> Phage_TAC_8  Phage tail assembly chaperone protein Gp14 ()A118
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       8.8   6.3e+03      37      54 ..      81      98 ..      57     108 .. 0.68
   2 ?   12.1   0.1   0.00024      0.18      36      98 ..     177     241 ..     163     245 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 8.8
                   Phage_TAC_8 37 likageeykkavdkleki 54
                                  +i+  ++ k+  d+l+++
  gi|13540867|ref|NP_110555.1| 81 IINFTDKIKEFTDELQDY 98
                                  566667777777777765 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00024
                   Phage_TAC_8  36 elikageeykkavdklekieiddpeelttddyialeekvke..llkealnkllddekaydkiykk 98 
                                   e +++ +++++  d l++  id+  ++  d ++ l e  ke  ++++ + ++  d   ++ iy +
  gi|13540867|ref|NP_110555.1| 177 EDVETVKKWERDPDLLNEAFIDEKGNIEKDYFLNLLEAFKEsnIMTKVYPVSSRDSFGFEDIYSN 241
                                   5577778999999************************988744799999***999999****987 PP

>> V-ATPase_H_N  V-ATPase subunit H
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00017      0.13      22      74 ..     170     222 ..     167     227 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00017
                  V-ATPase_H_N  22 rsqliseedlkliksldkakkeqraklldedgpqyvklllnLlsklskedtlq 74 
                                   + +l+s+ed++++k+ + ++   +++++de+g+  ++ +lnLl+  ++++++ 
  gi|13540867|ref|NP_110555.1| 170 KIDLVSDEDVETVKKWERDPDLLNEAFIDEKGNIEKDYFLNLLEAFKESNIMT 222
                                   5689******************999********************99888876 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00021      0.15      26      51 ..       4      28 ..       2     128 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00021
                        AAA_16 26 lvllsGesGvGKsslvrellralekd 51
                                   ++++G++G+GKs+   +l++ + ++
  gi|13540867|ref|NP_110555.1|  4 TLYVTGPAGTGKSTFSGALKE-WLQR 28
                                  589***********9988885.3333 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00041       0.3      24      42 ..       4      22 ..       1      27 [. 0.81

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00041
                        AAA_29 24 atlltGpsGsGKSTllDAi 42
                                  +  +tGp G+GKST+  A+
  gi|13540867|ref|NP_110555.1|  4 TLYVTGPAGTGKSTFSGAL 22
                                  5679**********86665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       626  (0.0349155); expected 358.6 (0.02)
Passed bias filter:                      551  (0.0307323); expected 358.6 (0.02)
Passed Vit filter:                       105  (0.00585643); 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: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.50
# Mc/sec: 1561.42
//
Query:       gi|13540868|ref|NP_110556.1|  [L=204]
Description: hypothetical protein TVN0037 [Thermoplasma volcanium GSS1]
Scores for complete 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-46  157.3   0.1      3e-46  157.1   0.1    1.0  1  DUF99     Protein of unknown function DUF99
  ------ inclusion threshold ------
      0.076   13.3   0.1        3.4    8.0   0.0    2.4  2  SepF      Cell division protein SepF


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 !  157.1   0.1   3.4e-50     3e-46       2     180 ..      30     202 ..      29     204 .] 0.95

  Alignments for each domain:
  == domain 1  score: 157.1 bits;  conditional E-value: 3.4e-50
                                   GSEEEEEEEEE.....-SS-EEEEEEEEETT.EEEEEEEEEE-TT-S-HHHHHHHHHCC-TTTTEEEEEESSSEETTTEE- CS
                         DUF99   2 eirvlGiddsfferkkkdgksvlvGvvmradrvvdgvafgrvtvdGtDateaiielvkrleredirvvlldGitiagFNvv 82 
                                   +ir lG+dds+f+  + ++ks++vGv+mr d ++++v+ +++t+dG D+te+i ++  +  ++ +rv++l+Gi ++gFN++
  gi|13540868|ref|NP_110556.1|  30 GIRLLGVDDSPFR--RGQQKSFIVGVIMRLDGYIEKVMKAQITIDGNDVTERISNMALKF-KDIVRVIVLSGISFGGFNIC 107
                                   79***********..459**************************************9977.899***************** PP

                                   -HHHHHHHH---EEEEESS---HHHHHHCCT.TSTTHHHHHHHHHHC.---EEETT....EEEEEESS-HHHHHHHHHHC- CS
                         DUF99  83 DlerlheetglPviavtreepdlgklekaLrkhfpdeeeRlelieklgerieevektgeelyvravGieleeaaklvrklt 163
                                   D+e l++ tg+Pvi+++++  + +++ +a++kh+ d+ e++ ++++l ++i+  ++ g++++ + +Gie e a++++r  t
  gi|13540868|ref|NP_110556.1| 108 DIELLFKLTGIPVISLFEKGGSASEMINAINKHLGDQ-EKIGILKRL-KPIALNNN-GYTIMANLAGIESESASRIIRMNT 185
                                   *******************************998665.7********.99998888.************************ PP

                                   SSSSS-HHHHHHHHHHH CS
                         DUF99 164 legriPEPlRvAhliAs 180
                                   ++g++PE++Rv +liA+
  gi|13540868|ref|NP_110556.1| 186 VRGKMPEAVRVPDLIAK 202
                                   ****************8 PP

>> SepF  Cell division protein SepF
   #    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      43      60 ..      49      66 ..      46      72 .. 0.85
   2 ?    8.0   0.0   0.00038       3.4      21      41 ..     161     181 ..     157     185 .. 0.92

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.018
                                  HHHHHHHHCT-EEEEECT CS
                          SepF 43 flsgvvyaldGdiqkvgk 60
                                  f+ gv+  ldG i+kv k
  gi|13540868|ref|NP_110556.1| 49 FIVGVIMRLDGYIEKVMK 66
                                  899************986 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00038
                                   TT-EEEEE-CCCTCHHHHHHH CS
                          SepF  21 egkiVilnledldkeeakriv 41 
                                   +g++++ nl ++++e+a ri+
  gi|13540868|ref|NP_110556.1| 161 NGYTIMANLAGIESESASRII 181
                                   89******************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       512  (0.0285571); 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:                         2  (0.000111551); expected 0.2 (1e-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: 1392.21
//
Query:       gi|13540869|ref|NP_110557.1|  [L=92]
Description: hypothetical protein TVN0038 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       342  (0.0190752); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 587.70
//
Query:       gi|13540870|ref|NP_110558.1|  [L=170]
Description: hypothetical protein TVN0039 [Thermoplasma volcanium GSS1]
Scores for complete 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-14   52.9   0.4    7.1e-14   52.6   0.4    1.2  1  Hemerythrin    Hemerythrin HHE cation binding domain
  ------ inclusion threshold ------
      0.079   12.8   0.1        0.1   12.4   0.1    1.3  1  Vac_ImportDeg  Vacuolar import and degradation protein
       0.13   12.1   0.0       0.15   11.8   0.0    1.3  1  BCDHK_Adom3    Mitochondrial branched-chain alpha-ketoacid de


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 !   52.6   0.4   1.2e-17   7.1e-14       3     130 ..       5     123 ..       3     124 .. 0.92

  Alignments for each domain:
  == domain 1  score: 52.6 bits;  conditional E-value: 1.2e-17
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHCCHHHHHHHHHHHHHHHHHHHHHHCHHHHH......CCC.HHHHHHHHH CS
                   Hemerythrin   3 vealdeeHralrallerlraladaaaevhgalrklaelldelvdeleaHhaaEEellfPlle.....drpggravldvler 78 
                                   +e+l+ eH  +r l + l    d+       l+ ++ + d+lv++   H ++EE++lfP++      d+++++a++++ ++
  gi|13540870|ref|NP_110558.1|   5 AELLMVEHTSIRLLSNFLY-GKDS-------LEIFEGFNDYLVKD---HVEIEEKILFPVIVdvdyeDKDQFKATVERIKN 74 
                                   7889999999999999765.4444.......78888888888887...********************************* PP

                                   HHHHHHHHHHHHHHHCHTCGGSTCHHHHHHHHHHHHHHHHHHHHHHHTHHHH CS
                   Hemerythrin  79 eHdeirelleelrellkgleepsaaafaelleeladllreHiakEesilfpl 130
                                   +H+ i+ l+ +l ++ ++ +   ++ f  +l  +++ l +H+  Ee+++fp+
  gi|13540870|ref|NP_110558.1|  75 DHRLIETLATNLIKWKRDGD---DDKFMLRLPLFYKTLTDHNSSEEELIFPR 123
                                   ********************...****************************6 PP

>> Vac_ImportDeg  Vacuolar import and degradation protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   1.7e-05       0.1      64     134 ..      80     166 ..      55     170 .] 0.65

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.7e-05
                 Vac_ImportDeg  64 ysfltkkkkwkaseetDlehWkkleafkkllak.dlenkelifmrwk............ekflvpde..........rvks 121
                                    +++t+  kwk + + D ++  +l+ f k l++ + +++elif rwk            e      +             +
  gi|13540870|ref|NP_110558.1|  80 ETLATNLIKWKRDGD-DDKFMLRLPLFYKTLTDhNSSEEELIFPRWKnidpelqkdalkE------AisiidtvnrdLYVR 153
                                   467788999987755.56889999998765554499999********5544444333332......033333233323334 PP

                 Vac_ImportDeg 122 iegasfeGfYYiv 134
                                   ++g+s +  YYi+
  gi|13540870|ref|NP_110558.1| 154 VTGISKDFIYYIS 166
                                   6777777777776 PP

>> BCDHK_Adom3  Mitochondrial branched-chain alpha-ketoacid dehydrogenase kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   2.6e-05      0.15      75     112 ..      58      94 ..       9     117 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.6e-05
                   BCDHK_Adom3  75 eleenekftelLekikkrHddvvttlaqGvlelkekrk 112
                                   + e++++f  ++e+ik++H+  ++tla  ++++k++ +
  gi|13540870|ref|NP_110558.1|  58 DYEDKDQFKATVERIKNDHR-LIETLATNLIKWKRDGD 94 
                                   367799*************6.79***********8743 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       505  (0.0281667); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 1019.40
//
Query:       gi|13540871|ref|NP_110559.1|  [L=94]
Description: hypothetical protein TVN0040 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.4e-05   23.4   2.6    7.3e-05   23.2   2.6    1.2  1  Rubrerythrin  Rubrerythrin
  ------ inclusion threshold ------
      0.014   15.6   0.2      0.024   14.8   0.2    1.4  1  Death         Death domain
      0.017   15.4   0.4      0.029   14.7   0.3    1.4  1  DUF2383       Domain of unknown function (DUF2383)
       0.03   14.1   0.3      0.032   14.0   0.3    1.2  1  COQ7          Ubiquinone biosynthesis protein COQ7
      0.054   13.5   0.0      0.059   13.4   0.0    1.1  1  DUF1326       Protein of unknown function (DUF1326)


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 !   23.2   2.6     2e-08   7.3e-05       6      61 ..      23      76 ..       5      91 .. 0.85

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 2e-08
                                  HHHHHHHHHHHHHHHHHCHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTHH CS
                  Rubrerythrin  6 AiagEssarrlYkelaekakegypqiaelFeelAeeEreHakilnklleklepele 61
                                  +++ E++a+++Y e a+ +k   ++++ ++e   ++E+eHa++l ++++  +p  +
  gi|13540871|ref|NP_110559.1| 23 SLIEEIEAMMFYDERADATK--DEDLKYIMEHNRDDEKEHAALLLEWIRRHDPAMD 76
                                  77889999999999999999..9999999999999999999999999999888877 PP

>> Death  Death domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.2   6.8e-06     0.024      28      70 ..      42      83 ..      37      90 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 6.8e-06
                                  HHHHHHHHHHSSSTHHHHHHHHHHHHHHHHTTTCSHHHHHHHH CS
                         Death 28 seeeidriekennslrsqsyalLqlWedregenatvgtLleaL 70
                                  ++e++++i ++n++  +   alL +W+ r+ + a  ++L+e+L
  gi|13540871|ref|NP_110559.1| 42 KDEDLKYIMEHNRDDEKEHAALLLEWIRRH-DPAMDKELHEIL 83
                                  6899*************************9.666677787777 PP

>> DUF2383  Domain of unknown function (DUF2383)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.3     8e-06     0.029       7      58 ..      22      72 ..      16      79 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 8e-06
                                  HHHHHHHHHHHHHHHHHHHT--SHHHHHHHHHHHHHHHHHHHHHHHHHHHCT CS
                       DUF2383  7 ndLietlkdgeegykeaaekvkdpqlktlleriaeereeaaeeLqseiralg 58
                                  ++Lie ++ ++ +y+e a+  kd++lk ++e+  ++ +e+a+ L + ir++ 
  gi|13540871|ref|NP_110559.1| 22 QSLIE-EIEAMMFYDERADATKDEDLKYIMEHNRDDEKEHAALLLEWIRRHD 72
                                  56666.467999**********************************999985 PP

>> COQ7  Ubiquinone biosynthesis protein COQ7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.3   9.1e-06     0.032      13      59 ..      27      71 ..       8      83 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 9.1e-06
                          COQ7 13 ElgAvaiYkgqlavlakkdpelkpllkemleqEkeHlatfeellker 59
                                  E+ A + Y+  +++  +kd++lk ++++  ++EkeH a++ e ++++
  gi|13540871|ref|NP_110559.1| 27 EIEAMMFYDERADA--TKDEDLKYIMEHNRDDEKEHAALLLEWIRRH 71
                                  77788888888888..6888888999999999999998888888777 PP

>> DUF1326  Protein of unknown function (DUF1326)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   1.7e-05     0.059      59      97 ..      27      65 ..      17      80 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.7e-05
                       DUF1326 59 nwkavlliDerAddeqreALeaifsGeaggplavlaslv 97
                                  +++a+++ DerAd+++ e L+ i++++  ++ +  a l+
  gi|13540871|ref|NP_110559.1| 27 EIEAMMFYDERADATKDEDLKYIMEHNRDDEKEHAALLL 65
                                  57899*********************9988866666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1063  (0.0592894); expected 358.6 (0.02)
Passed bias filter:                      541  (0.0301746); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-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 0.31s 00:00:00.78 Elapsed: 00:00:00.49
# Mc/sec: 571.26
//
Query:       gi|13540872|ref|NP_110560.1|  [L=199]
Description: regulator of amino acid metabolism [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00043   20.0   0.0     0.0012   18.6   0.0    1.7  2  HTH_23    Homeodomain-like domain
     0.0011   18.9   0.0     0.0045   16.9   0.0    2.0  2  HTH_11    HTH domain
     0.0017   18.3   0.0     0.0032   17.4   0.0    1.4  1  HTH_29    Winged helix-turn helix
     0.0022   18.2   0.0     0.0042   17.3   0.0    1.6  1  UPF0122   Putative helix-turn-helix protein, YlxM / p13 like
     0.0097   16.0   0.4      0.041   13.9   0.1    2.1  2  HTH_7     Helix-turn-helix domain of resolvase
  ------ inclusion threshold ------
      0.033   14.3   0.0      0.081   13.1   0.0    1.6  1  HTH_28    Helix-turn-helix domain
      0.042   13.9   0.1       0.32   11.1   0.1    2.3  1  HTH_22    HTH domain
      0.076   12.7   0.0        1.4    8.6   0.0    2.2  1  GntR      Bacterial regulatory proteins, gntR family
      0.082   13.5   0.1         11    6.7   0.0    3.0  3  ACT_4     ACT domain
      0.082   12.7   0.0       0.22   11.4   0.0    1.8  1  HTH_10    HTH DNA binding domain
       0.11   12.4   0.0       0.22   11.5   0.0    1.5  1  HTH_36    Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       4.1   6.6e+03      10      22 ..      18      31 ..      14      31 .. 0.55
   2 !   18.6   0.0   7.2e-07    0.0012      18      40 ..      41      63 ..      35      69 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 4.1
                        HTH_23 10 illllae.Glsvre 22
                                  i+  l + G+sv+e
  gi|13540872|ref|NP_110560.1| 18 IIEGLYRsGISVKE 31
                                  55444444887775 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 7.2e-07
                        HTH_23 18 lsvreIAreLgvsrrTvyrwlkr 40
                                  +s++eIA+ +gv+r Tvy  +k 
  gi|13540872|ref|NP_110560.1| 41 ISISEIAKTFGVNRKTVYDTVKL 63
                                  79****************99997 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   2.8e-06    0.0045      11      39 ..      36      64 ..      33      69 .. 0.86
   2 ?   -1.9   0.0       2.1   3.4e+03      31      36 ..     106     111 ..     106     123 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.8e-06
                        HTH_11 11 eargpisgeeLAeeLnvSrrtvrrdIkaL 39
                                  +++  is++e+A+ ++v r+tv+  +k  
  gi|13540872|ref|NP_110560.1| 36 ANDVEISISEIAKTFGVNRKTVYDTVKLV 64
                                  56667******************999976 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.1
                        HTH_11  31 tvrrdI 36 
                                   tv++d+
  gi|13540872|ref|NP_110560.1| 106 TVWKDV 111
                                   899997 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0     2e-06    0.0032      13      37 ..      42      65 ..      30      72 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2e-06
                        HTH_29 13 stvsqiAkllglsrrtvyrwlkrfe 37
                                  s +s+iAk  g+ r+tvy+++k+ e
  gi|13540872|ref|NP_110560.1| 42 S-ISEIAKTFGVNRKTVYDTVKLVE 65
                                  4.9*******************965 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 !   17.3   0.0   2.6e-06    0.0042      33      58 ..      40      65 ..      10      76 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2.6e-06
                       UPF0122 33 DlSlsEiAeefnvsrqavydnikrte 58
                                  ++S+sEiA +f v+r++vyd++k +e
  gi|13540872|ref|NP_110560.1| 40 EISISEIAKTFGVNRKTVYDTVKLVE 65
                                  479*******************9765 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 ?   -1.4   0.0       1.5   2.5e+03      17      25 ..      22      30 ..      13      31 .. 0.83
   2 !   13.9   0.1   2.5e-05     0.041      22      39 ..      41      58 ..      40      58 .. 0.97

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.5
                                  STTTT--ST CS
                         HTH_7 17 LleeGisis 25
                                  L+++Gis++
  gi|13540872|ref|NP_110560.1| 22 LYRSGISVK 30
                                  899999987 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 2.5e-05
                                  --STTTSSSS---SSSS- CS
                         HTH_7 22 isiskIAkevnisRsTvY 39
                                  isis+IAk +++ R TvY
  gi|13540872|ref|NP_110560.1| 41 ISISEIAKTFGVNRKTVY 58
                                  79**************** PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0     5e-05     0.081      14      35 ..      42      63 ..      34      68 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5e-05
                        HTH_28 14 svreaArelgisrrtvyrWikr 35
                                  s++e+A+ +g++r tvy+ +k 
  gi|13540872|ref|NP_110560.1| 42 SISEIAKTFGVNRKTVYDTVKL 63
                                  99***************97775 PP

>> HTH_22  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1    0.0002      0.32      41      60 ..      40      59 ..      11      62 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0002
                        HTH_22 41 kgavekvAekLgiSraTvYr 60
                                    +++++A+ +g+ r TvY 
  gi|13540872|ref|NP_110560.1| 40 EISISEIAKTFGVNRKTVYD 59
                                  5699***************7 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.0   0.00085       1.4      24      41 ..      41      57 ..      11      72 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00085
                                  ---HHHHHHHHTS-HHHH CS
                          GntR 24 LPsereLaaefgVsrttv 41
                                  + s +e+a+ fgV+r tv
  gi|13540872|ref|NP_110560.1| 41 I-SISEIAKTFGVNRKTV 57
                                  6.789************9 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0    0.0067        11      56      78 ..      64      86 ..      35      87 .. 0.90
   2 ?    3.0   0.0     0.093   1.5e+02      18      48 ..     106     136 ..      96     141 .. 0.86
   3 ?   -0.8   0.1       1.4   2.3e+03      63      78 ..     147     162 ..     147     163 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0067
                         ACT_4 56 VkdvehLsrviakLraipgVisV 78
                                  V+  +hL+rv++++  + +V +V
  gi|13540872|ref|NP_110560.1| 64 VEGNSHLKRVMESIMPMADVSNV 86
                                  8899*************999988 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.093
                         ACT_4  18 glLaditqviseekanivsvnaktrkkdgla 48 
                                    +++d+  +is+ +  i+++ +++ ++d+ +
  gi|13540872|ref|NP_110560.1| 106 TVWKDVFMAISKYGCYIREIFSRNMSQDESF 136
                                   6899****************99998886555 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 1.4
                         ACT_4  63 srviakLraipgVisV 78 
                                   +++i++++ai+g  +V
  gi|13540872|ref|NP_110560.1| 147 QKIIDQIKAIDGARNV 162
                                   5899*****9997777 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00013      0.22      17      48 ..      34      65 ..      28      78 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00013
                        HTH_10 17 YFdyPRrvtlkeLAkelGIskstlsehLrkae 48
                                  +F  + +++++e+Ak++G+ + t+++ ++ +e
  gi|13540872|ref|NP_110560.1| 34 FFANDVEISISEIAKTFGVNRKTVYDTVKLVE 65
                                  56666789****************99877655 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00013      0.22      17      50 ..      35      65 ..      27      70 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00013
                        HTH_36 17 fanknggcfpsqetlakrlglsknTvsraikeLe 50
                                  fan+ ++   s + +ak +g++++Tv+  +k+ e
  gi|13540872|ref|NP_110560.1| 35 FANDVEI---SISEIAKTFGVNRKTVYDTVKLVE 65
                                  4555555...9****************9999866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       755  (0.0421105); expected 358.6 (0.02)
Passed bias filter:                      568  (0.0316805); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 1208.72
//
Query:       gi|13540873|ref|NP_110561.1|  [L=90]
Description: hypothetical protein TVN0042 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       222  (0.0123822); expected 358.6 (0.02)
Passed bias filter:                      190  (0.0105974); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 595.12
//
Query:       gi|13540874|ref|NP_110562.1|  [L=174]
Description: hypothetical protein TVN0043, partial [Thermoplasma volcanium GSS1]
Scores for complete sequence (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   63.4   0.0      2e-17   62.8   0.0    1.3  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
  ------ inclusion threshold ------
      0.037   14.4   0.0      0.059   13.8   0.0    1.3  1  RuvX            Holliday junction resolvase


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 !   62.8   0.0   2.3e-21     2e-17       2      68 ..      41     108 ..      40     109 .. 0.95

  Alignments for each domain:
  == domain 1  score: 62.8 bits;  conditional E-value: 2.3e-21
                OrfB_Zn_ribbon   2 rklkeqleykakeyGikveevnpayTSktCseCgsknke.alsgrtfkCpnCgfeadrDvnAaiNilk 68 
                                   + ++++ e   +e G+kv++v++a+TSktCs Cg+ +++ + ++ +++C + g ++++D+n+aiNil+
  gi|13540874|ref|NP_110562.1|  41 GYIIRRFEGVGEELGVKVVKVDEAWTSKTCSLCGEAHDDgRIKRGLYRCLRIGKVINADLNGAINILH 108
                                   67788899999****************************9**************************96 PP

>> RuvX  Holliday junction resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   6.6e-06     0.059      40     103 ..       2      71 ..       1      85 [. 0.71

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6.6e-06
                                   HHHHHHHHHHTT--EEEEE------SSS---SS.TTHHHHHHHHHT........T-EEEEE--S----XXX CS
                          RuvX  40 leelkelvkeeeveeiVvGlPlnldgsegesak.kvrkfaeeLakrl......kklpvelvDErlttveae 103
                                   ++++ e +k++ v ei +G+P+++++++g++   ++ ++   + +r+       +++v+ vDE  t+++ +
  gi|13540874|ref|NP_110562.1|   2 VRKIMEEFKNKGVGEIAIGYPKEISKDHGNKLTvNFWNYGYII-RRFegvgeeLGVKVVKVDEAWTSKTCS 71 
                                   678999999**************97776655441444443333.233233444488***********9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       372  (0.0207485); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1202.59
//
Query:       gi|13540875|ref|NP_110563.1|  [L=242]
Description: TPR repeat-containing protein [Thermoplasma volcanium GSS1]
Scores for complete 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  150.9  12.2    3.3e-11   42.5   0.1    6.3  6  TPR_1         Tetratricopeptide repeat
    1.7e-44  146.4   9.2    1.7e-08   34.0   0.0    6.3  6  TPR_2         Tetratricopeptide repeat
    2.3e-38  127.2  14.4      2e-07   30.7   0.1    6.3  6  TPR_8         Tetratricopeptide repeat
    1.6e-37  126.9  18.8    2.2e-11   43.2   0.5    6.3  6  TPR_11        TPR repeat
    4.3e-30  103.8  12.0    3.3e-09   36.9   0.5    5.2  6  TPR_12        Tetratricopeptide repeat
    2.1e-25   89.1   0.9    1.9e-09   38.0   0.1    5.0  5  TPR_16        Tetratricopeptide repeat
    1.6e-22   78.2   0.1     0.0011   19.6   0.0    6.1  6  TPR_14        Tetratricopeptide repeat
    5.8e-22   78.0   5.6    1.1e-09   38.6   0.2    3.4  3  TPR_19        Tetratricopeptide repeat
    1.8e-20   72.8   0.2    7.7e-05   22.8   0.0    4.9  5  TPR_9         Tetratricopeptide repeat
    1.9e-20   71.7  10.9    6.1e-06   26.3   0.0    6.9  7  TPR_17        Tetratricopeptide repeat
    1.1e-18   65.8   3.0     0.0017   18.3   0.0    6.1  6  TPR_7         Tetratricopeptide repeat
    5.8e-16   57.8   7.7     0.0014   18.4   0.1    6.3  6  TPR_10        Tetratricopeptide repeat
    1.1e-15   57.1   4.8     0.0028   18.2   0.1    6.3  6  TPR_6         Tetratricopeptide repeat
    4.7e-15   55.6   4.8    0.00017   21.7   0.1    3.6  4  ANAPC3        Anaphase-promoting complex, cyclosome, subunit 
    7.2e-14   51.6   6.3    5.6e-07   28.8   0.1    3.0  3  NARP1         NMDA receptor-regulated protein 1
    4.9e-07   29.7  12.4      0.008   16.0   0.4    3.6  3  DUF5113       Domain of unknown function (DUF5113)
    2.4e-06   27.4   5.4       0.99    9.5   0.0    6.2  6  TPR_3         Tetratricopeptide repeat
    2.9e-06   27.3  13.2       0.11   12.5   0.2    5.5  6  Fis1_TPR_C    Fis1 C-terminal tetratricopeptide repeat
      3e-06   26.6   3.2       0.63    9.5   0.1    5.2  5  SHNi-TPR      SHNi-TPR
    1.1e-05   25.5   1.9       0.12   12.4   0.1    4.1  4  DUF3856       Domain of Unknown Function (DUF3856)
    5.1e-05   23.3  10.9     0.0045   17.0   1.4    2.9  3  SRP_TPR_like  Putative TPR-like repeat
    7.8e-05   22.2   5.3       0.41   10.3   0.0    5.2  5  HTH_Bact      Helix-turn-helix bacterial domain
    8.8e-05   23.0   0.1       0.63   10.5   0.0    2.8  2  BTAD          Bacterial transcriptional activator domain
     0.0002   21.7   0.0         16    6.5   0.0    5.0  5  TPR_4         Tetratricopeptide repeat
    0.00052   19.8   7.0        4.4    7.0   0.2    4.2  3  RPN7          26S proteasome subunit RPN7
    0.00064   18.8   0.1       0.27   10.2   0.0    2.3  2  ChAPs         ChAPs (Chs5p-Arf1p-binding proteins)
     0.0016   18.9   6.0         14    6.3   0.0    5.0  5  DUF4810       Domain of unknown function (DUF4810)
     0.0016   18.2   4.5      0.034   13.9   0.3    3.5  4  TPR_21        Tetratricopeptide repeat-like domain
     0.0018   17.9   0.1     0.0027   17.3   0.1    1.3  1  HrpB1_HrpK    Bacterial type III secretion protein (HrpB1_Hrp
     0.0021   18.4   0.9        1.5    9.2   0.0    3.7  4  TPR_20        Tetratricopeptide repeat
     0.0047   17.0   7.9         10    6.3   0.1    5.2  4  MIT           MIT (microtubule interacting and transport) dom
      0.005   16.5   5.2        7.6    6.3   0.1    4.7  6  SPOB_a        Sensor_kinase_SpoOB-type, alpha-helical domain
     0.0065   16.6   0.6         60    4.2   0.0    4.9  5  PPR           PPR repeat
  ------ inclusion threshold ------
      0.016   15.3   0.0        7.6    6.6   0.0    3.2  4  MAS20         MAS20 protein import receptor
      0.028   13.0   0.8       0.17   10.4   0.1    2.0  2  DUF1347       Protein of unknown function (DUF1347)
      0.054   13.4   0.4       0.49   10.3   0.1    2.4  2  PaREP1        Archaeal PaREP1/PaREP8 family


Domain annotation for each model (and alignments):
>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0   2.3e-08   1.1e-05       2      30 ..      23      51 ..      22      55 .. 0.91
   2 !   42.5   0.1   6.5e-14   3.3e-11       1      33 [.      56      88 ..      56      89 .. 0.97
   3 !   24.0   0.1   4.6e-08   2.3e-05       2      31 ..      91     120 ..      90     123 .. 0.92
   4 !   37.2   0.4   3.1e-12   1.6e-09       2      31 ..     125     154 ..     124     154 .. 0.94
   5 !   14.4   0.0   4.9e-05     0.025      10      32 ..     167     189 ..     166     191 .. 0.89
   6 !   11.6   0.2   0.00038      0.19       6      34 .]     197     225 ..     192     225 .. 0.90

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 2.3e-08
                                  HHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                         TPR_1  2 kalynlGnayfklgkydeAleyyekALel 30
                                  + ++ +G  yf+ gkyd+A+e + kA+++
  gi|13540875|ref|NP_110563.1| 23 DDYNERGISYFNIGKYDKAVEEFTKAISI 51
                                  569************************97 PP

  == domain 2  score: 42.5 bits;  conditional E-value: 6.5e-14
                                  HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                         TPR_1  1 akalynlGnayfklgkydeAleyyekALelnPn 33
                                  a+ + n+G+ay++++ yd+A+e++e+ ++l+Pn
  gi|13540875|ref|NP_110563.1| 56 ADLYHNRGMAYYSMKAYDQAIEDFERSISLDPN 88
                                  789*****************************9 PP

  == domain 3  score: 24.0 bits;  conditional E-value: 4.6e-08
                                   HHHHHHHHHHHHTT-HHHHHHHHHHHHHHS CS
                         TPR_1   2 kalynlGnayfklgkydeAleyyekALeln 31 
                                   + ++ lG +y  +g+y++Ale ++ A++l+
  gi|13540875|ref|NP_110563.1|  91 DYHNALGSVYEDMGNYEKALEEFNSAIRLE 120
                                   67999**********************997 PP

  == domain 4  score: 37.2 bits;  conditional E-value: 3.1e-12
                                   HHHHHHHHHHHHTT-HHHHHHHHHHHHHHS CS
                         TPR_1   2 kalynlGnayfklgkydeAleyyekALeln 31 
                                   + +yn+Gn+y klg+ ++A+++y+kA  l+
  gi|13540875|ref|NP_110563.1| 125 DYYYNRGNVYWKLGEIEKAIQDYSKAADLD 154
                                   78************************9887 PP

  == domain 5  score: 14.4 bits;  conditional E-value: 4.9e-05
                                   HHHHTT-HHHHHHHHHHHHHHST CS
                         TPR_1  10 ayfklgkydeAleyyekALelnP 32 
                                   a+ +lg+ydeAle  +kA+++ P
  gi|13540875|ref|NP_110563.1| 167 ALTSLGRYDEALETVDKAIKVVP 189
                                   6889***************9876 PP

  == domain 6  score: 11.6 bits;  conditional E-value: 0.00038
                                   HHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                         TPR_1   6 nlGnayfklgkydeAleyyekALelnPnn 34 
                                    ++ ++ k+++y+eA    e++ +lnP n
  gi|13540875|ref|NP_110563.1| 197 MKAELLIKMKRYEEARPVIEEVEKLNPGN 225
                                   689999*********************87 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.0   3.2e-08   1.6e-05       2      30 ..      23      51 ..      22      55 .. 0.90
   2 !   34.0   0.0   3.4e-11   1.7e-08       1      33 [.      56      88 ..      56      89 .. 0.96
   3 !   26.4   0.1     9e-09   4.5e-06       2      32 ..      91     121 ..      90     123 .. 0.93
   4 !   31.4   0.3   2.3e-10   1.1e-07       1      33 [.     124     156 ..     124     157 .. 0.93
   5 !   13.4   0.0   0.00013     0.065      10      34 .]     167     191 ..     166     191 .. 0.88
   6 !   17.6   0.1   5.9e-06     0.003       3      34 .]     194     225 ..     192     225 .. 0.93

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 3.2e-08
                         TPR_2  2 ealynlGlayyklgdyeeAleafekAlel 30
                                  + ++++G +y++ g+y++A+e f kA+++
  gi|13540875|ref|NP_110563.1| 23 DDYNERGISYFNIGKYDKAVEEFTKAISI 51
                                  6799***********************98 PP

  == domain 2  score: 34.0 bits;  conditional E-value: 3.4e-11
                         TPR_2  1 aealynlGlayyklgdyeeAleafekAleldPn 33
                                  a++++n+G+ayy ++ y++A+e+fe++++ldPn
  gi|13540875|ref|NP_110563.1| 56 ADLYHNRGMAYYSMKAYDQAIEDFERSISLDPN 88
                                  789*****************************9 PP

  == domain 3  score: 26.4 bits;  conditional E-value: 9e-09
                         TPR_2   2 ealynlGlayyklgdyeeAleafekAleldP 32 
                                   +++++lG +y+ +g+ye+Ale f+ A++l+ 
  gi|13540875|ref|NP_110563.1|  91 DYHNALGSVYEDMGNYEKALEEFNSAIRLED 121
                                   689*************************976 PP

  == domain 4  score: 31.4 bits;  conditional E-value: 2.3e-10
                         TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPn 33 
                                   ++++yn+G++y+klg+ e+A++++ kA  ld +
  gi|13540875|ref|NP_110563.1| 124 PDYYYNRGNVYWKLGEIEKAIQDYSKAADLDYT 156
                                   589***************************976 PP

  == domain 5  score: 13.4 bits;  conditional E-value: 0.00013
                         TPR_2  10 ayyklgdyeeAleafekAleldPnn 34 
                                   a+  lg+y+eAle  +kA++  P n
  gi|13540875|ref|NP_110563.1| 167 ALTSLGRYDEALETVDKAIKVVPAN 191
                                   56689***************99876 PP

  == domain 6  score: 17.6 bits;  conditional E-value: 5.9e-06
                         TPR_2   3 alynlGlayyklgdyeeAleafekAleldPnn 34 
                                   +l + +++++k+++yeeA+   e++ +l+P+n
  gi|13540875|ref|NP_110563.1| 194 YLAMKAELLIKMKRYEEARPVIEEVEKLNPGN 225
                                   677899************************97 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   1.5e-06   0.00074       4      33 ..      25      54 ..      25      55 .. 0.90
   2 !   30.7   0.1     4e-10     2e-07       1      33 [.      56      88 ..      56      89 .. 0.96
   3 !   23.8   0.1   6.6e-08   3.3e-05       2      31 ..      91     120 ..      90     123 .. 0.91
   4 !   29.4   0.3   1.1e-09   5.2e-07       2      31 ..     125     154 ..     124     157 .. 0.93
   5 !   10.7   0.0     0.001      0.52      10      30 ..     167     187 ..     166     191 .. 0.86
   6 !   19.0   0.1   2.3e-06    0.0011       3      33 ..     194     224 ..     192     225 .. 0.93

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.5e-06
                                  HHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                         TPR_8  4 yynlgsiylklgdyeeAkeyyekaleldpd 33
                                  y+  g  y++ g+y++A+e + ka+++  d
  gi|13540875|ref|NP_110563.1| 25 YNERGISYFNIGKYDKAVEEFTKAISIIND 54
                                  7778999*******************9766 PP

  == domain 2  score: 30.7 bits;  conditional E-value: 4e-10
                                  CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                         TPR_8  1 aeayynlgsiylklgdyeeAkeyyekaleldpd 33
                                  a++y+n g++y +++ y++A+e +e+ ++ldp+
  gi|13540875|ref|NP_110563.1| 56 ADLYHNRGMAYYSMKAYDQAIEDFERSISLDPN 88
                                  689*****************************8 PP

  == domain 3  score: 23.8 bits;  conditional E-value: 6.6e-08
                                   CHHHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
                         TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleld 31 
                                   ++++ lgs+y+++g+ye+A e ++ a++l+
  gi|13540875|ref|NP_110563.1|  91 DYHNALGSVYEDMGNYEKALEEFNSAIRLE 120
                                   57899**********************997 PP

  == domain 4  score: 29.4 bits;  conditional E-value: 1.1e-09
                                   CHHHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
                         TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleld 31 
                                   ++yyn g++y+klg++e+A++ y ka +ld
  gi|13540875|ref|NP_110563.1| 125 DYYYNRGNVYWKLGEIEKAIQDYSKAADLD 154
                                   69*************************998 PP

  == domain 5  score: 10.7 bits;  conditional E-value: 0.001
                                   HHHHTT-HHHHHHHHHHHHHH CS
                         TPR_8  10 iylklgdyeeAkeyyekalel 30 
                                   ++ +lg+y+eA e+  ka++ 
  gi|13540875|ref|NP_110563.1| 167 ALTSLGRYDEALETVDKAIKV 187
                                   5779***************96 PP

  == domain 6  score: 19.0 bits;  conditional E-value: 2.3e-06
                                   HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                         TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                   ++ +++ +++k+++yeeA  ++e++ +l+p 
  gi|13540875|ref|NP_110563.1| 194 YLAMKAELLIKMKRYEEARPVIEEVEKLNPG 224
                                   7899*************************96 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.7   0.2   2.1e-11     1e-08       3      41 ..      31      69 ..      29      70 .. 0.94
   2 !   34.9   0.0   1.8e-11     9e-09       3      42 .]      65     104 ..      64     104 .. 0.98
   3 !   43.2   0.5   4.4e-14   2.2e-11       7      42 .]     103     138 ..     102     138 .. 0.97
   4 !   14.8   0.8   3.3e-05     0.016       6      24 ..     136     154 ..     136     163 .. 0.90
   5 !   14.7   0.1   3.6e-05     0.018       3      28 ..     167     192 ..     166     196 .. 0.91
   6 ?    5.6   0.0     0.025        12       4      38 ..     202     236 ..     199     239 .. 0.83

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 2.1e-11
                        TPR_11  3 ayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykq 41
                                   y+  Gky++A+e++ kA+ + +d+a++y+n+G ayy +
  gi|13540875|ref|NP_110563.1| 31 SYFNIGKYDKAVEEFTKAISIINDDADLYHNRGMAYYSM 69
                                  59999********************************76 PP

  == domain 2  score: 34.9 bits;  conditional E-value: 1.8e-11
                        TPR_11   3 ayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                   ayy+   y++Aie++++ + ldP++ + +++LG +y  +G
  gi|13540875|ref|NP_110563.1|  65 AYYSMKAYDQAIEDFERSISLDPNSSDYHNALGSVYEDMG 104
                                   7************************************998 PP

  == domain 3  score: 43.2 bits;  conditional E-value: 4.4e-14
                        TPR_11   7 qGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                    G+ye+A+e+++ A++l  d ++ yyn+G++y+k+G
  gi|13540875|ref|NP_110563.1| 103 MGNYEKALEEFNSAIRLEDDLPDYYYNRGNVYWKLG 138
                                   7*********************************99 PP

  == domain 4  score: 14.8 bits;  conditional E-value: 3.3e-05
                        TPR_11   6 eqGkyeeAieaYkkAlkld 24 
                                   ++G++e+Ai++Y+kA +ld
  gi|13540875|ref|NP_110563.1| 136 KLGEIEKAIQDYSKAADLD 154
                                   58****************9 PP

  == domain 5  score: 14.7 bits;  conditional E-value: 3.6e-05
                        TPR_11   3 ayyeqGkyeeAieaYkkAlkldPdna 28 
                                   a++++G+y+eA+e   kA+k  P n 
  gi|13540875|ref|NP_110563.1| 167 ALTSLGRYDEALETVDKAIKVVPANY 192
                                   7899*******************995 PP

  == domain 6  score: 5.6 bits;  conditional E-value: 0.025
                        TPR_11   4 yyeqGkyeeAieaYkkAlkldPdnaeayynLGlay 38 
                                   + +  +yeeA  + ++  kl+P n++a   ++++ 
  gi|13540875|ref|NP_110563.1| 202 LIKMKRYEEARPVIEEVEKLNPGNPDAARLMAQIN 236
                                   567789********************977766665 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   0.0   3.7e-10   1.9e-07       6      75 ..      25      86 ..      20      88 .. 0.91
   2 !   36.9   0.5   6.6e-12   3.3e-09       3      74 ..      56     119 ..      54     122 .. 0.93
   3 !   32.4   0.3   1.7e-10   8.7e-08       7      74 ..      93     153 ..      88     156 .. 0.81
   4 !   20.4   0.1   9.4e-07   0.00047       6      73 ..     127     186 ..     122     187 .. 0.85
   5 !   14.3   0.0   7.5e-05     0.037      12      71 ..     167     218 ..     158     221 .. 0.84
   6 ?    6.9   0.0     0.015       7.5       9      47 ..     198     231 ..     190     235 .. 0.74

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 3.7e-10
                        TPR_12  6 lnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaia 75
                                  +n+++  ++  g+yd+A e + ka+ i+      d    a  ++n g++y+ ++ y++A+e +e+++ ++
  gi|13540875|ref|NP_110563.1| 25 YNERGISYFNIGKYDKAVEEFTKAISII-----ND---DADLYHNRGMAYYSMKAYDQAIEDFERSISLD 86
                                  567999**********************.....55...4899************************9876 PP

  == domain 2  score: 36.9 bits;  conditional E-value: 6.6e-12
                        TPR_12   3 atalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                   a +++n++++++ ++ yd+A+e +e+++ +      p++   + + ++Lg +y+ +g+ye+Ale ++ a+++
  gi|13540875|ref|NP_110563.1|  56 ADLYHNRGMAYYSMKAYDQAIEDFERSISLD-----PNS---SDYHNALGSVYEDMGNYEKALEEFNSAIRL 119
                                   7899***********************8888.....775...8899**********************9986 PP

  == domain 3  score: 32.4 bits;  conditional E-value: 1.7e-10
                        TPR_12   7 nn.laavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                   +n l++v+  +g+y++Ale ++ a+++   l  pd      +++n g +y++lg+ e+A++ + +a ++
  gi|13540875|ref|NP_110563.1|  93 HNaLGSVYEDMGNYEKALEEFNSAIRLEDDL--PD------YYYNRGNVYWKLGEIEKAIQDYSKAADL 153
                                   444*********************7777555..44......5888888888888888888888888765 PP

  == domain 4  score: 20.4 bits;  conditional E-value: 9.4e-07
                        TPR_12   6 lnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleeala 73 
                                   ++n+++v+++lg+ ++A++ + ka ++        + + + ++  +  l   lgry+eAle   +a++
  gi|13540875|ref|NP_110563.1| 127 YYNRGNVYWKLGEIEKAIQDYSKAADLD-------YTDQIYVYKKYEAL-TSLGRYDEALETVDKAIK 186
                                   78**********************8887.......44578899999888.599999999999888875 PP

  == domain 5  score: 14.3 bits;  conditional E-value: 7.5e-05
                        TPR_12  12 vlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleea 71 
                                   +l+ lgrydeAle  +ka+ ++     p +++   +l   ++l+ +++ryeeA+   ee+
  gi|13540875|ref|NP_110563.1| 167 ALTSLGRYDEALETVDKAIKVV-----PANYN---YLAMKAELLIKMKRYEEARPVIEEV 218
                                   6889**************9999.....55534...7899999999999999999877775 PP

  == domain 6  score: 6.9 bits;  conditional E-value: 0.015
                        TPR_12   9 laavlrrlgrydeAlellekaleiarrllGpdhpltatt 47 
                                    a++l +++ry+eA+   e++     + l+p +p++a+ 
  gi|13540875|ref|NP_110563.1| 198 KAELLIKMKRYEEARPVIEEVE----K-LNPGNPDAARL 231
                                   6899999999999999988882....2.24666666665 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0     0.038        19       3      24 ..      28      49 ..      22      59 .. 0.74
   2 !   15.6   0.0   3.9e-05     0.019       2      44 ..      61     100 ..      60     101 .. 0.90
   3 !   38.0   0.1   3.8e-12   1.9e-09       2      63 ..      95     153 ..      94     158 .. 0.94
   4 !    8.5   0.0    0.0064       3.2      38      66 ..     162     190 ..     154     192 .. 0.82
   5 !   18.9   0.0   3.5e-06    0.0017       2      39 ..     197     231 ..     196     241 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.038
                        TPR_16  3 laraalragdyddAaaaleaal 24
                                  ++ ++++ g+yd+A++ ++ a+
  gi|13540875|ref|NP_110563.1| 28 RGISYFNIGKYDKAVEEFTKAI 49
                                  4667777777777777776554 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 3.9e-05
                        TPR_16   2 alaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaa 44 
                                   ++++a++  + yd+A++ +e+ + +d   P   + +++lg ++
  gi|13540875|ref|NP_110563.1|  61 NRGMAYYSMKAYDQAIEDFERSISLD---PNSSDYHNALGSVY 100
                                   6899**********************...88888999999876 PP

  == domain 3  score: 38.0 bits;  conditional E-value: 3.8e-12
                        TPR_16   2 alaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalra 63 
                                   al+  + + g+y++A++ ++ a+++     d ++ ++++g++++++g+ ++A++ y +a++ 
  gi|13540875|ref|NP_110563.1|  95 ALGSVYEDMGNYEKALEEFNSAIRLE---DDLPDYYYNRGNVYWKLGEIEKAIQDYSKAADL 153
                                   78999*********************...99999*******************999999875 PP

  == domain 4  score: 8.5 bits;  conditional E-value: 0.0064
                        TPR_16  38 lllgdaalrqgrlaeAaalyraalraapd 66 
                                   + + +a+  +gr++eA++ +++a++  p 
  gi|13540875|ref|NP_110563.1| 162 YKKYEALTSLGRYDEALETVDKAIKVVPA 190
                                   56678999999999999999999877665 PP

  == domain 5  score: 18.9 bits;  conditional E-value: 3.5e-06
                        TPR_16   2 alaraalragdyddAaaaleaalkrdpssPdaaeAlll 39 
                                   ++a ++++ ++y++A+++ e++ k++p+ Pdaa+   l
  gi|13540875|ref|NP_110563.1| 197 MKAELLIKMKRYEEARPVIEEVEKLNPGNPDAAR---L 231
                                   7899**********************77777665...3 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.0    0.0094       4.7       6      38 ..      27      59 ..      22      63 .. 0.85
   2 !   12.1   0.0   0.00059      0.29       4      41 ..      59      96 ..      56      97 .. 0.86
   3 !   14.0   0.0   0.00014     0.071       6      36 ..      95     125 ..      90     129 .. 0.86
   4 !   10.6   0.0    0.0017      0.87       2      31 ..     125     154 ..     124     165 .. 0.84
   5 !   12.9   0.0    0.0003      0.15       9      44 .]     166     201 ..     160     201 .. 0.90
   6 !   19.6   0.0   2.2e-06    0.0011       4      44 .]     195     235 ..     192     235 .. 0.93

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0094
                        TPR_14  6 alaeallalGdpdeAiallrralalaPddaeaw 38
                                  +++  +++ G++d+A++ + +a++   dda+++
  gi|13540875|ref|NP_110563.1| 27 ERGISYFNIGKYDKAVEEFTKAISIINDDADLY 59
                                  688999******************988888776 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00059
                        TPR_14  4 llalaeallalGdpdeAiallrralalaPddaeawlll 41
                                  +  ++ a++    +d+Ai+ ++r ++l+P++ +++ +l
  gi|13540875|ref|NP_110563.1| 59 YHNRGMAYYSMKAYDQAIEDFERSISLDPNSSDYHNAL 96
                                  55678899999*******************99888766 PP

  == domain 3  score: 14.0 bits;  conditional E-value: 0.00014
                        TPR_14   6 alaeallalGdpdeAiallrralalaPddae 36 
                                   al+++++  G++++A++ ++ a++l  d ++
  gi|13540875|ref|NP_110563.1|  95 ALGSVYEDMGNYEKALEEFNSAIRLEDDLPD 125
                                   89*********************98877665 PP

  == domain 4  score: 10.6 bits;  conditional E-value: 0.0017
                        TPR_14   2 eallalaeallalGdpdeAiallrralala 31 
                                   + ++ ++ +++ lG+ ++Ai+ + +a +l+
  gi|13540875|ref|NP_110563.1| 125 DYYYNRGNVYWKLGEIEKAIQDYSKAADLD 154
                                   568889***************999998764 PP

  == domain 5  score: 12.9 bits;  conditional E-value: 0.0003
                        TPR_14   9 eallalGdpdeAiallrralalaPddaeawlllaql 44 
                                   eal  lG++deA++  ++a++  P++  ++ + a+l
  gi|13540875|ref|NP_110563.1| 166 EALTSLGRYDEALETVDKAIKVVPANYNYLAMKAEL 201
                                   78999*********************9999999876 PP

  == domain 6  score: 19.6 bits;  conditional E-value: 2.2e-06
                        TPR_14   4 llalaeallalGdpdeAiallrralalaPddaeawlllaql 44 
                                   l++ ae+l    +++eA+ + +++ +l+P++++a +l+aq+
  gi|13540875|ref|NP_110563.1| 195 LAMKAELLIKMKRYEEARPVIEEVEKLNPGNPDAARLMAQI 235
                                   56779**********************************96 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0   1.6e-07   7.8e-05       5      65 ..      36      96 ..      35      99 .. 0.97
   2 !   17.8   0.2   7.2e-06    0.0036       3      57 ..     102     156 ..     100     168 .. 0.87
   3 !   38.6   0.2   2.3e-12   1.1e-09       5      68 .]     172     235 ..     168     235 .. 0.97

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 1.6e-07
                        TPR_19  5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddaryasLl 65
                                  g+y+ A++ +++a++  +++a++  +   a+++++ +d+A++  ++    dp++++y+++l
  gi|13540875|ref|NP_110563.1| 36 GKYDKAVEEFTKAISIINDDADLYHNRGMAYYSMKAYDQAIEDFERSISLDPNSSDYHNAL 96
                                  89********************************************************987 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 7.2e-06
                        TPR_19   3 aegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpd 57 
                                   ++g+y+ Al+ + +a+  + + ++  ++  +++++lg++++A++  +++ + d  
  gi|13540875|ref|NP_110563.1| 102 DMGNYEKALEEFNSAIRLEDDLPDYYYNRGNVYWKLGEIEKAIQDYSKAADLDYT 156
                                   69****************************************9866666666555 PP

  == domain 3  score: 38.6 bits;  conditional E-value: 2.3e-12
                        TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddaryasLlAkl 68 
                                   g+y+eAl+   +a++  p n + ++  Ae+l+++++++eA+ +++++ + +p ++++a+L+A++
  gi|13540875|ref|NP_110563.1| 172 GRYDEALETVDKAIKVVPANYNYLAMKAELLIKMKRYEEARPVIEEVEKLNPGNPDAARLMAQI 235
                                   9************************9*************************************7 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.0    0.0028       1.4      29      64 ..      22      57 ..      17      59 .. 0.87
   2 !   22.8   0.0   1.5e-07   7.7e-05      26      65 ..      53      92 ..      48      96 .. 0.90
   3 !   17.8   0.0   5.6e-06    0.0028      19      64 ..      80     125 ..      80     127 .. 0.94
   4 !   20.7   0.0     7e-07   0.00035       3      60 ..      98     155 ..      96     160 .. 0.90
   5 !   15.2   0.0   3.7e-05     0.018       9      73 .]     172     236 ..     166     236 .. 0.95

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0028
                         TPR_9 29 peerrdRGlllaqlGclsaAladLeaylalapdapd 64
                                  ++++ +RG+ ++  G + +A++++  ++++  d++d
  gi|13540875|ref|NP_110563.1| 22 ADDYNERGISYFNIGKYDKAVEEFTKAISIINDDAD 57
                                  67889*********************9988777766 PP

  == domain 2  score: 22.8 bits;  conditional E-value: 1.5e-07
                         TPR_9 26 PddpeerrdRGlllaqlGclsaAladLeaylalapdapda 65
                                   dd++++  RG++++ + ++ +A++d+e+ ++l+p+  d 
  gi|13540875|ref|NP_110563.1| 53 NDDADLYHNRGMAYYSMKAYDQAIEDFERSISLDPNSSDY 92
                                  699********************************88775 PP

  == domain 3  score: 17.8 bits;  conditional E-value: 5.6e-06
                         TPR_9  19 erllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapd 64 
                                   er + l+P++ + +   G +++ +G++++Al++++ +++l++d pd
  gi|13540875|ref|NP_110563.1|  80 ERSISLDPNSSDYHNALGSVYEDMGNYEKALEEFNSAIRLEDDLPD 125
                                   7999***********************************9998877 PP

  == domain 4  score: 20.7 bits;  conditional E-value: 7e-07
                         TPR_9   3 aiaireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalap 60 
                                   +++    ++e+al+  ++ + l  d p+ ++ RG ++ +lG +++A++d   +++l+ 
  gi|13540875|ref|NP_110563.1|  98 SVYEDMGNYEKALEEFNSAIRLEDDLPDYYYNRGNVYWKLGEIEKAIQDYSKAADLDY 155
                                   567777899******************************************9999875 PP

  == domain 5  score: 15.2 bits;  conditional E-value: 3.7e-05
                         TPR_9   9 edweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapdaeairaqLn 73 
                                    ++++al++v+  + + P     +   + ll ++ ++++A+   e    l+p +pda++++aq+n
  gi|13540875|ref|NP_110563.1| 172 GRYDEALETVDKAIKVVPANYNYLAMKAELLIKMKRYEEARPVIEEVEKLNPGNPDAARLMAQIN 236
                                   6899***********************************************************97 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.1     0.014       7.2      13      34 .]      22      43 ..      15      43 .. 0.87
   2 !   14.7   0.1   5.8e-05     0.029       2      34 .]      45      77 ..      44      77 .. 0.92
   3 !   26.3   0.0   1.2e-08   6.1e-06       2      34 .]      79     111 ..      78     111 .. 0.96
   4 !    9.9   0.0     0.002      0.98       4      34 .]     115     145 ..     112     145 .. 0.90
   5 ?   -0.5   0.0       4.3   2.2e+03      22      34 .]     167     179 ..     160     179 .. 0.79
   6 !   10.0   0.1    0.0019      0.97       4      33 ..     183     212 ..     181     212 .. 0.96
   7 ?    4.5   0.0      0.11        54       7      26 ..     220     239 ..     218     242 .] 0.82

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.014
                        TPR_17 13 adaynnLAelllknGdlmtArq 34
                                  ad yn+++  + ++G++++A++
  gi|13540875|ref|NP_110563.1| 22 ADDYNERGISYFNIGKYDKAVE 43
                                  788****************975 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 5.8e-05
                        TPR_17  2 ylkaleldPnnadaynnLAelllknGdlmtArq 34
                                  ++ka+ +  ++ad+y+n++ ++++ + +++A++
  gi|13540875|ref|NP_110563.1| 45 FTKAISIINDDADLYHNRGMAYYSMKAYDQAIE 77
                                  789999999***************999999985 PP

  == domain 3  score: 26.3 bits;  conditional E-value: 1.2e-08
                        TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                   +++++ ldPn++d +n L+ +++  G++++A++
  gi|13540875|ref|NP_110563.1|  79 FERSISLDPNSSDYHNALGSVYEDMGNYEKALE 111
                                   89*****************************85 PP

  == domain 4  score: 9.9 bits;  conditional E-value: 0.002
                        TPR_17   4 kaleldPnnadaynnLAelllknGdlmtArq 34 
                                    a++l+ + +d y+n+++++ k+G+ ++A+q
  gi|13540875|ref|NP_110563.1| 115 SAIRLEDDLPDYYYNRGNVYWKLGEIEKAIQ 145
                                   589999999*****************99997 PP

  == domain 5  score: -0.5 bits;  conditional E-value: 4.3
                        TPR_17  22 lllknGdlmtArq 34 
                                   +l ++G++++A++
  gi|13540875|ref|NP_110563.1| 167 ALTSLGRYDEALE 179
                                   4568999999975 PP

  == domain 6  score: 10.0 bits;  conditional E-value: 0.0019
                        TPR_17   4 kaleldPnnadaynnLAelllknGdlmtAr 33 
                                   ka++  P n + + ++Aell k +++++Ar
  gi|13540875|ref|NP_110563.1| 183 KAIKVVPANYNYLAMKAELLIKMKRYEEAR 212
                                   99**************************97 PP

  == domain 7  score: 4.5 bits;  conditional E-value: 0.11
                        TPR_17   7 eldPnnadaynnLAelllkn 26 
                                   +l+P n+da  ++A++  k+
  gi|13540875|ref|NP_110563.1| 220 KLNPGNPDAARLMAQINMKR 239
                                   57************996554 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.0   0.00063      0.31       5      28 ..      28      51 ..      25      57 .. 0.78
   2 !   10.8   0.0   0.00081       0.4       2      33 ..      59      88 ..      58      91 .. 0.83
   3 !   18.3   0.0   3.3e-06    0.0017       3      31 ..      94     122 ..      92     125 .. 0.84
   4 !   13.2   0.2   0.00014     0.068       2      32 ..     127     157 ..     127     160 .. 0.88
   5 ?    6.0   0.0     0.028        14       8      24 ..     167     183 ..     166     192 .. 0.80
   6 ?    0.3   0.0       1.9   9.2e+02       6      24 ..     199     217 ..     195     227 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00063
                         TPR_7  5 LarlysrlGdyeeAielyeqsLal 28
                                   +  y++ G+y++A+e +++++ +
  gi|13540875|ref|NP_110563.1| 28 RGISYFNIGKYDKAVEEFTKAISI 51
                                  5778****************6554 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00081
                         TPR_7  2 LlnLarlysrlGdyeeAielyeqsLaltkdpe 33
                                  ++n + +y ++  y++Aie +e+   +  dp+
  gi|13540875|ref|NP_110563.1| 59 YHNRGMAYYSMKAYDQAIEDFER--SISLDPN 88
                                  899999*****************..5555554 PP

  == domain 3  score: 18.3 bits;  conditional E-value: 3.3e-06
                         TPR_7   3 lnLarlysrlGdyeeAielyeqsLaltkd 31 
                                   ++L+++y+++G+ye+A+e +  +++l++d
  gi|13540875|ref|NP_110563.1|  94 NALGSVYEDMGNYEKALEEFNSAIRLEDD 122
                                   89****************99886666666 PP

  == domain 4  score: 13.2 bits;  conditional E-value: 0.00014
                         TPR_7   2 LlnLarlysrlGdyeeAielyeqsLaltkdp 32 
                                   ++n +++y +lG+ e+Ai+ y ++  l++ +
  gi|13540875|ref|NP_110563.1| 127 YYNRGNVYWKLGEIEKAIQDYSKAADLDYTD 157
                                   7899******************988887766 PP

  == domain 5  score: 6.0 bits;  conditional E-value: 0.028
                         TPR_7   8 lysrlGdyeeAielyeq 24 
                                   +  +lG+y+eA+e   +
  gi|13540875|ref|NP_110563.1| 167 ALTSLGRYDEALETVDK 183
                                   6789********98766 PP

  == domain 6  score: 0.3 bits;  conditional E-value: 1.9
                         TPR_7   6 arlysrlGdyeeAielyeq 24 
                                   a+l  ++ +yeeA  + e+
  gi|13540875|ref|NP_110563.1| 199 AELLIKMKRYEEARPVIEE 217
                                   677788889****998887 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.0   0.00075      0.37       5      31 ..      25      51 ..      25      53 .. 0.94
   2 !   18.4   0.1   2.9e-06    0.0014       2      30 ..      56      84 ..      56      85 .. 0.93
   3 !    9.8   0.1    0.0015      0.74       6      30 ..      94     118 ..      94     120 .. 0.88
   4 !    8.8   0.1    0.0031       1.5       5      28 ..     127     150 ..     125     153 .. 0.88
   5 ?    6.4   0.0     0.018       8.7      11      29 ..     167     185 ..     166     187 .. 0.80
   6 ?    2.6   0.0      0.27   1.3e+02       9      27 ..     199     217 ..     193     218 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00075
                        TPR_10  5 lnNLanalrqrgrydeAealleealai 31
                                  +n  ++ +++ g+yd+A++ + +a++i
  gi|13540875|ref|NP_110563.1| 25 YNERGISYFNIGKYDKAVEEFTKAISI 51
                                  7899********************997 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 2.9e-06
                        TPR_10  2 AsslnNLanalrqrgrydeAealleeala 30
                                  A  ++N ++a+++++ yd+A +++e++++
  gi|13540875|ref|NP_110563.1| 56 ADLYHNRGMAYYSMKAYDQAIEDFERSIS 84
                                  6779**********************997 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.0015
                        TPR_10   6 nNLanalrqrgrydeAealleeala 30 
                                   n L+ ++ ++g+y++A++ +  a++
  gi|13540875|ref|NP_110563.1|  94 NALGSVYEDMGNYEKALEEFNSAIR 118
                                   88***************98877765 PP

  == domain 4  score: 8.8 bits;  conditional E-value: 0.0031
                        TPR_10   5 lnNLanalrqrgrydeAealleea 28 
                                   + N +n+++++g+ ++A +++ +a
  gi|13540875|ref|NP_110563.1| 127 YYNRGNVYWKLGEIEKAIQDYSKA 150
                                   7799***************99887 PP

  == domain 5  score: 6.4 bits;  conditional E-value: 0.018
                        TPR_10  11 alrqrgrydeAealleeal 29 
                                   al+++grydeA++  ++a+
  gi|13540875|ref|NP_110563.1| 167 ALTSLGRYDEALETVDKAI 185
                                   799********98666665 PP

  == domain 6  score: 2.6 bits;  conditional E-value: 0.27
                        TPR_10   9 analrqrgrydeAeallee 27 
                                   a +l +++ry+eA+   ee
  gi|13540875|ref|NP_110563.1| 199 AELLIKMKRYEEARPVIEE 217
                                   5677899******987776 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.0    0.0017      0.86       6      28 ..      28      50 ..      27      51 .. 0.89
   2 !   18.2   0.1   5.6e-06    0.0028       3      33 .]      59      89 ..      57      89 .. 0.93
   3 !    9.0   0.0    0.0048       2.4       6      28 ..      96     118 ..      95     122 .. 0.89
   4 !    9.9   0.1    0.0024       1.2       3      26 ..     127     150 ..     125     154 .. 0.88
   5 ?    1.9   0.0      0.88   4.4e+02      12      27 ..     170     185 ..     162     190 .. 0.75
   6 ?    3.7   0.0      0.23   1.1e+02       6      31 ..     198     223 ..     195     225 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0017
                                  HHHHHHHHHHHHHHHHHHHHHHH CS
                         TPR_6  6 lalsyrklgdtdkAlealerlik 28
                                  ++ sy++ g++dkA+e + + i+
  gi|13540875|ref|NP_110563.1| 28 RGISYFNIGKYDKAVEEFTKAIS 50
                                  699****88*********99885 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 5.6e-06
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHH-TT- CS
                         TPR_6  3 lyklalsyrklgdtdkAlealerlikeYPdS 33
                                  + +++++y++++ +d+A+e +er i+  P+S
  gi|13540875|ref|NP_110563.1| 59 YHNRGMAYYSMKAYDQAIEDFERSISLDPNS 89
                                  6789*************************98 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.0048
                                   HHHHHHHHHHHHHHHHHHHHHHH CS
                         TPR_6   6 lalsyrklgdtdkAlealerlik 28 
                                   l+  y+ +g+++kAle +++ i+
  gi|13540875|ref|NP_110563.1|  96 LGSVYEDMGNYEKALEEFNSAIR 118
                                   6889999***********99987 PP

  == domain 4  score: 9.9 bits;  conditional E-value: 0.0024
                                   HHHHHHHHHHHHHHHHHHHHHHHH CS
                         TPR_6   3 lyklalsyrklgdtdkAlealerl 26 
                                   +y+++  y klg+ +kA++ + + 
  gi|13540875|ref|NP_110563.1| 127 YYNRGNVYWKLGEIEKAIQDYSKA 150
                                   8*********99******999876 PP

  == domain 5  score: 1.9 bits;  conditional E-value: 0.88
                                   HHHHHHHHHHHHHHHH CS
                         TPR_6  12 klgdtdkAlealerli 27 
                                   +lg++d+Ale+ ++ i
  gi|13540875|ref|NP_110563.1| 170 SLGRYDEALETVDKAI 185
                                   469******9866666 PP

  == domain 6  score: 3.7 bits;  conditional E-value: 0.23
                                   HHHHHHHHHHHHHHHHHHHHHHHH-T CS
                         TPR_6   6 lalsyrklgdtdkAlealerlikeYP 31 
                                    a++++k++++++A+   e++ k  P
  gi|13540875|ref|NP_110563.1| 198 KAELLIKMKRYEEARPVIEEVEKLNP 223
                                   58999**9*******98888877766 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 ?    1.5   0.0      0.71   3.5e+02      32      48 ..      31      47 ..      15      59 .. 0.74
   2 !   21.7   0.1   3.4e-07   0.00017       4      79 ..      37     113 ..      34     116 .. 0.91
   3 !   18.5   1.0   3.5e-06    0.0017      25      81 ..     126     183 ..     116     184 .. 0.87
   4 !   16.0   0.0   2.1e-05      0.01      13      67 ..     182     237 ..     180     242 .] 0.89

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.71
                                  HHHHTT-HHHHHHHHHC CS
                        ANAPC3 32 clylngqykrAyellrk 48
                                  ++++ g+y++A e + k
  gi|13540875|ref|NP_110563.1| 31 SYFNIGKYDKAVEEFTK 47
                                  57777777777765555 PP

  == domain 2  score: 21.7 bits;  conditional E-value: 3.4e-07
                                   -HHHHHHHHHHHH.HHH--HHHHHHH.HHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH CS
                        ANAPC3   4 nyknAiflaerllaaetespedayll.AlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaL 79 
                                   +y++A+  + ++  +  +++ d+y   + ++y+++ y++A+e ++++  l+++s  ++  ++ ++ ++++ye+A+  +
  gi|13540875|ref|NP_110563.1|  37 KYDKAVEEFTKAI-SIINDDADLYHNrGMAYYSMKAYDQAIEDFERSiSLDPNSSDYHNALGSVYEDMGNYEKALEEF 113
                                   6888999999999.8888999988867***********************************************9765 PP

  == domain 3  score: 18.5 bits;  conditional E-value: 3.5e-06
                                   HHHHH..HHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                        ANAPC3  25 dayll..AlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                       +  + ++ ++g+ ++A++ ++ka +l+ +++ + y + ++l  L++y+eA+ + +k
  gi|13540875|ref|NP_110563.1| 126 YY--YnrGNVYWKLGEIEKAIQDYSKAaDLDYTDQIYVYKKYEALTSLGRYDEALETVDK 183
                                   33..33599******************999999999999999*************99887 PP

  == domain 4  score: 16.0 bits;  conditional E-value: 2.1e-05
                                   HHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHH CS
                        ANAPC3  13 erllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcll 67 
                                   +++ +  + +++ + ++A+ l ++++y++A  ++++  kln+ ++ ++ l+Aq   
  gi|13540875|ref|NP_110563.1| 182 DKAIKVVPANYNYLAMKAELLIKMKRYEEARPVIEEVeKLNPGNPDAARLMAQINM 237
                                   6777778999999999************************************9765 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.1   0.00096      0.48      17      80 ..      35      98 ..      30     101 .. 0.94
   2 !   28.8   0.1   1.1e-09   5.6e-07     201     260 ..      99     158 ..      96     164 .. 0.94
   3 !   17.3   0.3   3.5e-06    0.0017      13      71 ..     167     225 ..     158     240 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00096
                                  HTHHHHHHHHHHHHGGG---HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-CHHHHHHHH CS
                         NARP1 17 agkleeAlehLeekekqivDklavketkaelllkLgrkeeAeatyeaLlernpenskYyeglek 80
                                   gk+++A+e+++++ + i D   +  +++  +  ++ +++A + +e+ ++  p++s+Y+++l  
  gi|13540875|ref|NP_110563.1| 35 IGKYDKAVEEFTKAISIINDDADLYHNRGMAYYSMKAYDQAIEDFERSISLDPNSSDYHNALGS 98
                                  6999*******************************************************99865 PP

  == domain 2  score: 28.8 bits;  conditional E-value: 1.1e-09
                                   HHHHHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCTTT-H CS
                         NARP1 201 hydklgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklDlaDR 260
                                    y+ +g++ekAle  ++ai+ ++ l ++y+++++++ + G+++kA++   +a  lD  D 
  gi|13540875|ref|NP_110563.1|  99 VYEDMGNYEKALEEFNSAIRLEDDLPDYYYNRGNVYWKLGEIEKAIQDYSKAADLDYTDQ 158
                                   6999****************************************************9995 PP

  == domain 3  score: 17.3 bits;  conditional E-value: 3.5e-06
                                   HHHHHTHHHHHHHHHHHHGGG---HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT- CS
                         NARP1  13 iieeagkleeAlehLeekekqivDklavketkaelllkLgrkeeAeatyeaLlernpen 71 
                                    ++  g+++eAle ++++ k +  + +++ +kaell+k++r+eeA+ ++e+  + np n
  gi|13540875|ref|NP_110563.1| 167 ALTSLGRYDEALETVDKAIKVVPANYNYLAMKAELLIKMKRYEEARPVIEEVEKLNPGN 225
                                   55666777888888888888777888888888888888888888887777777766665 PP

>> DUF5113  Domain of unknown function (DUF5113)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.4   1.6e-05     0.008       6      49 ..      20      63 ..      15      79 .. 0.85
   2 ?    6.4   2.5     0.014       7.1       8      53 ..      89     134 ..      84     171 .. 0.65
   3 !   12.9   0.3   0.00014      0.07      19      64 ..     169     213 ..     152     224 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.6e-05
                       DUF5113  6 qiandYanlayylnvegeyeeALeyldsaleylNahyekYakkk 49
                                  q a+dY + +  ++  g+y++A+e +++a++++N   + Y ++ 
  gi|13540875|ref|NP_110563.1| 20 QLADDYNERGISYFNIGKYDKAVEEFTKAISIINDDADLYHNRG 63
                                  789********************************999998775 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.014
                       DUF5113   8 andYan.layylnvegeyeeALeyldsaleylNahyekYakkkadtl 53 
                                   ++dY n l++ +   g+ye+ALe ++sa+++     + Y+++  +  
  gi|13540875|ref|NP_110563.1|  89 SSDYHNaLGSVYEDMGNYEKALEEFNSAIRLEDDLPDYYYNRG-NVY 134
                                   567766257777888**************98777766666665.333 PP

  == domain 3  score: 12.9 bits;  conditional E-value: 0.00014
                       DUF5113  19 nvegeyeeALeyldsaleylNahyekYakkkadtldklkmllegeg 64 
                                      g+y+eALe++d+a++++ a y+  a k+ + l k+k ++e   
  gi|13540875|ref|NP_110563.1| 169 TSLGRYDEALETVDKAIKVVPANYNYLAMKA-ELLIKMKRYEEARP 213
                                   4569********************8666666.78877776666554 PP

>> TPR_3  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0     0.023        11       9      22 ..      30      43 ..      24      46 .. 0.86
   2 !    9.5   0.0     0.002      0.99       8      23 ..      63      78 ..      57      88 .. 0.84
   3 ?    4.1   0.0     0.095        47       6      23 ..      95     112 ..      90     119 .. 0.82
   4 ?    1.0   0.2      0.88   4.4e+02      15      23 ..     145     153 ..     127     155 .. 0.69
   5 ?    1.9   0.0      0.48   2.4e+02      15      23 ..     172     180 ..     170     182 .. 0.87
   6 ?    0.3   0.0       1.5   7.5e+02      14      21 ..     205     212 ..     204     214 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.023
                                  HHHHHTT-HHHHHH CS
                         TPR_3  9 aefynkkkyqeAre 22
                                   +++n +ky++A+e
  gi|13540875|ref|NP_110563.1| 30 ISYFNIGKYDKAVE 43
                                  5899********98 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.002
                                  HHHHHHTT-HHHHHHH CS
                         TPR_3  8 AaefynkkkyqeArel 23
                                  + ++y++k y++A+e 
  gi|13540875|ref|NP_110563.1| 63 GMAYYSMKAYDQAIED 78
                                  678***********96 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.095
                                   HHHHHHHHTT-HHHHHHH CS
                         TPR_3   6 syAaefynkkkyqeArel 23 
                                   +++ ++ ++++y++A+e 
  gi|13540875|ref|NP_110563.1|  95 ALGSVYEDMGNYEKALEE 112
                                   67788889*******985 PP

  == domain 4  score: 1.0 bits;  conditional E-value: 0.88
                                   T-HHHHHHH CS
                         TPR_3  15 kkyqeArel 23 
                                   ++y++A++l
  gi|13540875|ref|NP_110563.1| 145 QDYSKAADL 153
                                   356666665 PP

  == domain 5  score: 1.9 bits;  conditional E-value: 0.48
                                   T-HHHHHHH CS
                         TPR_3  15 kkyqeArel 23 
                                   ++y+eA+e+
  gi|13540875|ref|NP_110563.1| 172 GRYDEALET 180
                                   9*****997 PP

  == domain 6  score: 0.3 bits;  conditional E-value: 1.5
                                   TT-HHHHH CS
                         TPR_3  14 kkkyqeAr 21 
                                   +k+y+eAr
  gi|13540875|ref|NP_110563.1| 205 MKRYEEAR 212
                                   8******8 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0       1.2   5.8e+02       9      22 ..      30      43 ..      28      51 .. 0.80
   2 ?    4.4   0.1     0.079        40       7      33 ..      62      88 ..      57     102 .. 0.86
   3 ?    3.9   0.1      0.12        58      14      31 ..     103     120 ..      92     123 .. 0.81
   4 ?   -2.2   0.2       9.3   4.7e+03      13      20 ..     136     143 ..     125     152 .. 0.56
   5 !   10.9   0.0   0.00075      0.37      13      40 ..     170     197 ..     166     201 .. 0.86
   6 !   12.5   0.2   0.00023      0.11      12      47 ..     203     238 ..     202     242 .] 0.91

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 1.2
                                  HHHHHHT-HHHHHH CS
                    Fis1_TPR_C  9 lGhyklgeYseArr 22
                                  + ++ +g+Y++A +
  gi|13540875|ref|NP_110563.1| 30 ISYFNIGKYDKAVE 43
                                  66899******976 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.079
                                  HHHHHHHHT-HHHHHHHHHHHHHHTTS CS
                    Fis1_TPR_C  7 lAlGhyklgeYseArryvdalLeiEPe 33
                                    +++y ++ Y++A +  ++ ++++P+
  gi|13540875|ref|NP_110563.1| 62 RGMAYYSMKAYDQAIEDFERSISLDPN 88
                                  5789**********9999999998887 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.12
                                   HT-HHHHHHHHHHHHHHT CS
                    Fis1_TPR_C  14 lgeYseArryvdalLeiE 31 
                                   +g+Y++A++  +  +++E
  gi|13540875|ref|NP_110563.1| 103 MGNYEKALEEFNSAIRLE 120
                                   8********999988887 PP

  == domain 4  score: -2.2 bits;  conditional E-value: 9.3
                                   HHT-HHHH CS
                    Fis1_TPR_C  13 klgeYseA 20 
                                   klge ++A
  gi|13540875|ref|NP_110563.1| 136 KLGEIEKA 143
                                   55555554 PP

  == domain 5  score: 10.9 bits;  conditional E-value: 0.00075
                                   HHT-HHHHHHHHHHHHHHTTS-HHHHHH CS
                    Fis1_TPR_C  13 klgeYseArryvdalLeiEPenrQaqsL 40 
                                    lg+Y+eA++ vd  +++ P n + ++ 
  gi|13540875|ref|NP_110563.1| 170 SLGRYDEALETVDKAIKVVPANYNYLAM 197
                                   59********************887665 PP

  == domain 6  score: 12.5 bits;  conditional E-value: 0.00023
                                   HHHT-HHHHHHHHHHHHHHTTS-HHHHHHHHHHHHH CS
                    Fis1_TPR_C  12 yklgeYseArryvdalLeiEPenrQaqsLkeliedk 47 
                                   +k+++Y+eAr  ++ + ++ P+n  a+ L + i+ k
  gi|13540875|ref|NP_110563.1| 203 IKMKRYEEARPVIEEVEKLNPGNPDAARLMAQINMK 238
                                   69***************************9988765 PP

>> SHNi-TPR  SHNi-TPR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0     0.015       7.5      15      30 ..      36      51 ..      33      51 .. 0.89
   2 !    9.5   0.1    0.0013      0.63      17      30 ..      72      85 ..      71      85 .. 0.93
   3 ?    5.4   0.0     0.026        13      15      30 ..     104     119 ..      90     122 .. 0.83
   4 ?    1.0   0.1      0.58   2.9e+02      19      26 ..     142     149 ..     132     153 .. 0.57
   5 ?   -1.9   0.0       4.8   2.4e+03      16      27 ..     173     184 ..     172     186 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.015
                      SHNi-TPR 15 enFpqAveDlrkaLeL 30
                                  ++++ Ave+++ka+ +
  gi|13540875|ref|NP_110563.1| 36 GKYDKAVEEFTKAISI 51
                                  79***********976 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0013
                      SHNi-TPR 17 FpqAveDlrkaLeL 30
                                  ++qA+eD+++++ L
  gi|13540875|ref|NP_110563.1| 72 YDQAIEDFERSISL 85
                                  99*********987 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.026
                      SHNi-TPR  15 enFpqAveDlrkaLeL 30 
                                   +n++ A+e++++a+ L
  gi|13540875|ref|NP_110563.1| 104 GNYEKALEEFNSAIRL 119
                                   7************876 PP

  == domain 4  score: 1.0 bits;  conditional E-value: 0.58
                      SHNi-TPR  19 qAveDlrk 26 
                                    A++D+ k
  gi|13540875|ref|NP_110563.1| 142 KAIQDYSK 149
                                   35666655 PP

  == domain 5  score: -1.9 bits;  conditional E-value: 4.8
                      SHNi-TPR  16 nFpqAveDlrka 27 
                                   ++++A+e  +ka
  gi|13540875|ref|NP_110563.1| 173 RYDEALETVDKA 184
                                   899999865555 PP

>> DUF3856  Domain of Unknown Function (DUF3856)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0      0.15        75     105     132 ..      27      54 ..      16      57 .. 0.84
   2 ?    4.5   0.0     0.067        33      65      96 ..      32      63 ..      27      84 .. 0.65
   3 ?    4.9   0.1      0.05        25      58      91 ..      93     119 ..      85     154 .. 0.60
   4 !   12.4   0.1   0.00025      0.12      51      83 ..     154     186 ..     139     201 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.15
                                   HHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                       DUF3856 105 sravaleelGrkdealkafrmagemiae 132
                                   +r+ ++ ++G++d+a+++f +a  +i++
  gi|13540875|ref|NP_110563.1|  27 ERGISYFNIGKYDKAVEEFTKAISIIND 54 
                                   5777888899999999999999988875 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.067
                                  HHHTT-HHHHHHHHHHHHHHHHHH--TTSTHH CS
                       DUF3856 65 laklgrydealesadkalryfnrrGeleqdeG 96
                                  + ++g+yd+a+e   ka+   n   +l ++ G
  gi|13540875|ref|NP_110563.1| 32 YFNIGKYDKAVEEFTKAISIINDDADLYHNRG 63
                                  44556666666666666666666666655555 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.05
                                   HHHHHHHHHHTT-HHHHHHHHHHHHHHHHHH--T CS
                       DUF3856  58 haglsealaklgrydealesadkalryfnrrGel 91 
                                   h +l + +  +g+y++ale  ++a+r       l
  gi|13540875|ref|NP_110563.1|  93 HNALGSVYEDMGNYEKALEEFNSAIR-------L 119
                                   55666667777777777766666654.......3 PP

  == domain 4  score: 12.4 bits;  conditional E-value: 0.00025
                                   HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                       DUF3856  51 eGfdalchaglsealaklgrydealesadkalr 83 
                                   +  d +      eal+ lgrydeale++dka++
  gi|13540875|ref|NP_110563.1| 154 DYTDQIYVYKKYEALTSLGRYDEALETVDKAIK 186
                                   555555555667899999999999999999986 PP

>> SRP_TPR_like  Putative TPR-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.8   0.00052      0.26      20      98 ..      28     113 ..       9     125 .. 0.70
   2 ?    3.1   0.4      0.19        95      30      69 ..     106     148 ..      99     160 .. 0.68
   3 !   17.0   1.4     9e-06    0.0045      16      75 ..     160     222 ..     143     241 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00052
                  SRP_TPR_like  20 kvvaliklekyeeaLkllkkgs.alse..dvrfEkaYvlYklkkykkalkilkkveaee....kvkvlksqvlYrlgsyek 93 
                                   + +++ +++ky+ a++  +k+   +++  d+   +  ++Y +k y +a + +++  + +      +  +  v+  +g+yek
  gi|13540875|ref|NP_110563.1|  28 RGISYFNIGKYDKAVEEFTKAIsIINDdaDLYHNRGMAYYSMKAYDQAIEDFERSISLDpnssDYHNALGSVYEDMGNYEK 108
                                   789999********976655542555411678899**************99988654333112445556679999999999 PP

                  SRP_TPR_like  94 AYklL 98 
                                   A +  
  gi|13540875|ref|NP_110563.1| 109 ALEEF 113
                                   97765 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.19
                  SRP_TPR_like  30 yeeaLkllkkgsalse...dvrfEkaYvlYklkkykkalkilk 69 
                                   ye aL+  + +  l++   d  + +  v++kl + +ka +  +
  gi|13540875|ref|NP_110563.1| 106 YEKALEEFNSAIRLEDdlpDYYYNRGNVYWKLGEIEKAIQDYS 148
                                   555555555555444411167899**********999987555 PP

  == domain 3  score: 17.0 bits;  conditional E-value: 9e-06
                  SRP_TPR_like  16 lkkfkvvaliklekyeeaLkllkkgs...alsedvrfEkaYvlYklkkykkalkilkkveaee 75 
                                   +   k  al +l++y+eaL+ ++k+      + +    ka  l k+k+y++a  ++++ve+ +
  gi|13540875|ref|NP_110563.1| 160 YVYKKYEALTSLGRYDEALETVDKAIkvvPANYNYLAMKAELLIKMKRYEEARPVIEEVEKLN 222
                                   3333667999*************9983333345556689*******************99764 PP

>> HTH_Bact  Helix-turn-helix bacterial domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0      0.25   1.3e+02       1      15 [.      37      51 ..      37      54 .. 0.92
   2 ?   -0.8   0.0       2.3   1.2e+03       2      14 ..      72      84 ..      68      88 .. 0.79
   3 ?    2.9   0.0      0.16        80       2      14 ..     106     118 ..     105     120 .. 0.90
   4 ?    4.2   0.2     0.066        33      28      48 ..     126     146 ..     123     147 .. 0.90
   5 !   10.3   0.0   0.00082      0.41       1      15 [.     173     187 ..     173     193 .. 0.92

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.25
                                  -HHHHHHHHHHHHHH CS
                      HTH_Bact  1 rYeeaLeqvnkAiei 15
                                  +Y++a e   kAi i
  gi|13540875|ref|NP_110563.1| 37 KYDKAVEEFTKAISI 51
                                  6************86 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 2.3
                                  HHHHHHHHHHHHH CS
                      HTH_Bact  2 YeeaLeqvnkAie 14
                                  Y++a+e  ++ i 
  gi|13540875|ref|NP_110563.1| 72 YDQAIEDFERSIS 84
                                  8888888888775 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.16
                                   HHHHHHHHHHHHH CS
                      HTH_Bact   2 YeeaLeqvnkAie 14 
                                   Ye+aLe  n Ai 
  gi|13540875|ref|NP_110563.1| 106 YEKALEEFNSAIR 118
                                   ***********97 PP

  == domain 4  score: 4.2 bits;  conditional E-value: 0.066
                                   HHHHHHHHHHHTT--HHHHHH CS
                      HTH_Bact  28 LyYqkgecleklgfseeeIke 48 
                                    yY +g+   klg  e+ I++
  gi|13540875|ref|NP_110563.1| 126 YYYNRGNVYWKLGEIEKAIQD 146
                                   59************9999987 PP

  == domain 5  score: 10.3 bits;  conditional E-value: 0.00082
                                   -HHHHHHHHHHHHHH CS
                      HTH_Bact   1 rYeeaLeqvnkAiei 15 
                                   rY+eaLe v+kAi++
  gi|13540875|ref|NP_110563.1| 173 RYDEALETVDKAIKV 187
                                   7************96 PP

>> BTAD  Bacterial transcriptional activator domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.0    0.0013      0.63      71     124 ..      65     118 ..      53     125 .. 0.86
   2 !   10.2   0.0    0.0015      0.77      56     118 ..     118     180 ..     115     188 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0013
                                   HHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                          BTAD  71 aelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrr 124
                                   a  ++  +++a+++ e+ ++++P   ++h +l   +  +G+ ++ALe ++++ r
  gi|13540875|ref|NP_110563.1|  65 AYYSMKAYDQAIEDFERSISLDPNSSDYHNALGSVYEDMGNYEKALEEFNSAIR 118
                                   555667899****************************************99855 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0015
                                   HHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHH CS
                          BTAD  56 rleelrlealealaeaelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALev 118
                                   rle++  + +  + +  ++lG++e+a+++++++++++ ++  ++ +  +Al  +Gr  eALe+
  gi|13540875|ref|NP_110563.1| 118 RLEDDLPDYYYNRGNVYWKLGEIEKAIQDYSKAADLDYTDQIYVYKKYEALTSLGRYDEALET 180
                                   5666666667777888899******************************************97 PP

>> TPR_4  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0       1.9   9.5e+02       5      22 ..      94     111 ..      92     114 .. 0.84
   2 ?    5.6   0.0     0.062        31       4      20 ..     127     143 ..     124     145 .. 0.89
   3 ?    6.5   0.0     0.032        16      10      25 ..     167     182 ..     166     183 .. 0.81
   4 ?    1.1   0.0       1.8     9e+02      16      26 .]     207     217 ..     194     217 .. 0.73
   5 ?   -1.0   0.0       8.2   4.1e+03      15      21 ..     224     230 ..     224     234 .. 0.73

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 1.9
                         TPR_4   5 laLArallalGdldeAra 22 
                                    aL+ ++ + G+++ A++
  gi|13540875|ref|NP_110563.1|  94 NALGSVYEDMGNYEKALE 111
                                   5789999999******97 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.062
                         TPR_4   4 llaLArallalGdldeA 20 
                                   +++++ +++ lG+ + A
  gi|13540875|ref|NP_110563.1| 127 YYNRGNVYWKLGEIEKA 143
                                   799***********988 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.032
                         TPR_4  10 allalGdldeAralle 25 
                                   al  lG++deA+++++
  gi|13540875|ref|NP_110563.1| 167 ALTSLGRYDEALETVD 182
                                   66679*******9876 PP

  == domain 4  score: 1.1 bits;  conditional E-value: 1.8
                         TPR_4  16 dldeAraller 26 
                                   +++eAr + e+
  gi|13540875|ref|NP_110563.1| 207 RYEEARPVIEE 217
                                   89****99886 PP

  == domain 5  score: -1.0 bits;  conditional E-value: 8.2
                         TPR_4  15 GdldeAr 21 
                                   G++d+Ar
  gi|13540875|ref|NP_110563.1| 224 GNPDAAR 230
                                   7788887 PP

>> RPN7  26S proteasome subunit RPN7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.9   0.1    0.0096       4.8      32      62 ..      18      48 ..      11      53 .. 0.87
   2 !    7.0   0.2    0.0089       4.4      28      62 ..      82     116 ..      62     122 .. 0.78
   3 ?    6.7   0.0     0.011       5.2      38      64 ..     126     152 ..     119     160 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0096
                                  HHHHHHHHHHHHHHHHHCT-HHHHHHHHHTC CS
                          RPN7 32 keeirrakldlaehYlkigdleeAlkaysri 62
                                  ke+ ++ +++++  Y++ig++++A++ + ++
  gi|13540875|ref|NP_110563.1| 18 KEQLADDYNERGISYFNIGKYDKAVEEFTKA 48
                                  7889999999999************999886 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0089
                                   HTT-HHHHHHHHHHHHHHHHHCT-HHHHHHHHHTC CS
                          RPN7  28 enlgkeeirrakldlaehYlkigdleeAlkaysri 62 
                                   + + + +  + +++l+  Y ++g++e+Al+ ++ +
  gi|13540875|ref|NP_110563.1|  82 SISLDPNSSDYHNALGSVYEDMGNYEKALEEFNSA 116
                                   5555666678899*****************99985 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.011
                                   HHHHHHHHHHHCT-HHHHHHHHHTCCC CS
                          RPN7  38 akldlaehYlkigdleeAlkaysrire 64 
                                    ++++++ Y k g++e+A++ ys++ +
  gi|13540875|ref|NP_110563.1| 126 YYYNRGNVYWKLGEIEKAIQDYSKAAD 152
                                   578999*****************9876 PP

>> ChAPs  ChAPs (Chs5p-Arf1p-binding proteins)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.0   0.00054      0.27     218     293 ..      40     115 ..      31     129 .. 0.92
   2 !    6.6   0.0    0.0065       3.2     249     287 ..     173     211 ..     136     241 .. 0.55

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00054
                                   HHHHHHHHHH-SSS-HHHHHHHHHHHHHHSS--HHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHT CS
                         ChAPs 218 davkllneeleeeekdaelLllqaefllskkkeelAlevakravksaPsefktWalLvkvYikledienALltLNs 293
                                   +av+   ++++  ++da+l + +     s k ++ A+e  +r++++ P+ +     L  vY +++++e+AL   Ns
  gi|13540875|ref|NP_110563.1|  40 KAVEEFTKAISIINDDADLYHNRGMAYYSMKAYDQAIEDFERSISLDPNSSDYHNALGSVYEDMGNYEKALEEFNS 115
                                   5777888888888999999999999999999********************************************9 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0065
                                   --HHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHH CS
                         ChAPs 249 keelAlevakravksaPsefktWalLvkvYikledienA 287
                                   +++ Ale+ ++a+k+ P +++  a+ ++  ik++ +e+A
  gi|13540875|ref|NP_110563.1| 173 RYDEALETVDKAIKVVPANYNYLAMKAELLIKMKRYEEA 211
                                   335555555555555555555555555555555555544 PP

>> DUF4810  Domain of unknown function (DUF4810)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0      0.19        95      49      70 ..      26      47 ..      24      51 .. 0.88
   2 ?    6.3   0.0     0.028        14      48      84 ..      59      95 ..      57      96 .. 0.90
   3 ?    3.7   0.0      0.18        88      48      70 ..      93     115 ..      92     119 .. 0.88
   4 ?    2.4   0.0      0.45   2.2e+02      45      70 ..     124     149 ..     121     153 .. 0.87
   5 ?    2.6   0.6      0.41     2e+02       6      44 ..     154     189 ..     152     233 .. 0.63

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.19
                       DUF4810 49 AelGllylkegkkeeaieafek 70
                                   e G+ y++ gk ++a+e+f+k
  gi|13540875|ref|NP_110563.1| 26 NERGISYFNIGKYDKAVEEFTK 47
                                  578999*************986 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.028
                       DUF4810 48 yAelGllylkegkkeeaieafekEkelfPESatfmdf 84
                                  y + G+ y+++   ++aie fe+  +l P S+ + + 
  gi|13540875|ref|NP_110563.1| 59 YHNRGMAYYSMKAYDQAIEDFERSISLDPNSSDYHNA 95
                                  6678**************************9999765 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.18
                       DUF4810  48 yAelGllylkegkkeeaieafek 70 
                                   +  lG +y ++g+ e+a e+f++
  gi|13540875|ref|NP_110563.1|  93 HNALGSVYEDMGNYEKALEEFNS 115
                                   6679****************985 PP

  == domain 4  score: 2.4 bits;  conditional E-value: 0.45
                       DUF4810  45 PGlyAelGllylkegkkeeaieafek 70 
                                   P +y + G +y k g+ e+ai+ ++k
  gi|13540875|ref|NP_110563.1| 124 PDYYYNRGNVYWKLGEIEKAIQDYSK 149
                                   66788999*************99876 PP

  == domain 5  score: 2.6 bits;  conditional E-value: 0.41
                       DUF4810   6 nYqdavYeyykedeeskekqieklekiiekaeakgkkvp 44 
                                   +Y d++Y y+k    +  + + ++++++e+ +++ k vp
  gi|13540875|ref|NP_110563.1| 154 DYTDQIYVYKKY---EALTSLGRYDEALETVDKAIKVVP 189
                                   799999999995...445556677777777755555444 PP

>> TPR_21  Tetratricopeptide repeat-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0       1.1   5.7e+02     152     176 ..      28      52 ..      13      62 .. 0.75
   2 ?    5.5   0.1     0.025        12     123     174 ..      66     118 ..      29     127 .. 0.71
   3 !   13.9   0.3   6.8e-05     0.034     119     191 ..      96     168 ..      93     170 .. 0.80
   4 ?    2.1   0.0      0.27   1.3e+02     125     166 ..     170     212 ..     166     217 .. 0.66

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 1.1
                        TPR_21 152 rGDilvaqgkldeAraaYqaAlaal 176
                                   rG  +++ gk d+A +++++A++ +
  gi|13540875|ref|NP_110563.1|  28 RGISYFNIGKYDKAVEEFTKAISII 52 
                                   6777888999999999999998755 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.025
                        TPR_21 123 llaekkydeAlktLeak.keeafaalvaelrGDilvaqgkldeAraaYqaAla 174
                                   +  +k+yd+A++  e++ + +  ++ + +  G ++  +g+ ++A ++++ A++
  gi|13540875|ref|NP_110563.1|  66 YYSMKAYDQAIEDFERSiSLDPNSSDYHNALGSVYEDMGNYEKALEEFNSAIR 118
                                   56789999999999765155778889999999999999999999999999986 PP

  == domain 3  score: 13.9 bits;  conditional E-value: 6.8e-05
                        TPR_21 119 LarvllaekkydeAlktLeak.keeafaalvaelrGDilvaqgkldeAraaYqaAlaaleekarellqlKlddL 191
                                   L +v+ ++++y++Al++ +++ + e     +   rG+++ + g++++A + Y++A +   ++ + ++  K ++L
  gi|13540875|ref|NP_110563.1|  96 LGSVYEDMGNYEKALEEFNSAiRLEDDLPDYYYNRGNVYWKLGEIEKAIQDYSKAADLDYTD-QIYVYKKYEAL 168
                                   66799999*********97651556777889999*********************9876666.45666666655 PP

  == domain 4  score: 2.1 bits;  conditional E-value: 0.27
                        TPR_21 125 aekkydeAlktLeakkee.afaalvaelrGDilvaqgkldeAr 166
                                     + ydeAl+t++++ +    +  +  ++ ++l+++++ +eAr
  gi|13540875|ref|NP_110563.1| 170 SLGRYDEALETVDKAIKVvPANYNYLAMKAELLIKMKRYEEAR 212
                                   5678999999997654330333456667777777777777776 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 !   17.3   0.1   5.4e-06    0.0027      31      88 ..     179     235 ..     165     242 .] 0.81

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 5.4e-06
                    HrpB1_HrpK  31 ellLdalrvLrPevaeldllegvlliergrweeAlrlLreveaeasgtpyakaLlAlc 88 
                                   e++ +a++v  P + +  ++ + lli+ +r+eeA+ +++eve+ ++g p a+ L+A  
  gi|13540875|ref|NP_110563.1| 179 ETVDKAIKV-VPANYNYLAMKAELLIKMKRYEEARPVIEEVEKLNPGNPDAARLMAQI 235
                                   444445554.5899999999***********************************975 PP

>> TPR_20  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0       1.4   7.1e+02      30      50 ..      30      50 ..      14      65 .. 0.77
   2 ?    5.1   0.0     0.058        29       7      52 ..      41      86 ..      36      91 .. 0.84
   3 !    9.2   0.0     0.003       1.5       5      50 ..      73     118 ..      69     133 .. 0.89
   4 ?    3.4   0.0      0.19        94       6      41 ..     176     211 ..     172     217 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 1.4
                        TPR_20 30 lallaagryeeAleqLleilk 50
                                    ++  g+y++A+e++ + ++
  gi|13540875|ref|NP_110563.1| 30 ISYFNIGKYDKAVEEFTKAIS 50
                                  567888999999999887765 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.058
                        TPR_20  7 elaeleaalaanpddldarldlAlallaagryeeAleqLleilkrd 52
                                   ++e+ +a+    dd d+ ++   a+++ + y++A+e + + ++ d
  gi|13540875|ref|NP_110563.1| 41 AVEEFTKAISIINDDADLYHNRGMAYYSMKAYDQAIEDFERSISLD 86
                                  6788899999999***********************9886666655 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.003
                        TPR_20   5 apelaeleaalaanpddldarldlAlallaagryeeAleqLleilk 50 
                                   ++ ++++e+ +  +p+  d + +l  ++   g+ye+Ale++ + ++
  gi|13540875|ref|NP_110563.1|  73 DQAIEDFERSISLDPNSSDYHNALGSVYEDMGNYEKALEEFNSAIR 118
                                   678999*********************************9987776 PP

  == domain 4  score: 3.4 bits;  conditional E-value: 0.19
                        TPR_20   6 pelaeleaalaanpddldarldlAlallaagryeeA 41 
                                   + l+++++a++  p++++     A++l++ +ryeeA
  gi|13540875|ref|NP_110563.1| 176 EALETVDKAIKVVPANYNYLAMKAELLIKMKRYEEA 211
                                   56899999***************************9 PP

>> MIT  MIT (microtubule interacting and transport) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0     0.042        21      26      42 ..      37      54 ..      33      68 .. 0.69
   2 ?    6.3   0.1      0.02        10      14      32 ..     100     118 ..      73     123 .. 0.84
   3 ?    2.6   0.1      0.28   1.4e+02      18      33 ..     138     153 ..     136     154 .. 0.86
   4 ?    1.5   0.2      0.65   3.2e+02      27      39 ..     174     186 ..     165     212 .. 0.65

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.042
                           MIT 26 lYkealelLlqalke.kn 42
                                  +Y +a+e +++a++  ++
  gi|13540875|ref|NP_110563.1| 37 KYDKAVEEFTKAISIiND 54
                                  788888888888884344 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.02
                           MIT  14 eDnagnyeeAlelYkeale 32 
                                   ++  gnye+Ale + +a++
  gi|13540875|ref|NP_110563.1| 100 YEDMGNYEKALEEFNSAIR 118
                                   5566788888887777775 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.28
                           MIT  18 gnyeeAlelYkealel 33 
                                   g++e+A++ Y++a +l
  gi|13540875|ref|NP_110563.1| 138 GEIEKAIQDYSKAADL 153
                                   78999******99885 PP

  == domain 4  score: 1.5 bits;  conditional E-value: 0.65
                           MIT  27 YkealelLlqalk 39 
                                   Y eale   +a+k
  gi|13540875|ref|NP_110563.1| 174 YDEALETVDKAIK 186
                                   4444444444444 PP

>> SPOB_a  Sensor_kinase_SpoOB-type, alpha-helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0      0.32   1.6e+02      33      45 ..      32      44 ..      30      59 .. 0.80
   2 ?   -2.3   0.0       7.3   3.6e+03      33      44 ..      66      77 ..      65      81 .. 0.83
   3 ?   -0.6   0.0       2.3   1.1e+03      33      44 ..     100     111 ..      98     118 .. 0.77
   4 ?   -2.5   0.0         9   4.5e+03      33      42 ..     134     143 ..     133     150 .. 0.74
   5 ?    5.9   0.0     0.021        10      33      51 ..     168     186 ..     166     190 .. 0.89
   6 ?    6.3   0.1     0.015       7.6      33      49 ..     202     218 ..     200     220 .. 0.92

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.32
                        SPOB_a 33 ylqLgkydkaeey 45
                                  y  +gkydka+e 
  gi|13540875|ref|NP_110563.1| 32 YFNIGKYDKAVEE 44
                                  8899******985 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 7.3
                        SPOB_a 33 ylqLgkydkaee 44
                                  y  ++ yd+a e
  gi|13540875|ref|NP_110563.1| 66 YYSMKAYDQAIE 77
                                  788999999976 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 2.3
                        SPOB_a  33 ylqLgkydkaee 44 
                                   y ++g+y+ka e
  gi|13540875|ref|NP_110563.1| 100 YEDMGNYEKALE 111
                                   678999999987 PP

  == domain 4  score: -2.5 bits;  conditional E-value: 9
                        SPOB_a  33 ylqLgkydka 42 
                                   y +Lg+++ka
  gi|13540875|ref|NP_110563.1| 134 YWKLGEIEKA 143
                                   6678888887 PP

  == domain 5  score: 5.9 bits;  conditional E-value: 0.021
                        SPOB_a  33 ylqLgkydkaeeyieevvk 51 
                                   ++ Lg+yd+a e +++++k
  gi|13540875|ref|NP_110563.1| 168 LTSLGRYDEALETVDKAIK 186
                                   789************9987 PP

  == domain 6  score: 6.3 bits;  conditional E-value: 0.015
                        SPOB_a  33 ylqLgkydkaeeyieev 49 
                                   ++++++y++a+ +ieev
  gi|13540875|ref|NP_110563.1| 202 LIKMKRYEEARPVIEEV 218
                                   799************98 PP

>> PPR  PPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0       2.2   1.1e+03       9      21 ..      31      43 ..      30      43 .. 0.86
   2 ?    3.3   0.0      0.24   1.2e+02       4      21 ..      94     111 ..      93     117 .. 0.91
   3 ?    1.6   0.0      0.84   4.2e+02       8      20 ..     132     144 ..     132     145 .. 0.88
   4 ?    4.2   0.0      0.12        60       9      25 ..     167     183 ..     166     186 .. 0.83
   5 ?   -1.1   0.0       5.8   2.9e+03      11      19 ..     203     211 ..     200     221 .. 0.64

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 2.2
                           PPR  9 gycknGkleeAle 21
                                  +y   Gk+++A+e
  gi|13540875|ref|NP_110563.1| 31 SYFNIGKYDKAVE 43
                                  58889******86 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.24
                           PPR   4 nslIsgycknGkleeAle 21 
                                   n+l s+y   G++e+Ale
  gi|13540875|ref|NP_110563.1|  94 NALGSVYEDMGNYEKALE 111
                                   888899999*******97 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.84
                           PPR   8 sgycknGkleeAl 20 
                                   ++y k G++e+A+
  gi|13540875|ref|NP_110563.1| 132 NVYWKLGEIEKAI 144
                                   6799********7 PP

  == domain 4  score: 4.2 bits;  conditional E-value: 0.12
                           PPR   9 gycknGkleeAlelfke 25 
                                   ++ + G+++eAle  ++
  gi|13540875|ref|NP_110563.1| 167 ALTSLGRYDEALETVDK 183
                                   67889*******98776 PP

  == domain 5  score: -1.1 bits;  conditional E-value: 5.8
                           PPR  11 cknGkleeA 19 
                                    k  ++eeA
  gi|13540875|ref|NP_110563.1| 203 IKMKRYEEA 211
                                   455566665 PP

>> MAS20  MAS20 protein import receptor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0     0.015       7.6      85     112 ..      32      59 ..      16      62 .. 0.85
   2 ?   -1.5   0.0       5.1   2.5e+03      84     110 ..      65      91 ..      60     104 .. 0.79
   3 ?   -1.1   0.0       3.8   1.9e+03      87     104 ..     102     119 ..      94     122 .. 0.79
   4 ?    4.4   0.0     0.076        38      83     112 ..     166     195 ..     141     204 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.015
                         MAS20  85 llaqgeeeeaaehlynAlkvcpqPqeLl 112
                                   +++ g++++a+e +++A+++++  ++L 
  gi|13540875|ref|NP_110563.1|  32 YFNIGKYDKAVEEFTKAISIINDDADLY 59 
                                   555699**************99998886 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 5.1
                         MAS20  84 ellaqgeeeeaaehlynAlkvcpqPqe 110
                                    + + + +++a+e + + +++ p+ ++
  gi|13540875|ref|NP_110563.1|  65 AYYSMKAYDQAIEDFERSISLDPNSSD 91 
                                   566778999999999999998887765 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 3.8
                         MAS20  87 aqgeeeeaaehlynAlkv 104
                                     g++e+a+e +  A+++
  gi|13540875|ref|NP_110563.1| 102 DMGNYEKALEEFNSAIRL 119
                                   44999*******999986 PP

  == domain 4  score: 4.4 bits;  conditional E-value: 0.076
                         MAS20  83 EellaqgeeeeaaehlynAlkvcpqPqeLl 112
                                   E l + g+++ea+e   +A+kv+p   + l
  gi|13540875|ref|NP_110563.1| 166 EALTSLGRYDEALETVDKAIKVVPANYNYL 195
                                   788888*****************9876655 PP

>> DUF1347  Protein of unknown function (DUF1347)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.1       0.3   1.5e+02     143     213 ..      44     115 ..      39     129 .. 0.78
   2 ?   10.4   0.1   0.00035      0.17      86     154 ..     158     218 ..     137     222 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.3
                       DUF1347 143 eyaeGrvvlnrviekilkreydw.svdiydrlvlmlGrsyllelqesvrsdllpeyyetilfykkkvktidk 213
                                   e+++   ++n   + + +r +++ s   yd+++  + rs  l+ + s   + l   ye +  y+k ++ ++ 
  gi|13540875|ref|NP_110563.1|  44 EFTKAISIINDDADLYHNRGMAYySMKAYDQAIEDFERSISLDPNSSDYHNALGSVYEDMGNYEKALEEFNS 115
                                   666666777777777788877752678899999999999999999999999999999999999998888765 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00035
                       DUF1347  86 allaykkkqyslaldvlslwkehldstktslldenvqellsdyvleemeaeslieareyaeGrvvlnrv 154
                                    ++ ykk  y  al +l ++ e l+      +d+ ++ + ++y    m+ae li++++y e r v+++v
  gi|13540875|ref|NP_110563.1| 158 QIYVYKK--Y-EALTSLGRYDEALET-----VDKAIKVVPANYNYLAMKAELLIKMKRYEEARPVIEEV 218
                                   4444443..3.578888888888764.....688999999************************99886 PP

>> PaREP1  Archaeal PaREP1/PaREP8 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   0.00099      0.49      11      69 ..      20      78 ..      14     119 .. 0.82
   2 ?    0.7   0.0      0.98   4.9e+02      31      73 ..     108     150 ..     104     162 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00099
                        PaREP1 11 eeAeellekGdlrqAaeKaykAvkalvkalaeknnlklleeaeekerwstkellkavak 69
                                  ++A+++ e+G +    +K+ kAv+++ ka+ + n +  l  ++++  +s k + +a+++
  gi|13540875|ref|NP_110563.1| 20 QLADDYNERGISYFNIGKYDKAVEEFTKAISIINDDADLYHNRGMAYYSMKAYDQAIED 78
                                  67888888888888889*********************999999999888886666554 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.98
                        PaREP1  31 kAvkalvkalaeknnlklleeaeekerwstkellkavakllee 73 
                                   kA +++ +a+  +  l+ + +++++  w+ +e  ka+++ ++ 
  gi|13540875|ref|NP_110563.1| 108 KALEEFNSAIRLEDDLPDYYYNRGNVYWKLGEIEKAIQDYSKA 150
                                   7899999999999999999999999999999999998887754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       719  (0.0401026); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        36  (0.00200792); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              36  [number of targets reported over threshold]
# CPU time: 0.75u 0.33s 00:00:01.08 Elapsed: 00:00:00.61
# Mc/sec: 1203.84
//
Query:       gi|13540876|ref|NP_110564.1|  [L=118]
Description: hypothetical protein TVN0045 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       547  (0.0305092); 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: 0.45u 0.31s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 737.07
//
Query:       gi|13540877|ref|NP_110565.1|  [L=252]
Description: exonuclease III [Thermoplasma volcanium GSS1]
Scores for complete 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   70.3   0.1      2e-19   70.0   0.1    1.1  1  Exo_endo_phos    Endonuclease/Exonuclease/phosphatase family
      2e-06   27.6   0.1    2.9e-05   23.9   0.1    2.3  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   0.1   2.3e-23     2e-19       1     233 []       8     243 ..       8     243 .. 0.81

  Alignments for each domain:
  == domain 1  score: 70.0 bits;  conditional E-value: 2.3e-23
                                   EEEEESTGCHHHHTHHHHHHHHHHHHHHCTTS........EEEEEEEBSCTCHHHHHHHHH.TTCEEEEECCHECSSSTTS CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxx RF
                 Exo_endo_phos   1 ltwNvngqaspalgssrrsdrladlltaydaD........vlgLQEvdddelsriplllal.ggflgasstsptggggggg 72 
                                   l+wNvng              l++++++   D        ++++QE++ d  s++++   l +++++          ++g+
  gi|13540877|ref|NP_110565.1|   8 LSWNVNG--------------LRAVIKSGGLDlirngdyfAIAMQETKVDVKSVPEEMYHLgYHVYNN------PAKRKGY 68 
                                   79*****..............9****99955433333345999*********9986666655333333......4559*** PP

                                   SEEEEEECSTEEEEEEEEEEETSSSSGCEEEEEEEEEEEEEEE....CCCHHGHHHHHHHHHHHHHHHHHHHHHTTSEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Exo_endo_phos  73 nggavlsrfpltslfrrtfiefndlvaalrreplaakleqlni....ashrdhdlvrdlqllalllqvealnadrgapviv 149
                                    g ++lsr ++  +       ++++++++r+ +l  ++ ++ +    +s +     +     + +  + a+ +++++p+i+
  gi|13540877|ref|NP_110565.1|  69 SGTMTLSREKPIDV------SYGFESEEGRILNLEFDNFYFINayfpNSQHGLTRLDLKLDFDKKFLGYANDLRKKKPLII 143
                                   ***********666......5678888888888888888877799988999999999999999999999************ PP

                                   EEE-SSSTSGGGBSCGHHHHHHCTTTH...........H............SSCESCETTTTTTTTTTTEB-BEEEEEECH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxx...........x............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Exo_endo_phos 150 aGDfNarpsdddsrvlrtrglalapap...........v............glyllgggptptyvtraggsrlDrilaspa 207
                                   +GDfN+++ + d  ++ ++   +  ++           +            g+++ +++++++++ ++ g+r+D+  +s++
  gi|13540877|ref|NP_110565.1| 144 CGDFNVAHEEIDIARPKDNEHNAGFTIeertwmsqflsSgyvdtfrlfttdGGHYSWWSYRFNAREKNIGWRIDYFVVSDD 224
                                   ***********************99999888777766505667788899******************************84 PP

                                   HHCCEEEEEEECCHHEEC.TSSCSSSB CS
                                   xxxxxxxxxxxxxxxxxx.xxxxxxxx RF
                 Exo_endo_phos 208 lalfrsgvlppplalvrr.ealtlSDH 233
                                    +  +  +           e++++SDH
  gi|13540877|ref|NP_110565.1| 225 IKDKVKASR--------IlENVKGSDH 243
                                   333333333........256789**** PP

>> Exo_endo_phos_2  Endonuclease-reverse transcriptase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.1   3.3e-09   2.9e-05       2     118 ..     102     246 ..     101     247 .. 0.76

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 3.3e-09
               Exo_endo_phos_2   2 liisvYippsd.......elenlestlekllselksp.kiiilGDfNakhplWgsedtds........sargeeLieflee 66 
                                   ++i++Y p+s+          ++++++  + ++l+++ ++ii+GDfN+ h++ +  + ++         ++ + + +fl +
  gi|13540877|ref|NP_110565.1| 102 YFINAYFPNSQhgltrldLKLDFDKKFLGYANDLRKKkPLIICGDFNVAHEEIDIARPKDnehnagftIEERTWMSQFLSS 182
                                   899*******9999988655578888888888888888**************99855555566778875666666677766 PP

               Exo_endo_phos_2  67 hslsll...nllksgptfkssng.......sstiDltltsdnlals..kleleeedlgSDHrpi 118
                                     + ++    +   +  ++s +           iD +++sd++ ++  + ++ e+  gSDH p+
  gi|13540877|ref|NP_110565.1| 183 GYVDTFrlfTTDGGHYSWWSYRFnarekniGWRIDYFVVSDDIKDKvkASRILENVKGSDHAPV 246
                                   666655433444455667766556677455566***********999999999999*****998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 1534.68
//
Query:       gi|13540878|ref|NP_110566.1|  [L=426]
Description: serine hydroxymethyltransferase [Thermoplasma volcanium GSS1]
Scores for complete 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  210.6   0.0    3.5e-62  210.3   0.0    1.0  1  SHMT             Serine hydroxymethyltransferase
    4.5e-07   29.4   0.0    6.4e-06   25.6   0.0    2.0  1  Aminotran_1_2    Aminotransferase class I and II
    9.2e-06   25.1   0.0    1.4e-05   24.6   0.0    1.4  1  Beta_elim_lyase  Beta-eliminating lyase
    0.00014   21.0   0.3    0.00038   19.5   0.0    1.7  2  SelA             L-seryl-tRNA selenium transferase
  ------ inclusion threshold ------
      0.019   15.4   0.1      0.089   13.3   0.0    2.1  2  HMA              Heavy-metal-associated domain
      0.077   11.5   0.0       0.41    9.1   0.0    2.0  2  Met_gamma_lyase  Methionine gamma-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 !  210.3   0.0   1.2e-65   3.5e-62       9     399 .]      10     383 ..       3     383 .. 0.90

  Alignments for each domain:
  == domain 1  score: 210.3 bits;  conditional E-value: 1.2e-65
                                   HHHHHHHHHHHHHSEE-STT-----HHHHHHHTSGGGG----EETTEESSST-HHHHHHHHHHHHHHHHHCT-STTTEEEE CS
                          SHMT   9 aeiikkekerqkeeieliasenftskavlealGsvltnkyaeGyPGkryyGGcefvdeveelaqdrakelfkldpakwgvn 89 
                                    e+ ++ ++   +++ liasen++s+ + e++ s l+ +yaeG+P +ryy G++fvd +e+ +++   +lfk++    + +
  gi|13540878|ref|NP_110566.1|  10 RELAQQHNALFGDSVALIASENVMSPLAREVMISDLESRYAEGLPHHRYYQGNNFVDLIEDKTNELLSKLFKTE----QTD 86 
                                   556666666667899***********************************************************....999 PP

                                   ---SSHHHHHHHHHHHHT-TT-EEEEESCTTTSTGGGT-BTSS-B-SHHHHHSEEEEE-B-TTTSSB-HHHHHHHHHHH-- CS
                          SHMT  90 vqplsGsqanlavytallepgdrilgldladGGhlthGakveskkisassklfesveykvdketglidydelekkakefkP 170
                                    +p sG++an a   al +pgd +    l+ GGh++     e+  + + +   ++++y  dk+t ++d de  k  k+ kP
  gi|13540878|ref|NP_110566.1|  87 PRPISGTNANSAAIYALAKPGDLVAVPALSGGGHISAA---EFGILGMRG--VRTISYPYDKNTMTVDPDEASKIIKREKP 162
                                   ***********************************864...343345555..56788888899****************** PP

                                   SEEEEE-SST-S---HHHHHHHHHHTT-EEEEE-GGGHHHHHTTSS--GCC.TSSEEEEESSSTT-S-S-EEEEEC-SEEE CS
                          SHMT 171 klivaGtsaysrlidyarlreiadevgayllvdmahiaGlvaagvipsPfe.yadvvtttthktlrGprgglillrkgvks 250
                                   k+ + G+s +   +  + ++   devg  +  d ah+ Gl+a+  + +P++  ad+vt  thkt+ Gp+ g+il +     
  gi|13540878|ref|NP_110566.1| 163 KVCLFGQSVFMFPVPLKEMKGAFDEVGCKVWYDGAHVLGLIAGRKFQDPLReGADIVTGSTHKTFPGPQHGVILGN----- 238
                                   *************************************************96269********************99..... PP

                                   EETTTEEEEHHHHHHHHHHHTTTT-SS--HHHHHHHHHHHHHCTSHHH.HHHHHHHHHHHHHHHHHHHHTT-EEGGGS... CS
                          SHMT 251 vdktgkevleelekkinsavfPglqGGPlnhviaakavalkealepef.kvyqkqvlknakalaealkekgyklvsgG... 327
                                          ++ e  k +  avfPg+    +  ++aa+  ++  a e ef  +y++++++nakala +l + g+k++++    
  gi|13540878|ref|NP_110566.1| 239 -------TDSETWKSVRRAVFPGVLSNHHLNAMAAL--GITAAEELEFgEKYASDIIDNAKALAGELYSLGFKVLAEErgf 310
                                   .......56789999********9987666666655..5666777788457***********************9853234 PP

                                   -SSSEEEEEGGGGTS-HHHHHHHHHHTTEE-EEE--TTS..STTTT-SEEEEESHHHHHTT--HHHHHHHHHHH CS
                          SHMT 328 tdnhlvlvdlrekgldGkraekvlekvnitankntvPgd..ksalvtsGlrlGtpaltsrgfkeedlekvakfi 399
                                   t++h + vd++++g  Gk + + le+  i  nkn +P d  k++  +sG+r+G   +t+ g+++++++++a++i
  gi|13540878|ref|NP_110566.1| 311 TESHTMAVDVTQNG-GGKYVAETLEASGIILNKNLLPWDdnKKSQNPSGIRIGVQEVTRTGMGKSEMKEIASLI 383
                                   9********99877.7999******************9988999**************************9876 PP

>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.0   2.2e-09   6.4e-06      50     306 ..      73     310 ..      60     319 .. 0.79

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 2.2e-09
                                   HHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEEEESS-THHHHHHH.....HTTSEEEEEEBEET CS
                 Aminotran_1_2  50 eealakflgrseklklkreaavvvgsGagaliealifllklnpgdeilvpdptyasyknilr.....lsggevvryplyse 125
                                   +e l k+++       + ++    +sG++a+ +a+ +l+k  pgd + vp+++ + ++ +++     ++g+  ++yp y++
  gi|13540878|ref|NP_110566.1|  73 NELLSKLFK-------TEQTDPRPISGTNANSAAIYALAK--PGDLVAVPALSGGGHISAAEfgilgMRGVRTISYP-YDK 143
                                   566666666.......444466789**************9..****************9876444337888899999.779 PP

                                   TTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGG CS
                 Aminotran_1_2 126 edfhldlealeealkeapegnkktkvilvesphNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavatran 206
                                   +++++d ++  + +k+     k++ +++  s++       +l+e +      ++ ++ +  D a+  +     ++      
  gi|13540878|ref|NP_110566.1| 144 NTMTVDPDEASKIIKRE----KPKVCLFGQSVFM---FPVPLKEMKGA---FDEVGCKVWYDGAHVLGLIAGRKF---QDP 211
                                   ***************94....3556777788874...45788888888...***************999997666...557 PP

                                   STTSTTEEEEEESSSTT.SSGGG-EEEEEEEH..HHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                 Aminotran_1_2 207 veeepnllivgslsKaf.GlaGeRvGyilgna..avvsqlrklsrpflsssllqaavaaalsdallkqseleemrqrlqkr 284
                                   + e+ + +++gs  K f G      G ilgn   +  + +r+++ p+  s++   a aa   +a ++ ++ e+ ++ ++++
  gi|13540878|ref|NP_110566.1| 212 LREGAD-IVTGSTHKTFpG---PQHGVILGNTdsETWKSVRRAVFPGVLSNHHLNAMAALGITAAEELEFGEKYASDIIDN 288
                                   777766.*********944...446*****666766666666666666655555555555555555668************ PP

                                   HHHHHHHHHHSTEEEECCSCSS CS
                 Aminotran_1_2 285 rkelrdeLaelglkvlasqsgm 306
                                   +k l  eL +lg+kvla++ g+
  gi|13540878|ref|NP_110566.1| 289 AKALAGELYSLGFKVLAEERGF 310
                                   *****************99987 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.0   4.6e-09   1.4e-05      27     242 ..      58     318 ..       2     414 .. 0.80

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 4.6e-09
                                   CCT--HHHHHHHHHHHH....HTT-SEEEEES.-HHHHHHHHHHHH--TTEEEEEETT...-HHHHSSTTHHHHCC--EEE CS
               Beta_elim_lyase  27 sYgedktvnrLedavae....lfgkeaalfvp.qGtaAnsillkillqrgeevivtep...ahihfdetgaiaelagvklr 99 
                                    Y++++ v  +ed+++e    lf +e++ + p +Gt Ans ++ +l+++g+ v v      +hi   e g +  + gv+ +
  gi|13540878|ref|NP_110566.1|  58 YYQGNNFVDLIEDKTNEllskLFKTEQTDPRPiSGTNANSAAIYALAKPGDLVAVPALsggGHISAAEFGIL-GMRGVRTI 137
                                   4555555555566655544446666666666669*****************999888788899999999987.67777777 PP

                                   EE-EBTT.TBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEETTHHHHHHHHT CS
               Beta_elim_lyase 100 dlknkea.GkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgARfanaakslg 179
                                     + +++  ++d+++  ++ik+     ek+k+ +  + + +    +v+l+e++      ++ g ++++DgA ++    + +
  gi|13540878|ref|NP_110566.1| 138 SYPYDKNtMTVDPDEASKIIKR-----EKPKVCLFGQSVFM---FPVPLKEMKG---AFDEVGCKVWYDGAHVLGLI-AGR 206
                                   7776553277788899999999.....78999999999998...8999888775...5789***********99866.555 PP

                                   S-CHHHHTTSSEEEEESSSTT--SS-EEEEE-HH........................................HHHHHHH CS
               Beta_elim_lyase 180 eivkemfsyvDsvtmslkKdllanvGgvlafrddel....................................edylaerve 224
                                        + +++D+vt s  K    +  gv++++ d++                                    e+y +  + 
  gi|13540878|ref|NP_110566.1| 207 KFQDPLREGADIVTGSTHKTFPGPQHGVILGNTDSEtwksvrravfpgvlsnhhlnamaalgitaaeelefgEKYASDIID 287
                                   555556689*************************98********************************************* PP

                                   HHHHHT---SSTHHHHH.............. CS
               Beta_elim_lyase 225 qrkylggglrqagvlaa.............l 242
                                    +k+l+g+l++ g+++              +
  gi|13540878|ref|NP_110566.1| 288 NAKALAGELYSLGFKVLaeergfteshtmaV 318
                                   *************988743444433333330 PP

>> SelA  L-seryl-tRNA selenium transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   1.3e-07   0.00038     189     228 ..     201     240 ..     184     249 .. 0.89
   2 ?   -3.0   0.0      0.94   2.8e+03     305     346 ..     363     403 ..     350     410 .. 0.65

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.3e-07
                                   T-----BHHHHHHTT-SEEEEETTSTT-SSS-EEEEE-HH CS
                          SelA 189 glskePtvqealaeGvdlvsfsGDkllGgpqaGiivGkke 228
                                   gl    ++q+ l+eG+d+v+ s  k + gpq G+i+G+ +
  gi|13540878|ref|NP_110566.1| 201 GLIAGRKFQDPLREGADIVTGSTHKTFPGPQHGVILGNTD 240
                                   66777789*****************************975 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 0.94
                                   EEEEEE-TCSSS-SS--EEEEEEEEEESSS-HHHHHHHHHTS CS
                          SelA 305 vvkslsqvGsGslPveelpsaaltiaeekakleaLeerlral 346
                                   v++ +++ G G   ++e++s + +   +k++ ++++e+++ l
  gi|13540878|ref|NP_110566.1| 363 VQE-VTRTGMGKSEMKEIASLIYRAIVKKEEPSKIKEEVKDL 403
                                   443.47888898899999988876665566555555555544 PP

>> HMA  Heavy-metal-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0     3e-05     0.089      15      53 ..     123     157 ..     109     163 .. 0.78
   2 ?   -1.4   0.2       1.1   3.2e+03      45      59 ..     392     403 ..     381     405 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3e-05
                           HMA  15 kvekvLselpgVesvkvdlatktvtVegdaestklrkii 53 
                                   + e  ++++ gV++++  ++++t+tV+ d++s+     i
  gi|13540878|ref|NP_110566.1| 123 AAEFGILGMRGVRTISYPYDKNTMTVDPDEASKI----I 157
                                   55567899***********************933....3 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.1
                           HMA  45 estklrkiieaieka 59 
                                   e+   +ki+e+++++
  gi|13540878|ref|NP_110566.1| 392 EP---SKIKEEVKDL 403
                                   44...7788877764 PP

>> Met_gamma_lyase  Methionine gamma-lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.0   0.00014      0.41      45     100 ..      57     110 ..      43     138 .. 0.87
   2 ?   -0.5   0.0      0.11   3.4e+02     207     227 ..     209     229 ..     206     261 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00014
               Met_gamma_lyase  45 tgstGyGyddlGrdtldkvyaevfgaeaalvrpqlvsGthaiatalfgvlrpgdel 100
                                   +   G  + dl  d+ +++ +++f++e++  rp  +sGt a ++a+++  +pgd +
  gi|13540878|ref|NP_110566.1|  57 RYYQGNNFVDLIEDKTNELLSKLFKTEQTDPRP--ISGTNANSAAIYALAKPGDLV 110
                                   5567888999999***************98776..9*****************954 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.11
               Met_gamma_lyase 207 kePtevGadliaGsliknpGG 227
                                   ++P + Gad+++Gs  k   G
  gi|13540878|ref|NP_110566.1| 209 QDPLREGADIVTGSTHKTFPG 229
                                   689999********9998666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (426 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       648  (0.0361426); expected 358.6 (0.02)
Passed bias filter:                      620  (0.0345808); 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: 0.69u 0.31s 00:00:01.00 Elapsed: 00:00:00.50
# Mc/sec: 2571.55
//
Query:       gi|13540879|ref|NP_110567.1|  [L=75]
Description: H+-ATPase subunit K [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      3e-08   33.9  10.7    3.9e-08   33.5  10.7    1.1  1  ATP-synt_C  ATP synthase subunit C
  ------ inclusion threshold ------
        1.2    8.1   4.7        1.2    8.1   4.7    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 !   33.5  10.7   4.3e-12   3.9e-08       1      60 []      11      70 ..      11      70 .. 0.98

  Alignments for each domain:
  == domain 1  score: 33.5 bits;  conditional E-value: 4.3e-12
                                  HHHHHHH.GGGHHHHHHHHHHHHHHHHHHHHSGHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                    ATP-synt_C  1 lgaglavGlsalgsGigiGkagsagiravarnpklftksliilafaeaialygLivalil 60
                                  ++a ++++ + +g+G+++  +g+ag++++a++p+ f+++l +++++e++ ++gL  ++il
  gi|13540879|ref|NP_110567.1| 11 IAASISIAGGLIGTGMAQQGIGAAGMGIIAEKPEKFGQVLFFFVIPETLWVIGLALGIIL 70
                                  799*****************************************************9997 PP

>> PHO4  Phosphate transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   4.7   0.00013       1.2      85     137 ..       9      71 ..       1      75 [] 0.62

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00013
                          PHO4  85 lPvStthslvGaliGaalaaeggeavkw.......kklvkivlswvls...Pllggiiaallf 137
                                   l +  + s+ G+liG ++a +g  a  +       +k+++++++ v+     ++g++++++l+
  gi|13540879|ref|NP_110567.1|   9 LAIAASISIAGGLIGTGMAQQGIGAAGMgiiaekpEKFGQVLFFFVIPetlWVIGLALGIILL 71 
                                   5678899************85533333334555655888887776664211344555555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       500  (0.0278878); expected 358.6 (0.02)
Passed bias filter:                      231  (0.0128842); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.25s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 536.34
//
Query:       gi|13540880|ref|NP_110568.1|  [L=185]
Description: V-type ATP synthase subunit E [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    0.00059   19.3  16.4       0.22   10.9  13.6    2.2  2  vATP-synt_E   ATP synthase (E/31 kDa) subunit
  ------ inclusion threshold ------
        0.2   12.1   9.0        0.4   11.1   9.0    1.5  1  V-ATPase_G_2  Vacuolar (H+)-ATPase G subunit
       0.24   10.8   9.7       0.29   10.5   9.4    1.3  1  GBP_C         Guanylate-binding protein, C-terminal domain
       0.28   11.1   2.9        4.6    7.1   2.0    2.4  2  eIF-5_eIF-2B  Domain found in IF2B/IF5


Domain annotation for each model (and alignments):
>> vATP-synt_E  ATP synthase (E/31 kDa) subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9  13.6     5e-05      0.22       8     125 ..      11     131 ..       5     141 .. 0.74
   2 !   10.6   0.0   6.1e-05      0.27     157     198 ..     138     183 ..     118     183 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 5e-05
                                   HHHHHHHHHH.HHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHH....HHHHHHHHHHHHHH.HHHHHHHHHHHH CS
                   vATP-synt_E   8 ekAeeIkaka.eeefeiekaklveeeeekieeayekkeKqaelqkkiaiS....nalnkarlkvLkar.eevleevfeeae 82 
                                   e+ +eIk+k   e+ + +++k+++e++ ki+e+++  + ++ ++ +++      +a  +ar  +L+ + ee+le  +++a+
  gi|13540880|ref|NP_110568.1|  11 EQSQEIKKKEiLENTKNILDKMEAEKKAKIDEIRALYQEKMRAESSRITAsiidKANIEARS-ILRNKiEEILEGYVSAAQ 90 
                                   4556676554146678899*************998777776666555544022134455555.55555499********** PP

                                   HHHHHHTTSHHCCCCHHHHHHCCCCCCC-SSCEEEEECCCCHH CS
                   vATP-synt_E  83 kkLaeveedkdeYkellkkLivqalvkleepevivrarkeDae 125
                                   + L+++ +   eY  ll+k+i   + k  +++ i+++  +D+ 
  gi|13540880|ref|NP_110568.1|  91 EILRNIRNMP-EYPALLNKMIE-VAKKYLGQDCIIKVDSKDKA 131
                                   *********9.*********96.55667777788888888765 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 6.1e-05
                                   B....TTSSSEEEECCSSSCEEECCCHHHCHHHHHHHHHHCCCCCH CS
                   vATP-synt_E 157 l....edvlGGvvleaadgkikvnnTlearLelvleqllpeirkaL 198
                                   +    +d  GG+  +++dgk++++    +++e vle++  +i ++L
  gi|13540880|ref|NP_110568.1| 138 ItysnIDPYGGILASSRDGKVELDLRVSSIMEEVLEKIKVKIYTRL 183
                                   234468999**************************99988887766 PP

>> V-ATPase_G_2  Vacuolar (H+)-ATPase G subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   9.0     9e-05       0.4      20     101 ..       9      95 ..       2      98 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 9e-05
                                   HHHHHHHHHH.HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHCSHHH...HH CS
                  V-ATPase_G_2  20 rlEaArkeae.reveaAeaeAarilreAeakakalqaeyeqelaeevarireeararaeaeaqav.rkraearlqq...Av 95 
                                    +E+ ++  + + +e+ +   +++ +e +ak+ ++ a y++++++e +ri + +  +a+ ea+++ r++ e+ l++   A+
  gi|13540880|ref|NP_110568.1|   9 EIEQSQEIKKkEILENTKNILDKMEAEKKAKIDEIRALYQEKMRAESSRITASIIDKANIEARSIlRNKIEEILEGyvsAA 89 
                                   566666644404456666667778888888999*****************************9972555555555333377 PP

                                   HHHHHH CS
                  V-ATPase_G_2  96 elilka 101
                                   ++il++
  gi|13540880|ref|NP_110568.1|  90 QEILRN 95 
                                   888876 PP

>> GBP_C  Guanylate-binding protein, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   9.4   6.6e-05      0.29     223     289 ..       3      69 ..       1      81 [. 0.87

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 6.6e-05
                         GBP_C 223 leekqkeeeqrmeakeksleehvkqLkekleeereklleeqerllekklkeqeellkegfkeeaesl 289
                                   le+  ke eq+ e k+k++ e+ k++ +k+e+e++ +++e + l ++k++ + + ++++   +a+  
  gi|13540880|ref|NP_110568.1|   3 LEQVIKEIEQSQEIKKKEILENTKNILDKMEAEKKAKIDEIRALYQEKMRAESSRITASIIDKANIE 69 
                                   56667889999****************************************9999998887777655 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 ?    7.1   2.0     0.001       4.6      13      84 ..       7      86 ..       2      90 .. 0.56
   2 ?    2.8   0.0     0.022     1e+02      27      58 ..      95     126 ..      75     139 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.001
                                  STT--EEEETT.EEEETTHHHHHHHHTTSHHHHHHHHHH....HHTSEEEESETTEEEES.....SSSSCCHHHHHHHHHH CS
                  eIF-5_eIF-2B 13 mpklqvkvegkkktvivNfeeiakaLnrdpehvlkyllk....elgtqgsidengrliln.....gkfeakkleklldkyi 84
                                  +++++  +e kkk +++N ++i ++++ +++  ++ + +    ++ +++s   + ++i +      ++ ++k+e++l+ y+
  gi|13540880|ref|NP_110568.1|  7 IKEIEQSQEIKKKEILENTKNILDKMEAEKKAKIDEIRAlyqeKMRAESSR-ITASIIDKanieaRSILRNKIEEILEGYV 86
                                  678888999999***************998876554433000033333332.22222222000013334445555555555 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.022
                                   EETTHHHHHHHHTTSHHHHHHHHHHHHTSEEE CS
                  eIF-5_eIF-2B  27 vivNfeeiakaLnrdpehvlkyllkelgtqgs 58 
                                   +i+N+ e    Ln+  e   kyl+++  ++ +
  gi|13540880|ref|NP_110568.1|  95 NIRNMPEYPALLNKMIEVAKKYLGQDCIIKVD 126
                                   68999999999999999999999998766554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2080  (0.116013); expected 358.6 (0.02)
Passed bias filter:                      733  (0.0408835); expected 358.6 (0.02)
Passed Vit filter:                        93  (0.00518713); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 1180.71
//
Query:       gi|13540881|ref|NP_110569.1|  [L=356]
Description: V-type ATP synthase subunit C [Thermoplasma volcanium GSS1]
Scores for complete 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-45  155.7   5.4    2.4e-45  155.5   5.4    1.0  1  vATP-synt_AC39  ATP synthase (C/AC39) subunit


Domain annotation for each model (and alignments):
>> vATP-synt_AC39  ATP synthase (C/AC39) subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  155.5   5.4   1.3e-49   2.4e-45       3     333 ..      10     347 ..       8     350 .. 0.92

  Alignments for each domain:
  == domain 1  score: 155.5 bits;  conditional E-value: 1.3e-49
                                   HHHHHHGGGS--HHHHHHHTTS.-HHHHHHHHHTSGGGGG--.....SSSHHHHHHHHHHHHHHHTTTGGGGS-H..HHHH CS
                vATP-synt_AC39   3 ArvramrsglLteedyenLlqcesledvkryLketdYgnfladelseplsrsdiekalreklarefnklreqapgp.sref 82 
                                   +r+++++  +L+++ +e+L+  +  +d+ ++L  + Y+++    +s + +++  e a++++l+   n++ ++a  p +++ 
  gi|13540881|ref|NP_110569.1|  10 GRLKVYEVDFLKKDFLEHLISLDKPSDFSSVLYASVYKEDYDALTSIYREPDLTEMAINRHLV-RMNRIAAFAIPPlAKNA 89 
                                   799*************************************777778899*************9.6899************* PP

                                   HHHHHHHHHHHHHHHHHHHHHH..T-.....-GGGS-..--.S.S.SS-HHHHHHHHHSSSHHHHHHHHHT-HHHHHHHHH CS
                vATP-synt_AC39  83 ldyllyrydidNvklllrgklsg.dl.....dleeleeklhpl.g.elsaldldklieaksveelyeallgtpyakyleea 155
                                   l +++ ++di+N+k+++ +k+ g +l         +++  + l g  l+++d +++++  +ve ++++l    y++y+ ++
  gi|13540881|ref|NP_110569.1|  90 LTAYISKWDIENIKTVISSKFLGhGLketemFIVSFRDIPMGLiGgVLTNEDYRNMMNLPNVEAIINYLTRYGYGSYMLQF 170
                                   **********************877766666444444445555955*********************************** PP

                                   HCC...--SHHHHHHHHHHHHHHHHHHHHHTSS-HH...HHHHHHHHHHHHHHHHHHHTTTSS......T...--SS-S-- CS
                vATP-synt_AC39 156 ldeleetgdleiienaLdkayledllkfckklggetaeilreilgfeiDlrniniilrskkygelskedrkkllipggsly 236
                                   ++++++tgd++++  +Ld++y+++ll++ k  +g++   + +++++ iD+ n+n+il+ kk +  s e + + l++gg+++
  gi|13540881|ref|NP_110569.1| 171 IEDYRKTGDISPMLYSLDRYYYARLLESLKYYNGDE-GPVINYIRSDIDRINLNTILKGKKLN-ISYERFFSGLVDGGNIP 249
                                   ****************************99777655.6699********************77.667779999******** PP

                                   HHHHHHHHTT-G.....GG..GGSSTSSTTGGGTT--S.HHHHHHHHHHHHHHHHHT.TTSSSTSTHHHHHHHHHHHHHHH CS
                vATP-synt_AC39 237 peglealaeaedveellaal.kyteygelleealeeagslksledaldealvkllkk.afrqqfsvgvfyaYlklkeqEir 315
                                    + + +++  +d+ ++++ + +y++  +  ++++++ g+l +++  +++ ++ ++   + + ++s+  ++ ++++ e E +
  gi|13540881|ref|NP_110569.1| 250 INAIHDFYGNSDILSMIDSIkRYYDLEDAKNKYASD-GNLYHFDVSMRNIMITKYMGtMSMLPLSLDSIFYFIIRAEIERQ 329
                                   ************999999999999999988888776.66****************************************** PP

                                   HHHHHHHHHHHT--SHHH CS
                vATP-synt_AC39 316 nlrwIaegiaqglpkekI 333
                                   nlr+I e +  g pke I
  gi|13540881|ref|NP_110569.1| 330 NLRTIYEAKLHGAPKESI 347
                                   ***************999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (356 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.52
# Mc/sec: 2058.03
//
Query:       gi|13540882|ref|NP_110570.1|  [L=104]
Description: V-type ATP synthase subunit F [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    6.6e-15   55.2   0.3    7.5e-15   55.0   0.3    1.1  1  ATP-synt_F  ATP synthase (F/14-kDa) subunit
  ------ inclusion threshold ------
      0.063   13.3   0.0      0.074   13.0   0.0    1.1  1  TIR_3       Toll/interleukin-1 receptor domain


Domain annotation for each model (and alignments):
>> ATP-synt_F  ATP synthase (F/14-kDa) subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.0   0.3   8.3e-19   7.5e-15       1      90 [.       5      95 ..       5      96 .. 0.91

  Alignments for each domain:
  == domain 1  score: 55.0 bits;  conditional E-value: 8.3e-19
                                  EEEEESHHHHHHHHHTTCEEEECSSHHHHHHHHHHHHHHTTEEEEEEEHHHHCCCH.HHHHHCTCSSSSEEEEESCSCCGGSH CS
                    ATP-synt_F  1 iavIGdedtvtgfrlaGvgevevtdeeeieealkelleredigiilitekiaeeir.elideykeealPaileIPskegpyde 82
                                  i+vIG++d+v+gfrl+G++++ v++ +++ +++ e  e++ + +i+++e++ ++i+ +++++++ +++P+++ IP  + + +e
  gi|13540882|ref|NP_110570.1|  5 ITVIGERDVVLGFRLLGITNTIVAEGKDLVKKFMEEFENPHCSVIVVSEHLKNMIDkKTLRSIEVSSKPLVVFIPLPGFKEEE 87
                                  89***********************9999999999999*****************98999999999*********99887777 PP

                                  HCHHHHHH CS
                    ATP-synt_F 83 ekdsvrkk 90
                                  + +++ k+
  gi|13540882|ref|NP_110570.1| 88 SIETMAKR 95
                                  76666665 PP

>> TIR_3  Toll/interleukin-1 receptor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   8.3e-06     0.074      37     106 ..      27      94 ..      15      99 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 8.3e-06
                         TIR_3  37 leeetslkkeellslksskcilllLsaelleslyepkvlefLervlkppekvvvLlCGVeeselleelfk 106
                                   + e + l k+ ++++++ +c ++++s++l +++ ++k l+++e v + p  v + l G +e+e +e++ k
  gi|13540882|ref|NP_110570.1|  27 VAEGKDLVKKFMEEFENPHCSVIVVSEHLKNMI-DKKTLRSIE-VSSKPLVVFIPLPGFKEEESIETMAK 94 
                                   5556667778899***************98888.777777775.44444556666888888888877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       713  (0.039768); expected 358.6 (0.02)
Passed bias filter:                      632  (0.0352502); 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: 0.57u 0.37s 00:00:00.94 Elapsed: 00:00:00.57
# Mc/sec: 552.48
//
Query:       gi|13540883|ref|NP_110571.1|  [L=776]
Description: V-type ATP synthase subunit A [Thermoplasma volcanium GSS1]
Scores for complete 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-88  294.1   0.0    4.9e-80  268.2   0.0    2.4  2  ATP-synt_ab      ATP synthase alpha/beta family, nucleotide-b
    4.6e-41  139.5   0.7    2.8e-40  136.9   0.1    2.3  2  ATP-synt_ab_Xtn  ATPsynthase alpha/beta subunit N-term extens
    1.1e-19   70.7   0.0    2.6e-19   69.5   0.0    1.7  1  Intein_splicing  Intein splicing domain
    2.6e-11   43.9   2.7    2.6e-11   43.9   2.7    2.1  2  ATP-synt_ab_N    ATP synthase alpha/beta family, beta-barrel 
     0.0064   16.0   0.0       0.04   13.4   0.0    2.1  1  Hint             Hint module
  ------ inclusion threshold ------
      0.023   14.9   0.3        8.2    6.7   0.0    3.4  3  Peptidase_M23    Peptidase family M23
      0.025   14.5   0.1      0.099   12.6   0.1    2.0  2  RnfC_N           RnfC Barrel sandwich hybrid domain


Domain annotation for each model (and alignments):
>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0   1.4e-08   3.6e-05       1      29 [.     209     237 ..     209     278 .. 0.92
   2 !  268.2   0.0   1.9e-83   4.9e-80      27     213 .]     421     618 ..     408     618 .. 0.96

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 1.4e-08
                                   SSHHHHHHS-EBTT-EEEEEESTTSSHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   ATP-synt_ab   1 GirvlDalfpivqGqrtlipgafgvGktv 29 
                                   G+rv+Dalfp+++G++ ++pg fg Gk v
  gi|13540883|ref|NP_110571.1| 209 GQRVIDALFPVAKGGTAAVPGPFGSGKCV 237
                                   9**************************86 PP

  == domain 2  score: 268.2 bits;  conditional E-value: 1.9e-83
                                   HHHHHHHHHHHSSTSSEEEEEEESEEHHHHHHHHHHCHH......SS.GGGGEEEEEEETTS-HHHHHHHHHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   ATP-synt_ab  27 ktvisqslskqsnsddaiiyvgiGergnevaevleefpe......gt.imkrtvlvantsnepvaareasiytgitlAEyf 100
                                    tvi+++l+k+s+++ +++y+g+Gergne++e+l++fpe      g+ +m+rtvl+antsn+pvaareasiytgit+AEy+
  gi|13540883|ref|NP_110571.1| 421 NTVIQHQLAKWSDAN-IVVYIGCGERGNEMTEILTTFPElkdpvsGQpLMDRTVLIANTSNMPVAAREASIYTGITIAEYY 500
                                   699********9777.***********************988886337********************************* PP

                                   HHTTSEEEEEEETHHHHHHHHHHHHHHTTTSBEGGGSBTTHHHHHHHHHTTSEEE.....TSSEEEEEEEEEEE-GGCSTT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxx RF
                   ATP-synt_ab 101 rdqgknvlliadslsrwaeAlreislrlgempadqgypaylgaklaslyERagka.....pdrtGsvtivaavspaggDfs 176
                                   rd+g++v l+ads+srwaeAlreis+rl+emp+++gypaylg +++++yER+g+a     +dr Gs+t++ avsp+ggD+s
  gi|13540883|ref|NP_110571.1| 501 RDMGYDVALMADSTSRWAEALREISGRLEEMPGEEGYPAYLGRRISEFYERSGRArlvspEDRFGSITVIGAVSPPGGDIS 581
                                   ***********************************************************999******************* PP

                                   SHHHHHHHHHSSEEEEB-HHHHHTTBSSSBCTTTEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   ATP-synt_ab 177 dpvttatlgitdgfivLdkklaqrkhfPainvlvSvS 213
                                   +pv+++tl++t +f+ Ld +la+r+hfP+in+l+S+S
  gi|13540883|ref|NP_110571.1| 582 EPVSQNTLRVTRVFWALDASLANRRHFPSINWLNSYS 618
                                   ************************************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 !  136.9   0.1   1.1e-43   2.8e-40       1     121 []      82     200 ..      82     200 .. 0.98
   2 ?    0.0   0.0      0.29   7.4e+02      75     106 ..     336     366 ..     319     374 .. 0.73

  Alignments for each domain:
  == domain 1  score: 136.9 bits;  conditional E-value: 1.1e-43
                                   EETTS-BHHHHHHHHTSBE-TT----SS-SSS-EEEEESS-TT-EEETT-EEEEEECTTCEEEEEE--TT-EEEEEEE--E CS
               ATP-synt_ab_Xtn   1 yDGiqrpLekiaeksgsfierGvkvpaldrekkwefkpkvkvgdkvsggdilGtvqeteliehkimvppkvegkvkeiaee 81 
                                   yDGiqrpL+ i+e+sg+fi+rG++ p+ldr+k+w+f+p+vk+ d v +g+++Gtvqet+li+h+i+vp +v+gk+k+i  e
  gi|13540883|ref|NP_110571.1|  82 YDGIQRPLDVIKETSGDFIARGLNPPPLDRKKEWDFVPAVKKNDIVYPGQVIGTVQETSLITHRIIVPDGVSGKIKSIY-E 161
                                   9*****************************************************************************9.* PP

                                   EEE-TTSECEEECETT.ECEEEESSEEEETTS---ESEEE CS
               ATP-synt_ab_Xtn  82 geytvedtiaeveteegkekeltllqkwPvrkprpvkekl 121
                                   g+ tved++++++te+g +++++l+ +wPvrk+r v +kl
  gi|13540883|ref|NP_110571.1| 162 GKRTVEDVVCTISTEHG-DVDVNLMTTWPVRKARRVVRKL 200
                                   *************9996.9*****************9996 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.29
                                   EEEE--EEEE-TTSECEEECETT.ECEEEESS CS
               ATP-synt_ab_Xtn  75 vkeiaeegeytvedtiaeveteegkekeltll 106
                                   ++e++ +++ +v d+ia v ++e++ +++ + 
  gi|13540883|ref|NP_110571.1| 336 IEEVM-ASNLKVGDMIAAVAESESEARDCGMS 366
                                   66676.77788888888888888777777776 PP

>> Intein_splicing  Intein splicing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.5   0.0     1e-22   2.6e-19       3     134 .]     245     421 ..     243     421 .. 0.82

  Alignments for each domain:
  == domain 1  score: 69.5 bits;  conditional E-value: 1e-22
                                   ECTTCEEEEHHHHCC...ECTTEEEEEETTTTEEEEEE............EEEEEEEEEE....EEEEEEETTS-EEEEET CS
                                   xxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxx............xxxxxxxxxx....xxxxxxxxxxxxxxxxx RF
               Intein_splicing   3 ledgeekvkieelve...kegeevlslnledlklevks............vkkliklklk....elyeiklesgrkikaTp 64 
                                   l+dg+   ki++l++   k+++++++    ++ ++ k             v    +l +k     l++i++  gr++ +Tp
  gi|13540883|ref|NP_110571.1| 245 LADGKT-IKIKDLYSserKKEDNIVEAGSGEEIIHLKDpiqiysyvdgtiVRSRSRLLYKgkssYLVRIETIGGRSVSVTP 324
                                   667444.58999998666555555555443333333337788888888885544444444444799*************** PP

                                   T-EEEECCTTEEEEEECCC--TT-EEEEE........................HSCEEEEEEEEEEEEECEEEEEEEEETT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
               Intein_splicing  65 eHkllvvrdegivEkradeLkegdliavp........................dadvvwdkvksievedeeeyVYdltved 121
                                    Hkl+v++++gi E+ a++Lk+gd+ia +                          ++++d+vksi +e+ + +VYdl+v++
  gi|13540883|ref|NP_110571.1| 325 VHKLFVLTEKGIEEVMASNLKVGDMIAAVaeseseardcgmseecvmeaevytSLEATFDRVKSIAYEKGDFDVYDLSVPE 405
                                   ***************************99***********************9999***********************99 PP

                                   T.-EEEE.CTTE.EE- CS
                                   x.xxxxx.xxxx.xxx RF
               Intein_splicing 122 n.hNFva.ngii.vHN 134
                                   +  NF++ +g++ +HN
  gi|13540883|ref|NP_110571.1| 406 YgRNFIGgEGLLvLHN 421
                                   867*****999889*9 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 !   43.9   2.7     1e-14   2.6e-11       1      68 [.       4      65 ..       4      66 .. 0.98
   2 ?   -3.8   0.0         7   1.8e+04      32      45 ..     649     662 ..     643     663 .. 0.74

  Alignments for each domain:
  == domain 1  score: 43.9 bits;  conditional E-value: 1e-14
                                  EEEEETTEEEEESSTSCETCTTEEEEECCETCSTEEEEEEEEEETTEEEEEESS-STTBBTTSEEEEE CS
                 ATP-synt_ab_N  1 ivqviGpvvdvefgigrlpgiynalevelvefgtlllgvalnlgedkVrvivmgstdGlsrGteVkrT 68
                                  iv+++Gpvv +e+ +    ++y++++v+  e   +l+g+++++++++  ++v+++t G+++ ++V++T
  gi|13540883|ref|NP_110571.1|  4 IVRISGPVVVAEDIEN--AKMYDVVKVG--E--MGLIGEIIRIEGNRSTIQVYEDTAGIRPDEKVENT 65
                                  89**************..**********..9..*********************************99 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 7
                                   CSTEEEEEEEEEET CS
                 ATP-synt_ab_N  32 fgtlllgvalnlge 45 
                                    ++ l++va+ +g 
  gi|13540883|ref|NP_110571.1| 649 RESELQEVAQLVGY 662
                                   36899999999886 PP

>> Hint  Hint module
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.0   1.6e-05      0.04       9     120 ..     233     358 ..     229     367 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.6e-05
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXX.....XXXXXXXXXXXX....XXXXXXXXXXX..........XXXXXXXXXX CS
                          Hint   9 kggCFpgestvtvedgeqkslseLepGdk.....Vlavdesgevvf....sevllfldrds..........eqraefveie 70 
                                   +g C +ge  v ++dg+++++++L   ++     ++ + + +e+++     ++ +++d              ++   v ie
  gi|13540883|ref|NP_110571.1| 233 SGKCVSGETPVYLADGKTIKIKDLYSSERkkednIVEAGSGEEIIHlkdpIQIYSYVDGTIvrsrsrllykGKSSYLVRIE 313
                                   5788888888888888888888886654422222555555555554221123455555444666677887556666789** PP

                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..XXXX CS
                          Hint  71 tengekltlTpaHLvfvsenekssseeeeavfaskvregdyvlvedtask 120
                                   t  g+++++Tp H +fv +++  ++     v+as+ + gd++    ++++
  gi|13540883|ref|NP_110571.1| 314 TIGGRSVSVTPVHKLFVLTEKGIEE-----VMASNLKVGDMIAAVAESES 358
                                   *****************99886665.....9**********998444444 PP

>> Peptidase_M23  Peptidase family M23
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.19     5e+02      24      54 ..      25      55 ..      14      65 .. 0.80
   2 ?    6.7   0.0    0.0032       8.2      56      76 ..     120     140 ..     115     147 .. 0.89
   3 ?    2.4   0.0     0.069   1.8e+02      15      56 ..     284     329 ..     270     370 .. 0.66

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.19
                                  EEEEEEETTTEEEEEEEECTCEEEEEEEESE CS
                 Peptidase_M23 24 VvfagkkegyGnvviidhgdgystlyahlsk 54
                                  Vv++g+++ +G++++i+ +  ++++y     
  gi|13540883|ref|NP_110571.1| 25 VVKVGEMGLIGEIIRIEGNRSTIQVYEDTAG 55
                                  8999999667********9999999976655 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0032
                                   SS-TTEEE-TTCEEEEEBSTS CS
                 Peptidase_M23  56 svkegqkVkaGqvIGtvgstg 76 
                                   +vk+++ V  GqvIGtv +t 
  gi|13540883|ref|NP_110571.1| 120 AVKKNDIVYPGQVIGTVQETS 140
                                   49***************9886 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.069
                                   EEEESSSEEEEEEEE....ETTTEEEEEEEECTCEEEEEEEESEES CS
                 Peptidase_M23  15 pVlAaadGtVvfagk....kegyGnvviidhgdgystlyahlskis 56 
                                   ++++  dGt+v ++     k++   +v+i+  +g s     ++k+ 
  gi|13540883|ref|NP_110571.1| 284 QIYSYVDGTIVRSRSrllyKGKSSYLVRIETIGGRSVSVTPVHKLF 329
                                   699*******999996663334488899998776555544444443 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 ?   12.6   0.1   3.9e-05     0.099      43      85 ..     118     164 ..     108     177 .. 0.79
   2 ?   -3.5   0.0       4.1     1e+04      68      97 ..     284     313 ..     273     314 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.9e-05
                        RnfC_N  43 kplvkvgdkVlkGqkiaeaeg..fvsapvhas..vsGtVkaiekrlv 85 
                                    p vk++d V  Gq+i++ ++  +++  +  +  vsG++k+i + + 
  gi|13540883|ref|NP_110571.1| 118 VPAVKKNDIVYPGQVIGTVQEtsLITHRIIVPdgVSGKIKSIYEGKR 164
                                   689**************997656788888887669******987655 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 4.1
                        RnfC_N  68 pvhasvsGtVkaiekrlvahgsgveavvie 97 
                                   ++++ v Gt+++ ++rl  +g+    v ie
  gi|13540883|ref|NP_110571.1| 284 QIYSYVDGTIVRSRSRLLYKGKSSYLVRIE 313
                                   799999999999888888777776666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (776 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       523  (0.0291706); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.79u 0.37s 00:00:01.16 Elapsed: 00:00:00.55
# Mc/sec: 4250.49
//
Query:       gi|13540884|ref|NP_110572.1|  [L=460]
Description: V-type ATP synthase subunit B [Thermoplasma volcanium GSS1]
Scores for complete 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-66  223.6   0.0    2.9e-66  223.2   0.0    1.2  1  ATP-synt_ab    ATP synthase alpha/beta family, nucleotide-bin
    5.5e-11   42.8   1.6    6.1e-11   42.7   0.4    1.8  2  ATP-synt_ab_N  ATP synthase alpha/beta family, beta-barrel do
  ------ inclusion threshold ------
       0.09   12.9   0.1       0.21   11.7   0.1    1.7  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 !  223.2   0.0   4.9e-70   2.9e-66       1     213 []     132     350 ..     132     350 .. 0.98

  Alignments for each domain:
  == domain 1  score: 223.2 bits;  conditional E-value: 4.9e-70
                                   SSHHHHHHS-EBTT-EEEEEESTTSSHHHHHHHHHHHSSTS....S.EEEEEEESEEHHHHHHHHHHCHHSSGGGGEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....x.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   ATP-synt_ab   1 GirvlDalfpivqGqrtlipgafgvGktvisqslskqsnsd....d.aiiyvgiGergnevaevleefpegtimkrtvlva 76 
                                   Gi+++D + ++v+Gq++ i++++g++++++++++++q++      + a+++ ++G  ++e++ + ++f+e+++++r+v+++
  gi|13540884|ref|NP_110572.1| 132 GISAIDGMNTLVRGQKLPIFSGSGLPHNQLAAQIARQAKVLdsseNfAVVFGAMGITSEEANYFTNQFRETGALSRSVMFL 212
                                   89***********************************8654777778********************************** PP

                                   EETTS-HHHHHHHHHHHHHHHHHHHH.TTSEEEEEEETHHHHHHHHHHHHHHTTTSBEGGGSBTTHHHHHHHHHTTSEEET CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   ATP-synt_ab  77 ntsnepvaareasiytgitlAEyfrd.qgknvlliadslsrwaeAlreislrlgempadqgypaylgaklaslyERagkap 156
                                   n s++p ++r++ +++++t+AEy++  +++++l+i++++++++eAlreis + +e+p+++gyp+y++++l+++yERagk++
  gi|13540884|ref|NP_110572.1| 213 NLSSDPSMERIILPRIALTTAEYLAFqKEMHILVILTDMTNYCEALREISSAREEVPGRRGYPGYMYTDLSTIYERAGKLK 293
                                   *************************97899*************************************************** PP

                                   SSEEEEEEEEEEE-GGCSTTSHHHHHHHHHSSEEEEB-HHHHHTTBSSSBCTTTEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   ATP-synt_ab 157 drtGsvtivaavspaggDfsdpvttatlgitdgfivLdkklaqrkhfPainvlvSvS 213
                                    ++Gs+t++++++++g+D+++pv++ t +it+g++v++++l +++++P i+vl S+S
  gi|13540884|ref|NP_110572.1| 294 GNNGSITQIPILTMPGDDITHPVPDLTGYITEGQVVVSRDLNRKGIYPGIDVLLSLS 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   0.4     1e-14   6.1e-11       1      69 []       9      75 ..       9      75 .. 0.91
   2 ?   -3.7   0.0         3   1.8e+04      49      64 ..     132     147 ..     131     147 .. 0.79

  Alignments for each domain:
  == domain 1  score: 42.7 bits;  conditional E-value: 1e-14
                                  EEEEETTEEEEESSTSCETCTTEEEEECCETCSTEEEEEEEEEETTEEEEEESS-STTBBT.TSEEEEES CS
                 ATP-synt_ab_N  1 ivqviGpvvdvefgigrlpgiynalevelvefgtlllgvalnlgedkVrvivmgstdGlsr.GteVkrTG 69
                                  +++++Gp++ ve+++    ++++++ +el + g+ ++g++l  + + ++v+++g t+G+   Gt+Vk+ G
  gi|13540884|ref|NP_110572.1|  9 VSEISGPLLFVENVPN--AAYNEMVDIELDN-GETRQGQVLDTRKGLAIVQIFGATTGIGTeGTRVKFRG 75
                                  799*************..7777777777557.****************************99*****976 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 3
                                   EEEESS-STTBBTTSE CS
                 ATP-synt_ab_N  49 rvivmgstdGlsrGte 64 
                                   ++ +++++  l+rG++
  gi|13540884|ref|NP_110572.1| 132 GISAIDGMNTLVRGQK 147
                                   5778889999999975 PP

>> HAS-barrel  HAS barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   3.6e-05      0.21       5      49 ..       6      51 ..       4      90 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.6e-05
                    HAS-barrel  5 igests.sslifrvegskdvkvGeyVeielpdgeivlGmvtdirrg 49
                                  + +++  s+++ +ve++ +  + e+V iel+ ge + G+v+d r+g
  gi|13540884|ref|NP_110572.1|  6 YKSVSEiSGPLLFVENVPNAAYNEMVDIELDNGETRQGQVLDTRKG 51
                                  55667779***********************************993 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (460 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       292  (0.0162865); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); 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: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 2863.48
//
Query:       gi|13540885|ref|NP_110573.1|  [L=215]
Description: V-type ATP synthase subunit D [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.2e-46  159.0  11.5    1.4e-46  158.8  11.5    1.0  1  ATP-synt_D  ATP synthase subunit D


Domain annotation for each model (and alignments):
>> ATP-synt_D  ATP synthase subunit D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  158.8  11.5   7.6e-51   1.4e-46       1     196 []      15     206 ..      15     206 .. 0.97

  Alignments for each domain:
  == domain 1  score: 158.8 bits;  conditional E-value: 7.6e-51
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSTSTTSTSHHHHHHHSSS.SS-..TSS CS
                    ATP-synt_D   1 eLirlkkrlklaqrghslLkkKrdaLilefreilkelkelreeleeelkeayfslaeafaaggeediesavlesvklakvv 81 
                                   eLir ++r+kla++g++lLk+Kr+aLi ef +i + ++ +re+l++e+++a +++  a +++g+ ++e+++++s +     
  gi|13540885|ref|NP_110573.1|  15 ELIRTRRRIKLARKGLDLLKMKRSALIYEFLQISRTIRGMRENLRREVEDALNTIRTAEILEGQVALERIANMSSD----S 91 
                                   79******************************************************************99998876....8 PP

                                   -SEEEEEEBTTSEEEEEEE-..S.SSTSSSSSSSSTCHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                    ATP-synt_D  82 kvelktenvaGVkvpvfeleeeksdstelygllrtgaqldeavealrellellvelasletslelLdeeikktnrRvNaLe 162
                                   ++++ ++nv+GV +p+++l+ + s  ++ y  ++ +  +++a++++++l+ +l+++ ++e++l+ L  ei kt+rR Na+e
  gi|13540885|ref|NP_110573.1|  92 TINVDSRNVMGVVIPTLNLTYNLSILSDVYRTISVPVAINDAIDRFQRLFLNLIQILEKENALRNLLIEIDKTKRRSNAIE 172
                                   9******************999666678899999*********************************************** PP

                                   TTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                    ATP-synt_D 163 kvvIPrleetikyIkseLdEqereeffrlkkvkk 196
                                   +++IPrle + k Ik+ LdE+er +f+ lk +kk
  gi|13540885|ref|NP_110573.1| 173 NILIPRLEYQAKMIKMMLDERERDTFTTLKTIKK 206
                                   ********************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       697  (0.0388756); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 1446.49
//
Query:       gi|13540886|ref|NP_110574.1|  [L=111]
Description: V-type ATP synthase subunit H [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.018   15.5  15.6      0.078   13.5  15.6    1.9  1  V-ATPase_G       Vacuolar (H+)-ATPase G subunit
       0.04   13.8  14.2      0.047   13.6  14.2    1.1  1  ARGLU            Arginine and glutamate-rich 1
      0.041   13.3   7.2      0.048   13.1   7.2    1.2  1  RNase_E_G        Ribonuclease E/G family
       0.16   11.8  10.2       0.18   11.6  10.2    1.0  1  DUF445           Protein of unknown function (DUF445)
       0.26   10.3   3.8        0.3   10.1   3.8    1.0  1  ArAE_2_N         Putative ER transporter, 6TM, N-terminal
       0.38   10.3   5.6       0.46   10.0   5.6    1.1  1  HAUS6_N          HAUS augmin-like complex subunit 6 N-terminu
       0.38    9.5  13.9       0.44    9.3  13.9    1.1  1  Mitofilin        Mitochondrial inner membrane protein
       0.51   10.1   7.5       0.65    9.8   7.5    1.1  1  Selenoprotein_S  Selenoprotein S (SelS)
       0.59   10.6  14.1        1.1    9.7  14.1    1.5  1  V-ATPase_G_2     Vacuolar (H+)-ATPase G subunit
       0.75    7.9  11.9       0.79    7.8  11.9    1.0  1  HSP70            Hsp70 protein
        0.8   10.3   6.0        1.6    9.4   6.0    1.6  1  DUF883           Bacterial protein of unknown function (DUF88
        2.2    9.4   9.3        9.5    7.4   2.8    2.3  2  RNase_J_C        Ribonuclease J C-terminal domain
        2.4    8.8  11.1        3.3    8.3   0.7    2.1  2  YtxH             YtxH-like protein
        3.4    6.8   6.7        3.7    6.7   6.7    1.0  1  TMPIT            TMPIT-like protein
        6.7    6.3   7.2        8.3    6.0   5.5    1.8  2  DUF2321          Uncharacterized protein conserved in bacteri


Domain annotation for each model (and alignments):
>> V-ATPase_G  Vacuolar (H+)-ATPase G subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5  15.6   6.6e-05     0.078      13      83 ..      19      89 ..       9     105 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.6e-05
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHHHHHSSHHHHHHH CS
                    V-ATPase_G 13 EkeAaeivkeArkrkakrlkqAkeeAekEieeyrakkekefkekeaeklgseeelekkieketeekikelk 83
                                  E + ++ +++ +k + + +k+A ++ e+Ei+++ +++e+e++++  e+    e+ +k+i +e+++k +++ 
  gi|13540886|ref|NP_110574.1| 19 EISSDKEIEDLKKTQDDLVKEASQKNEEEIAKFTEEMEAEYRKFLDEQRKIAEDKAKSIIEEARQKASRIL 89
                                  566788999**************************************************999999988775 PP

>> ARGLU  Arginine and glutamate-rich 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6  14.2   3.9e-05     0.047      42     127 ..      13      95 ..       5     101 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.9e-05
                         ARGLU  42 rveearkkmekqveeelerereaeleeekrkeeeerkkreelerileenkrkveeaqrklaEerlaeleekrrlkeerqrl 122
                                   ++ +++++ +++  e+l++ +   ++e+ +k+eee +k +   +++e + rk  ++qrk aE++ + + e+ r+k  r  l
  gi|13540886|ref|NP_110574.1|  13 KIIKEKEISSDKEIEDLKKTQDDLVKEASQKNEEEIAKFT---EEMEAEYRKFLDEQRKIAEDKAKSIIEEARQKASRILL 90 
                                   77889999999999*******************9987654...467888999**************999999998887666 PP

                         ARGLU 123 kkeee 127
                                   +  e+
  gi|13540886|ref|NP_110574.1|  91 NISES 95 
                                   65555 PP

>> RNase_E_G  Ribonuclease E/G family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   7.2     4e-05     0.048      50     116 ..      39     108 ..       7     111 .] 0.80

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4e-05
                     RNase_E_G  50 aaegaseeelekdleelkkkweeileka...kkrkapsllyeeedlllrvlrdllnedieeivvddkely 116
                                   +a++++eee++k  ee++ ++++ l+++   ++ ka s++ e+++ ++r+l +++++++++iv+d+ ++y
  gi|13540886|ref|NP_110574.1|  39 EASQKNEEEIAKFTEEMEAEYRKFLDEQrkiAEDKAKSIIEEARQKASRILLNISESELTKIVIDTVNAY 108
                                   6888999999999999999999888887444448899****************************98877 PP

>> DUF445  Protein of unknown function (DUF445)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6  10.2   0.00015      0.18     228     325 ..       6     108 ..       4     111 .] 0.67

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00015
                        DUF445 228 aakveklkkkklsdlevqeyeealwealkdlllkdlneeesllrerisklleklgeklaed....pklreklnkflenaaa 304
                                   ++ +e++k  k +++ +++  e+l +   dl++++ +++e ++ + ++++++++ + l e+    ++ +++++++++++a+
  gi|13540886|ref|NP_110574.1|   6 MDDIEAIKIIKEKEISSDKEIEDLKKTQDDLVKEASQKNEEEIAKFTEEMEAEYRKFLDEQrkiaEDKAKSIIEEARQKAS 86 
                                   566677777777777777777777777777777766665567777777777777777777744454444555566666666 PP

                        DUF445 305 kv.lekyrldiskiveetvnaf 325
                                   ++ l++++++++kiv +tvna+
  gi|13540886|ref|NP_110574.1|  87 RIlLNISESELTKIVIDTVNAY 108
                                   651677899***********97 PP

>> ArAE_2_N  Putative ER transporter, 6TM, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   3.8   0.00025       0.3     326     404 ..      12      94 ..       3     107 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00025
                      ArAE_2_N 326 lravil..kserssklaa...nghakldseieekkrevgayetkksielleardaqrsltlsdldeviealrelsgeilea 401
                                   + ++i+  ++++++++++   ++   ++++ +++++e+++++++ ++e  +  d+qr+   ++ + +ie  r+  ++il  
  gi|13540886|ref|NP_110574.1|  12 I-KIIKekEISSDKEIEDlkkTQDDLVKEASQKNEEEIAKFTEEMEAEYRKFLDEQRKIAEDKAKSIIEEARQKASRILLN 91 
                                   4.334456455555566666366666777778888****************99************************9988 PP

                      ArAE_2_N 402 vee 404
                                   ++e
  gi|13540886|ref|NP_110574.1|  92 ISE 94 
                                   876 PP

>> HAUS6_N  HAUS augmin-like complex subunit 6 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   5.6   0.00038      0.46     126     197 ..      18      87 ..      11     107 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00038
                       HAUS6_N 126 kskklalevreaaskkaqdlsklvaahrvslrrflrekaaadrarqkyqenaqllekkerelraeleelqae 197
                                   k+ ++ +e+ ++ ++++  +++++++ + ++ +f +e++a++  r+ + e+ +  e+k +++ +e ++  ++
  gi|13540886|ref|NP_110574.1|  18 KEISSDKEIEDLKKTQDDLVKEASQKNEEEIAKFTEEMEAEY--RKFLDEQRKIAEDKAKSIIEEARQKASR 87 
                                   444455566666677777777777777777777777777776..7777777777777777776666663333 PP

>> Mitofilin  Mitochondrial inner membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3  13.9   0.00037      0.44     327     396 ..      16      84 ..       8      99 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00037
                     Mitofilin 327 keelekqeealsarleeerakeerqlrlelereleeireeyeekLrteLerqaeaheehLkdvlveqeie 396
                                   k e+e ++ + ++ l++ ++   ++  +++e+e+++ +ee+e + r+ L++q++++e++ k  ++e+++ 
  gi|13540886|ref|NP_110574.1|  16 K-EKEISSDKEIEDLKKTQDDLVKEASQKNEEEIAKFTEEMEAEYRKFLDEQRKIAEDKAKSIIEEARQK 84 
                                   3.45677888888888888888889999999999999999999999999999999999999999888876 PP

>> Selenoprotein_S  Selenoprotein S (SelS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   7.5   0.00054      0.65      37     121 ..       2      80 ..       1      87 [. 0.66

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00054
               Selenoprotein_S  37 GWylllgivllllliqklrkrlralrqresdksaaaldpdvvvkrqealeaaRlrmqeeldakaekfkekkkqleeekRrq 117
                                   GWy++  i ++ ++ +k  ++ +    + +d + ++ d  +++ +++  e    ++ ee++a+  kf ++++++ e+k + 
  gi|13540886|ref|NP_110574.1|   2 GWYMMDDIEAIKIIKEKEISSDK----EIEDLKKTQDDLVKEASQKN--EEEIAKFTEEMEAEYRKFLDEQRKIAEDKAKS 76 
                                   99999999999888765443322....22233332333333333333..34445789999999999999999999999999 PP

               Selenoprotein_S 118 kiem 121
                                    ie+
  gi|13540886|ref|NP_110574.1|  77 IIEE 80 
                                   9997 PP

>> V-ATPase_G_2  Vacuolar (H+)-ATPase G subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7  14.1   0.00091       1.1       6      91 ..      11     100 ..       6     111 .] 0.81

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00091
                                   HTHHHHHHHHHHHHHHHHHHHHHHHHHHHH....HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                  V-ATPase_G_2   6 llkeLaerEaeLdqrlEaArkeaereveaA....eaeAarilreAeakakalqaeyeqelaeevarireeararaeaeaqa 82 
                                    +k ++e+E   d+ +E+ +k+    v++A    e e a+  +e ea+ +++ +e ++  +++ + i eear++a+    +
  gi|13540886|ref|NP_110574.1|  11 AIKIIKEKEISSDKEIEDLKKTQDDLVKEAsqknEEEIAKFTEEMEAEYRKFLDEQRKIAEDKAKSIIEEARQKASRILLN 91 
                                   578899999999**********99999999444445778889999999999999999999999999*******99988888 PP

                                   HHHHHHCSH CS
                  V-ATPase_G_2  83 vrkraearl 91 
                                   ++++   ++
  gi|13540886|ref|NP_110574.1|  92 ISESELTKI 100
                                   777766664 PP

>> HSP70  Hsp70 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8  11.9   0.00066      0.79     493     580 ..      11      99 ..       4     111 .] 0.69

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00066
                                   EEEE.ECCSSSBHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGGGSTHHHHHHHHHHHHHHHCHT. CS
                         HSP70 493 eiti.easeglseeeiekmvkdaeesaeedkkkkeaieakneaeelvyslekkleeeaekvseaekekvesaieeLkeel. 571
                                    i+i +++e  s++eie + k +++  +e  ++k++ e  + +ee+  + +k l+e+++ +++++k+ +e+a ++ ++ l 
  gi|13540886|ref|NP_110574.1|  11 AIKIiKEKEISSDKEIEDLKKTQDDLVKEA-SQKNEEEIAKFTEEMEAEYRKFLDEQRKIAEDKAKSIIEEARQKASRILl 90 
                                   4555055555999*****998887766655.555566999999**************999999999888888777665541 PP

                                   TSSCHHHHH CS
                         HSP70 572 eeeekeeie 580
                                   + +e+e ++
  gi|13540886|ref|NP_110574.1|  91 NISESELTK 99 
                                   233344444 PP

>> DUF883  Bacterial protein of unknown function (DUF883)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   6.0    0.0013       1.6       4      67 ..      23      83 ..      18     102 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0013
                        DUF883  4 eaeleslladleellkeaadeageeaeelRerleerlerarerlrdaeeavaerakeaaeaadd 67
                                   +e+e+l ++ ++l+kea+++ +ee+++  e++e++ ++    l+++++ ++++ak+++e+a++
  gi|13540886|ref|NP_110574.1| 23 DKEIEDLKKTQDDLVKEASQKNEEEIAKFTEEMEAEYRKF---LDEQRKIAEDKAKSIIEEARQ 83
                                  589*********************9999988887665444...444444444555555554443 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 ?    7.4   2.8    0.0079       9.5      17      60 ..      24      67 ..      14      71 .. 0.85
   2 ?    6.0   0.7     0.021        25      12      57 ..      71     110 ..      68     111 .] 0.70

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0079
                     RNase_J_C 17 eLieeakkvvretieealeekesdwnelkrkirealkkflykkt 60
                                  + ie++kk+  + ++ea +++e + ++  +++  + +kfl ++ 
  gi|13540886|ref|NP_110574.1| 24 KEIEDLKKTQDDLVKEASQKNEEEIAKFTEEMEAEYRKFLDEQR 67
                                  55899999999999999999999999999999999999998875 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.021
                     RNase_J_C  12 vkeseeLieeakkvvretieealeekesdwnelkrkirealkkfly 57 
                                   +++++++ieea++++++++ ++ e+      el + + ++++ +l+
  gi|13540886|ref|NP_110574.1|  71 EDKAKSIIEEARQKASRILLNISES------ELTKIVIDTVNAYLE 110
                                   5566777777777777777776554......788888888888876 PP

>> YtxH  YtxH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   5.2     0.016        20      32      69 ..      24      61 ..      10      65 .. 0.83
   2 ?    8.3   0.7    0.0028       3.3      25      62 ..      58      95 ..      56     111 .] 0.73

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.016
                          YtxH 32 ekaddlkekakelleeakekakekaedlkekvkekade 69
                                  ++ +dlk+  ++l++ea++k +e++++++e+++ +  +
  gi|13540886|ref|NP_110574.1| 24 KEIEDLKKTQDDLVKEASQKNEEEIAKFTEEMEAEYRK 61
                                  4589999999999*****************99987766 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0028
                          YtxH 25 etRkdlkekaddlkekakelleeakeka........kekaedlkek 62
                                  e Rk l e+ + + +kak+++eea++ka        +        +
  gi|13540886|ref|NP_110574.1| 58 EYRKFLDEQRKIAEDKAKSIIEEARQKAsrillnisE--------S 95
                                  678889999999999*********9999555555542........2 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   6.7    0.0031       3.7      11      81 ..      12      83 ..       5     110 .. 0.61

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0031
                         TMPIT 11 fkeleetakeykqkleelsklqskcskeik.kqkkrlkelksslkklkksvkeeeeeeveelkeelkerkkv 81
                                  +k ++e++ +  +++e+l+k q++++ke++ k+++++ +++++++   ++  +e+++++e+ ++++ e+ ++
  gi|13540886|ref|NP_110574.1| 12 IKIIKEKEISSDKEIEDLKKTQDDLVKEASqKNEEEIAKFTEEMEAEYRKFLDEQRKIAEDKAKSIIEEARQ 83
                                  667889999999999999999999888775145667788888777766665556665555444444332222 PP

>> DUF2321  Uncharacterized protein conserved in bacteria (DUF2321)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   5.5     0.007       8.3      85     144 ..      11      70 ..       3      86 .. 0.69
   2 ?    2.5   0.5     0.084     1e+02     108     146 ..      66     103 ..      45     109 .. 0.45

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.007
                       DUF2321  85 aakelieeleelsddekeklkaslpdllvd.tpktklaavrfkkvlskaeksvadalrdiv 144
                                   a  ++i+e+e  sd+e e lk++ +dl+++ + k +  +++f   ++   ++ +d  r+i 
  gi|13540886|ref|NP_110574.1|  11 A-IKIIKEKEISSDKEIEDLKKTQDDLVKEaSQKNEEEIAKFTEEMEAEYRKFLDEQRKIA 70 
                                   4.45788888888999**************4445556667777666666665555555554 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.084
                       DUF2321 108 lpdllvdtpktklaavrfkkvlskaeksvadalrdivvd 146
                                      +  d +k  + ++r k   +   + + + l +iv+d
  gi|13540886|ref|NP_110574.1|  66 QRKIAEDKAKSIIEEARQKAS-RILLNISESELTKIVID 103
                                   334444444444444444432.22223333444455555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3152  (0.175805); expected 358.6 (0.02)
Passed bias filter:                      876  (0.0488594); expected 358.6 (0.02)
Passed Vit filter:                       105  (0.00585643); 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: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 712.79
//
Query:       gi|13540887|ref|NP_110575.1|  [L=643]
Description: V-type ATP synthase subunit I [Thermoplasma volcanium GSS1]
Scores for complete 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-33  114.2   0.0    2.9e-24   85.1   0.0    2.5  2  V_ATPase_I    V-type ATPase 116kDa subunit family
     0.0046   16.4   0.3       0.22   10.9   0.0    2.2  2  FliD_C        Flagellar hook-associated protein 2 C-terminus
     0.0094   15.7   0.5       0.92    9.3   0.1    2.2  2  Nsp1_C        Nsp1-like C-terminal region
  ------ inclusion threshold ------
       0.13   12.4   1.5       0.41   10.7   0.2    2.3  2  THUMP         THUMP domain
       0.19   11.8   0.3       0.38   10.8   0.0    1.6  2  Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C
        7.1    6.6   8.3        1.5    8.8   2.8    2.2  2  Prefoldin_2   Prefoldin subunit


Domain annotation for each model (and alignments):
>> V_ATPase_I  V-type ATPase 116kDa subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.1   0.0   9.6e-28   2.9e-24     205     464 ..     166     429 ..     136     440 .. 0.85
   2 !   26.2   0.1   6.2e-10   1.8e-06     716     812 ..     537     627 ..     534     628 .. 0.72

  Alignments for each domain:
  == domain 1  score: 85.1 bits;  conditional E-value: 9.6e-28
                    V_ATPase_I 205 veksvfiiffqgeqlkekikkicesfgaklyelpeseeereeklkeveeriedlekvleqteealkevleeiakeleewkl 285
                                   ++ + f +++  + ++  + k+++ +g +++++pe   + ++ ++++e++ +dle+++ + +++l+e+ +++ +++++++ 
  gi|13540887|ref|NP_110575.1| 166 TRMKGFSVITAPSLISGELAKVANRLGLQIIHIPEVIGKPADVISSLEQKKKDLEDAVASLNKRLEELSDKYYERIAQVRE 246
                                   4567799999999******************************************************************** PP

                    V_ATPase_I 286 kvkkekaiyhtLnlfnldvtkkvliaegWvpkeeleeiqkalkeateessssvpsilneietketpPTyfrtnkfteafQe 366
                                    ++ e +  ++ ++   + tk ++  egW+p e+ e++++al+++        + il++i+t+e+pPT  r  k  + f  
  gi|13540887|ref|NP_110575.1| 247 ALEIEAKKIDVEEKT--KGTKYTFAVEGWIPDEDYEKLHNALNRVI-----GGSFILSKIKTDEMPPTLLRNPKRISLFEF 320
                                   999998877777777..788999*********************88.....34689************************* PP

                    V_ATPase_I 367 ivdaYGiarYrEvNpalftiitFPFlFavMFGDiGHGlllllfalllvlkekklkkkkkdeilemlfsgRYiillmG.... 443
                                   ++  Y+ ++  E  p+l+    FP  F++M GD+G Gl++ll++l+++ + ++  +k  + i +++   R+i+++mG    
  gi|13540887|ref|NP_110575.1| 321 FIRFYSLPEGTEYDPTLIFALVFPLFFGLMVGDWGYGLFILLMSLWIIRRVDNPPAK--SHIPKVI--SRFILMIMGpqsl 397
                                   ************************************************999888876..3555544..5777777763333 PP

                    V_ATPase_I 444 ...........lfsiYtGliYNdifskslnlf 464
                                              + +i +G+++N++f+ s+  f
  gi|13540887|ref|NP_110575.1| 398 ktlaralipssIVAIVAGILFNEFFGFSILPF 429
                                   33333333333677888888888888877555 PP

  == domain 2  score: 26.2 bits;  conditional E-value: 6.2e-10
                    V_ATPase_I 716 ciSnTASYLRLWALSLAHaqLseVlwemvlkkallksksvlgvillvilfavfavltvavLllmeglsafLHaLRLhWVEf 796
                                   +iS+  SYLRL  + +A   ++e++    l++++ +  + +g+++l i++   +v+     +++ +++  +   RL  VEf
  gi|13540887|ref|NP_110575.1| 537 IISHILSYLRLVGILIASVVIAEIIDLVFLRSVV-S--HSIGLAILGIII---LVIGQLFNIILAVFEPGIQGARLIYVEF 611
                                   79**********9999988888887666666633.2..333333333333...333333334445567788899******* PP

                    V_ATPase_I 797 qsKFykgdGykFepfs 812
                                    sKFy+g+G +F+pf 
  gi|13540887|ref|NP_110575.1| 612 FSKFYHGNGKPFRPFR 627
                                   **************95 PP

>> FliD_C  Flagellar hook-associated protein 2 C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.1     0.016        49     193     225 ..      91     123 ..      76     127 .. 0.84
   2 !   10.9   0.0   7.2e-05      0.22     196     234 ..     209     247 ..     188     250 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.016
                                   HHHHHHXXXXHHHHHHHHHHHHHCHHHHHHHHH CS
                        FliD_C 193 qtasknltkqikdldkkiedldkrletleerlk 225
                                   + ++ n++++++ + +k+ed++++l+++e+rl+
  gi|13540887|ref|NP_110575.1|  91 EASKINIDEDLRIIVNKQEDIKSSLREIENRLY 123
                                   3456699************************97 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 7.2e-05
                                   HHHXXXXHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHH CS
                        FliD_C 196 sknltkqikdldkkiedldkrletleerlkkqfaaleka 234
                                   +++l++++kdl++ +++l+krle+l  ++++++a+  +a
  gi|13540887|ref|NP_110575.1| 209 ISSLEQKKKDLEDAVASLNKRLEELSDKYYERIAQVREA 247
                                   7899****************************9987765 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 !    9.3   0.1   0.00031      0.92      70     101 ..      91     122 ..      55     128 .. 0.84
   2 ?    4.4   0.0      0.01        30      15      45 ..     214     244 ..     203     247 .. 0.57

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00031
                        Nsp1_C  70 eqeqnkidqeLeyiesqqdeLeslLdnyEkel 101
                                   e+++ +id+ L +i ++q++++s L ++E++l
  gi|13540887|ref|NP_110575.1|  91 EASKINIDEDLRIIVNKQEDIKSSLREIENRL 122
                                   556778***********************976 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.01
                        Nsp1_C  15 lknktldelinkWtteLeeqekeFeeqakkv 45 
                                    k+k l++ +   ++ Lee ++++ e  ++v
  gi|13540887|ref|NP_110575.1| 214 QKKKDLEDAVASLNKRLEELSDKYYERIAQV 244
                                   3455666666666666666665555555555 PP

>> THUMP  THUMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1      0.41   1.2e+03      48      75 ..      65      96 ..      50     128 .. 0.60
   2 ?   10.7   0.2   0.00014      0.41      64     111 ..     245     293 ..     202     322 .. 0.72

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.41
                                  TTECEEEEE....EEEEESSHHHHHHHHHHHH CS
                         THUMP 48 rgiqrvipv....cevceadledileaakeiv 75
                                  rg ++++p       +++ +l+++l  a++i+
  gi|13540887|ref|NP_110575.1| 65 RGYESILPKrpvkNKAKFSGLDEVLQEASKIN 96
                                  55555555555555555555555555555554 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00014
                                   HHHHHHHHHHHHHHHHHHCT-.EEEEEEEESSSTSSSHHHHHHHHHHHH CS
                         THUMP  64 ledileaakeivkkkfeeeke.tFaVrvkrrgkhfeftsreinrevGka 111
                                    e ++  ak+i+ +++ ++++ tFaV+   +++++e   + +nr++G+ 
  gi|13540887|ref|NP_110575.1| 245 REALEIEAKKIDVEEKTKGTKyTFAVEGWIPDEDYEKLHNALNRVIGGS 293
                                   4556667889999999888889************************974 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 ?   -3.6   0.0       3.6   1.1e+04      51      64 ..     108     121 ..      93     123 .. 0.54
   2 ?   10.8   0.0   0.00013      0.38      17      88 ..     183     253 ..     180     258 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 3.6
                  Baculo_PEP_C  51 sedlksllaeldtr 64 
                                   +ed+ks+l e+++r
  gi|13540887|ref|NP_110575.1| 108 QEDIKSSLREIENR 121
                                   34444444444444 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00013
                  Baculo_PEP_C  17 dLtnvLnairlqnvqilaqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalqdtlrneLt 88 
                                   +L +v n + lq + i   + +  d i ++L++ ++dl++++a+l++rl++l+++  + ++++ ++l+ e +
  gi|13540887|ref|NP_110575.1| 183 ELAKVANRLGLQIIHIPEVIGKPADVI-SSLEQKKKDLEDAVASLNKRLEELSDKYYERIAQVREALEIEAK 253
                                   677788888888888866666666655.559999*****************************999987755 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.3      0.23   6.8e+02       9      97 ..      96     120 ..      89     125 .. 0.52
   2 ?    8.8   2.8   0.00051       1.5      62     101 ..     207     246 ..     204     263 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.23
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-TT--EEEEETTEEEEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                   Prefoldin_2   9 qlqqqlqqlaqqikqletqlkelelvleelelldedtkvyklvGdvlvkqdkeevkeeLeerketlekeiktlekqlekle 89 
                                   ++ ++l+ ++++ ++++  l+e+e                                                         
  gi|13540887|ref|NP_110575.1|  96 NIDEDLRIIVNKQEDIKSSLREIE--------------------------------------------------------- 119
                                   444455555555555555555554......................................................... PP

                                   HHHHHHHH CS
                   Prefoldin_2  90 keleelke 97 
                                          +
  gi|13540887|ref|NP_110575.1| 120 -------N 120
                                   .......4 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00051
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                   Prefoldin_2  62 evkeeLeerketlekeiktlekqleklekeleelkeelqk 101
                                   +v++ Le++k++le  +++l+k+le+l  ++ e  +++++
  gi|13540887|ref|NP_110575.1| 207 DVISSLEQKKKDLEDAVASLNKRLEELSDKYYERIAQVRE 246
                                   79999********************999887665555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (643 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1527  (0.0851693); expected 358.6 (0.02)
Passed bias filter:                     1018  (0.0567795); expected 358.6 (0.02)
Passed Vit filter:                       155  (0.00864521); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.81u 0.30s 00:00:01.11 Elapsed: 00:00:00.49
# Mc/sec: 3959.19
//
Query:       gi|13540888|ref|NP_110576.1|  [L=199]
Description: glutamine amidotransferase subunit PdxT [Thermoplasma volcanium GSS1]
Scores for complete 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-54  183.8   0.0    3.5e-54  183.5   0.0    1.0  1  SNO            SNO glutamine amidotransferase family
    2.5e-10   40.3   0.0    9.3e-10   38.4   0.0    1.8  1  GATase_3       CobB/CobQ-like glutamine amidotransferase doma
    0.00086   19.0   0.0     0.0011   18.7   0.0    1.2  1  Peptidase_S51  Peptidase family S51
  ------ inclusion threshold ------
      0.036   13.9   0.0       0.05   13.4   0.0    1.2  1  DJ-1_PfpI      DJ-1/PfpI family
      0.061   13.1   0.0      0.093   12.5   0.0    1.2  1  Thioredoxin_9  Thioredoxin


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 !  183.5   0.0   9.9e-58   3.5e-54       2     184 ..       6     187 ..       5     189 .. 0.96

  Alignments for each domain:
  == domain 1  score: 183.5 bits;  conditional E-value: 9.9e-58
                                   ESSSSSHHHHHHHHHHTTSEE.....EEE-SGGGGCC-SEEEE-SS-HHHHHHHHHHTT-HHHHHHHHHTT.--EEEETHH CS
                           SNO   2 lalqGaveehveaikkclaen.....ktvkrkedlaevdaliiPGGestamskliertglyedllefvknsekvvlGtCaG 77 
                                   +++qG+veeh+  +kk          + ++rkedl++ d+liiPGGest++ kli ++g+y+++   +k++  +v+ tCaG
  gi|13540888|ref|NP_110576.1|   6 IGFQGDVEEHIAIVKKISRRRkginvLRIRRKEDLDRSDSLIIPGGESTTIYKLISEYGIYDEIIRRAKEG-MPVMATCAG 85 
                                   789************99877667777999*****************************************9.9******** PP

                                   HHHHCCEETTBSS-SS--CCEEEETTTT-SCCGEEEEEEEETTTCSEEEEEESS--EEEEE-.TTTCEEEEECTTEEEEEE CS
                           SNO  78 lillskelenelvktlellkvkvkrnafGrqvdsfekeldfknliekftavfiraPvieeilddeavkvlyeldgeivvak 158
                                   lil+sk+++ + v+ ++ll+v++ rna+Grqv+sfe ++d+k+++  f avfiraP i+e +   +v+v+  ldg  v ++
  gi|13540888|ref|NP_110576.1|  86 LILISKDTNDDRVPGMNLLDVTIMRNAYGRQVNSFETDIDIKGIG-TFHAVFIRAPRIKEYG---NVDVMASLDGYPVMVR 162
                                   ********************************************9.**************99...899999999999**** PP

                                   ETTEEEESS-GGGSTTHCHHHHHHHH CS
                           SNO 159 qkkilatsfhPelaeddirvhdyfve 184
                                    ++il+++fhPel+ d + +h+yf+ 
  gi|13540888|ref|NP_110576.1| 163 SGNILGMTFHPELTGD-VSIHEYFLS 187
                                   **************99.9******86 PP

>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.4   0.0   2.6e-13   9.3e-10      24     126 ..      28     120 ..      22     173 .. 0.78

  Alignments for each domain:
  == domain 1  score: 38.4 bits;  conditional E-value: 2.6e-13
                      GATase_3  24 evrvrfvplkdeslgedadlvilpGgkdtiqdlallresgldeaikeaaeaggpvlgiCGGlqmLGeeiedpegvegeage 104
                                    ++v  ++ ++e+l++  d +i+pGg++t+  + l  e g+ ++i + a++g+pv++ C+Gl++ ++   d+        +
  gi|13540888|ref|NP_110576.1|  28 GINVLRIR-RKEDLDR-SDSLIIPGGESTTIYK-LISEYGIYDEIIRRAKEGMPVMATCAGLILISKDTNDD--------R 97 
                                   55666667.7899976.9*********997655.555669***************************98885........7 PP

                      GATase_3 105 veglglLdietefek.ekltgqv 126
                                   v+g++lLd+++  +   +++++ 
  gi|13540888|ref|NP_110576.1|  98 VPGMNLLDVTIMRNAyGRQVNSF 120
                                   9********98877644555444 PP

>> Peptidase_S51  Peptidase family S51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0     3e-07    0.0011      78     137 ..      38      97 ..      13     114 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 3e-07
                                   HHHHHSSEEEE--S-HHHHHHHHHHTTHHHHHHHHHHTT-EEEEETHHHHTTSSB-GGGT CS
                 Peptidase_S51  78 eklleadviyvgGGntfrLlkllketgldkllreavqqglvyiGvSAGaivagesietts 137
                                   e l ++d +++ GG+   + kl+ e g+ + ++++ ++g++++ + AG i +++  + + 
  gi|13540888|ref|NP_110576.1|  38 EDLDRSDSLIIPGGESTTIYKLISEYGIYDEIIRRAKEGMPVMATCAGLILISKDTNDDR 97 
                                   34666*******************************************999999877766 PP

>> DJ-1_PfpI  DJ-1/PfpI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   1.4e-05      0.05      59     111 ..      40      92 ..      14     112 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.4e-05
                                   CCG-SEEEE--BHHHHHH..HHTSHHHHHHHHHHHHTT-EEEEETTTHHHHHHTT CS
                     DJ-1_PfpI  59 aaeyDalvlpGGragper..lrenekvvelvkefaekgklvaaICagpqlLaaag 111
                                    ++ D l++pGG++   +  ++e   + e++ + a++g +v a Cag ++L++++
  gi|13540888|ref|NP_110576.1|  40 LDRSDSLIIPGGESTTIYklISEYGIYDEII-RRAKEGMPVMATCAG-LILISKD 92 
                                   5678********9965431144444555555.55799**********.6777665 PP

>> Thioredoxin_9  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   2.6e-05     0.093      54      92 ..      10      48 ..       7      69 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.6e-05
                                  HHHHHHHHHHHHHHHH-TTEEEEEE-HHHHHHHTTTTTT CS
                 Thioredoxin_9 54 gDaavnvPvlakiaelnpnievkillrdenlelmdqylt 92
                                  gD+ + +++++ki++  ++i+v  + r+e+l++ d+   
  gi|13540888|ref|NP_110576.1| 10 GDVEEHIAIVKKISRRRKGINVLRIRRKEDLDRSDSLII 48
                                  8********************************998766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       347  (0.0193541); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.50
# Mc/sec: 1201.74
//
Query:       gi|13540889|ref|NP_110577.1|  [L=362]
Description: aminomethyltransferase (glycine cleavage system T protein) [Thermoplasma volcanium GSS1]
Scores for complete 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-84  283.3   0.0    1.9e-84  283.0   0.0    1.1  1  GCV_T     Aminomethyltransferase folate-binding domain
    9.5e-19   67.1   0.0    1.8e-18   66.2   0.0    1.5  1  GCV_T_C   Glycine cleavage T-protein C-terminal barrel domain


Domain annotation for each model (and alignments):
>> GCV_T  Aminomethyltransferase folate-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  283.0   0.0   2.2e-88   1.9e-84       1     256 [.       8     262 ..       8     263 .. 0.97

  Alignments for each domain:
  == domain 1  score: 283.0 bits;  conditional E-value: 2.2e-88
                         GCV_T   1 lydrhkalgakfvefagwemPvqYasesikaehlavreaaglfDvShmgkievsGpdaaalLqrlltndisklkpgkatyt 81 
                                   lyd h++l+a+f++f+gw+mP++Y  +si++eh  vr++ag+fDvShmg+i v+G +a ++L+++++ ++s+l++g++ yt
  gi|13540889|ref|NP_110577.1|   8 LYDEHVKLNAHFTDFNGWDMPLYY--KSIIEEHMSVRKHAGIFDVSHMGDITVRGREAGKFLDHMFPTKVSSLNDGECIYT 86 
                                   79**********************..******************************************************* PP

                         GCV_T  82 lllnedGgvidDlivarldedefllvvnaankekdlawlekaaekkdldvevedvteelallalqGPkarevlskllgadl 162
                                   ++lne+G +idD+iv+r++ d++++v na++++k+++w++k  +  ++dv++e+v+++++ +alqGP++++v+s+l    +
  gi|13540889|ref|NP_110577.1|  87 AFLNEKGQMIDDTIVYRMSSDSYFFVPNAGTTDKIYEWVTKNSK--GFDVKIENVSSKISSIALQGPESESVISELG---F 162
                                   *****************************************655..*******************************...7 PP

                         GCV_T 163 selkffsfaevela......ggkkvlvsRtgytGedGfeiyipaeeaeelweaLleagkeegvkpaGlgArdtlRlEaglr 237
                                   s   +f+f+ v+ +      g++++++s tgytGe+G+e++ip+e+a elw++Ll+ +++ +  p+Glg rdtlR+E+g+ 
  gi|13540889|ref|NP_110577.1| 163 SYPGYFKFTYVNGKyknaitGKNDIIISGTGYTGEKGVEFIIPNEYAVELWRKLLSLVEKRSGLPCGLGSRDTLRMEKGML 243
                                   777888888888888899988889********************************************************* PP

                         GCV_T 238 lyghdldeettPleaglgw 256
                                   l ghd++e+ +P+ea++ +
  gi|13540889|ref|NP_110577.1| 244 LSGHDFNENRDPYEASISF 262
                                   ***************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 !   66.2   0.0     2e-22   1.8e-18       5      78 ..     289     360 ..     286     362 .] 0.93

  Alignments for each domain:
  == domain 1  score: 66.2 bits;  conditional E-value: 2e-22
                       GCV_T_C   5 glelddgapllrggepilrdgevvGhvTSgaysptlgksialAyvkaelaklgtevevevrgkrvpaevvkkpf 78 
                                   g+ l dg  ++r g+ +  +g+vvG++TSg  sp l+k ial+y+++e++k gt+v ve+rgk ++a+v+++  
  gi|13540889|ref|NP_110577.1| 289 GFILSDG--IPRSGNSVKVNGKVVGTLTSGSISPVLNKGIALGYIDKEYSKEGTKVFVEIRGKDHEATVSRPKI 360
                                   8889899..56******99**************************************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (362 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 2256.93
//
Query:       gi|13540890|ref|NP_110578.1|  [L=312]
Description: UDP-glucose 4-epimerase [Thermoplasma volcanium GSS1]
Scores for 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-48  163.0   0.0      1e-47  162.7   0.0    1.1  1  Epimerase        NAD dependent epimerase/dehydratase family
    1.8e-47  162.4   0.2    3.6e-47  161.4   0.2    1.4  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    1.6e-18   66.8   0.0    2.4e-18   66.3   0.0    1.2  1  RmlD_sub_bind    RmlD substrate binding domain
    3.4e-18   65.6   0.2    5.2e-18   65.0   0.2    1.2  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    7.5e-13   48.3   0.6    2.1e-11   43.5   0.6    2.6  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
    3.2e-12   46.2   0.1    1.7e-07   30.7   0.0    2.7  2  NAD_binding_4    Male sterility protein
     0.0029   17.5   0.0     0.0085   16.0   0.0    1.8  2  NAD_binding_10   NAD(P)H-binding
  ------ inclusion threshold ------
      0.012   15.0   0.5        2.4    7.6   0.0    2.6  2  adh_short        short chain dehydrogenase


Domain annotation for each model (and alignments):
>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  162.7   0.0   4.6e-51     1e-47       1     241 []       6     235 ..       6     235 .. 0.91

  Alignments for each domain:
  == domain 1  score: 162.7 bits;  conditional E-value: 4.6e-51
                                   EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC.....EEEE--TT-HHHHHHHHHHHT-SEEEE--S--- CS
                     Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledl.....elveldltdrsalerlfkeeqpdavihlAavgg 76 
                                   il+tG++GfiGs++v++ll k+ ev+++d+ls ++ +  ++       ++++ d++++      ++ ++ d+v+hlAa ++
  gi|13540890|ref|NP_110578.1|   6 ILITGGAGFIGSNMVEHLLPKN-EVTVIDNLSITDDRYIKKFYdnpnfKFIKKDILNG------IDGYHYDIVVHLAADSD 79 
                                   8******************987.99999999766666555444677778888888865......577899*********** PP

                                   HHHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHHHHHHHHHHH CS
                     Epimerase  77 vaassedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKlageklveaya 157
                                   v++ s++pa  ++ n++gt  +le++rk+++k +lf+sSs+vYG+ + +p+ e+   gpl p s Y+a+Kla+e  + aya
  gi|13540890|ref|NP_110578.1|  80 VRNGSSNPALDMKVNVEGTISVLEMMRKSDIKDILFASSSTVYGEAKVIPTPENY--GPLLPISSYGASKLAAEAFISAYA 158
                                   ************************************************9977777..9*********************** PP

                                   HHHT-EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHHHHHHHHHHTT-STTEEE CS
                     Epimerase 158 aqyglnaiilrlfnlyGprngegevsrvipalirkilegkqevtllgdgtalRdflyveDvaeaillvlehvdagdkgeiy 238
                                     yg+na+ +r  n++G++    + ++vi+ +i+k++++k+e+ +lgdgt+   +++veD++  +++v ehv+     e +
  gi|13540890|ref|NP_110578.1| 159 SYYGFNALLFRFANVVGKN----STHGVIFDFINKLKNNKKELEVLGDGTQAKSYIHVEDLIGSMIYVYEHVKG---VEPF 232
                                   *******************....9***********************************************554...4568 PP

                                   EES CS
                     Epimerase 239 niG 241
                                   n+G
  gi|13540890|ref|NP_110578.1| 233 NLG 235
                                   776 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 !  161.4   0.2   1.6e-50   3.6e-47       1     331 [.       7     302 ..       7     303 .. 0.90

  Alignments for each domain:
  == domain 1  score: 161.4 bits;  conditional E-value: 1.6e-50
                                   EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-SEEEE CS
                 GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpdevyn 81 
                                   LiTG+aGfiGs+++e+Ll k  ev++i+++s + + + i++ +++p      n+k++k D+ +       ++ ++ d v++
  gi|13540890|ref|NP_110578.1|   7 LITGGAGFIGSNMVEHLLPK-NEVTVIDNLSIT-DDRYIKKFYDNP------NFKFIKKDILN------GIDGYHYDIVVH 73 
                                   9******************9.789888887665.668999999755......79********9......5999******** PP

                                   --S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB-TT.S-----SHHHHHHHHHH CS
                 GDP_Man_Dehyd  82 LAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpqtEt.tpfyPrsPYaaaKlyad 161
                                   LAA s V++  ++P+  ++vnv Gt+ +Le++r+  ++    +++aS+s+vYG+++ +p  E+  p+ P s Y+a+Kl+a+
  gi|13540890|ref|NP_110578.1|  74 LAADSDVRNGSSNPALDMKVNVEGTISVLEMMRKSDIK---DILFASSSTVYGEAKVIPTPENyGPLLPISSYGASKLAAE 151
                                   **********************************9875...6889**************998868**************** PP

                                   HHHHHHHHHH---EEEEEE-EEESTTS-TTSCCCHHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHHHHHHHHHHHHC.SS CS
                 GDP_Man_Dehyd 162 wivvnyreayglfavngilfnhesprrgetfvtrkitravarialgkqevlylGnldakRdwghvkDyveamwlmlqq.dk 241
                                    ++ +y   yg+ a+  ++ n  +           i +++ + +++k+e  +lG++ + +++ hv+D +  m  + ++ + 
  gi|13540890|ref|NP_110578.1| 152 AFISAYASYYGFNALLFRFANVVGKNS----THGVIFDFINKLKNNKKELEVLGDGTQAKSYIHVEDLIGSMIYVYEHvKG 228
                                   *********************999994....4568**************99*************************99455 PP

                                   ---EEE-TT-EEECHHCHHCCHHCCCHHHHHH............TTGGCCCEECGG--SS--SB--B-THHHHHHH----S CS
                 GDP_Man_Dehyd 242 pedyviatgethsvrefvelaflelgktiewegkgeeevgrakesgkvvvevdpkyfrpgevdlllgdaskakeeLgWkpk 322
                                    e +++++ +++sv+++++  ++++g +               ++  v+      +  pg+v+  ++d++k+k + gWk k
  gi|13540890|ref|NP_110578.1| 229 VEPFNLGNDDVTSVDKIAKFVLEAMGLK---------------DTAIVHRGGYNGRGWPGDVKYAMMDIAKLK-KTGWKNK 293
                                   799****************999999974...............233344444556677**************9.89***** PP

                                   S-HHHHHHH CS
                 GDP_Man_Dehyd 323 vsfeelvre 331
                                   +s +e v++
  gi|13540890|ref|NP_110578.1| 294 YSSDEAVKK 302
                                   *****9986 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 !   66.3   0.0   1.1e-21   2.4e-18       2     285 ..       5     307 ..       4     309 .. 0.83

  Alignments for each domain:
  == domain 1  score: 66.3 bits;  conditional E-value: 1.1e-21
                                   EEEEESTTSHHHHHHHHHCTTTSEEEEEE-TTT--TTSHHHHHHHH................HHH--SEEEE------HHH CS
                 RmlD_sub_bind   2 kilvtGanGqlGseLakqlaeeglevlaltreeldltdaeavaell................keakpdvvvnaAAytavDk 66 
                                   +il+tG+ G +Gs++++ l  ++ ev+ +  ++l +td   ++++                 +  + d+vv++AA  +v +
  gi|13540890|ref|NP_110578.1|   5 RILITGGAGFIGSNMVEHLLPKN-EVTVI--DNLSITDDRYIKKFYdnpnfkfikkdilngiDGYHYDIVVHLAADSDVRN 82 
                                   89******************999.88888..5677777777777777777777777777777999**************** PP

                                   HHHSHHHHHHHHTHHHHHHHHHHHHCT-E.EEEEEEGGGS-S-TTS-.B-TTS----SSHHHHHHHHHHHHHHH....H-S CS
                 RmlD_sub_bind  67 aEseeeaayavnaeavealAeaaaavgal.LihvStDyVFdGekkrp.YeeddetsPlnvYGrtKlaGEqavla....agk 141
                                     s+++++++vn+e++  + e+ ++ +++ +++ S+  V+  +k  p  e+  +  P++ YG++Kla E  + a    +g 
  gi|13540890|ref|NP_110578.1|  83 GSSNPALDMKVNVEGTISVLEMMRKSDIKdILFASSSTVYGEAKVIPtPENYGPLLPISSYGASKLAAEAFISAyasyYGF 163
                                   ***************************9658899******9998888455567899*****************97666677 PP

                                   SEEEEEE-SEESS.SSS-HHHHHH.HHHHH-SEEEEESS..-EE--EEHHHHHHHHHHHHHHCHH.GGG-EEEE---BS-E CS
                 RmlD_sub_bind 142 kalivRtswvyge.kgknfvktml.rlakereelkvvaD..qlgsPTsardlAevllqllekaaeekelagvyHlaneget 218
                                   +al++R++ v g+ + +  ++ ++ +l ++++el+v  D  q  s  +++dl   ++++ e+ +      + + l+n+++t
  gi|13540890|ref|NP_110578.1| 164 NALLFRFANVVGKnSTHGVIFDFInKLKNNKKELEVLGDgtQAKSYIHVEDLIGSMIYVYEHVKG----VEPFNLGNDDVT 240
                                   9**********985455666655505568899*****9966777778899*********999997....889********* PP

                                   EHHHHHHHHHHHHCHTTSEEEEE-CCCS--SS---SBE-B--HHHHHCCT----BHHHHHHHHHHHH CS
                 RmlD_sub_bind 219 swlefArailkeagadseevkpistaeyptpAkRPanSvLdtekleatfgiklrewrealkevlkel 285
                                   s  ++A+ +l+++g + + +      +        +++++d +kl++t+  +  +  ea+k++++e+
  gi|13540890|ref|NP_110578.1| 241 SVDKIAKFVLEAMGLKDTAIVHRGGYNGRGWPGDVKYAMMDIAKLKKTGWKNKYSSDEAVKKSINEV 307
                                   **************98855543333332333345689999999999998888888999999988876 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.0   0.2   2.3e-21   5.2e-18       1     222 [.       7     216 ..       7     229 .. 0.84

  Alignments for each domain:
  == domain 1  score: 65.0 bits;  conditional E-value: 2.3e-21
                     3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkkviegDvtdkdkleealegvdvvihlaslvdvag 81 
                                   ++tGgaGF+G+++v++L+  +e+  +  l + ++  +++   + n k +i+ D+++  +        d+v+hla+ +dv++
  gi|13540890|ref|NP_110578.1|   7 LITGGAGFIGSNMVEHLLPKNEVTVIDNLSITDDRYIKKFYDNPNFK-FIKKDILNGIDG----YHYDIVVHLAADSDVRN 82 
                                   69****************99975555555588888887777777777.999999976443....3579***********98 PP

                     3Beta_HSD  82 .kltedeimkvnvkGTrnvleacvkagvrvlvYtSsaevvgpnslgeeilngdEeleyeslhqdaypesKalaEklvlkaN 161
                                      +    mkvnv+GT +vle+ +k++++ +++ Ss  v g+   ++ i    E  + + l+ + y  sK  aE+++ +  
  gi|13540890|ref|NP_110578.1|  83 gSSNPALDMKVNVEGTISVLEMMRKSDIKDILFASSSTVYGE---AKVIP-TPE-NYGPLLPISSYGASKLAAEAFISAYA 158
                                   577777789********************************9...55444.555.567899***************98776 PP

                     3Beta_HSD 162 grtlknggrlyTcaLRpagiyGegdk..llvpllkqlaklglalfkigdeevlsdrvYvgNva 222
                                         g  ++    R a + G  ++  +++ ++++l++++++l  +gd  + ++++ v+ + 
  gi|13540890|ref|NP_110578.1| 159 S---YYG--FNALLFRFANVVGKNSThgVIFDFINKLKNNKKELEVLGDGTQAKSYIHVEDLI 216
                                   6...344..888999*******99873358899**************************9876 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.5   0.6   9.2e-15   2.1e-11       1     251 [.       6     257 ..       6     268 .. 0.78

  Alignments for each domain:
  == domain 1  score: 43.5 bits;  conditional E-value: 9.2e-15
                                   EEEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T-SEE CS
               Polysacc_synt_2   1 vlvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelkvdvv 81 
                                   +l+tG++G iGs++v+++l k+  ++ ++++   + ++  k++   +++ ++k+           k+ + + ++ ++ d+v
  gi|13540890|ref|NP_110578.1|   6 ILITGGAGFIGSNMVEHLLPKN--EVTVIDNLSITDDRYIKKF---YDNPNFKFI----------KKDILNGIDGYHYDIV 71 
                                   89****************9875..6777777666555555554...466666555..........6677788899****** PP

                                   EE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEEG......GGSS.........--SHHHHHHHHHHH CS
               Polysacc_synt_2  82 fhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkvvliStD......KAvn.........PtnvmGatKrlaek 147
                                   +h AA   V    +np+  +k Nv gt +v+e+  ++++k++++ S+       K +          P++ +Ga+K++ae 
  gi|13540890|ref|NP_110578.1|  72 VHLAADSDVRNGSSNPALDMKVNVEGTISVLEMMRKSDIKDILFASSStvygeaKVIPtpenygpllPISSYGASKLAAEA 152
                                   *******************************************999752233224432333334444899*********** PP

                                   HHHHGGG--SSS--EEEEEEE-EETT..GTTSSHHHHHHHHHTT.SSEEE.S-TT-EEEEE-HHHHHHHHHHHHHH--SS- CS
               Polysacc_synt_2 148 llqalakeseekktkfvvvRfGNVlg..SrGSviplFkkqikeg.gpvtv.TdpemtRyfmtieeavqLvlqalalakgge 224
                                   ++ a+a++      + ++ Rf NV+g  S   vi  F +++k++ +++ v  d +  + ++ +e+ +  +++  ++ kg e
  gi|13540890|ref|NP_110578.1| 153 FISAYASYY---GFNALLFRFANVVGknSTHGVIFDFINKLKNNkKELEVlGDGTQAKSYIHVEDLIGSMIYVYEHVKGVE 230
                                   *******99...7899999******95455678888888888775788763566777778888888888888888888888 PP

                                   EEEE--.-EEEHHHHHHHH........ CS
               Polysacc_synt_2 225 ifvldmGepvkivdlakalielsglee 251
                                    f l   + +++ ++ak ++e +gl+ 
  gi|13540890|ref|NP_110578.1| 231 PFNLGNDDVTSVDKIAKFVLEAMGLKD 257
                                   888877777778888888777777654 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.0   2.7e-05      0.06       1      24 [.       8      30 ..       8      40 .. 0.88
   2 !   30.7   0.0   7.5e-11   1.7e-07      88     215 ..      68     183 ..      65     247 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.7e-05
                                  EE-TTSHHHHHHHHHHHHHS-.TE CS
                 NAD_binding_4  1 lTGaTGFLGkvLlekLLrttpevk 24
                                  +TG+ GF+G+ ++e LL +++ v+
  gi|13540890|ref|NP_110578.1|  8 ITGGAGFIGSNMVEHLLPKNE-VT 30
                                  8****************9886.44 PP

  == domain 2  score: 30.7 bits;  conditional E-value: 7.5e-11
                                   --EEEE--SS-S.STTSSE...EHHHHHHHHHHHHHHHTSSS--.-EEEEEEGGGTTS-TTT--SSS-H......HHH--E CS
                 NAD_binding_4  88 vdviihsaAtvnfdepyke...llrvNveGtrevlelakklkklkvllhvSTayvngeregeveekvyeegekeekldede 165
                                    d+++h aA+ ++ +  ++    ++vNveGt  vle+ +k   +  +l+ S+++v+ge +                  + e
  gi|13540890|ref|NP_110578.1|  68 YDIVVHLAADSDVRNGSSNpalDMKVNVEGTISVLEMMRKSDIK-DILFASSSTVYGEAK-V--------------IPTPE 132
                                   69********999886666444589**************99999.9************99.3..............45566 PP

                                   EEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEE-.-SSST-- CS
                 NAD_binding_4 166 raklkglpntYeqsKalaEklvrearrrsglpvvivRpsiitg.esktGwi 215
                                             Y  sK +aE  + ++++  g++++ +R  +++g +s+ G+i
  gi|13540890|ref|NP_110578.1| 133 NYGPLLPISSYGASKLAAEAFISAYASYYGFNALLFRFANVVGkNSTHGVI 183
                                   666666667*********************************976666765 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 !   16.0   0.0   3.8e-06    0.0085       1     132 [.      10     155 ..      10     185 .. 0.70
   2 ?   -3.3   0.0       3.2   7.2e+03     165     180 ..     237     252 ..     225     256 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 3.8e-06
                                   TTTSHHHHHHHHHHHHC-T-EE..EEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES---TCC...... CS
                NAD_binding_10   1 GAtGkvGrllvkellargghev..talvRnpeklaeleaeeglevvegdvtdvedlaealkgadaVvsalggggk...... 73 
                                   G+ G +G+  v++ll +++++v   + + +   ++++ ++++ + ++ d+++  d      ++d+Vv  ++ ++       
  gi|13540890|ref|NP_110578.1|  10 GGAGFIGSNMVEHLLPKNEVTVidNLSITDDRYIKKFYDNPNFKFIKKDILNGID----GYHYDIVVHLAADSDVrngssn 86 
                                   899*************985555333557788889999999******999986544....2345776666643333333333 PP

                                   ...HHHH......HHHHHHHHHHCT--EEEEEEETTTTSGCGCHHHHHHHH...CCHHHHHHHHHHHHHHH CS
                NAD_binding_10  74 ...deeg......aknivdaakeagvkRfvlvsaigvgdevpgefgewnke...llkaylaakraaeellr 132
                                      d  +      ++++++ ++++++k +++ s+  v+ e++    + n+     +++y a k aae+ + 
  gi|13540890|ref|NP_110578.1|  87 palD--MkvnvegTISVLEMMRKSDIKDILFASSSTVYGEAKVIPTPENYGpllPISSYGASKLAAEAFIS 155
                                   4452..1446666************************9865432222111122255677788888887775 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 3.2
                                   --EEEHHHHHHHHHHH CS
                NAD_binding_10 165 ggsisradVAdvlvav 180
                                   +  +s + +A++++++
  gi|13540890|ref|NP_110578.1| 237 DDVTSVDKIAKFVLEA 252
                                   4456777777777776 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0    0.0011       2.4       1      34 [.       4      36 ..       4      61 .. 0.70
   2 ?    3.8   1.6     0.015        34     146     165 ..     140     159 ..      90     164 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0011
                                  SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCH CS
                     adh_short  1 kvvlvtGassGIGraiakelakeGakvvvvdrse 34
                                  k +l+tG+++ IG +++++l+ ++ +v+v+d+ +
  gi|13540890|ref|NP_110578.1|  4 KRILITGGAGFIGSNMVEHLLPKN-EVTVIDNLS 36
                                  679*****************9884.555555544 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.015
                                   BHHHHHHHHHHHHHHHHHHH CS
                     adh_short 146 vaaYsAsKaavagltrslak 165
                                    ++Y+AsK a ++++++ a 
  gi|13540890|ref|NP_110578.1| 140 ISSYGASKLAAEAFISAYAS 159
                                   689***********999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       586  (0.0326845); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.55u 0.32s 00:00:00.87 Elapsed: 00:00:00.46
# Mc/sec: 2041.39
//
Query:       gi|13540891|ref|NP_110579.1|  [L=67]
Description: nucleic-acid-binding protein (Zn-ribbon) [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0017   18.3   0.8     0.0024   17.8   0.8    1.4  1  DUF2116          Uncharacterized protein containing a Zn-ribb
     0.0073   16.3   0.5     0.0083   16.1   0.5    1.2  1  zinc-ribbons_6   zinc-ribbons
  ------ inclusion threshold ------
      0.012   16.1   0.2       0.16   12.5   0.0    2.0  2  Zn_ribbon_recom  Recombinase zinc beta ribbon domain
      0.012   15.6   0.8      0.041   13.8   0.8    1.7  1  Gin              Inhibitor of sigma-G Gin


Domain annotation for each model (and alignments):
>> DUF2116  Uncharacterized protein containing a Zn-ribbon (DUF2116)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.8   5.4e-07    0.0024       5      33 ..       6      32 ..       2      39 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 5.4e-07
                       DUF2116  5 HCivCGkaIpldesfCsekCqeeyekkrk 33
                                  HC +CG++I ++   Cs+ C++e e+ r 
  gi|13540891|ref|NP_110579.1|  6 HCLICGTPIYSG-LYCSD-CESEMERSRT 32
                                  *********875.89*96.9999998875 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.5   1.9e-06    0.0083      15      44 ..       3      32 ..       1      48 [. 0.88

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.9e-06
                                  SEEE-TTT--EEEEEEE-SSS-S---EEEE CS
                zinc-ribbons_6 15 eqyhCeaCqedlkkealCpeCeqelevlka 44
                                  +++hC  C + +    +C +Ce+e+e+ + 
  gi|13540891|ref|NP_110579.1|  3 QKLHCLICGTPIYSGLYCSDCESEMERSRT 32
                                  689**********************98775 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 ?    2.2   0.2     0.057   2.6e+02       5      16 ..       4      15 ..       2      17 .. 0.80
   2 ?   12.5   0.0   3.6e-05      0.16       6      36 ..      18      50 ..      15      67 .] 0.75

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.057
               Zn_ribbon_recom  5 llrCgeCGspmt 16
                                  +l C  CG p +
  gi|13540891|ref|NP_110579.1|  4 KLHCLICGTPIY 15
                                  789999999865 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 3.6e-05
               Zn_ribbon_recom  6 lrCgeCGspmtrrkrkgkr..hyYrCstyrrkg 36
                                  l+C +C s m r++++ +   + ++ +t+ +++
  gi|13540891|ref|NP_110579.1| 18 LYCSDCESEMERSRTSDEEsfDEWISKTREKNR 50
                                  79**********887744446888888887776 PP

>> Gin  Inhibitor of sigma-G Gin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.8   9.2e-06     0.041      11      35 ..      11      35 ..       6      44 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 9.2e-06
                                  EE-SSS--EEHHHHHHHHHHS---S CS
                           Gin 11 GiiilgkfICeeCekkivntevddp 35
                                  G  i++ + C++Ce+++ + +++d+
  gi|13540891|ref|NP_110579.1| 11 GTPIYSGLYCSDCESEMERSRTSDE 35
                                  556888888***********99997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (67 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       691  (0.0385409); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 445.53
//
Query:       gi|13540892|ref|NP_110580.1|  [L=205]
Description: superoxide dismutase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.3e-25   88.2   0.2    5.4e-25   87.5   0.2    1.3  1  Sod_Fe_C  Iron/manganese superoxide dismutases, C-terminal do
    4.5e-09   36.6   0.1    1.4e-08   35.1   0.0    1.8  2  Sod_Fe_N  Iron/manganese superoxide dismutases, alpha-hairpin


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 !   87.5   0.2     6e-29   5.4e-25       4     101 ..      95     191 ..      93     192 .. 0.95

  Alignments for each domain:
  == domain 1  score: 87.5 bits;  conditional E-value: 6e-29
                                   HHHHHHHHHHSSHHHHHHHHHHHHHHSSSSEEEEEEEETT.TEEEEEEEETTTBGGGGTTCEEEEEE-SGGGTHHHHTT-H CS
                      Sod_Fe_C   4 elaeaieedfgslekfkkefkaaalavfgsGwawLvldkk.kkLeivttknqdnplvkeakplLalDvwehAYyldyqnkr 83 
                                   e+++a+ +dfgs+ek+ ++fka+++a   +Gwa+Lv+d + +kL+ + ++ ++  l++++ ++L++Dv+ehAYy+dy  kr
  gi|13540892|ref|NP_110580.1|  95 EFKDAVAKDFGSYEKWLEDFKATGTA--FRGWAILVFDLNyGKLRNIGSDAHNVGLIWNSIAILTMDVYEHAYYVDYGAKR 173
                                   67899********************9..89********8879*************************************** PP

                                   HHHHHHHGGGBBHHHHHH CS
                      Sod_Fe_C  84 adYieafwnvvnWkevee 101
                                   a Y++af++ vnW  v +
  gi|13540892|ref|NP_110580.1| 174 APYLDAFMKNVNWPVVLK 191
                                   *************99976 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 !   35.1   0.0   1.5e-12   1.4e-08      18      81 ..      19      85 ..       9      86 .. 0.84
   2 ?   -2.5   0.0      0.83   7.5e+03      33      53 ..     179     201 ..     176     204 .. 0.63

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 1.5e-12
                                  S-HHHHHHHHHTHHHHHHHHHHHHHHCH.HHHCHCCHHHHHH..HHHHHHHHHHHHHHHHHHHHHTB CS
                      Sod_Fe_N 18 isketlelHhdkHhktYvnnlNkalekl.eeakkkleelvlk..klekalrnnagghvnHslfwknl 81
                                  is  +++ H+d H+k+Yvn+lN++ ++l + +++k+++  ++  +l+ + ++n gg  +H+l+++ l
  gi|13540892|ref|NP_110580.1| 19 ISDVQIDNHFDVHYKGYVNKLNEIWSRLpDVDRSKANQNYSEfrALKLEETFNYGGSFLHELYFEGL 85
                                  788899******************99997666666665554444999999**************977 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.83
                                   HHHHHHH..HHHHCHHHHCHCCH CS
                      Sod_Fe_N  33 tYvnnlN..kalekleeakkkle 53 
                                   ++++n+N   +l++le+akk+ e
  gi|13540892|ref|NP_110580.1| 179 AFMKNVNwpVVLKRLEKAKKAYE 201
                                   56677773245677777777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       491  (0.0273858); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.53
# Mc/sec: 1172.02
//
Query:       gi|13540893|ref|NP_110581.1|  [L=204]
Description: N-glycosylase/DNA lyase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.11   13.0   0.0       0.18   12.3   0.0    1.4  1  HhH-GPD   HhH-GPD superfamily base excision DNA repair protei


Domain annotation for each model (and alignments):
>> HhH-GPD  HhH-GPD superfamily base excision DNA repair protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   9.8e-06      0.18      23      97 ..      64     167 ..      42     178 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 9.8e-06
                                   HHHSHCSHHHHHHSHHHHHHHHHTT..STTHHHHHHHHHHHHHHHH................................... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxx................................... RF
                       HhH-GPD  23 erfgfptpedladadeekLrelire..lGfyrrKakyikelArilv................................... 66 
                                   +         +++++e +Lre +++   +fy+ + +yi e  r +v                                   
  gi|13540893|ref|NP_110581.1|  64 KG--------FLYLSENELREKLKAfkYRFYNVRPRYIVES-RDIVdelpyivsmdnkeeardllvenvygfgykeashfl 135
                                   44........467788888888887779************6.66666********************************** PP

                                   ...S-SSS--TTSHHHHHHHHHHTTSSSSTTHHH CS
                                   ...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       HhH-GPD  67 ...gkpdvlivvDvhvrrilkrlrsikekktkkk 97 
                                      g  d + + D h+   l+r++++k++ t +k
  gi|13540893|ref|NP_110581.1| 136 rnvGVFD-FAILDKHILEWLSRYFQVKKN-TSRK 167
                                   9997667.9999***************97.4444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       688  (0.0383736); expected 358.6 (0.02)
Passed bias filter:                      505  (0.0281667); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1370.42
//
Query:       gi|13540894|ref|NP_110582.1|  [L=296]
Description: phosphate permease [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.7e-28   97.7  31.3    2.5e-26   92.5  31.3    2.1  1  PHO4             Phosphate transporter family
     0.0046   16.8   1.2      0.011   15.7   1.2    1.6  1  Pox_polyA_pol    Poxvirus poly(A) polymerase nucleotidyltrans
  ------ inclusion threshold ------
        3.2    7.8   4.4       0.49   10.4   0.1    1.8  2  DUF4501          Domain of unknown function (DUF4501)
        4.7    7.0   7.0         18    5.2   0.5    2.9  3  Gly-zipper_YMGG  YMGG-like Gly-zipper


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 !   92.5  31.3   5.5e-30   2.5e-26       4     332 ..      18     288 ..      15     293 .. 0.86

  Alignments for each domain:
  == domain 1  score: 92.5 bits;  conditional E-value: 5.5e-30
                          PHO4   4 nDvanafatsvgskaltlrqAvilaaifeflGavllGaeVaetirkgivdvelfdpselmlgmlaallgaavwlllatvlg 84 
                                   n ++   +t +gs+++     +++ a+  ++G+++ G+   ++++  +     f p     +++ a+l++++  ++a +++
  gi|13540894|ref|NP_110582.1|  18 NNTSAVSGTLIGSRMVGRYYGLLMTAVGYVAGYLIEGQFLKKAVSVLLP----FPP----EVVIYAILASFIIFVVAFFVK 90 
                                   7888999*****************************9866666665553....322....3888999999*********** PP

                          PHO4  85 lPvStthslvGaliGaalaaeggeavkw..kklvkivlswvlsPllggiiaallfllvkrlilvkeklknalralpvlvlv 163
                                   +P S t++lvG+ iG +l +    +v+   + l+ i+++w+l+P++++++++ l +++   ++                  
  gi|13540894|ref|NP_110582.1|  91 VPLSLTMALVGSSIGLSLKY----GVNLpkSFLLSIFVAWILAPIISVVLSYYLNVVMSGKNY-----G------------ 150
                                   *******************5....4555336899********************999999833.....1............ PP

                          PHO4 164 tiailalsilfkgeskkddeeteklfkflqvvsaalvsfahGanDvanaiGpllaalisiykaskevplwvlllgglaial 244
                                            ++         +  +++k l++++a + +f+ Gan    +iG +  ++           +   +++++a+ l
  gi|13540894|ref|NP_110582.1| 151 --------NIW---------KYASAVKLLLIFTALFTAFTLGAN----TIGFIGNVI-GF-------NTENNIVIVAAVFL 202
                                   ........122.........335569****************99....777775444.22.......2334578889999* PP

                          PHO4 245 GlllgGkrviktvGekitkkltpsrGfaaelaaaltvllasklglPvStThvlvgavvGvGlakkresavnwklvrnivla 325
                                   G++++   v+k v++++   l+++++f+ ++++al v + + + +P+S T++l+++v+G+Gl   + +a+  + +  iv++
  gi|13540894|ref|NP_110582.1| 203 GTFMFSSGVMKSVSQNMY-MLKYTNAFTSQIVSALAVEVSTLFSIPMSNTQTLTSSVLGAGLSY-KAKAIYLRPFLYIVVM 281
                                   ******************.5********************************************.78************** PP

                          PHO4 326 WvlTlpv 332
                                   W+++ ++
  gi|13540894|ref|NP_110582.1| 282 WIISPIL 288
                                   ***9766 PP

>> Pox_polyA_pol  Poxvirus poly(A) polymerase nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   1.2   2.4e-06     0.011      57     145 ..     137     222 ..     133     225 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.4e-06
                 Pox_polyA_pol  57 syslyllnreikygdidllqtnartflinlafliklitGrdvvllkvPylknyivlkdeedahiidsfnirqeilnv.ipk 136
                                   sy l ++ +  +yg+i  +    + +li+ a++  ++ G ++    + ++ n i ++ e+++ i+ ++++   +++  + k
  gi|13540894|ref|NP_110582.1| 137 SYYLNVVMSGKNYGNIWKYASAVKLLLIFTALFTAFTLGANT----IGFIGNVIGFNTENNIVIVAAVFLGTFMFSSgVMK 213
                                   778888888889****************************98....69**********************99888644999 PP

                 Pox_polyA_pol 137 ilidniyii 145
                                   ++ +n+y++
  gi|13540894|ref|NP_110582.1| 214 SVSQNMYML 222
                                   9999*9997 PP

>> DUF4501  Domain of unknown function (DUF4501)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.8       1.4   6.3e+03      94     102 ..      86      94 ..      60     140 .. 0.62
   2 ?   10.4   0.1   0.00011      0.49      86     113 ..     196     223 ..     183     234 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.4
                       DUF4501  94 tlfislfLi 102
                                    +f+ + L 
  gi|13540894|ref|NP_110582.1|  86 AFFVKVPLS 94 
                                   333333333 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00011
                       DUF4501  86 vaaslllgtlfislfLilsvasffylkr 113
                                   ++a+++lgt++ s++++ sv + +y+ +
  gi|13540894|ref|NP_110582.1| 196 IVAAVFLGTFMFSSGVMKSVSQNMYMLK 223
                                   6899****************99888643 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 ?    5.2   0.5    0.0039        18      15      45 ..      22      54 ..      15      55 .. 0.65
   2 ?   -3.0   0.0       1.4   6.4e+03      37      43 ..      98     104 ..      96     106 .. 0.40
   3 ?    4.6   0.2     0.006        27      16      35 ..     181     200 ..     180     200 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0039
                                  XXXXXXXXXXXXXX...XXXXXXXXXXXXXXXX- CS
               Gly-zipper_YMGG 15 AvvGaliGsgggkG...AaiGAaaGalaGgaiGa 45
                                  Av G liG ++  G    + + a+G +aG++i +
  gi|13540894|ref|NP_110582.1| 22 AVSGTLIG-SRMVGryyGLLMTAVGYVAGYLIEG 54
                                  45555566.4444455567778888888888865 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.4
                                   XXXXXXX CS
               Gly-zipper_YMGG  37 alaGgai 43 
                                   al+G  i
  gi|13540894|ref|NP_110582.1|  98 ALVGSSI 104
                                   2222222 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.006
                                   XXXXXXXXXXXXXXXXXXXX CS
               Gly-zipper_YMGG  16 vvGaliGsgggkGAaiGAaa 35 
                                    +G++iG ++ ++ +i Aa+
  gi|13540894|ref|NP_110582.1| 181 FIGNVIGFNTENNIVIVAAV 200
                                   69*****99999******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1065  (0.059401); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.60u 0.31s 00:00:00.90 Elapsed: 00:00:00.50
# Mc/sec: 1764.34
//
Query:       gi|13540895|ref|NP_110583.1|  [L=188]
Description: hypothetical protein TVN0064 [Thermoplasma volcanium GSS1]
Scores for complete 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   40.6   9.1      4e-10   39.4   9.1    1.6  1  PhoU_div  Protein of unknown function DUF47


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 !   39.4   9.1   2.2e-14     4e-10      36     211 ..       2     182 ..       1     185 [. 0.84

  Alignments for each domain:
  == domain 1  score: 39.4 bits;  conditional E-value: 2.2e-14
                      PhoU_div  36 egdyekveellkeiselEreADeikreirlklekglflPvdRedllelveslDeildvlediamlvtlrkvef...peelk 113
                                    +d+++  e  +e+ e+E+ +De+   i+  ++kg + P+   +l++lve+ D+ild    i   ++   ++     +   
  gi|13540895|ref|NP_110583.1|   2 MKDCSSLVERNEEVKEIEKVGDELNISIKQDITKGGISPNLMDNLIQLVEKSDDILDTSYFISREIKRMFLDYgrgMDRCS 82 
                                   5799999999***********************************************988887666555554400045556 PP

                      PhoU_div 114 deflallkktveaiealaevieeleklletalskk..diveeieslEdeiDqlqrklikklfsredasnplevlllveiie 192
                                     +++  ++ + + e  + +++ l+ +l    + k  +    ie+lE+++D+l+       + + d + +l +  lv++++
  gi|13540895|ref|NP_110583.1|  83 SIIQKCYSTFISMLEYNKGALKHLNAMLTAENDDKirEERIAIEKLEEKVDELKDDTFDYIYRNADDIPYLVFSHLVDLTH 163
                                   678888888888999888999999988876666434433345*************************************** PP

                      PhoU_div 193 klenvsdraedvadrisii 211
                                   k+  + d  ed+ad i  i
  gi|13540895|ref|NP_110583.1| 164 KVDDMLDDCEDAADLIITI 182
                                   **************87555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1069  (0.0596241); expected 358.6 (0.02)
Passed bias filter:                      608  (0.0339115); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 1136.52
//
Query:       gi|13540896|ref|NP_110584.1|  [L=212]
Description: MarC family integral membrane protein [Thermoplasma volcanium GSS1]
Scores for complete sequence (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  194.6  12.9    1.3e-57  194.5  12.9    1.0  1  MarC      MarC family integral membrane protein
  ------ inclusion threshold ------
       0.24   11.6   1.3       0.81   10.0   1.3    1.9  1  DUF2149   Uncharacterized conserved protein (DUF2149)
       0.28   11.0   2.0       0.39   10.5   2.0    1.1  1  RIFIN     Rifin
        4.6    7.4   7.0        2.4    8.4   0.2    2.6  2  DUF3302   Protein of unknown function (DUF3302)


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 !  194.5  12.9   2.9e-61   1.3e-57       3     200 ..       6     204 ..       4     207 .. 0.97

  Alignments for each domain:
  == domain 1  score: 194.5 bits;  conditional E-value: 2.9e-61
                          MarC   3 aiikafvsLlaiinplgnvpvflslleevskeerkrialkasilallillvfllfGelilklfgisidalkiaGgillfli 83 
                                   +++ +f+ L+a++np+g++pv+++++e +s+e  +r+++ a++  +l+l+ f+++G +i++++gi+id +k+aGg+llf++
  gi|13540896|ref|NP_110584.1|   6 FLVTVFIALFALVNPIGALPVLIAVTEGYSSEDFDRVVKNATVTEALMLFGFMFIGIYIFQVLGINIDDFKVAGGVLLFKV 86 
                                   68999**************************************************************************** PP

                          MarC  84 aidmlkakqkkekkkkseeeeseekdeiavvPLAlPliaGPgaittvlvlaseass.ivekvavvlaillaalitllilll 163
                                   a+dml+++++++k  + e+ee++e+ +i + P+ +Pl+aGPg+itt ++  +++s+ +++kv+v++a++l++++++l+l++
  gi|13540896|ref|NP_110584.1|  87 AFDMLQGRTSTTKLTPVEKEETAERSSIGIAPIGTPLLAGPGSITTAIIYFNSYSTnLTDKVLVIVAVFLVIVVSYLMLHY 167
                                   **********************************************9998877765499********************** PP

                          MarC 164 sslilrllgktginaleRlmGllLvalavqlivdGik 200
                                   ss++ + lg+tg  +++R+mGllL+a+av+++v+G++
  gi|13540896|ref|NP_110584.1| 168 SSILFKFLGNTGSLLISRIMGLLLAAIAVDFMVTGLA 204
                                   ***********************************97 PP

>> DUF2149  Uncharacterized conserved protein (DUF2149)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   1.3   0.00018      0.81       5      28 ..     142     165 ..     139     175 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00018
                       DUF2149   5 aNLfDvalVlavallvalvsslnl 28 
                                   +NL+D +lV+++++lv++vs l l
  gi|13540896|ref|NP_110584.1| 142 TNLTDKVLVIVAVFLVIVVSYLML 165
                                   7****************9998744 PP

>> RIFIN  Rifin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   2.0   8.8e-05      0.39     271     303 ..     135     167 ..     124     169 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 8.8e-05
                         RIFIN 271 attaslqtaiiasivaivvIvLimvIIYLiLRY 303
                                     ++s++t+++  +++iv + L++v+ YL+L+Y
  gi|13540896|ref|NP_110584.1| 135 IYFNSYSTNLTDKVLVIVAVFLVIVVSYLMLHY 167
                                   457899999************************ PP

>> DUF3302  Protein of unknown function (DUF3302)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.2   0.00053       2.4       6      66 ..       4      64 ..       2      68 .. 0.84
   2 ?    0.8   2.1      0.12   5.5e+02       6      19 ..     150     163 ..     145     173 .. 0.46

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00053
                       DUF3302  6 livlivvvlvlvygiivlhdiPyeiakrRnhPhadaihvagWvsLltlfvlWPllliWatl 66
                                  l  l++v++ l++++  ++ +P  ia    +  +d  +v   +++    +l+ +++i  ++
  gi|13540896|ref|NP_110584.1|  4 LLFLVTVFIALFALVNPIGALPVLIAVTEGYSSEDFDRVVKNATVTEALMLFGFMFIGIYI 64
                                  567999999******************9999999988888888888888888888876666 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.12
                       DUF3302   6 livlivvvlvlvyg 19 
                                   +iv +++v+v+ y+
  gi|13540896|ref|NP_110584.1| 150 VIVAVFLVIVVSYL 163
                                   22333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1266  (0.0706119); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); 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):               4  [number of targets reported over threshold]
# CPU time: 0.59u 0.35s 00:00:00.94 Elapsed: 00:00:00.55
# Mc/sec: 1165.07
//
Query:       gi|13540897|ref|NP_110585.1|  [L=164]
Description: 2'-5' RNA ligase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.6e-24   84.4   0.0    2.3e-15   56.5   0.0    2.2  2  LigT_PEase       LigT like Phosphoesterase
      3e-08   33.7   0.0    3.8e-08   33.4   0.0    1.1  1  2_5_RNA_ligase2  2'-5' RNA ligase superfamily
  ------ inclusion threshold ------
      0.042   13.6   0.0       0.14   11.9   0.0    1.8  2  LRR_8            Leucine rich repeat


Domain annotation for each model (and alignments):
>> LigT_PEase  LigT like Phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.5   0.0   3.9e-19   2.3e-15      14      87 .]      18      86 ..       7      86 .. 0.87
   2 !   25.9   0.0   1.4e-09   8.2e-06      30      87 .]     108     155 ..      90     155 .. 0.82

  Alignments for each domain:
  == domain 1  score: 56.5 bits;  conditional E-value: 3.9e-19
                                  HHHHHHHHHCCTTEEETSGGGSEEEEEEEEEESHHHHHHHHHHHHHHHHTSBEEEEEEEEEEEEEECCSCCEEE CS
                    LigT_PEase 14 laaeleralaklglkpvrpfnpHiTLaflgevdeekvpellealaeiasgaepfelkvdgvglfpsrlrprviy 87
                                  + + ++   +++++k+v++ n+HiTL+flg++d++ ++++++ l+++  ++++f++k  g+g+fp+ ++prvi+
  gi|13540897|ref|NP_110585.1| 18 ILSTFR---QSRNIKVVEDTNVHITLKFLGDIDDDFAKKICSGLSGL--KVHKFTIKTLGIGAFPNMRSPRVIF 86
                                  334444...677***********************************..999********************95 PP

  == domain 2  score: 25.9 bits;  conditional E-value: 1.4e-09
                                   TSGGGSEEEEEEEEEESHHHHHHHHHHHHHHHHTSBEEEEEEEEEEEEEECC.SCCEEE CS
                    LigT_PEase  30 vrpfnpHiTLaflgevdeekvpellealaeiasgaepfelkvdgvglfpsrl.rprviy 87 
                                   +++f pHiT++++++  + ++p l       ++ +e+  +++++v+lf+srl ++++iy
  gi|13540897|ref|NP_110585.1| 108 DKDFVPHITIGRIKA--KVRIPPL-------EFTQEE--YEAKEVCLFSSRLtPSGPIY 155
                                   589**********98..7888888.......334445..*******************9 PP

>> 2_5_RNA_ligase2  2'-5' RNA ligase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.4   0.0   6.4e-12   3.8e-08      10     117 ..      20     121 ..      10     143 .. 0.86

  Alignments for each domain:
  == domain 1  score: 33.4 bits;  conditional E-value: 6.4e-12
               2_5_RNA_ligase2  10 ealrrslydkayprwppHitLlypfvededl.adlaellsrlaketepfevrldgfgvFeh.kks.vvylsvsdsealqal 87 
                                    ++r+s + k +++  +HitL++++++d+d+ +++ + ls l     +f++ + g+g F+  ++  v++l+  +s+++++l
  gi|13540897|ref|NP_110585.1|  20 STFRQSRNIKVVEDTNVHITLKFLGDIDDDFaKKICSGLSGL--KVHKFTIKTLGIGAFPNmRSPrVIFLDL-QSNDIEKL 97 
                                   5566666777788899*************9888888888877..5778**************7778******.******** PP

               2_5_RNA_ligase2  88 raallealpeagdkedsgeftPHlTiaqsa 117
                                     ++ + ++        ++f+PH+Ti++ +
  gi|13540897|ref|NP_110585.1|  98 YIEIGRIVGID------KDFVPHITIGRIK 121
                                   *******9988......79*******9865 PP

>> LRR_8  Leucine rich repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   2.4e-05      0.14       5      61 .]      35      94 ..      34      94 .. 0.86
   2 ?   -1.3   0.0      0.32   1.9e+03       4      20 ..      95     111 ..      93     114 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.4e-05
                                  EEE-TTS--SEE-TTSSTT.-TT--EEE--SS---GGGGGGGTT--S..-.EEE--SS-- CS
                         LRR_8  5 sLdLsnNrltslddeaFkg.lsnLkvLdLsnNllttlspgafsgLps..LrsLdLsgNrL 61
                                  +++++   l ++dd++ k+ +s+L  L+    +++tl  gaf +++s  + +LdL++N++
  gi|13540897|ref|NP_110585.1| 35 NVHITLKFLGDIDDDFAKKiCSGLSGLKVHKFTIKTLGIGAFPNMRSprVIFLDLQSNDI 94
                                  6778888899********************************998662256788899986 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.32
                                   SEEE-TTS--SEE-TTS CS
                         LRR_8   4 tsLdLsnNrltslddea 20 
                                   ++L++   r+ ++d+++
  gi|13540897|ref|NP_110585.1|  95 EKLYIEIGRIVGIDKDF 111
                                   689999999*9999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       478  (0.0266607); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.46
# Mc/sec: 1069.07
//
Query:       gi|13540898|ref|NP_110586.1|  [L=169]
Description: hypothetical protein TVN0067 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score 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   12.4   0.1       0.11   11.9   0.1    1.2  1  PEP_mutase  Phosphoenolpyruvate phosphomutase
       0.12   12.6   6.9         15    5.9   6.9    2.2  1  DUF4064     Protein of unknown function (DUF4064)


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 ?   11.9   0.1   1.2e-05      0.11      23      74 ..      52     104 ..      46     123 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.2e-05
                    PEP_mutase  23 kiveeagfkalat.sSlavaaslGvpDgeelpleellaavraiaevvslPliv 74 
                                    + e  ++k l + sS +++ +l  pDg + +++ ++++  ++++v+s P ++
  gi|13540898|ref|NP_110586.1|  52 AVSEYLSYKILFVsSSSSISSYLSSPDGTHYTFSHTMNTSGSMMAVQSGPWSL 104
                                   55566677876651567899999***********************9988655 PP

>> DUF4064  Protein of unknown function (DUF4064)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   6.9    0.0017        15       9      81 ..       7     147 ..       3     154 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0017
                       DUF4064   9 glIGgilgillglllllflfllssgefsqeltee............................................... 42 
                                   g IG+++ +++ +l +  +f +s++ +s + t++                                               
  gi|13540898|ref|NP_110586.1|   7 GRIGVVIVLVSLILFGSSIFYISRDTSSYSHTITpgssieitkeaavseylsykilfvsssssissylsspdgthytfsht 87 
                                   556776666666666666666666666666666667666666666666666666666666666666666667777777777 PP

                       DUF4064  43 .....................qalsgedasavleflstllivlgvialiaivlgivgall 81 
                                                        + +++e+++ v +++ + +++++ i+l ++++gi++++l
  gi|13540898|ref|NP_110586.1|  88 mntsgsmmavqsgpwslivtnTGNTTENVEVVFSIVPQPVFFMLYISLALLAFGIAAIVL 147
                                   777888888888888888888889999999999***9******************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       738  (0.0411624); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1090.45
//
Query:       gi|13540899|ref|NP_110587.1|  [L=158]
Description: nucleic-acid-binding protein [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.3e-09   36.1   0.3    5.9e-09   35.6   0.3    1.2  1  DUF35_N        Rubredoxin-like zinc ribbon domain (DUF35_N)
    3.7e-07   30.0   0.0    5.9e-07   29.4   0.0    1.3  1  OB_aCoA_assoc  DUF35 OB-fold domain, acyl-CoA-associated
  ------ inclusion threshold ------
      0.024   14.7   0.1      0.034   14.2   0.1    1.2  1  DZR            Double zinc ribbon
       0.58   10.1   4.4        1.1    9.2   0.1    3.0  3  zinc_ribbon_4  zinc-ribbon domain
        1.3    8.8   4.1         12    5.8   4.2    2.1  1  zinc_ribbon_2  zinc-ribbon domain
          2    7.9   5.4        8.8    5.9   5.4    1.9  1  zf-ribbon_3    zinc-ribbon 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 !   35.6   0.3     2e-12   5.9e-09       1      37 []      40      77 ..      40      77 .. 0.92

  Alignments for each domain:
  == domain 1  score: 35.6 bits;  conditional E-value: 2e-12
                       DUF35_N  1 wdaaaegrLvgqrCpdCGtvqfPPravCphC.gsddle 37
                                  +da++ g ++++rCp CG+ +fPP+a C+ C  s+++e
  gi|13540899|ref|NP_110587.1| 40 FDALDKGIIMATRCPVCGAKYFPPEAWCSACgYSGEME 77
                                  69*****************************7777765 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 !   29.4   0.0     2e-10   5.9e-07       4      64 ..      81     141 ..      79     142 .. 0.87

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 2e-10
                                   E-GG-EEEEEEEEEE-TTS-EEEEEEEEEEEE-TT....-EE-EEEEEEES..TT-B-EEE- CS
                 OB_aCoA_assoc   4 lsgrGtvysftvvhrappgfaeeaPyvvgvVeLde.gvrimarlvgvdpdevriGmrVravf 64 
                                   +   Gt+ +ft + ++p +f+ ++ y+vg+ + d  g  ++a+l +  + + ++Gm+V++++
  gi|13540899|ref|NP_110587.1|  81 IETDGTLLTFTKIFAKPGSFSSFPDYTVGIARIDKeGFNVLAWLSDKIENP-KVGMPVKLRV 141
                                   5678*******6666666****************98999******998766.6******986 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   1.1e-05     0.034      28      49 .]      50      71 ..      21      71 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.1e-05
                           DZR 28 edrCpsCgekvdpearfCpeCG 49
                                  ++rCp Cg+k  p ++ C +CG
  gi|13540899|ref|NP_110587.1| 50 ATRCPVCGAKYFPPEAWCSACG 71
                                  789*******99999******9 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.38   1.1e+03      11      20 ..      28      37 ..      26      38 .. 0.85
   2 ?    9.2   0.1   0.00038       1.1       1      12 [.      49      60 ..      49      64 .. 0.94
   3 ?    0.7   0.1      0.17   5.2e+02      28      33 ..      67      72 ..      63      73 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.38
                 zinc_ribbon_4 11 kyeiddeklp 20
                                  ky+i+  k++
  gi|13540899|ref|NP_110587.1| 28 KYRIPVLKIK 37
                                  8****99997 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00038
                 zinc_ribbon_4  1 MkitCpsCkaky 12
                                  M ++Cp C+aky
  gi|13540899|ref|NP_110587.1| 49 MATRCPVCGAKY 60
                                  999********9 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.17
                 zinc_ribbon_4 28 CskCgh 33
                                  Cs+Cg 
  gi|13540899|ref|NP_110587.1| 67 CSACGY 72
                                  999985 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   4.2     0.004        12       1      21 [.      52      72 ..      52      74 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.004
                 zinc_ribbon_2  1 fCpnCGaelqdnakFCpyCGt 21
                                  +Cp CGa+  + +  C+ CG+
  gi|13540899|ref|NP_110587.1| 52 RCPVCGAKYFPPEAWCSACGY 72
                                  69*****99888888999997 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   5.4    0.0029       8.8       3      24 ..      51      72 ..      49      73 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0029
                   zf-ribbon_3  3 vrCPnCGaplssddnvCpyCGt 24
                                  +rCP CGa+  +    C  CG+
  gi|13540899|ref|NP_110587.1| 51 TRCPVCGAKYFPPEAWCSACGY 72
                                  79******65888888888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       538  (0.0300073); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-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: 00:00:00.47
# Mc/sec: 1013.85
//
Query:       gi|13540900|ref|NP_110588.1|  [L=390]
Description: acetyl-CoA acetyltransferase [Thermoplasma volcanium GSS1]
Scores for complete 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   96.3   0.0      3e-27   95.6   0.0    1.4  1  Thiolase_N     Thiolase, N-terminal domain
    1.1e-07   31.6   1.6      2e-07   30.7   0.0    2.2  3  Thiolase_C     Thiolase, C-terminal domain
    0.00011   21.9   4.8    0.00011   21.9   4.8    2.4  3  ketoacyl-synt  Beta-ketoacyl synthase, N-terminal domain
    0.00012   21.9   1.6     0.0069   16.2   0.4    2.6  2  ACP_syn_III    3-Oxoacyl-[acyl-carrier-protein (ACP)] synthas
  ------ inclusion threshold ------
       0.32   11.0   1.4       0.49   10.3   0.3    1.9  2  GA-like        GA-like 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 !   95.6   0.0   8.5e-31     3e-27       8     260 .]      11     223 ..       4     223 .. 0.94

  Alignments for each domain:
  == domain 1  score: 95.6 bits;  conditional E-value: 8.5e-31
                                   EE--EETTSTTTTS-HHHHHHHHHHHHHHHHTS-GGGCCEEEEEHSSCTTSTSCHHHHHHHHTTS-TTSEEEEEEHGGGHH CS
                    Thiolase_N   8 rtpigkfggslkdlsaeeLlaealkallekagvdpeevdevivGnvlqagegqniarqaalkagipeevpavtvnkvcsSg 88 
                                    +++gk     +d+s+ +L  ea++++l+  gvd+++v++++v+n+    +++ +a  a   +g  e + + +v+ +c+Sg
  gi|13540900|ref|NP_110588.1|  11 ISKFGK----RNDASMYDLIWEAGSEALKTSGVDKKDVEYLVVSNMGMWSSEELPAVVAGEVLGT-ERAGTNRVEAACASG 86 
                                   455555....99****************************************************9.9************** PP

                                   HHHHHHHHHHHHTTSHSEEEEEEEEESTTS-EEETCTTT..TGGSSSSEEEEEHHHHHHTEETTTTSEHHHHHHHHHHHHT CS
                    Thiolase_N  89 lkavalaaqsiaageadvvvagGvEsmsnaptaestdvr..sglklgdekakdllipdgladafneehmGltaenlakkyk 167
                                    +a+  a ++ia+g++ +++a GvE+ms+++t ++ +++  +g  l + +  +l+ p            +l+a  +++ky+
  gi|13540900|ref|NP_110588.1|  87 SSAISSAYDAIASGHVRMAMALGVEKMSEVDTGTAIELIgrAGNFLWEYEFFGLTFPG---------YYALHATAYLDKYG 158
                                   **********************************999876688899999999***999.........899*********** PP

                                   --HHHHHHHHHHHHHHHHHHHHTTTTTTTBE-EEEEESSSEEEE-S-TTS-TT--HHHHHTS-BSSSTTSS-BTTSB--BE CS
                    Thiolase_N 168 isReeqdefAvkshqkaaaaqkagkFkdeivPvkvkgkkgkktvdkdeairsevtaekLaklkpaFkkeGtvtAgnasqis 248
                                      e+++ + vk+h+ a+ ++ka+ F+++i              + ++ ++s+  a +L+ +             ++s+i+
  gi|13540900|ref|NP_110588.1| 159 GKEEDLALVSVKNHHYAHFNPKAQ-FTNDI--------------SVEDVMSSRYIASPLKLY-------------DSSPIT 211
                                   ************************.*****..............89****************.............****** PP

                                   EEEEEEEEEEHH CS
                    Thiolase_N 249 DGaaavllmses 260
                                   DGaaav+l+se+
  gi|13540900|ref|NP_110588.1| 212 DGAAAVVLASED 223
                                   *********996 PP

>> Thiolase_C  Thiolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       0.8   2.9e+03      27      45 ..      29      47 ..      22      51 .. 0.84
   2 ?   -3.7   0.2       2.5     9e+03     101     118 ..      74      91 ..      71      93 .. 0.73
   3 !   30.7   0.0   5.7e-11     2e-07      26     101 ..     261     358 ..     243     368 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.8
                                  HHHHHHHHHT--GGGESEE CS
                    Thiolase_C 27 aikkvlkkagltvedidlf 45
                                  a +++lk  g++ +d++++
  gi|13540900|ref|NP_110588.1| 29 AGSEALKTSGVDKKDVEYL 47
                                  5678999*****9999876 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 2.5
                                   TTSEEEEEEEETTTEEEE CS
                    Thiolase_C 101 ggklgvaalCigggqgva 118
                                    g+  v a+C++g+ +++
  gi|13540900|ref|NP_110588.1|  74 AGTNRVEAACASGSSAIS 91 
                                   566678899999988765 PP

  == domain 3  score: 30.7 bits;  conditional E-value: 5.7e-11
                                   HHHHHHHHHHT--GGG....ESEEEE--SBHHHHHHHHHHHT--G..................GGBSTT--HHHH-B-TTT CS
                    Thiolase_C  26 yaikkvlkkagltved....idlfEinEAFaaqaLavakaldldl..................ekvNvnGGaialGHPlGa 84 
                                    a++k+ k ag++ e+    id  ++++ F+   L++ ++l+++                     vNv GG i+ GHP+Ga
  gi|13540900|ref|NP_110588.1| 261 EAARKAYKVAGIDSEKpynfIDGADVHDCFSIAELMAYEDLGFAGkgealeliregqtyiggrIPVNVDGGLISKGHPIGA 341
                                   577888888888755444449999*******************9999**************9889**************** PP

                                   HHHHHHHHHHHHHHHCT CS
                    Thiolase_C  85 sGaRivvtllselkkeg 101
                                   +G+ ++v ++++l ++ 
  gi|13540900|ref|NP_110588.1| 342 TGVAMAVEATKQLLRKA 358
                                   ********999987753 PP

>> ketoacyl-synt  Beta-ketoacyl synthase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   4.8     3e-08   0.00011     165     209 ..      73     117 ..      21     128 .. 0.76
   2 ?   -3.0   0.0       1.2   4.4e+03     239     251 ..     211     223 ..     209     225 .. 0.82
   3 ?   -1.7   0.0      0.49   1.8e+03     144     173 ..     319     350 ..     256     367 .. 0.51

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 3e-08
                                   -SSEEEEESGGGHHHHHHHHHHHHHHTTS-SEEEEEEEE---SHH CS
                 ketoacyl-synt 165 rGpsvtvdtACsSslvavhaavqslrsgeadvalaGGvellltpe 209
                                   r+ +  v++AC+S+  a+  a++++ sg++ +a a Gve + +  
  gi|13540900|ref|NP_110588.1|  73 RAGTNRVEAACASGSSAISSAYDAIASGHVRMAMALGVEKMSEVD 117
                                   5666789********************************987765 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.2
                                   B-EEEEEEEEECH CS
                 ketoacyl-synt 239 GEGvGavvLkrle 251
                                   ++G++avvL +++
  gi|13540900|ref|NP_110588.1| 211 TDGAAAVVLASED 223
                                   69*******9876 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.49
                                   THHHHHSTTHHHHHHHHH..HT--SSEEEEES CS
                 ketoacyl-synt 144 kavgavlanviagrisya..lglrGpsvtvdt 173
                                   ++ g +  nv  g is     g++G++++v++
  gi|13540900|ref|NP_110588.1| 319 YIGGRIPVNVDGGLISKGhpIGATGVAMAVEA 350
                                   33444444444444543333555555555554 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 !   16.2   0.4   1.9e-06    0.0069       3      41 ..      79     116 ..      78     126 .. 0.93
   2 ?    4.0   0.0     0.012        45      53      65 ..     211     223 ..     207     237 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.9e-06
                                   EE-GGGHHHHHHHHHHHHHHTTS-SEEEEEEEEEGGGCS CS
                   ACP_syn_III   3 lnaaCsgfvyalsvAdaliesgaakrvLvigaetlskil 41 
                                   ++aaC++   a+s A ++i+sg+++ ++  g e++s+ +
  gi|13540900|ref|NP_110588.1|  79 VEAACASGSSAISSAYDAIASGHVRMAMALGVEKMSE-V 116
                                   689*********************************9.4 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.012
                                   -EEEEEEEEEEES CS
                   ACP_syn_III  53 GDGAgAvvlease 65 
                                    DGA+Avvl  ++
  gi|13540900|ref|NP_110588.1| 211 TDGAAAVVLASED 223
                                   5********9863 PP

>> GA-like  GA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       3.3   1.2e+04      17      26 ..      32      40 ..      29      42 .. 0.73
   2 ?   10.3   0.3   0.00014      0.49       9      37 ..     257     285 ..     254     286 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 3.3
                       GA-like 17 aeLkaaGits 26
                                  ++Lk  G+ +
  gi|13540900|ref|NP_110588.1| 32 EALKTSGV-D 40
                                  57888888.4 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00014
                       GA-like   9 keAKeaAkaeLkaaGitsdfyiekIdkAk 37 
                                   ++A+eaA ++ k aGi+s++  + Id+A+
  gi|13540900|ref|NP_110588.1| 257 EAAREAARKAYKVAGIDSEKPYNFIDGAD 285
                                   89************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (390 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); 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:                         5  (0.000278878); expected 0.2 (1e-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: 00:00:00.47
# Mc/sec: 2512.42
//
Query:       gi|13540901|ref|NP_110589.1|  [L=435]
Description: proline/betaine transport permease [Thermoplasma volcanium GSS1]
Scores for complete 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-23   82.0  49.8    3.7e-23   82.0  49.8    2.2  2  MFS_1     Major Facilitator Superfamily
    1.8e-22   79.8  37.4    1.6e-18   66.9  10.2    2.1  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 !   82.0  49.8   4.1e-27   3.7e-23      10     341 ..      32     374 ..      20     382 .. 0.75
   2 ?   -6.5   9.2         2   1.8e+04     138     253 ..     383     404 ..     370     427 .. 0.35

  Alignments for each domain:
  == domain 1  score: 82.0 bits;  conditional E-value: 4.1e-27
                         MFS_1  10 larsilgpalpl.alaedlgispseigl..lltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll.f....a 82 
                                    ++++l p++   +   ++g++   ig+  ++t+ +++  v+ l++Grl+dr+Gr+ ++ ++ll+++l  ++++ f    +
  gi|13540901|ref|NP_110589.1|  32 SMMFLLVPVIADlFFPAHYGLAI--IGTwsIYTTTFIFRPVGGLIFGRLGDRIGRKNTMTITLLGLGLI-TFATgFlpvyS 109
                                   34455555555445555556444..444569999***********************************.55555655442 PP

                         MFS_1  83 ...sslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslg........Wr 151
                                      +  + ll+++r+++G++ag+ + +g +++ + +  ++rg   + +++g+ lG+ l++++  +l   +         Wr
  gi|13540901|ref|NP_110589.1| 110 vigIAAPlLLFLFRIITGIFAGGEYGNGSSILMETVGAPKRGIWGAAIQSGYPLGYTLAAVIFLYLHYVFPgtefaitgWR 190
                                   566556768*******************************************************99966556********* PP

                         MFS_1 152 avfyilaivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlw..illialllfffgfsg..llt 228
                                   ++f+i  i +++++v      +  p +  + ++k++      a+ ++ ++ ++k++ l   i+  +l+++++++ +  +l 
  gi|13540901|ref|NP_110589.1| 191 WMFWIGIIPAIIGLV----IRLKMPESAMWIETKDR------AKKLT-LSDVFKNRRLTyeIITSVLAMTGIAWVYglTLG 260
                                   *************65....45555555555555555......34444.678999998855766666666666666655777 PP

                         MFS_1 229 llplylqevlgls..glllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavtssavllllvl 307
                                   ++p+   +  g+    ++l +  +  + lv++ + l +g+lsd++grr+ +++  +l++++++ l +l    +++ +  +l
  gi|13540901|ref|NP_110589.1| 261 FFPTV-LSFDGFLkfPYFLYV--VITAILVSLLGYLSSGYLSDHIGRRTVMVIYSILAIIFSIPLTFLIIK-HYLGFSGSL 337
                                   77774.333333333233333..33333344444899**************************99999999.666666666 PP

                         MFS_1 308 vl...iGfglgfvfpsllalasdlappeeagtasglf 341
                                   ++   i f    +++ + +++s+ +p+e + t +g+ 
  gi|13540901|ref|NP_110589.1| 338 IFasiIAFLTTGIYGVIPSFLSEKYPTEVRSTGTGIG 374
                                   66333666444459*************9999999975 PP

  == domain 2  score: -6.5 bits;  conditional E-value: 2
                         MFS_1 138 pllggllasslgWravfyilaivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialll 218
                                        +l+  ++++++f+                                                               
  gi|13540901|ref|NP_110589.1| 383 NWSTVFLLLIVSFTSPFF--------------------------------------------------------------- 400
                                   222222222222111111............................................................... PP

                         MFS_1 219 fffgfsglltllplylqevlglsglllaglllall 253
                                                                  ++  
  gi|13540901|ref|NP_110589.1| 401 -------------------------------FGWW 404
                                   ...............................1111 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.9  10.2   1.8e-22   1.6e-18      56     205 ..      65     224 ..      53     235 .. 0.90
   2 !   19.0  19.1   5.8e-08   0.00052     289     445 ..     274     430 ..     226     434 .. 0.66

  Alignments for each domain:
  == domain 1  score: 66.9 bits;  conditional E-value: 1.8e-22
                                   HHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTT.....SS-TGGGGGHHHHHHHHHHHHHHHHHHHHTTS CS
                      Sugar_tr  56 lvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgk.....nsvevlivgRvlvGigvGlasvlvPmyisEiA 131
                                   ++ + +G+l++g lgdr+GRk+++ i+ + +   ++ +++ + +      +  +l++ R+++Gi++G++++  +  + E  
  gi|13540901|ref|NP_110589.1|  65 FIFRPVGGLIFGRLGDRIGRKNTMTITLLGLGLITFATGFLPVYsvigiAAPLLLFLFRIITGIFAGGEYGNGSSILMETV 145
                                   56689*******************99887776666666666666666699999**************************** PP

                                   -SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-.....TTHHHHHHHCCHHHHHHHHHHGGGS---HHHHHHTT-HH CS
                      Sugar_tr 132 pkklRgalvslyqlaitfGilvaaifglglnktsn.....adgwrillglqlvpallllilllflPESPrylvekgkee 205
                                    + +Rg+ +   q+++ +G  +aa++ l l ++        +gwr+++++ ++pa++ l+++l +PES  +  +k++ +
  gi|13540901|ref|NP_110589.1| 146 GAPKRGIWGAAIQSGYPLGYTLAAVIFLYLHYVFPgtefaITGWRWMFWIGIIPAIIGLVIRLKMPESAMWIETKDRAK 224
                                   ******************************999999999989******************************9999876 PP

  == domain 2  score: 19.0 bits;  conditional E-value: 5.8e-08
                                   H...HHHHHHHHHHHHHHHHHHHHHHHHS-SHHHHHHHHHHHHHHHHHHH..HHHHTTSS...CHHHHHHHHHHHHHHHTT CS
                      Sugar_tr 289 s...llvtiivgvvnfvatfvaiflvdrfGRRtllllGaagmaicfvilgivalllvakskaasivaivfialfialfalg 366
                                       l+v i  + v  +  + + +l+d++GRRt++++ ++ ++i+ + l+  +l++++     ++     +a  ia+ ++g
  gi|13540901|ref|NP_110589.1| 274 FpyfLYVVITAILVSLLGYLSSGYLSDHIGRRTVMVIYSILAIIFSIPLT--FLIIKHY---LGFSGSLIFASIIAFLTTG 349
                                   24656777777777888888888999999999888888888888888886..5555555...2443444455667788888 PP

                                   TTHHHHHHHHHHSHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHT-HHHHHHHHHHHH...HHHHHHHHS--STT-- CS
                      Sugar_tr 367 wgpvpwvlvsElfpqsvRskalaiavavnwlanflisllfpiiteaigggyvflvfaglavl...fiifvfffvpetkgrt 444
                                   + +v+   +sE +p++vRs+++ i ++  ++     +++   i++  + +++f  +++++++   fi+   +   et g++
  gi|13540901|ref|NP_110589.1| 350 IYGVIPSFLSEKYPTEVRSTGTGIGFNGGFILGNWSTVFLLLIVSFTS-PFFFGWWGIFVIIgelFIFSSALLSKETRGLD 429
                                   888888888999999999999999999999999999999999999999.55555555555550004555555666666666 PP

                                   C CS
                      Sugar_tr 445 l 445
                                   l
  gi|13540901|ref|NP_110589.1| 430 L 430
                                   6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (435 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       728  (0.0406046); expected 358.6 (0.02)
Passed bias filter:                      230  (0.0128284); 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):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.28s 00:00:00.90 Elapsed: 00:00:00.46
# Mc/sec: 2812.15
//
Query:       gi|13540902|ref|NP_110590.1|  [L=316]
Description: threonine synthase [Thermoplasma volcanium GSS1]
Scores for complete 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-56  189.6   0.0    8.9e-56  189.4   0.0    1.0  1  PALP      Pyridoxal-phosphate dependent enzyme
  ------ inclusion threshold ------
      0.066   13.2   0.0       0.12   12.4   0.0    1.3  1  FlpD      Methyl-viologen-reducing hydrogenase, delta subunit


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 !  189.4   0.0   9.9e-60   8.9e-56       3     294 .]      10     313 ..       8     313 .. 0.94

  Alignments for each domain:
  == domain 1  score: 189.4 bits;  conditional E-value: 9.9e-60
                                   GCSSS--EEEECCTCCCCCCE.EEEEEGGGSTTSBTTHHHHHHHHHHHHTTTTTSEEEEEBSSHHHHHHHHHHHHHT-EEE CS
                          PALP   3 lgigpTPlvrlprlskelgvp.lflKlEslnptgSfKdRgaeyllarlkegtgaktvveassGNhgralAaaaallGlkvt 82 
                                    + g+TP +++ +l kel  + lflK E+ n tg  KdR  e  ++++ +  g  ++++++ GN g+++A++a+l+G+k++
  gi|13540902|ref|NP_110590.1|  10 KPPGRTPTIKAYALGKELRLNnLFLKFEGANATGTQKDRISEAHVLNAIRD-GYNGIAVGTCGNYGASIAYYANLYGIKSY 89 
                                   5679*******************************************9999.9**************************** PP

                                   EEEETTS-HHHHHHHHHTT-EEEEECCHHHHHHHHHHHHHHHSTTCEE--TTT.SHHHHHH.HHTHHHHHHHHTTTTEEEE CS
                          PALP  83 ivvpadaspekvallrllGaevvevggdydeavaaaaelaaegegaylvsqfd.nptvieg.ygtiglEileqlggkpdav 161
                                   i +p+  + ++ + + + +ae+  ++g y+e+v+ ++++a + ++ y +s+++ ++++    y+ i++Ei+e + ++pd+v
  gi|13540902|ref|NP_110590.1|  90 IGMPSAYTHDREDFMLSSNAEILYYNGKYEETVSFIHDYATD-NSLYDASPGSdHSYIDTKmYAGIAFEIYEAILKVPDYV 169
                                   ******************************************.**********744444446******************* PP

                                   EEE-SSSHHHHHHHHHHHH..HSTT....-EEEEEEECTTCGGTTCCS..S.SS..B.SSS.CCSTCS........CGTTC CS
                          PALP 162 vvpvGgGgliaGiaaglke..rrpd....vrvigvepegsdalarslragrrvtvpvsdtiadglavg........spsel 228
                                   +vpvG+G +++Gi+ g++    +++    +r++gv + g +++ +s+++g  + v+  +  +   av+         ++++
  gi|13540902|ref|NP_110590.1| 170 IVPVGNGTTLSGIYEGFHLmyLNGTidrmPRMVGVSTRGGNPIVSSWKRGYKKVVDLDPARIRETAVNeplvsyrsFDGDK 250
                                   *******************9944445689******************9998888888877777777777788899999*** PP

                                   CHHHHSEEEEEEEEEEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHHHHHHHHCCTTCEEEEEEE-B CS
                          PALP 229 afelldrlvdeivtvsdeealeamrllarregivvepssaaalaalklreagelkegdrvvviltg 294
                                   a+++++++ +++  vsd+e+++  +l++r+eg+ + p+sa a+aal      +l+++d vv ++tg
  gi|13540902|ref|NP_110590.1| 251 ALAAIRETHGKALYVSDDEMVRFSELMYREEGLNPLPASASAVAAL---VHLHLNPDDYVVSVITG 313
                                   **********************************************...***************98 PP

>> FlpD  Methyl-viologen-reducing hydrogenase, delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   1.3e-05      0.12      37      62 ..      47      72 ..      45      82 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.3e-05
                          FlpD 37 grvdpefilkalekGadgVlvlgChp 62
                                  +r++++++l+a+++G++g++v  C++
  gi|13540902|ref|NP_110590.1| 47 DRISEAHVLNAIRDGYNGIAVGTCGN 72
                                  699*********************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (316 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1943.04
//
Query:       gi|13540903|ref|NP_110591.1|  [L=344]
Description: hypothetical protein TVN0072 [Thermoplasma volcanium GSS1]
Scores for complete 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-68  227.8   0.0    1.2e-67  227.1   0.0    1.3  1  DUF1611    Domain of unknown function (DUF1611_C) P-loop doma
    4.8e-30  103.7   0.0    9.8e-30  102.6   0.0    1.6  1  DUF1611_N  Domain of unknown function (DUF1611_N) Rossmann-li
  ------ inclusion threshold ------
      0.051   13.7   0.0       0.25   11.4   0.0    2.2  2  DapB_N     Dihydrodipicolinate reductase, N-terminus
       0.08   13.0   0.0       0.39   10.8   0.0    2.1  2  CbiA       CobQ/CobB/MinD/ParA nucleotide binding domain


Domain annotation for each model (and alignments):
>> DUF1611  Domain of unknown function (DUF1611_C) P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  227.1   0.0   2.7e-71   1.2e-67       2     194 ..     140     331 ..     139     336 .. 0.98

  Alignments for each domain:
  == domain 1  score: 227.1 bits;  conditional E-value: 2.7e-71
                       DUF1611   2 vadgkarevkakrvlvvGTdcavGKrttaleleealeerGlkaafvaTgqtgili.agegvvldavvvdfvaGaveglvkk 81 
                                   +++g++++vkak+++v+GTd+a+GKrtta+ l++a+++ G k+ +++Tgqt++++  ++ vv+da+v+dfvaGa+e ++ +
  gi|13540903|ref|NP_110591.1| 140 FFTGNIEKVKAKKIAVLGTDSAIGKRTTAIYLNRAMKAIGKKSVMIGTGQTSWMQgFKYTVVVDAIVNDFVAGALETITYE 220
                                   6899***************************************************************************** PP

                       DUF1611  82 aaeeeepdlilveGQgsLthpaysgvtlglLlGsqPdalvLchrpgrkhirglpeialppleeeieliealaakkkvvgis 162
                                   a+++e+pd++++eGQgs++hpay+g +++++ + +Pda++L+h+p rk+++g+p +++pple++i+++e l+++k v++i+
  gi|13540903|ref|NP_110591.1| 221 AWDSERPDYMFIEGQGSVLHPAYPG-SFEIIGATRPDAIILQHAPMRKYFDGFPGYEIPPLEKYIKILELLSNRK-VIAIA 299
                                   *************************.************************************************9.***** PP

                       DUF1611 163 lNtknlseeeakealeeleeelglpvvdpvre 194
                                   lNt+n++e  +ke+  +l++++g+pv+dp+++
  gi|13540903|ref|NP_110591.1| 300 LNTENMDESMVKEEKSRLQAKFGIPVFDPLQR 331
                                   *****************************986 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 !  102.6   0.0   2.2e-33   9.8e-30       2      93 ..      39     132 ..      38     133 .. 0.98

  Alignments for each domain:
  == domain 1  score: 102.6 bits;  conditional E-value: 2.2e-33
                     DUF1611_N   2 ekaGkdagelldd..rgipvvssleealaagaevlviGiapeggklpeswreavkeAleaGldvvsGlHerLsddpelaal 80 
                                   ++aG+dag++l +   gip++ss+eea +  ae+l++Gia  gg+lpe++r+++++Al  G+++vsGlH+++sddpe++++
  gi|13540903|ref|NP_110591.1|  39 RLAGQDAGQVLMHkpSGIPIISSVEEAINGHAETLIVGIASDGGVLPENYRPYIRTALGYGMNIVSGLHDFVSDDPEFVKI 119
                                   79**********99******************************************************************* PP

                     DUF1611_N  81 akkkgvkiiDvRk 93 
                                   a+++g++i DvRk
  gi|13540903|ref|NP_110591.1| 120 ARRTGSRITDVRK 132
                                   ************8 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   5.7e-05      0.25      13      97 ..      17     105 ..      15     128 .. 0.76
   2 ?   -2.8   0.0       1.4   6.4e+03      25      62 ..     295     330 ..     285     336 .. 0.50

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 5.7e-05
                                   HHHHHHHHHHSTTEEEEEEEETTCSTTTTTBHHHHSSSS--S-BEBSSHHHHHHH.-S.EEEE-S.....-HHHHHHHHHH CS
                        DapB_N  13 Gkevvkaveeaedlelvaavdrkeselegkdagellglgklgvavtddleevlek.ad.vliDFT.....tpeavlenlkl 86 
                                   Gk+   +v+ ++++++++++d++   l g+dag++l  +++g+++ +++ee+++  a+  ++         pe    ++++
  gi|13540903|ref|NP_110591.1|  17 GKTANGLVRYSKRYHITSVIDSR---LAGQDAGQVLMHKPSGIPIISSVEEAINGhAEtLIVGIAsdggvLPENYRPYIRT 94 
                                   67777788889999999999996...59***********************999885524444431111245566666777 PP

                                   HHHTT-EEEE- CS
                        DapB_N  87 alekgvklViG 97 
                                   al +g+++V G
  gi|13540903|ref|NP_110591.1|  95 ALGYGMNIVSG 105
                                   77777777776 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.4
                                   TEEEEEEEETTCSTTTTTBHHHHSSSS.--S-BEBSSHH CS
                        DapB_N  25 dlelvaavdrkeselegkdagellglg.klgvavtddle 62 
                                    + ++   ++ ++++++++ ++l   + k g++v+d l+
  gi|13540903|ref|NP_110591.1| 295 VIAIALNTENMDESMVKEEKSRL---QaKFGIPVFDPLQ 330
                                   44444444444444444444332...2367777776665 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 ?   -2.7   0.0       1.3   5.7e+03      71      93 ..      27      49 ..      11      52 .. 0.69
   2 ?   10.8   0.0   8.7e-05      0.39       1     120 [.     153     337 ..     153     343 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.3
                                  HHH..EEEEEEEEESS...-TTC CS
                                  xxxxxxxxxxxxxxxxxxxxxxx RF
                          CbiA 71 alllkiagvvlnrvdgeneetll 93
                                  ++   i +v++ r  g+++ + l
  gi|13540903|ref|NP_110591.1| 27 SKRYHITSVIDSRLAGQDAGQVL 49
                                  33378889999999888877766 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 8.7e-05
                                   EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH........................... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................... RF
                          CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep........................... 54 
                                   ia+ +t +  GK t+a+ L ra++  g++ +++ ++  + +       +  +                             
  gi|13540903|ref|NP_110591.1| 153 IAVLGTDSAIGKRTTAIYLNRAMKAIGKKSVMIGTGQTSWMQG----FKYTVVVdaivndfvagaletityeawdserpdy 229
                                   799******************************9988865555....3333333444678888999999999999999999 PP

                                   .................................................CCHCCCHHHHHHCHCHHHH..EEEEEEEEESS CS
                                   .................................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          CbiA  55 .................................................dlkrllellealgkkkalllkiagvvlnrvdg 86 
                                                                                     l++++++le l+++     k++ + ln  + 
  gi|13540903|ref|NP_110591.1| 230 mfiegqgsvlhpaypgsfeiigatrpdaiilqhapmrkyfdgfpgyeipPLEKYIKILELLSNR-----KVIAIALNTENM 305
                                   9999999999999999999999999999999999999999999999999999999999999987.....788888888777 PP

                                   ...-TTCHHHHHHHHHHCTS-EEEEEE--CCHCC CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          CbiA  87 eneetllkealeelkqrygvpvlgviprdeavae 120
                                   +  e + ke   +l++++g+pv++ + r + v++
  gi|13540903|ref|NP_110591.1| 306 D--ESMVKEEKSRLQAKFGIPVFDPLQRLSTVTR 337
                                   7..666666666776777***9999998888766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       375  (0.0209158); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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 0.28s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 2208.87
//
Query:       gi|13540904|ref|NP_110592.1|  [L=466]
Description: metal-binding protein containing [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       575  (0.0320709); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); 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: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.46
# Mc/sec: 3067.85
//
Query:       gi|13540905|ref|NP_110593.1|  [L=333]
Description: D-mannonate dehydratase [Thermoplasma volcanium GSS1]
Scores for complete 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-88  294.4   0.0    3.2e-61  207.1   0.1    2.0  2  UxuA          D-mannonate dehydratase (UxuA)
    6.5e-10   38.8   0.0      8e-10   38.5   0.0    1.1  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 !   85.6   0.0   3.2e-28   2.8e-24      19     138 ..      24     149 ..       5     153 .. 0.91
   2 !  207.1   0.1   3.5e-65   3.2e-61     171     349 ..     153     331 ..     152     332 .. 0.97

  Alignments for each domain:
  == domain 1  score: 85.6 bits;  conditional E-value: 3.2e-28
                                   HHHHH.T--EEEE--TTS-T.......TS---HHHHHHHHHHHHHTT-EEEEEE-----HHHHHT-TTHHHHHHHHHHHHH CS
                          UxuA  19 eirqipGvkgvvsalhdipa.......gevWekeeilklkeeiekagltlevvesvpvhediklgteerdryienykqtir 92 
                                    ++qi Gv++vv+ l + p+       + +W+++++  lk+ + ++gltl+++e++p++e+ik+g + ++ ++en+ + i 
  gi|13540905|ref|NP_110593.1|  24 LLKQI-GVNEVVGTLPRDPSdwrgdqpDLPWDYAPLSSLKRRLSEYGLTLSAIEDNPPMEKIKYGVKGKEDELENVLRLIE 103
                                   35666.***********9999998888889*************************************************** PP

                                   HHHHTT--EEEE---SS--S--SEEEEE-TTS-EEEEE-HHHHHHH CS
                          UxuA  93 nlakiGvkvvCYnfmpvldWtrtdleykledgskalrfdkkeieal 138
                                   n++++ + v+CYn+m++ +W+r+ ++++   g++++ f  ++ie++
  gi|13540905|ref|NP_110593.1| 104 NMGRLKIGVWCYNWMAGQGWMRSRISIPDRGGAEVTGFSLSDIEEY 149
                                   *****************************************99987 PP

  == domain 2  score: 207.1 bits;  conditional E-value: 3.5e-65
                                   CCTT--HHHHHHHHHHHHHHHHHHHHHHT-EEEE---SSSS-.BTTB--SSSSHHHHHHHHHH--STTEEEEEEHHHHTTS CS
                          UxuA 171 aykkideeklrenlayFlkeiiPvaeevgvklaihPDDPPlp.ifGlpRivstkedlqrlldlvdspangitlCtGslgar 250
                                   ++ kid+e l++nla+Fl+++iPvae+ gvk+a+hPDDPPl  i+G+ Ri+++ +++++l+++++s++n+itlC+G+++++
  gi|13540905|ref|NP_110593.1| 153 KMGKIDAETLWKNLAWFLDNVIPVAEDSGVKIAMHPDDPPLEeIRGVSRIMNNVKAFDKLIEMKRSEYNTITLCQGNFTLM 233
                                   5889*************************************99************************************** PP

                                   TT--HHHHHHHHGG..GEEEEE--EEEE-SSTT-EEEE-TTSSSS-HHHHHHHHHHHHHHH-EE-----B-GGGG--STT- CS
                          UxuA 251 adndlvemikefad..riyFahlRnikreedeksFveaahleGsvdlaevvkalleeeyrrylRpDhgrlllddkklrPGY 329
                                   + +dl++ i++f+    + F+h+R++k +  + +F+e+ + +G++d a+++ a++ee++++++R Dh+++l +d+   PGY
  gi|13540905|ref|NP_110593.1| 234 T-EDLPSAIRHFVRkkAVSFVHFRDVKGK--KDNFIESFIDDGKTDTASCMSAYIEEGFDGIMRTDHTPTLYGDTYKVPGY 311
                                   9.9*********976689**********9..567*****************************************99**** PP

                                   -HHHHHHHHHHHHHHHHHHH CS
                          UxuA 330 slidRllgiaylrGlleale 349
                                   s+++Rl +i+y++Gl++ ++
  gi|13540905|ref|NP_110593.1| 312 SILGRLHAIGYIQGLIDGVS 331
                                   ***************99875 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 !   38.5   0.0   8.9e-14     8e-10      26     194 ..      54     266 ..      24     304 .. 0.85

  Alignments for each domain:
  == domain 1  score: 38.5 bits;  conditional E-value: 8.9e-14
                                   HHHHHHHHHHHHHHTTSEEEEEEECCCHSTCTHCHTTCSHHHHHHHHHHHHHHHHHH..TBSEEEEEBCC........... CS
                  AP_endonuc_2  26 sdeelrelrkaldelglriaslslftrfgypdederearreesvdalkraielaaaL..GapllvlhpGt........... 93 
                                   + + l  l+++l e+gl++++++ ++  +      + +  e+ ++++ r ie + +L  G+ + + ++G+           
  gi|13540905|ref|NP_110593.1|  54 DYAPLSSLKRRLSEYGLTLSAIEDNPPMEKIKY--GVKGKEDELENVLRLIENMGRLkiGVWCYNWMAGQgwmrsrisipd 132
                                   4567889***********999988877777433..2222567799999999999999888999****************** PP

                                   ..................GBCTTTSGHHHHHHHHHHHHHHHHHHHHHHTSEEEEE--TTTTSSSTC........HHHHHHH CS
                  AP_endonuc_2  94 ..................agagpkgseeeawerlaeslneladyaekegvklalEtlagsgvelgd........eelarll 148
                                                      +  +k ++e+ w++la  l+ ++++ae+ gvk+a+++ +++  e ++        + +++l+
  gi|13540905|ref|NP_110593.1| 133 rggaevtgfslsdieeypPPKMGKIDAETLWKNLAWFLDNVIPVAEDSGVKIAMHPDDPPLEEIRGvsrimnnvKAFDKLI 213
                                   ***************9886677888899********************************988888*************** PP

                                   HHHTTTTEEEEEEHHHHHHHTTTHHHHHHHHHGG..EEEEEE.EESS.....T CS
                  AP_endonuc_2 149 davdspnvgvclDtgHlliaeedvddalraladr..ikhvHikDakg.....d 194
                                   +  +s+   ++l  g++ ++ ed+ +a+r++ ++  +++vH+ D+kg      
  gi|13540905|ref|NP_110593.1| 214 EMKRSEYNTITLCQGNFTLMTEDLPSAIRHFVRKkaVSFVHFRDVKGkkdnfI 266
                                   **********************************************9555540 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       430  (0.0239835); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.33s 00:00:00.94 Elapsed: 00:00:00.55
# Mc/sec: 1814.13
//
Query:       gi|13540906|ref|NP_110594.1|  [L=261]
Description: aldose dehydrogenase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-64  217.3   0.8    2.9e-64  216.8   0.8    1.1  1  adh_short_C2     Enoyl-(Acyl carrier protein) reductase
    2.2e-48  164.3   3.0    3.4e-48  163.7   3.0    1.3  1  adh_short        short chain dehydrogenase
    1.2e-08   35.1   0.7    3.5e-07   30.3   0.7    2.2  1  KR               KR domain
    1.3e-06   28.3   0.1    2.4e-06   27.5   0.1    1.4  1  DFP              DNA / pantothenate metabolism flavoprotein
    0.00057   19.4   0.6    0.00092   18.7   0.6    1.5  1  Epimerase        NAD dependent epimerase/dehydratase family
     0.0063   15.6   0.1     0.0095   15.0   0.1    1.3  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
  ------ inclusion threshold ------
      0.017   14.9   0.2      0.051   13.3   0.2    1.8  1  Eno-Rase_NADH_b  NAD(P)H binding domain of trans-2-enoyl-CoA 
      0.025   14.6   0.0      0.052   13.5   0.0    1.5  1  ADH_zinc_N       Zinc-binding dehydrogenase
      0.088   12.7   0.4       0.14   12.0   0.4    1.5  1  NAD_binding_10   NAD(P)H-binding
       0.11   12.9   0.1       0.49   10.8   0.0    2.0  2  Radical_SAM      Radical SAM superfamily


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 !  216.8   0.8   1.6e-67   2.9e-64       3     233 ..      15     245 ..      11     246 .. 0.91

  Alignments for each domain:
  == domain 1  score: 216.8 bits;  conditional E-value: 1.6e-67
                                   TTSHHHHHHHHHHHTT-EEEEEESSGGHHHHHHHHHHHTT.SEEEE--TTSHHHHHHHHHHHHHHHSSEEEEEE-----EG CS
                  adh_short_C2   3 asgIGraiAkalaeeGaevvltdlneeakkrveelaeelg.aevlecDVtdeeqvealveevvekfgklDilvnnagiapk 82 
                                    sgIG a++ al + Ga+vv + l+e+++         ++ ++ +++DVt+ee+v+++ve++++k+g++Dilvnnagi + 
  gi|13540906|ref|NP_110594.1|  15 SSGIGLAVVDALVRYGAKVVSVSLDEKSD---------VNvSDHFKIDVTNEEEVKEAVEKTTKKYGRIDILVNNAGIEQY 86 
                                   59*************************92.........22145799*********************************** PP

                                   CSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHH.HCTSC.CEEEEEEEGGGTSBSTTTTHHHHHHHHHHHHHHHHHHHHGG CS
                  adh_short_C2  83 lkgpfletsreefdraldvnlyslfllakaalp.lmkeg.gsivnlssvgaervvpnynaygaaKaalealtrylAvelgp 161
                                     +p++ t+ e ++r++dvn+++ +l+ak+ +p +++ g gsi+n++sv++  +++n +ay ++K+al +ltr++A +++p
  gi|13540906|ref|NP_110594.1|  87 --SPLHLTPTEIWRRIIDVNVNGSYLMAKYTIPvMLAIGhGSIINIASVQSYAATKNAAAYVTSKHALLGLTRSVAIDYAP 165
                                   ..*******************************6556668***************************************** PP

                                   GTEEEEEEEE--BHCTGGGGSTT.........HHHHHHHHHHHSTTSS-B-HHHHHHHHHHHCSGGGTT--SEEEEESTTG CS
                  adh_short_C2 162 kgiRvNavspgpikTlaasgikg.........fdelleelearaplgrlgtpeevaeaalfLasdeasyitGqtlvvDgGl 233
                                    +iR+Nav+pg i T+++ ++++          ++ +ee+ +++p+gr+g+peevae+++fLasd++s+itG+ l vDgGl
  gi|13540906|ref|NP_110594.1| 166 -KIRCNAVCPGTIMTPMVIKAAKmevgedenaVERKIEEWGRQHPMGRIGRPEEVAEVVAFLASDRSSFITGACLTVDGGL 245
                                   .9***************555544344544333444778899***************************************7 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  163.7   3.0   1.9e-51   3.4e-48       1     193 [.       7     188 ..       7     190 .. 0.94

  Alignments for each domain:
  == domain 1  score: 163.7 bits;  conditional E-value: 1.9e-51
                                   SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSESEE CS
                     adh_short   1 kvvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkldvL 81 
                                   kv++vtG+ssGIG+a++++l++ Gakvv v+  e+   +v ++          +++Dvt++eev+++vek  kk+g++d+L
  gi|13540906|ref|NP_110594.1|   7 KVAIVTGGSSGIGLAVVDALVRYGAKVVSVSLDEKSDVNVSDH----------FKIDVTNEEEVKEAVEKTTKKYGRIDIL 77 
                                   89***************************99987766555544..........779************************* PP

                                   EE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHHHHHHHHHHH CS
                     adh_short  82 vnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsKaavagltrs 162
                                   vnNAGi++ +p + +  e w+r+i+vN++g +l+++  +p ml+   G+I+n++Sv++  + ++ aaY +sK+a+ gltrs
  gi|13540906|ref|NP_110594.1|  78 VNNAGIEQYSPLHLTPTEIWRRIIDVNVNGSYLMAKYTIPVMLAIGHGSIINIASVQSYAATKNAAAYVTSKHALLGLTRS 158
                                   *******99**99999999************************************************************** PP

                                   HHHHHGGGTEEEEEEEESSBSSHHHHHHCTH CS
                     adh_short 163 lakelaptgirvnavaPGlvdTdmakelrek 193
                                   +a ++ap+ ir+nav+PG + T+m+ ++ ++
  gi|13540906|ref|NP_110594.1| 159 VAIDYAPK-IRCNAVCPGTIMTPMVIKAAKM 188
                                   *******8.***************9887765 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.3   0.7   1.9e-10   3.5e-07       4     149 ..      10     145 ..       8     165 .. 0.76

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 1.9e-10
                                   EEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EE.EE----TT-HHHHHHHHHHHHHHSS--- CS
                            KR   4 litGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaev.evvaaDvsdkdavealleeikaeeppik 83 
                                   ++tGG  g+Gl++++ l++ ga+  v +s +    e+s+          ++v + +++Dv+++++v++++e+ +++ ++i 
  gi|13540906|ref|NP_110594.1|  10 IVTGGSSGIGLAVVDALVRYGAKV-VSVSLD----EKSD----------VNVsDHFKIDVTNEEEVKEAVEKTTKKYGRID 75 
                                   8********************984.445555....2222..........33316899************************ PP

                                   EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTT....S--SEEEEEEEHHHHH--TT-HHH CS
                            KR  84 GvihaAgvlrdklleemtaedleqvlapKvkGawnLhelled....esldffvlfSSiagllgsagqanY 149
                                     ++ Ag+ + ++l  + +e +++++   v+G+  + +++ +         ++ ++S+ +   ++  a+Y
  gi|13540906|ref|NP_110594.1|  76 ILVNNAGIEQYSPLHLTPTEIWRRIIDVNVNGSYLMAKYTIPvmlaIGHGSIINIASVQSYAATKNAAAY 145
                                   ***********************************99999762222222334444444444444444444 PP

>> DFP  DNA / pantothenate metabolism flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   0.1   1.4e-09   2.4e-06      15     101 ..       3      92 ..       1     106 [. 0.83

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 1.4e-09
                                   EECCTTEEEEE----HHHHHHHHHHHHTT-EEEEEE-S-SS---T.T-EEEE--SHHHHHHHHHHHHTT-...SEEEE--- CS
                           DFP  15 EaiDpVRfisNrSSGkmGyalAeaaaarGaeVtlvsgpvsletpe.gvevvkvesaeemleaveealkea...divimaAA 91 
                                   E  D+V +++  SSG  G+a+ +a+++ Ga+V  vs   + + +      ++v++ ee +eave+++k+    di++  A 
  gi|13540906|ref|NP_110594.1|   3 EFTDKVAIVTGGSSG-IGLAVVDALVRYGAKVVSVSLDEKSDVNVsDHFKIDVTNEEEVKEAVEKTTKKYgriDILVNNAG 82 
                                   788************.6******************98865554331445799999999999999998777778******** PP

                                   S--EEES--- CS
                           DFP  92 vaDyrpkeaa 101
                                   +  y+p + +
  gi|13540906|ref|NP_110594.1|  83 IEQYSPLHLT 92 
                                   ***9997665 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.6   5.2e-07   0.00092       2     160 ..      10     163 ..       9     229 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 5.2e-07
                                   EEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HH....HHHHHHHHH.T-SEEEE--S---H CS
                     Epimerase   2 lVtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrs....alerlfkee.qpdavihlAavggv 77 
                                   +VtG++  iG a+v+al + g +v+ ++ +++++ + +    +  ++d+t+++    a+e+  k++ ++d+ ++ A++  +
  gi|13540906|ref|NP_110594.1|  10 IVTGGSSGIGLAVVDALVRYGAKVVSVSLDEKSDVNVS----DHFKIDVTNEEevkeAVEKTTKKYgRIDILVNNAGIEQY 86 
                                   8**********************999998833333222....4589*****99666677777778889*******998888 PP

                                   HHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHHHHHHHHHHHH CS
                     Epimerase  78 aassedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKlageklveayaa 158
                                   +  + +p++++++ + +++n    + k+ +  +l ++  ++      q   +++    +k   +Y  +K+a   l++++a 
  gi|13540906|ref|NP_110594.1|  87 SPLHLTPTEIWRRIIDVNVNGSYLMAKYTIPVMLAIGHGSIINIASVQ---SYA---ATKNAAAYVTSKHALLGLTRSVAI 161
                                   877888888888777777777777777777666666666666544442...222...346666666666666666666655 PP

                                   HH CS
                     Epimerase 159 qy 160
                                   +y
  gi|13540906|ref|NP_110594.1| 162 DY 163
                                   55 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 !   15.0   0.1   5.3e-06    0.0095       1      67 [.      10      67 ..      10     113 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 5.3e-06
                     3Beta_HSD  1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkkviegDvtdkdkleealegv 67
                                  +vtGg+  +G a+v +Lvr +     +v+ +      l+e s vnv +  + Dvt++++++ea+e+ 
  gi|13540906|ref|NP_110594.1| 10 IVTGGSSGIGLAVVDALVRYGA----KVVSV-----SLDEKSDVNVSDHFKIDVTNEEEVKEAVEKT 67
                                  69*******************6....33333.....3466678999999**************9964 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 ?   13.3   0.2   2.9e-05     0.051      41      76 ..       7      41 ..       2      44 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.9e-05
                                  SEEEEESTSSHHHHHHHHHHHHSS--EEEEEE---- CS
               Eno-Rase_NADH_b 41 kkvLviGaStGYGLAsriaaafgagadtigVsfeke 76
                                  k ++v G+S+G GLA    a   +ga+ ++Vs + +
  gi|13540906|ref|NP_110594.1|  7 KVAIVTGGSSGIGLAVV-DALVRYGAKVVSVSLDEK 41
                                  8899**********974.4555579******99865 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   2.9e-05     0.052       1      70 [.      17      85 ..      17      93 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.9e-05
                                  HHHHHHHHHHHHTT-EEEEEESSHHHHHHHHH.TTESEEEETTTCHHHHHHHHHTT.TSSEEEEEESSCSHH CS
                    ADH_zinc_N  1 gvGlaavqlAkalGaeviavdsseeklelakk.lGadevinykeadlverikeltg.gegvdvvfecvGsga 70
                                  g+Gla+v ++  +Ga+v+ v+ +e+    + + +  d++  +   +++e++++ t+  + +d+ ++ +G+++
  gi|13540906|ref|NP_110594.1| 17 GIGLAVVDALVRYGAKVVSVSLDEKSDVNVSDhFKIDVTNEE---EVKEAVEKTTKkYGRIDILVNNAGIEQ 85
                                  8***********************955455553555555444...688999888875558999999999766 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.4   7.8e-05      0.14       1      61 [.      13      67 ..      13     147 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.8e-05
                                  TTTSHHHHHHHHHHHHC-T-EEEEEETT.HHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT- CS
                NAD_binding_10  1 GAtGkvGrllvkellargghevtalvRn.peklaeleaeeglevvegdvtdvedlaealkga 61
                                  G++ ++G ++v+ l++ g  +v+ +  + +++++ ++     + +++dvt++e+++ea++ +
  gi|13540906|ref|NP_110594.1| 13 GGSSGIGLAVVDALVRYG-AKVVSVSLDeKSDVN-VS-----DHFKIDVTNEEEVKEAVEKT 67
                                  8999*************6.888888655144444.44.....679*************9964 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00027      0.49      92     144 ..      21      74 ..       6      91 .. 0.85
   2 ?   -1.3   0.0       1.4   2.6e+03      77      94 ..     166     183 ..     145     229 .. 0.56

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00027
                                   HHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHTTSET CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  92 eklerllelgvdrvslgleaaddekvlklmn.rghtfeevlealeklreagikr 144
                                    ++++l+++g  +vs++l+  +d  v ++++ +  + eev+ea+ek +++ ++ 
  gi|13540906|ref|NP_110594.1|  21 AVVDALVRYGAKVVSVSLDEKSDVNVSDHFKiDVTNEEEVKEAVEKTTKKYGRI 74 
                                   5799********************9*******99***************98773 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.4
                                   TEEEEEEECSSCHGHHHH CS
                                   xxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  77 giritvetngtlpdeekl 94 
                                   +ir+  +++gt  ++ ++
  gi|13540906|ref|NP_110594.1| 166 KIRCNAVCPGTIMTPMVI 183
                                   555555555555542222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       985  (0.0549389); expected 358.6 (0.02)
Passed bias filter:                      754  (0.0420548); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.62u 0.33s 00:00:00.95 Elapsed: 00:00:00.53
# Mc/sec: 1489.10
//
Query:       gi|13540907|ref|NP_110595.1|  [L=164]
Description: hypothetical protein TVN0076 [Thermoplasma volcanium GSS1]
Scores for complete 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-41  138.7   0.0    9.6e-41  138.5   0.0    1.1  1  Ribo_biogen_C  Ribosome biogenesis protein, C-terminal
     0.0014   18.4   0.0     0.0025   17.6   0.0    1.3  1  RLI            Possible Fer4-like domain in RNase L inhibitor


Domain annotation for each model (and alignments):
>> Ribo_biogen_C  Ribosome biogenesis protein, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  138.5   0.0   1.1e-44   9.6e-41       1     126 [.      40     162 ..      40     163 .. 0.95

  Alignments for each domain:
  == domain 1  score: 138.5 bits;  conditional E-value: 1.1e-44
                                   EEE-TT-SSB--GGGHHHHHHT-EEEE---TTT--GGGTTT-E....EB--S-B--STTTTT-BS---HHHHHHHHHHHTT CS
                 Ribo_biogen_C   1 ivlspkakkvlspaDreiveksgiavvdcsWarleevkfkklkakeerlLPyLvAaNpvnYgkplkLscvEAlaaalyilg 81 
                                   +vl+p+a+ +ls++D+ ++ek+g++v++ sW++++++k  +lk + er+LP L+AaNpvnYgk   Ls+vEA aaalyi+g
  gi|13540907|ref|NP_110595.1|  40 LVLTPYADIFLSREDAVLYEKYGLCVIEGSWNKIDSIK--SLKFRIERRLPALLAANPVNYGKIGILSSVEATAAALYIIG 118
                                   69**********************************99..555689*********************************** PP

                                   -HHHHHHHHTSSTTHHHHHHHCHHHHHHH.TT--HHHHHHHHHHH CS
                 Ribo_biogen_C  82 lkeeaeellskfkwgeeFlelnkelleeYakckdseevvevqkey 126
                                   + ++a +llskf+wg +F++ln+++l+eY+ ++d++e+++++++y
  gi|13540907|ref|NP_110595.1| 119 YWDTAYALLSKFSWGLNFIKLNENPLNEYS-TADRSEIKKIEESY 162
                                   *****************************6.567889****9988 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 !   17.6   0.0   2.8e-07    0.0025       7      30 ..       8      31 ..       4      34 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2.8e-07
                                  S---------TTHHHHHTTSEEEE CS
                           RLI  7 dadqCdPKKCtgkkcarfcpvrlv 30
                                  +  q+dPKK t +k++rf++++ v
  gi|13540907|ref|NP_110595.1|  8 YLRQDDPKKATMRKLERFGLAKRV 31
                                  566******************654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 1052.27
//
Query:       gi|13540908|ref|NP_110596.1|  [L=256]
Description: hypothetical protein TVN0077 [Thermoplasma volcanium GSS1]
Scores for complete 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-59  199.9   0.0    3.8e-59  199.7   0.0    1.1  1  tRNA_deacylase  D-aminoacyl-tRNA deacylase


Domain annotation for each model (and alignments):
>> tRNA_deacylase  D-aminoacyl-tRNA deacylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  199.7   0.0   2.1e-63   3.8e-59       3     204 ..      56     253 ..      54     254 .. 0.97

  Alignments for each domain:
  == domain 1  score: 199.7 bits;  conditional E-value: 2.1e-63
                                   ---SEEEEEEEEE-TT---EEEEE--B-SS-.-TTSS-TT-B--B-HHHHHHHHHHHHGGGGGSTT-EEEE--S-SS---- CS
                tRNA_deacylase   3 edvdliiflSrHssesgkplLTvHvtGnlge.aelGGkpeelapaaPrllkallralkkiaekleefevtlEatHHGPtel 82 
                                   ++++++++lSrHss+++ ++LT+H+tGn+g+ a+lGG+p+++ +++P++++ +lr++ +   +  +f+vt+EatHHGP+ +
  gi|13540908|ref|NP_110596.1|  56 NNYEYAVVLSRHSSAADIKSLTAHPTGNFGPkADLGGRPKTINVSCPKYMSGTLRQMLESY-SGTKFQVTFEATHHGPI-F 134
                                   6899****************************************************99999.9****************.* PP

                                   -S-EEEEEEEESHHHHT-HHHHHHHHHHHHHHHH------EEEEEE-S-TT-HHHHHHHHHBSEEEEEEE-GGGGGG--HH CS
                tRNA_deacylase  83 kvPslFvEiGSteeeWkdedaaeavaeavlelleseeekekvlvgiGGgHYaprftklvletevavGhilskyaleelkee 163
                                   + P ++vEiG+te+eW+d+da ++ ++av++   ++    +++v++GGgHYap++ ++++++e+++Ghi+sk+ +++l+e 
  gi|13540908|ref|NP_110596.1| 135 DLPNYYVEIGTTENEWTDDDAKKTAVDAVINPDAKD---FPNFVAVGGGHYAPKILEYFRRNEINIGHIISKHDHDDLEEW 212
                                   ******************************996655...****************************************** PP

                                   HHHHHHHHH.T-SEEEE-TTT--HHHHHHHHHHHHHHT-EE CS
                tRNA_deacylase 164 vikqaleksegadvalidkkslkseqkeaieelleelgiev 204
                                    ik+a+ek+ +++ +l+d+k+++s+ +++++++ ++lg+e+
  gi|13540908|ref|NP_110596.1| 213 QIKDAVEKTPSCKGFLVDRKGTRSRVRDMVKSISDDLGLEL 253
                                   **************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       486  (0.0271069); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1736.70
//
Query:       gi|13540909|ref|NP_110597.1|  [L=335]
Description: histidinol-phosphate aminotransferase [Thermoplasma volcanium GSS1]
Scores for complete 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-20   71.1   0.0    1.2e-19   70.7   0.0    1.1  1  Aminotran_1_2  Aminotransferase class I and II


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.7   0.0   6.7e-24   1.2e-19      32     335 ..      29     299 ..      17     327 .. 0.83

  Alignments for each domain:
  == domain 1  score: 70.7 bits;  conditional E-value: 6.7e-24
                                   HHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHH CS
                 Aminotran_1_2  32 laggtlneygpidglpeleealakflgrseklklkreaavvvgsGagaliealifllklnpgdeilvpdptyasyknilrl 112
                                   l+ g++  y+ i  + + ee+l  + +        ++  +v g+G ++li   + + +    ++ ++  p++++yk i++ 
  gi|13540909|ref|NP_110597.1|  29 LDLGKYSLYPEIS-YTDIEEKLRVYTK-------STNMGIVIGPGLTHLIYKYFEFYQ---VKKPIIAMPNFSEYKGIAED 98 
                                   5667788888888.8888888888888.......55559************9999996...444567789*********** PP

                                   TTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTC CS
                 Aminotran_1_2 113 sggevvryplyseedfhldlealeealkeapegnkktkvilvesphNPtGtvatleeleklldlakkynlllfvDeaYagf 193
                                   +++ +  +p y      +  + l+  lk++      +  ++++sp+NP G ++++ +le++ ++ +k++ ++f+D a+ +f
  gi|13540909|ref|NP_110597.1|  99 RHLRFSAIPSY-----IIEKDPLI--LKNF-----DHDALFITSPSNPFGELFPESTLETVFEIEEKRGRRVFLDGAFMDF 167
                                   *********44.....44444443..4554.....6789****************************************** PP

                                   BSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEEEEEEHHHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHHHHHH CS
                 Aminotran_1_2 194 vfgsldavatranveeepnllivgslsKafGlaGeRvGyilgnaavvsqlrklsrpflsssllqaavaaalsdallkqsel 274
                                   v +   a++++     + n+ i +sl K ++++ +R Gy++   + ++  rk+  p+ ++ ++  ++  +  ++       
  gi|13540909|ref|NP_110597.1| 168 VPN--YAESIVQSSRSYFNVTIGRSLTKILAIPSLRAGYLIMERHEADLFRKAMEPWSICQPAIDFIRSIDINE-----VA 241
                                   ***..678889999******************************************988888887777665554.....46 PP

                                   HHHHHHHHHHHHHHHHHHHHSTEEEECCSCSSEEEEEETHHCHHHHHHHHHHTCTEEEEEG CS
                 Aminotran_1_2 275 eemrqrlqkrrkelrdeLaelglkvlasqsgmflltdlsaetakelskkLleevgvyvtpg 335
                                   +++++ ++ +r++l +eL++ g+kv++++s+ + +  +++   +e++  +l + g++v+  
  gi|13540909|ref|NP_110597.1| 242 KNSVALVNGEREYLISELKARGIKVIGNPSANYIVISMPRT--DEFYNFMLSK-GILVRLL 299
                                   899***************999********888888888877..8999999999.8888755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2384.97
//
Query:       gi|13540910|ref|NP_110598.1|  [L=295]
Description: hypothetical protein TVN0079 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.018   14.7   7.8      0.018   14.7   7.8    4.1  5  TEX13           Testis-expressed sequence 13 protein family
       0.36   11.1  28.4       0.16   12.2   1.4    4.2  4  DUF948          Bacterial protein of unknown function (DUF948
       0.91    9.6  17.8      0.074   13.1   1.9    3.4  3  Baculo_PEP_C    Baculovirus polyhedron envelope protein, PEP,
       0.91    9.3  24.4      0.034   13.9   2.6    3.2  3  MCPsignal       Methyl-accepting chemotaxis protein (MCP) sig
        2.6    7.3  45.6       0.24   10.7  36.9    2.4  2  ALIX_LYPXL_bnd  ALIX V-shaped domain binding to HIV
        2.9    6.3   7.9        1.3    7.4   0.2    2.0  2  FUSC            Fusaric acid resistance protein family
          6    7.3  21.5          7    7.1   1.3    4.9  4  LPP             Lipoprotein leucine-zipper


Domain annotation for each model (and alignments):
>> TEX13  Testis-expressed sequence 13 protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       1.4   3.5e+03     132     144 ..       5      17 ..       2      25 .. 0.74
   2 ?   14.7   7.8   6.9e-06     0.018      75     140 ..      36      97 ..      30     108 .. 0.76
   3 ?   -0.3  10.2      0.31   7.8e+02      77     141 ..     107     174 ..      99     183 .. 0.70
   4 ?    2.9   3.6     0.031        78      80     144 ..     155     215 ..     146     221 .. 0.76
   5 ?   -0.6   1.5      0.37   9.5e+02      85     121 ..     217     244 ..     206     285 .. 0.42

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.4
                         TEX13 132 laevqkerdlLrk 144
                                   l+e +++rdlL+k
  gi|13540910|ref|NP_110598.1|   5 LQEFEEKRDLLKK 17 
                                   7788888888876 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 6.9e-06
                         TEX13  75 aarqrelqarrvqkLqdqveehksaaqaLaselkrlreqqemerkeaasqlqlaqaalaevqkerd 140
                                    a qr++ + +v+ +++qv+e+ s  +aL+ e++++r+    e++e   +l   +++ +++++e +
  gi|13540910|ref|NP_110598.1|  36 YAEQRDQLNAKVHEMREQVKEKISQKNALIEEVQKVRA----EKEEHFKKLSDLRKDYKKLSEESN 97 
                                   56799999******************************....555555555555555555555443 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.31
                         TEX13  77 rqrelqarrvqkLqdqveehksaaqaLaselkrlreqqemerkeaasqlqla...qaalaevqkerdl 141
                                   + +e++ +++   q+ +++ k+    ++se+k+l+++ ++ +++ + ql+     ++ lae+ ke+ +
  gi|13540910|ref|NP_110598.1| 107 KAKEKELQKLITKQQTMQLTKAEEDKIVSEIKKLNNEIKKMKEDRTKQLNENekvKELLAEIDKEKTI 174
                                   3455555666666999999***************9977777777777776541114456666666655 PP

  == domain 4  score: 2.9 bits;  conditional E-value: 0.031
                         TEX13  80 elqarrvqkLqdqveehksaaqaLaselkrlreqqemerkeaasqlqlaqaalaevqkerdlLrk 144
                                    +++++v+ L   ++++k++a  L  + +++ +      +e+   ++ + ++l ev+k+ d +++
  gi|13540910|ref|NP_110598.1| 155 LNENEKVKELLAEIDKEKTIARDLKKKAEEISN----KISEISNDINKSLQDLDEVRKKADEMHE 215
                                   346789999999999999999999999999998....6677777777777777777777776655 PP

  == domain 5  score: -0.6 bits;  conditional E-value: 0.37
                         TEX13  85 rvqkLqdqveehksaaqaLaselkrlreqqemerkea 121
                                    v+  ++  +eh+++ qa  ++l+ l++        +
  gi|13540910|ref|NP_110598.1| 217 AVKYGKESEQEHEAFIQA-KNDLRDLEK--------V 244
                                   444444444444444433.222222222........1 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   2.6   0.00016      0.41      34      81 ..      25      72 ..      13     100 .. 0.62
   2 ?    2.7   5.2     0.059   1.5e+02      32      76 ..     120     164 ..     104     171 .. 0.79
   3 ?   12.2   1.4   6.4e-05      0.16      28      76 ..     168     216 ..     159     226 .. 0.58
   4 ?   -1.4   0.3       1.1   2.9e+03      30      70 ..     233     271 ..     228     283 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00016
                        DUF948 34 tieelekqvdpilkevedllakvnelledvneklekvdplteavadlg 81
                                    +e  +q +++ ++ ++l akv e+ e+v+ek+ + ++l+e+v+++ 
  gi|13540910|ref|NP_110598.1| 25 KRDEAAQQSRSYAEQRDQLNAKVHEMREQVKEKISQKNALIEEVQKVR 72
                                  555555666666666666666666666666666666666666666653 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.059
                        DUF948  32 aatieelekqvdpilkevedllakvnelledvneklekvdpltea 76 
                                   ++t++ ++ + d+i+ e+++l ++++++ ed +++l++ +++ e 
  gi|13540910|ref|NP_110598.1| 120 QQTMQLTKAEEDKIVSEIKKLNNEIKKMKEDRTKQLNENEKVKEL 164
                                   678899999999******************999988765555444 PP

  == domain 3  score: 12.2 bits;  conditional E-value: 6.4e-05
                        DUF948  28 ldeaaatieelekqvdpilkevedllakvnelledvneklekvdpltea 76 
                                   +d+ ++  ++l+k++++i++++ ++ + +n+ l+d+ e  +k d++ e 
  gi|13540910|ref|NP_110598.1| 168 IDKEKTIARDLKKKAEEISNKISEISNDINKSLQDLDEVRKKADEMHEM 216
                                   4444455566666666666666666666666666666666665555555 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 1.1
                        DUF948  30 eaaatieelekqvdpilkevedllakvnelledvneklekv 70 
                                   +a++ +++lek + ++ ++ +++ +k ++  +++++k e +
  gi|13540910|ref|NP_110598.1| 233 QAKNDLRDLEKVIAGLRTKKRATKKKEKD--DELQQKAEVL 271
                                   55666666776666666666666666666..6666666655 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 ?    1.3   0.2      0.13   3.3e+02      60      93 ..      31      64 ..       5      71 .. 0.68
   2 ?   -2.7  11.2       2.2   5.5e+03      40     100 ..      99     167 ..      37     169 .. 0.78
   3 ?   13.1   1.9   2.9e-05     0.074      18      63 ..     161     205 ..     153     251 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.13
                  Baculo_PEP_C 60 eldtrldtlltnLtdalnalqdtlrneLtnlnsi 93
                                  ++++  +++ ++L++++ ++ +++++++   n+ 
  gi|13540910|ref|NP_110598.1| 31 QQSRSYAEQRDQLNAKVHEMREQVKEKISQKNAL 64
                                  4444667777788888888888887777665554 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.2
                  Baculo_PEP_C  40 ldaietqLnalsedlksllaeldt.........rldtlltnLtdalnalqdtlrneLtnlnsiltnLlss 100
                                    +  +++++a +++l++l+++++t         ++ + +++L++ +++++++ +++L+  n ++ +Ll++
  gi|13540910|ref|NP_110598.1|  99 TNISQREIKAKEKELQKLITKQQTmqltkaeedKIVSEIKKLNNEIKKMKEDRTKQLNE-NEKVKELLAE 167
                                   44456677777788888888888777777777788888888888888888888888865.5666666665 PP

  == domain 3  score: 13.1 bits;  conditional E-value: 2.9e-05
                  Baculo_PEP_C  18 LtnvLnairlqnvqilaqlatlldaietqLnalsedlksllaeldt 63 
                                   + ++L+ i  ++ +i+ +l++  ++i ++++++s+d++++l++ld+
  gi|13540910|ref|NP_110598.1| 161 VKELLAEI-DKEKTIARDLKKKAEEISNKISEISNDINKSLQDLDE 205
                                   56789999.8889999**************************9997 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 ?    2.4   5.1     0.046   1.2e+02      81     135 ..      30      84 ..      19     117 .. 0.57
   2 ?    3.0   3.7     0.031        81     110     170 ..     110     170 ..      97     172 .. 0.75
   3 ?   13.9   2.6   1.3e-05     0.034      78     147 ..     172     241 ..     168     260 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.046
                                   HHHHHHHHHHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHH CS
                     MCPsignal  81 Aersaqaakeiealiieiqkeindsvesleetrqrveegselveetgealkeive 135
                                   A++s   a++ ++l +++++  +++ e +++ +  +ee  +  +e +e +k++++
  gi|13540910|ref|NP_110598.1|  30 AQQSRSYAEQRDQLNAKVHEMREQVKEKISQKNALIEEVQKVRAEKEEHFKKLSD 84 
                                   4555555555555555555555555555555555555555555555555555444 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.031
                                   HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     MCPsignal 110 eetrqrveegselveetgealkeiveavaevadlvqeiaaaseeqsasieevnqaveevak 170
                                   e+  q+  +  ++++ t+ +  +iv+++++++++++ ++   ++q +  e+v + ++e++k
  gi|13540910|ref|NP_110598.1| 110 EKELQKLITKQQTMQLTKAEEDKIVSEIKKLNNEIKKMKEDRTKQLNENEKVKELLAEIDK 170
                                   4444555556677788888889999999999999999999999999888888888887765 PP

  == domain 3  score: 13.9 bits;  conditional E-value: 1.3e-05
                                   HHHHHHHHHHHHHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHH CS
                     MCPsignal  78 rkLAersaqaakeiealiieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqei 147
                                   +++A+  +++a+ei++ i ei ++in+s++ l+e+r++++e  e++ + g++ ++  ea  + ++ ++++
  gi|13540910|ref|NP_110598.1| 172 KTIARDLKKKAEEISNKISEISNDINKSLQDLDEVRKKADEMHEMAVKYGKESEQEHEAFIQAKNDLRDL 241
                                   78899999*********************************99999888887777777666666666665 PP

>> ALIX_LYPXL_bnd  ALIX V-shaped domain binding to HIV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7  36.9   9.3e-05      0.24     103     280 ..       6     198 ..       1     208 [. 0.67
   2 ?   -2.2  12.1      0.75   1.9e+03     105     220 ..     158     240 ..     153     282 .. 0.37

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 9.3e-05
                ALIX_LYPXL_bnd 103 qenkedlelLsg.peeeleaa..lpssssa.............aasesveeqirklrsllekldelkaereqllkdlkeka 167
                                   qe++e+ +lL++  ee +++     ++s++             ++ e+v+e+i++   l+e++++++ae+e+  k+l +  
  gi|13540910|ref|NP_110598.1|   6 QEFEEKRDLLKKaVEEHIKKRdeAAQQSRSyaeqrdqlnakvhEMREQVKEKISQKNALIEEVQKVRAEKEEHFKKLSDLR 86 
                                   55555555553312222222222111111223444444433323389*************************999998644 PP

                ALIX_LYPXL_bnd 168 endDitpklltekkr.diaanefealfeeelekydplqeqleqslakqeellkeiqeaneefeqskksdseq..sqrqree 245
                                   ++    +kl +e+   +i+  e  +  e+el+k+   q+ ++ ++a+++++++ei+++n+e+++ k+++ +q   +++ +e
  gi|13540910|ref|NP_110598.1|  87 KDY---KKLSEESNYtNISQRE-IKAKEKELQKLITKQQTMQLTKAEEDKIVSEIKKLNNEIKKMKEDRTKQlnENEKVKE 163
                                   444...7777777764444444.677899*****************************************88533666667 PP

                ALIX_LYPXL_bnd 246 vlqkleaaydkykelksnleeglkFYndltellek 280
                                    l ++++  +  ++lk++ ee  +  ++ ++ ++k
  gi|13540910|ref|NP_110598.1| 164 LLAEIDKEKTIARDLKKKAEEISNKISEISNDINK 198
                                   77777777777777777777666554444444444 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.75
                ALIX_LYPXL_bnd 105 nkedlelLsg..peeeleaalpssssaaasesveeqirklrsllekldelkaereqllkdlkekaendDitpklltekkrd 183
                                   n++  elL+    e+ + + l ++++ ++s++ +e  +++ + l++lde++++ +++ ++                     
  gi|13540910|ref|NP_110598.1| 158 NEKVKELLAEidKEKTIARDLKKKAE-EISNKISEISNDINKSLQDLDEVRKKADEMHEMA-------------------- 217
                                   44444444322222223333443222.2344444444444444444444444444433333.................... PP

                ALIX_LYPXL_bnd 184 iaanefealfeeelekydplqeqleqslakqeellke 220
                                                  ky++  eq +++  + ++ l++
  gi|13540910|ref|NP_110598.1| 218 --------------VKYGKESEQEHEAFIQAKNDLRD 240
                                   ..............13333333333333222222333 PP

>> FUSC  Fusaric acid resistance protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   2.7     0.023        60     229     325 ..       2      93 ..       1     112 [. 0.55
   2 ?    7.4   0.2   0.00052       1.3     197     337 ..     137     264 ..     111     277 .. 0.50

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.023
                          FUSC 229 lallallsslarllarlraeeaaavpelaallaelaaleaaaaaealeaalaalrarlralrraleadadtaalllarlae 309
                                   ++ll+ + + ++ll+   +e+ + ++e a+  +  a+     + ++l a++ ++r+++++  ++  a  +  + + a+  e
  gi|13540910|ref|NP_110598.1|   2 TDLLQEFEEKRDLLKKAVEEHIKKRDEAAQQSRSYAE-----QRDQLNAKVHEMREQVKEKISQKNALIEEVQKVRAEKEE 77 
                                   5555556666666666666666665555554444444.....455555555555555555555555455555555555555 PP

                          FUSC 310 llaelaqllaslrale 325
                                   ++++l +l++++++l+
  gi|13540910|ref|NP_110598.1|  78 HFKKLSDLRKDYKKLS 93 
                                   5555555555555554 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.00052
                          FUSC 197 ilalealrsqaayesprirararalrrllsrmlallallsslarllarlraeeaaavpelaallaelaaleaaaaaealea 277
                                   i  l++ ++    + ++  ++++++++ll+++    ++++ l +  ++ + + ++   ++ + l++l+++           
  gi|13540910|ref|NP_110598.1| 137 IKKLNNEIKKMKEDRTKQLNENEKVKELLAEIDKEKTIARDLKKKAEEISNKISEISNDINKSLQDLDEV----------- 206
                                   4444444444444444444444444444444444444444444444444444444444444444444443........... PP

                          FUSC 278 alaalrarlralrrale..............adadtaalllarlaellaelaqllaslraleaaiaaarraerl 337
                                                                  ++++++++++ +++++l++l  + a lr+ ++a++++++   l
  gi|13540910|ref|NP_110598.1| 207 ----------------RkkademhemavkygKESEQEHEAFIQAKNDLRDLEKVIAGLRTKKRATKKKEKDDEL 264
                                   ................0333333334445656666777777777777777777777777777776664444433 PP

>> LPP  Lipoprotein leucine-zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   2.3     0.055   1.4e+02       3      33 ..      41      71 ..      36     100 .. 0.67
   2 ?   -0.5   0.0      0.64   1.6e+03       9      26 ..      82      99 ..      80     112 .. 0.63
   3 ?    6.8   1.7    0.0034       8.7       3      29 ..     131     157 ..     129     184 .. 0.80
   4 ?    7.1   1.3    0.0027         7      11      36 ..     184     209 ..     175     219 .. 0.54

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.055
                           LPP  3 deLssqVsqLkskvdqlssdvnsakaaaqaa 33
                                  d+L++ V ++ ++v++  s+ n++ +++q++
  gi|13540910|ref|NP_110598.1| 41 DQLNAKVHEMREQVKEKISQKNALIEEVQKV 71
                                  4555555555555554444444444444444 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.64
                           LPP  9 VsqLkskvdqlssdvnsa 26
                                  +s+L ++ ++ls++ n +
  gi|13540910|ref|NP_110598.1| 82 LSDLRKDYKKLSEESNYT 99
                                  577777888888775443 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.0034
                           LPP   3 deLssqVsqLkskvdqlssdvnsakaa 29 
                                   d++ s++++L+++++++++d ++  ++
  gi|13540910|ref|NP_110598.1| 131 DKIVSEIKKLNNEIKKMKEDRTKQLNE 157
                                   789999************994443333 PP

  == domain 4  score: 7.1 bits;  conditional E-value: 0.0027
                           LPP  11 qLkskvdqlssdvnsakaaaqaakeE 36 
                                   + ++k++++s+d+n++ ++++++++ 
  gi|13540910|ref|NP_110598.1| 184 EISNKISEISNDINKSLQDLDEVRKK 209
                                   34445555555555555554444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      5010  (0.279436); expected 358.6 (0.02)
Passed bias filter:                      702  (0.0391544); expected 358.6 (0.02)
Passed Vit filter:                       271  (0.0151152); expected 17.9 (0.001)
Passed Fwd filter:                       133  (0.00741815); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 2.13u 0.39s 00:00:02.52 Elapsed: 00:00:00.66
# Mc/sec: 1351.15
//
Query:       gi|13540911|ref|NP_110599.1|  [L=134]
Description: hypothetical protein TVN0080 [Thermoplasma volcanium GSS1]
Scores for complete 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   62.5   2.0    2.1e-17   62.5   2.0    2.8  3  DUF131          Protein of unknown function DUF131
  ------ inclusion threshold ------
      0.021   15.2   0.0       0.03   14.7   0.0    1.1  1  CpxA_peri       Two-component sensor protein CpxA, periplasmi
      0.032   13.3   0.1      0.032   13.3   0.1    1.8  2  DUF898          Bacterial protein of unknown function (DUF898
      0.082   13.3   0.9       0.26   11.7   0.0    1.9  2  G0-G1_switch_2  G0/G1 switch protein 2
       0.29   11.6   9.8       0.31   11.6   1.0    2.7  2  DUF3899         Domain of unknown function (DUF3899)
       0.85    8.6  15.2       0.35    9.9   8.6    2.0  2  DUF973          Protein of unknown function (DUF973)
        1.4    9.0   4.4        9.4    6.3   4.4    2.3  1  Jagunal         Jagunal, ER re-organisation during oogenesis
        4.7    7.1  11.1         26    4.7   8.6    2.1  2  DUF1461         Protein of unknown function (DUF1461)


Domain annotation for each model (and alignments):
>> DUF131  Protein of unknown function DUF131
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   1.3       1.1   2.4e+03      46      53 ..       9      16 ..       3      21 .. 0.54
   2 !    4.9   5.4    0.0091        20      34      58 ..      36      61 ..      34      65 .. 0.84
   3 !   62.5   2.0   9.4e-21   2.1e-17      13      61 ..      74     130 ..      63     131 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.1
                        DUF131 46 taiiLaIi 53
                                  ++ii+++i
  gi|13540911|ref|NP_110599.1|  9 ILIIIGVI 16
                                  33444433 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0091
                        DUF131 34 PIiFGsdkrlaktai.iLaIilmill 58
                                  P+i+G+  +++  +i +L+I++m+++
  gi|13540911|ref|NP_110599.1| 36 PVIYGTGLSVIPFLIiFLGIVIMFFA 61
                                  *********999876268*****976 PP

  == domain 3  score: 62.5 bits;  conditional E-value: 9.4e-21
                        DUF131  13 e........eaekeesrvkgGGVvliGPIPIiFGsdkrlaktaiiLaIilmilllil 61 
                                   +        e+++e++++ +GG+++iGPIPIiFG++k +++++i +aI+++++++++
  gi|13540911|ref|NP_110599.1|  74 PqdyvnkmeEEQEEKRKSSFGGLIMIGPIPIIFGNNKTIVYVSIAIAILILLVFILY 130
                                   3444444447888889999*******************************9999986 PP

>> 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 ?   14.7   0.0   1.3e-05      0.03      72     120 ..      68     117 ..      64     120 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.3e-05
                                   HHHHHHHHHHHHH-S-TTS-EEE.EETTEEEEEEEEEEETTEEEEEEEEE CS
                     CpxA_peri  72 dfklkalrnfvtsiespekPkqk.LYGrymlaGPlpitlakeelllyvGl 120
                                   ++++k  +++v  +e+ ++ k+k  +G  ++ GP+pi   ++++++yv +
  gi|13540911|ref|NP_110599.1|  68 RYEYKEPQDYVNKMEEEQEEKRKsSFGGLIMIGPIPIIFGNNKTIVYVSI 117
                                   5788889999*999988877766379*********************975 PP

>> DUF898  Bacterial protein of unknown function (DUF898)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   1.6      0.25   5.6e+02      67     102 ..       8      38 ..       2      46 .. 0.50
   2 ?   13.3   0.1   1.4e-05     0.032     185     250 ..      45     130 ..      41     134 .] 0.75

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.25
                        DUF898  67 flialvllvlysvasalapllglllllllflllpwa 102
                                   ++++++      v++ ++ ++   + ++lf+++p++
  gi|13540911|ref|NP_110599.1|   8 YILIIIG-----VIALVGLAALGQAHFALFVIFPVI 38 
                                   3333333.....333333334444455555555555 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 1.4e-05
                        DUF898 185 laavllfllglvlliallaalltevlakeaaatadaskseaellk......................lavllilalvllll 243
                                   ++ +l+++lg+v+++++++ + + +  ke+    +++++e+e +                       ++ ++i++++l+ll
  gi|13540911|ref|NP_110599.1|  45 VIPFLIIFLGIVIMFFAPFTMGGRYEYKEPQDYVNKMEEEQEEKRkssfgglimigpipiifgnnktIVYVSIAIAILILL 125
                                   56789999999999999999998888888877777766666655589999*99***********99866666666666444 PP

                        DUF898 244 allaaay 250
                                   +++   y
  gi|13540911|ref|NP_110599.1| 126 VFI--LY 130
                                   433..33 PP

>> G0-G1_switch_2  G0/G1 switch protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.9      0.94   2.1e+03      26      42 ..       3      18 ..       1      27 [. 0.73
   2 ?   11.7   0.0   0.00011      0.26      31      77 ..      44      90 ..      37      95 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.94
                G0-G1_switch_2 26 lYvlGsvLallGvvigl 42
                                  l+ lG +L ++Gv+  l
  gi|13540911|ref|NP_110599.1|  3 LFRLGYILIIIGVIA-L 18
                                  778899999999753.3 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00011
                G0-G1_switch_2 31 svLallGvviglvetvcspFssesrlreeeeavaklqaarekeaeek 77
                                  sv+ +l + +g+v + + pF+  +r + +e +   ++ ++e+e+++k
  gi|13540911|ref|NP_110599.1| 44 SVIPFLIIFLGIVIMFFAPFTMGGRYEYKEPQDYVNKMEEEQEEKRK 90
                                  8999999*****************88877776666655555555544 PP

>> DUF3899  Domain of unknown function (DUF3899)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   1.9     0.026        58       4      20 ..       3      19 ..       2      24 .. 0.90
   2 ?   11.6   1.0   0.00014      0.31       9      83 ..      45     130 ..      42     131 .. 0.65

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.026
                       DUF3899  4 lFllglllliigilliv 20
                                  lF lg++l+iig++++v
  gi|13540911|ref|NP_110599.1|  3 LFRLGYILIIIGVIALV 19
                                  799**********9987 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00014
                       DUF3899   9 lllliigillivlnsGfFdgfsygfrklkklflkkskkddsyyeykekkkes................skkstrplliiGl 73 
                                   +++++i +l iv+   fF  f+ g r   k   +  + + +++e++e+k +s                ++k +++  i++ 
  gi|13540911|ref|NP_110599.1|  45 VIPFLIIFLGIVIM--FFAPFTMGGRYEYKE--P-QDYVNKMEEEQEEKRKSsfgglimigpipiifgNNKTIVYVSIAIA 120
                                   55555555555554..555555555554433..2.4555666666666555558999999999999998888888888888 PP

                       DUF3899  74 llivlsivll 83 
                                   +li+l ++l+
  gi|13540911|ref|NP_110599.1| 121 ILILLVFILY 130
                                   8888888875 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   8.6   0.00016      0.35     102     163 ..       2      70 ..       1      75 [. 0.84
   2 ?    3.3   0.5     0.016        36     103     137 ..      96     130 ..      82     134 .] 0.56

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00016
                        DUF973 102 tliligaiiiiigvilaivsll........slilslillgviilligiilaliGqillglsfyklGevYn 163
                                   +l+  g+i+iiigvi a+v+l           +   +++g+ +++i +++++ G ++++++   +G +Y+
  gi|13540911|ref|NP_110599.1|   2 NLFRLGYILIIIGVI-ALVGLAalgqahfaLFVIFPVIYGTGLSVIPFLIIFLGIVIMFFAPFTMGGRYE 70 
                                   6788999******88.77788888988876556667889999999999*************999999997 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.016
                        DUF973 103 liligaiiiiigvilaivsllslilslillgviil 137
                                   li+ig i ii+g   +iv +  +i +lill +i++
  gi|13540911|ref|NP_110599.1|  96 LIMIGPIPIIFGNNKTIVYVSIAIAILILLVFILY 130
                                   44455555555555555444444444444444444 PP

>> Jagunal  Jagunal, ER re-organisation during oogenesis
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   4.4    0.0042       9.4     110     154 ..      51     104 ..       3     133 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0042
                       Jagunal 110 yligtlvlgllpllygaveylkevleylkskease.........eitllqgfpl 154
                                   + +g++++ ++p  +g  + +ke ++y++++e+++          + ++  +p+
  gi|13540911|ref|NP_110599.1|  51 IFLGIVIMFFAPFTMGGRYEYKEPQDYVNKMEEEQeekrkssfgGLIMIGPIPI 104
                                   467899999*********************999985666555554445555554 PP

>> DUF1461  Protein of unknown function (DUF1461)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   8.6     0.011        26      91     160 ..       2      65 ..       1      65 [. 0.71
   2 ?    3.1   0.0     0.035        79      93     115 ..     106     128 ..      73     133 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.011
                       DUF1461  91 kLfllglivrlvtlillvllllllivlkkkkkkirllkskslllavilllliliilgllalidFdkaFtl 160
                                   +Lf+lg+i+ ++ +i+l    + l+ l +   +++l+  + ++++++l +++++i++l ++i F + Ft+
  gi|13540911|ref|NP_110599.1|   2 NLFRLGYILIIIGVIAL----VGLAALGQA--HFALFVIFPVIYGTGLSVIPFLIIFLGIVIMFFAPFTM 65 
                                   46666666666665555....555444444..4455556899****************999999988875 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.035
                       DUF1461  93 fllglivrlvtlillvlllllli 115
                                   f ++ ++++v++++++l+ll++i
  gi|13540911|ref|NP_110599.1| 106 FGNNKTIVYVSIAIAILILLVFI 128
                                   55566666666666655555443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1232  (0.0687155); expected 358.6 (0.02)
Passed bias filter:                      599  (0.0334096); expected 358.6 (0.02)
Passed Vit filter:                        98  (0.005466); 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):               8  [number of targets reported over threshold]
# CPU time: 0.63u 0.31s 00:00:00.94 Elapsed: 00:00:00.48
# Mc/sec: 832.56
//
Query:       gi|13540912|ref|NP_110600.1|  [L=359]
Description: nucleoside-diphosphate-sugar pyrophosphorylase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-47  162.7   0.0    1.4e-47  162.4   0.0    1.1  1  NTP_transferase  Nucleotidyl transferase
      1e-10   42.2   0.0    1.3e-10   41.8   0.0    1.2  1  NTP_transf_3     MobA-like NTP transferase domain
      3e-07   29.9  11.8    0.00046   19.8   1.3    4.2  5  Hexapep          Bacterial transferase hexapeptide (six repea
    1.1e-06   27.1   2.9    1.6e-06   26.6   2.9    1.2  1  DUF4954          Domain of unknown function (DUF4954)
  ------ inclusion threshold ------
       0.01   15.6   0.7       0.01   15.6   0.7    2.7  3  Hexapep_2        Hexapeptide repeat of succinyl-transferase
      0.012   14.6   5.0       0.26   10.2   4.8    2.6  2  Fucokinase       L-fucokinase


Domain annotation for each model (and alignments):
>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  162.4   0.0   4.7e-51   1.4e-47       1     243 [.       4     231 ..       4     236 .. 0.93

  Alignments for each domain:
  == domain 1  score: 162.4 bits;  conditional E-value: 4.7e-51
                                   EEEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEEEEES CS
               NTP_transferase   1 kavILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevlialep 81 
                                   k+v++aGG+GtRL+P+t +++k+lvpv+gk ++i + l    n+g+++ i+++t ++ + + + + e++  + ++l+++e+
  gi|13540912|ref|NP_110600.1|   4 KGVLMAGGKGTRLRPITYSIPKPLVPVAGK-PVISYILDSFYNAGVKD-IIITTGYKFEALIKGVLENKFSDQNILFSVEK 82 
                                   69****************************.*****************.7777777777666666666544479******* PP

                                   S--BGGHHHHHTHHHHTTSSE..EEEEETTEEEESTTHHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEEEECTTSBEEEE CS
               NTP_transferase  82 egkgtAdAvalaaelledeksdelvlvLggDhlikdayeeavkkaiekaakgtvtfgivpveeateyGvieadeegrverf 162
                                    + gtA+ v+la+++++d++     +v +gD+li+ +++++++++++++a   +t+++++v++++++G++e+d+eg v+rf
  gi|13540912|ref|NP_110600.1|  83 DPAGTAGGVKLAENFIDDTF-----VVGSGDILIDFDVSKMIEEHKKRGA--NITIALTRVDDPSQFGIAEVDDEGYVKRF 156
                                   *****************877.....8************************..9**************************** PP

                                   ECS-SSHSH.CSEECCSEEEEETTHHHHHHHCCHHHTTSSCHHHHHHHHHHHTTEEEEEECSTTEE-EEEXSSHHHHHHHH CS
               NTP_transferase 163 vEKPkeaka.selassGiYvfnsevllflakdleelkrgedeitdilpkaleegkvalaflfkdaeyWsDvGtldsllean 242
                                    EKPk+ +  s+++++G+Yv +++vl+++     +   + d+ +d++pka+++g + + +  ++   W D G + +l++an
  gi|13540912|ref|NP_110600.1| 157 LEKPKKSETfSNTINAGVYVIEPSVLEYI-----PKGVQFDFAKDLFPKAMANGIKIYTYEING--VWLDAGRPGDLIKAN 230
                                   *****98877*******************.....778999************************..7*************9 PP

                                   H CS
               NTP_transferase 243 e 243
                                   +
  gi|13540912|ref|NP_110600.1| 231 Q 231
                                   7 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 !   41.8   0.0   4.4e-14   1.3e-10       1     124 [.       5     135 ..       5     183 .. 0.83

  Alignments for each domain:
  == domain 1  score: 41.8 bits;  conditional E-value: 4.4e-14
                                   EEEEEESS-TTTT..T...THHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSHC.......HHHHHHTTCTS-EEE-TTSS CS
                  NTP_transf_3   1 aviLAGGrSsRmg..g...dKallplggkpllervldalraagvdevvvvggde.......evlaalarlgvrvvededpg 69 
                                   +v++AGG+++R+   +   +K+l+p++gkp++ ++ld++  agv+++++ +g++        +++ + ++++ + +++dp 
  gi|13540912|ref|NP_110600.1|   5 GVLMAGGKGTRLRpiTysiPKPLVPVAGKPVISYILDSFYNAGVKDIIITTGYKfealikgVLENKFSDQNILFSVEKDP- 84 
                                   799*********8551559**********************************654555544445677888888777764. PP

                                   -SHHHHHHHHHHHH.SSSCEEEEETT-TT--HHHHHHHHHCHHHHTSSEEEEESS CS
                  NTP_transf_3  70 kgplaslaaalraaadadavlvlacDmPlltpelverllaaaaasgadvvvptye 124
                                   +g++++++ a + +  +d ++v ++D+ l++   v +++++++++ga+++++ ++
  gi|13540912|ref|NP_110600.1|  85 AGTAGGVKLAENFI--DDTFVVGSGDI-LID-FDVSKMIEEHKKRGANITIALTR 135
                                   8**********998..79999999999.444.56788888889999998777665 PP

>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.1       2.6   7.7e+03      10      16 ..     170     176 ..     168     181 .. 0.55
   2 !   10.8   0.5    0.0001      0.31       8      34 ..     251     277 ..     250     279 .. 0.88
   3 !   19.8   1.3   1.5e-07   0.00046       2      32 ..     263     298 ..     262     301 .. 0.91
   4 !   14.3   0.4   8.3e-06     0.025       1      29 [.     285     312 ..     279     315 .. 0.78
   5 !   14.2   0.3   8.7e-06     0.026       2      30 ..     297     330 ..     296     334 .. 0.73

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 2.6
                                   E-TTEEE CS
                       Hexapep  10 Igpfavi 16 
                                   I +++++
  gi|13540912|ref|NP_110600.1| 170 INAGVYV 176
                                   5555555 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.0001
                                   EEE-TTEEEETTEEE-TTEEEETTEEE CS
                       Hexapep   8 vlIgpfaviggnVkIGdnvkIgagvvi 34 
                                   + I  ++ + g++ IG++v Ig g+ i
  gi|13540912|ref|NP_110600.1| 251 ARIPDGVNVSGPTYIGEGVAIGKGSSI 277
                                   6788999***************99877 PP

  == domain 3  score: 19.8 bits;  conditional E-value: 1.5e-07
                                   EEEETTEEE-T.....TEEEETTEEE-TTEEEETTE CS
                       Hexapep   2 tvIGsnvlIgp.....faviggnVkIGdnvkIgagv 32 
                                   t IG++v Ig+      ++i+++V+IG++v I + v
  gi|13540912|ref|NP_110600.1| 263 TYIGEGVAIGKgssidSSTIYEGVQIGNDVEIKNSV 298
                                   789********99999****************9866 PP

  == domain 4  score: 14.3 bits;  conditional E-value: 8.3e-06
                                   TEEEETTEEE-TTEEEETTEEE-TTEEEE CS
                       Hexapep   1 stvIGsnvlIgpfaviggnVkIGdnvkIg 29 
                                   +++IG++v I  ++vi++ + I d++kI 
  gi|13540912|ref|NP_110600.1| 285 GVQIGNDVEIK-NSVIMSSCRILDGSKIS 312
                                   46677777777.99999999999999985 PP

  == domain 5  score: 14.2 bits;  conditional E-value: 8.7e-06
                                   EEEETTEEE-T.....TEEEETTEEE-TTEEEET CS
                       Hexapep   2 tvIGsnvlIgp.....faviggnVkIGdnvkIga 30 
                                   +vI s + I        +vi+ n++IG+ + I +
  gi|13540912|ref|NP_110600.1| 297 SVIMSSCRILDgskisDSVIMQNTVIGEACEIRN 330
                                   6888888888866666778888888888777766 PP

>> DUF4954  Domain of unknown function (DUF4954)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   2.9   5.5e-10   1.6e-06     176     274 ..     242     342 ..     225     349 .. 0.81

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 5.5e-10
                       DUF4954 176 igekvkilnaglikNvkigdyatiegaskl.engtinSsk.eapveiGegViledfiissGskikdgavisrcfvGqavkl 254
                                   i+ + +il+a++   v++   ++i     + +  +i Ss+  + v+iG++V++++++i+s ++i dg++is++++ q++ +
  gi|13540912|ref|NP_110600.1| 242 INGSRMILKARIPDGVNVSGPTYIGEGVAIgKGSSIDSSTiYEGVQIGNDVEIKNSVIMSSCRILDGSKISDSVIMQNTVI 322
                                   66667788888888888888888865555515567877652789************************************* PP

                       DUF4954 255 kkqfsaedsllfaNcqgeng 274
                                   ++   + +s+l +  ++++g
  gi|13540912|ref|NP_110600.1| 323 GEACEIRNSVLSQKLNLQKG 342
                                   ***********998887776 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 ?   -2.2   0.3       1.2   3.6e+03      26      32 ..     170     176 ..     169     177 .. 0.84
   2 ?   15.6   0.7   3.4e-06      0.01       1      28 [.     262     296 ..     262     300 .. 0.89
   3 ?   -1.5   0.1      0.75   2.2e+03       7      24 ..     319     326 ..     313     332 .. 0.56

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.2
                                   E-TT-EE CS
                     Hexapep_2  26 vgaGvvi 32 
                                   + aGv++
  gi|13540912|ref|NP_110600.1| 170 INAGVYV 176
                                   789**98 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 3.4e-06
                                   .EEE-TT-EE-TT-EE.......SEEE-TT-EE-T CS
                     Hexapep_2   1 pviIGdnCliGanagi.......GvslGdncvvga 28 
                                   p+ IG+ + iG+ + i       Gv++G+++ + +
  gi|13540912|ref|NP_110600.1| 262 PTYIGEGVAIGKGSSIdsstiyeGVQIGNDVEIKN 296
                                   899**********9977777899********9987 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 0.75
                                   T-EE-TT-EESEEE-TT- CS
                     Hexapep_2   7 nCliGanagiGvslGdnc 24 
                                   n++iG            c
  gi|13540912|ref|NP_110600.1| 319 NTVIGEA----------C 326
                                   3444433..........3 PP

>> Fucokinase  L-fucokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0     0.069     2e+02      49     121 ..      99     164 ..      91     185 .. 0.79
   2 ?   10.2   4.8   8.5e-05      0.26     271     329 ..     289     344 ..     259     357 .. 0.68

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.069
                    Fucokinase  49 kpGvlvtssDvlllfdseeisfdka..gvtalavpstldigtnHGVfvlddqsseeeeleirsvkkflhKpseee 121
                                     +++v s+D l+ fd +++  +++  g+ +    + +d  ++ G+  +dd+         ++vk+fl Kp ++e
  gi|13540912|ref|NP_110600.1|  99 DDTFVVGSGDILIDFDVSKMIEEHKkrGANITIALTRVDDPSQFGIAEVDDE---------GYVKRFLEKPKKSE 164
                                   6788999999999998887776665556666556678889999999999999.........99999999999887 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 8.5e-05
                    Fucokinase 271 kesavvinSvlessvsvgegsviehsslkgnvsigsnsivsglelesseeslelpddti 329
                                    + + + nSv+ ss+++ +gs i +s + +n+ ig+ + + +  l+++ +   l++ + 
  gi|13540912|ref|NP_110600.1| 289 GNDVEIKNSVIMSSCRILDGSKISDSVIMQNTVIGEACEIRNSVLSQKLN---LQKGSR 344
                                   55666778888888888888888888888888888888888877777644...444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (359 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       311  (0.0173462); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 2216.76
//
Query:       gi|13540913|ref|NP_110601.1|  [L=317]
Description: hypothetical protein TVN0082 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1111  (0.0619666); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); 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):               0  [number of targets reported over threshold]
# CPU time: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.45
# Mc/sec: 2121.48
//
Query:       gi|13540914|ref|NP_110602.1|  [L=455]
Description: cytochrome bd-type quinol oxidase, subunit 1 [Thermoplasma volcanium GSS1]
Scores for complete 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-94  314.5  28.2      1e-93  314.3  28.2    1.0  1  Cyt_bd_oxida_I  Cytochrome bd terminal oxidase subunit I


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 !  314.3  28.2   5.6e-98     1e-93       3     416 ..       9     437 ..       7     439 .. 0.94

  Alignments for each domain:
  == domain 1  score: 314.3 bits;  conditional E-value: 5.6e-98
                Cyt_bd_oxida_I   3 RlqfaltavfHflfvpltlGlalllailetlylrtgdekykklakfwgklfainFavGvvtGivlefqfgtnWseysrfvG 83 
                                   Rl fa+++ +H+++v+++++  ++l ++e+l ++ +d++y  lak+++k+f+i+Fa+G+++Giv++ +++ +++++ ++v+
  gi|13540914|ref|NP_110602.1|   9 RLLFAYSIGVHIILVTMSISTIVVLSVAEYLGIKYKDKYYDLLAKRLAKVFTIFFAIGTASGIVMAAELVILFPKFFSVVA 89 
                                   99******************************************************************************* PP

                Cyt_bd_oxida_I  84 difgapLaiEgllAFflEstflglmlfgwdrv.skklhllatwlvaigtllSalwIlaanswmqtPvGael..npdtgrae 161
                                    +++ p+++E ++AF++E +fl ++++ wd + ++ +h+++t+++  gtl Sa +I+++n+wm+tP+G+++   ++tg ++
  gi|13540914|ref|NP_110602.1|  90 AVAMVPFYLE-IFAFMTETIFLIIYIYYWDFFkNRITHWILTFFIGAGTLGSAAFIVMVNAWMNTPNGFNIgvYEKTGAIT 169
                                   **********.7*******************978889********************************995333455555 PP

                Cyt_bd_oxida_I 162 ltdflavlfnpsalakflHtvlaalltaaffvagvsawyllr....rekefarkslkialvvalvaallqallGdlsgkev 238
                                    ++++a l +ps++ +++H+v  +ll++ +++ g++a+++l+    +++ f++k +k++ ++ ++ ++l+ ++G l ++++
  gi|13540914|ref|NP_110602.1| 170 DVNPWASLNSPSFMSEIAHVVPVTLLAGTMLIGGYFAYRYLKaregEDRTFYKKGMKLTSALSMAYVILAGVSGSLAASDL 250
                                   56*****************************************8777777******************************* PP

                Cyt_bd_oxida_I 239 aetqpaKlAAmeglwetee..aplslfgipdeeeeknefaieiPgllsllat.gsldgev.kGlndlpkeevPpvalvfws 315
                                   + +qp+K+ A+e ++  ++  +p  lfg + +   +   ai+iPgl+s+la  g++   + kGl  +p++++Pp ++v+  
  gi|13540914|ref|NP_110602.1| 251 IVNQPLKYSAIELNYLGGRafEPEKLFGTIVN--GHVVGAIKIPGLQSFLAGtGNPAYVIpKGLAYYPQSMWPP-LIVHSL 328
                                   ***************9998899******9776..556789**********973555555535***********9.9***** PP

                Cyt_bd_oxida_I 316 frimvglgvlllllallalll..........rwllrllllaiplpfiaveaGWivtevGRqPWivygllrtadavspvsag 386
                                   f++mvg+g+l+ l++l+ l++          r++  + +++++l+++++e GW+v evGRqPWi+y+++ + +a+   +++
  gi|13540914|ref|NP_110602.1| 329 FDLMVGFGILIGLFLLAYLIMwilrsepysnRIMAGIYIILGFLAMFTMEDGWVVDEVGRQPWIIYNVMYVYQAI--NTST 407
                                   ***********9999988755679******998999***************************************..8999 PP

                Cyt_bd_oxida_I 387 evllslilflllylvLlvvevylllklikk 416
                                   +++   i+++++y++L+ v +y+ ++++++
  gi|13540914|ref|NP_110602.1| 408 SMIGPGIAMMAFYTLLIPVSFYFSARVFNR 437
                                   99999******************9999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (455 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       852  (0.0475208); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.63u 0.30s 00:00:00.93 Elapsed: 00:00:00.48
# Mc/sec: 2851.51
//
Query:       gi|13540915|ref|NP_110603.1|  [L=205]
Description: transcription activator [Thermoplasma volcanium GSS1]
Scores for complete 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-26   91.2   0.6    9.2e-26   91.0   0.6    1.0  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 !   91.0   0.6   5.1e-30   9.2e-26       3     209 ..       9     200 ..       7     201 .. 0.92

  Alignments for each domain:
  == domain 1  score: 91.0 bits;  conditional E-value: 5.1e-30
                                   HCHHHHHHHHCSHHHHHHHTT-S-HHHHHHHHHHHHHHHHHHHHHHHHHHHC-SSHHHHHHHHHHHHHHHHCHHHHHHHHH CS
                    TENA_THI-4   3 qlrpiwkeyinHpFvkalakGtlpreqfqayviqdylylknfvrvlaiilskssdlevrrelesrivdhdgeeielhlrla 83 
                                   +++ +w++y++H+Fv+++++ tlp ++f++y++qd ly+ ++vr++ i ++ s  +++ +e+ s+iv    + +e h +l 
  gi|13540915|ref|NP_110603.1|   9 RAEDLWEKYVKHEFVERMRDDTLPVDSFKFYLVQDSLYVEEMVRSV-IRAAASMPFDMAYEILSKIVLNRDKGMEVHGQLE 88 
                                   67899***************************************99.5555556688888********99999******** PP

                                   HHTT-HHHHHCTTT--HHHHHHHHHHHHHHCHS-HHHHHHHHHHHHHHHHHHHHHHCCHHHS-TSCHHHHHHHHHCSHHHH CS
                    TENA_THI-4  84 ealGlsreelsktkpspatkayvrylldlarrgslaeavaallpclfvyqeiaerlkeklralegpeyyewvkeyaseefr 164
                                   ++lG++ +     k + +t++y+r+l+  a++  + +++aa +pc ++y  i +++     a ++  +++w++ yas+++ 
  gi|13540915|ref|NP_110603.1|  89 RELGITGKG----KMTMTTYSYTRHLIY-ASTLGWPQFLAAWTPCMWGYSFIGKYVV----ATKNMYFKRWAEFYASDDYM 160
                                   *******99....99999*******996.66778*******************8888....6678999************* PP

                                   HHHHHHHHHHHHHHHTSHHHHHHHHHHHHHHHHHHHHHHHHHHHT CS
                    TENA_THI-4 165 aaveeakrllerllakvsdeqleelqeiflkalefetsfltmald 209
                                   ++v+   ++l+r   ++s+     l + f+ + ++e++f+++ald
  gi|13540915|ref|NP_110603.1| 161 ERVSVILKSLDRFNGDASE-----LSDLFKASVKYEIMFWQSALD 200
                                   ************9999666.....9*****************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       566  (0.031569); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1324.76
//
Query:       gi|13540916|ref|NP_110604.1|  [L=170]
Description: hypothetical protein TVN0085 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       766  (0.0427241); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1208.34
//
Query:       gi|13540917|ref|NP_110605.1|  [L=201]
Description: alpha/beta superfamily hydrolase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score 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   14.3   0.0      0.026   13.2   0.0    1.4  1  Ndr       Ndr family


Domain annotation for each model (and alignments):
>> Ndr  Ndr family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.5e-06     0.026      95     134 ..      91     130 ..      85     147 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.5e-06
                                   HHT---EEEEEETHHHHHHHHHHHHSGGGEEEEEEES--- CS
                           Ndr  95 hfklksviglGvgaGAyilarfalkhperveglvLinits 134
                                    ++lk+ + +G g+   + +r a+++per + ++ in+ +
  gi|13540917|ref|NP_110605.1|  91 SLHLKNTMLIGSGVNGDVALRCAMEYPERCSNIIVINAPG 130
                                   699*********************************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       402  (0.0224218); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.30s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 1387.92
//
Query:       gi|13540918|ref|NP_110606.1|  [L=137]
Description: molybdopterin converting factor, large subunit [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-38  130.8   0.1    2.9e-38  130.6   0.1    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 !  130.6   0.1   1.6e-42   2.9e-38       1     113 []       8     120 ..       8     120 .. 0.98

  Alignments for each domain:
  == domain 1  score: 130.6 bits;  conditional E-value: 1.6e-42
                                   EESS---HHHHHHHH--TT--EEEEEEEE------TS-EEEEEECC-HHHHHHHHHHHHHHHHCCCTTSEEEEEEE-EEEE CS
                          MoaE   1 lteepldvaeiealvaspkaGAvvlFvGtvRdsfdgkkvteLeyeayepmaektleeiaeearerwelervavvHrlGele 81 
                                   +te+++++ ++ + v++p+aGA+v+F GtvR+++dg +vt+L yeay++mae +++++++ea++++++ ++av+Hr+G + 
  gi|13540918|ref|NP_110606.1|   8 ITEKDINPLDLINRVRRPDAGAIVTFEGTVRNDSDGVRVTALYYEAYKEMAEMQIADLIDEAKKKYNILDAAVCHRIGLVG 88 
                                   67889999999999******************************************************************* PP

                                   TTSEEEEEEEEESSHHHHHHHHHHHHHHHHHH CS
                          MoaE  82 vgeasvvvavssahRkeafeaceylidelKkr 113
                                   ++e svv++vssahR +afeac+y+id++K+r
  gi|13540918|ref|NP_110606.1|  89 LTEDSVVISVSSAHRSSAFEACRYIIDTIKER 120
                                   ******************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 939.81
//
Query:       gi|13540919|ref|NP_110607.1|  [L=284]
Description: chromosome partitioning ATPase [Thermoplasma volcanium GSS1]
Scores for complete 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-98  326.5   0.5    1.2e-97  326.2   0.5    1.0  1  ParA             NUBPL iron-transfer P-loop NTPase
      4e-18   65.7   0.0    8.6e-18   64.6   0.0    1.5  1  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
    1.1e-14   54.8   4.4      9e-13   48.5   4.4    2.5  1  AAA_31           AAA domain
    2.6e-08   33.5   1.7      9e-08   31.7   1.7    1.8  1  MipZ             ATPase MipZ
    3.8e-06   26.3   5.3    5.9e-06   25.7   1.6    2.5  3  ArsA_ATPase      Anion-transporting ATPase
    6.2e-06   25.9   1.0      0.001   18.6   0.2    2.3  2  Fer4_NifH        4Fe-4S iron sulfur cluster binding proteins,
    6.2e-05   22.4   0.0     0.0001   21.7   0.0    1.3  1  VirC1            VirC1 protein
    7.1e-05   22.7   0.2      0.052   13.4   0.0    2.2  2  AAA_26           AAA domain
    8.2e-05   22.3   0.1    0.00018   21.1   0.1    1.6  1  AAA_25           AAA domain
    0.00068   19.2   0.3       0.22   11.0   0.1    2.1  2  CBP_BcsQ         Cellulose biosynthesis protein BcsQ
     0.0057   16.3   0.1     0.0091   15.6   0.1    1.4  1  SRP54            SRP54-type protein, GTPase domain
     0.0069   15.4   0.2      0.012   14.6   0.2    1.3  1  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
     0.0086   16.0   0.0      0.069   13.1   0.1    2.0  2  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
  ------ inclusion threshold ------
      0.011   15.5   0.1      0.073   12.8   0.2    1.9  2  IstB_IS21        IstB-like ATP binding protein
      0.013   15.4   0.1      0.023   14.6   0.1    1.4  1  APS_kinase       Adenylylsulphate kinase
      0.014   15.2   0.1      0.027   14.3   0.1    1.4  1  CLP1_P           mRNA cleavage and polyadenylation factor CLP
      0.018   14.7   0.7      0.033   13.8   0.7    1.4  1  Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
       0.02   14.3   0.0      0.038   13.3   0.0    1.4  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
      0.028   13.8   0.2       0.11   11.9   0.7    1.6  2  PhoH             PhoH-like protein
      0.039   13.9   0.4      0.065   13.1   0.4    1.3  1  RsgA_GTPase      RsgA GTPase
        0.1   12.0   0.0       0.18   11.2   0.0    1.3  1  KTI12            Chromatin associated protein KTI12
       0.11   12.2   0.2       0.19   11.4   0.2    1.4  1  zf-RRN7          Zinc-finger of RNA-polymerase I-specific TFI
       0.15   12.0   0.4       0.31   10.9   0.4    1.5  1  NTPase_1         NTPase


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 !  326.2   0.5  1.5e-100   1.2e-97       2     245 ..      28     271 ..      27     272 .. 0.98

  Alignments for each domain:
  == domain 1  score: 326.2 bits;  conditional E-value: 1.5e-100
                          ParA   2 vkkviavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgveeekpeqsekkliPvea.kgikvmSigfl 81 
                                   vk++i+v+SgKGGVGKStvavnlA++Lakkglkvgl+DaDi Gp+ p+llgve+ k  ++++++iP e+ +g+kv+S+gfl
  gi|13540919|ref|NP_110607.1|  28 VKHTITVMSGKGGVGKSTVAVNLAVSLAKKGLKVGLIDADINGPDDPKLLGVEDLKLYADDDGIIPAETkYGVKVVSMGFL 108
                                   9************************************************************9******999********** PP

                          ParA  82 lesedeavvwrGpmkskaikqllkdvewgelDyLiiDlPPGtgDeqltvaqkl.plagaviVttpqevaladvkkaiemfk 161
                                   l+s+d++v+wrG++++kai+q+l+dv+w++ Dy+++D+PPGtgD++l+vaq + + +g+viV tpq+val d+kkai++++
  gi|13540919|ref|NP_110607.1| 109 LPSQDTPVIWRGSLMHKAIQQFLEDVSWKDTDYVVLDMPPGTGDVALSVAQLVpESNGVVIVVTPQDVALLDAKKAINFAR 189
                                   *****************************************************77889*********************** PP

                          ParA 162 kvkvkvlGvveNmsgfvcpkcgekteifgkgggeklaeelgvpllgeipldpeireasdegkplvlkepeseaakaleeia 242
                                   ++k++++G++eNmsgfvcp+cg+ t+if++gggek a+e++vp+lg+ipl pei++++d+g p+v+ +  +++++++++ia
  gi|13540919|ref|NP_110607.1| 190 QLKLPIFGIIENMSGFVCPHCGNVTYIFKEGGGEKSAKEYNVPFLGKIPLVPEIADNGDKGIPAVEIN--DTIKSIFNDIA 268
                                   ***************************************************************99775..88999*****9 PP

                          ParA 243 ekv 245
                                   +k+
  gi|13540919|ref|NP_110607.1| 269 DKI 271
                                   998 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.6   0.0   1.1e-20   8.6e-18       1     127 [.      32     252 ..      32     253 .. 0.91

  Alignments for each domain:
  == domain 1  score: 64.6 bits;  conditional E-value: 1.1e-20
                                   EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH........................... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................... RF
                          CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep........................... 54 
                                   i+++s+kGGvGK+t+a+nLa++la++gl+V l+DaD  ++ +    +l + ++                            
  gi|13540919|ref|NP_110607.1|  32 ITVMSGKGGVGKSTVAVNLAVSLAKKGLKVGLIDADINGPDDP---KLLGVEDLklyadddgiipaetkygvkvvsmgfll 109
                                   799****************************************...333333334589999******************** PP

                                   ......................................................................CCHCCCHHHHH CS
                                   ......................................................................xxxxxxxxxxx RF
                          CbiA  55 ......................................................................dlkrllellea 65 
                                                                                                         d+k+ ++++++
  gi|13540919|ref|NP_110607.1| 110 psqdtpviwrgslmhkaiqqfledvswkdtdyvvldmppgtgdvalsvaqlvpesngvvivvtpqdvallDAKKAINFARQ 190
                                   ********************************************************************************* PP

                                   HCHCHHHH.....EEEEEEEEESS...-TTCHHHHHHHHHHCTS-EEEEEE--CCHCCCCHHTS- CS
                                   xxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          CbiA  66 lgkkkall...lkiagvvlnrvdgeneetllkealeelkqrygvpvlgviprdeavaeapargep 127
                                   l+ +   +    ++ g+v    ++  ++   + + e+  ++y+vp+lg+ip + ++a+   +g p
  gi|13540919|ref|NP_110607.1| 191 LKLP--IFgiiENMSGFVCPHCGNV-TYIFKEGGGEKSAKEYNVPFLGKIPLVPEIADNGDKGIP 252
                                   **77..5667888888888888876.5666666778888899**************998888765 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.5   4.4   1.2e-15     9e-13       3     168 ..      31     192 ..      29     200 .. 0.70

  Alignments for each domain:
  == domain 1  score: 48.5 bits;  conditional E-value: 1.2e-15
                        AAA_31   3 vIaianqKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQanattg.lgiekneiektlyevlieeknikeaiiktk..... 77 
                                   +I+++  KGGvGK+T +vnla++lak+g kv l+D+D  +    + lg+e    + +ly         ++ ii ++     
  gi|13540919|ref|NP_110607.1|  31 TITVMSGKGGVGKSTVAVNLAVSLAKKGLKVGLIDADINGPDDPKlLGVE----DLKLYAD-------DDGIIPAEtkygv 100
                                   89***********************************9886655304432....2334433.......3333322210000 PP

                        AAA_31  78 ..venldlipssidLaeaeielvelekkeeilkellekvk.deYDyiiiDcpPsLgllt..enaLv.asdsviipvqaeay 152
                                     v++  l+ps+   +    +l+     +++++++le+v+ ++ Dy+++D+pP  g ++  +  Lv  s+ v+i+v +++ 
  gi|13540919|ref|NP_110607.1| 101 kvVSMGFLLPSQDTPVIWRGSLM-----HKAIQQFLEDVSwKDTDYVVLDMPPGTGDVAlsVAQLVpESNGVVIVVTPQDV 176
                                   01344466666655555555553.....5567899999974679*********988554113344437************* PP

                        AAA_31 153 aleGleqllktieevk 168
                                   al  +++ +++ +++k
  gi|13540919|ref|NP_110607.1| 177 ALLDAKKAINFARQLK 192
                                   **99999999988876 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.7   1.7   1.2e-10     9e-08       1      41 [.      30      70 ..      30     182 .. 0.64

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 1.2e-10
                                  EEEEE--SSTTSSHHHHHHHHHHHHHTTT--EEEEE--TTT CS
                          MipZ  1 hvivlgnekGGsGksttavhvavaLlkkGarvaaidldlrq 41
                                  h i +   kGG Gkst+av +av+L+kkG++v+ id d+  
  gi|13540919|ref|NP_110607.1| 30 HTITVMSGKGGVGKSTVAVNLAVSLAKKGLKVGLIDADING 70
                                  67889999*****************************9864 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   1.6   7.6e-09   5.9e-06       3      38 ..      32      67 ..      30      69 .. 0.91
   2 ?    0.6   0.1      0.32   2.5e+02     113     137 ..     127     152 ..     123     167 .. 0.81
   3 ?   -1.1   0.0       1.1   8.3e+02     205     243 ..     163     201 ..     156     205 .. 0.83

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 7.6e-09
                                  EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-S CS
                   ArsA_ATPase  3 vilvgGKGGVGKttvsaatavklsekgkkvllistD 38
                                  + +++GKGGVGK+tv+  +av l++kg kv li  D
  gi|13540919|ref|NP_110607.1| 32 ITVMSGKGGVGKSTVAVNLAVSLAKKGLKVGLIDAD 67
                                  6789*************************9988776 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.32
                                   HHHHHHHHHCSSSSEEEEESBS.CCH CS
                   ArsA_ATPase 113 feellkyvkeeeydvvvlDtaP.TGh 137
                                    +++l+ v+ ++ d+vvlD +P TG+
  gi|13540919|ref|NP_110607.1| 127 IQQFLEDVSWKDTDYVVLDMPPgTGD 152
                                   5677788888999*******996664 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 1.1
                                   TTEEEEEEEESSHHHHHHHHHHHHHHHHTT-EEEEEEEE CS
                   ArsA_ATPase 205 ertsfrlVvipEklslkEteRaikeLkkygikvdavivN 243
                                   e   +++Vv+p  ++l + ++ai+   ++++ +  +i N
  gi|13540919|ref|NP_110607.1| 163 ESNGVVIVVTPQDVALLDAKKAINFARQLKLPIFGIIEN 201
                                   5567999***************99888888887777765 PP

>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.2   1.3e-06     0.001       5      37 ..      35      67 ..      31      78 .. 0.88
   2 ?    5.6   0.0     0.012         9     100     247 ..     123     274 ..      99     281 .. 0.63

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.3e-06
                     Fer4_NifH  5 iyGkGGiGksttsqnlsaalaemgkkvlivGCD 37
                                  + GkGG+Gkst + nl+ +la++g kv ++  D
  gi|13540919|ref|NP_110607.1| 35 MSGKGGVGKSTVAVNLAVSLAKKGLKVGLIDAD 67
                                  67************************9887666 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.012
                     Fer4_NifH 100 vitaielleelgayddlDfvlyDv...LGDvvCGGfalPiredkaqevyivtsgelmalyaanniakgiekyaksggvrlg 177
                                   + +ai+ + e   ++d+D+v++D+    GDv     a  +    ++ v+iv++ +  al  a +      ++a++ ++ + 
  gi|13540919|ref|NP_110607.1| 123 MHKAIQQFLEDVSWKDTDYVVLDMppgTGDVALS-VAQLVP--ESNGVVIVVTPQDVALLDAKKAI----NFARQLKLPIF 196
                                   5567776667778999999999994444666443.222222..34445555555555666554322....34455555555 PP

                     Fer4_NifH 178 Gliinsr........kvd..dereliekfaeelgtkvlevvPrdeivrkaelrkktvieyapeseqakeyrelarkilen 247
                                   G+i n          +v+   +++  ek a+e +++ l ++P+  ++  +  +    +e +++ +    ++++a+kil++
  gi|13540919|ref|NP_110607.1| 197 GIIENMSgfvcphcgNVTyiFKEGGGEKSAKEYNVPFLGKIPLVPEIADNGDKGIPAVEINDTIK--SIFNDIADKILKQ 274
                                   55444321111101122211345556788999999999999999999888888777777777776..8899999998765 PP

>> VirC1  VirC1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   1.3e-07    0.0001       3      43 ..      31      71 ..      29      74 .. 0.95

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 1.3e-07
                         VirC1  3 litfcslkGGaGkttalmglcsalasdgkrvalfeadenrP 43
                                   it+ s kGG Gk+t  + l  +la +g +v+l +ad n P
  gi|13540919|ref|NP_110607.1| 31 TITVMSGKGGVGKSTVAVNLAVSLAKKGLKVGLIDADINGP 71
                                  599**********************************9987 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.1    0.0044       3.5       1      33 [.      30      62 ..      30      75 .. 0.93
   2 !   13.4   0.0   6.7e-05     0.052     131     194 ..     167     243 ..     124     246 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0044
                        AAA_26  1 rtifvtgtdtgvGKTvvslgLvralkrkgvkvg 33
                                  +ti v +   gvGK++v+  L+ +l +kg kvg
  gi|13540919|ref|NP_110607.1| 30 HTITVMSGKGGVGKSTVAVNLAVSLAKKGLKVG 62
                                  6899999999*********************98 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 6.7e-05
                        AAA_26 131 vilVargglgtinqllltiealrqknvrvlGvilNk....vrnpenvetlekksg.........ipvlGvvPylpdl 194
                                   v++V+++++ ++ ++  +i+++rq +++++G+i N     +++  nv+ ++k +g         +p lG +P  p++
  gi|13540919|ref|NP_110607.1| 167 VVIVVTPQDVALLDAKKAINFARQLKLPIFGIIENMsgfvCPHCGNVTYIFKEGGgeksakeynVPFLGKIPLVPEI 243
                                   8999999999999********************99866544555799999999888888888889*******99886 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.1   2.3e-07   0.00018      29      61 ..      26      59 ..       3      71 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 2.3e-07
                        AAA_25 29 llpagelallaGapgtGKttlaldlalava.tGk 61
                                  +++++++++  G +g+GK+t+a++la+++a +G 
  gi|13540919|ref|NP_110607.1| 26 YRVKHTITVMSGKGGVGKSTVAVNLAVSLAkKGL 59
                                  667999************************6665 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.1   0.00028      0.22       8      38 ..      36      66 ..      30      77 .. 0.87
   2 !    6.4   0.0    0.0071       5.5     103     148 ..     125     174 ..      99     190 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00028
                      CBP_BcsQ  8 GvRGGvGttsllaaLawalhelgesvlviDl 38
                                    +GGvG++++++ La +l + g +v +iD+
  gi|13540919|ref|NP_110607.1| 36 SGKGGVGKSTVAVNLAVSLAKKGLKVGLIDA 66
                                  448**************************97 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0071
                      CBP_BcsQ 103 eallaalkelk.eqyrwillDlpagasalt...rellaladlvllvvepd 148
                                   +a++++l+ ++ ++ ++++lD+p g+ +++    +l+  ++ v+ vv+p+
  gi|13540919|ref|NP_110607.1| 125 KAIQQFLEDVSwKDTDYVVLDMPPGTGDVAlsvAQLVPESNGVVIVVTPQ 174
                                   678888999999999*********98887611156677789899999886 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   1.2e-05    0.0091       2      39 ..      31      68 ..      30     105 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.2e-05
                                  EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEEST CS
                         SRP54  2 nvillvGlqGaGKTttlaKLaallkkegkkvllvaaDt 39
                                  +++++ G  G+GK t +  La  l k+g kv l+ aD+
  gi|13540919|ref|NP_110607.1| 31 TITVMSGKGGVGKSTVAVNLAVSLAKKGLKVGLIDADI 68
                                  57899*****************************9997 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.2   1.6e-05     0.012      34      66 ..      35      67 ..      25      75 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.6e-05
                                  EEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE- CS
                          MeaB 34 ltGvPGaGkstlvealglelrrrGkrvavlavD 66
                                  + G  G+Gkst+  +l+++l+++G +v+++  D
  gi|13540919|ref|NP_110607.1| 35 MSGKGGVGKSTVAVNLAVSLAKKGLKVGLIDAD 67
                                  67999************************9877 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0         1   7.8e+02       5      18 ..     126     139 ..     125     143 .. 0.85
   2 !   13.1   0.1   8.9e-05     0.069      17      31 ..     203     217 ..     202     228 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 1
                 Zn_Tnp_IS1595   5 earalLealrWpng 18 
                                   +++++Le++ W+++
  gi|13540919|ref|NP_110607.1| 126 AIQQFLEDVSWKDT 139
                                   5789*******986 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 8.9e-05
                 Zn_Tnp_IS1595  17 ngfvCPhCgsrkayr 31 
                                   +gfvCPhCg+ ++++
  gi|13540919|ref|NP_110607.1| 203 SGFVCPHCGNVTYIF 217
                                   58*******987776 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 ?   12.8   0.2   9.3e-05     0.073      46      79 ..      29      62 ..      22      67 .. 0.86
   2 ?    0.1   0.0      0.73   5.7e+02      32      66 ..     124     158 ..     112     190 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 9.3e-05
                     IstB_IS21 46 kkenivllGpsGvGKshlaialgveavraglsvl 79
                                  k+   v+ G  GvGKs +a+ l+v+ +++gl+v 
  gi|13540919|ref|NP_110607.1| 29 KHTITVMSGKGGVGKSTVAVNLAVSLAKKGLKVG 62
                                  67778999***********************995 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.73
                     IstB_IS21  32 krkvk.eLatlsfiekkenivllGpsGvGKshlaia 66 
                                   +++++  L   s+ ++ + +vl  p+G+G   l++a
  gi|13540919|ref|NP_110607.1| 124 HKAIQqFLEDVSW-KDTDYVVLDMPPGTGDVALSVA 158
                                   4555514566677.55678999999***99877776 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1     3e-05     0.023       4      39 ..      32      67 ..      29      75 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3e-05
                                  EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHH CS
                    APS_kinase  4 vvwltGlsgsGKstianalekkLvekgisvylLdGd 39
                                  +  ++G  g GKst+a++l+ +L +kg +v l+d d
  gi|13540919|ref|NP_110607.1| 32 ITVMSGKGGVGKSTVAVNLAVSLAKKGLKVGLIDAD 67
                                  45689*************************999987 PP

>> CLP1_P  mRNA cleavage and polyadenylation factor CLP1 P-loop
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   3.4e-05     0.027       1      33 [.      37      69 ..      37      73 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.4e-05
                        CLP1_P  1 GpkdsGKSTlarlLlNyalrkgrkpvyvDlDvG 33
                                  G+  +GKST+a +L+  +++kg k+ ++D+D++
  gi|13540919|ref|NP_110607.1| 37 GKGGVGKSTVAVNLAVSLAKKGLKVGLIDADIN 69
                                  66789**************************97 PP

>> Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.7   4.3e-05     0.033       7      25 ..     205     223 ..     200     224 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.3e-05
                                   EE-TTT--EEEECC--SS- CS
               Desulfoferrod_N   7 YkCevCGniVeVleaGgGe 25 
                                   + C +CGn+  + ++GgGe
  gi|13540919|ref|NP_110607.1| 205 FVCPHCGNVTYIFKEGGGE 223
                                   77****************7 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   4.8e-05     0.038      31      80 ..     123     172 ..     120     192 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.8e-05
                                   THHHHHHHHHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES CS
               Ubie_methyltran  31 ihrlWkkfveklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDi 80 
                                   +h+  ++f+e+++ + +   vlD+  GtgD+a+++++ v e+  vv++  
  gi|13540919|ref|NP_110607.1| 123 MHKAIQQFLEDVSWKDTDYVVLDMPPGTGDVALSVAQLVPESNGVVIVVT 172
                                   699999*********************************98887666544 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.7   0.00014      0.11      18      47 ..      29      58 ..      22      64 .. 0.88
   2 ?   -2.2   0.0         3   2.4e+03      18      39 ..     138     159 ..     124     165 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00014
                                  H-SEEEEE--TTSSTTHHHHHHHHHHHHTT CS
                          PhoH 18 kndivfaiGpaGtGKtylavalavealkkk 47
                                  k++i+++ G+ G GK+ +av lav++ kk+
  gi|13540919|ref|NP_110607.1| 29 KHTITVMSGKGGVGKSTVAVNLAVSLAKKG 58
                                  799**********************99885 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 3
                                   H-SEEEEE--TTSSTTHHHHHH CS
                          PhoH  18 kndivfaiGpaGtGKtylaval 39 
                                   + d v+   p GtG   l+va 
  gi|13540919|ref|NP_110607.1| 138 DTDYVVLDMPPGTGDVALSVAQ 159
                                   6778888889999999999885 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.4   8.3e-05     0.065      96     122 ..      27      53 ..      21      69 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 8.3e-05
                                   HCTTSEEEEECSTTSSHHHHHHHHCTT CS
                   RsgA_GTPase  96 llkdktsvlvGqSGvGKStLinallpe 122
                                   ++k+ ++v+ G+ GvGKSt+  +l+ +
  gi|13540919|ref|NP_110607.1|  27 RVKHTITVMSGKGGVGKSTVAVNLAVS 53 
                                   67889**************98777654 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00023      0.18       5      38 ..      34      67 ..      31      75 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00023
                                  EEE--TTSSHHHHHHHHHHHHHHTT--EEEE-TH CS
                         KTI12  5 vltGlPssGKstrakeLakaleeekrsvvvidde 38
                                  v++G   +GKst+a +La  l++++ +v +id +
  gi|13540919|ref|NP_110607.1| 34 VMSGKGGVGKSTVAVNLAVSLAKKGLKVGLIDAD 67
                                  8999999*********************999976 PP

>> zf-RRN7  Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2   0.00024      0.19       3      20 ..     203     221 ..     201     222 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00024
                       zf-RRN7   3 kgppCgvCgcrsftl.ddG 20 
                                    g++C+ Cg++++ + + G
  gi|13540919|ref|NP_110607.1| 203 SGFVCPHCGNVTYIFkEGG 221
                                   689*******999886665 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.4    0.0004      0.31       3      31 ..      34      62 ..      32      67 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0004
                                  EEE--TTSSHHHHHHHHHHHH...GGGEE CS
                      NTPase_1  3 fiTGppGvGKtTlvkkvlellkssgvkvg 31
                                  +++G+ GvGK+T+  +++  l+++g+kvg
  gi|13540919|ref|NP_110607.1| 34 VMSGKGGVGKSTVAVNLAVSLAKKGLKVG 62
                                  578***********************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       683  (0.0380947); expected 358.6 (0.02)
Passed bias filter:                      647  (0.0360868); expected 358.6 (0.02)
Passed Vit filter:                       140  (0.00780858); 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: 0.63u 0.30s 00:00:00.93 Elapsed: 00:00:00.50
# Mc/sec: 1716.35
//
Query:       gi|13540920|ref|NP_110608.1|  [L=536]
Description: formyltetrahydrofolate synthetase [Thermoplasma volcanium GSS1]
Scores for complete 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-225  747.3   1.0   8.6e-225  747.1   1.0    1.0  1  FTHFS     Formate--tetrahydrofolate ligase
    6.2e-05   23.1   0.0      0.009   16.1   1.7    2.8  2  CbiA      CobQ/CobB/MinD/ParA nucleotide binding domain


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 !  747.1   1.0  9.5e-229  8.6e-225      12     554 .]       1     536 []       1     536 [] 0.99

  Alignments for each domain:
  == domain 1  score: 747.1 bits;  conditional E-value: 9.5e-229
                                   ---HHHHHHCTT--CCCEEEBSTTEEEE-CHHCCTCTTTS-.-EEEEEEESS--TT--SHHHHHHHHHHHHHHTT--EEEE CS
                         FTHFS  12 lkpieeiaeklglkeeelelyGkykakvslkvlerllkekkkgklilvtaitPtplGeGKttttigLaqalnklgkkavaa 92 
                                   +++ieei +++gl+++++elyG+y+ak+sl++ e    +kkk+klilvta+tPt +GeGKttttigL qa++klgk++++a
  gi|13540920|ref|NP_110608.1|   1 MRDIEEILHEMGLSKDDYELYGRYMAKLSLNLQE---VNKKKAKLILVTAMTPTAAGEGKTTTTIGLGQAFKKLGKNVAIA 78 
                                   578****************************885...47999*************************************** PP

                                   E----SHHHHCST--SCEETTEEEESHHHHHTTTTSHHHHHHHHHHHHHHHHHHHHHTTTTT-EECCCE---EEESS--GG CS
                         FTHFS  93 lRepslGPvfgiKGgAaGGGysqvvPmedinLhltGDihaitaannllaalidnrifheneldidpkkitwkrvlDvndra 173
                                   +RepslGP+fgiKGgA+GGG s+v P + inL +tGD+ ai+aa+nll+a+i+n+i+h+nel++dpk+it+ r++D+ndr+
  gi|13540920|ref|NP_110608.1|  79 IREPSLGPCFGIKGGATGGGKSKVEPSDRINLLFTGDFPAISAAHNLLSAMINNHIYHGNELNLDPKRITFPRTIDMNDRS 159
                                   ********************************************************************************* PP

                                   GSSEEES-SSTTS---EEE-EEEGGGSHHHHHHHH-SSHHHHHHHHHC-EEEEETTS-EEECCCCT-HHHHHHHTTTTTS- CS
                         FTHFS 174 LRkivvglggkekgvpretgfditvasEimailaLakdledlkerlgrivvaytkdgepvtaedlkvagalavllkdaikP 254
                                   LR+ivvg+g++  g   +++f it asE+mai  L+ +++dlke+l+ri+ ++t +++pv a+dlk++g++a+ll+da+kP
  gi|13540920|ref|NP_110608.1| 160 LRSIVVGVGPRDMGAIANDNFVITPASEVMAITGLSLNYKDLKEKLSRILAGFTVKNKPVFAADLKAEGSMAALLRDALKP 240
                                   ********************************************************************************* PP

                                   EEEEETT--EEEE-----SSSS--B--HHHHHHHHHH-SEEEEEBSSSTTTHHHHHHHTHHHHHT---SEEEEEEEHHHHH CS
                         FTHFS 255 nlvqtlegtpalvHggPFAniahGcnsviatklalkladyvvtEaGFgadlgaekfldikcrasglkpdavvlvatvraLk 335
                                   nlvqt+eg pa+vH+gPF niahG++s++a+++a++l dyv+tEaGFg+dlgaekf++i +r ++l  +avvlvat+raLk
  gi|13540920|ref|NP_110608.1| 241 NLVQTTEGVPAFVHTGPFGNIAHGTSSIVADRIAMNLFDYVITEAGFGSDLGAEKFFNIVSRIGNLPINAVVLVATIRALK 321
                                   ********************************************************************************* PP

                                   HHTT--CCCTTS--HHHHHHHHHHHHHHHHHHCTTT--EEEEEE--TT--HHHHHHHHHHHHCTTSEEEEE-HHHHGGGGG CS
                         FTHFS 336 lhggvekeelkeenlealekGlanlekhienvkkfgvpvvvainkfktDteaelelvkelaeakavevalsevwakGgeGa 416
                                   lhgg +k   + e++ea+++G +nl +h++n++kfgv+ vva+nkf+tDte+e+ ++ e++++++++ alsev++kGgeG+
  gi|13540920|ref|NP_110608.1| 322 LHGGSKK---QGEDVEAVKEGSKNLLRHVANIRKFGVEPVVALNKFPTDTENEIMAIGEILDSHGIKWALSEVFEKGGEGG 399
                                   ****877...579******************************************************************** PP

                                   HHHHHHHHHHCC--.---SS-TTS-HHHHHHHHHHHTT--SEEEE-HHHHHHHHHHHHTTCTTS-EEEE--SSSSSSSTT- CS
                         FTHFS 417 lelaeavvealeekefkflYdlelsieekietiakeiYgadgvelseeakkklkklekqgldklpvciaKtqySlsddpkl 497
                                   +ela++v++ + + ++k +Y+ ++++++kie+ia ++Ygadgv ++++a ++lkk e+  +++  vc+aKtqyS+sdd++l
  gi|13540920|ref|NP_110608.1| 400 IELANKVLSSIGDYQIKRTYEVREDLKTKIEKIAVNVYGADGVIFEKKALNDLKKAEEI-MNDPYVCMAKTQYSFSDDASL 479
                                   *******************************************************9987.77888**************** PP

                                   -SS--S-EEEEEEEEEETTTTEEEEESST--SS----SS-GGGC-EE-TTSEEES-- CS
                         FTHFS 498 kgapegftltvrevrlsaGagfivalageimtmPGlpkkpaaekidvdeegkieGlf 554
                                   ++ p+gf+++v++v++s+Gagf+v++ geimtmPGlpk+paae+id+ e+g+i+Glf
  gi|13540920|ref|NP_110608.1| 480 LNDPHGFKVRVQSVNISSGAGFVVPILGEIMTMPGLPKRPAAENIDLAEDGEITGLF 536
                                   ********************************************************8 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   1.7     1e-06     0.009       5      32 ..      50      77 ..      46      78 .. 0.89
   2 ?    2.0   0.0     0.023     2e+02      54      55 ..     244     399 ..     200     463 .. 0.47

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1e-06
                                  ESSTTSSHHHHHHHHHHHHHHTT--EEE CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          CbiA  5 stkGGvGKTtlaanLaralarrglrVll 32
                                   t  G+GKTt++++L++a+++ g++V+ 
  gi|13540920|ref|NP_110608.1| 50 PTAAGEGKTTTTIGLGQAFKKLGKNVAI 77
                                  5778*********************985 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.023
                                   H................................................................................ CS
                                   x................................................................................ RF
                          CbiA  54 p................................................................................ 54 
                                   +                                                                                
  gi|13540920|ref|NP_110608.1| 244 Qttegvpafvhtgpfgniahgtssivadriamnlfdyviteagfgsdlgaekffnivsrignlpinavvlvatiralklhg 324
                                   455555555555555555555555555555555555555555555555555555555555555555555555555555555 PP

                                   ..........................................................................C CS
                                   ..........................................................................x RF
                          CbiA  55 ..........................................................................d 55 
                                                                                                             +
  gi|13540920|ref|NP_110608.1| 325 gskkqgedveavkegsknllrhvanirkfgvepvvalnkfptdteneimaigeildshgikwalsevfekggegG 399
                                   444444444444444443333333344444444444455555555544444444444444444444444444441 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (536 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       629  (0.0350828); expected 358.6 (0.02)
Passed bias filter:                      583  (0.0325172); 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: 0.79u 0.37s 00:00:01.16 Elapsed: 00:00:00.57
# Mc/sec: 2838.81
//
Query:       gi|13540921|ref|NP_110609.1|  [L=204]
Description: formiminotetrahydrofolate cyclodeaminase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.1e-65  219.4   2.0    3.6e-65  219.1   2.0    1.1  1  FTCD_C        Formiminotransferase-cyclodeaminase
  ------ inclusion threshold ------
      0.054   13.3   5.4        1.5    8.6   0.4    2.4  2  Bacillus_HBL  Bacillus haemolytic enterotoxin (HBL)
       0.39   11.2   6.8        4.1    7.9   4.4    2.1  2  AAA_23        AAA domain
       0.63   10.4   9.4        1.2    9.6   2.5    2.2  2  DUF1690       Protein of Unknown function (DUF1690)
        2.9    8.6   7.5       0.39   11.4   2.8    1.8  2  YabA          Initiation control protein YabA


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 !  219.1   2.0     1e-68   3.6e-65       2     180 ..       4     182 ..       3     184 .. 0.98

  Alignments for each domain:
  == domain 1  score: 219.1 bits;  conditional E-value: 1e-68
                                   HHHHHHHHHSSSSSS-HHHHHHHHHHHHHHHHHHHHHTTTT-TT-GGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        FTCD_C   2 ieefleelaskspaPGGGsvaAlvgalgaaLgsmvanltlgkkkyedveeemeellekleelrkellelideDaeaFnevm 82 
                                    ++f+e+las spaPGGG+++A+v  +++aL+smv ++t+gkk ye++e+em+e++++ +++++el +li+eD+eaFn++m
  gi|13540921|ref|NP_110609.1|   4 YNNFIERLASPSPAPGGGAASAFVSIVASALISMVSQITMGKKGYEQYEDEMKEIISENSKIKEELEKLIEEDEEAFNSIM 84 
                                   579****************************************************************************** PP

                                   TTTT..........S-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-GGGHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        FTCD_C  83 eayklpketeeekaareeaiqealkkavevPlelarkalellelleelaekgnknavSDagvaaklleaavegallnVkiN 163
                                   +a+k+pk teeek++re+++q+al++ +evP+++a ++ +ll+l e+l+e+gnknav+Dag aa++l++a+e+al+nVkiN
  gi|13540921|ref|NP_110609.1|  85 AAIKMPKITEEEKKEREKKLQSALRHGIEVPWRIAARSFDLLKLSEKLVEHGNKNAVTDAGSAASILHSAIEAALYNVKIN 165
                                   ********************************************************************************* PP

                                   HTT---HHHHHHHHHHH CS
                        FTCD_C 164 lksikDeefaeelkaea 180
                                   lks+kD+e++++ k ++
  gi|13540921|ref|NP_110609.1| 166 LKSVKDQEYVSDQKMKI 182
                                   **********9887766 PP

>> Bacillus_HBL  Bacillus haemolytic enterotoxin (HBL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.3    0.0013       4.6      61     109 ..      25      75 ..      21      89 .. 0.78
   2 ?    8.6   0.4   0.00041       1.5       8      70 ..     138     200 ..     131     203 .. 0.92

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0013
                  Bacillus_HBL  61 ewlnevkPqliktiqdiigYstkFqsyyktlveav..dkkdkaellellek 109
                                    +++ v   li++ ++i   ++ +++y ++++e +  + k k+el +l+e+
  gi|13540921|ref|NP_110609.1|  25 AFVSIVASALISMVSQITMGKKGYEQYEDEMKEIIseNSKIKEELEKLIEE 75 
                                   56666777899999999999999************7777777777777765 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00041
                  Bacillus_HBL   8 kealekagsqalvmqaYanlilkqpdvnleeiknkellsklnqhqklakanakewlnevkPql 70 
                                   k+a+++ags+a ++ + ++++l +  +nl+ +k++e+ s+ +  +kl   n +e  + +k++l
  gi|13540921|ref|NP_110609.1| 138 KNAVTDAGSAASILHSAIEAALYNVKINLKSVKDQEYVSDQKMKIKLFLENSDEVYERIKKKL 200
                                   89**************************************99999999999999999998886 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   4.4    0.0011       4.1     156     192 ..      53     108 ..      26     113 .. 0.62
   2 ?    3.6   0.0     0.022        80      35      78 ..     151     197 ..     149     202 .. 0.67

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0011
                        AAA_23 156 eelekeleeledekkllekl...................eqekekekeleeleeel 192
                                   +e+++ + e++++k++lekl                   + e+ek+++ ++l+++l
  gi|13540921|ref|NP_110609.1|  53 DEMKEIISENSKIKEELEKLieedeeafnsimaaikmpkITEEEKKEREKKLQSAL 108
                                   34444455555555555555555566666666666777656666666666666665 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.022
                        AAA_23  35 ildAiklaLygetprlsrksgrgfe...ksdveiesegkvkayvelt 78 
                                   +  Ai  aLy+ + +l++ +++ ++   k +++++ e++++ y +++
  gi|13540921|ref|NP_110609.1| 151 LHSAIEAALYNVKINLKSVKDQEYVsdqKMKIKLFLENSDEVYERIK 197
                                   55799999999998888888776664445556666666666665554 PP

>> DUF1690  Protein of Unknown function (DUF1690)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   2.5   0.00032       1.2      36      80 ..      62     107 ..      34     114 .. 0.69
   2 ?    5.1   0.7    0.0077        28       7      69 ..     126     192 ..     122     203 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00032
                       DUF1690  36 qerVaeeLkkLraeeeetlkkfeeklekellkde.adakdelsska 80 
                                   +++++eeL+kL +e+ee+ +++ ++++  ++++e +++ +++ ++a
  gi|13540921|ref|NP_110609.1|  62 NSKIKEELEKLIEEDEEAFNSIMAAIKMPKITEEeKKEREKKLQSA 107
                                   469************************9999999433333333444 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0077
                       DUF1690   7 iqfSqslvsqLessketda.sraqalekliqe...rVaeeLkkLraeeeetlkkfeeklekellkde 69 
                                   +++S++lv++ ++++ tda s a+ l+  i++    V+ +Lk ++++e    +k++ kl  e++++ 
  gi|13540921|ref|NP_110609.1| 126 LKLSEKLVEHGNKNAVTDAgSAASILHSAIEAalyNVKINLKSVKDQEYVSDQKMKIKLFLENSDEV 192
                                   579****************888888999999844469999****99999999999999888877765 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   2.8   0.00011      0.39       9      65 ..      33     103 ..      28     114 .. 0.70
   2 ?   -1.5   0.2       1.1   3.9e+03      40      40 ..     183     183 ..     151     203 .. 0.45

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00011
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH..............XXXXXXXXXXXXX CS
                          YabA   9 kleeleeqleelleeleelkeelaelleenaeLeleneklrerl..............eeeekkekekkke 65 
                                   +l ++ +q++  ++  e+ ++e++e++ en++++ e ekl e+               + +e+++ke++k+
  gi|13540921|ref|NP_110609.1|  33 ALISMVSQITMGKKGYEQYEDEMKEIISENSKIKEELEKLIEEDeeafnsimaaikmpKITEEEKKEREKK 103
                                   67788888888889999999999999999999999988888777777788877776663333333333333 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.1
                                   H CS
                          YabA  40 e 40 
                                   +
  gi|13540921|ref|NP_110609.1| 183 K 183
                                   2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2669  (0.148865); expected 358.6 (0.02)
Passed bias filter:                      980  (0.05466); expected 358.6 (0.02)
Passed Vit filter:                       109  (0.00607954); expected 17.9 (0.001)
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: 0.61u 0.35s 00:00:00.96 Elapsed: 00:00:00.52
# Mc/sec: 1176.74
//
Query:       gi|13540922|ref|NP_110610.1|  [L=302]
Description: glutamate formiminotransferase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-66  223.3   0.0    2.4e-66  222.8   0.0    1.2  1  FTCD_N    Formiminotransferase domain, N-terminal subdomain
    7.8e-26   90.8   0.1    1.4e-25   90.0   0.1    1.4  1  FTCD      Formiminotransferase domain


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 !  222.8   0.0   2.7e-70   2.4e-66       1     176 []       3     179 ..       3     179 .. 0.99

  Alignments for each domain:
  == domain 1  score: 222.8 bits;  conditional E-value: 2.7e-70
                        FTCD_N   1 lvecvpnfSegrdkevieaiekaarkaegvklldvfsdedynRtvvtlvgepealkeaalaaakkAlelIDlrkhkGeHPr 81 
                                   l+ecvpnfSegrdk+ +++i++a+++ + v++ldv++d+++nR+v+t+v +  + +eaa+a +kkA+elID++kh+GeHPr
  gi|13540922|ref|NP_110610.1|   3 LIECVPNFSEGRDKSKVDQIKSAISAIPTVRILDVEMDSNHNRSVITFVCDDGKAVEAAFAGIKKAAELIDMDKHTGEHPR 83 
                                   79******************************************************************************* PP

                        FTCD_N  82 lGavDvipfiPlkevtleecaelAkelaeelgeelgvpvylygaaaqkeerknLaaiRrg..efeglkeklkeeewkpdfG 160
                                   +Ga Dvipf+Pl ++++ +c++lA+el++++g+el++pv+ly++aa+++er +LaaiR++  ++e+lk  +kee+wkpdfG
  gi|13540922|ref|NP_110610.1|  84 FGAADVIPFVPLDDTKMSRCVQLARELGKRVGDELNIPVFLYAEAATRPERADLAAIRNKsfQYEQLKGAIKEEKWKPDFG 164
                                   ************************************************************9*******999********** PP

                        FTCD_N 161 paevspkaGvtvvGAr 176
                                   p+ev  kaG+ ++GAr
  gi|13540922|ref|NP_110610.1| 165 PSEV-GKAGASIIGAR 179
                                   ***9.689*******7 PP

>> FTCD  Formiminotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.0   0.1   1.5e-29   1.4e-25       1     110 [.     181     285 ..     181     299 .. 0.92

  Alignments for each domain:
  == domain 1  score: 90.0 bits;  conditional E-value: 1.5e-29
                          FTCD   1 FLiAynvnlltt.keqakriAlniRekGrgkkepGrlkkvkaiGwyleeynlaqvslnltdievtplhvvfeevkkeaeel 80 
                                   FLiAynvnl+ +  e  k+iA  +R +       G l  vka+ +yl++ n+ q+s+nlt++++tp++ ++e vk ea++ 
  gi|13540922|ref|NP_110610.1| 181 FLIAYNVNLNISdVEIGKKIASALRAR------DGGLTFVKALAFYLKDRNIVQISMNLTNFRKTPIYRAYELVKLEASRY 255
                                   9*********988***********974......688********************************************* PP

                          FTCD  81 glevtgseivglvplealleaakyylekek 110
                                   g   + seivglvp +al++aak+yl+ + 
  gi|13540922|ref|NP_110610.1| 256 GAYPIESEIVGLVPEQALIDAAKFYLQLNG 285
                                   *************************98654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       422  (0.0235373); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); 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: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 1841.68
//
Query:       gi|13540923|ref|NP_110611.1|  [L=767]
Description: ribonucleotide-diphosphate reductase subunit alpha [Thermoplasma volcanium GSS1]
Scores for complete 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-163  544.5   0.0   8.7e-162  539.3   0.0    2.2  1  Ribonuc_red_lgC  Ribonucleotide reductase, barrel domain
    2.9e-33  113.7   0.1    8.4e-33  112.2   0.1    1.9  1  Ribonuc_red_lgN  Ribonucleotide reductase, all-alpha domain
    1.1e-18   67.5   1.7    1.1e-18   67.5   1.7    2.5  3  ATP-cone         ATP cone domain
  ------ inclusion threshold ------
      0.017   15.6   0.4        4.4    7.8   0.0    3.4  2  SPK              Domain of unknown function (DUF545)
      0.095   12.7   0.3          5    7.1   0.0    3.1  3  Cnd1             non-SMC mitotic condensation complex subunit


Domain annotation for each model (and alignments):
>> Ribonuc_red_lgC  Ribonucleotide reductase, barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  539.3   0.0  2.4e-165  8.7e-162       1     524 []     248     713 ..     248     713 .. 0.96

  Alignments for each domain:
  == domain 1  score: 539.3 bits;  conditional E-value: 2.4e-165
                                   EEE.....BSS-EEEE-X..............XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
               Ribonuc_red_lgC   1 ssCfvlsvedslesIletvkeaallskaggGvGlnlsklRakgslvkgtegaasGpvsfmklidavadvvkqgGkRrGAam 81 
                                   s+Cfvl v ds+e+I+et+k++al++k+ggG+G+++s+lR+k+++v++t+g asGpvsfmk++d ++dv+kqgGkRrGA+m
  gi|13540923|ref|NP_110611.1| 248 SACFVLPVGDSIEDIFETLKNTALIHKSGGGTGFSFSRLRPKDDIVGSTKGVASGPVSFMKIFDVTTDVIKQGGKRRGANM 328
                                   79******************************************************************************* PP

                                   XXXXXXXXXXXXXXXXXXXXXX..XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.................... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
               Ribonuc_red_lgC  82 vylevwHpDiekfidaKekntgeeenrlsnlnisvgvpdlFmeavkedkdwtLfsPrtvvkleklygeefeeeyeeleeka 162
                                   ++l+ +HpDi++f+  K      e+++lsn+nisvgv+d+F+e++ +d+ + L++Prt +k                    
  gi|13540923|ref|NP_110611.1| 329 GILNYNHPDIMEFVLSK-D---SENKVLSNFNISVGVTDEFFEKLDNDDYVDLINPRT-KK-------------------- 384
                                   *****************.4...5899*******************************3.22.................... PP

                                   .....XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXXXXXXX CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
               Ribonuc_red_lgC 163 kikkkevkakeLfeeiaesawetgePgvlfkDtiNrrnvlekakggkIratNlCgEiplleyesvavCnLasinLakfvkk 243
                                      +k++kakeL+++i+  aw+t++Pg++f D+iNr+n++  +++g I++tN+CgE+pll+yes   CnL+sinL+k+v  
  gi|13540923|ref|NP_110611.1| 385 --VTKRIKAKELWDAIIDQAWKTADPGLIFLDEINRKNPV--KNVGDIESTNPCGEQPLLPYES---CNLGSINLSKYV-- 456
                                   ..3469**********************************..999*******************...************.. PP

                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
               Ribonuc_red_lgC 244 deegkkefdwdelkkviqlvvraLdnvidvnkyplpeiekntkktRriGlGvmgladalaklgipydseealkfarkitel 324
                                      + k++d+d+l++++ l++r+Ld+vid+nk+p+++i+k t+ tR+iGlGvmg+ad+l+kl++py+s eal++a+k++++
  gi|13540923|ref|NP_110611.1| 457 ---NGKDIDYDRLRETVWLATRFLDDVIDANKFPVEQIKKVTRMTRKIGLGVMGFADLLIKLEVPYNSWEALEIAEKVMSF 534
                                   ...3569************************************************************************** PP

                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX......XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
               Ribonuc_red_lgC 325 ltyyaykaSvelAkergpfplfekskyskgilpvdefeekekedweeLreeikkyGlrnamvtalaPTgsiSliagtssgi 405
                                   ++ ++ kaS  lA+erg+fp + +s+++k                      ik   +rn+++t++aPTg+iS+iag+ss+i
  gi|13540923|ref|NP_110611.1| 535 INEESHKASQHLAEERGVFPAWYGSEWEKEG--------------------IK---MRNSTTTTIAPTGTISIIAGCSSSI 592
                                   **************************99883....................33...7************************ PP

                                   XXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                   xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
               Ribonuc_red_lgC 406 ePifalvykksvtv.geflevnpvfeeeLkklglwseellkkiles.vqgleeipeeikrvfktaldidqedhikaqaaiq 484
                                   ePifal++++ v +  e+levnp fee+ ++lgl+seel +k+ e+   +  ei+eeik++f+ta+++d+++h+ +qa+ q
  gi|13540923|ref|NP_110611.1| 593 EPIFALAFVRHVLNgQELLEVNPLFEEKTRSLGLYSEELMRKVAETgNLENIEINEEIKKIFVTAHEVDPQWHVLMQATFQ 673
                                   **************456**************************44434455689*************************** PP

                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
               Ribonuc_red_lgC 485 kwidqsiSktinlpneatvedvkelyllAwklGlKgvtyY 524
                                   ++ d+++Sktin++++at ed++++y  A +l +Kg+t+Y
  gi|13540923|ref|NP_110611.1| 674 RYCDSGVSKTINMKSDATREDIAKAYRMAKDLHCKGITVY 713
                                   ***************************************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 !  112.2   0.1   2.4e-36   8.4e-33       2      83 .]     110     245 ..     109     245 .. 0.99

  Alignments for each domain:
  == domain 1  score: 112.2 bits;  conditional E-value: 2.4e-36
               Ribonuc_red_lgN   2 kltynalkvledrYllkdengeivEspqqmfmRvAlalaiaealyd................................... 47 
                                   klt+na+kvle+rYllkde+g+i+E+p+qmf+RvA ++ i+ealyd                                   
  gi|13540923|ref|NP_110611.1| 110 KLTLNAVKVLEARYLLKDEDGKIIETPRQMFRRVASHIGIIEALYDfmeykktgkipenaekigkvsltqeevlrrafnym 190
                                   79******************************************************************************* PP

               Ribonuc_red_lgN  48 ...................kleedkdlaeefydlmssqkflpasPtlmnaGtelg 83 
                                                      k+++++ ++++f+++mss++f+p+sPtlmnaGt+lg
  gi|13540923|ref|NP_110611.1| 191 kedgimegtfeefmdflstKGTSAHLYINKFEEMMSSLDFVPNSPTLMNAGTKLG 245
                                   ****************************************************996 PP

>> ATP-cone  ATP cone domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.5   1.7   3.2e-22   1.1e-18       2      85 ..       4      94 ..       3      95 .. 0.81
   2 ?   -2.2   0.0       1.8   6.5e+03      45      68 ..     382     405 ..     345     410 .. 0.69
   3 ?   -3.6   0.0       4.9   1.8e+04      67      83 ..     689     705 ..     680     706 .. 0.65

  Alignments for each domain:
  == domain 1  score: 67.5 bits;  conditional E-value: 3.2e-22
                                  EEE-TTS-EEE--HHHHHHHHHHHHHH....-HHHHHHHHHHHHHHHHHHHIIT..-BHHHHHHHHHHHHH.....HSS-HHH CS
                      ATP-cone  2 kViKRdGtvepfdvekIkraiekAceg....seeeideiaeeveaevrkrlrdg..isteeIqdlvektli.....ehpdyav 73
                                   V+KRdGtv+pf+++kI+ ai kA+ +    s+ +++ +a++v     +rl++   +++e+Iqd+ve++l+      +   +v
  gi|13540923|ref|NP_110611.1|  4 EVVKRDGTVVPFEKGKIAMAIYKAMLSvkngSMRDAETLADKV----VERLKNIerPTVEQIQDIVEDVLMtskieGKIFTDV 82
                                  69*************************5555555555555555....444444445***************9998766778** PP

                                  HHHHHHHHHHHH CS
                      ATP-cone 74 aaayilyrnlrk 85
                                  a++yilyr++r+
  gi|13540923|ref|NP_110611.1| 83 AKSYILYREKRR 94
                                  *********996 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.8
                                   HHHHIIT-BHHHHHHHHHHHHHHS CS
                      ATP-cone  45 rkrlrdgisteeIqdlvektlieh 68 
                                    k+  + i+ +e+ d +++++ + 
  gi|13540923|ref|NP_110611.1| 382 TKKVTKRIKAKELWDAIIDQAWKT 405
                                   344556688888888888877655 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 4.9
                                   HSS-HHHHHHHHHHHHH CS
                      ATP-cone  67 ehpdyavaaayilyrnl 83 
                                   +++  ++a+ay + ++l
  gi|13540923|ref|NP_110611.1| 689 DATREDIAKAYRMAKDL 705
                                   45566778887776666 PP

>> SPK  Domain of unknown function (DUF545)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.1     0.022        80      56      87 ..     346     377 ..     331     387 .. 0.87
   2 ?    7.8   0.0    0.0012       4.4      36      74 ..     625     663 ..     608     678 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.022
                           SPK  56 dletkvrllFalsapvdedflkelrkdakvel 87 
                                   d e kv   F +s+ v+++f ++l +d  v l
  gi|13540923|ref|NP_110611.1| 346 DSENKVLSNFNISVGVTDEFFEKLDNDDYVDL 377
                                   77999999****************99977766 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0012
                           SPK  36 stlarrfrqllakihkleeydletkvrllFalsapvded 74 
                                     + +++ +++a+  +le++++++ ++ +F++ ++vd++
  gi|13540923|ref|NP_110611.1| 625 GLYSEELMRKVAETGNLENIEINEEIKKIFVTAHEVDPQ 663
                                   33667777888899**********************986 PP

>> Cnd1  non-SMC mitotic condensation complex subunit 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.0    0.0014         5     117     151 ..      22      56 ..      17      66 .. 0.87
   2 ?   -1.5   0.0      0.64   2.3e+03      66     105 ..     124     161 ..     117     216 .. 0.55
   3 ?    1.5   0.0     0.078   2.8e+02     111     136 ..     519     544 ..     478     549 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0014
                          Cnd1 117 itilefLlsyipkdkqeaeslveklcprlqhansa 151
                                   + i++++ls ++ + ++ae+l++k+++rl++ +  
  gi|13540923|ref|NP_110611.1|  22 MAIYKAMLSVKNGSMRDAETLADKVVERLKNIERP 56 
                                   68***************************987654 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.64
                          Cnd1  66 lleDenprVvanalaalteiseksenaiynllpdiiskls 105
                                   ll+De+ ++++  + ++  +++     i++ l d + + +
  gi|13540923|ref|NP_110611.1| 124 LLKDEDGKIIETPRQMFRRVASHI--GIIEALYDFMEYKK 161
                                   678888888888888887777774..23334444333333 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.078
                          Cnd1 111 csewgqitilefLlsyipkdkqeaes 136
                                    + w+  +i e ++s+i++++++a +
  gi|13540923|ref|NP_110611.1| 519 YNSWEALEIAEKVMSFINEESHKASQ 544
                                   6899***************9997654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (767 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       852  (0.0475208); expected 358.6 (0.02)
Passed bias filter:                      609  (0.0339673); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.71u 0.30s 00:00:01.01 Elapsed: 00:00:00.45
# Mc/sec: 5078.78
//
Query:       gi|13540924|ref|NP_110612.1|  [L=257]
Description: metal-dependent hydrolase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.3e-12   46.4   0.2    1.9e-11   43.9   0.2    1.9  1  Lactamase_B_2  Beta-lactamase superfamily domain
    1.1e-07   32.1   0.4    1.8e-07   31.4   0.4    1.6  1  Lactamase_B    Metallo-beta-lactamase superfamily
  ------ inclusion threshold ------
       0.02   15.0   0.1      0.086   12.9   0.1    2.0  2  DUF4513        Domain of unknown function (DUF4513)
       0.16   11.0   3.2        2.2    7.3   2.3    2.3  1  PDEase_II      cAMP phosphodiesterases class-II


Domain annotation for each model (and alignments):
>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.9   0.2   4.1e-15   1.9e-11      34     200 ..      59     212 ..      55     213 .. 0.86

  Alignments for each domain:
  == domain 1  score: 43.9 bits;  conditional E-value: 4.1e-15
                                   EE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHHHCHTTTTEEEEEE-TTSEEEECSTTEEEEEEEE-EE- CS
                 Lactamase_B_2  34 VllthaHyDHlaglltlrelrpkklplyapkgvlavleanfvylaleeepavnvheldwgesfelgdggleitatparhks 114
                                   ++++h+H+DH+ g+ ++++  +  +++y  + +++                 n++  ++++++ +g  ++ei a+ ++h++
  gi|13540924|ref|NP_110612.1|  59 IFISHEHADHVSGIRSVKKVDG--ADVYTRPATAEA---------------ANIKAYEIDNEVVIG--NFEILAFDVPHDA 120
                                   99*****************765..556655555443...............345578999*****9..789********** PP

                                   -CTCCE-TTTSEEEEEECTTEEEEEESS-S---HHHHHHHCT-SEEEEE-S-SSTTHHHH..............HHT---S CS
                 Lactamase_B_2 115 grrldrnagdtlGlriegggkrvyyigDtgyipeeigerlggadllllditayeddemir..............hmgHltp 181
                                   +          +++ +++++ ++  + D+g+++e +   +++ d+l ++ +  +d +m +              ++gHl+ 
  gi|13540924|ref|NP_110612.1| 121 AD--------PVAFTVKWKDLKISVVSDLGTVTENVISNIRDSDILAFESN--HDVSMLKtgrypaslkrrilsQHGHLSN 191
                                   *9........***************************9********99988..77777778999999999*********** PP

                                   TSHHHHCTTSS..SSEEEEES CS
                 Lactamase_B_2 182 eeaveaaadlg..akrlvliH 200
                                   e+ +ea+ ++    +  vl+H
  gi|13540924|ref|NP_110612.1| 192 EQSAEAISKAIneSTEIVLTH 212
                                   ******998874455677777 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.4   0.4   4.1e-11   1.8e-07       5      88 ..      19      99 ..      15     212 .. 0.76

  Alignments for each domain:
  == domain 1  score: 31.4 bits;  conditional E-value: 4.1e-11
                                  SSEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCHCHHH CS
                   Lactamase_B  5 pvnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalfmeea 87
                                   +ns++i++  ++i+iD G++  + ++a     l l++++ + ++++H H+DH++g + +++  ++ v+  +++a+a +  + 
  gi|13540924|ref|NP_110612.1| 19 KGNSTFIWDAHDLIVIDFGITMKKFKEAI--SELTLGGLN-KSIFISHEHADHVSGIRSVKKVDGADVYTRPATAEAANIKAY 98
                                  68*************************95..444444444.569*****************************9999887777 PP

                                  H CS
                   Lactamase_B 88 d 88
                                  +
  gi|13540924|ref|NP_110612.1| 99 E 99
                                  3 PP

>> DUF4513  Domain of unknown function (DUF4513)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.51   2.3e+03      66      84 ..      46      64 ..      37      78 .. 0.77
   2 ?   12.9   0.1   1.9e-05     0.086      10      78 ..     187     254 ..     179     256 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.51
                       DUF4513 66 evsgiyagpledslflnys 84
                                   +s +  g l++s+f++++
  gi|13540924|ref|NP_110612.1| 46 AISELTLGGLNKSIFISHE 64
                                  4677888999999999986 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 1.9e-05
                       DUF4513  10 pklanncsaensykpakkceeihlprfslkqgmiprryvmpwkenmkfrnvnlkkaevsgiyagpleds 78 
                                    +l+n++sae+  k  +++ ei l ++s ++   p+  +   k  +k r+++ k  e++  y g   +s
  gi|13540924|ref|NP_110612.1| 187 GHLSNEQSAEAISKAINESTEIVLTHLSQEN-NKPEIALNEVKSYLKNRDIKYKDVECADQYVGSSLKS 254
                                   5799**********************99765.579999********************99999976555 PP

>> PDEase_II  cAMP phosphodiesterases class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   2.3   0.00049       2.2      83     191 ..      58     168 ..      54     178 .. 0.54

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.00049
                                   EEE-S---GGGTHHHHHHGGGGGS-S.--EEEEE-HHHHHHHHHHTBSSSSB--GGGSTT-..............-EEEEE CS
                     PDEase_II  83 sylItHsHLDHvsglvinSaefykaqlkkktivGlpytInalqkhlFNnkvWPnlpsfkrvnl..........islvklie 153
                                   s +I+H H DHvsg+  +   ++ + +  +        I a   ++ N+ v  n++      +           ++vk ++
  gi|13540924|ref|NP_110612.1|  58 SIFISHEHADHVSGIRSVKKVDGAD-VYTRPATAEAANIKA--YEIDNEVVIGNFEILA---FdvphdaadpvAFTVKWKD 132
                                   679**********975444444443.222222222222222..2233444433333222...1223344444466777777 PP

                                   --TT--EE-SSSSEEEEE...........EEEEEEE-T CS
                     PDEase_II 154 lepkelnkltettldvvanefsfsvkvktfevnhgsli 191
                                   l+ + +  l   t++v+   +   + + +fe nh+ ++
  gi|13540924|ref|NP_110612.1| 133 LKISVVSDLGTVTENVIS--NIRDSDILAFESNHDVSM 168
                                   777777777777777776..566667777777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       888  (0.0495287); expected 358.6 (0.02)
Passed bias filter:                      577  (0.0321825); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 1590.06
//
Query:       gi|13540925|ref|NP_110613.1|  [L=592]
Description: chloride channel protein [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.2e-87  294.5  33.4    1.2e-87  294.5  33.4    2.1  2  Voltage_CLC  Voltage gated chloride channel
    2.2e-15   56.8   0.2    1.1e-07   32.2   0.0    3.2  3  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 !    3.4   0.4    0.0041        37     162     192 ..      18      48 ..       2      74 .. 0.78
   2 !  294.5  33.4   1.3e-91   1.2e-87       1     353 [.      85     436 ..      85     437 .. 0.97

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.0041
                                   GGHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                   Voltage_CLC 162 lelilfvllGilgGllgalfvrlllkverlf 192
                                   +++i+ +++G+++Gl + +f +    +e+lf
  gi|13540925|ref|NP_110613.1|  18 KWFIMGLIIGVISGLGALAFYFAIKLFEYLF 48 
                                   5789999***********9999888887766 PP

  == domain 2  score: 294.5 bits;  conditional E-value: 1.3e-91
                                   HHHHHHHHCCCCC-GGGSC-SHHHHHHHCTTSS---HHHHHHHHHHHHHHHHCTT-S-BTHHHHHHHHHHHHHHHHHHTT. CS
                   Voltage_CLC   1 lggllagllvklvapeaagsGipevkaalngvkgplslrvllvkflasvltvgsGlslGreGplvqiGAavgsglsrllkl 81 
                                   lggl++gl+v+ +apea+g+G++  ++a+++++g+++ r+ +vk++as++t+gsG+s+GreGp+ qi+A +gs++++l+ l
  gi|13540925|ref|NP_110613.1|  85 LGGLFSGLIVYTFAPEAEGHGTDAAIRAFHNEQGKIRRRIPVVKTIASAITIGSGGSAGREGPTAQISAGLGSLIADLFGL 165
                                   589****************************************************************************** PP

                                   --SHHHHHHHHHHHHHHHHHHHT-HHHHHHHHCTT.TSTSS--TTHHHHHHHHHHHHHHHHHHCTTS-S-.T---...--G CS
                   Voltage_CLC  82 srndrdrrlvaaGaAAGiAAaFnaPlgGvlfalEe.vsrefslrallpvfvasvvaalvlrlllgeepafgeveslfalsl 161
                                   s+ d +r+ va+G+++Gi+ +F++P+gG++++ E+ + r+++++a+ p++va +v++ ++ +++g ep+fg  ++  ++++
  gi|13540925|ref|NP_110613.1| 166 SDAD-RRIAVAVGIGSGIGTIFKTPIGGTMLGAEIlYKRDLETQAIYPSLVANAVGYSIFASVVGFEPIFGYYTA--SFQV 243
                                   9999.888***************************888*********************************7544..79** PP

                                   GGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHCHHHHHHHHHHHHHHHHHHHCCCSCC.CSSSSCCHHHHHCTT-S-. CS
                   Voltage_CLC 162 lelilfvllGilgGllgalfvrlllkverlfrkleklkikkrlepalvgllvgllglllpasvlgggyeliasllegstl. 241
                                     ++++++lG+++Gl+++++v++++ +  +f+kl   ki+++++p+++g l+g+++l++p+ ++ +gy++++ l++++   
  gi|13540925|ref|NP_110613.1| 244 IRIPYYMVLGVISGLFAIFYVKSFYGTVAFFKKL---KISNYYKPIIGGGLTGIIALFFPE-IMATGYGWVNLLMNQKLGe 320
                                   *********************************9...9999********************.*************998669 PP

                                   .....HHHHHH...HHHHHHHHHHHHHCTT-CSBSHHHHHHHHHHHHHHHHHHHHHH-CTSSC...HHHHHHCCTHHHHHC CS
                   Voltage_CLC 242 .....llsllllllllllkllataltlgsgvpgGifaPsLviGAalGrlvglvlalllpgaassdpgafalvGmaaflagv 317
                                        +  ll+l+ll ++k++at++t+gsg +gG++aP ++iGAalG +v+  +++l p+ ++ +++ f+++Gm +f++ +
  gi|13540925|ref|NP_110613.1| 321 iptfgIPLLLVLILLPFIKVIATSFTVGSGGSGGVYAPGIFIGAALGTVVAIGFHYLTPSIVP-TITPFVIIGMISFFGSA 400
                                   9999999999999********************************************997666.6789************* PP

                                   CS-HHHHHHHHHHCC--GCCHHHHHHHHHHHHHHHC CS
                   Voltage_CLC 318 trapltaiviviEltgdlelllplmlavliAkavad 353
                                    ++pl++i++v+E+tg+l+ll+  m+a++iA+++++
  gi|13540925|ref|NP_110613.1| 401 GKVPLSVILMVVEMTGSLQLLPGAMIATFIAYIISG 436
                                   ********************************9985 PP

>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.39   3.5e+03      21      36 ..     109     127 ..     107     130 .. 0.62
   2 !   20.5   0.2   5.4e-08   0.00048      10      53 ..     476     518 ..     467     519 .. 0.89
   3 !   32.2   0.0   1.2e-11   1.1e-07       1      54 [.     524     576 ..     524     579 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.39
                                   HHHHHHHHT.....SSEEEEE CS
                           CBS  21 alelmrekg.....vsrlPVV 36 
                                   a++ +  ++      +r+PVV
  gi|13540925|ref|NP_110613.1| 109 AIRAF--HNeqgkiRRRIPVV 127
                                   56666..33334633699**9 PP

  == domain 2  score: 20.5 bits;  conditional E-value: 5.4e-08
                                   EEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHH CS
                           CBS  10 vtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllr 53 
                                   ++v+ d+++e a   m+++g+ ++PVV  +gkl+G + l D+++
  gi|13540925|ref|NP_110613.1| 476 ISVSDDDDVEHAKTVMIDHGLASIPVV-VYGKLIGALYLFDIAE 518
                                   59***********************98.6************986 PP

  == domain 3  score: 32.2 bits;  conditional E-value: 1.2e-11
                                   HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHH CS
                           CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllra 54 
                                   V+++m+  + +++p++t eea e m +++ +  P+V  +gk+ Givtl D+l+a
  gi|13540925|ref|NP_110613.1| 524 VREYMRAGITYLRPTSTAEEAWEVMMRNKTTWCPIV-YEGKFKGIVTLNDILDA 576
                                   8999********************6577778*****.99*************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (592 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       610  (0.0340231); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); 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: 0.72u 0.33s 00:00:01.05 Elapsed: 00:00:00.54
# Mc/sec: 3306.09
//
Query:       gi|13540926|ref|NP_110614.1|  [L=322]
Description: cell wall biosynthesis glycosyltransferase [Thermoplasma volcanium GSS1]
Scores for complete 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   38.9   0.1    1.2e-09   38.2   0.1    1.4  1  Glycos_transf_2  Glycosyl transferase family 2
    1.4e-05   25.1   0.0      2e-05   24.6   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 !   38.2   0.1   1.4e-13   1.2e-09       1     101 [.       4      98 ..       4     161 .. 0.85

  Alignments for each domain:
  == domain 1  score: 38.2 bits;  conditional E-value: 1.4e-13
                                   EEEEEESS-TTTHHHHHHHHHHH.GGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-.HHHHHHHHHHHH-- CS
               Glycos_transf_2   1 svviptyNeektlletlesllaq.dpypdfeiivvDDgStDetveileelakedprvrvirreenv.Gkagalnaglraat 79 
                                   sv+i++  ++ ++ ++++s+l+q  p++dfeiiv +D       ++++e+     + r i ++en+   ++ +  ++ +++
  gi|13540926|ref|NP_110614.1|   4 SVIITAQGRKGYVMQAVRSVLSQnIPKEDFEIIVSKDFK----DDVIDEFL----DGRAIVLNENHiRSGSRVASAVLQSS 76 
                                   8**************************************....55555553....34457888899788888889****** PP

                                   SSEEEEEESSEEE-TTHHHHHH CS
               Glycos_transf_2  80 gdyilflDaDdepdpdwleklv 101
                                   g++++flD+Dd + p++l+++ 
  gi|13540926|ref|NP_110614.1|  77 GKILVFLDDDDLFYPGKLREVK 98 
                                   ******************9975 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 !   24.6   0.0   2.2e-09     2e-05       4     109 ..       3      98 ..       2     120 .. 0.83

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 2.2e-09
               Glyco_tranf_2_3   4 lavlVptfneedvlgevlesllaqeypr..vevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksralnea 82 
                                   l+v++++ ++  ++   ++s+l+q  p   +e++v  d +d+   e++++        r  +v n++  +s++++     a
  gi|13540926|ref|NP_110614.1|   3 LSVIITAQGRKGYVMQAVRSVLSQNIPKedFEIIVSKDFKDDVIDEFLDG--------R-AIVLNENHIRSGSRVA---SA 71 
                                   79*********************9875557************99999987........3.3555766557666655...88 PP

               Glyco_tranf_2_3  83 lravksdlvllvDdDtvvePdtlkrll 109
                                   + + ++++++++DdD++  P+ l+ + 
  gi|13540926|ref|NP_110614.1|  72 VLQSSGKILVFLDDDDLFYPGKLREVK 98 
                                   99999**************99998754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       589  (0.0328518); 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:                         2  (0.000111551); expected 0.2 (1e-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: 2079.11
//
Query:       gi|13540927|ref|NP_110615.1|  [L=212]
Description: 2-phosphosulfolactate phosphatase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.8e-41  141.1   0.1    1.6e-39  135.4   0.1    2.0  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 !  135.4   0.1   8.9e-44   1.6e-39       6     224 ..       7     204 ..       2     206 .. 0.90

  Alignments for each domain:
  == domain 1  score: 135.4 bits;  conditional E-value: 8.9e-44
                                   CTEE-GTTTEEEEE-TTTHHHHHHHHHHTT-SEEEEESSHHHHHHTCCH.HGCCEEEEE-BTTB--TTSSB-S-GGGHHHH CS
                    2-ph_phosp   6 eikeeklkdvvvviDvLRAtstivtaLanGakavipvssveealelakklpeekvllaGErgglkiegfdlgnSPleytke 86 
                                     kee+ + + ++iD++R+t+ti ++L++Ga+ ++p+++v +al++++k  +++v+l+GE+ g+k++ fd++nSP ++ ++
  gi|13540927|ref|NP_110615.1|   7 GRKEENWSSINIIIDIFRSTTTIPVILSRGARYIVPFKDVTSALNFKRK--NKNVVLIGEKYGIKPPFFDYDNSPAQIINA 85 
                                   5566678889**************************************7..578*************************** PP

                                   HHTTSEEEEE-CCHHHHHHHCCTSSEEEEE-STTHHHHHHHHHHHTSSEEEEE--BTTB--HHHHHHHHHHHHHHHHHS.S CS
                    2-ph_phosp  87 kvkgktvvltTtNGTralekaasakrvligsllNakavaeklkelakevvivcaGtegefsleDtlcAgalveelekeeel 167
                                   +++gk + +t+tNG  +l+++++  r+l  sl+N++a+++k+k +++ +++v + +    ++eD ++A++l  +le     
  gi|13540927|ref|NP_110615.1|  86 DLEGKIIAFTSTNGMYVLSRIKR-GRILFSSLVNMSATIKKVKGKDD-ILVVPSNRPIGKAVEDNIFAEMLKLALEG---- 160
                                   **********************6.9******************9997.****************************9.... PP

                                   EE-HHHHHHHHHHHC-STHHHHHHHSHHHHHHHHTT-HHHHHHHTSTSS----EEEE CS
                    2-ph_phosp 168 elsDaalaalalyeskedllealkksshgkrLkelgleeDleycaqldlldvVpvlk 224
                                   +  D  +++ ++ e+ke++   ++             ++Dle+c++ldlld+Vp++ 
  gi|13540927|ref|NP_110615.1| 161 KNYDREILVNRIRETKENTVVSIS-------------TQDLEICLKLDLLDCVPEYI 204
                                   457887877777777665554444.............56999999999999999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       625  (0.0348597); expected 358.6 (0.02)
Passed bias filter:                      514  (0.0286686); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.33s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 1282.82
//
Query:       gi|13540928|ref|NP_110616.1|  [L=342]
Description: Kef-type K+ transporter NAD-binding component [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-11   44.9   0.0    2.2e-11   44.1   0.0    1.4  1  TrkA_N          TrkA-N domain
      2e-10   40.5   5.9      2e-10   40.5   5.9    2.3  2  Ion_trans_2     Ion channel
     0.0023   17.2   7.8     0.0048   16.1   7.8    1.5  1  Ion_trans       Ion transport protein
  ------ inclusion threshold ------
      0.018   14.7   1.0      0.033   13.9   1.0    1.4  1  tRNA-synt_2_TM  Transmembrane region of lysyl-tRNA synthetase
      0.041   14.2   0.0      0.083   13.3   0.0    1.5  1  NTP_transf_3    MobA-like NTP transferase domain
      0.078   12.4   0.0       0.14   11.6   0.0    1.3  1  PEX11           Peroxisomal biogenesis factor 11 (PEX11)
       0.11   12.5   0.1       0.23   11.5   0.0    1.5  2  AdoHcyase_NAD   S-adenosyl-L-homocysteine hydrolase, NAD bind


Domain annotation for each model (and alignments):
>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.1   0.0   8.4e-15   2.2e-11       1     109 [.     212     323 ..     212     330 .. 0.92

  Alignments for each domain:
  == domain 1  score: 44.1 bits;  conditional E-value: 8.4e-15
                                   EEEES-SHHHHHHHHHHHH.TTEEEEEEESSHHHHHHHHHTTSEEEES-TTSHHHHHHTTGGGESEEEE-SSSHHHHHHHH CS
                        TrkA_N   1 iiiiGlGrvGrslaeeLse.ggkdvvvidkdeerveelreeglevvvgdatdeevLeeagiekadaviaatgddeanilav 80 
                                   ++++G++ + +s +  L++ g+  +v+++kd++ +++lr++g+ v++ +a d+++L +  +++a  +i+  +dd+ +++++
  gi|13540928|ref|NP_110616.1| 212 VLVCGYSPLLSSYLLMLKQmGK-VIVIVEKDPAIAAKLRDDGYIVLNQEADDQNLLSSFTMDDAYKIIIGPEDDAYSLIIA 291
                                   68*****************555.7********************************************************* PP

                                   HHHHHHTSS...SEEEEEESSGGGHHHHHHHT CS
                        TrkA_N  81 llakelnpk...kkiiaraqdpehaellkklg 109
                                   +++++  ++    k+ + + + +++++++  g
  gi|13540928|ref|NP_110616.1| 292 ATLRQVAGEkaaGKTRVIVYNTKNVKKFSPFG 323
                                   ****9999877777889999999998887655 PP

>> Ion_trans_2  Ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   1.3       2.6   6.6e+03      56      56 ..      50      50 ..      13      84 .. 0.64
   2 !   40.5   5.9   7.8e-14     2e-10       3      74 ..     111     185 ..     106     189 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 2.6
                                  H CS
                   Ion_trans_2 56 i 56
                                  +
  gi|13540928|ref|NP_110616.1| 50 T 50
                                  1 PP

  == domain 2  score: 40.5 bits;  conditional E-value: 7.8e-14
                                   HHHTCHHHHHHHHT.......T---HHHHHHHHHHHHTTS----SSTT-----HHHHHHHHHHHHHHHHHHHHHH CS
                   Ion_trans_2   3 lllvlifgaviysl..eeg.wekwsfldalYfsfvtltTiGYGdivpetdagrlftivyillGlalfalflavlg 74 
                                   +l+++++g+   +l  e++     s+ +alY++  t+tT+G+Gdi p++   rlfti +++lG+a+f+ +++ l+
  gi|13540928|ref|NP_110616.1| 111 VLFTIAYGVGGSILsgEQFkPPIRSLGTALYYTGETVTTLGFGDILPVDLESRLFTISLAFLGVAIFFSAMTALI 185
                                   677888888888889866667799************************8888****************9998765 PP

>> Ion_trans  Ion transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   7.8   1.9e-06    0.0048      56     238 ..      35     190 ..       8     192 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.9e-06
                                   HHTHHHHHHHCHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGGGGGGHHHCHSHHHHHHHHHHHHHHHHHHHHHHH CS
                     Ion_trans  56 algllikkrYlrdpwnilDflvvlpsllslvlseesllllsvlrlfrvlrllklisrleglrtlvtalirsvkdllnvlll 136
                                   ++gl   ++  r  w+i+   + l++ l +++   ++ ++ +  +f ++ +l li+r +    +v+  + + +  + +++l
  gi|13540928|ref|NP_110616.1|  35 GYGL---QEKTRAAWFIVTADAFLTFALLIISYARTYHIVFIGAIFDLYLILTLIKRRSE---FVYPSKTIGRPEVGIAIL 109
                                   4555...55566677777665555555555333334555555556688888888888888...66688889999999**** PP

                                   HHHHHHHHHHHHHHHHTTSCCCCCCSCCSTSSSTTTSSSSSSHHHHHHHHHHHHTTSSHHHHHHHHHHHSHHHHHHHHHHH CS
                     Ion_trans 137 llvvlfifaligvqlfkgklreknecaktwenpnngntnFdnfftallwlfrlmttegwgdilyatldekskvaliyfvif 217
                                   ++++ +++++ g  l +++++                +  ++++tal+ + ++ tt g+gdil++ l ++     ++ +++
  gi|13540928|ref|NP_110616.1| 110 TVLFTIAYGVGGSILSGEQFK----------------PPIRSLGTALYYTGETVTTLGFGDILPVDLESR-----LFTISL 169
                                   ************999955554................34679****************************.....999999 PP

                                   HHHHHHHHHHHHHHHHHHHHH CS
                     Ion_trans 218 iilgsflllNlliaviadnfq 238
                                    +lg+ ++++ + a+i+ +++
  gi|13540928|ref|NP_110616.1| 170 AFLGVAIFFSAMTALITPTIE 190
                                   *******99999999987765 PP

>> tRNA-synt_2_TM  Transmembrane region of lysyl-tRNA synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   1.0   1.3e-05     0.033      55     152 ..      28     118 ..      19     125 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.3e-05
                tRNA-synt_2_TM  55 avvLllLAaAlaarkriAwwllvvylvlllllnavllvasdlreqvaedinelvglavqvvvlvlLllarkeFyarvrr.G 134
                                   +++L l + +l+++ r+Aw+++++   l+ +l ++  +               +g+++++ ++++L+  r+eF+  +++ G
  gi|13540928|ref|NP_110616.1|  28 GFFLTLGGYGLQEKTRAAWFIVTADAFLTFALLIISYAR--------TYHIVFIGAIFDLYLILTLIKRRSEFVYPSKTiG 100
                                   6899999***************99988887777766666........5556789*******************75444324 PP

                tRNA-synt_2_TM 135 allkAllvlvaglavatl 152
                                       ++++l + +++a  
  gi|13540928|ref|NP_110616.1| 101 RPEVGIAILTVLFTIAYG 118
                                   455555555555555555 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 ?   13.3   0.0   3.2e-05     0.083      15      76 ..     208     269 ..     193     271 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.2e-05
                                   THHHHCCCC.CCHHHHHHHHHCTT.-CEEEEECSHCHHHHHHTTCTS-EEE-TTSS-SHHHHH CS
                  NTP_transf_3  15 dKallplgg.kpllervldalraagvdevvvvggdeevlaalarlgvrvvededpgkgplasl 76 
                                    K ++ ++g  pll   l +l+++g + +v+v +d++++a l++ g+ v+++e  +++ l+s+
  gi|13540928|ref|NP_110616.1| 208 LKDFVLVCGySPLLSSYLLMLKQMG-KVIVIVEKDPAIAAKLRDDGYIVLNQEADDQNLLSSF 269
                                   466777755269************7.788888899******************999*999985 PP

>> PEX11  Peroxisomal biogenesis factor 11 (PEX11)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   5.5e-05      0.14      90     142 ..     133     185 ..     131     193 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5.5e-05
                         PEX11  90 lrnlgyalYlllDhvlwlkklgllkvknakklsrlssrfwlfglvlslvrdly 142
                                   +r lg alY++ ++v+ l+   +l+v+ +++l ++s  f  +++++s +  l 
  gi|13540928|ref|NP_110616.1| 133 IRSLGTALYYTGETVTTLGFGDILPVDLESRLFTISLAFLGVAIFFSAMTALI 185
                                   6899*******************************************998775 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 ?   -4.0   0.1       5.3   1.4e+04      19      34 ..     140     155 ..     137     155 .. 0.78
   2 ?   11.5   0.0   9.1e-05      0.23      25      72 ..     211     258 ..     196     279 .. 0.86

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 5.3
                                   S--TTSEEEEE--SHH CS
                 AdoHcyase_NAD  19 vllaGkvavvaGyGdv 34 
                                   +  +G ++   G+Gd+
  gi|13540928|ref|NP_110616.1| 140 LYYTGETVTTLGFGDI 155
                                   5568999999999996 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 9.1e-05
                                   EEEEE--SHHHHHHHHHHHHCT-EEEEE-S-HHHHHHHHCTT-EE--H CS
                 AdoHcyase_NAD  25 vavvaGyGdvGkGcaaslkglGarvivtevdPicalqaameGfevvtl 72 
                                    ++v+Gy  +       lk++G  +++ e dP  a +   +G+ v + 
  gi|13540928|ref|NP_110616.1| 211 FVLVCGYSPLLSSYLLMLKQMGKVIVIVEKDPAIAAKLRDDGYIVLNQ 258
                                   689****************************************98654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (342 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       497  (0.0277205); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 2283.27
//
Query:       gi|13540929|ref|NP_110617.1|  [L=180]
Description: hypothetical protein TVN0098 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-41  142.7   0.0    1.2e-41  142.5   0.0    1.0  1  Cob_adeno_trans  Cobalamin adenosyltransferase


Domain annotation for each model (and alignments):
>> Cob_adeno_trans  Cobalamin adenosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  142.5   0.0   6.9e-46   1.2e-41       2     163 ..       2     159 ..       1     160 [. 0.93

  Alignments for each domain:
  == domain 1  score: 142.5 bits;  conditional E-value: 6.9e-46
                                   XXXXXXXXXXXXXXX.XXXTTHHHHHHHHHHHHHHHHHHHHHHHCTTTTHHHHHHHHHHHHHHHHHHHHHHT.-BTCCG-S CS
               Cob_adeno_trans   2 yTrtGDkGtTslvggervsKddprveayGtvDelnsaiglarallaeeeeelkeaLeeiqneLfdlgaelatpekkkekkk 82 
                                   +Tr+GD+G+T+l++  rv Kd+p+ve+ G +Deln++ig a+ l+  ++e+++++L +iqn+Lf lg++++t     + + 
  gi|13540929|ref|NP_110617.1|   2 FTRRGDTGETDLASRVRVGKDSPIVEVQGVIDELNAFIGQALVLT--KWEDIRKDLFKIQNDLFVLGEDVSTG---GKGRV 77 
                                   7*****************************************444..589********************865...44556 PP

                                   --HHHHHHHHHHHHHHHHHS--EESEEES-SSHHHHHHHHHHHHHHHHHHHHHHHHHHS..HHHHHHHHHHHHHHHHHHHH CS
               Cob_adeno_trans  83 iteeeveelekeideleaelpplksfilpggspaaaalhvaRtvcRraERavvelaeee.veeevlkylNRLSDlLfvlar 162
                                   +t e ++ le++++ l++e+ +++ f++pgg+ +a ++h+aRtv Rr ER++v +++ + ++++vl y NRLS+lLf++a 
  gi|13540929|ref|NP_110617.1|  78 VTREMIDYLEDRVNVLRKEIGKIELFVIPGGTLEATSVHIARTVSRRLERRIVFANHYTdINKNVLIYANRLSSLLFMIAM 158
                                   77888**************************************************8855899****************997 PP

                                   H CS
               Cob_adeno_trans 163 v 163
                                   v
  gi|13540929|ref|NP_110617.1| 159 V 159
                                   5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.32s 00:00:00.85 Elapsed: 00:00:00.52
# Mc/sec: 1034.22
//
Query:       gi|13540930|ref|NP_110618.1|  [L=436]
Description: dihydrolipoamide dehydrogenase [Thermoplasma volcanium GSS1]
Scores for complete 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   1.7    1.2e-65  221.6   1.7    1.2  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    6.3e-21   74.7   8.2    4.1e-20   72.1   1.2    3.1  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    3.7e-17   62.6   0.1    1.3e-16   60.8   0.1    2.0  1  Pyr_redox_dim   Pyridine nucleotide-disulphide oxidoreductase
    8.4e-16   58.1   4.3    4.1e-11   42.7   0.1    2.2  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    5.9e-10   38.4  11.9    0.00018   20.4   0.3    4.3  4  HI0933_like     HI0933-like protein
    1.5e-08   34.7   1.5    5.8e-05   23.2   0.1    2.8  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    5.2e-07   29.6  14.7      0.027   14.0   4.1    4.0  4  DAO             FAD dependent oxidoreductase
    5.9e-07   28.9   7.9    0.00013   21.2   0.9    3.2  3  FAD_binding_2   FAD binding domain
    2.2e-06   27.0  10.1     0.0012   18.0   0.1    3.9  5  GIDA            Glucose inhibited division protein A
    4.7e-06   26.0   3.1     0.0022   17.3   0.1    2.7  2  Thi4            Thi4 family
    9.8e-06   25.2   4.3     0.0011   18.4   0.2    2.3  2  FAD_oxidored    FAD dependent oxidoreductase
     0.0013   19.0   2.1       0.72   10.1   0.3    2.6  2  TrkA_N          TrkA-N domain
     0.0016   17.8   2.2       0.95    8.6   0.0    2.3  2  FAD_binding_3   FAD binding domain
     0.0026   17.4   0.5     0.0026   17.4   0.5    2.3  2  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
     0.0059   16.6   9.2       0.19   11.7   0.2    3.6  4  NAD_binding_9   FAD-NAD(P)-binding
  ------ inclusion threshold ------
      0.029   13.5   0.2       0.22   10.6   0.0    2.4  3  K_oxygenase     L-lysine 6-monooxygenase (NADPH-requiring)
      0.033   14.1   0.3      0.033   14.1   0.3    1.8  2  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
       0.07   12.2   6.3        2.9    6.8   0.6    3.1  3  Lycopene_cycl   Lycopene cyclase protein
      0.075   13.0   0.9         17    5.4   0.1    2.8  3  NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogen
      0.077   12.3   3.0       0.39   10.0   0.2    2.7  3  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
        0.1   12.6   0.0       0.25   11.3   0.0    1.6  1  CHB_HEX_C       Chitobiase/beta-hexosaminidase C-terminal dom
       0.18   12.3   0.7        3.3    8.2   0.2    2.5  2  NAD_binding_7   Putative NAD(P)-binding
       0.21   10.8   0.3       0.46    9.7   0.1    1.6  2  Amino_oxidase   Flavin containing amine oxidoreductase
        1.4    7.7   7.8       0.61    8.9   0.1    2.5  2  Trp_halogenase  Tryptophan halogenase


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  221.6   1.7   1.6e-68   1.2e-65       1     294 []       2     306 ..       2     306 .. 0.96

  Alignments for each domain:
  == domain 1  score: 221.6 bits;  conditional E-value: 1.6e-68
                                   CSEEEE--SHHHHHHHHHHHHHTS-EEEEE...TTHCHHHCSHHHHCHHHHHHHHHHHHH..................... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxx..................... RF
                   Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaqagakvtlve...legtclnggcllskallgvaedaeias..................... 57 
                                   +d vv+G+Gp+G+aaa++l+q + kv+++e    +g+cln gc++ska+ + a   + ++                     
  gi|13540930|ref|NP_110618.1|   2 YDAVVLGAGPGGYAAAIRLGQRKKKVAIIEkdkIGGECLNYGCIPSKAIIELANSINYLKempgvsinynvdmkkwqewkw 82 
                                   588**************************9999************************************************ PP

                                   HHHHCHHHHCCCCHCCTCEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHHHHHHCC CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2  58 evvkklnqgielllgeevvkidpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGvaenvgklvrtldsaealkl 138
                                     ++kl+ g+elll++ +v+i +g + +++++ ++ + + ++ d+lv+AtGs+p  +   G         + + + e l l
  gi|13540930|ref|NP_110618.1|  83 SMINKLTGGVELLLKAYGVDIFRGTGYIQDKNHVKVNDKVLETDSLVIATGSKPVSI--NGI-------NDVMYNREVLDL 154
                                   999************99******************999*************999776..666.......244778999999 PP

                                   SS-TSEEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTEEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2 139 kllpkrivvvGgGyiGvElAaalaklgkevtlveardrllraldkelsaaleealekeGvevklgtsvkeidgngeklevv 219
                                   +  p +iv++GgGyiGvE+ +alaklg++vt+ve ++ +l+++d el + + +++ + G++v +g +v    +nge ++v+
  gi|13540930|ref|NP_110618.1| 155 DHIPSSIVIIGGGYIGVEIGIALAKLGSKVTIVEMMPSILPGTDNELVRHVVRRMSQLGINVITGRKVLSTAKNGE-VTVK 234
                                   ***************************************************************************8.9*** PP

                                   ETTSCEEEESEEEE-S-EEES-HHCS.HCCT-EEEETTEEE--TTSBESSTTEEE-GGGCTECCSS--HHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2 220 ledgeeidadlvvvavGvrpstelle.eklglelderggivvdeflrtnvpgiyaiGDvaggkggpelaqaAvqqG 294
                                   l+dg+e+ a+ v++ vG+ p+te+++ e+l+l++ ++++i++d++  t+v+g+yaiGDv    g+p+la++A  ++
  gi|13540930|ref|NP_110618.1| 235 LDDGQELRAEKVLMTVGRIPNTEGFGlENLKLAM-DGRFIKTDSRKMTSVKGVYAIGDVS---GQPMLAHKAYYEA 306
                                   **********************************.999**********************...*********9876 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.2     0.028        21       2      30 ..       4      32 ..       3      38 .. 0.93
   2 !   72.1   1.2   5.5e-23   4.1e-20       1      79 [.     160     236 ..     160     238 .. 0.94

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.028
                                  EEEECSSHHHHHHHHHHHHTTSEEEEEES CS
                     Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvver 30
                                  +vv+G+G  g  +A  l + +kkV ++e 
  gi|13540930|ref|NP_110618.1|  4 AVVLGAGPGGYAAAIRLGQRKKKVAIIEK 32
                                  69*************************96 PP

  == domain 2  score: 72.1 bits;  conditional E-value: 5.5e-23
                                   EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTSEEEEEEE CS
                     Pyr_redox   1 kvvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekngievllntkveeiegsedgvesvklk 79 
                                   ++v++GgGyig+E + ala+lg+kVt+ve+++ +l++ D+e+ + + ++++++gi+v++++kv +  ++++ v+ vkl 
  gi|13540930|ref|NP_110618.1| 160 SIVIIGGGYIGVEIGIALAKLGSKVTIVEMMPSILPGTDNELVRHVVRRMSQLGINVITGRKVLSTAKNGE-VT-VKLD 236
                                   69*****************************************************************9998.65.7765 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 !   60.8   0.1   1.8e-19   1.3e-16       1     109 [.     325     423 ..     325     424 .. 0.94

  Alignments for each domain:
  == domain 1  score: 60.8 bits;  conditional E-value: 1.8e-19
                                   BEEEEESSSEEEEEES-HHHHHHHHSGEEEEEEEEECGHHHCHTTHTEEEEEEEEETTTTBEEEEEEECTTHHHHHHHHHH CS
                 Pyr_redox_dim   1 iptvvftdpevasvGlteeeAkaagieikvgkfpfkangralayaetkgfvKlvadaktgkvlGahivGpgageliqelav 81 
                                   +p v+++dpe+a++G+        g   k  +fp++angr+l+++e+ g++ + +d+ +g v Ga i +p+a+eli+e+++
  gi|13540930|ref|NP_110618.1| 325 MPYVIYSDPEIAYTGVK-------G--AKSTRFPVAANGRSLTMNENIGTFNIYYDE-KGIVTGAGIAAPHASELISEISL 395
                                   699************94.......4..56678*********************7776.9********************** PP

                                   HHHTTSBHHHHHTSBSSSSSTGGGGHCH CS
                 Pyr_redox_dim  82 aikagltvedladtihihPtlsealkea 109
                                   a++ gl + d+  tih+hPt+se +ke+
  gi|13540930|ref|NP_110618.1| 396 AVESGLMAMDIGLTIHPHPTVSEGVKES 423
                                   ************************9997 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.8   4.7e-06    0.0035       1      39 [.       5      42 ..       5      47 .. 0.92
   2 !   42.7   0.1   5.5e-14   4.1e-11     113     305 .]     113     290 ..     109     290 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 4.7e-06
                   Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkgnignsiyry 39
                                  ++ GaGP G aaai l + +  ++ i+Ek++ig    +y
  gi|13540930|ref|NP_110618.1|  5 VVLGAGPGGYAAAIRLGQRKK-KVAIIEKDKIGGECLNY 42
                                  689*****************8.7*********9888887 PP

  == domain 2  score: 42.7 bits;  conditional E-value: 5.5e-14
                   Pyr_redox_3 113 gfevetsketyeAkkviiAtGefdkPnklnipGeeklvkhyskvkefhkyagqkvvViGgknSavDaAlelvrkgaeVtvv 193
                                   + +v+ + +++e+++++iAtG   kP   +i+G +  v+ +++v +++      +v+iGg+  +v++ + l++ g++Vt+v
  gi|13540930|ref|NP_110618.1| 113 KNHVKVNDKVLETDSLVIATGS--KPV--SINGIN-DVMYNREVLDLD-HIPSSIVIIGGGYIGVEIGIALAKLGSKVTIV 187
                                   56799999*************9..776..6****9.79*********5.557899************************** PP

                   Pyr_redox_3 194 trgseiekeesdpsyslkpdienrleelvkeekikvlfnaevkeikekeeeykvktedgkkvevkddvvlatGykpdlsfl 274
                                       +i       + +l  ++  r+ +l   + i+v++  +v +  + + e++vk +dg+++++ ++v++ +G  p+++ +
  gi|13540930|ref|NP_110618.1| 188 EMMPSILPGT---DNELVRHVVRRMSQL---G-INVITGRKVLSTAK-NGEVTVKLDDGQELRA-EKVLMTVGRIPNTEGF 259
                                   *999777653...444555555566554...4.99999*99999876.5889********9987.6667779*******99 PP

                   Pyr_redox_3 275 kkslfeldedgrpvlteeteetnvpglflaG 305
                                     + ++l+ dgr   t++ + t v+g++ +G
  gi|13540930|ref|NP_110618.1| 260 GLENLKLAMDGRFIKTDSRKMTSVKGVYAIG 290
                                   999999999*******************999 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.3   2.4e-07   0.00018       2      36 ..       3      37 ..       2      43 .. 0.90
   2 ?    4.5   0.0     0.016        12     143     174 ..     114     144 ..      96     150 .. 0.80
   3 !    6.7   1.4    0.0032       2.4       2      35 ..     160     193 ..     159     196 .. 0.93
   4 !   11.4   0.2   0.00013     0.095     109     163 ..     199     251 ..     195     257 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 2.4e-07
                                  SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS- CS
                   HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakklg 36
                                  d +v+G+G+ G  aAi++++r+k+V+++ek k  g
  gi|13540930|ref|NP_110618.1|  3 DAVVLGAGPGGYAAAIRLGQRKKKVAIIEKDKIGG 37
                                  89****************************97555 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.016
                                   EEEEE.TTEEEEESEEEE----SS-GGGT--S CS
                   HI0933_like 143 frvktkseeeleadklvlAtGGlSiPklGstg 174
                                    +vk+ +++ le+d+lv+AtG++ +   G ++
  gi|13540930|ref|NP_110618.1| 114 NHVKV-NDKVLETDSLVIATGSKPVSINGIND 144
                                   57888.99*************99877666555 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.0032
                                   SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS CS
                   HI0933_like   2 dviviGgGaAGlmaAisaakrgkrVlllekakkl 35 
                                   ++++iGgG  G+   i++ak g++V+++e ++++
  gi|13540930|ref|NP_110618.1| 160 SIVIIGGGYIGVEIGIALAKLGSKVTIVEMMPSI 193
                                   68***************************99886 PP

  == domain 4  score: 11.4 bits;  conditional E-value: 0.00013
                                   HHHHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE--- CS
                   HI0933_like 109 edivdallkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtG 163
                                   +++v+  ++++++ g+++ + ++v s +k  +g+++vk+++++el+a+k+++++G
  gi|13540930|ref|NP_110618.1| 199 NELVRHVVRRMSQLGINVITGRKVLSTAK--NGEVTVKLDDGQELRAEKVLMTVG 251
                                   578999*********************55..55689*****************98 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.1   7.8e-08   5.8e-05       1      38 [.       6      42 ..       6      56 .. 0.93
   2 !    9.8   0.1    0.0012      0.93       1      30 [.     163     192 ..     163     198 .. 0.94

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 7.8e-08
                                  EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-EE CS
                 NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraasy 38
                                  ++GaG +G +aA +L +++++v ++ek d++GG +  y
  gi|13540930|ref|NP_110618.1|  6 VLGAGPGGYAAAIRLGQRKKKVAIIEK-DKIGGECLNY 42
                                  89************************9.69***99765 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0012
                                   EE--SHHHHHHHHHHHCCTEEEEEE-SSSS CS
                 NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrdr 30 
                                   I+G+G  G  +  +Lak g +v+++e+ ++
  gi|13540930|ref|NP_110618.1| 163 IIGGGYIGVEIGIALAKLGSKVTIVEMMPS 192
                                   9*************************8765 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.2   6.2e-05     0.046       1      33 [.       3      36 ..       3      41 .. 0.88
   2 ?    0.9   0.0      0.37   2.8e+02     147     202 ..      87     134 ..      81     147 .. 0.70
   3 !   14.0   4.1   3.6e-05     0.027       2      29 ..     161     190 ..     160     199 .. 0.90
   4 !    6.3   0.1    0.0084       6.3     147     201 ..     200     251 ..     196     307 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.2e-05
                                  EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTT CS
                           DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiag 33
                                  d v+ G+G  G ++A  L +r+  V+++ek+  +g
  gi|13540930|ref|NP_110618.1|  3 DAVVLGAGPGGYAAAIRLGQRKkkVAIIEKD-KIG 36
                                  78****************988669*******.555 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.37
                                   HHHHHHHHHHHHTT-EEEESECEEE.EEEEETCEEEEEEECT.EEEEEEEEEEE--GG CS
                           DAO 147 kltaalaraaealGveilegtevtg.leeedgkvwgverttp.gendaadavVnaaGa 202
                                   klt ++   ++a Gv+i++g   tg ++  d+  ++v +++  +     d +V+a+G 
  gi|13540930|ref|NP_110618.1|  87 KLTGGVELLLKAYGVDIFRG---TGyIQ--DKNHVKV-NDKVlE----TDSLVIATGS 134
                                   56666666788999*****9...66343..3345666.433222....499*****94 PP

  == domain 3  score: 14.0 bits;  conditional E-value: 3.6e-05
                                   EEEECTSHHHHHHHHHHHHTT..EEEEESS CS
                           DAO   2 vviiGGGiiGlstAyeLarrg..Vtllekg 29 
                                   +viiGGG+iG+ +  +La+ g  Vt++e+ 
  gi|13540930|ref|NP_110618.1| 161 IVIIGGGYIGVEIGIALAKLGskVTIVEMM 190
                                   9******************999******86 PP

  == domain 4  score: 6.3 bits;  conditional E-value: 0.0084
                                   HHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECTEEE.EEEEEEEE--G CS
                           DAO 147 kltaalaraaealGveilegtevtgleeedgkvwgverttpgen.daadavVnaaG 201
                                   +l++ + r++ +lG+++++g++v +  + +g  ++v+   +g++ +a ++v ++ G
  gi|13540930|ref|NP_110618.1| 200 ELVRHVVRRMSQLGINVITGRKVLSTAK-NGE-VTVK-LDDGQElRA-EKVLMTVG 251
                                   6899999******************844.444.6663.223666344.77887776 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.9   1.8e-07   0.00013       1      32 [.       3      34 ..       3      40 .. 0.94
   2 !    7.5   1.2    0.0025       1.9       2      32 ..     161     191 ..     160     194 .. 0.93
   3 ?    1.9   0.0      0.12        93     378     404 ..     275     295 ..     268     302 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 1.8e-07
                                  SEEEE--SHHHHHHHHHHHHTTT-EEEEESSS CS
                 FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeq 32
                                  D++V G+G +G+aAA+++ ++ +kva++ek +
  gi|13540930|ref|NP_110618.1|  3 DAVVLGAGPGGYAAAIRLGQRKKKVAIIEKDK 34
                                  89***************************975 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0025
                                   EEEE--SHHHHHHHHHHHHTTT-EEEEESSS CS
                 FAD_binding_2   2 viViGsGlAGLaAAleaaeaGlkvavvekeq 32 
                                   +++iG+G  G   ++++a+ G kv++ve ++
  gi|13540930|ref|NP_110618.1| 161 IVIIGGGYIGVEIGIALAKLGSKVTIVEMMP 191
                                   79*************************9876 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.12
                                   BETTSBESTTEEESSBTEEE-STCEES CS
                 FAD_binding_2 378 tdengrvldadgqpipGLYAaGevaag 404
                                   t      ++++ + ++G YA+G v + 
  gi|13540930|ref|NP_110618.1| 275 T------DSRKMTSVKGVYAIGDVSGQ 295
                                   3......4455569*********9865 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.1   1.7e-06    0.0012       1      46 [.       3      50 ..       3      74 .. 0.86
   2 ?   -0.2   0.0      0.53     4e+02     133     150 ..     117     134 ..      94     150 .. 0.81
   3 !   11.0   1.9   0.00021      0.16       2      28 ..     161     187 ..     160     215 .. 0.86
   4 ?    0.1   0.0      0.46   3.4e+02     105     150 ..     206     252 ..     196     282 .. 0.70
   5 ?   -2.6   0.0         3   2.2e+03     349     366 ..     277     294 ..     260     296 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.7e-06
                                  CEEEE-SSHHHHHHHHHHHHTT--EEEE..ES-GGGTT--SSSSEEE- CS
                          GIDA  1 dviViGgGhAGceAAlaaarlGakvlLi..thkldtiaelsCnpsigg 46
                                  d +V+G+G  G++AA+ + ++  kv++i   +  +++++ +C ps   
  gi|13540930|ref|NP_110618.1|  3 DAVVLGAGPGGYAAAIRLGQRKKKVAIIekDKIGGECLNYGCIPSKAI 50
                                  579*************************75556789********9865 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.53
                                   ETTS-EEEECEEEE--TT CS
                          GIDA 133 tedgetikakavviatGt 150
                                   + +++++++++ viatG+
  gi|13540930|ref|NP_110618.1| 117 KVNDKVLETDSLVIATGS 134
                                   5678899999*******9 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 0.00021
                                   EEEE-SSHHHHHHHHHHHHTT--EEEE CS
                          GIDA   2 viViGgGhAGceAAlaaarlGakvlLi 28 
                                   +++iGgG  G+e  +a+a+lG kv+++
  gi|13540930|ref|NP_110618.1| 161 IVIIGGGYIGVEIGIALAKLGSKVTIV 187
                                   89**********************998 PP

  == domain 4  score: 0.1 bits;  conditional E-value: 0.46
                                   HHTSTTEEEEES-EEEEEECT.TEEEEEEETTS-EEEECEEEE--TT CS
                          GIDA 105 lenepnleiieeeveelivee.kkvkgvvtedgetikakavviatGt 150
                                   +++  +l i   +  +++ +  +    v+++dg++++a++v ++ G 
  gi|13540930|ref|NP_110618.1| 206 VRRMSQLGINVITGRKVLSTAkNGEVTVKLDDGQELRAEKVLMTVGR 252
                                   555455555544555554444134445999**************996 PP

  == domain 5  score: -2.6 bits;  conditional E-value: 3
                                   TSBBSSSBTEEE-CGGGT CS
                          GIDA 349 tLetkkvkgLflAGqinG 366
                                   + ++ +vkg+++ G+++G
  gi|13540930|ref|NP_110618.1| 277 SRKMTSVKGVYAIGDVSG 294
                                   556778999999999999 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.1   2.9e-06    0.0022      19      79 ..       3      62 ..       1      77 [. 0.75
   2 !    8.2   0.5    0.0017       1.3      12      51 ..     154     191 ..     144     199 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2.9e-06
                                  EEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTTTTSTTBSEEEEE.TTTHHHHHH CS
                          Thi4 19 DvvivGaGssGLtaayylakkpdlkvailersvspGGGawlGGqlfsaivvr.kpakelLde 79
                                  D v+ GaG+ G +aa  l+++ + kvai+e+   +GG     G + s+ +++  ++ + L+e
  gi|13540930|ref|NP_110618.1|  3 DAVVLGAGPGGYAAAIRLGQR-KKKVAIIEKD-KIGGECLNYGCIPSKAIIElANSINYLKE 62
                                  89*******************.99******98.56666666666555555541444555555 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0017
                                   HHHHTEEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSS CS
                          Thi4  12 llkyaesDvvivGaGssGLtaayylakkpdlkvailersv 51 
                                   l +++ s +vi+G+G  G+  +  lak  + kv+i+e   
  gi|13540930|ref|NP_110618.1| 154 L-DHIPSSIVIIGGGYIGVEIGIALAKL-GSKVTIVEMMP 191
                                   4.456788*******************9.*******9765 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.2   1.4e-06    0.0011       1      36 [.       3      37 ..       3      47 .. 0.89
   2 !    7.9   0.6    0.0022       1.7       2      31 ..     161     190 ..     160     194 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.4e-06
                  FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGG 36
                                  D vV G+gp+G+aAAi   ++ +kv+++e+++ +GG
  gi|13540930|ref|NP_110618.1|  3 DAVVLGAGPGGYAAAIRLGQRKKKVAIIEKDK-IGG 37
                                  779**************************876.566 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0022
                  FAD_oxidored   2 vvVvGGgpaGvaAAiaAaraGakvlLveer 31 
                                   +v++GGg  Gv   ia a+ G kv +ve  
  gi|13540930|ref|NP_110618.1| 161 IVIIGGGYIGVEIGIALAKLGSKVTIVEMM 190
                                   8**************************965 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   0.1    0.0045       3.4       2      31 ..       5      34 ..       4      41 .. 0.93
   2 !   10.1   0.3   0.00097      0.72       1      43 [.     161     203 ..     161     214 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0045
                                  EEES-SHHHHHHHHHHHHTTEEEEEEESSH CS
                        TrkA_N  2 iiiGlGrvGrslaeeLseggkdvvvidkde 31
                                  +++G+G  G++ a +L +++k+v +i+kd+
  gi|13540930|ref|NP_110618.1|  5 VVLGAGPGGYAAAIRLGQRKKKVAIIEKDK 34
                                  8*****************8878******95 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00097
                                   EEEES-SHHHHHHHHHHHH.TTEEEEEEESSHHHHHHHHHTTSE CS
                        TrkA_N   1 iiiiGlGrvGrslaeeLse.ggkdvvvidkdeerveelreegle 43 
                                   i+iiG G +G ++   L + g+ +v++++  ++ +    +e ++
  gi|13540930|ref|NP_110618.1| 161 IVIIGGGYIGVEIGIALAKlGS-KVTIVEMMPSILPGTDNELVR 203
                                   89*****************777.6*****999888777776655 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.0    0.0013      0.95       3      33 ..       3      33 ..       1      35 [. 0.92
   2 !    8.5   0.5    0.0014         1       4      34 ..     161     191 ..     159     246 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0013
                                  EEEEE--SHHHHHHHHHHHHTTHHEEEEESS CS
                 FAD_binding_3  3 dVlIVGaGpaGlmlallLseaGvrvvlvekr 33
                                  d ++ GaGp G  +a  L ++  +v ++ek 
  gi|13540930|ref|NP_110618.1|  3 DAVVLGAGPGGYAAAIRLGQRKKKVAIIEKD 33
                                  7899*****************999*****96 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0014
                                   EEEE--SHHHHHHHHHHHHTTHHEEEEESSS CS
                 FAD_binding_3   4 VlIVGaGpaGlmlallLseaGvrvvlvekrs 34 
                                   ++I+G+G  G+  +  L++ G +v++ve + 
  gi|13540930|ref|NP_110618.1| 161 IVIIGGGYIGVEIGIALAKLGSKVTIVEMMP 191
                                   78*************************9875 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 ?   -0.2   0.2      0.87   6.5e+02       4      35 ..       5      36 ..       3      51 .. 0.83
   2 !   17.4   0.5   3.4e-06    0.0026       2      31 ..     160     189 ..     159     216 .. 0.94

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.87
                                  EEE--STTHHHHHHHHHHCTSEEEEE-S-HHH CS
                UDPG_MGDP_dh_N  4 sviGlGYvGlvtaavlaeighevigvDideek 35
                                  +v+G+G  G   a+ l ++ ++v ++ +d+  
  gi|13540930|ref|NP_110618.1|  5 VVLGAGPGGYAAAIRLGQRKKKVAIIEKDKIG 36
                                  5899*********************9999755 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 3.4e-06
                                   EEEEE--STTHHHHHHHHHHCTSEEEEE-S CS
                UDPG_MGDP_dh_N   2 kisviGlGYvGlvtaavlaeighevigvDi 31 
                                    i++iG GY+G+  +++la++g +v++v +
  gi|13540930|ref|NP_110618.1| 160 SIVIIGGGYIGVEIGIALAKLGSKVTIVEM 189
                                   599************************986 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.1    0.0055       4.1       1      40 [.       5      38 ..       5      56 .. 0.84
   2 ?   -1.4   0.0       2.7     2e+03     139     155 ..     118     134 ..     108     135 .. 0.81
   3 ?    0.8   0.7       0.6   4.4e+02       1      29 [.     162     185 ..     162     196 .. 0.79
   4 !   11.7   0.2   0.00026      0.19     102     155 ..     200     252 ..     199     253 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0055
                 NAD_binding_9  1 aivGaGprGlavlerLlarakkkspleitlfdpsepgagr 40
                                  ++ GaGp G a++ rL +r+      ++ +++++++g g 
  gi|13540930|ref|NP_110618.1|  5 VVLGAGPGGYAAAIRLGQRK-----KKVAIIEKDKIG-GE 38
                                  578***************95.....678888888887.54 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.7
                 NAD_binding_9 139 adgaslaadaVvLAlGh 155
                                    +++ l+ d++v+A+G 
  gi|13540930|ref|NP_110618.1| 118 VNDKVLETDSLVIATGS 134
                                   5678899********95 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.6
                 NAD_binding_9   1 aivGaGprGlavlerLlarakkkspleit 29 
                                   +i+G+G  G+ +  +L++        ++t
  gi|13540930|ref|NP_110618.1| 162 VIIGGGYIGVEIGIALAKLG-----SKVT 185
                                   7*************999984.....3333 PP

  == domain 4  score: 11.7 bits;  conditional E-value: 0.00026
                 NAD_binding_9 102 dlfeellarlpegvtvevhraevvdleeradgqavlladgaslaadaVvLAlGh 155
                                   +l++++++r++ ++ ++v++++ v  + ++++++v l+dg++l+a++V +++G 
  gi|13540930|ref|NP_110618.1| 200 ELVRHVVRRMS-QLGINVITGRKVLSTAKNGEVTVKLDDGQELRAEKVLMTVGR 252
                                   56788898886.589999999887778888889*******************95 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.81     6e+02       2      33 ..       1      30 [.       1      34 [. 0.80
   2 ?   10.6   0.0   0.00029      0.22     143     237 ..     119     202 ..     106     210 .. 0.77
   3 ?   -3.4   0.0       5.2   3.9e+03     135     160 ..     233     254 ..     219     255 .. 0.71

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.81
                   K_oxygenase  2 ilDligiGiGpsnLsLailleevkkelkalfl 33
                                  ++D +  G+Gp   + ai+l ++k  +k+  +
  gi|13540930|ref|NP_110618.1|  1 MYDAVVLGAGPGGYAAAIRLGQRK--KKVAII 30
                                  5899***************99999..444444 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00029
                   K_oxygenase 143 eeeelearnlvlgvGtepkiPevleklegkervvHsseylerkeellakkriaVvGsGqSaaeifedllrrqkkvelklvt 223
                                   + + le+ +lv+++G++p     ++ +   ++v+ + e+l      + + +i+++G+G  + ei   l++  +  ++++v 
  gi|13540930|ref|NP_110618.1| 119 NDKVLETDSLVIATGSKPV---SINGI---NDVMYNREVLDLD---HIPSSIVIIGGGYIGVEIGIALAKLGS--KVTIVE 188
                                   56778999999**999975...55554...5799999998775...799*******************99887..566666 PP

                   K_oxygenase 224 rsealeplddspfv 237
                                     +++ p  d ++v
  gi|13540930|ref|NP_110618.1| 189 MMPSILPGTDNELV 202
                                   66666666666665 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 5.2
                   K_oxygenase 135 veskdaegeeeelearnlvlgvGtep 160
                                   v+     ++ +el+a++++++vG  p
  gi|13540930|ref|NP_110618.1| 233 VK----LDDGQELRAEKVLMTVGRIP 254
                                   33....35678999999999999876 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   0.1       5.1   3.8e+03       4      31 ..       6      33 ..       4      35 .. 0.86
   2 ?   14.1   0.3   4.4e-05     0.033       2      52 ..     161     211 ..     160     246 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 5.1
                                  EE--SCCHHHHHHHHHHTT-EEEEE-S- CS
                       3HCDH_N  4 viGaGtmGagiaavfasagleVvlvdis 31
                                  v+GaG  G   a  + +++ +V +++ +
  gi|13540930|ref|NP_110618.1|  6 VLGAGPGGYAAAIRLGQRKKKVAIIEKD 33
                                  8999999999999999999999998865 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 4.4e-05
                                   EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTT CS
                       3HCDH_N   2 vaviGaGtmGagiaavfasagleVvlvdiseealekalekieksleklvek 52 
                                   + +iG G +G +i  ++a+ g +V++v++ +++l    +++ + + + +++
  gi|13540930|ref|NP_110618.1| 161 IVIIGGGYIGVEIGIALAKLGSKVTIVEMMPSILPGTDNELVRHVVRRMSQ 211
                                   789**************************9999988777776655555554 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.1     0.018        14       1      31 [.       3      31 ..       3      42 .. 0.86
   2 ?    6.8   0.6    0.0039       2.9       2      37 ..     161     194 ..     160     202 .. 0.91
   3 ?    2.7   0.0      0.07        53     113     140 ..     224     251 ..     197     276 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.018
                 Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvlie 31
                                  D vv GaGp g + A rl   + + kv +ie
  gi|13540930|ref|NP_110618.1|  3 DAVVLGAGPGGYAAAIRL--GQRKKKVAIIE 31
                                  789***************..66677777776 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0039
                 Lycopene_cycl   2 vvviGaGpAglslAarlteakpglkvvlieaspsll 37 
                                   +v+iG+G  g+ +   l  ak g kv+++e  ps+l
  gi|13540930|ref|NP_110618.1| 161 IVIIGGGYIGVEIGIAL--AKLGSKVTIVEMMPSIL 194
                                   89***************..***********999985 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.07
                 Lycopene_cycl 113 eeeeageslvvleggrkirarlvvdarg 140
                                     +++ge++v l++g+++ra  v+   g
  gi|13540930|ref|NP_110618.1| 224 STAKNGEVTVKLDDGQELRAEKVLMTVG 251
                                   3344589**************9998776 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0     0.025        19       3      46 ..       5      61 ..       3      77 .. 0.71
   2 ?    5.4   0.1     0.022        17       2      31 ..     161     190 ..     160     215 .. 0.88
   3 ?   -1.8   0.0       3.7   2.8e+03     127     152 ..     373     398 ..     340     400 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.025
                                  EEE--SHHHHHHHHHHHTTT--EEEE-S-H.............HHHHHHHHHSSBTT CS
                NAD_Gly3P_dh_N  3 avlGaGswGtalAkvlaenghevrlwvree.............elieeineehenvk 46
                                   vlGaG  G a A+ l+++ ++v ++ +++             + i e+ ++ +  k
  gi|13540930|ref|NP_110618.1|  5 VVLGAGPGGYAAAIRLGQRKKKVAIIEKDKiggeclnygcipsKAIIELANSINYLK 61
                                  59***********************99999777777777755533333333333334 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.022
                                   EEEE--SHHHHHHHHHHHTTT--EEEE-S- CS
                NAD_Gly3P_dh_N   2 iavlGaGswGtalAkvlaenghevrlwvre 31 
                                   i ++G+G  G  + ++la+ g++v++  + 
  gi|13540930|ref|NP_110618.1| 161 IVIIGGGYIGVEIGIALAKLGSKVTIVEMM 190
                                   89**********************997765 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 3.7
                                   EEEEESS--HHHHHTT--EEEEEEES CS
                NAD_Gly3P_dh_N 127 vavlsGpslAeEvakgkptavviask 152
                                    ++++G+ +A   a + ++++ +a++
  gi|13540930|ref|NP_110618.1| 373 KGIVTGAGIAAPHASELISEISLAVE 398
                                   68899999999999999999888865 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 ?    1.9   0.0      0.16   1.2e+02      32      61 ..       5      34 ..       3     132 .. 0.84
   2 ?   10.0   0.2   0.00052      0.39      28      65 ..     158     195 ..     154     234 .. 0.84
   3 ?   -2.1   0.0       2.6   1.9e+03      32      49 ..     375     392 ..     364     420 .. 0.74

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.16
                                  EEESTSHHHHHHHHHHHHTT-EEEEEESSH CS
                   AlaDh_PNT_C 32 lviGgGvaGlqAiatakglgakVtvlDvrp 61
                                  +v+G+G  G +A+    + + kV ++++++
  gi|13540930|ref|NP_110618.1|  5 VVLGAGPGGYAAAIRLGQRKKKVAIIEKDK 34
                                  89********99999999999999988876 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00052
                                   --EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHH CS
                   AlaDh_PNT_C  28 pakvlviGgGvaGlqAiatakglgakVtvlDvrparle 65 
                                   p+ +++iGgG  G++   + ++lg kVt++++ p+ l 
  gi|13540930|ref|NP_110618.1| 158 PSSIVIIGGGYIGVEIGIALAKLGSKVTIVEMMPSILP 195
                                   6899***********8888889********99887765 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 2.6
                                   EEESTSHHHHHHHHHHHH CS
                   AlaDh_PNT_C  32 lviGgGvaGlqAiatakg 49 
                                   +v G+G+a  +A +  ++
  gi|13540930|ref|NP_110618.1| 375 IVTGAGIAAPHASELISE 392
                                   677777777766554444 PP

>> CHB_HEX_C  Chitobiase/beta-hexosaminidase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00034      0.25      30      53 ..      61      83 ..      49     102 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00034
                     CHB_HEX_C 30 valPGltieYsldggetwqkytay 53
                                   ++PG++i Y +d ++ wq+++  
  gi|13540930|ref|NP_110618.1| 61 KEMPGVSINYNVDMKK-WQEWKWS 83
                                  589**********666.***9943 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0      0.31   2.3e+02      10      41 ..       4      44 ..       2     144 .. 0.70
   2 ?    8.2   0.2    0.0044       3.3       9      39 ..     160     190 ..     153     351 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.31
                 NAD_binding_7 10 vlvvGgGevAarkvrklleagakvtvvapev.........k 41
                                   +v G+G+ ++  + +l + ++kv ++ ++          +
  gi|13540930|ref|NP_110618.1|  4 AVVLGAGPGGYAAAIRLGQRKKKVAIIEKDKiggeclnygC 44
                                  5899***********************99965444444443 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0044
                 NAD_binding_7   9 kvlvvGgGevAarkvrklleagakvtvvape 39 
                                   +++++GgG ++ +    l++ g kvt+v   
  gi|13540930|ref|NP_110618.1| 160 SIVIIGGGYIGVEIGIALAKLGSKVTIVEMM 190
                                   689************************8654 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       7.4   5.5e+03       5      27 ..      15      36 ..      13      37 .. 0.80
   2 ?    9.7   0.1   0.00062      0.46     212     260 ..     205     250 ..     177     252 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 7.4
                                  HHHHHHHHTTEEEEEEESSSSSB CS
                 Amino_oxidase  5 aaArqLlsaGfdVtvlEardrvG 27
                                  aaA +L ++  +V ++E  d +G
  gi|13540930|ref|NP_110618.1| 15 AAAIRLGQRKKKVAIIEK-DKIG 36
                                  899999999999999996.4555 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00062
                                   HHHHHHHTTTTEEEETSEEEEEEEEETTCEEEEETTSTEEEESEEEE-S CS
                 Amino_oxidase 212 lpealaeelrgldirlntrVkeikregdgvtvtledgevveaDaVvvTv 260
                                   +++++++  +g ++ ++++V + ++ +++vtv+l dg++++a +V++Tv
  gi|13540930|ref|NP_110618.1| 205 VVRRMSQ--LGINVITGRKVLSTAK-NGEVTVKLDDGQELRAEKVLMTV 250
                                   4555555..999999999**99999.888*******************8 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.1   0.00081      0.61       3      38 ..       5      37 ..       3      56 .. 0.87
   2 ?    0.7   3.1      0.24   1.8e+02       2      34 ..     161     190 ..     160     229 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00081
                                  EEE--SHHHHHHHHHHHHHTTTSSEEEEEE-SSS-- CS
                Trp_halogenase  3 vivGGGtaGwlaAaalakalkgklevtlveseeigt 38
                                  v++G+G+ G+ aA+ l++      +v ++e+++ig 
  gi|13540930|ref|NP_110618.1|  5 VVLGAGPGGYAAAIRLGQRK---KKVAIIEKDKIGG 37
                                  89**************9988...56*********85 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.24
                                   EEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-S CS
                Trp_halogenase   2 ivivGGGtaGwlaAaalakalkgklevtlvese 34 
                                   ivi+GGG  G    +alak +    +vt+ve  
  gi|13540930|ref|NP_110618.1| 161 IVIIGGGYIGVEIGIALAKLG---SKVTIVEMM 190
                                   9*******************9...679999864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (436 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                        24  (0.00133861); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              24  [number of targets reported over threshold]
# CPU time: 0.65u 0.30s 00:00:00.95 Elapsed: 00:00:00.50
# Mc/sec: 2619.28
//
Query:       gi|13540931|ref|NP_110619.1|  [L=402]
Description: branched-chain alpha-keto acid dehydrogenase subunit E2 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-69  233.5   0.2      3e-69  233.0   0.2    1.2  1  2-oxoacid_dh     2-oxoacid dehydrogenases acyltransferase (ca
    3.2e-22   78.1   4.1    3.2e-22   78.1   4.1    2.0  2  Biotin_lipoyl    Biotin-requiring enzyme
    9.1e-16   57.9   0.7    2.3e-15   56.6   0.7    1.8  1  E3_binding       e3 binding domain
    6.8e-11   41.8   2.6    1.9e-06   27.6   0.1    2.5  2  Biotin_lipoyl_2  Biotin-lipoyl like
     0.0005   20.7   5.5      0.018   15.7   0.1    3.7  3  HlyD_3           HlyD family secretion protein
     0.0098   15.6   1.6       0.92    9.3   0.2    3.0  3  PTS_EIIA_1       phosphoenolpyruvate-dependent sugar phosphot
  ------ inclusion threshold ------
      0.033   13.4   2.2        2.1    7.5   0.0    2.6  3  HlyD_D23         Barrel-sandwich domain of CusB or HlyD membr
      0.044   13.7   1.4       0.12   12.2   0.5    2.1  2  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 !  233.0   0.2   1.4e-72     3e-69       4     232 ..     184     399 ..     181     400 .. 0.96

  Alignments for each domain:
  == domain 1  score: 233.0 bits;  conditional E-value: 1.4e-72
                                   XXXXXXXXXXXXXXXXXXXXX.XXXEEEEEEEEE-HHHHHHHHHHHHHHHHTT-----HHHHHHHHHHHHHHH-GGGG-EE CS
                  2-oxoacid_dh   4 eervplsgirkaiakrlteskqeiphftlsdevdvtallelrkelkekeakeekakltlldflikavalAlkefPelnasv 84 
                                   ee  ++ g+r++i++++t++kq +phft++++vdvt ++++ ++ k++ +     k+t++ +++++v + lk++P lna +
  gi|13540931|ref|NP_110619.1| 184 EEILEMHGLRRIIFDKMTKAKQIMPHFTVVEKVDVTGMISIIESAKSSGK-----KVTITGYIARIVPIVLKQYPYLNAIY 259
                                   67789******************************************998.....9************************* PP

                                   .EESEEEE--SS--EEEE--------EEEE--GGG--HHHHHHHHHHHHHHHTTT---GGGTSS-SEEEE----------- CS
                  2-oxoacid_dh  85 deeekeivvkkhvniGvAvatprGLlvPviknadkkslleiakelkelaekaregklkpedleggtftisNlGmlGvtsft 165
                                   de + ++ +kk++niG+Av+tp+GL v v+k+ad+ks++ei +e+++ ae+ar+++lk ++++++tfti+N+G++G+  +t
  gi|13540931|ref|NP_110619.1| 260 DEANRRYLIKKYYNIGIAVDTPDGLNVFVVKDADRKSMYEITAEITDKAERARNNQLKIDEVQDSTFTITNVGTIGGVLST 340
                                   ********************************************************************************* PP

                                   ----TT-SEEEEE---.B--TTSTT-HT---EEEEEEEEETTT--HHHHHHHHHHHHHTT-HHXXXX CS
                  2-oxoacid_dh 166 PiinppqvaIlgvgrikerpvvkegelvvrkvmtlslsaDHRvidGaeaarFlntlkkllenpeell 232
                                   Piin+p+vaIlgv+r+      ++g    +k+m+lsls+DHR+idGa a rF+ +lkk++e+p++l+
  gi|13540931|ref|NP_110619.1| 341 PIINYPEVAILGVHRVM----DENG----KKIMYLSLSCDHRLIDGAVATRFIMDLKKIIEDPNSLI 399
                                   ****************4....3444....69********************************9985 PP

>> Biotin_lipoyl  Biotin-requiring enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.1   4.1   1.4e-25   3.2e-22       2      73 .]       5      77 ..       4      77 .. 0.98
   2 ?   -2.4   0.1       1.9   4.3e+03      35      63 ..     224     234 ..     209     244 .. 0.49

  Alignments for each domain:
  == domain 1  score: 78.1 bits;  conditional E-value: 1.4e-25
                                  EEEESSSEEEEEE..ECSESSSTTCEE-TTSEEEEEECTTEEEEEEBSSSEEEEEESSTTTEEE-TTCEEEEE CS
                 Biotin_lipoyl  2 eiksPmiGesveeg.vvevlvkvGdkVkagqvlaeveamKmemeieapkaGvvkeilvkeGdtvevgdllaki 73
                                  e+k+P+iGe v+eg +v++ v++Gd+Vk++q l+ev ++K++++i++p++G++++il+keG+ v vg+ l++i
  gi|13540931|ref|NP_110619.1|  5 EFKLPDIGEGVTEGeIVKWDVAEGDEVKKDQDLVEVMTDKVTVKIPSPVNGKISKILYKEGQVVPVGSTLVQI 77
                                  79********************************************************************987 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.9
                                   EEECTTEEEEEEBSSSEEEEEESSTTTEE CS
                 Biotin_lipoyl  35 eveamKmemeieapkaGvvkeilvkeGdt 63 
                                   ++e+ K                  ++G++
  gi|13540931|ref|NP_110619.1| 224 IIESAK------------------SSGKK 234
                                   333333..................33444 PP

>> E3_binding  e3 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.6   0.7     1e-18   2.3e-15       1      35 [.     115     149 ..     115     150 .. 0.96

  Alignments for each domain:
  == domain 1  score: 56.6 bits;  conditional E-value: 1e-18
                                   SBE-HHHHHHHHHCT--TTTS---CTTTBE-HHHH CS
                    E3_binding   1 vlAsPaaRklAkelGidLsdvkGtGpgGRItkeDV 35 
                                   vlAsPa+R++A+e+GidL++vkGtG +GR+t +D 
  gi|13540931|ref|NP_110619.1| 115 VLASPAVRRIARENGIDLAKVKGTGDNGRVTLDDL 149
                                   79*****************************9996 PP

>> Biotin_lipoyl_2  Biotin-lipoyl like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.3   1.6e-05     0.035      10      32 ..      17      39 ..      14      44 .. 0.90
   2 !   27.6   0.1   8.5e-10   1.9e-06       3      47 ..      47      91 ..      39      94 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.6e-05
               Biotin_lipoyl_2 10 sGrVaqlnVkdGqrVkaGdvLae 32
                                   G ++++ V +G++Vk+ + L+e
  gi|13540931|ref|NP_110619.1| 17 EGEIVKWDVAEGDEVKKDQDLVE 39
                                  699****************9987 PP

  == domain 2  score: 27.6 bits;  conditional E-value: 8.5e-10
               Biotin_lipoyl_2  3 vsIaapvsGrVaqlnVkdGqrVkaGdvLaelDsralqlalaqaea 47
                                  v+I +pv+G++++++ k+Gq+V  G +L+++D+ +   ++  ae+
  gi|13540931|ref|NP_110619.1| 47 VKIPSPVNGKISKILYKEGQVVPVGSTLVQIDTGEETSQQTMAEE 91
                                  99******************************9888777777776 PP

>> HlyD_3  HlyD family secretion protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.2     0.021        46       7      39 ..      17      48 ..      15      50 .. 0.85
   2 !   15.7   0.1   8.1e-06     0.018       2      30 ..      49      77 ..      48      90 .. 0.92
   3 ?    0.7   0.0      0.38   8.4e+02      63      84 ..     231     252 ..     214     270 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.021
                        HlyD_3  7 dGvvvelnveegevvqagdelleiippdtllve 39
                                   G++v+++v eg+ v + + l+e++ +d++ v+
  gi|13540931|ref|NP_110619.1| 17 EGEIVKWDVAEGDEVKKDQDLVEVM-TDKVTVK 48
                                  599*********************9.5665554 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 8.1e-06
                        HlyD_3  2 lrApvdGvvvelnveegevvqagdellei 30
                                  + +pv G+++++ ++eg+vv+ g +l++i
  gi|13540931|ref|NP_110619.1| 49 IPSPVNGKISKILYKEGQVVPVGSTLVQI 77
                                  669************************99 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.38
                        HlyD_3  63 qgsdytlkgkierisptvdakt 84 
                                   +g++ t++g i ri p v ++ 
  gi|13540931|ref|NP_110619.1| 231 SGKKVTITGYIARIVPIVLKQY 252
                                   57888**********9998843 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 !    9.3   0.2   0.00041      0.92      80     111 ..      17      48 ..      11      54 .. 0.87
   2 ?    4.5   0.0     0.012        27      80     105 ..      54      79 ..      46      89 .. 0.82
   3 ?   -1.7   0.0         1   2.3e+03      12      28 ..     316     332 ..     314     338 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00041
                                   TTTTEEES----SEE-SEEEEEEE-HHHHGGG CS
                    PTS_EIIA_1  80 kgegFellvkegdkVkagdklvevdleaikka 111
                                   +ge  +  v+egd+Vk+ + lvev  ++++ +
  gi|13540931|ref|NP_110619.1|  17 EGEIVKWDVAEGDEVKKDQDLVEVMTDKVTVK 48 
                                   78999999****************99998765 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.012
                                   TTTTEEES----SEE-SEEEEEEE-H CS
                    PTS_EIIA_1  80 kgegFellvkegdkVkagdklvevdl 105
                                   +g+  ++l keg+ V  g++lv++d 
  gi|13540931|ref|NP_110619.1|  54 NGKISKILYKEGQVVPVGSTLVQIDT 79 
                                   88999999999999999999999996 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 1
                                   EEGGGSSSHHHHT-TTS CS
                    PTS_EIIA_1  12 vpleevpDevfaekmlG 28 
                                   ++++ev+D +f    +G
  gi|13540931|ref|NP_110619.1| 316 LKIDEVQDSTFTITNVG 332
                                   5799*******877776 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 ?    5.0   0.1    0.0056        13      26      54 ..      16      43 ..      12      47 .. 0.82
   2 ?    7.5   0.0   0.00094       2.1     108     140 ..      46      78 ..      42      83 .. 0.84
   3 ?   -3.0   0.0       1.6   3.5e+03      99     115 ..     200     216 ..     177     245 .. 0.55

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0056
                                  XXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                      HlyD_D23 26 veGwveklyvnatgdkVkkGqpLaelysp 54
                                  +eG + k +v  +gd+Vkk+q L+e+   
  gi|13540931|ref|NP_110619.1| 16 TEGEIVKWDVA-EGDEVKKDQDLVEVMTD 43
                                  57888888888.99999999999998765 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.00094
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                      HlyD_D23 108 tvtvkapisGvVteknvreGqyvqpgdtlftia 140
                                   tv++ +p++G + +    eGq+v  g+tl++i 
  gi|13540931|ref|NP_110619.1|  46 TVKIPSPVNGKISKILYKEGQVVPVGSTLVQID 78 
                                   678889999999999999999999999999985 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 1.6
                                   XXXXXXXXXXXXXXXXX CS
                      HlyD_D23  99 lektgkvqktvtvkapi 115
                                   ++k +++ +++tv  ++
  gi|13540931|ref|NP_110619.1| 200 MTKAKQIMPHFTVVEKV 216
                                   55555555555543322 PP

>> GCV_H  Glycine cleavage H-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.5   5.4e-05      0.12      31      73 ..      18      59 ..      13      95 .. 0.91
   2 ?   -1.2   0.0       0.8   1.8e+03      43      62 ..     214     233 ..     205     256 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 5.4e-05
                                  -SEEEEE---TT-EE-TT-EEEEEEESS-EEEEE-SSSEEEEE CS
                         GCV_H 31 gdvvfvelpevgtkvkkgeslaavEsvKaasevyapvsGevve 73
                                  g++v  ++  +g++vkk+++l  v + K + ++++pv+G++ +
  gi|13540931|ref|NP_110619.1| 18 GEIVKWDVA-EGDEVKKDQDLVEVMTDKVTVKIPSPVNGKISK 59
                                  666666665.69****************************975 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.8
                                   -EE-TT-EEEEEEESS-EEE CS
                         GCV_H  43 tkvkkgeslaavEsvKaase 62 
                                   +kv+    ++++Es K+ ++
  gi|13540931|ref|NP_110619.1| 214 EKVDVTGMISIIESAKSSGK 233
                                   56667777889999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (402 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       814  (0.0454013); expected 358.6 (0.02)
Passed bias filter:                      581  (0.0324056); 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: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 2531.78
//
Query:       gi|13540932|ref|NP_110620.1|  [L=319]
Description: thiamine pyrophosphate-dependent dehydrogenase, E1 component beta subunit [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-48  165.1   0.0    1.7e-48  164.7   0.0    1.2  1  Transket_pyr     Transketolase, pyrimidine binding domain
    4.2e-37  126.8   0.1      1e-36  125.5   0.0    1.7  2  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 !  164.7   0.0   1.9e-52   1.7e-48       5     176 ..       3     175 ..       1     177 [. 0.98

  Alignments for each domain:
  == domain 1  score: 164.7 bits;  conditional E-value: 1.9e-52
                                   HHHHHHHHHHHHHCTTTTEEEEESSTH..HHHTTCHCCHHEGGTTEGEEE--S-HHHHHHHHHHHHHHCTTEEEEEEEEHH CS
                  Transket_pyr   5 wrkaeaealaellkedpevvligaDva..ggtfsvrkgllhdqgegrvidsgisEqavlgfavGaalagpllviveaqFgd 83 
                                   + +a+++a++  ++ed++vv++g+Dv+  gg+f v+ gll + g++rvid++++E +++g+a+G+a++g l++i e+qF d
  gi|13540932|ref|NP_110620.1|   3 IVQALNNAMDIKMAEDNDVVVLGEDVGkdGGVFRVTDGLLAKYGPERVIDTPLTELGIVGMAIGMAVNG-LKPIPEIQFQD 82 
                                   6789*****************************************************************.9********** PP

                                   HHGGG..HHGGHHHHHCHHHHHT--EEEEESBSGGGSTTGTTTSBSSHHHHHHTSTTEEEE--SSHHHHHHHHHHHHHSSS CS
                  Transket_pyr  84 FangA..qiyadqairsgeakgklkvgvvtrlpigvgedGpehqsaeleaflrlipglkvvrPsdpaetkhllrrairred 162
                                   F+ +A  qi+++ a+++++++g ++v++v+r+p+g g +G   +s++ e ++++++gl+vv Ps+p+++k+ll   i+  +
  gi|13540932|ref|NP_110620.1|  83 FIYTAmdQIINQMAKIRYRSGGDYTVPLVLRTPVGGGIKGGLYHSQSGETYFAHTAGLTVVSPSNPYDAKGLLISSIE--S 161
                                   ******************************************************************************..6 PP

                                   .SEEEEEE-SSEEC CS
                  Transket_pyr 163 rkPvvlrlpksllr 176
                                   ++Pv++++pk+l+r
  gi|13540932|ref|NP_110620.1| 162 PDPVIFLEPKRLYR 175
                                   78***********9 PP

>> Transketolase_C  Transketolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0      0.48   4.3e+03      54      76 ..      12      34 ..       2      37 .. 0.75
   2 !  125.5   0.0   1.1e-40     1e-36       2     124 .]     192     308 ..     191     308 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.48
                                  HHHHHHHHSEEEEEEEEESTTSH CS
               Transketolase_C 54 ilesvkktgrlvvveeavkrgGi 76
                                    ++++  + +v+ e+  k gG+
  gi|13540932|ref|NP_110620.1| 12 DIKMAEDNDVVVLGEDVGKDGGV 34
                                  44678888889999999888886 PP

  == domain 2  score: 125.5 bits;  conditional E-value: 1.1e-40
                                   EEEEEETTSSEEEEEETTHHHHHHHHHHHHHTTTTCEEEEE-SEEESHHHHHHHHHHHHHSEEEEEEEEESTTSHHHHHHH CS
               Transketolase_C   2 kaeilregkdvtlvayGsmveealeAaeeLekegisaeVvdlrtvkplDketilesvkktgrlvvveeavkrgGigsevaa 82 
                                   ka++lreg+ vtlv+yGsmv+++l  ++   k+gi+a+Vvdlrt+ plDk+ti +svkktgr+v+v+ea ++ G+g+ev+a
  gi|13540932|ref|NP_110620.1| 192 KANLLREGNSVTLVTYGSMVPTVLSTVD---KNGIDADVVDLRTIAPLDKDTIISSVKKTGRVVIVHEAPRTLGVGAEVSA 269
                                   899*********************9985...67************************************************ PP

                                   HHHHCCCTTCSSEEEEEEE-SSSSSSGHHHHHHHTT-SHHHH CS
               Transketolase_C  83 alaeeafdgldapvkrvggpdviepgsaeelekafgldaeki 124
                                   +++e+a+++l ap++r++gpd++ p+    le++++++ ++i
  gi|13540932|ref|NP_110620.1| 270 MISERAIEYLYAPILRITGPDTPFPYR---LEDYYLPNEQRI 308
                                   **********************55555...********9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 2486.48
//
Query:       gi|13540933|ref|NP_110621.1|  [L=337]
Description: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit [Thermoplasma volcanium GSS1]
Scores for complete 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-86  289.0   0.0    3.5e-86  288.9   0.0    1.0  1  E1_dh            Dehydrogenase E1 component
    9.8e-07   28.7   0.4    4.4e-05   23.3   0.2    2.5  2  TPP_enzyme_C     Thiamine pyrophosphate enzyme, C-terminal TP
     0.0083   15.4   0.0      0.015   14.5   0.0    1.4  1  DXP_synthase_N   1-deoxy-D-xylulose-5-phosphate synthase
  ------ inclusion threshold ------
       0.01   16.2   0.0      0.021   15.2   0.0    1.5  1  Penicillinase_R  Penicillinase repressor


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 !  288.9   0.0   7.8e-90   3.5e-86       3     297 ..      19     310 ..      17     313 .. 0.97

  Alignments for each domain:
  == domain 1  score: 288.9 bits;  conditional E-value: 7.8e-90
                                   HHHHHHHHHHHHHHHHTTSS-S-----TT-HHHHHHHHHTS-TTSEEEESS--HHHHHHTT--HHHHHHHHTT-TTTSSGT CS
                         E1_dh   3 lvllrrvedaldalykrkkrigfyhlsagqealkvgiaaalekeDliiteYReagvllarglsleeilaeltgkvkgkggs 83 
                                   +++l r++d++ + ++r++ +gfy +++gqea++ g+a+al k+Dl+  +YR+   l++ g+++e+i+ +++g++++ +++
  gi|13540933|ref|NP_110621.1|  19 SMVLGRLFDKKVITAQRQGLVGFYTPMMGQEATQAGAAMALSKQDLVYGYYRDVTLLIYLGYPIEKIFDQIMGNAEDTSKG 99 
                                   6999***************************************************************************** PP

                                   T-..-E..BTT..BEEE-SSTTTHHHHHHHHHHHHHHHTS---EEEEEEGGGTT-HHHHHHHHHHHHTT--EEEEEEEESE CS
                         E1_dh  84 rh.elmyaekesrilggngivgaqvplvaGialaakiegkkevailliGDgAanqGdvyealnlaalwklpvifvveNNky 163
                                   r+ + +y++k ++++   ++v+++ pl+ G+a+a+k+++++ ++i+ +GDg+++  d+++a+n+a++++lpv+f +eNN++
  gi|13540933|ref|NP_110621.1| 100 RQmPSHYSAKAVNFMSVPSPVATNLPLAVGAAYAKKYRKEDGIVITSFGDGGTSTPDFHAAMNFASVYDLPVVFLCENNGW 180
                                   ********************************************************************************* PP

                                   ETTEEHHHH-S---GGG..TTTTS-EEEEETTSHHHHHHHHHHHHHHHHTTT--EEEEEEE--SS-SSTTSHSHSSSHHHH CS
                         E1_dh 164 gisTeaekasaskeladrargvgipglrVdgnDplavyeAvkfAaeraregkgpllielvtYRyggHsesDdpstyrtree 244
                                   +is ++e++++++ ++++a ++g+ g+ VdgnD++  y+Avk+A+e+ar+g  p+l+e+ +YR+g+Hs+sDdps+yr ++e
  gi|13540933|ref|NP_110621.1| 181 AISFPVERQTKAE-IYKKAEAYGMKGVYVDGNDFIKTYNAVKEAVEYARSG-NPILVEARSYRMGPHSTSDDPSKYR-QNE 258
                                   **********986.5666********************************6.6************************.*** PP

                                   HHHHHHHH-HHHHHHHHHHHTTSS-HHHHHHHHHHHHHHHHHHHHHHHHS--- CS
                         E1_dh 245 veevrkkkdpiqrlkelLvkkgvvseeelkeiekevrkeveeavkkaeskkel 297
                                   v+e +++ dp+ + ++++++kg++s+ e+++i++e rk+++e +++  + + +
  gi|13540933|ref|NP_110621.1| 259 VKEGDEN-DPLVIAEKAVISKGILSQSEVNRIKDESRKMIDEKFEERLKIPAP 310
                                   **99998.************************************986665555 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 !   23.3   0.2   9.8e-09   4.4e-05      30     152 ..     120     236 ..      99     237 .. 0.76
   2 ?   -3.2   0.0       1.4   6.2e+03     106     143 ..     260     297 ..     240     304 .. 0.55

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 9.8e-09
                                   TTTHHHHHHHHHHH....STTSEEEEEEEHHHHHHT.GGGHHH.HHHTT-SEEEEEEE-SBCCCHHHHHHHHTCCTTTTSB CS
                  TPP_enzyme_C  30 mGyglpaAiGakla....kpdrevvaivGDGgflmi.lqelat.avrrnlpitvvvlnNegygmtggqqepfggkrksgpa 104
                                       lp A+Ga+ a    k+d  v+   GDGg+    +++ ++ a  ++lp+++++ nN++         +f  +r     
  gi|13540933|ref|NP_110621.1| 120 VATNLPLAVGAAYAkkyrKEDGIVITSFGDGGTSTPdFHAAMNfASVYDLPVVFLCENNGWAI-------SFPVER----- 188
                                   5667999999999645435678**********999996555551667899*999999998762.......222222..... PP

                                   B.BS----HHHHHHHTTSEEEEESSH.HHHHHHHHHHHH...CSSSEEEEE CS
                  TPP_enzyme_C 105 gkdlkpvdfaklaealGakgarvekadveeleealkeal...ekkgpalie 152
                                      +++  + k aea+G+kg++v+ +d  ++ +a+kea+   +++ p l+e
  gi|13540933|ref|NP_110621.1| 189 ---QTKAEIYKKAEAYGMKGVYVDGNDFIKTYNAVKEAVeyaRSGNPILVE 236
                                   ...233467788*******999999999999******99777777788876 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.4
                                   .BS----HHHHHHHTTSE.EE.EESSH.HHHHHHHHHHHH CS
                  TPP_enzyme_C 106 kdlkpvdfaklaealGak.ga.rvekadveeleealkeal 143
                                   k++++ d+  +ae + ++ g+ +  +++v+ +++  ++++
  gi|13540933|ref|NP_110621.1| 260 KEGDENDPLVIAEKAVISkGIlS--QSEVNRIKDESRKMI 297
                                   24555577778877766655542..444455555555444 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 !   14.5   0.0   3.3e-06     0.015     114     179 ..     121     186 ..     114     242 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.3e-06
                DXP_synthase_N 114 stsisaalGlavardlkgekkkvvaviGDgaltgGmafealnnigelkkkllvilNdNemsisknv 179
                                   +t +  a+G a a+++++e+  v++  GDg+ ++   + a+n ++  +  ++ +  +N ++is +v
  gi|13540933|ref|NP_110621.1| 121 ATNLPLAVGAAYAKKYRKEDGIVITSFGDGGTSTPDFHAAMNFASVYDLPVVFLCENNGWAISFPV 186
                                   688999*******************************************************99887 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.0   4.7e-06     0.021      40      79 ..      20      59 ..       3      70 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 4.7e-06
                                  HHHHHHHHTTS-EEEEETTEEEEE----XXXXXXXXXXXX CS
               Penicillinase_R 40 tllrrLvkKgllsrekegrafiYsplvseeeavasavkql 79
                                   +l+rL +K++++++++g    Y+p + +e  +a+a+  l
  gi|13540933|ref|NP_110621.1| 20 MVLGRLFDKKVITAQRQGLVGFYTPMMGQEATQAGAAMAL 59
                                  689***************************9999887655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       604  (0.0336884); expected 358.6 (0.02)
Passed bias filter:                      538  (0.0300073); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.41
# Mc/sec: 2457.73
//
Query:       gi|13540934|ref|NP_110622.1|  [L=291]
Description: methionine aminopeptidase [Thermoplasma volcanium GSS1]
Scores for complete 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-40  137.8   0.0    4.3e-40  137.6   0.0    1.1  1  Peptidase_M24  Metallopeptidase family M24


Domain annotation for each model (and alignments):
>> Peptidase_M24  Metallopeptidase family M24
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.6   0.0   2.4e-44   4.3e-40       3     207 ..       9     280 ..       7     282 .. 0.78

  Alignments for each domain:
  == domain 1  score: 137.6 bits;  conditional E-value: 2.4e-44
                                   HHHHHHHHHHHHHHHHHHHHTTCBHHHHHHHHHHHHHHHTTTCEESSSSEEEEGGGGGSTTTBC...SSSB--TTEEEEEE CS
                 Peptidase_M24   3 irkaariasaaleavleaikpgvterelaaeieattlkrhgarglafppivasgenaavlhytp...ndrvlkegdlvlid 80 
                                   + +a+ri ++ale + + i+pg++  ++a+++e++ ++++ + ++afp  v +++n++++hytp   +++v+k gd+v++d
  gi|13540934|ref|NP_110622.1|   9 YIEAGRIGREALELARTLIEPGTKLLDVAEAMEKF-VIEQ-GAKPAFP--VNLSINNDAAHYTPasgDKKVFKTGDVVKVD 85 
                                   679************999***************99.4554.5689***..9999999999****9988899********** PP

                                   EEEEETTEEEEEEEEEECSSGSHHHHHHHHHHHHHHHHHHHC-STTSBHHHHHHHHHHHHHHTTBCCGBSSCSEEEESS.S CS
                 Peptidase_M24  81 agaeydgyasDitrTvlvGkftpeqrelyeavleaqeaaikavkpGvtlseidaaarevlesaglakffphglGHgvGl.e 160
                                   +ga++dgy+sD++ T+ vG ++ ++ +l++a++ea++aai++v+p ++++ei+  + +v+ s g+ k+++++ GHgv + +
  gi|13540934|ref|NP_110622.1|  86 FGAHIDGYMSDTAITLEVG-ESGKHSDLIDATREALDAAISLVRPMRSVNEIGGRIADVIGSFGF-KPVRNLGGHGVERyD 164
                                   ****************998.4567999**************************************.************99* PP

                                   SSEEEEEESS.STTCSSB--TTBEEEEEE...............EEEEETTT............................. CS
                 Peptidase_M24 161 vhdegpsvsr.esndgrkleeGmvftiEp...............giyfapge............................. 196
                                   +h    ++++ + ++ ++l++ + ++iEp                                                    
  gi|13540934|ref|NP_110622.1| 165 LHAT-LFIPNyDDGNVVRLQPDHAIAIEPfastgigmihsgppgN------Iyildapkvredeviyknfrtlpfaerwla 238
                                   **98.7776533447999***********8888554333333332......033333333444445555555555555566 PP

                                   ..............................E.EEEEBEEEEE CS
                 Peptidase_M24 197 ..............................g.gvriedtvlv 207
                                                                     + e+t+lv
  gi|13540934|ref|NP_110622.1| 239 glvedhktylksmvssrevspfpilrehnnTlISQAEHTILV 280
                                   666666666666666666666666666666336666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       297  (0.0165653); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1814.51
//
Query:       gi|13540935|ref|NP_110623.1|  [L=225]
Description: hypothetical protein TVN0104 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-47  161.6   0.1    1.8e-47  161.2   0.1    1.0  1  DUF3834   Protein of unknown function (DUF3834)


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 !  161.2   0.1     1e-51   1.8e-47       7     200 ..       6     195 ..       2     196 .. 0.95

  Alignments for each domain:
  == domain 1  score: 161.2 bits;  conditional E-value: 1e-51
                       DUF3834   7 P..GPVsyPliaatmkkkdiel..kfekeesadvvlDsivslvkrglridlvvikkllviipkigkekIavwrkGsaaDvl 83 
                                   P  GPVs+Pl++   ++  + +   +++ +++dvvlDsi+++ k+gl+i ++v +++++i ++  + +I+++rkG++aD++
  gi|13540935|ref|NP_110623.1|   6 PfaGPVSFPLLVI-EEELPFRIhnICSETGKFDVVLDSITNMPKYGLKIFAGVRIDMYSILGDESSGRIYTLRKGTLADFN 85 
                                   555********98.66777888879******************************************************** PP

                       DUF3834  84 lrilldlkkikaevvyaddpeevlkllnegevdsavvaselkkgeafedllkklgvyvpGsCgaavkeneeefidaYeeGI 164
                                   +ril+     ka+v++a d ++ +k++neg    a+v++e++ g++f + +k+lg+ +p sC +a+    +e+i+aYe+GI
  gi|13540935|ref|NP_110623.1|  86 ARILAYYD--KAQVINA-DGDTCIKMANEGYS--ALVGNEISIGKSFRNRMKELGLDLP-SCAMASTRRIDEVIEAYEQGI 160
                                   ****9954..6******.99**********76..*************************.********************* PP

                       DUF3834 165 elikedpeeaaeyiaskLpikidkefiknilknael 200
                                   ++ik++ e+aae+i++k + ++++e++k+i+  + +
  gi|13540935|ref|NP_110623.1| 161 DFIKNNHERAAEIISKK-SGYYSEEVMKKIIGIYGH 195
                                   *****************.*************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); 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 0.28s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1518.04
//
Query:       gi|13540936|ref|NP_110624.1|  [L=86]
Description: hypothetical protein TVN0105 [Thermoplasma volcanium GSS1]
Scores for complete 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   72.8   3.5    2.3e-20   72.6   3.5    1.1  1  CRISPR_Cas2     CRISPR associated protein Cas2
     0.0064   16.5   0.0     0.0067   16.5   0.0    1.1  1  Cas_Cas2CT1978  CRISPR-associated protein (Cas_Cas2CT1978)
  ------ inclusion threshold ------
      0.051   13.4   0.0      0.056   13.3   0.0    1.1  1  RhoGAP          RhoGAP domain


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 !   72.6   3.5   3.8e-24   2.3e-20       1      73 [.       1      69 [.       1      71 [. 0.96

  Alignments for each domain:
  == domain 1  score: 72.6 bits;  conditional E-value: 3.8e-24
                                  EEEEEEEECHCHHHHHHHHHHHHHHTTEEEEETTEEEEEESHHHHHHHHHHHHHHSHTTTCEEEEEEEETCHH CS
                   CRISPR_Cas2  1 mlvlvvYDikedrkrrrkvakilkkyGfqrvQySVFegelseaqleklkkrlkkiidpeedsiriykltekqf 73
                                  m+++vvYD+  d+ r++kv k+lk+y + + Q+SVFege+se+ ++ ++k + kii++e dsi+iyk++ k++
  gi|13540936|ref|NP_110624.1|  1 MYLIVVYDV--DESRVNKVNKYLKRY-LLWRQNSVFEGEISENLIDSMIKGITKIIKDE-DSIIIYKFKVKSY 69
                                  99*******..***************.******************************88.*******987765 PP

>> Cas_Cas2CT1978  CRISPR-associated protein (Cas_Cas2CT1978)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   1.1e-06    0.0067      13      75 ..      17      79 ..       1      85 [. 0.85

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.1e-06
                                  HHHHHHHHSEEEETTEEEEEE-HHHHHHHHHHHHHH-TSSEEEEEEE-SSSSSEEEEEESTTS CS
                Cas_Cas2CT1978 13 lRGeLtrwllEvragVyvgrvsarVreklwerveekieegsavmvysanneqgfeirtlGetr 75
                                  +  +L+r ll  + +V+ g++s++  +++++ +++ i+++  +++y+ + +++++  ++G+++
  gi|13540936|ref|NP_110624.1| 17 VNKYLKRYLLWRQNSVFEGEISENLIDSMIKGITKIIKDEDSIIIYKFKVKSYIDNIIIGNDK 79
                                  5668999****************************************9999999998888876 PP

>> RhoGAP  RhoGAP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   9.3e-06     0.056      47      83 ..       8      44 ..       3      69 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 9.3e-06
                                  TTTTSCHHHHHHHHHHHHHHSSSTTTTGGHHHHHHHH CS
                        RhoGAP 47 dleeedvhavaslLKrfLrelpepLltkelyeeliea 83
                                  d++e  v++v + LKr+L   +++++  e+ e+li+ 
  gi|13540936|ref|NP_110624.1|  8 DVDESRVNKVNKYLKRYLLWRQNSVFEGEISENLIDS 44
                                  678999***************************9953 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       693  (0.0386525); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.30s 00:00:00.73 Elapsed: 00:00:00.48
# Mc/sec: 534.42
//
Query:       gi|13540937|ref|NP_110625.1|  [L=322]
Description: hypothetical protein TVN0106 [Thermoplasma volcanium GSS1]
Scores for complete 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-73  246.2   0.1    4.1e-73  246.0   0.1    1.1  1  Cas_Cas1   CRISPR associated protein Cas1
  ------ inclusion threshold ------
       0.11   12.6   0.3       0.65   10.2   0.1    2.2  3  Tubulin_C  Tubulin C-terminal 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 !  246.0   0.1   4.5e-77   4.1e-73       2     283 .]       5     279 ..       4     279 .. 0.96

  Alignments for each domain:
  == domain 1  score: 246.0 bits;  conditional E-value: 4.5e-77
                                   EEESTEEEEEEETTEEEEEESSEEEEEEECCCEEEEEEESTEEEEHHHHHHHHHTT-EEEEE-TTS-EEEEEEE.SSSSTH CS
                      Cas_Cas1   2 yvteqgaylrkkgerlvvekegeekkeiplediesivifgevslstkalrllaekgipvvflsengkylgrlep.eesgnv 81 
                                   y+t++g+ ++++g++l++   +  k+++p+ ++++i+i  +vsls+ al +l++ gi v+++s ngky+++l+p ++++ +
  gi|13540937|ref|NP_110625.1|   5 YITQDGT-ITREGNTLYFIGPDF-KRHLPVMNVQEIIISAKVSLSSWALDYLSKLGIIVHIISTNGKYMSSLIPgNRNERG 83 
                                   9******.************988.9******************************************************** PP

                                   HHHHHHHHHHHSHHHHHHHHHHHHHHHHHHHHHHHHHCCHHCTTHHHHCHCHHHHHHHHHHHH-HSHHHHHHHHHHHHHHH CS
                      Cas_Cas1  82 elrraQyraaddeekrlelakkivagklenqrkvlrrlkrdreeeeleeaieeleelleklekaesleeLrgiEGeaakaY 162
                                   ++ ++Q++a+ +++ r+++a ++v+g  +n+ ++lr+++ ++   e+++ i+ +e++  +  + +++++++g+EG+++++Y
  gi|13540937|ref|NP_110625.1|  84 NTTVQQVKAYLSDK-RFKIAAEMVNGIKNNILANLRYYSDNN---EITKYIKAIESYNPDY-NSNDINKILGVEGNIWSTY 159
                                   ***********987.***********************9999...9*********966665.568**************** PP

                                   HHHHHHHCSCGGS-SS-SSSS-SSHHHHHHHHHHHHHHHHHHHHHHTSS--TT--SSS--TTSS-HHHHHHHHHHHHHHCH CS
                      Cas_Cas1 163 feafdkllkeefefegRsrrppkDpvNalLsfgYtllysevlsaieavgLdPyiGfLHedrpgrpsLalDLmEefRpllvD 243
                                   ++af+ + k+ +   +R+  ppkD++Na++s+g++lly++vl++i  +gL+P i+fLHe++++ +sLalD++++f+p++v+
  gi|13540937|ref|NP_110625.1| 160 YSAFPFIYKK-YPDFKREFYPPKDELNAMISYGNALLYATVLTKIFITGLNPSISFLHEPSERSFSLALDIADIFKPVIVE 239
                                   *****98865.55558***************************************************************** PP

                                   HHHHHHHHTTSS-GGGEEEETTEEEE-HHHHHHHHHHHHH CS
                      Cas_Cas1 244 rlvlslinkrqlkekdFekeengvlLteegrkkfleafee 283
                                   r++ +l+nk+++  ++F  e+ng++L+ +gr+kf+e ++e
  gi|13540937|ref|NP_110625.1| 240 RTIANLVNKNIMAHDSFRFEDNGCYLSLNGRRKFIEYYNE 279
                                   ************************************9986 PP

>> Tubulin_C  Tubulin C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1   7.2e-05      0.65      20      95 ..      40     119 ..      29     129 .. 0.83
   2 ?   -0.0   0.0       0.1   9.1e+02      46      69 ..     124     148 ..     110     150 .. 0.73
   3 ?   -2.2   0.0       0.5   4.5e+03      36      52 ..     247     266 ..     232     293 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 7.2e-05
                                   TCS-HHHHHHHHHTCSGGGBSSSTSTTTSSEEEEEE....EEEESSSHHHHHHHHHHHHHTTTS-BSTTSTTTEEEEEEE CS
                     Tubulin_C  20 avektsvqdvtrallepknimvkvdprkgkylaial....lirGdvepkevnkavqrikekkkaqfveWiptgikvalnk 95 
                                    ++k s++    + l++  i+v++   +gky++ ++      rG+ ++++v++ ++  + k  a++v+ i+++i  +l +
  gi|13540937|ref|NP_110625.1|  40 ISAKVSLSSWALDYLSKLGIIVHIISTNGKYMSSLIpgnrNERGNTTVQQVKAYLSDKRFKIAAEMVNGIKNNILANLRY 119
                                   556777777788889999999************9975545789*************************999999877765 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.1
                                   TT.SSEEEEEEEEEESSSHHHHHHH CS
                     Tubulin_C  46 rk.gkylaiallirGdvepkevnka 69 
                                   ++  ky+ ++  + +d +++++nk 
  gi|13540937|ref|NP_110625.1| 124 NEiTKYIKAIESYNPDYNSNDINKI 148
                                   22689***************99985 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 0.5
                                   GGGBSS..STSTTT.SSEEE CS
                     Tubulin_C  36 pknimv..kvdprk.gkyla 52 
                                   +knim+  +++ ++ g+yl+
  gi|13540937|ref|NP_110625.1| 247 NKNIMAhdSFRFEDnGCYLS 266
                                   45666522222222355554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       812  (0.0452898); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 1995.57
//
Query:       gi|13540938|ref|NP_110626.1|  [L=236]
Description: hypothetical protein TVN0107 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.6e-12   46.4   0.3      7e-12   45.5   0.3    1.5  1  Cas_NE0113   CRISPR-associated protein NE0113 (Cas_NE0113)
    2.5e-05   24.2   0.5    4.4e-05   23.4   0.5    1.3  1  Cas_APE2256  CRISPR-associated protein (Cas_APE2256)
  ------ inclusion threshold ------
      0.015   14.7   2.4      0.026   14.0   2.4    1.4  1  Bul1_C       Bul1 C terminus


Domain annotation for each model (and alignments):
>> Cas_NE0113  CRISPR-associated protein NE0113 (Cas_NE0113)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.5   0.3   1.2e-15     7e-12       1     153 [.       4     140 ..       4     203 .. 0.74

  Alignments for each domain:
  == domain 1  score: 45.5 bits;  conditional E-value: 1.2e-15
                    Cas_NE0113   1 sPqVvTetldaLlqegepvdevvvittkdgkvrealelLleeflkdygakikldesaihviedvsgeelaDirteedneal 81 
                                   sP V Te  + L+    ++++v++i+t ++ v++               k++l e++ h  ++ ++  ++Dir+++d  ++
  gi|13540938|ref|NP_110626.1|   4 SPMVATEMYEYLKD---EISDVILIYTDNKYVKAGTLAA----------KASL-EDKFHAHVHLQKLDFDDIRSDNDMIKF 70 
                                   68888998888888...99********999999876544..........3333.2233333489***************** PP

                    Cas_NE0113  82 lqlivrlvrelreneg.erlhlsiaGGRKtmsillalaaqLygreqDrlyHvlveeefesnreflyppkesai 153
                                   +++i + v++ + + g e++ ++ +GGRK+ +i+l + a+++    D +y + +++ + s +e +++ k++++
  gi|13540938|ref|NP_110626.1|  71 IKVISETVKKEKYQFGtEKIIVNASGGRKIETIILSVYASIFS--FDEVYNI-INKSVTSYNEEYEKIKDKIS 140
                                   **************9999*************************..*******.66666665555554444332 PP

>> Cas_APE2256  CRISPR-associated protein (Cas_APE2256)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.5   7.4e-09   4.4e-05      18     121 ..      16     118 ..       7     125 .. 0.73

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 7.4e-09
                   Cas_APE2256  18 kkeqkeelvllssdTaaGklvaeilkeyleeegaevevveieklsdlgreeFre..glrnLveklarevknkkre..gekv 94 
                                   k e    ++l+ +d +  k+ + + k  le  +++ +v    +l++l+ ++ r+   +++ ++ +++ vk++k +   ek+
  gi|13540938|ref|NP_110626.1|  16 KDEI-SDVILIYTDNKYVKAGTLAAKASLED-KFHAHV----HLQKLDFDDIRSdnDMIKFIKVISETVKKEKYQfgTEKI 90 
                                   3222.37899999999999999999999999.555555....345555555444349************98554322778* PP

                   Cas_APE2256  95 linaTgGfKpeiavltlvall.ladevy 121
                                   ++na+gG K e+ +l + a++   devy
  gi|13540938|ref|NP_110626.1|  91 IVNASGGRKIETIILSVYASIfSFDEVY 118
                                   ********************94445555 PP

>> Bul1_C  Bul1 C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   2.4   4.3e-06     0.026      77     153 ..     111     181 ..      97     223 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.3e-06
                        Bul1_C  77 lkeikktfkefekkikeykkkfeenkeklneLynlsreistkreLkFtdfiskqlanDveslanlkvkvtelnevfk 153
                                   + + +++++ ++k +++y++++e+ k+k+ e   ++ +  + +e k  d++ +  + D++ l  lkv v++l    k
  gi|13540938|ref|NP_110626.1| 111 IFSFDEVYNIINKSVTSYNEEYEKIKDKISEFDDENYKD-KYKEYK--DLLDHVFYPDMNDLYFLKVPVVKLP---K 181
                                   5678899************************98888777.666666..*******************999996...3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1383  (0.0771376); expected 358.6 (0.02)
Passed bias filter:                      521  (0.0290591); 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: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.63
# Mc/sec: 1133.44
//
Query:       gi|13540939|ref|NP_110627.1|  [L=385]
Description: hypothetical protein TVN0108 [Thermoplasma volcanium GSS1]
Scores for complete 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   91.1   0.0    2.8e-25   89.6   0.0    1.7  1  RAMPs          RAMP superfamily
  ------ inclusion threshold ------
      0.025   14.3   0.1       0.11   12.3   0.1    2.0  1  OxoGdeHyase_C  2-oxoglutarate dehydrogenase C-terminal


Domain annotation for each model (and alignments):
>> RAMPs  RAMP superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.6   0.0   3.1e-29   2.8e-25       2     210 ..       5     331 ..       4     334 .. 0.87

  Alignments for each domain:
  == domain 1  score: 89.6 bits;  conditional E-value: 3.1e-29
                                   EEESS-EE----..................................................................... CS
                         RAMPs   2 letltPlhiGdg..................................................................... 13 
                                   l++ +P++iG++                                                                     
  gi|13540939|ref|NP_110627.1|   5 LKVSSPVLIGNDyvnvtnmiinkdslymldmdklidnepkidqlaeyflsykssdkdeyskyneikrfynninaenykiep 85 
                                   788899999999999999999999999999999999999999999999999999999999999999999999999999999 PP

                                   ......................................---S----HHHHHHHHHHHHHHHHH.HHHTT-HHHHH.H.... CS
                         RAMPs  14 ........................kisdekeespefrdkgglPyIPGSSlkGalRsalekllgsekkekkdeysrkkekqr 70 
                                                            +   +      ++k+ +P+IPGS++kGa+R+a+++++ +++k++ +++++kk k++
  gi|13540939|ref|NP_110627.1|  86 eikgdkefyevinsndnkflkakdVKLTMGTYEVINNKKTFVPFIPGSTIKGAIRNAIRNEYIKKNKINITYDDHKKVKSY 166
                                   9999999999999999999988888888888899999******************************************** PP

                                   .........HHHHHH--S.............SS--SEEEEE.......................EEEEEEEEEEEEEEEEE CS
                         RAMPs  71 vkkgd....leeaiFGne..........eeskiagrvffeDarpvkipgqileeskqikstpspklsgselrelldhster 137
                                   + +g+    l eaiF +e          ++++ +++v++ D++p ++ ++i + +++ +s++  k +g++++ +++ s ++
  gi|13540939|ref|NP_110627.1| 167 NFNGNsygdLDEAIFYKEdqkrqnepkkISNDVFRFVEVDDFYPKEYSLKIYRIERIKLSNN--KRNGIPFYAISIDSGTF 245
                                   ***************7777788899**************************99999999999..***************** PP

                                   --SSS-EEEEEE....-TT-EEEEEEEESS..............................HHHHHHHHHHHHHH.HHH--- CS
                         RAMPs 138 rtrvaidrktktngk.kkgglftleaipae................rikfsgrirlenlsdeelgallklLdlldlhflgl 201
                                     +++i r++++  k +k++++ +  + ++                 i++   i  ++  d+ +++ ++  d +d   l +
  gi|13540939|ref|NP_110627.1| 246 TGNIKIGRSFDNIYKsDKNQFYAISKVFNKlidikindasdhtkneIINKMLCISGKYYRDILKKEKEHYNDNPDKEVLLI 326
                                   ****************99************9*9977777777777755555555555555555555555555557777777 PP

                                   STTTTBTTT CS
                         RAMPs 202 GggkplGfG 210
                                   G    +G+G
  gi|13540939|ref|NP_110627.1| 327 G----FGGG 331
                                   7....7777 PP

>> OxoGdeHyase_C  2-oxoglutarate dehydrogenase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   1.2e-05      0.11      17      54 ..     281     316 ..     262     326 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.2e-05
                 OxoGdeHyase_C  17 ledeeeealkepekvkrvvlcsGkvyydLlkerekkek 54 
                                   ++d ++   +++e +++++ +sGk y d+lk+ +++ +
  gi|13540939|ref|NP_110627.1| 281 INDASD--HTKNEIINKMLCISGKYYRDILKKEKEHYN 316
                                   344444..466899****************99887544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (385 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1078  (0.0601261); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); 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: 0.60u 0.31s 00:00:00.90 Elapsed: 00:00:00.49
# Mc/sec: 2380.15
//
Query:       gi|13540940|ref|NP_110628.1|  [L=296]
Description: hypothetical protein TVN0109 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0077   16.2   0.2        0.1   12.5   0.1    2.2  2  Rad17     Rad17 P-loop domain


Domain annotation for each model (and alignments):
>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.1   5.7e-06       0.1      86     140 ..      78     133 ..      36     159 .. 0.84
   2 ?    1.5   0.0     0.014   2.5e+02      93     132 ..     215     254 ..     197     256 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.7e-06
                         Rad17  86 dnqksdfkgltekesrflsqiesfkeleLkdakylklqklGd.dlrtdkklilved 140
                                   + ++   ++ ++  +++ s +e+fke   ++ +y k+++ G+ d +++ + il+ +
  gi|13540940|ref|NP_110628.1|  78 SIKNRKKRSEFIDIDELSSIVEAFKETGYQGVNYSKIKHEGNgDNKGKPHKILISE 133
                                   34788889999999999*********************999757788888888877 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.014
                         Rad17  93 kgltekesrflsqiesfkeleLkdakylklqklGddlrtd 132
                                    g+ +  s+f++  +  k++    ++y+    +G++++++
  gi|13540940|ref|NP_110628.1| 215 EGIYILLSSFIPDNDYIKNIDFERSRYNIKTLQGKNINGN 254
                                   567788899******************999999***9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       524  (0.0292264); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 2020.04
//
Query:       gi|13540941|ref|NP_110629.1|  [L=229]
Description: hypothetical protein TVN0110 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-16   60.9   3.5    2.4e-16   60.4   3.5    1.2  1  RAMPs     RAMP superfamily


Domain annotation for each model (and alignments):
>> RAMPs  RAMP superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.4   3.5   1.4e-20   2.4e-16       1     213 []      15     201 ..      15     201 .. 0.89

  Alignments for each domain:
  == domain 1  score: 60.4 bits;  conditional E-value: 1.4e-20
                                   EEEESS-EE----........................---S----HHHHHHHHHHHHHHHHH.HHHTT-HHHHH.H..... CS
                         RAMPs   1 kletltPlhiGdg..........kisdekeespefrdkgglPyIPGSSlkGalRsalekllgsekkekkdeysrkkekqrv 71 
                                   ++e+lt lhiG+                 + ++    + +lPyIPGSS+kG +Rs+le++     ++k+++ ++       
  gi|13540941|ref|NP_110629.1|  15 EIEVLTGLHIGGSneelkiggtdSPVITTKYLINNVEPCDLPYIPGSSIKGKIRSLLENV-----DYKGKNGDD------- 83 
                                   59******************99988888888999999*********************88.....567777777....... PP

                                   ....HHHHHH--S.......SS--SEEEEE.......................EEEEEEEEEEEEEEEEE--SSS-EEEEE CS
                         RAMPs  72 kkgdleeaiFGne....eeskiagrvffeDarpvkipgqileeskqikstpspklsgselrelldhsterrtrvaidrktk 148
                                       +++++FG      e+ k+  r++++Da +++                    ++++ +e+ ++  e++ +++id    
  gi|13540941|ref|NP_110629.1|  84 ----IVSKMFGYYpnagEGIKRLTRLIIRDAFLDD--------------------GHIKSAEDARNVIEIKSENKIDPIES 140
                                   ....******8888888889***********9955....................678999******************99 PP

                                   E...-TT-EEEEEEEESS.................HHHHHHHHHHHHHH.HHH---STTTTBTTT-EE CS
                         RAMPs 149 tngkkkgglftleaipae...rikfsgrirlenlsdeelgallklLdlldlhflglGggkplGfGsve 213
                                   ++ +       +e ++ +   + k+   i++ ++ +e  + l+  ++ll   +  lGg  ++G+Gsv+
  gi|13540941|ref|NP_110629.1| 141 KATP-----RFIERVRRGtkfKGKIILSIYEGDNEEEMIKCLKTGISLL--EDSYLGGNGTRGYGSVK 201
                                   9999.....8888888886666677777888888888888888888888..***************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.20s 00:00:00.55 Elapsed: 00:00:00.34
# Mc/sec: 2018.37
//
Query:       gi|13540942|ref|NP_110630.1|  [L=146]
Description: hypothetical protein TVN0111 [Thermoplasma volcanium GSS1]
Scores for complete 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-15   55.5   5.0    9.2e-15   55.5   5.0    1.9  2  Csm2_III-A  Csm2 Type III-A
     0.0099   15.4   2.1       0.01   15.3   2.1    1.2  1  14-3-3      14-3-3 protein


Domain annotation for each model (and alignments):
>> Csm2_III-A  Csm2 Type III-A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.1      0.12   1.1e+03      70      96 ..       3      29 ..       1      35 [. 0.58
   2 !   55.5   5.0     1e-18   9.2e-15       9     110 ..      40     138 ..      33     142 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.12
                                  HHHHHHHHHHHHHHHHHH--SH.HHHH CS
                    Csm2_III-A 70 reeavkelsevlkkaidkvkkskekfk 96
                                  ++   ke +e+++ +++k ++s+e+  
  gi|13540942|ref|NP_110630.1|  3 KQVRDKEVQEIMDYIMNKGEDSEERVY 29
                                  555566667777777777776664433 PP

  == domain 2  score: 55.5 bits;  conditional E-value: 1e-18
                                   HHHHHHHHHHH.TTS-STTTHHHHHHHHHHHHHHHHTHHHHHHHTHHHHHHHHHHHHHHHHHH..HHHHHHHHHHHHHHHH CS
                    Csm2_III-A   9 ekaeeigkelkkkklktsqiRkfydevkrieekikkkkeeeseeilrklkllkpklaYaagre..eavkelsevlkkaidk 87 
                                   e+a +i+++  +++ +++qiRkfyd++ +i++k +       ++++ kl ++ p++ Ya +r+  ++  ++++ l++ idk
  gi|13540942|ref|NP_110630.1|  40 EIACNISRNQ-NSETTQNQIRKFYDYTIKINSKDE-------KKAKIKLAMMMPQIYYAIQRKviSSDSPFVKFLEDSIDK 112
                                   5666777655.5779*****************952.......456789**************88899************** PP

                                   --SH....HHHHHHHHHHHHHHHHHH CS
                    Csm2_III-A  88 vkksk...ekfkrfvdffEAivAYhk 110
                                    +k +   + f+rf+++f AivAY k
  gi|13540942|ref|NP_110630.1| 113 LNKTEdfeNAFNRFLNVFQAIVAYSK 138
                                   *999888888999***********98 PP

>> 14-3-3  14-3-3 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   2.1   1.2e-06      0.01      91     164 ..      10      83 ..       3     133 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.2e-06
                                   HHHHHHCCHCH.-SHHHHHHHH.HHHHHHHHHHHCC--HHHHHHHHHHHHHHHHHHHHHHHTTTGCC-HHHHHHH CS
                        14-3-3  91 lelldktlipkatseeskvfyl.kmkgDyyRYlaEfaegeekkeaaekakeaYeeAleiakkelqpthpirLgla 164
                                   ++ + +++++k +++e++v+ l km g  y   +++++++++++++++ ++ Y   ++i +k+ ++   i+L+++
  gi|13540942|ref|NP_110630.1|  10 VQEIMDYIMNKGEDSEERVYKLfKMNGVIYEIACNISRNQNSETTQNQIRKFYDYTIKINSKD-EKKAKIKLAMM 83 
                                   44455677766899999997666************************************9554.33334444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1535  (0.0856155); expected 358.6 (0.02)
Passed bias filter:                      506  (0.0282224); 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: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 947.57
//
Query:       gi|13540943|ref|NP_110631.1|  [L=775]
Description: HD superfamily hydrolase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-16   59.9   0.2    4.9e-13   48.7   0.1    2.6  2  Csm1_B    Csm1 subunit domain B
    4.7e-12   46.2   3.5    1.6e-11   44.5   2.4    2.5  2  HD        HD domain
    1.2e-07   32.0   1.7    4.8e-05   23.7   0.2    3.0  2  mCpol     minimal CRISPR polymerase domain
  ------ inclusion threshold ------
       0.37   10.9   1.3        4.3    7.4   0.9    2.5  2  HD_6      HD domain


Domain annotation for each model (and alignments):
>> Csm1_B  Csm1 subunit domain B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.7   0.1   1.1e-16   4.9e-13       4      94 .]     250     339 ..     248     339 .. 0.93
   2 !    8.5   0.0   0.00038       1.7      22      84 ..     558     617 ..     540     625 .. 0.76

  Alignments for each domain:
  == domain 1  score: 48.7 bits;  conditional E-value: 1.1e-16
                                   S--HHHHHHHHHHHHHHHHHHHHHHHHHTT--CCCEEEEETTEEEEEEE--HHHHHHHHHHHHHHHHHCCCCTSSS-EEEE CS
                        Csm1_B   4 kgAlksLrgRSfylellleeivdelleklelsranllYagGGhfylLlpntekvkekleeiekelnewllkefkgkLylal 84 
                                   ++ +k+L+gRSf+++l+++ i  +++++ +l r n+++     f lL+ n+e++ +kle+i+k+++  l+++ k  +  ++
  gi|13540943|ref|NP_110631.1| 250 EKGTKRLKGRSFMIKLFTDSIESYIINEFNLYRFNVVWEKSDGFLLLMDNNEENIKKLEDIKKNIDLGLIEK-KRGITANI 329
                                   5678******************************************************************99.77888899 PP

                                   EEEEE-TTTT CS
                        Csm1_B  85 ayvelsaedl 94 
                                   a+v+ s +d+
  gi|13540943|ref|NP_110631.1| 330 AWVTASLDDF 339
                                   9988887775 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00038
                                   HHHHHHHHHHTT--CCCEEEEETTEEEEEEE--HHHHHHHHHHHHHHHHHCCCCTSSS-EEEE CS
                        Csm1_B  22 eeivdelleklelsranllYagGGhfylLlpntekvkekleeiekelnewllkefkgkLylal 84 
                                    + +de+ ++   ++  ++Y+gG  ++ + +  +k  + ++++++e+n+ + k+++ +  + +
  gi|13540943|ref|NP_110631.1| 558 SVKLDEIAQQ--NKDIYIVYSGGDDVTAVGE-INKLIKFISDFHNEFNKYFCKKINISAGVTV 617
                                   5555555554..4688999*99999987655.5569******************998877765 PP

>> HD  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.5   2.4   3.6e-15   1.6e-11      24     121 ..       4      86 ..       1      87 [. 0.88
   2 ?   -1.4   0.0      0.56   2.5e+03      63      93 ..     454     482 ..     435     511 .. 0.72

  Alignments for each domain:
  == domain 1  score: 44.5 bits;  conditional E-value: 3.6e-15
                                   HHHHHHHHHHHTTTTHHHHTS..HHHHHHCTCCHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHTTCCHHHHHHHHHHHHC CS
                            HD  24 drellllaaLlHDiGkgpfgdafekkeeefekflaHekvgaeilrevekrlgld.ledvaklirehheswegkkrprglae 103
                                   d+ +l +a +lHDiGk++++ +           ++H++ g++ ++e+++++  + +e +a+l+++hh++ + +     +  
  gi|13540943|ref|NP_110631.1|   4 DEFVLITASILHDIGKIQQRYK---------LSEKHADLGYQFIKEIKYSN--KdMERIANLVKHHHHDPDKT-----ELD 68 
                                   777899************7742.........3357****************..55****************77.....899 PP

                                   CTSCHHHHHHHHHHHHHH CS
                            HD 104 rqlslearivklaDrlaa 121
                                      +++++i+++aDr +a
  gi|13540943|ref|NP_110631.1|  69 GRDKKLLKILQIADRKSA 86 
                                   999999********9776 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.56
                                   HHHHHHHHHHHHHHHHHHHHHHHHTTCCHHH CS
                            HD  63 gaeilrevekrlgldledvaklirehheswe 93 
                                   g + ++ ++ ++++  ++v+k++ +++ +++
  gi|13540943|ref|NP_110631.1| 454 GNKYIKYYFSDHEE--KEVIKIYDYNNIDSN 482
                                   55556666666655..578888888777776 PP

>> mCpol  minimal CRISPR polymerase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.4   0.1    0.0024        11      22      81 ..     253     315 ..     237     337 .. 0.84
   2 !   23.7   0.2   1.1e-08   4.8e-05       5     104 ..     526     628 ..     522     640 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0024
                         mCpol  22 eeeleklskevkeaikklkkllkdel...gasvifaaGDsilakssleedllvelsrvyqkit 81 
                                    ++l+ +s  +k +++++++++ +e     ++v+++  D+ l+  + +e+++ +l+ + ++i 
  gi|13540943|ref|NP_110631.1| 253 TKRLKGRSFMIKLFTDSIESYIINEFnlyRFNVVWEKSDGFLLLMDNNEENIKKLEDIKKNID 315
                                   5678889999***********9999877899**************999999999888877765 PP

  == domain 2  score: 23.7 bits;  conditional E-value: 1.1e-08
                         mCpol   5 DGDdiGkklealllsndeeeleklskevkeai.kklkkllkdelgasvifaaGDsilaksslee..dllvelsrvyqkitg 82 
                                   D Dd G  + a l    +++l  l  e + ++  kl ++ +++    +++++GD+++a  ++++  + +++++++++k+  
  gi|13540943|ref|NP_110631.1| 526 DVDDMGLIVAAGLKRTTISKLASLTFEFEYFFsVKLDEIAQQNKDIYIVYSGGDDVTAVGEINKliKFISDFHNEFNKYFC 606
                                   6677777777777777777777777777665415899999***9*********************999************9 PP

                         mCpol  83 ltvSiGvGktlrealiaLkkAk 104
                                   +++ i++G t+ +   +L+ A 
  gi|13540943|ref|NP_110631.1| 607 KKINISAGVTVVSPKFPLRRAV 628
                                   9999999999999999998885 PP

>> HD_6  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.9   0.00095       4.3      55     121 ..       9      60 ..       2      95 .. 0.56
   2 ?   -1.8   0.0      0.62   2.8e+03      15      35 ..     190     210 ..     185     229 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.00095
                                   HHHHHCCCGGGSSHHHHTTS----TTS-.....-GGGT----HHHHHHHHHH......HHHHHHHHHHHTTTS CS
                          HD_6  55 aflaalHDlGKaspaFqakvpelaekleeaglelekelekarHdslgaalle......evarslaaavggHHG 121
                                   +   +lHD+GK+++++    ++                     ++lg+ + +      + ++++a++v  HH 
  gi|13540943|ref|NP_110631.1|   9 ITASILHDIGKIQQRYKLSEKH---------------------ADLGYQFIKeikysnKDMERIANLVKHHHH 60 
                                   5566789999998888776643.....................333333322222222222333333333333 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.62
                                   EHHHHHHHHHHHHHHHHHHTS CS
                          HD_6  15 pLvaHllDvaavaealldkwl 35 
                                   pL++Hl  +aa+a  l+++ +
  gi|13540943|ref|NP_110631.1| 190 PLYHHLKLTAAIALSLYRNLK 210
                                   899**********99998655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (775 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1094  (0.0610185); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.73u 0.33s 00:00:01.06 Elapsed: 00:00:00.51
# Mc/sec: 4541.76
//
Query:       gi|13540944|ref|NP_110632.1|  [L=237]
Description: hypothetical protein TVN0113 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.8e-21   75.6   4.2      1e-20   74.8   4.2    1.4  1  Cas_Cas6  CRISPR associated protein Cas6
  ------ inclusion threshold ------
      0.053   13.6   1.2      0.082   12.9   1.2    1.4  1  RAMPs     RAMP superfamily


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 !   74.8   4.2   1.1e-24     1e-20       2     145 ..      83     230 ..      82     231 .. 0.81

  Alignments for each domain:
  == domain 1  score: 74.8 bits;  conditional E-value: 1.1e-24
                                   HHCS-EEEETTEEEEEEEEEE----S--TCEE.EEESS-BBEEEEEEETTCCEEEEE-T.TSTTHHHHHHHHHHHHHHHHH CS
                      Cas_Cas6   2 llknkeirlgnnefkveevellkepeitssevvfktlSPivvrstkkengkkktyylsp.ddeeFsellkenlkkkykaly 81 
                                   l knk ++l++++f++ e++ ++ +   ++   f t SP+v++    +n+k+k+ ++++ +  +F ++lken++kk++++y
  gi|13540944|ref|NP_110632.1|  83 LDKNKIFYLSGYKFHIAEIKEFDINIS-KD---FITGSPVVLY---LDNKKNKYFSIKDdSIAFFLRRLKENAIKKFNLYY 156
                                   568999***************999996.23...99********...4577888888866599******************* PP

                                   SS...SS---EEEEE.EEEE..........TEEEEEEEEEEEE....EE-HHHHHHHHHC-SCS-CCCT-S-EE CS
                      Cas_Cas6  82 gee.keeklsikpdk.kvkkivvkkk....etyirGylgrfel....egdpellklaydaGlGeknsqGFGmve 145
                                   +e+ ++++l +++ k +++   + +k      +i ++ +++ l    + + +++++++daG+Gekns+GFG+++
  gi|13540944|ref|NP_110632.1| 157 HENiNINHLIFDKLKfHREVALLLRKgktsFNIIGTTWYNLHLnklnRDEIKFYNFIMDAGIGEKNSLGFGFLN 230
                                   *998777776666664444444444488853344444488888888899***********************98 PP

>> RAMPs  RAMP superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   1.2   9.1e-06     0.082      97     212 ..      72     229 ..       8     230 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9.1e-06
                                   E................................................................................ CS
                         RAMPs  97 Darpvkipgqileeskqikstpsp......................................................... 120
                                   D++++k+ ++il+++k++++++++                                                         
  gi|13540944|ref|NP_110632.1|  72 DSNIIKNIYNILDKNKIFYLSGYKfhiaeikefdiniskdfitgspvvlyldnkknkyfsikddsiafflrrlkenaikkf 152
                                   888899999999999999999999999999888888888888888888888888888888887777777777777777555 PP

                                   ...EEEEEEEEEEEEEEEEE--SSS-EEEEEE...-TT-EEEEEEEESS..............HHHHHHHHHHHHHH.HHH CS
                         RAMPs 121 ...klsgselrelldhsterrtrvaidrktktngkkkgglftleaipaerikfsgrirlenlsdeelgallklLdlldlhf 198
                                        + +++++l++ ++++  +va+  ++++++        + + + +         l+ l+++e ++++++ d+     
  gi|13540944|ref|NP_110632.1| 153 nlyYHENININHLIFDKLKFHREVALLLRKGKTSF-----NIIGTTWYN-------LHLNKLNRDEIKFYNFIMDAG---- 217
                                   55555556666666666666666665555555554.....224444444.......556666999999999999999.... PP

                                   ---STTTTBTTT-E CS
                         RAMPs 199 lglGggkplGfGsv 212
                                     +G + +lGfG++
  gi|13540944|ref|NP_110632.1| 218 --IGEKNSLGFGFL 229
                                   ..**********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       619  (0.0345251); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); 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: 0.52u 0.32s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 1420.38
//
Query:       gi|13540945|ref|NP_110633.1|  [L=406]
Description: hypothetical protein TVN0114 [Thermoplasma volcanium GSS1]
Scores for 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-06   27.6  33.6    4.2e-06   26.6  33.6    1.5  1  Cas_DxTHG  CRISPR-associated (Cas) DxTHG family


Domain annotation for each model (and alignments):
>> Cas_DxTHG  CRISPR-associated (Cas) DxTHG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6  33.6   2.3e-10   4.2e-06       2     280 ..       5     356 ..       4     405 .. 0.48

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 2.3e-10
                     Cas_DxTHG   2 lisflGt.gnykevkYelkeeeeeeketsfvqeallellaekedpdkvvilltdtlad.keaeek...eeaak.lkeelee 76 
                                   +is +G+  +++ ++Y+   ++ +++e+  +++ ++e +  k d    +i  + + +  +  +++   ++++  + ++l e
  gi|13540945|ref|NP_110633.1|   5 FISLWGNpERWNVTRYS---FNSKTCESITSSRVIYENF--KTD--YCIIYIPNSIYPgI-YKDDtylSQYQDlINSKLCE 77 
                                   9******999*******...778999***********99..666..89999999666652.22224676677778888844 PP

                     Cas_DxTHG  77 lle.........iekvdveiipgggte......eelwe........ife.kllekleende...iilDiThGfrylPvla. 129
                                    l+         +++   +i p+ g++        +++        +f+  +l++le+ d+   ii+DiThG+++l +++ 
  gi|13540945|ref|NP_110633.1|  78 FLNskdtesaefYKNSNKIIFPSKGSFtadnknY-IFDfdinyiysYFYrSILNYLESVDKinkIIVDITHGINFLEFIFl 157
                                   44456666788644444799*******9998640.44466666444444477777777655666*************9995 PP

                     Cas_DxTHG 130 ....llalaylrnvk.n..ltikgi.yYgaf................................keeeedPildlteflels 170
                                        ++  y+ ++k +  ++ +++ +Y +f                                +++++  ++ l+   +ls
  gi|13540945|ref|NP_110633.1| 158 eslmYALRVYALSNKiDvnIEYYNSdPYSNFailniykiksieieyknvlsiisrdfinmyrhNKKDIKDYFKLNFNEDLS 238
                                   555433333333444331133333344444444444444444443333333333333333333333333333333333333 PP

                     Cas_DxTHG 171 dwltaverflktgdaeklaellre.kkekkkek..............lkklk.klkeklkkelee...fskalelirplel 232
                                   d+++a +   ++    +l+ l+ + +k++                   +k++ ++ +k++ ++e    +  +++++ ++++
  gi|13540945|ref|NP_110633.1| 239 DYIKACSIMAQSVTVPYLMYLIINiYKKI---YeigsgglevhlnieDNKIRqTFDNKINVNIETlafLDTLIKINSSIKY 316
                                   55555554444444444444443332222...0222233333333331222223333333333320002223333332222 PP

                     Cas_DxTHG 233 lekaekleke...............iveklkeeleeiesleeeesakplellldeikkklekf 280
                                    ++  k+++                +   +k+                   +l +ik k e +
  gi|13540945|ref|NP_110633.1| 317 -DNGFKIPDIytftdnffsresyniF---IKN-------------------ELRKIKSKKEHY 356
                                   .1222222223323333222221210...222...................333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (406 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       962  (0.0536561); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.49
# Mc/sec: 2473.38
//
Query:       gi|13540946|ref|NP_110634.1|  [L=248]
Description: hypothetical protein TVN0115 [Thermoplasma volcanium GSS1]
Scores for complete sequence (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  120.3   0.1    1.3e-34  120.1   0.1    1.0  1  PAC2             PAC2 family
  ------ inclusion threshold ------
      0.054   12.9   0.4      0.086   12.3   0.4    1.2  1  FliD_C           Flagellar hook-associated protein 2 C-termin
      0.055   13.5   0.5      0.096   12.7   0.5    1.3  1  Laminin_II       Laminin Domain II
      0.074   13.0   1.1          2    8.3   0.1    2.8  3  Methyltransf_18  Methyltransferase domain
      0.077   13.0   5.9       0.14   12.1   5.9    1.4  1  FlxA             FlxA-like protein
      0.083   14.0   0.0       0.13   13.3   0.0    1.4  1  DUF5320          Family of unknown function (DUF5320)
       0.11   12.4   4.3       0.13   12.1   2.7    1.9  3  60KD_IMP         60Kd inner membrane protein
       0.18   11.4   1.0       0.28   10.7   1.0    1.2  1  SseC             Secretion system effector C (SseC) like fami
       0.32   11.2   4.1        1.4    9.1   3.8    2.1  2  DUF2802          Protein of unknown function (DUF2802)
        0.4   11.2   7.6        0.7   10.4   7.6    1.3  1  ZapB             Cell division protein ZapB
        1.1    9.1   6.5        1.9    8.3   6.5    1.3  1  DivIC            Septum formation initiator
          2    8.7   4.4        1.5    9.0   2.6    1.8  2  XhlA             Haemolysin XhlA


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 !  120.1   0.1     9e-38   1.3e-34       2     212 ..      25     228 ..      24     229 .. 0.92

  Alignments for each domain:
  == domain 1  score: 120.1 bits;  conditional E-value: 9e-38
                                   EEESSCGGGHHHHHHHHHHHHTTEEEEEEEEHCCHSBCCCC.SEEEEETTEEE-SEEEEEETTT.SEEEEEEEE-HSCHHH CS
                          PAC2   2 ilGfpgiGnVgqlavdlLiesleaekvgeidsdyllpfvgprpvvlveegrelepprlyakdsgsrdllvlqgrepilqye 82 
                                   i Gf +    g l+++++ie+l++++v+++ s++ +p     pv+++ +g+ ++p+r+ya++  s++llv ++  pil++ 
  gi|13540946|ref|NP_110634.1|  25 ICGFASSTPTGVLTASYMIETLGLHQVAHLISQH-VP-----PVTVFVGGKLRHPFRIYANN--SNTLLVAVCEVPILTSH 97 
                                   8899999***************************.**.....*****************996..59**************9 PP

                                   ..HHHHHHHHHHHHTTESEEEEEEEEEESS-ES..TTS-.EEEEEESSHHHHHHHH.....CT-CEEEEHHHHHHHHHHHH CS
                          PAC2  83 ..efakalldwaeelgvkevvvLggldageradvphtrpekvtgaatdeelleele.....eseyggivgitglLlsaake 156
                                     e+++al++w+ee+g +e+ v++g +      +p++r   v+ +a ++ +l++l+     ++e + i+g+ g +l+++  
  gi|13540946|ref|NP_110634.1|  98 iyEISNALMSWLEEIGASEIAVIEGSPVS---GIPEDRN--VYSVA-EKRRLDKLKkvgipAAESALIAGMGGGMLNECLV 172
                                   ***************************64...5577887..66666.6666678853666555****************** PP

                                   TT-EEEEEEEEEECCC--HHHHHHHHHHHHHHHT---HCHHHHHHHHHHHHHHHHH CS
                          PAC2 157 rgipavgllaevphylpdPkaaaalleflskllglevdtedLeedaeeleeqleel 212
                                   r ++++++  +++  +pdP a ++++++l+k+++l+++t+ Le++ +el  q++++
  gi|13540946|ref|NP_110634.1| 173 RRMSGISFITPTSADIPDPGAVLSVVNALNKVYNLNIETDLLEQQVKELNDQIKKI 228
                                   *****************************************************986 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 ?   12.3   0.4   5.7e-05     0.086     191     227 ..     206     242 ..     188     247 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.7e-05
                                   HHHHHHHHXXXXHHHHHHHHHHHHHCHHHHHHHHHHH CS
                        FliD_C 191 tlqtasknltkqikdldkkiedldkrletleerlkkq 227
                                   +l+ +++ l++q+k+l+++i+++++++++l++r k+ 
  gi|13540946|ref|NP_110634.1| 206 NLNIETDLLEQQVKELNDQIKKIEEQYKELQNRQKQE 242
                                   4567777788888888888888888888888876655 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.5   6.4e-05     0.096      45      84 ..     202     241 ..     181     245 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.4e-05
                                   XXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH CS
                    Laminin_II  45 ekvkdankairdArrsvkkLeklapqLldklkelkqleea 84 
                                   +kv ++n  +++ +++vk+L+ ++ +++++ kel++++++
  gi|13540946|ref|NP_110634.1| 202 NKVYNLNIETDLLEQQVKELNDQIKKIEEQYKELQNRQKQ 241
                                   5777899999999********************9998875 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.33   4.9e+02      80     103 ..      16      40 ..       7      58 .. 0.75
   2 ?    8.3   0.1    0.0013         2      67     102 ..     138     173 ..     128     182 .. 0.77
   3 ?    1.0   0.1      0.24   3.6e+02      19      62 ..     186     229 ..     173     240 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.33
               Methyltransf_18  80 eee.vdtvviaGmGgelileILeea 103
                                   +++  + +vi+G  +++ + +L+++
  gi|13540946|ref|NP_110634.1|  16 KRSyNNPIVICGFASSTPTGVLTAS 40 
                                   44446789*******9999999987 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0013
               Methyltransf_18  67 ievrlsdGleklkeeevdtvviaGmGgelileILee 102
                                    e r  d l+k+    ++ ++iaGmGg +  e L +
  gi|13540946|ref|NP_110634.1| 138 AEKRRLDKLKKVGIPAAESALIAGMGGGMLNECLVR 173
                                   556666778888767799*********999888765 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.24
               Methyltransf_18  19 aDiGtDHgylpiylvkegkakkviasDinegplekakeniekag 62 
                                   aDi    ++l++  + ++ ++  i +D+ e+ +++ +++i+k +
  gi|13540946|ref|NP_110634.1| 186 ADIPDPGAVLSVVNALNKVYNLNIETDLLEQQVKELNDQIKKIE 229
                                   66666668888888889999999999999999999999998854 PP

>> FlxA  FlxA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   5.9   9.5e-05      0.14      53      83 ..     213     243 ..     204     247 .. 0.55

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 9.5e-05
                          FlxA  53 liqaQIqqlqaQIaqlqqqqaekaqekqqse 83 
                                   l+++Q++ l+ QI+++++q +e +++++q+ 
  gi|13540946|ref|NP_110634.1| 213 LLEQQVKELNDQIKKIEEQYKELQNRQKQEP 243
                                   4555555555555555555544444444443 PP

>> DUF5320  Family of unknown function (DUF5320)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   8.7e-05      0.13      62      99 .]     188     235 ..     147     235 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 8.7e-05
                       DUF5320  62 a..........aaetaeaskeeekelLeeqaeaLeeeleaikkrlkel 99 
                                              +a ++ ++ + e++lLe+q + L++++++i+++ kel
  gi|13540946|ref|NP_110634.1| 188 IpdpgavlsvvNALNKVYNLNIETDLLEQQVKELNDQIKKIEEQYKEL 235
                                   25566666666666777888889*********************9997 PP

>> 60KD_IMP  60Kd inner membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0         3   4.5e+03     129     147 ..      19      37 ..       3      52 .. 0.74
   2 ?   -2.5   0.0       2.8   4.1e+03      69     101 ..      83     115 ..      76     125 .. 0.66
   3 ?   12.1   2.7     9e-05      0.13      19      59 ..     207     247 ..     197     248 .] 0.85

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 3
                      60KD_IMP 129 yvmplmilffslsfpaglv 147
                                   y  p++i  f+ s p+g++
  gi|13540946|ref|NP_110634.1|  19 YNNPIVICGFASSTPTGVL 37 
                                   6678888888889998886 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.8
                      60KD_IMP  69 GclplLiqlpifialyrvlrslasfwikdLsap 101
                                    +l+++  +pi+++  + ++++  +w+++++a+
  gi|13540946|ref|NP_110634.1|  83 TLLVAVCEVPILTSHIYEISNALMSWLEEIGAS 115
                                   567777788888876666666444477666665 PP

  == domain 3  score: 12.1 bits;  conditional E-value: 9e-05
                      60KD_IMP  19 ltlkqlkssakmqelqPelkeiqekykkdkqklqqemmklY 59 
                                   l++++    ++++el+ ++k+i+e+yk+ +++++qe + +Y
  gi|13540946|ref|NP_110634.1| 207 LNIETDLLEQQVKELNDQIKKIEEQYKELQNRQKQEPQSMY 247
                                   566666667899**************877999999999988 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 ?   10.7   1.0   0.00019      0.28     257     300 ..     203     246 ..     192     247 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00019
                          SseC 257 kaaqlqAdtkllravleqlqkvldeaaeeikellesiqellksm 300
                                   k+ +l+ +t+ll+ ++++l+++++++ e++kel++ +++  +sm
  gi|13540946|ref|NP_110634.1| 203 KVYNLNIETDLLEQQVKELNDQIKKIEEQYKELQNRQKQEPQSM 246
                                   677889999**************************999988887 PP

>> DUF2802  Protein of unknown function (DUF2802)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       1.1   1.6e+03      51      66 ..     147     162 ..     146     164 .. 0.84
   2 ?    9.1   3.8   0.00092       1.4       3      31 ..     215     243 ..     214     247 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1.1
                       DUF2802  51 eecgLsraEAeLllrL 66 
                                   +++g++ aE  L++ +
  gi|13540946|ref|NP_110634.1| 147 KKVGIPAAESALIAGM 162
                                   689******9999865 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00092
                       DUF2802   3 gqrlaelekrlkqleerleeleqqdpqsk 31 
                                   +q+++el+ ++k++ee+ +el+++++q++
  gi|13540946|ref|NP_110634.1| 215 EQQVKELNDQIKKIEEQYKELQNRQKQEP 243
                                   699******************99988765 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   7.6   0.00047       0.7      13      57 ..     197     241 ..     195     246 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00047
                          ZapB  13 iqkaidtitlLqmeieeLkeeneelkeenreleeeneqlkeerea 57 
                                   + +a++++  L  e + L+++++el+++++++ee+ ++l++ +++
  gi|13540946|ref|NP_110634.1| 197 VVNALNKVYNLNIETDLLEQQVKELNDQIKKIEEQYKELQNRQKQ 241
                                   678999*********************************988776 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   6.5    0.0013       1.9      13      53 ..     198     238 ..     193     242 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0013
                                   XXXXXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XXX CS
                         DivIC  13 kkgllaykqlkqeiaalqaelaklkaeneeLeaevkdLksd 53 
                                   ++ l++++ l+ e + l++++++l++++++ e++ k+L++ 
  gi|13540946|ref|NP_110634.1| 198 VNALNKVYNLNIETDLLEQQVKELNDQIKKIEEQYKELQNR 238
                                   67778888999999999999999999999999999999654 PP

>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       6.8     1e+04      19      26 ..     142     149 ..     139     156 .. 0.62
   2 ?    9.0   2.6     0.001       1.5      20      49 ..     204     233 ..     197     240 .. 0.76

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 6.8
                          XhlA  19 rvdkleek 26 
                                   r+dkl++ 
  gi|13540946|ref|NP_110634.1| 142 RLDKLKKV 149
                                   56666654 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.001
                          XhlA  20 vdkleekaaeaeekiknleedlkklesnqk 49 
                                   v  l+   +  e+++k+l++++kk+e++ k
  gi|13540946|ref|NP_110634.1| 204 VYNLNIETDLLEQQVKELNDQIKKIEEQYK 233
                                   555666677788999999999999998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2055  (0.114619); expected 358.6 (0.02)
Passed bias filter:                     1429  (0.0797033); expected 358.6 (0.02)
Passed Vit filter:                       285  (0.015896); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.65u 0.33s 00:00:00.98 Elapsed: 00:00:00.46
# Mc/sec: 1615.56
//
Query:       gi|13540947|ref|NP_110635.1|  [L=68]
Description: hypothetical protein TVN0116 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      3e-07   31.0   0.2    3.5e-07   30.8   0.2    1.0  1  ThiS            ThiS family
    3.3e-05   23.6   0.2    3.9e-05   23.4   0.2    1.1  1  Ub-Mut7C        Mut7-C ubiquitin
      0.003   17.6   0.3     0.0059   16.6   0.3    1.5  1  ThiS-like       ThiS-like ubiquitin
  ------ inclusion threshold ------
      0.041   14.0   0.3       0.12   12.5   0.1    1.7  2  DUF749          Domain of unknown function (DUF749)
      0.066   13.3   1.2       0.24   11.5   0.8    1.9  2  TGS             TGS domain
       0.12   12.3   0.0       0.12   12.3   0.0    1.1  1  Thioredoxin_15  Thioredoxin-like domain


Domain annotation for each model (and alignments):
>> ThiS  ThiS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.8   0.2   1.2e-10   3.5e-07      11      77 .]       9      68 .]       4      68 .] 0.92

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 1.2e-10
                                  HT..CEEEEESSTSBHHHHHHHHHHHTCHHGTTTTEEEEETTEEEGCCTTTSB--TTCEEEEEESTTC- CS
                          ThiS 11 ag..eeelelaegstvaelleaLgerypelalerrvavavNgeivprlwldtelkdgDevailppVaGG 77
                                  +g  ++ +e++ +++v+++l+ Lg +       +  +v vNg+ v     d+ +k+ D v+il +++GG
  gi|13540947|ref|NP_110635.1|  9 KGhiKKSVEIDREMSVGDILKDLGLPE------EEYVVIVNGKPVLA---DHTVKKDDDVVILEVFSGG 68
                                  556677889999***************......**************...******************9 PP

>> Ub-Mut7C  Mut7-C ubiquitin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.2   1.3e-08   3.9e-05      26      77 ..      15      65 ..       5      67 .. 0.89

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 1.3e-08
                      Ub-Mut7C 26 avafdeaatvkhviEalGVPhtEVelilvnGesvgfshiledGdrvavypvf 77
                                  +v++d+  +v++++  lG P  E  ++ vnG++v  +h +++ d v +  vf
  gi|13540947|ref|NP_110635.1| 15 SVEIDREMSVGDILKDLGLPEEEY-VVIVNGKPVLADHTVKKDDDVVILEVF 65
                                  688999**************9885.788****************99988776 PP

>> ThiS-like  ThiS-like ubiquitin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.3     2e-06    0.0059       8      54 ..      14      62 ..      13      64 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2e-06
                     ThiS-like  8 keveveegttlealkekik.pdaD.vvIlNGFpikeDteLkegDevflI 54
                                  k+ve++ + ++ ++ +++  p+++ vvI+NG p+  D ++k  D v++ 
  gi|13540947|ref|NP_110635.1| 14 KSVEIDREMSVGDILKDLGlPEEEyVVIVNGKPVLADHTVKKDDDVVIL 62
                                  6788888888888766654266679*********************986 PP

>> DUF749  Domain of unknown function (DUF749)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.45   1.3e+03      22      37 ..       6      22 ..       3      29 .. 0.57
   2 ?   12.5   0.1   3.9e-05      0.12      14      44 ..      33      64 ..      23      67 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.45
                                  THHHHCTTT-.--SS-- CS
                        DUF749 22 vklkaalekk.elkddd 37
                                  + +k ++ k  e++++ 
  gi|13540947|ref|NP_110635.1|  6 ITVKGHIKKSvEIDREM 22
                                  55666665544555544 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 3.9e-05
                                  -ST.TTS-STHHHHCTTT---SS--EEEEEE- CS
                        DUF749 14 Lpe.elekfvklkaalekkelkdddeiaIlni 44
                                  Lpe e+   v+ k  l+++ +k+dd+++Il++
  gi|13540947|ref|NP_110635.1| 33 LPEeEYVVIVNGKPVLADHTVKKDDDVVILEV 64
                                  6765999***********************98 PP

>> TGS  TGS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.18   5.3e+02      39      57 ..       8      29 ..       7      31 .. 0.77
   2 ?   11.5   0.8   8.1e-05      0.24      36      59 ..      39      62 ..      14      63 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.18
                                  ECS...EEEETTSBB-SSEEEE CS
                           TGS 39 VnG...qrvgldhvLedgdvve 57
                                  V G   + v +d+++  gd+++
  gi|13540947|ref|NP_110635.1|  8 VKGhikKSVEIDREMSVGDILK 29
                                  5566667889999999999875 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 8.1e-05
                                  EEEECSEEEETTSBB-SSEEEEEE CS
                           TGS 36 yAlVnGqrvgldhvLedgdvveIv 59
                                  + +VnG+ v  dh+++ +d v I+
  gi|13540947|ref|NP_110635.1| 39 VVIVNGKPVLADHTVKKDDDVVIL 62
                                  579*************99999886 PP

>> Thioredoxin_15  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0     4e-05      0.12     132     174 ..      22      62 ..       1      66 [. 0.75

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4e-05
                                   HHHHHHHHHTT--TT-EEEEETTEEEEEESSTTSS-HHHHHHH CS
                Thioredoxin_15 132 kalqkflrvlglepgqnavilNGRvvgpidedeefsaeDfelL 174
                                    ++  +l++lgl +++ +vi+NG+ v  +++ +  + +D   L
  gi|13540947|ref|NP_110635.1|  22 MSVGDILKDLGLPEEEYVVIVNGKPV--LADHTVKKDDDVVIL 62 
                                   578899******************99..666655555665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-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 0.29s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 437.61
//
Query:       gi|13540948|ref|NP_110636.1|  [L=437]
Description: tRNA CCA-pyrophosphorylase [Thermoplasma volcanium GSS1]
Scores for complete 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-40  135.7   0.0    1.4e-39  134.8   0.0    1.5  1  tRNA_NucTransf2  tRNA nucleotidyltransferase, second domain
    1.3e-18   67.0   0.0    3.4e-18   65.7   0.0    1.7  1  NTP_transf_2     Nucleotidyltransferase domain
      4e-06   27.1   0.1    1.2e-05   25.5   0.0    1.8  2  SMODS            Second Messenger Oligonucleotide or Dinucleo
      0.002   18.2   0.0     0.0049   16.9   0.0    1.6  1  Polbeta          Polymerase beta, Nucleotidyltransferase


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 !  134.8   0.0   3.2e-43   1.4e-39       1     112 [.     149     254 ..     149     255 .. 0.97

  Alignments for each domain:
  == domain 1  score: 134.8 bits;  conditional E-value: 3.2e-43
                                   HHHHHHHHHHHHTT-BSSSTTT-SB-HHHHHHHHHHHSSHHHHHHHHTT--TTEEEE......EEE..-SS-EEEETTEEE CS
               tRNA_NucTransf2   1 devrllKkflkgigvYGselkvkGfsGYlaEllvleygsfeevleaaakwkpkvvidleekeallkkfdeplvviDPvDpk 81 
                                   d+vrllK f+k++gvYG+e ++ GfsGYl+Ell+++yg+fe+vl+  ++ + +++id        ++f++p+v+iDPvDp+
  gi|13540948|ref|NP_110636.1| 149 DQVRLLKVFMKSVGVYGAEARTYGFSGYLCELLIIRYGNFENVLRLFSTTRGRLKID------DDERFEDPMVLIDPVDPD 223
                                   79******************************************************8......3578************** PP

                                   EETTTTS-HHHHHHHHHHHHHHHHS--GGGG CS
               tRNA_NucTransf2  82 RNvaaalsleklaefilaareflkkpseeff 112
                                   RNva+a+sle+l+++ +a+++fl++pse+ff
  gi|13540948|ref|NP_110636.1| 224 RNVASAVSLESLSRMRIASKMFLDNPSESFF 254
                                   ******************************9 PP

>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.7   0.0   7.5e-22   3.4e-18       3      94 ..      31     134 ..      30     135 .. 0.94

  Alignments for each domain:
  == domain 1  score: 65.7 bits;  conditional E-value: 7.5e-22
                                   HHHHHHHHHTTTSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHH............HHHEHHHHHHHHCCCEEECTTEEE CS
                  NTP_transf_2   3 klleelkelepvakvvlfGSyarGtalkgSDiDllvvlpeevsre............kkeegleklaeiikfleellglev 71 
                                   ++ e+++ ++  a+ vl+GSya+Gt+lk+ D+Dl++ ++++ ++               ++g+ek+ae++++  e+ g+++
  gi|13540948|ref|NP_110636.1|  31 RASEICRHKNIRADPVLVGSYAKGTNLKDGDLDLFIAFDRDYEEKimeklglsighdLLPNGKEKYAEHPYVSGEIDGIKI 111
                                   56799999999******************************6655************88899******************* PP

                                   EEECEEECCCCTEEEEEECEEEH CS
                  NTP_transf_2  72 dlvtrekledpllvksileerpl 94 
                                   d+v++ k+e+  +++s++++++l
  gi|13540948|ref|NP_110636.1| 112 DVVPCFKMEFGQKKISAVDRTLL 134
                                   **********9999999999876 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 !   25.5   0.0   2.8e-09   1.2e-05      11     140 ..       8     126 ..       3     132 .. 0.78
   2 ?   -3.2   0.1       1.8     8e+03      14      39 ..     384     409 ..     382     419 .. 0.70

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 2.8e-09
                         SMODS  11 lsnielsqttkdsissrvkaitkrLnkdfrelkskiaesllvGSyardTaikpvsdkdmlfeldvdllvvvnevegdepsd 91 
                                   l+  ++ +++ ++++s  + +t+r ++     k+  a+ +lvGSya++T +k   d+      d dl+++++    d  ++
  gi|13540948|ref|NP_110636.1|   8 LNRYRPDEQELQKLKSISEYLTTRASEIC-RHKNIRADPVLVGSYAKGTNLK---DG------DLDLFIAFDR---DYEEK 75 
                                   55566777777777777777777777666.5677788899***********9...55......7888888887...56679 PP

                         SMODS  92 lleklkkal..kktyksseirqdrqvvvvelneikidvvPavenkdgsyei 140
                                   ++ekl  ++  +   + +e+  +++ v  e+++ikidvvP+++ + g+ +i
  gi|13540948|ref|NP_110636.1|  76 IMEKLGLSIghDLLPNGKEKYAEHPYVSGEIDGIKIDVVPCFKMEFGQKKI 126
                                   9********84444456788899********************99887666 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.8
                         SMODS  14 ielsqttkdsissrvkaitkrLnkdf 39 
                                   i ls+  k si ++ +++++ ++ ++
  gi|13540948|ref|NP_110636.1| 384 IVLSNISKYSIGKNLDKLKNTIKVQK 409
                                   67777778888888888888877554 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   1.1e-06    0.0049      17      44 ..      46      75 ..      31      93 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.1e-06
                                  TEEEEEE-S------EEEEEEEESS-..-- CS
                       Polbeta 17 ylFGSrakgkareeSDiDlavllkek..ld 44
                                  +l GS+akg+  ++ D+Dl++ ++++  ++
  gi|13540948|ref|NP_110636.1| 46 VLVGSYAKGTNLKDGDLDLFIAFDRDyeEK 75
                                  789*********************993322 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (437 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       378  (0.0210832); 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: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 3185.12
//
Query:       gi|13540949|ref|NP_110637.1|  [L=119]
Description: nascent polypeptide-associated complex protein [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.3e-12   46.2   1.9    3.3e-12   46.2   1.9    1.5  2  NAC          NAC domain
     0.0092   16.5   0.4      0.012   16.2   0.4    1.4  1  SPT6_acidic  Acidic N-terminal SPT6
  ------ inclusion threshold ------
       0.11   12.5   1.0        0.2   11.7   0.7    1.6  2  DUF3764      Protein of unknown function (DUF3764)


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 !   46.2   1.9   5.5e-16   3.3e-12       2      56 ..       9      66 ..       8      67 .. 0.97
   2 ?   -2.8   0.0       1.1   6.7e+03      28      40 ..      82      94 ..      79     100 .. 0.58

  Alignments for each domain:
  == domain 1  score: 46.2 bits;  conditional E-value: 5.5e-16
                           NAC  2 kKlrkalkklgl..keipgieeVtirksdgkvlvfdnPkVq..kspgsntyvvfGeaee 56
                                  +++r+ ++++g+  +e++++++V++  ++ k +v++n++V+  +++g +t++v+G+++e
  gi|13540949|ref|NP_110637.1|  9 REMRRLMAQMGIksTEMDDVKKVIFVGKE-KDYVIENAQVTmiEAQGVKTFQVVGDFRE 66
                                  78************************999.**************************987 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.1
                           NAC 28 dgkvlvfdnPkVq 40
                                  d+  lv d+  V 
  gi|13540949|ref|NP_110637.1| 82 DDIKLVMDQTGVA 94
                                  4466666665554 PP

>> SPT6_acidic  Acidic N-terminal SPT6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.4     2e-06     0.012      47      76 ..      69      98 ..      23     107 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2e-06
                   SPT6_acidic 47 kkrreeeedaLdedDldLieentgvkvkrk 76
                                  kk++ ++e+   edD++L++++tgv +++ 
  gi|13540949|ref|NP_110637.1| 69 KKQEGKKEETFPEDDIKLVMDQTGVAREKA 98
                                  2333356679***************99875 PP

>> DUF3764  Protein of unknown function (DUF3764)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.7   3.4e-05       0.2      20      75 ..       6      54 ..       4      67 .. 0.91
   2 ?   -1.6   0.0      0.49     3e+03       6      21 ..      57      72 ..      53      96 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.4e-05
                       DUF3764 20 fdseeakkmhkevgikslyrGvskdDpkkvivifqapegvaekifedakelveasG 75
                                  ++s e++++++++giks    + +dD kkvi + + +  v+e+    +  ++ea+G
  gi|13540949|ref|NP_110637.1|  6 MNSREMRRLMAQMGIKS----TEMDDVKKVIFVGKEKDYVIENA---QVTMIEAQG 54
                                  89*************98....79**************9999988...788999998 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.49
                       DUF3764  6 tFkisktFeewaaifd 21
                                  tF++   F e  +  +
  gi|13540949|ref|NP_110637.1| 57 TFQVVGDFRETPKKQE 72
                                  6666666666554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       769  (0.0428914); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.32u 0.22s 00:00:00.54 Elapsed: 00:00:00.35
# Mc/sec: 1026.28
//
Query:       gi|13540950|ref|NP_110638.1|  [L=140]
Description: ferredoxin [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      6e-12   44.8  19.9    3.3e-07   29.8   3.3    2.5  3  Fer4      4Fe-4S binding domain
    3.8e-07   30.6  21.1      6e-06   26.8  12.9    2.1  2  Fer4_7    4Fe-4S dicluster domain
    5.6e-07   29.6  11.6    1.5e-05   25.0  12.2    2.2  2  Fer4_10   4Fe-4S dicluster domain
      2e-06   27.8  10.0    0.00034   20.7   2.0    2.2  2  Fer4_21   4Fe-4S dicluster domain
    8.1e-06   25.9  10.8    5.6e-05   23.2  11.3    1.9  2  Fer4_9    4Fe-4S dicluster domain
    0.00024   21.5  10.9    0.00087   19.7  10.7    1.9  2  Fer4_8    4Fe-4S dicluster domain
    0.00024   21.8  16.5     0.0082   17.0   4.9    2.4  2  Fer4_3    4Fe-4S binding domain
    0.00058   19.8  19.2      0.098   12.8   7.2    2.5  2  Fer4_6    4Fe-4S binding domain
     0.0013   19.3  10.5      0.016   15.7   0.4    2.6  3  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
     0.0015   19.4  23.6     0.0085   17.0  13.0    2.2  3  Fer4_16   4Fe-4S double cluster binding domain
  ------ inclusion threshold ------
      0.015   15.8  11.0       0.21   12.2  12.2    2.0  2  Fer4_17   4Fe-4S dicluster domain
      0.038   14.5  13.5       0.56   10.8   5.6    2.5  2  Fer4_4    4Fe-4S binding domain
      0.073   13.8   0.3      0.073   13.8   0.3    3.2  3  Fer4_15   4Fe-4S single cluster domain
       0.17   12.1  11.6        0.1   12.8   2.4    2.2  2  Fer4_18   4Fe-4S dicluster domain
       0.93    9.7  18.3        2.3    8.5   4.2    2.6  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 !   24.1   4.9   1.8e-08   2.1e-05       2      21 ..      60      79 ..      59      82 .. 0.92
   2 ?   -2.8   0.1       5.7   6.8e+03       5       8 ..     110     113 ..     108     114 .. 0.77
   3 !   29.8   3.3   2.7e-10   3.3e-07       3      24 .]     116     137 ..     115     137 .. 0.92

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 1.8e-08
                                  EEETTTSSS-THHHHHSTTT CS
                          Fer4  2 videekCigCGaCvevCPvg 21
                                   +d++ Ci+ GaC++vCPv+
  gi|13540950|ref|NP_110638.1| 60 AVDWDCCIADGACMDVCPVN 79
                                  69*****************8 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 5.7
                                   TTTS CS
                          Fer4   5 eekC 8  
                                   ++kC
  gi|13540950|ref|NP_110638.1| 110 TDKC 113
                                   6999 PP

  == domain 3  score: 29.8 bits;  conditional E-value: 2.7e-10
                                   EETTTSSS-THHHHHSTTTEEE CS
                          Fer4   3 ideekCigCGaCvevCPvgAIt 24 
                                   + e++Ci+C+aC++vCPv AI+
  gi|13540950|ref|NP_110638.1| 116 VRESDCIFCMACESVCPVRAIK 137
                                   6799*****************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 !   15.2   1.1     2e-05     0.024      29      51 ..      57      79 ..      23      80 .. 0.72
   2 !   26.8  12.9     5e-09     6e-06       2      52 .]      66     135 ..      65     135 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2e-05
                        Fer4_7 29 ekveidpekClgCgaCvavCPtg 51
                                   +v++d + C+  gaC++vCP++
  gi|13540950|ref|NP_110638.1| 57 THVAVDWDCCIADGACMDVCPVN 79
                                  677999999************97 PP

  == domain 2  score: 26.8 bits;  conditional E-value: 5e-09
                        Fer4_7   2 CigCgaCvaaCpvkaield..........eeenekgtekv.........eidpekClgCgaCvavCPtga 52 
                                   Ci  gaC+++Cpv+  e++          ++++ekg +++          +++++C++C aC++vCP+ a
  gi|13540950|ref|NP_110638.1|  66 CIADGACMDVCPVNLYEWNlnpgksgtgnDKKVEKGSDEWnkyrtdkcdPVRESDCIFCMACESVCPVRA 135
                                   9999*************99666655555434444444444444555443356778************976 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0  12.2   1.2e-08   1.5e-05       1      56 []      58     132 ..      58     132 .. 0.80
   2 !   12.5   3.4   9.7e-05      0.12       7      21 ..     119     133 ..     114     139 .. 0.77

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 1.2e-08
                       Fer4_10   1 kvvidddtCirCgkCvkaCPadl...................tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                   +v +d d+Ci  g+C+++CP++l                   ++++  +++  ++ + +  ++C++c aC ++CP
  gi|13540950|ref|NP_110638.1|  58 HVAVDWDCCIADGACMDVCPVNLyewnlnpgksgtgndkkveKGSDEWNKYRTDKCDPVRESDCIFCMACESVCP 132
                                   5678999**************99***********88877777555555555555555556678888********9 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 9.7e-05
                       Fer4_10   7 dtCirCgkCvkaCPa 21 
                                   + Ci C +C ++CP+
  gi|13540950|ref|NP_110638.1| 119 SDCIFCMACESVCPV 133
                                   678888888888888 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   1.3   0.00017       0.2      32      53 ..      57      78 ..      49      81 .. 0.87
   2 !   20.7   2.0   2.9e-07   0.00034      29      58 ..     109     137 ..      98     138 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00017
                       Fer4_21 32 tvlkvvedeCvGCnlCssvCPv 53
                                  t+++v  d C++   C++vCPv
  gi|13540950|ref|NP_110638.1| 57 THVAVDWDCCIADGACMDVCPV 78
                                  67888999*************9 PP

  == domain 2  score: 20.7 bits;  conditional E-value: 2.9e-07
                       Fer4_21  29 daktvlkvvedeCvGCnlCssvCPvedcie 58 
                                    +++  +v+e++C+ C  C svCPv  +i+
  gi|13540950|ref|NP_110638.1| 109 RTDKCDPVRESDCIFCMACESVCPV-RAIK 137
                                   56677799****************9.7775 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   1.0    0.0018       2.1      33      49 ..      54      79 ..      27      81 .. 0.63
   2 !   23.2  11.3   4.6e-08   5.6e-05       2      51 .]      66     136 ..      63     136 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0018
                        Fer4_9 33 e........eaC.igCgaCveaCpkg 49
                                           ++C i  gaC+++Cp +
  gi|13540950|ref|NP_110638.1| 54 IhgthvavdWDCcIADGACMDVCPVN 79
                                  04445555544438888899999975 PP

  == domain 2  score: 23.2 bits;  conditional E-value: 4.6e-08
                        Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraase.....................eaCigCgaCveaCpkgai 51 
                                   C+  gaC+++Cp ++++   +++k    ++++                     ++Ci+C+aC+ +Cp  ai
  gi|13540950|ref|NP_110638.1|  66 CIADGACMDVCPVNLYEWNLNPGKSGTGNDKKvekgsdewnkyrtdkcdpvreSDCIFCMACESVCPVRAI 136
                                   666699***********999999999888777999******************99************9887 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.9   0.00018      0.22      44      64 ..      49      79 ..      21      80 .. 0.59
   2 !   19.7  10.7   7.3e-07   0.00087       3      63 ..      64     133 ..      62     135 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00018
                        Fer4_8 44 e..........eealwsCttcgaCtevCpvg 64
                                             +  ++ C + gaC +vCpv+
  gi|13540950|ref|NP_110638.1| 49 PtklgihgthvAVDWDCCIADGACMDVCPVN 79
                                  0334444444466678889999999999987 PP

  == domain 2  score: 19.7 bits;  conditional E-value: 7.3e-07
                        Fer4_8   3 ekCieCgaCqsaCpvlrr.tk.khlldargeaae.....dvqeeqvlee.......eealwsCttcgaCtevCpv 63 
                                   + Ci  gaC++ Cpv    ++ +  ++  g+ ++     d+++     +             C  c+aC++vCpv
  gi|13540950|ref|NP_110638.1|  64 DCCIADGACMDVCPVNLYeWNlNPGKSGTGNDKKvekgsDEWN-----KyrtdkcdPVRESDCIFCMACESVCPV 133
                                   569999********64442333555555555555555442222.....13334566666799************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 !   10.3   3.7   0.00096       1.1       1      14 [.      66      79 ..      64      79 .. 0.76
   2 !   17.0   4.9   6.8e-06    0.0082       1      15 []     121     135 ..     121     135 .. 0.97

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00096
                        Fer4_3  1 CtgCgaCvevCPvg 14
                                  C+  gaC++vCPv+
  gi|13540950|ref|NP_110638.1| 66 CIADGACMDVCPVN 79
                                  33337*******97 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 6.8e-06
                        Fer4_3   1 CtgCgaCvevCPvgA 15 
                                   C+ C+aC+ vCPv+A
  gi|13540950|ref|NP_110638.1| 121 CIFCMACESVCPVRA 135
                                   *************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 !   12.6   4.1   9.5e-05      0.11       2      22 ..      59      79 ..      58      81 .. 0.87
   2 !   12.8   7.2   8.2e-05     0.098       6      24 .]     118     136 ..     108     136 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 9.5e-05
                        Fer4_6  2 veidpdkCigCgdCvrvCPeg 22
                                  v++d d Ci  g+C++vCP +
  gi|13540950|ref|NP_110638.1| 59 VAVDWDCCIADGACMDVCPVN 79
                                  6788899************87 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 8.2e-05
                        Fer4_6   6 pdkCigCgdCvrvCPegai 24 
                                   ++ Ci C++C++vCP  ai
  gi|13540950|ref|NP_110638.1| 118 ESDCIFCMACESVCPVRAI 136
                                   344556*********9997 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       9.9   1.2e+04      19      34 ..      14      27 ..      13      41 .. 0.54
   2 !   15.7   0.4   1.3e-05     0.016       1      21 [.      61      82 ..      61     107 .. 0.79
   3 !    8.7   2.5    0.0021       2.5       4      17 ..     119     132 ..     116     136 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 9.9
                       Fer4_13 19 vFeeddeggasvvaeq 34
                                  +F e+d++  + ++ q
  gi|13540950|ref|NP_110638.1| 14 HFLENDKD--YPITGQ 27
                                  56666653..333333 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 1.3e-05
                       Fer4_13  1 VDrdtCiacgaCvelaP.dvFe 21
                                  VD d Cia+gaC +++P +++e
  gi|13540950|ref|NP_110638.1| 61 VDWDCCIADGACMDVCPvNLYE 82
                                  899**************44555 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.0021
                       Fer4_13   4 dtCiacgaCvelaP 17 
                                   + Ci c+aC +++P
  gi|13540950|ref|NP_110638.1| 119 SDCIFCMACESVCP 132
                                   78***********9 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   1.8    0.0036       4.3      55      67 .]      67      79 ..      54      79 .. 0.65
   2 !   17.0  13.0   7.1e-06    0.0085       2      66 ..      66     133 ..      65     134 .. 0.69
   3 !   14.5   2.8   4.4e-05     0.052       2      18 ..     121     137 ..     120     139 .. 0.92

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0036
                       Fer4_16 55 tgCdiCqdvCPan 67
                                  +  ++C+dvCP+n
  gi|13540950|ref|NP_110638.1| 67 IADGACMDVCPVN 79
                                  3334677777766 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 7.1e-06
                       Fer4_16   2 CgtCgkCaevCPtnaikek....kekeiearecisyntaekkdlaedeekckkqeaitgCdiCqdvCPa 66 
                                   C+  g+C++vCP+n  + +    k+ +  +++++++  +e +++++d+    ++ ++++C +C+ vCP+
  gi|13540950|ref|NP_110638.1|  66 CIADGACMDVCPVNLYEWNlnpgKSGT-GNDKKVEKGSDEWNKYRTDKCDPVRESDCIFCMACESVCPV 133
                                   88889*********9775521112222.233344445566667777777777889*************7 PP

  == domain 3  score: 14.5 bits;  conditional E-value: 4.4e-05
                       Fer4_16   2 CgtCgkCaevCPtnaik 18 
                                   C+ C +C +vCP++aik
  gi|13540950|ref|NP_110638.1| 121 CIFCMACESVCPVRAIK 137
                                   999************97 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.6   0.00059      0.71      41      60 ..      61      80 ..      23      81 .. 0.71
   2 ?   12.2  12.2   0.00018      0.21       2      57 ..      66     132 ..      65     135 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00059
                       Fer4_17 41 ekaslCieCgeCerkCPqgl 60
                                    ++ Ci  g C  +CP +l
  gi|13540950|ref|NP_110638.1| 61 VDWDCCIADGACMDVCPVNL 80
                                  47899************887 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00018
                       Fer4_17   2 CiqCgyClpeCps..yeaydnepkk.llraakl.....glleeaeke..e.kaslCieCgeCerkCP 57 
                                   Ci  g+C+++Cp   ye++ n  k+ + ++ k+     + +++  ++  + + s+Ci C  Ce++CP
  gi|13540950|ref|NP_110638.1|  66 CIADGACMDVCPVnlYEWNLNPGKSgTGNDKKVekgsdEWNKYRTDKcdPvRESDCIFCMACESVCP 132
                                   88889*******744666666544324444444333332333333333334789************* PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   1.0    0.0036       4.3       4      17 .]      66      79 ..      61      83 .. 0.85
   2 ?   10.8   5.6   0.00047      0.56       4      16 ..     121     133 ..     110     134 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0036
                        Fer4_4  4 CigCgsCvaaCPqg 17
                                  Ci  g+C+++CP++
  gi|13540950|ref|NP_110638.1| 66 CIADGACMDVCPVN 79
                                  666699******75 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00047
                        Fer4_4   4 CigCgsCvaaCPq 16 
                                   Ci C++C+++CP+
  gi|13540950|ref|NP_110638.1| 121 CIFCMACESVCPV 133
                                   899*********7 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.3   6.1e-05     0.073       1      19 [.      59      77 ..      59     105 .. 0.92
   2 ?   -0.9   5.2       2.4   2.9e+03       6      19 ..     119     132 ..     116     135 .. 0.86
   3 ?    2.8   1.2      0.17     2e+02      57      66 .]     129     138 ..     126     138 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6.1e-05
                       Fer4_15  1 VvvDrdaCigcglCvaeap 19
                                  V vD+d Ci +g+C++++p
  gi|13540950|ref|NP_110638.1| 59 VAVDWDCCIADGACMDVCP 77
                                  89****************8 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 2.4
                       Fer4_15   6 daCigcglCvaeap 19 
                                   + Ci c +C  ++p
  gi|13540950|ref|NP_110638.1| 119 SDCIFCMACESVCP 132
                                   68*******99998 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.17
                       Fer4_15  57 raCPvdAIrv 66 
                                   ++CPv AI +
  gi|13540950|ref|NP_110638.1| 129 SVCPVRAIKI 138
                                   58******87 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   1.7     0.021        25      59      74 ..      64      79 ..      31      84 .. 0.80
   2 ?   12.8   2.4   8.7e-05       0.1      44      74 ..     104     134 ..      81     139 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.021
                       Fer4_18 59 gdcidcescvkvcPtg 74
                                    ci+ ++c++vcP++
  gi|13540950|ref|NP_110638.1| 64 DCCIADGACMDVCPVN 79
                                  45899999******86 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 8.7e-05
                       Fer4_18  44 kkalkekeerkekgagdcidcescvkvcPtg 74 
                                   + ++ ++++     ++dci c +c +vcP+ 
  gi|13540950|ref|NP_110638.1| 104 EWNKYRTDKCDPVRESDCIFCMACESVCPVR 134
                                   3344455666778899*************85 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   4.2    0.0019       2.3       2      21 ..      58      77 ..      57      78 .. 0.89
   2 ?    6.7   6.2    0.0072       8.6       7      21 ..     119     132 ..     108     133 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0019
                        Fer4_2  2 pvvvdtdrCigCgaCvsaCP 21
                                  +v+vd d Ci+ gaC ++CP
  gi|13540950|ref|NP_110638.1| 58 HVAVDWDCCIADGACMDVCP 77
                                  789999999987******** PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0072
                        Fer4_2   7 tdrCigCgaCvsaCP 21 
                                   +d Ci C aC s+CP
  gi|13540950|ref|NP_110638.1| 119 SD-CIFCMACESVCP 132
                                   45.999********* PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); expected 358.6 (0.02)
Passed bias filter:                      201  (0.0112109); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 851.04
//
Query:       gi|13540951|ref|NP_110639.1|  [L=163]
Description: hypothetical protein TVN0120 [Thermoplasma volcanium GSS1]
Scores for complete 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   59.1   0.0    7.9e-16   58.3   0.0    1.4  1  PIN_6         PIN domain of ribonuclease
    2.7e-05   23.7   0.1     0.0008   18.9   0.0    2.1  2  PIN_5         PINc domain ribonuclease
    7.6e-05   22.7   0.5     0.0005   20.0   0.3    2.4  2  DUF4411       Domain of unknown function (DUF4411)
     0.0017   18.6   0.1     0.0045   17.2   0.0    1.7  2  PIN_2         PIN domain
     0.0036   17.4   1.8     0.0064   16.6   1.8    1.3  1  NOB1_Zn_bind  Nin one binding (NOB1) Zn-ribbon like
  ------ inclusion threshold ------
      0.011   16.2   0.4      0.086   13.3   0.4    2.2  1  PIN           PIN domain
      0.039   14.0   0.0      0.057   13.5   0.0    1.2  1  Mut7-C        Mut7-C RNAse domain
      0.057   13.6   0.3      0.095   12.9   0.3    1.3  1  zf-piccolo    Piccolo Zn-finger
       0.09   12.9   3.0       0.21   11.8   3.0    1.6  1  Zn-ribbon_8   Zinc ribbon domain
       0.11   12.2   0.1        0.2   11.4   0.1    1.4  1  DUF5615       Domain of unknown function (DUF5615)
       0.98    9.5   4.3        1.7    8.7   4.3    1.4  1  ADK_lid       Adenylate kinase, active site lid
        2.7    8.6   6.0         13    6.5   0.9    2.3  2  zf-C2H2       Zinc finger, C2H2 type


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 !   58.3   0.0   5.3e-19   7.9e-16       2      88 ..       4      87 ..       3      88 .. 0.96

  Alignments for each domain:
  == domain 1  score: 58.3 bits;  conditional E-value: 5.3e-19
                         PIN_6  2 VlDagaliknslsslqnlaeklyttpeVvaEirdkkarerlellplelevrePspesvkkvtefakktGDlsvLSktDievlA 84
                                  VlD++a+i++   +++ l   l+  ++V+ Eir+ k +  l+ l   +++ +P++ +v+ v+++a+ktGDl  LS tDiev+A
  gi|13540951|ref|NP_110639.1|  4 VLDTSAIISR---NINLLDGDLLFPSSVIGEIRKGKLKYMLDALFPMIRIVDPDQYYVRSVEDAAHKTGDLMNLSGTDIEVIA 83
                                  9*******98...7888899************************99************************************* PP

                         PIN_6 85 Ltye 88
                                  ++++
  gi|13540951|ref|NP_110639.1| 84 VAMQ 87
                                  9986 PP

>> PIN_5  PINc domain ribonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0      0.04        60       1      15 [.       2      16 ..       2      52 .. 0.80
   2 !   18.9   0.0   5.4e-07    0.0008     156     195 ..      75     114 ..      64     122 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.04
                         PIN_5  1 rfvlDTsaltdpevr 15
                                  ++vlDTsa++ +++ 
  gi|13540951|ref|NP_110639.1|  2 KYVLDTSAIISRNIN 16
                                  79*******998875 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 5.4e-07
                         PIN_5 156 saeDldvllLAkELdaavvssDeGikkwaeklGlrlveak 195
                                   s  D++v+  A+   a++v++D  i+++a+ l + +++a+
  gi|13540951|ref|NP_110639.1|  75 SGTDIEVIAVAMQYGATIVTDDYSIQNVASALKIAFMNAN 114
                                   678**********************************995 PP

>> DUF4411  Domain of unknown function (DUF4411)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.35   5.2e+02       1      11 [.       3      13 ..       3      26 .. 0.86
   2 !   20.0   0.3   3.3e-07    0.0005      96     138 ..      68     109 ..       9     154 .. 0.66

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.35
                       DUF4411  1 YllDtnvfiea 11
                                  Y+lDt+++i+ 
  gi|13540951|ref|NP_110639.1|  3 YVLDTSAIISR 13
                                  9*******964 PP

  == domain 2  score: 20.0 bits;  conditional E-value: 3.3e-07
                       DUF4411  96 aakkeflsvaDpfliAaAlaknatvVTkEvkkpnkkknkvkIP 138
                                   + +   ls  D  +iA+A++++at+VT + + +n    + kI 
  gi|13540951|ref|NP_110639.1|  68 TGDLMNLSGTDIEVIAVAMQYGATIVTDDYSIQNVAS-ALKIA 109
                                   224455699**********************666666.44442 PP

>> PIN_2  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       3.3     5e+03       1      13 [.       4      16 ..       4      29 .. 0.75
   2 !   17.2   0.0     3e-06    0.0045      52     114 ..      32      98 ..      27     108 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 3.3
                         PIN_2  1 VvdaNivvsallk 13
                                  V+d+ +++s+ ++
  gi|13540951|ref|NP_110639.1|  4 VLDTSAIISRNIN 16
                                  7899999998886 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 3e-06
                         PIN_2  52 lseeeleellelletkikiveeslye..skikeAker..iarvDpdDtpfvAlaLlleapiWTeDkd 114
                                   + + +l+ +l++l+  i+iv+  +y+  s++  A++   + +    D+ ++A+a++  a i T+D  
  gi|13540951|ref|NP_110639.1|  32 IRKGKLKYMLDALFPMIRIVDPDQYYvrSVEDAAHKTgdLMNLSGTDIEVIAVAMQYGATIVTDDYS 98 
                                   66778999************99988884555555554222344679*******************75 PP

>> NOB1_Zn_bind  Nin one binding (NOB1) Zn-ribbon like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   1.8   4.3e-06    0.0064       3      32 ..     120     148 ..     118     155 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 4.3e-06
                  NOB1_Zn_bind   3 rvkswvlrChaCfkvtkdmtkkFCpkCGnk 32 
                                   +  swv+rC++C k++++  k+ C+ CG++
  gi|13540951|ref|NP_110639.1| 120 KQISWVYRCTGCKKIFHEPVKV-CDICGHN 148
                                   5669************998886.*****97 PP

>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.4   5.8e-05     0.086      64     120 ..      44     103 ..       3     105 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.8e-05
                                   HHHTSEEEEBCHHHHHHHHHHHHHHH....SBHHHHHHHHHHHHHT-EEE.ESSTHHHHHH CS
                           PIN  64 llsalkilpidaeiaeeaaeialkyg....llpnDaliaAtAkehgikliatfDedfrrva 120
                                   l + ++i++ d   ++ +++ a k g    l+  D  ++A+A ++g++++ t D  + +va
  gi|13540951|ref|NP_110639.1|  44 LFPMIRIVDPDQYYVRSVEDAAHKTGdlmnLSGTDIEVIAVAMQYGATIV-TDDYSIQNVA 103
                                   467789999999999999999999999999*****************888.***9999887 PP

>> Mut7-C  Mut7-C RNAse domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   3.8e-05     0.057       8     104 ..      40     153 ..      36     162 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.8e-05
                        Mut7-C   8 mlgklakyLRllGydalyasdv...............edeellalaakekrillTrdreLlkraklkkg..vlltsrdvee 71 
                                   ml  l  ++R++  d  y ++v               +d e++a a++ + +++T d ++ + a++ k   +  + +++++
  gi|13540951|ref|NP_110639.1|  40 MLDALFPMIRIVDPDQYYVRSVedaahktgdlmnlsgTDIEVIAVAMQYGATIVTDDYSIQNVASALKIafMNANIKSISK 120
                                   7777777788888888877766677788888888888999********************9999988775444477899** PP

                        Mut7-C  72 qlreviarlglklslkpelsrCvaCngeleeve 104
                                   q+  v +  g+k  +++ ++ C  C +++++  
  gi|13540951|ref|NP_110639.1| 121 QISWVYRCTGCKKIFHEPVKVCDICGHNVKRHY 153
                                   *************99999********9998754 PP

>> zf-piccolo  Piccolo Zn-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.3   6.3e-05     0.095      13      45 ..     118     156 ..     109     159 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.3e-05
                    zf-piccolo  13 gskeppnyntCteCkk......qvCnlCGFnptphltek 45 
                                    sk+      Ct Ckk      +vC  CG n + h  +k
  gi|13540951|ref|NP_110639.1| 118 ISKQISWVYRCTGCKKifhepvKVCDICGHNVKRHYDKK 156
                                   4555566678****985555557*********9998876 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   3.0   0.00014      0.21       6      38 ..     126     151 ..     124     153 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00014
                   Zn-ribbon_8   6 YrCeeCghefevlqsisdapltaCPeCgsevrr 38 
                                   YrC+ C++ f        +p ++C  Cg++v+r
  gi|13540951|ref|NP_110639.1| 126 YRCTGCKKIFH-------EPVKVCDICGHNVKR 151
                                   *******9998.......35567********99 PP

>> DUF5615  Domain of unknown function (DUF5615)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00013       0.2      29      57 ..      70      98 ..      48     108 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00013
                       DUF5615 29 elglegasDeeileyAkeedriivTkDkD 57
                                  +l + + +D e++++A + +++ivT D  
  gi|13540951|ref|NP_110639.1| 70 DLMNLSGTDIEVIAVAMQYGATIVTDDYS 98
                                  44444579******************965 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 ?    8.7   4.3    0.0011       1.7       4      30 ..     128     148 ..     126     154 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0011
                                   -TTT--EEETTTB--SSTTB-TTT--. CS
                       ADK_lid   4 CpkCGrsYhvvfnpPkveglCDkCGep 30 
                                   C  C++++h    p     +CD CG +
  gi|13540951|ref|NP_110639.1| 128 CTGCKKIFH---EP---VKVCDICGHN 148
                                   99*******...33...579*****86 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.9    0.0085        13       1      10 [.     126     135 ..     126     138 .. 0.92
   2 ?    4.6   0.3     0.033        49       2      15 ..     141     154 ..     140     157 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0085
                                   EEETTTTEEE CS
                       zf-C2H2   1 ykCpdCgksF 10 
                                   y+C++C+k F
  gi|13540951|ref|NP_110639.1| 126 YRCTGCKKIF 135
                                   9*******99 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.033
                                   EETTTTEEESSHHH CS
                       zf-C2H2   2 kCpdCgksFkrksn 15 
                                   +C++Cg   kr ++
  gi|13540951|ref|NP_110639.1| 141 VCDICGHNVKRHYD 154
                                   6*****99999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       941  (0.0524848); expected 358.6 (0.02)
Passed bias filter:                      604  (0.0336884); 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: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1039.54
//
Query:       gi|13540952|ref|NP_110640.1|  [L=129]
Description: hypothetical protein TVN0121 [Thermoplasma volcanium GSS1]
Scores for complete 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   40.1   0.0    5.5e-10   39.0   0.0    1.6  2  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 !   39.0   0.0   3.1e-14   5.5e-10       1      58 [.      33      89 ..      33      93 .. 0.97
   2 ?   -2.3   0.0      0.23   4.2e+03       7      20 ..      90     103 ..      89     103 .. 0.80

  Alignments for each domain:
  == domain 1  score: 39.0 bits;  conditional E-value: 3.1e-14
                                  EEHHHHHHCTT-S--S-EEEEEEE-HHHHHHHHCC-GGGGGG-SEEEEEEEETTEEEE CS
                        DUF302  1 iDvqatlkkklgedlrpykilgaCnPklatealqadpeiglllPcrvvVyekdgkttv 58
                                  iD q++l k+ g++++p +i+++ nP +a+ + +++  +g+  P+r+ Vy ++gkt+ 
  gi|13540952|ref|NP_110640.1| 33 IDPQQNL-KNAGISIEPQHIFEIFNPVYAKSVFDQNILAGIVPPLRIFVYVSEGKTWM 89
                                  899****.************************************************96 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.23
                                   HHCTT-S--S-EEE CS
                        DUF302   7 lkkklgedlrpyki 20 
                                   +++   e++rpy i
  gi|13540952|ref|NP_110640.1|  90 MRESAIEKFRPYNI 103
                                   67788899999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       733  (0.0408835); expected 358.6 (0.02)
Passed bias filter:                      525  (0.0292822); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 840.57
//
Query:       gi|13540953|ref|NP_110641.1|  [L=526]
Description: Acyl-coenzyme A synthetase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-69  235.1   0.0    1.3e-69  234.9   0.0    1.0  1  AMP-binding      AMP-binding enzyme
    3.5e-26   92.0   0.1    8.8e-26   90.7   0.1    1.7  1  AMP-binding_C    AMP-binding enzyme C-terminal domain
  ------ inclusion threshold ------
       0.04   13.6   0.0         14    5.5   0.0    2.8  2  Glyco_hydro_42C  Beta-galactosidase 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 !  234.9   0.0   2.2e-73   1.3e-69       8     422 ..      14     403 ..       6     404 .. 0.83

  Alignments for each domain:
  == domain 1  score: 234.9 bits;  conditional E-value: 2.2e-73
                                   STTSEEEEE...CCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEETTS-HHH CS
                   AMP-binding   8 tpdkvalvd...sgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvplnptltaee 85 
                                    + k+a+++   + + +  TY+ l +++ +l++++r+l +k g+r++i+++ns++++ ++ a   aG+v++p  p l+ ++
  gi|13540953|ref|NP_110641.1|  14 DKRKTAVIMsdeNLSSKNETYGTLLKESYKLSNFMRQLRLKAGNRILIMMENSLDLYHVVTASIAAGMVYAPTAPILPDDQ 94 
                                   3478888777786678899************************************************************** PP

                                   HHHHHHHHTESEEEETCTCCCHHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS-TSCCCS-BTTSEEEEEE CS
                   AMP-binding  86 layiledseakvliatvdselleklleaaakleavklvivldadellkeeelkeeeeseekaekpeeeeelkpddlayiiY 166
                                   ++y +e+ +ak+++  vd+   ++ +e+ ++     +v ++d     + +++++++ ++  + +  e+ e++ ++   +++
  gi|13540953|ref|NP_110641.1|  95 IKYRVEQLKAKAIF--VDAGT-HQKAEQFGD----IVVNMSD-----EGTRVEISKMDDTFN-DF-ET-EIDGEH--AVFF 158
                                   **************..76544.222222332....2233333.....233344444333222.13.22.355555..789* PP

                                   E--SSSS-EEEEEEHHHHHHHHHHHHHHHCSCCTTT-EEEES.S-TTSCHHHHHHHHHHHHTT-EEEE-TTCGCCHHHHHH CS
                   AMP-binding 167 TSGTTGkPKGVmlshrnlvanvaslkletrfklkeddvvlsi.lplahifglilelllallsGatvvllpkdaaldpklll 246
                                   TSGT G+PK V ++ r+     +++k     +l++ddv + i  p +   g+ ++ + ++++G++v  ++   ++dp++ l
  gi|13540953|ref|NP_110641.1| 159 TSGTEGMPKMVLHTNRYPEGHRTTVK---WLDLNRDDVHWNIsSPGWAKWGW-SSYYSPFIAGSAVFGMSYR-RFDPERAL 234
                                   *****************977767764...3447889***9996677777899.***********99888844.5799999* PP

                                   HHHHHHT-SEEEEEHHHHHHHHHCCCHHCHHHHCCGTT-SEEEEESS-EBHHHHHHHHHHHTCEEEEEEEEGGGSSECEEC CS
                   AMP-binding 247 elieklkvtviagvPrvleallesgalkaakkakdlsslrlvllggeplspellrffralfgeevlegYGlTEttgvvtvl 327
                                   ++++k+++t ++++P+v++++l+++  +      +   l+ + ++gepl+pe++++f++ +g ++ +gYG+TE t +v +l
  gi|13540953|ref|NP_110641.1| 235 DAMSKFQITSVCAPPTVWRMFLQHDVGS------RALYLKKAASAGEPLNPEVIERFEKYTGVKIKDGYGQTESTLMVGNL 309
                                   ***********************97665......444499999**********************************9634 PP

                                   HCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEEEEEEEET....TS-SEBTT-HHHHHHHEEETCCEEEEEEEEEE CS
                   AMP-binding 328 pleedkkklgsvGkplpgvevkivDeetgepvpdgeeGellvrgp....gvmkgYlkkpeataeafdsegrwlrTGDlgrl 404
                                   +  + k+k+gs Gk l   +++ivDe+ g++++ + +G + v+ +    g+++ Y +++++t ++f+ + +++ TGD g++
  gi|13540953|ref|NP_110641.1| 310 T--GMKVKPGSMGKSLEPYDIRIVDEN-GNELGVNRTGFIAVKAEkrpeGLFSAYINDKKLTHDRFK-N-GYYYTGDTGYR 385
                                   4..55569******************9.9*************98877789****************8.5.7********** PP

                                   ETTSEEEEEEECCCEEEE CS
                   AMP-binding 405 dedGyleivgRkkdlikl 422
                                   dedGy+++v R++d+ik 
  gi|13540953|ref|NP_110641.1| 386 DEDGYIWFVSRSDDVIKA 403
                                   ****************96 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 !   90.7   0.1   1.5e-29   8.8e-26       1      76 []     412     490 ..     412     490 .. 0.96

  Alignments for each domain:
  == domain 1  score: 90.7 bits;  conditional E-value: 1.5e-29
                                   HHHHHHHSSTTEEEEEEE-----TTS---EEEEEE------...HHHHHHHHHHHHT-TTTS-SEEEE-S---B-TTS- CS
                 AMP-binding_C   1 evEsalvshpaVaeaaVvGvpdevkGealvafVvlkdgsea...leeeLkahvrkelgpyavpkkvvfvdelpktrsGK 76 
                                   evEsal++hpaV e aVvG pd+++G +++a+Vvlk+g+e+   l++eL   vr ++gp+a+pk+++fv++lpkt sGK
  gi|13540953|ref|NP_110641.1| 412 EVESALLRHPAVVESAVVGSPDDIRGDIVKAYVVLKKGYEPsyeLARELSMLVRNTIGPHARPKRIEFVEDLPKTISGK 490
                                   8**********************************999755578**********************************9 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 ?    5.5   0.0    0.0023        14      16      32 ..     123     140 ..     121     143 .. 0.82
   2 ?    4.9   0.0    0.0036        21      45      57 ..     317     332 ..     307     333 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0023
                                   EEEE-SSS-EE---.-TT CS
               Glyco_hydro_42C  16 FvlNfsneevtvtl.pas 32 
                                   +v+N+s+e ++v++ +++
  gi|13540953|ref|NP_110641.1| 123 IVVNMSDEGTRVEIsKMD 140
                                   89***********95544 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0036
                                   ....SEE-TTEEEEEE CS
               Glyco_hydro_42C  45 g...vtlePygvaVlr 57 
                                   g   + lePy+++++ 
  gi|13540953|ref|NP_110641.1| 317 GsmgKSLEPYDIRIVD 332
                                   445599********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (526 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       611  (0.0340789); 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:                         3  (0.000167327); expected 0.2 (1e-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 0.33s 00:00:01.00 Elapsed: 00:00:00.51
# Mc/sec: 3098.16
//
Query:       gi|13540954|ref|NP_110642.1|  [L=471]
Description: phosphate ABC transporter permease [Thermoplasma volcanium GSS1]
Scores for complete sequence (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  186.0  23.9    1.5e-54  185.6  23.9    1.1  1  Sugar_tr  Sugar (and other) transporter
    1.8e-32  112.7  46.4    3.9e-27   95.1  37.1    2.0  2  MFS_1     Major Facilitator Superfamily
    4.4e-06   26.3  20.6    1.2e-05   24.8   7.4    3.3  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 !  185.6  23.9   2.6e-58   1.5e-54      10     447 ..      34     462 ..      17     465 .. 0.84

  Alignments for each domain:
  == domain 1  score: 185.6 bits;  conditional E-value: 2.6e-58
                                   HHHHHHHHCGGGTHHHHHHHHTSTT--SHHHHHH...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHH CS
                      Sugar_tr  10 llfgYdtgvigafltllkfaknfglsksksskeessvlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfviga 90 
                                   +   Yd+++ig+++++l      g++k       ++++s+l+ s +l+ a+iG+l++g l+d++GRk ++    +++++ga
  gi|13540954|ref|NP_110642.1|  34 FTDAYDLFIIGVVTSILV---LSGWNKF------TTLQSSLLDSTALLSAVIGALIFGRLIDKLGRKTVYGLELIILIVGA 105
                                   555566666666655555...2222222......45678999*************************************** PP

                                   HHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-..TTH CS
                      Sugar_tr  91 vlqaaakgknsvevlivgRvlvGigvGlasvlvPmyisEiApkklRgalvslyqlaitfGilvaaifglglnktsn..adg 169
                                   + +a+ +  n v+vli+ R+++Gig+G+ ++++++ ++E++ +++Rg+lv++  ++ ++G l +  ++lgl +++   +  
  gi|13540954|ref|NP_110642.1| 106 LGSAFLTPLNGVYVLIIWRFILGIGIGGDYATSSTIMAEYSNTAHRGKLVGMVFSMQSLGLLAGPLITLGLLYSGMslSLV 186
                                   ***********************************************************************88888899** PP

                                   HHHHHHCCHHHHHHHHHHGGGS---HHHH.HHTT-HHHHHHHHHHHHHC.HHHHHHHHHHHHHHHHHHH.....HTTHHHH CS
                      Sugar_tr 170 wrillglqlvpallllilllflPESPryl.vekgkeeeakevlaklrge.edadrelaeekdsleaeqeeekaswkellss 248
                                   w++ll++ ++pal++++++  +PE+Pryl   kg+ e+a +  +k  g  + ad +++ +k+s  +   ++k ++ +l+++
  gi|13540954|ref|NP_110642.1| 187 WKLLLAFGAIPALIVVYFRRKMPETPRYLlRVKGDAEAAVKNWEKYTGIeASADAQAEVIKKSWTQI-IKQKEFLITLVGT 266
                                   *****************************55677777888888886666244555555555555555.4456888888888 PP

                                   SH...HHHHHHHHHHHHHHTTHHHHHHHTTTHHHHSS-THH.....HHHHHHHHHHHHHHHHHHHHHHHHS-SHHHHHHHH CS
                      Sugar_tr 249 ktvrqrlligvvlqifqqltGinaimyysptifenlglsks.....llvtiivgvvnfvatfvaiflvdrfGRRtllllGa 324
                                    +       +++++++   + i++   ++  + +++   +      ++  +i+g+  f     a f++dr+GR+t+  +G+
  gi|13540954|ref|NP_110642.1| 267 AG------AWFLMDWALYGNSIMSSSMLGVLVPSSVTGLDHlirttIYSAMIFGFAAFPGYWLATFTIDRIGRKTIQSIGF 341
                                   77......899999999999999999999999888754444255556666677777777777888**************** PP

                                   HHHHHHHHHHH..HHHHTTSS...CHHHHHHHHHHHHHHHTTTTHHHHHHHHHHSHTTTHHHHHHHHHHHHHHHHHHHHHH CS
                      Sugar_tr 325 agmaicfvilgivalllvakskaasivaivfialfialfalgwgpvpwvlvsElfpqsvRskalaiavavnwlanflisll 405
                                   a ma+ f ilg v++ l + s  +   ++   + + ++ ++g++ + +++ +E+fp++vR++++  ++a   +  f+ ++l
  gi|13540954|ref|NP_110642.1| 342 AAMALSFGILG-VFHQLLSPS-YIVQFLLLYGMSY-FFINFGPNVTTFIYPPEVFPTKVRGLGAGASAAGGKIGAFVGTFL 419
                                   **********9.777777774.4444444444444.68899**************************************** PP

                                   HHHHH.CHHHT-HHHHHHHHHHHHHHHHHHHHS--STT--CCC CS
                      Sugar_tr 406 fpiit.eaigggyvflvfaglavlfiifvfffvpetkgrtlee 447
                                     ii+ ++ig+ + f++ a la++++i++++ +pe k ++l+e
  gi|13540954|ref|NP_110642.1| 420 NAIILrSSIGESGLFMILALLAAFGLIITLVLLPEPKKLDLDE 462
                                   99876267889**************************999987 PP

>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.1  37.1   6.6e-31   3.9e-27       3     320 ..      31     381 ..      29     390 .. 0.77
   2 !   23.3   2.0   4.5e-09   2.7e-05     111     186 ..     390     466 ..     382     469 .. 0.89

  Alignments for each domain:
  == domain 1  score: 95.1 bits;  conditional E-value: 6.6e-31
                         MFS_1   3 laaflsalarsilgpalpl.alaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfa 82 
                                   l++f  a++ +i+g++ ++  l+    ++  + +ll ++  l a++++l++Grl+d++Gr+ v+ l l+++++g+l  +f 
  gi|13540954|ref|NP_110642.1|  31 LGFFTDAYDLFIIGVVTSIlVLSGWNKFTTLQSSLLDSTALLSAVIGALIFGRLIDKLGRKTVYGLELIILIVGALGSAFL 111
                                   78999999999999999998888878899999******************************************6666673 PP

                         MFS_1  83 ...sslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllgglla.sslg......Wrav 153
                                      +++++l++ r++ G+g g+ ++++ +++a++++  +rg+ +g++ ++ slG + gpl+   l+ s  g      W ++
  gi|13540954|ref|NP_110642.1| 112 tplNGVYVLIIWRFILGIGIGGDYATSSTIMAEYSNTAHRGKLVGMVFSMQSLGLLAGPLITLGLLyS--GmslslvWKLL 190
                                   4689999*******************************************************988834..34688888888 PP

                         MFS_1 154 fyilaivsllafvlfllllpeepperkrkspkeee.............kgtgpaplvp.awkallkdpvl..........w 210
                                     + ai +l++ v f   +pe+p+   r+++  e              + +++a++++  w+++ k++ +          w
  gi|13540954|ref|NP_110642.1| 191 LAFGAIPALIV-VYFRRKMPETPRYLLRVKGDAEAavknwekytgieaSADAQAEVIKkSWTQIIKQKEFlitlvgtagaW 270
                                   88888888887.433333344444444444444449998888888888444444444467999999998855555555444 PP

                         MFS_1 211 .illialllf.ffgfsg..lltllplylqevlgls..glllaglllallalvgailallagrlsdrlgrrrrlllalllll 285
                                    ++ +al+++  +   +  l +l+p+   +v gl+     ++ +  ++++++++++  la++ +dr+gr+++  +++++++
  gi|13540954|ref|NP_110642.1| 271 fLMDWALYGNsIMS--SsmLGVLVPS---SVTGLDhlI-RTTIYSAMIFGFAAFPGYWLATFTIDRIGRKTIQSIGFAAMA 345
                                   32223333332223..2457777777...666666442.4555556777777777788888888***************** PP

                         MFS_1 286 laalglallavtssavllllvlvliGfglgfv.fps 320
                                   l++ +l ++    s++ ++ +l+l+G+ ++f+ f++
  gi|13540954|ref|NP_110642.1| 346 LSFGILGVFHQLLSPSYIVQFLLLYGMSYFFInFGP 381
                                   ************88888888*******777664433 PP

  == domain 2  score: 23.3 bits;  conditional E-value: 4.5e-09
                         MFS_1 111 adwfpkeergraigllsagfslGailgpllgglla.sslgWravfyilaivsllafvlfllllpeepperkrkspke 186
                                    ++fp + rg++ g  +ag  +Ga +g  l ++++ ss+g +++f+ila+++++++++ l+llpe+++    +s+ e
  gi|13540954|ref|NP_110642.1| 390 PEVFPTKVRGLGAGASAAGGKIGAFVGTFLNAIILrSSIGESGLFMILALLAAFGLIITLVLLPEPKKLDLDESSGE 466
                                   689****************************************************9998899988887776666655 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 !   24.8   7.4   2.1e-09   1.2e-05      24     171 ..      57     207 ..      49     228 .. 0.83
   2 ?    1.6   5.9     0.023   1.4e+02     233     341 ..     311     427 ..     304     450 .. 0.57
   3 !    4.4   0.6    0.0033        20     124     173 ..     407     456 ..     398     468 .. 0.87

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 2.1e-09
                         MFS_4  24 qlslsqagllaaaNylGYLvGallaafalsagaeRlr....llagllatvllllamaltesfaaflliRflaGvasAvvlv 100
                                   +++  q +ll +  +l   +Gal++  +l  +  R +     l+ l++ +l  +    ++++ +++++Rf++G++ +    
  gi|13540954|ref|NP_110642.1|  57 KFTTLQSSLLDSTALLSAVIGALIF-GRLIDKLGRKTvyglELIILIVGALGSAFLTPLNGVYVLIIWRFILGIGIGGDYA 136
                                   68888999***************99.55555555655355433444444444455555789999***************** PP

                         MFS_4 101 fgsslvlahaaaarrervgallfaGvGlGiavsgllvllllqlglsasslWlalavlsavllllvalllpr 171
                                     s+++ + ++ a r+++ +++f+   lG +++ l+ l ll  g+s s +W +l ++ a+  l+v+  +++
  gi|13540954|ref|NP_110642.1| 137 TSSTIMAEYSNTAHRGKLVGMVFSMQSLGLLAGPLITLGLLYSGMSLSLVWKLLLAFGAIPALIVVYFRRK 207
                                   9999999********************************************99988888888888776653 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.023
                         MFS_4 233 llvGlaaivgvlvwlrvakrsglrralaaalliea.....vgvllsllspsplglivssvllGltflaitalvlqlarela 308
                                   +++G aa++g ++ +   +r g +++  + ++  a     +gv+  llsps+++  +   ll ++    ++++ +++ +++
  gi|13540954|ref|NP_110642.1| 311 MIFGFAAFPGYWLATFTIDRIGRKTIQSIGFAAMAlsfgiLGVFHQLLSPSYIVQFL---LLYGMSYFFINFGPNVTTFIY 388
                                   599******************999988776665552222268999999888854444...333333334455555555555 PP

                         MFS_4 309 ppat.....rrllglmTasfg.igQilGpllasllaeat 341
                                   pp++     r l + + a+ g ig  +G  l +++   +
  gi|13540954|ref|NP_110642.1| 389 PPEVfptkvRGLGAGASAAGGkIGAFVGTFLNAIILRSS 427
                                   555443221333333333332366666666666655544 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.0033
                         MFS_4 124 aGvGlGiavsgllvllllqlglsasslWlalavlsavllllvalllpraa 173
                                   aG  +G  v+  l +++l+   ++s l ++la+l+a  l++ ++llp+ +
  gi|13540954|ref|NP_110642.1| 407 AGGKIGAFVGTFLNAIILRSSIGESGLFMILALLAAFGLIITLVLLPEPK 456
                                   67779999**************************************9443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (471 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       691  (0.0385409); 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:                         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: 0.64u 0.29s 00:00:00.93 Elapsed: 00:00:00.48
# Mc/sec: 2972.38
//
Query:       gi|13540955|ref|NP_110643.1|  [L=337]
Description: adenine specific DNA methylase [Thermoplasma volcanium GSS1]
Scores for complete 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   72.3   0.9    5.8e-20   72.0   0.9    1.2  1  N6_N4_Mtase    DNA methylase
  ------ inclusion threshold ------
      0.077   12.6   0.0       0.17   11.5   0.0    1.6  1  Cons_hypoth95  Conserved hypothetical protein 95


Domain annotation for each model (and alignments):
>> N6_N4_Mtase  DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.0   0.9   6.4e-24   5.8e-20       1     129 [.     106     247 ..     106     312 .. 0.82

  Alignments for each domain:
  == domain 1  score: 72.0 bits;  conditional E-value: 6.4e-24
                                   EEEEEE--SSSSSCS........................GCCGCCHHHHHHHHHHHHHHHHHHHEEEEEEEEEEE-CCCHH CS
                   N6_N4_Mtase   1 vdlivtdpPYntgkdy...................endeqyeeedsyeeyleflekvlkevrrvLkddgsifiniddseik 62 
                                   +dli++dpP+  + +y                   ++ ++   +d  + yle ++++l +++++L++ gsi+++id +  +
  gi|13540955|ref|NP_110643.1| 106 IDLIYIDPPFDSKANYrtkihlptadveqmpsvieQFAYSDTWKDGTKSYLEMIVPRLVLMKELLSEKGSIYVHIDWHVGH 186
                                   89*****************************886533344444566889******************************** PP

                                   THHHHHHHHHTT-EEEEEEEEEEESSSTTTSTCCS-B--EEEEEEEESSTT-..---GGGSSBSS-H CS
                   N6_N4_Mtase  63 kelkaladeifggffllnvivwkkpnsmpesnkdrltsthEyilvfsknkkyllkfnldaikvpyee 129
                                   + +k ++deifg+ ++ n ivwkk+n  p+ +++++  +h+ +++++k+ ++   fn  +ik++++e
  gi|13540955|ref|NP_110643.1| 187 Y-VKVIMDEIFGRENFVNEIVWKKTN-SPKAQSKGFGTQHDVLYIYRKTPQF--IFN--QIKKEPDE 247
                                   9.**********999*********95.5555556******************..444..33333333 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   1.9e-05      0.17     109     132 ..     101     124 ..      69     133 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 1.9e-05
                                   -SS-EEEEEEE--SSSTTCH.HHH CS
                 Cons_hypoth95 109 kkkeefdivflDPPyakellieev 132
                                   +  +++d++++DPP+ +++ +++ 
  gi|13540955|ref|NP_110643.1| 101 SMRGKIDLIYIDPPFDSKANYRTK 124
                                   456789*********999876655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       576  (0.0321267); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 2271.89
//
Query:       gi|13540956|ref|NP_110644.1|  [L=348]
Description: adenine specific DNA methylase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-17   64.4   0.0    2.5e-17   63.4   0.0    1.5  1  N6_N4_Mtase    DNA methylase
  ------ inclusion threshold ------
      0.065   12.9   0.0       0.12   12.0   0.0    1.5  1  Cons_hypoth95  Conserved hypothetical protein 95


Domain annotation for each model (and alignments):
>> N6_N4_Mtase  DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.4   0.0   2.8e-21   2.5e-17     172     226 ..      11      65 ..       2      70 .. 0.89

  Alignments for each domain:
  == domain 1  score: 63.4 bits;  conditional E-value: 2.8e-21
                                   -SS---HHHHHHHHHHHS-TT-EEEETT-TTTHHHHHHHHTT-EEEEEESSHHHH CS
                   N6_N4_Mtase 172 HpaqkPvallerlIklstkkgdivlDpFaGSGtTavaakelgrkfiGieieeeyv 226
                                   + +qkP+all+r+I++s+ +++iv+D+FaGSGt +++a++lgrk+i +++ + ++
  gi|13540956|ref|NP_110644.1|  11 YVTQKPEALLKRIIEASSLPDSIVADFFAGSGTLGAVAEKLGRKWIMCDVGKPAC 65 
                                   78***********************************************988666 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   1.3e-05      0.12      40      99 ..      29      96 ..      17     169 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.3e-05
                                  HCC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--T.........TTEEEEES CS
                 Cons_hypoth95 40 iegarvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelklee.........etaelked 99
                                  + ++ v D faGsG+lg  A   g +k ++ +  k a+ i+++ l+ l+++          + +++k++
  gi|13540956|ref|NP_110644.1| 29 LPDSIVADFFAGSGTLGAVAEKLG-RKWIMCDVGKPACMIMRKRLSDLNARPflyqsigdyQKEQFKRS 96
                                  7788899**********7554444.56999******************987664333333223333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (348 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       409  (0.0228122); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.20s 00:00:00.58 Elapsed: 00:00:00.34
# Mc/sec: 3056.13
//
Query:       gi|13540957|ref|NP_110645.1|  [L=502]
Description: Acyl-CoA synthetase (AMP-forming) [Thermoplasma volcanium GSS1]
Scores for complete 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   87.3   0.0    6.9e-16   57.9   0.0    2.8  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 !   25.7   0.0   2.2e-10   3.9e-06       4      79 ..      21      92 ..      18     127 .. 0.85
   2 !   57.9   0.0   3.8e-20   6.9e-16     200     412 ..     210     397 ..     189     402 .. 0.83

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 2.2e-10
                                  HHHHSTTSEEEEECCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEET CS
                   AMP-binding  4 qaaktpdkvalvdsgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvplnp 79
                                   a+k+  +va+++   g+ +TY+ l + v+++A  L+sl+v  gd V+i+l+nsp+ ++++la+ ++G+ +  ln 
  gi|13540957|ref|NP_110645.1| 21 IAEKNSSQVAIYY--LGKPITYSALISMVDSFAFNLKSLDVD-GD-VGIMLRNSPQILISILALNRLGLPAFILNQ 92
                                  6889999****99..9**********************8886.44.**********************99888876 PP

  == domain 2  score: 57.9 bits;  conditional E-value: 3.8e-20
                                   TTT-EEEESS-TTSCHHHHHHHHHHHHTT-EEEE-TTCGCCHHHHHHHHHHHHT-SEEEEEHHHHH.HHHHCCCHHCHHHH CS
                   AMP-binding 200 keddvvlsilplahifglilelllallsGatvvllpkdaaldpklllelieklkvtviagvPrvle.allesgalkaakka 279
                                   + ++ v ++ +l hi +l ++ l++l+sG t+ l+p++ + +    +++iek + ++++g   ++e +ll++         
  gi|13540957|ref|NP_110645.1| 210 GYRKDVAVYSSLNHISSL-IFSLIPLFSGRTLTLMPEFYEVE--KTIKAIEKAESSMLVGNTYLYEeMLLKN--V------ 279
                                   23667899*********9.*****************998844..4689******************444554..2...... PP

                                   CCGTT.-SEEEEESS-EBHHHHHHHHHHHTCEEEEEEEEGGGSSECEECHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBE CS
                   AMP-binding 280 kdlss.lrlvllggeplspellrffralfgeevlegYGlTEttgvvtvlpleedkkklgsvGkplpgvevkivDeetgepv 359
                                    ++++ +r++++ ge ++pe l+ f  ++g+ +  gY  + +tg v+ ++ e  k+   svG +lp++ v i D + g+p+
  gi|13540957|ref|NP_110645.1| 280 -EMPKtIRYLFSIGEYIRPEFLKDFFVKYGKDIKIGYDISAATGLVC-MQ-ELMKNDFDSVGVALPDCTVSISDRS-GKPL 356
                                   .34555**************999999999999**************9.55.44446899***************98.**** PP

                                   ETTSEEEEEEEETTS-SEBTT-HHHHHHHEEETCCEEEEEEEEEEETTSEEEE CS
                   AMP-binding 360 pdgeeGellvrgpgvmkgYlkkpeataeafdsegrwlrTGDlgrldedGylei 412
                                   p ge G + ++++ +        ++t e     g+ l TGDlg++de G+l++
  gi|13540957|ref|NP_110645.1| 357 PVGENGLVKIKSNRIV-------DKTDE-----GGSLSTGDLGHIDESGHLYL 397
                                   ************9665.......45554.....469*************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (502 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.65u 0.30s 00:00:00.95 Elapsed: 00:00:00.49
# Mc/sec: 3051.82
//
Query:       gi|13540958|ref|NP_110646.1|  [L=460]
Description: sugar kinase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      5e-43  147.3   0.2    1.1e-42  146.2   0.0    1.7  2  Carb_kinase      Carbohydrate kinase
    1.4e-35  122.7   0.2    2.7e-35  121.8   0.2    1.5  1  YjeF_N           YjeF-related protein N-terminus
    4.8e-08   32.7   0.0    1.2e-07   31.3   0.0    1.8  1  HK               Hydroxyethylthiazole kinase family
     0.0089   15.4   0.0      0.024   14.0   0.0    1.7  2  Phos_pyr_kin     Phosphomethylpyrimidine kinase
  ------ inclusion threshold ------
       0.08   12.6   0.0       0.17   11.6   0.0    1.5  1  Cation_ATPase_N  Cation transporter/ATPase, N-terminus
      0.086   12.6   0.1        1.8    8.3   0.0    2.4  2  Cupin_2          Cupin domain
       0.13   12.2   0.2       0.29   11.0   0.2    1.6  1  Alba             Alba
       0.13   11.7   1.7       0.15   11.4   0.3    1.8  2  PALP             Pyridoxal-phosphate dependent enzyme
       0.14   12.7   1.1         22    5.7   0.1    3.5  3  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent


Domain annotation for each model (and alignments):
>> Carb_kinase  Carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       1.3   2.5e+03       2      19 ..      47      64 ..      46     101 .. 0.68
   2 !  146.2   0.0   5.6e-46   1.1e-42       2     243 ..     219     452 ..     218     453 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.3
                                  EEEE-BTTCHHHHHHHHH CS
                   Carb_kinase  2 lvigGsedytGAallaal 19
                                  +v++G  + +G a+ aa+
  gi|13540958|ref|NP_110646.1| 47 CVVCGTGNNAGDAIVAAE 64
                                  677777777777766664 PP

  == domain 2  score: 146.2 bits;  conditional E-value: 5.6e-46
                                   EEEE-BTTCHHHHHHHHHHHHCTT-SEEEEEESSTTTCCCCTTTTTCEECCTTHTTTS...--SSS-SEEEE-TT-SSSHC CS
                   Carb_kinase   2 lvigGsedytGAallaalaalrlgaglvsvateseaiavlksylpevivhplledeqakileklerldavviGpGLgrdek 82 
                                   ++++G  +y G  ++aalaa +lg++lv++ +  ++   + sy p +iv  ++ + qa   e+  r +a++iGpGLg+  +
  gi|13540958|ref|NP_110646.1| 219 GIVAG-WEYHGSSVIAALAAENLGLDLVRIYVTNKNYEIVSSYDPGIIVRLFDYKRQA-SYEEVWRNSALLIGPGLGTSHE 297
                                   78999.89********************************************955555.678888**************99 PP

                                   HHHHCHH.HCCCCS-EEEEGGGGGSGGGG...TTTTSSEEEE--HHHHHHHCTTTCHHCCSHHHHHHHHHHHHTTEEEEES CS
                   Carb_kinase  83 ikkllee.vlekdeplviDAdgLnllaqknelserkaeviLTPhkkEfkrLlkaivkkeddrlelarelaqklnavvllkg 162
                                   ++ +l+  v    +p+viDAdg++ll+++  +  + ++++ TPhk Ef +L++          e a e+a++ + +++lkg
  gi|13540958|ref|NP_110646.1| 298 AEIALKRlVNGSAVPIVIDADGITLLSKHL-SIIKGKKIVVTPHKNEFRKLTGTEP-----NEENAVEFAKEKGIIIVLKG 372
                                   998776515567789*************94.77788899***************99.....556677889999******** PP

                                   TTSEEEECTTEEEEE----GGG-STTHHHHHHHHHHHHHHCTSSHHHHHHHHHHHHHHHHHHHCCCT-TS-HCHHHHHHHC CS
                   Carb_kinase 163 ekdvivspegevlinstgssalakGGsGDvLaGligalLaqneasyeaaiaaawlhgaasdeaaekkgvgmlatelskiip 243
                                   ++d+i + ++ev   + g++ ++ GG+GD LaGli+++++   +++ + + +++l+ +++++a +kkg+ ++ t+++++ip
  gi|13540958|ref|NP_110646.1| 373 KVDIITD-GKEVHYAKGGNARMTMGGTGDLLAGLISSFISKGIDPMRSCLMGTYLNKRIGELAYDKKGLFYKITDMIDEIP 452
                                   ***9998.*************************************************************999999999997 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 !  121.8   0.2   1.4e-38   2.7e-35       3     171 .]      23     171 ..      21     171 .. 0.88

  Alignments for each domain:
  == domain 1  score: 121.8 bits;  conditional E-value: 1.4e-38
                        YjeF_N   3 eLmenagravaevlrallgnspaekkvlvlvGsgnnGgdglaaArhLaqegakVtvllleeeekldedaeralellkkagg 83 
                                    Lm+nag++va+v+++ +    +++kv+v++G gnn gd+++aA  L +++++Vtvll++     +e a+   ++l+++gg
  gi|13540958|ref|NP_110646.1|  23 PLMKNAGSSVAKVIEKNF---ASGQKVCVVCGTGNNAGDAIVAAELL-RTKFEVTVLLVNG--LKSELAK---KALQEYGG 94 
                                   69****************...9*********************9999.9*******98855..4555555...55677789 PP

                        YjeF_N  84 kvveekpeedleeklsapvdlviDAllGiglrgelreelaeliewlnsseapvlavDiPSGldadtGavsgtavkadvtvt 164
                                   +vv  +  ++    l   +d++iD+++G+g++ge +e++++ ie++n+s++++++vD+PSGl    G     av++d+tvt
  gi|13540958|ref|NP_110646.1|  95 NVVDASHIDEC---L--AADIIIDGIFGVGISGEPKEPYKSTIEKINASGKKIVSVDVPSGL----GTNC--AVRPDITVT 164
                                   99965554444...4..39*******************************************....5556..8******** PP

                        YjeF_N 165 fgapkrg 171
                                   f+ +k g
  gi|13540958|ref|NP_110646.1| 165 FTSLKYG 171
                                   **99965 PP

>> HK  Hydroxyethylthiazole kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   0.0   6.2e-11   1.2e-07     142     228 ..     355     439 ..     288     456 .. 0.79

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 6.2e-11
                                   HHHHHHHHHHTSEEEEESSSEEEEESSEEEEEE-S-GGGGGSTTHHHHHHHHHHHHHTTBSSHHHHHHHHHHHHHHHH.HH CS
                            HK 142 aavqkvAqklrvvvvvtGevDvvsdgkkvyklknGtellgkitasGCllgsvvaaflavkkdkllaaveavllykvAgkea 222
                                   + + + A++ ++++v+ G+vD+++dgk+v   k+G+  ++ + ++G ll+  +++f++   d++ + + ++ l k  g+ a
  gi|13540958|ref|NP_110646.1| 355 ENAVEFAKEKGIIIVLKGKVDIITDGKEVHYAKGGNARMT-MGGTGDLLAGLISSFISKGIDPMRSCLMGTYLNKRIGELA 434
                                   34567899******************************98.79************************99999999999555 PP

                                   HHHHHT CS
                            HK 223 aarseg 228
                                      ++g
  gi|13540958|ref|NP_110646.1| 435 YD-KKG 439
                                   44.344 PP

>> Phos_pyr_kin  Phosphomethylpyrimidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       2.6   5.2e+03      19      33 ..     225     239 ..     218     242 .. 0.80
   2 !   14.0   0.0   1.2e-05     0.024     119     221 ..     333     420 ..     303     433 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 2.6
                                   TEEEEEEEEEEEEEE CS
                  Phos_pyr_kin  19 gvygmsvitaltaqn 33 
                                   + +g svi al a n
  gi|13540958|ref|NP_110646.1| 225 EYHGSSVIAALAAEN 239
                                   568889999998887 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 1.2e-05
                                   G-SEEE-BHHHHHHHHT---SSHHHHHHHHHHHHHTT-SEEEEEEGGS-SSSEEEEEEEETSSEEEEEEEE----S--BTH CS
                  Phos_pyr_kin 119 latvitPNlpEaeaLlgekikteedmkeaakkllklgakaVlikGghlegeeavvtdvlydgeeveeleaerietknthGt 199
                                   +  v+tP   E ++L+g++ +     +e a +++k +   +++kG+          d++ dg+ev+  ++      ++ Gt
  gi|13540958|ref|NP_110646.1| 333 KKIVVTPHKNEFRKLTGTEPN-----EENAVEFAKEKGIIIVLKGKV---------DIITDGKEVHYAKGGNAR-MTMGGT 398
                                   4569*************5555.....444555556555567779974.........999999999999999988.999*** PP

                                   HHHHHHHHHHHHHCTSSHHHHH CS
                  Phos_pyr_kin 200 GCtlssaiaaelakgesleeAv 221
                                   G+ l+  i + ++kg ++  + 
  gi|13540958|ref|NP_110646.1| 399 GDLLAGLISSFISKGIDPMRSC 420
                                   ***************9987765 PP

>> Cation_ATPase_N  Cation transporter/ATPase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   8.4e-05      0.17      17      41 ..      76     100 ..      61     106 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 8.4e-05
               Cation_ATPase_N  17 lenGLtqaeaaerlkkyGpNelkek 41 
                                   l nGL+++ a++ l++yG N++++ 
  gi|13540958|ref|NP_110646.1|  76 LVNGLKSELAKKALQEYGGNVVDAS 100
                                   389*****************99765 PP

>> Cupin_2  Cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0      0.12   2.3e+02      28      51 ..     178     205 ..     176     214 .. 0.74
   2 ?    8.3   0.0   0.00091       1.8      21      44 ..     365     388 ..     350     394 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.12
                                   SEEEEE.EC...TEEEEEETTEEEEE-T CS
                       Cupin_2  28 Gegelt.vd...geeveleaGdsvyfpa 51 
                                   Ge+ +  ++   + +   ++Gd++y p+
  gi|13540958|ref|NP_110646.1| 178 GEIIVAdIGipdDVRKYAGPGDLIYYPR 205
                                   5555555555547788899*******97 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00091
                                   EEEEEEESEEEEEECTEEEEEETT CS
                       Cupin_2  21 effyVleGegeltvdgeeveleaG 44 
                                    +++Vl+G++ ++ dg+ev++ +G
  gi|13540958|ref|NP_110646.1| 365 GIIIVLKGKVDIITDGKEVHYAKG 388
                                   589****************99998 PP

>> Alba  Alba
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.2   0.00014      0.29      15      55 ..      33      72 ..      26      83 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00014
                                  HHHHHHHHTHTTESEEEEEEETTHHHHHHHHHHHHHHHTCT CS
                          Alba 15 vkralklLsnkkeeeVvlkatGraIskAvsvaeilkrrfgk 55
                                  +k + k +  +++++ v+++tG++   A+  ae l+ +f+ 
  gi|13540958|ref|NP_110646.1| 33 AKVIEKNF-ASGQKVCVVCGTGNNAGDAIVAAELLRTKFEV 72
                                  56667778.8899999*********************9954 PP

>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.3   7.6e-05      0.15      47     117 ..      33     108 ..      25     119 .. 0.77
   2 ?   -3.6   0.0       2.8   5.6e+03     165     184 ..     396     415 ..     393     418 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 7.6e-05
                                   HHHHTT...TTTSEEEEEBSSHHHHHHHHHHHHH..T-EEEEEEETTS-.HHHHHHHHHTT-EEEEECCHHHHHHHH CS
                          PALP  47 arlkeg...tgaktvveassGNhgralAaaaall..Glkvtivvpadas.pekvallrllGaevvevggdydeavaa 117
                                   a+  e+    g+k+ v++++GN +  ++ aa ll  +++vt+++ ++ + +  +++l+++G +vv   +  de++aa
  gi|13540958|ref|NP_110646.1|  33 AKVIEKnfaSGQKVCVVCGTGNNAGDAIVAAELLrtKFEVTVLLVNGLKsELAKKALQEYGGNVVDA-SHIDECLAA 108
                                   55344446668999999999999999999999776689999997777663688999*********99.668888876 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 2.8
                                   -SSSHHHHHHHHHHHHHSTT CS
                          PALP 165 vGgGgliaGiaaglkerrpd 184
                                    G+G l+aG+   + +++ d
  gi|13540958|ref|NP_110646.1| 396 GGTGDLLAGLISSFISKGID 415
                                   599*******9999887765 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.1     0.011        22       2      66 ..      46     112 ..      45     146 .. 0.82
   2 ?    1.3   0.0      0.27   5.4e+02      28      51 ..     347     369 ..     333     383 .. 0.77
   3 ?    1.9   0.0      0.17   3.3e+02       6      27 ..     397     419 ..     394     447 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.011
                                   EEEE.TTSHHH.H.HHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEE CS
                 F420_oxidored   2 igii.GaGnmg.e.alasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvv 66 
                                   ++++ G+Gn +    +a  ll++ ++ + ++ +n  + e a+++ +e+g +v   ++ + +  ad+++
  gi|13540958|ref|NP_110646.1|  46 VCVVcGTGNNAgDaIVAAELLRTKFEVTVLL-VNGLKSELAKKALQEYGGNVVDASHIDECLAADIII 112
                                   6677799986523245778999986665555.88999************9999999999888999997 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.27
                                   EEEEEESSCCCHHHHHHHHC-EEE CS
                 F420_oxidored  28 ivvansrnpekaeelaeelgvkvt 51 
                                   ++ ++++n+e a e+a+e g+ + 
  gi|13540958|ref|NP_110646.1| 347 LT-GTEPNEENAVEFAKEKGIIIV 369
                                   55.88999********99996554 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.17
                                   TTSHHHHHHHHHHHHTTS.-GGC CS
                 F420_oxidored   6 GaGnmgealasgllaaga.qphe 27 
                                   G+G++ ++l+s ++++g  + ++
  gi|13540958|ref|NP_110646.1| 397 GTGDLLAGLISSFISKGIdPMRS 419
                                   9****************854444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (460 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); 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: 0.62u 0.32s 00:00:00.94 Elapsed: 00:00:00.50
# Mc/sec: 2747.35
//
Query:       gi|13540959|ref|NP_110647.1|  [L=339]
Description: oxidoreductase [Thermoplasma volcanium GSS1]
Scores for complete 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-68  230.4   0.0    2.8e-68  230.3   0.0    1.0  1  Aldo_ket_red     Aldo/keto reductase family
  ------ inclusion threshold ------
      0.099   12.5   0.1        2.7    7.9   0.0    2.4  2  ThiC-associated  ThiC-associated domain


Domain annotation for each model (and alignments):
>> Aldo_ket_red  Aldo/keto reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  230.3   0.0   3.2e-72   2.8e-68       2     292 ..      16     314 ..      15     316 .. 0.96

  Alignments for each domain:
  == domain 1  score: 230.3 bits;  conditional E-value: 3.2e-72
                                   EEEE-SSS-ST......TS-HHHHHHHHHHHHHTT--EEE--TT-TTTHHHHHHHHHHHH-TTTGGG-EEEEEE..--SSS CS
                  Aldo_ket_red   2 lglGtwqlgsk.....eeiskeealellrraleaGinffDtAevYgkgqseellGealkksrkkreeviiatKv..dlrda 75 
                                   l +G++++g +     + +++e + ++++ra++aGin+fDtA+vY +g se +lG+ lk     r++v+iatKv  + +++
  gi|13540959|ref|NP_110647.1|  16 LSFGAMTFGERnrwklGGVTQELSDRMVKRAYDAGINLFDTADVYDDGDSEVMLGRSLKP---YRDSVMIATKVrgKIGQG 93 
                                   789******99*************************************************...***********99999** PP

                                   TTSSSS-HHHHHHHHHHHHHHHT-S-EEEEEE-S--TTS-.HHHHHHHHHHHHHTTSEEEEEEES--HHHHHHH....HHT CS
                  Aldo_ket_red  76 eiksglskeniresleeslkrLgtdyvDllllHrpdpslpsieevldaleelvkeGkiraiGvSnfsveqleka....kkk 152
                                    ++sgls+ +++ ++++sl+rLgt+ +D+++ H +d++    ee l+++e +v++G++ + +vSnf+++q++ +     + 
  gi|13540959|ref|NP_110647.1|  94 VNSSGLSRHHMHIAIKKSLERLGTEWIDIYQYHGWDVYGN-FEEFLETMESFVEQGLVIYPAVSNFTAWQISVLqtmaIER 173
                                   ****************************************.*******************************999999999 PP

                                   TT--EEEEE-B-BTT-HHHHTTHHHHHHHTT-EEEEBSTTGGGTTGTTTSS---SSSCCC-------...TS-HHHHHHHH CS
                  Aldo_ket_red 153 kkvkivavqveynllreleeegllelckkkgvpliaysplggGlltgkyqseedkedkeprkdlkrd...ertsknldaae 230
                                   ++ +  + q++y+ll+++ e ++l+++k  g+ l  +spl+gG l gky++ e++ ++++  + + +   +  +   d +e
  gi|13540959|ref|NP_110647.1| 174 GYARYESAQMNYSLLNRDVEYEVLPFMKYSGMTLLSWSPLHGGVLAGKYKKGEKPATGTRMGNRGFFfpyFDEDHGWDVVE 254
                                   ******************************************************999888777666699966666779*** PP

                                   HHHHHHHHTT--HHHHHHHHHTTSTT-SEEEE--SSHHHHHHHHGGGG----HHHHHHHHHH CS
                  Aldo_ket_red 231 elselakehgvslaqlalryalsqpavgivipgasnieqlednldalelklseeevaeldel 292
                                   e++++a+e+g++++q+al++++  ++  ++i+ga+++eqle+nl++l+++l++e++++ld++
  gi|13540959|ref|NP_110647.1| 255 EVKKVAQEQGCKPSQVALAWII--SKSHVAILGARSMEQLEENLGSLDVQLTKEQMDRLDNV 314
                                   **********************..99999*******************************87 PP

>> ThiC-associated  ThiC-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0   0.00031       2.7      39      72 ..      46      79 ..      34      85 .. 0.83
   2 ?    1.8   0.0     0.023   2.1e+02      54      75 ..     100     121 ..      95     124 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00031
                                  G----EEEE---GGGG-TTS---TTT-S--TTHH CS
               ThiC-associated 39 eenepvrvYDtSGpYtdpeveidvrkGLprlRea 72
                                  + ++ + ++Dt+ +Y d + e+ + + L++ R++
  gi|13540959|ref|NP_110647.1| 46 AYDAGINLFDTADVYDDGDSEVMLGRSLKPYRDS 79
                                  4677899************************986 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.023
                                   G-TTS---TTT-S--TTHHHHH CS
               ThiC-associated  54 tdpeveidvrkGLprlReaWie 75 
                                   +  +++i ++k L+rl ++Wi+
  gi|13540959|ref|NP_110647.1| 100 SRHHMHIAIKKSLERLGTEWID 121
                                   567899**************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (339 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       656  (0.0365888); expected 358.6 (0.02)
Passed bias filter:                      553  (0.0308439); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 2071.83
//
Query:       gi|13540960|ref|NP_110648.1|  [L=89]
Description: hypothetical protein TVN0129 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       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:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.48
# Mc/sec: 553.64
//
Query:       gi|13540961|ref|NP_110649.1|  [L=351]
Description: hypothetical protein TVN0130 [Thermoplasma volcanium GSS1]
Scores for complete 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   39.4   0.0    1.6e-09   37.8   0.0    1.8  1  ACP_syn_III_C   3-Oxoacyl-[acyl-carrier-protein (ACP)] syntha
    2.6e-05   24.0   0.2     0.0034   17.0   0.0    2.2  2  HMG_CoA_synt_C  Hydroxymethylglutaryl-coenzyme A synthase C t
    0.00037   19.9   0.1    0.00062   19.2   0.1    1.3  1  Thiolase_N      Thiolase, N-terminal domain
      0.001   18.8   4.2     0.0013   18.6   1.0    2.4  2  ACP_syn_III     3-Oxoacyl-[acyl-carrier-protein (ACP)] syntha
  ------ inclusion threshold ------
      0.071   12.7   0.0       0.14   11.8   0.0    1.5  1  SatD            SatD family (SatD)
      0.085   12.7   0.0       0.18   11.6   0.0    1.5  1  HMG_CoA_synt_N  Hydroxymethylglutaryl-coenzyme A synthase N t
       0.11   12.6   0.1       0.64   10.3   0.0    2.2  2  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind


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 !   37.8   0.0   6.1e-13   1.6e-09       2      81 ..     219     298 ..     218     304 .. 0.92

  Alignments for each domain:
  == domain 1  score: 37.8 bits;  conditional E-value: 6.1e-13
                                   HHTT--GGG-SEEEE-SSSHHHHHHHHHHHT--GGGB--TH..HHH-B-GGGHHHHHHHHHHHTTSS-TT-EEEEEEEETT CS
                 ACP_syn_III_C   2 ekagltpedidalvphqanlriidavakklglpeekvvvnl..deyGntsaasiplaLdeaveegklkpgdlvllvgfGaG 80 
                                   e+ + +p+d d++v+hq n ++   +ak lg++e+++   l    +Gnt + s++  L+  ++    kpgd++l v+fG G
  gi|13540961|ref|NP_110649.1| 219 ERMETQPKDYDYVVFHQPNGKFPTRAAKLLGFEEKQYKDGLitPYIGNTYSGSMMTGLSSILD--VSKPGDHILAVSFGSG 297
                                   677899*****************************88776655899*****************..88*************9 PP

                                   T CS
                 ACP_syn_III_C  81 l 81 
                                    
  gi|13540961|ref|NP_110649.1| 298 A 298
                                   6 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 !    5.4   0.1    0.0049        12      62      90 ..     220     248 ..     204     256 .. 0.69
   2 !   17.0   0.0   1.3e-06    0.0034     141     215 ..     251     324 ..     245     343 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0049
                                   -----GGG-SEEEE--SSHHHHHHHHHHH CS
                HMG_CoA_synt_C  62 dkeftlddfdyvifhsPfcklvqkslarl 90 
                                     e+  +d+dyv+fh P  k+ +++   l
  gi|13540961|ref|NP_110649.1| 220 RMETQPKDYDYVVFHQPNGKFPTRAAKLL 248
                                   44556689***********9988775555 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 1.3e-06
                                   HHHTGGGGHHHHHH---GGGHHHHHHHHHHHHS-HHHHTT-EEEEEEEETTTEEEEEEEEE-S--STTSHHH...HHT CS
                HMG_CoA_synt_C 141 kkkvkpsllvptevGnmYtaslyaalasllskvsadelagkriglfsYGsGlaaslfslrvkqdvsedsild...iak 215
                                   ++k  +  l++  +Gn Y  s+ + l s+l      +  g  i++ s+GsG  +  f ++v++  +e + ++   i+k
  gi|13540961|ref|NP_110649.1| 251 EEKQYKDGLITPYIGNTYSGSMMTGLSSILD----VSKPGDHILAVSFGSGAGSDAFDITVTDRIEEMDRNKaptIKK 324
                                   55555566677789****************3....334699*********************9988854443332333 PP

>> Thiolase_N  Thiolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.1   2.4e-07   0.00062      24     113 ..      51     140 ..      41     151 .. 0.94

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 2.4e-07
                                   HHHHHHHHHHHHHHHTS-GGGCCEEEEEHSSCTTSTSCHHHHHHHHTTS-TTSEEEEEEHGGGHHHHHHHHHHHHHHTTSH CS
                    Thiolase_N  24 eeLlaealkallekagvdpeevdevivGnvlqagegqniarqaalkagipeevpavtvnkvcsSglkavalaaqsiaagea 104
                                     ++ ea++++l++ +++p+e+  ++vG   +  + +  a  +  ++g+  +  a   + +c  g +++ ++  ++ ag +
  gi|13540961|ref|NP_110649.1|  51 ATISVEAARNALKRKKINPKEIGAIYVGSESHPYAVKPTATIVGSAIGVDFSLFAADYEFACKAGTAGMQNVKAMVDAGMI 131
                                   56788999************************************************************************* PP

                                   SEEEEEEEE CS
                    Thiolase_N 105 dvvvagGvE 113
                                   +  +a+G+ 
  gi|13540961|ref|NP_110649.1| 132 KYGLAIGAD 140
                                   *******85 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 !   18.6   1.0     5e-07    0.0013       2      64 ..     107     166 ..     106     181 .. 0.77
   2 ?    0.3   0.1      0.26   6.6e+02      37      57 ..     276     299 ..     274     309 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 5e-07
                                   EEE-GGGHHHHHHHHHHHHHHTTS-SEEEEEEEEEGGGCS-TTTHHHHTTB-EEEEEEEEEEE CS
                   ACP_syn_III   2 DlnaaCsgfvyalsvAdaliesgaakrvLvigaetlskilDwkdrstavlfGDGAgAvvleas 64 
                                   D + aC++ ++++++++a++++g++k+ L iga+t s+       +  +  + G+ A++++++
  gi|13540961|ref|NP_110649.1| 107 DYEFACKAGTAGMQNVKAMVDAGMIKYGLAIGADT-SQGA--PGDALEYSASAGGSAFIIGKD 166
                                   77889*****************************9.5432..234455556667777777665 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.26
                                   GGGCS-TT...THHHHTTB-EEEE CS
                   ACP_syn_III  37 lskilDwk...drstavlfGDGAg 57 
                                   ls+ilD +   d   av fG GAg
  gi|13540961|ref|NP_110649.1| 276 LSSILDVSkpgDHILAVSFGSGAG 299
                                   688899885556888999****98 PP

>> SatD  SatD family (SatD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   5.4e-05      0.14      79     105 ..     161     187 ..     148     194 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5.4e-05
                          SatD  79 fGvGvGeilteinpelsiGadGPaywe 105
                                   f +G  ++++ein+ ls+ +d P +w+
  gi|13540961|ref|NP_110649.1| 161 FIIGKDDVIAEINSTLSVASDTPDFWR 187
                                   789***********************7 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 ?   11.6   0.0   7.2e-05      0.18       6     171 ..       3     165 ..       2     168 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 7.2e-05
                HMG_CoA_synt_N   6 gilaleiylpaqyvdqaelekfdgveagkytiglgqtrmgfvsdredinslsltvvqkllertkldydaigrlevgtetii 86 
                                   gi++   y+p   ++  e+ +  g +  +   g+     +  +  ed+ ++s+   ++ l+r+k++ + ig + vg+e+  
  gi|13540961|ref|NP_110649.1|   3 GIVTYGSYIPRYRIKPDEIARVWGENPERIKNGIFILSKSVPAPDEDVATISVEAARNALKRKKINPKEIGAIYVGSESHP 83 
                                   566666677777777777777666666666667777777778889*********************************987 PP

                HMG_CoA_synt_N  87 dksksvksvlmqlfeesgntdiegidtlnacyggtaalfnavnwiessawdgryalvvagdiaiydsgnarp.tggagava 166
                                      k   +++   ++   +  +   d   ac  gta + n    +++ +   +y l +  d +  + g+a   +  ag  a
  gi|13540961|ref|NP_110649.1|  84 YAVKPTATIVGSAIGV--DFSLFAADYEFACKAGTAGMQNVKAMVDAGMI--KYGLAIGADTSQGAPGDALEySASAGGSA 160
                                   7777766666665554..66788999999********9999999887765..68888888888888777754156677778 PP

                HMG_CoA_synt_N 167 lligp 171
                                   ++ig 
  gi|13540961|ref|NP_110649.1| 161 FIIGK 165
                                   87776 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       1.3   3.4e+03      27      37 ..     275     285 ..     272     286 .. 0.85
   2 ?   10.3   0.0   0.00025      0.64      35      58 ..     318     341 ..     305     342 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.3
                                   HHHHHHTS-HH CS
                Fe_dep_repress  27 dlaerLnvsps 37 
                                    l+++L+vs++
  gi|13540961|ref|NP_110649.1| 275 GLSSILDVSKP 285
                                   699******97 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00025
                                   -HHHHHHHHHHHHHTTSEEEETTT CS
                Fe_dep_repress  35 spssVsemlkkLekdGyveyekyk 58 
                                   +++++ +ml+k +   y +y+kyk
  gi|13540961|ref|NP_110649.1| 318 KAPTIKKMLEKIKWVDYAIYAKYK 341
                                   789********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (351 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 2241.82
//
Query:       gi|13540962|ref|NP_110650.1|  [L=389]
Description: acetyl-CoA acetyltransferase [Thermoplasma volcanium GSS1]
Scores for complete 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  108.6   5.3    9.5e-31  107.1   3.0    2.3  2  Thiolase_N     Thiolase, N-terminal domain
    4.4e-10   39.3   0.0    1.1e-09   38.0   0.0    1.7  1  Thiolase_C     Thiolase, C-terminal domain
    2.3e-06   27.4   2.3    2.5e-05   24.0   0.7    2.6  3  ketoacyl-synt  Beta-ketoacyl synthase, N-terminal domain


Domain annotation for each model (and alignments):
>> Thiolase_N  Thiolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.1   3.0   1.6e-34   9.5e-31       1     259 [.       7     228 ..       7     229 .. 0.95
   2 ?    1.1   0.0     0.034     2e+02      17      46 ..     255     284 ..     239     289 .. 0.77

  Alignments for each domain:
  == domain 1  score: 107.1 bits;  conditional E-value: 1.6e-34
                                   EEEEEEEEE--EETTSTTTTS-HHHHHHHHHHHHHHHHTS-GGGCCEEEEEHSSCT..TSTSCHHHHHHHHTTS-.TTSEE CS
                    Thiolase_N   1 vvivsaartpigkfggslkdlsaeeLlaealkallekagvdpeevdevivGnvlqa..gegqniarqaalkagip.eevpa 78 
                                   v+i++a  t++g+    l d s ++L+ ea+ +++++a++ +++++ ++ +n l++  +e +nia  aa  +gi+ ++vpa
  gi|13540962|ref|NP_110650.1|   7 VYIIGAGETKFGE----LWDKSLRDLAVEAGLEAIKDANIYSKDLQMLYASNSLAGtiNEQSNIAALAADFSGIAeNHVPA 83 
                                   89***********....*************************************9985556669999999999972689** PP

                                   EEEEHGGGHHHHHHHHHHHHHHTTSHSEEEEEEEEESTTS-EEETCTTTTGGSSSSEEEEEHHHHHHTEETTTTSEHHHHH CS
                    Thiolase_N  79 vtvnkvcsSglkavalaaqsiaageadvvvagGvEsmsnaptaestdvrsglklgdekakdllipdgladafneehmGlta 159
                                   v+v+   +Sg +av +a  +i++ge+dvv++gGvE+m++ +  e  dv s++   + +  +   p          +++++a
  gi|13540962|ref|NP_110650.1|  84 VRVEASTASGGAAVREAYLAIKSGEYDVVMVGGVEKMTDIYGTEIIDVQSSILDREWESFNGATPA--------AMAAIAA 156
                                   ****************************************************99999999999999........7899*** PP

                                   HHHHHHHT--HHHHHHHHHHHHHHHHHHHHTTTTTTTBE-EEEEESSSEEEE-S-TTS-TT--HHHHHTS-BSSSTTSS-B CS
                    Thiolase_N 160 enlakkykisReeqdefAvkshqkaaaaqkagkFkdeivPvkvkgkkgkktvdkdeairsevtaekLaklkpaFkkeGtvt 240
                                   +++ +++++ Re+   +Av+ h++a+ +++a+ ++++i              + d+ ++s+ +ae+L+             
  gi|13540962|ref|NP_110650.1| 157 RRYMHDFNVEREAISMVAVNDHANASLNPDAQ-YRNKI--------------TVDQVLNSDPVAEPLNVF----------- 211
                                   ********************************.99999..............8899*************9........... PP

                                   TTSB--BEEEEEEEEEEEH CS
                    Thiolase_N 241 AgnasqisDGaaavllmse 259
                                     ++s+i+DGa+a++l+se
  gi|13540962|ref|NP_110650.1| 212 --DCSPITDGASAIILASE 228
                                   ..**************997 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.034
                                   TTTTS-HHHHHHHHHHHHHHHHTS-GGGCC CS
                    Thiolase_N  17 slkdlsaeeLlaealkallekagvdpeevd 46 
                                   s k++ + e  ++a +++l+kag++ e+v+
  gi|13540962|ref|NP_110650.1| 255 SRKSIYTLESTKIATEEALKKAGIKREDVS 284
                                   4556666666788999*********99996 PP

>> Thiolase_C  Thiolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.0   0.0   1.8e-13   1.1e-09      25     106 ..     266     364 ..     244     387 .. 0.88

  Alignments for each domain:
  == domain 1  score: 38.0 bits;  conditional E-value: 1.8e-13
                                   HHHHHHHHHHHT--GGGESEEEE--SBHHHHHHHHHHHT--G.................GGBSTT--HHHH-B-TTTHHHH CS
                    Thiolase_C  25 ayaikkvlkkagltvedidlfEinEAFaaqaLavakaldldl.................ekvNvnGGaialGHPlGasGaR 88 
                                     a++++lkkag++ ed+ ++E+n+ ++   L  ++++++++                   vN  GG  a G PlGa+G+ 
  gi|13540962|ref|NP_110650.1| 266 KIATEEALKKAGIKREDVSFLELNDSYSIYGLLELEDMGFAEkgkakdlvyddiklngrLPVNPSGGLKAKGNPLGATGVS 346
                                   5799****************************************************99888******************** PP

                                   HHHHHHHHHHHCTTSEEE CS
                    Thiolase_C  89 ivvtllselkkeggklgv 106
                                   ++  +  +lk + g+  v
  gi|13540962|ref|NP_110650.1| 347 QFFEAYLQLKGKAGQRQV 364
                                   *****9999988777655 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 ?    1.8   0.1     0.024   1.5e+02      91     133 ..      28      70 ..      22      79 .. 0.82
   2 !   24.0   0.7   4.2e-09   2.5e-05     162     213 ..      77     128 ..      47     143 .. 0.79
   3 ?   -1.3   0.0      0.22   1.3e+03      95     110 ..     268     283 ..     266     291 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.024
                                   HHHHHHHHHHHHHTS-HHTCTTGGEEEEEEESSTHHHHHHHHH CS
                 ketoacyl-synt  91 llleaawealedagltpeeldgsrvgvfiGvgagdyaalaald 133
                                   l++ea  ea++da++  ++l+   + + ++ ++++++++aal 
  gi|13540962|ref|NP_110650.1|  28 LAVEAGLEAIKDANIYSKDLQMLYASNSLAGTINEQSNIAALA 70 
                                   899**************99988778888888888777766665 PP

  == domain 2  score: 24.0 bits;  conditional E-value: 4.2e-09
                                   HT--SSEEEEESGGGHHHHHHHHHHHHHHTTS-SEEEEEEEE---SHHHHHH CS
                 ketoacyl-synt 162 lglrGpsvtvdtACsSslvavhaavqslrsgeadvalaGGvellltpeavag 213
                                      + p+v v++  +S+ +av  a+ +++sge dv+ +GGve ++   ++  
  gi|13540962|ref|NP_110650.1|  77 AENHVPAVRVEASTASGGAAVREAYLAIKSGEYDVVMVGGVEKMTDIYGTEI 128
                                   4446699***********************************9998776655 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 0.22
                                   HHHHHHHHHTS-HHTC CS
                 ketoacyl-synt  95 aawealedagltpeel 110
                                   a++eal++ag++ e++
  gi|13540962|ref|NP_110650.1| 268 ATEEALKKAGIKREDV 283
                                   789********99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       440  (0.0245412); 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:                         3  (0.000167327); expected 0.2 (1e-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 0.26s 00:00:00.93 Elapsed: 00:00:00.52
# Mc/sec: 2270.60
//
Query:       gi|13540963|ref|NP_110651.1|  [L=133]
Description: nucleic-acid-binding protein [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.5e-22   76.9   0.1    1.2e-21   76.4   0.1    1.2  1  OB_aCoA_assoc  DUF35 OB-fold domain, acyl-CoA-associated
    6.5e-13   48.3   3.9    1.1e-12   47.6   3.9    1.3  1  DUF35_N        Rubredoxin-like zinc ribbon domain (DUF35_N)
     0.0055   16.8   1.2     0.0091   16.1   1.2    1.4  1  Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (
  ------ inclusion threshold ------
      0.039   13.6   0.1       0.05   13.3   0.1    1.1  1  TackOD1        Thaumarchaeal output domain 1
       0.17   11.8   3.2        7.1    6.6   1.3    2.5  2  Nudix_N_2      Nudix N-terminal


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 !   76.4   0.1   3.4e-25   1.2e-21       2      65 .]      50     113 ..      49     113 .. 0.98

  Alignments for each domain:
  == domain 1  score: 76.4 bits;  conditional E-value: 3.4e-25
                                   EEE-GG-EEEEEEEEEE-TTS-EEEEEEEEEEEE-TT...-EE-EEEEEEES..TT-B-EEE-S CS
                 OB_aCoA_assoc   2 velsgrGtvysftvvhrappgfaeeaPyvvgvVeLdegvrimarlvgvdpdevriGmrVravfr 65 
                                   +elsg G+++sftvvh+app+f+ ++Py++++++ +eg+ +++++v++dpdev+iG +V avfr
  gi|13540963|ref|NP_110651.1|  50 IELSGDGVIESFTVVHEAPPRFSRQRPYILALIKTEEGPMLTGQIVDADPDEVEIGKKVHAVFR 113
                                   59*************************************************************7 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.6   3.9   2.9e-16   1.1e-12       6      35 ..      14      43 ..      12      45 .. 0.95

  Alignments for each domain:
  == domain 1  score: 47.6 bits;  conditional E-value: 2.9e-16
                       DUF35_N  6 egrLvgqrCpdCGtvqfPPravCphCgsdd 35
                                  ++rL+g++C +CGtv+fPPr vCp C++d+
  gi|13540963|ref|NP_110651.1| 14 RYRLLGSKCGNCGTVYFPPREVCPTCHRDS 43
                                  79*************************985 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 !   16.1   1.2   2.5e-06    0.0091      11      39 ..      15      39 ..      12      40 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2.5e-06
                 Auto_anti-p27 11 wtMLaetCpvCgvPLmrdrkggkvyCvaC 39
                                  +++L++ C +Cg++ +  r     +C++C
  gi|13540963|ref|NP_110651.1| 15 YRLLGSKCGNCGTVYFPPR----EVCPTC 39
                                  89***************54....4***** PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   1.4e-05      0.05      75     104 ..      21      50 ..      10      60 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.4e-05
                       TackOD1  75 lCpsCksghlnvrevCpkCkSidieeqeli 104
                                    C +C +  +  revCp C+   i + + i
  gi|13540963|ref|NP_110651.1|  21 KCGNCGTVYFPPREVCPTCHRDSIGKMKDI 50 
                                   6*******************9999887765 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0    0.0088        32      25      31 ..      22      28 ..       3      30 .. 0.70
   2 ?    6.6   1.3     0.002       7.1      21      29 ..      32      40 ..      31      41 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.0088
                                  ETTTTEE CS
                     Nudix_N_2 25 CpaCgti 31
                                  C +Cgt+
  gi|13540963|ref|NP_110651.1| 22 CGNCGTV 28
                                  9999998 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.002
                                  -EEEETTTT CS
                     Nudix_N_2 21 eRlvCpaCg 29
                                  +R vCp C+
  gi|13540963|ref|NP_110651.1| 32 PREVCPTCH 40
                                  8*******8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); 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: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 923.91
//
Query:       gi|13540964|ref|NP_110652.1|  [L=219]
Description: ribonuclease HII [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.7e-46  158.6   0.1    2.1e-46  158.3   0.1    1.1  1  RNase_HII  Ribonuclease HII
     0.0046   16.7   0.1     0.0093   15.7   0.1    1.5  1  DUF835     Protein of unknown function (DUF835)


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 !  158.3   0.1   2.3e-50   2.1e-46       1     197 [.      14     203 ..      14     204 .. 0.91

  Alignments for each domain:
  == domain 1  score: 158.3 bits;  conditional E-value: 2.3e-50
                                   EEEEEE-TT-SBS-EEEEEEEECGHHHHHHHCTTGTTGTTS-HHHHHHHHHHHHSEEEEEEE-HHHHH..HHTTTS-HHHH CS
                     RNase_HII   1 iGiDEaGrGpvlGplvvaavavekereeelkklgvkDSKkLskqkreeLaklikkkiekrklvaeeiky.aseneinlnei 80 
                                   +GiDEaGrGpv+Gp+v+  v +++e+    +++gvkDSK Ls ++re+L+ +i k+  ++++v +     +++++ +ln+i
  gi|13540964|ref|NP_110652.1|  14 CGIDEAGRGPVIGPMVISIVCCKEEYL---REIGVKDSKMLSRKRREYLFDKITKNCAYSYVVVSPETLnKDMASESLNKI 91 
                                   7*********************99987...9***********************999999888887766588888899999 PP

                                   HHHHHHHHHHHHHHTCEECCECCCE--SS.HHHHHHHHHHHHCCEEEEETTGGGT-HHHHHHHHHHHHHHHHHHHHHHHHC CS
                     RNase_HII  81 kaaltlaviklleklgvkvdeilvdgvtt.peslkkkleqiikikvtvekkadekyllvaaASiiAkverdeelellkrkp 160
                                   +++ +l++  + e        +++d ++  +e+ +k++++  + +v+ ++kad++y++v+aASi+ kv rd e++++++k+
  gi|13540964|ref|NP_110652.1|  92 EENYILELLSKAEG------IVYIDCFDViEERAEKYIREKSGKEVVCKHKADSIYPAVSAASIVSKVIRDREIDKIAEKY 166
                                   98888887766543......46777777768889999******9************************************9 PP

                                   SH.--TTSSTTSHHHHHHHHHHHHH..S--TTB-TTSHH CS
                     RNase_HII 161 gtldkgsGyasdektrallkkgats..klpdivrlsfkt 197
                                   g   +gsGy+sd++t  +l+k +++   l++++r +++t
  gi|13540964|ref|NP_110652.1| 167 G--FFGSGYPSDPRTIDFLRKAMQQglDLRSVARIHWET 203
                                   8..99********************999*********97 PP

>> DUF835  Protein of unknown function (DUF835)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1     1e-06    0.0093      21      88 ..      47     115 ..      36     120 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1e-06
                        DUF835  21 kvlaitRenpkkirekv.kienvkviwltkveeentvsPtnlekltetivkflkeaekgvvliDgleyL 88 
                                   +  +++R++++ + +k+ k+   +++ ++ +  ++ +  ++l+k++e  +  l ++ +g+v+iD+++ +
  gi|13540964|ref|NP_110652.1|  47 DSKMLSRKRREYLFDKItKNCAYSYVVVSPETLNKDMASESLNKIEENYILELLSKAEGIVYIDCFDVI 115
                                   56789************5555556666666667999**********9876666666668*******976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       570  (0.0317921); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1538.63
//
Query:       gi|13540965|ref|NP_110653.1|  [L=176]
Description: hypothetical protein TVN0134 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0043   17.1   0.1     0.0068   16.4   0.1    1.3  1  DUF727    Protein of unknown function (DUF727)


Domain annotation for each model (and alignments):
>> DUF727  Protein of unknown function (DUF727)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1   3.8e-07    0.0068      46      91 ..      83     132 ..      81     147 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3.8e-07
                        DUF727  46 velsakGfrvvsskydeveeeeekedeeky....fetlyaLLdkiSpeyr 91 
                                   ++l+ kGf+++ s  d+ +++e+++  +      + +l +LLd++ ++y 
  gi|13540965|ref|NP_110653.1|  83 IRLTNKGFKIAASVWDHLTDFEKQQIFDVKstfnYMSLTELLDTVYSRYP 132
                                   89****************7777776543323445*********9988885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       601  (0.0335211); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.51
# Mc/sec: 1045.86
//
Query:       gi|13540966|ref|NP_110654.1|  [L=163]
Description: hypothetical protein TVN0135 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00017   22.1   0.1     0.0009   19.7   0.1    2.0  1  PIN       PIN domain
  ------ inclusion threshold ------
      0.012   16.4   0.1      0.042   14.6   0.1    1.8  1  PIN_3     PIN domain


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.1     1e-07    0.0009       2      48 ..       4      60 ..       3     144 .. 0.71

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1e-07
                                  EE-HHHHHHHH....TTSHHHHHHHHHHHTSSEEEEEHHHHHHHHHHHHS......S CS
                           PIN  2 vlDTsvliall....rgeekaeaarklleeleelvtsalvlaEllyvlar......r 48
                                  ++DT+v++a+l     ++ +a+ +r+ +++l++ +t+++ + El + l        +
  gi|13540966|ref|NP_110654.1|  4 IIDTNVVLAYLisgsARSSNAKVCRRVVNGLDKAFTCDILYGELKRLLDLdpdlieK 60
                                  79*************999999***********************9988876666551 PP

>> PIN_3  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1   4.7e-06     0.042       1     115 [.       2     135 ..       2     136 .. 0.61

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4.7e-06
                         PIN_3   1 rvvlDtnvlldallfdsp..aarkildaletgaitlvvsprlldElervl..............arelaypqfklraadka 65 
                                   r ++Dtnv+l++l++ s   +++k+ + + +g   ++++  l  El+r l              ++e++ +++  +     
  gi|13540966|ref|NP_110654.1|   2 RLIIDTNVVLAYLISGSArsSNAKVCRRVVNGLDKAFTCDILYGELKRLLdldpdliekisiigKKEGDVFRALYN----- 77 
                                   789***********88878899999999999999999999999999999976666665554444222222221111..... PP

                         PIN_3  66 allakvaler................kavapdaelrpllkcrDp.dDqkvlelAlaaradvlVTkdr 115
                                            +                  v+ +  +   ++++D  +D  ++ +A     d++VT+++
  gi|13540966|ref|NP_110654.1|  78 ---------AkteylnsrldpyvmqlNFVKTENLAIDPVAIKDIgNDWYMISIAKSVSIDYIVTWNT 135
                                   .........1122222233444444433333222222333456426777888888888888888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       498  (0.0277762); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); 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 0.29s 00:00:00.78 Elapsed: 00:00:00.49
# Mc/sec: 1001.58
//
Query:       gi|13540967|ref|NP_110655.1|  [L=74]
Description: integrase/recombinase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       508  (0.028334); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.51
# Mc/sec: 434.03
//
Query:       gi|13540968|ref|NP_110656.1|  [L=182]
Description: integrase/recombinase, partial [Thermoplasma volcanium GSS1]
Scores for complete sequence (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   0.0    3.8e-05   23.5   0.0    1.7  2  PRK       Phosphoribulokinase / Uridine kinase family


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 ?   -1.3   0.0     0.087   1.6e+03     147     164 ..       3      20 ..       1      28 [. 0.85
   2 !   23.5   0.0   2.1e-09   3.8e-05      66     134 ..     102     182 .]      90     182 .] 0.87

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.087
                           PRK 147 klqRDiaeRGrsleavld 164
                                   ++ R  ++RGr   a+++
  gi|13540968|ref|NP_110656.1|   3 RILRKATSRGRVAIAIMA 20 
                                   89999******9999886 PP

  == domain 2  score: 23.5 bits;  conditional E-value: 2.1e-09
                           PRK  66 peandfdllyevlkelkegkk.vdkpiYsheteeaapdkeeliegadvlviEGlhalyder...........vaelldlki 134
                                   pe  d++ l +   elk+gk+ +d+p Ysh   +++p k +++e++dvl++EGl  l  +r           v ++ld++i
  gi|13540968|ref|NP_110656.1| 102 PESYDLKALIKFPYELKSGKEnIDIPQYSHIIYDIVPGKFKTVENPDVLILEGLNVLQTRRtdtippasellVSDFLDFSI 182
                                   8999999999999******8549*******************************988888777777777777777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       277  (0.0154498); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.32s 00:00:00.82 Elapsed: 00:00:00.50
# Mc/sec: 1104.07
//
Query:       gi|13540969|ref|NP_110657.1|  [L=395]
Description: multidrug efflux permease [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-41  141.9  36.6    2.4e-41  141.9  36.6    1.9  2  MFS_1     Major Facilitator Superfamily
    2.1e-05   23.1   1.3    2.1e-05   23.1   1.3    2.0  2  MFS_3     Transmembrane secretion effector
    0.00074   18.5  12.0    0.00074   18.5  12.0    2.5  2  Sugar_tr  Sugar (and other) transporter
     0.0015   17.1  38.0      0.063   11.8   7.0    3.1  3  MFS_2     MFS/sugar transport protein
  ------ inclusion threshold ------
       0.12   12.1   0.0       0.12   12.1   0.0    3.6  3  DUF4538   Domain of unknown function (DUF4538)
        0.5   10.3   0.1        0.5   10.3   0.1    3.0  5  TRIQK     Triple QxxK/R motif-containing protein 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 !  141.9  36.6     8e-45   2.4e-41       4     352 ..      18     345 ..      15     346 .. 0.78
   2 ?    0.6   1.6     0.071   2.1e+02     257     296 ..     346     384 ..     343     389 .. 0.71

  Alignments for each domain:
  == domain 1  score: 141.9 bits;  conditional E-value: 8e-45
                         MFS_1   4 aaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfa.s 83 
                                   + +l +++++++ p+++ ++++ +  sp  ig+++++y+l++a+++ p+G +sdrfGr+ v++lg++ +++g l+++ +  
  gi|13540969|ref|NP_110657.1|  18 IEVLRMFGIFLVVPVFT-LYGKLFSNSPILIGIAFGAYGLTMALFQAPFGIISDRFGRKNVIILGMIPYIVGNLIAW-HpV 96 
                                   56789999*********.9*****************************************************55555.558 PP

                         MFS_1  84 slwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivslla 164
                                   +++ l+v+r+++G ga  ++++g+a++ + +p+e+r++a++ll++ +++++++g +lg+l+++ lg   +f+i a++++++
  gi|13540969|ref|NP_110657.1|  97 NIFGLIVGRLVAGSGA--VTSSGMAMVQESVPPERRNLAMALLGIPIGFAFMIGIVLGPLISARLGADTLFLISALLGIIS 175
                                   8889*********985..*************************************************************** PP

                         MFS_1 165 fv.lfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsg..lltllplylqevlglsg 242
                                   ++ + ++  + +p  r+ +++k          + p       +     +l+++++f + +++  ++++lply    +g  g
  gi|13540969|ref|NP_110657.1| 176 IIpMTAIK-YHKPEYRAEERKKAG-------RIEP-------KT----VLVGVVGFLVSLYMivFFYYLPLYGTRAYGSHG 237
                                   99442222.223333333322222.......2222.......33....3333333333344446********888888888 PP

                         MFS_1 243 lllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavt.ssavllllvlvliGfglgfvfpsll 322
                                   + l++  +  + ++g+i a+ ++ ++dr +   + ++al+l+l+++ +++l +v+  +  ++ ++ +++  g++++ + ++
  gi|13540969|ref|NP_110657.1| 238 YELLL--FWSVVIGGII-AVASSSFADRGKTTLFSIIALILMLVSTPFVFLEPVAtGNRDWFFIGTIIFFAGFSIYEIVFT 315
                                   66666..4444444433.5799******4444444444444444444444444447777777777777777********** PP

                         MFS_1 323 alasdlappeeagtasglfntagslggalg 352
                                    l+s+l  +e  g+ +g++nt++ lg + g
  gi|13540969|ref|NP_110657.1| 316 PLVSKLSKKESYGANIGIYNTMQFLGQFAG 345
                                   **************************9987 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.071
                         MFS_1 257 gailallagrlsdrlgrrrrlllallllllaalglallav 296
                                   g+ +++l++  +d ++++ r+ ++l++l+l++lg++++++
  gi|13540969|ref|NP_110657.1| 346 GITGGVLVTLTLD-YNSMLRTSMILAVLVLISLGFLYIPT 384
                                   3444556666666.58888888888888888888888875 PP

>> MFS_3  Transmembrane secretion effector
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   1.3   7.2e-09   2.1e-05      41     196 ..      41     189 ..      35     200 .. 0.86
   2 ?    1.2   0.4     0.031        94     253     303 ..     331     379 ..     246     393 .. 0.65

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 7.2e-09
                         MFS_3  41 sasplmvAlvqaaatLPifllsilaGalaDnfdrRkvllavqlllalvsvlltvlaalgllspwlllaltlligiGaalnd 121
                                   s sp+ + +   a  L + l+  + G+++D f r++v++ +++  +++ +++        ++ + l++  l++g Ga    
  gi|13540969|ref|NP_110657.1|  41 SNSPILIGIAFGAYGLTMALFQAPFGIISDRFGRKNVIILGMIPYIVGNLIA-----WHPVNIFGLIVGRLVAGSGAVT-- 114
                                   678888888888999************************9988777766543.....4556677788888888888643.. PP

                         MFS_3 122 PaWqAsvgelvkrrdvpaAvaLnsvginiaRsvGPAlgGvlvaavGaalafavnalsylalivallrwkrevrks 196
                                    +  A+v+e v+ +  + A+aL  + i  a  +G  lg ++ a +Ga + f + al  ++ i+ ++++k ++++ 
  gi|13540969|ref|NP_110657.1| 115 SSGMAMVQESVPPERRNLAMALLGIPIGFAFMIGIVLGPLISARLGADTLFLISALLGIISIIPMTAIKYHKPEY 189
                                   466899*****************************************************9999999999988765 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.031
                         MFS_3 253 alvyGil..lgalGvGAilgalllsrLRerlsserlvllaavalAlvllslal 303
                                     +y ++  lg + +G i+g++l++    +l+ + +++++++   lvl+sl++
  gi|13540969|ref|NP_110657.1| 331 IGIYNTMqfLGQF-AGGITGGVLVT---LTLDYNSMLRTSMILAVLVLISLGF 379
                                   3333333223333.23333333322...2456666666666666666665554 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  12.0   2.5e-07   0.00074      46     185 ..      45     180 ..       7     190 .. 0.83
   2 ?    2.9  16.1     0.013        40      17     191 ..     208     380 ..     206     384 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2.5e-07
                                   .HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHHHH CS
                      Sugar_tr  46 vlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlvPmy 126
                                   +l+g+ ++++ +  ++ +  +g+++drfGRk++++ + + +++g+++        ++  livgR+++G g+ + s+++   
  gi|13540969|ref|NP_110657.1|  45 ILIGIAFGAYGLTMALFQAPFGIISDRFGRKNVIILGMIPYIVGNLIAWHPV---NIFGLIVGRLVAGSGAVTSSGMA--M 120
                                   566666777777777777789**************************99999...9************9988888886..7 PP

                                   HHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHH.HTSS-TTHHHHHHHCCHHHHHHHH CS
                      Sugar_tr 127 isEiApkklRgalvslyqlaitfGilvaaifglgl.nktsnadgwrillglqlvpallll 185
                                   ++E  p++ R   + l    i f +++++++g  + ++ ++++ + i   l +++ + + 
  gi|13540969|ref|NP_110657.1| 121 VQESVPPERRNLAMALLGIPIGFAFMIGIVLGPLIsARLGADTLFLISALLGIISIIPMT 180
                                   9******************************98887888885555555555555555444 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.013
                                   HCGGGTHHHHHHHHTSTT--SHHHHHH...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TT CS
                      Sugar_tr  17 gvigafltllkfaknfglsksksskeessvlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaak 97 
                                   gv+g+ ++l+  +++++l  + +  + s  +  l++ ++++G+ii    ++ ++dr       +ia +l+++++   ++ +
  gi|13540969|ref|NP_110657.1| 208 GVVGFLVSLYMIVFFYYLPLYGTRAYGSHGYELLLFWSVVIGGIIAVASSS-FADRGKTTLFSIIALILMLVSTPFVFLEP 287
                                   899999999999999999999988888888888888888888888666555.55555555555556666666653333333 PP

                                   TT.SS-TGGGGGHHHHHHHHHHHHHHHHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-TTHHHHHHHCC CS
                      Sugar_tr  98 gk.nsvevlivgRvlvGigvGlasvlvPmyisEiApkklRgalvslyqlaitfGilvaaifglglnktsnadgwrillglq 177
                                    +  +   +++g ++   g  +  ++ + ++s++++k+  ga +++y+++  +G++ + i+g +l + +    +  +l  +
  gi|13540969|ref|NP_110657.1| 288 VAtGNRDWFFIGTIIFFAGFSIYEIVFTPLVSKLSKKESYGANIGIYNTMQFLGQFAGGITGGVLVTLTL--DYNSMLRTS 366
                                   2247789999**99999999999999999********************************999955555..4******** PP

                                   HHHHHHHHHHGGGS CS
                      Sugar_tr 178 lvpallllilllfl 191
                                   +++a+l+li l fl
  gi|13540969|ref|NP_110657.1| 367 MILAVLVLISLGFL 380
                                   ******99987665 PP

>> MFS_2  MFS/sugar transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   7.0   2.1e-05     0.063     228     339 ..      14     121 ..       3     125 .. 0.86
   2 !    5.1   5.4    0.0023       6.9     261     332 ..     133     222 ..     127     230 .. 0.73
   3 !    8.2  16.3   0.00027       0.8       9     198 ..     207     389 ..     202     395 .] 0.77

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.1e-05
                         MFS_2 228 illllfllaalalgvlnglllYyltyvlgngsaasvfllvvtisallgiplwqplakrlgkkntyllgalltivllvlvll 308
                                   +++++ +l+++++++    + +y + + ++   + + +++  + ++l+ + +  +  r+g+kn+++lg++ +iv+ ++++ 
  gi|13540969|ref|NP_110657.1|  14 AVAVIEVLRMFGIFLVVPVFTLYGKLFSNSPILIGIAFGAYGLTMALFQAPFGIISDRFGRKNVIILGMIPYIVGNLIAW- 93 
                                   67888899999999999999*********************99999999999**********************998876. PP

                         MFS_2 309 lqpsnlllflvllviagfgvgvaallpwsml 339
                                    +p n+  ++v  ++ag g+++  +  ++m+
  gi|13540969|ref|NP_110657.1|  94 -HPVNIFGLIVGRLVAGSGAVT--SSGMAMV 121
                                   .479*******99999999555..4455554 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0023
                         MFS_2 261 asvfllvvtisal.lgiplwqplakrlgkkntyllgalltivllvlvlll.................qpsnlllflvllvi 323
                                   a+++l++++  a+ +gi+l + + +rlg  +++l++all i+  + + ++                  + +++l+ v+ ++
  gi|13540969|ref|NP_110657.1| 133 AMALLGIPIGFAFmIGIVLGPLISARLGADTLFLISALLGIISIIPMTAIkyhkpeyraeerkkagrIEPKTVLVGVVGFL 213
                                   4555555655555699*************************9999999999999999999988666544445555555555 PP

                         MFS_2 324 agfgvgvaa 332
                                   +++ ++v++
  gi|13540969|ref|NP_110657.1| 214 VSLYMIVFF 222
                                   555555544 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.00027
                         MFS_2   9 anilsvllatylli.FytdvlglsaalvglvllvarlvDaitDpivGtlidktstrwGrrrPwlllsaiilavsiillftp 88 
                                   +++++ l+++y+ + Fy   l  + a+ +  + +  ++++++  i+++ ++ + + +G+ + +  +++i++ vs+ ++f+ 
  gi|13540969|ref|NP_110657.1| 207 VGVVGFLVSLYMIVfFYYLPLYGTRAYGSHGYELLLFWSVVIGGIIAVASS-SFADRGKTTLFSIIALILMLVSTPFVFLE 286
                                   567777777776543555555556678899999999999999999987655.55569**99999***************** PP

                         MFS_2  89 pelsqsakfiwllvtyillrilytlfeipyvslvpvltkdydeRtsltsvrsflsvlggvlaailafllvlilgglkserk 169
                                   p +  ++   w+++  i++   ++ +ei ++ lv+ l+k+ +    +  + ++++ lg +++ i  ++lv  +        
  gi|13540969|ref|NP_110657.1| 287 PVA--TGNRDWFFIGTIIFFAGFSIYEIVFTPLVSKLSKKESYGANIGIY-NTMQFLGQFAGGITGGVLVTLTLD----YN 360
                                   *94..69*********************************9988888655.455666666666666666555554....45 PP

                         MFS_2 170 gylifaliialLmllgviivvlgtkerve 198
                                    +l + +i a+L+l++  ++++ tk r+ 
  gi|13540969|ref|NP_110657.1| 361 SMLRTSMILAVLVLISLGFLYIPTKFREI 389
                                   56888888999999998888888887754 PP

>> DUF4538  Domain of unknown function (DUF4538)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   1.1       0.3   9.1e+02       9      26 ..     205     221 ..     201     229 .. 0.84
   2 ?   -2.7   0.3       1.7   5.2e+03       8      16 ..     246     254 ..     244     257 .. 0.82
   3 ?   12.1   0.0   4.1e-05      0.12       3      31 ..     291     319 ..     289     327 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.3
                       DUF4538   9 lvggvvgliglalYPiii 26 
                                   +++gvvg+  ++lY i++
  gi|13540969|ref|NP_110657.1| 205 VLVGVVGF-LVSLYMIVF 221
                                   67899999.689999997 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.7
                       DUF4538   8 llvggvvgl 16 
                                   +++gg++++
  gi|13540969|ref|NP_110657.1| 246 VVIGGIIAV 254
                                   789***987 PP

  == domain 3  score: 12.1 bits;  conditional E-value: 4.1e-05
                       DUF4538   3 glkyvllvggvvgliglalYPiiiaPllh 31 
                                   g +   ++g+++ + g ++Y i++ Pl+ 
  gi|13540969|ref|NP_110657.1| 291 GNRDWFFIGTIIFFAGFSIYEIVFTPLVS 319
                                   567778********************986 PP

>> TRIQK  Triple QxxK/R motif-containing protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.2       3.1   9.3e+03      55      70 ..      23      40 ..       9      42 .. 0.52
   2 ?   10.3   0.1   0.00017       0.5      38      72 ..     190     223 ..     181     227 .. 0.80
   3 ?   -3.7   0.5       3.9   1.2e+04      55      63 ..     270     278 ..     264     285 .. 0.45
   4 ?   -1.6   0.1      0.85   2.5e+03      47      73 ..     291     317 ..     288     322 .. 0.70
   5 ?   -2.7   0.6       1.9   5.7e+03      54      62 ..     367     375 ..     364     382 .. 0.74

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 3.1
                         TRIQK 55 lvailvl..llalYalff 70
                                  + +i+++  +++lY+ +f
  gi|13540969|ref|NP_110657.1| 23 MFGIFLVvpVFTLYGKLF 40
                                  344443312566776555 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00017
                         TRIQK  38 kAeakksasgikevllvlvailvlllalYalffln 72 
                                   +Ae +k a  i e + vlv+++ +l++lY ++f+ 
  gi|13540969|ref|NP_110657.1| 190 RAEERKKAGRI-EPKTVLVGVVGFLVSLYMIVFFY 223
                                   68888888766.56889************976654 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 3.9
                         TRIQK  55 lvailvlll 63 
                                   ++a++++l+
  gi|13540969|ref|NP_110657.1| 270 IIALILMLV 278
                                   444333333 PP

  == domain 4  score: -1.6 bits;  conditional E-value: 0.85
                         TRIQK  47 gikevllvlvailvlllalYalfflnl 73 
                                   g ++ +++   i++  +++Y ++f  l
  gi|13540969|ref|NP_110657.1| 291 GNRDWFFIGTIIFFAGFSIYEIVFTPL 317
                                   556666666667777799999999755 PP

  == domain 5  score: -2.7 bits;  conditional E-value: 1.9
                         TRIQK  54 vlvailvll 62 
                                   +++a+lvl+
  gi|13540969|ref|NP_110657.1| 367 MILAVLVLI 375
                                   889999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (395 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       893  (0.0498076); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.70u 0.27s 00:00:00.97 Elapsed: 00:00:00.46
# Mc/sec: 2595.34
//
Query:       gi|13540970|ref|NP_110658.1|  [L=148]
Description: hypothetical protein TVN0139 [Thermoplasma volcanium GSS1]
Scores for complete 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   43.9   0.0    3.1e-11   43.6   0.0    1.1  1  DDE_Tnp_1_5  Transposase DDE 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 !   43.6   0.0   1.7e-15   3.1e-11       7     110 ..      26     128 ..      24     130 .. 0.88

  Alignments for each domain:
  == domain 1  score: 43.6 bits;  conditional E-value: 1.7e-15
                   DDE_Tnp_1_5   7 tiwldeeaiaawkekkkn...gkrgrpqvysdaaiqtcltvkvlfklplRqlqGfvqsllklaglellvpdystlsrrakt 84 
                                   t+ ++ +++++w+++++n   gkrg p+ +++ +++++++ k++  l +R+l+G+ +sl ++ +++ +   y+t+++r ++
  gi|13540970|ref|NP_110658.1|  26 TFLFNLDFVQQWDQEVTNmnrGKRGSPYLFPESFMKFMMMWKQF--LDYRALEGMARSLADMKKIP-QYGYYTTVWHRIHD 103
                                   6889999*****98844333599********************9..679****************5.7889********** PP

                   DDE_Tnp_1_5  85 levkipvkrkskglhlvvdstGlkvl 110
                                   ++ ++ +++ + +  l  d+tGlk  
  gi|13540970|ref|NP_110658.1| 104 MKPTLDISDLRYA-DLGTDGTGLKTN 128
                                   *****99888855.999******975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       324  (0.0180713); expected 358.6 (0.02)
Passed bias filter:                      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: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1134.97
//
Query:       gi|13540971|ref|NP_110659.1|  [L=69]
Description: transposon-encoded protein [Thermoplasma volcanium GSS1]
Scores for complete 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-17   61.5   0.2    6.3e-17   61.1   0.2    1.2  1  DUF2080          Putative transposon-encoded protein (DUF2080
  ------ inclusion threshold ------
      0.075   13.5   0.1      0.089   13.3   0.1    1.1  1  Phage_int_SAM_4  Phage integrase, N-terminal SAM-like domain


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 !   61.1   0.2     7e-21   6.3e-17       1      50 []      16      65 ..      16      65 .. 0.97

  Alignments for each domain:
  == domain 1  score: 61.1 bits;  conditional E-value: 7e-21
                       DUF2080  1 veIrkktwlkvkeilpffegkVkpfGnSAkvsiPkeylGkkvylvIlddd 50
                                  v+++++ +  + +i+   e+ V++fG++Akv++PkeylGk+v l+I +dd
  gi|13540971|ref|NP_110659.1| 16 VKVKEANEITAHNIEAYMERTVTKFGSGAKVDCPKEYLGKRVCLIIKKDD 65
                                  799*******************************************9997 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 ?   13.3   0.1     1e-05     0.089      22      53 ..       5      36 ..       2      46 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1e-05
               Phage_int_SAM_4 22 YlsaikrflrflkkkapeeltkedieaYlnyL 53
                                   ++ i+ f++++k k+ +e+t + ieaY++  
  gi|13540971|ref|NP_110659.1|  5 NIYCIYTFVKKVKVKEANEITAHNIEAYMERT 36
                                  567899***********************875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       645  (0.0359752); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.32s 00:00:00.80 Elapsed: 00:00:00.50
# Mc/sec: 414.46
//
Query:       gi|13540972|ref|NP_110660.1|  [L=170]
Description: hypothetical protein TVN0141, partial [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.46
# Mc/sec: 1112.72
//
Query:       gi|13540973|ref|NP_110661.1|  [L=58]
Description: hypothetical protein TVN0142, partial [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0082   15.8   0.1      0.011   15.4   0.1    1.2  1  RIIa      Regulatory subunit of type II PKA R-subunit


Domain annotation for each model (and alignments):
>> RIIa  Regulatory subunit of type II PKA R-subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   6.1e-07     0.011      20      32 ..       2      14 ..       2      18 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 6.1e-07
                                  S-HHHHHHHHHHH CS
                          RIIa 20 sDvlqFaadYFek 32
                                  sD+++F+++YF++
  gi|13540973|ref|NP_110661.1|  2 SDPMEFLKEYFKR 14
                                  8**********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       332  (0.0185175); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); 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 0.30s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 375.10
//
Query:       gi|13540974|ref|NP_110662.1|  [L=131]
Description: hypothetical protein TVN0143 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.028   14.6   5.5      0.028   14.6   5.5    2.6  3  YtpI      YtpI-like protein
        2.7    7.7   5.8       0.81    9.5   2.6    1.7  2  TMEM40    Transmembrane protein 40 family
        8.3    6.3  16.7        4.2    7.3   2.7    2.2  2  DUF2721   Protein of unknown function (DUF2721)


Domain annotation for each model (and alignments):
>> YtpI  YtpI-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.4      0.12   7.4e+02      53      71 ..       7      25 ..       4      40 .. 0.75
   2 ?   -0.5   0.5      0.23   1.4e+03      39      65 ..      34      61 ..      25      61 .. 0.78
   3 ?   14.6   5.5   4.7e-06     0.028      33      82 ..      73     128 ..      67     131 .] 0.77

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.12
                          YtpI 53 lestvalvvgavflvlGla 71
                                  ++s + +vvg+ +l l ++
  gi|13540974|ref|NP_110662.1|  7 YKSILFYVVGLALLYLSIF 25
                                  5666777777777777665 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.23
                          YtpI 39 Glflilfgin.qllllestvalvvgavf 65
                                  G f++++ i+  l+++   ++++v +++
  gi|13540974|ref|NP_110662.1| 34 GHFISALPIVlPLVFSAASIGVAVILIM 61
                                  7788888888777778888888877775 PP

  == domain 3  score: 14.6 bits;  conditional E-value: 4.7e-06
                          YtpI  33 kasialGlflilfgin.qllllestv...alvvgavflvlGlanlf..aGiraykh 82 
                                    +s+++G+ l+lfgi  ++l  es v   ++v+g++f++ +++ l+   G+  y++
  gi|13540974|ref|NP_110662.1|  73 IMSLVIGITLFLFGILtFYLGVESLVwagSVVIGILFIIAAMVRLIiqGGLSTYRK 128
                                   599*************777888887755689********99987651146666655 PP

>> TMEM40  Transmembrane protein 40 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1      0.27   1.6e+03      61      73 ..      25      37 ..       2      64 .. 0.46
   2 ?    9.5   2.6   0.00014      0.81      48     113 ..      68     130 ..      56     131 .] 0.80

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.27
                        TMEM40 61 llvsyhyyadwfm 73
                                  +l     y   f+
  gi|13540974|ref|NP_110662.1| 25 FLSNILKYNGHFI 37
                                  3333333333333 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00014
                        TMEM40  48 ffhfvllcfaigallvsyhyyadwfmslgvglltfasletvgiyfglvyrihsvlqgfiplfqkir 113
                                   ff   ++ + ig  l  +       + lgv  l +a    +gi f +   +  ++qg +  ++kir
  gi|13540974|ref|NP_110662.1|  68 FFRTGIMSLVIGITLFLFGI---LTFYLGVESLVWAGSVVIGILFIIAAMVRLIIQGGLSTYRKIR 130
                                   66667777777766655544...44679*************************************9 PP

>> DUF2721  Protein of unknown function (DUF2721)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   2.7   0.00071       4.2      59     114 ..       2      58 ..       1      62 [. 0.63
   2 ?    4.9   6.3    0.0038        23      66     111 ..      74     119 ..      67     126 .. 0.60

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.00071
                       DUF2721  59 Rarlirrailllvlsallvvlvvlllflsall.sldlsllaailfvlalllllvsll 114
                                   R + i ++il++v++++l+ l+++l  + ++  ++  +l +++  v++ +++ v+++
  gi|13540974|ref|NP_110662.1|   2 RYQNIYKSILFYVVGLALLYLSIFLSNILKYNgHFISALPIVLPLVFSAASIGVAVI 58 
                                   8889999*************9999988844442222223333334444444444444 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0038
                       DUF2721  66 ailllvlsallvvlvvlllflsallsldlsllaailfvlalllllv 111
                                   + l++ ++++l+ ++ + l +++l+ +   ++  ++ ++a++ l++
  gi|13540974|ref|NP_110662.1|  74 MSLVIGITLFLFGILTFYLGVESLVWAGSVVIGILFIIAAMVRLII 119
                                   3344455666666677777776666555555555555567777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1123  (0.062636); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); 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: 0.53u 0.34s 00:00:00.87 Elapsed: 00:00:00.51
# Mc/sec: 777.10
//
Query:       gi|13540975|ref|NP_110663.1|  [L=210]
Description: hypothetical protein TVN0144 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.28   11.3   4.8       0.53   10.5   0.5    2.6  2  CD225     Interferon-induced transmembrane protein
       0.48   10.4   7.0        1.4    8.9   2.9    2.3  2  DUF2755   Protein of unknown function (DUF2755)
        6.1    7.7  18.2         37    5.1  14.2    2.2  2  DUF4282   Domain of unknown function (DUF4282)


Domain annotation for each model (and alignments):
>> CD225  Interferon-induced transmembrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.4     0.036   2.2e+02      47      68 .]      77      98 ..      66     106 .. 0.70
   2 ?   10.5   0.5   8.9e-05      0.53       8      65 ..     138     193 ..     136     196 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.036
                         CD225 47 sstAkllniialvlgiiliill 68
                                  + ++++l  +a  ++i+ +i++
  gi|13540975|ref|NP_110663.1| 77 AGSSRTLVTVAYAISILSVIAY 98
                                  5566777777777777666654 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 8.9e-05
                         CD225   8 wsifntlfcclplGivAlvySvkvrdrkmvGdvegAqsasstAkllniialvlgiili 65 
                                    si+++l+ +l++ i  +v  +k r+   +Gd+e A +  +++  + ++al++g +l+
  gi|13540975|ref|NP_110663.1| 138 ISILVFLIIFLVIDIYIVVRISKIRSYIINGDYESAYQ--KNSVGFGVVALIFGGLLT 193
                                   69**********************************87..566678888888887765 PP

>> DUF2755  Protein of unknown function (DUF2755)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   2.9   0.00023       1.4      10      97 ..      72     157 ..      64     162 .. 0.80
   2 ?    3.1   0.1     0.014        86      75      95 ..     181     201 ..     175     206 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00023
                       DUF2755  10 llsdkkreastsgnvayalfvllclwaGaqllnl.lvhapGvlerlmqaqesarpqveislavGtlfglvpflaGlvilgv 89 
                                   ++ +  +++ t   vaya+ +l  +   a ++++ ++   G+    m     ++      +a G l gl+ +l+ l+i+ v
  gi|13540975|ref|NP_110663.1|  72 MVEGNAGSSRTLVTVAYAISILSVI---AYIISIaIISLDGIASTHMYSSYGGQGIGYTNVATGALVGLISILVFLIIFLV 149
                                   6677788889999999999876544...566665256779999999999999999888999*****************999 PP

                       DUF2755  90 lalilrlr 97 
                                   + + + +r
  gi|13540975|ref|NP_110663.1| 150 IDIYIVVR 157
                                   98776655 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.014
                       DUF2755  75 fglvpflaGlvilgvlalilr 95 
                                   fg+v ++ G ++ g+l li r
  gi|13540975|ref|NP_110663.1| 181 FGVVALIFGGLLTGILLLIAR 201
                                   9***************99987 PP

>> DUF4282  Domain of unknown function (DUF4282)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1  14.2    0.0062        37      10      62 ..      81     150 ..      78     160 .. 0.86
   2 ?    4.7   0.2    0.0087        52      31      71 ..     164     205 ..     151     209 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0062
                       DUF4282  10 pkllkvlYilgivlialvllslivgafaal.................seslsagggllllllaviafllm 62 
                                   ++l+ v+Y + i+ ++ +++s+ + +++ +                 + +++a++gl+++l+++i+fl++
  gi|13540975|ref|NP_110663.1|  81 RTLVTVAYAISILSVIAYIISIAIISLDGIasthmyssyggqgigytNVATGALVGLISILVFLIIFLVI 150
                                   789999999999999999999999999999999999999999***999999****************886 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0087
                       DUF4282  31 livgafaal.seslsagggllllllaviafllmilllRivlE 71 
                                    i+++  ++ ++++s+g g+++l+++ +   + +l++R  lE
  gi|13540975|ref|NP_110663.1| 164 YIINGDYESaYQKNSVGFGVVALIFGGLLTGILLLIARGDLE 205
                                   44444444468999***********99999999999986666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1550  (0.0864521); expected 358.6 (0.02)
Passed bias filter:                      608  (0.0339115); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 1281.40
//
Query:       gi|13540976|ref|NP_110664.1|  [L=173]
Description: hypothetical protein TVN0145 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       393  (0.0219198); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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 0.31s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1100.43
//
Query:       gi|13540977|ref|NP_110665.1|  [L=482]
Description: Na+/proline symporter permease [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-23   83.3  31.3    2.7e-23   82.5  31.3    1.4  1  SSF       Sodium:solute symporter family


Domain annotation for each model (and alignments):
>> SSF  Sodium:solute symporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.5  31.3   1.5e-27   2.7e-23       3     406 .]      37     429 ..      35     429 .. 0.81

  Alignments for each domain:
  == domain 1  score: 82.5 bits;  conditional E-value: 1.5e-27
                           SSF   3 lagrsltgfvlglslaasnisaasfvGlaGavaasGlavvllelgalllvlllllllae.rlr...nagalTlpdylskRf 79 
                                   ++gr+++ + +   la++   a  f+G++G ++a G   + ++l   +l++l  +++ + ++r   +++ +T pd++++R+
  gi|13540977|ref|NP_110665.1|  37 VGGRNIGALLIWFLLAGEIYTAFTFLGVPGYAYAFGA-PAYYALSYGVLAYLTSYFILPkIWRiskKKNIMTQPDFFKERY 116
                                   79**********************************6.5677777777666666655550556999*************** PP

                           SSF  80 kgkrilvylsalslllvitlklsvdlvggaklielalGlnyet...avlllaaltalYtviGGllAvvytdtiq.avlmlv 156
                                   ++  +  ++++ + +++++ +l  ++ +   ++e ++G n+ +    +++  +lta Y+++ Gl++ ++t   + ++ ++v
  gi|13540977|ref|NP_110665.1| 117 QSTLLATIVAV-VGVVFMVPYLELQVSAITDILE-VMGYNVIMpayVMIITFVLTAGYVIMNGLRSATFTAFFKdGLALIV 195
                                   ***96666655.56789999*****888777776.6888876521135666789999***************995344555 PP

                           SSF 157 galilliivllevGgleslveklkeaapkvvdlltpdslkllrdpltalslwlglvlGvaglphilvRflaakdakailkg 237
                                     + l +i  +++G l+++++++ +       l+ p+  +l ++     +  l   lG ++ ph  +  ++ak+ + + k 
  gi|13540977|ref|NP_110665.1| 196 IFSALIVIPAVQFGDLNNMMHRMVTNYS--EYLYFPGHSELGLSWFVSVV--LMSALGFFMWPHSFQSYISAKNDNVLKKN 272
                                   55667778889**********9988777..55666666544333333333..46889****************98888777 PP

                           SSF 238 vlkltivlilvligmisiilfaiklagavpkavgtevgvsniaypeLvvkllpnllaGlllavmlAaimstltslllsass 318
                                    +  ++v  ++l+ ++++++ a  +         +++ +++ a+   + + +p++  G++  ++    m   + ll+++s+
  gi|13540977|ref|NP_110665.1| 273 AVF-LPVYNVLLVITVFMGFAALLY--------NPHLSNADDAFLIVARASFPSWWNGVVAGAITLGSMVPASVLLIASST 344
                                   654.677777777778888766433........45688999*******************98887778888999******* PP

                           SSF 319 aftkDlYkkirrkasakekelvgvsriivlvvislaillavqeeqkgvlklvelafaglasavlavillalfwkrvneqGA 399
                                   +++k lYk ++ k+ a++  ++ ++++ v +++ +a+l a++++    + l  l  +g++  +++ i++++ w +v++ G 
  gi|13540977|ref|NP_110665.1| 345 IISKNLYKDLINKK-ASDSSVKFIAQVFVAIITGVALLFAIEFPAL-FVNLLLLGYSGIT-LFFPGIVMGITWRKVTAVGV 422
                                   ************99.99***************************99.6666666666664.799***************** PP

                           SSF 400 lagliiG 406
                                   ++g+i+G
  gi|13540977|ref|NP_110665.1| 423 ISGIITG 429
                                   *****98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (482 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1121  (0.0625244); 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:                         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: 0.65u 0.30s 00:00:00.95 Elapsed: 00:00:00.48
# Mc/sec: 3010.99
//
Query:       gi|13540978|ref|NP_110666.1|  [L=64]
Description: hypothetical protein TVN0147 [Thermoplasma volcanium GSS1]
Scores for complete 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-13   48.0   5.7    9.3e-13   47.9   5.7    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 !   47.9   5.7   5.2e-17   9.3e-13       2      54 ..      10      62 ..       9      64 .] 0.97

  Alignments for each domain:
  == domain 1  score: 47.9 bits;  conditional E-value: 5.2e-17
                       DUF3311  2 lllvpvlvalllvpfynrvdpvllGlPffywwqllwvllasvvtwlayrlakr 54
                                  lll+p++ +l++ p++n+   ++l +P++++w++ w++l+ +vt+++yr ++r
  gi|13540978|ref|NP_110666.1| 10 LLLIPYIAILVIAPLLNSIHILVLDMPLIMFWLFIWFFLTPIVTYMIYREDRR 62
                                  89***********************************************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       825  (0.0460148); 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):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 456.72
//
Query:       gi|13540979|ref|NP_110667.1|  [L=1344]
Description: multitransmembrane protein [Thermoplasma volcanium GSS1]
Scores for complete 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-63  214.0  13.7    2.4e-63  214.0  13.7    4.2  5  Thermopsin      Thermopsin
      5e-25   88.5   0.0    1.2e-24   87.3   0.0    1.7  1  Pro-kuma_activ  Pro-kumamolisin, activation domain
  ------ inclusion threshold ------
      0.041   13.1   0.1      0.077   12.2   0.1    1.3  1  Peptidase_S8    Subtilase family
        1.8    7.8  35.8      0.028   13.7  27.3    2.4  2  NosD            Periplasmic copper-binding protein (NosD)


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 !  214.0  13.7   5.3e-67   2.4e-63       7     259 ..      91     372 ..      87     373 .. 0.93
   2 ?   -3.8   0.3       1.5   6.9e+03     108     155 ..     491     544 ..     488     562 .. 0.60
   3 ?   -0.6   4.7      0.17   7.5e+02      97     138 ..     705     750 ..     675     761 .. 0.77
   4 ?   -4.0   0.3       1.8     8e+03     135     171 ..     869     906 ..     858     932 .. 0.71
   5 ?   -3.2   0.0      0.99   4.5e+03      94     105 ..    1010    1021 ..    1007    1031 .. 0.83

  Alignments for each domain:
  == domain 1  score: 214.0 bits;  conditional E-value: 5.3e-67
                    Thermopsin   7 slyssepaPmGiadyGiknnsgkltpysyntssvlGevnisslsaynsssnspesaslQLNvvlevvt..ggktysywvQn 85 
                                    ly+++paPmGi+ +G++n++g+l+  +y   s+ ++vn+++ls++n++++ p+s+s+QLN+vl+++t  g+++y+yw+Qn
  gi|13540979|ref|NP_110667.1|  91 LLYTQSPAPMGIGFFGLENKNGQLMGSNYYAYSFSATVNLTNLSVFNLANDGPNSISIQLNTVLDNTTilGTSNYTYWTQN 171
                                   689******************************************************************9*********** PP

                    Thermopsin  86 VvsfnttekqltfidNiWNftspsanlsnsai.sGnGtvyasskgefYyayateylelslPltlkLvinvsltsngvpevs 165
                                   V+ ++ ++++l+fidNiWNf+sp+a ++ ++i +  G+v    +  ++ a++++ + l +P+tl+L++n+s + ng+++v+
  gi|13540979|ref|NP_110667.1| 172 VAFYSVRTHELEFIDNIWNFSSPTAVMTPNTIlNSTGQVL--PYPGVHIAIGPT-YYLPTPFTLTLYLNTSEI-NGNNVVY 248
                                   ******************************99899*****..89999*******.899************999.8888*** PP

                    Thermopsin 166 FgYsid..ggvvtYDnvtinstgkasa.......eilvngssltpsgllyDaeLvlgGpgngekttfnslnatlsLyY... 234
                                   F+Ysi   g   tYD+vt+nst ++         ++ v+g++ltp gllyDae+++gGpg+g++tt++ +n t+sL+Y   
  gi|13540979|ref|NP_110667.1| 249 FNYSIPqiGAEGTYDRVTFNSTYGMPPaykapysYFRVSGTQLTPLGLLYDAEIMIGGPGGGSTTTIMGINGTMSLKYipa 329
                                   ****9899999***********999888999***********************************************988 PP

                    Thermopsin 235 .............lngtn.....yqpvknaydfGsdTaEtaen 259
                                                 ng       y++v++a+dfG+dT+Et+ +
  gi|13540979|ref|NP_110667.1| 330 gqsrvtpppppppPNGPAspqmdYVNVPSAFDFGTDTGETSIG 372
                                   88777777777763333356677*****************976 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 1.5
                    Thermopsin 108 psanlsnsaisGnGtvy..asskgefYyayatey...lelslP.ltlkLvinvs 155
                                   ++a+l n ++sG Gt       +++ Y ++++      ++s+P ++  +++ +s
  gi|13540979|ref|NP_110667.1| 491 NNAQLANISMSGAGTAKdpYVLYNNEYGYISPLFgqiNDYSFPqFAGVMLLGTS 544
                                   688999999999999885534444444444443355466666644455555554 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.17
                    Thermopsin  97 tfidNiWNftspsanlsnsai...sGnGtvy..asskgefYyayate 138
                                   ++  NiWN++++  n  +  +   +  G+++  + ++g+++y+++ +
  gi|13540979|ref|NP_110667.1| 705 AVYTNIWNISKEPVNYVRI-VdgfKLSGSIIggKYQGGNYWYNFNGT 750
                                   6789*******99887544.455577999997777777888877655 PP

  == domain 4  score: -4.0 bits;  conditional E-value: 1.8
                    Thermopsin 135 yatey.lelslPltlkLvinvsltsngvpevsFgYsid 171
                                   ++ +  +    Pl + L  nvs+ +++  +  F Y++ 
  gi|13540979|ref|NP_110667.1| 869 LGFKVwSYWYAPLVIVLQGNVSMFEHAFGTMLFEYMFT 906
                                   44444344456999999999999999999999999865 PP

  == domain 5  score: -3.2 bits;  conditional E-value: 0.99
                    Thermopsin   94 kqltfidNiWNf 105 
                                     +++ idN WN 
  gi|13540979|ref|NP_110667.1| 1010 ANISAIDNFWNQ 1021
                                    67999******7 PP

>> Pro-kuma_activ  Pro-kumamolisin, activation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.3   0.0   2.6e-28   1.2e-24       6     140 ..     801     939 ..     796     941 .. 0.94

  Alignments for each domain:
  == domain 1  score: 87.3 bits;  conditional E-value: 2.6e-28
                Pro-kuma_activ   6 rgraasstllpvrigLkqnnlekledflmdvsdpkspnygkhltaeevaelfapseeaidaVrnwLessgiaasrhsdtkg 86 
                                    g+a++st+++v+++L+++ ++ le+f+ +v++p+sp+++++l++++++++++ps++ i++++n+ e+ g+++ +      
  gi|13540979|ref|NP_110667.1| 801 LGPANQSTVINVTLYLNFTHIQALEQFVSQVNSPNSPEFRHYLSPSQFESMYYPSSSVINSIENYYEKLGFKVWSYWYAPL 881
                                   689****************************************************************************** PP

                Pro-kuma_activ  87 wiafsatvaqverllktsfeaYshk....kgssslarcdeyslPealknyvdyihptd 140
                                   +i+++++v+ +e +++t +  Y       +g  +++++ ++++P + k ++ ++ +++
  gi|13540979|ref|NP_110667.1| 882 VIVLQGNVSMFEHAFGTMLFEYMFTypggDGAVFMTNTANPYIPIEFKGVIMHVYGLS 939
                                   *****************9988884446668888999******************9986 PP

>> Peptidase_S8  Subtilase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   1.7e-05     0.077     201     266 ..    1211    1260 ..    1146    1273 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.7e-05
                                    TT--B-TT.......-EEEE-S-CCCCCCCCCHHHTTTHHEEEE-SHHHCHHHHHHHHHHHHHHHT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Peptidase_S8  201 pfSsrGpssdgklkpdivapGgnivstwsrqsnnsaglssyqsmsGTSmAsPnaagaaAlllsalp 266 
                                    +f++rG        pdi++p++++v  +++               GTS+A+P  ag++A + +++ 
  gi|13540979|ref|NP_110667.1| 1211 TFTNRGQ-------PDIAMPAAKMVFAYKNFF---------GVAGGTSFATPISAGIFADIEQGYM 1260
                                    5555554.......9********999998886.........6789****************99775 PP

>> NosD  Periplasmic copper-binding protein (NosD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.6   1.3       2.4   1.1e+04     161     178 ..     145     162 ..     116     187 .. 0.58
   2 ?   13.7  27.3   6.2e-06     0.028      81     220 ..     576     758 ..     570     775 .. 0.78

  Alignments for each domain:
  == domain 1  score: -4.6 bits;  conditional E-value: 2.4
                          NosD 161 gntiynNyFinnsenvky 178
                                   + +i  N+ ++n++ +  
  gi|13540979|ref|NP_110667.1| 145 SISIQLNTVLDNTTILGT 162
                                   333334444333333222 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 6.2e-06
                          NosD  81 nesGialmsssnntlenNtisnnen........yGillsdssnntisnNtisnnnkGiflensssntitgNriesn..... 148
                                   n+ G+++++ss+ ++++++i++           + i+l + s++ i+ N +++ ++ + + + s+nt+ gN++ ++     
  gi|13540979|ref|NP_110667.1| 576 NYLGYWIYNSSHVVVRQSEITGWFFtddsgfplANIILWNTSDSLIASNYFLSMDSSLLIFGGSNNTVWGNYFFNSplian 656
                                   67899999999889999998763223345699999****************************************999977 PP

                          NosD 149 ...........qkiGilllsssegntiynNyFinnsenvkydgsn........nneW................nttktsgt 194
                                              +  G  l  +s++ntiynN F    + ++ ++s          n W                +       
  gi|13540979|ref|NP_110667.1| 657 pslyaawnlwgEALG--LAVYSSNNTIYNNFFATQLTAISPSTSIytgnpavyTNIWniskepvnyvrivdgfKL----SG 731
                                   877777777544444..5589999********7766666555544666678888999888888888876654433....34 PP

                          NosD 195 niiggpylgGNyWsdydg.eDadgDGi 220
                                    iigg+y gGNyW +++g    +++G+
  gi|13540979|ref|NP_110667.1| 732 SIIGGKYQGGNYWYNFNGtIPYNNNGM 758
                                   79****************533555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       587  (0.0327403); 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:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.94u 0.33s 00:00:01.27 Elapsed: 00:00:00.55
# Mc/sec: 7391.00
//
Query:       gi|13540980|ref|NP_110668.1|  [L=239]
Description: ABC-type multidrug transport system, ATPase component [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.7e-30  103.9   0.0    1.5e-29  103.2   0.0    1.3  1  ABC_tran         ABC transporter
    8.9e-13   48.7   3.0    4.4e-06   26.7   0.1    2.1  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    6.5e-05   22.5   0.1       0.11   11.9   0.0    2.2  2  SMC_N            RecF/RecN/SMC N terminal domain
    0.00037   20.2   0.1    0.00072   19.3   0.1    1.4  1  AAA_29           P-loop containing region of AAA domain
     0.0038   17.0   0.2     0.0057   16.4   0.2    1.6  1  AAA_15           AAA ATPase domain
     0.0051   17.3   0.1     0.0054   17.3   0.1    1.4  1  AAA_23           AAA domain
  ------ inclusion threshold ------
      0.013   15.9   0.0      0.018   15.5   0.0    1.4  1  AAA_16           AAA ATPase domain
      0.014   15.0   0.0      0.042   13.5   0.0    1.7  2  SRP54            SRP54-type protein, GTPase domain
       0.02   14.8   0.0      0.041   13.8   0.0    1.4  1  RsgA_GTPase      RsgA GTPase
      0.023   15.0   0.2      0.083   13.2   0.2    2.1  1  AAA_22           AAA domain
      0.026   14.4   0.6      0.079   12.9   0.1    1.9  2  Rad17            Rad17 P-loop domain
      0.034   13.9   0.0      0.056   13.2   0.0    1.3  1  AAA_30           AAA domain
      0.035   14.5   0.1      0.087   13.3   0.1    1.9  1  AAA              ATPase family associated with various cellul
      0.042   13.7   0.0      0.085   12.6   0.0    1.5  1  MukB             MukB N-terminal
      0.067   12.6   0.0       0.13   11.6   0.0    1.4  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
       0.08   12.6   0.0       0.18   11.5   0.0    1.6  2  AAA_24           AAA domain
       0.16   11.6   0.0        0.4   10.3   0.0    1.6  2  Thymidylate_kin  Thymidylate kinase


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.2   0.0   1.4e-32   1.5e-29       2     137 .]      20     159 ..      19     159 .. 0.96

  Alignments for each domain:
  == domain 1  score: 103.2 bits;  conditional E-value: 1.4e-32
                                   EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx... RF
                      ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren... 79 
                                   + +++ l  ge +a++G+nGaGKSt lk+lag lkp++G++ + g d ++   + +rk +g+lp+++    +l+vren   
  gi|13540980|ref|NP_110668.1|  20 DGLTFRLDCGESMALIGPNGAGKSTTLKILAGILKPDSGSVSISGYDPST---NDARKIVGYLPEDAAPYFTLSVRENley 97 
                                   6899****************************************998888...99***********99999999******* PP

                                   ........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                   ........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  80 ........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                           + +++++ +++ lgl + ++ +v    s LS G +q++a+a +l+ +pk+lllDEp +
  gi|13540980|ref|NP_110668.1|  98 igalrgvqNLNSRMDFLMELLGLGNYRNVKV----SALSRGNRQKLAIALVLIHDPKVLLLDEPLN 159
                                   ********9****************999999....*****************************86 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.4   3.9e-08   4.1e-05       2      31 ..      32      57 ..      31      84 .. 0.65
   2 !   26.7   0.1   4.2e-09   4.4e-06     190     299 ..      77     187 ..      60     191 .. 0.79

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 3.9e-08
                        AAA_21  2 nvliGpNgsGKSnLLdaldllarldrdveg 31
                                  ++liGpNg+GKS+ L++l ++       ++
  gi|13540980|ref|NP_110668.1| 32 MALIGPNGAGKSTTLKILAGILKP----DS 57
                                  68****************998642....22 PP

  == domain 2  score: 26.7 bits;  conditional E-value: 4.2e-09
                        AAA_21 190 rslklveielsdlgegeeliasvderlrer.......gvvflengdgqelparelSdGtkrllalltallralkkgsllli 263
                                   + l ++ +++ +l ++e+l +  ++r  ++        + +l  g+++++ ++ lS G ++ la+++ l+ ++   ++ll+
  gi|13540980|ref|NP_110668.1|  77 GYLPEDAAPYFTLSVRENLEYIGALRGVQNlnsrmdfLMELLGLGNYRNVKVSALSRGNRQKLAIALVLIHDP---KVLLL 154
                                   44555555555666666666666666666688888889999999******************99999999988...9**** PP

                        AAA_21 264 DEpEngLHPkllrrllellkelsrngaQviltTHSp 299
                                   DEp n L+   ++ + + + +l   +a ++++TH  
  gi|13540980|ref|NP_110668.1| 155 DEPLNYLDIPSQEAITKYFHSL---KATFLVSTHIM 187
                                   ****************888555...459******65 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.0    0.0011       1.1      27      41 ..      32      46 ..      16      55 .. 0.84
   2 !   11.9   0.0   0.00011      0.11     129     205 ..     123     193 ..     101     207 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0011
                                  EEEEESTTSSHHHHH CS
                                  xxxxxxxxxxxxxxx RF
                         SMC_N 27 taivGpNGSGKsnll 41
                                   a++GpNG+GKs  l
  gi|13540980|ref|NP_110668.1| 32 MALIGPNGAGKSTTL 46
                                  589*********865 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00011
                                   CTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC- CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 129 sagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislreemleka 205
                                     +++ ++LS+G+++ +a+aL++ i+  +p+ + llDe    LD    +++ +++++ +  a f+v ++   + e+ 
  gi|13540980|ref|NP_110668.1| 123 YRNVKVSALSRGNRQKLAIALVL-IH--DPK-VLLLDEPLNYLDIPSQEAITKYFHSLK--ATFLVSTHIMSIAERF 193
                                   56778889*************96.33..444.5699********************999..99***99987777665 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 !   19.3   0.1   6.8e-07   0.00072      12      49 ..      19      56 ..      17      61 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 6.8e-07
                        AAA_29 12 fdghtieidlkgatlltGpsGsGKSTllDAiqalLvpa 49
                                  +dg t+++d  +++ l+Gp+G+GKST l  ++ +L p+
  gi|13540980|ref|NP_110668.1| 19 IDGLTFRLDCGESMALIGPNGAGKSTTLKILAGILKPD 56
                                  577889999888**************987776666665 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.2   5.4e-06    0.0057      23      50 ..      30      56 ..      22     221 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 5.4e-06
                        AAA_15 23 eeltvliGkNnsGKSsilealdlFlnnk 50
                                  e  + liG+N++GKS+ l++l  +l+ +
  gi|13540980|ref|NP_110668.1| 30 E-SMALIGPNGAGKSTTLKILAGILKPD 56
                                  5.689****************8887765 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.1   5.1e-06    0.0054      13      64 ..      22      73 ..       4     218 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 5.1e-06
                        AAA_23 13 qeidFsk.gltlItGpNGaGKTTildAiklaLygetprlsrksgrgfeksdve 64
                                   ++ ++     +++GpNGaGK+T l  +  +L  ++ +  + sg +  ++d +
  gi|13540980|ref|NP_110668.1| 22 LTFRLDCgESMALIGPNGAGKSTTLKILAGILKPDS-GSVSISGYDPSTNDAR 73
                                  55555442356899************9999997764.4555566666666665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.0   1.7e-05     0.018       3      63 ..      13      69 ..      11     186 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.7e-05
                        AAA_16  3 vGReeeleqLlsalervrsgrpelvllsGesGvGKsslvrellralekdggif.lrgkcdql 63
                                  +G+++ ++ L+  l+      +e++ l+G+ G GKs+ ++ l+  l+ d g + ++g   + 
  gi|13540980|ref|NP_110668.1| 13 YGKKRAIDGLTFRLD-----CGESMALIGPNGAGKSTTLKILAGILKPDSGSVsISGYDPST 69
                                  566666666666555.....5599*****************999998886666455555444 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0     4e-05     0.042       4      38 ..      32      66 ..      30      76 .. 0.90
   2 ?   -2.0   0.0       2.2   2.3e+03     159     186 ..     186     215 ..     184     222 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4e-05
                                  EEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEES CS
                         SRP54  4 illvGlqGaGKTttlaKLaallkkegkkvllvaaD 38
                                  ++l+G++GaGK ttl  La +lk +  +v +   D
  gi|13540980|ref|NP_110668.1| 32 MALIGPNGAGKSTTLKILAGILKPDSGSVSISGYD 66
                                  689********************999999888777 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.2
                                   HHHHHHHHTS-EEEEE-SSST..TGEEE-- CS
                         SRP54 159 alsiaaelklPikfigvGeki..edleefd 186
                                   ++sia+++ + i +i +G k+   d+++++
  gi|13540980|ref|NP_110668.1| 186 IMSIAERFTSRILIINNGRKVweGDIQQIK 215
                                   689999999999999999998766777765 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   3.9e-05     0.041      86     131 ..      15      61 ..       4      66 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.9e-05
                                   THTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT-----S--- CS
                   RsgA_GTPase  86 tkegleelkellkd.ktsvlvGqSGvGKStLinallpelelktgevs 131
                                   +k++++ l+ +l+  + ++l+G+ G+GKSt ++ l++ l+   g+vs
  gi|13540980|ref|NP_110668.1|  15 KKRAIDGLTFRLDCgESMALIGPNGAGKSTTLKILAGILKPDSGSVS 61 
                                   56788889999987799*****************9998777777666 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.2   7.9e-05     0.083       7      29 ..      31      53 ..      28     176 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7.9e-05
                        AAA_22  7 ilvvtGesGtGKTtllrrlleql 29
                                  +++++G+ G+GK+t+l+ l+  l
  gi|13540980|ref|NP_110668.1| 31 SMALIGPNGAGKSTTLKILAGIL 53
                                  689**************998777 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   0.1   7.5e-05     0.079      50      71 ..      34      55 ..      23      64 .. 0.88
   2 ?   -0.7   0.0       1.1   1.2e+03     132     140 ..     140     148 ..      93     205 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.5e-05
                         Rad17 50 isGPsGCgkstvvkvLskelgi 71
                                  + GP G gkst++k+L+ +l +
  gi|13540980|ref|NP_110668.1| 34 LIGPNGAGKSTTLKILAGILKP 55
                                  67***************98865 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.1
                         Rad17 132 dkklilved 140
                                      l+l+ d
  gi|13540980|ref|NP_110668.1| 140 AIALVLIHD 148
                                   333444443 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   5.3e-05     0.056      21      60 ..      32      73 ..      24      95 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.3e-05
                        AAA_30 21 avltGpAGtGKttalkalreaweaa.g.grviglAptgkaAk 60
                                  ++l Gp G+GK+t+lk l+ +++ + g  ++ g+ p+ + A+
  gi|13540980|ref|NP_110668.1| 32 MALIGPNGAGKSTTLKILAGILKPDsGsVSISGYDPSTNDAR 73
                                  6899***************99998844455556666665555 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   8.2e-05     0.087       1      31 [.      32      64 ..      32     157 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 8.2e-05
                                  EEEESSTTSSHHHHHHHHHHHHT..HEEEEEET CS
                           AAA  1 vllyGppGtGKTllakavakelg..vefleisg 31
                                  + l+Gp G GK+++ k +a  l+  +  ++isg
  gi|13540980|ref|NP_110668.1| 32 MALIGPNGAGKSTTLKILAGILKpdSGSVSISG 64
                                  679*****************9973333444444 PP

>> MukB  MukB N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   8.1e-05     0.085      21      55 ..      23      58 ..      19      74 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 8.1e-05
                                  EE-HHH.HHHHHHS--SHHHHHHHHHHHHHHS--TT CS
                          MukB 21 tfdlde.lvttlsGgnGaGksttmaafvtaliPdls 55
                                  tf ld     +l G nGaGkstt+  +  +l Pd  
  gi|13540980|ref|NP_110668.1| 23 TFRLDCgESMALIGPNGAGKSTTLKILAGILKPDSG 58
                                  5666642456899********************975 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   0.00013      0.13       7      49 ..      14      56 ..       8      64 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00013
                  Mg_chelatase  7 GqeeakraleiaaaGgHnlllvGppGsGKtmlakrlpsllppl 49
                                  G+++a   l+     g ++ l+Gp G+GK+   k l+++l p 
  gi|13540980|ref|NP_110668.1| 14 GKKRAIDGLTFRLDCGESMALIGPNGAGKSTTLKILAGILKPD 56
                                  6777777777777788899********************9875 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   0.00017      0.18       4      42 ..      31      66 ..      28      91 .. 0.67
   2 ?   -2.2   0.0       2.6   2.8e+03      59      91 ..     176     220 ..     156     226 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00017
                        AAA_24  4 kiliyGpsgiGKTtlakelgpkplfidtekGlksldadk 42
                                  +++++Gp+g+GK+t++k l   + ++  + G+ s+ + +
  gi|13540980|ref|NP_110668.1| 31 SMALIGPNGAGKSTTLKIL---AGILKPDSGSVSISGYD 66
                                  799*************999...55666666665555555 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.6
                        AAA_24  59 l............aaeladyktlviDtideleelclaevirqnek 91 
                                   l             ae  + ++l+i +  +++e  ++++++q+++
  gi|13540980|ref|NP_110668.1| 176 LkatflvsthimsIAERFTSRILIINNGRKVWEGDIQQIKDQSNR 220
                                   444455555555555555667788888888888888888887765 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00038       0.4       3      47 ..      36      80 ..      35      95 .. 0.87
   2 ?   -2.6   0.0       3.5   3.7e+03     156     172 ..     183     200 ..     151     206 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00038
                                  ESTTSSHHHHHHHHHHHHHHTTE.EEEESSSTTSHHHHHHHHHHH CS
               Thymidylate_kin  3 GlDGaGKttqaellkerlkeegikvvltrepggteiGekirelll 47
                                  G +GaGK+t +++l+  lk    +v ++  + +t+ ++ki ++l 
  gi|13540980|ref|NP_110668.1| 36 GPNGAGKSTTLKILAGILKPDSGSVSISGYDPSTNDARKIVGYLP 80
                                  889*****************9999999988888999999988886 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 3.5
                                   HHHHHHHHH.TTSTEEEE CS
               Thymidylate_kin 156 rerylelak.ederilii 172
                                    ++ +++a+ ++ rilii
  gi|13540980|ref|NP_110668.1| 183 STHIMSIAErFTSRILII 200
                                   344455555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        79  (0.00440627); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 1477.50
//
Query:       gi|13540981|ref|NP_110669.1|  [L=469]
Description: hypothetical protein TVN0150 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (469 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       880  (0.0490825); expected 358.6 (0.02)
Passed bias filter:                      223  (0.0124379); 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):               0  [number of targets reported over threshold]
# CPU time: 0.67u 0.28s 00:00:00.95 Elapsed: 00:00:00.48
# Mc/sec: 2909.54
//
Query:       gi|13540982|ref|NP_110670.1|  [L=432]
Description: amino acid transporter [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0042   16.0  66.7     0.0064   15.4  66.7    1.2  1  AA_permease_2  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 !   15.4  66.7   3.6e-07    0.0064      17     408 ..      26     421 ..       6     429 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 3.6e-07
                 AA_permease_2  17 sgifvknlaasggpalilwvwiavligslavllvyaEl.ssa.lprsgGiyvytkaafgkkvaflsawfnwfayvpvlasi 95 
                                   +g+f +  +as   + +++++i+++i+  +++ +y+ + +s+ + ++gG y+   +++gk+ + ++++++++  +++++si
  gi|13540982|ref|NP_110670.1|  26 VGVF-A-IIASFSSINLVYIVIGAFII--SLVNIYMPYrASKiIRSNGGYYTLNGIFMGKRTGLFVSILYLIYGFAAFPSI 102
                                   2222.2.46666666677777777775..78999999999999************************************** PP

                 AA_permease_2  96 lsvaasyllnalgpdlqgntwltyliaiaililvalinirgikesakiqnilgilkillpliiliilglitvdgggfssls 176
                                   ++  +s l ++  ++l    +++++ a ai + +a+++  g+  sak+ +ilg l i +++++l +  +  ++g +++   
  gi|13540982|ref|NP_110670.1| 103 TIFTVSILYYLS-GSL----TMSVVAADAIAASIAFVTMGGTYVSAKVLKILGALEI-MFIVLLDVSMISHGSGVISP--- 174
                                   *99999999965.466....47889999*****************************.89888887777777777777... PP

                 AA_permease_2 177 tetdtffpn.gwpgvllgllivlwsfdGfesaanvseevkk.k.dvpkaifigllivlvlyllvniaflgvvpddeianls 254
                                       + +++ + p ++ g++  l+ f+G  s+  +se  k+ k  v+++i i+ ++++ l +++++a+   ++ +    +s
  gi|13540982|ref|NP_110670.1| 175 ----YALSSaTTPNFWYGIMFGLLMFSGLGSSLFISENTKNsKvSVSRGIAIAYAVSGSLMVVTALAIERFLGNNISYYSS 251
                                   ....555553444477777777889***************98856******************999975555555444445 PP

                 AA_permease_2 255 nlgsvaalffeavggkvvaiivvilialsllgaintavigssrvlealardgvlPrffakvnkfgspiraiiltaivslil 335
                                   n  ++++ +   +g    +++ ++++++s+  a n av++ + + +++++ g+    +a  ++++    ++ l+ + s+++
  gi|13540982|ref|NP_110670.1| 252 NPFYIIGSVKSVLG----SYFYIFFLFFSVSSAFNLAVAYLNAFSNSAVKMGE-DGIIAPLSRRKVLAISLALDIVASSVF 327
                                   53446677766666....55555555555555555555555555554444443.256788899999************999 PP

                 AA_permease_2 336 lllfllassaaynfllsvsslgliisyllliigalilrkkrphl.kr........pgk...............ilvaiiga 392
                                    +lf   +  a+ +++ + s +++ + l+  +++ ++   +++  ++                          +lv i++a
  gi|13540982|ref|NP_110670.1| 328 PILFG--PFVAFVTITGLVSASYLTVHLISNVSLYKHISASREViGKimliassfT-VlvtlaysiladiytsMLVDIFFA 405
                                   87775..5567888888888888888888888888777777766577776665540.145555555666666689999999 PP

                 AA_permease_2 393 lfllfllvalffppkg 408
                                   + ll++++  f+++  
  gi|13540982|ref|NP_110670.1| 406 IALLVAIYSVFYILRS 421
                                   9999999999987655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (432 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       906  (0.0505327); expected 358.6 (0.02)
Passed bias filter:                      217  (0.0121033); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.65u 0.31s 00:00:00.96 Elapsed: 00:00:00.50
# Mc/sec: 2584.32
//
Query:       gi|13540983|ref|NP_110671.1|  [L=341]
Description: hypothetical protein TVN0152 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       253  (0.0141112); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 00:00:00.47
# Mc/sec: 2194.11
//
Query:       gi|13540984|ref|NP_110672.1|  [L=340]
Description: dihydropteroate synthase [Thermoplasma volcanium GSS1]
Scores for complete 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-58  197.2   0.0      4e-58  197.0   0.0    1.1  1  Pterin_bind  Pterin binding enzyme


Domain annotation for each model (and alignments):
>> Pterin_bind  Pterin binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  197.0   0.0   2.2e-62     4e-58       1     244 []      88     323 ..      88     323 .. 0.97

  Alignments for each domain:
  == domain 1  score: 197.0 bits;  conditional E-value: 2.2e-62
                                   EEEEETTTTTCHCCHHCTHHHHHHHHHHHHHHTT-SEEEEESS-TSTT--CCHHHHHHHHHHHHHHHHHHHCTSEEEEE-S CS
                   Pterin_bind   1 mgilNvtpdsfsdggkfedldkalaqarkmveeGAdilDiggestrPgaervdeeeelervvpvlealrdeadvpisiDtt 81 
                                   mgi+N+tpdsf+ g++++  ++ +    k ++e  di+D+g+estrPg+++vd+ +e er++pv++ +rd +d+p+siD+ 
  gi|13540984|ref|NP_110672.1|  88 MGIINATPDSFYSGSRVLGNEDLIF---KIIDEKPDIVDVGAESTRPGSKPVDPTKEYERLLPVIKIIRDYSDIPVSIDSR 165
                                   9****************77776654...6789999***********************************99********* PP

                                   -HHHHHHHHHTTSEEEEETTTTSSSTTHHHHHHHHT-EEEEESECSSTTTHCCCCCCCSSHHHHHHHHHHHHHHHHHHTT- CS
                   Pterin_bind  82 kaevaeaAlkagadivNdvsgeerdpkmlelvaeagaavvvmhmrgtpktmqeeegqyedvveeveaflearveaaeeaGv 162
                                   +++v+++ +k   +++Nd+sg++ +++m+ l++++++ +vvmhmrg p++mq+ + +y+dv+ +v  fl  r++++ +  v
  gi|13540984|ref|NP_110672.1| 166 HPSVIKNLVKYEINYINDISGFT-NKEMIDLAKDSSLYCVVMHMRGSPQDMQNFT-NYDDVIVDVIGFLLDRANNLLANDV 244
                                   ***********************.*******************************.************************* PP

                                   -GGGEEEETTTTSSTTHHHHHHHHHTHHHHHHTTSSEBEEEGTTGHHHHHHHCTTCHGHHHHHHHHHHHHHHHTT-SEEEE CS
                   Pterin_bind 163 aperillDpgigfgkteehnlellrrldelrealevpvllGvSrksflgrllelgkaeeRdagtaaflalaaaaGadivrV 243
                                   a  ri+ Dpgigf+k+ + n+e+lr+++ +  + ++p+l+G+Srk f+g ++  +++e R  gt+ ++ + a++ ++i+rV
  gi|13540984|ref|NP_110672.1| 245 AFGRIISDPGIGFAKDLKGNIEILRNIKSF--HIGMPLLVGTSRKTFIGTIT-GQAVEGRLPGTIGTSIYLANNRVSIIRV 322
                                   ******************************..99****************98.34599*********************** PP

                                   S CS
                   Pterin_bind 244 h 244
                                   h
  gi|13540984|ref|NP_110672.1| 323 H 323
                                   9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (340 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       319  (0.0177924); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 2045.30
//
Query:       gi|13540985|ref|NP_110673.1|  [L=426]
Description: histidyl-tRNA synthetase [Thermoplasma volcanium GSS1]
Scores for complete sequence (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  155.8   0.0    2.8e-45  155.0   0.0    1.4  1  tRNA-synt_His   Histidyl-tRNA synthetase
    4.1e-12   46.1   0.0    7.6e-12   45.2   0.0    1.4  1  HGTP_anticodon  Anticodon binding domain
    1.2e-09   38.4   0.0      2e-09   37.7   0.0    1.4  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 !  155.0   0.0   4.6e-49   2.8e-45       1     304 [.       8     310 ..       8     312 .. 0.86

  Alignments for each domain:
  == domain 1  score: 155.0 bits;  conditional E-value: 4.6e-49
                                   T---EETCHHHHHHHHHHHHHHHHHHTT-EEEE--SEEEHHHHCTTSTCC.HHHS-EEE-TTSSEEEE-SSSHHHHHHHHH CS
                 tRNA-synt_His   1 glrdllpeeaekieelrrrlldlfeswGYelVspPllEyldslltgaged.ldqtfklvDqsgrllglRaDiTpqvaRiaa 80 
                                   g+rd++pe++e ++ + ++ ++++es+G++++  P+lEy+d +  ++ge+ l+qt+ ++D  gr + l ++ Tp+ +R+ +
  gi|13540985|ref|NP_110673.1|   8 GFRDFYPEDMEIEKFIFETASSVAESYGFKRIDFPSLEYIDLYRIKSGEElLNQTYSFTDRGGREVTLIPEATPSTVRMLT 88 
                                   89*********************************************999567**************************** PP

                                   HHHHTSS-EEEEEEEEEEESS-SSTT--CCEEEEEEEEESS-SHHHHHHHHHHHHHHHHHHCTS.SSEEEEEEETCHHHHH CS
                 tRNA-synt_His  81 hrlnrerplRlcYaGsvlrtrpdglgrsreplQvGaEliGaegleadlEvlslllealeaaagv.kelrldlghvglvral 160
                                    r    +p R++++ +v+r ++ ++gr re +Q+ a ++G ++ ead+E++sl+  +l+  +g+    ++ +++  +++ +
  gi|13540985|ref|NP_110673.1|  89 SRKDIAKPVRWYSFPKVWRYEEPQAGRFREHYQFNADIFGPSNEEADAEIISLASGILD-GLGLsGAYEIRVNSRIMMEDI 168
                                   **********************************************************8.999637789************ PP

                                   HHHTT--HHHHHHHHHHHHCT-HHHHHHHHH...CCTTHHHCCHCC....HCCHCCCHHHHCHCCHCTHHHHHHHHHHHHH CS
                 tRNA-synt_His 161 leaaglsesleeallaalarkdlaelkelaa...eaglkealrellkal.elygdaevleealealaaapalqaaldelee 237
                                   l+ +g+++    +++++++r   ++ +++++   + gl+e++ +++  + + ++++  +    + l ++ ++ +a ++l +
  gi|13540985|ref|NP_110673.1| 169 LNGMGIADP--YTVFSIVDRFHKVSKETFVDdlmSVGLSEENSNTIYRMcSEASEPGGI----SGLFGSGKVSKAAERLIR 243
                                   *****9875..556666666555554444441112356666666665543334444444....456889999999999999 PP

                                   HHHHHHHHHHH-TTEEE-TT--TTTTT--SEEEEEEETT-S.S-SEEEEEECTTTGGG.T---EEEEEE CS
                 tRNA-synt_His 238 laallealakpevrvtlDlaelrgyeYytGlvFaayaegvg.qaiarGGrYdelgaaf.grarpAtGfs 304
                                   + ++l++++    +v++D++ +rg++YytGlvF+ay ++ + +ai++GGrYd+l + f  +  pA+Gf 
  gi|13540985|ref|NP_110673.1| 244 TIDILKEYG--VKSVKYDFSIVRGLSYYTGLVFEAYDKSGQfRAILGGGRYDNLAKLFsEQDIPAVGFG 310
                                   999999997..689**********************9854437***************999*******6 PP

>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.2   0.0   1.3e-15   7.6e-12       4      93 ..     336     422 ..     333     423 .. 0.90

  Alignments for each domain:
  == domain 1  score: 45.2 bits;  conditional E-value: 1.3e-15
                                   EEESSSSHHHHHHHHHHHHHHHHTTTSEEEEESSSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEEETTTCEEEEEET CS
                HGTP_anticodon   4 viplnekaeeleeyakklaeeLraagirvelddsnesigkkireadllgipfavvvGekelekgtvtvrdrdtreqervsl 84 
                                   v  +++      e   ++ + Lr  g+ v     ++s+  ++++a   g+ +av+ Ge++le+++vtvrd+ t+eqe v+l
  gi|13540985|ref|NP_110673.1| 336 VCRVGT---VKAERIASISKMLRSSGFIVSAEIMDRSLSSQLKYASYEGCEYAVIAGERDLENNSVTVRDLSTGEQEIVTL 413
                                   555555...34577889**************99************************************************ PP

                                   THHHHHHHH CS
                HGTP_anticodon  85 delveklke 93 
                                    +lv +l++
  gi|13540985|ref|NP_110673.1| 414 GDLVPFLEK 422
                                   ****99976 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 !   37.7   0.0   3.4e-13     2e-09       1     125 [.      63     342 ..      63     393 .. 0.76

  Alignments for each domain:
  == domain 1  score: 37.7 bits;  conditional E-value: 3.4e-13
                                   EEEEETTSEEEEE-SSSHHHHHHHHHHHEEEBGGSSEEEEEEEEEEBTTTSTBCTTTB-SEEEEEEEEEEESGGGHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  tRNA-synt_2b   1 YkledrndreyiLkPtneetfvelirdevlrskrLPlklyqiqtkyRdEksdsrGLlRvreFhqkdgyvfhaeaslddslr 81 
                                   Y + dr +re +L+P++++  v++   +    k  P++ y +  ++R+E++ + G  R re  q ++ +f+  +  ++ ++
  gi|13540985|ref|NP_110673.1|  63 YSFTDRGGREVTLIPEATPSTVRMLTSRKDIAK--PVRWYSFPKVWRYEEP-QAG--RFREHYQFNADIFGPSN--EEADA 136
                                   899**********************98844446..****************.99*..***************88..899** PP

                                   HHHHHHHHHHHHTT.SCEEEEEEGTTSC..................................................... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxx..................................................... RF
                  tRNA-synt_2b  82 dlikaisriferlglefraiielmsaks..................................................... 109
                                   ++i ++s i+  lgl+    i+++s++                                                      
  gi|13540985|ref|NP_110673.1| 137 EIISLASGILDGLGLSGAYEIRVNSRIMmedilngmgiadpytvfsivdrfhkvsketfvddlmsvglseensntiyrmcs 217
                                   ***************985445554444345566778788899999999999999999999999999988888888888888 PP

                                   ................................................BTTSEEEEEEEEETT.................. CS
                                   ................................................xxxxxxxxxxxxxxx.................. RF
                  tRNA-synt_2b 110 ................................................adykdkkefeavses.................. 124
                                                                                   ++y+  ++fea+++s                  
  gi|13540985|ref|NP_110673.1| 218 easepggisglfgsgkvskaaerlirtidilkeygvksvkydfsivrgLSYYTGLVFEAYDKSgqfrailgggrydnlakl 298
                                   888888888888888888888888888888888888888888888888888888888888886666666666666666666 PP

                                   ...........................................T CS
                                   ...........................................x RF
                  tRNA-synt_2b 125 ...........................................l 125
                                                                              +
  gi|13540985|ref|NP_110673.1| 299 fseqdipavgfgmgdavislllkskgvkaphakksvyvcrvgtV 342
                                   66666666666666666666666666666665555555555551 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (426 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       481  (0.026828); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.61u 0.32s 00:00:00.93 Elapsed: 00:00:00.52
# Mc/sec: 2465.46
//
Query:       gi|13540986|ref|NP_110674.1|  [L=495]
Description: ATP-dependent protease [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.8e-15   54.5   0.0    1.3e-08   34.5   0.0    2.3  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    6.4e-13   48.3   0.1    2.8e-07   29.7   0.1    3.1  3  AAA_32           AAA domain
    5.3e-10   39.2   0.0     0.0001   22.1   0.0    2.3  2  Sigma54_activat  Sigma-54 interaction domain
    1.6e-08   34.6   0.0      7e-05   22.8   0.0    2.5  2  AAA_5            AAA domain (dynein-related subfamily)
      8e-07   28.9   0.0     0.0086   15.8   0.0    2.4  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
      1e-06   29.2   0.0     0.0011   19.4   0.0    2.6  2  AAA              ATPase family associated with various cellul
    1.9e-05   23.9   0.0      0.028   13.5   0.0    2.2  2  MCM              MCM P-loop domain
    0.00023   21.4   0.0     0.0093   16.2   0.0    2.5  2  AAA_22           AAA domain
    0.00037   20.9   0.0    0.00085   19.7   0.0    1.6  1  AAA_16           AAA ATPase domain
     0.0022   18.4   0.0      0.006   17.0   0.0    1.8  1  MCM_lid          MCM AAA-lid domain
     0.0025   17.7   1.6     0.0051   16.7   1.6    1.5  1  DUF35_N          Rubredoxin-like zinc ribbon domain (DUF35_N)
     0.0033   17.5   0.0       0.28   11.3   0.0    2.3  2  Sigma54_activ_2  Sigma-54 interaction domain
     0.0077   15.8   0.0      0.015   14.8   0.0    1.4  1  AAA_7            P-loop containing dynein motor region
      0.008   15.9   0.0      0.015   15.1   0.0    1.3  1  IstB_IS21        IstB-like ATP binding protein
  ------ inclusion threshold ------
      0.011   15.2   0.0       0.02   14.3   0.0    1.3  1  SMC_N            RecF/RecN/SMC N terminal domain
      0.012   15.7   0.0        5.2    7.1   0.0    3.2  3  AAA_14           AAA domain
      0.012   14.9   0.3        1.4    8.0   0.0    2.9  3  TIP49            TIP49 P-loop domain
       0.02   15.5   0.0      0.086   13.4   0.0    2.1  2  AAA_18           AAA domain
      0.028   13.8   4.5      0.052   13.0   4.5    1.4  1  zf-ribbon_3      zinc-ribbon domain
      0.034   14.1   0.0      0.065   13.2   0.0    1.4  1  Rad17            Rad17 P-loop domain
       0.04   14.0   0.5      0.068   13.2   0.5    1.3  1  DZR              Double zinc ribbon
       0.04   13.3   0.0       0.25   10.7   0.0    2.1  2  TniB             Bacterial TniB protein
      0.044   13.8   0.2       0.11   12.5   0.2    1.6  1  HypA             Hydrogenase/urease nickel incorporation, met
      0.055   12.4   0.0       0.27   10.1   0.0    2.0  2  AAA_PrkA         PrkA AAA domain
      0.068   13.5   0.0        2.4    8.5   0.0    2.3  2  AAA_19           AAA domain
      0.081   13.4   0.0       0.24   11.9   0.0    1.9  1  ABC_tran         ABC transporter
        0.1   12.3   0.0       0.24   11.1   0.0    1.6  1  AAA_30           AAA domain
       0.11   12.7   0.0       0.26   11.4   0.0    1.6  1  DUF2318          Predicted membrane protein (DUF2318)
       0.18   11.4   0.0       0.31   10.7   0.0    1.3  1  TackOD1          Thaumarchaeal output domain 1
       0.19   11.9   2.4       0.43   10.7   2.4    1.6  1  Zn-ribbon_8      Zinc ribbon domain
       0.21   11.3   3.7        0.4   10.5   3.7    1.5  1  Rubredoxin_2     Rubredoxin metal binding domain
       0.31   10.8   4.5       0.58    9.9   4.5    1.5  1  zinc_ribbon_2    zinc-ribbon domain
       0.36   10.4   2.8        2.9    7.5   0.2    2.5  2  TF_Zn_Ribbon     TFIIB zinc-binding
        2.2    7.7   4.7        3.4    7.1   4.7    1.3  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 !   34.5   0.0   2.4e-11   1.3e-08       2      46 ..      25      69 ..      24      80 .. 0.90
   2 !   17.6   0.0   3.6e-06    0.0019      97     158 ..     267     335 ..     260     347 .. 0.82

  Alignments for each domain:
  == domain 1  score: 34.5 bits;  conditional E-value: 2.4e-11
                  Mg_chelatase  2 lkdvkGqeeakraleiaaaGgHnlllvGppGsGKtmlakrlpsll 46
                                  l  v+Gq+ea r   +aa  + +lllvGppG GK+m+a++l+  +
  gi|13540986|ref|NP_110674.1| 25 LDRVIGQDEAVRIASVAARQRRHLLLVGPPGVGKSMIAQALSFYI 69
                                  6789***********************************998655 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 3.6e-06
                  Mg_chelatase  97 pkpGeislahnGvLfLDElpe...fkrkvlevLRe...Pledgevtisrakakv.efparfqlvaamNp 158
                                   +  G++  ah+GvLf+DE+++   ++r +l ++ e   P+  ++ + + a+ +v + pa+f lvaa N 
  gi|13540986|ref|NP_110674.1| 267 VIAGAVHEAHEGVLFIDEITHlgnLQRYILTAMQEkvfPITGRNPQSAGASVRVdKVPADFILVAACNI 335
                                   5689**************986222688999999886778888888888888777579*********996 PP

>> AAA_32  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.2   0.0    0.0073       3.9       5      76 ..      23      88 ..      21      90 .. 0.69
   2 !    8.7   0.0    0.0012      0.64     291     341 ..     230     283 ..     183     295 .. 0.86
   3 !   29.7   0.1   5.4e-10   2.8e-07     422     509 ..     359     451 ..     356     453 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0073
                        AAA_32  5 epleeiigqeRAvealefglkikkkgYNifvlGesgtGrttlvkrlleeiakkeptpdDwcYvnnfdnpeeP 76
                                  +pl+++igq+ Av+  +++    ++  ++ ++G++g+G++++++ l   i    +  +++  v+n + pe+P
  gi|13540986|ref|NP_110674.1| 23 NPLDRVIGQDEAVRIASVAA---RQRRHLLLVGPPGVGKSMIAQALSFYI---GRPNEEIRVVHNPQYPERP 88
                                  58999****98887777765...56669***********99887664333...2233455556666666655 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0012
                        AAA_32 291 gaPVvvednptyanLfGkieyesemg..alvt.dftlIkaGaLhkAnGGyLild 341
                                     P v  +  + ++L+G + ++ + g   l t  ++++ aGa+h+A+ G+L +d
  gi|13540986|ref|NP_110674.1| 230 RNPFVLATGASETELLGDVRHDPYGGhpQLGTlPYERVIAGAVHEAHEGVLFID 283
                                   6788999999999*********9999554444379****************987 PP

  == domain 3  score: 29.7 bits;  conditional E-value: 5.4e-10
                        AAA_32 422 ddemerteenekkyarfiasivk.kekllpfdrsavarlieyssrlae....dqeklstrfseiadllrEAdywakkegae 497
                                   +++m+ teen  ky++fia+ ++ + k+++++ +a + +ie++ + a     +++ l++r++e+  l+r A  +a  +g++
  gi|13540986|ref|NP_110674.1| 359 KTTMKDTEENRMKYLQFIAQEINmDGKIPHMTMDAAQLIIEEGRKRAKlidrKNNELTLRLRELGGLIRAAGDIAVFKGNK 439
                                   689***************9877626689**************98877533336788************************* PP

                        AAA_32 498 vveaehVekAle 509
                                   ++++e+Ve+A++
  gi|13540986|ref|NP_110674.1| 440 LIDKEDVEEAIK 451
                                   **********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 !   14.7   0.0   3.5e-05     0.019      11      56 ..      34      79 ..      29      91 .. 0.78
   2 !   22.1   0.0   1.9e-07    0.0001      86     136 ..     269     319 ..     264     327 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.5e-05
                                  HHHHHHHHCTSSS-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEE CS
               Sigma54_activat 11 lleqikkvaktdlsvlitGesGtGKellaraiheaskrkekpfvav 56
                                  +++ ++ +a+++ ++l++G  G+GK+++a+a+     r ++++  v
  gi|13540986|ref|NP_110674.1| 34 AVRIASVAARQRRHLLLVGPPGVGKSMIAQALSFYIGRPNEEIRVV 79
                                  566777888999*******************977766666655555 PP

  == domain 2  score: 22.1 bits;  conditional E-value: 1.9e-07
                                   EHHHHHTTTSEEEEETGGGS-HHHHHHHHHHHHHSEEESBTSS.SEEE--EE CS
               Sigma54_activat  86 kGlfekadgGtlfLDeigelplelQekLlrvlqegevervGss.keikvdvr 136
                                   +G++++a++G+lf+Dei++l  +lQ  +l+++qe+ +   G + ++  ++vr
  gi|13540986|ref|NP_110674.1| 269 AGAVHEAHEGVLFIDEITHLG-NLQRYILTAMQEKVFPITGRNpQSAGASVR 319
                                   59******************7.79************9999977345556666 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 !   22.8   0.0   1.3e-07     7e-05       1      30 [.      47      76 ..      47      95 .. 0.82
   2 !    9.2   0.0    0.0021       1.1      65     137 ..     276     348 ..     233     349 .. 0.77

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 1.3e-07
                                  EEEEE--SSSSHHHHHHHGGGGBS--EEEE CS
                         AAA_5  1 dvlLvGppGtgKselaerlaaalnreveyv 30
                                  ++lLvGppG+gKs++a+ l+  ++r+ e++
  gi|13540986|ref|NP_110674.1| 47 HLLLVGPPGVGKSMIAQALSFYIGRPNEEI 76
                                  79*********************5554443 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0021
                                   G-SEEEEESGGG--.HHHHHHHHHHHHSSEEE..-SSSEEE---..........-EEEEEESS--.-TT-TTHHHHTT CS
                         AAA_5  65 egeilvlDEverae.sevlnsLlslleerrllleeggelvkakndd.ller...frviatanpldrslnelspalrsR 137
                                   +  +l++DE++  +  + +   l+ + e+ ++   g++ ++a +     +    f ++a++n +d  l  + ++lrsR
  gi|13540986|ref|NP_110674.1| 276 HEGVLFIDEIT--HlGNLQRYILTAMQEKVFP-ITGRNPQSAGASVrVDKVpadFILVAACNIND--LPYILSPLRSR 348
                                   4569*******..4479999999********9.556666666664434444999***********..99999999998 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.6e-05    0.0086      10      55 ..      29      67 ..      21      84 .. 0.75
   2 !   10.5   0.0   0.00073      0.38      84     153 ..     276     349 ..     264     353 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.6e-05
                        RuvB_N 10 igqekvkeklkifieaakkreealdhvllyGpPGlGkttlakiiak 55
                                  igq++    ++i+  aa++r+    h+ll+GpPG+Gk+ +a+ ++ 
  gi|13540986|ref|NP_110674.1| 29 IGQDE---AVRIASVAARQRR----HLLLVGPPGVGKSMIAQALSF 67
                                  55543...4566666777765....9**************998875 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00073
                        RuvB_N  84 ekdvlfideihrlsraveevlysamedfrldivigkGpsa.rsikldl..pkftlvgattragl..lssPlrdrf 153
                                   ++ vlfidei  l +  + ++ +am++  + i+  + +sa  s+++d   + f lv+a   + l  + sPlr+r+
  gi|13540986|ref|NP_110674.1| 276 HEGVLFIDEITHLGNL-QRYILTAMQEKVFPITGRNPQSAgASVRVDKvpADFILVAACNINDLpyILSPLRSRI 349
                                   567**********875.5667799*99999987655554424566653223699999987654333889999986 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 !   19.4   0.0   2.1e-06    0.0011       1      34 [.      48      97 ..      48     118 .. 0.69
   2 ?    7.0   0.0     0.014       7.3      54     113 ..     272     337 ..     264     352 .. 0.63

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 2.1e-06
                                  EEEESSTTSSHHHHHHHHHHHHTHE................EEEEETTTC CS
                           AAA  1 vllyGppGtGKTllakavakelgve................fleisgsel 34
                                  +ll+GppG+GK+++a+a+   +g++                f+ei+  e 
  gi|13540986|ref|NP_110674.1| 48 LLLVGPPGVGKSMIAQALSFYIGRPneeirvvhnpqyperpFVEIKTREE 97
                                  69****************99986443333333333444444777666655 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.014
                                   HHTSTSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTS..............SSTEEEEEEESSGG CS
                           AAA  54 kekakpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkk..............eskvivigatnrpd 113
                                    ++a+  +lfiDEi  l++ +        + ++ ++ +++   + +               +++i+++a+n  d
  gi|13540986|ref|NP_110674.1| 272 VHEAHEGVLFIDEITHLGNLQ--------RYILTAMQEKVFPITGRnpqsagasvrvdkvPADFILVAACNIND 337
                                   4444349**********8877........444444444444444445556777777777767788888888744 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.0    0.0025       1.3      52      77 ..      40      65 ..      27      72 .. 0.82
   2 !   13.5   0.0   5.2e-05     0.028      82     152 ..     229     306 ..     222     337 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0025
                                  SBBCSS-EEEEEESSTSTHHHHHHHH CS
                           MCM 52 tklrgdinvllvgdpgtaKsqlLkyv 77
                                  +  r + ++llvg pg++Ks + +++
  gi|13540986|ref|NP_110674.1| 40 VAARQRRHLLLVGPPGVGKSMIAQAL 65
                                  5689999*************997765 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 5.2e-05
                                   SSEEEEESSSSSSSHSSSEEEEESSSSS........EEEEETHHHHTTTSEEEEESGGGSTCHHHHHHHHHHHHSEEEE CS
                           MCM  82 pravytsgkgssaagLtaavvrdeetge........fvleaGalvladkGvcciDefdkmkeedrsalhEamEqqtisi 152
                                   +r+ ++ ++g+s+++L   v++d+  g+          + aGa+  a++Gv+ iDe+ +  +  + +++ am ++   i
  gi|13540986|ref|NP_110674.1| 229 DRNPFVLATGASETELLGDVRHDPYGGHpqlgtlpyERVIAGAVHEAHEGVLFIDEITHLGN-LQRYILTAMQEKVFPI 306
                                   57778888888888998888888887765554444334679*******************99.8999999998876655 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   1.8e-05    0.0093       2      25 ..      43      65 ..      41      76 .. 0.92
   2 ?    2.3   0.0      0.36   1.9e+02      83     104 ..     269     289 ..     229     307 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.8e-05
                        AAA_22  2 rktagilvvtGesGtGKTtllrrl 25
                                  r ++++l+++G++G+GK++ ++ l
  gi|13540986|ref|NP_110674.1| 43 R-QRRHLLLVGPPGVGKSMIAQAL 65
                                  4.899***************9986 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.36
                        AAA_22  83 eqalraravielliiDEaqhlr 104
                                   + a+++++  ++l iDE+ hl 
  gi|13540986|ref|NP_110674.1| 269 AGAVHEAHE-GVLFIDEITHLG 289
                                   445666666.9*********93 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   1.6e-06   0.00085      18      92 ..      39     109 ..      28     176 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.6e-06
                        AAA_16  18 rvrsgrpelvllsGesGvGKsslvrellralekd..ggiflrgkcdqlesaipy..salaqalareellrqlldeaesa 92 
                                   +v++ + + +ll+G++GvGKs ++++l  ++ +   +      + +++     y   +++++ +ree++ + ++e++++
  gi|13540986|ref|NP_110674.1|  39 SVAARQRRHLLLVGPPGVGKSMIAQALSFYIGRPneE-----IRVVHN---PQYpeRPFVEIKTREEVMLEREEESSTS 109
                                   455666699******************9988888432.....222222...2222235777777777777777775554 PP

>> MCM_lid  MCM AAA-lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   1.1e-05     0.006      18      83 ..     389     453 ..     370     456 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.1e-05
                                   ETCHHHHHHHHHHHHHHHHH..TSSTSSSST--HHHHHHHHHHHHHHHHHHTSSSE-HHHHHHHHHHH CS
                       MCM_lid  18 lseeakeklseaYvelRkee..edskrksipitvRqLesliRLseAlAklrlsevvteedveeairll 83 
                                   ++ +a++ +     e Rk++   d+k+++++   R+L  liR +  +A  + ++ +++edveeai+l+
  gi|13540986|ref|NP_110674.1| 389 MTMDAAQLII---EEGRKRAklIDRKNNELTLRLRELGGLIRAAGDIAVFKGNKLIDKEDVEEAIKLY 453
                                   4444444444...355666644445788999999*******************************996 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 !   16.7   1.6   9.6e-06    0.0051      11      33 ..     127     149 ..     126     152 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 9.6e-06
                       DUF35_N  11 gqrCpdCGtvqfPPravCphCgs 33 
                                   g rC++CG +  P + vCp+C s
  gi|13540986|ref|NP_110674.1| 127 GYRCSKCGFYSSPTEMVCPNCNS 149
                                   88*********9999******55 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 !   11.3   0.0   0.00052      0.28      16      44 ..      40      68 ..      33     101 .. 0.78
   2 ?    3.7   0.0      0.12        63      65      92 ..     272     298 ..     242     319 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00052
                                  HHHT-SS-EEEEEETT--HHHHHHCC--T CS
               Sigma54_activ_2 16 qaaqsklpvfltGekGsgkelvArlLhkn 44
                                  +aa++   ++l+G++G gk+++A++L+  
  gi|13540986|ref|NP_110674.1| 40 VAARQRRHLLLVGPPGVGKSMIAQALSFY 68
                                  45688899******************854 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.12
                                   HHHTTTSEEEEEE-TT--HHHHHHHHHH CS
               Sigma54_activ_2  65 leqakggtLylkdiadlskaeqkeLlel 92 
                                   + +a++g+L++ +i +l++ +  ++l +
  gi|13540986|ref|NP_110674.1| 272 VHEAHEGVLFIDEITHLGNLQ-RYILTA 298
                                   56799************9654.444444 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   2.8e-05     0.015      28      53 ..      40      65 ..      33      79 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.8e-05
                         AAA_7 28 lllknkkpvllvGptGtGKtviikdl 53
                                     ++++++llvGp G+GK++i++ l
  gi|13540986|ref|NP_110674.1| 40 VAARQRRHLLLVGPPGVGKSMIAQAL 65
                                  567899****************9975 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   2.8e-05     0.015      46      70 ..      44      68 ..      33      83 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.8e-05
                     IstB_IS21 46 kkenivllGpsGvGKshlaialgve 70
                                  ++  ++l+Gp+GvGKs +a al+  
  gi|13540986|ref|NP_110674.1| 44 QRRHLLLVGPPGVGKSMIAQALSFY 68
                                  567899***************9865 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   3.8e-05      0.02      23      58 ..      44      78 ..      37      84 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.8e-05
                                  TSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTC CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 23 sksftaivGpNGSGKsnlldAilFvLGersakklrs 58
                                  ++++  +vGp G GKs + +A++F++G   ++++r 
  gi|13540986|ref|NP_110674.1| 44 QRRHLLLVGPPGVGKSMIAQALSFYIGR-PNEEIRV 78
                                  5677899********************5.5557775 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.057        30       2      36 ..      45      79 ..      44     114 .. 0.67
   2 ?   -1.4   0.0       4.4   2.3e+03      90     116 ..     229     255 ..     184     265 .. 0.75
   3 ?    7.1   0.0    0.0098       5.2      62      90 ..     274     302 ..     258     316 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.057
                        AAA_14  2 rkilvitGaRrvGKTtllkqlikell.vkkesilyi 36
                                  r+ l+++G+  vGK+++++ l   ++  ++e+i  +
  gi|13540986|ref|NP_110674.1| 45 RRHLLLVGPPGVGKSMIAQALS-FYIgRPNEEIRVV 79
                                  57789************87764.3334555555555 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 4.4
                        AAA_14  90 gknldvivtGSnskllskeiatslagr 116
                                   ++n  v++tG +   l+ ++++++ g 
  gi|13540986|ref|NP_110674.1| 229 DRNPFVLATGASETELLGDVRHDPYGG 255
                                   456678899999999888888877765 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.0098
                        AAA_14  62 eekktylflDEiqevpewekalkslvdeg 90 
                                   e ++ +lf+DEi ++ ++++++   ++e+
  gi|13540986|ref|NP_110674.1| 274 EAHEGVLFIDEITHLGNLQRYILTAMQEK 302
                                   457789***************99999877 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.0    0.0027       1.4      50      75 ..      45      70 ..      19      81 .. 0.74
   2 ?    1.5   0.0      0.26   1.3e+02     279     309 ..     277     306 ..     267     309 .. 0.73
   3 ?    1.2   0.1      0.31   1.6e+02      70     139 ..     376     446 ..     373     473 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0027
                                  XXXXXXXXXXXXXXXXXXXXXXXXXX CS
                         TIP49 50 GravLlaGpsgtGktalaiaiskelg 75
                                   r +Ll+Gp+g Gk+ +a a+s  +g
  gi|13540986|ref|NP_110674.1| 45 RRHLLLVGPPGVGKSMIAQALSFYIG 70
                                  3789*****************98887 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.26
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                         TIP49 279 pGvlfiDevhmlDiecfsylnraleselaPi 309
                                    GvlfiDe+  l  +   y+  a+ +++ Pi
  gi|13540986|ref|NP_110674.1| 277 EGVLFIDEITHLG-NLQRYILTAMQEKVFPI 306
                                   7*******87664.44566777777777666 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.31
                                   XXXXXX..XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX-S-EEEEEEEEEEE...-SSS-..TT CS
                         TIP49  70 iskelg..edvpfvalsgsevyslevkktevltqalrksigvrikeekevleGevveleveeaenplskekk 139
                                   i++e++   ++p +++ ++++   e +k   l++     + +r++e   ++     ++ v++ ++ ++ke  
  gi|13540986|ref|NP_110674.1| 376 IAQEINmdGKIPHMTMDAAQLIIEEGRKRAKLIDRKNNELTLRLRELGGLIRA-AGDIAVFKGNKLIDKEDV 446
                                   7788875468************************************9887764.345556555566654444 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   0.00016     0.086       2      21 ..      49      68 ..      48     115 .. 0.66
   2 ?   -2.1   0.2       9.8   5.2e+03      97     114 ..     203     220 ..     187     225 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00016
                        AAA_18  2 lltGtpGvGKttlakeLskr 21
                                  ll G+pGvGK+ +a++Ls  
  gi|13540986|ref|NP_110674.1| 49 LLVGPPGVGKSMIAQALSFY 68
                                  689**************644 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 9.8
                        AAA_18  97 vvLtaspeelleRlekRg 114
                                    vL+ ++ e+++Rlek +
  gi|13540986|ref|NP_110674.1| 203 RVLDEKTLERRRRLEKKS 220
                                   466667777888888754 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   4.5   9.9e-05     0.052       3      22 ..     128     147 ..     127     150 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 9.9e-05
                   zf-ribbon_3   3 vrCPnCGa.plssddnvCpyC 22 
                                   +rC++CG    s+  +vCp+C
  gi|13540986|ref|NP_110674.1| 128 YRCSKCGFyS-SPTEMVCPNC 147
                                   79********.********** PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   0.00012     0.065      34      70 ..      34      70 ..      27     102 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00012
                         Rad17 34 wlkadvLesrkkriLLisGPsGCgkstvvkvLskelg 70
                                  +++  ++  r++r LL+ GP+G gks + + Ls   g
  gi|13540986|ref|NP_110674.1| 34 AVRIASVAARQRRHLLLVGPPGVGKSMIAQALSFYIG 70
                                  55566677788999*****************997665 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.5   0.00013     0.068      27      48 ..     124     147 ..     103     148 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00013
                           DZR  27 a..edrCpsCgekvdpearfCpeC 48 
                                   +   +rC++Cg   +p++ +Cp+C
  gi|13540986|ref|NP_110674.1| 124 ErlGYRCSKCGFYSSPTEMVCPNC 147
                                   15679******************* PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00048      0.25      30      54 ..      41      64 ..      33     100 .. 0.76
   2 ?   -0.7   0.0       1.5   8.1e+02     115     131 ..     272     288 ..     263     298 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00048
                          TniB 30 pkrkrmpnlllvGdsnnGKtmivek 54
                                  + r+r ++lllvG++ +GK+mi++ 
  gi|13540986|ref|NP_110674.1| 41 AARQR-RHLLLVGPPGVGKSMIAQA 64
                                  55667.89**************985 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.5
                          TniB 115 lrelkvrvLiiDEihnl 131
                                    +e +  vL iDEi +l
  gi|13540986|ref|NP_110674.1| 272 VHEAHEGVLFIDEITHL 288
                                   56777889******998 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2   0.00021      0.11      68      99 ..     125     154 ..     100     160 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00021
                                   --EEEETTTS-EEECHHHHHS-TTTSSS-EEE CS
                          HypA  68 pvkvrCreCgkefeleekalrCpkCgsadvei 99 
                                   ++ +rC++Cg   + +  ++ Cp+C+s + +i
  gi|13540986|ref|NP_110674.1| 125 RLGYRCSKCGFYSSPT--EMVCPNCNSPKAQI 154
                                   56689*****777766..579******99987 PP

>> AAA_PrkA  PrkA AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00051      0.27      85     145 ..      42     104 ..      23     119 .. 0.79
   2 ?   -0.8   0.0       1.1   5.6e+02     227     267 ..     270     309 ..     265     370 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00051
                      AAA_PrkA  85 eerkqilyllGPvggGksslverlkklleaa..piyalegsPvfeePlhlipeelrkkleeey 145
                                     +++ l+l+GP g Gks ++++l   +      i ++++    e P+  i ++ + +le+e 
  gi|13540986|ref|NP_110674.1|  42 ARQRRHLLLVGPPGVGKSMIAQALSFYIGRPneEIRVVHNPQYPERPFVEIKTREEVMLEREE 104
                                   45677899****************998876555899999888889999988888888887765 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.1
                      AAA_PrkA 227 GalnranrGllefvemfkadikvlhplltatqegnykstek 267
                                   Ga+  a +G+l   e+     ++   +lta qe+ ++ t++
  gi|13540986|ref|NP_110674.1| 270 GAVHEAHEGVLFIDEI-THLGNLQRYILTAMQEKVFPITGR 309
                                   6777777777744444.344456677999999999988876 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.0    0.0046       2.4       5      29 ..      40      64 ..      31     124 .. 0.86
   2 ?    2.7   0.0      0.28   1.5e+02     103     126 ..     276     300 ..     249     314 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0046
                        AAA_19  5 vealkekvllvtaGpGtGKTrvlkh 29
                                  v+a ++++ll++++pG GK+ + ++
  gi|13540986|ref|NP_110674.1| 40 VAARQRRHLLLVGPPGVGKSMIAQA 64
                                  3478999************987654 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.28
                        AAA_19 103 ee.llivDEfqdvdelqyrLlkall 126
                                   +e +l++DE+  +  lq  +l a+ 
  gi|13540986|ref|NP_110674.1| 276 HEgVLFIDEITHLGNLQRYILTAMQ 300
                                   3459**************9999998 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   0.00046      0.24       6      45 ..      40      79 ..      35     119 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00046
                                  EEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEET CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  6 lklkegekvaivGenGaGKStLlkllagllkpteGeilld 45
                                  +  ++ + + +vG+ G GKS ++++l+      ++ei++ 
  gi|13540986|ref|NP_110674.1| 40 VAARQRRHLLLVGPPGVGKSMIAQALSFYIGRPNEEIRVV 79
                                  5667778899****************98777777777554 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00046      0.24       6      39 ..      31      66 ..      29      79 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00046
                        AAA_30  6 Qaaave..alltsgdrvavltGpAGtGKttalkalr 39
                                  Q +av+  ++++ ++r  +l+Gp+G GK+++ +al 
  gi|13540986|ref|NP_110674.1| 31 QDEAVRiaSVAARQRRHLLLVGPPGVGKSMIAQALS 66
                                  6666542278899999**************998875 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   0.0    0.0005      0.26      23      60 ..     113     150 ..      97     160 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0005
                       DUF2318  23 vkksdgklrvaldaCevCekkgYvqegeelvCknCgvr 60 
                                   +  +d  ++va      C+k g++ +  e+vC nC++ 
  gi|13540986|ref|NP_110674.1| 113 IDPKDAPTSVAERLGYRCSKCGFYSSPTEMVCPNCNSP 150
                                   55566666667777778******************974 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00059      0.31      16      99 ..      67     153 ..      57     157 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00059
                       TackOD1  16 yllsrdeeklepvldpkske..lysypllealskekeeseelleelvkrglleeelvdri.rlCpsCksghlnvrevCpkC 93 
                                   + + r++e+++ v++p+ +e  +++ +  e ++ e+ee++++  +l + +   +++++r+   C++C  ++     vCp+C
  gi|13540986|ref|NP_110674.1|  67 FYIGRPNEEIRVVHNPQYPErpFVEIKTREEVMLEREEESSTSGTLIDPKDAPTSVAERLgYRCSKCGFYSSPTEMVCPNC 147
                                   555566666666666666555556666666666666666666666666666666666666357****************** PP

                       TackOD1  94 kSidie 99 
                                   +S + +
  gi|13540986|ref|NP_110674.1| 148 NSPKAQ 153
                                   **8765 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   2.4   0.00082      0.43       6      36 ..     128     152 ..     127     154 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00082
                   Zn-ribbon_8   6 YrCeeCghefevlqsisdapltaCPeCgs.ev 36 
                                   YrC +Cg  f      s + + +CP+C+s ++
  gi|13540986|ref|NP_110674.1| 128 YRCSKCG--FY-----SSPTEMVCPNCNSpKA 152
                                   9******..33.....2345778*****9665 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   3.7   0.00076       0.4       1      22 [.     128     149 ..     128     149 .. 0.95

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00076
                  Rubredoxin_2   1 YvCsqCGfesakwfGrCpsCgs 22 
                                   Y+Cs+CGf s+     Cp+C+s
  gi|13540986|ref|NP_110674.1| 128 YRCSKCGFYSSPTEMVCPNCNS 149
                                   9*********99999*****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 ?    9.9   4.5    0.0011      0.58       1      21 [.     129     149 ..     129     151 .. 0.92

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0011
                 zinc_ribbon_2   1 fCpnCGaelqdnakFCpyCGt 21 
                                   +C++CG   ++++  Cp+C +
  gi|13540986|ref|NP_110674.1| 129 RCSKCGFYSSPTEMVCPNCNS 149
                                   6******************66 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.2      0.22   1.2e+02      16      26 ..     124     134 ..     122     135 .. 0.85
   2 ?    7.5   0.2    0.0054       2.9       1      10 [.     142     151 ..     142     157 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.22
                                   STTCEEESSSS CS
                  TF_Zn_Ribbon  16 ergelvCtdCG 26 
                                   er  ++C++CG
  gi|13540986|ref|NP_110674.1| 124 ERLGYRCSKCG 134
                                   677899****9 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0054
                                   EEETTTTCEE CS
                  TF_Zn_Ribbon   1 ykCPnCgstn 10 
                                   ++CPnC+s++
  gi|13540986|ref|NP_110674.1| 142 MVCPNCNSPK 151
                                   79*****986 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   4.7    0.0065       3.4       7      28 ..     130     151 ..     129     153 .. 0.95

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0065
                                   -SSS--EEESSSSB-TTT--BT CS
                      zf-RanBP   7 CskClvqNfawstkCvaCqapk 28 
                                   CskC+++ +++ ++C +C +pk
  gi|13540986|ref|NP_110674.1| 130 CSKCGFYSSPTEMVCPNCNSPK 151
                                   *********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (495 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       796  (0.0443973); expected 358.6 (0.02)
Passed bias filter:                      704  (0.039266); expected 358.6 (0.02)
Passed Vit filter:                       137  (0.00764125); 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: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 3095.24
//
Query:       gi|13540987|ref|NP_110675.1|  [L=430]
Description: DNA primase [Thermoplasma volcanium GSS1]
Scores for complete 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-12   45.6   0.8    5.1e-11   42.9   0.1    2.8  3  Toprim_4    Toprim domain
    4.7e-07   30.1   0.1    6.5e-06   26.5   0.0    2.8  4  Toprim_2    Toprim-like
    0.00082   19.6   1.4     0.0031   17.7   0.1    2.6  2  Toprim      Toprim domain
  ------ inclusion threshold ------
      0.062   13.4   0.6       0.13   12.3   0.1    1.8  2  sCache_3_2  Single cache domain 3
       0.27   11.7   3.8       0.24   11.8   0.8    2.3  2  CelTOS      Cell-traversal protein for ookinetes and sporozoi
        5.3    7.4   5.9        4.3    7.7   0.6    2.4  2  DUF349      Domain of Unknown Function (DUF349)


Domain annotation for each model (and alignments):
>> Toprim_4  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.85   2.5e+03      25      45 ..      84     105 ..      80     122 .. 0.72
   2 !   42.9   0.1   1.7e-14   5.1e-11       2      76 ..     173     234 ..     172     271 .. 0.76
   3 ?   -3.4   0.0       4.9   1.5e+04      16      31 ..     399     414 ..     398     421 .. 0.72

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.85
                      Toprim_4  25 avlggalspldgirpeklkt.e 45 
                                   a+l  al++ d i+p k k   
  gi|13540987|ref|NP_110675.1|  84 AILAAALETIDRIGPCKAKVeI 105
                                   7789999999999999998833 PP

  == domain 2  score: 42.9 bits;  conditional E-value: 1.7e-14
                      Toprim_4   2 eiiiVEgyaDvlalekagiknvvavlggalspldgirpeklktenlveaekkvkevilaldgDaeGeataerlae 76 
                                    ii+VEg++Dvl+l k+gikn++av g+++  ++ ++  kl +e         + v+++ldgD  G+   ++ ++
  gi|13540987|ref|NP_110675.1| 173 SIIVVEGRNDVLNLLKYGIKNTIAVQGTNI--PETVK--KLSKE---------RTVTVFLDGDRGGDLILKEMLQ 234
                                   69****************************..66666..44443.........5677777777777655554444 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 4.9
                      Toprim_4  16 ekagiknvvavlggal 31 
                                   ++agikn++    g +
  gi|13540987|ref|NP_110675.1| 399 YNAGIKNIYGLKLGHI 414
                                   5789999997655555 PP

>> Toprim_2  Toprim-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.58   1.7e+03      36      77 ..     117     154 ..     107     170 .. 0.70
   2 !   26.5   0.0   2.2e-09   6.5e-06       1      69 [.     175     237 ..     175     254 .. 0.80
   3 ?   -3.0   0.0       3.5     1e+04      22      39 ..     270     285 ..     261     304 .. 0.58
   4 ?   -3.3   0.0       4.4   1.3e+04       4      15 ..     329     340 ..     329     366 .. 0.66

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.58
                      Toprim_2  36 lkllerypekkvvlalDnDkaGrkaakrlaellreagvreki 77 
                                    k++er   kk  +  D + +G++  + l++ +re+  + +i
  gi|13540987|ref|NP_110675.1| 117 QKIIERA--KK--IYQDMNSKGDDLSESLVKSVREEVEKSEI 154
                                   4555555..32..45699999999999999888877655554 PP

  == domain 2  score: 26.5 bits;  conditional E-value: 2.2e-09
                      Toprim_2   1 vvfEgaiDalSlaqlgikektnvvalgGtalteaalkllerypekkvvlalDnDkaGrkaakrlaellr 69 
                                   +v+Eg  D+l l+++gik   n +a+ Gt + ++ +k l+++  ++v + lD D+ G+   k++ ++++
  gi|13540987|ref|NP_110675.1| 175 IVVEGRNDVLNLLKYGIK---NTIAVQGT-NIPETVKKLSKE--RTVTVFLDGDRGGDLILKEMLQVAE 237
                                   69***************9...********.555556666666..68*************9999888774 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 3.5
                      Toprim_2  22 nvvalgGtalteaalkll 39 
                                   +++++ G    +++ ++ 
  gi|13540987|ref|NP_110675.1| 270 QYLSMHGM--NDELKEYS 285
                                   67777776..23332222 PP

  == domain 4  score: -3.3 bits;  conditional E-value: 4.4
                      Toprim_2   4 EgaiDalSlaql 15 
                                   Eg++D+l  + +
  gi|13540987|ref|NP_110675.1| 329 EGYLDLLNPHDV 340
                                   778887765554 PP

>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.2      0.53   1.6e+03       6       6 ..      60      60 ..      21     155 .. 0.48
   2 !   17.7   0.1     1e-06    0.0031       2      98 ..     174     248 ..     173     253 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.53
                                  S CS
                        Toprim  6 E 6 
                                  E
  gi|13540987|ref|NP_110675.1| 60 E 60
                                  0 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 1e-06
                                   EEEESSHHHHHHHHHTHTSTEEEEEEESSSSEEEHSTTEEEEEECTTTHHHHHHHHHHHHHHSEEEEECSSSHHHHHHHHH CS
                        Toprim   2 lvivEgpsdaktiakalgsgfqavtaslGhildletefkpvyeeiedkkkvlkalkelakradeiilatDpDreGeaiawe 82 
                                   +++vEg +d+ ++ k+   g ++++a++G+ +  +                    k+l+ +   + + +D+Dr G  i +e
  gi|13540987|ref|NP_110675.1| 174 IIVVEGRNDVLNLLKY---GIKNTIAVQGTNIPETV-------------------KKLS-KERTVTVFLDGDRGGDLILKE 231
                                   89**************...9*********9886554...................5555.66799999************* PP

                                   HHHHHT.HHHTTTEEEE CS
                        Toprim  83 llevlk.ellenkigrv 98 
                                   +l+v++ +++ ++ + +
  gi|13540987|ref|NP_110675.1| 232 MLQVAEvDFVARAPPGT 248
                                   **999876666655555 PP

>> sCache_3_2  Single cache domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.1       2.4   7.2e+03       7      27 ..     116     136 ..     112     152 .. 0.67
   2 ?   12.3   0.1   4.5e-05      0.13      44      97 ..     340     395 ..     297     401 .. 0.78

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 2.4
                    sCache_3_2   7 aealeeralalatsvagsriv 27 
                                   +++ +era+++ +++  +  +
  gi|13540987|ref|NP_110675.1| 116 RQKIIERAKKIYQDMNSKGDD 136
                                   577788888888888766655 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 4.5e-05
                    sCache_3_2  44 v.ddvrritgvdyvvitDeegrvlah.pdpaevgrklsgpataaalkagrayvgtv 97 
                                   v  ++++++++++  i+D+ g+++a+ p  ++v r +++p++++++++g +  + +
  gi|13540987|ref|NP_110675.1| 340 VsRRIEALSQLKTTEIYDSNGQRIASfPVAEAVDRIIQDPQGNTIVTGGIISQRLI 395
                                   258899999999**************9********************997766655 PP

>> CelTOS  Cell-traversal protein for ookinetes and sporozoites
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.8   8.2e-05      0.24      10      50 ..     116     155 ..     107     161 .. 0.85
   2 ?   -0.6   0.1      0.59   1.7e+03      76     107 ..     228     260 ..     181     266 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 8.2e-05
                        CelTOS  10 qkslssklseiiradldskgdelvdliandlekelqknslv 50 
                                   +++++++ ++ i +d++skgd+l + +++ + +e++k +++
  gi|13540987|ref|NP_110675.1| 116 RQKIIERAKK-IYQDMNSKGDDLSESLVKSVREEVEKSEII 155
                                   4567888888.99************************9865 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.59
                        CelTOS  76 vlksllpvvek.ivadavkPPvvdravYsvlvk 107
                                   +lk++l+v e  +va a     v++ +Y+ +vk
  gi|13540987|ref|NP_110675.1| 228 ILKEMLQVAEVdFVARAPPGTEVEELTYKQIVK 260
                                   566666666631444443333566667776665 PP

>> DUF349  Domain of Unknown Function (DUF349)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.6    0.0014       4.3      28      59 ..     109     137 ..     100     148 .. 0.76
   2 ?    1.7   0.5      0.11   3.2e+02      30      46 ..     295     311 ..     277     326 .. 0.60

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0014
                        DUF349  28 reenlekKealieeaealaksttdwksatkrl 59 
                                   ++   +k++++ie+a+++ +++   +s+ + l
  gi|13540987|ref|NP_110675.1| 109 EDVRVQKRQKIIERAKKIYQDM---NSKGDDL 137
                                   566789************8877...6655444 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.11
                        DUF349  30 enlekKealieeaeala 46 
                                   +n e+K++ +ee ea +
  gi|13540987|ref|NP_110675.1| 295 HNSEQKKEVLEEPEAEK 311
                                   45555555555544432 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (430 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       849  (0.0473534); expected 358.6 (0.02)
Passed bias filter:                      486  (0.0271069); 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: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 3287.98
//
Query:       gi|13540988|ref|NP_110676.1|  [L=341]
Description: endonuclease IV [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.6e-11   42.9   0.0    5.6e-11   42.3   0.0    1.2  1  AP_endonuc_2  Xylose isomerase-like TIM barrel
  ------ inclusion threshold ------
      0.012   14.8   0.0      0.023   14.0   0.0    1.4  1  UvdE          UV-endonuclease UvdE
       0.11   13.2   0.1        1.1    9.9   0.0    2.4  3  DUF493        Protein of unknown function (DUF493)
        0.2   11.5   0.4       0.65    9.9   0.2    2.0  2  TrkA_C        TrkA-C 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 !   42.3   0.0   1.2e-14   5.6e-11      13     184 ..      92     256 ..      91     273 .. 0.91

  Alignments for each domain:
  == domain 1  score: 42.3 bits;  conditional E-value: 1.2e-14
                                   EEECCTCSHHHHCHHHHHHHHHHHHHHTTSEEEEEEECCCHSTCTHCHTTCSHHHHHHHHHHHHHHHHHHTBSEEEEEBCC CS
                  AP_endonuc_2  13 ElfgrdlvpvselsdeelrelrkaldelglriaslslftrfgypdederearreesvdalkraielaaaLGapllvlhpGt 93 
                                   Elf+  +++++     +l++  ++++el+++++++ +++ +   + d  ++     +++l+ a+ l + +Ga+ +++h+G 
  gi|13540988|ref|NP_110676.1|  92 ELFWNMARNYD-----DLETGGQLARELDITLSMHAPYYMDMIAGNDVADKS----INHLRWALILGKYMGAKRVITHSG- 162
                                   78888888887.....58*************************998766666....************************. PP

                                   GBCTTTSGHHHHHHHHHHHHHHHHHHHH.HHT.SEEEEE--TTTTSSSTCHHHHHHHHHHTTTTEEEEEEHHHHHHH.... CS
                  AP_endonuc_2  94 agagpkgseeeawerlaeslneladyae.keg.vklalEtlagsgvelgdeelarlldavdspnvgvclDtgHllia.... 168
                                       + g++++a++++ae+  +l+ ++  ++g   +++Et  +++v+   +e+ +l ++v+   +   l+++H ++     
  gi|13540988|ref|NP_110676.1| 163 ---FYHGQKKDAVKKFAEVYADLVNEFPpDAGyPYIGVETSGKQEVFGTVKEVTDLAKKVN---IEPILNFAHVHAItggs 237
                                   ...455666669***************98888777**********99999**********9...***************** PP

                                   ...TTTHHHHHHHHHGGEE CS
                  AP_endonuc_2 169 ...eedvddalraladrik 184
                                        d+++++++++++ k
  gi|13540988|ref|NP_110676.1| 238 lmeIKDFESIINEFKKYAK 256
                                   **************99966 PP

>> UvdE  UV-endonuclease UvdE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0     5e-06     0.023      87     212 ..     102     229 ..      92     257 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5e-06
                          UvdE  87 eeleevGelakelglRltfHPeqftllnSdrkevtesairdlayHdklldalklaeqqdavliiHvGGkfgdkeaalerfk 167
                                   + le  G+la+el++ l++H   ++ + +  ++v +++i+ l     l + ++ ++     +i H G  +g+k++a+++f+
  gi|13540988|ref|NP_110676.1| 102 DDLETGGQLARELDITLSMHAPYYMDMIAG-NDVADKSINHLRWALILGKYMGAKR-----VITHSGFYHGQKKDAVKKFA 176
                                   568888****************9*999875.689********99877777777544.....699***99************ PP

                          UvdE 168 enikrlpdsv.....kerlvLEND...dksytvadlLpvceelniPlVlDyHH 212
                                   e +++l ++         + +E     ++  tv+++  ++++ ni  +l + H
  gi|13540988|ref|NP_110676.1| 177 EVYADLVNEFppdagYPYIGVETSgkqEVFGTVKEVTDLAKKVNIEPILNFAH 229
                                   *****976651111134566665311133446677777777777766666544 PP

>> DUF493  Protein of unknown function (DUF493)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00024       1.1      44      74 ..      66      97 ..      46     102 .. 0.83
   2 ?   -0.1   0.0      0.32   1.5e+03       4      34 ..     184     213 ..     181     223 .. 0.71
   3 ?   -2.9   0.0       2.4   1.1e+04       3      12 ..     293     302 ..     291     302 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00024
                        DUF493 44 v.resskgkYlSvtvtvrveseeqldalyqeL 74
                                  v r+ ++g+Y+Sv ++ ++e+ + +++l+ ++
  gi|13540988|ref|NP_110676.1| 66 VmRQDEEGNYVSVGINTEIEEDDIVRELFWNM 97
                                  348999********************999776 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.32
                        DUF493   4 ieFPcdfpikviGkaeedfaqavvevverha 34 
                                    eFP d  +  iG ++ + +q+v+  v+++ 
  gi|13540988|ref|NP_110676.1| 184 NEFPPDAGYPYIGVETSG-KQEVFGTVKEVT 213
                                   699***99*99*996554.466666666554 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 2.4
                        DUF493   3 lieFPcdfpi 12 
                                   li++P d++i
  gi|13540988|ref|NP_110676.1| 293 LIDYPDDMTI 302
                                   89***99987 PP

>> TrkA_C  TrkA-C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.2   0.00014      0.65      22      53 ..      53      90 ..      46      91 .. 0.84
   2 ?   -2.4   0.0         1   4.5e+03       9      24 ..     131     144 ..     129     149 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00014
                                  HHHH...S-EEEEEE-T...-EEES--TT-B--TT-EE CS
                        TrkA_C 22 lrar...gvlvvairRg...geliipsgdtvLeeGDvl 53
                                  lr r   + +++ + R+   g +++ + +t++ee+D++
  gi|13540988|ref|NP_110676.1| 53 LRPRdveDSIIIDVMRQdeeGNYVSVGINTEIEEDDIV 90
                                  55555599******88889999999999********98 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1
                                   -GGGTTSBHHHHTHHH CS
                        TrkA_C   9 gsplvGktlkelnlra 24 
                                   g  +++k++ +  lr 
  gi|13540988|ref|NP_110676.1| 131 GNDVADKSINH--LRW 144
                                   667999***99..554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 2079.73
//
Query:       gi|13540989|ref|NP_110677.1|  [L=96]
Description: hypothetical protein TVN0158 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.5e-21   75.6   0.1      5e-21   75.5   0.1    1.0  1  DUF5611   Domain of unknown function (DUF5611)


Domain annotation for each model (and alignments):
>> DUF5611  Domain of unknown function (DUF5611)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.5   0.1   2.8e-25     5e-21       1     103 []       1      95 [.       1      95 [. 0.96

  Alignments for each domain:
  == domain 1  score: 75.5 bits;  conditional E-value: 2.8e-25
                                   -EEE---SSS--SH.HHHHHHHHHHT.-EEEEETTEEEEE-TTBS-EEEEE..-SS-EEEEE--.B...-TTS-HHHHHHH CS
                       DUF5611   1 mreYkiKrGfkkeeeerlkelleeyfggeveeegdllvvsfgaikklevkisskkkklvvdteerdaeeeddeaaldtvkk 81 
                                   mr+Y++K+G+ +++ e++ +ll+ +   +++ egd++v+s ++i+++e+k   +k+kl+v+t++      d  + l+++k+
  gi|13540989|ref|NP_110677.1|   1 MRDYPVKKGIANTL-ESIADLLSGMG-YQFSIEGDIIVTSLPGISRIEIKP--EKRKLLVNTSD-Y---SDGVDKLQIIKN 73 
                                   9*************.*********99.9***********************..*********99.4...688999****** PP

                                   HHHHHHHHH---GGGHHHHH-- CS
                       DUF5611  82 fndFLeeaTGydaKeRkkkakk 103
                                   +nd++e++TGy+aKeRkk+++k
  gi|13540989|ref|NP_110677.1|  74 YNDLIEKLTGYSAKERKKMMTK 95 
                                   ********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       636  (0.0354733); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.48
# Mc/sec: 606.20
//
Query:       gi|13540990|ref|NP_110678.1|  [L=166]
Description: hypothetical protein TVN0159 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.9e-07   30.8   4.3    2.9e-07   30.8   4.3    1.5  2  CopD             Copper resistance protein D
    0.00034   20.7  10.4    0.00052   20.1  10.4    1.3  1  DUF2269          Predicted integral membrane protein (DUF2269
      0.003   17.8   1.4      0.003   17.8   1.4    2.1  2  DUF4149          Domain of unknown function (DUF4149)
  ------ inclusion threshold ------
      0.025   15.0   1.0       0.11   13.0   0.1    2.1  2  FLILHELTA        Hypothetical protein FLILHELTA
      0.067   13.0  10.1      0.042   13.7   2.0    2.3  2  TatC             Sec-independent protein translocase protein 
       0.97    9.1  10.6          2    8.1   3.7    2.0  2  PhoLip_ATPase_C  Phospholipid-translocating P-type ATPase C-t
        1.1    9.2  12.5        2.1    8.4   8.3    2.6  2  Cytochrom_B_N_2  Cytochrome b(N-terminal)/b6/petB
        4.6    7.3   7.8        8.5    6.5   2.2    2.2  2  DHHC             DHHC palmitoyltransferase


Domain annotation for each model (and alignments):
>> CopD  Copper resistance protein D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.2       3.5   7.9e+03      14      14 ..      16      16 ..       6      39 .. 0.54
   2 !   30.8   4.3   1.3e-10   2.9e-07       5     103 ..      55     159 ..      51     161 .. 0.70

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 3.5
                          CopD 14 a 14
                                   
  gi|13540990|ref|NP_110678.1| 16 F 16
                                  1 PP

  == domain 2  score: 30.8 bits;  conditional E-value: 1.3e-10
                          CopD   5 rrFsrlalaavavvlvtGvvnallrvg..lagllttayGrlllaKlalllvllalaalnrf...rlvprleaa.tgaggqa 79 
                                   r F+++  a +a+++v+G +++  ++   ++ l+tt  G++llaK++++ ++++l  +n      l+ rl+++ + ++ + 
  gi|13540990|ref|NP_110678.1|  55 RYFGWWTDATIAILVVSGGYLGYEYIHgnFGLLTTTIGGKILLAKVIVVWIMIVLMYANNIyhgKLIMRLAEEkKYDEMK- 134
                                   568888999999999******987777778888889999*********************99998999994432222222. PP

                          CopD  80 lrhrlrrsaa....lelvlalvvlllaa 103
                                      r+r+  +    + l+l l++++la+
  gi|13540990|ref|NP_110678.1| 135 ---RIRKITHvasfITLGLILAIMGLAV 159
                                   ...3333333000134445555555555 PP

>> DUF2269  Predicted integral membrane protein (DUF2269)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1  10.4   2.3e-07   0.00052       3     148 ..      10     157 ..       8     160 .. 0.72

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 2.3e-07
                       DUF2269   3 lkllHilsavlllgtgigiafyllras..rtrdaaviaevarlvvladwlftatavillpvtGlwlvhla...gwplkqsW 78 
                                   + ++H++++++++g+ + i+f+++ as  +t+d  + ++++ ++ +   + t  ++ +l+v+G +l +     ++ l ++ 
  gi|13540990|ref|NP_110678.1|  10 VLIIHVFASIMFIGGSFFIWFIVWPASykMTKDESMRTKIVGIIGRYFGWWTDATIAILVVSGGYLGYEYihgNFGLLTT- 89 
                                   779*********************99733689999999999999887777888889999*******98765544444444. PP

                       DUF2269  79 lllslvLyllagalwlpVvwlqirlrrlaeaaeeegaalpeeyvrlfriwfalgvlaflaliaifvLMva 148
                                    +++ +L + ++++w+++v +   +++  +     + a +++y ++ ri  +++v +f+ l +i+++M++
  gi|13540990|ref|NP_110678.1|  90 TIGGKILLAKVIVVWIMIVLM--YANNIYHGKLIMRLAEEKKYDEMKRIRKITHVASFITLGLILAIMGL 157
                                   567777778888888887753..33333333333344456677777777777777777777777777754 PP

>> DUF4149  Domain of unknown function (DUF4149)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   1.4   1.3e-06     0.003       5     101 ..      20     129 ..      16     130 .. 0.92
   2 ?   -0.3   0.2      0.62   1.4e+03      72      86 ..     149     163 ..     134     165 .. 0.56

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.3e-06
                       DUF4149   5 lllGsqlwvtfvvapvlfrsL.prhqfgelqsklFplyfglglalsvlllltevavg............seklaseellql 72 
                                     +G+ +++ f+v p  ++   ++    ++++ +  ++ ++  a+ ++l+++ ++ g            +   ++  l+++
  gi|13540990|ref|NP_110678.1|  20 MFIGGSFFIWFIVWPASYKMTkDESMRTKIVGIIGRYFGWWTDATIAILVVSGGYLGyeyihgnfglltTTIGGKILLAKV 100
                                   579*****************87999***************************99999999******98777777888**** PP

                       DUF4149  73 llllvvllltllnafylepritslkeqre 101
                                   +++ ++++l  +n+ y +  i +l e+++
  gi|13540990|ref|NP_110678.1| 101 IVVWIMIVLMYANNIYHGKLIMRLAEEKK 129
                                   ***********************999875 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.62
                       DUF4149  72 lllllvvllltllna 86 
                                    l+l+++ l +ll++
  gi|13540990|ref|NP_110678.1| 149 GLILAIMGLAVLLQF 163
                                   344455555555554 PP

>> FLILHELTA  Hypothetical protein FLILHELTA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.1      0.35   7.9e+02      24      42 ..       6      24 ..       2      64 .. 0.59
   2 ?   13.0   0.1   4.7e-05      0.11       2      47 ..     120     164 ..     119     166 .] 0.88

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.35
                     FLILHELTA 24 hvtsFLiLHElTAivPllg 42
                                   +++ Li+H +  i+ + g
  gi|13540990|ref|NP_110678.1|  6 LIMAVLIIHVFASIMFIGG 24
                                  5788899998888865443 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 4.7e-05
                     FLILHELTA   2 llkrlPkflrkytrklrsapvshvtsFLiLHElTAivPllglfalf 47 
                                   l++rl    +ky++  r   ++hv+sF+ L  + Ai+ l +l  +f
  gi|13540990|ref|NP_110678.1| 120 LIMRL-AEEKKYDEMKRIRKITHVASFITLGLILAIMGLAVLLQFF 164
                                   56666.5678999*****************************9998 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 ?   13.7   2.0   1.9e-05     0.042      95     131 ..       9      45 ..       7      80 .. 0.74
   2 ?    4.0   1.3     0.017        39      16      64 ..     100     153 ..      91     165 .. 0.48

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.9e-05
                                   TTHHHHHHHHHHHHHHHHHHHHTHHHHHHHHHTTTTS CS
                          TatC  95 lvlvfliaslllfllGaafayfvvlplvlkfllseev 131
                                   +vl + ++++++f++G +f +f+v p+++k+  +e++
  gi|13540990|ref|NP_110678.1|   9 AVLIIHVFASIMFIGGSFFIWFIVWPASYKMTKDESM 45 
                                   5788899**********************98873333 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.017
                                   HHHHHHHHHHHTHHHHHH..HCCHHHHC..CTTS-EE..--SSS-HHHHHHHHH CS
                          TatC  16 avaiafiitfvfaeelia..fllepleea.eeeveli..vlspleafllklkvs 64 
                                   ++++ ++i++++a+++++  ++++  ee+   e++ i  +++++  ++l l ++
  gi|13540990|ref|NP_110678.1| 100 VIVVWIMIVLMYANNIYHgkLIMRLAEEKkYDEMKRIrkITHVASFITLGLILA 153
                                   233333333358999999987776666653332222232333333333333333 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 ?    8.1   3.7   0.00091         2     170     244 ..       7      82 ..       1      87 [. 0.67
   2 ?    5.8   0.7    0.0046        10     180     237 ..      99     163 ..      83     165 .. 0.59

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00091
               PhoLip_ATPase_C 170 aletktwtl.iliililgsillyflflllyssllpsssefygvleelfsspsfwlvlllvvvvallpdllikvlkr 244
                                   ++ +  +++  +i++i gs++++f+++ +  ++++ +s  ++++  + +   +w+   ++++v+    l +++++ 
  gi|13540990|ref|NP_110678.1|   7 IMAVLIIHVfASIMFIGGSFFIWFIVWPASYKMTKDESMRTKIVGIIGRYFGWWTDATIAILVVSGGYLGYEYIHG 82 
                                   4444455540455555559999999887666666666667766777777788888788888888888888888865 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0046
               PhoLip_ATPase_C 180 liililgsillyflflllyssllps.....ssefygvleelfsspsfwlv..lllvvvvallpdl 237
                                    +i++++ i+l+++ ++ + +l++      +++ ++ ++++ + +sf ++  +l ++ +a+l+++
  gi|13540990|ref|NP_110678.1|  99 KVIVVWIMIVLMYANNIYHGKLIMRlaeekKYDEMKRIRKITHVASFITLglILAIMGLAVLLQF 163
                                   46677777777777776666655558877755555566666666666665434444444444444 PP

>> 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 ?    2.1   0.1     0.077   1.7e+02      89     124 ..       6      42 ..       2      52 .. 0.66
   2 ?    8.4   8.3   0.00092       2.1      24      93 ..      55     124 ..      53     166 .] 0.95

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.077
               Cytochrom_B_N_2  89 llsrlyalHilllpalllalivahlllv.ekkgqtps 124
                                   l+  ++++H++   ++++  +++ ++++  ++++t++
  gi|13540990|ref|NP_110678.1|   6 LIMAVLIIHVFASIMFIGGSFFIWFIVWpASYKMTKD 42 
                                   5566788888777788888888888887444444443 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00092
               Cytochrom_B_N_2  24 RelnWiiGvllllltllegflGysLpddllsvtalrvgagiissvPvvgtwlvellfGgelpgeallsrl 93 
                                   R + W++  ++ +l++  g+lGy  +    +  ++++g +i+ +  +v  +++ l+ ++++++ +l+ rl
  gi|13540990|ref|NP_110678.1|  55 RYFGWWTDATIAILVVSGGYLGYEYIHGNFGLLTTTIGGKILLAKVIVVWIMIVLMYANNIYHGKLIMRL 124
                                   5678***************************************999988888999999***999999997 PP

>> DHHC  DHHC palmitoyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.3     0.019        43      95     132 ..       9      46 ..       2      48 .. 0.75
   2 ?    6.5   2.2    0.0038       8.5      55     114 ..     102     162 ..      59     165 .. 0.65

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.019
                          DHHC  95 lsilllvlsllfllllgllllfhlylilrnlTtieamk 132
                                    ++++ v++ ++++  ++++ f ++ ++ ++T+ e m+
  gi|13540990|ref|NP_110678.1|   9 AVLIIHVFASIMFIGGSFFIWFIVWPASYKMTKDESMR 46 
                                   45667777778888888888888889999999999887 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0038
                          DHHC  55 llylllllilalv.lllialvklveeekkseflavtllkkllsilllvlsllfllllglll 114
                                   +++++++l++a    +   + +l ee+k +e+ ++++++ + s+++l l l ++ l +ll 
  gi|13540990|ref|NP_110678.1| 102 VVWIMIVLMYANNiYHGKLIMRLAEEKKYDEMKRIRKITHVASFITLGLILAIMGLAVLLQ 162
                                   3333333333333155556666667777777777777666555555554444443333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1262  (0.0703888); expected 358.6 (0.02)
Passed bias filter:                      524  (0.0292264); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        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 0.29s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 1093.25
//
Query:       gi|13540991|ref|NP_110679.1|  [L=90]
Description: nucleoid DNA-binding protein (HB-related) [Thermoplasma volcanium GSS1]
Scores for complete 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-20   71.3   2.5    7.1e-20   71.0   2.5    1.0  1  Bac_DNA_binding  Bacterial DNA-binding protein
    2.8e-05   24.2   0.1    3.3e-05   24.0   0.1    1.0  1  HU-HIG           HU domain fused to wHTH, Ig, or Glycine-rich
  ------ inclusion threshold ------
      0.027   14.4   0.0      0.044   13.6   0.0    1.3  1  HU-CCDC81_bac_2  CCDC81-like prokaryotic HU domain 2
       0.57   10.5   4.3        4.1    7.8   0.7    2.1  2  DUF5024          Domain of unknown function (DUF5024)


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 !   71.0   2.5   1.6e-23   7.1e-20       4      86 ..       5      87 ..       3      89 .. 0.97

  Alignments for each domain:
  == domain 1  score: 71.0 bits;  conditional E-value: 1.6e-23
                                  HHHHHHHHTT----HHHHHHHHHHHHHHHHHHHHTT-EEEETTTEEEEEEEE--BS-B-TTT--B--B--EEEEEEEE-HHHH CS
               Bac_DNA_binding  4 keLieeiaektgltkkdakrvveafldtikeaLkkgekvelsgFGtfkvkerkartgrnpkTgekvkiparkvvkFkpskelk 86
                                  +eL + +a+k++ t+k a++v+++fld+i ++ + g+k++l gFG f+ +++ +r++rnp+T++ +++p++k+  F++s+++k
  gi|13540991|ref|NP_110679.1|  5 SELSKDVAKKANTTQKVARTVIKSFLDEIVAQANGGQKINLAGFGIFERRTQGPRKARNPQTKKVIEVPSKKKFVFRASSKIK 87
                                  7999****************************************************************************998 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 !   24.0   0.1   7.4e-09   3.3e-05      32     115 ..       2      87 ..       1      89 [. 0.88

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 7.4e-09
                        HU-HIG  32 vdfeeLceeiskrstlsrgdvkavldaledelkeaLadGerVeLgelGyFslslks.kgved.ekevransikkkkinfrp 110
                                   v ++eL+++++k    ++   + v++++ de++ + + G+ ++L ++G F    +  +++ + + +   +  +kkk +fr+
  gi|13540991|ref|NP_110679.1|   2 VGISELSKDVAKKANTTQKVARTVIKSFLDEIVAQANGGQKINLAGFGIFERRTQGpRKARNpQTKKVIEVPSKKKFVFRA 82 
                                   7789**************************************************9986655535555578889999****9 PP

                        HU-HIG 111 gkklk 115
                                   ++k+k
  gi|13540991|ref|NP_110679.1|  83 SSKIK 87 
                                   99987 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 ?   13.6   0.0   9.9e-06     0.044       5      52 ..       9      56 ..       7      58 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 9.9e-06
               HU-CCDC81_bac_2  5 nsiaeaegisyeeAlqkiekeveelkqeLeeegrveleniGeLslnee 52
                                  + +a++ +++ + A++ i+++ +e+  + + +++++l + G + +  +
  gi|13540991|ref|NP_110679.1|  9 KDVAKKANTTQKVARTVIKSFLDEIVAQANGGQKINLAGFGIFERRTQ 56
                                  568999*************************************88765 PP

>> DUF5024  Domain of unknown function (DUF5024)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.2     0.008        36      22      51 ..      11      44 ..       5      60 .. 0.71
   2 ?    7.8   0.7   0.00092       4.1      24      36 ..      61      73 ..      52      88 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.008
                       DUF5024 22 vtkrdPkTrkVvk.vVksfsvk...deglgkelk 51
                                  v k+   T+kV + v+ksf  +   ++++g+++ 
  gi|13540991|ref|NP_110679.1| 11 VAKKANTTQKVARtVIKSFLDEivaQANGGQKIN 44
                                  6788889999975378999543323666666665 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.00092
                       DUF5024 24 krdPkTrkVvkvV 36
                                   r+P+T+kV+ v 
  gi|13540991|ref|NP_110679.1| 61 ARNPQTKKVIEVP 73
                                  69********995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       698  (0.0389313); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 600.85
//
Query:       gi|13540992|ref|NP_110680.1|  [L=459]
Description: hypothetical protein TVN0161 [Thermoplasma volcanium GSS1]
Scores for complete 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-14   51.5   0.0    2.2e-13   50.4   0.0    1.6  1  DDE_Tnp_1     Transposase DDE domain
     0.0013   18.0   0.0      0.002   17.3   0.0    1.2  1  ANF_receptor  Receptor family ligand binding region
  ------ inclusion threshold ------
      0.018   13.3   0.1       0.11   10.7   0.1    1.9  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 !   50.4   0.0   3.7e-17   2.2e-13      26     214 .]     186     399 ..     153     399 .. 0.81

  Alignments for each domain:
  == domain 1  score: 50.4 bits;  conditional E-value: 3.7e-17
                     DDE_Tnp_1  26 gyk.ggkykygyklhiavdtrsglilsvvitpgnvhdskglkqlldelrprkgklvlaDaGYasaelldtleekgvdyiir 105
                                   g++ +g + + +++ ++++    +++ v+i pg+  d  ++  ++d++   + ++++aD+G++sa ++++l+ ++++yii+
  gi|13540992|ref|NP_110680.1| 186 GHNsKGMHLPQINVMMLFSSTRTMPTFVRILPGSIRDASAMSKTIDMAGV-DRCVIVADKGFFSAINVKKLKRRHLSYIIP 265
                                   555466678888999999998889***********************999.****************************** PP

                     DDE_Tnp_1 106 lkkntklyrk.....................g.....aeskrrgrlrkhdrnkiltksqkrrnkskkekgdvyy.vtntns 159
                                   l+ n+ l                        +     ++   r++++k++  +i + +++r+ +  +e++++   ++++++
  gi|13540992|ref|NP_110680.1| 266 LRRNSSLIPEpehfmgvfsydgkpvkywkreNdvyifEDPVLRSEEEKDFLLRIEENKRSRKQY--DENEINFGkLYLLSD 344
                                   *****99999999998888777766666655055555555566666666666666666666666..555554440566666 PP

                     DDE_Tnp_1 160 ellsaeevaelyrlRwqiErvFkwlkrkfgldrlryrglnrveaqllllllalnl 214
                                      ++e + +ly++R  +E  F   k+++  dr ++r+    +++++l ll+l l
  gi|13540992|ref|NP_110680.1| 345 LNEEPERIYRLYKQREYVEYAFNVYKNDLEADRSYLRDDHMLFTYMFLNLLSLYL 399
                                   6789*********************************************999865 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 !   17.3   0.0   3.4e-07     0.002      52     129 ..     171     245 ..     147     265 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3.4e-07
                                   EEEEE-SSHHHHHHHHHHHCCTT-EEEESS---GGGG-TTTTTTEEESS--CHHHHHHHHHHHHHTT--EEEEEEESS CS
                  ANF_receptor  52 vaviGpssssvsdavaslanlfkiPvisygstspelsdknryptflrtvpsdtsqaqAivdilkhfgWkkvaliysdd 129
                                    a++  s ++++  + + ++ +++P+i ++     +s+++  ptf+r+ p + + a A+++++ + g ++ +++++++
  gi|13540992|ref|NP_110680.1| 171 TAIFSRSENMSFLELGHNSKGMHLPQINVMM---LFSSTRTMPTFVRILPGSIRDASAMSKTIDMAGVDRCVIVADKG 245
                                   577777888888888888999******7544...89999************************************997 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 ?   10.7   0.1   1.8e-05      0.11     218     350 ..     238     380 ..     224     406 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 1.8e-05
                   DDE_Tnp_1_4 218 ilvRgDSafarpellkwceergvdYviglaknsrlealiaelvekak....teaaekkek.........ereyrefayqae 285
                                    ++ +D +f +   +k +++r+++Y+i l++ns l  + ++++   +      ++ k+e+                  ++e
  gi|13540992|ref|NP_110680.1| 238 CVIVADKGFFSAINVKKLKRRHLSYIIPLRRNSSLIPEPEHFMGVFSydgkPVKYWKRENdvyifedpvL--------RSE 310
                                   5677899999999999999999999999999999999888876544300002222222223333333331........333 PP

                   DDE_Tnp_1_4 286 s.......WskerrVvakaerpaeglnl..rfvvTslaklspeelyeqlYcaRGemEnrIKeakldlaadrtss 350
                                            ++++r   ++++ ++++n+   + +++l+  +pe++y +lY++R  +E  +   k+dl+adr  +
  gi|13540992|ref|NP_110680.1| 311 EekdfllrIEENKR--SRKQYDENEINFgkLYLLSDLN-EEPERIY-RLYKQREYVEYAFNVYKNDLEADRSYL 380
                                   12333322222222..5677777777777778899999.9******.***********************9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (459 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       558  (0.0311228); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 3507.91
//
Query:       gi|13540993|ref|NP_110681.1|  [L=186]
Description: 30S ribosomal protein S7P [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.1e-42  142.6   1.3    8.8e-42  142.3   1.3    1.1  1  Ribosomal_S7   Ribosomal protein S7p/S5e
  ------ inclusion threshold ------
      0.012   14.0   0.1      0.017   13.4   0.1    1.2  1  Peptidase_S80  Bacteriophage T4-like capsid assembly protein 


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 !  142.3   1.3   9.8e-46   8.8e-42      17     149 .]      45     186 .]      38     186 .] 0.97

  Alignments for each domain:
  == domain 1  score: 142.3 bits;  conditional E-value: 9.8e-46
                                   STTSBHHHHHHHHHSB....TTBHHHHHHHHHHHHHHHHHHHSS-HHHHHHHHHHHCS-SEEEEEEBSSSSBEEEEEEE-H CS
                  Ribosomal_S7  17 kynselveklinklmk....dGkkslAekivygaldiieektkkdplevleeAlenvkPrvevksrrvGGatyqvpvevrp 93 
                                   k n+++ve+linklm+    +Gkk  A+ki ++a+dii++ktk++pl++l +A+en+ Pr+ev+++++GG++++ +v+v+p
  gi|13540993|ref|NP_110681.1|  45 KINMNVVERLINKLMRtekwTGKKYSAYKITKDAFDIIADKTKQNPLQILINAIENAGPREEVTRLKYGGIAVPKSVDVSP 125
                                   57899**************************************************************************** PP

                                   HHHHHHHHHHHHHHH...STSSSS-HHHHHHHHHHHHHTT-..SHHHHHHHHHHHHHHHTG CS
                  Ribosomal_S7  94 kRrqalAlrwiieaa...rkrkeksmaekLaeElidAaege..gaavkkreethrmAeanr 149
                                   +Rr++ Alr+i+++a   +++++ks++++La+E++ Aa+++  + a++k+ee++r+A+++r
  gi|13540993|ref|NP_110681.1| 126 SRRVDEALRNIATGAtnaSFKSKKSIVNCLADEIMLAAKNDasSFAISKKEEIERVAQSAR 186
                                   *************9999899*********************999**************987 PP

>> Peptidase_S80  Bacteriophage T4-like capsid assembly protein (Gp20)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   1.9e-06     0.017     446     498 ..      39      91 ..      28      95 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.9e-06
                                   -HHHHHHHTTHHHHHHHHHHHHT-TTTTTTS-HHHHHHHTS---HHHHHHHHH CS
                 Peptidase_S80 446 dsyfeelkeleilerrinalrdiedyigkyishktiqkdilrlsdeeieaeak 498
                                    sy++   +++++er in l   e++ gk +s   i kd + +  ++ +++  
  gi|13540993|ref|NP_110681.1|  39 SSYYAGKINMNVVERLINKLMRTEKWTGKKYSAYKITKDAFDIIADKTKQNPL 91 
                                   69**************************************9999988887655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       585  (0.0326287); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 1431.42
//
Query:       gi|13540994|ref|NP_110682.1|  [L=142]
Description: 30S ribosomal protein S12P [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.2e-48  162.1   2.5      4e-48  161.8   2.5    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 !  161.8   2.5   2.2e-52     4e-48       1     113 [.      27     140 ..      27     141 .. 0.98

  Alignments for each domain:
  == domain 1  score: 161.8 bits;  conditional E-value: 2.2e-52
                                   --------S-TSSTTSSEEEEEEEEEEEE---TT--S-EEEEEEEET.TSEEEEEEE-SSS..----TT-EEEEEE--... CS
               Ribosom_S12_S23   1 rkelrkktksdalegapqkrGvvlekvtveakkPnsAlRkvvrvrLikngkevtafipgegalnfldEhdevlvrGirrk. 80 
                                   r+ l++k ksd+legapq++G+ +ekv++eak+PnsA+Rk+v+v+Likng+++taf+ g+ga+n++dEhdev+v+Gi+++ 
  gi|13540994|ref|NP_110682.1|  27 RRVLQLKRKSDPLEGAPQAKGIAIEKVGIEAKQPNSAIRKCVKVQLIKNGRQITAFAVGDGAINYIDEHDEVTVEGIGGRm 107
                                   678899***********************************************************************9999 PP

                                   ...BTTSTTEEEEBETS---TSSSTTTTT---- CS
               Ribosom_S12_S23  81 gkavkDlpGvrykvvkvagvslkalskykkekp 113
                                   g++++D+pGvrykvv v+g+slk+l+k++kek 
  gi|13540994|ref|NP_110682.1| 108 GRSKGDIPGVRYKVVAVNGISLKELVKGRKEKT 140
                                   *******************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       379  (0.0211389); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.24s 00:00:00.58 Elapsed: 00:00:00.38
# Mc/sec: 1130.13
//
Query:       gi|13540995|ref|NP_110683.1|  [L=338]
Description: phosphoribosylaminoimidazole synthetase [Thermoplasma volcanium GSS1]
Scores for complete 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-20   73.2   0.0    4.5e-20   72.3   0.0    1.4  1  AIRS_C    AIR synthase related protein, C-terminal domain
    4.3e-13   49.7   1.9      9e-13   48.7   1.9    1.5  1  AIRS      AIR synthase related protein, N-terminal domain


Domain annotation for each model (and alignments):
>> AIRS_C  AIR synthase related protein, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.3   0.0   5.1e-24   4.5e-20       1     152 [.     166     326 ..     166     328 .. 0.91

  Alignments for each domain:
  == domain 1  score: 72.3 bits;  conditional E-value: 5.1e-24
                                   STTEEEEEEETSSCTCCHHHHHHHCHHHCTSHTT......TSEHHHHHHHHHHHHHHHHHHHH.HTTECEEEE--TTHHHH CS
                        AIRS_C   1 kpGdvliltgslGlggagtslkrkileeegldds......avqlgdvlleptliyvkralaal.kglvkaahDvTgGGLlg 74 
                                   k+Gdv+i++gs+Gl+++g+  +rki+ +++ +++      +++  +vllept+iyv ++l  +   ++k+++ +TgGG+  
  gi|13540995|ref|NP_110683.1| 166 KEGDVIIGLGSSGLHSNGFTTVRKIISDNEINLFdnfpgeSKKTYEVLLEPTRIYVREILDVMgIIQIKGMANITGGGF-K 245
                                   79****************************9999*****8888*********************************987.8 PP

                                   HHHHHHHTTTEEEEEECG..THHHHHHHH.....HHHHHHHCSTTTEEEEEEEHGGH.HHHHHHHHHTTCCCEEEEEEEEE CS
                        AIRS_C  75 alaemapasgvgaeidld..kvpifdele.....splemllsensGrllvavppeea.davlaileeeglpeaavIGevta 147
                                   ++ +m +    + +id +     +f  l+     +  +m+ ++n+G ++v+v  e++   ++++l+ + +p  +vIG+v++
  gi|13540995|ref|NP_110683.1| 246 NITRMKDM---KYVIDDPmePQNVFVRLMelgnlNYKQMYEIFNMGTGFVVVIGEDDkIDFINTLKNR-VP-LKVIGHVEN 321
                                   999**665...5777777778888888888899************************99*******76.76.********9 PP

                                   SSSEE CS
                        AIRS_C 148 keels 152
                                   + +++
  gi|13540995|ref|NP_110683.1| 322 GTGVE 326
                                   98765 PP

>> AIRS  AIR synthase related protein, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.7   1.9     1e-16     9e-13       5      94 .]      52     154 ..      46     154 .. 0.91

  Alignments for each domain:
  == domain 1  score: 48.7 bits;  conditional E-value: 1e-16
                                   EEEEEEEEE.EECC....TCCCCHHHHHHHHHHHHHHTTTEEEEEEEEEEEEC.....HHHHHHHHHHHHHHHTT-EEEEE CS
                          AIRS   5 vvvttdshnrpvlv....epvhfiGakavavnlsDlaamGArPlalllslalp.....wleevvrglaeaaeelgvplvgG 76 
                                   + +  d++++++++    ++++++G  +va+n++D +++G +P+a++++la+      +++++ +g++ +a+ +++++vgG
  gi|13540995|ref|NP_110683.1|  52 LSFNNDGVGTKTMIaeqaNKYDTLGIDCVAMNVNDAITVGSEPIAMVDYLAVRdlnedIAKQLGNGFNVGAQIANISIVGG 132
                                   56778899999999655566777***********************************99********************* PP

                                   EEEEESS....EEEEEEEEEEE CS
                          AIRS  77 dtsfsne....ptisvtavGlv 94 
                                   +t++ +e    + +s +++G+v
  gi|13540995|ref|NP_110683.1| 133 ETAVVPEivnhIDVSGAVIGIV 154
                                   *****999999999*****997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (338 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       560  (0.0312343); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.33s 00:00:00.92 Elapsed: 00:00:00.52
# Mc/sec: 1957.99
//
Query:       gi|13540996|ref|NP_110684.1|  [L=305]
Description: ABC-type multidrug transport system, ATPase component [Thermoplasma volcanium GSS1]
Scores for complete 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-24   84.8   0.0    1.7e-23   83.7   0.0    1.5  2  ABC_tran  ABC transporter
      9e-11   42.1   1.8    2.3e-06   27.6   0.0    2.2  2  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
  ------ inclusion threshold ------
      0.016   14.6   0.3       0.24   10.8   0.3    2.4  1  SMC_N     RecF/RecN/SMC N terminal domain
      0.036   14.0   0.0      0.064   13.2   0.0    1.4  1  Rad17     Rad17 P-loop domain
      0.077   12.7   0.1       0.14   11.9   0.1    1.3  1  AAA_30    AAA domain
      0.093   12.5   0.2       0.22   11.3   0.2    1.6  1  AAA_29    P-loop containing region of AAA domain
        0.1   13.1   0.9       0.24   11.9   0.2    1.9  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 !   83.7   0.0   6.4e-27   1.7e-23       1     137 []      19     162 ..      19     162 .. 0.87
   2 ?   -2.4   0.0       2.4   6.3e+03      30      35 ..     228     233 ..     194     276 .. 0.65

  Alignments for each domain:
  == domain 1  score: 83.7 bits;  conditional E-value: 6.4e-27
                                   EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                      ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren.. 79 
                                   l+ vs+k      ++ +G+nGaGK+t lk+l++l kp  G  l++g ++++++ + +    +v+ + p+ fp  t+ ++  
  gi|13540996|ref|NP_110684.1|  19 LDGVSFKYDGEGAIGYLGPNGAGKTTTLKILTNLIKPSTGVALINGINVNKEPVKAFAVTGSVI-ESPSPFPYFTIMDSlm 98 
                                   689999999999***************************************8888887765555.667999999999999* PP

                                   ...........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                   ...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  80 ...........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                              e+++ i+++++ l+l+   d+++      LS+Gq+qrv++a+al+ +p++lllDEpt+
  gi|13540996|ref|NP_110684.1|  99 fvadirkidhrEAKKSIDEYADILKLPP-LDSKI----GDLSKGQRQRVVIAAALMPDPEILLLDEPTS 162
                                   **99999776666666777777777777.44444....9****************************96 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.4
                                   HHTTSS CS
                                   xxxxxx RF
                      ABC_tran  30 llagll 35 
                                   l+a+ l
  gi|13540996|ref|NP_110684.1| 228 LIAETL 233
                                   333333 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 !   13.6   0.6   1.7e-05     0.043       6      23 ..      36      53 ..      35      80 .. 0.76
   2 !   27.6   0.0   9.1e-10   2.3e-06     234     297 ..     131     190 ..      83     196 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.7e-05
                        AAA_21  6 GpNgsGKSnLLdaldlla 23
                                  GpNg+GK++ L++l  l 
  gi|13540996|ref|NP_110684.1| 36 GPNGAGKTTTLKILTNLI 53
                                  **************7773 PP

  == domain 2  score: 27.6 bits;  conditional E-value: 9.1e-10
                        AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTH 297
                                   + +lS G+++   +++a l  ++   +ll+DEp +gL+P  ++ + +l+k+ ++ +  +++++H
  gi|13540996|ref|NP_110684.1| 131 IGDLSKGQRQR-VVIAAALMPDP--EILLLDEPTSGLDPFEMKIIRDLIKAYKK-DKLILMSSH 190
                                   5688****999.55555555554..9*************999999999988877.777899999 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 ?   10.8   0.3   9.3e-05      0.24      31     208 ..      36     202 ..      14     210 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 9.3e-05
                                   ESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--.BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEEEEETTSEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N  31 GpNGSGKsnlldAilFvLGersakklrseklsdlihk.skekasvkkaeveitfdnedkklkiekeevsisrrvkrkgese 110
                                   GpNG+GK+  l  +       +   ++ ++  +li+  + +k+ vk   v+  + ++ +      + ++i+ +++   +  
  gi|13540996|ref|NP_110684.1|  36 GPNGAGKTTTLKIL----T--N--LIKPSTGVALINGiNVNKEPVKAFAVTGSVIESPSP----FPYFTIMDSLMFVAD-I 103
                                   55555555555443....1..1..344445555555533334444444444433333322....344555544444444.3 PP

                                   EEETTEEE-H..HHHHHHHHCTT-STT..CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHC CS
                                   xxxxxxxxxx..xxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 111 ykingkevtk..kevsellesagiske..lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeks 187
                                    ki+ +e++k   e++++l+   ++++   LS G+++ v +a   A  + +p+ + llDe  + LD  ++k++ +l+k+ +
  gi|13540996|ref|NP_110684.1| 104 RKIDHREAKKsiDEYADILKLPPLDSKigDLSKGQRQRVVIA---AALMPDPE-ILLLDEPTSGLDPFEMKIIRDLIKAYK 180
                                   4566666655446777777666655443379***99877655...44455555.779***********************9 PP

                                   TTSEEEEE-SS.HHHCCC-SCE CS
                                   xxxxxxxxxxx.xxxxxxxxxx RF
                         SMC_N 188 knaQfivislr.eemlekadkl 208
                                   k+  +++ s+  +e+ e +d +
  gi|13540996|ref|NP_110684.1| 181 KDKLILMSSHLlSEVSEVCDDV 202
                                   9988888887414444444555 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   2.5e-05     0.064      52      98 ..      36      83 ..      30     117 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.5e-05
                         Rad17 52 GPsGCgkstvvkvLskelgikl.rewlnpvslkepdnqksdfkgltek 98
                                  GP G gk+t++k+L+    ++     +n++++++ + +   + g ++ 
  gi|13540996|ref|NP_110684.1| 36 GPNGAGKTTTLKILTNLIKPSTgVALINGINVNKEPVKAFAVTGSVIE 83
                                  9**************998887635779999988777776666555544 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   5.3e-05      0.14      24      55 ..      35      78 ..      26      84 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 5.3e-05
                        AAA_30 24 tGpAGtGKttalkalreaweaa.g...........grviglApt 55
                                   Gp G+GKtt+lk l+++++ + g           ++v ++A t
  gi|13540996|ref|NP_110684.1| 35 LGPNGAGKTTTLKILTNLIKPStGvalinginvnkEPVKAFAVT 78
                                  69***************999886666666655555555555555 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.2   8.6e-05      0.22      13      50 ..      20      57 ..      14      64 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 8.6e-05
                        AAA_29 13 dghtieidlkgatlltGpsGsGKSTllDAiqalLvpak 50
                                  dg +++ d +ga+   Gp+G+GK+T l  ++ l+ p++
  gi|13540996|ref|NP_110684.1| 20 DGVSFKYDGEGAIGYLGPNGAGKTTTLKILTNLIKPST 57
                                  5667777777788889**********999999988887 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.2   9.4e-05      0.24      18      39 ..      28      49 ..       3      53 .. 0.69
   2 ?   -0.6   0.0      0.64   1.6e+03     103     103 ..     231     231 ..     128     297 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 9.4e-05
                        AAA_23 18 skgltlItGpNGaGKTTildAi 39
                                  + g     GpNGaGKTT l  +
  gi|13540996|ref|NP_110684.1| 28 GEGAIGYLGPNGAGKTTTLKIL 49
                                  55666667*********99766 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.64
                        AAA_23 103 t 103
                                   +
  gi|13540996|ref|NP_110684.1| 231 E 231
                                   1 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       581  (0.0324056); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 2027.49
//
Query:       gi|13540997|ref|NP_110685.1|  [L=275]
Description: ABC transporter permease [Thermoplasma volcanium GSS1]
Scores for complete 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-08   32.3  33.1    2.2e-07   30.5  33.1    1.7  1  ABC2_membrane_2  ABC-2 family transporter protein
     0.0042   16.7  23.8     0.0042   16.7  23.8    3.1  3  ABC2_membrane_5  ABC-2 family transporter protein
  ------ inclusion threshold ------
       0.22   11.8   3.9        7.9    6.8   0.1    2.9  2  DUF2537          Protein of unknown function (DUF2537)
        2.2    7.3  45.2        4.9    6.2  45.2    1.6  1  ABC2_membrane_3  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 !   30.5  33.1   4.9e-11   2.2e-07       8     286 ..      21     271 ..      14     273 .. 0.77

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 4.9e-11
               ABC2_membrane_2   8 frdlvrsrrfllltvllplidvalaylkdlgsslqseakaikeatlaleyveaasasdeaedtdqdlkvvstimavlipvi 88 
                                   f   +rs+rf++l +l ++i  a  +++dl    ++ + +++ a  +  +++                     ++++++vi
  gi|13540997|ref|NP_110685.1|  21 FTYYIRSKRFIGLLILTIVI-TAALIMLDLHYKYTTLKTENS-AIFFNGFLSS-------------------DLITFFAVI 80 
                                   56679***************.565666665555444333332.2222222222...................4678999** PP

               ABC2_membrane_2  89 aalfgadaiagEkergTlkllLskPvsRdeillgKfigglaiglaiavallatvllalaiilalgivlaledllllvvasv 169
                                   aa fg d+++ +    T    L +P+ R+ +++g   + +++    av++l++++ ++a++l+l  +++    + ++ +++
  gi|13540997|ref|NP_110685.1|  81 AAFFGGDLVSMDLGTNTAYYTLVQPIRRSVLYIGRYTSAFLA---SAVMVLIVYIGGMAMSLYLYGNITDITGISFA-LAL 157
                                   ******************************************...****************9998888655444444.444 PP

               ABC2_membrane_2 170 lllllvvflalglllSsvarssreaaalalglfvvlailvpivlygvaellagpavpqeindflsllsptsayntllneil 250
                                   l++l+  +l+++ l+S+++r+ +  + ++++++++ + +++++l+g+a  +  + v  ++   +++l     y+t   +  
  gi|13540997|ref|NP_110685.1| 158 LYMLA--LLSFSSLFSAIFRTPTIGLVMSIIFLIIIYPAIQGILSGLAGVNPWMFV--TYAGQILYLVFEKKYTTYAVTHV 234
                                   45553..49*************************************9999998877..56666666655555555444444 PP

               ABC2_membrane_2 251 agsdlna.lgstatnllilllllavllvlgyvlFkrk 286
                                    + ++ +      +++ i+l++++++l +++ +F  k
  gi|13540997|ref|NP_110685.1| 235 GRISFYTfNPTLLESIYIMLGYIVIFLLISAAVFTYK 271
                                   44434443445567899**************999866 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 ?    0.7   2.5     0.071   3.2e+02     121     143 ..      33      55 ..      10      71 .. 0.50
   2 !   16.7  23.8   9.3e-07    0.0042      31     162 ..      68     196 ..      61     223 .. 0.77
   3 ?    1.2   3.8      0.05   2.2e+02     108     135 ..     241     268 ..     226     271 .. 0.70

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.071
               ABC2_membrane_5 121 liglvialiflaivlPlyfkfgv 143
                                   l++l i++++  i+l l +k+ +
  gi|13540997|ref|NP_110685.1|  33 LLILTIVITAALIMLDLHYKYTT 55 
                                   23333444444444444444444 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 9.3e-07
               ABC2_membrane_5  31 flndsvllifsilslvisiililttlsyDekskwnkylltLPvtrkeiVksKYlfvlililiailitllllii.avlikgn 110
                                   fl++++++    +++vi+++    ++s D   ++ +y+l  P++r+ + + +Y ++++ +++++li+++ ++  + +++gn
  gi|13540997|ref|NP_110685.1|  68 FLSSDLIT----FFAVIAAFFGGDLVSMDLGTNTAYYTLVQPIRRSVLYIGRYTSAFLASAVMVLIVYIGGMAmSLYLYGN 144
                                   44444444....44555555567899********************************************9864889**** PP

               ABC2_membrane_5 111 vtisevllsiliglvialiflaivlPlyfkfgvekgrivliiiifgiif.llv 162
                                   +t + + +s++++l+++l++l+++  +  +f + ++ +v+ ii+++ii+  + 
  gi|13540997|ref|NP_110685.1| 145 IT-DITGISFALALLYMLALLSFSSLFSAIFRTPTIGLVMSIIFLIIIYpAIQ 196
                                   97.99999*********999999999999999999998888888887653332 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.05
               ABC2_membrane_5 108 kgnvtisevllsiliglvialiflaivl 135
                                   + n t+ e+++ +l ++vi+l+++a v+
  gi|13540997|ref|NP_110685.1| 241 TFNPTLLESIYIMLGYIVIFLLISAAVF 268
                                   3345677888889999999998888877 PP

>> DUF2537  Protein of unknown function (DUF2537)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.6    0.0065        29      33      54 ..     121     142 ..      97     164 .. 0.75
   2 ?    6.8   0.1    0.0018       7.9       5      38 ..     179     212 ..     176     216 .. 0.93

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0065
                       DUF2537  33 pllavvvnvvvvaGlaPtvwll 54 
                                    + av+v +v  +G+a +++l+
  gi|13540997|ref|NP_110685.1| 121 LASAVMVLIVYIGGMAMSLYLY 142
                                   4457777777778888777765 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0018
                       DUF2537   5 tGltvavfvavvvavavvalslalaevhpllavv 38 
                                    Gl++++++ +++  a+  + ++la v+p++ v 
  gi|13540997|ref|NP_110685.1| 179 IGLVMSIIFLIIIYPAIQGILSGLAGVNPWMFVT 212
                                   69****************************9885 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 ?    6.2  45.2    0.0011       4.9     142     344 ..      48     265 ..       4     266 .. 0.63

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0011
               ABC2_membrane_3 142 saninvestqleeelsnvasflvg.liliilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllql 221
                                      ++++++ +e+++  ++ fl + li ++++ i a+f    +  +  +++    lv +++++ ++++++++ fl++++++
  gi|13540997|ref|NP_110685.1|  48 DLHYKYTTLKTENSAIFFNGFLSSdLITFFAV-IAAFFGGDLVSMDLGTNTAYYTLVQPIRRSVLYIGRYTSAFLASAVMV 127
                                   33444444444555555555655554444444.4444466666777888888899999**********************9 PP

               ABC2_membrane_3 222 llill..lafglgipfg.nl....glllllfllfglayialgyllsslfknsetaqilifivilllsgffgglfp.ledlp 294
                                   l++ +  +a +  +  + n+    g+ + l ll++la+++++ l+s++f++++ + ++ +i+++++  ++ g+ + l  ++
  gi|13540997|ref|NP_110685.1| 128 LIVYIggMAMS--LYLYgNItditGISFALALLYMLALLSFSSLFSAIFRTPTIGLVMSIIFLIIIYPAIQGILSgLAGVN 206
                                   98776586555..333323344458999************************99998666666655555555543344444 PP

               ABC2_membrane_3 295 .....salkwifsii....Pffapglgllrlitgdplweillsliilalfavvylllal 344
                                        +++ +i++++     +++      r+++++ + ++l s+ i+++ +v++ll+++
  gi|13540997|ref|NP_110685.1| 207 pwmfvTYAGQILYLVfekkYTTYAVTHVGRISFYTFNPTLLESIYIMLGYIVIFLLISA 265
                                   45444334444444333333444444444666777444588***************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       958  (0.053433); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); 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):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.32s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 1724.49
//
Query:       gi|13540998|ref|NP_110686.1|  [L=202]
Description: Zn-dependent hydrolase [Thermoplasma volcanium GSS1]
Scores for complete 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-23   81.8   1.2    7.2e-23   81.6   1.2    1.0  1  Lactamase_B    Metallo-beta-lactamase superfamily
    7.1e-07   28.9   0.0      1e-06   28.4   0.0    1.3  1  Lactamase_B_2  Beta-lactamase superfamily domain
      3e-05   24.0   0.0    5.1e-05   23.2   0.0    1.7  1  Lactamase_B_3  Beta-lactamase superfamily domain
    4.6e-05   22.9   0.0    0.00014   21.4   0.0    1.7  2  Lactamase_B_6  Metallo-beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.6   1.2   1.6e-26   7.2e-23       3     197 .]      12     196 ..      10     196 .. 0.93

  Alignments for each domain:
  == domain 1  score: 81.6 bits;  conditional E-value: 1.6e-26
                                   CCSSEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCH CS
                   Lactamase_B   3 pdpvnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalf 83 
                                   ++ +n+y +  ++ ++L+D+Gt +  +++     + ++ + ++d v++TH+H+DHiGgl ++ve++  +v++  +e++   
  gi|13540998|ref|NP_110686.1|  12 GVVANCYSLKIGDVTVLVDSGTRSGGKKII---DYYERSGGKPDVVVITHHHADHIGGLSEIVERFHPKVYVPDLELKIVS 89 
                                   5678************************95...79999******************************************* PP

                                   CHHHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTSSHHCCCCCC.T CS
                   Lactamase_B  84 meeaddaasrkglllagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDallagetgridltl 164
                                   +ee+ +a+  + + +++++  k  +++ + +   +++++ +v+ +pgh+ g+ ++ +++ k++f+GDa  +    ++    
  gi|13540998|ref|NP_110686.1|  90 GEEKPPAPKSF-IGRIIARSLKFNPVKAIVPASKLDVPGIEVMATPGHTIGSTSYILDDFKLIFSGDAAVESGGKLVIN-- 167
                                   ****5554444.4499999999************************************************777777777.. PP

                                   TCEEE-SHCHHHHHHHHHHHHHHHCHSEEEESS CS
                   Lactamase_B 165 rgaevrdpsdaekyldsllklaglkaevlvpgH 197
                                         ++++   + +sl+ +a +k  +++pgH
  gi|13540998|ref|NP_110686.1| 168 ----KTFTYEINGAERSLETIASMKGHTVLPGH 196
                                   ....79*************************** PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.0   2.3e-10     1e-06      29     110 ..      49     135 ..      27     161 .. 0.70

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 2.3e-10
                                   .SEEEEE-SS--HHHHGGGGCCCC.C--EEEEEEEEHHHHHHCCTTCGHHHCHTT.........TTEEEEEE-TTSEEEEC CS
                 Lactamase_B_2  29 ppidaVllthaHyDHlaglltlre.lrpkklplyapkgvlavleanfvylaleee.........pavnvheldwgesfelg 99 
                                    + d+V++th H+DH+ gl  + e ++pk   +y+p+  l++++ + ++ a +           ++ +v+ + +  ++++ 
  gi|13540998|ref|NP_110686.1|  49 GKPDVVVITHHHADHIGGLSEIVErFHPK---VYVPDLELKIVSGEEKPPAPKSFigriiarslKFNPVKAIVPASKLDVP 126
                                   578*********************99985...9999887777777765555444455556644444444444455555553 PP

                                   STTEEEEEEEE CS
                 Lactamase_B_2 100 dggleitatpa 110
                                     g+e+ atp 
  gi|13540998|ref|NP_110686.1| 127 --GIEVMATPG 135
                                   ..666666665 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 !   23.2   0.0   1.1e-08   5.1e-05       8      50 ..      16      64 ..      13     196 .. 0.85

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 1.1e-08
                 Lactamase_B_3  8 nsflletagarilvDPf.....ka.nlgyeppaeeaDlvlisqaledHa 50
                                  n++ l+++++++lvD +     k+    ye++  ++D+v+i+++++dH 
  gi|13540998|ref|NP_110686.1| 16 NCYSLKIGDVTVLVDSGtrsggKKiIDYYERSGGKPDVVVITHHHADHI 64
                                  9**************996555422233455555***************6 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 !   21.4   0.0   3.1e-08   0.00014       2      61 ..      20      76 ..      19      81 .. 0.90
   2 ?   -1.7   0.0      0.35   1.6e+03     138     149 ..     134     145 ..     117     148 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 3.1e-08
                 Lactamase_B_6  2 LeldnvkiLlDvGwdeskvslesalkelekviptvdliLLshatlehlGayallyakfks 61
                                  L++ +v++L+D G+++     +++++++e+   + d+++++h  ++h+G+++ ++ +f+ 
  gi|13540998|ref|NP_110686.1| 20 LKIGDVTVLVDSGTRSGG---KKIIDYYERSGGKPDVVVITHHHADHIGGLSEIVERFHP 76
                                  7899***********973...579***************************999988865 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.35
                 Lactamase_B_6 138 aGhtlGGtiWki 149
                                    Ght+G t + +
  gi|13540998|ref|NP_110686.1| 134 PGHTIGSTSYIL 145
                                   59****998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       342  (0.0190752); 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 0.33s 00:00:00.82 Elapsed: 00:00:00.50
# Mc/sec: 1216.45
//
Query:       gi|13540999|ref|NP_110687.1|  [L=398]
Description: galactonate dehydratase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.4e-49  167.4   0.0    4.8e-49  166.9   0.0    1.1  1  MR_MLE_C  Enolase C-terminal domain-like
    7.1e-12   45.6   0.0    1.3e-11   44.8   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 !  166.9   0.0   5.3e-53   4.8e-49       2     213 ..     145     361 ..     144     367 .. 0.95

  Alignments for each domain:
  == domain 1  score: 166.9 bits;  conditional E-value: 5.3e-53
                                   HHHHHHHHHHHHT-SEEEEETSSS........HHHHHHHHHHHHHHHHTTTSTSEEEEE-TTTSBHHHHHHHHHHHGGGTE CS
                      MR_MLE_C   2 laeearelvaeqgfravKlkvggd........dvaedvervravreavgpgddvdlmvDanqawdlatAirvareleeldl 74 
                                   ++++a+e v++ gf+a+K++++gd         ++     v a+r ++g+  +vdl+++ +++++  +Ai+ + +lee+++
  gi|13540999|ref|NP_110687.1| 145 FVKKAKEVVKM-GFTAMKFDPFGDnydtitneGIENARNIVGALRSEFGE--KVDLLIEYHGRFSKIAAIKAGMALEEFKP 222
                                   57789886666.************************************66..67*************************** PP

                                   SEEESSSSTTTHHHHHHHHHHHH.SSEEEESTTSSSHHHHHHHHHHTSESEEEEBHHHHTSHHHHHHHHHHHHHTT-EEEE CS
                      MR_MLE_C  75 lwlEEPvppeddleglaelrara.sipiaagEslysradfrelleagavdivqpdvsrvgGitearkvaalaeafgvpvap 154
                                   +++EEP++p d  ++l +l+ +  ++pia+gE++ + + f+++++++ vdi+qpd++++gGi ea+k+aa+a+ fg+p+ap
  gi|13540999|ref|NP_110687.1| 223 YFYEEPLHP-DLDHDLLDLK-QYyKVPIALGERVLNKKIFARFISQKLVDIIQPDLTNSGGILEAKKIAAIADGFGIPIAP 301
                                   *********.6788899999.6679******************************************************** PP

                                   BSCSSHHHHHHHHHHHHTTTTBEEEEEEGGGGH.TSGCSBSSSSEEETTEEECTSSSBTS CS
                      MR_MLE_C 155 Hsgsgglglaaslhlaaaipnllileyfldael.leeelleeplevedGrvtvpdgpGlG 213
                                   H+  g++++aa+l + +++ n+ i+e+f+ +++ ++++l  + ++ e+G++++    G+G
  gi|13540999|ref|NP_110687.1| 302 HNAFGPIQTAATLNVDTTLTNFAIQESFEMFWPdWKKNLMASGYKLENGYFRLTGDAGIG 361
                                   **658*************************************************999999 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 !   44.8   0.0   1.4e-15   1.3e-11      27     117 .]      27     121 ..      19     121 .. 0.94

  Alignments for each domain:
  == domain 1  score: 44.8 bits;  conditional E-value: 1.4e-15
                                   EEEEEEEEECTTEEEEEEEE-STTGHHHHHHHHHHHHHHHHTTSBTTHHHHHHHHHHHHCSS......CHHHHHHHHHHHH CS
                      MR_MLE_N  27 slvlvkietseGvvGigeatsvggraetikaelddhlapllvgkdaanisdlaqllkravlg......nmsAkaaidmAlw 101
                                   ++ lvk+++++G+vG gea +   + + +   +++ +a    gkd  n+++ +  ++r  ++      ++sA +a ++A w
  gi|13540999|ref|NP_110687.1|  27 TILLVKLTSADGLVGYGEAPTTL-MTLPVLESMKE-VARVFKGKDFFNVEQNVFDFYRNSFYlpvsmeATSALSAFEIASW 105
                                   6789**************98888.88999888887.************************999***999************ PP

                                   HHHHHHTTSBHHHHTT CS
                      MR_MLE_N 102 DlkakalnlpladLlG 117
                                   Dl +k l++p+++L+G
  gi|13540999|ref|NP_110687.1| 106 DLIGKELGTPVYKLIG 121
                                   ***************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (398 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       386  (0.0215294); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.60u 0.31s 00:00:00.90 Elapsed: 00:00:00.53
# Mc/sec: 2262.43
//
Query:       gi|13541000|ref|NP_110688.1|  [L=238]
Description: ATPase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-10   39.8   0.0    3.8e-10   39.5   0.0    1.1  1  ATPase    KaiC
  ------ inclusion threshold ------
      0.067   12.5   0.0       0.08   12.3   0.0    1.2  1  DnaB_C    DnaB-like helicase C terminal 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 !   39.5   0.0   4.2e-14   3.8e-10       1     160 [.      14     171 ..      14     193 .. 0.78

  Alignments for each domain:
  == domain 1  score: 39.5 bits;  conditional E-value: 4.2e-14
                        ATPase   1 vktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdlekleeeg 81 
                                   ++tgI+  De+l+gG+  +  + ++G+  + K  f  +F+ ++a++ g +++++ v+ ++e+l  + ++ G dle++    
  gi|13541000|ref|NP_110688.1|  14 ISTGIPRVDELLYGGFDGRDNIVVSGNNFSQKRSFIYNFIKSSANS-GMKVIIINVDGSSESLLADLARRGTDLENII--- 90 
                                   68*****************************************999.***************************8764... PP

                        ATPase  82 klaiidasesaeesaee...kdkedleelieelaeaikeika.krvvi..DsitglayeekeavaReilrqlvrvlkklgv 156
                                      ++d ++++ +++     +  +d++++++ l++++ + +  k  +    s t++   + +++ R+ + qlv++ +k+ +
  gi|13541000|ref|NP_110688.1|  91 ---LLDGFSKNFQEKVPpnaEVIDDPSNVSSVLKQYMLRAQKeKDFIFvfLSATPY-LMDFNDQNRKFFVQLVHWNRKNSL 167
                                   ...55555554443322455888899999999988876655524444301455555.788888899999999988877766 PP

                        ATPase 157 Tail 160
                                    +  
  gi|13541000|ref|NP_110688.1| 168 LSTY 171
                                   5555 PP

>> DnaB_C  DnaB-like helicase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0     9e-06      0.08       2      69 ..      14      81 ..      13     136 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 9e-06
                                  BXSSTHHHHHHC.TSBXTTXEEEEEEXTTSSHHHHHHHHHHHHHHCSTSEEEEEESSSXHHHHHHHHHH CS
                                  xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        DnaB_C  2 lstgfkdLDklt.sGlqkgdliiiAarpsmGktalalniaenaavkeklpvavfslemsaeqlvqRlls 69
                                  +stg  ++D+l+ +G+   d i++ +     k ++  n++++ a+ + ++v++++++ s+e+l++ l  
  gi|13541000|ref|NP_110688.1| 14 ISTGIPRVDELLyGGFDGRDNIVVSGNNFSQKRSFIYNFIKSSAN-SGMKVIIINVDGSSESLLADLAR 81
                                  7899999**8752789999**********************9996.7889************9876655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       543  (0.0302861); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1534.43
//
Query:       gi|13541001|ref|NP_110689.1|  [L=69]
Description: hypothetical protein TVN0170 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      1e-09   38.5   1.9    1.5e-09   37.9   1.1    1.7  2  zf-CDGSH    Iron-binding zinc finger CDGSH type
  ------ inclusion threshold ------
      0.065   13.7   0.0      0.081   13.4   0.0    1.1  1  S-l_SbsC_C  S-layer protein SbsC C-terminal domain
      0.094   11.8   0.0      0.094   11.8   0.0    1.1  1  LigB        Catalytic LigB subunit of aromatic ring-opening d


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 !   37.9   1.1   2.5e-13   1.5e-09      19      48 .]      12      41 ..       3      41 .. 0.79
   2 ?   -1.7   0.0      0.57   3.4e+03       9      21 ..      49      61 ..      43      65 .. 0.61

  Alignments for each domain:
  == domain 1  score: 37.9 bits;  conditional E-value: 2.5e-13
                      zf-CDGSH 19 svelregrevvaLCrCgrSknkPfCDgsHk 48
                                  ++ ++ g+++v +C Cg+S++kP+CDg+Hk
  gi|13541001|ref|NP_110689.1| 12 PYVVKVGDREVHICGCGLSSHKPYCDGTHK 41
                                  4555555566*******************7 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.57
                      zf-CDGSH  9 dvelvdadgesve 21
                                  ++ + dad+++ e
  gi|13541001|ref|NP_110689.1| 49 KIYIYDADKKREE 61
                                  4555666666554 PP

>> S-l_SbsC_C  S-layer protein SbsC C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   1.4e-05     0.081      17      72 ..       8      58 ..       2      60 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.4e-05
                    S-l_SbsC_C 17 stgnsykykvssssvetpaagsklsgaaaaytsgtditditatagqyillyeVDas 72
                                  + ++ y++kv++ +v +   g +  +   +y  gt   +it  +g++i +y  D++
  gi|13541001|ref|NP_110689.1|  8 TRDHPYVVKVGDREVHICGCGLSSHK---PYCDGTH--KITTDEGEKIYIYDADKK 58
                                  567889*****888888888876555...7999966..68**************86 PP

>> LigB  Catalytic LigB subunit of aromatic ring-opening dioxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   1.6e-05     0.094     167     196 ..      16      52 ..      11      69 .] 0.73

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.6e-05
                          LigB 167 el.dknvlilgsGglsHqlegdeaakadaq......t 196
                                   +  d++v+i g G  sH++ +d + k +++      +
  gi|13541001|ref|NP_110689.1|  16 KVgDREVHICGCGLSSHKPYCDGTHKITTDegekiyI 52 
                                   4459******************999877765555540 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); 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:                         3  (0.000167327); expected 0.2 (1e-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 0.31s 00:00:00.71 Elapsed: 00:00:00.47
# Mc/sec: 445.50
//
Query:       gi|13541002|ref|NP_110690.1|  [L=200]
Description: folate-dependent phosphoribosylglycinamide formyltransferase [Thermoplasma volcanium GSS1]
Scores for complete 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-44  149.7   0.0    8.2e-44  149.5   0.0    1.1  1  Formyl_trans_N  Formyl transferase


Domain annotation for each model (and alignments):
>> Formyl_trans_N  Formyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  149.5   0.0   4.6e-48   8.2e-44       2     181 .]       3     181 ..       2     181 .. 0.96

  Alignments for each domain:
  == domain 1  score: 149.5 bits;  conditional E-value: 4.6e-48
                                   EEEEEESESSHHHHHHHHHHHHTTSECEEEEEEESCTTEHCHHHHHHCCHCCCECHHCCSCCCCCCCHHHHHHHHCTT-SE CS
                Formyl_trans_N   2 kivvlisgtgsnlqalldalkkgsleadvvlvvsnkdkaaglekaeaasiptkvfeekkleprsqfeeelaeelkelkadl 82 
                                   ki v++sg+g+ lqa++da+k++++++++  v+ +++ +a +++ae+++ip +++++ ++     f+++l+ee+++ k d+
  gi|13541002|ref|NP_110690.1|   3 KICVMVSGNGTTLQAIIDAVKNKKIDVEISKVIADRECLA-IKRAEDNNIPYRILKRGEY-----FQRDLKEEMRSSKCDF 77 
                                   89********************************987666.*************988776.....555999********** PP

                                   EEEES--S---HHHHHSSTTSEEEEESSSTTTT.....BSS-HHHHHHHTTSSEEEEEEEE--SSSSTS-EEEEEEEE--T CS
                Formyl_trans_N  83 ivlagymkllpkelvqavrlkilniHpSLLPrf.....kGaaaiqraleaGdketGvtihfvdeelDtGailaqkkveiia 158
                                    vlag++ +++ke+ +++r +i+n HpSLLP+f     +G +++++++++G k++G+t+hfv++e+D G+i++q  v +  
  gi|13541002|ref|NP_110690.1|  78 FVLAGFLSIIGKEITDEFRYRIINTHPSLLPCFgghgfYGRKVHEAVIKSGMKYSGCTVHFVTDEVDGGPIILQRCVSVED 158
                                   *********************************9999999***************************************** PP

                                   T--HHHHHHHHHHHHHHHHHHHH CS
                Formyl_trans_N 159 edtkeeleqrvadaehkalveal 181
                                    d++++le++++  eh+a+vea+
  gi|13541002|ref|NP_110690.1| 159 VDDAQSLEEKIHGIEHSAIVEAI 181
                                   ********************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       658  (0.0367003); expected 358.6 (0.02)
Passed bias filter:                      559  (0.0311785); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.33s 00:00:00.83 Elapsed: 00:00:00.50
# Mc/sec: 1207.20
//
Query:       gi|13541003|ref|NP_110691.1|  [L=126]
Description: hypothetical protein TVN0172 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       292  (0.0162865); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 791.75
//
Query:       gi|13541004|ref|NP_110692.1|  [L=190]
Description: thymidylate kinase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.3e-25   88.2   0.4    1.2e-24   87.0   0.4    1.6  1  Thymidylate_kin  Thymidylate kinase
    6.8e-08   32.6   0.1    4.2e-07   30.0   0.1    1.9  1  dNK              Deoxynucleoside kinase
    2.5e-05   24.8   0.2    0.00016   22.3   0.2    2.2  1  AAA_18           AAA domain
    0.00035   20.1   0.0    0.00049   19.6   0.0    1.2  1  KTI12            Chromatin associated protein KTI12
     0.0004   20.7   0.0    0.00051   20.3   0.0    1.4  1  AAA_28           AAA domain
     0.0031   17.7   0.0     0.0054   16.9   0.0    1.5  1  AAA_33           AAA domain
     0.0035   17.4   0.2     0.0062   16.6   0.2    1.8  1  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
     0.0066   16.7   0.0      0.009   16.3   0.0    1.6  1  AAA_22           AAA domain
     0.0073   16.8   0.0      0.012   16.2   0.0    1.6  1  ABC_tran         ABC transporter
     0.0079   15.9   0.0      0.012   15.3   0.0    1.3  1  AAA_30           AAA domain
     0.0083   15.8   0.0      0.021   14.5   0.0    1.6  2  SRP54            SRP54-type protein, GTPase domain
  ------ inclusion threshold ------
      0.012   15.6   0.0       0.03   14.2   0.0    1.7  2  MobB             Molybdopterin guanine dinucleotide synthesis
      0.022   14.7   0.0      0.045   13.7   0.0    1.5  1  NACHT            NACHT domain
      0.026   14.6   0.7       0.15   12.1   0.7    1.9  1  tRNA_lig_kinase  tRNA ligase kinase domain
       0.03   14.7   0.0      0.031   14.7   0.0    1.3  1  AAA_16           AAA ATPase domain
      0.034   14.0   0.1      0.092   12.6   0.0    1.7  2  NTPase_1         NTPase
      0.037   13.3   0.0       0.33   10.2   0.0    2.0  2  Herpes_TK        Thymidine kinase from herpesvirus
      0.045   13.6   0.1      0.081   12.8   0.1    1.5  1  APS_kinase       Adenylylsulphate kinase
      0.078   12.7   0.1       0.11   12.2   0.1    1.6  1  AAA_24           AAA domain
      0.082   13.9   0.0       0.18   12.8   0.0    1.9  1  LytR_C           LytR cell envelope-related transcriptional a


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 !   87.0   0.4   1.3e-27   1.2e-24       1     160 [.       5     159 ..       5     180 .. 0.81

  Alignments for each domain:
  == domain 1  score: 87.0 bits;  conditional E-value: 1.3e-27
                                   EEESTTSSHHHHHHHHHHHHHHTTE.EEEESSSTTSHHHHHHHHHHHTCS---HHHHHHHHHHHHHHTTHHHHHHHHHTT- CS
               Thymidylate_kin   1 iEGlDGaGKttqaellkerlkeegikvvltrepggteiGekirelllkeeeleeqteallfaadriehleekikpalkqgk 81 
                                   +EG+DGaGKtt a+ l + l++eg +v+ltrep+     + ir++     e ++  + + f+ dr ++++++i ++l++g+
  gi|13541004|ref|NP_110692.1|   5 VEGIDGAGKTTLAKSLSSLLEKEGFRVFLTREPT-----DDIRNY-----EGDDVELFIKFTLDR-YKHQKEIRKKLNEGF 74 
                                   7*********************************.....677777.....5588999999*****.777779********* PP

                                   EEEEES-HHHHHHHH..HTTTTTTC.....HHHHHHGGGTTSE-SEEEEEESSHHHHHTSCCTTSSTTTSHHHHHHHHHHH CS
               Thymidylate_kin  82 tvivdRylfSslaYq..gakegvdl.....dlvlslnedvllkPdltflldvdpevalkRlakrdeldeeeeeqldflrkv 155
                                   +vi+dRy+ Ss+aY+  ga+ +++      +++ ++++ ++ +Pd+ +l++vd++v+l R++kr+    + +eq++ l++ 
  gi|13541004|ref|NP_110692.1|  75 VVISDRYIRSSYAYEmkGAAAALGSeekakEWMDCVSNIITIRPDINILVQVDVQVGLDRISKRNG-TITHFEQRERLNEA 154
                                   **************7334566666511111455566555555***********************9.89999999988877 PP

                                   HHHHH CS
               Thymidylate_kin 156 reryl 160
                                    + y+
  gi|13541004|ref|NP_110692.1| 155 LKIYN 159
                                   66554 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   0.1   4.7e-10   4.2e-07       1     146 [.       3     141 ..       3     163 .. 0.77

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 4.7e-10
                                   EEEEESTTSSHHHHHHHHHCCST...CEEE..E-HHHHCCSSSSHHHHHHHHSHHHHHHHHHHHHHHHHHHHHHCHHSSS- CS
                           dNK   1 ivveGnIgaGKstlvklLskklg...vkvf..eEpvdkwtnvqknlLekfYkdpsrwsfalqtyvllsrlkqqlealatkq 76 
                                   i+veG  gaGK+tl+k Ls  l+   + vf  +Ep d+ +n ++  +e+f k      f+l+ y   + +++    l+++ 
  gi|13541004|ref|NP_110692.1|   3 IAVEGIDGAGKTTLAKSLSSLLEkegFRVFltREPTDDIRNYEGDDVELFIK------FTLDRYKHQKEIRKK---LNEGF 74 
                                   89**************999988766666653379999998888888888755......666666666666655...4889* PP

                                   EEEEES-HHHHHHTHHHHHHHTTSS.-HHHHHHHHHHHHHHHHHCCH-SEEEEEE--HHHHHHHHHHCTTC CS
                           dNK  77 vvvleRsiysdryiFakalaekgtl.seeelkiykelldnlleelakpdlliYLkasletclerikkRgre 146
                                   vv+ +R i s+   + ++  +   l see+ k + +  +n++ ++  pd+ i +++++++ l ri kR+ +
  gi|13541004|ref|NP_110692.1|  75 VVISDRYIRSSY-AY-EMKGAAAALgSEEKAKEWMDCVSNII-TIR-PDINILVQVDVQVGLDRISKRNGT 141
                                   *********999.44.55555555416666777777777777.565.*********************976 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.2   1.7e-07   0.00016       1     114 [.       3     139 ..       3     155 .. 0.56

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 1.7e-07
                        AAA_18   1 IlltGtpGvGKttlakeLskrlgfgvnlrdvakenglllevdpe.....aldeskrldedkldklldaleenssaleegkn 76 
                                   I++ G+ G+GKttlak Ls++l    +   v+  +++ ++  ++     +      l ++++    +  +e++++l eg +
  gi|13541004|ref|NP_110692.1|   3 IAVEGIDGAGKTTLAKSLSSLL--EKEGFRVFLTREPTDDIRNYegddvE------LFIKFTLDRYKHQKEIRKKLNEGFV 75 
                                   89******************99..77777777777777777777433221......2333333333333333333333333 PP

                        AAA_18  77 lvidghlaeleseaakdikk...........................vvLtaspeelleRlekRg 114
                                   ++ d  +   + +++k +                             + ++++ ++ l+R++kR+
  gi|13541004|ref|NP_110692.1|  76 VISDRYIRSSYAYEMKGA-AaalgseekakewmdcvsniitirpdinILVQVDVQVGLDRISKRN 139
                                   222222222222222222.1244444444445555556666666666777777777777777776 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   5.4e-07   0.00049       4      90 ..       3      91 ..       1     102 [. 0.81

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 5.4e-07
                                  EEEE--TTSSHHHHHHHHHHHHHHTT--EEEE-...THHHH.TTSSS--GGGHHHHHHHHHHHHHHHHTT.SEEEE-S---SH CS
                         KTI12  4 vvltGlPssGKstrakeLakaleeekrsvvvid...deslgiekdsykdsakekalRsslrsavkrdLskekvVIvDslnyik 83
                                  + + G+  +GK+t+ak L++ le+e+ +v + +   d+  + e d+++   k    R + +++++++L++  vVI D   yi+
  gi|13541004|ref|NP_110692.1|  3 IAVEGIDGAGKTTLAKSLSSLLEKEGFRVFLTReptDDIRNYEGDDVELFIKFTLDRYKHQKEIRKKLNEGFVVISDR--YIR 83
                                  667888899**********************99442344447777788888888889*******************96..776 PP

                                  .HHHHHHH CS
                         KTI12 84 .gfRYeLy 90
                                   ++ Ye+ 
  gi|13541004|ref|NP_110692.1| 84 sSYAYEMK 91
                                  35778875 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   5.7e-07   0.00051       2      89 ..       3      89 ..       2     161 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 5.7e-07
                        AAA_28  2 ivitGgestGKTtlleaLa...ar.gypvv..pEaareileeklakgedalpwvedllafaervleeqleeeaaaaankvlfc 78
                                  i++ G  ++GKTtl++ L+   ++ g++v+  +E+  +i + ++++        e +++f   + ++q+e  ++ +++ v+++
  gi|13541004|ref|NP_110692.1|  3 IAVEGIDGAGKTTLAKSLSsllEKeGFRVFltREPTDDIRNYEGDDV-------ELFIKFTLDRYKHQKEIRKKLNEGFVVIS 78
                                  7889999************5552269999977888887775444333.......34799999999***9999999******** PP

                        AAA_28 79 DrglldtlaYa 89
                                  Dr +  ++aY 
  gi|13541004|ref|NP_110692.1| 79 DRYIRSSYAYE 89
                                  ****9999995 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0     6e-06    0.0054       3     120 ..       4     140 ..       2     158 .. 0.61

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 6e-06
                        AAA_33   3 llvGlpGsGKstlaerl...lkklg..avllssdtlrrrlfgtdqqsktdytrvldrlyqilnelarkalsagrnvildat 78 
                                    + G  G+GK+tla++l   l+k+g  ++l +++t  + +++ + ++ +  ++++ + y+++ + +rk+l +g+ vi d  
  gi|13541004|ref|NP_110692.1|   4 AVEGIDGAGKTTLAKSLsslLEKEGfrVFLTREPT--DDIRNYEGDDVELFIKFTLDRYKHQ-KEIRKKLNEGFVVISDRY 81 
                                   578*************8666777777444445554..7788877777777888887777776.788889999988888876 PP

                        AAA_33  79 nls..................rrerarflklarrlgvpvrivvvetdeetlkeRlakRaa 120
                                    +s                  ++e+++ ++    +  p+  + v++d ++  +R+ kR+ 
  gi|13541004|ref|NP_110692.1|  82 IRSsyayemkgaaaalgseekAKEWMDCVSNIITIR-PDINILVQVDVQVGLDRISKRNG 140
                                   554333333333333333222222222222222222.45556666666666666666665 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.2   6.9e-06    0.0062       9      32 ..      10      33 ..       2     168 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 6.9e-06
                                  TSSHHHHHHHHHHHHHHTT--EEE CS
                                  xxxxxxxxxxxxxxxxxxxxxxxx RF
                          CbiA  9 GvGKTtlaanLaralarrglrVll 32
                                  G+GKTtla +L  +l ++g+rV+l
  gi|13541004|ref|NP_110692.1| 10 GAGKTTLAKSLSSLLEKEGFRVFL 33
                                  9*********************87 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0     1e-05     0.009       7      65 ..       2      75 ..       1     176 [. 0.79

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1e-05
                        AAA_22  7 ilvvtGesGtGKTtllrrlleqldeeakaee..............erpevv.fvtlpsstsskdllrellralg 65
                                  +++v G  G+GKTtl++ l + l++e +                  ++e++ ++tl   + +k+++++l + + 
  gi|13541004|ref|NP_110692.1|  2 FIAVEGIDGAGKTTLAKSLSSLLEKEGFRVFltreptddirnyegDDVELFiKFTLDRYKHQKEIRKKLNEGFV 75
                                  7999******************9765444337777777777776533333347777777777777777776665 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   1.3e-05     0.012      15      80 ..       4      85 ..       2     181 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.3e-05
                                  EEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS..--S-TTSBHHHH...............H CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxx...............x RF
                      ABC_tran 15 aivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe..pqlfpeltvren...............e 80
                                  a+ G  GaGK+tL+k l+ ll+++  ++ l  +++++  ++     ++ + +   ++ + ++++r++                
  gi|13541004|ref|NP_110692.1|  4 AVEGIDGAGKTTLAKSLSSLLEKEGFRVFLTREPTDD-IRNYEGDDVELFIKFtlDRYKHQKEIRKKlnegfvvisdryirsS 85
                                  677899***************9887788555555555.333333333333333223333333333334455555555554442 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.4e-05     0.012      22      51 ..       4      33 ..       1      40 [. 0.92

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.4e-05
                        AAA_30 22 vltGpAGtGKttalkalreaweaaggrvig 51
                                  +++G  G+GKtt+ k+l  ++e++g+rv++
  gi|13541004|ref|NP_110692.1|  4 AVEGIDGAGKTTLAKSLSSLLEKEGFRVFL 33
                                  789************************986 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   2.3e-05     0.021       4      35 ..       3      34 ..       1      43 [. 0.90
   2 ?   -2.1   0.0       2.8   2.6e+03      96     131 ..     101     136 ..      97     158 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.3e-05
                                  EEEEESTTSSHHHHHHHHHHHHHHTTS-EEEE CS
                         SRP54  4 illvGlqGaGKTttlaKLaallkkegkkvllv 35
                                  i++ G+ GaGKTt +  L+ ll+keg +v l 
  gi|13541004|ref|NP_110692.1|  3 IAVEGIDGAGKTTLAKSLSSLLEKEGFRVFLT 34
                                  6788***********************99885 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.8
                                   TTHHHHHHHHHHHHHHHSSSEEEEEEETTBHTHHHH CS
                         SRP54  96 qndkelmeelkkikkvvkpdevllvldattgqeavk 131
                                   ++ ke m+ +++i ++  ++++l+ +d  +g + ++
  gi|13541004|ref|NP_110692.1| 101 EKAKEWMDCVSNIITIRPDINILVQVDVQVGLDRIS 136
                                   556677777777777766666666677777766554 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   3.4e-05      0.03       2      33 ..       3      34 ..       2      48 .. 0.86
   2 ?   -3.0   0.0       7.1   6.4e+03      71      92 ..     142     162 ..     135     168 .. 0.64

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.4e-05
                          MobB  2 lgivgksgsGKTtLleklipelkarglrvgti 33
                                  +++ g  g+GKTtL + l + l+++g+rv + 
  gi|13541004|ref|NP_110692.1|  3 IAVEGIDGAGKTTLAKSLSSLLEKEGFRVFLT 34
                                  5678999*********************9765 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 7.1
                          MobB  71 ikeleeaelsleellarlsevD 92 
                                   i++ e+ + +l+e l+ +++ D
  gi|13541004|ref|NP_110692.1| 142 ITHFEQ-RERLNEALKIYNSFD 162
                                   444333.567888888887766 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   5.1e-05     0.045       3      28 ..       3      28 ..       1      37 [. 0.89

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.1e-05
                                  EEEEC-TTTCHHHHHHHHHHHHCTS- CS
                         NACHT  3 vilqGeaGsGKTtLlqklalawaegk 28
                                  ++++G  G GKTtL+++l +++ ++ 
  gi|13541004|ref|NP_110692.1|  3 IAVEGIDGAGKTTLAKSLSSLLEKEG 28
                                  789*****************998865 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 ?   12.1   0.7   0.00017      0.15       9     164 ..      10     166 ..       1     170 [. 0.66

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00017
                                   TSSHHHHHHHHHHH-TT..SEEEEGGGS-TT-SS-HHHHHHHTTSSTT--EEEEES---SHHHHHHHHHHHHHHHHHH-.. CS
               tRNA_lig_kinase   9 GCGkttvaltlenlfge..WghvqnDnitgkdkkklvkealellkkdeskvvlvDrnnhqkreRkqlfeeidelkeeyl.. 85 
                                   G Gktt a+ l++l  +  + +    +  + d +++  + +el+    +    +Dr  hqk+ Rk+l e +  + ++y+  
  gi|13541004|ref|NP_110692.1|  10 GAGKTTLAKSLSSLLEKegFRVFLTREP-TDDIRNYEGDDVELF----I-KFTLDRYKHQKEIRKKLNEGFVVISDRYIrs 84 
                                   7788888888888877543333333222.224455555566666....2.2468*************************44 PP

                                   -TT-EEEEEEEE-S-TT-HHHHHHHHHHHHH-------------..-HHHHHHHHHHHHHT-...----TTSTTGGG-SEE CS
               tRNA_lig_kinase  86 sydvnvkvvalsFvdeddleevreltkdRvlkRGdnhqsikves.edekkvkkimegfikrf...qpvnkekepDnkfDlv 162
                                   sy  ++k  a    +e++ +e ++ + + ++ R d    ++v+   + ++++k  +g i +f   +++n++ +  n+fD  
  gi|13541004|ref|NP_110692.1|  85 SYAYEMKGAAAALGSEEKAKEWMDCVSNIITIRPDINILVQVDVqVGLDRISK-RNGTITHFeqrERLNEALKIYNSFDWD 164
                                   46778999999999999999999*99999999999877777664135555543.233333331114566666666666666 PP

                                   EE CS
               tRNA_lig_kinase 163 ie 164
                                   i+
  gi|13541004|ref|NP_110692.1| 165 IK 166
                                   65 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   3.5e-05     0.031      27      92 ..       3      68 ..       1     156 [. 0.73

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.5e-05
                        AAA_16 27 vllsGesGvGKsslvrellralekdg.gif.lrgkcdqlesaipysa.laqalareellrqlldeaesa 92
                                  + + G  G GK++l+++l   lek+g  +f +r+ +d+    + y    ++++ + +l r  ++++  +
  gi|13541004|ref|NP_110692.1|  3 IAVEGIDGAGKTTLAKSLSSLLEKEGfRVFlTREPTDDI---RNYEGdDVELFIKFTLDRYKHQKEIRK 68
                                  5688999************99999995455455555555...555444555555555555555555555 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0    0.0001     0.092       2      30 ..       3      31 ..       2      44 .. 0.88
   2 ?   -2.0   0.1       3.2   2.9e+03     108     151 ..     100     141 ..     100     156 .. 0.55

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.0001
                                  EEEE--TTSSHHHHHHHHHHHH...GGGE CS
                      NTPase_1  2 vfiTGppGvGKtTlvkkvlellkssgvkv 30
                                  +++ G  G GKtTl k +++ll+++g++v
  gi|13541004|ref|NP_110692.1|  3 IAVEGIDGAGKTTLAKSLSSLLEKEGFRV 31
                                  5678999*******************998 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.2
                                   GGG-HHHHHHHHHHHT..TTSEEEEE--SS--SHHHHHHHT-TT-E CS
                      NTPase_1 108 ElkskkfkeaveevLk..sekpvlavihrrkdlalveeirerkdvk 151
                                   E k+k++ + v ++++  ++ ++l+ + ++     +++i++r+ ++
  gi|13541004|ref|NP_110692.1| 100 EEKAKEWMDCVSNIITirPDINILVQVDVQ---VGLDRISKRN-GT 141
                                   566777777777777643444444444444...3466666663.33 PP

>> Herpes_TK  Thymidine kinase from herpesvirus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00037      0.33       3      58 ..       9      66 ..       7     103 .. 0.80
   2 ?    0.6   0.0       0.3   2.7e+02     152     171 ..     122     141 ..     106     148 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00037
                                  TTSSHHHHH.HHHHHHSTT.TTEEEE---HHHHHTTSSSSHHHHHHHHHHH.HHTTSS CS
                     Herpes_TK  3 fGiGkttvleellkalair.drilyveEPlkyWrvlfaedaiteiyttqer.rdrGei 58
                                   G Gktt ++ l + l  + +r+ +  EP    r++ ++d+   i  t +r +++ ei
  gi|13541004|ref|NP_110692.1|  9 DGAGKTTLAKSLSSLLEKEgFRVFLTREPTDDIRNYEGDDVELFIKFTLDRyKHQKEI 66
                                  699********99998877799*****************9999999888873445566 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.3
                                   EEEE--HHHHHHHHHHS-TT CS
                     Herpes_TK 152 vivdlseeehvsRlskRqRp 171
                                   ++v+++++  ++R+skR+ +
  gi|13541004|ref|NP_110692.1| 122 ILVQVDVQVGLDRISKRNGT 141
                                   4678999**********865 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1     9e-05     0.081       5      35 ..       3      33 ..       1      77 [. 0.86

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 9e-05
                                  EEEESSTTSSHHHHHHHHHHHHHHTT--EEE CS
                    APS_kinase  5 vwltGlsgsGKstianalekkLvekgisvyl 35
                                  + + G+ g+GK+t+a+ l++ L+++g +v l
  gi|13541004|ref|NP_110692.1|  3 IAVEGIDGAGKTTLAKSLSSLLEKEGFRVFL 33
                                  56789*********************88754 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00013      0.11       5      52 ..       3      55 ..       1     163 [. 0.81

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00013
                        AAA_24  5 iliyGpsgiGKTtlakel.....gpkplfidtekGlksldadkfpdieswedf 52
                                  i++ G  g+GKTtlak+l     ++ + ++ t + ++++ + +++d+e +++f
  gi|13541004|ref|NP_110692.1|  3 IAVEGIDGAGKTTLAKSLsslleKEGFRVFLTREPTDDIRNYEGDDVELFIKF 55
                                  678899************88888666666666666888888888888744444 PP

>> LytR_C  LytR cell envelope-related transcriptional attenuator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0    0.0002      0.18       7      35 ..       8      36 ..       3     133 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.0002
                        LytR_C  7 lNgtgvsGlAarvadaLeerGftvgevgn 35
                                   +g+g++ lA++++++Le++Gf+v  + +
  gi|13541004|ref|NP_110692.1|  8 IDGAGKTTLAKSLSSLLEKEGFRVFLTRE 36
                                  589*******************9987443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       707  (0.0394333); expected 358.6 (0.02)
Passed bias filter:                      558  (0.0311228); expected 358.6 (0.02)
Passed Vit filter:                       102  (0.00568911); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.49
# Mc/sec: 1162.63
//
Query:       gi|13541005|ref|NP_110693.1|  [L=389]
Description: cystathionine gamma-lyase [Thermoplasma volcanium GSS1]
Scores for complete 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-123  411.4   0.0   2.8e-123  411.3   0.0    1.0  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
     0.0087   15.4   0.0      0.014   14.7   0.0    1.3  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
  ------ inclusion threshold ------
       0.03   13.5   0.0      0.057   12.6   0.0    1.5  1  Aminotran_1_2    Aminotransferase class I and II
       0.13   12.0   0.0       0.56    9.9   0.0    1.9  2  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl


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 !  411.3   0.0  6.2e-127  2.8e-123       2     381 ..      12     383 ..      11     384 .. 0.96

  Alignments for each domain:
  == domain 1  score: 411.3 bits;  conditional E-value: 6.2e-127
                                   HHHHHTTTTCHTTTTBSS--B---SBBBESSHHHH...CTTCSSS-SBTTT--HHHHHHHHHHHHHHT-SEEEEESSHHHH CS
               Cys_Met_Meta_PP   2 Tllvhagqekdeqtgavavpiyltstykfkdvdea...fageekgyeYsRsgnptrsvleeriaaLeggeaalavssGmaA 79 
                                   T +v++g+ +d+++g+v++pi++tst++f ++++     + ++  y+Y+R gnpt++++ee+ a Le++e+al +ssGm+A
  gi|13541005|ref|NP_110693.1|  12 TRAVQSGELRDPRFGNVTTPIFETSTFVFPNSEKDayiDNTRNLPYIYTRWGNPTVQAFEEKYASLEKAEHALSFSSGMGA 92 
                                   899***************************999988866666666************************************ PP

                                   HHHHHHTTS-TTEEEEEESTSSHHHHHHHHHTHHHTTCEEEEESTTSHHHHHHHCCT.TEEEEEEESS-TTTT----HHHH CS
               Cys_Met_Meta_PP  80 iaaailallkaGdeivvsddlYggtqrllkkvlkklgievkfvdtsdleelekaike.ntklvylEtptnpllkvvDieki 159
                                   i+++ilal++ Gd+i++ +dlYg t+ +l+kvl++ gi+v+++ t+ l++ e  +k+   +++ylE++tnp+lkv+Di+++
  gi|13541005|ref|NP_110693.1|  93 ITSVILALAERGDKILSVSDLYGQTFYFLNKVLPEYGISVEYISTDRLNSGE--FKPsDYDIIYLESITNPTLKVPDIKAV 171
                                   *********************************************9998765..4443789******************** PP

                                   HHHHHHTT-EEEEEGTTTHTTTS-GGGGT-SEEEEETTTTTTCSSS--EEEEEESSCHHHHHHHHHHHHHHT-B--HHHHH CS
               Cys_Met_Meta_PP 160 aklakkagvlvvvDntfaspllqrplklgaDivvhSaTKylgGhsdvvaGvivvkgkeelkkelkflqnalGavlspfdaw 240
                                   ++  ++ g  ++vD+tfasp++q+pl+lgaD+v+hSaTKy++Ghsdvv+Gv  +++ +++ +++ +  +++G+  +p +++
  gi|13541005|ref|NP_110693.1| 172 SE--RSTGKKIIVDATFASPYNQNPLDLGADVVIHSATKYISGHSDVVMGVFSTND-KSIFDKVVVRRKTFGSNPDPIQSY 249
                                   98..67788899********************************************.88888899999************* PP

                                   HHHHHHTTHHHHHHHHHHHHHHHHHHHHTSTTEEEEE-TTSTTSTTHHHHHHHSSSG-SEEEEEESSHHHHHHHHHHC-SS CS
               Cys_Met_Meta_PP 241 lllrGlkTLslRlerhqenAlkvAefLekhpkvekvyYpglpshpqhelakkqlkgaggvlsFelkseeekakkfvdnlkl 321
                                   l lrG+kTL+lR+e+h++n +++A++L+++p++++vyYp      + e+ kk l+g+gg++sFel+ e+  ++ f+ nlk+
  gi|13541005|ref|NP_110693.1| 250 LALRGIKTLGLRMEKHNKNGMELAKYLRTEPRISHVYYP------DTEIGKKVLRGFGGMISFELRPEL-DVHVFMRNLKI 323
                                   ***************************************......899******************995.6********** PP

                                   SEECSS-SSSS-EEEETTTTTTTTSCHHHHHHTTS-TTEEEEE--SS-HHHHHHHHHHHH CS
               Cys_Met_Meta_PP 322 fslaeslGgveslielpasmthasipkeereaagvtddliRlsvGiEdvdDliaDlkqal 381
                                    ++a+slGgvesli+lp+ ++h s++keere+ g+td+l+R+s+GiEd  Dli+D+kqal
  gi|13541005|ref|NP_110693.1| 324 PMVAASLGGVESLITLPVETSHSSMTKEERERIGITDNLVRFSIGIEDHVDLIDDIKQAL 383
                                   ***********************************************************9 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   3.2e-06     0.014      21      67 ..      61     108 ..      45     118 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.2e-06
                                   S..SHHHHHHHHHHHHHHT-SEEEEESSHHHHHHHHHHHTTTTTT-EEE CS
               DegT_DnrJ_EryC1  21 s..gpeveeFEkafaaylgvkhaiavssGtaAlhlaLralgvgpgdeVI 67 
                                   +  +p+v++FE++ a   +++ha+++ssG  A+  ++ al    gd+++
  gi|13541005|ref|NP_110693.1|  61 RwgNPTVQAFEEKYASLEKAEHALSFSSGMGAITSVILALAER-GDKIL 108
                                   345799***************************9999998876.88776 PP

>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   1.3e-05     0.057      46     170 ..      67     171 ..      58     224 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.3e-05
                                   HHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEEEE....SS-THHHHHHHHTTSEEEEEEB CS
                 Aminotran_1_2  46 lpeleealakflgrseklklkreaavvvgsGagaliealifllklnpgdeilvpd....ptyasyknilrlsggevvrypl 122
                                    +++ee+ a++ +        +e a+ ++sG ga+ +++ +l++  +gd+il+ +    +t+   +++l  +g+ v ++++
  gi|13541005|ref|NP_110693.1|  67 VQAFEEKYASLEK--------AEHALSFSSGMGAITSVILALAE--RGDKILSVSdlygQTFYFLNKVLPEYGISVEYIST 137
                                   5678888888888........9*********************8..******87633336667778888888888888884 PP

                                   EETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHH CS
                 Aminotran_1_2 123 yseedfhldlealeealkeapegnkktkvilvesphNPtGtvatleel 170
                                   +     +l+  +++         +    +i++es+ NPt +v++ + +
  gi|13541005|ref|NP_110693.1| 138 D-----RLNSGEFKP-------SDY--DIIYLESITNPTLKVPDIKAV 171
                                   4.....333333333.......223..567777777777555555544 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 ?    9.9   0.0   0.00012      0.56      32     105 ..      37     111 ..      26     159 .. 0.88
   2 ?   -0.7   0.0      0.22   9.7e+02      34      58 ..     182     205 ..     168     243 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00012
                                   GGSSCGGGGGTTSSS-EEEETTEE.E--HHHHHHHHHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEE CS
                          PCMT  32 efvpesfkekaYedaplsigynat.iSaphmvalalellelkkgarvLevGsGsGyltavlarlvgekgrvvsie 105
                                   +fv  + ++ aY d++ ++ y  t   +p + a+  ++ +l+k +++L   sG G  t v+  l ++  +++s+ 
  gi|13541005|ref|NP_110693.1|  37 TFVFPNSEKDAYIDNTRNLPYIYTrWGNPTVQAFEEKYASLEKAEHALSFSSGMGAITSVILALAERGDKILSVS 111
                                   5666666889999999999998662689*********************************99999999999985 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.22
                                   SSCGGGGGTTSSS-EEEETTEEE-- CS
                          PCMT  34 vpesfkekaYedaplsigynatiSa 58 
                                   v+++f  ++Y+++pl++g+++ i +
  gi|13541005|ref|NP_110693.1| 182 VDATF-ASPYNQNPLDLGADVVIHS 205
                                   55555.689999***9999987743 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       373  (0.0208043); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.47
# Mc/sec: 2489.87
//
Query:       gi|13541006|ref|NP_110694.1|  [L=249]
Description: deoxyribose-phosphate aldolase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.9e-05   22.6   0.0    0.00012   21.8   0.0    1.6  1  DeoC      DeoC/LacD family aldolase


Domain annotation for each model (and alignments):
>> DeoC  DeoC/LacD family aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   6.8e-09   0.00012      94     215 ..      90     216 ..       7     233 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 6.8e-09
                                   -SEEEEEEEEHTTTTCHHHHHHHHHHHHHHHHHHHTEEEEEEEEE-CTTBSSTTCHHHHHHHHHHHHTCCT-SEEEE--S. CS
                          DeoC  94 AdavkvvvyyradgseeeqqklaeikrvkeacheeglplilelylrdeaikdekvdpdlvaeAarvsaelGaDiiKvevp. 173
                                   Ad++++v+++ + +s ++ ++ ++i+ v ++++++gl++ +  +    +  dek       +   + +    D+iK++++ 
  gi|13541006|ref|NP_110694.1|  90 ADEIDMVIPIGYVKSHRWDKVEQDINDVVSTARDLGLVSKIITEDGYLTL-DEK------LKTYDIVIRSAPDFIKTSTGf 163
                                   9************************************9988776666663.444......57778999999********** PP

                                   .........SCC.B.HHHHHHHHHHHHHCHSSTE.EEEETTS.SHHHHHHHHH CS
                          DeoC 174 .........kevvnateedaevfkdvikaapvpg.vvlsGGv.seedfletve 215
                                            +    at+e ++ +++ +k++     ++ +GG+ +  ++ + ++
  gi|13541006|ref|NP_110694.1| 164 adkefckslGNETGATPENVKLMSEIAKKIGSNIgIKAAGGIhTYDQVEKIID 216
                                   ********98889*****************99966*******55555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1666.45
//
Query:       gi|13541007|ref|NP_110695.1|  [L=470]
Description: major facilitator superfamily permease [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.7e-46  158.8  35.8    1.7e-46  158.8  35.8    1.6  1  MFS_1      Major Facilitator Superfamily
  ------ inclusion threshold ------
      0.023   15.0   0.1       0.21   11.9   0.1    2.6  1  ASFV_L11L  African swine fever virus (ASFV) L11L protein
       0.98    7.6   9.8         16    3.7   8.2    3.0  3  OATP       Organic Anion Transporter Polypeptide (OATP) famil


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 !  158.8  35.8   2.9e-50   1.7e-46       1     350 [.      27     409 ..      27     412 .. 0.85

  Alignments for each domain:
  == domain 1  score: 158.8 bits;  conditional E-value: 2.9e-50
                         MFS_1   1 lllaaflsalarsilgpalplalaedlgispse..........igllltlyalgaavaslplGrlsdrfGrrrvlllglll 71 
                                   l++a+++++++r i +++ p a a ++g+s s           i+l+l + +l +a++++p+G+++d++G r+ + +++++
  gi|13541007|ref|NP_110695.1|  27 LFIAILFNYADREIWIVSEP-AFAYSFGWSYSPthldalaihnISLILFFWSLSYAIFNFPGGWIVDKLGLRKSMTTMFAI 106
                                   799***********999999.9******9888877777777778889999******************************* PP

                         MFS_1  72 falglllllfa.sslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWr 151
                                   ++++ ++l+ a  ++ +++++r+++G+g+g ++p+   ++  w+++ + ++ + l++ag ++G+++g ++gg+l++++gW+
  gi|13541007|ref|NP_110695.1| 107 WSIF-TALTAAtFNFITMAIVRIVMGAGEGPVWPINSKVVKGWASRFDESKSFTLAGAGQAVGPVIGLIAGGILVTLFGWP 186
                                   ****.455423356668**************************************************************** PP

                         MFS_1 152 avfyilaivsllafvlfllllpeepperkrkspkeee...........kgtgpaplvp.......awkallkdpvlw.... 210
                                   ++f+++++++l+++ +++++++++p+e +++++ e+            +     +++p         ++++          
  gi|13541007|ref|NP_110695.1| 187 SAFIFFGVLGLIFVAIWFFYVRDRPSEDSKVNENELAyiiegktneekE----EKILPskvnwkiSARMIFG----Tqagl 259
                                   *************99999999**********999999*99887754432....2222234433332223333....13344 PP

                         MFS_1 211 illialllfffgfsglltllplylqevlgls....glllaglllallalvgail.allagrlsdrlgrrrrlllallllll 286
                                     l+++l+f+ +++++l++lp ++ +++  +    gl++a+  + ++ ++g+ + +++   l++r++  ++l   l++++ 
  gi|13541007|ref|NP_110695.1| 260 GTLLVFLSFGYVLFTFLYWLPPLMFSTFAHTveksGLYSAA--IDVALIAGFLGsGPFNDGLLKRFPDNKPLARRLGAIIP 338
                                   8******************************9999988888..55555555555689************************ PP

                         MFS_1 287 aalglallavt...ssavllllvlvliGfglgfv...fpsllalasdlappeeagtasglfn.tagslgga 350
                                   ++l++++++++    +a+ l+   +++G+g+g++   ++s+++ a+dlap+  ++t++g++n +++ +g++
  gi|13541007|ref|NP_110695.1| 339 MVLMIVMVGLSyftGKAHNLVGTAIFLGVGSGLMnltVGSWAVNAVDLAPAGTSATVYGIYNgSLNFIGAF 409
                                   ******9999987433333333777799999999888999999999999*************777778775 PP

>> ASFV_L11L  African swine fever virus (ASFV) L11L protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   3.5e-05      0.21       9      38 ..     335     367 ..     331     372 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.5e-05
                     ASFV_L11L   9 apiplvlifl...ysyfkiklhklitialflgc 38 
                                   a ip+vl+++    syf  k h l+  a+flg 
  gi|13541007|ref|NP_110695.1| 335 AIIPMVLMIVmvgLSYFTGKAHNLVGTAIFLGV 367
                                   45676665542236*****************95 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 ?    0.6   0.2     0.022   1.3e+02     348     386 ..      84     121 ..      71     124 .. 0.68
   2 ?    3.7   8.2    0.0026        16     132     352 ..     120     313 ..      97     363 .. 0.66
   3 ?   -1.3   0.1     0.082   4.9e+02      50      83 ..     342     372 ..     333     381 .. 0.68

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.022
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          OATP 348 illgGllvkklklsakklaklvlvvsllsllllllllfl 386
                                    + gG++v kl l+ + + ++ ++ s++++l+ +++ f+
  gi|13541007|ref|NP_110695.1|  84 NFPGGWIVDKLGLRKSMTTMF-AIWSIFTALTAATFNFI 121
                                   577*********996655544.45555555555555554 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.0026
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          OATP 132 vllfflaqlllGiGatpiytlGisYidDnvkkknsplylgilyalrilGpalGfllGslllklyvdidseisltpkdprWv 212
                                   ++ + +  +++G+G+ p++++    +   +++ + +  + ++ a +++Gp++G + G++l+ l+                 
  gi|13541007|ref|NP_110695.1| 120 FITMAIVRIVMGAGEGPVWPINSKVVKGWASRFDESKSFTLAGAGQAVGPVIGLIAGGILVTLF----------------- 183
                                   347888999*************************************************999987................. PP

                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          OATP 213 gaWWlgflilgvllllaaiplffFPkelpkkkeerakkkseeesaekkeekkkkeksksseeeelkslkdfpkalkrllkn 293
                                     W   f+++gvl l+++ + ff+ +  p++  + ++ ++ +   e k++++k+ek   s+        +   + ++++  
  gi|13541007|ref|NP_110695.1| 184 -GWPSAFIFFGVLGLIFVAIWFFYVRDRPSEDSKVNE-NELAYIIEGKTNEEKEEKILPSK-------VNWKISARMIFGT 255
                                   .466789999999999999999999998855555544.44433322222222222222222.......2222333444444 PP

                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          OATP 294 pifllvilssvfeillvaGfitFlpkylEtqFslsaseAnlltGvvvipgaalGillgG 352
                                   +  l ++l   +  +++  f  +lp  + + F  +  ++ l+ +++ + + ++G+l +G
  gi|13541007|ref|NP_110695.1| 256 QAGLGTLLVFLSFGYVLFTFLYWLPPLMFSTFAHTVEKSGLYSAAIDV-ALIAGFLGSG 313
                                   444444444444555555566666777777777777777777666554.3445555555 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 0.082
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          OATP  50 illilfvsYfggrghrPrwigigallmalgslll 83 
                                   +++++ +sYf g++h   ++g+++ ++++gs l+
  gi|13541007|ref|NP_110695.1| 342 MIVMVGLSYFTGKAHN--LVGTAI-FLGVGSGLM 372
                                   67888899***99996..344333.334444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (470 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       821  (0.0457917); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.62u 0.28s 00:00:00.90 Elapsed: 00:00:00.47
# Mc/sec: 2991.25
//
Query:       gi|13541008|ref|NP_110696.1|  [L=62]
Description: hypothetical protein TVN0177 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.5e-05   23.6   0.0    3.5e-05   23.6   0.0    1.0  1  Stk19          Serine-threonine protein kinase 19
  ------ inclusion threshold ------
      0.016   14.9   0.1      0.018   14.6   0.1    1.0  1  SMC_ScpB       Segregation and condensation complex subunit S
       0.04   13.9   2.5      0.048   13.7   2.5    1.2  1  DUF4342        Domain of unknown function (DUF4342)
       0.09   12.8   1.4       0.13   12.3   1.1    1.4  1  DNA_pol3_a_NI  DNA polymerase III polC-type N-terminus I
       0.11   12.7   0.1       0.14   12.4   0.1    1.2  1  HTH_17         Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> Stk19  Serine-threonine protein kinase 19
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   9.8e-09   3.5e-05      21      71 ..       3      52 ..       1      60 [. 0.87

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 9.8e-09
                         Stk19 21 evlklrrslP.plvtvahlhsllaqsptkvereleelirkgklrklvingrg 71
                                  ++l + ++ P  + t +++ s++  + ++v+++l+el+++gkl+k+ +n+++
  gi|13541008|ref|NP_110696.1|  3 QILDIFNENPdVFLTEEQIMSIV--GTKDVDKKLKELVKEGKLKKIEVNKKS 52
                                  57888888885678999******..699********************9986 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 ?   14.6   0.1   5.1e-06     0.018      99     142 ..      17      61 ..      13      62 .] 0.94

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 5.1e-06
                      SMC_ScpB  99 traeieeiRGvn.sdsvvrtLlerglieekgrkeepgrpilYgtT 142
                                   t ++i +i G + +d+ +++L+++g  ++ + ++++gr i Yg++
  gi|13541008|ref|NP_110696.1|  17 TEEQIMSIVGTKdVDKKLKELVKEGKLKKIEVNKKSGRKIYYGIS 61 
                                   7899******999*****************************987 PP

>> DUF4342  Domain of unknown function (DUF4342)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   2.5   1.3e-05     0.048      13      40 ..      28      56 ..      17      57 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.3e-05
                       DUF4342 13 eelvekvKelikkgnvtriiikk.dgktl 40
                                  +++ +k+Kel+k+g+ ++i + k +g+ +
  gi|13541008|ref|NP_110696.1| 28 KDVDKKLKELVKEGKLKKIEVNKkSGRKI 56
                                  56779****************99888865 PP

>> DNA_pol3_a_NI  DNA polymerase III polC-type N-terminus I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   1.1   3.6e-05      0.13      11      33 ..      30      52 ..      26      55 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.6e-05
                 DNA_pol3_a_NI 11 lpdelkslfedaeiekvvvhkks 33
                                  ++++lk+l ++++++k++v+kks
  gi|13541008|ref|NP_110696.1| 30 VDKKLKELVKEGKLKKIEVNKKS 52
                                  56899*****************9 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   3.9e-05      0.14      15      38 ..      31      58 ..      15      59 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.9e-05
                        HTH_17 15 rstvyrlirrgelpaa....kiGrrwri 38
                                  ++++ +l+++g+l+      k Gr++++
  gi|13541008|ref|NP_110696.1| 31 DKKLKELVKEGKLKKIevnkKSGRKIYY 58
                                  6789**************966****997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (62 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1295  (0.0722293); expected 358.6 (0.02)
Passed bias filter:                      697  (0.0388756); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 434.42
//
Query:       gi|13541009|ref|NP_110697.1|  [L=172]
Description: C4-type Zn finger protein [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-34  119.5   0.1    1.4e-34  119.3   0.1    1.0  1  zf-ZPR1         ZPR1 zinc-finger domain
  ------ inclusion threshold ------
      0.059   13.5   4.2        2.1    8.5   1.3    2.4  2  Zn-ribbon_8     Zinc ribbon domain
      0.067   13.2   0.3       0.16   12.0   0.3    1.6  1  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
      0.096   12.9   1.4       0.14   12.4   1.3    1.5  1  MCM6_C          MCM6 C-terminal winged-helix domain
       0.11   12.5   0.1       0.36   10.9   0.1    1.9  1  DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domai
       0.26   11.2   2.8        4.8    7.1   2.8    2.4  1  RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit


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 !  119.3   0.1   4.6e-38   1.4e-34       2     159 .]      12     163 ..      11     163 .. 0.93

  Alignments for each domain:
  == domain 1  score: 119.3 bits;  conditional E-value: 4.6e-38
                       zf-ZPR1   2 lCpsCgkengetrllltkiPyfkeviimsfeCehCgyknnevksageieekGkritlkveseedlnrqvlkSetatveipe 82 
                                   +Cp Cg +     ++ t+iPy + + i +++C++C y+++ev + +e+++  +ritlk+es+edl++ v++S +a + ipe
  gi|13541009|ref|NP_110697.1|  12 ECPVCG-SLLYLLTYDTDIPYEGRISIYTYQCKKCMYRKTEVYQEEEKNP--VRITLKIESPEDLKTLVYRSRKADIYIPE 89 
                                   7****7.8788888899*********************************..***************************** PP

                       zf-ZPR1  83 leleippg.tlegrlttvEGlLeqikeelekeegdqaeredeekekieeflekleeliegee.pftlildDpagnSfie 159
                                   +e +i++    +g++ttvEG++ +i e+l+     +   +deeke+++e+ +k++++i+g   +ftli++D +g+S+ie
  gi|13541009|ref|NP_110697.1|  90 IEASIDSAeYANGEITTVEGIIYRIGEKLD---LLSY--DDEEKEAVKEVRKKIDDIINGYFgSFTLIITDESGKSVIE 163
                                   *****99889*******************3...3333..346799**************9878**************96 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.1    0.0063        19      26      34 ..      10      18 ..       4      21 .. 0.75
   2 ?    8.5   1.3   0.00072       2.1       3      16 ..      37      50 ..      36      61 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0063
                   Zn-ribbon_8 26 ltaCPeCgs 34
                                  + +CP Cgs
  gi|13541009|ref|NP_110697.1| 10 NMECPVCGS 18
                                  456*****8 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00072
                   Zn-ribbon_8  3 iYeYrCeeCghefe 16
                                  iY Y+C++C  + +
  gi|13541009|ref|NP_110697.1| 37 IYTYQCKKCMYRKT 50
                                  8********86655 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   0.3   5.2e-05      0.16      19      45 ..      11      47 ..       8      48 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 5.2e-05
                 Zn_Tnp_IS1595 19 fvCPhCgsr.kayrikt.........rglfqCkeCrk 45
                                    CP Cgs   + ++ t            +qCk+C +
  gi|13541009|ref|NP_110697.1| 11 MECPVCGSLlYLLTYDTdipyegrisIYTYQCKKCMY 47
                                  57*****998778888899**99999999******76 PP

>> MCM6_C  MCM6 C-terminal winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   1.3   4.8e-05      0.14      30      88 ..      74     132 ..      47     169 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.8e-05
                        MCM6_C  30 eegiekeeLvewYleqieeeleseeeleeekklvekvlkrLvkdkvLlevreeaeesee 88 
                                   ++ + +++  + Y+ +ie++++s e  + e ++ve ++ r+ +   Ll+ ++e++e+ +
  gi|13541009|ref|NP_110697.1|  74 KTLVYRSRKADIYIPEIEASIDSAEYANGEITTVEGIIYRIGEKLDLLSYDDEEKEAVK 132
                                   466667777899*****************************999999999999888533 PP

>> DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00012      0.36       1       9 [.      12      20 ..      12      22 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00012
                DNA_ligase_ZBD  1 hCPvCGsav 9 
                                  +CPvCGs +
  gi|13541009|ref|NP_110697.1| 12 ECPVCGSLL 20
                                  5******76 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   2.8    0.0016       4.8       4      30 ..      13      48 ..      13      50 .. 0.63

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0016
                                  ESTTTSBEE........EEECSCCCE....EEESSSS-E CS
                RNA_POL_M_15KD  4 CpkCgNlLl........pkedkegkn....feCrqCgYe 30
                                  Cp Cg+lL+        p    eg++    + C +C Y 
  gi|13541009|ref|NP_110697.1| 13 CPVCGSLLYlltydtdiPY---EGRIsiytYQCKKCMYR 48
                                  9******984442222233...44444459999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       947  (0.0528195); expected 358.6 (0.02)
Passed bias filter:                      604  (0.0336884); 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: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1105.21
//
Query:       gi|13541010|ref|NP_110698.1|  [L=347]
Description: isopentenyl pyrophosphate isomerase [Thermoplasma volcanium GSS1]
Scores for complete 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-19   68.6   0.1    1.3e-12   47.5   0.1    2.5  2  FMN_dh        FMN-dependent dehydrogenase
     0.0003   19.9   0.7       0.33    9.9   0.0    3.7  4  IMPDH         IMP dehydrogenase / GMP reductase domain
    0.00054   19.2   0.7      0.002   17.4   0.7    1.8  1  Glu_synthase  Conserved region in glutamate synthase
  ------ inclusion threshold ------
      0.044   13.0   0.0      0.086   12.0   0.0    1.4  1  DHO_dh        Dihydroorotate dehydrogenase


Domain annotation for each model (and alignments):
>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0     2e-07   0.00088      29      99 ..      24      96 ..       2     118 .. 0.80
   2 !   47.5   0.1   2.8e-16   1.3e-12     208     344 ..     174     333 ..     147     336 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 2e-07
                                  GGGGEEE---SSSS-S..S-B--EEETTEEESSSEEE--BSTGGGTSTTHHHHHHHHHHHHTS-EEEETT-SS CS
                        FMN_dh 29 aferirlrprvlrdvs..kvdlsttllGqklslPvliaPvglaklahpdgelalaraaakagipfvlstvast 99
                                   ++++ l +++  +v+  ++d+ +++lG++l +P++i+++     ++++ + +la  a+k ++ ++++++  +
  gi|13541010|ref|NP_110698.1| 24 YWDDVYLMHEADPEVNydDIDTGVDFLGKHLGFPMVISSMTGGAEIAKKINYNLATVAEKYQLAMGVGSMRAA 96
                                  45666666666555541167999*****************777777789******************999765 PP

  == domain 2  score: 47.5 bits;  conditional E-value: 2.8e-16
                                   HHHHHHHHS.SEEEEEEE...-SHHHHHHHHHTTESEEEE--GGG.........TSSTT---HHHCH...........HHH CS
                        FMN_dh 208 ikwlreqtk.lplvvKGv...ltaedakraveaGvdgivvSNHGG.........RqldgapatidvL...........pei 264
                                   ik+++e     +++ K+     ++++a+r+++aGv++i vS   G         R  +   a    +           p+ 
  gi|13541010|ref|NP_110698.1| 174 IKRIKELSGsFNIIAKETgsgFSKATAQRLADAGVKAIEVSGLSGttfaaveyyRAKNEGNAEKMRIgetfwnwgipsPAS 254
                                   56666655435777777766678899*******************888888888544444444444434444444444555 PP

                                   HHHH..SS-EEEESS--SHHHHHHHHHTT-SEEEESHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-SBHHHHHCG CS
                        FMN_dh 265 veavggrievlvDgGirrGsDvlkAlalGAdavllGRpflyglaagGeeGvervleilraelertmallGvksvaeldrs 344
                                   v ++ + ++v+ +gG r+G D +kA+ lGA++ +++R +l   a +  e v+r +e++++e++ +m l+G k+v el+++
  gi|13541010|ref|NP_110698.1| 255 VYYCSDVLPVIGSGGLRNGLDLAKAISLGASLGGFARTLLKD-ADQSVEAVSRNVEMIEREFKVAMFLTGNKNVYELRKT 333
                                   8888999********************************888.668999*************************999875 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     0.096   4.3e+02     254     279 ..      81     108 ..      25     138 .. 0.69
   2 !    3.5   0.1    0.0066        30     129     172 ..     170     213 ..     163     220 .. 0.78
   3 !    9.9   0.0   7.3e-05      0.33     208     231 ..     262     285 ..     244     293 .. 0.85
   4 ?    1.5   0.0     0.027   1.2e+02     298     331 ..     303     336 ..     295     339 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.096
                                   TEEEEEEEETTSHHHH..HH-SS-TTS- CS
                                   xxxxxxxxxxxxxxxx..xxxxxxxxxx RF
                         IMPDH 254 grkyKeyrGmgslgam..kkgskdryfq 279
                                    +ky+   G+gs++a   +++ +d y  
  gi|13541010|ref|NP_110698.1|  81 AEKYQLAMGVGSMRAAivNRSLSDTYSV 108
                                   5667777888888888644456667743 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.0066
                                   SHHHHHHHHHHHHHTTTSEEEEEEE-SHHHHHHHHHTT-SEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         IMPDH 129 sekvleavkeikkkveeveviaGnvataegakaLieagadavkv 172
                                    e+v++ +ke+  +++ +   +G+  +++ a++L++ag++a+ v
  gi|13541010|ref|NP_110698.1| 170 AEGVIKRIKELSGSFNIIAKETGSGFSKATAQRLADAGVKAIEV 213
                                   456677777777777556666799999***************98 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 7.3e-05
                                   -EEEEES---SHHHHHHHHHTT-S CS
                                   xxxxxxxxxxxxxxxxxxxxxxxx RF
                         IMPDH 208 vpviaDGGikysgdivkAlaaGad 231
                                    pvi  GG+++  d++kA+++Ga+
  gi|13541010|ref|NP_110698.1| 262 LPVIGSGGLRNGLDLAKAISLGAS 285
                                   69*********************8 PP

  == domain 4  score: 1.5 bits;  conditional E-value: 0.027
                                   -HHHHHHHHHHHHHHHHHHHT-SSHHHHHHH-EE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         IMPDH 298 svkevveqlvgglrsgmgylGaktieelkekakf 331
                                    v++ ve +  + + +m  +G k++ el+++ k+
  gi|13541010|ref|NP_110698.1| 303 AVSRNVEMIEREFKVAMFLTGNKNVYELRKTKKV 336
                                   578889999999*****************98876 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 !   17.4   0.7   4.4e-07     0.002     193     305 ..     173     292 ..     165     295 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 4.4e-07
                                   HHHHHHHH-TTSEEEEEEE-STTHHHHHHHHHHTT-SEEEEE-TT---SSEE.HHHHHHB---HHHHHHHHHHHH...... CS
                  Glu_synthase 193 liedLkevnkeakvsvKlvaeagvetiaagvakanadiilidGleGGTGAsp.kssikhaGlPlelalaevdqtl...... 266
                                   +i+ +ke++ + ++  K +     ++ a  +a+a++ +i ++Gl+G T A+  +  +k+ G    + + e+          
  gi|13541010|ref|NP_110698.1| 173 VIKRIKELSGSFNIIAKETGSGFSKATAQRLADAGVKAIEVSGLSGTTFAAVeYYRAKNEGNAEKMRIGETFWNWgipspa 253
                                   688999999999999998777777777777******************877515667999*99999998875432111111 PP

                                   HHTT-GGG-EEEEESS--SHHHHHHHHHHT-SEEE-SHH CS
                  Glu_synthase 267 keeglrdrvsliadGglktgadvvkalalGAdavgigta 305
                                     +   d + +i +Ggl+ g d++ka+ lGA   g++++
  gi|13541010|ref|NP_110698.1| 254 SVYYCSDVLPVIGSGGLRNGLDLAKAISLGASLGGFART 292
                                   45667788899********************98888875 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   1.9e-05     0.086     241     291 ..     258     308 ..     253     311 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.9e-05
                                   TTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHHHHHGTCHHHHHHHHH CS
                        DHO_dh 241 lkkeipiIgvGGiesgeDalekieaGAslvqvytalvfegpkiakkikkel 291
                                    ++ +p+Ig+GG+  g D    i  GAsl      l ++  ++++ + +++
  gi|13541010|ref|NP_110698.1| 258 CSDVLPVIGSGGLRNGLDLAKAISLGASLGGFARTLLKDADQSVEAVSRNV 308
                                   45689***********************98888888788777777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       429  (0.0239277); 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:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.47
# Mc/sec: 2230.46
//
Query:       gi|13541011|ref|NP_110699.1|  [L=244]
Description: kinase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      1e-30  107.2   0.0    1.1e-30  107.0   0.0    1.0  1  AA_kinase  Amino acid kinase family


Domain annotation for each model (and alignments):
>> AA_kinase  Amino acid kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.0   0.0   6.3e-35   1.1e-30       2     230 ..       1     213 [.       1     223 [. 0.87

  Alignments for each domain:
  == domain 1  score: 107.0 bits;  conditional E-value: 6.3e-35
                                   EEEEEE-TTCCCCTCC......HHHHHHHHHHHHHHHHTTEEEEEE--HHHHHHHHHHTCCCCCHHHC....E..HHHHHH CS
                     AA_kinase   2 rvVvKlGGssltdkee......aslrrlaeqiaalkesgnklvvVhGggsftdgllalksglssgelaaglrstleeagev 76 
                                   ++++KlGGs++t+k+       +  ++++++ia+     ++ v++hGggsf++  +++ +gl+ + ++      l  ag+ 
  gi|13541011|ref|NP_110699.1|   1 MIIIKLGGSLITEKNSyrvfreSETKKAIREIAND---FEDFVIIHGGGSFGHIKAKE-YGLPGEINK------LSSAGFS 71 
                                   58**********999999*9995555555555555...3445****************.***999988......899**** PP

                                   HHHHHHHHHHHHHHHHHHHTTHGEEEE-GGGTCEECCCE..HHHTTTCEEECCHHHHHHHTT-EEEEESEEEEETTTEEEE CS
                     AA_kinase  77 atrdalaslgerlvaallaaglpavglsaaaldateagrdegsdgnvesvdaeaieelleagvvpvltgfigldeegelgr 157
                                   + +  +  l+  +v+ ++++gl+ + ++ +++  +++++           d   ++++ + g+vpv  g++ + +++  g+
  gi|13541011|ref|NP_110699.1|  72 VVHNDMSYLNHLVVSIMISEGLKPMTVPISSMI-FNGNF-----------DYTMLKKYHDLGFVPVSYGDVYVKNNNFYGI 140
                                   **********************99999999887.55666...........89999999999******************** PP

                                   E-HHHHHHHHHHHCTSSEEEEEESSSSCESSTTTTCCTTCECCEEEHHHCHHCSSS.TTTHHHHCHHHHHHHH CS
                     AA_kinase 158 gssDtiaallAealgAdkliiltdVdGVydadpkkvpdarllpeisvdeaeesaselatgGmkvkhpaalaaa 230
                                    s+D i   l + +++d + +l+dVdG++d+dpkk  da+ll++i+ +   ++ ++++tgG++ k+  ++ + 
  gi|13541011|ref|NP_110699.1| 141 YSGDNIVLDLSKIFNPDFVAFLSDVDGIFDKDPKKYRDAKLLRTINTKVEFSKPENDVTGGIENKLNTMFLIR 213
                                   *********************************************77766666888*********99887764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       466  (0.0259914); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 1685.47
//
Query:       gi|13541012|ref|NP_110700.1|  [L=176]
Description: acetyltransferase [Thermoplasma volcanium GSS1]
Scores for complete 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   65.5   0.0    9.2e-18   65.3   0.0    1.1  1  Acetyltransf_3   Acetyltransferase (GNAT) domain
    1.3e-15   57.9   0.1    1.7e-15   57.5   0.1    1.2  1  Acetyltransf_4   Acetyltransferase (GNAT) domain
    3.3e-10   40.2   0.1    4.2e-10   39.9   0.1    1.2  1  Acetyltransf_1   Acetyltransferase (GNAT) family
  ------ inclusion threshold ------
      0.065   13.7   0.1        0.1   13.1   0.1    1.4  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
      0.078   12.9   0.0        0.1   12.5   0.0    1.2  1  Acetyltransf_10  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 !   65.3   0.0   2.6e-21   9.2e-18      10     137 ..      19     149 ..      11     150 .. 0.84

  Alignments for each domain:
  == domain 1  score: 65.3 bits;  conditional E-value: 2.6e-21
                Acetyltransf_3  10 eDlealfelrsdpevmry.....lpepltleeaeewlerawaeeseeegyg..waivlkdtgviGsvglrdleeedeeael 83 
                                   e ++++++l++d+++ r      +p p+t e+a  ++e   ++++ +e++   ++i  k++   G++gl ++++ d++a++
  gi|13541012|ref|NP_110700.1|  19 EYADDIARLANDRTIKRNigshsFPYPYTKEDAIFFIE--AERGYGKEAFRidFLIKYKGG-PAGIIGLSEIDRTDKKAHV 96 
                                   5578999999****999654445555999999988888..455555566555588833444.8****************** PP

                Acetyltransf_3  84 gymlapsfwgkGyateavralleyafeelglerlvavidkeNeaSirvleklGf 137
                                   gy+++++f+gkG+ate +r ++eya ++ g +rl+  + + N  S  vl++ Gf
  gi|13541012|ref|NP_110700.1|  97 GYWIGKKFRGKGIATESLRLIVEYA-KNDGFHRLYTSVIEGNYPSMIVLMRNGF 149
                                   *************************.8888***********************9 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.5   0.1   4.6e-19   1.7e-15      32     152 ..      46     167 ..      18     169 .. 0.84

  Alignments for each domain:
  == domain 1  score: 57.5 bits;  conditional E-value: 4.6e-19
                Acetyltransf_4  32 ssveefekfleal.dsek...eyvflvaesdrivGyaylgqfkkrakdwkaelsvylaerdnnkeglgrelidaleqvlke 108
                                   +++e++  f+ea  + +k   ++ fl+ +++  +G+  l++++    d+ka + +++  ++ + +g++ e + ++++++k+
  gi|13541012|ref|NP_110700.1|  46 YTKEDAIFFIEAErGYGKeafRIDFLIKYKGGPAGIIGLSEIDR--TDKKAHVGYWIG-KKFRGKGIATESLRLIVEYAKN 123
                                   566666677777644333335888********************..***********7.89******************** PP

                Acetyltransf_4 109 qnienllaeiaspnensiqfhkalGFelvgifkkcikkngrwiD 152
                                    ++++l+++++  n +s+ ++ + GF+++g +k+ i +++r++D
  gi|13541012|ref|NP_110700.1| 124 DGFHRLYTSVIEGNYPSMIVLMRNGFSIEGVEKDSIRIGNRYYD 167
                                   *******************************************9 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.9   0.1   1.2e-13   4.2e-10      34     117 .]      68     149 ..      28     149 .. 0.78

  Alignments for each domain:
  == domain 1  score: 39.9 bits;  conditional E-value: 1.2e-13
                                   EEEEEEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTESEEEEEEETTEHHHHHHHHH CS
                Acetyltransf_1  34 gllvaeedgeliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeerareegikkivlaveedndaairlYek 114
                                     +++++ g ++G i+l+ i+    ++a++ ++++ +++rgkG++++ l+ ++e+a++ g+++++  v e n +++ ++++
  gi|13541012|ref|NP_110700.1|  68 IDFLIKYKGGPAGIIGLSEIDR-TDKKAHV-GYWIGKKFRGKGIATESLRLIVEYAKNDGFHRLYTSVIEGNYPSMIVLMR 146
                                   23448888**************.7899999.9******************************************9999989 PP

                                   TTE CS
                Acetyltransf_1 115 lGF 117
                                    GF
  gi|13541012|ref|NP_110700.1| 147 NGF 149
                                   988 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   2.8e-05       0.1       7      48 ..      71     116 ..      49     149 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.8e-05
                                   EEEETTEEEEEEEEEEES....TCTEEEEE-GGGTTSSHHHHHHHH CS
                Acetyltransf_7   7 VaeddgkivGfialslld....aeitrlaVdpeyrgkGiGraLlea 48 
                                   +++ +g++ G i+ls++d      + + ++ +++rgkGi+++ l++
  gi|13541012|ref|NP_110700.1|  71 LIKYKGGPAGIIGLSEIDrtdkKAHVGYWIGKKFRGKGIATESLRL 116
                                   35556888899999999886544444499************98885 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   2.8e-05       0.1      42      93 ..      81     135 ..      54     157 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.8e-05
               Acetyltransf_10  42 ivGviel.rdgs.hisllfVdpeyrgqGigkaLleaveeeaekdgikl.eltvna 93 
                                   i+G  e+ r+++       + +++rg+Gi+++ l  + e+a++dg +   ++v +
  gi|13541012|ref|NP_110700.1|  81 IIGLSEIdRTDKkAHVGYWIGKKFRGKGIATESLRLIVEYAKNDGFHRlYTSVIE 135
                                   4555578555555334568*************************99977777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       235  (0.0131073); expected 358.6 (0.02)
Passed bias filter:                      226  (0.0126053); 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: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 1163.42
//
Query:       gi|13541013|ref|NP_110701.1|  [L=263]
Description: Zn-dependent hydrolase [Thermoplasma volcanium GSS1]
Scores for complete 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-19   68.1   0.0    1.4e-18   67.6   0.0    1.2  1  Lactamase_B    Metallo-beta-lactamase superfamily
      0.002   17.7   0.0     0.0027   17.2   0.0    1.2  1  Lactamase_B_2  Beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.6   0.0   1.6e-22   1.4e-18       4     197 .]      44     240 ..      41     240 .. 0.93

  Alignments for each domain:
  == domain 1  score: 67.6 bits;  conditional E-value: 1.6e-22
                                   CSSEEEEEE.ETTCEEEES--SCHHHHHHHH............HHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCE CS
                   Lactamase_B   4 dpvnsylie.gdggviLiDtGtsteaaraal............elaalglkpkdvdavilTHlHlDHiGglgglveatdvp 71 
                                   + +n+ +i+  dg+ iL+D+G+++ ++++++            e+ +l+ +p+ v+ +i++HlH+DH+G ++++++a+ ++
  gi|13541013|ref|NP_110701.1|  44 LATNVLYITeSDGTSILVDSGIGNKFDDKFRkiyrvekqsdiyEYIRLHGDPNSVRMIINSHLHFDHVGHNADFKNAYAYA 124
                                   6789999999*********************************************************************** PP

                                   ETCCEHHHHCCHCHHHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTT CS
                   Lactamase_B  72 vgavaeeapalfmeeaddaasrkglllagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDal 152
                                   ++ + ++a++ ++  +  ++   +        + +  +e ++     g  ++  t g+++gh ++ + +gg+k+ + GD +
  gi|13541013|ref|NP_110701.1| 125 QADEFKAARYRNYITKANYRLSAS--------QIKNKVEIGGSKRINGFIRVIKTDGHTPGHQVILINAGGRKIMYFGDIV 197
                                   ****99999999999999988764........67889999999999999******************************** PP

                                   SSHHCCCCCC.TTCEEE-SHCHHHHHHHHHHHHHHHCHSEEEESS CS
                   Lactamase_B 153 lagetgridltlrgaevrdpsdaekyldsllklaglkaevlvpgH 197
                                   ++  +++++   r a ++dp    +  + l k+a  ++ ++++ H
  gi|13541013|ref|NP_110701.1| 198 PSTFHLKLPY--RTAIDLDPLKTIEFKKNLVKMAIRENYICIFNH 240
                                   *999999999..*******99999999999999988887777655 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   3.1e-07    0.0027       3     144 ..      59     197 ..      57     210 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 3.1e-07
                                   EEES--TT..........HHHHHTCGG.S--SSS--..SEEEEE-SS--HHHHGGGGCCCC.C--EEEEEE.EEHHHHHHC CS
                 Lactamase_B_2   3 iLiDagpd..........lrqqalral.qPvelrdelppidaVllthaHyDHlaglltlre.lrpkklply.apkgvlavl 70 
                                   iL+D g +           r   ++   +  +l  +++++ +++ +h H+DH+    +++   ++ +++ + a +    + 
  gi|13541013|ref|NP_110701.1|  59 ILVDSGIGnkfddkfrkiYRVEKQSDIyEYIRLHGDPNSVRMIINSHLHFDHVGHNADFKNaYAYAQADEFkAARYRNYIT 139
                                   6777777777777766653333233332444478899****************6666676643333333332555555566 PP

                                   CTTCGHHHCHTTTTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S CS
                 Lactamase_B_2  71 eanfvylaleeepavnvheldwgesfelgdggleitatparhksgrrldrnagdtlGlriegggkrvyyigDtg 144
                                   +an    a++ +     +++++g+s +++  g+ i+++   + ++             +i  gg++++y gD  
  gi|13541013|ref|NP_110701.1| 140 KANYRLSASQIK-----NKVEIGGSKRIN--GF-IRVIKTDGHTPG--------HQVILINAGGRKIMYFGDIV 197
                                   666666666666.....889999999998..55.999999999988........66778889999999999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       569  (0.0317363); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1693.73
//
Query:       gi|13541014|ref|NP_110702.1|  [L=321]
Description: phosphate uptake regulator [Thermoplasma volcanium GSS1]
Scores for complete 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   8.8      7e-15   55.3   3.1    2.9  2  PhoU            PhoU domain
    4.5e-08   32.9   0.2      1e-07   31.7   0.2    1.6  1  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an
  ------ inclusion threshold ------
       0.01   14.9   0.1      0.016   14.3   0.1    1.2  1  Fungal_trans    Fungal specific transcription factor domain
      0.024   14.5   0.0        0.1   12.5   0.0    1.9  2  Rossmann-like   Rossmann-like domain


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 !   55.3   3.1   1.6e-18     7e-15       1      86 [.     140     218 ..     140     221 .. 0.87
   2 !   12.7   0.3     3e-05      0.13      10      88 ..     242     306 ..     234     307 .. 0.83

  Alignments for each domain:
  == domain 1  score: 55.3 bits;  conditional E-value: 1.6e-18
                                   HHHHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SHHHHHHHHHHHHHHHHHHHHHH CS
                          PhoU   1 lrrmaeiveemlddalealeekdtelarevierddeidrlekeiersllealakrqplaedlrellsllriardlERigDh 81 
                                   +rrm+  v +m++d+++a+e++d+el + vierdde+dr++  i+r+ ++   +++  +      + +l ++r lER++Dh
  gi|13541014|ref|NP_110702.1| 140 IRRMSLNVGTMIEDTIKAIEDYDEELFQNVIERDDEVDRYQWYIYRE-VKNHCQYEDSN------VFMLVLSRILERMADH 213
                                   79*********************************************.44444544322......227889********** PP

                                   HHHHH CS
                          PhoU  82 avnia 86 
                                    vni+
  gi|13541014|ref|NP_110702.1| 214 TVNIC 218
                                   ****8 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 3e-05
                                   HHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          PhoU  10 emlddalealeekdtelarevierddeidrlekeiersllealakrqplaedlrellsllriardlERigDhavniaer 88 
                                   +  + a+e++++k+ + ++ +i++  ei++  +++    l++l+         + +  l +ia ++ Rig + ++iae 
  gi|13541014|ref|NP_110702.1| 242 DVYNHAVESFYSKNFKVLDGIINQKSEINERKFKL----LKILSY--------DVV--LSSIAEEISRIGLYGTDIAEL 306
                                   566889********9****************9998....555632........222..5679***************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 !   31.7   0.2   2.2e-11     1e-07       2      39 ..      11      48 ..      10      53 .. 0.94

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 2.2e-11
                                  EETTEEEEEE-CCCHHHCCEECTCEEEEEECTTCCCCC CS
                MazE_antitoxin  2 kvGnsgavriPkevrfelgireGdevelevdgdkiilr 39
                                  ++G++ +v++P e+++ +gi +G+e+ ++ dg++++++
  gi|13541014|ref|NP_110702.1| 11 TGGSTFIVSLPPEWVKRNGITKGSEISISDDGNDLVIS 48
                                  79******************************999997 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 ?   14.3   0.1   3.5e-06     0.016     192     266 ..     161     245 ..     152     246 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.5e-06
                  Fungal_trans 192 lwesddaseetlvetk..........lsneeksrkiasfllaLkkilskiagsllsiekqlqqrdlqseklswveeleral 262
                                   ++e ++ + +++ + +          ++n+++ ++ + f+l L++il  +a+ + +i+  ++ r+ ++   ++++ l ++l
  gi|13541014|ref|NP_110702.1| 161 YDEELFQNVIERDDEVdryqwyiyreVKNHCQYEDSNVFMLVLSRILERMADHTVNICIAMKDRKAVNGRMEMIDNLKFSL 241
                                   444444444555444466666666778**************************************9999999999999999 PP

                  Fungal_trans 263 dnWr 266
                                   d+++
  gi|13541014|ref|NP_110702.1| 242 DVYN 245
                                   9876 PP

>> Rossmann-like  Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   2.3e-05       0.1      13      72 ..      87     146 ..      81     158 .. 0.92
   2 ?   -1.3   0.0      0.41   1.8e+03      24      44 ..     202     223 ..     200     247 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.3e-05
                 Rossmann-like  13 vGiisaGrvGtalgaaleraghvvvgisaisaasreraerrlPdvpvlevedvaaraell 72 
                                   + i+s  ++G+ l   ++r   vv+gi  i ++s+    + + +v+  ++ + ++r  l 
  gi|13541014|ref|NP_110702.1|  87 LSIVSKEKMGSELRDDIKRFSKVVMGIEIIEETSKSVVLQNVLNVKTFPLSKAIRRMSLN 146
                                   579***********************************************9999998875 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.41
                 Rossmann-like  24 algaaler.aghvvvgisaisa 44 
                                   +l+  ler a+h+v  + a+ +
  gi|13541014|ref|NP_110702.1| 202 VLSRILERmADHTVNICIAMKD 223
                                   5777788757999999988865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       769  (0.0428914); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 2068.93
//
Query:       gi|13541015|ref|NP_110703.1|  [L=237]
Description: hypothetical protein TVN0184 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       886  (0.0494171); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1516.60
//
Query:       gi|13541016|ref|NP_110704.1|  [L=194]
Description: transcription regulator [Thermoplasma volcanium GSS1]
Scores for complete 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-23   80.4   1.2    1.4e-14   54.2   0.1    2.5  2  CBS             CBS domain
    7.4e-15   54.8   0.5    1.6e-14   53.6   0.5    1.6  1  HTH_3           Helix-turn-helix
    8.6e-12   44.9   0.2    3.3e-11   43.0   0.2    2.0  2  HTH_19          Helix-turn-helix domain
    6.5e-11   42.4   0.0    1.3e-10   41.5   0.0    1.5  1  HTH_31          Helix-turn-helix domain
    2.9e-05   23.8   0.0    5.9e-05   22.8   0.0    1.5  1  HTH_25          Helix-turn-helix domain
    0.00011   22.5   0.1     0.0005   20.4   0.0    2.1  2  HTH_26          Cro/C1-type HTH DNA-binding domain
    0.00025   20.9   0.1      0.002   18.1   0.0    2.1  2  HTH_37          Helix-turn-helix domain
    0.00084   19.4   0.0     0.0014   18.7   0.0    1.4  1  MqsA_antitoxin  Antitoxin component of bacterial toxin-antito
     0.0039   17.8   0.0     0.0062   17.2   0.0    1.3  1  HNF-1_N         Hepatocyte nuclear factor 1 (HNF-1), N termin
  ------ inclusion threshold ------
      0.013   15.4   0.0      0.047   13.7   0.0    1.9  1  Pou             Pou domain - N-terminal to homeobox domain
      0.018   14.6   0.0      0.059   12.9   0.0    1.9  1  HTH_24          Winged helix-turn-helix DNA-binding
      0.064   13.1   0.0        0.2   11.5   0.0    1.8  1  HTH_23          Homeodomain-like domain
      0.073   13.0   0.0       0.16   11.8   0.0    1.6  1  MarR_2          MarR family
       0.14   12.1   0.8       0.39   10.7   0.1    2.0  2  DUF3659         Protein of unknown function (DUF3659)


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.2   0.1   1.1e-17   1.4e-14       3      51 ..      73     121 ..      71     127 .. 0.94
   2 !   24.6   0.1   1.9e-08   2.5e-05       2      55 ..     140     190 ..     139     192 .. 0.82

  Alignments for each domain:
  == domain 1  score: 54.2 bits;  conditional E-value: 1.1e-17
                                   HHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHH CS
                           CBS   3 dimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDl 51 
                                    imtr+vv+++ d+++ +al+lmr++g+s+lPVV+e++k++G vt++ +
  gi|13541016|ref|NP_110704.1|  73 KIMTRNVVVCRADDSILKALNLMRDRGYSQLPVVNEENKVIGTVTESNI 121
                                   59********************************************987 PP

  == domain 2  score: 24.6 bits;  conditional E-value: 1.9e-08
                                   HHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                           CBS   2 gdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                   + +m + ++ v+ +t++  + +l+ ++  ++++V+ ++g+l Gi+t+ D+l+ +
  gi|13541016|ref|NP_110704.1| 140 RRVMGDVLPQVDKNTPINVIYQLL-KY-SNAVLVL-DSGNLTGIITKADILKTV 190
                                   56666667899*************.62.3688888.6999***********976 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.6   0.5   1.3e-17   1.6e-14       1      48 [.      10      57 ..      10      62 .. 0.94

  Alignments for each domain:
  == domain 1  score: 53.6 bits;  conditional E-value: 1.3e-17
                                  HHHHHHHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHHH CS
                         HTH_3  1 lkelRkqlglsqeeLAeklGvsrstisriEnGernPsletlkklakaL 48
                                  l+++Rk lg+sq++LA+++Gvs+s+i+r+E+G  nP+ +++k++ ++L
  gi|13541016|ref|NP_110704.1| 10 LRKMRKNLGISQKDLARVTGVSQSYIARLEKGTINPTYSKIKAIYEYL 57
                                  89*****************************************98877 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.0   0.2   2.6e-14   3.3e-11       4      52 ..      10      57 ..       7      58 .. 0.97
   2 ?   -1.6   0.0       2.3   2.9e+03      11      22 ..     135     146 ..     133     167 .. 0.67

  Alignments for each domain:
  == domain 1  score: 43.0 bits;  conditional E-value: 2.6e-14
                        HTH_19  4 LkeaReelgltqeelaerlgisrskisaiEngkkdvpsaelllkiaeal 52
                                  L+++R++lg++q++la+ +g+s+s+i+ +E+g + +p+++++++i+e+l
  gi|13541016|ref|NP_110704.1| 10 LRKMRKNLGISQKDLARVTGVSQSYIARLEKGTI-NPTYSKIKAIYEYL 57
                                  9*********************************.************97 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.3
                        HTH_19  11 lgltqeelaerl 22 
                                   +glt + +++++
  gi|13541016|ref|NP_110704.1| 135 RGLTVRRVMGDV 146
                                   688888887743 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.5   0.0     1e-13   1.3e-10       5      53 ..       9      56 ..       8      61 .. 0.93

  Alignments for each domain:
  == domain 1  score: 41.5 bits;  conditional E-value: 1e-13
                        HTH_31  5 lLralReraGLsqeevAerlgvsestlsrlEqGrrgrpspavlealara 53
                                  +Lr +R+  G+sq+++A+ +gvs+s++ rlE G++ +p+ + + a+ ++
  gi|13541016|ref|NP_110704.1|  9 ELRKMRKNLGISQKDLARVTGVSQSYIARLEKGTI-NPTYSKIKAIYEY 56
                                  8**********************************.6*****9998665 PP

>> HTH_25  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0   4.6e-08   5.9e-05       2      35 ..      10      43 ..       9      50 .. 0.94

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 4.6e-08
                                  HHHHHHTTT--HHHHHHHSS--HHHHHHHHCT-- CS
                        HTH_25  2 LraaRearglsleevaketkIrkdylealEeddf 35
                                  Lr+ R+ +g+s +++a+ t ++++y+ +lE++ +
  gi|13541016|ref|NP_110704.1| 10 LRKMRKNLGISQKDLARVTGVSQSYIARLEKGTI 43
                                  9*****************************9976 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 !   20.4   0.0   3.9e-07    0.0005       2      46 ..      10      53 ..       9      58 .. 0.86
   2 ?   -1.9   0.0       3.8   4.9e+03       4      12 ..      93     101 ..      86     102 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 3.9e-07
                        HTH_26  2 LrelmadrgitkseLargtgisaatlsrlvkgkpervsldtLdki 46
                                  Lr++ +  gi++++Lar tg+s++ ++rl kg++ +++ + + +i
  gi|13541016|ref|NP_110704.1| 10 LRKMRKNLGISQKDLARVTGVSQSYIARLEKGTI-NPTYSKIKAI 53
                                  99******************************97.6666666666 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3.8
                        HTH_26   4 elmadrgit 12 
                                   +lm+drg++
  gi|13541016|ref|NP_110704.1|  93 NLMRDRGYS 101
                                   588888876 PP

>> HTH_37  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   1.5e-06     0.002      22      57 ..       9      44 ..       3      49 .. 0.92
   2 ?    0.0   0.0      0.65   8.3e+02      43      66 ..     116     136 ..     107     141 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.5e-06
                                  HHHHHHHHCT--HHHHHHHHT--HHHHHHHHTT--T CS
                        HTH_37 22 aiaeliekrelsqseaaqllgiaqPkvsrllrgkls 57
                                  +++++++ +++sq+++a+ +g++q+ + rl++g ++
  gi|13541016|ref|NP_110704.1|  9 ELRKMRKNLGISQKDLARVTGVSQSYIARLEKGTIN 44
                                  58999***************************9876 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.65
                                   --HHHHHHHHTT--TT--HHHHHH CS
                        HTH_37  43 iaqPkvsrllrgklsrfsldkLln 66 
                                   +++++++++l   l+ +s+d+L+ 
  gi|13541016|ref|NP_110704.1| 116 VTESNINDML---LKGMSVDSLRG 136
                                   7888888988...99999999986 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 !   18.7   0.0   1.1e-06    0.0014      72     116 ..       8      52 ..       2      67 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.1e-06
                MqsA_antitoxin  72 afiarvrkkleldqreaaeifGgGvnafsryekGkvrpplalvkl 116
                                   ++++++rk+l+++q+++a++ G+     +r ekG ++p  + +k 
  gi|13541016|ref|NP_110704.1|   8 DELRKMRKNLGISQKDLARVTGVSQSYIARLEKGTINPTYSKIKA 52 
                                   57899**********************************999985 PP

>> HNF-1_N  Hepatocyte nuclear factor 1 (HNF-1), N terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   4.9e-06    0.0062     150     190 ..      15      55 ..       7      59 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 4.9e-06
                       HNF-1_N 150 qqhrIsQrevvdvTGlsQShlSqwLlkGt.pmktqkraalYr 190
                                   ++  IsQ+  + vTG+sQS++ + L kGt +   +k +a+Y+
  gi|13541016|ref|NP_110704.1|  15 KNLGISQKDLARVTGVSQSYIAR-LEKGTiNPTYSKIKAIYE 55 
                                   5667*****************97.676651444566677776 PP

>> Pou  Pou domain - N-terminal to homeobox domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   3.6e-05     0.047      12      54 ..       9      45 ..       5      62 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.6e-05
                           Pou 12 efkqkRiklgltQadvglaLgklygkefSqttIcrFEkLdlsl 54
                                  e+++ R +lg++Q+d+++       + +Sq+ I r+Ek ++++
  gi|13541016|ref|NP_110704.1|  9 ELRKMRKNLGISQKDLARV------TGVSQSYIARLEKGTINP 45
                                  899************9886......679*********977765 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   4.6e-05     0.059      14      36 ..      15      37 ..      10      38 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.6e-05
                        HTH_24 14 knprisqreLAerlglSpstvnr 36
                                  kn +isq++LA+ +g+S+s + r
  gi|13541016|ref|NP_110704.1| 15 KNLGISQKDLARVTGVSQSYIAR 37
                                  6669*************998765 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00016       0.2      13      39 ..      13      40 ..       9      42 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00016
                        HTH_23 13 llae.GlsvreIAreLgvsrrTvyrwlk 39
                                  + ++ G+s+++ Ar  gvs++ + r  k
  gi|13541016|ref|NP_110704.1| 13 MRKNlGISQKDLARVTGVSQSYIARLEK 40
                                  44558******************99865 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00013      0.16      17      41 ..      16      38 ..       8      40 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00013
                                  TTTSEEEHHHHHHHHTSSHHHHHHH CS
                        MarR_2 17 rpgrdltvgelarrlglsksavsri 41
                                  + g  +++++lar +g+s+s++ r+
  gi|13541016|ref|NP_110704.1| 16 NLG--ISQKDLARVTGVSQSYIARL 38
                                  445..89***************986 PP

>> DUF3659  Protein of unknown function (DUF3659)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1    0.0003      0.39      14      39 ..     105     132 ..     104     147 .. 0.87
   2 ?   -1.6   0.0         2   2.6e+03      17      29 ..     173     185 ..     167     193 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0003
                       DUF3659  14 vvdeeGnvvGrvveGdlkkLa..Gkkvd 39 
                                   vv+ee +v+G v+e +++++   G++vd
  gi|13541016|ref|NP_110704.1| 105 VVNEENKVIGTVTESNINDMLlkGMSVD 132
                                   9*************98888765588887 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2
                       DUF3659  17 eeGnvvGrvveGd 29 
                                   ++Gn  G +++ d
  gi|13541016|ref|NP_110704.1| 173 DSGNLTGIITKAD 185
                                   4888888888764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       769  (0.0428914); expected 358.6 (0.02)
Passed bias filter:                      575  (0.0320709); 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):              14  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 1196.43
//
Query:       gi|13541017|ref|NP_110705.1|  [L=177]
Description: hypothetical protein TVN0186 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.9e-36  123.9   8.7    7.6e-36  123.7   8.7    1.0  1  CarS-like     CDP-archaeol synthase
    1.4e-08   34.9   7.1    1.4e-08   34.9   7.1    1.5  1  CTP_transf_1  Cytidylyltransferase family
  ------ inclusion threshold ------
        6.9    6.2   9.8         12    5.4   9.4    1.7  1  PMT_4TMC      C-terminal four TMM region of protein-O-mannosy


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 !  123.7   8.7   1.3e-39   7.6e-36       7     175 .]       3     177 .]       1     177 [] 0.91

  Alignments for each domain:
  == domain 1  score: 123.7 bits;  conditional E-value: 1.3e-39
                     CarS-like   7 ksiylllpayvanasavlvGGGtpvdlGktlvdGrrliGdGvtyrGtvaGvlvGvlvgliqglleklsilaldssgsvlef 87 
                                   ++i l++pa +an  avl GG   +d Gk+++dGrr++GdG+t  G ++G ++G++ g+i + +   +   l  +gs+   
  gi|13541017|ref|NP_110705.1|   3 QAIILFVPALIANSGAVLTGGYFVLDRGKNFIDGRRILGDGKTLSGYLGGSFIGIVSGVIIYWISYATHFILGNYGSIALS 83 
                                   578899**********************************************************8888899********** PP

                     CarS-like  88 vilalllafGallGdavGsfikrrlkierGkpalildqldfvlgalllayp......vkllpieliilivlitlvlhlsan 162
                                   + +  ++afG+l Gd+ Gsf+krr++i+ G +  +ldq  f l+a+l+ +       +    +  ii+i+ i + lh ++n
  gi|13541017|ref|NP_110705.1|  84 IEIPAVMAFGSLTGDILGSFVKRRIGIKSGGKGGLLDQWPFALVAFLFLFLmerpffLHYYFFAGIIVILAIVPPLHRAVN 164
                                   *********************************************998855222232334444557888888999****** PP

                     CarS-like 163 iiayklglkdvwy 175
                                   ii ykl  kdv++
  gi|13541017|ref|NP_110705.1| 165 IIGYKLHKKDVPW 177
                                   ************9 PP

>> CTP_transf_1  Cytidylyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.9   7.1   2.3e-12   1.4e-08     170     261 ..      43     134 ..      40     139 .. 0.90

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 2.3e-12
                                   --BHHHHHHHHHHHHHHHHHHHHHHHCTS.....---TTSHHHHHHHHHHHHHHHHHHHHHHHHHHT-SSS-S-SSSSS-H CS
                  CTP_transf_1 170 kKTveGfigGlvaavvvglllalvlskal.....alsllhllllslllslvavfGDLveSglKRafgiKDsGkliPGhGGi 245
                                   +KT++G++gG+++ +v g++++++   +      + s+  ++ + +++++ +  GD++ S +KR++giK  Gk     GG+
  gi|13541017|ref|NP_110705.1|  43 GKTLSGYLGGSFIGIVSGVIIYWISYATHfilgnYGSIALSIEIPAVMAFGSLTGDILGSFVKRRIGIKSGGK-----GGL 118
                                   6***********************999889999999999999999************************8877.....*** PP

                                   HHHHHHHHHHHHHHHH CS
                  CTP_transf_1 246 lDRlDsllfaapvvyl 261
                                   lD     l+a+ +++l
  gi|13541017|ref|NP_110705.1| 119 LDQWPFALVAFLFLFL 134
                                   **98777777766665 PP

>> 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 ?    5.4   9.4    0.0021        12     109     138 ..     128     157 ..      60     173 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0021
                      PMT_4TMC 109 hylPfflmgRvlflhhYlpAllfailllaa 138
                                    +l  flm+R  flh Y+ A ++ il++  
  gi|13541017|ref|NP_110705.1| 128 AFLFLFLMERPFFLHYYFFAGIIVILAIVP 157
                                   4566799*******************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      231  (0.0128842); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.34u 0.26s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 1314.07
//
Query:       gi|13541018|ref|NP_110706.1|  [L=117]
Description: peptidyl-tRNA hydrolase [Thermoplasma volcanium GSS1]
Scores for complete 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  134.3   0.2    2.5e-39  134.2   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 !  134.2   0.2   1.4e-43   2.5e-39       1     117 []       3     117 .]       3     117 .] 0.98

  Alignments for each domain:
  == domain 1  score: 134.2 bits;  conditional E-value: 1.4e-43
                                   EEEEEEEESSSSS-HHHHHHHHHHHHHHHHHHHHHH.CHHHHHHHHHHTTTSEEEEEESSHHHHHHHHHHHHHTT-SEEEE CS
                          PTH2   1 lkmvlvvrkDLkmskGkiaaqcahAavalvkkllkesnekellkeWeeegqkkivlkveseeeLlelaakakalglpaali 81 
                                   +k+v+ vrkDL m+kGkiaaq+ahAav+++ k++ke ++ ++++eW++egqkkiv+kv++ +e+  +++ka++ g+ +++i
  gi|13541018|ref|NP_110706.1|   3 VKLVVAVRKDLDMGKGKIAAQVAHAAVSCAIKAMKE-KK-KIFDEWMDEGQKKIVVKVPNVDEIYIIKKKADSMGIINEVI 81 
                                   599********************************9.67.8**************************************** PP

                                   EETSSSSSSTTCEEEEEEEEEEHHHHHHHHTTSEB- CS
                          PTH2  82 rDagrtqiepgtkTvlaigPapksivdkvtgkLkll 117
                                   +D g tq+epgt+T++++gP  +  +d +tgk+kll
  gi|13541018|ref|NP_110706.1|  82 QDRGYTQVEPGTVTCIGLGPDYEVYLDDITGKYKLL 117
                                   **********************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       884  (0.0493056); expected 358.6 (0.02)
Passed bias filter:                      586  (0.0326845); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 822.18
//
Query:       gi|13541019|ref|NP_110707.1|  [L=56]
Description: hypothetical protein TVN0188 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       768  (0.0428356); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 380.68
//
Query:       gi|13541020|ref|NP_110708.1|  [L=881]
Description: aconitate hydratase [Thermoplasma volcanium GSS1]
Scores for complete 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-177  588.7   0.0   1.2e-176  588.3   0.0    1.1  1  Aconitase    Aconitase family (aconitate hydratase)
    8.2e-43  145.9   0.0    1.8e-42  144.8   0.0    1.6  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 !  588.3   0.0  1.4e-180  1.2e-176       4     461 .]      64     556 ..      56     556 .. 0.94

  Alignments for each domain:
  == domain 1  score: 588.3 bits;  conditional E-value: 1.4e-180
                     Aconitase   4 wdahlveeegiayvpdrvllqdvtgvqalvdlaaareavrrlggtlatidhlvpvdlvidhsv.....gaeealeknlede 79 
                                   w+  +v +++i ++++rv++qd+tgv+a+vdla++r++v++lg++++ i+++v vdlvidhsv     g++ a+ekn e e
  gi|13541020|ref|NP_110708.1|  64 WNPSNVPDKEIRFKVSRVVMQDFTGVPAVVDLASMRDTVKKLGKDPELINPQVRVDLVIDHSVqvdyyGESFAIEKNEELE 144
                                   664445444499*******************************************************99999********* PP

                     Aconitase  80 fernkeryefLksaakaf.girvvppgqGIvHqvnlEy.............glalpgktvvgtDSHTtmigglGvlaiGvG 146
                                   f+rn ery+fLk+a+k+f ++rv+ppg+GI+HqvnlEy              +a+ + t+vgtDSHTtmi+g+Gvl++GvG
  gi|13541020|ref|NP_110708.1| 145 FNRNLERYKFLKWAQKSFkNFRVIPPGTGIIHQVNLEYlaevifdyeekgkRYAYFD-TLVGTDSHTTMINGIGVLGWGVG 224
                                   ********************************************99998655*****.*********************** PP

                     Aconitase 147 gieaeavllgqplelkipkvvgvkltGklkegvtakDlvlavigklrkkgvvgkvvEffGegvesLsledraTiaNMaaEv 227
                                   gieaea+llgqp+++++p+v+gv+l+G+l++gvta+Dlvl++++ lrk +vv+k+vEffG+ v+ Ls+ +raT++NM++E+
  gi|13541020|ref|NP_110708.1| 225 GIEAEAALLGQPITISLPEVIGVRLHGELNPGVTATDLVLTITELLRKVNVVDKFVEFFGPSVKYLSVPERATVSNMCPEY 305
                                   ********************************************************************************* PP

                     Aconitase 228 GAttglfpvdektleYLkatgreeaav.lveaydkaqalfelaadedaeydkvleldlstlepsvagpkrPqdavplselv 307
                                   GAt +lfp+d++tl+YL++tgr+++++ l+++y + q++f   ++e+ ey+kv++ldlst++psvagpk Pq++++l ++v
  gi|13541020|ref|NP_110708.1| 306 GATLALFPIDDQTLDYLRTTGRSDHKIkLIKKYLELQGMFG--ESEGVEYTKVIDLDLSTVKPSVAGPKLPQQRLDL-DQV 383
                                   **************************9999********994..7889******************************.788 PP

                     Aconitase 308 kkefkeelekeaaekaley......klkegtklkdgkvdiaaigSCTNssnedvraaaglla.kavekglkvkpgvktsva 381
                                   +++f +++e+++ ++ +++       ++++++l+dg+++iaai+SCTN+sn+ v++aagl+a kave glkv+p+vkts+a
  gi|13541020|ref|NP_110708.1| 384 PSSFLSSVESNSDSHLVSLrkvplkLKGQDVELSDGDIVIAAITSCTNTSNPYVMLAAGLVAkKAVELGLKVNPKVKTSLA 464
                                   778888888666666555555666546689*************************************************** PP

                     Aconitase 382 PGSevvkayleaeGlleiLekaGfevvgagCstCignsdrle........ege...aivsssNRNFegRqgpntra.yLaS 450
                                   PGS+vv++yl+++Gl ++L+k+Gf +vg+gC+tCigns++l+        +++   ++v+s+NRNFe+R++++++a yL+S
  gi|13541020|ref|NP_110708.1| 465 PGSRVVTDYLTESGLIDYLDKLGFYLVGYGCTTCIGNSGPLDkdvdeaiiKNNlnvVSVLSGNRNFEARIHKDVKAnYLMS 545
                                   *****************************************978777776444889************************* PP

                     Aconitase 451 PelvvaaAlaG 461
                                   P+lvva+A+aG
  gi|13541020|ref|NP_110708.1| 546 PPLVVAYAIAG 556
                                   **********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 !  144.8   0.0     2e-46   1.8e-42       3     129 ..     684     809 ..     682     811 .. 0.98

  Alignments for each domain:
  == domain 1  score: 144.8 bits;  conditional E-value: 2e-46
                                   CCCCCTT--CHHHHSTGGGCCGHCCHHHCCCGGTTTCCCCTTTSBBSEEEETTTTEEEEHHHHHHHHHHTT--EEEE--SS CS
                   Aconitase_C   3 kllklkGlttedeksnvdtdlkipkqfegtianiglgnelveekrankttdlddgekedvvdaaerykkegaklvviagkn 83 
                                   k+l ++G+++ed++s+++++++++++++gt+an++++n +v+ k+ + t+  +d+++++v+daa++y++ g++lvv+ag +
  gi|13541020|ref|NP_110708.1| 684 KYLIEHGVKPEDFNSYGSRRGNHEVMMRGTFANVRIRNLMVN-KEGGYTIFIPDNKEMSVYDAAMKYRSMGIPLVVVAGRE 763
                                   7999***********************************999.9************************************* PP

                                   BTBS---THHHHHHHHTTEEEEEES-B-HHHHHHHHHTT-EEEEES CS
                   Aconitase_C  84 fGeGSSRehAAkalrllGikaviaeSFerIfennliknglLplefk 129
                                   +G+GSSR++AAk+++llG++av+a+S+erI+++nl+++g++p+e++
  gi|13541020|ref|NP_110708.1| 764 YGTGSSRDWAAKGTYLLGVRAVLAKSYERIHRSNLVGMGVIPIEYE 809
                                   *******************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (881 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); 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:                         2  (0.000111551); expected 0.2 (1e-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 0.34s 00:00:01.07 Elapsed: 00:00:00.51
# Mc/sec: 5242.33
//
Query:       gi|13541021|ref|NP_110709.1|  [L=406]
Description: threonine dehydratase [Thermoplasma volcanium GSS1]
Scores for complete 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-86  288.7   0.6    6.7e-86  288.3   0.6    1.1  1  PALP      Pyridoxal-phosphate dependent enzyme
    7.6e-10   39.3   0.0    1.8e-09   38.0   0.0    1.6  1  ACT_4     ACT domain
     0.0024   17.6   0.0      0.005   16.6   0.0    1.6  1  ACT       ACT domain
     0.0036   17.2   0.0      0.006   16.4   0.0    1.3  1  AAA_26    AAA 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 !  288.3   0.6   1.5e-89   6.7e-86       3     294 .]      21     308 ..      19     308 .. 0.98

  Alignments for each domain:
  == domain 1  score: 288.3 bits;  conditional E-value: 1.5e-89
                                   GCSSS--EEEECCTCCCCCCEEEEEEGGGSTTSBTTHHHHHHHHHHHHTTTTTSEEEEEBSSHHHHHHHHHHHHHT-EEEE CS
                          PALP   3 lgigpTPlvrlprlskelgvplflKlEslnptgSfKdRgaeyllarlkegtgaktvveassGNhgralAaaaallGlkvti 83 
                                   + + +TPl+r+  + ke+g+++++KlE++++tgSfK Rga +++++l e +++ +v++as+GNh++++A+aa   G+++ i
  gi|13541021|ref|NP_110709.1|  21 GKVNRTPLIRSTTIGKEYGADIYFKLENFQKTGSFKSRGAIFRFSKLSEDEKRHGVITASAGNHAQGVAYAAMINGIDAKI 101
                                   66789*****************************************99999****************************** PP

                                   EEETTS-HHHHHHHHHTT-EEEEECCHHHHHHHHHHHHHHHSTTCEE--TTTSHHHHHHHHTHHHHHHHHTTTTEEEEEEE CS
                          PALP  84 vvpadaspekvallrllGaevvevggdydeavaaaaelaaegegaylvsqfdnptviegygtiglEileqlggkpdavvvp 164
                                   v+p+ + p+kv +  ++Ga+v++ g+dydea ++a e+a++ eg++++  f++ +vi g+gtiglEi+e+l +++d ++vp
  gi|13541021|ref|NP_110709.1| 102 VMPEYTIPQKVNAVISYGAHVILKGSDYDEAHRYADEIAKQ-EGRIFIEAFNDRWVISGQGTIGLEIMEDL-PDVDIILVP 180
                                   *****************************************.*****************************.6******** PP

                                   -SSSHHHHHHHHHHHHHSTT-EEEEEEECTTCGGTTCCS..S.SS..B.SSS.CCSTCSCGTTCCHHHHSEEEEEEEEEEH CS
                          PALP 165 vGgGgliaGiaaglkerrpdvrvigvepegsdalarslragrrvtvpvsdtiadglavgspselafelldrlvdeivtvsd 245
                                   vGgGgli+Gia + k++  +v+vig+e+e sd++ +slr+g+ v  +++ +i+dg++v+ p++l+f++++++vd+ivtv++
  gi|13541021|ref|NP_110709.1| 181 VGGGGLISGIALAAKHASNKVKVIGIESELSDSMKASLREGKIVAHTSGVSICDGISVKYPGVLTFDIARKYVDDIVTVTE 261
                                   ********************************************************************************* PP

                                   HHHHHHHHHHHHHHSB-B-HHHHHHHHHHHHHHHHCCTTCEEEEEEE-B CS
                          PALP 246 eealeamrllarregivvepssaaalaalklreagelkegdrvvviltg 294
                                   e + +a+ +l +r++iv+eps+a++laa+ ++ + ++k++ +v ++++g
  gi|13541021|ref|NP_110709.1| 262 EYVSKAIYKLFERNKIVAEPSGAVGLAAI-MEGKVDVKGK-KVAIVVSG 308
                                   *****************************.9999999999.99999998 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.0   0.0   4.1e-13   1.8e-09       6      72 ..     330     399 ..     325     405 .. 0.94

  Alignments for each domain:
  == domain 1  score: 38.0 bits;  conditional E-value: 4.1e-13
                         ACT_4   6 tvrleveaedrkglLaditqviseekanivsvnaktrkk...dglaeikitveVkdvehLsrviakLrai 72 
                                    vr+e +  dr+g L +i+ +i+e+++ni + ++++ +k    g+ ++++tv+V+  +hL+r+i +Lr++
  gi|13541021|ref|NP_110709.1| 330 LVRIECTIPDRPGNLYRIAMAIAENGGNIYHAEVDNLRKetpPGFQSVTFTVNVRGQDHLDRIIGSLREM 399
                                   599*********************************99888889***********************986 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   1.1e-06     0.005       2      58 ..     332     392 ..     331     399 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.1e-06
                                   EEEEEEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTT....ECEEEEEEEEEEHHHHHHH CS
                           ACT   2 vlrvgvpDrPGlLarvfgaladrgiNidsieqrssedk....vagivfvvivvdeedleev 58 
                                   ++++  pDrPG L r++ a+a++g Ni ++e+   + +    + + +f+v v ++++l+ +
  gi|13541021|ref|NP_110709.1| 332 RIECTIPDRPGNLYRIAMAIAENGGNIYHAEVDNLRKEtppgFQSVTFTVNVRGQDHLDRI 392
                                   688999*********************9999987777776556666666665555555555 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   1.3e-06     0.006      85     162 ..     128     206 ..      93     206 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.3e-06
                        AAA_26  85 did.lekivkelekdadivvVEGagglgvpiteellnadiaknl.gapvilVargglgtinqllltiealrqknvrvlGv 162
                                   d d   ++ +e++k++  +++E++   +v + ++++  +i++ l ++++ilV  gg g i  ++l+++++ + +v+v+G+
  gi|13541021|ref|NP_110709.1| 128 DYDeAHRYADEIAKQEGRIFIEAFNDRWVISGQGTIGLEIMEDLpDVDIILVPVGGGGLISGIALAAKHASN-KVKVIGI 206
                                   44445566699*********************************99**********************9988.6999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (406 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       574  (0.0320152); expected 358.6 (0.02)
Passed bias filter:                      494  (0.0275531); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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: 2621.46
//
Query:       gi|13541022|ref|NP_110710.1|  [L=183]
Description: RNA methylase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-15   57.6   0.0    1.7e-15   57.0   0.0    1.3  1  MTS              Methyltransferase small domain
    5.5e-08   33.4   0.0    8.1e-08   32.9   0.0    1.3  1  Methyltransf_25  Methyltransferase domain
    4.3e-07   29.9   0.0    4.9e-07   29.7   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
    9.5e-07   28.5   0.0    1.3e-06   28.0   0.0    1.1  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
      1e-05   25.2   0.0    1.2e-05   24.9   0.0    1.3  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
    1.2e-05   25.8   0.1    2.2e-05   25.0   0.1    1.5  1  Methyltransf_11  Methyltransferase domain
    1.7e-05   25.5   0.1      4e-05   24.3   0.0    1.6  2  Methyltransf_12  Methyltransferase domain
    5.4e-05   23.0   0.0    0.00011   22.0   0.0    1.5  2  Methyltransf_16  Lysine methyltransferase
    5.4e-05   23.0   0.0    7.5e-05   22.5   0.0    1.2  1  UPF0020          Putative RNA methylase family UPF0020
    0.00015   21.3   0.0    0.00024   20.6   0.0    1.3  1  TehB             Tellurite resistance protein TehB
     0.0036   17.1   0.0     0.0045   16.8   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
     0.0081   16.4   0.0     0.0094   16.2   0.0    1.1  1  DUF2431          Domain of unknown function (DUF2431)
     0.0094   15.8   0.0      0.018   14.9   0.0    1.4  1  UPF0146          Uncharacterised protein family (UPF0146)
  ------ inclusion threshold ------
        0.1   12.5   0.1        0.5   10.3   0.0    2.0  2  Methyltransf_18  Methyltransferase domain


Domain annotation for each model (and alignments):
>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.0   0.0   1.3e-18   1.7e-15      25     149 ..      26     155 ..      19     167 .. 0.81

  Alignments for each domain:
  == domain 1  score: 57.0 bits;  conditional E-value: 1.3e-18
                                   HHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTSTTS-EEEEEE-- CS
                           MTS  25 etlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvleeveekkfdlivsNP 105
                                    +  +  +g+++ +GcG+G++++ ++k+  +  +++vd +  A++++k+n+e n+++++v+asd++e++  + +d+++ N 
  gi|13541022|ref|NP_110710.1|  26 MQYAE-CKGRAIEIGCGTGLVSIYFKKRGCN--IECVDLNQSAVDCTKRNAEINGVSLNVYASDLFEAAR-GVYDTVLFNA 102
                                   33333.6889*****************9888..9************************************.********** PP

                                   -STTTCH........CHHHHHHHHHHHHHHHEEEEEEEEEEEETTSCHHHH.H CS
                           MTS 106 Pfhagka........telavaeeliaeAkeaLkegGeLliVanrklgyesl.l 149
                                   P+   ++        ++ +++ ++++e+k++ + + +++iV     + esl +
  gi|13541022|ref|NP_110710.1| 103 PYLPVSDedmawsggKSMELISRFLRESKNHINRSSNIFIVLTDLTDNESLfM 155
                                   9864333011111114678999*******************998887777644 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.9   0.0   6.3e-11   8.1e-08       2      80 ..      36     110 ..      35     130 .. 0.81

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 6.3e-11
                                   EEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGSSHH CS
               Methyltransf_25   2 LdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhlsde 80 
                                   +++GcGtG +++++ kr+  +++ +vD+++++++ ++++ae +g++++++  d+ +   + g +D v+ +  +  +sde
  gi|13541022|ref|NP_110710.1|  36 IEIGCGTGLVSIYFKKRG--CNIECVDLNQSAVDCTKRNAEINGVSLNVYASDLFEA--ARGVYDTVLFNAPYLPVSDE 110
                                   58***************5..********************99999999999998554..57789999985332224444 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.7   0.0   3.8e-10   4.9e-07       9      62 ..      18      79 ..       9     151 .. 0.79

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 3.8e-10
               Methyltransf_23  9 lsdklerllpklraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae........k 62
                                  +sd +  l+++ + +gr ++iGcGtG ++ +++++g++++ vDl+  av+  +        +
  gi|13541022|ref|NP_110710.1| 18 PSDDTFLLMQYAECKGRAIEIGCGTGLVSIYFKKRGCNIECVDLNQSAVDCTKrnaeingvS 79
                                  555555677889999*****************************998887665555444442 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.0     1e-09   1.3e-06     156     231 ..      26      99 ..      22     102 .. 0.79

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 1e-09
                          PrmA 156 eklvkegeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveaklevalseellk..eekadviv 231
                                    ++ + + + + +G+G+G+ +i  +k g  ++  vD+++ Av+ +k+Nae+N+v+ ++     ++l++  ++ +d ++
  gi|13541022|ref|NP_110710.1|  26 MQYAECKGRAIEIGCGTGLVSIYFKKRGC-NIECVDLNQSAVDCTKRNAEINGVSLNVYA---SDLFEaaRGVYDTVL 99 
                                   5666677789****************997.699*********************998843...444432346666666 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.0   9.5e-09   1.2e-05       4      63 ..      35      92 ..      32     147 .. 0.87

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 9.5e-09
               Methyltransf_15  4 ilDlfsGaGGnviqfalvfekviaieinleklacaqhNaevYgvsdkitlvlgdvfella 63
                                   + + +G+G  +i f++ ++++ +++ n++ + c+++Nae+ gvs ++     d+fe+ +
  gi|13541022|ref|NP_110710.1| 35 AIEIGCGTGLVSIYFKKRGCNIECVDLNQSAVDCTKRNAEINGVSLNVY--ASDLFEAAR 92
                                  57888***************************************98775..567776554 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.1   1.7e-08   2.2e-05       2      66 ..      37      99 ..      36     129 .. 0.85

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 1.7e-08
                                  EET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEE CS
               Methyltransf_11  2 dvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvv 66
                                  ++GcGtG+++ +++krg+++ +vDl++ ++++ k++a+ +g+++++  +d+ +   + + +D v+
  gi|13541022|ref|NP_110710.1| 37 EIGCGTGLVSIYFKKRGCNIECVDLNQSAVDCTKRNAEINGVSLNVYASDLFE--AARGVYDTVL 99
                                  89************************************999865565555544..5566666665 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.0   3.2e-08     4e-05       2      72 ..      37     100 ..      36     105 .. 0.80
   2 ?   -2.3   0.0       6.1   7.9e+03      19      29 ..     138     148 ..     122     163 .. 0.54

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 3.2e-08
               Methyltransf_12   2 eiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvva 72 
                                   eiGcGtG ++ ++ ++  ++++ +vD+++sa+ d  ++ a++++ +    ++ a dl++ + g  +D+v+ 
  gi|13541022|ref|NP_110710.1|  37 EIGCGTGLVSIYFKKR--GCNIECVDLNQSAV-DCTKRNAEINGVSL---NVYASDLFEAARG-VYDTVLF 100
                                   9***************..**************.99999999998554...4444444444443.8898875 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 6.1
               Methyltransf_12  19 pdieytgvDis 29 
                                   ++i ++ +D+ 
  gi|13541022|ref|NP_110710.1| 138 SNIFIVLTDLT 148
                                   33444444433 PP

>> Methyltransf_16  Lysine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   8.7e-08   0.00011      48     105 ..      33      87 ..      13     104 .. 0.87
   2 ?   -2.3   0.0       2.4   3.1e+03      70      83 ..     139     152 ..     118     157 .. 0.60

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 8.7e-08
               Methyltransf_16  48 lsvlELGsGtGlvGlavaellpeakviltDlee.llellkknielnknalkskvkvevL 105
                                    +++E+G GtGlv + +++   ++++   Dl++ ++++ k+n e+n+  ++ +v ++ L
  gi|13541022|ref|NP_110710.1|  33 GRAIEIGCGTGLVSIYFKKR--GCNIECVDLNQsAVDCTKRNAEING--VSLNVYASDL 87 
                                   4789***************9..*********9989**********76..7777766655 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.4
               Methyltransf_16  70 eakviltDleelle 83 
                                   ++ ++ltDl + + 
  gi|13541022|ref|NP_110710.1| 139 NIFIVLTDLTDNES 152
                                   33444555544433 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0   5.9e-08   7.5e-05      77     177 ..      54     155 ..      40     167 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 5.9e-08
                                   --EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EEEE----------H.....HHHHHHHHHHHHHH CS
                       UPF0020  77 lklygsDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdvivtnpPYGerlgsk.....kalekLYseflrel 152
                                    ++ ++Dl++++v+++++Nae  gv+  + +s++    +++++g +d+++ n PY    ++      ++  +L s flre 
  gi|13541022|ref|NP_110710.1|  54 CNIECVDLNQSAVDCTKRNAEINGVSLNVYASDL----FEAARGVYDTVLFNAPYLPVSDEDmawsgGKSMELISRFLRES 130
                                   4588**********************99999983....3357789**********97665541111156689********* PP

                                   HHH-TT..-EEEEEESSHHHHHCC- CS
                       UPF0020 153 krvlrgggrlvlltsenkalekale 177
                                   k+++++++ + +++++  + e+++ 
  gi|13541022|ref|NP_110710.1| 131 KNHINRSSNIFIVLTDLTDNESLFM 155
                                   ******9999999999888887765 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   1.9e-07   0.00024      32      90 ..      33      90 ..      27     109 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 1.9e-07
                                  -EEEEES-TTSHHHHHHHHTT-EEEEEES-HHHHHHHHHHHHHTT-TTEEEEE--GGG- CS
                          TehB 32 gkvldlgcgqgrnslylsllgydvtawdknensiafleeikekenlknistalydinea 90
                                  g+++++gcg g  s+y++  g +++++d n++++   ++ +e++ ++ ++    d+ ea
  gi|13541022|ref|NP_110710.1| 33 GRAIEIGCGTGLVSIYFKKRGCNIECVDLNQSAVDCTKRNAEINGVS-LNVYASDLFEA 90
                                  6899******************************9999999988776.66666666554 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   3.5e-06    0.0045       6      91 ..      34     111 ..      31     170 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 3.5e-06
               Methyltransf_31   6 rvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsnevlna 86 
                                   r +++GCGtG  ++ + ++   ++++  +D ++ a+   + na+ +g++ +++ ++d +e+     +  +D +l n++   
  gi|13541022|ref|NP_110710.1|  34 RAIEIGCGTGLVSIYFKKR---GCNIECVDLNQSAVDCTKRNAEINGVS-LNVYASDLFEAA----RGVYDTVLFNAPYLP 106
                                   5789*****9999999855...56688*********************8.999*******66....489*****9977633 PP

               Methyltransf_31  87 ladpd 91 
                                   ++d d
  gi|13541022|ref|NP_110710.1| 107 VSDED 111
                                   33333 PP

>> DUF2431  Domain of unknown function (DUF2431)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   7.3e-06    0.0094      58     131 ..      65     147 ..      40     178 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 7.3e-06
                       DUF2431  58 gVDatkleks.........kl.qeklkkekfdriifnFPhvggkstdvnrqvranqeLlvsffksakellsekpgeilvtl 128
                                    VD+tk ++          ++   ++ ++ +d ++fn P    + +d+     ++ eL+ +f++++k+++++  ++i + l
  gi|13541022|ref|NP_110710.1|  65 AVDCTKRNAEingvslnvyASdLFEAARGVYDTVLFNAPYLPVSDEDMAWSGGKSMELISRFLRESKNHINRS-SNIFIVL 144
                                   577777776678887776633234445555***********999999999999********************.9999988 PP

                       DUF2431 129 feg 131
                                   ++ 
  gi|13541022|ref|NP_110710.1| 145 TDL 147
                                   765 PP

>> UPF0146  Uncharacterised protein family (UPF0146)
   #    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      12      69 ..      29      96 ..      21     100 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.4e-05
                                  S-SS.EEEEET-TT--HHHHHHHHHS-EEEEE-SS-S..............STTEE---SSS--HHHHT CS
                       UPF0146 12 narg.kvvEvGiGrkldvaealakrgvdlvatDikek.........kak.egvrivrDDvtdPnleiYk 69
                                  ++++ + +E+G G+ l v+ +++krg+++  +D++++         +++  +++++  D+++  + +Y 
  gi|13541022|ref|NP_110710.1| 29 AECKgRAIEIGCGTGL-VSIYFKKRGCNIECVDLNQSavdctkrnaEINgVSLNVYASDLFEAARGVYD 96
                                  45555********976.9****************99977766653323345678888888888888886 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00039       0.5      13      73 ..      30      86 ..      24     100 .. 0.78
   2 ?   -0.4   0.0      0.79     1e+03     136     150 ..     149     163 ..     116     164 .. 0.58

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00039
               Methyltransf_18 13 ekgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievrlsd 73
                                  e + r + iG+  g+++iy  k+g    +  +D+n+++++  k+n+e +g++  ++v+ sd
  gi|13541022|ref|NP_110710.1| 30 ECKGRAIEIGCGTGLVSIYFKKRGCN--IECVDLNQSAVDCTKRNAEINGVS--LNVYASD 86
                                  44558999************988765..7789*************9999984..4555555 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.79
               Methyltransf_18 136 edEelvkeegkiYei 150
                                    +E+l+ +eg +Ye+
  gi|13541022|ref|NP_110710.1| 149 DNESLFMDEGFLYEV 163
                                   355666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       480  (0.0267723); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); 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: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1224.16
//
Query:       gi|13541023|ref|NP_110711.1|  [L=151]
Description: transcription regulator [Thermoplasma volcanium GSS1]
Scores for complete 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   25.9   0.0    1.3e-05   25.1   0.0    1.4  1  HTH_20       Helix-turn-helix domain
    1.1e-05   25.2   0.0      2e-05   24.4   0.0    1.5  1  HTH_5        Bacterial regulatory protein, arsR family
    2.2e-05   24.5   0.3    6.5e-05   23.0   0.1    1.9  2  HTH_17       Helix-turn-helix domain
    5.6e-05   23.0   0.0    0.00012   21.9   0.0    1.5  1  HTH_11       HTH domain
    0.00018   21.4   0.0    0.00028   20.8   0.0    1.3  1  HTH_Crp_2    Crp-like helix-turn-helix domain
    0.00043   20.1   0.0    0.00072   19.4   0.0    1.4  1  TrmB         Sugar-specific transcriptional regulator TrmB
     0.0017   18.9   0.0     0.0026   18.3   0.0    1.3  1  Mga          Mga helix-turn-helix domain
     0.0078   16.0   0.0      0.012   15.4   0.0    1.3  1  HTH_IclR     IclR helix-turn-helix domain
  ------ inclusion threshold ------
      0.044   13.7   0.0      0.079   12.9   0.0    1.3  1  MarR_2       MarR family
      0.051   13.7   0.0      0.095   12.9   0.0    1.5  1  HTH_Tnp_1_2  Helix-turn-helix of insertion element transposas
      0.064   13.4   0.0       0.11   12.6   0.0    1.4  1  FUR          Ferric uptake regulator family
       0.12   12.5   0.1       0.29   11.2   0.1    1.7  1  HTH_7        Helix-turn-helix domain of resolvase
       0.16   12.1   0.0        0.3   11.2   0.0    1.5  2  GP3_package  DNA-packaging protein gp3
       0.17   12.4   0.0       0.28   11.7   0.0    1.3  1  HTH_27       Winged helix DNA-binding domain


Domain annotation for each model (and alignments):
>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.0     1e-08   1.3e-05      25      60 ..      65     100 ..      46     101 .. 0.88

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 1e-08
                                   B-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTE CS
                        HTH_20  25 ltaselaerldlskntlsyHLrvLeeagLvevvreg 60 
                                    t++el+  l++s++tl++HL++L   +L+e v+ g
  gi|13541023|ref|NP_110711.1|  65 WTPEELMSYLGTSRSTLYRHLNKLKYMDLLEEVKDG 100
                                   699*********************99*******988 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.0   1.6e-08     2e-05      17      46 ..      66      95 ..      56      96 .. 0.85

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 1.6e-08
                                  EHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                         HTH_5 17 cvcelaeelglsqstvShHLkkLreaGLVe 46
                                  +  el+ +lg s+st+ +HL+kL+ ++L+e
  gi|13541023|ref|NP_110711.1| 66 TPEELMSYLGTSRSTLYRHLNKLKYMDLLE 95
                                  5679**********************9986 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0         5   6.4e+03      37      47 ..      12      22 ..      12      23 .. 0.80
   2 !   23.0   0.1     5e-08   6.5e-05       3      43 ..      66     112 ..      64     116 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 5
                        HTH_17 37 riprsdleewl 47
                                  r++ sdl++ l
  gi|13541023|ref|NP_110711.1| 12 RVDVSDLDRSL 22
                                  78999999865 PP

  == domain 2  score: 23.0 bits;  conditional E-value: 5e-08
                        HTH_17   3 tveEaAelLgvsrstvyrlirrgelpaa.........kiGrrwriprsdl 43 
                                   t+eE++ +Lg srst+yr +  ++l+++         ki +++ri+  d+
  gi|13541023|ref|NP_110711.1|  66 TPEELMSYLGTSRSTLYRHL--NKLKYMdlleevkdgKI-KKYRIRSGDI 112
                                   99****************88..66666666666655445.5688887766 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   9.3e-08   0.00012       8      41 ..      57      90 ..      52      97 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 9.3e-08
                        HTH_11  8 lLleargpisgeeLAeeLnvSrrtvrrdIkaLee 41
                                  +L++ + +++ eeL+ +L+ Sr+t +r++ +L+ 
  gi|13541023|ref|NP_110711.1| 57 FLMNGERFWTPEELMSYLGTSRSTLYRHLNKLKY 90
                                  46666777************************85 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   2.2e-07   0.00028      23      55 ..      66     101 ..      57     116 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 2.2e-07
                                   HHHHHHHHTTSSHHHHHHHHHHHHHTTSEE..E.TE CS
                     HTH_Crp_2  23 tqeelAsmlGltretvsrilseLkreglis..r.gr 55 
                                   t eel s+lG++r+t+ r l++Lk   l++  + g+
  gi|13541023|ref|NP_110711.1|  66 TPEELMSYLGTSRSTLYRHLNKLKYMDLLEevKdGK 101
                                   6799*************************9743332 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   5.6e-07   0.00072      24      63 ..      66     106 ..      47     109 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 5.6e-07
                                   HHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES.STTTEEE CS
                          TrmB  24 tadeiaeelgvprskvYevLrsLedkGlVerek.grpklYr 63 
                                   t +e+ + lg +rs+ Y+ L++L+ ++l e +k g+ k+Yr
  gi|13541023|ref|NP_110711.1|  66 TPEELMSYLGTSRSTLYRHLNKLKYMDLLEEVKdGKIKKYR 106
                                   7899***************************9955677887 PP

>> Mga  Mga helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0     2e-06    0.0026      11      56 ..      42      90 ..      38     111 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 2e-06
                                  HHHHHSHHHHHHHHHH...HHSEEEHHHHHHHCT--HHHHHHHHHHHHH CS
                           Mga 11 ellkeslkyqllkflf...eeeevsieelaqelyiSestlkrkikelnk 56
                                  +++k+s+ ++l k  f    e++ + eel   l  S+stl+r++++l+ 
  gi|13541023|ref|NP_110711.1| 42 NSIKNSVYFRLFKECFlmnGERFWTPEELMSYLGTSRSTLYRHLNKLKY 90
                                  67899******99999898899999*********************995 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   9.4e-06     0.012      19      50 ..      65      96 ..      55      98 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 9.4e-06
                                  -BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                      HTH_IclR 19 ltlselArrtglpkStvhRlLqtLvelGyveq 50
                                  +t  el   +g ++St +R+L+ L  + ++e 
  gi|13541023|ref|NP_110711.1| 65 WTPEELMSYLGTSRSTLYRHLNKLKYMDLLEE 96
                                  68889********************9999985 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   6.2e-05     0.079      17      56 ..      61      99 ..      55     102 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.2e-05
                                  TTTSEE.EHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEES CS
                        MarR_2 17 rpgrdl.tvgelarrlglsksavsrilkrLvaaGLverrpg 56
                                  +++  + t+ el  +lg s+s++ r+l++L    L+e++++
  gi|13541023|ref|NP_110711.1| 61 GER--FwTPEELMSYLGTSRSTLYRHLNKLKYMDLLEEVKD 99
                                  443..779***********************9999999875 PP

>> HTH_Tnp_1_2  Helix-turn-helix of insertion element transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   7.4e-05     0.095      27      65 ..      65     103 ..      53     138 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.4e-05
                                   S-HHHHHHHHTS-HHHHHHHHH-HHHHHHHHHHHHHHHH CS
                   HTH_Tnp_1_2  27 ltldeiaeevgvsrsTlykWkkkkeFieyvnelaeefle 65 
                                    t +e+ + +g srsTly+ ++k ++++ ++e+ +  ++
  gi|13541023|ref|NP_110711.1|  65 WTPEELMSYLGTSRSTLYRHLNKLKYMDLLEEVKDGKIK 103
                                   5788999**********************9999886555 PP

>> FUR  Ferric uptake regulator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   8.7e-05      0.11      39      73 ..      75     108 ..      57     114 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 8.7e-05
                                   T--HHHHHHHHHHHHHTTSEEEEEETTSEEEEEES CS
                           FUR  39 eislaTVYrtLklleeaglvkelefedgesryela 73 
                                     s +T+Yr L+ l+ ++l++e++   + ++y+++
  gi|13541023|ref|NP_110711.1|  75 GTSRSTLYRHLNKLKYMDLLEEVKDG-KIKKYRIR 108
                                   5799******************9866.67777766 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 ?   11.2   0.1   0.00023      0.29      31      44 ..      74      87 ..      71      88 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00023
                                  S---SSSS--SS-- CS
                         HTH_7 31 vnisRsTvYRylad 44
                                  +++sRsT+YR l++
  gi|13541023|ref|NP_110711.1| 74 LGTSRSTLYRHLNK 87
                                  589*******9997 PP

>> GP3_package  DNA-packaging protein gp3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00023       0.3      35      78 ..      57      99 ..      21     111 .. 0.83
   2 ?   -2.7   0.0       5.1   6.5e+03      58      77 ..     126     142 ..     117     145 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00023
                                  .EEEE-----HHHHHHHHT--HHHHHHHGG..SHHHHHHHHHHH CS
                   GP3_package 35 yevvgdraptvtGLalyLgisrstlkeyekrkrefsetierikq 78
                                  +   g+r+ t + L+ yLg srstl++  ++  ++ +++e +k+
  gi|13541023|ref|NP_110711.1| 57 FLMNGERFWTPEELMSYLGTSRSTLYRHLNKL-KYMDLLEEVKD 99
                                  4556789999999**************99977.99999998875 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 5.1
                                   HHHHHGG..SHHHHHHHHHH CS
                   GP3_package  58 tlkeyekrkrefsetierik 77 
                                    +++y++   +++ ++++i+
  gi|13541023|ref|NP_110711.1| 126 AMDNYRS---NVEHIVDLIR 142
                                   5566666...4555555555 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00022      0.28      22      63 ..      68     106 ..      57     107 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00022
                        HTH_27  22 adlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvr 63 
                                   ++l+ +l ++ s+    l+kL  ++L+e+    +d++ k +r
  gi|13541023|ref|NP_110711.1|  68 EELMSYLGTSRSTLYRHLNKLKYMDLLEEV---KDGKIKKYR 106
                                   799************************999...556666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       628  (0.0350271); expected 358.6 (0.02)
Passed bias filter:                      499  (0.027832); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.52u 0.31s 00:00:00.83 Elapsed: 00:00:00.51
# Mc/sec: 885.25
//
Query:       gi|13541024|ref|NP_110712.1|  [L=192]
Description: SAM-dependent methyltransferase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.6e-11   42.9   0.0    8.9e-11   42.3   0.0    1.3  1  Methyltransf_11  Methyltransferase domain
    1.4e-06   28.9   0.0      3e-06   27.9   0.0    1.5  1  Methyltransf_25  Methyltransferase domain
    5.1e-05   23.2   0.0    0.00012   21.9   0.0    1.6  1  Methyltransf_23  Methyltransferase domain
     0.0068   17.1   0.0      0.022   15.5   0.0    1.8  1  Methyltransf_12  Methyltransferase domain


Domain annotation for each model (and alignments):
>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.3   0.0     2e-14   8.9e-11       2      89 ..      45     122 ..      44     124 .. 0.94

  Alignments for each domain:
  == domain 1  score: 42.3 bits;  conditional E-value: 2e-14
                                   EET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-CCHHHHHH CS
               Methyltransf_11   2 dvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhvedpekalk 82 
                                   ++G+GtGr+a++l       vgvD+s+ ml++a +++  +      + a a +lpf +++fD+ +   +l+++edp +alk
  gi|13541024|ref|NP_110712.1|  45 EIGVGTGRFAQKLG----IKVGVDPSEGMLRIAAARGIFP------ILAYADRLPFISKYFDFSLFVVTLCFLEDPVSALK 115
                                   89************....789***********98888777......899******************************** PP

                                   HHHHHEE CS
               Methyltransf_11  83 eiaRvLk 89 
                                   e++Rv k
  gi|13541024|ref|NP_110712.1| 116 EAKRVSK 122
                                   *****77 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.0   6.6e-10     3e-06       3      94 ..      45     122 ..      44     123 .. 0.90

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 6.6e-10
                                   EET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGSSHHHHH CS
               Methyltransf_25   3 dlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhlsdedle 83 
                                   ++G GtGr++++l  +      +gvD+se+ml++a++r       +  + + a++lpf ++ fD+ + + +l++l+  d  
  gi|13541024|ref|NP_110712.1|  45 EIGVGTGRFAQKLGIK------VGVDPSEGMLRIAAARG------IFPILAYADRLPFISKYFDFSLFVVTLCFLE--DPV 111
                                   89*******9999866......69*************99......899********************87799988..566 PP

                                   HHHHHHHHHEE CS
               Methyltransf_25  84 kalkeiarvLk 94 
                                    alke++rv k
  gi|13541024|ref|NP_110712.1| 112 SALKEAKRVSK 122
                                   9*******977 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   2.8e-08   0.00012       7     163 ..      25     170 ..      16     172 .. 0.76

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 2.8e-08
               Methyltransf_23   7 eelsdklerllpklraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiaekakkaqkdqfdeqeaaepqgkfdlIv 87 
                                   +e+++ ++ l +   ++g+ ++iG GtG++++ l  +    +gvD+s+ +  ia  a+  ++  ++++  ++ +++fd+  
  gi|13541024|ref|NP_110712.1|  25 REYQEQIK-LIKDAIRKGNDVEIGVGTGRFAQKLGIK----VGVDPSEGMLRIA-AARGIFPILAYADRLPFISKYFDFSL 99 
                                   67777777.555688999999***********99888....9*******99999.89999999999999999********* PP

               Methyltransf_23  88 lrevlehvpdppellrqiatllkpgGylllseplaslkedrllldwlylvpagrhisffsarslkelleeaGlevv 163
                                      +l+ ++dp ++l+ +++  k+   ++++   ++     ++l+ + +       +f+s+r+l +   eaGle v
  gi|13541024|ref|NP_110712.1| 100 FVVTLCFLEDPVSALKEAKRVSKDVFSAIIEKGSSY----ADFLEKKKEGFY-AYAHFYSERELLDFYSEAGLEAV 170
                                   ********************8885433433333222....233333333222.34478888888888888888866 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0     5e-06     0.022       1      92 [.      44     120 ..      44     123 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 5e-06
               Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhhlkd 81 
                                   +eiG GtG++++ l  k      +gvD+s+ ++  a+++  + +         + l  ++    ++fD  +   +l+ l+d
  gi|13541024|ref|NP_110712.1|  44 VEIGVGTGRFAQKLGIK------VGVDPSEGMLRIAAARGIFPIL-----AYADRLPFIS----KYFDFSLFVVTLCFLED 109
                                   69***************......**********666666666554.....2222222222....38999888889999999 PP

               Methyltransf_12  82 irevldnirkl 92 
                                   + ++l++++++
  gi|13541024|ref|NP_110712.1| 110 PVSALKEAKRV 120
                                   99998888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       600  (0.0334653); expected 358.6 (0.02)
Passed bias filter:                      546  (0.0304535); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 1247.87
//
Query:       gi|13541025|ref|NP_110713.1|  [L=230]
Description: 3-dehydroquinate dehydratase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      4e-14   53.4   0.6      6e-14   52.8   0.6    1.3  1  DHquinase_I  Type I 3-dehydroquinase
     0.0004   19.6   0.0       0.24   10.4   0.0    2.1  2  GcpE         GcpE protein
  ------ inclusion threshold ------
       0.01   15.4   0.1      0.014   14.9   0.1    1.1  1  HMGL-like    HMGL-like
       0.57   10.6   0.1       0.57   10.6   0.1    2.1  3  HSP9_HSP12   Heat shock protein 9/12


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 !   52.8   0.6   1.3e-17     6e-14       4     223 ..      27     217 ..      24     223 .. 0.77

  Alignments for each domain:
  == domain 1  score: 52.8 bits;  conditional E-value: 1.3e-17
                                   E--SSHHHHHHHHHHHTT.S-SEEEEEGGG-.TT.THHHHHHHHHHHHHH.T.TS-EEEE---GGGT-S.SSS-HHHHHHH CS
                   DHquinase_I   4 itgktleeilaelesgke.kaDlvElRlDllketseaedvseeleelrst.s.dlpliftlrtkaeggrfkrkseeeylel 81 
                                   i   + + + ++ e  k  +  l E+R Dl+++     ++ eele +r   + d+  ift+r    g+  +       +++
  gi|13541025|ref|NP_110713.1|  27 IFDHDAKSLTEKFETKKLsDKNLYEIRFDLFDKV----NIDEELEIIRALdEmDIDYIFTYR----GHD-P-------EKI 91 
                                   55566666666666655567899********544....455666666666545*********....444.4.......678 PP

                                   HHHHHHCT-SEEEEEGG-.HHGHHHHHHHHHHHTT-EEEEEEEESS----HHHHHHHHHHHHHTT-SEEEEEE--SSHHHH CS
                   DHquinase_I  82 lrtaielgadyvDvElteapeeskkrlieekreggtkvIvSyhdfegtpsaeelkallekmqalgaDivKiavmaksieDv 162
                                   ++tai   +  vD++l ++     +++ +  r+  t+++vSyh     +s ++++++l +m + +aDivK+a+  k+ ++ 
  gi|13541025|ref|NP_110713.1|  92 YETAITKMVPAVDMDL-SLL----NKVNR--RSPDTRIMVSYHT----DSSKDMIEKLDEMLKANADIVKVACNYKDEKNF 161
                                   99999988899*****.566....24554..459*********5....5566799**********************8888 PP

                                   HH.HHHHHHHHHHHT-SS-EEEEE-TTTTGHHHCHHHHHTB-EEEEESSS-..SSTT-EEHH CS
                   DHquinase_I 163 lr.llsltseakeekdeaplIamamGelGkiSRilgevfGspvtfasleeakasapGqltar 223
                                   ++ l ++  + ke    +p+  + mG+   + R+++ ++ s + +a  +++  +a Gq++ +
  gi|13541025|ref|NP_110713.1| 162 FKdLIEIA-QRKE-ISGKPVLFIPMGKS--FLRVISAYYVSDMVYAKYDKE--TAMGQPDPD 217
                                   75266665.4444.467**********5..89******99*******7777..9****9866 PP

>> GcpE  GcpE protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.5   0.0   0.00041       1.9       2      68 ..       7      72 ..       6     106 .. 0.78
   2 !   10.4   0.0   5.4e-05      0.24      21      72 ..     122     173 ..     110     180 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.00041
                                  --EEETTEEESTTS--EEEEE--S-TT-HHHHHHHHHHHHHCT-SEEEEEE-SHHHHHHHHHHHHHH CS
                          GcpE  2 revkvgkvkiGgeapiavqsMtntdtadveatvkqikrlaeaGaelvRvtvqdeeeaealkeikekl 68
                                  ++v++g+++iGg+ pi++ s+ + d + +++  + +k+l+++    +R+   d+ ++++  ei + l
  gi|13541025|ref|NP_110713.1|  7 SRVNIGRFTIGGSIPIVIISIFDHDAKSLTEKFE-TKKLSDKNLYEIRFDLFDKVNIDEELEIIRAL 72
                                  579**********************999988875.56677777777777766666666655555555 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 5.4e-05
                                   EE--S-TT-HHHHHHHHHHHHHCT-SEEEEEE-SHHHHHHHHHHHHHHHHTT CS
                          GcpE  21 sMtntdtadveatvkqikrlaeaGaelvRvtvqdeeeaealkeikeklkkkg 72 
                                    M++ +t+  +++++++ ++ +a a++v+v+++ ++e + +k++ e  ++k+
  gi|13541025|ref|NP_110713.1| 122 IMVSYHTDSSKDMIEKLDEMLKANADIVKVACNYKDEKNFFKDLIEIAQRKE 173
                                   59999*********************************99999887766555 PP

>> HMGL-like  HMGL-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.1   3.2e-06     0.014      18     118 ..      58     171 ..      46     174 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.2e-06
                                   S---HHHHHHHHHHHHHHT-SEE--................TSGGGT.THHHHHHHS---TT-B....--EE-SSHHHHHH CS
                     HMGL-like  18 aalsveeklaiakaLdeagvdeiEv................gfpaaseddfevvraiakavkkar..ilalvrarekdika 80 
                                   ++++++e l+i++aLde+ +d+i +                 +pa    d+  + ++ +  +++r  +  +  + ++ i++
  gi|13541025|ref|NP_110713.1|  58 DKVNIDEELEIIRALDEMDIDYIFTyrghdpekiyetaitkMVPAVD-MDLSLLNKVNRRSPDTRimVSYHTDSSKDMIEK 137
                                   6789**********************************999999988.9****************5333333444555666 PP

                                   HHH....TT-SEEEEEEES-HHHHHHHHSSTHHHHHHH CS
                     HMGL-like  81 avealkgagakrvhvfiatselhlkaklkkdreevakk 118
                                     e + +a+a++v+v+    +   ++++ kd  e+a++
  gi|13541025|ref|NP_110713.1| 138 LDE-MLKANADIVKVACNYKD---EKNFFKDLIEIAQR 171
                                   666.999********999988...88888888777765 PP

>> HSP9_HSP12  Heat shock protein 9/12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.2       1.8   8.2e+03      22      30 ..      32      40 ..      30      47 .. 0.66
   2 ?   10.6   0.1   0.00013      0.57       6      52 ..     115     161 ..     112     165 .. 0.84
   3 ?   -2.0   0.0       1.1     5e+03      30      47 ..     198     215 ..     196     217 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.8
                                  SHCHHHHHH CS
                    HSP9_HSP12 22 qKStlekak 30
                                   KS +ek  
  gi|13541025|ref|NP_110713.1| 32 AKSLTEKFE 40
                                  577777754 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00013
                                   SSCHHHHHHHHCS--SSHCHHHHHHHHHHHHHHHHHHCS-TTCHHCC CS
                    HSP9_HSP12   6 RkdftdkakeevtPDsqKStlekaketvtdaaDklarklqpddqKst 52 
                                   R++  +++  +   Ds+K + ek+ e ++ +aD +  + + +d+K++
  gi|13541025|ref|NP_110713.1| 115 RRSPDTRIMVSYHTDSSKDMIEKLDEMLKANADIVKVACNYKDEKNF 161
                                   55555666666677*********************999999999986 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 1.1
                                   HHHHHHHHHHHHHCS-TT CS
                    HSP9_HSP12  30 ketvtdaaDklarklqpd 47 
                                   ++ v  ++Dk     qpd
  gi|13541025|ref|NP_110713.1| 198 SDMVYAKYDKETAMGQPD 215
                                   677888889988888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       825  (0.0460148); expected 358.6 (0.02)
Passed bias filter:                      526  (0.0293379); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 1505.94
//
Query:       gi|13541026|ref|NP_110714.1|  [L=405]
Description: isocitrate dehydrogenase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   1.4e-108  363.1   0.0   1.7e-108  362.9   0.0    1.0  1  Iso_dh    Isocitrate/isopropylmalate dehydrogenase


Domain annotation for each model (and alignments):
>> Iso_dh  Isocitrate/isopropylmalate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  362.9   0.0  9.4e-113  1.7e-108       2     348 .]      20     396 ..      19     396 .. 0.98

  Alignments for each domain:
  == domain 1  score: 362.9 bits;  conditional E-value: 9.4e-113
                                   EEEEEESTTHHHHHHHHHHHHHHHHHHHT...-EEEEEE---THHHHHHHSSSS-HHHHHHHHHSSEEEEEE---CSSSSS CS
                        Iso_dh   2 iallegdgiGpevveaalkvlkaakekag...lelefeevdvGgaaidetgeplpeetleaikeadvvllgavgtpkekev 79 
                                   i  +egdgiGp++++ +++v++aa e a+   +++e+++v +G +a+d+tg+ lp+ +le +k+  v+++g+++tp +++ 
  gi|13541026|ref|NP_110714.1|  20 IGYIEGDGIGPDITKTTINVINAALEVAYggkRSIEWHKVLAGDEAYDKTGNRLPDSSLEELKKCVVSIKGPLTTPIGEGF 100
                                   889***********************9999999************************************************ PP

                                   SHHHHHHHHHHHTTEEEEEEEEE-BCCTTCCSSBTHHHHCT-EEEEEEE-SSCGGCSSEEEEET..............TG. CS
                        Iso_dh  80 rpengLlaLrkeldlfanlrpvkvfeklkvksplkrevveevdlvivReltggiYfgeekekkg..............si. 145
                                   r+ n  ++Lr+ ldl+an+rpv++f   +v+sp+ +  +e +++v++Re+t+++Y+g+e  +++              +i 
  gi|13541026|ref|NP_110714.1| 101 RSLN--VTLRQYLDLYANIRPVRYF--PGVPSPVLH--PEYMNMVVFRENTEDLYAGIEWRYDSedaekvraflsstfNIn 175
                                   ****..9******************..79*****97..899******************9999999***********9666 PP

                                   .GGGEEEEEEEEEHHHHHHHHHHHHHHHHHTTTSEEEEEESTTTTHHHH.HHHHHHHHHHCC..................T CS
                        Iso_dh 146 fteevavdtklyseeeieriaraafelAlkrgkkkvtlvdKanvlksse.lwrkiveevaee..................e 207
                                    t ++++++k++s+  + r++r a+++A+++g+k+vtlv+K+n++k +e ++r++ +eva+                    
  gi|13541026|ref|NP_110714.1| 176 LTPDTGIGIKPISKFKSTRLVRKAIQYAIANGRKSVTLVHKGNIMKYTEgAFRDWGYEVARTefgdytvteaeylkdpekY 256
                                   78999**************************************************************************88 PP

                                   TTTSEEEEEEHHHHHHHHHHSGGGGSEEEE-HHHHHHHHHHHHHHTTSGCC-EEEEEETSS-EEEEESS---CCCTTSS-S CS
                        Iso_dh 208 ypdielehqlvDsaamqlvkspkqfdVivtkNlfGDilSDeaaalvGslGllpSaslgekkvaifEavHGsapdiagkdka 288
                                   +++i +++++ D++ +q++++ +++dVi+t+Nl+GD+lSD++aa+vG++Gl+p+a++g ++ a+fEavHG+ap++ag d+a
  gi|13541026|ref|NP_110714.1| 257 ANKIVIKDRITDNMFQQVLTRTQEYDVIATPNLNGDYLSDALAAQVGGIGLAPGANIG-DHYAVFEAVHGTAPKYAGLDVA 336
                                   899*******************************************************.78******************** PP

                                   -THHHHHHHHHHHHHTTT-HHHHHHHHHHHHHHHHHTSCCHHHCTTS.TCCCHHHHHHHHH CS
                        Iso_dh 289 NpiavilSaalmLryslgleeaAdkiekAvekvleagivTkDlagea.akevstsefgdav 348
                                   Np++ ilSa++mL + +g++ea++ +++A+ ++ +++++T+D+a+    k++++sefg+++
  gi|13541026|ref|NP_110714.1| 337 NPTSLILSAEMMLDH-IGWKEASKILDDAIMQTYRDQKLTQDIARLLnLKALKCSEFGEEI 396
                                   ***************.*****************************98789*********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (405 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 2646.55
//
Query:       gi|13541027|ref|NP_110715.1|  [L=235]
Description: hypothetical protein TVN0196 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.7e-23   83.6   0.0    2.4e-23   83.1   0.0    1.1  1  PTS_2-RNA  RNA 2'-phosphotransferase, Tpt1 / KptA family
  ------ inclusion threshold ------
      0.061   13.3   0.0        3.2    7.8   0.0    2.2  2  DUF2846    Protein of unknown function (DUF2846)


Domain annotation for each model (and alignments):
>> PTS_2-RNA  RNA 2'-phosphotransferase, Tpt1 / KptA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.1   0.0   2.7e-27   2.4e-23       4     180 ..      33     199 ..      30     199 .. 0.89

  Alignments for each domain:
  == domain 1  score: 83.1 bits;  conditional E-value: 2.7e-27
                     PTS_2-RNA   4 vqlskaLsyiLRhgaekegLkiredGyvkvedlLelp.klkslk.vtleeikevVesndKqRFelveleelliranqghsi 82 
                                    ++s++L+ +LRh + + g++++++Gy++++ l+++  k k ++ +t +++  + e+++++R++   ++++lira+ gh+i
  gi|13541027|ref|NP_110715.1|  33 NEVSRTLAAVLRHDPGRYGIRLDSHGYARISSLVSMFrKRKGMRwMTDDHLVYLAETDPRKRYQ---ISGVLIRAVYGHTI 110
                                   579******************************9943133444489999***************...888**********7 PP

                     PTS_2-RNA  83 kkvesselllepiesaeelpevvvHgTylkawesilasggLkrmsrnhihlatglpgekevisgmrk.saevliyidveka 162
                                       +    l+ + ++  +p+++++  ++++ + ++ + g+ +  ++ ihl+ +    k+ +sg  + +  +++ ++++++
  gi|13541027|ref|NP_110715.1| 111 D---V---DLTDLPTDG-IPDTLYYQSSTAEAPLVK-EAGIYPSDKSWIHLSGTYR--KSFVSGLYHiDDPLVLAVNARSM 181
                                   2...2...389986655.9*****************.99************99865..78*****998999********** PP

                     PTS_2-RNA 163 ladgikfyvsengviLte 180
                                   +++gi +++s+++++Lt+
  gi|13541027|ref|NP_110715.1| 182 IENGIDIFRSNDDIYLTK 199
                                   ****************96 PP

>> DUF2846  Protein of unknown function (DUF2846)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0    0.0089        80      24      57 ..      23      56 ..      11      78 .. 0.83
   2 ?    7.8   0.0   0.00036       3.2      16      59 ..     171     214 ..     157     226 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.0089
                       DUF2846 24 pdvfvngkkigelankeYfvaevepGeykister 57
                                  +++ +n+++i e+++   +v++ +pG+y i   +
  gi|13541027|ref|NP_110715.1| 23 GKIMMNEAEINEVSRTLAAVLRHDPGRYGIRLDS 56
                                  57999***********************998877 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.00036
                       DUF2846  16 wlkeeaeapdvfvngkkigelankeYfvaevepGeykisteref 59 
                                   +l+ +++a ++  ng +i++++++ Y+ ++v+p   +i+ ++e 
  gi|13541027|ref|NP_110715.1| 171 PLVLAVNARSMIENGIDIFRSNDDIYLTKQVPPEYITIAEKEEV 214
                                   6777888899999********************99999888754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       521  (0.0290591); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); 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: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.50
# Mc/sec: 1402.41
//
Query:       gi|13541028|ref|NP_110716.1|  [L=286]
Description: ribose-phosphate pyrophosphokinase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.9e-27   93.5   0.6      3e-25   88.4   0.0    2.5  3  Pribosyltran_N   N-terminal domain of ribose phosphate pyroph
    1.7e-14   53.6   0.4    9.5e-14   51.2   0.6    2.0  3  Pribosyltran     Phosphoribosyl transferase domain
    5.3e-11   42.9   0.4      1e-10   42.0   0.4    1.5  1  Pribosyl_synth   Phosphoribosyl synthetase-associated domain
     0.0017   17.8   0.0     0.0032   16.9   0.0    1.4  1  UPRTase          Uracil phosphoribosyltransferase
  ------ inclusion threshold ------
      0.036   14.0   1.5       0.25   11.3   1.5    2.1  1  Intein_splicing  Intein splicing domain
      0.076   12.5   0.1       0.15   11.6   0.1    1.4  1  PRTase_2         Phosphoribosyl transferase


Domain annotation for each model (and alignments):
>> Pribosyltran_N  N-terminal domain of ribose phosphate pyrophosphokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.4   0.0     1e-28     3e-25       1     113 [.       1     112 [.       1     114 [. 0.97
   2 ?    2.9   0.0     0.033        99      15      57 ..     170     213 ..     165     239 .. 0.90
   3 ?   -2.6   0.0       1.7   4.9e+03      21      46 ..     257     282 ..     245     285 .. 0.64

  Alignments for each domain:
  == domain 1  score: 88.4 bits;  conditional E-value: 1e-28
                Pribosyltran_N   1 lkifagssskeLaekiakrlgvelgkakvsrfadgEikveieesvrgkdvfiiqslskpvndnlmelllmidalrrasakr 81 
                                   +ki+a++ss +La++ia++l++e + ++ +rf+dgE +++++e++ g+++fii +++++   ++me++l+++a++    k+
  gi|13541028|ref|NP_110716.1|   1 MKIIALRSSLKLAARIAEELKTEPVMPDERRFPDGELYLRYDEDLTGHNIFIIGNTHSD--AEVMEMILTLSAIQDYRTKS 79 
                                   89******************************************************998..89****************** PP

                Pribosyltran_N  82 itaViPylgysrqdrk.ksrepisaklvaklLe 113
                                   ++++ Py+gy+rq+++ k+ epis++++ ++++
  gi|13541028|ref|NP_110716.1|  80 VNIIAPYYGYARQHQRyKNGEPISSQILTEIYS 112
                                   ****************999*******9988876 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.033
                Pribosyltran_N  15 kiakrlgvelgkakvsrfadgEikveiee.svrgkdvfiiqsls 57 
                                   +i+++lg +   ++ +r  d  +++++ + +v gk++ i+ ++ 
  gi|13541028|ref|NP_110716.1| 170 DISAKLGKKHFFIEKKRIDDRTVEMKVPNvDVNGKKLLIVDDII 213
                                   799999999999**************98879********99875 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 1.7
                Pribosyltran_N  21 gvelgkakvsrfadgEikveieesvr 46 
                                   +++++++  s+f+d  ++ e+ + +r
  gi|13541028|ref|NP_110716.1| 257 EIHVTDTVESKFSDISVYQEVCNYIR 282
                                   45666677777777666666655554 PP

>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       2.2   6.7e+03      38      52 ..       7      21 ..       6      32 .. 0.64
   2 ?   -1.5   0.0      0.51   1.5e+03     103     131 ..      65      93 ..      64     108 .. 0.73
   3 !   51.2   0.6   3.2e-17   9.5e-14      26     125 ..     150     243 ..     139     275 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 2.2
                                  TTTHHHHHHHHHHST CS
                  Pribosyltran 38 rgGvpfakiladeLe 52
                                  r ++ +a ++a eL+
  gi|13541028|ref|NP_110716.1|  7 RSSLKLAARIAEELK 21
                                  556667777777774 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.51
                                   HHHHHHHHHCC-BSEEEEEEEEE-HHHHH CS
                  Pribosyltran 103 llaalelLkekgpeevriavlvdkpatee 131
                                   ++ +l ++ +++ ++v i+++++  a++ 
  gi|13541028|ref|NP_110716.1|  65 MILTLSAIQDYRTKSVNIIAPYYGYARQH 93 
                                   66778888888899999999885544444 PP

  == domain 3  score: 51.2 bits;  conditional E-value: 3.2e-17
                                   --GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE........EE----TTSEEEEE-SEESSSHHHHHH CS
                  Pribosyltran  26 yngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdesrlledpagkkVliVDDildtGgTllaa 106
                                   +n   d+vv ++ gG+ ++ +++ +L+ + ++++k++ ++ + e  +        +  d+ gkk liVDDi++tGgT+ + 
  gi|13541028|ref|NP_110716.1| 150 KNVDVDYVVSPDDGGLARVADISAKLGKKHFFIEKKRIDDRTVEMKV--------PNVDVNGKKLLIVDDIISTGGTIAKS 222
                                   456679*********************99999999998888888887........6679********************** PP

                                   HHHHHCC-BSEEEEEEEE..E CS
                  Pribosyltran 107 lelLkekgpeevriavlv..d 125
                                     lL+ekg+ ++ + +++   
  gi|13541028|ref|NP_110716.1| 223 SGLLREKGASKIYVSAVHglF 243
                                   **********98777666553 PP

>> Pribosyl_synth  Phosphoribosyl synthetase-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.0   0.4   3.4e-14     1e-10      80     151 ..     200     270 ..     179     286 .] 0.84

  Alignments for each domain:
  == domain 1  score: 42.0 bits;  conditional E-value: 3.4e-14
                                   --TTSEEEEEEEEE-S-HHHHHHHHHHHHTT--EEEEEEEEE---TTHHHHHHHSS--EEEEESSS--HHHH CS
                Pribosyl_synth  80 dvgGriaiivddliddvesfvaaaevlkerGaykiyvlathGllssdaprlleesaidevvvtntipheiqk 151
                                   dv+G+  +ivdd+i    ++ +++ +l+e+Ga kiyv a hGl+ + + +++ +   de+ vt+t+  +   
  gi|13541028|ref|NP_110716.1| 200 DVNGKKLLIVDDIISTGGTIAKSSGLLREKGASKIYVSAVHGLFVNGSENKILQN-ADEIHVTDTVESKFSD 270
                                   9*******************************************99988888664.6*********876543 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   1.1e-06    0.0032     101     175 ..     182     257 ..     167     272 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.1e-06
                       UPRTase 101 reeetlepveyynkLPkki.aertvlllDpviaTGgsaaaaiqlLkergvgeekIlvlsvlaseegvkrlaeefpk 175
                                    e++  + + +  k+P+   + ++ l++D +i+TGg++a+   lL+e+g+ +  +  +  l  +   ++++++  +
  gi|13541028|ref|NP_110716.1| 182 IEKKRIDDRTVEMKVPNVDvNGKKLLIVDDIISTGGTIAKSSGLLREKGASKIYVSAVHGLFVNGSENKILQNADE 257
                                   555555666666788875459999***********************99876666666666555555555555555 PP

>> Intein_splicing  Intein splicing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   1.5   8.3e-05      0.25      37      96 ..     205     270 ..     101     283 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 8.3e-05
                                   E...EEEEEEEEEE...EEEEEEETTS-EEEEETT-EEEECCT.TEEEEEECCC--TT-EEEEEHSC CS
                                   x...xxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx RF
               Intein_splicing  37 s...vkkliklklk...elyeiklesgrkikaTpeHkllvvrd.egivEkradeLkegdliavpdad 96 
                                   +   v  +i+++ +       ++ +  +ki++++ H l+v    ++i+ ++ade+++ d++    +d
  gi|13541028|ref|NP_110716.1| 205 KlliVDDIISTGGTiakSSGLLREKGASKIYVSAVHGLFVNGSeNKIL-QNADEIHVTDTVESKFSD 270
                                   1444555555555443244557788899*************8877875.9*********99876666 PP

>> PRTase_2  Phosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   4.9e-05      0.15     120     155 ..     202     237 ..     186     268 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4.9e-05
                      PRTase_2 120 aakelvLvDDEistGktalnliralqeklprkryvv 155
                                   + k+l++vDD istG t+++    l+ek  +k yv 
  gi|13541028|ref|NP_110716.1| 202 NGKKLLIVDDIISTGGTIAKSSGLLREKGASKIYVS 237
                                   5689***************99999998887776654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       519  (0.0289475); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); 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 0.31s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 1745.86
//
Query:       gi|13541029|ref|NP_110717.1|  [L=243]
Description: enoyl-CoA hydratase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.4e-51  172.9   0.0    8.4e-51  172.7   0.0    1.0  1  ECH_1          Enoyl-CoA hydratase/isomerase
    1.9e-37  129.5   0.0    2.1e-37  129.4   0.0    1.0  1  ECH_2          Enoyl-CoA hydratase/isomerase
    0.00024   21.1   0.8      0.057   13.4   0.1    2.5  2  Peptidase_S49  Peptidase family S49
  ------ inclusion threshold ------
      0.052   13.4   0.6       0.85    9.5   0.0    2.4  2  CLP_protease   Clp protease
       0.12   11.9   0.0       0.33   10.5   0.0    1.7  1  Phage_TTP_13   Phage tail tube protein family


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 !  172.7   0.0   2.4e-54   8.4e-51       8     229 ..      13     230 ..       6     241 .. 0.96

  Alignments for each domain:
  == domain 1  score: 172.7 bits;  conditional E-value: 2.4e-54
                                   EEEE--CGCTTEE-HHHHHHHHHHHHHHHHSTTECEEEEEEBTSEEEEEB-HHHHHHHHCHHHHHHHCCHHHHHHHHHHSS CS
                         ECH_1   8 viklnrPeavNalsaelltEliqalekleddksvravvLtGgdkaFaaGadlkemaeeekakqallkeevlelwtklytvp 88 
                                   +i l rPe++Na++ e+l++l++ + k+e++   r++v+tG++k F+aGad++ +a   +a + +++ ++++  +++++++
  gi|13541029|ref|NP_110717.1|  13 LIVLSRPEKLNAINLEMLADLADQFSKAEKE-DTRVIVITGYGKNFSAGADINMLASFDPASAYSFRLKMNSIAQRIRKSD 92 
                                   6899***************************.9************************************************ PP

                                   SEEEEEE-SEEETHHHHHHHHSSEEEEETTTEEE-GGGGGTS--CTTCHHHHHHHHHHHHHHHHHHHT-EEEHHHHHHCTS CS
                         ECH_1  89 kpviaavnGaaigGGlelalacDiviaadnasfglnelklGlipgaggtqilarkvGkskAeeilllgkkisaqealkvGl 169
                                   kpvia ++G+++gGGlela  +Di+ia  +a++g++e+ +G+ +gagg  il++ vG+  A ++++ gkk++aqea   Gl
  gi|13541029|ref|NP_110717.1|  93 KPVIALLKGYSMGGGLELAESADIRIAMSDAVIGQPESSIGINAGAGGNVILPKLVGRGSAAYLAMSGKKLNAQEAMALGL 173
                                   ********************************************************************************* PP

                                   SSEEESGGGHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCT CS
                         ECH_1 170 vdkvvpeeqlleealelaeklaekspaalrqlkealnakledalaeqleaeaklfestfs 229
                                   vd+vv +e    +a +++  + +k+++ l+++k a+n  +++ l+ ++++ea  f+ +f 
  gi|13541029|ref|NP_110717.1| 174 VDEVVDDE---AKAWKIIDDICKKPKKTLQFIKRAINSSYDMGLESAMDQEALYFSLLFT 230
                                   *****986...69**************************************999987766 PP

>> ECH_2  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.4   0.0     6e-41   2.1e-37       3     201 ..      13     208 ..      11     240 .. 0.88

  Alignments for each domain:
  == domain 1  score: 129.4 bits;  conditional E-value: 6e-41
                                   EEEE--GGGTT-B-HHHHHHHHHHHHHHCC-TT-SEEEEEESSSSECE--B--HHHHHHHHCS-THHHHHHHHHHHHHHHH CS
                         ECH_2   3 vitLnrpkalNaLslemvralkealkewekddevklvvlkgagekafCAGgDvralyeaakegkkeeeeffreeYklnyli 83 
                                   +i L rp++lNa++lem+ +l++++++ e +++++++v++g g k f+AG D+++l++   +++ +   f  +  ++ ++i
  gi|13541029|ref|NP_110717.1|  13 LIVLSRPEKLNAINLEMLADLADQFSKAE-KEDTRVIVITGYG-KNFSAGADINMLASFDPASAYS---FRLKMNSIAQRI 88 
                                   799************************76.566899*****88.*************999997766...8889999***** PP

                                   HC-SS-EEEEE-BEEETHHHHHHTTSSEEEE-TT-EEE--GGGGT----TTHHHHHHCSST.THHHHHHHH---B-HHHHH CS
                         ECH_2  84 atypkpvvalmdGivmGgGvGlsvhgsfrvvtertvfAmPEtaIGlfPDvGgsyfLsrlpg.elGlylalTGarlkgadal 163
                                    +  kpv+al+ G+ mGgG+ l+ ++ +r++  ++v+  PE +IG+    Gg  +L++l g   + yla++G++l++++a+
  gi|13541029|ref|NP_110717.1|  89 RKSDKPVIALLKGYSMGGGLELAESADIRIAMSDAVIGQPESSIGINAGAGGNVILPKLVGrGSAAYLAMSGKKLNAQEAM 169
                                   **********************************************************977589***************** PP

                                   HTTS--EE--GGGH.HHHHHHHHTT........------ CS
                         ECH_2 164 aaglathyvpsekl.ealeeaLaelessdeeaveevlee 201
                                   a+gl + +v++e+   ++ +++++  +++ + +++++++
  gi|13541029|ref|NP_110717.1| 170 ALGLVDEVVDDEAKaWKIIDDICKKPKKTLQFIKRAINS 208
                                   *********987542689999999776665555555554 PP

>> Peptidase_S49  Peptidase family S49
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.1   1.6e-05     0.057       3      40 ..      89     126 ..      87     138 .. 0.88
   2 !    5.8   0.1    0.0035        13     119     139 ..     159     179 ..     153     190 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.6e-05
                                   HHTT--EEEEEEEEEETHHHHHHTTSSEEEE-TT-EEE CS
                 Peptidase_S49   3 kkakkPvvasaenvaaSggYylasaadkivanpstivg 40 
                                   +k+ kPv+a+ ++++  gg  la  ad  +a + +++g
  gi|13541029|ref|NP_110717.1|  89 RKSDKPVIALLKGYSMGGGLELAESADIRIAMSDAVIG 126
                                   799*********************************99 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0035
                                   CCHEEEHHHHHHTTSSSEETS CS
                 Peptidase_S49 119 egrvltgqqAlklgLvdelgt 139
                                   +g+ l +q+A +lgLvde+  
  gi|13541029|ref|NP_110717.1| 159 SGKKLNAQEAMALGLVDEVVD 179
                                   478999************975 PP

>> CLP_protease  Clp protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.1     0.056     2e+02      74     121 ..      90     135 ..      81     138 .. 0.78
   2 ?    9.5   0.0   0.00024      0.85     163     181 ..     162     180 ..     157     181 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.056
                                   SS-EEEEEEEEEETHHHHHHHTS-TTGEEEETTEEEEES-TEEEEEEE CS
                  CLP_protease  74 kpdvsticlGlaaSmgslllaagekgkRfalpnarimihqPlggaqgq 121
                                   k+d  +i+l  + Smg  l +a + + R+a+  +  +i qP + ++ +
  gi|13541029|ref|NP_110717.1|  90 KSDKPVIALLKGYSMGGGLELAESADIRIAM--SDAVIGQPESSIGIN 135
                                   6666677777889*************99886..566889998877665 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00024
                                   EEEHHHHHHHTSSSEE-SS CS
                  CLP_protease 163 flsaeeAveyGLideviek 181
                                    l+a+eA++ GL+dev++ 
  gi|13541029|ref|NP_110717.1| 162 KLNAQEAMALGLVDEVVDD 180
                                   589*************975 PP

>> Phage_TTP_13  Phage tail tube protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   9.3e-05      0.33      31      91 ..     170     227 ..     147     242 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 9.3e-05
                  Phage_TTP_13  31 atgltgsfvdcttlidtqkqsisdlpegpekslgfiddpknsdfveflnaaekrdtvqfyv 91 
                                   a+gl    vd  +      + i d+ + p+k+l fi    ns +   l++a +++++ f +
  gi|13541029|ref|NP_110717.1| 170 ALGLVDEVVDDEA---KAWKIIDDICKKPKKTLQFIKRAINSSYDMGLESAMDQEALYFSL 227
                                   3444444444322...234689***************************999999887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       552  (0.0307881); 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:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1523.48
//
Query:       gi|13541030|ref|NP_110718.1|  [L=339]
Description: N-acetylglucosamine kinase [Thermoplasma volcanium GSS1]
Scores for 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-43  149.8   2.6    1.2e-43  149.5   2.6    1.1  1  BcrAD_BadFG  BadF/BadG/BcrA/BcrD ATPase family
     0.0017   17.9   0.4        1.5    8.2   0.1    2.1  2  ROK          ROK family
  ------ inclusion threshold ------
      0.025   14.2   0.0      0.036   13.6   0.0    1.2  1  FGGY_N       FGGY family of carbohydrate kinases, N-terminal 


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 !  149.5   2.6     2e-47   1.2e-43       1     266 [.       9     294 ..       9     295 .. 0.95

  Alignments for each domain:
  == domain 1  score: 149.5 bits;  conditional E-value: 2e-47
                                   EEEEE-SSEEEEEEEETTTE.EEEEEEE--TTS-HHH.........HHHHHHHHHHT--GGGECEE..EEESTTCCCTCTT CS
                   BcrAD_BadFG   1 vGiDgGsTttkavlmdekge.vlgrgitnsanlesvrfeaaekvleealtealerageeeadieetylvgtgyGratlpek 80 
                                   +G+DgGsT+t av++d+++  ++g gi+++an+++  +e+a k++++ + ea++ a  + +di   +++++g+G++++ ++
  gi|13541030|ref|NP_110718.1|   9 LGVDGGSTKTVAVVYDDESGrIAGVGISGPANYTNSPREEAMKNIKNSVYEAVDDADVNIEDIGFKVFGLAGIGDSKEATA 89 
                                   7**************976555************************************************************ PP

                                   BSEEE-.....HHHHHHHHHHHH-TT--...EEEEEETTEEEEEEEETTEEEEEEEESS--TTSHHHHHHHHHHHT--TTT CS
                   BcrAD_BadFG  81 fekeiirs...eilvhgdGavalypgtr...tvldigGqdskgiqidkgkvenfqmndrcaageGrylgiiadelnmglre 155
                                    ++ei+rs   e  v +dG+ a++ ++    + ++  G++s+g+++ +gk  +f+++++++++e+++ ++++++l ++ re
  gi|13541030|ref|NP_110718.1|  90 EGEEIVRSiagEAIVVNDGYAAYKFANLnenGLVFAPGTGSVGFTMIDGKLSRFGGWGWFIGDEASASWMAKEALIYAERE 170
                                   ********************************************************************************* PP

                                   HHHHHTT--....................S-------SHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHHHHHTT--- CS
                   BcrAD_BadFG 156 ldglaekat....................kkarinstcavfaeaelrdalsggekaedIlaglhraialrvialisrsggv 216
                                   +dg+ e +                     k +  ++t+a+f++   + a +g+++a++I++++ ++ia++++a    + g 
  gi|13541030|ref|NP_110718.1| 171 KDGIIEAGIadkaetyfnldlyevvykimKGTIPKRTVAAFSPIISELAVEGNKYAISIFEEASNYIADLINAKSGIFSGK 251
                                   ****************************88888899*************************************99999888 PP

                                   SS.EEEESGGGG-HHHHHHH.....HHHH-S-EE--GGGGGHHHHHHHHH CS
                   BcrAD_BadFG 217 tdevtltGGvakneaavkelrklvkenygevkininpdsiytgalGAalf 266
                                      + + GG++ +  +++++   +k++ +  +  +n++  y+ ++G++++
  gi|13541030|ref|NP_110718.1| 252 A-IFSVLGGTMLAGRFYWDM---IKKKTMV-P--VNIHFGYQVVIGDIII 294
                                   5.6**********8888888...8777765.4..6777788889998765 PP

>> ROK  ROK family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.1   0.00025       1.5       2      67 ..       9      78 ..       8      94 .. 0.72
   2 !    7.9   0.0   0.00031       1.9     200     269 ..     215     286 ..     205     297 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00025
                                  EEEEE-SSEEEEEEEETTS-EEEEEEE.......EEHCCHHCCHHHHHHHHHHCCCHCCHTEEEEEEEEESSE CS
                           ROK  2 igidiGgtkialalvdeegeilarekv.......etptetteetlvdaiaelvdeaerkadeliavgigspGl 67
                                  +g+d G tk+++ + d+e+   a   +       + p+e+  + + +++ e+vd+a+ + +    +g  ++Gl
  gi|13541030|ref|NP_110718.1|  9 LGVDGGSTKTVAVVYDDESGRIAGVGIsgpanytNSPREEAMKNIKNSVYEAVDDADVNIE---DIGFKVFGL 78
                                  79**************999888888886766555666666677777777777777766555...666666665 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.00031
                                   HHHHHCTT-HHHHHHHHHHHHHHHHHHHHHHHHH--SEE..EEEHCCCTSTTHH.HHHHHHHHHCCTTTTCCC CS
                           ROK 200 iiklaekgdevaeevverlaeylakaiadlinlfdpqai..vlgGgvseadkll.eairklvkkylnkklevp 269
                                   i++la +g++ a  + e+  +y+a +i     +f+ +ai  vlgG  + a +++ ++i+k++   +n  +  +
  gi|13541030|ref|NP_110718.1| 215 ISELAVEGNKYAISIFEEASNYIADLINAKSGIFSGKAIfsVLGGT-MLAGRFYwDMIKKKTMVPVNIHFGYQ 286
                                   778999*******************************996556555.56666666****99977776666555 PP

>> FGGY_N  FGGY family of carbohydrate kinases, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0     6e-06     0.036       1     112 [.       7     119 ..       7     137 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6e-06
                                   EEEEEEEESSEEEEEEEE.TTS-EEEEEEEE--EB-SSTT--EE-HHHHHHHHHHHHHHHHHHC.T.-GCCEEEEEEEE-S CS
                        FGGY_N   1 lilglDcGttstkaivld.ekgkvvasaqaelelsspkegwaeqdpeeiwqalaeairkvleqa.gisekqikaIgisgqr 79 
                                   +ilg+D G t+t a+v+d e g++++++    + +++  + +e+ +++i ++++ea+  +  +  +i  k     gi+  +
  gi|13541030|ref|NP_110718.1|   7 MILGVDGGSTKTVAVVYDdESGRIAGVGISGPANYTN--SPREEAMKNIKNSVYEAVDDADVNIeDIGFKVFGLAGIGDSK 85 
                                   79****************9********9998888887..568999999999999998876444434555544455556666 PP

                                   S-EEEEETTT.EESSEEE-TT--TTHHHHHHHHH CS
                        FGGY_N  80 eglvllDknd.kpLynailwkdrrtaeiveklke 112
                                   e ++  ++   +  ++ai+ +d  +a    +l+e
  gi|13541030|ref|NP_110718.1|  86 EATAEGEEIVrSIAGEAIVVNDGYAAYKFANLNE 119
                                   6666666666344456777777777777666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (339 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       735  (0.040995); expected 358.6 (0.02)
Passed bias filter:                      581  (0.0324056); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.47
# Mc/sec: 2162.47
//
Query:       gi|13541031|ref|NP_110719.1|  [L=589]
Description: phosphoenolpyruvate carboxykinase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
   1.5e-148  494.5   0.1   2.1e-148  493.9   0.1    1.2  1  PEPCK_GTP  Phosphoenolpyruvate carboxykinase C-terminal P-loo
    3.2e-65  219.8   0.0    4.3e-65  219.4   0.0    1.2  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 !  493.9   0.1  2.4e-152  2.1e-148       1     358 []     232     587 ..     232     587 .. 0.98

  Alignments for each domain:
  == domain 1  score: 493.9 bits;  conditional E-value: 2.4e-152
                                   -EEES-EEEEEE-TTS-EEEEEEE-TTTSSHHHHHT---S....STT-EEEEEESS-EEEEE-TTSBEEEE---SEEEEE- CS
                     PEPCK_GTP   1 wLaEhmlilgvtspegkkkyvaaafpsacGKtnlamlept....legwkvetvgdDiawlkfgedgrlraiNpeaGfFgva 77 
                                   wLaEhml+l+v++p+gk++++++afpsa+GKtnlam++p+      gw  ++++dDi+w+k+  dg+++a Npe+GfF+v+
  gi|13541031|ref|NP_110719.1| 232 WLAEHMLLLEVKDPQGKSHFITGAFPSASGKTNLAMISPPkdyrDAGWSTRLISDDISWIKIV-DGKFMATNPENGFFAVV 311
                                   9**************************************8777678****************9.***************** PP

                                   TT-STTT-HHHHHHTTBS-EEES-EEETTS-EE-TT--------EE-TTSSEE-T.T-SSS-TT-EEEEEGGGSTTB-TTT CS
                     PEPCK_GTP  78 pgtnektnpnalktlkkntiftNvaltedgdvwWegleeeapaelidwkgkkwtkekekaahpnsrftvpakqlpiiapew 158
                                   pgtn++tn+na++tl+kntiftNv lt  gd+wWegl+   + el+dwkg+k + ++e++ahpnsr+t p++++p +++ +
  gi|13541031|ref|NP_110719.1| 312 PGTNYNTNKNAMATLSKNTIFTNVGLTMSGDPWWEGLDPVYD-ELYDWKGNKRKIGGEPIAHPNSRYTSPLTNYPYLSDLY 391
                                   *************************************86555.9************************************* PP

                                   T-TT-EEEEEEEEEEB-SSSS-SEEE-SSHHHHHHHHHT-EEE--TTSSS-TT-EEE-GGG-GGG-SS-HHHHHHHHHHHT CS
                     PEPCK_GTP 159 edpeGvpisaiifggrrsetvplvleafdwehGvflgatlesetTaaaegkvgvvrrdPfamlpFlgynlgdYlehwlelg 239
                                   edpeGvp+sai+fggrr++ +plv+eaf+w+hGvflgat++ e+Taa+egkvg +rrdP+am+pF+gyn+ +Y++hw+e+g
  gi|13541031|ref|NP_110719.1| 392 EDPEGVPVSAILFGGRRATLIPLVFEAFNWNHGVFLGATMGVERTAASEGKVGDLRRDPMAMRPFCGYNINEYFRHWIEIG 472
                                   ********************************************************************************* PP

                                   TSTT-B--EEEEEES--B-TTSSBSS--GGGHHHHHHHHHHHHTT..S-EEETTEEEE-BTTC--TT-..TT--HHHHS-- CS
                     PEPCK_GTP 240 kklekklPkifsvNwfrkdeegkflWPGfgenlrvlkWilkrvegeakavetpiGlvPkkedldlkgldlskedleellsv 320
                                   ++ +k++Pkif+vNwfr+ ++g+f+WPGf+en+rvl+Wi+ r++++ +avetpiG++P+  +l+l+gl++s+ed++el+++
  gi|13541031|ref|NP_110719.1| 473 ER-SKNKPKIFYVNWFRRRADGTFIWPGFAENFRVLEWIIYRTSHNDNAVETPIGYIPE--SLNLAGLNISEEDVKELFRI 550
                                   99.99****************************************999**********6..588***************** PP

                                   -HHHHHHHHHHHHHHHHHTGGGS-HHHHHHHHHHHHHH CS
                     PEPCK_GTP 321 dkeewkeeveeieelfeklgeklPkelleeleelekrl 358
                                   dke wkee++ei+++f++lg ++P+e+l+e+e  +krl
  gi|13541031|ref|NP_110719.1| 551 DKEGWKEEMNEIQKYFSELG-NVPEEILKEFELEKKRL 587
                                   ******************88.9*********9999986 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 !  219.4   0.0   4.8e-69   4.3e-65       2     218 .]      16     228 ..      15     228 .. 0.96

  Alignments for each domain:
  == domain 1  score: 219.4 bits;  conditional E-value: 4.8e-69
                                   HHHHHHHHH--SEEEE----HHHHHHHHHHHHHTTSEEE-..TTSBS-EEE---TTSSS--GGGEEEE-SSHHHH-SS--E CS
                       PEPCK_N   2 fveevaelcqPdkvvvcdgseeeneellkelvekgelikl..ekypnsylarsdpkDvARvesrTfictekeedagplnnw 80 
                                   ++ ++a++++P++++vcdg++ee + l++ +v++ge+ikl  ++ +nsyl+rs+ +DvAR+e+rTfi +++++ +gplnn 
  gi|13541031|ref|NP_110719.1|  16 WIVSIAKHLNPSSIYVCDGTKEEFDDLASAMVKDGEMIKLneKNFKNSYLYRSNATDVARTEERTFISARDKSFVGPLNNF 96 
                                   9***************************************98899************************************ PP

                                   E-HHHHHHHHHHHSTTTTTTSEEEEEEEEES-TTSTT-EEEEEEES-HHHHHHHHHHSEESHHHHTT-SS..TSEEEEEE- CS
                       PEPCK_N  81 mdpeemkeelkelfkgcmkGrtmyVipfsmGpvgsplskigveiTdsaYVvlsmrimtrvgkkvleklgeeeefvkclHsv 161
                                      +++k+ ++++fkg+++G+tm+Vip+ +   +s+++ +g+e+Tds+YVvl+ +++tr+gk v+ek+g  ++f+k +H++
  gi|13541031|ref|NP_110719.1|  97 LPLDRVKQVWNQFFKGAYTGKTMFVIPYALSSPESKFADFGIEVTDSKYVVLNLHYITRMGKGVIEKIG--DRFIKGVHAT 175
                                   *********************************************************************..58******** PP

                                   S--SS-SS-BTB---G.G-EEEEEGGGTE......EEEES--SHHHH-TCCHHHHCHHHHHHHH CS
                       PEPCK_N 162 gaplegqkdvkWpcne.kkyivhfpeere......ilsvgsgYgGNaLlgKkcfalRiasviar 218
                                   g+ +           + +k+i+h+p e+       ilsv+++YgGNaLl+Kkc+alRiasv ar
  gi|13541031|ref|NP_110719.1| 176 GNLD-----------PgNKFIIHMPWEKPegvdadILSVNTNYGGNALLSKKCHALRIASVRAR 228
                                   *733...........4489******9987788888**************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (589 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       469  (0.0261587); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 4292.68
//
Query:       gi|13541032|ref|NP_110720.1|  [L=242]
Description: metal-dependent hydrolase related to alanyl-tRNA synthetase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      8e-17   60.9   0.2    1.8e-16   59.8   0.1    1.6  2  tRNA-synt_2c  tRNA synthetases class II (A)
    1.9e-07   31.0   1.1    5.4e-07   29.6   1.1    1.8  1  tRNA_SAD      Threonyl and Alanyl tRNA synthetase second addi
  ------ inclusion threshold ------
       0.12   12.9   0.3        2.7    8.6   0.1    2.3  2  MBF2          Transcription activator MBF2


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 !   59.8   0.1   3.1e-20   1.8e-16     473     552 .]      13      91 ..       3      91 .. 0.95
   2 ?   -2.4   0.0      0.21   1.3e+03     317     347 ..     138     171 ..     120     177 .. 0.59

  Alignments for each domain:
  == domain 1  score: 59.8 bits;  conditional E-value: 3.1e-20
                                   SEEEEEEEEEETTEEEESEEXXXXSSSSCSXXXEEEEESSEEEEESEEEEETTEEEEEXSS.XSXXXTTSEEEEEEXHHH CS
                  tRNA-synt_2c 473 kefveeveegeevgvvLdrTpfYaesGGqigDeGliekegaefrvkdvqkakgvvlhkgkleegklkvgdkvkaevdeer 552
                                   kef  +v e++e+ ++LdrT+fY+++GGq +D+G+i++ g+e rv+dv k +  v+h+++ +   l+ g kv++++d++r
  gi|13541032|ref|NP_110720.1|  13 KEFDGNVIEVKENRLILDRTAFYPTGGGQPNDTGVIFCCGKEYRVNDVTKDGDEVIHVVDDS-TGLSAGAKVHGTIDWDR 91 
                                   789999******************************************************97.88************986 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.21
                                   -SSTHHHHHHHHHHHHHTT...TGCCHHCCHHHH CS
                  tRNA-synt_2c 317 lkekflaklvavvvevlgd...vypelkekeekv 347
                                   + ++f++k+++   +++++   vyp++  kee +
  gi|13541032|ref|NP_110720.1| 138 FTKEFVDKIIEESNSFMKEghrVYPDILTKEEAI 171
                                   4445555555555555543223566666666555 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 !   29.6   1.1     9e-11   5.4e-07       1      44 []     192     235 ..     192     235 .. 0.95

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 9e-11
                                   EEEEEETT.EEEEESS---SBGGGC-SEEEECCECCCTCEEEEE CS
                      tRNA_SAD   1 vrvvsiGdisvelCgGtHvpnTgeIgafkilseesiakglrRIy 44 
                                   vr++ i+  + +  gGtHv+nT+e+g + + + e+++k + RI+
  gi|13541032|ref|NP_110720.1| 192 VRIIVIEGLDEQSDGGTHVSNTKEVGTIFVRKIENKGKRNKRIE 235
                                   8999997799*********************************7 PP

>> MBF2  Transcription activator MBF2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.1   0.00045       2.7      39      75 ..      97     134 ..      60     144 .. 0.74
   2 ?    2.2   0.0     0.044   2.6e+02      39      86 ..     192     238 ..     157     239 .. 0.63

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00045
                          MBF2  39 ytItaievydltkn.gngatasltsGGvgqnfvtlklk 75 
                                   +  tai+v+d + n  +g +a lt+G + +  + + + 
  gi|13541032|ref|NP_110720.1|  97 RYHTAIHVIDGVVNvMHGSEALLTGGQIYEDRARIDMN 134
                                   5559*******9999***********999988888775 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.044
                          MBF2  39 ytItaievydltkngngatasltsGGvgqnfv.tlklksqrgrglnfqv 86 
                                    +I  ie +d+  +++g+t       vg+ fv ++  k++r++++ fq+
  gi|13541032|ref|NP_110720.1| 192 VRIIVIEGLDE--QSDGGTHVSNTKEVGTIFVrKIENKGKRNKRIEFQL 238
                                   55666666666..667777777777899999977999999999999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       521  (0.0290591); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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 0.31s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1530.91
//
Query:       gi|13541033|ref|NP_110721.1|  [L=220]
Description: glutaredoxin [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.9e-27   95.1   1.2    9.1e-17   60.9   0.1    2.2  2  Thioredoxin_3   Thioredoxin domain
    2.9e-14   53.0   1.1    2.1e-09   37.5   0.1    2.4  2  Glutaredoxin    Glutaredoxin
    1.6e-09   37.6   0.1    0.00042   19.9   0.0    2.1  2  ABC_transp_aux  ABC-type uncharacterized transport system
    1.7e-09   37.6   0.5    0.00028   20.8   0.1    2.2  2  Thioredoxin     Thioredoxin
    2.5e-08   33.8   0.0    0.00078   19.2   0.0    2.2  2  Thioredoxin_9   Thioredoxin
    5.7e-06   26.7   2.1      0.092   13.2   0.0    3.1  2  Thioredoxin_2   Thioredoxin-like domain
    0.00018   21.4   0.0       0.61    9.9   0.0    3.1  2  TraF            F plasmid transfer operon protein
  ------ inclusion threshold ------
      0.011   15.9   4.9        2.3    8.4   0.3    3.0  3  Thioredoxin_4   Thioredoxin
      0.016   15.3   0.1      0.038   14.1   0.1    1.6  1  Polbeta         Polymerase beta, Nucleotidyltransferase
      0.042   13.6   1.0       0.68    9.7   0.0    2.7  3  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 !   33.3   0.1     2e-11   3.6e-08       8      76 .]      35     110 ..      25     110 .. 0.89
   2 !   60.9   0.1   5.1e-20   9.1e-17       2      72 ..     138     211 ..     137     215 .. 0.93

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 2e-11
                                   SSSTTCHHHHHHHHHHCHCC.TCECEEECC.TTHHHHHHCT-SSSSEEECT......TCEEEESS---CCHHHHHHH CS
                 Thioredoxin_3   8 pgCakCpklekavkeaaaek.gikaevekv.tdfeeiekygVmsvPalvid......gkvvvsGkvpseeeirklle 76 
                                    +C++C++++++++e+ + + +i+++v++  +d ++++ ygV++ Pa+++       g++v+ G +ps++e+ +l+e
  gi|13541033|ref|NP_110721.1|  35 ENCRYCKETVQLATEVSEINpKIHLKVYNFdEDKDQVKAYGVEKYPATIVSkagvedGRIVYYG-LPSGYEFGSLIE 110
                                   68****************9978********8999999************97777777*******.******998875 PP

  == domain 2  score: 60.9 bits;  conditional E-value: 5.1e-20
                                   EEEE.ESSSSTTCH.HHHHHHHHHCHCCTCECEEECCTTHHHH.HHCT-SSSSEEECTTCEEEESS---CCHHH CS
                 Thioredoxin_3   2 eikv.lgpgCakCp.klekavkeaaaekgikaevekvtdfeei.ekygVmsvPalvidgkvvvsGkvpseeeir 72 
                                   +ikv ++p+C++Cp ++ +a+k a+ +++ik e++++ +fe+  e+ gV svP++vi+  v++ G+ p+ ++ +
  gi|13541033|ref|NP_110721.1| 138 TIKVyVTPTCPYCPrAVGTAHKFALMNPNIKGEMIEALEFENEaEEVGVSSVPHIVINNDVTFIGAYPDDQFAE 211
                                   69************99*********************8888777************************999876 PP

>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.2   2.4e-05     0.043       2      52 ..      28      81 ..      27      87 .. 0.76
   2 !   37.5   0.1   1.2e-12   2.1e-09       1      59 [.     139     198 ..     139     199 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.4e-05
                                  EEEES..TSSHHHHHHHHHHHHTT.....GGEEEEEGCCSHHHHHHHHHHHTSSSSSE CS
                  Glutaredoxin  2 vlftk..ptCpyCkkakrlLkelg.....vkfeeidvdkdeeireelkelsgvrtvPq 52
                                  v+ft+   +C yCk +++l++e       +  ++++ d+d   ++++k++ gv++ P 
  gi|13541033|ref|NP_110721.1| 28 VVFTSndENCRYCKETVQLATEVSeinpkIHLKVYNFDED---KDQVKAY-GVEKYPA 81
                                  899999**************77776444455666666665...8888888.8888886 PP

  == domain 2  score: 37.5 bits;  conditional E-value: 1.2e-12
                                   EEEEESTSSHHHHHHHHHHHHTT.....GGEEEEEGCCSHHHHHHHHHHHTSSSSSEEEETTEE CS
                  Glutaredoxin   1 vvlftkptCpyCkkakrlLkelg.....vkfeeidvdkdeeireelkelsgvrtvPqvfidgkh 59 
                                   + ++++ptCpyC++a+ +++++      +k e+i+ ++ e++ ee+    gv++vP+++i++++
  gi|13541033|ref|NP_110721.1| 139 IKVYVTPTCPYCPRAVGTAHKFAlmnpnIKGEMIEALEFENEAEEV----GVSSVPHIVINNDV 198
                                   689****************99998888899*********9999999....***********975 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 !   15.8   0.1   4.1e-06    0.0073      22     109 ..      20      99 ..      16     107 .. 0.84
   2 !   19.9   0.0   2.4e-07   0.00042      13      98 ..     123     197 ..     121     214 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 4.1e-06
                ABC_transp_aux  22 nleepvtikvylsenlalppelkalekevkdlLeeyaaysggkisvefidpspneeeeeeaeaygitpvqisveekdelkt 102
                                    l+++v + v+ s++++      ++ ke+ +l +e  + ++ ki++++++ +++   +++ +ayg+++ + + + k  ++ 
  gi|13541033|ref|NP_110721.1|  20 YLKNDVDLVVFTSNDEN-----CRYCKETVQLATEVSEINP-KIHLKVYNFDED---KDQVKAYGVEKYPATIVSKAGVED 91 
                                   5789999*****99963.....478**************99.**********55...588888999999988886666666 PP

                ABC_transp_aux 103 .krvymgl 109
                                     +vy gl
  gi|13541033|ref|NP_110721.1|  92 gRIVYYGL 99 
                                   68888876 PP

  == domain 2  score: 19.9 bits;  conditional E-value: 2.4e-07
                ABC_transp_aux  13 sdatkellknleepvtikvylsenlalppelkalekevkdlLeeyaaysggkisvefidpspneeeeeeaeaygitpvqis 93 
                                   s+++ el++++++p+tikvy+++    p     +  ++  + +++a  ++ +i+ e+i++ ++e   +eae+ g+++v+  
  gi|13541033|ref|NP_110721.1| 123 SSKAAELISKIDKPITIKVYVTPTC--P-----YCPRAVGTAHKFALMNP-NIKGEMIEALEFE---NEAEEVGVSSVPHI 192
                                   778899******************4..3.....367888999******99.**********888...77777899999876 PP

                ABC_transp_aux  94 veekd 98 
                                   v ++d
  gi|13541033|ref|NP_110721.1| 193 VINND 197
                                   66544 PP

>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.1   1.6e-07   0.00028       7      85 ..      14      91 ..      10      98 .. 0.81
   2 !   15.1   0.1   9.2e-06     0.017      12      88 ..     128     200 ..     119     215 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 1.6e-07
                                  HHHHHHHHTTTSSEEEEEEE-TTSHHHHCHHHHHHHHHHHCTTTSEEEEEETTTSHHHHHHTT-SSSSEEEEEETTEEE CS
                   Thioredoxin  7 kenFeeevakekklvlveFyApwCghCkalaPeleklaeelkdkvklakvdvdenedlakkyevegiPtlklfkngkev 85
                                  k +F++ ++++ +lv+     + C  Ck+     ++++e    k+ l   + de +d +k y+ve +P+ ++ k+g e 
  gi|13541033|ref|NP_110721.1| 14 KGEFDKYLKNDVDLVVFTSNDENCRYCKETVQLATEVSEINP-KIHLKVYNFDEDKDQVKAYGVEKYPATIVSKAGVED 91
                                  5689****996666666666789*****97777777766655.88888889999999*************999999765 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 9.2e-06
                                   HHHTTTSSEEEEEEE.-TTSHHHHCHHHHHHHHHHHCTTTSEEEEEETTTSHHHHHHTT-SSSSEEEEEETTEEEEEE CS
                   Thioredoxin  12 eevakekklvlveFy.ApwCghCkalaPeleklaeelkdkvklakvdvdenedlakkyevegiPtlklfkngkevkky 88 
                                   e ++k +k++ ++ y  p C+ C +  ++ +k+a     ++k   +++ e e+ a++++v+++P +++ ++      +
  gi|13541033|ref|NP_110721.1| 128 ELISKIDKPITIKVYvTPTCPYCPRAVGTAHKFALMNP-NIKGEMIEALEFENEAEEVGVSSVPHIVINNDVT----F 200
                                   567778889999877368*************9998888.***************************8766543....4 PP

>> Thioredoxin_9  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.0   4.9e-05     0.088      41     109 ..      23      90 ..       4     101 .. 0.81
   2 !   19.2   0.0   4.4e-07   0.00078      27     105 ..     121     196 ..     113     217 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.9e-05
                                   S-EEEEEE--..TT-HHHHHHHHHHHHHHHH-TTEEEEEE-HHHHHHHTTTTTT-SS--SSEEEEE-TT-- CS
                 Thioredoxin_9  41 kklkilvlte..dwCgDaavnvPvlakiaelnpnievkillrdenlelmdqyltngaraiPtliildeege 109
                                   ++++++v+t   + C  + ++v    +++e+np+i++k+   de+++ ++ y   g ++ P+ i+ ++++e
  gi|13541033|ref|NP_110721.1|  23 NDVDLVVFTSndENCRYCKETVQLATEVSEINPKIHLKVYNFDEDKDQVKAY---GVEKYPATIVSKAGVE 90 
                                   55566666642256888999999999*********************99999...7888898888776655 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 4.4e-07
                                   HHH---HHHHHT--S-EEEEEE--TT-HHHHHHHHHHHHHHHH-TTEEEEEE-HHHHHHHTTTTTT-SS--SSEEEEE- CS
                 Thioredoxin_9  27 elseeteekiksiekklkilvltedwCgDaavnvPvlakiaelnpnievkillrdenlelmdqyltngaraiPtliild 105
                                    +s++  e i++i+k+++i v  ++ C+ + + v   +k+a  npni+ +++   e le+ ++  + g  ++P ++i +
  gi|13541033|ref|NP_110721.1| 121 DVSSKAAELISKIDKPITIKVYVTPTCPYCPRAVGTAHKFALMNPNIKGEMI---EALEFENEAEEVGVSSVPHIVINN 196
                                   57888899****************************************9988...667777777777888888877654 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.0   5.1e-05     0.092       9      90 ..      27      89 ..      21     108 .. 0.72
   2 !   10.4   0.7   0.00039      0.69       9     108 ..     139     212 ..     131     213 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.1e-05
                 Thioredoxin_2  9 lvvft..dpdCpyCkklkkelkelddvtvrvllfplkpsfepkavaiwcakekkkafkdieenvelarkygvrgtPt.ivfld 88
                                  lvvft  d++C yCk   +   e+++         ++p+++ k+ +++ +k+++             ++ygv+  P+ iv   
  gi|13541033|ref|NP_110721.1| 27 LVVFTsnDENCRYCKETVQLATEVSE---------INPKIHLKVYNFDEDKDQV-------------KAYGVEKYPAtIVSKA 87
                                  5666658999*****97776666633.........4888999999999999997.............7888888888444444 PP

                 Thioredoxin_2 89 gk 90
                                  g 
  gi|13541033|ref|NP_110721.1| 88 GV 89
                                  44 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00039
                 Thioredoxin_2   9 lvvftdpdCpyCkklkkelkelddvtvrvllfplkpsfepkavaiwcakekkkafkdieenvelarkygvrgtPtivfldg 89 
                                   + v+ +p+CpyC +   +  +            ++p+++ ++++    +++             a+++gv+++P iv+ + 
  gi|13541033|ref|NP_110721.1| 139 IKVYVTPTCPYCPRAVGTAHKF----AL-----MNPNIKGEMIEALEFENE-------------AEEVGVSSVPHIVINND 197
                                   5566688999998866666666....22.....788877777777777777.............5999************9 PP

                 Thioredoxin_2  90 keivarlpGyvpaeeleal 108
                                        +  G++p ++++++
  gi|13541033|ref|NP_110721.1| 198 V----TFIGAYPDDQFAEY 212
                                   9....999*******9986 PP

>> TraF  F plasmid transfer operon protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.0   0.00034      0.61     127     214 ..      21     100 ..       2     105 .. 0.69
   2 !    7.1   0.0    0.0024       4.3     118     198 ..     124     194 ..     114     200 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00034
                          TraF 127 lakeygLlfFyrgk..cpyceaqapilqafadkyglevraVsvdgrplpelpnarvdkgqaarlgvkrtPalvlvdpksqk 205
                                   l++++ L++F +++  c yc++ ++   ++ +          ++ +++ ++ n+  dk+q +++gv+  Pa+++ +   ++
  gi|13541033|ref|NP_110721.1|  21 LKNDVDLVVFTSNDenCRYCKETVQLATEVSE----------INPKIHLKVYNFDEDKDQVKAYGVEKYPATIVSKAGVED 91 
                                   56666666666633337777666655554443..........344444446667777888999********9999988888 PP

                          TraF 206 vvpvaaGll 214
                                     +v +Gl 
  gi|13541033|ref|NP_110721.1|  92 GRIVYYGLP 100
                                   888888875 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0024
                          TraF 118 eekeaalkklakeygLlfFyrgkcpyceaqapilqafadkyglevraVsvdgrplpelpnarvdkgqaarlgvkrtPalvl 198
                                    + ++ ++k+ k   + + + ++cpyc  ++ +        +++++  ++ g++++ l+     ++ a++ gv+++P +v+
  gi|13541033|ref|NP_110721.1| 124 SKAAELISKIDKPITIKVYVTPTCPYCPRAVGTAH------KFALMNPNIKGEMIEALEF----ENEAEEVGVSSVPHIVI 194
                                   5677899999999999999********98887765......5567777888888876444....55788888888888877 PP

>> Thioredoxin_4  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.2      0.68   1.2e+03      22      55 ..      34      64 ..      22      81 .. 0.62
   2 ?    8.4   0.3    0.0013       2.3      12      31 ..     134     153 ..     129     174 .. 0.77
   3 ?    8.4   0.0    0.0013       2.3     128     164 ..     176     213 ..     167     215 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.68
                                  -TT-HHHHHHHHHHHHHHHHHHHTTSEEEEEEE- CS
                 Thioredoxin_4 22 dlrCphCakfeeeveklleeyidtGkvkfiirdf 55
                                  d +C +C++  +   ++ e    + k+ + + +f
  gi|13541033|ref|NP_110721.1| 34 DENCRYCKETVQLATEVSEI---NPKIHLKVYNF 64
                                  66788888876666555444...35555555555 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0013
                                   T-SEEEEEEE-TT-HHHHHH CS
                 Thioredoxin_4  12 dApvtvieyedlrCphCakf 31 
                                   d p+t+ +y+  +Cp+C + 
  gi|13541033|ref|NP_110721.1| 134 DKPITIKVYVTPTCPYCPRA 153
                                   5699*************764 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.0013
                                   HHHHHHHHHT--SS-EEEETTEE.E-TT--HHHHHHHH CS
                 Thioredoxin_4 128 aeskeakkagiestPtfiingek.veepqtyeelkali 164
                                   ++ +ea++ g++s+P ++in  + + ++ + +++ +++
  gi|13541033|ref|NP_110721.1| 176 EFENEAEEVGVSSVPHIVINNDVtFIGAYPDDQFAEYV 213
                                   67899**************8777688888888888876 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   2.1e-05     0.038      30      72 ..      22      68 ..      12      87 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.1e-05
                                  --EEEEEEEESS-...--HHHHHHHHHHHHHH.SSSEEEEEETT.TS CS
                       Polbeta 30 eSDiDlavllkek...ldleeelelaaelediklgkkvDlvdln.ea 72
                                  + D+Dl v+++++   +  +e ++la+e+++i+++  +++ +++ ++
  gi|13541033|ref|NP_110721.1| 22 KNDVDLVVFTSNDencRYCKETVQLATEVSEINPKIHLKVYNFDeDK 68
                                  78***********887777889**********665555555555333 PP

>> DSBA  DSBA-like thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.16   2.8e+02       7      53 ..      34      78 ..      28      91 .. 0.68
   2 ?   -0.8   0.1      0.62   1.1e+03       1      14 [.     138     151 ..     138     168 .. 0.82
   3 ?    9.7   0.0   0.00038      0.68     155     191 ..     176     212 ..     167     214 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.16
                                  BTTBHHHHHHHHHHHHHHHHCCTEEEEEEE-SSSCHHHHCT.S.GGG CS
                          DSBA  7 DvlCPyCylgkerleklaarspdvkvvlrpfelagakkasgnvgpse 53
                                  D +C yC+   +  +++ +++p+++++ + f+ +++  +++++g+++
  gi|13541033|ref|NP_110721.1| 34 DENCRYCKETVQLATEVSEINPKIHLKVYNFDEDKD--QVKAYGVEK 78
                                  567888888777777777777777776666654444..666666555 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.62
                                   EEEEEEBTTBHHHH CS
                          DSBA   1 tvdeffDvlCPyCy 14 
                                   t++++    CPyC 
  gi|13541033|ref|NP_110721.1| 138 TIKVYVTPTCPYCP 151
                                   688888889****6 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.00038
                                   HHHHHHHHTT-SSSSEEEETTCEEEESSSSHHHHHHH CS
                          DSBA 155 entaaaqslgvtGvPtvvvdgkrmvfGadrldtlada 191
                                   e +++a+++gv+ vP +v+++ +++ Ga + d++a++
  gi|13541033|ref|NP_110721.1| 176 EFENEAEEVGVSSVPHIVINNDVTFIGAYPDDQFAEY 212
                                   5789***************9999**********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       616  (0.0343577); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.51
# Mc/sec: 1287.27
//
Query:       gi|13541034|ref|NP_110722.1|  [L=77]
Description: hypothetical protein TVN0203 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.083   12.9   0.4      0.091   12.8   0.4    1.0  1  FTCD      Formiminotransferase domain
        0.1   12.8   0.2       0.13   12.4   0.2    1.2  1  Apo-CII   Apolipoprotein C-II


Domain annotation for each model (and alignments):
>> FTCD  Formiminotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.4     1e-05     0.091      57     124 ..       3      70 ..       1      75 [. 0.92

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1e-05
                          FTCD  57 nltdievtplhvvfeevkkeaeelglevtgseivglvplealleaakyylekeklfileeeekiklai 124
                                   n++ + v  + + f++  +++++++l+ +  +i  l +l+++ ++  +++  + l+  +e+++i++ +
  gi|13541034|ref|NP_110722.1|   3 NILKMIVILIIQSFQTLSRKSKKIDLHSINKKITHLYSLKSIAAVDXFMMYMQVLSYRKEKKTINIRV 70 
                                   7777788889999**************************************************99876 PP

>> Apo-CII  Apolipoprotein C-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.2   1.4e-05      0.13      37      63 ..      24      51 ..      15      61 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.4e-05
                       Apo-CII 37 kktylptvdekirdmYs.kstaAvstYa 63
                                  kk  l ++++ki  +Ys ks aAv  ++
  gi|13541034|ref|NP_110722.1| 24 KKIDLHSINKKITHLYSlKSIAAVDXFM 51
                                  677899**********989999998764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       862  (0.0480785); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); 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: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 471.60
//
Query:       gi|13541035|ref|NP_110723.1|  [L=122]
Description: hypothetical protein TVN0204 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.054   13.1   0.1       0.07   12.8   0.1    1.2  1  DDE_Tnp_1  Transposase DDE domain


Domain annotation for each model (and alignments):
>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   3.9e-06      0.07      69     214 .]       2     109 ..       1     109 [. 0.71

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.9e-06
                     DDE_Tnp_1  69 ldelrprkgklvlaDaGYasaelldtle.ekgvdyiirlkkntklyrkgaeskrrgrlrkhdrnkiltksqkrrnkskkek 148
                                   +d++r  + +++++D+ Y+  e++d++    +v +ii                 ++++r+  ++k +  s++  n      
  gi|13541035|ref|NP_110723.1|   2 IDSIR--YFSYLFVDSLYDASEIYDYVLeNTHVIPIID----------------ASERRGIVTEKLPDNSRIDINL----- 59 
                                   67777..999****************994555555554................4444444444444444444444..... PP

                     DDE_Tnp_1 149 gdvyyvtntnsellsaeevaelyrlRwqiErvFkwlkrkfgldrlryrglnrveaqllllllalnl 214
                                                   +++  ly+l+ +iEr F  l+ +++l  +++r++    +++ l+++++nl
  gi|13541035|ref|NP_110723.1|  60 ---------------RRKYPSLYSLKFGIERMFTILEISYKLSIWDVRNRSY-NTAVGLKIIVYNL 109
                                   ...............446689****************999988888877663.4556677888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       313  (0.0174578); expected 358.6 (0.02)
Passed bias filter:                      210  (0.0117129); 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 0.28s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 783.14
//
Query:       gi|13541036|ref|NP_110724.1|  [L=519]
Description: sugar-binding protein [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.6e-18   66.6   8.6    6.5e-18   65.7   8.6    1.3  1  SBP_bac_1  Bacterial extracellular solute-binding protein
  ------ inclusion threshold ------
      0.013   16.4   0.3      0.039   14.9   0.3    1.8  1  Pilin_N    Archaeal Type IV pilin, N-terminal
       0.19   12.1   1.1        1.8    8.9   0.4    2.5  2  Wzz        Chain length determinant protein


Domain annotation for each model (and alignments):
>> SBP_bac_1  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.7   8.6   1.1e-21   6.5e-18      13     300 ..      64     363 ..      55     375 .. 0.75

  Alignments for each domain:
  == domain 1  score: 65.7 bits;  conditional E-value: 1.1e-21
                                   HHHHH...HHHHHTTEEEEEEEE....CHHHHHHHHHHHHHTTSSSCSEEEECGGHHHHHHHTTSBECCHHHHHHTTECTT CS
                     SBP_bac_1  13 lvaka...fekehpgikVeiesv....gsgslaqkltlaiaaGdgpaDviavdndwiarlakaglllpldpyvkaylapgv 86 
                                   ++++a   +++ehp++kVe++      + g++++kl l +++++ ++ v+  d +++a++ ++g l+pl++y++       
  gi|13541036|ref|NP_110724.1|  64 FINNAtksWQAEHPNVKVEFIGPlgasSEGQYYTKLDLLTSSSSTAPTVMLEDMFYTATYQSEGILAPLNSYINSS----- 139
                                   33333445***********998888889999999**********888****************************9..... PP

                                   CCTEEEEHHHHTHHHHCE.EE...ES.EEEE.EEEEEEEETTTHHCTTGGG.......SHBHHHHHHHHHHHHHHCTCT.. CS
                     SBP_bac_1  87 kdaadklsssvlpkilds.kv...ly.vPly.aargliYNkdlfekagldp.......pwtWdelveaakklkekgkkp.. 152
                                         +++  +p+ l+  +    +y +P + + ++++YN +l+ kag+ p       p++W e++ aak +         
  gi|13541036|ref|NP_110724.1| 140 ------FFNNIFPSALGQmTIggiHYgLPAQvTDTLIYYNITLLQKAGVIPsdsttwqPTNWTEIINAAKQINSTLVPNdp 214
                                   ......44445555555434488********55**************************************9998876655 PP

                                   ...HCCHCCEEHHHHHHHHHHHHHHHHTGGGEECCCTHHCSHHHHSHHHHHHHHHHHHHHHHHHHTTEEECSSHHHHHHHH CS
                     SBP_bac_1 153 ...iggarggsasgtayyfalalakslggkvfdkdgggldnpegvtaatylvklyavanltkelkgkgaenkdgaaalalf 230
                                      +  ++ g  +++a+ f+                    +++  + ++y+ + +    + k ++  + +n++ +++++ f
  gi|13541036|ref|NP_110724.1| 215 gliPLNIYEGVKGDEASSFT-------------------GFEGLLYGTGYGLYNF---TDHKWYGYSPGLNETFEFYKTVF 273
                                   55555555555555555554...................2223333444444444...33344444444444444444444 PP

                                   H.....................TTSCSEEEEEHHHHHHHHCEEEEECHHCHHHHTTSTEEEECEEBETTTTSEE...EEEE CS
                     SBP_bac_1 231 e.....................aGeaamaivglwaalaamkvapkvafaadkekpkeelgvaplPagkggkpgi...lgay 287
                                                         +G+ a+ i+g+w+        ++ ++  + +++ +++gva +P+  g +pg    +g++
  gi|13541036|ref|NP_110724.1| 274 GeglatpalsatpyitagqymqEGKLAIDIDGSWM----YGYQWAPGAQHPISNFSKYIGVAKIPTYSGQAPGFntmVGGW 350
                                   44444444445555778888889999999999998....55556777777778888899********************** PP

                                   EEEEBTTCSTHHH CS
                     SBP_bac_1 288 glaipkgsknpea 300
                                   g+a+++g++  e 
  gi|13541036|ref|NP_110724.1| 351 GWAMYNGTPSSEK 363
                                   *******997665 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 ?   14.9   0.3   6.4e-06     0.039      13      51 ..      18      59 ..      17      82 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 6.4e-06
                       Pilin_N 13 vaitvIlaAviaafvlglasneekapqasievk...idssas 51
                                  ++i+v+laAvi+++v  ++  ++ + q++i+v    ++ssa+
  gi|13541036|ref|NP_110724.1| 18 IVIVVVLAAVIGGVVYYYSTLPHPTKQVTITVAapvYSSSAT 59
                                  79****************999999999999887765555544 PP

>> Wzz  Chain length determinant protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.4    0.0003       1.8      18      53 ..      18      53 ..      11      78 .. 0.80
   2 ?    0.8   0.0       0.1   6.2e+02      62      90 ..     450     478 ..     434     480 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0003
                                  XXXXXXXXXXXXXXXXXXXXXX-EEEEEEEES--CH CS
                           Wzz 18 lIilvtllfallaviyaflatpkYtataqilvpekk 53
                                  ++i+v+l++++++v+y +   p  t + +i+v  + 
  gi|13541036|ref|NP_110724.1| 18 IVIVVVLAAVIGGVVYYYSTLPHPTKQVTITVAAPV 53
                                  567777777888888889999**********98775 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.1
                                   CCHHHHHHHHHHHHHHHHHSSSS--EEEE CS
                           Wzz  62 aqdvqanlqlasteieilkSrdvlekvis 90 
                                   ++d  +++++ast++++l+S    ++v+s
  gi|13541036|ref|NP_110724.1| 450 VSDGYSVSKAASTYNSLLTSAVGASNVMS 478
                                   4577788899**********988888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (519 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       745  (0.0415528); expected 358.6 (0.02)
Passed bias filter:                      535  (0.0298399); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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 0.29s 00:00:00.94 Elapsed: 00:00:00.47
# Mc/sec: 3345.33
//
Query:       gi|13541037|ref|NP_110725.1|  [L=296]
Description: ABC-type sugar transporter, permease component [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.1e-17   62.0  27.6    6.1e-17   62.0  27.6    2.2  2  BPD_transp_1  Binding-protein-dependent transport system inne
  ------ inclusion threshold ------
       0.55   10.4   6.6       0.19   11.9   3.1    2.0  2  TM_PBP2_N     N-terminal of TM subunit in PBP-dependent ABC t
        8.4    6.0  10.8       0.12   12.0   2.7    2.0  2  CPP1-like     Protein CHAPERONE-LIKE PROTEIN OF POR1-like


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 ?  -10.5  18.1         3   1.8e+04      25      58 ..      16      97 ..       8     103 .. 0.67
   2 !   62.0  27.6     1e-20   6.1e-17       2     176 ..      91     293 ..      90     296 .] 0.92

  Alignments for each domain:
  == domain 1  score: -10.5 bits;  conditional E-value: 3
                  BPD_transp_1 25 ivllslPsfv..laillvlvf...............................................vilsilghlilpvii 58
                                  i+l  +Psf+  ++++++  +                                               v++ i+g+++l+ i+
  gi|13541037|ref|NP_110725.1| 16 IFLILIPSFIylIIFFIYP-IflsfkysftnlslydinkysfigftnyvdlfksdlflksiyitiiflVVSAIIGQMFLGSIL 97
                                  7888999999643333333.358889999999999999999999999999888885555544444444444555555555444 PP

  == domain 2  score: 62.0 bits;  conditional E-value: 1e-20
                  BPD_transp_1   2 illGilaa...lnrnkkldkllrpliivllslPsfvlaillvlvf...................vilsilghlilpviill 60 
                                   ++lG+++a   +  +k ++ +++++i + +++P +  +i+++  +                   + + +++++i ++ii+ 
  gi|13541037|ref|NP_110725.1|  91 MFLGSILAyllTLTHKYFKTVVTTIILIAWATPQVTAGIMWYSTLsyipegtinvilknmgfhpIDFFSIHNAIYSIIIAN 171
                                   689999999999************************99998887799999999999******98444468888888***** PP

                  BPD_transp_1  61 llsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtll 141
                                   ++  +++ +li+ ++++s++ + ++a++++Ga+++++f+ +++P++++ iit l+l   + lg ++l++ l+++++ g++ 
  gi|13541037|ref|NP_110725.1| 172 IWIGLGFSVLIFLGGIQSIDPSIIKASYIDGAKPFRRFFSIIFPLLKTNIITDLLLITLFTLGTFTLIYVLTAGGPAGSTE 252
                                   ***************************************************************************9**999 PP

                  BPD_transp_1 142 leailgydyseis......nggvlalviavlllnlvadilq 176
                                   l +i +y + + +      n++ ++++i+ l+l+l++  + 
  gi|13541037|ref|NP_110725.1| 253 LLTIYQYETGFSLfslglaNAIGVIIIIIALVLSLIYLRFI 293
                                   9999999999999**99998888888888888888887765 PP

>> TM_PBP2_N  N-terminal of TM subunit in PBP-dependent ABC transporters
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   3.1   3.1e-05      0.19       1      23 [.      25      47 ..      25      48 .. 0.94
   2 ?   -2.9   0.1       1.3   7.8e+03      17      24 ..      57      64 ..      55      64 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.1e-05
                     TM_PBP2_N  1 llLlvfqvfpvlyTistafTNyG 23
                                  ++L++f ++p++ +++++fTN++
  gi|13541037|ref|NP_110725.1| 25 IYLIIFFIYPIFLSFKYSFTNLS 47
                                  68*******************85 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.3
                     TM_PBP2_N 17 tafTNyGd 24
                                  ++fTNy d
  gi|13541037|ref|NP_110725.1| 57 IGFTNYVD 64
                                  68***976 PP

>> CPP1-like  Protein CHAPERONE-LIKE PROTEIN OF POR1-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   2.7     2e-05      0.12     137     193 ..      67     120 ..      55     122 .. 0.82
   2 ?   -2.9   1.1      0.74   4.4e+03     111     111 ..     256     256 ..     223     288 .. 0.52

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2e-05
                     CPP1-like 137 KekklgravlltlvgLvvGlllGsllasllqvdvalsglsseellvslvtlvllwlv 193
                                   K+  +++++ +t+++Lvv++++G+++ +++       ++ + + + ++vt ++l + 
  gi|13541037|ref|NP_110725.1|  67 KSDLFLKSIYITIIFLVVSAIIGQMFLGSILA---YLLTLTHKYFKTVVTTIILIAW 120
                                   66779**********************99955...3344677778999998888765 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 0.74
                     CPP1-like 111 l 111
                                   +
  gi|13541037|ref|NP_110725.1| 256 I 256
                                   1 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1081  (0.0602934); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 1946.97
//
Query:       gi|13541038|ref|NP_110726.1|  [L=268]
Description: sugar permease [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-14   54.6  17.8    1.1e-14   54.6  17.8    2.1  2  BPD_transp_1     Binding-protein-dependent transport system i
  ------ inclusion threshold ------
      0.079   12.4   0.8        6.2    6.3   0.0    2.7  2  ATP1G1_PLM_MAT8  ATP1G1/PLM/MAT8 family


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   6.6      0.78     7e+03      20      49 ..      11      71 ..       2      91 .. 0.43
   2 !   54.6  17.8   1.3e-18   1.1e-14      10     182 ..      89     261 ..      77     264 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 0.78
                  BPD_transp_1 20 lrpliivllslPsfvlaillvlvf...............................vilsil 49
                                  ++ l  vl+ +P+++l+   +  +                                +++++
  gi|13541038|ref|NP_110726.1| 11 FLSLLGVLFLIPFIWLINEAFSPLndiglkfpsyytlvpfynvmtnkifvnsiyeGLIQSF 71
                                  4444445555555554443332223333333333333444444466664333333333333 PP

  == domain 2  score: 54.6 bits;  conditional E-value: 1.3e-18
                  BPD_transp_1  10 lnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilpviillllsaapyvrlirraalrslpkdlveaaral 90 
                                    +++++++  l+  i +l ++P+f l+i+ + vf+++++l++  ++vi+ l + ++p+ ++i ++ ++++p+  ++a++++
  gi|13541038|ref|NP_110726.1|  89 SRKRFRFRIPLLLGILLLTGFPVFSLLIPEY-VFYVKTSLYNNLIGVILFLGVLNVPIDIWILKNSFDQIPSAIENASYID 168
                                   4678889999999999*********999955.7899********************************************* PP

                  BPD_transp_1  91 GasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydyseis...nggvlalviavlll 168
                                   Gas ++ + ++ lP+a p+++ ++il f++++g++ ++++l+s+    ++ +++++++ + + +   n ++++ +i++++ 
  gi|13541038|ref|NP_110726.1| 169 GASSFKSMLYIFLPLATPVLAVLIILDFVINWGNFYVPYILLSS--ARLFPVSVEIYSFFGAYNvkyNELAAFSIIYTVPA 247
                                   ******************************************87..5666666666666666669*9************** PP

                  BPD_transp_1 169 nlvadilqrlldpr 182
                                   ++++ + q++  + 
  gi|13541038|ref|NP_110726.1| 248 VILYIFAQKYMIKA 261
                                   ********998765 PP

>> ATP1G1_PLM_MAT8  ATP1G1/PLM/MAT8 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.3    0.0051        46      21      33 ..      15      27 ..      12      32 .. 0.84
   2 ?    6.3   0.0   0.00069       6.2      14      36 ..      69      91 ..      64      96 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.0051
                                  HHHHHHHHHHHHH CS
               ATP1G1_PLM_MAT8 21 AglLfivGiliil 33
                                   g+Lf++++++++
  gi|13541038|ref|NP_110726.1| 15 LGVLFLIPFIWLI 27
                                  59*********97 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.00069
                                  HHHHHHHHHHHHHHHHHHHHCCH CS
               ATP1G1_PLM_MAT8 14 rlgGLifAglLfivGiliilSkk 36
                                  +  G +f  +Lf vG + i+S+k
  gi|13541038|ref|NP_110726.1| 69 QSFGATFLSVLFSVGPAYIFSRK 91
                                  777999999************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       698  (0.0389313); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 1845.20
//
Query:       gi|13541039|ref|NP_110727.1|  [L=350]
Description: ABC-type sugar transporter, ATPase component [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.6e-32  112.2   0.0    5.1e-32  111.3   0.0    1.5  1  ABC_tran     ABC transporter
    7.4e-09   35.8   0.4     0.0019   18.1   0.0    2.4  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    5.3e-06   26.4   0.2    1.5e-05   25.0   0.0    1.8  2  RsgA_GTPase  RsgA GTPase
     0.0005   19.6   0.8     0.0056   16.1   0.8    2.1  1  SMC_N        RecF/RecN/SMC N terminal domain
     0.0027   17.4   0.1     0.0063   16.2   0.1    1.5  1  AAA_29       P-loop containing region of AAA domain
     0.0051   17.3   0.6      0.026   15.0   0.2    2.1  2  AAA_23       AAA domain
     0.0072   16.5   0.0      0.014   15.6   0.0    1.5  1  TOBE_2       TOBE domain
  ------ inclusion threshold ------
      0.012   16.4   0.0      0.038   14.8   0.0    2.0  1  OB_MalK      MalK OB fold domain
      0.025   14.7   0.0      0.081   13.0   0.0    1.9  2  MMR_HSR1     50S ribosome-binding GTPase
      0.061   12.8   0.0       0.51    9.7   0.0    2.1  2  PhoH         PhoH-like protein
      0.087   12.6   0.0       0.16   11.7   0.0    1.4  1  IstB_IS21    IstB-like ATP binding protein
       0.11   12.5   0.3       0.25   11.4   0.2    1.6  2  Dynamin_N    Dynamin family
       0.14   12.4   0.0       0.25   11.6   0.0    1.4  1  AAA_28       AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.3   0.0   3.7e-35   5.1e-32       1     136 [.      19     161 ..      19     162 .. 0.96

  Alignments for each domain:
  == domain 1  score: 111.3 bits;  conditional E-value: 3.7e-35
                                   EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                      ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren.. 79 
                                   lk ++++++ ge  +++G++GaGKStLl++lagl+  ++G+i +d+k +++  l+ +++ +++++q+  l p++tv++n  
  gi|13541039|ref|NP_110727.1|  19 LKGINFNIEDGEFFVLLGSSGAGKSTLLNILAGLEAVDSGSIFFDDKIVND--LPPVERGVAMVFQNYALYPHMTVYKNma 97 
                                   789*****************************************9999999..**************************** PP

                                   .......HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                   .......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  80 .......esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                          ++++ i+++++k+  + + +  +++ p++LSgGq qrval ral+++pk++llDEp 
  gi|13541039|ref|NP_110727.1|  98 fplkmlnYKKDSIDRIVKKVAETLDITWLLNRYPRELSGGQAQRVALGRALVRDPKIFLLDEPL 161
                                   ******9899999999999999998888898889*****************************7 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.4   9.3e-06     0.013       1      44 [.      31      65 ..      31      98 .. 0.70
   2 !   18.1   0.0   1.4e-06    0.0019     231     298 ..     128     193 ..      97     198 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 9.3e-06
                        AAA_21  1 lnvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirk 44
                                  + vl G  g+GKS+LL +l +l  +         ++++++  +k
  gi|13541039|ref|NP_110727.1| 31 FFVLLGSSGAGKSTLLNILAGLEAV---------DSGSIFFDDK 65
                                  689******************9655.........2333333333 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 1.4e-06
                        AAA_21 231 elparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHS 298
                                   ++ +relS G+ +  al  al r++   +++l+DEp ++L+  + +++   lk+ ++  +  +i +TH+
  gi|13541039|ref|NP_110727.1| 128 NRYPRELSGGQAQRVALGRALVRDP---KIFLLDEPLSNLDANIRSKIRNELKLMQKqLNKTFIYVTHD 193
                                   5678999999988889999999999...9********************99988888778899*****8 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0   1.1e-08   1.5e-05      86     126 ..      15      56 ..       2      65 .. 0.80
   2 ?   -3.0   0.0       4.2   5.7e+03      41      60 ..     323     342 ..     301     347 .. 0.57

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 1.1e-08
                                   THTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT---- CS
                   RsgA_GTPase  86 tkegleelkellkd.ktsvlvGqSGvGKStLinallpelelk 126
                                   + + l+ ++ +++d ++ vl+G+SG+GKStL+n l++ + + 
  gi|13541039|ref|NP_110727.1|  15 KVQVLKGINFNIEDgEFFVLLGSSGAGKSTLLNILAGLEAVD 56 
                                   4567788899999989*******************9866555 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 4.2
                                   HHHHTT-EEEEEEE-GGG-- CS
                   RsgA_GTPase  41 laeekgiepvivlnKiDlle 60 
                                   +   k+i++ i lnK+ + +
  gi|13541039|ref|NP_110727.1| 323 ISIGKEIPIYINLNKCLIFN 342
                                   44456788888888875555 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 !   16.1   0.8     4e-06    0.0056       8     209 ..       8     204 ..       1     212 [. 0.63

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 4e-06
                                   ESETTEECEEEEE..ET...TSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEE CS
                                   xxxxxxxxxxxxx..xx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N   8 enFksyagktvil..pf...sksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitf 83 
                                   + +ksy + +v    +f   + +f +++G+ G+GKs ll+ +    G ++     s  ++d i +  + + v+   v+++f
  gi|13541039|ref|NP_110727.1|   8 DVYKSYGKVQVLKgiNFnieDGEFFVLLGSSGAGKSTLLNIL---AGLEAV-DSGSIFFDDKIVN--DLPPVE-RGVAMVF 81 
                                   556777654443211221113457888899999999888866...444333.3445555555555..334443.3466667 PP

                                   EETTEE...SSSSSSCEEEEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SE CS
                                   xxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N  84 dnedkk...lkiekeevsisrrvkrkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpapl 161
                                   +n       ++ ++  + ++   ++k+ s  +i +k ++  +++ ll++   ++ +LSgG+ + val        v+   +
  gi|13541039|ref|NP_110727.1|  82 QNYALYphmTVYKNMAFPLKMLNYKKD-SIDRIVKKVAETLDITWLLNR---YPRELSGGQAQRVALGRA----LVRDPKI 154
                                   766655432444555555555555544.466677777777777777776...6889*****998776433....3566779 PP

                                   EEECTTTTTS-HHHHHHHHHHHHHHCTT..SEEEEE-SSHHHCCC-SCEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 162 yllDeidaaLDeknvkkvaellkekskn..aQfivislreemlekadklv 209
                                   +llDe  ++LD++ ++k+ + lk  +k+    fi +++++         +
  gi|13541039|ref|NP_110727.1| 155 FLLDEPLSNLDANIRSKIRNELKLMQKQlnKTFIYVTHDQMEAMSLGDHI 204
                                   9********************99655552277888888775555444555 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   4.5e-06    0.0063      17      39 ..      24      46 ..      15      52 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 4.5e-06
                        AAA_29 17 ieidlkg.atlltGpsGsGKSTll 39
                                  ++i+  g +++l G sG+GKSTll
  gi|13541039|ref|NP_110727.1| 24 FNIED-GeFFVLLGSSGAGKSTLL 46
                                  55654.4599*************8 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.2   1.9e-05     0.026      14      39 ..      20      49 ..       9      51 .. 0.76
   2 ?   -0.0   0.0      0.76   1.1e+03     118     133 ..     169     185 ..     101     232 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.9e-05
                        AAA_23 14 e.idF...skgltlItGpNGaGKTTildAi 39
                                  + i+F   +  ++++ G  GaGK+T+l+ +
  gi|13541039|ref|NP_110727.1| 20 KgINFnieDGEFFVLLGSSGAGKSTLLNIL 49
                                  25788887779****************976 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.76
                        AAA_23 118 eqfisellgskkiil.n 133
                                   + +i+++l+  +++l +
  gi|13541039|ref|NP_110727.1| 169 RSKIRNELKLMQKQLnK 185
                                   22222233322222213 PP

>> TOBE_2  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0     1e-05     0.014       1      75 [.     270     340 ..     270     341 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1e-05
                        TOBE_2   1 laiRPEklrlaaagg.anglsGtV..edveylGsstryvvelaggqlvvvrqpnadrdsalapGdtVelswdpddavv 75 
                                   l+iRPE++ l+   + +n ++G++  +  e lGs+t++  ++++ ++ +v  + +    ++ +G ++ + ++  ++++
  gi|13541039|ref|NP_110727.1| 270 LGIRPENIYLH--RQnDNDIEGKIipKVSELLGSHTLIIGSVENKEIRIVT-EET----NISIGKEIPIYINLNKCLI 340
                                   79********5..44368*****9767899**************9995554.444....4667777766666666665 PP

>> OB_MalK  MalK OB fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   2.8e-05     0.038      39      53 .]     263     277 ..     235     277 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.8e-05
                       OB_MalK  39 yagkevilGiRPEhi 53 
                                    + k+++lGiRPE+i
  gi|13541039|ref|NP_110727.1| 263 LDDKKITLGIRPENI 277
                                   367**********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 ?   13.0   0.0   5.8e-05     0.081       3      22 ..      33      52 ..      31      75 .. 0.83
   2 ?   -2.3   0.0       3.4   4.7e+03      91     109 ..     170     188 ..     137     193 .. 0.49

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.8e-05
                                  EEEESTTSSHHHHHHHHHTS CS
                      MMR_HSR1  3 aivGrpNvGKStLinaltge 22
                                  +++G + +GKStL+n l g 
  gi|13541039|ref|NP_110727.1| 33 VLLGSSGAGKSTLLNILAGL 52
                                  799*************9984 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 3.4
                                   HHHHHHHHHHHHHTTSEEE CS
                      MMR_HSR1  91 kpldeeleelleeakkpli 109
                                   +++++el+ ++++ +k +i
  gi|13541039|ref|NP_110727.1| 170 SKIRNELKLMQKQLNKTFI 188
                                   2233344444333445444 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   0.00037      0.51      16      80 ..      26      94 ..      12     125 .. 0.82
   2 ?    0.7   0.0      0.22     3e+02      43      97 ..     178     240 ..     137     250 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00037
                                  HHH-SEEEEE--TTSST.THHHHHHHHHHHHTTS-...SEEEEEE-S--TT----SS---------TTT CS
                          PhoH 16 lkkndivfaiGpaGtGK.tylavalavealkkkkv...kriiltrpaveageelGflpgdleekvdpyl 80
                                  +++ ++ + +G++G+GK t+l + +++ea+ ++++   ++i+   p ve g  + f++  l   + +y 
  gi|13541039|ref|NP_110727.1| 26 IEDGEFFVLLGSSGAGKsTLLNILAGLEAVDSGSIffdDKIVNDLPPVERGVAMVFQNYALYPHMTVYK 94
                                  556779999********77899*********98875557999999999999999998888777777765 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.22
                                   HHHTTS-SEEEE.EE-S--T...T----SS-.------...--TTTHHHHHHHTTTS-TTCHH CS
                          PhoH  43 alkkkkvkriil.trpavea...geelGflp.gdleek...vdpylrplydaLkdllgaekve 97 
                                   +++k+  k +i+ t  ++ea   g+++G+l  g le++   +d+y +p+ + + ++lg+ +++
  gi|13541039|ref|NP_110727.1| 178 LMQKQLNKTFIYvTHDQMEAmslGDHIGILHnGVLEQYgrpIDIYNNPINEYIATFLGDPEIN 240
                                   444444555554145555656668888887614444434446788888888888887776665 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00011      0.16      34      75 ..      15      58 ..       9      70 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00011
                     IstB_IS21 34 kvkeLatlsf.iekkenivllGpsGvGKshlaial.gveavrag 75
                                  kv+ L + +f ie+ e +vllG sG+GKs l   l g eav +g
  gi|13541039|ref|NP_110727.1| 15 KVQVLKGINFnIEDGEFFVLLGSSGAGKSTLLNILaGLEAVDSG 58
                                  57778888887999**************9875544277888776 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2   0.00018      0.25       2      28 ..      33      59 ..      32      68 .. 0.85
   2 ?   -2.6   0.0       3.7   5.1e+03      75      86 ..     171     182 ..     128     231 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00018
                                  EEEEBTTTTHHHHHHHHHTS--S---S CS
                     Dynamin_N  2 avvGsqSsGKSSvlnaLlgedilprgp 28
                                  +++Gs  +GKS++ln L g +   +g+
  gi|13541039|ref|NP_110727.1| 33 VLLGSSGAGKSTLLNILAGLEAVDSGS 59
                                  678****************98776666 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 3.7
                                   HHHHHHTSSSS- CS
                     Dynamin_N  75 etekiagankgi 86 
                                   + ++  + +++ 
  gi|13541039|ref|NP_110727.1| 171 KIRNELKLMQKQ 182
                                   332222222222 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00018      0.25       2      20 ..      32      50 ..      31      67 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00018
                        AAA_28  2 ivitGgestGKTtlleaLa 20
                                  +v++G +++GK+tll+ La
  gi|13541039|ref|NP_110727.1| 32 FVLLGSSGAGKSTLLNILA 50
                                  79***************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (350 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       548  (0.030565); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        83  (0.00462937); 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 0.31s 00:00:00.92 Elapsed: 00:00:00.47
# Mc/sec: 2223.49
//
Query:       gi|13541040|ref|NP_110728.1|  [L=1013]
Description: Alpha-mannosidase [Thermoplasma volcanium GSS1]
Scores for complete 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-63  212.5   0.2    1.3e-62  211.8   0.2    1.3  1  Glyco_hydro_38N  Glycosyl hydrolases family 38 N-terminal dom
    1.2e-33  117.0   0.1    2.3e-33  116.1   0.1    1.5  1  Glyco_hydro_38C  Glycosyl hydrolases family 38 C-terminal dom
    2.4e-18   66.1   0.0    4.6e-18   65.2   0.0    1.5  1  Alpha-mann_mid   Alpha mannosidase middle domain
    5.5e-12   45.6   0.1    1.3e-11   44.4   0.1    1.7  1  Glyco_hydro38C2  Glycosyl hydrolases family 38 C-terminal bet


Domain annotation for each model (and alignments):
>> Glyco_hydro_38N  Glycosyl hydrolases family 38 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  211.8   0.2   2.9e-66   1.3e-62       1     272 [.     249     497 ..     249     507 .. 0.94

  Alignments for each domain:
  == domain 1  score: 211.8 bits;  conditional E-value: 2.9e-66
                                   EEEEEEEEE--SSSSS-HHHHHCCTCHHHHHHHHHHHHHSTT--EEES-CHHHHHHHCCS-CCCHHHHHHHHHCTSEEECT CS
               Glyco_hydro_38N   1 kvhvvpHsHiDvgWlktvdeyqrrkvqrilssvlellerdpdrkFilseaslferwweeapeekkelvkklvaegrlevvg 81 
                                   kv++ +H+HiDv+Wl++ +e+  rk++r++ +vl+l+e   ++ F++s+a ++ ++++++   ++++ ++lv++g++ +vg
  gi|13541040|ref|NP_110728.1| 249 KVFAFGHCHIDVAWLWPYSET-LRKIERSFLNVLKLYEMGFNFVFAQSTALYYYEIEKRNVYIFNKI-RRLVNDGKWFIVG 327
                                   79*******************.*********************************************.************* PP

                                   T-SS-B-SSSS-HHHHHHHHHCCCHHHHCCH--EESEEEESSSSSB-TCHHHHHHCTT--EEEESSS-HHCHCCHHHTT-S CS
               Glyco_hydro_38N  82 GgwvenDealpsgeslirqlleGqrflkeefgvrpkvaWliDpFGysatlPqllkkaGidsfltqrlsyndknkfaeqkhl 162
                                   G+wve+D++l+ gesl+rqll+Gq+++ke f+  +++aWl+D+FG+s +lPql+ k+G++ f+t++  +nd+++f   +++
  gi|13541040|ref|NP_110728.1| 328 GMWVESDTNLIRGESLARQLLYGQGYFKEVFNRYSRIAWLPDTFGFSGQLPQLFVKSGMEVFVTHKPMWNDTTEF---PYH 405
                                   ***************************************************************************...*** PP

                                   CEEEE-TTSTEEEEEE--TT.SSHCCCCCC.GGGTTTHHHCHHHHHHCHHHHHTTSSSSEEEEEECEETHCCCCHHHHCCH CS
               Glyco_hydro_38N 163 efiWrgsdgteilthmlpadsydptygfqfdfkrdenvkeraekllaqvkklaektrtnevllplGddfadgqggntekll 243
                                    f W g+dgt i+t +++      +y+ ++          +++++++++k+ ++k+    + +++G++  dg+gg+  +++
  gi|13541040|ref|NP_110728.1| 406 CFKWFGIDGTPIITSIVNL-----SYNENL----------DFDSVVNAYKSNKNKNLP--ITYLYGYG--DGGGGPDIEMM 467
                                   ******************8.....577888..........88*********9999996..55556666..66999999999 PP

                                   HHHHHHHHHCSSEEEEC--H.HHHHHHHHH CS
               Glyco_hydro_38N 244 eeinrsnekeslpkvqfgtp.seYfdalek 272
                                    ++++ ++ +++p+v+ +   +eY+d+ ++
  gi|13541040|ref|NP_110728.1| 468 LKLEQIKDLQFMPNVNGSFSeQEYIDSFKE 497
                                   99999**********998877899999888 PP

>> Glyco_hydro_38C  Glycosyl hydrolases family 38 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.1   0.1   5.2e-37   2.3e-33       1     213 [.     688     885 ..     688     886 .. 0.92

  Alignments for each domain:
  == domain 1  score: 116.1 bits;  conditional E-value: 5.2e-37
                                   XTTSS-EEEE.TTTSSEEEEESTTTS-EEE...EEEEEEEEEEECS-S-SSS--BSTT-EEEE--..S-EEECEE-SS-EE CS
               Glyco_hydro_38C   1 leNgflkveidaknGtlksiydkeakrevlkeqvgnqfaayedapdssdaydfkpdneekplevse.keveviesgplvae 80 
                                   +eN+++k+ i +  G ++ +y+  +kr ++k   gn +++y+d p ++d+++++++n +k l  +e k  + + s  +   
  gi|13541040|ref|NP_110728.1| 688 IENKIIKLII-NSVGIISFFYN--NKRYIKK---GNIVKIYNDIPANFDSWNINAQNIRKDLFMDEiKTEIRVISKNIIGM 762
                                   8*********.9*****88888..7788774...89******************************966667777799*** PP

                                   EEEEETTES...EEEEEEEEECCCCEEEEEEEE-TTECEEEEEEEE---TTCEEEEETTTCEEEEESSTTTT...S..SEG CS
               Glyco_hydro_38C  81 vtvkfkieaestisqeirLykgkkriefevkvdweekevllkvafpidiqaefatdengfgvikRptdqntsweaakfevi 161
                                   v++k  +e+ s+i q+i +++g++ +efe+++ ++++e+l+kv+f+   +a+ ++ e++fg+i  + ++++++++      
  gi|13541040|ref|NP_110728.1| 763 VEIKKIFEDGSSIIQKIIIRPGSSIVEFENTLLLKNREKLVKVVFQPYFHADYIKREIPFGYIMTKLNSKNEKTRP----- 838
                                   ****99999999****************************************************999999433333..... PP

                                   GGG-EEESSEEEEE-SSEEEEEEECS-EEEEE-SSTTEEEEEEEEEBSSS-T CS
               Glyco_hydro_38C 162 agnyypiqsfvdlqdesygvavlndskyGvssleqggqleLsLlRrplypdp 213
                                       +p+ + vd++d+s+g+++l+++++G+s    +g+l +s+ + plyp+p
  gi|13541040|ref|NP_110728.1| 839 ---EFPALRYVDYSDNSHGFSILSRESHGYSF--INGELGISIAKVPLYPNP 885
                                   ...34***************************..67**************97 PP

>> Alpha-mann_mid  Alpha mannosidase middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.2   0.0     1e-21   4.6e-18       1      95 [.     512     604 ..     512     605 .. 0.97

  Alignments for each domain:
  == domain 1  score: 65.2 bits;  conditional E-value: 1e-21
                                   EE--GGGTSSCHHHHHHHHHHHHHHHHHHHCCTTT-SCGC-HHHHHHHHHHHHHHHTCTTTTTT-S-HHHHHHCCHHHHHH CS
                Alpha-mann_mid   1 elhrgtfTSrarlKrlnrkleslLraaellssaaaskgyeypkeeleelwkalllnqfHDilpGtsieeVyedaeerlaea 81 
                                   e hrg++T++ ++K++  ++e++L  ++ ++s  ++++++   ++ ++lw  ll +qfHDilpG+++ + ye+a ++l ++
  gi|13541040|ref|NP_110728.1| 512 ENHRGVYTTNLEIKKYVANIEDKLIMLDFINS--MIYNSKLYISNTKKLWYGLLKAQFHDILPGSAYYYAYEEAFAELDDI 590
                                   68******************************..789******************************************** PP

                                   HHHHHHHCCCCCCC CS
                Alpha-mann_mid  82 lkelekllesalrk 95 
                                   + e++k++e a+rk
  gi|13541040|ref|NP_110728.1| 591 ILEIDKITEFAIRK 604
                                   *********99987 PP

>> Glyco_hydro38C2  Glycosyl hydrolases family 38 C-terminal beta sandwich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.4   0.1     3e-15   1.3e-11       1      68 [.     941    1006 ..     941    1007 .. 0.90

  Alignments for each domain:
  == domain 1  score: 44.4 bits;  conditional E-value: 3e-15
                                    TEEEEEEEE-TTT--EEEEEEESSSSSBEEE-EETT.SCEEEEE-TTSSB-....-TTSEEXTTXEEEE CS
               Glyco_hydro38C2    1 nvhlltlkkaededdlllRlynlseegedatlslsqpvksvnvknllEttlape.eleielkPmEIrTf 68  
                                    n++l+++k aed+ +l++R+yn+s++ ++++l++  p   ++++++lE+++  +   +i +kP+EI+T+
  gi|13541040|ref|NP_110728.1|  941 NIILENIKVAEDNSGLVTRFYNCSDKMSTLELNF--PGGDIYETDILENKQV-KyNKNIIFKPFEIKTL 1006
                                    79**************************996665..658************3.3588***********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1013 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       769  (0.0428914); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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: 6434.41
//
Query:       gi|13541041|ref|NP_110729.1|  [L=118]
Description: transcription regulator [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-19   70.1   0.2    1.4e-19   69.7   0.2    1.1  1  HxlR      HxlR-like helix-turn-helix
     0.0035   17.3   0.1     0.0054   16.7   0.1    1.4  1  HTH_45    Winged helix-turn-helix
     0.0054   16.7   0.1     0.0088   16.0   0.1    1.3  1  PadR      Transcriptional regulator PadR-like family


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 !   69.7   0.2   2.4e-23   1.4e-19       3      88 ..      16     101 ..      14     104 .. 0.95

  Alignments for each domain:
  == domain 1  score: 69.7 bits;  conditional E-value: 2.4e-23
                                   HSTTHHHHHHHHTTS-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSS-EEEEEE-TCGGGGHHHHHHHHHHH CS
                          HxlR   3 ggkWkllilvellkgkkRfselkralpkisqkmLaqrLreLeqdglierevypevPpkveYsltekGrslepvlqelkkwg 83 
                                   g+   ll+++ l +    f+++ +  +k+s k+L+ +L++L ++++i r+v++++P +v+Y+ltekG++l++vl+ l +wg
  gi|13541041|ref|NP_110729.1|  16 GKENDLLVIRLLSDNDLGFNQILKLAGKMSPKTLSVTLKRLTEKKIIYRDVVSTQPFRVKYRLTEKGQELRNVLNDLGQWG 96 
                                   66667899999********************************************************************** PP

                                   HHHHH CS
                          HxlR  84 eeyle 88 
                                   e+++ 
  gi|13541041|ref|NP_110729.1|  97 ERWIL 101
                                   ***85 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.1   9.1e-07    0.0054      31      72 ..      44      92 ..      23      95 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 9.1e-07
                        HTH_45 31 LsykllnkYLdmLvekgli.......kkskekYvlTekGlelleklkel 72
                                  +s k+l+  L+ L+ek++i       +    kY+lTekG+el + l++l
  gi|13541041|ref|NP_110729.1| 44 MSPKTLSVTLKRLTEKKIIyrdvvstQPFRVKYRLTEKGQELRNVLNDL 92
                                  777888889999******9999988555899***********9988875 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1   1.5e-06    0.0088      33      71 ..      48      84 ..      34      87 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.5e-06
                                  HHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCH CS
                          PadR 33 slYpaLkrLekeglveseweesgegpprkyYrlTdaGrr 71
                                  +l  +LkrL +++++ +  +   ++p r  YrlT++G++
  gi|13541041|ref|NP_110729.1| 48 TLSVTLKRLTEKKIIYRDVVS--TQPFRVKYRLTEKGQE 84
                                  55568************9986..69************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       511  (0.0285013); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.29s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 777.65
//
Query:       gi|13541042|ref|NP_110730.1|  [L=177]
Description: hypothetical protein TVN0211 [Thermoplasma volcanium GSS1]
Scores for complete 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-43  146.8   0.6      7e-43  146.7   0.6    1.0  1  YceI      YceI-like domain


Domain annotation for each model (and alignments):
>> YceI  YceI-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  146.7   0.6   3.9e-47     7e-43       1     145 [.       7     172 ..       7     173 .. 0.93

  Alignments for each domain:
  == domain 1  score: 146.7 bits;  conditional E-value: 3.9e-47
                                   EEE-CCC-EEEE........-EEEEECTECCEEEE..TTT..EEEEEEEEGGGEESS.HCHHHHHHCTCTT-TTT--EEEE CS
                          YceI   1 YtldpahssvtftvkhlgvskvtGrfkkvsgelsvdeddp.essvevtidvasidtgnakrdehlksadffdvakyPtatF 80 
                                   +t d+ahss++f v+h++vskv+G+f++++  +  d+dd+ ++++e+t++vasi+tg+a+rd+hl+s+dff v+k+P+++F
  gi|13541042|ref|NP_110730.1|   7 WTPDKAHSSIEFVVRHMMVSKVRGSFNDFDIVFIGDPDDLaQGKAEATVRVASITTGEADRDQHLRSQDFFYVEKFPEIKF 87 
                                   889*************************99986669****99*************************************** PP

                                   CCCCEE.......EEEEEEETTEEEEEEEEEEEEEEE........CCEECEEEEEGGGGTC.........TTTC-SEEEEE CS
                          YceI  81 vstsve.....akvtGdLtikGvtkpvtlpvtvngaa........agfsatgtidrtdFGlkr.......galvgdevele 141
                                    st +      +k++G+Ltik+vtk+v+++ +++g+         +gf+a+++idr dFGl +       g lvg++v++e
  gi|13541042|ref|NP_110730.1|  88 SSTDIMkagdgYKINGKLTIKDVTKDVSFEGELEGKIkdpygkqrFGFTARTVIDRRDFGLMWnmaldngGILVGNTVNVE 168
                                   ****655****99********************9853456666668899***********999999*99999********* PP

                                   EEEE CS
                          YceI 142 iele 145
                                   i+le
  gi|13541042|ref|NP_110730.1| 169 ISLE 172
                                   *998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       274  (0.0152825); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); 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: 1204.24
//
Query:       gi|13541043|ref|NP_110731.1|  [L=304]
Description: Pirin-related protein [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-29  102.5   0.0    1.9e-29  101.8   0.0    1.3  1  Pirin     Pirin
    2.2e-24   85.8   0.0    3.6e-24   85.1   0.0    1.4  1  Pirin_C   Pirin C-terminal cupin domain
  ------ inclusion threshold ------
       0.12   12.5   0.0       0.59   10.2   0.0    1.9  2  DUF1877   Domain of unknown function (DUF1877)


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 !  101.8   0.0   3.1e-33   1.9e-29       2     108 .]      21     132 ..      20     132 .. 0.92

  Alignments for each domain:
  == domain 1  score: 101.8 bits;  conditional E-value: 3.1e-33
                                   EEECCGTCC.TTCCEECTCEECCEEESS.S.ETTEEEET-EEEEEEEBSEEEEEEEECSEEEEEETTS-EEEEETT-EEEE CS
                         Pirin   2 vrvrralgkaaelqsvdpFlfldefdpaelevgeedvigagfpphphrgletvtylleGevehrDslGnkgvirpGdvqwm 82 
                                   v+++r +g+  ++q +dpFl+ld f++++l+    d+ + gfp+hphrg+et+t+ l+G+  h+Ds+G+kg i pG++qwm
  gi|13541043|ref|NP_110731.1|  21 VKLERIFGSPRTVQITDPFLLLDFFGSSKLS----DY-ENGFPWHPHRGIETITLQLRGKTYHEDSEGHKGIILPGELQWM 96 
                                   67889999999******************95....33.39***************************************** PP

                                   E-TT-EEEEEEE-SS..........SS-EEEEEEEE CS
                         Pirin  83 tAgsGivhsEmneee..........eesleglqlWv 108
                                   tAgsGi+h+Em+++           +    g+qlW+
  gi|13541043|ref|NP_110731.1|  97 TAGSGIFHQEMPKPIyygdkvpsikDDANAGIQLWL 132
                                   ************998899999999878888999995 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 !   85.1   0.0     6e-28   3.6e-24       1     104 []     194     296 ..     194     296 .. 0.94

  Alignments for each domain:
  == domain 1  score: 85.1 bits;  conditional E-value: 6e-28
                                   EEEEEE-TT-EEEEE--TT-EEEEEEEES-EEESSTTEEE-TTEEEEE-.SSSEEEEE--SS-EEEEEEEE----S--EEE CS
                       Pirin_C   1 yldltleagaelelplpegleaavyvleGelevggerseieeeqlavlg.dgdslvvkaeekgarvlLlaGePlgepvvqy 80 
                                   yl ++  a+ ++e ++peg++a+++v+ G ++v++++  ++e++ ++l+ +g+ l + a+ +++ v+++aG+Pl+ep+ +y
  gi|13541043|ref|NP_110731.1| 194 YLRIKTIAKGKFETNIPEGHRAIIFVIGGLISVNDKE-LVSEGRAVILStKGKLLSFYAD-QPSDVIIIAGRPLNEPISWY 272
                                   5667777899**************************7.***********88888888888.******************** PP

                                   TTEEESSHHHHHHHHHHHHTT-TT CS
                       Pirin_C  81 GpfVmntkeeieqafedyregrfg 104
                                   Gp+Vmnt+eei+qa+++ ++g+f+
  gi|13541043|ref|NP_110731.1| 273 GPIVMNTREEIAQAIKELNDGTFI 296
                                   **********************95 PP

>> DUF1877  Domain of unknown function (DUF1877)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0       0.2   1.2e+03      79     117 ..     156     194 ..     130     204 .. 0.77
   2 ?   10.2   0.0   9.9e-05      0.59      61     105 ..     250     294 ..     238     299 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.2
                       DUF1877  79 edegygparlltpeqVkevaeaLaeldfeelrerfdaee 117
                                   e+++yg    + +   k+va aL+e  + el+e+ ++  
  gi|13541043|ref|NP_110731.1| 156 EEDDYGNKIGVISGNFKKVAGALNESFQYELAEKINPYY 194
                                   667777777777788899999999999999999988755 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 9.9e-05
                       DUF1877  61 egenplsevvlGgeelgeedegygparlltpeqVkevaeaLaeld 105
                                    +++p + +++ g++l+e+ + ygp+ + t e+++++ + L++ +
  gi|13541043|ref|NP_110731.1| 250 YADQPSDVIIIAGRPLNEPISWYGPIVMNTREEIAQAIKELNDGT 294
                                   567999**********99**********************99755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       365  (0.0203581); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.55
# Mc/sec: 1668.21
//
Query:       gi|13541044|ref|NP_110732.1|  [L=352]
Description: transcription regulator [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      5e-60  202.6   0.0    6.1e-60  202.3   0.0    1.1  1  Regulator_TrmB  Archaeal transcriptional regulator TrmB
    4.5e-22   77.7   0.2    9.1e-22   76.7   0.2    1.5  1  TrmB            Sugar-specific transcriptional regulator TrmB
     0.0079   16.2   0.4      0.013   15.4   0.4    1.2  1  CemA            CemA family
  ------ inclusion threshold ------
       0.02   15.2   0.2      0.042   14.2   0.2    1.5  1  NADH-UOR_E      putative NADH-ubiquinone oxidoreductase chain


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 !  202.3   0.0   1.4e-63   6.1e-60       1     231 [.     112     336 ..     112     338 .. 0.99

  Alignments for each domain:
  == domain 1  score: 202.3 bits;  conditional E-value: 1.4e-63
                                   -EEEESSHHHHHHHHHHHHHH-SSEEEEEE-GGGHHHHHHHHHHHHHTT-EEEEEESS----GGGSSSSEEEEEE-S---S CS
                Regulator_TrmB   1 avwvvksretvierieelIesAenelivslpselLeelreeliaaaergvtVllliypdedleeldleevatevrvrrsga 81 
                                   ++w++k++ ++ e+++++I++ ++e+i sl++e+L++l++++i+a+++g tV+l+++pd+++++l+++    ++++r + a
  gi|13541044|ref|NP_110732.1| 112 YLWMIKNNFQIREKMKDVITNSKYEIITSLNYENLRYLKRYFIDAVKKGLTVVLVVFPDAESDFLKTLPDDIVIKKRPGSA 192
                                   58******************************************************************************* PP

                                   .EEEEETTTEEEEE-SSS-EEEE--HHHHHHHHHHHHHH........HHH-EEEEEEES-TT-EEES-HHHHHHHHHHHT. CS
                Regulator_TrmB  82 pllvivDrkrgvvaprevlrdkeeeyaiifkekelihvlshyFlttlWktseviktdepvekpitfssirlavedikkllr 162
                                   ++++i+Dr+ g++++++  ++++e ya++f+e+elih+l++yF++t+W +se+ + d+p++ +++f++ +l++e+i+++l+
  gi|13541044|ref|NP_110732.1| 193 SQVIISDRNDGIINVES--KEDSEGYALYFNESELIHILNYYFYHTIWGPSEIYH-DFPEKPDLKFTTAWLSCEAINSFLK 270
                                   ****************9..*********************************999.************************* PP

                                   TTS-EEEEEEEEETTT--EEEEEEEEEEEEEETTTT.EEEEEEEETTEEEEEE-TT--SSSEEEEEEEEE CS
                Regulator_TrmB 163 aglkveaeveGrdtetgeevtieGrvveatlnstpg.vaslvvetedgevtVGGlgAvlEDieaeeitle 231
                                   + +++++++eG+    +++v+i G++++  ++  pg +++++++ +d+ ++VGG++A++EDi+ + ++++
  gi|13541044|ref|NP_110732.1| 271 RSYSITGSLEGIG--FNGPVKINGTITG--TDLVPGfKQTFFIKDGDRIYSVGGKTARMEDIKLTNLVIN 336
                                   ************9..9************..**********************************999885 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.7   0.2     2e-25   9.1e-22       1      67 [.      12      78 ..      12      79 .. 0.98

  Alignments for each domain:
  == domain 1  score: 76.7 bits;  conditional E-value: 2e-25
                                  HHHCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEEE--H CS
                          TrmB  1 LqklGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpklYravdp 67
                                  L+klGL+ yE+k+Y++Ll +gp++a+e a+ + vp+++vY++ +sLe+kG Ve+++g++k+Yrav++
  gi|13541044|ref|NP_110732.1| 12 LSKLGLTPYEIKIYKTLLIYGPKSATETAKLSRVPQPRVYDIFESLESKGAVEVSPGKKKIYRAVPV 78
                                  89***************************************************************97 PP

>> CemA  CemA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.4     3e-06     0.013      33     142 ..      76     184 ..      66     188 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 3e-06
                          CemA  33 plvdrflekeqaelflnkeleeealeelkefeekleleeligeapelseeeieeelkekaeelakeyreesseaiknifad 113
                                     vd+f++++  e++  k+  ++++e+ k+f+e+     +i+++ ++ +e++++ ++++  e+ ++ ++e+ + +k  f d
  gi|13541044|ref|NP_110732.1|  76 VPVDNFIDRKLIEIKDYKQRIQSYIEKQKKFKETAPYLWMIKNNFQI-REKMKDVITNSKYEIITSLNYENLRYLKRYFID 155
                                   4589999999999999999999**********************987.7899***************************** PP

                          CemA 114 lvsliafvvllllskeeleilksfldevl 142
                                    v     vvl+++   e   lk+  d+++
  gi|13541044|ref|NP_110732.1| 156 AVKKGLTVVLVVFPDAESDFLKTLPDDIV 184
                                   **********************9999987 PP

>> NADH-UOR_E  putative NADH-ubiquinone oxidoreductase chain E
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.2   9.5e-06     0.042      12      65 ..      91     145 ..      83     148 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 9.5e-06
                                   TTHHHHHHHHHTTS-TT-EEEEEE-S.S--SHHHHHHHTT-TTT-EE-S---TTS CS
                    NADH-UOR_E  12 nllerlkelldkevkegevaiflfev.gdFsavqksadlikergdeLlnsLkFne 65 
                                   +  +r++  ++k+ k +e+a +l+ + ++F++ +k  d+i++  +e++ sL + +
  gi|13541044|ref|NP_110732.1|  91 DYKQRIQSYIEKQKKFKETAPYLWMIkNNFQIREKMKDVITNSKYEIITSLNYEN 145
                                   5789**********************5689999******************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (352 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       699  (0.0389871); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.61u 0.27s 00:00:00.88 Elapsed: 00:00:00.50
# Mc/sec: 2126.64
//
Query:       gi|13541045|ref|NP_110733.1|  [L=121]
Description: hypothetical protein TVN0214 [Thermoplasma volcanium GSS1]
Scores for complete 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   0.4    8.2e-15   54.3   0.4    1.2  1  Cupin_2          Cupin domain
    1.6e-09   37.8   0.0    1.8e-09   37.6   0.0    1.1  1  AraC_binding     AraC-like ligand binding domain
    1.8e-07   31.2   0.2      2e-07   31.0   0.2    1.1  1  MannoseP_isomer  Mannose-6-phosphate isomerase
    1.9e-06   27.7   0.1    2.4e-06   27.4   0.1    1.1  1  Cupin_7          ChrR Cupin-like domain
    0.00014   21.5   0.4    0.00021   21.0   0.4    1.1  1  DMSP_lyase       Dimethlysulfonioproprionate lyase
     0.0014   18.9   0.2     0.0016   18.6   0.2    1.1  1  Ectoine_synth    Ectoine synthase
     0.0015   17.9   0.0     0.0017   17.7   0.0    1.1  1  KduI             KduI/IolB family
     0.0036   17.0   0.0     0.0054   16.4   0.0    1.3  1  Cupin_3          Protein of unknown function (DUF861)
     0.0056   15.8   0.1     0.0061   15.7   0.1    1.1  1  DUF4437          Domain of unknown function (DUF4437)
  ------ inclusion threshold ------
      0.015   15.5   0.0      0.022   14.9   0.0    1.3  1  CENP-C_C         Mif2/CENP-C like
       0.02   14.6   0.2      0.029   14.0   0.2    1.4  1  Auxin_BP         Auxin binding protein
      0.047   13.5   0.0      0.056   13.2   0.0    1.1  1  EutQ             Ethanolamine utilisation protein EutQ
      0.093   12.0   0.2       0.11   11.8   0.2    1.2  1  Lyx_isomer       D-lyxose isomerase


Domain annotation for each model (and alignments):
>> Cupin_2  Cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.3   0.4     6e-18   8.2e-15       2      70 ..      44     109 ..      43     111 .. 0.90

  Alignments for each domain:
  == domain 1  score: 54.3 bits;  conditional E-value: 6e-18
                                   EEEEETTEEEEEECSSSEEEEEEEEESEEEEEECTEEEEEETTEEEEE-TT-EEEEEE-SSS-EEEEEE CS
                       Cupin_2   2 lvelppGesapshrHpgedeffyVleGegeltvdgeeveleaGdsvyfpagtpHrfrNtgdeparllvv 70 
                                   l+++++G s+p h+H++e + +++++G+++++++++e+  +++d++++p++++H++  ++d+ + +  +
  gi|13541045|ref|NP_110733.1|  44 LITVQKGKSTPHHHHDYE-HEIFIISGKVKVKLGEQEYMAGQDDFIFIPPNVEHGMNAEEDTRMIC--I 109
                                   689***************.*************************************8888655554..3 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 !   37.6   0.0   1.3e-12   1.8e-09      13      66 ..      50     103 ..      39     118 .. 0.88

  Alignments for each domain:
  == domain 1  score: 37.6 bits;  conditional E-value: 1.3e-12
                                   T-SEEEETT-SEEEEEEEEE-EEEEETTEEEEE-TT-EEEE-TTS-EEEEE-TT CS
                  AraC_binding  13 dhsfpphvhdeyvihyvteGtgrlrlngrtydlgpGdlfLlppgepHdyesdse 66 
                                   + s+p h+hd+ + + +++G+++++l++++y +g++d +++pp++ H + ++++
  gi|13541045|ref|NP_110733.1|  50 GKSTPHHHHDYEHEIFIISGKVKVKLGEQEYMAGQDDFIFIPPNVEHGMNAEED 103
                                   678999****9999999*********************************9985 PP

>> MannoseP_isomer  Mannose-6-phosphate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   0.2   1.5e-10     2e-07      60     136 ..      37     113 ..      29     121 .] 0.82

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 1.5e-10
               MannoseP_isomer  60 geryqvkritvkPgeklslqkhhhraehWv.vvkGtakvtvddevlllkenestyiplgaihrlenpGki.plelievq 136
                                   +++y ++ itv+ g+  s  +hhh  eh + +++G  kv+ ++++++  +++ ++ip ++ h ++    + ++ ++ ++
  gi|13541045|ref|NP_110733.1|  37 AKNYSMRLITVQKGK--STPHHHHDYEHEIfIISGKVKVKLGEQEYMAGQDDFIFIPPNVEHGMNAEEDTrMICIVPIK 113
                                   689********9998..6789999****88478*****************************99876554144455555 PP

>> Cupin_7  ChrR Cupin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.1   1.8e-09   2.4e-06      14      85 ..      31     105 ..      20     114 .. 0.80

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 1.8e-09
                                   EEEEESSSS-EEEEEEEE-TTEE---EE-TT-EEEEEEEEEEEET..TEEEETT..EEEEE-TT-EE--EESS-EE CS
                       Cupin_7  14 pLerdgeekaratslvryapgsafsahkHpggeeilVLeGvfsde..egdypaG..sylrnppgsshapvseeGct 85 
                                   + + +++ k+++ +l+ +++g++ ++h+H+   ei++++G+ + +  e++y aG  ++++ pp+ +h   +ee++ 
  gi|13541045|ref|NP_110733.1|  31 ITH-KNGAKNYSMRLITVQKGKSTPHHHHDYEHEIFIISGKVKVKlgEQEYMAGqdDFIFIPPNVEHGMNAEEDTR 105
                                   344.45566999****************************99876226689888446***********99999854 PP

>> DMSP_lyase  Dimethlysulfonioproprionate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.4   1.5e-07   0.00021     109     159 ..      54     103 ..      52     107 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.5e-07
                    DMSP_lyase 109 PdHhhaaeelYlvlsggaefrqgeaewlsrgiGevifnepgikhamrsaee 159
                                   P Hhh +e    ++sg + ++ ge+e++  g+++ if +p+++h m ++e+
  gi|13541045|ref|NP_110733.1|  54 PHHHHDYEHEIFIISGKVKVKLGEQEYM-AGQDDFIFIPPNVEHGMNAEED 103
                                   99****966666678888********87.5899*************99965 PP

>> Ectoine_synth  Ectoine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.2   1.2e-06    0.0016      27     106 ..      31     109 ..       7     115 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.2e-06
                                   E-GGGS.SSSEEEEEEE-TT--EEEE-TT-EEEEEEEE--EEEEETTT--EEEE-TTEEEEETTT-EEEEEESS-EEEEEE CS
                 Ectoine_synth  27 llkddg.mGfslhettikagtetelkYknHleavycieGegeveeledgevyeikpgtlYlldkhdkHllrakkelrlvcv 106
                                   + +++g   +s+   t+++g++t  + +++   +++i+G+ +v+     ++y   + ++  +  + +H ++a+++ r++c+
  gi|13541045|ref|NP_110733.1|  31 ITHKNGaKNYSMRLITVQKGKSTPHHHHDYEHEIFIISGKVKVKLG--EQEYMAGQDDFIFIPPNVEHGMNAEEDTRMICI 109
                                   4444441479*************9999999999******9999875..5788888888888889999*************8 PP

>> KduI  KduI/IolB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   1.3e-06    0.0017      18     102 ..      31     106 ..      15     116 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.3e-06
                                   TCCCCCCCCBECCCEEEECHHCHHCHGCSEEEEEEEECCEEEECCTT.EEEEE-TTSSGGGS..EEEEE-TT--EEEEESS CS
                          KduI  18 tpesagweyvgfsvlkLaagesleletedrEvcvvllaGkvtvevageefeelgeRksvFegkpdavYvpkgakvtitaet 98 
                                     ++ g +  +++++++++g+s  ++ +d+E  + +++Gkv+v+ + e+ +  g+         d++++p++ +  + ae+
  gi|13541045|ref|NP_110733.1|  31 ITHKNGAKNYSMRLITVQKGKSTPHHHHDYEHEIFIISGKVKVKLG-EQEYMAGQD--------DFIFIPPNVEHGMNAEE 102
                                   344556788899*********************************4.466666655........88888888888888877 PP

                                   TEEE CS
                          KduI  99 daev 102
                                   d ++
  gi|13541045|ref|NP_110733.1| 103 DTRM 106
                                   7665 PP

>> Cupin_3  Protein of unknown function (DUF861)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   3.9e-06    0.0054      12      61 ..      47      95 ..      36     108 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3.9e-06
                                  EEEECEEEEECESSEEEEEEEECEEEEEETTTEEEEEETTEEEEE-TTEE CS
                       Cupin_3 12 wectpGkfrltyeedEfcyileGevkvtpeggetvelraGDlvvlpkgls 61
                                  ++  +++ + + +++  ++i++G+vkv+  g++++  ++ D++++p++ +
  gi|13541045|ref|NP_110733.1| 47 VQKGKSTPHHHHDYEHEIFIISGKVKVKL-GEQEYMAGQDDFIFIPPNVE 95
                                  4444555555566666679**********.9999************9875 PP

>> DUF4437  Domain of unknown function (DUF4437)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1   4.4e-06    0.0061      27     103 ..      30     107 ..       4     118 .. 0.62

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 4.4e-06
                                   EEEE-.TT.S-EEEEEEE-TT-EE--BEESS-EEEEEEESEEEETTEE.....E-TTEEEEE-TT.-EEEETTS-EE.E CS
                       DUF4437  27 Lwgdrted.gasgflvkfkkgFespphihnvdyrgvVikGalhnddekaekmWlpkgsywtqPaG.evhitaaeetenl 103
                                   L + +++  + s  l++++kg + p h h+ + ++++i+G+++    + ++   ++  + ++P   e  + a+e+t+ +
  gi|13541045|ref|NP_110733.1|  30 LITHKNGAkNYSMRLITVQKGKSTPHHHHDYEHEIFIISGKVKVKLGE-QEYMAGQDDFIFIPPNvEHGMNAEEDTRMI 107
                                   444444330345556777778888888888888888888887665444.334456778888887734444444444444 PP

>> CENP-C_C  Mif2/CENP-C like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   1.6e-05     0.022      26      71 ..      53      98 ..      41     107 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.6e-05
                                  EEEE--SEEEEEEEEESEEEEEETTEEEEEETT-EEEE-TT-EEEE CS
                      CENP-C_C 26 kkknskkatlvFyViqGrvevtvsktsfvigkgsvFqvPagneysi 71
                                  ++++ ++     ++i G+v+v++ ++++++g+ +   +P   e  +
  gi|13541045|ref|NP_110733.1| 53 TPHHHHDYEHEIFIISGKVKVKLGEQEYMAGQDDFIFIPPNVEHGM 98
                                  4556666777899*********************999997666555 PP

>> Auxin_BP  Auxin binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.2   2.1e-05     0.029      38      83 ..      34      79 ..      20     121 .] 0.78

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.1e-05
                                  HH--SSEEEEEEEE-TT-B--EEEESS-EEEEEEE--EEEEE--SS CS
                      Auxin_BP 38 lhgmkevevwlqtlapgsrtpihrhsceevfvvlkgkgtlylasss 83
                                  + g k+  + l t+  g+ tp h h  e  + ++ gk  + l++ +
  gi|13541045|ref|NP_110733.1| 34 KNGAKNYSMRLITVQKGKSTPHHHHDYEHEIFIISGKVKVKLGEQE 79
                                  46899999*******************9888889999999998754 PP

>> EutQ  Ethanolamine utilisation protein EutQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0     4e-05     0.056      80     143 ..      45     108 ..       4     113 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4e-05
                          EutQ  80 GlmemkettfdwtlnydeidyvieGrldvlidGrkvvaeaGdviliPkgskiefsvtdeakfly 143
                                     ++  ++t     +y+   ++i G+++v    ++ +a+  d i+iP + +  +   ++++++ 
  gi|13541045|ref|NP_110733.1|  45 ITVQKGKSTPHHHHDYEHEIFIISGKVKVKLGEQEYMAGQDDFIFIPPNVEHGMNAEEDTRMIC 108
                                   33444556677788999888***************************99888888888777775 PP

>> Lyx_isomer  D-lyxose isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.2   7.7e-05      0.11      80     113 ..      34      67 ..      28     104 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 7.7e-05
                    Lyx_isomer  80 kkkkklYaekllivkegqvtpmHfHwskaeDiin 113
                                   k+  k Y+ +l++v++g+ tp H H +  e  i 
  gi|13541045|ref|NP_110733.1|  34 KNGAKNYSMRLITVQKGKSTPHHHHDYEHEIFII 67 
                                   55789********************999996664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       398  (0.0221987); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 736.04
//
Query:       gi|13541046|ref|NP_110734.1|  [L=201]
Description: hypothetical protein TVN0215 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      1e-37  129.4   0.0    1.3e-37  129.1   0.0    1.1  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 !  129.1   0.0   7.2e-42   1.3e-37       5     172 .]      26     169 ..      22     169 .. 0.97

  Alignments for each domain:
  == domain 1  score: 129.1 bits;  conditional E-value: 7.2e-42
                                   --.GCCC-EEEEESTCSSEEEEEHHHHHHC-EEEEEEEEE-TTTTHHHHCHH--SS----TTSEEEEEEEEEEHHHHHHHT CS
                Oxidored_molyb   5 pkvdpekwrlevdglvekplslslddLkalpavevtatlqCagnrrkelnkkkvkglqwgagavsnaeWtGvrlrdvLeka 85 
                                   p++d+ kw+l v+glv+k + +s++dL+++++ e++++++C++              +w   ++ ++ W+G++l++++e+ 
  gi|13541046|ref|NP_110734.1|  26 PDIDIRKWKLCVNGLVDKVKCYSFSDLQSMRQLEYISDFNCVT--------------RW---SIKDIVWKGPSLKEIIENS 89 
                                   678999*************************************..............7*...9****************** PP

                                   TB-ETT..EEEEEEEEE-TCCTEEEEEEEHHHHCTTT-EEEEEETTEE--CCCTTT-EEE-TTB-GGGSBTTEEEEEEESS CS
                Oxidored_molyb  86 gvkkpearhvvfegadeeleeskygasiplekaleddvlLAyemngepLppdhGyPlRlvvpglvgarsvKwlkrievsde 166
                                   g+k +ear+v+f +ad      +y++ +p+e+a+++++++A+ mng pL++++GyP R + p+l+g++s+Kw+++ie+ +e
  gi|13541046|ref|NP_110734.1|  90 GPK-REARWVMFWSAD------GYSTPVPIEYAMDEKAIIAISMNGAPLKKENGYPARPFLPQLYGWKSAKWITEIELIPE 163
                                   **7.9**********9......5***********889******************************************** PP

                                   ---SHH CS
                Oxidored_molyb 167 esegyw 172
                                    ++gyw
  gi|13541046|ref|NP_110734.1| 164 YKDGYW 169
                                   *****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 1262.88
//
Query:       gi|13541047|ref|NP_110735.1|  [L=409]
Description: major facilitator superfamily permease [Thermoplasma volcanium GSS1]
Scores for 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-06   27.0  47.7    0.00015   20.8  21.7    2.2  2  MFS_1     Major Facilitator Superfamily
  ------ inclusion threshold ------
        1.2    9.5   6.6        1.5    9.1   0.7    2.9  3  DUF2149   Uncharacterized conserved protein (DUF2149)


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 !   17.2  42.3   2.1e-07    0.0019      19     311 ..      39     338 ..      28     349 .. 0.68
   2 !   20.8  21.7   1.7e-08   0.00015       2     166 ..     235     402 ..     231     408 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.1e-07
                         MFS_1  19 lplalaed.........lgispseigllltlyalgaavaslplGrlsdrfGrrr.vlllglllfalg.lllllfa....ss 84 
                                   ++  l+++         +g +++ +g+++++  l+  +++l + ++  ++   + v +++ +l  l  ll+++++    + 
  gi|13541047|ref|NP_110735.1|  39 YS-SLTQQyviplaiflFG-TVAPVGFITGIPLLAVPFSQLSAYWILKKIDNLKvVTIITTFLDRLPwLLIAILIlfrpAY 117
                                   44.4444433333333367.88889*********999999999999999*9888777777776555533333332345577 PP

                         MFS_1  85 lw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWrav..fyilaivsl 162
                                   +  ++++l ++ +++a+++ ++   ++  + ++e+r r++++ ++++ ++ ++g+ ++ l+   + +++   f i+++ +l
  gi|13541047|ref|NP_110735.1| 118 FLyIFIALLIIRAFFASLSGTTWTLWVPGLISEEKRDRYFSVRNMAMRASGLIGYFIAMLVFIFIKFHGFdyFTIFTVSFL 198
                                   8889*****************************************************997777777777763344444333 PP

                         MFS_1 163 lafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsg..lltllplylqevlgls 241
                                   ++    ++ +   p ++ ++ +++              k+  +++ ++ill+++ +f++g+++   ++ll+++ ++ l+ s
  gi|13541047|ref|NP_110735.1| 199 FSSA-SIAIMKKIPEAKTNDVKITS-------------KKTYTSQKFFILLFTVSIFALGYNFsqPYILLFILGKDYLNSS 265
                                   3322.23444444444444444444.............3444444444455555555556666446666666677777777 PP

                         MFS_1 242 glllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavtssavllllvlvl....iG 311
                                     ++ ++ll +++lv+++++ l+  l+ r+g  + ll++ ++l++++++++++ ++ +a++l  ++ +    ++
  gi|13541047|ref|NP_110735.1| 266 -SIIYTFLLIAGSLVFIASQKLGYNLISRYGYGKSLLISSIILSMTVFAWIFVRNIIEAMILFSLSSIpvsvYS 338
                                   .56777777777777777799999999*****************************444443332222222233 PP

  == domain 2  score: 20.8 bits;  conditional E-value: 1.7e-08
                         MFS_1   2 llaaflsalarsilgpalpl.alaed.lgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll 80 
                                   l+++ + al++++  p + l +l++d l++s   + +ll + +l++++++ ++  l+ r+G  + ll++ ++++ + ++++
  gi|13541047|ref|NP_110735.1| 235 LFTVSIFALGYNFSQPYILLfILGKDyLNSSSIIYTFLLIAGSLVFIASQKLGYNLISRYGYGKSLLISSIILSMT-VFAW 314
                                   5666777777777777777766666637778888888***************************999999999999.5555 PP

                         MFS_1  81 .fasslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslg.Wravfyilai 159
                                    f+ ++   ++l  l+++  +++  +g  +++  + +e r + ++l+++++s+++++gp+++ l++  +     +f+i  +
  gi|13541047|ref|NP_110735.1| 315 iFVRNIIEAMILFSLSSIPVSVYSLSGFNFVVSGSGGEGRVKRTSLYTLFNSISTAVGPIIANLVYVKVEnILDIFLISSA 395
                                   4778888999999*****************************************************443336666888888 PP

                         MFS_1 160 vsllafv 166
                                   ++++a+v
  gi|13541047|ref|NP_110735.1| 396 ILMVAAV 402
                                   8887766 PP

>> DUF2149  Uncharacterized conserved protein (DUF2149)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0     0.019   1.7e+02       8      45 ..     187     225 ..     186     233 .. 0.83
   2 ?   -2.5   0.1      0.72   6.4e+03       4      17 ..     317     330 ..     316     345 .. 0.78
   3 ?    9.1   0.7   0.00017       1.5       4      28 ..     383     406 ..     381     409 .] 0.90

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.019
                       DUF2149   8 fDvalVlavallvalvsslnlqellss.eedvtvvkkpg 45 
                                   fD + ++ v +l + +s   ++++ ++ ++dv+++ k++
  gi|13541047|ref|NP_110735.1| 187 FDYFTIFTVSFLFSSASIAIMKKIPEAkTNDVKITSKKT 225
                                   89999********99999999999988777888887766 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.72
                       DUF2149   4 vaNLfDvalVlava 17 
                                   v N++++++ +++ 
  gi|13541047|ref|NP_110735.1| 317 VRNIIEAMILFSLS 330
                                   67999999999886 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.00017
                       DUF2149   4 vaNLfDvalVlavallvalvsslnl 28 
                                   v N++D++l+ ++ l+va+vss+ l
  gi|13541047|ref|NP_110735.1| 383 VENILDIFLISSAILMVAAVSSW-L 406
                                   78********************9.4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (409 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1004  (0.0559987); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.49
# Mc/sec: 2515.37
//
Query:       gi|13541048|ref|NP_110736.1|  [L=616]
Description: glycosidase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.2e-59  201.2   5.3    1.2e-58  199.2   5.3    1.9  1  Alpha-amylase  Alpha amylase, catalytic domain
  ------ inclusion threshold ------
      0.018   14.2   0.5      0.039   13.1   0.0    1.8  2  hDGE_amylase   Glycogen debranching enzyme, glucanotransferas


Domain annotation for each model (and alignments):
>> Alpha-amylase  Alpha amylase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  199.2   5.3   1.4e-62   1.2e-58       1     337 []     222     521 ..     222     521 .. 0.85

  Alignments for each domain:
  == domain 1  score: 199.2 bits;  conditional E-value: 1.4e-62
                                   --CHHHHCTCCCCCCCT-SCEEE-B-CE-S-TTTTSS-SCECCE-CCC--CCCCCCHHHHHHCTT-EEEEEE--SC--TTS CS
                 Alpha-amylase   1 GDLkGiiekLdYlkeLGvtaiwlsPifkspqadhgYdiadytkidpefGtnedlkeLiskahekgikvilDlVvNHtsdeh 81 
                                   G L+Gi+ek+ Y+k L v+ i+l+P++ks  ++h Yd+ dy +id   G  +d+ eL+++ahe+gik++ D+V+NHts+++
  gi|13541048|ref|NP_110736.1| 222 GNLRGITEKIGYIKALNVDTIYLNPVYKSK-SNHRYDVDDYFSIDGLLGGEQDFIELVNEAHENGIKIVADMVFNHTSTDF 301
                                   89***************************9.************************************************** PP

                                   CCCHCCHHSTTSGGGCCC-E......ESS-STTC-TTTTCSCEECTTTTCEEESSS-TTS-BB-TTTCCCCCCCCCCCCCC CS
                 Alpha-amylase  82 ewfkeslkkkgepkrdyyiwkegkeekeppnnwkslfdgsaweydekaqeyylhlflkklpdLnteneevrkelkdvvkfw 162
                                    +f ++lk+ +  +++y++w       +   +   +fdg a   ++    y +++++ ++p+Ln++n evrk   dv+k++
  gi|13541048|ref|NP_110736.1| 302 PYFLDALKNGK--NSKYWNWY------IFHGEGAAVFDGRAKGKTKPL--YETFMGVGRMPKLNHKNAEVRKFCIDVMKYY 372
                                   ********666..55555553......333333344555554433333..446779************************* PP

                                   CTTT.-SEEEETTCCCTTTCCCCHCCHCCHHHHHHHHHHHTCCGTT-EEEEE-TT-SCCCHCCCC-CGG-SICECCITTCG CS
                 Alpha-amylase 163 lekg.idGfRlDvvkhvskvealesngeflheftqalnetvasrkevmtvgEvssdasedlrvyttearlelemvldfphl 242
                                    +k+ +dGfR Dv++ +             + f +a++e+    +e+  +gE +   s    + +  ++      ++f+ +
  gi|13541048|ref|NP_110736.1| 373 KNKFgVDGFRYDVAHSIYP-----------EFFLEAVKEFG---NEMLHIGEAWCLPS----MFMLSGYW-----NSFTNY 430
                                   ***99*************9...........55778888775...88899999998444....23333333.....355555 PP

                                   GGCC-CTSTTSB-SS-HHHHHHHHHHHHHHS-C.CCTTCEEES--TTS--HHHHTTSSTTTTHHHHHHHHHCCCTSSSEEE CS
                 Alpha-amylase 243 dvaqkakikeqlksisakklkellkkwlkalee.aaeeavtflgnHDqeRilsrlgddsaeaekklklaaillltlrGvpv 322
                                   ++++++  k   ++i++ +++++++++  ++    +++ +++l++HD+eRil  ++ ++    kk+kla  +l++++G + 
  gi|13541048|ref|NP_110736.1| 431 YLRNAII-KFVREEINITEFYNMIQNMIISYGPlIQQNVMNILDSHDTERILRAFKGNK----KKVKLAYSILFMFDGFAT 506
                                   5555554.7778999**********998888776999**********************....7***************** PP

                                   EETTCCCT----STT CS
                 Alpha-amylase 323 iYyGeEigmtggkdp 337
                                   iYyG+E+g+ gg+dp
  gi|13541048|ref|NP_110736.1| 507 IYYGDEVGLDGGRDP 521
                                   ***********9987 PP

>> hDGE_amylase  Glycogen debranching enzyme, glucanotransferase 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     0.039      19     112 ..     222     306 ..     214     321 .. 0.83
   2 ?   -3.6   0.1      0.48   4.3e+03     374     400 ..     507     534 ..     506     539 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.3e-06
                                   -SHHHHHHHHHHHHHTT--EEEES--EEE-TT--TTSEEEEEEE-TTT-.....SSC.HHHHHHHHHHHHHH--EEEEEE- CS
                  hDGE_amylase  19 GpleeWekvlkeikekgYnmiHftPlqelGesnSpYSiadqleldkelfeekdkeekeedveklvkklekeygllsltDvV 99 
                                   G+l+  ++++  ik  + ++i + P+ +  +sn  Y + d  ++d  l        +e+d+ +lv++++ e+g+  + D+V
  gi|13541048|ref|NP_110736.1| 222 GNLRGITEKIGYIKALNVDTIYLNPVYKS-KSNHRYDVDDYFSIDGLL-------GGEQDFIELVNEAH-ENGIKIVADMV 293
                                   47777888889999999999999999875.799999999999999877.......467899****9987.579******** PP

                                   -SEEETT-CCCCC CS
                  hDGE_amylase 100 lnHtannskwlee 112
                                   +nHt+++ ++  +
  gi|13541048|ref|NP_110736.1| 294 FNHTSTDFPYFLD 306
                                   *****99888765 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 0.48
                                   EEECCEEEB---SSGGGSH.HHHHHHHH CS
                  hDGE_amylase 374 ivWgDcvKLrYGkkpedsp.fLWehmte 400
                                   i +gD v L  G+ p+d   f W+ m e
  gi|13541048|ref|NP_110736.1| 507 IYYGDEVGLDGGRDPDDRRcFPWDNMDE 534
                                   7789*************86367999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (616 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       600  (0.0334653); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.70u 0.35s 00:00:01.04 Elapsed: 00:00:00.53
# Mc/sec: 3490.57
//
Query:       gi|13541049|ref|NP_110737.1|  [L=533]
Description: amino acid transporter [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.4e-38  131.6  58.2    3.4e-38  131.6  58.2    1.4  1  AA_permease_2  Amino acid permease
    9.8e-27   93.7  59.4    1.4e-26   93.1  59.1    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 !  131.6  58.2   3.8e-42   3.4e-38       1     403 [.      31     436 ..      31     479 .. 0.86

  Alignments for each domain:
  == domain 1  score: 131.6 bits;  conditional E-value: 3.8e-42
                 AA_permease_2   1 lsllsafalvigsvigsgifvkn..laasggpalilwvwiavligslavllvyaElssalprsgGiyvytkaafgkkvafl 79 
                                   l+ll++f++ i+ vigsg ++++  +a+++gpa+i +++++  ++ l+v+lv+ +l   ++  gGi  y +++ g +++ +
  gi|13541049|ref|NP_110737.1|  31 LGLLDLFMIGITGVIGSGWLFSPlyAANAAGPASIASWVLGGALV-LMVGLVFSQLMRFKSEAGGITRYPYYTNGALAGTI 110
                                   799********************988888****999999988888.8*********99899******************** PP

                 AA_permease_2  80 sawfnwfayvpvlasilsvaasyllnalgpdlqgn...twltyliaiaililvalinirgikesakiqnilgilkillpli 157
                                   ++w++w+ay+   +s +s +++y+ + + p l+ n   t   + iai ++ l++l+n++g+ + +ki n ++ lk+++p i
  gi|13541049|ref|NP_110737.1| 111 TGWTLWLAYSMNPPSESSGLVQYMSSYV-PGLYINgalTPVGLAIAISFMGLFVLVNYFGVVIFSKIINAITALKLVVPTI 190
                                   ***********99999999*****9877.533333223457899************************************* PP

                 AA_permease_2 158 iliilglitvdgggfsslstetdtffpngwpgvllglli..vlwsfdGfesaanvsee..vkkkdvpkaifigllivlvly 234
                                   +++ l l+ ++ + fs        + p g  +v++++ +  +++s+ Gf +++n + e  ++k+d p+ +++++++++v+y
  gi|13541049|ref|NP_110737.1| 191 TMVTLFLVSFKLRNFS-----AYGVAPYGPFSVVSAIVTsgIVYSYLGFQAVINLAGEsrNPKRDGPLSLILVIIFSVVFY 266
                                   ***9999999999998.....433444444446666644459****************666679***************** PP

                 AA_permease_2 235 llvniaflgvvpddeianlsnlgsvaalffeavggk...vvaiivvilialsllgaintavigssrvlealardgvlPrff 312
                                   ++++iaf+g vp + i++   ++s+ ++f++ + +    ++ +++++  + s  g+ ++av+++sr l+al++ g+lP+ff
  gi|13541049|ref|NP_110737.1| 267 VVLQIAFIGSVPASDISKGWAFLSLPSPFADIAVSFnmfWLYTLIIADSIYSPSGSSMAAVASNSRNLYALSKNGTLPSFF 347
                                   ****************8866666666666666653223599999************************************* PP

                 AA_permease_2 313 akvn.kfgspiraiiltaivslillllfllassaaynfllsvsslgliisyllliigalilrkkrphlkr.pgkilvaiig 391
                                    +v+  +g+p ra+ +++++sli+l ++ l   +  +++ +++ l+li++++ ++ +++i  +kr    + p +++v++i 
  gi|13541049|ref|NP_110737.1| 348 LRVDnNTGIPRRALLFNFVISLIVL-VT-L--KSWHQIIETLGILLLISFIGSAVSSGVIGSIKRYSSIKmPFIVIVSAIV 424
                                   ***99****************6653.34.4..4678999999999999999999999999999999886635556777777 PP

                 AA_permease_2 392 alfllfllvalf 403
                                   ++f+ +++ +  
  gi|13541049|ref|NP_110737.1| 425 FVFSGLIISISS 436
                                   777776665544 PP

>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.1  59.1   1.6e-30   1.4e-26       2     436 ..      36     442 ..      35     490 .. 0.82

  Alignments for each domain:
  == domain 1  score: 93.1 bits;  conditional E-value: 1.6e-30
                   AA_permease   2 vlvialggviGtglfvglgvvlsqaGplgallayllagvviflvmlslgeiatngpksggfytyasrflgpelGfviGlny 82 
                                   +++i + gviG g +++  +++++aGp+  + +++l+g+ +++v+l ++++  +++++gg++ y   + g  +G  +G+ +
  gi|13541049|ref|NP_110737.1|  36 LFMIGITGVIGSGWLFSPLYAANAAGPA-SIASWVLGGALVLMVGLVFSQLMRFKSEAGGITRYPYYTNGALAGTITGWTL 115
                                   78*************************5.56*************************************************8 PP

                   AA_permease  83 lfswitvlaleltaasiliqfwel.vtdlpkawvt........gavflvvlliinlvgvkvygea.efilalikiiaiiaf 153
                                   ++ + ++ + e   +s l+q++++ v+ l  + +         ++ f+++++++n++gv  + ++   i+al +++  i +
  gi|13541049|ref|NP_110737.1| 116 WLAYSMNPPSE---SSGLVQYMSSyVPGLY-INGAltpvglaiAISFMGLFVLVNYFGVVIFSKIiNAITALKLVVPTITM 192
                                   88888888888...7777777733144444.444489*****8777*****************952444444455555555 PP

                   AA_permease 154 iivgiillaggkpnkgagfrflgdngsifknnlppgfakeeegafknf.isvfvivvfaftGielvaiiagEvkdPeksiP 233
                                   + ++   l++ k+ ++       ++++   +  +p          + + ++v + +v ++ G+ +v+++agE+++P+++ P
  gi|13541049|ref|NP_110737.1| 193 VTLF---LVSFKLRNF-------SAYG--VAPYGPF---------SVVsAIVTSGIVYSYLGFQAVINLAGESRNPKRDGP 252
                                   5554...566666666.......2222..1223333.........3331456667788999******************** PP

                   AA_permease 234 kailqvviritifYvlsllligllvprndlgllndsasaaspfvifikesgvsvlaplinaviltaalssansslysasRv 314
                                    + + v+i  ++fYv + ++ +  vp +d +   + +s  spf  + ++ ++  l +li+a ++ +  +s++++++s sR 
  gi|13541049|ref|NP_110737.1| 253 LSLILVIIFSVVFYVVLQIAFIGSVPASDISKGWAFLSLPSPFADIAVSFNMFWLYTLIIADSIYSPSGSSMAAVASNSRN 333
                                   ******************999999*****99998888889***************************************** PP

                   AA_permease 315 lyslakdglaP.kvlkkvskrgvPlraillsmiisllalllaslnlaapivfnfllaisaliglivwlliilsylrfRkal 394
                                   ly+l+k+g++P ++l++ +  g P ra+l+ ++isl++l+  ++  +       ++   ++  li ++ +++s+ ++   +
  gi|13541049|ref|NP_110737.1| 334 LYALSKNGTLPsFFLRVDNNTGIPRRALLFNFVISLIVLVTLKSWHQ-------IIETLGILLLISFIGSAVSSGVIGSIK 407
                                   ***********999999**********************99998888.......889999**************9888887 PP

                   AA_permease 395 kyqgrsieelgfkaallplgvilvlaaliiillilalyaylt 436
                                   +y+++       k+++++  + +v+++  +i+ i ++ ++l 
  gi|13541049|ref|NP_110737.1| 408 RYSSI-------KMPFIVIVSAIVFVFSGLIISISSFSKVLV 442
                                   77777.......556666666666666666666666555543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (533 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1077  (0.0600703); 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:                         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: 0.70u 0.34s 00:00:01.04 Elapsed: 00:00:00.49
# Mc/sec: 3261.48
//
Query:       gi|13541050|ref|NP_110738.1|  [L=408]
Description: multidrug efflux permease [Thermoplasma volcanium GSS1]
Scores for complete 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  105.7  45.7    1.4e-19   70.2  26.2    2.1  2  MFS_1       Major Facilitator Superfamily
    2.4e-07   29.9   9.2    2.4e-07   29.9   9.2    2.6  3  MFS_1_like  MFS_1 like family
    0.00012   21.0  27.0      0.012   14.4   5.0    2.5  2  LacY_symp   LacY proton/sugar symporter


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.2  26.2   2.4e-23   1.4e-19       3     271 ..      22     277 ..      20     279 .. 0.86
   2 !   48.3  20.4   1.1e-16   6.8e-13      10     165 ..     231     389 ..     216     402 .. 0.82

  Alignments for each domain:
  == domain 1  score: 70.2 bits;  conditional E-value: 2.4e-23
                         MFS_1   3 laaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrr.vlllglllfalglllllfa 82 
                                    a+f+  lars +++++p++l+e  +i + ++g l+ l a+ a+ +s+ +G l+dr+Grrr  +l+ +l+++l  +l +++
  gi|13541050|ref|NP_110738.1|  22 SAQFIRVLARSQIWIFVPIYLTEIRHIPVYFMGVLFFLTAVIALPFSVYGGNLIDRIGRRRvAVLIPFLVSILL-FLTSIS 101
                                   689**********************************************************6666666666555.333332 PP

                         MFS_1  83 .....sslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyila 158
                                        + +++++ +  +  l   + + a  +++ad+++++er  ++g+l ++ ++G+ +gp++gg++a ++++ ++f++ a
  gi|13541050|ref|NP_110738.1| 102 imlrmQAIYIIIEFLSIEPLS-VVQWIADSVIMADVTSEDERLDGFGILRIAGNIGFSVGPAIGGFIA-QYSYAYIFLASA 180
                                   233445555566666666666.699*******************************************.99********** PP

                         MFS_1 159 ivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsg.lltllplylqevl 238
                                   i +l+ f+l +++++e+ + ++++++               +++ ++d+ ++ l+++l++ + ++sg   t+l+l+l  v 
  gi|13541050|ref|NP_110738.1| 181 IGALIEFILYFAWITETGVYSRTNRK---------------ISIPFNDRAFM-LVASLIGLSYFVSGqWGTTLTLFLSIVD 245
                                   ********999999999999999965...............77779999884.88888888777777899*********** PP

                         MFS_1 239 glsglllaglllallalvgailallagrlsdrl 271
                                   ++++  ++g+l+++ ++ ++ l++ + rl++++
  gi|13541050|ref|NP_110738.1| 246 KITN-SSVGILYSINGITVVLLQIPIIRLIRKM 277
                                   ***5.*********************9999997 PP

  == domain 2  score: 48.3 bits;  conditional E-value: 1.1e-16
                         MFS_1  10 larsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll.fasslwlll 89 
                                    +++++++++   + +   i+ s++g+l+++ +++ +++++p+ rl+ ++     l +g +++a+g+++l+ f ss+w+++
  gi|13541050|ref|NP_110738.1| 231 GQWGTTLTLFL-SIVDK--ITNSSVGILYSINGITVVLLQIPIIRLIRKMDGFQQLAIGSIVYASGFFALAfF-SSFWIIA 307
                                   34444444444.56777..889****************************8888************5555536.******* PP

                         MFS_1  90 vlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslg......Wravfyilaivslla 164
                                   +  v+  +g+ ++ p++++++a+++p+++rg ++g +s+++++ + ++p+lg  l+  +       W  vf+i  iv++  
  gi|13541050|ref|NP_110738.1| 308 LDVVVLTIGENIVSPVSNSIVAKLAPPDKRGEYYGAMSLFVGFISPIAPVLGTSLLYRYEsnslflWGPVFLIGIIVAIAT 388
                                   ********************************************************8888566666666666655555554 PP

                         MFS_1 165 f 165
                                   +
  gi|13541050|ref|NP_110738.1| 389 L 389
                                   3 PP

>> MFS_1_like  MFS_1 like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   9.2   4.1e-11   2.4e-07     217     377 ..       7     170 ..       1     178 [. 0.78
   2 !   12.5  15.3   8.3e-06      0.05     126     355 ..     122     345 ..     109     372 .. 0.75
   3 ?   -1.9   0.0       0.2   1.2e+03     257     283 ..     369     395 ..     360     402 .. 0.80

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 4.1e-11
                    MFS_1_like 217 vllnilknpeviifllvalilgmswgiienFlflYL.kelgasntllGslvalgvvaeiplfffaeklleklGhvklli.i 295
                                   ++l++ +++ vi++  + +i   + + i+ F+ +YL +    + +++G+l +l++v  +p+ +++ +l++++G +++ + i
  gi|13541050|ref|NP_110738.1|   7 HILRVARKRPVIVVSSAQFIRVLARSQIWIFVPIYLtEIRHIPVYFMGVLFFLTAVIALPFSVYGGNLIDRIGRRRVAVlI 87 
                                   56788899999999**********************777889********************************9996614 PP

                    MFS_1_like 296 allayilrfllyaii...enawlvlpievLh..gisfgllwaaaveyvskiapksleatgqgllsg...lyfglGralGsl 368
                                    +l+ il f l +i    +   + ++ie+L+  ++s+ + w a    +++++++  +  g g+l +   + f++G+a+G +
  gi|13541050|ref|NP_110738.1|  88 PFLVSILLF-LTSISimlRMQAIYIIIEFLSiePLSV-VQWIADSVIMADVTSEDERLDGFGILRIagnIGFSVGPAIGGF 166
                                   555555555.4444335888999999***96225554.56999999*******9999999999887112456666666666 PP

                    MFS_1_like 369 iGGllwdlk 377
                                   i+    + +
  gi|13541050|ref|NP_110738.1| 167 IA----Q-Y 170
                                   65....3.3 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 8.3e-06
                    MFS_1_like 126 aailvlldaatlkel..gedrkd.yGrqrlfGsvGyaifafitGilidhysvnllpysallyvlaallvisllvvlilnet 203
                                   + +  ++d++++ ++  +++r d +G  r+ G +G+ +  +i G++ ++++     y  +++  a+  +i +++      +
  gi|13541050|ref|NP_110738.1| 122 SVVQWIADSVIMADVtsEDERLDgFGILRIAGNIGFSVGPAIGGFIAQYSYA----Y--IFLASAIGALIEFIL-----YF 191
                                   455678999999999753333347*************998888888777777....4..566666666666666.....34 PP

                    MFS_1_like 204 ekesklkvtkslqvllnilknpeviifllvalilgmswgiienF...lflYL.kelgasntllGslvalgvvaeiplfffa 280
                                    + ++++v    +  + i  n +  +f+lva ++g s+ + +++   l+l+L    + +n+ +G+l  +  +  + l +  
  gi|13541050|ref|NP_110738.1| 192 AWITETGVYSRTNRKISIPFNDR--AFMLVASLIGLSYFVSGQWgttLTLFLsIVDKITNSSVGILYSINGITVVLLQIPI 270
                                   45555555544444455544444..5777777777777666666666*****667789*********************** PP

                    MFS_1_like 281 eklleklGhvklliiallayilrfllyaiienawlvlpievLhgisfgllwaaaveyvskiapksleatgqglls 355
                                    +l++k+   + l i+ ++y+  f+ +a+++++w++ +  v   i   ++  +  + v+k+ap+  ++ + g +s
  gi|13541050|ref|NP_110738.1| 271 IRLIRKMDGFQQLAIGSIVYASGFFALAFFSSFWIIALDVVVLTIGENIVSPVSNSIVAKLAPPDKRGEYYGAMS 345
                                   *******9999999999*****************99887777788888887888888888888888887766444 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 0.2
                    MFS_1_like 257 asntllGslvalgvvaeiplfffaekl 283
                                    s +l+G +  +g +  i ++++++kl
  gi|13541050|ref|NP_110738.1| 369 NSLFLWGPVFLIGIIVAIATLMIGSKL 395
                                   567889999999999999999998887 PP

>> LacY_symp  LacY proton/sugar symporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9  14.1   1.2e-05      0.07      14     187 ..      22     192 ..      10     201 .. 0.71
   2 !   14.4   5.0     2e-06     0.012       2      87 ..     209     295 ..     208     321 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.2e-05
                     LacY_symp  14 lffffyffimsayfplfpvwlkevlglsktetGivfsvislfsilfqplfGlisdklGlkke..ll.wvislllvlfapfl 91 
                                   +  f+  +  s ++ + p++l+e+ ++    +G++f    ++++ f +  G + d++G ++   l+ + +s+ll l++   
  gi|13541050|ref|NP_110738.1|  22 SAQFIRVLARSQIWIFVPIYLTEIRHIPVYFMGVLFFLTAVIALPFSVYGGNLIDRIGRRRVavLIpFLVSILLFLTS-IS 101
                                   455566666899**********************************************99862234223344443333.33 PP

                     LacY_symp  92 iyvfepllqlnilvGalvGgvflGlvysagagaieayiekvsraskfeyGkarvfGclGyalcaslaGilfsidpslvfwl 172
                                   i +   +  + i++  l       + + a + ++   +    r     +G  r+ G +G++++ ++ G + + +    f l
  gi|13541050|ref|NP_110738.1| 102 IML--RMQAIYIIIEFLSIEPLSVVQWIADSVIMADVTSEDERLDG--FGILRIAGNIGFSVGPAIGGFIAQYSYAYIF-L 177
                                   322..23333344444433334445566666666666655555554..79******************99999888776.7 PP

                     LacY_symp 173 asgfalillllllls 187
                                   as +++++ ++l+++
  gi|13541050|ref|NP_110738.1| 178 ASAIGALIEFILYFA 192
                                   888888888887765 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 2e-06
                     LacY_symp   2 iplkntnfylfalffffyffimsayfplfpvwlkevlglsktetGivfsvislfsilfq.plfGlisdklGlkkellwvis 81 
                                   ip+++++f+l a+   + +f+ + + + ++++l+ v +++++ +Gi++s++ ++ +l+q p++ li+   G+++  + +i 
  gi|13541050|ref|NP_110738.1| 209 IPFNDRAFMLVASLIGLSYFVSGQWGTTLTLFLSIVDKITNSSVGILYSINGITVVLLQiPIIRLIRKMDGFQQLAIGSIV 289
                                   57788899**********************************************998875799999999999988777775 PP

                     LacY_symp  82 lllvlf 87 
                                   +   +f
  gi|13541050|ref|NP_110738.1| 290 YASGFF 295
                                   443333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (408 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       901  (0.0502538); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.69u 0.32s 00:00:01.01 Elapsed: 00:00:00.52
# Mc/sec: 2348.59
//
Query:       gi|13541051|ref|NP_110739.1|  [L=188]
Description: hypothetical protein TVN0220 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score 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   13.7   1.6       0.62    9.4   1.6    2.3  1  DUF3575    Protein of unknown function (DUF3575)
       0.15   11.3   0.0       0.19   11.0   0.0    1.1  1  LCIB_C_CA  Limiting CO2-inducible proteins B/C beta carbonyic


Domain annotation for each model (and alignments):
>> DUF3575  Protein of unknown function (DUF3575)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   1.6   6.9e-05      0.62      17      76 ..      92     150 ..      83     188 .] 0.85

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 6.9e-05
                       DUF3575  17 kvavktNllydatttpNlgvevalgkkwtldlsvnynpwkfsdnkklkhllvqpelRyWl 76 
                                   ++ vk N+l+ + tt+N  +e + ++  t++ +v    ++  +++ +  +  ++el  W 
  gi|13541051|ref|NP_110739.1|  92 EFVVKLNVLDIINTTVNSYLESYWKSAETVNSEVTDSLFRA-KHRLMTAMFPEMELETWE 150
                                   788*******************************9999999.446777777777777775 PP

>> LCIB_C_CA  Limiting CO2-inducible proteins B/C beta carbonyic anhydrases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   2.2e-05      0.19     109     193 ..      66     150 ..      51     171 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 2.2e-05
                                   -BTTHHHHHHHHHHH---------------TTTHHHHHHHHHHGGGHH.HHHH-SSHHHHHHHHHHHHHHHHHHHHHHHTG CS
                     LCIB_C_CA 109 skaCGAlvaalkelkkeglekeskepgaldelDaeqsiikqrllkrle.eiekaeddlveltkvayeaikddlekliektt 188
                                    + CGA + ++k++ ++ ++ ++++p+ + +l++ ++ii++ ++++le   ++ae+   e+t  + +a +++++++  +  
  gi|13541051|ref|NP_110739.1|  66 VSFCGADESKYKKFYEDYVNINKSSPEFVVKLNV-LDIINTTVNSYLEsYWKSAETVNSEVTDSLFRAKHRLMTAMFPEME 145
                                   568**********99999*****99999987776.899999999999944588999999**************99988765 PP

                                   GS-TT CS
                     LCIB_C_CA 189 vdekk 193
                                    ++++
  gi|13541051|ref|NP_110739.1| 146 LETWE 150
                                   55544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       715  (0.0398795); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); 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: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.51
# Mc/sec: 1102.96
//
Query:       gi|13541052|ref|NP_110740.1|  [L=267]
Description: Signal peptidase I [Thermoplasma volcanium GSS1]
Scores for complete sequence (score 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   0.0       0.19   11.7   0.0    2.1  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 ?   11.7   0.0   1.1e-05      0.19       2      45 ..      39     107 ..      38     110 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.1e-05
                                   XXSSTT......CCT.XXTTXEEEEECTS...................---TTSEEEEEETTCE-EEEEE CS
                 Peptidase_S24   2 vpGdSM......ept.lldGdlilVdkfs...................epkrGdivvfrlpgeeeayiKr 45 
                                   v+++SM      ep+ ++ Gd++l +k +                     + Gd++  + p++e ++i+r
  gi|13541052|ref|NP_110740.1|  39 VESESMehgsswEPGvINTGDIVLLKKVNdplnnivtyvdgrsigfktYGEYGDVILYNAPDGE-IIIHR 107
                                   8999998888887754899*******9999*****************999*************8.99998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       868  (0.0484132); expected 358.6 (0.02)
Passed bias filter:                      575  (0.0320709); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 1691.25
//
Query:       gi|13541053|ref|NP_110741.1|  [L=174]
Description: peroxiredoxin [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-39  135.1   0.3    1.3e-39  134.9   0.3    1.1  1  AhpC-TSA       AhpC/TSA family
    8.3e-17   61.3   0.1    9.8e-17   61.0   0.1    1.0  1  Redoxin        Redoxin
      0.003   17.5   0.0     0.0043   17.0   0.0    1.4  1  SCO1-SenC      SCO1/SenC
     0.0034   17.2   0.1      0.017   15.0   0.0    2.1  2  1-cysPrx_C     C-terminal domain of 1-Cys peroxiredoxin
     0.0058   16.9   0.2     0.0085   16.4   0.2    1.3  1  Thioredoxin_8  Thioredoxin-like
  ------ inclusion threshold ------
       0.14   12.3   0.0        0.2   11.7   0.0    1.2  1  DUF4715        Domain of unknown function (DUF4715)


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 !  134.9   0.3   4.5e-43   1.3e-39       1     123 [.       4     133 ..       4     134 .. 0.98

  Alignments for each domain:
  == domain 1  score: 134.9 bits;  conditional E-value: 4.5e-43
                                   TTSB----EEE...STTCEEEECHHHTTSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCHHHHHHHH CS
                      AhpC-TSA   1 vgdkapdfelk...nadgetvslsdykgkpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvdspeshkkfie 78 
                                   v+++apdfe++   n++ ++++ls y+gk+vvlffyp+d+++vC+te++ +a+ ye+fk+++ evi vs d+++ hk++++
  gi|13541053|ref|NP_110741.1|   4 VNKAAPDFEANafvNGEVKKIRLSSYRGKWVVLFFYPADFTFVCPTEVEGFAEDYEKFKKKNTEVISVSEDTVYVHKAWVQ 84 
                                   6899***************************************************************************** PP

                                   H-H.....SSEEEE-TTSHHHHHTT-EETTTTECSCEEEEE-TTSBEEE CS
                      AhpC-TSA  79 kes....lnfpllsDeegkvakaygvlkeekglalratfvidkegkiry 123
                                    ++     ++p++ D++g +a+ay+v++ee+g a+r+ f+i+++g+++y
  gi|13541053|ref|NP_110741.1|  85 YDErvakAKYPMVEDRKGIIARAYDVYNEETGNAQRGLFIINPDGIVKY 133
                                   9999*******************************************99 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.0   0.1   3.3e-20   9.8e-17       2     138 ..       4     142 ..       3     152 .. 0.84

  Alignments for each domain:
  == domain 1  score: 61.0 bits;  conditional E-value: 3.3e-20
                                   TTSBB---E...CCEETTCEEEEEHHHHTTSEEEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEEEEESSSHHHHHH CS
                       Redoxin   2 agdkaPdft...lplaatdgnsvslsefkgkkvvvnfvpgafcPtCsaehpyleklaellkekgvdvvavvadndafvkef 79 
                                   ++++aPdf+   +  ++ + +++ ls+++gk vv++f+p+ f+ +C +e+  +++ +e++k+k+ +v+ v + +  +v ++
  gi|13541053|ref|NP_110741.1|   4 VNKAAPDFEanaF--VNGEVKKIRLSSYRGKWVVLFFYPADFTFVCPTEVEGFAEDYEKFKKKNTEVISV-SEDTVYVHKA 81 
                                   67889***97554..679999******************************7777777779999998444.455566**** PP

                                   HHH.....TT-TSEEEE-TTSHHHHHTT-TTEEE.GGGEEE-EEEEEEETTEEEEEEESSSCHT CS
                       Redoxin  80 wgk.....eglkfpvlsDgsaaftkalGlrleedaseglrtpryavidedgkvvylevepepet 138
                                   w +      + k+p++ D+++ +++a++++ +e  +   + + +++i+ dg v+y+   +++++
  gi|13541053|ref|NP_110741.1|  82 WVQydervAKAKYPMVEDRKGIIARAYDVY-NEETG--NAQRGLFIINPDGIVKYVVITDDNVG 142
                                   ********888*****************99.33333..599**************999888876 PP

>> SCO1-SenC  SCO1/SenC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   1.4e-06    0.0043       6      64 ..      16      72 ..      11     128 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.4e-06
                     SCO1-SenC  6 lvdqdgeavteedlegkpslvffgFthCpdvCpttlanmaevldalgeeaekvqplfiT 64
                                  +v+ + ++++ ++++gk++++ff  +  + vCpt+++  ae +++++++  + ++++++
  gi|13541053|ref|NP_110741.1| 16 FVNGEVKKIRLSSYRGKWVVLFFYPADFTFVCPTEVEGFAEDYEKFKKK--NTEVISVS 72
                                  7899999****************************************99..55555555 PP

>> 1-cysPrx_C  C-terminal domain of 1-Cys peroxiredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.57   1.7e+03      17      31 ..      63      74 ..      63      78 .. 0.82
   2 !   15.0   0.0   5.5e-06     0.017       8      23 ..     157     172 ..     154     174 .] 0.88

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.57
                                  .TBT-EEE---SSHH CS
                    1-cysPrx_C 17 kpGdkvivpPpatee 31
                                  k++++vi   +++e+
  gi|13541053|ref|NP_110741.1| 63 KKNTEVI---SVSED 74
                                  57999**...99998 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 5.5e-06
                                   HT-BB-TTT.TBT-EE CS
                    1-cysPrx_C   8 hgvatPAnWkpGdkvi 23 
                                   +g  +P+nW +G++++
  gi|13541053|ref|NP_110741.1| 157 SGGLCPVNWHEGEPTL 172
                                   6889**********99 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.2   2.8e-06    0.0085       1      93 [.      31     129 ..      31     141 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 2.8e-06
                                   .SEEEEEE-.-SSSHHHHHHHHHHHHHHHHHHHTTSEEEEEEE-S..S-HHHHHHHGGGS-TTSEE.EE-TT-HHHHTT-S CS
                 Thioredoxin_8   1 gkvvlLyfg.aswcppckaftpklkelyeklkkkkkveivyvsld..kkeeefekylkknkkpwlsvpfddkkrnklkkky 78 
                                   gk+v+L+f+ a++   c + ++   e yek+k kk+ e+++vs d     +++ +y +    +   +p  ++++  +++ y
  gi|13541053|ref|NP_110741.1|  31 GKWVVLFFYpADFTFVCPTEVEGFAEDYEKFK-KKNTEVISVSEDtvYVHKAWVQYDERV--AKAKYPMVEDRKGIIARAY 108
                                   5788887774788889***************9.7**********8432356666666666..6679999999999999999 PP

                                   --TT......-SEEEEE-TT- CS
                 Thioredoxin_8  79 nvka......iPtlvvldkng 93 
                                   +v +         l++++++g
  gi|13541053|ref|NP_110741.1| 109 DVYNeetgnaQRGLFIINPDG 129
                                   998877777744455555544 PP

>> DUF4715  Domain of unknown function (DUF4715)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   6.6e-05       0.2      53     110 ..      49     104 ..      28     111 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 6.6e-05
                       DUF4715  53 qkvagvqreledfkkealkaihrledaycemsralveqeeqaarvkqrlreeedrgiv 110
                                     v g   + e fkk+  + i   ed+   + +a v+ +e+ a+ k  + e+  +gi+
  gi|13541053|ref|NP_110741.1|  49 TEVEGFAEDYEKFKKKNTEVISVSEDTV-YVHKAWVQYDERVAKAKYPMVEDR-KGII 104
                                   579999*******************985.5899************99987765.4554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); 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:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1136.60
//
Query:       gi|13541054|ref|NP_110742.1|  [L=226]
Description: cell wall biosynthesis glycosyltransferase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-24   87.0   0.0    1.6e-24   86.6   0.0    1.1  1  Glycos_transf_2  Glycosyl transferase family 2
    1.7e-11   44.4   0.0    1.9e-11   44.3   0.0    1.1  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    0.00025   20.6   0.0    0.00035   20.1   0.0    1.3  1  Glyco_tranf_2_2  Glycosyltransferase like family 2
  ------ inclusion threshold ------
      0.071   13.6   0.0       0.11   13.0   0.0    1.4  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 !   86.6   0.0   3.5e-28   1.6e-24       1     168 [.      10     166 ..      10     168 .. 0.95

  Alignments for each domain:
  == domain 1  score: 86.6 bits;  conditional E-value: 3.5e-28
                                   EEEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH--SS CS
               Glycos_transf_2   1 svviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglraatgd 81 
                                   s vipt Neekt+  +++ + ++   p+ eii+vD +StD+t+ei+++      + +vi  +++ G+++a+ +g+ aa+gd
  gi|13541054|ref|NP_110742.1|  10 SFVIPTINEEKTIGSVIDGIHEN--FPNAEIILVDTNSTDKTKEIAKSK-----GATVIEEPRK-GYGRAYQTGIPAAKGD 82 
                                   78******************999..************************.....9*******87.**************** PP

                                   EEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SSEEEECCHCCCCHCCCCCCSTTCSTCCCEEE CS
               Glycos_transf_2  82 yilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrvgenerlyfkerkrslkgnlsfeigsaallr 162
                                   +i+++D D +++ d +++l+e l  d +d + + r  ++ +t+  + ++     +++ + + +   k  + +  ++++++r
  gi|13541054|ref|NP_110742.1|  83 IIVCMDGDGTYPTDIVKPLIEILILDKVDFISCDRITFRTSTNYTTLHY---VGNMVLNLTIRILFKVRMVDSQSGMWIFR 160
                                   ******************************9999999999999999986...69999999999999999999999999999 PP

                                   EHHHHH CS
               Glycos_transf_2 163 realee 168
                                    e++++
  gi|13541054|ref|NP_110742.1| 161 SELYKK 166
                                   998876 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 !   44.3   0.0   4.2e-15   1.9e-11       3     132 ..       8     125 ..       6     186 .. 0.85

  Alignments for each domain:
  == domain 1  score: 44.3 bits;  conditional E-value: 4.2e-15
               Glyco_tranf_2_3   3 dlavlVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksralneal 83 
                                   ++++++pt+nee+++g+v++ +  +  p+ e+++v+++s+++t e a+       + + +v+     ++ +g+ ra++ ++
  gi|13541054|ref|NP_110742.1|   8 KISFVIPTINEEKTIGSVIDGIHEN-FPNAEIILVDTNSTDKTKEIAKS------K-GATVIEE---PR-KGYGRAYQTGI 76 
                                   589********************94.8******************9975......3.5689844...55.6999******* PP

               Glyco_tranf_2_3  84 ravksdlvllvDdDtvvePdtlkrllqffltpkvgavgtpvfllnrstl 132
                                   +a+k+d+++ +D+D     d++k l  ++  +kv+++ +++ + + st 
  gi|13541054|ref|NP_110742.1|  77 PAAKGDIIVCMDGDGTYPTDIVKPLIEILILDKVDFISCDRITFRTSTN 125
                                   **************99999999999999977779999888766554444 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 !   20.1   0.0   7.8e-08   0.00035       1     106 [.      10     105 ..      10     132 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 7.8e-08
               Glyco_tranf_2_2   1 svviplraseerhyieervlqkakyydeeielivvddgSsekfleevssiidlnllvylkdeddkayslaaarNrGaskae 81 
                                   s vip  ++e++  i   +  +   + ++ e+i+vd  S++k     + i + ++     +e+ k y+  +a   G+  a+
  gi|13541054|ref|NP_110742.1|  10 SFVIPTINEEKT--IGSVIDGIHENF-PNAEIILVDTNSTDK----TKEIAKSKGATV-IEEPRKGYG--RAYQTGIPAAK 80 
                                   6799**9*9999..999997666653.99*************....455666666665.567788775..67899****** PP

               Glyco_tranf_2_2  82 sdlvlFlDaDcfissDkfekilkli 106
                                   +d+++ +D+D  + +D ++ +++++
  gi|13541054|ref|NP_110742.1|  81 GDIIVCMDGDGTYPTDIVKPLIEIL 105
                                   **********999999888777755 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   2.5e-05      0.11       2      54 ..      17      70 ..      16      90 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.5e-05
               Glyco_tranf_2_4  2 neadiLpefla.hhlalgfdrilvydndstDgtrailkelpevkllhvdksyed 54
                                  ne+++++++++  h+++   +i+++d +stD+t +i k+  +  + + +k y +
  gi|13541054|ref|NP_110742.1| 17 NEEKTIGSVIDgIHENFPNAEIILVDTNSTDKTKEIAKSKGATVIEEPRKGYGR 70
                                  899999999985788998899****************99877666666666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 1500.05
//
Query:       gi|13541055|ref|NP_110743.1|  [L=397]
Description: major facilitator superfamily permease [Thermoplasma volcanium GSS1]
Scores for complete 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  34.8    9.9e-07   28.0  34.8    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 !   28.0  34.8   5.5e-11   9.9e-07       3     329 ..      26     334 ..      24     349 .. 0.73
   2 ?   -0.5   2.6     0.026   4.7e+02     208     240 ..     358     392 ..     339     393 .. 0.65

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 5.5e-11
                         MFS_1   3 laaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfa. 82 
                                   +++ l a++ +++g+++ ++  + ++   s++   +++ + ++ ++ ++ G+l+  + ++ v+ +g  + +l +++l++a 
  gi|13541055|ref|NP_110743.1|  26 ISYNLFAFSNGLFGTFINIFFFSKFN-LISVVEYQAAIQG-TQTLMFVFSGYLIRILNAKYVYSIGNYARSLIIFALILAk 104
                                   56677888888888888887778888.3333333444433.68999999********9999************44444676 PP

                         MFS_1  83 sslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllgglla.sslg.....Wravfyil 157
                                    +l+  +++ ++ G+ +g+++++ ++l  +++  ++r   ++  s+ ++++ +++pll+g+++  s+g     ++  f+i 
  gi|13541055|ref|NP_110743.1| 105 GPLFNPIIFGLIYGIPSGIFWSGNNTLSQAVTRSKDRFGFLSTNSTIAGAAGLVAPLLAGFIIsISYGrglerYSTDFLIS 185
                                   666656888889***************************************************55555888877777**** PP

                         MFS_1 158 aivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsglltllplylqevl 238
                                   a+++++a+ +  +   +e+ e ++k  ++         ++   +  + ++    + + ++l  + + +++t +ply  + l
  gi|13541055|ref|NP_110743.1| 186 ALLLIIAGTV--AIAIREKGEGRWKYRARN-------TIIG--RDEKYSK----FKTYFFLSNILTITVSTIVPLY-IFSL 250
                                   *******995..555555555555555444.......2333..6666667....78888888888999********.8888 PP

                         MFS_1 239 glsglllaglllallalvgailallagrls.drlgrrrrlllallllllaalglallavtssavllll.vlvliGfglgfv 317
                                     s ++l+g++  +l+lv++i+   a+ +s +r     +++  ++++++++ +l+++ + +++v++++ +++   +   f+
  gi|13541055|ref|NP_110743.1| 251 TKS-YVLIGFFGTFLSLVNLIS--NATVVSlRR---IVPNISQISIVVVMLSSLLYFIHVWNNVASAYvASA---LIIYFM 322
                                   888.9**************999..888888455...445555555555555555555555334443332222...244444 PP

                         MFS_1 318 fpsllalasdla 329
                                   +p+ ++++s+++
  gi|13541055|ref|NP_110743.1| 323 VPLNNSAMSNFM 334
                                   555555555554 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.026
                         MFS_1 208 vlw..illialllfffgfsglltllplylqevlgl 240
                                    ++  ++l++l + +f + +l++ lp++  +vlg+
  gi|13541055|ref|NP_110743.1| 358 RIFsfAVLAVLSSLGFPIGLLMFSLPVFSLSVLGF 392
                                   33333566666666777777888888887777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (397 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       891  (0.049696); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.28s 00:00:00.90 Elapsed: 00:00:00.48
# Mc/sec: 2476.10
//
Query:       gi|13541056|ref|NP_110744.1|  [L=119]
Description: hypothetical protein TVN0225 [Thermoplasma volcanium GSS1]
Scores for complete 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   52.5   0.2    5.8e-14   52.1   0.2    1.1  1  SepF      Cell division protein SepF


Domain annotation for each model (and alignments):
>> SepF  Cell division protein SepF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.1   0.2   3.2e-18   5.8e-14       1      72 []      36     108 ..      36     108 .. 0.97

  Alignments for each domain:
  == domain 1  score: 52.1 bits;  conditional E-value: 3.2e-18
                                   EEEEE-SSGGGHHHHHHHHHTT-EEEEE-CCCTC.HHHHHHHHHHHHHHHHCT-EEEEECTTEEEEE-TT-EE CS
                          SepF   1 vvvveprsfedaqeiadalkegkiVilnledldk.eeakrivdflsgvvyaldGdiqkvgkkvflitPknvdi 72 
                                   v+v+e+ s+ed  e +++ ++g+i+i++++++++   ++ri+++++ + ++++Gd+++v+k++++itP++++i
  gi|13541056|ref|NP_110744.1|  36 VKVAEVYSYEDLLETVKYPYSGNILIVDISGVSDeMASRRIMEKCATIGKEINGDVARVSKNMIMITPNGIKI 108
                                   89********************************667799*******************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       522  (0.0291148); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.30s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 773.15
//
Query:       gi|13541057|ref|NP_110745.1|  [L=430]
Description: major facilitator superfamily permease [Thermoplasma volcanium GSS1]
Scores for complete 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-38  130.2  62.4    2.9e-32  112.0  42.4    2.0  2  MFS_1     Major Facilitator Superfamily
     0.0049   15.8   7.4     0.0049   15.8   7.4    3.6  3  Sugar_tr  Sugar (and other) transporter
  ------ inclusion threshold ------
       0.48    8.7  18.5        0.8    8.0   5.1    2.5  3  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 !  112.0  42.4   4.8e-36   2.9e-32       2     343 ..       7     367 ..       6     368 .. 0.83
   2 !   32.1  12.0   9.4e-12   5.6e-08      64     172 ..     305     411 ..     303     425 .. 0.83

  Alignments for each domain:
  == domain 1  score: 112.0 bits;  conditional E-value: 4.8e-36
                         MFS_1   2 llaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll.f 81 
                                   ++++++s++a+++++p++pl++   l++++ ++g + ++ +++++ a +++G lsd ++rr+v++l  ++ a++++l++ f
  gi|13541057|ref|NP_110745.1|   7 FISYLMSSMASGLTNPMIPLFVVVYLHSNVFFVGVASAVSSAASVPALIFWGNLSDSLSRRKVFILIGFFGAFASFLPIfF 87 
                                   899***********************************************************6655555555554666647 PP

                         MFS_1  82 asslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllgglla.sslg...Wravfyil 157
                                   + +++ ++++l ++q l++ a++p++ ++i +   +++ +++i+ +s+ +++G+++g ++g +++   ++    ++v+++ 
  gi|13541057|ref|NP_110745.1|  88 VRNIYeYMAILILFQVLAM-ASVPVSTVMILEQNDRSQWPQVISNFSMISGVGSVIGLVIGTVFItLEYSpsaLPLVYILS 167
                                   8****99*****9999997.9*****************************************999555559999999**** PP

                         MFS_1 158 aivsllafvlfllllpeepperkrkspkeee.......kgtgpaplvp.......awkallkdpvlwillialllfffgfs 224
                                    i++l+a+v  ++ l  ep ++ + +++++        ++ +p++++          ++ l ++v++++ ++++l+ fgf+
  gi|13541057|ref|NP_110745.1| 168 SIIYLIAGVT-AIKLISEPGRHITRNDVPLHtfrvverARYFPTSVIHflslssgKNGENLDKNVFLFITMTAFLM-FGFQ 246
                                   *********4.45666777777777777774555554444444444445555555444444444665344444444.5*** PP

                         MFS_1 225 glltllplylqevlglsglllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavtssavllll 305
                                   ++++  p+ ++  +g ++ +l+ +++al +l++ i+++++gr+++rlg ++ l++a+++ ++++ + a ++++   + +l+
  gi|13541057|ref|NP_110745.1| 247 LFFVPYPV-MVIKFGGNN-ILIFVMYALNSLLSTISFMFTGRIVTRLGGKTSLFIAVFSRVIIFSAAAAIPMFLYGTYALV 325
                                   ********.5*******5.899999***************************************99999999944444444 PP

                         MFS_1 306 ....vlvliGfglgfvfpsllalasdlappeeagtasglfnt 343
                                       v++++G  ++++++s ++++s++ +++++g+a+gl+n+
  gi|13541057|ref|NP_110745.1| 326 savaVYAVLGGIWSIISVSQTNYISRNSGQKARGKAIGLYNS 367
                                   44567777********************************97 PP

  == domain 2  score: 32.1 bits;  conditional E-value: 9.4e-12
                         MFS_1  64 vlllglllfalglllllfasslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggl 143
                                   v+++++++ + ++l++++   l  +++v  vl G+  +++  +   +i++ + ++ rg+aigl+++  ++G ilg l +g+
  gi|13541057|ref|NP_110745.1| 305 VIIFSAAAAIPMFLYGTY--ALVsAVAVYAVLGGIW-SIISVSQTNYISRNSGQKARGKAIGLYNSLLGVGQILGGLTSGI 382
                                   555555555555444444..34448***********.8******************************************* PP

                         MFS_1 144 lasslgWravfyilaivsllafvlfllll 172
                                   +++++g++  ++  a++ + ++v+++  +
  gi|13541057|ref|NP_110745.1| 383 ITTLYGYSIDYITSALIIMAGLVIMMKIY 411
                                   ******99999999999999988655444 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2  11.7     0.058   3.5e+02     295     437 ..      45     181 ..      26     190 .. 0.57
   2 ?    2.1  18.8     0.012        70      45     153 ..     263     375 ..     231     375 .. 0.72
   3 !   15.8   7.4   8.3e-07    0.0049      16      94 ..     331     408 ..     330     417 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.058
                                   HHHHHHHHHHHHHHHHHHHS-SHHHHHHHHHHHHHHHHHHH..HHHHTTSS...CHHHHHHHHHHHHHHHTTTTHHHHHHH CS
                      Sugar_tr 295 ivgvvnfvatfvaiflvdrfGRRtllllGaagmaicfvilgivalllvakskaasivaivfialfialfalgwgpvpwvlv 375
                                   + ++  + a +++  l+d ++RR++++l ++++a++ ++     +++++    ++++ai  ++ ++a+ +    pv  v++
  gi|13541057|ref|NP_110745.1|  45 VSSAASVPALIFWGNLSDSLSRRKVFILIGFFGAFASFLP---IFFVRNI---YEYMAILILFQVLAMAS---VPVSTVMI 116
                                   3333334444444578999999999876666665555555...3455555...36666655555554444...44444444 PP

                                   HHHSHTTTHHHHHH...HHHHHHHHHHHHHHHHHHHHHCHHHT-HHHHHHHHHHHHHHHHHHHHS CS
                      Sugar_tr 376 sElfpqsvRskala...iavavnwlanflisllfpiiteaigggyvflvfaglavlfiifvfffv 437
                                    E  + s  + +++   +   v  ++ ++i+++f ++  + ++ +  ++  ++ +l + ++ +++
  gi|13541057|ref|NP_110745.1| 117 LEQNDRSQWPQVISnfsMISGVGSVIGLVIGTVFITLEYSPSALPLVYILSSIIYLIAGVTAIKL 181
                                   44444443333333100222344456677777887777777777777777777777777777766 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.012
                                   ..HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHH....HHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHH CS
                      Sugar_tr  45 svlsglivsiflvGaiiGslfagllgdrfGRkkslliaav....lfvigavlqaaakgknsvevlivgRvlvGigvGlasv 121
                                   ++l+ ++ ++ ++ ++i+ +f+g +++r+G k sl ia++    +f+++a++ ++  g+ ++   ++   ++G  + ++sv
  gi|13541057|ref|NP_110745.1| 263 NILIFVMYALNSLLSTISFMFTGRIVTRLGGKTSLFIAVFsrviIFSAAAAIPMFLYGTYALVSAVAVYAVLGGIWSIISV 343
                                   3456778888899999*******************997652222555566665555555444444444677777799999* PP

                                   HHHHHHHTTS-SCCHHHHHHHHHHHHHHHHHH CS
                      Sugar_tr 122 lvPmyisEiApkklRgalvslyqlaitfGilv 153
                                     + yis ++ +k Rg+ ++ly++ + +G+++
  gi|13541057|ref|NP_110745.1| 344 SQTNYISRNSGQKARGKAIGLYNSLLGVGQIL 375
                                   *****************************986 PP

  == domain 3  score: 15.8 bits;  conditional E-value: 8.3e-07
                                   HHCGGGTHHHHHHHHTSTT--SHHHHHH...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH CS
                      Sugar_tr  16 tgvigafltllkfaknfglsksksskeessvlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqa 94 
                                   ++v+g++ +++++   ++ s+++++k++  + +gl  s++ vG+i+G+l++g++++ +G+   ++++a++ ++g v+++
  gi|13541057|ref|NP_110745.1| 331 YAVLGGIWSIISVSQTNYISRNSGQKAR-GKAIGLYNSLLGVGQILGGLTSGIITTLYGYSIDYITSALIIMAGLVIMM 408
                                   5899999999999999999999998885.9***********************************************97 PP

>> MFS_3  Transmembrane secretion effector
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   5.1   0.00013       0.8      50     164 ..      45     152 ..      27     206 .. 0.68
   2 ?   -2.7   0.0      0.24   1.4e+03      58      86 ..     213     241 ..     202     253 .. 0.81
   3 ?    6.8   4.6   0.00031       1.9     295     392 ..     312     409 ..     286     420 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00013
                         MFS_3  50 vqaaatLPifllsilaGalaDnfdrRkvllavqlllalvsvlltvlaalgllspwlllaltlligiGaalndPaWqAsvge 130
                                   v  aa++P ++   + G l+D+++rRkv++ +  + a +s l + + + ++ + +++l+l  ++++      P    ++ e
  gi|13541057|ref|NP_110745.1|  45 VSSAASVPALI---FWGNLSDSLSRRKVFILIGFFGAFASFLPIFF-VRNIYEYMAILILFQVLAMA---SVPVSTVMILE 118
                                   67788888875...68*****************9999999765555.55666666666555444432...34666677777 PP

                         MFS_3 131 lvkrrdvpaAvaLnsvginiaRsvGPAlgGvlva 164
                                   + +r++ p+ +   s+   +   +G  +g v ++
  gi|13541057|ref|NP_110745.1| 119 QNDRSQWPQVISNFSMISGVGSVIGLVIGTVFIT 152
                                   7777777777777676666666666666666554 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.24
                         MFS_3  58 ifllsilaGalaDnfdrRkvllavqllla 86 
                                   i +ls+ +G   +n+d+  +l+++++  +
  gi|13541057|ref|NP_110745.1| 213 IHFLSLSSGKNGENLDKNVFLFITMTAFL 241
                                   6799*************999998766544 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.00031
                         MFS_3 295 AlvllslalasslwvavlvlllgGaaW.italstlnvavqlavPrWvvgRalavYltvlaGglaaGsllWGavaealsvtl 374
                                   A++ + l  +  l+ av v +++G+ W i+++s+ n  +   + +  +g+a+ +Y  +l  g  +G+l  G ++  ++ ++
  gi|13541057|ref|NP_110745.1| 312 AAIPMFLYGTYALVSAVAVYAVLGGIWsIISVSQTN-YISRNSGQKARGKAIGLYNSLLGVGQILGGLTSGIITTLYGYSI 391
                                   34444444455667788899999****455555555.567788899*************9999****************** PP

                         MFS_3 375 aLlaaaaalllaaailll 392
                                     +++a+ ++++ +i+++
  gi|13541057|ref|NP_110745.1| 392 DYITSALIIMAGLVIMMK 409
                                   ******999999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (430 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       774  (0.0431703); expected 358.6 (0.02)
Passed bias filter:                      198  (0.0110436); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.44
# Mc/sec: 2925.66
//
Query:       gi|13541058|ref|NP_110746.1|  [L=895]
Description: chromosome segregation protein [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-20   74.7  26.2    1.4e-20   74.7  26.2    6.2  1  AAA_23          AAA domain
    8.4e-17   61.3  45.3      4e-16   59.1  45.3    2.3  1  SMC_N           RecF/RecN/SMC N terminal domain
    2.6e-11   43.8  20.9    2.6e-11   43.8  20.9    3.3  3  AAA_15          AAA ATPase domain
    1.5e-10   40.4  71.7    0.00018   20.4  14.0    5.1  4  AAA_13          AAA domain
    9.5e-08   31.7   0.0      2e-07   30.6   0.0    1.6  1  AAA_29          P-loop containing region of AAA domain
    2.3e-07   30.6   0.0    2.3e-07   30.6   0.0    5.7  4  Rad50_zn_hook   Rad50 zinc hook motif
    9.8e-07   28.6   0.1    9.8e-07   28.6   0.1    4.0  5  AAA_27          AAA domain
    2.6e-05   24.4   0.1    5.8e-05   23.3   0.1    1.7  1  SbcCD_C         Putative exonuclease SbcCD, C subunit
      4e-05   23.6   4.9      4e-05   23.6   4.9    4.2  4  AAA_21          AAA domain, putative AbiEii toxin, Type IV TA
     0.0011   19.2  10.0     0.0011   19.2  10.0    7.5  6  TMF_TATA_bd     TATA element modulatory factor 1 TATA binding
     0.0021   18.6  19.5     0.0021   18.6  19.5    4.4  3  Fez1            Fez1
  ------ inclusion threshold ------
      0.015   15.8  27.1       0.12   12.9   0.0    5.2  2  ABC_tran        ABC transporter
       0.13   12.1   0.0       0.13   12.1   0.0    3.8  4  RsgA_GTPase     RsgA GTPase
       0.19   10.6  83.6        0.3    9.9  12.0    5.6  5  Spc7            Spc7 kinetochore protein
       0.67   10.2   6.8         20    5.5   1.7    4.1  3  Mac             Maltose acetyltransferase
        1.6    9.0   7.9        8.5    6.7   0.2    3.2  3  AFP_2           Bacterial antifreeze protein repeat
        2.3    7.4   8.6        0.2   10.8   1.5    2.5  2  Dynein_C        Dynein heavy chain C-terminal domain
        3.1    8.1   5.8        1.4    9.3   0.1    3.4  3  AAA_16          AAA ATPase domain
        7.8    6.4   9.6        0.5   10.2   1.1    3.3  4  DYW_deaminase   DYW family of nucleic acid deaminases


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 !   74.7  26.2   1.4e-23   1.4e-20       1     196 [.       5     255 ..       5     288 .. 0.74

  Alignments for each domain:
  == domain 1  score: 74.7 bits;  conditional E-value: 1.4e-23
                        AAA_23   1 kLkienfrsfrdqeidFskgltlItGpNGaGKTTildAiklaLygetprlsrks..grgfeksdveiesegkvkay.velt 78 
                                   +++++nf s++d +i F+ g++ I+G+NGaGK++i+dAi++aL+ ++++ ++++  ++g    +ve+ ++ ++ +y +++t
  gi|13541058|ref|NP_110746.1|   5 RIRLRNFLSHSDSDIYFDTGINMIIGQNGAGKSSIVDAIRFALFSDKRTRRTEDmiKKGERYMEVELYFRSEGHSYrIRRT 85 
                                   79*******************************************987666666777777788888888877778889999 PP

                        AAA_23  79 fenkdgry...........................trsiererelskkkgkttkkaklelleideleqfisellgskki.. 130
                                   +e+ ++                               +i  + +l++   ++  +++l + +++e++++++e+l+++    
  gi|13541058|ref|NP_110746.1|  86 IERRGKSIstdaeierdgsiitrgasdvsnyveknVLNINKDVFLTSIFVRQGEMDALVSKDPAERKKILDEILNIDRLea 166
                                   888877667777888888888888888887777776677777777777777777777777777888888888777665533 PP

                        AAA_23 131 ..............ilnlilflgqerfeefel.kdkkerleelekeleeledekkllekleqekekek........eleel 188
                                                 + + +++l+ e + ++++  + ++++eele +l+ +e e+k le+++++ke++k        +l++ 
  gi|13541058|ref|NP_110746.1| 167 gylllkeviddltaNVSDYDYLKNELQSKINEiDNNNKQIEELESKLRLIEPEIKALEEEINIKENKKdhlneelhRLNAQ 247
                                   444444444444333344444444433333334666669999999999999999999999888888888888855544444 PP

                        AAA_23 189 eeeleeil 196
                                    e++++++
  gi|13541058|ref|NP_110746.1| 248 LETIKKYE 255
                                   44444544 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 !   59.1  45.3   4.2e-19     4e-16       2     217 ..       3     887 ..       2     890 .. 0.97

  Alignments for each domain:
  == domain 1  score: 59.1 bits;  conditional E-value: 4.2e-19
                                   EEEEEEESETTEECEEEEEETTSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N   2 lkrleienFksyagktvilpfsksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveit 82 
                                   ++r++++nF s   +  ++ f++++++i+G+NG+GKs+++dAi+F L  +++   r ++++d+i+k          eve++
  gi|13541058|ref|NP_110746.1|   3 IERIRLRNFLSH--SDSDIYFDTGINMIIGQNGAGKSSIVDAIRFALF-SDK---RTRRTEDMIKK-----GERYMEVELY 72 
                                   89**********..69999****************************8.344...8999******8.....556789**** PP

                                   EEETTEESSSSSSCEEEEEEEETTSE.....EEEEETTEEE-H..HHHHHHHHCTT-STT..................... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxx..xxxxxxxxxxxxxxx..................... RF
                         SMC_N  83 fdnedkklkiekeevsisrrvkrkge.....seykingkevtk..kevsellesagiske..................... 135
                                   f+ e+++       + i+r+++r g+      e++ +g+ +t+  ++vs+ +e+  ++++                     
  gi|13541058|ref|NP_110746.1|  73 FRSEGHS-------YRIRRTIERRGKsistdAEIERDGSIITRgaSDVSNYVEKNVLNINkdvfltsifvrqgemdalvsk 146
                                   ******9.......77777777776644423566779999998889*********9999999******************* PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                         SMC_N 136 ................................................................................. 135
                                                                                                                    
  gi|13541058|ref|NP_110746.1| 147 dpaerkkildeilnidrleagylllkeviddltanvsdydylknelqskineidnnnkqieelesklrliepeikaleeei 227
                                   ********************************************************************************* PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                         SMC_N 136 ................................................................................. 135
                                                                                                                    
  gi|13541058|ref|NP_110746.1| 228 nikenkkdhlneelhrlnaqletikkyemelaesqsrkasiemevvklpsieeelkrlennaavvkrneiieyinlkkdlg 308
                                   ********************************************************************************* PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                         SMC_N 136 ................................................................................. 135
                                                                                                                    
  gi|13541058|ref|NP_110746.1| 309 slseiieglksdlskydeahrkledlqsfrseflekkkrkedldklrsslkedednyqsavrnienikkwieneekeierm 389
                                   ********************************************************************************* PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                         SMC_N 136 ................................................................................. 135
                                                                                                                    
  gi|13541058|ref|NP_110746.1| 390 safiseilkiqeitpeiinsrraeinsslmqiegkiaslnasidamrshkmeveenaamlsgrgvcpvcgthlgteksedl 470
                                   ********************************************************************************* PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                         SMC_N 136 ................................................................................. 135
                                                                                                                    
  gi|13541058|ref|NP_110746.1| 471 vkhygeeasrleedinkteneikkldeerkhqkklldringkdverliasynllsskraelkkfmddearlkeahlkaeaa 551
                                   ********************************************************************************* PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                         SMC_N 136 ................................................................................. 135
                                                                                                                    
  gi|13541058|ref|NP_110746.1| 552 isqynsidlgdleakneewlkanavissidienirsrfeeknkqlndiikrmneievnipdvesynenslkrideelnslr 632
                                   ********************************************************************************* PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                         SMC_N 136 ................................................................................. 135
                                                                                                                    
  gi|13541058|ref|NP_110746.1| 633 nkknelyakkaamdeiqktiehfkeeiskkkgiedsqaevnaqllqinddlkqlssrldkinvdqyewkslhkvllqdnek 713
                                   ********************************************************************************* PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                         SMC_N 136 ................................................................................. 135
                                                                                                                    
  gi|13541058|ref|NP_110746.1| 714 lniavadirkrlekketiikaiadlkrvreafskdgvpaiirksasefitnqtrqyiqrfeldiddvdvdqdfnitvfrgg 794
                                   ********************************************************************************* PP

                                   ......CS-HHHHHHHHHHHHHHHHCC..S--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTS....EEEEE-SSHHHCCC CS
                                   ......xxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxx RF
                         SMC_N 136 ......lLSgGektLvalaLlfAiqkv..kpaplyllDeidaaLDeknvkkvaellkekskna....Qfivislreemlek 204
                                         +LSgGe+  va aL++Ai ++  k  +l ++De  a LDe +++ +a++++ + k++    Q+i+is+++e+l+ 
  gi|13541058|ref|NP_110746.1| 795 iaegidSLSGGERMAVAFALRVAIAQFlnKDVSLLVMDEPTAFLDEDRRSDLANIIEYSLKDSsgipQVIMISHHRELLSA 875
                                   ***********************999744789************************96555533444************** PP

                                   -SCEEEEEEEETT CS
                                   xxxxxxxxxxxxx RF
                         SMC_N 205 adklvgvtkveng 217
                                   +d  + v+k +ng
  gi|13541058|ref|NP_110746.1| 876 SDLALEVKK-RNG 887
                                   **9999999.554 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.8  20.9   2.8e-14   2.6e-11       1     268 [.       1     282 [.       1     300 [. 0.72
   2 ?    0.1  20.3      0.54   5.1e+02      89     262 ..     297     512 ..     264     538 .. 0.69
   3 !    6.9  22.9    0.0047       4.4      56     364 ..     537     868 ..     518     873 .. 0.61

  Alignments for each domain:
  == domain 1  score: 43.8 bits;  conditional E-value: 2.8e-14
                        AAA_15   1 MkIkkikikNFRslkdveidlseeltvliGkNnsGKSsilealdl.Flnnkekkn..kkvikiekedleif.eniseskdi 77 
                                   M+I++i+++NF s++d +i ++  ++ +iG N++GKSsi++a+ + +++ k+     ++ ik+ +  +e++   +se  + 
  gi|13541058|ref|NP_110746.1|   1 MIIERIRLRNFLSHSDSDIYFDTGINMIIGQNGAGKSSIVDAIRFaLFSDKRT-RrtEDMIKKGERYMEVElYFRSEGHSY 80 
                                   9******************************************8744454422.235555555555555431445666666 PP

                        AAA_15  78 kIdvefaekekakeyektlkskekkkadlllkkkesdlkktikdkklklkknelsdekisvekkks....kkelpkekeek 154
                                   +I+ +    e + +  +++ + e++ +  ++++  sd +++++++ l+++k+ + ++++  + +++    k   + +k  +
  gi|13541058|ref|NP_110746.1|  81 RIRRTI---ERRGK--SISTDAEIERDGSIITRGASDVSNYVEKNVLNINKDVFLTSIFVRQGEMDalvsKDPAERKKILD 156
                                   666666...33333..3334445555566899**************************99999999997666666666667 PP

                        AAA_15 155 lekekeelkidkedlkklikkleeslkkeeelknvlksaiiklllisakRnvsdedsekkssllgklkekileealqekle 235
                                   + ++++ l+     lk++i++l+ +++ ++ lkn l+s+i +++ ++++ +  +++   +++ + +l e+i+ + ++   +
  gi|13541058|ref|NP_110746.1| 157 EILNIDRLEAGYLLLKEVIDDLTANVSDYDYLKNELQSKINEIDNNNKQIEELESKLRLIEPEIKALEEEINIKENK---K 234
                                   77899999999*******************99999999999999888888888888888888888888888876444...5 PP

                        AAA_15 236 eelteklkeiqeklkeidkklaeelk................kilkkki 268
                                   + l+e+l +++  l++i+k+ ++el+                 ++++ +
  gi|13541058|ref|NP_110746.1| 235 DHLNEELHRLNAQLETIKKY-EMELAesqsrkasiemevvklPSIEEEL 282
                                   66677777777777666555.4555534444444444444443333333 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.54
                        AAA_15  89 akeyektlkskekkkadlllkkkesdlkktikdkklklkknelsdekisvekkkskkelpkekeeklekekeelkidkedl 169
                                    +ey+ ++k+ ++ +   +++ ++sdl+k+ + +       +l++ + +  +kk++ke+ ++ +++l++++++++    ++
  gi|13541058|ref|NP_110746.1| 297 IIEYINLKKDLGSLS--EIIEGLKSDLSKYDEAHRKLE---DLQSFRSEFLEKKKRKEDLDKLRSSLKEDEDNYQSAVRNI 372
                                   344555555444444..479999999****99999985...5888888888899999999998888888888888886666 PP

                        AAA_15 170 kklikkleeslkkee...elknvlksaiiklllisakRnvsdedsekkssllgklkekileealqekl............. 234
                                   +++ k +e+  k+ e    + + + + ++ +  i + R ++ + s  + + +++ ++  ++  ++++              
  gi|13541058|ref|NP_110746.1| 373 ENIKKWIENEEKEIErmsAFISEILKIQEITPEIINSRRAEINSSLMQIEGKIASLNASIDA-MRSHKmeveenaamlsgr 452
                                   65555333333333355544455555555555566666666666666777777777777775.44444588899******* PP

                        AAA_15 235 .........................eeelteklkeiqeklkeidkklaeelk.......k 262
                                                              +l+e+++++++++k++d++ + ++k       k
  gi|13541058|ref|NP_110746.1| 453 gvcpvcgthlgteksedlvkhygeeASRLEEDINKTENEIKKLDEERKHQKKlldringK 512
                                   ***********9999999999999877889999999999999998874444444433331 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.0047
                        AAA_15  56 kvikiekedleifeniseskdikIdvefaek...ekakeyektlkskekkkadlllkkkesdlkktikdkklklkknelsd 133
                                   ++  +++  l+ +  is  ++i++   +a++    ka+  +++ + ++++++    ++k++     ++d +   +++e++ 
  gi|13541058|ref|NP_110746.1| 537 DEARLKEAHLKAEAAISQYNSIDLGDLEAKNeewLKANAVISSIDIENIRSRF---EEKNK----QLNDIIKRMNEIEVNI 610
                                   34444444455555555555555555552222334444444444444444443...33333....3344444444444555 PP

                        AAA_15 134 ekisvekkkskkelpkekeeklekekeelkid..kedlkklikkleeslkkee.......elknvlksaiiklllisakRn 205
                                     ++ ++++s k +++e ++ ++k++e + ++   ++++k+i+ ++e ++k++       e       ++++l+++ + ++
  gi|13541058|ref|NP_110746.1| 611 PDVESYNENSLKRIDEELNSLRNKKNELYAKKaaMDEIQKTIEHFKEEISKKKgiedsqaE------VNAQLLQINDDLKQ 685
                                   5556666667666666667777766666666677999999999999999888832222221......22222222222222 PP

                        AAA_15 206 vsdedsekkssllgklkekileealqekl.........eeelteklkeiqeklkeidkklaeelk..........kilkkk 267
                                    s+      +  ++++++  +                 +e+l+ +  +i + l++++ ++++ +           + +  +
  gi|13541058|ref|NP_110746.1| 686 LSS------RLDKINVDQYEW-------KslhkvllqdNEKLNIAVADIRKRLEKKETIIKAIADlkrvreafskDGVPAI 753
                                   222......122222222222.......12233334555555555555555555555555555555556666666555555 PP

                        AAA_15 268 idkikkfnykgkkneeieik...................ddeelplnknGsGvqrllllillileaekkdekeeknvilli 329
                                   i k+ ++ + +++ ++i+ +                    +    ++  + G + ++ ++l  + a+     +++  +l++
  gi|13541058|ref|NP_110746.1| 754 IRKSASEFITNQTRQYIQRFeldiddvdvdqdfnitvfrGGIAEGIDSLSGGERMAVAFALRVAIAQFL---NKDVSLLVM 831
                                   55555555666666666666777778888888888899999999*************************...9******** PP

                        AAA_15 330 EEPEahLHpqaqkvlikllkelandnkt..QviitTH 364
                                   +EP a L  +  + l++ +   ++d+++  Qvi+ +H
  gi|13541058|ref|NP_110746.1| 832 DEPTAFLDEDRRSDLANIIEYSLKDSSGipQVIMISH 868
                                   *****************999999999999****9999 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.0   0.00067      0.63      18      38 ..      25      45 ..      17      64 .. 0.87
   2 !    9.5  12.5   0.00035      0.33     348     458 ..     145     253 ..      63     264 .. 0.81
   3 !   19.1  12.4   4.4e-07   0.00041     280     444 ..     326     504 ..     310     512 .. 0.75
   4 !   20.4  14.0   1.9e-07   0.00018     327     578 ..     614     877 ..     607     889 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00067
                        AAA_13 18 iNliYGwNGaGKTtLSrllrs 38
                                  iN+i G+NGaGK+++  ++r 
  gi|13541058|ref|NP_110746.1| 25 INMIIGQNGAGKSSIVDAIRF 45
                                  8**************999986 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00035
                        AAA_13 348 rkepfksvelesvkakiesikklvaeineliakhNekvanleeekeeakkklelhlveeleseldeykkkykklekaiekl 428
                                    k+p+++ ++ +   +i++++     ++e+i +  + v++++  k+e+++k+    + + +++++e+++k++ +e +i+ l
  gi|13541058|ref|NP_110746.1| 145 SKDPAERKKILDEILNIDRLEAGYLLLKEVIDDLTANVSDYDYLKNELQSKINE--IDNNNKQIEELESKLRLIEPEIKAL 223
                                   4678888888888888999999999999***********************998..888999******************* PP

                        AAA_13 429 ekelkeeeaelkkleeeikeLekqlrdekp 458
                                   e+e++ +e+++  l+ee   L +ql+++k+
  gi|13541058|ref|NP_110746.1| 224 EEEINIKENKKDHLNEELHRLNAQLETIKK 253
                                   ************************999887 PP

  == domain 3  score: 19.1 bits;  conditional E-value: 4.4e-07
                        AAA_13 280 efeekqerLekliekveskkselleklkavsdeasensafeedkeelkaeaealeeqLkglqraleaKrkepfksvelesv 360
                                   e ++k e+L++  ++ ++kk+  +e l    +  s  ++ e++++ + +++e++++++++ ++++e+    +++ ++++++
  gi|13541058|ref|NP_110746.1| 326 EAHRKLEDLQSFRSEFLEKKK-RKEDL---DKLRSSLKEDEDNYQSAVRNIENIKKWIENEEKEIERMSAFISEILKIQEI 402
                                   233334444444445544442.33444...3444455667888999999******************************** PP

                        AAA_13 361 kaki.....esikklvaeineliakhNekvanleeekeeakkklelhlv.............eeleseldeykkkykklek 423
                                   +++i      +i++++ +i+  ia+ N+ ++ + + k e++++                   e+ e+ +++y ++ ++le+
  gi|13541058|ref|NP_110746.1| 403 TPEIinsrrAEINSSLMQIEGKIASLNASIDAMRSHKMEVEENAAMLSGrgvcpvcgthlgtEKSEDLVKHYGEEASRLEE 483
                                   ****8877779****************************999988877678888888888887777888888888888888 PP

                        AAA_13 424 aieklekelkeeeaelkklee 444
                                   +i+k+e+e+k+  +e k  ++
  gi|13541058|ref|NP_110746.1| 484 DINKTENEIKKLDEERKHQKK 504
                                   888888888887777766554 PP

  == domain 4  score: 20.4 bits;  conditional E-value: 1.9e-07
                        AAA_13 327 kaeaealeeqLkglqraleaKrkepfk.svelesvkakiesikklvae...ineliakhNekvanleeekeeakkklelhl 403
                                   ++  e+  +++++  + l +K++e+ + ++ ++++++ ie++k+++++   i+++ a+ N++  +++++ +++ + l +  
  gi|13541058|ref|NP_110746.1| 614 ESYNENSLKRIDEELNSLRNKKNELYAkKAAMDEIQKTIEHFKEEISKkkgIEDSQAEVNAQLLQINDDLKQLSSRLDKIN 694
                                   5556667788999999999999999775888*********99999876555889999999999999999999999999999 PP

                        AAA_13 404 veeleseldeyk....kkykklekaieklekelkeeeaelkkleeeikeLekqlrd.....ekpaaee.inkeLkafGlge 474
                                   v ++e +   ++    ++ +kl+ a+ +  k+l+++e+ +k++++  +  e+  +d     ++++a+e i+++ +++ +++
  gi|13541058|ref|NP_110746.1| 695 VDQYEWK--SLHkvllQDNEKLNIAVADIRKRLEKKETIIKAIADLKRVREAFSKDgvpaiIRKSASEfITNQTRQY-IQR 772
                                   9877533..44422236777777777777777777777777777665555555666333333445544489999999.*** PP

                        AAA_13 475 leLkfeee..kkgYrivrkggsqaa..etLSeGEktaIaflYFlkslkeddseigkdkivviDDPvSSLDsnslfivfsli 551
                                   +eL++ +   ++ ++i+  +g  a+  ++LS GE+ a+af   ++  +  +++       v+D P   LD +     ++ i
  gi|13541058|ref|NP_110746.1| 773 FELDIDDVdvDQDFNITVFRGGIAEgiDSLSGGERMAVAFALRVAIAQFLNKD---VSLLVMDEPTAFLDEDRRSDLANII 850
                                   *****98888899999887776665569************9888888833344...4789********************* PP

                        AAA_13 552 ksrllkkkkakQlfiLTHnleffkevk 578
                                   +  l++++ + Q++   H+ e++   +
  gi|13541058|ref|NP_110746.1| 851 EYSLKDSSGIPQVIMISHHRELLSASD 877
                                   ***98**************99886655 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 !   30.6   0.0   2.2e-10     2e-07       2      52 ..       4      53 ..       3      56 .. 0.89

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 2.2e-10
                        AAA_29  2 krlqlvNWgtfdghtieidlkgatlltGpsGsGKSTllDAiqalLvpakkv 52
                                  +r++l N  + ++ +i +d  g+ +++G++G+GKS+++DAi + L ++k++
  gi|13541058|ref|NP_110746.1|  4 ERIRLRNFLSHSDSDIYFD-TGINMIIGQNGAGKSSIVDAIRFALFSDKRT 53
                                  68899999999999999*9.779**********************998854 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 ?   -0.6   0.1       1.3   1.2e+03      37      49 ..     188     200 ..     187     203 .. 0.69
   2 ?   -2.0   0.2       3.5   3.3e+03      38      46 ..     206     214 ..     193     220 .. 0.58
   3 !   30.6   0.0   2.4e-10   2.3e-07       5      51 ..     439     484 ..     435     485 .. 0.90
   4 ?   -2.4   0.2       4.7   4.4e+03       3      16 ..     650     663 ..     648     667 .. 0.71

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 1.3
                                   HHHHHHHHHHHHH CS
                 Rad50_zn_hook  37 Likelqsklerlp 49 
                                   L +elqsk++++ 
  gi|13541058|ref|NP_110746.1| 188 LKNELQSKINEID 200
                                   5677888887765 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.5
                                   HHHHHHHHH CS
                 Rad50_zn_hook  38 ikelqskle 46 
                                   i+el+skl+
  gi|13541058|ref|NP_110746.1| 206 IEELESKLR 214
                                   455555555 PP

  == domain 3  score: 30.6 bits;  conditional E-value: 2.4e-10
                                   HHHHHHHHHHHTT-SEE-TTT--EE-HHHHHHHHHHHHHHHHHHH.. CS
                 Rad50_zn_hook   5 teelnkkieelkeakgcCPlCgReldeehrseLikelqsklerlpee 51 
                                   + e ++++ +l+ ++  CP+Cg  l++e+ ++L+k++ ++  rl+e 
  gi|13541058|ref|NP_110746.1| 439 KMEVEENAAMLSGRG-VCPVCGTHLGTEKSEDLVKHYGEEASRLEED 484
                                   5678899*****999.****************************996 PP

  == domain 4  score: -2.4 bits;  conditional E-value: 4.7
                                   HHHHHHHHHHHHHT CS
                 Rad50_zn_hook   3 qeteelnkkieelk 16 
                                   +++e +++ i++ k
  gi|13541058|ref|NP_110746.1| 650 KTIEHFKEEISKKK 663
                                   67888888888766 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.1     1e-09   9.8e-07       1     100 [.       1      98 [.       1     123 [. 0.85
   2 ?   -2.4   0.1       3.1   2.9e+03     174     174 ..     229     229 ..     166     275 .. 0.60
   3 ?   -2.4   0.2       3.2     3e+03     158     198 ..     327     366 ..     309     374 .. 0.71
   4 ?   -1.8   0.5       2.1   1.9e+03     135     199 ..     532     598 ..     469     606 .. 0.64
   5 ?    2.7   0.4     0.089        84     155     196 ..     621     661 ..     616     700 .. 0.81

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 1e-09
                        AAA_27   1 MrlerLdLeryGkftdrsldfsaeeadlhliyGpNEAGKstalrAisdllfGip..ertkdnflhdakkLrigavleeadg 79 
                                   M +er++L+ + + +d+ + f+   +++ +i+G N AGKs++++Ai+  lf+ +  +rt+d     ++ ++++  + +++g
  gi|13541058|ref|NP_110746.1|   1 MIIERIRLRNFLSHSDSDIYFD---TGINMIIGQNGAGKSSIVDAIRFALFSDKrtRRTEDMIKKGERYMEVELYF-RSEG 77 
                                   99*******************8...8*************************965215677777888899******9.8899 PP

                        AAA_27  80 eelefaRrkgrkktlldaddq 100
                                   ++ +++R  +r+ + +++d +
  gi|13541058|ref|NP_110746.1|  78 HSYRIRRTIERRGKSISTDAE 98 
                                   999**9998777666665554 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 3.1
                        AAA_27 174 k 174
                                    
  gi|13541058|ref|NP_110746.1| 229 I 229
                                   2 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 3.2
                        AAA_27 158 lrevleaLeaeadelfkprkskkrainealeeleeakkelr 198
                                    ++ le+L++ ++e+ +++k+k+  + + +++l+e + +++
  gi|13541058|ref|NP_110746.1| 327 AHRKLEDLQSFRSEFLEKKKRKE-DLDKLRSSLKEDEDNYQ 366
                                   55667777777777777777777.77777777777666555 PP

  == domain 4  score: -1.8 bits;  conditional E-value: 2.1
                        AAA_27 135 ealleaegelgqlLfeasaGlaslrev.leaLeaeadelfkprkskk.rainealeeleeakkelre 199
                                   ++ ++ e +l ++ ++a+a++++ +++ l +Lea+ +e+ k ++  +   i + ++++ee +k+l++
  gi|13541058|ref|NP_110746.1| 532 KKFMDDEARLKEAHLKAEAAISQYNSIdLGDLEAKNEEWLKANAVISsIDIENIRSRFEEKNKQLND 598
                                   4455566666666677777777776664566777777777766665545666666777777666665 PP

  == domain 5  score: 2.7 bits;  conditional E-value: 0.089
                        AAA_27 155 laslrevleaLeaeadelfkprkskkrainealeeleeakke 196
                                   l+++ e l++L+++++el++++++ + +i+++ e+++e  ++
  gi|13541058|ref|NP_110746.1| 621 LKRIDEELNSLRNKKNELYAKKAAMD-EIQKTIEHFKEEISK 661
                                   67788889999999999999999998.888887777765544 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 !   23.3   0.1   6.1e-08   5.8e-05      24      88 ..     793     850 ..     764     852 .. 0.77

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 6.1e-08
                       SbcCD_C  24 kelsrssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllell 88 
                                   + + + + +lSGGe+ +++++al  a+a+ +++      +++l+++DE  + lDe++++ l +++
  gi|13541058|ref|NP_110746.1| 793 GGIAEGIDSLSGGER-MAVAFALRVAIAQFLNK------DVSLLVMDEPTAFLDEDRRSDLANII 850
                                   346778999******.*************9999......69*****************9999876 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   4.9   4.3e-08     4e-05       1     213 [.      25     234 ..      25     258 .. 0.65
   2 ?   -1.7   1.2       2.1   1.9e+03     141     202 ..     303     368 ..     278     419 .. 0.51
   3 ?   -1.9   4.5       2.4   2.3e+03      87     214 ..     471     602 ..     462     623 .. 0.84
   4 !   13.1   7.1   6.7e-05     0.063      84     302 ..     604     873 ..     575     874 .. 0.62

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 4.3e-08
                        AAA_21   1 lnvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeieeflsqgvryryglrlers 81 
                                   +n++iG Ng+GKS++ da++++ + d+  +++ d   +g  + +++ ++++   +++++ +ie    +++  + +++ + s
  gi|13541058|ref|NP_110746.1|  25 INMIIGQNGAGKSSIVDAIRFALFSDKRTRRTEDMIKKGERYMEVELYFRSEGHSYRIRRTIE-RRGKSISTDAEIERDGS 104
                                   79********************99888888888888888888888888888888888888888.66666666666666666 PP

                        AAA_21  82 qv.eeklssvetllesgllldkrsleeedvfnpeargirggvsvfslkelsvsepndlqfgkaltditsrawsllllldgl 161
                                   ++ +    +++ +++  l  +k++     ++ + + ++ + +++ ++k ++ ++ n++  ++ ++++++ +++l  +  + 
  gi|13541058|ref|NP_110746.1| 105 IItRGASDVSNYVEKNVLNINKDVFLTSIFVRQGEMDALVSKDPAERKKILDEILNIDRLEAGYLLLKEVIDDLTANVSDY 185
                                   665555555555555555555555555555555555555555555555555555555555555555555555555555443 PP

                        AAA_21 162 rkerigllnifadyfgfakekrllqrlvrslklveielsdlgegeeliasvd 213
                                      + + ++++ +    +++++++++l+++l+l+e+e+ +l+e ++  +  +
  gi|13541058|ref|NP_110746.1| 186 ---DYLKNELQSKINEIDNNNKQIEELESKLRLIEPEIKALEEEINIKENKK 234
                                   ...5555555555556666666666666666666666666665555544444 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.1
                        AAA_21 141 gkaltditsrawsllllldglrke....rigllnifadyfgfakekrllqrlvrslklveielsdl 202
                                    k  + + s++ + l+++ + ++e      +l+++  +++ ++k+k+ l++l +slk++e++++  
  gi|13541058|ref|NP_110746.1| 303 LKKDLGSLSEIIEGLKSDLSKYDEahrkLEDLQSFRSEFLEKKKRKEDLDKLRSSLKEDEDNYQSA 368
                                   444444444444444444444444444333333333333333333333333333333333333333 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 2.4
                        AAA_21  87 lssvetllesgllldkrsleeedvfnpeargirggvsvfslkelsvsepndlqfgkaltditsrawsllllldglrke... 164
                                   ++++++  ++ + + ++ ++e+++ + e ++++++++    k  ++ +++ +  ++ + +++++ ++ + l+++ +k+   
  gi|13541058|ref|NP_110746.1| 471 VKHYGEEASRLEEDINKTENEIKKLDEERKHQKKLLDRINGKDVERLIASYNLLSSKRAELKKFMDDEARLKEAHLKAeaa 551
                                   567777888888999999999999999999999999999999999999999999999999999999999999999999997 PP

                        AAA_21 165 .rigllnifadyfgfakekrllqrlvrslklveielsdlgegeeliasvde 214
                                       +  + +d+  +++e+  +   ++s++  +i+ +++++ ++l++ +++
  gi|13541058|ref|NP_110746.1| 552 iSQYNSIDLGDLEAKNEEWLKANAVISSIDIENIRSRFEEKNKQLNDIIKR 602
                                   777777777888888888888888888888888888888888888777765 PP

  == domain 4  score: 13.1 bits;  conditional E-value: 6.7e-05
                        AAA_21  84 eeklssvetllesgllldkrsleeedvfnpeargirggvsvfslkelsvsepndlqfgkaltditsrawsllllldglrke 164
                                    e   + +++++  + + kr++ee +   +++ + ++ +    +++++++ + +++++k  ++++   + + ll+ +  + 
  gi|13541058|ref|NP_110746.1| 604 NEIEVNIPDVESYNENSLKRIDEELNSLRNKKNELYAKKAAMDEIQKTIEHFKEEISKKKGIEDSQAEVNAQLLQINDDL- 683
                                   55555555556666666666666666666666666666666666666666666666666666655555555554444333. PP

                        AAA_21 165 rigllnifadyfgfakekrllqrlvrslklveielsdlgegeeliasvderlrer.......................... 219
                                   + +  ++ + ++ +++ k l + l+    + +i + d++++ e+ ++++ ++ +                           
  gi|13541058|ref|NP_110746.1| 684 KQLSSRLDKINVDQYEWKSLHKVLLQDNEKLNIAVADIRKRLEKKETIIKAIADLkrvreafskdgvpaiirksasefitn 764
                                   333333333333333333333333333333333333333333333333333222244456666667777777777777777 PP

                        AAA_21 220 ....................gvvflengdgqelparelSdGtkrll..alltallralkkg.sllliDEpEngLHPkllrr 277
                                                       ++ + +  +g    +++lS G + +   al +a+++ l k+ sll+ DEp ++L+  + + 
  gi|13541058|ref|NP_110746.1| 765 qtrqyiqrfeldiddvdvdqDFNITVFRGGIAEGIDSLSGGERMAVafALRVAIAQFLNKDvSLLVMDEPTAFLDEDRRSD 845
                                   88888888999999999999***********************9953588888888888889******************* PP

                        AAA_21 278 llell...kelsr...ngaQviltTHSplll 302
                                   l+ ++       +   +  Qvi+ +H  +ll
  gi|13541058|ref|NP_110746.1| 846 LANIIeysL---KdssGIPQVIMISHHRELL 873
                                   *****6442...335679********98887 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 !   19.2  10.0   1.2e-06    0.0011       7      76 ..     199     268 ..     193     278 .. 0.90
   2 ?    2.4   5.1      0.18   1.7e+02      28      87 ..     275     335 ..     265     360 .. 0.72
   3 ?   -0.8   4.6       1.9   1.8e+03       5      78 ..     363     437 ..     350     445 .. 0.66
   4 ?   -0.7   8.1       1.7   1.6e+03       9      51 ..     466     508 ..     460     605 .. 0.78
   5 ?   -1.3   0.2       2.7   2.5e+03      54      78 ..     591     615 ..     575     631 .. 0.56
   6 ?   -0.2  11.5       1.2   1.1e+03      19      82 ..     629     692 ..     608     744 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.2e-06
                   TMF_TATA_bd   7 agpsvqlverlsseirrlEgElaslkeelerleaerdeareeivklmkeneelkelkkeleelekeleel 76 
                                     ++ + +e+l+s++r  E E+++l+ee++  e+++d ++ee+ +l ++ e+ k+++ el+e +++ +++
  gi|13541058|ref|NP_110746.1| 199 IDNNNKQIEELESKLRLIEPEIKALEEEINIKENKKDHLNEELHRLNAQLETIKKYEMELAESQSRKASI 268
                                   5688899*****************************************************9999876555 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.18
                   TMF_TATA_bd  28 laslkeelerleaerdea.reeivklmkeneelkelkkeleelekeleelqeryetlLell 87 
                                   l s++eel+rle++   + r+ei++ ++   +l +l++ +e l++ l++ +e + +l  l 
  gi|13541058|ref|NP_110746.1| 275 LPSIEEELKRLENNAAVVkRNEIIEYINLKKDLGSLSEIIEGLKSDLSKYDEAHRKLEDLQ 335
                                   4567899999998887653789*********************998888777776654444 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 1.9
                   TMF_TATA_bd   5 ssagpsvqlverlsseirrlEgElaslkeelerleaerdeareeivklm..keneelkelkkeleelekeleelqe 78 
                                    + ++ v+ +e++++ i   E E++ +   ++++ + ++ ++ ei++    + n +l + ++++++l+++++++++
  gi|13541058|ref|NP_110746.1| 363 DNYQSAVRNIENIKKWIENEEKEIERMSAFISEILKIQE-ITPEIINSRraEINSSLMQIEGKIASLNASIDAMRS 437
                                   456667777777777788888888888777777777754.455555544224466677777777777777777665 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 1.7
                   TMF_TATA_bd   9 psvqlverlsseirrlEgElaslkeelerleaerdeareeivk 51 
                                   +s  lv++ + e  rlE +++++++e+++l +er+  ++ + +
  gi|13541058|ref|NP_110746.1| 466 KSEDLVKHYGEEASRLEEDINKTENEIKKLDEERKHQKKLLDR 508
                                   5667788888888888888888888888888888776554433 PP

  == domain 5  score: -1.3 bits;  conditional E-value: 2.7
                   TMF_TATA_bd  54 keneelkelkkeleelekeleelqe 78 
                                   ++n +l++  k+++e+e ++ ++++
  gi|13541058|ref|NP_110746.1| 591 EKNKQLNDIIKRMNEIEVNIPDVES 615
                                   3444444444444444444444444 PP

  == domain 6  score: -0.2 bits;  conditional E-value: 1.2
                   TMF_TATA_bd  19 seirrlEgElaslkeelerleaerdeareeivklmkeneelkelkkeleelekeleelqeryet 82 
                                    ++r + +El + k  + ++++  +  +eei k     ++++e +++l +++  l++l++r+++
  gi|13541058|ref|NP_110746.1| 629 NSLRNKKNELYAKKAAMDEIQKTIEHFKEEISKKKGIEDSQAEVNAQLLQINDDLKQLSSRLDK 692
                                   4567777777777777777777777777777777777777777777777777777777777665 PP

>> Fez1  Fez1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6  19.5   2.2e-06    0.0021      19     161 ..     171     340 ..     169     349 .. 0.78
   2 ?   -2.6  22.2       6.6   6.2e+03      26     164 ..     344     501 ..     341     605 .. 0.85
   3 ?    0.2  15.4      0.96     9e+02      39     141 ..     595     694 ..     562     768 .. 0.52

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2.2e-06
                          Fez1  19 Lkdsqaevtqklseivalkaqlrelrakleekeeeikeleesleektlelevcenelqrkkseaellrekvekleeelkel 99 
                                   Lk++  ++t+ +s++  lk++l+   +++++++++i+ele++l+  + e++ +e+e++ k+++++ l+e++++l+++l+ +
  gi|13541058|ref|NP_110746.1| 171 LKEVIDDLTANVSDYDYLKNELQSKINEIDNNNKQIEELESKLRLIEPEIKALEEEINIKENKKDHLNEELHRLNAQLETI 251
                                   89999**************************************************************************** PP

                          Fez1 100 reelselsleeeeaa..................lesdeakaqrqe.......aeeleelkreverlraeLkeerqk..kee 153
                                   ++   el+++++++a                  le ++a ++r+e       +++l++l++ +e l++ L++  ++  k e
  gi|13541058|ref|NP_110746.1| 252 KKYEMELAESQSRKAsiemevvklpsieeelkrLENNAAVVKRNEiieyinlKKDLGSLSEIIEGLKSDLSKYDEAhrKLE 332
                                   996555554444433578888887776666665455555555555888998888999999999999999987554400333 PP

                          Fez1 154 qassFeqE 161
                                     +sF +E
  gi|13541058|ref|NP_110746.1| 333 DLQSFRSE 340
                                   44555555 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 6.6
                          Fez1  26 vtqklseivalkaqlrelrakleekeeeikeleesleektlelevcenelqrkkseaellrekvekleeelkelreelsel 106
                                     ++ +++ +l+++l+e + + ++  ++i+++++ +e+ ++e+e++ + +++  + +e++ e +++  +e+++   +++ +
  gi|13541058|ref|NP_110746.1| 344 KKKRKEDLDKLRSSLKEDEDNYQSAVRNIENIKKWIENEEKEIERMSAFISEILKIQEITPEIINSRRAEINSSLMQIEGK 424
                                   5678888889************************************99999997777777777777777776655555554 PP

                          Fez1 107 sleeeeaalesdeakaqrqe...................aeeleelkreverlraeLkeerqkkeeqassFeqERrt 164
                                    ++ + ++ +++++k++ +e                   +e++e+l ++  +  ++L+e+ +k+e++ ++ ++ER+ 
  gi|13541058|ref|NP_110746.1| 425 IASLNASIDAMRSHKMEVEEnaamlsgrgvcpvcgthlgTEKSEDLVKHYGEEASRLEEDINKTENEIKKLDEERKH 501
                                   44444444444444444444567899999999999999988888888888888888888888888888999999876 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.96
                          Fez1  39 qlrelrakleekeeeikeleesleektlelevcenelqrkkseaellrekvekleeelkelreelselsleeeeaa..... 114
                                   ql ++ ++++e e +i ++e+  e+  + +++  n l++kk+e   ++  ++++++ +++++ee+s+++  e+++a     
  gi|13541058|ref|NP_110746.1| 595 QLNDIIKRMNEIEVNIPDVESYNENSLKRIDEELNSLRNKKNELYAKKAAMDEIQKTIEHFKEEISKKKGIEDSQAevnaq 675
                                   222222333333333333333333333333333333334455555555555666666666666666644332222222233 PP

                          Fez1 115 ....lesdeakaqrqeaeeleelkreverlr 141
                                       +            ++l++l++++++++
  gi|13541058|ref|NP_110746.1| 676 llqiN------------DDLKQLSSRLDKIN 694
                                   32220............22333333332222 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00012      0.12      15      32 ..      27      44 ..      21      96 .. 0.92
   2 ?    7.8  10.5    0.0046       4.4      96     137 .]     781     836 ..     393     836 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00012
                                  EEEESTTSSHHHHHHHHT CS
                                  xxxxxxxxxxxxxxxxxx RF
                      ABC_tran 15 aivGenGaGKStLlklla 32
                                   i+G+nGaGKS+++ ++ 
  gi|13541058|ref|NP_110746.1| 27 MIIGQNGAGKSSIVDAIR 44
                                  69************9985 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0046
                                   G.........TTCBGESTTSGGS-HHHHH......HHHHHHHHHHTSSEEEEESTTT CS
                                   x.........xxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  96 e.........lkdtvvksspssLSgGqkq......rvalarallkkpkllllDEpta 137
                                   +         ++  ++ ++  sLSgG++       rva+a+ l k+ +ll++DEpta
  gi|13541058|ref|NP_110746.1| 781 DvdqdfnitvFRGGIA-EGIDSLSGGERMavafalRVAIAQFLNKDVSLLVMDEPTA 836
                                   1333433332555554.6669*******988888999******************97 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00014      0.13      98     137 ..      22      63 ..      14      76 .. 0.81
   2 ?   -1.6   0.5       2.3   2.1e+03      50      82 ..     228     261 ..     194     291 .. 0.64
   3 ?   -1.5   0.2       2.2   2.1e+03      55      99 ..     318     360 ..     303     363 .. 0.81
   4 ?   -0.7   0.1       1.2   1.2e+03      61      98 ..     592     629 ..     570     635 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00014
                                   TTSEEEEECSTTSSHHHHHHHHCTT-..----S--------- CS
                   RsgA_GTPase  98 kdktsvlvGqSGvGKStLinallpel..elktgevseklgrG 137
                                   +  + +++Gq G+GKS++++a++  l  + +t+ + +  ++G
  gi|13541058|ref|NP_110746.1|  22 DTGINMIIGQNGAGKSSIVDAIRFALfsDKRTRRTEDMIKKG 63 
                                   557899***************998643377777777777777 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.3
                                   EEEEE-GGG--HHH.HHHHHHHHHHHTTSEEEE- CS
                   RsgA_GTPase  50 vivlnKiDlleeee.eleelkeelealgyevllv 82 
                                    i  nK D l+ee  +l+++ e+++++++e+   
  gi|13541058|ref|NP_110746.1| 228 NIKENKKDHLNEELhRLNAQLETIKKYEMELAES 261
                                   3444677777666545555555555555554444 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 2.2
                                   -GGG--HHHHHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHHCTT CS
                   RsgA_GTPase  55 KiDlleeeeeleelkeelealgyevllvsaktkegleelkellkd 99 
                                   K Dl + +e +++  e+l+++  e+l   +k+ke+l++l++ lk+
  gi|13541058|ref|NP_110746.1| 318 KSDLSKYDE-AHRKLEDLQSFRSEFLEK-KKRKEDLDKLRSSLKE 360
                                   788888888.888888899998887776.5559999**9999986 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 1.2
                                   HHHHHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHHCT CS
                   RsgA_GTPase  61 eeeeleelkeelealgyevllvsaktkegleelkellk 98 
                                   ++++l+++ ++++++++++  v++ ++++l+++ e+l+
  gi|13541058|ref|NP_110746.1| 592 KNKQLNDIIKRMNEIEVNIPDVESYNENSLKRIDEELN 629
                                   334799999***********999999999999999987 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2  16.8    0.0011         1     149     259 ..     162     271 ..     153     311 .. 0.61
   2 ?    9.9  12.0   0.00032       0.3     157     254 ..     302     400 ..     282     421 .. 0.75
   3 ?    0.0   6.9      0.33   3.1e+02     215     276 ..     464     522 ..     405     528 .. 0.50
   4 ?    6.5  11.8    0.0035       3.3     146     276 ..     512     636 ..     500     638 .. 0.82
   5 ?    5.8  16.4    0.0057       5.4     143     259 ..     623     744 ..     618     766 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0011
                          Spc7 149 egleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeql 229
                                   + le+ + lL++  + l++ + +++  k+el+++++++ + ++++e+++  +L+ +  e+++l++ei+ k+++ + l+e+l
  gi|13541058|ref|NP_110746.1| 162 DRLEAGYLLLKEVIDDLTANVSDYDYLKNELQSKINEIDNNNKQIEELE-SKLRLIEPEIKALEEEINIKENKKDHLNEEL 241
                                   5566666667777777777777777777777777777777777776654.4567777777777777777777777777777 PP

                          Spc7 230 eeleekieelkeqkseleeeiaeaervlee 259
                                    +l++++e++k+   el e  +++ ++ +e
  gi|13541058|ref|NP_110746.1| 242 HRLNAQLETIKKYEMELAESQSRKASIEME 271
                                   777777777765555544444433333332 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00032
                          Spc7 157 lLekqeeeldellpelee...ekaeleeeleklqeaaeelesid..keeLeelreelaelkaeieekkkelaelqeqleel 232
                                   +L+k+   l+e+ + l++   +++e +++le+lq+++ e+ + +  ke+L +lr++l+e + ++++  +++++ ++ +e+ 
  gi|13541058|ref|NP_110746.1| 302 NLKKDLGSLSEIIEGLKSdlsKYDEAHRKLEDLQSFRSEFLEKKkrKEDLDKLRSSLKEDEDNYQSAVRNIENIKKWIENE 382
                                   56666666666666666422267799999999**9888875533369********************************** PP

                          Spc7 233 eekieelkeqkseleeeiaeae 254
                                   e++ie +++ +se+ +     +
  gi|13541058|ref|NP_110746.1| 383 EKEIERMSAFISEILK----IQ 400
                                   ****888666666554....33 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 0.33
                          Spc7 215 ieekkkelaelqeqleeleekieelkeqkseleeeiaeaervleeckgwsesevsrlkeevk 276
                                    e+ ++ ++   e+  +lee+i+++++++++l ee ++++++l+   +++ ++v+rl ++++
  gi|13541058|ref|NP_110746.1| 464 TEKSEDLVKHYGEEASRLEEDINKTENEIKKLDEERKHQKKLLD---RINGKDVERLIASYN 522
                                   34444455566667777777777777777777777777777766...555566666666655 PP

  == domain 4  score: 6.5 bits;  conditional E-value: 0.0035
                          Spc7 146 enlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelq 226
                                   + +e l + ++lL+++++el+++++     +a+l+e + k ++a  + +sid  +Le+  ee  +++a i+  + ++++ +
  gi|13541058|ref|NP_110746.1| 512 KDVERLIASYNLLSSKRAELKKFMD----DEARLKEAHLKAEAAISQYNSIDLGDLEAKNEEWLKANAVIS--SIDIENIR 586
                                   5567777777777777777766554....456677777777777888899*********************..89****** PP

                          Spc7 227 eqleeleekieelkeqkseleeeiaeaervleeckgwsesevsrlkeevk 276
                                   ++ ee++++++++ ++++e+e +i   e++ e+  +  ++e+++l+++ +
  gi|13541058|ref|NP_110746.1| 587 SRFEEKNKQLNDIIKRMNEIEVNIPDVESYNENSLKRIDEELNSLRNKKN 636
                                   *********************************99999999999998755 PP

  == domain 5  score: 5.8 bits;  conditional E-value: 0.0057
                          Spc7 143 gleenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeeles..id.keeLeelreelaelkaeieekkk 220
                                   +++e+l++l++ k++L ++++ +de+ + +e+ k+e++++   + ++ae +++  ++ +++L++l ++l++++++  e k 
  gi|13541058|ref|NP_110746.1| 623 RIDEELNSLRNKKNELYAKKAAMDEIQKTIEHFKEEISKKKGIEDSQAE-VNAqlLQiNDDLKQLSSRLDKINVDQYEWKS 702
                                   578999*******************************999877776444.333346679***************9999999 PP

                          Spc7 221 elaelqeqleeleekieelk...eqkseleeeiaeaervlee 259
                                    ++ l ++ e+l+ ++++++   e+k+++ ++ia  +rv+e+
  gi|13541058|ref|NP_110746.1| 703 LHKVLLQDNEKLNIAVADIRkrlEKKETIIKAIADLKRVREA 744
                                   999988888888888887772225666777777777777775 PP

>> Mac  Maltose acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.48   4.6e+02      37      49 ..     147     159 ..     132     161 .. 0.89
   2 ?    5.5   1.7     0.021        20      15      39 ..     494     513 ..     488     573 .. 0.78
   3 ?   -2.3   0.1       5.8   5.5e+03       8      26 ..     616     638 ..     614     641 .. 0.74

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.48
                                   -HHHHHHHHHHHS CS
                           Mac  37 dkdeRrelLrell 49 
                                   d++eR+++L e+l
  gi|13541058|ref|NP_110746.1| 147 DPAERKKILDEIL 159
                                   899*********9 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.021
                                   HHHHHHHHHHHHHHHHHTSTTT-HH CS
                           Mac  15 eLvaeRlrarelcrryNqtrpsdkd 39 
                                   +L +eR++ ++l+ r N      kd
  gi|13541058|ref|NP_110746.1| 494 KLDEERKHQKKLLDRING-----KD 513
                                   799999999999999993.....22 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 5.8
                                   BETTT....SHHHHHHHHHHHHH CS
                           Mac   8 Ydafs....DpeLvaeRlrarel 26 
                                   Y+++s    D+eL  +R +  el
  gi|13541058|ref|NP_110746.1| 616 YNENSlkriDEELNSLRNKKNEL 638
                                   77766777789999999887665 PP

>> AFP_2  Bacterial antifreeze protein repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   1.2      0.04        38      18      37 ..     182     201 ..     175     204 .. 0.89
   2 ?    6.7   0.2     0.009       8.5      22      39 ..     359     376 ..     355     377 .. 0.90
   3 ?   -2.5   0.0       6.7   6.3e+03      24      35 ..     644     655 ..     640     659 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.04
                         AFP_2  18 kadyyanvdniQnkvsnFEN 37 
                                   ++dy++ ++++Q+k+++ +N
  gi|13541058|ref|NP_110746.1| 182 VSDYDYLKNELQSKINEIDN 201
                                   79*************99887 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.009
                         AFP_2  22 yanvdniQnkvsnFENIK 39 
                                   + + dn Q+ v n ENIK
  gi|13541058|ref|NP_110746.1| 359 KEDEDNYQSAVRNIENIK 376
                                   5789*************9 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 6.7
                         AFP_2  24 nvdniQnkvsnF 35 
                                     d+iQ+ ++ F
  gi|13541058|ref|NP_110746.1| 644 AMDEIQKTIEHF 655
                                   5799*****999 PP

>> Dynein_C  Dynein heavy chain C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.9      0.63   5.9e+02      36      85 ..     205     254 ..     152     333 .. 0.70
   2 ?   10.8   1.5   0.00021       0.2      17     122 ..     658     757 ..     624     778 .. 0.62

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.63
                                   ----------.....----..........-HHHHHHHHHHHHHHHHHHHHHHH CS
                      Dynein_C  36 laadileklp...elfdleeaekkpteyeeplntvllqElerfnkLleeirrs 85 
                                    ++++ +kl    +  +++ a +++ + +e  +  l  El+r+n+ le+i++ 
  gi|13541058|ref|NP_110746.1| 205 QIEELESKLRlieP--EIK-ALEEEINIKENKKDHLNEELHRLNAQLETIKKY 254
                                   33333333331111..222.112245566666667777777777777777764 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00021
                                   TTT-------..CCH--------------........----..........-HHHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                      Dynein_C  17 ressssgsggssreekvlelaadileklpe......lfdleeaekkpteyeeplntvllqElerfnkLleeirrsLkelqk 91 
                                   + s+++g   ++++ +v++ + +i + l +      ++++      ++ + ++l  vllq  e++n  ++ ir+ L++ + 
  gi|13541058|ref|NP_110746.1| 658 EISKKKG--IEDSQAEVNAQLLQINDDLKQlssrldKINV------DQYEWKSLHKVLLQDNEKLNIAVADIRKRLEKKET 730
                                   2221111..1112223333333333333321111111243......466789**************************999 PP

                                   ---------HHHHHHHHHHHHTS--GGG.-- CS
                      Dynein_C  92 aikGevvmseeleelansllngkvPesWakk 122
                                    ik      ++l+ + ++++++ vP+  +k+
  gi|13541058|ref|NP_110746.1| 731 IIKA----IADLKRVREAFSKDGVPAIIRKS 757
                                   9993....46899999999999999987544 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.1    0.0015       1.4      25      51 ..      24      50 ..       4     254 .. 0.84
   2 ?   -1.5   0.2       3.1     3e+03     135     135 ..     347     347 ..     277     424 .. 0.57
   3 ?   -0.7   0.2       1.7   1.6e+03      44     127 ..     741     818 ..     650     847 .. 0.55

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0015
                        AAA_16 25 elvllsGesGvGKsslvrellralekd 51
                                  ++ +++G+ G GKss+v++++ al  d
  gi|13541058|ref|NP_110746.1| 24 GINMIIGQNGAGKSSIVDAIRFALFSD 50
                                  66789**************99777666 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 3.1
                        AAA_16 135 r 135
                                   r
  gi|13541058|ref|NP_110746.1| 347 R 347
                                   1 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 1.7
                        AAA_16  44 llralekdg.giflrgkcdqlesaipysalaqalareellrqlldeaesaeleawrekleeala.....avpelagaeasr 118
                                   +++a++kdg    +r  + ++        ++++  r ++++  + + +  +++ ++++  ++++      +++l+g e+ +
  gi|13541058|ref|NP_110746.1| 741 VREAFSKDGvPAIIRKSASEF--------ITNQT-R-QYIQRFELDID--DVDVDQDFNITVFRggiaeGIDSLSGGERMA 809
                                   333333333222233333333........23333.2.33333333311..2333333333333344444555555555555 PP

                        AAA_16 119 llellkrll 127
                                   ++ +l+ ++
  gi|13541058|ref|NP_110746.1| 810 VAFALRVAI 818
                                   555555555 PP

>> DYW_deaminase  DYW family of nucleic acid deaminases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1       3.7   3.5e+03      14      65 ..     336     389 ..     329     416 .. 0.59
   2 ?   -1.6   0.1       2.4   2.3e+03      27      62 ..     413     447 ..     374     479 .. 0.72
   3 ?   -1.2   0.1       1.9   1.8e+03      29      51 ..     593     616 ..     581     661 .. 0.68
   4 ?   10.2   1.1   0.00053       0.5      23      94 ..     674     738 ..     655     743 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 3.7
                 DYW_deaminase  14 kfasgdkahpeskeieekleelsqrl..lsigyapdlekalhdvkeeekekkpl 65 
                                   +f+s +    + ke  +kl++ +++    ++  + + e ++  +++eeke + +
  gi|13541058|ref|NP_110746.1| 336 SFRSEFLEKKKRKEDLDKLRSSLKEDedNYQSAVRNIENIKKWIENEEKEIERM 389
                                   566666666666666666666555542233444455566665666666644334 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.4
                 DYW_deaminase  27 eieekleelsqrllsigyapdlekalhdvkeeekek 62 
                                   ei+  l+++  ++ s+    +  +  h++++ee+  
  gi|13541058|ref|NP_110746.1| 413 EINSSLMQIEGKIASLNA-SIDAMRSHKMEVEENAA 447
                                   555666666666655543.34445567777777744 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 1.9
                 DYW_deaminase  29 eekleelsqrllsigya.pdleka 51 
                                   +++l+++++r+ +i +  pd+e+ 
  gi|13541058|ref|NP_110746.1| 593 NKQLNDIIKRMNEIEVNiPDVESY 616
                                   457899999999998877777654 PP

  == domain 4  score: 10.2 bits;  conditional E-value: 0.00053
                 DYW_deaminase  23 peskeieekleelsqrllsigyapdlekalhdvkeeekekkplllsHsEKlalaygllktesg.aqiriiknl 94 
                                    + ++i++ l++ls rl +i + +  +k lh+v  + +ek  l       +a+a+++ ++e++ + i++i  l
  gi|13541058|ref|NP_110746.1| 674 AQLLQINDDLKQLSSRLDKINVDQYEWKSLHKVLLQDNEK--L------NIAVADIRKRLEKKeTIIKAIADL 738
                                   45569***************************99888876..2......478888888888883445566555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (895 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2618  (0.14602); expected 358.6 (0.02)
Passed bias filter:                      618  (0.0344693); expected 358.6 (0.02)
Passed Vit filter:                       158  (0.00881254); expected 17.9 (0.001)
Passed Fwd filter:                       100  (0.00557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 2.27u 0.47s 00:00:02.74 Elapsed: 00:00:00.75
# Mc/sec: 3617.55
//
Query:       gi|13541059|ref|NP_110747.1|  [L=368]
Description: DNA repair exonuclease [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.6e-09   37.9   0.6    4.9e-09   37.0   0.6    1.5  1  Metallophos    Calcineurin-like phosphoesterase
    5.5e-09   36.4   0.0      1e-08   35.6   0.0    1.4  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
  ------ inclusion threshold ------
      0.048   13.1   0.0      0.093   12.1   0.0    1.4  1  HBM            Helical bimodular sensor domain
      0.074   13.2   0.0       0.15   12.1   0.0    1.5  1  OSCP           ATP synthase delta (OSCP) subunit
       0.14   11.8   0.0       0.33   10.6   0.0    1.6  1  PRP8_domainIV  PRP8 domain IV core


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 !   37.0   0.6   1.4e-12   4.9e-09       6     118 ..       1     111 [.       1     191 [. 0.58

  Alignments for each domain:
  == domain 1  score: 37.0 bits;  conditional E-value: 1.4e-12
                                   EESBTB........TTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSSHHHHHHHHHHHHHHHH....TSEEEEEC-TT CS
                   Metallophos   6 igDlHl........algggqlddllkllddllreekpdlvllaGDlvdrgdlekellellaalvky....pipvylllGNH 74 
                                   ++D+H+        +++   +d+++++++ +++e k+d++++ GDl+d+  + ++ ++ ++   +      ipv+ + G H
  gi|13541059|ref|NP_110747.1|   1 MSDTHIgaksltieEREQDYYDTFQEAVEIAIDE-KVDFIIHSGDLFDTWIPGNRSMKVFRDAMMKlndrQIPVFYVFGDH 80 
                                   59***********999999999999999888888.**************977777777765555556677*********** PP

                                   S........CHHHHHHHHHHHHHHHHHHHEHHHCEEETSEEEEEETTE.EEEE CS
                   Metallophos  75 e........gfeeellnkygylgifsepwrsdaevfnnlplaslgsgs.lkvl 118
                                   +        +                      a+ f++l l  lg +    + 
  gi|13541059|ref|NP_110747.1|  81 DrprrnsesA----------------------AGIFDFLGLHILGRDEfAGIE 111
                                   *444333330......................444444444443333222222 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 !   35.6   0.0   2.8e-12     1e-08       6     153 ..       1     213 [.       1     231 [. 0.79

  Alignments for each domain:
  == domain 1  score: 35.6 bits;  conditional E-value: 2.8e-12
                 Metallophos_2   6 iSDlH.............snldaleavlealkevgvdaiihaGD.....leeeep.........evleellela.pvlaVr 58 
                                   +SD+H             + +d  ++++e++ +++vd iih+GD     +    p         +++++l ++  pv +V+
  gi|13541059|ref|NP_110747.1|   1 MSDTHigaksltieereqDYYDTFQEAVEIAIDEKVDFIIHSGDlfdtwI----PgnrsmkvfrDAMMKLNDRQiPVFYVF 77 
                                   599**9999999999988889999999*****************444432....133344555457777777779****** PP

                 Metallophos_2  59 GNnD...................................eev....veedvlreaaelgtdlpeeaelelagek..vlliH 98 
                                   G++D                                   ++v    + ++ +   ++l++++++++  +  g k  +l+ H
  gi|13541059|ref|NP_110747.1|  78 GDHDrprrnsesaagifdflglhilgrdefagierefsgMKVfiggISNMKGYLRNQLKEEYKKAESAST-GYKnsILISH 157
                                   **********************999999999999988874444556677777777777777776666664.3334599999 PP

                 Metallophos_2  99 gdpl..gvkdalaellkeaeegsdvvvcGHtHvpevekeggvlvvnPGsvgeprdgd 153
                                   +  +    +++ ++ +++  ++  ++++GH H    +++ g l+ +PGs + ++d++
  gi|13541059|ref|NP_110747.1| 158 QALDpiFIPEQCEAKVNDLPMNYSYIAMGHLHDFVEREI-GPLLSYPGSTELKSDRE 213
                                   984478777777777777555566********9988888.9999*****99987765 PP

>> HBM  Helical bimodular sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   2.6e-05     0.093     186     240 ..     250     304 ..     233     310 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.6e-05
                                   -GG.GHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           HBM 186 lasdpraalqqlesalskYRaaleqfkaavaaieqarkemteqgdeivkisdeLy 240
                                    +sdp++ l++++s l+kY +a+ + k++v+ i++ + +m+e  +++ ki+ ++ 
  gi|13541059|ref|NP_110747.1| 250 VESDPENYLEEIKSILDKYANAIGEKKPIVNLIINGQISMEEVYEDLKKINGAIF 304
                                   448999********************************************99986 PP

>> OSCP  ATP synthase delta (OSCP) subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   4.3e-05      0.15      17      89 ..     287     362 ..     264     366 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.3e-05
                          OSCP  17 galeeveeelealeavlaedkklaellsnpavsaee..kkdlleelfke.klseavknflkllaenkRlalLpeia 89 
                                    ++eev+e+l++++ ++ + +++ ++++ p+v++    +++ +++++k+ kl+++  ++++  a+ +++a++ e a
  gi|13541059|ref|NP_110747.1| 287 ISMEEVYEDLKKINGAIFNRPQILKIVDMPNVPSGSseLREYFQAFLKDqKLTDLAMKVFQHTADGDKEAIIREAA 362
                                   4799****************************97544499*****9998899999999999999999999988765 PP

>> PRP8_domainIV  PRP8 domain IV core
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   9.2e-05      0.33     116     150 ..     311     345 ..     296     350 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 9.2e-05
                 PRP8_domainIV 116 hlldfPnivikgselkLPfkavlkiekladlvlka 150
                                   +++d Pn+   +sel+  f+a+lk +kl+dl +k 
  gi|13541059|ref|NP_110747.1| 311 KIVDMPNVPSGSSELREYFQAFLKDQKLTDLAMKV 345
                                   689****************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (368 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       623  (0.0347482); expected 358.6 (0.02)
Passed bias filter:                      486  (0.0271069); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-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 0.33s 00:00:00.96 Elapsed: 00:00:00.52
# Mc/sec: 2112.60
//
Query:       gi|13541060|ref|NP_110748.1|  [L=518]
Description: ATPase [Thermoplasma volcanium GSS1]
Scores for complete 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-35  121.0   1.3    1.8e-34  119.8   1.3    1.6  1  DUF87            Helicase HerA, central domain
    7.6e-10   38.8   0.4    2.9e-09   37.0   0.2    2.2  2  HAS-barrel       HAS barrel domain
    5.6e-07   28.5   0.0    0.00071   18.3   0.0    2.2  2  DUF853           Bacterial protein of unknown function (DUF85
    2.1e-06   26.9   0.2     0.0021   17.0   0.0    2.6  3  TrwB_AAD_bind    Type IV secretion-system coupling protein DN
    3.6e-05   22.8   0.0      7e-05   21.8   0.0    1.4  1  T4SS-DNA_transf  Type IV secretory system Conjugative DNA tra
      0.003   18.0   0.0      0.019   15.4   0.0    2.3  2  AAA              ATPase family associated with various cellul
     0.0032   17.5   2.0      0.013   15.5   1.9    2.1  1  ResIII           Type III restriction enzyme, res subunit
     0.0092   15.4   0.0       0.65    9.3   0.0    2.4  2  FtsK_SpoIIIE     FtsK/SpoIIIE family
  ------ inclusion threshold ------
      0.028   14.7   0.0       0.83    9.9   0.0    2.5  2  AAA_22           AAA domain
      0.065   12.9   0.0        3.1    7.4   0.0    2.4  2  Zot              Zonular occludens toxin (Zot)
      0.073   12.9   0.1       0.17   11.7   0.1    1.7  2  Helicase_RecD    Helicase
       0.17   12.4   1.2       0.49   11.0   1.2    1.8  1  DUF1053          Domain of Unknown Function (DUF1053)


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 !  119.8   1.3   1.2e-37   1.8e-34       1     224 [.     136     343 ..     136     346 .. 0.94

  Alignments for each domain:
  == domain 1  score: 119.8 bits;  conditional E-value: 1.2e-37
                         DUF87   1 ieiGrllsgsevpvyldlnklvtrHlAilgsTGsGKSntvavLleellekkgatililDpHGEYgkal...ekllsekvkv 78 
                                   +eiG+l+++ +v++  ++n l +rHl i+++TG+GKS+t++vL+eell kkga+i++lDpH +Y+ ++   +  +++++kv
  gi|13541060|ref|NP_110748.1| 136 LEIGYLADQPDVKIFANINGL-RRHLSIIAQTGAGKSHTAGVLMEELL-KKGASIIVLDPHADYVLMKnsdKAIYRDNIKV 214
                                   58****************999.**************************.********************99999******* PP

                         DUF87  79 itpspsa........kdkelkinpwsldpeelldlleeddkpaaavqrsvleealdqakakeekeklssdepveklleelk 151
                                   ++++ s+        k  e++i++++l+ ee+ +++++   ++  +q +++++++++     + ++ ++de+++       
  gi|13541060|ref|NP_110748.1| 215 FRTPMSTgrytaklgKVDEFTIKFQDLNDEEVREIMGI--HENFVNQSKIVKDVMEK-----LTGRKDVDEFIQ------- 281
                                   ***9888*******************************..99*9************4.....558888888888....... PP

                         DUF87 152 kekeelrklknqaiarlldkledllrkggsfsnsstdliallleklekegkitiidlsgvdelaqqlvvsvil 224
                                         ++++ ++++r+ +++++l++ ++ f++++td+ + l      ++++++idlsg+d++ +++++  ++
  gi|13541060|ref|NP_110748.1| 282 ------KSEQIDTEKRIAARIKYLKKIKAIFGDKTTDVSEYL-----APSRMSVIDLSGLDQSLANYFAYKVI 343
                                   ......46678889****************************.....*******************9876655 PP

>> HAS-barrel  HAS barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.0   0.2   1.9e-12   2.9e-09       1      92 []      15     100 ..      15     100 .. 0.95
   2 ?   -2.9   0.0       5.2   7.7e+03      35      55 ..     288     311 ..     275     319 .. 0.59

  Alignments for each domain:
  == domain 1  score: 37.0 bits;  conditional E-value: 1.9e-12
                    HAS-barrel   1 iGevigestssslifrvegskdvkvGeyVeielpdgeivlGmvtdirrgnselsndlalvlsleeleeangddevalated 81 
                                   iG  +g   s+ ++f++ +   ++ +eyV+i+   ++ +lG+++d+ ++ s+l+nd+++++s++++  +n  d v + ++ 
  gi|13541060|ref|NP_110748.1|  15 IGLTVGDNRSDIFTFVISPESQIRKWEYVYIKAG-ETNLLGRIEDLLSK-SDLLNDRMDYESVKKYTTSNIKDNVDICVV- 92 
                                   567788888899**********************.*************5.******************************. PP

                    HAS-barrel  82 tgvkvlGeved 92 
                                      k++G v+d
  gi|13541060|ref|NP_110748.1|  93 ---KIIGAVKD 100
                                   ...*****997 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 5.2
                    HAS-barrel  35 dgeivlGmvtdirrgn...selsn 55 
                                   +++++  ++  +++++   +++ +
  gi|13541060|ref|NP_110748.1| 288 TEKRIAARIKYLKKIKaifGDKTT 311
                                   556777777777776655544444 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 !    8.0   0.0   0.00065      0.97       7      61 ..     143     197 ..     138     214 .. 0.87
   2 !   18.3   0.0   4.7e-07   0.00071     261     361 ..     361     462 ..     336     472 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00065
                        DUF853   7 keaeqelalalklanrhGliaGatGtGktvtLqvlaeslseaGvpvfladvkGdL 61 
                                   ++++ +++ +++   rh  i   tG+Gk  t  vl e+l + G ++++ d   d 
  gi|13541060|ref|NP_110748.1| 143 DQPDVKIFANINGLRRHLSIIAQTGAGKSHTAGVLMEELLKKGASIIVLDPHADY 197
                                   566677888888899*******************************999977775 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 4.7e-07
                        DUF853 261 fffdeahLLf.......ndapkallekveqvvrLirskGvGvyfvtqnPldlPdtvLaqLGnrvqhalraftpkdqkavka 334
                                   +f +eah +         + +++l + + ++    r  G+ +  +tq P  + ++vL+q  +++   lr   p dqka+  
  gi|13541060|ref|NP_110748.1| 361 LFIEEAHNFAppmkvkgSGVSQMLYDTIKKIAAEGRKFGIFLVIITQRPGKIDQDVLSQCNSQI--ILRITNPSDQKAILE 439
                                   566777754211111113456667777777777667777777778**************98765..7************99 PP

                        DUF853 335 aadtfranpefdveeaiteLgvGealv 361
                                   +++ + +    ++++ + +L+vGea++
  gi|13541060|ref|NP_110748.1| 440 SSENISE----SLMSDLPSLDVGEAII 462
                                   9876655....6778889999999997 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   1.4e-06    0.0021      15      56 ..     157     198 ..     149     206 .. 0.93
   2 ?   -2.3   0.0       1.1   1.6e+03      97     162 ..     279     345 ..     261     355 .. 0.64
   3 !    6.9   0.0    0.0017       2.5     260     312 ..     387     431 ..     384     449 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.4e-06
                 TrwB_AAD_bind  15 tqhilivGttGsGKtqalekllrairargdraivlDltGafv 56 
                                   ++h+ i+  tG+GK+ ++  l++++ ++g  +ivlD++ ++v
  gi|13541060|ref|NP_110748.1| 157 RRHLSIIAQTGAGKSHTAGVLMEELLKKGASIIVLDPHADYV 198
                                   68***********************************99987 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.1
                 TrwB_AAD_bind  97 lipedggssdpfWaeaartvlaetlrelvrekkksnaallr..alltadleeLkellagteaaalvae 162
                                   +i +  ++ d     aar+   + ++++  +k ++ +++l+  ++ + dl+ L + la+++a++++++
  gi|13541060|ref|NP_110748.1| 279 FIQK-SEQIDTEKRIAARIKYLKKIKAIFGDKTTDVSEYLApsRMSVIDLSGLDQSLANYFAYKVISQ 345
                                   5555.555566666666666666677777777777766654225666778888888888888888774 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.0017
                 TrwB_AAD_bind 260 elksllaegRkfGgavvlglqsiaqlrevYGedaaqsilslvntklilrvsda 312
                                   ++k+++aegRkfG+ +v+  q   ++         q +ls +n+++ilr+++ 
  gi|13541060|ref|NP_110748.1| 387 TIKKIAAEGRKFGIFLVIITQRPGKID--------QDVLSQCNSQIILRITNP 431
                                   7899******************99986........467777888888776643 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 !   21.8   0.0   4.7e-08     7e-05      39      83 ..     152     198 ..     118     236 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 4.7e-08
               T4SS-DNA_transf  39 ntdGdfehvlvvAptrsgK..gvgvviPnllkwkqsiVvlDpkgEla 83 
                                   n +G   h +++A t++gK  ++gv +  llk++ si+vlDp ++ +
  gi|13541060|ref|NP_110748.1| 152 NINGLRRHLSIIAQTGAGKshTAGVLMEELLKKGASIIVLDPHADYV 198
                                   5566669************6669*******************99965 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 ?   -1.1   0.0       1.5   2.3e+03       6      25 ..     165     187 ..     161     209 .. 0.72
   2 !   15.4   0.0   1.3e-05     0.019      56     129 ..     352     425 ..     302     428 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.5
                                   STTSSHHHHHHHHHHHH...THE CS
                           AAA   6 ppGtGKTllakavakel...gve 25 
                                     G GK+ +a  +++el   g++
  gi|13541060|ref|NP_110748.1| 165 QTGAGKSHTAGVLMEELlkkGAS 187
                                   56899999999999997544333 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 1.3e-05
                                   TS...TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHSTTSSEEEE CS
                           AAA  56 ka...kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallrgRfdrkie 129
                                         p+ lfi+E++++a+  + + s++++ + +++ +   + +k    ++++++t+rp k+d+ +l + ++++i 
  gi|13541060|ref|NP_110748.1| 352 TGsfeYPVFLFIEEAHNFAPPMKVKGSGVSQMLYDTIKKIAAEGRKF--GIFLVIITQRPGKIDQDVL-SQCNSQII 425
                                   33565689*************96666666666666666666666664..5999***************.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 !   15.5   1.9   8.7e-06     0.013      21     121 ..     146     269 ..     110     394 .. 0.59

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 8.7e-06
                                   ..........TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHH.HHHHHHHHG.................. CS
                        ResIII  21 s........krdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprks.lleqtleef.................. 74 
                                   +          ++++ i + TG+GK+ +a  l+e+llkkg    +++l p  + +l +  ++                   
  gi|13541060|ref|NP_110748.1| 146 DvkifaninGLRRHLSIIAQTGAGKSHTAGVLMEELLKKGA--SIIVLDPHADyVLMKNSDKAiyrdnikvfrtpmstgry 224
                                   0555555523345667**********************988..56666555431222222221233333333433333333 PP

                                   ...................GGGTGG....GEEEESSS-B--.......-SEEEEEHHHHHHTH... CS
                        ResIII  75 ...................kkflseaykeigkkvsgdkkkakekdstnkkilvttiqsldadseee 121
                                                      +                     + +++  ++  +++ +++ +d +e+
  gi|13541060|ref|NP_110748.1| 225 taklgkvdeftikfqdlndE---------------------EVREIMGIHENFVNQSKIVKDVMEK 269
                                   33333333333333222220.....................2444455555555555555554444 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0     0.028        42      15      64 ..     133     182 ..     123     188 .. 0.82
   2 !    9.3   0.0   0.00044      0.65     213     242 ..     381     410 ..     367     441 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.028
                                   --TTEEEEEEETTS-EEEEEGGGS-.SEEEE--TTSSHHHHHHHHHHHHH CS
                  FtsK_SpoIIIE  15 ssqlpvalgkeisgnplvldlkkmashllvaGatgsGKStalntLilSla 64 
                                   + +l++    ++ + ++ +++++   hl ++  tg GKS +  +L+  l+
  gi|13541060|ref|NP_110748.1| 133 QRSLEIGYLADQPDVKIFANINGLRRHLSIIAQTGAGKSHTAGVLMEELL 182
                                   55666667777778888888888889**************9999987665 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00044
                                   ...HHHHHHHHHHHCGGGTEEEEEEES--- CS
                  FtsK_SpoIIIE 213 svlvedaivRlarkgraaglHlllatqrls 242
                                   s++  d i+++a+ gr+ g++l+++tqr++
  gi|13541060|ref|NP_110748.1| 381 SQMLYDTIKKIAAEGRKFGIFLVIITQRPG 410
                                   566678899999999999999999999986 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00056      0.83       5      32 ..     157     184 ..     153     217 .. 0.75
   2 ?    2.0   0.0      0.15   2.2e+02      91     126 ..     352     401 ..     296     435 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00056
                        AAA_22   5 agilvvtGesGtGKTtllrrlleqldee 32 
                                   +++l +++++G+GK++++  l+e+l + 
  gi|13541060|ref|NP_110748.1| 157 RRHLSIIAQTGAGKSHTAGVLMEELLKK 184
                                   6899**************9999998644 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.15
                        AAA_22  91 v.....ielliiDEaqhlr.....s.....eealeeLrsllnlsrkgvqli 126
                                   +     +++l i+Ea+++      +     + ++ ++++++  +  ++ ++
  gi|13541060|ref|NP_110748.1| 352 TgsfeyPVFLFIEEAHNFAppmkvKgsgvsQMLYDTIKKIAA-EGRKFGIF 401
                                   2556778899*******9776544144553444444555544.33333333 PP

>> Zot  Zonular occludens toxin (Zot)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0     0.051        76      29      59 ..     146     178 ..     136     201 .. 0.81
   2 ?    7.4   0.0    0.0021       3.1      83     138 ..     360     420 ..     274     427 .. 0.73

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.051
                           Zot  29 gRkiitnidGlr..lerieqvlgekvstarlir 59 
                                   + ki++ni+Glr  l  i+q    k +ta ++ 
  gi|13541060|ref|NP_110748.1| 146 DVKIFANINGLRrhLSIIAQTGAGKSHTAGVLM 178
                                   5689*******9999999998888888887665 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0021
                           Zot  83 llviDEcqeifpvrakegrkd.....pevinaftehRhlgwDivlltqdiskihkevrala 138
                                   +l+i E++++ p  + +g  +     + + +  +e R++g  +v++tq + ki+++v   +
  gi|13541060|ref|NP_110748.1| 360 FLFIEEAHNFAPPMKVKGSGVsqmlyDTIKKIAAEGRKFGIFLVIITQRPGKIDQDVLSQC 420
                                   899999999888777665555555644444777899*******************997666 PP

>> Helicase_RecD  Helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   0.00011      0.17       2      36 ..     162     195 ..     161     254 .. 0.82
   2 ?   -3.1   0.0       3.9   5.9e+03      51      82 ..     268     302 ..     241     313 .. 0.52

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00011
                 Helicase_RecD   2 ltAdRGRGKSaalGlalaaliaegksnilvtapsk 36 
                                   ++A+ G GKS ++G+++++l+++g  +i+v  p+ 
  gi|13541060|ref|NP_110748.1| 162 IIAQTGAGKSHTAGVLMEELLKKGA-SIIVLDPHA 195
                                   89*********************98.677766655 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 3.9
                 Helicase_RecD  51 ealglke....eekkkkaekaelrvr.kqrieyiapd 82 
                                   e+l+ ++      +k+++  + +++r   ri+y++  
  gi|13541060|ref|NP_110748.1| 268 EKLTGRKdvdeFIQKSEQ--IDTEKRiAARIKYLKKI 302
                                   333333322112222222..22333356677776655 PP

>> DUF1053  Domain of Unknown Function (DUF1053)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   1.2   0.00033      0.49      30      90 ..     251     310 ..     227     316 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00033
                       DUF1053  30 eiplkksklqdkkersasekarleeelderleqaIdglsskklwkrsedlkkftliFkeks 90 
                                   +i ++  + q k  +++ ek +   ++de+++++ ++   k++  r ++lkk+  iF +k 
  gi|13541060|ref|NP_110748.1| 251 GIHENFVN-QSKIVKDVMEKLTGRKDVDEFIQKSEQIDTEKRIAARIKYLKKIKAIFGDKT 310
                                   55555444.578889999999************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (518 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       901  (0.0502538); expected 358.6 (0.02)
Passed bias filter:                      564  (0.0314574); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.73u 0.36s 00:00:01.08 Elapsed: 00:00:00.55
# Mc/sec: 2823.83
//
Query:       gi|13541061|ref|NP_110749.1|  [L=335]
Description: hypothetical protein TVN0230 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.7e-22   78.4   0.5    8.8e-22   78.0   0.5    1.2  1  NurA      NurA domain
  ------ inclusion threshold ------
      0.023   14.6   0.1      0.042   13.8   0.1    1.4  1  APC1_C    Anaphase-promoting complex sub unit 1 C-terminal do


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 !   78.0   0.5   9.8e-26   8.8e-22       2     242 .]      60     301 ..      59     301 .. 0.92

  Alignments for each domain:
  == domain 1  score: 78.0 bits;  conditional E-value: 9.8e-26
                                   EEEEEEEEEEEE.EETTCEEEEEEEEEEECCEEECCCEEEECEBTCCHHEEEEEHHHHHHHHHHHHHHHHHHHCGGCCSCE CS
                          NurA   2 rvaAvDGSngvv.rlsggilyilsayavvgggkerleealslasvdsispsdelerrirllmetlElklgallleekgedl 81 
                                   ++ A+D+S +++  +sg++++++++y   g + ++  e + l+  +++      +  + ++me++E++  ++ l+++++d 
  gi|13541061|ref|NP_110749.1|  60 KISATDSSEFSReLYSGNFFILVRGYTRLGDSIYNKLEVSFLSIGPEDV-----KKETMIMMENVEHLSMLECLKKENPDF 135
                                   578*********99*************9999998888887777777777.....**************999999******* PP

                                   EEEECSHHCCCH.HHHHHHHHHHHHHHHHHHHHHTT-....TTCEEEEESS-SCTCCHCCC..............S--HHH CS
                          NurA  82 lllDGsligslv.efdelheeleyeeylyslsrllea....glnlvgvaKsfrskellnll........letlligesisD 149
                                   +l+DGs++  ++ +++ +   +    y+ +l++lle+    +  +++v+Ks+rs+ + n          l +l+++ +  D
  gi|13541061|ref|NP_110749.1| 136 MLVDGSILSRILrCEKYQSSLDRENDYCLMLRELLEQrkksNFAIAFVSKSSRSTLIRNSIldqiedkaLANLERNSNHFD 216
                                   ************55555555666778*************9999999******999999988******************** PP

                                   HCCHHCCHCH---STTS-HHHHTT-HCCHHHHHH-EEEEEEESSTTTTEEEEEHHHHHHCCHHHHHHHHHH..TTB-SSSB CS
                          NurA 150 iallgallrkpgytspllkilrekpllrealidkeiyfaYvrlegggsilrleipaevstakdedvlsllasqrlsisGYp 230
                                   + l+++l++kpgyt+pl         +++ + ++++ ++ +    ++ + r+e  +++ ++++ed++ l+    +s+ GY 
  gi|13541061|ref|NP_110749.1| 217 HFLVKSLAKKPGYTKPLE------TSINIGNFSDHVLVTDILPRSEDLPIRVE--MIGNRDRFEDLVDLMF---WSYGGYK 286
                                   ******************......899**************************..8878***********9...******* PP

                                   CC...HHHHHHHHCC CS
                          NurA 231 rp...LalAhelaki 242
                                   ++   L  +++l+k+
  gi|13541061|ref|NP_110749.1| 287 VYniwLSEVDNLVKF 301
                                   99999*******996 PP

>> APC1_C  Anaphase-promoting complex sub unit 1 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   4.7e-06     0.042      37     140 ..     121     225 ..     101     251 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.7e-06
                                   HHHHHHHHHTT-TTHHHHHHHHHHHHHHHHHT---S-HHHHHHHHHHHHHSSSGGGTTTTS....SS-SSSSS-STTHHHH CS
                        APC1_C  37 ssaLleCltkDkpelLplylslykllqtlakqssaaslalwdlrlvlefyssearlsalgaa..eeksresLlrpsllesl 115
                                   +  +leCl k+ p+ + +  s+++ + +++k++  +    +d  l+l+   ++ ++s+   a  +++sr +L+r s+l+++
  gi|13541061|ref|NP_110749.1| 121 HLSMLECLKKENPDFMLVDGSILSRILRCEKYQ-SSLDRENDYCLMLRELLEQRKKSNFAIAfvSKSSRSTLIRNSILDQI 200
                                   6679********************999999984.66667778888887777777777777778899*************** PP

                                   HHHHHHHHHHHHHH.TTHHHHHHHHS CS
                        APC1_C 116 eqrvdalldswgke.gsakllsrylr 140
                                   e +  a l+  ++   +  l++++ +
  gi|13541061|ref|NP_110749.1| 201 EDKALANLERNSNHfDHF-LVKSLAK 225
                                   *99988888776553444.5555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       641  (0.0357521); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 2051.51
//
Query:       gi|13541062|ref|NP_110750.1|  [L=287]
Description: 3-hydroxyisobutyrate dehydrogenase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      6e-30  104.5   1.3    8.9e-30  103.9   1.3    1.3  1  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
    1.7e-24   86.4   0.0    2.9e-24   85.6   0.0    1.4  1  NAD_binding_11  NAD-binding of NADP-dependent 3-hydroxyisobut
    4.6e-07   30.0   0.1      8e-07   29.2   0.1    1.4  1  Shikimate_DH    Shikimate / quinate 5-dehydrogenase
    8.4e-06   26.3   0.1    1.6e-05   25.4   0.1    1.5  1  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
    1.7e-05   25.6   0.0      3e-05   24.8   0.0    1.4  1  GFO_IDH_MocA    Oxidoreductase family, NAD-binding Rossmann f
    0.00084   18.9   0.1     0.0014   18.2   0.1    1.4  1  IlvN            Acetohydroxy acid isomeroreductase, NADPH-bin
     0.0015   17.9   0.1     0.0023   17.3   0.1    1.2  1  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
     0.0071   16.2   0.0      0.012   15.5   0.0    1.4  1  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
  ------ inclusion threshold ------
       0.03   14.5   0.1      0.053   13.7   0.1    1.3  1  DUF4030         Protein of unknown function (DUF4030)
      0.073   13.2   0.1       0.14   12.3   0.1    1.6  1  DapB_N          Dihydrodipicolinate reductase, N-terminus


Domain annotation for each model (and alignments):
>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.9   1.3     5e-33   8.9e-30       2     158 .]       5     160 ..       4     160 .. 0.96

  Alignments for each domain:
  == domain 1  score: 103.9 bits;  conditional E-value: 5e-33
                                   EEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHT.TEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHSHCCC-- CS
                 NAD_binding_2   2 igfiGlGvMGsnmalnllkagykvavynrtkekveelvae.gakaaesieelvasldvvitmvkagkavdeviegllealk 81 
                                   + +iGlG+MG  +a n++kag+   v++r+ ek+e++ ++ g + +++ie++v+s dv++tm+ +++ v +v+++ ++ ++
  gi|13541062|ref|NP_110750.1|   5 VVLIGLGIMGYRIAANFKKAGMLNGVFDRKIEKAEAFSKQfGSEFYKDIESAVKSNDVIVTMLYDDSSVIDVYSKAMD-YA 84 
                                   679***********************************99679********************************777.67 PP

                                   TT-EEEE-S---HHHHHHHHHHHHHTT-EEEEEEEESHHHHHHHT-EEEEEEE-HHHHHHHHHHHHHHEEEEEEE-E CS
                 NAD_binding_2  82 kgdilidgstsspedtrelakelkekglkfldaPVSGGeegAekGtLsimvGGseeafervkpvleaigakvthviG 158
                                   +g+i++d+st+spe++++++k++++kg ++ daPV G+    ek  L++++GG+++ +  +++++ a +++v+ ++G
  gi|13541062|ref|NP_110750.1|  85 AGKIFVDMSTISPETSIRVSKDIESKGGEMYDAPVIGTSVVVEKKGLTVLIGGPRDNVGLIEELMGATATSVV-YVG 160
                                   9*********************************************************************999.667 PP

>> NAD_binding_11  NAD-binding of NADP-dependent 3-hydroxyisobutyrate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.6   0.0   1.6e-27   2.9e-24       1     122 []     163     284 ..     163     284 .. 0.96

  Alignments for each domain:
  == domain 1  score: 85.6 bits;  conditional E-value: 1.6e-27
                NAD_binding_11   1 GaGqavKlvnnlllainlaaasEalvlaekaGldpekvlev.inassgrsnalenklpqrvlsrdfdpgFaldlmlKDlgl 80 
                                   G+G  +Klvnnl l+  + a++Ea+ +++  Gld +++  v i+ ss+rs ++e k+p+ ++++d  ++F+++ mlKDl++
  gi|13541062|ref|NP_110750.1| 163 GSGLYAKLVNNLFLGSYMEALAEAVRFGRSTGLDDNVISSVlIKYSSARSPTSELKVPK-MMAGDHSTQFSVKNMLKDLEI 242
                                   899***********************************9984588*************5.89999**************** PP

                NAD_binding_11  81 alelareagaplpllalaeqlyaaaaaegggdaDhsaivrll 122
                                   + ++ar+  +p+p ++ a q+y+ +a++g++++D s+i+++l
  gi|13541062|ref|NP_110750.1| 243 IEDTARRKSVPIPSASIALQFYRYLASSGHSEEDISSIYKVL 284
                                   ***************************************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 !   29.2   0.1   4.5e-10     8e-07      12     112 ..       2      93 ..       1     107 [. 0.84

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 4.5e-10
                                   T-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEEEE-SSSSS-SB-H CS
                  Shikimate_DH  12 ekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeiealkleelkellaeadvvisataseepilek 92 
                                   ekkv+liG G m+ ++a ++ ++g+    v+ R +e+a+++ +++++e      +++++++++++dv+++     + +++ 
  gi|13541062|ref|NP_110750.1|   2 EKKVVLIGLGIMGYRIAANFKKAGML-NGVFDRKIEKAEAFSKQFGSE-----FYKDIESAVKSNDVIVTMLYDDSSVIDV 76 
                                   68*********************998.68****************887.....789**************99988888875 PP

                                   HHHHCCHHH.S..EEEEE-- CS
                  Shikimate_DH  93 eeveealkkrkkplllvDia 112
                                    +  +  +     +++vD++
  gi|13541062|ref|NP_110750.1|  77 YSKAMDYA---AGKIFVDMS 93 
                                   43332221...345666665 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.1   9.1e-09   1.6e-05       1      94 [.       4      92 ..       4      94 .. 0.86

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 9.1e-09
                                  EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S.-HHHHHHHHHHCG CS
                 F420_oxidored  1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlav.kpedveevlsela 82
                                  k+ +iG G mg  +a ++ +ag   + +    +r+ ekae++ +++g +  + d e a++++dv+v  +   + v +v s++ 
  gi|13541062|ref|NP_110750.1|  4 KVVLIGLGIMGYRIAANFKKAG-MLNGVF---DRKIEKAEAFSKQFGSEFYK-DIESAVKSNDVIVTMLyDDSSVIDVYSKA- 80
                                  6889******************.444444...9**************99999.***********997652567889999999. PP

                                  HHHHTTSEEEEE CS
                 F420_oxidored 83 kdalkgklvisv 94
                                   d  +gk+++++
  gi|13541062|ref|NP_110750.1| 81 MDYAAGKIFVDM 92
                                  777999999997 PP

>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0   1.7e-08     3e-05       2      62 ..       4      61 ..       3      77 .. 0.89

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 1.7e-08
                                  EEEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHEEESSHHHHHTCTT CS
                  GFO_IDH_MocA  2 rvaiiGaGkigskhlrplnesqrleevvalldpdaeraeavaesfgveaysdleelladpe 62
                                  +v++iG+G +g++ +++++++     + +++d++ e+aea++++fg e+y+d+e  +++ +
  gi|13541062|ref|NP_110750.1|  4 KVVLIGLGIMGYRIAANFKKA---GMLNGVFDRKIEKAEAFSKQFGSEFYKDIESAVKSND 61
                                  89************9777766...79****************************9988664 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 !   18.2   0.1     8e-07    0.0014       4      81 ..       2      81 ..       1      90 [. 0.82

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 8e-07
                                  TS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEE.EHHHHHHT-SEEE.E-S-HHHHHHHHHHHT CS
                          IlvN  4 gkkiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevl.tvaeavkkadvvm.iliPDelqkevyeeei 81
                                  +kk+++iG G  G   a n++ +g+   v  r+ +k  +  k+ g e + +++ avk+ dv++ +l  D+   +vy++++
  gi|13541062|ref|NP_110750.1|  2 EKKVVLIGLGIMGYRIAANFKKAGMLNGVFDRKIEKAEAFSKQFGSEFYkDIESAVKSNDVIVtMLYDDSSVIDVYSKAM 81
                                  79**********************9877778888878888888888876258999*****98715566677789997765 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 !   17.3   0.1   1.3e-06    0.0023      36      98 ..       2      66 ..       1      78 [. 0.88

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.3e-06
                                  TSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHH.CHHHHTCEEC.SHHHHHHH-SEEEE- CS
                  2-Hacid_dh_C 36 gktvGiiGlGrIGqavakrlkafgmkviaydrskkkee.eeeelgvelv.sleellaesDivslh 98
                                  +k+v +iGlG +G ++a  +k+ gm   ++dr+ +k e   ++ g e+  ++e ++++ D+++ +
  gi|13541062|ref|NP_110750.1|  2 EKKVVLIGLGIMGYRIAANFKKAGMLNGVFDRKIEKAEaFSKQFGSEFYkDIESAVKSNDVIVTM 66
                                  699******************************99888656666776655************976 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   6.7e-06     0.012       1      52 [.       4      55 ..       4      85 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 6.7e-06
                                  EEEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTT CS
                       3HCDH_N  1 kvaviGaGtmGagiaavfasagleVvlvdiseealekalekieksleklvek 52
                                  kv  iG G+mG  iaa f +ag+   ++d++ e++e+  ++  +++ k +e+
  gi|13541062|ref|NP_110750.1|  4 KVVLIGLGIMGYRIAANFKKAGMLNGVFDRKIEKAEAFSKQFGSEFYKDIES 55
                                  6889*****************************9999999998877766554 PP

>> DUF4030  Protein of unknown function (DUF4030)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1     3e-05     0.053      80     138 ..      20      79 ..       8      82 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3e-05
                       DUF4030  80 nveseqpvtlaiktkissadsGakelGkkiekevddllktkkvk.kwiendsytieiysq 138
                                   n+++   +      ki++a++ +k++G    k++++ +k+++v    + +ds  i++ys+
  gi|13541062|ref|NP_110750.1|  20 NFKKAGMLNGVFDRKIEKAEAFSKQFGSEFYKDIESAVKSNDVIvTMLYDDSSVIDVYSK 79 
                                   566666666667789*************************99852678999*******97 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   7.8e-05      0.14       2      72 ..       4      64 ..       3     109 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 7.8e-05
                                  EEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTCSTTTTTBHHHHSSSS--S-BEBSSHHHHHHH-SEEE CS
                        DapB_N  2 kvavvGasGrmGkevvkaveeaedlelvaavdrkeselegkdagellglgklgvavtddleevlekadvli 72
                                  kv+++G  G mG +++   ++     l +++drk +   + +a     +++ g ++++d+e++++++dv++
  gi|13541062|ref|NP_110750.1|  4 KVVLIGL-GIMGYRIAANFKK--AGMLNGVFDRKIE---KAEA----FSKQFGSEFYKDIESAVKSNDVIV 64
                                  899***8.********99999..6679999999862...2222....2358999***************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       497  (0.0277205); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1914.00
//
Query:       gi|13541063|ref|NP_110751.1|  [L=547]
Description: NADH:flavin oxidoreductase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-69  235.2   0.0    2.8e-69  234.0   0.0    1.5  1  Oxidored_FMN   NADH:flavin oxidoreductase / NADH oxidase fami
    4.4e-08   33.2   0.0    5.9e-07   29.6   0.0    2.7  3  NAD_binding_8  NAD(P)-binding Rossmann-like domain
      5e-07   29.4   0.0    7.3e-07   28.9   0.0    1.2  1  FAD_oxidored   FAD dependent oxidoreductase
    5.7e-06   26.8   0.8    0.00015   22.3   0.4    3.1  3  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
    1.6e-05   24.6   0.0    2.9e-05   23.8   0.0    1.5  1  DAO            FAD dependent oxidoreductase
    2.4e-05   23.7   0.0    5.4e-05   22.6   0.0    1.5  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    0.00013   21.2   0.4    0.00019   20.7   0.4    1.2  1  FAD_binding_2  FAD binding domain
     0.0006   19.2   0.0      0.001   18.4   0.0    1.3  1  AlaDh_PNT_C    Alanine dehydrogenase/PNT, C-terminal domain
    0.00074   18.7   0.0      0.001   18.2   0.0    1.3  1  GIDA           Glucose inhibited division protein A
      0.001   18.4   0.0     0.0017   17.6   0.0    1.3  1  Thi4           Thi4 family
     0.0021   16.8   0.2     0.0034   16.1   0.2    1.3  1  HI0933_like    HI0933-like protein
  ------ inclusion threshold ------
      0.032   13.7   0.0        1.8    8.0   0.0    2.6  2  BtpA           BtpA family
      0.085   12.7   0.0       0.18   11.7   0.0    1.5  1  3HCDH_N        3-hydroxyacyl-CoA dehydrogenase, NAD binding d
        0.1   11.8   0.2       0.15   11.2   0.2    1.2  1  FAD_binding_3  FAD binding domain
       0.17   11.1   0.0       0.34   10.2   0.0    1.4  1  Amino_oxidase  Flavin containing amine oxidoreductase
        0.2   10.7   0.0          2    7.4   0.0    2.2  2  Dus            Dihydrouridine synthase (Dus)


Domain annotation for each model (and alignments):
>> Oxidored_FMN  NADH:flavin oxidoreductase / NADH oxidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  234.0   0.0   2.5e-72   2.8e-69       8     335 ..      10     314 ..       9     319 .. 0.86

  Alignments for each domain:
  == domain 1  score: 234.0 bits;  conditional E-value: 2.5e-72
                                   ETTEEESSSEEE----S-TTTTTCS.HHHHHHHHHHHHHHTT-SEEEEEEEESSCCC-.SCTTSEE-SSGGGHHHHHHHHH CS
                  Oxidored_FMN   8 ignmtLknRivmapmtrlraldkgnvledlaaeyysqraeipvtliiteaafvnpksg.gfdnapgiwdeeqieewrklte 87 
                                   ign+++knRivmapm    a+ +g+ +e   + y+++ra+++++liite++ v+p+sg g +n+ gi+d+  ++++  l+e
  gi|13541063|ref|NP_110751.1|  10 IGNVEIKNRIVMAPMISNIANSDGSPSE-PYISYMRERARGGIGLIITEYTYVDPESGkGSRNQLGIYDDIFLPKFSRLAE 89 
                                   9**************9999999996666.9**************************998********************** PP

                                   HHHHTT-EEEEEEE--GGGS..SCSTCEC..SS.ESSSSSTTT-.S...CS-EE--HHHHHHHHHHHHHHHHHHHHTT-SE CS
                  Oxidored_FMN  88 avhengskvvvqlwhlGreakseyladqevdspsdpvaldaqeeesaeevykkeltkeeikqliqefveAAkraieAgfDg 168
                                   avh++gsk++vql h+G++a   +  +     ps ++ +d++         ++e++ ++i+ +i+++ +AA  a+ AgfDg
  gi|13541063|ref|NP_110751.1|  90 AVHDYGSKIFVQLVHAGAKALPSSSYKIA---PS-KTSFDKN---------AREMDSSDIERVIRNYERAASIARRAGFDG 157
                                   ********************443333333...55.6666666.........48**************************** PP

                                   EEEEE-CTSHHHHHH-TTT----STTSSSHHHHHHHHHHHHHHHHHHH-SSS.EEEEEECE--STTS--HHHHHHHHHHHC CS
                  Oxidored_FMN 169 VeihganGYLlnqFlspksnkrtDeygGslenRarFllevvdaVkeavgeer.vgyRlSpedvvekgldfaetaqkivllk 248
                                   +eihga+GYL+++F+sp+ n+rtD+ygGsle R++F+ ev+daVk     +  vg+RlS +++   g +  +    i+++k
  gi|13541063|ref|NP_110751.1| 158 IEIHGAHGYLVDEFISPYWNRRTDKYGGSLEGRIKFPQEVIDAVKSE--VDIpVGIRLSLYEDEVGGYG-PDY--GIKVAK 233
                                   ***********************************************..5777*******998765544.444..344433 PP

                                   HCCEEEEEEETT-SSSSSTTS-TTTTHHHCCTT.HHH..HHHCCCHSSEEEE-SS--SHHHHHHHHHTTS-SEEEESTHHH CS
                  Oxidored_FMN 249 elekrlkdgkklalvhaaeprkrgagsvrteqe.knt..efvkevwkkplitvgriadeekaaeivaegeadLvamgRefl 326
                                        l    ++++vh     +  +gs+   +  ++   ++    ++kp+i vg+ + +e  ++    + ad va+gR++l
  gi|13541063|ref|NP_110751.1| 234 S----L---VNIDYVHFSAGNNDPPGSSAPFYSnHTHilSKFPGGSNKPTILVGSVTTAE--DVRNVLKVADFVAVGRAVL 305
                                   3....3...367788877777777777766655333234889999***************..77777799*********** PP

                                   H-TTHHHHH CS
                  Oxidored_FMN 327 adpdlvekl 335
                                   adp +++k+
  gi|13541063|ref|NP_110751.1| 306 ADPYFARKV 314
                                   ******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 ?   -2.4   0.0       5.1   5.7e+03      43      53 ..      90     100 ..      84     105 .. 0.80
   2 !   29.6   0.0   5.2e-10   5.9e-07       1      39 [.     362     400 ..     362     419 .. 0.88
   3 ?   -0.7   0.0       1.5   1.7e+03      16      37 ..     507     530 ..     503     539 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 5.1
                                   CEECTS---EE CS
                 NAD_binding_8  43 vrvdygahifh 53 
                                    ++dyg  if 
  gi|13541063|ref|NP_110751.1|  90 AVHDYGSKIFV 100
                                   689****9996 PP

  == domain 2  score: 29.6 bits;  conditional E-value: 5.2e-10
                                   EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-EEC CS
                 NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraasye 39 
                                   IvG+G+ Gl aA+++a +g++v+l+e+ d++GG++ ++ 
  gi|13541063|ref|NP_110751.1| 362 IVGGGVKGLEAARFAALNGLSVTLYEQDDKIGGQLNTIY 400
                                   9*********************************99974 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 1.5
                                   HCC.TEEEEEE-SSSS.SSGGG-E CS
                 NAD_binding_8  16 aka.gfdvlllekrdr.lGGraas 37 
                                    ka ++dv ++e  ++ +G  ++s
  gi|13541063|ref|NP_110751.1| 507 EKAdNYDVSIYEEKQYdIGEAMKS 530
                                   565599*****9765437766655 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   0.0   6.5e-10   7.3e-07       1      38 [.     359     396 ..     359     436 .. 0.89

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 6.5e-10
                  FAD_oxidored   1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGll 38 
                                   Dvv+vGGg+ G+ AA  Aa +G +v L e+++ +GG+l
  gi|13541063|ref|NP_110751.1| 359 DVVIVGGGVKGLEAARFAALNGLSVTLYEQDDKIGGQL 396
                                   9***********************************98 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       5.7   6.4e+03      14      35 ..      87     110 ..      86     114 .. 0.76
   2 !   22.3   0.4   1.3e-07   0.00015       2      61 ..     360     430 ..     359     434 .. 0.70
   3 ?    0.5   0.0      0.81   9.1e+02      31      61 ..     482     509 ..     467     519 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 5.7
                                   HHHHHHHTTSEE..EEEESSSSSS CS
                     Pyr_redox  14 lAgalaelgkkV..tvversdkll 35 
                                   lA+a +++g+k+  ++v+++ k l
  gi|13541063|ref|NP_110751.1|  87 LAEAVHDYGSKIfvQLVHAGAKAL 110
                                   689999999886448888887776 PP

  == domain 2  score: 22.3 bits;  conditional E-value: 1.3e-07
                                   EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS....TTSSHHHHHHH.......HHHHHHTTEEEECSE CS
                     Pyr_redox   2 vvvvGgGyiglElAgalaelgkkVtvversdkll....rllDeeaskil.......qeklekngievllnt 61 
                                   vv+vGgG+ glE+A ++a  g +Vt+ e  dk+       +De+ +k++       +e l ++g+e+++++
  gi|13541063|ref|NP_110751.1| 360 VVIVGGGVKGLEAARFAALNGLSVTLYEQDDKIGgqlnTIYDEAKRKEFnrlieyyKEVLDRLGVEIITSE 430
                                   8********************************95445556666555552222222333333366666665 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.81
                                   SSSSSTTSSHHHHHHHHHHHHHTTEEEECSE CS
                     Pyr_redox  31 sdkllrllDeeaskilqeklekngievllnt 61 
                                   s   l+ lD++  +++ +  e +gi+++ ++
  gi|13541063|ref|NP_110751.1| 482 S---LSSLDRARKAAFLKIAESRGIKFIEKA 509
                                   4...4456999999999999*******9876 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.0   2.6e-08   2.9e-05       1      36 [.     359     395 ..     359     448 .. 0.96

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 2.6e-08
                                   EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSG CS
                           DAO   1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiagsga 36 
                                   dvvi+GGG+ Gl +A+++a  g  Vtl+e++d +g g+
  gi|13541063|ref|NP_110751.1| 359 DVVIVGGGVKGLEAARFAALNGlsVTLYEQDDKIG-GQ 395
                                   9******************************9999.64 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   4.8e-08   5.4e-05       2      70 ..     359     429 ..     355     453 .. 0.68

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 4.8e-08
                                   SEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH.....HHHHCHHHHCCCC CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxx RF
                   Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeias.....evvkklnqgiell 70 
                                   dvv++GgG+ Gl+aa+++a +g+ vtl+e+++ + ++   ++ ++ + + ++   +     ev+++l+ +i++ 
  gi|13541063|ref|NP_110751.1| 359 DVVIVGGGVKGLEAARFAALNGLSVTLYEQDDKIGGQLNTIYDEAKRKEFNR---LieyykEVLDRLGVEIITS 429
                                   8999999999999999999999999999766655444333333333333333...2224666666666666555 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.4   1.7e-07   0.00019       1      38 [.     359     396 ..     359     399 .. 0.96

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 1.7e-07
                                   SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGG CS
                 FAD_binding_2   1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefggat 38 
                                   Dv+++G+G+ GL AA  aa +Gl+v++ e+ ++ gg++
  gi|13541063|ref|NP_110751.1| 359 DVVIVGGGVKGLEAARFAALNGLSVTLYEQDDKIGGQL 396
                                   9********************************99975 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   9.2e-07     0.001      29      69 ..     358     398 ..     354     427 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 9.2e-07
                                   -EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHH CS
                   AlaDh_PNT_C  29 akvlviGgGvaGlqAiatakglgakVtvlDvrparleqles 69 
                                   + v+++GgGv Gl+A++ a+  g +Vt+++ + +   ql++
  gi|13541063|ref|NP_110751.1| 358 GDVVIVGGGVKGLEAARFAALNGLSVTLYEQDDKIGGQLNT 398
                                   78****************************99988888877 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   9.3e-07     0.001       1      36 [.     359     393 ..     359     443 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 9.3e-07
                                   CEEEE-SSHHHHHHHHHHHHTT--EEEEES-GGGTT CS
                          GIDA   1 dviViGgGhAGceAAlaaarlGakvlLithkldtia 36 
                                   dv+++GgG  G+eAA  aa  G++v+L+ ++ d+i+
  gi|13541063|ref|NP_110751.1| 359 DVVIVGGGVKGLEAARFAALNGLSVTLY-EQDDKIG 393
                                   79**************************.5555555 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   1.5e-06    0.0017      17      56 ..     357     395 ..     346     432 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.5e-06
                                   EEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TT CS
                          Thi4  17 esDvvivGaGssGLtaayylakkpdlkvailersvspGGG 56 
                                     DvvivG+G  GL aa+  a + +l v++ e+   +GG 
  gi|13541063|ref|NP_110751.1| 357 SGDVVIVGGGVKGLEAARFAALN-GLSVTLYEQDDKIGGQ 395
                                   57*********************.*********9999985 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.2     3e-06    0.0034       2      38 ..     359     395 ..     358     398 .. 0.94

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 3e-06
                                   SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-HH CS
                   HI0933_like   2 dviviGgGaAGlmaAisaakrgkrVlllekakklgrK 38 
                                   dv+++GgG  Gl aA  aa +g +V+l+e+ +k+g  
  gi|13541063|ref|NP_110751.1| 359 DVVIVGGGVKGLEAARFAALNGLSVTLYEQDDKIGGQ 395
                                   89*******************************9965 PP

>> BtpA  BtpA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.0    0.0016       1.8      15      95 ..     119     222 ..      97     239 .. 0.70
   2 ?    2.5   0.0     0.072        81     202     233 ..     276     307 ..     271     319 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0016
                          BtpA  15 Pgsaeyka........nleevidkAvkeakaleegGvDav.......ilenygdaPflke.vdpetvaamtvi......vk 73 
                                   P+ +++++        ++e vi + ++ a+    +G+D++        l +++  P+ ++ +d+   +   +i      ++
  gi|13541063|ref|NP_110751.1| 119 PSKTSFDKnaremdssDIERVIRNYERAASIARRAGFDGIeihgahgYLVDEFISPYWNRrTDKYGGSLEGRIkfpqevID 199
                                   44455554777777788999999999999999999999993333333233566778876636666544444432222229* PP

                          BtpA  74 evksdvsiplGvnv.Lrndavaa 95 
                                   +vks+v ip+G+ + L +d v+ 
  gi|13541063|ref|NP_110751.1| 200 AVKSEVDIPVGIRLsLYEDEVGG 222
                                   ************87577777765 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.072
                          BtpA 202 kvlvgsGvseenlekllsiadGvivgtsikkd 233
                                    +lvgs +++e+++++l++ad v vg  +  d
  gi|13541063|ref|NP_110751.1| 276 TILVGSVTTAEDVRNVLKVADFVAVGRAVLAD 307
                                   589*******************9999877655 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 ?   11.7   0.0   0.00016      0.18       2      35 ..     360     393 ..     359     435 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00016
                                   EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHH CS
                       3HCDH_N   2 vaviGaGtmGagiaavfasagleVvlvdiseeal 35 
                                   v ++G G+ G + a  +a +gl+V+l++ ++++ 
  gi|13541063|ref|NP_110751.1| 360 VVIVGGGVKGLEAARFAALNGLSVTLYEQDDKIG 393
                                   89*************************9987643 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.2   0.00014      0.15       3      33 ..     359     389 ..     357     393 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00014
                                   EEEEE--SHHHHHHHHHHHHTTHHEEEEESS CS
                 FAD_binding_3   3 dVlIVGaGpaGlmlallLseaGvrvvlvekr 33 
                                   dV+IVG+G  Gl +a++ +  G +v+l e+ 
  gi|13541063|ref|NP_110751.1| 359 DVVIVGGGVKGLEAARFAALNGLSVTLYEQD 389
                                   8************************998876 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0    0.0003      0.34       3      36 ..     369     402 ..     369     414 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0003
                                   HHHHHHHHHHTTEEEEEEESSSSSBTTS-EEEET CS
                 Amino_oxidase   3 GLaaArqLlsaGfdVtvlEardrvGGRirtvrsd 36 
                                   GL aAr  + +G++Vt++E +d +GG ++t++++
  gi|13541063|ref|NP_110751.1| 369 GLEAARFAALNGLSVTLYEQDDKIGGQLNTIYDE 402
                                   566666666789******************9987 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.27     3e+02     107     134 ..     191     218 ..     176     231 .. 0.79
   2 ?    7.4   0.0    0.0018         2     187     225 ..     277     313 ..     272     334 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.27
                                   HHHHHHHHHHHHCCSSS-EEEEEESESS CS
                           Dus 107 pdlvaqivkavvkaveiPvtvkirigid 134
                                    +  ++++ av++ v+iPv ++ ++  d
  gi|13541063|ref|NP_110751.1| 191 IKFPQEVIDAVKSEVDIPVGIRLSLYED 218
                                   555578999**********998887666 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0018
                                   EEESS--SHHHHHHHHHHH--SEEEESCHHCCSTTHHHH CS
                           Dus 187 iaNGdIkdaedaqaileetGadgvmigrgalgnPwlfae 225
                                   i  G +++aed++++l+   ad v +gr+ l +P++ ++
  gi|13541063|ref|NP_110751.1| 277 ILVGSVTTAEDVRNVLKV--ADFVAVGRAVLADPYFARK 313
                                   56699*************..**************99874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (547 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       485  (0.0270511); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.70u 0.34s 00:00:01.04 Elapsed: 00:00:00.55
# Mc/sec: 2994.03
//
Query:       gi|13541064|ref|NP_110752.1|  [L=133]
Description: hypothetical protein TVN0233 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00051   20.3  17.1    0.00051   20.3  17.1    2.0  2  EI24      Etoposide-induced protein 2.4 (EI24)
  ------ inclusion threshold ------
      0.096   11.0   2.0       0.17   10.3   2.0    1.3  1  DUF3292   Protein of unknown function (DUF3292)
        1.1    9.4   9.8       0.74   10.0   1.6    2.7  2  CbtB      Probable cobalt transporter subunit (CbtB)
        2.5    7.8  33.9         24    4.6  33.9    1.9  1  Yip1      Yip1 domain


Domain annotation for each model (and alignments):
>> EI24  Etoposide-induced protein 2.4 (EI24)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3  17.1   1.1e-07   0.00051      47     138 ..       3      92 ..       1      95 [. 0.76
   2 ?    1.2   4.7     0.087   3.9e+02      41     113 ..      97     117 ..      87     132 .. 0.50

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 1.1e-07
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHCCTTSHHHHHHHHHHHHHHHH.HHHHH.HH.TTHHH....HHHHH CS
                          EI24  47 vllllllplwlfplvalllaapfygllaekvekrhlglvkslaeslkslllllllll.vllpl.li.Pvvglilsplllsw 124
                                   ++++ l+++ +++lv+l++a++ +++ a++v+kr        ++++  +ll l+++  +l+++ ++ P++g i  ++  +w
  gi|13541064|ref|NP_110752.1|   3 IIIGDLIAFVISVLVTLIIASVPVWVAAKIVAKRST-----FGQAVAATLLSLIIFFiLLFVFsIFtPFIGGIFGFIGALW 78 
                                   5566677788888*******************9764.....44555555555554440444458667************** PP

                                   HHHHHHHHHHHHHH CS
                          EI24 125 ltayfycfeyldla 138
                                   ++ ++y +  +d+ 
  gi|13541064|ref|NP_110752.1|  79 VFRKVYNIGWVDSL 92 
                                   ******99888875 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.087
                                   THHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHCCTTSHHHHHHHHHHHHHHHHHHHHHHHTTH CS
                          EI24  41 llasllvllllllplwlfplvalllaapfygllaekvekrhlglvkslaeslkslllllllllvllplliPvv 113
                                   ++ +++++++++l ++lfp                                                    v+
  gi|13541064|ref|NP_110752.1|  97 IAIFIAIMIYIILGAFLFP----------------------------------------------------VI 117
                                   2223444444444455554....................................................32 PP

>> DUF3292  Protein of unknown function (DUF3292)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   2.0   3.7e-05      0.17     129     176 ..      79     125 ..      77     130 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 3.7e-05
                       DUF3292 129 afcavYfvaWlldllvpllvavlivLilvpeaRellFPpaplalvdsk 176
                                   +f  vY + W+ d l+ +++a++i+++++    ++lFP   +++++++
  gi|13541064|ref|NP_110752.1|  79 VFRKVYNIGWV-DSLALTIIAIFIAIMIYIILGAFLFPVIHTSMIHEH 125
                                   6899******5.9******************************99875 PP

>> CbtB  Probable cobalt transporter subunit (CbtB)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   1.6   0.00016      0.74       3      30 ..      32      59 ..      30      62 .. 0.89
   2 ?    3.4   1.4     0.018        81       9      38 ..      91     120 ..      88     126 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00016
                          CbtB  3 ssasaqrllqlvaAllLGlllvylvgfs 30
                                   +a+++++ q+vaA+lL l++ +++ f+
  gi|13541064|ref|NP_110752.1| 32 IVAKRSTFGQAVAATLLSLIIFFILLFV 59
                                  5678999****************99996 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.018
                          CbtB   9 rllqlvaAllLGlllvylvgfsqaaalHna 38 
                                   +l+ ++ A++++++++ ++g    +++H +
  gi|13541064|ref|NP_110752.1|  91 SLALTIIAIFIAIMIYIILGAFLFPVIHTS 120
                                   577889999999999999998877777755 PP

>> Yip1  Yip1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6  33.9    0.0054        24      66     167 ..       8     103 ..       1     132 [. 0.72

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.0054
                          Yip1  66 iiggylglllgllllalllhliakllggkgsfkqtlsvvgyallPlilgaliaillllllgt.........llllvgllal 137
                                   +i++++ +l++l++ ++ ++++ak+   + +f+q+++++ ++l++++++++++ ++ ++ g+         +         
  gi|13541064|ref|NP_110752.1|   8 LIAFVISVLVTLIIASVPVWVAAKIVAKRSTFGQAVAATLLSLIIFFILLFVFSIFTPFIGGifgfigalwV--------- 79 
                                   78888888999*******************************************998776664444444440......... PP

                          Yip1 138 iWslvllylglkaahnlskkkallaali....ll 167
                                             +++++n+ +  +l+ ++i    ++
  gi|13541064|ref|NP_110752.1|  80 ----------FRKVYNIGWVDSLALTIIaifiAI 103
                                   ..........455555555544444444322222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1403  (0.0782531); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); 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):               4  [number of targets reported over threshold]
# CPU time: 0.62u 0.33s 00:00:00.95 Elapsed: 00:00:00.50
# Mc/sec: 802.70
//
Query:       gi|13541065|ref|NP_110753.1|  [L=260]
Description: Zn-ribbon domain-containing protein [Thermoplasma volcanium GSS1]
Scores for complete 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-06   25.8   3.1    1.6e-05   24.9   3.1    1.3  1  UPF0547         Uncharacterised protein family UPF0547
    1.5e-05   24.2   2.9    2.4e-05   23.6   2.9    1.2  1  zf-ribbon_3     zinc-ribbon domain
    3.8e-05   23.8  13.7    3.8e-05   23.8  13.7    2.4  3  SpoIIM          Stage II sporulation protein M
    8.2e-05   22.6   0.1    0.00012   22.0   0.1    1.2  1  DZR             Double zinc ribbon
    0.00029   20.4   1.1    0.00041   20.0   1.1    1.2  1  zinc_ribbon_2   zinc-ribbon domain
     0.0029   17.1   0.9     0.0043   16.6   0.9    1.3  1  RecR            RecR protein
  ------ inclusion threshold ------
        0.1   12.2   0.2       0.18   11.5   0.2    1.3  1  zf-P11          P-11 zinc finger
       0.12   13.1   0.7       0.23   12.2   0.7    1.5  1  zinc_ribbon_15  zinc-ribbon family
       0.19   11.6   0.7         17    5.3   0.3    2.2  2  zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
        0.3   10.7   3.3        0.6    9.8   3.3    1.5  1  zf-tcix         Putative treble-clef, zinc-finger, Zn-binding
       0.31   11.0   1.5       0.52   10.3   1.5    1.3  1  Prok-RING_1     Prokaryotic RING finger family 1
       0.42   10.7   1.1        7.9    6.6   0.3    2.5  3  zf-ACC          Acetyl-coA carboxylase zinc finger domain


Domain annotation for each model (and alignments):
>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   3.1   1.1e-08   1.6e-05       2      22 ..       5      25 ..       5      28 .. 0.96

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 1.1e-08
                       UPF0547  2 vCPeCeakvPvaaqfCphCGy 22
                                  +CP+C +++P+   +Cp CGy
  gi|13541065|ref|NP_110753.1|  5 QCPQCGTIIPAGSDVCPICGY 25
                                  6*******************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 !   23.6   2.9   1.6e-08   2.4e-05       4      24 ..       5      25 ..       3      27 .. 0.92

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 1.6e-08
                   zf-ribbon_3  4 rCPnCGaplssddnvCpyCGt 24
                                  +CP+CG+++ ++  vCp CG+
  gi|13541065|ref|NP_110753.1|  5 QCPQCGTIIPAGSDVCPICGY 25
                                  7******99***********8 PP

>> SpoIIM  Stage II sporulation protein M
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   1.0     0.033        50      26      67 ..      29      71 ..      19      81 .. 0.72
   2 !   23.8  13.7   2.6e-08   3.8e-05       2     153 ..      53     211 ..      52     213 .. 0.75
   3 ?   -1.2   0.1       1.2   1.9e+03      58      69 ..     226     238 ..     218     255 .. 0.56

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.033
                        SpoIIM 26 seskensalslflaifan.NlrvalllfllGllllgiptilvl 67
                                  +++++ns   +f++ifa   + +++l+f++ ++l+ ++t++ +
  gi|13541065|ref|NP_110753.1| 29 KKTTDNSWRGIFASIFARrRILTMVLVFIFEIALMFVITAIPM 71
                                  4556677778899999988888889999988876666666554 PP

  == domain 2  score: 23.8 bits;  conditional E-value: 2.6e-08
                        SpoIIM   2 lllflvgillgallaa..........snfaeqis.......seskensalslflaifanNlrvalllf..llGllllgipt 63 
                                   +l+f++ i+l ++++a                         +   + + ls +++if +N ++a + +  + G      ++
  gi|13541065|ref|NP_110753.1|  53 VLVFIFEIALMFVITAipmsfsqakaI------AgqtepslQAVRSLPILSRSVSIFSHNYEIASIEIvpVIG-----QIF 122
                                   678999999999999887665443330......2444466666677788999***********9999834444.....444 PP

                        SpoIIM  64 ilvl.linGfvlGavaalvaef..gglllflllilPhgilelpaiiiagaaglrlgkalrsrrkalkeakrellklllllv 141
                                   +++    +++vl a+   + +   g + lf ll+lP  +lelp++ ia++ g  l  ++   rk+++ ++++++ + ll+ 
  gi|13541065|ref|NP_110753.1| 123 FVIStYSTAIVLDAL--AIGQGvpGPIALFTLLLLPYSWLELPSYAIAATEGGFLIASIF--RKQFRVEIKRAVIVWLLVG 199
                                   444435556666655..333334599************************9988888884..5899999999999999999 PP

                        SpoIIM 142 pllliAaliEaf 153
                                   + ll A+++E++
  gi|13541065|ref|NP_110753.1| 200 IELLTAGIFESW 211
                                   9*********96 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 1.2
                        SpoIIM  58 llgiptilvl.li 69 
                                   + +ip++++l ++
  gi|13541065|ref|NP_110753.1| 226 ITWIPYVIILaIF 238
                                   3333333333222 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.1   7.9e-08   0.00012       1      25 [.       6      30 ..       6      50 .. 0.91

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 7.9e-08
                           DZR  1 CpqCgeelppdarfCseCgtklkav 25
                                  CpqCg+ +p+++ +C+ Cg +lk+ 
  gi|13541065|ref|NP_110753.1|  6 CPQCGTIIPAGSDVCPICGYTLKKK 30
                                  **********************965 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   1.1   2.7e-07   0.00041       2      22 ..       6      26 ..       5      27 .. 0.95

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 2.7e-07
                 zinc_ribbon_2  2 CpnCGaelqdnakFCpyCGtp 22
                                  Cp+CG+ ++ ++  Cp CG+ 
  gi|13541065|ref|NP_110753.1|  6 CPQCGTIIPAGSDVCPICGYT 26
                                  *******************95 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.9   2.9e-06    0.0043      15      34 ..       2      23 ..       1      26 [. 0.93

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.9e-06
                                  H-EE-TTT--E..ESSSS-CCC CS
                          RecR 15 kvrhCsrCgnl..teedlCaIC 34
                                  kv +C++Cg++  + +d+C+IC
  gi|13541065|ref|NP_110753.1|  2 KVEQCPQCGTIipAGSDVCPIC 23
                                  7899********999******* PP

>> zf-P11  P-11 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.2   0.00012      0.18      24      45 ..       6      27 ..       4      31 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00012
                                  EHHHHHHHHHHSSBETTTSSB- CS
                        zf-P11 24 ClrClqllLsvserCpiCkkPL 45
                                  C +C +++   s+ CpiC + L
  gi|13541065|ref|NP_110753.1|  6 CPQCGTIIPAGSDVCPICGYTL 27
                                  99****************9877 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.7   0.00016      0.23      65      86 .]       3      24 ..       1      24 [. 0.94

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00016
                zinc_ribbon_15 65 kkeCknCgkeveeefkyCpkCg 86
                                  +++C++Cg+ + + ++ Cp Cg
  gi|13541065|ref|NP_110753.1|  3 VEQCPQCGTIIPAGSDVCPICG 24
                                  689******************9 PP

>> zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.3     0.011        17       1       8 [.       3      10 ..       3      13 .. 0.85
   2 ?    4.6   0.0     0.018        27       3      17 ..      19      33 ..      17      41 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.011
                                  -EE-SSS- CS
                zf-C4_Topoisom  1 vekCPkCg 8 
                                  ve+CP+Cg
  gi|13541065|ref|NP_110753.1|  3 VEQCPQCG 10
                                  589****9 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.018
                                  E-SSS--EEEEEE-S CS
                zf-C4_Topoisom  3 kCPkCggdLvlkrgk 17
                                   CP Cg  L +k++ 
  gi|13541065|ref|NP_110753.1| 19 VCPICGYTLKKKTTD 33
                                  5********999885 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 ?    9.8   3.3    0.0004       0.6      10      39 ..       3      30 ..       2      33 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0004
                       zf-tcix 10 vrkCpkCGtyNGtRglsCkNkaCdqvfkkk 39
                                  v +Cp+CGt+ +  + +C  + C + +kkk
  gi|13541065|ref|NP_110753.1|  3 VEQCPQCGTIIPAGSDVC--PICGYTLKKK 30
                                  669*******99999999..6777777665 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   1.5   0.00035      0.52       5      27 ..       4      24 ..       1      31 [. 0.89

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00035
                   Prok-RING_1  5 kkCpvCgkelkeedDiVvCpeCg 27
                                  ++Cp Cg  +  ++D  vCp Cg
  gi|13541065|ref|NP_110753.1|  4 EQCPQCGTIIPAGSD--VCPICG 24
                                  68*************..6****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 ?    6.6   0.3    0.0053       7.9       3      11 ..       5      13 ..       5      14 .. 0.92
   2 ?    2.0   0.0      0.15   2.2e+02       4      15 ..      20      31 ..      19      37 .. 0.80
   3 ?   -3.1   0.0         6   8.9e+03      10      16 ..     178     184 ..     177     185 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0053
                        zf-ACC  3 KCpsCgeml 11
                                  +Cp+Cg+++
  gi|13541065|ref|NP_110753.1|  5 QCPQCGTII 13
                                  7*****997 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.15
                        zf-ACC  4 CpsCgemlykke 15
                                  Cp Cg +l kk 
  gi|13541065|ref|NP_110753.1| 20 CPICGYTLKKKT 31
                                  999999999986 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 6
                        zf-ACC  10 mlykkeL 16 
                                   ++++k++
  gi|13541065|ref|NP_110753.1| 178 SIFRKQF 184
                                   79***97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1183  (0.0659825); expected 358.6 (0.02)
Passed bias filter:                      620  (0.0345808); expected 358.6 (0.02)
Passed Vit filter:                        95  (0.00529868); 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: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 1902.34
//
Query:       gi|13541066|ref|NP_110754.1|  [L=86]
Description: hypothetical protein TVN0235 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       311  (0.0173462); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 629.64
//
Query:       gi|13541067|ref|NP_110755.1|  [L=232]
Description: DNA-binding protein [Thermoplasma volcanium GSS1]
Scores for 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   77.4   0.1    1.2e-21   76.2   0.1    1.6  2  HTH_10           HTH DNA binding domain
     0.0014   18.3   0.1      0.027   14.2   0.0    2.9  3  HTH_psq          helix-turn-helix, Psq domain
     0.0036   17.9   0.1      0.008   16.7   0.1    1.7  1  Mga              Mga helix-turn-helix domain
      0.008   16.2   0.0       0.02   14.9   0.0    1.6  1  DUF2089          Protein of unknown function (DUF2089)
  ------ inclusion threshold ------
      0.035   13.7   0.3       0.08   12.5   0.0    1.7  2  HTH_24           Winged helix-turn-helix DNA-binding
      0.043   13.6   0.0         17    5.3   0.0    3.3  3  MerR             MerR family regulatory protein
      0.065   13.5   0.5       0.17   12.1   0.5    1.7  1  UPF0122          Putative helix-turn-helix protein, YlxM / p1
      0.093   12.5   0.0       0.56   10.0   0.0    2.3  2  CUE              CUE domain
      0.098   12.5   0.1        1.5    8.7   0.1    2.4  2  HU-CCDC81_bac_2  CCDC81-like prokaryotic HU domain 2
       0.21   11.8   0.2        2.5    8.3   0.0    2.6  3  HTH_28           Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       3.6   6.5e+03      32      41 ..      81      90 ..      78      92 .. 0.73
   2 !   76.2   0.1   6.8e-25   1.2e-21       1      53 []     163     215 ..     163     215 .. 0.99

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 3.6
                        HTH_10 32 elGIskstls 41
                                  + ++s+st+ 
  gi|13541067|ref|NP_110755.1| 81 RCNVSNSTIR 90
                                  6789999986 PP

  == domain 2  score: 76.2 bits;  conditional E-value: 6.8e-25
                        HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaesklie 53 
                                   LT+kql++l  Ay++GYFd+P+r+++ eLAk+++Is stl+ehL+ka +k+++
  gi|13541067|ref|NP_110755.1| 163 LTEKQLRYLVSAYHNGYFDVPKRTNIVELAKQFNISYSTLQEHLEKAVNKIMK 215
                                   9**************************************************96 PP

>> HTH_psq  helix-turn-helix, Psq domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       1.3   2.4e+03      27      35 ..      83      91 ..      83      93 .. 0.82
   2 ?   -0.5   0.0      0.59   1.1e+03      25      32 ..     179     186 ..     178     186 .. 0.90
   3 !   14.2   0.0   1.5e-05     0.027      21      39 ..     190     208 ..     188     216 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.3
                       HTH_psq 27 giPrsTLwr 35
                                  ++++sT+++
  gi|13541067|ref|NP_110755.1| 83 NVSNSTIRK 91
                                  599***985 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.59
                       HTH_psq  25 kYgiPrsT 32 
                                   ++++P++T
  gi|13541067|ref|NP_110755.1| 179 YFDVPKRT 186
                                   79****99 PP

  == domain 3  score: 14.2 bits;  conditional E-value: 1.5e-05
                       HTH_psq  21 kAArkYgiPrsTLwrrkrg 39 
                                   ++A+ ++i++sTL+++++ 
  gi|13541067|ref|NP_110755.1| 190 ELAKQFNISYSTLQEHLEK 208
                                   58*************9986 PP

>> Mga  Mga helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.1   4.5e-06     0.008       4      57 ..     155     212 ..     152     229 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 4.5e-06
                                   XTHHHHHHHHHHSHHHHHHHHHH....HHSEEEHHHHHHHCT--HHHHHHHHHHHHHH CS
                           Mga   4 sleellqellkeslkyqllkflf....eeeevsieelaqelyiSestlkrkikelnkl 57 
                                   sl++l+++l +++l y + ++        ++++i ela+++ iS+stl+ ++++  + 
  gi|13541067|ref|NP_110755.1| 155 SLSDLFSDLTEKQLRYLVSAYHNgyfdVPKRTNIVELAKQFNISYSTLQEHLEKAVNK 212
                                   5566666666666666665543222256899*******************99764333 PP

>> DUF2089  Protein of unknown function (DUF2089)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   1.1e-05      0.02      46      77 ..     182     213 ..     153     220 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.1e-05
                       DUF2089  46 ikarGnlkevekelgisYpTvrnrldeileaL 77 
                                   + +r n+ e++k+++isY T++++l++ ++++
  gi|13541067|ref|NP_110755.1| 182 VPKRTNIVELAKQFNISYSTLQEHLEKAVNKI 213
                                   45789*********************999886 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 ?   -3.0   0.1       3.1   5.5e+03      26      35 ..      81      90 ..      79      91 .. 0.84
   2 ?   12.5   0.0   4.5e-05      0.08      17      43 ..     185     211 ..     184     212 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 3.1
                        HTH_24 26 rlglSpstvn 35
                                  r+++S st++
  gi|13541067|ref|NP_110755.1| 81 RCNVSNSTIR 90
                                  7899999986 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 4.5e-05
                        HTH_24  17 risqreLAerlglSpstvnrrlkrLee 43 
                                   r+++ eLA++ ++S st+ ++l++ ++
  gi|13541067|ref|NP_110755.1| 185 RTNIVELAKQFNISYSTLQEHLEKAVN 211
                                   78999*****************99766 PP

>> MerR  MerR family regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.14   2.6e+02       8      18 ..      81      91 ..      78      98 .. 0.84
   2 ?    2.4   0.0     0.073   1.3e+02       8      20 ..     160     172 ..     156     175 .. 0.83
   3 ?    5.3   0.0    0.0093        17       2      16 ..     188     202 ..     187     204 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.14
                                  HHTTTHHHHHH CS
                          MerR  8 ltGvsprtLRy 18
                                  +++vs +t+R 
  gi|13541067|ref|NP_110755.1| 81 RCNVSNSTIRK 91
                                  689*******5 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.073
                                   HHTTTHHHHHHHH CS
                          MerR   8 ltGvsprtLRyYE 20 
                                   +++++ + LRy+ 
  gi|13541067|ref|NP_110755.1| 160 FSDLTEKQLRYLV 172
                                   58*********85 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.0093
                                   HHHHHHHHTTTHHHH CS
                          MerR   2 IgevAeltGvsprtL 16 
                                   I e+A+ +++s +tL
  gi|13541067|ref|NP_110755.1| 188 IVELAKQFNISYSTL 202
                                   88************9 PP

>> UPF0122  Putative helix-turn-helix protein, YlxM / p13 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.5   9.4e-05      0.17       9      70 ..     155     223 ..     147     228 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 9.4e-05
                       UPF0122   9 aLfdiYqsLLTekqanylelyyadDl.......SlsEiAeefnvsrqavydnikr.tekllekyEekLkl 70 
                                    L d++ + LTekq +yl   y++ +        + E+A +fn+s +++ +++++ ++k+++  E  L++
  gi|13541067|ref|NP_110755.1| 155 SLSDLFSD-LTEKQLRYLVSAYHNGYfdvpkrtNIVELAKQFNISYSTLQEHLEKaVNKIMKGIEPYLTI 223
                                   56666655.7*******9766665543334333689*****************77368888888877765 PP

>> CUE  CUE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00031      0.56       8      29 ..     156     177 ..     155     177 .. 0.93
   2 ?   -2.0   0.0       1.7   3.1e+03      31      40 ..     206     215 ..     203     216 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00031
                                   HHHHSTTS-HHHHHHHHHHCTT CS
                           CUE   8 LkemFPdldeevIravLrasng 29 
                                   L+++F dl+e ++r+  +a+++
  gi|13541067|ref|NP_110755.1| 156 LSDLFSDLTEKQLRYLVSAYHN 177
                                   99***************99986 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.7
                                   HHHHHHHHHH CS
                           CUE  31 vEatinaLLe 40 
                                   +E ++n+++ 
  gi|13541067|ref|NP_110755.1| 206 LEKAVNKIMK 215
                                   799***9986 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 ?    0.8   0.0      0.26   4.7e+02      20      40 ..      47      67 ..      42      76 .. 0.78
   2 ?    8.7   0.1   0.00084       1.5       8      41 ..     192     225 ..     189     229 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.26
               HU-CCDC81_bac_2 20 qkiekeveelkqeLeeegrve 40
                                    +ek+v e+++ L+++  + 
  gi|13541067|ref|NP_110755.1| 47 DSLEKYVPEIEKSLNTNSLYR 67
                                  5789**********9987665 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00084
               HU-CCDC81_bac_2   8 aeaegisyeeAlqkiekeveelkqeLeeegrvel 41 
                                   a++ +isy + ++ +ek+v+++ + +e   ++ l
  gi|13541067|ref|NP_110755.1| 192 AKQFNISYSTLQEHLEKAVNKIMKGIEPYLTIAL 225
                                   7889******************998876666665 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1      0.63   1.1e+03      18      31 ..      78      91 ..      66      95 .. 0.78
   2 ?   -2.7   0.0       3.7   6.6e+03      24      38 ..     163     177 ..     162     179 .. 0.83
   3 ?    8.3   0.0    0.0014       2.5      14      32 ..     187     205 ..     182     210 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.63
                        HTH_28 18 aArelgisrrtvyr 31
                                  ++++ ++s +t+++
  gi|13541067|ref|NP_110755.1| 78 LSCRCNVSNSTIRK 91
                                  5788999****997 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 3.7
                        HTH_28  24 isrrtvyrWikryee 38 
                                   +++ +++ ++++y  
  gi|13541067|ref|NP_110755.1| 163 LTEKQLRYLVSAYHN 177
                                   688999999999976 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.0014
                        HTH_28  14 svreaArelgisrrtvyrW 32 
                                   ++ e+A++++is++t++  
  gi|13541067|ref|NP_110755.1| 187 NIVELAKQFNISYSTLQEH 205
                                   7889***********9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       780  (0.0435049); expected 358.6 (0.02)
Passed bias filter:                      689  (0.0384294); 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: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.52
# Mc/sec: 1335.04
//
Query:       gi|13541068|ref|NP_110756.1|  [L=998]
Description: thermopsin [Thermoplasma volcanium GSS1]
Scores for complete 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-74  249.9  16.7    2.6e-74  249.9  16.7    2.9  2  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 !  249.9  16.7   1.5e-78   2.6e-74      10     260 .]      79     334 ..      72     334 .. 0.95
   2 ?   -7.6   7.5         1   1.8e+04     122     153 ..     788     816 ..     768     972 .. 0.71

  Alignments for each domain:
  == domain 1  score: 249.9 bits;  conditional E-value: 1.5e-78
                    Thermopsin  10 ssepaPmGiadyGiknnsgkltpysyntssvlGevnisslsaynsssnspesaslQLNvvlevvt..ggktysywvQnVvs 88 
                                     +p+PmG++d G++nnsg+l++y+++ ssv+Ge++++s + y+++ ++p+s+s+QLN+vl++vt  g+ +y +w+QnVv 
  gi|13541068|ref|NP_110756.1|  79 IASPSPMGLSDIGLYNNSGHLSAYNVTSSSVMGEITLNSSNEYYLDDDMPNSFSIQLNAVLNNVTlhGTPKYVFWTQNVVV 159
                                   57899************************************************************99999*********** PP

                    Thermopsin  89 fnttekqltfidNiWNftsp.sanlsnsaisGnGtvyasskgefYyayateylelslPltlkLvinvsltsngvpevsFgY 168
                                   ++ ++++ltfidN+WNf+s+ s+ l  s+++G+G+++   ++++Yy+++++ l++s+P+tlkL++n s + ng++ v+F+Y
  gi|13541068|ref|NP_110756.1| 160 YSVRTHELTFIDNVWNFSSRsSFALPLSTLEGKGKIV---SNKYYYYVGPT-LNISFPFTLKLYLNYSFA-NGNDLVYFNY 235
                                   *******************94567999**********...99999999**9.***************998.9999****** PP

                    Thermopsin 169 sid....ggvvtYDnvtinstgkasa.eilvngssltpsgllyDaeLvlgGpgngekttfnslnatlsLyYlngtn..yqp 242
                                   si     ++  +YD vt+ns+++ s  ++ v+g+ ++psgll DaeLv+gGpg+g++++f+s+n t+sLy +n+t   y+p
  gi|13541068|ref|NP_110756.1| 236 SILnpsySKSGSYDMVTFNSNSSESGaYYFVSGYVTSPSGLLNDAELVIGGPGGGSNANFYSINGTMSLYLFNETAhaYEP 316
                                   *999**9999***********998888********************************************9999888*** PP

                    Thermopsin 243 vknaydfGsdTaEtaenv 260
                                   vk+ayd+G dT+Et+++v
  gi|13541068|ref|NP_110756.1| 317 VKSAYDYGFDTGETSYGV 334
                                   ***************987 PP

  == domain 2  score: -7.6 bits;  conditional E-value: 1
                    Thermopsin 122 tvyasskgefYyayateylelslPltlkLvin 153
                                   ++y  s++++ yay+++ + +++ ++  ++ +
  gi|13541068|ref|NP_110756.1| 788 YIY--SGENYIYAYKNN-TYYNFTVNTGVLFS 816
                                   455..233333333333.22222222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (998 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       503  (0.0280551); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.76u 0.30s 00:00:01.06 Elapsed: 00:00:00.49
# Mc/sec: 6108.07
//
Query:       gi|13541069|ref|NP_110757.1|  [L=169]
Description: hypothetical protein TVN0238 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       421  (0.0234815); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); 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: 0.43u 0.30s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1160.01
//
Query:       gi|13541070|ref|NP_110758.1|  [L=386]
Description: citrate synthase [Thermoplasma volcanium GSS1]
Scores for complete 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-103  345.6   0.0   3.6e-103  345.4   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 !  345.4   0.0    2e-107  3.6e-103       1     361 []      11     368 ..      11     368 .. 0.94

  Alignments for each domain:
  == domain 1  score: 345.4 bits;  conditional E-value: 2e-107
                                   GGTTEEEEEESSEEEETTTTEEEETTEEHHHHHHHHS-HHHHHHHHHHSS---HHHHHHHHHHHHCTTS--HHHHHHHHCS CS
                  Citrate_synt   1 glrgvaaleteisevdgekgelrYRGydieeLaeekssfeevaylLltgelPtkeelkefkeelaearklpekvlealeal 81 
                                   gl++v +  t+++++dg+kg+lrY Gy++e+++++ ++ ee+ yl+l+gelP+++elk fke++++  ++p+ v++ +++l
  gi|13541070|ref|NP_110758.1|  11 GLEDVNIKWTRLTTIDGNKGILRYGGYSVEDIINNGAQAEEIQYLFLYGELPNAQELKIFKENVQKGYNIPDFVINSIRQL 91 
                                   788999999************************99********************************************** PP

                                   STTS-HHHHHHHHHHHHHHHSTT.CTCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS.--.---TTSSHHHHHHHHHH CS
                  Citrate_synt  82 pkdahpmavlraavsalsaddee.seakeeseeaalrdalkliAklptiaaaiyrarlgrepl.epddklsyaenflymlr 160
                                   p++++ +a+  aav++++a++ + + +k++ ++ a    +++i+++++i+a++yr+ lg  p+ +p++++syae+fl++ +
  gi|13541070|ref|NP_110758.1|  92 PRESDAVAMQMAAVASMAASEIKfKWNKDTDRDVA----AQMIGSMSAITANVYRHILGM-PAeRPKPSDSYAESFLKAAF 167
                                   *9999999999999999999876545555544433....46*****************97.78689999************ PP

                                   SS---HHHHHHHHHHHHHHS--SSSHHHHHHHHHHTTT--HHHHHHHHHHHHTSTTTTTHHHHHHHHHHHHSSGG.GHHHH CS
                  Citrate_synt 161 gkkpdeeeaklldlalvlhaDHelnaSTfaarvvaStladlysaiaagigalkGplhgganeavlkmleeigsaeveveey 241
                                   g++ ++ee++++++al+l+ DHe+ aST a  v+ Stl+d+ys i+a+++alkGplhgga ea+++ ++ei++++ +ve++
  gi|13541070|ref|NP_110758.1| 168 GRNVTKEEVDAINTALILYTDHEVPASTTAGLVAVSTLSDIYSGITAALAALKGPLHGGAAEAAIAQFDEIKEPS-NVEKW 247
                                   ***********************************************************************9999.***** PP

                                   HHHHHHTTTS--TTBC-SSSSS--HHHHHHHHHHHHHHTC.HTHHHHHHHHHHHHHHHHHHHHCHHGCT-EB-THHHHHHH CS
                  Citrate_synt 242 lekvlakekerlpGfGHrvykksDpRakilkelaeelaee.kgkdpllklaeeleevapevlkekeeknlypNvDfysgvl 321
                                    ++++ ++k+rl+GfGHrvyk++DpRaki+k +ae+l+++  + ++ +++a++le++  +  ++ + k++ypN D++sg++
  gi|13541070|ref|NP_110758.1| 248 FNDNIINGKKRLMGFGHRVYKTYDPRAKIFKGIAENLSKNnAEVKKIYDIATKLEDLGVK--QFGS-KGIYPNTDYFSGIV 325
                                   ****9999*******************************9888999***********999..7789.************** PP

                                   HHHTT--GGG..HHHHHHHHHHHHHHHHHHHHH.HT------E CS
                  Citrate_synt 322 yralgipeel..ftvlfaisRvaGwlAhileql.adnkiiRPr 361
                                   y ++g+p +   +t+lfa+sRv+Gw Ah +e+  +++++iRPr
  gi|13541070|ref|NP_110758.1| 326 YMSVGFPLRNniYTALFALSRVTGWEAHFIEYVeEQQRLIRPR 368
                                   *******98666*******************98789******8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (386 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       593  (0.0330749); expected 358.6 (0.02)
Passed bias filter:                      508  (0.028334); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.28s 00:00:00.90 Elapsed: 00:00:00.47
# Mc/sec: 2443.39
//
Query:       gi|13541071|ref|NP_110759.1|  [L=105]
Description: hypothetical protein TVN0240 [Thermoplasma volcanium GSS1]
Scores for complete 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-07   30.8   0.0    4.1e-07   30.4   0.0    1.5  1  DrsE      DsrE/DsrF-like family
     0.0083   16.0   0.0     0.0096   15.8   0.0    1.4  1  DrsE_2    DsrE/DsrF/DrsH-like family
  ------ inclusion threshold ------
      0.012   15.8   0.0      0.014   15.5   0.0    1.2  1  DsrH      DsrH like protein


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 !   30.4   0.0   6.9e-11   4.1e-07      67     116 ..      54     104 ..       8     105 .] 0.92

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 6.9e-11
                                   CGGGT-EEEEEHHHHHHTT--GGGE-.T--EEEE-HHHHHHHHHH-SEEEE CS
                          DrsE  67 lkeygvklyvCgqaakargldededl.gvgvevsglgelaelqnegdrvit 116
                                   lk+++v++++Cg++++ar++ +de+  gv  ++++l e+++  +eg+ +++
  gi|13541071|ref|NP_110759.1|  54 LKNKKVQVVACGTSMEARNIQKDELApGVVYVPASLKEIIKRKQEGYMYLV 104
                                   77888****************776558999*****************9986 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 !   15.8   0.0   1.6e-06    0.0096     106     147 ..      55      98 ..       5     104 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.6e-06
                                   HHTT-EEEEEHHHHHHHT--GGGB-TT-..EEE-HHHHHHHHHC CS
                        DrsE_2 106 keagvklvaCqmtmdlmglkkeelidgv..eiagaatylkeaee 147
                                   k++ v++vaC  +m+  +++k+el +gv   +a  ++ +k+ +e
  gi|13541071|ref|NP_110759.1|  55 KNKKVQVVACGTSMEARNIQKDELAPGVvyVPASLKEIIKRKQE 98 
                                   6899************************5344555666666666 PP

>> DsrH  DsrH like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.0   2.4e-06     0.014      21      72 ..      33      85 ..      14      92 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.4e-06
                                  EEEE-GGGGGGGBTTBTTHHHHHTSSSEEEEEHHHHHHTT-T.TSB-TTSEEE CS
                          DsrH 21 avlLieDgVyaalkgsrllkalkeasvklyaLkeDleARGlt.eqlsegvkvi 72
                                  +v+ +  g+ a+++++r+   lk+++v+++a    +eAR+++ ++l++gv  +
  gi|13541071|ref|NP_110759.1| 33 EVVYLNGGIAAVTEKNRIGPILKNKKVQVVACGTSMEARNIQkDELAPGVVYV 85
                                  57778889**********************************88899998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       358  (0.0199677); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.46
# Mc/sec: 691.46
//
Query:       gi|13541072|ref|NP_110760.1|  [L=128]
Description: hypothetical protein TVN0241 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score 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   0.4       0.28   11.3   0.4    1.5  1  TM_PBP2_N  N-terminal of TM subunit in PBP-dependent ABC tran


Domain annotation for each model (and alignments):
>> TM_PBP2_N  N-terminal of TM subunit in PBP-dependent ABC transporters
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.4   1.6e-05      0.28       5      23 ..       6      24 ..       3      26 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 1.6e-05
                     TM_PBP2_N  5 vfqvfpvlyTistafTNyG 23
                                  +fq  pvly ++tafT yG
  gi|13541072|ref|NP_110760.1|  6 AFQASPVLYMAATAFTAYG 24
                                  79****************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       698  (0.0389313); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 837.48
//
Query:       gi|13541073|ref|NP_110761.1|  [L=59]
Description: hypothetical protein TVN0242 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       292  (0.0162865); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 410.28
//
Query:       gi|13541074|ref|NP_110762.1|  [L=984]
Description: hypothetical protein TVN0243 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-79  268.1   0.0    1.7e-79  267.8   0.0    1.1  1  Molybdopterin    Molybdopterin oxidoreductase
    7.9e-24   83.8   0.0    1.4e-23   83.0   0.0    1.4  1  Molydop_binding  Molydopterin dinucleotide binding domain
    5.8e-18   64.6   0.2    5.8e-18   64.6   0.2    2.3  1  Molybdop_Fe4S4   Molybdopterin oxidoreductase Fe4S4 domain
    3.8e-12   46.1   0.0    8.2e-12   45.0   0.0    1.6  1  Fer2_4           2Fe-2S iron-sulfur cluster binding domain
    2.5e-11   42.9  19.1    3.9e-07   29.6   2.6    3.4  3  Fer4             4Fe-4S binding domain
      7e-11   41.5   4.6    2.2e-10   39.9   3.8    2.4  2  NADH-G_4Fe-4S_3  NADH-ubiquinone oxidoreductase-G iron-sulfur
    1.7e-10   40.5  13.2    4.5e-06   26.5   2.2    2.8  2  Fer4_6           4Fe-4S binding domain
    1.8e-09   37.6  12.1    4.7e-05   23.4   2.4    3.6  3  Fer4_10          4Fe-4S dicluster domain
    1.3e-08   34.8   8.2    1.3e-08   34.8   8.2    2.9  3  Fer4_21          4Fe-4S dicluster domain
    1.4e-08   35.2   7.7    1.4e-08   35.2   7.7    3.5  3  Fer4_7           4Fe-4S dicluster domain
    5.3e-07   29.5   0.0    5.3e-07   29.5   0.0    1.9  1  Fer2             2Fe-2S iron-sulfur cluster binding domain
    1.3e-06   28.4   9.3    1.3e-06   28.4   9.3    3.5  3  Fer4_9           4Fe-4S dicluster domain
    4.4e-06   27.1   7.0    4.4e-06   27.1   7.0    3.0  2  Fer4_8           4Fe-4S dicluster domain
    0.00033   20.6  24.4     0.0035   17.3   4.7    3.3  2  Fer4_2           4Fe-4S binding domain
    0.00065   20.4   4.0       0.37   11.5   1.0    2.6  2  Fer4_15          4Fe-4S single cluster domain
     0.0024   18.7  19.6      0.023   15.6   5.4    4.1  3  Fer4_16          4Fe-4S double cluster binding domain
     0.0093   16.4   0.8          4    7.9   0.1    2.6  2  zf-C2HE          C2HE / C2H2 / C2HC zinc-binding finger
  ------ inclusion threshold ------
      0.014   15.2   0.0        7.5    6.3   0.0    2.6  2  TPP_enzyme_M     Thiamine pyrophosphate enzyme, central domai
      0.024   15.2  11.6          2    9.0   1.9    3.1  3  Fer4_13          4Fe-4S single cluster domain of Ferredoxin I
        0.6   11.0  14.3        2.7    8.9   3.0    3.1  3  Fer4_22          4Fe-4S dicluster domain
        1.6    9.3  22.8      0.063   13.8  11.4    3.4  4  Fer4_17          4Fe-4S dicluster domain
        4.3    8.1  19.8       0.47   11.1   2.3    3.1  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 !  267.8   0.0   2.1e-82   1.7e-79       1     431 [.     322     745 ..     322     746 .. 0.91

  Alignments for each domain:
  == domain 1  score: 267.8 bits;  conditional E-value: 2.1e-82
                                   B--S-EEECTTTTTSEEEE--HHHHHHHHHHHHHHHHHHCSGGGEEEEEBTSSCSHHHHHHHHHHHHHTT-EEE-BEECCG CS
                 Molybdopterin   1 RlkyPmvRkqargeGkFvrvsWdeAleliaaslkytikkygpdrvagfssgplmsmeslaslkkllsllggknlsfydwya 81 
                                   Rl+ P++R       +F+r++W+eAl+l+a++l+++++kyg d++ + +s++ + +e+ ++++kl++ ++g  ++++d+  
  gi|13541074|ref|NP_110762.1| 322 RLTSPLIR---D-GERFRRATWEEALDLVAKKLREIKDKYGGDAIEFIASSKGT-NEEAYLMQKLARQVFG--TNNVDNSS 395
                                   9*******...5.667******************************87777777.9***************..89****** PP

                                   GGTTHHHH....CHHCCCCCTTTS-SS-CCGGGG-SEEEEESS-HHHHSHHHHHHHHHHHHTTC-EEEEECSSB-HCGGGC CS
                 Molybdopterin  82 dlppasaq....qtigsdsrsnyessnpledlensdliilwGsNvreerpilnarirkaalkkkakvivigpryaellkfa 158
                                   + + a a     +t+g++       s +++d++ +dl+i++G+N +e +p+l +r+ +a++ ++ k+iv + r +e++++a
  gi|13541074|ref|NP_110762.1| 396 RFCQAPATtglwRTVGYGGD-----SGSIQDIYMADLVIAIGTNTAESHPVLATRVKRAHKLNGQKLIVSDLRMHEMARRA 471
                                   ***99988556655554433.....5589*********************************99***************** PP

                                   SEEEEEHTTTHHHHHHHHHHHHHHCCCCTCHHHHHHEECHHHCCCCCCCEECCSHHHHHHCCHHHHHHHHHHHHHHTSSEE CS
                 Molybdopterin 159 dewlaikpgtdaalalamghvilqelkvdkeflrkytygkeetdmpllvtleeetgkkkevvariarelarnaaktagksm 239
                                   d+ l +kpgtd   + a  ++il+++++dk+f+r + +g+e + + l+  + e +++ +++ +++  ++ +n++ +a+++ 
  gi|13541074|ref|NP_110762.1| 472 DLFLHPKPGTDIVWLSAVTKYILDKGWEDKSFIRERVSGFEDYVKSLEPFTMEFAEEATGISKETLMKV-ANMIHEAKNMV 551
                                   *****************************************************5555555555555555.566666666** PP

                                   EEECHHHHTSTTHHHHHHHHHHHHHHCTHCSSTTCEEEEESSCTTHHHCHHHHTCCTTCCCCCCCTT..HHHHHCCCTTTC CS
                 Molybdopterin 240 iivGaglnhrqdgdaiyravinLallvgnvgqpgGgwahlnGqlilagaaekvgalpvllsvkslke..ekikfaaeqpgn 318
                                   i++ +g++++q g+++  a+ nL+l++gn+g++g+g   l+G ++++ga    ++++ l+ ++ +     ++kf + +  +
  gi|13541074|ref|NP_110762.1| 552 ILWAMGVTQHQAGSDTSTAISNLLLITGNYGRHGTGAYPLRGHNNVQGASDFGAMNAYLPGYQPVSDptVRKKFEDAWHCT 632
                                   ************************************************777777776666666655588889999999999 PP

                                   STSS--ECGGCHHHHHHTTSSSEEEEESH.HHHHSTTSCCCHCHHHCSSEEEEEESCSSHHHHTSSEEEEBE-CCGSEEEE CS
                 Molybdopterin 319 lgnfprnlfversnllkssgkkvlyllgnnpevdhadenevekalekldlvvvldgrltstalyaDiiLPaatwyEkedly 399
                                   ++ +p+ +     + + +++++++y++g++ + + +d n + ++lekld++vv d +l++ta+yaD++LPa++ +Eke+++
  gi|13541074|ref|NP_110762.1| 633 IPEKPGLDNNTCLEGIMNGKIRAMYVVGEELVETGSDSNFIRDQLEKLDFLVVEDLFLSETAKYADVVLPASASLEKEGTF 713
                                   ********************************************************************************* PP

                                   E-TTSEEEEEEESSS-STT-BEHHHHHHHHHH CS
                 Molybdopterin 400 tndegrfqhlkqavsppgeaksdwkIlkaLak 431
                                   +n+e+r+q++  ++ p    ++dw+I++++a+
  gi|13541074|ref|NP_110762.1| 714 VNTERRIQRIYEVMAPLPGTRPDWQIIQDIAN 745
                                   ******************************97 PP

>> Molydop_binding  Molydopterin dinucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.0   0.0   1.7e-26   1.4e-23       1     110 [.     829     935 ..     829     936 .. 0.98

  Alignments for each domain:
  == domain 1  score: 83.0 bits;  conditional E-value: 1.7e-26
                                   EEEEEE-BTTBSTTTTTCGCCHHHHCSSS.-EEEEEHHHHHHHT--TT-EEEEEETTEEEEEEEEEESSB-TTEEEEESSH CS
               Molydop_binding   1 lrLitgrsldqlhsqtrtrpvlrlakpep.evveinpedAaalGikdGdlVevesrrGsvevrakvtervrpGvvfmpfgw 80 
                                   l+L++gr l+++h + +t +++  +++ p  +ve++p+ A+++G+++GdlV+++s++Gs++v + v++rv    ++mp+++
  gi|13541074|ref|NP_110762.1| 829 LHLNNGRLLEHFHEGNETYKSPGIRSKVPgTFVEVSPDLAKERGLETGDLVRITSEYGSIKVSVLVSDRVSGKELYMPMNA 909
                                   79******************************************************************************* PP

                                   CC.....S-GHCTS--SCSTTT--CSTT-E CS
               Molydop_binding  81 weagekggnaNaltddatdplsgtpefksv 110
                                          +++N lt + +dp++ tp++k+v
  gi|13541074|ref|NP_110762.1| 910 SG----DSAVNLLTGRLMDPTAHTPAYKEV 935
                                   99....**********************87 PP

>> Molybdop_Fe4S4  Molybdopterin oxidoreductase Fe4S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.6   0.2   7.2e-21   5.8e-18       1      55 []     265     319 ..     265     319 .. 0.97

  Alignments for each domain:
  == domain 1  score: 64.6 bits;  conditional E-value: 7.2e-21
                                   SEEEEEE-SSBTT--EEEEEEETTEEEEEEE-TTSTTTTT---HHHHTCHHCCCB CS
                Molybdop_Fe4S4   1 ekvvktaCpyCgvgCglevhvkdgkivkvegdpdhpvnegrlCvKGrtllervyn 55 
                                   +k++kt+C+yCgvgC++e+++ + +i kv+++p++p+n   +C+KG++++++v++
  gi|13541074|ref|NP_110762.1| 265 IKKTKTVCTYCGVGCSFEMWTMGREILKVQPQPESPANGISTCIKGKFGWDFVNS 319
                                   589**************************************************96 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 !   45.0   0.0     1e-14   8.2e-12       4      78 ..      10      79 ..       7      83 .. 0.92

  Alignments for each domain:
  == domain 1  score: 45.0 bits;  conditional E-value: 1e-14
                        Fer2_4  4 vtltfDGkevtvpeGdtvasAllangvdvprsckygrprgelcaggeCrnClVevegepnvracstpvedGlkve 78
                                  ++++   k++++++++t+++All ng+d+p+ c++      l++++ C +ClV+++g+  vr+cst +e+G k+ 
  gi|13541074|ref|NP_110762.1| 10 IEFYAGSKSLKGEKNQTILQALLLNGIDIPHICYH----PSLGPINTCDTCLVDMNGKI-VRSCSTYLEQGAKID 79
                                  7778888999*************************....99****************98.***********9986 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   3.4   1.8e-07   0.00015       1      18 [.     146     163 ..     146     165 .. 0.94
   2 !   29.6   2.6   4.8e-10   3.9e-07       1      23 [.     189     211 ..     189     212 .. 0.94
   3 ?    0.3   0.2      0.85   6.9e+02       6      12 ..     270     276 ..     265     277 .. 0.80

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 1.8e-07
                                   EEEETTTSSS-THHHHHS CS
                          Fer4   1 vvideekCigCGaCvevC 18 
                                   +v+d++ Ci CG+Cve+C
  gi|13541074|ref|NP_110762.1| 146 YVYDPNQCILCGRCVEAC 163
                                   689*************** PP

  == domain 2  score: 29.6 bits;  conditional E-value: 4.8e-10
                                   EEEETTTSSS-THHHHHSTTTEE CS
                          Fer4   1 vvideekCigCGaCvevCPvgAI 23 
                                   v i+e+ C+ CG Cv vCPv+A+
  gi|13541074|ref|NP_110762.1| 189 VPINESSCVSCGHCVTVCPVNAL 211
                                   579*******************7 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.85
                                   TTSSS-T CS
                          Fer4   6 ekCigCG 12 
                                     C++CG
  gi|13541074|ref|NP_110762.1| 270 TVCTYCG 276
                                   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 !   39.9   3.8   2.7e-13   2.2e-10       1      39 [.      89     128 ..      89     129 .. 0.95
   2 ?   -3.0   0.0       6.8   5.5e+03      28      36 ..     741     749 ..     740     750 .. 0.87

  Alignments for each domain:
  == domain 1  score: 39.9 bits;  conditional E-value: 2.7e-13
               NADH-G_4Fe-4S_3   1 RktilellLanHpldCltCdkn.GnCeLQdlayelgvees 39 
                                   ++++++ +L nH+l+C++Cd+n G+C L++ +++l ++++
  gi|13541074|ref|NP_110762.1|  89 QREAVQRMLHNHDLYCTVCDNNnGDCPLHNAVHDLEIDNQ 128
                                   6899*********************************987 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 6.8
               NADH-G_4Fe-4S_3  28 Qdlayelgv 36 
                                   Qd+a++lg 
  gi|13541074|ref|NP_110762.1| 741 QDIANRLGA 749
                                   9******96 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   3.5   2.1e-06    0.0017       3      19 ..     147     163 ..     147     167 .. 0.95
   2 !   26.5   2.2   5.5e-09   4.5e-06       4      24 .]     191     211 ..     191     211 .. 0.95

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 2.1e-06
                        Fer4_6   3 eidpdkCigCgdCvrvC 19 
                                   ++dp+ Ci Cg+Cv +C
  gi|13541074|ref|NP_110762.1| 147 VYDPNQCILCGRCVEAC 163
                                   68*************** PP

  == domain 2  score: 26.5 bits;  conditional E-value: 5.5e-09
                        Fer4_6   4 idpdkCigCgdCvrvCPegai 24 
                                   i++++C++Cg Cv+vCP +a+
  gi|13541074|ref|NP_110762.1| 191 INESSCVSCGHCVTVCPVNAL 211
                                   79****************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 ?    0.6   0.1      0.74   6.1e+02       6      24 ..     101     124 ..      96     140 .. 0.68
   2 !   17.9   0.3   3.2e-06    0.0026       3      21 ..     147     164 ..     145     184 .. 0.77
   3 !   23.4   2.4   5.7e-08   4.7e-05       4      51 ..     191     279 ..     188     281 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.74
                       Fer4_10   6 ddtCirCgkCvkaCPadl.....t 24 
                                   d  C+ C + +  CP ++     +
  gi|13541074|ref|NP_110762.1| 101 DLYCTVCDNNNGDCPLHNavhdlE 124
                                   5569999999999**955443331 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 3.2e-06
                       Fer4_10   3 vidddtCirCgkCvkaCPa 21 
                                   v+d+++Ci Cg+Cv+aC +
  gi|13541074|ref|NP_110762.1| 147 VYDPNQCILCGRCVEAC-Q 164
                                   799**************.3 PP

  == domain 3  score: 23.4 bits;  conditional E-value: 5.7e-08
                       Fer4_10   4 idddtCirCgkCvkaCPadl........................................tsvgakgeaseeeavrkkvek 44 
                                   i++++C+ Cg Cv++CP+++                                         + ++++ ++++++++k    
  gi|13541074|ref|NP_110762.1| 191 INESSCVSCGHCVTVCPVNAlmektmlgkagfltglekntkqkmidvvksiepeitmspiMAISNIESKMRSSRIKKTKTV 271
                                   899***************99*******************999999999999999999999999999999999999999999 PP

                       Fer4_10  45 Ctgcg.aC 51 
                                   Ct cg  C
  gi|13541074|ref|NP_110762.1| 272 CTYCGvGC 279
                                   99998566 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.1      0.23   1.9e+02      32      57 ..      95     120 ..      76     122 .. 0.72
   2 !   34.8   8.2   1.6e-11   1.3e-08       4      55 ..     149     210 ..     147     214 .. 0.74
   3 ?   -2.2   0.2       5.7   4.7e+03      11      18 ..     272     279 ..     251     283 .. 0.54

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.23
                       Fer4_21  32 tvlkvvedeCvGCnlCssvCPvedci 57 
                                   ++l+  +  C+ C+     CP+++++
  gi|13541074|ref|NP_110762.1|  95 RMLHNHDLYCTVCDNNNGDCPLHNAV 120
                                   3444455689999999999**99987 PP

  == domain 2  score: 34.8 bits;  conditional E-value: 1.6e-11
                       Fer4_21   4 dedkCigCgkCliaCedtshq.ai.........eidaktvlkvvedeCvGCnlCssvCPved 55 
                                   d+++Ci Cg+C+ aC+d  ++  +         ++  ++ +++ e++Cv C  C++vCPv+ 
  gi|13541074|ref|NP_110762.1| 149 DPNQCILCGRCVEACQDVQVNeTLsidwsrerpRVVWDNDVPINESSCVSCGHCVTVCPVNA 210
                                   889**************776524444444443333344456999****************54 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 5.7
                       Fer4_21  11 CgkCliaC 18 
                                   C+ C + C
  gi|13541074|ref|NP_110762.1| 272 CTYCGVGC 279
                                   33333333 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   1.5         2   1.6e+03      24      49 ..      90     115 ..      51     119 .. 0.62
   2 !   35.2   7.7   1.7e-11   1.4e-08       1      52 []     152     210 ..     143     210 .. 0.79
   3 ?    2.2   0.2      0.34   2.8e+02       4      20 ..     271     287 ..     259     312 .. 0.74

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 2
                        Fer4_7  24 nekgtekveidpekClgCgaCvavCP 49 
                                   +e+ ++ ++ +  +C+ C++    CP
  gi|13541074|ref|NP_110762.1|  90 REAVQRMLHNHDLYCTVCDNNNGDCP 115
                                   22222334555669999999888888 PP

  == domain 2  score: 35.2 bits;  conditional E-value: 1.7e-11
                        Fer4_7   1 rCigCgaCvaaCp....vkaieldeeenekgt...ekveidpekClgCgaCvavCPtga 52 
                                   +Ci Cg+Cv+aC     ++++++d + + +++    +v i++++C++Cg+Cv+vCP++a
  gi|13541074|ref|NP_110762.1| 152 QCILCGRCVEACQdvqvNETLSIDWSRERPRVvwdNDVPINESSCVSCGHCVTVCPVNA 210
                                   6***********875556666666543333324667789999***************97 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.34
                        Fer4_7   4 gCgaCvaaCpvkaield 20 
                                    C +C + C+ +  ++ 
  gi|13541074|ref|NP_110762.1| 271 VCTYCGVGCSFEMWTMG 287
                                   59999999987766654 PP

>> Fer2  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   0.0   6.5e-10   5.3e-07      12      62 ..      21      75 ..      14      85 .. 0.83

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 6.5e-10
                                  EETTTHBHHHHHHHTTTTTSTTSSSS......SSSSTTEEEEEESCECTTSSSSTHH CS
                          Fer2 12 vadgettlldaaeenggidipysCgg......ggCgtClvevlegevqsdetelege 62
                                   ++++t +l+a+  n gidip+ C++      ++C tClv+++ + v+s++t+le  
  gi|13541074|ref|NP_110762.1| 21 GEKNQT-ILQALLLN-GIDIPHICYHpslgpiNTCDTCLVDMNGKIVRSCSTYLEQG 75
                                  567888.******88.**************9777*********66668888887765 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   7.7    0.0007      0.57       2      48 ..     104     165 ..     103     169 .. 0.68
   2 !   28.4   9.3   1.6e-09   1.3e-06       1      50 [.     152     210 ..     152     211 .. 0.75
   3 ?    2.1   0.5      0.28   2.3e+02       4      26 ..     271     293 ..     268     309 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0007
                        Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraase...............eaCigCgaCveaCpk 48 
                                   Ct C++    Cp + +v d      ++  + +               ++Ci Cg+CveaC+ 
  gi|13541074|ref|NP_110762.1| 104 CTVCDNNNGDCPLHNAVHDLEIDNQKYPYEPKpypvddsnpfyvydpNQCILCGRCVEACQD 165
                                   7777776677766665555444443333222256888888888889999***********85 PP

  == domain 2  score: 28.4 bits;  conditional E-value: 1.6e-09
                        Fer4_9   1 kCtgCgaCveaC....pagvvvedaaerkarlraase.....eaCigCgaCveaCpkga 50 
                                   +C+ Cg+CveaC     +++ + d++++  r+ ++++     ++C++Cg Cv +Cp +a
  gi|13541074|ref|NP_110762.1| 152 QCILCGRCVEACqdvqVNETLSIDWSRERPRVVWDNDvpineSSCVSCGHCVTVCPVNA 210
                                   6***********5554444445555555555555555****999************986 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.28
                        Fer4_9   4 gCgaCveaCpagvvvedaaerka 26 
                                    C++C   C ++++++ +   k+
  gi|13541074|ref|NP_110762.1| 271 VCTYCGVGCSFEMWTMGREILKV 293
                                   59*******99998877665555 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   2.9      0.23   1.9e+02       7      64 ..      52     117 ..      51     118 .. 0.79
   2 !   27.1   7.0   5.4e-09   4.4e-06       3      64 ..     151     209 ..     149     210 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.23
                        Fer4_8   7 eCgaCq........saCpvlrrtkkhlldargeaaedvqeeqvlee.eealwsCttcgaCtevCpvg 64 
                                    C  C          +C ++ +++  + ++ +++ e  q+e v+   ++   +Ct c + +  Cp +
  gi|13541074|ref|NP_110762.1|  52 TCDTCLvdmngkivRSCSTYLEQGAKIDYNSNRVLE-LQREAVQRMlHNHDLYCTVCDNNNGDCPLH 117
                                   5888887777777778*******9888888888888.6666664445888889******99999987 PP

  == domain 2  score: 27.1 bits;  conditional E-value: 5.4e-09
                        Fer4_8   3 ekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64 
                                   ++Ci Cg+C +aC  ++     + d   e+   v++++v     +  sC++cg+C++vCpv+
  gi|13541074|ref|NP_110762.1| 151 NQCILCGRCVEACQDVQVNETLSIDWSRERPRVVWDNDV---PINESSCVSCGHCVTVCPVN 209
                                   68************9999997777777777774777777...77899*************97 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   2.4   7.3e-06    0.0059       3      20 ..     146     163 ..     144     164 .. 0.93
   2 !   17.3   4.7   4.4e-06    0.0035       5      21 ..     191     207 ..     188     208 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 7.3e-06
                        Fer4_2   3 vvvdtdrCigCgaCvsaC 20 
                                   +v+d++ Ci Cg Cv aC
  gi|13541074|ref|NP_110762.1| 146 YVYDPNQCILCGRCVEAC 163
                                   89**************** PP

  == domain 2  score: 17.3 bits;  conditional E-value: 4.4e-06
                        Fer4_2   5 vdtdrCigCgaCvsaCP 21 
                                   +++ +C++Cg Cv++CP
  gi|13541074|ref|NP_110762.1| 191 INESSCVSCGHCVTVCP 207
                                   8999************* PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   1.0   0.00046      0.37       3      24 ..     148     169 ..     147     177 .. 0.88
   2 !    9.0   0.1    0.0028       2.2       2      20 ..     190     208 ..     189     240 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00046
                       Fer4_15   3 vDrdaCigcglCvaeapevfel 24 
                                   +D ++Ci cg+Cv+++++v ++
  gi|13541074|ref|NP_110762.1| 148 YDPNQCILCGRCVEACQDVQVN 169
                                   799*************998665 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0028
                       Fer4_15   2 vvDrdaCigcglCvaeape 20 
                                    ++++ C +cg Cv+++p 
  gi|13541074|ref|NP_110762.1| 190 PINESSCVSCGHCVTVCPV 208
                                   58899************73 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   1.1      0.66   5.4e+02      24      62 ..      71     109 ..      51     116 .. 0.78
   2 !    8.8   0.4    0.0039       3.1       1      15 [.     152     166 ..     152     188 .. 0.80
   3 !   15.6   5.4   2.8e-05     0.023       2      23 ..     196     215 ..     195     282 .. 0.69

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.66
                       Fer4_16  24 eiearecisyntaekkdlaedeekckkqeaitgCdiCqd 62 
                                    +e+ ++i+yn +   +l+ ++ +++ +++  +C +C +
  gi|13541074|ref|NP_110762.1|  71 YLEQGAKIDYNSNRVLELQREAVQRMLHNHDLYCTVCDN 109
                                   466777888888888888888888889999999999975 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0039
                       Fer4_16   1 rCgtCgkCaevCPtn 15 
                                   +C+ Cg+C+e+C   
  gi|13541074|ref|NP_110762.1| 152 QCILCGRCVEACQDV 166
                                   5***********665 PP

  == domain 3  score: 15.6 bits;  conditional E-value: 2.8e-05
                       Fer4_16   2 CgtCgkCaevCPtnaikekkek 23 
                                   C++Cg C+ vCP+na+ ek  +
  gi|13541074|ref|NP_110762.1| 196 CVSCGHCVTVCPVNALMEK--T 215
                                   ****************998..2 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 !    7.9   0.1     0.005         4      22      47 ..      87     111 ..      65     113 .. 0.75
   2 ?    6.2   0.0     0.018        14      22      44 ..     254     276 ..     223     282 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.005
                       zf-C2HE  22 eslseeqskelilktpLkCtrCganf 47 
                                   e l++e  ++ + +++L Ct C++n 
  gi|13541074|ref|NP_110762.1|  87 E-LQREAVQRMLHNHDLYCTVCDNNN 111
                                   3.7888889999***********765 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.018
                       zf-C2HE  22 eslseeqskelilktpLkCtrCg 44 
                                   ++++++  ++ i+kt+  Ct+Cg
  gi|13541074|ref|NP_110762.1| 254 SNIESKMRSSRIKKTKTVCTYCG 276
                                   556667777788**********9 PP

>> TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0    0.0092       7.5      63     119 ..     410     470 ..     401     480 .. 0.65
   2 ?    5.9   0.0     0.012       9.7       3      30 ..     539     566 ..     537     598 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0092
                                   SGGGSCHHHHHHHHH-SEEEEES-SSSTCCC....TT.TTT.TTTTT-.EEEEEESSCCCCTTC CS
                  TPP_enzyme_M  63 lglhgskaanealeeaDlvlalGarfddirt....tg.sep.efapea.kiihididpaeigkn 119
                                   +g+ g++   + +  aDlv+a+G++  + ++    t  +   + +  + k+i  d   +e+ ++
  gi|13541074|ref|NP_110762.1| 410 VGYGGDSGSIQDIYMADLVIAIGTNTAE-SHpvlaTRvKRAhKLN--GqKLIVSDLRMHEMARR 470
                                   677777788888899********99665.2222213332221222..33777777777666665 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.012
                                   HHHHHHHH-SSEEEEE-CHHCHTTGHHH CS
                  TPP_enzyme_M   3 kaaellkaakrpvilvGggvarsgasee 30 
                                   k+a+++++ak+ vil   gv +++a  +
  gi|13541074|ref|NP_110762.1| 539 KVANMIHEAKNMVILWAMGVTQHQAGSD 566
                                   79******************99987665 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   1.9    0.0025         2       2      19 ..     149     166 ..     148     170 .. 0.93
   2 ?    8.9   3.1    0.0027       2.2       1      17 [.     191     207 ..     191     209 .. 0.93
   3 ?   -1.8   0.0       5.7   4.7e+03      14      38 ..     380     404 ..     379     409 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0025
                       Fer4_13   2 DrdtCiacgaCvelaPdv 19 
                                   D ++Ci cg Cve++ dv
  gi|13541074|ref|NP_110762.1| 149 DPNQCILCGRCVEACQDV 166
                                   779************997 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0027
                       Fer4_13   1 VDrdtCiacgaCvelaP 17 
                                   +++++C++cg Cv ++P
  gi|13541074|ref|NP_110762.1| 191 INESSCVSCGHCVTVCP 207
                                   7899************9 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 5.7
                       Fer4_13  14 elaPdvFeeddeggasvvaeqptse 38 
                                   +la +vF  ++ ++ s++ + p ++
  gi|13541074|ref|NP_110762.1| 380 KLARQVFGTNNVDNSSRFCQAPATT 404
                                   57999************99988765 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   0.5    0.0039       3.1      78      93 ..     149     164 ..     141     167 .. 0.86
   2 ?    8.9   3.0    0.0033       2.7      78      95 ..     192     209 ..     182     210 .. 0.79
   3 ?    2.8   8.2      0.26   2.1e+02       2      18 ..     196     212 ..     195     280 .. 0.61

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0039
                       Fer4_22  78 gesgCvGCgRCieacp 93 
                                   + ++C+ CgRC+eac+
  gi|13541074|ref|NP_110762.1| 149 DPNQCILCGRCVEACQ 164
                                   6789***********7 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0033
                       Fer4_22  78 gesgCvGCgRCieacpvk 95 
                                   +es+Cv Cg C+++cpv+
  gi|13541074|ref|NP_110762.1| 192 NESSCVSCGHCVTVCPVN 209
                                   678899999999999875 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.26
                       Fer4_22   2 ClsCgaCtlvCptCsCf 18 
                                   C+sCg+C +vCp    +
  gi|13541074|ref|NP_110762.1| 196 CVSCGHCVTVCPVNALM 212
                                   88888888888876554 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   5.8    0.0055       4.4       5      57 ..     104     164 ..     102     166 .. 0.64
   2 ?   13.8  11.4   7.7e-05     0.063       1      58 [.     152     208 ..     152     211 .. 0.74
   3 ?    4.7   8.2     0.056        45       2      18 ..     196     212 ..     195     281 .. 0.57
   4 ?   -1.0   0.3       3.3   2.7e+03       5      17 ..     272     284 ..     269     308 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0055
                       Fer4_17   5 CgyClp...eCpsyea.ydn..epkkllraaklglleeaeke..ekaslCieCgeCerkCP 57 
                                   C  C +    Cp ++a +d   +++k+ ++ k+  +++ +       ++Ci Cg+C+++C 
  gi|13541074|ref|NP_110762.1| 104 CTVCDNnngDCPLHNAvHDLeiDNQKYPYEPKPYPVDDSNPFyvYDPNQCILCGRCVEACQ 164
                                   66666555578887775333235677777766654555333244578*************5 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 7.7e-05
                       Fer4_17   1 rCiqCgyClpeCpsyeaydnepkkllraakl..glleeaekeekaslCieCgeCerkCPq 58 
                                   +Ci Cg C+++C   + +++    + r+     +  ++     + s+C++Cg C+++CP 
  gi|13541074|ref|NP_110762.1| 152 QCILCGRCVEACQDVQVNETLSIDWSRERPRvvW--DN-DVPINESSCVSCGHCVTVCPV 208
                                   5*************99988866666666333122..22.2235789*************6 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.056
                       Fer4_17   2 CiqCgyClpeCpsyeay 18 
                                   C +Cg+C+ +Cp ++ +
  gi|13541074|ref|NP_110762.1| 196 CVSCGHCVTVCPVNALM 212
                                   88888888888876653 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 3.3
                       Fer4_17   5 CgyClpeCpsyea 17 
                                   C yC   C++ ++
  gi|13541074|ref|NP_110762.1| 272 CTYCGVGCSFEMW 284
                                   8888888887666 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   3.5     0.011       8.6       3      14 ..     152     163 ..     150     167 .. 0.88
   2 ?   11.1   2.3   0.00058      0.47       3      17 .]     195     209 ..     193     212 .. 0.91

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.011
                        Fer4_4   3 rCigCgsCvaaC 14 
                                    Ci Cg+Cv aC
  gi|13541074|ref|NP_110762.1| 152 QCILCGRCVEAC 163
                                   5*********** PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00058
                        Fer4_4   3 rCigCgsCvaaCPqg 17 
                                   +C+ Cg Cv +CP++
  gi|13541074|ref|NP_110762.1| 195 SCVSCGHCVTVCPVN 209
                                   8************75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (984 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       621  (0.0346366); expected 358.6 (0.02)
Passed bias filter:                      501  (0.0279436); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); 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):              22  [number of targets reported over threshold]
# CPU time: 0.82u 0.30s 00:00:01.11 Elapsed: 00:00:00.48
# Mc/sec: 6151.00
//
Query:       gi|13541075|ref|NP_110763.1|  [L=99]
Description: hypothetical protein TVN0244, partial [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-08   34.5   0.2    2.2e-08   33.8   0.2    1.4  1  DUF1641   Protein of unknown function (DUF1641)
  ------ inclusion threshold ------
        0.1   13.1   0.2       0.18   12.3   0.2    1.4  1  Rnk_N     Rnk N-terminus


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 !   33.8   0.2   2.4e-12   2.2e-08       2      37 ..      58      93 ..      57      95 .. 0.93

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 2.4e-12
                       DUF1641  2 gleepkpvGlfgLlraLrDPDVqrGLGfllalLKal 37
                                  +l+++  ++l+++ ++L+DPDV++G+++ll+++K++
  gi|13541075|ref|NP_110763.1| 58 KLKAEGSLSLLKIGSQLKDPDVSAGVRVLLSVAKGF 93
                                  67888999**************************98 PP

>> Rnk_N  Rnk N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.2     2e-05      0.18       5      34 ..      34      62 ..      33      62 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2e-05
                                  EEHHHHHHHHHHHHCTTTTSSTTHHHHHHH CS
                         Rnk_N  5 itelDleRLeaLldsladrdppaaeaLeaE 34
                                  +++ D eRL++ ++++a ++ + a++L aE
  gi|13541075|ref|NP_110763.1| 34 LSSIDSERLRKFMENAA-KSIESADKLKAE 62
                                  699***********665.455889999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       873  (0.0486921); 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: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 686.03
//
Query:       gi|13541076|ref|NP_110764.1|  [L=279]
Description: hypothetical protein TVN0245 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.8e-69  233.4   0.0    3.2e-69  233.2   0.0    1.0  1  FdhD-NarQ  FdhD/NarQ family
  ------ inclusion threshold ------
       0.21   11.9   0.0       0.44   10.9   0.0    1.5  1  DUF5110    Domain of unknown function (DUF5110)


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 !  233.2   0.0   3.6e-73   3.2e-69       2     236 ..      33     277 ..      32     278 .. 0.87

  Alignments for each domain:
  == domain 1  score: 233.2 bits;  conditional E-value: 3.6e-73
                                   --EEEEEEETT.....EEEEEEEE-SSSHHHHHHHHHHHCTS--SGGGEEEEEEETTTEE.......EE-S.........- CS
                     FdhD-NarQ   2 eEepltivvng.....relatlmatpadleelalGfllsegliesaediesievdedeas.......vavatrakaedkee 70 
                                   +Eepl+i +       ++  ++m+tp +++ la+Gfl+seg++ +++ i+ ie  + e++       v++++r+      +
  gi|13541076|ref|NP_110764.1|  33 QEEPLEIKFRIgsdkeKSAGIVMRTPVHDDWLAVGFLYSEGILHDRRWINGIEGVSIEGKaqdnivtVNIDPRNGSF---D 110
                                   677877776433344477889***********************998887666554444444466445555555444...3 PP

                                   --------------.---...--.H-----------EEGGGHHHHHHHHHTS-SHHHHHS--EEEEEEE.TTEEEEEEEES CS
                     FdhD-NarQ  71 rrtakrvvtsgCglcgkesleel.letlelpesdlklsaeallrlmdalrekqelfketggvHaaalfdadgellavreDv 150
                                      ++r v+s+Cg+cgk+ ++ + l+  + +++++k+++  +++l+  ++  q+lf++tgg+Haaalf+adg+ ++++eD+
  gi|13541076|ref|NP_110764.1| 111 PDYRERFVNSSCGICGKSTINGIfLRMGKIKRDNIKIDPGVIVSLPVIMKGMQQLFSKTGGIHAAALFSADGKPIVTAEDI 191
                                   4555669*************9997667777788************************************************ PP

                                   SHHHHHHHHHHHHHT.TSS-SSSEEEESS-B-HHHHHHHHHHT-SEEEESS-B-HHHHHHHHHHT-EEEEEEETTEEEEEE CS
                     FdhD-NarQ 151 GRHnAlDkviGaallegldlsdkilvvsgRlssemvqKaaragipvlvsvsaptslavelAeeagltlvgfvrgkrfnvYt 231
                                   GRHnA+Dkv+G  l+eg+d+s  il vsgR+ +e+v Kaa agipv++svsap+sla+e++e++gltl++fvrg++fnvYt
  gi|13541076|ref|NP_110764.1| 192 GRHNAVDKVVGFSLIEGIDTSTLILQVSGRAGFEIVEKAAIAGIPVICSVSAPSSLAIEVCESLGLTLICFVRGSSFNVYT 272
                                   ********************************************************************************* PP

                                   -GGGE CS
                     FdhD-NarQ 232 gaeRi 236
                                   +aeRi
  gi|13541076|ref|NP_110764.1| 273 HAERI 277
                                   ****9 PP

>> DUF5110  Domain of unknown function (DUF5110)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   4.9e-05      0.44      34      63 ..      87     114 ..      77     120 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 4.9e-05
                                   EEEEEEC-STTCEEEEEEEEEE-TT..S.C CS
                       DUF5110  34 tkftveadggkltltigpreGsykgmpker 63 
                                   ++++ +a+++ +t++i+pr+Gs+++  ++r
  gi|13541076|ref|NP_110764.1|  87 VSIEGKAQDNIVTVNIDPRNGSFDP--DYR 114
                                   567888899***************9..333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 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:                        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: 00:00:00.44
# Mc/sec: 1915.65
//
Query:       gi|13541077|ref|NP_110765.1|  [L=431]
Description: major facilitator superfamily permease [Thermoplasma volcanium GSS1]
Scores for complete 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-22   79.7  36.9    2.8e-22   79.2  36.9    1.2  1  Sugar_tr  Sugar (and other) transporter
    4.9e-22   78.3  40.3    4.9e-22   78.3  40.3    1.7  1  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 !   79.2  36.9   3.1e-26   2.8e-22      13     434 ..      17     426 ..       6     429 .. 0.80

  Alignments for each domain:
  == domain 1  score: 79.2 bits;  conditional E-value: 3.1e-26
                                   HHHHHCGGGTHHHHHHHHTSTT--SHHHHHH.......HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHH CS
                      Sugar_tr  13 gYdtgvigafltllkfaknfglsksksskee....ssvlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvig 89 
                                   gY +++i +++ +l+++    ls   +   +    s +++++ vs++++Ga++Gs+ + +l++rfGRk  ll   ++f+++
  gi|13541077|ref|NP_110765.1|  17 GYSIAIIVSASIFLDVWDLASLSFVITFFRSyfylSGLTLSVAVSSANIGAVMGSISGAYLVERFGRKRMLLSNMLIFFAS 97 
                                   555555555555555555444444443333344447778899*************************************** PP

                                   HHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-.TTH CS
                      Sugar_tr  90 avlqaaakgknsvevlivgRvlvGigvGlasvlvPmyisEiApkklRgalvslyqlaitfGilvaaifglglnktsn.adg 169
                                   ++ +++++   s++++i  R+l+G+g+G   v+  +yi E+A ++ R ++  l+  + ++  ++a+++ ++   +   ++ 
  gi|13541077|ref|NP_110765.1|  98 SIAIVFSP---SIYLVIPFRILMGFGIGSDVVTGFTYIYEYANERQRQTFYPLWGYSFSAIAILAIVVVFVSHLFVTwDQL 175
                                   ********...*********************************************999999999999999999998899* PP

                                   HHHHHHCCHHHHHHHHHHGGGS---HHHHHHTT-HHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHH.....HTTHHHHSH CS
                      Sugar_tr 170 wrillglqlvpallllilllflPESPrylvekgkeeeakevlaklrgeedadrelaeekdsleaeqeeekaswkellsskt 250
                                   w+i + +++++++ +l+l++ l E+P +l+ ++k++e + v++k        + +    d   +e     ++ ++l+  ++
  gi|13541077|ref|NP_110765.1| 176 WKIVFMIAAIFSVSMLFLRYRLMETPLWLYLNRKYSELENVMEK-----AYGKTILSLSDPPSRE----RIFGDSLKFLRS 247
                                   ********************************************.....4444444444444444....566677777755 PP

                                   ...HHHHHHHHHHHHHHTTHHHHHHHTTTHHHHSS-THH...HHHHHHHHHHHHHHHHHHHHHHHHS-SHHHHHHHHHHHH CS
                      Sugar_tr 251 vrqrlligvvlqifqqltGinaimyysptifenlglsks...llvtiivgvvnfvatfvaiflvdrfGRRtllllGaagma 328
                                     +r+  ++ l+ +  + G+  + +y +++++ l+l +    l + +i++    +a  ++ ++++rfG  +  ++ +a   
  gi|13541077|ref|NP_110765.1| 248 --KRMAFVLSLNGIVGFIGWG-FSFYVTYMLSALHLYTFnsiLGIDMIIYGSALIAAYISGYISKRFGVYKSTVVPSALSV 325
                                   ..789999***********65.66778999999999888777778889999999999999999999997666665544433 PP

                                   HHHHHHH..HHHHTTSS...CHHHHHHHHHHHHHHHTTTTHHHHHHHHHHS.HTTTHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Sugar_tr 329 icfvilgivalllvakskaasivaivfialfialfalgwgpvpwvlvsElf.pqsvRskalaiavavnwlanflisllfpi 408
                                   + ++ l +v+l +  +      +++v +++ +++f   +gp+ +  v  ++  +++Rs+a  + ++vn ++  + +l   +
  gi|13541077|ref|NP_110765.1| 326 ASLLALVMVFLGYLPQ------LFVVPLIIAVIFFD-YLGPMAYNAVLNIYvNPETRSAANGMNYMVNKVIESASGLSAGM 399
                                   3333333256666666......77777777777888.689999988888863689**********************9999 PP

                                   HHCHHH...T-HHHHHHHHHHHHHHHHHH CS
                      Sugar_tr 409 iteaig...ggyvflvfaglavlfiifvf 434
                                   i+   g   ++ +  + ag++ +f+   +
  gi|13541077|ref|NP_110765.1| 400 ILIEFGlgiNTLMLTIIAGVLFVFAA--Y 426
                                   99999975545555555555544443..3 PP

>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.3  40.3   5.5e-26   4.9e-22       3     346 ..      26     387 ..      24     394 .. 0.75

  Alignments for each domain:
  == domain 1  score: 78.3 bits;  conditional E-value: 5.5e-26
                         MFS_1   3 laaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfas 83 
                                    ++fl  ++ + l+++++ +  + + +s+ +++ +++   +ga+ +s+ +++l++rfGr+r+ll  +l+f++++++++f++
  gi|13541077|ref|NP_110765.1|  26 ASIFLDVWDLASLSFVIT-FFRSYFYLSGLTLSVAVSSANIGAVMGSISGAYLVERFGRKRMLLSNMLIFFASSIAIVFSP 105
                                   568999999999999999.******************************************99999999999967777878 PP

                         MFS_1  84 slwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailg..pllggllasslg.....Wravfyil 157
                                   s++l++ +r+l+G+g g+ + +g ++i +++++++r   + l++ +fs+ ail+   ++ + l          W  vf+i+
  gi|13541077|ref|NP_110765.1| 106 SIYLVIPFRILMGFGIGSDVVTGFTYIYEYANERQRQTFYPLWGYSFSAIAILAivVVFVSHLF---VtwdqlWKIVFMIA 183
                                   888*************************************888887777776662133333333...23458********* PP

                         MFS_1 158 aivsllafvlfllll........peepperkrkspkeee.......kgtgpaplvp..........awkallkdpvlwill 213
                                   ai+s+ ++   l +         + +++ ++ ++  e+                ++           +k l++++    + 
  gi|13541077|ref|NP_110765.1| 184 AIFSVSMLF--LRYRlmetplwlYLNRKYSELENVMEKAygktilsL-------SDppsrerifgdSLKFLRSKR----MA 251
                                   *******55..344444555555444444444444444344554441.......224544555677888888888....55 PP

                         MFS_1 214 ialllfffgfsg...lltllplylqevlglsglllaglllallalvgailallagrlsdrlgrrrrlllallllllaalgl 291
                                   ++l l++++ ++   +++++ +y+ + l+l ++ +++++ ++++  ++i+a ++g++s+r+g  + +++  +l ++++l+l
  gi|13541077|ref|NP_110765.1| 252 FVLSLNGIVGFIgwgFSFYV-TYMLSALHLYTFNSILGIDMIIYGSALIAAYISGYISKRFGVYKSTVVPSALSVASLLAL 331
                                   55555544444445233333.3345555555344444456666666677799****************9999999999999 PP

                         MFS_1 292 allavtssavllllvlvliGfglgfvfpsllalasdla.ppeeagtasglfntags 346
                                   +++ +   + l++++l+++ +++    p++ +++ + +  pe + +a+g + +++ 
  gi|13541077|ref|NP_110765.1| 332 VMVFLGYLPQLFVVPLIIAVIFFDYLGPMAYNAVLNIYvNPETRSAANGMNYMVNK 387
                                   99999988999999999988888888777776666666699*********999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (431 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       960  (0.0535445); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.69u 0.32s 00:00:01.01 Elapsed: 00:00:00.54
# Mc/sec: 2409.07
//
Query:       gi|13541078|ref|NP_110766.1|  [L=252]
Description: SAM-dependent methyltransferase [Thermoplasma volcanium GSS1]
Scores for complete 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   53.8   0.0    3.6e-14   53.2   0.0    1.3  1  Methyltransf_11  Methyltransferase domain
    2.7e-13   50.4   0.0    4.4e-13   49.7   0.0    1.3  1  Methyltransf_25  Methyltransferase domain
      2e-08   34.9   0.0    3.1e-08   34.3   0.0    1.3  1  Methyltransf_12  Methyltransferase domain
    1.2e-05   25.2   0.0    1.9e-05   24.5   0.0    1.4  2  Methyltransf_31  Methyltransferase domain
    6.3e-05   22.6   0.0    9.5e-05   22.0   0.0    1.3  1  MTS              Methyltransferase small domain
      9e-05   22.4   0.0    0.00011   22.1   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
    0.00063   20.1   0.4      0.006   16.9   0.1    2.2  2  AdoMet_MTase     Predicted AdoMet-dependent methyltransferase
     0.0039   17.2   0.0     0.0057   16.7   0.0    1.2  1  Methyltransf_32  Methyltransferase domain
      0.005   15.9   0.0     0.0073   15.4   0.0    1.2  1  RrnaAD           Ribosomal RNA adenine dimethylase
     0.0086   16.0   0.2      0.017   15.1   0.0    1.5  2  Methyltransf_18  Methyltransferase domain
  ------ inclusion threshold ------
      0.011   15.0   0.0      0.019   14.3   0.0    1.4  1  CMAS             Mycolic acid cyclopropane synthetase
      0.027   14.3   0.0      0.052   13.4   0.0    1.6  1  Methyltransf_8   Hypothetical methyltransferase
      0.044   13.5   0.0      0.074   12.8   0.0    1.3  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
      0.062   12.2   0.0      0.096   11.6   0.0    1.2  1  Methyltransf_9   Protein of unknown function (DUF1698)
      0.076   12.4   0.0        0.1   12.0   0.0    1.2  1  PrmA             Ribosomal protein L11 methyltransferase (Prm


Domain annotation for each model (and alignments):
>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.2   0.0     3e-17   3.6e-14       2      88 ..      44     128 ..      43     131 .. 0.95

  Alignments for each domain:
  == domain 1  score: 53.2 bits;  conditional E-value: 3e-17
                                   EET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-CCHHHHHH CS
               Methyltransf_11   2 dvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhvedpekalk 82 
                                   d+GcGtG+la+ + ++g +v+++D++ emlk ak++ s  g+   +v+++ae++ +ed+s+ ++ + +++h++ d +ka  
  gi|13541078|ref|NP_110766.1|  44 DIGCGTGILARMFLENGNKVYCIDPNGEMLKFAKDELSSFGN-AIIVRGSAENTGLEDHSVNVISAGQSFHWF-DTDKAKV 122
                                   9*************************************9996.789***************************.6999999 PP

                                   HHHHHE CS
               Methyltransf_11  83 eiaRvL 88 
                                   e++R+L
  gi|13541078|ref|NP_110766.1| 123 EFRRIL 128
                                   999998 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.7   0.0   3.7e-16   4.4e-13       1      92 [.      42     127 ..      42     130 .. 0.86

  Alignments for each domain:
  == domain 1  score: 49.7 bits;  conditional E-value: 3.7e-16
                                   EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEEST.GGGSSHH CS
               Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssga.lhhlsde 80 
                                   + d+GcGtG l++++++++   kv+++D++ eml+ a+ ++++ g n+ +v+g+ae+  +ed+s++++ + g+ +h+++ +
  gi|13541078|ref|NP_110766.1|  42 IADIGCGTGILARMFLENG--NKVYCIDPNGEMLKFAKDELSSFG-NAIIVRGSAENTGLEDHSVNVISA-GQsFHWFDTD 118
                                   78****************5..9*******************7655.************************.565**99855 PP

                                   HHHHHHHHHHHH CS
               Methyltransf_25  81 dlekalkeiarv 92 
                                   +   a  e++r+
  gi|13541078|ref|NP_110766.1| 119 K---AKVEFRRI 127
                                   4...44455555 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.3   0.0   2.6e-11   3.1e-08       2      86 ..      44     121 ..      43     130 .. 0.82

  Alignments for each domain:
  == domain 1  score: 34.3 bits;  conditional E-value: 2.6e-11
               Methyltransf_12   2 eiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhhlkdi 82 
                                   +iGcGtG l+r++le+  + +++++D++ ++++ ak +l++ +n    +   e++ l+d+    s+ ++ a + +h++ d+
  gi|13541078|ref|NP_110766.1|  44 DIGCGTGILARMFLEN--GNKVYCIDPNGEMLKFAKDELSSFGNAIIVRGSAENTGLEDH----SVNVISAGQSFHWF-DT 117
                                   9***************..*************************87766666665555544....*************8.44 PP

               Methyltransf_12  83 revl 86 
                                   +++ 
  gi|13541078|ref|NP_110766.1| 118 DKAK 121
                                   4443 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.0   1.5e-08   1.9e-05       2     101 ..      37     128 ..      36     182 .. 0.81
   2 ?   -3.7   0.0       7.9   9.5e+03      91     112 ..     221     242 ..     216     243 .. 0.76

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 1.5e-08
               Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsne 82 
                                   +k++++ D+GCGtG l+  + e+   + +v+ iD + e++++A+ +++   + n+   +g++e+    led ++++i + +
  gi|13541078|ref|NP_110766.1|  37 KKEMVIADIGCGTGILARMFLEN---GNKVYCIDPNGEMLKFAKDELS--SFGNAIIVRGSAENTG--LEDHSVNVISAGQ 110
                                   799**********9999988855...457****************755..7889999999999977..8899999987766 PP

               Methyltransf_31  83 vlnaladpdkileeiervl 101
                                    + +  d dk+  e  r l
  gi|13541078|ref|NP_110766.1| 111 SF-HWFDTDKAKVEFRRIL 128
                                   55.5556665555555555 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 7.9
               Methyltransf_31  91 dkileeiervlkpggilliedp 112
                                    k+le ++++++ +g + i+++
  gi|13541078|ref|NP_110766.1| 221 MKALETAFNAFSVDGKVRIRYI 242
                                   5778888888888998888876 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0     8e-08   9.5e-05      31     102 ..      38     107 ..      26     132 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 8e-08
                                   TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTSTTS-EEEEE CS
                           MTS  31 lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvleeveekkfdliv 102
                                   ++  ++D+GcG+G+l+ +++++ ++  v ++d + + l++ak  l++ + ++ v+ s     +e++++++i 
  gi|13541078|ref|NP_110766.1|  38 KEMVIADIGCGTGILARMFLENGNK--VYCIDPNGEMLKFAKDELSSFGNAIIVRGSAENTGLEDHSVNVIS 107
                                   45569**************997777..9******************99999888888888889999998885 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   9.1e-08   0.00011      20      62 ..      36      90 ..      15     163 .. 0.72

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 9.1e-08
               Methyltransf_23 20 lraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae............k 62
                                  l++ + + diGcGtGil++ + eng +v+ +D++ e+ + a+             
  gi|13541078|ref|NP_110766.1| 36 LKKEMVIADIGCGTGILARMFLENGNKVYCIDPNGEMLKFAKdelssfgnaiivR 90
                                  67778888**************************998887655555444333330 PP

>> AdoMet_MTase  Predicted AdoMet-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.1     5e-06     0.006      51      87 ..      31      67 ..      24      74 .. 0.86
   2 ?    0.7   0.0      0.52   6.3e+02      29      53 ..     116     141 ..     104     154 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 5e-06
                  AdoMet_MTase 51 kktrseeketsfvdvgcgngllvyvlaaegykgygid 87
                                   +++  +ke+ ++d+gcg g+l  +++ +g k y id
  gi|13541078|ref|NP_110766.1| 31 TDKYGLKKEMVIADIGCGTGILARMFLENGNKVYCID 67
                                  55666789999***********************999 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.52
                  AdoMet_MTase  29 stdplkfvfedlaiaaylivl.wkkt 53 
                                    td  k  f  +  a y++vl w++ 
  gi|13541078|ref|NP_110766.1| 116 DTDKAKVEFRRILTAPYMVVLiWNDR 141
                                   48999999*********998736544 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   4.8e-06    0.0057      15      87 ..      29      96 ..      24     130 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 4.8e-06
               Methyltransf_32 15 kllkelakesgaltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklgkkfnkrlsfael 87
                                   l+++    ++++ ++D+G+G g L+++       ++ kv++id + e+ + a++  + +g+++  r s +++
  gi|13541078|ref|NP_110766.1| 29 MLTDK-YGLKKEMVIADIGCGTGILARMFLE----NGNKVYCIDPNGEMLKFAKDELSSFGNAIIVRGSAENT 96
                                  44444.45577899*************9988....699********999998888877777666555555555 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   6.1e-06    0.0073      22      81 ..      30      89 ..      24     125 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 6.1e-06
                                  HHHHH-GGTTSEEEEES-TTTCCHHHHHCC-SEEEEE-S-HHHHHHHHCHTTTCCCEEEE CS
                        RrnaAD 22 IldklnleekltvleigpGkGilTeeLakrakqvvvlElderLakllqkklskdeklkvv 81
                                    dk  l++++ + +ig G+Gil + +++  ++v  +    +++k+ +++ls+ ++  +v
  gi|13541078|ref|NP_110766.1| 30 LTDKYGLKKEMVIADIGCGTGILARMFLENGNKVYCIDPNGEMLKFAKDELSSFGNAIIV 89
                                  5689999******************************************99977766665 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   1.4e-05     0.017      13      78 ..      37      98 ..      31     109 .. 0.79
   2 ?   -3.1   0.1       5.6   6.6e+03     130     149 ..     144     163 ..     142     163 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.4e-05
               Methyltransf_18 13 ekgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievrlsdGlekl 78
                                  +k+ ++aDiG+  g+l+ + +++g+  kv+ +D n + l+ ak+++++ g  + i vr s   + l
  gi|13541078|ref|NP_110766.1| 37 KKEMVIADIGCGTGILARMFLENGN--KVYCIDPNGEMLKFAKDELSSFG--NAIIVRGSAENTGL 98
                                  56779****************9885..7*****************98865..46666655555555 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 5.6
               Methyltransf_18 130 engfkiedEelvkeegkiYe 149
                                   + gf+ e E++v   gk Y+
  gi|13541078|ref|NP_110766.1| 144 DDGFTAEYEKIVSAYGKNYQ 163
                                   57899999999999999996 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   1.6e-05     0.019      51     111 ..      27      86 ..      25     129 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.6e-05
                                   HHHHHTTTT--TT-EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SS CS
                          CMAS  51 ldlileklelkpGmtlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvdeldle 111
                                   ++++ +k +lk+ m + diGcG G l+r   e+ + kv  +    e  k ak+++ + +++
  gi|13541078|ref|NP_110766.1|  27 VKMLTDKYGLKKEMVIADIGCGTGILARMFLEN-GNKVYCIDPNGEMLKFAKDELSSFGNA 86 
                                   57899**********************999999.999999999999999999888887765 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   4.4e-05     0.052      58     100 ..      22      67 ..       6     136 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.4e-05
                                   -HHHHHHHHHCTS...-TTS-EEEES-TT-HHH.HH--S-..EEEEE CS
                Methyltransf_8  58 nPldviirklkkk...kdnlvvadlGcGeakia.eavrekekvrsfd 100
                                    P+  i++ l  k   k+++v+ad+GcG   +a +  ++ +kv ++d
  gi|13541078|ref|NP_110766.1|  22 YPVG-IVKMLTDKyglKKEMVIADIGCGTGILArMFLENGNKVYCID 67 
                                   4543.344444332226789*************55567788999998 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   6.2e-05     0.074      63     122 ..      28      84 ..      20     107 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.2e-05
                                   HHHHHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTC.EEEEEESBHHHHHHHHHHHHHCT CS
                          PCMT  63 alalellelkkgarvLevGsGsGyltavlarlvgekg.rvvsierikelveeakrnlkkld 122
                                    ++++   lkk + + ++G+G+G+l+    r++ e+g +v  i+   e+ + ak +l   +
  gi|13541078|ref|NP_110766.1|  28 KMLTDKYGLKKEMVIADIGCGTGILA----RMFLENGnKVYCIDPNGEMLKFAKDELSSFG 84 
                                   45666677***************765....5555555467788888888888888776655 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 ?   11.6   0.0   8.1e-05     0.096     115     150 ..      38      72 ..      28      81 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 8.1e-05
                                   TT-EEEEET-TTSHHHHHHHHCT-SEEEEE---HHH CS
                Methyltransf_9 115 kgrtildvGcgnGyhlwrmvgegaklvvGidPself 150
                                   k+ +i+d+Gcg+G  l rm  e+ + v  idP+   
  gi|13541078|ref|NP_110766.1|  38 KEMVIADIGCGTGI-LARMFLENGNKVYCIDPNGEM 72 
                                   567899*******7.78***************8654 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   8.5e-05       0.1     156     201 ..      32      77 ..      26     108 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 8.5e-05
                          PrmA 156 eklvkegeevl.DvGtGSGiLaiaaakLgakkvvavDiDevAvkvak 201
                                   +k+  ++e v+ D+G+G+GiLa   +  g +kv+ +D +   +k ak
  gi|13541078|ref|NP_110766.1|  32 DKYGLKKEMVIaDIGCGTGILARMFLENG-NKVYCIDPNGEMLKFAK 77 
                                   555556666666*********96555444.56777776665555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       600  (0.0334653); expected 358.6 (0.02)
Passed bias filter:                      522  (0.0291148); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.52
# Mc/sec: 1453.82
//
Query:       gi|13541079|ref|NP_110767.1|  [L=393]
Description: transposase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.3e-16   58.6   0.2      1e-15   57.4   0.2    1.7  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    0.00083   19.1   1.9       0.22   11.1   0.1    2.2  2  DUF2229         CoA enzyme activase uncharacterised domain (D
     0.0059   16.6   0.5     0.0059   16.6   0.5    1.6  2  PBECR5          phage-Barnase-EndoU-ColicinE5/D-RelE like nuc
  ------ inclusion threshold ------
      0.082   13.0   0.9       0.15   12.1   0.9    1.4  1  DZR             Double zinc ribbon
       0.42   10.5   1.9       0.77    9.7   1.9    1.4  1  C1_1            Phorbol esters/diacylglycerol binding domain 


Domain annotation for each model (and alignments):
>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.4   0.2   2.8e-19     1e-15       1      67 [.     288     356 ..     288     358 .. 0.89

  Alignments for each domain:
  == domain 1  score: 57.4 bits;  conditional E-value: 2.8e-19
                OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnp...ayTSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNil 67 
                                   ++ l  q+ yka ++G +v+e  +   ++TS  Cs+C    +   +gr +kC++Cg+e+drDvnA+iNi+
  gi|13541079|ref|NP_110767.1| 288 YGMLASQVMYKASWEGLPVIELTRketRNTSRMCSVCDTLARI-EHGRILKCDSCGLEIDRDVNACINIA 356
                                   5678899*************986522256**********9999.9************************8 PP

>> DUF2229  CoA enzyme activase uncharacterised domain (DUF2229)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.1   6.2e-05      0.22     113     173 ..      34     103 ..      12     134 .. 0.63
   2 !    7.2   0.2   0.00097       3.5      90     179 ..     165     257 ..     156     260 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 6.2e-05
                       DUF2229 113 llspvldle.dkke.....lakqlle...elgiskkeikkAvekAleaqkafkeelrkkgeelleeleee 173
                                   +++ ++++  +k+      + +++++   e++i      +A++kA++  k+++++l+kk++++++++e+ 
  gi|13541079|ref|NP_110767.1|  34 MVNFTINIMiEKNLtsrnsVSNEVYHklkEYEIPSYYYIEAINKAVALVKTYRKRLKKKQKATVPHVEKP 103
                                   3333333332222222222223333234488********************************9987774 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.00097
                       DUF2229  90 eynCpivqglpeviknnleeeikllspvldledkkelakqlle...elgiskkeikkAv..ekAleaqkafkeelrkkgee 165
                                      C+ + g+  +++n++  ++++ ++++dl++  e+++++ +   +++++ ++i++ +  + + ++ +++k+ +++  ++
  gi|13541079|ref|NP_110767.1| 165 AIECTTTVGVDRNLRNAT-VGNEFHHEIYDLSNVVEIKQRYRKkesHFHRNDRRIREKIlsKYGKRERNRVKQIMHETSKA 244
                                   567***************.68899999999999999888888667788999999999873366888888888888888888 PP

                       DUF2229 166 lleeleeegkkgiv 179
                                   +++++++ +k+ iv
  gi|13541079|ref|NP_110767.1| 245 IVANAST-RKEMIV 257
                                   8876333.334444 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 ?   -2.5   0.1       1.1   4.1e+03     133     176 ..      48      91 ..      29     101 .. 0.55
   2 !   16.6   0.5   1.6e-06    0.0059     132     228 ..     169     266 ..     142     281 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.1
                        PBECR5 133 tsegse.keLaekllndeavkaaYLadkGeevevayvekektfte 176
                                   ts +s+ +e   kl++ e   + Y+ +  ++v  ++   +k++++
  gi|13541079|ref|NP_110767.1|  48 TSRNSVsNEVYHKLKEYEIPSYYYIEAINKAVALVKTY-RKRLKK 91 
                                   44444313444555555555555555555555553333.234444 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 1.6e-06
                        PBECR5 132 ltsegsekeLaekllndeavkaaYLadkGeevevayvekektfteeqvevlekltdalgddeee.geelaekiieekaeia 211
                                    t+ g  ++L +   ++e  +++Y  ++  e++++y++ke +f  ++++  ek+  ++g+ e + ++++ +++++   ++a
  gi|13541079|ref|NP_110767.1| 169 TTTVGVDRNLRNATVGNEFHHEIYDLSNVVEIKQRYRKKESHFHRNDRRIREKILSKYGKRERNrVKQIMHETSKAIVANA 249
                                   4556778999999999********9999***********99*****************98877768999999999999999 PP

                        PBECR5 212 kseakdrketekdkmed 228
                                    ++ + ++ ++++ +++
  gi|13541079|ref|NP_110767.1| 250 STRKEMIVLENIRGINK 266
                                   98888888888877766 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.9   4.2e-05      0.15       7      46 ..     313     353 ..     311     354 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.2e-05
                           DZR   7 elppdarfCseCgtklkavaa..edrCpsCgekvdpearfCp 46 
                                   e+++ +r+Cs C t  +  ++    +C+sCg ++d + + C 
  gi|13541079|ref|NP_110767.1| 313 ETRNTSRMCSVCDTLAR-IEHgrILKCDSCGLEIDRDVNACI 353
                                   678899*******9876.4445799**************996 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 ?    9.7   1.9   0.00021      0.77       9      44 ..     316     354 ..     311     362 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00021
                                   SS--B-TTT-SB--SSSS-EEEETTT--EE-CC...CCT CS
                          C1_1   9 kqptfCkhCgeflwgkekqglkCswCkllvHkk...Che 44 
                                   + +  C+ C+ + + +  ++lkC+ C+l ++ +   C++
  gi|13541079|ref|NP_110767.1| 316 NTSRMCSVCDTLARIEHGRILKCDSCGLEIDRDvnaCIN 354
                                   56789*******955*************99887667766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1244  (0.0693848); expected 358.6 (0.02)
Passed bias filter:                      550  (0.0306766); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.61u 0.33s 00:00:00.94 Elapsed: 00:00:00.52
# Mc/sec: 2255.74
//
Query:       gi|13541080|ref|NP_110768.1|  [L=158]
Description: HIT (histidine triad) family protein [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.8e-22   78.5   1.8    6.4e-22   78.1   1.8    1.2  1  HIT       HIT domain
    3.2e-16   59.8   0.8    4.5e-16   59.4   0.8    1.2  1  DcpS_C    Scavenger mRNA decapping enzyme C-term binding
    2.3e-07   30.7   0.5    3.3e-07   30.2   0.5    1.1  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 !   78.1   1.8   1.1e-25   6.4e-22       3      97 ..      29     121 ..      27     122 .. 0.95

  Alignments for each domain:
  == domain 1  score: 78.1 bits;  conditional E-value: 1.1e-25
                                   CC-CCEEEE-SSEEEEE-SS-SSSSEEEEEESSTGCSGGGCCHHHHHHHHHHHHHHHHHHHTCTTCCCEEEEEEESGGGT- CS
                           HIT   3 eipstvvyeddlvlafldidpkapghlLvipkkhlselhdlteeelakllsavkkvakalqkkfknkglrvvinngahagq 83 
                                   +i s+vvy d++++afld +p  +gh+L++p+kh +++ +++ee  +kl+ +v+ + +a++   + +g+ ++inn  +  q
  gi|13541080|ref|NP_110768.1|  29 KIASNVVYSDEHFIAFLDHKPLFKGHTLLVPRKHFENIYEMDEETSSKLMHEVQLISRAVEIATSSDGTFIAINN--KVSQ 107
                                   6889**********************************************************9999999999987..567* PP

                                   SSSS-EEEEEEC-T CS
                           HIT  84 svahlHiHviprre 97 
                                   sv+h+H+H++pr++
  gi|13541080|ref|NP_110768.1| 108 SVPHVHVHIVPRKQ 121
                                   ************87 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 !   59.4   0.8   7.5e-20   4.5e-16       1     105 [.      19     122 ..      19     127 .. 0.94

  Alignments for each domain:
  == domain 1  score: 59.4 bits;  conditional E-value: 7.5e-20
                                   T-HHHHHHTTSS-B-EEEE-SSEEEEE-SS-SSSEEEEEEESS---SGGG--TTTTTHHHHHHHHHHHHHHHTT-T-EEEE CS
                        DcpS_C   1 kwvfnilakgkepervvyedekfvvlkDikpkaklhllvipkrdikslrdLtkehlpllkemrekakkvieekynevdaee 81 
                                   k+ f+++++gk++++vvy+de+f+++ D kp  k h l +p++++++++++++e  + l + ++ +  ++e    + d  +
  gi|13541080|ref|NP_110768.1|  19 KCKFCDIISGKIASNVVYSDEHFIAFLDHKPLFKGHTLLVPRKHFENIYEMDEETSSKLMHEVQLISRAVEIAT-SSDGTF 98 
                                   699*******************************************************************7777.67**** PP

                                   E--SCCCT--S-S--EEEEE.... CS
                        DcpS_C  82 lrvgvhyqPsvyhlHlHvisldfe 105
                                   + +  ++ +sv h+H+H++  +++
  gi|13541080|ref|NP_110768.1|  99 IAINNKVSQSVPHVHVHIVPRKQK 122
                                   ******************985554 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 !   30.2   0.5   5.4e-11   3.3e-07       9     112 ..      15     122 ..      11     128 .. 0.70

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 5.4e-11
                                   HHHHH-S----SS---SS--S-B-SSEEEE---.S-SSTT-EEEEESS--SSTTSS-H....HHHHHHHHHHHHHHHHHHH CS
                      CwfJ_C_1   9 asldsClfClsnpklekhlivsignkvYlalpk.gpLssgHvliipieHisallslde....evldeirkfrkalvkmykk 84 
                                   +++ +C+fC   +     ++v  +++ ++a    +pL +gH l++p +H ++  ++de    +++ e++   +a+ ++ ++
  gi|13541080|ref|NP_110768.1|  15 NEVVKCKFCDIISGKIASNVVY-SDEHFIAFLDhKPLFKGHTLLVPRKHFENIYEMDEetssKLMHEVQLISRAV-EIATS 93 
                                   5677899994444444444444.56666665555***********************944444455666666665.45666 PP

                                   TT--EEEEEE-.SSS-----EEEEE--HH CS
                      CwfJ_C_1  85 qdkdavvfEis.sersvHlaiqvipvpks 112
                                    d   +   ++ s++ +H++++++p +++
  gi|13541080|ref|NP_110768.1|  94 SDGTFIAINNKvSQSVPHVHVHIVPRKQK 122
                                   666666666656************97765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       790  (0.0440627); expected 358.6 (0.02)
Passed bias filter:                      583  (0.0325172); 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: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 960.39
//
Query:       gi|13541081|ref|NP_110769.1|  [L=380]
Description: major facilitator superfamily permease [Thermoplasma volcanium GSS1]
Scores for complete 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-42  143.1  82.6    1.6e-32  112.8  42.7    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 !  112.8  42.7     9e-37   1.6e-32      10     353 .]      22     333 ..       7     333 .. 0.87
   2 !   44.0  31.8   7.4e-16   1.3e-11       2     174 ..     199     366 ..     198     377 .. 0.88

  Alignments for each domain:
  == domain 1  score: 112.8 bits;  conditional E-value: 9e-37
                         MFS_1  10 larsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll.fasslwlll 89 
                                   l++sil++ +p      +  +  e gl+++l+++g+++ ++p G++sdrf+   v+ ++l++ a++ ++l+ ++ +++  +
  gi|13541081|ref|NP_110769.1|  22 LSWSILSVYMP------FRPTIEEEGLAFSLFFVGYVIVQIPSGFVSDRFSGGCVIGIALIGVAIS-AILSsLSKNITDEY 95 
                                   56666677776......77888899*************************8888************.66665767777799 PP

                         MFS_1  90 vlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllafvlfll 170
                                   ++ +l+G++ag+++pa++ ++ +++++ +r+ +ig++s+++ l++++  l+ + +a  +gW++ +y  a +++++++    
  gi|13541081|ref|NP_110769.1|  96 LSSILMGFTAGWVYPASINVMNHYYKD-RRSVYIGYYSIAWPLAIVISGLVLPTIAVRIGWQWGYYTSAMAAVVVAIA--- 172
                                   **************************9.********************999999999******************994... PP

                         MFS_1 171 llpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsglltllplylqevlglsglllagllla 251
                                    +  +  + + +               + +++++ ++vl+ l ++ llff+ +++l+ +   y    +g++  l++g++++
  gi|13541081|ref|NP_110769.1| 173 AFKLRTEKAGYSI--------------D-FSLIKDRNVLL-LSLGGLLFFLSYWSLTLYAYKY-FVGMGID-PLISGFIFS 235
                                   4444444444442..............2.77888899997.99999*****************.*******.8******** PP

                         MFS_1 252 llalvgailallagrlsdrlgrrrrlllallllllaalglallavtssavllllvlvliGfglgfvfpsllalasdlappe 332
                                   ++a+ g+++ +++g+l+ rlg ++  +++l++  l  +++a +  +   ++l+l+++l+Gf+ ++++p    la +   +e
  gi|13541081|ref|NP_110769.1| 236 AMAISGLFSTPVSGFLISRLGLKPSVIISLIIYGLPIMSFAEVRSA---AVLILISLLMGFFRFIITPGNSDLAIEIG-RE 312
                                   *********************9777777777766666666666666...77777899999999999999999999986.7* PP

                         MFS_1 333 eagtasglfntagslggalgp 353
                                   +ag++sg++n++++ +g++gp
  gi|13541081|ref|NP_110769.1| 313 RAGSVSGIANMFWQSSGIIGP 333
                                   ********************8 PP

  == domain 2  score: 44.0 bits;  conditional E-value: 7.4e-16
                         MFS_1   2 llaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfa 82 
                                   +l+++l +l+++ l++ +   +    gi+p   g+++++ a+  ++++++ G+l+ r+G ++ ++++l++++l   +++fa
  gi|13541081|ref|NP_110769.1| 199 SLGGLLFFLSYWSLTLYAY-KYFVGMGIDPLISGFIFSAMAISGLFSTPVSGFLISRLGLKPSVIISLIIYGLP--IMSFA 276
                                   6788888888888888887.5556789***********************************************..77777 PP

                         MFS_1  83 .sslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivs 161
                                      +  +l++  +l+G++  +++p+   l+ ++  + + g++ g+++++++ + i+gpl+++l+++s+g+ ++++ila++ 
  gi|13541081|ref|NP_110769.1| 277 eVRSAaVLILISLLMGFFRFIITPGNSDLAIEIGRE-RAGSVSGIANMFWQSSGIIGPLVSSLIITSVGFNVLWIILAAIV 356
                                   7666669***********877777777777776666.******************************************** PP

                         MFS_1 162 llafvlfllllpe 174
                                   + + v   l+++ 
  gi|13541081|ref|NP_110769.1| 357 ISSSV---LYYMI 366
                                   ***99...66655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (380 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       836  (0.0466284); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.67u 0.28s 00:00:00.95 Elapsed: 00:00:00.48
# Mc/sec: 2365.11
//
Query:       gi|13541082|ref|NP_110770.1|  [L=471]
Description: mercuric reductase [Thermoplasma volcanium GSS1]
Scores for complete 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-54  183.7   0.3    6.2e-54  183.2   0.3    1.2  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    6.1e-24   84.4   0.1    1.1e-23   83.5   0.1    1.5  1  Pyr_redox_dim   Pyridine nucleotide-disulphide oxidoreductase
    9.2e-17   61.4   3.4    2.1e-16   60.2   0.3    2.8  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    2.3e-08   33.7   0.6    5.9e-08   32.3   0.6    1.7  1  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    1.1e-05   24.8   0.2     0.0038   16.4   0.0    2.9  3  K_oxygenase     L-lysine 6-monooxygenase (NADPH-requiring)
    8.2e-05   22.6   2.3     0.0092   15.9   0.1    2.4  2  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
     0.0021   17.4   5.4      0.019   14.3   0.1    3.1  4  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
  ------ inclusion threshold ------
      0.016   14.8   1.1       0.12   12.0   0.2    2.4  2  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
       0.14   11.8   0.4       0.34   10.5   0.4    1.6  1  ApbA            Ketopantoate reductase PanE/ApbA
       0.22   11.8   3.9       0.48   10.7   0.1    2.4  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
       0.41    9.3   8.1        8.5    4.9   0.7    3.3  3  HI0933_like     HI0933-like protein
        7.9    5.4   5.7         11    5.0   0.6    2.3  2  Lycopene_cycl   Lycopene cyclase protein


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  183.2   0.3   4.2e-57   6.2e-54       1     290 [.       6     323 ..       6     327 .. 0.85

  Alignments for each domain:
  == domain 1  score: 183.2 bits;  conditional E-value: 4.2e-57
                                   CSEEEE--SHHHHHHHHHHHH...HTS-EEEEE...TTHCHHHCSHHHHCHHHHHHHHHHHHH.................. CS
                                   xxxxxxxxxxxxxxxxxxxxx...xxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxx.................. RF
                   Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaq...agakvtlve...legtclnggcllskallgvaedaeias.................. 57 
                                   +d+v++G G+A+++aa+++++    +a++++v+   l+gtc+n gc++sk l +++   +  +                  
  gi|13541082|ref|NP_110770.1|   6 YDLVIVGRGAAAFSAAIRASEitsGQARIAMVGngpLGGTCVNTGCVPSKLLISISNSFQNSLkprypglpsverppetev 86 
                                   689******************9977*******999****************9999999987779***************** PP

                                   ..............HHHHCHHHHCCCCHC...CTCEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC.T CS
                                   ..............xxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2  58 ..............evvkklnqgielllg...eevvkidpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGvae 121
                                                 +   k++  +e + +    +++++ +g+k++ +     ++ +++   ++++AtGs+p  +gi+G++e
  gi|13541082|ref|NP_110770.1|  87 imdfiresvhgerkK---KYEDVVESYENidlYTGTAVFTGEKEILV-----DSSHSLFGYNVLIATGSRPYVPGIKGLNE 159
                                   *******99985541...44444444444111112555555555555.....5556777789*****************55 PP

                                   TBEECCSECHHHHHHCCSS-TSEEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2 122 nvgklvrtldsaealklkllpkrivvvGgGyiGvElAaalaklgkevtlveardrllraldkelsaaleealekeGvevkl 202
                                   +      +++++  ++lk +p++i++ GgG++GvE+ +al++lg+ev+++e  +++l++ + +++ ++e+ l+++G  + +
  gi|13541082|ref|NP_110770.1| 160 TS-----YITTDSVWELKHVPASIAILGGGAVGVEIGQALSRLGSEVHIIEVSNQILPGIPADMASIIERSLREDGMVINT 235
                                   54.....799*********************************************************************** PP

                                   SCEEEEEEETTE..EEEEEETTSCE...EEESEEEE-S-EEES-HHCSHCCT-EEEETTEEE--TTSBESSTTEEE-GGGC CS
                                   xxxxxxxxxxxx..xxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2 203 gtsvkeidgnge..klevvledgee...idadlvvvavGvrpstelleeklglelderggivvdeflrtnvpgiyaiGDva 278
                                    tsv e+ g +      ++l+  +    ++++ ++va+G+ p+ +l+ ek g++  +++gi vde+lrt+  +iya+GDv+
  gi|13541082|ref|NP_110770.1| 236 STSVDEVSGGEGkkY--LKLNGTNIndtLEVEEILVATGRAPNIDLALEKTGVKY-SKRGIAVDEYLRTSNRKIYAAGDVV 313
                                   ********9999322..33333333557******************77*******.9999********************* PP

                                   TECCSS--HHHH CS
                                   xxxxxxxxxxxx RF
                   Pyr_redox_2 279 ggkggpelaqaA 290
                                   ++  +++l + A
  gi|13541082|ref|NP_110770.1| 314 DQ--KYKLETLA 323
                                   55..44444444 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 !   83.5   0.1   7.5e-27   1.1e-23       1     109 [.     347     455 ..     347     456 .. 0.97

  Alignments for each domain:
  == domain 1  score: 83.5 bits;  conditional E-value: 7.5e-27
                                   BEEEEESSSEEEEEES-HHHHHHHHSGEEEEEEEEECGHHHCHTTHTEEEEEEEEETTTTBEEEEEEECTTHHHHHHHHHH CS
                 Pyr_redox_dim   1 iptvvftdpevasvGlteeeAkaagieikvgkfpfkangralayaetkgfvKlvadaktgkvlGahivGpgageliqelav 81 
                                   +p +vf++p +asvG+t++eA++agi+ +  +++ k+++  +++a+++g++ +va+a+t++++G++iv+++a eli+e+++
  gi|13541082|ref|NP_110770.1| 347 VPFAVFCSPGYASVGYTQDEATKAGIKTEARRISTKDVASERIHANREGIINIVAEADTKEIVGVQIVAENAPELINEASA 427
                                   6889***************************************************************************** PP

                                   HHHTTSBHHHHHTSBSSSSSTGGGGHCH CS
                 Pyr_redox_dim  82 aikagltvedladtihihPtlsealkea 109
                                   +++++ +++dl++t+h+ Pt +e lk a
  gi|13541082|ref|NP_110770.1| 428 ILSKRFKTDDLINTVHVFPTENEGLKLA 455
                                   *********************9998865 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.2      0.65   9.7e+02       2      22 ..       8      28 ..       7      41 .. 0.85
   2 !   60.2   0.3   1.4e-19   2.1e-16       1      72 [.     177     248 ..     177     259 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.65
                                  EEEECSSHHHHHHHHHHHHTT CS
                     Pyr_redox  2 vvvvGgGyiglElAgalaelg 22
                                  +v+vG G  +  +A  ++e+ 
  gi|13541082|ref|NP_110770.1|  8 LVIVGRGAAAFSAAIRASEIT 28
                                  79********99998887765 PP

  == domain 2  score: 60.2 bits;  conditional E-value: 1.4e-19
                                   EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTS CS
                     Pyr_redox   1 kvvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekngievllntkveeiegsedg 72 
                                   +++++GgG +g+E ++al++lg++V+++e s+++l+++++++++i++++l++ g+ + ++t+v e+ g e +
  gi|13541082|ref|NP_110770.1| 177 SIAILGGGAVGVEIGQALSRLGSEVHIIEVSNQILPGIPADMASIIERSLREDGMVINTSTSVDEVSGGEGK 248
                                   689****************************************************************88875 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 !   32.3   0.6   3.9e-11   5.9e-08      55     305 .]      70     310 ..       9     310 .. 0.70

  Alignments for each domain:
  == domain 1  score: 32.3 bits;  conditional E-value: 3.9e-11
                   Pyr_redox_3  55 leipdlnaise..etspafslkeeklsrkealeYlrevaksfelpiklfeeVesvkkedegfevetsketyeAkkviiAtG 133
                                      p+l++++   et+  + + +e ++++   +Y + v ++++++  + + V + +k   +  v+ s++++   +v+iAtG
  gi|13541082|ref|NP_110770.1|  70 PRYPGLPSVERppETEVIMDFIRESVHGERKKKYEDVVESYENIDLYTGTAVFTGEK---EILVD-SSHSLFGYNVLIATG 146
                                   455666666641144445556799999999999999999999999999988865443...45555.55678889******* PP

                   Pyr_redox_3 134 efdkPnklnipGeeklvkhyskvkefhkya..gqkvvViGgknSavDaAlelvrkgaeVtvvtrgseiekeesdpsyslkp 212
                                      +P++++i+G ++      +++ + +++     +++ Gg+  +v++   l r g+eV+++  +++i          + +
  gi|13541082|ref|NP_110770.1| 147 S--RPYVPGIKGLNE-TSYITTDSVW-ELKhvPASIAILGGGAVGVEIGQALSRLGSEVHIIEVSNQILPG-------IPA 216
                                   9..**********95.3323333333.444236899****************************9976664.......777 PP

                   Pyr_redox_3 213 dienrleelvkeekikvlfnaevkeikekeee.y.kvktedgkkvevkddvvlatGykpdlsf.lkkslfeldedgrpvlt 290
                                   d+ + +e+ ++e+ + + + ++v+e++  e + y k++ ++ + + + +++++atG  p++++ l+k ++++++ g+ ++ 
  gi|13541082|ref|NP_110770.1| 217 DMASIIERSLREDGMVINTSTSVDEVSGGEGKkYlKLNGTNINDTLEVEEILVATGRAPNIDLaLEKTGVKYSKRGI-AV- 295
                                   888888888888779999********9554431336666666666667888999********977778888855444.33. PP

                   Pyr_redox_3 291 eeteetnvpglflaG 305
                                   +e   t    ++ aG
  gi|13541082|ref|NP_110770.1| 296 DEYLRTSNRKIYAAG 310
                                   455555566677666 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0      0.01        15       2      25 ..       5      28 ..       4      38 .. 0.85
   2 !   16.4   0.0   2.5e-06    0.0038     140     219 ..     129     203 ..      89     220 .. 0.77
   3 ?   -0.3   0.0      0.31   4.6e+02     131     165 ..     249     280 ..     225     308 .. 0.61

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.01
                   K_oxygenase  2 ilDligiGiGpsnLsLailleevk 25
                                   +Dl+++G G+++ s ai+++e+ 
  gi|13541082|ref|NP_110770.1|  5 KYDLVIVGRGAAAFSAAIRASEIT 28
                                  69*****************99987 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 2.5e-06
                   K_oxygenase 140 aegeeeelearnlvlgvGtepkiPevleklegkervvHsseylerkeellakkriaVvGsGqSaaeifedllrrqkkvel 219
                                     +++++l   n+++++G++p++P + + l++    + ++++ e k   + + +ia+ G+G  + ei + l r  ++v++
  gi|13541082|ref|NP_110770.1| 129 LVDSSHSLFGYNVLIATGSRPYVPGI-KGLNE-TSYITTDSVWELK---HVPASIAILGGGAVGVEIGQALSRLGSEVHI 203
                                   56678889999*************86.66874.7788888887777...7899**************9999887765444 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.31
                   K_oxygenase 131 elltveskdaegeeeelearnlvlgvGtepkiPev 165
                                   ++l+++    ++ +++le +++++++G  p+i  +
  gi|13541082|ref|NP_110770.1| 249 KYLKLNG---TNINDTLEVEEILVATGRAPNIDLA 280
                                   4455554...3445566666677777776666555 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 !   15.9   0.1   6.1e-06    0.0092       2      50 ..     178     226 ..     177     244 .. 0.86
   2 !    6.2   0.2    0.0058       8.7      30      91 ..     364     423 ..     350     435 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 6.1e-06
                                   EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCT CS
                       3HCDH_N   2 vaviGaGtmGagiaavfasagleVvlvdiseealekalekieksleklv 50 
                                   +a++G G +G +i +++ + g eV+++++s+++l    + +++ +e+  
  gi|13541082|ref|NP_110770.1| 178 IAILGGGAVGVEIGQALSRLGSEVHIIEVSNQILPGIPADMASIIERSL 226
                                   8*******************************99888888887777654 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0058
                                   S-HHHHHHHHHHHHHHHHCCTTTTSS-HHHHCCCHHCEEEES-HHHHHC-SEEEE-S-SSHH CS
                       3HCDH_N  30 iseealekalekieksleklvekgklkeeeveaalarisfttdleeavdadlviEavvEnle 91 
                                    +e++ +  + ++++   k v++++++    ++ + +i +++d++e+v++++v E+++E ++
  gi|13541082|ref|NP_110770.1| 364 QDEATKAGIKTEARRISTKDVASERIH--ANREGIINIVAEADTKEIVGVQIVAENAPELIN 423
                                   444444444444455555556666666..445566778899*****************9775 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 ?   -1.4   0.4      0.79   1.2e+03      31      50 ..       8      27 ..       4      53 .. 0.87
   2 ?   -3.0   0.0       2.4   3.6e+03      78     105 ..      99     126 ..      55     130 .. 0.78
   3 !   14.3   0.1   1.3e-05     0.019      28      69 ..     175     216 ..     167     276 .. 0.78
   4 ?    4.3   0.1     0.014        21      77     113 ..     381     425 ..     334     429 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.79
                                  EEEESTSHHHHHHHHHHHHT CS
                   AlaDh_PNT_C 31 vlviGgGvaGlqAiatakgl 50
                                   +++G G a  +A+  a+++
  gi|13541082|ref|NP_110770.1|  8 LVIVGRGAAAFSAAIRASEI 27
                                  68999999999999888765 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2.4
                                   HCHHHHHHHHHHHH-SEEEE---BTTSS CS
                   AlaDh_PNT_C  78 lksqeellaeavkeadvvigtvlipGkk 105
                                   +k++ e + e+ ++ d+  gt+  +G+k
  gi|13541082|ref|NP_110770.1|  99 RKKKYEDVVESYENIDLYTGTAVFTGEK 126
                                   5667777888888899999999888876 PP

  == domain 3  score: 14.3 bits;  conditional E-value: 1.3e-05
                                   --EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHH CS
                   AlaDh_PNT_C  28 pakvlviGgGvaGlqAiatakglgakVtvlDvrparleqles 69 
                                   pa + ++GgG +G++  ++ ++lg +V +++v+ + l  + +
  gi|13541082|ref|NP_110770.1| 175 PASIAILGGGAVGVEIGQALSRLGSEVHIIEVSNQILPGIPA 216
                                   89******************************9987766655 PP

  == domain 4  score: 4.3 bits;  conditional E-value: 0.014
                                   E.......HCHHHHHHHHHHHH-SE.EEE---BTTSS---SC-HH CS
                   AlaDh_PNT_C  77 v.......lksqeellaeavkeadv.vigtvlipGkkaPkLvtee 113
                                   +       +++++e + + v+ead   i  v+i +++aP L++e+
  gi|13541082|ref|NP_110770.1| 381 TkdvaserIHANREGIINIVAEADTkEIVGVQIVAENAPELINEA 425
                                   2444446699999***********844889************975 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.2   7.9e-05      0.12       2      53 ..     177     228 ..     176     241 .. 0.94
   2 ?    0.6   0.1      0.24   3.5e+02     126     162 ..     390     428 ..     371     440 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.9e-05
                                   EEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHHCTTS-SS--TTHHH CS
                UDPG_MGDP_dh_N   2 kisviGlGYvGlvtaavlaeighevigvDideekvdklnsgkipiyepgLee 53 
                                    i+++G G vG+  + +l+++g ev ++ ++++    + ++  +i+e+ L+e
  gi|13541082|ref|NP_110770.1| 177 SIAILGGGAVGVEIGQALSRLGSEVHIIEVSNQILPGIPADMASIIERSLRE 228
                                   69*********************************************99976 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.24
                                   THHHHCHHHHHHHHCSS-..TTCEEEEE------TTSHH CS
                UDPG_MGDP_dh_N 126 gtaeelvkkileeaskkk..gvdfdvvsnPEflregsav 162
                                    +++e + +i++ea++k+  gv++     PE ++e sa+
  gi|13541082|ref|NP_110770.1| 390 HANREGIINIVAEADTKEivGVQIVAENAPELINEASAI 428
                                   466667788888888888444444444679999998887 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.4   0.00023      0.34       1      29 [.     178     206 ..     178     219 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00023
                                   EEEES-SHHHHHHHHHHHHHTHCEEEE-S CS
                          ApbA   1 iailGaGaiGsllaakLakagadvtlilr 29 
                                   iailG Ga+G  ++  L++ g +v++i  
  gi|13541082|ref|NP_110770.1| 178 IAILGGGAVGVEIGQALSRLGSEVHIIEV 206
                                   89***********************9865 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 ?    1.5   0.8      0.24   3.6e+02       1      17 [.      10      26 ..      10      49 .. 0.81
   2 ?   10.7   0.1   0.00032      0.48       1      31 [.     180     210 ..     180     232 .. 0.94

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.24
                                  EE--SHHHHHHHHHHHC CS
                 NAD_binding_8  1 IvGaGlsGlvaAylLak 17
                                  IvG G+++ +aA ++++
  gi|13541082|ref|NP_110770.1| 10 IVGRGAAAFSAAIRASE 26
                                  9***********99886 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00032
                                   EE--SHHHHHHHHHHHCCTEEEEEE-SSSSS CS
                 NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrdrl 31 
                                   I+G+G+ G  + ++L++ g +v+++e ++++
  gi|13541082|ref|NP_110770.1| 180 ILGGGAVGVEIGQALSRLGSEVHIIEVSNQI 210
                                   89************************98875 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.5      0.03        45       2      21 ..       7      26 ..       6      42 .. 0.84
   2 ?    4.9   0.7    0.0057       8.5       2      35 ..     177     210 ..     176     214 .. 0.92
   3 ?    4.5   0.0    0.0077        11     112     164 ..     219     273 ..     215     292 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.03
                                  SEEEE--SHHHHHHHHHHHH CS
                   HI0933_like  2 dviviGgGaAGlmaAisaak 21
                                  d++++G GaA + aAi+a++
  gi|13541082|ref|NP_110770.1|  7 DLVIVGRGAAAFSAAIRASE 26
                                  89***************965 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0057
                                   SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS CS
                   HI0933_like   2 dviviGgGaAGlmaAisaakrgkrVlllekakkl 35 
                                   +++++GgGa G+    ++++ g++V ++e  +++
  gi|13541082|ref|NP_110770.1| 177 SIAILGGGAVGVEIGQALSRLGSEVHIIEVSNQI 210
                                   589**************************99887 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.0077
                                   HHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE....TTEEEEESEEEE---- CS
                   HI0933_like 112 vdallkelkeagvklrletevksvekeedgkfrvkt...kseeeleadklvlAtGG 164
                                    +++++ l+e g+ ++++t+v +v+  e++   +k+   + +++le +++++AtG 
  gi|13541082|ref|NP_110770.1| 219 ASIIERSLREDGMVINTSTSVDEVSGGEGK-KYLKLngtNINDTLEVEEILVATGR 273
                                   5678899*****************776655.55555123457799*********95 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.3     0.038        57       1      27 [.       7      36 ..       7      42 .. 0.75
   2 ?    5.0   0.6    0.0073        11       2      37 ..     178     211 ..     177     215 .. 0.93

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.038
                 Lycopene_cycl  1 DvvviGaGpAglslAarl...teakpglkv 27
                                  D+v++G G+A  s A r    t+ ++++++
  gi|13541082|ref|NP_110770.1|  7 DLVIVGRGAAAFSAAIRAseiTSGQARIAM 36
                                  9************99887333555555554 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0073
                 Lycopene_cycl   2 vvviGaGpAglslAarlteakpglkvvlieaspsll 37 
                                   +++ G+G+ g+ + + l  ++ g +v +ie s+++l
  gi|13541082|ref|NP_110770.1| 178 IAILGGGAVGVEIGQAL--SRLGSEVHIIEVSNQIL 211
                                   789**************..************99884 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (471 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                        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: 0.64u 0.29s 00:00:00.93 Elapsed: 00:00:00.48
# Mc/sec: 2943.51
//
Query:       gi|13541083|ref|NP_110771.1|  [L=74]
Description: copper chaperone [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      7e-11   42.4   0.6    8.3e-11   42.2   0.6    1.1  1  HMA          Heavy-metal-associated domain
  ------ inclusion threshold ------
       0.11   12.6   0.0       0.14   12.3   0.0    1.2  1  ZoocinA_TRD  Target recognition domain of lytic exoenzyme


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 !   42.2   0.6   9.3e-15   8.3e-11       3      53 ..       7      56 ..       5      64 .. 0.88

  Alignments for each domain:
  == domain 1  score: 42.2 bits;  conditional E-value: 9.3e-15
                           HMA  3 rvsgmhCagCaakvekvLselpgVesvkvdlatktvtVegdaestklrkii 53
                                  r+ gm+C  C+a+vek L++++gV  v+v+l  ++++V++d++  +++k+ 
  gi|13541083|ref|NP_110771.1|  7 RIYGMTCNDCVATVEKGLKSVDGVLWVSVSLPDGSAVVKVDDSV-DPEKLE 56
                                  788*************************************8876.556654 PP

>> ZoocinA_TRD  Target recognition domain of lytic exoenzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   1.6e-05      0.14      60      97 ..       9      45 ..       2      54 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.6e-05
                   ZoocinA_TRD 60 yfvfnPksvlsveepiygvaGltfakvkfaegesiWls 97
                                  y +   ++v +ve+++++v G+ +  v +++g+ +  +
  gi|13541083|ref|NP_110771.1|  9 YGMTCNDCVATVEKGLKSVDGVLWVSVSLPDGSAVV-K 45
                                  5555679************************87764.4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       519  (0.0289475); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); 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 0.28s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 480.35
//
Query:       gi|13541084|ref|NP_110772.1|  [L=128]
Description: hypothetical protein TVN0253 [Thermoplasma volcanium GSS1]
Scores for complete 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-10   39.7   2.5    5.8e-10   39.4   2.5    1.1  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 !   39.4   2.5   3.2e-14   5.8e-10       1     103 [.       7     103 ..       7     119 .. 0.80

  Alignments for each domain:
  == domain 1  score: 39.4 bits;  conditional E-value: 3.2e-14
                           HPP   1 liaslGAsavllfavpesplaqPrnvvgGhlisalvGvaiaklfglsllwlaaalavalaialmlltrtlhPPagAtalia 81 
                                   l ++++ sa+l+    + ++++P +++++ +   l  +++  l+g  + ++++ l v++  +l+ +tr  hPPa+A a++ 
  gi|13541084|ref|NP_110772.1|   7 LAPPFAVSAYLISVEHRGRFSKPDSLIVSYVAVILSTTLLHILLG--TGVIQLYLNVVIISILITFTRFKHPPAIALAVFS 85 
                                   679**************************9988888888777777..5667****************************** PP

                           HPP  82 vlgkeikelgwafllvpvllgs 103
                                    ++++    +++f+ +++++  
  gi|13541084|ref|NP_110772.1|  86 YIEHN----DVKFVESSIIILI 103
                                   ****9....4555443222221 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       770  (0.0429472); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.31s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 808.62
//
Query:       gi|13541085|ref|NP_110773.1|  [L=359]
Description: membrane-associated Zn-dependent protease 1 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      1e-11   44.6  11.0    4.5e-06   26.1   1.9    2.9  3  Peptidase_M50  Peptidase family M50


Domain annotation for each model (and alignments):
>> Peptidase_M50  Peptidase family M50
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0     0.084   1.5e+03      36      57 ..      96     117 ..      76     124 .. 0.56
   2 !   26.1   1.9   2.5e-10   4.5e-06       2     108 ..     132     210 ..     131     237 .. 0.87
   3 !   23.4   0.8   1.7e-09   3.1e-05     188     227 ..     248     287 ..     229     305 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.084
                                   XXXXXXXXXXXXXXXXXXXXXX CS
                                   xxxxxxxxxxxxxxxxxxxxxx RF
                 Peptidase_M50  36 GpkllsfkkgeteYaiallpLG 57 
                                     ++ls+   + +Y+i ++p G
  gi|13541085|ref|NP_110773.1|  96 VATILSTMYVGSQYSINFVPRG 117
                                   2334444444555555555555 PP

  == domain 2  score: 26.1 bits;  conditional E-value: 2.5e-10
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....XXXX CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Peptidase_M50   2 filllgilvvvHElGHflvAklcgvkveefsigfGpkllsfkkgeteYaiallpLGGyVkmageepeeelseeeakaflkk 82 
                                   f + l++++ +HE +HflvAk+++vk    s+ f           +++ + +  +G+++++++  p+++            
  gi|13541085|ref|NP_110773.1| 132 FSAPLLLILGIHESAHFLVAKRHHVKA---SLPF----------FIPFPVGIGTFGAFISLRDPLPNRK------------ 187
                                   7788999*******************9...7776..........4678889999***********9988............ PP

                                   XXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Peptidase_M50  83 spwqrllivlAGplanfilailvfvv 108
                                      +   i +AGp+a+f+ a+ +++v
  gi|13541085|ref|NP_110773.1| 188 ---AMTEIGAAGPIAGFLTALPLLFV 210
                                   ...8889**************99998 PP

  == domain 3  score: 23.4 bits;  conditional E-value: 1.7e-09
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Peptidase_M50 188 lssflqllalisvnLgilNLlPipvLDGghllfalleair 227
                                    + ++ +++++++  + +NL+P  +LDG h+l+ +l   +
  gi|13541085|ref|NP_110773.1| 248 PIFPMVFAVWVGMFATAMNLIPAGQLDGSHILRGVLGNRA 287
                                   4567899**************************9998766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (359 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       648  (0.0361426); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 2543.73
//
Query:       gi|13541086|ref|NP_110774.1|  [L=368]
Description: major facilitator superfamily permease [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (368 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       804  (0.0448435); expected 358.6 (0.02)
Passed bias filter:                      237  (0.0132188); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.64u 0.31s 00:00:00.95 Elapsed: 00:00:00.51
# Mc/sec: 2162.97
//
Query:       gi|13541087|ref|NP_110775.1|  [L=403]
Description: multidrug efflux permease [Thermoplasma volcanium GSS1]
Scores for complete 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-60  203.1  58.0    2.2e-44  151.8  36.4    2.0  2  MFS_1      Major Facilitator Superfamily
    1.5e-09   36.9  15.7    3.4e-06   25.7   8.8    2.2  2  MFS_3      Transmembrane secretion effector
    2.1e-08   33.4  17.6    2.1e-08   33.4  17.6    2.6  3  LacY_symp  LacY proton/sugar symporter


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  151.8  36.4   3.7e-48   2.2e-44       3     353 .]      21     351 ..      19     351 .. 0.89
   2 !   65.1  13.6     9e-22   5.4e-18       5     176 ..     218     395 ..     213     400 .. 0.92

  Alignments for each domain:
  == domain 1  score: 151.8 bits;  conditional E-value: 3.7e-48
                         MFS_1   3 laaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalg.lllllfa 82 
                                    aa++ ++++++++p++  + +e l++s  ++g+++tl a++++v+sl++G+lsd +Gr+++l+ g ++ ++  +ll+l++
  gi|13541087|ref|NP_110775.1|  21 TAAAVRSIGYGATWPFMAVYFNEYLHLSLIFVGFIFTLNAALSIVFSLFAGYLSDVIGRKWTLISGSVAGFILyALLALLV 101
                                   578889999****************************************************66666665555536666655 PP

                         MFS_1  83 .sslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsl 162
                                      + +  +l v++++ +++++p+++a+++d++++++r +++ ++ ++++lG ++gpl+++++   +g++ +f+++a++ l
  gi|13541087|ref|NP_110775.1| 102 yRAVLIASALFVMTAFSGSLVYPSANAIVSDVTTEKNREMGYTVYRIMANLGWAVGPLISSFIF-RYGFEFIFLFVAVANL 181
                                   344558889999999999**********************************************.**************** PP

                         MFS_1 163 lafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsglltllplylqevlglsgl 243
                                   l+ ++ ll++ ++ + r+ k+             v+       + +  ++ i ++l  ++ s+++++lp++++e+l++  +
  gi|13541087|ref|NP_110775.1| 182 LSTIVSLLYVKRNVRYREAKRNFFV---------VD------YRLY--LFSIPVFLLIMVSSQFSVTLPIFVVEDLHIV-V 244
                                   ****877888777777777755444.........33......2222..277778888889*******************.* PP

                         MFS_1 244 llaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavtssavllllvlvliGfglgfvfpsllal 324
                                     +g+++a+ + v++i++  +++l+ r++    ++  ++++++ ++g+++++++ + + l++ +++i++g  +++p ++++
  gi|13541087|ref|NP_110775.1| 245 SNLGYFYAVNGTVVVIGQYPISKLMSRYP---DIYALVFGAIFYSIGYLMVSFSRNLPSLIIDMIIITIGENLTSPNINTV 322
                                   ***************************55...5999999999999999999999999************************ PP

                         MFS_1 325 asdlappeeagtasglfntagslggalgp 353
                                   +s+ ap+e  g+ +g+++++++l++a +p
  gi|13541087|ref|NP_110775.1| 323 VSKIAPKESVGQFMGFIGMVNQLARAAAP 351
                                   *************************9998 PP

  == domain 2  score: 65.1 bits;  conditional E-value: 9e-22
                         MFS_1   5 aflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll.fass 84 
                                   +fl ++ +s ++++lp+++ edl+i +s +g  +++ + + +++++p++ l+ r+     l++g++++++g +l++ f+ +
  gi|13541087|ref|NP_110775.1| 218 VFLLIMVSSQFSVTLPIFVVEDLHIVVSNLGYFYAVNGTVVVIGQYPISKLMSRYPDIYALVFGAIFYSIG-YLMVsFSRN 297
                                   6899999999*********************************************5555************.666659777 PP

                         MFS_1  85 lwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslg......Wrav..fyil 157
                                   l+ l++  ++  +g+ +  p++++++++++pke  g+ +g++++ ++l+ + +p +g l++ slg      W+++  f i 
  gi|13541087|ref|NP_110775.1| 298 LPSLIIDMIIITIGENLTSPNINTVVSKIAPKESVGQFMGFIGMVNQLARAAAPSVGTLILYSLGqrpglvWPVIdiFGIS 378
                                   779**********************************************************99999********9999999 PP

                         MFS_1 158 aivsllafvlfllllpeep 176
                                   a++++++  + +l++p+++
  gi|13541087|ref|NP_110775.1| 379 AAILFFS--FRGLFVPRKR 395
                                   9999999..5556766655 PP

>> MFS_3  Transmembrane secretion effector
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   8.8   5.7e-10   3.4e-06      54     201 ..      60     203 ..      14     298 .. 0.84
   2 !   15.4   0.9   7.7e-07    0.0046     105     169 ..     300     364 ..     275     387 .. 0.85

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 5.7e-10
                         MFS_3  54 atLPifllsilaGalaDnfdrRkvllavqlllalvsvlltvlaalgllspwlllaltlligiGaalndPaWqAsvgelvkr 134
                                   a+L  +++s++aG l+D + r++ l+ + +   +  +ll++l++  +l  ++l ++t   +   +l  P+ +A+v+++ + 
  gi|13541087|ref|NP_110775.1|  60 AALS-IVFSLFAGYLSDVIGRKWTLISGSVAGFILYALLALLVYRAVLIASALFVMT---AFSGSLVYPSANAIVSDVTTE 136
                                   4444.568********************99888888888888888877777776665...55669**************** PP

                         MFS_3 135 rdvpaAvaLnsvginiaRsvGPAlgGvlvaavGaalafavnals.ylalivallrwkrevrksslprE 201
                                   ++ +   ++  +  n+  +vGP ++  +    G  + f + a++  l  iv ll +kr+vr ++  r+
  gi|13541087|ref|NP_110775.1| 137 KNREMGYTVYRIMANLGWAVGPLISSFIF-RYGFEFIFLFVAVAnLLSTIVSLLYVKRNVRYREAKRN 203
                                   *************************9987.57999999877666156799**********99887765 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 7.7e-07
                         MFS_3 105 lllaltlligiGaalndPaWqAsvgelvkrrdvpaAvaLnsvginiaRsvGPAlgGvlvaavGaa 169
                                   +l++  ++i iG  l++P  + +v+ + +++ v + +    +   +aR++ P +g +++ ++G  
  gi|13541087|ref|NP_110775.1| 300 SLIIDMIIITIGENLTSPNINTVVSKIAPKESVGQFMGFIGMVNQLARAAAPSVGTLILYSLGQR 364
                                   577778899**************************************************999975 PP

>> LacY_symp  LacY proton/sugar symporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.4  17.6   3.5e-12   2.1e-08      23     186 ..      30     189 ..       9     208 .. 0.82
   2 !    3.1   4.0    0.0056        34       9      58 ..     211     260 ..     199     298 .. 0.82
   3 ?   -2.9   0.2      0.36   2.1e+03      64      97 ..     355     388 ..     333     391 .. 0.66

  Alignments for each domain:
  == domain 1  score: 33.4 bits;  conditional E-value: 3.5e-12
                     LacY_symp  23 msayfplfpvwlkevlglsktetGivfsvislfsilfqplfGlisdklGlkkellwvislllvlfapfliyvfepllqlni 103
                                   ++a +p+++v+++e+l+ls   +G +f+ +  +si+f  + G +sd +G k  l+      ++l+a + + v+  +l    
  gi|13541087|ref|NP_110775.1|  30 YGATWPFMAVYFNEYLHLSLIFVGFIFTLNAALSIVFSLFAGYLSDVIGRKWTLISGSVAGFILYALLALLVYRAVLIA-- 108
                                   7899***************************************************99999999**********998744.. PP

                     LacY_symp 104 lvGalvGgvflG.lvysagagaieayiekvsraskfeyGkarvfGclGyalcaslaGilfsidpslvfwlasgfalillll 183
                                      ++v + f G lvy +  +++   +     + ++ y   r++  lG+a++  ++  +f    ++ f +++ + l+ +++
  gi|13541087|ref|NP_110775.1| 109 -SALFVMTAFSGsLVYPSANAIVSDVTTEK--NREMGYTVYRIMANLGWAVGPLISSFIFRYGFEFIFLFVAVANLLSTIV 186
                                   .44455555555378887777776666554..456678999***************************9999888776655 PP

                     LacY_symp 184 lll 186
                                    ll
  gi|13541087|ref|NP_110775.1| 187 SLL 189
                                   433 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.0056
                     LacY_symp   9 fylfalffffyffimsayfplfpvwlkevlglsktetGivfsvislfsil 58 
                                    ylf++  f++ ++ s +   +p+++ e l++  +++G  ++v+  + ++
  gi|13541087|ref|NP_110775.1| 211 LYLFSIPVFLLIMVSSQFSVTLPIFVVEDLHIVVSNLGYFYAVNGTVVVI 260
                                   4677777777777777777789*********************9877665 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 0.36
                     LacY_symp  64 GlisdklGlkkellwvislllvlfapfliyvfep 97 
                                    li   lG +  l+w +  ++ + a  l + f  
  gi|13541087|ref|NP_110775.1| 355 TLILYSLGQRPGLVWPVIDIFGISAAILFFSFRG 388
                                   4566677777777887777777777777776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (403 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       910  (0.0507558); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.64u 0.28s 00:00:00.92 Elapsed: 00:00:00.47
# Mc/sec: 2569.81
//
Query:       gi|13541088|ref|NP_110776.1|  [L=201]
Description: phosphoglycerate mutase [Thermoplasma volcanium GSS1]
Scores for complete 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  114.1   0.0    8.2e-33  113.7   0.0    1.1  1  His_Phos_1       Histidine phosphatase superfamily (branch 1)
  ------ inclusion threshold ------
      0.048   13.6   0.0       0.78    9.7   0.0    2.7  3  DEK_C            DEK C terminal domain
      0.068   13.5   0.0       0.12   12.7   0.0    1.4  1  Gal_mutarotas_2  Galactose mutarotase-like


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 !  113.7   0.0   1.4e-36   8.2e-33       2     183 ..       5     178 ..       4     184 .. 0.88

  Alignments for each domain:
  == domain 1  score: 113.7 bits;  conditional E-value: 1.4e-36
                                   EEEE---BTTB--....TT----.B-HHHHHHHHHHHHHHTTS---EEEE-SSHHHHHHHHHHHHCTT--EEE-GGGS--- CS
                    His_Phos_1   2 yLvRHGetewnaegrlqgrtdvp.LteeGreqAealaerlagepidaiysSplkRarqTaeliaealglpveldegLrEid 81 
                                   +L+RHGe++ n++g+l+   d   Lte+G++qAe + + l g +i+ +ysSp+ Rar+Tae+ia   g +v +d++LrEi 
  gi|13541088|ref|NP_110776.1|   5 ILIRHGESDINVKGILSDSIDGNsLTERGIRQAEHARDQLTGLEIKNVYSSPINRARETAEIIASSFGKEVVIDDRLREIG 85 
                                   79*************999988766********************************************************* PP

                                   -GGGTT-B.HHHHHH..HSHHHHHHHHH-GGG-BS-BHHHHHHHHHHHHHHHHHHTTTSEEEEEE-HHHHHHHHHHHHT-- CS
                    His_Phos_1  82 fGdweglttaeiaeeypeeleawlrdpadvrppggEsledvaaRvaaaleelaarhegetvlvVsHggvirallarllglp 162
                                   +G+  g+  ++ ++e    +  + +++   +  + E +  ++ Rv++al   aar++    +  +H  +ira+++++l+l 
  gi|13541088|ref|NP_110776.1|  86 LGKASGRRASDFRDE---LYTGHISGSI-RKELEMEEWTSLQTRVVEAL---AAREGI--NVYTTHSDPIRAAISYFLELG 157
                                   *******87777777...4444444443.345679********998776...455554..4899***************** PP

                                   GGGGGGB---TT-EEEEEE-S CS
                    His_Phos_1 163 leelrrleldnaslsvlefde 183
                                     e   + ++nas++ ++++ 
  gi|13541088|ref|NP_110776.1| 158 EPESYGISIKNASMTFIDVEI 178
                                   ***************999875 PP

>> DEK_C  DEK C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   0.00013      0.78      10      30 ..      16      37 ..      15      41 .. 0.94
   2 ?   -1.6   0.0      0.45   2.7e+03      26      32 ..     109     115 ..     107     117 .. 0.82
   3 ?   -0.2   0.0      0.16   9.5e+02      26      53 ..     125     153 ..     123     154 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00013
                         DEK_C 10 ireiLrea.DLdtvTkkkvReq 30
                                  ++ iL+++ D +++T++ +R++
  gi|13541088|ref|NP_110776.1| 16 VKGILSDSiDGNSLTERGIRQA 37
                                  899*****************96 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.45
                         DEK_C  26 kvReqLe 32 
                                   ++R++Le
  gi|13541088|ref|NP_110776.1| 109 SIRKELE 115
                                   79***99 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.16
                         DEK_C  26 kvReqLeeklgvd.LsekKafIkalIdei 53 
                                    v+e+L ++ g++  + + + I+a+I  +
  gi|13541088|ref|NP_110776.1| 125 RVVEALAAREGINvYTTHSDPIRAAISYF 153
                                   58999999999997799999999999766 PP

>> Gal_mutarotas_2  Galactose mutarotase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0     2e-05      0.12      31      66 .]     139     175 ..     127     175 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2e-05
                                   -HCC.CTS-SCEEEEEEEE..TCEEEEEE--SSSEEEE CS
               Gal_mutarotas_2  31 yeaessdplYgsiPfmisl..segyGvfvdnpaetwfD 66 
                                   y+++ sdp + +i ++++l   e+yG+ + n++ t++D
  gi|13541088|ref|NP_110776.1| 139 YTTH-SDPIRAAISYFLELgePESYGISIKNASMTFID 175
                                   5555.9***************777************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       391  (0.0218082); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.47
# Mc/sec: 1288.59
//
Query:       gi|13541089|ref|NP_110777.1|  [L=423]
Description: hypothetical protein TVN0258 [Thermoplasma volcanium GSS1]
Scores for complete sequence (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   90.5   0.1      7e-25   88.4   0.1    1.8  1  Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosp
    2.3e-05   24.6   0.0    0.00099   19.2   0.1    2.2  2  PglZ          PglZ domain
  ------ inclusion threshold ------
      0.022   14.2   0.0      0.045   13.1   0.0    1.7  1  Sulfatase     Sulfatase


Domain annotation for each model (and alignments):
>> Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.4   0.1   1.2e-28     7e-25       2     355 ..      63     401 ..      62     403 .. 0.73

  Alignments for each domain:
  == domain 1  score: 88.4 bits;  conditional E-value: 1.2e-28
                                   EEEEETT-BTTHHHHHGS..TSHHHHHHHHHSEEESEEE-SSS-SHHHHHHHHHHSS-HHHHS--SSSEE...ETTTTEEE CS
                  Phosphodiest   2 lvislDGlradlldrlae..llpnlaaLakegvsapnlrpvfPtlTfpnhaslvTGlyPgeHGivgNtfy...drktgeyv 77 
                                   +++ lDGl  d++    +  +   +++++++g++a+ +++vfP++T+++ +++ TGl P eHG      y       + ++
  gi|13541089|ref|NP_110777.1|  63 VFFYLDGLGYDTFAS--DkfKNGIFKQIINNGYYAA-ITTVFPSTTAAANTTINTGLAPLEHGLLEWILYfdeA---RTVA 137
                                   67889********99..4369999************.*****************************77775552...4443 PP

                                   ...EEETTTTGG.........GGGCTTS-HHHHHHHTHTTCEEEESETTTTSEBTTCT.SC.TBHHSBTCT.CSTTSCHHH CS
                  Phosphodiest  78 ...vfvtededa.........prwwqgepiwdtaakarglkaaalfwpgsevdystyyylvsetppryleddfnakvpled 146
                                      ++++ ++++         + + +g  i+ +++ + g+++ ++  +  ++              + + +d ++ v++  
  gi|13541089|ref|NP_110777.1| 138 ltlPYRPITQRYrrrfnsmnpSYLFKGKTIFRKMKED-GVRSVSFLKA--NIVNGE--------YTKLI-QDGSDVVGYSY 206
                                   0004444444436666666645566667777777777.****999774..233221........11223.56778999999 PP

                                   HHHHHHHHHHHHCHTHSHHHHHCTSSESEEEEEECCCHHHHHHH-TTSHHHHHHHHHHHHHHHHHHHHHHHTTGTTTEEEE CS
                  Phosphodiest 147 kvdkavlqtwldaafakvvlekelekpdlllvyleetDtvgHkfGpdspevedalrrvDkaigdLlealderglsaetnii 227
                                   + d  +l   l++   +       + +d++++yl+++D++gH +Gp s+  + ++++  k+i++++e+l+ + ++  t +i
  gi|13541089|ref|NP_110777.1| 207 TTDGLLL---LKNYLLN-------GAYDYYYFYLDNIDHIGHVYGPSSEMYALEVQTTSKMIEETFEQLPME-VRRRTLVI 276
                                   9998444...7777777.......999*******************************************98.999999** PP

                                   EEES---EEEHTTSEEEGGGTSTGGHGEEEEECBHHS.SSE.....EEEEESTEEE.CCCTTHHHHHHHHHHTCHHCCHST CS
                  Phosphodiest 228 lvSDHGmadvsddkvielndlleekgllhlkdegkggakal.....iainpkarelnrvaeaeaeevyaelkakleelrkk 303
                                   ++SDHG  dv+  + i+ln++ +   +++lk++g ++ +++     +        +  v++ + e+  +  k+kl++ +  
  gi|13541089|ref|NP_110777.1| 277 ITSDHGHIDVDPLRTIYLNSFRKL--YDSLKSDGRYKIPPVgsprdV--------FLFVKNDALESTIDYTKRKLASSLVM 347
                                   **********88********9776..899999995555555333332........44455666677777777776676644 PP

                                   .HTT..TEEEEEGGGS-GGGCHSTTS-SEEEEE-TT...EEEESSTTCSSBS-SEE-- CS
                  Phosphodiest 304 .ege..alavylkeaipkrlhykkrapdlvlvadpg...wsitskdkpdeyeikgthG 355
                                    + e   + ++  +a+p  +   +ra+  ++++  +   w+ +++    + ++kg+hG
  gi|13541089|ref|NP_110777.1| 348 sTQEsfDYGLFGGGAVPDSFY--RRAGNMLILPSGNdliWYRMTGLR--DSRMKGMHG 401
                                   455555777777778888876..788888885544311133333333..447777777 PP

>> PglZ  PglZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0     0.012        71       2      79 ..      61     140 ..      60     210 .. 0.72
   2 !   19.2   0.1   1.7e-07   0.00099     109     170 ..     220     284 ..     186     287 .. 0.71

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.012
                          PglZ   2 kvfvIisDalryea..weelkqlLnkedrfeaelsavlgvlPslTklgraallpgkkllykeksaldvlvdeesseglen 79 
                                   k+++   D+l+y+    ++ k+ + k+ + +    a+ +v Ps T  +   +  g ++l +   +  ++ de ++ +l  
  gi|13541089|ref|NP_110777.1|  61 KIVFFYLDGLGYDTfaSDKFKNGIFKQIINNGYYAAITTVFPSTTAAANTTINTGLAPLEHGLLEWILYFDEARTVALTL 140
                                   6778889999999622567999999999999999999*********9999998888887766666666666666555555 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 1.7e-07
                          PglZ 109 lkdkevvyivhnkvDalgd....kasteqksfeaveeslkelkelvksllee..ngykvlltaDHGfi 170
                                    + +++ y +++++D++g+    +    ++    v+++ k ++e++++l  e    + v++t+DHG i
  gi|13541089|ref|NP_110777.1| 220 NGAYDYYYFYLDNIDHIGHvygpS---SEMYALEVQTTSKMIEETFEQLPMEvrRRTLVIITSDHGHI 284
                                   467899*************64331...2222333444445555555555333245699********98 PP

>> Sulfatase  Sulfatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   7.6e-06     0.045     212     251 ..     245     283 ..     141     318 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7.6e-06
                                   HHHHHHHHHHHHHHHHHHHHHHHTTTGGGEEEEEEESSSS CS
                     Sulfatase 212 eaylnsveyvDdligrvlaaLeenglldntlvvftSDhga 251
                                   e y+  v  + ++i++ +++L   ++++ tlv++tSDhg+
  gi|13541089|ref|NP_110777.1| 245 EMYALEVQTTSKMIEETFEQL-PMEVRRRTLVIITSDHGH 283
                                   557777888999*********.99***************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (423 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       559  (0.0311785); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 2727.43
//
Query:       gi|13541090|ref|NP_110778.1|  [L=305]
Description: carbamate kinase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.6e-31  109.7   0.0    2.5e-31  109.1   0.0    1.3  1  AA_kinase  Amino acid kinase family
  ------ inclusion threshold ------
      0.052   14.0   0.2       0.17   12.4   0.2    1.9  1  CBS        CBS domain


Domain annotation for each model (and alignments):
>> AA_kinase  Amino acid kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.1   0.0   2.8e-35   2.5e-31       2     241 .]       3     287 ..       2     287 .. 0.85

  Alignments for each domain:
  == domain 1  score: 109.1 bits;  conditional E-value: 2.8e-35
                                   EEEEEE-TTCCC.CTCC.......HHHHHHHHHHHHHHHHTTEEEEEE--HHHHHHHHHHTCCCCCHHHC........... CS
                     AA_kinase   2 rvVvKlGGsslt.dkee.......aslrrlaeqiaalkesgnklvvVhGggsftdgllalksglssgelaa.......... 64 
                                   r+V++lGG++l  ++e        +   + +++i+++ +++n+ v+ hG+g+++  + +  +++s  ++++          
  gi|13541090|ref|NP_110778.1|   3 RIVIALGGNALLrNGEPrnyevqySHAIETFKIIRDI-TEKNETVITHGNGPQVGDIQQS-HEISGIMANLhqsvamsqgy 81 
                                   8********77758888*****998888999******.9999***************999.78887777755445555444 PP

                                   ....E..HHHHHHHHH............HHHHHHHHHHHHHHHHTTHGEEEE-GGGTCEECCCE................. CS
                     AA_kinase  65 .glrstleeagevatr............dalaslgerlvaallaaglpavglsaaaldateagr................. 115
                                    g+                          +  s+ +++++++++   pa+  + ++++    ++                 
  gi|13541090|ref|NP_110778.1|  82 iGE------------IlanaydevrskySLSKSIFTIITRSVVNRNDPAFASPEKPIGRYYSDQevdeakrngwvmkkfkd 150
                                   322............12223333444445555666666666666666777777777777766668889999********** PP

                                   ......HHHTTTCEEECCHHHHHHHTT-EEEEESEEEEETTTE.......EEEE-HHHHHHHHHHHCTSSEEEEEESSSSC CS
                     AA_kinase 116 ....degsdgnvesvdaeaieelleagvvpvltgfigldeege.......lgrgssDtiaallAealgAdkliiltdVdGV 185
                                        ++s++++e ++++aieel+ +g++p   g++g+++ +e        +++++D +++llA+ l+Ad+ +iltdV+ V
  gi|13541090|ref|NP_110778.1| 151 gwrrVVPSPEPIEILEEKAIEELVREGHIPLAVGGGGIPVVKEngrivgiDAVIDKDIASSLLAAQLKADYFMILTDVESV 231
                                   **********************************998888888888999978***************************** PP

                                   ESSTTTTCCTTCECCEEEHHHCHH..CSSS.TTTHHHHCHHHHHHHHHCTT-EEEEEE CS
                     AA_kinase 186 ydadpkkvpdarllpeisvdeaee..saselatgGmkvkhpaalaaarrggipvvItn 241
                                   y + +k +   ++l +i  +e+e+   ++++a g+mk+k++aa++++++gg  ++Itn
  gi|13541090|ref|NP_110778.1| 232 YVNFGKPD--QKPLGRIHLNEIEKyyAEGQFADGSMKPKVRAAINFVKNGGKAAFITN 287
                                   ****9876..7*********************************************98 PP

>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.2   1.9e-05      0.17      19      45 ..     167     200 ..     156     200 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.9e-05
                                   HHHHHHHHHHT.S......SEEEEEETTTBEEEE CS
                           CBS  19 eealelmrekg.v......srlPVVdedgklvGi 45 
                                   e+a+e+++++g +      +++PVV e+g++vGi
  gi|13541090|ref|NP_110778.1| 167 EKAIEELVREGhIplavggGGIPVVKENGRIVGI 200
                                   57888887888437777778*************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       459  (0.025601); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        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: 00:00:00.39
# Mc/sec: 2339.99
//
Query:       gi|13541091|ref|NP_110779.1|  [L=217]
Description: phosphoribosyltransferase [Thermoplasma volcanium GSS1]
Scores for complete 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-21   73.9   0.0    1.5e-20   73.4   0.0    1.2  1  Pribosyltran  Phosphoribosyl transferase domain
  ------ inclusion threshold ------
       0.14   11.6   0.0       0.18   11.2   0.0    1.2  1  UPRTase       Uracil phosphoribosyltransferase
       0.15   12.3   0.0       0.29   11.4   0.0    1.5  1  DUF4777       Domain of unknown function (DUF4777)


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 !   73.4   0.0   2.4e-24   1.5e-20      14     155 ..      14     156 ..       6     159 .. 0.82

  Alignments for each domain:
  == domain 1  score: 73.4 bits;  conditional E-value: 2.4e-24
                                   EEEETTEEEEEE..--GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE.........EE----TTSEEE CS
                  Pribosyltran  14 avarlaaeilee..yngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdes.rlledpagkkVl 91 
                                   +++r+  +i+++  + +k d+++giargGv++a il+d+L v   ++++vk +++g + ++ g  +   +  +d++g+kVl
  gi|13541091|ref|NP_110779.1|  14 DIDRWCGKISRDvaDTFKVDTIIGIARGGVVPARILSDRLWV--KDMLSVKTEHWGLTATKDGEAVLKtKIDTDLRGRKVL 92 
                                   6778888888888888************************73..4555555566555555554433334799********* PP

                                   EE-SEESSSHHHHHHHHHHHCC-BSEEEEEEEEE-HHHHHHHHHH-TTS.....EEEEEEE-SE CS
                  Pribosyltran  92 iVDDildtGgTllaalelLkekgpeevriavlvdkpateeevdknakrvfslspdnfvavvgfe 155
                                   +VDDi dtG ++  a + +k+  p e+++a+ +  + ++  +d++a  + + +  +f ++++++
  gi|13541091|ref|NP_110779.1|  93 VVDDITDTGESMSVAYNYIKSLHPDELKSATMLHINRSKYVPDYYAELITEKNWAWFIFPWNVY 156
                                   *********************************8888888888888866655588999998887 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   3.1e-05      0.18     109     148 ..      76     115 ..      33     129 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3.1e-05
                       UPRTase 109 veyynkLPkkiaertvlllDpviaTGgsaaaaiqlLkerg 148
                                       +k+ ++++ r+vl++D +  TG+s+  a + +k+ +
  gi|13541091|ref|NP_110779.1|  76 AVLKTKIDTDLRGRKVLVVDDITDTGESMSVAYNYIKSLH 115
                                   35567999************************99999865 PP

>> DUF4777  Domain of unknown function (DUF4777)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   4.9e-05      0.29      36      65 ..     185     214 ..     163     215 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 4.9e-05
                       DUF4777  36 seeelkkvVkntLeaAvrhGFlkkengrYs 65 
                                    ++  + +++ +Le+ v++G +k++n+rY 
  gi|13541091|ref|NP_110779.1| 185 DLDTSNLDIETILEDLVHFGKMKRQNNRYV 214
                                   34566789*********************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       505  (0.0281667); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1476.17
//
Query:       gi|13541092|ref|NP_110780.1|  [L=109]
Description: NTP pyrophosphohydrolase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-09   37.2   0.0      3e-09   37.0   0.0    1.0  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 !   37.0   0.0   1.7e-13     3e-09       7      86 ..      13      92 ..       8     107 .. 0.65

  Alignments for each domain:
  == domain 1  score: 37.0 bits;  conditional E-value: 1.7e-13
                                  EEEEEETTSEEEEEEESSSSTTT..EESSEEECBTTSHHHHHHHHHHHHHHSEEE.EEEEEEEEEEEEEEEEEEEEE..EEEE CS
                         NUDIX  7 gvvllnekgevLlvrrskkpfpg..WelPgGkvepgEtpeeAArREleEEtGlea.ellellgrlhylapydgpygd..ehei 84
                                   ++ + ek evL+++   +p +g  W+++ G ve +E++ + ++RE++EEtGl +   + ++    + +++d+   d   he 
  gi|13541092|ref|NP_110780.1| 13 VIFRCKEKPEVLILHY--RPEHGsfWQTVSGNVELNEDLLDSLIREVKEETGLGKeCIINVYP---DIYSFDFHAHDmdFHET 90
                                  4445555555999983..3666677***************************95523334444...44444444444223333 PP

                                  EE CS
                         NUDIX 85 ly 86
                                  ++
  gi|13541092|ref|NP_110780.1| 91 VF 92
                                  33 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       312  (0.017402); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 692.11
//
Query:       gi|13541093|ref|NP_110781.1|  [L=354]
Description: geranylgeranyl pyrophosphate synthase [Thermoplasma volcanium GSS1]
Scores for complete 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  180.3   0.0    4.4e-53  179.9   0.0    1.1  1  polyprenyl_synt  Polyprenyl synthetase


Domain annotation for each model (and alignments):
>> polyprenyl_synt  Polyprenyl synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  179.9   0.0   2.5e-57   4.4e-53       4     255 ..      42     304 ..      39     305 .. 0.91

  Alignments for each domain:
  == domain 1  score: 179.9 bits;  conditional E-value: 2.5e-57
                                   HHHHHHHHHHSSS--HHHHHHHHHHHHHSCGHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEETTEE-HH......... CS
               polyprenyl_synt   4 leealeylveagGKrlRpllvllaaealkeeeeelekaavlawivellhaasLvhDDimDdsetRRGqpcah......... 75 
                                   + ++++ ++e gGKrlRp++++l +++++ +ee  +   ++   +el +++ L+hDD++D+s++RRG+p++h         
  gi|13541093|ref|NP_110781.1|  42 VIKIIRDYTEGGGKRLRPIFMILGYRLFS-PEE--KGIFDASISIELAQSYLLIHDDVIDKSDVRRGKPSMHirledafva 119
                                   5578888999*******************.443..788999*******************************888888887 PP

                                   .....HCTCHHHHHHHHHHHHHHHHHHHHHHH..STT.HHHHHHHHHHHHHHHHHHHHHHHHTTTTTCCC.SHHHHHHHHH CS
               polyprenyl_synt  76 .....rlvGnklAindgdfllarafellaklf..eks.lellelfsevllqtveGqlldleeekdddlskfsleeyleivk 148
                                        r   + lAi++gd+ ++ a e l +    +++ +++   +s+++  t  Gq+ld+ ++  dd++   + +  + + 
  gi|13541093|ref|NP_110781.1| 120 gcpqsRSTAEGLAIVAGDLAESYAHEALLRSGfySENlVKADLELSKTIEMTGYGQFLDILSTTMDDFN---EGDLIRLHL 197
                                   777765588889**************999876686677899899****************766556666...********* PP

                                   HHTH.HHCHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-HHHHSS-TSHHHHTT---HHHHHHHHCT- CS
               polyprenyl_synt 149 yKTa.ylfalpvalaallagasdeelealkdiglelGlaFQiqDDylDlfgdpevlgKpagtDiqegkctlpilkalelas 228
                                   +KTa y+++ p+a++a+l+g+ + +++al+++g+ lG+aFQ+ DD+l lfgd++++gK + +D++egk tl+++ka+e  +
  gi|13541093|ref|NP_110781.1| 198 WKTAkYTLEGPLAMGAILSGT-EYDITALREYGRVLGIAFQLKDDILGLFGDEKTIGKSVYSDVNEGKKTLLMIKAMEWGD 277
                                   ********************7.5569******************************************************* PP

                                   HHHHHHHHHHTTSSHHHHHHHHHHHHH CS
               polyprenyl_synt 229 peqrkvlkeilgkkaekeedvkealel 255
                                   +++++ ++++l+k + ++e+ +++ +l
  gi|13541093|ref|NP_110781.1| 278 RDDANFIRKMLRKGNVTNEEFERIKKL 304
                                   ************999898888887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (354 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       486  (0.0271069); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 2325.05
//
Query:       gi|13541094|ref|NP_110782.1|  [L=283]
Description: integrase/recombinase [Thermoplasma volcanium GSS1]
Scores for complete 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-50  170.5   0.0    3.5e-50  170.1   0.0    1.1  1  Phage_integrase  Phage integrase family
    1.2e-13   51.3   0.8    3.1e-13   50.0   0.4    1.9  2  Phage_int_SAM_4  Phage integrase, N-terminal SAM-like domain
     0.0052   17.1   1.5      0.026   14.9   1.1    2.1  2  Phage_int_SAM_5  Phage integrase SAM-like domain
  ------ inclusion threshold ------
      0.027   13.4   0.1      0.083   11.8   0.0    1.8  2  DUF3435          Protein of unknown function (DUF3435)


Domain annotation for each model (and alignments):
>> Phage_integrase  Phage integrase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  170.1   0.0   7.9e-54   3.5e-50       2     171 ..     104     269 ..     103     270 .. 0.99

  Alignments for each domain:
  == domain 1  score: 170.1 bits;  conditional E-value: 7.9e-54
                                   HHHHHHHHHHHHCCGCHHHHHHHHHHHHHHHHT--HHHHTT-BGGGEECTTTEEEEEEEECSSSSEEEEECTHHHHHHHHH CS
               Phage_integrase   2 vltedeverllaaleeslkirdklllellyetGlRisEllsLrvkdldlengvilvheregKgskeravplseealellke 82 
                                   +l e+e++rll+a+++  +++  +++ +l  tG+R++El++Lr++d+d+++g+i+v  + gKg k+r+v +++e +++lke
  gi|13541094|ref|NP_110782.1| 104 YLNEEEASRLLSASKK--SVKYSAVISVLAYTGIRVGELCNLRIGDVDMQEGIIYV--KSGKGDKDRIVVMPNECVSALKE 180
                                   699*************..**************************************..*********************** PP

                                   HHHHHCHCCTTTSBSSBETTSSB--HHHHHHHHHHHHHHCT-SSC--TTHHHHHHHHHHHHHCTSHHHHHHHHT-SSCCHH CS
               Phage_integrase  83 llskaleeaeksellfaskrgkplsrqtvrkafkraveeagiekpltpHtlRhsfataLleagvdlrvvqkllGHssistt 163
                                   +l+ + + + ++++lf+s ++++   +tv++++kr+ +eagi+k++tpH lRh+fat  l++g d+r++q++lGHss++tt
  gi|13541094|ref|NP_110782.1| 181 YLNWRISVETPHDFLFISNKKSRYDPSTVERMVKRLSQEAGINKRVTPHVLRHTFATSVLRNGGDIRFIQQILGHSSVATT 261
                                   ********************************************************************************* PP

                                   HHHHCCCH CS
               Phage_integrase 164 qiYthvak 171
                                   qiYth+++
  gi|13541094|ref|NP_110782.1| 262 QIYTHLDD 269
                                   *****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 !   50.0   0.4     7e-17   3.1e-13       3      78 ..      10      84 ..       9      89 .. 0.95
   2 ?   -3.1   0.0       2.5   1.1e+04      46      54 ..     178     186 ..     176     190 .. 0.76

  Alignments for each domain:
  == domain 1  score: 50.0 bits;  conditional E-value: 7e-17
               Phage_int_SAM_4  3 erfrealrlaglserTiksYlsaikrflrflkkkapeeltkedieaYlnyLanerklsastqknalnalsffykkv 78
                                  e+f  ++  +++s+ Tik Y++ +  fl+f+  k+p+e+t+ die+Y + La + ++s+++q  a++a++ fyk +
  gi|13541094|ref|NP_110782.1| 10 ENFVSYMVGERKSKYTIKEYKFLVSKFLAFVG-KTPAEVTPMDIERYKTFLASKAHYSKASQYLAIKAIKLFYKSL 84
                                  678999999***********************.****************************************984 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2.5
               Phage_int_SAM_4  46 ieaYlnyLa 54 
                                   +++Yln+ +
  gi|13541094|ref|NP_110782.1| 178 LKEYLNWRI 186
                                   678999876 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 !   14.9   1.1   5.7e-06     0.026       5      81 ..       8      82 ..       6      83 .. 0.86
   2 ?   -0.5   0.0      0.35   1.6e+03      55      77 ..     179     217 ..     163     229 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 5.7e-06
                                  HHHHHTHHHHTTS.-HHHHHHHHHHHHHTTTS-..S---TTT--HHHHHHHHHHHHHTS---HHHHHHHHHHHHHHHH CS
               Phage_int_SAM_5  5 yfkeyiekkkkkg.skgtlrnykstlkhlkkFlkkkditfeeidkefleeFedYLkkkkglsentiskyfkklkavln 81
                                  y++++++ +  ++ sk t++ yk ++ ++  F      t  e+++  +e+++++L +k ++s+++++  +k +k +++
  gi|13541094|ref|NP_110782.1|  8 YVENFVSYMVGERkSKYTIKEYKFLVSKFLAFV---GKTPAEVTPMDIERYKTFLASKAHYSKASQYLAIKAIKLFYK 82
                                  55666666655544889****************...999****************9999******9999999998775 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.35
                                   HHHH................HHTS---HHHHHHHHHHHH CS
               Phage_int_SAM_5  55 edYL................kkkkglsentiskyfkklk 77 
                                   ++YL                +kk+++ ++t+ +++k+l 
  gi|13541094|ref|NP_110782.1| 179 KEYLnwrisvetphdflfisNKKSRYDPSTVERMVKRLS 217
                                   444444455555555557777777888888888777775 PP

>> DUF3435  Protein of unknown function (DUF3435)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.26   1.2e+03      25      54 ..     120     149 ..     112     151 .. 0.84
   2 ?   11.8   0.0   1.9e-05     0.083     167     230 ..     197     260 ..     179     280 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.26
                       DUF3435  25 rvqlllllllaaftsnRpgalleLryrDle 54 
                                    v+ + ++ + a+t+ R g l +Lr  D+ 
  gi|13541094|ref|NP_110782.1| 120 SVKYSAVISVLAYTGIRVGELCNLRIGDVD 149
                                   566777888999*************99986 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 1.9e-05
                       DUF3435 167 il.kdealtastlnsrlkrlgeiagfeepitpYklRrgaakalne.SgevseaqrnlilqHassrt 230
                                   i+ k+ + ++st++  +krl++ ag+++ +tp+ lR   a  + +  g++     ++il+H+s +t
  gi|13541094|ref|NP_110782.1| 197 ISnKKSRYDPSTVERMVKRLSQEAGINKRVTPHVLRHTFATSVLRnGGDI--RFIQQILGHSSVAT 260
                                   4556778899**************************99887664402333..33456777777655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       470  (0.0262145); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1932.06
//
Query:       gi|13541095|ref|NP_110783.1|  [L=211]
Description: ribulose-phosphate 3-epimerase [Thermoplasma volcanium GSS1]
Scores for complete sequence (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  201.2   0.0    1.2e-59  201.0   0.0    1.0  1  Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family
  ------ inclusion threshold ------
      0.056   13.2   0.1      0.092   12.5   0.1    1.3  1  QRPTase_C       Quinolinate phosphoribosyl transferase, C-ter
       0.15   12.3   0.1        2.1    8.6   0.0    2.2  2  HGTP_anticodon  Anticodon binding domain


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 !  201.0   0.0     2e-63   1.2e-59       2     198 .]       3     197 ..       2     197 .. 0.98

  Alignments for each domain:
  == domain 1  score: 201.0 bits;  conditional E-value: 2e-63
                                   EEEBGGGS-GGGHHHHHHHHHHTT-SEEEEEEEBSSSSS-B-B-HHHHHHHGGGE-S-EEEEEESSSHHHCHHHHHHCT-S CS
                Ribul_P_3_epim   2 iapSllsadfarlgeevkaveeagadllHvDvmDghfvpNltigplvvealrkltelpldvHLmveevdrivpefaeagas 82 
                                   ++pS+++a  ++ + +vk+ e+aga ++H+DvmDg+fvpN+t+gp    alr+++++p+d HLmv+++d + ++f++ + +
  gi|13541095|ref|NP_110783.1|   3 VSPSIVAASLTKFQAQVKECEDAGAYSFHLDVMDGNFVPNITVGPDFYFALRSISKIPIDTHLMVDRPDYYYEKFLSQN-D 82 
                                   79**************************************************************************987.9 PP

                                   EEEEE-ST-TTHHHHHHHHHHTTSEEEEEE-TT--GGGGTTTCCC-SEEEEESS-TT-SS----CCHHHHHHHHHHHHHHH CS
                Ribul_P_3_epim  83 iisvHaEalehlkrtiqeikeaGakaglvlnpatplealeyllekldlvllmsvePgfgGQkFipevlekikkvrklidek 163
                                   ++ +H+E+  ++k +i+++ + G+k glv+np+tp + +++lle+ +++l+msv Pgf+GQkFi+ v ekik++r++i+e 
  gi|13541095|ref|NP_110783.1|  83 RVLIHYESPINIKGLIKKMENEGVKYGLVINPNTPFSKVSDLLERAEILLIMSVYPGFSGQKFID-VSEKIKEARNYIKEM 162
                                   99**************************************************************7.78************* PP

                                   T---EEEEESS--TTTCHHHHHHT--EEEESHHHH CS
                Ribul_P_3_epim 164 eldlkievDGGvkldnieqiaeagadvlVagsavf 198
                                   +l + ievDGG+++++++ + +agad++V++s++f
  gi|13541095|ref|NP_110783.1| 163 GLRTMIEVDGGINENTAKIVKNAGADIVVSASYLF 197
                                   ********************************998 PP

>> QRPTase_C  Quinolinate phosphoribosyl transferase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   1.5e-05     0.092     111     155 ..     149     193 ..     133     205 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.5e-05
                                   HHHHHHHHHHHHHHSTTSEEEEESS--TTTHHHHHCTT-SEEEEC CS
                     QRPTase_C 111 veelkkaveelkeknkrvlievSGgvtlenveeyaksgvdvisvg 155
                                   +e++k+a +++ke+  r +iev Gg+++++ + +++ g d++ ++
  gi|13541095|ref|NP_110783.1| 149 SEKIKEARNYIKEMGLRTMIEVDGGINENTAKIVKNAGADIVVSA 193
                                   4899**************************999999998876554 PP

>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.0   0.00034       2.1      22      63 ..      74     116 ..      59     130 .. 0.85
   2 ?    1.5   0.0     0.055   3.3e+02      34      60 ..     145     171 ..     133     185 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00034
                                   HHHHHTTTSEEEEES.SSSTHHHHHHHHHHTT-SEEEEE-HHH CS
                HGTP_anticodon  22 aeeLraagirveldd.snesigkkireadllgipfavvvGeke 63 
                                   +e+++ ++ rv + + s  +i+  i+++++ g+ + +v+ +++
  gi|13541095|ref|NP_110783.1|  74 YEKFLSQNDRVLIHYeSPINIKGLIKKMENEGVKYGLVINPNT 116
                                   5666666669999999999********************9886 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.055
                                   EESSSSTHHHHHHHHHHTT-SEEEEE- CS
                HGTP_anticodon  34 lddsnesigkkireadllgipfavvvG 60 
                                   + d +e+i+++ ++ +++g + +++v+
  gi|13541095|ref|NP_110783.1| 145 FIDVSEKIKEARNYIKEMGLRTMIEVD 171
                                   5578999999999999***99999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       642  (0.0358079); expected 358.6 (0.02)
Passed bias filter:                      545  (0.0303977); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 1334.33
//
Query:       gi|13541096|ref|NP_110784.1|  [L=328]
Description: alcohol dehydrogenase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.3e-19   68.4   0.2    6.6e-19   67.8   0.2    1.3  1  ADH_N         Alcohol dehydrogenase GroES-like domain
    2.6e-13   50.1   0.0    5.7e-13   49.0   0.0    1.5  1  ADH_zinc_N    Zinc-binding dehydrogenase
    1.3e-05   26.2   0.0    2.5e-05   25.3   0.0    1.5  1  ADH_zinc_N_2  Zinc-binding dehydrogenase
  ------ inclusion threshold ------
      0.047   13.2   0.0      0.094   12.2   0.0    1.5  1  Glu_dehyd_C   Glucose dehydrogenase C-terminus


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 !   67.8   0.2   1.5e-22   6.6e-19       2     108 ..      28     132 ..      27     133 .. 0.93

  Alignments for each domain:
  == domain 1  score: 67.8 bits;  conditional E-value: 1.5e-22
                                   TEEEEEEEEEEE-HHHHHHHTTS.TTTTSSSSEE---EEEEEEEEESTT-CS--TT-EEEE-SEEE-SSSHHHHTT-GGG- CS
                         ADH_N   2 gevlikvkaagiCgsDlhilkgg.kelevklplilGHEivGeveevgpevkklkvGdrVvvepliscgeCaaCkegeenlC 81 
                                   g+v+i+vk ag++  D+ +++g+     ++lp i+G E+ G+v+e      ++k+G+rV+v+  i +g+C++C +g+e+lC
  gi|13541096|ref|NP_110784.1|  28 GKVIIEVKKAGLNPIDYNVINGKiVYRLNPLPHIPGSEVYGIVKEDS---GSFKKGERVIVYNRIFDGTCSQCISGNEHLC 105
                                   79********************865667899************9933...4699*************************** PP

                                   TTBEETTTSS-SSSBSEEEECGGGEEE CS
                         ADH_N  82 eeakllgvsldGgfaeyvvvpekklvk 108
                                   e+++++gv  +Gg+++ v ++ek++++
  gi|13541096|ref|NP_110784.1| 106 ENGGIWGVVSNGGYSQLVQIDEKNVFR 132
                                   ***********************9986 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.0   0.0   1.3e-16   5.7e-13       3     129 ..     177     289 ..     176     290 .. 0.90

  Alignments for each domain:
  == domain 1  score: 49.0 bits;  conditional E-value: 1.3e-16
                                   HHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTESEEEETTTCHHHHHHHHHTTTSSEEEEEESSCSHHHHHHHHHCEEEEE CS
                    ADH_zinc_N   3 GlaavqlAkalGaeviavdsseeklelakklGadevinykeadlverikeltggegvdvvfecvGsgatleaalkllkpgG 83 
                                   G++avqlA ++G+ v+av++++      +++Ga ev+ +++         +  + ++d++++ +G    + +alk l+ +G
  gi|13541096|ref|NP_110784.1| 177 GMFAVQLASMMGCDVYAVSRKDW----IESFGAIEVFRPDN---------IPPDMKFDIIINPLG-SLFWGDALKHLRTRG 243
                                   99******************997....************33.........333448*********.*************** PP

                                   EEEECSC.TSSEEEEEHHHHHHTT-EEEEE-SSCHHHHHHHHHHHHH CS
                    ADH_zinc_N  84 rlvvvGg.gkgeeefdlrnlllkeksilGsllgslreefkealdlla 129
                                    lv +G+  + e ++d+++l   ek+ilGs++g+ re+++ +l++++
  gi|13541096|ref|NP_110784.1| 244 ILVSFGVlTGREGSIDIADLYTGEKKILGSTGGT-REDLRGLLEFMK 289
                                   *******6444444********************.*******99975 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 !   25.3   0.0   5.6e-09   2.5e-05      22     125 ..     219     316 ..     203     323 .. 0.74

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 5.6e-09
                                   -EEEEEES-HHHHH.HHHHHHEEEEEEEEE----.S-EEE-CHHHCTTT-EEEE--GGG...-.-HHHHHHHHHHHHHHH- CS
                  ADH_zinc_N_2  22 gvDvvldtvggealleaslkvlpggGrlvsiggpplsaallkpakkrkgrsvkyeflfsmkasaqadileelaalieeGkl 102
                                   ++D++++ +g+  +  ++lk+l+ +G lvs g    +++  + a    ++  k+   +    + ++d l+ l+++++ ++l
  gi|13541096|ref|NP_110784.1| 219 KFDIIINPLGSLFW-GDALKHLRTRGILVSFGVLTGREGSIDIAD-LYTGEKKILGST---GGTRED-LRGLLEFMKTHEL 293
                                   59********7755.99999**999***99884333333333333.433444443333...234888.************* PP

                                   ---EEEEEEGGGHHHHHHHHHSS CS
                  ADH_zinc_N_2 103 rpvvdrvfpleeaaeAhrylesg 125
                                   r+ + r+f+++e+++A++y  + 
  gi|13541096|ref|NP_110784.1| 294 RVKIAREFKINEIKDALKYYSET 316
                                   ******************98654 PP

>> Glu_dehyd_C  Glucose dehydrogenase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   2.1e-05     0.094      16     168 ..     149     282 ..     142     318 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.1e-05
                   Glu_dehyd_C  16 aielaeasrsafewepesalvlGa.GslGLLalalleaeerglervyvlgrrdrpdptidlveelGatYvdsretpvdeip 95 
                                   a+   +a+r +     +s l+ Ga G+ G+ a ++l++  +g + vy + r+d        +e+ Ga  v       d+ip
  gi|13541096|ref|NP_110784.1| 149 ALTSFRAIRISGCSPGRSILIYGAsGNTGMFA-VQLAS-MMGCD-VYAVSRKD-------WIESFGAIEVF----RPDNIP 215
                                   555556666666666789999997699***99.55554.47887.99999865.......5999***9885....346665 PP

                   Glu_dehyd_C  96 easeemdlvvEaTGsakhafeaiealapnGvaaLlGvpedsevevdggelhrelvleNkalvGsvNanrrhfe 168
                                     + ++d+++   Gs     +a+++l++ G+ +  Gv +++e ++d+ +l +      k ++Gs+   r+  +
  gi|13541096|ref|NP_110784.1| 216 -PDMKFDIIINPLGSL-FWGDALKHLRTRGILVSFGVLTGREGSIDIADLYTG----EKKILGSTGGTREDLR 282
                                   .4679*********85.678**************************9988765....7888888877776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       562  (0.0313459); expected 358.6 (0.02)
Passed bias filter:                      531  (0.0296168); 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: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 2102.94
//
Query:       gi|13541097|ref|NP_110785.1|  [L=178]
Description: hypothetical protein TVN0266 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score 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   14.6   0.7          2    8.4   0.0    2.4  2  Herpes_pp38  Herpesvirus pp38 phosphoprotein
       0.87    9.6  10.7       0.04   13.9   5.3    1.6  2  DUF1453      Protein of unknown function (DUF1453)
        2.4    7.6   5.1        1.7    8.1   3.4    1.6  1  DUF1129      Protein of unknown function (DUF1129)


Domain annotation for each model (and alignments):
>> Herpes_pp38  Herpesvirus pp38 phosphoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.3    0.0068        41       9      36 ..      61      88 ..      56     102 .. 0.84
   2 ?    8.4   0.0   0.00033         2      24      40 ..     141     157 ..     133     164 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.0068
                   Herpes_pp38  9 ylviLivsakiLllGsCisFaaGtLvGk 36
                                  +lv L+ s++   +   +  +aG LvG 
  gi|13541097|ref|NP_110785.1| 61 ILVLLDFSTQYYYYSVLLLIIAGYLVGV 88
                                  68999*****9999999999*****994 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00033
                   Herpes_pp38  24 sCisFaaGtLvGktadv 40 
                                   s +sF +G+L+G t ++
  gi|13541097|ref|NP_110785.1| 141 SILSFTTGLLIGETVNI 157
                                   779**********9987 PP

>> DUF1453  Protein of unknown function (DUF1453)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.2       2.2   1.3e+04     120     127 ..       3      10 ..       2      12 .. 0.70
   2 ?   13.9   5.3   6.7e-06      0.04       5     112 ..      23     131 ..      16     152 .. 0.80

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 2.2
                       DUF1453 120 sglFflla 127
                                   + +Ff+l+
  gi|13541097|ref|NP_110785.1|   3 TVMFFMLV 10 
                                   66888874 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 6.7e-06
                       DUF1453   5 lvaivmallvifirikaskrpveakkiilPplfmstGa.lmfvfpefrltllevleallvGalfsipliktskfevrdgki 84 
                                   +  + + ll  + r+ + +r + a+   +P++     + l+++  +++     vl  +++G l+++ +++ ++f  r+  +
  gi|13541097|ref|NP_110785.1|  23 IGILALLLLRSAYRSFKGRRYRPARVFRIPAVYALLTViLVLLDFSTQYYYYSVLLLIIAGYLVGVRVGTSVRFFYRGTVL 103
                                   34445555566677778888888888999999998777245555567789999**************************** PP

                       DUF1453  85 ylkrskafifillgLlvvRlvlksvlss 112
                                   y +rs  + +i+   l  R++l+ ++  
  gi|13541097|ref|NP_110785.1| 104 YYRRSPGVYVIWAVSLFSRVILEFLMPG 131
                                   *************999999999988765 PP

>> DUF1129  Protein of unknown function (DUF1129)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   3.4   0.00028       1.7      90     188 ..      53     153 ..      47     164 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00028
                       DUF1129  90 alfallfgilalfskkkqtasiGlitlllvalvgGlamvlvyrlltre..kkkkkrpplwkrllilllllvvwlvlftlva 168
                                   a++all+ il l++ ++q  + +++ l++ + ++G+   + +r+++r       + p++  +++++l++ v++ +l+   +
  gi|13541097|ref|NP_110785.1|  53 AVYALLTVILVLLDFSTQYYYYSVLLLIIAGYLVGVRVGTSVRFFYRGtvLYYRRSPGVYVIWAVSLFSRVILEFLMPGNS 133
                                   567889999999999999999**************************8754555556777788888999999999999999 PP

                       DUF1129 169 llpaviNpvLpplvliiigv 188
                                   l   ++   L+    ++ig 
  gi|13541097|ref|NP_110785.1| 134 LAEVSVDSILSFTTGLLIGE 153
                                   99999999999998888885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       650  (0.0362541); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.35s 00:00:00.87 Elapsed: 00:00:00.53
# Mc/sec: 1007.56
//
Query:       gi|13541098|ref|NP_110786.1|  [L=49]
Description: 50S ribosomal protein L40e [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      2e-09   37.2   8.1    2.4e-09   36.9   8.1    1.1  1  Ribosomal_L40e  Ribosomal L40e family
     0.0027   17.3   7.0     0.0042   16.7   7.0    1.4  1  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
     0.0047   16.6   0.8     0.0062   16.2   0.8    1.2  1  zinc_ribbon_2   zinc-ribbon domain
     0.0073   16.3   0.6     0.0083   16.1   0.6    1.2  1  DZR             Double zinc ribbon
  ------ inclusion threshold ------
       0.17   11.8   1.0       0.17   11.8   1.0    1.9  2  DUF35_N         Rubredoxin-like zinc ribbon domain (DUF35_N)


Domain annotation for each model (and alignments):
>> Ribosomal_L40e  Ribosomal L40e family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.9   8.1   6.7e-13   2.4e-09      12      49 ..       9      43 ..       6      44 .. 0.89

  Alignments for each domain:
  == domain 1  score: 36.9 bits;  conditional E-value: 6.7e-13
                Ribosomal_L40e 12 yncdKmiCrkCYArlpprAtnCrkkkCghsnnlrpKKk 49
                                   + +K+iC +CYAr ++rAt Cr  kCg +  lr KKk
  gi|13541098|ref|NP_110786.1|  9 RRLNKKICMRCYARNSIRATRCR--KCGYTG-LRLKKK 43
                                  6899*******************..9**996.888887 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 !   16.7   7.0   1.2e-06    0.0042       2      25 ..      15      35 ..      15      45 .. 0.94

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.2e-06
                                  B-SSS--B----SSS----SSS-- CS
                DNA_RNApol_7kD  2 iCgeCgaevslkkgdpiRCkeCGh 25
                                  iC++C a++s++++   RC++CG+
  gi|13541098|ref|NP_110786.1| 15 ICMRCYARNSIRAT---RCRKCGY 35
                                  8*************...******8 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.8   1.7e-06    0.0062       2      21 ..      16      35 ..      15      37 .. 0.95

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.7e-06
                 zinc_ribbon_2  2 CpnCGaelqdnakFCpyCGt 21
                                  C +C a ++ +a+ C +CG+
  gi|13541098|ref|NP_110786.1| 16 CMRCYARNSIRATRCRKCGY 35
                                  *******************8 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.6   2.3e-06    0.0083      28      49 .]      13      34 ..       4      43 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2.3e-06
                           DZR 28 edrCpsCgekvdpearfCpeCG 49
                                  ++ C++C + ++ +a+ C +CG
  gi|13541098|ref|NP_110786.1| 13 KKICMRCYARNSIRATRCRKCG 34
                                  5677777777777777777776 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.2     0.095   3.4e+02      27      35 ..      15      23 ..      13      24 .. 0.80
   2 ?   11.8   1.0   4.7e-05      0.17       5      18 ..      21      34 ..      20      36 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.095
                       DUF35_N 27 vCphCgsdd 35
                                  +C +C +++
  gi|13541098|ref|NP_110786.1| 15 ICMRCYARN 23
                                  7****8765 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 4.7e-05
                       DUF35_N  5 aegrLvgqrCpdCG 18
                                  a++ ++++rC++CG
  gi|13541098|ref|NP_110786.1| 21 ARNSIRATRCRKCG 34
                                  68899********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (49 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       789  (0.0440069); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); 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: 0.41u 0.30s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 329.40
//
Query:       gi|13541099|ref|NP_110787.1|  [L=258]
Description: phosphoribosylformylglycinamidine synthase I [Thermoplasma volcanium GSS1]
Scores for complete 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-61  205.8   0.0    6.6e-61  205.7   0.0    1.0  1  GATase_5       CobB/CobQ-like glutamine amidotransferase doma
    4.6e-07   29.8   0.0    9.1e-07   28.8   0.0    1.5  1  DJ-1_PfpI      DJ-1/PfpI family
    9.8e-06   25.5   0.0      2e-05   24.5   0.0    1.5  1  GATase         Glutamine amidotransferase class-I
    1.2e-05   25.0   0.0    2.7e-05   23.9   0.0    1.5  1  GATase_3       CobB/CobQ-like glutamine amidotransferase doma
    2.6e-05   24.1   0.0      8e-05   22.5   0.0    1.7  1  Peptidase_C26  Peptidase C26
  ------ inclusion threshold ------
      0.069   13.0   0.0       0.13   12.1   0.0    1.4  1  SNO            SNO glutamine amidotransferase family


Domain annotation for each model (and alignments):
>> GATase_5  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  205.7   0.0   2.2e-64   6.6e-61       2     254 ..       5     246 ..       4     253 .. 0.91

  Alignments for each domain:
  == domain 1  score: 205.7 bits;  conditional E-value: 2.2e-64
                      GATase_5   2 pkvailreeGvngeyemaaafekaGfeavdvhmsdllegrvslddfqilalpGGfsygDelgsgkgwakslllneklreal 82 
                                   pk+ il  eG+n e e+ ++++++G + + +h++dl +gr++++d+ +l++pGGfs+gD + +g ++a++l   + + +++
  gi|13541099|ref|NP_110787.1|   5 PKIGILLMEGTNNETEVYYSVKRSGGSPDFIHINDLSAGRKRVSDYDGLIIPGGFSAGDYIRAGVIFAARLG--AVAGKEI 83 
                                   8999************************99***************************************999..89***** PP

                      GATase_5  83 ekflnredtlaLGiCnGfqlLvklglvpggeieeaeksptltrNksgrfesrlvsvvvsekspsvflkgme...glslpva 160
                                   ++f+++ ++  +GiCnGfq+L+++gl+        ++++tlt+N+s+rfe+r +++++ ++ + +f +g     ++++pva
  gi|13541099|ref|NP_110787.1|  84 REFVDD-GKPLIGICNGFQVLMEMGLIYD------RSKITLTNNESNRFECRYTYMKM-TSRNRIFQSGFYgkgVFQVPVA 156
                                   ******.********************87......9********************98.67777777776434699***** PP

                      GATase_5 161 hGeGrfvfkseevlkeleangqvalrYvdeegkpteeyplNPNgSpegiagitspdGRvlalmpHpervveavqksiipee 241
                                   h+eGr+ +++++vlk+l++n qv+++Y +e +++t eyp+NPNgS +++a++ ++ G v++lmpHper++ ++q  ++++e
  gi|13541099|ref|NP_110787.1| 157 HAEGRIAVSERSVLKKLYENDQVVFKYSNE-NDVTDEYPWNPNGSIDSVASLSNEAGNVIGLMPHPERIYYRYQAMYLETE 236
                                   ***************************988.899******************************************98765 PP

                      GATase_5 242 eeeevspwlrlFe 254
                                   ++   +   ++F+
  gi|13541099|ref|NP_110787.1| 237 KD---EVAGKIFY 246
                                   54...33444443 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 !   28.8   0.0     3e-10   9.1e-07      56     116 ..      44     112 ..      24     132 .. 0.81

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 3e-10
                                   GCTCCG-SEEEE--BHHHHHHHHTSH........HHHHHHHHHHHTT-EEEEETTTHHHHHHTTTTTTS CS
                     DJ-1_PfpI  56 dvkaaeyDalvlpGGragperlrene........kvvelvkefaekgklvaaICagpqlLaaagvlkgr 116
                                     ++++yD l++pGG +  +++r+          ++++ ++ef+++gk++  IC g q+L++ g++  r
  gi|13541099|ref|NP_110787.1|  44 RKRVSDYDGLIIPGGFSAGDYIRAGVifaarlgaVAGKEIREFVDDGKPLIGICNGFQVLMEMGLIYDR 112
                                   557899***************9875433333333778889************************98665 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.0   6.6e-09     2e-05      39     161 ..      46     221 ..      18     230 .. 0.60

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 6.6e-09
                                   THHSTSEEEEEEESSCTT............TTTHHHHHHHHCTSTS-EEEETHHHHHHHHHTTT................. CS
                        GATase  39 llknpdgilvsgGpgspg............vegkieaikearenkiPiLGICLGmQllaiefgr................. 90 
                                     +++dg++++gG+ +                 + + i+e+ + ++P++GIC G+Q+l++ +g                  
  gi|13541099|ref|NP_110787.1|  46 RVSDYDGLIIPGGFSAGDyiragvifaarlGAVAGKEIREFVDDGKPLIGICNGFQVLME-MGLiydrskitltnnesnrf 125
                                   4789**********998889888888744333333445555569*************975.55546677666666666555 PP

                                   .......................EEEEEECEEEEEEEEEEEETTT.CGGTTTTSEEEEEEEEEEEEESGCHHHTT..EEEE CS
                        GATase  91 .......................kvvkekekehhggtmrlgddet.allyglknevierhrHryevnpkelepag..levt 145
                                                           v +     h  g + + +++  ++ly+++++v  + + +++ ++  + p+g    v+
  gi|13541099|ref|NP_110787.1| 126 ecrytymkmtsrnrifqsgfygkGVFQVP-VAHAEGRIAVSERSVlKKLYENDQVVFKYSNENDVTDEYPWNPNGsiDSVA 205
                                   55555555555543333333332222222.333333333333333667777777777777777777766666666433333 PP

                                   EEEETTEEEEEEEEET CS
                        GATase 146 akseddeelmeiiekk 161
                                     s++ + +++++ ++
  gi|13541099|ref|NP_110787.1| 206 SLSNEAGNVIGLMPHP 221
                                   3344444555555555 PP

>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.0   8.9e-09   2.7e-05      35      90 ..      45     105 ..      26     123 .. 0.74

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 8.9e-09
                      GATase_3  35 eslgedadlvilpGgkdtiqdla....llre..sgldeaikeaaeaggpvlgiCGGlqmLGe 90 
                                   +++ +d+d +i+pGg++  + +     ++++      ++i+e++ +g+p++giC G+q+L e
  gi|13541099|ref|NP_110787.1|  45 KRV-SDYDGLIIPGGFSAGDYIRagviFAARlgAVAGKEIREFVDDGKPLIGICNGFQVLME 105
                                   333.78*********98654433111122222356789**********************87 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0   2.7e-08     8e-05      30     175 ..      22     158 ..      12     187 .. 0.68

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 2.7e-08
                 Peptidase_C26  30 veavekagglpvllpieedeedvkaildkldgllltGgqdvePslygeepsekeeeadpeR.dalelaLiraalergvPil 109
                                   + +v+++gg p  + i+ d +  ++ ++  dgl+++Gg        + +   + + + ++R  a+  + ir+ ++ g+P++
  gi|13541099|ref|NP_110787.1|  22 YYSVKRSGGSPDFIHIN-DLSAGRKRVSDYDGLIIPGGFS------AGD-YIRAGVIFAARlGAVAGKEIREFVDDGKPLI 94 
                                   5589*************.999*****************87......333.344466666663799999************* PP

                 Peptidase_C26 110 giCrGlqllnvalGGtlyqdieeqsgltdhreheqsaashavkve.kgsllaell.gseeievnslHh 175
                                   giC G+q+l     G +y + + + ++++   ++ +     +k++  ++++++ + g+  ++v   H 
  gi|13541099|ref|NP_110787.1|  95 GICNGFQVL--MEMGLIYDRSKITLTNNES--NRFECRYTYMKMTsRNRIFQSGFyGKGVFQVPVAHA 158
                                   ********9..5567777665532222222..221111222222213344443331456666666665 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   4.3e-05      0.13      31      82 ..      47     104 ..      36     125 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.3e-05
                                   GCC-SEEEE-SS-HHH..HH...HHHHHTT-H..HHHHHHHHTT.--EEEETHHHHHHC CS
                           SNO  31 laevdaliiPGGesta..ms...kliertgly..edllefvknsekvvlGtCaGlills 82 
                                   + + d+liiPGG s+   ++    ++ r g +  ++++efv ++ k+++G C G+ +l 
  gi|13541099|ref|NP_110787.1|  47 VSDYDGLIIPGGFSAGdyIRagvIFAARLGAVagKEIREFVDDG-KPLIGICNGFQVLM 104
                                   6789********9974333211135677776533689******9.*********86654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       534  (0.0297841); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); 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: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1820.29
//
Query:       gi|13541100|ref|NP_110788.1|  [L=415]
Description: dihydroorotase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.5e-13   49.6   0.0    4.2e-12   46.0   0.0    2.1  1  Amidohydro_1  Amidohydrolase family
    5.2e-05   22.9   0.0    0.00095   18.7   0.0    2.1  2  Amidohydro_3  Amidohydrolase family
  ------ inclusion threshold ------
      0.098   12.1   0.0       0.17   11.4   0.0    1.3  1  DUF4916       Domain of unknown function (DUF4916)


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 !   46.0   0.0   7.1e-16   4.2e-12       2     344 .]      46     391 ..      45     391 .. 0.65

  Alignments for each domain:
  == domain 1  score: 46.0 bits;  conditional E-value: 7.1e-16
                                   EEE-EEEEEEECETTECSSSGHHHHHSTTHHHHHHHHHHHHHHHHTTEEEEEEEEHSSTHHHHHHHHHHHTSSSEEEEEEE CS
                  Amidohydro_1   2 vlPGlIDaHvHleqsllrgatledwlvppetaaealesgiktalksGtttvadmgattstgiealleaaeelplglrilgg 82 
                                   vlP+  D+HvH++             +p+et +e + +g   a+ +Gtt v dm+++ + +i++    +++l  g  ++ g
  gi|13541100|ref|NP_110788.1|  46 VLPAATDIHVHFR-------------TPGETDKEDFSTGSLSAIFGGTTLVMDMPNNII-PIKDYNAFSDKL--G--VING 108
                                   89**********9.............******************************533.555555555554..4..3333 PP

                                   SSEGGS......GCCCSHHHHHHHHHHHHHHHHHHCTTTCEEEEEEECGTCCSHHHHHHHHHHHHHHHTTEEEEEETSSCH CS
                  Amidohydro_1  83 kvsldr......gsaetskasreklkagaaetikgkadgvvkvalapheapafsdeelkealkeakkrdlpvaiHaletkg 157
                                    +s++       +   t  +s     + +   +k+  +      ++ ++  a++d e +++     +++  v +H  e+++
  gi|13541100|ref|NP_110788.1| 109 -TSYSDfalysmE---TGSNSLIVDSRSI--GLKVYLG----GSTNAAGTMAIPDQEAEMIN----EKGFTVIFHG-ELEE 174
                                   .444434664443...3333333333333..2243333....55557777777777776666....79*******9.4444 PP

                                   HHHHHHHHHTTTEEEETTTTSTCC........HHTTTHCCEEEHCTCEEEHHHHHHHHHHHHHHCEE..........HHHH CS
                  Amidohydro_1 158 evedaeaafgetiehgthlevaes........lglldeiklilahgvhltpteaellkerlkeagva..........hcpf 220
                                       ++ + ++  eh   l+++ +        +g l+    i+ah   +++               +          h+  
  gi|13541100|ref|NP_110788.1| 175 CLRKHQSETKNLREH--NLSRPIEcelaaagyVGSLNLKSKIMAHVSSPEV---------------SgdflrevtphHLLL 238
                                   444444444444444..5555555222222224444444455555555554...............233333333333333 PP

                                   HHHH.............SEHHHHHHHHHHHHTSCEEEEEECT....TSSCCGGHHHHHHHHHHHHHHCCTT.TTHCHCHHH CS
                  Amidohydro_1 221 snsi.............lrsgrealrkaldeGvkvglgtDga....asgnslnlleelrlalklqrgllye.deegglslk 283
                                   +++               r   e+l  a  +G + +l++D+a         ++  ++++++++++ +l    + + ++  +
  gi|13541100|ref|NP_110788.1| 239 NDEMplgsigkvnpplrDRNTQERLLYAYISGQFDILSSDHAphteKDKAEFEYAKSGIIGVETRIPLMLAlV-KKKILFL 318
                                   3333455555566665566777778888888*************99777788889999999988887777766.6669*** PP

                                   HHHHHHTHH.HHHHTT-TTTSSSS-TTSB--EEEECC...CT...........CGGGTTTCTSEEEEEEEETTEEE CS
                  Amidohydro_1 284 ealrmaTin.gAkalglddkvGsievGkdADlvvvdl...di...........laafvglkkdgnvkkvivkGklv 344
                                   ++l+++ i  +  ++g+  ++G+ievG+dAD+  vd    ++            ++f+g+   + + +v+ +G++v
  gi|13541100|ref|NP_110788.1| 319 DVLYKTGIErPPSIFGI--RKGKIEVGYDADFMCVDFtneKKvnedrlhsklpRSPFNGMDAIF-PSHVVMRGEVV 391
                                   **9999996488*****..*****************9765225667777788778888776544.77777777665 PP

>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.1      0.02   1.2e+02       9      45 ..      45      77 ..      44      82 .. 0.83
   2 !   18.7   0.0   1.6e-07   0.00095     430     473 .]     336     392 ..     327     392 .. 0.94

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.02
                  Amidohydro_3  9 lvlPGFvDsHtHlagggvnlrllrlpdarvtslegvl 45
                                   vlP+ +D+H H  + g    +++ +d +  sl +++
  gi|13541100|ref|NP_110788.1| 45 AVLPAATDIHVHFRTPG----ETDKEDFSTGSLSAIF 77
                                  69**********77777....9999998888887765 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 1.6e-07
                  Amidohydro_3 430 rkGtLevGadADlvvld.adpldvdppelaear............vrltvvdGrvvy 473
                                   rkG +evG+dAD++  d ++  +v +++l++++            ++++v +G+vv+
  gi|13541100|ref|NP_110788.1| 336 RKGKIEVGYDADFMCVDfTNEKKVNEDRLHSKLprspfngmdaifPSHVVMRGEVVI 392
                                   67*****************************************************95 PP

>> DUF4916  Domain of unknown function (DUF4916)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   2.8e-05      0.17      61     109 ..      16      67 ..       9      77 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.8e-05
                                   -TT-.-HHHHHHHHHHHHH-TT--B---SS---SE..EEEEESSTTSSSEE- CS
                       DUF4916  61 lyhe.tvreallrhiekdlGelalpqlPaslqPft..vaeyfPtpgvseytd 109
                                    y e tv++ ++  i+kd G++a + lP ++ P +  +  +f tpg ++  d
  gi|13541100|ref|NP_110788.1|  16 DYLEvTVKDGVIESIKKDAGNIARSYLPGAVLPAAtdIHVHFRTPGETDKED 67 
                                   5555489***********************99975337889*****998777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (415 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); 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: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 2693.53
//
Query:       gi|13541101|ref|NP_110789.1|  [L=197]
Description: RNA methylase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.9e-12   45.6   0.2    8.8e-12   45.0   0.2    1.2  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    5.2e-10   39.3   0.0    7.4e-10   38.8   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    2.4e-09   37.0   0.0      4e-09   36.2   0.0    1.3  1  MTS              Methyltransferase small domain
    8.3e-08   32.8   0.0    1.4e-07   32.1   0.0    1.4  1  Methyltransf_25  Methyltransferase domain
    6.1e-05   23.6   0.0    0.00012   22.6   0.0    1.6  1  Methyltransf_11  Methyltransferase domain
    6.6e-05   22.8   0.0    6.7e-05   22.8   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
    0.00025   21.1   0.0    0.00038   20.5   0.0    1.3  1  Methyltransf_32  Methyltransferase domain
    0.00098   18.9   0.0     0.0016   18.2   0.0    1.3  1  UPF0020          Putative RNA methylase family UPF0020
  ------ inclusion threshold ------
      0.013   16.2   0.0      0.031   15.0   0.0    1.6  1  Methyltransf_12  Methyltransferase domain
      0.016   14.9   0.0      0.029   14.0   0.0    1.5  1  Cons_hypoth95    Conserved hypothetical protein 95
       0.04   13.7   0.1       0.18   11.6   0.2    2.0  2  N6-adenineMlase  Probable N6-adenine methyltransferase
      0.063   13.0   0.0      0.078   12.7   0.0    1.2  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl


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 !   45.0   0.2   5.9e-15   8.8e-12     152     210 ..      39      95 ..      35     114 .. 0.84

  Alignments for each domain:
  == domain 1  score: 45.0 bits;  conditional E-value: 5.9e-15
                          PrmA 152 lealeklvkegeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkve 210
                                   +e+le+ + +g++v+D GtG GiLa +a  Lga++v++ DiD   v++ak+N +  +v+
  gi|13541101|ref|NP_110789.1|  39 VEILEDGNIKGRTVVDAGTGNGILACGAYYLGAATVLGFDIDVSMVEIAKQNCN--NVK 95 
                                   5789999999******************************************75..443 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.8   0.0     5e-13   7.4e-10       4      84 ..      49     117 ..      47     152 .. 0.86

  Alignments for each domain:
  == domain 1  score: 38.8 bits;  conditional E-value: 5e-13
               Methyltransf_31   4 glrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsnevl 84 
                                   g +v+D+G+G+G l+  ++  lg  a+v G+Di+  ++e A++n+      nv+Fe+ ++ +++      kfD ++ n ++
  gi|13541101|ref|NP_110789.1|  49 GRTVVDAGTGNGILACGAY-YLG-AATVLGFDIDVSMVEIAKQNCN-----NVKFEVRNVKDIS-----GKFDTWIMNPPF 117
                                   6789***************.766.5******************976.....***********99.....89*****99554 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.2   0.0   2.7e-12     4e-09      19     119 ..      34     126 ..      26     139 .. 0.79

  Alignments for each domain:
  == domain 1  score: 36.2 bits;  conditional E-value: 2.7e-12
                                   HHHHHHHHCHCC..TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTSTTS- CS
                           MTS  19 GsklLletlpke..lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvleeveekk 97 
                                   ++ +L+e l++   + ++v+D G+G+G+l++ +      a+v  +d+d   +e+ak+n+++ k+ev+      +++++ +k
  gi|13541101|ref|NP_110789.1|  34 AAYFLVEILEDGniKGRTVVDAGTGNGILACGAYYLGA-ATVLGFDIDVSMVEIAKQNCNNVKFEVRN-----VKDIS-GK 107
                                   567999999988878889************99887655.58*****************9887765443.....35677.8* PP

                                   EEEEEE---STTTCHCHHHHHH CS
                           MTS  98 fdlivsNPPfhagkatelavae 119
                                   fd+ ++NPPf +  +   ++ +
  gi|13541101|ref|NP_110789.1| 108 FDTWIMNPPFGSVMK---HADR 126
                                   **********88766...3333 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.1   0.0   9.7e-11   1.4e-07       1      85 [.      52     132 ..      52     137 .. 0.78

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 9.7e-11
                                   EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEE...EST.GGGS CS
               Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvs...sga.lhhl 77 
                                   v+d+G+G+G l+  +    g+a+v+g+Di+ +m+e+a++++     nv+f++ +++d++   g+fD  ++   +g+ + h 
  gi|13541101|ref|NP_110789.1|  52 VVDAGTGNGILACGAYYL-GAATVLGFDIDVSMVEIAKQNC----NNVKFEVRNVKDIS---GKFDTWIMnppFGSvMKHA 124
                                   89*******999999977.79********************....49********9997...8999999933333333444 PP

                                   SHHHHHHH CS
               Methyltransf_25  78 sdedleka 85 
                                   +++ +eka
  gi|13541101|ref|NP_110789.1| 125 DRPFIEKA 132
                                   44444444 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   8.2e-08   0.00012       1      54 [.      53     103 ..      53     133 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 8.2e-08
                                   EEET-TTSHHHHHHHHTT.SEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCC CS
               Methyltransf_11   1 LdvGcGtGrlaealakrg.arvvgvDlskemlklakekaseeglkvefvvadaek 54 
                                   +d+G+G+G+la+     g a+v+g+D++  m+++ak++ ++ +    f v ++++
  gi|13541101|ref|NP_110789.1|  53 VDAGTGNGILACGAYYLGaATVLGFDIDVSMVEIAKQNCNNVK----FEVRNVKD 103
                                   599************9999********************9976....45555555 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0   4.5e-08   6.7e-05      13      87 ..      38     112 ..      20     184 .. 0.77

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 4.5e-08
               Methyltransf_23  13 lerllpk.lraggrvLdiGcGtGillevlrengf.svtgvDlspeaveiaekakkaqkdqfdeqeaaepqgkfdlIv 87 
                                   l ++l+  + +g  v+d G+G Gil+  + + g+ +v g+D++  +veia+  ++ ++++f   + ++ +gkfd+ +
  gi|13541101|ref|NP_110789.1|  38 LVEILEDgNIKGRTVVDAGTGNGILACGAYYLGAaTVLGFDIDVSMVEIAK--QNCNNVKFEVRNVKDISGKFDTWI 112
                                   4444444478899**********999999888987999***********95..444444444455556666666644 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   2.5e-07   0.00038       2      78 ..      13      96 ..      12     117 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 2.5e-07
               Methyltransf_32  2 Klheverlaelvakllkel............akesgaltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekrae 72
                                  Kl++ e++a+ +++ ++++            + + +  tvvD+G G+g L+   ++        v+g+d+  ++ve a++  +
  gi|13541101|ref|NP_110789.1| 13 KLKQPEHYANYLEQYMTDAssaayflveileDGNIKGRTVVDAGTGNGILACGAYY---LGAATVLGFDIDVSMVEIAKQNCN 92
                                  89999999999999888888899999998876677889******************...778999999999999999888877 PP

               Methyltransf_32 73 klgkkf 78
                                  +++  f
  gi|13541101|ref|NP_110789.1| 93 NVK--F 96
                                  777..3 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   1.1e-06    0.0016      78     138 ..      73     124 ..      65     130 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.1e-06
                                   -EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EEEE----------H CS
                       UPF0020  78 klygsDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdvivtnpPYGerlgsk 138
                                    + g+D+d ++v+ a++N ++      ++f++ +++++    g++d+ + npP+G  ++++
  gi|13541101|ref|NP_110789.1|  73 TVLGFDIDVSMVEIAKQNCNN------VKFEVRNVKDIS---GKFDTWIMNPPFGSVMKHA 124
                                   589***************987......678889999999...78***********988865 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0     2e-05     0.031       5      73 ..      55     114 ..      53     134 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2e-05
               Methyltransf_12   5 cGtGsllrallekl.pdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvas 73 
                                   +GtG+ + a+ ++    ++++g Di+ s++        ++ ++n+nnv++e++++ d +g  +fD+ +++
  gi|13541101|ref|NP_110789.1|  55 AGTGNGILACGAYYlGAATVLGFDIDVSMV--------EIAKQNCNNVKFEVRNVKDISG--KFDTWIMN 114
                                   577777777777775677888*********........4444556788888888766655..9****997 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   1.9e-05     0.029      38      95 ..      44     100 ..      28     150 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.9e-05
                                   CC.HCC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEE CS
                 Cons_hypoth95  38 ae.iegarvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkleeetae 95 
                                      i+g +v+D   G+G l++ A   ga+ ++ ++ d ++v+i k+n++++k+e   ++
  gi|13541101|ref|NP_110789.1|  44 DGnIKGRTVVDAGTGNGILACGAYYLGAATVLGFDIDVSMVEIAKQNCNNVKFEV--RN 100
                                   435999**********************************************874..22 PP

>> N6-adenineMlase  Probable N6-adenine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.2   0.00012      0.18      70     145 ..      93     167 ..      22     180 .. 0.69
   2 ?    1.9   0.0      0.12   1.8e+02      32      49 ..     167     184 ..     134     193 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00012
               N6-adenineMlase  70 fvfYdlnnpeelpeelkgkfdviviDPPF......lseeclkklaktaklllkklilctgevmee..lekllgvkktkfep 142
                                    v ++++n     ++++gkfd  ++ PPF        +++++k+ +t k++      + g+  +e  l++++ ++   f+ 
  gi|13541101|ref|NP_110789.1|  93 NVKFEVRNV----KDISGKFDTWIMNPPFgsvmkhADRPFIEKAFETSKFI-----YSIGNAKAEsfLSREFSARGDIFRE 164
                                   344444444....569*************9977776667777766666655.....4444444444566666666666666 PP

               N6-adenineMlase 143 ehe 145
                                   eh 
  gi|13541101|ref|NP_110789.1| 165 EHI 167
                                   655 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.12
               N6-adenineMlase  32 aclsaPsvyealkkekkk 49 
                                   + ls P++ye+ kk+  +
  gi|13541101|ref|NP_110789.1| 167 IDLSVPRIYEHHKKDWTR 184
                                   559*******99987654 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   5.2e-05     0.078      65     127 ..      38     102 ..      10     137 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.2e-05
                                   HHHHTT..--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTC..SEE CS
                          PCMT  65 alelle..lkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldle..nvi 127
                                   ++e le    kg  v++ G+G G+l a+ a ++g+ + v++ +   ++ve ak+n ++ + e  nv+
  gi|13541101|ref|NP_110789.1|  38 LVEILEdgNIKGRTVVDAGTGNGIL-ACGAYYLGAAT-VLGFDIDVSMVEIAKQNCNNVKFEvrNVK 102
                                   34666665557999*********98.69999999988.******************99988744554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       565  (0.0315132); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); 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: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 1226.71
//
Query:       gi|13541102|ref|NP_110790.1|  [L=101]
Description: hypothetical protein TVN0271 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score 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   12.7   0.1      0.052   12.7   0.1    1.2  1  HAP1_N    HAP1 N-terminal conserved region


Domain annotation for each model (and alignments):
>> HAP1_N  HAP1 N-terminal conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   2.9e-06     0.052      42      92 ..      43      92 ..       7      94 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.9e-06
                        HAP1_N 42 qieetleYflLcservsqvtktyeDievvtrLLeEkerDLelaArIGqsLl 92
                                    +e  +Y++L+++      k +  ++ + +LL+E+    e +ArI ++++
  gi|13541102|ref|NP_110790.1| 43 VDREIAKYIVLAAHENGTW-KRQRAMKKIEKLLQERGESKENSARIAKEII 92
                                  5699**********88887.88999*********************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1209  (0.0674327); expected 358.6 (0.02)
Passed bias filter:                      775  (0.0432261); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 699.41
//
Query:       gi|13541103|ref|NP_110791.1|  [L=307]
Description: ornithine carbamoyltransferase [Thermoplasma volcanium GSS1]
Scores for complete 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  194.0   0.0    2.4e-57  193.4   0.0    1.3  1  OTCace    Aspartate/ornithine carbamoyltransferase, Asp/Orn b
    1.5e-42  145.1   0.0    2.4e-42  144.4   0.0    1.3  1  OTCace_N  Aspartate/ornithine carbamoyltransferase, carbamoyl


Domain annotation for each model (and alignments):
>> OTCace  Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  193.4   0.0   2.7e-61   2.4e-57       2     156 ..     150     303 ..     149     304 .. 0.99

  Alignments for each domain:
  == domain 1  score: 193.4 bits;  conditional E-value: 2.7e-61
                                   C.EEEEESSTTSHHHHHHHHHHHHCT-EEEEES-TTSSH-HHHHHHHHHHHHHHT-EEEEESSCHHHHTT-SEEEE--SSE CS
                        OTCace   2 glkiafvGdkknnvanslikllarlgmdvvlvaPkglepdkevleeakknakksggsititedleeavkgaDvvytdvwvs 82 
                                   glk+ ++Gd+ nn+ansl+ ++a+lg+d+++++P g+ep+ e++++ak+ ak+ g+++ it+d  ea+k+aDv+ytdvw+s
  gi|13541103|ref|NP_110791.1| 150 GLKFSYIGDG-NNMANSLMLGAAILGVDIYVATPHGYEPKSEFVDKAKQVAKERGSKVIITNDAIEAAKDADVIYTDVWIS 229
                                   89********.********************************************************************** PP

                                   TTCCGGHHHHHHHHCCCSB-HHHHHHS-TT-EEEE-S---BTTTB-HHHHTSTTBHHHHHHHHHHHHHHHHHHH CS
                        OTCace  83 mgeekereerlkklkdyqvteellklakkdaivlHcLPakrgeEvtdeVfdsprsvvfeqaeNrlhtikAllvl 156
                                   mgee++r e+ k++++yq++++l+++akkd i++HcLPa+rg Evtd+V ds +sv+f++aeNrlh +k +l+ 
  gi|13541103|ref|NP_110791.1| 230 MGEESKRGEKEKAFTKYQINSDLVSNAKKDYIFMHCLPAHRGLEVTDDVADSINSVIFDEAENRLHSEKGVLYK 303
                                   ***********************************************************************985 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 !  144.4   0.0   2.7e-46   2.4e-42       1     148 []       6     143 ..       6     143 .. 0.96

  Alignments for each domain:
  == domain 1  score: 144.4 bits;  conditional E-value: 2.7e-46
                                   S-BSSGGGS-HHHHHHHHHHHHHHHHHHHTTT-STTTTT-EEEEEESS--HHHHHHHHHHHHHTTSEEEEEESTTTSCTTT CS
                      OTCace_N   1 rhllsledlskeeieelldlaaelkekvkkekkekllkgktlallFeepStRTrvSfevAakrlGgkvlslseaediqlss 81 
                                   r++ls+ d++ ++++e+++l+ elk+++   ++ ++l++k+l+l+Fe+pStRTr+S evA+ +lGg++++l+ ++++ql+ 
  gi|13541103|ref|NP_110791.1|   6 RDILSVLDMK-NDLDEIINLSIELKKNRY--RSYESLRNKMLGLIFEKPSTRTRTSLEVAIDQLGGHAVYLN-PSEMQLG- 81 
                                   7899999997.99************9987..89999************************************.889***9. PP

                                   GGSTTSSCHHHHHHHHHHHTSEEEEEESSHHHHHHHHHHHSSEEEEEEETSSB-HHHHHHHHHHHHH CS
                      OTCace_N  82 vskgrkEsleDtarvlsryvdaiviRhpgaeeleelakyasvpviNagdgdgeHPtQaLaDlltire 148
                                       r+E+++Dt  vlsr+ dai++R+++++++ ela+  s+pviNa+  d eHP+Q+ aD++t++e
  gi|13541103|ref|NP_110791.1|  82 ----RGETISDTGHVLSRFLDAIAYRAFDHKNVVELARSTSIPVINAL-DDVEHPLQIVADFMTVKE 143
                                   ....78******************************************.999************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 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:                        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: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 1937.26
//
Query:       gi|13541104|ref|NP_110792.1|  [L=285]
Description: succinyl-CoA synthetase subunit alpha [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      5e-22   78.4   0.9      5e-22   78.4   0.9    2.4  2  CoA_binding   CoA binding domain
    2.8e-19   69.4   0.2    4.8e-19   68.7   0.2    1.4  1  Ligase_CoA    CoA-ligase
    4.4e-12   46.0   0.0    7.8e-12   45.2   0.0    1.4  1  Succ_CoA_lig  Succinyl-CoA ligase like flavodoxin domain
    2.9e-05   23.7   0.4    4.7e-05   23.0   0.4    1.4  1  IlvN          Acetohydroxy acid isomeroreductase, NADPH-bindi
      0.005   17.0   0.0      0.024   14.9   0.0    2.2  1  DUF1611_N     Domain of unknown function (DUF1611_N) Rossmann


Domain annotation for each model (and alignments):
>> CoA_binding  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.4   0.9   1.4e-25     5e-22       1      96 []       5      98 ..       5      98 .. 0.96
   2 ?   -0.3   0.3       0.5   1.8e+03      27      50 ..     168     193 ..     142     234 .. 0.56

  Alignments for each domain:
  == domain 1  score: 78.4 bits;  conditional E-value: 1.4e-25
                                  CTTEEEEEETTTSHHHHHHHHHHHHHHECEEEEEEC-TTTTTCEET.TEEEESCHHHHHHHCTTTEEEEES-HHHHHHHHHHH CS
                   CoA_binding  1 dkdtkviviGagglgiaglyhfkeklkygikavfgvnprkvgtevl.glpvyksvdeleektevdvavitvPaesaqeavdel 82
                                  dk+tkviv+G++g   +g +h+ e+lk+g+++v+g+ p+k+gt+    +p+ +sv+e+++  e+d+++i vPa+++++a+ e+
  gi|13541104|ref|NP_110792.1|  5 DKNTKVIVQGITGH--QGSFHTGEMLKFGTNVVAGIAPGKGGTKFAdKVPIVNSVAEAMQY-EPDATMISVPAPFVKDAAYEA 84
                                  699********999..**************************887658*************.********************* PP

                                  HHTT-SEEEEESST CS
                   CoA_binding 83 veagikgiviiteg 96
                                  +++g k + i te+
  gi|13541104|ref|NP_110792.1| 85 IDNGLKIVYILTEH 98
                                  ***********985 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.5
                                   HECEEEEEEC-TT.TTT.CEETTEEE CS
                   CoA_binding  27 kygikavfgvnpr.kvg.tevlglpv 50 
                                   ++g + v+g +++  vg + ++ l++
  gi|13541104|ref|NP_110792.1| 168 GMGESTVIGLGGDrVVGlSFIDVLKM 193
                                   55555555555442233233333333 PP

>> Ligase_CoA  CoA-ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.7   0.2   1.4e-22   4.8e-19       2     151 ..     151     269 ..     150     271 .. 0.95

  Alignments for each domain:
  == domain 1  score: 68.7 bits;  conditional E-value: 1.4e-22
                                   ESSHHHHHHHHHHHHHT..............T--BSEEEE-TSS--..........HHHHHHHHHHHHS-TT-SEEEEEEE CS
                    Ligase_CoA   2 vnGGtLayeamdlikealgdvasnkklknvlgseqheiidlGddaftkGrpHPmiDptkriealkklaadpevkvilldiv 82 
                                   +++GtL+ye +++i++a              g +++++i+lG+d+           + ++i+ lk + +dp++k i+l ++
  gi|13541104|ref|NP_110792.1| 151 SRSGTLTYEIVYAITKA--------------GMGESTVIGLGGDRVV---------GLSFIDVLKMFENDPKTKKIVLVGE 208
                                   69***************..............***************8.........9************************ PP

                                   ESSSEHHHHHHHHHHHHHHTT...--S-EEEEEECTTHH.....HHHHHHHTTTSSEEE-SSHHHHHHH CS
                    Ligase_CoA  83 lGygahedpaaellkaikeakaegrelpvvarvaGteadpqelseqakaleeagveiasskaqalraak 151
                                   +G g++e+ aae++k+  + k       vva++aG +a+p++++++a+a+ e gv +a+sk +a   a+
  gi|13541104|ref|NP_110792.1| 209 IG-GNNEELAAEYIKKNVKKK-------VVAYIAGRSAPPGKRMGHAGAIIERGVGTAESKLKAFNSAG 269
                                   **.***********9877766.......*********************************99987765 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 !   45.2   0.0   2.2e-15   7.8e-12       2     107 ..     145     251 ..     144     283 .. 0.81

  Alignments for each domain:
  == domain 1  score: 45.2 bits;  conditional E-value: 2.2e-15
                  Succ_CoA_lig   2 GkialisqSGalalalldwaasrglgfskvvslGn..eadvdvadlleylaedpetkvillylEsirdgrkflsaarraar 80 
                                   G++a+ s SG+l  +++ + ++ g+g s+v+ lG    + +++ d+l+++++dp+tk i+l+ E  ++ +++++   + + 
  gi|13541104|ref|NP_110792.1| 145 GDVAVASRSGTLTYEIVYAITKAGMGESTVIGLGGdrVVGLSFIDVLKMFENDPKTKKIVLVGEIGGNNEELAAEYIKKNV 225
                                   99********************************8334667899****************************998888888 PP

                  Succ_CoA_lig  81 kkpvvvlksGrseagaraaashtgala 107
                                   kk+vv++ +Grs+   +  + h ga+ 
  gi|13541104|ref|NP_110792.1| 226 KKKVVAYIAGRSAPPGKR-MGHAGAII 251
                                   9**********8754443.45666664 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 !   23.0   0.4   1.3e-08   4.7e-05       3     126 ..       6     130 ..       3     168 .. 0.87

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 1.3e-08
                                   HTS-EEEES-.SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEHHHHHH.T-SEEEE-S-HHHHHHHHHHHT CS
                          IlvN   3 kgkkiaviGy.GsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevltvaeavk.kadvvmiliPDelqkevyeeei 81 
                                   k+ k+ v G  G qG  ++ ++   g +vv g+  g+  +k A +  + v +vaea++ + d  mi +P  + k+   e+i
  gi|13541104|ref|NP_110792.1|   6 KNTKVIVQGItGHQGSFHTGEMLKFGTNVVAGIAPGKGGTKFADKVPI-VNSVAEAMQyEPDATMISVPAPFVKDAAYEAI 85 
                                   567888888559*************************99998887765.788888877478**********9999999*** PP

                                   GGG--TT-EEEESSSHHHHTTSS---TTSEEEEEEESS-SHHHHH CS
                          IlvN  82 epnlkegkalafahGfnihfglikppkdvdvvlvAPkgpGhlvre 126
                                    + lk   +l+    ++  ++ +k  +  +++++ P gpG +v  
  gi|13541104|ref|NP_110792.1|  86 DNGLKIVYILTEHVPYQDTMEIVKEAQLRNITVLGPNGPGITVPF 130
                                   ***********999**************************99854 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 !   14.9   0.0   6.6e-06     0.024       5      87 ..      44     117 ..      40     119 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 6.6e-06
                     DUF1611_N   5 GkdagellddrgipvvssleealaagaevlviGiapeggklpeswreavkeAleaGldvvsGl..HerLsddpelaalakk 83 
                                   G++++     +++p+v+s++ea++ ++++ +i++ ++  ++    + a+ eA+++Gl +v  l  H + +d  e+++ a+ 
  gi|13541104|ref|NP_110792.1|  44 GTKFA-----DKVPIVNSVAEAMQYEPDATMISVPAP--FV----KDAAYEAIDNGLKIVYILteHVPYQDTMEIVKEAQL 113
                                   66666.....99********************99654..45....8899**********9888446688999999999987 PP

                     DUF1611_N  84 kgvk 87 
                                   ++++
  gi|13541104|ref|NP_110792.1| 114 RNIT 117
                                   7765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); 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: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1753.51
//
Query:       gi|13541105|ref|NP_110793.1|  [L=365]
Description: succinyl-CoA synthetase subunit beta [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.3e-55  185.9   0.0    2.8e-54  183.8   0.0    1.8  2  ATP-grasp_2  ATP-grasp domain
    2.9e-12   46.7   0.2    4.9e-12   45.9   0.2    1.4  1  Ligase_CoA   CoA-ligase
    5.1e-09   35.9   0.1    5.7e-06   25.9   0.0    2.3  2  ATP-grasp_5  ATP-grasp domain
    0.00071   19.1   0.1     0.0019   17.8   0.0    1.7  2  CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP bindin
     0.0021   17.9   0.0     0.0041   16.9   0.0    1.5  1  GARS_A       Phosphoribosylglycinamide synthetase, ATP-grasp 


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 !  183.8   0.0   7.8e-58   2.8e-54       1     202 []       2     188 ..       2     188 .. 0.97
   2 ?   -0.2   0.0      0.17     6e+02     153     177 ..     333     355 ..     291     365 .] 0.60

  Alignments for each domain:
  == domain 1  score: 183.8 bits;  conditional E-value: 7.8e-58
                                   BE-HHHHHHHHHCTT----SEEEESSHHHHHHHHHHHTSSSEEEEE--SSSTCCCTTCEEEESSHHHHHHHHHCCTTSEEE CS
                   ATP-grasp_2   1 nlhEyqakeilakygvkvpegevaesaeeaeeaakklgekelvvKaQvlaGGRGKagGvklvkskeeakeaakellgkelv 81 
                                   nl+Ey +k+i+++yg++vp+g v++s++++++ ++      ++vK+Q+l GGRGKagG+k++k+ ee+k+a+++ll+++++
  gi|13541105|ref|NP_110793.1|   2 NLYEYMGKDIFREYGIPVPNGYVVSSPQDVKKFTNP-----VAVKSQILLGGRGKAGGIKFAKTDEELKNAVSTLLSTKVR 77 
                                   79***************************9877544.....59*************************************9 PP

                                   -TTS-TT-EEE--EEEEE---ECEEEEEEEEEETTTTEEEEEEESSTTS-HHHHHHH-GGGEEEEEEBTTTB--HHHHHHH CS
                   ATP-grasp_2  82 tkqtgkeGkkvekvlveealdikkElYlsivlDraskkvvviaSseGGvdiEevaakkPekiikvaidpakglkeeqarei 162
                                            +v kvl+e++l+ik+E+Y+si l ra+k++++iaS++GG++iE+v +   +ki+k  idp+ g +++  re 
  gi|13541105|ref|NP_110793.1|  78 -------NMTVTKVLIEDMLNIKHEYYVSIALNRAAKSPMLIASAMGGMEIENVPD---DKIFKRIIDPSLGYSDFIGREA 148
                                   .......789********************************************76...79******************** PP

                                   HHHCT--CHHHHHHHHHHHHHHHHHHHTTEEEEEEEEEEE CS
                   ATP-grasp_2 163 akklglekelvkkaakiikklyklfveldatlvEiNPLvv 202
                                    + +gl+ el k++ +i+kkly++++ +d++lvEiNPLv+
  gi|13541105|ref|NP_110793.1| 149 SQFMGLPPELSKQFLDILKKLYNVYRGEDCELVEINPLVE 188
                                   **************************************96 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.17
                                   B--HHHHHHHHHHCT--CHHHHHHH CS
                   ATP-grasp_2 153 glkeeqareiakklglekelvkkaa 177
                                   g++e + r+i+++ g+e+  +++++
  gi|13541105|ref|NP_110793.1| 333 GVHEVEGRKILQDNGIEA--FSEMM 355
                                   455555555555555543..34444 PP

>> Ligase_CoA  CoA-ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.9   0.2   1.4e-15   4.9e-12       2     141 ..     246     352 ..     245     364 .. 0.92

  Alignments for each domain:
  == domain 1  score: 45.9 bits;  conditional E-value: 1.4e-15
                                   ESSHHHHHHHHHHHHHT..............T--BSEEEE-TSS--..........HHHHHHHHHHHHS-TT-SEEEEEEE CS
                    Ligase_CoA   2 vnGGtLayeamdlikealgdvasnkklknvlgseqheiidlGddaftkGrpHPmiDptkriealkklaadpevkvilldiv 82 
                                    nG++L+++++d++ ++              ++++ +++dlG+ +            + +i+a+  +++  + k+il++i+
  gi|13541105|ref|NP_110793.1| 246 ANGAGLTMATLDALLLH--------------KGKPRNFLDLGGTDN----------VDIVINAFDLVLEA-KPKAILVNIF 301
                                   69***************..............************999..........799*****999876.569******* PP

                                   ESSSEHHHHHHHHHHHHHHTT...--S-EEEEEECTTHH.....HHHHHHHTTTSSEEE CS
                    Ligase_CoA  83 lGygahedpaaellkaikeakaegrelpvvarvaGteadpqelseqakaleeagveias 141
                                   +G  +++++a+++++a k+ +    ++pvv+r+ G ++      e++k+l++ g+e  s
  gi|13541105|ref|NP_110793.1| 302 GGVTKCDTVAQGIVEAKKKFD---IKIPVVVRLSGVHEV-----EGRKILQDNGIEAFS 352
                                   ********************9...*************99.....999****99998766 PP

>> ATP-grasp_5  ATP-grasp 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   5.7e-06      10     141 ..       3     126 ..       1     133 [. 0.87
   2 !    7.8   0.0   0.00055         2     200     222 .]     180     203 ..     148     203 .. 0.85

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 1.6e-09
                   ATP-grasp_5  10 LteaeakelleaygipvvetrlassaeeaveaaeeigypvvlKivspdilhKtdvgGvrlnlkdaeevraaaeeilervke 90 
                                   L+e+  k++++ ygipv++  ++ss+++    ++++  pv++K ++  +  + ++gG+++  k++ee+++a++++l++   
  gi|13541105|ref|NP_110793.1|   3 LYEYMGKDIFREYGIPVPNGYVVSSPQD----VKKFTNPVAVKSQIL-LGGRGKAGGIKF-AKTDEELKNAVSTLLSTK-- 75 
                                   899***********************88....678899*****9864.778*********.99***********99873.. PP

                   ATP-grasp_5  91 kspeariegvlVqemakr.ggrElivgvteDpvFGpvilfGlGGtavevlkd 141
                                      +  +++vl++ m +  +++ + + +++ +    +i+  +GG+++e + d
  gi|13541105|ref|NP_110793.1|  76 -VRNMTVTKVLIEDMLNIkHEYYVSIALNRAAKSPMLIASAMGGMEIENVPD 126
                                   .45789*********8866788888888888888888899999999987765 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.00055
                   ATP-grasp_5 200 eldinPllveeeg.vvalDarirl 222
                                    ++inPl+ +++g ++a+Da++++
  gi|13541105|ref|NP_110793.1| 180 LVEINPLVETGDGkLIAADAKVVI 203
                                   589********998*******987 PP

>> CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   5.2e-07    0.0019      34      94 ..      31      95 ..       9     116 .. 0.84
   2 ?   -2.1   0.0      0.64   2.3e+03      36      59 ..     322     345 ..     293     357 .. 0.68

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 5.2e-07
                                  HHHH-SSEEEEETTCCTTTTE....EEESSHHHHHHHHHHHHHHHHHHHSTS-EEEEE--SSSEE CS
                   CPSase_L_D2 34 akeigyPviikaafglGGkGm....rvarneeelaelvkkalaeakaafgnkqvlvekslkgpke 94
                                  +k++  Pv +k+ + lGG+G     ++a+++eel+++v++ l++    ++  +vl+e +l+  +e
  gi|13541105|ref|NP_110793.1| 31 VKKFTNPVAVKSQILLGGRGKaggiKFAKTDEELKNAVSTLLSTKVRNMTVTKVLIEDMLNIKHE 95
                                  577788************97433339******************999**********99976555 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.64
                                   HH-SSEEEEETTCCTTTTEEEESS CS
                   CPSase_L_D2  36 eigyPviikaafglGGkGmrvarn 59 
                                   +i+ Pv+++ +     +G ++ ++
  gi|13541105|ref|NP_110793.1| 322 DIKIPVVVRLSGVHEVEGRKILQD 345
                                   588899999888777777777766 PP

>> GARS_A  Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   1.1e-06    0.0041       7      90 ..       9      91 ..       5     114 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.1e-06
                                  HHHHHHTT--B--EEEESSHHHHHHHHHHHSSSEEEEEESC-GGGT-EEEESSHHHHHHHHHHHCTS-TTCCCCSSEEEEE-- CS
                        GARS_A  7 kdllkkagiptaeyeaftdpeeakeyieeatakalVvKadglaagKgvivakseeealkavkeilekkkfGeagekvviEell 89
                                  kd+++++gip ++  ++++p+++k++ + +  k  ++   g     g++ ak+ ee  +av+ +l++k    + +kv+iE++l
  gi|13541105|ref|NP_110793.1|  9 KDIFREYGIPVPNGYVVSSPQDVKKFTNPVAVKSQIL-LGGRGKAGGIKFAKTDEELKNAVSTLLSTKVRNMTVTKVLIEDML 90
                                  99********************999987776666333.34444445899********************************99 PP

                                  - CS
                        GARS_A 90 e 90
                                  +
  gi|13541105|ref|NP_110793.1| 91 N 91
                                  7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (365 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-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: 00:00:00.45
# Mc/sec: 2424.73
//
Query:       gi|13541106|ref|NP_110794.1|  [L=406]
Description: hypothetical protein TVN0275 [Thermoplasma volcanium GSS1]
Scores for complete 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   83.7   6.6    2.4e-23   83.3   6.6    1.1  1  Cas_DxTHG  CRISPR-associated (Cas) DxTHG family


Domain annotation for each model (and alignments):
>> Cas_DxTHG  CRISPR-associated (Cas) DxTHG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.3   6.6   1.4e-27   2.4e-23       2     359 .]       4     376 ..       3     376 .. 0.63

  Alignments for each domain:
  == domain 1  score: 83.3 bits;  conditional E-value: 1.4e-27
                     Cas_DxTHG   2 lisflGt.gnykevkYelkeeeeeeketsfvqeallellaekedpdkvvilltdtladkeaeek..eeaak.lkeeleell 78 
                                   l++++G+ +ny+evkY+  +       + + + a  + ++e+ + d++++ +  +l++ +++++   ++ + + + ++++l
  gi|13541106|ref|NP_110794.1|   4 LFAPIGDpKNYDEVKYR-ID------GKDYPSNASFKVIKEALNMDETIVYAGLSLCT-NSNYNdyVSCSNyISNLVKDKL 76 
                                   89***************.32......46788888888888888999************.4444437557787888888777 PP

                     Cas_DxTHG  79 eiekvdveiipgggte........ee.lwe.ifekllekleen..deiilDiThGfrylPvla.....llalaylrnvk.. 140
                                   ++++ +v++ p++           +  +++ i+++ l++le++  dei++DiThG++y+P+la     l++  yl   +  
  gi|13541106|ref|NP_110794.1|  77 QLNDESVIVAPNIYGDkftqpdgkNTlYFDfIYYNTLKILENEkpDEIYIDITHGINYMPLLAtdairLATYTYLLGRNsi 157
                                   788999*******999777777766655559999*****99999**********************997777776544424 PP

                     Cas_DxTHG 141 nltikgiyYgafkeeeedPil...............dlteflels.dwltaverflktgdaeklaellrekkekkkeklkk 205
                                   +l i ++          +P++               +    l ++   l  +  fl++++++++ + +             
  gi|13541106|ref|NP_110794.1| 158 DLAIFNS----------EPVIkgysgpynianvyseR----LYVRqALLSVLMPFLSNENKNNITNKV------------- 211
                                   5888888..........**********9777754331....222212334444999999999999999............. PP

                     Cas_DxTHG 206 lkklkeklkkeleefskalelirp.lellekaeklekeiveklkeeleei.esleeeesakplel................ 268
                                   lk +++++++++++ ++al  +   + ll +             +e+e++ +s e++ ++  +++                
  gi|13541106|ref|NP_110794.1| 212 LKGINNCNSDLIYSNANALFSGIFpFVLL-SR------------REIEQCiKSVERKIKILDYNNfgiefntshkpvykdt 279
                                   88999999999998888888876323333.22............2222222222222222222223333333444444488 PP

                     Cas_DxTHG 269 ..........lldeikkklekf.........lkkq.ikwclekgliqqaltllreliislllegedilnkkkrreeieeel 329
                                             l       +ek+         +k   ik ++++  +        e+i +l++++ d ++k +++++  + l
  gi|13541106|ref|NP_110794.1| 280 mpielsylhsL----LYIIEKIignmpdsscVKISdIKDLAKRFST-------SETISKLVESEIDSIEKLQNISDKPQLL 349
                                   88888845543....4444444333343333111122222222222.......2222111222334444444445555555 PP

                     Cas_DxTHG 330 knlskvekksseekeek..lsniRNdiaHaGl 359
                                        v+k s+++ +++   +++RN +aH+G+
  gi|13541106|ref|NP_110794.1| 350 ----AVIKHSQSS-PKSicQADKRNLLAHGGF 376
                                   ....333333332.222467***********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (406 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       782  (0.0436165); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.25s 00:00:00.82 Elapsed: 00:00:00.43
# Mc/sec: 2814.44
//
Query:       gi|13541107|ref|NP_110795.1|  [L=179]
Description: hypothetical protein TVN0276 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.3e-13   49.6   0.1      7e-13   49.2   0.1    1.1  1  AAA_17           AAA domain
      2e-12   47.8   0.1    2.7e-12   47.3   0.1    1.2  1  AAA_18           AAA domain
     0.0041   17.3   0.0     0.0057   16.8   0.0    1.2  1  AAA_33           AAA domain
  ------ inclusion threshold ------
      0.037   14.0   0.1      0.063   13.2   0.1    1.4  1  P-mevalo_kinase  Phosphomevalonate kinase


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 !   49.2   0.1   1.6e-16     7e-13       1     130 [.       5     126 ..       5     131 .. 0.80

  Alignments for each domain:
  == domain 1  score: 49.2 bits;  conditional E-value: 1.6e-16
                                   EE-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTTTSHSSHHHHCTSHHHH.HHHHHHHHHHHHHHHH.HSSEEEEEE- CS
                        AAA_17   1 lGgPGsGKgtqceklvekygfthlsaGdllreeakrgglakardemrklplee.kkelqkeaaekiaeea.kkkgvlvdgh 79 
                                   +G+PG+GK + + k+++ +gf  l +G  +re a+r+g  ++++e+ +   +e kk  +++ a++ ae+  +++  ++dg 
  gi|13541107|ref|NP_110795.1|   5 TGMPGAGKDEFV-KVARSLGFMDLHMGNTVREYASRNGIPDDDKEIGNFAASErKKFGMDIWARRTAEKIeSDELTVIDGV 84 
                                   7***********.**************************8888899876555514455677777888775255558****8 PP

                                   SEEEETTEEEESSHHHHHHHH..SEEEEEE--HHHHHHHHHHHTTST-TS- CS
                        AAA_17  80 prikeqagfldglpkevleelkpdaiilleadpeeilerrlkdrtrgrddd 130
                                     +ke++++++++ k    ++    ++ + a+ ++ ler lk+  r +d  
  gi|13541107|ref|NP_110795.1|  85 R-NKEEMDYFSKFSK----SI---YVVAIFANRKTRLERILKR-DRPDDIR 126
                                   6.7899999999997....45...7999*************94.4554544 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.3   0.1   6.1e-16   2.7e-12       1     119 [.       2     125 ..       2     140 .. 0.86

  Alignments for each domain:
  == domain 1  score: 47.3 bits;  conditional E-value: 6.1e-16
                        AAA_18   1 IlltGtpGvGKttlakeLskrlgf.....gvnlrdvakenglllevdpe.aldeskrldedkldklldaleenssaleegk 75 
                                   I++tG+pG+GK ++ k  +++ gf     g  +r++a+ ng+ +++ +   +  s+r + +++  + ++ e++ s     +
  gi|13541107|ref|NP_110795.1|   2 IIVTGMPGAGKDEFVKVARSL-GFmdlhmGNTVREYASRNGIPDDDKEIgNFAASERKKFGMDIWARRTAEKIES----DE 77 
                                   9****************9777.78899***********************8888999999998899999999866....67 PP

                        AAA_18  76 nlvidghlaeleseaakdikk....vvLtaspeelleRlekRgyeeak 119
                                     vidg++++ e +++ +  k    v + a+ +++leR+ kR++ ++ 
  gi|13541107|ref|NP_110795.1|  78 LTVIDGVRNKEEMDYFSKFSKsiyvVAIFANRKTRLERILKRDRPDDI 125
                                   77**********8877765557999*****************966544 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   1.3e-06    0.0057       1     125 [.       1     126 [.       1     137 [. 0.80

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.3e-06
                        AAA_33   1 lvllvGlpGsGKstlaerllkklg......avllssdtlrrrlfgtdqqskt..dytrvldrlyqilnelarkalsagrnv 73 
                                   ++++ G+pG+GK  +++ +++ lg      + ++++ + r+ +  +d++  +   + r ++ +  + +++a+k  s + +v
  gi|13541107|ref|NP_110795.1|   1 MIIVTGMPGAGKDEFVK-VARSLGfmdlhmGNTVREYASRNGIPDDDKEIGNfaASERKKFGMDIWARRTAEKIESDELTV 80 
                                   6899************9.799999988888888888888888888877755522333333446667778898777777776 PP

                        AAA_33  74 ildatnlsrrerarflklarrlgvpvrivvvetdeetlkeRlakRaangddr 125
                                   i   + ++++e++ f k+ +     + +v++ + ++t  eR+ kR ++ d r
  gi|13541107|ref|NP_110795.1|  81 I--DGVRNKEEMDYFSKFSK----SIYVVAIFANRKTRLERILKRDRPDDIR 126
                                   6..689999********999....799*******************997755 PP

>> P-mevalo_kinase  Phosphomevalonate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   1.4e-05     0.063      70     110 ..      57      95 ..      47      99 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.4e-05
               P-mevalo_kinase  70 krkkdpglFcraaiekieaakkdvliisDiRrktdleyfke 110
                                   ++k  + ++ r+  eki  ++ ++ +i+++R+k++++yf++
  gi|13541107|ref|NP_110795.1|  57 RKKFGMDIWARRTAEKI--ESDELTVIDGVRNKEEMDYFSK 95 
                                   34446778*******87..5567****************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (179 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1154.53
//
Query:       gi|13541108|ref|NP_110796.1|  [L=199]
Description: hypothetical protein TVN0277 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       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:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.50
# Mc/sec: 1196.70
//
Query:       gi|13541109|ref|NP_110797.1|  [L=75]
Description: hypothetical protein TVN0278 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       288  (0.0160634); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); 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 0.28s 00:00:00.70 Elapsed: 00:00:00.46
# Mc/sec: 490.05
//
Query:       gi|13541110|ref|NP_110798.1|  [L=90]
Description: RNAse P protein subunit RPR2 [Thermoplasma volcanium GSS1]
Scores for complete sequence (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   31.9   2.4    2.2e-07   31.1   2.4    1.5  1  Rpr2           RNAse P Rpr2/Rpp21/SNM1 subunit domain
  ------ inclusion threshold ------
       0.51   10.3   7.5       0.53   10.3   4.9    2.2  3  zinc_ribbon_4  zinc-ribbon domain


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 !   31.1   2.4   2.4e-11   2.2e-07      22      90 .]      28      81 ..      14      81 .. 0.87

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 2.4e-11
                                  HHHHHHHHHHHHHCT---SSTCCCTB-TTT--B--CTTTEEEEEE-SSS-E.........EEEEETTTT CS
                          Rpr2 22 rylakqlrevskkaqlrlppsvkrtvCkkCgsvlipgvtcsvrvenkskkkkkkkkkadvlvvtClaCg 90
                                  +++++ ++++ +++ + lp+++kr +CkkC++ +    +++vr+++            +v++vtCl+Cg
  gi|13541110|ref|NP_110798.1| 28 ERYIDLMERIGRRMDITLPQDIKRMYCKKCKKPY---KNVRVRLKK------------NVITVTCLECG 81
                                  78*****************************966...999999964............4789******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 ?   -0.9   0.0      0.18   1.6e+03      11      19 ..       7      15 ..       5      16 .. 0.84
   2 ?    6.2   1.1    0.0011       9.9      19      33 ..      45      59 ..      42      62 .. 0.72
   3 ?   10.3   4.9   5.9e-05      0.53       4      33 ..      53      82 ..      51      83 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.18
                 zinc_ribbon_4 11 kyeiddekl 19
                                  +y++++e+l
  gi|13541110|ref|NP_110798.1|  7 VYRVANERL 15
                                  8****9986 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0011
                 zinc_ribbon_4 19 lpakgvkvrCskCgh 33
                                  lp++++++ C+kC++
  gi|13541110|ref|NP_110798.1| 45 LPQDIKRMYCKKCKK 59
                                  677778888888865 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 5.9e-05
                 zinc_ribbon_4  4 tCpsCkakyeiddeklpakgvkvrCskCgh 33
                                   C++Ck+ y+    +l+++   v+C  Cg 
  gi|13541110|ref|NP_110798.1| 53 YCKKCKKPYKNVRVRLKKNVITVTCLECGD 82
                                  6********877779*************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       855  (0.0476881); expected 358.6 (0.02)
Passed bias filter:                      536  (0.0298957); 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: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 567.97
//
Query:       gi|13541111|ref|NP_110799.1|  [L=224]
Description: phosphoglycolate phosphatase [Thermoplasma volcanium GSS1]
Scores for complete sequence (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  100.5   0.4    4.4e-15   56.1   0.0    2.0  2  Hydrolase_3  haloacid dehalogenase-like hydrolase
    6.7e-09   35.6   0.0    1.8e-07   30.9   0.0    2.1  2  S6PP         Sucrose-6F-phosphate phosphohydrolase
    1.3e-07   32.2   2.4      0.045   14.1   0.0    3.3  3  HAD          haloacid dehalogenase-like hydrolase
    6.8e-06   26.5   3.0      0.041   14.2   0.0    3.0  2  Hydrolase    haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.017   15.2   0.1      0.069   13.3   0.0    2.0  2  Hydrolase_6  Haloacid dehalogenase-like hydrolase
      0.034   14.2   1.6        1.6    8.8   0.0    2.8  3  HAD_2        Haloacid dehalogenase-like hydrolase
      0.057   13.2   0.1      0.091   12.5   0.1    1.3  1  CAP_assoc_N  CAP-associated N-terminal
      0.062   13.7   1.4      0.086   13.3   0.6    1.7  2  DUF4367      Domain of unknown function (DUF4367)


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 !   42.8   0.1   2.3e-14     5e-11       1      99 [.       5     101 ..       5     110 .. 0.86
   2 !   56.1   0.0     2e-18   4.4e-15     156     245 ..     123     208 ..     108     216 .. 0.88

  Alignments for each domain:
  == domain 1  score: 42.8 bits;  conditional E-value: 2.3e-14
                                   EEEEIIIIIS-TTS---HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCCSEEEEGGGTEEECTTTEEEEE--B-H CS
                   Hydrolase_3   1 ialDlDGTLlnsdkkisektkeaikklkekgikvviATGRslravlpvleelgldlpvialNGaliddekgkilykstisk 81 
                                   +a+D+DGTL ++d  is +++e i+k+++kgi v + +G+ +  v  +   +g++ pv + NG++  + ++  + ++ +s+
  gi|13541111|ref|NP_110799.1|   5 VAIDVDGTLTDKDRLISTRAIEFIRKAEKKGIIVSLLSGNVIPVVYALKVFIGINGPVFGENGGVM-FDNDGSI-TKFFSN 83 
                                   79**************************************666666666667888***********.8888888.899999 PP

                                   HHHHHHHHHHHHTTCEEE CS
                   Hydrolase_3  82 edvkeiikllkennveil 99 
                                   e+ +++++ ++++     
  gi|13541111|ref|NP_110799.1|  84 EKTNSFLDEMSKKTSMRS 101
                                   999999999988874444 PP

  == domain 2  score: 56.1 bits;  conditional E-value: 2e-18
                                   HHHHHHHHHCTTTEEEEEESTTEEEEEETT-SHHHHHHHHHHHCT--GGGEEEEESSGGGHHHHHHSSEEEEETTS-HHHH CS
                   Hydrolase_3 156 elekelksklnklltitssskgyleimpkgvsKgtalkklakelnisleeviafGDgeNDieMLeaaglgvAmgnaseevk 236
                                    +++e +++      ++ +s++++ +m+kg +Kg a+k l ++++++ ee++++GD++ND++M+e   +  + +na+++vk
  gi|13541111|ref|NP_110799.1| 123 YVKAEAEKR----GLVVFYSGYSWHLMNKGEDKGFAVKILKEKYGLNYEEILVVGDSNNDMPMFELPVFKACPANATDNVK 199
                                   444444444....37999*************************************************************** PP

                                   HHSSEEE-- CS
                   Hydrolase_3 237 kaAdyvtks 245
                                   ka+d+v+ +
  gi|13541111|ref|NP_110799.1| 200 KASDFVSSY 208
                                   ******976 PP

>> S6PP  Sucrose-6F-phosphate phosphohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0      0.03        68       3      42 ..       3      42 ..       1      53 [. 0.78
   2 !   30.9   0.0   8.2e-11   1.8e-07     149     212 ..     134     197 ..     118     223 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.03
                                  EEEEE-TBTTTB.S-HHHHHHHHHHHH.GGGGGEEEEEE- CS
                          S6PP  3 lllvsdLDntlvdgdnealarlnelleaeerkdvllvfaT 42
                                  +l+++d+D+tl+d+d+    r  e+++++e+k + + + +
  gi|13541111|ref|NP_110799.1|  3 KLVAIDVDGTLTDKDRLISTRAIEFIRKAEKKGIIVSLLS 42
                                  58899*******9999988888787776777766665555 PP

  == domain 2  score: 30.9 bits;  conditional E-value: 8.2e-11
                                   EEEETTTEEEEEETT-SHHHHHHHHHHHHT--GGGEEEEE-SGGGHHHHTSSSEEEE-TT--HH CS
                          S6PP 149 viyssgkdlDvlPkraskgeAlryLakkleleleqilvcGdsgnDeellignvlgVvVgnaqee 212
                                   v++ sg    ++ k+ +kg A++ L +k++l+ e+ilv+Gds+nD  +++  v   + +na  +
  gi|13541111|ref|NP_110799.1| 134 VVFYSGYSWHLMNKGEDKGFAVKILKEKYGLNYEEILVVGDSNNDMPMFELPVFKACPANATDN 197
                                   67888888899999***********************************877777777776666 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.7     0.025        55       3      15 ..       7      19 ..       5      23 .. 0.84
   2 !   12.9   0.0   4.8e-05      0.11      85     139 ..      19      63 ..      16      86 .. 0.79
   3 !   14.1   0.0     2e-05     0.045     151     188 .]     148     183 ..     112     183 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.025
                           HAD  3 fDfDgTLldgdsl 15
                                   D+DgTL+d+d l
  gi|13541111|ref|NP_110799.1|  7 IDVDGTLTDKDRL 19
                                  6*********976 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 4.8e-05
                           HAD  85 lldpgalellaahraaGdrvvvvSgglrplvepllaelgadevlatelevddrlt 139
                                   l+   a e+++++ ++G+ v ++Sg+  p+v +l  + g    ++        ++
  gi|13541111|ref|NP_110799.1|  19 LISTRAIEFIRKAEKKGIIVSLLSGNVIPVVYALKVFIG----ING------PVF 63 
                                   5556899**************************999999....776......333 PP

  == domain 3  score: 14.1 bits;  conditional E-value: 2e-05
                           HAD 151 gegkvaalrewlaaegegidleevvayGDspsDlpllr 188
                                   ge+k  a++    +e++g+ +ee+ ++GDs +D+p+++
  gi|13541111|ref|NP_110799.1| 148 GEDKGFAVKI--LKEKYGLNYEEILVVGDSNNDMPMFE 183
                                   5555566666..899*********************86 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   1.5    0.0002      0.45       1      24 [.       2      29 ..       2     130 .. 0.79
   2 !   14.2   0.0   1.8e-05     0.041     176     207 ..     148     183 ..     125     184 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0002
                                  SSEEEEESBTTTBCHH....HHHHHHHH CS
                                  xxxxxxxxxxxxxxxx....xxxxxxxx RF
                     Hydrolase  1 iktvvfDkdGTLttge....psvedviv 24
                                  ik+v++D+dGTLt+       +  ++i+
  gi|13541111|ref|NP_110799.1|  2 IKLVAIDVDGTLTDKDrlisTRAIEFIR 29
                                  89***********988433333333333 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 1.8e-05
                                   HHHHHHHHHHHT....STGGGEEEEESSHHHHHHHH CS
                                   xxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxx RF
                     Hydrolase 176 pegkvaaireLq....gkpeevamVGDgvnDaaala 207
                                    e+k  a++ L+     + ee+++VGD+ nD+++++
  gi|13541111|ref|NP_110799.1| 148 GEDKGFAVKILKekygLNYEEILVVGDSNNDMPMFE 183
                                   566777777776444488***************985 PP

>> Hydrolase_6  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   3.1e-05     0.069       1      38 [.       5      43 ..       5      51 .. 0.84
   2 ?   -2.0   0.0       1.7   3.8e+03       3      12 ..      71      80 ..      69     112 .. 0.56

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.1e-05
                                  EEEESTTTSEETTEE-T.THHHHHHHHHHTT-EEEEEE- CS
                   Hydrolase_6  1 flfDidGvLwrgdkaip.gaaealnalraagkpvvllTN 38
                                  +++D+dG+L ++d++i   a e+++  +++g+ v ll+ 
  gi|13541111|ref|NP_110799.1|  5 VAIDVDGTLTDKDRLIStRAIEFIRKAEKKGIIVSLLSG 43
                                  579***********9962689999999999988888875 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.7
                                  EESTTTSEET CS
                   Hydrolase_6  3 fDidGvLwrg 12
                                  fD dG + ++
  gi|13541111|ref|NP_110799.1| 71 FDNDGSITKF 80
                                  6666655543 PP

>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.1     0.051   1.1e+02       4      18 ..       8      22 ..       5      39 .. 0.82
   2 ?   -0.3   0.0      0.44   9.8e+02      83     108 ..      85     110 ..      71     116 .. 0.75
   3 ?    8.8   0.0   0.00071       1.6     145     165 ..     159     179 ..     149     181 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.051
                         HAD_2  4 DlDgTlldteeliiq 18
                                  D+DgTl d+  li +
  gi|13541111|ref|NP_110799.1|  8 DVDGTLTDKDRLIST 22
                                  9********999865 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.44
                         HAD_2  83 gvkelLeeLkeagyklgivTsksrea 108
                                     +++L+e++++     i T+k rea
  gi|13541111|ref|NP_110799.1|  85 KTNSFLDEMSKKTSMRSIFTNKWREA 110
                                   45677888888888888888888776 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.00071
                         HAD_2 145 leklklkkeeviyvGDsptDi 165
                                    ek++l+ ee+++vGDs++D+
  gi|13541111|ref|NP_110799.1| 159 KEKYGLNYEEILVVGDSNNDM 179
                                   5789****************8 PP

>> CAP_assoc_N  CAP-associated N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1     4e-05     0.091      43     133 ..      72     162 ..      68     168 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4e-05
                   CAP_assoc_N  43 ed.gkVvtlytngeeia.ikpfkigesleevekklgipeeveveikkgsyrfelseedlnerplvkvdgtyatlffDqetn 121
                                   ++ g +++ ++n+++++   +++  +s+ +++++   +++  ++i+++++++   e +  +r lv +   y    +++ ++
  gi|13541111|ref|NP_110799.1|  72 DNdGSITKFFSNEKTNSfLDEMSKKTSMRSIFTNKWREASTGFDIDGKDVDYVKAEAE--KRGLVVFYSGYSWHLMNKGED 150
                                   55599***********************************************888887..********************* PP

                   CAP_assoc_N 122 kvtsvryldket 133
                                   k ++v++l+++ 
  gi|13541111|ref|NP_110799.1| 151 KGFAVKILKEKY 162
                                   ********9875 PP

>> DUF4367  Domain of unknown function (DUF4367)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.6   3.8e-05     0.086      20      98 ..      72     149 ..      64     160 .. 0.82
   2 ?   -3.3   0.0       5.6   1.2e+04      18      37 ..     197     214 ..     188     216 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.8e-05
                       DUF4367  20 edsesalleYkdengelisfsiskqskeesqklsidtedaevekieingikatyyekedgeyvlvwedegvvytlsg.ni 98 
                                   ++++s++ ++   n+++ sf  ++++k +  ++ +++    ++ ++i+g++  y++ e ++  lv+ + g++++l++   
  gi|13541111|ref|NP_110799.1|  72 DNDGSITKFF--SNEKTNSFLDEMSKKTSMRSIFTNKWREASTGFDIDGKDVDYVKAEAEKRGLVVFYSGYSWHLMNkGE 149
                                   7889999999..999999**966666666677777777779********************999999*******997444 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 5.6
                       DUF4367  18 isedsesalleYkdengeli 37 
                                    ++++++++  Y   +ge+i
  gi|13541111|ref|NP_110799.1| 197 NVKKASDFVSSY--SYGEEI 214
                                   456677788888..777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       513  (0.0286129); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.50
# Mc/sec: 1350.92
//
Query:       gi|13541112|ref|NP_110800.1|  [L=271]
Description: solute-binding protein [Thermoplasma volcanium GSS1]
Scores for complete 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-74  249.8   0.0    3.6e-74  249.6   0.0    1.0  1  VitK2_biosynth  Menaquinone biosynthesis
    0.00061   19.8   0.0     0.0015   18.5   0.0    1.6  2  NMT1            NMT1/THI5 like
  ------ inclusion threshold ------
      0.011   15.3   0.0      0.014   14.9   0.0    1.3  1  YhfZ_C          YhfZ C-terminal domain


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 !  249.6   0.0     6e-78   3.6e-74       2     265 ..       4     258 ..       3     259 .. 0.97

  Alignments for each domain:
  == domain 1  score: 249.6 bits;  conditional E-value: 6e-78
                                   EEEEESSHHHHHHHHHHHTTSS..SGCCEEEEEE-HHHHHHHHHTTS-SEEEEEHHHHTTCTTTEEEESEESCEEEESSSS CS
                VitK2_biosynth   2 rlGhspylNdlflfyaLvegkvdsegleveivledpetlnrallegelDvakiSsaayariaddyalLpdlsisalGrvyg 82 
                                    ++h+p+++d+f+fy+++egk+++  +++e v++d+etln++  eg+++v++iS+  y++++d y l +  s++++G  yg
  gi|13541112|ref|NP_110800.1|   4 MVAHTPDPDDAFMFYGMFEGKIRTS-NQYEQVIKDIETLNKESKEGKYEVTAISANGYVQVRDLYKLTR--SGASFGISYG 81 
                                   69********************999.59*****************************************..********** PP

                                   EEEEESS-CCC-SSS..T.EEEESTTTSHHHHHHHHHHCSTS----EEEEE-GGGHHHHHHTTS.SEEEEECCHHHTGGGG CS
                VitK2_biosynth  83 vllvskvpleelegel.gkrvalpgestTsvlLlrlllaeryglkprlvevpfdeieaavlege.dagLlIgesaltyaee 161
                                   +++v+++   e++  l ++r  +pg +t+s+lL+r++ +e+     ++ve++fdei++a+l+g+ dag+lI++++lt++++
  gi|13541112|ref|NP_110800.1|  82 PIVVARN---EID--LsKSRMGVPGFMTSSYLLYRMFGPEAK----EYVEIKFDEIPDAILTGKvDAGILIHDEQLTFQKR 153
                                   *****88...443..4467**********************8....*********************************** PP

                                   TTEEEEEHHHHHHHHH.SS-EEEEEEEEECCCHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHHCCSTTS.HHHHHHHHHHH CS
                VitK2_biosynth 162 glkkvlDLgelWeelt.glPlvlglwvvrrdlaaeaakeleealreSveyalahldevaeyaaeraqemddevlekhlelY 241
                                   glk+v D+  +W+  + +lP++lg +++r+dl++++++++  ++++S++ya+ah +e+++ya+++a+ +d +  ++++++Y
  gi|13541112|ref|NP_110800.1| 154 GLKEVFDIYSAWKSYAgNLPIPLGFNAIRKDLDEDTVNKFLYDFERSIRYAMAHEEEAVKYAMKYARYTDLDLERRFVRMY 234
                                   ****************56***************************************************99********** PP

                                   CSHHHHS-CHHHHHHHHHHHHHHH CS
                VitK2_biosynth 242 vnelsydlgeegragleeflelaa 265
                                   vnels+d+g+ gr++le ++++aa
  gi|13541112|ref|NP_110800.1| 235 VNELSIDFGDTGRKALELYYNRAA 258
                                   *********************996 PP

>> NMT1  NMT1/THI5 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       0.5     3e+03      41      57 ..      72      88 ..      64      93 .. 0.80
   2 !   18.5   0.0   2.5e-07    0.0015     119     216 .]     115     211 ..      91     211 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.5
                                  TS-SEEEE-HHHHHHHH CS
                          NMT1 41 gkadfgvsyqesllaar 57
                                    a fg+sy + ++a+ 
  gi|13541112|ref|NP_110800.1| 72 SGASFGISYGPIVVARN 88
                                  5689******9999875 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 2.5e-07
                                   GGG-EEEE-.TT-HHHHHHCTSSSEEECEETTTHHHHHHHTT--EEEE-GGGTT-----SEE.EEEEHHHHHH-HHHHHHH CS
                          NMT1 119 psdvtlvnvggtslakalltgkvDaaiggyenwegvelesegkelrifaladlgvpdyyslv.litnekllkenpelvkkF 198
                                   p++ + v++++++  +a+ltgkvDa+i  + + e+++ +++g +  ++ ++ +   +   ++ l  n    + ++++v kF
  gi|13541112|ref|NP_110800.1| 115 PEAKEYVEIKFDEIPDAILTGKVDAGI-LIHD-EQLTFQKRGLKEVFDIYSAWKSYAGNLPIpLGFNAIRKDLDEDTVNKF 193
                                   6667788998888888***********.8888.9*********99999999999864444441334444444488****** PP

                                   HHHHHHHHHHHHHSHHHH CS
                          NMT1 199 lrAlkkGyeyalahPeea 216
                                   l   ++++ ya+ah eea
  gi|13541112|ref|NP_110800.1| 194 LYDFERSIRYAMAHEEEA 211
                                   **************9998 PP

>> YhfZ_C  YhfZ C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   2.4e-06     0.014     130     168 ..     109     147 ..      52     164 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.4e-06
                        YhfZ_C 130 teaifegkdvelveisynqllelllkgkiDavvWnldev 168
                                     ++f  +  e+vei+++++++++l gk+Da +   de 
  gi|13541112|ref|NP_110800.1| 109 LYRMFGPEAKEYVEIKFDEIPDAILTGKVDAGILIHDEQ 147
                                   4567777888***********************988843 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); 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:                         3  (0.000167327); expected 0.2 (1e-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: 1794.63
//
Query:       gi|13541113|ref|NP_110801.1|  [L=260]
Description: hypothetical protein TVN0282 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1054  (0.0587874); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.61u 0.36s 00:00:00.97 Elapsed: 00:00:00.54
# Mc/sec: 1455.99
//
Query:       gi|13541114|ref|NP_110802.1|  [L=354]
Description: ABC-type Fe3+-siderophores transporter, permease component [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.5e-84  282.9  31.7    3.1e-84  282.6  31.7    1.0  1  FecCD            FecCD transport family
      4e-07   29.8  21.3    6.2e-07   29.2  19.2    2.2  2  ABC-3            ABC 3 transport family


Domain annotation for each model (and alignments):
>> FecCD  FecCD transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  282.6  31.7   3.5e-88   3.1e-84       1     312 []      25     346 ..      25     346 .. 0.98

  Alignments for each domain:
  == domain 1  score: 282.6 bits;  conditional E-value: 3.5e-88
                         FecCD   1 llllllllslllgavkispsevfeallgka...........dsleaeivlelrlprvlaallvGaaLavaGallQtvtrNp 70 
                                   ll+++ l+sl +g+v+++++++ e++ ++              ++  i+++lr p+++ +++vG  Lav G+++Q+++rNp
  gi|13541114|ref|NP_110802.1|  25 LLAFVSLISLGIGSVNVPLKNTAEIIWDQIpflnalhyfsvPYTQYAIITQLREPQIVGGIIVGSTLAVGGTVVQSIFRNP 105
                                   68999**********************99999988888877666667********************************** PP

                         FecCD  71 LadPsilGissgaalgavlalllllgslslfalplaaflgallalllvlllarkrkgasplkliLaGiavsallsaltsll 151
                                   + +P+i+Gissgaalgav++++l l  l+ ++l + af+++++++++v+ll+ ++++a p+ l+L+Gi +s+++s+++s+l
  gi|13541114|ref|NP_110802.1| 106 ITEPYIIGISSGAALGAVMTIALSLNFLGYYTLETNAFVFSIITVVIVYLLSFRHGRAPPTFLLLIGISLSFFASSIVSFL 186
                                   ***********************999******************************************************* PP

                         FecCD 152 llllneealesilfwllGslsgaswskvllllvllllllllllllarkldllalgdetAkslGvnvervrllllllvallt 232
                                   +++ n + + s +fwllGsl++ +w+++ +l++++ll+ +++++++++ld+l++gde A+s+Gvnver + +l++lv+l t
  gi|13541114|ref|NP_110802.1| 187 IFT-NVNLAGSEYFWLLGSLQTLNWQEISMLIPISLLTSIAIFFMRNELDALQMGDEHAHSIGVNVERSKAMLIALVTLST 266
                                   *99.99*************************************************************************** PP

                         FecCD 233 avavalvGpigFvGLivPhiarllvgadhrkllplsallGallllladllarlllsptelpvgivtaliGapffiylllr 312
                                   +++v+++G igFvGLi+Phi r+++g ++++++p+sal+Ga++l+la+ l ++++    +p+gi+t +iG+pffiyll r
  gi|13541114|ref|NP_110802.1| 267 SAVVSVSGLIGFVGLIMPHISRIIFGGSNKYVIPSSALFGAIFLILANDLTKVVVHGEVVPIGIITGIIGVPFFIYLLSR 346
                                   *****************************************************************************976 PP

>> ABC-3  ABC 3 transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2  19.2   6.9e-11   6.2e-07      41     225 ..     117     310 ..      79     313 .. 0.78
   2 ?    0.9   0.3     0.029   2.6e+02     113     140 ..     302     329 ..     289     345 .. 0.84

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 6.9e-11
                         ABC-3  41 aalpGvalayllgvn......lllgailvgliaavalellkrktklkedt...aigivlsvflalglvlvslikk..skvd 110
                                    a  G ++ ++l++n      l + a+++++i  v++ ll+ +   +  t   +igi ls+f a ++v + +  +   + +
  gi|13541114|ref|NP_110802.1| 117 GAALGAVMTIALSLNflgyytLETNAFVFSIITVVIVYLLSFRHGRAPPTfllLIGISLSFF-ASSIVSFLIFTNvnLAGS 196
                                   34445555555555555766677889999999888888887666655554222678877755.555554444444115555 PP

                         ABC-3 111 ldsyLfGniltisqedliliaiieavvllllllfwkelllitfdeelAkveglsvkllkllllalialavvvalqavGviL 191
                                      +L+G++ t++ +++ +++ i++++ +++++++ el ++ +  e+A+++g++v++ k +l+al+ l+ ++++ + G+i 
  gi|13541114|ref|NP_110802.1| 197 EYFWLLGSLQTLNWQEISMLIPISLLTSIAIFFMRNELDALQMGDEHAHSIGVNVERSKAMLIALVTLSTSAVVSVSGLIG 277
                                   55679*************************************************************************998 PP

                         ABC-3 192 vialliiPaatArrltrslesllivAillglvsv 225
                                    +  li+P +  + ++ s + ++  ++l+g++++
  gi|13541114|ref|NP_110802.1| 278 FVG-LIMPHISRIIFGGSNKYVIPSSALFGAIFL 310
                                   777.578988888888888888888888887765 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.029
                         ABC-3 113 syLfGniltisqedliliaiieavvlll 140
                                   s LfG i  i  +dl  +++   vv + 
  gi|13541114|ref|NP_110802.1| 302 SALFGAIFLILANDLTKVVVHGEVVPIG 329
                                   579***********99999887777554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (354 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       735  (0.040995); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.30s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 2247.44
//
Query:       gi|13541115|ref|NP_110803.1|  [L=321]
Description: ABC-type Fe3+-siderophores transporter, solute-binding component [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.4e-26   93.6   0.3    1.8e-26   93.2   0.3    1.1  1  Peripla_BP_2  Periplasmic binding protein


Domain annotation for each model (and alignments):
>> Peripla_BP_2  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.2   0.3     1e-30   1.8e-26       1     202 [.      53     249 ..      53     275 .. 0.90

  Alignments for each domain:
  == domain 1  score: 93.2 bits;  conditional E-value: 1e-30
                                   EEE-SHHHHHHHHHTT-GGGEEEB-GGG--GGGGGGT..TS-BSBESSSB-HHHHHHH--SEEEE-GGG...GGGHHHHHH CS
                  Peripla_BP_2   1 iaslspsvteillalGatdkvvgvdtttsdpldadkleeaivevgadgeidvEklaalkPDlvilskglgltdedeellks 81 
                                   i+sl ps+t  l+alGa++ +vg++t+t +p        +i+ vg+ +++++E+l+++ P  vi  +++ ++  + ++ + 
  gi|13541115|ref|NP_110803.1|  53 IVSLLPSITTNLYALGAEKDIVGISTYTTYPKNISL---KIPIVGQLDSVNYEELLNVSPQAVITIPSYYPQNVINKIVDM 130
                                   899***************************998863...9*****************************9*********** PP

                                   HS-EEE----TTSHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTS-TT....-EEEEEEEETTE..EEEE-TTST CS
                  Peripla_BP_2  82 giptvivessntgeslkeqiralgellgledeaeklvaeidsklaaaksaidse...kpkpvlvfggadeggyvvagsnsy 159
                                   gip+++v ++n+   ++ qi +lg ++g+e +a ++v+++ + la + ++++ +   ++k+v+++  + eggy  ag+ ++
  gi|13541115|ref|NP_110803.1| 131 GIPVIEVGQNNF-TQIEQQIFELGNITGTEGNASAIVNWMANSLAYLHTDANMLsngTEKTVFYLL-STEGGYWTAGNETF 209
                                   ***********8.************************************99999975555555555.6678********** PP

                                   TTHHHHTS--EESTTT--STT-EEE-HHHHHHH--SEEEEEEH CS
                  Peripla_BP_2 160 igdlldalgieniaaeskkseyeeisaEqilasdpdvifvsgr 202
                                   i+d++++++++nia e    +y +i+   i+++dp+v++ +  
  gi|13541115|ref|NP_110803.1| 210 INDFFRIADLRNIANE---TGYYTIPSSLIVKEDPEVVILDQY 249
                                   *************777...5888999999**********9877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       645  (0.0359752); 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:                         1  (5.57756e-05); expected 0.2 (1e-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 0.31s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 2053.87
//
Query:       gi|13541116|ref|NP_110804.1|  [L=431]
Description: arsenite transport permease [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     1e-103  347.9  40.7   1.3e-103  347.6  40.7    1.0  1  ArsB      Arsenical pump membrane protein
    1.2e-15   57.5  42.3    1.2e-15   57.5  42.3    2.0  2  CitMHS    Citrate transporter


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 !  347.6  40.7  1.4e-107  1.3e-103       2     421 ..       9     425 ..       8     427 .. 0.98

  Alignments for each domain:
  == domain 1  score: 347.6 bits;  conditional E-value: 1.4e-107
                          ArsB   2 avfiflltlvlviwqpknlsigwsacggavlaliagvvnfhdvltvtgivwnatlafvaiilislildnigffewaalhma 82 
                                   a ++f++tl+lv  +p ++ ig+ a  ga +++i g+    dv+ v  i+wn t++fvaii +sl+ld  gffe+ a++++
  gi|13541116|ref|NP_110804.1|   9 AAIVFIFTLILVTVRPWKIDIGYGALIGAFVSIILGISTPADVIKVWNIIWNPTFTFVAIIAMSLVLDYAGFFEYYAIRIS 89 
                                   5679999************************************************************************** PP

                          ArsB  83 kaakgygvrmfvyvsllgaivaalfandgaaliltpivlamvralhfneklvfpfiiasgfiadttslpfvvsnlvnivsa 163
                                   k a g g+++fv++ +lg++ aa+fandga l+ltpivl+++    + +k  + +i+a gfi+d++slpfv+snlvni+ +
  gi|13541116|ref|NP_110804.1|  90 KFAGGNGIKLFVFIVILGSLTAAFFANDGAVLVLTPIVLSIMDMTGIGKKGAVAYIMAIGFISDSSSLPFVISNLVNIIGS 170
                                   ********************************************************************************* PP

                          ArsB 164 dyfhitfidyasrmvvpylfsllasiivlylffrksipkrydltevkkpveaikdqnmfrlswyilgllligyfaseffsi 244
                                    yf i+f  ya  mv+p ++s+++s+ +l l++rk ip+ y++  + +p + ikd  +f+l++  + ++++ yf + f  +
  gi|13541116|ref|NP_110804.1| 171 GYFGISFASYAKVMVIPDIISVVSSLGLLLLYYRKDIPRIYQVESLPNPKNVIKDPLIFKLAFPFMAIVVLAYFLTSFDLV 251
                                   ********************************************************************************* PP

                          ArsB 245 pvsvvagsiaiifliaaqkspavhtkkvvkeapwaivffsigmyvvvygvrnagltdvlsdviqaaadqglfagtigmgfi 325
                                   pvs va   a i+++ a+ +  + t+ ++ eapw +v+fs+gmy+vvyg  + glt vl  v ++    g    t+  g++
  gi|13541116|ref|NP_110804.1| 252 PVSFVAVPAATILIVVARYNHRINTRSIIAEAPWQVVVFSLGMYIVVYGFGDNGLTSVLVHVTKSILLLGNPLSTVLAGLL 332
                                   ********************************************************************************* PP

                          ArsB 326 aailssimnnlptvmidalaiagtdthgmmrealiyanvigsdlgpkitpigslatllwlhvlshk.gmkiswgtyfktgi 405
                                      ++  mnnlp+vm+ al+i+  +        liyanvig+d+gpk tpigslatllw++ l +k g++i+   y+k g 
  gi|13541116|ref|NP_110804.1| 333 FGAMAGSMNNLPSVMMGALTISHLN----QNSFLIYANVIGNDIGPKFTPIGSLATLLWIYTLQRKhGVQITPIYYMKVGF 409
                                   *******************998655....55679****************************987659************* PP

                          ArsB 406 iltiptllitlvglyi 421
                                   i++ p l++tl+ ly 
  gi|13541116|ref|NP_110804.1| 410 IIAFPVLVLTLLSLYA 425
                                   **************96 PP

>> CitMHS  Citrate transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.5  42.3   1.4e-19   1.2e-15       8     283 ..      22     355 ..       7     369 .. 0.67
   2 ?   -0.5   4.4     0.061   5.4e+02     101     164 ..     351     424 ..     346     431 .] 0.51

  Alignments for each domain:
  == domain 1  score: 57.5 bits;  conditional E-value: 1.4e-19
                                   x....xxxxxxxxxxxxxx.xxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx RF
                        CitMHS   8 k....lrldvvallvlvll.vltiee.....alsgiaspiillllgamiigaaleetGlfdrlaakllrlaggkrd.llvl 77 
                                   +    +++   al+++ +  +l+i +      +  i ++ ++++++ + ++ +l+ +G+f++ a ++ ++agg+   l+v+
  gi|13541116|ref|NP_110804.1|  22 VrpwkIDIGYGALIGAFVSiILGISTpadviKVWNIIWNPTFTFVAIIAMSLVLDYAGFFEYYAIRISKFAGGNGIkLFVF 102
                                   24556777777777777767444444333432333555556**************************************** PP

                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxx............. RF
                        CitMHS  78 lvlltallsafvsndgvvlimipivlslakrlkklppl....lliplalaaniggaltpiGtpttraa............. 141
                                   +v+l  l +af+ ndg+vl+++pivls++  ++++       +++++++++   ++   i +     +             
  gi|13541116|ref|NP_110804.1| 103 IVILGSLTAAFFANDGAVLVLTPIVLSIMD-MTGIGKKgavaYIMAIGFISDSSSLPFVISNLVN--Iigsgyfgisfasy 180
                                   *****************************9.6888888877888888888888876666666622..12344444444444 PP

                                   ....................................xxxxxxxxxxxxxxx.............xxxxxxxxxxxxxxxxx RF
                        CitMHS 142 ....................................arpglslpnllllal.............llvgllplvllfmfgva 173
                                                                                                   ++ +++++vl++  + +
  gi|13541116|ref|NP_110804.1| 181 akvmvipdiisvvsslgllllyyrkdipriyqveslP-------------NpknvikdplifklAFPFMAIVVLAYFLTSF 248
                                   4444444333333333333333333333333333330.............0333333333333344444444444444444 PP

                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        CitMHS 174 lalpvnapkvkkqkaiieaiarsllpvatillla............ykkveWsvlllfaGvfllvgaleqtGilealadll 242
                                   + +pv +                ++p+atil+++            + + +W+v+++  G+ ++v ++++ G+   l++++
  gi|13541116|ref|NP_110804.1| 249 DLVPVSF---------------VAVPAATILIVVarynhrintrsiIAEAPWQVVVFSLGMYIVVYGFGDNGLTSVLVHVT 314
                                   5555554...............36666777766678888888888888********************************* PP

                                   xx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        CitMHS 243 ga....ggplvalalvlgliallsafisnvavaalmapialgmap 283
                                   ++    g+p ++ +l+ +l++++   ++n + +   + +al+++ 
  gi|13541116|ref|NP_110804.1| 315 KSilllGNP-LSTVLAGLLFGAMAGSMNNLPSV---MMGALTISH 355
                                   668876555.445788999999**********7...444444333 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.061
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........................xxx RF
                        CitMHS 101 ivlslakrlkklppllliplalaaniggaltpiGtpttraaarpglslpnlll.........................lal 156
                                   +++s  ++ + + ++   + ++++ ig  +tpiG             ++ l++                         ++l
  gi|13541116|ref|NP_110804.1| 351 LTISHLNQ-NSFLIY---ANVIGNDIGPKFTPIGSL-----------ATLLWIytlqrkhgvqitpiyymkvgfiiafPVL 416
                                   44444443.333333...478899999999999999...........3444444444555555555554444443444444 PP

                                   xxxxxxxx RF
                        CitMHS 157 llvgllpl 164
                                   +l++l   
  gi|13541116|ref|NP_110804.1| 417 VLTLLSLY 424
                                   44444333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (431 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       703  (0.0392102); expected 358.6 (0.02)
Passed bias filter:                      233  (0.0129957); 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):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.31s 00:00:00.93 Elapsed: 00:00:00.50
# Mc/sec: 2575.24
//
Query:       gi|13541117|ref|NP_110805.1|  [L=157]
Description: peroxiredoxin [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      6e-38  129.5   0.0    7.1e-38  129.3   0.0    1.1  1  AhpC-TSA    AhpC/TSA family
    1.5e-23   83.2   0.1    1.8e-23   82.9   0.1    1.0  1  Redoxin     Redoxin
     0.0037   17.2   0.0     0.0046   16.9   0.0    1.2  1  SCO1-SenC   SCO1/SenC
     0.0078   16.3   0.0      0.016   15.3   0.0    1.6  2  AhpC-TSA_2  AhpC/TSA antioxidant enzyme


Domain annotation for each model (and alignments):
>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.3   0.0   1.6e-41   7.1e-38       1     123 [.       5     133 ..       5     134 .. 0.98

  Alignments for each domain:
  == domain 1  score: 129.3 bits;  conditional E-value: 1.6e-41
                                   TTSB----EEESTTCEEEECHHHTTSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCHHHHHHHHH-H CS
                      AhpC-TSA   1 vgdkapdfelknadgetvslsdykgkpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvdspeshkkfiekes 81 
                                   v++kapdfe++++  +  +ls+++g+ vvl f+p++++ vCt+e++ +++ + +f + +++vig+svdsp+s+++f++k++
  gi|13541117|ref|NP_110805.1|   5 VNEKAPDFEAPDTALKMRKLSEFRGQNVVLAFFPGAFTSVCTKEMCTFRDSMANFNKFKAKVIGISVDSPFSLAEFAKKNN 85 
                                   689****************************************************************************** PP

                                   .SSEEEE-TTSHHHHHTT-EETT......TTECSCEEEEE-TTSBEEE CS
                      AhpC-TSA  82 lnfpllsDeegkvakaygvlkee......kglalratfvidkegkiry 123
                                   l+f+llsD++++++k+y+vl+++       ++  r++f+id +g++ry
  gi|13541117|ref|NP_110805.1|  86 LTFDLLSDSNREISKKYDVLHQNfagvpgLTASKRSVFIIDGDGIVRY 133
                                   *********************99*****999****************9 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.9   0.1     4e-27   1.8e-23       1     145 [.       4     148 ..       4     149 .. 0.87

  Alignments for each domain:
  == domain 1  score: 82.9 bits;  conditional E-value: 4e-27
                                   -TTSBB---ECCEETTCEEEEEHHHHTTSEEEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEEEEESSSHHHHHHHH CS
                       Redoxin   1 kagdkaPdftlplaatdgnsvslsefkgkkvvvnfvpgafcPtCsaehpyleklaellkekgvdvvavvadndafvkefwg 81 
                                   k+++kaPdf+ p+  t  +  +lsef+g++vv+ f+pgaf+ +C++e++ +++  + +++   +v+++++d+     ef++
  gi|13541117|ref|NP_110805.1|   4 KVNEKAPDFEAPD--TALKMRKLSEFRGQNVVLAFFPGAFTSVCTKEMCTFRDSMANFNKFKAKVIGISVDSPFSLAEFAK 82 
                                   6899******988..**********************************666665555888999***99999988****** PP

                                   HTT-TSEEEE-TTSHHHHHTT-TTEEE.GGG.....EEE-EEEEEEETTEEEEEEESSSCHTSTTSHHH CS
                       Redoxin  82 keglkfpvlsDgsaaftkalGlrleedaseg.....lrtpryavidedgkvvylevepepeteesnaea 145
                                   k++l+f +lsD + +++k++++    ++ +g        +++++id dg v+y  v ++p  +e++++a
  gi|13541117|ref|NP_110805.1|  83 KNNLTFDLLSDSNREISKKYDVL--HQNFAGvpgltASKRSVFIIDGDGIVRYAWVSDDPG-KEPDYKA 148
                                   *********************65..5555557788455556889999***********995.5888876 PP

>> SCO1-SenC  SCO1/SenC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0     1e-06    0.0046       3     132 ..      11     129 ..       9     131 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1e-06
                     SCO1-SenC   3 pFelvdqdgeavteedlegkpslvffgFthCpdvCpttlanmaevldalgeeaekvqplfiTvDPerDtpevlkeyleafd 83 
                                   +Fe  d+  + ++ ++++g+ +++ f+    ++vC++++ + ++ ++++++   k +++ i+v    D+p  l+e++++ +
  gi|13541117|ref|NP_110805.1|  11 DFEAPDTALKMRKLSEFRGQNVVLAFFPGAFTSVCTKEMCTFRDSMANFNKF--KAKVIGISV----DSPFSLAEFAKKNN 85 
                                   899999999*****************************************99..888999999....5899********** PP

                     SCO1-SenC  84 priigltGskeeiakaakefrvyvekvedeesdytvdHsssvyLvdpdg 132
                                     +  l++s+ ei+k   ++ v +++     +  +     sv+++d dg
  gi|13541117|ref|NP_110805.1|  86 LTFDLLSDSNREISK---KYDVLHQNFAGVPG--LTASKRSVFIIDGDG 129
                                   ********9998865...66666666666655..445566666666665 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 !   15.3   0.0   3.6e-06     0.016       7      50 ..      57     101 ..      51     120 .. 0.88
   2 ?   -2.5   0.0       1.2   5.5e+03      96     111 ..     122     137 ..     121     139 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3.6e-06
                    AhpC-TSA_2   7 peldaagvklvaigigdp.sakkFvkltgfpfelyvDpsaklyqa 50 
                                   + +++   k+++i++++p s+ +F+k ++  f+l+ D ++++ ++
  gi|13541117|ref|NP_110805.1|  57 ANFNKFKAKVIGISVDSPfSLAEFAKKNNLTFDLLSDSNREISKK 101
                                   666777889*******************************99876 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.2
                    AhpC-TSA_2  96 tflfdkqgelvyehrd 111
                                   +f++d +g ++y++  
  gi|13541117|ref|NP_110805.1| 122 VFIIDGDGIVRYAWVS 137
                                   6999999999999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       474  (0.0264376); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.57u 0.33s 00:00:00.89 Elapsed: 00:00:00.56
# Mc/sec: 845.88
//
Query:       gi|13541118|ref|NP_110806.1|  [L=436]
Description: adenylosuccinate synthetase [Thermoplasma volcanium GSS1]
Scores for complete 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-154  514.0   0.1   3.3e-154  513.8   0.1    1.0  1  Adenylsucc_synt  Adenylosuccinate synthetase
  ------ inclusion threshold ------
      0.034   14.8   0.0       0.15   12.7   0.0    2.0  2  Phage_int_SAM_2  Phage integrase, N-terminal
      0.071   13.2   0.0       0.14   12.3   0.0    1.4  1  IGR              IGR protein motif


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 !  513.8   0.1  5.5e-158  3.3e-154       2     419 .]      14     432 ..      13     432 .. 0.95

  Alignments for each domain:
  == domain 1  score: 513.8 bits;  conditional E-value: 5.5e-158
                                   EEEE-SSS-S-HHHHHHHHHTT-SEEEE-SB-TTSSEEEEETTEEEEESSS-GGGGSTT-EEEE-TTBEE-HHHHHHHHTT CS
               Adenylsucc_synt   2 vvvGaqwGDEGKGkivDllaeeadvvvRfqGGanAGHtvvvdgkkyklhllpSGilnpgvvnviGngvvvdpealleEiee 82 
                                   vvvG+q+GDEGKGki+D+l+e++dvvvRf+GG nAGHtvvv++++yk+hllpSG l+++ v v+G+g+v+dp++l++Eie 
  gi|13541118|ref|NP_110806.1|  14 VVVGLQFGDEGKGKITDFLSESYDVVVRFNGGTNAGHTVVVGNETYKFHLLPSGSLRTK-VVVLGSGMVIDPQSLISEIEI 93 
                                   9*******************************************************865.55******************* PP

                                   SS-TT......TEEEETTSEE--HHHHHHHHHHHHH----------TTHHHHHHHHHTT---BGGGGGSHHHHHHHHHHHH CS
               Adenylsucc_synt  83 leakgvelskerllisdrahlvlpyhkalDkleeaakgkkkiGtTkkGiGpayadkvarrgirvgdlldeeeleeklekll 163
                                   +++++ +l    +++s++ah+v+++hk lD  ee+ +++  iGtT +GiGp+y+dk+ar+g+r+ dlld +++ ekl+ ++
  gi|13541118|ref|NP_110806.1|  94 VKKNNSNL---AVVVSSNAHVVTKIHKYLDVEEEKIRSSMVIGTTAQGIGPTYEDKYARSGLRMIDLLDYKTIIEKLDIIY 171
                                   ***98877...8************************999****************************************** PP

                                   HHTHHHHHHT.....T-----HHHHHHHHHHHHGGGEE-HHHHHHHHHHTT--EEEE--S-GGG-TTTSSTTSS-SS--SH CS
               Adenylsucc_synt 164 elknkllekldk..eeleveelleellkyaerlkpyvvdtvallnealkegkkvLfEGaqgtllDidhGtYPfvTsSntta 242
                                   +++++ll++ +    +++ e+l++el +y ++lk+y+  t  l+n+ ++eg+++LfEGaqg+llD d+G+YP+vTsSnt++
  gi|13541118|ref|NP_110806.1| 172 RMHENLLSRSEFsdPSVR-ENLAKELYSYGQELKKYMYYTDILINKLYNEGRTILFEGAQGVLLDPDFGFYPYVTSSNTIS 251
                                   ******998755534555.88************************************************************ PP

                                   HHHHHHTT--GGGEEEEEEEEESSEEESSSS--TTB--SHHHHHHHHHTT-B-TTT--B-EEE-EEHHHHHHHHHHHT-SE CS
               Adenylsucc_synt 243 ggaltglglapkkidevlgvvKAyttrvGeGpfptelkdevgeklrekGkEfgtttgrpRrcGwlDlvllryavrvngvte 323
                                   ++ +tg+g++++ki++v+gv+KAy+++vG+Gpfptel+d+ ++k+r++G+E+gtttgrpRr+GwlD++ll+yav+++ v+e
  gi|13541118|ref|NP_110806.1| 252 ASSYTGTGFSMRKIKKVIGVAKAYVSKVGAGPFPTELNDDLAKKIRDAGGEYGTTTGRPRRVGWLDVPLLKYAVQIDDVDE 332
                                   ********************************************************************************* PP

                                   EEEE-GGGGTT-SEEEEEEEEEETTEEESS--S.....-GEEEEEEEEE--.S--TT-....--GGGS-HHHHHHHHHHHH CS
               Adenylsucc_synt 324 laltklDvldgldeikvcvaYkldgkeldefpasleelekvepvyeelpgWkedisgv....rsfedlpenakkyvefiee 400
                                   +altk+D+l  l++ikvc +Y+ldgk++d++p++++e+++v+p yee++gW +  s++     +  ++p+++++y++fiee
  gi|13541118|ref|NP_110806.1| 333 IALTKVDTLGILHTIKVCYSYELDGKQIDYIPKHISEVSRVKPLYEEFEGWGDLSSSLlhpkMRKWEIPQQLRRYIDFIEE 413
                                   ***************************************************65555546666444579************* PP

                                   HHTS-EEEEE-SSSTT-EE CS
               Adenylsucc_synt 401 llgvpvkiisvGpereqti 419
                                    +g pv+iis G++r++t+
  gi|13541118|ref|NP_110806.1| 414 QIGRPVTIISSGKDRSKTV 432
                                   ***************9986 PP

>> Phage_int_SAM_2  Phage integrase, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.97   5.8e+03      19      37 ..     160     178 ..     159     181 .. 0.89
   2 ?   12.7   0.0   2.5e-05      0.15       3      55 ..     287     339 ..     286     344 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.97
               Phage_int_SAM_2  19 ykTvndrerilqrlareLl 37 
                                   ykT  ++  i+ r+ ++Ll
  gi|13541118|ref|NP_110806.1| 160 YKTIIEKLDIIYRMHENLL 178
                                   9999999********9997 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 2.5e-05
               Phage_int_SAM_2   3 kLskdlkrlakqagGsykTvndrerilqrlareLlalniqvrdvkslKarHie 55 
                                   +L+ dl +  ++agG y+T   r r +  l+  Ll+  +q+ dv ++    ++
  gi|13541118|ref|NP_110806.1| 287 ELNDDLAKKIRDAGGEYGTTTGRPRRVGWLDVPLLKYAVQIDDVDEIALTKVD 339
                                   69999*999***********************************999776665 PP

>> IGR  IGR protein motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   2.4e-05      0.14      16      45 ..     378     408 ..     372     413 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.4e-05
                           IGR  16 ekfeswekLfe.lsskqlkelGipvrqRRYi 45 
                                   e fe w +L + l   ++++  ip + RRYi
  gi|13541118|ref|NP_110806.1| 378 EEFEGWGDLSSsLLHPKMRKWEIPQQLRRYI 408
                                   78999****998999***************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (436 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); 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: 0.69u 0.34s 00:00:01.03 Elapsed: 00:00:00.57
# Mc/sec: 2306.69
//
Query:       gi|13541119|ref|NP_110807.1|  [L=122]
Description: glycine cleavage system protein H [Thermoplasma volcanium GSS1]
Scores for complete 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-37  126.1   2.3    7.6e-37  125.9   2.3    1.0  1  GCV_H          Glycine cleavage H-protein
    0.00022   21.0   0.6    0.00035   20.3   0.2    1.6  2  Biotin_lipoyl  Biotin-requiring enzyme
  ------ inclusion threshold ------
      0.012   15.6   0.0      0.017   15.1   0.0    1.2  1  RnfC_N         RnfC Barrel sandwich hybrid domain


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 !  125.9   2.3   1.3e-40   7.6e-37       1     119 [.       8     121 ..       8     122 .] 0.94

  Alignments for each domain:
  == domain 1  score: 125.9 bits;  conditional E-value: 1.3e-40
                                   -EE-TTSEEEEEETT.EEEEEE-HHHHHHH-SEEEEE---TT-EE-TT-EEEEEEESS-EEEEE-SSSEEEEEE-GGGTT- CS
                         GCV_H   1 lyytkehewvkveedgvatvGitdfaqeelgdvvfvelpevgtkvkkgeslaavEsvKaasevyapvsGevvevNekleee 81 
                                   l+ytk hew kv++ g+atvGitd+aq+++ d+v+v+lpevg+k k g+ l ++EsvK+a +vy+p++Ge++evN++l+++
  gi|13541119|ref|NP_110807.1|   8 LKYTKTHEWYKVDN-GIATVGITDYAQSQMTDIVYVDLPEVGDKKKVGDVLLTIESVKSAEDVYSPLTGEITEVNQELTKH 87 
                                   79**********88.5***************************************************************** PP

                                   TTHHHH-TTTTT--EEEEES-GGGGGGSEEHHHHHHHH CS
                         GCV_H  82 peliNkdpyeegWliklklsnleeleeLlsaeeyekll 119
                                   pe iNkdpy   Wl+k+k+++   + e l+ae+y+kl+
  gi|13541119|ref|NP_110807.1|  88 PENINKDPY-GNWLVKMKVEK---EGEYLTAEQYRKLI 121
                                   *********.67******977...45567889998876 PP

>> Biotin_lipoyl  Biotin-requiring enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.2   5.8e-08   0.00035      22      59 ..      46      83 ..      31      87 .. 0.92
   2 ?   -3.0   0.0       1.1   6.8e+03      42      42 ..     106     106 ..      98     116 .. 0.52

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 5.8e-08
                                  STTCEE-TTSEEEEEECTTEEEEEEBSSSEEEEEESST CS
                 Biotin_lipoyl 22 kvGdkVkagqvlaeveamKmemeieapkaGvvkeilvk 59
                                  +vGdk k g+vl+++e+ K   ++ +p +G ++e+ ++
  gi|13541119|ref|NP_110807.1| 46 EVGDKKKVGDVLLTIESVKSAEDVYSPLTGEITEVNQE 83
                                  79********************************9876 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.1
                                   E CS
                 Biotin_lipoyl  42 e 42 
                                   e
  gi|13541119|ref|NP_110807.1| 106 E 106
                                   2 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 ?   15.1   0.0   2.9e-06     0.017      47      91 ..      46      91 ..      34      94 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.9e-06
                        RnfC_N 47 kvgdkVlkGqkiaeaegfvsa.pvhasvsGtVkaiekrlvahgsgv 91
                                  +vgdk + G+++ + e++ sa  v+++ +G+++++++ l++h++++
  gi|13541119|ref|NP_110807.1| 46 EVGDKKKVGDVLLTIESVKSAeDVYSPLTGEITEVNQELTKHPENI 91
                                  79**********99999777636*******************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       601  (0.0335211); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.32s 00:00:00.81 Elapsed: 00:00:00.51
# Mc/sec: 721.06
//
Query:       gi|13541120|ref|NP_110808.1|  [L=197]
Description: methyltransferase involved in cell division [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-43  149.3   0.0    1.3e-43  149.1   0.0    1.0  1  FtsJ             FtsJ-like methyltransferase
  ------ inclusion threshold ------
      0.063   13.1   0.0       0.11   12.4   0.0    1.4  1  Methyltransf_23  Methyltransferase domain
      0.067   13.4   0.0       0.11   12.7   0.0    1.3  1  Arteri_nsp7a     Arterivirus nonstructural protein 7 alpha


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 !  149.1   0.0   2.2e-47   1.3e-43       1     177 []      18     194 ..      18     194 .. 0.97

  Alignments for each domain:
  == domain 1  score: 149.1 bits;  conditional E-value: 2.2e-47
                                   CCCCHHHHHHHHHHHHT-S-TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSSHHHTTEEEECS-CCCSSHHHHHCH CS
                          FtsJ   1 yrsRsayKLleidekfklfkpgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpmaplpgvttiqgditdpetiekike 81 
                                   +rsR+a+KL+ ++++++++++g++v+++g++PGgw+qvl+    a  k++++Dlq+m+ + gv++i++di++++  + i +
  gi|13541120|ref|NP_110808.1|  18 LRSRAAFKLEFLLDRYRVVRKGDAVIEIGSSPGGWTQVLNSL--A-RKIISIDLQEMEEIAGVRFIRCDIFKETIFDDIDR 95 
                                   59*************************************999..3.79********************************* PP

                                   CHHH...SSEEEEEE--S-SS-CHHHHHHHHHCCCCHHHHCCHCCCCECCCEEEECCCHCCCHHHHHHHHHCCEEEEEEEE CS
                          FtsJ  82 alse...rkvdlvvsDgapdvsgvhdldeylqsqLllaalelalkllkpggtfvlkifrgeeteallkqlkkfFekvsvvk 159
                                   al e   +kvd vvsD   +vsg+ + d++++ q+ ++ +e+a++ l++gg+++lk f+g+ t+++++  +k F++ ++ k
  gi|13541120|ref|NP_110808.1|  96 ALREegiEKVDDVVSDAMAKVSGIPSRDHAVSYQIGQRVMEIAVRYLRNGGNVLLKQFQGDMTNDFIAIWRKNFSSYKISK 176
                                   **9999999*******999************************************************************** PP

                                   -SS--CCG-EEEEEEEEC CS
                          FtsJ 160 Pkssrsesseeflvcrgf 177
                                   P++sr +sse++++  gf
  gi|13541120|ref|NP_110808.1| 177 PPASRGSSSEIYIMFFGF 194
                                   *************98776 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   1.8e-05      0.11       4     119 ..      17     152 ..      10     174 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.8e-05
               Methyltransf_23   4 qreeelsdklerllpk...lraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae..kakkaqkdqfdeqeaaep 79 
                                   q++ +++ kle+ll++    r+g  v++iG   G +++vl     +++ +Dl  e+ eia    +++ +++ +        
  gi|13541120|ref|NP_110808.1|  17 QLRSRAAFKLEFLLDRyrvVRKGDAVIEIGSSPGGWTQVLNSLARKIISIDLQ-EMEEIAGvrFIRCDIFKET-------I 89 
                                   555666778899997766568889****************888889*****96.5677764444444444444.......1 PP

               Methyltransf_23  80 qgkfdlIvlrevlehvpdpp.......................ellrqiatllkpgGylllse 119
                                    + +d +   e++e v+d+                        +++  + ++l+ gG++ll  
  gi|13541120|ref|NP_110808.1|  90 FDDIDRALREEGIEKVDDVVsdamakvsgipsrdhavsyqigqRVMEIAVRYLRNGGNVLLKQ 152
                                   123344444555555555444555555555555555555555577777777777777777765 PP

>> Arteri_nsp7a  Arterivirus nonstructural protein 7 alpha
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   1.8e-05      0.11      67     129 ..      25      87 ..      10      88 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.8e-05
                  Arteri_nsp7a  67 kLedFaegvskelkpGDvvvllGkkpvgelvdikvgdkelv..lkpietrvvaGskcticevvke 129
                                   kL +F+    + ++ GD v+ +G++p g  +++     +++  +  +e + +aG+++  c++ ke
  gi|13541120|ref|NP_110808.1|  25 KL-EFLLDRYRVVRKGDAVIEIGSSP-GGWTQVLNSLARKIisIDLQEMEEIAGVRFIRCDIFKE 87 
                                   44.477788899************99.66666655555555125679999**********99887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       552  (0.0307881); expected 358.6 (0.02)
Passed bias filter:                      509  (0.0283898); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.52
# Mc/sec: 1140.74
//
Query:       gi|13541121|ref|NP_110809.1|  [L=208]
Description: hypothetical protein TVN0290 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       713  (0.039768); expected 358.6 (0.02)
Passed bias filter:                      517  (0.028836); 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: 0.50u 0.34s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 1287.20
//
Query:       gi|13541122|ref|NP_110810.1|  [L=312]
Description: hypothetical protein TVN0291 [Thermoplasma volcanium GSS1]
Scores for complete 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-07   29.0   2.0    1.6e-06   28.0   0.1    2.6  3  HTH_3       Helix-turn-helix
      3e-06   27.2   2.0    8.5e-06   25.7   1.3    2.3  2  HTH_19      Helix-turn-helix domain
     0.0044   17.3   0.2      0.016   15.6   0.0    2.0  2  HTH_31      Helix-turn-helix domain
  ------ inclusion threshold ------
      0.092   12.6   0.0       0.37   10.7   0.0    2.0  2  PTS_EIIA_2  Phosphoenolpyruvate-dependent sugar phosphotransf


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 ?   -2.1   0.1      0.96   4.3e+03      41      49 ..      64      72 ..      60      76 .. 0.79
   2 !   28.0   0.1   3.6e-10   1.6e-06       1      49 [.     133     180 ..     133     185 .. 0.93
   3 ?   -2.6   0.0       1.3   5.9e+03      38      48 ..     256     266 ..     255     267 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.96
                                  HHHHHHHHT CS
                         HTH_3 41 lkklakaLg 49
                                  l+klak L 
  gi|13541122|ref|NP_110810.1| 64 LIKLAKLLR 72
                                  789999886 PP

  == domain 2  score: 28.0 bits;  conditional E-value: 3.6e-10
                                   HHHHHHHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHHHT CS
                         HTH_3   1 lkelRkqlglsqeeLAeklGvsrstisriEnGernPsletlkklakaLg 49 
                                   l+e+R++l+ls+  ++ +lGvsr+++s +EnG ++ ++++ ++l + L+
  gi|13541122|ref|NP_110810.1| 133 LRERRNELNLSIGNISSYLGVSRRSVSLYENG-SAATIDIFIRLRNILK 180
                                   89******************************.88******99988775 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 1.3
                                   HHHHHHHHHHH CS
                         HTH_3  38 letlkklakaL 48 
                                   +++lkk+++++
  gi|13541122|ref|NP_110810.1| 256 VRILKKISDVF 266
                                   56899999998 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   1.3   1.9e-09   8.5e-06       1      55 [.     130     182 ..     130     219 .. 0.92
   2 ?   -3.2   0.0       1.9   8.7e+03      27      53 ..     241     267 ..     235     270 .. 0.54

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 1.9e-09
                        HTH_19   1 GerLkeaReelgltqeelaerlgisrskisaiEngkkdvpsaelllkiaealgid 55 
                                   Ge L+e R el+l++  +++ lg+sr++ s +Eng+   ++++ + ++ ++l+ d
  gi|13541122|ref|NP_110810.1| 130 GELLRERRNELNLSIGNISSYLGVSRRSVSLYENGSA--ATIDIFIRLRNILKAD 182
                                   89*********************************87..6668999998888876 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.9
                        HTH_19  27 skisaiEngkkdvps.aelllkiaealg 53 
                                   s i+a++++   +p+  + l+ki+  ++
  gi|13541122|ref|NP_110810.1| 241 SLIAALIGDAP-EPErVRILKKISDVFE 267
                                   55666665522.3332333477776666 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.1       2.5   1.1e+04      48      57 ..      65      74 ..      62      76 .. 0.63
   2 !   15.6   0.0   3.5e-06     0.016       3      39 ..     130     166 ..     130     186 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 2.5
                        HTH_31 48 ealaralgld 57
                                   +la +l+++
  gi|13541122|ref|NP_110810.1| 65 IKLAKLLRAT 74
                                  5667777665 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 3.5e-06
                        HTH_31   3 GalLralReraGLsqeevAerlgvsestlsrlEqGrr 39 
                                   G+lLr++R++ +Ls       lgvs+  +s +E+G  
  gi|13541122|ref|NP_110810.1| 130 GELLRERRNELNLSIGNISSYLGVSRRSVSLYENGSA 166
                                   89*********************************86 PP

>> PTS_EIIA_2  Phosphoenolpyruvate-dependent sugar phosphotransferase system, EIIA 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0         1   4.5e+03      17      33 ..       5      21 ..       3      26 .. 0.69
   2 ?   10.7   0.0   8.3e-05      0.37      81     125 ..     228     272 ..     225     281 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1
                                  HHHHHHHHHHHHHHTTS CS
                    PTS_EIIA_2 17 keeaieqlaqklaeaga 33
                                  +e +i +l ++l+e+g+
  gi|13541122|ref|NP_110810.1|  5 REALISKLMNMLVENGF 21
                                  56667777777777764 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 8.3e-05
                                   EEEE-T-GCC-CEEEEEEEE-SSCHH.HHHHHHHHHHHHCSCCHH CS
                    PTS_EIIA_2  81 epvdfeasdgkpvklifllalpekdaehlkilaqLaellkdeefv 125
                                    p d  a+d ++++li +l+   ++ e ++il++++++++d+ f+
  gi|13541122|ref|NP_110810.1| 228 VPFDIVAKDSDEISLIAALIGDAPEPERVRILKKISDVFEDDAFL 272
                                   455555999**************9999**************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       468  (0.026103); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); 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: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1974.68
//
Query:       gi|13541123|ref|NP_110811.1|  [L=148]
Description: Fe2+ uptake regulation protein [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-24   86.1   0.0    2.3e-24   85.8   0.0    1.1  1  FUR              Ferric uptake regulator family
  ------ inclusion threshold ------
      0.015   14.8   1.0       0.77    9.3   0.1    2.3  2  TF_Zn_Ribbon     TFIIB zinc-binding
      0.052   13.7   0.0      0.082   13.1   0.0    1.3  1  TRAM_2           TRAM domain
      0.058   13.0   1.1       0.17   11.5   1.1    1.7  1  Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
       0.12   12.5   0.8        6.7    6.9   0.1    2.3  2  zf-UDP           Zinc-binding RING-finger
        1.3    8.5   4.2         21    4.6   4.2    2.5  1  DNAP_B_exo_N     DNA polymerase family B exonuclease domain, 


Domain annotation for each model (and alignments):
>> FUR  Ferric uptake regulator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.8   0.0   7.7e-28   2.3e-24       2      99 ..      12     106 ..      11     126 .. 0.89

  Alignments for each domain:
  == domain 1  score: 85.8 bits;  conditional E-value: 7.7e-28
                                   TTHCHHHHHHHHHHHHHHHSSSBEHHHHHHHHHHTTTT--HHHHHHHHHHHHHTTSEEEEEETTSEEEEEESSSSSEEEEE CS
                           FUR   2 aglklTkqRekilevlekseehlsaeevykelkeedpeislaTVYrtLklleeaglvkelefedgesryelakkehhdhli 82 
                                   ag+k+T+qR++++e+l+k + h++a++vyke+++  p+i laTVY++Lk ++++  +++++++ g++ +e +  e h++l+
  gi|13541123|ref|NP_110811.1|  12 AGYKITPQRLAVIEYLKKGPGHFTANDVYKEIRKSIPTITLATVYNILKAFADVRCINSFDVD-GTTWFENE-VELHANLM 90 
                                   79************************************************************9.999***99.6******* PP

                                   ETTT--EEEE--HHHHH CS
                           FUR  83 cekCgkviefkddeiek 99 
                                   c+ Cg++ ++k d+ ek
  gi|13541123|ref|NP_110811.1|  91 CKVCGNIVDIKIDK-EK 106
                                   *********99763.33 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.1   0.00026      0.77      17      37 ..      86     105 ..      75     108 .. 0.81
   2 ?    4.0   0.1     0.012        35       2      14 ..     129     140 ..     128     143 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00026
                                   TTCEEESSSSBEEEECCCCCC CS
                  TF_Zn_Ribbon  17 rgelvCtdCGlVlednsideg 37 
                                   +++l C+ CG++++   id++
  gi|13541123|ref|NP_110811.1|  86 HANLMCKVCGNIVD-IKIDKE 105
                                   57899*******96.557766 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.012
                                   EETTTTCEECHEE CS
                  TF_Zn_Ribbon   2 kCPnCgstnlveD 14 
                                   +CP C+ ++ +eD
  gi|13541123|ref|NP_110811.1| 129 VCPSCKARQ-EED 140
                                   688888763.655 PP

>> TRAM_2  TRAM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   2.7e-05     0.082      24      62 ..      69     113 ..      66     114 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.7e-05
                                   S-TTTS--EEEES---T.........T-EEEEEEEEEETTEEEEE CS
                        TRAM_2  24 dAPEvDgevyvtgaekl.sk.....vGdfvkvkItdadeyDLiGe 62 
                                   ++ +vDg++ ++++ +l ++     +G++v++kI++ +   L+Ge
  gi|13541123|ref|NP_110811.1|  69 NSFDVDGTTWFENEVELhANlmckvCGNIVDIKIDKEKLIKLLGE 113
                                   5779********999886669**************9999999997 PP

>> Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   1.1   5.7e-05      0.17       9      18 ..      91     100 ..      88     101 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 5.7e-05
                                   -TTT--EEEE CS
               Desulfoferrod_N   9 CevCGniVeV 18 
                                   C+vCGniV +
  gi|13541123|ref|NP_110811.1|  91 CKVCGNIVDI 100
                                   ********87 PP

>> zf-UDP  Zinc-binding RING-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.1    0.0023       6.7       8      27 ..      88     107 ..      82     113 .. 0.83
   2 ?    4.0   0.1     0.019        56      52      66 ..     129     143 ..     125     148 .] 0.75

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0023
                        zf-UDP   8 gqiCqiCgddvgltedgelF 27 
                                   + +C++Cg+ v+++ d+e  
  gi|13541123|ref|NP_110811.1|  88 NLMCKVCGNIVDIKIDKEKL 107
                                   568*********99998865 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.019
                        zf-UDP  52 sCPqCktrykrlkgs 66 
                                   +CP Ck+r +    s
  gi|13541123|ref|NP_110811.1| 129 VCPSCKARQEEDMRS 143
                                   8******98776555 PP

>> DNAP_B_exo_N  DNA polymerase family B exonuclease domain, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   4.2     0.007        21       2      11 ..      64      81 ..      63      86 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.007
                  DNAP_B_exo_N  2 dikClN........WFEn 11
                                  d++C+N        WFEn
  gi|13541123|ref|NP_110811.1| 64 DVRCINsfdvdgttWFEN 81
                                  99****777777778887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       759  (0.0423336); expected 358.6 (0.02)
Passed bias filter:                      586  (0.0326845); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-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: 00:00:00.47
# Mc/sec: 956.31
//
Query:       gi|13541124|ref|NP_110812.1|  [L=310]
Description: GMP synthase subunit B [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-33  115.2   0.0    2.5e-33  114.0   0.0    1.7  1  GMP_synt_C    GMP synthase C terminal domain
    1.3e-06   27.8   0.1    1.9e-05   23.9   0.0    2.1  2  NAD_synthase  NAD synthase
    1.3e-05   24.8   0.0    0.00032   20.3   0.0    2.1  1  QueC          Queuosine biosynthesis protein QueC
    2.6e-05   24.0   0.0    3.9e-05   23.5   0.0    1.2  1  ATP_bind_3    PP-loop family
     0.0034   17.5   0.0     0.0049   16.9   0.0    1.2  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 !  114.0   0.0   6.9e-37   2.5e-33       9      92 .]     226     309 ..     217     309 .. 0.96

  Alignments for each domain:
  == domain 1  score: 114.0 bits;  conditional E-value: 6.9e-37
                                   GGGSSEEEEEEEEEEE----------EEEEEEEEE---------B----HHHHHHHHHHHHHHSTT---EEEE---TTTS- CS
                    GMP_synt_C   9 ykkiwQafavllpvksvGvmgdkRtyeyvvalRaveseDamtadvaelpyevLekissrivnevkgvnrvvyditskPpat 89 
                                   +++ wQ+favllpv+++Gv+gd+R+y+ +v +R++e++Damt ++++  +++Le+is+ i++e++++nrvvydit+kPpat
  gi|13541124|ref|NP_110812.1| 226 ESRPWQYFAVLLPVRTTGVHGDRRAYGLTVGIRMIETTDAMTGTFSKPSWDLLEDISNTITDEIPEINRVVYDITNKPPAT 306
                                   5677***************************************************************************** PP

                                   S-- CS
                    GMP_synt_C  90 iEw 92 
                                   iEw
  gi|13541124|ref|NP_110812.1| 307 IEW 309
                                   *** PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.0   5.3e-09   1.9e-05       7      85 ..       8      85 ..       3     103 .. 0.87
   2 ?    1.6   0.0     0.035   1.3e+02     148     172 ..     160     184 ..     154     216 .. 0.89

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 5.3e-09
                                  HHHHHHHHHCTTSEEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--SSSTTHHHHHHHHHHHHHHTSEEEE---HHHH CS
                  NAD_synthase  7 dflkeyvkkagakgvvlGlSGGvDSslvaalavkalgkenvlalllPssvsseedvedalalaenlgievktidikpiv 85
                                    +k++++++   ++++ +SGG+DSsl + la ++l  +n l + + +    ++++   + + e+ ++++  +d +++ 
  gi|13541124|ref|NP_110812.1|  8 SRIKDNIRNSIKGKAIIAVSGGQDSSLLSLLASEVL-GNNLLCVFIDTGLLRKNETGRVKDFFEKHSMNYVIVDAADTF 85
                                  56888999999999**********************.67999****999999******************999988765 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.035
                                   BETTTTS-HHHHHHHHHHTT--HHH CS
                  NAD_synthase 148 lapiaellKtevkeLakelnvPerv 172
                                   ++p+ + +K e++ ++kel+ P  +
  gi|13541124|ref|NP_110812.1| 160 VEPLRDYYKDEIRGMSKELGLPTDI 184
                                   579*******************987 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   8.9e-08   0.00032       1     177 [.      21     182 ..      21     185 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 8.9e-08
                                   EEEEE--SSHHHHHHHHHHHHH.-SEEEEEEEESS-TTSHHHHHHHHHHHHT--.-EEEEE-GGGGGGSCGGG-------- CS
                          QueC   1 kavvllSGGlDSttvlalakke.gkevealtfdYgqrhkkeleaakkiakelgveehkildldllkelggsaLtdeeievp 80 
                                   ka++ +SGG+DS+ + +la++  g+++ ++ +d g  +k+e+  +k++++++ + +  i+d          + +++ + v+
  gi|13541124|ref|NP_110812.1|  21 KAIIAVSGGQDSSLLSLLASEVlGNNLLCVFIDTGLLRKNETGRVKDFFEKHSM-NYVIVDAA-------DTFINNLKGVT 93 
                                   79************9999988626999***************************.77787776.......45555556677 PP

                                   ---...--------TTHHHHHHHHHHHHHHHHT-SEEEE---S-STT--GGGSHHHHHHHHHHHHHHHTS--EEE-TTTT- CS
                          QueC  81 keeleeeelpntfVpaRNliflslaasyaealgaeaiiiGvneedfsgYPDcrdefvkalnkalnlgedkkieieaPlidl 161
                                   + e +++ + +tf++        + +  a++ gae ++ G  + d       +++++k+ +++  l +d k++++ Pl d 
  gi|13541124|ref|NP_110812.1|  94 DPEEKRKIIGKTFID--------VLSEQAQNFGAEYLLQGTIAPDWIESGGQKRDTIKSHHNVGGLPKDMKLKLVEPLRDY 166
                                   766777888888876........5678899*************************************************** PP

                                   -HHHHHHHHHHTTHHH CS
                          QueC 162 sKaeivklgkelgvpl 177
                                    K ei  ++kelg+p+
  gi|13541124|ref|NP_110812.1| 167 YKDEIRGMSKELGLPT 182
                                   *************875 PP

>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0   1.1e-08   3.9e-05       2     158 ..      22     177 ..      21     183 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 1.1e-08
                                   EEEE--SCHHHHHHHHHHHHHCTTTTTEEEEEEEE-SSSTCHHHHHHHHHHHHHHTT-EEEEEE--H...HHCTTSTCCCH CS
                    ATP_bind_3   2 vlvAvSgGlDSmaLllllaklkkklgiklvaihvdhglreeskeeaelvkelckklnikleiekvdv...akkkgknleea 79 
                                   +++AvSgG DS +L ll+ +    lg +l ++ +d gl    k+e+  vk++ +k++++++i ++     ++ kg +  e+
  gi|13541124|ref|NP_110812.1|  22 AIIAVSGGQDSSLLSLLASEV---LGNNLLCVFIDTGLLR--KNETGRVKDFFEKHSMNYVIVDAADtfiNNLKGVTDPEE 97 
                                   79**********999999888...56699******99964..567788999999999998887766667766666666666 PP

                                   HHHH....HHHHHHHCHHCCT.CEEE---BHHHHHHHHHHHHCCT--CCHHH-S-SEEEETTCCEE-CCCT--HHHHHHHH CS
                    ATP_bind_3  80 ARel....RYevlkealkkegievlllAhhadDqaEtfllrlargsglaglagikeaseiasirlvRPlLkvskeeleeyl 156
                                    R++      +vl+e +++ g+e+ll +  a D +E    +    ++ +++ g+++     + +lv Pl +++k+e++ + 
  gi|13541124|ref|NP_110812.1|  98 KRKIigktFIDVLSEQAQNFGAEYLLQGTIAPDWIESGGQKRDTIKSHHNVGGLPKDM---KLKLVEPLRDYYKDEIRGMS 175
                                   77652221568899999999******************99999999999999999977...799*************9887 PP

                                   HH CS
                    ATP_bind_3 157 ke 158
                                   ke
  gi|13541124|ref|NP_110812.1| 176 KE 177
                                   76 PP

>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   1.4e-06    0.0049       2      61 ..      22      82 ..      21     115 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.4e-06
                                  EEEE--SSCTCHHHHHHHHHHCTTH.EEEEEE-STB-HHHHHHHHHHHHHTT-EEEEEE-S CS
                   PAPS_reduct  2 lvvsvsgGkdslVllhLalkafkpv.pvvfvdtghefpetiefvdeleeryglrlkvyepe 61
                                   +++vsgG ds+ l  La++++ +    vf+dtg   ++ +  v+++ e+  ++  +++  
  gi|13541124|ref|NP_110812.1| 22 AIIAVSGGQDSSLLSLLASEVLGNNlLCVFIDTGLLRKNETGRVKDFFEKHSMNYVIVDAA 82
                                  5799******************99637*******987665555555555555665554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-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: 00:00:00.47
# Mc/sec: 1971.87
//
Query:       gi|13541125|ref|NP_110813.1|  [L=105]
Description: hypothetical protein TVN0294 [Thermoplasma volcanium GSS1]
Scores for complete sequence (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    8.2  22.2       0.28   11.5  10.4    2.2  2  DUF4064    Protein of unknown function (DUF4064)
          9    5.6   7.3       0.97    8.7   2.1    1.7  2  SLATT_5    SMODS and SLOG-associating 2TM effector domain fam
        9.8    6.4  14.2         12    6.1   4.9    2.6  2  DUF2613    Protein of unknown function (DUF2613)


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 ?   11.5  10.4   4.6e-05      0.28      60     102 ..      13      55 ..       8      56 .. 0.92
   2 ?    2.8   3.9     0.023   1.4e+02      66      82 ..      81      97 ..      69     105 .] 0.48

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4.6e-05
                       DUF4064  60 llivlgvialiaivlgivgalllkknkkvsGilfiiaailslf 102
                                   ll++l+++al +i+lgi+ a++ +++++v+G+ ++++++++++
  gi|13541125|ref|NP_110813.1|  13 LLVILALLALSLIILGILTAYFGSGKSRVAGAAILVIGLVVAV 55 
                                   78899999******************************99875 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.023
                       DUF4064 66 vialiaivlgivgalll 82
                                  ++ ++a+v+g+v  ll+
  gi|13541125|ref|NP_110813.1| 81 IFYVVAAVIGVVIGLLV 97
                                  22333333333332222 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 ?    8.7   2.1   0.00016      0.97      32      74 ..      12      56 ..       9      63 .. 0.91
   2 ?   -0.4   0.3       0.1   6.1e+02      64      81 ..      79      96 ..      63     101 .. 0.59

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00016
                       SLATT_5 32 lstfslsllSvylivlslls..nkssestinenlldflsiilSil 74
                                  +++ +l+ll+++li+l +l+  + s +s   ++++ +++++++++
  gi|13541125|ref|NP_110813.1| 12 FLLVILALLALSLIILGILTayFGSGKSRVAGAAILVIGLVVAVI 56
                                  67889***************9999999**************9998 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.1
                       SLATT_5 64 ldflsiilSilvlvisll 81
                                   +++ ++++++ +vi+ll
  gi|13541125|ref|NP_110813.1| 79 GTIFYVVAAVIGVVIGLL 96
                                  344445555555555554 PP

>> DUF2613  Protein of unknown function (DUF2613)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   1.8    0.0039        23       4      23 ..      41      60 ..      38      64 .. 0.87
   2 ?    6.1   4.9     0.002        12       7      23 ..      84     100 ..      78     103 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0039
                       DUF2613  4 gPaaaSaVaGivlGvvavfg 23
                                  +++aa  V+G+v++v+ ++g
  gi|13541125|ref|NP_110813.1| 41 VAGAAILVIGLVVAVIDIIG 60
                                  7899999*******998887 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.002
                       DUF2613   7 aaSaVaGivlGvvavfg 23 
                                   +++aV+G+v+G+ + +g
  gi|13541125|ref|NP_110813.1|  84 VVAAVIGVVIGLLVFLG 100
                                   89*********988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1222  (0.0681577); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        85  (0.00474092); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 759.62
//
Query:       gi|13541126|ref|NP_110814.1|  [L=77]
Description: transcription regulator [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-12   47.4   0.1    1.6e-12   47.2   0.1    1.0  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain
    0.00089   19.3   0.1     0.0011   19.0   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 !   47.2   0.1   1.8e-16   1.6e-12       1      70 [.       6      72 ..       6      76 .. 0.96

  Alignments for each domain:
  == domain 1  score: 47.2 bits;  conditional E-value: 1.8e-16
                                  EEEEE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEE CS
                AsnC_trans_reg  1 vlvslepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartets 70
                                  vl+s+ pg+    +e+  ++ ++  Vve++ + G+yd+++k   +d  ++ +++ ek+++++gv +t+t+
  gi|13541126|ref|NP_110814.1|  6 VLISTVPGK---EHEVYNKVLKINGVVEAHPLFGEYDIIVKLDMKDFTEIGEVVIEKIRTIDGVIDTKTL 72
                                  7899999**...*********************************************************8 PP

>> NapD  NapD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.1   1.2e-07    0.0011       1      67 [.       1      69 [.       1      72 [. 0.92

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.2e-07
                          NapD  1 lhIsSlvVqarperlaavkaalaalpg.vEvhasdeegklVvviEaesedeladt.ieaiealpgVlsa 67
                                  ++I+ +++ + p++  +v +++ ++ g vE h   +e  ++v ++ ++  e+ +  ie+i++++gV+++
  gi|13541126|ref|NP_110814.1|  1 MSIAFVLISTVPGKEHEVYNKVLKINGvVEAHPLFGEYDIIVKLDMKDFTEIGEVvIEKIRTIDGVIDT 69
                                  678889*******************9945***********************9963899********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.46
# Mc/sec: 503.64
//
Query:       gi|13541127|ref|NP_110815.1|  [L=209]
Description: organic radical activating protein [Thermoplasma volcanium GSS1]
Scores for complete 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   53.8   0.0    3.7e-14   53.4   0.0    1.2  1  Radical_SAM  Radical SAM superfamily
    4.5e-11   42.9   0.1    1.1e-10   41.7   0.1    1.6  2  Fer4_14      4Fe-4S single cluster domain
    4.3e-06   27.0   0.0    5.6e-06   26.7   0.0    1.2  1  Fer4_12      4Fe-4S single cluster domain
  ------ inclusion threshold ------
       0.13   12.3   0.0       0.24   11.4   0.0    1.4  1  ADK_lid      Adenylate kinase, active site lid


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.4   0.0   8.3e-18   3.7e-14       2     123 ..      24     129 ..      23     152 .. 0.89

  Alignments for each domain:
  == domain 1  score: 53.4 bits;  conditional E-value: 8.3e-18
                                   EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgiritv 82 
                                   v t+ Cn rC +C++++   + + gr++ + +il++vke+k       v ++ggepl+++d   ++e   kl   g +i +
  gi|13541127|ref|NP_110815.1|  24 VRTNVCNIRCEWCDTKY---SFYGGREIALSDILNIVKEAK----EQWVCFTGGEPLVQRDALSFVEGSLKL---GKKILI 94 
                                   6899************9...7*******************9....678***********************9...****** PP

                                   EECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTC CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  83 etngtlpdeeklerllelgvdrvslgleaaddekvlklmnr 123
                                   etngt+p    ++ +      ++ +++++++ + v+k++  
  gi|13541127|ref|NP_110815.1|  95 ETNGTVP----IRNFTISDNIVLDVDVKSPSAK-VRKPF-L 129
                                   ******9....66666666899**********9.99987.4 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 !   41.7   0.1   2.3e-14   1.1e-10       1      93 [.      22     102 ..      22     119 .. 0.82
   2 ?   -2.1   0.0      0.88   3.9e+03      60      94 ..     134     167 ..     126     190 .. 0.55

  Alignments for each domain:
  == domain 1  score: 41.7 bits;  conditional E-value: 2.3e-14
                       Fer4_14   1 lfvrlsgCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeeypek 81 
                                   lfvr++ Cn+ C +Cd+k   ++  g + +  ++ +i+   k  e k q + +tGGePL    +++ l +v+   + +  k
  gi|13541127|ref|NP_110815.1|  22 LFVRTNVCNIRCEWCDTKY--SFYGGREIALSDILNIV---K--EAKEQWVCFTGGEPLV---QRDALSFVEGSLKLG--K 90 
                                   7***************987..77788777777777777...3..3333678********4...589999999999999..* PP

                       Fer4_14  82 kiwletngtlei 93 
                                   ki +etngt+ i
  gi|13541127|ref|NP_110815.1|  91 KILIETNGTVPI 102
                                   ********9875 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.88
                       Fer4_14  60 hyenkkellklvkrlkeeypekkiwletngtleie 94 
                                    y ++++ lk+v + +e   ++ i +  +   +++
  gi|13541127|ref|NP_110815.1| 134 KYIRDTDYLKIVIKDREDL-DFAINFIRGHRKNLN 167
                                   4445555555554444444.555555555555555 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.0   1.3e-09   5.6e-06       2      94 ..      11      99 ..      10     127 .. 0.80

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 1.3e-09
                       Fer4_12  2 nGeGvrl.....slfvsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelvkev 79
                                  +GeG+ +     +++++ Cn++C+ C      sf +g+e+    + +i++++   + + + ++GGEPl+   +++ l++v+  
  gi|13541127|ref|NP_110815.1| 11 QGEGTLIgipmlFVRTNVCNIRCEWCD--TKYSFYGGREIALSDILNIVKEA---KEQWVCFTGGEPLV---QRDALSFVEGS 85
                                  899976555644777999*******86..45589999999988888888776...8999**********...77888999988 PP

                       Fer4_12 80 keekpekdiwlytgy 94
                                   + +  k  ++++g+
  gi|13541127|ref|NP_110815.1| 86 LKLGK-KILIETNGT 99
                                  88876.789999997 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 ?   11.4   0.0   5.3e-05      0.24      15      35 ..      57      77 ..      32      77 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 5.3e-05
                                  TB--SSTTB-TTT--.-B--G CS
                       ADK_lid 15 fnpPkveglCDkCGepLvqRs 35
                                   +  k+  +C   GepLvqR+
  gi|13541127|ref|NP_110815.1| 57 VKEAKEQWVCFTGGEPLVQRD 77
                                  46789***************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       562  (0.0313459); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); 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 0.26s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1430.00
//
Query:       gi|13541128|ref|NP_110816.1|  [L=434]
Description: glycine dehydrogenase subunit 1 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   1.1e-108  363.9   0.0   1.2e-108  363.8   0.0    1.0  1  GDC-P          Glycine cleavage system P-protein
    5.4e-05   22.5   0.0    8.9e-05   21.8   0.0    1.3  1  Aminotran_1_2  Aminotransferase class I and II
     0.0017   17.4   0.0     0.0025   16.8   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 !  363.8   0.0    2e-112  1.2e-108      11     429 ..       4     429 ..       1     430 [. 0.93

  Alignments for each domain:
  == domain 1  score: 363.8 bits;  conditional E-value: 2e-112
                                   HHHHHHHHT-SSHHHHHHHHS-GGGB--S---------HHHHHHHHHHHHTTB--.-EE--BTTB------HHHHHHTTT- CS
                         GDC-P  11 qkemLetlGlkslddliekavPkeiklkkelkleapksEeellaelekiasknkv.vksfiGaGyydtilPaviqrnilen 90 
                                     +mL+ lG+ks ++l+ +++P ++  kke  + +p +E+ +l++ +k as n + + +f+G+G+yd+ +P++++  i+++
  gi|13541128|ref|NP_110816.1|   4 ISSMLDYLGIKSTEELF-SDIPLSV-RKKEIGIGSPLDEHLVLERARKYASLNSTeMLNFLGNGIYDRVIPEAVNY-IISK 81 
                                   578**************.9******.578999*******************88877******************99.**** PP

                                   HHHHS--S-SSGGG-HHHHHHHHHHHHHHHHHHT-SEE-S-BS-HHHHHHHHHHHHHHH-SSS--EEEEETTS-HHHHHHH CS
                         GDC-P  91 pewytaYtPYqaEisqGrLeallnfqtlvadltGldianasllDegtAaaEAvllaaraskkkakkvvvdkkvhpqtlevl 171
                                   +e++ +YtPYq+E+sqG L++++++q+l++dl  +d +nas++D+ +A++EA+ +a+r++ k+  k+++ ++ +  +l+vl
  gi|13541128|ref|NP_110816.1|  82 SEFLDSYTPYQPEVSQGMLQSIFEYQSLISDLFKMDFTNASMYDGYSALGEAARMAYRINGKN--KILIPESTYDSKLSVL 160
                                   **********************************************************99888..**************** PP

                                   HHHHGGGT-EEEEE-GGG--S-..........S-EEEEEEEES-TTSB----HHHHHHHHHTT-EEEEEE-TTGGGTB--H CS
                         GDC-P 172 ktrakglgieivevdlteekvtd.......kekevagvlvqypnteGriedlkelvekakkkkslvvvaadllaLtllkpP 245
                                   k +  gl ++i++ ++ ee++ d          ++++v+v  pn  G i +    ++++k k+sl++  +d+++L++lkpP
  gi|13541128|ref|NP_110816.1| 161 KNYVWGLSMKIEKYKMNEEGKIDiddlqsrIDGDTSAVVVENPNGYGVIDENVFRISEIK-KESLLISYVDPISLGVLKPP 240
                                   ******************999999999998889****************88655555555.56788889************ PP

                                   HHHT-SEEEEE-TTTT---GGG----EEEEE-GGGGGG--S-EEEEEEBTTS-EEEEEE-CCGSHHCCHHHCS-S--S--H CS
                         GDC-P 246 gelgaDivvGsaqrfGvPlgyGGPhagffAvkeklkRkiPGRlvGvskDaegkralrlalqtREqHirRdkAtsniCtaqa 326
                                   ge+g+Di++ ++q++G+P+ +GGP  g +  k++++Rk PGRl+G s Da+gkra++++lqtREqHirR kAtsniC++qa
  gi|13541128|ref|NP_110816.1| 241 GEYGSDIAIAEGQQLGIPMNFGGPLLGIMSFKADYVRKSPGRLIGESVDADGKRAFVMTLQTREQHIRRAKATSNICSNQA 321
                                   ********************************************************************************* PP

                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT..T-EE--SSBSSEEEEE--TTTHHHHHHHHHHTTEE-EEES CS
                         GDC-P 327 LlAnlaalyavyhGkeglkeiarrihkkteilakelkkk.leeelkkkkffdtllieveekaaekvlkkaekeglnlrkve 406
                                   Ll ++a  y  ++G++glk++a  + k+++ la+ l +  +e++++  +f dtl +  + + +  + kk++  g++l++  
  gi|13541128|ref|NP_110816.1| 322 LLTLAAGSYLSILGSSGLKKVALLTIKHSKNLAESLGNIgIEKVFDSISFSDTLFRIDK-NVMLDLAKKGILGGIKLTSLI 401
                                   **************************************9999************99666.555579999999999888765 PP

                                   TT.....EEEEE--TT--HHHHHHHHHH CS
                         GDC-P 407 lk.....tvgialdEtvtkedieallkv 429
                                   ++      +  + +E++ +e+i+al+++
  gi|13541128|ref|NP_110816.1| 402 KDskyssGTFFTATEKTDNEKIKALVNA 429
                                   5421212356789999999999999876 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 !   21.8   0.0   1.5e-08   8.9e-05      68     158 ..     119     204 ..      51     206 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1.5e-08
                                   GEGEEEESHHHHHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHT....TSEEEEEEBEETTTTEE-HHHHHHHHTTHHC CS
                 Aminotran_1_2  68 eaavvvgsGagaliealifllklnpgdeilvpdptyasyknilrls....ggevvryplyseedfhldlealeealkeape 144
                                     +  +  G++al ea+ ++ ++n + +il+p+ ty+s   +l+++     +++ +y+++  e+ ++d+++l+  ++    
  gi|13541128|ref|NP_110816.1| 119 T-NASMYDGYSALGEAARMAYRINGKNKILIPESTYDSKLSVLKNYvwglSMKIEKYKMN--EEGKIDIDDLQSRIDG--- 193
                                   4.667889******************************8888887733224555555544..9**************9... PP

                                   TTETEEEEEEESS- CS
                 Aminotran_1_2 145 gnkktkvilvesph 158
                                       t  ++ve+p+
  gi|13541128|ref|NP_110816.1| 194 ---DTSAVVVENPN 204
                                   ...8899****997 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   4.2e-07    0.0025      83     175 ..     138     230 ..     128     258 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 4.2e-07
                                   CC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--TTEEEEEEESBETTTTEB--.HHHHH CS
                   Aminotran_5  83 rslkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldelekllnektklvaithvsnvtGtiqp.veeig 162
                                   ++++ +++i++ e+ + ++l   ++      +k+++++++eeg++d+d+l++ ++ +t++v +  + n  G+i++ v +i 
  gi|13541128|ref|NP_110816.1| 138 YRINGKNKILIPESTYDSKLSVLKNYVWGLSMKIEKYKMNEEGKIDIDDLQSRIDGDTSAVVV-ENPNGYGVIDEnVFRIS 217
                                   45889999************999999999*******************************987.57888999875255555 PP

                                   HHHHHTT-EEEEE CS
                   Aminotran_5 163 klakkkgalvlvD 175
                                   ++ k++  +  vD
  gi|13541128|ref|NP_110816.1| 218 EIKKESLLISYVD 230
                                   5545455555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (434 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       333  (0.0185733); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 2795.58
//
Query:       gi|13541129|ref|NP_110817.1|  [L=472]
Description: glycine dehydrogenase subunit 2 [Thermoplasma volcanium GSS1]
Scores for complete 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   56.6   0.0    1.5e-14   53.7   0.0    1.9  1  GDC-P            Glycine cleavage system P-protein
    7.5e-11   41.6   0.0    2.1e-10   40.1   0.0    1.7  2  Aminotran_5      Aminotransferase class-V
    9.6e-05   21.8   0.0    0.00014   21.2   0.0    1.2  1  Beta_elim_lyase  Beta-eliminating lyase
  ------ inclusion threshold ------
      0.037   13.4   0.0      0.056   12.7   0.0    1.2  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family


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 !   53.7   0.0   3.2e-18   1.5e-14      28     428 ..      30     434 ..      16     436 .. 0.77

  Alignments for each domain:
  == domain 1  score: 53.7 bits;  conditional E-value: 3.2e-18
                                   HHHS-GGGB--S---------HHHHHHHHHHHHTTB---EE--.BTTB.------HHHHHHTTT-HHHHS--S-SSGG.G- CS
                         GDC-P  28 ekavPkeiklkkelkleapksEeellaelekiasknkvvksfi.GaGy.ydtilPaviqrnilenpewytaYtPYqaE.is 105
                                   e+ +P+++ ++k+l+l++ +sE++++++ +++++ n +v   i   G  + ++ P+  +r  ++  + + +  P+q+E   
  gi|13541129|ref|NP_110817.1|  30 ESILPENL-KRKDLELPE-VSEYDVVRHYTRLSQMNYTVDVGIyPLGScTMKYNPKFADR--VSAIDGFRNIHPFQPEnTV 106
                                   45678888.567777775.79*************99875433313454145678999999..8899999999*****9456 PP

                                   HHHHHHHHHHHHHHHHHHT-SEE-S-BS-HHHHHHHH..HHHHHHH..-SSS.--EEEEETTS-HHHHHHHHHHHGGGT-E CS
                         GDC-P 106 qGrLeallnfqtlvadltGldianasllDegtAaaEA..vllaara..skkk.akkvvvdkkvhpqtlevlktrakglgie 181
                                   qG L+ + + q  +  +  +d    sl   + A +E   +l++++   +k++ ++++++  + h  +       a   g++
  gi|13541129|ref|NP_110817.1| 107 QGALHVMYDLQEYLKKISDMDA--VSLQPMAGADGEFtgILIVKKYfeDKGEdRTEIIIPDSAHGTNP----ASATMGGFD 181
                                   *****************98875..68888888888861144444431134442445566555555443....467778999 PP

                                   EEEE-GGG--S-..........S-EEEEEEEES-TTSB---.-HHHHHHHHHTT-EEEE.EE-TTGGGTB--HHHHT-SEE CS
                         GDC-P 182 ivevdlteekvtd.......kekevagvlvqypnteGried.lkelvekakkkkslvvv.aadllaLtllkpPgelgaDiv 253
                                   +vev++ ++++ d       ++k++a+ ++  pnt G  e+ ++e+++ +++  +l+    a+l a+  +++Pg +g Div
  gi|13541129|ref|NP_110817.1| 182 VVEVPSDDKGMVDlealraaVSKKTAAFMITNPNTLGIFEQnIEEIAKIIHNAGALLYYdGANLNAIFGITSPGLMGFDIV 262
                                   9999999999999999999999***************998769**********999876379999***************9 PP

                                   .EEE-TTTT---GGG----EEEEE-GGGGGG--S-EEEEEEBTTS-EEEEEE-CCGSHHCCHHHCS-S--S--HHHHHHHH CS
                         GDC-P 254 .vGsaqrfGvPlgyGGPhagffAvkeklkRkiPGRlvGvskDaegkralrlalqtREqHirRdkAtsniCtaqaLlAnlaa 333
                                    +   + f  P g GGP ag +Avk+ lk  +P  +v    D +g+ ++rl    +       k +s   +   Ll   a 
  gi|13541129|ref|NP_110817.1| 263 hFNLHKSFATPHGGGGPGAGPVAVKSFLKDFLPVPIV----DFDGN-SYRLNYELKK---TIGKVSSFYGSFSILLR--AW 333
                                   4566789******************99******9998....67776.6999876654...45789999988888875..67 PP

                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT...T-EE--SSBSSEEEEE--TTTHH..H.HHHHHHHTT.EE-EEESTT CS
                         GDC-P 334 lyavyhGkeglkeiarrihkkteilakelkkk..leeelkkkkffdtllieveekaae..k.vlkkaekeg.lnlrkvelk 408
                                    y++  G +glk+++ r   ++++l+k+l+k   +     kk+ f   + +++++a +  k +l++++++  + +    ++
  gi|13541129|ref|NP_110817.1| 334 SYIIRNGDDGLKNVSARAVLNSNYLKKKLEKYydIPYYPLKKHEFVLSTENTGKRALDigKyILDNGIHSPtVYFPLIVKE 414
                                   8*****************************974433333344444444444555665322358888888874556666677 PP

                                   EEEEE--TT--HHHHHHHHH CS
                         GDC-P 409 tvgialdEtvtkedieallk 428
                                   ++ i  +Etv k+d+++  +
  gi|13541129|ref|NP_110817.1| 415 AMMIEPTETVSKADLDNYAD 434
                                   999999****9999998665 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.1   0.0   4.7e-14   2.1e-10      84     207 ..     154     275 ..     139     278 .. 0.82
   2 ?   -2.9   0.0      0.57   2.6e+03     272     333 ..     343     401 ..     340     402 .. 0.79

  Alignments for each domain:
  == domain 1  score: 40.1 bits;  conditional E-value: 4.7e-14
                                   C-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--TTEEEEEEESBETTTTE.B--HHHHHH CS
                   Aminotran_5  84 slkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldelekllnektklvaithvsnvtGt.iqpveeigk 163
                                   + ++++ei++ ++ h  n   + +     g++v+ +p d++g +dl++l++++++kt++ +it + n++G+  q +eei+k
  gi|13541129|ref|NP_110817.1| 154 KGEDRTEIIIPDSAHGTNP--ASAT--MGGFDVVEVPSDDKGMVDLEALRAAVSKKTAAFMIT-NPNTLGIfEQNIEEIAK 229
                                   4677888999988888777..4444..47******************************9998.568899989******** PP

                                   HHHHTT-EEEEE-TTTTTTS--.-HHHHTESEEEEETTT.TTSSTT CS
                   Aminotran_5 164 lakkkgalvlvDaaqavghipi.dvkklgvDflafsghK.llgPtG 207
                                   +++++gal+  D+a       i     +g D++ f  hK +  P G
  gi|13541129|ref|NP_110817.1| 230 IIHNAGALLYYDGANLNAIFGItSPGLMGFDIVHFNLHKsFATPHG 275
                                   **************866555551456789**********8888888 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 0.57
                                   HHHHHHHHHHHHHHHHHHHHCTSTTEEEES.-B-CTCBSEEEEEETTCSHHHHHHHHHHTTE CS
                   Aminotran_5 272 gleaiekhekelaeyllerlkslpgvrlygpdkaerrasivsfnfkgvhaedvatlLdeegI 333
                                   gl+++ +++   ++yl+++l+++ ++  y     ++++ ++s   +g  a d+++++ ++gI
  gi|13541129|ref|NP_110817.1| 343 GLKNVSARAVLNSNYLKKKLEKYYDIPYYP---LKKHEFVLSTENTGKRALDIGKYILDNGI 401
                                   678888888889999999999999998855...47777888888888888888888777777 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   3.2e-08   0.00014      80     206 ..     167     276 ..     106     292 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 3.2e-08
                                   -HHHHSSTTHHHHCC--EEEEE-EBTTTBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHC CS
               Beta_elim_lyase  80 ahihfdetgaiaelagvklrdlknkeaGkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakky 160
                                   ah+   ++ a a+++g  +++++++++G +dle+l+aa+ +      k+++ ++t+ n    G  +  ++++e+a+i ++ 
  gi|13541129|ref|NP_110817.1| 167 AHG---TNPASATMGGFDVVEVPSDDKGMVDLEALRAAVSK------KTAAFMITNPNTL--G--IFEQNIEEIAKIIHNA 234
                                   444...55688999**************************9......4667777777776..4..5789************ PP

                                   T-EEEEEETTHHHHHHHHTS-CHHHHTTSSEEEEESSSTT--SS-E CS
               Beta_elim_lyase 161 giplhlDgARfanaakslgeivkemfsyvDsvtmslkKdllanvGg 206
                                   g  l +DgA    +  ++  i +  + ++D+v + l K   ++ Gg
  gi|13541129|ref|NP_110817.1| 235 GALLYYDGA----NLNAIFGITSPGLMGFDIVHFNLHKSFATPHGG 276
                                   *********....556667777777888888888888888888776 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 ?   12.7   0.0   1.3e-05     0.056      63     147 ..     158     244 ..     150     277 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.3e-05
                                   T-EEEEESSS-THHHHHHHHTT-EEEEE-B-TTTSSB-GGGCGGG--TTEEEEEEB..-GGGB--.-HHHHHHHHHHCT-E CS
               DegT_DnrJ_EryC1  63 gdeVIvpsltFvatanavlelgakpvfvDvdpdtynidpaaieaaitertkaIlpV..hlyGqva.dmdalkaiaakhglk 140
                                   ++e+I+p     +  ++++  g ++v v  d d  ++d +a++aa+ ++t+a ++   +++G +  +++++ +i ++ g  
  gi|13541129|ref|NP_110817.1| 158 RTEIIIPDSAHGTNPASATMGGFDVVEVPSD-DKGMVDLEALRAAVSKKTAAFMITnpNTLGIFEqNIEEIAKIIHNAGAL 237
                                   68999999999999999999999*9999999.99*****************9888733588998889************** PP

                                   EEEE-TT CS
               DegT_DnrJ_EryC1 141 vieDaAh 147
                                   +  D A+
  gi|13541129|ref|NP_110817.1| 238 LYYDGAN 244
                                   *999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (472 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.63u 0.33s 00:00:00.96 Elapsed: 00:00:00.53
# Mc/sec: 2683.53
//
Query:       gi|13541130|ref|NP_110818.1|  [L=336]
Description: heme d1 biosynthesis protein (NirJ-related) [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      1e-30  106.3   4.2    1.6e-30  105.6   4.2    1.3  1  DUF3463      Domain of unknown function (DUF3463)
    4.7e-18   66.1   0.0    7.3e-18   65.5   0.0    1.3  1  Radical_SAM  Radical SAM superfamily
    1.8e-07   31.5   0.0      2e-06   28.1   0.0    2.2  2  Fer4_12      4Fe-4S single cluster domain
     0.0042   17.2   1.5      0.011   15.8   0.0    2.2  3  Fer4_14      4Fe-4S single cluster domain
  ------ inclusion threshold ------
      0.095   12.7   0.0       0.24   11.4   0.0    1.6  1  MraZ         MraZ protein, putative antitoxin-like
      0.097   12.5   0.0       0.13   12.1   0.0    1.2  1  DUF2100      Uncharacterized protein conserved in archaea (DU


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 !  105.6   4.2   5.3e-34   1.6e-30       1     132 [.     188     323 ..     188     325 .. 0.94

  Alignments for each domain:
  == domain 1  score: 105.6 bits;  conditional E-value: 5.3e-34
                       DUF3463   1 itvspgysYekapdqdlflerektkelfrkilelkkkkyklnesplyldflag....kqeykCtpWgnptrnvlG.wqkPC 76 
                                   i+v+++y+Y++a  ++l++e++ + +++ ++ ++k+++y +++s++y+d l+       ++ C+pW++++++++G +++PC
  gi|13541130|ref|NP_110818.1| 188 INVQVSYDYSTA--NNLSPEKKALYDVLLSLKKMKEDGYPIVNSKEYFDTLISswyyGIKWACKPWSTVNIDPQGrIVMPC 266
                                   689*********..9*************************************96764459********************* PP

                       DUF3463  77 Ylleegyaktfk.......elleetdwekygkgkdpkCanCmvhsgyEasavsdtvksllkal 132
                                   Y+l ++ya + k        l++++dw++y+     +C++C +++++E+s++s++  s+++++
  gi|13541130|ref|NP_110818.1| 267 YVL-NEYAGSSKvwetdivRLWNTYDWSQYE-----SCNKCSLSCYLEPSIFSWKKLSMVNER 323
                                   ***.99****9999999999**********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 !   65.5   0.0   2.4e-21   7.3e-18       6     166 ..      35     180 ..      31     189 .. 0.92

  Alignments for each domain:
  == domain 1  score: 65.5 bits;  conditional E-value: 2.4e-21
                                   EESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEEEECS CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM   6 gCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgiritvetng 86 
                                    CnlrC  C+++    r++++r ls++e +  +++l a+ gv ++ + ggepll+ d++++l++ +++    ++++++tng
  gi|13541130|ref|NP_110818.1|  35 TCNLRCDMCPFW----RRKDERLLSIDEEIMMMDSL-ASAGVSFMGFEGGEPLLRNDLEDILRESHRR----FHTSLVTNG 106
                                   7***********....6*******************.8********************9999999995....********* PP

                                   SCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  87 tlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglpGendeeleellel 166
                                    l+ +  +  ++++  d++ ++++ + +  + k  + +++fe+ le++e ++++ +   v + + +  +n+ e+ +++el
  gi|13541130|ref|NP_110818.1| 107 WLL-KNRASSIAKYL-DYLFVSIDGLKET-HDKQRGVPGSFEHALEGIEEAKKY-VQ--VAISTTITTYNMNEITKVVEL 180
                                   ***.*********99.************9.******99****************.88..677777777777777776665 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.0   6.8e-10     2e-06      12     124 ..      33     136 ..      26     146 .. 0.89
   2 ?    0.9   0.0      0.17     5e+02      87     133 ..     160     207 ..     139     213 .. 0.62

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 6.8e-10
                       Fer4_12  12 vsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelvkevkeekpekdiwlyt 92 
                                   +  Cnl+C+ C     w+ k ++  + + +  ++++l+   ++ + + GGEPll   +++l ++++e  +++   + ++++
  gi|13541130|ref|NP_110818.1|  33 LYTCNLRCDMCP---FWRRKDERLLSIDEEIMMMDSLASAGVSFMGFEGGEPLL---RNDLEDILRESHRRFH--TSLVTN 105
                                   568*******76...9**********999999**********************...99*************9..7899** PP

                       Fer4_12  93 gytleelskkekeellkeidvlvdGkfeesle 124
                                   g  l++  + +  + l+++ v +dG  e + +
  gi|13541130|ref|NP_110818.1| 106 GWLLKNRAS-SIAKYLDYLFVSIDGLKETHDK 136
                                   ****99986.5999999999*****7775544 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.17
                       Fer4_12  87 diwlytgytleelskkekeellkeidvlvdGkfeesledes.lrfrgs 133
                                   + +++t +t++  + +++ el k + v + ++ + ++ + + l+ + +
  gi|13541130|ref|NP_110818.1| 160 VAISTTITTYNMNEITKVVELAKDLGVGINVQVSYDYSTANnLSPEKK 207
                                   445555555554444478999999998888887766654431445555 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   3.7e-06     0.011       7      88 ..      35     105 ..      32     129 .. 0.73
   2 ?   -0.4   0.1      0.41   1.2e+03      62     103 ..     169     208 ..     151     223 .. 0.73
   3 ?   -4.3   0.4         6   1.8e+04       6      12 ..     299     305 ..     297     314 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 3.7e-06
                       Fer4_14   7 gCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeeypekkiwlet 87 
                                    Cnl C +C     ++++l  +++e ++ + l       +  +++ + GGePL+    ++l +++++ ++++   +  l t
  gi|13541130|ref|NP_110818.1|  35 TCNLRCDMCPFWRRKDERLLSIDEEIMMMDSL---ASAGV--SFMGFEGGEPLLR---NDLEDILRESHRRF---HTSLVT 104
                                   6*********9998999999999999995555...55555..788999*****66...56677777777776...344445 PP

                       Fer4_14  88 n 88 
                                   n
  gi|13541130|ref|NP_110818.1| 105 N 105
                                   5 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.41
                       Fer4_14  62 enkkellklvkrlkeeypekkiwletngtleielektpdlke 103
                                   +n +e+ k+v+  k+ +  +++++   ++ + +l   p+ k+
  gi|13541130|ref|NP_110818.1| 169 YNMNEITKVVELAKDLGVGINVQVSYDYSTANNLS--PEKKA 208
                                   57888889998888888777777777777776655..44443 PP

  == domain 3  score: -4.3 bits;  conditional E-value: 6
                       Fer4_14   6 sgCnlsC 12 
                                   ++C+lsC
  gi|13541130|ref|NP_110818.1| 299 NKCSLSC 305
                                   6888888 PP

>> MraZ  MraZ protein, putative antitoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   8.2e-05      0.24       7      57 ..     253     299 ..     250     306 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 8.2e-05
                                   EEEB-TTSEEE--C.HHHHHTTSCSEEEEEECCSEEEEEEHHHHHHHHHCHH CS
                          MraZ   7 evelDakGRlllPa.klreeaklekevvviGvsncLeiwpraeWekyeeela 57 
                                   +v++D +GR+  P   l e+a+ +k+  +++v     +w   +W++ye+  +
  gi|13541130|ref|NP_110818.1| 253 TVNIDPQGRIVMPCyVLNEYAGSSKVWETDIV----RLWNTYDWSQYESC-N 299
                                   79***********6368889999988888776....59999999999986.4 PP

>> DUF2100  Uncharacterized protein conserved in archaea (DUF2100)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   4.4e-05      0.13     131     191 ..     121     181 ..      86     206 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.4e-05
                                   SSXEEEXSSXSSSHHHHTT..XXXSTTTTTSHHHHHHHHHHHHHHHHHHXXSXEEEEXS.. CS
                       DUF2100 131 dlniisteGvLeieDmkeiNPkipekalkgieKkveivkeeieklikklkpekvvvvveed 191
                                   d   +s++G  e  D +   P   e+al+gie   + v+  i+ +i+ ++ +++  vve  
  gi|13541130|ref|NP_110818.1| 121 DYLFVSIDGLKETHDKQRGVPGSFEHALEGIEEAKKYVQVAISTTITTYNMNEITKVVELA 181
                                   55679999*99999998888**********************************9999864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       756  (0.0421663); expected 358.6 (0.02)
Passed bias filter:                      571  (0.0318478); 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: 0.59u 0.34s 00:00:00.93 Elapsed: 00:00:00.51
# Mc/sec: 1966.85
//
Query:       gi|13541131|ref|NP_110819.1|  [L=168]
Description: hypothetical protein TVN0300 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     0.0026   18.2   2.2     0.0036   17.7   2.2    1.3  1  Rubrerythrin  Rubrerythrin
  ------ inclusion threshold ------
      0.027   14.8   5.1        1.3    9.5   1.5    2.3  2  DNA_PPF       DNA polymerase processivity factor
      0.046   13.0   4.6      0.049   13.0   0.7    2.1  2  DUF2113       Uncharacterized protein conserved in archaea (D
      0.083   12.8   4.2        5.2    7.0   0.6    2.6  2  Ferritin      Ferritin-like domain


Domain annotation for each model (and alignments):
>> Rubrerythrin  Rubrerythrin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   2.2     8e-07    0.0036      28     136 ..      49     158 ..      32     159 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 8e-07
                                   -HHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTHH..B.SSBBS-------TTGGHHHHHHHHHHHHHHHHHCHHHHHHHHH CS
                  Rubrerythrin  28 ypqiaelFeelAeeEreHakilnklleklepele.levkekvreyaeakpkflttaknLeeaiegayaeeeemyrfyeela 107
                                     +++ +++++A++E++ +++++++++k e +    + + ++  +  +k + ++   ++++++   ++eeee++r +e + 
  gi|13541131|ref|NP_110819.1|  49 PDNVRSMMLRVADMEEQTRRRIEDAIRKKEFDVSiNNTNSYAMIEHIVKNSDVSDISDVKSVLLKSMKEEEELHRILEVMS 129
                                   467999**********************99999966666667777777777777778899********************* PP

                                   HHTTSHHHHHHHHHHHHHHHHHHHHHHHH CS
                  Rubrerythrin 108 ekegneeakklfkklaeaEkkHeerlrkl 136
                                   ++    +++k++++++e E+  ++ l+ l
  gi|13541131|ref|NP_110819.1| 130 KEYNGTNIEKTLRSIIECEENNKNALADL 158
                                   *******************9888887776 PP

>> DNA_PPF  DNA polymerase processivity factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.1    0.0012       5.6      61     100 ..      51      90 ..      36      94 .. 0.88
   2 ?    9.5   1.5   0.00028       1.3      49     108 ..      94     153 ..      89     157 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0012
                                   HHHHHHTTS-TT........-EEEE-TTSSEEEEESSEE- CS
                       DNA_PPF  61 qltsilapakndedNitkLlaeikksedgnvkiadasSyl 100
                                    + s+++ + + e+  +  +++ +++++ +v i++++Sy 
  gi|13541131|ref|NP_110819.1|  51 NVRSMMLRVADMEEQTRRRIEDAIRKKEFDVSINNTNSYA 90 
                                   68899999999999999*********************96 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00028
                                   EE-S-EEESTHHHHHHHHTTS-TT........-EEEE-TTSSEEEEESSEE--B-GGGS- CS
                       DNA_PPF  49 vvpadsditdvnqltsilapakndedNitkLlaeikksedgnvkiadasSyleaykslvs 108
                                    + ++sd+ d++ ++s+l+   + e+ ++ +l+ ++k+ +g    + ++S  e +++ ++
  gi|13541131|ref|NP_110819.1|  94 HIVKNSDVSDISDVKSVLLKSMKEEEELHRILEVMSKEYNGTNIEKTLRSIIECEENNKN 153
                                   5789*****************************999997765545667776666655555 PP

>> DUF2113  Uncharacterized protein conserved in archaea (DUF2113)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.2     0.026   1.2e+02     120     141 ..      54      75 ..       4      77 .. 0.65
   2 ?   13.0   0.7   1.1e-05     0.049      58     120 ..      96     155 ..      86     165 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.026
                       DUF2113 120 leelvVaDpkeelkkkvidali 141
                                      l VaD++e+ ++++ da+ 
  gi|13541131|ref|NP_110819.1|  54 SMMLRVADMEEQTRRRIEDAIR 75 
                                   2345699999999999999985 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 1.1e-05
                       DUF2113  58 iklgdvaeveedkeegkvkikiedEtylpelLkkLwekygrenveqpdRfeiiiesdedleel 120
                                   +k +dv++++    +  +  ++++E+ l+++L+++ ++y   n+e++ R  i+ e++++   l
  gi|13541131|ref|NP_110819.1|  96 VKNSDVSDISD--VKSVLLKSMKEEEELHRILEVMSKEYNGTNIEKTLRSIIECEENNKN-AL 155
                                   56677777777..66688889********************************9997755.33 PP

>> Ferritin  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.3    0.0012       5.3      48     105 ..      22      76 ..      15     111 .. 0.75
   2 ?    7.0   0.6    0.0012       5.2      94     124 ..     135     165 ..      82     166 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0012
                                   HHHHHHHHHHTTS....SHHHHHHC-SSSS..CSSHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Ferritin  48 adklaerilalGgtpvltraeleeieapke..fgsveevleaalehekkvteslreliel 105
                                    + l+ ri +l        +el   +  ++   ++v++++  + ++e+++ ++++++i+ 
  gi|13541131|ref|NP_110819.1|  22 LEGLLRRIAQLKR-----NRELNYRKMANSnvPDNVRSMMLRVADMEEQTRRRIEDAIRK 76 
                                   5667778888887.....4444442222233244**********************9976 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0012
                                   HHHHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                      Ferritin  94 kvteslrelielaeeegDpatadfledflee 124
                                   + +e+  + i  +ee++ +a+ad++ed+++e
  gi|13541131|ref|NP_110819.1| 135 TNIEKTLRSIIECEENNKNALADLYEDYVNE 165
                                   566777778888****************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1997  (0.111384); expected 358.6 (0.02)
Passed bias filter:                      667  (0.0372023); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 1012.39
//
Query:       gi|13541132|ref|NP_110820.1|  [L=276]
Description: metal-dependent hydrolase [Thermoplasma volcanium GSS1]
Scores for complete 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-20   71.4   0.0    9.3e-20   71.1   0.0    1.1  1  TatD_DNase  TatD related DNase


Domain annotation for each model (and alignments):
>> TatD_DNase  TatD related DNase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.1   0.0   5.2e-24   9.3e-20       1     248 [.       7     262 ..       7     269 .. 0.82

  Alignments for each domain:
  == domain 1  score: 71.1 bits;  conditional E-value: 5.2e-24
                                   EEEEE-TTSCCCTTTHHHHHHHHHHTTEEEEEEE-SSG.............GGHHHHHHHHTT.TTTEEEEE---GGGGGC CS
                    TatD_DNase   1 iDaHcHldskefeedreeileraeeagvaavvvvgtss.............kdskavlelakkypnkvyavlGiHPnevde 68 
                                   +D+H Hl+      +++e++ r+ +ag++ +  +++ +              ++k  +++ +++ ++v++++G +P + + 
  gi|13541132|ref|NP_110820.1|   7 FDNHFHLNP---GGNYKEAIGRFIKAGGTSINLTNLPLhdrtsgyyenlyeWNIKMSEKIRSEFGIEVVVTIGPYPFDYQF 84 
                                   7********...456899999999999999987777778888899999953355588888888*************99888 PP

                                   .......C.CCHHHHHHHH.HHCCCTSEEEEEEEEEET-CCCCCGHHHHHHHHHHHHHHHHHTTEEEEEEEES...-HHHH CS
                    TatD_DNase  69 .......asedlleelkel.anvkhskvvaiGeiGLDyysreestkeaqeevFeeqlrlAkelklplviHlrk...aeedl 138
                                          + +++ + l+ + + v ++k+ aiGeiG ++ +++++ +++  e++ e +++A  ++ p+++H+ +    + + 
  gi|13541132|ref|NP_110820.1|  85 fsnagldPINEMRHGLELAaKLVSEEKADAIGEIGYPHIQVDKELMDVYTEMLSEAFEIAGNIDSPVILHTYDldcKDYER 165
                                   7777776555556899999899***************************************************87444477 PP

                                   HHHHHHCGGCCSEEEETT--S-HHHHHHHHHTTEEEEE-GGGGTTTTHHHHHHH.HHS-GGGEEE---TTSSEECCCTTSE CS
                    TatD_DNase 139 leilkeaaeakakvvlHsfsgsaeeakkflklgyyislsglltfknakelrelv.kavpldrlLiETDaPyltpkpyrgkr 218
                                   le+l++  ++++kvv H+   + + +k  +   ++ s+++          ++++  +  ++++L+ETD  ++++  yr+k 
  gi|13541132|ref|NP_110820.1| 166 LESLSSSFGKNVKVVKHH--ARPNDLKCNT--HIFRSIGAS--------RKNVIeSTALSKKFLLETD--FIDDPLYRNKY 232
                                   888888778888******..6677777777..89*****92........2344434556889******..888879999** PP

                                   --GGGHHHHHHHHHHHHTS-HHHHHHHHHH CS
                    TatD_DNase 219 nepanvayvveklaelkaltleelaeitae 248
                                     p  v++ + ++ ++ + + e l+ i +e
  gi|13541132|ref|NP_110820.1| 233 LPPDSVPKRALMIQQQIENADELLYSIFEE 262
                                   ***********9999888777777666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       362  (0.0201908); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 1697.53
//
Query:       gi|13541133|ref|NP_110821.1|  [L=404]
Description: hypothetical protein TVN0302 [Thermoplasma volcanium GSS1]
Scores for complete 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-72  242.8   0.0      7e-72  242.5   0.0    1.1  1  Nre_N     Archaeal Nre, N-terminal
    9.4e-33  112.4   0.0      2e-32  111.3   0.0    1.5  1  Nre_C     Archaeal Nre, C-terminal


Domain annotation for each model (and alignments):
>> Nre_N  Archaeal Nre, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  242.5   0.0   7.8e-76     7e-72       1     269 [.      28     287 ..      28     288 .. 0.96

  Alignments for each domain:
  == domain 1  score: 242.5 bits;  conditional E-value: 7.8e-76
                         Nre_N   1 LcglkkcpileklravekakkkisskeleGsspPsvfVGrygYPkVsvgplvppvegdasvldspekwlglslediiklrl 81 
                                   +cgl+ cpile++++v  +++ +   +++ s+pPs+f+G+y+YP+V+ g++      d++     ++ ++l + +ii++++
  gi|13541133|ref|NP_110821.1|  28 MCGLRVCPILERFQEVFPRLDLH--GDISTSTPPSIFIGEYNYPSVYGGIMSV---VDPERPYARRDMFDLGMPEIIERNA 103
                                   6*****************99988..9***********************7732...3677777788999************ PP

                         Nre_N  82 slvrgekkvkvkkakedklleeiqelalsekpvdvevelekkpkaklkfdevlaPvGpsaeleklkvaenpkvprkveklv 162
                                   +l+r+ k+v+v++ + +k++e+iqe+a++ + + ve ++  k   + +fd + +PvGp  + e++kv +n+k+pr+ + ++
  gi|13541133|ref|NP_110821.1| 104 NLFRNVKTVSVHNLS-EKTVEQIQEAAMALNELRVESRIVGK---EKHFDFFDSPVGPMYKSENIKVYGNAKTPRAAQDVI 180
                                   **************9.9*******************999999...67899999**************************** PP

                         Nre_N 163 eDtdlkAeeavveLyrsgvdvykiqrlLSvGlLGekkkrrlVPTrWsITAvddivgkelkkeikdlpeidevevfsgeylg 243
                                   +D dl+++ea+  Ly + +d+++i+ lLS GlLG +kkr+lVPTrWsITAvdd+++++lk++  ++++id+ +vfs++ +g
  gi|13541133|ref|NP_110821.1| 181 YDIDLNSTEALKILYMNSIDINYITGLLSGGLLGIEKKRKLVPTRWSITAVDDTISRYLKSDALNYESIDKPMVFSYSRFG 261
                                   ********************************************************************************* PP

                         Nre_N 244 NrflviLaPgkwsfelvEawapgslw 269
                                   N+f +iL+P+  +fe+ E w+ gslw
  gi|13541133|ref|NP_110821.1| 262 NHFNIILLPRGTAFEMQEYWEIGSLW 287
                                   ************************** PP

>> Nre_C  Archaeal Nre, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.3   0.0   2.3e-36     2e-32       5     109 ..     302     402 ..     298     403 .. 0.93

  Alignments for each domain:
  == domain 1  score: 111.3 bits;  conditional E-value: 2.3e-36
                         Nre_C   5 grkeyse.iaGaYyaarlavleaLekikrqakvivlreitpeYwaPvGvWqvReavrkalekkpkefesleealeevsekl 84 
                                    r++y++ i+GaYyaarlav e+L++i+r+a++ivlr+i+p+Y+aP+GvW++Re+vr+al++kp+ fesle+ ++     +
  gi|13541133|ref|NP_110821.1| 302 PRNSYASeITGAYYAARLAVFEYLSRIRRSASAIVLRRISPDYFAPLGVWVIRESVRNALKGKPAIFESLEDLFK-----V 377
                                   68899988***************************************************************9985.....5 PP

                         Nre_C  85 klplkkllkkskllkelkkqktLdd 109
                                   +l+++++++ s ++k++++qktL+d
  gi|13541133|ref|NP_110821.1| 378 RLEIAEWKRYSPVIKRFMTQKTLTD 402
                                   666799*****************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (404 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       560  (0.0312343); expected 358.6 (0.02)
Passed bias filter:                      525  (0.0292822); 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: 0.70u 0.36s 00:00:01.06 Elapsed: 00:00:00.59
# Mc/sec: 2061.36
//
Query:       gi|13541134|ref|NP_110822.1|  [L=465]
Description: phosphate ABC transporter permease [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.8e-42  145.2  26.8    3.7e-42  144.8  26.8    1.1  1  Sugar_tr        Sugar (and other) transporter
    1.1e-21   77.2  47.8    8.7e-21   74.2  36.4    2.0  2  MFS_1           Major Facilitator Superfamily
  ------ inclusion threshold ------
      0.012   15.5   0.4      0.012   15.5   0.4    2.4  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 !  144.8  26.8   6.1e-46   3.7e-42      47     449 ..      51     451 ..      16     453 .. 0.82

  Alignments for each domain:
  == domain 1  score: 144.8 bits;  conditional E-value: 6.1e-46
                                   HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHHHHH CS
                      Sugar_tr  47 lsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlvPmyi 127
                                    s l++s +++Ga+iG++++gl++d++GRk+++    +l   g++lq++a    ++ +l++ R+++G+g+G+ +vl+P+ +
  gi|13541134|ref|NP_110822.1|  51 ESALMTSGAFIGAAIGAILFGLIADKIGRKPVYGLDLALITLGSFLQFFAV---NFTLLLIFRIILGLGIGGDYVLSPIIT 128
                                   347999*********************************************...*************************** PP

                                   HTTS-SCCHHH.HHHHHHHHHHHHHHHHHHHHHHH.HTSS-TTHHHHHHHCCHHHHHHHHHHGGGS---HHHHHHTT-HHH CS
                      Sugar_tr 128 sEiApkklRga.lvslyqlaitfGilvaaifglgl.nktsnadgwrillglqlvpallllilllflPESPrylvekgkeee 206
                                   +E+A  + Rg+ +++ +  + +fG ++aa+++ +      ++  w+i l++  vpal++++++  + E+ ry  +++  + 
  gi|13541134|ref|NP_110822.1| 129 AENANSRDRGKlMIMTFPIMAAFGAMLAAFVDQVStILLPSSLVWKIVLAFGGVPALFVIYFRRKITETARYSAIVKGSSV 209
                                   *********7615677899*************9995556669***********************************9999 PP

                                   HHHHHHHHHHCHHHHHHHHHHHHHHHHHHH.....HTTHHHHSH...HHHHHHHHHHHHHHTTHHHHHHHTTTHHHHSS-T CS
                      Sugar_tr 207 akevlaklrgeedadrelaeekdsleaeqeeekaswkellssktvrqrlligvvlqifqqltGinaimyysptifenlgls 287
                                   + ++++k   e++ + e+    +++ +               kt +  +li  vl+i+  +    + +y + ti +nlgl+
  gi|13541134|ref|NP_110822.1| 210 DIMSIEK---ETGTKIEITRDTKTYSYR-------------LKTSLVLVLISSVLWILYDMYSSTFAIYGPITIAKNLGLT 274
                                   9999999...444444444444444444.............3334567899999999999999888889999********* PP

                                   HHHHHHHHHHHHHHHHHHHHHHHHHHS-SHHHHHHHHHHHHHHHHHHH....HHHHTTSS.................CHHH CS
                      Sugar_tr 288 ksllvtiivgvvnfvatfvaiflvdrfGRRtllllGaagmaicfvilg..ivalllvaks..............kaasiva 352
                                   +   +    ++  +   +v+++l+d++GR++l  +G +g ++ ++++g   +  +                    + +  a
  gi|13541134|ref|NP_110822.1| 275 PISFTYYAEIFAGIPGAIVSAMLIDKIGRKRLITIGYLGVFFWLLLYGllLMKSP----IfgskilsgilptglVGEAAFA 351
                                   *94444444444455667888**************************95522222....2344467888998544444445 PP

                                   HHHHHHHHHHH.HTTTTHHH..HHHHHHHSHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHT-HHHHHHHHHHHHHH CS
                      Sugar_tr 353 ivfialfialf.algwgpvp..wvlvsElfpqsvRskalaiavavnwlanflisllfpiiteaigggyvflvfaglavlfi 430
                                    + ++++  lf a+g+++++  +++ +E+ p++ R++ +ai+v +  +a  l  + fp ++ ++g ++  l f ++a+l+i
  gi|13541134|ref|NP_110822.1| 352 GFSFYIMNYLFsAMGPASIIggAMVTPEITPTKARGTSQAITVGLDRTADALGLTAFPLLLARLGLPFLILGFSAIAILSI 432
                                   55555555555568999997446899***************************************99999*********** PP

                                   HHHHHHS--STT--CCCCG CS
                      Sugar_tr 431 ifvfffvpetkgrtleeie 449
                                   i++ +++pe  g++leei+
  gi|13541134|ref|NP_110822.1| 433 IIMNVGIPEARGKSLEEIT 451
                                   *****************96 PP

>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.2  36.4   1.5e-24   8.7e-21       6     297 ..      25     327 ..      18     358 .. 0.72
   2 !    4.3   9.5    0.0026        15      70     184 ..     340     449 ..     327     461 .. 0.77

  Alignments for each domain:
  == domain 1  score: 74.2 bits;  conditional E-value: 1.5e-24
                         MFS_1   6 flsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfasslw 86 
                                   f  +++ +++++++  + a  l+++p e  l++++ ++gaa++++++G ++d++Gr++v+ l l+l  lg++l +fa +++
  gi|13541134|ref|NP_110822.1|  25 FSDSYNLYAIALVYY-IAAFYLNLTPPESALMTSGAFIGAAIGAILFGLIADKIGRKPVYGLDLALITLGSFLQFFAVNFT 104
                                   444455555555555.88999*************************************************55555789988 PP

                         MFS_1  87 lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllgg.......lla.sslgWravfyilai 159
                                   lll++r++ Glg g+ + ++ +++a+ ++ ++rg+ +    ++f + a++g++l++       +l+ ssl W  v  + ++
  gi|13541134|ref|NP_110822.1| 105 LLLIFRIILGLGIGGDYVLSPIITAENANSRDRGKLM---IMTFPIMAAFGAMLAAfvdqvstILLpSSLVWKIVLAFGGV 182
                                   ***********************************99...67777777777777773333444444455559999999999 PP

                         MFS_1 160 vsllafvlfllllpeepperkrkspkeee..............kgtgpaplvpawkallkdpvlwillialllfffgfsg. 225
                                    +l++     ++++++ +e +r s + ++              k    +  ++ +++ lk   +  l++++ + ++ + + 
  gi|13541134|ref|NP_110822.1| 183 PALFV-----IYFRRKITETARYSAIVKGssvdimsieketgtKIEITRDTKT-YSYRLKTSLV--LVLISSVLWILYDMy 255
                                   99888.....5555555555555555554556699887554444444444444.6666666644..333333344567664 PP

                         MFS_1 226 ...lltllplylqevlglsglllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavt 297
                                      + ++ p+ + + lgl+    +++++ +  ++g+++a++++ l+d++gr+r +++++l++++++l++ ll + 
  gi|13541134|ref|NP_110822.1| 256 sstFAIYGPITIAKNLGLT---PISFTYYAEIFAGIPGAIVSAMLIDKIGRKRLITIGYLGVFFWLLLYGLLLMK 327
                                   4555555565456666666...45555999999999********************************9999888 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.0026
                         MFS_1  70 llfalglllllfasslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgW 150
                                   l ++l    ++f +++  ++++  l ++++ a++ +ga ++ +++p + rg   ++  +    + +lg  + +ll++ lg 
  gi|13541134|ref|NP_110822.1| 340 LPTGLV-GEAAF-AGFS-FYIMNYLFSAMGPASIIGGAMVTPEITPTKARGTSQAITVGLDRTADALGLTAFPLLLARLGL 417
                                   333333.22224.7777.5555555555558************************************************** PP

                         MFS_1 151 ravfyilaivsllafvlfllllpeepperkrksp 184
                                   + + + + ++++l++++  + +  ++ + k  ++
  gi|13541134|ref|NP_110822.1| 418 PFLILGFSAIAILSIII--MNVGIPEARGKSLEE 449
                                   *9999999999999887..665555555555444 PP

>> Gly-zipper_Omp  Glycine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.4   2.1e-06     0.012      22      44 ..      57      79 ..      51      81 .. 0.89
   2 ?   -2.6   0.1      0.94   5.6e+03      32      42 ..     149     159 ..     149     162 .. 0.49

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.1e-06
                Gly-zipper_Omp 22 tGaliGAavGaavGgliGaamdk 44
                                   Ga+iGAa+Ga++ gli++++++
  gi|13541134|ref|NP_110822.1| 57 SGAFIGAAIGAILFGLIADKIGR 79
                                  69*************99999876 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.94
                Gly-zipper_Omp  32 aavGgliGaam 42 
                                   aa G++ +a +
  gi|13541134|ref|NP_110822.1| 149 AAFGAMLAAFV 159
                                   44555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (465 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       669  (0.0373138); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.69u 0.35s 00:00:01.04 Elapsed: 00:00:00.54
# Mc/sec: 2599.78
//
Query:       gi|13541135|ref|NP_110823.1|  [L=233]
Description: proteasome subunit alpha [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-60  204.3   0.2    1.4e-60  204.0   0.2    1.1  1  Proteasome      Proteasome subunit
    2.2e-14   52.8   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 !  204.0   0.2   1.6e-64   1.4e-60       1     181 [.      31     208 ..      31     217 .. 0.96

  Alignments for each domain:
  == domain 1  score: 204.0 bits;  conditional E-value: 1.6e-64
                                   HHHS-EEEEEEETTEEEEEEEEEEEETTEEEESSSSTSEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHSSGTCH CS
                    Proteasome   1 vkkGttvvGikgkdgvvlaadkratagskllskstveKifkiddhigvafaGlaaDartlvrraraeaqlyrlrygrpipv 81 
                                   vkkG+t++G+k+++gv+l++dk++   skl++++++eKi  idd+++++++Gl+aDar+l+++ar  aq+++++yg  +++
  gi|13541135|ref|NP_110823.1|  31 VKKGSTALGLKFSNGVLLISDKKIR--SKLIEQNSLEKIQLIDDYVAAVTSGLVADARVLIDFARISAQQEKVTYGSLVNI 109
                                   79***********************..****************************************************** PP

                                   HHHHHHHHHHHHHHHHHCTTTTTSEEEEEEEEETTTEEEEEEEETTSEEEEESSEEEESTTHHHHHHHHHHHHSTTBSHHH CS
                    Proteasome  82 erlvarvaaklqaytqrsgrrpfgvslliagvdeeggpeLyqidpsGsyieekdavaiGsgseaaktalekeykedltlee 162
                                   e+lv+rva+++q+ytq++g+rp+gvsl++ag+d+ g p+L+ +dp+G++ e+k a+aiGsg++a+ ++lekeyke l+++e
  gi|13541135|ref|NP_110823.1| 110 ENLVKRVADQMQQYTQYGGVRPYGVSLIFAGIDQIG-PRLFDCDPAGTINEYK-ATAIGSGKDAVVSFLEKEYKEGLSEKE 188
                                   *********************************998.***************8.*************************** PP

                                   HHHHHHHHHHHHHH.HBTTS CS
                    Proteasome 163 avelavkalkeale.rdkls 181
                                   av+l +kalk++le +++l+
  gi|13541135|ref|NP_110823.1| 189 AVTLGIKALKASLEeGEELK 208
                                   ************96255555 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|13541135|ref|NP_110823.1|  8 YDRAITVFSPDGRLFQVEYAREA 30
                                  *********************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       589  (0.0328518); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.31s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 1412.24
//
Query:       gi|13541136|ref|NP_110824.1|  [L=230]
Description: RNA-associated protein [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-21   75.3   0.3      3e-21   75.3   0.3    1.5  2  SBDS      Shwachman-Bodian-Diamond syndrome (SBDS) protein
    7.8e-19   67.8   0.0    1.5e-18   66.9   0.0    1.5  1  SBDS_C    SBDS protein C-terminal domain


Domain annotation for each model (and alignments):
>> SBDS  Shwachman-Bodian-Diamond syndrome (SBDS) protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.3   0.3   3.3e-25     3e-21       3      88 .]       8      92 ..       6      92 .. 0.97
   2 ?   -3.6   0.0       1.4   1.2e+04      67      78 ..      99     110 ..      96     117 .. 0.72

  Alignments for each domain:
  == domain 1  score: 75.3 bits;  conditional E-value: 3.3e-25
                                  EEEEEEETTEEEEEEE-HHHHHHHHCTT---HHHHBSSSS-EEETTTTEE--HHHHHHHHS---HHHHHHHHHHHSEEE--HH CS
                          SBDS  3 sivrykkgkkrFeiavyknklleyregkeidLsevlqsekiFtnaskGetaskselekafgteskdeiikeILkkGeiqvsae 85
                                   ++r+++++ +Fei+v+++++++ r+g +id+++ l+ ++++++a+kGe+as+++l++af+t++  +i+  I+kkG+iq+++e
  gi|13541136|ref|NP_110824.1|  8 IVARLESHGYKFEILVDPDAIERIRKG-NIDIENDLAMPEVYKDARKGEKASEESLKEAFKTTDIAQIVVDIVKKGQIQLTTE 89
                                  6799***********************.8****************************************************** PP

                                  HHH CS
                          SBDS 86 erk 88
                                  +r+
  gi|13541136|ref|NP_110824.1| 90 QRR 92
                                  996 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 1.4
                                   HHHHHHHHHHHS CS
                          SBDS  67 kdeiikeILkkG 78 
                                    ++i+++I ++G
  gi|13541136|ref|NP_110824.1|  99 RKQIVNIIAREG 110
                                   578888888888 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 !   66.9   0.0   1.6e-22   1.5e-18       2     111 ..      99     212 ..      98     217 .. 0.82

  Alignments for each domain:
  == domain 1  score: 66.9 bits;  conditional E-value: 1.6e-22
                                   HHHHHHHHHHHEEBTTTTB---HHHHHHHHHHTT----TTS-CCCCHHHHHHHHTTTS--EE-EEEEEEEE-...CCCHHH CS
                        SBDS_C   2 ekeiieivaeklvnpqtkrpytttmIekalkelgtsvktnksaksQalevikaLiqeipiqrarmrlritcptsikdkilk 82 
                                   +k+i++i+a++ +npqt++p+t+ +I++a++e+++++++ ksa++Q++ v+ka+  +ipi++++ +l++++     d   k
  gi|13541136|ref|NP_110824.1|  99 RKQIVNIIAREGINPQTNTPHTPYRISQAMEEAKVKIDPFKSAEEQVQGVLKAIMPIIPIRFEKAKLAVKLV---GDAYGK 176
                                   69*********************************************************************9...888888 PP

                                   HHHHH.HH.....S.EE.....EEEE.EEGGGHHHH CS
                        SBDS_C  83 lieqv.esqkvaekewe.....vvvl.iePgaykel 111
                                   l+ ++ +s  ++++ew      + +l +++g + ++
  gi|13541136|ref|NP_110824.1| 177 LYGELaKSGYITKEEWGkdgswMGILeVPAGIQGDI 212
                                   888884443344444433444344444666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       854  (0.0476323); expected 358.6 (0.02)
Passed bias filter:                      563  (0.0314016); 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: 0.59u 0.33s 00:00:00.92 Elapsed: 00:00:00.54
# Mc/sec: 1277.37
//
Query:       gi|13541137|ref|NP_110825.1|  [L=236]
Description: exosome complex RNA-binding protein Rrp4 [Thermoplasma volcanium GSS1]
Scores for 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-06   27.5   1.1    4.4e-06   26.4   1.1    1.6  1  KH_1           KH domain
    1.6e-05   24.6   1.3    2.8e-05   23.8   0.5    1.8  2  KH_2           KH domain
    0.00015   22.0   0.7    0.00024   21.4   0.7    1.4  1  KH_6           KH domain
    0.00074   19.8   0.0     0.0076   16.6   0.0    2.5  3  S1             S1 RNA binding domain
       0.01   15.5   0.1      0.034   13.8   0.0    1.9  2  TFA2_Winged_2  TFA2 Winged helix domain 2


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 !   26.4   1.1   1.2e-09   4.4e-06       4      65 ..     146     200 ..     144     201 .. 0.91

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 1.2e-09
                                   EEEGGGHHHHHHTGGGHHHHHHHHHHT-EEEEESSTT...T.-EEEEEESHHHHHHHHHHHH CS
                          KH_1   4 ilvPsslvgriIGkgGsnIkeIreetgakIkvpksedegsderevtisGspeavekAkelie 65 
                                   +l+++s v+r+IGkgG +++  +e t ++I +  ++     +  + i G+ e+v  A+++ie
  gi|13541137|ref|NP_110825.1| 146 VLIHASRVPRVIGKGGGMVNMVKELTSTRIII--GQ-----NGLIWIDGPIEGVTMAIAAIE 200
                                   699****************************6..43.....469**************9996 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.5   7.9e-09   2.8e-05      28      68 ..     145     185 ..     135     190 .. 0.91
   2 ?   -3.5   0.0       2.6   9.3e+03      26      35 ..     198     207 ..     191     210 .. 0.65

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 7.9e-09
                                   EEEEEESCHHHHHTGGGHHHHHHHHHHHHHHHHHHTTCEEE CS
                          KH_2  28 iiviresqpgivIGkgGsnikkigkelrkdieklegkkVkl 68 
                                    + i++s+  +vIGkgG +++++++    +i + +++ +++
  gi|13541137|ref|NP_110825.1| 145 MVLIHASRVPRVIGKGGGMVNMVKELTSTRIIIGQNGLIWI 185
                                   689****************************9999998987 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 2.6
                                   EEEEEEEESC CS
                          KH_2  26 rviiviresq 35 
                                   ++++++re++
  gi|13541137|ref|NP_110825.1| 198 AIEMIEREAH 207
                                   5566666665 PP

>> KH_6  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.7   6.8e-08   0.00024       1      43 [.     143     188 ..     143     191 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 6.8e-08
                          KH_6   1 GmlfeVslslvrRll......nhvLeeLgkagpfeiavGlNGriWvkse 43 
                                   G ++ +  s v+R++      +    ++++  +  i++G+NG iW++++
  gi|13541137|ref|NP_110825.1| 143 GHMVLIHASRVPRVIgkgggmV---NMVKELTSTRIIIGQNGLIWIDGP 188
                                   6678888999999998887442...444455779************987 PP

>> S1  S1 RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1       1.6   5.7e+03      47      59 ..       8      20 ..       5      20 .. 0.78
   2 !   16.6   0.0   2.1e-06    0.0076       2      67 ..      61     126 ..      60     133 .. 0.94
   3 ?   -0.0   0.0      0.32   1.2e+03      26      40 ..     142     156 ..     139     180 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.6
                                  HHCEETTEEEEEE CS
                            S1 47 devlkvGdevkvk 59
                                  ++ + +Gd+v+v+
  gi|13541137|ref|NP_110825.1|  8 KKIVLPGDPVEVQ 20
                                  6678899999995 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 2.1e-06
                                   STTTCEEEEEEEEEETTEEEEEETTTEEEEEEGGGSSSSCEESCHHHCEETTEEEEEEEEEEETTT CS
                            S1   2 pekgevveGeVtsvtkgGafVelgngvegfvpaselsrdarvedpdevlkvGdevkvkvlkvdkdr 67 
                                   p+kg+ v G++++v +    V++  +  ++++ ++ +++ +  d ++ l  Gd v++k+  v++ +
  gi|13541137|ref|NP_110825.1|  61 PRKGDKVIGKIIEVGPSTWTVDINSPYFAMLHMNDTPWRISSGDLKRYLNSGDYVYAKIMSVNEIK 126
                                   79*********************************************************9998765 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 0.32
                                   TTEEEEEEGGGSSSS CS
                            S1  26 ngvegfvpaselsrd 40 
                                   +g+ ++++as ++r 
  gi|13541137|ref|NP_110825.1| 142 GGHMVLIHASRVPRV 156
                                   588899****99986 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 !   13.8   0.0   9.4e-06     0.034       4      47 ..     103     149 ..     101     177 .. 0.84
   2 ?   -2.0   0.0      0.84     3e+03      31      42 ..     215     226 ..     212     227 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 9.4e-06
                 TFA2_Winged_2   4 eeLlalLkkrp..kaeGikvkdLkdswpdv.eealeeLeaegeilvl 47 
                                    +L+++L + +   a+ ++v+++k+sw    e+ l++Le+ + +l+ 
  gi|13541137|ref|NP_110825.1| 103 GDLKRYLNSGDyvYAKIMSVNEIKESWLTLkEPGLKKLEGGHMVLIH 149
                                   689999988876569**************72567******9999987 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.84
                 TFA2_Winged_2  31 veealeeLeaeg 42 
                                   ve +l+eL +++
  gi|13541137|ref|NP_110825.1| 215 VESFLKELRGDK 226
                                   89999**99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       338  (0.0188521); 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:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 1411.00
//
Query:       gi|13541138|ref|NP_110826.1|  [L=248]
Description: exosome complex exonuclease Rrp41 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.5e-34  118.2   0.0    4.9e-34  117.7   0.0    1.2  1  RNase_PH    3' exoribonuclease family, domain 1
      4e-14   52.4   0.5    8.5e-14   51.3   0.5    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 !  117.7   0.0   5.5e-38   4.9e-34       1     132 []      26     155 ..      26     155 .. 0.93

  Alignments for each domain:
  == domain 1  score: 117.7 bits;  conditional E-value: 5.5e-38
                                   EEEEEEEEESSSSTTSEEEEEEECCEEEEEEEEEEEEEE-TCCG..--CCEEEECCCCECCCCEC-C...S...HHHHHHH CS
                      RNase_PH   1 elRslsietgvlsqanGSaylelGdtkvlasvtgpieerpseer..ddaegaldveveyapfasgerrregrpsdeeiels 79 
                                   elR+++ie gvl +a+GSay+e G +k++++v+gp+e+ p+ ++  d+a  ++++++++a f+  er+r   p+++++e+s
  gi|13541138|ref|NP_110826.1|  26 ELRPIKIEAGVLNRADGSAYIEWGGNKIIVGVYGPKEAYPKHSQdiDHA--VVKARYNMAAFSVDERKR-PGPDRRTMEIS 103
                                   79***********************************955555311444..5***************87.56********* PP

                                   HHHHHHHCCTC-CCGCCTCEEEEEEEEEECCCS-CHHHCHHHHHHHHHCTCEE CS
                      RNase_PH  80 rlleralrpsillekkpkstididitvlssdggslldalinaaslALadagip 132
                                   +++ +al++si++e++p+ +id++i+vl++d  ++  a  +aa++ALadagip
  gi|13541138|ref|NP_110826.1| 104 KVISEALSSSIMIEQFPRAEIDVYIEVLQADA-GTRIAGLTAATVALADAGIP 155
                                   ********************************.*******************9 PP

>> RNase_PH_C  3' exoribonuclease family, domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.3   0.5   9.5e-18   8.5e-14       1      60 [.     158     216 ..     158     220 .. 0.96

  Alignments for each domain:
  == domain 1  score: 51.3 bits;  conditional E-value: 9.5e-18
                                   S--EEEEEEEETTEEEES--HHHHHHSSEEEEEEEETTSEEEEEEEECSSCEEHHHHHHH CS
                    RNase_PH_C   1 apviavtvgkvddqfvlDptkeEedlsegdltlavagtkevvtlmkeggsqldeetllea 60 
                                   ++v+++t gkvd+++vlD++keE++ +e+d+++a+  +  +++l++++g  ++e+++ ea
  gi|13541138|ref|NP_110826.1| 158 DMVVGCTAGKVDGHIVLDLSKEEDNFGEADIPMAIMPKTGEIVLLQMDGD-VTEDEFYEA 216
                                   69*********************************9999999********.******998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); 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: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.53
# Mc/sec: 1420.09
//
Query:       gi|13541139|ref|NP_110827.1|  [L=260]
Description: exosome complex RNA-binding protein Rrp42 [Thermoplasma volcanium GSS1]
Scores for complete 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-29  101.9   0.0    5.8e-29  101.3   0.0    1.3  1  RNase_PH    3' exoribonuclease family, domain 1
    4.9e-13   48.9   0.2    9.3e-13   48.0   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 !  101.3   0.0   6.4e-33   5.8e-29       1     132 []      34     169 ..      34     169 .. 0.94

  Alignments for each domain:
  == domain 1  score: 101.3 bits;  conditional E-value: 6.4e-33
                                   EEEEEEEEESSSSTTSEEEEEEECCEEEEEEEEEEEEEE-TCCG.--CCEEEECCCCECCCCEC-C...S...HHHHHHHH CS
                      RNase_PH   1 elRslsietgvlsqanGSaylelGdtkvlasvtgpieerpseer.ddaegaldveveyapfasgerrregrpsdeeielsr 80 
                                   e+R+++i  + +++anGSay+ lG+t v+a+v+ +  e p++++ d  +g+l+++ve+ p+a ++++  g p+d +ie+sr
  gi|13541139|ref|NP_110827.1|  34 EFREITIIENYVPRANGSAYVALGKTRVVAGVKIEAGE-PFPDTpD--QGVLTTNVELLPIAFPSFEA-GPPNDLAIEVSR 110
                                   89**********************************99.8888744..589***************55.9*********** PP

                                   HHHHHHCCTC-C........CGCCTCEEEEEEEEEECCCS-CHHHCHHHHHHHHHCTCEE CS
                      RNase_PH  81 lleralrpsill........ekkpkstididitvlssdggslldalinaaslALadagip 132
                                   +++r +r+s ++        ++k+ + + +di vl++dg +l+da+ +aa  AL +a +p
  gi|13541139|ref|NP_110827.1| 111 VVDRGIRESKMIspdklvieQGKKVWIVFLDINVLDYDG-NLIDACTIAAVSALRNAIVP 169
                                   ***********99999999988999**************.***************99776 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   0.2     1e-16   9.3e-13       3      66 ..     186     249 ..     184     250 .. 0.95

  Alignments for each domain:
  == domain 1  score: 48.0 bits;  conditional E-value: 1e-16
                                   -EEEEEEEETTEEEES--HHHHHHSSEEEEEEEETTSEEEEEEEECSSC.EEHHHHHHHHHHHHH CS
                    RNase_PH_C   3 viavtvgkvddqfvlDptkeEedlsegdltlavagtkevvtlmkeggsq.ldeetlleaielAkk 66 
                                   +i+vt+ k++d++v+Dp++eE++++ g++t++ ++++ +   m+ g+ + ++ +++++ai++++k
  gi|13541139|ref|NP_110827.1| 186 PISVTMVKIGDTLVCDPSLEEDQICGGRITVTTTEDGHI-RAMQKGEIGvFTLDDVKKAIKMSLK 249
                                   99***********************************99.9999999999************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); 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: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.52
# Mc/sec: 1513.24
//
Query:       gi|13541140|ref|NP_110828.1|  [L=80]
Description: 50S ribosomal protein L37Ae [Thermoplasma volcanium GSS1]
Scores for complete sequence (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   95.5   4.1    1.7e-27   95.4   4.1    1.0  1  Ribosomal_L37ae  Ribosomal L37ae protein family
     0.0003   20.7   3.1     0.0004   20.3   3.1    1.3  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
     0.0012   18.6   1.6     0.0013   18.5   1.6    1.1  1  Rep_fac-A_C      Replication factor-A C terminal domain
     0.0018   18.2   0.7     0.0028   17.5   0.7    1.3  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
     0.0051   16.7   3.9       0.01   15.7   3.9    1.5  1  Zn_ribbon_SprT   SprT-like zinc ribbon domain
  ------ inclusion threshold ------
       0.01   16.0   0.5       0.42   10.8   0.0    2.2  2  Zn-ribbon_8      Zinc ribbon domain
      0.022   14.2   5.6       0.25   10.8   5.6    2.1  1  zf-ribbon_3      zinc-ribbon domain
      0.031   14.9   0.1      0.039   14.5   0.1    1.2  1  RPA_interact_C   Replication protein A interacting C-terminal
      0.051   13.5   0.1        5.4    7.0   0.0    2.2  2  PhnA_Zn_Ribbon   PhnA Zinc-Ribbon
      0.053   13.1   0.1       0.08   12.5   0.1    1.3  1  TF_Zn_Ribbon     TFIIB zinc-binding
       0.14   12.6   7.0        1.8    9.2   1.8    2.2  2  zf-H2C2_2        Zinc-finger double domain
       0.16   12.0   1.6        1.4    9.0   0.1    2.1  2  CpXC             CpXC protein
       0.18   11.9   2.1        9.7    6.3   0.1    2.3  2  Rubredoxin       Rubredoxin
       0.42   10.4   7.3       0.33   10.7   0.7    2.4  2  Rubredoxin_2     Rubredoxin metal binding domain
       0.46   10.5   3.9        3.2    7.7   0.4    2.3  2  zinc_ribbon_4    zinc-ribbon domain
       0.63    9.8   4.3         19    5.1   0.3    2.2  2  zinc_ribbon_10   Predicted integral membrane zinc-ribbon meta
       0.66   10.3   5.9        3.5    8.0   5.9    2.0  1  Prim_Zn_Ribbon   Zinc-binding domain of primase-helicase
        0.7   10.0   9.5         12    6.1   9.5    2.2  1  UPF0547          Uncharacterised protein family UPF0547
          1    9.3   4.0         12    5.9   4.1    2.1  2  RNA_POL_M_15KD   RNA polymerases M/15 Kd subunit
        1.3    9.7   4.9         11    6.7   0.3    2.3  2  zf-C2H2          Zinc finger, C2H2 type


Domain annotation for each model (and alignments):
>> Ribosomal_L37ae  Ribosomal L37ae protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.4   4.1   1.8e-30   1.7e-27       1      72 [.       4      75 ..       4      79 .. 0.95

  Alignments for each domain:
  == domain 1  score: 95.4 bits;  conditional E-value: 1.8e-30
                                  XXXXXX-GGGGTTSS-HHHHHHHHHHHHHHHS-BEESSSSSSEEEEEETTEEEETTTTEEEE-BSSSSS-HH CS
               Ribosomal_L37ae  1 rtkkvgiaGkygtrYGaslrkrvkkieisqhakytCpfcgktkvkRkavgiwkCkkcgktvaGgAytpetts 72
                                  rt kvg aG++g+rYG+++rk++++i +++ a ytCp+c+k++vkR a+giw C++cg+++aGgAy p  + 
  gi|13541140|ref|NP_110828.1|  4 RTLKVGAAGRFGPRYGVTIRKEWNEIYKQKIALYTCPSCKKKRVKRLAAGIWVCRHCGYKFAGGAYNPAYEV 75
                                  688***************************************************************997665 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 !   20.3   3.1   4.5e-07    0.0004      19      45 ..      37      62 ..      25      63 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 4.5e-07
                 Zn_Tnp_IS1595 19 fvCPhCgsrkayriktrglfqCkeCrk 45
                                   +CP C+++++ r+++ g + C++C++
  gi|13541140|ref|NP_110828.1| 37 YTCPSCKKKRVKRLAA-GIWVCRHCGY 62
                                  58*************9.********98 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 !   18.5   1.6   1.5e-06    0.0013      10      54 ..      28      71 ..      20      79 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.5e-06
                                  EEETTTTEEEB--STT---B-EEE.TTTEEEETTTTEEESS--EEE CS
                   Rep_fac-A_C 10 fikkdnlvYkACpsedCnkKvvee.edgewrCekCdkeveepkyry 54
                                   i+k++++   Cp   C+kK v++ + g w C +C  +++   y+ 
  gi|13541140|ref|NP_110828.1| 28 EIYKQKIALYTCP--SCKKKRVKRlAAGIWVCRHCGYKFAGGAYNP 71
                                  56777777778**..********9899********99998777765 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.7   3.2e-06    0.0028      30      56 ..      38      64 ..      35      70 .. 0.94

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 3.2e-06
                OrfB_Zn_ribbon 30 tCseCgsknkealsgrtfkCpnCgfea 56
                                  tC+ C +k  ++l+   ++C++Cg+++
  gi|13541140|ref|NP_110828.1| 38 TCPSCKKKRVKRLAAGIWVCRHCGYKF 64
                                  8***********************986 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 !   15.7   3.9   1.1e-05      0.01       5      31 ..      37      61 ..      36      66 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.1e-05
                Zn_ribbon_SprT  5 YrCtgCgreythhlsirrhn...YrCrrCk 31
                                  Y+C++C++      +++r +   + Cr+C+
  gi|13541140|ref|NP_110828.1| 37 YTCPSCKK-----KRVKRLAagiWVCRHCG 61
                                  *******4.....4554444477******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 ?   10.8   0.0   0.00047      0.42      26      39 ..      36      50 ..      25      51 .. 0.82
   2 ?    3.6   0.1     0.084        76       7      15 ..      56      64 ..      54      68 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00047
                   Zn-ribbon_8 26 ltaCPeCgs.evrrv 39
                                  l +CP+C++ +v+r+
  gi|13541140|ref|NP_110828.1| 36 LYTCPSCKKkRVKRL 50
                                  678******999996 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.084
                   Zn-ribbon_8  7 rCeeCghef 15
                                   C+ Cg +f
  gi|13541140|ref|NP_110828.1| 56 VCRHCGYKF 64
                                  599999887 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   5.6   0.00028      0.25       3      26 .]      37      64 ..      35      64 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00028
                   zf-ribbon_3  3 vrCPnCGap.lssddn...vCpyCGtkl 26
                                  ++CP+C+++ ++  +    vC +CG+k+
  gi|13541140|ref|NP_110828.1| 37 YTCPSCKKKrVKRLAAgiwVCRHCGYKF 64
                                  78******55999887777******985 PP

>> RPA_interact_C  Replication protein A interacting C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   4.3e-05     0.039       1      27 [.      38      66 ..      38      77 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.3e-05
                RPA_interact_C  1 lCPvCkkrklkets.evifCe.Cglrlet 27
                                  +CP Ckk+++k+    + +C+ Cg +++ 
  gi|13541140|ref|NP_110828.1| 38 TCPSCKKKRVKRLAaGIWVCRhCGYKFAG 66
                                  5**********97758889*99**99875 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.032        29      18      26 ..      35      43 ..      18      44 .. 0.86
   2 ?    7.0   0.0    0.0061       5.4      19      27 ..      54      62 ..      52      65 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.032
                PhnA_Zn_Ribbon 18 allvCpeCa 26
                                  al+ Cp C+
  gi|13541140|ref|NP_110828.1| 35 ALYTCPSCK 43
                                  688999997 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0061
                PhnA_Zn_Ribbon 19 llvCpeCah 27
                                  ++vC +C++
  gi|13541140|ref|NP_110828.1| 54 IWVCRHCGY 62
                                  8******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   0.1     9e-05      0.08       1      27 [.      37      62 ..      37      65 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 9e-05
                                  EEETTTTCEECHEETSTTCEEESSSSB CS
                  TF_Zn_Ribbon  1 ykCPnCgstnlveDpergelvCtdCGl 27
                                  y+CP C+ ++ v   + g  vC  CG+
  gi|13541140|ref|NP_110828.1| 37 YTCPSCKKKR-VKRLAAGIWVCRHCGY 62
                                  89*****986.***************8 PP

>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   1.8     0.002       1.8      13      23 ..      33      45 ..      30      48 .. 0.81
   2 ?    6.6   0.3     0.012        11      15      25 ..      55      65 ..      46      65 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.002
                     zf-H2C2_2 13 kp..yeCplCdka 23
                                  k+  y+Cp+C+k+
  gi|13541140|ref|NP_110828.1| 33 KIalYTCPSCKKK 45
                                  5555*******96 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.012
                     zf-H2C2_2 15 yeCplCdkaFk 25
                                  + C  C+++F+
  gi|13541140|ref|NP_110828.1| 55 WVCRHCGYKFA 65
                                  68********6 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.1    0.0016       1.4      29      47 ..      28      46 ..      22      54 .. 0.87
   2 ?    2.9   0.1      0.12     1e+02      38      47 ..      55      64 ..      47      73 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0016
                          CpXC 29 klldgslfeatCpkCgata 47
                                  ++ ++++  +tCp+C +++
  gi|13541140|ref|NP_110828.1| 28 EIYKQKIALYTCPSCKKKR 46
                                  7889999********9986 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.12
                          CpXC 38 atCpkCgata 47
                                  ++C +Cg+++
  gi|13541140|ref|NP_110828.1| 55 WVCRHCGYKF 64
                                  7899999987 PP

>> Rubredoxin  Rubredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.1     0.011       9.7      35      44 ..      37      46 ..      16      48 .. 0.82
   2 ?    5.4   0.4     0.021        18       2      11 ..      55      64 ..      54      75 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.011
                                  -BBTTTB-BG CS
                    Rubredoxin 35 WvCPdCgvek 44
                                  ++CP+C+ ++
  gi|13541140|ref|NP_110828.1| 37 YTCPSCKKKR 46
                                  89****9876 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.021
                                  EEETTT-BEE CS
                    Rubredoxin  2 yeCkvCgyvY 11
                                  + C+ Cgy +
  gi|13541140|ref|NP_110828.1| 55 WVCRHCGYKF 64
                                  8899999975 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.9       0.1        91      17      21 ..      39      43 ..      38      44 .. 0.87
   2 ?   10.7   0.7   0.00036      0.33       1      10 [.      55      64 ..      55      66 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.1
                  Rubredoxin_2 17 CpsCg 21
                                  CpsC+
  gi|13541140|ref|NP_110828.1| 39 CPSCK 43
                                  ****8 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00036
                  Rubredoxin_2  1 YvCsqCGfes 10
                                  +vC++CG+++
  gi|13541140|ref|NP_110828.1| 55 WVCRHCGYKF 64
                                  89******87 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.4    0.0036       3.2       4      12 ..      38      46 ..      36      47 .. 0.87
   2 ?    3.9   0.2     0.059        53      28      35 ..      57      64 ..      53      65 .. 0.68

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0036
                 zinc_ribbon_4  4 tCpsCkaky 12
                                  tCpsCk+k+
  gi|13541140|ref|NP_110828.1| 38 TCPSCKKKR 46
                                  8*****985 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.059
                 zinc_ribbon_4 28 CskCghvF 35
                                  C +Cg +F
  gi|13541140|ref|NP_110828.1| 57 CRHCGYKF 64
                                  66666665 PP

>> zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.3     0.022        19      44      53 ..      36      45 ..      26      46 .. 0.78
   2 ?    3.4   4.4     0.069        62      38      53 ..      48      63 ..      39      64 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.022
                zinc_ribbon_10 44 kyrCpkCgal 53
                                   y Cp+C+ +
  gi|13541140|ref|NP_110828.1| 36 LYTCPSCKKK 45
                                  699****875 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.069
                zinc_ribbon_10 38 eeleevkyrCpkCgal 53
                                  ++l+   ++C +Cg +
  gi|13541140|ref|NP_110828.1| 48 KRLAAGIWVCRHCGYK 63
                                  5566668******975 PP

>> Prim_Zn_Ribbon  Zinc-binding domain of primase-helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   5.9     0.004       3.5      21      33 ..      50      61 ..      37      68 .. 0.62

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.004
                                  ...S-EEETTTTB CS
                Prim_Zn_Ribbon 21 dgrGtwfCrqCgg 33
                                    +G w+Cr+C g
  gi|13541140|ref|NP_110828.1| 50 LAAGIWVCRHC-G 61
                                  3349*******.5 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   9.5     0.014        12       2      24 ..      38      64 ..      38      65 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.014
                       UPF0547  2 vCPeCeak....vPvaaqfCphCGyvF 24
                                  +CP C  k    +++   +C+hCGy F
  gi|13541140|ref|NP_110828.1| 38 TCPSCKKKrvkrLAAGIWVCRHCGYKF 64
                                  6888887665557788889******99 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.4      0.29   2.6e+02       4       8 ..      39      43 ..      30      49 .. 0.71
   2 ?    5.9   4.1     0.013        12      20      31 ..      55      64 ..      36      66 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.29
                                  ESTTT CS
                RNA_POL_M_15KD  4 CpkCg 8 
                                  Cp+C+
  gi|13541140|ref|NP_110828.1| 39 CPSCK 43
                                  55554 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.013
                                  CEEEESSSS-EE CS
                RNA_POL_M_15KD 20 knfeCrqCgYee 31
                                  ++  Cr CgY++
  gi|13541140|ref|NP_110828.1| 55 WV--CRHCGYKF 64
                                  33..******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 ?    5.0   0.6     0.044        39       1       9 [.      37      45 ..      37      50 .. 0.85
   2 ?    6.7   0.3     0.012        11       2      10 ..      56      64 ..      55      66 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.044
                                  EEETTTTEE CS
                       zf-C2H2  1 ykCpdCgks 9 
                                  y+Cp C+k+
  gi|13541140|ref|NP_110828.1| 37 YTCPSCKKK 45
                                  9*****974 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.012
                                  EETTTTEEE CS
                       zf-C2H2  2 kCpdCgksF 10
                                  +C +Cg++F
  gi|13541140|ref|NP_110828.1| 56 VCRHCGYKF 64
                                  7******99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       882  (0.049194); expected 358.6 (0.02)
Passed bias filter:                      656  (0.0365888); expected 358.6 (0.02)
Passed Vit filter:                       109  (0.00607954); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.57u 0.32s 00:00:00.88 Elapsed: 00:00:00.53
# Mc/sec: 453.88
//
Query:       gi|13541141|ref|NP_110829.1|  [L=45]
Description: DNA-directed RNA polymerase subunit P [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00011   21.8   2.9    0.00017   21.2   2.9    1.3  1  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
    0.00071   19.8   1.8    0.00073   19.8   1.8    1.0  1  DUF1922         Domain of unknown function (DUF1922)
     0.0034   17.5   2.1     0.0049   17.0   2.1    1.2  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 !   21.2   2.9   2.8e-08   0.00017       1      32 []       4      35 ..       4      35 .. 0.93

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 2.8e-08
                                  -B-SSS--B--.--SSS----SSS-----B--- CS
                DNA_RNApol_7kD  1 YiCgeCgaevs.lkkgdpiRCkeCGhRilYKkR 32
                                  Y+C +Cg + +    +  i C  CG+R++ K+R
  gi|13541141|ref|NP_110829.1|  4 YKCVRCGRPLEkTMGTTEIECE-CGSRVFVKER 35
                                  9**********7777789***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 !   19.8   1.8   1.2e-07   0.00073       4      40 ..       4      41 ..       2      45 .] 0.89

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 1.2e-07
                                  EEET.TS--EEEETT-SEEEETTTEEEE--SSS-BS-- CS
                       DUF1922  4 fRCd.CGRvlYakegaktrkCvCGktikvkerrilkka 40
                                  ++C  CGR l    g+   +C CG ++ vker  ++k+
  gi|13541141|ref|NP_110829.1|  4 YKCVrCGRPLEKTMGTTEIECECGSRVFVKERPSIEKT 41
                                  78977**************************9877776 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   2.1   8.1e-07    0.0049       5      36 ..       3      30 ..       3      33 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 8.1e-07
                   Zn-ribbon_8  5 eYrCeeCghefevlqsisdapltaCPeCgsev 36
                                  eY+C +Cg+  e+ +  +   +++C eCgs+v
  gi|13541141|ref|NP_110829.1|  3 EYKCVRCGRPLEKTMGTT---EIEC-ECGSRV 30
                                  8***********998766...788*.999965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (45 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.33s 00:00:00.79 Elapsed: 00:00:00.50
# Mc/sec: 273.09
//
Query:       gi|13541142|ref|NP_110830.1|  [L=388]
Description: pseudouridylate synthase [Thermoplasma volcanium GSS1]
Scores for complete 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-08   33.2   0.7    1.3e-07   31.8   0.7    1.8  1  THUMP     THUMP domain
     0.0036   17.7   0.2     0.0076   16.6   0.2    1.6  1  TruB_N    TruB family pseudouridylate synthase (N terminal do


Domain annotation for each model (and alignments):
>> THUMP  THUMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.8   0.7   1.4e-11   1.3e-07      57     142 ..      58     157 ..      18     159 .. 0.84

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 1.4e-11
                                   EEEEESSHHHHHHHHHHHHHHHHHHCT-EEEEEEEESSSTS..............SSHHHHHHHHHHHHHHCCTT-EE-SS CS
                         THUMP  57 cevceadledileaakeivkkkfeeeketFaVrvkrrgkhf..............eftsreinrevGkaivektglkVdle 123
                                   ce+c   ++++  + + +  k +e e  tF V++ ++++ +              e +++e+nre Gk+i  ktg++ + e
  gi|13541142|ref|NP_110830.1|  58 CEICHGIFDKFSVFLSLVEDKLKEIEYSTFVVGSVFPKEWIelenkiqeafgahgESIKKEFNREFGKYITAKTGKEYRKE 138
                                   7777777777777776666665555444***********99**************************************** PP

                                   S-SEEEEEEEETTEEEEEE CS
                         THUMP 124 nPdivvrveiikdkayisi 142
                                   +Pdi++ v +  + + +si
  gi|13541142|ref|NP_110830.1| 139 DPDITIAVNVEYEFVNVSI 157
                                   **********988887777 PP

>> TruB_N  TruB family pseudouridylate synthase (N terminal domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.2   8.5e-07    0.0076      69     149 .]     269     351 ..     247     351 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 8.5e-07
                                   -TT--HHHHHHHHHHC-EEE-------------------------------..--EEEEEEEEEEEEEEEEEEEEEESTTT CS
                        TruB_N  69 veklteekleevlkkftGeieqvppmySAvkvnGkrlyelaregeeverkk..rkvtiyelelleveepevelevecskGt 147
                                   +++ +++k+ +++ +   +i++     +  ++nGk++y+ +   ++  r+   r+ +i+++el++ve +e+e+ v+ ++Gt
  gi|13541142|ref|NP_110830.1| 269 IKEEKHSKVYDCIIEGDTDIDKLKLEEACTEMNGKNIYQRTPLRVAQRRSDliRTRKIERMELVAVEGKEAEIVVQAEAGT 349
                                   334444556666777778899999999999********987555555554445**************************** PP

                                   TH CS
                        TruB_N 148 Yi 149
                                   Yi
  gi|13541142|ref|NP_110830.1| 350 YI 351
                                   *9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (388 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       667  (0.0372023); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.28s 00:00:00.90 Elapsed: 00:00:00.49
# Mc/sec: 2379.91
//
Query:       gi|13541143|ref|NP_110831.1|  [L=98]
Description: 50S ribosomal protein L21e [Thermoplasma volcanium GSS1]
Scores for complete 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   90.3   1.8    6.2e-26   90.2   1.8    1.0  1  Ribosomal_L21e  Ribosomal protein L21e
  ------ inclusion threshold ------
      0.077   12.9   0.0      0.097   12.6   0.0    1.2  1  Ribosomal_L19   Ribosomal protein L19


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 !   90.2   1.8   6.9e-30   6.2e-26       2     100 ..       3      97 ..       2      98 .] 0.98

  Alignments for each domain:
  == domain 1  score: 90.2 bits;  conditional E-value: 6.9e-30
                                   --S-STTTT-TTTTS--GGG-SS--SHHHH----TT-EEEE---TT--SS---GGGTT-EEEE..EEEETTEEEEEEEETT CS
                Ribosomal_L21e   2 knskglrrgtrklfskkfrkkgvpplstylreykkGdkVdikidpsvqkgmphkryhGktgrvynvtkravgvivnkkvgg 82 
                                   k+s+g+r+g+r++++k+  ++  + + ++++e+  Gd+V+i+i+psv++gmp++r++G tg v   + ++ +++v +kvg+
  gi|13541143|ref|NP_110831.1|   3 KMSHGPRSGSRRKLTKSKEERKKSIIGRMMQEFSPGDRVAIDIEPSVHNGMPYHRFQGYTGIV--EGAQGNCYKVGVKVGS 81 
                                   78*************************************************************..***************9 PP

                                   E..EEEEEE-GGGEEE-- CS
                Ribosomal_L21e  83 kileKriivriehlkksk 100
                                      +K +i+ + hlk++k
  gi|13541143|ref|NP_110831.1|  82 L--TKYVIASPVHLKRIK 97 
                                   9..************987 PP

>> Ribosomal_L19  Ribosomal protein L19
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   1.1e-05     0.097       8      53 ..      25      73 ..      16      89 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.1e-05
                 Ribosomal_L19  8 keqlkkdlpefkvGdtvkVkvk..ikegk.keRiqafeGvviarkgkgi 53
                                  k+ + + + ef++Gd v ++++  +++g   +R q ++G+v   +g+  
  gi|13541143|ref|NP_110831.1| 25 KSIIGRMMQEFSPGDRVAIDIEpsVHNGMpYHRFQGYTGIVEGAQGNCY 73
                                  444567799******99988753378884489********988777655 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:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.34s 00:00:00.89 Elapsed: 00:00:00.53
# Mc/sec: 554.53
//
Query:       gi|13541144|ref|NP_110832.1|  [L=103]
Description: hypothetical protein TVN0313 [Thermoplasma volcanium GSS1]
Scores for complete 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   19.7   0.0     0.0015   18.8   0.0    1.4  1  RNA_pol_Rpb4  RNA polymerase Rpb4
     0.0089   16.6   0.0       0.08   13.5   0.0    2.0  2  POTRA         Surface antigen variable number repeat
  ------ inclusion threshold ------
       0.11   12.4   0.3       0.15   11.9   0.3    1.3  1  Ost4          Oligosaccaryltransferase


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 !   18.8   0.0   2.6e-07    0.0015      37     122 ..      17     101 ..       5     102 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 2.6e-07
                                   HTCHHCHHHHHHHHHHHCTHHTTSSHHHHHHHHHHHTTST.STHHHHHHHHHCSTSSHHHHHHHSTTGTTTSTSHHHHHHH CS
                  RNA_pol_Rpb4  37 vkgnlnkilkktleyltnkfsrlkneekfnelvellksfe.LtkaEklqlvnlkPesavelktlieeleerfedeqleeiL 116
                                    k++l+ + k++ley  + fsr + ++ +  +   ++ +  L ++ ++++++lkP + +++ ++    +  ++de+l+++ 
  gi|13541144|ref|NP_110832.1|  17 KKEQLTDMEKENLEYAGK-FSRVD-PSVIDRVKGDISGIAkLPEKVIVKILDLKPGTPADITSILSTYNVMISDEDLNALA 95 
                                   5778999999*******9.****9.8888888888887667***************************************9 PP

                                   HHHHHH CS
                  RNA_pol_Rpb4 117 delkev 122
                                   d lk++
  gi|13541144|ref|NP_110832.1|  96 DYLKKL 101
                                   999987 PP

>> POTRA  Surface antigen variable number repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0     0.065   3.9e+02      37      61 ..      21      42 ..       8      51 .. 0.65
   2 !   13.5   0.0   1.3e-05      0.08       8      50 ..      50     101 ..      45     103 .] 0.90

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.065
                                  HHHHHHHHHHHHCTT-EE.EEEEEE CS
                         POTRA 37 eadkealksryanlGyfdasVqvel 61
                                   +d e  k++++  G f+ +V+++ 
  gi|13541144|ref|NP_110832.1| 21 LTDME--KENLEYAGKFS-RVDPSV 42
                                  34444..68999999999.996655 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 1.3e-05
                                   EES.SSS-HHHHHTTTSSSTT.........SBHCHHHHHHHHHHHHHHHHCT CS
                         POTRA   8 feGnkktkdeelrrelelkeg.........dvynpekleadkealksryanl 50 
                                   ++G  k++++++ ++l lk+g          +yn    ++d++al++++ +l
  gi|13541144|ref|NP_110832.1|  50 ISGIAKLPEKVIVKILDLKPGtpaditsilSTYNVMISDEDLNALADYLKKL 101
                                   78977****************99999999999999999**********9865 PP

>> Ost4  Oligosaccaryltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.3   2.6e-05      0.15       1      11 [.      85      95 ..      85      98 .. 0.96

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.6e-05
                                  X-SHHHHHHHH CS
                          Ost4  1 MIsDnqLytLA 11
                                  MIsD++L+ LA
  gi|13541144|ref|NP_110832.1| 85 MISDEDLNALA 95
                                  **********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       711  (0.0396564); expected 358.6 (0.02)
Passed bias filter:                      543  (0.0302861); 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 0.33s 00:00:00.88 Elapsed: 00:00:00.52
# Mc/sec: 601.00
//
Query:       gi|13541145|ref|NP_110833.1|  [L=182]
Description: RNA-binding protein [Thermoplasma volcanium GSS1]
Scores for 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-69  232.6   0.7    3.3e-69  232.5   0.7    1.0  1  DUF655    Protein of unknown function (DUF655)
    5.9e-06   26.5   0.0    1.5e-05   25.1   0.0    1.7  2  HHH_6     Helix-hairpin-helix motif
    0.00079   19.6   0.0     0.0018   18.5   0.0    1.6  1  HHH_3     Helix-hairpin-helix motif
  ------ inclusion threshold ------
      0.018   15.6   0.4          2    9.1   0.3    3.2  3  HHH_5     Helix-hairpin-helix domain


Domain annotation for each model (and alignments):
>> DUF655  Protein of unknown function (DUF655)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  232.5   0.7   7.4e-73   3.3e-69       1     180 [.       1     180 [.       1     181 [. 0.98

  Alignments for each domain:
  == domain 1  score: 232.5 bits;  conditional E-value: 7.4e-73
                                   X--EEEEEEEETT--TT--S-GGG---EEEEEETTT--EEEEEE-TT----TT-EEE-SSS..--SSEEEEEEE--GGGS- CS
                        DUF655   1 leeeaivLDylpeGypddkhrehrdkpvvqalgereltLlelvplkevdilkldevaigkg..ksdkivkikreisyedLt 79 
                                   +ee+a+vLDylp+G+pdd++  +r +p+v a+ge+e++Llel+p+++  i + ++v+igk+  +++ki +++r+i y+dLt
  gi|13541145|ref|NP_110833.1|   1 MEEYAYVLDYLPQGRPDDRS--YRMNPLVLAIGESEFKLLELIPKPNEIITVGEKVYIGKNpeMRKKILSVRRRITYKDLT 79 
                                   79****************96..************************************98633799*************** PP

                                   HHHHHHHHHHHHHHHHTTHHHHHHHH-----B-SSSBGGGGSTT--HHHHHHHHHHHHHS---SHHHHHHHSTT---HHHH CS
                        DUF655  80 dvaraeLpdvvekivkekEdrfveffneaepitiRlHaLelLpgvgkklarkileeRerrrFesFedvkkrvkglkdpaei 160
                                   ++a++eLp+v+e+iv+++ +rf++ffneaepi+ RlH+LelLpg+g+k++++ileeR++++F+sFed+ +rvk++++p+++
  gi|13541145|ref|NP_110833.1|  80 NSAQNELPYVLEDIVNKQQERFIKFFNEAEPINARLHSLELLPGLGNKTMWAILEERKKKPFDSFEDLVNRVKSIHNPQKM 160
                                   ********************************************************************************* PP

                                   HHHHHHHHHH-TTSS--SS- CS
                        DUF655 161 lverileEiedktekYylFv 180
                                   ++ ri+eE++d+ ekY+lFv
  gi|13541145|ref|NP_110833.1| 161 IAGRIIEELKDRYEKYKLFV 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 ?   -2.6   0.0       1.5   6.9e+03      41      58 ..      64      80 ..      57      89 .. 0.72
   2 !   25.1   0.0   3.4e-09   1.5e-05      28      66 ..     117     155 ..      94     172 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.5
                         HHH_6 41 erivaeRekegpfksled 58
                                  ++i++ R+ +  +k+l++
  gi|13541145|ref|NP_110833.1| 64 KKILSVRR-RITYKDLTN 80
                                  67777777.677777765 PP

  == domain 2  score: 25.1 bits;  conditional E-value: 3.4e-09
                         HHH_6  28 GLaaikglgeaaaerivaeRekegpfksledlarrvds.l 66 
                                   +L+ + glg++++ +i++eR+ ++pf s+edl++rv+s  
  gi|13541145|ref|NP_110833.1| 117 SLELLPGLGNKTMWAILEERK-KKPFDSFEDLVNRVKSiH 155
                                   577788**************9.8*************9742 PP

>> HHH_3  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   3.9e-07    0.0018      11      51 ..     113     153 ..     111     167 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 3.9e-07
                         HHH_3  11 AsaeeLqklpGlgpklAknIvayReknGpfksreeLl.kvkg 51 
                                   A +  L+ lpGlg k+  +I++ R k++pf s+e+L+ +vk 
  gi|13541145|ref|NP_110833.1| 113 ARLHSLELLPGLGNKTMWAILEER-KKKPFDSFEDLVnRVKS 153
                                   778899******************.666********955665 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.41   1.8e+03      11      37 ..      59      86 ..      57      99 .. 0.73
   2 ?    7.3   0.0    0.0016       7.1      36      57 .]     117     138 ..      88     139 .. 0.86
   3 ?    9.1   0.3   0.00044         2       7      57 .]     121     171 ..     117     171 .. 0.65

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.41
                                  -HHHHHHHHTTT--...SHHHHHHS-HHHH CS
                         HHH_5 11 GpktAlallsaGie...svedlaaadveeL 37
                                  +p++ +++ls   +   ++ dl + +++eL
  gi|13541145|ref|NP_110833.1| 59 NPEMRKKILSV--RrriTYKDLTNSAQNEL 86
                                  68888888888..32347788877766664 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0016
                                   HHHTSTTS-HHHHHHHHHHHHH CS
                         HHH_5  36 eLakipGiGkktAeriilelkd 57 
                                    L  +pG+G+kt   i++e k+
  gi|13541145|ref|NP_110833.1| 117 SLELLPGLGNKTMWAILEERKK 138
                                   47778********999999886 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.00044
                                   STT--HHHHHHHHTT...T.--SHHHHHHS-HHHHHTSTTS-HHHHHHHHHHHHH CS
                         HHH_5   7 vsGiGpktAlallsa...G.iesvedlaaadveeLakipGiGkktAeriilelkd 57 
                                   ++G+G kt  a+l+      ++s+edl    v+++ +i+   k  A rii+elkd
  gi|13541145|ref|NP_110833.1| 121 LPGLGNKTMWAILEErkkKpFDSFEDL----VNRVKSIHNPQKMIAGRIIEELKD 171
                                   688888888888888322112234444....556777777777788999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       645  (0.0359752); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.60u 0.34s 00:00:00.94 Elapsed: 00:00:00.54
# Mc/sec: 1018.09
//
Query:       gi|13541146|ref|NP_110834.1|  [L=237]
Description: rRNA dimethyladenosine transferase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.2e-34  117.3   0.1    8.1e-34  116.9   0.1    1.0  1  RrnaAD           Ribosomal RNA adenine dimethylase
    0.00027   20.8   0.0    0.00041   20.2   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
  ------ inclusion threshold ------
       0.04   13.3   1.5        0.2   11.0   0.1    2.4  3  TehB             Tellurite resistance protein TehB
      0.055   13.7   2.9       0.65   10.2   0.0    2.3  2  DUF1229          Protein of unknown function (DUF1229)
      0.055   14.2   0.0      0.098   13.4   0.0    1.4  1  Methyltransf_25  Methyltransferase domain
      0.063   12.8   0.0       0.11   12.1   0.0    1.3  1  MTS              Methyltransferase small domain
       0.12   12.1   0.0       0.19   11.4   0.0    1.3  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl


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 !  116.9   0.1   3.2e-37   8.1e-34       6     230 ..       5     209 ..       2     225 .. 0.94

  Alignments for each domain:
  == domain 1  score: 116.9 bits;  conditional E-value: 3.2e-37
                                   XGCG--EE--HHHHHHHHHHH-GGTTSEEEEES-TTTCCHHHHHCC-SEEEEE-S-HHHHHHHHCHTTTCCCEEEE-S-CC CS
                        RrnaAD   6 ksygqnflknkkvineIldklnleekltvleigpGkGilTeeLakrakqvvvlElderLakllqkklskdeklkvvhqDfl 86 
                                   k++gq fl+++ +++  +d ln  + + vleigpG GilT +L++r   v+++E+d+  +++l     k+++l++ + Dfl
  gi|13541146|ref|NP_110834.1|   5 KRLGQVFLRSRRIAEYEVDLLNGHPGDSVLEIGPGHGILTSILLDRGYYVTAVEKDRFVYNELLS--IKNKNLNLFNMDFL 83 
                                   789*******************************************************9999998..67************ PP

                                   GHHHHHHHCTTTCCCCEEEEEEE--TTTHHHHHHHHHHGGGGCEEEEEEEEEHHHHHHHH--TTSTT-SHHHHHHHHHEEE CS
                        RrnaAD  87 kfetpeevtekdsihqeflvvanlPyeistqlvkqlleesrfglvkmllwlqkefarrllarpgskkrsrlsvlreaftdv 167
                                   ++   +             +++n+Py+is++ +++l +   f ++ +++++qkefa +l++    k+ srl v++ +  ++
  gi|13541146|ref|NP_110834.1|  84 DMPPQKYD----------FIIGNIPYYISSDVIFKLYD---FEFSASVIMVQKEFADKLTN---VKDSSRLYVNAYVRYEI 148
                                   *9888833..........689**************987...7779****************...79*************** PP

                                   EEEEEC-GGCECS--SSSEEEEEEEE-SS-S--S-HHHHHHHHHHHHCTTTSBCCCHCCCTST CS
                        RrnaAD 168 klvakveksifsPppkvdsalvelerkdedlpqkdlkkyesvvrkllnrkrktlstslksllp 230
                                    l   v++++f P+pkvdsa++ l++k+ +l +  l+ ++s ++ ++ +krk +s+ ++ ++p
  gi|13541146|ref|NP_110834.1| 149 DLKRYVGRKNFNPQPKVDSAILLLKKKKINL-DIPLDYLDSKLKVMFSKKRKMISNIFE-IYP 209
                                   *****************************97.8999*******************9987.665 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   1.6e-07   0.00041      20      88 ..      27      95 ..       8      97 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 1.6e-07
               Methyltransf_23 20 lraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiaekakkaqkdqfdeqeaaepqgkfdlIvl 88
                                    +g +vL+iG+G+Gil+++l ++g+ vt+v+ ++   +++ ++k+ +   f+ ++ + p +k+d+I+ 
  gi|13541146|ref|NP_110834.1| 27 GHPGDSVLEIGPGHGILTSILLDRGYYVTAVEKDRFVYNELLSIKNKNLNLFNMDFLDMPPQKYDFIIG 95
                                  457789**************************998766666699999999999999999********86 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1     8e-05       0.2      33     103 ..      32      97 ..      22     112 .. 0.80
   2 ?    0.3   0.1      0.15   3.9e+02      87     109 ..     101     123 ..      95     140 .. 0.75
   3 ?   -0.8   0.0      0.32   8.3e+02      89     117 ..     176     205 ..     162     212 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 8e-05
                                   EEEEES-TTSHHHHHHHHTT-EEEEEES-HHHHHHHHHHHHHTT-TTEEEEE--GGG---.-S-EEEEEEES CS
                          TehB  33 kvldlgcgqgrnslylsllgydvtawdknensiafleeikekenlknistalydineakl.derydfilstv 103
                                    vl++g g+g  +  l   gy vta++k+    + l +ik+k nl+     l++++ +++  ++ydfi+  +
  gi|13541146|ref|NP_110834.1|  32 SVLEIGPGHGILTSILLDRGYYVTAVEKDRFVYNELLSIKNK-NLN-----LFNMDFLDMpPQKYDFIIGNI 97 
                                   489*******99999999************999999999876.677.....555555555247899999765 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.15
                                   GGG----S-EEEEEEESSGGGS- CS
                          TehB  87 ineaklderydfilstvvlmfle 109
                                   i +  + + ydf +s+ v+m  +
  gi|13541146|ref|NP_110834.1| 101 ISSDVIFKLYDFEFSASVIMVQK 123
                                   666677889*******9999754 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.32
                                   G----S-EEEEEEESSGGGS-G.GGHHHHH CS
                          TehB  89 eaklderydfilstvvlmflea.eripsii 117
                                   +++ld   d++ s + +mf ++ ++i++i 
  gi|13541146|ref|NP_110834.1| 176 KINLDIPLDYLDSKLKVMFSKKrKMISNIF 205
                                   567888899999999999986515666665 PP

>> DUF1229  Protein of unknown function (DUF1229)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00025      0.65      42      72 ..      41      71 ..      36      87 .. 0.79
   2 ?    3.3   1.0     0.035        89       8      40 ..      88     120 ..      81     155 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00025
                       DUF1229 42 siaseklnehvdywnavkkdffvypkitigs 72
                                  +i + +l+++ +y  av+kd fvy ++    
  gi|13541146|ref|NP_110834.1| 41 GILTSILLDRGYYVTAVEKDRFVYNELLSIK 71
                                  899*********************9875444 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.035
                       DUF1229   8 vlykfiigflilllssseiyfflketyiGqrii 40 
                                     y fiig + + +ss  i+      +    i+
  gi|13541146|ref|NP_110834.1|  88 QKYDFIIGNIPYYISSDVIFKLYDFEFSASVIM 120
                                   679***********9998776555555555554 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   3.8e-05     0.098       1      70 [.      33      95 ..      33     111 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.8e-05
                                  EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEE CS
               Methyltransf_25  1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvs 70
                                  vL++G G+G lt  l++r+  + vt+v+ +    ++  +     + n+++ ++d+ d+p   +++D+++ 
  gi|13541146|ref|NP_110834.1| 33 VLEIGPGHGILTSILLDRG--YYVTAVEKDRFVYNELLSIK---NKNLNLFNMDFLDMPP--QKYDFIIG 95
                                  9*****************5..*******9988777665544...4589999999999985..46898886 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   4.2e-05      0.11      27     110 ..      25     102 ..      20     114 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.2e-05
                                   CHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTSTTS-EEEEEE---S CS
                           MTS  27 lpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvleeveekkfdlivsNPPf 107
                                   l+ +  ++vl +G G G+l+  l+++     vt+v++d       +e l+ ++ ++++++ d l+  + +k+d+i+ N P+
  gi|13541146|ref|NP_110834.1|  25 LNGHPGDSVLEIGPGHGILTSILLDRGYY--VTAVEKDRFVY---NELLSIKNKNLNLFNMDFLDMPP-QKYDFIIGNIPY 99 
                                   55667788****************98877..99***998743...4445555555799******9999.*********998 PP

                                   TTT CS
                           MTS 108 hag 110
                                     +
  gi|13541146|ref|NP_110834.1| 100 YIS 102
                                   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 ?   11.4   0.0   7.5e-05      0.19      65      92 ..      21      48 ..       9      81 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 7.5e-05
                                  HHHHTT--TT-EEEEES-TTSHHHHHHH CS
                          PCMT 65 alellelkkgarvLevGsGsGyltavla 92
                                   ++ll+ ++g++vLe+G G G+lt +l 
  gi|13541146|ref|NP_110834.1| 21 EVDLLNGHPGDSVLEIGPGHGILTSILL 48
                                  57889999****************9974 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       526  (0.0293379); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-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 0.33s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 1440.54
//
Query:       gi|13541147|ref|NP_110835.1|  [L=274]
Description: membrane protease subunit [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-31  109.5   3.6    2.5e-31  109.1   3.6    1.2  1  Band_7    SPFH domain / Band 7 family
     0.0016   18.2   0.9     0.0027   17.5   0.2    1.8  2  Band_7_1  SPFH domain-Band 7 family
      0.007   16.3   0.2      0.017   15.0   0.2    1.6  1  DUF2605   Protein of unknown function (DUF2605)


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 !  109.1   3.6   4.2e-35   2.5e-31       4     177 ..      27     194 ..      24     201 .. 0.95

  Alignments for each domain:
  == domain 1  score: 109.1 bits;  conditional E-value: 4.2e-35
                        Band_7   4 eegevgvvvrfGklsrvlepGlhfilPfgrsvtvvsvrvqtldvsvsltvptkDglpvtidvtviyrvpddapklvaaver 84 
                                   +e e+++v + G++ ++++pG+ fi P++++ + vs+r+q ++++    + tkD++pv++d++++y+v  d+ k+v+++  
  gi|13541147|ref|NP_110835.1|  27 KEWERAIVLTLGRYGGIRGPGIIFITPIVSRGIYVSTRIQPVQFKT-EATFTKDNVPVNVDAIMYYQV-IDPQKAVLNI-- 103
                                   7889******************************************.8888*****************.**********.. PP

                        Band_7  85 esanldnlirrvlesalrevisemtleellsnreelaeelknelneqlrkyGvevldvritdidpppevaqalaakqaaea 165
                                     +n+    + +++ +lrevi++  ++ells+re++ e +++ + ++ + +Gv v +v i+d+  p ++++a+ + + ae+
  gi|13541147|ref|NP_110835.1| 104 --ENYSVGTNYAAQTTLREVIGKSMFDELLSEREKVGETAREIIDQKTEAWGVKVASVEIRDVIVPSQLQEAMSRQASAER 182
                                   ..******************************************************************************* PP

                        Band_7 166 eaqaeiaraeae 177
                                   e++ ++  a+ae
  gi|13541147|ref|NP_110835.1| 183 ERRSRVTLAQAE 194
                                   **6666666665 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 !   17.5   0.2   4.4e-07    0.0027     158     209 ..     129     180 ..      82     182 .. 0.87
   2 ?   -3.7   0.0       1.3   7.9e+03     161     190 ..     192     222 ..     186     229 .. 0.60

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 4.4e-07
                      Band_7_1 158 dlaakseelaeklkealkeelaeyGlelekleienislpeevekaldkrasm 209
                                   +l ++ e+++e+ +e ++++ ++ G+++ ++ei+++ +p ++++a++++as+
  gi|13541147|ref|NP_110835.1| 129 ELLSEREKVGETAREIIDQKTEAWGVKVASVEIRDVIVPSQLQEAMSRQASA 180
                                   6788999*****************************************9986 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 1.3
                      Band_7_1 161 akseelaeklkealkeel.aeyGleleklei 190
                                     + e a+k+ ea k+ + + +Gl+l  ++i
  gi|13541147|ref|NP_110835.1| 192 QAEVEAAQKMVEASKQYVdNPVGLQLRWMQI 222
                                   4445556666666666665567777776654 PP

>> DUF2605  Protein of unknown function (DUF2605)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.2   2.9e-06     0.017      42      87 ..     181     226 ..     162     228 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.9e-06
                       DUF2605  42 qadllarvkeaqqeveaakaLfkatdgqvgvevevlvpWHqLvtec 87 
                                   +++  +rv+ aq+eveaa+ +++a+++ v   v + ++W q++ e+
  gi|13541147|ref|NP_110835.1| 181 ERERRSRVTLAQAEVEAAQKMVEASKQYVDNPVGLQLRWMQIIYEI 226
                                   4456789*********************999999999999999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1075  (0.0599587); expected 358.6 (0.02)
Passed bias filter:                      600  (0.0334653); 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: 0.65u 0.37s 00:00:01.02 Elapsed: 00:00:00.54
# Mc/sec: 1522.78
//
Query:       gi|13541148|ref|NP_110836.1|  [L=134]
Description: transcription regulator [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-09   37.7   0.5    2.6e-09   36.9   0.5    1.4  1  HTH_45           Winged helix-turn-helix
  ------ inclusion threshold ------
      0.061   12.8   0.0      0.069   12.6   0.0    1.2  1  Methyltrn_RNA_3  Putative RNA methyltransferase


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 !   36.9   0.5   2.9e-13   2.6e-09       1      70 [.      56     130 ..      56     133 .. 0.89

  Alignments for each domain:
  == domain 1  score: 36.9 bits;  conditional E-value: 2.9e-13
                        HTH_45   1 rRskleIiadILeais.egeakkTkimykanLsykllnkYLdmLvekgli....kkskekYvlTekGlelleklk 70 
                                   r  k +Ii+dIL+ i+  +++   +i+y+ nL+y+++ k    + ++g      + +++kY lT kG ++le ++
  gi|13541148|ref|NP_110836.1|  56 RKQKAKIIFDILSFIKtPECTGIKSIIYNCNLNYRTAIKIQREMESRGPKekqqEGRNGKYILTSKGTDFLEAIQ 130
                                   56899**********9778899999***********************97554344889************9986 PP

>> Methyltrn_RNA_3  Putative RNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   7.7e-06     0.069      26      70 ..      12      74 ..       5     114 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 7.7e-06
               Methyltrn_RNA_3 26 qIARaaaiFnVdeivvfddseseeekkek...................pseflarlLqYletPp 70
                                  ++A++++i+ V++i+ ++++++++e  ++                   +++++  +L++++tP+
  gi|13541148|ref|NP_110836.1| 12 MLAKSLSIYFVSKII-YHKPDGSSEVIKNeeeninlrfsqsvvtgrkqKAKIIFDILSFIKTPE 74
                                  79***********97.55555554443335899******************************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); 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: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.50
# Mc/sec: 808.43
//
Query:       gi|13541149|ref|NP_110837.1|  [L=127]
Description: hypothetical protein TVN0318 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score 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   12.5   2.2       0.39   11.2   0.2    2.0  2  PP2C_C    Protein serine/threonine phosphatase 2C, C-terminal
       0.35   11.0   4.5       0.19   11.8   1.6    2.1  2  KH_8      Krr1 KH1 domain


Domain annotation for each model (and alignments):
>> PP2C_C  Protein serine/threonine phosphatase 2C, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.2   4.3e-05      0.39      23      60 ..      18      55 ..      13      64 .. 0.90
   2 ?    0.9   0.1     0.073   6.5e+02      13      31 ..      88     106 ..      86     121 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 4.3e-05
                        PP2C_C 23 eldekleervkeiiekeekkeeldlekvlkvLasedip 60
                                  +ld++ +e  + i+e+++++e+l++++v+ +L+ e+i+
  gi|13541149|ref|NP_110837.1| 18 KLDKAFQEIFEHIVEQKKNPEDLQFDQVILQLNLEEIK 55
                                  89******************************988886 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.073
                        PP2C_C  13 vseeavkkEkeldekleer 31 
                                   vse+  +k +e+++ l+++
  gi|13541149|ref|NP_110837.1|  88 VSEDVHEKTEEVEKILKNK 106
                                   5666666667777777643 PP

>> KH_8  Krr1 KH1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.1      0.11     1e+03       9      42 ..      13      47 ..       7      73 .. 0.57
   2 ?   11.8   1.6   2.2e-05      0.19      11      42 ..      88     119 ..      69     127 .] 0.84

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.11
                          KH_8  9 kyrekylkeveekikkll.eekklklevdlkersl 42
                                  k+  + l + +++i + + e+kk   ++++++ +l
  gi|13541149|ref|NP_110837.1| 13 KFEWSKLDKAFQEIFEHIvEQKKNPEDLQFDQVIL 47
                                  55555555554444433324444444444444433 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 2.2e-05
                          KH_8  11 rekylkeveekikklleekklklevdlkersl 42 
                                     + ++e++e+++k+l++kk+k +vd+++  l
  gi|13541149|ref|NP_110837.1|  88 VSEDVHEKTEEVEKILKNKKIKYTVDYDKMLL 119
                                   566788999******************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1493  (0.0832729); expected 358.6 (0.02)
Passed bias filter:                      542  (0.0302304); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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 0.35s 00:00:00.91 Elapsed: 00:00:00.53
# Mc/sec: 717.62
//
Query:       gi|13541150|ref|NP_110838.1|  [L=55]
Description: preprotein translocase subunit SecG [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.8e-13   49.7   0.1    3.1e-13   49.5   0.1    1.1  1  Sec61_beta  Sec61beta family
  ------ inclusion threshold ------
       0.11   12.6   0.0       0.12   12.4   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 !   49.5   0.1   3.5e-17   3.1e-13       1      41 []      12      53 ..      12      53 .. 0.96

  Alignments for each domain:
  == domain 1  score: 49.5 bits;  conditional E-value: 3.5e-17
                                  XXXXXXXXXX.----SS-B-THHHHHHHHHHHHHHHHHTSS- CS
                    Sec61_beta  1 SsaGLlryye.edapgikidPkvVlvlsvafiasVilLhila 41
                                  S+aGL+ry+e e+ +g+ +dPk V+++++a++++V l++i++
  gi|13541150|ref|NP_110838.1| 12 SGAGLIRYFEeEEIKGPALDPKLVVYIGIAVAIMVELAKIFW 53
                                  89********8889*************************986 PP

>> Adeno_E3A  Adenovirus E3A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   1.3e-05      0.12      19      65 ..       6      50 ..       2      53 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.3e-05
                     Adeno_E3A 19 rhkcfargsgefcyfelpeehiegpahgvrlttqveltrslireftk 65
                                  + + f  g+g + yfe  ee i+gpa   +l   + ++ +++ e++k
  gi|13541150|ref|NP_110838.1|  6 KSEGFQSGAGLIRYFE--EEEIKGPALDPKLVVYIGIAVAIMVELAK 50
                                  5667999********8..899************99999999998877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (55 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       240  (0.0133861); expected 358.6 (0.02)
Passed bias filter:                      203  (0.0113224); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.33s 00:00:00.81 Elapsed: 00:00:00.52
# Mc/sec: 318.05
//
Query:       gi|13541151|ref|NP_110839.1|  [L=320]
Description: mevalonate pyrophosphate decarboxylase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
     0.0068   15.9   0.1     0.0094   15.4   0.1    1.1  1  SbmA_BacA  SbmA/BacA-like family


Domain annotation for each model (and alignments):
>> SbmA_BacA  SbmA/BacA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   5.2e-07    0.0094      96     145 ..     215     265 ..     189     273 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 5.2e-07
                     SbmA_BacA  96 iskwdklreieGasqrvqedtmrfakiledlGvslvkaim.tliaflPvlf 145
                                   i++ ++  +ieG   +  edt  + +il ++Gv +++  m  li+f+ +l 
  gi|13541151|ref|NP_110839.1| 215 IKEMARTDDIEGIFEKAEEDTEEYHSILREVGVLVIRENMqKLIEFIKILR 265
                                   566777889**************************9865527*****9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       846  (0.0471861); expected 358.6 (0.02)
Passed bias filter:                      598  (0.0333538); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.63u 0.33s 00:00:00.96 Elapsed: 00:00:00.52
# Mc/sec: 1837.24
//
Query:       gi|13541152|ref|NP_110840.1|  [L=272]
Description: hypothetical protein TVN0321 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.5e-11   43.3   5.0    4.5e-11   43.3   5.0    1.9  3  SNARE_assoc  SNARE associated Golgi protein


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 ?   -2.4   0.1      0.36   6.4e+03      79      79 ..      50      50 ..      29      70 .. 0.52
   2 !   43.3   5.0   2.5e-15   4.5e-11       2     119 ..     100     225 ..      99     226 .. 0.88
   3 ?   -4.0   0.1         1   1.8e+04     105     114 ..     246     255 ..     241     261 .. 0.41

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.36
                   SNARE_assoc 79 i 79
                                  i
  gi|13541152|ref|NP_110840.1| 50 I 50
                                  1 PP

  == domain 2  score: 43.3 bits;  conditional E-value: 2.5e-15
                   SNARE_assoc   2 PsevllvaaGvlf.....glllgtlvtslgallGaslayllgrylgrkalrrkllsekrvka.....lerlverygflall 72 
                                   P +++l + G+l      +++l++lv+++++l  + + y+ gr +g + l  k+ls+ ++ +     ++++++ +g++ ++
  gi|13541152|ref|NP_110840.1| 100 PDYLILPFYGYLSsvgefNIFLTFLVSVAAMLFEMGIEYAGGRLAG-RPLLLKVLSYFKITEkdlevADHWIKDHGSFSIF 179
                                   5555666666666555558899************************.88888888888888888888************** PP

                   SNARE_assoc  73 llrllpivPrdlvnyvaGltrvsfkrFflatfiGsipwalvyaylGs 119
                                   ++ ++p + +++++++aG+++++   Ffl +++G +++  +++y+G+
  gi|13541152|ref|NP_110840.1| 180 IATFIPYF-KNVTSLAAGTLKMNAGLFFLSNLVGFSIRFGLLLYIGY 225
                                   ******99.*************************************8 PP

  == domain 3  score: -4.0 bits;  conditional E-value: 1
                   SNARE_assoc 105 iGsipwalvy 114
                                   +G +  + ++
  gi|13541152|ref|NP_110840.1| 246 VGVLALMYII 255
                                   3333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       536  (0.0298957); expected 358.6 (0.02)
Passed bias filter:                      200  (0.0111551); 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 0.30s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 1680.61
//
Query:       gi|13541153|ref|NP_110841.1|  [L=509]
Description: membrane-associated Zn-dependent protease 1 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-33  116.5   4.0    1.8e-33  115.9   4.0    1.3  1  Peptidase_M50    Peptidase family M50
    3.1e-06   27.4   0.3    6.9e-06   26.3   0.3    1.5  1  PDZ_2            PDZ domain
     0.0041   17.4   1.2      0.066   13.6   0.3    2.5  2  PDZ              PDZ domain
  ------ inclusion threshold ------
        9.8    6.1  12.4        2.6    8.0   0.1    3.7  4  Flp_Fap          Flp/Fap pilin component


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 !  115.9   4.0   3.9e-37   1.8e-33       2     249 ..     116     494 ..     115     495 .. 0.93

  Alignments for each domain:
  == domain 1  score: 115.9 bits;  conditional E-value: 3.9e-37
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....XXXX CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Peptidase_M50   2 filllgilvvvHElGHflvAklcgvkveefsigfGpkllsfkkgeteYaiallpLGGyVkmageepeeelseeeakaflkk 82 
                                    +l+++i+vv+HE++H+++A+++g+kv++++ +f                 ++p+G++V+ +++e            ++k+
  gi|13541153|ref|NP_110841.1| 116 GLLAIVISVVIHEMMHGITARKHGLKVDSVGALF----------------FIVPVGAFVEPNQDE------------MTKA 168
                                   5899*************************99999................99*************............899* PP

                                   XXXXXXXXXXXXXXXXXXXXXXXXXX....................................................... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxx....................................................... RF
                 Peptidase_M50  83 spwqrllivlAGplanfilailvfvv....................................................... 108
                                   +p+ r +i++AGp +n+i++i+++v+                                                       
  gi|13541153|ref|NP_110841.1| 169 DPVIRRRIFAAGPSINIIIGIIFAVIlstamfagaqpihqglyiessdttvnphilpgtelislgnysgsavmqalqsptf 249
                                   *************************9******************************************************* PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                 Peptidase_M50 109 ................................................................................. 108
                                                                                                                    
  gi|13541153|ref|NP_110841.1| 250 lpgsnvtvetfdghsvskgeavagviivsvisgypaekvpgnsvilsidnktiynlttlddvlnsikpgthismkilelps 330
                                   ********************************************************************************* PP

                                   .....................-EEECE...CTTTSCEE-SEEEC-XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.X CS
                                   .....................xxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x RF
                 Peptidase_M50 109 .....................pkkske...seeekrgviGvspkpvkkegllealkegvektlkvvvltvkalgklitg.k 164
                                                        p    +   +  +++++iGvs ++    g+     + +++ + +  + ++ ++++it   
  gi|13541153|ref|NP_110841.1| 331 yslqsytmvtaskysyyqqydP----SansVIYKNQSFIGVSVSY---MGISGYPLNELRNIIFLKEIYANPIDGFITSiG 404
                                   **********999888776654....133589999**********...55555555555555555566666********** PP

                                   XXXX.XXXXXXXXXXXXXXXXXXXXX....XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                   xxxx.xxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Peptidase_M50 165 lslk.tlggpisiaqlaseaaeagls....sflqllalisvnLgilNLlPipvLDGghllfalleairrkplserkeevan 240
                                   l++     +p+s+a++ s  ++ +l     ++l+++++i++ Lgi+N+lP+ ++DGg++++ +l+ + r+  s r e+++n
  gi|13541153|ref|NP_110841.1| 405 LPFYgLNPVPVSLASMFSVPVNPTLFwgtvNILFWMFWINIVLGITNALPFAFFDGGQFFKDTLTIWGRHIKSLRSEKTVN 485
                                   ****8999*********9999888877888*************************************************** PP

                                   XXXXXXXXX CS
                                   xxxxxxxxx RF
                 Peptidase_M50 241 lvglallll 249
                                   +v+++l ++
  gi|13541153|ref|NP_110841.1| 486 QVMYFLSFI 494
                                   ****99876 PP

>> PDZ_2  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.3   1.5e-09   6.9e-06       6      69 ..     264     325 ..     254     328 .. 0.90

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 1.5e-09
                                   X------..-EEEEEE-TTSGGGGT.--TT-EEEEETTB--SSHHHHHHHHHTS-TT-EEEEEE CS
                         PDZ_2   6 svsdeedtggvlvvsVkeggPaakaglkagDvilkvdgkkvksledlislllkkkpGdtVkltv 69 
                                   svs+ e   gv++vsV +g Pa+k     + vil++d+k++ +l++l+  l++ kpG+ ++ ++
  gi|13541153|ref|NP_110841.1| 264 SVSKGEAVAGVIIVSVISGYPAEKV--PGNSVILSIDNKTIYNLTTLDDVLNSIKPGTHISMKI 325
                                   5566666789***********8886..999******************************9987 PP

>> PDZ  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0      0.07   3.1e+02      27      47 ..     123     143 ..     114     145 .. 0.87
   2 !   13.6   0.3   1.5e-05     0.066      11      81 ..     260     325 ..     254     326 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.07
                                   SEEEEEECTTSHHHHHTSSTT CS
                           PDZ  27 gifvsevlpggaaeadglkvG 47 
                                   ++++ e+++g  a + glkv+
  gi|13541153|ref|NP_110841.1| 123 SVVIHEMMHGITARKHGLKVD 143
                                   689*******88888889986 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 1.5e-05
                                   ESSEEEEEETTSSSSSSEEEEEECTTSHHHHHTSSTTEEEEEETTEETTTSHHHHHHHHHHTTTSEEEEEE CS
                           PDZ  11 glGfslkggsdqrgdkgifvsevlpggaaeadglkvGDkIlsvNgvdvenvsheeavqaikgskgkvtLti 81 
                                   + G s++ g++     g+++ +v  g +ae+     + +Ils++++++ n++ ++ v+   +++ +++++i
  gi|13541153|ref|NP_110841.1| 260 FDGHSVSKGEAV---AGVIIVSVISGYPAEKV--PGNSVILSIDNKTIYNLTTLDDVLNSIKPGTHISMKI 325
                                   567778877776...6**********888888..57789************66666555555556888888 PP

>> Flp_Fap  Flp/Fap pilin component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       1.3   5.9e+03      15      27 ..      11      24 ..      11      33 .. 0.73
   2 ?    3.4   1.8     0.015        67      16      28 ..      71      83 ..      64      89 .. 0.91
   3 ?    8.0   0.1   0.00057       2.6      13      24 ..     115     126 ..     113     140 .. 0.92
   4 ?   -0.8   0.1      0.31   1.4e+03      17      35 ..     192     210 ..     188     211 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.3
                       Flp_Fap 15 LIaaliAvvii.ay 27
                                  LIa ++A+ ++  y
  gi|13541153|ref|NP_110841.1| 11 LIAWIMAIYLLsPY 24
                                  89999999887545 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.015
                       Flp_Fap 16 IaaliAvviiayv 28
                                  Ia+++++v+++y+
  gi|13541153|ref|NP_110841.1| 71 IAGIVSLVMLFYS 83
                                  9*********997 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.00057
                       Flp_Fap  13 YgLIaaliAvvi 24 
                                   YgL+a++i+vvi
  gi|13541153|ref|NP_110841.1| 115 YGLLAIVISVVI 126
                                   ***********9 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 0.31
                       Flp_Fap  17 aaliAvviiayvttlgtaL 35 
                                   a++ +++++a+++ + ++L
  gi|13541153|ref|NP_110841.1| 192 AVILSTAMFAGAQPIHQGL 210
                                   8999*****9999887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (509 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       905  (0.0504769); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); 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):               4  [number of targets reported over threshold]
# CPU time: 0.68u 0.32s 00:00:01.00 Elapsed: 00:00:00.52
# Mc/sec: 2936.03
//
Query:       gi|13541154|ref|NP_110842.1|  [L=135]
Description: hypothetical protein TVN0323 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.4e-16   57.7   0.3    1.3e-15   57.1   0.3    1.3  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
  ------ inclusion threshold ------
      0.012   15.6   0.9      0.021   14.9   0.9    1.3  1  DZR             Double zinc ribbon
       0.06   13.7   1.2       0.11   12.8   1.1    1.5  1  C1_2            C1 domain
      0.097   12.6   1.6       0.15   12.0   1.6    1.3  1  C1_1            Phorbol esters/diacylglycerol binding domain 
       0.18   11.7   2.2       0.32   10.9   2.2    1.5  1  PHD             PHD-finger
       0.33   10.7   4.4       0.39   10.4   2.8    1.9  2  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
       0.37   10.5   2.6          6    6.6   2.3    2.2  2  zf-NADH-PPase   NADH pyrophosphatase 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 !   57.1   0.3     5e-19   1.3e-15       1      67 [.      30      98 ..      30     100 .. 0.87

  Alignments for each domain:
  == domain 1  score: 57.1 bits;  conditional E-value: 5e-19
                OrfB_Zn_ribbon  1 frklkeqleykakeyGikveevnp...ayTSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNil 67
                                  ++ l  q+ yka ++G + +e  +   ++TS  Cs+C    +   +gr +kC++Cg e+drDvnA+iNi+
  gi|13541154|ref|NP_110842.1| 30 YGMLASQVMYKASWEGLPAIELTRketRNTSRMCSVCDTLARI-EHGRILKCDSCGIEIDRDVNACINIA 98
                                  5678899*********9888765411167**********9999.9************************8 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.9   8.1e-06     0.021       7      46 ..      55      95 ..      53      96 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 8.1e-06
                           DZR  7 elppdarfCseCgtklkavaa..edrCpsCgekvdpearfCp 46
                                  e+++ +r+Cs C t  +  ++    +C+sCg ++d + + C 
  gi|13541154|ref|NP_110842.1| 55 ETRNTSRMCSVCDTLAR-IEHgrILKCDSCGIEIDRDVNACI 95
                                  678899*******9876.4445799**************996 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   1.1   4.3e-05      0.11       9      43 ..      51      88 ..      47      95 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.3e-05
                          C1_2  9 lskgedssesfnCsaCgrk..idgff.YsCseCdfslh 43
                                  l+++e+++ s+ Cs+C++   i+  +  +C+ C + ++
  gi|13541154|ref|NP_110842.1| 51 LTRKETRNTSRMCSVCDTLarIEHGRiLKCDSCGIEID 88
                                  556799999**********88544447******98887 PP

>> C1_1  Phorbol esters/diacylglycerol binding domain (C1 domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   1.6   5.9e-05      0.15       9      44 ..      58      96 ..      53     105 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 5.9e-05
                                  SS--B-TTT-SB--SSSS-EEEETTT--EE-CC...CCT CS
                          C1_1  9 kqptfCkhCgeflwgkekqglkCswCkllvHkk...Che 44
                                  + +  C+ C+ + + +  ++lkC+ C++ ++ +   C++
  gi|13541154|ref|NP_110842.1| 58 NTSRMCSVCDTLARIEHGRILKCDSCGIEIDRDvnaCIN 96
                                  56789*******955************999887777766 PP

>> PHD  PHD-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   2.2   0.00012      0.32       1      22 [.      62      84 ..      62     100 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00012
                                  SBTTTTS.TTSTTSCEEEETTTS CS
                           PHD  1 rCavCkk.ksdeeeelvqCdgCk 22
                                  +C+vC+  +  e+++++ Cd+C+
  gi|13541154|ref|NP_110842.1| 62 MCSVCDTlARIEHGRILKCDSCG 84
                                  5******98999**********7 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       1.1   2.8e+03      26      31 ..      36      41 ..      35      41 .. 0.79
   2 ?   10.4   2.8   0.00015      0.39       3      25 ..      63      85 ..      62      87 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.1
                                  ---B-- CS
                DNA_RNApol_7kD 26 RilYKk 31
                                   ++YK+
  gi|13541154|ref|NP_110842.1| 36 QVMYKA 41
                                  69***5 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00015
                                  -SSS--B----SSS----SSS-- CS
                DNA_RNApol_7kD  3 CgeCgaevslkkgdpiRCkeCGh 25
                                  C  C++  ++++g +++C  CG 
  gi|13541154|ref|NP_110842.1| 63 CSVCDTLARIEHGRILKCDSCGI 85
                                  999*******************7 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.4     0.032        81      20      29 ..      59      68 ..      52      70 .. 0.75
   2 ?    6.6   2.3    0.0024         6      13      30 ..      69      86 ..      58      87 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.032
                 zf-NADH-PPase 20 warvCpaCgl 29
                                  ++r C+ C++
  gi|13541154|ref|NP_110842.1| 59 TSRMCSVCDT 68
                                  6899999986 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0024
                 zf-NADH-PPase 13 tepaeggwarvCpaCgle 30
                                   ++ e+g+ + C++Cg e
  gi|13541154|ref|NP_110842.1| 69 LARIEHGRILKCDSCGIE 86
                                  5678999********976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-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 0.33s 00:00:00.83 Elapsed: 00:00:00.51
# Mc/sec: 789.61
//
Query:       gi|13541155|ref|NP_110843.1|  [L=331]
Description: 50S ribosomal protein L3P [Thermoplasma volcanium GSS1]
Scores for complete 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-73  246.4   0.7    4.1e-53  180.7   0.1    2.0  2  Ribosomal_L3  Ribosomal protein L3


Domain annotation for each model (and alignments):
>> Ribosomal_L3  Ribosomal protein L3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.7   0.1   3.9e-22     7e-18       7     118 ..       5     115 ..       1     127 [. 0.88
   2 !  180.7   0.1   2.3e-57   4.1e-53     157     369 .]     130     330 ..     117     330 .. 0.94

  Alignments for each domain:
  == domain 1  score: 64.7 bits;  conditional E-value: 3.9e-22
                                   XXXXSSXCCCTTXSBXSXSSXXXSX.XXSBTTTTTXBSEEEEEEEEEEEEEEECHHTTSCCCCCEEEEEEEEEEC--EEEE CS
                  Ribosomal_L3   7 eaprhgslGflprkRaerergkvksfPkddtskpvkltaflGyKaGmthiVrevdkpgskldkkevveavtvvetppmviv 87 
                                   ++ r+gs+ + pr Ra++  ++++s+P+   s pvk+++f+G+K Gmth+  ++ + +s + ++ + ++vtv+e pp+ ++
  gi|13541155|ref|NP_110843.1|   5 HHSRRGSMAYYPRVRAKSIEPRIRSWPEI--SGPVKVQGFAGFKVGMTHVEMVDYRKTSVTAGQPIFVPVTVIEVPPLDVI 83 
                                   56899**********************75..567*********************************************** PP

                                   EEEEEEEETTEEEE.EEEEESSS.SHHHHCCC CS
                  Ribosomal_L3  88 gvvgyvetprGlrs.lktvwaehlseevkrrl 118
                                   g+++y e + G +  + ++w+++l +e+ +++
  gi|13541155|ref|NP_110843.1|  84 GIRLYDEDEEGNMVvVYEKWTQNLDKELFKKI 115
                                   ***********8862679****8888876665 PP

  == domain 2  score: 180.7 bits;  conditional E-value: 2.3e-57
                                   CSCEEEEEEEECCCSS-SCCSSHHEEEEECHCS.CHHHHHHHHHHCCTCEEECCCCS-TTSEEEEEEEE---EEE-HHHHC CS
                  Ribosomal_L3 157 asvvrviahtvirktkslaqKkahllEiqvngG.tiaekldfarealektvavaavFrqgeliDvigvtkGkGfeGvvkRW 236
                                    + vr+i+ t  ++++++  Kk+++ E++++gG ++ e++++a+++l kt+ +++  ++g+++Dv +vtkGkGf G v+R+
  gi|13541155|ref|NP_110843.1| 130 YADVRLIVATRNKDVPGIPSKKPEIFELRIGGGnSVKERFEYATAHLGKTIRFEDFSKPGKFVDVLSVTKGKGFTGHVQRF 210
                                   5679*****************************88999******************************************* PP

                                   T----STTTSSSSSS-S-SS-SSSSS--TTS--SEEESCCEEEEEEEEEEEEETTTSSTTTSSTTT.SS..SS.TTTCTTC CS
                  Ribosomal_L3 237 gvkklprkthrglRkvaaigawdparVsstvaraGqkGyhhRtelnkkiyrigkgedaknastefdltekeitPmGGfvhy 317
                                   gvk lprk  + +R ++++g+w+p  V+ tv++aGq+Gy +Rt  n ++ +  kgeda           ++i+  GGf hy
  gi|13541155|ref|NP_110843.1| 211 GVKLLPRKNRKHRRMIGTLGPWHPDWVRNTVPQAGQMGYQQRTISNVRVLKYSKGEDA-----------DTINVRGGFLHY 280
                                   ******************************************************8875...........689********* PP

                                   B..TSCEEEEES--SSSTTEEEEEEE-SSGGGSCCCSS-EEEEEE-TTCTSS CS
                  Ribosomal_L3 318 GevkndfilvkGsvpGpkkrlvklrkslltqtsrkaeeevslkfidtaskfg 369
                                   G vknd++l+ GsvpGp krl+k+r+  + +    + ++v+l++i+  sk+g
  gi|13541155|ref|NP_110843.1| 281 GLVKNDYVLLFGSVPGPAKRLIKMRDPARQKVP--DIDNVKLDYISLESKQG 330
                                   **************************9876655..5667888*******998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       496  (0.0276647); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.33s 00:00:00.94 Elapsed: 00:00:00.53
# Mc/sec: 1879.51
//
Query:       gi|13541156|ref|NP_110844.1|  [L=255]
Description: 50S ribosomal protein L4P [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-33  116.3   0.1    1.5e-33  116.1   0.1    1.0  1  Ribosomal_L4  Ribosomal protein L4/L1 family


Domain annotation for each model (and alignments):
>> Ribosomal_L4  Ribosomal protein L4/L1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.1   0.1   8.2e-38   1.5e-33       1     191 [.      18     252 ..      18     253 .. 0.91

  Alignments for each domain:
  == domain 1  score: 116.1 bits;  conditional E-value: 8.2e-38
                                   EEE-HHHHSS---HHHHHHHHHHHHHSS-EE-----.-TTTSS---S-SS-SSSSSS---S-TT.......STTSTT---S CS
                  Ribosomal_L4   1 veLspkvFaapirrdlihravvaylanrrqgtastk.arsevsgsgrklwkQKGtGrARvgsir.......spiargGgva 73 
                                   ++L p++F+  +r+dli++a++a + + rq+++s++ a+ +  g++ k++     G +R+++i         + a+gG+ a
  gi|13541156|ref|NP_110844.1|  18 IDL-PEIFNYSVREDLIRKAFRAISLSLRQPYGSSPlAGLRRVGHTTKPGL----GISRMPRIAggsrvvgIASAVGGKSA 93 
                                   578.9***************************************9888866....****************9********* PP

                                   S---S.EEHHHHHHHHHHHHHHHHHHHHHHHTT-EEEES.---..-S...........S--HHHHHHHHHHTT-....... CS
                  Ribosomal_L4  74 hgpkperdystklnkKvrrlAlrsaLsakakqglllvvd.nle.ple...........esktkelvellkklgl....... 134
                                   h p+ +++ +  +n+K+r++A  sa++ +a+++ ++ ++  ++  l+           ++ktk++v+llk++gl       
  gi|13541156|ref|NP_110844.1|  94 HSPRSTKKLYVGINEKERKMAKFSAIAMTASADAVRKRGhRFSeSLPlpvvvedavsgIKKTKDAVNLLKSIGLyedilrs 174
                                   ***************************************845445556688999999**************9998888888 PP

                                   ...................TTSSEEEEESSSSCHHHHHHTT-TTEEEEESTT--CHHHHHSSE....EEEEHHHHHHHHH CS
                  Ribosomal_L4 135 ...................ksksvLivvsekdenlvlaarnlpgvevieveslnvydllkadk....vvitksaveklee 191
                                                       +ks+Liv    d+  +++++ lpgv+v++++sl++++l+++      +v+t+sa+ekl+e
  gi|13541156|ref|NP_110844.1| 175 kegkhiragrgkmrnrrykVPKSLLIVGT--DSVSLKVFKSLPGVDVASMDSLSIRKLAPGGVggrlTVYTESAIEKLRE 252
                                   88888888888887777755667666664..799********************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       372  (0.0207485); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.34s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 1532.51
//
Query:       gi|13541157|ref|NP_110845.1|  [L=83]
Description: 50S ribosomal protein L23P [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.7e-15   56.5   5.4    3.4e-14   53.0   5.4    1.9  1  Ribosomal_L23  Ribosomal protein L23
  ------ inclusion threshold ------
      0.017   14.0   0.2      0.018   13.9   0.2    1.0  1  Fmp27_WPPW     RNA pol II promoter Fmp27 protein domain
       0.05   13.0   0.0      0.057   12.8   0.0    1.1  1  VPS13_mid_rpt  Repeating coiled region of VPS13


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 !   53.0   5.4   5.7e-18   3.4e-14       1      78 [.       3      67 ..       3      75 .. 0.87

  Alignments for each domain:
  == domain 1  score: 53.0 bits;  conditional E-value: 5.7e-18
                                  SSEEEE--SHHHHHHHTT.E.EEEEE-SS-THHHHHHHHHHHHT--EEEEEEEEE--EBESSSSSEEBE--EEEEEEEE CS
                 Ribosomal_L23  1 dvilkPvitEkstklaek.nkyvFeVakdanKleikkaveklFgVkVekVntlnvkgkkkrvgrkvgrrksyKkaiVtL 78
                                  dvil+Pv tEk+  laek nk+++ V+++a+K +ik+ ve+ F VkVe +n+l+ k+ kk              aiV+L
  gi|13541157|ref|NP_110845.1|  3 DVILSPVSTEKTALLAEKeNKLTLIVDRKATKEDIKREVESRFSVKVEGINILITKKGKK--------------AIVKL 67
                                  79***************988**********************************998655..............33333 PP

>> Fmp27_WPPW  RNA pol II promoter Fmp27 protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.2     3e-06     0.018     398     454 ..       9      63 ..       4      76 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3e-06
                    Fmp27_WPPW 398 knpksvvlvtakdielkivsiedkervsddvsglverRfgvllddaqfFvlkkkdfs 454
                                     +++++l++ k+ +l    i d++  ++d+++ ve+Rf+v+++ +++ ++kk +  
  gi|13541157|ref|NP_110845.1|   9 VSTEKTALLAEKENKLTL--IVDRKATKEDIKREVESRFSVKVEGINILITKKGKKA 63 
                                   566777788877766655..567777999***********************95443 PP

>> VPS13_mid_rpt  Repeating coiled region of VPS13
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   9.5e-06     0.057     137     186 ..      32      81 ..       2      82 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 9.5e-06
                 VPS13_mid_rpt 137 edleeleelmYDkfslklsdtqvllgdsgedwkealsedssklhilepin 186
                                    + e++++++ ++fs+k++ + +l++++g+++  +l ++ s   i e+i+
  gi|13541157|ref|NP_110845.1|  32 ATKEDIKREVESRFSVKVEGINILITKKGKKAIVKLAKEYSAEEIAERIG 81 
                                   23677999999*********************999998877778998886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       824  (0.0459591); 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:                         3  (0.000167327); expected 0.2 (1e-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 0.32s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 528.84
//
Query:       gi|13541158|ref|NP_110846.1|  [L=234]
Description: 50S ribosomal protein L2P [Thermoplasma volcanium GSS1]
Scores for complete 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-41  139.4   0.8    1.2e-40  138.6   0.8    1.3  1  Ribosomal_L2_C  Ribosomal Proteins L2, C-terminal domain
    0.00013   21.9   0.0    0.00038   20.4   0.0    1.9  1  Ribosomal_L2    Ribosomal Proteins L2, RNA binding domain


Domain annotation for each model (and alignments):
>> Ribosomal_L2_C  Ribosomal Proteins L2, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  138.6   0.8   1.3e-44   1.2e-40       1     121 [.      85     215 ..      85     219 .. 0.91

  Alignments for each domain:
  == domain 1  score: 138.6 bits;  conditional E-value: 1.3e-44
                                   SSSS-EBSSSS-TTB-BBSE-SSTTS--SSS-SSSB-EEBB-B.SSEEEEEETTS-EEEEETTSBEBES-BS-TTCTT--- CS
                Ribosomal_L2_C   1 kvGnvlplknipeGtivhnielkpgkggklarsaGtyaqvvakegkkvtvklpSgevrkvssecrAtiGvvsngehkekkl 81 
                                   ++G ++ l+nip G++v+nie++pg+gg+++rsaGt+a vv++  ++vt+klpSg++r ++ +crAt+Gvv+ ++  + ++
  gi|13541158|ref|NP_110846.1|  85 NPGTTTVLANIPDGSYVYNIESSPGDGGEFCRSAGTFALVVSHG-SRVTLKLPSGSMRDFDPRCRATVGVVAASGIIDAPI 164
                                   58999*************************************96.9*********************************** PP

                                   -STTHHHHT.....TBS----SSSS-TTTSSS--SS....SS..--SSSST CS
                Ribosomal_L2_C  82 gkAgrkrwl.....grrpkvrGvamnpvdHphGGGe....Gk..tksrkap 121
                                   +kAg++ +      +r  +vrGvamn+v+HphGGG+    G+  t++r+ap
  gi|13541158|ref|NP_110846.1| 165 LKAGTHVHYlrskaKRPYTVRGVAMNAVNHPHGGGNhqhvGRpsTVGRNAP 215
                                   ******9998998555559*****************777776656666665 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 !   20.4   0.0   4.2e-08   0.00038      25      76 ..      27      77 ..       9      78 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 4.2e-08
                                  --S-.--SS--EEEEEEE--TT-SS-EEEEEETTTEEEEEE--SS--SS-EE- CS
                  Ribosomal_L2 25 dfkr.nkekvkgkVveieyDpgRsApiAlvkyedgekryiiapeglkvGdtvv 76
                                  d k  +++++  +V++i++ pgR++p+  ++   g+k y ia  g  vG+++v
  gi|13541158|ref|NP_110846.1| 27 DVKHlKPGEY--VVKDIIHAPGRNSPLLELVDSTGKKVYQIAFTGAYVGQKIV 77
                                  4544444444..9*************99999999*****************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 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:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.51
# Mc/sec: 1389.68
//
Query:       gi|13541159|ref|NP_110847.1|  [L=151]
Description: 30S ribosomal protein S19P [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-25   88.8   0.2    1.6e-25   88.8   0.2    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 ?   -3.2   0.1      0.44   7.8e+03       8       8 ..      17      17 ..       5      29 .. 0.48
   2 !   88.8   0.2   8.8e-30   1.6e-25       2      81 .]      59     134 ..      55     134 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 0.44
                                  T CS
                 Ribosomal_S19  8 f 8 
                                  +
  gi|13541159|ref|NP_110847.1| 17 R 17
                                  1 PP

  == domain 2  score: 88.8 bits;  conditional E-value: 8.8e-30
                                   HHHSS.TTCCCHHHHHHHHHHTS-----EEES-TT-B--GGGTT-EEEEE-SSSEEEEE--CCCTTSBCGGGT-SS----S CS
                 Ribosomal_S19   2 slkkg.pfvqesllkkvrkakaekkkevikthsRdstIlPemvgltvgVynGktfvpveikeemvGhkLgEFspTrkpvkh 81 
                                   sl ++ ++ q++l++k++     ++ + ikth+Rd++IlP++vg  v+VynG+++ ++eik+em+Gh+LgEF++Trk vkh
  gi|13541159|ref|NP_110847.1|  59 SLSREmNHDQKKLVEKLE-----GDYDDIKTHVRDVIILPSYVGKIVEVYNGNSYSKFEIKPEMIGHYLGEFVMTRKEVKH 134
                                   555665566666666554.....355679***************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       961  (0.0536003); expected 358.6 (0.02)
Passed bias filter:                      624  (0.0348039); 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: 0.56u 0.32s 00:00:00.88 Elapsed: 00:00:00.52
# Mc/sec: 873.96
//
Query:       gi|13541160|ref|NP_110848.1|  [L=151]
Description: 50S ribosomal protein L22P [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.1e-26   90.7   0.1    7.5e-26   90.4   0.1    1.1  1  Ribosomal_L22  Ribosomal protein L22p/L17e


Domain annotation for each model (and alignments):
>> Ribosomal_L22  Ribosomal protein L22p/L17e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.4   0.1   4.2e-30   7.5e-26       2     103 .]      19     147 ..      18     147 .. 0.96

  Alignments for each domain:
  == domain 1  score: 90.4 bits;  conditional E-value: 4.2e-30
                                   EEEEESS-HHHHHHHHHHHTTSBHHHHHHHHHT..-SST.........................THHHHHHHHHHHHHHHH CS
                 Ribosomal_L22   2 kgsnlrvsfkklrevarlIrgmkveeAlkyLkf..skkk.........................aakfvlklLknaeanae 55 
                                   ++ ++ +s k + ++a+ Irgmk++ A+++L++  skk                          aak +++lL n+e+nae
  gi|13541160|ref|NP_110848.1|  19 RIVEADISLKDAVNIAHHIRGMKLDYAKQILEDvvSKKYaipyfryldsvshrpgkgpgrypvkAAKVFIDLLSNVENNAE 99 
                                   566789***************************965555****************************************** PP

                                   ..HT-GGGEEEEEEEEEEEEEEEEEEEESTTEEEEEEEEEEEEEEEEE CS
                 Ribosomal_L22  56 lkgldvdslvIeeiqvnkgpklkrrtyrArGrinpirkspchievvlk 103
                                    kg++ dsl+I+++ +nkg+++k++t++A Gr++   k  +++ev+++
  gi|13541160|ref|NP_110848.1| 100 FKGMNTDSLIIKHVAANKGRMIKKYTPKAYGRAGANFKDLINLEVIVT 147
                                   **********************************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); 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:                         1  (5.57756e-05); expected 0.2 (1e-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 0.31s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 925.88
//
Query:       gi|13541161|ref|NP_110849.1|  [L=225]
Description: 30S ribosomal protein S3P [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-18   67.5   0.8    2.1e-18   66.6   0.8    1.5  1  Ribosomal_S3_C  Ribosomal protein S3, C-terminal domain
    4.3e-13   48.9   0.0      1e-12   47.7   0.0    1.6  1  KH_2            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 !   66.6   0.8   2.4e-22   2.1e-18       1      83 []      98     181 ..      98     181 .. 0.99

  Alignments for each domain:
  == domain 1  score: 66.6 bits;  conditional E-value: 2.4e-22
                                   HHHHHHTT--HHHHHHHHHHHHHHCC-SEEEEEEEC-SS.TTT--EEEEEEC----..TCHHHH-EEEEEEEEETTEEEEE CS
                Ribosomal_S3_C   1 iaeqlekrvsfRramkkairramkagakGikiqvsGrLggaeiarsekykeGrvpl..htlradidyavaeaktkyGiiGv 79 
                                   ia +lek++s+R+a +++++r+++aga+G+ i++sG+++ +e+ar +k+  G+v+   ++ ++ +  ++++ak+k Gi+Gv
  gi|13541161|ref|NP_110849.1|  98 IALSLEKGWSYRKAGNTSLKRTIDAGARGVLIKISGKIS-GERARYQKFIYGNVKYsgEPGSKGMLVGFSTAKLKVGILGV 177
                                   8999***********************************.9***************9************************ PP

                                   EEEE CS
                Ribosomal_S3_C  80 kVwI 83 
                                   +V+I
  gi|13541161|ref|NP_110849.1| 178 TVKI 181
                                   **98 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.7   0.0   1.1e-16     1e-12       2      76 ..      16      87 ..      15      89 .. 0.93

  Alignments for each domain:
  == domain 1  score: 47.7 bits;  conditional E-value: 1.1e-16
                                  HHHHHHHHTECETEEEEEEECCSCEEEEEEEESCHHHHHTGGGHHHHHHHHHHHHHHHHHHTTCEEEEEEEETTT CS
                          KH_2  2 ipeslaveikkagvskveIertanrviiviresqpgivIGkgGsnikkigkelrkdieklegkkVklnivkVkkp 76
                                  ++e+l +e+++ag +k+  +rt+ +++i++++++pg+vIG++Gs++++++++l+k+  ++e  +++  +++Vk p
  gi|13541161|ref|NP_110849.1| 16 VYEYLVKETENAGFGKMSMKRTPFGTNITLYVNRPGLVIGRRGSKVQQMTETLEKKY-AIETPQIE--VKDVKDP 87
                                  6899*****************************************************.6******9..5666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       388  (0.0216409); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); 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 0.34s 00:00:00.95 Elapsed: 00:00:00.58
# Mc/sec: 1170.38
//
Query:       gi|13541162|ref|NP_110850.1|  [L=66]
Description: 50S ribosomal protein L29P [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.3e-15   56.3   1.5    3.1e-15   55.9   1.5    1.1  1  Ribosomal_L29  Ribosomal L29 protein
     0.0057   17.1   1.9     0.0057   17.1   1.9    1.3  1  Enkurin        Calmodulin-binding
  ------ inclusion threshold ------
      0.031   14.3   0.1      0.045   13.8   0.1    1.3  1  Spectrin_like  Spectrin like 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 !   55.9   1.5   5.2e-19   3.1e-15       1      56 [.       7      63 ..       7      63 .. 0.97

  Alignments for each domain:
  == domain 1  score: 55.9 bits;  conditional E-value: 5.2e-19
                                  HHHHHS-HHHHHHHHHHHHHHHHHHHHHHHHT.SSS-CHHHHHHHHHHHHHHHHHHH CS
                 Ribosomal_L29  1 kelrelsdeeLkeklkelkkeLfnLrfqkatg.qlenpsrirkvRkdIARikTvlre 56
                                  k++r++s+ee ++ lk+lk+ L+  r   ++g +   p+++r +R++IAR++Tv re
  gi|13541162|ref|NP_110850.1|  7 KQIRQMSKEERQQTLKNLKESLLHERALVSMGgSSPSPGKVRSIRRQIARLLTVERE 63
                                  68******************************8888*******************98 PP

>> Enkurin  Calmodulin-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   1.9   9.5e-07    0.0057      33      54 ..       7      28 ..       2      66 .] 0.86

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 9.5e-07
                       Enkurin 33 pgmrllseeerqellegLkkkw 54
                                  +++r++s+eerq++l++Lk+++
  gi|13541162|ref|NP_110850.1|  7 KQIRQMSKEERQQTLKNLKESL 28
                                  789****************986 PP

>> Spectrin_like  Spectrin like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   7.6e-06     0.045      19      38 ..       7      26 ..       3      41 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 7.6e-06
                 Spectrin_like 19 amlktmkpeeyrqvlknLel 38
                                  +++++m+ ee++q+lknL+ 
  gi|13541162|ref|NP_110850.1|  7 KQIRQMSKEERQQTLKNLKE 26
                                  789***************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1122  (0.0625802); expected 358.6 (0.02)
Passed bias filter:                      553  (0.0308439); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.32s 00:00:00.81 Elapsed: 00:00:00.51
# Mc/sec: 392.94
//
Query:       gi|13541163|ref|NP_110851.1|  [L=100]
Description: translation initiation factor Sui1 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-22   79.7   2.4    2.1e-22   79.4   2.4    1.1  1  SUI1      Translation initiation factor SUI1
    1.2e-05   25.5   0.4    1.5e-05   25.2   0.4    1.2  1  Img2      Mitochondrial large subunit ribosomal protein (Img2
  ------ inclusion threshold ------
      0.019   14.7   0.0      0.042   13.6   0.0    1.6  1  DUF2179   Uncharacterized protein conserved in bacteria (DUF2


Domain annotation for each model (and alignments):
>> SUI1  Translation initiation factor SUI1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.4   2.4   3.5e-26   2.1e-22       2      77 .]      23      95 ..      22      95 .. 0.94

  Alignments for each domain:
  == domain 1  score: 79.4 bits;  conditional E-value: 3.5e-26
                          SUI1  2 kpkihirleqrggrKkvTtvsgleafgidlkklakelkkkfacsgsvvkdggeeiqvQGdqrkkvaelLtekygvp 77
                                  ++ ++i +++r+ +K vT+++g++++  d++k+akelkkk+a++g+v k+g   i++QGd+r++v+++L+++ g++
  gi|13541163|ref|NP_110851.1| 23 AQAVKIVVDKRRYGKFVTIIEGIDPKIEDIEKIAKELKKKVASGGTV-KEG-RIIELQGDHRQEVKKFLEDM-GFK 95
                                  688*******************************************9.655.79*****************9.885 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 !   25.2   0.4   2.5e-09   1.5e-05      36      80 .]      51      94 ..      24      94 .. 0.81

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 2.5e-09
                          Img2 36 DiaalredLrkaleelvkvnevtgkieikGdrveevkkfLeskgF 80
                                  Di++++++L+k ++ +    ++ + ie++Gd+++evkkfLe+ gF
  gi|13541163|ref|NP_110851.1| 51 DIEKIAKELKKKVA-SGGTVKEGRIIELQGDHRQEVKKFLEDMGF 94
                                  88899999999999.78888899*********************9 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 ?   13.6   0.0     7e-06     0.042      14      42 ..      20      48 ..      16      49 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 7e-06
                       DUF2179 14 geekkvlytvvsrkelsklkeiikeiDpk 42
                                  g+e + + +vv ++ + k+ +ii+ iDpk
  gi|13541163|ref|NP_110851.1| 20 GREAQAVKIVVDKRRYGKFVTIIEGIDPK 48
                                  55788899********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1076  (0.0600145); expected 358.6 (0.02)
Passed bias filter:                      747  (0.0416643); 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: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.52
# Mc/sec: 576.51
//
Query:       gi|13541164|ref|NP_110852.1|  [L=89]
Description: ribonuclease P protein component 1 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-19   69.5   0.2    1.9e-19   69.3   0.2    1.0  1  UPF0086   Domain of unknown function UPF0086


Domain annotation for each model (and alignments):
>> UPF0086  Domain of unknown function UPF0086
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.3   0.2   1.1e-23   1.9e-19       6      82 ..       5      76 ..       1      78 [. 0.95

  Alignments for each domain:
  == domain 1  score: 69.3 bits;  conditional E-value: 1.1e-23
                                  SXXSS-EEEEEECSSTTTTTEEEEEEEEETTEEEEEECTTEEEEEESTTCEEEEEE.TTEEEEEECCCCSSXHHHHH CS
                       UPF0086  6 adlhGaeveVvrsknpslvgikGiVvkEtkntlkivtkksrvktvpKegsvFefevkdvlevevdGsqlryrpadRa 82
                                   +++G +veV++s+n+  vgi+G V  Etknt++i +  ++  +vpKeg +F+f+ k    ++vdGs ++yrp+dR 
  gi|13541164|ref|NP_110852.1|  5 SEFIGRHVEVIQSSNRYDVGISGQVSFETKNTFEITK-GTGKVIVPKEGRIFTFDGK----FKVDGSLINYRPEDRL 76
                                  69*********************************97.999***************8....***************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.33s 00:00:00.82 Elapsed: 00:00:00.51
# Mc/sec: 523.58
//
Query:       gi|13541165|ref|NP_110853.1|  [L=109]
Description: 30S ribosomal protein S17P [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.3e-24   84.4   3.0    5.3e-24   84.1   3.0    1.1  1  Ribosomal_S17    Ribosomal protein S17
     0.0041   17.5   0.1     0.0097   16.3   0.0    1.7  2  Ribosomal_S17_N  Ribosomal_S17 N-terminal


Domain annotation for each model (and alignments):
>> Ribosomal_S17  Ribosomal protein S17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.1   3.0   5.9e-28   5.3e-24       1      68 []      37     105 ..      37     105 .. 0.99

  Alignments for each domain:
  == domain 1  score: 84.1 bits;  conditional E-value: 5.9e-28
                                   EEEEE--STTEEEEEEEEEEEETTTTEEEEEEEEEEEE-TTTS.--TT-EEEEEEECECSSSEEEEEEE CS
                 Ribosomal_S17   1 GvVvsdkmdkTvvVrverlvkhpkykkyvkrrkkylahdenns.vkvGDiVrieecrPlSktkrfvvve 68 
                                   G+V+s+ m+++vvV++e+++++pky++  ++ kky++h ++++ ++vGD+Vr++ecr+l+kt++fvvve
  gi|13541165|ref|NP_110853.1|  37 GKVISTAMTRSVVVAREYQQYIPKYERKATKIKKYHVHVPDCIeLRVGDTVRFAECRKLAKTISFVVVE 105
                                   99*****************************************************************97 PP

>> Ribosomal_S17_N  Ribosomal_S17 N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   1.1e-06    0.0097      34      69 .]       4      35 ..       2      35 .. 0.84
   2 ?   -2.9   0.1         1   9.1e+03      16      16 ..      62      62 ..      51      74 .. 0.50

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.1e-06
                                  ----TT----GGGGS-----TTSSSSSS----S-EE CS
               Ribosomal_S17_N 34 knvglgfktPkeAiegtYiDkKCPFtGnvsirGriL 69
                                  +n+gl  ++P++    +  D  CPF Gn  +rG++L
  gi|13541165|ref|NP_110853.1|  4 RNIGLDVSVPEK----ECTDPHCPFHGNLPVRGQVL 35
                                  688888888865....55699*************98 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1
                                  - CS
               Ribosomal_S17_N 16 k 16
                                  +
  gi|13541165|ref|NP_110853.1| 62 E 62
                                  1 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       469  (0.0261587); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.31s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 682.49
//
Query:       gi|13541166|ref|NP_110854.1|  [L=132]
Description: 50S ribosomal protein L14P [Thermoplasma volcanium GSS1]
Scores for 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-35  119.4   0.1    1.1e-34  119.2   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 !  119.2   0.1   5.9e-39   1.1e-34       5     121 ..      15     131 ..      12     132 .] 0.92

  Alignments for each domain:
  == domain 1  score: 119.2 bits;  conditional E-value: 5.9e-39
                                   S-EEE--SSSSBSEEEEEEETT-.....---EE-SSSEEEEEESSS-T...TTSSCEEEEEEEE-SS-EE-TTS-EEEESS CS
                 Ribosomal_L14   5 ktrlkvaDNsgakevecikvlggk....krkaasvGdiivvsvkkakpkgkvkkgdvvkavvvrtkkevrrkdGsvirfdd 81 
                                   ++++ +aDN+ga+++ +i v  ++    + +aa vGd+ ++svkk++p   +++++vv+avv+r+k+++rr+dG++++f+d
  gi|13541166|ref|NP_110854.1|  15 GANIVCADNTGARSISLIDVKAYHgkarRIPAAGVGDMFIASVKKGTP---EMRSKVVYAVVIRQKRPYRRPDGTMVEFED 92 
                                   67899**************997664443449*****************...899*************************** PP

                                   -EEEEB-TTS-BSS-.B-SBEEHHHHHH.-HHHHHTBSBE CS
                 Ribosomal_L14  82 naaVllnkkgeplGtrifgpvarelrekkflkivslApev 121
                                   naaVl++ +ge++G++i+gpvare++e+ +++i+++A+ +
  gi|13541166|ref|NP_110854.1|  93 NAAVLVTPDGEVRGSEIKGPVAREAAER-WPRIAAIASII 131
                                   ***************************9.********977 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       344  (0.0191868); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.34s 00:00:00.85 Elapsed: 00:00:00.52
# Mc/sec: 760.67
//
Query:       gi|13541167|ref|NP_110855.1|  [L=145]
Description: 50S ribosomal protein L24P [Thermoplasma volcanium GSS1]
Scores for complete 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-13   48.7   0.0    9.9e-12   45.2   0.0    2.0  2  Ribosomal_L26  Ribosomal proteins L26 eukaryotic, L24P archae
    0.00021   21.1   6.8    0.00021   21.1   6.8    1.9  2  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 !   45.2   0.0   1.1e-15   9.9e-12      23      79 ..       5      94 ..       2      97 .. 0.94
   2 ?    2.0   0.1     0.032   2.9e+02      35      65 ..      98     130 ..      91     141 .. 0.79

  Alignments for each domain:
  == domain 1  score: 45.2 bits;  conditional E-value: 1.1e-15
                                  xxxxxxxxxxxxxxxxxxxxx................................xxxxxxxxxxxxxxxxxxxxxxxxxxxx.x RF
                 Ribosomal_L26 23 msapLskeLrekygvrslpir................................gvtrekangttvpvgihpSkvvItklkl.D 72
                                  ++  Lsk+Lr+kyg+rs+pi                                 g+t  k +g++  +gi+p k++It l+l  
  gi|13541167|ref|NP_110855.1|  5 LNVALSKDLRKKYGIRSFPIVkgdvvkvvsgarkgeggkvaevdhhsglviveGITIAKIDGKQKGFGISPEKLQITHLDLsR 87
                                  5778*****************************************************************************77 PP

                                  xxxxxxx RF
                 Ribosomal_L26 73 kdrkkiL 79
                                   +r + +
  gi|13541167|ref|NP_110855.1| 88 SERFQKI 94
                                  7777766 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.032
                                   xxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxx RF
                 Ribosomal_L26  35 ygvrslpir..gvtrekangttvpvgihpSkvv 65 
                                    +++++ i+   +++e+++ ++++  i p +v 
  gi|13541167|ref|NP_110855.1|  98 ANIKHITIQeePIQEEQQKTEETKQEIAPEEVE 130
                                   588999999887899999999999999998886 PP

>> KOW  KOW motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   6.8   2.3e-08   0.00021       1      32 []      26      57 ..      26      57 .. 0.96
   2 ?   -1.4   0.1       0.3   2.7e+03       8      15 ..      64      71 ..      63      71 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 2.3e-08
                                  TTSEEEESSSTTTTCEEEEEEEETTTTEEEEE CS
                           KOW  1 pGdhVkVvsGphkGktGkVvkvdqhkvrVfvd 32
                                  +Gd+VkVvsG  kG+ GkV +vd h   V+v+
  gi|13541167|ref|NP_110855.1| 26 KGDVVKVVSGARKGEGGKVAEVDHHSGLVIVE 57
                                  7*************************999886 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.3
                                  SSSTTTTC CS
                           KOW  8 vsGphkGk 15
                                  ++G+ kG+
  gi|13541167|ref|NP_110855.1| 64 IDGKQKGF 71
                                  78999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2017  (0.112499); expected 358.6 (0.02)
Passed bias filter:                      564  (0.0314574); 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 0.33s 00:00:00.87 Elapsed: 00:00:00.51
# Mc/sec: 858.44
//
Query:       gi|13541168|ref|NP_110856.1|  [L=235]
Description: 30S ribosomal protein S4e [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      1e-18   67.0   0.0    2.5e-18   65.7   0.0    1.7  1  Ribosomal_S4e  Ribosomal family S4e
    2.6e-06   27.0   0.1    5.2e-06   26.1   0.1    1.5  1  S4             S4 domain
    0.00019   21.5   1.1    0.00031   20.8   1.1    1.3  1  RS4NT          RS4NT (NUC023) domain
    0.00032   20.5   3.6    0.00062   19.6   0.0    3.2  3  KOW            KOW motif
     0.0062   16.3   2.8     0.0062   16.3   0.6    2.1  3  S4_2           S4 domain


Domain annotation for each model (and alignments):
>> Ribosomal_S4e  Ribosomal family S4e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.7   0.0     7e-22   2.5e-18       2      75 .]      90     163 ..      89     163 .. 0.99

  Alignments for each domain:
  == domain 1  score: 65.7 bits;  conditional E-value: 7e-22
                                   TEEEEEEE-TTSSEEEEEE-TTCCCEEEEEECEEEEECCCEEEEEETTS-EEEESSTT-STTEEEEEETTTTEE CS
                 Ribosomal_S4e   2 genyrllydtkgrfalhkItseeakyKLcKikkkttvkkgipqlvthdGrtirypdpdikvnDtvkidleenkI 75 
                                   ge+yr++y+++g ++l+  +++ a++K +++k+k + +++++ql +hdGr + ++d +i+v+D+v  +l++ kI
  gi|13541168|ref|NP_110856.1|  90 GESYRVVYNNQGALVLVSESKDRANMKPLQVKNKVIAPGNKIQLGFHDGRVMVTEDRSISVGDVVIASLPDMKI 163
                                   8**********************************************************************998 PP

>> S4  S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.1   1.4e-09   5.2e-06      17      48 .]      55      86 ..      41      86 .. 0.95

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 1.4e-09
                                  HHHHHHHHTTTEEETTEEE--TT-EE-TTCEE CS
                            S4 17 reArqlIehGrVlVNGkvvkdpsyrVkpgDvi 48
                                  reA ++   G V+V+Gkvvk  ++ V+++Dvi
  gi|13541168|ref|NP_110856.1| 55 REATRILANGLVKVDGKVVKERKFGVGFMDVI 86
                                  8*****************************98 PP

>> RS4NT  RS4NT (NUC023) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   1.1   8.6e-08   0.00031       7      36 ..       5      34 ..       3      35 .. 0.94

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 8.6e-08
                                  EETTTS-TTS---SSSSSEE----SSSS-T CS
                         RS4NT  7 LKrlaAPkhWpldkkegvfavkPspGPHkl 36
                                   Krl+ P++  +++k++ + ++P pG Hk+
  gi|13541168|ref|NP_110856.1|  5 TKRLMVPRTVKIPRKTYFWGPTPLPGRHKA 34
                                  6***************************97 PP

>> KOW  KOW motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.3      0.63   2.3e+03      20      27 ..      66      73 ..      65      76 .. 0.74
   2 !   19.6   0.0   1.7e-07   0.00062       1      30 [.     171     204 ..     171     206 .. 0.86
   3 ?   -1.1   0.1       0.6   2.2e+03       2       9 ..     213     220 ..     212     220 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.63
                                  EEEETTTT CS
                           KOW 20 vkvdqhkv 27
                                  vkvd ++v
  gi|13541168|ref|NP_110856.1| 66 VKVDGKVV 73
                                  78888875 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 1.7e-07
                                   TTSEEEESSSTTTTCEEEEEEEETTT....TEEE CS
                           KOW   1 pGdhVkVvsGphkGktGkVvkvdqhk....vrVf 30 
                                   pG+   +++G h G+tG++ k++ +     + V+
  gi|13541168|ref|NP_110856.1| 171 PGNKAFITGGSHVGETGTISKIEIKEsssaNLVH 204
                                   8*********************988766666666 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.6
                                   TSEEEESS CS
                           KOW   2 GdhVkVvs 9  
                                    dhV V++
  gi|13541168|ref|NP_110856.1| 213 KDHVFVIG 220
                                   69999985 PP

>> S4_2  S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.6   1.7e-06    0.0062      25      65 .]      56      96 ..      51      96 .. 0.94
   2 ?   -2.5   0.0       1.3   4.7e+03      45      58 ..     121     134 ..     106     143 .. 0.68
   3 ?   -2.7   0.0       1.5   5.2e+03      46      55 ..     145     154 ..     132     163 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.7e-06
                          S4_2 25 eaKafiaegeVkvNGevetrRgkKlraGdvVeidgetievv 65
                                  ea  ++a+g Vkv+G+v ++R+  +   dv+ei ge+++vv
  gi|13541168|ref|NP_110856.1| 56 EATRILANGLVKVDGKVVKERKFGVGFMDVIEISGESYRVV 96
                                  67789**********************************95 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.3
                          S4_2  45 RgkKlraGdvVeid 58 
                                   ++k + +G  ++++
  gi|13541168|ref|NP_110856.1| 121 KNKVIAPGNKIQLG 134
                                   67777888888774 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 1.5
                          S4_2  46 gkKlraGdvV 55 
                                    + +  GdvV
  gi|13541168|ref|NP_110856.1| 145 DRSISVGDVV 154
                                   5667778887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       492  (0.0274416); 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:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.51u 0.32s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 1467.59
//
Query:       gi|13541169|ref|NP_110857.1|  [L=170]
Description: 50S ribosomal protein L5P [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.6e-24   84.1   0.2    1.3e-22   79.7   0.1    2.3  2  Ribosomal_L5_C  ribosomal L5P family C-terminus
      6e-21   74.5   0.5    1.2e-20   73.6   0.5    1.5  1  Ribosomal_L5    Ribosomal protein L5


Domain annotation for each model (and alignments):
>> Ribosomal_L5_C  ribosomal L5P family C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.7   0.1   1.5e-26   1.3e-22       1      79 [.      59     135 ..      59     159 .. 0.88
   2 ?    2.9   0.0     0.013   1.2e+02       5      25 ..     148     168 ..     144     170 .] 0.83

  Alignments for each domain:
  == domain 1  score: 79.7 bits;  conditional E-value: 1.5e-26
                Ribosomal_L5_C   1 piGvkvtLrgekmyefldkllevvlprlrdFkGiskssfdgrGnvsfGikeqiifpeieydkdkgifGmditivttak... 78 
                                   piGvkvtLr++++++fl+k+l v+ +++       ++sfd++Gn  fGi+++++f++++yd+d+gifGmd++iv++++   
  gi|13541169|ref|NP_110857.1|  59 PIGVKVTLRKDDAVNFLNKALYVKDYKIP------DYSFDKHGNAYFGISDYTDFKGMKYDPDIGIFGMDVAIVLKRRggy 133
                                   8****************************......77***************************************98664 PP

                Ribosomal_L5_C  79 .t 79 
                                    +
  gi|13541169|ref|NP_110857.1| 134 rI 135
                                   32 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.013
                Ribosomal_L5_C   5 kvtLrgekmyefldkllevvl 25 
                                   ++ +++++++efl+k ++v +
  gi|13541169|ref|NP_110857.1| 148 SIRIKKDEAVEFLEKNFKVSV 168
                                   57899**********999865 PP

>> Ribosomal_L5  Ribosomal protein L5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.6   0.5   1.3e-24   1.2e-20       1      57 []       2      55 ..       2      55 .. 0.99

  Alignments for each domain:
  == domain 1  score: 73.6 bits;  conditional E-value: 1.3e-24
                                  SCTTS-EEEEEEEEEE-SSSSSCHHHHHCCHHHHCCCHSS--EECC--TTCTTTCSC CS
                  Ribosomal_L5  1 NvMqvPrleKivinmgvGeagedkkllekaakeLaeItGQkPvvtkakksianFkiR 57
                                  N Mq++ ++K+v+n+gvG+ag++   l+kaak+L+ +tG kP++t akks+++F+iR
  gi|13541169|ref|NP_110857.1|  2 NQMQEIIIDKVVVNIGVGQAGDR---LTKAAKVLEMLTGHKPTQTLAKKSVRDFNIR 55
                                  89*********************...******************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); 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:                         2  (0.000111551); expected 0.2 (1e-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 0.35s 00:00:00.89 Elapsed: 00:00:00.54
# Mc/sec: 956.29
//
Query:       gi|13541170|ref|NP_110858.1|  [L=53]
Description: 30S ribosomal protein S14P [Thermoplasma volcanium GSS1]
Scores for complete 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-13   48.9   3.3    4.6e-13   48.7   3.3    1.1  1  Ribosomal_S14  Ribosomal protein S14p/S29e


Domain annotation for each model (and alignments):
>> Ribosomal_S14  Ribosomal protein S14p/S29e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.7   3.3   2.6e-17   4.6e-13      17      54 .]      17      53 .]       4      53 .] 0.91

  Alignments for each domain:
  == domain 1  score: 48.7 bits;  conditional E-value: 2.6e-17
                                  --SSS--SSSEE-GGG-..EHHHHHHHTTT...TT-EE-- CS
                 Ribosomal_S14 17 rCrvtGrprGvirkfgL..sRicfRelAlkgelpGvkKaS 54
                                   C+ +Gr rG++rk+gL  +R+cfRe A++    G++K+S
  gi|13541170|ref|NP_110858.1| 17 GCVRCGRKRGIVRKYGLhlCRQCFRETARQ---LGFEKYS 53
                                  6*****************************...******8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (53 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.48
# Mc/sec: 331.03
//
Query:       gi|13541171|ref|NP_110859.1|  [L=129]
Description: 30S ribosomal protein S8P [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.7e-25   88.3   0.2    4.4e-25   88.1   0.2    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 !   88.1   0.2   2.5e-29   4.4e-25       1     127 []       4     129 .]       4     129 .] 0.91

  Alignments for each domain:
  == domain 1  score: 88.1 bits;  conditional E-value: 2.5e-29
                                   -HHHHHHHHHHHHHHTT-SEEEE.E--HHHHHHHHHHHHCTSEEEEEEE.CCCCCCEEEEE-BSSS-SBSSSEEEE-SBTT CS
                  Ribosomal_S8   1 DpiadmltrirNaekakkeevev.pasklkeeilkvLkeeGyikdfeve.eekkkkikielkynkkkksvikklkrvskpg 79 
                                   D+++d++++i+Na++ +++e+   pa+kl+ ++lkv+++ +yik+fev  e++  k+ki l+ + ++++vik    v++  
  gi|13541171|ref|NP_110859.1|   4 DTLNDVINSIKNASRLGRREIIAePAAKLIGKVLKVMQDYNYIKSFEVIdESRGGKFKIVLNTTINNCGVIKPRFPVKNEN 84 
                                   89******************9999************************9666677788888888888*****999999999 PP

                                   C--EE-CCC---CGGGTSEEEEEETTEEEEHHHHHHCT--EEEEEEEE CS
                  Ribosomal_S8  80 rrvYakvkelpkvlnglGiaivsTskGvmtdkeArkkkvGGevlayvw 127
                                   ++ Y + + lp   + +Gi+i++T+kGvm++ eArk ++GG++layv+
  gi|13541171|ref|NP_110859.1|  85 LEKYES-RYLP--AEDFGILILTTTKGVMSNIEARKLGIGGKLLAYVY 129
                                   997765.4555..589*******************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.33s 00:00:00.85 Elapsed: 00:00:00.52
# Mc/sec: 746.07
//
Query:       gi|13541172|ref|NP_110860.1|  [L=178]
Description: 50S ribosomal protein L6P [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.8e-16   59.9   5.1    2.3e-08   34.6   0.2    2.1  2  Ribosomal_L6  Ribosomal protein L6


Domain annotation for each model (and alignments):
>> Ribosomal_L6  Ribosomal protein L6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.8   1.8e-10   3.2e-06       1      76 []      12      84 ..      12      84 .. 0.90
   2 !   34.6   0.2   1.3e-12   2.3e-08       1      76 []      96     170 ..      96     170 .. 0.98

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 1.8e-10
                                  CSTTEEEEEETTTEEEEEESSEEEEEE-CTTSEEEEEECSTEEEEEECSESCHHHHHHHHHHHHHHHHHHHHHHTC CS
                  Ribosomal_L6  1 iPvgvrvsikggqlvlvlGpkgeltreipegvtvevkvegnkvtvivvsgidkekvAligtvrslinnmikGVteg 76
                                  iP++v+v + g  l +  G k  l+ ++ ++  v++ ve+nk++ +  + +++e+   +gt+ s i+nm+kG +eg
  gi|13541172|ref|NP_110860.1| 12 IPKDVKVGLSGTMLSMTFGNK-KLEKKFADN-YVRLLVEDNKIKIVKSKNNSRERG-IVGTWASEISNMVKGLKEG 84
                                  8*********96666666655.79******9.7777799*****************.***************9997 PP

  == domain 2  score: 34.6 bits;  conditional E-value: 1.3e-12
                                   CSTTEEEEEETTTEEEEEESSEEEEEE-CTTSEEEEEECSTEEEEEECSESCHHHH....HHHHHHHHHHHHHHHHHHTC CS
                  Ribosomal_L6   1 iPvgvrvsikggqlvlvlGpkgeltreipegvtvevkvegnkvtvivvsgidkekv....AligtvrslinnmikGVteg 76 
                                   +P+ v+v++k + ++++ G++ ++t+ei  +++v vk     ++   ++g +k++v    A+i+ ++ ++  + +++++g
  gi|13541172|ref|NP_110860.1|  96 FPMRVSVKGKTVVIENFFGERSPRTAEIVGETQVSVK-----GDRLFLNGPSKKDVgetaANIERATIIKGFDPRVFQDG 170
                                   79*********************************99.....************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1179.85
//
Query:       gi|13541173|ref|NP_110861.1|  [L=128]
Description: 50S ribosomal protein L32e [Thermoplasma volcanium GSS1]
Scores for complete 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-39  132.4   1.0      1e-38  132.1   0.2    1.5  2  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 ?   -1.9   0.0      0.25   4.6e+03      23      39 ..       3      19 ..       2      22 .. 0.73
   2 !  132.1   0.2   5.7e-43     1e-38       3     108 .]      25     128 .]      23     128 .] 0.99

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.25
                                  --TT-TTTTT-TTS--- CS
                Ribosomal_L32e 23 rGidnrvrrrfkgqilm 39
                                  r +d++vrr +k ++ m
  gi|13541173|ref|NP_110861.1|  3 RALDDEVRRLLKIKNYM 19
                                  56788888888877766 PP

  == domain 2  score: 132.1 bits;  conditional E-value: 5.7e-43
                                   ----TTTTT-TTS-SS------TT-TTTTT-TTS-----GGG---TTTTT--TTS-EEEEESSGGGGTT--TTTE..EEEE CS
                Ribosomal_L32e   3 kFirhqsdryvklkeswrkprGidnrvrrrfkgqilmpkiGYgspkktrgllpsGfkkvlVhnvkeLevllmenksyaaei 83 
                                   +F+r+++ ry+kl++ wrkprG+++++r++++ +++++++G++sp+k+rg++psG+ +vlV+n+k++e+++++ +  aa+i
  gi|13541173|ref|NP_110861.1|  25 EFHRQEWFRYKKLGDAWRKPRGKHSKLREHLSRRPPIVDAGFRSPAKVRGMHPSGYYEVLVYNLKDIENIDPKIQ--AARI 103
                                   8**************************************************************************..**** PP

                                   -TTS-HHHHHHHHHHHHHTT-EBSS CS
                Ribosomal_L32e  84 ahsVsskkrkeiverAaelgikVtN 108
                                   a+sV+s+kr+ei++r ael+ikV+N
  gi|13541173|ref|NP_110861.1| 104 ASSVGSRKREEIAKRCAELNIKVLN 128
                                   ************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       605  (0.0337442); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        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 0.30s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 799.96
//
Query:       gi|13541174|ref|NP_110862.1|  [L=149]
Description: 50S ribosomal protein L19e [Thermoplasma volcanium GSS1]
Scores for complete 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-42  143.9  10.9    3.7e-42  143.8  10.9    1.0  1  Ribosomal_L19e  Ribosomal protein L19e
  ------ inclusion threshold ------
      0.028   14.0   1.2       0.22   11.1   1.3    2.2  1  TPD52           Tumour protein D52 family
       0.12   12.3   1.2       0.29   11.0   0.0    2.1  3  betaPIX_CC      betaPIX coiled coil


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 !  143.8  10.9   6.2e-46   3.7e-42       3     143 ..       4     144 ..       2     145 .. 0.98

  Alignments for each domain:
  == domain 1  score: 143.8 bits;  conditional E-value: 6.2e-46
                                   HHHHHHHHHHTTS-GGGEEE-GGGHHHHHH--SHHHHHHHHHTTSEEE-------THHHHHHHHHHHTT-S-SGGG--S-H CS
                Ribosomal_L19e   3 klqkrlaasvlkvGknrvwldpeeleeiaeAitredirklikdglIikkpkkgnsrararerkekkrkgrrrgsGkrkGtk 83 
                                   +++kr+ +++ +vG++rv++d+++l++i eA+tr+di +li++++++ k+kkg s++r+++r ++ +k+rrrg+G+ +Gt+
  gi|13541174|ref|NP_110862.1|   4 ETVKRIVSDLKGVGTSRVYIDTNKLDKIDEAATRSDILALIEQDVVKIKQKKGISNGRLKKRIKQLSKDRRRGPGSLRGTR 84 
                                   689****************************************************************************** PP

                                   HHHS-HHHHHHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHTT--SSHHHHHHHHT-X CS
                Ribosomal_L19e  84 eaRlpekelWikriRalRrlLkelrekkkidkktYrelYrkakGgefknkavLkeyiekk 143
                                   +aR ++ke+Wi++iRalR++L++l++++kid   Yr++Yr +k+g++k++a+L ++i+++
  gi|13541174|ref|NP_110862.1|  85 NARYKRKERWIDTIRALRDELRKLKKDGKIDPAVYRKYYRIIKSGSIKSRAQLVSHIKSA 144
                                   *********************************************************975 PP

>> TPD52  Tumour protein D52 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   1.3   3.6e-05      0.22      34     139 ..      26     143 ..      23     145 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 3.6e-05
                         TPD52  34 seLakleeeivtLrqvLaakekhlaelkrklGltalneLrqnlskswhdvq.........tsnaYkktsetlsqagqktsa 105
                                   ++L k++e  +t +++La  e+ ++++k+k G++    L++ + +  +d +             Yk+ +  ++++     +
  gi|13541174|ref|NP_110862.1|  26 NKLDKIDEA-ATRSDILALIEQDVVKIKQKKGISN-GRLKKRIKQLSKDRRrgpgslrgtRNARYKRKERWIDTIRALRDE 104
                                   578898877.999********************97.556655544444443444444463344476655545443322222 PP

                         TPD52 106 ..als...tvgsaisrklgdmrnsptFkSfEekvetlks 139
                                      l    ++  a+ rk+  + +s + kS  ++v  +ks
  gi|13541174|ref|NP_110862.1| 105 lrKLKkdgKIDPAVYRKYYRIIKSGSIKSRAQLVSHIKS 143
                                   002221114566888888888888888888888888887 PP

>> betaPIX_CC  betaPIX coiled coil
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.2      0.21   1.2e+03      53      65 ..      61      73 ..      38      84 .. 0.64
   2 ?   -1.3   0.1      0.34     2e+03      40      53 ..      62      75 ..      60      92 .. 0.66
   3 ?   11.0   0.0   4.9e-05      0.29      33      52 ..      94     113 ..      79     115 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.21
                    betaPIX_CC 53 klkksleeEqkaR 65
                                  +lkk + +  k R
  gi|13541174|ref|NP_110862.1| 61 RLKKRIKQLSKDR 73
                                  4444444444444 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.34
                    betaPIX_CC 40 Lkdevqelkqenkk 53
                                  Lk  +++l ++ ++
  gi|13541174|ref|NP_110862.1| 62 LKKRIKQLSKDRRR 75
                                  56666666666655 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 4.9e-05
                    betaPIX_CC  33 lVDtVYaLkdevqelkqenk 52 
                                    +Dt+ aL+de+++lk++ k
  gi|13541174|ref|NP_110862.1|  94 WIDTIRALRDELRKLKKDGK 113
                                   58***************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       991  (0.0552736); expected 358.6 (0.02)
Passed bias filter:                      567  (0.0316247); 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: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 898.44
//
Query:       gi|13541175|ref|NP_110863.1|  [L=160]
Description: 50S ribosomal protein L18P [Thermoplasma volcanium GSS1]
Scores for 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   74.4   4.2    4.3e-14   52.8   1.2    2.2  2  Ribosomal_L5e   Ribosomal large subunit proteins 60S L5, and 
     0.0036   17.7   0.2     0.0047   17.3   0.2    1.2  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 !   52.8   1.2   4.8e-18   4.3e-14       7      93 ..       3      82 ..       1      89 [. 0.91
   2 !   22.8   0.1   8.5e-09   7.6e-05     127     162 ..      89     124 ..      83     125 .. 0.90

  Alignments for each domain:
  == domain 1  score: 52.8 bits;  conditional E-value: 4.8e-18
                 Ribosomal_L5e  7 frrrregktdYyarkrliiqdknkyntpkyRlvVrvtnkdiicqiayakiegdkvlaaayskelpkygvkvgltnyaaaYatg 89
                                  f+r+  gktdY +r rl+         +  R++Vr+tnk ii+qia+ +++gd++la+ + k l+kyg+++  +n +++Y++g
  gi|13541175|ref|NP_110863.1|  3 FKRKVLGKTDYGRRLRLLKS-------KDRRFIVRITNKGIIAQIAEYSVNGDRILATITDKALSKYGIELRGNNLQICYLVG 78
                                  8999*************854.......4469**************************************************** PP

                 Ribosomal_L5e 90 llla 93
                                  +  +
  gi|13541175|ref|NP_110863.1| 79 YAAG 82
                                  9765 PP

  == domain 2  score: 22.8 bits;  conditional E-value: 8.5e-09
                 Ribosomal_L5e 127 rafkaiLdvGLartttgakvfgalkgavdgglsiph 162
                                   +  +a+Ld+G ++  +g ++ ++lkg++d+g++iph
  gi|13541175|ref|NP_110863.1|  89 GVETAVLDIGRKKFRKGGRIAACLKGITDSGVDIPH 124
                                   55689******************************9 PP

>> Ribosomal_L18p  Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.2   5.2e-07    0.0047      24     114 ..      24     120 ..       6     122 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 5.2e-07
                                   S-EEEEEE-SS-EEEEEE-TT.T-.-EEEEECS-SCCCT....S-SSSCHHHHHHHHHHHHHHHCHHCHTC-EE--TTSSS CS
                Ribosomal_L18p  24 rprlvvfrsnrhiyaQviddv.kg.ktlasastlekelk....lkstknkeaakkvgeliAerakekgiekvvfDrggykY 98 
                                     r +v  +n+ i aQ+ + + +g ++la++   +k+l        ++n +    vg +   +a+++g+e++v D g +k+
  gi|13541175|ref|NP_110863.1|  24 DRRFIVRITNKGIIAQIAEYSvNGdRILATIT--DKALSkygiELRGNNLQICYLVGYAAGVEAQKAGVETAVLDIGRKKF 102
                                   35788888*********986513314444443..4444435655778899999**********************888877 PP

                                   ..-CHHHHHHHHHHCTSS CS
                Ribosomal_L18p  99 ..hGrvaalAdaaReaGl 114
                                      Gr+aa  +++ + G+
  gi|13541175|ref|NP_110863.1| 103 rkGGRIAACLKGITDSGV 120
                                   336****99888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       479  (0.0267165); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.33s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 944.65
//
Query:       gi|13541176|ref|NP_110864.1|  [L=221]
Description: 30S ribosomal protein S5P [Thermoplasma volcanium GSS1]
Scores for complete 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   85.4   0.2    4.1e-24   84.3   0.2    1.6  1  Ribosomal_S5    Ribosomal protein S5, N-terminal domain
    3.3e-18   64.9   0.7    6.3e-18   64.0   0.4    1.6  2  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 !   84.3   0.2   4.5e-28   4.1e-24       2      65 .]      47     110 ..      46     110 .. 0.98

  Alignments for each domain:
  == domain 1  score: 84.3 bits;  conditional E-value: 4.5e-28
                                   EEEEEEEEEEEEEETTEEEEEEEEEEEEEETTTEEEEEEEEESSHHHHHHHHHHHHHHTEEE-- CS
                  Ribosomal_S5   2 kekvlkikrvqkvtkgGrrtsfsalvvvGdgnGlvGlGvgkakevatAirkAiekAkknlvpvp 65 
                                   k++v++ikr q++t++Grr+++s++vvvG+++G++GlG+g +ke a AirkA ++Ak+n+++++
  gi|13541176|ref|NP_110864.1|  47 KDEVIDIKRAQRMTDSGRRMTYSITVVVGNEDGYIGLGIGRSKEAAPAIRKALINAKLNIMEIR 110
                                   89***********************************************************996 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 ?   -3.2   0.0      0.65   5.8e+03      20      32 ..      14      26 ..      13      27 .. 0.82
   2 !   64.0   0.4     7e-22   6.3e-18       1      66 [.     131     197 ..     131     199 .. 0.97

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 0.65
                                  EES-HHHHHHHHH CS
                Ribosomal_S5_C 20 iiaggavravlel 32
                                  ++a+g ++++ e+
  gi|13541176|ref|NP_110864.1| 14 LVASGQIKTISEA 26
                                  6899999999876 PP

  == domain 2  score: 64.0 bits;  conditional E-value: 7e-22
                                   EEEETTEEEEEEE--TT--EES-HHHHHHHHHHT--SEE---BS.-SSHHHHHHHHHHHHHHTTTT- CS
                Ribosomal_S5_C   1 tgkfgavkvllkpaprGtGiiaggavravlelaGikDvlakslg.srnpinvvkAtfeALkklrspe 66 
                                   +gk g+v+++lkpaprG G+ +g++++ +l++aGi+D +  + g +++++n + A+++ALk++ +++
  gi|13541176|ref|NP_110864.1| 131 EGKSGSVRITLKPAPRGVGLAVGNVAKIILRMAGIEDAWGFAAGhTKTTVNYALAVYNALKETAKVR 197
                                   59************************************************************98875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.33s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 1321.88
//
Query:       gi|13541177|ref|NP_110865.1|  [L=165]
Description: 50S ribosomal protein L30P [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-14   53.7   0.3    2.7e-14   52.8   0.3    1.5  1  Ribosomal_L30  Ribosomal protein L30p/L7e


Domain annotation for each model (and alignments):
>> Ribosomal_L30  Ribosomal protein L30p/L7e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.8   0.3   1.5e-18   2.7e-14       1      51 []       2      52 ..       2      52 .. 0.95

  Alignments for each domain:
  == domain 1  score: 52.8 bits;  conditional E-value: 1.5e-18
                                  EEEEE-S-STTS-HHHHHHHHHTT-SSTTEEEE--SSHHHHHHHHHCCCGE CS
                 Ribosomal_L30  1 lfVtrirsiigvppkvrktLqlLgLrkingtvvklntpsirGmLkkVkhlV 51
                                  l+V+rir+  g+++++ +t +lL+L++in+ v +   + ++GmL+kVk++V
  gi|13541177|ref|NP_110865.1|  2 LAVIRIRGRTGIKQDIEDTAHLLRLNRINHLVLLQEDAVTKGMLQKVKDYV 52
                                  68***************************88888888*************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); expected 358.6 (0.02)
Passed Vit filter:                        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 0.32s 00:00:00.84 Elapsed: 00:00:00.51
# Mc/sec: 981.65
//
Query:       gi|13541178|ref|NP_110866.1|  [L=145]
Description: 50S ribosomal protein L15P [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.6e-17   63.7   0.5      4e-17   63.1   0.5    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 !   63.1   0.5   2.2e-21     4e-17       1     127 [.      24     138 ..      24     139 .. 0.88

  Alignments for each domain:
  == domain 1  score: 63.1 bits;  conditional E-value: 2.2e-21
                                   GGGGTSSTTTTTTTTT-..S--........S--.........---GGG..---EEEEHHHHHHTTTTGTTS.--...---- CS
                Ribosomal_L27A   1 kGktgGrGhkGqkkrsg..vkk.kpg.feGGqmplyrrlpkrGfknskfkkeykvvnlkdLdelideerle.la...deae 73 
                                   kGk+gGrG++G+ k+++  + k  p  f  G           Gf++++ ++ + ++nl++L++++++++ +      ++++
  gi|13541178|ref|NP_110866.1|  24 KGKKGGRGNAGMGKHKWiwMVKyDPLhF--GGK---------GFTSHHLSTPDVPINLGELENIFENLKADgFVreeNGET 93 
                                   6****************96444344468..555.........7*966778999***************9986558877899 PP

                                   EEEGGGTTTTSSS....SE.EEE--S---.--EEEESEE-HHHHHHHHHTT-EEE CS
                Ribosomal_L27A  74 eidleelaeaglikkkdgv.KvlgkgeltkklkvkaskfSkkAkekIeaaGGkve 127
                                   ++dl++           g+ K+lg+g+++ k  +  +k+++kA++k  a G k+e
  gi|13541178|ref|NP_110866.1|  94 VVDLKAA----------GYdKLLGSGNFSVKSRIIIDKATEKAISKLSAIGSKIE 138
                                   *******..........**********************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.51u 0.32s 00:00:00.83 Elapsed: 00:00:00.51
# Mc/sec: 854.17
//
Query:       gi|13541179|ref|NP_110867.1|  [L=586]
Description: preprotein translocase SecY [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-68  231.4  17.9    1.4e-68  231.4  17.9    1.8  2  SecY             SecY translocase
    1.2e-10   41.0   1.1    4.5e-10   39.2   0.5    2.4  2  Plug_translocon  Plug domain of Sec61p
  ------ inclusion threshold ------
        0.4   10.5   3.5       0.23   11.2   0.2    2.4  2  SPC25            Microsomal signal peptidase 25 kDa subunit (


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 ?   -6.3   4.9         3   1.8e+04     222     222 ..      28      28 ..       5     117 .. 0.61
   2 !  231.4  17.9   2.3e-72   1.4e-68       1     306 []     133     564 ..     133     564 .. 0.81

  Alignments for each domain:
  == domain 1  score: -6.3 bits;  conditional E-value: 3
                                   H CS
                          SecY 222 f 222
                                   f
  gi|13541179|ref|NP_110867.1|  28 F 28 
                                   2 PP

  == domain 2  score: 231.4 bits;  conditional E-value: 2.3e-72
                                   BTTSSTCHHHHHHHHHHHHH.HHHSSSSSSTS-SSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC............... CS
                          SecY   1 sifaLGImPyitasIilqLl.tvvipkleelkkegeegrkkinqitryltvvlalvqalgialslg............... 65 
                                   s++ LGI+P++tasI++qL+ ++   k+ +l+ ++ e+++ +++++++l++++++v+a+  a+++                
  gi|13541179|ref|NP_110867.1| 133 SLMDLGIGPIVTASIVMQLFvGA---KIFNLDLQNSEDKAIYQGVQKLLVIIMIFVEAIPQAFGYLvpdtkfvnsinsvlp 210
                                   89******************999...55666656999**********************9887655899************ PP

                                   .....HH.HHHHHHHHHHHHHHHHHHHHHHHHSSTTHHHHHHHHHHHHHHC.CHSS.....................-HHH CS
                          SecY  66 .....lalllivlqltagtvllmwLgEqitekGiGnGisllifagivarlp.kals.....................glie 119
                                        la ++i++ql++g++l+++++E+++++GiG+Gisl+i+a ++++l+ +a++                     +   
  gi|13541179|ref|NP_110867.1| 211 gygefLAQTTIIMQLFFGSYLVFLMDEVVSKYGIGSGISLFIAADVSEQLFiGAFNwqalnnaltyslknppagafpK--- 288
                                   *****8899******************************************999998777766666555555544441... PP

                                   H...........SS...........THHHHHHHHHHHHHHHHHCHHHHBEEEECBBBS.TT....S.S-EEEEETTCCCSC CS
                          SecY 120 l...........ale.........gilallllllvtllvillvvyveeaerripvqya.krgrkggqssylPlklnyagvi 179
                                   +                       +  + ++++l tll+++lv y++++++++p+ ++  r    g+++++Pl+l+ya++i
  gi|13541179|ref|NP_110867.1| 289 MfyiimhsssayL-LtngvvqilfAPPNPMIAVLGTLLIFFLVAYFQSSKIELPIAHErVR----GARGRYPLQLLYASNI 364
                                   1544444444441.0444443334333789999*************************666....9*************** PP

                                   HHHHHHHHHH.......................................................HHHCCCCS........ CS
                          SecY 180 PiIfasslla.......................................................lpstiaqfl....... 198
                                   P+I+a++lla                                                                       
  gi|13541179|ref|NP_110867.1| 365 PVILATALLAnvsmwtllfwsspvlskvpllghnkflgsypsaaqaaalnissttptgglayylfS-------Pnglsdwl 438
                                   **********77777777777777777777777776666666666666666655555555555441.......04443333 PP

                                   .........TCCCS........THHHHHHHHHHHHHH....HHHHHHTCT.THHHHHHHCCHHTBSSSCTTT.TCHHHHHH CS
                          SecY 199 .........lalls........psvlyvvlyvlliif....Fayfyteit.fnpkevaenlkksggfipgir.pgketaky 256
                                            +   +        +++++++++++++++    Fa+f++e+t + ++ va++++ sg++ipg+r + + ++++
  gi|13541179|ref|NP_110867.1| 439 fpilqpsayQ---NillghtpiEEAIHIIVFTAFMVGfsvlFAIFWIETTnMGASAVAKQIQSSGMQIPGFRrDPRVMERV 516
                                   4444444331...0333455666778999999999988999*******************************999****** PP

                                   HHHHHHHHHHHHHHHHHHHHHHHHHHTTS.TT.TTHHHHHHHHHHHHHHH CS
                          SecY 257 LekvlsritliGalflaliavlpdllgasligafggtslLivVgvaletv 306
                                   L+k+++ it+++++ ++l+a+ ++l+g+  +g  +gt+lL++Vg++++++
  gi|13541179|ref|NP_110867.1| 517 LKKYIPAITIFSGAAVGLLAAGANLIGT--VGDTSGTGLLLAVGIIIQFY 564
                                   ****************************..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 !   39.2   0.5   7.5e-14   4.5e-10       1      35 []      98     132 ..      98     132 .. 0.98
   2 ?   -2.4   0.0      0.76   4.5e+03       5      13 ..     388     396 ..     388     396 .. 0.91

  Alignments for each domain:
  == domain 1  score: 39.2 bits;  conditional E-value: 7.5e-14
                                   HHHHHHCCSB-TT--SSS-TCCHTTTCCCCTSSTT CS
               Plug_translocon   1 llYlvlsqiPLyGissssssDpfywlRaifAsnrG 35 
                                   +lY+ ls+i++yG+ +++++D f+ +R ifA+++G
  gi|13541179|ref|NP_110867.1|  98 ILYFALSNIYIYGLNTAKTIDVFASFREIFAGASG 132
                                   89******************************998 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.76
                                   HHCCSB-TT CS
               Plug_translocon   5 vlsqiPLyG 13 
                                   vls +PL G
  gi|13541179|ref|NP_110867.1| 388 VLSKVPLLG 396
                                   79*****98 PP

>> SPC25  Microsomal signal peptidase 25 kDa subunit (SPC25)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.4      0.38   2.3e+03      54      77 ..       6      29 ..       3      41 .. 0.82
   2 ?   11.2   0.2   3.9e-05      0.23      49      76 ..      83     110 ..      77     205 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.38
                         SPC25 54 eskpvlaiavvlYfilsgiltlys 77
                                  ++++v +++ ++Y+i+ ++++++ 
  gi|13541179|ref|NP_110867.1|  6 RNNSVAFPIFIFYVIIVVAFWYFG 29
                                  567788888999999999999975 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 3.9e-05
                         SPC25  49 kveFeeskpvlaiavvlYfilsgiltly 76 
                                   +veF+ +  ++a++v+lYf+ls i+ + 
  gi|13541179|ref|NP_110867.1|  83 HVEFKYKMLWTAVIVILYFALSNIYIYG 110
                                   4799*******************99775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (586 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       711  (0.0396564); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.65u 0.31s 00:00:00.96 Elapsed: 00:00:00.50
# Mc/sec: 3537.00
//
Query:       gi|13541180|ref|NP_110868.1|  [L=181]
Description: adenylate kinase [Thermoplasma volcanium GSS1]
Scores for complete 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   0.0      9e-35  120.1   0.0    1.1  1  AAA_17           AAA domain
      4e-08   33.9   0.0      6e-08   33.3   0.0    1.3  1  AAA_18           AAA domain
     0.0004   20.5   0.1     0.0025   17.9   0.1    2.0  1  SKI              Shikimate kinase
     0.0015   18.7   0.2      0.004   17.3   0.2    1.8  1  AAA_33           AAA domain
     0.0022   18.2   0.2     0.0048   17.1   0.2    1.7  1  AAA_28           AAA domain
     0.0025   18.3   0.1     0.0039   17.6   0.1    1.7  1  AAA              ATPase family associated with various cellul
     0.0041   17.0   0.0       0.36   10.7   0.0    2.1  2  dNK              Deoxynucleoside kinase
  ------ inclusion threshold ------
      0.013   15.3   0.0      0.018   14.8   0.0    1.3  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase
      0.022   14.7   3.1       0.13   12.2   0.5    2.3  2  NTPase_1         NTPase
       0.03   14.0   0.1      0.052   13.3   0.1    1.4  1  AAA_30           AAA domain
      0.051   14.0   0.1      0.063   13.7   0.1    1.5  1  AAA_16           AAA ATPase domain
       0.09   11.0   0.0       0.14   10.4   0.0    1.2  1  TcdA_TcdB_pore   TcdA/TcdB pore forming domain
      0.096   13.2   0.0       0.11   13.1   0.0    1.3  1  ABC_tran         ABC transporter
       0.11   12.5   0.0       0.19   11.7   0.0    1.4  1  AAA_14           AAA domain
       0.12   12.2   0.0       0.28   10.9   0.0    1.6  1  AAA_29           P-loop containing region of AAA domain
       0.15   12.3   0.0       0.23   11.7   0.0    1.4  1  AAA_22           AAA domain


Domain annotation for each model (and alignments):
>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.1   0.0     8e-38     9e-35       1     136 []       6     138 ..       6     138 .. 0.98

  Alignments for each domain:
  == domain 1  score: 120.1 bits;  conditional E-value: 8e-38
                                   EE-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTTTSHSSHHHHCTSHHHHHHHHHHHHHHHHHHHHHSSEEEEEE-SE CS
                        AAA_17   1 lGgPGsGKgtqceklvekygfthlsaGdllreeakrgglakardemrklpleekkelqkeaaekiaeeakkkgvlvdghpr 81 
                                   +G+ G+GK+t+++ ++++ g++++++G l++e+akr+gl+++rd++rkl+ e + +lqk+a e+i ++   ++++vd+h++
  gi|13541180|ref|NP_110868.1|   6 TGVAGVGKTTVLDIVARESGIPVVNYGTLMFEVAKRRGLVENRDQIRKLSRETQVDLQKLAGEEIGKM---ENAIVDTHMS 83 
                                   69****************************************************************96...89******** PP

                                   EEETTEEEESSHHHHHHHH..SEEEEEE--HHHHHHHHHHHTTST-TS-SHHHHH CS
                        AAA_17  82 ikeqagfldglpkevleelkpdaiilleadpeeilerrlkdrtrgrdddneesik 136
                                   ik++ g+l+glp++vl++++ ++++++eadp  i +rr +d tr rdd+  +si+
  gi|13541180|ref|NP_110868.1|  84 IKTPFGYLPGLPEWVLRSINASVFVIIEADPAIIKRRRDNDPTRARDDEGVDSIR 138
                                   ********************************9999999************9997 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.3   0.0   5.4e-11     6e-08       2     120 ..       4     131 ..       4     146 .. 0.76

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 5.4e-11
                        AAA_18   2 lltGtpGvGKttlakeLskrlgf.....gvnlrdvakenglllevdpealdeskrldedkldklldaleenssaleegknl 77 
                                   ++tG++GvGKtt+ + ++++ g+     g+   +vak +gl++ +d+   ++  r+ +     l+++  e +   ++ +n 
  gi|13541180|ref|NP_110868.1|   4 VITGVAGVGKTTVLDIVARESGIpvvnyGTLMFEVAKRRGLVENRDQI--RKLSRETQVD---LQKLAGEEI---GKMENA 76 
                                   69***************9998899999999999999999999999999..3333333333...333333322...345777 PP

                        AAA_18  78 vidghlaeleseaakdikk............vvLtaspeelleRlekRgyeeaki 120
                                   ++d h++   +  +  +              v+++a+p + ++R  ++ ++ ++ 
  gi|13541180|ref|NP_110868.1|  77 IVDTHMSIKTPFGYLPGLPewvlrsinasvfVIIEADPAIIKRRRDNDPTRARDD 131
                                   88888888888887776667777888888889999**999999998888776554 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.1   2.3e-06    0.0025       2     157 ..      10     180 ..       9     181 .] 0.74

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.3e-06
                                   TSSHHHHHHHHHHHHTSEEEEHHHHHHHHHTS-HHHHHHHHHHHHHHHHHHHH.HHHHCCCS.....SEEEEE-TTGGGSH CS
                           SKI   2 GaGKstvGkllAkklglefiDlDeliekrtgksiaeifeeegeegFrelEsev.lkelleee.....glViatGGGavlse 76 
                                   G+GK+tv  ++A++ g++++   +l+ ++++   + ++e++++ +   +E++v l++l+ ee     ++++ t  +++ ++
  gi|13541180|ref|NP_110868.1|  10 GVGKTTVLDIVARESGIPVVNYGTLMFEVAK--RRGLVENRDQIRKLSRETQVdLQKLAGEEigkmeNAIVDT-HMSIKTP 87 
                                   99*********************99877776..556666666666666666666555555555555599**99.5555555 PP

                                   H......HHHHHH..HHSEEEEEE--HHHHHHHHHHTTSSGGGCSCHH...HHHHHHHHH.HHHHHHCCSSCEEEECTSSH CS
                           SKI  77 e......nrellk..ekgiviyLdvsleellerlkadkeRPllqeksk...eeelleela.ereplyeeaadvvvdesees 145
                                            ++l+  +  +++ +++++  + +r ++d++R+   e      e+++++ ++ +  ++++ a  ++v+++e +
  gi|13541180|ref|NP_110868.1|  88 FgylpglPEWVLRsiNASVFVIIEADPAIIKRRRDNDPTRARDDEGVDsirEHQEMNRYFaAAYSIFSGATVKIVKNEEGK 168
                                   4444443334444889999********************855444333666666666667699999999999999999999 PP

                                   HHHHHHHHHHHH CS
                           SKI 146 keevaeeileal 157
                                   +e+ a+ei++++
  gi|13541180|ref|NP_110868.1| 169 PEQAADEIVRVI 180
                                   9********987 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.2   3.6e-06     0.004       4      77 ..       5      80 ..       3     148 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3.6e-06
                        AAA_33  4 lvGlpGsGKstlaerllkklgavllssdtlrrrlfg.....tdqqsktdytr.vldrlyqilnelarkalsagrnvilda 77
                                  + G++G+GK+t+++ ++++ g  +++  tl++ +++     +     +d++r ++ ++   l++la +   +  n+i+d 
  gi|13541180|ref|NP_110868.1|  5 ITGVAGVGKTTVLDIVARESGIPVVNYGTLMFEVAKrrglvE----NRDQIRkLSRETQVDLQKLAGEEIGKMENAIVDT 80
                                  67***************************9999998543322....3345552334455567788888888888888875 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.2   4.3e-06    0.0048       2      94 ..       3      89 ..       2     167 .. 0.59

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 4.3e-06
                        AAA_28  2 ivitGgestGKTtlleaLaar.gypvvpEaareileeklakgedalpwvedllafaervleeqleeeaaaaankvlfcDrgll 83
                                   vitG  + GKTt+l   a++ g+pvv  +++ ++e   ++g       e++ +++++  e q+  ++  a++++  ++  ++
  gi|13541180|ref|NP_110868.1|  3 SVITGVAGVGKTTVLDIVAREsGIPVVN-YGTLMFEVAKRRGLV-----ENRDQIRKLSRETQVDLQKL-AGEEIGKMENAIV 78
                                  59*****************887***994.888888666655553.....34455555555555543333.3555555555555 PP

                        AAA_28 84 dtlaYaraygg 94
                                  dt + +++ +g
  gi|13541180|ref|NP_110868.1| 79 DTHMSIKTPFG 89
                                  55555555555 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.1   3.5e-06    0.0039       3      50 ..       5      55 ..       3     137 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 3.5e-06
                                  EESSTTSSHHHHHHHHHHHHTHEEEEEETTTCS.SS..STTHHHHHHHHHH CS
                           AAA  3 lyGppGtGKTllakavakelgvefleisgsell.sk..yvgesekkirelf 50
                                  ++G  G+GKT++   va+e+g+++++     +   k   + e+ ++ir+l 
  gi|13541180|ref|NP_110868.1|  5 ITGVAGVGKTTVLDIVARESGIPVVNYGTLMFEvAKrrGLVENRDQIRKLS 55
                                  789*****************9998776555544333334445555555554 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.0   0.00032      0.36       2      28 ..       4      30 ..       3      63 .. 0.88
   2 ?    4.8   0.0      0.02        23     112     197 ..      94     178 ..      74     181 .] 0.83

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00032
                                  EEEESTTSSHHHHHHHHHCCSTCEEEE CS
                           dNK  2 vveGnIgaGKstlvklLskklgvkvfe 28
                                  v+ G  g+GK+t++++ +++ g++v++
  gi|13541180|ref|NP_110868.1|  4 VITGVAGVGKTTVLDIVARESGIPVVN 30
                                  799*****************9998876 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.02
                                   HHHHHHHHCCH-SEEEEEE--HHHHHHHHHH...CTTCCCTTS-HHHHHHHHHHHHHHHTSGGCS-EEEEETSS.-TTTHC CS
                           dNK 112 lldnlleelakpdlliYLkasletclerikk...RgreeekkieldYlekLhekyeewlkklnevpvlvidveeldlvaee 189
                                   l +++l+ ++  ++++ ++a++  +++r  +   R+r +e   +++  +++++++ ++++ ++ ++v ++  ee    + e
  gi|13541180|ref|NP_110868.1|  94 LPEWVLRSIN-ASVFVIIEADPAIIKRRRDNdptRARDDEGVDSIREHQEMNRYFAAAYSIFSGATVKIVKNEE---GKPE 170
                                   5688998888.999*********9999987544499999998889999*******************9999999...5677 PP

                                   CHHHHHHH CS
                           dNK 190 ekredvve 197
                                   ++ +++v+
  gi|13541180|ref|NP_110868.1| 171 QAADEIVR 178
                                   77777765 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   1.6e-05     0.018       2      39 ..       4      43 ..       3      91 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.6e-05
               Viral_helicase1  2 vvhGvpGcGKStlirkllrts..liltvnrptaelltegk 39
                                  v+ Gv+G GK+t++  ++r+s   +++ ++  +e+++++ 
  gi|13541180|ref|NP_110868.1|  4 VITGVAGVGKTTVLDIVARESgiPVVNYGTLMFEVAKRRG 43
                                  89*************9999987644555555566665555 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.5   0.00012      0.13       3      22 ..       4      23 ..       2      44 .. 0.84
   2 ?    2.8   0.1     0.088        99     102     115 ..      68      81 ..      30      88 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00012
                                  EEE--TTSSHHHHHHHHHHH CS
                      NTPase_1  3 fiTGppGvGKtTlvkkvlel 22
                                  +iTG  GvGKtT+++ v+++
  gi|13541180|ref|NP_110868.1|  4 VITGVAGVGKTTVLDIVARE 23
                                  79************999875 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.088
                                   ---STTGGG-HHHH CS
                      NTPase_1 102 DEiGkmElkskkfk 115
                                    EiGkmE  +   +
  gi|13541180|ref|NP_110868.1|  68 EEIGKMENAIVDTH 81 
                                   69*****9876655 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   4.7e-05     0.052      21      39 ..       3      21 ..       1      32 [. 0.88

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.7e-05
                        AAA_30 21 avltGpAGtGKttalkalr 39
                                  +v+tG+AG GKtt+l  ++
  gi|13541180|ref|NP_110868.1|  3 SVITGVAGVGKTTVLDIVA 21
                                  69*************9875 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   5.6e-05     0.063      28      48 ..       4      24 ..       2     158 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.6e-05
                        AAA_16 28 llsGesGvGKsslvrellral 48
                                  +++G +GvGK+++++ ++r+ 
  gi|13541180|ref|NP_110868.1|  4 VITGVAGVGKTTVLDIVARES 24
                                  69************9999754 PP

>> TcdA_TcdB_pore  TcdA/TcdB pore forming domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00013      0.14     399     437 ..     127     165 ..     123     168 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00013
                TcdA_TcdB_pore 399 tsreddGlDviRrleedkrFdydfyaFpaeevirrikpe 437
                                   ++r+d+G+D+iR+ +e +r+    y  ++ ++++ +k+e
  gi|13541180|ref|NP_110868.1| 127 RARDDEGVDSIREHQEMNRYFAAAYSIFSGATVKIVKNE 165
                                   89****************998888888889999999875 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   9.5e-05      0.11      15      79 ..       4      69 ..       1     163 [. 0.70

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 9.5e-05
                                  EEEESTTSSHHHHHHHHTTSS--...SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH CS
                                  xxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran 15 aivGenGaGKStLlkllagllkp...teGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren 79
                                  +i+G  G GK+t+l ++a+++     + G++ ++ ++   + l + r +i+ l+ e+q++ ++ ++e+
  gi|13541180|ref|NP_110868.1|  4 VITGVAGVGKTTVLDIVARESGIpvvNYGTLMFEVAKR--RGLVENRDQIRKLSRETQVDLQKLAGEE 69
                                  799***************99865566778876663333..4477777777777777766666655555 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00017      0.19       6      44 ..       4      42 ..       2      81 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00017
                        AAA_14  6 vitGaRrvGKTtllkqlikellvkkesilyinldderdk 44
                                  vitG+  vGKTt+l  +++e+ ++  ++  + ++  + +
  gi|13541180|ref|NP_110868.1|  4 VITGVAGVGKTTVLDIVARESGIPVVNYGTLMFEVAKRR 42
                                  8*************9999998855555555555444443 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00025      0.28      26      40 ..       4      18 ..       2      22 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00025
                        AAA_29 26 lltGpsGsGKSTllD 40
                                  ++tG  G+GK+T+lD
  gi|13541180|ref|NP_110868.1|  4 VITGVAGVGKTTVLD 18
                                  79************9 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00021      0.23       9      29 ..       4      24 ..       3      86 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00021
                        AAA_22  9 vvtGesGtGKTtllrrlleql 29
                                  v+tG +G+GKTt+l  ++++ 
  gi|13541180|ref|NP_110868.1|  4 VITGVAGVGKTTVLDIVARES 24
                                  89***********99888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       595  (0.0331865); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); 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 0.33s 00:00:00.98 Elapsed: 00:00:00.55
# Mc/sec: 985.74
//
Query:       gi|13541181|ref|NP_110869.1|  [L=225]
Description: hypothetical protein TVN0350 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      1e-21   77.4  14.5      1e-21   77.4  14.5    2.2  2  EMC3_TMCO1    Integral membrane protein EMC3/TMCO1-like
  ------ inclusion threshold ------
      0.061   13.4   0.1       0.23   11.6   0.1    2.0  2  ANAPC5        Anaphase-promoting complex subunit 5
       0.96    9.3   0.0       0.96    9.3   0.0    3.0  3  LapA_dom      Lipopolysaccharide assembly protein A domain
        2.8    8.1   8.0       0.81    9.8   2.5    2.6  2  DUF2107       Predicted membrane protein (DUF2107)


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 !    5.3   2.7    0.0034        15      78     108 ..       3      33 ..       1      43 [. 0.73
   2 !   77.4  14.5   2.3e-25     1e-21       1     167 [.      48     208 ..      48     221 .. 0.94

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0034
                    EMC3_TMCO1  78 eelmedqsemmmdqmkpmivtmipqiliffw 108
                                   e ++++q+e m+++m  ++  m++++   f 
  gi|13541181|ref|NP_110869.1|   3 ETYNKEQQEAMKKMMSFQMLYMLIMLGSLFI 33 
                                   5678888888888888777777777665544 PP

  == domain 2  score: 77.4 bits;  conditional E-value: 2.3e-25
                    EMC3_TMCO1   1 dlvldplirdwvllPivivillvgiltgllsellqkllidkkkmekeqkrekelqkrarelqkngdklklkklekrqeelm 81 
                                   ++vl p i + + +P+ + i+l+g++ g++ ++ +++++d+ km k+q ++k++ ++ r++ +++d +k  kl+++++++ 
  gi|13541181|ref|NP_110869.1|  48 NVVLIPTIGFGYRYPL-LSIILTGVIIGVILSIPRYFFTDWVKMGKMQNTMKAFNEAIRAAYRERDMKKINKLNSMRMQMS 127
                                   68899999999999*9.99************************************************************** PP

                    EMC3_TMCO1  82 edqsemmmdqmkpmivtmipqiliffwlnsffsgfvvaklpfpltgrfksllqrglesldvrfvssiswYflcsfglsqii 162
                                    dq +++m++mkp +v+ +++il ++wl+ f+ ++ +  + fp  + ++ ++    +   ++++++i++Yfl+ + +s  i
  gi|13541181|ref|NP_110869.1| 128 MDQYQLSMNTMKPLLVISVLTILFYAWLFVFVGKIPYNYIAFPWDFNIN-IS----TAHFWIMPYWIFMYFLTEIVVSYFI 203
                                   *********************************9999999999999998.77....7999999999999999999999988 PP

                    EMC3_TMCO1 163 rklLg 167
                                   + +++
  gi|13541181|ref|NP_110869.1| 204 TMIMK 208
                                   88875 PP

>> ANAPC5  Anaphase-promoting complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1     5e-05      0.23      53      89 ..      89     125 ..      84     130 .. 0.86
   2 ?   -0.2   0.0      0.24   1.1e+03      44      65 ..     118     139 ..     115     141 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5e-05
                        ANAPC5  53 dfghneeAvkaleeairlArenkDkscLalalawlar 89 
                                   ++g+ ++ +ka++eair A  ++D++ ++  +++ ++
  gi|13541181|ref|NP_110869.1|  89 KMGKMQNTMKAFNEAIRAAYRERDMKKINKLNSMRMQ 125
                                   7999********************9999887776555 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.24
                        ANAPC5  44 lLnlaslhadfghneeAvkale 65 
                                    Ln++++++++++++ ++++++
  gi|13541181|ref|NP_110869.1| 118 KLNSMRMQMSMDQYQLSMNTMK 139
                                   5899999999999999998875 PP

>> LapA_dom  Lipopolysaccharide assembly protein A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0   0.00021      0.96      23      56 ..      63     104 ..      55     120 .. 0.74
   2 ?   -2.8   1.5       1.3   5.7e+03      23      39 ..     142     158 ..     141     163 .. 0.62
   3 ?   -0.3   0.1      0.21   9.5e+02      35      55 ..     202     222 ..     188     224 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00021
                      LapA_dom  23 llvafgiGallgwllslwsyl........rlrrelrrlkkki 56 
                                   ll  ++ G+++g++ls+++y+        + +  +++ ++ i
  gi|13541181|ref|NP_110869.1|  63 LLSIILTGVIIGVILSIPRYFftdwvkmgKMQNTMKAFNEAI 104
                                   56678899*********9998666666565555555555544 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.3
                      LapA_dom  23 llvafgiGallgwllsl 39 
                                   l+++++  ++ +wl+ +
  gi|13541181|ref|NP_110869.1| 142 LVISVLTILFYAWLFVF 158
                                   55555555667777766 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.21
                      LapA_dom  35 wllslwsylrlrrelrrlkkk 55 
                                   +++++++y+   ++lrr  ++
  gi|13541181|ref|NP_110869.1| 202 FITMIMKYIDFTLRLRRISRE 222
                                   566778888777777776665 PP

>> DUF2107  Predicted membrane protein (DUF2107)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   2.5   0.00018      0.81       5      37 ..      23      56 ..      19      79 .. 0.85
   2 ?    0.1   0.3       0.2   9.2e+02      50      65 ..     192     207 ..     175     211 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00018
                       DUF2107  5 lilliiGtlaaaiGPrekdplvrllnlE.vpavG 37
                                  ++l+++G+l+ +i P ++d +  lln+  +p++G
  gi|13541181|ref|NP_110869.1| 23 YMLIMLGSLFIVITPSSRDAVGNLLNVVlIPTIG 56
                                  78999*********************74378887 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.2
                       DUF2107  50 ALlTfiavtaiitlvl 65 
                                     lT i v+ +it+++
  gi|13541181|ref|NP_110869.1| 192 YFLTEIVVSYFITMIM 207
                                   5799999999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1424  (0.0794244); expected 358.6 (0.02)
Passed bias filter:                      524  (0.0292264); 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):               4  [number of targets reported over threshold]
# CPU time: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.51
# Mc/sec: 1317.93
//
Query:       gi|13541182|ref|NP_110870.1|  [L=190]
Description: cytidylate kinase [Thermoplasma volcanium GSS1]
Scores for complete 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   79.7   1.4    1.3e-20   74.3   1.4    2.1  1  Cytidylate_kin2  Cytidylate kinase-like family
    5.2e-14   52.9   0.0      7e-14   52.5   0.0    1.2  1  AAA_18           AAA domain
    2.6e-08   33.9   0.9    0.00061   19.6   0.2    2.2  2  Cytidylate_kin   Cytidylate kinase
    7.3e-08   32.9   0.1    1.5e-07   31.9   0.0    1.6  2  AAA_17           AAA domain
    0.00054   19.9   0.0     0.0011   18.9   0.0    1.6  1  dNK              Deoxynucleoside kinase
     0.0023   17.7   1.6       0.15   11.8   1.3    2.2  2  PRK              Phosphoribulokinase / Uridine kinase family
     0.0055   16.4   0.0      0.046   13.4   0.1    2.0  2  CoaE             Dephospho-CoA kinase
     0.0063   15.8   0.0      0.011   15.0   0.0    1.4  1  Zeta_toxin       Zeta toxin
     0.0084   16.3   0.0     0.0094   16.1   0.0    1.2  1  AAA_33           AAA domain
  ------ inclusion threshold ------
      0.025   14.6   0.1      0.045   13.7   0.0    1.6  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
      0.033   14.1   0.1      0.057   13.3   0.1    1.6  1  Rad17            Rad17 P-loop domain
      0.048   13.8   0.2      0.049   13.8   0.2    1.5  1  SKI              Shikimate kinase
      0.052   13.7   0.0      0.086   12.9   0.0    1.5  1  ADK              Adenylate kinase
      0.087   12.9   0.0       0.13   12.3   0.0    1.3  1  PglZ             PglZ domain
      0.091   11.9   0.1        3.9    6.5   0.0    2.1  2  G-alpha          G-protein alpha subunit
        0.2   11.4   0.2        0.4   10.5   0.2    1.4  1  AAA_29           P-loop containing region of AAA domain
       0.23   11.1   1.0          5    6.7   0.4    2.1  2  ATP-synt_ab      ATP synthase alpha/beta family, nucleotide-b


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 !   74.3   1.4   1.2e-23   1.3e-20       2     178 ..       3     158 ..       2     159 .. 0.94

  Alignments for each domain:
  == domain 1  score: 74.3 bits;  conditional E-value: 1.2e-23
               Cytidylate_kin2   2 ITIsreyGsgGetigeaLAekLglpfydr.eiieevakelglseeeveevdersrlssflskllaarvagdtldeklddel 81 
                                   ITI+++ Gsg++t+ +++++  g+ +y+    ++e ak++g+s e + ++ e+ +                    + d + 
  gi|13541182|ref|NP_110870.1|   3 ITIAGKIGSGKSTVSQEISKITGYSVYSSgTFFRESAKKMGMSIEDFNRYAETHP--------------------EADYAT 63 
                                   9****************************999********************333....................455556 PP

               Cytidylate_kin2  82 feaqervirelaaeesvVivGRgadliLkdrp.nvlrvfltapledrvkrvaereglseeearekiketDkrrakyykkyt 161
                                     +q++++++    +++++ GR a  i+k ++  +++vfl+a++  r+ r++ reg++ +ea+++++e++  ++k+y  ++
  gi|13541182|ref|NP_110870.1|  64 DGMQKDFMETH---DNIIVEGRLAGWICKIYSiSAFKVFLYATRYTRLVRFSNREGIEIDEAAKLLDEREISEKKRYLDLY 141
                                   67899999998...49**************7779*********************************************** PP

               Cytidylate_kin2 162 gqdwgdaenYdlvlnts 178
                                   g d++d + Yd+v+nt+
  gi|13541182|ref|NP_110870.1| 142 GIDIDDLSIYDIVVNTE 158
                                   ***************96 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.5   0.0   6.6e-17     7e-14       1     121 [.       3     122 ..       3     137 .. 0.82

  Alignments for each domain:
  == domain 1  score: 52.5 bits;  conditional E-value: 6.6e-17
                        AAA_18   1 IlltGtpGvGKttlakeLskrlgf.....gvnlrdvakenglllevdpealdeskrldedkldklldaleenssaleegkn 76 
                                   I ++G++G+GK+t+++e+sk +g+     g+  r+ ak+ g+++e+++  + e++ + +  +d  ++ ++e       ++n
  gi|13541182|ref|NP_110870.1|   3 ITIAGKIGSGKSTVSQEISKITGYsvyssGTFFRESAKKMGMSIEDFNR-YAETHPEADYATDGMQKDFME------THDN 76 
                                   89*******************999*************************.555555555554445555555......589* PP

                        AAA_18  77 lvidghlaele.seaakdikkvvLtaspeelleRlekRgyeeakik 121
                                   ++++g+la ++ + + + + kv+L+a   ++l R+++R+  e + +
  gi|13541182|ref|NP_110870.1|  77 IIVEGRLAGWIcKIYSISAFKVFLYATRYTRLVRFSNREGIEIDEA 122
                                   ********9996666777777*****************97776644 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.2   5.8e-07   0.00061       1      37 [.       3      39 ..       3      61 .. 0.89
   2 !   13.6   0.0   3.9e-05     0.041     103     174 ..      64     133 ..      44     174 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 5.8e-07
                                  EEEE-STTSSHHHHHHHHHHHHT-EEEEHHHHHHHHH CS
                Cytidylate_kin  1 iaiDGPagsGKssvaralaeklglkyldtgalYRala 37
                                  i+i G  gsGKs+v++++++  g+++ ++g+++R  a
  gi|13541182|ref|NP_110870.1|  3 ITIAGKIGSGKSTVSQEISKITGYSVYSSGTFFRESA 39
                                  8999******************************877 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 3.9e-05
                                   HHHHHTT-B.SSBEEEEESSII..IIISTT-SEEEEEE--HHHHHHHHHHHHHHTT----HHHHHHHHHHHHHHH CS
                Cytidylate_kin 103 vkklrelvk.karvvveGRDig..tvvfpdaelKifldAsveeRakRRlkqlkakgtsvsleellaeikeRDklD 174
                                      ++++++ +++++veGR  g   ++   + +K+fl A  ++R  R  +    +g +  ++e  + + eR    
  gi|13541182|ref|NP_110870.1|  64 DGMQKDFMEtHDNIIVEGRLAGwiCKIYSISAFKVFLYATRYTRLVRFSNR---EGIE--IDEAAKLLDEREISE 133
                                   567888888799*******999657899****************9986655...3433..444444444455444 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.9   0.0   1.4e-10   1.5e-07       2      79 ..       7      82 ..       6      99 .. 0.79
   2 ?   -2.0   0.0       4.1   4.3e+03      52      61 ..     132     141 ..     107     180 .. 0.53

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 1.4e-10
                                  E-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTTTS.HSSHHHHCTSHHHHHHHHHHHHHHHHHHHHHSSEEEEEE- CS
                        AAA_17  2 GgPGsGKgtqceklvekygfthlsaGdllreeakrggl.akardemrklpleekkelqkeaaekiaeeakkkgvlvdgh 79
                                  G  GsGK+t+++++ +  g++++s G  +re ak+ g+ +++++++++   e + +++ + ++  +e   +++++v+g 
  gi|13541182|ref|NP_110870.1|  7 GKIGSGKSTVSQEISKITGYSVYSSGTFFRESAKKMGMsIEDFNRYAETHPEADYATDGMQKD-FME--THDNIIVEGR 82
                                  667**********************************96777777777766666655555444.333..3567777776 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 4.1
                                   HHHHHHHHHH CS
                        AAA_17  52 eekkelqkea 61 
                                   +ekk+++++ 
  gi|13541182|ref|NP_110870.1| 132 SEKKRYLDLY 141
                                   3333333333 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0     1e-06    0.0011       1      53 [.       3      53 ..       3      80 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1e-06
                                  EEEEESTTSSHHHHHHHHHCCSTCEEEE-HHHHCCSSSSHHHHHHHHSHHHHH CS
                           dNK  1 ivveGnIgaGKstlvklLskklgvkvfeEpvdkwtnvqknlLekfYkdpsrws 53
                                  i++ G+Ig+GKst+ + +sk +g+ v++    ++    ++ + +  +d++r++
  gi|13541182|ref|NP_110870.1|  3 ITIAGKIGSGKSTVSQEISKITGYSVYSS--GTFFRESAKKMGMSIEDFNRYA 53
                                  89**********************99975..4555566677777777777776 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   1.3   0.00014      0.15       2      26 ..       3      27 ..       2      56 .. 0.73
   2 ?    4.6   0.0     0.023        25     101     140 ..      61     104 ..      33     118 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00014
                           PRK  2 IgvagsSGaGkttvarklekifgre 26
                                  I +ag+ G+Gk+tv++++ ki g  
  gi|13541182|ref|NP_110870.1|  3 ITIAGKIGSGKSTVSQEISKITGYS 27
                                  89******************98833 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.023
                           PRK 101 p....dkeeliegadvlviEGlhalydervaelldlkiyvdisi 140
                                         +++++e  d +++EG +a++  ++ +   +k+++ +  
  gi|13541182|ref|NP_110870.1|  61 YatdgMQKDFMETHDNIIVEGRLAGWICKIYSISAFKVFLYATR 104
                                   24444567999****************************97765 PP

>> CoaE  Dephospho-CoA kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.1   4.3e-05     0.046       3      26 ..       3      27 ..       1      52 [. 0.85
   2 ?    0.8   0.0      0.31   3.3e+02     128     163 ..     100     135 ..      74     144 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.3e-05
                                  EEEEESTTSSHHHHHHHHHH.TT-E CS
                          CoaE  3 vgltGgiasGKstvanlfad.lgvp 26
                                  + ++G i+sGKstv++ +++ +g+ 
  gi|13541182|ref|NP_110870.1|  3 ITIAGKIGSGKSTVSQEISKiTGYS 27
                                  889*************999855554 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.31
                                   EE--HHHHHHHHHHCCTSTHHHHHHHHHHS--HHHH CS
                          CoaE 128 vdvelelqveRlvardgvseeevkaiiaaQlseeer 163
                                   + ++  +++ R  +r+g++ +e+++ +     +e++
  gi|13541182|ref|NP_110870.1| 100 LYATRYTRLVRFSNREGIEIDEAAKLLDEREISEKK 135
                                   44667789999999****999999998765444444 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0     1e-05     0.011      19     105 ..       3      84 ..       1      91 [. 0.88

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1e-05
                    Zeta_toxin  19 illgGqpGAGKselaellkdelerqgnvvrldpDdlRelhPeyeeilkadpkkaseltqkdaselvekllqeaiengynii 99 
                                   i ++G  G+GKs++++++ +    +g  v  +++ +Re   +  + +  ++ + ++ t+++a   ++ + +  +e   nii
  gi|13541182|ref|NP_110870.1|   3 ITIAGKIGSGKSTVSQEISKI---TGYSVYSSGTFFRESAKKM-G-MSIEDFNRYAETHPEADYATDGMQKDFMETHDNII 78 
                                   679***************998...599***********99764.4.34467777788************************ PP

                    Zeta_toxin 100 vegtlr 105
                                   veg l+
  gi|13541182|ref|NP_110870.1|  79 VEGRLA 84 
                                   **9775 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   8.9e-06    0.0094       4      67 ..       5      71 ..       3     132 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 8.9e-06
                        AAA_33  4 lvGlpGsGKstlaerllkklgavllssdtlrrrlfgtdqqskt...dytrvldrlyqilnelarkal 67
                                  + G  GsGKst+++++ k +g+ + ss t++r  +++   s++   +y++  +++ + + ++ ++ +
  gi|13541182|ref|NP_110870.1|  5 IAGKIGSGKSTVSQEISKITGYSVYSSGTFFRESAKKMGMSIEdfnRYAETHPEADYATDGMQKDFM 71
                                  6799*************************99977775555555111444444446666555555555 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   4.3e-05     0.045      22      54 ..       3      35 ..       1      82 [. 0.88
   2 ?   -3.3   0.0       8.1   8.6e+03      69      86 ..     138     156 ..     134     170 .. 0.52

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.3e-05
                                  EEEEESTTSSHHHHHHHHHHHTT------TTTT CS
                          TsaE 22 ilLeGdLGaGKTtlvrglakalgveevkSPTFt 54
                                  i++ G++G+GK+t ++++ k  g++  +S TF 
  gi|13541182|ref|NP_110870.1|  3 ITIAGKIGSGKSTVSQEISKITGYSVYSSGTFF 35
                                  7889********************999999995 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 8.1
                                   EE-TT-S.STHHHHHCTTC CS
                          TsaE  69 fDlYRle.deeeleelgle 86 
                                   +DlY ++ d+ +++++ ++
  gi|13541182|ref|NP_110870.1| 138 LDLYGIDiDDLSIYDIVVN 156
                                   5677663222233444333 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   5.4e-05     0.057      50      88 ..       5      41 ..       2     115 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.4e-05
                         Rad17 50 isGPsGCgkstvvkvLskelgiklrewlnpvslkepdnq 88
                                  i+G  G gkstv +++sk+ g+++  ++ ++ ++e+  +
  gi|13541182|ref|NP_110870.1|  5 IAGKIGSGKSTVSQEISKITGYSV--YSSGTFFRESAKK 41
                                  89999****************998..5678888877665 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.2   4.7e-05     0.049       2      38 ..      10      49 ..       9     173 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.7e-05
                                  TSSHHHHHHHHHHHHTSEEEEHHHHH...HHHHTS-HHHH CS
                           SKI  2 GaGKstvGkllAkklglefiDlDeli...ekrtgksiaei 38
                                  G+GKstv ++++k  g++++ + +++    k++g+si+++
  gi|13541182|ref|NP_110870.1| 10 GSGKSTVSQEISKITGYSVYSSGTFFresAKKMGMSIEDF 49
                                  9**********************99954455667777764 PP

>> ADK  Adenylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   8.2e-05     0.086       2      37 ..       6      41 ..       5      79 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 8.2e-05
                                  EESTTSSHHHHHHHHHHHHTSEEEEHHHHHHHHHHC CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ADK  2 lGaPgaGKGtqaeklvkkyglahlstGdllRaevks 37
                                   G  g+GK t+++++ k  g+   s+G ++R++ k+
  gi|13541182|ref|NP_110870.1|  6 AGKIGSGKSTVSQEISKITGYSVYSSGTFFRESAKK 41
                                  6899***************************98875 PP

>> PglZ  PglZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00013      0.13      79     130 ..     128     181 ..      97     189 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00013
                          PglZ  79 nrekilekkl...glavkaddllelkkderrellkdkevvyivhnkvDalgdkas 130
                                   +r +i+ekk     + +  ddl  ++     e++k +ev ++v+n++D+++ k++
  gi|13541182|ref|NP_110870.1| 128 ER-EISEKKRyldLYGIDIDDLSIYDIVVNTEFMKPEEVAVLVLNRIDEMSRKEV 181
                                   33.33333334578889999999999999999******************99865 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0    0.0037       3.9      24      50 ..       1      27 [.       1      80 [. 0.82
   2 ?    3.9   0.0     0.024        25     251     285 ..     115     179 ..      84     186 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0037
                                  EEEEEEESTTSSHHHHHHHHHHHCS-- CS
                       G-alpha 24 vkllllGqseSGKsTilkqlkllykkg 50
                                  +++ + G+ +SGKsT+ +++ ++ + +
  gi|13541182|ref|NP_110870.1|  1 MRITIAGKIGSGKSTVSQEISKITGYS 27
                                  578999*************99887554 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.024
                                   H.............................HHHHHHHHCCCC-GGGT.TSEEEEEEE-HHHHHHH CS
                       G-alpha 251 l.............................eeslklFkeicnnkllk.ntpiiLflnKlDileeK 285
                                                                  + l++++ ++n +++k +   +L+ln +D +++K
  gi|13541182|ref|NP_110870.1| 115 EgieideaaklldereisekkryldlygidIDDLSIYDIVVNTEFMKpEEVAVLVLNRIDEMSRK 179
                                   0555555555555555555555556666666889999*********735558********99998 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.2   0.00038       0.4      26      38 ..       4      16 ..       2      20 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00038
                        AAA_29 26 lltGpsGsGKSTl 38
                                   ++G++GsGKST+
  gi|13541182|ref|NP_110870.1|  4 TIAGKIGSGKSTV 16
                                  599*********6 PP

>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.4    0.0047         5      16      38 ..       2      24 ..       1      31 [. 0.84
   2 ?    3.5   0.0     0.046        48      94     124 ..      29      59 ..      23      70 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0047
                                  EEEEEESTTSSHHHHHHHHHHHS CS
                                  xxxxxxxxxxxxxxxxxxxxxxx RF
                   ATP-synt_ab 16 rtlipgafgvGktvisqslskqs 38
                                  r+ i g+ g Gk+++sq++sk +
  gi|13541182|ref|NP_110870.1|  2 RITIAGKIGSGKSTVSQEISKIT 24
                                  789*****************984 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.046
                                   HHHHHHHHHTTSEEEEEEETHHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   ATP-synt_ab  94 itlAEyfrdqgknvlliadslsrwaeAlrei 124
                                    + + +fr+  k++ + +++  r+ae   e 
  gi|13541182|ref|NP_110870.1|  29 YSSGTFFRESAKKMGMSIEDFNRYAETHPEA 59 
                                   566789********************98775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       635  (0.0354175); expected 358.6 (0.02)
Passed bias filter:                      508  (0.028334); expected 358.6 (0.02)
Passed Vit filter:                        86  (0.0047967); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.57u 0.34s 00:00:00.90 Elapsed: 00:00:00.61
# Mc/sec: 943.11
//
Query:       gi|13541183|ref|NP_110871.1|  [L=353]
Description: H/ACA RNA-protein complex component Cbf5p [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-26   93.3   1.9    3.2e-16   60.1   0.1    3.2  2  TruB_N           TruB family pseudouridylate synthase (N term
    1.6e-15   57.0   0.0    2.6e-15   56.3   0.0    1.4  1  TruB_C_2         tRNA pseudouridylate synthase B C-terminal d
      2e-13   50.1   0.1    5.7e-13   48.6   0.1    1.8  1  PUA              PUA domain
    2.6e-06   27.6   0.3    8.6e-06   25.9   0.1    2.1  2  UPF0113          UPF0113 PUA domain
     0.0002   21.3   0.0    0.00052   20.0   0.0    1.7  1  DKCLD            DKCLD (NUC011) domain
  ------ inclusion threshold ------
      0.056   13.5   0.1       0.14   12.2   0.1    1.7  1  PseudoU_synth_2  RNA pseudouridylate synthase
       0.13   12.1   0.0       0.37   10.6   0.0    1.8  1  PUA_3            PUA-like domain


Domain annotation for each model (and alignments):
>> TruB_N  TruB family pseudouridylate synthase (N terminal domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.1   0.1   1.2e-19   3.2e-16       1      52 [.      30      81 ..      30      84 .. 0.96
   2 !   29.7   0.3   2.8e-10   7.1e-07      71     149 .]      82     143 ..      80     143 .. 0.97

  Alignments for each domain:
  == domain 1  score: 60.1 bits;  conditional E-value: 1.2e-19
                                  HHHTT-S-EEESS---TT-EEEEEEEEGGGGGGHHHCTTS-EEEEEEEEETE CS
                        TruB_N  1 krllkakkvGhtGtLDplatGvLvvavgeaTklleylleadKeYeatirlga 52
                                  +++l+++kvGh GtLDp++tGvLv+a+g+a +l+++++e++KeY+ ++r++ 
  gi|13541183|ref|NP_110871.1| 30 RQILGTEKVGHIGTLDPNVTGVLVMAIGKAVRLIDVVHEKPKEYVGVMRFHS 81
                                  789**********************************************987 PP

  == domain 2  score: 29.7 bits;  conditional E-value: 2.8e-10
                                   T--HHHHHHHHHHC-EEE---------------------------------EEEEEEEEEEEEEEEEEEEEEESTTTTH CS
                        TruB_N  71 klteekleevlkkftGeieqvppmySAvkvnGkrlyelaregeeverkkrkvtiyelelleveepevelevecskGtYi 149
                                   +++ee+++ev++kft +i+q pp+ SAv                  rk r  tiyel+++e +++ v ++v+c++GtYi
  gi|13541183|ref|NP_110871.1|  82 DISEEEVREVFRKFTTRIYQLPPVRSAVS-----------------RKVRIKTIYELDMIEKKDKIVLFHVKCESGTYI 143
                                   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 !   56.3   0.0     1e-18   2.6e-15       1      63 [.     144     208 ..     144     209 .. 0.93

  Alignments for each domain:
  == domain 1  score: 56.3 bits;  conditional E-value: 1e-18
                                   HHHHHHHHHHTTS-EEEEEEEEEEETTEGG-..B-HHHHHHHHHHHHT.--H.HHHHEEEGGGGG CS
                      TruB_C_2   1 RtLcdDiGeaLgcgAhveeLRRtrvgpfdeedmvtledLedavllyke.dee.LdrlllPlesal 63 
                                   RtLc+DiG + g g+++ +LRR+++gpf+e+ ++tl+dL++ v l+ke ++e  +++ l +  a+
  gi|13541183|ref|NP_110871.1| 144 RTLCTDIGYVSGKGGQMVDLRRISTGPFKEDIAITLQDLQAYVDLAKEgKDElFRSHFLDMTYAF 208
                                   9*******************************************999996666999999987775 PP

>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.6   0.1   2.2e-16   5.7e-13       1      59 [.     212     270 ..     212     274 .. 0.97

  Alignments for each domain:
  == domain 1  score: 48.6 bits;  conditional E-value: 2.2e-16
                                   CEEEE-HHHHHHHHTT-EEEGGGEEEEETT--TTSEEEEEETTSCEEEEEEESS-HHHH CS
                           PUA   1 grvvvddgAvkallsgasLlapGvvevegdfeegdvVaivdedgelvavGlanysseel 59 
                                   +++v +++Av+ +++g++L++ Gv  ++g+f++gd V +++ed+el++ G+a+++s+ l
  gi|13541183|ref|NP_110871.1| 212 PKIVAKKSAVENIAHGSDLYVGGVKLIDGNFQKGDRVCVLSEDNELLGTGIARCDSSNL 270
                                   699*****************************************************976 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       2.6   6.7e+03      59      75 ..     127     144 ..     117     145 .. 0.60
   2 !   25.9   0.1   3.4e-09   8.6e-06       1      56 [.     213     273 ..     213     294 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 2.6
                       UPF0113  59 pgkivvknl.aDiGeYlR 75 
                                   ++kiv+ ++ +  G+Y+R
  gi|13541183|ref|NP_110871.1| 127 KDKIVLFHVkCESGTYIR 144
                                   344444443268899998 PP

  == domain 2  score: 25.9 bits;  conditional E-value: 3.4e-09
                       UPF0113   1 kvvvkekaeklFLYGrdvlkesilkitesvkenqvvvVlnengeplGiGkirkdt.....k 56 
                                   k+v k++a +++  G d++  +++ i+++++++++v Vl+e++e+lG G++r+d+     k
  gi|13541183|ref|NP_110871.1| 213 KIVAKKSAVENIAHGSDLYVGGVKLIDGNFQKGDRVCVLSEDNELLGTGIARCDSsnlfmK 273
                                   78999************************************************88655444 PP

>> DKCLD  DKCLD (NUC011) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0     2e-07   0.00052      42      57 ..      10      25 ..       4      26 .. 0.94

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 2e-07
                                  EEEEEEE-SSS-HHHH CS
                         DKCLD 42 GvinLDKPsnPsSHEV 57
                                  G+i +DKP++P+SH+V
  gi|13541183|ref|NP_110871.1| 10 GFIVIDKPQGPTSHQV 25
                                  9*************99 PP

>> PseudoU_synth_2  RNA pseudouridylate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   5.4e-05      0.14       2      84 ..      11      77 ..      10     142 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 5.4e-05
               PseudoU_synth_2  2 lvvvnKPagvpvqpeakdgsekekettatssraeeekkelklvhRLDkatsGllllAksseaanklakafeerkvrKkYlalv 84
                                  ++v++KP+g ++++ +            +  r+   ++++++++ LD +++G+l++A  ++a+ +l +    ++  K+Y+++ 
  gi|13541183|ref|NP_110871.1| 11 FIVIDKPQGPTSHQVD------------YWVRQILGTEKVGHIGTLDPNVTGVLVMAI-GKAV-RLID--VVHEKPKEYVGVM 77
                                  6788888888888877............5567779999*******************7.4433.3333..3345555666555 PP

>> PUA_3  PUA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00014      0.37      21      51 ..     233     263 ..     216     268 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00014
                         PUA_3  21 neiasvegeledGdvVdvfsekgkflGtGyy 51 
                                   + ++ ++g+++ Gd V v se+++ lGtG+ 
  gi|13541183|ref|NP_110871.1| 233 GGVKLIDGNFQKGDRVCVLSEDNELLGTGIA 263
                                   55666788999******************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); 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:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.60u 0.35s 00:00:00.95 Elapsed: 00:00:00.54
# Mc/sec: 1972.85
//
Query:       gi|13541184|ref|NP_110872.1|  [L=183]
Description: Nop56p-related protein (ribosomal biogenesis) [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-33  115.5   0.1    3.2e-33  115.1   0.1    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 !  115.1   0.1   1.8e-37   3.2e-33      85     229 ..      37     179 ..      32     181 .. 0.89

  Alignments for each domain:
  == domain 1  score: 115.1 bits;  conditional E-value: 1.8e-37
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHCHHHHHHHHHHHHSSHHHHHCS-HHHHTTTT-HHHHCCCHH. CS
                           Nop  85 lknikelcdrvleleelrkelleYlesrmsaiAPNlsaLvGeevaarLishaGgLtnLakmPastiqilGaekalfralk. 164
                                   ++ i+el +   ++ ++r +l e +++  ++i PN +aLvGe++a  L+ ha gL++La mP+s iq+lGae+alf+a++ 
  gi|13541184|ref|NP_110872.1|  37 IDGISELFSYGSKMCDFRGQLDERVKEMARQILPNTTALVGERLAMDLLVHAHGLKRLAYMPSSSIQMLGAERALFTAIQk 117
                                   56788888999999******************************************************************6 PP

                                   T---SSSCHHHCSHHHHHTS-CCCHHHHHHHHHHHHHHHHHHHHTT----SHHHHHHHHHHHHHH CS
                           Nop 165 kkntpkyGliyhselvqkatppklkkkiaRllaaKvalaaRiDafsekdgslGkklreeiekklk 229
                                   ++ntpkyG++++ + ++ ++ p++++kiaR++a+Kva+ aR D  +  ++   +++re+i++ +k
  gi|13541184|ref|NP_110872.1| 118 RGNTPKYGVLFKYPKLS-TLRPRQRGKIARIIANKVAITARADLLG--TKVDAESFREKIDNMIK 179
                                   66**************9.88***********************663..34444566666666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       364  (0.0203023); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.33s 00:00:00.87 Elapsed: 00:00:00.53
# Mc/sec: 1037.21
//
Query:       gi|13541185|ref|NP_110873.1|  [L=474]
Description: amidophosphoribosyltransferase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.8e-24   84.1   0.0    4.8e-23   81.4   0.0    2.1  2  GATase_7      Glutamine amidotransferase domain
    2.9e-21   76.1   0.0      5e-21   75.3   0.0    1.4  1  GATase_6      Glutamine amidotransferase domain
    2.9e-07   30.2   0.0    1.1e-06   28.3   0.0    1.9  2  Pribosyltran  Phosphoribosyl transferase domain
    0.00043   19.3   0.0    0.00075   18.5   0.0    1.3  1  GATase_4      Glutamine amidotransferases class-II
     0.0053   15.5   0.1        3.1    6.4   0.0    3.0  3  GATase_2      Glutamine amidotransferases class-II


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 ?   -0.1   0.0      0.22     8e+02      11      52 ..       6      49 ..       2      61 .. 0.72
   2 !   81.4   0.0   1.3e-26   4.8e-23      12     122 ..     101     217 ..      88     218 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.22
                      GATase_7 11 agaQPmvs.sedgr.lvivfnGeiyNykelreeLeakghrfrtk 52
                                  +g+ P+   + +++  v+ f G+i  y+ +   L++ +hr +++
  gi|13541185|ref|NP_110873.1|  6 QGSDPINGqKPSEDcAVVGFKGKINAYNPIITALRTLQHRGQES 49
                                  55566655433334157779**********99999998876655 PP

  == domain 2  score: 81.4 bits;  conditional E-value: 1.3e-26
                      GATase_7  12 gaQPmvs.sedgrlvivfnGeiyNykelreeLeakghrfrtksDtevllallea........ewgeealerlnGmfAfaiw 83 
                                   +a P+v+ s+ g ++i +nGei+N +elr+ ++++g++f+++sDtev+la l++        ++ e+ +e l+G +A ai 
  gi|13541185|ref|NP_110873.1| 101 NAGPFVMnSSFGYITISHNGEIVNADELRDSMKKEGITFQSDSDTEVMLAELSRniskyglkRGFEQSMESLRGAYACAIS 181
                                   5668888789999**********************************99888889*******9*****************9 PP

                      GATase_7  84 deeekrlllaRDrlGikPLyygedkgdallfaSelkall 122
                                    +++  l+++RD+ Gi+PL +g+++ d++++aSe  a+ 
  gi|13541185|ref|NP_110873.1| 182 INDR--LYAVRDPNGIRPLVIGKNN-DGYIVASESCAID 217
                                   9999..******************6.7********9986 PP

>> GATase_6  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.3   0.0   1.4e-24     5e-21      12     134 .]      82     212 ..      61     212 .. 0.88

  Alignments for each domain:
  == domain 1  score: 75.3 bits;  conditional E-value: 1.4e-24
                      GATase_6  12 devalaHvRlaivglaeeegaqPf..psedgrlllvhNGeiynykelreelpalkglafrsrsDtevlla.ll...eelG. 85 
                                   + v+++H+R ++ g ++   a Pf   s+ g ++++hNGei n++elr+ +++ +g +f+s+sDtev+la l    +++G 
  gi|13541185|ref|NP_110873.1|  82 GYVGVGHTRYSTAGSKNVVNAGPFvmNSSFGYITISHNGEIVNADELRDSMKK-EGITFQSDSDTEVMLAeLSrniSKYGl 161
                                   349*************88888***877777889********************.****************55588877779 PP

                      GATase_6  86 ....eevlerlrGmfafaiwdkrentlilardrlgvkplyyavdesglafase 134
                                       e+ +e+lrG++a ai  + +++l  +rd  g++pl+++ +++g ++ase
  gi|13541185|ref|NP_110873.1| 162 krgfEQSMESLRGAYACAI--SINDRLYAVRDPNGIRPLVIGKNNDGYIVASE 212
                                   9999*********999976..478899999**********************8 PP

>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       0.6   2.1e+03     104     149 ..      36      81 ..      35      89 .. 0.78
   2 !   28.3   0.0     3e-10   1.1e-06      30     120 ..     292     389 ..     270     394 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.6
                                   HHHHHHHHCC-BSEEEEEEEEE-HHHHHHHHHH-TTS.....EEEE CS
                  Pribosyltran 104 laalelLkekgpeevriavlvdkpateeevdknakrvfslspdnfv 149
                                   + al+ L  +g e+ + av+  k+ t ++ +  ++ vf++ +d+++
  gi|13541185|ref|NP_110873.1|  36 ITALRTLQHRGQESAGMAVFDGKKVTLKKGSGLVTDVFNPATDDIK 81 
                                   6799999999999999999999999999888888888877755444 PP

  == domain 2  score: 28.3 bits;  conditional E-value: 3e-10
                                   GEEEEEEETTTHHHHHHHHHHSTT-EE.-EEEEEE-TTT--EE................EE----TTSEEEEE-SEESSSH CS
                  Pribosyltran  30 pdvvvgiargGvpfakiladeLevpla.yvrkvkyrpdgseeaargssdes........rlledpagkkVliVDDildtGg 101
                                    d+vv+++  G   a  ++ e + p++  + k +y++ +    ++ s d             e + gkkV++VDD +  G+
  gi|13541185|ref|NP_110873.1| 292 ADIVVPVPDSGRSQAIGYSMESGMPYTeGLIKNRYSERTFIMPTQ-S-DRKaaihlklnPIREVIGGKKVVLVDDSIVRGN 370
                                   567777777777777777777777777344444444444333332.2.2224677888667777889************** PP

                                   HHHHHHHHHHCC-BSEEEE CS
                  Pribosyltran 102 TllaalelLkekgpeevri 120
                                   T++ ++ l++++g++e+++
  gi|13541185|ref|NP_110873.1| 371 TMRFIVGLMRKYGAKEIHV 389
                                   ***************9985 PP

>> GATase_4  Glutamine amidotransferases class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   2.1e-07   0.00075      68     145 ..      79     160 ..      31     181 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2.1e-07
                      GATase_4  68 piksknvvaHiRkatqGevklenthpFvRelwgrewifAHnGdlkeykpkl....egrfePvGsTDsElafCelleelasr 144
                                   +ik  + v H R  t G+ +  n+ pFv +    ++++ HnG++ + ++ +    ++  +   + D+E+++ el ++++++
  gi|13541185|ref|NP_110873.1|  79 DIKGYVGVGHTRYSTAGSKNVVNAGPFVMNSSFGYITISHNGEIVNADELRdsmkKEGITFQSDSDTEVMLAELSRNISKY 159
                                   6999999*************************************7744333322333344446789999999998888876 PP

                      GATase_4 145 f 145
                                    
  gi|13541185|ref|NP_110873.1| 160 G 160
                                   6 PP

>> GATase_2  Glutamine amidotransferases class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0     0.016        59      22      57 ..      36      71 ..      26      80 .. 0.83
   2 !    3.1   0.0     0.009        32     200     254 ..      79     141 ..      73     157 .. 0.72
   3 !    6.4   0.0   0.00086       3.1     337     396 ..     181     237 ..     165     257 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.016
                                  HHHHHHGGGGS-B-TTSSSBSEEEEEEE--HHHHHH CS
                      GATase_2 22 lealenleHRGavgadektGDGaGillqiPdeflrk 57
                                  ++al++l+HRG  +a     DG  + l++ + ++++
  gi|13541185|ref|NP_110873.1| 36 ITALRTLQHRGQESAGMAVFDGKKVTLKKGSGLVTD 71
                                  789*******************99988877766655 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.009
                                   T--BSEEEEEE---SSSS--GGGSSS-SS........EEEEE--TTHHHHHHHHHHHCTT--B CS
                      GATase_2 200 elesalalvHsRfstntfPsWelaqPlRl........laHnGEintlrGnknwmkareaelks 254
                                   +++ ++ + H+R+st    +   a P+ +        ++HnGEi      ++ mk    +++s
  gi|13541185|ref|NP_110873.1|  79 DIKGYVGVGHTRYSTAGSKNVVNAGPFVMnssfgyitISHNGEIVNADELRDSMKKEGITFQS 141
                                   667788999******999999999987543333333388999997766666666666666655 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.00086
                                   E-SSEEEEEE-TT--S--EEEEETT--EEEESSTTSS---GGGEEEEEE--TT-EEEEET CS
                      GATase_2 337 tdGkvvgavLDRnGLRPaRylvtkddlvvlasEvGvldleeeevvekgrlqPGrmllvdl 396
                                   +    + av D nG+RP  +   +d++ ++asE+  +d  e ++++   ++PG+++ +  
  gi|13541185|ref|NP_110873.1| 181 SINDRLYAVRDPNGIRPLVIGKNNDGY-IVASESCAIDALEGTLIK--NIEPGEVVEISD 237
                                   4455667899*******9887777776.579***999998888876..589999987754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (474 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-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: 00:00:00.51
# Mc/sec: 2779.25
//
Query:       gi|13541186|ref|NP_110874.1|  [L=54]
Description: 50S ribosomal protein L37e [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.2e-23   81.6   8.5    3.4e-23   81.5   8.5    1.0  1  Ribosomal_L37e  Ribosomal protein L37e
     0.0012   18.7   2.4     0.0015   18.4   2.4    1.1  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
     0.0018   18.3   0.6     0.0019   18.2   0.6    1.1  1  HypA            Hydrogenase/urease nickel incorporation, meta
     0.0048   16.9   0.7     0.0058   16.6   0.7    1.2  1  DZR             Double zinc ribbon
     0.0059   16.3   2.7       0.33   10.7   0.1    2.3  2  Rubredoxin_2    Rubredoxin metal binding domain
     0.0064   16.6   0.1     0.0069   16.5   0.1    1.1  1  SelR            SelR domain
  ------ inclusion threshold ------
       0.02   14.3   3.1       0.58    9.6   0.3    2.1  2  zf-ribbon_3     zinc-ribbon domain
      0.039   13.6   5.4       0.65    9.7   0.6    2.2  2  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
      0.049   13.6   4.9       0.54   10.2   0.8    2.2  2  zinc_ribbon_4   zinc-ribbon domain
      0.069   12.9   6.0        0.6    9.9   6.1    2.0  2  zinc_ribbon_2   zinc-ribbon domain
       0.13   11.8   1.8        8.2    6.0   0.3    2.2  2  zn-ribbon_14    Zinc-ribbon
       0.14   12.2   6.0       0.34   11.1   0.3    2.2  2  UPF0547         Uncharacterised protein family UPF0547
       0.16   12.1   0.2       0.18   11.9   0.2    1.1  1  DUF2614         Zinc-ribbon containing domain
        0.2   11.8   3.2        2.9    8.1   3.7    2.0  2  Zn-ribbon_8     Zinc ribbon domain
       0.26   11.4   4.9        1.1    9.4   0.3    2.1  2  zf-Mss51        Zinc-finger of mitochondrial splicing suppres
       0.46   10.1   3.0        3.9    7.1   0.3    2.1  2  zf_UBZ          Ubiquitin-Binding Zinc Finger
       0.49   10.6   3.9       0.89    9.8   1.5    2.0  2  zinc_ribbon_13  Nucleic-acid-binding protein containing Zn-ri
        1.6    8.8   5.2        3.1    7.8   0.4    2.2  2  YhfH            YhfH-like protein
        2.4    8.1   8.8        4.2    7.3   8.8    1.5  1  DUF35_N         Rubredoxin-like zinc ribbon domain (DUF35_N)


Domain annotation for each model (and alignments):
>> Ribosomal_L37e  Ribosomal protein L37e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.5   8.5   3.6e-26   3.4e-23       2      51 ..       3      52 ..       2      54 .] 0.96

  Alignments for each domain:
  == domain 1  score: 81.5 bits;  conditional E-value: 3.6e-26
                Ribosomal_L37e  2 kGtssfGkrqkkktHilCrrCgkrsyhvqkktCascGypsaklrkynWsa 51
                                  +Gt+ +Gk ++kktHi+CrrCg+++y+v++k+C++cG+p+ ++r+y+W++
  gi|13541186|ref|NP_110874.1|  3 NGTAVMGKINNKKTHITCRRCGHHTYNVRTKRCSHCGFPAPRIRSYKWAK 52
                                  8***********************************************86 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   2.4   1.6e-06    0.0015      21      56 ..      10      42 ..       4      44 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.6e-06
                OrfB_Zn_ribbon 21 evnpayTSktCseCgsknkealsgrtfkCpnCgfea 56
                                  ++n   T  tC +Cg+  ++    rt +C++Cgf a
  gi|13541186|ref|NP_110874.1| 10 KINNKKTHITCRRCGHHTYN---VRTKRCSHCGFPA 42
                                  68889999********9999...**********965 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.6     2e-06    0.0019      63      96 ..      10      42 ..       2      49 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2e-06
                                  EEEEE--EEEETTTS-EEECHHHHHS-TTTSSS- CS
                          HypA 63 eieevpvkvrCreCgkefeleekalrCpkCgsad 96
                                  +i++++ +++Cr+Cg+++   + + rC +Cg   
  gi|13541186|ref|NP_110874.1| 10 KINNKKTHITCRRCGHHTYNVR-TKRCSHCGFPA 42
                                  588999*********8887543.469****9765 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.7   6.2e-06    0.0058       8      38 ..      13      42 ..       6      48 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 6.2e-06
                           DZR  8 lppdarfCseCgtklkavaaedrCpsCgekv 38
                                  +++  ++C +Cg++     + +rC++Cg ++
  gi|13541186|ref|NP_110874.1| 13 NKKTHITCRRCGHHTY-NVRTKRCSHCGFPA 42
                                  5666778888888853.33478888888765 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.5     0.013        12       3      10 ..      20      27 ..      19      30 .. 0.80
   2 !   10.7   0.1   0.00035      0.33       2      12 ..      34      44 ..      34      46 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.013
                  Rubredoxin_2  3 CsqCGfes 10
                                  C++CG+ +
  gi|13541186|ref|NP_110874.1| 20 CRRCGHHT 27
                                  99999976 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00035
                  Rubredoxin_2  2 vCsqCGfesak 12
                                  +Cs+CGf +++
  gi|13541186|ref|NP_110874.1| 34 RCSHCGFPAPR 44
                                  8******8887 PP

>> SelR  SelR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1   7.3e-06    0.0069      30      60 ..      12      42 ..       3      49 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 7.3e-06
                                  --SSCEEEETTTS-EEEECCCCE-STTSSSE CS
                          SelR 30 ekekGvyecavcgepLfssetkfdsgcGwps 60
                                  +++k   +c+ cg++ ++ +tk  s+cG+p+
  gi|13541186|ref|NP_110874.1| 12 NNKKTHITCRRCGHHTYNVRTKRCSHCGFPA 42
                                  44567789**********************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 ?    5.7   0.2     0.011        10      16      24 ..      17      25 ..       9      27 .. 0.66
   2 ?    9.6   0.3   0.00062      0.58       2       9 ..      32      39 ..      31      44 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.011
                   zf-ribbon_3 16 dnvCpyCGt 24
                                   ++C  CG+
  gi|13541186|ref|NP_110874.1| 17 HITCRRCGH 25
                                  466666665 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00062
                   zf-ribbon_3  2 tvrCPnCG 9 
                                  t+rC++CG
  gi|13541186|ref|NP_110874.1| 32 TKRCSHCG 39
                                  89999999 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.6   0.00069      0.65      15      25 ..      15      25 ..      10      28 .. 0.83
   2 ?    6.5   0.4    0.0073       6.9      19      25 ..      34      40 ..      30      42 .. 0.93

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00069
                                  SS----SSS-- CS
                DNA_RNApol_7kD 15 gdpiRCkeCGh 25
                                  +  i C+ CGh
  gi|13541186|ref|NP_110874.1| 15 KTHITCRRCGH 25
                                  56899*****9 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0073
                                  --SSS-- CS
                DNA_RNApol_7kD 19 RCkeCGh 25
                                  RC +CG+
  gi|13541186|ref|NP_110874.1| 34 RCSHCGF 40
                                  9*****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 ?   10.2   0.8   0.00057      0.54      18      33 ..      10      25 ..       8      26 .. 0.90
   2 ?    5.4   0.2     0.018        17      27      32 ..      34      39 ..      28      41 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00057
                 zinc_ribbon_4 18 klpakgvkvrCskCgh 33
                                  k+  k++ ++C +Cgh
  gi|13541186|ref|NP_110874.1| 10 KINNKKTHITCRRCGH 25
                                  78889999*******9 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.018
                 zinc_ribbon_4 27 rCskCg 32
                                  rCs+Cg
  gi|13541186|ref|NP_110874.1| 34 RCSHCG 39
                                  899997 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.3    0.0041       3.8      11      22 ..      15      26 ..       9      27 .. 0.71
   2 ?    9.9   6.1   0.00064       0.6       2      22 ..      20      41 ..      19      42 .. 0.92

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0041
                 zinc_ribbon_2 11 dnakFCpyCGtp 22
                                  ++   C +CG++
  gi|13541186|ref|NP_110874.1| 15 KTHITCRRCGHH 26
                                  555669999986 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00064
                 zinc_ribbon_2  2 CpnCGaelqd.nakFCpyCGtp 22
                                  C +CG+   + + k C++CG+p
  gi|13541186|ref|NP_110874.1| 20 CRRCGHHTYNvRTKRCSHCGFP 41
                                  ********9889999*****97 PP

>> zn-ribbon_14  Zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.3    0.0087       8.2       2       8 ..      19      25 ..      18      29 .. 0.83
   2 ?    5.3   0.1     0.015        14       2       9 ..      34      41 ..      33      43 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0087
                  zn-ribbon_14  2 kCerCGy 8 
                                  +C+rCG+
  gi|13541186|ref|NP_110874.1| 19 TCRRCGH 25
                                  7*****7 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.015
                  zn-ribbon_14  2 kCerCGyl 9 
                                  +C+ CG+ 
  gi|13541186|ref|NP_110874.1| 34 RCSHCGFP 41
                                  8*****85 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   1.0      0.06        57      17      22 ..      20      25 ..      18      26 .. 0.84
   2 ?   11.1   0.3   0.00036      0.34      14      22 ..      32      40 ..      30      41 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.06
                       UPF0547 17 CphCGy 22
                                  C+ CG+
  gi|13541186|ref|NP_110874.1| 20 CRRCGH 25
                                  999**9 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00036
                       UPF0547 14 aqfCphCGy 22
                                  +++C+hCG+
  gi|13541186|ref|NP_110874.1| 32 TKRCSHCGF 40
                                  689*****9 PP

>> DUF2614  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.2   0.00019      0.18      57      92 ..       7      41 ..       4      49 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00019
                       DUF2614 57 wiGllstkavqvvcpeceketkvlGrvdlcmhcdep 92
                                  ++G +  k  +++c  c+++t  + r   c hc  p
  gi|13541186|ref|NP_110874.1|  7 VMGKINNKKTHITCRRCGHHTYNV-RTKRCSHCGFP 41
                                  5799999*************9765.999*****876 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.1    0.0044       4.1      18      35 ..       8      26 ..       3      31 .. 0.71
   2 ?    8.1   3.7    0.0031       2.9       8      38 ..      20      44 ..      18      46 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0044
                   Zn-ribbon_8 18 lqsis.dapltaCPeCgse 35
                                  + +i+ ++  ++C +Cg++
  gi|13541186|ref|NP_110874.1|  8 MGKINnKKTHITCRRCGHH 26
                                  5667756667779999873 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0031
                   Zn-ribbon_8  8 CeeCghefevlqsisdapltaCPeCgsevrr 38
                                  C++Cgh    ++       + C +Cg ++ r
  gi|13541186|ref|NP_110874.1| 20 CRRCGHHTYNVR------TKRCSHCGFPAPR 44
                                  *****9988887......455****988877 PP

>> zf-Mss51  Zinc-finger of mitochondrial splicing suppressor 51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.3    0.0012       1.1      11      28 ..      12      29 ..       3      34 .. 0.84
   2 ?    5.0   0.4     0.028        27      18      26 ..      34      42 ..      30      52 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0012
                      zf-Mss51 11 apkhvdfeCpdCGiptyc 28
                                  ++k+ +++C +CG  ty 
  gi|13541186|ref|NP_110874.1| 12 NNKKTHITCRRCGHHTYN 29
                                  578999********9996 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.028
                      zf-Mss51 18 eCpdCGipt 26
                                   C +CG+p 
  gi|13541186|ref|NP_110874.1| 34 RCSHCGFPA 42
                                  6******96 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.3    0.0041       3.9       2      11 ..      17      26 ..      16      28 .. 0.87
   2 ?    3.8   0.2     0.047        44       2      11 ..      32      41 ..      31      44 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0041
                        zf_UBZ  2 tylCerCgke 11
                                  +++C rCg++
  gi|13541186|ref|NP_110874.1| 17 HITCRRCGHH 26
                                  78******97 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.047
                        zf_UBZ  2 tylCerCgke 11
                                  t  C+ Cg +
  gi|13541186|ref|NP_110874.1| 32 TKRCSHCGFP 41
                                  678****965 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 ?    9.8   1.5   0.00094      0.89      30      48 ..      12      29 ..       3      36 .. 0.70
   2 ?    1.8   0.3       0.3   2.8e+02      37      43 ..      34      40 ..      29      42 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00094
                zinc_ribbon_13 30 nkkfitvsCknCgYtelYk 48
                                  n+k + ++C++Cg+   Y+
  gi|13541186|ref|NP_110874.1| 12 NNKKTHITCRRCGHH-TYN 29
                                  556688899999875.355 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.3
                zinc_ribbon_13 37 sCknCgY 43
                                   C++Cg+
  gi|13541186|ref|NP_110874.1| 34 RCSHCGF 40
                                  5888887 PP

>> YhfH  YhfH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.5      0.07        66      15      22 ..      19      26 ..      11      29 .. 0.86
   2 ?    7.8   0.4    0.0033       3.1      10      20 ..      29      39 ..      27      41 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.07
                          YhfH 15 kCteCGke 22
                                  +C  CG +
  gi|13541186|ref|NP_110874.1| 19 TCRRCGHH 26
                                  7999*986 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0033
                          YhfH 10 nLPkKkCteCG 20
                                  n  +K C++CG
  gi|13541186|ref|NP_110874.1| 29 NVRTKRCSHCG 39
                                  5668******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 ?    7.3   8.8    0.0045       4.2      14      32 ..      20      39 ..      18      42 .. 0.95

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0045
                       DUF35_N 14 CpdCGtvqfPPr.avCphCg 32
                                  C+ CG++ +  r   C+hCg
  gi|13541186|ref|NP_110874.1| 20 CRRCGHHTYNVRtKRCSHCG 39
                                  *******************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (54 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       728  (0.0406046); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.45u 0.33s 00:00:00.78 Elapsed: 00:00:00.50
# Mc/sec: 325.38
//
Query:       gi|13541187|ref|NP_110875.1|  [L=83]
Description: small nuclear ribonucleoprotein [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.9e-20   70.7   1.1    6.7e-20   70.6   1.1    1.0  1  LSM       LSM domain
    0.00026   21.1   0.0    0.00029   20.9   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 !   70.6   1.1   7.4e-24   6.7e-20       2      67 .]      13      77 ..      12      77 .. 0.97

  Alignments for each domain:
  == domain 1  score: 70.6 bits;  conditional E-value: 7.4e-24
                                  HHHHTTTSEEEEEETTSEEEEEEEEEEETTSEEEEEEEEEEETTETEEEEEEEEEEEGGGEEEEEE CS
                           LSM  2 flkklinkkvtvelkngrelrGtLkgfDqfmNlvLedveetlkdkkekrklglvliRGnnivlisl 67
                                   lk+ + ++v++  k++re++G+L+g+D +mN+vL++++e+++++ +k + +++l+RG+n++++s+
  gi|13541187|ref|NP_110875.1| 13 VLKNALSRNVLIDVKGNREYSGILEGYDVYMNVVLQNASEIINGE-NKGVFDRILVRGDNVIFVSP 77
                                  699*****************************************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 !   20.9   0.0   3.2e-08   0.00029       8      53 ..      14      56 ..       7      75 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 3.2e-08
                                  HHTTTTSEEEEEETTS-EEEEEEEEE-T..T--EEEEEEEETTS.. CS
                        SM-ATX  8 ltslvGkevevtvknGevyeGifstvslekdfsvvLkmarkvkkan 53
                                  l++   ++v + vk    y+Gi+ ++++   ++vvL++a ++ + +
  gi|13541187|ref|NP_110875.1| 14 LKNALSRNVLIDVKGNREYSGILEGYDV--YMNVVLQNASEIIN-G 56
                                  555666899*******************..**********9988.2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       231  (0.0128842); expected 358.6 (0.02)
Passed bias filter:                      199  (0.0110993); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.34s 00:00:00.81 Elapsed: 00:00:00.51
# Mc/sec: 491.48
//
Query:       gi|13541188|ref|NP_110876.1|  [L=277]
Description: nucleoside-diphosphate-sugar epimerase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.3e-10   39.4   0.3    2.4e-07   30.1   0.4    2.4  2  3Beta_HSD       3-beta hydroxysteroid dehydrogenase/isomerase
    4.8e-10   39.6   0.1    2.6e-09   37.2   0.0    2.1  3  NAD_binding_10  NAD(P)H-binding
    1.6e-08   34.3   0.1    3.5e-08   33.2   0.1    1.5  2  Epimerase       NAD dependent epimerase/dehydratase family
    1.1e-05   24.7   0.0     0.0011   18.2   0.0    2.1  1  RmlD_sub_bind   RmlD substrate binding domain
    2.4e-05   24.0   1.0    9.3e-05   22.1   1.0    2.1  1  NmrA            NmrA-like family
  ------ inclusion threshold ------
      0.072   12.0   0.0       0.23   10.3   0.0    1.7  2  DUF677          Protein of unknown function (DUF677)
      0.084   12.3   0.1       0.23   10.8   0.1    1.7  1  GDP_Man_Dehyd   GDP-mannose 4,6 dehydratase
       0.13   11.4   0.0        6.2    5.9   0.0    2.3  2  NAD_binding_4   Male sterility protein


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 !   30.1   0.4   1.1e-10   2.4e-07       1     108 [.       4      98 ..       4     110 .. 0.82
   2 !    7.0   0.0    0.0011       2.6     158     223 ..     124     179 ..     107     185 .. 0.74

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 1.1e-10
                     3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkkviegDvtdkdkleealegvdvvihlaslvdvag 81 
                                   +v Gg+GF+G+++v++L +   +  v  + l++++++     k n +  i+gDvtd +k+e+ + g d v++   + d a 
  gi|13541188|ref|NP_110876.1|   4 IVFGGSGFIGSHIVNSL-E---ADSVAYYSLEKGTNV-----KRNDAVWIQGDVTDYSKVEASMAGYDTVFFA--VEDWAA 73 
                                   699************98.3...345888888887777.....3344448*********************997..999998 PP

                     3Beta_HSD  82 kltedeimkvnvkGTrnvleacvkagv 108
                                      ++   ++ ++G +nv++a +ka+ 
  gi|13541188|ref|NP_110876.1|  74 DEARN--REILLNGIKNVVSAIKKAST 98 
                                   66666..899************99876 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0011
                     3Beta_HSD 158 lkaNgrtlknggrlyTcaLRpagiyGegdkllvpllkqlaklglalfkigdeevlsdrvYvgNvaw 223
                                   ++ N r+lkng       +R ++++G+gd+++ +++k + +      ++ +e +   +vYvg v+ 
  gi|13541188|ref|NP_110876.1| 124 VEDNTRVLKNG-----LVVRLSIVFGDGDHFTDRFVKLAEQVS----HLPEEGN-LAPVYVGDVVT 179
                                   45588999999.....679**********99887776555544....4444444.56899999875 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.2   0.0   1.2e-12   2.6e-09       1      92 [.       7     100 ..       7     129 .. 0.78
   2 ?   -3.3   0.0       3.3   7.3e+03      23      48 ..     151     177 ..     145     183 .. 0.68
   3 ?   -0.8   0.0      0.53   1.2e+03     108     137 ..     234     266 ..     225     268 .. 0.75

  Alignments for each domain:
  == domain 1  score: 37.2 bits;  conditional E-value: 1.2e-12
                                   TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES-....--TCCHHHH CS
                NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtdvedlaealkgadaVvsal....ggggkdeeg 77 
                                   G++G +G+++v+ l a++ +   a+  + ek ++++ ++ +  ++gdvtd +++++ ++g+d+V++a+    +    de  
  gi|13541188|ref|NP_110876.1|   7 GGSGFIGSHIVNSLEADS-V---AY-YSLEKGTNVK-RNDAVWIQGDVTDYSKVEASMAGYDTVFFAVedwaA----DEAR 77 
                                   9*************9996.3...33.3567777786.68999**************************66642....2222 PP

                                   ........HHHHHHHHHHCT--E CS
                NAD_binding_10  78 ........aknivdaakeagvkR 92 
                                            kn+v a k+a + +
  gi|13541188|ref|NP_110876.1|  78 nreillngIKNVVSAIKKASTDQ 100
                                   23346666**********98744 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 3.3
                                   EEEETTHHHCHHHHCTTTCEEEE.--T CS
                NAD_binding_10  23 talvRnpeklaeleaeeglevve.gdv 48 
                                     +v  +e++++l++e +l  v  gdv
  gi|13541188|ref|NP_110876.1| 151 DRFVKLAEQVSHLPEEGNLAPVYvGDV 177
                                   557777888998988888765542666 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.53
                                   HHHHHHHH.CCHHHHHHHHHHHHHHHH..SSSE CS
                NAD_binding_10 108 efgewnke.llkaylaakraaeellra..sgld 137
                                    f+++  e ++++y+++    ++++++  s ld
  gi|13541188|ref|NP_110876.1| 234 LFSRYEAElMFQDYYRETSILDRYVKNptSYLD 266
                                   455665554899************999666666 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.2   0.1   1.6e-11   3.5e-08       2     113 ..       4     105 ..       3     108 .. 0.83
   2 ?   -2.4   0.0       1.1   2.6e+03     166     187 ..     136     155 ..     121     188 .. 0.59

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 1.6e-11
                                   EEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE--S---HHHHHH CS
                     Epimerase   2 lVtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfkeeqpdavihlAavggvaasse 82 
                                   +V G++GfiGs++v+ l++  +    l + ++ ++    +d+ ++++d+td s++e+ ++  + d+v+ +  v ++aa   
  gi|13541188|ref|NP_110876.1|   4 IVFGGSGFIGSHIVNSLEADSVAYYSLEKGTNVKR----NDAVWIQGDVTDYSKVEASMA--GYDTVFFA--VEDWAADEA 76 
                                   79*****************9999999988855444....34489****************..9*******..888888888 PP

                                   SHHHHHHHHTHHHHHHHHHHHHHTCT.EEEEE CS
                     Epimerase  83 dpadfieknlqgtlnlleaarkagvk.rllfl 113
                                   ++ +++   l+g  n+++a++ka  + +l+ +
  gi|13541188|ref|NP_110876.1|  77 RNREIL---LNGIKNVVSAIKKASTDqKLVSF 105
                                   877755...78889999999998776566665 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.1
                                   EEEESEEESTTS-TTSTTSHHH CS
                     Epimerase 166 ilrlfnlyGprngegevsrvip 187
                                   ++rl+ ++G +  +++ +r++ 
  gi|13541188|ref|NP_110876.1| 136 VVRLSIVFGDG--DHFTDRFVK 155
                                   66666666666..333333332 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   4.8e-07    0.0011       1     199 [.       1     187 [.       1     195 [. 0.73

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 4.8e-07
                                   EEEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT.T--TTSHHHHHHHHHHH--SEEEE------HHHHHHSHHHHHHHHTH CS
                 RmlD_sub_bind   1 mkilvtGanGqlGseLakqlaeeglevlaltre.eldltdaeavaellkeakpdvvvnaAAytavDkaEseeeaayavnae 80 
                                   mk +v+G++G +Gs+++++l+++ +++++l++  ++  +da  ++  + +   +v  ++A y  v+ a ++ +a++a n  
  gi|13541188|ref|NP_110876.1|   1 MKAIVFGGSGFIGSHIVNSLEADSVAYYSLEKGtNVKRNDAVWIQGDVTDY-SKVEASMAGYDTVFFAVEDWAADEARNR- 79 
                                   7889**************************554344444444444445553.3355778888888777666555555444. PP

                                   HHHHHHHHHHHCT-EEEEEEEGGGS-S-TTS-B-TTS----SSHHHHHHHHHHHHHHHH-SSEEEEEE-SEESSSSS-HHH CS
                 RmlD_sub_bind  81 avealAeaaaavgalLihvStDyVFdGekkrpYeeddetsPlnvYGrtKlaGEqavlaagkkalivRtswvygekgknfvk 161
                                     e l +  ++v + +   StD     +k   ++  +++s    Y rtK + E   +   k+ l+vR s v+g+ g  f  
  gi|13541188|ref|NP_110876.1|  80 --EILLNGIKNVVSAIKKASTD-----QKLVSFSMINQPSYPLEYFRTKRLVEDNTR-VLKNGLVVRLSIVFGD-GDHFTD 151
                                   ..33444555555556667998.....4666677766666555788*********99.89999**********9.899*** PP

                                   HHHHHHHH-SEEEEESS-EE--EEHHHHHHHHHHHHHH CS
                 RmlD_sub_bind 162 tmlrlakereelkvvaDqlgsPTsardlAevllqllek 199
                                   ++++la++  +l   +    +P ++ d+  v+ +++++
  gi|13541188|ref|NP_110876.1| 152 RFVKLAEQVSHLP--EEGNLAPVYVGDVVTVVNSIIKR 187
                                   ******9988775..66677777777777777777765 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   1.0   4.1e-08   9.3e-05       2     134 ..       4     135 ..       3     259 .. 0.77

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 4.1e-08
                                   EESSTTSHHHHHHHHHHHHHT-EEEEEES-S-SHHHHHHHHSTTEEEES-TT-HHHHHHHHTT-SEEEE---GG....... CS
                          NmrA   2 lviGaTGrqGksvvrallkaghkvralvRdtkselakslkeaGvelvkgdlddkeslvealkgvdvvfsvtgfy....... 75 
                                   +v+G++G +G+++v+ l ++      l      e+ +++k + ++ ++gd+ d++ +++ + g d+vf++++ +       
  gi|13541188|ref|NP_110876.1|   4 IVFGGSGFIGSHIVNSLEADSVAYYSL------EKGTNVKRNDAVWIQGDVTDYSKVEASMAGYDTVFFAVEDWaadearn 78 
                                   599**********99988877665544......6778899********************************99*999995 PP

                                   .S-HHHHHHHHHHHHHHHS.-SEEEEEE---GG.GT.SSS---TTTHHHHHHHHHHHHC..TS CS
                          NmrA  76 .skeiedgkklvdAakeaG.vkhfiySslgddndrsnaeepavphfdsKaeieeyvral..gi 134
                                    +  ++  k++v+A+k+a   ++++  s+ ++   +      ++ f +K  +e+ +r l  g+
  gi|13541188|ref|NP_110876.1|  79 rEILLNGIKNVVSAIKKAStDQKLVSFSMINQP-SY-----PLEYFRTKRLVEDNTRVLknGL 135
                                   3333444589*********66777766777776.44.....5889999999999998775543 PP

>> DUF677  Protein of unknown function (DUF677)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0    0.0001      0.23     237     309 ..      19      95 ..      10     102 .. 0.81
   2 ?   -1.3   0.0      0.36   8.1e+02     208     252 ..     188     234 ..     151     240 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0001
                        DUF677 237 alkrqkeivssmekgievakkdvenisilverleseiksil..ktvefAvekeene..aavklaleeikkkveklte 309
                                   +l     +  s+ekg++v+ +d   i+ +v + ++++ s+    tv fAve+ + +   + ++ l+ ik+ v  +++
  gi|13541188|ref|NP_110876.1|  19 SLEADSVAYYSLEKGTNVKRNDAVWIQGDVTDYSKVEASMAgyDTVFFAVEDWAADeaRNREILLNGIKNVVSAIKK 95 
                                   56666677889*****************************64479******96544014556888999988888877 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.36
                        DUF677 208 avva.vagalavPleavgkwvasaw.kkyeealkrqkeivssmekgi 252
                                    +v  + +   +Pl+ + +++ +   kk+  ++k +k++    e+g+
  gi|13541188|ref|NP_110876.1| 188 EGVYdICSNDNLPLIRIINYIRKNIgKKEIGSVKLEKGLSMLTETGL 234
                                   33444888888999998889886551556678888888877666665 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 ?   10.8   0.1    0.0001      0.23       2      71 ..       5      58 ..       4      66 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0001
                                  EETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHH CS
                 GDP_Man_Dehyd  2 iTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerll 71
                                  + G++GfiGs++++ L +     +    +++ +n++r +++             +++gD+tD s++e  +
  gi|13541188|ref|NP_110876.1|  5 VFGGSGFIGSHIVNSLEADSVAYYS---LEKGTNVKRNDAV-------------WIQGDVTDYSKVEASM 58
                                  89*************9887665554...4455555554443.............5677777777776655 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0     0.013        30       3      16 ..       7      20 ..       5      41 .. 0.91
   2 ?    5.9   0.0    0.0028       6.2     155     209 ..      96     145 ..      44     198 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.013
                                  -TTSHHHHHHHHHH CS
                 NAD_binding_4  3 GaTGFLGkvLlekL 16
                                  G++GF+G+++++ L
  gi|13541188|ref|NP_110876.1|  7 GGSGFIGSHIVNSL 20
                                  9**********987 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0028
                                   .....HHH--EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEE-- CS
                 NAD_binding_4 155 gekeekldederaklkglpntYeqsKalaEklvrearrrsglpvvivRpsiitge 209
                                     +++kl + ++ ++ ++p +Y ++K l E+  r  +  +gl   +vR+si+ g+
  gi|13541188|ref|NP_110876.1|  96 ASTDQKLVSFSMINQPSYPLEYFRTKRLVEDNTRVLK--NGL---VVRLSIVFGD 145
                                   33778888888999999*************9999999..455...9******994 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.56u 0.33s 00:00:00.89 Elapsed: 00:00:00.50
# Mc/sec: 1677.97
//
Query:       gi|13541189|ref|NP_110877.1|  [L=155]
Description: hypothetical protein TVN0358 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-55  187.7   0.3    1.2e-55  187.5   0.3    1.0  1  DUF1940          Domain of unknown function (DUF1940)
     0.0044   17.2   0.0     0.0064   16.6   0.0    1.4  1  Cob_adeno_trans  Cobalamin adenosyltransferase
  ------ inclusion threshold ------
      0.013   14.7   0.1      0.015   14.5   0.1    1.1  1  SNAD3            Secreted Novel AID/APOBEC-like Deaminase 3


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 !  187.5   0.3   2.1e-59   1.2e-55       1     143 []       9     151 ..       9     151 .. 1.00

  Alignments for each domain:
  == domain 1  score: 187.5 bits;  conditional E-value: 2.1e-59
                                   EETTTTEEEETT-HHHHHHHHHHHHHHHHHHHHHT-SSHHHHHHHHHHHHHHHHTTT-------HHHHHHHHH-------H CS
                       DUF1940   1 yCdvlddeldaespyfkyrseiklaeaslGlaiseGikvqatrelldilDtlyqslsDpeskLkDeqrkkLnhadevWlDi 81 
                                   yC+v+dd l+ ++++fk+rsei+ aea++Gla+seG+kv++trelld+lDt+y+sl+D+eskL+++q+k+L +++e+W+Di
  gi|13541189|ref|NP_110877.1|   9 YCPVIDDNLPLDHVFFKFRSEIESAEAFIGLAVSEGVKVNETRELLDMLDTVYNSLYDEESKLNEFQEKRLKFTEEEWYDI 89 
                                   9******************************************************************************** PP

                                   HHHHHHT-HHHHHHHHHHHHHHHHHHHHHHHHTSTTTTTT--HHHHHHHHHHHHHHHHHHH- CS
                       DUF1940  82 kekmsnGdrraayllaaaahlekavaylvrmkedeefkeivkdylikyllklsvfiyreaig 143
                                   kek + G ++++yl+ a++h+++av++l +++ede+f + v+d++i  l k++ +i+re++g
  gi|13541189|ref|NP_110877.1|  90 KEKCNSGSKWSLYLMLARSHIDNAVYWLSKLREDERFVNKVSDENIMALYKIGAVILREGLG 151
                                   ***********************************************************997 PP

>> Cob_adeno_trans  Cobalamin adenosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   1.1e-06    0.0064      20      93 ..      18      91 ..      12     139 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.1e-06
                                  XTTHHHHHHHHHHHHHHHHHHHHHHHCTTT..THHHHHHHHHHHHHHHHHHHHHHT.-BTCCG-S--HHHHHHHHH CS
               Cob_adeno_trans 20 sKddprveayGtvDelnsaiglarallaee..eeelkeaLeeiqneLfdlgaelatpekkkekkkiteeeveelek 93
                                  + d+  +++  ++++++++igla +   +   ++el ++L  + n+L d  ++l   e ++++ k+teee  ++ +
  gi|13541189|ref|NP_110877.1| 18 PLDHVFFKFRSEIESAEAFIGLAVSEGVKVneTRELLDMLDTVYNSLYDEESKLN--EFQEKRLKFTEEEWYDIKE 91
                                  558999******************765554777889999999**********995..3445555566553333333 PP

>> SNAD3  Secreted Novel AID/APOBEC-like Deaminase 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   2.5e-06     0.015     273     323 ..      43      94 ..      30     123 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.5e-06
                         SNAD3 273 keekkvltkelslmLeaaepsllekketleefaekGeslalk..fdlskeice 323
                                   + +k   t+el  mL+ +  sl +++  l+ef+ek  ++ ++  +d+ ke c+
  gi|13541189|ref|NP_110877.1|  43 EGVKVNETRELLDMLDTVYNSLYDEESKLNEFQEKRLKFTEEewYDI-KEKCN 94 
                                   5678889****************************999987632343.44455 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       796  (0.0443973); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); 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: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 956.73
//
Query:       gi|13541190|ref|NP_110878.1|  [L=299]
Description: GTPase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.6e-11   44.4   0.3    3.3e-11   43.4   0.3    1.6  1  GTP_EFTU_D2  Elongation factor Tu domain 2
     0.0009   19.1   0.2     0.0024   17.7   0.2    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 !   43.4   0.3   3.6e-15   3.3e-11       1      73 [.     153     219 ..     153     220 .. 0.97

  Alignments for each domain:
  == domain 1  score: 43.4 bits;  conditional E-value: 3.6e-15
                                   EEEEEEEEEESEEETTEEEEEECTCTTSEEEEEEEEEEEEETEEESEEETTSEEEEEEEESSCCSGSSTTCEE CS
                   GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilgndtskkeivtrissletfhededeavaganaGvivaikgledaiivGdtl 73 
                                   Gtv+lg v sG++kk d +++  ++++++   ++i+s++++  d+dea+ag ++G+ ++ +++e+ + +G+ l
  gi|13541190|ref|NP_110878.1| 153 GTVVLGFVLSGIVKKHDDLYL--SEVNRQ---VQIRSIQVNDVDVDEAEAGTRVGLALRNVEVEE-LSRGMFL 219
                                   9********************..999899...*********************************.9***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 !   17.7   0.2   2.7e-07    0.0024       8      72 ..     143     207 ..     138     214 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2.7e-07
                                   EEEEEEETCC.CEEEEEEEEEEEEETT-EEEETTE.EEEEEEEEEETTEEESEEETT-EEEEEEES CS
                   GTP_EFTU_D4   8 lpgvvfrrsd.paivGvevlgGvikpgvklikedGrevGeilqiqdkgkkleeakaGqevaisieg 72 
                                   ++++ +++s   ++ G  vl+G++k   +l  ++ ++  +i++iq ++  ++ea+aG++v++++++
  gi|13541190|ref|NP_110878.1| 143 IDHYFKVKSVgTVVLG-FVLSGIVKKHDDLYLSEVNRQVQIRSIQVNDVDVDEAEAGTRVGLALRN 207
                                   5666666665146667.9*************99999999**********************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.33s 00:00:00.89 Elapsed: 00:00:00.52
# Mc/sec: 1715.50
//
Query:       gi|13541191|ref|NP_110879.1|  [L=234]
Description: hypothetical protein TVN0360 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 1427.01
//
Query:       gi|13541192|ref|NP_110880.1|  [L=416]
Description: hypothetical protein TVN0361 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (416 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1005  (0.0560544); 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:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.60u 0.31s 00:00:00.90 Elapsed: 00:00:00.49
# Mc/sec: 2564.02
//
Query:       gi|13541193|ref|NP_110881.1|  [L=649]
Description: polyferredoxin [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.5e-05   23.4   8.4      0.012   16.2   0.2    3.1  4  Fer4_7    4Fe-4S dicluster domain
     0.0012   18.9   8.8      0.042   14.0   0.1    3.0  3  Fer4_10   4Fe-4S dicluster domain
     0.0014   18.6  14.5     0.0063   16.5   0.3    2.6  2  Fer4_6    4Fe-4S binding domain
  ------ inclusion threshold ------
      0.012   15.8   7.8       0.11   12.6   6.1    2.5  3  Fer4_9    4Fe-4S dicluster domain
      0.017   14.9   0.4      0.017   14.9   0.4    3.3  3  Fer4      4Fe-4S binding domain
      0.021   14.9   3.9      0.021   14.9   3.9    1.8  2  Fer4_21   4Fe-4S dicluster domain
      0.023   14.7   0.6      0.023   14.7   0.6    4.6  4  Fer4_5    4Fe-4S binding domain
      0.058   13.5   2.7      0.061   13.5   0.7    1.9  2  Fer4_11   4Fe-4S dicluster domain
      0.077   13.1  14.0       0.08   13.1   0.2    3.0  3  Fer4_2    4Fe-4S binding domain
       0.42   11.6   3.4        3.4    8.7   0.0    2.9  3  Fer4_16   4Fe-4S double cluster binding domain
        3.4    8.4  10.6       0.35   11.5   0.8    2.5  2  Fer4_4    4Fe-4S binding 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 ?    1.7   0.0      0.25     4e+02       7      19 ..     430     442 ..     428     458 .. 0.78
   2 !    6.9   2.4    0.0059       9.6      34      52 .]     562     582 ..     541     582 .. 0.78
   3 !   14.2  10.0     3e-05     0.049       2      51 ..     566     613 ..     565     614 .. 0.88
   4 !   16.2   0.2   7.1e-06     0.012       1      21 [.     599     619 ..     599     646 .. 0.74

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.25
                        Fer4_7   7 aCvaaCpvkaiel 19 
                                   +C   Cp+ +++ 
  gi|13541193|ref|NP_110881.1| 430 YCSTLCPSAVMYG 442
                                   7888888888765 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0059
                        Fer4_7  34 dpekClgCga..CvavCPtga 52 
                                   dp+ Cl C+   C+++C +ga
  gi|13541193|ref|NP_110881.1| 562 DPSICLKCETkaCATACEVGA 582
                                   688999998666999999987 PP

  == domain 3  score: 14.2 bits;  conditional E-value: 3e-05
                        Fer4_7   2 CigC..gaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtg 51 
                                   C +C  +aC+ aC v+a +l+ +  ++     ++++ kC+g g+Cv +CP++
  gi|13541193|ref|NP_110881.1| 566 CLKCetKACATACEVGAGDLPGQFIKQ----GYFKSAKCVGSGSCVIACPYN 613
                                   9999555*************9986555....5******************97 PP

  == domain 4  score: 16.2 bits;  conditional E-value: 7.1e-06
                        Fer4_7   1 rCigCgaCvaaCpvkaielde 21 
                                   +C+g g Cv aCp++ i++ +
  gi|13541193|ref|NP_110881.1| 599 KCVGSGSCVIACPYNNIYFYD 619
                                   7****************9864 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   0.0      0.25     4e+02      14      34 ..     430     446 ..     427     464 .. 0.69
   2 !   11.6  10.1   0.00014      0.23       3      56 .]     560     611 ..     558     611 .. 0.84
   3 !   14.0   0.1   2.6e-05     0.042       5      35 ..     596     621 ..     592     640 .. 0.70

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.25
                       Fer4_10  14 kCvkaCPadltsvgakgease 34 
                                    C + CP+     + +g + +
  gi|13541193|ref|NP_110881.1| 430 YCSTLCPS----AVMYGGTLG 446
                                   6******9....444444444 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00014
                       Fer4_10   3 vidddtCirCg..kCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                   v+d++ C++C+  +C +aC    +   +      +++   k+ kC g g+Cv aCP
  gi|13541193|ref|NP_110881.1| 560 VRDPSICLKCEtkACATAC----EVGAGDLPGQFIKQGYFKSAKCVGSGSCVIACP 611
                                   789*******9999*****....24556666677777777***************9 PP

  == domain 3  score: 14.0 bits;  conditional E-value: 2.6e-05
                       Fer4_10   5 dddtCirCgkCvkaCPadltsvgakgeasee 35 
                                    + +C++ g Cv aCP+     ++++++++ 
  gi|13541193|ref|NP_110881.1| 596 KSAKCVGSGSCVIACPY-----NNIYFYDIR 621
                                   5789*************.....444444433 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   2.6   0.00026      0.42       4      23 ..     561     582 ..     560     583 .. 0.89
   2 !   16.5   0.3   3.9e-06    0.0063       4      24 .]     595     615 ..     594     615 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00026
                        Fer4_6   4 idpdkCigCgd..CvrvCPega 23 
                                    dp+ C+ C+   C+++C  ga
  gi|13541193|ref|NP_110881.1| 561 RDPSICLKCETkaCATACEVGA 582
                                   69*******7779*****9987 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 3.9e-06
                        Fer4_6   4 idpdkCigCgdCvrvCPegai 24 
                                   ++  kC+g g Cv++CP++ i
  gi|13541193|ref|NP_110881.1| 595 FKSAKCVGSGSCVIACPYNNI 615
                                   7889*************9865 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0      0.17   2.8e+02       7      26 ..     430     449 ..     429     457 .. 0.79
   2 ?    3.5   3.3     0.051        84      32      49 ..     562     581 ..     540     583 .. 0.74
   3 ?   12.6   6.1     7e-05      0.11       2      49 ..     566     613 ..     565     615 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.17
                        Fer4_9   7 aCveaCpagvvvedaaerka 26 
                                   +C + Cp+ v+ +   ++ +
  gi|13541193|ref|NP_110881.1| 430 YCSTLCPSAVMYGGTLGQAM 449
                                   7*******999887777766 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.051
                        Fer4_9  32 seeaCigCga..CveaCpkg 49 
                                   + + C++C++  C+ aC+ g
  gi|13541193|ref|NP_110881.1| 562 DPSICLKCETkaCATACEVG 581
                                   44569999988899999876 PP

  == domain 3  score: 12.6 bits;  conditional E-value: 7e-05
                        Fer4_9   2 CtgCga..CveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkg 49 
                                   C +C +  C +aC+ g+  +d  ++++++  ++  +C+g g+Cv aCp +
  gi|13541193|ref|NP_110881.1| 566 CLKCETkaCATACEVGA--GDLPGQFIKQGYFKSAKCVGSGSCVIACPYN 613
                                   99995444*99998776..55566666666666679************86 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1       1.5   2.5e+03      14      21 ..     431     438 ..     430     441 .. 0.79
   2 ?   -0.8   6.1      0.98   1.6e+03      12      22 ..     572     582 ..     559     582 .. 0.70
   3 ?   14.9   0.4     1e-05     0.017       6      23 ..     598     615 ..     594     616 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.5
                                   HHHHSTTT CS
                          Fer4  14 CvevCPvg 21 
                                   C   CP  
  gi|13541193|ref|NP_110881.1| 431 CSTLCPSA 438
                                   999***75 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.98
                                   THHHHHSTTTE CS
                          Fer4  12 GaCvevCPvgA 22 
                                   +aC+ +C vgA
  gi|13541193|ref|NP_110881.1| 572 KACATACEVGA 582
                                   48*****9998 PP

  == domain 3  score: 14.9 bits;  conditional E-value: 1e-05
                                   TTSSS-THHHHHSTTTEE CS
                          Fer4   6 ekCigCGaCvevCPvgAI 23 
                                    kC+g G Cv +CP++ I
  gi|13541193|ref|NP_110881.1| 598 AKCVGSGSCVIACPYNNI 615
                                   69*************988 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.3         4   6.5e+03      46      52 ..     430     436 ..     429     439 .. 0.80
   2 ?   14.9   3.9   1.3e-05     0.021       4      54 ..     562     613 ..     560     617 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 4
                       Fer4_21  46 lCssvCP 52 
                                    Cs+ CP
  gi|13541193|ref|NP_110881.1| 430 YCSTLCP 436
                                   5999999 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 1.3e-05
                       Fer4_21   4 dedkCigCg..kCliaCedtshqai.eidaktvlkvvedeCvGCnlCssvCPve 54 
                                   d++ C++C+   C++aCe ++ +   ++ ++ +    + +CvG   C++ CP +
  gi|13541193|ref|NP_110881.1| 562 DPSICLKCEtkACATACEVGAGDLPgQFIKQGY--FKSAKCVGSGSCVIACPYN 613
                                   6678****7336******888776544555555..6789*************64 PP

>> Fer4_5  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   1.3       6.3     1e+04       3      13 ..     182     192 ..     180     192 .. 0.67
   2 ?   -3.6   0.5       6.9   1.1e+04       9      16 ..     211     218 ..     208     224 .. 0.47
   3 ?   14.7   0.6   1.4e-05     0.023      13      30 ..     419     437 ..     407     443 .. 0.73
   4 ?   -2.1   4.1       2.4     4e+03       2      24 ..     517     541 ..     516     561 .. 0.74

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 6.3
                        Fer4_5   3 llllilflaiv 13 
                                   ++++i++++i+
  gi|13541193|ref|NP_110881.1| 182 ISMVIFMIIIF 192
                                   56777777775 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 6.9
                        Fer4_5   9 flaivlvt 16 
                                   +++++++t
  gi|13541193|ref|NP_110881.1| 211 VILFLIFT 218
                                   23333333 PP

  == domain 3  score: 14.7 bits;  conditional E-value: 1.4e-05
                        Fer4_5  13 vlvtllfGR.afCgWiCPf 30 
                                    +++llfGR  +C+ +CP 
  gi|13541193|ref|NP_110881.1| 419 AILALLFGRrSYCSTLCPS 437
                                   4566679999********5 PP

  == domain 4  score: -2.1 bits;  conditional E-value: 2.4
                        Fer4_5   2 allllilflaivlvtll.fGR.afC 24 
                                   +++++++f+ i l+ +   +R  +C
  gi|13541193|ref|NP_110881.1| 517 NVMWYLFFISIPLIGMSpCRRyGWC 541
                                   6789999996666666668888888 PP

>> Fer4_11  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1       1.5   2.4e+03      81      98 ..     426     443 ..     425     445 .. 0.83
   2 ?   13.5   0.7   3.7e-05     0.061       6      62 ..     562     618 ..     559     642 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.5
                       Fer4_11  81 Gllpacvescptgalnfg 98 
                                   G+   c++ cp+ +++ g
  gi|13541193|ref|NP_110881.1| 426 GRRSYCSTLCPSAVMYGG 443
                                   667889*****9999876 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 3.7e-05
                       Fer4_11   6 lpeqCrhCleppCvasapse......aivkdeetGaVlldektkkeevrevveacPykivrkn 62 
                                    p++C +C++++C+++++++       ++k+       +++ ++  +  ++v acPy+ ++  
  gi|13541193|ref|NP_110881.1| 562 DPSICLKCETKACATACEVGagdlpgQFIKQG-----YFKSAKCV-GSGSCVIACPYNNIYFY 618
                                   599****************9433333333333.....67788886.99*********988764 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.5       1.9   3.2e+03      15      21 ..     430     436 ..     429     437 .. 0.84
   2 ?    7.7   2.3    0.0025         4       5      20 ..     561     578 ..     557     580 .. 0.86
   3 ?   13.1   0.2   4.9e-05      0.08       4      22 .]     594     612 ..     592     612 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.9
                        Fer4_2  15 aCvsaCP 21 
                                    C + CP
  gi|13541193|ref|NP_110881.1| 430 YCSTLCP 436
                                   5*999*9 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0025
                        Fer4_2   5 vdtdrCigCg..aCvsaC 20 
                                    d+ +C+ C+  aC +aC
  gi|13541193|ref|NP_110881.1| 561 RDPSICLKCEtkACATAC 578
                                   6999*****667****** PP

  == domain 3  score: 13.1 bits;  conditional E-value: 4.9e-05
                        Fer4_2   4 vvdtdrCigCgaCvsaCPa 22 
                                   ++ +++C+g g+Cv aCP+
  gi|13541193|ref|NP_110881.1| 594 YFKSAKCVGSGSCVIACPY 612
                                   57889*************5 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       1.6   2.7e+03       7      19 ..     430     442 ..     427     462 .. 0.79
   2 ?    0.7   1.5      0.65   1.1e+03       2      16 ..     566     582 ..     565     593 .. 0.77
   3 ?    8.7   0.0    0.0021       3.4       1      27 [.     599     625 ..     599     646 .. 0.72

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 1.6
                       Fer4_16   7 kCaevCPtnaike 19 
                                    C   CP++++ +
  gi|13541193|ref|NP_110881.1| 430 YCSTLCPSAVMYG 442
                                   5999999988765 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.65
                       Fer4_16   2 CgtCgk..CaevCPtna 16 
                                   C +C+   Ca +C ++a
  gi|13541193|ref|NP_110881.1| 566 CLKCETkaCATACEVGA 582
                                   88886445*****9887 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.0021
                       Fer4_16   1 rCgtCgkCaevCPtnaikekkekeiea 27 
                                   +C++ g C+ +CP n i     +++ +
  gi|13541193|ref|NP_110881.1| 599 KCVGSGSCVIACPYNNIYFYDIRSFIS 625
                                   599999*********998775555544 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   3.1      0.62     1e+03       4      17 .]     566     581 ..     563     581 .. 0.79
   2 ?   11.5   0.8   0.00022      0.35       3      17 .]     599     613 ..     597     613 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.62
                        Fer4_4   4 CigCg..sCvaaCPqg 17 
                                   C+ C   +C  aC++g
  gi|13541193|ref|NP_110881.1| 566 CLKCEtkACATACEVG 581
                                   99999546*****975 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00022
                        Fer4_4   3 rCigCgsCvaaCPqg 17 
                                   +C+g gsCv+aCP++
  gi|13541193|ref|NP_110881.1| 599 KCVGSGSCVIACPYN 613
                                   8************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (649 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1014  (0.0565564); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.67u 0.30s 00:00:00.97 Elapsed: 00:00:00.48
# Mc/sec: 4055.47
//
Query:       gi|13541194|ref|NP_110882.1|  [L=224]
Description: enoyl-CoA hydratase [Thermoplasma volcanium GSS1]
Scores for complete 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   50.6   0.1      4e-13   49.2   0.1    1.7  1  ECH_1     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 !   49.2   0.1   2.3e-17     4e-13       4     125 ..      18     135 ..      16     197 .. 0.86

  Alignments for each domain:
  == domain 1  score: 49.2 bits;  conditional E-value: 2.3e-17
                                   TTEEEEEE--CGCTTEE-HHHHHHHHHHHHHHHHSTTECEEEEEEBTSEEEEEB-HHHHHHHHCHHHHHHHCCHHHHHHHH CS
                         ECH_1   4 agvaviklnrPeavNalsaelltEliqalekleddksvravvLtGgdkaFaaGadlkemaeeekakqallkeevlelwtkl 84 
                                   +g+ +i ++   ++  +s ++l+E++ al  +  d++v+ v  tG +k+Fa G+      ++  + ++l+++   + ++ +
  gi|13541194|ref|NP_110882.1|  18 DGIGLIVIKSD-VNGIISRNCLDEMVSALGLASMDPNVKCVAFTGINKVFAKGMKPDGDDGR--SLYELMQS-SSSFLSMV 94 
                                   56777777776.6667899**********************************988887776..56666655.5678899* PP

                                   HHSSSEEEEEE-SEEETHHHHHHHHSSEEEEETTTEEE-GG CS
                         ECH_1  85 ytvpkpviaavnGaaigGGlelalacDiviaadnasfglne 125
                                   y++pkp+ + +nG a   G e+al  D++i a++a+ g n+
  gi|13541194|ref|NP_110882.1|  95 YSLPKPIFSILNGDATNEGYEIALSSDLIISAEDANVGFNQ 135
                                   ***********************************966554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       365  (0.0203581); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.35s 00:00:00.90 Elapsed: 00:00:00.53
# Mc/sec: 1274.37
//
Query:       gi|13541195|ref|NP_110883.1|  [L=209]
Description: DNA-binding protein [Thermoplasma volcanium GSS1]
Scores for complete 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-17   60.7   0.7    1.7e-16   59.8   0.0    1.8  2  HTH_10         HTH DNA binding domain
    1.7e-06   27.5   0.0    1.6e-05   24.3   0.0    2.1  2  Sigma70_r4     Sigma-70, region 4
  ------ inclusion threshold ------
      0.025   14.4   0.6      0.053   13.3   0.6    1.5  1  Rep_3          Initiator Replication protein
       0.05   13.2   0.1       0.41   10.2   0.0    2.2  2  HTH_24         Winged helix-turn-helix DNA-binding
       0.12   12.9   0.2        2.4    8.7   0.0    2.7  3  Ribosomal_L26  Ribosomal proteins L26 eukaryotic, L24P archae


Domain annotation for each model (and alignments):
>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.2         1   3.8e+03      43      51 ..     121     129 ..     119     131 .. 0.81
   2 !   59.8   0.0   4.7e-20   1.7e-16       1      52 [.     149     200 ..     149     201 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1
                        HTH_10  43 hLrkaeskl 51 
                                    L+ka++kl
  gi|13541195|ref|NP_110883.1| 121 ELNKAIRKL 129
                                   589999998 PP

  == domain 2  score: 59.8 bits;  conditional E-value: 4.7e-20
                        HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaeskli 52 
                                   LT+++ e++ +A+++GYFd +R++++k+LAk +GI+ +++s+ +r+a +k++
  gi|13541195|ref|NP_110883.1| 149 LTPREKEIINAAFKLGYFDIDRQISMKDLAKNFGIKTASISDVMRRALKKIV 200
                                   9*************************************************97 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.12   4.3e+02       1      15 [.     125     139 ..     122     145 .. 0.68
   2 !   24.3   0.0   4.4e-09   1.6e-05       4      48 ..     148     199 ..     147     199 .. 0.98

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.12
                                   HHHHS-HHHHHHHHH CS
                    Sigma70_r4   1 aLasLpererevlel 15 
                                   a+++L e++ +v++l
  gi|13541195|ref|NP_110883.1| 125 AIRKLKEEDLNVIVL 139
                                   456666666666666 PP

  == domain 2  score: 24.3 bits;  conditional E-value: 4.4e-09
                                   HS-HHHHHHHHHHH.......TTT--HHHHHHHHTS-HHHHHHHHHHHHHHH CS
                    Sigma70_r4   4 sLpererevlelrf.......geglTleEIgerlgiSrerVrqiekrAlrkL 48 
                                   +L++re+e++   f       ++  +++++++ +gi    ++  ++rAl+k+
  gi|13541195|ref|NP_110883.1| 148 ELTPREKEIINAAFklgyfdiDRQISMKDLAKNFGIKTASISDVMRRALKKI 199
                                   7*************************************************96 PP

>> Rep_3  Initiator Replication protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.6   1.5e-05     0.053       5      72 ..     116     198 ..     112     206 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.5e-05
                                   EEEEGGGHHHHHHS-HHHHHHHHHHHHTS-TT..S---SS..............EEEEHHHHH....HHHT--HHHHHHHH CS
                         Rep_3   5 vvksndlvqaaykltlmelklfvlalskikkk..dedeke..............ykisasdlaeellgvkaegaykrlkea 69 
                                    + +n+l++a  kl++ +l+++vl +s  +k    ++eke               +is++dla+ + g+k+ +  +  + a
  gi|13541195|ref|NP_110883.1| 116 APSRNELNKAIRKLKEEDLNVIVLSISEYNKVelTPREKEiinaafklgyfdidRQISMKDLAKNF-GIKTASISDVMRRA 195
                                   5789***************************96544444489999888886666666899999777.88887755555555 PP

                                   HHH CS
                         Rep_3  70 ler 72 
                                   l++
  gi|13541195|ref|NP_110883.1| 196 LKK 198
                                   554 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.1      0.13   4.5e+02      32      45 ..     120     133 ..     118     134 .. 0.80
   2 ?   10.2   0.0   0.00011      0.41      15      43 ..     169     197 ..     149     198 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.13
                        HTH_24  32 stvnrrlkrLeeeG 45 
                                   + +n+ +++L+ee 
  gi|13541195|ref|NP_110883.1| 120 NELNKAIRKLKEED 133
                                   55799******996 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00011
                        HTH_24  15 nprisqreLAerlglSpstvnrrlkrLee 43 
                                   +  is+++LA+  g+  + ++  ++r  +
  gi|13541195|ref|NP_110883.1| 169 DRQISMKDLAKNFGIKTASISDVMRRALK 197
                                   667*******************9999766 PP

>> Ribosomal_L26  Ribosomal proteins L26 eukaryotic, L24P archaeal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.0   0.00068       2.4      48      81 ..       3      36 ..       1      37 [. 0.86
   2 ?   -2.9   0.0       2.8     1e+04       6      27 ..      52      73 ..      49      74 .. 0.71
   3 ?    0.9   0.0      0.18   6.4e+02      29      47 ..     175     193 ..     172     202 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00068
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Ribosomal_L26 48 ekangttvpvgihpSkvvItklklDkdrkkiLer 81
                                  +++n  +  + ++ S + +t+l lD d+++ +er
  gi|13541195|ref|NP_110883.1|  3 QNKNPVEALIEVERSDCWVTNLVLDRDKDAKIER 36
                                  56666677789999******************98 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.8
                                  xxxxxxxxxxxxxxxxxxxxxx RF
                 Ribosomal_L26  6 kqrKahfnapshirrklmsapL 27
                                   +r+a+fn  ++    +++a+L
  gi|13541195|ref|NP_110883.1| 52 MDRRALFNDLKKYPGIILKANL 73
                                  5788999887777777777766 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.18
                                   xxxxxxxxxxxxxxxxxxx RF
                 Ribosomal_L26  29 keLrekygvrslpirgvtr 47 
                                   k+L +++g+++  i  v r
  gi|13541195|ref|NP_110883.1| 175 KDLAKNFGIKTASISDVMR 193
                                   89**********9997665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       974  (0.0543254); expected 358.6 (0.02)
Passed bias filter:                      760  (0.0423894); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.56u 0.33s 00:00:00.89 Elapsed: 00:00:00.52
# Mc/sec: 1201.58
//
Query:       gi|13541196|ref|NP_110884.1|  [L=172]
Description: hypothetical protein TVN0365 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-22   80.6   0.0    1.9e-22   80.4   0.0    1.0  1  YceI      YceI-like domain


Domain annotation for each model (and alignments):
>> YceI  YceI-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.4   0.0     1e-26   1.9e-22       2     146 .]       9     168 ..       8     168 .. 0.87

  Alignments for each domain:
  == domain 1  score: 80.4 bits;  conditional E-value: 1e-26
                                   EE-CCC-EEEE........-EEEEECTECCEEEE...TTT..EEEEEEEEGGGEESS.HCHHHHHHCTCTT-TTT--EEEE CS
                          YceI   2 tldpahssvtftvkhlgvskvtGrfkkvsgelsv.deddp.essvevtidvasidtgnakrdehlksadffdvakyPtatF 80 
                                   tl++a+s+++ft++hl++skv G+f+++ g +++    d+    +e++id +s++tgn+ rd++l+++++f+ +kyP++  
  gi|13541196|ref|NP_110884.1|   9 TLNKAKSQISFTIDHLVISKVVGKFNTFGGYIETcG--DLcVDYAELDIDSESLETGNSVRDRNLRGKNYFNCKKYPEILC 87 
                                   6899***************************99833..55456799*********************************66 PP

                                   CCCCEE........EEEEEEETTEEEEEEEEEEEE.E..EECCEECEEEEEGGGGTC........TTTC-SEEEEEEEEEE CS
                          YceI  81 vstsve......akvtGdLtikGvtkpvtlpvtvn.g..aaagfsatgtidrtdFGlkr......galvgdeveleielea 146
                                   +  +v+      ++v+ + +ik+++k++++++ +  +  + ++ +  g+i+  dF+lk+       a++g+e ++e  l++
  gi|13541196|ref|NP_110884.1|  88 TVRNVKlknyftNTVEVNVKIKDIEKTLKFDLFLLsYslKNISVRVIGKINTGDFNLKWqspfipSAVIGSEARVEAYLTF 168
                                   55555555999977******************9984432235467*******************9899******9998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       459  (0.025601); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.33s 00:00:00.85 Elapsed: 00:00:00.52
# Mc/sec: 991.27
//
Query:       gi|13541197|ref|NP_110885.1|  [L=242]
Description: Rieske Fe-S protein [Thermoplasma volcanium GSS1]
Scores for complete sequence (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   34.7   0.1    2.2e-08   33.9   0.1    1.4  1  Rieske      Rieske [2Fe-2S] domain
  ------ inclusion threshold ------
      0.082   12.8   0.1       0.19   11.6   0.1    1.6  1  TAT_signal  TAT (twin-arginine translocation) pathway signal 


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 !   33.9   0.1   2.5e-12   2.2e-08      34      87 ..     122     192 ..      92     194 .. 0.85

  Alignments for each domain:
  == domain 1  score: 33.9 bits;  conditional E-value: 2.5e-12
                                   S-EEEEESC-TTTT-BC................GGSEEETT.EEE-TTT--EEE..TTSBEEE-TTHHHEEE CS
                        Rieske  34 gevyAlsdvCtHrgapl................segkidekgvleCpcHgwayd..adGkvikgPaprplat 87 
                                   ++v+A s +C+H+g+ +                 +g+  + g ++C+cHg++yd  +  +v++gP+++pl++
  gi|13541197|ref|NP_110885.1| 122 KSVVASSAICQHLGCVPpeihyyppgtpipstsISGSS-NHGLIHCNCHGSTYDplNGFSVVTGPTTHPLPS 192
                                   6899************999999999*999986433666.788*************6666999******9987 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   2.1e-05      0.19       2      20 ..       5      23 ..       4      28 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.1e-05
                    TAT_signal  2 lSRRdFLKgsAAaaAAaal 20
                                   SRR+F+K+ +    Aa++
  gi|13541197|ref|NP_110885.1|  5 PSRRNFIKAMGIISIAAVA 23
                                  7*******87766655544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       322  (0.0179597); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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 0.34s 00:00:00.86 Elapsed: 00:00:00.52
# Mc/sec: 1404.27
//
Query:       gi|13541198|ref|NP_110886.1|  [L=537]
Description: cytochrome b subunit of the bc complex [Thermoplasma volcanium GSS1]
Scores for complete 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-57  192.8   2.4    4.2e-57  192.8   2.4    3.6  3  Cytochrom_B_N_2  Cytochrome b(N-terminal)/b6/petB
    2.2e-26   92.9   9.6    2.2e-26   92.9   9.6    2.8  4  Cytochrome_B     Cytochrome b/b6/petB
    7.8e-05   22.4  21.4      0.067   12.8   1.5    3.6  3  Ni_hydr_CYTB     Prokaryotic cytochrome b561
    8.7e-05   22.8   0.7    8.7e-05   22.8   0.7    3.7  4  Cytochrom_B_C    Cytochrome b(C-terminal)/b6/petD
    0.00046   20.7   3.3    0.00046   20.7   3.3    3.9  3  DUF4405          Domain of unknown function (DUF4405)


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 ?    2.1   0.5     0.047   1.7e+02      27      77 ..      37      87 ..      29      92 .. 0.84
   2 !  192.8   2.4   1.2e-60   4.2e-57       1     168 [.      93     278 ..      93     279 .. 0.88
   3 ?    1.8   1.0     0.059   2.1e+02     106     165 ..     450     505 ..     445     509 .. 0.57

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.047
               Cytochrom_B_N_2 27 nWiiGvllllltllegflGysLpddllsvtalrvgagiissvPvvgtwlve 77
                                   +++G l ++  l e ++G +L + +   +a + ++ +++svP+   +l +
  gi|13541198|ref|NP_110886.1| 37 WYWTGALTMFAFLYEVVTGIILLFYYQPSNAYTSTETFLHSVPYGEIILTT 87
                                  5799999************************************94444444 PP

  == domain 2  score: 192.8 bits;  conditional E-value: 1.2e-60
               Cytochrom_B_N_2   1 yimiiliyvHmlrvfftGaYkkpRelnWiiGvllllltllegflGysLpddllsvtalrvgagiissvPvvgtwlvellfG 81 
                                   yimi+l+y+H+lr++f+GaYk+pR+ ++++G+llllltl++g++GysL++d+ls++a++vg+gi++++P++g++l+e++fG
  gi|13541198|ref|NP_110886.1|  93 YIMIALVYIHLLRNIFVGAYKRPRRDQFLSGILLLLLTLGVGYFGYSLSGDVLSADATDVGRGIAQGFPYIGNYLMEIIFG 173
                                   79******************************************************************************* PP

               Cytochrom_B_N_2  82 gelpgeallsrlyalHilllpalllalivahlllvekkgqtpsrrkeknv..........vgeplvpvnavkml.llflvl 151
                                   + ++ + l++rl+a+Hi ll++l+++li+ah++l+e+++++p+r +e+n+          +++p++p+n+++m+ l+f+++
  gi|13541198|ref|NP_110886.1| 174 NGTQ-TSLFHRLLAWHI-LLAGLIAVLIAAHFFLAEARTIMPKR-SESNYrvpaidkekpDYKPWYPYNMLYMVeLGFFSV 251
                                   ***8.889*********.************************97.77765334444333355***********98888877 PP

               Cytochrom_B_N_2 152 valli..........alalinPvpllg 168
                                   + ++i          +++l++P+p+l 
  gi|13541198|ref|NP_110886.1| 252 ALIFIlpslaalvpgVPMLFSPFPQLP 278
                                   666666766666666666888887765 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.059
               Cytochrom_B_N_2 106 lalivahlllvekkgqtpsrrkeknvvgeplvpvnavkmlllflvlvallialalinPvp 165
                                    +l+++ l+l++ +g ++s+   ++++      +++v+ +l+f+ +++l+ ++ ++nP  
  gi|13541198|ref|NP_110886.1| 450 TVLVLIFLVLMKVEGYFKST---TPKKPMSKRSYILVSAILGFF-TLFLATIVSTMNPTS 505
                                   56666777777888888775...333333334444555554444.445666777788865 PP

>> Cytochrome_B  Cytochrome b/b6/petB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.9   9.6   6.1e-30   2.2e-26      11     184 ..      35     205 ..      26     210 .. 0.95
   2 ?   -3.6   0.0       2.4   8.4e+03     124     137 ..     312     325 ..     303     339 .. 0.68
   3 ?   -2.4   0.1      0.98   3.5e+03     130     144 ..     408     422 ..     380     436 .. 0.70
   4 ?    0.0   0.8      0.18   6.5e+02      94     149 ..     443     501 ..     429     523 .. 0.68

  Alignments for each domain:
  == domain 1  score: 92.9 bits;  conditional E-value: 6.1e-30
                  Cytochrome_B  11 siiynlGsllllvlvlqiltGvalafyytptvtlaflsvqyilrdvnfGwlirsvhangasllflllylhifrglllgglk 91 
                                    i+y  G+l+++ ++  ++tG++l fyy+p+  +a++s + +l+ v +G +i + h +ga +++ l+y+h+ r +++g++k
  gi|13541198|ref|NP_110886.1|  35 GIWYWTGALTMFAFLYEVVTGIILLFYYQPS--NAYTSTETFLHSVPYGEIILTTHLYGAYIMIALVYIHLLRNIFVGAYK 113
                                   589*************************996..799********************************************* PP

                  Cytochrome_B  92 ktrelvWviGvillllvivtafiGyvLpwdqmsyWavtvitnllsaiPviGstlvellwgsvsvddatLtrffslhfllPf 172
                                   ++r+  +++G++llll++ +++ Gy+L  d +s  a+ v  ++++ +P+iG+ l+e+++g  + + + ++r+ + h+ll  
  gi|13541198|ref|NP_110886.1| 114 RPRRDQFLSGILLLLLTLGVGYFGYSLSGDVLSADATDVGRGIAQGFPYIGNYLMEIIFGNGT-QTSLFHRLLAWHILLAG 193
                                   ***********************************************************9765.77889************ PP

                  Cytochrome_B 173 lllillllhlll 184
                                   l+++l+  h++l
  gi|13541198|ref|NP_110886.1| 194 LIAVLIAAHFFL 205
                                   *********986 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 2.4
                  Cytochrome_B 124 syWavtvitnllsa 137
                                    +Wa++++++l+ a
  gi|13541198|ref|NP_110886.1| 312 PFWATVLFAGLPLA 325
                                   48888888887655 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 0.98
                  Cytochrome_B 130 vitnllsaiPviGst 144
                                   v  +++ ++PviG++
  gi|13541198|ref|NP_110886.1| 408 VHIGVIGTVPVIGFF 422
                                   444566677777765 PP

  == domain 4  score: 0.0 bits;  conditional E-value: 0.18
                  Cytochrome_B  94 relvWviGvillllvivtafiGy...vLpwdqmsyWavtvitnllsaiPviGstlvell 149
                                      +++  v++l++++ + + Gy   + p + ms  +  +++++l  + ++  t+v+ +
  gi|13541198|ref|NP_110886.1| 443 EASIFMATVLVLIFLVLMKVEGYfksTTPKKPMSKRSYILVSAILGFFTLFLATIVSTM 501
                                   55667777888888888888888332345666777777777777766666666666554 PP

>> Ni_hydr_CYTB  Prokaryotic cytochrome b561
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   1.5   1.9e-05     0.067      91     171 ..      20     112 ..       3     123 .. 0.72
   2 !   12.5   3.8   2.3e-05     0.083      41     109 ..     165     256 ..     120     329 .. 0.69
   3 !    8.0   1.3   0.00055         2      43     115 ..     440     522 ..     378     528 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.9e-05
                                   -----------TT.......THHHHHHHHHHHHHHHHHHHT........HHHHHHHH...HTS-THHHHHHH.HHHHHHHH CS
                  Ni_hydr_CYTB  91 kpeagknnplqkl.......vhlllyvllvvliltGlllsf........aatagfplllddkggaqlarelHellaaalla 156
                                   +p +++ +   +         ++l +++++  ++tG++l f        +     + +l +  + +++ + H + a++++a
  gi|13541198|ref|NP_110886.1|  20 EPLPRRVPDYMRKaggiwywTGALTMFAFLYEVVTGIILLFyyqpsnayT---STETFLHSVPYGEIILTTHLYGAYIMIA 97 
                                   444444444444455666667778888888899******99998885443...4444467************77788888* PP

                                   HHHHHHHHHHHHHH- CS
                  Ni_hydr_CYTB 157 fvvlHiaaallhgpv 171
                                   +v +H++  ++ g+ 
  gi|13541198|ref|NP_110886.1|  98 LVYIHLLRNIFVGAY 112
                                   *****9877776655 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 2.3e-05
                                   -..................HHHHHHHHHHHHHHHHHHHHHHH------------STTTSSSSS----------------TT CS
                  Ni_hydr_CYTB  41 k..................aralHklaGlvllalllfrllwlkkakkpspriifrqikrdltlllrgrkpeagknnplqkl 103
                                                      ++a+H+l++ ++++l+++ ++++    + ++   +r   ++ +  + ++kp+++++ p ++l
  gi|13541198|ref|NP_110886.1| 165 NylmeiifgngtqtslfhrLLAWHILLAGLIAVLIAAHFFLA----EARTIMPKRSESNYRVPAIDKEKPDYKPWYPYNML 241
                                   03334444444444444566999***9999999999999999....66666666777778888999999999999999999 PP

                                   .........THHHHH CS
                  Ni_hydr_CYTB 104 .........vhllly 109
                                            v+l+++
  gi|13541198|ref|NP_110886.1| 242 ymvelgffsVALIFI 256
                                   565544444333333 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.00055
                                   HHHHHHHHHHHHHHHHHHHHHH..........------------STTTSSSSS----------------TTTHHHHHHHHH CS
                  Ni_hydr_CYTB  43 ralHklaGlvllalllfrllwl..........kkakkpspriifrqikrdltlllrgrkpeagknnplqklvhlllyvllv 113
                                   + l  ++ ++ +++l+f +l+           kk++++++ i  ++i   +tl+l +    + ++++  ++++++ + +++
  gi|13541198|ref|NP_110886.1| 440 IYLEASIFMATVLVLIFLVLMKvegyfksttpKKPMSKRSYILVSAILGFFTLFLATIVSTMNPTSITDEAFYAMGIGFIF 520
                                   44444443444444444444446899*****99**************************************5444444444 PP

                                   HH CS
                  Ni_hydr_CYTB 114 vl 115
                                   ++
  gi|13541198|ref|NP_110886.1| 521 IA 522
                                   33 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 ?   -2.9   2.5       2.3   8.4e+03      15      38 ..      37      60 ..      32     135 .. 0.75
   2 ?   -3.6   0.2         4   1.4e+04      38      50 ..     248     260 ..     235     262 .. 0.66
   3 !   22.8   0.7   2.4e-08   8.7e-05       4      96 ..     282     378 ..     279     384 .. 0.80
   4 ?    3.0   0.5     0.034   1.2e+02      36      84 ..     447     497 ..     439     519 .. 0.59

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2.3
                                  GGGHHHHHHHHCSSSHHHHHHHHH CS
                 Cytochrom_B_C 15 WYflpfYaiLraipakllGvvamg 38
                                  WY++ + +++  + + + G+++++
  gi|13541198|ref|NP_110886.1| 37 WYWTGALTMFAFLYEVVTGIILLF 60
                                  888877777777777777776665 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 4
                                   HHHHHGGGCHHHH CS
                 Cytochrom_B_C  38 gaaivilfllpwl 50 
                                   +++++++f+lp l
  gi|13541198|ref|NP_110886.1| 248 FFSVALIFILPSL 260
                                   5667777777765 PP

  == domain 3  score: 22.8 bits;  conditional E-value: 2.4e-08
                                   TTC--TT----GGGHHHHHHHHCSSSHHHH.....HHHHHHHHHGGGCHHHH---SSSSSTT-.HHHHHHHHHHHHHHHHH CS
                 Cytochrom_B_C   4 plktPahIaPeWYflpfYaiLraipakllG.....vvamgaaivilfllpwldrskvksiryrkplakvllallvvsfvvL 79 
                                   p   +   +P W++l++Y+ L  + a+ +G     v+  g  ++ l+llp++d+s   +i+ r p+++ l+++ ++ ++ L
  gi|13541198|ref|NP_110886.1| 282 PAAAALPAYPPWFLLFMYKELDFTFAQSMGpfwatVLFAGLPLAYLILLPYIDTSISLKISER-PIFNGLAIVGILYLIGL 361
                                   555556668*************9965555443334666688899*******************.***************** PP

                                   HHHHTS-SSCCHHHHHH CS
                 Cytochrom_B_C  80 gylGvqppeevavllsq 96 
                                    +lG+  p +++ +l  
  gi|13541198|ref|NP_110886.1| 362 SVLGALTPGQPIPTLDA 378
                                   *****888777666555 PP

  == domain 4  score: 3.0 bits;  conditional E-value: 0.034
                                   HHHHHHHGGGCHHH.H---SSSSSTT-.HHHHHHHHH..HHHHHHHHHHHHT CS
                 Cytochrom_B_C  36 amgaaivilfllpw.ldrskvksiryrkplakvllal..lvvsfvvLgylGv 84 
                                    m+  +++l++l +   +   ks++ +kp++k  ++l   ++ f++L ++ +
  gi|13541198|ref|NP_110886.1| 447 FMA-TVLVLIFLVLmKVEGYFKSTTPKKPMSKRSYILvsAILGFFTLFLATI 497
                                   444.444555554404456778888888888876655224555555544443 PP

>> DUF4405  Domain of unknown function (DUF4405)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   3.3   1.3e-07   0.00046       1      65 [.      39     106 ..      39     107 .. 0.87
   2 ?   -0.2   7.5      0.42   1.5e+03      12      64 ..     137     205 ..     120     206 .. 0.62
   3 ?   -5.8   2.2         5   1.8e+04       5      13 ..     451     459 ..     448     460 .. 0.53

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 1.3e-07
                       DUF4405   1 iidlllllsflvlaiSGillsfavlpsgrgaywa.flgl..skhqwrdiHeilgllflilvvlHlglh 65 
                                   ++ +l+ ++fl  +++Gi+l f + ps  +  +  fl+     + +   H + ++++++lv +Hl+ +
  gi|13541198|ref|NP_110886.1|  39 WTGALTMFAFLYEVVTGIILLFYYQPSNAYTSTEtFLHSvpYGEIILTTHLYGAYIMIALVYIHLLRN 106
                                   56788999***************9997666655598887888999*******************9755 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.42
                       DUF4405  12 vlaiSGillsfavlpsgrgaywa.....................flglskhqwrdiHeilgllflilvvlHlgl 64 
                                   +  +SG +ls+ +   grg +++                     f     h + ++H++l+ l  +l++ H++l
  gi|13541198|ref|NP_110886.1| 137 GYSLSGDVLSADATDVGRGIAQGfpyignylmeiifgngtqtslF-----HRLLAWHILLAGLIAVLIAAHFFL 205
                                   555666666666555555555556666666555433333333333.....566788888888999999999876 PP

  == domain 3  score: -5.8 bits;  conditional E-value: 5
                       DUF4405   5 llllsflvl 13 
                                   +l+l flvl
  gi|13541198|ref|NP_110886.1| 451 VLVLIFLVL 459
                                   455555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (537 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       965  (0.0538234); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.77u 0.35s 00:00:01.12 Elapsed: 00:00:00.51
# Mc/sec: 3195.95
//
Query:       gi|13541199|ref|NP_110887.1|  [L=293]
Description: carboxyphosphonoenolpyruvate phosphonomutase [Thermoplasma volcanium GSS1]
Scores for complete 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-52  176.6   1.8    7.2e-52  176.2   1.8    1.1  1  PEP_mutase  Phosphoenolpyruvate phosphomutase
    1.1e-16   60.4   0.9    1.4e-16   60.1   0.9    1.1  1  ICL         Isocitrate lyase family
  ------ inclusion threshold ------
      0.026   14.0   1.0      0.073   12.5   0.9    1.8  2  ComA        (2R)-phospho-3-sulfolactate synthase (ComA)


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 !  176.2   1.8   1.2e-55   7.2e-52       1     238 [.      12     253 ..      12     254 .. 0.93

  Alignments for each domain:
  == domain 1  score: 176.2 bits;  conditional E-value: 1.2e-55
                    PEP_mutase   1 lraLhakgeplvlpnawDalsakiveeagfkalatsSlavaaslGvpDgeelpleellaavraiaevvslPlivDledGyg 81 
                                   lr+L ++ +++v+p +  +++a i+e+ gfka  +s+ +va ++G+pD + ++++e+ + v++i++  +lPlivD+++G+g
  gi|13541199|ref|NP_110887.1|  12 LRRLLRE-DIVVAPGVVGGIGALIAEKRGFKAAYLSGSQVAGMMGLPDLSVTTMNEVAEEVQRITAISRLPLIVDVDTGFG 91 
                                   5777777.89*********************************************************************** PP

                    PEP_mutase  82 espeevaetvrrliaaGvvgvniEDk....kknd.aerqlldieefaekiaaaraaaeeagfvinARtdalllsagaglee 157
                                   e + +v +tvr ++a G++++++ED+    k++  ++++++d +e+ +ki+aa++a ++++f+i+ARtda    a +gle+
  gi|13541199|ref|NP_110887.1|  92 E-VVNVIRTVRVMEASGASAIHMEDQelpkKCGHlNGKKVIDRDEMIRKISAAASARKNEDFMIIARTDAR---AVNGLED 168
                                   9.99**********************998655566889999*****************************3...6789*** PP

                    PEP_mutase 158 aieRaraYaeAGAdgvfvpglqkdaeiaelvaavdvplnvvp.lkgt...lsvaelaelGvarislgnhllraalaalrea 234
                                   ai+Ra+aY+eAGAd++f   l++++e +++ ++v++ l + + ++g+   lsv++l+ +G +++++   ++r +l+a++ +
  gi|13541199|ref|NP_110887.1| 169 AIDRANAYLEAGADAIFTEALESKEEFEKMRKQVKGYLLANMtEDGKsplLSVDDLRSIGYNIVIFPLTAFRTMLKAIDSI 249
                                   **********************************9887777734333577***************************9988 PP

                    PEP_mutase 235 aeei 238
                                    ++i
  gi|13541199|ref|NP_110887.1| 250 YADI 253
                                   7765 PP

>> ICL  Isocitrate lyase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.1   0.9   2.4e-20   1.4e-16     137     255 ..      68     182 ..      60     214 .. 0.83

  Alignments for each domain:
  == domain 1  score: 60.1 bits;  conditional E-value: 2.4e-20
                                   HHHHTTS--------EEEE-TT-SSSHHHHHHHHHHHHHTT-SEEEE-SB-TT---------EEE--HHHHHHHHHHHHHH CS
                           ICL 137 keereklanvdylrpiiadadtGhGGltavvkltklfierGaaGihiedqasgtkkcGhmaGkvlvpiqehinrlvairaq 217
                                    ee ++++ +  l p+i d dtG+G +  v++ ++++   Ga+ ih+edq    kkcGh+ Gk ++  +e i ++ a+ a+
  gi|13541199|ref|NP_110887.1|  68 AEEVQRITAISRL-PLIVDVDTGFGEVVNVIRTVRVMEASGASAIHMEDQE-LPKKCGHLNGKKVIDRDEMIRKISAA-AS 145
                                   4556666666665.99**********************************6.679***************99876665.44 PP

                                   HHHTT---EEEEE--GGGEEEES-TT-GGGGGGEEEE- CS
                           ICL 218 adilgsdllvvartdseaatlitstidtrdhafilGat 255
                                   a   + d +++artd+ a + ++ +id+ + ++  Ga 
  gi|13541199|ref|NP_110887.1| 146 AR-KNEDFMIIARTDARAVNGLEDAIDRANAYLEAGAD 182
                                   43.5789********************99999888875 PP

>> ComA  (2R)-phospho-3-sulfolactate synthase (ComA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.1     0.068   4.1e+02     146     191 ..      95     141 ..      55     153 .. 0.76
   2 ?   12.5   0.9   1.2e-05     0.073     134     185 ..     157     201 ..      83     215 .. 0.71

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.068
                                   HHHHHHHHHHHHTECEEEE--TTT--SSTTB-TTS-B-HH.HHHHHH CS
                          ComA 146 klieeakrdleaGaekviiEaresGitegvydekgevrtd.vvekii 191
                                   ++i++++   + Ga+++ +E +e  ++ g ++ k+ ++ d +++ki 
  gi|13541199|ref|NP_110887.1|  95 NVIRTVRVMEASGASAIHMEDQELPKKCGHLNGKKVIDRDeMIRKIS 141
                                   56777777778899999999998877777777776664441455554 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 1.2e-05
                                   SSHHHHTT--CCHHHHHHHHHHHHTECEEEE--TTT--SSTTB-TTS-B-HH CS
                          ComA 134 kdgelesesdveklieeakrdleaGaekviiEaresGitegvydekgevrtd 185
                                   +  + ++   +e+ i++a++ leaGa+++ +Ea es    ++    +++r++
  gi|13541199|ref|NP_110887.1| 157 RT-DARAVNGLEDAIDRANAYLEAGADAIFTEALESKE--EF----EKMRKQ 201
                                   22.346668999**********************9755..55....333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       648  (0.0361426); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.33s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 1786.85
//
Query:       gi|13541200|ref|NP_110888.1|  [L=443]
Description: hypothetical protein TVN0369 [Thermoplasma volcanium GSS1]
Scores for complete 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-105  352.5   0.0   3.1e-105  352.3   0.0    1.0  1  MmgE_PrpD  MmgE/PrpD family
  ------ inclusion threshold ------
      0.036   14.1   0.0       0.24   11.5   0.0    2.2  2  Band_7_C   C-terminal region of band_7


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 !  352.3   0.0  3.4e-109  3.1e-105       3     420 ..       7     413 ..       5     430 .. 0.97

  Alignments for each domain:
  == domain 1  score: 352.3 bits;  conditional E-value: 3.4e-109
                                   HHHHHHHH-----H..HHHHHHHHHHHHHHHHHHHHTT-HHHHTT-SSSTT-B-TT-EE-TTSS-EE-HHHHHHHHHHHHH CS
                     MmgE_PrpD   3 qlaefvaelryddlpeevverakrlilDtlGvalaglrepavkkaleavkgtggpggatvigtgerlspvkAAfvnGaaih 83 
                                    l +++ +++++d+ ++  e++k++i D++  a+ ++++p++k++l+ + +  g+ ++t++++++++  ++A ++nG++++
  gi|13541200|ref|NP_110888.1|   7 VLEDYANSTSFSDINDDEKEAIKMRIADSFITAFTAISSPPTKILLNTIGDVRGQMDSTIYFSKRKVFTPYAVMLNGCMTR 87 
                                   5789***************************************************************************** PP

                                   CTS-S-BEESSSEE-GGGGHHHHHHHHHHHHHHBHHHHHHHHHHHHHHHHHCCC--SCCCT.B-THHHHHHHHHHHHHHHT CS
                     MmgE_PrpD  84 alDfdDthlaaelhhpsdvlpaalAvAealgasgkdlLtAivvGyEvqgrlglalsfnhygfhdtvtlgtfgaaaaaakLl 164
                                   ++D++Dt+l++e  hpsd++p+++ +Ae+ + +gkd+++A+ v+y++ + +++a+s +++g +d+v + ++++ aa a++l
  gi|13541200|ref|NP_110888.1|  88 YMDYNDTYLSKEALHPSDNIPPLITMAETKELEGKDVIRAVKVAYDIVCSFADAVSIRDRG-WDHVNYDSISSSAALASML 167
                                   *************************************************************.******************* PP

                                   T--HHHHHHHHHHHHCT-B-BSGGGSTTT--CHHCHHHHHHHHHHHHHHHHHTT---TTTTT-TTTSHHHHHSTT-----S CS
                     MmgE_PrpD 165 gLdaeqianAlgiaatqaaglrqyrhagtkskklwaaGdAarnGveaallAkrGftGpsdilegewGflavlsggkdlele 245
                                   +L+ e+++nA+++ +  + ++rq+r+++ +++k +  +  +++   a+l A++G+tGpsdi+ege+Gf +++sg+ +le +
  gi|13541200|ref|NP_110888.1| 168 ELNGEKFENAVSLSIINNISMRQTRAGKLSMWKGCTVAYETMSSTLAVLNASAGLTGPSDIFEGEMGFKKQVSGEFQLEIK 248
                                   ***************************************************************************666666 PP

                                   .S-SS...SHHHHC-B---SSS-CCCHHHHHHHHHHHHHHCCTCCCEEEEEEEE-HHHHHHC---S...---SHHHHCT-C CS
                     MmgE_PrpD 246 vkplgegesweienvlfKpypaerhthaaidaalklraelklkpddIesieirtseaalriigkkg...ppenradadhSl 323
                                             +++++++K yp+e+h+ +a++aa +l ++l+    +I++i+++t+++a+ ii k++   +p+n+++adhS+
  gi|13541200|ref|NP_110888.1| 249 ---------PHVMKTMIKNYPVEYHAMSAAQAAANLKDKLDG---NIKKIDVETFKVAHTIIIKDPeklRPQNKETADHSM 317
                                   .........3799****************************9...*******************999************** PP

                                   CHHHHHHHHCS---CCCCSCCCCTSCHHCCHHCCEEEEE-HHHHHHHTTT---EEEEETTS-B---EEESS-TTSGGHHHH CS
                     MmgE_PrpD 324 qyvvAvalldgrvtledfederladpevqaLrekvevvedpeltadypekrsivvvvlkdggrtleerveypkGhprnpls 404
                                   +y++A  l +g+  +++++d+ l+d+++ + ++k+++++ ++++++ype  + v++ ++d++++ ee+++ pkGh+r p +
  gi|13541200|ref|NP_110888.1| 318 PYIIAYTLNYGEPDVHSYDDKYLNDKKILDTIDKIHFKVTERFDKMYPEYLP-VKISVTDQTSVKEEEIDVPKGHFRDPYT 397
                                   ****************************************************.**************************** PP

                                   HHHHHHHHHHHHHCCS CS
                     MmgE_PrpD 405 reeleeKfrrlaegvl 420
                                   +++le+K rr+  + +
  gi|13541200|ref|NP_110888.1| 398 WKDLEAKARRVNPNLV 413
                                   *********9876655 PP

>> Band_7_C  C-terminal region of band_7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   2.7e-05      0.24      11      40 ..      23      52 ..      18      65 .. 0.78
   2 ?   -0.9   0.0       0.2   1.8e+03       8      20 ..     170     182 ..     167     184 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.7e-05
                      Band_7_C 11 ggqeAvsLrvAeqYveaFgkLAkesntvil 40
                                  + +eA+++r+A  +++aF  +    + ++l
  gi|13541200|ref|NP_110888.1| 23 DEKEAIKMRIADSFITAFTAISSPPTKILL 52
                                  5689***************99877766666 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.2
                      Band_7_C   8 kkpggqeAvsLrv 20 
                                   + +++++AvsL++
  gi|13541200|ref|NP_110888.1| 170 NGEKFENAVSLSI 182
                                   567899*****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (443 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       514  (0.0286686); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.34s 00:00:00.94 Elapsed: 00:00:00.52
# Mc/sec: 2566.57
//
Query:       gi|13541201|ref|NP_110889.1|  [L=272]
Description: Sec-independent protein secretion pathway component (TatC-related) [Thermoplasma volcanium GSS1]
Scores for complete 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-45  155.1  20.5    2.7e-45  154.7  20.5    1.1  1  TatC       Sec-independent protein translocase protein (TatC)
  ------ inclusion threshold ------
      0.026   14.2   2.2      0.026   14.2   2.2    2.8  3  PDR_assoc  Plant PDR ABC transporter associated


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 !  154.7  20.5     3e-49   2.7e-45       3     207 .]      13     243 ..      11     243 .. 0.89

  Alignments for each domain:
  == domain 1  score: 154.7 bits;  conditional E-value: 3e-49
                                   HHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHCCHHHHC..C....................TTS-EE--SSS-HHHHHHH CS
                          TatC   3 LeeLrkrlirallavaiafiitfvfaeeliafllepleea.e....................eevelivlspleafllklk 62 
                                   ++eLr r+ ral++++++f+i+f+f  e+i++l + +    +                    ++veli+++p++a+++ + 
  gi|13541201|ref|NP_110889.1|  13 IDELRLRVTRALIGFFVFFLIFFTFRFEYINMLGRKIPMLyPdpysnvgaqflvlaeshvlpKKVELIAVKPTDAMVADIY 93 
                                   79*********************998887775554433222244444455666666666665669**************** PP

                                   HHHHHHHHHSHHHHHHHHHCCCTTTTS---STTTHHHHHHHHHHHHHHHHHHHHTHHHHHHHHHT....TTTSSTTEEHHH CS
                          TatC  63 vslvaglvlasPvilyqlwafvapgLykherrlvlvfliaslllfllGaafayfvvlplvlkfll....seevepllslse 139
                                     +++++++++P+i+ ++ +fv pgL+k+e  +++ + i + +lf++G +f++++++p ++k+++    s ++ p++s+s+
  gi|13541201|ref|NP_110889.1|  94 SVMFLAILFSMPIIVTEIGRFVGPGLRKQEISAIRSLGIPAAVLFAIGSIFGFWFIFPDLFKIFFyfdsSVGAYPTMSISS 174
                                   **************************************************************88878665555889***** PP

                                   HHHHHHHHHHHHHHHTTHHHHHHHHHHTTSS-HHHHHTTHHHHHHHHHHHHHHH-S..SHHHHHHHHHH CS
                          TatC 140 ylsfvlllllafgiaFelPlvlvllarlglvsaetlrkkrryaivvilvvaavltP.pdvisqlllavP 207
                                   + sf++  ++ fg++Fe+P+++v l+rl+lv+a+++ +++rya+v++l+++ v++P    +s++++a+P
  gi|13541201|ref|NP_110889.1| 175 FTSFLFVYIISFGLSFEMPVIMVALTRLKLVQANFWLRNWRYAVVGSLIFGLVFSPgVLGVSMMIMALP 243
                                   *******************************************************************99 PP

>> PDR_assoc  Plant PDR ABC transporter associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   2.2   2.9e-06     0.026      36      61 ..      23      48 ..      21      52 .. 0.92
   2 ?    0.1   2.2     0.074   6.6e+02      33      54 ..     139     160 ..     137     167 .. 0.82
   3 ?   -3.9   0.2       1.3   1.2e+04      37      45 ..     179     187 ..     177     193 .. 0.52

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.9e-06
                     PDR_assoc 36 allgftiLFNilftlaLtYLnplgks 61
                                  al+gf ++F i+ft+  +Y+n lg++
  gi|13541201|ref|NP_110889.1| 23 ALIGFFVFFLIFFTFRFEYINMLGRK 48
                                  9*********************9976 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.074
                     PDR_assoc  33 gvgallgftiLFNilftlaLtY 54 
                                   ++g ++gf ++F  lf ++  +
  gi|13541201|ref|NP_110889.1| 139 AIGSIFGFWFIFPDLFKIFFYF 160
                                   68999*******9999887665 PP

  == domain 3  score: -3.9 bits;  conditional E-value: 1.3
                     PDR_assoc  37 llgftiLFN 45 
                                   l+ ++i F 
  gi|13541201|ref|NP_110889.1| 179 LFVYIISFG 187
                                   445554443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       651  (0.0363099); 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:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 1694.83
//
Query:       gi|13541202|ref|NP_110890.1|  [L=100]
Description: Sec-independent protein secretion pathway component [Thermoplasma volcanium GSS1]
Scores for complete sequence (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   53.0   0.4    9.2e-14   50.5   0.1    1.9  2  MttA_Hcf106   mttA/Hcf106 family
     0.0062   17.0   0.0       0.19   12.2   0.0    2.1  2  PhoU          PhoU domain
  ------ inclusion threshold ------
      0.026   14.3   0.3      0.049   13.4   0.3    1.4  1  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b
      0.085   13.5   0.3       0.57   10.9   0.1    2.2  3  DUF5395       Family of unknown function (DUF5395)
       0.12   12.1   0.1        2.2    8.1   0.0    2.1  2  PHP_C         PHP-associated


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 !   50.5   0.1   2.6e-17   9.2e-14       2      49 ..       4      52 ..       4      65 .. 0.90
   2 ?    0.9   0.0      0.08   2.9e+02      30      43 ..      82      95 ..      71     100 .] 0.86

  Alignments for each domain:
  == domain 1  score: 50.5 bits;  conditional E-value: 2.6e-17
                                  -HHHHHHHHHHHHHHS-.TTTHHHHHHHHHHHHHHHHHHHHHHHH---X CS
                   MttA_Hcf106  2 gapelliIlvValllFG.pkkLPEvaraLGktLreFkkavkeleeenek 49
                                  +a e+li+ vV+l+lFG +kk PE+ar+ G++  eFk  + e e+e +k
  gi|13541202|ref|NP_110890.1|  4 SAIEWLIVIVVILVLFGsAKKVPELARNVGRATGEFKRGQMEIEQELRK 52
                                  688**************779***********************999665 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.08
                                  HHHHHHHHHHHHHH CS
                   MttA_Hcf106 30 GktLreFkkavkel 43
                                  Gk++ e k +++e 
  gi|13541202|ref|NP_110890.1| 82 GKSIDELKAEIQEK 95
                                  89999999999986 PP

>> PhoU  PhoU domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.0   5.3e-05      0.19      21      73 ..      23      74 ..      14      76 .. 0.88
   2 ?    3.0   0.0     0.041   1.5e+02      35      50 ..      83      98 ..      77     100 .] 0.82

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 5.3e-05
                                  CT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SHHHHHHHHHHHHHH CS
                          PhoU 21 ekdtelarevierddeidrlekeiersllealakrqplaedlrellsllriar 73
                                  +k  elar v +   e  r ++eie + l++++++++ a+   + ++++++a+
  gi|13541202|ref|NP_110890.1| 23 KKVPELARNVGRATGEFKRGQMEIEQE-LRKAMNSNNTAQTASQGVDYISVAK 74
                                  5678***********************.777778888888899********98 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.041
                                  HHHHHHHHHHHHHHHH CS
                          PhoU 35 deidrlekeierslle 50
                                  ++id+l  ei+++l +
  gi|13541202|ref|NP_110890.1| 83 KSIDELKAEIQEKLKN 98
                                  78**********9755 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 ?   13.4   0.3   1.4e-05     0.049      92     144 ..      48      97 ..      40     100 .] 0.59

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.4e-05
                                   HHHHTCCTTTTSBB.BS----HHHHHHHTTSEEE..EESSH.HHHHHHHHHHHHC CS
                  TPP_enzyme_C  92 qepfggkrksgpagkdlkpvdfaklaealGakga..rvekadveeleealkeale 144
                                   qe + + ++ ++a+  ++ vd+  +a+ +G++    +     ++el++ ++e l+
  gi|13541202|ref|NP_110890.1|  48 QELRKAMNSNNTAQTASQGVDYISVAKTMGIETEgkS-----IDELKAEIQEKLK 97 
                                   444444444444444699**************55434.....4555555555443 PP

>> DUF5395  Family of unknown function (DUF5395)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.44   1.6e+03      23      37 ..      21      35 ..       7      58 .. 0.64
   2 ?   -0.1   0.0      0.43   1.6e+03      33      47 ..      45      59 ..      31      71 .. 0.64
   3 ?   10.9   0.1   0.00016      0.57      14      41 ..      72      99 ..      65     100 .] 0.91

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.44
                       DUF5395 23 kgktleeLDenlake 37
                                  ++k++ eL +n+ ++
  gi|13541202|ref|NP_110890.1| 21 SAKKVPELARNVGRA 35
                                  566666666666554 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.43
                       DUF5395 33 nlakelkkrgdfkgk 47
                                  ++++el+k+ + +++
  gi|13541202|ref|NP_110890.1| 45 EIEQELRKAMNSNNT 59
                                  566666666443333 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 0.00016
                       DUF5395 14 iaeneelvvkgktleeLDenlakelkkr 41
                                  +a++ +++ +gk+++eL ++++++lk++
  gi|13541202|ref|NP_110890.1| 72 VAKTMGIETEGKSIDELKAEIQEKLKNA 99
                                  7889999*******************97 PP

>> PHP_C  PHP-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.0    0.0006       2.2      27      55 ..      29      58 ..      28      59 .. 0.78
   2 ?    2.1   0.0     0.047   1.7e+02      35      53 ..      75      94 ..      67      95 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0006
                         PHP_C 27 leeVGrayTef...eepiatpdelleairegr 55
                                  +++VGra  ef   +++i+  +el +a+ +  
  gi|13541202|ref|NP_110890.1| 29 ARNVGRATGEFkrgQMEIE--QELRKAMNSNN 58
                                  78*********65555555..99999998765 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.047
                         PHP_C 35 Tef.eepiatpdelleaire 53
                                  T+  e++ +++del ++i e
  gi|13541202|ref|NP_110890.1| 75 TMGiETEGKSIDELKAEIQE 94
                                  55458888999******987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1504  (0.0838864); expected 358.6 (0.02)
Passed bias filter:                      830  (0.0462937); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.61u 0.35s 00:00:00.96 Elapsed: 00:00:00.58
# Mc/sec: 521.71
//
Query:       gi|13541203|ref|NP_110891.1|  [L=279]
Description: Rieske Fe-S protein [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.2e-06   27.0   0.0    6.1e-06   26.1   0.0    1.5  1  Rieske      Rieske [2Fe-2S] domain
  ------ inclusion threshold ------
       0.02   14.8   0.6      0.033   14.0   0.6    1.3  1  TAT_signal  TAT (twin-arginine translocation) pathway signal 


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 !   26.1   0.0   6.9e-10   6.1e-06      34      74 ..     122     183 ..      87     203 .. 0.79

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 6.9e-10
                                   S-EEEEESC-TTTT-BC....................GGSEEE....TT.EEE-TTT--EEE.TTS CS
                        Rieske  34 gevyAlsdvCtHrgapl....................segkid....ekgvleCpcHgwayd.adG 74 
                                   +++ A+s++C+H+g+++                    +    +    e g l C cHg++yd  +G
  gi|13541203|ref|NP_110891.1| 122 DSITAYSGICQHLGCTVplldyhpgnsipfeaqligyT----KknwpEYGLLYCKCHGSQYDpIRG 183
                                   5789************9999*********999655442....333448889***********7555 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.6   3.7e-06     0.033       4      22 ..      15      33 ..      15      36 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.7e-06
                    TAT_signal  4 RRdFLKgsAAaaAAaalgg 22
                                  RR+FLKg+A+    +alg+
  gi|13541203|ref|NP_110891.1| 15 RRSFLKGAAVSLFSLALGS 33
                                  9********9877777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       223  (0.0124379); expected 358.6 (0.02)
Passed bias filter:                      212  (0.0118244); 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: 0.54u 0.35s 00:00:00.89 Elapsed: 00:00:00.53
# Mc/sec: 1593.23
//
Query:       gi|13541204|ref|NP_110892.1|  [L=391]
Description: cytochrome b subunit of the bc complex [Thermoplasma volcanium GSS1]
Scores for complete 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-49  166.8  20.8    6.9e-47  159.6  16.2    2.5  2  Cytochrom_B_N_2  Cytochrome b(N-terminal)/b6/petB
    7.2e-17   61.8  21.4    7.2e-17   61.8  21.4    2.0  3  Cytochrome_B     Cytochrome b/b6/petB
    0.00024   21.3   2.1    0.00024   21.3   2.1    3.4  3  Cytochrom_B_C    Cytochrome b(C-terminal)/b6/petD


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 !    9.0   0.1   0.00022       1.3      22      73 ..      33      84 ..      23      91 .. 0.88
   2 !  159.6  16.2   1.2e-50   6.9e-47       1     167 [.      94     265 ..      94     267 .. 0.97

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00022
               Cytochrom_B_N_2 22 kpRelnWiiGvllllltllegflGysLpddllsvtalrvgagiissvPvvgt 73
                                  k  +l +++G +l+  +   ++ G +L + + s+   + + +iissvP+   
  gi|13541204|ref|NP_110892.1| 33 KEFRLDYWTGSFLMAAVAYLAVSGMLLFYYYQSGHPFSSTISIISSVPFGYA 84
                                  555799******************************************9444 PP

  == domain 2  score: 159.6 bits;  conditional E-value: 1.2e-50
               Cytochrom_B_N_2   1 yimiiliyvHmlrvfftGaYk.kpRelnWiiGvllllltllegflGysLpddllsvtalrvgagiiss......vPvvgtw 74 
                                   y+mi+l+y+Hmlr++f+GaYk k+R+l+Wi+Gv+l++l+++++++Gy+L+++++sv+a++vg+ +i++      +P + +w
  gi|13541204|ref|NP_110892.1|  94 YAMIVLVYAHMLRNYFVGAYKgKWRWLQWILGVILFILVYTTAIVGYMLTYTYISVAATHVGELLIERsiigrlLPGLANW 174
                                   79*****************************************************************99************ PP

               Cytochrom_B_N_2  75 lvellfGgelpgeallsrlyalHilllpalllalivahlllvekkgqtpsrrkeknvvgeplvpvnavkmlllflvlvall 155
                                   lv++l+G+ ++ ++++s++++lH+++l++l++++ ++h++l+ek+g +  +  +kn++++p++pvn++++++l+l+++ ++
  gi|13541204|ref|NP_110892.1| 175 LVSILIGDGTT-SQTFSHILGLHVMILSTLIIVIAFVHFFLFEKSGPYGVK-YDKNEKMVPWFPVNLLYTIFLSLMFIGVI 253
                                   **********8.999*********************************996.99***********************9999 PP

               Cytochrom_B_N_2 156 ialalinPvpll 167
                                   +++ +++P+  +
  gi|13541204|ref|NP_110892.1| 254 LIFSAAFPQVIP 265
                                   999999998765 PP

>> Cytochrome_B  Cytochrome b/b6/petB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.8  21.4   1.2e-20   7.2e-17      13     188 ..      38     218 ..      28     219 .. 0.84
   2 ?   -3.4   0.3       1.2   7.3e+03      66      79 ..     241     254 ..     231     261 .. 0.57
   3 ?   -2.8   1.2      0.76   4.5e+03      89     117 ..     324     352 ..     302     378 .. 0.49

  Alignments for each domain:
  == domain 1  score: 61.8 bits;  conditional E-value: 1.2e-20
                  Cytochrome_B  13 iynlGsllllvlvlqiltGvalafyytptvtlaflsvqyilrdvnfGwlirsvhangasllflllylhifrglllgglk.k 92 
                                    y  Gs l+  ++   ++G++l +yy++   + f+s   i+  v fG+ + + h + a  +++l+y h+ r +++g++k k
  gi|13541204|ref|NP_110892.1|  38 DYWTGSFLMAAVAYLAVSGMLLFYYYQSG--HPFSSTISIISSVPFGYALLTSHLYMAYAMIVLVYAHMLRNYFVGAYKgK 116
                                   57789999999999999***999999875..689******************************************99834 PP

                  Cytochrome_B  93 trelvWviGvillllvivtafiGyvLpwdqmsyWavtvitnlls......aiPviGstlvellwgsvsvddatLtrffslh 167
                                    r l W++Gvil++lv +ta++Gy L ++ +s  a+ v   l++       +P + ++lv++l g  +  + t+ ++  lh
  gi|13541204|ref|NP_110892.1| 117 WRWLQWILGVILFILVYTTAIVGYMLTYTYISVAATHVGELLIErsiigrLLPGLANWLVSILIGDGTT-SQTFSHILGLH 196
                                   57799***************************9888875544431111115788888888888887665.568999999** PP

                  Cytochrome_B 168 .fllPflllillllhllllhkt 188
                                    ++l  l+++++ +h++l+ k 
  gi|13541204|ref|NP_110892.1| 197 vMILSTLIIVIAFVHFFLFEKS 218
                                   8899************998875 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 1.2
                  Cytochrome_B  66 hangasllflllyl 79 
                                   ++ + sl+f+ ++l
  gi|13541204|ref|NP_110892.1| 241 YTIFLSLMFIGVIL 254
                                   34444555554444 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 0.76
                  Cytochrome_B  89 glkktrelvWviGvillllvivtafiGyv 117
                                   +    r  +   G+ +++ + v+a+ G +
  gi|13541204|ref|NP_110892.1| 324 SHPLDRPMITAFGIFIIIGIPVIALWGAS 352
                                   33334444444555555555555555544 PP

>> Cytochrom_B_C  Cytochrome b(C-terminal)/b6/petD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   3.4      0.14   8.1e+02      35      84 ..      90     136 ..      69     155 .. 0.63
   2 ?   -1.5   1.5       0.5     3e+03      51      60 ..     216     225 ..     184     267 .. 0.45
   3 !   21.3   2.1     4e-08   0.00024      13      90 ..     279     357 ..     274     372 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.14
                                   HHHHHHHHGGGCHHHH---SSSSSTT-.HHHHHHHHHHHHHHHHHHHHHT CS
                 Cytochrom_B_C  35 vamgaaivilfllpwldrskvksiryrkplakvllallvvsfvvLgylGv 84 
                                   + m+ a+++l+   +l +  v +++ +  + ++   +l v +++L y  +
  gi|13541204|ref|NP_110892.1|  90 LYMAYAMIVLVYAHMLRNYFVGAYKGKWRWLQW---ILGVILFILVYTTA 136
                                   678889999999998888888766666444444...44444444444332 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.5
                                   ---SSSSSTT CS
                 Cytochrom_B_C  51 drskvksiry 60 
                                   ++s    ++y
  gi|13541204|ref|NP_110892.1| 216 EKSGPYGVKY 225
                                   2332223333 PP

  == domain 3  score: 21.3 bits;  conditional E-value: 4e-08
                                   --GGGHHHHHHHHCS..SSHHHHHHHHHHHHHGGGCHHHH---SSSSSTT-.HHHHHHHHHHHHHHHHHHHHHTS-SSCC CS
                 Cytochrom_B_C  13 PeWYflpfYaiLrai..pakllGvvamgaaivilfllpwldrskvksiryrkplakvllallvvsfvvLgylGvqppeev 90 
                                   P WY lp+Y+++ +      ++Gv ++++ ++ l++lp++dr + +    r p+ +++ +++++ + v+++ G+++p  +
  gi|13541204|ref|NP_110892.1| 279 PDWYILPVYKLMDTAgyGLTTGGVPLVIVFFLFLLILPFIDRYSGSHPLDR-PMITAFGIFIIIGIPVIALWGASQPGLT 357
                                   99**********99744678899*999************************.8888888888899999999998776443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1039  (0.0579508); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                        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: 0.73u 0.35s 00:00:01.08 Elapsed: 00:00:00.53
# Mc/sec: 2223.62
//
Query:       gi|13541205|ref|NP_110893.1|  [L=63]
Description: hypothetical protein TVN0374 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0062   16.5   3.2     0.0078   16.2   3.2    1.1  1  DUF981    Protein of unknown function (DUF981)
  ------ inclusion threshold ------
      0.019   14.4   2.4       0.02   14.3   2.4    1.0  1  DUF1084   Protein of unknown function (DUF1084)
      0.042   14.2   6.4      0.055   13.8   6.4    1.1  1  DUF308    Short repeat of unknown function (DUF308)
       0.15   12.1   3.2       0.19   11.8   3.2    1.2  1  DUF2892   Protein of unknown function (DUF2892)


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 !   16.2   3.2   1.7e-06    0.0078     131     176 ..       6      55 ..       3      58 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.7e-06
                        DUF981 131 lllyilvGLagllsplvllkldksrs....vllvlaavlliiagllalli 176
                                   l++y ++G+  +++ ++++   ++      ++ v++a+ li++g++a++i
  gi|13541205|ref|NP_110893.1|   6 LAVYSIAGIQFVIAIILWILAVTNPTgnqrIWSVVFAIDLILSGIIAFII 55 
                                   677888887655555444444333323345******************99 PP

>> DUF1084  Protein of unknown function (DUF1084)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   2.4   4.4e-06      0.02     127     174 ..       8      55 ..       2      62 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.4e-06
                       DUF1084 127 fllinaviyviqiilWilllvkpaellekvsklflaavsllaalgfll 174
                                    + i ++ +vi iilWil +++p+    + s +f   + l   ++f++
  gi|13541205|ref|NP_110893.1|   8 VYSIAGIQFVIAIILWILAVTNPTGNQRIWSVVFAIDLILSGIIAFII 55 
                                   57899999**************************************97 PP

>> DUF308  Short repeat of unknown function (DUF308)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   6.4   1.2e-05     0.055      22      72 ..       5      53 ..       2      54 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.2e-05
                        DUF308 22 lalvllfGilllvsGivqiiaafaarkknrggrwlglllGilyliaGllll 72
                                  +  v+ ++ + +v +i+ +i a+   + ++ +r+++++++i +++ G++++
  gi|13541205|ref|NP_110893.1|  5 VLAVYSIAGIQFVIAIILWILAV--TNPTGNQRIWSVVFAIDLILSGIIAF 53
                                  56789999999999999999999..4445777899*********9999998 PP

>> DUF2892  Protein of unknown function (DUF2892)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   3.2   4.3e-05      0.19      12      51 ..      14      53 ..       7      57 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4.3e-05
                       DUF2892 12 lrivvGlvllllallglsggwgwllglvGavllltgltgf 51
                                  +++v++++l +la+++ +g   ++++++++ l+l+g++ f
  gi|13541205|ref|NP_110893.1| 14 IQFVIAIILWILAVTNPTGNQRIWSVVFAIDLILSGIIAF 53
                                  788999999999999998888999*************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       926  (0.0516482); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 394.27
//
Query:       gi|13541206|ref|NP_110894.1|  [L=100]
Description: hypothetical protein TVN0375 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score 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   0.8      0.018   14.5   0.8    1.6  2  DUF599       Protein of unknown function, DUF599
      0.057   13.5   1.9      0.061   13.4   1.2    1.5  1  PgaD         PgaD-like protein
       0.12   10.9  11.5       0.14   10.5  11.5    1.0  1  ABC_export   Putative ABC exporter
          1    8.8   6.7        1.1    8.6   6.7    1.0  1  DUF373       Domain of unknown function (DUF373)
        2.3    7.8   7.2       0.59    9.8   3.9    1.6  2  Tetraspanin  Tetraspanin family
        4.9    6.9  11.1       0.24   11.1   1.0    2.7  3  DUF131       Protein of unknown function DUF131


Domain annotation for each model (and alignments):
>> DUF599  Protein of unknown function, DUF599
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.8     6e-06     0.018      65     130 ..       3      67 ..       1      80 [. 0.86
   2 ?   -0.8   0.1      0.29   8.7e+02     114     123 ..      84      93 ..      67      98 .. 0.63

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 6e-06
                        DUF599  65 stllAstaillisglaallsstd..klsdllkslpvfgatsealfelKlllllliflvAFlkfvqsir 130
                                   + ++ s++++l ++++  ++ ++  +++++    pvfg+ +++lf+l l++ ++i++v+++ f +si 
  gi|13541206|ref|NP_110894.1|   3 VYIFGSITLILYTLIIKPIALMYhePINQM--VSPVFGNYARYLFSLELFT-MIIMVVSLILFLLSIY 67 
                                   56899***********99999997777774..469*************999.88999********995 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.29
                        DUF599 114 llliflvAFl 123
                                    +l+f++AF+
  gi|13541206|ref|NP_110894.1|  84 PVLLFAFAFV 93 
                                   3344444444 PP

>> PgaD  PgaD-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   1.2   2.1e-05     0.061      47      99 ..      23      72 ..       2      86 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.1e-05
                          PgaD 47 lfeaeillglfseasasevegslseletlrlYalilvviavlLilWaklnrv.r 99
                                  l+++e     + ++ ++ + +++  l +l l+ +i++v++++L+l++ + ++ r
  gi|13541206|ref|NP_110894.1| 23 LMYHEP----INQMVSPVFGNYARYLFSLELFTMIIMVVSLILFLLSIYHNHiR 72
                                  333333....467778889999999************************98833 PP

>> ABC_export  Putative ABC exporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5  11.5   4.8e-05      0.14     112     203 ..       3      94 ..       2      99 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 4.8e-05
                    ABC_export 112 vllYglvkqiltsllvslfaifqlpnlgsglgltvgkivalllglilllialllsvillliYllsskekklkkivkaiivl 192
                                   v+++g ++ il +l++  +a+++   + ++++  +g+   +l++l l+ +++++  ++l++ ++++++ + +ki+k +i+ 
  gi|13541206|ref|NP_110894.1|   3 VYIFGSITLILYTLIIKPIALMYHEPINQMVSPVFGNYARYLFSLELFTMIIMVVSLILFLLSIYHNHIRNGKISKPTIIT 83 
                                   89*****************************96666666666666666655555555555577788888999999999999 PP

                    ABC_export 193 vlvlllvavvl 203
                                     +l++ a+vl
  gi|13541206|ref|NP_110894.1|  84 PVLLFAFAFVL 94 
                                   75555555554 PP

>> DUF373  Domain of unknown function (DUF373)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   6.7   0.00037       1.1     225     316 ..       6     100 .]       1     100 [] 0.60

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00037
                        DUF373 225 vvallllligiisgyislesvss..asvssglltlilafiyg...avewlalailtaslgkiideylkreekdiarllllp 300
                                   + ++ l+l  +i   i+   + +  +++ s ++   + ++++   ++ +++++ l+++l +i ++ + r+ k  + ++++p
  gi|13541206|ref|NP_110894.1|   6 FGSITLILYTLIIKPIA-LMYHEpiNQMVSPVFGNYARYLFSlelFTMIIMVVSLILFLLSIYHNHI-RNGKISKPTIITP 84 
                                   33344444444444333.2222235444455555555544444446666677777788888888888.6689999999*** PP

                        DUF373 301 flvlaiglvlygasay 316
                                   +l++a+++vl g+s++
  gi|13541206|ref|NP_110894.1|  85 VLLFAFAFVLLGVSGF 100
                                   **********999987 PP

>> Tetraspanin  Tetraspanin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1      0.38   1.1e+03      81     110 ..       3      32 ..       1      44 [. 0.63
   2 ?    9.8   3.9    0.0002      0.59       4      67 ..      46      99 ..      41     100 .] 0.74

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.38
                                   XXXXXXXXXXXXXXXXXXXXX--HHH.... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Tetraspanin  81 tfsllllvlfllelaagilgfvfsdkargk 110
                                   ++++  + l+l  l++  +++++++  ++ 
  gi|13541206|ref|NP_110894.1|   3 VYIFGSITLILYTLIIKPIALMYHEPINQM 32 
                                   677777777777777666777666664444 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0002
                                  XXXXXXXXXXXXXXXXXXXXXXXXXXXX.....................XXXXXXXXXXXXXXX CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Tetraspanin  4 llfffnllfwligivllavGvwlrlkhaeaalacllsesaedpailaillivvGvllfllgflG 67
                                  +l +f +++++++++l+ ++++   +h         + + ++p+i+ ++++++ ++++llg+ G
  gi|13541206|ref|NP_110894.1| 46 SLELFTMIIMVVSLILFLLSIYH--NHI-------RNGKISKPTII-TPVLLFAFAFVLLGVSG 99
                                  6889****************999..233.......33446666666.67777777777777777 PP

>> DUF131  Protein of unknown function DUF131
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.7     0.058   1.7e+02      36      55 ..       5      24 ..       2      26 .. 0.85
   2 ?   11.1   1.0     8e-05      0.24      36      62 .]      36      62 ..      35      62 .. 0.97
   3 ?   -1.2   0.1      0.54   1.6e+03      46      61 ..      79      94 ..      73      95 .. 0.62

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.058
                        DUF131 36 iFGsdkrlaktaiiLaIilm 55
                                  iFGs   +++t+ii  I lm
  gi|13541206|ref|NP_110894.1|  5 IFGSITLILYTLIIKPIALM 24
                                  89999999999999888887 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 8e-05
                        DUF131 36 iFGsdkrlaktaiiLaIilmilllilf 62
                                  +FG+  r +  + ++++i+m+++lilf
  gi|13541206|ref|NP_110894.1| 36 VFGNYARYLFSLELFTMIIMVVSLILF 62
                                  8************************97 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.54
                        DUF131 46 taiiLaIilmilllil 61
                                   +ii  ++l++++++l
  gi|13541206|ref|NP_110894.1| 79 PTIITPVLLFAFAFVL 94
                                  5566667777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1186  (0.0661498); expected 358.6 (0.02)
Passed bias filter:                      496  (0.0276647); 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):               6  [number of targets reported over threshold]
# CPU time: 0.56u 0.35s 00:00:00.91 Elapsed: 00:00:00.53
# Mc/sec: 570.28
//
Query:       gi|13541207|ref|NP_110895.1|  [L=74]
Description: hypothetical protein TVN0376 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.031   13.3   2.0      0.036   13.1   2.0    1.1  1  DUF973    Protein of unknown function (DUF973)
      0.038   13.5   0.1      0.044   13.3   0.1    1.1  1  UPF0220   Uncharacterised protein family (UPF0220)
      0.078   13.4   4.0        1.1    9.7   0.7    2.0  2  DUF202    Domain of unknown function (DUF202)


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 ?   13.1   2.0   6.1e-06     0.036     106     155 ..      19      69 ..       8      72 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.1e-06
                        DUF973 106 igaiiiiigvilai.vsllslilslillgviilligiilaliGqillglsf 155
                                   +g+++++i++ + +   ++++i s+i    i + ++ ++ +iG+il+++++
  gi|13541207|ref|NP_110895.1|  19 AGIVLLVIAIPVFLdYKVFPVINSEIGPHQIGSWLALLFSFIGFILIIVGM 69 
                                   344444444332221245577777777777777777777777777777654 PP

>> UPF0220  Uncharacterised protein family (UPF0220)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   7.4e-06     0.044      17      75 ..       7      65 ..       1      69 [. 0.85

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 7.4e-06
                       UPF0220 17 nsakrravgvylaGa.LfalgfwlliDaaivskkanasdvhvtfvdwipgicstlgmliv 75
                                   ++krr++g ++aG+ L  +++ +++D  ++ +  n+     ++  w+ +++s +g++++
  gi|13541207|ref|NP_110895.1|  7 AKEKRRSFGKVVAGIvLLVIAIPVFLDYKVF-PVINSEIGPHQIGSWLALLFSFIGFILI 65
                                  6799**********64899*********998.55567777888999**********9977 PP

>> DUF202  Domain of unknown function (DUF202)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.2    0.0044        26      34      54 ..      10      30 ..       3      33 .. 0.66
   2 ?    9.7   0.7   0.00019       1.1      33      60 ..      43      70 ..      30      73 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0044
                        DUF202 34 gepsalgkilglilivlgilt 54
                                  + +s + +++g++l+v++i +
  gi|13541207|ref|NP_110895.1| 10 KRRSFGKVVAGIVLLVIAIPV 30
                                  444444588899999999865 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00019
                        DUF202 33 tgepsalgkilglilivlgiltllvglv 60
                                  + +p ++g++l+l++  +g+++++vg+ 
  gi|13541207|ref|NP_110895.1| 43 EIGPHQIGSWLALLFSFIGFILIIVGMG 70
                                  6788899******************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       759  (0.0423336); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.32s 00:00:00.87 Elapsed: 00:00:00.53
# Mc/sec: 418.19
//
Query:       gi|13541208|ref|NP_110896.1|  [L=175]
Description: transcription regulator [Thermoplasma volcanium GSS1]
Scores for complete 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-16   57.8   4.2    1.9e-15   56.9   4.2    1.6  1  Arc_trans_TRASH  Archaeal TRASH domain
    2.4e-10   39.8   2.0    2.4e-10   39.8   2.0    2.0  2  HTH_24           Winged helix-turn-helix DNA-binding
      2e-08   34.0   0.3    3.3e-08   33.3   0.3    1.4  1  TrmB             Sugar-specific transcriptional regulator Trm
    2.2e-06   27.5   0.0    3.6e-06   26.7   0.0    1.4  1  MarR_2           MarR family
    2.9e-06   27.1   0.2    7.2e-06   25.9   0.0    1.8  1  HTH_36           Helix-turn-helix domain
    3.9e-06   26.7   0.1    1.3e-05   25.0   0.1    1.9  1  HTH_Crp_2        Crp-like helix-turn-helix domain
    8.7e-05   22.2   0.1    0.00016   21.3   0.1    1.4  1  HTH_23           Homeodomain-like domain
    9.5e-05   22.3   1.6    0.00021   21.2   0.2    2.0  2  MarR             MarR family
    0.00015   22.0   0.0    0.00024   21.4   0.0    1.3  1  Rrf2             Transcriptional regulator
    0.00031   20.5   0.2    0.00056   19.7   0.2    1.5  1  HTH_AsnC-type    AsnC-type helix-turn-helix domain
    0.00083   19.3   0.7     0.0015   18.4   0.7    1.4  1  HTH_11           HTH domain
      0.001   18.8   0.0     0.0016   18.2   0.0    1.2  1  HTH_IclR         IclR helix-turn-helix domain
     0.0014   18.7   0.0     0.0022   18.0   0.0    1.3  1  HTH_20           Helix-turn-helix domain
     0.0016   18.5   0.0     0.0029   17.7   0.0    1.4  1  HTH_28           Helix-turn-helix domain
      0.002   18.6   0.1     0.0033   17.9   0.1    1.4  1  HTH_27           Winged helix DNA-binding domain
     0.0055   16.6   0.2      0.014   15.3   0.2    1.7  1  TFIIE_alpha      TFIIE alpha subunit
     0.0056   16.5   0.1      0.015   15.2   0.0    1.7  1  HTH_5            Bacterial regulatory protein, arsR family
     0.0071   16.1   0.1      0.011   15.5   0.1    1.3  1  FtsK_gamma       Ftsk gamma domain
     0.0087   16.1   0.1      0.019   15.0   0.1    1.6  1  HTH_3            Helix-turn-helix
  ------ inclusion threshold ------
      0.015   14.7   0.1      0.028   13.8   0.1    1.4  1  RepL             Firmicute plasmid replication protein (RepL)
      0.018   14.6   0.2       0.04   13.4   0.2    1.6  1  Sigma70_r4       Sigma-70, region 4
       0.02   15.3   0.0      0.042   14.3   0.0    1.5  1  HTH_26           Cro/C1-type HTH DNA-binding domain
      0.021   15.0   0.6       0.11   12.7   0.0    2.2  2  Fe_dep_repress   Iron dependent repressor, N-terminal DNA bin
      0.023   14.7   0.0      0.042   13.9   0.0    1.4  1  HTH_29           Winged helix-turn helix
      0.026   14.6   0.0      0.045   13.9   0.0    1.3  1  DprA_WH          DprA winged helix domain
      0.033   14.2   0.6      0.058   13.4   0.6    1.3  1  DZR              Double zinc ribbon
      0.036   14.3   0.1      0.091   13.0   0.1    1.7  1  HTH_17           Helix-turn-helix domain
      0.037   14.1   0.2       0.06   13.5   0.2    1.4  1  DUF2250          Uncharacterized protein conserved in archaea
      0.055   13.1   0.0        0.1   12.3   0.0    1.4  1  GntR             Bacterial regulatory proteins, gntR family
      0.057   13.8   0.1      0.098   13.0   0.1    1.3  1  Penicillinase_R  Penicillinase repressor
       0.06   12.9   0.2       0.14   11.7   0.0    1.7  2  HTH_47           winged helix-turn-helix
      0.064   13.3   1.1       0.12   12.4   1.1    1.5  1  HTH_19           Helix-turn-helix domain
      0.065   12.2   0.1      0.075   12.0   0.1    1.2  1  TnsD             Tn7-like transposition protein D
      0.069   12.7   0.2       0.15   11.6   0.2    1.6  1  GerE             Bacterial regulatory proteins, luxR family
      0.072   13.1   0.4       0.15   12.1   0.4    1.6  1  HTH_46           Winged helix-turn-helix DNA binding
      0.076   12.4   0.0       0.12   11.8   0.0    1.3  1  HTH_Tnp_ISL3     Helix-turn-helix domain of transposase famil
      0.078   12.9   0.0       0.15   12.0   0.0    1.4  1  HTH_43           Winged helix-turn helix
        0.1   12.7   0.0       0.18   12.0   0.0    1.4  1  HTH_9            RNA polymerase III subunit RPC82 helix-turn-
        0.1   13.2   0.0       0.19   12.4   0.0    1.4  1  HHH_5            Helix-hairpin-helix domain
       0.11   13.2   1.8       0.26   12.0   1.1    1.9  2  ATPase-cat_bd    Putative metal-binding domain of cation tran
       0.13   11.8   3.5        1.6    8.4   0.9    2.2  2  Sgf11            Sgf11 (transcriptional regulation protein)
       0.13   12.1   0.3        0.4   10.5   0.0    1.9  2  HTH_10           HTH DNA binding domain
       0.25   10.8   5.1        3.1    7.3   0.1    2.4  2  zf-ribbon_3      zinc-ribbon domain
       0.37   10.8   3.4       0.34   10.9   0.5    2.0  2  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
        8.2    6.2   8.3       0.24   11.1   1.1    2.0  2  zf-RRN7          Zinc-finger of RNA-polymerase I-specific TFI


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 !   56.9   4.2   4.9e-18   1.9e-15       1      37 []     134     170 ..     134     170 .. 0.98

  Alignments for each domain:
  == domain 1  score: 56.9 bits;  conditional E-value: 4.9e-18
               Arc_trans_TRASH   1 CDYCGkeivgePivyklknkvYyvCCktCkselkkkl 37 
                                   CDYCG+ i g+Pi +k kn++Y vCC++C++++ k+l
  gi|13541208|ref|NP_110896.1| 134 CDYCGNQIHGDPISVKWKNRTYLVCCPNCEKDMLKRL 170
                                   *********************************9985 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.8   2.0     6e-13   2.4e-10       4      48 .]      11      55 ..       8      55 .. 0.94
   2 ?   -0.4   0.2       2.2   8.9e+02      37      44 ..     166     173 ..     164     174 .. 0.83

  Alignments for each domain:
  == domain 1  score: 39.8 bits;  conditional E-value: 6e-13
                        HTH_24  4 tdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                  ++ ++L++L +++r s  e++er+g+ ++tv++ +k Le++G+Ik
  gi|13541208|ref|NP_110896.1| 11 LESRVLRELIDDSRSSVEEISERTGIGRNTVSKIIKDLERNGIIK 55
                                  56799***************************************8 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 2.2
                        HTH_24  37 rlkrLeee 44 
                                    lkrLe++
  gi|13541208|ref|NP_110896.1| 166 MLKRLEKD 173
                                   69****98 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.3   0.3   8.4e-11   3.3e-08       5      56 ..       7      58 ..       4      75 .. 0.91

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 8.4e-11
                                  HHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES CS
                          TrmB  5 GLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerek 56
                                  +Ls  E++v   L+   +++++ei+e++g+ r++v ++++ Le+ G++++  
  gi|13541208|ref|NP_110896.1|  7 NLSNLESRVLRELIDDSRSSVEEISERTGIGRNTVSKIIKDLERNGIIKKYT 58
                                  89**********************************************9865 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.0   9.2e-09   3.6e-06       3      53 ..       8      56 ..       6      66 .. 0.91

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 9.2e-09
                                  --HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEE CS
                        MarR_2  3 ltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLver 53
                                  l+  + rvL +L +  +   +v e+ +r+g+ + +vs+i+k+L++ G + +
  gi|13541208|ref|NP_110896.1|  8 LSNLESRVLRELIDDSR--SSVEEISERTGIGRNTVSKIIKDLERNGIIKK 56
                                  566799*********98..8***************************9975 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.0   1.8e-08   7.2e-06      27      55 .]      26      54 ..      15      54 .. 0.95

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 1.8e-08
                        HTH_36 27 sqetlakrlglsknTvsraikeLeqlGyi 55
                                  s+e +++r+g+ +nTvs++ik Le+ G+i
  gi|13541208|ref|NP_110896.1| 26 SVEEISERTGIGRNTVSKIIKDLERNGII 54
                                  799************************98 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.1   3.3e-08   1.3e-05      21      54 ..      24      57 ..       8      62 .. 0.85

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 3.3e-08
                                  EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEET CS
                     HTH_Crp_2 21 pltqeelAsmlGltretvsrilseLkreglisrg 54
                                  + + ee++++ G+ r tvs+i+++L+r g+i++ 
  gi|13541208|ref|NP_110896.1| 24 RSSVEEISERTGIGRNTVSKIIKDLERNGIIKKY 57
                                  56789**************************964 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.1   4.1e-07   0.00016      12      46 ..      17      53 ..      13      56 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 4.1e-07
                        HTH_23 12 lllae..GlsvreIAreLgvsrrTvyrwlkryreeGl 46
                                  + l +  + sv+eI+++ g+ r+Tv++++k  +++G+
  gi|13541208|ref|NP_110896.1| 17 RELIDdsRSSVEEISERTGIGRNTVSKIIKDLERNGI 53
                                  555555899**********************987986 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.2   5.2e-07   0.00021       3      51 ..      10      58 ..       8      62 .. 0.88
   2 ?   -0.2   0.1       2.5   9.8e+02      37      44 ..     166     173 ..     165     174 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 5.2e-07
                                  HHHHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE CS
                          MarR  3 ltqfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRsk 51
                                    + ++Lr l +    sv e+ ++ g+ + tv+++++ Le++G i+++ 
  gi|13541208|ref|NP_110896.1| 10 NLESRVLRELIDDSRSSVEEISERTGIGRNTVSKIIKDLERNGIIKKYT 58
                                  56678888888999999****************************9986 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 2.5
                                   HHHHHHHT CS
                          MarR  37 vldrLekk 44 
                                   +l+rLek+
  gi|13541208|ref|NP_110896.1| 166 MLKRLEKD 173
                                   89****97 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   6.1e-07   0.00024      22      56 ..      21      55 ..      13      58 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 6.1e-07
                                  TCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          Rrf2 22 eeepvsseeiaerqnispsylekilakLrkaglvk 56
                                  +++  s+eei+er++i ++ ++ki++ L+++g++k
  gi|13541208|ref|NP_110896.1| 21 DDSRSSVEEISERTGIGRNTVSKIIKDLERNGIIK 55
                                  455589***************************98 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.2   1.4e-06   0.00056       7      41 ..      14      48 ..       8      49 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.4e-06
                 HTH_AsnC-type  7 kILeaLqedaRisyaeLAervGlSestvlrRvrrL 41
                                  + L++L  d+R s++e++er+G+ ++tv + ++ L
  gi|13541208|ref|NP_110896.1| 14 RVLRELIDDSRSSVEEISERTGIGRNTVSKIIKDL 48
                                  78**************************8766666 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.7   3.8e-06    0.0015       5      44 ..      15      53 ..      12      62 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 3.8e-06
                        HTH_11  5 ilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgv 44
                                  +l+ L   ++  s ee++e++++ r tv + Ik+Le  g+
  gi|13541208|ref|NP_110896.1| 15 VLREL-IDDSRSSVEEISERTGIGRNTVSKIIKDLERNGI 53
                                  56677.444457**************************93 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     4e-06    0.0016      18      49 ..      24      55 ..      14      57 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 4e-06
                                  S-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                      HTH_IclR 18 eltlselArrtglpkStvhRlLqtLvelGyve 49
                                  + ++ e+++rtg+ + tv+ +++ L++ G+++
  gi|13541208|ref|NP_110896.1| 24 RSSVEEISERTGIGRNTVSKIIKDLERNGIIK 55
                                  3589*************************987 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   5.5e-06    0.0022      14      56 ..      14      56 ..       8      60 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 5.5e-06
                                  HHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEE CS
                        HTH_20 14 rilraLaraegltaselaerldlskntlsyHLrvLeeagLvev 56
                                  r+lr+L ++   +++e+ er ++ +nt+s+ ++ Le+ g+++ 
  gi|13541208|ref|NP_110896.1| 14 RVLRELIDDSRSSVEEISERTGIGRNTVSKIIKDLERNGIIKK 56
                                  89****999999****************************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 !   17.7   0.0   7.2e-06    0.0029       4      41 ..      14      53 ..      14      60 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 7.2e-06
                        HTH_28  4 eiikllaaG.h.svreaArelgisrrtvyrWikryeegGi 41
                                  +++++l++  + sv e++++ gi+r tv++ ik +e  Gi
  gi|13541208|ref|NP_110896.1| 14 RVLRELIDDsRsSVEEISERTGIGRNTVSKIIKDLERNGI 53
                                  578888854268************************9997 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.1   8.2e-06    0.0033       2      50 ..       9      56 ..       8      76 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 8.2e-06
                        HTH_27  2 trqqalvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLver 50
                                  +++++ vL+ +   + r++ +++++r+ ++  ++s+++k L+++G +++
  gi|13541208|ref|NP_110896.1|  9 SNLESRVLRELI-DDSRSSVEEISERTGIGRNTVSKIIKDLERNGIIKK 56
                                  567777888777.7999999*************************9944 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.2   3.5e-05     0.014      17      59 ..      14      56 ..       8      78 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3.5e-05
                                  HHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEE CS
                   TFIIE_alpha 17 lvldvLlekgevteedlakelkidlnelrklLnrLyearlvky 59
                                   vl  L+ ++  + e++++ ++i +n + k++ +L   +++k 
  gi|13541208|ref|NP_110896.1| 14 RVLRELIDDSRSSVEEISERTGIGRNTVSKIIKDLERNGIIKK 56
                                  69999**********************************9984 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 !   15.2   0.0   3.7e-05     0.015       6      47 .]      14      56 ..      12      56 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3.7e-05
                                  HHHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                         HTH_5  6 kILklLae.gelcvcelaeelglsqstvShHLkkLreaGLVek 47
                                  ++L+ L + +  +v e++e +g+ + tvS   k L+  G+++k
  gi|13541208|ref|NP_110896.1| 14 RVLRELIDdSRSSVEEISERTGIGRNTVSKIIKDLERNGIIKK 56
                                  6888999955599***************************986 PP

>> FtsK_gamma  Ftsk gamma domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1   2.9e-05     0.011      10      52 ..      15      57 ..       8      64 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.9e-05
                    FtsK_gamma 10 avelvveegkaStSllQRrlriGYnRAarlidqLeeeGiVgpa 52
                                  +++  +++ + S+  +  r  iG n  +++i +Le++Gi+ ++
  gi|13541208|ref|NP_110896.1| 15 VLRELIDDSRSSVEEISERTGIGRNTVSKIIKDLERNGIIKKY 57
                                  66778899999*****************************986 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1   4.9e-05     0.019      11      34 ..      26      50 ..      16      51 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 4.9e-05
                                  HHHHHHHHHTSSHHHHHHHHTT.SS CS
                         HTH_3 11 sqeeLAeklGvsrstisriEnG.er 34
                                  s ee++e++G+ r+t+s+i+++ er
  gi|13541208|ref|NP_110896.1| 26 SVEEISERTGIGRNTVSKIIKDlER 50
                                  669****************998665 PP

>> RepL  Firmicute plasmid replication protein (RepL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   7.1e-05     0.028      78     109 ..      27      58 ..      10      62 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 7.1e-05
                          RepL  78 nRelaeetgislktvsetlkileeanilkkka 109
                                   + e++e+tgi  +tvs+ +k le  +i+kk +
  gi|13541208|ref|NP_110896.1|  27 VEEISERTGIGRNTVSKIIKDLERNGIIKKYT 58 
                                   4689*************************976 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.2    0.0001      0.04       9      42 ..      12      46 ..       6      48 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.0001
                                  HHHHHHHHH.TTT--HHHHHHHHTS-HHHHHHHHH CS
                    Sigma70_r4  9 erevlelrf.geglTleEIgerlgiSrerVrqiek 42
                                  e +vl+    +   + eEI+er gi r +V+ i+k
  gi|13541208|ref|NP_110896.1| 12 ESRVLRELIdDSRSSVEEISERTGIGRNTVSKIIK 46
                                  5555554444666799*****************98 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 ?   14.3   0.0   0.00011     0.042       2      33 ..      16      47 ..      15      51 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 0.00011
                        HTH_26  2 LrelmadrgitkseLargtgisaatlsrlvkg 33
                                  Lrel+ d + ++ e +++tgi ++t+s++ k+
  gi|13541208|ref|NP_110896.1| 16 LRELIDDSRSSVEEISERTGIGRNTVSKIIKD 47
                                  99***************************987 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00029      0.11      24      53 ..      26      55 ..      16      62 .. 0.89
   2 ?    0.0   0.2       2.5     1e+03      41      49 ..     165     173 ..     164     174 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00029
                                  -HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                Fe_dep_repress 24 ktkdlaerLnvspssVsemlkkLekdGyve 53
                                  ++ +++er ++   +Vs+ +k Le++G ++
  gi|13541208|ref|NP_110896.1| 26 SVEEISERTGIGRNTVSKIIKDLERNGIIK 55
                                  7899***********************765 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 2.5
                                   HHHHHHHHT CS
                Fe_dep_repress  41 emlkkLekd 49 
                                    mlk+Lekd
  gi|13541208|ref|NP_110896.1| 165 DMLKRLEKD 173
                                   5******97 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   0.00011     0.042       8      41 ..      20      53 ..      18      71 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 0.00011
                        HTH_29  8 laeGvstvsqiAkllglsrrtvyrwlkrfeegGl 41
                                  +++  s+v +i +++g+ r tv +++k+ e  G+
  gi|13541208|ref|NP_110896.1| 20 IDDSRSSVEEISERTGIGRNTVSKIIKDLERNGI 53
                                  5566678***********************9997 PP

>> DprA_WH  DprA winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   0.00011     0.045       5      54 ..       3      53 ..       2      57 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 0.00011
                       DprA_WH  5 paepplddlerrvL.aaLgpePvhvDqLvrrtglpaaevsaaLleLELaGl 54
                                  p  + l+ le rvL +++  +  +v+++++rtg+   +vs +   LE  G 
  gi|13541208|ref|NP_110896.1|  3 PEKRNLSNLESRVLrELIDDSRSSVEEISERTGIGRNTVSKIIKDLERNGI 53
                                  5678899*******555577788*****************99999986665 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.6   0.00014     0.058      13      37 ..     132     165 ..     124     170 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00014
                           DZR  13 rfCseCgtklkavaa.........edrCpsCgek 37 
                                    +C++Cg+++   +             Cp+C+++
  gi|13541208|ref|NP_110896.1| 132 LYCDYCGNQIHGDPIsvkwknrtyLVCCPNCEKD 165
                                   59*******986555999999**99******987 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   0.00023     0.091       3      32 ..      26      59 ..      26      67 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00023
                        HTH_17  3 tveEaAelLgvsrstvyrli....rrgelpaaki 32
                                  +veE++e  g++r+tv + i    r+g ++ + i
  gi|13541208|ref|NP_110896.1| 26 SVEEISERTGIGRNTVSKIIkdleRNGIIKKYTI 59
                                  69****************9977776999988854 PP

>> DUF2250  Uncharacterized protein conserved in archaea (DUF2250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.2   0.00015      0.06      27      59 ..      29      61 ..       5      73 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00015
                       DUF2250 27 siakeleipleevrellkkLeelGLlervegkt 59
                                   i++++ i ++ v++++k+Le+ G++++++ kt
  gi|13541208|ref|NP_110896.1| 29 EISERTGIGRNTVSKIIKDLERNGIIKKYTIKT 61
                                  6899*************************9665 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00026       0.1      26      54 ..      26      54 ..      15      56 .. 0.95

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00026
                                  -HHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                          GntR 26 sereLaaefgVsrttvReALrrLeaeglv 54
                                  s++e++++ g++r+tv + ++ Le+ g++
  gi|13541208|ref|NP_110896.1| 26 SVEEISERTGIGRNTVSKIIKDLERNGII 54
                                  689************************97 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   0.00025     0.098       1      58 [.       8      61 ..       8      64 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00025
                                  ---S-SHHHHHHHHHS-EEHHHHHHT--GGG---HHHHHHHHHHHHHTTS-EEEEETT CS
               Penicillinase_R  1 lgelEaevmeilwekgeatvkevveeleeekelaysTVktllrrLvkKgllsrekegr 58
                                  l++lE+ v++ l + ++ +v+e+ e+        ++TV  +++ L++ g++++++ + 
  gi|13541208|ref|NP_110896.1|  8 LSNLESRVLRELIDDSRSSVEEISERTGIG----RNTVSKIIKDLERNGIIKKYTIKT 61
                                  6899***************99999887777....*****************9987655 PP

>> HTH_47  winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00035      0.14      44      77 ..      22      55 ..      14      56 .. 0.91
   2 ?   -2.5   0.1        10     4e+03       2      14 ..     154     166 ..     153     169 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00035
                                  EEEEEHHHHHHHHT--HHHHHHHHHHHHHTT-EE CS
                        HTH_47 44 DGkrsLldiAeriglpfdrvaaiaraLaeaglla 77
                                  D + s+ +i+er+g++ ++v +i++ L+++g+++
  gi|13541208|ref|NP_110896.1| 22 DSRSSVEEISERTGIGRNTVSKIIKDLERNGIIK 55
                                  55678889************************97 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 10
                                   EEEES--SS---T CS
                        HTH_47   2 vykntsplgEPqL 14 
                                   +y   +p +E  +
  gi|13541208|ref|NP_110896.1| 154 TYLVCCPNCEKDM 166
                                   7888999999655 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   1.1   0.00031      0.12       4      36 ..      16      50 ..      14      70 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00031
                        HTH_19  4 LkeaReelgltqeelaerlgisrskisaiEng..k 36
                                  L+e++     + ee++er+gi r+  s+i+++  +
  gi|13541208|ref|NP_110896.1| 16 LRELIDDSRSSVEEISERTGIGRNTVSKIIKDleR 50
                                  88888888999*******************98753 PP

>> TnsD  Tn7-like transposition protein D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00019     0.075     189     237 ..      14      62 ..       9     116 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00019
                          TnsD 189 erlkeLveeeglslkeiAkelgvdiktVlryakklgllkekkkqkkesr 237
                                   + l+eL++++  s++ei+++ g+  +tV ++ k l+ +   kk   + +
  gi|13541208|ref|NP_110896.1|  14 RVLRELIDDSRSSVEEISERTGIGRNTVSKIIKDLERNGIIKKYTIKTS 62 
                                   5699*****************************9888775444444333 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.2   0.00038      0.15       2      35 ..       7      42 ..       6      50 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00038
                                  SS-HHHHHHHHHHCTTS..-HHHHHHHHTS-HHHHH CS
                          GerE  2 sLskRErevLrllaeGk..snkeIAeelniSekTVk 35
                                  +Ls+ E+ vLr l++    s++eI+e+ +i  +TV+
  gi|13541208|ref|NP_110896.1|  7 NLSNLESRVLRELIDDSrsSVEEISERTGIGRNTVS 42
                                  69999**********964489**************8 PP

>> HTH_46  Winged helix-turn-helix DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.4   0.00039      0.15      29      54 ..      30      55 ..      14      60 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00039
                        HTH_46 29 IqkrtnLSrSsimkvLseLkkggyIe 54
                                  I++rt + r ++ k++ +L ++g I+
  gi|13541208|ref|NP_110896.1| 30 ISERTGIGRNTVSKIIKDLERNGIIK 55
                                  99*******************99986 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0    0.0003      0.12      17      51 ..      12      48 ..      10      49 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0003
                  HTH_Tnp_ISL3 17 eayilellles..rsvkavArqlgvSwtTVwrildry 51
                                  e  +l++l+++   sv ++++++g++ +TV  i++++
  gi|13541208|ref|NP_110896.1| 12 ESRVLRELIDDsrSSVEEISERTGIGRNTVSKIIKDL 48
                                  56677777777778********************985 PP

>> HTH_43  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00037      0.15      13      51 ..      17      55 ..       7      70 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00037
                                  HHHHHHS-B-HHHHHHHH---HHHHHHHHHGGGGGT-EE CS
                        HTH_43 13 aylideeeanvpklieltgmPRRtlqDtlkalaeldiel 51
                                    lid+++++v ++ e tg+ R t+  ++k l+  +i  
  gi|13541208|ref|NP_110896.1| 17 RELIDDSRSSVEEISERTGIGRNTVSKIIKDLERNGIIK 55
                                  569***************************999877755 PP

>> HTH_9  RNA polymerase III subunit RPC82 helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00044      0.18      16      47 ..      13      44 ..      10      55 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00044
                                  HHHHHHHHHHSSBEHHHHHHHHSSTHHHHHHH CS
                         HTH_9 16 akVvetLlrkgrltlrelvkktkLsldqVkks 47
                                  ++V + L++ +r+++ e++++t++ ++ V k+
  gi|13541208|ref|NP_110896.1| 13 SRVLRELIDDSRSSVEEISERTGIGRNTVSKI 44
                                  689999*********************99887 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00047      0.19      27      56 ..      17      49 ..       6      50 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00047
                                  HHHHHS...-HHHHHTSTTS-HHHHHHHHHHHH CS
                         HHH_5 27 edlaaa...dveeLakipGiGkktAeriilelk 56
                                   +l++    +vee+++ +GiG  t+ +ii  l+
  gi|13541208|ref|NP_110896.1| 17 RELIDDsrsSVEEISERTGIGRNTVSKIIKDLE 49
                                  56666433379******************9986 PP

>> ATPase-cat_bd  Putative metal-binding domain of cation transport ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       9.5   3.8e+03      35      57 ..      45      67 ..      37      80 .. 0.64
   2 ?   12.0   1.1   0.00066      0.26       2      32 ..     134     163 ..     133     171 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 9.5
                 ATPase-cat_bd 35 aqliveaglesyYklrtekakka 57
                                  ++ + ++g+ + Y+++t+ ++++
  gi|13541208|ref|NP_110896.1| 45 IKDLERNGIIKKYTIKTSYEESE 67
                                  45566677777787777444433 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00066
                 ATPase-cat_bd   2 CyHCglpveesaklkaeiegeerefCCkGCq 32 
                                   C  Cg++++   +++++ ++++  +CC+ C+
  gi|13541208|ref|NP_110896.1| 134 CDYCGNQIHG-DPISVKWKNRTYLVCCPNCE 163
                                   9*******66.69*****************8 PP

>> Sgf11  Sgf11 (transcriptional regulation protein)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.1      0.11        42       4      15 ..     131     142 ..     128     143 .. 0.81
   2 ?    8.4   0.9     0.004       1.6       3      14 ..     155     166 ..     153     168 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.11
                                   EEE-TTTSSEEE CS
                         Sgf11   4 yvtCpnCgRqia 15 
                                   +  C++Cg qi+
  gi|13541208|ref|NP_110896.1| 131 TLYCDYCGNQIH 142
                                   678*******98 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.004
                                   -EEE-TTTSSEE CS
                         Sgf11   3 eyvtCpnCgRqi 14 
                                    +v+CpnC++++
  gi|13541208|ref|NP_110896.1| 155 YLVCCPNCEKDM 166
                                   589*****9986 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0     0.001       0.4      23      49 ..      24      50 ..      21      54 .. 0.90
   2 ?   -1.4   0.0       5.2   2.1e+03      35      52 ..      54      71 ..      51      72 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.001
                        HTH_10 23 rvtlkeLAkelGIskstlsehLrkaes 49
                                  r +++e++++ GI ++t+s++++  e+
  gi|13541208|ref|NP_110896.1| 24 RSSVEEISERTGIGRNTVSKIIKDLER 50
                                  6789*****************998887 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 5.2
                        HTH_10 35 IskstlsehLrkaeskli 52
                                  I+k t++   +++e+k+i
  gi|13541208|ref|NP_110896.1| 54 IKKYTIKTSYEESEKKII 71
                                  677788888889999998 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.1    0.0077       3.1       3      12 ..     132     141 ..     130     145 .. 0.72
   2 ?    4.5   1.5     0.059        23      18      25 ..     158     165 ..     157     166 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0077
                   zf-ribbon_3   3 vrCPnCGapl 12 
                                    +C +CG+++
  gi|13541208|ref|NP_110896.1| 132 LYCDYCGNQI 141
                                   5788888854 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.059
                   zf-ribbon_3  18 vCpyCGtk 25 
                                   +Cp+C ++
  gi|13541208|ref|NP_110896.1| 158 CCPNCEKD 165
                                   89999876 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.1       1.9   7.7e+02      21      27 ..     134     140 ..     128     149 .. 0.75
   2 ?   10.9   0.5   0.00085      0.34      14      28 ..     149     166 ..     145     172 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 1.9
                 Zn_Tnp_IS1595  21 CPhCgsr 27 
                                   C +Cg++
  gi|13541208|ref|NP_110896.1| 134 CDYCGNQ 140
                                   8899987 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00085
                 Zn_Tnp_IS1595  14 rWpng...fvCPhCgsrk 28 
                                    W+n+   ++CP+C+++ 
  gi|13541208|ref|NP_110896.1| 149 KWKNRtylVCCPNCEKDM 166
                                   6******999****9874 PP

>> zf-RRN7  Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   1.1   0.00061      0.24      22      31 ..     132     141 ..     131     142 .. 0.89
   2 ?   -1.5   1.0       5.4   2.2e+03       5      10 ..     157     162 ..     153     164 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00061
                       zf-RRN7  22 yyCrrChtqe 31 
                                    yC++C++q+
  gi|13541208|ref|NP_110896.1| 132 LYCDYCGNQI 141
                                   6********8 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 5.4
                       zf-RRN7   5 ppCgvC 10 
                                    +C+ C
  gi|13541208|ref|NP_110896.1| 157 VCCPNC 162
                                   579999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       987  (0.0550505); expected 358.6 (0.02)
Passed bias filter:                      674  (0.0375927); expected 358.6 (0.02)
Passed Vit filter:                       138  (0.00769703); 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: 0.61u 0.35s 00:00:00.96 Elapsed: 00:00:00.56
# Mc/sec: 941.80
//
Query:       gi|13541209|ref|NP_110897.1|  [L=56]
Description: transcription regulator (HTH) [Thermoplasma volcanium GSS1]
Scores for complete 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   21.3   0.0    0.00022   21.0   0.0    1.2  1  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an
     0.0021   18.4   0.0     0.0023   18.3   0.0    1.1  1  PrlF_antitoxin  prlF antitoxin for toxin YhaV_toxin
  ------ inclusion threshold ------
       0.17   11.1   0.0       0.19   11.0   0.0    1.0  1  BNR_3           BNR repeat-like domain


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 !   21.0   0.0   3.7e-08   0.00022       4      37 ..      17      51 ..      14      56 .] 0.83

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 3.7e-08
                                  TTEEEEEE-CCCHHHCCEECTCEEEEEECTT.CCC CS
                MazE_antitoxin  4 GnsgavriPkevrfelgireGdevelevdgd.kii 37
                                  G+s +v++Pk v ++l+++  d + +++ +d +  
  gi|13541209|ref|NP_110897.1| 17 GSSVRVTLPKKVLKKLNLKDEDLIAFYEGEDgRVY 51
                                  99*****************9888888888875554 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 !   18.3   0.0   3.8e-07    0.0023       3      42 ..      12      53 ..      10      56 .] 0.84

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 3.8e-07
                PrlF_antitoxin  3 tlterg...qttiPasvRkaLklkkgrdkiaytilddgkvvis 42
                                  ++t+rg     t+P+ v k L+lk  +d ia+   +dg+v+i+
  gi|13541209|ref|NP_110897.1| 12 RMTKRGssvRVTLPKKVLKKLNLKD-EDLIAFYEGEDGRVYIE 53
                                  56776522257*************8.99*************97 PP

>> BNR_3  BNR repeat-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   3.2e-05      0.19     267     310 .]       1      44 [.       1      44 [. 0.78

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 3.2e-05
                         BNR_3 267 lTDnthivdigpvssedd..dvaaSslLyksgeennkkeeLialYE 310
                                   +TDn +i+di  ++       v+ ++   k+ +   k+e Lia YE
  gi|13541209|ref|NP_110897.1|   1 MTDNRRIMDIARMTKRGSsvRVTLPKKVLKKLN--LKDEDLIAFYE 44 
                                   6***********976665335677776666664..89********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       491  (0.0273858); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.34s 00:00:00.83 Elapsed: 00:00:00.52
# Mc/sec: 323.10
//
Query:       gi|13541210|ref|NP_110898.1|  [L=632]
Description: ATPase [Thermoplasma volcanium GSS1]
Scores for complete 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   55.8   0.0      2e-14   53.4   0.0    1.9  1  TrwB_AAD_bind    Type IV secretion-system coupling protein DN
      1e-10   41.7   0.0    2.8e-10   40.3   0.0    1.8  1  TraG-D_C         TraM recognition site of TraD and TraG
    1.5e-10   41.6   0.1    3.2e-10   40.5   0.1    1.6  1  DUF87            Helicase HerA, central domain
    1.1e-06   29.0   0.0      0.064   13.5   0.0    2.8  2  AAA_22           AAA domain
      3e-05   23.0   0.6    0.00053   18.9   0.6    2.2  1  T4SS-DNA_transf  Type IV secretory system Conjugative DNA tra
    0.00012   21.5   0.0      0.001   18.5   0.0    2.1  2  FtsK_SpoIIIE     FtsK/SpoIIIE family
     0.0032   17.3   0.0        1.9    8.3   0.0    2.3  2  Helicase_RecD    Helicase
     0.0058   16.2   0.1      0.022   14.3   0.0    1.9  2  AAA_7            P-loop containing dynein motor region
     0.0061   15.5   0.1      0.011   14.7   0.1    1.3  1  AAA_10           AAA-like domain
  ------ inclusion threshold ------
      0.014   15.5   0.0      0.082   13.0   0.0    1.9  2  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
      0.023   15.2   0.1        2.7    8.5   0.0    2.5  2  AAA_18           AAA domain
      0.024   13.8   0.1        2.1    7.5   0.0    2.3  2  DUF815           Protein of unknown function (DUF815)
      0.029   13.5   0.0      0.053   12.6   0.0    1.3  1  T2SSE            Type II/IV secretion system protein
      0.029   14.1   0.0       0.11   12.3   0.0    1.9  2  DEAD             DEAD/DEAH box helicase
      0.032   14.3   0.1         11    6.1   0.0    3.4  3  AAA_14           AAA domain
      0.054   12.9   0.1       0.41   10.1   0.1    2.2  2  Pox_A32          Poxvirus A32 protein
      0.068   11.7   0.0       0.13   10.8   0.0    1.4  1  DUF853           Bacterial protein of unknown function (DUF85
      0.075   12.7   0.0        6.2    6.5   0.0    2.5  2  AAA_30           AAA domain
       0.11   12.0   0.0        5.1    6.5   0.0    2.5  2  PhoH             PhoH-like protein
       0.11   13.0   0.0       0.26   11.8   0.0    1.6  1  ABC_tran         ABC transporter
       0.14   12.5   0.0        1.8    8.9   0.0    2.6  2  AAA_16           AAA ATPase domain


Domain annotation for each model (and alignments):
>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.4   0.0   2.3e-17     2e-14      14     333 ..      36     366 ..      30     382 .. 0.76

  Alignments for each domain:
  == domain 1  score: 53.4 bits;  conditional E-value: 2.3e-17
                 TrwB_AAD_bind  14 etqhilivGttGsGKtqalekllrairargdraivlDltGafvsrfydegkdil...lnPlDaRsaaWsvfaei.keksdf 90 
                                      h+ i+G tG+GK+  l  ll+++ +    ++v+D++G++ ++ y+ +k ++   l+ ++++ a+ ++  ++ ++  d+
  gi|13541210|ref|NP_110898.1|  36 LSGHLSITGKTGTGKSSYLVYLLKNLDKERANVVVIDPHGTLKDAVYNTKKKVIylgLDRVEKNGASYQMKMNVlDRRFDA 116
                                   5679*************************************************9555666678999999877662555677 PP

                 TrwB_AAD_bind  91 aeiAaal..ipedggssdpfWaeaartvlaetlrelvrekkksn.aallralltadleeLkellagteaaalva......e 162
                                   + +   +  i +++  s++ W    + ++ ++l e+ + + + + ++ +r  +++d+  +  ++ + e +a+ +       
  gi|13541210|ref|NP_110898.1| 117 NMLGGWIrsIFSSKAVSNNTWGPRLEVMFRSVLAEYIKSQDNPTlSEFFR--IVSDVTSMRMFIGEIENDAVRSliksfiS 195
                                   76654322245558999****************99988766655488888..77889999998887777776664435542 PP

                 TrwB_AAD_bind 163 eaertaasiratlatnlevlelLa......ekgerFSireWleeedesgwlfltskaeqr..al.lrpllsawldlaikal 234
                                   + +   +   +tl++ l +++         +++   S+  + e   +++++f+  ++ ++  ++ ++     ++++   al
  gi|13541210|ref|NP_110898.1| 196 DRSYWREYSASTLNKILPLISDESvndlvsSSK--NSLDLYTEMATADRFVFVDVAKGKMpsEVsTQIAFLFLMKIWFDAL 274
                                   333233333344444444443322223312333..588888888888******998877622331344455689******* PP

                 TrwB_AAD_bind 235 lslpesrerrlWfflDElpaLgrleelksllaegRkfGgavvlglqsiaqlrevYGedaaqsilslvntklilrvsdaetA 315
                                   ++ ++s   ++++++DE ++++  + l+++l egRk+G+ ++l  q i+q++  Y++    ++ ++v++ + + vs ++ A
  gi|13541210|ref|NP_110898.1| 275 VRYNRSGPVKTYVVVDEAQNVPP-DILETILSEGRKYGISLILSNQYISQMEG-YSS----AVYGNVRNFISFLVSHED-A 348
                                   ********************997.99************************974.666....899****99999888665.6 PP

                 TrwB_AAD_bind 316 eelsellGeqeverstes 333
                                    +ls+++G++ v+r+ e 
  gi|13541210|ref|NP_110898.1| 349 AYLSRTVGNHPVSRKLER 366
                                   68999****999998765 PP

>> TraG-D_C  TraM recognition site of TraD and TraG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.3   0.0   3.3e-13   2.8e-10       3      87 ..     286     363 ..     284     384 .. 0.89

  Alignments for each domain:
  == domain 1  score: 40.3 bits;  conditional E-value: 3.3e-13
                      TraG-D_C   3 lfllDEfanlgkipdleellstgrsrgislvlilQsiaqleelYgkegaetilgncdvklflgvndeetaeelSkllGekt 83 
                                   ++++DE++n+++ + le++ls+gr++gisl+l  Q i+q+e  Y     ++++gn+ + + + + ++e a +lS+ +G++ 
  gi|13541210|ref|NP_110898.1| 286 YVVVDEAQNVPP-DILETILSEGRKYGISLILSNQYISQME-GYS----SAVYGNVRNFISF-LVSHEDAAYLSRTVGNHP 359
                                   789******977.99*************************9.674....89*********77.589**************9 PP

                      TraG-D_C  84 vese 87 
                                   v+++
  gi|13541210|ref|NP_110898.1| 360 VSRK 363
                                   9865 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.5   0.1   3.8e-13   3.2e-10       8      68 ..      23      81 ..      18     118 .. 0.80

  Alignments for each domain:
  == domain 1  score: 40.5 bits;  conditional E-value: 3.8e-13
                         DUF87  8 sgsevpvyldlnklvtrHlAilgsTGsGKSntvavLleellekkgatililDpHGEYgkal 68
                                  ++ + p y++ n+l + Hl i g+TG+GKS    +Ll++l  k +a+++++DpHG  ++a 
  gi|13541210|ref|NP_110898.1| 23 DQYGRPFYINYNSL-SGHLSITGKTGTGKSSYLVYLLKNLD-KERANVVVIDPHGTLKDAV 81
                                  5566799****999.**************************.*************766665 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   7.5e-05     0.064       6      47 ..      38      73 ..      34      88 .. 0.85
   2 !   12.3   0.0   0.00019      0.16      86     128 ..     278     317 ..     227     322 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7.5e-05
                        AAA_22  6 gilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtl 47
                                  g+l +tG +GtGK+  l  ll++ld+e      r+ vv +++
  gi|13541210|ref|NP_110898.1| 38 GHLSITGKTGTGKSSYLVYLLKNLDKE------RANVVVIDP 73
                                  899*********************876......777776665 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00019
                        AAA_22  86 lraravielliiDEaqhlrseealeeLrsllnlsrkgvqliLv 128
                                    r+  v+  +++DEaq++ ++++le++ s     ++g++liL 
  gi|13541210|ref|NP_110898.1| 278 NRSGPVKTYVVVDEAQNV-PPDILETILSEGR--KYGISLILS 317
                                   3333337899********.********77666..999999996 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 !   18.9   0.6   6.2e-07   0.00053      45     389 ..      38     361 ..      15     375 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 6.2e-07
               T4SS-DNA_transf  45 ehvlvvAptrsgKgvgvv..iPnllkwkqsiVvlDpkgElaeltskiRkkqgr.kVfvlePanlktsdrfNpldyidlkse 122
                                    h ++ + t+ gK+  +v  + nl k+  ++Vv+Dp g l + +++ +kk  +    ++e   +  + + N ld  +++ +
  gi|13541210|ref|NP_110898.1|  38 GHLSITGKTGTGKSSYLVylLKNLDKERANVVVIDPHGTLKDAVYNTKKKVIYlGLDRVEKNGASYQMKMNVLDR-RFDAN 117
                                   58899999999999865533788888888**********************999999999999999999**9997.89999 PP

               T4SS-DNA_transf 123 vetedilsvaslilkkkgkgkddffsntarqLlvaliaevllkketetegqtlkvvramlsepnledenkeeaklleelkg 203
                                   +    i+s+ s  + ++     + +      ++ +++ae+  ++ ++t +++ ++v+ + s    +   +e++++ + +k 
  gi|13541210|ref|NP_110898.1| 118 MLGGWIRSIFSSKAVSN-----NTWGPRLEVMFRSVLAEYIKSQDNPTLSEFFRIVSDVTSMRMFI-GEIENDAVRSLIKS 192
                                   99999999988888777.....57***********9999999999999999999999888877333.44444444444444 PP

               T4SS-DNA_transf 204 keedrvgdnlrvlvektdetrsSvlgtakselalyadplvrnatSksdFdlr...dlrrkkvsvyvivnpkd..levvapl 279
                                   + +dr+           +e ++   +t+++ l l +d+ v+ ++S+s  +l+   +++  +  v+v v   +  +ev  ++
  gi|13541210|ref|NP_110898.1| 193 FISDRS---------YWREYSA---STLNKILPLISDESVNDLVSSSKNSLDlytEMATADRFVFVDVAKGKmpSEVSTQI 261
                                   444443.........3343333...5668999************9988877622245555555555544322113444444 PP

               T4SS-DNA_transf 280 lrlffnmvvellkrklpnkde.rpkevlflLDEfpslGkleileealatiagYgirltlIiQsisqlketYgkegaksils 359
                                   + lf   ++++  ++l   ++  p+++    DE +++   +ile+ l  +++Ygi+l+l  Q isq+++ Y      ++ +
  gi|13541210|ref|NP_110898.1| 262 AFLF---LMKIWFDALVRYNRsGPVKTYVVVDEAQNVP-PDILETILSEGRKYGISLILSNQYISQMEG-YS----SAVYG 333
                                   4333...4455555444444314688999*******96.59**************************86.43....46778 PP

               T4SS-DNA_transf 360 nsavvivfaasndeetaeyiSkllGktTve 389
                                   n    i+f +s   e+a y+S+ +G+  v 
  gi|13541210|ref|NP_110898.1| 334 NVRNFISFLVSH--EDAAYLSRTVGNHPVS 361
                                   888899999999..9**********98665 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   1.2e-06     0.001      22      77 ..      20      71 ..      14      85 .. 0.82
   2 ?    0.1   0.0      0.49   4.2e+02     168     237 ..     302     378 ..     282     383 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.2e-06
                                  EEEETTS-EEEEEGGGS-.SEEEE--TTSSHHHHHHHHHHHHHTT--TTTEEEEEE CS
                  FtsK_SpoIIIE 22 lgkeisgnplvldlkkmashllvaGatgsGKStalntLilSlatthtPeeVqlili 77
                                  +g ++ g+p+++++++  +hl + G tg+GKS +l  L+ +l      e+ + ++i
  gi|13541210|ref|NP_110898.1| 20 IGMDQYGRPFYINYNSLSGHLSITGKTGTGKSSYLVYLLKNLDK----ERANVVVI 71
                                  577889*****************************999988754....55555555 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.49
                                   ........-----------B--...---EEEEEEC-HHHHHHHHHHH.......HHHHHHHHHHH.CGGGTEEEEEE CS
                  FtsK_SpoIIIE 168 sLsnqgpsygvhvlvtagrele...krpslvvivderieLrlaapkds...svlvedaivRlark.graaglHllla 237
                                    + ++g +yg+ ++++++  ++      ++  +v ++i   +++++ +   +     +++R  ++   +++lH l+a
  gi|13541210|ref|NP_110898.1| 302 TILSEGRKYGISLILSNQYISQmegYSSAVYGNVRNFISFLVSHEDAAylsRTVGNHPVSRKLERiLTTQSLHKLVA 378
                                   577889999999999988544422566789999******99999999888766677777776666466999999987 PP

>> Helicase_RecD  Helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.0    0.0022       1.9       2      57 ..      42      95 ..      41     117 .. 0.72
   2 !    6.7   0.0    0.0068       5.8      79     116 ..     272     309 ..     216     349 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0022
                 Helicase_RecD  2 ltAdRGRGKSaalGlalaaliaegksnilvtapskenvktlfeflakglealglke 57
                                  +t++ G+GKS+ l  +l++l +e+ +n++v  p+ +  + +++  +k    lgl++
  gi|13541210|ref|NP_110898.1| 42 ITGKTGTGKSSYLVYLLKNLDKER-ANVVVIDPHGTLKDAVYNTKKKV-IYLGLDR 95
                                  89*****************99996.59999988877655555555433.3455554 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0068
                 Helicase_RecD  79 iapdellklkeqadllvvDEAAaiplpllkkllekfkr 116
                                    a  +  ++   +  +vvDEA  +p ++l+++l++ ++
  gi|13541210|ref|NP_110898.1| 272 DALVRYNRSGPVKTYVVVDEAQNVPPDILETILSEGRK 309
                                   444555555556689*****************976554 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   2.5e-05     0.022      35      67 ..      39      71 ..      32      79 .. 0.89
   2 ?   -2.0   0.0       2.6   2.2e+03      94     141 ..     234     282 ..     225     290 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.5e-05
                         AAA_7 35 pvllvGptGtGKtviikdllkkldkekylslti 67
                                  ++ ++G+tGtGK++++  llk+ldke+ ++++i
  gi|13541210|ref|NP_110898.1| 39 HLSITGKTGTGKSSYLVYLLKNLDKERANVVVI 71
                                  66789********************99988876 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.6
                         AAA_7  94 ygPpggkklvvFvDDlnmpakekygaqpp.iellRqlldyggwYdrkkl 141
                                   y   ++    vFvD     ++ +  +q + + l++ ++d    Y+r+  
  gi|13541210|ref|NP_110898.1| 234 YTEMATADRFVFVDVAKGKMPSEVSTQIAfLFLMKIWFDALVRYNRSGP 282
                                   5555666667888888888888888887625688999999999999754 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.1   1.3e-05     0.011      21      83 ..      37      96 ..      31     108 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.3e-05
                        AAA_10 21 asasliiGdlGnGKSvlakllvlyisllggkaliiDpkkerekfketlpeiakkinvvtLdse 83
                                  + +  i+G++G GKS    +l  ++      +++iDp    + ++++ +   kk+ ++ Ld+ 
  gi|13541210|ref|NP_110898.1| 37 SGHLSITGKTGTGKSSYLVYLLKNLDKERANVVVIDPHGTLKDAVYNTK---KKVIYLGLDRV 96
                                  56889********************************998655555544...45555555554 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   9.7e-05     0.082       5      37 ..      43      73 ..      40     131 .. 0.78
   2 ?   -2.4   0.0       5.5   4.7e+03      36      69 ..     400     487 ..     388     508 .. 0.56

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 9.7e-05
                                  ESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEE CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          CbiA  5 stkGGvGKTtlaanLaralarrglrVllvDaDp 37
                                   +k G+GK++ ++ L++ l +++ +V+++D  p
  gi|13541210|ref|NP_110898.1| 43 TGKTGTGKSSYLVYLLKNLDKERANVVVID--P 73
                                  69***************************9..3 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 5.5
                                   EESSCCCCHHTTEB-HHHH......................................................CCHCCCHH CS
                                   xxxxxxxxxxxxxxxxxxx......................................................xxxxxxxx RF
                          CbiA  36 Dpqannlaileglendiep......................................................dlkrllel 62 
                                   D   + + + +g+++ +++                                                      d++  +++
  gi|13541210|ref|NP_110898.1| 400 DERIEESIVEFGSKGTERKteseesdhsklisafakyldghgiqvnfghagkyipdsffyygdrlfiveaensDIDHKERI 480
                                   555555555555555555555555555555555555555555555555555555555555555555555666655555555 PP

                                   HHHHCHC CS
                                   xxxxxxx RF
                          CbiA  63 lealgkk 69 
                                   l +l+++
  gi|13541210|ref|NP_110898.1| 481 LDKLKHH 487
                                   5555554 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.0    0.0032       2.7       3      32 ..      42      81 ..      41     155 .. 0.68
   2 ?    4.1   0.0     0.073        63      24     114 ..     379     484 ..     355     503 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0032
                        AAA_18  3 ltGtpGvGKttlakeL.....skrlgf.........gvnlrdva 32
                                  +tG+ G+GK++   +L     +              +  l+d +
  gi|13541210|ref|NP_110898.1| 42 ITGKTGTGKSSYLVYLlknldK----EranvvvidpHGTLKDAV 81
                                  8**************9444432....133346666633333333 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.073
                        AAA_18  24 f...........gvnlrdvakenglllevdpe...aldeskrldedkldklldaleenssaleegknlvidghlaelesea 90 
                                               g+n+  +ak+++++++  ++    ++++ + +e  + kl++a+ +  +    g+ + +   +a  + ++
  gi|13541210|ref|NP_110898.1| 379 WstdgsygpvslGFNVVPIAKDERIEESIVEFgskGTERKTESEESDHSKLISAFAKYLD----GHGIQVNFGHAGKYIPD 455
                                   14444556667799******************9999999999999999999999999754....77776655555555555 PP

                        AAA_18  91 akdikk...vvLtasp..eelleRlekRg 114
                                    +++++   ++++a++    ++eR+ +  
  gi|13541210|ref|NP_110898.1| 456 SFFYYGdrlFIVEAENsdIDHKERILDKL 484
                                   55555559977777663256777777665 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0    0.0024       2.1      56      89 ..      40      73 ..      32      95 .. 0.85
   2 ?    3.8   0.0     0.032        28      78     113 ..     460     495 ..     456     502 .. 0.91

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0024
                        DUF815 56 vLLwGarGtGKSslvkallneyaeegLrlievek 89
                                  + ++G+ GtGKSs +  ll+++ +e   ++ ++ 
  gi|13541210|ref|NP_110898.1| 40 LSITGKTGTGKSSYLVYLLKNLDKERANVVVIDP 73
                                  5689******************999988887765 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.032
                        DUF815  78 aeegLrlievekedlkelpklvellrerperfilfv 113
                                     + L ++e e++d+++ ++++++l++ + r i+f+
  gi|13541210|ref|NP_110898.1| 460 YGDRLFIVEAENSDIDHKERILDKLKHHNWRKIVFL 495
                                   566799****************************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 ?   12.6   0.0   6.2e-05     0.053     131     163 ..      39      71 ..      31      82 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6.2e-05
                         T2SSE 131 lilvsGgTgsGKttllyallkeinksderivtv 163
                                    + ++G Tg+GK+  l  llk ++k+  ++v++
  gi|13541210|ref|NP_110898.1|  39 HLSITGKTGTGKSSYLVYLLKNLDKERANVVVI 71 
                                   5669**********************9999987 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00013      0.11      16      97 ..      39     113 ..      31     127 .. 0.81
   2 ?   -2.2   0.0       3.4   2.9e+03     123     132 ..     285     294 ..     256     298 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00013
                                   EEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTT.STSEEEEEETTSSHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD  16 dvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkky.idlrvlliiggvaardqlskld 95 
                                   ++ + ++TG+GK+  +l+ +l+++    +k++  ++++ P   L   ++n+ kk++   +d rv+   +g +++ ++++ld
  gi|13541210|ref|NP_110898.1|  39 HLSITGKTGTGKSS-YLVYLLKNL----DKERANVVVIDPHGTLKDAVYNTKKKVIYLgLD-RVE--KNGASYQMKMNVLD 111
                                   667889******96.688899888....79999*****************99999984344.443..67888888888887 PP

                                   TT CS
                                   xx RF
                          DEAD  96 ng 97 
                                   ++
  gi|13541210|ref|NP_110898.1| 112 RR 113
                                   66 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 3.4
                                   EEEEEETHHH CS
                                   xxxxxxxxxx RF
                          DEAD 123 rflVlDEadr 132
                                   +++V+DEa++
  gi|13541210|ref|NP_110898.1| 285 TYVVVDEAQN 294
                                   589****986 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.076        65       5      39 ..      40      74 ..      37     133 .. 0.67
   2 ?    6.1   0.0     0.013        11      62     104 ..     278     321 ..     227     345 .. 0.71
   3 ?   -0.2   0.0       1.1   9.3e+02      54      87 ..     584     618 ..     551     627 .. 0.69

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.076
                        AAA_14  5 lvitGaRrvGKTtllkqlikellvkkesilyinld 39
                                  l itG   +GK+ +l  l+k+l  ++ +++ i+  
  gi|13541210|ref|NP_110898.1| 40 LSITGKTGTGKSSYLVYLLKNLDKERANVVVIDPH 74
                                  6799999*******999998888666666666533 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.013
                        AAA_14  62 e...ekktylflDEiqevpewekalkslvdegknldvivtGSnskl 104
                                   +   + kty++ DE+q+vp   ++l  ++ eg+++ + +  Sn+++
  gi|13541210|ref|NP_110898.1| 278 NrsgPVKTYVVVDEAQNVPP--DILETILSEGRKYGISLILSNQYI 321
                                   1344679***********84..667777777766666666666655 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 1.1
                        AAA_14  54 elileklkeekktylflDEiqevpewe.kalkslv 87 
                                    ++ +++k++++ +l +D i  ++++  +a++++v
  gi|13541210|ref|NP_110898.1| 584 AAVYSEMKTKRQFILNIDNITSLNNFTnDAIRRFV 618
                                   34444444568888999999999998525777766 PP

>> Pox_A32  Poxvirus A32 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1   0.00048      0.41      15      49 ..      39      73 ..      30      99 .. 0.81
   2 ?   -0.2   0.0      0.64   5.5e+02     112     168 ..     295     354 ..     272     373 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00048
                       Pox_A32 15 rlalvGgsGsGktvyLlsLlrtlvkkykhifLltp 49
                                  +l ++G++G Gk  yL  Ll++l k+   + ++ p
  gi|13541210|ref|NP_110898.1| 39 HLSITGKTGTGKSSYLVYLLKNLDKERANVVVIDP 73
                                  5899******************9887776666666 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.64
                       Pox_A32 112 tksktLlellnvgRhlnvsiilLcqtykhvp...vngrasithlvcinvsssdienllrs 168
                                   +   +L ++l  gR   +s+il  q    ++   +    ++  ++++ vs++d   l r+
  gi|13541210|ref|NP_110898.1| 295 VPPDILETILSEGRKYGISLILSNQYISQMEgysSAVYGNVRNFISFLVSHEDAAYLSRT 354
                                   55678999999*********9988876666511144455777788888888887777665 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 ?   10.8   0.0   0.00015      0.13       6      64 ..      22      80 ..      18     109 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00015
                        DUF853  6 akeaeqelalalklanrhGliaGatGtGktvtLqvlaeslseaGvpvfladvkGdLsgi 64
                                   ++  ++ +++ +    h  i+G tGtGk   L  l ++l +    v++ d  G L + 
  gi|13541210|ref|NP_110898.1| 22 MDQYGRPFYINYNSLSGHLSITGKTGTGKSSYLVYLLKNLDKERANVVVIDPHGTLKDA 80
                                  56777888999999999**********************************99999765 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0    0.0072       6.2      22      57 ..      41      76 ..      34      88 .. 0.84
   2 ?    3.4   0.0     0.063        53      88     121 ..     282     316 ..     238     318 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0072
                        AAA_30 22 vltGpAGtGKttalkalreaweaaggrviglAptgk 57
                                   +tG  GtGK+  l  l + ++++  +v+++ p g+
  gi|13541210|ref|NP_110898.1| 41 SITGKTGTGKSSYLVYLLKNLDKERANVVVIDPHGT 76
                                  589************999999999889999877766 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.063
                        AAA_30  88 pg.tllivDEagmvdtkqlaallkaaekagakvil 121
                                   p  t ++vDEa  v  + l+++l++ +k+g+++il
  gi|13541210|ref|NP_110898.1| 282 PVkTYVVVDEAQNVPPDILETILSEGRKYGISLIL 316
                                   44499******************999999999887 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0     0.093        80      23      53 ..      41      70 ..      28     123 .. 0.68
   2 ?    6.5   0.0     0.006       5.1     121     140 ..     285     304 ..     283     311 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.093
                                  EEE--TTSSTTHHHHHHHHHHHHTTS-SEEE CS
                          PhoH 23 faiGpaGtGKtylavalavealkkkkvkrii 53
                                   ++G++GtGK+    ++ ++ l k++ + ++
  gi|13541210|ref|NP_110898.1| 41 SITGKTGTGKSSYL-VYLLKNLDKERANVVV 70
                                  689*******8542.3445555555555444 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.006
                                   EEEEE-SGGG--HHHHHHHH CS
                          PhoH 121 afvilDEAQnttkeqmkmfl 140
                                   ++v++DEAQn+ +  ++++l
  gi|13541210|ref|NP_110898.1| 285 TYVVVDEAQNVPPDILETIL 304
                                   79*********999988887 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00031      0.26      13      65 ..      39      92 ..      34     162 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00031
                                  EEEEEESTTSSHHHHHHHHTTSS--SEEEE.EETTCEGGGB-HHHCCHCEEEE- CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran 13 kvaivGenGaGKStLlkllagllkpteGei.lldgkdlkeqeleslrkeigvlp 65
                                   + i+G++G+GKS+ l  l+++l+++  ++  +d + + ++    ++k++ +l 
  gi|13541210|ref|NP_110898.1| 39 HLSITGKTGTGKSSYLVYLLKNLDKERANVvVIDPHGTLKDAVYNTKKKVIYLG 92
                                  578***********9988888888765554256655555556666666665555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0    0.0021       1.8      25      55 ..      38      68 ..      32      99 .. 0.83
   2 ?    0.1   0.0       1.1   9.4e+02     124     147 ..     272     295 ..     146     309 .. 0.48

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0021
                        AAA_16 25 elvllsGesGvGKsslvrellralekdggif 55
                                  + + ++G  G+GKss +  ll+ l k+++ +
  gi|13541210|ref|NP_110898.1| 38 GHLSITGKTGTGKSSYLVYLLKNLDKERANV 68
                                  5788*******************99995433 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1.1
                        AAA_16 124 krllallsrderplvlvlDdlqwa 147
                                    +l+++ +++  ++++v+D++q +
  gi|13541210|ref|NP_110898.1| 272 DALVRYNRSGPVKTYVVVDEAQNV 295
                                   222244444333466677766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (632 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       685  (0.0382063); expected 358.6 (0.02)
Passed bias filter:                      591  (0.0329634); expected 358.6 (0.02)
Passed Vit filter:                        93  (0.00518713); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.79u 0.32s 00:00:01.11 Elapsed: 00:00:00.50
# Mc/sec: 3777.48
//
Query:       gi|13541211|ref|NP_110899.1|  [L=206]
Description: hypothetical protein TVN0380 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.068   12.9   0.0        0.1   12.4   0.0    1.2  1  NUDIX_5   NUDIX, or N-terminal NPxY motif-rich,  region of KR


Domain annotation for each model (and alignments):
>> NUDIX_5  NUDIX, or N-terminal NPxY motif-rich,  region of KRIT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   5.6e-06       0.1      29      70 ..     137     177 ..     133     198 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5.6e-06
                       NUDIX_5  29 kKvLlevklraseeksksildyvlettksvspsnqGikgkRv 70 
                                   +K+ l +++ + ee +k+i+++++++++s   +  Gik kR 
  gi|13541211|ref|NP_110899.1| 137 RKYGLFIRISSCEEYNKEIMEFLDQQIRSLK-KRHGIKMKRC 177
                                   6888999**********************88.9*******95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       686  (0.038262); expected 358.6 (0.02)
Passed bias filter:                      605  (0.0337442); 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: 0.56u 0.32s 00:00:00.88 Elapsed: 00:00:00.52
# Mc/sec: 1189.62
//
Query:       gi|13541212|ref|NP_110900.1|  [L=155]
Description: hypothetical protein TVN0381 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.34s 00:00:00.87 Elapsed: 00:00:00.53
# Mc/sec: 879.98
//
Query:       gi|13541213|ref|NP_110901.1|  [L=375]
Description: ATPase of the AAA+ class involved in cell division [Thermoplasma volcanium GSS1]
Scores for complete 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-41  139.9   0.0    1.2e-40  139.0   0.0    1.5  1  AAA              ATPase family associated with various cellul
    2.6e-11   43.1   0.0    5.8e-11   42.0   0.0    1.6  1  AAA_lid_3        AAA+ lid domain
    1.7e-06   28.3   0.0    4.3e-06   27.0   0.0    1.7  1  AAA_2            AAA domain (Cdc48 subfamily)
    5.9e-06   26.8   0.0    1.4e-05   25.6   0.0    1.6  1  AAA_16           AAA ATPase domain
    2.4e-05   24.3   0.0    7.7e-05   22.7   0.0    2.0  1  AAA_5            AAA domain (dynein-related subfamily)
    3.2e-05   23.8   0.0    6.2e-05   22.9   0.0    1.5  1  AAA_3            ATPase family associated with various cellul
    0.00091   19.0   0.0     0.0027   17.5   0.0    1.8  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
     0.0013   18.0   0.0     0.0025   17.1   0.0    1.4  1  TIP49            TIP49 P-loop domain
     0.0017   18.7   0.0     0.0086   16.4   0.0    2.0  2  AAA_22           AAA domain
     0.0022   18.0   0.0     0.0075   16.3   0.0    1.9  1  AAA_14           AAA domain
     0.0026   17.8   2.0      0.011   15.7   2.2    2.0  2  MIT              MIT (microtubule interacting and transport) 
     0.0036   17.0   0.0       0.03   14.0   0.0    2.2  1  Sigma54_activat  Sigma-54 interaction domain
      0.004   17.7   0.0     0.0086   16.6   0.0    1.5  1  ABC_tran         ABC transporter
     0.0047   16.7   0.0     0.0078   16.0   0.0    1.4  1  IstB_IS21        IstB-like ATP binding protein
     0.0052   17.2   0.0      0.013   15.9   0.0    1.7  1  RNA_helicase     RNA helicase
      0.006   16.1   0.0     0.0098   15.4   0.0    1.4  1  AAA_7            P-loop containing dynein motor region
  ------ inclusion threshold ------
       0.01   16.4   0.0      0.023   15.3   0.0    1.6  1  AAA_18           AAA domain
      0.011   15.5   0.0      0.027   14.3   0.0    1.8  1  Bac_DnaA         Bacterial dnaA  protein
      0.013   14.7   0.0      0.026   13.7   0.0    1.7  1  DUF815           Protein of unknown function (DUF815)
      0.013   15.3   0.2      0.031   14.0   0.0    1.7  2  AAA_11           AAA domain
      0.016   15.2   0.1       0.13   12.3   0.0    2.5  3  Vps4_C           Vps4 C terminal oligomerisation domain
      0.016   15.5   0.0      0.039   14.3   0.0    1.6  1  AAA_19           AAA domain
      0.018   14.7   0.1        0.4   10.2   0.0    2.2  2  AAA_25           AAA domain
      0.018   15.2   0.0      0.032   14.4   0.0    1.5  1  AAA_33           AAA domain
       0.02   14.6   0.0      0.036   13.8   0.0    1.3  1  AAA_30           AAA domain
      0.026   14.2   0.0      0.049   13.4   0.0    1.4  1  AAA_24           AAA domain
      0.032   14.2   0.0      0.063   13.3   0.0    1.4  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
      0.039   13.2   0.0      0.058   12.6   0.0    1.2  1  KAP_NTPase       KAP family P-loop domain
      0.045   13.7   0.0      0.077   12.9   0.0    1.5  1  Rad17            Rad17 P-loop domain
      0.047   12.9   0.0      0.087   12.0   0.0    1.4  1  PIF1             PIF1-like helicase
      0.054   12.6   0.0       0.11   11.6   0.0    1.4  1  MCM              MCM P-loop domain
      0.054   12.9   0.0       0.13   11.7   0.0    1.5  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
      0.058   13.1   0.0       0.11   12.2   0.0    1.4  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase
      0.088   11.8   0.0       0.24   10.3   0.0    1.7  1  AAA_6            Hydrolytic ATP binding site of dynein motor 
       0.12   11.5   0.0       0.21   10.6   0.0    1.3  1  Parvo_NS1        Parvovirus non-structural protein NS1
       0.12   12.3   0.0       0.77    9.6   0.0    2.0  2  NACHT            NACHT domain
       0.14   11.9   0.0       0.29   10.9   0.0    1.4  1  AAA_29           P-loop containing region of AAA domain


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.0   0.0   2.5e-43   1.2e-40       1     131 [.     148     279 ..     148     280 .. 0.97

  Alignments for each domain:
  == domain 1  score: 139.0 bits;  conditional E-value: 2.5e-43
                                   EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCHH CS
                           AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsgsesee 81 
                                   +llyGppGtGKT ++ka+a+e++++f++++ s+l s+++g  ek+i++lf++a+  + p i+f+DEidal+++r++s+s+ 
  gi|13541213|ref|NP_110901.1| 148 MLLYGPPGTGKTFIVKAIANEVKARFINVNPSTLYSEWFGVFEKNISKLFRAASLLS-PAIIFFDEIDALVPKRDTSNSDA 227
                                   89**************************************************99998.*********************** PP

                                   HHHHHHHHHHHHHHTTTS.SSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                           AAA  82 eervvnqLlteldgvkkk.eskvivigatnrpdkldpallr.gRfdrkieie 131
                                   ++r v+qLl+e+ g +++ ++++++i+atn+p+++d+a+lr gRfd+ki+++
  gi|13541213|ref|NP_110901.1| 228 AKRGVAQLLNEVGGINSQkNKNIFIIAATNNPWEVDEAMLRpGRFDIKIYVP 279
                                   **************998856789999************************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 !   42.0   0.0   1.2e-13   5.8e-11       1      42 [.     302     348 ..     302     351 .. 0.84

  Alignments for each domain:
  == domain 1  score: 42.0 bits;  conditional E-value: 1.2e-13
                     AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAa....llAlrrgike.itmed 42 
                                   +vd++ LAe+TeGySGAD++ +c++Aa    ++A++ g    ++++d
  gi|13541213|ref|NP_110901.1| 302 NVDYDLLAEETEGYSGADIEFICKKAAqnvfMEAVKTGKSRpVETRD 348
                                   7**************************77777788877765577776 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.0   8.9e-09   4.3e-06       6     128 ..     148     257 ..     145     268 .. 0.82

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 8.9e-09
                                   EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG---..----THHHHHHHHHTTT-HHHHTTSEEEEETGGG----. CS
                         AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselle..eeevehlvsrligappgyvgaeegGivllDEidKihpk. 83 
                                   +ll gp g+Gkt++ ka+a+  ++    ++i ++ s+l        e+ +s+l  a+          i+++DEid   pk 
  gi|13541213|ref|NP_110901.1| 148 MLLYGPPGTGKTFIVKAIANEVKA----RFINVNPSTLYSewFGVFEKNISKLFRAASLLS----PAIIFFDEIDALVPKr 220
                                   6899*****************995....999999999888233445677777777766665....67************** PP

                                   ---------HHHHHHHHHHHH--EE-------EE-TT-EEEEEE- CS
                         AAA_2  84 essgadvSregVqrdLLqileggtltdkqgrkvdtknilfImtga 128
                                   ++s++d  + gV ++L  +   g ++ +++     kni +I++++
  gi|13541213|ref|NP_110901.1| 221 DTSNSDAAKRGVAQLLNEV---GGINSQKN-----KNIFIIAATN 257
                                   **************98654...77777777.....7888888877 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.0   2.9e-08   1.4e-05      25     132 ..     146     245 ..     135     254 .. 0.71

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 2.9e-08
                        AAA_16  25 elvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesaeleawrekleeal 105
                                   + +ll+G++G+GK+ +v++++++++++   f++ +   l     ys +  ++++  + +   +++  + +  + +++++ +
  gi|13541213|ref|NP_110901.1| 146 GGMLLYGPPGTGKTFIVKAIANEVKAR---FINVNPSTL-----YSEWFGVFEK-NISKLFRAASLLSPAIIFFDEIDALV 217
                                   789*******************99988...999999999.....8889999954.66666666666666666666666666 PP

                        AAA_16 106 aavpelagaeasrllellkrll.allsr 132
                                      +   +++a+r  ++l + +    s+
  gi|13541213|ref|NP_110901.1| 218 PKRDTSNSDAAKRGVAQLLNEVgGINSQ 245
                                   6555555555666666666655455555 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.0   1.6e-07   7.7e-05       2      80 ..     148     219 ..     147     269 .. 0.72

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 1.6e-07
                                   EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGGG--HH CS
                         AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEveraese 80 
                                   +lL GppGtgK+++++ +a  +++++  ++ + +t +++ +g  e          s+l raa   +++i+++DE++ + ++
  gi|13541213|ref|NP_110901.1| 148 MLLYGPPGTGKTFIVKAIANEVKARF--INVNPSTLYSEWFGVFE-------KNISKLFRAASllSPAIIFFDEIDALVPK 219
                                   89*****************9887765..67788888888888888.......4668999999999**********976655 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 !   22.9   0.0   1.3e-07   6.2e-05       2     116 ..     148     263 ..     147     271 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 1.3e-07
                         AAA_3   2 vllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeekekefefkkGpvfanllladeinrappktqsal 82 
                                   +ll g PG++kt +vka+a+ ++++f  i + p  l s+  G  vfe++ +++   +  +   +++ dei+   pk +++ 
  gi|13541213|ref|NP_110901.1| 148 MLLYGPPGTGKTFIVKAIANEVKARF--INVNPSTLYSEWFG--VFEKNISKLFRAASLLSPAIIFFDEIDALVPKRDTSN 224
                                   6899****************999888..77889******999..699999888777777778999***********99999 PP

                         AAA_3  83 leameerqvtv....eg.ethklpepflvlatqnPieqe 116
                                    +a +     +    +g +++k ++ f++ at+nP e +
  gi|13541213|ref|NP_110901.1| 225 SDAAKRGVAQLlnevGGiNSQKNKNIFIIAATNNPWEVD 263
                                   9988765443311113324566677899999****9875 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   5.6e-06    0.0027      36      64 ..     148     176 ..     137     222 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 5.6e-06
                        RuvB_N  36 vllyGpPGlGkttlakiiakelgvklkit 64 
                                   +llyGpPG Gkt + k ia+e+++++   
  gi|13541213|ref|NP_110901.1| 148 MLLYGPPGTGKTFIVKAIANEVKARFINV 176
                                   79********************9987554 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   5.1e-06    0.0025      50      92 ..     145     185 ..     132     202 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 5.1e-06
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                         TIP49  50 GravLlaGpsgtGktalaiaiskelgedvpfvalsgsevysle 92 
                                   G ++Ll Gp+gtGkt +  ai++e+     f+ ++ s +ys  
  gi|13541213|ref|NP_110901.1| 145 GGGMLLYGPPGTGKTFIVKAIANEVK--ARFINVNPSTLYSEW 185
                                   7799********************97..78**********975 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   1.8e-05    0.0086       8      48 ..     148     179 ..     144     201 .. 0.83
   2 ?   -0.7   0.0       3.2   1.5e+03      88     105 ..     199     220 ..     186     253 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.8e-05
                        AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlp 48 
                                   ++++G++GtGKT+ ++ ++++          +++++ v+++
  gi|13541213|ref|NP_110901.1| 148 MLLYGPPGTGKTFIVKAIANEV---------KARFINVNPS 179
                                   789*****************99.........7777777665 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 3.2
                        AAA_22  88 arav..ielliiDEaqhlr..s 105
                                   a++   ++++  DE++ l   +
  gi|13541213|ref|NP_110901.1| 199 AASLlsPAIIFFDEIDALVpkR 220
                                   333366789999**99996541 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   1.5e-05    0.0075       6      76 ..     149     216 ..     146     260 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.5e-05
                        AAA_14   6 vitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpe.kllelilek.lkeekktylflDEiqev 76 
                                   ++ G+  +GKT+++k +++e      +++ +n  +   + +  +e ++ +l+++  l      ++f+DEi  +
  gi|13541213|ref|NP_110901.1| 149 LLYGPPGTGKTFIVKAIANEVK---ARFINVNPSTLYSEWFGVFEkNISKLFRAAsL--LSPAIIFFDEIDAL 216
                                   7899*************98777...88888888887777777776234455555442..45799******876 PP

>> MIT  MIT (microtubule interacting and transport) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   2.2   2.3e-05     0.011       1      51 [.       9      59 ..       9      70 .. 0.82
   2 ?   -1.6   0.0         6   2.9e+03      29      48 ..     327     349 ..     326     352 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.3e-05
                           MIT  1 ldkAlelvkkAveeDnagnyeeAlelYkealelLlqalkekneerrellre 51
                                  ++kA +l+++ ++e+++g+ ++A e+Y  a +++l+a + + +  +++   
  gi|13541213|ref|NP_110901.1|  9 IEKATKLLHAGIKEEENGHKDKAKEYYLVAYRVMLEAANDSPSDLKKKRLD 59
                                  68************************************9533344444444 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 6
                           MIT  29 ealelLlqalk.e.kne.errel 48 
                                    a +++++a+k   + + e+r+ 
  gi|13541213|ref|NP_110901.1| 327 AAQNVFMEAVKtGkSRPvETRDV 349
                                   57789999999544333566665 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.0   6.1e-05      0.03      25     144 ..     148     259 ..     132     278 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 6.1e-05
                                   EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS-TTCHHHHHHEBSSSSSTTTSS-BEHHHHHTTTSEEEEETGGGS CS
               Sigma54_activat  25 vlitGesGtGKellaraiheaskrkekpfvavncaaipeelleseLFGhekGaFtGAekekkGlfekadgGtlfLDeigel 105
                                   +l+ G  GtGK+++ +ai ++ k   ++f++vn      + l se FG+    F    ++   + +  +  ++f+Dei  l
  gi|13541213|ref|NP_110901.1| 148 MLLYGPPGTGKTFIVKAIANEVK---ARFINVNP-----STLYSEWFGV----FEKNISKLFRAASLLSPAIIFFDEIDAL 216
                                   79****************98766...78999984.....5567888876....5555555545556667789999999999 PP

                                   -HHHHHHHHHHHHHSE...EESBTS.SSEEE--EEEEEEESS- CS
               Sigma54_activat 106 plelQekLlrvlqege...vervGs.skeikvdvriiaatned 144
                                    ++  +    + ++g    ++ vG+ +++++ ++ iiaatn+ 
  gi|13541213|ref|NP_110901.1| 217 VPKRDTSNSDAAKRGVaqlLNEVGGiNSQKNKNIFIIAATNNP 259
                                   9988888777777665112567776356777888888888875 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   1.8e-05    0.0086      10      97 ..     144     244 ..     138     256 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.8e-05
                                   TTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS.--S-TTSBHHHH.......... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx.......... RF
                      ABC_tran  10 egekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe.pqlfpeltvren.......... 79 
                                    g  + + G+ G+GK+ ++k++a+++k     i+++   l ++   +++k+i+ l+   + l p +   ++          
  gi|13541213|ref|NP_110901.1| 144 FGGGMLLYGPPGTGKTFIVKAIANEVKA--RFINVNPSTLYSEWFGVFEKNISKLFRAaSLLSPAIIFFDEidalvpkrdt 222
                                   56667899*****************985..56777988888899************9966667777666668999988887 PP

                                   ....HHHTCHHHHHHHSTTGGT CS
                                   ....xxxxxxxxxxxxxxxxxx RF
                      ABC_tran  80 ....esdeeiekalsklglkel 97 
                                       ++++ ++++l+++g ++ 
  gi|13541213|ref|NP_110901.1| 223 snsdAAKRGVAQLLNEVGGINS 244
                                   7655555558888888876664 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 !   16.0   0.0   1.6e-05    0.0078      34      71 ..     132     169 ..     111     213 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.6e-05
                     IstB_IS21  34 kvkeLatlsfiekkenivllGpsGvGKshlaialgvea 71 
                                   k+keL +   i+   +++l Gp+G+GK+++  a++ e 
  gi|13541213|ref|NP_110901.1| 132 KFKELSQEYNIQFGGGMLLYGPPGTGKTFIVKAIANEV 169
                                   6778888888888999***************9999875 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   2.7e-05     0.013       2      35 ..     149     182 ..     148     227 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.7e-05
                  RNA_helicase   2 wlyGpsgeGKStlakeLakallkklklkkkdsvy 35 
                                   +lyGp+g+GK+ ++k +a+++  ++ + + +++y
  gi|13541213|ref|NP_110901.1| 149 LLYGPPGTGKTFIVKAIANEVKARFINVNPSTLY 182
                                   79*******************9888444444444 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 !   15.4   0.0     2e-05    0.0098      35      84 ..     147     191 ..     134     257 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2e-05
                         AAA_7  35 pvllvGptGtGKtviikdllkkldkekylsltinfsaqtsanqlqdiies 84 
                                    +ll+Gp GtGKt i+k + ++++       +in++ +t  ++   ++e+
  gi|13541213|ref|NP_110901.1| 147 GMLLYGPPGTGKTFIVKAIANEVK-----ARFINVNPSTLYSEWFGVFEK 191
                                   68****************999988.....555555555555555555555 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.0   4.7e-05     0.023       2      90 ..     149     264 ..     148     300 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 4.7e-05
                        AAA_18   2 lltGtpGvGKttlakeLskrlgf..................gvnlrdvakenglllevdpealdeskrldedkldklldal 64 
                                   ll G+pG+GKt + k+++++ +                     n++++++   ll +   + +de + l+ +++ +++da 
  gi|13541213|ref|NP_110901.1| 149 LLYGPPGTGKTFIVKAIANEVKArfinvnpstlysewfgvfEKNISKLFRAASLLSPAIIF-FDEIDALVPKRDTSNSDAA 228
                                   689**************88853346777999999999999988888888888888888888.5555555555554444444 PP

                        AAA_18  65 eenss.........aleegknl.vidghlaelesea 90 
                                   ++  +         +++++kn+ +i    + +e ++
  gi|13541213|ref|NP_110901.1| 229 KRGVAqllnevggiNSQKNKNIfIIAATNNPWEVDE 264
                                   444444444444444588888767777777777554 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   5.5e-05     0.027      37      75 ..     148     186 ..     134     308 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 5.5e-05
                                   EEEE-SSSSSHHHHHHHHHHHHHHHSSSS-EEEEEHHHH CS
                      Bac_DnaA  37 lfiygevGlGktHLlkaignevlenapelrvvYltaeeF 75 
                                   +++yg+ G Gkt ++kai+nev++++ +   + l +e F
  gi|13541213|ref|NP_110901.1| 148 MLLYGPPGTGKTFIVKAIANEVKARFINVNPSTLYSEWF 186
                                   79********************99998887777777766 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   5.3e-05     0.026      55      85 ..     147     174 ..      92     259 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.3e-05
                        DUF815  55 nvLLwGarGtGKSslvkallneyaeegLrli 85 
                                    +LL+G  GtGK  +vka+ ne++++    i
  gi|13541213|ref|NP_110901.1| 147 GMLLYGPPGTGKTFIVKAIANEVKARF---I 174
                                   58********************98754...3 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.3       4.1     2e+03     128     168 ..       4      44 ..       1      90 [. 0.50
   2 ?   14.0   0.0   6.5e-05     0.031      20      42 ..     148     170 ..     135     274 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 4.1
                        AAA_11 128 eiskeleklakelrafeeeeekeklkkskekskskleqerr 168
                                   ++++++ek  k l+a  +eee+  ++k+ke+    +++ ++
  gi|13541213|ref|NP_110901.1|   4 DVQNKIEKATKLLHAGIKEEENGHKDKAKEYYLVAYRVMLE 44 
                                   45555555555555555554442222222222222222222 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 6.5e-05
                        AAA_11  20 tliqGPPGtgKTktivellsqll 42 
                                    l+ GPPGtgKT+ + ++ +++ 
  gi|13541213|ref|NP_110901.1| 148 MLLYGPPGTGKTFIVKAIANEVK 170
                                   6899*********9999999885 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 ?   -1.9   0.0       7.3   3.5e+03      17      34 ..      96     113 ..      91     114 .. 0.74
   2 ?   -1.7   0.0         6   2.9e+03      21      48 ..     199     226 ..     189     230 .. 0.79
   3 ?   12.3   0.0   0.00027      0.13      26      58 ..     341     373 ..     327     375 .] 0.90

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 7.3
                        Vps4_C  17 mdipsdkllePpvtlkDf 34 
                                   ++i  +k   P+vt++D+
  gi|13541213|ref|NP_110901.1|  96 EEIGIEKPEIPKVTFEDV 113
                                   566667777799999996 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 6
                        Vps4_C  21 sdkllePpvtlkDflkalkkarptVske 48 
                                   +  ll P + + D ++al   r t +++
  gi|13541213|ref|NP_110901.1| 199 AASLLSPAIIFFDEIDALVPKRDTSNSD 226
                                   7789999999999999999998887765 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 0.00027
                        Vps4_C  26 ePpvtlkDflkalkkarptVskeDLekheeFTk 58 
                                    +pv+ +D+++++ + +p++  e Lek+ ++ +
  gi|13541213|ref|NP_110901.1| 341 SRPVETRDVIDVIGSIKPSIDYELLEKYSKYGS 373
                                   579*************************99865 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   8.1e-05     0.039      13      36 ..     148     171 ..     141     183 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 8.1e-05
                        AAA_19  13 llvtaGpGtGKTrvlkhivallve 36 
                                   +l+ ++pGtGKT ++k+i +++++
  gi|13541213|ref|NP_110901.1| 148 MLLYGPPGTGKTFIVKAIANEVKA 171
                                   899*************99988765 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00083       0.4      36      54 ..     148     166 ..     142     172 .. 0.83
   2 ?    2.1   0.0      0.26   1.2e+02     132     172 ..     195     235 ..     185     253 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00083
                        AAA_25  36 allaGapgtGKttlaldla 54 
                                    ll+G+pgtGKt+++  +a
  gi|13541213|ref|NP_110901.1| 148 MLLYGPPGTGKTFIVKAIA 166
                                   69***********986665 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.26
                        AAA_25 132 aleaaieevegvrlvviDplsralggdensnsdv.galveal 172
                                   +l +a+     ++ + +D ++++++   +snsd+ ++ v++l
  gi|13541213|ref|NP_110901.1| 195 KLFRAASL-LSPAIIFFDEIDALVPKRDTSNSDAaKRGVAQL 235
                                   55555555.45999************8888888667777776 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   6.7e-05     0.032       3      78 ..     149     256 ..     148     282 .. 0.61

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 6.7e-05
                        AAA_33   3 llvGlpGsGKstlaerllkklg..avllssdt...............................lrrrlfgtdqqsktdytr 50 
                                   ll G+pG+GK++ ++ ++++ +  ++ ++  t                               ++++l+++ ++s +d   
  gi|13541213|ref|NP_110901.1| 149 LLYGPPGTGKTFIVKAIANEVKarFINVNPSTlysewfgvfeknisklfraasllspaiiffdEIDALVPKRDTSNSD--A 227
                                   688***************999966666666665555555555555555555555555555555555555433333322..2 PP

                        AAA_33  51 vldrlyqilnelarkalsagrn.vildat 78 
                                   ++  + q lne+  ++ ++++n +i+ at
  gi|13541213|ref|NP_110901.1| 228 AKRGVAQLLNEVGGINSQKNKNiFIIAAT 256
                                   22224455555555555555553455555 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   7.4e-05     0.036      21      44 ..     148     171 ..     142     181 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 7.4e-05
                        AAA_30  21 avltGpAGtGKttalkalreawea 44 
                                   ++l Gp+GtGKt+++ka+++ ++a
  gi|13541213|ref|NP_110901.1| 148 MLLYGPPGTGKTFIVKAIANEVKA 171
                                   5789**************887665 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0    0.0001     0.049       5      35 ..     148     180 ..     147     221 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.0001
                        AAA_24   5 iliyGpsgiGKTtlakel..gpkplfidtekGl 35 
                                   +l+yGp+g+GKT ++k +  + k+ fi+++ ++
  gi|13541213|ref|NP_110901.1| 148 MLLYGPPGTGKTFIVKAIanEVKARFINVNPST 180
                                   79**************99887777777776655 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   0.00013     0.063      13      49 ..     139     177 ..     125     185 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00013
                                   HHHHCHTEEEEEEESTTSSHHHHHHHHHHHTT--..--- CS
                          TsaE  13 klakalgdvilLeGdLGaGKTtlvrglakalgve..evk 49 
                                   +   ++g  +lL+G+ G+GKT +v+++a++++ +  +v+
  gi|13541213|ref|NP_110901.1| 139 EYNIQFGGGMLLYGPPGTGKTFIVKAIANEVKARfiNVN 177
                                   3333335559*******************9988765555 PP

>> KAP_NTPase  KAP family P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00012     0.058      24      98 ..     149     256 ..     140     295 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00012
                    KAP_NTPase  24 gLygkWGsGKssllnkledelkefa..............................kpvrflfaefnawsfk...ggddava 71 
                                    Lyg+ G+GK+++++ + +e k +                                p  ++f e++a+ +k   +++da +
  gi|13541213|ref|NP_110901.1| 149 LLYGPPGTGKTFIVKAIANEVKARFinvnpstlysewfgvfeknisklfraasllSPAIIFFDEIDALVPKrdtSNSDAAK 229
                                   69*********************9999999999999999999999999999999988888888899998872223567888 PP

                    KAP_NTPase  72 ellaaLadaleeeygqlatkllrakkl 98 
                                   + +a+L+++++   +q+++++++  ++
  gi|13541213|ref|NP_110901.1| 230 RGVAQLLNEVGGINSQKNKNIFIIAAT 256
                                   888999999999888888888887665 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   0.00016     0.077      48     112 ..     148     213 ..     127     263 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00016
                         Rad17  48 LLisGPsGCgkstvvkvLskelgiklrewlnpvslkepdn..qksdfkgltekesrflsqiesfkel 112
                                   +L+ GP+G gk+ +vk ++ e   +++ ++np +l +  +   ++++  l+   s + + i  f e+
  gi|13541213|ref|NP_110901.1| 148 MLLYGPPGTGKTFIVKAIANEVKARFI-NVNPSTLYSEWFgvFEKNISKLFRAASLLSPAIIFFDEI 213
                                   6999*****************999998.689999888877555666777777777777777777776 PP

>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00018     0.087      20      49 ..     143     172 ..     132     183 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00018
                                   HCTS-EEEEESTTSSCHHHHHHHHHHCHCT CS
                          PIF1  20 ekgklfFvtGsgGtgKtflwkallkklrse 49 
                                   + g+ + ++G  GtgKtf+ ka+ + ++++
  gi|13541213|ref|NP_110901.1| 143 QFGGGMLLYGPPGTGKTFIVKAIANEVKAR 172
                                   56788999*****************99987 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00023      0.11      20      86 ..     107     173 ..      98     183 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00023
                                   HHSSTTSSS-HHHHHHHHHHHH---E.BBBSSSSBBCSS-EEEEEESSTSTHHHHHHHHHHHSSSEEE CS
                           MCM  20 ksiapsiyghedvkkaillqlfggvk.kkledktklrgdinvllvgdpgtaKsqlLkyveklapravy 86 
                                   k  ++ + g +dvk+ il +++ ++k k+l+++ +++    +ll g pgt+K+ ++k++++ + +a +
  gi|13541213|ref|NP_110901.1| 107 KVTFEDVAGLDDVKNEILGKIIYPMKfKELSQEYNIQFGGGMLLYGPPGTGKTFIVKAIANEV-KARF 173
                                   6678899****************99867888889999999******************99554.4444 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   0.00026      0.13      25      43 ..     148     166 ..     140     172 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00026
                  Mg_chelatase  25 lllvGppGsGKtmlakrlp 43 
                                   +ll+GppG+GKt + k+++
  gi|13541213|ref|NP_110901.1| 148 MLLYGPPGTGKTFIVKAIA 166
                                   89************99875 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00022      0.11       5      71 ..     152     213 ..     148     218 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00022
               Viral_helicase1   5 GvpGcGKStlirkllrts.liltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDEy 71 
                                   G pG GK+ +++ ++++    +  ++p   l++e++   +++  + ++++    ++     i+++DE+
  gi|13541213|ref|NP_110901.1| 152 GPPGTGKTFIVKAIANEVkARFINVNP-STLYSEWFGVFEKNISKLFRAASLL-SP----AIIFFDEI 213
                                   78***************9955545555.69******66666666666654443.33....48999997 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 ?   10.3   0.0    0.0005      0.24      24      65 ..     135     178 ..     128     190 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0005
                         AAA_6  24 tltqAlklklgg..apaGpagtGKtEtvkdLakalakqvvvfnc 65 
                                    l q +++++gg   ++Gp gtGKt  vk +a+++   ++ +n 
  gi|13541213|ref|NP_110901.1| 135 ELSQEYNIQFGGgmLLYGPPGTGKTFIVKAIANEVKARFINVNP 178
                                   56777888887722468****************99888877775 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   0.00044      0.21     118     139 ..     149     170 ..     140     181 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00044
                     Parvo_NS1 118 wfyGpantGktnlaeaIakavp 139
                                   ++yGp+ tGkt + +aIa+ v+
  gi|13541213|ref|NP_110901.1| 149 LLYGPPGTGKTFIVKAIANEVK 170
                                   79****************9875 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0    0.0016      0.77       3      27 ..     148     172 ..     147     182 .. 0.89
   2 ?   -0.1   0.0       1.6   7.8e+02      84     131 ..     207     258 ..     181     275 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0016
                                   EEEEC-TTTCHHHHHHHHHHHHCTS CS
                         NACHT   3 vilqGeaGsGKTtLlqklalawaeg 27 
                                   ++l G++G GKT  ++ +a + +++
  gi|13541213|ref|NP_110901.1| 148 MLLYGPPGTGKTFIVKAIANEVKAR 172
                                   6899***************998865 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.6
                                   EEEEE-STT-SS-TCH.............HHHHHCTTTTT--EEEEEEECCC CS
                         NACHT  84 LlilDglDelvtdlgq....kekqpvrtlLselirkkllpeasllltvrpra 131
                                    + +D +D lv + +     + k+ v +lL+e    ++ ++  +++++ +++
  gi|13541213|ref|NP_110901.1| 207 IIFFDEIDALVPKRDTsnsdAAKRGVAQLLNEVGGINSQKNKNIFIIAATNN 258
                                   3778999999987777777777788888888776666666666666665555 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0    0.0006      0.29      15      43 ..     138     166 ..     132     177 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0006
                        AAA_29  15 htieidlkgatlltGpsGsGKSTllDAiq 43 
                                   ++++i+  g +ll Gp G+GK+ ++ Ai+
  gi|13541213|ref|NP_110901.1| 138 QEYNIQFGGGMLLYGPPGTGKTFIVKAIA 166
                                   5566777789**************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (375 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       631  (0.0351944); expected 358.6 (0.02)
Passed bias filter:                      541  (0.0301746); expected 358.6 (0.02)
Passed Vit filter:                        99  (0.00552178); expected 17.9 (0.001)
Passed Fwd filter:                        37  (0.0020637); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              37  [number of targets reported over threshold]
# CPU time: 0.70u 0.34s 00:00:01.04 Elapsed: 00:00:00.52
# Mc/sec: 2184.61
//
Query:       gi|13541214|ref|NP_110902.1|  [L=212]
Description: coiled-coil domain-containing protein [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.2e-11   43.7  10.8    2.2e-11   43.7  10.8    1.6  2  Snf7           Snf7
     0.0071   16.5   2.3      0.011   15.9   1.3    1.9  2  Rad21_Rec8_N   N terminus of Rad21 / Rec8 like protein
  ------ inclusion threshold ------
      0.011   16.0   1.3      0.011   16.0   1.3    2.3  2  USP8_dimer     USP8 dimerisation domain
      0.046   13.4   4.0      0.063   13.0   4.0    1.1  1  SpoIISA_toxin  Toxin SpoIISA, type II toxin-antitoxin system
      0.056   12.9   0.1      0.064   12.7   0.1    1.2  1  DUF4152        Protein of unknown function (DUF4152)
        0.1   12.7   3.7       0.28   11.3   0.8    2.7  3  DUF2443        Protein of unknown function (DUF2443)
        1.1    9.4   6.1       0.37   10.9   2.2    2.2  2  YojJ           Bacterial membrane-spanning protein N-terminus


Domain annotation for each model (and alignments):
>> Snf7  Snf7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.7  10.8   8.6e-15   2.2e-11       4     159 ..      19     179 ..      16     190 .. 0.90
   2 ?   -0.4   0.1       0.3   7.7e+02     137     157 ..     187     207 ..     180     212 .] 0.76

  Alignments for each domain:
  == domain 1  score: 43.7 bits;  conditional E-value: 8.6e-15
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Snf7   4 rsLrkaerkldkkqeslekkikkleaelkklakkgnkdralllLKqkkryekqldqldnqlanleqvslaienlksnkevl 84 
                                   +++ k + ++d+ +++ ek  +   +++k   ++gn ++a++++  ++ +e+ +  l++ +  le++ l ++++ ++k+v 
  gi|13541214|ref|NP_110902.1|  19 SRISKWKSDIDRAIRQYEKNREMNIQNAKISLRDGNLEKARVFASNIVSLESAIRGLKDYKLFLENIDLNLQFADTTKKVW 99 
                                   67888999************************************************************************* PP

                                   HHHHHHHHHHHHHHHCTCCHHHHHHHHHHHHHHHHHTCHHHHHHHHHTT-.......GGTTHHHHHHHHHHHHHHHHHCSH CS
                          Snf7  85 namkqgakamkamnkkvdidkidklmdeiedqmekaeeisEalsrsldda.......deedEeeleaeLdaLeqelgdeel 158
                                   +++k+g + + + +  +   ++ ++++++e+ +  +++i+E ls++ld +        e + e ++++L+ L  + +++++
  gi|13541214|ref|NP_110902.1| 100 ASLKEGSEDLLKSQ--LTEKQVIQMQQNVEKIINSSDQIQERLSSQLDQIttavnqrGEYNVESVDKILETLKGDTEASKS 178
                                   *********97755..5556***************************9988878777788889999999999998888875 PP

                                   . CS
                          Snf7 159 l 159
                                   +
  gi|13541214|ref|NP_110902.1| 179 A 179
                                   4 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.3
                                   TTHHHHHHHHHHHHHHHHHCS CS
                          Snf7 137 edEeeleaeLdaLeqelgdee 157
                                   + E+ +++eL++L++ lg  +
  gi|13541214|ref|NP_110902.1| 187 QGEATTDKELEDLLKSLGGVK 207
                                   568889999999999877655 PP

>> Rad21_Rec8_N  N terminus of Rad21 / Rec8 like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.98   2.5e+03      26      43 ..      54      71 ..      38      90 .. 0.74
   2 !   15.9   1.3   4.1e-06     0.011      13     106 ..      94     191 ..      80     195 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.98
                  Rad21_Rec8_N 26 klskkeilevniekavee 43
                                  +l+k+ +++ ni +  ++
  gi|13541214|ref|NP_110902.1| 54 NLEKARVFASNIVSLESA 71
                                  678888888888765554 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 4.1e-06
                  Rad21_Rec8_N  13 plakvWlaAtl.ekklskkeilevni...ekaveeIlnpeaplaLrlsgqLllGvvriyskkvkyllsDceealekikkaf 89 
                                     +kvW   +  ++ l k++++e ++   ++ ve+I+n++ ++  rls+qL   ++   +++ +y ++ + ++le++k   
  gi|13541214|ref|NP_110902.1|  94 TTKKVWASLKEgSEDLLKSQLTEKQViqmQQNVEKIINSSDQIQERLSSQLDQ-ITTAVNQRGEYNVESVDKILETLKGDT 173
                                   567889444444557777777765542226889*****************987.77777999****************988 PP

                  Rad21_Rec8_N  90 ksikea.kidlpeekkae 106
                                   + +k+a ++ +p++ +a+
  gi|13541214|ref|NP_110902.1| 174 EASKSAsRTSEPAQGEAT 191
                                   877634377777766554 PP

>> USP8_dimer  USP8 dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   16.0   1.3   4.1e-06     0.011      24     109 ..      25     110 ..       8     117 .. 0.73
   2 ?    1.1   0.2      0.17   4.4e+02      86     110 ..     118     142 ..     110     157 .. 0.64

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 4.1e-06
                    USP8_dimer  24 kdkknksikrllrsaeklfkkAeeyrlegdeEkAYvlymkylnllelIrkksdykekkasvkellgdkkankvildklekL 104
                                   k++ +++i+++ ++ e  +++A+   ++g+ EkA v+    ++l ++Ir  +dyk + ++++ +l+ ++  k +  +l++ 
  gi|13541214|ref|NP_110902.1|  25 KSDIDRAIRQYEKNREMNIQNAKISLRDGNLEKARVFASNIVSLESAIRGLKDYKLFLENIDLNLQFADTTKKVWASLKEG 105
                                   333344554455555555899***********************************9999999888555555546666665 PP

                    USP8_dimer 105 kesLk 109
                                   +e L 
  gi|13541214|ref|NP_110902.1| 106 SEDLL 110
                                   55554 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.17
                    USP8_dimer  86 ellgdkkankvildklekLkesLkk 110
                                   ++++ +++ + i+++ ++++e+L+ 
  gi|13541214|ref|NP_110902.1| 118 QVIQMQQNVEKIINSSDQIQERLSS 142
                                   4444455555555666666666654 PP

>> SpoIISA_toxin  Toxin SpoIISA, type II toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   4.0   2.4e-05     0.063      91     203 ..      23     157 ..      15     167 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.4e-05
                                   XXXXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-EEEE...ESSHHHHHHHHHHHHHHHHHTTTSEEEEEE-SSH..... CS
                 SpoIISA_toxin  91 elekdiektikenekvlkanlrrvetftellqnesihvy.eeygskeayieglkkllksyadkfeisvsivpfevk..... 165
                                   + + di + i+++ek +++n + ++   +  + e+  v+ ++  s e+ i+glk++ k++ + ++++++    + k     
  gi|13541214|ref|NP_110902.1|  23 KWKSDIDRAIRQYEKNREMNIQNAKISLRDGNLEKARVFaSNIVSLESAIRGLKDY-KLFLENIDLNLQFADTTKKvwasl 102
                                   567889********************************999**************9.9**********99999988***** PP

                                   .................HHHHHHHTTSS-HHH.....HHHHHHTT--EE-TTSSE CS
                 SpoIISA_toxin 166 .................eekdelleaieqqlstikeevaekLdrqevvylkeekl 203
                                                     + +++ e+i ++ ++i+e + ++Ld+  + ++++++ 
  gi|13541214|ref|NP_110902.1| 103 kegsedllksqltekqvIQMQQNVEKIINSSDQIQERLSSQLDQITTAVNQRGEY 157
                                   **************9999999**************************99999886 PP

>> DUF4152  Protein of unknown function (DUF4152)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   2.5e-05     0.064      66     125 ..      55     115 ..      29     169 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.5e-05
                                   HHHHHHH--SEEEESS-SSS-BGGG--HHHHH.TSSS-HHHHHHHHHHHHHHHHHHHHHHH CS
                       DUF4152  66 velarkvkpdvvhldstlggielrkldeptie.algisdkgkevwkelskdlqplakklwe 125
                                   +e ar    ++v l+s++ g++  kl    i+  l  +d  k+vw  l +  + l k    
  gi|13541214|ref|NP_110902.1|  55 LEKARVFASNIVSLESAIRGLKDYKLFLENIDlNLQFADTTKKVWASLKEGSEDLLKSQLT 115
                                   6899999*******************999999569**********9887766665554333 PP

>> DUF2443  Protein of unknown function (DUF2443)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.18   4.5e+02      10      32 ..      30      52 ..      20      57 .. 0.75
   2 ?   11.3   0.8   0.00011      0.28      15      65 ..      81     132 ..      67     144 .. 0.82
   3 ?   -1.4   0.0      0.99   2.5e+03      51      63 ..     143     155 ..     132     170 .. 0.54

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.18
                                  HHHHHHHHHHHHHHHHHT--HHH CS
                       DUF2443 10 kdiedskeeielLLklakislvd 32
                                  + i + +++ e+ ++ akisl d
  gi|13541214|ref|NP_110902.1| 30 RAIRQYEKNREMNIQNAKISLRD 52
                                  445555566678899999*9988 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00011
                                   HHHHHHHHHHHHT--HHHHHHHHTTSS---T.TS-HHHHHHHHHHHHHHHHH CS
                       DUF2443  15 skeeielLLklakislvdyilikrGsldmPe.sldvafltqideevekLkea 65 
                                     e+i+l L++a+ +   +  +k Gs d+ + +l+   + q++++vek+ + 
  gi|13541214|ref|NP_110902.1|  81 FLENIDLNLQFADTTKKVWASLKEGSEDLLKsQLTEKQVIQMQQNVEKIINS 132
                                   4589************************865279*************98554 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.99
                                   HHHHHHHHHHHHH CS
                       DUF2443  51 fltqideevekLk 63 
                                    l qi + v++  
  gi|13541214|ref|NP_110902.1| 143 QLDQITTAVNQRG 155
                                   4555655555443 PP

>> YojJ  Bacterial membrane-spanning protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1       1.6   4.2e+03       9      25 ..      23      39 ..      16      49 .. 0.72
   2 ?   10.9   2.2   0.00014      0.37       6      51 ..     106     152 ..     102     156 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.6
                          YojJ  9 elkeklkeeLeqiekel 25
                                  + k+++ + ++q ek+ 
  gi|13541214|ref|NP_110902.1| 23 KWKSDIDRAIRQYEKNR 39
                                  67888888888877765 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00014
                          YojJ   6 leeelkeklk.eeLeqiekeleevlkaldeedeClLcelesirekfa 51 
                                   +e  lk++l  ++  q ++++e+++++ d+ +e+l ++l++i + ++
  gi|13541214|ref|NP_110902.1| 106 SEDLLKSQLTeKQVIQMQQNVEKIINSSDQIQERLSSQLDQITTAVN 152
                                   6777999986257999**************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2589  (0.144403); 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:                         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: 0.60u 0.34s 00:00:00.94 Elapsed: 00:00:00.51
# Mc/sec: 1253.89
//
Query:       gi|13541215|ref|NP_110903.1|  [L=102]
Description: hypothetical protein TVN0384 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.54    9.5   2.8       0.28   10.4   1.1    1.3  1  Pox_A11   Poxvirus A11 Protein
        2.4    8.3   8.9       0.46   10.6   4.8    2.0  2  DUF2198   Uncharacterized protein conserved in bacteria (DUF2


Domain annotation for each model (and alignments):
>> Pox_A11  Poxvirus A11 Protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   1.1   3.1e-05      0.28     240     306 ..      28      94 ..      22      99 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 3.1e-05
                       Pox_A11 240 vtnfiiiviivleqllvklGfeeikGlsteltselid.veiGedceaiavklGisnsPvlniilfivk 306
                                   vt fi+i+i ++    v + f     l t++t++l+  ++   d  + a  +G++ s  l i+lf++ 
  gi|13541215|ref|NP_110903.1|  28 VTSFILIIIALIISTYVGFSFAPHVSL-TNVTAKLVPyIKTYADQITKAISIGFGGSLSLTIVLFLIG 94 
                                   89*********9998887777766555.799999996256666666668899**************96 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 ?   10.6   4.8   5.1e-05      0.46      25      66 ..      11      52 ..       1      57 [. 0.81
   2 ?   -0.8   0.1      0.19   1.7e+03      25      31 ..      84      90 ..      57      98 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 5.1e-05
                       DUF2198 25 vGllltvaLivasvykgYtkelyiividiiSllaGflyakkm 66
                                  + +l+  +L   ++ kg t+ + ii++ iiS+ +Gf +a ++
  gi|13541215|ref|NP_110903.1| 11 IVALIDGLLFGLAIKKGVTSFILIIIALIISTYVGFSFAPHV 52
                                  4445555677899************************99765 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.19
                       DUF2198 25 vGllltv 31
                                  + l++++
  gi|13541215|ref|NP_110903.1| 84 LSLTIVL 90
                                  3334444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1108  (0.0617993); expected 358.6 (0.02)
Passed bias filter:                      510  (0.0284455); 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):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.35s 00:00:00.89 Elapsed: 00:00:00.53
# Mc/sec: 578.41
//
Query:       gi|13541216|ref|NP_110904.1|  [L=328]
Description: homoserine dehydrogenase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.1e-28   97.7   0.0    2.7e-27   95.8   0.0    1.8  2  Homoserine_dh  Homoserine dehydrogenase
      4e-11   43.6   0.0      8e-11   42.6   0.0    1.5  1  NAD_binding_3  Homoserine dehydrogenase, NAD binding domain


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 ?   -0.7   0.0      0.13   1.2e+03      88     115 ..     118     145 ..      66     150 .. 0.79
   2 !   95.8   0.0   3.1e-31   2.7e-27       1     173 []     151     321 ..     151     321 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.13
                                   EE--STTS-HHHHHHHHCTTEEEEEEEE CS
                 Homoserine_dh  88 evegiskltaedikeakeegkvlklvas 115
                                   + +g+ +  +e +++a+++++++++ a+
  gi|13541216|ref|NP_110904.1| 118 NKSGLANFWPEIMEYARSNNRRIRYEAT 145
                                   4456666677779999999999999776 PP

  == domain 2  score: 95.8 bits;  conditional E-value: 3.1e-31
                                   --HHHHHHTCTTSEEEEEEEE--HHHHHHHHHHHCHTT-HHHHHHHHHHTTSS-SSTHHHHTTHHHHHHHHHHHHHHCTTT CS
                 Homoserine_dh   1 PiiktlkeilsgdritrieGilngtlnyiltemeeegasfsevlkeaqelGyaeaDptdDveGlDaarKlailarlafgle 81 
                                   P+++ ++ +   +ri++++Gi++ t+ny + e+++ +++f++vl+ea++lG+ e++ +dD+ GlDaarK +il ++++g++
  gi|13541216|ref|NP_110904.1| 151 PLFSFIDYSVLPSRIKKFRGIVSLTINYFIRELAN-KREFDDVLSEATKLGIVEKNYKDDLTGLDAARKSVILCNHLYGSS 230
                                   788899999999**********************8.566****************************************** PP

                                   --GGGSEE--STTS-HHHHHHHHCTTEEEEEEEEE..C....EEEEEEEEEETTSGGGHSSST-EEEEEEESSSEEEEEEE CS
                 Homoserine_dh  82 veledvevegiskltaedikeakeegkvlklvasa..v....earVkpelvpkshplasvkgsenavlvetdrlgelviqG 156
                                   ++l+dv  egi +       + ++ gk  +lv ++  v    +a+ +++++++++ l ++ +   + +++td  g+l ++ 
  gi|13541216|ref|NP_110904.1| 231 YRLSDVFYEGILD-------QDRSFGKNERLVTETgiVngkpSAESRIKSLDSNDYLLTLGKGSLGYQLQTDTNGTLNVSD 304
                                   ***********74.......55667778888888765245559************************************** PP

                                   S-SSHHHHHHHHHHHHH CS
                 Homoserine_dh 157 pgaGaepTAsavlsDll 173
                                      G+++TA av++Dl+
  gi|13541216|ref|NP_110904.1| 305 LYDGPYETAGAVMNDLV 321
                                   ***************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 !   42.6   0.0   8.9e-15     8e-11       1     117 []      10     143 ..      10     143 .. 0.81

  Alignments for each domain:
  == domain 1  score: 42.6 bits;  conditional E-value: 8.9e-15
                                   --SHHHHHHHHHHHH---S....SEEEEEEEEESS.EEE-TT.........HHHHHT--CB---HHHHHHHH.S-EEEEE- CS
                 NAD_binding_3   1 GlGaiGsavleqlkrqqse....ielelvavadrd.sllskd.........rkallasealtldlddliahl.dpdvvVEc 66 
                                   GlG++G  +l+++++ ++e    +++++v+vad+  s  +++         +++   +  +++++ +  a + d d+vV++
  gi|13541216|ref|NP_110904.1|  10 GLGNVGLNLLRIIRSFNEEnrlgLKFNVVFVADSLhSYYNERidigkvisyKEKGSLDSLEYESISASEALArDFDIVVDA 90 
                                   9**************99999**************9888888899999988844444444444444443333338******* PP

                                   S--HH..HHT..THHHHHHTTEEEE-S--CGGG-HHHHHHHTSSSTTS--.EE-G CS
                 NAD_binding_3  67 assea..vae..lvlkaLkagkdvvtankgaladealyeeLreaaeangakiyve 117
                                   ++ +a   +e  ++ +  ++gkdvvtank+ la  + + e++e a++n+++i++e
  gi|13541216|ref|NP_110904.1|  91 TPASAdgKKElaFYKETFENGKDVVTANKSGLA--NFWPEIMEYARSNNRRIRYE 143
                                   7665521333337999*****************..*****************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       457  (0.0254894); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.32s 00:00:00.90 Elapsed: 00:00:00.52
# Mc/sec: 1902.20
//
Query:       gi|13541217|ref|NP_110905.1|  [L=270]
Description: ABC-type nitrate transporter, ATPase component [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      6e-29  101.3   0.0    8.2e-29  100.9   0.0    1.2  1  ABC_tran      ABC transporter
    5.3e-06   26.5   1.0      0.007   16.2   0.4    2.2  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    3.7e-05   23.7   0.0      8e-05   22.6   0.0    1.5  1  RsgA_GTPase   RsgA GTPase
    0.00017   22.0   0.0     0.0003   21.2   0.0    1.4  1  AAA_16        AAA ATPase domain
    0.00024   20.9   0.0    0.00036   20.4   0.0    1.3  1  AAA_15        AAA ATPase domain
    0.00099   18.8   0.0     0.0033   17.1   0.0    1.8  2  AAA_29        P-loop containing region of AAA domain
     0.0018   17.8   0.4       0.93    8.9   0.1    2.2  2  SMC_N         RecF/RecN/SMC N terminal domain
     0.0033   17.7   0.1     0.0091   16.3   0.1    2.0  1  AAA_22        AAA domain
      0.006   17.1   0.1     0.0091   16.5   0.1    1.3  1  AAA_23        AAA domain
  ------ inclusion threshold ------
      0.015   15.4   0.1      0.062   13.4   0.1    2.1  1  MMR_HSR1      50S ribosome-binding GTPase
      0.033   14.6   0.0       0.12   12.8   0.0    1.9  1  AAA           ATPase family associated with various cellular 
      0.034   13.9   0.0       0.05   13.3   0.0    1.4  1  AAA_24        AAA domain
       0.12   12.1   0.0       0.21   11.3   0.0    1.4  1  IstB_IS21     IstB-like ATP binding protein
       0.13   12.2   0.0       0.26   11.2   0.0    1.5  1  Rad17         Rad17 P-loop domain
       0.15   11.2   0.0       0.26   10.4   0.0    1.3  1  NB-ARC        NB-ARC domain
       0.16   12.4   0.0       0.37   11.2   0.0    1.6  1  RNA_helicase  RNA helicase
       0.16   11.9   0.1       0.32   10.9   0.1    1.5  1  NACHT         NACHT domain
       0.26   11.5   0.3       0.68   10.2   0.1    1.8  2  AAA_28        AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.9   0.0   8.2e-32   8.2e-29       2     137 .]      38     177 ..      37     177 .. 0.95

  Alignments for each domain:
  == domain 1  score: 100.9 bits;  conditional E-value: 8.2e-32
                                   EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx... RF
                      ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren... 79 
                                   ++++l+l+++e vaivG++G GKStLl++l g lkp++G++ l gk++++         i  ++q    fp +t+ en   
  gi|13541217|ref|NP_110905.1|  38 EDINLSLNRNEFVAIVGPSGIGKSTLLRILGGFLKPDKGSVYLMGKKINR-----PTPDIVLIHQSIVTFPWMTALENvmv 113
                                   689**************************************999999988.....9999********************** PP

                                   ..........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                   ..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  80 ..........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                             +++e +++al+++gl++++d       +++SgG++qrva+aral+ +p ++l+DEp+a
  gi|13541217|ref|NP_110905.1| 114 slkakhipndKAEEMAKEALETVGLQGFEDLYP----KEMSGGMRQRVAIARALAADPLVFLMDEPFA 177
                                   ******998777777************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 !   16.2   0.4     7e-06     0.007       1      23 [.      49      71 ..      49      90 .. 0.82
   2 !    8.8   0.0    0.0013       1.3     196     271 ..     119     180 ..      95     216 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 7e-06
                        AAA_21  1 lnvliGpNgsGKSnLLdaldlla 23
                                  + +++Gp g GKS+LL++l ++ 
  gi|13541217|ref|NP_110905.1| 49 FVAIVGPSGIGKSTLLRILGGFL 71
                                  679****************8774 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0013
                        AAA_21 196 eielsdlgegeeliasvderlrergvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLH 271
                                   +i+ ++ +e+ ++  ++  ++           +  +l + e+S G+++  a++ al++++    ++l DEp ++L+
  gi|13541217|ref|NP_110905.1| 119 HIPNDKAEEMAKEALETVGLQ-----------GFEDLYPKEMSGGMRQRVAIARALAADP---LVFLMDEPFAHLD 180
                                   444444444444444444443...........347888999********99999999988...89**********8 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0     8e-08     8e-05      57     121 ..       4      69 ..       2      87 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 8e-08
                                   GG--HHHHHHHHHHHHHHTTSEEEE--TTTH.TTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCT CS
                   RsgA_GTPase  57 Dlleeeeeleelkeelealgyevllvsaktk.egleelkellkd.ktsvlvGqSGvGKStLinallp 121
                                   Dl+ e++ +e+ ++  + l+ + +  s +++ + +e+++  l+  +++++vG+SG+GKStL+  l +
  gi|13541217|ref|NP_110905.1|   4 DLVRESQ-IEKPSNSSSVLEAANIDFSYENGyKVFEDINLSLNRnEFVAIVGPSGIGKSTLLRILGG 69 
                                   7777877.77777777777766666666665478899*99998879****************98865 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   3.1e-07    0.0003      23     142 ..      46     173 ..      37     208 .. 0.53

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 3.1e-07
                        AAA_16  23 rpelvllsGesGvGKsslvrellralekdggif.lrgkcdql........esaipysalaqalareellrqllde..aesa 92 
                                   r e v ++G+sG+GKs+l+r l   l+ d+g + l gk            +++i   ++ +al +  ++  l+++  +++ 
  gi|13541217|ref|NP_110905.1|  46 RNEFVAIVGPSGIGKSTLLRILGGFLKPDKGSVyLMGKKINRptpdivliHQSIVTFPWMTAL-E-NVMVSLKAKhiPND- 123
                                   45789*****************99999995333366665555322222332222223566666.3.44444444432222. PP

                        AAA_16  93 eleawrekleeala.......avpelagaeasrllellkrll..allsrderplvlvlD 142
                                   ++e+ +++ +e+++                 + +   +++ +  a++   ++plv+++D
  gi|13541217|ref|NP_110905.1| 124 KAEEMAKEALETVGlqgfedlYP--------KEMSGGMRQRVaiARALA-ADPLVFLMD 173
                                   22222222222222343333322........333333333332122222.457888887 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   3.6e-07   0.00036      10      56 ..      33      76 ..      31     140 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 3.6e-07
                        AAA_15 10 NFRslkdveidlsee.ltvliGkNnsGKSsilealdlFlnnkekknkk 56
                                   ++ ++d+ ++l+ + +  ++G+ ++GKS++l++l  Fl+ +    k 
  gi|13541217|ref|NP_110905.1| 33 GYKVFEDINLSLNRNeFVAIVGPSGIGKSTLLRILGGFLKPD----KG 76
                                  599****999999999***********************987....23 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   3.3e-06    0.0033      12      39 ..      37      64 ..      33      76 .. 0.86
   2 ?   -2.7   0.0       5.1     5e+03      38      50 ..     254     266 ..     254     268 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 3.3e-06
                        AAA_29 12 fdghtieidlkgatlltGpsGsGKSTll 39
                                  f++  +++++++++ ++GpsG GKSTll
  gi|13541217|ref|NP_110905.1| 37 FEDINLSLNRNEFVAIVGPSGIGKSTLL 64
                                  666677888888***************8 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 5.1
                        AAA_29  38 llDAiqalLvpak 50 
                                   llD++   L+p+k
  gi|13541217|ref|NP_110905.1| 254 LLDSLYNYLTPPK 266
                                   79999999*9997 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.1   0.00094      0.93       9      41 ..      33      64 ..      30      70 .. 0.75
   2 !    7.1   0.0    0.0034       3.4     130     169 ..     142     184 ..     105     199 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00094
                                  SETTEECEEEEEETTSSEEEEEESTTSSHHHHH CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N  9 nFksyagktvilpfsksftaivGpNGSGKsnll 41
                                  ++k +++ + +l+  ++f aivGp G GKs ll
  gi|13541217|ref|NP_110905.1| 33 GYKVFEDINLSLNR-NEFVAIVGPSGIGKSTLL 64
                                  66777544444444.45*************987 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0034
                                   TT-STTCS-HHHHHHHHHHHHHH...HHCCS--SEEEECTTTT CS
                                   xxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxx RF
                         SMC_N 130 agiskelLSgGektLvalaLlfA...iqkvkpaplyllDeida 169
                                   ++++++++SgG ++ va+a  +A   +     +p+  lDe+ a
  gi|13541217|ref|NP_110905.1| 142 EDLYPKEMSGGMRQRVAIARALAadpLVFLMDEPFAHLDELTA 184
                                   4577889************999955555566667777776655 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   9.2e-06    0.0091       6      29 ..      48      71 ..      44     216 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 9.2e-06
                        AAA_22  6 gilvvtGesGtGKTtllrrlleql 29
                                   +++++G+sG+GK+tllr l   l
  gi|13541217|ref|NP_110905.1| 48 EFVAIVGPSGIGKSTLLRILGGFL 71
                                  6899*************9887776 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1   9.2e-06    0.0091       6      39 ..      33      67 ..      28      92 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 9.2e-06
                        AAA_23  6 nfrsfrdqeidF.skgltlItGpNGaGKTTildAi 39
                                  +++ f+d ++ +  + +++I+Gp G GK+T+l+ +
  gi|13541217|ref|NP_110905.1| 33 GYKVFEDINLSLnRNEFVAIVGPSGIGKSTLLRIL 67
                                  556677777777555899*************9865 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   6.2e-05     0.062       2      21 ..      50      69 ..      49     227 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.2e-05
                                  EEEEESTTSSHHHHHHHHHT CS
                      MMR_HSR1  2 vaivGrpNvGKStLinaltg 21
                                  vaivG +  GKStL++ l g
  gi|13541217|ref|NP_110905.1| 50 VAIVGPSGIGKSTLLRILGG 69
                                  8**************98865 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00012      0.12       2      66 ..      51     174 ..      50     197 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00012
                                   EEESSTTSSHHHHHHHHHHHHTHE.....................................EEEEETTTCSSS........ CS
                           AAA   2 llyGppGtGKTllakavakelgve.....................................fleisgsellsk........ 37 
                                    ++Gp G+GK++l + +   l+ +                                     +++++++ + ++        
  gi|13541217|ref|NP_110905.1|  51 AIVGPSGIGKSTLLRILGGFLKPDkgsvylmgkkinrptpdivlihqsivtfpwmtalenvMVSLKAKHIPNDkaeemake 131
                                   589*****************9643344445566666777777777777777777777777766666666664479999999 PP

                                   .............STTHHHHHHHHHHHHHHHTS.TSEEEEEET CS
                           AAA  38 .............yvgesekkirelfkeakeka.kpsilfiDE 66 
                                                y +e++  +r+ ++ a++ a +p ++++DE
  gi|13541217|ref|NP_110905.1| 132 aletvglqgfedlYPKEMSGGMRQRVAIARALAaDPLVFLMDE 174
                                   9999999999999*************99999999999999999 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   5.1e-05      0.05       5      45 ..      50      87 ..      46     135 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.1e-05
                        AAA_24  5 iliyGpsgiGKTtlakelgpkplfidtekGlksldadkfpd 45
                                  ++i+GpsgiGK+tl++ l     f+  +kG+  l ++k+++
  gi|13541217|ref|NP_110905.1| 50 VAIVGPSGIGKSTLLRIL---GGFLKPDKGSVYLMGKKINR 87
                                  79*************999...33555666666666666555 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00021      0.21      44      68 ..      44      68 ..      21      80 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00021
                     IstB_IS21 44 iekkenivllGpsGvGKshlaialg 68
                                  ++++e ++++GpsG+GKs l   lg
  gi|13541217|ref|NP_110905.1| 44 LNRNEFVAIVGPSGIGKSTLLRILG 68
                                  578999************9876665 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00026      0.26      44      66 ..      46      68 ..      35      79 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00026
                         Rad17 44 kkriLLisGPsGCgkstvvkvLs 66
                                  +++ + i GPsG gkst +++L 
  gi|13541217|ref|NP_110905.1| 46 RNEFVAIVGPSGIGKSTLLRILG 68
                                  4568889**************97 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00027      0.26      21      38 ..      48      65 ..      35      67 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00027
                                  EEEEEEESTTSSHHHHHH CS
                        NB-ARC 21 lvvalvGmgGvGKttlak 38
                                   +va+vG  G+GK+tl++
  gi|13541217|ref|NP_110905.1| 48 EFVAIVGPSGIGKSTLLR 65
                                  49*************975 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00037      0.37       2      38 ..      51      82 ..      50      87 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00037
                  RNA_helicase  2 wlyGpsgeGKStlakeLakallkklklkkkdsvysrn 38
                                   ++Gpsg+GKStl +      l+ + ++ k+svy  +
  gi|13541217|ref|NP_110905.1| 51 AIVGPSGIGKSTLLRI-----LGGFLKPDKGSVYLMG 82
                                  689***********99.....4444467778888755 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   0.00032      0.32       3      19 ..      50      66 ..      48      75 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00032
                                  EEEEC-TTTCHHHHHHH CS
                         NACHT  3 vilqGeaGsGKTtLlqk 19
                                  v++ G++G+GK+tLl+ 
  gi|13541217|ref|NP_110905.1| 50 VAIVGPSGIGKSTLLRI 66
                                  89*************85 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1   0.00068      0.68       2      19 ..      50      67 ..      49      78 .. 0.92
   2 ?   -2.3   0.0       4.7   4.7e+03     102     110 ..     158     166 ..     121     189 .. 0.54

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00068
                        AAA_28  2 ivitGgestGKTtlleaL 19
                                  ++i+G+++ GK+tll+ L
  gi|13541217|ref|NP_110905.1| 50 VAIVGPSGIGKSTLLRIL 67
                                  89*************988 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 4.7
                        AAA_28 102 aaarekryd 110
                                   a+ar+   d
  gi|13541217|ref|NP_110905.1| 158 AIARALAAD 166
                                   222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       402  (0.0224218); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); 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: 0.56u 0.34s 00:00:00.90 Elapsed: 00:00:00.50
# Mc/sec: 1637.84
//
Query:       gi|13541218|ref|NP_110906.1|  [L=541]
Description: ABC-type nitrate transport permease [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.7e-16   58.6  42.7    5.5e-11   42.5  13.2    3.2  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 !   25.8  14.9   4.3e-10   7.8e-06       2     177 ..      26     206 ..      25     214 .. 0.81
   2 ?    0.4   0.2     0.027   4.8e+02     154     179 ..     270     299 ..     234     305 .. 0.73
   3 !   42.5  13.2   3.1e-15   5.5e-11       2     182 ..     340     531 ..     335     534 .. 0.90

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 4.3e-10
                  BPD_transp_1   2 illGilaa..lnrnkkldkllrpliivllslPsfvlaillvlvf.vilsilghlilpviillllsaapyvrlirraalrsl 79 
                                   i++G+++a    ++k++ ++   li+v+ s+P++ ++++++ +f   +++     l++ +l+++  ++ + +  ++a++++
  gi|13541218|ref|NP_110906.1|  26 IVTGWFLAylAIKGKFFENIYIALIEVFESVPVISFFPIVLIIFvTRIGGPLGVELAADFLVFTAVVWNIWMGEYQAFKTV 106
                                   899******999***************************999995333333334444555555555555555679****** PP

                  BPD_transp_1  80 pkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydyseis.....n 155
                                   pk+ +e+a  + +s   ++ ++ +P + p i++ l+ ++   +   ++ e ++   G+  +  ++ +g+ +++ +     n
  gi|13541218|ref|NP_110906.1| 107 PKEMIEVADNYRMSFLSRMARIYIPFSYPRIAANLFPSVSDGFFYITVSEVFT--VGIH-TYATFGIGSVLDSLAptgktN 184
                                   **************************************************999..4433.555666666666666788898 PP

                  BPD_transp_1 156 ggvlalviavlllnlvadilqr 177
                                    ++lal+++ +++ ++++il +
  gi|13541218|ref|NP_110906.1| 185 YVYLALLVLAVVIGAIIYILRE 206
                                   8888888888888888888765 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.027
                  BPD_transp_1 154 s....nggvlalviavlllnlvadilqrll 179
                                   +    +g++++ +i +++l+l+++  + ++
  gi|13541218|ref|NP_110906.1| 270 YpqrkIGSYVMSGIGIIILILLVYSAYSVI 299
                                   044447888888888888888888887766 PP

  == domain 3  score: 42.5 bits;  conditional E-value: 3.1e-15
                  BPD_transp_1   2 illGilaalnrnkkldkllrpliivllslPsfvlaillvlvf....vilsilghlilpviillllsaapyvrlirraalrs 78 
                                   i+lG+ +a   + +   +  pl +vl++ P+ + +++++++      +l +  +  + vi l+++s++ y+++ + +++++
  gi|13541218|ref|NP_110906.1| 340 IFLGYSLA--IHTRAEGIGVPLLQVLSAYPPPIYFPFVFAASytwiHNLMGPVTNEFFVIGLGFISTFYYMFYSFWMGVKA 418
                                   56666666..99*********************99998876688777777888888889********************** PP

                  BPD_transp_1  79 lpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydyseis..... 154
                                   lp+++ e+++ l ++ ++ +r ++lP ++p++i+g+  ++ +++gg ++ e+     G  tl ++  +++ ++  +     
  gi|13541218|ref|NP_110906.1| 419 LPSEYFEVMKNLNLGFFKKMRMIILPGTFPYLISGISSTINSAWGGLMIGEYWPDIVGDKTLQIHYGIMKFIDIQTeagni 499
                                   ******************************************************999988888888888888866699999 PP

                  BPD_transp_1 155 ....nggvlalviavlllnlvadilqrlldpr 182
                                       ++++++++++v+  +l+++ +++l  +r
  gi|13541218|ref|NP_110906.1| 500 ayagWASFIFGIVVVIYSILFTRRMMDLARKR 531
                                   ***9*******************999998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (541 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       760  (0.0423894); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.71u 0.34s 00:00:01.05 Elapsed: 00:00:00.52
# Mc/sec: 3143.55
//
Query:       gi|13541219|ref|NP_110907.1|  [L=153]
Description: hypothetical protein TVN0388 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.54   10.1   5.9        0.5   10.2   4.6    1.5  1  VIT1      VIT family


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 ?   10.2   4.6   2.8e-05       0.5     135     206 ..      74     142 ..      44     149 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 2.8e-05
                          VIT1 135 lkaAlssalsfliGgliPllpylfvesvglalvvsiavtllalllfGavkalltgssklvsalrmlliGalA 206
                                   l+    s++s + G+liPl++ + +++ g++ +v    +++al ++G+  a+  +   +  al m+l+G+l 
  gi|13541219|ref|NP_110907.1|  74 LEGTTLSGFSGFAGALIPLASDVYLHQLGEVPFVI---SIAALSILGIGLARSISGHYATWALGMALLGVLM 142
                                   445667899999***********999666655555...8999999999999999999999999999999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       466  (0.0259914); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); 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 0.31s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 967.10
//
Query:       gi|13541220|ref|NP_110908.1|  [L=97]
Description: hypothetical protein TVN0389 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-34  117.2   3.9      3e-34  117.0   3.9    1.0  1  DUF211    Uncharacterized ArCR, COG1888
  ------ inclusion threshold ------
      0.027   14.9   0.2       0.14   12.6   0.2    2.1  1  HMA       Heavy-metal-associated domain


Domain annotation for each model (and alignments):
>> DUF211  Uncharacterized ArCR, COG1888
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.0   3.9   3.4e-38     3e-34       1      88 [.       4      92 ..       4      93 .. 0.98

  Alignments for each domain:
  == domain 1  score: 117.0 bits;  conditional E-value: 3.4e-38
                                  SEEEEEEEEEEE.SSS-HHHHHHHHHTSTTEEEEEEEEEEE-SSEEEEEEEEEESSE-HHHHHHHHHCTT-EEEEEEEEEEES CS
                        DUF211  1 kirrlvLDvlkp.hepsivelakklaelegvdgvnitvkevDketenlkitieGenidyeeieeaieelggvihSiDevvaGk 82
                                  +irr+vLDv+k  ++p++vela++++++ gv++vni+v+e+D+et++++it+eG+ni+yee+ e+ie++g++ihS+De+++Gk
  gi|13541220|ref|NP_110908.1|  4 NIRRIVLDVDKGlNRPTLVELASAIERVPGVEAVNIIVTEMDMETMGTNITVEGTNINYEELIESIENTGSAIHSVDEIAVGK 86
                                  69********************************************************************************* PP

                                  S----- CS
                        DUF211 83 kiveev 88
                                  +++e+v
  gi|13541220|ref|NP_110908.1| 87 RLIENV 92
                                  ****97 PP

>> HMA  Heavy-metal-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.2   1.6e-05      0.14      18      60 ..      26      73 ..      24      74 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.6e-05
                           HMA 18 kvLselpgVesvkvdlatktvtVeg.....daestklrkiieaiekag 60
                                  ++++++pgVe+v++ + +  ++ +g     + + ++++++ie+ie++g
  gi|13541220|ref|NP_110908.1| 26 SAIERVPGVEAVNIIVTEMDMETMGtnitvEGTNINYEELIESIENTG 73
                                  6899*****9999866666655555554337777888********998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       604  (0.0336884); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.31s 00:00:00.78 Elapsed: 00:00:00.49
# Mc/sec: 598.69
//
Query:       gi|13541221|ref|NP_110909.1|  [L=321]
Description: dehydrogenase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.6e-20   71.6   0.2    1.4e-19   71.0   0.2    1.3  1  GFO_IDH_MocA    Oxidoreductase family, NAD-binding Rossmann f
      8e-07   29.1   0.1    1.7e-06   28.1   0.1    1.5  1  GFO_IDH_MocA_C  Oxidoreductase family, C-terminal alpha/beta 
  ------ inclusion threshold ------
      0.011   16.3   0.2      0.039   14.5   0.0    1.9  2  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
      0.015   15.4   0.0      0.029   14.5   0.0    1.4  1  Fn3-like        Fibronectin type III-like domain


Domain annotation for each model (and alignments):
>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.0   0.2   3.2e-23   1.4e-19       1     118 [.       1     115 [.       1     117 [. 0.95

  Alignments for each domain:
  == domain 1  score: 71.0 bits;  conditional E-value: 3.2e-23
                                   EEEEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHE.EESSHHHHHTCTTESEEEE-S-GGGHHHHHH CS
                  GFO_IDH_MocA   1 lrvaiiGaGkigskhlrplnesqrleevvalldpdaeraeavaesfgve.aysdleelladpeidavivatpngtheelak 80 
                                   ++v iiG+  +g+ hl+++ +++ + e++   ++++e  e++ ++++++ +y +lee l+ +++++  ++ p + h+++a 
  gi|13541221|ref|NP_110909.1|   1 MKVNIIGLNGFGKVHLEAWSKTDVDIEIT---ERKKEIVEELKQKYNISkVYGSLEEALR-SDAEIFDIVLPHSMHRDVAV 77 
                                   5899******************7666666...9**************************9.67****************** PP

                                   HHHHTT-EEEEESSS-SSHHHHHHHHHHHHHHTS-EEE CS
                  GFO_IDH_MocA  81 aaleagkhvllEKPlattveeakelvelaekkgklvsv 118
                                   + le gkhvl+EKP+at v++a+ ++ +aek++++++v
  gi|13541221|ref|NP_110909.1|  78 KSLESGKHVLIEKPIATEVRDAQIMISTAEKNKRKFMV 115
                                   ***********************************998 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 !   28.1   0.1   3.7e-10   1.7e-06       4      60 ..     132     185 ..     128     220 .. 0.81

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 3.7e-10
                                   HHTTTTSSEEEEEEEEECBEEECHHHHCCGGSHHCSTSHHHHTCHHHHHHHHHHHTS CS
                GFO_IDH_MocA_C   4 IengklGevvsvdvwtldtragaeakkrwkrrkkksgGvlgdlgiHdiDllqwLfGq 60 
                                   I++g +G+v+s+   ++d+r++++  +r  ++  ++gG+l+d giH+iD l  + G 
  gi|13541221|ref|NP_110909.1| 132 IKAGDIGKVHSI--IIRDQRKYNWHGWRAEAE-HMGGGSLIDGGIHFIDTLLNIGGD 185
                                   999999999999..699999999999999977.5***************99766554 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 ?   14.5   0.0   8.8e-06     0.039       1      79 [.       2      77 ..       2      90 .. 0.80
   2 ?   -1.0   0.0      0.62   2.8e+03      14      46 ..      87     119 ..      80     137 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 8.8e-06
                                  EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHH.H-SEEEE-S-HHHHHHHHH CS
                 F420_oxidored  1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaae.eadvvvlavkpedveevls 79
                                  k+ iiG   +g+  ++ +++++    +i ++ +r++e +eel+++++++   ++ eea++ +a++  + ++ +++ +v+ 
  gi|13541221|ref|NP_110909.1|  2 KVNIIGLNGFGKVHLEAWSKTD---VDIEIT-ERKKEIVEELKQKYNISKVYGSLEEALRsDAEIFDIVLPHSMHRDVAV 77
                                  678999999*************...999955.***************888888******956666556667777777764 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.62
                                   HHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHH CS
                 F420_oxidored  14 lasgllaagaqpheivvansrnpekaeelaeel 46 
                                   l+++ +a+ +++ +i++ +  ++++    a+++
  gi|13541221|ref|NP_110909.1|  87 LIEKPIATEVRDAQIMISTAEKNKRKFMVADQY 119
                                   556666666677888888777777766666666 PP

>> Fn3-like  Fibronectin type III-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   6.6e-06     0.029      21      58 ..       8      45 ..       3      51 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 6.6e-06
                                  EEEEEEEEE-TT-EEEEEEEEECGGG-EEETTTTEEE- CS
                      Fn3-like 21 LkgFekveLapGesktvtftldrkdlsvwdeekqkwvv 58
                                  L gF kv+L++  +++v ++++++   +++e kqk+ +
  gi|13541221|ref|NP_110909.1|  8 LNGFGKVHLEAWSKTDVDIEITERKKEIVEELKQKYNI 45
                                  89***********************9999999998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       792  (0.0441742); expected 358.6 (0.02)
Passed bias filter:                      612  (0.0341346); 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: 0.62u 0.34s 00:00:00.96 Elapsed: 00:00:00.54
# Mc/sec: 1797.58
//
Query:       gi|13541222|ref|NP_110910.1|  [L=114]
Description: hypothetical protein TVN0391 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score 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   15.9   1.5      0.018   15.6   1.5    1.2  1  AF0941-like  AF0941-like


Domain annotation for each model (and alignments):
>> AF0941-like  AF0941-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.6   1.5     1e-06     0.018       5      92 ..      29     110 ..      16     114 .] 0.83

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1e-06
                                   -HHHHHHHHHHT...TSS-GGGHHHHT-HHHHHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHHHHTHHHHHHHHHH CS
                   AF0941-like   5 ntyleklgellkkeviddiekvldelldkeeieelfrsdvedvleklkagdieeeeakknlklLkvyvvsqLdehykrvle 85 
                                    +ylekl  +lk   i d +  ++ l++   +++l   d+  ++ ++ +g+i  ee  +n ++L  y+  +++ h++r ++
  gi|13541222|ref|NP_110910.1|  29 KAYLEKL--ILK--NIADTDSIMQRLVEGRTVKKL-NPDISPIIRQYLEGNISAEELLRNDDVLD-YIAVKIKDHHDRYMD 103
                                   5677776..554..6889999************97.89**********************99998.555578888888888 PP

                                   HHHCTT- CS
                   AF0941-like  86 lledkek 92 
                                    +    k
  gi|13541222|ref|NP_110910.1| 104 CIRFIYK 110
                                   8765555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       688  (0.0383736); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 752.02
//
Query:       gi|13541223|ref|NP_110911.1|  [L=156]
Description: hypothetical protein TVN0392 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.4e-29  101.4   0.0    5.6e-29  101.1   0.0    1.1  1  AAA_assoc_C  C-terminal AAA-associated domain


Domain annotation for each model (and alignments):
>> AAA_assoc_C  C-terminal AAA-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.1   0.0   3.1e-33   5.6e-29       1     119 []      32     148 ..      32     148 .. 0.94

  Alignments for each domain:
  == domain 1  score: 101.1 bits;  conditional E-value: 3.1e-33
                   AAA_assoc_C   1 yeLaeelelevddLlpiveaaelLglveveegdielTelGrkfveadikerKeifreqllklvplaaairrvLderenkrl 81 
                                   y+L++e+e+++ddL+piv++a+ Lg+v++e+gdi++Te+G+++++a+ik+rKei+re+l +++p+ +a++        +++
  gi|13541223|ref|NP_110911.1|  32 YQLEKEMEVDIDDLMPIVYTASRLGFVSAESGDIIVTEEGKEYIRASIKRRKEIIREALRNIEPFRTALDL-------RNF 105
                                   89*******************************************************************98.......789 PP

                   AAA_assoc_C  82 peerfldeLeek.ls...eeeaertletai.eWgrYaelfeyd 119
                                   + e +++ L++k ++   +++ +++le+++ eWg+Y++l+  d
  gi|13541223|ref|NP_110911.1| 106 DCETLMENLQRKgVQtfnSPSGKHDLEVILiEWGVYSGLLRKD 148
                                   9999999999886556669********9988********9877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       661  (0.0368676); expected 358.6 (0.02)
Passed bias filter:                      599  (0.0334096); 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: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.51
# Mc/sec: 929.24
//
Query:       gi|13541224|ref|NP_110912.1|  [L=393]
Description: Kef-type K+ transport system, membrane component [Thermoplasma volcanium GSS1]
Scores for complete 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-31  107.1  52.4      1e-30  106.8  52.4    1.0  1  Na_H_Exchanger  Sodium/hydrogen exchanger family


Domain annotation for each model (and alignments):
>> Na_H_Exchanger  Sodium/hydrogen exchanger family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.8  52.4   5.8e-35     1e-30       3     379 ..      11     378 ..       9     380 .. 0.85

  Alignments for each domain:
  == domain 1  score: 106.8 bits;  conditional E-value: 5.8e-35
                                   HHHHHHHHHHHHHHHTTSXHHHHHHHHHHHHTTTTTS.....HHHCHCCHHHHCHHCCHHHHCTCGCCTGCCTHHHHHHHH CS
                Na_H_Exchanger   3 llillallvgllarrlklpeivgliiaGlllGpsglgliepseedlevlselglilllFlaGleldlrelrknlksillla 83 
                                   +l+++++l+g+l++++k+p++v++i++G+l+G+ +l++++ps   ++ +  + l+++++++G+e + +++  n + +++l 
  gi|13541224|ref|NP_110912.1|  11 ILLFVSMLLGVLFSKFKIPDVVAYILTGVLVGNGFLKIVSPS-VPISDIESVSLFFIILAIGVEANTEYIYGNVRRSIILT 90 
                                   556667777778*****************************9.999*********************************** PP

                                   HHHHHHHHHHHHHHHH.HHTXTTCHHHHHHHHHHHTSSXHHHHHHHC.CCCTSTCCCCCCHHHHHHHHHHHCCCCCHHHHH CS
                Na_H_Exchanger  84 llgvlitvvliGlllylllilgiplleallfgailsatdpvvvlailkeegrvperlgtlllgesvlnDavavvllavlla 164
                                   + +++++  l G+l     +  +p++ a+++++ + + ++ +++ +l ++ +++ + g+l+l+  vl+D +a+++l++  +
  gi|13541224|ref|NP_110912.1|  91 ISSFIAPSML-GFLYLQ-AVAHLPIIPAFVLSMSVGVPSISIISVLLMRYDLLKLNAGRLILSSVVLTDTSAFIILSSTYE 169
                                   **********.997776.789*********************************************************999 PP

                                   HTXXXXXTSSSTSXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSCTHHHHH.HHHHHHHHHHH..HHHHHTSXXXHHHHHH CS
                Na_H_Exchanger 165 lakeeaggetslllllliflvvavgglllglvigwllrlitrftdddrele.vllvlllalla..allaellgvsgilgaf 242
                                    +   +   +s + ++l+++ + ++ +l+++  g + + i+r+   d+++e +l++l+++ ++  + l e +g++ +lgaf
  gi|13541224|ref|NP_110912.1| 170 SV---TKVLISFGFVVLFLFAIWLFDILIRRRAGRIIEWISRRE-TDNNMEyILFSLVIIAGLlvSTLFEFIGITYVLGAF 246
                                   98...777777777777777788888888888888888888885.444444044444444333448899999********* PP

                                   HHHHHHHHHHHHTTHHHHHHHHHH....HHHHHHHHHHHHHHSXHHHHHXXHHHHHHHHHHHHHHHTHHHHHHHHHTTTXS CS
                Na_H_Exchanger 243 laGlvlseyefsnklseklesfre....glfnplfFvlvGlsldlkvlnnhlsvlilvllilvaillgrilavflllrllg 319
                                    aG+++ e + ++k ++ + ++++    ++f+plfF++ G+s+ l+ +    s +++ l +l++++ +    ++l++ +l+
  gi|13541224|ref|NP_110912.1| 247 YAGILIHEASIGQKYHKIILNTIKrindSFFIPLFFSIAGISMILPKI----SIFMIFLPALLILMGASGGLTYLVSHRLI 323
                                   *******999999855554444444555****************5555....45555555555555678888899999999 PP

                                   SXHHHHHHCCCCSS.BHHHHHHHHHHHHHHXHHHHTT.SSTTTCSTSXHHHHHHHHHHHHH CS
                Na_H_Exchanger 320 lslrealiigfgglqrgavalalaalgpalgllarel.yallivvvlftvlvqGlslkpll 379
                                    sl    +++++g  rgav +++a ++ ++g+++ ++   +li++v+f+++      +pl+
  gi|13541224|ref|NP_110912.1| 324 RSLEPIKVVSILGG-RGAVGVIIATIAFQSGIIDVAVySLALIGTVIFSLV-----MTPLV 378
                                   9999999******9.**********************8889999*****99.....66665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       938  (0.0523175); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.51
# Mc/sec: 2298.54
//
Query:       gi|13541225|ref|NP_110913.1|  [L=348]
Description: major facilitator superfamily permease [Thermoplasma volcanium GSS1]
Scores for complete 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-09   35.6  28.3    3.3e-05   23.0  23.7    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 !   19.1  13.0   2.9e-08   0.00052      48     296 ..      17     247 ..       2     253 .. 0.69
   2 !   23.0  23.7   1.8e-09   3.3e-05       8     171 ..     174     340 ..     165     346 .. 0.70

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 2.9e-08
                         MFS_1  48 aslplGrlsdrfGrrrvlllglllfalglllllfasslwlllvlrvlqGlga.galfpagaaliadwfpkeergraiglls 127
                                   +s+++Grl d ++++++ +lg  l  l++l++l  ++ ++ + +  + G+ +  + +p   ++i + +++e+ +rai ll 
  gi|13541225|ref|NP_110913.1|  17 FSYIGGRLWDSHSPKKLTILGNSLIPLMSLIGL--AGTYIGASALYIGGWWSrNFRNPPPRVMIIQSSKEEDISRAICLLH 95 
                                   789*************************77887..8888899999999*9999999************************* PP

                         MFS_1 128 agfslGailgpllggllasslg..Wravfyilaivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkd 206
                                   +    G  ++ +l   ++ +lg   + vf++  + ++++ +     l+++ ++ + ++++e     + +++ +   a   +
  gi|13541225|ref|NP_110913.1|  96 GLDITGGTIAGILPLSFT-ALGlpLSRVFLFSIAPLVVSNL-----LVASTRSVHXVKQEEV----KIKNVDS---AKAEK 163
                                   **************9999.7773455558888888888844.....4444444444444444....2222222...33344 PP

                         MFS_1 207 pvlwillialllfffgfsglltllplylqevlglsglllaglllallalvgailallagrlsdr..lgrrrrlllalllll 285
                                   +v++ +++a l+f  gfs+ ++ +p++       +   ++g  l l+ +++a  + ++g+l  r  ++++ rll  l+ +l
  gi|13541225|ref|NP_110913.1| 164 NVVYGVFLATLSF--GFSYHSIGFPIL-TAAQSAD-STISG--LVLFPVFMAS-SSVGGFLYSRlrISKEVRLLGYLGYTL 237
                                   5443355555555..777888888885.4444444.26666..3333333333.457788887744555555555555555 PP

                         MFS_1 286 laalglallav 296
                                   +++ g +l+++
  gi|13541225|ref|NP_110913.1| 238 TGV-GTLLISL 247
                                   555.5555444 PP

  == domain 2  score: 23.0 bits;  conditional E-value: 1.8e-09
                         MFS_1   8 salarsilgpalplalaedlgispseigl.lltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll...fa.. 82 
                                    ++++s  ++ +p +l+ +  ++ +  gl l+ ++++ ++v+ ++++rl  r+ ++ v llg+l++ l+++  l   ++  
  gi|13541225|ref|NP_110913.1| 174 LSFGFSYHSIGFP-ILTAAQSADSTISGLvLFPVFMASSSVGGFLYSRL--RI-SKEVRLLGYLGYTLTGVGTLlisLVyl 250
                                   3344444556666.55555445555566644445666666666666666..55.333555555555555333331123355 PP

                         MFS_1  83 ..sslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivs 161
                                     ++  + +++ v+ Glg++++ +   ++i+++ ++++ g+++g+l++++s+G     +l gll+  ++  ++++ +++++
  gi|13541225|ref|NP_110913.1| 251 yrAPELYYYLSAVVIGLGTSGVETFEPTIISKIIKGSRTGSGVGYLTSFISIGLFTSNILMGLLYYEISPLSAYLYAGLAA 331
                                   6655556**************************************************************999999999999 PP

                         MFS_1 162 llafvlflll 171
                                   +l+++++ l+
  gi|13541225|ref|NP_110913.1| 332 ILGGLII-LF 340
                                   9998852.33 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (348 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       469  (0.0261587); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); 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):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 2205.44
//
Query:       gi|13541226|ref|NP_110914.1|  [L=134]
Description: sterol carrier protein [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.9e-11   43.3   0.0    4.5e-11   43.1   0.0    1.1  1  SCP2      SCP-2 sterol transfer family


Domain annotation for each model (and alignments):
>> SCP2  SCP-2 sterol transfer family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.1   0.0   2.5e-15   4.5e-11       3     100 ..      12     120 ..      10     121 .. 0.90

  Alignments for each domain:
  == domain 1  score: 43.1 bits;  conditional E-value: 2.5e-15
                                   HHHHHH.HHHHHHHHHCCH-EEEEEEECTC.T.....EEEEEETTSTEEE....SSCTT.BS-SEEEEEEHHHHHHHHCTS CS
                          SCP2   3 qllerl.kdpekkealkklagvlrfdltdlkg.....sltldlkegqldv....aakde.gkadvtlslsledllelaegk 72 
                                   ++++rl ++p++++a k ++g + f +++ ++     ++++dl +g+++      ++ e  ka++   +++ ++++l++++
  gi|13541226|ref|NP_110914.1|  12 EYCNRLnNNPDYADAGKTWEGDILFVVQPDENyskteYIYIDLYHGKCRSakyvHEGEEvPKAEFRYVGKYGNWIRLLNKE 92 
                                   5677784456********************999*************9999999655556789999999************* PP

                                   S-HHHHHHTTSSEEEC-HHHHHHHHHHH CS
                          SCP2  73 lnpqkafmqgkLkieGDielaqkleall 100
                                   ++p + +++gk k+eG +++ +++ +++
  gi|13541226|ref|NP_110914.1|  93 IDPIQGILTGKFKLEGSMMKIMRYTKAA 120
                                   ***********************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.49
# Mc/sec: 826.99
//
Query:       gi|13541227|ref|NP_110915.1|  [L=373]
Description: alcohol dehydrogenase IV [Thermoplasma volcanium GSS1]
Scores for complete 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-97  324.4   0.0    8.7e-97  324.2   0.0    1.0  1  Fe-ADH    Iron-containing alcohol dehydrogenase
    5.3e-20   72.2   0.0    1.1e-09   38.3   0.2    2.1  2  Fe-ADH_2  Iron-containing alcohol dehydrogenase
  ------ inclusion threshold ------
      0.021   14.4   0.0      0.076   12.6   0.0    1.9  2  DUF4417   Domain of unknown function (DUF4417)


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 !  324.2   0.0  1.4e-100   8.7e-97       2     363 ..       7     364 ..       6     365 .. 0.95

  Alignments for each domain:
  == domain 1  score: 324.2 bits;  conditional E-value: 1.4e-100
                                   SEEEEETTGGGGHHHHHTTT-..EEEEEEEHHHH.HH.THHHHHHHHHCTT-EEEE.EEE-S---HHHHHHHHTTS-TT.- CS
                        Fe-ADH   2 trivfgkgaleelgellkklgakralivtdkgslkksglldkvlesleeagievtvfdgvepnptleeveeaaalareega 82 
                                   +ri+fg+++l+ l ++      +++l+vtd++++ ++++l++vl++l  +g +++vf++++p+p+l+e+ ++ +la   ++
  gi|13541227|ref|NP_110915.1|   7 PRIIFGEDSLSFLDDHS----SSKILVVTDNFLS-NTPILKEVLSHL--SGKDIKVFSEISPEPRLSEILKGRELASRLDP 80 
                                   49********7777766....479********88.************..999***************************** PP

                                   -EEEEEESHHHHHHHHHHHHHTT....................--EEEEESS-S-S-TT-SEEEEE.-TTSEEEEE-..SS CS
                        Fe-ADH  83 dvviavGGGsviDtAKaialllanpe..vedylgegkakkkkalpliaiPTtaGtGsevtplavitdeeegeklsifdpel 161
                                   d++i++GGGs++D+AK++ +l + p+  + d+  ++  k +++ +li iPTt+GtGse++++av++d+ e++k +i++pe+
  gi|13541227|ref|NP_110915.1|  81 DTIIGLGGGSSMDAAKILFALHEMPDlsPFDISPINSIKLHQKSELIEIPTTSGTGSECSWAAVFSDDTEERKNEIASPEI 161
                                   ***********************98756666668888889999***********************99999********** PP

                                   --SEEEEEHHHHHHS-HHHHHHHHHHHHHHHHHHHHHHT---TTSSB--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        Fe-ADH 162 lPdlaivDpeltltlPkrvtaatglDalahalEayvskkanplsdalaleairliaknleravadgedleareqmllastl 242
                                   ++d+ai+Dp+l+l+lPk +t++t+ Da++ha+Eay+s+ +np+sda+a++a+ li++nl++++ +++d++ar  +++++ +
  gi|13541227|ref|NP_110915.1| 162 MADYAILDPKLVLDLPKGITVNTATDAITHAIEAYTSQWRNPYSDAMAEKALDLILNNLPTVLVNPKDINARNSVHIGASM 242
                                   ********************************************************************************* PP

                                   HHHHHHSS---HHHHHHHHHHC.CGGGGGS-HHHHHHHHH..........HHHHHHT.......T--HHHHHHHHHHHHHT CS
                        Fe-ADH 243 aglafsnaglgavHalahalgalfgiphglanaillpavlrfnaeaaperlaqlaralggesdeeaaeeliealrellkel 323
                                   ag++fsn+++g++Hal+halga+f++phg+++++ lp+v++fn+eaa++r+ ++   +    de + +++ e +r  l+++
  gi|13541227|ref|NP_110915.1| 243 AGISFSNSQIGLAHALGHALGAIFKTPHGESVGLYLPHVTEFNYEAAKDRYDKINSFF---PDEYRTDKVWETIRSYLNAI 320
                                   *********************************************************9...588***************** PP

                                   T---SHHHHT-TT-....HHHHHHHHHT-TSGGGGSSS---HHH CS
                        Fe-ADH 324 glptsLselgvdee....dldklaeaalkdrslannpreltaed 363
                                   g  t++se g++++    +l k+++ a ++  + +n r ++ +d
  gi|13541227|ref|NP_110915.1| 321 GQVTNVSEAGIERSkyekELGKIVSLASESTGVITNARDASTKD 364
                                   *************7477777999999999977778888887776 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 !   31.7   0.0     2e-11   1.2e-07      12      99 ..      17     103 ..      12     108 .. 0.89
   2 !   38.3   0.2   1.9e-13   1.1e-09      97     250 .]     121     275 ..     110     275 .. 0.91

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 2e-11
                      Fe-ADH_2  12 ellkelelkkvllvadentkka.agekveeslkeagikvevveeveeeadleeveklvealreketdlvvavGgGtiiDia 91 
                                   ++l +++ +k+l+v+d+  +++ + ++v ++l+ ++ikv  ++e ++e+ l+e+ k  e ++  + d ++++GgG+ +D+a
  gi|13541227|ref|NP_110915.1|  17 SFLDDHSSSKILVVTDNFLSNTpILKEVLSHLSGKDIKV--FSEISPEPRLSEILKGRELASRLDPDTIIGLGGGSSMDAA 95 
                                   68999999**********88877************7766..789************************************* PP

                      Fe-ADH_2  92 kyvsakln 99 
                                   k++ a  +
  gi|13541227|ref|NP_110915.1|  96 KILFALHE 103
                                   *9866655 PP

  == domain 2  score: 38.3 bits;  conditional E-value: 1.9e-13
                      Fe-ADH_2  97 klnvpyvsvpTaaSvDGfaspgaslvvd..gkkrtv.akaaaPlaviaDldvlaeAPrrllasGvGDllgkytaladwkla 174
                                   +++ +++ +pT+    + +s  a +  d  ++k  +  +  ++   i+D +++ + P+ ++     D++   +  ++++  
  gi|13541227|ref|NP_110915.1| 121 HQKSELIEIPTTSGTGSECSWAAVFSDDteERKNEIaSPEIMADYAILDPKLVLDLPKGITVNTATDAITHAIEAYTSQWR 201
                                   5677899********99*******9999666666676555555566889******************************** PP

                      Fe-ADH_2 175 nevseplaklsaamvqeaaeklvedkketealeellealalsgigisrpaSGsEHliSHaldmlalkqalHGeqVG 250
                                   n +s+ +a+++ + + +++ +++ ++k+++a + +  +  ++gi++s++  G  H + Hal +++  ++ HGe+VG
  gi|13541227|ref|NP_110915.1| 202 NPYSDAMAEKALDLILNNLPTVLVNPKDINARNSVHIGASMAGISFSNSQIGLAHALGHALGAIF--KTPHGESVG 275
                                   *****************************************************************..99******9 PP

>> DUF4417  Domain of unknown function (DUF4417)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.35   2.1e+03     155     179 ..      73      97 ..      64     107 .. 0.77
   2 ?   12.6   0.0   1.3e-05     0.076      24      70 ..     281     326 ..     272     331 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.35
                       DUF4417 155 emvkrlkPklilvyGaqpeelfakl 179
                                   e  +rl+P +i+  G+     +ak+
  gi|13541227|ref|NP_110915.1|  73 ELASRLDPDTIIGLGGGSSMDAAKI 97 
                                   67789*******9887776666664 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 1.3e-05
                       DUF4417  24 ligFskarskkkderelvhffadDyqferlwnsPekylaaLkqlsav 70 
                                   +  F+++   k++ +++  ff d+y+  ++w++ + yl+a+ q++ v
  gi|13541227|ref|NP_110915.1| 281 VTEFNYE-AAKDRYDKINSFFPDEYRTDKVWETIRSYLNAIGQVTNV 326
                                   5679999.999999**************************9998766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       450  (0.025099); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.23s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 2678.97
//
Query:       gi|13541228|ref|NP_110916.1|  [L=498]
Description: NAD-dependent aldehyde dehydrogenase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   1.5e-155  518.3   0.0   1.8e-155  518.0   0.0    1.0  1  Aldedh    Aldehyde dehydrogenase family
    1.9e-06   27.2   0.0    3.9e-06   26.2   0.0    1.5  2  LuxC      Acyl-CoA reductase (LuxC)


Domain annotation for each model (and alignments):
>> Aldedh  Aldehyde dehydrogenase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  518.0   0.0    2e-159  1.8e-155      10     461 ..      23     475 ..      15     476 .. 0.97

  Alignments for each domain:
  == domain 1  score: 518.0 bits;  conditional E-value: 2e-159
                                   EEEETTTCEEEEEEE-B-HHHHHHHHHHHHH.HHHHHTTS-HHHHHHHHHHHHHHHHHTHHHHHHHHHHHH---HHHHHH. CS
                        Aldedh  10 evinPatgeviakvpaataedvdaavaaAke.afkawaklpaeeRaeiLrkaadlleerkeelaeletletGkplaeara. 88 
                                    v +P++g++ia+v  a+++ v +a++++ +  +k w+k +++eR+++L+k+ad ++e+ e+ a+le+l+tGk+l++++  
  gi|13541228|ref|NP_110916.1|  23 IVKSPVDGSPIASVYFADRDAVSKAIDSSYDsYYKVWSKFTLSERKKLLAKLADRIQEKSERYATLESLNTGKTLRQSMLm 103
                                   5789*************************9967779*******************************************99 PP

                                   HHHHHHHHHHHHHHHHHH.HSEEEEEEC.TTEEEEEEEEE-SEEEEEE-SSSCCHHHHHHHHHHHHTT-EEEEEE-TTSHH CS
                        Aldedh  89 eveeaidvlryyaelaek.legevlpss.egklalvrrePlGvvgaItPWNfPlllaawklapalaaGNtvvlKPaeetpl 167
                                   +++  i++lry+a++ e  +e +++  + ++++ +v++ P+GvvgaItPWN+P+l+a+wk+apal+aGNtvv+KP++ tpl
  gi|13541228|ref|NP_110916.1| 104 DIPLGIEHLRYFATETEFkMERQITHPEyPDSHGIVQYVPMGVVGAITPWNVPFLMAVWKAAPALLAGNTVVIKPSSFTPL 184
                                   ***************99856667766645**************************************************** PP

                                   HHHHHHHHHHHTTS-TTSEEE--SSTCCHHHHHHH-TTESEEEEES-HHHHHHHHHHHHCTTSEEEEEE---EEEEE-TTS CS
                        Aldedh 168 salllaelfeeaglPkgvlnvvtgsgsevgealvehpevdkvsftGstevgrkiakaaaknlkrvtlElGGknplivleda 248
                                   +++ +a+ +  +g+P+gvlnvv+g+g++vge+l+++++v+++sftGst +g++i +  +  +k+vtlElGGk+p+iv++da
  gi|13541228|ref|NP_110916.1| 185 TTIEMARDAISVGFPPGVLNVVNGRGETVGEELARNKKVRMLSFTGSTYTGKRITEITG--IKKVTLELGGKSPNIVFDDA 263
                                   *********************************************************99..9******************* PP

                                   HHHHHHHHHHHHHHGGGGTSTTSEEEEEEEHHHHHHHHHHHHHHHHT--BS-TTSTT-SB---SSHHHHHHHHHHHHHHHH CS
                        Aldedh 249 DldkaveaivkgafgnaGQvCiaasrllvqesiydefveklveaakklkvgdpldedtdvGPliseaqlekvekyveeake 329
                                   Dl++a+ ++++g+++n+GQ C ++srllvq+si d+f++ l+ +++k++ g+p+  +td+ ++++++q++k+ek+v+++ +
  gi|13541228|ref|NP_110916.1| 264 DLERAALGVMFGIYLNSGQLCESGSRLLVQSSIKDKFLNLLKSKIEKMRPGNPMSMETDISAITTKNQRDKIEKMVNSGLK 344
                                   ********************************************************************************* PP

                                   TTSEEEE-TTE.SB-SSSTTEE--EEEES-TTTSHHHHS---SSEEEEEEESSHHHHHHHHHSSSEESEEEEE-SBHHHHH CS
                        Aldedh 330 egaklllGgereeaglekgyfvePtvlanvtpdmriaqeEiFGPVlsvikfkdeeeaieiaNdteyGLaagvftkdlerae 410
                                   +g  + +  + + + ++ g ++ Pt+l++v++dm++a+eEiFGPVlsv++f+de++ai++aN t+yGLaagv+t+d e+a 
  gi|13541228|ref|NP_110916.1| 345 DGSVIFYQKSIDGSVPKGGLYFPPTILDKVSEDMEVAKEEIFGPVLSVMEFDDEADAIDKANMTDYGLAAGVWTQDSEKAT 425
                                   *****99888889999***************************************************************** PP

                                   HHHHHS-SSEEEESSSST--TTTSEB--CGGGEES-BSHHHHHHHTEEEEE CS
                        Aldedh 411 rvaerleaGnvyiNdsttgaaealpfgGvkqSglGreggkegleeytevkt 461
                                   rva+++eaG+v+iN+++  +a a p gG+k+Sg+Gre g +g++e+t++++
  gi|13541228|ref|NP_110916.1| 426 RVASSIEAGTVWINEYHLLSAAA-PRGGFKNSGVGRELGLDGIMEFTQTRH 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 !   26.2   0.0   4.3e-10   3.9e-06      64     292 ..     118     336 ..      65     360 .. 0.78
   2 ?   -3.4   0.0      0.42   3.7e+03     198     221 ..     385     405 ..     373     415 .. 0.75

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 4.3e-10
                          LuxC  64 eseLgqpeiLdeflktkeksyekaqprglvlhvlsgNvp.llpvmsilqglLvknvnllkvSssdpflaaallksladvde 143
                                   e e++ ++ + ++ + + ++  +++p g+v  +++ Nvp l++v+  + +lL++n  ++k+Ss  p +++++++  + v  
  gi|13541228|ref|NP_110916.1| 118 ETEFKMERQITHPEYPDSHGIVQYVPMGVVGAITPWNVPfLMAVWKAAPALLAGNTVVIKPSSFTPLTTIEMARDAISVGF 198
                                   66787788888888888899******************94568********************************999998 PP

                          LuxC 144 nhtladslsvvyfksgdtkleeeivqnaDvv..vawGgeeaikaiseklkpgkqlikfGakvSfavvdkealeeealdkaa 222
                                          l vv  ++  +++ ee+  n  v+  +  G+ ++ k i e    +k  ++ G k    v+d ++     l+ aa
  gi|13541228|ref|NP_110916.1| 199 P---PGVLNVV--NGRGETVGEELARNKKVRmlSFTGSTYTGKRITEITGIKKVTLELGGKSPNIVFDDAD-----LERAA 269
                                   6...7889999..88999999999965555411679*************************9999999877.....77777 PP

                          LuxC 223 eraAkDiivfdQqAClspqvvfvekddkieidefaeaLaaaLekrarilpkakldedeaakisskraelk 292
                                     +   i     q C s   ++v+++     d+f ++L +++ek     p +   +  a  ++++r +++
  gi|13541228|ref|NP_110916.1| 270 LGVMFGIYLNSGQLCESGSRLLVQSS---IKDKFLNLLKSKIEKMRPGNPMSMETDISAITTKNQRDKIE 336
                                   77777788888888888888888855...66888888888888888888887777777766666666643 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 0.42
                          LuxC 198 kfGakvSfavvdkealeeealdka 221
                                   +fG+ +S++ +d ea   +a+dka
  gi|13541228|ref|NP_110916.1| 385 IFGPVLSVMEFDDEA---DAIDKA 405
                                   488888999998888...555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (498 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       594  (0.0331307); expected 358.6 (0.02)
Passed bias filter:                      557  (0.031067); 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 0.29s 00:00:00.84 Elapsed: 00:00:00.44
# Mc/sec: 3416.19
//
Query:       gi|13541229|ref|NP_110917.1|  [L=393]
Description: 2-amino-3-ketobutyrate coenzyme A ligase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.7e-65  220.1   0.0    5.3e-65  219.9   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
    0.00027   19.6   0.0    0.00039   19.1   0.0    1.2  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
  ------ inclusion threshold ------
      0.059   12.3   0.0      0.091   11.7   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 !  219.9   0.0   8.9e-69   5.3e-65       2     362 ..      40     382 ..      39     383 .. 0.96

  Alignments for each domain:
  == domain 1  score: 219.9 bits;  conditional E-value: 8.9e-69
                                   EEEESSSSSTTSTTSS.HHHHHHHHHHHH.HHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHH CS
                 Aminotran_1_2   2 dvinLgsneylgdsgk.ptlpevakaeke.galaggtlneygpidglpeleealakflgrseklklkreaavvvgsGagal 80 
                                   +v+n++sn+ylg +++ +t +++++a  e g++ag  + + g+ +++ +lee++a+f +         eaa+v+ +G  a+
  gi|13541229|ref|NP_110917.1|  40 QVLNMCSNNYLGFANHpETKKAAIEAIEEyGVGAGAVRSIAGTDEIHIKLEEKIASFKH--------SEAALVYQGGLLAN 112
                                   799*************7777777777777*999999999999999**************........9************* PP

                                   HHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT CS
                 Aminotran_1_2  81 iealifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilvesphNPt 161
                                   + ++++l    ++d i++ ++++as++++ rls ++ + y+       hl +++le++ ke+ +  k + ++++ ++++++
  gi|13541229|ref|NP_110917.1| 113 LGTVPALVG--KDDIIFSEELNHASIIDGTRLSPAKRIVYK-------HLSVDDLEKQAKENRSSGK-KALVITDGVFSMD 183
                                   ********9..******************************.......*************887777.99*********** PP

                                   --B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSS..HTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEEEEEEHHHH CS
                 Aminotran_1_2 162 GtvatleeleklldlakkynlllfvDeaYagfvfgsl..davatranveeepnllivgslsKafGlaGeRvGyilgnaavv 240
                                   G++a+l+e++++   a+ky ++++vD+a++++v+g++  +   +++ +e++++ + +g++sKa+G++G   G+++g+a+++
  gi|13541229|ref|NP_110917.1| 184 GDIAPLPEIVDI---AEKYDIMTYVDDAHGEGVLGDHgrGI-VNYFHLEDKVD-IEMGTFSKALGSMG---GFVAGSAEMI 256
                                   ************...********************997433.33*********.**************...********** PP

                                   HHHHHHHHHHTSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCSCSSEEEEEETHHCHHHHH CS
                 Aminotran_1_2 241 sqlrklsrpflsssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLaelglkvlasqsgmflltdlsaetakels 321
                                   + l++ +rpfl+ss+l +  aaa+ +a ++ ++ +  +++l+++++ l+++La+lg +   s++ + ++  +++++  els
  gi|13541229|ref|NP_110917.1| 257 DLLKQKARPFLFSSALNPGDAAAVLKAIEILEKDDSLVKKLWENADLLKKSLADLGYNTGHSKTPITPVIIGDEKKTVELS 337
                                   ********************************************************************************* PP

                                   HHHHHTCTEEEEEGGGGTS...TTEEEEEC.TTS-HHHHHHHHHH CS
                 Aminotran_1_2 322 kkLleevgvyvtpgtsftv...pgrlRitv.Aglteeeleelvea 362
                                    kL ee++v  +p+ ++tv   ++r+R+ + A +t+e++  +v+a
  gi|13541229|ref|NP_110917.1| 338 TKLYEEKNVFASPIVYPTVpkgTARIRLMPsAVHTHEDIMTAVNA 382
                                   ********************9999***************999987 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 !   19.1   0.0   6.5e-08   0.00039      56     181 ..      88     214 ..      80     295 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 6.5e-08
                                   HHHHHHHHHHT-SEEEEESSHHHHHHHHHHTTS-TTEEEEEESTSSHHHHHHHHHTHHHTTCEEEEESTTSHHHHHHHCCT CS
               Cys_Met_Meta_PP  56 vleeriaaLeggeaalavssGmaAiaaailallkaGdeivvsddlYggtqrllkkvlkklgievkfvdtsdleelekaike 136
                                    lee+ia  +++eaal++  G+ A   ++ al+ + d+i+ s++l   +    +++ +   i +k+  ++dle+ +k  ++
  gi|13541229|ref|NP_110917.1|  88 KLEEKIASFKHSEAALVYQGGLLANLGTVPALVGK-DDIIFSEELNHASIIDGTRLSPAKRIVYKHLSVDDLEKQAKENRS 167
                                   79***********************9999999987.789999999999999999999999999999999888888877776 PP

                                   ..TEEEEEEESS-TTTT----HHHHHHHHHHTT-EEEEEGTTTHTTT CS
               Cys_Met_Meta_PP 137 ..ntklvylEtptnpllkvvDiekiaklakkagvlvvvDntfaspll 181
                                     +  lv ++ + +   +++ +++i+++a k ++++ vD +   ++l
  gi|13541229|ref|NP_110917.1| 168 sgKKALVITDGVFSMDGDIAPLPEIVDIAEKYDIMTYVDDAHGEGVL 214
                                   447778888888899999**********************9988876 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   1.5e-05     0.091      86     177 ..     120     208 ..      57     212 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.5e-05
                                   TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH-.....-TTEEEEEEESBETTTTEB--HHHH CS
                   Aminotran_5  86 kpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldelekll.....nektklvaithvsnvtGtiqpveei 161
                                     +d i+ +e   ha ++   +l+ ++ +  k++++        d+lek+      + k +lv+   v ++ G i p++ei
  gi|13541229|ref|NP_110917.1| 120 VGKDDIIFSEELNHASIIDGTRLSPAKRIVYKHLSV--------DDLEKQAkenrsSGKKALVITDGVFSMDGDIAPLPEI 192
                                   455666665555555554555555444444444444........44444432222267889999999************** PP

                                   HHHHHHTT-EEEEE-T CS
                   Aminotran_5 162 gklakkkgalvlvDaa 177
                                   +++a k+++++ vD a
  gi|13541229|ref|NP_110917.1| 193 VDIAEKYDIMTYVDDA 208
                                   **************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       492  (0.0274416); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.43
# Mc/sec: 2756.70
//
Query:       gi|13541230|ref|NP_110918.1|  [L=199]
Description: 30S ribosomal protein S2 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      2e-29  102.4   0.5    1.5e-14   53.8   0.5    2.1  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 !   46.9   0.0   1.1e-16   1.9e-12       3      95 ..      14     103 ..      13     113 .. 0.92
   2 !   53.8   0.5   8.2e-19   1.5e-14     150     213 ..     113     176 ..     106     178 .. 0.95

  Alignments for each domain:
  == domain 1  score: 46.9 bits;  conditional E-value: 1.1e-16
                  Ribosomal_S2   3 eagvhfGhqtrrwnpkmkpyIygern.gihiidlektlaalrraykvvkevaakggkilfvgtkkqakeavkeaakrangy 82 
                                   ++gvh+G q +    +mkpyI++ rn g +i+d++kt ++l  a k++ ++  + + il v+ ++ a + v++ a+ ++++
  gi|13541230|ref|NP_110918.1|  14 KSGVHIGTQVK--SSDMKPYIFKIRNdGLYILDVKKTNSKLIAAGKMLARF--DPQDILVVAQRQYAFRPVAKFAEVTGAV 90 
                                   589****8887..789********9868*******************9986..6678************************ PP

                  Ribosomal_S2  83 yvnerWlgGtLTN 95 
                                    ++ r+ +GtLTN
  gi|13541230|ref|NP_110918.1|  91 SITGRFNPGTLTN 103
                                   ************* PP

  == domain 2  score: 53.8 bits;  conditional E-value: 8.2e-19
                  Ribosomal_S2 150 dlvvvldpkkekiavkEakklgipviaivDtnvdpdlvdypIpaNddsirsiklilgvladaie 213
                                   +++vv+dp  +  a+kEa k gip+ia++D n  +d vd +Ip N++  rs+ +i+ +la+ i 
  gi|13541230|ref|NP_110918.1| 113 KVIVVTDPLADVQAMKEAIKIGIPIIALCDANNKTDFVDLVIPTNNKGRRSLAVIYWLLAREIL 176
                                   68**********************************************************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1345.65
//
Query:       gi|13541231|ref|NP_110919.1|  [L=292]
Description: tRNA splicing endonuclease [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-21   75.9   3.8    7.5e-20   70.8   0.8    2.5  2  tRNA_int_endo    tRNA intron endonuclease, catalytic C-termin
     0.0024   17.5   0.1     0.0069   16.0   0.1    1.7  1  tRNA_int_endo_N  tRNA intron endonuclease, N-terminal domain


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 !    5.4   0.1    0.0021        19       3      21 ..      72      90 ..      71     122 .. 0.79
   2 !   70.8   0.8   8.4e-24   7.5e-20       6      85 .]     206     281 ..     203     281 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0021
                                  HHHHHHHHHHHTT-EEEEC CS
                 tRNA_int_endo  3 lkyavyrdLrekGyvvrsG 21
                                  ++y++y+ L++kGy v ++
  gi|13541231|ref|NP_110919.1| 72 ERYTAYTLLKNKGYRVHED 90
                                  58*************9876 PP

  == domain 2  score: 70.8 bits;  conditional E-value: 8.4e-24
                                   HHHHHHHHTT-EEEECGGGTSSEEEETSCTTTSSCSEEEEEEETTSEEEHHHHHHHHHHHHHTTSEEEEEEETTTSCEEE CS
                 tRNA_int_endo   6 avyrdLrekGyvvrsGlkFGadFrvYqrrpslehseylVvvvsedeeldwpdlsaavrlahsvkKklilaivdaegdvty 85 
                                    vyrdL ++G +v++G+k+G++FrvY ++++ eh+eylV vv+   +l w+ +s+avr+a sv+Kk+i+ ++  +g+++y
  gi|13541231|ref|NP_110919.1| 206 EVYRDLLSRGCIVKTGFKYGTNFRVY-EGEKSEHAEYLVSVVE--NKLIWYYISRAVRVASSVRKKMIFTTI-IDGKIKY 281
                                   69************************.99999********954..4555********************999.6667776 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 !   16.0   0.1   7.7e-07    0.0069      33      59 ..      33      59 ..      24      65 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 7.7e-07
                                  TSSEEEEHHHHHHHHHTTSEEEETTSE CS
               tRNA_int_endo_N 33 depLqLslvEAlYLlekGklevvkgge 59
                                  +  L+L+++E lYL  kG+++ ++++e
  gi|13541231|ref|NP_110919.1| 33 QGILFLDPYECLYLYFKGRITFEDSEE 59
                                  5679******************96665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       402  (0.0224218); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        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 0.32s 00:00:00.83 Elapsed: 00:00:00.50
# Mc/sec: 1755.06
//
Query:       gi|13541232|ref|NP_110920.1|  [L=171]
Description: GTPase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.6e-14   53.8   2.4    1.3e-13   50.9   2.4    1.9  1  Ras           Ras family
    5.4e-05   23.4   0.3     0.0014   18.8   0.3    2.3  1  Roc           Ras of Complex, Roc, domain of DAPkinase
    0.00039   20.4   0.7    0.00059   19.8   0.7    1.3  1  MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
    0.00041   20.3   2.6       0.17   11.8   0.3    2.2  2  RsgA_GTPase   RsgA GTPase
    0.00051   19.5   0.3    0.00082   18.9   0.3    1.6  1  Arf           ADP-ribosylation factor family
     0.0021   18.1   0.6        1.1    9.3   0.1    2.2  2  Dynamin_N     Dynamin family
     0.0033   17.0   0.1      0.082   12.4   0.3    2.2  2  GTP_EFTU      Elongation factor Tu GTP binding domain
  ------ inclusion threshold ------
      0.012   15.3   0.3        1.7    8.2   0.2    2.2  2  cobW          CobW/HypB/UreG, nucleotide-binding domain
      0.014   15.9   0.2      0.025   15.1   0.2    1.5  1  AAA_23        AAA domain
      0.039   14.0   1.1       0.86    9.7   1.1    2.3  1  MMR_HSR1      50S ribosome-binding GTPase
      0.068   12.9   1.1       0.19   11.5   1.1    1.9  1  AAA_24        AAA domain


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 !   50.9   2.4     8e-17   1.3e-13       1     160 [.       9     160 ..       9     162 .. 0.87

  Alignments for each domain:
  == domain 1  score: 50.9 bits;  conditional E-value: 8e-17
                                   EEEEEESTTSSHHHHHHHHHHSSCSSSCTTTSSEEEEEEEEEETTEEEEEEEEEETTSGGGHHHHHHHHTTESEEEEEEET CS
                           Ras   1 KlvlvGdsavGKtslllrfvkdkFkeeyesTigvdfytkeievdgkevkleiwDTAGqeefkslrelyyrdaegillvydi 81 
                                   K+v+ G+++ GK+s++   v ++        +   +++ + e++g+++ ++i+     +e +   e+++ +a+++++v d+
  gi|13541232|ref|NP_110920.1|   9 KFVIAGSKGAGKSSFISYIVYGEPAPILPRSL--VKKSLNREINGHKLAVDIL----FQEVDGGIENFIPTATAFIIVVDV 83 
                                   78999999999999999888888777666666..3455556677888887777....345677778899************ PP

                                   TBHHHHHTHHHHHHHHHHHSTTTSEEEEEEETTTGGGG-SS-HHHHHHHHHHHTSEEEEEBTTTTCTHHHHHHHHHHHH CS
                           Ras  82 tsresfenvkkwveeikrvaeenvpivLvGnKvDleekravsteegeelakelglkfletSAktnenveeafeellrei 160
                                   ts++s++++++++ eik+ +++  +i ++GnK+Dl+ + ++  ++ eel +++++k++ +S k+  ++e+++e+++++i
  gi|13541232|ref|NP_110920.1|  84 TSADSLSEARNIIMEIKNAKKN--NIFVIGNKIDLKYEAQIWIDDMEELKNKFSTKYYMVSCKDGIGFETLLEDIINSI 160
                                   *******************996..899************************************************9987 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 !   18.8   0.3   8.7e-07    0.0014       1     120 []       9     116 ..       9     116 .. 0.67

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 8.7e-07
                                   EEEEESSTTSSHHHHHHCHCT-CCC-EEETTTTEEEEEEECGGSGGCTTBTTTTCEEEEEEEE-SGGCTTTT-HHHHCTSC CS
                           Roc   1 KvvlvGdsgvGKtsllkrfvedkfsekekstigvdfltkevtkikgvendkkvkkvklniWDtaGqerfrslhplylreaa 81 
                                   K v+ G +g+GK+s+++ +v ++  +        ++++k+++  ++      ++  kl++ D+  qe    + + ++  a 
  gi|13541232|ref|NP_110920.1|   9 KFVIAGSKGAGKSSFISYIVYGEPAPIL----PRSLVKKSLN--RE------INGHKLAV-DILFQEVDGGI-ENFIPTAT 75 
                                   78999***********999988876554....4444444431..11......12233444.88999887776.56788888 PP

                                   EEEEEEEGHHH...HCHHHHHHHHHHHCSSS-EEEEEE-TTT CS
                           Roc  82 lailvydsrss...enlkeWlkelkkvagkspvilvgnkiDl 120
                                   ++i+v+d +s    +++++ + e+k+ a+k++++++gnkiDl
  gi|13541232|ref|NP_110920.1|  76 AFIIVVDVTSAdslSEARNIIMEIKN-AKKNNIFVIGNKIDL 116
                                   88888886655112455667777765.6678899******95 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 !   19.8   0.7   3.6e-07   0.00059      52     103 ..     101     159 ..      69     161 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 3.6e-07
                  MMR_HSR1_Xtn  52 nrvYipclyvlNKiDl.....isleeldelare..pnsvviSaekelnldeLkekiwee 103
                                   n +  + +++ NKiDl     i +++++el+++   ++ ++S+++++++++L+e+i ++
  gi|13541232|ref|NP_110920.1| 101 NAKKNNIFVIGNKIDLkyeaqIWIDDMEELKNKfsTKYYMVSCKDGIGFETLLEDIINS 159
                                   55556677888****9999889999999999976579*****************99775 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.1    0.0011       1.8     103     120 ..      11      28 ..       5      36 .. 0.88
   2 !   11.8   0.3    0.0001      0.17      20      99 ..      78     158 ..      67     166 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0011
                                   EEECSTTSSHHHHHHHHC CS
                   RsgA_GTPase 103 vlvGqSGvGKStLinall 120
                                   v++G+ G+GKS++i  ++
  gi|13541232|ref|NP_110920.1|  11 VIAGSKGAGKSSFISYIV 28 
                                   89***********98875 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.0001
                                   EEEEESTTTT--HHHHHHHHHHHHHTT-.EEEEEEE-GGG--HHH.HHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHHCT CS
                   RsgA_GTPase  20 livvslkepelslnlldrfLvlaeekgi.epvivlnKiDlleeee.eleelkeelealgyevllvsaktkegleelkellk 98 
                                   +ivv ++    sl+    +++++++++  ++ ++ nKiDl  e++  +++++e  +++ ++ ++vs k++ g+e+l e + 
  gi|13541232|ref|NP_110920.1|  78 IIVVDVT-SADSLSEARNIIMEIKNAKKnNIFVIGNKIDLKYEAQiWIDDMEELKNKFSTKYYMVSCKDGIGFETLLEDII 157
                                   5566665.3445555556666666555526666779999999999888888888999999999999999999999988765 PP

                                   T CS
                   RsgA_GTPase  99 d 99 
                                   +
  gi|13541232|ref|NP_110920.1| 158 N 158
                                   5 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.3   5.1e-07   0.00082      76     132 ..      68     121 ..       4     160 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 5.1e-07
                                   GGGCTTESEEEEEEETT-CTTHHHHHHHHHHHCTSGCCTTSEEEEEEE-TTSTTSS- CS
                           Arf  76 knYfektdavifvvDsadreRleeakeeLkalleeeelkevallvlaNKqDlpeals 132
                                   +n+ ++ +a i vvD++  + l+ea++ +   +e ++ k+  + v++NK+Dl+  ++
  gi|13541232|ref|NP_110920.1|  68 ENFIPTATAFIIVVDVTSADSLSEARNII---MEIKNAKKNNIFVIGNKIDLKYEAQ 121
                                   577888999****************9865...56677777889*********97654 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.0    0.0027       4.4       2      20 ..      11      29 ..      10      41 .. 0.78
   2 !    9.3   0.1   0.00068       1.1     122     165 ..      67     110 ..      46     113 .. 0.92

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0027
                                  EEEEBTTTTHHHHHHHHHT CS
                     Dynamin_N  2 avvGsqSsGKSSvlnaLlg 20
                                  ++ Gs  +GKSS++  ++ 
  gi|13541232|ref|NP_110920.1| 11 VIAGSKGAGKSSFISYIVY 29
                                  578999********99984 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00068
                                   HHHHHSTTEEEEEEEETTS-CCC-CHHHHHHHHSTTBTTEEEEE CS
                     Dynamin_N 122 vkeyikkadiilavtsanhdlsnsealflarevdpkgkrtivvl 165
                                   ++++i  a++++ v++  ++ s sea+++  e+++ +k+ i+v+
  gi|13541232|ref|NP_110920.1|  67 IENFIPTATAFIIVVDVTSADSLSEARNIIMEIKNAKKNNIFVI 110
                                   6889999********************************99998 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0     0.062     1e+02       5      28 ..       9      32 ..       6      77 .. 0.73
   2 !   12.4   0.3     5e-05     0.082      97     192 ..      77     160 ..      71     162 .. 0.69

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.062
                                  EEEEEESTTSSHHHHHHHHHHHTT CS
                      GTP_EFTU  5 nigiighvDhGKtTLtdrLlyktg 28
                                  +++i+g   +GK++++  ++y   
  gi|13541232|ref|NP_110920.1|  9 KFVIAGSKGAGKSSFISYIVYGEP 32
                                  58999999********99999764 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 5e-05
                                   EEEEEETTTB.STHHHHHHHHHHHHTTTE.EEEEEESCGSTHHHHHHH..HHHHHHHHHHHHHHHHHHHHTTTTTEEEEEE CS
                      GTP_EFTU  97 avlvvdaveG.vepqteevlrlalkegvp.iivfiNKmDrlkaelkei..veevkqklsrkeeklekygekgekevpvvfg 173
                                    ++vvd+++    +  ++++  +++ + + i+v+ NK+D   +   +i   ee+k+k+                 ++ +++
  gi|13541232|ref|NP_110920.1|  77 FIIVVDVTSAdSLSEARNIIMEIKNAKKNnIFVIGNKIDLKYEAQIWIddMEELKNKF----------------STKYYMV 141
                                   57788877432667777777777777777578888****9844433330034444444................35699** PP

                                   BTTTTBTHHHHHHHHHHHS CS
                      GTP_EFTU 174 Salkgegvktllealvell 192
                                   S+++g g++tlle +++ +
  gi|13541232|ref|NP_110920.1| 142 SCKDGIGFETLLEDIINSI 160
                                   *************999866 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0    0.0088        14       3      21 ..      10      28 ..       9      35 .. 0.87
   2 ?    8.2   0.2    0.0011       1.7     111     171 ..      73     136 ..      47     142 .. 0.69

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0088
                                  EEEEESTTCCHHHHHHHHH CS
                          cobW  3 tvltGflGsGKTtLlnhll 21
                                  +v++G+ G+GK+++++ ++
  gi|13541232|ref|NP_110920.1| 10 FVIAGSKGAGKSSFISYIV 28
                                  589***********99886 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0011
                                   CECEEEEEEETTTH...CCHCCHHHHHHHHHHTSSEEEEE-HHHHCHC...HHHHHHHHHHHHT CS
                          cobW 111 tldavvavvDaknl..eaeeekieekaedqlaaadllvlnKtDlldee.allekleerlrqlnp 171
                                   t++a + vvD++ +   +e ++i  ++++  +   +++ nK+Dl  e+   ++ +ee  +++++
  gi|13541232|ref|NP_110920.1|  73 TATAFIIVVDVTSAdsLSEARNIIMEIKNAKKNNIFVIGNKIDLKYEAqIWIDDMEELKNKFST 136
                                   56788999**97764444555555555555555557888*****88885666777777776665 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.2   1.6e-05     0.025      22     142 ..      10     114 ..       9     171 .] 0.48

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.6e-05
                        AAA_23  22 tlItGpNGaGKTTildAiklaLygetprlsrksgrgfeksdveiesegkvkayveltfenkdgry................ 86 
                                   ++I G  GaGK+++   i ++ yge+++  ++   +++k + + e +g  k  v++ f+  dg+                 
  gi|13541232|ref|NP_110920.1|  10 FVIAGSKGAGKSSF---ISYIVYGEPAPILPR---SLVKKSLNREING-HKLAVDILFQEVDGGIenfiptatafiivvdv 83 
                                   89**********95...7999***99666553...3344444433333.35568888888777644444444444444444 PP

                        AAA_23  87 ........trsiererelskkkgkttkkaklelleideleqfisellgskkiilnlilflgqer 142
                                            r+i  e++++k                                  n+i+ +g + 
  gi|13541232|ref|NP_110920.1|  84 tsadslseARNIIMEIKNAK---------------------------------KNNIFVIGNKI 114
                                   44333333222222222222.................................22222222222 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   1.1   0.00052      0.86       2      21 ..      10      29 ..       9     113 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00052
                                  EEEEESTTSSHHHHHHHHHT CS
                      MMR_HSR1  2 vaivGrpNvGKStLinaltg 21
                                  ++i+G   +GKS++i+ ++ 
  gi|13541232|ref|NP_110920.1| 10 FVIAGSKGAGKSSFISYIVY 29
                                  689*************9984 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   1.1   0.00011      0.19       2      24 ..       7      32 ..       6     142 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00011
                        AAA_24  2 klkiliyGpsgiGKTtlakel...gp 24
                                  ++k++i G+ g+GK+++++ +   +p
  gi|13541232|ref|NP_110920.1|  7 AWKFVIAGSKGAGKSSFISYIvygEP 32
                                  689***************99876533 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       666  (0.0371465); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 1083.01
//
Query:       gi|13541233|ref|NP_110921.1|  [L=402]
Description: transcription regulator [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-41  142.5   0.0    2.1e-41  142.3   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
    1.6e-11   43.7   0.0    8.2e-11   41.3   0.0    1.9  1  Aminotran_MocR   Alanine-glyoxylate amino-transferase
    0.00015   21.2   0.0    0.00023   20.6   0.0    1.3  1  Beta_elim_lyase  Beta-eliminating lyase
    0.00016   21.1   0.0    0.00028   20.3   0.0    1.3  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
  ------ inclusion threshold ------
       0.01   15.7   0.0      0.023   14.6   0.0    1.5  1  MreC             rod shape-determining protein MreC
      0.014   14.1   0.0       0.12   11.0   0.0    2.0  2  Aminotran_3      Aminotransferase class-III
       0.08   11.6   0.0       0.13   11.0   0.0    1.2  1  Pyridoxal_deC    Pyridoxal-dependent decarboxylase conserved 
      0.084   12.5   0.0       0.15   11.7   0.0    1.3  1  PAR1             PAR1 protein


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  142.3   0.0   9.6e-45   2.1e-41      29     358 ..      53     385 ..      30     390 .. 0.87

  Alignments for each domain:
  == domain 1  score: 142.3 bits;  conditional E-value: 9.6e-45
                                   H.HHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEEEESS-THHHH CS
                 Aminotran_1_2  29 e.galaggtlneygpidglpeleealakflgrseklklkreaavvvgsGagaliealifllklnpgdeilvpdptyasykn 108
                                   +   + g+++ +yg+++gl+ l+ +lak++ + e+++ kre ++++++G+++++ a++ ++ +np d ++   pty   + 
  gi|13541233|ref|NP_110921.1|  53 DiMDNYGKKALQYGTTEGLDVLRDELAKYVLKTEGINAKRE-EIILTTGSQQALYAIAKIF-VNPNDPVITEGPTYVGAIS 131
                                   3444778999*******************************.*******************.9****************** PP

                                   HHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEE.EEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEE CS
                 Aminotran_1_2 109 ilrlsggevvryplyseedfhldlealeealkeapegnkktkvi.lvesphNPtGtvatleeleklldlakkynlllfvDe 188
                                   +++++++ ++ + ++   + ++++++le+++ke++++  k+k+i ++ + +NP Gt ++l+  + ll++ ++y++ ++ D 
  gi|13541233|ref|NP_110921.1| 132 AFNANTANMMAIDID---ENGMNVDELEAKIKELSQNGLKPKFIyVIPTFQNPAGTTMSLDRRKRLLEISERYEIPIVEDN 209
                                   *************66...779***********************45799******************************** PP

                                   TTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEEEEEEHHHHHHHHHHHHHHTS.SHHHHHHHHHHHHHHH CS
                 Aminotran_1_2 189 aYagfvfgsldavatranveeepnllivgslsKafGlaGeRvGyilgnaavvsqlrklsrpfls.ssllqaavaaalsdal 268
                                    Y+ + ++ + +++ +  +++  n++ +g++sK + ++G+R+Gy+++  +v++ ++ l++++   s +l++++a    +  
  gi|13541233|ref|NP_110921.1| 210 PYGQLRYDGEPVQS-IKSMDKNGNVIYLGTFSKVM-APGLRLGYVIAPREVIDKINLLKQGLDLaSDSLSEYIAYEYLKRG 288
                                   *******9776555.******************99.5************************98886666666665555555 PP

                                   HHHHHHHHHHHHHHHHHHHHHHHHHHS...TEEEECCSCSSEEEEEETHH..CHHHHHHHHHHTCTEEEEEGGGGTS.... CS
                 Aminotran_1_2 269 lkqseleemrqrlqkrrkelrdeLael...glkvlasqsgmflltdlsae..takelskkLleevgvyvtpgtsftv.... 340
                                    + +++ ++++ + k+r+ + ++L+e      +++++++gmfl++ l++   t k l ++L  +  v+ + g+ f+     
  gi|13541233|ref|NP_110921.1| 289 AIYRQIPKTVDLYRKKRDLMIKSLEEYfpeAATWTKPHGGMFLWVSLDERidTTKMLDRALKAK--VAYVSGSAFYPhgek 367
                                   5667********************999**999999999**********9996656666666555..666677888777899 PP

                                   TTEEEEECTTS-HHHHHH CS
                 Aminotran_1_2 341 pgrlRitvAglteeelee 358
                                    ++ R+++   +++++ e
  gi|13541233|ref|NP_110921.1| 368 HNSMRLNFTYSDDDKIVE 385
                                   889999995555555544 PP

>> Aminotran_MocR  Alanine-glyoxylate amino-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.3   0.0   3.7e-14   8.2e-11     127     394 ..     119     379 ..      52     397 .. 0.80

  Alignments for each domain:
  == domain 1  score: 41.3 bits;  conditional E-value: 3.7e-14
                                   EEEEES--HHHHHHHHHHT-EEEEEEEETTEE-HHH....HHHHHHC-TTEEEEEE-SSS-TTT-----HHHHHHHHT--- CS
                Aminotran_MocR 127 llvtvpGydrhfllleelGielltvdlqddGpdvda....veklvaedasvkGilavpkysnptGetiseevarrlaalka 203
                                   ++   p y       +    +++++d++++G +vd     +++l  +    k i+++p++ np+G+t+s ++ +rl  +  
  gi|13541233|ref|NP_110921.1| 119 VITEGPTYVGAISAFNANTANMMAIDIDENGMNVDEleakIKELSQNGLKPKFIYVIPTFQNPAGTTMSLDRRKRLLEISE 199
                                   566677777777788888999*************9622226788888999999***********************99976 PP

                                   SSTT-EEEEE-TTSS-BS.SSSS----HHHHHHHHT-TTSEEEEEESTTTS-TTSS-EEEEE-HHHHHHHHHHHHHC-S-- CS
                Aminotran_MocR 204 aapdfrifaddayavhdlvaeedkdanivalardaGhpdrafvlastskitfaGaGvafvassedniawlkkylGlqsiGp 284
                                      +  i  d+ y    l  +++  + i     +       + l + sk+   G  +++v +  + i  ++       +  
  gi|13541233|ref|NP_110921.1| 200 -RYEIPIVEDNPYGQ--LRYDGEPVQSIK----SMDKNGNVIYLGTFSKVMAPGLRLGYVIAPREVIDKINLLKQGLDLAS 273
                                   .57899*******75..545666655554....44444567889999***************9999998887666666788 PP

                                   -HHHHHHHHHHHHHSTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTSSEEE---SBSS-..EEEEESSS-HHHHHHHHHH CS
                Aminotran_MocR 285 dkveqlrhvkflkdyeGlealmrdhaeliapkfeavlevleaelggaevatwteprGGyf..isldtldgvakrvvklaee 363
                                   d + +     +lk    +  ++ +  +l + k + + + le+ +   e atwt+p+GG f  +sld    ++ +++  a +
  gi|13541233|ref|NP_110921.1| 274 DSLSEYIAYEYLKRG-AIYRQIPKTVDLYRKKRDLMIKSLEEYFP--EAATWTKPHGGMFlwVSLDERIDTT-KMLDRALK 350
                                   888887777777654.57778888999999999999999999875..78*********99456887654444.5778899* PP

                                   CTEE---TTTTSSTT--SSS-EEEE--SSS- CS
                Aminotran_MocR 364 aGvsltaaGatypaGedpkdrnirlaptlpp 394
                                   a v+  +  a yp+Ge   ++ +rl  t   
  gi|13541233|ref|NP_110921.1| 351 AKVAYVSGSAFYPHGEK--HNSMRLNFTYSD 379
                                   ***************95..445666666555 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0     1e-07   0.00023      88     167 ..     128     208 ..      42     209 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 1e-07
                                   THHHHC..C--EEEEE-EBTTTBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEE CS
               Beta_elim_lyase  88 gaiael..agvklrdlknkeaGkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhl 166
                                   gai+++  + +++  ++++e + m++++lea+ike ++   k+k+i++  T +  +G+ +sl+  +++ +i ++y+ip++ 
  gi|13541233|ref|NP_110921.1| 128 GAISAFnaNTANMMAIDIDE-NGMNVDELEAKIKELSQNGLKPKFIYVIPTFQNPAGTTMSLDRRKRLLEISERYEIPIVE 207
                                   44444433556667778888.88************999999*************************************987 PP

                                   E CS
               Beta_elim_lyase 167 D 167
                                   D
  gi|13541233|ref|NP_110921.1| 208 D 208
                                   7 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   1.2e-07   0.00028      42     146 ..      95     210 ..      76     229 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 1.2e-07
                                   EEESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHHHHHHTT-EEEEE-B-TTTSSB-GGGCGGG--TTE......EEEE CS
               DegT_DnrJ_EryC1  42 iavssGtaAlhlaLralgvgpgdeVIvpsltFvatanavlelgakpvfvDvdpdtynidpaaieaaitert......kaIl 116
                                   i +++G++  + a+  + v+p+d VI+   t+v+ ++a   + a+ + +D+d++ +n+d  ++ea+i e +      k I 
  gi|13541233|ref|NP_110921.1|  95 IILTTGSQQALYAIAKIFVNPNDPVITEGPTYVGAISAFNANTANMMAIDIDENGMNVD--ELEAKIKELSqnglkpKFIY 173
                                   556778888888888899**********************************9988876..78999999988899999999 PP

                                   EB-GGGB--..-H..H...HHHHHHHHCT-EEEEE-T CS
               DegT_DnrJ_EryC1 117 pVhlyGqva..dm..d...alkaiaakhglkvieDaA 146
                                   ++ ++ ++a   m  d   +l +i+++++++++eD  
  gi|13541233|ref|NP_110921.1| 174 VIPTFQNPAgtTMslDrrkRLLEISERYEIPIVEDNP 210
                                   99887666644342244336999************65 PP

>> MreC  rod shape-determining protein MreC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0     1e-05     0.023      10     119 ..      92     253 ..      85     269 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1e-05
                                   TTEEEES--GGGT........--TT-EEEETTE.EEEEEEEE-SS-EEEEETTSCCE.EEE.....EEE.CTTEEEE.... CS
                          MreC  10 nssltIdkGskdg........vkkgmpVvsgkg.lVGkVtevgknssrVllitdssssvsv.....kvkrtgergil.... 72 
                                   ++++++  Gs++         v++++pV+++    VG ++  ++n++  + i  ++  + v     k+k+     +     
  gi|13541233|ref|NP_110921.1|  92 REEIILTTGSQQAlyaiakifVNPNDPVITEGPtYVGAISAFNANTANMMAIDIDENGMNVdeleaKIKE-----LSqngl 167
                                   678999999999999999999********99559****************99777777777211112332.....113333 PP

                                   ...........................................EEEETTTTEEEEEEE.CT..-..--TT-EEEEE-TTSS CS
                          MreC  73 ...........................................egkddekkeleleylpke..aadvkkgdlvvTsglggv 108
                                                                                     ++l+++  p +  ++  k+g+ ++   +++v
  gi|13541233|ref|NP_110921.1| 168 kpkfiyviptfqnpagttmsldrrkrlleiseryeipivednpY------GQLRYDGEPVQsiKSMDKNGNVIYLGTFSKV 242
                                   35555667777778777788888888888877776665544332......3444432222223445577888888999999 PP

                                   S-CCEEEEEEE CS
                          MreC 109 fpkglpvGtVe 119
                                   + +gl  G+V 
  gi|13541233|ref|NP_110921.1| 243 MAPGLRLGYVI 253
                                   99999999985 PP

>> Aminotran_3  Aminotransferase class-III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0     0.062   1.4e+02     286     335 ..     117     169 ..      99     193 .. 0.76
   2 ?   11.0   0.0   5.5e-05      0.12     258     380 ..     238     367 ..     227     394 .. 0.72

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.062
                                   S....B--TTTT-HHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHCTT- CS
                   Aminotran_3 286 s....hgsTfgGnplacavalavleiieeekllenaqelgaalkegLeelqkky 335
                                   +     g+T+ G  +a  +  a + +i  ++   n++el+a++ke L++   k+
  gi|13541233|ref|NP_110921.1| 117 DpvitEGPTYVGAISAFNANTANMMAIDIDENGMNVDELEAKIKE-LSQNGLKP 169
                                   14455899*******999999999999999999999999998865.55444444 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 5.5e-05
                                   EE-GGGGTTSS-EEEEEEHHHHTTS-TTSB--TTTT-HHHHHHHHHHHH..HHHH..TTHHHHHHHHHHHHHHHHHHHCTT CS
                   Aminotran_3 258 tlaKaltgGlplsavlataevmqalapgshgsTfgGnplacavalavle..iiee..ekllenaqelgaalkegLeelqkk 334
                                   t++K+++ Gl l  v+a++ev + ++  ++g   + + l   +a + l+  +i +   k ++  +++++ + + Lee   +
  gi|13541233|ref|NP_110921.1| 238 TFSKVMAPGLRLGYVIAPREVIDKINLLKQGLDLASDSLSEYIAYEYLKrgAIYRqiPKTVDLYRKKRDLMIKSLEEYFPE 318
                                   8***********************************************844344457788889999999999999998866 PP

                                   -TTEEEEEEETTEEEEEEBCCCETTC....HHHHHHHHHCTEE-EEETTT CS
                   Aminotran_3 335 yevikevRgkGlmiaielkeeaevke....keilkkakekGvlilsaGdn 380
                                        + +  G+++ + l e+ ++++    +  +k a   G  +++ G++
  gi|13541233|ref|NP_110921.1| 319 A-ATWTKPHGGMFLWVSLDERIDTTKmldrALKAKVAYVSGSAFYPHGEK 367
                                   5.556666778888888888777664443211122233345556666664 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 ?   11.0   0.0   5.6e-05      0.13     168     231 ..     139     205 ..     126     213 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 5.6e-05
                                   EEEEE--BTTTBB-HHHHHHHHHHHHCTT.EE..EEEEEEB....S-TTT-BB--HHHHHHHHHHCT-EE CS
                 Pyridoxal_deC 168 klrvipldengklrgaalekaieedkekGlip..ffvvatl....GttvlgaFddlkelgdicekydlwl 231
                                   ++ +i +deng + +++le++i+e  ++Gl p  ++v +t+    Gtt+  + d  k l +i e+y++++
  gi|13541233|ref|NP_110921.1| 139 NMMAIDIDENG-MNVDELEAKIKELSQNGLKPkfIYVIPTFqnpaGTTM--SLDRRKRLLEISERYEIPI 205
                                   5999*****99.******************9854577888644447776..5788888888888887776 PP

>> PAR1  PAR1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   6.5e-05      0.15      26     101 ..     225     302 ..     222     306 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 6.5e-05
                          PAR1  26 ksvkrsgeeeytcrtseveae..klkelietdecvkacGvdrksvGissdsllesqftkklcspaclnkcPnivdlyf 101
                                   ks+ ++g+ +y    s+v+a   +l  +i   e +++  + ++ + ++sdsl e    + l   a +++ P  vdly 
  gi|13541233|ref|NP_110921.1| 225 KSMDKNGNVIYLGTFSKVMAPglRLGYVIAPREVIDKINLLKQGLDLASDSLSEYIAYEYLKRGAIYRQIPKTVDLYR 302
                                   678899**************9667788999***********************************************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (402 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       621  (0.0346366); expected 358.6 (0.02)
Passed bias filter:                      567  (0.0316247); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.65u 0.32s 00:00:00.97 Elapsed: 00:00:00.51
# Mc/sec: 2381.16
//
Query:       gi|13541234|ref|NP_110922.1|  [L=328]
Description: phosphopantetheine adenylyltransferase/unknown domain fusion protein [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.5e-33  114.7   0.0    6.2e-33  113.9   0.0    1.4  2  NTPase_I-T       Protein of unknown function DUF84
    1.6e-14   54.3   0.0    2.6e-14   53.6   0.0    1.4  1  CTP_transf_like  Cytidylyltransferase-like


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 ?   -3.8   0.0       1.1   9.7e+03     137     151 ..      32      46 ..      28      47 .. 0.86
   2 !  113.9   0.0   6.9e-37   6.2e-33       1     162 [.     156     315 ..     156     316 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 1.1
                                   HHHHTTTSS-HHHHH CS
                    NTPase_I-T 137 igllTkglvtRedly 151
                                   igl +++ v+R+++y
  gi|13541234|ref|NP_110922.1|  32 IGLTSDEYVKRNKVY 46 
                                   899999999999987 PP

  == domain 2  score: 113.9 bits;  conditional E-value: 6.9e-37
                                   S---HHHHHHHHHHHHHHCTTEEEEEEE---SS-SS-BSHHHHHHHHHHHHHHHHHHSTTSSEEEEEEEEE..ET....TE CS
                    NTPase_I-T   1 gSkNpvKveAvkeafeklfkdvevegvsvpsgvsdqPmgdeetlkGAinRaknaleaaeeadygvGlEgGv..eeleekll 79 
                                   +++N +K++A+++ f+kl+k+++v +    +   +qP+g e t++ A++Ra + l +    dy++G+E+G+  e+++ k++
  gi|13541234|ref|NP_110922.1| 156 ATNNSAKLKATNDFFHKLMKNFDVIQNTDYKLETQQPFG-EVTMNMATKRAMQSLGD---NDYAIGIESGIvyERFSRKYF 232
                                   699************************************.***************99...79********955667777** PP

                                   EEEEE.EEEESS-EEEEE---EE--HHHHHHHCTT--HHHHHHHHHTHCCHHHTTHHHHHHTTTSS-HHHHHHHHHHHHTH CS
                    NTPase_I-T  80 dvawaavvdkegrvsvgrsasfelPeevveevkegeelgevmdelfgtenikqkeGaigllTkglvtRedlyeqavilAli 160
                                   d+++++v+d+ g+v+ g+s++fe+P+++++++k+++ ++++  ++++t++i  ++G++g +++g+v+R dl+ +++  A+i
  gi|13541234|ref|NP_110922.1| 233 DFHYCVVIDRFGNVTRGSSSGFEVPDRIIDLIKRDMSFSQAYGKVIDTNGIDDSTGIVGKISNGRVRRYDLIMECIRNAFI 313
                                   ********************************************************************************* PP

                                   HH CS
                    NTPase_I-T 161 pf 162
                                   p+
  gi|13541234|ref|NP_110922.1| 314 PR 315
                                   96 PP

>> CTP_transf_like  Cytidylyltransferase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.6   0.0   2.9e-18   2.6e-14       2     142 ..       5     138 ..       4     139 .. 0.91

  Alignments for each domain:
  == domain 1  score: 53.6 bits;  conditional E-value: 2.9e-18
                                   EEE--TT--HHHHHHHHHHHHHSSESEEEEEESSTHCSST-.SCSSTHHHHHHHHHHH.TTCTTEEEEEEESEHH.HHHHH CS
               CTP_transf_like   2 agGtFDpiHlGHlrlleqakklleedlivgvpsdeppkkkk.kplasaeeRlemlela.kevdevisvdpweltr.evlkk 79 
                                   +gGtF  +H+GH +lle+a + ++e +++g++sde +k++k  p ++++eR+++l  +  ++ + ++++p++  + +   +
  gi|13541234|ref|NP_110922.1|   5 VGGTFSKLHKGHKALLEKAIETGNE-IVIGLTSDEYVKRNKvYPAIPYKERYRNLYNYmVKKTNKFRIRPIDDRNgNAPYE 84 
                                   79***********************.**************99****************95666669999999888766666 PP

                                   TTTTEEEEEEEHHHHHHHHCHHHHHHHHHHHHHEEEEEEHTTCEEEEEEECCTTTCSHHHHHH CS
               CTP_transf_like  80 lkpdklylvigadvledfsewkeleeilgnvklvvvsrpekqanvllkaekrtngiSstkire 142
                                   ++ +  ++v++ ++++   + +e++   g  +l ++++p       +  +++  +iSst+i++
  gi|13541234|ref|NP_110922.1|  85 RDYE--IIVVSPETYQRSLKINEIRIQNGLPPLKIIRVP-------YVLAEDLFPISSTRIIN 138
                                   6668..999999999999999999999999999999999.......9999***********86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       594  (0.0331307); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 1956.05
//
Query:       gi|13541235|ref|NP_110923.1|  [L=296]
Description: Ca2+/Na+ antiporter [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-12   47.5  36.5    9.5e-07   28.9  12.6    2.1  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 !   24.8  15.9   9.8e-10   1.8e-05       6     141 ..      22     148 ..      17     157 .. 0.79
   2 !   28.9  12.6   5.3e-11   9.5e-07       2     132 ..     171     291 ..     170     295 .. 0.88

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 9.8e-10
                                   HHHHHHHHHHHHHHHHHHHHHHHHHTTCTHHHHHHHHHHHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHTHHHHH CS
                      Na_Ca_ex   6 filslllisvladflvssaeeiakslgisgsvlGltllAlgnslpElissiiaaltgevdlaignvlGsnifnlllviGli 86 
                                   +i+++++++v++d++++ a++    +g s++++G ++ A +  + E+ +si++++   + ++ g+v Gsn++ ll+ +  +
  gi|13541235|ref|NP_110923.1|  22 LIFAMAVLIVSSDRFFDEATAAMGRIGFSDRFSGSIFAAMVAVADEISLSIFSVILRTPLVGFGAVEGSNLVTLLFFVVWM 102
                                   7899999999******666666658***************************************************99999 PP

                                   HHHHHBTTSSCECCHHHHHHHHHHHHHHHHHHHTCHHHHHHTEEHHHHHHHHHHH CS
                      Na_Ca_ex  87 aligslkvdseslkldlgllllvallllllvlllllplfvpgrltvleglvllll 141
                                    l+   ++   ++++ +++  +++lll+++++ + +   v+   ++  g++l l+
  gi|13541235|ref|NP_110923.1| 103 PLF---SI---QKTRAFRADAVFVLLLSIITYYFST---VSSDFKIIAGILLSLF 148
                                   999...44...4567777766777777665555553...3477777777766544 PP

  == domain 2  score: 28.9 bits;  conditional E-value: 5.3e-11
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCTHHHHHHHHHHHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHTH CS
                      Na_Ca_ex   2 lfvlfilslllisvladflvssaeeiakslgisgsvlGltllAlgnslpElissiiaaltgevdlaignvlGsnifnlllv 82 
                                   ++++++ls++l+ ++++++v+ + ++++  +i  + l++  + +++ +pE++++i+a ++++vd++ig + Gs +  + ++
  gi|13541235|ref|NP_110923.1| 171 SLIMLVLSIVLLTAASQIIVEDTIALSELDHIDIAALSIYGIGIASAIPETVMIIVASIKKKVDISIGVLAGSSVYKMSII 251
                                   7899***********************7558888888888899*************************************9 PP

                                   HHHHHHHHHBTTSSCECCHHHHHHHHHHHHHHHHHHHTCHHHHHHTEEHH CS
                      Na_Ca_ex  83 iGlialigslkvdseslkldlgllllvallllllvlllllplfvpgrltv 132
                                    Gl +  g+     e++ ldl+l+ +++l +++l+++l+      g++++
  gi|13541235|ref|NP_110923.1| 252 PGLLIMTGK----IETTGLDLPLMTIMILSVIFLFYTLY------GTIKF 291
                                   999888844....6678999*999999999999999988......66655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       883  (0.0492498); expected 358.6 (0.02)
Passed bias filter:                      235  (0.0131073); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 1920.17
//
Query:       gi|13541236|ref|NP_110924.1|  [L=130]
Description: S-adenosylmethionine decarboxylase proenzyme [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.8e-33  114.4   0.0    3.2e-33  114.2   0.0    1.0  1  AdoMet_dc  S-adenosylmethionine decarboxylase


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 !  114.2   0.0   1.8e-37   3.2e-33       1     106 []       8     114 ..       8     114 .. 0.99

  Alignments for each domain:
  == domain 1  score: 114.2 bits;  conditional E-value: 1.8e-37
                                   EEEEEEES--HHHCTSHHHHHHHHHHHHHHCT-EEEEEEEEE-SSS-EEEEEEETTEEEEEEEEGGGTEEEEEEEEEST.H CS
                     AdoMet_dc   1 hllvdlygcdpelledaelleqilteaaeaigatvlsvafhkfepeGvsvvvliaeShlsiHtwpetgyaaiDvftcge.i 80 
                                   h+++d+yg+d++l++ +e++  i+++a++   +t +s+ +++f+p+G+s+vvl+aeShls Htwpe+g +++D++tcg+  
  gi|13541236|ref|NP_110924.1|   8 HIIADFYGVDSKLISTTERMYPIIEGAVKYGRLTKISSDYYQFRPQGASGVVLLAESHLSFHTWPEYGLVTLDIYTCGDpK 88 
                                   9******************************************************************************** PP

                                   HHHHHHHHHHHHHT-SEEEEEEEEEE CS
                     AdoMet_dc  81 spekaleylieafkadrvtvdelkRG 106
                                   +++ a+eyl++++k+++vt+++++RG
  gi|13541236|ref|NP_110924.1|  89 TADDAFEYLTRELKPTSVTTRKIVRG 114
                                   *************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       319  (0.0177924); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 882.60
//
Query:       gi|13541237|ref|NP_110925.1|  [L=252]
Description: transcription regulator [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00079   19.9   0.0     0.0018   18.7   0.0    1.6  1  HTH_27    Winged helix DNA-binding domain
     0.0052   16.3   0.1      0.018   14.6   0.0    1.9  2  HTH_24    Winged helix-turn-helix DNA-binding
     0.0059   16.4   0.1      0.029   14.3   0.0    2.2  2  HTH_5     Bacterial regulatory protein, arsR family
  ------ inclusion threshold ------
       0.11   12.6   0.0       0.41   10.8   0.0    1.9  2  HTH_20    Helix-turn-helix domain
       0.16   11.9   0.0       0.27   11.2   0.0    1.3  1  MIP-T3_C  Microtubule-binding protein MIP-T3 C-terminal regio


Domain annotation for each model (and alignments):
>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   4.9e-07    0.0018       4      56 ..       9      55 ..       7      61 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 4.9e-07
                        HTH_27  4 qqalvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdead 56
                                  +q++vL +++  ++r k +++++ ++++ + ++y lk L +  ++    de++
  gi|13541237|ref|NP_110925.1|  9 NQVIVLLNVY--HGRRKPSEISKNMDITLQGVIYHLKNLRKSRYI----DEEN 55
                                  699*******..7777789**************************....5544 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     5e-06     0.018      16      47 ..      20      51 ..      14      52 .. 0.91
   2 ?   -2.7   0.0       1.2   4.4e+03      24      32 ..     191     199 ..     191     199 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 5e-06
                        HTH_24 16 prisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                  +r   +e+++  +++++ v ++lk+L ++ +I
  gi|13541237|ref|NP_110925.1| 20 GRRKPSEISKNMDITLQGVIYHLKNLRKSRYI 51
                                  667789**********************9998 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.2
                        HTH_24  24 AerlglSps 32 
                                   A++lgl ps
  gi|13541237|ref|NP_110925.1| 191 ARKLGLNPS 199
                                   89****987 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0     8e-06     0.029      11      46 ..      15      52 ..       7      53 .. 0.83
   2 ?   -2.7   0.0       1.6   5.6e+03      15      28 ..     210     223 ..     210     224 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 8e-06
                                  HTT..SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                         HTH_5 11 Lae..gelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                  L+   g ++ +e+++ ++++   v +HLk Lr++++++
  gi|13541237|ref|NP_110925.1| 15 LNVyhGRRKPSEISKNMDITLQGVIYHLKNLRKSRYID 52
                                  4445588999*************************996 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.6
                                   SEEHHHHHHHHTS- CS
                         HTH_5  15 elcvcelaeelgls 28 
                                   e+cv  ++ +l +s
  gi|13541237|ref|NP_110925.1| 210 EACVRGISVILLVS 223
                                   68999999888666 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00011      0.41      27      56 ..      24      53 ..      18      56 .. 0.90
   2 ?   -2.0   0.0       1.1   3.9e+03       9      17 ..     242     250 ..     242     252 .] 0.84

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00011
                                  HHHHHHHHTS-HHHHHHHHHHHHHCTTEEE CS
                        HTH_20 27 aselaerldlskntlsyHLrvLeeagLvev 56
                                  +se+ + +d++ + + yHL+ L++  +++ 
  gi|13541237|ref|NP_110925.1| 24 PSEISKNMDITLQGVIYHLKNLRKSRYIDE 53
                                  69*********************9988876 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.1
                                   -HHHHHHHH CS
                        HTH_20   9 hPvRrrilr 17 
                                   +PvR+ i +
  gi|13541237|ref|NP_110925.1| 242 NPVRAHIID 250
                                   7****9987 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 ?   11.2   0.0   7.6e-05      0.27      97     135 ..      47      85 ..      35      88 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 7.6e-05
                      MIP-T3_C  97 qaeelaeerrateealeplkaqlaeleeaIkdqkekisn 135
                                   ++  + ee+r+t+e  + l++ql+e+ e I+++   ++ 
  gi|13541237|ref|NP_110925.1|  47 KSRYIDEENRITKEGFQFLYDQLSEMREFINENITDLDS 85 
                                   5566789*************************9887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       552  (0.0307881); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); 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 0.25s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 1767.19
//
Query:       gi|13541238|ref|NP_110926.1|  [L=286]
Description: prenyltransferase [Thermoplasma volcanium GSS1]
Scores for complete 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-36  124.1  21.2    7.6e-36  123.7  21.2    1.1  1  UbiA           UbiA prenyltransferase family


Domain annotation for each model (and alignments):
>> UbiA  UbiA prenyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.7  21.2   4.2e-40   7.6e-36       3     251 ..      20     266 ..      19     280 .. 0.95

  Alignments for each domain:
  == domain 1  score: 123.7 bits;  conditional E-value: 4.2e-40
                          UbiA   3 ipalvglalaaggspdlllllllllgtllaaaaanalNdyfDreiDadmertpnRPlvsGrispkealifaivllilglll 83 
                                   +++l g+++aag s+ +  ++l+l++++ a+++a+ +N++     D  ++r+++ +lvsGr++++ea+++ i+++++  + 
  gi|13541238|ref|NP_110926.1|  20 PFILSGYVIAAGTSIFPYKIILILIAAVTARSSAMSINRIEGLRYDLTNPRKKEWALVSGRMTVREAIALTILFIAVFEIS 100
                                   678999**************************************************************************9 PP

                          UbiA  84 lalllnpltallgllalllyvvYtglrlKrrtllgtvvggiafglppllgwaavtgsl..sllalllalavflltwaiala 162
                                   + +lln l+++l+ ++++l v  +   lKr+t ++++  g a g++ l+g+ av  ++  +l++++l++a  l++++++++
  gi|13541238|ref|NP_110926.1| 101 A-FLLNRLVFILSPIVIFLFVSDP--ILKRYTEWRHFYMGSAIGIGTLAGYLAVIPEFpsNLAIYFLFIASSLWIAGFDMI 178
                                   9.*****************9***9..********************************8888888899999********** PP

                          UbiA 163 ndlrdregDrkagiktlpvvlGrkaarillalllavlllallllllalllllylllalllaalallraarlvrrrdakkaa 243
                                   + ++d+e D+k  +kt  +++G k  +  +  ++ ++ l++++l+l+++ ++++l++l+++++++++++ +v+  d+ +++
  gi|13541238|ref|NP_110926.1| 179 YVIPDIEYDQKNKLKTVMTKYGIKLGLL-ISDITHLAALIFFWLMLYYFRTIWYLAGLIIITILVIYQHIIVDPADPLSIR 258
                                   ***************************9.6666666666678999************************************ PP

                          UbiA 244 kfflflss 251
                                   k+f++ +s
  gi|13541238|ref|NP_110926.1| 259 KSFFNANS 266
                                   ***66554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       839  (0.0467957); 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:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 1845.76
//
Query:       gi|13541239|ref|NP_110927.1|  [L=481]
Description: 4-hydroxybenzoate decarboxylase [Thermoplasma volcanium GSS1]
Scores for complete 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-147  491.6   0.0   1.8e-147  491.4   0.0    1.0  1  UbiD          3-octaprenyl-4-hydroxybenzoate carboxy-lyase
     0.0037   17.1   0.2     0.0088   15.9   0.2    1.6  2  Galactosyl_T  Galactosyltransferase


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 !  491.4   0.0    2e-151  1.8e-147       2     405 ..      11     421 ..      10     422 .. 0.96

  Alignments for each domain:
  == domain 1  score: 491.4 bits;  conditional E-value: 2e-151
                                   HHCCCTTSEEEEESEB-TBTHHHHHHHHH.HHHT--EEEEEEBTTB.TT-EEEE-TTS-HCHHHHHHTS-GHHHHHHHHHH CS
                          UbiD   2 ealekagelvrikeevdpelEiaeiarrv.leeggpallFenvkgkgskfpvltnlfgtrervalalglssleeileklae 81 
                                   + l k+++lv+i+eevdp+l+++ i+ +     +g+ +lF+nvk  gs++p+++nlf+t e+++ +lg ++   i+ k+a+
  gi|13541239|ref|NP_110927.1|  11 DYLAKKNDLVTITEEVDPNLDLTYILSEEeRMGRGRTILFKNVK--GSQVPAVGNLFSTNEKLKAVLG-DDPYSIGVKIAD 88 
                                   6799************************9866789********6..568*******************.999********* PP

                                   HHHS..-...................---EE--GCG-GGGSEEECCCCC--HHHS---BSSTTSSS-EEECEEEEEE-TTT CS
                          UbiD  82 llepkpp...................ippkvvesekapcqeevvlegddvdLskLPvltlwpgDgGpyitlglvitrdpet 143
                                   +++p  p                   ++pkv +s   p       e ++vdL + P++++wp+DgGp+itl+lvit+dp t
  gi|13541239|ref|NP_110927.1|  89 IVKP--PrdsesfigkglemmrelsgLRPKVSNS--IPSGY---SELEKVDLYRYPICKTWPDDGGPFITLPLVITKDPST 162
                                   ***7..55789***************99*99865..55552...34579******************************** PP

                                   T-EEEEEEEEEEEETTEEEE--TTTHCHHHHHHHHHHCCT--EEEEEEES--HHHHHHCTS--TTT-TCHHHHHHHHTS-- CS
                          UbiD 144 gkrnlgiyRmqvldknklglhwqihkggaehlrkakkkggeplpvavaiGvdPaltlaAvaplPeglsElefaGalrgepv 224
                                   g rn+g+yRmqv+d +++g+hw+ihkgg e++ k k+kg ++++vav+iG dP+++++AvaplP g++E++f G+++ ++ 
  gi|13541239|ref|NP_110927.1| 163 GIRNMGMYRMQVYDSETTGMHWHIHKGGSENFLKEKEKG-KAMDVAVVIGSDPLTIFSAVAPLPNGIDEFMFRGLISRKRS 242
                                   ***************************************.8**************************************** PP

                                   EEEE-SSSSSEEETT-SEEEEEEEECCEEEECTTTC-TTSCEEC--CCEEEEEEEEEEE-TT-EEEE-SSSCCSHHHHCHH CS
                          UbiD 225 elvkcetvdlevpadAEivleGeidpgetapEGPfgdhtGyysevrdefpvfkVtaithRkdpiypttvvgkppeedallg 305
                                   elvk +tvdle p + EivleG+idp+et+ EGPfgdhtGyys + +efpvf+V++i+ R+d iyptt+vgk + ed++lg
  gi|13541239|ref|NP_110927.1| 243 ELVKGKTVDLEYPRNFEIVLEGYIDPSETRVEGPFGDHTGYYSLE-EEFPVFHVKNIIERNDRIYPTTIVGKLWHEDVVLG 322
                                   ******************************************766.66********************************* PP

                                   HHHHHHHHHHHHCCSTTEEEEEE-GGGTTTCEEEEECHHHTCCHHHHHHHHHHCCTTGGC-SEEEEEEETTS-TTSHHHHH CS
                          UbiD 306 kalealflpllkkqvpevkdvhlpeeggfhllavvsikkrypghakkvmealwalkqqlsltKlvivvDedvdvrdlkevl 386
                                   ka+e++flpl+++ +pev+d++++ee++fh++++vsikkrypghakkvm+alw+l+q l+++K+++vvD+d+++++ ke++
  gi|13541239|ref|NP_110927.1| 323 KAVERMFLPLIQMVLPEVVDINTMEEAVFHNMVIVSIKKRYPGHAKKVMFALWGLGQ-LMFSKIIVVVDDDINIHNRKELI 402
                                   *******************************************************88.*********************** PP

                                   HHHHHC--CCCCEEEECCC CS
                          UbiD 387 waiatrvdpdrDlviiegt 405
                                   wa++tr+dpdrD++ii+gt
  gi|13541239|ref|NP_110927.1| 403 WAMTTRIDPDRDVIIIPGT 421
                                   ****************997 PP

>> Galactosyl_T  Galactosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0      0.42   3.8e+03     172     192 ..     313     333 ..     309     336 .. 0.80
   2 !   15.9   0.2   9.9e-07    0.0088      39     113 ..     342     415 ..     315     430 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.42
                  Galactosyl_T 172 flkleDvlvGilaedlgvsrv 192
                                   +l+ eDv++G  +e++ ++ +
  gi|13541239|ref|NP_110927.1| 313 KLWHEDVVLGKAVERMFLPLI 333
                                   5789******99999877665 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 9.9e-07
                  Galactosyl_T  39 elvmeeaklygDivvvdledsYenltlKtltlllwavskvpeaklilkvDdDvyv.npdkLlsllkrelidpsess 113
                                   ++   e++ ++ +v v+++ +Y   + K ++  lw+  +   +k+i+ vDdD+ + n ++L+  +  + idp+ + 
  gi|13541239|ref|NP_110927.1| 342 DINTMEEAVFHNMVIVSIKKRYPGHAKKVMF-ALWGLGQLMFSKIIVVVDDDINIhNRKELIWAMTTR-IDPDRDV 415
                                   444556667*************998866655.5688888888***********983457788888877.7776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (481 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       370  (0.020637); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.48
# Mc/sec: 3020.93
//
Query:       gi|13541240|ref|NP_110928.1|  [L=454]
Description: cobyrinic acid a,c-diamide synthase [Thermoplasma volcanium GSS1]
Scores for complete 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-42  143.0   0.0    1.2e-41  142.5   0.0    1.2  1  GATase_3  CobB/CobQ-like glutamine amidotransferase domain
    2.9e-19   69.4   0.1    5.3e-19   68.5   0.1    1.5  1  CbiA      CobQ/CobB/MinD/ParA nucleotide binding domain
    1.8e-13   50.8   1.4    2.4e-06   27.5   0.0    2.4  2  AAA_26    AAA domain
    3.2e-05   23.3   0.1    5.8e-05   22.5   0.1    1.4  1  DUF1611   Domain of unknown function (DUF1611_C) P-loop domai
  ------ inclusion threshold ------
      0.044   13.7   0.7      0.091   12.7   0.7    1.5  1  NTPase_1  NTPase
      0.059   13.3   0.1       0.16   11.8   0.0    1.7  2  MobB      Molybdopterin guanine dinucleotide synthesis protei
      0.078   12.9   0.1       0.14   12.1   0.1    1.3  1  AAA_31    AAA domain
       0.18   11.1   0.1       0.29   10.4   0.1    1.3  1  MipZ      ATPase MipZ


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 !  142.5   0.0   5.2e-45   1.2e-41       1     194 [.     244     433 ..     244     435 .. 0.91

  Alignments for each domain:
  == domain 1  score: 142.5 bits;  conditional E-value: 5.2e-45
                      GATase_3   1 kiavirlpaisnyt..dldpLeaepevrvrfvplkdeslgedadlvilpGgkdtiqdlallresgldeaikeaaeaggpvl 79 
                                   kiav++++a+ +y+  ++++L++ +++ v+f+pl++e  +ed d ++++Gg++++++++l+ + + +e+i++++++g+p l
  gi|13541240|ref|NP_110928.1| 244 KIAVAYDSAFDFYYeeNFRVLRNLGAELVFFSPLNNEIPPEDTDGLYIGGGYPEVFAKKLAYAVDARENIAKLIKKGVPTL 324
                                   79*******************************8888888***************************************** PP

                      GATase_3  80 giCGGlqmLGeeiedpegvegeageveglglLdietefekekltgqvegevel........aaegeevkGyEiHsGrtilk 152
                                   ++CGG+++L ++i+ ++g+     e++g+g+++++t +++ kl+    g+ e          ++ge+ +G+E+H+++ + +
  gi|13541240|ref|NP_110928.1| 325 AECGGYMYLTRTIVGQDGI-----EYPGVGIVPAKTFLTD-KLI---LGYREIvsktsnmlLRHGETARGHEFHRSTIQFQ 396
                                   *******************.....****************.666...333333344688988889**************** PP

                      GATase_3 153 ekakpllkvkvggnng.ekdGavkksedgnvlGtYlHglfdnr 194
                                   +k+++ + +k+  +++ e+dG +++    nv+++Y+H++f+++
  gi|13541240|ref|NP_110928.1| 397 DKVDHPFVLKY--KDRfEEDGYYSN----NVVASYVHIHFLSN 433
                                   **999999943..33369*****88....***********975 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.5   0.1   2.4e-22   5.3e-19       1     126 [.       6     190 ..       6     193 .. 0.91

  Alignments for each domain:
  == domain 1  score: 68.5 bits;  conditional E-value: 2.4e-22
                                   EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH........................... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................... RF
                          CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep........................... 54 
                                   ++ia+t +GvGKTt++++ + al+++gl+V +++++p+                                           
  gi|13541240|ref|NP_110928.1|   6 VIIAGTNSGVGKTTTTLAVISALKNKGLKVKPYKVGPDYIDPQF---------Hsllagatsdnldlwmiprerifqllad 77 
                                   68************************************555553.........033333334467799************* PP

                                   ...........................................CCHCCCHHHHHHCHCHHHH....EEEEEEEEESS...- CS
                                   ...........................................xxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxx RF
                          CbiA  55 ...........................................dlkrllellealgkkkall..lkiagvvlnrvdgenee 90 
                                                                              d   l+++++a++k+++++   ++agv+++rv ge+++
  gi|13541240|ref|NP_110928.1|  78 astsfnisviegvmglldgfgstdegstldlaritgtpiilviDGYGLSGSAAAIVKGFKDFsgDLLAGVIVTRVSGERHY 158
                                   *******************************************99999********************************* PP

                                   TTCHHHHHHHHHHCTS-EEEEEE--CCHCCCCHHTS CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          CbiA  91 tllkealeelkqrygvpvlgviprdeavaeaparge 126
                                    l+k+a+e+     +v+vlg i ++++v ++++r++
  gi|13541240|ref|NP_110928.1| 159 DLIKKAIEDNT---NVRVLGYIEKNDEV-RLESRHL 190
                                   *********88...*************9.8888876 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   1.0   1.1e-07   0.00025       3      33 ..       6      36 ..       4      41 .. 0.92
   2 !   27.5   0.0   1.1e-09   2.4e-06      97     195 ..      80     184 ..      65     187 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 1.1e-07
                        AAA_26  3 ifvtgtdtgvGKTvvslgLvralkrkgvkvg 33
                                  ++++gt  gvGKT+++l++++alk+kg kv+
  gi|13541240|ref|NP_110928.1|  6 VIIAGTNSGVGKTTTTLAVISALKNKGLKVK 36
                                  79**************************997 PP

  == domain 2  score: 27.5 bits;  conditional E-value: 1.1e-09
                        AAA_26  97 kdadivvVEGagglgvp..iteellnadiaknlgapvilVargglgtinqllltiealrq.knvrvlGvilNkvrnpenve 174
                                      +i v+EG+ gl+++  +t+e ++ d+a+  g p+ilV+ g+      +++ ++ +++  +  ++Gvi+ +v  ++ ++
  gi|13541240|ref|NP_110928.1|  80 TSFNISVIEGVMGLLDGfgSTDEGSTLDLARITGTPIILVIDGYG-LSGSAAAIVKGFKDfSGDLLAGVIVTRVSGERHYD 159
                                   567899*********87558999******************9864.4455666666677647889************8777 PP

                        AAA_26 175 tlekksg....ipvlGvvPylpdle 195
                                    ++k+++    ++vlG ++ +++++
  gi|13541240|ref|NP_110928.1| 160 LIKKAIEdntnVRVLGYIEKNDEVR 184
                                   66666554544********998875 PP

>> DUF1611  Domain of unknown function (DUF1611_C) P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.1   2.6e-08   5.8e-05      11      47 ..       2      38 ..       1      45 [. 0.90

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 2.6e-08
                       DUF1611 11 kakrvlvvGTdcavGKrttaleleealeerGlkaafv 47
                                  k +rv++ GT + vGK tt+l++  al+++Glk++  
  gi|13541240|ref|NP_110928.1|  2 KVPRVIIAGTNSGVGKTTTTLAVISALKNKGLKVKPY 38
                                  679*****************************99865 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.7   4.1e-05     0.091       2      31 ..       6      36 ..       5      39 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.1e-05
                                  EEEE-.-TTSSHHHHHHHHHHHH...GGGEE CS
                      NTPase_1  2 vfiTG.ppGvGKtTlvkkvlellkssgvkvg 31
                                  v+i G ++GvGKtT    v+++lk++g+kv+
  gi|13541240|ref|NP_110928.1|  6 VIIAGtNSGVGKTTTTLAVISALKNKGLKVK 36
                                  67777358********************996 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 ?   11.8   0.0   7.3e-05      0.16       4      32 ..       8      37 ..       5      47 .. 0.84
   2 ?   -3.4   0.0       3.8   8.4e+03      55      79 ..     145     169 ..     143     183 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 7.3e-05
                          MobB  4 ivgk.sgsGKTtLleklipelkarglrvgt 32
                                  i+g+ sg GKTt    +i++lk++gl+v  
  gi|13541240|ref|NP_110928.1|  8 IAGTnSGVGKTTTTLAVISALKNKGLKVKP 37
                                  554439*********************975 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 3.8
                          MobB  55 AGAkevlvaskerlalikeleeael 79 
                                   AG   + v++++++ lik+  e+++
  gi|13541240|ref|NP_110928.1| 145 AGVIVTRVSGERHYDLIKKAIEDNT 169
                                   7788888899999999988744233 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   6.1e-05      0.14       9      33 ..      11      35 ..       5      61 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6.1e-05
                        AAA_31  9 qKGGvGKTTtsvnlaaalaklgkkv 33
                                     GvGKTTt++++ +al ++g kv
  gi|13541240|ref|NP_110928.1| 11 TNSGVGKTTTTLAVISALKNKGLKV 35
                                  446********************99 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   0.00013      0.29       3      33 ..       6      36 ..       4      42 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00013
                                  EEE--SSTTSSHHHHHHHHHHHHHTTT--EE CS
                          MipZ  3 ivlgnekGGsGksttavhvavaLlkkGarva 33
                                  ++++    G Gk+tt++ v+ aL +kG++v 
  gi|13541240|ref|NP_110928.1|  6 VIIAGTNSGVGKTTTTLAVISALKNKGLKVK 36
                                  67788889********************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (454 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       409  (0.0228122); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 2928.70
//
Query:       gi|13541241|ref|NP_110929.1|  [L=251]
Description: hypothetical protein TVN0410 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    9.7e-47  159.7   0.0    1.1e-46  159.5   0.0    1.0  1  PAC2        PAC2 family
  ------ inclusion threshold ------
      0.065   13.6   0.0       0.12   12.7   0.0    1.5  1  PP-binding  Phosphopantetheine attachment site


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 !  159.5   0.0   1.2e-50   1.1e-46       1     211 [.      19     233 ..      19     235 .. 0.92

  Alignments for each domain:
  == domain 1  score: 159.5 bits;  conditional E-value: 1.2e-50
                                   EEEESSCGGGHHHHHHHHHHHHTTEEEEEEEEHCCHSBCCCC.SEEEEETT..EEE-SEEEEEE.TTT.SEEEEEEE.... CS
                          PAC2   1 LilGfpgiGnVgqlavdlLiesleaekvgeidsdyllpfvgprpvvlveeg..relepprlyak.dsgsrdllvlqg.... 74 
                                   Li G+pgiGnVg++a+d+++e+l+++k+  i s+y lp     p+v+++++   +l  +++y+k   g++dllvl g    
  gi|13541241|ref|NP_110929.1|  19 LIGGLPGIGNVGKIAADYIVEKLNMVKIYDIFSEY-LP-----PQVFINDDseIHLVRNSIYYKkMRGKHDLLVLGGdfqg 93 
                                   799********************************.9*.....********55555555559998888*******999999 PP

                                   E-HSCHHHHHHHHHHHHHHHTTESEEEEEEEEEESS-ES..TTS-.EEEEEESSHHHHHHHHCT........-CEEEEHHH CS
                          PAC2  75 repilqyeefakalldwaeelgvkevvvLggldageradvphtrpekvtgaatdeelleelees........eyggivgit 147
                                    ++++qye ++ ++l++a++++v+ev++Lgg+  g+      +rp +v ga+td++l+ ele++        ++ggivg +
  gi|13541241|ref|NP_110929.1|  94 TTQEAQYE-LSYKMLELAKDMNVSEVYTLGGYSVGKIV----ERP-RVLGAVTDKKLIPELEKNgvifpkgePGGGIVGSA 168
                                   ********.************************88775....799.***************74446677788********* PP

                                   HHHHHHH.HHTT-EEEEEEEEEECCC--HHHHHHHHHHHHHHHT---HCHHHHHHHHHHHHHHHH CS
                          PAC2 148 glLlsaa.kergipavgllaevphylpdPkaaaalleflskllglevdtedLeedaeeleeqlee 211
                                   gl+l+++ +  +i++++l++e+++y+ dPk+a ++l++l+k +g+++d++d e +++++e+   +
  gi|13541241|ref|NP_110929.1| 169 GLILGLGmEIFKINGACLMGETSGYFADPKSAMEVLNVLQKQIGIKIDMSDIETRSKQIEQITGK 233
                                   *******9999*************************************************97666 PP

>> PP-binding  Phosphopantetheine attachment site
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   1.4e-05      0.12      29      62 ..     195     229 ..     191     234 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.4e-05
                    PP-binding  29 lDSllavellaaleeefgveiplsdlfe.hptlae 62 
                                    D  +a+e+l+ l+++ g++i++sd+ +  + +++
  gi|13541241|ref|NP_110929.1| 195 ADPKSAMEVLNVLQKQIGIKIDMSDIETrSKQIEQ 229
                                   57779*********************765666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       812  (0.0452898); expected 358.6 (0.02)
Passed bias filter:                      648  (0.0361426); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.31s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 1505.95
//
Query:       gi|13541242|ref|NP_110930.1|  [L=62]
Description: H/ACA RNA-protein complex component Nop10p [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.3e-21   74.2   1.5    8.5e-21   73.7   1.5    1.1  1  Nop10p         Nucleolar RNA-binding protein, Nop10p family
    7.6e-06   25.4   1.0    9.3e-06   25.1   1.0    1.2  1  RecR           RecR protein
     0.0012   16.8   0.1     0.0012   16.8   0.1    1.0  1  PolC_DP2       DNA polymerase II large subunit DP2
     0.0033   17.3   3.2     0.0075   16.1   3.2    1.6  1  DUF35_N        Rubredoxin-like zinc ribbon domain (DUF35_N)
  ------ inclusion threshold ------
      0.011   14.6   0.3      0.011   14.5   0.3    1.0  1  NRDD           Anaerobic ribonucleoside-triphosphate reductas
      0.034   13.6   1.3        1.3    8.6   0.2    2.2  2  zf-ribbon_3    zinc-ribbon domain
      0.049   13.7   0.4      0.058   13.4   0.4    1.1  1  HypA           Hydrogenase/urease nickel incorporation, metal
      0.052   13.6   0.5       0.27   11.3   0.5    1.9  1  Elf1           Transcription elongation factor Elf1 like
      0.063   13.0   3.4      0.063   13.0   0.2    2.2  2  zf-RRN7        Zinc-finger of RNA-polymerase I-specific TFIIB
      0.065   12.8   3.6       0.46   10.0   0.2    2.2  2  TF_Zn_Ribbon   TFIIB zinc-binding
        1.2    9.0   5.6        9.4    6.1   0.1    2.3  2  zinc_ribbon_2  zinc-ribbon domain


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 !   73.7   1.5   5.2e-24   8.5e-21       1      47 [.       1      47 [.       1      48 [. 0.98

  Alignments for each domain:
  == domain 1  score: 73.7 bits;  conditional E-value: 5.2e-24
                                  .----EE-TTT--EESSSB-TTT-SB-B-SS--S--TT-TTCHHHHH CS
                        Nop10p  1 mksylrkcgkcrvYTLkkvcpecggptksahPaRFSPdDkyskyRra 47
                                  mks +rkc+kc++YT++++cp cg++t  a P+RFSP D++ kyR++
  gi|13541242|ref|NP_110930.1|  1 MKSLIRKCRKCGRYTMEEICPVCGSQTYIAVPPRFSPVDRFKKYRME 47
                                  9********************************************85 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   1.0   5.7e-09   9.3e-06      13      36 ..       2      25 ..       1      27 [. 0.90

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 5.7e-09
                                  HHH-EE-TTT--EESSSS-CCCCS CS
                          RecR 13 kekvrhCsrCgnlteedlCaICsd 36
                                  k+ +r C++Cg +t e++C++C +
  gi|13541242|ref|NP_110930.1|  2 KSLIRKCRKCGRYTMEEICPVCGS 25
                                  6779******************76 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 !   16.8   0.1   7.6e-07    0.0012     618     642 ..       5      29 ..       1      55 [. 0.88

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 7.6e-07
                      PolC_DP2 618 rrkCkkCgketlearCeeCgektee 642
                                    rkC+kCg+ t+e  C+ Cg++t  
  gi|13541242|ref|NP_110930.1|   5 IRKCRKCGRYTMEEICPVCGSQTYI 29 
                                   589******************9976 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 !   16.1   3.2   4.6e-06    0.0075      11      35 ..       5      27 ..       4      28 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 4.6e-06
                       DUF35_N 11 gqrCpdCGtvqfPPravCphCgsdd 35
                                  +++C++CG++    + +Cp Cgs +
  gi|13541242|ref|NP_110930.1|  5 IRKCRKCGRYTM--EEICPVCGSQT 27
                                  78********98..9*******975 PP

>> NRDD  Anaerobic ribonucleoside-triphosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.3   6.9e-06     0.011     508     555 ..       6      49 ..       3      54 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 6.9e-06
                                   EEETT.--EESSSB-TTT--BE.EEEEEESSSSEEEHHHHHHHHHHHS CS
                          NRDD 508 dvCnecgykgeiekCpkCgseeevevirRitGYlrpvsswnkgkkaEl 555
                                     C++cg+    e Cp+Cgs+  + v  R    ++pv++++k + +El
  gi|13541242|ref|NP_110930.1|   6 RKCRKCGRYTMEEICPVCGSQTYIAVPPR----FSPVDRFKKYRMEEL 49 
                                   67******777777*****7665777777....567777777777776 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.1     0.018        30      17      23 ..       6      12 ..       2      13 .. 0.86
   2 ?    8.6   0.2   0.00077       1.3       2      11 ..      17      26 ..      16      27 .. 0.72

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.018
                   zf-ribbon_3 17 nvCpyCG 23
                                  ++C +CG
  gi|13541242|ref|NP_110930.1|  6 RKCRKCG 12
                                  5899999 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00077
                   zf-ribbon_3  2 tvrCPnCGap 11
                                  +  CP CG++
  gi|13541242|ref|NP_110930.1| 17 EEICPVCGSQ 26
                                  5679999975 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.4   3.5e-05     0.058      71      96 ..       6      27 ..       1      35 [. 0.75

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.5e-05
                                  EEETTTS-EEECHHHHHS-TTTSSS- CS
                          HypA 71 vrCreCgkefeleekalrCpkCgsad 96
                                   +Cr+Cg ++++e   + Cp Cgs+ 
  gi|13541242|ref|NP_110930.1|  6 RKCRKCG-RYTME---EICPVCGSQT 27
                                  58*****.55544...36*****986 PP

>> Elf1  Transcription elongation factor Elf1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.5   0.00016      0.27      47      72 ..      19      44 ..       2      49 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00016
                          Elf1 47 sCkvCgesfetkvnalsepvDvYskw 72
                                   C vCg+++ + v++  +pvD ++k+
  gi|13541242|ref|NP_110930.1| 19 ICPVCGSQTYIAVPPRFSPVDRFKKY 44
                                  59*******************99987 PP

>> zf-RRN7  Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.3      0.45   7.3e+02      24      28 ..       8      12 ..       8      13 .. 0.85
   2 ?   13.0   0.2   3.9e-05     0.063       2      15 ..      15      28 ..      14      29 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.45
                       zf-RRN7 24 CrrCh 28
                                  Cr C+
  gi|13541242|ref|NP_110930.1|  8 CRKCG 12
                                  99998 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 3.9e-05
                       zf-RRN7  2 ekgppCgvCgcrsf 15
                                  +++++C+vCg+ ++
  gi|13541242|ref|NP_110930.1| 15 TMEEICPVCGSQTY 28
                                  6799*******766 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.4     0.022        35       2      10 ..       7      15 ..       6      18 .. 0.74
   2 ?   10.0   0.2   0.00028      0.46       2      13 ..      19      31 ..      18      35 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.022
                                  EETTTTCEE CS
                  TF_Zn_Ribbon  2 kCPnCgstn 10
                                  kC +Cg ++
  gi|13541242|ref|NP_110930.1|  7 KCRKCGRYT 15
                                  899999865 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00028
                                  EETTTTC.EECHE CS
                  TF_Zn_Ribbon  2 kCPnCgs.tnlve 13
                                  +CP+Cgs t++ +
  gi|13541242|ref|NP_110930.1| 19 ICPVCGSqTYIAV 31
                                  6******554755 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   1.5     0.015        25       1       7 [.       7      13 ..       7      14 .. 0.83
   2 ?    6.1   0.1    0.0058       9.4      16      21 ..      20      25 ..      17      27 .. 0.65

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.015
                 zinc_ribbon_2  1 fCpnCGa 7 
                                  +C +CG+
  gi|13541242|ref|NP_110930.1|  7 KCRKCGR 13
                                  7999996 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0058
                 zinc_ribbon_2 16 CpyCGt 21
                                  Cp CG+
  gi|13541242|ref|NP_110930.1| 20 CPVCGS 25
                                  666664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (62 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       749  (0.0417759); expected 358.6 (0.02)
Passed bias filter:                      560  (0.0312343); expected 358.6 (0.02)
Passed Vit filter:                       100  (0.00557756); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 379.88
//
Query:       gi|13541243|ref|NP_110931.1|  [L=254]
Description: translation initiation factor IF-2 subunit alpha [Thermoplasma volcanium GSS1]
Scores for complete 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   63.2   0.0    2.3e-15   56.7   0.0    2.6  2  EIF_2_alpha  Eukaryotic translation initiation factor 2 alpha
    5.4e-09   36.3   0.7    5.4e-09   36.3   0.7    2.2  2  S1           S1 RNA binding domain
  ------ inclusion threshold ------
      0.035   14.1   0.6       0.11   12.6   0.1    2.0  2  TRAM         TRAM domain
       0.22   12.2   1.7        3.6    8.2   0.1    2.5  2  EXOSC1       Exosome component EXOSC1/CSL4
       0.46   10.7   5.3        1.3    9.2   0.4    2.5  2  FlaG         FlaG protein


Domain annotation for each model (and alignments):
>> EIF_2_alpha  Eukaryotic translation initiation factor 2 alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0     0.015        55      58      95 ..      35      76 ..      20      86 .. 0.74
   2 !   56.7   0.0   6.3e-19   2.3e-15       3     116 .]     121     224 ..     119     224 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.015
                                  EEEEEEEEE-STTHHHHHHHHHHHHST.S......TTSSSEE CS
                   EIF_2_alpha 58 iradieltcftkdGveaIkeaLkageeasne....eeveeee 95
                                  ++++i+++ ++   v++I++ L++g+++  +    +++ +++
  gi|13541243|ref|NP_110931.1| 35 VEGYIHISEVATGWVKHIRSYLREGQRVVCKvinvNQERKNV 76
                                  77889999999999*********9998655544333333333 PP

  == domain 2  score: 56.7 bits;  conditional E-value: 6.3e-19
                                   HCTHHHHTTTTS-HHHHH.HHHHSTTHHHHHTTS-TTTHHHHHHCTHHHHHHT-EEEEEEEEEEE-STTHHHHHHHHHHHH CS
                   EIF_2_alpha   3 eevgwklyekyghaydaF.klaitdeevldkleipeeveeaLveiikkklkpqkvkiradieltcftkdGveaIkeaLkag 82 
                                   +e+g  l e yg+++ aF  +a  + e l +  i+ ++++++ve +k+++++++v + +++e  + ++dGve+Ike+L+  
  gi|13541243|ref|NP_110931.1| 121 KEFGVRLVELYGTLFAAFeSAAAAEGEWLPD--INGDWKDTFVEVAKENITIPEVSVAGYFEAYSLASDGVEKIKEVLT-- 197
                                   789***************7777788888988..89********************************************.. PP

                                   ST.S..TTSSSEEEEEEEESSSSEEEEEEEES.. CS
                   EIF_2_alpha  83 eeasneeeveeeeevkikliapPeYvltvetldk 116
                                             e  + +++++++P+Y++ v+ +d+
  gi|13541243|ref|NP_110931.1| 198 -------IPPEIGKAELEYVGAPRYRIVVRDKDY 224
                                   .......233457899*************99886 PP

>> S1  S1 RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.3   0.7   1.5e-12   5.4e-09       2      75 .]       7      81 ..       6      81 .. 0.96
   2 ?   -0.7   0.6      0.54   1.9e+03      43      60 ..     217     234 ..     177     250 .. 0.62

  Alignments for each domain:
  == domain 1  score: 36.3 bits;  conditional E-value: 1.5e-12
                                  STTTCEEEEEEEEEETTEEEEEET..TTEEEEEEGGGSSSSCEESCHHHCEETTEEEEEEEEEEETTTTEEEEEEC CS
                            S1  2 pekgevveGeVtsvtkgGafVelg..ngvegfvpaselsrdarvedpdevlkvGdevkvkvlkvdkdrrriilsik 75
                                  pe+g+ v  ++t+v ++Ga   l+   gveg++++se++    v+++   l++G++v  kv++v+ +r++++ls+k
  gi|13541243|ref|NP_110931.1|  7 PEVGDLVVVKITEVKNFGANGILEeyPGVEGYIHISEVATG-WVKHIRSYLREGQRVVCKVINVNQERKNVDLSLK 81
                                  899**************9998888889*************9.9*******************************86 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.54
                                   ESCHHHCEETTEEEEEEE CS
                            S1  43 vedpdevlkvGdevkvkv 60 
                                   + ++d+ +k+ +e  +k+
  gi|13541243|ref|NP_110931.1| 217 IVVRDKDYKKAEETLKKI 234
                                   444555555444433333 PP

>> TRAM  TRAM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1     3e-05      0.11      38      59 ..       6      27 ..       2      29 .. 0.85
   2 ?   -1.8   0.1       0.9   3.2e+03      42      53 ..      59      70 ..      56      72 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3e-05
                                  -T..TEEEEEEEEEE-SSEEEE CS
                          TRAM 38 lpgIGdfVeVkItkvkrqyLrG 59
                                  lp++Gd V VkIt+vk++ + G
  gi|13541243|ref|NP_110931.1|  6 LPEVGDLVVVKITEVKNFGANG 27
                                  7999************987766 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.9
                                  TEEEEEEEEEE- CS
                          TRAM 42 GdfVeVkItkvk 53
                                  G++V +k+  v+
  gi|13541243|ref|NP_110931.1| 59 GQRVVCKVINVN 70
                                  999999999876 PP

>> EXOSC1  Exosome component EXOSC1/CSL4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.1     0.001       3.6       1      21 [.       6      26 ..       6      56 .. 0.74
   2 ?    2.5   0.3     0.061   2.2e+02      18      49 ..      60      90 ..      55     129 .. 0.50

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.001
                                  -S-TT-EEEEEEEEEESSEEE CS
                        EXOSC1  1 lPkegdvVLarvtrlrkkqal 21
                                  lP++gd+V +++t++++  a+
  gi|13541243|ref|NP_110931.1|  6 LPEVGDLVVVKITEVKNFGAN 26
                                  8**************997775 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.061
                                  SEEEEEEEEECTBSBCCCEEECCCTTSS--ST CS
                        EXOSC1 18 kqalveilsvegennvlsdsgvgangegavke 49
                                  +++++++  v++e +   d+ +  +++ + +e
  gi|13541243|ref|NP_110931.1| 60 QRVVCKVINVNQE-RKNVDLSLKRVNQHQSRE 90
                                  4555555555333.444444444444333333 PP

>> FlaG  FlaG protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.5     0.028     1e+02      13      51 ..      83     122 ..      59     126 .. 0.61
   2 ?    9.2   0.4   0.00036       1.3      25      56 ..     222     253 ..     217     254 .] 0.87

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.028
                                   HHHS-----SS-------HHH.HHHHHHHHHHHHTTSS-- CS
                          FlaG  13 qkseeekaekaeeekevseee.leeaveklnkklsslnte 51 
                                    ++ +++++ ae ++e+++++  e + +klnk+l++ ++e
  gi|13541243|ref|NP_110931.1|  83 VNQHQSREKIAEWKNEQKADKlFEIVCSKLNKDLEACKKE 122
                                   2333333333333333334442555889999999877654 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00036
                                   ------HHHHHHHHHHHHHHHTTSS--EEEEE CS
                          FlaG  25 eekevseeeleeaveklnkklsslnteleFsv 56 
                                   ++ ++ ee+l+++v+++ +k+++l+ eleFs 
  gi|13541243|ref|NP_110931.1| 222 KDYKKAEETLKKIVQSVTDKAKKLQVELEFSR 253
                                   566777888*********************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1697  (0.0946511); expected 358.6 (0.02)
Passed bias filter:                      858  (0.0478554); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.63u 0.30s 00:00:00.93 Elapsed: 00:00:00.48
# Mc/sec: 1580.54
//
Query:       gi|13541244|ref|NP_110932.1|  [L=65]
Description: 30S ribosomal protein S27e [Thermoplasma volcanium GSS1]
Scores for complete sequence (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   66.2   2.0    1.7e-18   66.0   2.0    1.1  1  Ribosomal_S27e   Ribosomal protein S27
     0.0042   17.1   0.4       0.15   12.1   0.0    2.1  2  zf-BED           BED zinc finger
      0.005   16.2   2.3       0.49    9.9   0.2    2.3  2  zf-ribbon_3      zinc-ribbon domain
     0.0085   16.2   0.4      0.014   15.5   0.4    1.3  1  Zn-ribbon_8      Zinc ribbon domain
  ------ inclusion threshold ------
      0.023   14.7   1.8      0.075   13.1   1.9    1.7  2  zinc_ribbon_6    Zinc-ribbon
      0.027   14.4   2.4       0.37   10.7   0.3    2.1  2  zinc_ribbon_4    zinc-ribbon domain
      0.041   13.8   0.2      0.051   13.5   0.2    1.3  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
      0.084   12.8   0.6       0.88    9.5   0.1    2.1  2  zf-trcl          Probable zinc-ribbon domain
      0.094   13.1   0.9       0.54   10.7   0.9    1.9  1  Lar_restr_allev  Restriction alleviation protein Lar
      0.095   13.2   1.8        2.4    8.8   0.1    2.4  2  zf-C2H2          Zinc finger, C2H2 type
       0.22   11.4   4.1       0.75    9.7   0.3    2.1  2  ZZ               Zinc finger, ZZ type
       0.28   10.9   4.3        2.3    8.0   0.6    2.2  2  DNA_RNApol_7kD   DNA directed RNA polymerase, 7 kDa subunit
        1.1    8.9   8.3        2.8    7.6   1.5    2.3  2  Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
        2.7    7.9   6.2        1.4    8.8   1.8    2.1  2  zf-CCHC_6        Zinc knuckle


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 !   66.0   2.0   1.4e-21   1.7e-18       3      52 ..      14      63 ..      12      65 .] 0.91

  Alignments for each domain:
  == domain 1  score: 66.0 bits;  conditional E-value: 1.4e-21
                                  --EEEEE-TTTS-EEEEESS-SS-EEESSSTCEEEEECSSSEEESSCEEE CS
                Ribosomal_S27e  3 skFldvkCpdCenetvvFshaatvvkCisCgkvLvePtGGkaklkaqile 52
                                  ++Fl++kC+dC+n +vvF ++++vv+C +Cg ++++PtGG +  + +++e
  gi|13541244|ref|NP_110932.1| 14 GHFLKIKCKDCGNVQVVFARPSSVVTCNICGATIAKPTGGVLETSGEVIE 63
                                  68**************************************8887777766 PP

>> zf-BED  BED zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.1     0.055        70      16      25 ..      18      27 ..       9      29 .. 0.85
   2 !   12.1   0.0   0.00012      0.15      15      28 ..      36      49 ..      31      59 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.055
                                  --EETTTTEE CS
                        zf-BED 16 kavCryCgki 25
                                  k++C+ Cg++
  gi|13541244|ref|NP_110932.1| 18 KIKCKDCGNV 27
                                  899****986 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00012
                                  S--EETTTTEE--- CS
                        zf-BED 15 qkavCryCgkilsr 28
                                   +++C++Cg++++ 
  gi|13541244|ref|NP_110932.1| 36 SVVTCNICGATIAK 49
                                  689********986 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.4   0.2    0.0049       6.3      17      25 ..      19      27 ..      16      28 .. 0.83
   2 !    9.9   0.2   0.00038      0.49       3      14 ..      38      50 ..      36      51 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0049
                   zf-ribbon_3 17 nvCpyCGtk 25
                                  ++C+ CG +
  gi|13541244|ref|NP_110932.1| 19 IKCKDCGNV 27
                                  68****987 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00038
                   zf-ribbon_3  3 vrCPnCGa.plss 14
                                  v+C+ CGa ++++
  gi|13541244|ref|NP_110932.1| 38 VTCNICGAtIAKP 50
                                  89******88776 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.4   1.1e-05     0.014       7      37 ..      20      48 ..      18      49 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.1e-05
                   Zn-ribbon_8  7 rCeeCghefevlqsisdaplta.CPeCgsevr 37
                                  +C++Cg++  v+++ s    ++ C  Cg++  
  gi|13541244|ref|NP_110932.1| 20 KCKDCGNVQVVFARPS---SVVtCNICGATIA 48
                                  8*****8888888655...5566*****9765 PP

>> zinc_ribbon_6  Zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   1.9   5.8e-05     0.075      20      54 ..       9      44 ..       3      45 .. 0.79
   2 ?    1.8   0.1      0.19   2.4e+02      28      38 ..      36      46 ..      30      50 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.8e-05
                 zinc_ribbon_6 20 peeyknkkvkilCnDCekksevkfhvl.glkCkeCg 54
                                  p++++ +  ki C+DC++ + v  +    + C+ Cg
  gi|13541244|ref|NP_110932.1|  9 PKNVSGHFLKIKCKDCGNVQVVFARPSsVVTCNICG 44
                                  7888999999******99998877765146788886 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.19
                 zinc_ribbon_6 28 vkilCnDCekk 38
                                    ++Cn C+++
  gi|13541244|ref|NP_110932.1| 36 SVVTCNICGAT 46
                                  57899999876 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.3   0.00029      0.37      17      34 ..      10      27 ..       7      28 .. 0.83
   2 ?    3.7   0.1     0.048        61      25      35 ..      37      47 ..      33      48 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00029
                 zinc_ribbon_4 17 eklpakgvkvrCskCghv 34
                                  + ++++  k++C+ Cg+v
  gi|13541244|ref|NP_110932.1| 10 KNVSGHFLKIKCKDCGNV 27
                                  56888889********97 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.048
                 zinc_ribbon_4 25 kvrCskCghvF 35
                                   v+C  Cg+++
  gi|13541244|ref|NP_110932.1| 37 VVTCNICGATI 47
                                  58888888775 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   0.2     4e-05     0.051       7      39 ..      16      48 ..       3      59 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4e-05
                OrfB_Zn_ribbon  7 qleykakeyGikveevnpayTSktCseCgsknk 39
                                  +l+ k+k+ G   ++  +  +  tC+ Cg++  
  gi|13541244|ref|NP_110932.1| 16 FLKIKCKDCGNVQVVFARPSSVVTCNICGATIA 48
                                  556666666544444444445556666665554 PP

>> zf-trcl  Probable zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.1   0.00069      0.88       4      16 ..      18      30 ..      17      34 .. 0.78
   2 ?    1.9   0.1      0.16   2.1e+02       4      13 ..      37      46 ..      35      48 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00069
                       zf-trcl  4 tltCkdCgaefvF 16
                                  +++CkdCg+ +v 
  gi|13541244|ref|NP_110932.1| 18 KIKCKDCGNVQVV 30
                                  589*****97764 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.16
                       zf-trcl  4 tltCkdCgae 13
                                  ++tC+ Cga+
  gi|13541244|ref|NP_110932.1| 37 VVTCNICGAT 46
                                  579****985 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.9   0.00042      0.54       6      37 ..      21      50 ..       2      64 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00042
               Lar_restr_allev  6 CPfCggravlersqrvvaeigqcvyCadCga....s 37
                                  C  Cg+ +v++ +++       +v+C  Cga     
  gi|13541244|ref|NP_110932.1| 21 CKDCGNVQVVFARPSS------VVTCNICGAtiakP 50
                                  7778888888888766......58998899944332 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.1    0.0019       2.4       2      15 ..      20      36 ..      19      39 .. 0.88
   2 ?    4.1   0.1     0.057        73       2       9 ..      39      46 ..      38      51 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0019
                                  EETTTT...EEESSHHH CS
                       zf-C2H2  2 kCpdCg...ksFkrksn 15
                                  kC+dCg    +F r+s+
  gi|13541244|ref|NP_110932.1| 20 KCKDCGnvqVVFARPSS 36
                                  8*****99999999997 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.057
                                  EETTTTEE CS
                       zf-C2H2  2 kCpdCgks 9 
                                  +C++Cg +
  gi|13541244|ref|NP_110932.1| 39 TCNICGAT 46
                                  7****955 PP

>> ZZ  Zinc finger, ZZ type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.3     0.035        45       5      19 ..      19      33 ..      17      38 .. 0.74
   2 ?    9.7   0.3   0.00059      0.75       3      13 ..      36      46 ..      34      50 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.035
                                  EE-TTT-S..EESSE CS
                            ZZ  5 ytCdgCseapligvR 19
                                   +C  C++  ++ +R
  gi|13541244|ref|NP_110932.1| 19 IKCKDCGNVQVVFAR 33
                                  7999**996666555 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00059
                                  S-EE-TTT-S. CS
                            ZZ  3 kkytCdgCsea 13
                                   ++tC++C+++
  gi|13541244|ref|NP_110932.1| 36 SVVTCNICGAT 46
                                  689******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 ?    8.0   0.6    0.0018       2.3      18      24 ..      19      25 ..      17      31 .. 0.88
   2 ?    4.8   0.1     0.018        23      13      26 ..      33      46 ..      26      48 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0018
                                  ---SSS- CS
                DNA_RNApol_7kD 18 iRCkeCG 24
                                  i+Ck+CG
  gi|13541244|ref|NP_110932.1| 19 IKCKDCG 25
                                  9*****9 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.018
                                  -SSS----SSS--- CS
                DNA_RNApol_7kD 13 kkgdpiRCkeCGhR 26
                                  +++ ++ C  CG  
  gi|13541244|ref|NP_110932.1| 33 RPSSVVTCNICGAT 46
                                  578899******75 PP

>> Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   1.5    0.0022       2.8       8      18 ..      20      30 ..      15      33 .. 0.84
   2 ?    5.7   0.7    0.0089        11       6      14 ..      37      45 ..      32      56 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0022
                                  E-TTT--EEEE CS
               Desulfoferrod_N  8 kCevCGniVeV 18
                                  kC+ CGn+ +V
  gi|13541244|ref|NP_110932.1| 20 KCKDCGNVQVV 30
                                  9******8666 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0089
                                  EEE-TTT-- CS
               Desulfoferrod_N  6 vYkCevCGn 14
                                  v  C++CG 
  gi|13541244|ref|NP_110932.1| 37 VVTCNICGA 45
                                  667*****6 PP

>> zf-CCHC_6  Zinc knuckle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   1.8    0.0011       1.4       1       8 [.      18      25 ..      18      27 .. 0.90
   2 ?    1.3   0.2      0.24   3.1e+02       2       9 ..      38      45 ..      37      46 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0011
                     zf-CCHC_6  1 rvKCknCG 8 
                                  ++KCk+CG
  gi|13541244|ref|NP_110932.1| 18 KIKCKDCG 25
                                  79*****9 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.24
                     zf-CCHC_6  2 vKCknCGA 9 
                                  v C  CGA
  gi|13541244|ref|NP_110932.1| 38 VTCNICGA 45
                                  6799***9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       546  (0.0304535); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.47
# Mc/sec: 419.49
//
Query:       gi|13541245|ref|NP_110933.1|  [L=93]
Description: 50S ribosomal protein L44e [Thermoplasma volcanium GSS1]
Scores for complete sequence (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   2.4    1.7e-30  105.3   2.4    1.2  1  Ribosomal_L44  Ribosomal protein L44
    0.00046   20.6   2.6      0.014   15.9   1.5    2.4  2  Ribosomal_L33  Ribosomal protein L33
     0.0028   17.4   0.9     0.0064   16.2   0.5    1.7  2  zf-U1          U1 zinc finger
  ------ inclusion threshold ------
      0.024   14.8   0.6      0.052   13.8   0.6    1.5  1  DUF4451        Domain of unknown function (DUF4451)
      0.097   12.7   2.3        1.2    9.1   0.5    2.2  2  Zn_Tnp_IS1595  Transposase zinc-ribbon domain
      0.098   12.9   2.3       0.36   11.1   0.4    2.0  2  zf-LITAF-like  LITAF-like zinc ribbon domain
       0.14   12.6   4.1        6.4    7.4   1.7    2.4  2  zf-H2C2_2      Zinc-finger double domain


Domain annotation for each model (and alignments):
>> Ribosomal_L44  Ribosomal protein L44
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.3   2.4   6.5e-34   1.7e-30       1      76 []      16      91 ..      16      91 .. 0.99

  Alignments for each domain:
  == domain 1  score: 105.3 bits;  conditional E-value: 6.5e-34
                                  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+f++++K+tK+i lrl C eC+k+++ +++Rakkfe+v
  gi|13541245|ref|NP_110933.1| 16 KHTTHSVERVRKRKASELKAGQRRFRRVTSGYGGFPRPRFEGREKPTKRIALRLVCDECHKAITPPGIRAKKFEIV 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 !   15.9   1.5   5.3e-06     0.014      33      43 ..      10      20 ..       4      23 .. 0.90
   2 ?    3.6   0.0     0.037        95       3      12 ..      67      76 ..      65      88 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 5.3e-06
                                  EETTTTEEEEE CS
                 Ribosomal_L33 33 Ycprcrkhtlh 43
                                  Ycp+c+kht+h
  gi|13541245|ref|NP_110933.1| 10 YCPYCKKHTTH 20
                                  **********9 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.037
                                  EEEEET.... CS
                 Ribosomal_L33  3 vtLeCtecks 12
                                   +L+C ec++
  gi|13541245|ref|NP_110933.1| 67 LRLVCDECHK 76
                                  58******97 PP

>> zf-U1  U1 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.5   2.5e-06    0.0064       5      22 ..      10      27 ..       3      30 .. 0.85
   2 ?   -1.6   0.0      0.91   2.3e+03       6      13 ..      71      78 ..      68      86 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.5e-06
                                  EETTTTEEESS-SHHHHH CS
                         zf-U1  5 yCdYCdiyLthDspsvRk 22
                                  yC YC++  th+  +vRk
  gi|13541245|ref|NP_110933.1| 10 YCPYCKKHTTHSVERVRK 27
                                  *****************9 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.91
                                  ETTTTEEE CS
                         zf-U1  6 CdYCdiyL 13
                                  Cd C++ +
  gi|13541245|ref|NP_110933.1| 71 CDECHKAI 78
                                  89898755 PP

>> DUF4451  Domain of unknown function (DUF4451)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.6     2e-05     0.052      21      96 ..       6      79 ..       2      91 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2e-05
                       DUF4451 21 kkeglCpiCeeev.ekkekflklknssyekhlsfeHGvlsngslvpePillrskkrrkakekekegivCpkCneiie 96
                                  k +  Cp+C++++ ++ e+  k k s+ +   +    v s    +p P +     r+k +++ +  +vC +C++ i+
  gi|13541245|ref|NP_110933.1|  6 KIVTYCPYCKKHTtHSVERVRKRKASELKAGQRRFRRVTSGYGGFPRPRFE---GREKPTKRIALRLVCDECHKAIT 79
                                  66789*****888666888999999*99999999999**99999****876...777778888899*******9886 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 ?    9.1   0.5   0.00048       1.2      21      37 ..      11      27 ..       4      42 .. 0.78
   2 ?    3.4   0.1      0.03        76      19      37 ..      69      87 ..      61      89 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00048
                 Zn_Tnp_IS1595 21 CPhCgsrkayriktrgl 37
                                  CP+C++ + +++++ ++
  gi|13541245|ref|NP_110933.1| 11 CPYCKKHTTHSVERVRK 27
                                  *****999999999443 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.03
                 Zn_Tnp_IS1595 19 fvCPhCgsr.kayriktrgl 37
                                   vC  C+++ ++  i++ ++
  gi|13541245|ref|NP_110933.1| 69 LVCDECHKAiTPPGIRA-KK 87
                                  68888988877777776.55 PP

>> zf-LITAF-like  LITAF-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.4   0.00014      0.36       5      24 ..       8      27 ..       4      34 .. 0.81
   2 ?    1.6   0.1      0.13   3.5e+02       6      15 ..      69      78 ..      66      81 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00014
                 zf-LITAF-like  5 qvdCpaCqqrvvTsveyksg 24
                                   ++Cp+C+++++ sve+  +
  gi|13541245|ref|NP_110933.1|  8 VTYCPYCKKHTTHSVERVRK 27
                                  679*******9999999876 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.13
                 zf-LITAF-like  6 vdCpaCqqrv 15
                                  + C  C++ +
  gi|13541245|ref|NP_110933.1| 69 LVCDECHKAI 78
                                  5677777765 PP

>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   1.7    0.0025       6.4      16      26 .]      10      20 ..       2      20 .. 0.75
   2 ?    5.4   0.0     0.011        27      15      23 ..      69      77 ..      57      79 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0025
                     zf-H2C2_2 16 eCplCdkaFkt 26
                                   Cp+C+k +++
  gi|13541245|ref|NP_110933.1| 10 YCPYCKKHTTH 20
                                  8******9987 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.011
                     zf-H2C2_2 15 yeCplCdka 23
                                  + C++C+ka
  gi|13541245|ref|NP_110933.1| 69 LVCDECHKA 77
                                  68*****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       792  (0.0441742); expected 358.6 (0.02)
Passed bias filter:                      552  (0.0307881); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 611.75
//
Query:       gi|13541246|ref|NP_110934.1|  [L=95]
Description: hypothetical protein TVN0415 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.9e-23   80.6   0.8    9.9e-23   80.3   0.8    1.1  1  DUF1805   Domain of unknown function (DUF1805)


Domain annotation for each model (and alignments):
>> DUF1805  Domain of unknown function (DUF1805)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.3   0.8   5.5e-27   9.9e-23       1      63 []      37      95 .]      37      95 .] 0.99

  Alignments for each domain:
  == domain 1  score: 80.3 bits;  conditional E-value: 5.5e-27
                                  E-TT--HHHHHHTT--EEE-....-S--SHHHHHHSB-SEE-HHHHHTT--TT-BHHHHGGGG CS
                       DUF1805  1 mCGaLdvealeklgdlaarvivagsGVrtledllaapvesvteaAeelGikeGmtgkeaLekl 63
                                  mCG+L+++a+eklgd+a+r+    +G++tl+d+l++++++vt+aA++lGik+G  +k++L+kl
  gi|13541246|ref|NP_110934.1| 37 MCGYLNLDAAEKLGDTAVRI----TGIKTLDDMLNGKIVEVTSAASALGIKKGDVLKDVLSKL 95
                                  9*******************....************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       328  (0.0182944); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.48
# Mc/sec: 599.71
//
Query:       gi|13541247|ref|NP_110935.1|  [L=121]
Description: hypothetical protein TVN0416 [Thermoplasma volcanium GSS1]
Scores for complete 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   77.5   1.8    7.3e-22   77.0   1.8    1.3  1  DUF3198   Protein of unknown function (DUF3198)
  ------ inclusion threshold ------
      0.027   14.1   0.1      0.029   14.0   0.1    1.1  1  DUF4131   Domain of unknown function (DUF4131)
       0.04   13.8   0.2      0.051   13.5   0.2    1.1  1  Wzy_C_2   Virulence factor membrane-bound polymerase, C-termi
       0.17   12.0   2.6       0.22   11.6   2.6    1.2  1  DHHC      DHHC palmitoyltransferase


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 !   77.0   1.8   1.6e-25   7.3e-22       1      50 []      72     121 .]      72     121 .] 0.98

  Alignments for each domain:
  == domain 1  score: 77.0 bits;  conditional E-value: 1.6e-25
                                   -HHHHHHHHHHS--HHHHHHHHHHHHHHHHHH-SHHHHHHHHHHHHH--- CS
                       DUF3198   1 kdrrkFeelInSdSKstFvknlkeLekiarklGssYqqrLeeakekWkvk 50 
                                   +d+ +Fe+lInS SKs+Fv+nl eLe++a+klG+ Y  +Le+akekWkvk
  gi|13541247|ref|NP_110935.1|  72 RDTSRFESLINSSSKSVFVRNLDELERLAKKLGKGYLIQLENAKEKWKVK 121
                                   6999*********************************************8 PP

>> DUF4131  Domain of unknown function (DUF4131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   6.5e-06     0.029      13      72 ..      17      91 ..       7     119 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 6.5e-06
                       DUF4131 13 llllllllllllrr................rprrrvllllllllllallgfalrapqpnandlsqlles.gqevive 72
                                  +++ +++l+++  +                   + +++++  +++++++g+  +a  + ++++++l++s +++v+v+
  gi|13541247|ref|NP_110935.1| 17 FVISMAVLVIV--SnqlifhnsflndaqfnVGDWVYWIFAVSFIAAIMFGYSMWANLRDTSRFESLINSsSKSVFVR 91
                                  22222222222..2235555568999888866677788888888888888888888888888888888878888875 PP

>> Wzy_C_2  Virulence factor membrane-bound polymerase, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.2   1.1e-05     0.051      22      93 ..      13      92 ..      11     103 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.1e-05
                       Wzy_C_2 22 Yspfllaaflvlgllds.........ksrsrrlrlrpklvlrvvalvlallglalllsilhdyqrleqlyltsepneaalr 93
                                  Y +++++ + vl+++++         ++ + + +  ++ ++++v++++a++  + +  +l+d++r+e l+ +s++   +++
  gi|13541247|ref|NP_110935.1| 13 YAALFVISMAVLVIVSNqlifhnsflNDAQFNVGD-WVYWIFAVSFIAAIMFGYSMWANLRDTSRFESLINSSSKSVFVRN 92
                                  67777777888877777799987766666666663.8889999999999999999999***********999988766555 PP

>> DHHC  DHHC palmitoyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   2.6   4.8e-05      0.22      51     120 ..       8      73 ..       2      86 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4.8e-05
                          DHHC  51 Fllfllylllllilalvlllialvklveeekkseflavtllkkllsilllvlsllfllllgllllfhlyl 120
                                   F +f++y +l++i ++vl +++ + +++++  ++++        +++ ++++s+++++++g+ +  +l  
  gi|13541247|ref|NP_110935.1|   8 F-QFIIYAALFVISMAVLVIVSNQLIFHNSFLNDAQFNVGD---WVYWIFAVSFIAAIMFGYSMWANLRD 73 
                                   5.899999999999999999999999999988888855544...78999999999999999998876655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1203  (0.067098); expected 358.6 (0.02)
Passed bias filter:                      583  (0.0325172); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.31s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 767.26
//
Query:       gi|13541248|ref|NP_110936.1|  [L=273]
Description: spermidine synthase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.7e-49  166.7   0.0      5e-49  166.3   0.0    1.2  1  Spermine_synth   Spermine/spermidine synthase domain
    4.8e-15   55.2   0.1    1.1e-14   54.0   0.1    1.7  1  Spermine_synt_N  Spermidine synthase tetramerisation domain
  ------ inclusion threshold ------
      0.019   14.8   0.0      0.035   14.0   0.0    1.4  1  Methyltransf_30  S-adenosyl-L-methionine-dependent methyltran


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 !  166.3   0.0   8.4e-53     5e-49       2     185 ..      62     243 ..      61     246 .. 0.96

  Alignments for each domain:
  == domain 1  score: 166.3 bits;  conditional E-value: 8.4e-53
                                   HHHHHHHHHHHHCCSS.ST-EEEEESSTTSHHHHHHTTSTT-SEEEEEES-HHHHHHHHHHSHHHHTTCGGCTTEEEEEST CS
                Spermine_synth   2 faykemiahvplmlhk.npkevLiiGGgDGgvlrevvkhntvekitlvdiDqkvidfskkflpslaisafndarvklvlgd 81 
                                    +y+e+i+ +p +  k  p+  L+iGGgDGg++r+++ +  ++ki+ v+iD +v+++sk+f+p+l+   f d+rv+l+++d
  gi|13541248|ref|NP_110936.1|  62 YIYHELITMIPYHMTKnPPQSALVIGGGDGGAARRLLDLG-LNKIVNVEIDGQVVEVSKRFFPDLSSA-FTDKRVNLIIDD 140
                                   68*********9777725799*******************.*************************99.************ PP

                                   CHHHHCTCSS-EEEEEEECCSTTCSSCGCSSHHHHHHHHHTEEEEEEEEEEEEETTTCHHHHHHHHHHHHTTSSCEEEEEE CS
                Spermine_synth  82 gfkflkayekkfdvvivdsldpvgpaenlFskeffdllkkvlkedGviilqaekpelekelvinvdksgkqvfalqvepsa 162
                                   g+k+++++++kfd vi ds+dp+gpae lFs ef+  + k+l ++Gvi++q+ +p+++ + ++ + + ++ +f+ +v++++
  gi|13541248|ref|NP_110936.1| 141 GIKYVRKCNEKFDLVIIDSTDPEGPAEGLFSMEFYSDITKILSDGGVIVSQSGSPFYQPKALKLAYTGMRRLFK-DVKVYT 220
                                   ************************************************************************99.****** PP

                                   EETTTSCSCEEEEEEEESSTT.. CS
                Spermine_synth 163 vlvPtylsgminfvveskknlvt 185
                                     +Pty+sg+++f+++s+++ + 
  gi|13541248|ref|NP_110936.1| 221 GFIPTYPSGFWSFTIASEDAMNP 243
                                   *****************996555 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 !   54.0   0.1   1.9e-18   1.1e-14       2      53 .]       7      58 ..       6      58 .. 0.99

  Alignments for each domain:
  == domain 1  score: 54.0 bits;  conditional E-value: 1.9e-18
                                  EEEEEEETTEEEEEEEEEEEEEEEESSSEEEEEEETTTEEEEEETTEEEEET CS
               Spermine_synt_N  2 WfteisdpglalelkVekvLyeekSeyQdieifesktfGkvLvLDgvvqltE 53
                                  Wf+e+++++l l+++V++ L+  k++yQ i +f++++fGk L++Dg+vqltE
  gi|13541248|ref|NP_110936.1|  7 WFSERYSDNLQLSFRVSDQLLSIKTDYQRIDLFDTYDFGKLLAIDGTVQLTE 58
                                  ***************************************************9 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 ?   14.0   0.0   5.9e-06     0.035      28      94 ..     129     196 ..     112     210 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.9e-06
                                   TTTEEEEEEES-HHHHHHHC-T-EEEEEE-SS-TTTSGG.GCSHHHHHHHHHHEEEEEEEEES---HH CS
               Methyltransf_30  28 aeevtlklligdarealkeldekadawFlDgFsPaknPe.lwseellkelarllkkkgtlatyssAga 94 
                                     + +++l+i d  + + +++ek+d +  D   P+   e l+s e+++ + ++l+++g++++ s + +
  gi|13541248|ref|NP_110936.1| 129 FTDKRVNLIIDDGIKYVRKCNEKFDLVIIDSTDPEGPAEgLFSMEFYSDITKILSDGGVIVSQSGSPF 196
                                   45678999**************************987666********************99876655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       302  (0.0168442); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 2030.56
//
Query:       gi|13541249|ref|NP_110937.1|  [L=310]
Description: deoxyhypusine synthase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   1.6e-105  352.5   0.0   1.8e-105  352.4   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 !  352.4   0.0  9.8e-110  1.8e-105       2     286 ..      25     307 ..      24     309 .. 0.98

  Alignments for each domain:
  == domain 1  score: 352.4 bits;  conditional E-value: 9.8e-110
                            DS   2 llesyeki.gfqatslgeaidilnkmrkdekctiflgltsnlissGlreiiadlvkeklvdvivtTaggieeDlikalgkk 81 
                                   l++++++i gf+a++l+ea +i+++m   e+ t+fl++ + +is+Glr++i d+vk+klvdvi+tT g++++D+++++gk 
  gi|13541249|ref|NP_110937.1|  25 LMAQFSNIgGFTAAKLYEAHSIISDMF-LEDNTTFLSFPADIISTGLRGLINDVVKRKLVDVIITTSGTLDHDIARTFGK- 103
                                   899*****9*****************6.5677***********************************************9. PP

                            DS  82 tylgdfelddeeLrekginRignllvpneny.ckfedwvreildkleeeqkvwspselikelGkeindeeSilywAykndi 161
                                   +y+g+f+++d eLre +inR+gn+lvp+e+y + +e+ v+e l+kl + +k+w++ +like+G  in+e+Sily A+kndi
  gi|13541249|ref|NP_110937.1| 104 YYCGSFNYSDVELREININRLGNVLVPDESYgELIEEKVMEQLEKLYSIKKEWATVDLIKEIGLSINNESSILYNAAKNDI 184
                                   *******************************999*********************************************** PP

                            DS 162 pvfcpaltDgslGdqlllfhsvkekkklkldivkDirelndialkakktgaiilGGGvpKhhilnanlmrngadyavyitt 242
                                   p+f+p++tDgs+G ql+ f+  ++++++k+++++D ++l+di+++akktgai++GGG++Khh++++n++r+g+dyavyitt
  gi|13541249|ref|NP_110937.1| 185 PIFVPGITDGSFGSQLWSFY--EQHHDFKINLLEDEHRLSDIIFDAKKTGAIMVGGGISKHHTIWWNQFRDGLDYAVYITT 263
                                   ********************..69999****************************************************** PP

                            DS 243 aqefdGslsgatldEavSwgkikaeaksvkvyaDaTivlPLlva 286
                                   aqe+dGslsga+l+Ea+Sw k++++a+ v++y+DaT+++P+l+a
  gi|13541249|ref|NP_110937.1| 264 AQEYDGSLSGAKLEEAISWKKVRPNARFVNIYGDATVIMPILMA 307
                                   ******************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       492  (0.0274416); 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: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 1989.46
//
Query:       gi|13541250|ref|NP_110938.1|  [L=152]
Description: peroxiredoxin [Thermoplasma volcanium GSS1]
Scores for complete 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-46  155.6   0.1    6.1e-46  155.4   0.1    1.1  1  AhpC-TSA       AhpC/TSA family
    5.7e-30  104.0   0.2    6.4e-30  103.8   0.2    1.0  1  Redoxin        Redoxin
    5.2e-07   29.6   0.0    6.9e-07   29.2   0.0    1.3  1  SCO1-SenC      SCO1/SenC
      2e-05   24.8   0.0    3.3e-05   24.1   0.0    1.3  1  Thioredoxin_8  Thioredoxin-like
    0.00012   22.1   0.1    0.00077   19.6   0.0    1.9  2  AhpC-TSA_2     AhpC/TSA antioxidant enzyme


Domain annotation for each model (and alignments):
>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  155.4   0.1   1.7e-49   6.1e-46       1     123 [.       6     126 ..       6     127 .. 0.98

  Alignments for each domain:
  == domain 1  score: 155.4 bits;  conditional E-value: 1.7e-49
                                   TTSB----EEESTTCEEEECHHHTTSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCHHHHHHHHH-H CS
                      AhpC-TSA   1 vgdkapdfelknadgetvslsdykgkpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvdspeshkkfiekes 81 
                                   vgd+apdfe  ++ g +v+lsd+kg+pvvl+fypkd++p+Ctte+++++++++ fke+g++vigvsvdspeshk+f+ek++
  gi|13541250|ref|NP_110938.1|   6 VGDQAPDFETVDQSGSKVRLSDFKGQPVVLYFYPKDNTPGCTTEACNFRDNFNSFKEAGIKVIGVSVDSPESHKRFAEKYQ 86 
                                   8******************************************************************************** PP

                                   .SSEEEE-TTSHHHHHTT-EETTTTECSCEEEEE-TTSBEEE CS
                      AhpC-TSA  82 lnfpllsDeegkvakaygvlkeekglalratfvidkegkiry 123
                                   lnf+l+sD+e++++k+ygvl     +a r t++id++gki+y
  gi|13541250|ref|NP_110938.1|  87 LNFTLASDKEKEICKKYGVLGL--ATAKRVTYIIDRDGKIVY 126
                                   ********************55..69**************99 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.8   0.2   1.8e-33   6.4e-30       1     141 [.       5     139 ..       5     145 .. 0.91

  Alignments for each domain:
  == domain 1  score: 103.8 bits;  conditional E-value: 1.8e-33
                                   -TTSBB---ECCEETTCEEEEEHHHHTTSEEEEEEESTTT-HHHHHTHH.HHHTHHHHHHCSTTTEEEEEESSSHHHHHHH CS
                       Redoxin   1 kagdkaPdftlplaatdgnsvslsefkgkkvvvnfvpgafcPtCsaehp.yleklaellkekgvdvvavvadndafvkefw 80 
                                   k+gd+aPdf++  +++ g++v ls+fkg++vv++f+p   +P C++e++ + ++++ + ke g++v++v++d+ +  k+f+
  gi|13541250|ref|NP_110938.1|   5 KVGDQAPDFET--VDQSGSKVRLSDFKGQPVVLYFYPKDNTPGCTTEACnFRDNFNSF-KEAGIKVIGVSVDSPESHKRFA 82 
                                   69********7..66**********************************99999*999.********************** PP

                                   HHTT-TSEEEE-TTSHHHHHTT-TTEEE.GGGEEE-EEEEEEETTEEEEEEESSSCHT.STT CS
                       Redoxin  81 gkeglkfpvlsDgsaaftkalGlrleedaseglrtpryavidedgkvvylevepepet.ees 141
                                   +k++l+f+++sD ++++ k++G+   +      + + + +id+dgk+vy++  + p++  ++
  gi|13541250|ref|NP_110938.1|  83 EKYQLNFTLASDKEKEICKKYGVLGLA-----TAKRVTYIIDRDGKIVYVYPKVTPKDhAVE 139
                                   **********************77433.....2778899************99999655444 PP

>> SCO1-SenC  SCO1/SenC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   0.0   1.9e-10   6.9e-07       2      98 ..      11     101 ..      10     130 .. 0.88

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 1.9e-10
                     SCO1-SenC   2 gpFelvdqdgeavteedlegkpslvffgFthCpdvCpttlanmaevldalgeeaekvqplfiTvDPerDtpevlkeyleaf 82 
                                    +Fe vdq+g +v+ +d++g+p++++f     +  C+t+  n ++  + ++e+   ++++ ++v    D+pe  k+++e++
  gi|13541250|ref|NP_110938.1|  11 PDFETVDQSGSKVRLSDFKGQPVVLYFYPKDNTPGCTTEACNFRDNFNSFKEA--GIKVIGVSV----DSPESHKRFAEKY 85 
                                   58*************************9999999*******************..677788888....589********** PP

                     SCO1-SenC  83 dpriigltGskeeiak 98 
                                   + +++  +++++ei k
  gi|13541250|ref|NP_110938.1|  86 QLNFTLASDKEKEICK 101
                                   ****999999988754 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.0   9.3e-09   3.3e-05       2      95 .]      31     124 ..      30     124 .. 0.78

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 9.3e-09
                                   SEEEEEE--S.SSHHHHHHHHHHHHHHHHHHHTTSEEEEEEE-SS-HHHHHHHGGGS-TTSEE.EE-TT-HHHHTT-S--T CS
                 Thioredoxin_8   2 kvvlLyfgas.wcppckaftpklkelyeklkkkkkveivyvsldkkeeefekylkknkkpwlsvpfddkkrnklkkkynvk 81 
                                   + v+Lyf+ + + p c++   +  + ++++k + +++++ vs+d+   e +k +++     l+++  ++k ++++kky+v 
  gi|13541250|ref|NP_110938.1|  31 QPVVLYFYPKdNTPGCTTEACNFRDNFNSFK-EAGIKVIGVSVDSP--ESHKRFAEK--YQLNFTLASDKEKEICKKYGVL 106
                                   678888886526677*******999999999.7************6..555555555..5999999*************99 PP

                                   T-SE....EEEE-TT-BE CS
                 Thioredoxin_8  82 aiPt....lvvldkngev 95 
                                   ++ t    ++++d++g++
  gi|13541250|ref|NP_110938.1| 107 GLATakrvTYIIDRDGKI 124
                                   854422225778877775 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 !   19.6   0.0   2.1e-07   0.00077       4      52 ..      55     104 ..      52     112 .. 0.90
   2 ?    0.2   0.0      0.22   8.1e+02      96     109 ..     115     128 ..     110     131 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 2.1e-07
                    AhpC-TSA_2   4 rdkpeldaagvklvaigigdp.sakkFvkltgfpfelyvDpsaklyqalg 52 
                                   +  +++++ag+k++++++++p s k+F++  + +f l  D+++++ ++ g
  gi|13541250|ref|NP_110938.1|  55 DNFNSFKEAGIKVIGVSVDSPeSHKRFAEKYQLNFTLASDKEKEICKKYG 104
                                   557899***************77********************9988877 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.22
                    AhpC-TSA_2  96 tflfdkqgelvyeh 109
                                   t+++d++g++vy +
  gi|13541250|ref|NP_110938.1| 115 TYIIDRDGKIVYVY 128
                                   799*********76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       597  (0.033298); expected 358.6 (0.02)
Passed bias filter:                      527  (0.0293937); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1032.44
//
Query:       gi|13541251|ref|NP_110939.1|  [L=104]
Description: 50S ribosomal protein L12P [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-20   74.1  13.1    1.3e-20   73.7  13.1    1.2  1  Ribosomal_60s  60s Acidic ribosomal protein
  ------ inclusion threshold ------
       0.01   15.8   3.9      0.013   15.4   3.9    1.2  1  Sigma70_ner    Sigma-70, non-essential region
      0.029   14.7   1.1      0.048   14.0   0.0    1.7  2  EF-hand_14     EF-hand domain
      0.034   14.3   3.2      0.041   14.0   3.2    1.1  1  YceD           Large ribosomal RNA subunit accumulation prote
       0.04   14.0   1.6      0.051   13.7   1.6    1.3  1  tRNA_bind      Putative tRNA binding domain
       0.14   12.7   5.1       0.17   12.4   5.1    1.2  1  DUF3391        Domain of unknown function (DUF3391)
       0.37   10.5   3.4       0.43   10.3   3.3    1.2  1  EIIBC-GUT_N    Sorbitol phosphotransferase enzyme II N-termin
       0.77    9.9   9.5        0.2   11.8   6.5    1.5  2  DUF3408        Protein of unknown function (DUF3408)
        0.9    9.6   6.1        6.9    6.7   0.1    2.3  2  PepSY_2        Peptidase propeptide and YPEB domain
       0.97    9.7   5.8        3.4    8.0   5.8    2.0  1  PhetRS_B1      Phe-tRNA synthetase beta subunit B1 domain
        1.4    7.3   4.8        1.7    7.0   4.8    1.1  1  TMEM214        TMEM214, C-terminal, caspase 4 activator
        2.6    6.4   4.6        2.8    6.3   4.6    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 !   73.7  13.1   8.8e-24   1.3e-20       1      88 []      16     103 ..      10     103 .. 0.91

  Alignments for each domain:
  == domain 1  score: 73.7 bits;  conditional E-value: 8.8e-24
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..XX-- CS
                 Ribosomal_60s   1 eptaenikkvlkaagveveaarvkllvkalegkdieellangaaklaaaaaaaaaaaaaaaaaaaaeekkkeeeee.Eeed 80 
                                   e+++e++kkvl+++gv+v++ar+k+lv+ l++++i+e+l+n++ +  ++aaa+aa ++++++++++eekkkee +e Eee+
  gi|13541251|ref|NP_110939.1|  16 EVDEEKLKKVLEDVGVQVDEARLKTLVSGLKDVNIDEVLKNATVA--PVAAAPAAPQEKKEEPKKKEEKKKEENKEqEEEE 94 
                                   6899**************************************988..9999999999999999999999999988867777 PP

                                   SS--.STTT CS
                 Ribosomal_60s  81 ddmG.fgLF 88 
                                    + G  +LF
  gi|13541251|ref|NP_110939.1|  95 AMSGlSALF 103
                                   788988898 PP

>> Sigma70_ner  Sigma-70, non-essential region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   3.9   8.5e-06     0.013      15      65 ..      31      96 ..      14     101 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 8.5e-06
                   Sigma70_ner 15 veageirLrdiidGflD......................eeeeeeeeeeeedeeeeeeeedddeeeseseaad 65
                                  v+ +e rL+ +++G+ D                      +       e++e+ +++ee+++++++e+e+e+a+
  gi|13541251|ref|NP_110939.1| 31 VQVDEARLKTLVSGLKDvnidevlknatvapvaaapaapQ-------EKKEEPKKKEEKKKEENKEQEEEEAM 96
                                  6789*********************999999865543331.......22222222222222222333444444 PP

>> EF-hand_14  EF-hand domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   3.2e-05     0.048      14      51 ..      14      51 ..       3      63 .. 0.84
   2 ?   -1.5   0.8       2.2   3.3e+03      48      55 ..      83      88 ..      69      98 .. 0.46

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.2e-05
                    EF-hand_14 14 tdklsvakllkaLaetGirkdDpRLkellkklkkveke 51
                                   +++  +kl k+L+++G++ d  RLk l++ lk+v+ +
  gi|13541251|ref|NP_110939.1| 14 GKEVDEEKLKKVLEDVGVQVDEARLKTLVSGLKDVNID 51
                                  4678889*************************998765 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.2
                    EF-hand_14 48 vekeksea 55
                                   ++e  ++
  gi|13541251|ref|NP_110939.1| 83 KKEE--NK 88
                                  1111..12 PP

>> YceD  Large ribosomal RNA subunit accumulation protein YceD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   3.2   2.8e-05     0.041      38     110 ..      16      96 ..       6     103 .. 0.64

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.8e-05
                          YceD  38 eaedeedee.........deedeeeilaeedeiDlselireelllalPlkplckpdckgeklcsqcganlneeecdceeek 109
                                   e ++e++++         de    +++ + ++++++e+++ + +  +   p   p+ k+e++ ++++++++e+++++eee 
  gi|13541251|ref|NP_110939.1|  16 EVDEEKLKKvledvgvqvDEARLKTLVSGLKDVNIDEVLKNATVAPVAAAPAA-PQEKKEEPKKKEEKKKEENKEQEEEEA 95 
                                   33344343355557777455555555668999***********9999999999.777776677777776666664444443 PP

                          YceD 110 e 110
                                   +
  gi|13541251|ref|NP_110939.1|  96 M 96 
                                   3 PP

>> tRNA_bind  Putative tRNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   1.6   3.4e-05     0.051      16      60 ..      23      68 ..      15      96 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.4e-05
                                  ST.EEEEEEEESSSSEEEEEESCTTTSTHHHHTTEEEEEETTSESE CS
                     tRNA_bind 16 dk.LlvlkvdvGeeeprqivsgaknvyepeelvakkvvvvanlkpk 60
                                  +k L  + v+v e++ ++ vsg+k+v+ +e+l +  v+ va   ++
  gi|13541251|ref|NP_110939.1| 23 KKvLEDVGVQVDEARLKTLVSGLKDVNIDEVLKNATVAPVAAAPAA 68
                                  44488899********************************987665 PP

>> DUF3391  Domain of unknown function (DUF3391)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   5.1   0.00011      0.17      46     100 ..      43      94 ..      15     101 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00011
                       DUF3391  46 sgiqeVwidtdksdeeelagldvpaaeaaeeakaaeesaeleeekqerperleae 100
                                   sg++ V id   ++++     +v+aa+aa+++k++e+++++e++k+e++e++e+e
  gi|13541251|ref|NP_110939.1|  43 SGLKDVNIDEVLKNATV---APVAAAPAAPQEKKEEPKKKEEKKKEENKEQEEEE 94 
                                   45777777766633333...44555555555555566666666666666655554 PP

>> EIIBC-GUT_N  Sorbitol phosphotransferase enzyme II N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   3.3   0.00029      0.43     105     161 ..      40      96 ..      29     104 .] 0.52

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00029
                   EIIBC-GUT_N 105 iyvSgvkeeqieladeeeeeeeeeeeekeeaeekekkketkkkiteqeekekkkgli 161
                                   + vSg k  +i  + ++++ +  +++ ++ +e+ke+ k++++k++e+++++++++ +
  gi|13541251|ref|NP_110939.1|  40 TLVSGLKDVNIDEVLKNATVAPVAAAPAAPQEKKEEPKKKEEKKKEENKEQEEEEAM 96 
                                   568999999998774444444333333333333333333333333333333333333 PP

>> DUF3408  Protein of unknown function (DUF3408)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       2.8   4.2e+03       2      11 ..      17      26 ..      16      31 .. 0.66
   2 ?   11.8   6.5   0.00013       0.2       1      59 [.      32      92 ..      32     100 .. 0.52

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 2.8
                       DUF3408  2 vdEellkeli 11
                                  vdEe+lk++ 
  gi|13541251|ref|NP_110939.1| 17 VDEEKLKKVL 26
                                  7788877765 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00013
                       DUF3408  1 evdEellkeli..vkkiplksk.........peeeetpakeekeeakeeeeeeaeeeeekekkekkkris 59
                                  +vdE+ lk l+   k++ +++          +         ++ +a++e++ee++++eek+k+e k++++
  gi|13541251|ref|NP_110939.1| 32 QVDEARLKTLVsgLKDVNIDEVlknatvapvA---------AAPAAPQEKKEEPKKKEEKKKEENKEQEE 92
                                  69999999999887777777774444444442.........44444444444443333333333332222 PP

>> PepSY_2  Peptidase propeptide and YPEB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.1    0.0047       6.9      28      51 ..      15      38 ..      11      41 .. 0.88
   2 ?    4.7   2.0     0.021        31       6      40 ..      58      92 ..      53     102 .. 0.54

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0047
                       PepSY_2 28 dwlpreklvakleaqGykvkkiev 51
                                  +++++ekl++ le+ G +v+++++
  gi|13541251|ref|NP_110939.1| 15 KEVDEEKLKKVLEDVGVQVDEARL 38
                                  7789****************9876 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.021
                       PepSY_2  6 lalallaaaAlAgrrdtdspkadwlpreklvakle 40
                                  +++ ++aa+A  ++++++ +k+++ ++e+ +++ e
  gi|13541251|ref|NP_110939.1| 58 TVAPVAAAPAAPQEKKEEPKKKEEKKKEENKEQEE 92
                                  44455555555545554444555555555555444 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 ?    8.0   5.8    0.0023       3.4       9      41 ..       7      39 ..       3      99 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0023
                     PhetRS_B1  9 eaLfkalgkelteeeledllfefGlElDeivee 41
                                  + L++a gke++ee+l+++l + G+ +De+  +
  gi|13541251|ref|NP_110939.1|  7 ALLLHAAGKEVDEEKLKKVLEDVGVQVDEARLK 39
                                  6789999**********************8765 PP

>> TMEM214  TMEM214, C-terminal, caspase 4 activator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   4.8    0.0011       1.7      27      98 ..      23      94 ..      10     102 .. 0.58

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0011
                       TMEM214 27 kkiae.napkledllplkqvktlyeldfekenkkqnkeqvpekstseaeekkksnkkkkkkksekkkeepkek 98
                                  kk+ e  + ++ ++     v+ l +++++++ k+ + + v ++  ++++ekk++ kkk++kk e++ke+++e+
  gi|13541251|ref|NP_110939.1| 23 KKVLEdVGVQVDEARLKTLVSGLKDVNIDEVLKNATVAPVAAA-PAAPQEKKEEPKKKEEKKKEENKEQEEEE 94
                                  3333303344444444455666777899999999999988777.55666666666666655555555444443 PP

>> Cytomega_UL84  Cytomegalovirus UL84 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   4.6    0.0019       2.8     143     173 ..      63      93 ..      39     100 .. 0.66

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0019
                 Cytomega_UL84 143 qtapatsqeeetaashepekkkekeekkeee 173
                                    +apa+ qe++    ++ ekkke ++ +eee
  gi|13541251|ref|NP_110939.1|  63 AAAPAAPQEKKEEPKKKEEKKKEENKEQEEE 93 
                                   4577777777665555555555443333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2882  (0.160745); expected 358.6 (0.02)
Passed bias filter:                     1367  (0.0762452); expected 358.6 (0.02)
Passed Vit filter:                       189  (0.0105416); 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 0.32s 00:00:00.86 Elapsed: 00:00:00.46
# Mc/sec: 682.62
//
Query:       gi|13541252|ref|NP_110940.1|  [L=314]
Description: acidic ribosomal protein P0 [Thermoplasma volcanium GSS1]
Scores for 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   5.4    1.9e-20   72.8   5.4    1.7  1  Ribosomal_L10  Ribosomal protein L10
    2.5e-18   65.9   0.2    6.4e-18   64.5   0.2    1.8  1  RL10P_insert   Insertion domain in 60S ribosomal protein L10P
  ------ inclusion threshold ------
      0.071   13.1   0.1       0.22   11.5   0.1    1.8  1  Feld-I_B       Allergen Fel d I-B chain


Domain annotation for each model (and alignments):
>> Ribosomal_L10  Ribosomal protein L10
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.8   5.4   3.2e-24   1.9e-20       3      97 ..       5     100 ..       3     101 .. 0.94

  Alignments for each domain:
  == domain 1  score: 72.8 bits;  conditional E-value: 3.2e-24
                                   CCCHCCCCCCCCCCCTTSSEEEEEE-TTS-HHHHHHCCCHHHHHGCEEEEESCCCCCCCCHCCTSS.S...SCGCCSSSEE CS
                 Ribosomal_L10   3 kekKeelvkelkellkkyksvvvvdyegltvaqlqelRkklrengaelkvvKntlmrrAleetgeeek...lkellkgpva 80 
                                   + kK+e+v+el + + k+k+v++vd++g+++ q+q++R+k r++ +++kvvK+tl+ +Al+  ++e k   lk+  +g++a
  gi|13541252|ref|NP_110940.1|   5 NPKKKEIVSELAQDITKSKAVAIVDIKGVRTRQMQDIRAKNRDK-VKIKVVKKTLLFKALDSINDE-KltkLKDATTGQIA 83 
                                   679****************************************9.*****************9998.4457********** PP

                                   EEEESS-TCHHHHCCCC CS
                 Ribosomal_L10  81 lvftnedpvalakvlee 97 
                                   ++ ++ dp ++++++++
  gi|13541252|ref|NP_110940.1|  84 VLTSQLDPTEIYQMVQA 100
                                   ***********999875 PP

>> RL10P_insert  Insertion domain in 60S ribosomal protein L10P
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.5   0.2   1.1e-21   6.4e-18       2      71 .]     108     177 ..     107     177 .. 0.99

  Alignments for each domain:
  == domain 1  score: 64.5 bits;  conditional E-value: 1.1e-21
                  RL10P_insert   2 raGtiAtedviipagplelaPgsiepeLrklglptklkkGkivleedylvckkGetltseqaqlLklLgi 71 
                                   r G++A+ d++++++ ++  Pg++ +e++k+gl+t ++kGki ++++ +++kkGe++ +++a++  +L+i
  gi|13541252|ref|NP_110940.1| 108 RGGEVAPADITVEPMVTGFPPGPMMTEFQKVGLQTGVEKGKIAIKKEAVLVKKGEVIPKDKAKIMAMLDI 177
                                   88******************************************************************98 PP

>> Feld-I_B  Allergen Fel d I-B chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   3.7e-05      0.22       7      35 ..     262     290 ..     260     295 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.7e-05
                                   HHHHHHTT-HHHHHHHHHHTT--HHHHHH CS
                      Feld-I_B   7 vygavlsgsrllLnaeLslvnaTeeEkeA 35 
                                    ++a+++++ ++Ln+eL++ n Te+E e 
  gi|13541252|ref|NP_110940.1| 262 EFLAIANRNAIILNNELNKGNTTEKESEK 290
                                   699***********************875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1123  (0.062636); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); 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: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 1922.76
//
Query:       gi|13541253|ref|NP_110941.1|  [L=217]
Description: 50S ribosomal protein L1P [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      5e-43  147.2   1.2      6e-43  147.0   1.2    1.0  1  Ribosomal_L1     Ribosomal protein L1p/L10e family
      0.009   15.2   0.0      0.015   14.5   0.0    1.3  1  DUF4317          Domain of unknown function (DUF4317)
  ------ inclusion threshold ------
        0.1   12.7   0.1       0.36   10.9   0.0    1.9  3  Sigma54_activ_2  Sigma-54 interaction domain


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 !  147.0   1.2     1e-46     6e-43       6     203 ..      19     206 ..      10     207 .. 0.93

  Alignments for each domain:
  == domain 1  score: 147.0 bits;  conditional E-value: 1e-46
                                   -SSS--EEEEEEEESSS-TTSGGG--EEEEE-STSTSSCS-EEEEE-HHHHH...HHHHTT..-SEEETCHHHHHHT-HHH CS
                  Ribosomal_L1   6 kkkfdesveialnlttkkpkkadqrkpgkipLphplgkevkiclitkdpqaeyakeakeagriakviglkklkkkyksfea 86 
                                   ++kf+esveia+nl+++++  +++r++++i Lp++ gk+vk++++  ++ ++     k++g  + + g +++ k  ++++a
  gi|13541253|ref|NP_110941.1|  19 QRKFEESVEIAINLKDIDMTNPKNRINEEILLPNGRGKDVKVVIFGSEELKA-----KAKGVADYIFGPEDISKFAEDKKA 94 
                                   88********************************************999766.....556655888899999999999*** PP

                                   HHHTCCH-SEEEEEGGGHHHHHHHCHHHHGGGT-S-ECC..CT.BTS-HHHHHHHHCTTEEEEE-TTTSEEEEEEEETTSS CS
                  Ribosomal_L1  87 krkllkefdlfladdrimpllpklLGkvfgkrkkmPipvltkgtvkedvkkevekalkstvvvrldkgtclsvkvGklsft 167
                                    +k+ ++  +f+a+  +m  ++k LG+v+g+r+kmP p+       +d    ++ +++ tv+ r++++ +l+v+vG+ s++
  gi|13541253|ref|NP_110941.1|  95 FKKIVNDAYFFIAEATLMANIGKSLGQVLGPRGKMPRPI-PP---GQDPVPLIKALKN-TVKARSRNSLTLHVPVGTRSMD 170
                                   ***************************************.33...4689999998888.********************** PP

                                   HHHHHHHHHHHHHHHHHTSTTTSGSEEEEEEEETTS CS
                  Ribosomal_L1 168 aeelaeNieavvkalvekvpkkwkniksiylkttms 203
                                   ++++ eNi+a+++ ++ k++++ +nik++y+kttm+
  gi|13541253|ref|NP_110941.1| 171 TQKISENIMAILNRITGKLERGHSNIKNVYVKTTMG 206
                                   ***********************************9 PP

>> DUF4317  Domain of unknown function (DUF4317)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   2.5e-06     0.015     197     267 ..      53     123 ..      50     135 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.5e-06
                       DUF4317 197 drstDinsvlYytkkakepheefieevLgceakltaeeqketFqeivkevlgeelekevvkeiqeelnemi 267
                                    r +D++ v++ +++ k   + + + ++g e     +e+k++F++iv+++     e +++++i ++l +++
  gi|13541253|ref|NP_110941.1|  53 GRGKDVKVVIFGSEELKAKAKGVADYIFGPEDISKFAEDKKAFKKIVNDAYFFIAEATLMANIGKSLGQVL 123
                                   6899***********************************************************99998875 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0     6e-05      0.36      55     116 ..      12      73 ..       2      77 .. 0.89
   2 ?   -2.5   0.0      0.85   5.1e+03       6      26 ..     142     162 ..     141     171 .. 0.80
   3 ?   -3.4   0.0       1.6   9.5e+03       7      31 ..     182     206 ..     179     209 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 6e-05
                                   THHHH-HHHHHHHTTTSEEEEEE-TT--HHHHHHHHHHHHHHTTTT-EEEEEEEE-TTT..- CS
               Sigma54_activ_2  55 erlaklpldlleqakggtLylkdiadlskaeqkeLlellakaeksslrlVstsskdleqlle 116
                                   +   ++p++ +e++ +  + lkdi+  ++++  +   ll+++ ++++++V  +s++l+++++
  gi|13541253|ref|NP_110941.1|  12 AVKQSSPQRKFEESVEIAINLKDIDMTNPKNRINEEILLPNGRGKDVKVVIFGSEELKAKAK 73 
                                   4455799***************************************************9876 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.85
                                   HHHHHHHHHHHHHT-SS-EEE CS
               Sigma54_activ_2   6 aiqelkerLeqaaqsklpvfl 26 
                                   +i++lk+++++ ++++l +++
  gi|13541253|ref|NP_110941.1| 142 LIKALKNTVKARSRNSLTLHV 162
                                   578889999888888888876 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 1.6
                                   HHHHHHHHHHHHT-SS-EEEEEETT CS
               Sigma54_activ_2   7 iqelkerLeqaaqsklpvfltGekG 31 
                                    ++++ +Le   ++  +v+++   G
  gi|13541253|ref|NP_110941.1| 182 LNRITGKLERGHSNIKNVYVKTTMG 206
                                   5678888888888888888877666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       503  (0.0280551); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1466.06
//
Query:       gi|13541254|ref|NP_110942.1|  [L=158]
Description: 50S ribosomal protein L11P [Thermoplasma volcanium GSS1]
Scores for complete 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-24   83.0   2.0    1.7e-23   82.2   2.0    1.5  1  Ribosomal_L11_N  Ribosomal protein L11, N-terminal domain
    3.8e-19   69.0   1.8    3.8e-19   69.0   1.8    1.6  2  Ribosomal_L11    Ribosomal protein L11, RNA binding domain
  ------ inclusion threshold ------
      0.029   14.6   0.2         13    6.1   0.0    2.5  2  Poly_export      Polysaccharide biosynthesis/export protein


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 !   82.2   2.0   2.8e-27   1.7e-23       5      59 ..       2      56 ..       1      64 [. 0.93

  Alignments for each domain:
  == domain 1  score: 82.2 bits;  conditional E-value: 2.8e-27
               Ribosomal_L11_N  5 vkvvklrvpaGkAtpaPplGpaLGplGlnikkfckefnkaTkdkkglripVkitv 59
                                  ++ vk++v++GkAt +Pp+GpaLGplGln+++++ke+n++Tk+++g+++pV++tv
  gi|13541254|ref|NP_110942.1|  2 AQSVKTMVEGGKATTGPPIGPALGPLGLNVAQVVKEINEKTKEFQGMQVPVTVTV 56
                                  5789**************************************************9 PP

>> Ribosomal_L11  Ribosomal protein L11, RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       2.8   1.7e+04      56      59 ..      35      38 ..      29      48 .. 0.49
   2 !   69.0   1.8   6.3e-23   3.8e-19       2      70 .]      70     137 ..      69     137 .. 0.97

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 2.8
                                  HHHH CS
                 Ribosomal_L11 56 vksi 59
                                  vk+i
  gi|13541254|ref|NP_110942.1| 35 VKEI 38
                                  3332 PP

  == domain 2  score: 69.0 bits;  conditional E-value: 6.3e-23
                                   --SHHHHHHHHHTXSSXXSSTTTSXXEEEEHHHHHHHHHHHGGGHTXS.SHHHHHHHHHHHHCTTTEEE CS
                 Ribosomal_L11   2 tPptsylLkkaagiekgsgkpgketvGtvslkqvyeIAkiKksdlnaalsleaavksilgtArsmGikV 70 
                                   +Ppts+lLkk++g+ekg++k+++ ++G+ +l+q++++A  K++++ a+ +l++av ++lgt+  mGi+V
  gi|13541254|ref|NP_110942.1|  70 VPPTSALLKKELGLEKGASKKKEAVAGNATLEQIKNVAIKKMPSMLAK-DLKSAVLEVLGTCVAMGINV 137
                                   6********************99999****************999988.******************98 PP

>> Poly_export  Polysaccharide biosynthesis/export protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0    0.0022        13      54      81 ..      28      54 ..      21      56 .. 0.89
   2 ?    6.0   0.0    0.0023        14      50      66 ..     135     151 ..     129     156 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0022
                   Poly_export 54 GltveelreeieeklskylkdpqvtVrv 81
                                  Gl v+++ +ei ek ++ ++  qv V+v
  gi|13541254|ref|NP_110942.1| 28 GLNVAQVVKEINEKTKE-FQGMQVPVTV 54
                                  99*************98.5999998887 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0023
                   Poly_export  50 ikvaGltveelreeiee 66 
                                   i+v+G+ ++e++++i++
  gi|13541254|ref|NP_110942.1| 135 INVEGKDPKEVQKLIKS 151
                                   99*************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       828  (0.0461822); expected 358.6 (0.02)
Passed bias filter:                      545  (0.0303977); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 1202.13
//
Query:       gi|13541255|ref|NP_110943.1|  [L=186]
Description: intracellular protease [Thermoplasma volcanium GSS1]
Scores for complete 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  156.7   0.0    5.3e-46  156.4   0.0    1.1  1  DJ-1_PfpI  DJ-1/PfpI family
  ------ inclusion threshold ------
      0.082   12.6   0.0        5.7    6.6   0.0    2.1  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 !  156.4   0.0   5.9e-50   5.3e-46       2     164 ..       3     178 ..       2     179 .. 0.99

  Alignments for each domain:
  == domain 1  score: 156.4 bits;  conditional E-value: 5.9e-50
                                   EEEEEEETTBEHHHHHHHHHHHHHTTEEEEEEESS..............TSEEEETTSEEEE-SEEGGGCTCCG-SEEEE- CS
                     DJ-1_PfpI   2 kvlvlladgvedvElivpvdvlkragikvdvvsvd..............keevkgsrGlkvtvdaslddvkaaeyDalvlp 68 
                                   kvl++++d  e++E+++p+++l ++g++vd++ ++               ++++++ G+ v+++++++dv+++ey a+v+p
  gi|13541255|ref|NP_110943.1|   3 KVLIITGDAGESLEVMYPYQRLLEEGYEVDIAAPSakyvqtvvhdfvpgFDTYTEKPGYLVKANKAFKDVNPEEYAAIVIP 83 
                                   9***********************************************999****************************** PP

                                   -BHHHHHHHHTSHHHHHHHHHHHHTT-EEEEETTTHHHHHHTTTTTTSEE--SGGGHHHHHHTTSEE-SSSEEEETTEEEE CS
                     DJ-1_PfpI  69 GGragperlrenekvvelvkefaekgklvaaICagpqlLaaagvlkgrrvTsypavkdklekagakyvdkrvvvdgnlvTs 149
                                   GGra pe++r+++ v+ +vk f++k+ +va +C++p++L +ag+lkgr++++ypa+k ++e ag +++d+ +vvd n+v++
  gi|13541255|ref|NP_110943.1|  84 GGRA-PEYIRNDPDVQRIVKYFFNKDAPVAELCHAPLILGSAGLLKGRKTAAYPALKSDVEIAGGTFIDEGAVVDRNIVSA 163
                                   ****.**************************************************************************** PP

                                   SSGGGHHHHHHHHHH CS
                     DJ-1_PfpI 150 rgpgaaiefalelle 164
                                   r++++++ +++e+++
  gi|13541255|ref|NP_110943.1| 164 RAWPDHPSWMREFMK 178
                                   ************987 PP

>> ThiJ_like  ThiJ/PfpI family-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0   0.00064       5.7      10      33 ..      16      39 ..       9      55 .. 0.83
   2 ?    4.1   0.0    0.0036        33      83     136 ..      75     119 ..      55     148 .. 0.66

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.00064
                     ThiJ_like 10 evaipwkvlkdagfsveFvtekgk 33
                                  ev  p++ l ++g++v+ ++++ k
  gi|13541255|ref|NP_110943.1| 16 EVMYPYQRLLEEGYEVDIAAPSAK 39
                                  899****************99987 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.0036
                     ThiJ_like  83 eeydlvllpGGsdkavrelleserlhsllveylklvkrekepskvlgaicqgvl 136
                                   eey ++ +pGG+ +    + +++ +++ ++ ++       +++  ++  c+  l
  gi|13541255|ref|NP_110943.1|  75 EEYAAIVIPGGRAPEY--IRNDPDVQRIVKYFF-------NKDAPVAELCHAPL 119
                                   689********99854..334444444444443.......23334555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       322  (0.0179597); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1240.44
//
Query:       gi|13541256|ref|NP_110944.1|  [L=341]
Description: hypothetical protein TVN0425 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); 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: 0.59u 0.26s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 2098.06
//
Query:       gi|13541257|ref|NP_110945.1|  [L=369]
Description: mevalonate pyrophosphate decarboxylase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
       0.11   12.7   0.5       0.23   11.7   0.5    1.5  1  GHMP_kinases_N  GHMP kinases N terminal domain


Domain annotation for each model (and alignments):
>> GHMP_kinases_N  GHMP kinases N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.5   1.3e-05      0.23      11      32 ..     136     158 ..     131     190 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.3e-05
                                   TSSSCHHHHHHHHHHHHHHH.HT CS
                GHMP_kinases_N  11 gaGLGSSAAlavalvaAlla.ll 32 
                                   ++GL+ S+A+a+a+ +Al +  +
  gi|13541257|ref|NP_110945.1| 136 AKGLSESSAVAAAVSRALIKnVF 158
                                   57***************954244 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 2247.41
//
Query:       gi|13541258|ref|NP_110946.1|  [L=101]
Description: hypothetical protein TVN0427 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       593  (0.0330749); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 639.32
//
Query:       gi|13541259|ref|NP_110947.1|  [L=636]
Description: hypothetical protein TVN0428 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.4e-23   82.1   2.0    6.5e-18   64.7   2.3    2.8  2  Glyco_hydro_15   Glycosyl hydrolases family 15
    1.6e-05   24.2   0.7    2.6e-05   23.6   0.7    1.4  1  DUF608           Glycosyl-hydrolase family 116, catalytic reg
    3.7e-05   23.1   1.6    3.7e-05   23.1   1.6    2.3  3  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 !   64.7   2.3   1.1e-21   6.5e-18      35     349 ..     293     572 ..     275     584 .. 0.80
   2 !   13.8   0.0   3.1e-06     0.019     406     444 ..     584     622 ..     576     626 .. 0.84

  Alignments for each domain:
  == domain 1  score: 64.7 bits;  conditional E-value: 1.1e-21
                                   S......B--SEEHHHHHHHHHHHH.......HHHHHTTT-HCCHHHHHHHHHHHHHHCTS-BTTB-TTSCGGGG--EE-T CS
                Glyco_hydro_15  35 p......DYrytWvRDsvyvilavwglgyrdedrakayeleqslvklmrglleamvrqagkvekfketqstkgLhakyftk 109
                                          +Y+y+W RD+++ + a+   g  + +r++   +e s+ +  +g+l+  ++ +gk        s+   +++   +
  gi|13541259|ref|NP_110947.1| 293 IlkmshdGYYYVWPRDASIAAYALSISGHSETARRFFALMESSMSE--EGYLYHKYNVDGKIA------SS---WLPHVIN 362
                                   33555559*****************777778888888888888877..9***********933......34...6665443 PP

                                   TS-B--S-..-S--BTTHHHHHHHHHHHHHCTTHCHCCCCHHH.HTHHHHHHHHHHHTT.....S-EE-TTS--ECEEHH. CS
                Glyco_hydro_15 110 tgstvvGddewghlQlDatslyllalaqmtasglqiistldev.afvqnlvdYieaayk.....tpdfglWEenqgeseln 184
                                    g+++++      +Q D t+l++ +l+++  +   i +t+  + + + +  d+ ++  +     +p+f+lWEe+ g + + 
  gi|13541259|ref|NP_110947.1| 363 -GKHIYP------IQEDETALVVWVLWEYFHKYNDIGFTAPYYeKLITKAADFMTRFVDsdglpQPSFDLWEERYGVHAY- 435
                                   .555555......6***************8888888888887777888888888876542222289**************. PP

                                   .HHHHHHHHHHHHHHHHHHCT-HHHHCCHHHHHHHHHHHHHSTTT..GGGEETTCCECECSCH.....HHHTTS--S-BCH CS
                Glyco_hydro_15 185 assvgmakAlleaideadlfgakgdaqlvektkdeilnklqgkygckrgfwplfntylildgsfaedkeqvqeyrealdas 265
                                    + + + +Al  a ++a+ fg+ + ++++ + ++ +++        ++ + ++ ++y ++  +         + +  +d++
  gi|13541259|ref|NP_110947.1| 436 -TVATVYAALKAASNFANVFGDGDLSEKYLSAAERMYEAF-----EEKFYSEEYGYYARAILD--------GKPDFTVDSA 502
                                   .************************************999.....334445555555544444........347899**** PP

                                   HHHHHHHCS-TTS-TT-TT-TTTSHHHHHHHHHHHHHHHHHSGGGTT-STTS--SBTT--CGSSSBSCT--BHHHHHHHHH CS
                Glyco_hydro_15 266 llllpelyfvpaddvdeeyqnpqsprllaqslyildsllsegflavgeldplvrRysedvkpdklglsGrpyylctlwtve 346
                                   l  l++ ++  + d          p++++++ +i d+l   g    g    ++ Ry   +  d+ +  G+p+ ++tlw+++
  gi|13541259|ref|NP_110947.1| 503 LTSLVIFGMKDPRD----------PKIVSTMEKISDTLWVNGV--GGIARYQNDRYMRVK--DDTNIPGNPWIITTLWMAR 569
                                   **************..........******************9..565556666666665..569999**********888 PP

                                   HHH CS
                Glyco_hydro_15 347 tll 349
                                    +l
  gi|13541259|ref|NP_110947.1| 570 YYL 572
                                   765 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 3.1e-06
                                   HHHHHHHS-TTS---SEE-TTT--EESSTT-HHHHHHHH CS
                Glyco_hydro_15 406 iveaveednslgvLteevdvylgeliraqpllfsealll 444
                                   i+ +   ++++g+++e+++ y g++++ +pl +s+a+++
  gi|13541259|ref|NP_110947.1| 584 IMWVKSHRQKSGIFSEQINPYNGQPLSVSPLVWSHAEFI 622
                                   55555558999*************************998 PP

>> DUF608  Glycosyl-hydrolase family 116, catalytic region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.7   4.3e-09   2.6e-05     145     218 ..     412     486 ..     370     600 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 4.3e-09
                        DUF608 145 lienegfadqtYDaws.vkGvsaycgglwlaaLeaaiemaellgdkkdaeeykellekakkvyekkLwnGeYfky 218
                                   +++++g ++ ++D w+   Gv ay+    +aaL+aa+++a++ gd +  e+y +  e+  +++e+k+++ eY  y
  gi|13541259|ref|NP_110947.1| 412 FVDSDGLPQPSFDLWEeRYGVHAYTVATVYAALKAASNFANVFGDGDLSEKYLSAAERMYEAFEEKFYSEEYGYY 486
                                   56777888888****7257*************************************************9998555 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 ?   -3.4   0.1      0.73   4.4e+03     127     158 ..      58     102 ..      56     122 .. 0.59
   2 ?   -2.0   0.1      0.28   1.7e+03     303     318 ..     243     258 ..     236     265 .. 0.72
   3 !   23.1   1.6   6.2e-09   3.7e-05      56     223 ..     316     488 ..     303     496 .. 0.73

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 0.73
                                   HHHHHHHHHHTSBT......TB..--S-S--STT........... CS
               Bac_rhamnosid6H 127 mkryldylkqrsdd.....gle.elskfqlgDWldpe.......a 158
                                   + +y+dy++++         ++ + ++++l+D ++         +
  gi|13541259|ref|NP_110947.1|  58 CIKYMDYYDHTMVGiinynVDDiNFENHDLVDIYKNIyvrqitaE 102
                                   667888888877776666533447777778887755565444332 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.28
                                   TT-SS--SSTTSB--- CS
               Bac_rhamnosid6H 303 nGaTtiwErWdsmlnp 318
                                   + +T  wE W+s   p
  gi|13541259|ref|NP_110947.1| 243 KRTTNYWELWSSKVTP 258
                                   568999****997644 PP

  == domain 3  score: 23.1 bits;  conditional E-value: 6.2e-09
                                   HHHB--HHHHHHHHHHHHHH--TT..........S.--BSBSS--T...T--B--TTTTTHHHHHHHHHHHHH--HHHHHH CS
               Bac_rhamnosid6H  56 sylydveaflekwlrdladeqren..........g.avptvaPevl...galsetaeWadaivivpwelyetygDkeilkk 122
                                     + +++++++++++ +++++ e+          g     + P+v+   + +  +   ++++v v we++++y+D  + + 
  gi|13541259|ref|NP_110947.1| 316 LSISGHSETARRFFALMESSMSEEgylyhkynvdGkIASSWLPHVIngkHIYPIQEDETALVVWVLWEYFHKYNDIGFTAP 396
                                   455667777777777777777776455555555532455677777766333333444456678899999************ PP

                                   HHHHHHHHHHHHHHTSBT.TB.--S-S--STT.....-SS----HHHHHHHHHHHHHHHHHHHHHHTTS..--HHHHHHHH CS
               Bac_rhamnosid6H 123 qYesmkryldylkqrsddgleelskfqlgDWldpeardgaaktekalvataylvrslklvakiaellgkeedakkyaalae 203
                                   +Ye++        +r  d  ++l +  +  W            + ++vat+y   +lk ++++a+++g  + ++ky + ae
  gi|13541259|ref|NP_110947.1| 397 YYEKLITKAADFMTRFVD-SDGLPQPSFDLWE------ERYGVHAYTVATVY--AALKAASNFANVFGDGDLSEKYLSAAE 468
                                   ****88777777777777.4667777777777......34456667777766..67999*********9888********* PP

                                   HHHHHHHHHHB.-TTS-BTT CS
               Bac_rhamnosid6H 204 elkaafnkkyldsetgsvan 223
                                   ++++af++k++ +e g +a 
  gi|13541259|ref|NP_110947.1| 469 RMYEAFEEKFYSEEYGYYAR 488
                                   ***********888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (636 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       572  (0.0319036); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); 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: 0.66u 0.34s 00:00:01.00 Elapsed: 00:00:00.49
# Mc/sec: 3902.49
//
Query:       gi|13541260|ref|NP_110948.1|  [L=601]
Description: glycogen debranching protein [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.4e-91  304.9   0.0      1e-90  304.5   0.0    1.1  1  GDE_C            Amylo-alpha-1,6-glucosidase
    4.1e-54  183.3   0.1    6.8e-54  182.6   0.1    1.3  1  GDE_N            Glycogen debranching enzyme N terminal
    8.7e-07   27.9   0.0      0.025   13.3   0.0    2.1  2  Glyco_hydro_100  Alkaline and neutral invertase
  ------ inclusion threshold ------
      0.017   14.3   0.0      0.033   13.4   0.0    1.4  1  DUF608           Glycosyl-hydrolase family 116, catalytic reg


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 !  304.5   0.0   2.3e-94     1e-90      22     383 .]     261     587 ..     245     587 .. 0.90

  Alignments for each domain:
  == domain 1  score: 304.5 bits;  conditional E-value: 2.3e-94
                         GDE_C  22 vsliAGlpwFsdWGRDtfIaLsGllLvtgrfeeAreilltFaktlrhGliPNlldegqealyntvdaslwlieaiekYley 102
                                    ++iAG++wF  WGRD+fI+L+GllL++g +++A ++l++++++  +Gli N   eg + ly ++d slw+++ai+k++ey
  gi|13541260|ref|NP_110948.1| 261 DNIIAGFHWFGPWGRDAFISLPGLLLIPGMYDKAANVLRHYSEQSVDGLILNSA-EGGNVLY-SADSSLWFVYAIQKFYEY 339
                                   579*************************************************97.7888888.67**************** PP

                         GDE_C 103 agdaeilrriypvlqeilqkyvqGtkykigldeedglisagerlnqlTWmDakvkgepvtPRdGkaveinaLwyaaLkile 183
                                   ++++++lr++y+ +q+i+ +y++G++ +++++    +++      + TWmDa ++g++vtPR+G ++einaLwy++Lk+++
  gi|13541260|ref|NP_110948.1| 340 TKNKAFLREMYNKVQNIIYAYLKGNE-NFHIE--GKFVRVTG--SPMTWMDAVIDGKAVTPRSGLPIEINALWYNTLKAYT 415
                                   **************************.99998..66665443..5************************************ PP

                         GDE_C 184 elaekalgeakkssykelaekikesfekkFwdeaaaavakreilaDvlksseekdlslRpNflialslapellseekakkv 264
                                    ++   lg++ k++  e+ +  +++f+k F         + + + D+  +   +d+s+RpNfl+a++l++ ll+++     
  gi|13541260|ref|NP_110948.1| 416 DFSA-LLGKEPKKEAIEILDGFEDEFKKAF--------VRGTHILDIAFP---DDYSFRPNFLFAYFLPYPLLKDKI---W 481
                                   ****.6666466666666666666666666........346667787766...89******************9987...8 PP

                         GDE_C 265 lekaeeeLltplGlktLdpedpeYkgnYdgsedsrdaaYHqGtvWvwllgsyveallkfgeklgkskealeevkalLegle 345
                                   ++ a  +L+tp+Gl++Ldp++p++ g+Y g++ srd aYH+GtvW++l+g++++a++k+g +   + + l+ +k+l++   
  gi|13541260|ref|NP_110948.1| 482 IDYAIDKLVTPYGLRSLDPSNPSFIGKYAGDRFSRDNAYHNGTVWPYLAGIFIKAAIKVGYD---RIKLLNIFKPLFD--- 556
                                   9************************************************************8...5555666666665... PP

                         GDE_C 346 khleeaglgslsElfdgdaellpkgciaQAWSvaellr 383
                                           ++++E++dg ++ +p+gci+QAWS++e++r
  gi|13541260|ref|NP_110948.1| 557 -------SARIPEIYDGINPGVPRGCIMQAWSHGEVIR 587
                                   .......578*************************997 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 !  182.6   0.1   1.5e-57   6.8e-54       2     210 ..       6     210 ..       5     216 .. 0.91

  Alignments for each domain:
  == domain 1  score: 182.6 bits;  conditional E-value: 1.5e-57
                         GDE_N   2 EwllTNglGGYasgtvagantRryhGlLvaalnppsgRtlllskldeslevsgkvfeLstneypgeiepeGyeyLesFele 82 
                                   Ewl++N +G+Y+s+t a antR+yhGlLv+++n+  +R++llsk++e++ ++g+ +++ tn+y+g+++p+G++y+ +++  
  gi|13541260|ref|NP_110948.1|   6 EWLMSNERGSYSSSTFAFANTRTYHGLLVVNTNEYYDRYVLLSKISEEIGYDGEYISIDTNFYEGGVYPDGFKYIYEYRDF 86 
                                   9******************************************************************************** PP

                         GDE_N  83 pvptwtyrv.gdvllekqivmpkgentvliaYrlenadepatLrlrpllafRdfheltkanellqksqeeglveiqaseae 162
                                   p+p + +++ gd +l+k+ivm+k ++ v+i+Y+ ++ ++p +L l+pl+a R+fh + +++e++++ + ++     + + +
  gi|13541260|ref|NP_110948.1|  87 PYPSVSFKFpGDRRLKKSIVMDKVSDLVIIRYEFQG-ERPKSLVLTPLIALRSFHRTLNSKEKNFDVHISNF---YVFS-D 162
                                   *********666************************.55********************8766666544433...3333.3 PP

                         GDE_N 163 pslrlqaskegefqeepvwyynveypeEaerGlddredlyspgyfeve 210
                                    ++++ ++k g+f   ++wyyn++yp+E+erG+++ edly+pg++ ++
  gi|13541260|ref|NP_110948.1| 163 GKYSFSMNKVGKFYGPGYWYYNFRYPREEERGTNSLEDLYNPGRIVID 210
                                   3466777779*********************************99776 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 !   13.3   0.0   5.6e-06     0.025     112     200 ..     321     417 ..     313     447 .. 0.69
   2 !   12.5   0.0   9.8e-06     0.044     352     406 ..     516     568 ..     507     588 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.6e-06
                                   --HHHHHHHHHHHHHHHHHH---HHHHS..HHHHHHHHHHHHHHT---SSSSSS--B-SS-SS......S-S-SS-..-BS CS
               Glyco_hydro_100 112 apvDsslWWiillraYvkatgdlslaee..eevqkgiklilelvlaerfdeaPtllvpdgafm......idRrlgv..yga 182
                                    ++DsslW++  ++ + + t+++++ +e  ++vq+ i   l+   +e+f+    ++   g+ m      id +      g 
  gi|13541260|ref|NP_110948.1| 321 YSADSSLWFVYAIQKFYEYTKNKAFLREmyNKVQNIIYAYLK--GNENFHIEGKFVRVTGSPMtwmdavIDGKAVTprSGL 399
                                   589**********************98622467777776664..2355555555555555544221111443322222699 PP

                                   BHHHHHHHHHHHHHHHHH CS
               Glyco_hydro_100 183 pleiqaLlyaalrsakel 200
                                   p+ei+aL+y++l++ +++
  gi|13541260|ref|NP_110948.1| 400 PIEINALWYNTLKAYTDF 417
                                   *************98764 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 9.8e-06
                                   -TTBTTBT-B-GGGHHHHHHHHHHTT-HHHHHHHHHHHHTTHTTTT--S-EESTT CS
               Glyco_hydro_100 352 tpwsYhngGsWpvllWllvaaalkterkelaekaielaekrlskdewaeYydgkt 406
                                   +  +Yhng  Wp l  +++ aa+k++ +++  k +++ +  +++ + +e ydg +
  gi|13541260|ref|NP_110948.1| 516 RDNAYHNGTVWPYLAGIFIKAAIKVGYDRI--KLLNIFKPLFDSARIPEIYDGIN 568
                                   5568**********************9998..56777888899999999999976 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 ?   13.4   0.0   7.4e-06     0.033      99     201 ..     324     435 ..     318     456 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7.4e-06
                        DUF608  99 DlnlkfvLqvYRdyvitedkeflkemypkvkkvleklle.fDk.d.kdglienegfa....dqtYDa...wsvkGvsaycg 169
                                   D  l fv  + + y  t++k+fl+emy+kv++++   l+   + + +  ++  +g +    d   D    +  +G    ++
  gi|13541260|ref|NP_110948.1| 324 DSSLWFVYAIQKFYEYTKNKAFLREMYNKVQNIIYAYLKgNENfHiEGKFVRVTGSPmtwmDAVIDGkavTPRSGLPIEIN 404
                                   66677899999999*******************99888742221213345566665411116666664434456888889* PP

                        DUF608 170 glwlaaLeaaiemaellgdkkdaeeykellek 201
                                    lw+ +L+a+++++ llg++ ++e   e+l+ 
  gi|13541260|ref|NP_110948.1| 405 ALWYNTLKAYTDFSALLGKEPKKEA-IEILDG 435
                                   *****************98877764.445554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (601 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.64u 0.30s 00:00:00.94 Elapsed: 00:00:00.48
# Mc/sec: 3750.27
//
Query:       gi|13541261|ref|NP_110949.1|  [L=369]
Description: glycosyltransferase [Thermoplasma volcanium GSS1]
Scores for complete sequence (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   76.8   0.0    2.2e-21   76.1   0.0    1.3  1  Glycos_transf_1  Glycosyl transferases group 1
    3.4e-21   76.0   0.0    5.2e-21   75.4   0.0    1.3  1  Glyco_transf_4   Glycosyltransferase Family 4
    1.1e-20   74.4   0.0    1.8e-20   73.8   0.0    1.3  1  Glyco_trans_1_4  Glycosyl transferases group 1
    6.6e-11   42.9   0.0      1e-10   42.3   0.0    1.3  1  Glyco_trans_4_4  Glycosyl transferase 4-like domain
    1.7e-09   37.7   0.1    3.7e-08   33.4   0.0    2.5  2  Glyco_transf_5   Starch synthase catalytic domain
    2.7e-05   24.5   0.0    6.8e-05   23.2   0.0    1.7  1  Glyco_trans_1_2  Glycosyl transferases group 1


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.1   0.0   7.4e-25   2.2e-21      13     133 ..     194     313 ..     189     349 .. 0.86

  Alignments for each domain:
  == domain 1  score: 76.1 bits;  conditional E-value: 7.4e-25
                                   TT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSSSHHHHHHCE CS
               Glycos_transf_1  13 ekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsredleellkna 93 
                                   +k++ +l+ gr++++Kg++ + + ++++ +  +  ++++iaG ge + e+k+ a      d+++f g+v   + + ++k++
  gi|13541261|ref|NP_110949.1| 194 KKERNVLYFGRVTNQKGPKFFMETAKKVLEF-DRTIRFTIAGTGELLGEMKSYAMDNDFFDHIEFPGFVHFRKAIWYYKRS 273
                                   68999************************97.**************************************55566688999 PP

                                   SEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHT CS
               Glycos_transf_1  94 difvlpsisEgfGivllEAmaaglpviasnaggpaevvkd 133
                                   ++f++p+ sE+fG+++lEAm +g+pvi s + g+ e + +
  gi|13541261|ref|NP_110949.1| 274 SAFIIPAVSEPFGMTVLEAMVSGTPVILSRTTGVGEALHH 313
                                   *********************************9998876 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.4   0.0   1.8e-24   5.2e-21      63     169 ..      83     185 ..      34     186 .. 0.79

  Alignments for each domain:
  == domain 1  score: 75.4 bits;  conditional E-value: 1.8e-24
                Glyco_transf_4  63 rlrrllkrekpDvvHahspaalgaallalrrrlgiplVltvHglyekrllkarlkplsrllralerrllrradrviavSea 143
                                   ++  +++ +++ +vH+h+++++  a++a++ ++gipl++t+H+++      a+ +p++  + ++er   + adr+i+vS+ 
  gi|13541261|ref|NP_110949.1|  83 KVVDAFDPNGVKLVHCHDWITF-PAGIAIKEKYGIPLIVTYHSTEF--DRSAYFNPQE-KIMKIEREGGKEADRIITVSNL 159
                                   455566666999*********8.677899999*************5..2333444444.455679999************* PP

                Glyco_transf_4 144 tadelrerygvppekitVipnGvDle 169
                                   t+  ++e+y+++peki++++nGvD +
  gi|13541261|ref|NP_110949.1| 160 TKSIVVEKYNIDPEKIVTVYNGVDAT 185
                                   ************************75 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.8   0.0   5.9e-24   1.8e-20       2     133 ..     197     334 ..     196     335 .. 0.86

  Alignments for each domain:
  == domain 1  score: 73.8 bits;  conditional E-value: 5.9e-24
                                   EEEEEES---GG.GTHHHHHHHHHHHH.HH..EEEEEES---...HHHHHHHT..T-T.TEEEE---..THHHHHHHH-SE CS
               Glyco_trans_1_4   2 pvilfvGrleenvkgvdllleavpllrkkd..vrlvivGdgp.rpeeleelaa..gleerveftGfv..edlaellaaadv 75 
                                   +++l++Gr+  n+kg ++++e ++++++ d  +r++i+G g+    e++++a   ++ +++ef Gfv   +   ++++++ 
  gi|13541261|ref|NP_110949.1| 197 RNVLYFGRV-TNQKGPKFFMETAKKVLEFDrtIRFTIAGTGElLG-EMKSYAMdnDFFDHIEFPGFVhfRKAIWYYKRSSA 275
                                   689******.799**********999966557*********9875.8988774467779********88889999****** PP

                                   EEE--..---SHHHHHHHHTT-EEEE-TGGGTTT--TTSSEE-.-TT-HHHHHHHHHHHHH CS
               Glyco_trans_1_4  76 fvaPs..egfglkllEamaaglpvVatdvggiaevvgengllv.ppgdpealaeailrLle 133
                                   f++P   e fg+++lEam +g+pv+ +++ g+ e++  + +l  +  d++ +a  ++ +l+
  gi|13541261|ref|NP_110949.1| 276 FIIPAvsEPFGMTVLEAMVSGTPVILSRTTGVGEAL--HHVLSaDFWDTDRMATYVVSILN 334
                                   ******9**********************9*99944..44444155689999999988876 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 !   42.3   0.0   3.4e-14     1e-10      73     160 .]      92     181 ..      62     181 .. 0.87

  Alignments for each domain:
  == domain 1  score: 42.3 bits;  conditional E-value: 3.4e-14
               Glyco_trans_4_4  73 rpdvvhahsptaglaarlarrrrgiplvvtlhglllrrg..sgavrrlyralerrllrradavlvvseaeaeelra.lgvp 150
                                   ++ +vh+h++ + +a+ +++ + gipl+vt+h+++++r     ++  +   +er   + ad++++vs+     +++ ++++
  gi|13541261|ref|NP_110949.1|  92 GVKLVHCHDWITFPAGIAIKEKYGIPLIVTYHSTEFDRSayFNPQEKI-MKIEREGGKEADRIITVSNLTKSIVVEkYNID 171
                                   5679****************899************9999654444444.59*************************999** PP

               Glyco_trans_4_4 151 adrvvvvpng 160
                                   ++++v+v ng
  gi|13541261|ref|NP_110949.1| 172 PEKIVTVYNG 181
                                   ********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 ?    1.2   0.0     0.082   2.5e+02       1      21 [.       2      21 ..       2      26 .. 0.90
   2 !   33.4   0.0   1.2e-11   3.7e-08     118     230 ..      73     165 ..      63     175 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.082
                Glyco_transf_5  1 kilfvasEvaplaktGGLadv 21
                                  ki ++++E +p a  GGL+ +
  gi|13541261|ref|NP_110949.1|  2 KIAVIGWELPP-AFSGGLGIH 21
                                  7999*******.******966 PP

  == domain 2  score: 33.4 bits;  conditional E-value: 1.2e-11
                Glyco_transf_5 118 fsraalellekl.....gwkpdvihahDWhtalvpallkelykerglfkkiktvftiHNlayqgrfpkdel.aalglpaed 192
                                   f  a++++ ek+     ++++ ++h+hDW t  +++ +ke y        i++++t H+++++++   ++  +        
  gi|13541261|ref|NP_110949.1|  73 FYEAVMDYNEKVvdafdPNGVKLVHCHDWITFPAGIAIKEKY-------GIPLIVTYHSTEFDRSAYFNPQeK-------- 138
                                   6677777777766766556799*******************9.......5*************9988654312........ PP

                Glyco_transf_5 193 fekldglefygkvnflkagivyadavttVSptyakEil 230
                                               ++  + g ++ad+++tVS+ ++  ++
  gi|13541261|ref|NP_110949.1| 139 -----------IMKIEREGGKEADRIITVSNLTKSIVV 165
                                   ...........356667999999999999987766555 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 !   23.2   0.0   2.3e-08   6.8e-05       5      90 ..     279     362 ..     273     364 .. 0.90

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 2.3e-08
               Glyco_trans_1_2   5 psrsespnlrlfEaaacGafaltddaegleelftpgkevilfe..dleelaekiryllanpeerraiaeaarervlaehty 83 
                                   p  se + + ++Ea+ +G++++ ++++g++e +   ++v+ ++  d++ +a  +   l++++  + +++ +++++l  +t+
  gi|13541261|ref|NP_110949.1| 279 PAVSEPFGMTVLEAMVSGTPVILSRTTGVGEAL---HHVLSADfwDTDRMATYVVSILNHRGILETMSRYGKAEAL-GFTW 355
                                   6778999*************************9...677777788*****************************55.99** PP

               Glyco_trans_1_2  84 dhraeql 90 
                                   d++a++ 
  gi|13541261|ref|NP_110949.1| 356 DKAAAKT 362
                                   **99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       422  (0.0235373); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-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 0.25s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 2516.83
//
Query:       gi|13541262|ref|NP_110950.1|  [L=378]
Description: Alpha-amylase [Thermoplasma volcanium GSS1]
Scores for complete 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-67  226.2   4.7      8e-67  225.7   4.7    1.2  1  Glyco_hydro_57   Glycosyl hydrolase family 57
    8.6e-07   28.9   0.0    1.4e-06   28.2   0.0    1.3  1  Polysacc_deac_1  Polysaccharide deacetylase


Domain annotation for each model (and alignments):
>> Glyco_hydro_57  Glycosyl hydrolase family 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  225.7   4.7   8.9e-71     8e-67       2     325 .]       6     283 ..       5     283 .. 0.98

  Alignments for each domain:
  == domain 1  score: 225.7 bits;  conditional E-value: 8.9e-71
                                   EEEEE-----TTS-SSSSSHHHHHHHHHHTHHHHHHHHHHHHHTT----EEEEE-HHHHHHHT-HHHHHHHHHHHHHHHHH CS
                Glyco_hydro_57   2 fvfhqHqplykkpgkgeytlpwvrehaaedYiklalilekfpkvhvtfeLsgsLiaqLeeylngekksylpateellelie 82 
                                   f+f+ Hqp++ +p+      + ++++  +++++++++ e+f++v+                    ++sy+pat++l+e+  
  gi|13541262|ref|NP_110950.1|   6 FYFEIHQPFRLRPT------NLYDVKSEQNVFWDEKNEEIFRRVA--------------------ERSYIPATRNLMEY-- 58 
                                   99************......99***********************....................**************.. PP

                                   HHHHH---HHHHHHHHHHHHHHHHHHHHHHHT.TT-HHHHHHHHHHCTSEEEEEE-TT-B-GGG-S-HHHHHHHHHHHHHH CS
                Glyco_hydro_57  83 eglerctelkldlavlfnlaisgplleqiqkwlnkevlelfrelqesgqvElltspyyHpllpllpdsedieaqvkkarel 163
                                           +k       +++i+g+ +eq+ ++ n +v+++++++++sg +E+l+++yyH+l++++++ +++++qv ++r+l
  gi|13541262|ref|NP_110950.1|  59 -------GIK------SSFSITGTAVEQALMY-NTKVIDAIDDYVKSGLCEMLSETYYHSLASIWNY-DEFKRQVDMHRDL 124
                                   .......799......9***************.**********************************.************* PP

                                   HHHHHSS--SBEE-GGG-B--SHHHHHHHTT--EEEE-C------------TTS-EE-TTS.-EEEE--CHH-TTTSGGG- CS
                Glyco_hydro_57 164 yeeyfgqePrgfwlpElavspeileilaelGfeylftdelaeiledkskespyrpyllknggiavffRdreLsddigFrys 244
                                   ++++f++ P++f+++El+++++i+e+++ +Gf  ++t+++++i++d+   sp+++y ++ g +++++R++ +sd+i+Fr+s
  gi|13541262|ref|NP_110950.1| 125 MKRIFNVVPKVFRNTELIYDDRIAEMVKRMGFTSIITEGTDSIVKDH---SPNYRYASPSG-LNLYLRNYVMSDNISFRFS 201
                                   ***********************************************...*********88.******************* PP

                                   ................TTSB..........-TT---TTT-..-BB-TT-S---HHHHHHHHHHHHHHHHHHHHHHHHHSS- CS
                Glyco_hydro_57 245 ....eqypleavddfinwlkkvkkaksevvtialdgEnwg..hypetgkkeFleklyeeleenglielvtpsefikklkpk 319
                                       + ypl ++d++++w++++   ++++v++++d+E++g  +++etg+++F+++l+ ++   g ie++t+se+ k+++ k
  gi|13541262|ref|NP_110950.1| 202 ntkwKDYPL-TADKYAKWINES---EGDMVNLFMDYETFGehQTQETGIFDFMKYLPVYFRDYG-IETITISEAEKRHRVK 277
                                   ****99***.**********88...***************99**********************.***************9 PP

                                   EEEEEE CS
                Glyco_hydro_57 320 gliklp 325
                                   +++++p
  gi|13541262|ref|NP_110950.1| 278 DVLSIP 283
                                   998876 PP

>> Polysacc_deac_1  Polysaccharide deacetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2   0.0   1.6e-10   1.4e-06      28     122 ..      55     157 ..      45     159 .. 0.95

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 1.6e-10
                                   HHHCT--EEEEE-HHHHCH-.......HHHHHHHHHTT.EEEEE--SS--EGGGSHHHHHHHHHHHHHHHHHHHHS----E CS
               Polysacc_deac_1  28 Lkkykvkatffvigglvedy.......pdevremaasG.veignHtinhsnlkrlseeevrreierakdalrkalgreprl 100
                                   L +y++k  f ++g+ ve+         d +   ++sG +e  + t+ hs  + +  +e++r++++ +d ++++++  p++
  gi|13541262|ref|NP_110950.1|  55 LMEYGIKSSFSITGTAVEQAlmyntkvIDAIDDYVKSGlCEMLSETYYHSLASIWNYDEFKRQVDMHRDLMKRIFNVVPKV 135
                                   889***********999999999*999****************************************************** PP

                                   EE-GGGEE-HHHHHHHHHTT.E CS
               Polysacc_deac_1 101 fryPygsasatvlevarelgfa 122
                                   fr   + +++++ e+++++gf+
  gi|13541262|ref|NP_110950.1| 136 FRNTELIYDDRIAEMVKRMGFT 157
                                   ********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (378 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       572  (0.0319036); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.32s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 2315.11
//
Query:       gi|13541263|ref|NP_110951.1|  [L=274]
Description: asparaginase [Thermoplasma volcanium GSS1]
Scores for complete sequence (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  201.7   0.0    2.2e-59  201.0   0.0    1.3  1  Asparaginase_2  Asparaginase


Domain annotation for each model (and alignments):
>> Asparaginase_2  Asparaginase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  201.0   0.0   1.2e-63   2.2e-59       2     278 ..       4     257 ..       3     268 .. 0.87

  Alignments for each domain:
  == domain 1  score: 201.0 bits;  conditional E-value: 1.2e-63
                                   EEEEEEEEESE-G-HHHHHHHHHCHHHHHHHHHHHHHTT--HHHHHHHHHHHHHCTCCCSSSTTSS-BTTS---EEEEEEE CS
                Asparaginase_2   2 vlvihGGAgsilktkereeavrkalkealeagykvLkeggsaldaVeaavrllEddplfnaGkGsvltedgeveldAsimd 82 
                                   vl+ihGGAgs ++       +   l++ ++ +    +e+ sald  ++av  +Eddp+fnaG+Gsv+  dg +++dA++m 
  gi|13541263|ref|NP_110951.1|   4 VLLIHGGAGSDPS-------YSGRLNSYASFA----SEEISALDNAVKAVVKMEDDPDFNAGTGSVPRLDGSIQMDAAVMI 73 
                                   6899999998888.......666666655544....567788988888999*****************************7 PP

                                   TTTTEEEEEEEESSBS-HHHHHHHHHHHCS-SEEEHHHHHHHHHHTT-----CGGG--HHHHHHHHHHHHCCCHS..B-S- CS
                Asparaginase_2  83 gktlraGaVagvkrvknpislArlvmeksehvlLvgegAeefareqglelvdeesllteerlkelekakkekaekkeaknv 163
                                       ++G+V++++rvknp+ +Ar vm ks+h++++g+gA +far +g+   +++++ te+++k l+++++e +++++  + 
  gi|13541263|ref|NP_110951.1|  74 PG--HFGSVINIERVKNPVLVARDVMAKSPHIMISGDGAVKFARLMGY---PDYDPTTEKAKKLLQQFEEEAEKNEIPDK- 148
                                   65..57******************************************...99999999999999999777777544333. PP

                                   BS-TTT..TT---EEEEEE-TTS-EEEEEEE--STTB-TTEE-STTSTTTSEEEETTTEEEEEEE-HHHHCCTTHHHHHHH CS
                Asparaginase_2 164 sekelk..aklgTvGaValDsegnlAaaTSTgGltnklvGRvGDspiiGaGtYAdnkvgAvsaTGkGeeiirellaadiva 242
                                    +   k  + + TvGaVa   eg++A a STgG    + GRvGDspi+GaG Y+  + gAv aTG Geei +++l+ +i  
  gi|13541263|ref|NP_110951.1| 149 FKIYFKyvKPHDTVGAVAR-VEGEFAGAVSTGGSFPMVRGRVGDSPIPGAGIYV-GEKGAVVATGIGEEIAKNILSFRIYN 227
                                   333344678999******7.79********************************.888*********************** PP

                                   HHHTTT--HHHHHHHHHHCHHHHTTT-EEEEEEETT CS
                Asparaginase_2 243 lmeykglsleeAaekvieeklkrvkgsgGviavdkk 278
                                   ++ +      +   ++++e+++++  s+G+iavd+k
  gi|13541263|ref|NP_110951.1| 228 RIGE------KRLYDIVKEEVDKFSVSVGIIAVDEK 257
                                   **99......44567778888888899*******87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       545  (0.0303977); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 1847.78
//
Query:       gi|13541264|ref|NP_110952.1|  [L=121]
Description: hypothetical protein TVN0433 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       290  (0.0161749); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 864.37
//
Query:       gi|13541265|ref|NP_110953.1|  [L=117]
Description: hypothetical protein TVN0434 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.082   11.3   0.1       0.09   11.2   0.1    1.1  1  DUF2863   Protein of unknown function (DUF2863)


Domain annotation for each model (and alignments):
>> DUF2863  Protein of unknown function (DUF2863)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1     5e-06      0.09     297     343 ..      59     106 ..      31     115 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 5e-06
                       DUF2863 297 rleEyRigftlresneviyGvvWpllg.eeeeeeeeadeaeeeaalee 343
                                   +leEy i  t re+ +v++G +W + + +  +++  + ++e++++ +e
  gi|13541265|ref|NP_110953.1|  59 NLEEYGILETYREEVSVMHGKIWRVNQwRYRKDKILELASEKDTVKKE 106
                                   79***********************99666666655555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       582  (0.0324614); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 866.67
//
Query:       gi|13541266|ref|NP_110954.1|  [L=314]
Description: nucleoside-diphosphate-sugar pyrophosphorylase [Thermoplasma volcanium GSS1]
Scores for complete 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   89.5   0.0    2.9e-25   89.3   0.0    1.1  1  NTP_transferase  Nucleotidyl transferase
    2.5e-08   34.4   0.0    3.3e-08   34.0   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 !   89.3   0.0   3.2e-29   2.9e-25       2     245 ..       3     225 ..       2     228 .. 0.86

  Alignments for each domain:
  == domain 1  score: 89.3 bits;  conditional E-value: 3.2e-29
                                   EEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEEEEESS CS
               NTP_transferase   2 avILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevlialepe 82 
                                   + ILaGG+G+RL P+t +++k lv + +++++++ +l    n g++e +++l+ +    +ee +++ +  ++++ ++ e++
  gi|13541266|ref|NP_110954.1|   3 GAILAGGYGKRLKPITDSIPKALVEIKDNYTIMDRQLFDFRNIGVKE-VYILSGYLGNKIEERYGDLY-NDMNMYYLREEK 81 
                                   67*********************************************.*******************9.588********* PP

                                   --BGGHHHHHTHHHHTTSSE..EEEEETTEEEESTTHHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEEEECTTSBEEEEE CS
               NTP_transferase  83 gkgtAdAvalaaelledeksdelvlvLggDhlikdayeeavkkaiekaakgtvtfgivpveeateyGvieadeegrverfv 163
                                   + gt  +++  ++   d++    ++  +gD +++ ++  ++kka++++a     + i  ++ ++ +G++e+ + ++v +f 
  gi|13541266|ref|NP_110954.1|  82 PLGTLYSLRNLLDKRSDDD----IILRNGDTITDINFLSFIKKAQSQQA----FITIHITKMKSPFGIVETFG-DQVSEFR 153
                                   ****999988887777777....8999*******************999....556666677889*****987.59***** PP

                                   CS-SSHSHCSEECCSEEEEETTHHHHHHHCCHHHTTSSCHHHHHHHHHHHTTEEEEEECSTTEE-EEEXSSHHHHHHHHHH CS
               NTP_transferase 164 EKPkeakaselassGiYvfnsevllflakdleelkrgedeitdilpkaleegkvalaflfkdaeyWsDvGtldslleanek 244
                                   EKP+ +    ++++G+Y+ +++++ +    +ee+   +d  t ++pk+++ g va +   +da  W+ + + ++l ++ e+
  gi|13541266|ref|NP_110954.1| 154 EKPELDH---YINAGLYYIKQDAFPYF---YEEY-MYRDLETTVFPKLTKLGLVASY--HEDA-LWMGIDSEKDLEKIREE 224
                                   *****88...**************999...4566.4555556788888888877755..3332.58777777777766665 PP

                                   H CS
               NTP_transferase 245 l 245
                                   +
  gi|13541266|ref|NP_110954.1| 225 Y 225
                                   5 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.0   0.0   3.7e-12   3.3e-08       1      97 [.       3     109 ..       3     164 .. 0.76

  Alignments for each domain:
  == domain 1  score: 34.0 bits;  conditional E-value: 3.7e-12
                                   EEEEEESS-TTTT..T...THHHHCC.CCCCHHHHHHHHHCTT.-CEEEEECSH..CHHHH....HHTTCTS-EEE-TTSS CS
                  NTP_transf_3   1 aviLAGGrSsRmg..g...dKallpl.ggkpllervldalraagvdevvvvggd..eevla....alarlgvrvvededpg 69 
                                   ++iLAGG ++R++  +   +Kal+++ ++ ++++r+l  +r  gv+ev++  g+  +++++     +++ ++ ++++e+  
  gi|13541266|ref|NP_110954.1|   3 GAILAGGYGKRLKpiTdsiPKALVEIkDNYTIMDRQLFDFRNIGVKEVYILSGYlgNKIEErygdLYNDMNMYYLREEK-P 82 
                                   68**********8551459*******9999**********************998855665222255666899999986.5 PP

                                   -SHHHHHHHHHHHH.SSSCEEEEETT-T CS
                  NTP_transf_3  70 kgplaslaaalraaadadavlvlacDmP 97 
                                    g+l+sl+  l++  ++d +++  +D++
  gi|13541266|ref|NP_110954.1|  83 LGTLYSLRNLLDKR-SDDDIILRNGDTI 109
                                   9***********97.7899999888884 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       532  (0.0296726); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 2152.94
//
Query:       gi|13541267|ref|NP_110955.1|  [L=445]
Description: major facilitator superfamily permease [Thermoplasma volcanium GSS1]
Scores for complete 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-56  192.0  29.2    2.5e-56  191.5  29.2    1.1  1  Sugar_tr  Sugar (and other) transporter
    1.9e-37  129.0  46.7    2.5e-28   99.1  20.2    2.0  2  MFS_1     Major Facilitator Superfamily
      0.001   17.7  34.4     0.0049   15.5   4.8    3.8  4  MFS_2     MFS/sugar transport protein
  ------ inclusion threshold ------
       0.18   10.2  12.7      0.011   14.2   4.2    2.2  2  TRI12     Fungal trichothecene efflux pump (TRI12)
        1.1    7.6   3.2        1.7    6.9   3.2    1.3  1  CBP_BcsG  Cellulose biosynthesis protein BcsG
        2.5    7.4   6.0        4.8    6.4   0.1    2.6  2  DUF3810   Protein of unknown function (DUF3810)


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 !  191.5  29.2   8.3e-60   2.5e-56       3     448 ..      21     440 ..      19     442 .. 0.89

  Alignments for each domain:
  == domain 1  score: 191.5 bits;  conditional E-value: 8.3e-60
                                   HHHHHHHHHHHHHHHCGGGTHHHHHHHHTSTT--SHHHHHH...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHH CS
                      Sugar_tr   3 lvaalggllfgYdtgvigafltllkfaknfglsksksskeessvlsglivsiflvGaiiGslfagllgdrfGRkkslliaa 83 
                                   ++a++g +l gYd+ vi  ++ l+ ++ +fg   +            l+  ++++G iiG+ ++g l+dr+GRkk++ i  
  gi|13541267|ref|NP_110955.1|  21 ILASMGMFLDGYDLSVITMAILLMPTQLHFGKLDY-----------ILVNVSAFIGMIIGAPLLGRLSDRIGRKKIFGIDL 90 
                                   6799999******************8888875544...........47888899*************************** PP

                                   HHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTS CS
                      Sugar_tr  84 vlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlvPmyisEiApkklRgalvslyqlaitfGilvaaifglglnkt 164
                                   +lfv+ a+  ++a+   ++ +l+++R+ +Gig+G+ + ++++ +sE++p ++Rg+l      ++ +G +++a++++ ++ t
  gi|13541267|ref|NP_110955.1|  91 LLFVVFAITAGLAT---NFAMLFISRLMLGIGIGGDYPISSTMVSEFSPVSKRGTLLYGMVGMYWLGSFFSAVMNYTFAFT 168
                                   **************...**************************************************************** PP

                                   S-TTHHHHHHHCCHHHHHHHHHHGGGS---HHHHHHTT-HHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHH.....HTTH CS
                      Sugar_tr 165 snadgwrillglqlvpallllilllflPESPrylvekgkeeeakevlaklrgeedadrelaeekdsleaeqeeekaswkel 245
                                    +   wr+++ +  v+a+ +++l++ +PESPr+l+ +g ++ a+ v+++    ++++++++e k++ e+e   e+++ ++l
  gi|13541267|ref|NP_110955.1| 169 PY--FWRYTFIVGGVIAIPIIFLRMRIPESPRWLIGHGMTKSAESVVED---LTGRKPDVEEGKAEAEQE---ESVKFSSL 241
                                   **..9********************************************...677778888888888888...34568888 PP

                                   HHHSH...HHHHHHHHHHHHHHTTHHHHHHHTTTHHHHSS-THH..........HHHHHHHHHHHHHHHHHHHHHHHHS-S CS
                      Sugar_tr 246 lssktvrqrlligvvlqifqqltGinaimyysptifenlglsks..........llvtiivgvvnfvatfvaiflvdrfGR 316
                                   +ssk     +++  v  +f   ++   i +y pt++++lgl             ++ ++iv v  ++  +va++l dr+GR
  gi|13541267|ref|NP_110955.1| 242 FSSKFLASTIFVLSVWFLFDVASY--GIGFYYPTLIDKLGLASHvlntaglraiAESSMIVAVGAILGYLVAMPLADRIGR 320
                                   888544444444444444444444..6666667788888888888888888888999************************ PP

                                   HHHHHHHHHHHHHHHHHHH..HHHHTTSS...CHHHHHHHHHHHHHHHTTTTHHHHHHHHHHSHTTTHHHHHHHHHHHHHH CS
                      Sugar_tr 317 RtllllGaagmaicfvilgivalllvakskaasivaivfialfialfalgwgpvpwvlvsElfpqsvRskalaiavavnwl 397
                                   R l + G+++m++++++ +     +v+ s   + + +v++++ ++lf+  +g    ++ +Elfp++ Rs+ + ia+ v+ +
  gi|13541267|ref|NP_110955.1| 321 RILTISGLFVMFLLLLLGS-----VVKIS---TLLPVVAFFFSFVLFEQWVGAATLFYPTELFPTNYRSTIQGIATSVSRV 393
                                   *999999999999887776.....33333...6789999999999************************************ PP

                                   HHHHHHHHHHHHHCHHHT-HHHHHHHHHHHHHHHHHHHHS--STT--CCCC CS
                      Sugar_tr 398 anflisllfpiiteaigggyvflvfaglavlfiifvfffvpetkgrtleei 448
                                     +   ++fp        + + ++fa+l++l++i+ ++f petk  +le+i
  gi|13541267|ref|NP_110955.1| 394 GAIMGIVVFPLYP----VFHSIFIFAILMALALIISVIFAPETKKTPLEKI 440
                                   ***9999999865....46669***************************98 PP

>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.1  20.2   8.2e-32   2.5e-28       3     253 ..      25     294 ..      23     302 .. 0.86
   2 !   35.0  20.5   2.4e-12   7.2e-09      39     182 ..     298     437 ..     292     444 .. 0.82

  Alignments for each domain:
  == domain 1  score: 99.1 bits;  conditional E-value: 8.2e-32
                         MFS_1   3 laaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll.fa 82 
                                   ++ fl +++ s++++a+  ++ ++l++ +  + l+ +  ++g+++++++lGrlsdr+Gr++++ + lllf+++ ++ + +a
  gi|13541267|ref|NP_110955.1|  25 MGMFLDGYDLSVITMAIL-LMPTQLHFGKLDYILVNVSAFIGMIIGAPLLGRLSDRIGRKKIFGIDLLLFVVF-AITAgLA 103
                                   789**************9.999***************************************************.5555476 PP

                         MFS_1  83 sslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllgglla.sslgWravfyilaivsl 162
                                   +++ +l+++r++ G+g g+ +p++ +++++ +p ++rg  +  + +++ lG+ + ++    +a + + Wr++f++ +++++
  gi|13541267|ref|NP_110955.1| 104 TNFAMLFISRLMLGIGIGGDYPISSTMVSEFSPVSKRGTLLYGMVGMYWLGSFFSAVMNYTFAfTPYFWRYTFIVGGVIAI 184
                                   7777*************************************9999***************99988888************* PP

                         MFS_1 163 lafvlfllllpeepperkrkspkeee....................kgtgpaplvpawkallkdpvlw...illialllff 220
                                     +    l ++ ++++r+   +   +                    +  ++ + v+ +++l+++++l    ++l +++lf 
  gi|13541267|ref|NP_110955.1| 185 PIIF---LRMRIPESPRWLIGHGMTKsaesvvedltgrkpdveegkAEAEQEESVK-FSSLFSSKFLAstiFVLSVWFLFD 261
                                   *977...8889999999999998888999999988888888766665555555555.999999998854556888888888 PP

                         MFS_1 221 fgfsglltllplylqevlgls.glllaglllall 253
                                   ++ +g+ ++ p+ l + lgl+  +l +++l a++
  gi|13541267|ref|NP_110955.1| 262 VASYGIGFYYPT-LIDKLGLAsHVLNTAGLRAIA 294
                                   88888*******.5*******7545555554444 PP

  == domain 2  score: 35.0 bits;  conditional E-value: 2.4e-12
                         MFS_1  39 tlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfa..sslwlllvlrvlqGlgagalfpagaaliadwfpke 117
                                    ++a+ga+++ l++++l+dr+Grr + + gl++++l lll++++  s+l +++++ +   l++ ++ +a + + +++fp +
  gi|13541267|ref|NP_110955.1| 298 MIVAVGAILGYLVAMPLADRIGRRILTISGLFVMFLLLLLGSVVkiSTLLPVVAFFFSFVLFEQWVGAATLFYPTELFPTN 378
                                   57899********************77777777777746666557577669****************************** PP

                         MFS_1 118 ergraigllsagfslGailgpllggllasslgWravfyilaivsllafvlfllllpeepperkrk 182
                                    r+   g++++ + +Gai+g ++ +l      ++++f+++ +++l +++    +++++++++ + 
  gi|13541267|ref|NP_110955.1| 379 YRSTIQGIATSVSRVGAIMGIVVFPLYP---VFHSIFIFAILMALALII---SVIFAPETKKTPL 437
                                   ********************77777554...488998888888888777...6666666555544 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   4.8   1.6e-06    0.0049     261     341 ..      55     133 ..      37     151 .. 0.87
   2 ?   -2.5   2.5      0.45   1.4e+03     233     334 ..     154     183 ..     111     199 .. 0.61
   3 !   15.4   5.5   1.7e-06    0.0052     198     325 ..     224     357 ..     211     377 .. 0.78
   4 !    4.2   1.6    0.0044        13     132     199 ..     380     435 ..     376     445 .] 0.63

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.6e-06
                         MFS_2 261 asvfllvvtisallgiplwqplakrlgkkntyllgalltivllvlvlllqpsnlllflvllviagfgvgvaallpwsmlad 341
                                   + ++ + ++i++++g+pl  +l  r+g+k+++ + +ll +v+ + + l+  +n +++++  ++ g+g+g+ + +   m+++
  gi|13541267|ref|NP_110955.1|  55 YILVNVSAFIGMIIGAPLLGRLSDRIGRKKIFGIDLLLFVVFAITAGLA--TNFAMLFISRLMLGIGIGGDYPISSTMVSE 133
                                   55677889***********************999999888888888777..9*******9999999999888888888765 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.45
                         MFS_2 233 fllaalalgvlnglllYyltyvlgngsaasvfllvvtisallgiplwqplakrlgkkntyllgalltivllvlvlllqpsn 313
                                   ++++++                                                                          n
  gi|13541267|ref|NP_110955.1| 154 GSFFSA------------------------------------------------------------------------VMN 162
                                   222222........................................................................245 PP

                         MFS_2 314 lllflvllviagfgvgvaall 334
                                   ++++++ ++  ++++++ +++
  gi|13541267|ref|NP_110955.1| 163 YTFAFTPYFWRYTFIVGGVIA 183
                                   555555555555554444444 PP

  == domain 3  score: 15.4 bits;  conditional E-value: 1.7e-06
                         MFS_2 198 emrkkekteqkeklslleqlkevfrnraflillllfllaalalgvlnglllY.....yltyvlg..ngsaasvfllvvtis 271
                                   e + k ++eq+e+++++  + + f      +l + fl+ ++++g+++    +      + +vl+    +a++ ++++v ++
  gi|13541267|ref|NP_110955.1| 224 E-EGKAEAEQEESVKFSSLFSSKFLASTIFVLSVWFLFDVASYGIGFYYPTLidklgLASHVLNtaGLRAIAESSMIVAVG 303
                                   3.5778888889999999999999998888888888888888888775444422223789999963336788899****** PP

                         MFS_2 272 allgiplwqplakrlgkkntyllgalltivllvlvlllqpsnlllflvllviag 325
                                   a+lg +++ pla r+g++ ++++g+ ++++ll+l  +++ s ll+++++++ + 
  gi|13541267|ref|NP_110955.1| 304 AILGYLVAMPLADRIGRRILTISGLFVMFLLLLLGSVVKISTLLPVVAFFFSFV 357
                                   ***********************************9997777777666655443 PP

  == domain 4  score: 4.2 bits;  conditional E-value: 0.0044
                         MFS_2 132 RtsltsvrsflsvlggvlaailafllvlilgglkserkgylifaliialLmllgviivvlgtkervem 199
                                   R++++++   +s +g +++ i++f+l  ++             ++i+a+Lm+l+ ii+v++  e ++ 
  gi|13541267|ref|NP_110955.1| 380 RSTIQGIATSVSRVGAIMG-IVVFPLYPVFH-----------SIFIFAILMALALIISVIFAPETKKT 435
                                   5555555555555554433.33344433333...........47999999999999999999988654 PP

>> TRI12  Fungal trichothecene efflux pump (TRI12)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   4.2   3.5e-06     0.011      90     235 ..      65     210 ..      55     219 .. 0.72
   2 ?    0.8   1.3     0.042   1.2e+02      84     137 ..     297     349 ..     281     433 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.5e-06
                         TRI12  90 gqavsilvmgrltdrfgrrpfvilthilglvgaivgctatkfntllaamtllgvaagpa.gasplfvgelmsnktkflgll 169
                                   g  +   ++grl+dr+gr+ +  +  +l +v ai    at+f  l+ +  +lg+  g     s  +v e+ s  +k   ll
  gi|13541267|ref|NP_110955.1|  65 GMIIGAPLLGRLSDRIGRKKIFGIDLLLFVVFAITAGLATNFAMLFISRLMLGIGIGGDyPISSTMVSEF-SPVSKRGTLL 144
                                   556666789***********99999*****************************8775415566677775.4444444444 PP

                         TRI12 170 ivsipvvvtsglspylgqrlaiqgswrwif..yiyiitsaiavllivvwy.yppsfaqlhgkkvrkree 235
                                        +v +  l+ ++   +    ++   f  y +i+   ia+ +i +    p s + l g+ ++k  e
  gi|13541267|ref|NP_110955.1| 145 Y---GMVGMYWLGSFFSAVMNYTFAFTPYFwrYTFIVGGVIAIPIIFLRMrIPESPRWLIGHGMTKSAE 210
                                   3...45666667777777666666555444226678888888888877651466777777777776665 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.042
                         TRI12  84 stlwttgqavsilvmgrltdrfgrrpfvilthilglvgaivgctatkfntllaa 137
                                   s + ++g  +  lv   l+dr+grr + i    + ++  ++g    k+ tll  
  gi|13541267|ref|NP_110955.1| 297 SMIVAVGAILGYLVAMPLADRIGRRILTISGLFVMFLLLLLGS-VVKISTLLPV 349
                                   55667888889999999********999987666665555554.3466666654 PP

>> CBP_BcsG  Cellulose biosynthesis protein BcsG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   3.2   0.00058       1.7       3     120 ..     256     370 ..     255     394 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.00058
                      CBP_BcsG   3 lYFllklaLllagylkfhlllnllflallllplrskllrklrqliaipvglaLlyhdswlPplerllsqasqlagfslsYl 83 
                                   ++Fl+ +a + +g    +l+  l ++  +l +   + +      + ++vg++L y    +P  +r+ + +  ++g+ + +l
  gi|13541267|ref|NP_110955.1| 256 VWFLFDVASYGIGFYYPTLIDKLGLASHVLNTAGLRAIAES--SMIVAVGAILGYL-VAMPLADRIGRRILTISGLFVMFL 333
                                   67777777788888777777777777777766666655544..4555678888887.679********************* PP

                      CBP_BcsG  84 vellgrfinlkmllalivllivylllsqwirvttlvl 120
                                   + llg ++++++ll +++ +  ++l++qw+  +tl +
  gi|13541267|ref|NP_110955.1| 334 LLLLGSVVKISTLLPVVAFFFSFVLFEQWVGAATLFY 370
                                   ******************************9888764 PP

>> DUF3810  Protein of unknown function (DUF3810)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.1    0.0016       4.8      12     109 ..     160     296 ..     150     301 .. 0.63
   2 ?    2.8   1.1      0.02        60      12      45 ..     392     428 ..     379     443 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0016
                       DUF3810  12 ilsrlsglfpFSvgellivllillvilylvlai........klkkrkkkkkrllk.......................... 58 
                                   ++++ + + p+     +iv  ++++ +++++++        +                                       
  gi|13541267|ref|NP_110955.1| 160 VMNYTFAFTPYFWRYTFIVGGVIAIPIIFLRMRipesprwlI------------Ghgmtksaesvvedltgrkpdveegka 228
                                   444555555555555555555555555544444444444431............123333344444455566666666666 PP

                       DUF3810  59 .................vllrvllvllvvyflftllwglnYyreplserlglkkeeyseeelaelaek 109
                                                    +l ++++vl+v +++ ++ +g+ +y ++l ++lgl+++  +++ l+++ae+
  gi|13541267|ref|NP_110955.1| 229 eaeqeesvkfsslfsskFLASTIFVLSVWFLFDVASYGIGFYYPTLIDKLGLASHVLNTAGLRAIAES 296
                                   666666666777776657777777777777777889****************9999999999998875 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.02
                       DUF3810  12 ilsrlsglfpFSvgellivllillvilylvlai...k 45 
                                    +++++g++ F ++ ++  ++i++++++l+l+i   +
  gi|13541267|ref|NP_110955.1| 392 RVGAIMGIVVFPLYPVFHSIFIFAILMALALIIsviF 428
                                   57899*************9999999999999995321 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (445 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       831  (0.0463495); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                        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: 0.69u 0.31s 00:00:01.00 Elapsed: 00:00:00.49
# Mc/sec: 2731.17
//
Query:       gi|13541268|ref|NP_110956.1|  [L=407]
Description: RNA processing exonuclease [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-12   47.5   0.0    2.7e-12   46.5   0.0    1.6  1  RMMBL            Zn-dependent metallo-hydrolase RNA specifici
    1.6e-12   47.7   0.0    3.1e-12   46.7   0.0    1.5  1  Beta-Casp        Beta-Casp domain
    3.2e-11   43.1   0.0    3.2e-09   36.6   0.0    2.2  2  Lactamase_B_2    Beta-lactamase superfamily domain
      6e-10   38.9   0.0    9.3e-10   38.2   0.0    1.3  1  Lactamase_B_6    Metallo-beta-lactamase superfamily domain
    1.6e-06   28.3   0.0    2.9e-06   27.4   0.0    1.5  1  Lactamase_B      Metallo-beta-lactamase superfamily
     0.0012   18.7   0.1     0.0081   16.1   0.0    2.3  2  Lactamase_B_3    Beta-lactamase superfamily domain
  ------ inclusion threshold ------
      0.022   13.9   0.1      0.036   13.2   0.1    1.3  1  PDEase_II        cAMP phosphodiesterases class-II
      0.061   12.6   0.0       0.11   11.7   0.0    1.4  1  Beta_lactamase3  Putative beta-lactamase-like family


Domain annotation for each model (and alignments):
>> RMMBL  Zn-dependent metallo-hydrolase RNA specificity domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.5   0.0   1.2e-15   2.7e-12       3      43 ..     345     385 ..     343     399 .. 0.92

  Alignments for each domain:
  == domain 1  score: 46.5 bits;  conditional E-value: 1.2e-15
                         RMMBL   3 pvkarieeidfSgHadknellelirklkprnvilvHGeeea 43 
                                   + k+r+e++d+S+Ha+++el  +i+ ++p++v+l HG++++
  gi|13541268|ref|NP_110956.1| 345 KPKMRVEFFDMSAHAGHDELVSFIKAINPEKVVLMHGDHRE 385
                                   679***********************************997 PP

>> Beta-Casp  Beta-Casp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.7   0.0   1.4e-15   3.1e-12      22     110 .]     236     331 ..     222     331 .. 0.72

  Alignments for each domain:
  == domain 1  score: 46.7 bits;  conditional E-value: 1.4e-15
                                   -EEEEE-HHHHHHHHHGGGGGG..............E-SHH....HHH.H..HHHS-SSEEEEES-TTSSSSHHHHHHHHH CS
                     Beta-Casp  22 lpiyldsplaskatevYkeyae..............veakslewmesk.keelnsskgpkvilassgmlegGrsrellkkl 87 
                                   + + +d+ +++++ ++Y + +               v++ +     ++ + e  +  +  +i+++sgml+gG++  +++kl
  gi|13541268|ref|NP_110956.1| 236 YDVSVDG-MGNDISSIYLNTPGflkskrdflralgkVREVK----GRRmR-E--NAINSDIIISTSGMLDGGPVLGYIQKL 308
                                   4566677.777888887777777765555555544322222....22212.2..223568********************* PP

                                   TTSTTSEEEESS---TTSHHHHH CS
                     Beta-Casp  88 ledprntvilvgyqaegTlgrkl 110
                                   +ed++++++ +gyq+egT gr+l
  gi|13541268|ref|NP_110956.1| 309 MEDEKSAIFVTGYQVEGTNGRSL 331
                                   ********************986 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.6   0.0   1.4e-12   3.2e-09      28     174 ..      44     193 ..      31     217 .. 0.73
   2 ?    4.4   0.0     0.011        24     125     200 ..     301     380 ..     291     381 .. 0.71

  Alignments for each domain:
  == domain 1  score: 36.6 bits;  conditional E-value: 1.4e-12
                                   ..SEEEEE-SS--HHHHGGGGCCCC.C--EEEEEEEEHHHHH.............HCCTTCGHHHCHTT.....TTEEEEE CS
                 Lactamase_B_2  28 lppidaVllthaHyDHlaglltlre.lrpkklplyapkgvla.............vleanfvylaleee.....pavnvhe 89 
                                   ++p+da ++th+H DH+  ++   + ++p   +lya++++l              +le      a+ +e     +  n+++
  gi|13541268|ref|NP_110956.1|  44 PEPVDAMFITHSHLDHIGAIPVYYHkGEP---DLYATQMTLNcmkpllndslkvtNLEGY---PAMFNEddintALANMKP 118
                                   67***************888888885555...69******99777777777743333333...333333565555666666 PP

                                   E-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S---HHHHHHHCT..-SEEEEE-S-SS CS
                 Lactamase_B_2  90 ldwgesfelgdggleitatparhksgrrldrnagdtlGlriegggkrvyyigDtgyipeeigerlgg..adllllditaye 168
                                       esf++g  ++++t+ pa h  g          + + +e +gk++  +gD+++i+  + +  ++   d+l+++ t+  
  gi|13541268|ref|NP_110956.1| 119 ARYFESFDVG--DFKVTPYPAGHIPGS---------AMWKFE-DGKSITVTGDVNTIDTYLINGAKPikTDVLIIESTYAG 187
                                   6677777777..566777777777777.........99****.9**************998878887679******99988 PP

                                   TTHHHH CS
                 Lactamase_B_2 169 ddemir 174
                                   ++  +r
  gi|13541268|ref|NP_110956.1| 188 KNHESR 193
                                   777665 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.011
                                   SEEEEEE..CTTEEEEEESS-S---HHHHHHHCT-SEEEEE-S-SSTTHHHH....HHT---STSHHHHCTTSSSSEEEEE CS
                 Lactamase_B_2 125 tlGlrie..gggkrvyyigDtgyipeeigerlggadllllditayeddemir....hmgHltpeeaveaaadlgakrlvli 199
                                   +lG++ +  +++k++ ++++ +      + +l++  +++  +t  +++ m+        H+  +e v ++++++++++vl+
  gi|13541268|ref|NP_110956.1| 301 VLGYIQKlmEDEKSAIFVTGYQVEGTNGRSLLENGTITVAGVT-MKPK-MRVeffdMSAHAGHDELVSFIKAINPEKVVLM 379
                                   6666666667777788888877544556677777777775555.3333.33346866779999****************** PP

                                   S CS
                 Lactamase_B_2 200 H 200
                                   H
  gi|13541268|ref|NP_110956.1| 380 H 380
                                   * 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 !   38.2   0.0   4.2e-13   9.3e-10      35     173 ..      46     171 ..      21     185 .. 0.83

  Alignments for each domain:
  == domain 1  score: 38.2 bits;  conditional E-value: 4.2e-13
                 Lactamase_B_6  35 tvdliLLshatlehlGayallyakfksklllnipvyatlpvvkLGrvslldlyaskgllgpedseeleledideafdkikt 115
                                    vd+  ++h+ l+h+Ga ++ y+k       +   yat+ + +  + +l d+ + ++l+g    + ++ +di++a  ++k+
  gi|13541268|ref|NP_110956.1|  46 PVDAMFITHSHLDHIGAIPVYYHK------GEPDLYATQMTLNCMKPLLNDSLKVTNLEGYP--AMFNEDDINTALANMKP 118
                                   599**************8744443......36789*********************999855..46899************ PP

                 Lactamase_B_6 116 lkYsQklelkskldgltitaynaGhtlGGtiWkiskesekivYavdwnhakeshLnga 173
                                    +Y  ++++ +      +t+y aGh +G ++Wk +++  +i    d+n     ++nga
  gi|13541268|ref|NP_110956.1| 119 ARYFESFDVGD----FKVTPYPAGHIPGSAMWKFEDGK-SITVTGDVNTIDTYLINGA 171
                                   ******99985....89****************98764.4555666666666666655 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.0   1.3e-09   2.9e-06      15      71 ..      23      73 ..      18     160 .. 0.84

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 1.3e-09
                                  TCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCE CS
                   Lactamase_B 15 ggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvp 71
                                  ++ +++D G+ ++++ +         +p++vda ++TH+HlDHiG+ +   ++    
  gi|13541268|ref|NP_110956.1| 23 NTSVIVDYGVIPDKPPQY------PMPPEPVDAMFITHSHLDHIGAIPVYYHKGEPD 73
                                  566677777777777766......689*******************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 !   16.1   0.0   3.6e-06    0.0081      11      52 ..      18      62 ..      12     155 .. 0.84
   2 ?   -0.5   0.0      0.45     1e+03     142     163 .]     359     380 ..     352     380 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 3.6e-06
                 Lactamase_B_3 11 lletagarilvDPf...kanlgyeppaeeaDlvlisqaledHahl 52
                                   +++++++++vD++   ++  +y  p+e +D+  i++++ dH  +
  gi|13541268|ref|NP_110956.1| 18 KITDRNTSVIVDYGvipDKPPQYPMPPEPVDAMFITHSHLDHIGA 62
                                  68899*********776447899999****************755 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.45
                 Lactamase_B_3 142 lgqeealelakrLkpklvlPmh 163
                                    g +e +  +k+++p+ v+ mh
  gi|13541268|ref|NP_110956.1| 359 AGHDELVSFIKAINPEKVVLMH 380
                                   57889999***********998 PP

>> PDEase_II  cAMP phosphodiesterases class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   1.6e-05     0.036      81      97 ..      47      63 ..      44      92 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.6e-05
                                  EEEEE-S---GGGTHHH CS
                     PDEase_II 81 iksylItHsHLDHvsgl 97
                                  +   +ItHsHLDH++++
  gi|13541268|ref|NP_110956.1| 47 VDAMFITHSHLDHIGAI 63
                                  5678**********986 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 ?   11.7   0.0     5e-05      0.11      60     199 ..      46     183 ..      41     196 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5e-05
               Beta_lactamase3  60 nidkifvtssn.....slgifFlkkdvpiYiTkpvYeqlllrlkellslqvvyeeeeekqdlkiveeidierlkrnvkfir 135
                                    +d +f+t+s      ++ +++ k + ++Y T+     ++  l++ l++      e       + +e di+ +  n+k  r
  gi|13541268|ref|NP_110956.1|  46 PVDAMFITHSHldhigAIPVYYHKGEPDLYATQMTLNCMKPLLNDSLKVTN---LEGY---PAMFNEDDINTALANMKPAR 120
                                   577777777744444467788888888888888888777777776544332...2333...3578999************* PP

               Beta_lactamase3 136 yneliyfddltieakaagtflGWvnyllevekkkilayissl.slkkklslemkpiksdvlllnv 199
                                   y e + + d+++++ +ag   G  ++++e +k +  + +  + +++  l    kpik+dvl++  
  gi|13541268|ref|NP_110956.1| 121 YFESFDVGDFKVTPYPAGHIPGSAMWKFEDGKSI--TVTGDVnTIDTYLINGAKPIKTDVLIIES 183
                                   **************************99887766..666666155666677899******99854 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (407 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 2498.05
//
Query:       gi|13541269|ref|NP_110957.1|  [L=257]
Description: 5'-methylthioadenosine phosphorylase II [Thermoplasma volcanium GSS1]
Scores for complete 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-48  162.5   0.0      1e-47  162.4   0.0    1.0  1  PNP_UDP_1  Phosphorylase superfamily
  ------ inclusion threshold ------
       0.14   12.0   0.0       0.29   11.0   0.0    1.4  1  CutA1      CutA1 divalent ion tolerance protein


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 !  162.4   0.0   1.1e-51     1e-47       2     229 ..       4     233 ..       3     238 .. 0.95

  Alignments for each domain:
  == domain 1  score: 162.4 bits;  conditional E-value: 1.1e-51
                                   EEEEESSH.HHHHHHHHHEEEEEEEEEE.TTEEEEEEEETTEEE.EEEE--....SSHHHHHHHHHHHHHHHC--SEEEEE CS
                     PNP_UDP_1   2 iaiivgsp.gevellaespleetpfgregrgfkfvtGtlkgkpv.vivstG....iGkpnaavvaeirllkefgvkaiiri 76 
                                   i+ii+gs+ +++ + +++   +tp+g++  +  + +G+++g++v ++ ++G    i ++ ++++a+i++l+++gv++ii  
  gi|13541269|ref|NP_110957.1|   4 IGIIGGSGlYDLMAESKKVDVDTPYGKP--SDLIEIGEVNGVEVaFLPRHGkkhtIPPHKVNYRANIWALHDLGVERIIGL 82 
                                   9*******87777777779*********..*********8888879*********************************** PP

                                   EEEEESSTTT-TT-EEEEEEEEESSSCCGCCTHHCCTCCCCTTSSEE--HHHHHHHHHCHHTTTTTEEE.EEEEEESESS- CS
                     PNP_UDP_1  77 GtaGglnpdlkvGDvvipddainfdgrsplygpkeegqyfpdsydapadpelrallkeaaealgikvhr.Gvvatadgfya 156
                                   +++G+l++d+k+GD+vipd++i+f+ r+ l++++ + +y++ ++d+ ++pe+ +l  + a+ l i+vh  G+++t +g+++
  gi|13541269|ref|NP_110957.1|  83 NAVGSLREDYKPGDIVIPDQYIDFTKRRELTFYDGPQVYHISEADP-FCPEMNELFYQTAKNLKIPVHNtGTYITIEGPRF 162
                                   ************************************9999999999.*********************99*********** PP

                                   CHHHHHHHHHHTC-CEEESSHHHHHHHHHHTT--EEEEEEEEETTTBETTCTCH.HCCCHHHHHHHHHHHHHH CS
                     PNP_UDP_1 157 eteaelrllrrlgadaveMEtaavaqlArelgipfaairvvsdlaaggadaeatheeveefaqeaaknaaall 229
                                   +t+ae++++r++  d+++M+ ++++ lA el +++ +i++++d ++ + +++ + +ev+  ++++ k++  +l
  gi|13541269|ref|NP_110957.1| 163 STRAESKMFRQFA-DIIGMTLVPEVGLAGELALCYSVIASITD-YDVWSEKPVDAREVMTIMKQNDKKVRDIL 233
                                   ************9.*****************************.888*******9999999999988887776 PP

>> CutA1  CutA1 divalent ion tolerance protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   3.3e-05      0.29      22      65 ..     189     232 ..     180     237 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 3.3e-05
                                   HTTS-SEEEEEEEEEEEEEETTEEEEEEEEEEEEEEEGGGHHHH CS
                         CutA1  22 eeklaACvnilpkieSvYrWkgkieedkEvllliktreekveel 65 
                                   + +la C +++ +i+ + +W +k  +++Ev+ ++k +++kv ++
  gi|13541269|ref|NP_110957.1| 189 AGELALCYSVIASITDYDVWSEKPVDAREVMTIMKQNDKKVRDI 232
                                   6689**********************************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); 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: 1692.98
//
Query:       gi|13541270|ref|NP_110958.1|  [L=236]
Description: asparagine synthase, partial [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.8e-16   59.4   0.1      1e-07   32.0   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 !   32.0   0.0   5.6e-12     1e-07      23     138 ..      26     133 ..      22     143 .. 0.83
   2 !   25.7   0.0   4.5e-10     8e-06     213     293 ..     142     222 ..     134     231 .. 0.89

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 5.6e-12
                  Asn_synthase  23 lLSGGlDSSliaalaarqsksplktFsigfeekgsdeakyakevaehlgtehtelvlteeelldalpdviyhlee..pfad 101
                                    +SGGlDSSl+  + +r    +l  +++g+    s ++  ak v   l+     + l+e  +++    ++++l    p ++
  gi|13541270|ref|NP_110958.1|  26 AFSGGLDSSLLYVISDR----NLVPYTVGY--SFSHDVNRAKFVLSLLNGSGKYVTLDEINIEN----YVKYLKSeyPDIN 96 
                                   68***************....5678*****..*******************7555555555544....444444336999* PP

                  Asn_synthase 102 rsaiplyllsrla.krkgvkvvLsGeGaDElfgGYpyf 138
                                   + +i+  l+ + + ++ ++  + +G+GaDElf GY+ +
  gi|13541270|ref|NP_110958.1|  97 KVEISFELVLEILlENVDSDLLVTGQGADELFFGYK-R 133
                                   *****999999987899999***************9.4 PP

  == domain 2  score: 25.7 bits;  conditional E-value: 4.5e-10
                  Asn_synthase 213 ldlktllpgdllrkDrasmahglEaRvPflDhrlvevalrlppelklrggieKyiLRealegy.lPeeileRpKegfsapv 292
                                   l++++ll+ ++ r+  ++ ++g E+ +PflD+r++++a ++ p++      +K  LRe+++   lPee++  +K+++++++
  gi|13541270|ref|NP_110958.1| 142 LQMERLLKRTIPREKDMAKRQGKELVTPFLDDRILKLASEISPAYHCL-YGGKKALREIAKIAgLPEEVYGYRKKAAQYGS 221
                                   568999***************************************987.789999*****9988******99999999876 PP

                  Asn_synthase 293 g 293
                                   g
  gi|13541270|ref|NP_110958.1| 222 G 222
                                   6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       479  (0.0267165); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1593.35
//
Query:       gi|13541271|ref|NP_110959.1|  [L=593]
Description: ATPase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.1e-09   35.3   0.4    1.5e-08   34.0   0.1    1.8  2  T2SSE            Type II/IV secretion system protein
    9.7e-08   31.7   2.7    4.9e-07   29.5   2.7    2.3  1  KH_1             KH domain
    7.5e-05   23.0   0.0    0.00047   20.4   0.0    2.3  2  PIN_4            PIN domain
     0.0001   22.1   0.7     0.0004   20.2   0.2    2.4  1  KH_4             KH domain
    0.00034   19.7   0.0    0.00075   18.6   0.0    1.5  1  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
    0.00038   20.3   0.0      0.001   18.9   0.0    1.7  2  ATP_bind_1       Conserved hypothetical ATP binding protein
    0.00039   20.7   0.2     0.0029   17.9   0.1    2.4  2  PIN_9            PIN like domain
    0.00055   20.4   0.0      0.001   19.5   0.0    1.5  1  AAA_16           AAA ATPase domain
     0.0011   19.5   0.0     0.0079   16.7   0.0    2.3  2  AAA_18           AAA domain
     0.0036   16.7   0.0     0.0077   15.6   0.0    1.5  1  FtsK_SpoIIIE     FtsK/SpoIIIE family
     0.0043   16.8   0.0      0.013   15.2   0.0    1.8  1  AAA_29           P-loop containing region of AAA domain
     0.0045   16.3   0.0     0.0092   15.3   0.0    1.5  1  Zeta_toxin       Zeta toxin
      0.005   16.8   0.0       0.17   11.8   0.0    2.8  2  NTPase_1         NTPase
     0.0075   16.8   0.1      0.031   14.8   0.0    2.0  2  ABC_tran         ABC transporter
     0.0093   15.7   0.2      0.026   14.2   0.0    1.8  1  AAA_30           AAA domain
  ------ inclusion threshold ------
      0.011   15.4   0.1      0.049   13.3   0.0    2.1  2  Thymidylate_kin  Thymidylate kinase
      0.015   15.6   0.0      0.056   13.7   0.0    2.0  1  AAA_22           AAA domain
      0.015   15.4   3.4      0.026   14.6   0.7    2.8  2  KH_5             NusA-like KH domain
      0.015   14.5   0.0      0.027   13.6   0.0    1.3  1  DUF815           Protein of unknown function (DUF815)
      0.044   13.9   0.0       0.11   12.6   0.0    1.7  1  MMR_HSR1         50S ribosome-binding GTPase
      0.048   13.7   0.0        0.1   12.6   0.0    1.5  1  AAA_5            AAA domain (dynein-related subfamily)
      0.052   13.3   0.0       0.12   12.1   0.0    1.6  1  PRK              Phosphoribulokinase / Uridine kinase family
      0.054   13.5   0.0       0.14   12.1   0.0    1.7  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
      0.068   13.3   0.0       0.21   11.8   0.0    1.8  1  AAA_33           AAA domain
      0.081   12.7   0.0       0.15   11.7   0.0    1.5  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase
      0.089   12.2   0.0       0.17   11.3   0.0    1.4  1  KTI12            Chromatin associated protein KTI12
       0.17   11.4   0.2        0.4   10.2   0.2    1.6  1  AAA_25           AAA domain
        1.2    9.0   8.2       0.68    9.8   4.2    2.7  2  KH_2             KH domain


Domain annotation for each model (and alignments):
>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       2.3   1.5e+03      22      86 ..      64     128 ..      60     135 .. 0.62
   2 !   34.0   0.1   2.4e-11   1.5e-08      76     243 ..     210     366 ..     169     394 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 2.3
                         T2SSE  22 pervkvrervdgielreveelekaalerlisriaalakldiseerplq.darlpekgvrlrvvllP 86 
                                   ++++ ++   ++ +  ++++ ++ ++  +i+++a+   +++ +  ++q d ++  kg+ ++++ +P
  gi|13541271|ref|NP_110959.1|  64 EGKISIEIEGERPKEWQIKRAKSGEIDEMIRQVAFQYDATLVTGDIIQrDVAIV-KGITVEYLSPP 128
                                   556666333333555567777777777777777777777766666665345555.77777777766 PP

  == domain 2  score: 34.0 bits;  conditional E-value: 2.4e-11
                         T2SSE  76 kgvrlrvvllPvvag.ealviRkksakeltlddlgaeealkekiaevlrkavrerglilvsGgTgsGKttllyallkeink 155
                                   k++r+ +  +P + + e  ++R     +l +d +  + ++ke+    l++       ilv+G  g GK+t++ al +++n+
  gi|13541271|ref|NP_110959.1| 210 KNIRIVITRPPFSDDmEITAVR--PIVKLGIDYYELNDKVKER----LEST---ANGILVAGSPGAGKSTFVQALAEFFNA 281
                                   5777777778888887778888..3455666666666555555....5555...5779*********************** PP

                         T2SSE 156 sderivtvEDpvEiqlega..nqvqlnakkakvtfadllraaLRlrPDrimvGEiRdketlei.lkAvnTGHlgslsTlHa 233
                                   + + + t+E p+ ++++++  ++++l+ +   +++   +  +L  rPD  +  E+R ++ +++       G  g ++ +Ha
  gi|13541271|ref|NP_110959.1| 282 RGKIVKTMERPRDLDVSKDitQYTELEGS---MEMTGDI--LLLVRPDYTIFDEMRVTDDFKVyADLRLAG-VGMVGVVHA 356
                                   *88888*********97751144445544...5555444..46689************9999954444455.55589**** PP

                         T2SSE 234 nsaagalerL 243
                                     a++al+r 
  gi|13541271|ref|NP_110959.1| 357 TRAIDALQRF 366
                                   ********96 PP

>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   2.7   7.6e-10   4.9e-07       4      43 ..     483     530 ..     480     548 .. 0.74

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 7.6e-10
                                   EEEGGGHHHHHHTGGGHHHHHHHHHHT-EEEEES.STT.......... CS
                          KH_1   4 ilvPsslvgriIGkgGsnIkeIreetgakIkvpk.sedeg.......s 43 
                                   + v+ ++++++IG++G+nI eI+++ g kI+v++ + +++        
  gi|13541271|ref|NP_110959.1| 483 VRVDPKYIPKLIGRNGRNISEIEKKLGIKIDVEEaGGSSErekagveI 530
                                   6899********************77*****98434333234455554 PP

>> PIN_4  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   7.4e-07   0.00047       1     128 [.       3     123 ..       3     126 .. 0.79
   2 ?   -1.1   0.0       3.3   2.1e+03       2      33 ..     378     409 ..     377     411 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 7.4e-07
                         PIN_4   1 fVlDTnvlLhdp.e.alksfkeehdvviPitVleELdklKkgsserelarlarqanrlldellekesgrlkvqtsaeelpe 79 
                                   +V DT+v+ +   + ++ + +e  +v++P   l+E++++ ++ +   ++ +a + ++ l+++ ++ + ++ ++ ++ +  +
  gi|13541271|ref|NP_110959.1|   3 YVPDTSVIVDGRfTaFISE-REGSNVILPEAMLSEIEHQANEGR--AIGFAALEELKKLRKMESEGKISIEIEGERPKEWQ 80 
                                   899******8641313333.69**************99999998..99999999999999998888888877777433333 PP

                         PIN_4  80 e.eseseknDnrIlavalelkeekpdrkvvLvskDinlrikAkalgieae 128
                                      ++s + D++I +va +++ +       Lv+ Di  r  A ++gi +e
  gi|13541271|ref|NP_110959.1|  81 IkRAKSGEIDEMIRQVAFQYDAT-------LVTGDIIQRDVAIVKGITVE 123
                                   22234679***********9986.......79999999999999999776 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 3.3
                         PIN_4   2 VlDTnvlLhdpealksfkeehdvviPitVleE 33 
                                   ++DT + +++ ++ + ++ e+ v iP+   +E
  gi|13541271|ref|NP_110959.1| 378 IIDTIIYISNGQVAQVLSTEYTVKIPYGMTQE 409
                                   79**********999999********977666 PP

>> KH_4  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.2   6.2e-07    0.0004       3      52 ..     457     502 ..     455     505 .. 0.91

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 6.2e-07
                          KH_4   3 lvedilkalvddpeevevteeeeeeeveielnvegedlGrvIGkrGrtld 52 
                                    +ed++k+++ + ++vev++     + +  ++v+++ + ++IG++Gr+++
  gi|13541271|ref|NP_110959.1| 457 RIEDYIKKVL-KSDDVEVKMV---GDSRAIVRVDPKYIPKLIGRNGRNIS 502
                                   69*******9.689******8...678999999**************996 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   1.2e-06   0.00075      29      60 ..     255     286 ..     242     290 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.2e-06
                                   SEEEEEEE-TTSSHHHHHHHHHHHHHCTT--E CS
                          MeaB  29 aqvvGltGvPGaGkstlvealglelrrrGkrv 60 
                                   a+ + + G+PGaGkst+v+al++ + +rGk v
  gi|13541271|ref|NP_110959.1| 255 ANGILVAGSPGAGKSTFVQALAEFFNARGKIV 286
                                   5567799**********************987 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   1.6e-06     0.001       1      30 [.     260     289 ..     260     312 .. 0.85
   2 ?   -3.3   0.0       9.4     6e+03     210     231 ..     432     453 ..     430     458 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.6e-06
                    ATP_bind_1   1 vvGpaGsGKttfvgalseilelrgrsvavv 30 
                                   v+G +G+GK+tfv+al+e++++rg+ v+++
  gi|13541271|ref|NP_110959.1| 260 VAGSPGAGKSTFVQALAEFFNARGKIVKTM 289
                                   89*********************9988765 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 9.4
                    ATP_bind_1 210 efalvlrflplssekeesiedl 231
                                    f+++++++p++ ++e+s+++l
  gi|13541271|ref|NP_110959.1| 432 SFGEQIVVVPVKEKTESSVSRL 453
                                   57788899**********9988 PP

>> PIN_9  PIN like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       4.3   2.8e+03      30      48 ..      26      44 ..      23      51 .. 0.83
   2 !   17.9   0.1   4.5e-06    0.0029      37     113 ..      51     125 ..      46     126 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 4.3
                         PIN_9 30 elvvpkavleELerlakag 48
                                  ++++p+a+l+E+e+ a++g
  gi|13541271|ref|NP_110959.1| 26 NVILPEAMLSEIEHQANEG 44
                                  689*********9986655 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 4.5e-06
                         PIN_9  37 vleELerlakagkgkertaakvalsLaerceiveaeeekaDdailelakeldaavlvTnDreLkkrllekgipvilL 113
                                    leEL++l ++++++ + ++++  +  ++ +i +a++++ D++i ++a ++da+ + T D+  ++ ++ kgi+v +L
  gi|13541271|ref|NP_110959.1|  51 ALEELKKL-RKMESEGKISIEIEGERPKEWQIKRAKSGEIDEMIRQVAFQYDATLV-TGDIIQRDVAIVKGITVEYL 125
                                   589*****.99999**************************************7766.***************99776 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   1.6e-06     0.001      12      62 ..     243     294 ..     238     373 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.6e-06
                        AAA_16  12 LlsalervrsgrpelvllsGesGvGKsslvrellralekdggif.lrgkcdq 62 
                                   L++ ++   +++ + +l+ G +G GKs+ v++l++ ++++g i+ + ++ ++
  gi|13541271|ref|NP_110959.1| 243 LNDKVKERLESTANGILVAGSPGAGKSTFVQALAEFFNARGKIVkTMERPRD 294
                                   6777777777888*********************998888644434444444 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       3.9   2.5e+03      29      99 ..      59     148 ..      50     157 .. 0.53
   2 !   16.7   0.0   1.2e-05    0.0079       1      42 [.     258     300 ..     258     319 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 3.9
                        AAA_18  29 rdvakenglllevdpe..aldeskrldedkldklldaleenss......aleegknlvidghlaeleseaakdikk..... 96 
                                   r++ +e+ +++e + e  +  + kr++ +  d+ ++++  +++      +  + ++ ++ g+ +e++s+  k+ik      
  gi|13541271|ref|NP_110959.1|  59 RKMESEGKISIEIEGErpKEWQIKRAKSGEIDEMIRQVAFQYDatlvtgDIIQRDVAIVKGITVEYLSPPEKIIKNieeff 139
                                   444445555555555555344444444444444444444444454444544555555777777777776666665555555 PP

                        AAA_18  97 ......vvL 99 
                                         v+L
  gi|13541271|ref|NP_110959.1| 140 eettmsVHL 148
                                   555555555 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 1.2e-05
                        AAA_18   1 IlltGtpGvGKttlakeLskrlgf.gvnlrdvakenglllevd 42 
                                   Il++G pG+GK+t+ ++L++  +  g +++ + + ++l  + d
  gi|13541271|ref|NP_110959.1| 258 ILVAGSPGAGKSTFVQALAEFFNArGKIVKTMERPRDLDVSKD 300
                                   99****************9976446777777666666666555 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.2e-05    0.0077      29      59 ..     245     275 ..     223     276 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.2e-05
                                   -EEEEEGGGS-.SEEEE--TTSSHHHHHHHH CS
                  FtsK_SpoIIIE  29 nplvldlkkmashllvaGatgsGKStalntL 59 
                                   ++++  l + a+ +lvaG++g GKSt++++L
  gi|13541271|ref|NP_110959.1| 245 DKVKERLESTANGILVAGSPGAGKSTFVQAL 275
                                   55555666777889***************98 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0     2e-05     0.013      18      45 ..     252     278 ..     241     286 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2e-05
                        AAA_29  18 eidlkgatlltGpsGsGKSTllDAiqal 45 
                                   e + +g +l++G  G+GKST++ A++  
  gi|13541271|ref|NP_110959.1| 252 ESTANG-ILVAGSPGAGKSTFVQALAEF 278
                                   555566.9**************999765 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.4e-05    0.0092      19      47 ..     258     286 ..     243     290 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.4e-05
                    Zeta_toxin  19 illgGqpGAGKselaellkdelerqgnvv 47 
                                   il++G+pGAGKs+  ++l++ ++++g++v
  gi|13541271|ref|NP_110959.1| 258 ILVAGSPGAGKSTFVQALAEFFNARGKIV 286
                                   89****************99999888888 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0      0.35   2.3e+02      60     107 ..     156     205 ..     144     225 .. 0.73
   2 !   11.8   0.0   0.00027      0.17       2      30 ..     258     286 ..     257     293 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.35
                                   EEETT.---SSEETTEEE-HHHHHHHHHHHHHHHHHHH-.EEEE---STT CS
                      NTPase_1  60 Larve.akreprvgkyvvdvesfeelalealrkalsead.viviDEiGkm 107
                                   L   + ++ +++   yv++ +++e++a++++++   e+d  i +D  G  
  gi|13541271|ref|NP_110959.1| 156 LKDGKpGNVKYKRLDYVINRNDLENIASNIVKRGKLEPDsFIEMDALGAT 205
                                   5444444445556679****************999888867778888865 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00027
                                   EEEE--TTSSHHHHHHHHHHHH...GGGE CS
                      NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkv 30 
                                   +++ G+pG GK+T+v+ ++e  + +g  v
  gi|13541271|ref|NP_110959.1| 258 ILVAGSPGAGKSTFVQALAEFFNARGKIV 286
                                   789*****************998888776 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1       5.4   3.4e+03      52      80 ..     126     164 ..      56     191 .. 0.52
   2 !   14.8   0.0   4.8e-05     0.031      15      59 ..     259     309 ..     252     395 .. 0.65

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 5.4
                                   B-HHHCCHCEEEE-SS--S-TTSBHHHH..........H CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxx..........x RF
                      ABC_tran  52 qeleslrkeigvlpqepqlfpeltvren..........e 80 
                                    + e+  k+i+ +++e+++  +l++++n           
  gi|13541271|ref|NP_110959.1| 126 SPPEKIIKNIEEFFEETTMSVHLKAGTNpvlkdgkpgnV 164
                                   333444444555555555555555555555555555544 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 4.8e-05
                                   EEEESTTSSHHHHHHHHTTSS--SEEEE........EET.TCEGGGB-HHHCCH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxx.xxxxxxxxxxxxxx RF
                      ABC_tran  15 aivGenGaGKStLlkllagllkpteGei........lld.gkdlkeqeleslrk 59 
                                    + G+ GaGKSt++++la+  + + G+i         ld +kd+++   ++l+ 
  gi|13541271|ref|NP_110959.1| 259 LVAGSPGAGKSTFVQALAEFFN-ARGKIvktmerprDLDvSKDITQ--YTELEG 309
                                   578*****************98.69999554444443333333333..333333 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   4.1e-05     0.026      11      49 ..     248     286 ..     244     293 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.1e-05
                        AAA_30  11 ealltsgdrvavltGpAGtGKttalkalreaweaaggrv 49 
                                   ++ l+s++   ++ G +G+GK+t ++al+e ++a+g+ v
  gi|13541271|ref|NP_110959.1| 248 KERLESTANGILVAGSPGAGKSTFVQALAEFFNARGKIV 286
                                   5556677777899********************999655 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   7.7e-05     0.049       3      49 ..     262     308 ..     260     321 .. 0.80
   2 ?   -0.7   0.0       1.5   9.5e+02     109     128 ..     312     333 ..     303     338 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 7.7e-05
                                   ESTTSSHHHHHHHHHHHHHHTTE.EEEESSSTTSHHHHHHHHHHHTC CS
               Thymidylate_kin   3 GlDGaGKttqaellkerlkeegikvvltrepggteiGekirelllke 49 
                                   G  GaGK+t++++l+e ++++g+ v +   p++ ++ + i ++ + e
  gi|13541271|ref|NP_110959.1| 262 GSPGAGKSTFVQALAEFFNARGKIVKTMERPRDLDVSKDITQYTELE 308
                                   6679******************6566666699999999999997744 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.5
                                   HHGGGTTS..E-SEEEEEESSH CS
               Thymidylate_kin 109 slnedvll..kPdltflldvdp 128
                                   +++ d+ll  +Pd+t++ ++ +
  gi|13541271|ref|NP_110959.1| 312 EMTGDILLlvRPDYTIFDEMRV 333
                                   5666676678*******98765 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   8.8e-05     0.056       3      37 ..     253     287 ..     249     319 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 8.8e-05
                        AAA_22   3 ktagilvvtGesGtGKTtllrrlleqldeeakaee 37 
                                   +ta+ ++v G +G+GK+t ++ l+e ++++ k+ +
  gi|13541271|ref|NP_110959.1| 253 STANGILVAGSPGAGKSTFVQALAEFFNARGKIVK 287
                                   578889********************987655544 PP

>> KH_5  NusA-like KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1       3.8   2.4e+03      39      54 ..     434     461 ..     417     476 .. 0.66
   2 ?   14.6   0.7   4.1e-05     0.026       4      44 ..     480     514 ..     477     517 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 3.8
                          KH_5  39 gekidvvewseD............laef 54 
                                   ge+i vv+ +e             ++ +
  gi|13541271|ref|NP_110959.1| 434 GEQIVVVPVKEKtessvsrlavdrIEDY 461
                                   8888888888774444444444445555 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 4.1e-05
                          KH_5   4 rtkvaVkshnpnvdpvGaivgkkGsrikavsseLkgekidv 44 
                                   r++v V  +      + +++g++G++i++++++L g kidv
  gi|13541271|ref|NP_110959.1| 480 RAIVRVDPKY-----IPKLIGRNGRNISEIEKKL-GIKIDV 514
                                   6666666666.....899****************.*****8 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   4.3e-05     0.027      51      81 ..     253     283 ..     239     307 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.3e-05
                        DUF815  51 lpannvLLwGarGtGKSslvkallneyaeeg 81 
                                    +an +L+ G+ G+GKS+ v+al + ++++g
  gi|13541271|ref|NP_110959.1| 253 STANGILVAGSPGAGKSTFVQALAEFFNARG 283
                                   579********************99888877 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   0.00017      0.11       2      26 ..     258     285 ..     257     321 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00017
                                   EEEEESTTSSHHHHHHHHHT...STEEE CS
                      MMR_HSR1   2 vaivGrpNvGKStLinaltg...ekaiv 26 
                                   ++++G p +GKSt+++al +   ++ ++
  gi|13541271|ref|NP_110959.1| 258 ILVAGSPGAGKSTFVQALAEffnARGKI 285
                                   789***************8633233333 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 ?   12.6   0.0   0.00016       0.1       2      31 ..     258     287 ..     257     329 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00016
                                   EEEE--SSSSHHHHHHHGGGGBS--EEEEE CS
                         AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvq 31 
                                   +l+ G pG gKs++++ la+++n++  +v 
  gi|13541271|ref|NP_110959.1| 258 ILVAGSPGAGKSTFVQALAEFFNARGKIVK 287
                                   7889******************66544443 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00018      0.12       2      35 ..     258     291 ..     258     331 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00018
                           PRK   2 IgvagsSGaGkttvarklekifgrekvkaaeieg 35 
                                   I vags GaGk+t+ ++l + f+  ++  +++e 
  gi|13541271|ref|NP_110959.1| 258 ILVAGSPGAGKSTFVQALAEFFNARGKIVKTMER 291
                                   669********************87776555544 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   0.00023      0.14      14      46 ..     247     282 ..     238     288 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00023
                                   HHHCH...TEEEEEEESTTSSHHHHHHHHHHHTT-- CS
                          TsaE  14 lakal...gdvilLeGdLGaGKTtlvrglakalgve 46 
                                   +++ l   ++ il  G  GaGK+t+v++la+ ++ +
  gi|13541271|ref|NP_110959.1| 247 VKERLestANGILVAGSPGAGKSTFVQALAEFFNAR 282
                                   333332224459******************988765 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   0.00032      0.21       2      21 ..     258     277 ..     258     296 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00032
                        AAA_33   2 vllvGlpGsGKstlaerllk 21 
                                   +l+ G pG+GKst+++ l++
  gi|13541271|ref|NP_110959.1| 258 ILVAGSPGAGKSTFVQALAE 277
                                   6789************9985 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 ?   11.7   0.0   0.00024      0.15       1      21 [.     258     278 ..     258     330 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00024
               Viral_helicase1   1 ivvhGvpGcGKStlirkllrt 21 
                                   i+v+G pG+GKSt ++ l++ 
  gi|13541271|ref|NP_110959.1| 258 ILVAGSPGAGKSTFVQALAEF 278
                                   68***************9987 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00027      0.17       4      36 ..     258     290 ..     257     321 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00027
                                   EEEE--TTSSHHHHHHHHHHHHHHTT--EEEE- CS
                         KTI12   4 vvltGlPssGKstrakeLakaleeekrsvvvid 36 
                                   +++ G P +GKst+++ La+ ++++++ v  ++
  gi|13541271|ref|NP_110959.1| 258 ILVAGSPGAGKSTFVQALAEFFNARGKIVKTME 290
                                   799*********************998877655 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.2   0.00063       0.4      36     150 ..     258     381 ..     245     390 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00063
                        AAA_25  36 allaGapgtGKttlaldlalava.tGkpwlg.....pvapeqgkVlyvsaEdsedelrrRlravgealrddarllvldlag 110
                                   +l+aG pg+GK+t++  la     +Gk +       ++ + +  + y  +E+s + +   l  v+ +++  ++ +v+d  +
  gi|13541271|ref|NP_110959.1| 258 ILVAGSPGAGKSTFVQALAEFFNaRGKIVKTmerprDLDVSKDITQYTELEGSMEMTGDILLLVRPDYTIFDEMRVTDDFK 338
                                   689**************9966544777443366655555566666677777777677777777777775555555666566 PP

                        AAA_25 111 v.eslpLfakdrggtl.ltadvdaleaaieevegvrlv..viDp 150
                                   v  +l+L+  +  g + +t+++dal++ i ++e ++l+  +iD+
  gi|13541271|ref|NP_110959.1| 339 VyADLRLAGVGMVGVVhATRAIDALQRFIGRIE-LGLIpqIIDT 381
                                   667777777777777777777777777777765.6666556665 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1       4.3   2.8e+03      10      20 ..      61      71 ..      37      82 .. 0.53
   2 ?    9.8   4.2    0.0011      0.68       6      59 ..     462     513 ..     457     539 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 4.3
                                  TECETEEEEEE CS
                          KH_2 10 ikkagvskveI 20
                                  ++++g+ ++eI
  gi|13541271|ref|NP_110959.1| 61 MESEGKISIEI 71
                                  22333333333 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0011
                                   HHHHTECETEEEEEEEC.CSCEEEEEEEESCHHHHHTGGGHHHHHHHHHHHHHHH CS
                          KH_2   6 laveikkagvskveIer.tanrviiviresqpgivIGkgGsnikkigkelrkdie 59 
                                   +++++k+ +   ve++     r+i+ +       +IG++G+ni +i+k+l+ +i+
  gi|13541271|ref|NP_110959.1| 462 IKKVLKSDD---VEVKMvGDSRAIVRVDPKYIPKLIGRNGRNISEIEKKLGIKID 513
                                   555544333...3333322278999999999999****************99995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (593 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       673  (0.037537); expected 358.6 (0.02)
Passed bias filter:                      534  (0.0297841); expected 358.6 (0.02)
Passed Vit filter:                       109  (0.00607954); 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: 0.75u 0.29s 00:00:01.04 Elapsed: 00:00:00.48
# Mc/sec: 3686.74
//
Query:       gi|13541272|ref|NP_110960.1|  [L=170]
Description: hypothetical protein TVN0441 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.9e-33  113.4   7.7    2.3e-32  110.9   7.0    2.0  2  DUF2250   Uncharacterized protein conserved in archaea (DUF22
  ------ inclusion threshold ------
      0.015   15.0   0.1      0.023   14.4   0.1    1.4  1  DUF4423   Domain of unknown function (DUF4423)
      0.038   13.9   0.0      0.098   12.5   0.0    1.7  1  HTH_5     Bacterial regulatory protein, arsR family


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 !  110.9   7.0   3.9e-36   2.3e-32       3      93 .]      12     102 ..      10     102 .. 0.97
   2 ?    1.0   0.0     0.077   4.6e+02      40      54 ..     129     143 ..     116     148 .. 0.82

  Alignments for each domain:
  == domain 1  score: 110.9 bits;  conditional E-value: 3.9e-36
                       DUF2250   3 eleedelalkvlkhlkkanvdYaksiakeleipleevrellkkLeelGLlervegktikrteaklKkksevhkhHtYYrlt 83 
                                    l++d+++l+vlkh++ a+vdYak+i++++eip+ +vr +l++L+e+GLl+++++++ikrteaklKk++evhkhHtYY+++
  gi|13541272|ref|NP_110960.1|  12 DLINDYDMLRVLKHFTVAHVDYAKNITRYTEIPQIRVRAYLERLKEMGLLDYYTNTSIKRTEAKLKKSAEVHKHHTYYQIN 92 
                                   57899**************************************************************************** PP

                       DUF2250  84 reGelllrel 93 
                                   +++e++l+e+
  gi|13541272|ref|NP_110960.1|  93 KKAEAVLKEI 102
                                   *******986 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.077
                       DUF2250  40 rellkkLeelGLler 54 
                                    + +  L+ +GL+++
  gi|13541272|ref|NP_110960.1| 129 PDRCTGLQAMGLIDK 143
                                   577899*******97 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   3.8e-06     0.023      40      91 ..      35      84 ..      15     106 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.8e-06
                       DUF4423 40 eelakrlrpkisaeevekalefLlklgllkkdedgkyrqtekslttssevks 91
                                  +++ + +   i++ +v++ le+L+++gll+   +  +++te++l+ s+ev +
  gi|13541272|ref|NP_110960.1| 35 KNITRYTE--IPQIRVRAYLERLKEMGLLDYYTNTSIKRTEAKLKKSAEVHK 84
                                  56777777..***********************************8887765 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   1.6e-05     0.098      20      47 .]      36      63 ..      32      63 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.6e-05
                                  HHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                         HTH_5 20 elaeelglsqstvShHLkkLreaGLVek 47
                                   ++++++++q  v+ +L +L+e+GL+++
  gi|13541272|ref|NP_110960.1| 36 NITRYTEIPQIRVRAYLERLKEMGLLDY 63
                                  5899*********************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       836  (0.0466284); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.31s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 1045.54
//
Query:       gi|13541273|ref|NP_110961.1|  [L=347]
Description: adenine-specific DNA methylase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.4e-25   87.8   0.1    1.7e-15   57.3   0.0    2.2  2  N6_N4_Mtase      DNA methylase
    3.3e-05   23.7   0.0    9.1e-05   22.2   0.0    1.7  1  UPF0020          Putative RNA methylase family UPF0020
    0.00056   19.6   0.0     0.0011   18.7   0.0    1.4  1  Cons_hypoth95    Conserved hypothetical protein 95
  ------ inclusion threshold ------
      0.029   14.0   0.0      0.046   13.3   0.0    1.4  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase


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 !   57.3   0.0   3.9e-19   1.7e-15     175     228 ..     129     182 ..      59     185 .. 0.87
   2 !   28.6   0.1   2.3e-10     1e-06       2     111 ..     221     347 .]     220     347 .] 0.86

  Alignments for each domain:
  == domain 1  score: 57.3 bits;  conditional E-value: 3.9e-19
                                   ---HHHHHHHHHHHS-TT-EEEETT-TTTHHHHHHHHTT-EEEEEESSHHHHHH CS
                   N6_N4_Mtase 175 qkPvallerlIklstkkgdivlDpFaGSGtTavaakelgrkfiGieieeeyvel 228
                                    +  ++++ lI+ +++k+++vlDpF GSGtT+++ak+lgr+++Giei+ee ++ 
  gi|13541273|ref|NP_110961.1| 129 NFVPQIPRQLILRFSRKDEWVLDPFSGSGTTLIEAKKLGRNSLGIEINEEVCKK 182
                                   55568899******************************************9984 PP

  == domain 2  score: 28.6 bits;  conditional E-value: 2.3e-10
                                   EEEEE--SSSSSCS......GCCGCCHHHHHHHHHHHHHHHHHHHEEEEEEEEEEE-CCCHHT......HHHHHHHHHTT- CS
                   N6_N4_Mtase   2 dlivtdpPYntgkdy.endeqyeeedsyeeyleflekvlkevrrvLkddgsifiniddseikk......elkaladeifgg 75 
                                   +l++  pPY+   ++   + ++    + +e+l+ l kv ++v + L+++ ++ + i+d++ +       +  ++   ++g 
  gi|13541273|ref|NP_110961.1| 221 NLVIMHPPYHDIIKFtDIGGDLSNARDTKEFLSMLGKVTRNVSKYLQKGRFLALVIGDKYSNGewiplgFYSMQKVMDQG- 300
                                   89********999976677888888899**************************************99988888888888. PP

                                   EEEEEEEEEEES...SSTTTSTCC..........S-B--EEEEEEEESS CS
                   N6_N4_Mtase  76 ffllnvivwkkp...nsmpesnkd..........rltsthEyilvfskn 111
                                   f l+++iv++ +   +   +s++d          +++  hEyi+vf+k+
  gi|13541273|ref|NP_110961.1| 301 FRLKSTIVKNFEytrG--KASSSDlwryralaggFYVFKHEYIFVFQKT 347
                                   99*****998885432..3333335688999999999**********96 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0     2e-08   9.1e-05      27      69 ..     144     186 ..     139     212 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 2e-08
                                   -TTS-EEETT-TTSHHHHHHHHHHTT--TTTT----SSHHHHH CS
                       UPF0020  27 kpgepllDPmCGsGtilIEaallganiapgllrefvlelkaea 69 
                                   +++e  lDP++GsGt lIEa  lg+n   + + e+v+++  e+
  gi|13541273|ref|NP_110961.1| 144 RKDEWVLDPFSGSGTTLIEAKKLGRNSLGIEINEEVCKKSLEI 186
                                   578999*********************9999988888865555 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   2.4e-07    0.0011      42     125 ..     146     231 ..     139     244 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2.4e-07
                                   C-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--T.TTEEEEES-HHHHCTS--..SS-EEEEEEE CS
                 Cons_hypoth95  42 garvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelklee.etaelkedaleallklak..kkeefdivfl 119
                                   ++ vLD f+GsG+  +EA   g ++++ +e ++e++k   e l++++ ++ +ta+  ++a+ +l k  +    +ef++v +
  gi|13541273|ref|NP_110961.1| 146 DEWVLDPFSGSGTTLIEAKKLG-RNSLGIEINEEVCKKSLEILNSIDGDGfSTAISGDSASVNLTKVMEyyGIPEFNLVIM 225
                                   6679**************7777.67999*********99999999998874444444444445554443113579****** PP

                                   --SSST CS
                 Cons_hypoth95 120 DPPyak 125
                                    PPy++
  gi|13541273|ref|NP_110961.1| 226 HPPYHD 231
                                   ****97 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0     1e-05     0.046       3      80 ..     148     228 ..     146     268 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1e-05
               Methyltransf_15   3 vilDlfsGaGGnviqfalvfekviaieinleklacaqhNaevYgvsdkitlvlgdvfe..llaklkleki.kvdlvflSpP 80 
                                    +lD+fsG+G   i+ ++ +++  +iein+e ++ + +  ++ + +   t + gd  +  l++ ++   i +++lv++ pP
  gi|13541273|ref|NP_110961.1| 148 WVLDPFSGSGTTLIEAKKLGRNSLGIEINEEVCKKSLEILNSIDGDGFSTAISGDSASvnLTKVMEYYGIpEFNLVIMHPP 228
                                   69******************************9988877777776666677777765532222222222255566666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.50
# Mc/sec: 2094.33
//
Query:       gi|13541274|ref|NP_110962.1|  [L=44]
Description: peroxiredoxin fragment (inactivated), partial [Thermoplasma volcanium GSS1]
Scores for 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   25.4   0.0      1e-05   25.4   0.0    1.0  1  AhpC-TSA  AhpC/TSA family
  ------ inclusion threshold ------
      0.026   14.5   0.1      0.029   14.4   0.1    1.2  1  MNSV_P7B  Melon necrotic spot virus P7B 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 !   25.4   0.0   1.2e-09     1e-05      22      59 ..       6      43 ..       1      44 [] 0.93

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 1.2e-09
                                  HHTTSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTT CS
                      AhpC-TSA 22 dykgkpvvlffypkdwcpvCttelpalaklyeefkerg 59
                                  dy+gk++vlf + +d++pv  te +++a++++e + ++
  gi|13541274|ref|NP_110962.1|  6 DYSGKWLVLFSHFGDFTPVRATEFFSFARRNDEPERLN 43
                                  9*******************************998777 PP

>> MNSV_P7B  Melon necrotic spot virus P7B protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   3.2e-06     0.029      10      25 ..       4      19 ..       2      32 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.2e-06
                      MNSV_P7B 10 pGdysGallilfisfv 25
                                  pGdysG  l+lf  f 
  gi|13541274|ref|NP_110962.1|  4 PGDYSGKWLVLFSHFG 19
                                  9***********9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (44 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       126  (0.00702772); expected 358.6 (0.02)
Passed bias filter:                      120  (0.00669307); expected 358.6 (0.02)
Passed Vit filter:                         6  (0.000334653); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.45
# Mc/sec: 296.31
//
Query:       gi|13541275|ref|NP_110963.1|  [L=89]
Description: peroxiredoxin fragment (inactivated), partial [Thermoplasma volcanium GSS1]
Scores for complete 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   24.0   0.7    7.4e-05   22.5   0.7    1.7  1  1-cysPrx_C   C-terminal domain of 1-Cys peroxiredoxin
  ------ inclusion threshold ------
      0.091   13.1   0.0       0.12   12.7   0.0    1.3  1  Glu-tRNAGln  Glu-tRNAGln amidotransferase C subunit


Domain annotation for each model (and alignments):
>> 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 !   22.5   0.7   8.2e-09   7.4e-05       1      33 [.      37      73 ..      37      78 .. 0.93

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 8.2e-09
                                  HHHHHHHHT-BB-TTT.T.....BT-EEE---SSHHHH CS
                    1-cysPrx_C  1 ALQladkhgvatPAnWkp.....GdkvivpPpateeda 33
                                  ALQ++dk++v tPA  +p      dk i+pPp+t +d+
  gi|13541275|ref|NP_110963.1| 37 ALQMVDKYKVETPAS-RPdneliKDKSIIPPPVTIDDI 73
                                  9**************.69*****************996 PP

>> Glu-tRNAGln  Glu-tRNAGln amidotransferase C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   1.4e-05      0.12      11      44 ..      26      56 ..      23      83 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.4e-05
                                  HHHHHHHHHHTTCGCS--TT----S..-EB-S-- CS
                   Glu-tRNAGln 11 kelnsildyveqLqevdttgveplthpvlReDev 44
                                  + l++il ++++Lq vd  +ve    p  R+D +
  gi|13541275|ref|NP_110963.1| 26 RNLSEILRMIKALQMVDKYKVET---PASRPDNE 56
                                  789**************669974...32377743 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       318  (0.0177366); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); 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: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 664.21
//
Query:       gi|13541276|ref|NP_110964.1|  [L=309]
Description: ATPase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-11   44.8   0.0    2.2e-11   43.8   0.0    1.5  1  ATP_bind_3     PP-loop family
    5.1e-07   28.8   0.0    7.3e-07   28.3   0.0    1.2  1  tRNA_Me_trans  tRNA methyl transferase
      4e-05   23.5   0.0    6.6e-05   22.7   0.0    1.3  1  Asn_synthase   Asparagine synthase
    0.00034   20.1   1.4    0.00034   20.1   1.4    2.4  3  RecR           RecR protein
     0.0008   19.0   0.1     0.0067   15.9   0.0    2.5  2  QueC           Queuosine biosynthesis protein QueC
     0.0018   17.4   0.0     0.0028   16.8   0.0    1.3  1  NAD_synthase   NAD synthase
     0.0043   16.5   1.0     0.0043   16.5   1.0    2.3  2  zn-ribbon_14   Zinc-ribbon
      0.006   16.6   0.0       0.18   11.8   0.0    2.3  2  PAPS_reduct    Phosphoadenosine phosphosulfate reductase fami
  ------ inclusion threshold ------
      0.091   13.0   0.4       0.19   12.0   0.4    1.5  1  CTU2           Cytoplasmic tRNA 2-thiolation protein 2


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 !   43.8   0.0   1.1e-14   2.2e-11       2     181 ..      51     242 ..      50     243 .. 0.84

  Alignments for each domain:
  == domain 1  score: 43.8 bits;  conditional E-value: 1.1e-14
                                   EEEE--SCHHHHHHHHHHHHH.CTTTTTEEEEEEEE-SSSTCHHHHHHHHHHHHHHTT-EEEEEE--H..........HHC CS
                    ATP_bind_3   2 vlvAvSgGlDSmaLllllakl.kkklgiklvaihvdhglreeskeeaelvkelckklnikleiekvdv..........akk 71 
                                   + vA+SgG DS + l ll+k   +++++k+ a++vd g+     +  e  k+lc++l+i++e+ ++            +++
  gi|13541276|ref|NP_110964.1|  51 ISVALSGGKDSSVTLFLLHKIlGNRKNMKIKAFTVDEGIDGYRPSGLESAKRLCTSLGIDHETISFYDsygltldsivKTN 131
                                   679*******988777777761566677**********************************9999877999997765444 PP

                                   TTSTCCCHHHHHHHHHHHHCHHCCT.CEEE---BHHHHHHHHHHHHCCT--CCHHH-S-SEEEETTCCEE-..CCCT--HH CS
                    ATP_bind_3  72 kgknleeaARelRYevlkealkkegievlllAhhadDqaEtfllrlargsglaglagikeaseiasirlvR..PlLkvske 150
                                     k   +    lR ++++e++ k+++++++l+ + dD+   +l+++a+g     ++ +++++ ++ + + R  Pl ++  +
  gi|13541276|ref|NP_110964.1| 132 PVKIPCAYCGPLRRKLINEMADKQDADYVALGLNLDDYSQSILMNVAKGDFD-RFIRMSPQTDRKVGLVRRiaPLRTILEK 211
                                   45555567889*************************************9986.66777777766654444455******** PP

                                   HHHHHHHHTT---B--CGGGCTTSHHHHHHH CS
                    ATP_bind_3 151 eleeylkekkikwveDesNadekyeRnriRk 181
                                   e+  y+ +++i++      + ++ +Rn +R+
  gi|13541276|ref|NP_110964.1| 212 EVVLYAVTNDIPFDSSWCPYYSRAQRNVFRE 242
                                   ************9988888888888998885 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   0.0   3.6e-10   7.3e-07       2      75 ..      50     121 ..      49     163 .. 0.87

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 3.6e-10
                 tRNA_Me_trans   2 kvvvalSgGVDSsvaaallkeqgyevigvflklweeedeegkeccaeedlkdaervaeklgiplevvdfekeyk 75 
                                   ++ valSgG DSsv+++ll++   + + + +k  + ++         + l+ a+r +  lgi +e+++f ++y 
  gi|13541276|ref|NP_110964.1|  50 TISVALSGGKDSSVTLFLLHKILGNRKNMKIKAFTVDEGI--DGYRPSGLESAKRLCTSLGIDHETISFYDSYG 121
                                   589*********************9999999988884333..578889**********************9995 PP

>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.0   3.3e-08   6.6e-05      16      79 ..      47     116 ..      33     132 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 3.3e-08
                  Asn_synthase  16 advpvGalLSGGlDSSliaalaarqsk....splktFsigf..eekgsdeakyakevaehlgtehtelvl 79 
                                    dv +++ LSGG DSS+  +l+ + +      ++k+F+++   +  + + ++ ak+++  lg++h ++ +
  gi|13541276|ref|NP_110964.1|  47 DDVTISVALSGGKDSSVTLFLLHKILGnrknMKIKAFTVDEgiDGYRPSGLESAKRLCTSLGIDHETISF 116
                                   79**********************999999999******9854558888999*************98876 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.5       3.2   6.4e+03      19      22 ..       3       6 ..       2       8 .. 0.74
   2 ?   -1.8   0.2       1.2   2.4e+03      30      35 ..     136     141 ..     133     145 .. 0.66
   3 !   20.1   1.4   1.7e-07   0.00034      15      36 ..     277     298 ..     275     300 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 3.2
                                  -TTT CS
                          RecR 19 CsrC 22
                                  Cs+C
  gi|13541276|ref|NP_110964.1|  3 CSKC 6 
                                  8888 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.2
                                   S-CCCC CS
                          RecR  30 lCaICs 35 
                                   +Ca C 
  gi|13541276|ref|NP_110964.1| 136 PCAYCG 141
                                   577774 PP

  == domain 3  score: 20.1 bits;  conditional E-value: 1.7e-07
                                   H-EE-TTT--EESSSS-CCCCS CS
                          RecR  15 kvrhCsrCgnlteedlCaICsd 36 
                                   k+++C++Cg  te+d+C+ Cs+
  gi|13541276|ref|NP_110964.1| 277 KLKRCKICGAPTERDVCTACSS 298
                                   689*****************97 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   3.4e-06    0.0067       4     186 ..      53     233 ..      50     242 .. 0.69
   2 ?   -2.4   0.2       1.4   2.8e+03     175     197 ..     276     297 ..     258     301 .. 0.63

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 3.4e-06
                                   EE--SSHHHHHHHHHHHH.....H-SEEEEEEEESS-T..TSHHHHHHHHHHHHT--.-EEEEE-GGGGGGSCGGG----- CS
                          QueC   4 vllSGGlDSttvlalakk.....egkevealtfdYgqr..hkkeleaakkiakelgveehkildldllkelggsaLtdeei 77 
                                   v lSGG DS++ l+l +k     +  +++a t+d g    + + le+ak+++++lg+ +h++++        +  Lt ++i
  gi|13541276|ref|NP_110964.1|  53 VALSGGKDSSVTLFLLHKilgnrKNMKIKAFTVDEGIDgyRPSGLESAKRLCTSLGI-DHETISFY-----DSYGLTLDSI 127
                                   679**********99875222225689*******9988667889*************.88877665.....6677777775 PP

                                   ------...--------.TTHHHHHHHHHHHHHHHHT-SEEEE---S-STT--GGGSHHHHHHHHHHHHHH..HTS--EE. CS
                          QueC  78 evpkeeleeeelpntfV.paRNliflslaasyaealgaeaiiiGvneedfsgYPDcrdefvkalnkalnlg..edkkiei. 154
                                    v++   +  ++p  +  p R  ++       a++++a+ +++G+n  d+s      +     ++++++++  +d+k+ + 
  gi|13541276|ref|NP_110964.1| 128 -VKT---NPVKIPCAYCgPLRRKLIN----EMADKQDADYVALGLNLDDYSQSI-LMNVAKGDFDRFIRMSpqTDRKVGLv 199
                                   .555...5567888776577876654....456888999999999988887632.22222334555555555533443332 PP

                                   ..E-TTTT--HHHHHHHHHHTTHHHHH-B-STTS CS
                          QueC 155 ..eaPlidlsKaeivklgkelgvpleetlsCYeg 186
                                      aPl ++  +e+v  +   ++p++ ++  Y +
  gi|13541276|ref|NP_110964.1| 200 rrIAPLRTILEKEVVLYAVTNDIPFDSSWCPYYS 233
                                   2257777777777777777777777777777765 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.4
                                   HHHHH-B-STTS.-BTTTTSSSH CS
                          QueC 175 vpleetlsCYegeeegkaCgeCd 197
                                   v+l+    C +++ e++ C  C 
  gi|13541276|ref|NP_110964.1| 276 VKLKRCKICGAPT-ERDVCTACS 297
                                   5556666666663.336666665 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   1.4e-06    0.0028       6      90 ..      35     125 ..      30     161 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.4e-06
                                   HHHHHHHHHHCTT.SEEEEEE-SSHHHHHHHHHHHHHHTCGEEE...EEE--..SSSTTHHHHHHHHHHHHHHTSEEEE-- CS
                  NAD_synthase   6 vdflkeyvkkaga.kgvvlGlSGGvDSslvaalavkalgkenvl...alllP..ssvsseedvedalalaenlgievktid 80 
                                   ++ ++++v+ +g    + + lSGG DSs++  l  k+lg+ + +   a  +        ++ +e a+ l+ +lgi+ +ti+
  gi|13541276|ref|NP_110964.1|  35 KKEIRKQVEFHGDdVTISVALSGGKDSSVTLFLLHKILGNRKNMkikAFTVDegIDGYRPSGLESAKRLCTSLGIDHETIS 115
                                   56678888877773456689******************8765541115555521233567889****************99 PP

                                   -HHHHHHHHH CS
                  NAD_synthase  81 ikpivrafeq 90 
                                     + +    +
  gi|13541276|ref|NP_110964.1| 116 FYDSYGLTLD 125
                                   8887765555 PP

>> zn-ribbon_14  Zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.4      0.34   6.9e+02       2       7 ..       2       7 ..       1       8 [. 0.82
   2 !   16.5   1.0   2.2e-06    0.0043       2      26 ..     280     304 ..     279     308 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.34
                  zn-ribbon_14 2 kCerCG 7
                                 kC++C 
  gi|13541276|ref|NP_110964.1| 2 KCSKCS 7
                                 8****5 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 2.2e-06
                  zn-ribbon_14   2 kCerCGylSSqkiCkACvLLegLnk 26 
                                   +C+ CG  +  ++C AC  L++ n 
  gi|13541276|ref|NP_110964.1| 280 RCKICGAPTERDVCTACSSLQEVNE 304
                                   8****************88877665 PP

>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.0   8.9e-05      0.18       2      27 ..      51      81 ..      50      92 .. 0.78
   2 ?    2.7   0.0     0.058   1.2e+02     123     155 ..     192     224 ..     108     239 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 8.9e-05
                                  EEEE--SSCTCHHHHHHHHHHCTTH.....E CS
                   PAPS_reduct  2 lvvsvsgGkdslVllhLalkafkpv.....p 27
                                  + v+ sgGkds+V+l L+ k++ ++     +
  gi|13541276|ref|NP_110964.1| 51 ISVALSGGKDSSVTLFLLHKILGNRknmkiK 81
                                  6799****************99986344444 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.058
                                   ECTTT-SCEEE-CCCT--HHHHHHHHHHCT--B CS
                   PAPS_reduct 123 idedfekslrvfPllnWteedvwqyilrenipy 155
                                   +d++   + r+ Pl    e++v  y+ +++ip 
  gi|13541276|ref|NP_110964.1| 192 TDRKVGLVRRIAPLRTILEKEVVLYAVTNDIPF 224
                                   444555477999******************996 PP

>> CTU2  Cytoplasmic tRNA 2-thiolation protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.4   9.4e-05      0.19       7      58 ..     241     291 ..     237     307 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 9.4e-05
                          CTU2   7 ekFilklekdfpstvstvvrTgeKLvknksseeaeletsekCalCglplddk 58 
                                   ++ ++kl ++ pst   +++  + + +n ++ ++   + ++C++Cg+p +++
  gi|13541276|ref|NP_110964.1| 241 REVVNKLSEENPSTKFAILKFFDRVRENITTGHE-EVKLKRCKICGAPTERD 291
                                   66789***********************998655.57899********9554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       757  (0.0422221); expected 358.6 (0.02)
Passed bias filter:                      580  (0.0323498); 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):               9  [number of targets reported over threshold]
# CPU time: 0.65u 0.29s 00:00:00.94 Elapsed: 00:00:00.51
# Mc/sec: 1828.69
//
Query:       gi|13541277|ref|NP_110965.1|  [L=100]
Description: hypothetical protein TVN0446 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.2e-15   55.7   0.6    4.8e-15   55.6   0.6    1.0  1  rhaM      L-rhamnose mutarotase
  ------ inclusion threshold ------
      0.018   15.1   0.3      0.022   14.8   0.3    1.3  1  DUF1398   Protein of unknown function (DUF1398)


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 !   55.6   0.6   5.3e-19   4.8e-15       1     107 [.       2      98 ..       2      99 .. 0.86

  Alignments for each domain:
  == domain 1  score: 55.6 bits;  conditional E-value: 5.3e-19
                          rhaM   1 RyaqvlklkpeaieeYkklHaevwpevlealkeagirnysIyldeegntLfailevgddeeadaaaaaadpkvqeWwalma 81 
                                   Ry ++lk++  + +eY + H++vw+e+ ++lk+agirny+++   +++ +  ++e+gd     + + +  +  ++W+++m 
  gi|13541277|ref|NP_110965.1|   2 RYFFTLKIDGTRKAEYIEKHRRVWDEMIAELKKAGIRNYTLF--IDDDNVYXYWEYGDISTVVNYLFN-REIDKKWQEYMG 79 
                                   8999**************************************..57999*******955555555555.************ PP

                          rhaM  82 klqeaapsaspakeeekwteleevFh 107
                                   ++  +  ++ p+       + +evFh
  gi|13541277|ref|NP_110965.1|  80 NIILERTDTFPN-------KFTEVFH 98 
                                   *99988875555.......5677777 PP

>> DUF1398  Protein of unknown function (DUF1398)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.3   2.5e-06     0.022      13      43 ..      25      55 ..      14      80 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.5e-06
                                  -HHHHHHHHHH-SSEEEEETTTSEEEEE-SS CS
                       DUF1398 13 fpafiqelkrlgvskYeyfvadgnvkyvgen 43
                                  +++ i elk+ g+++Y+ f+ d+nv  + e 
  gi|13541277|ref|NP_110965.1| 25 WDEMIAELKKAGIRNYTLFIDDDNVYXYWEY 55
                                  67899*******************9776554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       827  (0.0461264); expected 358.6 (0.02)
Passed bias filter:                      563  (0.0314016); 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: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 742.84
//
Query:       gi|13541278|ref|NP_110966.1|  [L=238]
Description: DNA-binding protein [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-17   63.6   0.1      2e-17   62.7   0.1    1.5  1  HTH_10        HTH DNA binding domain
      0.003   17.3   0.0     0.0048   16.7   0.0    1.4  1  HTH_IclR      IclR helix-turn-helix domain
     0.0032   17.4   0.0      0.006   16.5   0.0    1.4  1  HTH_36        Helix-turn-helix domain
     0.0041   17.0   0.0     0.0089   15.9   0.0    1.5  1  HTH_5         Bacterial regulatory protein, arsR family
     0.0081   16.3   0.0      0.022   14.9   0.0    1.7  1  HTH_17        Helix-turn-helix domain
     0.0085   15.7   0.0      0.019   14.6   0.0    1.5  1  Sigma70_r4_2  Sigma-70, region 4
     0.0089   16.1   0.0      0.021   14.9   0.0    1.6  1  SpoIIID       Stage III sporulation protein D
  ------ inclusion threshold ------
      0.017   15.0   0.0      0.051   13.5   0.0    1.7  1  MarR_2        MarR family
      0.034   13.7   0.0      0.067   12.8   0.0    1.5  1  HTH_24        Winged helix-turn-helix DNA-binding
      0.041   13.6   0.0       0.17   11.6   0.0    2.0  2  HTH_Tnp_4     Helix-turn-helix of DDE superfamily endonucleas
      0.064   13.3   0.0       0.14   12.2   0.0    1.5  1  HTH_3         Helix-turn-helix
      0.072   13.2   0.2       0.18   11.9   0.2    1.7  1  MetOD2        Metanogen output domain 2
      0.085   12.7   0.0       0.34   10.8   0.0    1.9  2  HTH_23        Homeodomain-like domain
       0.13   11.9   0.0       0.25   11.0   0.0    1.4  1  GntR          Bacterial regulatory proteins, gntR family


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 !   62.7   0.1   1.6e-20     2e-17       2      52 ..     174     224 ..     173     225 .. 0.98

  Alignments for each domain:
  == domain 1  score: 62.7 bits;  conditional E-value: 1.6e-20
                        HTH_10   2 TdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaeskli 52 
                                   T+ +++++++A+  GY+  PR v +++LA+ +G skst++e+Lrkae+k +
  gi|13541278|ref|NP_110966.1| 174 TPSEMQIIAEAVSRGYYSIPRHVGIRDLAEYFGMSKSTVQEYLRKAEQKTM 224
                                   899**********************************************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 !   16.7   0.0   3.7e-06    0.0048      17      40 ..     194     217 ..     178     231 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 3.7e-06
                                   SS-BHHHHHHHHTS-HHHHHHHHH CS
                      HTH_IclR  17 qeltlselArrtglpkStvhRlLq 40 
                                   + +++++lA+ +g++kStv  +L+
  gi|13541278|ref|NP_110966.1| 194 RHVGIRDLAEYFGMSKSTVQEYLR 217
                                   4589*****************996 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   4.7e-06     0.006      28      52 ..     198     222 ..     176     223 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 4.7e-06
                        HTH_36  28 qetlakrlglsknTvsraikeLeql 52 
                                    ++la+ +g+sk+Tv+ ++++ eq+
  gi|13541278|ref|NP_110966.1| 198 IRDLAEYFGMSKSTVQEYLRKAEQK 222
                                   689*******************997 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   6.9e-06    0.0089      19      38 ..     199     218 ..     197     221 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 6.9e-06
                                   HHHHHHHTS-HHHHHHHHHH CS
                         HTH_5  19 celaeelglsqstvShHLkk 38 
                                    +lae++g+s+stv ++L+k
  gi|13541278|ref|NP_110966.1| 199 RDLAEYFGMSKSTVQEYLRK 218
                                   79****************97 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   1.7e-05     0.022       4      24 ..     198     218 ..     196     224 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.7e-05
                        HTH_17   4 veEaAelLgvsrstvyrlirr 24 
                                   + ++Ae++g+s+stv++++r+
  gi|13541278|ref|NP_110966.1| 198 IRDLAEYFGMSKSTVQEYLRK 218
                                   789**************9986 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   1.5e-05     0.019      30      53 ..     199     222 ..     196     222 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.5e-05
                                   HHHHHHHT--HHHHHHHHHHHHHH CS
                  Sigma70_r4_2  30 kEIAellgisegtVksrlsRArkk 53 
                                   ++ Ae++g+s +tV+ +l++A +k
  gi|13541278|ref|NP_110966.1| 199 RDLAEYFGMSKSTVQEYLRKAEQK 222
                                   789******************876 PP

>> SpoIIID  Stage III sporulation protein D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   1.7e-05     0.021       8      40 ..     184     216 ..     178     236 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.7e-05
                       SpoIIID   8 vleiakyiveskatvRkaakvfgvskstvhkDv 40 
                                   +++ ++y + ++  +R+ a+ fg+skstv   +
  gi|13541278|ref|NP_110966.1| 184 AVSRGYYSIPRHVGIRDLAEYFGMSKSTVQEYL 216
                                   5666789999999***************98655 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0     4e-05     0.051      24      48 ..     198     222 ..     173     223 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4e-05
                                   HHHHHHHHTSSHHHHHHHHHHHHHT CS
                        MarR_2  24 vgelarrlglsksavsrilkrLvaa 48 
                                   +++la+++g+sks+v+  l++++++
  gi|13541278|ref|NP_110966.1| 198 IRDLAEYFGMSKSTVQEYLRKAEQK 222
                                   68*******************9975 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   5.2e-05     0.067      20      44 ..     198     222 ..     194     222 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.2e-05
                        HTH_24  20 qreLAerlglSpstvnrrlkrLeee 44 
                                   +r+LAe  g+S+stv ++l++ e++
  gi|13541278|ref|NP_110966.1| 198 IRDLAEYFGMSKSTVQEYLRKAEQK 222
                                   69*******************9985 PP

>> HTH_Tnp_4  Helix-turn-helix of DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       5.7   7.3e+03       4      15 ..       9      20 ..       8      21 .. 0.81
   2 ?   11.6   0.0   0.00014      0.17      23      43 ..     199     219 ..     195     222 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 5.7
                     HTH_Tnp_4  4 sledqllltLvy 15
                                  s+ d++ +++++
  gi|13541278|ref|NP_110966.1|  9 SPDDRFSMVYFK 20
                                  788999999887 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00014
                     HTH_Tnp_4  23 qdLayrFgvsestvsrifhkw 43 
                                   +dLa  Fg+s stv+ + +k 
  gi|13541278|ref|NP_110966.1| 199 RDLAEYFGMSKSTVQEYLRKA 219
                                   69***************9986 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00011      0.14      13      42 ..     199     228 ..     198     232 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00011
                                   HHHHHHHTSSHHHHHHHHTTSSCSBHHHHH CS
                         HTH_3  13 eeLAeklGvsrstisriEnGernPsletlk 42 
                                   ++LAe+ G+s+st++ + +   + ++ +lk
  gi|13541278|ref|NP_110966.1| 199 RDLAEYFGMSKSTVQEYLRKAEQKTMNNLK 228
                                   79***************9985556666665 PP

>> MetOD2  Metanogen output domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.2   0.00014      0.18      11      45 ..     201     236 ..     197     238 .] 0.86

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00014
                        MetOD2  11 rAkkaGvdkeiidEYarLaksvevnk.rllslLsqt 45 
                                    A+  G++k+ ++EY r+a +  +n+ +ll+l++++
  gi|13541278|ref|NP_110966.1| 201 LAEYFGMSKSTVQEYLRKAEQKTMNNlKLLKLMNEM 236
                                   68889**************99888766999999876 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       2.9   3.8e+03      20      35 ..      27      42 ..      10      54 .. 0.72
   2 ?   10.8   0.0   0.00026      0.34      20      41 ..     198     219 ..     195     223 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 2.9
                        HTH_23 20 vreIAreLgvsrrTvy 35
                                  ++ I +e+++  +T+ 
  gi|13541278|ref|NP_110966.1| 27 WTGITKEHNIAIHTLK 42
                                  5567788888888876 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00026
                        HTH_23  20 vreIAreLgvsrrTvyrwlkry 41 
                                   +r+ A+ +g+s++Tv+ +l++ 
  gi|13541278|ref|NP_110966.1| 198 IRDLAEYFGMSKSTVQEYLRKA 219
                                   6899*************99984 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00019      0.25      13      51 ..     185     222 ..     178     224 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00019
                                   HHTTSS-TTSB---HHHHHHHHTS-HHHHHHHHHHHHHT CS
                          GntR  13 IlsgelrpGdkLPsereLaaefgVsrttvReALrrLeae 51 
                                   +++g ++        r+La+ fg s++tv+e Lr+ e++
  gi|13541278|ref|NP_110966.1| 185 VSRGYYSIPRHV-GIRDLAEYFGMSKSTVQEYLRKAEQK 222
                                   555555555666.789***************99998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       807  (0.0450109); expected 358.6 (0.02)
Passed bias filter:                      557  (0.031067); 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: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 1741.20
//
Query:       gi|13541279|ref|NP_110967.1|  [L=367]
Description: dehydrogenase [Thermoplasma volcanium GSS1]
Scores for complete 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-40  138.5   0.0    3.3e-40  138.1   0.0    1.2  1  adh_short_C2    Enoyl-(Acyl carrier protein) reductase
      5e-30  104.4   0.3    4.8e-29  101.2   0.0    2.0  2  adh_short       short chain dehydrogenase
    1.1e-26   92.8   0.1    2.9e-26   91.5   0.1    1.7  2  ADH_N           Alcohol dehydrogenase GroES-like domain
     0.0026   17.1   0.1     0.0057   16.0   0.1    1.6  1  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
     0.0038   17.2   0.0      0.013   15.5   0.0    1.7  2  KR              KR domain
     0.0059   16.2   0.1      0.009   15.6   0.1    1.4  1  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
  ------ inclusion threshold ------
      0.011   15.2   0.0       0.02   14.4   0.0    1.3  1  Glu_dehyd_C     Glucose dehydrogenase C-terminus
       0.02   15.0   0.1      0.037   14.1   0.1    1.5  1  Shikimate_DH    Shikimate / quinate 5-dehydrogenase
      0.025   13.8   0.0      0.039   13.2   0.0    1.3  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
       0.14   11.5   0.0       0.24   10.8   0.0    1.3  1  SecD_SecF       Protein export membrane protein
       0.17   11.8   0.1       0.31   10.9   0.1    1.4  1  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD 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 !  138.1   0.0     2e-43   3.3e-40      65     233 ..     193     362 ..     184     363 .. 0.96

  Alignments for each domain:
  == domain 1  score: 138.1 bits;  conditional E-value: 2e-43
                                   HHHSSEEEEEE-----EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHH.HCTSC..CEEEEEEEGGGTSBSTTTTHHH CS
                  adh_short_C2  65 ekfgklDilvnnagiapklkgpfletsreefdraldvnlyslfllakaalp.lmkeg..gsivnlssvgaervvpnynayg 142
                                   ++++++Dil+nnagi+p   ++f +++ + f+++ +vn+ s + +++a+ + ++++g  g+i+ +ss++++++ + +++y+
  gi|13541279|ref|NP_110967.1| 193 NRLEHVDILINNAGICPF--EDFFKIDIDLFEKVWKVNVESHYFITQAVSKhMIEKGikGRILIMSSISGRVGGEFQTHYT 271
                                   57799*************..*******************************566666************************ PP

                                   HHHHHHHHHHHHHHHHHGGGTEEEEEEEE--BHCTGGGGSTTHHHHHHHHHHHSTTSS-B-HHHHHHHHHHHCSGGGTT-- CS
                  adh_short_C2 143 aaKaalealtrylAvelgpkgiRvNavspgpikTlaasgikgfdelleelearaplgrlgtpeevaeaalfLasdeasyit 223
                                   ++K al+++++++A  lg++gi vN+  pg i T+++++  +++e ++++e+r+ +grlg+pe++ + alfL+sd+++y+t
  gi|13541279|ref|NP_110967.1| 272 TTKSALNGFMHSVAIVLGRYGILVNSLEPGTITTDINKDDLSNEEKRKYMERRTVVGRLGDPEDMVAPALFLVSDDNTYVT 352
                                   ************************************999999*************************************** PP

                                   SEEEEESTTG CS
                  adh_short_C2 224 GqtlvvDgGl 233
                                   G++l +DgG+
  gi|13541279|ref|NP_110967.1| 353 GSELLADGGM 362
                                   *********8 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.1     0.012        19       3      40 ..     161     198 ..     159     198 .. 0.92
   2 !  101.2   0.0   2.9e-32   4.8e-29      74     192 ..     194     313 ..     192     316 .. 0.96

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.012
                                   EEEESTTSHHHHHHHHHHHHTT-EEEE.EESCHHHHHHH CS
                     adh_short   3 vlvtGassGIGraiakelakeGakvvv.vdrseekleev 40 
                                   +lv+Ga+  IG+   k + + G++ vv +d+++++le+v
  gi|13541279|ref|NP_110967.1| 161 ALVIGAG-TIGLLATKIFSSVGCRKVVsMDINDNRLEHV 198
                                   8999998.9**************99999*******9875 PP

  == domain 2  score: 101.2 bits;  conditional E-value: 2.9e-32
                                   HHSSESEEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHH.HCTTEEEEEEEEGGGTSB-TTBHHHHHHH CS
                     adh_short  74 klgkldvLvnNAGitgsgpfselseeewervievNltgvflltravlpaml.kqssGrIvnvsSvagkvpvagvaaYsAsK 153
                                   +l+++d+L+nNAGi  +++f +++ + +e+v +vN+ + + +t+av ++m+ k+ +GrI  +sS+ g+v+ + ++ Y+++K
  gi|13541279|ref|NP_110967.1| 194 RLEHVDILINNAGICPFEDFFKIDIDLFEKVWKVNVESHYFITQAVSKHMIeKGIKGRILIMSSISGRVGGEFQTHYTTTK 274
                                   7899***********************************************999*************************** PP

                                   HHHHHHHHHHHHHHGGGTEEEEEEEESSBSSHHHHHHCT CS
                     adh_short 154 aavagltrslakelaptgirvnavaPGlvdTdmakelre 192
                                    a++g+++s+a  l ++gi vn++ PG + Td++k+  +
  gi|13541279|ref|NP_110967.1| 275 SALNGFMHSVAIVLGRYGILVNSLEPGTITTDINKDDLS 313
                                   *********************************998765 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 !   91.5   0.1   1.8e-29   2.9e-26       2     108 ..      25     130 ..      24     131 .. 0.95
   2 ?   -2.5   0.0       2.9   4.7e+03       3      15 ..     197     209 ..     196     217 .. 0.83

  Alignments for each domain:
  == domain 1  score: 91.5 bits;  conditional E-value: 1.8e-29
                                   TEEEEEEEEEEE-HHHHHHHTTSTTTTSSSSEE---EEEEEEEEESTT-CS--TT-EEEE-SEEE-SSSHHHHTT-GGG-T CS
                         ADH_N   2 gevlikvkaagiCgsDlhilkggkelevklplilGHEivGeveevgpevkklkvGdrVvvepliscgeCaaCkegeenlCe 82 
                                   g+v++kv++agi gs+l  + g ++  +k   ++GHE++G+v+++g++v+     ++V+v+pl++cg+C++Ck+g+++lC 
  gi|13541279|ref|NP_110967.1|  25 GWVTLKVNYAGIRGSELSAFVG-QNELRKSLSVMGHEFTGKVVKLGEDVDPKLLNKNVAVNPLVTCGKCRYCKTGNRQLCL 104
                                   79********************.677777778************************************************* PP

                                   TBEETTTSS-SSSBSEEEECGGGEEE CS
                         ADH_N  83 eakllgvsldGgfaeyvvvpekklvk 108
                                   e+kl+gv+++G+faeyv vpe ++++
  gi|13541279|ref|NP_110967.1| 105 ERKLIGVDYPGAFAEYVNVPEYSCYE 130
                                   *********************99987 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.9
                                   EEEEEEEEEEE-H CS
                         ADH_N   3 evlikvkaagiCg 15 
                                    v i ++ agiC 
  gi|13541279|ref|NP_110967.1| 197 HVDILINNAGICP 209
                                   57899999****5 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1   3.5e-06    0.0057      30      72 ..     160     203 ..     143     287 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 3.5e-06
                                   EEEEESTSHHHHHHHHHHHHTT-.EEEEEESSHHHHHHHHHTTT CS
                   AlaDh_PNT_C  30 kvlviGgGvaGlqAiatakglga.kVtvlDvrparleqleslga 72 
                                   + lviG+G+ Gl A ++ +++g  kV+ +D++ +rle+++ l +
  gi|13541279|ref|NP_110967.1| 160 RALVIGAGTIGLLATKIFSSVGCrKVVSMDINDNRLEHVDILIN 203
                                   789******************9637**************98444 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       1.3   2.2e+03       6      30 ..     164     187 ..     160     197 .. 0.83
   2 !   15.5   0.0   7.7e-06     0.013      80     162 ..     196     283 ..     184     286 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.3
                                   ETTTSHHHHHHHHHHHHHHS-EEEE CS
                            KR   6 tGGlGgLGlelarwlaekgarhlvl 30 
                                   + G+G +Gl  ++   + g r++v 
  gi|13541279|ref|NP_110967.1| 164 I-GAGTIGLLATKIFSSVGCRKVVS 187
                                   5.58999*99999999999998885 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 7.7e-06
                                   S---EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTTS--S.....EEEEEEEHHHHH--TT-HHHHHHHHH CS
                            KR  80 ppikGvihaAgvlrdklleemtaedleqvlapKvkGawnLhelledesld.....ffvlfSSiagllgsagqanYaaaNaf 155
                                   + +   i+ Ag+   + + + + + +e+v +  v+    + ++++++ ++      ++++SSi+g +g   q++Y+++ + 
  gi|13541279|ref|NP_110967.1| 196 EHVDILINNAGICPFEDFFKIDIDLFEKVWKVNVESHYFITQAVSKHMIEkgikgRILIMSSISGRVGGEFQTHYTTTKSA 276
                                   667778999*********************************999955542222258899********************* PP

                                   HHHHHHH CS
                            KR 156 lDalaey 162
                                   l++++++
  gi|13541279|ref|NP_110967.1| 277 LNGFMHS 283
                                   ****986 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   5.5e-06     0.009       4      39 ..     162     198 ..     159     247 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 5.5e-06
                                   EEE--STTHHHHHHHHHHCT.SEEEEE-S-HHHHHHH CS
                UDPG_MGDP_dh_N   4 sviGlGYvGlvtaavlaeig.hevigvDideekvdkl 39 
                                    viG+G +Gl    +++++g  +v+ +Di++++ +++
  gi|13541279|ref|NP_110967.1| 162 LVIGAGTIGLLATKIFSSVGcRKVVSMDINDNRLEHV 198
                                   69****************9989*********998865 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 ?   14.4   0.0   1.2e-05      0.02      32      75 ..     159     200 ..     140     208 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.2e-05
                   Glu_dehyd_C  32 esalvlGaGslGLLalalleaeerglervyvlgrrdrpdptidl 75 
                                   ++alv+GaG++GLLa+ ++++   g  +v  ++ +d+    +d+
  gi|13541279|ref|NP_110967.1| 159 DRALVIGAGTIGLLATKIFSS--VGCRKVVSMDINDNRLEHVDI 200
                                   58*************999985..789999999988877777776 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   2.3e-05     0.037      12      52 ..     158     198 ..     151     254 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.3e-05
                                   T-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHH CS
                  Shikimate_DH  12 ekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakel 52 
                                   + ++l+iGaG ++ l++k +++ g++kvv +  + +r +++
  gi|13541279|ref|NP_110967.1| 158 DDRALVIGAGTIGLLATKIFSSVGCRKVVSMDINDNRLEHV 198
                                   5799************************9777666666555 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   2.4e-05     0.039     109     178 ..     116     195 ..     111     257 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.4e-05
                                   EEE-BCTCTTC.TTBEECCSECHHHHHHCCSS-T.........SEEEEES-SHHHHHHHHHHHHHT-E.EEEEESSSSSS CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx RF
                   Pyr_redox_2 109 ssprdlgipGvaenvgklvrtldsaealklkllp.........krivvvGgGyiGvElAaalaklgke.vtlveardrll 178
                                   + +   ++p    + +k + +   ae+l  +l+          +r++v+G+G iG+  +  ++++g++ v+ ++ +d+ l
  gi|13541279|ref|NP_110967.1| 116 AFAEYVNVPEYSCYEIKEIPEASLAEPLATALRGvlqagpeidDRALVIGAGTIGLLATKIFSSVGCRkVVSMDINDNRL 195
                                   55555555555444444445555555555555557777779999***********************7677666665555 PP

>> SecD_SecF  Protein export membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00014      0.24      12      87 ..     226     303 ..     217     305 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00014
                                   -EEEEEEEEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-HHHHH..HHHHHHHHHHHHHHHHHHHTT----HHHH CS
                     SecD_SecF  12 daekisvetvgpsvskelaekavlallialvliliyvalrFewrval..aaiialvhDviitvgvlsllgievdlatv 87 
                                   ++++ s  ++ + vsk+++ek++   ++ +  i   v+  F+ ++ +  +a+   +h v i++g + +l   +++ t+
  gi|13541279|ref|NP_110967.1| 226 KVNVESHYFITQAVSKHMIEKGIKGRILIMSSISGRVGGEFQTHYTTtkSALNGFMHSVAIVLGRYGILVNSLEPGTI 303
                                   57788999**********************************999873357777*************99988888777 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00019      0.31       4      38 ..     163     198 ..     160     207 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00019
                                   EE--SCCHHHHHHHHHHTT-.EEEEE-S-HHHHHHH CS
                       3HCDH_N   4 viGaGtmGagiaavfasagl.eVvlvdiseealeka 38 
                                   viGaGt+G   +++f s g+ +Vv +di++++le++
  gi|13541279|ref|NP_110967.1| 163 VIGAGTIGLLATKIFSSVGCrKVVSMDINDNRLEHV 198
                                   9*****************984699*******99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (367 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 2438.26
//
Query:       gi|13541280|ref|NP_110968.1|  [L=121]
Description: 50S ribosomal protein L7Ae [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      1e-24   86.1   0.3    1.2e-24   85.8   0.3    1.1  1  Ribosomal_L7Ae  Ribosomal protein L7Ae/L30e/S12e/Gadd45 famil
     0.0048   17.0   0.0     0.0053   16.8   0.0    1.0  1  RNase_P_pop3    RNase P subunit Pop3


Domain annotation for each model (and alignments):
>> Ribosomal_L7Ae  Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.8   0.3   1.3e-28   1.2e-24       3      94 ..      18     108 ..      16     109 .. 0.93

  Alignments for each domain:
  == domain 1  score: 85.8 bits;  conditional E-value: 1.3e-28
                                   HHHHHHHHHHHTEEEESHHHHHHHHHTTTESEEEEETTSSSGGHHHHHHHHHHHTTEEEEEESCHHHHHHHTTSSSECSEE CS
                Ribosomal_L7Ae   3 ieevlkkakkagklvlGlkevtkalergeaklvilAedvepeekkkllealckekevpyvkvkskkeLGelvgkkrpvsal 83 
                                   + ++++ a ++gk+++G++ev+k++erge klv++Aedv+p+e + +l+ lc++k+vpyv+vk k++LG  vg    ++++
  gi|13541280|ref|NP_110968.1|  18 ALDLVESAFRSGKIKKGTNEVIKSIERGESKLVVIAEDVNPPEVVYYLPSLCEDKKVPYVYVKKKADLGSKVGIA-SAASV 97 
                                   567788899******************************************************************.68889 PP

                                   EEEESTTTHHH CS
                Ribosomal_L7Ae  84 aikdegdskdl 94 
                                   +i+d+g+ ++l
  gi|13541280|ref|NP_110968.1|  98 SIVDYGKNEEL 108
                                   99999988776 PP

>> RNase_P_pop3  RNase P subunit Pop3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   5.9e-07    0.0053      47     151 ..      23     119 ..       5     121 .] 0.74

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 5.9e-07
                  RNase_P_pop3  47 eskeneeseltvglneivelLecsesddvvllvcnkD.tPsvLlsqlpllvavanltvklvqlpksaqakldeklGlskag 126
                                   e       ++  g ne+++ +e  es    l+v+ +D +P   +  lp l++ ++  v+ v + k+  a l +k+G  +a 
  gi|13541280|ref|NP_110968.1|  23 E-SAFRSGKIKKGTNEVIKSIERGES---KLVVIAEDvNPPEVVYYLPSLCEDKK--VPYVYVKKK--ADLGSKVGIASAA 95 
                                   4.4556678999*********94444...466677776699999********999..999988776..6799999*99998 PP

                  RNase_P_pop3 127 mllvrkdasldkklaklvskkveel 151
                                    + + +  + ++ +++ vs+ ve+l
  gi|13541280|ref|NP_110968.1|  96 SVSIVDYGKNEELYKSIVSA-VEQL 119
                                   88777777777555555555.8876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       587  (0.0327403); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 906.03
//
Query:       gi|13541281|ref|NP_110969.1|  [L=69]
Description: 30S ribosomal protein S28e [Thermoplasma volcanium GSS1]
Scores for complete 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  106.3   2.0    6.5e-31  106.1   2.0    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 !  106.1   2.0   3.6e-35   6.5e-31       2      64 .]       4      66 ..       3      66 .. 0.98

  Alignments for each domain:
  == domain 1  score: 106.1 bits;  conditional E-value: 3.6e-35
                                  --EEEEEEEEEE---SSSSEEEEEEEE-S-SS-S-EEEEEEES---TT-EEEES--S--TT-- CS
                Ribosomal_S28e  2 eaklAeVikvlgrtGsrGevtqVrvellegkdkgriiiRnVkGPvreGDiLtLlEterEArrL 64
                                  ea++AeV++++grtG++Ge+t V+v++l+g+d+grii RnV GPvr+GDiL+L+Et+rEA++L
  gi|13541281|ref|NP_110969.1|  4 EATPAEVVEIIGRTGMTGEATTVKVRILSGRDQGRIIARNVLGPVRVGDILMLMETAREAKKL 66
                                  789**********************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       218  (0.0121591); expected 358.6 (0.02)
Passed bias filter:                      180  (0.0100396); 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: 0.33u 0.23s 00:00:00.56 Elapsed: 00:00:00.40
# Mc/sec: 514.10
//
Query:       gi|13541282|ref|NP_110970.1|  [L=66]
Description: 50S ribosomal protein L24e [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.8e-23   81.9   1.0    2.9e-23   81.9   1.0    1.0  1  Ribosomal_L24e   Ribosomal protein L24e
    1.7e-06   27.8   0.7    2.6e-06   27.3   0.7    1.3  1  zf-FCS           MYM-type Zinc finger with FCS sequence motif
    1.9e-05   24.7   0.2    2.9e-05   24.1   0.2    1.2  1  YHS              YHS domain
    5.1e-05   22.7   0.4    7.4e-05   22.1   0.4    1.2  1  zf-FLZ           zinc-finger of the FCS-type, C2-C2
     0.0068   16.7   0.1      0.008   16.4   0.1    1.1  1  Ta0938           Ta0938
  ------ inclusion threshold ------
      0.023   15.0   0.3      0.023   15.0   0.3    1.1  1  DUF3268          zinc-finger-containing domain
      0.041   13.9   0.6        8.2    6.5   0.0    2.3  2  DUF2116          Uncharacterized protein containing a Zn-ribb
       0.05   14.0   2.3       0.05   14.0   2.3    1.6  2  Arc_trans_TRASH  Archaeal TRASH domain
        0.3   11.0   3.5        1.3    9.0   3.5    1.8  1  VATC             Vms1-associating treble clef domain
       0.31   11.0   4.0       0.51   10.3   4.0    1.6  1  zf-C4_ClpX       ClpX C4-type zinc finger
          1    9.1   3.9        5.1    6.9   3.9    2.3  1  YacG             DNA gyrase inhibitor YacG


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 !   81.9   1.0   1.8e-26   2.9e-23       3      63 ..       3      64 ..       1      66 [] 0.94

  Alignments for each domain:
  == domain 1  score: 81.9 bits;  conditional E-value: 1.8e-26
                                  X-B-TTT-SB--SS--EEEE-TTS-EEEESSHHH.HHHHHTT--GGGSTTSTTT-XXXXXXX CS
                Ribosomal_L24e  3 tekCsFsgykiyPGhGkrfvrnDgkvfrFlssKc.eklfkqkrnPrklkWTkayRrahkkel 63
                                   ++CsF+g+ i+PG+G+++vr+Dg ++ F+s+Kc ++++   r Pr ++WT+ y++ +k+++
  gi|13541282|ref|NP_110970.1|  3 ARTCSFCGKTIEPGTGIMYVRKDGAILYFCSNKCkKNMIGLNRVPRYVRWTNEYHELKKMRT 64
                                  689*******************************888999******************9876 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 !   27.3   0.7   1.6e-09   2.6e-06       4      39 ..       4      38 ..       2      39 .. 0.91

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 1.6e-09
                        zf-FCS  4 krCwfCkkyikgkpeftyvlendgvvgqFCStsCld 39
                                  ++C+fC+k i+ ++    ++ +dg + +FCS  C++
  gi|13541282|ref|NP_110970.1|  4 RTCSFCGKTIEPGT-GIMYVRKDGAILYFCSNKCKK 38
                                  79********9999.57889999***********86 PP

>> YHS  YHS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.2   1.8e-08   2.9e-05       6      35 ..       9      38 ..       8      39 .. 0.96

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 1.8e-08
                           YHS  6 cgmkvdkekaeekseYkGkeYyFcSegCkd 35
                                  cg+++++++   +++ +G+  yFcS +Ck 
  gi|13541282|ref|NP_110970.1|  9 CGKTIEPGTGIMYVRKDGAILYFCSNKCKK 38
                                  ****************************96 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 !   22.1   0.4   4.6e-08   7.4e-05      14      48 ..       4      41 ..       2      45 .. 0.91

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 4.6e-08
                        zf-FLZ 14 saCflCkkkLgegkDiymYrGdka...FCSeeCRqqqi 48
                                  ++C++C k +++g  i   r d a   FCS+ C ++ i
  gi|13541282|ref|NP_110970.1|  4 RTCSFCGKTIEPGTGIMYVRKDGAilyFCSNKCKKNMI 41
                                  68**************99999999999*******9987 PP

>> Ta0938  Ta0938
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1   4.9e-06     0.008      15      61 ..       4      53 ..       2      63 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 4.9e-06
                                  GS-SS---S-....--SS-B-TT--BSSS--SSSS-TTS-THHHHHHHHHH CS
                        Ta0938 15 kgcalcgatw....gdyyeevdgeklffccdicakefvnllnevkkrtgls 61
                                  + c++cg t     g  y   dg  l+fc + c k+++  ln+v + + ++
  gi|13541282|ref|NP_110970.1|  4 RTCSFCGKTIepgtGIMYVRKDGAILYFCSNKCKKNMIG-LNRVPRYVRWT 53
                                  579****9954444889*****************99886.57777766665 PP

>> DUF3268  zinc-finger-containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.3   1.4e-05     0.023       3      38 ..       4      38 ..       2      66 .] 0.73

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.4e-05
                       DUF3268  3 trCpyCGekvilvsaseiYkerskgkllylC.pkCda 38
                                   +C++CG+++       +Y  r+ g++ly C +kC  
  gi|13541282|ref|NP_110970.1|  4 RTCSFCGKTIEPG-TGIMY-VRKDGAILYFCsNKCKK 38
                                  68*****987654.44567.99*********989974 PP

>> DUF2116  Uncharacterized protein containing a Zn-ribbon (DUF2116)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.1    0.0097        16       5      16 ..       5      16 ..       3      19 .. 0.86
   2 ?    6.5   0.0     0.005       8.2      19      27 ..      31      39 ..      28      46 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0097
                       DUF2116  5 HCivCGkaIpld 16
                                   C  CGk I+++
  gi|13541282|ref|NP_110970.1|  5 TCSFCGKTIEPG 16
                                  6********985 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.005
                       DUF2116 19 fCsekCqee 27
                                  fCs+kC+++
  gi|13541282|ref|NP_110970.1| 31 FCSNKCKKN 39
                                  9*****986 PP

>> Arc_trans_TRASH  Archaeal TRASH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   2.3     3e-05      0.05       1      32 [.       6      39 ..       6      41 .. 0.78
   2 ?   -2.7   0.1       4.9   8.1e+03      31      36 ..      57      62 ..      56      63 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3e-05
               Arc_trans_TRASH  1 CDYCGkeiv.gePivyklkn.kvYyvCCktCkse 32
                                  C +CGk i  g+ i+y  k   + y+C + Ck++
  gi|13541282|ref|NP_110970.1|  6 CSFCGKTIEpGTGIMYVRKDgAILYFCSNKCKKN 39
                                  99******746777764443379*********87 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 4.9
               Arc_trans_TRASH 31 selkkk 36
                                  +elkk 
  gi|13541282|ref|NP_110970.1| 57 HELKKM 62
                                  689985 PP

>> VATC  Vms1-associating treble clef domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   3.5   0.00077       1.3       4      31 ..       4      36 ..       3      39 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00077
                          VATC  4 lrCsiCgesleg...kvyFekfd..frYCstkC 31
                                  ++Cs+Cg+ +e+   + y +k      +Cs kC
  gi|13541282|ref|NP_110970.1|  4 RTCSFCGKTIEPgtgIMYVRKDGaiLYFCSNKC 36
                                  78*********8553446665332245899999 PP

>> zf-C4_ClpX  ClpX C4-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   4.0   0.00031      0.51       2      10 ..       5      13 ..       4      40 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00031
                    zf-C4_ClpX  2 rCSFCgkse 10
                                  +CSFCgk+ 
  gi|13541282|ref|NP_110970.1|  5 TCSFCGKTI 13
                                  7******96 PP

>> YacG  DNA gyrase inhibitor YacG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   3.9    0.0031       5.1      20      28 ..      30      38 ..       4      66 .] 0.69

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0031
                          YacG 20 PFCSeRCkl 28
                                   FCS++Ck+
  gi|13541282|ref|NP_110970.1| 30 YFCSNKCKK 38
                                  5******96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       544  (0.0303419); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.41u 0.29s 00:00:00.70 Elapsed: 00:00:00.46
# Mc/sec: 426.74
//
Query:       gi|13541283|ref|NP_110971.1|  [L=147]
Description: nucleoside diphosphate kinase [Thermoplasma volcanium GSS1]
Scores for complete 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-55  185.5   0.1    4.6e-55  185.3   0.1    1.0  1  NDK       Nucleoside diphosphate kinase


Domain annotation for each model (and alignments):
>> NDK  Nucleoside diphosphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  185.3   0.1   2.5e-59   4.6e-55       2     135 .]       3     136 ..       2     136 .. 0.99

  Alignments for each domain:
  == domain 1  score: 185.3 bits;  conditional E-value: 2.5e-59
                                   EEEEEE-HHHHHTT-HHHHHHHHHHHT-EEEEEEEECE-HHHHHHHTGGGTTSTTHHHHHHHHTSSEEEEEEEESTTHHHH CS
                           NDK   2 rtlvliKPdavkrgligeiisrleekglkivalkmlrlteeqaeehYaehkgkpffeelvefmtsgpvvalvlegedaiek 82 
                                   rtlvl+KPdavkr+l+g+ii+r+eekglkiva+k++++t++qa++hY+ h++kpff++lv+++tsgp+va++leg +aie 
  gi|13541283|ref|NP_110971.1|   3 RTLVLLKPDAVKRRLVGKIIERFEEKGLKIVAMKFMQMTKDQAKTHYSVHQNKPFFNDLVNYITSGPIVAMILEGAHAIEI 83 
                                   9******************************************************************************** PP

                                   HHHHH--SSTTTSSTTSHHHHH-SSSTT-SEEE-SSHHHHHHHHHHHSTGGGS CS
                           NDK  83 vreliGatnpaeaapgtiRadfgvslgeNlvHgSdseesaereiklfFkeeei 135
                                   vr + Gat+ ++a+pgtiR+d+++ +++N++H+Sds e+ ++e+ +fF+++ei
  gi|13541283|ref|NP_110971.1|  84 VRLMSGATDGSKAQPGTIRGDYSMGIEKNIIHASDSLEAYNHEMPIFFSDNEI 136
                                   *************************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       583  (0.0325172); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 897.14
//
Query:       gi|13541284|ref|NP_110972.1|  [L=589]
Description: translation initiation factor IF-2 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-32  112.7   1.7    1.9e-31  109.1   1.7    2.4  1  GTP_EFTU         Elongation factor Tu GTP binding domain
    1.5e-22   79.3   0.2      1e-21   76.6   0.2    2.5  1  GTP_EFTU_D4      Elongation factor Tu domain 4
    2.5e-20   72.6   3.4    6.4e-20   71.2   3.4    1.8  1  IF-2             Translation-initiation factor 2
    7.2e-09   35.7   1.1      2e-08   34.3   0.3    2.2  2  MMR_HSR1         50S ribosome-binding GTPase
    2.6e-08   34.1   5.0    0.00012   22.4   0.5    3.0  2  GTP_EFTU_D2      Elongation factor Tu domain 2
     0.0013   18.8   0.4       0.24   11.4   0.0    3.0  3  Dynamin_N        Dynamin family
     0.0043   16.9   0.0      0.015   15.1   0.0    1.9  1  ATP_bind_1       Conserved hypothetical ATP binding protein
  ------ inclusion threshold ------
      0.011   15.7   0.1      0.026   14.5   0.1    1.5  1  Spore_coat_CotO  Spore coat protein CotO
      0.033   14.4   0.0       0.11   12.7   0.0    2.0  1  Roc              Ras of Complex, Roc, domain of DAPkinase
       0.04   13.2   0.2       0.12   11.6   0.0    1.8  2  Septin           Septin
       0.43   10.5   5.6       0.15   11.9   1.9    2.2  2  NUFIP1           Nuclear fragile X mental retardation-interac


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 !  109.1   1.7   1.2e-34   1.9e-31       5     189 ..      18     221 ..      15     226 .. 0.81

  Alignments for each domain:
  == domain 1  score: 109.1 bits;  conditional E-value: 1.2e-34
                                   EEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEETTCSSEEEEEEEESSSGGGHH CS
                      GTP_EFTU   5 nigiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaisleketkkylinliDtPGHvdFsk 85 
                                    ++++ghvDhGKtTL+d +  ++ a ++ g  ++ + +  t +  +    T k ++  ++       + +iDtPGHv Fs+
  gi|13541284|ref|NP_110972.1|  18 IVCVLGHVDHGKTTLLDIIRGTAVANKEPGGITQ-RIAATTVDINKILKATEKLNNKGMK----IPGLLFIDTPGHVAFSN 93 
                                   68***************99977777777665554.3334455555555566666666665....8999************* PP

                                   HHHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTEEEEEEESCGST...............HHHHHHHHHHHHHHHH CS
                      GTP_EFTU  86 evirglrvlDgavlvvdaveGvepqteevlrlalkegvpiivfiNKmDrl...............kaelkeiveevkqkls 151
                                      rg + +D+avlv+d++eG++pqt e + +++k ++p+i++ NK+D +               +++ +e v+e+  ++ 
  gi|13541284|ref|NP_110972.1|  94 MRARGGALADIAVLVIDINEGIMPQTVESIDILKKFKTPFIIAANKIDLIpfftdvktnlftefiRKQRQEYVNELDARIY 174
                                   ****************************************************99999888855554444555555555554 PP

                                   HHHHHHHHHHHTTT.........TTEEEEEEBTTTTBTHHHHHHHHH CS
                      GTP_EFTU 152 rkeeklekygekge.........kevpvvfgSalkgegvktllealv 189
                                   +  +kl +yg +++         k++ +v++Sa+k+ gv ++l +l 
  gi|13541284|ref|NP_110972.1| 175 NIVNKLYEYGLNSDrfdrisdftKTIAIVPVSAKKNIGVPEILMVLA 221
                                   447777777777669999999999****************9998776 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 !   76.6   0.2   6.4e-25     1e-21       2      86 .]     463     547 ..     462     547 .. 0.99

  Alignments for each domain:
  == domain 1  score: 76.6 bits;  conditional E-value: 6.4e-25
                                   -CEEEEEEEEEEETCCCEEEEEEEEEEEEETT-EEEETTE.EEEEEEEEEETTEEESEEETT-EEEEEEESS-TTTS--TT CS
                   GTP_EFTU_D4   2 PgkikilpgvvfrrsdpaivGvevlgGvikpgvklikedGrevGeilqiqdkgkkleeakaGqevaisiegkivGrqikeg 82 
                                   P+ki+ilp+++fr+s+p+ivG++v +G+ik+g +li++dG+  G+i++i++ + +++   a +eva++i++ ++ rqi  +
  gi|13541284|ref|NP_110972.1| 463 PAKIRILPQYIFRASKPVIVGIRVETGQIKVGDNLIRSDGKYAGTIKSIRNDEVSVRYQDAPAEVAVAIDNVTLNRQIFPD 543
                                   9******************************************************************************** PP

                                   -EEE CS
                   GTP_EFTU_D4  83 dily 86 
                                   d+ly
  gi|13541284|ref|NP_110972.1| 544 DVLY 547
                                   ***9 PP

>> IF-2  Translation-initiation factor 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.2   3.4   3.9e-23   6.4e-20       4     104 ..     336     441 ..     333     442 .. 0.88

  Alignments for each domain:
  == domain 1  score: 71.2 bits;  conditional E-value: 3.9e-23
                                   HHHCCCSCS......SCCEEEEEESSHHHHHHHHHHHHCTT.SSTEEEECEEEESSB-HHHHHHHHH....STEEEEEESS CS
                          IF-2   4 lfeeikeeg......kelnviikaDvqGsleAlkeaLekleseevkvkvihsgvGaitesDvelasa....snaiiigFnv 74 
                                   +++ei+e        +e ++++ka+  GsleA++  L+k       +k+  ++vG+it++Dv+ +++     n iiigFnv
  gi|13541284|ref|NP_110972.1| 336 VMKEIEEASkvdiplDENGIYVKAEAIGSLEAISYELNKQ-----GIKIRAAAVGDITKRDVMDVQTlqdpLNRIIIGFNV 411
                                   5555554445556778999********************8.....4*********************755446******** PP

                                   SCTHHHHHCCCCCTSEEEEESSHHHHHHHH CS
                          IF-2  75 kvskkakklaekegvkirlynvIYkliddv 104
                                   ++ ++ak+++e+++v +++ ++IYk+++d 
  gi|13541284|ref|NP_110972.1| 412 SILPEAKDAIESSDVGVITGDIIYKIVEDT 441
                                   ****************************96 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.3   0.3   1.2e-11     2e-08       2     114 .]      19     139 ..      18     139 .. 0.71
   2 ?   -3.5   0.0       6.5   1.1e+04      38     101 ..     435     445 ..     414     462 .. 0.46

  Alignments for each domain:
  == domain 1  score: 34.3 bits;  conditional E-value: 1.2e-11
                                   EEEEESTTSSHHHHHHHHHT.....S..TEEESSSTTSSSSEEEEEEEETTEE...........EEEEECGGCSSHHHHHH CS
                      MMR_HSR1   2 vaivGrpNvGKStLinaltg.....e..kaivsdkpgtTrdinegrvklkgke...........ielvDtpGliegaseek 64 
                                   v+++G+   GK+tL+  + g     +    i+++++ tT din++  ++   e           + ++DtpG +       
  gi|13541284|ref|NP_110972.1|  19 VCVLGHVDHGKTTLLDIIRGtavanKepGGITQRIAATTVDINKILKAT---EklnnkgmkipgLLFIDTPGHVA------ 90 
                                   899**************99833332222346677777777776663332...0233455666669*******444...... PP

                                   HHHHHHHHHHC.TSEEEEEEETTTTCSHHHHHHHHHHHHHTTSEEEEEEES CS
                      MMR_HSR1  65 glgkaflalee.adlillvvdaseeklkpldeeleelleeakkplilvlnk 114
                                    +++  ++    ad+++lv+d++ e++ p+  e  ++l++ k p+i+++nk
  gi|13541284|ref|NP_110972.1|  91 -FSNMRARGGAlADIAVLVIDIN-EGIMPQTVESIDILKKFKTPFIIAANK 139
                                   .333333333347********99.77*9*********************98 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 6.5
                                   EEEEEETTEEEEEEECGGCSSHHHHHHHHHHHHHHHHCTSEEEEEEETTTTCSHHHHHHHHHHH CS
                      MMR_HSR1  38 egrvklkgkeielvDtpGliegaseekglgkaflaleeadlillvvdaseeklkpldeeleell 101
                                   ++ v                                                     e+ ++++
  gi|13541284|ref|NP_110972.1| 435 YKIV-----------------------------------------------------EDTQKWI 445
                                   2222.....................................................2222222 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 !   22.4   0.5   7.1e-08   0.00012       5      73 ..     257     326 ..     253     327 .. 0.89
   2 !   12.5   0.4   8.8e-05      0.14       3      56 ..     481     527 ..     480     539 .. 0.68

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 7.1e-08
                                   EEEEEESEEETTEEEEEECTCTTSEEEEEEEEEEEEETEEESEE.....ETTSEEEEEEEESSCCSGSSTTCEE CS
                   GTP_EFTU_D2   5 lgrvysGtlkkGdevrilgndtskkeivtrissletfhededea.....vaganaGvivaikgledaiivGdtl 73 
                                   ++++y+Gt+ +Gd+v +  n+ +  + +t++++l+++ ++ +        + a+ G+ v+i +  d +i G++l
  gi|13541284|ref|NP_110972.1| 257 DAVLYQGTISVGDTVAV--NT-KTGPVTTKVKALFVNTGKSQRSlkeveTVSAAEGIRVLISDKLD-VISGSPL 326
                                   6789*************..85.4667*************9888889988999999**********9.9*99987 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 8.8e-05
                                   EEEEEEEESEEETTEEEEEECTCTTSEEEEEEEEEEEEETEEESEEETTSEEEE CS
                   GTP_EFTU_D2   3 valgrvysGtlkkGdevrilgndtskkeivtrissletfhededeavaganaGv 56 
                                   ++++rv++G++k+Gd++    +d +     ++i+s+   +  ++     a+a v
  gi|13541284|ref|NP_110972.1| 481 IVGIRVETGQIKVGDNLIR--SDGKYA---GTIKSIRNDEVSVRY--QDAPAEV 527
                                   899*************998..665455...888888877444443..3333333 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.0   0.00015      0.24       1      35 [.      19      53 ..      19      57 .. 0.95
   2 ?    4.3   0.0     0.023        37      83     112 ..      60      89 ..      53     126 .. 0.85
   3 ?   -3.6   0.0       6.4     1e+04      67      88 ..     440     461 ..     432     471 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00015
                                  EEEEEBTTTTHHHHHHHHHTS--S---SSS---S- CS
                     Dynamin_N  1 iavvGsqSsGKSSvlnaLlgedilprgpnptTrrp 35
                                  ++v+G++ +GK+++l+ + g ++  ++p+ +T+r+
  gi|13541284|ref|NP_110972.1| 19 VCVLGHVDHGKTTLLDIIRGTAVANKEPGGITQRI 53
                                  78******************************997 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.023
                                   SSS--SS-EEEEEEETTS-SEEEEE---B- CS
                     Dynamin_N  83 nkgiskkvillkilsllvkgltlvDlPGld 112
                                    ++i k  ++l++++ + +gl ++D+PG  
  gi|13541284|ref|NP_110972.1|  60 INKILKATEKLNNKGMKIPGLLFIDTPGHV 89 
                                   6788899999******************65 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 6.4
                                   HHHHHHHHHHHHHHTSSSS--S CS
                     Dynamin_N  67 evreeieketekiagankgisk 88 
                                   + ++ ie+++++++++ k+   
  gi|13541284|ref|NP_110972.1| 440 DTQKWIEERKKQLSQKRKEAMP 461
                                   4455566666666655555544 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   9.1e-06     0.015      84     227 ..      68     212 ..      47     225 .. 0.64

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 9.1e-06
                    ATP_bind_1  84 eeleke.ed..dyllfDtPGQielfthseslakiveeLesefalvvvyLvDsqrltdptkfisgllsalsamlrlelPhvv 161
                                   e+l+++  +   +l +DtPG + + ++++ +           a ++v ++D +    p +       ++ ++ + ++P+++
  gi|13541284|ref|NP_110972.1|  68 EKLNNKgMKipGLLFIDTPGHVAFSNMRARGG--------ALADIAVLVIDINEGIMPQTVE-----SIDILKKFKTPFII 135
                                   4444443334468999*************999........5566888888887665555443.....3588999******* PP

                    ATP_bind_1 162 vlnkfDllkeklekeleffedvealslllekee...........ekykklaeaiaelleefalvlrflplssekees 227
                                   + nk+Dl+   ++ + + f+++ + ++ +  +e            +   l+++  + +++f+ ++ ++p+s++k+ +
  gi|13541284|ref|NP_110972.1| 136 AANKIDLIPFFTDVKTNLFTEFIRKQRQEYVNEldariynivnkLYEYGLNSDRFDRISDFTKTIAIVPVSAKKNIG 212
                                   *******8744666777777664333322222233456655553222335555556666666666666666666555 PP

>> Spore_coat_CotO  Spore coat protein CotO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   1.6e-05     0.026     152     185 ..     502     535 ..     495     540 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.6e-05
               Spore_coat_CotO 152 ktYrgvilerredivsiktfssmeetelaiddIt 185
                                    +Y g i + r+d+vs++ ++ ++e+ +aid++t
  gi|13541284|ref|NP_110972.1| 502 GKYAGTIKSIRNDEVSVRYQDAPAEVAVAIDNVT 535
                                   58*****************************997 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 ?   12.7   0.0     7e-05      0.11       2     119 ..      19     141 ..      18     142 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7e-05
                                   EEEESSTTSSHHHHHHCHCT-CCC-EEETTTTEEEEE..EECGGSG...GCTTBTTTTCEEEEEEEE-SGGCTTTT-HHHH CS
                           Roc   2 vvlvGdsgvGKtsllkrfvedkfsekekstigvdflt..kevtkik...gvendkkvkkvklniWDtaGqerfrslhplyl 77 
                                   v+++G    GKt+ll+ +    + +ke   i   ++    +++ki    +  n+k +k   l + Dt G+  f++++    
  gi|13541284|ref|NP_110972.1|  19 VCVLGHVDHGKTTLLDIIRGTAVANKEPGGITQRIAAttVDINKILkatEKLNNKGMKIPGLLFIDTPGHVAFSNMRARGG 99 
                                   689************99998888877654333333330033333221102223444555668999**************** PP

                                   CTSCEEEEEEEGHHHHCHHHHHHHHHHHCS.SS-EEEEEE-TT CS
                           Roc  78 reaalailvydsrssenlkeWlkelkkvag.kspvilvgnkiD 119
                                     a++a+lv+d ++   + + +++++   + k+p+i+ +nkiD
  gi|13541284|ref|NP_110972.1| 100 ALADIAVLVIDINE-GIMPQTVESIDILKKfKTPFIIAANKID 141
                                   ***********854.44556677777776657899999***99 PP

>> Septin  Septin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   7.3e-05      0.12       7      75 ..      19      91 ..      16     101 .. 0.78
   2 ?   -2.8   0.0       1.8   2.9e+03     134     152 ..     192     210 ..     149     238 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 7.3e-05
                                  EEEEEBTTSSCCCCCCTTSSSS------------------S-E...EEEEEEEETTCEEE.EEEEE---BSSS CS
                        Septin  7 lmvvGesglGkttlintlfetdlieeekleeasekkkktveik...kkkvvieedgvkln.ltviDtpgfGda 75
                                  + v G+   Gkttl++ +  t + ++e    ++  +++tv+i+   k++++++++g+k+  l  iDtpg+  +
  gi|13541284|ref|NP_110972.1| 19 VCVLGHVDHGKTTLLDIIRGTAVANKEPGGITQRIAATTVDINkilKATEKLNNKGMKIPgLLFIDTPGHVAF 91
                                  5688*******************9996544444455555555533389999********5499******8655 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.8
                                   HHHHHTTTS-EEEEESSGG CS
                        Septin 134 lmkklsekvnliPviaKaD 152
                                    +   ++++ ++Pv aK +
  gi|13541284|ref|NP_110972.1| 192 RISDFTKTIAIVPVSAKKN 210
                                   4556677788888888865 PP

>> NUFIP1  Nuclear fragile X mental retardation-interacting protein 1 (NUFIP1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   1.9   9.3e-05      0.15      19      30 ..     439     450 ..     432     451 .. 0.92
   2 ?   -2.6   0.1       3.2   5.2e+03       9      23 ..     562     576 ..     558     576 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 9.3e-05
                        NUFIP1  19 eeIakWreERkK 30 
                                   e+ +kW+eERkK
  gi|13541284|ref|NP_110972.1| 439 EDTQKWIEERKK 450
                                   899********9 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 3.2
                        NUFIP1   9 egtsitleTpeeIak 23 
                                   +  + +++T eeI k
  gi|13541284|ref|NP_110972.1| 562 PMEKEIMDTLEEIIK 576
                                   566778999999965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (589 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       843  (0.0470188); expected 358.6 (0.02)
Passed bias filter:                      605  (0.0337442); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.69u 0.29s 00:00:00.98 Elapsed: 00:00:00.48
# Mc/sec: 3710.22
//
Query:       gi|13541285|ref|NP_110973.1|  [L=317]
Description: UDP-glucose 4-epimerase [Thermoplasma volcanium GSS1]
Scores for 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  105.1   0.1    4.7e-30  104.8   0.1    1.2  1  Epimerase        NAD dependent epimerase/dehydratase family
    4.1e-23   82.3   0.2    9.7e-23   81.1   0.2    1.8  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    5.4e-17   61.7   0.0    8.9e-17   61.0   0.0    1.4  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    5.7e-15   55.2   0.0    7.4e-15   54.8   0.0    1.1  1  RmlD_sub_bind    RmlD substrate binding domain
    4.5e-12   45.7   0.4    2.3e-10   40.1   0.4    2.8  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
    2.5e-10   40.5   0.0    5.3e-10   39.5   0.0    1.5  2  NAD_binding_10   NAD(P)H-binding
    9.2e-09   34.8   0.0    7.1e-08   31.9   0.0    2.2  2  NAD_binding_4    Male sterility protein
    1.5e-05   24.9   0.0    0.00034   20.6   0.0    2.2  1  KR               KR domain
    0.00057   19.4   0.1     0.0013   18.2   0.1    1.6  1  adh_short        short chain dehydrogenase
  ------ inclusion threshold ------
      0.036   13.6   0.0      0.062   12.8   0.0    1.5  1  adh_short_C2     Enoyl-(Acyl carrier protein) reductase
       0.19   11.6   0.0        0.3   11.0   0.0    1.3  1  VasL             Type VI secretion system, EvfB, or VasL


Domain annotation for each model (and alignments):
>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.8   0.1   2.9e-33   4.7e-30       1     177 [.       2     173 ..       2     237 .. 0.80

  Alignments for each domain:
  == domain 1  score: 104.8 bits;  conditional E-value: 2.9e-33
                                   EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE--S.---HHHH CS
                     Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfkeeqpdavihlAa.vggvaas 80 
                                   ilVtG +G+iG+ lv +l+ek  +  +++++  ++ t+    +++++ld+ +r++++r+++++ +da++hlA+  +  ++ 
  gi|13541285|ref|NP_110973.1|   2 ILVTGSSGQIGTELVPYLAEKYGKKNVIASDIVQRDTG---GIKFITLDVSNRDEIDRAVEKYSIDAIFHLAGiLSAKGE- 78 
                                   8********************96655555553344433...348*****************************8888777. PP

                                   HHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS--.--SSHHHHHHHHHHHHHHHHHHHH CS
                     Epimerase  81 sedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqpkeettltgpl.kpnspYaaaKlageklveayaaqy 160
                                    +dpa  ++ n++gt+n+leaa+++ v++++  s+  v+G+ ++  k+++     + +p++ Y+++K+a+e l ++y +++
  gi|13541285|ref|NP_110973.1|  79 -KDPALAYKVNMNGTYNILEAAKQHRVEKVVIPSTIGVFGPETP--KNKVPSI-TItRPRTMYGVTKIAAELLGQYYYEKF 155
                                   .9**************************************9988..5666633.445************************ PP

                                   T-EEEEEEESEEESTT.S CS
                     Epimerase 161 glnaiilrlfnlyGpr.n 177
                                   gl++ +lr+  +++   +
  gi|13541285|ref|NP_110973.1| 156 GLDVRSLRYPGIISYKaE 173
                                   *********999998852 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 !   81.1   0.2     6e-26   9.7e-23       1     255 [.       3     238 ..       3     301 .. 0.70

  Alignments for each domain:
  == domain 1  score: 81.1 bits;  conditional E-value: 6e-26
                                   EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-SEEEE CS
                 GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpdevyn 81 
                                   L+TG +G+iG  l+ +L ek+ +  +i    +s     i  +++d     ++ +k++  D++++++++r+++++ +d++++
  gi|13541285|ref|NP_110973.1|   3 LVTGSSGQIGTELVPYLAEKYGKKNVI----AS----DI--VQRD-----TGGIKFITLDVSNRDEIDRAVEKYSIDAIFH 68 
                                   9******************94444333....12....22..3332.....35799************************** PP

                                   --S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-S.SSSB-TTS-----SHHHHHHHHHH CS
                 GDP_Man_Dehyd  82 LAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvq.evpqtEttpfyPrsPYaaaKlyad 161
                                   LA+    +   ++P+  ++vn+ Gt+++Lea++++ +e   ++++ St  v+G  + + ++   t ++Pr  Y+++K++a+
  gi|13541285|ref|NP_110973.1|  69 LAGILSAKG-EKDPALAYKVNMNGTYNILEAAKQHRVE---KVVIPSTIGVFGPETpKNKVPSITITRPRTMYGVTKIAAE 145
                                   ***977665.478**********************987...899*********88646778889***************** PP

                                   HHHHHHHHHH---EEEEEE-EEESTTS-TTSCCCHHHHHHHHHHTTS-C.-EECTTTT-EEEEEEHHHHHHHHHHHHHCSS CS
                 GDP_Man_Dehyd 162 wivvnyreayglfavngilfnhesprrgetfvtrkitravarialgkqe.vlylGnldakRdwghvkDyveamwlmlqqdk 241
                                    + + y+e++gl + + ++    s + ++t  t      +   a+++++ + yl   +a     +  D  +a++ + ++d+
  gi|13541285|ref|NP_110973.1| 146 LLGQYYYEKFGLDVRSLRYPGIISYKAEPTAGTTDYAVEIFYYAVKREKyKCYLAPNRA-LPMMYMPDALKALVDLYEADR 225
                                   ************99998775555544444443333333333333322220223332222.234566666666666666554 PP

                                   ---EEE-TT-EEEC CS
                 GDP_Man_Dehyd 242 pedyviatgethsv 255
                                    ++ v+ +g +++ 
  gi|13541285|ref|NP_110973.1| 226 -DKLVLRNGYNVTA 238
                                   .5566666555555 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 !   61.0   0.0   5.5e-20   8.9e-17       1     130 [.       3     126 ..       3     147 .. 0.88

  Alignments for each domain:
  == domain 1  score: 61.0 bits;  conditional E-value: 5.5e-20
                     3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkkviegDvtdkdkleeale..gvdvvihlaslvdv 79 
                                   +vtG++G +G +lv  L +   +k+v + D++++++        ++k +i+ Dv + d++++a+e  ++d+++hla++   
  gi|13541285|ref|NP_110973.1|   3 LVTGSSGQIGTELVPYLAEKYGKKNVIASDIVQRDTG-------GIK-FITLDVSNRDEIDRAVEkySIDAIFHLAGILSA 75 
                                   69****************9999*********998877.......566.9***************9444789********** PP

                     3Beta_HSD  80 agkltedeimkvnvkGTrnvleacvkagvrvlvYtSsaevvgpnslgeeil 130
                                   +g+      +kvn++GT n+lea++++ v+++v  S+++v gp + ++++ 
  gi|13541285|ref|NP_110973.1|  76 KGEKDPALAYKVNMNGTYNILEAAKQHRVEKVVIPSTIGVFGPETPKNKVP 126
                                   *******************************************87777664 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.8   0.0   4.6e-18   7.4e-15       3     133 ..       2     145 ..       1     155 [. 0.88

  Alignments for each domain:
  == domain 1  score: 54.8 bits;  conditional E-value: 4.6e-18
                                   EEEESTTSHHHHHHHHHCTTT..SEEEEEE-TT..........T--TTSHHHHHHHHHHH--SEEEE------HHHHHHSH CS
                 RmlD_sub_bind   3 ilvtGanGqlGseLakqlaee..glevlaltre..........eldltdaeavaellkeakpdvvvnaAAytavDkaEsee 71 
                                   ilvtG++Gq+G+eL+  lae+  + +v+a +            +ld+++++++++++++ + d++ ++A      k E+++
  gi|13541285|ref|NP_110973.1|   2 ILVTGSSGQIGTELVPYLAEKygKKNVIASDIVqrdtggikfiTLDVSNRDEIDRAVEKYSIDAIFHLAGILS-AKGEKDP 81 
                                   9***************99986223456666433678*********************************9876.589**** PP

                                   HHHHHHHTHHHHHHHHHHHHCT-.EEEEEEEGGGS-S-TTS-.B-TTS----SSHHHHHHHHHH CS
                 RmlD_sub_bind  72 eaayavnaeavealAeaaaavga.lLihvStDyVFdGekkrp.YeeddetsPlnvYGrtKlaGE 133
                                   ++ay+vn++++ ++ eaa+++ + +++  St  VF  e++++       t P+++YG tK+a E
  gi|13541285|ref|NP_110973.1|  82 ALAYKVNMNGTYNILEAAKQHRVeKVVIPSTIGVFGPETPKNkVPSITITRPRTMYGVTKIAAE 145
                                   *******************9998358899******99977664888899************999 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.1   0.4   1.4e-13   2.3e-10       1     128 [.       2     112 ..       2     164 .. 0.76

  Alignments for each domain:
  == domain 1  score: 40.1 bits;  conditional E-value: 1.4e-13
                                   EEEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T-SEE CS
               Polysacc_synt_2   1 vlvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelkvdvv 81 
                                   +lvtG++G iG elv  +++k  kk ++ +       +i ++      +  +k+    +  dv +++++++a+e++++d++
  gi|13541285|ref|NP_110973.1|   2 ILVTGSSGQIGTELVPYLAEKYGKKNVIAS-------DIVQRD-----TGGIKF----ITLDVSNRDEIDRAVEKYSIDAI 66 
                                   89****************999777777655.......333332.....223444....478******************** PP

                                   EE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEE CS
               Polysacc_synt_2  82 fhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkvvliSt 128
                                   fh A +      e+ p+ a k N+ gt n++eaa++++v+kvv+ St
  gi|13541285|ref|NP_110973.1|  67 FHLAGILS-AKGEKDPALAYKVNMNGTYNILEAAKQHRVEKVVIPST 112
                                   ****9976.568********************************998 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.5   0.0   3.3e-13   5.3e-10       1     146 [.       6     167 ..       6     191 .. 0.68
   2 ?   -2.5   0.0       2.4   3.9e+03      14      33 ..     228     247 ..     226     270 .. 0.67

  Alignments for each domain:
  == domain 1  score: 39.5 bits;  conditional E-value: 3.3e-13
                                   TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-..SEEEES-....--TCC.. CS
                NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtdvedlaealkga..daVvsal....ggggk.. 73 
                                   G +G++G +lv  l+++   +  +++ +  +     ++ g++ +++dv++ +++ +a++ +  da++  +    ++g+k  
  gi|13541285|ref|NP_110973.1|   6 GSSGQIGTELVPYLAEKY-GKKNVIASDIVQR----DTGGIKFITLDVSNRDEIDRAVEKYsiDAIFHLAgilsAKGEKdp 81 
                                   89**************97.3445555555554....479*******************96633788888777753333345 PP

                                   ......HHHHHHHHHHHHHHCT--EEEEEEETTTTS.GCG.CHHHHHHHHCCHHHH.....HHHHHHHHHHHHSSSEEEEE CS
                NAD_binding_10  74 ......deegaknivdaakeagvkRfvlvsaigvgd.evp.gefgewnkellkayl.....aakraaeellrasgldwTiv 141
                                         + +g+ ni++aak++ v+++v+ s+igv   e+p +++++++ +  ++++     aa      + ++ gld   +
  gi|13541285|ref|NP_110973.1|  82 alaykvNMNGTYNILEAAKQHRVEKVVIPSTIGVFGpETPkNKVPSITITRPRTMYgvtkiAAELLGQYYYEKFGLDVRSL 162
                                   5655555555************************64244313344444444444442112233333444445567777777 PP

                                   EE-CE CS
                NAD_binding_10 142 rpggL 146
                                   r +g+
  gi|13541285|ref|NP_110973.1| 163 RYPGI 167
                                   76665 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.4
                                   HHHC-T-EEEEEETTHHHCH CS
                NAD_binding_10  14 llargghevtalvRnpekla 33 
                                   l+ r+g++vta++ +p++l 
  gi|13541285|ref|NP_110973.1| 228 LVLRNGYNVTAYTFTPSELY 247
                                   45555799999998888874 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.33   5.4e+02       1      21 [.       4      24 ..       4      37 .. 0.83
   2 !   31.9   0.0   4.4e-11   7.1e-08      87     240 ..      62     201 ..      46     212 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.33
                                  EE-TTSHHHHHHHHHHHHHS- CS
                 NAD_binding_4  1 lTGaTGFLGkvLlekLLrttp 21
                                  +TG++G +G+ L+  L ++  
  gi|13541285|ref|NP_110973.1|  4 VTGSSGQIGTELVPYLAEKYG 24
                                  7***********998877655 PP

  == domain 2  score: 31.9 bits;  conditional E-value: 4.4e-11
                                   H--EEEE--SS-S.STTSSE..EHHHHHHHHHHHHHHHTSSS--.-EEEEEE.GGGTTS-TTT--SSS-H......HHH-- CS
                 NAD_binding_4  87 evdviihsaAtvnfdepyke..llrvNveGtrevlelakklkklkvllhvST.ayvngeregeveekvyeegekeeklded 164
                                   ++d+i+h a+ ++ +++ +   +++vN++Gt ++le ak+ +    ++  ST +++ +e  +                ++ 
  gi|13541285|ref|NP_110973.1|  62 SIDAIFHLAGILSAKGEKDPalAYKVNMNGTYNILEAAKQHRVE-KVVIPSTiGVFGPETPK----------------NKV 125
                                   79**********9999777645889**************99888.9999***9999988884................445 PP

                                   EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEE-...-SSST---TTSHHHHHHHHHHHH-EEES-SB- CS
                 NAD_binding_4 165 eraklkglpntYeqsKalaEklvrearrrsglpvvivRpsiitg...esktGwingsdlgirgllgliakgvlpeilgd 240
                                      + +   + Y  +K +aE l + + ++ gl v  +R + i++   e++ G +   d+ ++ + ++++++++++ l+ 
  gi|13541285|ref|NP_110973.1| 126 PSITITRPRTMYGVTKIAAELLGQYYYEKFGLDVRSLRYPGIISykaEPTAGTT---DYAVEIFYYAVKREKYKCYLAP 201
                                   55666677789**************************96666664545555444...4477888889998888876654 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   2.1e-07   0.00034       3     137 ..       2     113 ..       1     122 [. 0.82

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 2.1e-07
                                   EEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHSS--- CS
                            KR   3 ylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaeeppik 83 
                                    l+tG  G++G+el+  laek  ++ v+ s    ++           +    ++++ +Dvs++d++ +++e+++     i 
  gi|13541285|ref|NP_110973.1|   2 ILVTGSSGQIGTELVPYLAEKYGKKNVIASDI--VQ-----------RDTGGIKFITLDVSNRDEIDRAVEKYS-----ID 64 
                                   58999999999999999999887777777766..22...........2334799******************97.....99 PP

                                   EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTTS--SEEEEEEEH CS
                            KR  84 GvihaAgvlrdklleemtaedleqvlapKvkGawnLhelledesldffvlfSSi 137
                                    ++h Ag+l       + ++d + +++  ++G+ n+ e+ ++++++ +v+ S i
  gi|13541285|ref|NP_110973.1|  65 AIFHLAGILS-----AKGEKDPALAYKVNMNGTYNILEAAKQHRVEKVVIPSTI 113
                                   *******976.....556777788888899999999999999999998887765 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.1   8.1e-07    0.0013       3     122 ..       2     102 ..       1     116 [. 0.80

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 8.1e-07
                                   EEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSESEEEE CS
                     adh_short   3 vlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkldvLvn 83 
                                   +lvtG s+ IG +++  la++  k  v+++    +  v          + +i++Dv++r+e++++vek      ++d++ +
  gi|13541285|ref|NP_110973.1|   2 ILVTGSSGQIGTELVPYLAEKYGKKNVIASD---I--VQRD----TGGIKFITLDVSNRDEIDRAVEKY-----SIDAIFH 68 
                                   89*****************985555443333...2..2223....3459*******************9.....9****** PP

                                   ---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHH CS
                     adh_short  84 NAGitgsgpfselseeewervievNltgvflltravlpa 122
                                    AGi      s   e++    ++vN++g++++ +a+ ++
  gi|13541285|ref|NP_110973.1|  69 LAGI-----LSAKGEKDPALAYKVNMNGTYNILEAAKQH 102
                                   ****.....555666778888999999999998887655 PP

>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   3.8e-05     0.062      41     119 ..      39     105 ..      14     151 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.8e-05
                                   TTSEEEE--TTSHHHHHHHHHHHHHHHSSEEEEEE-----EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHHHCTS CS
                  adh_short_C2  41 lgaevlecDVtdeeqvealveevvekfgklDilvnnagiapklkgpfletsreefdraldvnlyslfllakaalplmke 119
                                   +g +++ +DV+++++++++ve+      ++D +++ agi  + kg      +++ + a +vn+++++++++aa+++  e
  gi|13541285|ref|NP_110973.1|  39 GGIKFITLDVSNRDEIDRAVEKY-----SIDAIFHLAGILSA-KG------EKDPALAYKVNMNGTYNILEAAKQHRVE 105
                                   34568*************99984.....7************9.33......5899999***********9999986555 PP

>> VasL  Type VI secretion system, EvfB, or VasL
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00018       0.3       7      46 ..     249     288 ..     244     300 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00018
                          VasL   7 rLeklsplaalrygeqlveqaqqlwPdsaavkaltrqWqq 46 
                                   +++++ p ++++y e  ++++   wP+s++  +++++W  
  gi|13541285|ref|NP_110973.1| 249 KIKERIPEFEIEYKEDFRDKIAATWPESLDSSEASNEWGF 288
                                   6788899*******************************75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       511  (0.0285013); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.60u 0.33s 00:00:00.93 Elapsed: 00:00:00.48
# Mc/sec: 1966.61
//
Query:       gi|13541286|ref|NP_110974.1|  [L=358]
Description: phosphoribosylaminoimidazole carboxylase ATPase subunit [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-36  125.4   0.0    2.3e-36  124.9   0.0    1.2  1  ATP-grasp       ATP-grasp domain
    2.6e-15   55.8   0.2    2.8e-14   52.5   0.0    2.2  2  PurK_C          Phosphoribosylaminoimidazole carboxylase C-te
     0.0026   17.8   0.0     0.0059   16.7   0.0    1.6  1  ATP-grasp_3     ATP-grasp domain
     0.0064   16.3   0.1      0.011   15.6   0.1    1.3  1  Heme_oxygenase  Heme oxygenase
  ------ inclusion threshold ------
      0.011   15.1   0.0      0.018   14.4   0.0    1.3  1  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
      0.026   14.7   0.0      0.061   13.5   0.0    1.6  1  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
       0.11   12.6   0.1        0.2   11.7   0.1    1.4  1  DUF5346         Family of unknown function (DUF5346)


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 !  124.9   0.0   9.1e-40   2.3e-36       4     170 ..     104     258 ..     101     259 .. 0.93

  Alignments for each domain:
  == domain 1  score: 124.9 bits;  conditional E-value: 9.1e-40
                                   TT--B-EEEEECCHHHHHHHHHHH-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHCGTTCEEEEE----SEEEEEEEEE CS
                     ATP-grasp   4 lglpvprflaveskeeleeaaeelglpvvvKarrlgydGkGqsvvrseedleqalealkeekvivEefvpfekElsvlvvr 84 
                                    gl+v+++ +++s +e+ + a+++g  +++K++ +gydGkGq++  + +      e+lk+ek++vEefv+f++E s+++ r
  gi|13541286|ref|NP_110974.1| 104 IGLKVANYRVAHSFSEAVRYAKDFGK-AMIKNSFGGYDGKGQTIYDNGN-----YEELKGEKFVVEEFVDFDYEASIIASR 178
                                   689*********************96.679************9987654.....56678999******************* PP

                                   ETTC-EEE--EEEEEEETTEEEEEEECEE-SCHHHHHHHHHHHHHHHHHTSSEEEEEEEEEETTCTEEEEEEESS--GGGG CS
                     ATP-grasp  85 saeGetafypvvetvqedgilrlsvapaevsekaqkkaeeiakkiveeLggvGvfavElFvledgellvnElapRpHnsGh 165
                                   s++ +++  ++  +++++ i+ +++ap  +     ++  +iakk++++L++vGv+++E++v+ +ge+++nE+apR+HnsGh
  gi|13541286|ref|NP_110974.1| 179 SEDKSFRYHDPSFNYNRNAIFIYNYAPI-M----PANMPDIAKKLMDSLDYVGVMGIEFYVK-NGEVIINEFAPRVHNSGH 253
                                   ***************************9.3....58999********************999.****************** PP

                                   GHHHH CS
                     ATP-grasp 166 vtlda 170
                                    tl +
  gi|13541286|ref|NP_110974.1| 254 HTLLG 258
                                   **965 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 ?    0.9   0.1      0.15   3.7e+02      41      55 ..     252     266 ..     251     267 .. 0.90
   2 !   52.5   0.0   1.1e-17   2.8e-14       4      54 ..     288     339 ..     285     341 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.15
                        PurK_C  41 GHitvvgdsaeelee 55 
                                   GH t++g+s  + ee
  gi|13541286|ref|NP_110974.1| 252 GHHTLLGSSISQFEE 266
                                   9********999886 PP

  == domain 2  score: 52.5 bits;  conditional E-value: 1.1e-17
                        PurK_C   4 vNlLGedae.ekleellaipgahlHlYgKeearpgRKmGHitvvgdsaeele 54 
                                   +N+LG++ + ++++++l++  +++++YgKee r+ RK+GH++v++ + e+l 
  gi|13541286|ref|NP_110974.1| 288 INILGTKLStDAWNSILSMSSTQIYWYGKEEIRRRRKVGHVNVTAGTVEALI 339
                                   8*******9999999******************************9999875 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   2.3e-06    0.0059      31     159 ..     128     249 ..     101     251 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 2.3e-06
                                   SSSEEEEESS-------B--SS--TTE.......EEEE---SEEEEEEEEE.SSSEEEEEEEEEEEET....TEEEEEEES CS
                   ATP-grasp_3  31 ekklvvKprdGaggesvrvveekeeaeaaieevelvqefieGkplSvsllsdgekvlvlavnrqliekaekefvyaGnvtp 111
                                    k+++   + G +g++ ++ ++++ +e + e+  +v ef++  ++ +s++++ ++ + +   +   + + ++ ++  n +p
  gi|13541286|ref|NP_110974.1| 128 GKAMIKNSFGGYDGKGQTIYDNGNYEELKGEKF-VVEEFVDF-DYEASIIASRSEDKSFRYHDPSFNYN-RNAIFIYNYAP 205
                                   566777777889***********9999888876.******95.68899999999999999999999774.44667668999 PP

                                   ----HHHHHHHHHHHHHTTSTT--EEEEEEEEESS.SEEEEEEESS-- CS
                   ATP-grasp_3 112 ietelkeevvelaeevvekleglaGyvGvDlvlkdeepyviEvNPRlt 159
                                   i      ++ ++a++++ +l + +G++G+++ +k++e ++ E  PR+ 
  gi|13541286|ref|NP_110974.1| 206 IM---PANMPDIAKKLMDSL-DYVGVMGIEFYVKNGEVIINEFAPRVH 249
                                   98...899************.**************9999999999986 PP

>> Heme_oxygenase  Heme oxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   4.2e-06     0.011      33      82 ..      46     100 ..      37     132 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 4.2e-06
                                   -HHHHHHHHHH....HHHHHHHHHHHHHHCTTSTTCGGGS-G.GG--HHHHHHHH CS
                Heme_oxygenase  33 dkeaYkkllan....lyelykalEeeleenkdspviapilfp.eLhRkaaLerdl 82 
                                   ++++Yk+++ +     ye+ + lEe+l   +d++ ++p ++p eL+++ +Le+d 
  gi|13541286|ref|NP_110974.1|  46 SVDQYKEFVDKcdvvTYEFEHVLEEALLYAEDQHKLKPSIRPvELKKDRSLEKDY 100
                                   55667777665333369************************************95 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   7.2e-06     0.018      38      98 ..       2      63 ..       1      83 [. 0.89

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 7.2e-06
                                  EEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHH.CHHHHTCEECSHHHHHHH-SEEEE- CS
                  2-Hacid_dh_C 38 tvGiiGlGrIGqavakrlkafgmkviaydrskkkee.eeeelgvelvsleellaesDivslh 98
                                   vGiiG G++G  +++  + +g k ++ d +    +   ++ ++++++ +e++ ++D+v+  
  gi|13541286|ref|NP_110974.1|  2 NVGIIGSGQLGYMMINEGRRLGNKYFVLDSNGVGPAsLIADAHFSVDQYKEFVDKCDVVTYE 63
                                  69*****************************9866657788899***************975 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   2.4e-05     0.061       1      60 [.       2      61 ..       2      67 .. 0.96

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.4e-05
                                  EEEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTTEEE-SSHHHHHHHCSEEE CS
                 NAD_binding_2  1 kigfiGlGvMGsnmalnllkagykvavynrtkekveelvaegakaaesieelvasldvvi 60
                                  ++g+iG G++G  m+++  + g k  v + +     +l+a+    +++ +e+v+++dvv 
  gi|13541286|ref|NP_110974.1|  2 NVGIIGSGQLGYMMINEGRRLGNKYFVLDSNGVGPASLIADAHFSVDQYKEFVDKCDVVT 61
                                  69****************************************99*************996 PP

>> DUF5346  Family of unknown function (DUF5346)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   7.6e-05       0.2      64      86 ..     195     217 ..     188     223 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 7.6e-05
                       DUF5346  64 rpaapfynyvpalpanwpdvvkl 86 
                                   r a   yny p +pan pd++k 
  gi|13541286|ref|NP_110974.1| 195 RNAIFIYNYAPIMPANMPDIAKK 217
                                   666778*************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (358 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-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: 00:00:00.47
# Mc/sec: 2299.76
//
Query:       gi|13541287|ref|NP_110975.1|  [L=171]
Description: regulator of amino acid metabolism [Thermoplasma volcanium GSS1]
Scores for 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   38.3   0.5    1.5e-09   37.4   0.5    1.5  1  ACT       ACT domain
     0.0032   18.0   0.7      0.005   17.4   0.1    1.6  2  ACT_4     ACT domain
      0.008   15.9   0.2      0.025   14.4   0.2    1.8  2  ACT_7     ACT domain


Domain annotation for each model (and alignments):
>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.4   0.5   2.6e-13   1.5e-09       3      66 ..     102     163 ..     100     164 .. 0.94

  Alignments for each domain:
  == domain 1  score: 37.4 bits;  conditional E-value: 2.6e-13
                                   EEEEEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHHHHHHHHHHHTTC CS
                           ACT   3 lrvgvpDrPGlLarvfgaladrgiNidsieqrssedkvagivfvvivvdeedleevlealkkle 66 
                                   ++ + +++PG++a +++++a+++i+i+ + +   e   ++    v+v+d+++++e++ +l+++ 
  gi|13541287|ref|NP_110975.1| 102 IIPESANKPGIIAGISSIIAKHNISIRQVIVDDPEI--VEDPKAVVVTDQKVPAELIPELRSVD 163
                                   566789******************************..9**********************985 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       2.8   1.7e+04      23      26 ..      65      68 ..      57      74 .. 0.46
   2 !   17.4   0.1   8.3e-07     0.005      12      77 ..     105     167 ..     100     169 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 2.8
                         ACT_4 23 itqv 26
                                  +++ 
  gi|13541287|ref|NP_110975.1| 65 VINR 68
                                  2333 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 8.3e-07
                         ACT_4  12 eaedrkglLaditqviseekanivsvnaktrkkdglaeikitveVkdvehLsrviakLraipgVis 77 
                                   e+ +++g++a i+++i++++++i+ v +++   + ++e    v V d +  +++i  Lr+++gV+ 
  gi|13541287|ref|NP_110975.1| 105 ESANKPGIIAGISSIIAKHNISIRQVIVDD--PE-IVEDPKAVVVTDQKVPAELIPELRSVDGVKG 167
                                   5689*************************9..55.999999999*****************99975 PP

>> 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       0.7   4.2e+03      16      29 ..      12      24 ..       4      25 .. 0.77
   2 !   14.4   0.2   4.2e-06     0.025      19      41 ..     108     130 ..      93     134 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.7
                                  ---SS--HHHHHHH CS
                         ACT_7 16 lpfdvtGivaklas 29
                                   p+ + +iv+k++s
  gi|13541287|ref|NP_110975.1| 12 SPS-QLKIVKKMIS 24
                                  555.7899999987 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 4.2e-06
                                   SS--HHHHHHHHHHTTT---EEE CS
                         ACT_7  19 dvtGivaklaspLaeagIsifqi 41 
                                   + +Gi+a+++s  a+++Isi q+
  gi|13541287|ref|NP_110975.1| 108 NKPGIIAGISSIIAKHNISIRQV 130
                                   68******************876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        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 0.25s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1199.23
//
Query:       gi|13541288|ref|NP_110976.1|  [L=323]
Description: DNA repair and recombination protein RadA [Thermoplasma volcanium GSS1]
Scores for complete 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-86  287.4   0.0    9.8e-86  287.1   0.0    1.0  1  Rad51            Rad51
    4.8e-12   46.3   1.0    1.4e-11   44.8   1.0    1.8  1  HHH_5            Helix-hairpin-helix domain
    1.4e-10   41.1   0.1    1.9e-10   40.6   0.1    1.2  1  RecA             recA bacterial DNA recombination protein
    5.6e-08   32.4   0.1    9.5e-08   31.7   0.1    1.4  1  ATPase           KaiC
    3.5e-07   29.8   2.5     0.0077   16.0   0.1    2.6  2  HHH              Helix-hairpin-helix motif
    4.5e-06   26.4   0.0    7.5e-06   25.6   0.0    1.3  1  AAA_25           AAA domain
    1.4e-05   25.0   0.1    4.5e-05   23.5   0.1    1.9  1  HHH_2            Helix-hairpin-helix motif
    0.00014   22.0   0.0       0.13   12.6   0.0    2.8  2  IMS_HHH          IMS family HHH motif
    0.00019   21.7   0.6       0.31   11.4   0.0    2.7  2  HHH_8            Helix-hairpin-helix domain
    0.00048   20.3   0.0    0.00093   19.4   0.0    1.5  1  Cdd1             Pathogenicity locus
    0.00089   19.5   0.5       0.24   11.7   0.0    2.8  2  HHH_3            Helix-hairpin-helix motif
     0.0011   18.8   0.7       0.19   11.6   0.0    3.5  3  DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
     0.0054   17.1   0.2       0.16   12.4   0.0    2.9  3  BAF              Barrier to autointegration factor
  ------ inclusion threshold ------
      0.093   13.0   0.0       0.18   12.1   0.0    1.4  1  AAA_22           AAA domain
       0.13   12.9   0.7          3    8.5   0.2    2.4  2  5_3_exonuc       5'-3' exonuclease, C-terminal SAM fold


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 !  287.1   0.0   8.2e-89   9.8e-86       3     254 ..      74     321 ..      72     322 .. 0.99

  Alignments for each domain:
  == domain 1  score: 287.1 bits;  conditional E-value: 8.2e-89
                                   -EBHHHHHHHHHSS-EE--S-HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHHHHHHTTS-TTTS--SSEEEEEESSS-- CS
                         Rad51   3 fvsavellekrsellqlttGskklDelLgGGietgsiteifGefrsGktqlchtlcvtvqlplelgGgegkavyidtegtf 83 
                                   f ++ e+le+r+++ +lttGsk+lD+lLgGG+et++ite fGef+sGktq+ h+l+v + +p+e+gG ++ ++ idte tf
  gi|13541288|ref|NP_110976.1|  74 FETGEEILERRKTIQKLTTGSKNLDDLLGGGLETQAITEFFGEFGSGKTQIMHQLAVNCTMPKEKGGFDSDVMMIDTENTF 154
                                   78999**************************************************************************** PP

                                   -GGGGHHHHHHTT--HHHHGGGEEEEE--STTHHHHHHHHTHHHHHHS-EEEEEEETTTGGGCH-------THHHHHHHHH CS
                         Rad51  84 rperlveiaerykldkeevlenvayaRaytiehqeellqqaaallaedkfallivDsvtalyRtdfsgrgelakRqqklgk 164
                                   rper++++a+  +ld++e+l+++ +aRay++ hq  l ++a ++ +e +++llivDs+ta++R+++ grg la+Rqq l+k
  gi|13541288|ref|NP_110976.1| 155 RPERIIQMAKSKGLDPDETLKRIHVARAYNSHHQILLAEKAQETAKEFNIRLLIVDSLTAHFRSEYVGRGSLAERQQLLNK 235
                                   ***********************************9999****************************************** PP

                                   HHHHHHHHHHHH--EEEEEEE-------.------------HHHHHHHH-SEEEEEEE-STTEEEEEEES-SSS-S-EEEE CS
                         Rad51 165 llrtLrkladefevavvitnqvvaqvdgqaalfsadpkkPigGlvlahasttRlalrkgkgeeRivkvvdsPnlpeleavf 245
                                   +++ L ++   +++ + +tnqv+a++d     f +dp+ PigG++++h++t R++lrk kg +Ri++++dsP lpe e+v+
  gi|13541288|ref|NP_110976.1| 236 HMHDLLRFGTIYNAVIAVTNQVSARPDV----FFGDPMAPIGGNIVGHTATFRVYLRKSKGGKRIARLIDSPYLPEGETVI 312
                                   ***************************9....99*********************************************** PP

                                   EEETTEEE- CS
                         Rad51 246 aigeeGied 254
                                   +i+eeG++d
  gi|13541288|ref|NP_110976.1| 313 QISEEGVND 321
                                   *******98 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.8   1.0   1.2e-14   1.4e-11       3      57 .]      13      67 ..      11      67 .. 0.97

  Alignments for each domain:
  == domain 1  score: 44.8 bits;  conditional E-value: 1.2e-14
                                  HHHTSTT--HHHHHHHHTTT--SHHHHHHS-HHHHHTSTTS-HHHHHHHHHHHHH CS
                         HHH_5  3 eLlsvsGiGpktAlallsaGiesvedlaaadveeLakipGiGkktAeriilelkd 57
                                   L +++G+G++tA +l ++G++ + ++a a++++L++++GiG+  A +ii ++++
  gi|13541288|ref|NP_110976.1| 13 TLEDLPGVGEATAEKLRENGYDDIMAIAVASPKDLSDVTGIGEGAAAKIIAAARK 67
                                  6899************************************************997 PP

>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.6   0.1   1.6e-13   1.9e-10      27     224 ..      83     292 ..      60     302 .. 0.77

  Alignments for each domain:
  == domain 1  score: 40.6 bits;  conditional E-value: 1.6e-13
                                   .-----EE--S-HHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHH...HHTT--...EEEEESS----H....HH CS
                          RecA  27 eklkvetissGslaldialGiGGlpkGriieiyGpessGkttlalhaiaea...qkkggv...aafidaehaldp....ky 97 
                                   ++++++ +++Gs  ld  lG GGl    i+e +G   sGkt +  ++ +++   ++kgg+   + +id+e ++ p    + 
  gi|13541288|ref|NP_110976.1|  83 RRKTIQKLTTGSKNLDDLLG-GGLETQAITEFFGEFGSGKTQIMHQLAVNCtmpKEKGGFdsdVMMIDTENTFRPeriiQM 162
                                   46789***************.********************9976655444222456665444789*******99444347 PP

                                   HHHTT--GGG-E....EE--SSHHHHH...HHHHHHHTTT--SEEEEE-TTT---STT-----------HHHHHHHHHHHH CS
                          RecA  98 akklGvdidell....vsqpdtGeqal...eiadalvrsgaidlivvdsvaalvpkaeieGemgdskvglqarlmsqalrk 171
                                   ak  G+d de l    v++  +  + +   e a+   +   i l++vds++a   ++e     g  +++ + +l+ + +  
  gi|13541288|ref|NP_110976.1| 163 AKSKGLDPDETLkrihVARAYNSHHQIllaEKAQETAKEFNIRLLIVDSLTAHF-RSEYV---GRGSLAERQQLLNKHMHD 239
                                   9999**98875433338888777766613344555677779*********9976.45543...445566666777777777 PP

                                   HHHHHTTT--EEEEEEE-----------------HHHHHHH-SEEEEEEEES- CS
                          RecA 172 ltgaisksntvvifinqirekiGvmfgnpetttGGralkfyasvrldvrriee 224
                                   l    +  n+v+   nq+  +  v fg+p +  GG+ +   a+ r+ +r+++ 
  gi|13541288|ref|NP_110976.1| 240 LLRFGTIYNAVIAVTNQVSARPDVFFGDPMAPIGGNIVGHTATFRVYLRKSKG 292
                                   777777778889999**********************************9875 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.7   0.1     8e-11   9.5e-08       2     141 ..      91     223 ..      90     241 .. 0.79

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 8e-11
                        ATPase   2 ktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaek.....ygepgvfvtveepa..edlrenakslGwdle 75 
                                    tg + lD++l gG+  ++++   Ge G+GKt +  q +++  +      ++  ++++ +e +   e +++ aks G d +
  gi|13541288|ref|NP_110976.1|  91 TTGSKNLDDLLGGGLETQAITEFFGEFGSGKTQIMHQLAVNCTMPkekggFDSDVMMIDTENTFrpERIIQMAKSKGLDPD 171
                                   6999************************************9876512222567889*****98666*************** PP

                        ATPase  76 kleeegklaiidasesaeesaeekdkedleelieelaeaikeikakrvviDsitglayeekeavaR 141
                                   +  ++  + +  a++s ++            l+e+ +e  ke++++ +++Ds+t++    +e v R
  gi|13541288|ref|NP_110976.1| 172 ETLKR--IHVARAYNSHHQ----------ILLAEKAQETAKEFNIRLLIVDSLTAH--FRSEYVGR 223
                                   *****..555555544433..........348888999999999999999999988..44455555 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1   6.5e-06    0.0077      12      28 ..      13      29 ..       5      30 .. 0.88
   2 !   12.9   0.6   6.7e-05      0.08       5      29 ..      39      63 ..      38      64 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 6.5e-06
                                  HHHTSTT-SHHHHHHHH CS
                           HHH 12 eLlalPGVGpktAeaIl 28
                                   L++lPGVG++tAe+ +
  gi|13541288|ref|NP_110976.1| 13 TLEDLPGVGEATAEKLR 29
                                  699***********975 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 6.7e-05
                                  HHTSSHHHHHTSTT-SHHHHHHHHH CS
                           HHH  5 lipasreeLlalPGVGpktAeaIls 29
                                  +  as+++L ++ G+G+  A +I++
  gi|13541288|ref|NP_110976.1| 39 IAVASPKDLSDVTGIGEGAAAKIIA 63
                                  678*******************986 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.0   6.3e-09   7.5e-06      12     156 ..      87     217 ..      78     244 .. 0.80

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 6.3e-09
                        AAA_25  12 vadlaapppprrwlvkgllpagelallaGapgtGKttlaldlalava..tGkpwlgpvapeqgkVlyvsaEdsedelrrRl 90 
                                   + +l +  + +++l++g l  ++++ ++G  g+GKt +  +la+ ++  + k  +         V+++++E++    ++R+
  gi|13541288|ref|NP_110976.1|  87 IQKLTTGSKNLDDLLGGGLETQAITEFFGEFGSGKTQIMHQLAVNCTmpKEKGGF------DSDVMMIDTENTF--RPERI 159
                                   55566777889999**999****************************65333223......459*********9..67777 PP

                        AAA_25  91 ravg..ealrddarllvldlagveslpLfakdrggtl.ltadvdaleaaieevegvrlvviDplsralg 156
                                    ++   + l++d++l  +++a+       ++  ++++ l++   + +++++e  ++rl+++D+l++ ++
  gi|13541288|ref|NP_110976.1| 160 IQMAksKGLDPDETLKRIHVARA------YNS-HHQIlLAE---KAQETAKE-FNIRLLIVDSLTAHFR 217
                                   777756777999***99999886......444.55552555...5799****.67*********98665 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.1   3.7e-08   4.5e-05       9      53 ..      18      63 ..      16      71 .. 0.92

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 3.7e-08
                         HHH_2  9 rhVGektAklLakr.FksldaLkkasleeLlevddiGeeiAqsive 53
                                  + VGe+tA++L ++ ++++ a++ as ++L+ v +iGe  A++i+ 
  gi|13541288|ref|NP_110976.1| 18 PGVGEATAEKLRENgYDDIMAIAVASPKDLSDVTGIGEGAAAKIIA 63
                                  78*********9866***************************9975 PP

>> IMS_HHH  IMS family HHH motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.0   0.00011      0.13      11      31 ..      12      32 ..      10      33 .. 0.86
   2 ?    6.3   0.0     0.011        13      10      27 ..      44      61 ..      43      65 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00011
                       IMS_HHH 11 lpitkipGiGgklgekLeklG 31
                                  + + ++pG+G  ++ekL+  G
  gi|13541288|ref|NP_110976.1| 12 TTLEDLPGVGEATAEKLRENG 32
                                  5689************99766 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.011
                       IMS_HHH 10 plpitkipGiGgklgekL 27
                                  p +++++ GiG   ++k+
  gi|13541288|ref|NP_110976.1| 44 PKDLSDVTGIGEGAAAKI 61
                                  679*********999994 PP

>> HHH_8  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.0   0.00026      0.31      47      65 ..      11      30 ..       3      31 .. 0.82
   2 !    7.9   0.1    0.0033         4      42      64 ..      41      62 ..      36      66 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00026
                                  T.HCTTSTT--HHHHHHHHH CS
                         HHH_8 47 e.eltklpgiGkkiaakiee 65
                                  + +l++lpg+G+++a+k++e
  gi|13541288|ref|NP_110976.1| 11 KtTLEDLPGVGEATAEKLRE 30
                                  24699************998 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0033
                                  HHHHTTHCTTSTT--HHHHHHHH CS
                         HHH_8 42 itsleeeltklpgiGkkiaakie 64
                                  ++s ++ l+++ giG++ aaki 
  gi|13541288|ref|NP_110976.1| 41 VASPKD-LSDVTGIGEGAAAKII 62
                                  566565.**************96 PP

>> Cdd1  Pathogenicity locus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   7.8e-07   0.00093       3      43 ..       9      49 ..       7      61 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 7.8e-07
                          Cdd1  3 kalkelqdiPniGkalaedlvelGirsveelkgedpeelye 43
                                  ++ ++l+d+P++G+a+ae+l+e G+ ++  ++  +p++l +
  gi|13541288|ref|NP_110976.1|  9 EKKTTLEDLPGVGEATAEKLRENGYDDIMAIAVASPKDLSD 49
                                  56789*******************************99865 PP

>> HHH_3  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0     0.025        29      12      30 ..      10      28 ..       7      31 .. 0.81
   2 !   11.7   0.0    0.0002      0.24      10      46 ..      41      80 ..      37      91 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.025
                         HHH_3 12 saeeLqklpGlgpklAknI 30
                                  +++ L+ lpG+g+++A+++
  gi|13541288|ref|NP_110976.1| 10 KKTTLEDLPGVGEATAEKL 28
                                  5678999999999999986 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.0002
                         HHH_3 10 tAsaeeLqklpGlgpklAknIva.yRekn..GpfksreeL 46
                                   As ++L+ + G+g+  A +I+a +R+    G+f++ ee 
  gi|13541288|ref|NP_110976.1| 41 VASPKDLSDVTGIGEGAAAKIIAaARKFAdiGNFETGEEI 80
                                  69************87777777615542233566665555 PP

>> DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.0   0.00016      0.19       7      38 ..      18      50 ..      12      54 .. 0.77
   2 ?    4.7   0.2     0.023        27       3      20 ..      47      64 ..      45     101 .. 0.72
   3 ?   -0.6   0.0         1   1.2e+03      31      49 ..     222     240 ..     209     241 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00016
               DNA_pol_lambd_f  7 yGVGpktAkkwyakGirtledlra.krakLtre 38
                                   GVG +tA+k+ ++G+ ++  +    +++L+ +
  gi|13541288|ref|NP_110976.1| 18 PGVGEATAEKLRENGYDDIMAIAVaSPKDLSDV 50
                                  5***************99987766555666655 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.023
               DNA_pol_lambd_f  3 FtkvyGVGpktAkkwyak 20
                                  ++ v+G+G  +A k +a+
  gi|13541288|ref|NP_110976.1| 47 LSDVTGIGEGAAAKIIAA 64
                                  789*****8888877764 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 1
               DNA_pol_lambd_f  31 krakLtreqqiGlkyyeDl 49 
                                   +r +L + qq+  k+ +Dl
  gi|13541288|ref|NP_110976.1| 222 GRGSLAERQQLLNKHMHDL 240
                                   5678999999999999998 PP

>> BAF  Barrier to autointegration factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.0   0.00014      0.16      19      42 ..      13      36 ..       4      42 .. 0.81
   2 ?    0.8   0.0      0.56   6.7e+02      18      36 ..      45      63 ..      41      71 .. 0.83
   3 ?   -1.0   0.0         2   2.4e+03      32      60 ..     172     200 ..     167     213 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00014
                           BAF 19 evtalaGigevlgkkLeekGfdkA 42
                                  + ++l+G+ge  ++kL+e+G+d  
  gi|13541288|ref|NP_110976.1| 13 TLEDLPGVGEATAEKLRENGYDDI 36
                                  4679*****************975 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.56
                           BAF 18 KevtalaGigevlgkkLee 36
                                  K+ +++ Gige  ++k+ +
  gi|13541288|ref|NP_110976.1| 45 KDLSDVTGIGEGAAAKIIA 63
                                  8999*******99988765 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 2
                           BAF  32 kkLeekGfdkAyvvlgqfLvlkkdeelFk 60 
                                   + L++  + +Ay+   q L+ +k +e+ k
  gi|13541288|ref|NP_110976.1| 172 ETLKRIHVARAYNSHHQILLAEKAQETAK 200
                                   56777788899999999999999887655 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00015      0.18       4     102 ..     107     214 ..     105     249 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00015
                        AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaee.erpevvfvtlpsstsskdllrellralglelka.........erls 74 
                                   t+ i+  +Ge G+GKT  + +l+ + +  +k +   +++v+ ++  +   ++ + ++  ++  ++ ++         ++  
  gi|13541288|ref|NP_110976.1| 107 TQAITEFFGEFGSGKTQIMHQLAVNCT-MPKEKGgFDSDVMMIDTENTFRPERIIQMAKSKGLDPDETlkrihvaraYNSH 186
                                   6788889****************9964.444444699*******9999999999888877777666669888888876777 PP

                        AAA_22  75 seellealeqalraravielliiDEaqh 102
                                    + ll+  +q   + + i+lli+D    
  gi|13541288|ref|NP_110976.1| 187 HQILLAEKAQETAKEFNIRLLIVDSLTA 214
                                   7777766666666666679**9997654 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 ?    2.4   0.0       0.2   2.4e+02      22      35 ..      16      29 ..      10      43 .. 0.78
   2 ?    8.5   0.2    0.0025         3      19      63 ..      46      93 ..      31     100 .. 0.69

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.2
                    5_3_exonuc 22 GvpgiGektAakLl 35
                                    pg+Ge tA kL 
  gi|13541288|ref|NP_110976.1| 16 DLPGVGEATAEKLR 29
                                  579********995 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0025
                    5_3_exonuc 19 nipGvpgiGektAakLlkeygsleeilenld...e.lkekklkekLeen 63
                                  ++  v giGe +Aak+++   + ++i +  +   e l++ k+ +kL+++
  gi|13541288|ref|NP_110976.1| 46 DLSDVTGIGEGAAAKIIAAARKFADIGN-FEtgeEiLERRKTIQKLTTG 93
                                  6778**************9999998876.32122323335555666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       617  (0.0344135); expected 358.6 (0.02)
Passed bias filter:                      548  (0.030565); 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: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 2151.18
//
Query:       gi|13541289|ref|NP_110977.1|  [L=338]
Description: glyceraldehyde-3-phosphate dehydrogenase [Thermoplasma volcanium GSS1]
Scores for complete 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    4.9e-23   81.5   0.5    1.2  1  Gp_dh_C        Glyceraldehyde 3-phosphate dehydrogenase, C-te
      3e-11   43.5   0.2    8.5e-11   42.1   0.1    1.8  1  DapB_N         Dihydrodipicolinate reductase, N-terminus
    1.4e-06   28.6   0.1    5.8e-06   26.6   0.1    2.1  1  Gp_dh_N        Glyceraldehyde 3-phosphate dehydrogenase, NAD 
     0.0014   18.9   0.1     0.0033   17.7   0.1    1.7  1  TrkA_N         TrkA-N domain
     0.0063   17.3   0.4      0.039   14.8   0.0    2.4  3  GFO_IDH_MocA   Oxidoreductase family, NAD-binding Rossmann fo
  ------ inclusion threshold ------
      0.014   16.0   0.2       0.91   10.2   0.0    2.6  2  NAD_binding_3  Homoserine dehydrogenase, NAD binding domain
      0.025   13.9   0.4       0.19   11.1   0.4    2.3  1  2-Hacid_dh_C   D-isomer specific 2-hydroxyacid dehydrogenase,
       0.14   12.2   0.5       0.44   10.5   0.1    2.0  2  DUF3113        Protein of unknown function (DUF3113)


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 !   81.5   0.5   2.2e-26   4.9e-23       1     158 []     144     297 ..     144     297 .. 0.97

  Alignments for each domain:
  == domain 1  score: 81.5 bits;  conditional E-value: 2.2e-26
                                   HHHHHHHHHHHHEEEEEEEEEEEECTTTSBSSSS--.SSTTTTSBTT.CSSEEEE-THHHHHHHHSGGGTTTEEEEEEEES CS
                       Gp_dh_C   1 LaplakvlndkfgikkglmttvhaytndQkllDgpskkdlrraraaa.eniiptstgaakavglVlpelkgkldglAvrVP 80 
                                   La++++ ++++fg+k++ +t+++++t++         +d  +++++a e   ++++++a+++++V+   +++++++A++VP
  gi|13541289|ref|NP_110977.1| 144 LARTLYPIQQAFGVKHVEATLIRRATDQ---------NDSSKGPINAvEPSLKIPSHHAPDLKTVMG--NIDVNTVAIKVP 213
                                   89*************************9.........99********8999****************..6999******** PP

                                   SSSEEEEEEEEEESSTS-HHHHHHHHHHHHH....TTTTTTEEEEHSHHHGGGGTTGCS..SEEEEGGGCEEETTTEEEEE CS
                       Gp_dh_C  81 tpnvsvvdlvvelekevtveevnaalkeaae....galkgilsyteeelvssDlvgdph..ssifdaketivveenlvkvv 155
                                   t+ ++v+ + v++ek+++ + v +a ++  +    ++ +gi s+++ +  ++++ +d+   ++i  ++ +   + n++ ++
  gi|13541289|ref|NP_110977.1| 214 TTLMHVHVVQVDTEKNASNDGVLEAWNNYRRiihvKKDDGIKSTAQIMDLAREFGRDRSdlYEIAIWEGSVSAKANRISYI 294
                                   **********************************99*********************9999*******************9 PP

                                   EEE CS
                       Gp_dh_C 156 awy 158
                                   +++
  gi|13541289|ref|NP_110977.1| 295 QAV 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 !   42.1   0.1   3.8e-14   8.5e-11       1      93 [.       2     102 ..       2     119 .. 0.84

  Alignments for each domain:
  == domain 1  score: 42.1 bits;  conditional E-value: 3.8e-14
                                   EEEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTCSTTTTTBHH...........HHSSSS--S-BEBSSHHHHHHH-SE CS
                        DapB_N   1 ikvavvGasGrmGkevvkaveeaedlelvaavdrkeselegkdag...........ellglgklgvavtddleevlekadv 70 
                                   i+v+++G+ G++G++v++av++++d+ +v+ v++k+ +++++ a+            +  ++  g++v+ +l+++l++a++
  gi|13541289|ref|NP_110977.1|   2 IRVGINGY-GTIGRRVANAVSSQDDMIVVGIVKTKP-DYISEVASrrfkifvpdssYMKAFQDAGIKVEGTLDNLLDDAEI 80 
                                   79******.**************************9.55555555688899999954555559****************** PP

                                   EEE-S-HHHHHHHHHHHHHTT-E CS
                        DapB_N  71 liDFTtpeavlenlklalekgvk 93 
                                   ++D T pe++ e+ k ++ k+++
  gi|13541289|ref|NP_110977.1|  81 IVDAT-PEGMGEKNKPLYIKKKA 102
                                   *****.88888888877665443 PP

>> Gp_dh_N  Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.1   2.6e-09   5.8e-06       1      38 [.       2      38 ..       2      70 .. 0.88

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 2.6e-09
                                  CEEEEESTSHHHHHHHHHHHHHTTCEEEEEE-TS-HHH CS
                       Gp_dh_N  1 vkvainGfGRIGrlvlralleekelevvaindltdlet 38
                                  ++v+inG+G IGr v+ a+ +++++ vv i + t++++
  gi|13541289|ref|NP_110977.1|  2 IRVGINGYGTIGRRVANAVSSQDDMIVVGIVK-TKPDY 38
                                  69****************************98.44444 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.1   1.5e-06    0.0033       3      61 ..       6      66 ..       4      82 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.5e-06
                                  EES-SHHHHHHHHHHHHTT..EEEEEEESSHHHHHHHHHTTSEEEES-TTSHHHHHHTTGG CS
                        TrkA_N  3 iiGlGrvGrslaeeLsegg..kdvvvidkdeerveelreeglevvvgdatdeevLeeagie 61
                                  i G+G++Gr++a+ +s++   + v ++ ++++ + e++ + ++++v d +  ++ ++agi+
  gi|13541289|ref|NP_110977.1|  6 INGYGTIGRRVANAVSSQDdmIVVGIVKTKPDYISEVASRRFKIFVPDSSYMKAFQDAGIK 66
                                  77***************5546545678889999**************************96 PP

>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   1.8e-05     0.039       1      74 [.       2      89 ..       2     108 .. 0.73
   2 ?   -1.8   0.0       2.4   5.3e+03      43      67 ..     114     138 ..      96     164 .. 0.69
   3 ?   -0.9   0.0       1.2   2.7e+03      44      78 ..     184     220 ..     158     230 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.8e-05
                                  EEEEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHH.........HHHTTHEEESS........HHHHHTCTTESEE CS
                  GFO_IDH_MocA  1 lrvaiiGaGkigskhlrplnesqrleevvalldpdaeraeav.........aesfgveaysd........leelladpeidav 66
                                  +rv+i G+G ig++ ++++  sq++  vv+++++++    +v          +s  ++a++d        l++ll+  +++++
  gi|13541289|ref|NP_110977.1|  2 IRVGINGYGTIGRRVANAV-SSQDDMIVVGIVKTKPDYISEVasrrfkifvPDSSYMKAFQDagikvegtLDNLLD--DAEII 81
                                  69**************555.566***********999998887443333343333333555588888888888888..66777 PP

                                  EE-S-GGG CS
                  GFO_IDH_MocA 67 ivatpngt 74
                                  + atp g 
  gi|13541289|ref|NP_110977.1| 82 VDATPEGM 89
                                  77777654 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2.4
                                   HHHTTHEEESSHHHHHTCTTESEEE CS
                  GFO_IDH_MocA  43 aesfgveaysdleelladpeidavi 67 
                                    +++ ++ays++++   ++ +++v+
  gi|13541289|ref|NP_110977.1| 114 VAETSFNAYSNYNDAIGKSYVRVVS 138
                                   4566677899988888866555544 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 1.2
                                   HHTTHE..EESSHHHHHTCTTESEEEE-S-GGGHHHH CS
                  GFO_IDH_MocA  44 esfgve..aysdleelladpeidavivatpngtheel 78 
                                    s++++     dl+ ++ + +++ v + +p+++ + +
  gi|13541289|ref|NP_110977.1| 184 PSLKIPshHAPDLKTVMGNIDVNTVAIKVPTTLMHVH 220
                                   4555555566678888887788888888888774443 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 ?   10.2   0.0   0.00041      0.91       1      68 [.       8      86 ..       8      93 .. 0.74
   2 ?    2.7   0.0     0.083   1.9e+02      69      95 ..     286     312 ..     281     325 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00041
                                  --SHHHHHHHHHHHH---SSEEEEEEEEESS.EEE-TT...............HHHHHT--CB---HHHHHHHHS-EEEEE-S CS
                 NAD_binding_3  1 GlGaiGsavleqlkrqqseielelvavadrd.sllskd...............rkallasealtldlddliahldpdvvVEca 67
                                  G+G+iG++v++++ +q +   + +v++++ + + +s+                ++ + a  ++   ld+l++  d+ ++V+++
  gi|13541289|ref|NP_110977.1|  8 GYGTIGRRVANAVSSQDD---MIVVGIVKTKpDYISEVasrrfkifvpdssymKAFQDAGIKVEGTLDNLLD--DAEIIVDAT 85
                                  99**************97...566666666655555556667666666677655555556677777888888..999999998 PP

                                  - CS
                 NAD_binding_3 68 s 68
                                  +
  gi|13541289|ref|NP_110977.1| 86 P 86
                                  6 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.083
                                   -HHHHTTHHHHHHTTEEEE-S--CGGG CS
                 NAD_binding_3  69 seavaelvlkaLkagkdvvtankgala 95 
                                    +a +  + +a+ +  dv+  n++a+ 
  gi|13541289|ref|NP_110977.1| 286 AKANRISYIQAVHQESDVIPENVDAIR 312
                                   56778899****************985 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 ?   11.1   0.4   8.5e-05      0.19      38      67 ..       3      33 ..       2      99 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 8.5e-05
                                  EEEEES-SHHHHHHHHHHH.HTT-EEEEESS CS
                  2-Hacid_dh_C 38 tvGiiGlGrIGqavakrlk.afgmkviaydr 67
                                  +vGi G+G IG++va+ ++ + +m v+++ +
  gi|13541289|ref|NP_110977.1|  3 RVGINGYGTIGRRVANAVSsQDDMIVVGIVK 33
                                  69**************998455666665544 PP

>> DUF3113  Protein of unknown function (DUF3113)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   0.00019      0.44      10      33 ..     207     230 ..     203     240 .. 0.90
   2 ?   -1.9   0.1       1.5   3.3e+03      15      32 ..     304     323 ..     293     325 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00019
                       DUF3113  10 svDiRiPtevesvnyddvDdeken 33 
                                   +v i++Pt    v+  +vD ek+ 
  gi|13541289|ref|NP_110977.1| 207 TVAIKVPTTLMHVHVVQVDTEKNA 230
                                   899*******************86 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.5
                       DUF3113  15 iPtevesv..nyddvDdeke 32 
                                   iP +v+     ++  D+ek 
  gi|13541289|ref|NP_110977.1| 304 IPENVDAIraMFNLADKEKS 323
                                   66666654115899999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (338 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       621  (0.0346366); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.31s 00:00:00.88 Elapsed: 00:00:00.50
# Mc/sec: 2023.45
//
Query:       gi|13541290|ref|NP_110978.1|  [L=1161]
Description: hypothetical protein TVN0459 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.062   13.1   0.1       0.16   11.8   0.1    1.7  1  WIYLD     Ubiquitin-binding WIYLD domain


Domain annotation for each model (and alignments):
>> WIYLD  Ubiquitin-binding WIYLD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   8.7e-06      0.16       4      32 ..    1106    1134 ..    1104    1137 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 8.7e-06
                         WIYLD    4 gkeRidaAidamkelGfskeqvrpvlkkL 32  
                                    +++R da i+ mk+l ++k+++++++k+L
  gi|13541290|ref|NP_110978.1| 1106 EDKRLDALIKEMKRLRYTKRTINKTIKEL 1134
                                    689************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       677  (0.0377601); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.84u 0.31s 00:00:01.14 Elapsed: 00:00:00.58
# Mc/sec: 6065.88
//
Query:       gi|13541291|ref|NP_110979.1|  [L=181]
Description: hypothetical protein TVN0460 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       641  (0.0357521); 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:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 1121.15
//
Query:       gi|13541292|ref|NP_110980.1|  [L=182]
Description: aromatic acid decarboxylase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.3e-28   98.4   0.0    6.4e-28   97.5   0.0    1.4  1  Flavoprotein  Flavoprotein


Domain annotation for each model (and alignments):
>> Flavoprotein  Flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.5   0.0   3.6e-32   6.4e-28       1     125 [.       1     161 [.       1     174 [. 0.89

  Alignments for each domain:
  == domain 1  score: 97.5 bits;  conditional E-value: 3.6e-32
                                   EEEEEEE-SSCGGGCHHHHHHHHHHTTEEEEEEESCHHHHCCHHGGS....TCSSHHHHHHCT.................T CS
                  Flavoprotein   1 kkillgiTGsvaaikalellekLkkegievqvvltkaAkkfiskeklklaaredpilhielrr.................w 64 
                                   ++i++g++G++++ +a++lle+L +   ev+++++++Akk+++ e   +  ++dp    +l+                   
  gi|13541292|ref|NP_110980.1|   1 MRIVVGVSGASGIPYAVKLLENLGQ--NEVHLIISENAKKVMKYE---M--NQDPSYLSSLASytysdddftapvssgsfL 74 
                                   79**********************7..9***************88...2..23455555555566777788888888889* PP

                                   ESEEEEEEEEHHHHHHHHTT--SSHH..............................HHHHHTHCCTTEEEEE.--HHCCTC CS
                  Flavoprotein  65 adllviaPasantlakianGiadnll..............................tlilratakkpiliaPamnpamyen 115
                                   +d++vi+P+s+ tl+kia Gi+d+l+                              +l l   ++ +++iaP ++p +y++
  gi|13541292|ref|NP_110980.1|  75 FDAMVIVPCSISTLSKIAVGISDTLItraaavsikerrrliivpremplssidlknMLSL---SENGVIIAP-ASPGFYNK 151
                                   ****************************************************98777777...99*******.******** PP

                                   STCHHHHHHH CS
                  Flavoprotein 116 pqtlknlekl 125
                                   p+++++l+++
  gi|13541292|ref|NP_110980.1| 152 PKSIDDLVSF 161
                                   *********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1219.74
//
Query:       gi|13541293|ref|NP_110981.1|  [L=157]
Description: hypothetical protein TVN0462 [Thermoplasma volcanium GSS1]
Scores for complete 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-32  110.5   0.0    1.2e-31  109.8   0.0    1.3  1  Mut7-C           Mut7-C RNAse domain
    1.1e-05   25.0   0.0    1.8e-05   24.4   0.0    1.3  1  DUF5615          Domain of unknown function (DUF5615)
     0.0018   18.4   0.8       0.33   11.1   0.0    2.3  2  Zn-ribbon_8      Zinc ribbon domain
  ------ inclusion threshold ------
      0.011   15.8   0.6      0.017   15.1   0.6    1.4  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
      0.014   15.8   0.5        6.4    7.2   0.1    2.2  2  Lar_restr_allev  Restriction alleviation protein Lar
      0.015   15.7   3.6        1.6    9.3   0.3    2.3  2  zf-H2C2_2        Zinc-finger double domain
      0.016   14.8   1.2       0.24   11.0   0.1    2.3  2  Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
       0.29   12.1   3.6         16    6.7   0.2    2.6  2  zf-C2H2_4        C2H2-type zinc finger


Domain annotation for each model (and alignments):
>> Mut7-C  Mut7-C RNAse domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.8   0.0   5.4e-35   1.2e-31       2     145 ..      13     145 ..      12     146 .. 0.91

  Alignments for each domain:
  == domain 1  score: 109.8 bits;  conditional E-value: 5.4e-35
                        Mut7-C   2 rfllDamlgklakyLRllGydalyas.dvedeellalaakekrillTrdreLlkraklkkgvlltsrdveeqlreviarlg 81 
                                   ++ +D+mlgkla+++Rl+Gyd+ y   +v+d+e+++ +++e+ril+T+d eL++r  l+  ++   +++ +ql + +  ++
  gi|13541293|ref|NP_110981.1|  13 KLTVDQMLGKLARWIRLMGYDVYYPAgNVSDNEIIEVSKNEGRILITKDYELYSRYPLS--IYELYSNIDDQLYDFV--FH 89 
                                   789*********************99899****************************99..9999***********5..55 PP

                        Mut7-C  82 lklslkpelsrCvaCngeleevekeevkervpekvyeeadeftrCekCrkvfWkGshwerveel 145
                                   ++ ++++e++rC  Cng+l++v ++         v + +++++rCe C+k++WkG+h++++ ++
  gi|13541293|ref|NP_110981.1|  90 FRKRTEEEFKRCPVCNGKLVKVYASPH-------VLN-HRDLYRCEFCGKLYWKGTHYKKIYRK 145
                                   56778999************9988744.......554.5569******************9876 PP

>> DUF5615  Domain of unknown function (DUF5615)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.0     8e-09   1.8e-05       2      56 ..      13      62 ..      12      73 .. 0.88

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 8e-09
                       DUF5615  2 klllDenlsprlvellreaghdvlhvrelglegasDeeileyAkeedriivTkDk 56
                                  kl +D+ l  +l++++r  g+dv +       ++sD+ei+e+ k+e+ri++TkD 
  gi|13541293|ref|NP_110981.1| 13 KLTVDQMLG-KLARWIRLMGYDVYYP----AGNVSDNEIIEVSKNEGRILITKDY 62
                                  778888888.99***********999....5589********************4 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.0   0.00015      0.33      18      39 ..      90     111 ..      83     112 .. 0.81
   2 !    5.4   0.4     0.009        20       6      13 ..     124     131 ..     123     134 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00015
                   Zn-ribbon_8  18 lqsisdapltaCPeCgsevrrv 39 
                                   +++ ++++ + CP C++++ +v
  gi|13541293|ref|NP_110981.1|  90 FRKRTEEEFKRCPVCNGKLVKV 111
                                   56666888899******99998 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.009
                   Zn-ribbon_8   6 YrCeeCgh 13 
                                   YrCe Cg+
  gi|13541293|ref|NP_110981.1| 124 YRCEFCGK 131
                                   9******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 ?   15.1   0.6   7.5e-06     0.017      19      45 ..      99     131 ..      80     132 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 7.5e-06
                 Zn_Tnp_IS1595  19 fvCPhCgsr..kayrikt....rglfqCkeCrk 45 
                                    +CP C ++  k+y   +    r l++C+ C+k
  gi|13541293|ref|NP_110981.1|  99 KRCPVCNGKlvKVYASPHvlnhRDLYRCEFCGK 131
                                   45*******9988887778888*********86 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.1    0.0028       6.4       1      15 [.      96     110 ..      96     117 .. 0.82
   2 ?    6.9   0.0    0.0037       8.2       2      20 ..     122     140 ..     121     147 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0028
               Lar_restr_allev   1 eeLkpCPfCggravl 15 
                                   ee k CP C+g+ v+
  gi|13541293|ref|NP_110981.1|  96 EEFKRCPVCNGKLVK 110
                                   689*******98765 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0037
               Lar_restr_allev   2 eLkpCPfCggravlersqr 20 
                                   +L+ C fCg+   ++++++
  gi|13541293|ref|NP_110981.1| 122 DLYRCEFCGKLYWKGTHYK 140
                                   79*******8776666665 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 ?    9.3   0.3   0.00072       1.6       2      21 ..      86     105 ..      85     112 .. 0.87
   2 ?    7.3   0.2    0.0031       6.9      14      24 ..     123     133 ..     116     135 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00072
                     zf-H2C2_2   2 LrrHirkHtgekpyeCplCd 21 
                                   ++ H+rk t e +  Cp+C+
  gi|13541293|ref|NP_110981.1|  86 FVFHFRKRTEEEFKRCPVCN 105
                                   678********999*****8 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0031
                     zf-H2C2_2  14 pyeCplCdkaF 24 
                                    y C++C+k +
  gi|13541293|ref|NP_110981.1| 123 LYRCEFCGKLY 133
                                   59******976 PP

>> Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.1     0.053   1.2e+02       8      18 ..     100     111 ..      93     114 .. 0.81
   2 ?   11.0   0.1   0.00011      0.24       2      14 ..     119     131 ..     118     132 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.053
                                   E-TTT.--EEEE CS
               Desulfoferrod_N   8 kCevC.GniVeV 18 
                                   +C vC G  V+V
  gi|13541293|ref|NP_110981.1| 100 RCPVCnGKLVKV 111
                                   8****9999998 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00011
                                   -TT-EEE-TTT-- CS
               Desulfoferrod_N   2 eklevYkCevCGn 14 
                                   ++ + Y+Ce CG 
  gi|13541293|ref|NP_110981.1| 119 NHRDLYRCEFCGK 131
                                   67899*******6 PP

>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.2     0.007        16       2      23 ..     100     120 ..      99     121 .. 0.83
   2 ?    5.8   0.4     0.014        31       1      10 [.     124     133 ..     124     142 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.007
                     zf-C2H2_4   2 kCpiCgksFsskkaLlrHlkth 23 
                                   +Cp+C++     +a + H+++h
  gi|13541293|ref|NP_110981.1| 100 RCPVCNGKLVKVYA-SPHVLNH 120
                                   7****999988888.7788777 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.014
                     zf-C2H2_4   1 fkCpiCgksF 10 
                                   ++C++Cgk +
  gi|13541293|ref|NP_110981.1| 124 YRCEFCGKLY 133
                                   89****9977 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       786  (0.0438396); expected 358.6 (0.02)
Passed bias filter:                      610  (0.0340231); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 1135.57
//
Query:       gi|13541294|ref|NP_110982.1|  [L=340]
Description: RNA-binding protein (pelota-related) [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.4e-26   91.4   2.0      1e-25   90.2   0.9    2.0  2  eRF1_1    eRF1 domain 1
    1.3e-19   70.8   0.1    6.2e-19   68.5   0.1    2.2  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 !   90.2   0.9   1.1e-29     1e-25       1     128 [.       1     124 [.       1     125 [. 0.92
   2 ?   -0.2   0.0       0.1   9.3e+02      16      50 ..     216     250 ..     206     306 .. 0.75

  Alignments for each domain:
  == domain 1  score: 90.2 bits;  conditional E-value: 1.1e-29
                                   HEEEEECTBTTSCCEEEEEE-SCHHHHHHHHHCHTTHEEEEEEEECHHH........--CEEEEEEEEEEEEEEECTTSSE CS
                        eRF1_1   1 mkllkrdlekdgsgsvtLipeddedlwhlynliapgdsvrastvrkvqr.esstgsreservklkLtikvekvdfdkdagv 80 
                                   m+ll +d +    g  tL++e+ +dlw+l n+iapgd+++a+t+r++++ +  + sre+er+ ++ ti+vek++f+  +++
  gi|13541294|ref|NP_110982.1|   1 MRLLDKDEK---LGRYTLRIENLDDLWYLKNIIAPGDKISAVTFRRIEEsSDMQRSREKERIPIRVTIEVEKIEFQDFENR 78 
                                   666666544...7999*******************************88335677889*********************** PP

                                   EEEEEEEEEGGGG--TTSEEEEEE-TTSEEEEEECEESHHHHHHHHHH CS
                        eRF1_1  81 lrisGkvieenehvklgafhtldlelkrpftiikeewdsfalerLkea 128
                                   lri Gkv+++ e   +g++ ++++  + ++ +ik  wd   +++Lkea
  gi|13541294|ref|NP_110982.1|  79 LRILGKVTNGPE-DTIGKYQSITVSEETELDVIK-VWDDDSINMLKEA 124
                                   ************.59*******************.9***********9 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.1
                                   EEEEE-SCHHHHHHHHHCHTTHEEEEEEEECHHH. CS
                        eRF1_1  16 vtLipeddedlwhlynliapgdsvrastvrkvqre 50 
                                   v +   +  d   +y+ i+++d+ +   + ++ r+
  gi|13541294|ref|NP_110982.1| 216 VAVSSSNRTDQGAIYEFISSEDGKKLISKEQISRD 250
                                   55555666677778889999998888888877764 PP

>> eRF1_3  eRF1 domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.5   0.1     7e-23   6.2e-19       2     113 .]     248     338 ..     247     338 .. 0.95

  Alignments for each domain:
  == domain 1  score: 68.5 bits;  conditional E-value: 7e-23
                                   HHHHHHHHHHHHHHHCTCSSEEESHHHHHHHHHTT-EEEEEEEHCHHTSSSHHHHHS-HHH-HHHHHHHHHHHHHHHHHTT CS
                        eRF1_3   2 iqekklleefleelakdtgkavYGveevlkalemgAvetLLvseelersrdtlkekvketgeelelvelieelvenveesg 82 
                                   ++++++++ fl++l+++  + +YG ee++k+lemgA+++L+++++ +rs+         tg         +el++ ++++g
  gi|13541294|ref|NP_110982.1| 248 SRDNEIVSAFLSSLRRG--SGIYGSEEIRKYLEMGALSDLIITDKKFRSE---------TG---------RELLSLARSVG 308
                                   68999**********88..99***************************96.........34.........89********* PP

                                   -EEEEE-TTSHHHHHHHHHTTTEEEEESS-- CS
                        eRF1_3  83 akveiisseseeGeqlvkafgGiaaiLRykv 113
                                   ++++i+s++++ Ge + ++fgG+a+iLRykv
  gi|13541294|ref|NP_110982.1| 309 TDIHIVSTSNDMGEII-EKFGGYAGILRYKV 338
                                   ****************.************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (340 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.50
# Mc/sec: 2036.05
//
Query:       gi|13541295|ref|NP_110983.1|  [L=152]
Description: restriction endonuclease S subunit fragment, partial [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.7e-09   36.7   0.0    6.5e-09   36.2   0.0    1.3  1  Methylase_S  Type I restriction modification DNA specificity 


Domain annotation for each model (and alignments):
>> Methylase_S  Type I restriction modification DNA specificity domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.2   0.0   3.6e-13   6.5e-09      68     148 ..       9      89 ..       2     120 .. 0.87

  Alignments for each domain:
  == domain 1  score: 36.2 bits;  conditional E-value: 3.6e-13
                                   SSTT-EEEESS-BEE-TTEEEEEESTTT--HHHHHHHHHHCHHHHHHHCCSSTTT---HHHHCC-EEEE--HHHHHHHHHH CS
                   Methylase_S  68 atiGkvayrdkkyylnqsvivlipknkkkineflylylllklkklkslsvgstqpkltkenlkkikIplPpleeQkkIaki 148
                                    t G v + +++ ++nqs+  +++++  ++ ++ly++l+ k+k++  l +   +  l+++ l+++ Ip+P+l+eQ  I  +
  gi|13541295|ref|NP_110983.1|   9 KTKGMVGILKVESTCNQSLAAFNVNERTLHYRYLYYFLKSKYKQMRGLVGDDLRDGLSLSVLRELRIPVPSLQEQFAISNY 89 
                                   6779999*****************776677899999999********99999999*******************9888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       813  (0.0453455); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 998.83
//
Query:       gi|13541296|ref|NP_110984.1|  [L=82]
Description: restriction endonuclease S subunit fragment, partial [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.058   13.6   0.6       0.06   13.6   0.6    1.0  1  Methylase_S  Type I restriction modification DNA specificity 


Domain annotation for each model (and alignments):
>> Methylase_S  Type I restriction modification DNA specificity domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.6   3.3e-06      0.06       2      53 ..      14      73 ..      13      82 .] 0.78

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.3e-06
                                  TT-EEEEHHHHEEEEE-----TT..GGTTT--EEEE-HH.HCCT.....EE-HHHHCCTT CS
                   Methylase_S  2 edwevvkLgdvfeikkgktpkkk..elkengkypyirag.ilnn.....kvvkdglgykk 53
                                  ++w +vk+  + ++k++ tp k   e++e+gk+ + ++g i+ +     ++++  lgyk+
  gi|13541296|ref|NP_110984.1| 14 SKWPIVKIIYFSKLKTCGTPDKRvlEYWEDGKINWMSSGeINKDliyevEGKITELGYKN 73
                                  789999999999***************************666558888844444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); 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 0.28s 00:00:00.71 Elapsed: 00:00:00.47
# Mc/sec: 528.26
//
Query:       gi|13541297|ref|NP_110985.1|  [L=209]
Description: hypothetical protein TVN0466, partial [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.2e-36  125.3   0.2    3.7e-36  125.1   0.2    1.1  1  DDE_Tnp_ISL3  Transposase


Domain annotation for each model (and alignments):
>> DDE_Tnp_ISL3  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.1   0.2   2.1e-40   3.7e-36       1     169 [.      42     208 ..      42     209 .] 0.96

  Alignments for each domain:
  == domain 1  score: 125.1 bits;  conditional E-value: 2.1e-40
                  DDE_Tnp_ISL3   1 lgiDEislkkghkyvtvvvdllvdggrlldilpgRkketlkafleslsekerekveavvmDmsaayksavkealPnAk..i 79 
                                   +giDE  + k+h+y+t v ++  d +++ +i  +Rk+e l+ + +s++e+   ++ea+ mDm+ +++ ++k ++ +A+  i
  gi|13541297|ref|NP_110985.1|  42 IGIDEKYYGKHHRYITLVFNH--DDHSVEFISLDRKQESLDLYYRSIGEEASGSIEAAPMDMWDPFIVSTKSNVTDAEskI 120
                                   8********************..*****************************************************9777* PP

                  DDE_Tnp_ISL3  80 vvDrFHvvklanealdevRrreqkelreekrkklkrsrrlllknpenlteeqkqrldelleaspelekaYelkeelrevfr 160
                                   v+DrFHv+k++n ald+vR  e + +  e+++ ++++r l+l +penl ++  +r + l e++ +++++Y++ke+lr++++
  gi|13541297|ref|NP_110985.1| 121 VFDRFHVMKHMNMALDDVRWMESRMA--EYKEMFRKTRCLWLYSPENLPDKYGERYEILKESDLKTARVYAIKENLRNLWN 199
                                   ********************999976..57999**********************99999********************* PP

                  DDE_Tnp_ISL3 161 kkdkeeark 169
                                   ++ ++ear+
  gi|13541297|ref|NP_110985.1| 200 CSGEDEARS 208
                                   998888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       630  (0.0351386); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1463.09
//
Query:       gi|13541298|ref|NP_110986.1|  [L=256]
Description: hypothetical protein TVN0467 [Thermoplasma volcanium GSS1]
Scores for complete 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   80.0   1.6    5.7e-22   78.6   1.6    1.7  1  HEPN_AbiV  AbiV


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 !   78.6   1.6   3.2e-26   5.7e-22       6     155 ..      31     219 ..      26     230 .. 0.84

  Alignments for each domain:
  == domain 1  score: 78.6 bits;  conditional E-value: 3.2e-26
                     HEPN_AbiV   6 akalleNAeeLledAelLaengsyarAysLlilaiEElgKalllydalegfws.....edkdlkrlkkafrdHkkKhnlay 81 
                                   +k++++NAe+Ll+dA    ++ s+++  +Ll l++EE +K++lly +l+++++     ++ + + l++ f++Hk K++   
  gi|13541298|ref|NP_110986.1|  31 CKLCMRNAERLLDDA--SNNSLSIQTRMALLELSFEETAKSILLYFYLLSHDKgqllvKGSVEENLRDIFKNHKTKIE--- 106
                                   79*************..999*******************************99***99999999**************... PP

                     HEPN_AbiV  82 lflkaftlllsaeesasfgaerldefeeliqleaeeela......................................kkln 124
                                    ++k ++ +l     a+  a++ld +e++ ++++e e +                                      + +n
  gi|13541298|ref|NP_110986.1| 107 -IMKNVMSFLAENIPAFDMASDLDYIERIVRYGTEGEKRdsreakismarqialddrssiikkmvkeiidflnlqdvDYYN 186
                                   .4444555555555554666666666666665555555566666666667777799************************* PP

                     HEPN_AbiV 125 llKnaglYVdldkng..issPseviskeaaeei 155
                                   +lKn++lYVd+d ++  +++P e  +k++ +++
  gi|13541298|ref|NP_110986.1| 187 DLKNKSLYVDIDPSTdrLQLPLEPKNKKIMDYM 219
                                   **************9*************99988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1034  (0.0576719); expected 358.6 (0.02)
Passed bias filter:                      548  (0.030565); 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 0.31s 00:00:00.87 Elapsed: 00:00:00.52
# Mc/sec: 1473.23
//
Query:       gi|13541299|ref|NP_110987.1|  [L=295]
Description: hypothetical protein TVN0468 [Thermoplasma volcanium GSS1]
Scores for complete 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-30  104.9   0.2    3.1e-30  104.9   0.2    1.8  2  OrfB_IS605  Probable transposase


Domain annotation for each model (and alignments):
>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.3      0.15   2.7e+03      60      89 ..      38      65 ..      13      77 .. 0.73
   2 !  104.9   0.2   1.7e-34   3.1e-30       1     113 [.     170     279 ..     170     285 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.15
                    OrfB_IS605 60 lqsklkksknykkasrklarlhrkrsrrrk 89
                                  +q+++k+++     s+ ++ +++k ++++k
  gi|13541299|ref|NP_110987.1| 38 MQQFKKGER--VDFSKTEKEVYEKYKQILK 65
                                  566666665..6777777777777777665 PP

  == domain 2  score: 104.9 bits;  conditional E-value: 1.7e-34
                    OrfB_IS605   1 sipvevevelpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrklarlh 81 
                                   +ipvev++   k++ + +a+iD+Gi n atv++edg+w+++kg ++ s+y+y++k+i   q++l+++k  +  sr++++lh
  gi|13541299|ref|NP_110987.1| 170 YIPVEVQN-DVKAEDKLKASIDIGIVNSATVYVEDGSWYIFKGGSVLSQYEYYSKRISVAQKTLARHK--QGGSREMKLLH 247
                                   589****8.89999******************************************************..*********** PP

                    OrfB_IS605  82 rkrsrrrkhllhklathliktlkevgvetLnv 113
                                   +kr+r++kh+l++++++++++lk++ v+ +  
  gi|13541299|ref|NP_110987.1| 248 EKRKRFLKHALNSMVRKIMEELKKKDVGAVFT 279
                                   **************************998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1416  (0.0789782); expected 358.6 (0.02)
Passed bias filter:                      558  (0.0311228); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 1936.87
//
Query:       gi|13541300|ref|NP_110988.1|  [L=121]
Description: hypothetical protein TVN0469 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-35  121.5   0.1    2.3e-35  121.3   0.1    1.0  1  Y1_Tnp    Transposase IS200 like
  ------ inclusion threshold ------
      0.064   13.3   0.2         17    5.5   0.0    2.6  3  HTH_3     Helix-turn-helix


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 !  121.3   0.1   2.5e-39   2.3e-35       2     116 ..      11     121 .]      10     121 .] 0.96

  Alignments for each domain:
  == domain 1  score: 121.3 bits;  conditional E-value: 2.5e-39
                        Y1_Tnp   2 snlkyhivlvtkyRrkvltgeveerlkeiikeiaekkevkilelelmpDHvHllvelppklsiskivkalkgassrlinke 82 
                                   + ++yh  +++kyRr +lt+ev+e  ke++k+ia++ +++i++le+mpDH+Hl+v++pp++s+s + + +kg+s+rli k+
  gi|13541300|ref|NP_110988.1|  11 YLCNYHYLWIPKYRRAILTNEVAEYTKEVLKSIAKELGCEIIALEVMPDHIHLFVNCPPRYSPSYLTNYFKGKSARLILKK 91 
                                   78*****************************************************************************99 PP

                        Y1_Tnp  83 fpelkkkklkkeslWqrgYfvstvgeasletvkr 116
                                    pel++   k  +lW+r+Yfvst+g++s et++r
  gi|13541300|ref|NP_110988.1|  92 SPELRRY--K--KLWSRSYFVSTAGNVSSETIQR 121
                                   9998843..4..5******************986 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0    0.0021        18      37      52 ..      36      51 ..      28      54 .. 0.87
   2 ?    5.5   0.0    0.0019        17      22      34 ..      72      84 ..      70     101 .. 0.87
   3 ?   -1.9   0.0       0.4   3.6e+03       7      27 ..      99     120 ..      94     121 .] 0.51

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0021
                                  BHHHHHHHHHHHTSEH CS
                         HTH_3 37 sletlkklakaLgvsl 52
                                  + e+lk +ak Lg+++
  gi|13541300|ref|NP_110988.1| 36 TKEVLKSIAKELGCEI 51
                                  789***********87 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0019
                                  SHHHHHHHHTTSS CS
                         HTH_3 22 srstisriEnGer 34
                                  s+s+++++++G++
  gi|13541300|ref|NP_110988.1| 72 SPSYLTNYFKGKS 84
                                  9**********76 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 0.4
                                   HTTHHH.HHHHHHHTSSHHHHH CS
                         HTH_3   7 qlglsq.eeLAeklGvsrstis 27 
                                   ++ +s+   ++ + +vs  ti+
  gi|13541300|ref|NP_110988.1|  99 KKLWSRsYFVSTAGNVSSETIQ 120
                                   5555553334444557766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       600  (0.0334653); expected 358.6 (0.02)
Passed bias filter:                      517  (0.028836); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.35s 00:00:00.85 Elapsed: 00:00:00.53
# Mc/sec: 683.84
//
Query:       gi|13541301|ref|NP_110989.1|  [L=100]
Description: thioredoxin reductase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-06   27.5   0.1      2e-06   27.3   0.1    1.0  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    3.5e-06   26.4   0.3    4.7e-06   26.0   0.3    1.1  1  Thi4            Thi4 family
    3.7e-05   23.0   1.9    4.9e-05   22.6   1.9    1.2  1  FAD_binding_2   FAD binding domain
    7.9e-05   22.2   0.1    7.9e-05   22.2   0.1    1.0  1  FAD_oxidored    FAD dependent oxidoreductase
    0.00075   19.7   1.0      0.001   19.2   1.0    1.3  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
     0.0021   17.2   0.2     0.0021   17.2   0.2    1.2  1  GIDA            Glucose inhibited division protein A
     0.0026   17.4   0.2     0.0026   17.4   0.2    1.1  1  DAO             FAD dependent oxidoreductase
     0.0043   15.8   1.1     0.0069   15.1   1.1    1.3  1  HI0933_like     HI0933-like protein
  ------ inclusion threshold ------
      0.014   15.9   0.3      0.091   13.3   0.3    2.0  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
      0.017   14.4   0.5      0.022   14.0   0.5    1.1  1  FAD_binding_3   FAD binding domain
      0.025   14.5   0.1      0.031   14.2   0.1    1.2  1  PS_pyruv_trans  Polysaccharide pyruvyl transferase
       0.08   12.2   0.1      0.086   12.1   0.1    1.2  1  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
       0.12   11.4   0.4       0.18   10.8   0.4    1.2  1  Lycopene_cycl   Lycopene cyclase protein
       0.16   10.7   0.2       0.17   10.6   0.2    1.0  1  MCRA            MCRA family


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.1   1.5e-09     2e-06       1      72 [.      17      94 ..      17      99 .. 0.70

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 1.5e-09
                                  CSEEEE--SHHHHHHHHHHHHHTS-EEEEE..TTHCHHHCSHHHHCHHHHHHHHHHHHH....HHHHCHHHHCCCCHC CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxx RF
                   Pyr_redox_2  1 kdvvviGgGpAGlaaaltlaqagakvtlve..legtclnggcllskallgvaedaeias....evvkklnqgielllg 72
                                  +d v+iG+G+ G++aa + a++g+kv++++    g +  + +l+ + l   a ++  ++    ++ ++++q i++ l+
  gi|13541301|ref|NP_110989.1| 17 YDAVIIGSGAPGMSAAVYTARYGLKVVILGqsVAGGLTAEAPLVENYLGYKAIKGTDLAsnfaKHAQEYSQIIDNTLR 94
                                  588**************************8774444555555554443333333333335666888999999998887 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.3   3.7e-09   4.7e-06      13      54 ..      12      52 ..       4      57 .. 0.88

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 3.7e-09
                                  HHHTEEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS-- CS
                          Thi4 13 lkyaesDvvivGaGssGLtaayylakkpdlkvailersvspG 54
                                  ++  + D vi+G+G+ G++aa y a+  +lkv+il +sv+ G
  gi|13541301|ref|NP_110989.1| 12 IEARDYDAVIIGSGAPGMSAAVYTARY-GLKVVILGQSVAGG 52
                                  5666789********************.***********966 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   1.9   3.8e-08   4.9e-05       1      33 [.      18      50 ..      18      58 .. 0.88

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 3.8e-08
                                  SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSG CS
                 FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqe 33
                                  D+++iGsG+ G++AA+  a+ Glkv+++ +  +
  gi|13541301|ref|NP_110989.1| 18 DAVIIGSGAPGMSAAVYTARYGLKVVILGQSVA 50
                                  89*************************988776 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.1   6.2e-08   7.9e-05       1      58 [.      18      71 ..      18      98 .. 0.71

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 6.2e-08
                  FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsg.lvatdignkaeeqvvtg 58
                                  D v++G+g+ G+ AA+  ar G kv+++ +  v GGl++ + lv + +g+k    +++g
  gi|13541301|ref|NP_110989.1| 18 DAVIIGSGAPGMSAAVYTARYGLKVVILGQ-SVAGGLTAEApLVENYLGYK----AIKG 71
                                  779************************986.68899888662334444433....4444 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   1.0   8.1e-07     0.001       1      34 [.      21      53 ..      21      82 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 8.1e-07
                                  EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGG CS
                 NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGr 34
                                  I+G+G+ G++aA + a++g++v++l + +  GG 
  gi|13541301|ref|NP_110989.1| 21 IIGSGAPGMSAAVYTARYGLKVVILGQ-SVAGGL 53
                                  9***********************954.456655 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.2   1.7e-06    0.0021       1      31 [.      18      48 ..      18      93 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.7e-06
                                  CEEEE-SSHHHHHHHHHHHHTT--EEEEES- CS
                          GIDA  1 dviViGgGhAGceAAlaaarlGakvlLithk 31
                                  d ++iG G  G+ AA+ +ar G+kv+++ ++
  gi|13541301|ref|NP_110989.1| 18 DAVIIGSGAPGMSAAVYTARYGLKVVILGQS 48
                                  579***********************99554 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.2   2.1e-06    0.0026       1      35 [.      18      52 ..      18      96 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2.1e-06
                                  EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSS CS
                           DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiagsg 35
                                  d viiG+G  G+s+A + ar g  V++l ++  ag g
  gi|13541301|ref|NP_110989.1| 18 DAVIIGSGAPGMSAAVYTARYGlkVVILGQS-VAG-G 52
                                  78************************99988.666.4 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   1.1   5.4e-06    0.0069       2      31 ..      18      47 ..      17      52 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 5.4e-06
                                  SEEEE--SHHHHHHHHHHHHTT--EEEE-S CS
                   HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllek 31
                                  d ++iG Ga G+ aA+  a+ g +V++l +
  gi|13541301|ref|NP_110989.1| 18 DAVIIGSGAPGMSAAVYTARYGLKVVILGQ 47
                                  89************************9865 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   0.3   7.1e-05     0.091       2      28 ..      19      45 ..      18      50 .. 0.92
   2 ?    0.0   0.0         1   1.3e+03      11      26 ..      71      86 ..      69      94 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 7.1e-05
                                  EEEECSSHHHHHHHHHHHHTTSEEEEE CS
                     Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvv 28
                                  +v++G+G  g+ +A + a++g kV ++
  gi|13541301|ref|NP_110989.1| 19 AVIIGSGAPGMSAAVYTARYGLKVVIL 45
                                  69**********************886 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 1
                                  HHHHHHHHHHTTSEEE CS
                     Pyr_redox 11 glElAgalaelgkkVt 26
                                  g +lA+++a+++++ +
  gi|13541301|ref|NP_110989.1| 71 GTDLASNFAKHAQEYS 86
                                  7789999999998874 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.5   1.7e-05     0.022       2      31 ..      17      46 ..      16      51 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.7e-05
                                  EEEEEE--SHHHHHHHHHHHHTTHHEEEEE CS
                 FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlve 31
                                  +d +I+G+G  G+++a   +++G +vv++ 
  gi|13541301|ref|NP_110989.1| 17 YDAVIIGSGAPGMSAAVYTARYGLKVVILG 46
                                  7899***********************985 PP

>> PS_pyruv_trans  Polysaccharide pyruvyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   2.5e-05     0.031      62     110 ..      14      51 ..       3      85 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.5e-05
                                   .....EEE--E......EEEETT-HHHHHHHHHHHHHS-SSEEEE-SEEE.. CS
                PS_pyruv_trans  62 ddaddviivGgd..gtlgndgdlsrlpdalrllflakkagkpviilgqgi.G 110
                                    +++d++i+G++  g              ++ + +  + g +v+ilgq++ G
  gi|13541301|ref|NP_110989.1|  14 ARDYDAVIIGSGapG--------------MSAAVYTARYGLKVVILGQSVaG 51 
                                   5799*******6555..............********************962 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   6.7e-05     0.086       1      30 [.      20      48 ..      20      87 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6.7e-05
                   Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkg 30
                                  +IiG G+ G++aa+   + gl +++il + 
  gi|13541301|ref|NP_110989.1| 20 VIIGSGAPGMSAAVYTARYGL-KVVILGQS 48
                                  7********************.79999766 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   0.4   0.00014      0.18       1      34 [.      18      47 ..      18      56 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00014
                 Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvlieasp 34
                                  D v+iG+G+ g+s A     a++glkvv++  ++
  gi|13541301|ref|NP_110989.1| 18 DAVIIGSGAPGMSAAVYT--ARYGLKVVIL--GQ 47
                                  88***********99999..*********9..44 PP

>> MCRA  MCRA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.2   0.00013      0.17       3      66 ..      18      78 ..      16      92 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00013
                                  EEEEE--SHHHHHHHHHHHHTT---GGGEEEE-SS----------..-------CCC----B-TT- CS
                          MCRA  3 kaylvGsGiasLaaAvyLirdakvpgenihileelkvaggsldga..gdpekGyvlrggreleehy 66
                                  +a ++GsG  +++aAvy  r     g ++ il ++ vagg + +a   ++  Gy +  g  l +++
  gi|13541301|ref|NP_110989.1| 18 DAVIIGSGAPGMSAAVYTARY----GLKVVILGQS-VAGGLTAEAplVENYLGYKAIKGTDLASNF 78
                                  689**************8886....5788888854.577766666233444588777777775555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 715.30
//
Query:       gi|13541302|ref|NP_110990.1|  [L=208]
Description: transcription regulator (HTH) [Thermoplasma volcanium GSS1]
Scores for complete 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-06   26.8   0.1    7.1e-06   25.8   0.1    1.4  1  TrmB          Sugar-specific transcriptional regulator TrmB
    7.4e-05   22.5   0.7    0.00016   21.5   0.2    1.8  2  HTH_5         Bacterial regulatory protein, arsR family
    0.00042   20.2   0.3     0.0012   18.8   0.4    1.7  2  MarR          MarR family
    0.00057   19.7   0.0      0.001   18.9   0.0    1.3  1  MarR_2        MarR family
     0.0013   18.3   0.2     0.0032   17.0   0.2    1.8  1  HTH_24        Winged helix-turn-helix DNA-binding
     0.0041   16.8   0.5     0.0079   15.9   0.1    1.6  2  DUF4423       Domain of unknown function (DUF4423)
  ------ inclusion threshold ------
      0.013   16.0   0.0      0.022   15.2   0.0    1.3  1  HTH_27        Winged helix DNA-binding domain
      0.082   12.3   0.0       0.13   11.7   0.0    1.3  1  HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family I
      0.087   12.9   0.0       0.12   12.4   0.0    1.2  1  Replic_Relax  Replication-relaxation
       0.11   12.5   0.0       0.22   11.6   0.0    1.4  1  HTH_20        Helix-turn-helix domain
       0.13   12.2   1.2       0.42   10.5   0.5    2.1  2  RuvB_C        RuvB C-terminal winged helix domain
       0.54   10.3   4.0       0.23   11.4   0.9    2.0  2  HTH_11        HTH domain
       0.87    9.6   2.6        1.1    9.3   0.4    2.1  2  RWP-RK        RWP-RK 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 !   25.8   0.1   5.1e-09   7.1e-06      14      64 ..     142     199 ..     140     202 .. 0.89

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 5.1e-09
                                   CHHHH...HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST....TTEEEE CS
                          TrmB  14 YlaLl...klgpatadeiaeelgvprskvYevLrsLedkGlVerekgr....pklYra 64 
                                   Y++L+   +++p+t++++++ l+++ s++ + L+sL++ ++++r  +     p+lY+ 
  gi|13541302|ref|NP_110990.1| 142 YITLIreiSKDPKTIKDLSRSLKIDTSTISRRLKSLLSLDMIMRLGKGtrnyPYLYKL 199
                                   7888877799**********************************97556999999986 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0         4   5.5e+03       3      11 ..      44      52 ..      43      54 .. 0.83
   2 !   21.5   0.2   1.1e-07   0.00016       8      44 ..     146     182 ..     143     184 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 4
                                  HHHHHHHHH CS
                         HTH_5  3 tRlkILklL 11
                                  +R +IL +L
  gi|13541302|ref|NP_110990.1| 44 ARKEILDFL 52
                                  6999*9988 PP

  == domain 2  score: 21.5 bits;  conditional E-value: 1.1e-07
                                   HHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTS CS
                         HTH_5   8 LklLaegelcvcelaeelglsqstvShHLkkLreaGL 44 
                                   ++  ++ ++++ +l++ l++  st+S+ Lk L  +++
  gi|13541302|ref|NP_110990.1| 146 IREISKDPKTIKDLSRSLKIDTSTISRRLKSLLSLDM 182
                                   566789**************************88766 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       7.5     1e+04       5      15 ..      27      37 ..      26      38 .. 0.75
   2 !   18.8   0.4   8.4e-07    0.0012      16      50 ..     152     186 ..     142     188 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 7.5
                                  HHHHHHHHHHS CS
                          MarR  5 qfviLrilyeq 15
                                   +++L i+y++
  gi|13541302|ref|NP_110990.1| 27 KISTLSIIYDR 37
                                  57889999976 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 8.4e-07
                                   TTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                          MarR  16 gplsvseLakklgvskstvtrvldrLekkGlieRs 50 
                                   +p ++++L + l++++st++r l+ L   ++i+R 
  gi|13541302|ref|NP_110990.1| 152 DPKTIKDLSRSLKIDTSTISRRLKSLLSLDMIMRL 186
                                   7889*************************999995 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   7.5e-07     0.001      10      51 ..     145     183 ..     141     190 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 7.5e-07
                                   HHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSE CS
                        MarR_2  10 vLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLv 51 
                                   ++ ++   p    t+++l r l+++ s++sr+lk L +  ++
  gi|13541302|ref|NP_110990.1| 145 LIREISKDPK---TIKDLSRSLKIDTSTISRRLKSLLSLDMI 183
                                   5677778887...***********************998877 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.2   2.3e-06    0.0032      19      47 ..     155     183 ..     143     184 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 2.3e-06
                        HTH_24  19 sqreLAerlglSpstvnrrlkrLeeeGlI 47 
                                   ++++L++ l +  st++rrlk L +   I
  gi|13541302|ref|NP_110990.1| 155 TIKDLSRSLKIDTSTISRRLKSLLSLDMI 183
                                   89*********************887666 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       2.7   3.7e+03     130     142 ..      40      52 ..      36      54 .. 0.64
   2 !   15.9   0.1   5.7e-06    0.0079      14      75 ..     134     190 ..     123     193 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 2.7
                       DUF4423 130 dyekikkeirefr 142
                                   +ye+++kei +f 
  gi|13541302|ref|NP_110990.1|  40 EYEQARKEILDFL 52 
                                   4666666666554 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 5.7e-06
                       DUF4423  14 efeyfssWyypvirellplkdfkadpeelakrlrpkisaeevekalefLlklgllkkdedgk 75 
                                   ++ ++++ y++ ire+   kd  ++++ l++ l+  i+++ +++ l+ Ll+l+++ + ++g+
  gi|13541302|ref|NP_110990.1| 134 KINIYNNKYITLIREIS--KDP-KTIKDLSRSLK--IDTSTISRRLKSLLSLDMIMRLGKGT 190
                                   56799*********933..344.78*********..********************999875 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.0   1.6e-05     0.022      12      51 ..     149     186 ..     140     197 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.6e-05
                        HTH_27  12 irhrrrrkkladlcgrlnvedshisyslkkLtekGLvert 51 
                                   i    ++k+++dl++ l+++ s+is  lk L   + ++r 
  gi|13541302|ref|NP_110990.1| 149 IS--KDPKTIKDLSRSLKIDTSTISRRLKSLLSLDMIMRL 186
                                   44..89**************************99988765 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   9.7e-05      0.13      25      51 ..     151     177 ..     142     178 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 9.7e-05
                  HTH_Tnp_ISL3  25 lesrsvkavArqlgvSwtTVwrildry 51 
                                   ++ +++k+ +r l ++++T+ r+l+++
  gi|13541302|ref|NP_110990.1| 151 KDPKTIKDLSRSLKIDTSTISRRLKSL 177
                                   4458********************976 PP

>> Replic_Relax  Replication-relaxation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   8.9e-05      0.12      16      68 ..     160     206 ..     133     207 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 8.9e-05
                  Replic_Relax  16 arllfashratarrrLarLrelgllsrlrkrvggarggsepyvYaLtpkGarl 68 
                                    r l  + ++ ++rrL+ L +l++++rl k   ++++   py Y L+  G+ l
  gi|13541302|ref|NP_110990.1| 160 SRSLKIDTST-ISRRLKSLLSLDMIMRLGKG--TRNY---PYLYKLNDFGKIL 206
                                   4444455555.9***************9998..5555...******9988655 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00016      0.22      16      55 ..     146     184 ..     143     189 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00016
                                   HHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEE CS
                        HTH_20  16 lraLaraegltaselaerldlskntlsyHLrvLeeagLve 55 
                                    r++ ++++ t ++l + l ++ +t+s++L+ L + + + 
  gi|13541302|ref|NP_110990.1| 146 IREI-SKDPKTIKDLSRSLKIDTSTISRRLKSLLSLDMIM 184
                                   6777.99***************************999886 PP

>> RuvB_C  RuvB C-terminal winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       1.5   2.1e+03      46      57 ..     113     124 ..      99     127 .. 0.84
   2 ?   10.5   0.5   0.00031      0.42       8      60 ..     139     189 ..     135     193 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.5
                                   HHHHHTTSEEEE CS
                        RuvB_C  46 PyLlkeglIert 57 
                                   P+ ++ ++I +t
  gi|13541302|ref|NP_110990.1| 113 PMVIYDKYIDKT 124
                                   888999999998 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00031
                                   HHHHHHHHHHT.TT--B-HHHHHHHTT--HHHHHHTTHHHHHHTTSEEEETTE CS
                        RuvB_C   8 dikyLkllkekfkggpvglktlaailgeeketiedviEPyLlkeglIertsrG 60 
                                   + ky+ l+ e  ++ p  +k l+  l+++++ti+      Ll   +I+r  +G
  gi|13541302|ref|NP_110990.1| 139 NNKYITLIREI-SKDPKTIKDLSRSLKIDTSTISRRLK-SLLSLDMIMRLGKG 189
                                   57899999876.99********************9885.78999999998888 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1       3.8   5.3e+03      36      47 ..       7      18 ..       6      19 .. 0.77
   2 ?   11.4   0.9   0.00017      0.23      12      40 ..     150     178 ..     140     183 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 3.8
                        HTH_11 36 IkaLeelgvpIe 47
                                  I++Le  g  I+
  gi|13541302|ref|NP_110990.1|  7 IAILEREGEYII 18
                                  899999996654 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00017
                        HTH_11  12 argpisgeeLAeeLnvSrrtvrrdIkaLe 40 
                                   +++p ++++L++ L++ ++t+ r++k+L 
  gi|13541302|ref|NP_110990.1| 150 SKDPKTIKDLSRSLKIDTSTISRRLKSLL 178
                                   344579********************995 PP

>> RWP-RK  RWP-RK domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.4   0.00077       1.1      29      41 ..      77      89 ..      75      89 .. 0.94
   2 ?   -1.1   0.1       1.4   1.9e+03      14      32 ..     155     173 ..     154     177 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00077
                        RWP-RK 29 LKricRelgIsRW 41
                                  L +ic+  gI+RW
  gi|13541302|ref|NP_110990.1| 77 LQKICKTKGIPRW 89
                                  89*********** PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.4
                        RWP-RK  14 plkeAAksLgvskttLKri 32 
                                   ++k+ ++sL++ ++t+ r+
  gi|13541302|ref|NP_110990.1| 155 TIKDLSRSLKIDTSTISRR 173
                                   5777788888888777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       914  (0.0509789); expected 358.6 (0.02)
Passed bias filter:                      644  (0.0359195); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 1240.51
//
Query:       gi|13541303|ref|NP_110991.1|  [L=465]
Description: transporter component [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.7e-27   95.4  20.9    4.7e-27   95.4  20.9    1.7  2  Sulf_transp  Sulphur transport


Domain annotation for each model (and alignments):
>> Sulf_transp  Sulphur transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.3      0.15   2.7e+03      21      39 ..      28      46 ..      17      61 .. 0.59
   2 !   95.4  20.9   2.6e-31   4.7e-27      12     310 .]      81     448 ..      72     448 .. 0.67

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.15
                   Sulf_transp 21 llralllaiavaavgfqll 39
                                   l +l+la+++  +++q+l
  gi|13541303|ref|NP_110991.1| 28 ALLILALALLIGGIIMQVL 46
                                  4444444444444444444 PP

  == domain 2  score: 95.4 bits;  conditional E-value: 2.6e-31
                   Sulf_transp  12 divvekdgrllralllaiavaavgfqllaaaglidlpksafpvvglivGGllFGvGMalaGgCasgtlyrvGeGslralit 92 
                                   +++ ++d  l+  + +ai++ ++++ l+a ++  ++  + f v g+++GGl+FG+G  laG  +++ ++ +G+G+  a+++
  gi|13541303|ref|NP_110991.1|  81 RVMAFQDRFLMVCFGFAIGLGSIILYLVAIFTHPNFGIKDFFVPGIVIGGLIFGIGVGLAGYFPGTIWIALGQGRRDAIYA 161
                                   789999999***************************999****************************************** PP

                   Sulf_transp  93 llffilgava...lltgilsswleqllestvskesly...etlglsplllialllliallllvkelrkek........... 156
                                    ++  lga+    +   +  +++++l + ++++ s++   +++g+ ++ l++ ++l+ + ll+ +  k+k           
  gi|13541303|ref|NP_110991.1| 162 SFGGLLGAFTwsiIFGNVKWFFWDTLNFGPITWASVAgisSKFGVFAVSLVFGIILLLVFLLLPRYPKSKvkdscgyhmlg 242
                                   *******97522233334446667788888888776533366666554444443333333333222222234667777777 PP

                   Sulf_transp 157 ..................lqeaeklektslakk.lfrkpwslvlgavllgllavlawllsaktgrsfglg........ft. 209
                                                     + +a+ +  t+l+++   +++  ++  ++++ ++av++++l + +g s++++        ++ 
  gi|13541303|ref|NP_110991.1| 243 ksektitfdlvisedfekYPKAN-RYLTKLINEsSKENARMTIPLGLAFTITAVAVIILHQIFGESTTFSwigaqlsyLAn 322
                                   77777777776655544333333.444455544144444455556777777777777777666666554321111212111 PP

                   Sulf_transp 210 .vpgakilqyl..........vlgtskf.......lnwgvvlvlGiilGaflaallsge....fkleapk.ar.......e 260
                                    +++a+ ++++          v     +       + w+ +++l+ +lG ++aa l  +    fk+++pk ++       +
  gi|13541303|ref|NP_110991.1| 323 pTWAASNAYFQlfgglhmvngV-----PvnhpfseIGWEPFTDLSSFLGGLIAATLISKrymaFKPQVPKiWShshnpkyR 398
                                   1333333333222333222211.....222222334467888888888888888765542333666666655477788889 PP

                   Sulf_transp 261 llaallGGllMGfGarlAgGCniGaglsgiaslslsgwlalvflllGavl 310
                                    + a+lG++++ fGar+A+GC +G++lsg  ++++s++++++f+llGa++
  gi|13541303|ref|NP_110991.1| 399 PIGAFLGAFMVLFGARMANGCASGHILSGNIQMAISSFVFMIFVLLGAWV 448
                                   9***********************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (465 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       879  (0.0490267); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        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: 0.68u 0.30s 00:00:00.98 Elapsed: 00:00:00.49
# Mc/sec: 2849.15
//
Query:       gi|13541304|ref|NP_110992.1|  [L=388]
Description: NAD(FAD)-dependent dehydrogenase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.2e-14   52.8   0.0    2.3e-13   50.1   0.0    2.0  2  Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
  ------ inclusion threshold ------
       0.11   13.1   0.1          1   10.0   0.0    2.3  2  Pyr_redox    Pyridine nucleotide-disulphide oxidoreductase


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.1   0.0   2.5e-17   2.3e-13       1     278 [.       3     289 ..       3     306 .. 0.78
   2 ?   -4.4   0.1         1     9e+03     103     110 ..     331     338 ..     330     340 .. 0.84

  Alignments for each domain:
  == domain 1  score: 50.1 bits;  conditional E-value: 2.5e-17
                                   CSEEEE--SHHHHHHHHHHHH....HTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH.HHHHCHHHH.CCCCHCCTC CS
                                   xxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx.xxxxxxxxx RF
                   Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaq....agakvtlvelegtclnggcllskallgvaedaeias.evvkklnqg.ielllgeev 75 
                                   k++v+iG+G++G     +l++      +++t+++ +      +  +s+++l++++++   + + ++ ln g ++++++ ev
  gi|13541304|ref|NP_110992.1|   3 KKIVIIGAGAGGGISLSKLRRvlkdEDVDITIID-KLGR--TDFQPSYIFLSIGQKRVKDLsRDFNLLNGGhVKTVKD-EV 79 
                                   589*********999999*9999878*******5.3323..3455666888877777666676677788887888888.** PP

                                   EEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHHHHHHCCSS-TSEEEEES-SHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2  76 vkidpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGvaenvgklvrtldsaealklkllpkrivvvGgGyiGvE 156
                                   v++d +++ v    +k     k+ yd+l++ +G   ++   +G   +++++v tl++  +l+ k ++       gG i + 
  gi|13541304|ref|NP_110992.1|  80 VSVDAQNRIVNT--LK----GKYSYDYLIMSPGPDIKKDSFEGI--EATDSVWTLEDSLKLRAKIKE-----FNGGKILIS 147
                                   ****99966655..33....37***********87777789999..566788999*********999.....336777777 PP

                                   HHHHH.......HHHT-..................EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEET CS
                                   xxxxx.......xxxxx..................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2 157 lAaal.......aklgk..................evtlveardrllraldkelsaaleealekeGvevklgtsvkeidgn 212
                                   +++++       +   +                  e+t+ +  +++++++++ ls+  ++ lek+ +    g++   id+ 
  gi|13541304|ref|NP_110992.1| 148 VSSQWykcppvpW---EmalllddyfrkknmrdkvEITVAHPVSKPMEMYGPGLSDPFAKMLEKRSIGGLYGKKLLGIDAS 225
                                   7777634444441...03334444444566677779********************************************9 PP

                                   TEEEEEEETTSCEEEESEEEE-S-EEES-HHCSHCCT-EEEETTEE..E--TTSBESSTTEEE-GGGC CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2 213 geklevvledgeeidadlvvvavGvrpstelleeklglelderggi..vvdeflrtnvpgiyaiGDva 278
                                   ++  e v ed +++  dl +va   +p + ++ ++  l   ++g+     ++f + + ++i+aiGDv+
  gi|13541304|ref|NP_110992.1| 226 KK--EAVFEDDDRLRFDLSIVAPPHSPPSFIK-DNEYLRS-KNGWAstNLKDFRNPKYDDIFAIGDVI 289
                                   99..9**********************99887.6666665.7777733666777889**********9 PP

  == domain 2  score: -4.4 bits;  conditional E-value: 1
                                   EEE---EE CS
                                   xxxxxxxx RF
                   Pyr_redox_2 103 lvlAtGss 110
                                   +++AtGss
  gi|13541304|ref|NP_110992.1| 331 CIIATGSS 338
                                   69****97 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      0.13   1.1e+03       1      11 [.       4      14 ..       4      40 .. 0.76
   2 ?   10.0   0.0   0.00011         1      23      72 ..     179     228 ..     160     234 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.13
                                  EEEEECSSHHH CS
                     Pyr_redox  1 kvvvvGgGyig 11
                                  k+v++G+G  g
  gi|13541304|ref|NP_110992.1|  4 KIVIIGAGAGG 14
                                  699***99754 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00011
                                   SEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTS CS
                     Pyr_redox  23 kkVtvversdkllrllDeeaskilqeklekngievllntkveeiegsedg 72 
                                    ++tv +  +k++ ++++ +s+ +++ lek+ i  l+++k+  i+ s+++
  gi|13541304|ref|NP_110992.1| 179 VEITVAHPVSKPMEMYGPGLSDPFAKMLEKRSIGGLYGKKLLGIDASKKE 228
                                   467******************************************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (388 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       402  (0.0224218); 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: 0.62u 0.31s 00:00:00.93 Elapsed: 00:00:00.52
# Mc/sec: 2251.79
//
Query:       gi|13541305|ref|NP_110993.1|  [L=140]
Description: hypothetical protein TVN0474 [Thermoplasma volcanium GSS1]
Scores for complete 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   17.8   0.8       0.27   11.5   0.1    2.6  3  YlbD_coat       Putative coat protein
  ------ inclusion threshold ------
      0.016   15.1   0.2      0.042   13.7   0.1    1.8  2  DUF1641         Protein of unknown function (DUF1641)
      0.027   14.8   4.0        0.2   12.0   0.8    2.3  2  TEX12           Testis-expressed 12
      0.031   14.0   0.1       0.12   12.2   0.0    1.8  2  SKA2            Spindle and kinetochore-associated protein 2
      0.053   12.4   0.1      0.053   12.4   0.1    1.1  1  Polyoma_lg_T_C  Polyomavirus large T antigen C-terminus
      0.072   12.5   1.7      0.095   12.1   1.7    1.3  1  Not3            Not1 N-terminal domain, CCR4-Not complex comp
       0.17   11.8   0.6       0.35   10.7   0.3    1.6  2  PCRF            PCRF domain


Domain annotation for each model (and alignments):
>> YlbD_coat  Putative coat protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.1     0.017        44      77     103 ..       5      31 ..       1      40 [. 0.82
   2 !   11.5   0.1    0.0001      0.27      67     107 ..      43      83 ..      34     108 .. 0.89
   3 ?    0.1   0.0      0.36   9.3e+02      94     108 ..      88     102 ..      76     123 .. 0.43

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.017
                     YlbD_coat  77 kkldvdklqehlnqlskalasvqelik 103
                                   k+ d+++++++ln+l+  ++ ++++ +
  gi|13541305|ref|NP_110993.1|   5 KEKDINDISKELNKLKPTIDLLKSMQE 31 
                                   556999*********999999988765 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.0001
                     YlbD_coat  67 dllsqllnllkkldvdklqehlnqlskalasvqelikqfqe 107
                                   ++ ++++nl  ++d+ ++  +l++lsk  as++++  ++ +
  gi|13541305|ref|NP_110993.1|  43 ENYDTIFNLTARMDIYDIATGLKKLSKLAASLSSIDDNYFD 83 
                                   567899***************************99887765 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.36
                     YlbD_coat  94 alasvqelikqfqek 108
                                   +++++ e+i++ +++
  gi|13541305|ref|NP_110993.1|  88 IVKNLPEVIEKSNKA 102
                                   333333333322222 PP

>> DUF1641  Protein of unknown function (DUF1641)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       3.3   8.5e+03      32      37 ..      24      29 ..      23      30 .. 0.56
   2 ?   13.7   0.1   1.6e-05     0.042       2      23 ..     102     123 ..     101     124 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 3.3
                       DUF1641 32 alLKal 37
                                   lLK++
  gi|13541305|ref|NP_110993.1| 24 DLLKSM 29
                                  456655 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 1.6e-05
                       DUF1641   2 gleepkpvGlfgLlraLrDPDV 23 
                                   +++e+k +G++gLl+++r  D+
  gi|13541305|ref|NP_110993.1| 102 AADENKNIGVLGLLKLMRSNDI 123
                                   689**************97665 PP

>> TEX12  Testis-expressed 12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.8   7.8e-05       0.2      24      67 ..       2      49 ..       1      58 [. 0.63
   2 ?    3.8   0.1     0.029        73      42      70 ..      64      92 ..      54     107 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.8e-05
                         TEX12 24 devlekvlndmskeinlllskya..kilseraavda.sy.ieeidalf 67
                                  de  ek++nd+ske+n l  +    k + e    ++  y +e++d++f
  gi|13541305|ref|NP_110993.1|  2 DENKEKDINDISKELNKLKPTIDllKSMQETGMTETlKYlVENYDTIF 49
                                  7899************99876541133344444333223245566666 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.029
                         TEX12 42 lskyakilseraavdasyieeidalfkea 70
                                  l k +k+ +  +++d  y +e+  + k+ 
  gi|13541305|ref|NP_110993.1| 64 LKKLSKLAASLSSIDDNYFDELARIVKNL 92
                                  66777777888899********9999974 PP

>> SKA2  Spindle and kinetochore-associated protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   4.6e-05      0.12      45      95 ..       7      57 ..       6      63 .. 0.93
   2 ?   -1.3   0.0      0.69   1.8e+03      35      56 ..      79     101 ..      67     109 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4.6e-05
                          SKA2 45 erlkkvkeelqaLkeqceellaekkelidkirttlvanrellqqLqasael 95
                                  ++++++ +el++Lk  ++ l + ++  ++++ + lv+n+ ++ +L a++ +
  gi|13541305|ref|NP_110993.1|  7 KDINDISKELNKLKPTIDLLKSMQETGMTETLKYLVENYDTIFNLTARMDI 57
                                  57999****************************************999854 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.69
                          SKA2  35 dna.eNpvkLlerlkkvkeelqa 56 
                                   dn   ++++++++l +v e+ ++
  gi|13541305|ref|NP_110993.1|  79 DNYfDELARIVKNLPEVIEKSNK 101
                                   44445556666666666555544 PP

>> Polyoma_lg_T_C  Polyomavirus large T antigen C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   2.1e-05     0.053      75     154 ..      12      94 ..       1     134 [. 0.81

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.1e-05
                Polyoma_lg_T_C  75 qavdtvlakkrvdslhltreemlterfndlldkmdlifgahgnavleeymagvawlhcl...lpkmdsviydflkcivlni 152
                                    + +    k  +d l+  +e  +te +++l+++ d if  +   ++ +  +g+  l  l   l  +d   +d l  iv n+
  gi|13541305|ref|NP_110993.1|  12 ISKELNKLKPTIDLLKSMQETGMTETLKYLVENYDTIFNLTARMDIYDIATGLKKLSKLaasLSSIDDNYFDELARIVKNL 92 
                                   555555668889*************************************999887765522277888899*********** PP

                Polyoma_lg_T_C 153 pk 154
                                   p 
  gi|13541305|ref|NP_110993.1|  93 PE 94 
                                   97 PP

>> Not3  Not1 N-terminal domain, CCR4-Not complex component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   1.7   3.7e-05     0.095      37     107 ..       3      73 ..       1     109 [. 0.74

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.7e-05
                          Not3  37 sqkeKleadLKkeikKLqrlRdqiktwlssneikdkkkLlenrkliEeamerFkavEkesKtKafSkegla 107
                                   ++keK  +d  ke+ KL+   d +k+++++   ++ k L en ++i +   r      ++ +K+ Sk + +
  gi|13541305|ref|NP_110993.1|   3 ENKEKDINDISKELNKLKPTIDLLKSMQETGMTETLKYLVENYDTIFNLTARMDIYDIATGLKKLSKLAAS 73 
                                   68******************************************997544444444556666666665555 PP

>> PCRF  PCRF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.3   0.00013      0.35      19      95 ..       4      79 ..       2      90 .. 0.80
   2 ?    2.2   0.0     0.056   1.4e+02       6      53 ..      65     111 ..      60     123 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00013
                                  TTGGGSSSTTHHHHHTHHHHHHHHHHHHHTTTHHH...HT.....-S-..-GGGTHHHHHHHHHH..HHHHHT-..SS CS
                          PCRF 19 edqekakklskelaeleeivealeeleealedleeakelle.edeelaelaeeeleelekeleeleeelkklLlpkde 95
                                  +++++++++skel++l+++++ l++++e+    e++k l+e  d+ ++  a+ ++ ++++ l++l ++l   L+  d 
  gi|13541305|ref|NP_110993.1|  4 NKEKDINDISKELNKLKPTIDLLKSMQETGM-TETLKYLVEnYDTIFNLTARMDIYDIATGLKKL-SKLAASLSSIDD 79
                                  4678999******************988654.566677885577777777899999999999999.888888886555 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.056
                                   TTTTTST.-GGGTTTGGGSSSTTHHHHHTHHHHHHHHHHHHHTTTHHH CS
                          PCRF   6 eelekklsdpevwedqekakklskelaeleeivealeeleealedlee 53 
                                   ++l+k +++ + ++d + + +l++ +++l e++e+ +++ ++++++  
  gi|13541305|ref|NP_110993.1|  65 KKLSKLAASLSSIDD-NYFDELARIVKNLPEVIEKSNKAADENKNIGV 111
                                   566666666666654.77889999999999999999998888887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       982  (0.0547716); expected 358.6 (0.02)
Passed bias filter:                      571  (0.0318478); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.52u 0.31s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 852.88
//
Query:       gi|13541306|ref|NP_110994.1|  [L=240]
Description: hypothetical protein TVN0475 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.8e-54  183.5   0.0    6.5e-54  183.3   0.0    1.0  1  DUF72           Protein of unknown function DUF72
  ------ inclusion threshold ------
       0.11   12.0   0.0       0.15   11.5   0.0    1.2  1  Porphobil_deam  Porphobilinogen deaminase, dipyromethane cofa
       0.12   12.2   2.6        6.8    6.5   0.1    2.3  2  PAZ_siRNAbind   PAZ domain


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 !  183.3   0.0   1.1e-57   6.5e-54       1     216 [.      21     233 ..      21     235 .. 0.93

  Alignments for each domain:
  == domain 1  score: 183.3 bits;  conditional E-value: 1.1e-57
                                   B.TT..CCCHHHHHCCT-SEEEE-HHCCSSS-HHHHHHHHCTS-TT-EEEEE--CCCCCS.G-.SCHHHHHHHHHH.CHHH CS
                         DUF72   1 YpeglkkkerLeyYarhfntVEinstFYalpspetvakwaaqtpedFrFavKapraitherne.daeealerflesalepL 80 
                                   Ype++ +k +++yY+++fntVE+nstFY++ps++t+  w+++ pe+F++++K++r+ith ++  d++e++ +f++    +L
  gi|13541306|ref|NP_110994.1|  21 YPEDIHTKYWFRYYSSRFNTVELNSTFYRFPSDKTALGWYNSSPENFTYSLKINRSITHIKRLrDTDEEILKFYNV-AGKL 100
                                   9**********************************************************752337**********6.**** PP

                                   CT-EEEEEEE--TT--S.HHHHHHHHHH.TTTS-SEEEE--BGGGH.H.HHHHHHHTT-EEEE.E--SSC--------SST CS
                         DUF72  81 geklgpllfQlppsfkfdeenlerLeaf.laalpllavEvRhrswf.e.llellrehgvavvl.depkkpklpledvttad 157
                                   +eklg+llfQ+ppsfk++een++ ++++ l+++   ++E+Rh+swf + +l+ l ++g+ + + +   +++lp+  +  + 
  gi|13541306|ref|NP_110994.1| 101 KEKLGCLLFQFPPSFKYSEENVSLIAKIpLSKYC-RVLEFRHKSWFdKkILSSLVDNGFHIATvS---SKDLPFLLIQ-DV 176
                                   ******************99*********99774.8**********955*********9955524...6789997777.88 PP

                                   EEEEEE--SHHTTB----HHHHHHHHHHHHHHHTCSSEEEEEE-SBCCCHHHHHHHHHH CS
                         DUF72 158 fvyvRlhgreeryayrYseeelaewaerikawaaegrevyvffnndaegqaplnaraLa 216
                                    +y+R+hg+ + ya++Y  e+l+++++ri +++   + +y++fnnd++g+ap+na++++
  gi|13541306|ref|NP_110994.1| 177 IIYMRMHGDTNGYATDYPLEKLKDMLNRIIDLSP--DYAYIYFNNDYNGYAPKNAEEIK 233
                                   9*******989*********************99..79******************997 PP

>> 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 ?   11.5   0.0   2.6e-05      0.15      46      88 ..     137     179 ..     127     199 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.6e-05
                Porphobil_deam  46 akiggkglFtkeleeaLlegeidlaVhSlKDlptelpeglela 88 
                                    ++ +k+ F k++   L+++ +++a  S KDlp  l +++ + 
  gi|13541306|ref|NP_110994.1| 137 LEFRHKSWFDKKILSSLVDNGFHIATVSSKDLPFLLIQDVIIY 179
                                   57889****************************9998887765 PP

>> PAZ_siRNAbind  PAZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.7    0.0024        15      65      88 ..      27      49 ..      15      56 .. 0.86
   2 ?    6.5   0.1    0.0011       6.8      71     110 ..      78     117 ..      60     133 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0024
                                  HHHHHHHHHHHH--SHHHHHHHHH CS
                 PAZ_siRNAbind 65 vkywynyhierywntpeaklefyr 88
                                   kyw+ y+  r+ nt e +  fyr
  gi|13541306|ref|NP_110994.1| 27 TKYWFRYYSSRF-NTVELNSTFYR 49
                                  69******9985.9********99 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0011
                                   HHHHHH--SHHHHHHHHHHT-S--TTS-EEEEEES----- CS
                 PAZ_siRNAbind  71 yhierywntpeaklefyrkfgqvdlkqpailakfaskikk 110
                                    hi+r  +t e  l+fy   g++  k  ++l +f    k 
  gi|13541306|ref|NP_110994.1|  78 THIKRLRDTDEEILKFYNVAGKLKEKLGCLLFQFPPSFKY 117
                                   59************************99999999877664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.32s 00:00:00.88 Elapsed: 00:00:00.53
# Mc/sec: 1355.82
//
Query:       gi|13541307|ref|NP_110995.1|  [L=402]
Description: transporter component [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.9e-23   82.9  20.9    7.6e-23   81.5  20.9    1.6  1  Sulf_transp  Sulphur transport


Domain annotation for each model (and alignments):
>> Sulf_transp  Sulphur transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.5  20.9   4.3e-27   7.6e-23      24     305 ..      47     389 ..      36     393 .. 0.69

  Alignments for each domain:
  == domain 1  score: 81.5 bits;  conditional E-value: 4.3e-27
                   Sulf_transp  24 alllaiavaavgfqllaaaglidlpksafpv.vglivGGllFGvGMalaGgCasgtlyrvGeGslralitllffilgaval 103
                                    +++ai++ a+++  l+a+g+   ++ +  + +g+++GG++FG G+a++G  ++++++ +GeG+  a++++l+  lga+ +
  gi|13541307|ref|NP_110995.1|  47 CIAIAIGAGAIVLYGLSALGVSFHWGIKPDYvIGVALGGIIFGTGIAISGYVPGTVWMALGEGRRDAIYAVLGGLLGAASW 127
                                   457888888999999999999999997776659********************************************9865 PP

                   Sulf_transp 104 ltgils...swle.qllestvskesly..etlglsplllialllliallllvk...elrkek................... 156
                                   +  +      wl+  l + ++   ++    +++l++ ++ia++++i + ++++   + rk k                   
  gi|13541307|ref|NP_110995.1| 128 TLIYQTsfgHWLTtYLNFGQI---YFGgkVGTDLKLGFIIAIVWAIIMFVIAYtlpRYRKGKscaylsthknykldaeeek 205
                                   443333111333303333333...222113334455556666655555555442233344337778888888888888888 PP

                   Sulf_transp 157 ................lqeae..klektslakklfrkpwslvlgavllgllavlawllsaktgrs..fglgftvpgakilq 217
                                                   + +++  ++ ++ ++ +     ++++  ++++gl++vl ++l + +g s  +++ ++  +  + +
  gi|13541307|ref|NP_110995.1| 206 eyietanflmegtsmpIGKNNlpEKVNYHWTVSSKLFGVTMLSVGIIIGLTVVLEMFLHQIFGESttYSWIVAQIWLPAGY 286
                                   888888888777777644444332333344433333467788899*********999998888872244555554444444 PP

                   Sulf_transp 218 ylv.lgtskflnwgvvlvlGiilGaflaall.sgefk.le..apk.a.........rellaallGGllMGfGarlAgGCni 283
                                   ++  +     + w+ ++++G ++Gafla+++ +++f+ +   +p+ +         ++++ a+ G+ lM  Gar+A GC +
  gi|13541307|ref|NP_110995.1| 287 WQYsTIVVHTIGWEPFSDIGTLFGAFLASIFfTRRFQaFSnvIPPsWkerfgnsqiKRAAGAFSGAYLMLLGARMADGCAS 367
                                   433134456799*****************9725556412221333235555555555************************ PP

                   Sulf_transp 284 Gaglsgiaslslsgwlalvfll 305
                                   G++lsg  ++++s+  +++f++
  gi|13541307|ref|NP_110995.1| 368 GHILSGDLQMAVSSLEFFIFVV 389
                                   ******9999999988888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (402 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       971  (0.0541581); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); 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):               1  [number of targets reported over threshold]
# CPU time: 0.64u 0.30s 00:00:00.94 Elapsed: 00:00:00.50
# Mc/sec: 2411.21
//
Query:       gi|13541308|ref|NP_110996.1|  [L=418]
Description: arginine deiminase [Thermoplasma volcanium GSS1]
Scores for complete 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-41  141.8   0.0    3.7e-41  141.3   0.0    1.2  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 !  141.3   0.0   2.1e-45   3.7e-41       2     340 .]      16     417 ..      15     417 .. 0.82

  Alignments for each domain:
  == domain 1  score: 141.3 bits;  conditional E-value: 2.1e-45
                                   ----HHHHT--TTTTTTTT-SS---HHHHHHHHHHHHHHHHTTT-EEEEHHHHHHHHCTSHHHHHHHHHHHSSTTTTITTT CS
                 Amidinotransf   2 vrPgrflenltetasdnllqddeiilekaqkEHdafvqvLrekGveVlvledllaealeaeearkekldeklleselgikl 82 
                                   +rP  ++e  + ++   l+ ++++ ++ka++EH  + + Lre+G++V+ le++   + + + +++e l + +    + i  
  gi|13541308|ref|NP_110996.1|  16 HRPSIEIEYAMLAPRPFLF-ERVFSVKKAIEEHIRLEEILRENGIKVYRLEEEIIKKADYDANFRELLLNYV----RSI-V 90 
                                   99*******9998888777.********************************97644444444444333322....222.1 PP

                                   .............................GGGS-S-HHHHHHHHHHHHH----EEE---GGGG-TTTTEEEEBSEEEE--- CS
                 Amidinotransf  83 .............................gvklseeikiekleladkatsnnsflipplpnlvFtrdwfstigggvvlnpm 134
                                                                +   +e+ + +k+   ++ +    +   pl nl+F+rd+++ ++ gv++++m
  gi|13541308|ref|NP_110996.1|  91 hfygriedirraenefaenirqidsktllDYLILEPSIDLKNDYENSGNYPTVYSNIPLANLYFMRDQQAVADSGVIIGNM 171
                                   34557888***************999988777788888888888888888888888999********************** PP

                                   SSGGGHHHHHHHHHHHHHSHTSB-EEEEE-TTS--TT----GGGEEEEETTEEEEEESSSS-HHHHHHHHHHHHHT...TS CS
                 Amidinotransf 135 aapnRrrErllaeliykkhpgvkvakvldisgkeeesktlEGGdfvvlskgvvaigvssRtdeegieelakklfyk...tv 212
                                   + ++R+ E+  + + + +   +       +  k+ +++ +EGGdf++ +++  + g +sRtd+ g+ +  ++ + +   + 
  gi|13541308|ref|NP_110996.1| 172 KREQRKSESDITSFVLLN--VFGE----TDAFKMPQNAHFEGGDFMPAGDFAFI-GTGSRTDYNGAFQALSSGKIDcdeVL 245
                                   ******************..2221....23367889*************99876.*********99887776555533433 PP

                                   -SEEEEEE--GGSST..S-GGGTEEEEETTEEEE-HHHH.TT-E...........SS-HHHHHHHHTT-SS-EEEE-CS-S CS
                 Amidinotransf 213 afkviaieipkgrai..mHldtvftvvdddavvclpsildaegv...........kakereavaqaLkekgleiIeigeee 280
                                   + +  + e+ ++ ++  mHldt f+ + d  +v   +  +++++           ++  ++ +++ Lkekg+++I+ +  e
  gi|13541308|ref|NP_110996.1| 246 VVENPKYEFSQEDNMvnMHLDTYFNLAGDGIAVTSTYLAKRAKArvygkksrsryEKLSETNLYEYLKEKGFNFIDLTVPE 326
                                   333335555555554449*********************999779******999988889999****************** PP

                                   S-B---S-EEEETTEE...............EEETTGHHHHHHHHHT...................T-EEEEE-HTTTGGG CS
                 Amidinotransf 281 qwnfggNvLelkpgvv...............vaydrntvtnekleea...................gievievpiselerG 327
                                   q ++ +N+L++++ ++               +a+d+ t++ +k                       gi+ i  ++ el+ G
  gi|13541308|ref|NP_110996.1| 327 QLAYSSNFLTISDRKIisvnvesvikrlisqRAFDKSTEEVIK---TelskigekifpnrkeikdfGIDFIDAELIELTGG 404
                                   ***********99999666666666666555555555555444...25559****************************** PP

                                   S--TTTT-EEEEE CS
                 Amidinotransf 328 gGgarCmsaplfr 340
                                   +Gga+Cm+a l r
  gi|13541308|ref|NP_110996.1| 405 YGGAHCMTATLNR 417
                                   ********98865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (418 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       811  (0.045234); expected 358.6 (0.02)
Passed bias filter:                      581  (0.0324056); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 2906.35
//
Query:       gi|13541309|ref|NP_110997.1|  [L=335]
Description: NMD protein (ribosome stability and mRNA decay protein) [Thermoplasma volcanium GSS1]
Scores for complete 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-41  139.8   0.3    1.3e-40  139.4   0.3    1.2  1  NMD3             NMD3 family
     0.0023   17.8   2.2       0.63    9.9   0.1    2.7  2  eIF-5_eIF-2B     Domain found in IF2B/IF5
  ------ inclusion threshold ------
      0.033   14.3   2.1      0.039   14.1   0.6    1.9  2  MqsA_antitoxin   Antitoxin component of bacterial toxin-antit
      0.042   14.0   0.5         15    5.8   0.1    2.7  2  CxC7             CxC7 like cysteine cluster associated with K
       0.24   11.7   2.1         34    4.9   1.4    2.9  2  GFA              Glutathione-dependent formaldehyde-activatin
       0.34   11.0   5.5        3.3    7.8   3.9    2.5  2  DZR              Double zinc ribbon
       0.48   10.7   5.2         16    5.8   0.0    3.1  3  Ribosomal_L32p   Ribosomal L32p protein family
       0.48   10.7   3.5       0.58   10.4   0.1    2.5  2  Yippee-Mis18     Yippee zinc-binding/DNA-binding /Mis18, cent
       0.64    9.9   7.5        4.9    7.1   0.1    3.2  3  DUF3797          Domain of unknown function (DUF3797)
       0.66    9.9   3.9       0.77    9.7   0.8    2.4  2  zf-C3HC4         Zinc finger, C3HC4 type (RING finger)
       0.68   10.4   2.5        3.1    8.3   0.3    2.6  2  Lar_restr_allev  Restriction alleviation protein Lar
       0.69   10.4   3.7         15    6.2   1.7    2.7  2  zf-C4pol         C4-type zinc-finger of DNA polymerase delta
        2.3    8.1   4.6         50    3.9   0.1    3.5  3  TFIIS_C          Transcription factor S-II (TFIIS)
        5.6    6.9   6.2        3.4    7.6   0.1    3.1  3  RNA_POL_M_15KD   RNA polymerases M/15 Kd subunit
          6    6.4  13.4       0.63    9.5   0.1    3.3  3  zf-ribbon_3      zinc-ribbon domain


Domain annotation for each model (and alignments):
>> NMD3  NMD3 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.4   0.3   1.1e-43   1.3e-40       1     243 []       3     231 ..       3     231 .. 0.87

  Alignments for each domain:
  == domain 1  score: 139.4 bits;  conditional E-value: 1.1e-43
                          NMD3   1 CcrCGkeieelinglCedCllkevditegiekievevCkeCgrylpkgkWvkaeleseellaeclkklvekgLkvseevee 81 
                                   C+ CG+++   ++g+C++C+ ++++ +e+i  +++ +C++Cg+++ ++kW++     ++ll  +l ++  + ++       
  gi|13541309|ref|NP_110997.1|   3 CVVCGRNEA-VEHGMCSSCIYDNTN-VENIGPVSLVFCPKCGSIRIGKKWYRD-SYGNKLLPMLLDEVKCSDVN------- 73 
                                   ********7.7799*******9997.788888******************665.67778888888888333333....... PP

                          NMD3  82 vkvelvdaefiwtephskrikvkvtvqgevrgenetilqqevevevkvkrqqCprCsriaggyyeaivQvRqkrelteeeh 162
                                    ++   d + i   +++k+i + vt++++  + +     q+v +++ v++  Cp+C++i+g+y+ea++Q+R+ ++  ++  
  gi|13541309|ref|NP_110997.1|  74 ARIS-GDEKGIFFDEKNKQIILPVTIKRSNMKDK----IQNVAIPYSVTYISCPTCNKITGSYFEATIQLRTVSTKYDNIL 149
                                   3343.33333444444899999999999985533....59*********************************89999999 PP

                          NMD3 163 krtfelleqli...lkhdahafiskikevkeGlDfyfgsksaArklveflksevggkvkeseklvsedkksgkevyrltys 240
                                   + + e +e ++   +k+da++fisk+++++eG+D+y+g+++++  +++f+ +++  ++  +++l++  k+ gk+ +r+tys
  gi|13541309|ref|NP_110997.1| 150 ESVLESIEAIVekrKKEDAESFISKVEKKPEGIDIYLGKRTDGDVVSSFVLDHFFSSIIVTKTLAGV-KD-GKKFFRFTYS 228
                                   999999999999999999*************************************************.88.********** PP

                          NMD3 241 vrl 243
                                   +r+
  gi|13541309|ref|NP_110997.1| 229 LRI 231
                                   *98 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 !    6.7   0.3    0.0052       6.3      89     116 ..      16      43 ..      12      44 .. 0.94
   2 !    9.9   0.1   0.00053      0.63      65      96 ..      96     127 ..      82     141 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0052
                                   STSSSTSTCEEECCSSSCEEEEESSSTC CS
                  eIF-5_eIF-2B  89 lCkeCkspetelekeerllvlkCkaCga 116
                                   +C++C   +t++e  + ++++ C +Cg+
  gi|13541309|ref|NP_110997.1|  16 MCSSCIYDNTNVENIGPVSLVFCPKCGS 43 
                                   7*************************97 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00053
                                   EEESSSSSCCHHHHHHHHHHHHHTSTSSSTST CS
                  eIF-5_eIF-2B  65 lilngkfeakkleklldkyieeyVlCkeCksp 96 
                                   ++++ +  ++k++++   y  +y+ C++C++ 
  gi|13541309|ref|NP_110997.1|  96 VTIKRSNMKDKIQNVAIPYSVTYISCPTCNKI 127
                                   345666667777777788***********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 ?   14.1   0.6   3.2e-05     0.039       1      53 [.       1      55 [.       1      77 [. 0.79
   2 ?   -1.9   0.0       2.8   3.3e+03      51      80 ..     136     165 ..     106     178 .. 0.51

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.2e-05
                MqsA_antitoxin  1 mkCpvCgkaelvrdtrdvpytykgekt.vikavtgdfCarCGegvldeee.edrl 53
                                  mkC+vCg+ e v++    +  y   ++  i  v+  fC++CG   ++++   d +
  gi|13541309|ref|NP_110997.1|  1 MKCVVCGRNEAVEHGMCSSCIYDNTNVeNIGPVSLVFCPKCGSIRIGKKWyRDSY 55
                                  9*************999999998766527999**********9888776324455 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.8
                MqsA_antitoxin  51 drlseellefrkkvnaelvdpafiarvrkk 80 
                                    +l +  +++ + ++++l   + i++ rkk
  gi|13541309|ref|NP_110997.1| 136 IQLRTVSTKYDNILESVLESIEAIVEKRKK 165
                                   222333333444444444444445555544 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 ?    5.8   0.1     0.013        15      12      28 ..      28      44 ..      19      56 .. 0.84
   2 ?    5.8   0.1     0.013        16      12      28 ..     109     127 ..     101     131 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.013
                          CxC7 12 efrvPfsliecsecgdi 28
                                  e+  P+sl+ c++cg i
  gi|13541309|ref|NP_110997.1| 28 ENIGPVSLVFCPKCGSI 44
                                  7777**********986 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.013
                          CxC7  12 efrvPfsli..ecsecgdi 28 
                                   +  +P+s++   c+ c++i
  gi|13541309|ref|NP_110997.1| 109 NVAIPYSVTyiSCPTCNKI 127
                                   5679**995438*****97 PP

>> GFA  Glutathione-dependent formaldehyde-activating enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   1.4     0.028        34      23      59 ..       8      45 ..       1      59 [. 0.68
   2 ?    4.3   0.0     0.044        53       5      26 ..     121     142 ..     118     167 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.028
                           GFA 23 kaealelleg..elkeykkt.adsgnkvtrsfCpeCgspl 59
                                  ++ea+e  +g  +   y++t  ++  +v+  fCp+Cgs  
  gi|13541309|ref|NP_110997.1|  8 RNEAVE--HGmcSSCIYDNTnVENIGPVSLVFCPKCGSIR 45
                                  555555..33335555666657778889999******865 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.044
                           GFA   5 CsdCrkasgsaftanavvkaea 26 
                                   C +C k++gs f a + +++ +
  gi|13541309|ref|NP_110997.1| 121 CPTCNKITGSYFEATIQLRTVS 142
                                   9***********9998877655 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   3.9    0.0028       3.3      15      49 .]       3      42 ..       1      42 [. 0.72
   2 ?    0.9   0.0       0.4   4.8e+02      29      36 ..     119     126 ..      98     133 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0028
                           DZR 15 CseCgtk..lkavaaedrCpsCgekvdpearf.......CpeCG 49
                                  C  Cg +  ++    + +C+sC +++++ +++       Cp+CG
  gi|13541309|ref|NP_110997.1|  3 CVVCGRNeaVE----HGMCSSCIYDNTNVENIgpvslvfCPKCG 42
                                  77777763343....78888888888888887777777788887 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.4
                           DZR  29 drCpsCge 36 
                                   + Cp C++
  gi|13541309|ref|NP_110997.1| 119 ISCPTCNK 126
                                   56777765 PP

>> Ribosomal_L32p  Ribosomal L32p protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   1.0     0.021        25      28      54 ..       2      28 ..       1      30 [. 0.88
   2 ?    5.8   0.0     0.013        16      24      39 ..      33      48 ..      29      58 .. 0.81
   3 ?   -1.0   0.0       1.8   2.2e+03      25      34 ..     117     126 ..      99     128 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.021
                                  EETTTC.CEECTTC-BTTTTBSSSBXSX CS
                Ribosomal_L32p 28 ecpncg.elklpHrvcpscGyYkgrevi 54
                                  +c +cg +  + H +c+sc  Y++  v+
  gi|13541309|ref|NP_110997.1|  2 KCVVCGrNEAVEHGMCSSC-IYDNTNVE 28
                                  7999999999*********.**999886 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.013
                                  --EEEETTTCCEECTT CS
                Ribosomal_L32p 24 pnlvecpncgelklpH 39
                                   +lv cp+cg+ ++ +
  gi|13541309|ref|NP_110997.1| 33 VSLVFCPKCGSIRIGK 48
                                  489*******999876 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 1.8
                                   -EEEETTTCC CS
                Ribosomal_L32p  25 nlvecpncge 34 
                                   +   cp+c++
  gi|13541309|ref|NP_110997.1| 117 TYISCPTCNK 126
                                   4578999987 PP

>> Yippee-Mis18  Yippee zinc-binding/DNA-binding /Mis18, centromere assembly
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   1.1         1   1.2e+03      53      70 ..      33      51 ..       3      59 .. 0.77
   2 ?   10.4   0.1   0.00049      0.58      29      74 ..      84     137 ..      63     167 .. 0.71

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1
                                  EEEEEETTT--E.EEEEEE CS
                  Yippee-Mis18 53 ystlsCkgCnsv.lGwkYk 70
                                  +s ++C +C+s+ +G+k++
  gi|13541309|ref|NP_110997.1| 33 VSLVFCPKCGSIrIGKKWY 51
                                  6789999999854887765 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00049
                                   ES---CCCEEEECEEEETTSTT........EEEEEEEETTT--EEEEEEEECSC CS
                  Yippee-Mis18  29 vlkkvtrnvvvgkelvtdeegk........ctystlsCkgCnsvlGwkYkstee 74 
                                   ++++ ++++++  + ++++ ++        ++++ +sC +Cn++ G  +++t +
  gi|13541309|ref|NP_110997.1|  84 FFDEKNKQIILPVTIKRSNMKDkiqnvaipYSVTYISCPTCNKITGSYFEATIQ 137
                                   44555555554444444422222445778899**************99998855 PP

>> DUF3797  Domain of unknown function (DUF3797)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   1.2       5.9   7.1e+03      15      23 ..       2      10 ..       1      31 [. 0.65
   2 ?    6.4   0.1    0.0069       8.2      14      25 ..      36      47 ..      32      49 .. 0.89
   3 ?    7.1   0.1    0.0041       4.9       6      22 ..     111     127 ..     103     142 .. 0.75

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 5.9
                       DUF3797 15 qCPeCgNnk 23
                                  +C +Cg n 
  gi|13541309|ref|NP_110997.1|  2 KCVVCGRNE 10
                                  577887443 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0069
                       DUF3797 14 vqCPeCgNnkvl 25
                                  v CP+Cg ++++
  gi|13541309|ref|NP_110997.1| 36 VFCPKCGSIRIG 47
                                  78********97 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.0041
                       DUF3797   6 ivkLdekYvqCPeCgNn 22 
                                   +++ +  Y+ CP C  +
  gi|13541309|ref|NP_110997.1| 111 AIPYSVTYISCPTCNKI 127
                                   5778888*******765 PP

>> zf-C3HC4  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.8   0.00065      0.77      18      41 .]      13      41 ..      11      41 .. 0.80
   2 ?    0.0   0.1      0.68   8.1e+02      34      41 .]     117     124 ..     107     124 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00065
                                  S--B-CHHHHHHHHC.....TSSB--TTT CS
                      zf-C3HC4 18 kHsfCskCirkilks.....rkkvkCPlC 41
                                  +H +Cs+Ci   ++       + v CP+C
  gi|13541309|ref|NP_110997.1| 13 EHGMCSSCIYDNTNVenigpVSLVFCPKC 41
                                  5********9999986666555566**99 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.68
                                   SSB--TTT CS
                      zf-C3HC4  34 kkvkCPlC 41 
                                   ++ +CP+C
  gi|13541309|ref|NP_110997.1| 117 TYISCPTC 124
                                   5678***9 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.6     0.032        39      28      37 ..      35      47 ..       2      57 .. 0.62
   2 ?    8.3   0.3    0.0026       3.1       6      38 ..      38     128 ..      33     143 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.032
               Lar_restr_allev 28 cvyCadCga...s 37
                                   v+C +Cg    +
  gi|13541309|ref|NP_110997.1| 35 LVFCPKCGSiriG 47
                                  6777777763333 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0026
               Lar_restr_allev   6 CPfCggravlersqrvvaeigq........................................................... 27 
                                   CP Cg+  + ++ +r +++  +                                                           
  gi|13541309|ref|NP_110997.1|  38 CPKCGSIRIGKKWYRDSYGN-Kllpmlldevkcsdvnarisgdekgiffdeknkqiilpvtikrsnmkdkiqnvaipysvt 117
                                   99999999999998888754.259999998888888888888888888888888888888888888888888889999999 PP

               Lar_restr_allev  28 cvyCadCgast 38 
                                   +++C  C+  t
  gi|13541309|ref|NP_110997.1| 118 YISCPTCNKIT 128
                                   99999998743 PP

>> zf-C4pol  C4-type zinc-finger of DNA polymerase delta
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   1.7     0.012        15       1      20 [.       3      24 ..       3      44 .. 0.81
   2 ?    3.5   0.0     0.086     1e+02      12      42 ..     120     149 ..     101     164 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.012
                      zf-C4pol  1 ClvCk..eklkkalCkkCrsdk 20
                                  C+vC+  e +++ +C++C  d+
  gi|13541309|ref|NP_110997.1|  3 CVVCGrnEAVEHGMCSSCIYDN 24
                                  *****5544559******7444 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.086
                      zf-C4pol  12 lCkkCrsdkqesllkllsrlkelekklnele 42 
                                    C +C+ + + s+++   +l+++ +k++++ 
  gi|13541309|ref|NP_110997.1| 120 SCPTCN-KITGSYFEATIQLRTVSTKYDNIL 149
                                   6****4.88888**********999999875 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 ?    1.1   0.2      0.31   3.7e+02       2      12 ..       2      12 ..       1      13 [. 0.77
   2 ?    2.7   0.1     0.097   1.2e+02       2       8 ..      37      43 ..      36      46 .. 0.82
   3 ?    3.9   0.1     0.042        50       2      19 ..     120     139 ..     119     141 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.31
                       TFIIS_C  2 kCpkCgsreay 12
                                  kC  Cg +ea+
  gi|13541309|ref|NP_110997.1|  2 KCVVCGRNEAV 12
                                  78888888875 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.097
                       TFIIS_C  2 kCpkCgs 8 
                                   CpkCgs
  gi|13541309|ref|NP_110997.1| 37 FCPKCGS 43
                                  5****97 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.042
                       TFIIS_C   2 kCpkCgsreayff..qlQtR 19 
                                    Cp C++   ++f  ++Q+R
  gi|13541309|ref|NP_110997.1| 120 SCPTCNKITGSYFeaTIQLR 139
                                   7******9999996677877 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 ?   -0.4   0.1      0.93   1.1e+03      24      29 ..      17      22 ..       9      24 .. 0.75
   2 ?    7.6   0.1    0.0028       3.4       2       9 ..      36      43 ..      35      46 .. 0.86
   3 ?    0.3   0.3      0.54   6.5e+02       4       8 ..     121     125 ..     119     127 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.93
                                  ESSSS- CS
                RNA_POL_M_15KD 24 CrqCgY 29
                                  C++C Y
  gi|13541309|ref|NP_110997.1| 17 CSSCIY 22
                                  99**88 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0028
                                  EBESTTTS CS
                RNA_POL_M_15KD  2 kFCpkCgN 9 
                                   FCpkCg+
  gi|13541309|ref|NP_110997.1| 36 VFCPKCGS 43
                                  5*****97 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.54
                                   ESTTT CS
                RNA_POL_M_15KD   4 CpkCg 8  
                                   Cp+C+
  gi|13541309|ref|NP_110997.1| 121 CPTCN 125
                                   ****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 ?   -3.2   3.3       5.4   6.5e+03       5      11 ..       3       9 ..       2      20 .. 0.55
   2 ?    9.5   0.1   0.00053      0.63       3      11 ..      36      44 ..      34      49 .. 0.78
   3 ?    5.1   0.3     0.013        16       3      11 ..     119     127 ..     118     130 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 5.4
                   zf-ribbon_3  5 CPnCGap 11
                                  C  CG +
  gi|13541309|ref|NP_110997.1|  3 CVVCGRN 9 
                                  8888864 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00053
                   zf-ribbon_3  3 vrCPnCGap 11
                                  v+CP+CG++
  gi|13541309|ref|NP_110997.1| 36 VFCPKCGSI 44
                                  799999986 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.013
                   zf-ribbon_3   3 vrCPnCGap 11 
                                   ++CP C+++
  gi|13541309|ref|NP_110997.1| 119 ISCPTCNKI 127
                                   79****997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1249  (0.0696637); expected 358.6 (0.02)
Passed bias filter:                      826  (0.0460706); expected 358.6 (0.02)
Passed Vit filter:                       105  (0.00585643); 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: 0.64u 0.27s 00:00:00.91 Elapsed: 00:00:00.48
# Mc/sec: 2083.26
//
Query:       gi|13541310|ref|NP_110998.1|  [L=204]
Description: hypothetical protein TVN0479 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-19   69.4  13.3    3.4e-19   69.1  13.3    1.1  1  DUF998    Protein of unknown function (DUF998)
    0.00076   17.9   9.0    0.00085   17.7   9.0    1.1  1  YfhO      Bacterial membrane protein YfhO


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 !   69.1  13.3   3.8e-23   3.4e-19       1     182 [.      14     188 ..      14     191 .. 0.93

  Alignments for each domain:
  == domain 1  score: 69.1 bits;  conditional E-value: 3.8e-23
                        DUF998   1 vaaallalavilaaallrpgydplrhaiSeLgaeg........gpggwlfnaglvllgllvlalavgllraargragragr 73 
                                   +aa++ a+++i+++   +p ++   +a+S+Lg+ +        ++ ++++n+gl++++llv+ ++v+ +++  ++++ +g 
  gi|13541310|ref|NP_110998.1|  14 IAAIICAWLTIAISIHFNPWFRINVNALSDLGGGNfisnghpaPTYPFIYNGGLMVTALLVFSFSVLSISHVNSKVEIMGL 94 
                                   6899999**************************99***********************************9********** PP

                        DUF998  74 lllavaglglvlagvfptdpgggspslsglvHglasavaflalavavlllasaarrrawallrlvggvallllvaalvwll 154
                                    ++++++l+l+l+g+++++++         +H+++s+++f++  +++++++           +++g++ +l+++a++++  
  gi|13541310|ref|NP_110998.1|  95 SFFIISALFLALIGIYHEGTY---------PHAFVSIWFFILSSISFVTIG---IGMYLVGDKKFGITIILIILASWIVYS 163
                                   *********************.........9********************...777777778888888888888877777 PP

                        DUF998 155 aaaldgslllGlaerllvlaitawllal 182
                                    +   ++ +++  e +++ +i +++ ++
  gi|13541310|ref|NP_110998.1| 164 SV---RWGSVAEGEVFGISVIDIVVSIY 188
                                   77...9*************999998876 PP

>> YfhO  Bacterial membrane protein YfhO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   9.0   9.5e-08   0.00085     276     384 ..      56     164 ..      31     202 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 9.5e-08
                          YfhO 276 mgslpniyvgllpll.llilyFvlkkiklkeklafallllllilsfllpplnlvwhgfqaPvgfpyRfsfilsflllllaa 355
                                    +++p+iy g l+++ ll++ F+  +i++ +  + ++ l ++i+s l+ +l  ++h +++P  f+  + fils ++ +++ 
  gi|13541310|ref|NP_110998.1|  56 APTYPFIYNGGLMVTaLLVFSFSVLSISHVNSKVEIMGLSFFIISALFLALIGIYHEGTYPHAFVSIWFFILSSISFVTIG 136
                                   24489999876555515566677778877665555555599999*****************************99999999 PP

                          YfhO 356 ealkelkqlkklkllaailllvlllliil 384
                                    ++  l   kk ++++++++l++ ++++ 
  gi|13541310|ref|NP_110998.1| 137 IGMY-LVGDKKFGITIILIILASWIVYSS 164
                                   9985.443435555555555555555443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       994  (0.0554409); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                        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: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 1344.82
//
Query:       gi|13541311|ref|NP_110999.1|  [L=360]
Description: hypothetical protein TVN0480 [Thermoplasma volcanium GSS1]
Scores for complete 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-101  337.5   0.0   8.4e-101  337.2   0.0    1.1  1  DUF763    Protein of unknown function (DUF763)


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 !  337.2   0.0  4.7e-105  8.4e-101       1     312 []       5     316 ..       5     316 .. 0.94

  Alignments for each domain:
  == domain 1  score: 337.2 bits;  conditional E-value: 4.7e-105
                        DUF763   1 GiadLpLhegkvPewllermkkLskaiveliveeygkeellerlsdPlwFqslgnvlGmdWdsSGsTtvvlgalkealkse 81 
                                   G++ LpLh+g++Pe+l+ r +kLs+++ el++e+yg eel++r++dP+wF+s++ ++G+dW+sSG+T   l+alk++++++
  gi|13541311|ref|NP_110999.1|   5 GTSILPLHYGHPPEYLYCRAVKLSGLLSELVIENYGVEELIRRIADPFWFHSMSLAIGFDWNSSGTTVFALSALKDYFSKR 85 
                                   7899***************************************************************************** PP

                        DUF763  82 elgilvaGGkGkksrktpeeleklaeklgldeek...lvkasrlvakvdnaalqdgyqlYlhalivsekgkwaviqQGmne 159
                                     +i+++GGkGkk+ ++++ele++     + +++   l   ++ vak+dn++lqdg+++Yl++l+vs+kg++av+qQGmn+
  gi|13541311|ref|NP_110999.1|  86 PGEIVICGGKGKKMGSMQDELESARALGFITASEsnkLSVDAKRVAKIDNNLLQDGFDIYLQFLVVSSKGTHAVVQQGMNT 166
                                   *********************9988765554444445999***************************************** PP

                        DUF763 160 eerlARRYhwlseelesfveephsgiagekkeeevlnlvskeseearkaildlvkekpekllkelkelkallkgekklklp 240
                                   + r ARRYhw+  + + +  ++++gi++e   +++l+l++kese +rk i+d+++ek   +l+   e +a+l+g    +l+
  gi|13541311|ref|NP_110999.1| 167 QLRSARRYHWTLGN-TFAGIDGRNGISSELVLDRTLDLSAKESEGNRKGIVDVIREKS--FLNVPGEKQATLDGFVMPELR 244
                                   **********9444.444569**********************************965..777777777888888888899 PP

                        DUF763 241 akhevlekvlekayelqpedfeellllkgvGpktlraLalvaeliygekasfkDPvkysfavGgKdgvPypv 312
                                    + ++++++++++ye++++dfe++ +++g+G++t+raL+++ae++ygek+sfkDPvkysfa+GgKdgvP+pv
  gi|13541311|ref|NP_110999.1| 245 MDYRINWNKVRNLYEYNVDDFEQVYMAPGIGKSTIRALSFLAEIVYGEKPSFKDPVKYSFALGGKDGVPKPV 316
                                   9999*******************************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       391  (0.0218082); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); 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 0.30s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 2228.64
//
Query:       gi|13541312|ref|NP_111000.1|  [L=100]
Description: hypothetical protein TVN0481 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.3e-24   84.6   0.1    4.8e-24   84.5   0.1    1.0  1  DUF2175     Uncharacterized protein conserved in archaea (DUF
     0.0033   17.8   0.1     0.0053   17.1   0.0    1.4  1  Syntaxin_2  Syntaxin-like protein
  ------ inclusion threshold ------
      0.017   15.3   0.1      0.031   14.5   0.1    1.3  1  DUF2685     Protein of unknown function (DUF2685)


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 !   84.5   0.1     8e-28   4.8e-24       2      98 .]       3      99 ..       2      99 .. 0.97

  Alignments for each domain:
  == domain 1  score: 84.5 bits;  conditional E-value: 8e-28
                       DUF2175  2 kwkCyiCgkeivegekFTftkkgvvHyeClvekarkklkesedaaaLleleevlneeivklkelerv.aedeevkkvleqkrk 83
                                  ++kCy+C+k + +gekFTftkkg+vHy+C+ +++r+kl e e+ + L+ l+ +l++ + +l ++  v a++ e+ ++ +q  +
  gi|13541312|ref|NP_111000.1|  3 EYKCYVCEKPVKTGEKFTFTKKGSVHYDCFIADKRNKLGE-EKLENLRVLSILLDSNLQNLVNVLGVpADSPELAEIKRQNIQ 84
                                  8**************************************8.999***********************99999*********** PP

                       DUF2175 84 elEkaaakltkklek 98
                                  ++Ek a+ +t+k+e+
  gi|13541312|ref|NP_111000.1| 85 SIEKMAGDITRKIEE 99
                                  ************986 PP

>> Syntaxin_2  Syntaxin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   8.9e-07    0.0053      13      56 ..      57     100 .]      46     100 .] 0.94

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 8.9e-07
                    Syntaxin_2  13 stleklvkqLgtkkdteelreklhelieeinelikktnellkkl 56 
                                   s+l++lv+ Lg + d++el e  +++i++i +++ ++++++++l
  gi|13541312|ref|NP_111000.1|  57 SNLQNLVNVLGVPADSPELAEIKRQNIQSIEKMAGDITRKIEEL 100
                                   79*************************************99876 PP

>> DUF2685  Protein of unknown function (DUF2685)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   5.1e-06     0.031       3      26 ..       5      28 ..       3      33 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 5.1e-06
                       DUF2685  3 iCvvCKqPideadvtvdtdkGtvH 26
                                   C vC +P++ ++    t kG+vH
  gi|13541312|ref|NP_111000.1|  5 KCYVCEKPVKTGEKFTFTKKGSVH 28
                                  6************9999******* PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       833  (0.046461); expected 358.6 (0.02)
Passed bias filter:                      623  (0.0347482); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 694.15
//
Query:       gi|13541313|ref|NP_111001.1|  [L=55]
Description: 30S ribosomal protein S27ae [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.3e-19   67.7   1.8    9.2e-19   67.3   1.8    1.2  1  Ribosomal_S27   Ribosomal protein S27a
    7.1e-05   22.9   2.2    9.2e-05   22.5   2.2    1.2  1  Ribosomal_L37e  Ribosomal protein L37e
    0.00048   19.7   1.2    0.00048   19.7   1.2    2.2  2  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain
  ------ inclusion threshold ------
      0.015   15.6   1.4       0.29   11.5   0.0    2.0  2  GFA             Glutathione-dependent formaldehyde-activating
      0.018   15.0   6.6       0.11   12.4   6.6    2.0  1  Nudix_N_2       Nudix N-terminal
       0.03   14.0   4.2       0.42   10.4   0.2    2.3  2  zinc_ribbon_2   zinc-ribbon domain
      0.054   13.5   6.4       0.28   11.2   6.3    2.1  3  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
      0.061   13.4   3.4       0.24   11.5   3.4    1.8  1  DZR             Double zinc ribbon
      0.082   13.0   0.1      0.099   12.7   0.1    1.3  1  MqsA_antitoxin  Antitoxin component of bacterial toxin-antito
       0.13   12.5   3.1       0.17   12.0   0.5    2.1  2  zinc_ribbon_13  Nucleic-acid-binding protein containing Zn-ri
       0.26   11.6   5.4       0.79   10.0   0.6    2.1  2  Ribosomal_L32p  Ribosomal L32p protein family
       0.45   10.7   5.9        2.9    8.1   0.8    2.1  2  NOB1_Zn_bind    Nin one binding (NOB1) Zn-ribbon like
       0.67    9.9   6.0        7.4    6.5   6.0    2.2  1  RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
          1    8.9   5.2          3    7.4   5.2    1.7  1  TF_Zn_Ribbon    TFIIB zinc-binding
        4.6    6.9   8.8         12    5.6   1.0    2.5  2  zf_UBZ          Ubiquitin-Binding Zinc Finger


Domain annotation for each model (and alignments):
>> Ribosomal_S27  Ribosomal protein S27a
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.3   1.8   7.7e-22   9.2e-19       3      45 .]       5      45 ..       3      45 .. 0.97

  Alignments for each domain:
  == domain 1  score: 67.3 bits;  conditional E-value: 7.7e-22
                                  SSCCESSSSSEEESS-B-SS-S-TTSBEEECTTEEEESSTTTE CS
                 Ribosomal_S27  3 kyYkvddsgkverlrkeCpreCGaGvfMAehkdRkyCGkCglT 45
                                  ++Y++ d gk  r+++ Cpr CG+Gvf+Aeh+dR +CG+Cg+T
  gi|13541313|ref|NP_111001.1|  5 ELYEIAD-GKLVRKHRFCPR-CGPGVFLAEHADRFTCGRCGYT 45
                                  57*****.************.*********************9 PP

>> Ribosomal_L37e  Ribosomal protein L37e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   2.2   7.7e-08   9.2e-05       8      46 ..      12      52 ..       9      54 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 7.7e-08
                Ribosomal_L37e  8 GkrqkkktHilCrrCgkrsy...hvqkktCascGy.psaklrk 46
                                  Gk    + H +C rCg   +   h  + tC+ cGy   +k++k
  gi|13541313|ref|NP_111001.1| 12 GKL--VRKHRFCPRCGPGVFlaeHADRFTCGRCGYtEFKKVKK 52
                                  666..456************77788888*******66677665 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 !   19.7   1.2     4e-07   0.00048       1      11 [.      16      26 ..      16      33 .. 0.80
   2 ?    3.8   1.8     0.038        45       6      10 ..      39      43 ..      38      44 .. 0.96

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 4e-07
                 zf-NADH-PPase  1 rthrFCgrCGa 11
                                  r+hrFC+rCG 
  gi|13541313|ref|NP_111001.1| 16 RKHRFCPRCGP 26
                                  79********5 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.038
                 zf-NADH-PPase  6 CgrCG 10
                                  CgrCG
  gi|13541313|ref|NP_111001.1| 39 CGRCG 43
                                  ****9 PP

>> GFA  Glutathione-dependent formaldehyde-activating enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00024      0.29      42      63 ..      11      32 ..       2      37 .. 0.68
   2 ?    5.3   0.2     0.021        25      45      64 ..      32      51 ..      29      55 .] 0.76

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00024
                           GFA 42 dsgnkvtrsfCpeCgsplysee 63
                                  d +   +++fCp+Cg  ++  e
  gi|13541313|ref|NP_111001.1| 11 DGKLVRKHRFCPRCGPGVFLAE 32
                                  334445569******9999754 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.021
                           GFA 45 nkvtrsfCpeCgsplysees 64
                                  ++++r  C +Cg + + + +
  gi|13541313|ref|NP_111001.1| 32 EHADRFTCGRCGYTEFKKVK 51
                                  5788999*****99886644 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   6.6   9.1e-05      0.11       1      32 [.      19      46 ..      19      48 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 9.1e-05
                                  -B-TTT--B-EEE--TT-SS-EEEETTTTEEE CS
                     Nudix_N_2  1 kFCsqCGtpvelripdgDnreRlvCpaCgtih 32
                                  +FC+ CG  v l+    ++  R++C +Cg++ 
  gi|13541313|ref|NP_111001.1| 19 RFCPRCGPGVFLA----EHADRFTCGRCGYTE 46
                                  8******998776....6999********975 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.2   0.00035      0.42      14      20 ..      19      25 ..      13      25 .. 0.80
   2 ?    5.1   0.5     0.016        19      15      21 ..      37      44 ..      34      45 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00035
                 zinc_ribbon_2 14 kFCpyCG 20
                                  +FCp+CG
  gi|13541313|ref|NP_111001.1| 19 RFCPRCG 25
                                  6888888 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.016
                 zinc_ribbon_2 15 F.CpyCGt 21
                                  F C +CG+
  gi|13541313|ref|NP_111001.1| 37 FtCGRCGY 44
                                  56889986 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   1.7     0.013        16      18      25 ..      18      25 ..       2      25 .. 0.71
   2 ?   11.2   6.3   0.00024      0.28      18      46 .]      18      45 ..      10      45 .. 0.77
   3 ?    9.3   0.2   0.00094       1.1      16      33 ..      34      51 ..      29      54 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.013
                 Zn_Tnp_IS1595 18 gfvCPhCg 25
                                  ++ CP+Cg
  gi|13541313|ref|NP_111001.1| 18 HRFCPRCG 25
                                  34488887 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00024
                 Zn_Tnp_IS1595 18 gfvCPhCgsrkayriktrglfqCkeCrkq 46
                                  ++ CP+Cg   ++  +++ +f C +C+++
  gi|13541313|ref|NP_111001.1| 18 HRFCPRCG-PGVFLAEHADRFTCGRCGYT 45
                                  355*****.5555555689*******985 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.00094
                 Zn_Tnp_IS1595 16 pngfvCPhCgsrkayrik 33
                                  +++f+C +Cg++++ ++k
  gi|13541313|ref|NP_111001.1| 34 ADRFTCGRCGYTEFKKVK 51
                                  477899999988776665 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   3.4    0.0002      0.24      10      37 ..      16      45 ..      11      53 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0002
                           DZR 10 pdarfCseCgtklkavaa..edrCpsCgek 37
                                   + rfC++Cg  +  +++    +C +Cg+ 
  gi|13541313|ref|NP_111001.1| 16 RKHRFCPRCGPGVFLAEHadRFTCGRCGYT 45
                                  678999999988544444448889999875 PP

>> MqsA_antitoxin  Antitoxin component of bacterial toxin-antitoxin system, MqsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   8.3e-05     0.099      35      59 ..      19      43 ..       9      55 .] 0.77

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 8.3e-05
                MqsA_antitoxin 35 dfCarCGegvldeeeedrlseelle 59
                                   fC+rCG gv+ +e+ dr++     
  gi|13541313|ref|NP_111001.1| 19 RFCPRCGPGVFLAEHADRFTCGRCG 43
                                  6*****************9875443 PP

>> zinc_ribbon_13  Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.1      0.39   4.6e+02       2       7 ..      21      26 ..      20      34 .. 0.79
   2 ?   12.0   0.5   0.00015      0.17      37      49 ..      38      50 ..      32      55 .] 0.81

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.39
                zinc_ribbon_13  2 CpKCgn 7 
                                  Cp+Cg 
  gi|13541313|ref|NP_111001.1| 21 CPRCGP 26
                                  999985 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00015
                zinc_ribbon_13 37 sCknCgYtelYka 49
                                  +C +CgYte+ k 
  gi|13541313|ref|NP_111001.1| 38 TCGRCGYTEFKKV 50
                                  8********9665 PP

>> Ribosomal_L32p  Ribosomal L32p protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.6   0.00066      0.79      33      46 ..      12      25 ..       7      32 .. 0.89
   2 ?    4.5   0.4     0.034        41      39      54 ..      36      51 ..      31      53 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00066
                                  CCEECTTC-BTTTT CS
                Ribosomal_L32p 33 gelklpHrvcpscG 46
                                  g+l + Hr cp cG
  gi|13541313|ref|NP_111001.1| 12 GKLVRKHRFCPRCG 25
                                  8999*********8 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.034
                                  TC-BTTTTBSSSBXSX CS
                Ribosomal_L32p 39 HrvcpscGyYkgrevi 54
                                  +  c  cGy + ++v 
  gi|13541313|ref|NP_111001.1| 36 RFTCGRCGYTEFKKVK 51
                                  678*****99999885 PP

>> NOB1_Zn_bind  Nin one binding (NOB1) Zn-ribbon like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.8    0.0025       2.9      22      30 ..      17      25 ..      11      31 .. 0.85
   2 ?    5.9   0.4     0.012        15      21      38 ..      34      51 ..      28      54 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0025
                  NOB1_Zn_bind 22 tkkFCpkCG 30
                                  + +FCp+CG
  gi|13541313|ref|NP_111001.1| 17 KHRFCPRCG 25
                                  678*****9 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.012
                  NOB1_Zn_bind 21 mtkkFCpkCGnktLkrva 38
                                   ++  C +CG    k+v+
  gi|13541313|ref|NP_111001.1| 34 ADRFTCGRCGYTEFKKVK 51
                                  55666**********996 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   6.0    0.0062       7.4       2      31 ..      19      46 ..      19      48 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0062
                                  EBESTTTSBEEEEECSCCCEEEESSSS-EE CS
                RNA_POL_M_15KD  2 kFCpkCgNlLlpkedkegknfeCrqCgYee 31
                                  +FCp Cg     +e      f C  CgY e
  gi|13541313|ref|NP_111001.1| 19 RFCPRCGPGVFLAEHADR--FTCGRCGYTE 46
                                  7*****975555554444..55****9975 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   5.2    0.0025         3       2      27 ..      20      44 ..      19      46 .. 0.69

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0025
                                  EETTTTC.EECHEETSTTCEEESSSSB CS
                  TF_Zn_Ribbon  2 kCPnCgs.tnlveDpergelvCtdCGl 27
                                   CP Cg    ++ +++   ++C++CG+
  gi|13541313|ref|NP_111001.1| 20 FCPRCGPgV-FLAEHA-DRFTCGRCGY 44
                                  6*****633.344433.467******6 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   2.2     0.017        20       3       9 ..      19      25 ..      17      35 .. 0.78
   2 ?    5.6   1.0      0.01        12       1       9 [.      35      43 ..      35      45 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.017
                        zf_UBZ  3 ylCerCg 9 
                                   +C+rCg
  gi|13541313|ref|NP_111001.1| 19 RFCPRCG 25
                                  69****9 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.01
                        zf_UBZ  1 dtylCerCg 9 
                                  d ++C rCg
  gi|13541313|ref|NP_111001.1| 35 DRFTCGRCG 43
                                  679*****8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (55 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       505  (0.0281667); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); 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: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 378.36
//
Query:       gi|13541314|ref|NP_111002.1|  [L=99]
Description: 30S ribosomal protein S24e [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.4e-19   67.9   1.9    6.9e-19   67.6   1.9    1.2  1  Ribosomal_S24e  Ribosomal protein S24e


Domain annotation for each model (and alignments):
>> Ribosomal_S24e  Ribosomal protein S24e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.6   1.9   3.8e-23   6.9e-19       3      78 ..      23      98 ..      14      99 .] 0.96

  Alignments for each domain:
  == domain 1  score: 67.6 bits;  conditional E-value: 3.8e-23
                                  EEE-SSS-S--HHHHHHHHHHHHTS-CTTEEEEEEEE-SSSSEEEEEEEEES-HHHHHHHS-HHHHHHTTSS---S CS
                Ribosomal_S24e  3 dvlHpgkatpskteireklakmykvdpdlvvvfgfrthfGggkttGfakiYdsleaakkfEpkhrlaRnglaekkk 78
                                  ++ +++  tps++ei+e +ak   ++++l++v + ++  G+++  G+ kiY+++++a+ +Ep++ l+Rngl++k++
  gi|13541314|ref|NP_111002.1| 23 TLKFENARTPSREEIKEIIAKHEGAQKELIIVESNKQLTGKHEIVGYTKIYQDKASAMLYEPDYELIRNGLKQKEA 98
                                  568999*******************************************************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       842  (0.046963); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 646.83
//
Query:       gi|13541315|ref|NP_111003.1|  [L=166]
Description: hypothetical protein TVN0484 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.5e-34  117.1   0.2    5.9e-34  116.4   0.2    1.3  1  DUF359        Protein of unknown function (DUF359)
  ------ inclusion threshold ------
        0.1   11.2   0.1       0.13   10.9   0.1    1.1  1  A-2_8-polyST  Alpha-2,8-polysialyltransferase (POLYST)


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 !  116.4   0.2   6.6e-38   5.9e-34       1     125 [.      48     163 ..      48     164 .. 0.96

  Alignments for each domain:
  == domain 1  score: 116.4 bits;  conditional E-value: 6.6e-38
                        DUF359   1 vtknllkagikPdlaivDgktkReeveeeekeeekekekekevievkNpaGtiteelieaikealeseekvlilVdGEEDL 81 
                                   +t nl++ag k  l ivD ktkR          e++ ++e+ +i+v+N +Gti+ +lieaik+++e++++++i+V GEEDL
  gi|13541315|ref|NP_111003.1|  48 TTTNLRRAGAKLFLQIVDLKTKRG---------ESIFQHEEGSITVRNDPGTISFDLIEAIKSSIENNKPTRIEVIGEEDL 119
                                   799*********************.........335778999*************************************** PP

                        DUF359  82 avlpaillapegsvvvYGqpdeGvvlvkvteeakeeaeellekf 125
                                   avlp+i++ ++++v+ YG+pd G+++++vt++++++++e++ k+
  gi|13541315|ref|NP_111003.1| 120 AVLPIIYYSKNNTVIAYGIPDVGMAALTVTDDLRDHVTEVIAKM 163
                                   *****************************************998 PP

>> A-2_8-polyST  Alpha-2,8-polysialyltransferase (POLYST)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   1.4e-05      0.13     265     325 ..      74     135 ..      62     161 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 1.4e-05
                  A-2_8-polyST 265 islriegkifiklhPkemenkyimslflnivkinpr.lvvinekdflieplikltkikgiiG 325
                                   i ++ eg i ++  P  +  + i ++  +i + +p  + vi e+d+ + p+i+ +k   +i 
  gi|13541315|ref|NP_111003.1|  74 IFQHEEGSITVRNDPGTISFDLIEAIKSSIENNKPTrIEVIGEEDLAVLPIIYYSKNNTVIA 135
                                   66788999**********************9999854*******************999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       693  (0.0386525); expected 358.6 (0.02)
Passed bias filter:                      512  (0.0285571); 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: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1109.45
//
Query:       gi|13541316|ref|NP_111004.1|  [L=64]
Description: DNA-directed RNA polymerase subunit E'' [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.2e-14   52.8   0.0    4.4e-14   52.3   0.0    1.2  1  Spt4      Spt4/RpoE2 zinc finger
  ------ inclusion threshold ------
      0.063   13.1   0.0      0.091   12.6   0.0    1.2  1  TetR_N    Bacterial regulatory proteins, tetR family


Domain annotation for each model (and alignments):
>> Spt4  Spt4/RpoE2 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.3   0.0   4.9e-18   4.4e-14       1      77 []       5      63 ..       5      63 .. 0.97

  Alignments for each domain:
  == domain 1  score: 52.3 bits;  conditional E-value: 4.9e-18
                          Spt4  1 lrACllCklvktedqFeeegCpnCeilelkgdkekvsectseefeGlvaildpekSwvAkwqrldkkvpglYAlkve 77
                                  +rAC++Ck++++e++     Cp++            +e+t++e+ G+++i++pe S +Ak+   + ++pg+YA+kv+
  gi|13541316|ref|NP_111004.1|  5 YRACKKCKRLTPEKT-----CPIH-----------PDEKTTTEWFGFLIITEPEFSAIAKR--AGISEPGMYAIKVR 63
                                  59*************.....****...........9*************************..************96 PP

>> TetR_N  Bacterial regulatory proteins, tetR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0     1e-05     0.091      20      34 ..      44      58 ..      42      59 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1e-05
                                  HHHHHHHTSSHHHHH CS
                        TetR_N 20 reIAkrAGvskgalY 34
                                  ++IAkrAG+s++ +Y
  gi|13541316|ref|NP_111004.1| 44 SAIAKRAGISEPGMY 58
                                  79**********999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       631  (0.0351944); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 479.27
//
Query:       gi|13541317|ref|NP_111005.1|  [L=192]
Description: DNA-directed RNA polymerase subunit E' [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      1e-14   54.6   0.1    1.6e-14   54.0   0.1    1.3  1  SHS2_Rpb7-N    SHS2 domain found in N terminus of Rpb7p/Rpc25
    1.3e-11   44.7   0.8    1.3e-11   44.7   0.8    1.8  2  S1             S1 RNA binding domain
  ------ inclusion threshold ------
       0.14   12.1   1.2       0.15   12.0   0.1    1.7  2  RNase_II_C_S1  RNase II-type exonuclease C-terminal S1 domain
       0.18   12.0   2.6        1.4    9.1   0.1    3.0  4  CSD2           Cold shock domain


Domain annotation for each model (and alignments):
>> SHS2_Rpb7-N  SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.0   0.1   3.5e-18   1.6e-14       2      70 .]       9      87 ..       8      87 .. 0.97

  Alignments for each domain:
  == domain 1  score: 54.0 bits;  conditional E-value: 3.5e-18
                                  EEEEE-GGGTTSTHHHHHHHHHHHHHTTBEETTTE..........EEEEEEEEEEECCEEE-TTTSSEEEEEEEEEEEE CS
                   SHS2_Rpb7-N  2 dtvrlePsylgstledallerllekyegkvvpslG..........vivavldiaeysegkvlggsGsvyvrVtfralvF 70
                                  ++ r++P +lg+++++a++e +++ +egk+v+ ++          +++++  ++ ++eg++++g+G+vy++V++ alvF
  gi|13541317|ref|NP_111005.1|  9 YIARIPPDMLGEDYDKAVEEVTKRSLEGKLVDVVNektgvnegkyLVISIISTKAVGEGSIVHGDGGVYQEVKYSALVF 87
                                  6789*****************************999999***************************************9 PP

>> S1  S1 RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1       1.5   6.9e+03       9      16 ..      35      42 ..      21      55 .. 0.56
   2 !   44.7   0.8   2.9e-15   1.3e-11       2      64 ..      89     160 ..      88     167 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.5
                                  EEEEEEEE CS
                            S1  9 eGeVtsvt 16
                                  eG+ ++v+
  gi|13541317|ref|NP_111005.1| 35 EGKLVDVV 42
                                  22222222 PP

  == domain 2  score: 44.7 bits;  conditional E-value: 2.9e-15
                                   STTTCEEEEEEEEEETTEEEEEETTTEEEEEEGGGSSSS..........CEESCHHHCEETTEEEEEEEEEEE CS
                            S1   2 pekgevveGeVtsvtkgGafVelgngvegfvpaselsrd..........arvedpdevlkvGdevkvkvlkvd 64 
                                   pe  e+v+GeV+sv k+GafV +    eg++++s++++d            ++d ++ lkvGd+v+v++  ++
  gi|13541317|ref|NP_111005.1|  89 PEMQEIVDGEVVSVQKFGAFVKFS-SFEGLLHISQIMDDridvdlenkrFIGKDTKRDLKVGDKVRVRIVALN 160
                                   67789*******************.*********************999778999**************9876 PP

>> RNase_II_C_S1  RNase II-type exonuclease C-terminal S1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.2       2.2   9.9e+03       3      12 ..      95     104 ..      93     109 .. 0.60
   2 ?   12.0   0.1   3.4e-05      0.15      31      54 ..     143     166 ..     127     167 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 2.2
                 RNase_II_C_S1   3 FdAvVvdvdd 12 
                                    d+ Vv+v +
  gi|13541317|ref|NP_111005.1|  95 VDGEVVSVQK 104
                                   5666777766 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 3.4e-05
                 RNase_II_C_S1  31 gaglplGervrVrLveADvatrrv 54 
                                   +++l++G++vrVr+v+ ++a+  v
  gi|13541317|ref|NP_111005.1| 143 KRDLKVGDKVRVRIVALNLASSSV 166
                                   569**************9999877 PP

>> CSD2  Cold shock domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1      0.13   5.7e+02      15      51 ..      13      43 ..       2      56 .. 0.71
   2 ?   -0.2   0.1      0.26   1.2e+03      19      36 ..      44      61 ..      30      71 .. 0.64
   3 ?   -0.9   0.0      0.42   1.9e+03      16      32 ..      89     103 ..      78     107 .. 0.72
   4 ?    9.1   0.1   0.00031       1.4       9      35 ..     132     158 ..     127     167 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.13
                          CSD2 15 ipkeklkgakdGdkVvveiteypdkknpeGevievLG 51
                                  ip++ l+  +d dk+v e+t++    ++eG+ ++v  
  gi|13541317|ref|NP_111005.1| 13 IPPDMLG--EDYDKAVEEVTKR----SLEGKLVDVVN 43
                                  5655444..7778888888874....57888888865 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.26
                          CSD2 19 klkgakdGdkVvveitey 36
                                  ++ g+++G+  v+ i++ 
  gi|13541317|ref|NP_111005.1| 44 EKTGVNEGKYLVISIIST 61
                                  344688888888888774 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.42
                          CSD2  16 pkeklkgakdGdkVvve 32 
                                   p  + ++ +dG++V v+
  gi|13541317|ref|NP_111005.1|  89 P--EMQEIVDGEVVSVQ 103
                                   4..46778888888875 PP

  == domain 4  score: 9.1 bits;  conditional E-value: 0.00031
                          CSD2   9 lkqdifipkeklkgakdGdkVvveite 35 
                                   l ++ fi k+ + ++k GdkV v+i+ 
  gi|13541317|ref|NP_111005.1| 132 LENKRFIGKDTKRDLKVGDKVRVRIVA 158
                                   5667799999999***********975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); 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:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.42
# Mc/sec: 1367.39
//
Query:       gi|13541318|ref|NP_111006.1|  [L=365]
Description: chaperone protein DnaJ [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      5e-38  130.5   0.1    6.5e-38  130.1   0.1    1.1  1  DnaJ_C          DnaJ C terminal domain
    6.3e-29   99.9   2.8    6.3e-29   99.9   2.8    2.1  2  DnaJ            DnaJ domain
    9.7e-14   51.5  16.8    1.8e-13   50.6  16.8    1.5  1  DnaJ_CXXCXGXG   DnaJ central domain
    0.00023   21.1  18.6      0.032   14.2   5.9    2.5  2  Anti-TRAP       Tryptophan RNA-binding attenuator protein inh
     0.0015   18.5   8.9       0.21   11.6   0.8    2.3  2  HypA            Hydrogenase/urease nickel incorporation, meta
  ------ inclusion threshold ------
      0.033   14.2   0.0      0.077   13.1   0.0    1.6  1  DUF4460         Domain of unknown function (DUF4460)
      0.041   13.6   5.9       0.75    9.4   0.4    2.2  2  TackOD1         Thaumarchaeal output domain 1
      0.068   13.1   0.1       0.15   12.1   0.1    1.6  1  RPT             A repeated domain in UCH-protein
        0.2   11.4   2.8         12    5.7   0.1    3.2  3  Zn_Tnp_IS1      InsA N-terminal domain
       0.33   10.8   4.2       0.67    9.8   4.2    1.5  1  FdhE            Protein involved in formate dehydrogenase for
       0.38   10.0  14.8        4.8    6.4   3.2    3.5  2  DUF1356         Protein of unknown function (DUF1356)
       0.54    9.6  11.7        2.1    7.8   2.2    3.4  3  zf-TFIIB        Transcription factor zinc-finger
          2    8.5   8.8         54    3.9   0.1    2.2  2  zinc-ribbons_6  zinc-ribbons
        3.2    7.8   6.2         61    3.7   0.1    3.5  4  PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
        8.4    6.7  27.0        8.5    6.7   1.8    4.7  4  DUF5351         Family of unknown function (DUF5351)


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 !  130.1   0.1   5.4e-41   6.5e-38       3     148 .]     127     339 ..     125     339 .. 0.97

  Alignments for each domain:
  == domain 1  score: 130.1 bits;  conditional E-value: 5.4e-41
                                   EEEEE-HHHHHH-.EEE.EEEE........................................................... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxx........................................................ RF
                        DnaJ_C   3 veleisleelykGktkkikikrnvi........................................................ 27 
                                   ++l+islee+y G++k+ik++rn i                                                        
  gi|13541318|ref|NP_111006.1| 127 TNLDISLEEAYYGTEKRIKFRRNAIcpdckgtgakngklitcptchgtgqqrvvrgqgffrmvtvttcntcggkgripeek 207
                                   789********************99******************************************************** PP

                                   .............TEEEEEE-TT--TT-EEEETT-SSSS..S---EEEEEEE---SS-EEETTEEEEEEEEEHHHHHHTEE CS
                                   .........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        DnaJ_C  28 .........kkekktlevkipaGikdgqkirlegeGdeeggepGDlivtikvkphpvFkrkgndlyveveislaeallGgk 99 
                                            ++ ++ ++vkip+G  d+ ++r++g+G++  g++GDl+v+++ k++++++r ++dl+++ +i++ +a+lG+ 
  gi|13541318|ref|NP_111006.1| 208 cprcngtgtIVVDEDITVKIPRGATDNLRLRVSGKGQSYDGRTGDLYVILRIKQDKNLQRINDDLLLDQKINFGQAALGAD 288
                                   *******99667778*********************9777***********99**************************** PP

                                   EEEE-SS-EEEEEE...--TT-EEEETT-S-EET...TEE--EEEEEEEE-- CS
                                   xxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        DnaJ_C 100 levptldgkvklki...tqpgevlrikgkGmpklkkpgkrGdlyvevkvefP 148
                                   + ++++++k +lki   tqpg+v++ikg Gmp+l+ +++ Gdl+v+++ve+P
  gi|13541318|ref|NP_111006.1| 289 IPIQIFNEKYNLKIpegTQPGDVIKIKGAGMPHLN-GHGSGDLLVRINVEVP 339
                                   **********************************7.***************9 PP

>> DnaJ  DnaJ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.9   2.8   5.3e-32   6.3e-29       1      63 []       4      67 ..       4      67 .. 0.99
   2 ?   -0.0   0.1      0.84     1e+03       1      18 [.     252     269 ..     252     271 .. 0.87

  Alignments for each domain:
  == domain 1  score: 99.9 bits;  conditional E-value: 5.3e-32
                                  HHHHHHTSSTTG-HHHHHHHHHHHHHHHSTTTSCCHH.HHHHHHHHHHHHHHHHTSHHHHHHHH CS
                          DnaJ  1 dyYeiLgvskdasedeIkkaYrklalkyHPDknpkdp.eaeekFkeineAyevLsdpekRkqYD 63
                                  dyY+iLgv+++ase++Ikka+r+la+k+HPD +p+++ eaeekFkei+eAyevLsdpekR++YD
  gi|13541318|ref|NP_111006.1|  4 DYYKILGVDRNASEEDIKKAFRELAKKWHPDLHPDNKaEAEEKFKEISEAYEVLSDPEKRRIYD 67
                                  8**************************************************************9 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.84
                                   HHHHHHTSSTTG-HHHHH CS
                          DnaJ   1 dyYeiLgvskdasedeIk 18 
                                   d+Y iL +++d + + I 
  gi|13541318|ref|NP_111006.1| 252 DLYVILRIKQDKNLQRIN 269
                                   79********99988875 PP

>> DnaJ_CXXCXGXG  DnaJ central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.6  16.8   1.5e-16   1.8e-13       1      67 []     152     215 ..     152     215 .. 0.84

  Alignments for each domain:
  == domain 1  score: 50.6 bits;  conditional E-value: 1.5e-16
                 DnaJ_CXXCXGXG   1 CkkCkGsgakkgkkktCktCkGsGvvreeqktlgpfvqqsqstCpeCeGtGkvikekdkCkkCkGkg 67 
                                   C++CkG+gak+gk  tC+tC+G+G++r+ +   g+f + + +tC++C+G+G++   ++kC++C+G+g
  gi|13541318|ref|NP_111006.1| 152 CPDCKGTGAKNGKLITCPTCHGTGQQRVVRG-QGFFRMVTVTTCNTCGGKGRIP--EEKCPRCNGTG 215
                                   *************99*********7655553.4445556889**********88..668******86 PP

>> Anti-TRAP  Tryptophan RNA-binding attenuator protein inhibitory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   4.7    0.0001      0.13      12      47 ..     151     182 ..     149     190 .. 0.84
   2 !   14.2   5.9   2.6e-05     0.032      11      43 ..     192     218 ..     189     224 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.0001
                                   E-TTTTTTSEETTE......E-TTTTTSSEEE-HHH CS
                     Anti-TRAP  12 kCdaCngsGkiepeeprasleCPkCsGkglipTaqG 47 
                                    C+ C+g+G  +++     + CP C G g      G
  gi|13541318|ref|NP_111006.1| 151 ICPDCKGTGAKNGK----LITCPTCHGTGQQRVVRG 182
                                   5**********999....99*******997655555 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 2.6e-05
                                   EE-TTTTTTSEETTE......E-TTTTTSSEEE CS
                     Anti-TRAP  11 tkCdaCngsGkiepeeprasleCPkCsGkglip 43 
                                   t+C++C g G+i+ e      +CP+C+G g i 
  gi|13541318|ref|NP_111006.1| 192 TTCNTCGGKGRIPEE------KCPRCNGTGTIV 218
                                   79*************......*********986 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.8   0.00017      0.21      70     105 ..     149     185 ..     134     191 .. 0.85
   2 !   11.4   1.4    0.0002      0.24      70     105 ..     191     223 ..     185     227 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00017
                                   EEEETTTS-EEECHHHHHS-TTTSSS.-EEEEESSSE CS
                          HypA  70 kvrCreCgkefeleekalrCpkCgsa.dveivsGeel 105
                                   ++ C +C+ ++ ++ k ++Cp+C+++ + ++v+G+++
  gi|13541318|ref|NP_111006.1| 149 NAICPDCKGTGAKNGKLITCPTCHGTgQQRVVRGQGF 185
                                   678*****99998877789****99867788999876 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.0002
                                   EEEETTTS-EEECHHHHHS-TTTSSS-EEEEESSSE CS
                          HypA  70 kvrCreCgkefeleekalrCpkCgsadveivsGeel 105
                                   +++C++Cg ++++ e  ++Cp+C+++++ iv  e++
  gi|13541318|ref|NP_111006.1| 191 VTTCNTCGGKGRIPE--EKCPRCNGTGT-IVVDEDI 223
                                   578******999884..48*****9875.4445555 PP

>> DUF4460  Domain of unknown function (DUF4460)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   6.4e-05     0.077       3      67 ..      13      74 ..      11      75 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.4e-05
                       DUF4460  3 ralskkelrnaLrpFYlavhPDlfgqyPkekkvNeeSLklLnsyleelkkeekksikpekkkLtF 67
                                  r++s++++++a r++ ++ hPDl   +P++k   ee  k +++  e l+ +ek++i  ++ ++ F
  gi|13541318|ref|NP_111006.1| 13 RNASEEDIKKAFRELAKKWHPDL---HPDNKAEAEEKFKEISEAYEVLSDPEKRRIYDQTGSVDF 74
                                  78999*****************6...9************************99988887777766 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.4   0.00062      0.75      85     116 ..     147     178 ..     142     185 .. 0.83
   2 ?    6.6   0.7    0.0048       5.7      72      95 ..     190     213 ..     183     220 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00062
                       TackOD1  85 nvrevCpkCkSidieeqelihhftCgnvgpee 116
                                       +Cp+Ck +  ++ +li + tC  +g+++
  gi|13541318|ref|NP_111006.1| 147 RRNAICPDCKGTGAKNGKLITCPTCHGTGQQR 178
                                   55679********************8887765 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0048
                       TackOD1  72 rirlCpsCksghlnvrevCpkCkS 95 
                                   ++ +C++C ++     e Cp C+ 
  gi|13541318|ref|NP_111006.1| 190 TVTTCNTCGGKGRIPEEKCPRCNG 213
                                   6789******************86 PP

>> RPT  A repeated domain in UCH-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   0.00012      0.15       6      47 ..       6      52 ..       3      56 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00012
                           RPT  6 yklLgidentdDdviitayqvkled.....dpsqkdklrrALkvIAe 47
                                  yk+Lg+d+n++++ i +a++    +     +p++k+++ + +k I+e
  gi|13541318|ref|NP_111006.1|  6 YKILGVDRNASEEDIKKAFRELAKKwhpdlHPDNKAEAEEKFKEISE 52
                                  9******************954433666789********99999987 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 ?    0.1   0.0      0.58   6.9e+02       8      14 ..     152     158 ..     149     164 .. 0.79
   2 ?    5.7   0.1      0.01        12       6      18 ..     166     181 ..     165     184 .. 0.73
   3 ?    3.5   0.1     0.051        61       7      14 ..     207     214 ..     206     219 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.58
                    Zn_Tnp_IS1   8 CPrCsst 14 
                                   CP C+ t
  gi|13541318|ref|NP_111006.1| 152 CPDCKGT 158
                                   9999876 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.01
                    Zn_Tnp_IS1   6 ihCPrCsst..d.VyR 18 
                                   i CP C+ t  + V+R
  gi|13541318|ref|NP_111006.1| 166 ITCPTCHGTgqQrVVR 181
                                   89*****873236666 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.051
                    Zn_Tnp_IS1   7 hCPrCsst 14 
                                    CPrC+ t
  gi|13541318|ref|NP_111006.1| 207 KCPRCNGT 214
                                   5****987 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 ?    9.8   4.2   0.00056      0.67     168     220 ..     165     217 ..     145     221 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00056
                                   -SS-TTT---EEEEEEE-------EEEEEETTT--EEE--TTS-TTT---SS- CS
                          FdhE 168 kglCPvCgsaPvasvvriggeaeglRylhCslCeteWhvvRvkCsnCeetkel 220
                                     +CP C ++    vvr +g  + +   +C++C  + ++   kC  C+ t  +
  gi|13541318|ref|NP_111006.1| 165 LITCPTCHGTGQQRVVRGQGFFRMVTVTTCNTCGGKGRIPEEKCPRCNGTGTI 217
                                   568*****************9999999********************998776 PP

>> DUF1356  Protein of unknown function (DUF1356)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   3.2     0.004       4.8      21      43 ..     154     176 ..     134     183 .. 0.77
   2 ?    6.1   3.9    0.0049       5.9      32      48 ..     191     207 ..     179     238 .. 0.92

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.004
                       DUF1356  21 qvpyveatgrdsvtCptCqGtGe 43 
                                       + a   + +tCptC GtG+
  gi|13541318|ref|NP_111006.1| 154 DCKGTGAKNGKLITCPTCHGTGQ 176
                                   445556667789**********7 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0049
                       DUF1356  32 svtCptCqGtGeiPreq 48 
                                     tC tC G+G+iP+e+
  gi|13541318|ref|NP_111006.1| 191 VTTCNTCGGKGRIPEEK 207
                                   569***********996 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.3      0.14   1.7e+02      22      27 ..     152     157 ..     150     158 .. 0.78
   2 ?    7.8   2.2    0.0017       2.1       2      27 ..     168     199 ..     167     200 .. 0.88
   3 ?    5.0   0.1     0.013        16       1       9 [.     207     215 ..     203     226 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.14
                      zf-TFIIB  22 CpqCrG 27 
                                   Cp+C+G
  gi|13541318|ref|NP_111006.1| 152 CPDCKG 157
                                   899988 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0017
                      zf-TFIIB   2 CPkCqdele......eserggveidyCpqCrG 27 
                                   CP+C+ + +      +  ++ v++ +C+ C+G
  gi|13541318|ref|NP_111006.1| 168 CPTCHGTGQqrvvrgQGFFRMVTVTTCNTCGG 199
                                   *****99997777777777************9 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.013
                      zf-TFIIB   1 kCPkCqdel 9  
                                   kCP+C+ + 
  gi|13541318|ref|NP_111006.1| 207 KCPRCNGTG 215
                                   688887665 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.1     0.045        54      25      36 ..     145     156 ..     134     161 .. 0.85
   2 ?    3.4   9.1     0.065        78       2      36 ..     151     198 ..     150     217 .. 0.70

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.045
                                   EEEEEEE-SSS- CS
                zinc-ribbons_6  25 dlkkealCpeCe 36 
                                   +++++a+Cp+C+
  gi|13541318|ref|NP_111006.1| 145 KFRRNAICPDCK 156
                                   78999******7 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.065
                                   --SSS-S--EE-SSEEE-TTT--.............EEEEEEE-SSS- CS
                zinc-ribbons_6   2 kCpeCqqelekrgeqyhCeaCqe.............dlkkealCpeCe 36 
                                   +Cp+C+    k+g+ ++C +C+              ++  +++C++C+
  gi|13541318|ref|NP_111006.1| 151 ICPDCKGTGAKNGKLITCPTCHGtgqqrvvrgqgffRMVTVTTCNTCG 198
                                   588888888888888888888776666666666666666666666665 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0      0.08        95      21      26 ..     151     156 ..     146     157 .. 0.84
   2 ?    3.7   0.1     0.051        61      17      26 ..     163     172 ..     161     173 .. 0.79
   3 ?   -2.3   0.1       3.9   4.7e+03      22      26 ..     194     198 ..     190     199 .. 0.74
   4 ?    2.1   0.0      0.16   1.9e+02       4       9 ..     207     212 ..     203     220 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.08
                PhnA_Zn_Ribbon  21 vCpeCa 26 
                                   +Cp+C+
  gi|13541318|ref|NP_111006.1| 151 ICPDCK 156
                                   999997 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.051
                PhnA_Zn_Ribbon  17 gallvCpeCa 26 
                                   g l  Cp+C+
  gi|13541318|ref|NP_111006.1| 163 GKLITCPTCH 172
                                   66788****8 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 3.9
                PhnA_Zn_Ribbon  22 CpeCa 26 
                                   C +C+
  gi|13541318|ref|NP_111006.1| 194 CNTCG 198
                                   88887 PP

  == domain 4  score: 2.1 bits;  conditional E-value: 0.16
                PhnA_Zn_Ribbon   4 kCplCa 9  
                                   kCp C+
  gi|13541318|ref|NP_111006.1| 207 KCPRCN 212
                                   9****8 PP

>> DUF5351  Family of unknown function (DUF5351)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.5     0.034        40      20      28 ..     152     160 ..     151     161 .. 0.87
   2 ?    6.7   1.8    0.0071       8.5      19      28 ..     167     176 ..     166     177 .. 0.92
   3 ?    4.0   3.4     0.047        56       6      27 ..     182     201 ..     181     203 .. 0.72
   4 ?    6.0   0.9     0.012        14      18      28 ..     206     216 ..     205     217 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.034
                       DUF5351  20 CesCeGtgk 28 
                                   C+ C+Gtg 
  gi|13541318|ref|NP_111006.1| 152 CPDCKGTGA 160
                                   99****996 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0071
                       DUF5351  19 TCesCeGtgk 28 
                                   TC+ C+Gtg+
  gi|13541318|ref|NP_111006.1| 167 TCPTCHGTGQ 176
                                   9********8 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.047
                       DUF5351   6 GkGYfqLlLGGSETCesCeGtg 27 
                                   G+G+f+++     TC+ C G+g
  gi|13541318|ref|NP_111006.1| 182 GQGFFRMVT--VTTCNTCGGKG 201
                                   566666553..469*******9 PP

  == domain 4  score: 6.0 bits;  conditional E-value: 0.012
                       DUF5351  18 ETCesCeGtgk 28 
                                   E C+ C+Gtg+
  gi|13541318|ref|NP_111006.1| 206 EKCPRCNGTGT 216
                                   78*******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (365 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       833  (0.046461); expected 358.6 (0.02)
Passed bias filter:                      686  (0.038262); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); 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):              15  [number of targets reported over threshold]
# CPU time: 0.59u 0.26s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 2327.01
//
Query:       gi|13541319|ref|NP_111007.1|  [L=615]
Description: molecular chaperone DnaK [Thermoplasma volcanium GSS1]
Scores for complete 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-213  708.5  15.6   3.1e-193  643.3  13.4    2.0  2  HSP70          Hsp70 protein
    7.8e-19   67.7   2.6    4.1e-18   65.3   2.6    2.2  1  MreB_Mbl       MreB/Mbl protein
    1.1e-05   25.8   5.7       0.19   12.2   0.0    4.4  4  FtsA           Cell division protein FtsA
     0.0081   15.4   0.1     0.0081   15.4   0.1    2.2  2  StbA           StbA protein
     0.0093   15.6  12.3       0.02   14.5  12.3    1.5  1  DUF4795        Domain of unknown function (DUF4795)
  ------ inclusion threshold ------
        0.3   11.3   6.5       0.66   10.2   6.5    1.6  1  SesA           N-terminal domain on NACHT_NTPase and P-loop N
       0.52   10.1   6.5      0.075   12.8   1.9    2.0  2  TRAF_BIRC3_bd  TNF receptor-associated factor BIRC3 binding d
       0.93    8.9   6.6        1.6    8.1   6.6    1.4  1  Allexi_40kDa   Allexivirus 40kDa protein
        2.5    8.3   6.2        2.8    8.2   0.5    2.4  2  SMBP           Small metal-binding protein
        3.4    7.3   0.0        3.4    7.3   0.0    3.5  4  Raco_middle    RACo middle region
        5.3    5.8   4.6        8.1    5.2   4.6    1.3  1  LMBR1          LMBR1-like membrane protein


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 !   67.7   0.0   3.6e-22   5.8e-19       1      80 [.       6      90 ..       6      91 .. 0.91
   2 !  643.3  13.4  1.9e-196  3.1e-193     102     599 .]      86     583 ..      83     583 .. 0.99

  Alignments for each domain:
  == domain 1  score: 67.7 bits;  conditional E-value: 3.6e-22
                                  EEEEEEXSSEEEEEEEETTEEEEEXXTTS....XSSEESEEEEXTT.SEEETHHHHHCTTTTGGGEEEXGGGTTTXBTTSHHH CS
                         HSP70  1 viGiDLGttnsvvavmeggkievianeeg....nrttPsvvaFtkk.erlvGeaAkrqavtnpkntvfsvKrliGrkfsdpev 78
                                  +iGiDLGt ns+ av+ +gk++vi  +eg     ++ Ps+vaFtk+ + lvGe+A+rqa  np+ t+f++Kr +G++++ +++
  gi|13541319|ref|NP_111007.1|  6 IIGIDLGTSNSAAAVVISGKPTVIPSSEGvsigGKAFPSYVAFTKDgQMLVGEPARRQALLNPEGTIFAAKRKMGTDYKFKVF 88
                                  69************************99722226899*********99******************************98776 PP

                                  HH CS
                         HSP70 79 qk 80
                                  +k
  gi|13541319|ref|NP_111007.1| 89 DK 90
                                  65 PP

  == domain 2  score: 643.3 bits;  conditional E-value: 1.9e-196
                                   EETTEEEEHHHHHHHHHHHHHHHHHHHHTSBEEEEEEEEXTTXXHHHHHHHHHHHHHTTXEEEEEEEHHHHHHHHHHTCCS CS
                         HSP70 102 eaagekftpeqisamvLkklketaeaylgkkvtdavitvPaYfndaqRqatkdAgkiAGLnvlRivNepTAaalaYGldkk 182
                                   ++ +++ftp+qisa++L+k+k++aea+lg++v++avitvPaYfnd+qRqatkdAg+iAG++v Ri+NepTAaalaYG+dk+
  gi|13541319|ref|NP_111007.1|  86 KVFDKEFTPQQISAFILQKIKKDAEAFLGEPVNEAVITVPAYFNDNQRQATKDAGTIAGFDVKRIINEPTAAALAYGVDKS 166
                                   56789**************************************************************************** PP

                                   SSCEEEEEEEEXSSXEEEEEEEEE.TTEEEEEEEEEETTXSHHHHHHHHHHHHHHHHHHHHSXXGGGSHHHHHHHHHHHHH CS
                         HSP70 183 dkernvlvyDlGggtfdvSilele.kGvfevkaTagDthlGGedfDealvehlveefkkkegidlskdkkalqrlkeaaek 262
                                    k++++lv+DlGggt dv i+e++ +  ++v++T+gDt+lGG d+Dea+v++++++f+kkegidl+kd+ a+ rl++aaek
  gi|13541319|ref|NP_111007.1| 167 GKSEKILVFDLGGGTLDVTIIEISkRPNVQVLSTSGDTQLGGTDMDEAIVNYIADDFQKKEGIDLRKDRGAYIRLRDAAEK 247
                                   ***********************83569***************************************************** PP

                                   HHHHTTTSSCSEEEEEEEEEETTT.EEEEEEEEHHHHHHHHHHHHHHTHHHHHHHHHHCTEEGGGCSEEEEESGGGGSHHH CS
                         HSP70 263 aKkeLSsskqteinleietvdedg.kdlseklsRakfeelvedllertlepvekalkdaklkkeeidevvlvGGstRiPkv 342
                                   aK+eLS++ +++i+l+++tv+++g k+++++l+Rak+eel+++++er++ p+ kal+ aklkk +i +++ vGG tRiP v
  gi|13541319|ref|NP_111007.1| 248 AKIELSTTLSSDIDLPYITVTSSGpKHIKMTLTRAKLEELISPIVERVKAPIDKALEGAKLKKTDITKLLFVGGPTRIPYV 328
                                   ********************************************************************************* PP

                                   HHHHHHHTTCHHBSSSHTTTHHHHHHHHHHHHHCTCGCSHCCEEEEBESS-EEEEETTTEEEEEESTTCBSSEEEEEEEEE CS
                         HSP70 343 qelvkelfgkepsktvnpDeavaiGAAvqagvlsgeeevkdllllDvtpLslgietlggvmtkliernttiptkksqvfst 423
                                   ++ v++++g +++ +v+p eavaiGAA+q++vl+g  e+kd++llDvtpL+l++etlgg++t +i+ nttip +ksqvf+t
  gi|13541319|ref|NP_111007.1| 329 RKYVEDYLGIKAEGGVDPMEAVAIGAAIQGAVLKG--EIKDIVLLDVTPLTLSVETLGGIATPIIPANTTIPVRKSQVFTT 407
                                   ***********************************..******************************************** PP

                                   SSTTSSSEEEEEEESSSSBGGGSEEEEEEEEECESSCSTTCSEEEEEEEEETTSCEEEEEEETTTCCEEEEEEECCSSSBH CS
                         HSP70 424 aadnqtaveievlqgerelvkdnkllgsfeldgippaprGvpqieVtfdidanGiltvsakdketgkeeeitieaseglse 504
                                   a+d qt+v+i+v+qger l+kdn +lg f+l+gi paprG pqieVtfdid nGil+v+a dk+tgk++ iti+as++ls+
  gi|13541319|ref|NP_111007.1| 408 AEDMQTTVTIHVVQGERPLAKDNVSLGMFNLTGIAPAPRGIPQIEVTFDIDSNGILNVTAVDKATGKKQGITITASTKLSK 488
                                   ********************************************************************************* PP

                                   HHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGGGSTHHHHHHHHHHHHHHHCHTTSSCHHHHHHHHHH CS
                         HSP70 505 eeiekmvkdaeesaeedkkkkeaieakneaeelvyslekkleeeaekvseaekekvesaieeLkeeleeeekeeieaktee 585
                                   +eie+m k+ae++ae+d+k ke+ie+ n+ae+l+ys+ek+l+e+++kv++++k+++ s++++L++++ee++ +++++ +e+
  gi|13541319|ref|NP_111007.1| 489 DEIERMKKEAEQYAEQDRKMKEQIETLNNAESLAYSVEKTLNEAGDKVDKETKDRILSEVKDLRKAIEEKNMDNVKTLMEK 569
                                   ********************************************************************************* PP

                                   HHHHHHHHHHHHHH CS
                         HSP70 586 lkkvvekiaeklye 599
                                   ++k ++++++k+y+
  gi|13541319|ref|NP_111007.1| 570 ISKDIQEVGTKMYQ 583
                                   ***********996 PP

>> MreB_Mbl  MreB/Mbl protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.3   2.6   2.5e-21   4.1e-18       2     317 ..       5     356 ..       4     364 .. 0.68

  Alignments for each domain:
  == domain 1  score: 65.3 bits;  conditional E-value: 2.5e-21
                                   SEEEEEE-SSEEE..EEETTTEEEEEEES-EEEETT.........T--EEEESHHHHT.TTTS-GTTEEEE.-SEETTE.. CS
                      MreB_Mbl   2 kdlgiDLGtantl..vyvkgkgivlnepsvvAikkk.........tkkvlavGeeAkk.mlgktpgnikav.rPlkdGv.. 67 
                                   k +giDLGt n    v ++gk  v+     v i  k         +   + vGe A++  l   +g+i a  r +  G+  
  gi|13541319|ref|NP_111007.1|   5 KIIGIDLGTSNSAaaVVISGKPTVIPSSEGVSIGGKafpsyvaftKDGQMLVGEPARRqALLNPEGTIFAAkRKM--GTdy 83 
                                   5699*****997522678888888866555555554433333332333445677775413444455554431445..3322 PP

                                   ...ESSHHHHHHHHHHHH.HHHHT.SS-S...S--EEEEEE-SS--HHHHHHHHHHHHHTT-SEEEEEEHHHHHHHHTT-- CS
                      MreB_Mbl  68 ...iadlevaeellkyfi.kkvkk.kksl...skprvvicvPsgiteverrAvkeaakkaGarevllieeplaAAiGaglp 140
                                      + d e + + +  fi +k+kk ++++   + ++ vi+vP   ++ +r+A k+a + aG +   +i+ep aAA+  g++
  gi|13541319|ref|NP_111007.1|  84 kfkVFDKEFTPQQISAFIlQKIKKdAEAFlgePVNEAVITVPAYFNDNQRQATKDAGTIAGFDVKRIINEPTAAALAYGVD 164
                                   3337888999999988762566665333334445689*******************************************9 PP

                                   TT.SSS-EEEEEE-SS-EEEEEEETTE......EEEEEEES-SHHHHHHHHHHHHHHHHSEE--H..HHHHHHHHHH-BSS CS
                      MreB_Mbl 141 ve.epsgnmvvdiGggttevavislgg......ivtsksvrvaGdeldeaiikyirkkynlliGe..rtaekikieigsav 212
                                    + +++  +v d+Gggt +v++i ++       + ts   +++G ++deai++yi  +++   G   r+ +   i++  a+
  gi|13541319|ref|NP_111007.1| 165 KSgKSEKILVFDLGGGTLDVTIIEISKrpnvqvLSTSGDTQLGGTDMDEAIVNYIADDFQKKEGIdlRKDRGAYIRLRDAA 245
                                   87255667899***********97754222211345556899999**********99998765541144444445554444 PP

                                   --HHHH.......EEEEEEEETTTTCEEEEE..EEHHHHHHHHHHHHHHHHHHHHHHHHTS-HHHHHHHHHH-EEEESGGG CS
                      MreB_Mbl 213 keeeee.......kmeikGrdlvtglpkeve..vsseevrealkepvsaiveavkevLektppeLaadivdrgivltGGga 284
                                   ++++ e        +++    +++  pk+++  ++ ++++e ++  v+++   + ++Le ++    +di++  ++++GG +
  gi|13541319|ref|NP_111007.1| 246 EKAKIElsttlssDIDLPYITVTSSGPKHIKmtLTRAKLEELISPIVERVKAPIDKALEGAKLK-KTDITK--LLFVGGPT 323
                                   4444433233322344445566777788665115667777788888888888888888865543.467764..6778**** PP

                                   GSBTHHHHHHHHHSS-EEE-SSTTTHHHHHHHH CS
                      MreB_Mbl 285 llkgldkllseetglpvkvaedpltcvakGtgk 317
                                    +  ++k++++ +g++ + + dp+++va G+++
  gi|13541319|ref|NP_111007.1| 324 RIPYVRKYVEDYLGIKAEGGVDPMEAVAIGAAI 356
                                   ******************************975 PP

>> FtsA  Cell division protein FtsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.1     0.072   1.2e+02       1      30 [.       7      39 ..       7      47 .. 0.76
   2 ?   -1.0   0.0       1.5   2.4e+03      31      48 ..     103     120 ..      96     124 .. 0.91
   3 !   12.2   0.0   0.00012      0.19       2      86 ..     174     336 ..     173     355 .. 0.70
   4 !    9.5   0.4   0.00078       1.3      36     101 ..     471     585 ..     430     600 .. 0.73

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.072
                                  EEEEE-SSSEEEEEEETTEEEE...EEEES--H CS
                                  xxxxxxxxxxxxxxxxxxxxxx...xxxxxxxx RF
                          FtsA  1 alvDiGagktdvavaedgalvh...lrvigvgg 30
                                  +++D+G++ + +av+  g+++    ++ + +gg
  gi|13541319|ref|NP_111007.1|  7 IGIDLGTSNSAAAVVISGKPTVipsSEGVSIGG 39
                                  58*************999876544455555555 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.5
                                   HHHHHHHHHHHT--HHHH CS
                                   xxxxxxxxxxxxxxxxxx RF
                          FtsA  31 ngitkdiakalrtaveeA 48 
                                   + i+kd++  l+++v+eA
  gi|13541319|ref|NP_111007.1| 103 QKIKKDAEAFLGEPVNEA 120
                                   579*************99 PP

  == domain 3  score: 12.2 bits;  conditional E-value: 0.00012
                                   EEEE-SSSEEEEEEETTEEEEEEEES-......-HHHHHHHHHHHHT--HHHHHHHHH..HH--S--.............. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxx.............. RF
                          FtsA   2 lvDiGagktdvavaedgalvhlrvigv......ggngitkdiakalrtaveeAeriki..kyGsala.............. 60 
                                   + D+G+g+ dv+++e ++  +++v+ +      gg  +++ i++ +   +++ e i    + G+ ++              
  gi|13541319|ref|NP_111007.1| 174 VFDLGGGTLDVTIIEISKRPNVQVLSTsgdtqlGGTDMDEAIVNYIADDFQKKEGIDLrkDRGAYIRlrdaaekakielst 254
                                   56****************999******9999*****************999999998422455555576665555444433 PP

                                   .EEEEEHHHHH...............................................................GGGGSTT CS
                                   .xxxxxxxxxx...............................................................xxxxxxx RF
                          FtsA  61 .ekeigrkels...............................................................ggsalpn 77 
                                             s                                                               g + +p 
  gi|13541319|ref|NP_111007.1| 255 tL--------SsdidlpyitvtssgpkhikmtltrakleelispivervkapidkalegaklkktditkllfvgGPTRIPY 327
                                   30........14444555555566666666666566666777777777777777777777777777778888877777888 PP

                                   HHHHHHHHH CS
                                   xxxxxxxxx RF
                          FtsA  78 leelaeral 86 
                                   +++++e+ l
  gi|13541319|ref|NP_111007.1| 328 VRKYVEDYL 336
                                   877777776 PP

  == domain 4  score: 9.5 bits;  conditional E-value: 0.00078
                                   H........HHHHHT--HHHHHHHHHHH--S--..EEEEEHHHHH.................................... CS
                                   x........xxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxx.................................... RF
                          FtsA  36 d........iakalrtaveeAerikikyGsala..ekeigrkels.................................... 70 
                                            i  + + + +e er+k+  + ++a  +++++ ++++                                    
  gi|13541319|ref|NP_111007.1| 471 AtgkkqgitITASTKLSKDEIERMKK-EAEQYAeqDRKMK-EQIEtlnnaeslaysvektlneagdkvdketkdrilsevk 549
                                   13334446688888999999999994.3333334533333.3344444777888888888888888888999999999999 PP

                                   ......GGGGSTTHHHHHHHHHT-..HHHT-GGGHHH CS
                                   ......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          FtsA  71 ......ggsalpnleelaeralspkleevsdpeyasa 101
                                         ++ ++ n+++l+e++ +   +ev + +y sa
  gi|13541319|ref|NP_111007.1| 550 dlrkaiEEKNMDNVKTLMEKISKD-IQEVGTKMYQSA 585
                                   ********************9633.333555555554 PP

>> StbA  StbA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1     5e-06    0.0081     138     211 ..     146     221 ..     130     256 .. 0.73
   2 ?   -1.5   1.3      0.71   1.2e+03     204     262 ..     524     581 ..     478     592 .. 0.64

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 5e-06
                          StbA 138 tikkvkvlPeslPagfealkeldeleslLiiDlGGttLDvakvr.gk..legiskvkgdskiGvslitdavkealet 211
                                    +k +   P +   ++ ++k+  + e+ L+ DlGG tLDv+ ++ +k    ++  + gd ++G   + +a+ ++++ 
  gi|13541319|ref|NP_111007.1| 146 DVKRIINEPTAAALAYGVDKS-GKSEKILVFDLGGGTLDVTIIEiSKrpNVQVLSTSGDTQLGGTDMDEAIVNYIAD 221
                                   555555445554445555544.6789***************99623312346778899***********99999875 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.71
                          StbA 204 avkealetaktrtssfladeliknrkdeeyLkrri..ndedkresvlevinekvkkLkerv 262
                                   +v+++l++a  ++ + + d+++++ kd   L++ i  ++ d++++++e i++  +++  ++
  gi|13541319|ref|NP_111007.1| 524 SVEKTLNEAGDKVDKETKDRILSEVKD---LRKAIeeKNMDNVKTLMEKISKDIQEVGTKM 581
                                   455566666666666666666665555...3333311344455555555555555555555 PP

>> DUF4795  Domain of unknown function (DUF4795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5  12.3   1.3e-05      0.02      13     103 ..     488     577 ..     463     608 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.3e-05
                       DUF4795  13 qeaieklqeelekleekvkelekrledkekklealkkqieelekvkadkeeveeelaekadkeaLatkvsrdqfDeakkeL 93 
                                   +++ie +++e e+  e+ +++++++e++  + e+l  ++e++ ++ +dk + e++ ++ +  ++L++ ++++++D++k+++
  gi|13541319|ref|NP_111007.1| 488 KDEIERMKKEAEQYAEQDRKMKEQIETL-NNAESLAYSVEKTLNEAGDKVDKETKDRILSEVKDLRKAIEEKNMDNVKTLM 567
                                   3678888888888888888888888765.46788888888888888999999***************************** PP

                       DUF4795  94 ekmleellek 103
                                   ek+ +++ e 
  gi|13541319|ref|NP_111007.1| 568 EKISKDIQEV 577
                                   **99777664 PP

>> SesA  N-terminal domain on NACHT_NTPase and P-loop NTPases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   6.5   0.00041      0.66      46     121 ..     495     576 ..     482     577 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00041
                          SesA  46 ksqlesskldedtesaikpvlesckekatkleeifekv....apapad...srleryrkavrslgkgskVEtLmkgiledl 119
                                   k+++e+  +++ + ++  ++l++ ++ a ++e+ +++      ++++d   s+++  rka+ + ++ ++V tLm++i +d+
  gi|13541319|ref|NP_111007.1| 495 KKEAEQYAEQDRKMKEQIETLNNAESLAYSVEKTLNEAgdkvDKETKDrilSEVKDLRKAIEE-KNMDNVKTLMEKISKDI 574
                                   555555555555555577788888888888888888887766444444688999999999988.***************** PP

                          SesA 120 ql 121
                                   q+
  gi|13541319|ref|NP_111007.1| 575 QE 576
                                   97 PP

>> TRAF_BIRC3_bd  TNF receptor-associated factor BIRC3 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   1.9   4.6e-05     0.075      26      53 ..     490     517 ..     484     522 .. 0.93
   2 ?   -3.0   0.2       3.9   6.4e+03      43      56 ..     558     571 ..     542     573 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.6e-05
                 TRAF_BIRC3_bd  26 EverssttieaverqrrldqekieaLek 53 
                                   E+er++ ++e++++q r+ +e ie+L++
  gi|13541319|ref|NP_111007.1| 490 EIERMKKEAEQYAEQDRKMKEQIETLNN 517
                                   9*************************97 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 3.9
                 TRAF_BIRC3_bd  43 ldqekieaLekKvr 56 
                                   ++ + +++L +K+ 
  gi|13541319|ref|NP_111007.1| 558 KNMDNVKTLMEKIS 571
                                   45577888888875 PP

>> Allexi_40kDa  Allexivirus 40kDa protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   6.6     0.001       1.6      62     159 ..     509     606 ..     487     613 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.001
                  Allexi_40kDa  62 dsiinklnpvslls..qttlLselrdalrtltklldklksvekklelsaetasdskllkklesietsleelhakldelsss 140
                                    + i++ln+ ++l+   +++L+e  d++ +  ++ d++ s  k l++ +e+++  ++ + +e i ++++e+++k+ + +ss
  gi|13541319|ref|NP_111007.1| 509 KEQIETLNNAESLAysVEKTLNEAGDKVDK--ETKDRILSEVKDLRKAIEEKNMDNVKTLMEKISKDIQEVGTKMYQSASS 587
                                   556889999988763367788888888875..56688999999999999998888888999**************999999 PP

                  Allexi_40kDa 141 etsesegPsssptkassae 159
                                   +t++ +g ++s+++++ + 
  gi|13541319|ref|NP_111007.1| 588 TTQTGSGNQNSSKQENDKT 606
                                   9999999888888776654 PP

>> SMBP  Small metal-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   1.2      0.11   1.9e+02      58      86 ..     492     519 ..     466     524 .. 0.69
   2 ?    8.2   0.5    0.0017       2.8      55      99 ..     527     568 ..     517     578 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.11
                                   HHHHHH...-------HHHHHHHHHHHHH CS
                          SMBP  58 khakaaaekakeeekehldegikhLeeAI 86 
                                   +  k+ ++++ +e++++++e i+ L++A 
  gi|13541319|ref|NP_111007.1| 492 ERMKK-EAEQYAEQDRKMKEQIETLNNAE 519
                                   33344.4789999*************996 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0017
                                   HHHHHHHHH...-------HHHHHHHHHHHHHHHHHCT-HHHHHH CS
                          SMBP  55 ealkhakaaaekakeeekehldegikhLeeAIkhgkaghadvAtk 99 
                                   +    +++a +k ++e k+++   +k L++AI++ ++++ +   +
  gi|13541319|ref|NP_111007.1| 527 K---TLNEAGDKVDKETKDRILSEVKDLRKAIEEKNMDNVKTLME 568
                                   3...345555669999999*******************9986555 PP

>> Raco_middle  RACo middle region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.2      0.87   1.4e+03       4      31 ..     174     201 ..     173     217 .. 0.83
   2 ?    7.3   0.0    0.0021       3.4      47      93 ..     277     322 ..     273     335 .. 0.89
   3 ?   -1.9   0.1       1.5   2.4e+03      34      67 ..     483     516 ..     455     532 .. 0.65
   4 ?    0.3   0.2       0.3     5e+02      46      80 ..     554     588 ..     547     593 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.87
                   Raco_middle   4 avDiGtTtvvaaLvdletgkelaeasal 31 
                                    +D+G  t+ +++++++++  +++ s+ 
  gi|13541319|ref|NP_111007.1| 174 VFDLGGGTLDVTIIEISKRPNVQVLSTS 201
                                   79**************999998887765 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0021
                   Raco_middle  47 yakeeeegleklqkavveeinelieelleeagiekeeiyevvvagNt 93 
                                   ++ + + +le+l + +ve ++  i+++le a+++k++i+++ ++g  
  gi|13541319|ref|NP_111007.1| 277 MTLT-RAKLEELISPIVERVKAPIDKALEGAKLKKTDITKLLFVGGP 322
                                   5555.7899********************************999965 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 1.5
                   Raco_middle  34 QikyGeDvlsRiayakeeeegleklqkavveein 67 
                                    +k+ +D + R++ ++e+  + ++  k+ +e++n
  gi|13541319|ref|NP_111007.1| 483 STKLSKDEIERMKKEAEQYAEQDRKMKEQIETLN 516
                                   4556666677776666644444444444444554 PP

  == domain 4  score: 0.3 bits;  conditional E-value: 0.3
                   Raco_middle  46 ayakeeeegleklqkavveeinelieelleeagie 80 
                                   a+++++ +++++l +++ ++i+e+ +++ ++a+ +
  gi|13541319|ref|NP_111007.1| 554 AIEEKNMDNVKTLMEKISKDIQEVGTKMYQSASST 588
                                   55677889999999999999999999998887655 PP

>> LMBR1  LMBR1-like membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   4.6     0.005       8.1     199     265 ..     488     591 ..     440     614 .. 0.63

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.005
                         LMBR1 199 deelkklyfeaaklntekeeae.............................reledllkevkklrksisesdplrkyleei 250
                                   ++e+++++ ea++  +++ +++                             +  + +l+evk lrk i+e++   ++++++
  gi|13541319|ref|NP_111007.1| 488 KDEIERMKKEAEQYAEQDRKMKeqietlnnaeslaysvektlneagdkvdkETKDRILSEVKDLRKAIEEKN--MDNVKTL 566
                                   455555555555555555444444555555555555555555555555555555578888888888888877..6888888 PP

                         LMBR1 251 lkkvPeeiaeklks..........n 265
                                   ++k+ ++i+e   +          +
  gi|13541319|ref|NP_111007.1| 567 MEKISKDIQEVGTKmyqsassttqT 591
                                   8888887777644444333333221 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (615 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2359  (0.131575); expected 358.6 (0.02)
Passed bias filter:                      724  (0.0403815); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); 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 0.33s 00:00:01.12 Elapsed: 00:00:00.49
# Mc/sec: 3786.04
//
Query:       gi|13541320|ref|NP_111008.1|  [L=176]
Description: molecular chaperone GrpE (heat shock protein) [Thermoplasma volcanium GSS1]
Scores for complete sequence (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  119.6   4.4    1.9e-34  118.7   4.4    1.4  1  GrpE      GrpE
  ------ inclusion threshold ------
      0.077   13.0   4.4       0.11   12.4   4.4    1.2  1  Stathmin  Stathmin family


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 !  118.7   4.4   2.1e-38   1.9e-34       8     166 .]      26     175 ..      15     175 .. 0.86

  Alignments for each domain:
  == domain 1  score: 118.7 bits;  conditional E-value: 2.1e-38
                                   TTTHHHHCCCCCC.TTCHHHCTTSCCCCCCTTTTTTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC..HHH- CS
                          GrpE   8 eeeedeeeeleee.leelekevkelkekllrllaefenlrkrtekekeeakkfaiekfakdLLpvlDnleralksakenee 87 
                                    ++++ee+ l +   e+  ++++e++e+++++la++en+ k  ++e e ++k a+e+++kd+Lpv+D+++ a+++     +
  gi|13541320|ref|NP_111008.1|  26 LKKRAEEAILYRSiAEQSSRKLAEISEAYKHKLADMENYLKIKDRETEIIRKNANESLIKDFLPVIDSMDAAIQAE----K 102
                                   34444444444442445677*****************************************************974....3 PP

                                   HHHHHHHHHHHHHHHHHHHHHTT-EE---TTSB--TTTEEEEEEECSSC...TBEEEEEE--EEETTEEEE-EEEEEEE CS
                          GrpE  88 ekslleGvemtlkqllkiLekhgvekiepkgepFDpnlheavstveddekeegtvvevvqkGYklkdrvlRpAmVkVsk 166
                                    ++l+     +++q+l+iL+k+g+++i+++ge+FDp lhea+ +++d e  +g++  +vq+GY+l+++vlR+++V+V+k
  gi|13541320|ref|NP_111008.1| 103 DNNLI----RIRDQMLSILSKYGLQPIKAEGEKFDPYLHEAIGMTQDGE--DGKIKYEVQRGYTLNNSVLRTSKVIVVK 175
                                   34333....49*************************************9..**************************97 PP

>> Stathmin  Stathmin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   4.4   1.3e-05      0.11      77     135 ..      23      81 ..      11      82 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.3e-05
                      Stathmin  77 evlqKaaeennnfskaaeeklkqkmeaskenreaqlaalkekLkekekhveevrknkeq 135
                                     + K+  e++  ++   e+ ++k+ ++ e  + +la++++ Lk k+++ e +rkn ++
  gi|13541320|ref|NP_111008.1|  23 TRNLKKRAEEAILYRSIAEQSSRKLAEISEAYKHKLADMENYLKIKDRETEIIRKNANE 81 
                                   456789999999999****************************************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1010  (0.0563333); 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:                         2  (0.000111551); expected 0.2 (1e-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: 1025.38
//
Query:       gi|13541321|ref|NP_111009.1|  [L=410]
Description: multidrug efflux permease [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-35  122.5  42.6    1.8e-35  122.5  42.6    1.9  2  MFS_1     Major Facilitator Superfamily
    6.5e-09   34.7   6.8      8e-09   34.4   4.2    1.9  2  MFS_3     Transmembrane secretion effector
  ------ inclusion threshold ------
       0.22   12.0   0.2       0.22   12.0   0.2    2.7  3  DUF4231   Protein of unknown function (DUF4231)


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 !  122.5  42.6   3.1e-39   1.8e-35       3     352 ..      19     356 ..      17     357 .. 0.88
   2 ?   -0.5   2.7     0.078   4.6e+02     261     297 ..     357     393 ..     354     406 .. 0.52

  Alignments for each domain:
  == domain 1  score: 122.5 bits;  conditional E-value: 3.1e-39
                         MFS_1   3 laaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfa. 82 
                                   l+ ++ a +r   +++lpl+  e + is    gl+l+  a+++a+ ++  Gr++dr+Grr +l++  +  a++ ++l+f+ 
  gi|13541321|ref|NP_111009.1|  19 LSRLIRASGRVSSFIFLPLIFIEIYSISFLITGLILGSSAIAMAFVQYYSGRWTDRIGRRFFLIVIPIPAAVF-YFLMFTt 98 
                                   5556666777778889999888***************************************************.7777743 PP

                         MFS_1  83 ...sslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilai 159
                                      + +  ll++++  + ++ ++ +pa+ a +ad+++ +er +++ l+ ++++lGa++gpl+gg+la  ++++++f+++ i
  gi|13541321|ref|NP_111009.1|  99 vylHMSViLLIIFWYGTIITNSLQYPAIEASVADVTSTSERLSGYTLIRIMANLGAAVGPLAGGFLA-GINFSYIFLLASI 178
                                   566666768999999999999**********************************************.888********** PP

                         MFS_1 160 vsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsglltllplylqevlgl 240
                                   ++++   lf+l++ ++++  +  + +e+         ++ +k++++d+++  +l++l+++f   ++l +  p++++  ++l
  gi|13541321|ref|NP_111009.1| 179 FTVIE--LFILYYNVRETFLPARAIAEK---------IK-LKIFKTDRFF--FLFTLVGVF-LGFTLRQNGPTLTVYAFDL 244
                                   *****..888***999999999988888.........77.999*****88..888888887.4445666666655555555 PP

                         MFS_1 241 s..glllaglllallalvgailallagrls.drlgrrrrlllallllllaalglallavtssavllllvlvliGfglgfvf 318
                                   +   l+ +g+l++l ++v+++l++ + rl+  r    ++ ++ +++++  ++g+++l+ + + + +ll+++++++g  f++
  gi|13541321|ref|NP_111009.1| 245 KnlPLMDIGYLYSLNGIVVIALQMPILRLMsSR---SNPVFWRGIGTIYYSIGFVILGIAPTFLYILLAMFIFTVGEDFMS 322
                                   5666******************55555555266...66999999999999999999999988899999************* PP

                         MFS_1 319 psllalasdlappeeagtasglfntagslggalg 352
                                   p+ +++++ lap+e+ g+++g +n++ s+g+++g
  gi|13541321|ref|NP_111009.1| 323 PTTQTIITTLAPAEKKGSYIGSYNLLTSFGRFFG 356
                                   ********************************99 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.078
                         MFS_1 261 allagrlsdrlgrrrrlllallllllaalglallavt 297
                                    +++ +++  +++ +++++++++++++++gl+++ ++
  gi|13541321|ref|NP_111009.1| 357 TIFGLYFLFIYQKTTFTFWIIIATSTGVIGLLYIFMS 393
                                   3333333344444555555555555555555555554 PP

>> MFS_3  Transmembrane secretion effector
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.4   4.2   1.3e-12     8e-09      43     205 ..      46     207 ..      39     224 .. 0.78
   2 ?    0.5   0.0     0.026   1.6e+02     104     136 ..     305     337 ..     286     380 .. 0.78

  Alignments for each domain:
  == domain 1  score: 34.4 bits;  conditional E-value: 1.3e-12
                         MFS_3  43 splmvAlvqaaatLPifllsilaGalaDnfdrRkvllavqlllalvsvlltvlaalgllspwlllaltlligiGaalndPa 123
                                   s l   l+  ++++ + ++   +G  +D + rR +l+++  + a+v  +l+ ++++  +s++ll+++ + + i  +l+ Pa
  gi|13541321|ref|NP_111009.1|  46 SFLITGLILGSSAIAMAFVQYYSGRWTDRIGRRFFLIVIP-IPAAVFYFLMFTTVYLHMSVILLIIFWYGTIITNSLQYPA 125
                                   5566678999999******************998888776.567788899999999999********************** PP

                         MFS_3 124 WqAsvgelvkrrdvpaAvaLnsvginiaRsvGPAlgGvlvaavGaalafavnalsylalival.lrwkrevrksslprEkl 203
                                    +Asv ++ + ++  +  +L  +  n+  +vGP  gG l a +   + f ++++  ++ +++l  +++ +  + +  +Ek+
  gi|13541321|ref|NP_111009.1| 126 IEASVADVTSTSERLSGYTLIRIMANLGAAVGPLAGGFL-AGINFSYIFLLASIFTVIELFILyYNVRETFLPARAIAEKI 205
                                   *********************************999976.44455555555554444444444134455555555556665 PP

                         MFS_3 204 le 205
                                     
  gi|13541321|ref|NP_111009.1| 206 KL 207
                                   55 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.026
                         MFS_3 104 wlllaltlligiGaalndPaWqAsvgelvkrrd 136
                                     +l   ++  +G  +++P+ q ++  l ++++
  gi|13541321|ref|NP_111009.1| 305 LYILLAMFIFTVGEDFMSPTTQTIITTLAPAEK 337
                                   3466678999**************998887765 PP

>> DUF4231  Protein of unknown function (DUF4231)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.2   3.6e-05      0.22      16      86 ..     142     208 ..     129     212 .. 0.77
   2 ?   -1.7   0.2      0.68   4.1e+03      26      60 ..     263     297 ..     254     334 .. 0.57
   3 ?   -3.0   0.1       1.7     1e+04      41      53 ..     370     382 ..     336     396 .. 0.51

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.6e-05
                       DUF4231  16 rfrllrlitivlgallpilvssklgagvsvlkiltallsalvailaaleeffrykerWrryRstaEsLkte 86 
                                    + l+r+++ +++a+ p++      ag ++    ++ll+++ ++++ ++  ++++e++  +R++aE +k  
  gi|13541321|ref|NP_111009.1| 142 GYTLIRIMANLGAAVGPLAGG--FLAGINFS--YIFLLASIFTVIELFILYYNVRETFLPARAIAEKIKLK 208
                                   566677777777777777777..33334433..457889999999***********************975 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.68
                       DUF4231  26 vlgallpilvssklgagvsvlkiltallsalvail 60 
                                   v++   pil  + ++++  ++  + ++ +++  ++
  gi|13541321|ref|NP_111009.1| 263 VIALQMPILRLMSSRSNPVFWRGIGTIYYSIGFVI 297
                                   45555555555333333333333333333332222 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 1.7
                       DUF4231  41 agvsvlkiltall 53 
                                   + ++++ i+++  
  gi|13541321|ref|NP_111009.1| 370 TTFTFWIIIATST 382
                                   3333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (410 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       951  (0.0530426); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.68u 0.31s 00:00:00.99 Elapsed: 00:00:00.51
# Mc/sec: 2436.99
//
Query:       gi|13541322|ref|NP_111010.1|  [L=148]
Description: phospholipid-binding protein [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.2e-30  104.8   0.0      5e-30  104.5   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 !  104.5   0.0   2.8e-34     5e-30       2     132 .]      14     144 ..      13     144 .. 0.90

  Alignments for each domain:
  == domain 1  score: 104.5 bits;  conditional E-value: 2.8e-34
                                   --GGG..CSBGGS-EEEEES--TTSSEEEEEEEETTSCCTCTTEEEEEEEEEETTSSEE-TTC......EE-B-TTSSCCC CS
                           PBP   2 lpkky..egentsPplswsdvpegtksyalvviDpDapkvsetflHwvvtnipasvtslpega......vqgknslgeese 74 
                                   +p+k+  +ge+  P ls++dvp+++k +alvv DpDap  +  f+H ++++ip s+ ++ +          g n++ge   
  gi|13541322|ref|NP_111010.1|  14 IPTKFtcDGEDEMPVLSVTDVPKEAKCLALVVDDPDAP-SGL-FTHCIIYDIPLSKMEIDSSIlnekgvKAGINDFGE--- 89 
                                   7899888999999*************************.333.**********999999874456677799*******... PP

                                   CS---B--STTS..EEEEEEEEEESSSG--BGSS-SHHHHHHHHCTTEEEEEEEEEEE CS
                           PBP  75 sgYlgpcPpkgdgkHrYvfllyaldvealdlkagftraelgaaiaghvlakatlagnY 132
                                   +gY+gpcPp+g+ +HrY+f++yal++e +  + g +r+e++++i++h+++k +++g+Y
  gi|13541322|ref|NP_111010.1|  90 KGYRGPCPPPGK-PHRYYFTVYALNTEIK--EDGLKRREFDKEIKNHIIEKVSYMGTY 144
                                   ************.7***********9953..466999*******************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       389  (0.0216967); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); 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: 00:00:00.44
# Mc/sec: 1002.80
//
Query:       gi|13541323|ref|NP_111011.1|  [L=439]
Description: membrane-bound serine protease [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.6e-18   64.9   1.3    2.8e-17   62.8   1.3    2.1  1  NfeD           NfeD-like C-terminal, partner-binding
    4.4e-08   33.2   5.2      8e-08   32.4   5.2    1.4  1  CLP_protease   Clp protease
     0.0025   16.9   0.3      0.004   16.2   0.3    1.3  1  SDH_sah        Serine dehydrogenase proteinase
       0.01   15.8   0.8      0.019   14.9   0.8    1.5  1  Peptidase_S49  Peptidase family S49
  ------ inclusion threshold ------
      0.017   15.4   9.7      0.017   15.4   9.7    3.4  3  DUF308         Short repeat of unknown function (DUF308)
        0.1   11.9   0.1       0.16   11.2   0.1    1.4  1  ECH_1          Enoyl-CoA hydratase/isomerase


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 !   62.8   1.3   9.5e-21   2.8e-17       3      84 .]     344     427 ..     341     427 .. 0.82

  Alignments for each domain:
  == domain 1  score: 62.8 bits;  conditional E-value: 9.5e-21
                                   XXXXXXXXXXXXXXS---SSS--S..S---GGTTSEEEEEE-B.S-EEEEETTEEEEEE-.SS..B-TT-EEEEEEE-SSS CS
                          NfeD   3 avvsvlllvllrplllkklkkkek.ktnaealiGkegvvledi.gtGrvkvdGeeWsarsege..iekgerVrVveveGlt 79 
                                   ++v+  l + +r++++  +   +   t+ae+liG+ ++++++i + G+v vdG eW+a+s+++  i+kge+V++v+++Gl 
  gi|13541323|ref|NP_111011.1| 344 VIVAGFLAFYIRRIVRTIK--FRGrWTGAESLIGRSAKAVSNInSHGWVSVDGIEWQAKSNDGkpINKGEPVKIVDRSGLV 422
                                   5666666677777666633..233349****************758**************87779**************** PP

                                   EEEEE CS
                          NfeD  80 liVep 84 
                                   liVe+
  gi|13541323|ref|NP_111011.1| 423 LIVER 427
                                   ***97 PP

>> CLP_protease  Clp protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.4   5.2   2.7e-11     8e-08      18     178 ..      37     194 ..      28     197 .. 0.73

  Alignments for each domain:
  == domain 1  score: 32.4 bits;  conditional E-value: 2.7e-11
                                   EEEEES-BSHHHHHHHHHHHHHHHHH-SSS-EEEEEEE--B-HHHHHHHHHHHHHS.SS-EEEEEE....EEEETHHHHHH CS
                  CLP_protease  18 iiflgseiddevankiiaqLllLeaedpdkdillyinspGGsvtaglaIydtmqyi.kpdvsticl....GlaaSmgslll 93 
                                   +i l +eid  +an i+++L  + +++ +  +++y+n+pGG +++++ +  ++  + +  ++ti      G+aaS+gs ++
  gi|13541323|ref|NP_111011.1|  37 VINLDEEIDAGSANMITSTLSSV-SNSTTAAVVIYMNTPGGILENMMQMVSAISSVeNQGIITITYvpvdGMAASAGSYVA 116
                                   68899******************.999999**************************54556666433445*********** PP

                                   HTS-TTGEEEETTEEEEES-TEEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHTS-HHHHHHHHCSTEEEEHHHHHHHTS CS
                  CLP_protease  94 aagekgkRfalpnarimihqPlggaqgqasdieieaeellkikerlneilakhtgqslekiekdldrdtflsaeeAveyGL 174
                                   +a ++   f+ + + i    P   a+   + +e++      +++ ++++ ++h g++   + + ++++t  +  eA + G+
  gi|13541323|ref|NP_111011.1| 117 MACDYI--FMGNGSYIGPSTPIVVAG---TSLEQQH-TTSAMEQYMVSLAEQH-GRNTTAVFSMVSNNTAYTDVEAYKIGI 190
                                   ***998..444444443333433333...4555543.4566777777665555.555555566666677777777888877 PP

                                   SSEE CS
                  CLP_protease 175 idev 178
                                    + +
  gi|13541323|ref|NP_111011.1| 191 SNGI 194
                                   6665 PP

>> SDH_sah  Serine dehydrogenase proteinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.3   1.3e-06     0.004      96     159 ..      69     137 ..      44     162 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.3e-06
                       SDH_sah  96 liihtpGGlvlaatqiakalkehkak.....trvivphyamsGGtlialaadeiildenavlGpvdpql 159
                                   + + tpGG+     q+  a+ + + +     t v v   a s G+ +a+a d i + + + +Gp  p +
  gi|13541323|ref|NP_111011.1|  69 IYMNTPGGILENMMQMVSAISSVENQgiitiTYVPVDGMAASAGSYVAMACDYIFMGNGSYIGPSTPIV 137
                                   5578*************9998766552221123344567889**********************99976 PP

>> Peptidase_S49  Peptidase family S49
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.8   6.5e-06     0.019      10      40 ..     101     131 ..      96     174 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 6.5e-06
                                   EEEEEEEEETHHHHHHTTSSEEEE-TT-EEE CS
                 Peptidase_S49  10 vasaenvaaSggYylasaadkivanpstivg 40 
                                   ++ ++++aaS+g y+a+a+d+i++   + +g
  gi|13541323|ref|NP_111011.1| 101 YVPVDGMAASAGSYVAMACDYIFMGNGSYIG 131
                                   57799*******************9999998 PP

>> DUF308  Short repeat of unknown function (DUF308)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.3      0.49   1.5e+03      20      39 ..       7      26 ..       4      33 .. 0.78
   2 ?    6.2  10.6    0.0044        13       5      40 ..     235     270 ..     234     276 .. 0.92
   3 ?   15.4   9.7   5.9e-06     0.017       1      72 [.     277     351 ..     277     352 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.49
                        DUF308 20 allalvllfGilllvsGivq 39
                                   ll++v+++  lllv Gi++
  gi|13541323|ref|NP_111011.1|  7 LLLIIVIFILSLLLVEGIGN 26
                                  56788888888999999976 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0044
                        DUF308   5 llivlGilalllPvaallalvllfGilllvsGivqi 40 
                                   ++i+lG++a++l+   ++++ +++Gi llv G++++
  gi|13541323|ref|NP_111011.1| 235 IFILLGFVAIMLDIYHGSVVLTVIGIALLVLGFLGL 270
                                   79******************************9987 PP

  == domain 3  score: 15.4 bits;  conditional E-value: 5.9e-06
                        DUF308   1 llGillivlGilalllPvaallalvllfGilllvsGivqii..aafaarkknrggrw.lglllGilyliaGllll 72 
                                   l+G+ll++lG +++ll + ++  ++ll G+++ + G + ++   + ++ +++ + +  ++ll +il +i++ +l 
  gi|13541323|ref|NP_111011.1| 277 LVGVLLLILGSVLILLEAKMGHGFALLSGVVIGLVGTFMLAspYYSSNPGYSPSPFTtFDLLTSILIVIVAGFLA 351
                                   69**************************************84445599999999998999999999999888775 PP

>> ECH_1  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   5.4e-05      0.16      94     122 ..     103     131 ..      78     195 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 5.4e-05
                                   EE-SEEETHHHHHHHHSSEEEEETTTEEE CS
                         ECH_1  94 avnGaaigGGlelalacDiviaadnasfg 122
                                    v G a+ +G  +a+acD++ +++ + +g
  gi|13541323|ref|NP_111011.1| 103 PVDGMAASAGSYVAMACDYIFMGNGSYIG 131
                                   379******************99887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (439 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1007  (0.056166); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); 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):               6  [number of targets reported over threshold]
# CPU time: 0.64u 0.34s 00:00:00.98 Elapsed: 00:00:00.49
# Mc/sec: 2693.96
//
Query:       gi|13541324|ref|NP_111012.1|  [L=113]
Description: hypothetical protein TVN0493 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.4e-31  106.9   0.1    4.3e-31  106.6   0.1    1.1  1  DUF1495   Winged helix DNA-binding domain (DUF1495)


Domain annotation for each model (and alignments):
>> DUF1495  Winged helix DNA-binding domain (DUF1495)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.6   0.1   2.4e-35   4.3e-31       1      82 [.       9      90 ..       9      96 .. 0.97

  Alignments for each domain:
  == domain 1  score: 106.6 bits;  conditional E-value: 2.4e-35
                       DUF1495  1 ilrslnkSkvRkkvllyLysiypeksnlqeisrrvrskpsnvkGaleGmgkrynsessLielGLveeeeeseglklYkltee 82
                                  ilrsln+S++R+kvl+yL+siyp +s+l+eisr+v+s+psnvkG+leG g ry++e+sLi lGLv  e++++g+k++k+++e
  gi|13541324|ref|NP_111012.1|  9 ILRSLNRSELRRKVLFYLLSIYPYRSYLSEISRAVKSDPSNVKGCLEGLGVRYTGEESLIGLGLVIVEQSKNGFKYFKINPE 90
                                  89*****************************************************************************994 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); 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: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 776.04
//
Query:       gi|13541325|ref|NP_111013.1|  [L=655]
Description: ATP-dependent protease Lon [Thermoplasma volcanium GSS1]
Scores for complete 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  108.1   0.0    6.8e-24   84.5   0.0    2.2  2  AAA_32           AAA domain
      7e-30  104.1   7.8    1.2e-29  103.4   7.8    1.3  1  Lon_C            Lon protease (S16) C-terminal proteolytic do
    5.7e-15   55.3   0.0    1.4e-08   34.4   0.0    2.5  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    1.1e-13   51.3   0.0    2.5e-07   30.6   0.0    2.7  2  Sigma54_activat  Sigma-54 interaction domain
    8.3e-11   42.0   0.0    0.00051   20.1   0.0    2.7  2  AAA_5            AAA domain (dynein-related subfamily)
    8.7e-09   35.3   0.6    2.4e-08   33.9   0.6    1.8  1  ChlI             Subunit ChlI of Mg-chelatase
    7.8e-08   31.7   0.1      0.007   15.5   0.0    2.9  3  MCM              MCM P-loop domain
    1.2e-06   28.9   0.0    0.00014   22.1   0.0    2.9  3  AAA_22           AAA domain
    2.7e-06   27.8   0.0       0.11   12.9   0.0    2.7  2  AAA              ATPase family associated with various cellul
    0.00012   22.2   0.0       0.52   10.4   0.0    2.7  2  Sigma54_activ_2  Sigma-54 interaction domain
    0.00019   21.8   0.0      0.057   13.8   0.0    2.8  2  AAA_16           AAA ATPase domain
    0.00021   20.9   0.0     0.0024   17.4   0.0    2.4  2  AAA_7            P-loop containing dynein motor region
    0.00027   20.8   0.0       0.19   11.6   0.0    3.1  3  AAA_3            ATPase family associated with various cellul
    0.00098   19.1   0.0     0.0035   17.3   0.0    1.9  2  NACHT            NACHT domain
     0.0014   18.4   0.0       0.59    9.9   0.0    2.6  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
     0.0014   19.0   0.0       0.18   12.1   0.0    2.8  2  AAA_19           AAA domain
  ------ inclusion threshold ------
      0.014   14.8   1.4       0.14   11.5   0.7    2.2  2  DUF4191          Domain of unknown function (DUF4191)
      0.035   13.8   0.0       0.27   10.9   0.0    2.3  3  AAA_30           AAA domain
      0.053   12.4   0.2       0.17   10.8   0.0    1.9  2  AAA_10           AAA-like domain
      0.059   13.8   0.0       0.37   11.2   0.0    2.2  2  RNA_helicase     RNA helicase
      0.064   12.5   0.0       0.43    9.7   0.0    2.1  2  DUF2075          Uncharacterized conserved protein (DUF2075)
      0.092   12.5   0.0       0.29   10.9   0.0    1.8  1  IstB_IS21        IstB-like ATP binding protein
       0.13   11.9   0.0       0.35   10.4   0.0    1.7  1  AAA_25           AAA domain
       0.15   10.8   0.7       0.31    9.8   0.7    1.4  1  DUF2207          Predicted membrane protein (DUF2207)


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 !   21.3   0.0   1.3e-07   9.9e-05       8      94 ..      31     112 ..      26     125 .. 0.84
   2 !   84.5   0.0   9.2e-27   6.8e-24     281     507 ..     179     404 ..     172     409 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 1.3e-07
                        AAA_32   8 eeiigqeRAvealefglkikkkgYNifvlGesgtGrttlvkrlleeiakkeptpdDwcYvnnfdnpeePkalsLpaGkGke 88 
                                   +++igq++A e ++ +     +  ++ ++Ge+gtG+++l++++++   k  +  +D++   n ++p++Pk+  +paGkGke
  gi|13541325|ref|NP_111013.1|  31 DQVIGQDQAGEIVKKAAL---QRRHVILIGEPGTGKSMLAQSMVDFLPK--SELEDILVFPNPEDPNKPKIKTVPAGKGKE 106
                                   678888888888877654...345899*****************88754..5679*************************9 PP

                        AAA_32  89 lkkdme 94 
                                     ++ +
  gi|13541325|ref|NP_111013.1| 107 IVRQYQ 112
                                   988765 PP

  == domain 2  score: 84.5 bits;  conditional E-value: 9.2e-27
                        AAA_32 281 nvlvdnsetegaPVvvednptyanLfGkieyesemg.alvt.dftlIkaGaLhkAnGGyLildaedlLeeplaWeaLkraL 359
                                   ++lv++s+t++ P v  +  +   L+G + ++  +   l t  +++++aG +hkA+ G+L +d  +lL+ +   +a+  aL
  gi|13541325|ref|NP_111013.1| 179 KLLVSHSSTDKPPFVDSTGAHSGALLGDVRHDPFQSgGLETpAHERVEAGNIHKAHKGVLFIDEINLLRPE-DQQAILTAL 258
                                   79****************************997544355553899**********************9855.5688999** PP

                        AAA_32 360 rskeikiesleeqlglistvsLkPepipldvKViLiGsrelYylLseyDpdfkklFk...vkadFddemerteenekkyar 437
                                   ++k+  i+      + ++    + ep+p+d   +  G+   Y+ + ++ p ++   +    ++  +d m+ ++en kk+++
  gi|13541325|ref|NP_111013.1| 259 QEKKYPISGQ---SERSAGAMVQTEPVPCDFVLVAAGN---YDAIRNMHPALRSRIRgygYEVVVNDYMDDNDENRKKLVQ 333
                                   ********53...34567788999******98777776...7788888888876644333899****************** PP

                        AAA_32 438 fiasivkk.ekllpfdrsavarlieyssrlaedqeklstrfseiadllrEAdywakkegaevveaehVekA 507
                                   fia+ v+k +k+++fd+sa+ ++i+++ + +++++kl++r++e+  l+r A  +a ++++++v+a++V +A
  gi|13541325|ref|NP_111013.1| 334 FIAQEVEKdKKIPHFDKSAIVEIIKEAQKRSGRRNKLTLRLRELGGLVRVAGDIAVSQKRNIVTASDVIAA 404
                                   ***988652789********************************************************988 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 !  103.4   7.8   1.5e-32   1.2e-29      20     204 ..     438     617 ..     415     618 .. 0.82

  Alignments for each domain:
  == domain 1  score: 103.4 bits;  conditional E-value: 1.5e-32
                                   SSSS--BSSEEEEEEEETTEEEEEEEEEEEES....S-S-EEEEES--HHHHHHHHHHHHHHTSS-GGGSS-SS-TTT-EE CS
                         Lon_C  20 eaekedqvGvvtGlawtevGGdlltieavllp....gkgklkltGklgdvmkesaqaalsyvrsraeelgidkevfekkdi 96 
                                    ++    vG+ tG+a  e+ G +l i a ++p    g g+++ tGklgd+ ke++    ++++ + +      +  +++di
  gi|13541325|ref|NP_111013.1| 438 MVNGLAVVGADTGMA--EYTGVVLPIVAEVTPaehkGAGNIIATGKLGDIAKEAVLNVSAVFK-KIT-----GKDISNMDI 510
                                   344445667777766..6778999988776653344889**************8865444443.333.....3335689** PP

                                   EEEE-S-B-GGGGGGGHHHHHHHHHHHHTS--B-TTBEE--EE-TT-BEE--S-HHHHHHHHHHTT-SBEEEEGGGGGGTT CS
                         Lon_C  97 hihvPeGavPkdGPsaGvtlatalvslltgkkvrkdvamtGeitLrGrvlpiGGlkekllaakragikkvilPkenekdle 177
                                   hi +       +G sa v++ata++s++ +++v++ vamtG +++rG vlp+GG+  k+ aa  ag+ kvi+P+ n +d+ 
  gi|13541325|ref|NP_111013.1| 511 HIQFVGTYEGVEGDSASVSIATAVISAIENIPVDQSVAMTGSLSVRGDVLPVGGVTAKVEAAIEAGMAKVIVPELNYNDII 591
                                   ****9999999********************************************************************98 PP

                                   TS-HHHHTS-B--EESBHHHHHHHHB- CS
                         Lon_C 178 diPeevreeleiilveevdevlkaalv 204
                                    +  e  + ++ii+++++++vlk+alv
  gi|13541325|ref|NP_111013.1| 592 -LDAEHINRIQIIPARTIEDVLKVALV 617
                                   .55566689****************97 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.4   0.0   1.9e-11   1.4e-08       2      55 ..      30      83 ..      29      87 .. 0.94
   2 !   18.2   0.0   1.7e-06    0.0013      96     157 ..     224     293 ..     215     304 .. 0.71

  Alignments for each domain:
  == domain 1  score: 34.4 bits;  conditional E-value: 1.9e-11
                  Mg_chelatase  2 lkdvkGqeeakraleiaaaGgHnlllvGppGsGKtmlakrlpsllpplseeeal 55
                                  + +v+Gq++a + ++ aa  + +++l+G pG+GK+mla+ +   lp+ + e++l
  gi|13541325|ref|NP_111013.1| 30 FDQVIGQDQAGEIVKKAALQRRHVILIGEPGTGKSMLAQSMVDFLPKSELEDIL 83
                                  679*******************************************99888765 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 1.7e-06
                  Mg_chelatase  96 kpkpGeislahnGvLfLDElpefkrkvlevLRePledgevtis....rak....akvefparfqlvaamN 157
                                   +++ G+i +ah+GvLf+DE+  ++ +  +++ + l++++  is    r++    ++   p++f lvaa N
  gi|13541325|ref|NP_111013.1| 224 RVEAGNIHKAHKGVLFIDEINLLRPEDQQAILTALQEKKYPISgqseRSAgamvQTEPVPCDFVLVAAGN 293
                                   6789****************88888877777777777777776222222211112234688888888877 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   2.9e-06    0.0022      11      46 ..      39      74 ..      33      85 .. 0.85
   2 !   30.6   0.0   3.3e-10   2.5e-07      80     129 ..     220     270 ..     174     302 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2.9e-06
                                  HHHHHHHHCTSSS-EEEECSTTSSHHHHHHHHHHHS CS
               Sigma54_activat 11 lleqikkvaktdlsvlitGesGtGKellaraiheas 46
                                  + e +kk+a ++ +v++ Ge GtGK++la+++ +  
  gi|13541325|ref|NP_111013.1| 39 AGEIVKKAALQRRHVILIGEPGTGKSMLAQSMVDFL 74
                                  5577999***********************997754 PP

  == domain 2  score: 30.6 bits;  conditional E-value: 3.3e-10
                                   TTSS-BE.HHHHHTTTSEEEEETGGGS-HHHHHHHHHHHHHSEEESBTSSS CS
               Sigma54_activat  80 GAekekk.GlfekadgGtlfLDeigelplelQekLlrvlqegevervGssk 129
                                    A+++ + G ++ka++G+lf+Dei+ l +e Q+ +l++lqe+++   G+s+
  gi|13541325|ref|NP_111013.1| 220 PAHERVEaGNIHKAHKGVLFIDEINLLRPEDQQAILTALQEKKYPISGQSE 270
                                   45555445***********************************98777655 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 !   20.1   0.0   6.8e-07   0.00051       1      25 [.      52      77 ..      52      85 .. 0.86
   2 !   19.1   0.0   1.4e-06     0.001      62     137 ..     227     307 ..     205     308 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 6.8e-07
                                  EEEEE--SSSSHHHHHHHGGGGB.S- CS
                         AAA_5  1 dvlLvGppGtgKselaerlaaal.nr 25
                                  +v+L+G+pGtgKs+la+++  +l ++
  gi|13541325|ref|NP_111013.1| 52 HVILIGEPGTGKSMLAQSMVDFLpKS 77
                                  79*****************9998554 PP

  == domain 2  score: 19.1 bits;  conditional E-value: 1.4e-06
                                   ---....G-SEEEEESGGG--HHHHHHHHHHHHSSEEE..-SSSEEE---............-EEEEEESS--.-TT-TTH CS
                         AAA_5  62 aar....egeilvlDEveraesevlnsLlslleerrllleeggelvkaknddller......frviatanpldrslnelsp 132
                                   a++    ++ +l++DE++ +++e +++ l+ l e++++  +g+ + +a +  +  +      f ++a++n       ++ p
  gi|13541325|ref|NP_111013.1| 227 AGNihkaHKGVLFIDEINLLRPEDQQAILTALQEKKYP-ISGQSERSAGAMVQ--TepvpcdFVLVAAGNYDA--IRNMHP 302
                                   4446666899****************************.55555555555223..24589**********998..666799 PP

                                   HHHTT CS
                         AAA_5 133 alrsR 137
                                   alrsR
  gi|13541325|ref|NP_111013.1| 303 ALRSR 307
                                   ***99 PP

>> ChlI  Subunit ChlI of Mg-chelatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.9   0.6   3.2e-11   2.4e-08       9     121 .]     473     586 ..     464     586 .. 0.91

  Alignments for each domain:
  == domain 1  score: 33.9 bits;  conditional E-value: 3.2e-11
                          ChlI   9 lpkftivGlpdtavkeskervrsalkn.sgfefpakkitvnLaPadlkkeGsafDLpiAigilaaleqieaeeetlflGeL 88 
                                     ++  +G +    ke+   v +  k+ +g ++ ++ i +         eG + + +iA ++++a+e+i++++++ + G L
  gi|13541325|ref|NP_111013.1| 473 AGNIIATGKLGDIAKEAVLNVSAVFKKiTGKDISNMDIHIQFVGTYEGVEGDSASVSIATAVISAIENIPVDQSVAMTGSL 553
                                   55566677788888999999999999978999*************999********************************* PP

                          ChlI  89 sldGslrpvkgvlpialaakkegikkvivpken 121
                                   s  G++ pv gv++ + aa ++g++kvivp+ n
  gi|13541325|ref|NP_111013.1| 554 SVRGDVLPVGGVTAKVEAAIEAGMAKVIVPELN 586
                                   ******************************865 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.0   6.3e-05     0.047      54      84 ..      47      77 ..      17      82 .. 0.82
   2 !   15.5   0.0   9.3e-06     0.007     111     149 ..     224     262 ..     185     270 .. 0.89
   3 ?   -3.3   0.0       5.3   3.9e+03      21      50 ..     495     524 ..     487     541 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.3e-05
                                  BCSS-EEEEEESSTSTHHHHHHHHHHHSSSE CS
                           MCM 54 lrgdinvllvgdpgtaKsqlLkyveklapra 84
                                     + +v+l+g+pgt+Ks l +++ +++p++
  gi|13541325|ref|NP_111013.1| 47 ALQRRHVILIGEPGTGKSMLAQSMVDFLPKS 77
                                  45677*******************9999987 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 9.3e-06
                                   EEEETHHHHTTTSEEEEESGGGSTCHHHHHHHHHHHHSE CS
                           MCM 111 vleaGalvladkGvcciDefdkmkeedrsalhEamEqqt 149
                                    +eaG +  a+kGv+ iDe++  + ed++a++ a+ +++
  gi|13541325|ref|NP_111013.1| 224 RVEAGNIHKAHKGVLFIDEINLLRPEDQQAILTALQEKK 262
                                   589******************************998776 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 5.3
                                   HSSTTSSS-HHHHHHHHHHHH---EBBBSS CS
                           MCM  21 siapsiyghedvkkaillqlfggvkkkled 50 
                                   +++++i+g++     i +q +g+++  + d
  gi|13541325|ref|NP_111013.1| 495 AVFKKITGKDISNMDIHIQFVGTYEGVEGD 524
                                   566777777777777777777776655554 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   1.9e-07   0.00014       4      59 ..      49     110 ..      46     134 .. 0.70
   2 ?    3.0   0.0      0.15   1.1e+02      86     112 ..     230     258 ..     218     270 .. 0.76
   3 ?   -2.1   0.0       5.9   4.4e+03      50      83 ..     325     358 ..     305     376 .. 0.56

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 1.9e-07
                        AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaee......erpevvfvtlpsstsskdllre 59 
                                   ++++++++Ge+GtGK++l++ +++ l++ +  +       e+p   +++    ++ k++ r+
  gi|13541325|ref|NP_111013.1|  49 QRRHVILIGEPGTGKSMLAQSMVDFLPKSELEDIlvfpnpEDPNKPKIKTVPAGKGKEIVRQ 110
                                   6899**********************876555447777764444444444444444555555 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.15
                        AAA_22  86 lraravielliiDEaqhlr...seealeeL 112
                                   ++++++ ++l iDE+  lr   ++++l+ L
  gi|13541325|ref|NP_111013.1| 230 IHKAHK-GVLFIDEINLLRpedQQAILTAL 258
                                   677777.9**********754334444444 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 5.9
                        AAA_22  50 stsskdllrellralglelkaerlsseelleale 83 
                                   ++++k+l + ++++++ ++k +  ++++++e + 
  gi|13541325|ref|NP_111013.1| 325 DENRKKLVQFIAQEVEKDKKIPHFDKSAIVEIIK 358
                                   3345556666666666555543344443333333 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.0   0.00015      0.11       1      21 [.      53      73 ..      53     129 .. 0.80
   2 !   12.0   0.0   0.00028      0.21      56     124 ..     233     308 ..     218     311 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00015
                                  EEEESSTTSSHHHHHHHHHHH CS
                           AAA  1 vllyGppGtGKTllakavake 21
                                  v+l+G pGtGK++la++++  
  gi|13541325|ref|NP_111013.1| 53 VILIGEPGTGKSMLAQSMVDF 73
                                  68*************998765 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00028
                                   TSTSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTS..................SSTEEEEEEESS..GGGST CS
                           AAA  56 kakpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkk..................eskvivigatnr..pdkld 116
                                     ++ +lfiDEi  l +++           ++++lt+l++ k                      ++++++a+n+  ++++ 
  gi|13541325|ref|NP_111013.1| 233 A-HKGVLFIDEINLLRPED-----------QQAILTALQEKKYPisgqsersagamvqtepvPCDFVLVAAGNYdaIRNMH 301
                                   2.359**********9999...........999999999998889999999*********99667*********999**** PP

                                   HHHHSTTS CS
                           AAA 117 pallrgRf 124
                                   pal+ +R+
  gi|13541325|ref|NP_111013.1| 302 PALR-SRI 308
                                   ****.887 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.0    0.0022       1.7      14      43 ..      43      72 ..      39      86 .. 0.86
   2 !   10.4   0.0    0.0007      0.52      62      97 ..     227     262 ..     173     300 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0022
                                  HHHHHT-SS-EEEEEETT--HHHHHHCC-- CS
               Sigma54_activ_2 14 LeqaaqsklpvfltGekGsgkelvArlLhk 43
                                  +++aa +   v l+Ge+G+gk++ A+ + +
  gi|13541325|ref|NP_111013.1| 43 VKKAALQRRHVILIGEPGTGKSMLAQSMVD 72
                                  6888999999***************98765 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0007
                                   HHHHHHTTTSEEEEEE-TT--HHHHHHHHHHHHHHT CS
               Sigma54_activ_2  62 ldlleqakggtLylkdiadlskaeqkeLlellakae 97 
                                   +  + +a+ g+L++ +i+ l +++q+ +l +l++++
  gi|13541325|ref|NP_111013.1| 227 AGNIHKAHKGVLFIDEINLLRPEDQQAILTALQEKK 262
                                   4445679*************************9963 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   7.7e-05     0.057      23      51 ..      50      77 ..      37     124 .. 0.82
   2 ?    4.8   0.0     0.046        34     132     159 ..     232     259 ..     222     269 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 7.7e-05
                        AAA_16 23 rpelvllsGesGvGKsslvrellralekd 51
                                  r + v+l+Ge+G+GKs l+++  + l k+
  gi|13541325|ref|NP_111013.1| 50 R-RHVILIGEPGTGKSMLAQSMVDFLPKS 77
                                  3.89***************9988766666 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.046
                        AAA_16 132 rderplvlvlDdlqwadeaslql.laaLl 159
                                   + +++ vl++D++  ++++++q+ l aL 
  gi|13541325|ref|NP_111013.1| 232 K-AHKGVLFIDEINLLRPEDQQAiLTALQ 259
                                   3.6778*****************666554 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   3.2e-06    0.0024      25      62 ..      42      79 ..      37      85 .. 0.87
   2 ?   -0.0   0.0      0.71   5.3e+02     100     116 ..     234     250 ..     230     256 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3.2e-06
                         AAA_7 25 llelllknkkpvllvGptGtGKtviikdllkkldkeky 62
                                  ++++   ++++v+l+G+ GtGK+++++++++ l+k+++
  gi|13541325|ref|NP_111013.1| 42 IVKKAALQRRHVILIGEPGTGKSMLAQSMVDFLPKSEL 79
                                  567778899********************999998776 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.71
                         AAA_7 100 kklvvFvDDlnmpakek 116
                                   +k v+F+D++n+ ++e+
  gi|13541325|ref|NP_111013.1| 234 HKGVLFIDEINLLRPED 250
                                   6789*******988876 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.019        14       1      23 [.      52      74 ..      52      86 .. 0.89
   2 !   11.6   0.0   0.00025      0.19      63      98 ..     235     270 ..     219     292 .. 0.85
   3 ?   -2.1   0.0       4.4   3.3e+03      26      51 ..     596     621 ..     576     634 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.019
                         AAA_3  1 hvllegvPGlaktllvkalakal 23
                                  hv+l g PG++k +l++++ + l
  gi|13541325|ref|NP_111013.1| 52 HVILIGEPGTGKSMLAQSMVDFL 74
                                  9****************998766 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00025
                         AAA_3  63 anllladeinrappktqsalleameerqvtvegeth 98 
                                   + +l+ dein   p  q a+l a++e++  ++g++ 
  gi|13541325|ref|NP_111013.1| 235 KGVLFIDEINLLRPEDQQAILTALQEKKYPISGQSE 270
                                   46899***********************99988765 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 4.4
                         AAA_3  26 efkriqftpdllPsdilGtevfeeke 51 
                                   +++riq+ p     d+l + ++++ e
  gi|13541325|ref|NP_111013.1| 596 HINRIQIIPARTIEDVLKVALVNSPE 621
                                   46899999988888888888877655 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   4.7e-06    0.0035       1      31 [.      51      81 ..      51     135 .. 0.85
   2 ?   -1.9   0.0       3.6   2.7e+03      79     109 ..     232     255 ..     218     266 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 4.7e-06
                                  SCEEEEC-TTTCHHHHHHHHHHHHCTS-SCC CS
                         NACHT  1 rlvilqGeaGsGKTtLlqklalawaegklpq 31
                                  r vil Ge+G GK++L+q++++ + +++l+ 
  gi|13541325|ref|NP_111013.1| 51 RHVILIGEPGTGKSMLAQSMVDFLPKSELED 81
                                  579******************9999988776 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3.6
                                   SCCCEEEEEE-STT-SS-TCH.........H CS
                         NACHT  79 lperlLlilDglDelvtdlgqkekqpvrtlL 109
                                    +++ +l +D ++ l+ +++q         L
  gi|13541325|ref|NP_111013.1| 232 KAHKGVLFIDEINLLRPEDQQ-------AIL 255
                                   577888999*****9998888.......223 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 !    9.9   0.0   0.00079      0.59       7      53 ..      31      70 ..      26      77 .. 0.76
   2 ?    5.5   0.0     0.017        13      84     116 ..     234     266 ..     225     308 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00079
                        RuvB_N  7 eeyigqekvkeklkifieaakkreealdhvllyGpPGlGkttlakii 53
                                  ++ igq++  e   i+ +aa +r+    hv+l+G PG Gk+ la+ +
  gi|13541325|ref|NP_111013.1| 31 DQVIGQDQAGE---IVKKAALQRR----HVILIGEPGTGKSMLAQSM 70
                                  56667766554...5667777775....9**************9855 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.017
                        RuvB_N  84 ekdvlfideihrlsraveevlysamedfrldiv 116
                                   +k vlfidei  l+++ ++ + +a+++ +  i 
  gi|13541325|ref|NP_111013.1| 234 HKGVLFIDEINLLRPEDQQAILTALQEKKYPIS 266
                                   578*************99999999998777665 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.0   0.00024      0.18       6      37 ..      45      77 ..      40      87 .. 0.81
   2 ?    3.7   0.0     0.095        71      98     128 ..     229     261 ..      91     266 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00024
                        AAA_19  6 e.alkekvllvtaGpGtGKTrvlkhivallvel 37
                                  + al+++++++++ pGtGK+ + + +v  l + 
  gi|13541325|ref|NP_111013.1| 45 KaALQRRHVILIGEPGTGKSMLAQSMVDFLPKS 77
                                  35799***************9999988877655 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.095
                        AAA_19  98 kklqeee.llivDEfqdvd.elqyrLlkallge 128
                                   +  ++++ +l++DE+  +  e q+++l al ++
  gi|13541325|ref|NP_111013.1| 229 NIHKAHKgVLFIDEINLLRpEDQQAILTALQEK 261
                                   333445569**********999*****999854 PP

>> DUF4191  Domain of unknown function (DUF4191)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.7   0.00018      0.14       8      68 ..     104     164 ..      98     178 .. 0.74
   2 ?    1.2   0.0      0.27     2e+02     124     178 ..     287     342 ..     283     362 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00018
                       DUF4191   8 lkqiaqvfkltrkedkkllwlllaaflvvvvvfvvlglllgslilllilgillgllvaliv 68 
                                    k+i++ ++++++++k+     +++++  vv++ ++  ++ + i+l++++i++++ + + +
  gi|13541325|ref|NP_111013.1| 104 GKEIVRQYQIKAEREKRDRSRSIMFVIFSVVLLGIIAAIVLRSITLIFFAIMAAAFLYMAM 164
                                   5789999****99999966666666666666666666666689999999999877666644 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.27
                       DUF4191 124 vLvgEGnkkrvkkllaqekkrikrvvadvpvyeivvGngegqvplkk.Lqktlkkl 178
                                   vLv+ Gn+++++++  + + ri+   ++v v +++  n+e++ +l + +++++ k 
  gi|13541325|ref|NP_111013.1| 287 VLVAAGNYDAIRNMHPALRSRIRGYGYEVVVNDYMDDNDENRKKLVQfIAQEVEKD 342
                                   9**********************************999999988766245666664 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00036      0.27       5      42 ..      37      74 ..      34      86 .. 0.72
   2 ?   -1.1   0.0       1.8   1.3e+03      87     115 ..     233     261 ..     208     266 .. 0.80
   3 ?   -2.6   0.0         5   3.7e+03      47      64 ..     392     409 ..     350     451 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00036
                        AAA_30  5 eQaaavealltsgdrvavltGpAGtGKttalkalreaw 42
                                  +Qa  + + ++ ++r ++l G +GtGK+++ +++++ +
  gi|13541325|ref|NP_111013.1| 37 DQAGEIVKKAALQRRHVILIGEPGTGKSMLAQSMVDFL 74
                                  5554444444455569*************998887765 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.8
                        AAA_30  87 epgtllivDEagmvdtkqlaallkaaeka 115
                                   +++ +l +DE+ ++  ++ +a+l+a++++
  gi|13541325|ref|NP_111013.1| 233 AHKGVLFIDEINLLRPEDQQAILTALQEK 261
                                   3457999*****99999999999998875 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 5
                        AAA_30  47 grviglAptgkaAkvLae 64 
                                   +r i+ A+   aAk+L++
  gi|13541325|ref|NP_111013.1| 392 KRNIVTASDVIAAKALSK 409
                                   455566666666666664 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00023      0.17      14      49 ..      43      78 ..      35     126 .. 0.77
   2 ?   -2.1   0.2       1.8   1.3e+03     121     156 ..     329     364 ..     314     419 .. 0.59

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00023
                        AAA_10 14 vkgsktnasasliiGdlGnGKSvlakllvlyisllg 49
                                  vk +  +  ++++iG++G GKS+la+ +v ++   +
  gi|13541325|ref|NP_111013.1| 43 VKKAALQRRHVILIGEPGTGKSMLAQSMVDFLPKSE 78
                                  56666677899*****************99876555 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.8
                        AAA_10 121 sekkaalseaveavlegkqrgllavieelrkedekv 156
                                   ++ ++++++ ve+ ++ ++ +  a++e +++ +++ 
  gi|13541325|ref|NP_111013.1| 329 KKLVQFIAQEVEKDKKIPHFDKSAIVEIIKEAQKRS 364
                                   222334444444444444444444555444444433 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0    0.0005      0.37       1      27 [.      53      89 ..      53     116 .. 0.65
   2 ?   -0.9   0.1       2.8   2.1e+03      53      86 ..     315     348 ..     309     352 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0005
                  RNA_helicase  1 iwlyGpsgeGKStlakeLakallkkl..........k 27
                                  ++l G++g+GKS+la+++++ l k+           +
  gi|13541325|ref|NP_111013.1| 53 VILIGEPGTGKSMLAQSMVDFLPKSEledilvfpnpE 89
                                  6799*************76655543345555555553 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 2.8
                  RNA_helicase  53 vvidDfgqvkdeenpsdlaelirlvsstpyplnm 86 
                                   vv+ D + ++de+ ++ ++++ + v+  + +++ 
  gi|13541325|ref|NP_111013.1| 315 VVVNDYMDDNDENRKKLVQFIAQEVEKDKKIPHF 348
                                   7889999999984445888888888888877776 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   0.00058      0.43       4      42 ..      53      89 ..      50     125 .. 0.76
   2 ?   -0.2   0.1       0.6   4.5e+02     162     228 ..     360     439 ..     314     444 .. 0.65

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00058
                       DUF2075  4 vlVtGvaGtGKtvvllnllaeleddeeertavylsvNhp 42
                                  v+  G++GtGK++++ +++  l   ++e + +++  N +
  gi|13541325|ref|NP_111013.1| 53 VILIGEPGTGKSMLAQSMVDFL--PKSELEDILVFPNPE 89
                                  4556***************999..777777777777765 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.6
                       DUF2075 162 v...............hLksqfRvaaseaviewvdalldgkkekakplssqenfdirvfddleelkkalkeknkesgrsrl 227
                                                   +L   +Rva++ av++  + +++ + ++ak l  ++  + +++d+  e+kk +k+  +e+  +++
  gi|13541325|ref|NP_111013.1| 360 AqkrsgrrnkltlrlrELGGLVRVAGDIAVSQKRNIVTASDVIAAKAL--SKPLEQQIADKSIEIKKIYKTFRTEGSVVGM 438
                                   033333333444455577778888888888888888888888888887..6888888888888888888888888777888 PP

                       DUF2075 228 v 228
                                   v
  gi|13541325|ref|NP_111013.1| 439 V 439
                                   7 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   0.00038      0.29      47      67 ..      50      70 ..      25      75 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00038
                     IstB_IS21 47 kenivllGpsGvGKshlaial 67
                                  +  ++l+G +G+GKs la ++
  gi|13541325|ref|NP_111013.1| 50 RRHVILIGEPGTGKSMLAQSM 70
                                  45799*************987 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00047      0.35      34      54 ..      51      71 ..      29      75 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00047
                        AAA_25 34 elallaGapgtGKttlaldla 54
                                    ++l+G pgtGK++la +++
  gi|13541325|ref|NP_111013.1| 51 RHVILIGEPGTGKSMLAQSMV 71
                                  5689*************9886 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.7   0.00042      0.31     367     432 ..     107     165 ..      92     176 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00042
                       DUF2207 367 kergyfdkkgkkklkklsalglgliilglilillallllvlllvfllilllillliaiivlllfsr 432
                                     r+y  k++++k+ +++ + ++++ ++l++i++a       +v+ +i+l++++++a+++l+++ +
  gi|13541325|ref|NP_111013.1| 107 IVRQYQIKAEREKRDRSRSIMFVIFSVVLLGIIAA-------IVLRSITLIFFAIMAAAFLYMAMA 165
                                   56889999999999999999999999998888888.......556666666666666666655544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (655 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1400  (0.0780858); expected 358.6 (0.02)
Passed bias filter:                      914  (0.0509789); expected 358.6 (0.02)
Passed Vit filter:                       145  (0.00808746); 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: 0.86u 0.40s 00:00:01.26 Elapsed: 00:00:00.55
# Mc/sec: 3562.88
//
Query:       gi|297616201|ref|YP_003710340.1|  [L=141]
Description: KEOPS complex Cgi121-like subunit [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-06   27.8   0.0    2.8e-06   27.5   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 !   27.5   0.0   1.6e-10   2.8e-06      20      91 ..      27      97 ..       9     127 .. 0.79

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 1.6e-10
                                      CTT-EEE-GGG---HHHHHHHHHHHHHHHHHS---SSSHHHH...HHHHHSSSS-HHHHHHHHB--TT-S-EEEE CS
                           CGI-121 20 eldfafldaslilskehllsAvlrallaaargklktktlhsE...ilfsLspnnnIgealkrfgisdkttsllvv 91
                                      +  f ++d +++ls++++lsA+ ra   +     k   +++E   il+  s +++I  a+  +g++++++   ++
  gi|297616201|ref|YP_003710340.1| 27 KNLFQLIDGRCLLSQTQILSAISRAGRRYI----KGSRVNNEgilILMFVSASTQIDSAISSCGLKPDSSTAALI 97
                                      33489*********************8886....6666777644477888******************7755544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       315  (0.0175693); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 1007.17
//
Query:       gi|13541326|ref|NP_111014.1|  [L=258]
Description: cobalamin synthase [Thermoplasma volcanium GSS1]
Scores for complete 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-29  102.4   8.8    4.5e-29  102.1   8.8    1.1  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 !  102.1   8.8   2.5e-33   4.5e-29       2     202 ..       9     230 ..       8     232 .. 0.74

  Alignments for each domain:
  == domain 1  score: 102.1 bits;  conditional E-value: 2.5e-33
                          CobS   2 lsflTrlPvp..elaralaffPlvGlllGlll.llallllllllllaallavaalvlltgglHlDGlaDtaDglgsgrdre 79 
                                   +sf+T +P    ++++ + f+Plv  + +l+   ++++++++++l+a++l++  +++  g +H+D  aD++D+l+ + d++
  gi|13541326|ref|NP_111014.1|   9 FSFFTLVPSRqkDIGNPITFLPLVVTVGALIGdSILYITWQFSHLIASFLSISSIIIYNGLNHFDATADLGDALMVR-DKS 88 
                                   89*******74344779999999877777777777888888877889***9999999*****************996.*** PP

                          CobS  80 rrleImkDsrvGafGvlalvlvlllkvaalaala.......lllapvlsRlaallaiallpya.eeglgalfae.aqkk.. 149
                                   r+ e++kD +vGa+G++a+++v ++ v++la  +       +l+ +v+s  ++++++  +++  + gl+ +f++  +k+  
  gi|13541326|ref|NP_111014.1|  89 RIPEVIKDHHVGAGGIFAVIFVYGIAVLSLARSTlyiglvgILIGQVVSGSSMMISLIGSQPFvP-GLADYFISlFRKHsv 168
                                   ***************************99743334467778677788888877777777776645.999999984333344 PP

                          CobS 150 ......lvllal......avlllllalllaallvalllrrlarrklggvtGDvlGavieltellv 202
                                         l   a+      ++  l+++++++ ll++ l++ +  r++gg++GDv+G++ e ++ l+
  gi|13541326|ref|NP_111014.1| 169 gytiefL---AIpiivsfIFSPLYVVIVALNLLIVQLTKTMISRRFGGINGDVIGFLGEFSRSLF 230
                                   4433221...11333332111112222233333444667777777**************999877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       763  (0.0425568); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1875.79
//
Query:       gi|13541327|ref|NP_111015.1|  [L=345]
Description: aspartate aminotransferase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-18   67.6   0.0    2.2e-18   66.6   0.0    1.5  1  Aminotran_1_2  Aminotransferase class I and II


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.6   0.0   1.3e-22   2.2e-18      50     358 ..      57     335 ..      15     340 .. 0.79

  Alignments for each domain:
  == domain 1  score: 66.6 bits;  conditional E-value: 1.3e-22
                                   HHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE CS
                 Aminotran_1_2  50 eealakflgrseklklkreaavvvgsGagaliealifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhl 130
                                    eal + l+      ++++  ++ + G +++i ++   l    +++i vp p y+++  + +  g+e  +++       + 
  gi|13541327|ref|NP_111015.1|  57 TEALSRRLR------VDQD-LIIPTVGGTEAIFIALSHL-SSVSKRIHVPLPEYEPMFLVPESLGIETSKIE-------SK 122
                                   445555555......5555.6666666666666666666.46777777777777777777777777777777.......33 PP

                                   -HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTST CS
                 Aminotran_1_2 131 dlealeealkeapegnkktkvilvesphNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeep 211
                                    + + +           k+  i+ + p+NPt +  ++  l +    +   + l+++De++ +f         tr+++ ++ 
  gi|13541327|ref|NP_111015.1| 123 VMPGRIS----------KNESIAMTLPNNPTAQYSDRISLLDN---VIHSEGLIYIDETFRDFLPS-----GTRPTLFDGS 185
                                   4444444..........55679*************99888776...55569**************9.....5588888888 PP

                                   T.EEEEEESSSTTSSGGG-EEEEEEEHHHHHHHHHHHHHHTS..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                 Aminotran_1_2 212 n.llivgslsKafGlaGeRvGyilgnaavvsqlrklsrpfls..ssllqaavaaalsdallkqseleemrqrlqkrrkelr 289
                                   + +++ g++ K +Gl ++R G+i+++++ v  +r+++    +   s   +++a+a+++ +    + e++   ++k+ ++ r
  gi|13541327|ref|NP_111015.1| 186 EtMVVSGTMTKFYGLSNLRTGWIISSEHNVAGMRRIKDLTSInnASFSLYIAAQAIQKWNY---FKEAEDNLINKNLRVAR 263
                                   88999**********************************9999788888888888888773...55666667788999999 PP

                                   HHHHHS.TEEEECCSCSSEEEEEETHH.CHHHHHHHHHHTCTEEEEEGGGGTSTTEEEEEC.TTS-HHHHHH CS
                 Aminotran_1_2 290 deLael.glkvlasqsgmflltdlsae.takelskkLleevgvyvtpgtsftvpgrlRitv.Aglteeelee 358
                                   + L+ l g+++ +++++ f +  +s+  +  +l+k  +e++g++  pg+ f+ + ++R+++ ++ +ee+ + 
  gi|13541327|ref|NP_111015.1| 264 EYLEGLpGISYKEPEGAPFIFLSYSKNiESVKLAKLAVERYGILFAPGSFFGEEHHIRVCLtSNKPEEDFNV 335
                                   99*999*********999999999999899999999*************************88888877655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       284  (0.0158403); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); 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: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 2244.06
//
Query:       gi|13541328|ref|NP_111016.1|  [L=160]
Description: hypothetical protein TVN0497 [Thermoplasma volcanium GSS1]
Scores for complete 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-70  233.7   0.2    8.6e-70  233.5   0.2    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 !  233.5   0.2   4.8e-74   8.6e-70       1     154 []       6     159 ..       6     159 .. 0.99

  Alignments for each domain:
  == domain 1  score: 233.5 bits;  conditional E-value: 4.8e-74
                                   EEE---TTEEEEEEEESSTTHHHHHHHHHHCCSTTSEEEEEEE--STT-EEEEEESSHHHHHHHHHHHHHH--TTEEEEEE CS
                 Adenosine_kin   1 vkiekpeevnvilgqshfiktvedlyealvtsvpgikfglafcEasgkrLvrvegndeelvelavknalaigaghvfvill 81 
                                   v++ +p++ n+i+g+shfiktvedl+e++ ts+p++++++af+Easg+rL+r+egnd+elv++a++n+++i+agh+fvill
  gi|13541328|ref|NP_111016.1|   6 VDMIVPNDSNIIVGYSHFIKTVEDLNEIVHTSMPKCRYAIAFSEASGDRLIRYEGNDDELVNAAIENIKRISAGHTFVILL 86 
                                   67889**************************************************************************** PP

                                   EST-HHHHHHHHHHCTTCEEEEEEESSSEEEEEEEETTEEEEEEEEES---SEE--HHHHHHHHHHHHHTTS- CS
                 Adenosine_kin  82 knafPinvlnaiksvpevvkifaAtanplevivaeteqgrgvlgvvDGfspkgveeeedkkerkellrkigYk 154
                                   ++a+Pin+lna+ks++ev  ifaAtan l++i+ + e+g+gvlgv+DG+sp gve+++dkk+r++llrkigYk
  gi|13541328|ref|NP_111016.1|  87 RDAYPINILNAVKSCQEVGGIFAATANSLKIIIYKGENGNGVLGVIDGMSPVGVESDDDKKKRRDLLRKIGYK 159
                                   ************************************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.31s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1036.74
//
Query:       gi|13541329|ref|NP_111017.1|  [L=515]
Description: RNA polymerase II complex ELP3 subunit [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-30  105.2   0.2    2.4e-30  104.4   0.2    1.4  1  Radical_SAM_C    Radical_SAM C-terminal domain
    4.2e-21   76.0   0.7      2e-19   70.6   0.0    3.0  3  Radical_SAM      Radical SAM superfamily
    1.9e-06   28.1   0.2    4.3e-06   27.0   0.2    1.6  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    8.8e-06   25.7   0.0    0.00063   19.7   0.0    2.3  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 !  104.4   0.2   5.3e-34   2.4e-30       1      81 [.     286     366 ..     286     367 .. 0.98

  Alignments for each domain:
  == domain 1  score: 104.4 bits;  conditional E-value: 5.3e-34
                 Radical_SAM_C   1 pdgvKlypllvikgTeLaelyksgeykplsleeyvdlvadilellppdirvhRltgdipkelliagpwhknlreliekrlk 81 
                                   pd++K+yp+lv+kgT L++l+k+g+y+p+++ee v+l++d+++++pp+irv+R+++dip + ++ag++++ lr l+e+r++
  gi|13541329|ref|NP_111017.1| 286 PDMLKIYPTLVTKGTALYNLWKNGKYRPYTTEETVELIVDFMKMMPPWIRVQRIQRDIPVQFIVAGVKRSDLRNLVEERIR 366
                                   8******************************************************************************96 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0      0.05   2.2e+02      91     126 ..      24      63 ..       6      67 .. 0.81
   2 !   70.6   0.0   4.4e-23     2e-19       5     156 ..      79     267 ..      75     276 .. 0.84
   3 ?   -1.4   0.0      0.58   2.6e+03      22      52 ..     378     408 ..     365     449 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.05
                                   HHHHHHHHHTT-SEEEEEEBSSSHH....HHHHHHTCTSH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxx RF
                   Radical_SAM  91 eeklerllelgvdrvslgleaadde....kvlklmnrght 126
                                   + k+e+ +++++d+v  ++e++++     +v+ +++r++t
  gi|13541329|ref|NP_111017.1|  24 DLKVELSRKYHLDYVPGDVEILNSYefddDVKSMLRRKPT 63 
                                   668999*****************99888878888777665 PP

  == domain 2  score: 70.6 bits;  conditional E-value: 4.4e-23
                                   SEESS-.-TTTSCCTT.................HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHH CS
                                   xxxxxx.xxxxxxxxx.................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM   5 rgCnlr.CsfCarpet.................vrregrgrslsveeileevkelkaekgvkevilgggepllypdfvell 67 
                                     C+++ C+fC+ + +                   +++++++ +  +i+++  ++ ++  +  +i++gg+ +++p  ++  
  gi|13541329|ref|NP_111017.1|  79 DRCPHGkCIFCPGGVDnnspqsytgfepaalrgRNNRYDPYMETFSRIKQLETIG-HDTSKIDLIVMGGTFTARPVDYQNS 158
                                   5788888*************************77777777777777777777777.68779999999*******5555555 PP

                                   HHHHHTC..................CCTEEEEEEECSSCHG...HHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHH CS
                                   xxxxxxx..................xxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  68 erlakla..................vpgiritvetngtlpd...eeklerllelgvdrvslgleaaddekvlklmnrghtf 127
                                   +    l+                   ++ r+   t +t+pd   e+ ++  l++g++ v+lg++ ++d+ +l+++nrght+
  gi|13541329|ref|NP_111017.1| 159 FIKGCLDamngyisndlyqaikineTSEHRCIGLTVETKPDwffEKEIDDALNYGTTKVELGVQNINDR-ILRINNRGHTV 238
                                   55555555666666666666666678999999999999999999*************************.*********** PP

                                   HHHHHHHHHHHHTTSETEEEEEEEBTTTS CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM 128 eevlealeklreagikrvvdrivglpGen 156
                                   e++ ++++++r+ag+k v+++++g+ G +
  gi|13541329|ref|NP_111017.1| 239 EDIARSTQLARDAGLKIVYHIMPGMYGSS 267
                                   *************************9976 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.58
                                   HHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx RF
                   Radical_SAM  22 regrgrslsveeileevkelkaekg.vkevil 52 
                                   re  +++ sve+i   v+++ +  g ++++i+
  gi|13541329|ref|NP_111017.1| 378 REIGHYNGSVENIHLSVDKY-EAAGgTEYFIS 408
                                   56678888888888888888.66664555554 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.2   9.5e-10   4.3e-06      32     117 .]     403     503 ..     368     503 .. 0.81

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 9.5e-10
                                   TCEEEE..EEETTEEEEEEEEEEEET.....TSTTEEEEEEEEE...........SGGGTTSSHHHHHHHHHHHHHHHT.T CS
                Acetyltransf_1  32 aegllv..aeedgeliGfisllkipd.....ekggvayieslaV...........speyrgkGlGsaLlealeeraree.g 93 
                                   + ++++  + +d+ ++Gf++l++  +     e  g a++++l V            ++++++G+G +L+e++e++ar+  g
  gi|13541329|ref|NP_111017.1| 403 T-EYFIsyVTDDDHIVGFVRLRQPSEmahrqEMLGSAIVRELKVfgqevpvgrrdLKNWQHHGYGMRLMEEAERIARDDlG 482
                                   3.44444888999*************8888866677777777779999999****************************** PP

                                   ESEE.EEEEETTEHHHHHHHHHTTE CS
                Acetyltransf_1  94 ikki.vlaveedndaairlYeklGF 117
                                   +++i v+    +  + + +++k G+
  gi|13541329|ref|NP_111017.1| 483 LDRIlVI----SGIGVRQYFRKIGY 503
                                   *998555....77777888866776 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.014        62      29      53 ..     403     427 ..     386     435 .. 0.80
   2 !   19.7   0.0   1.4e-07   0.00063      61     111 ..     458     508 ..     457     513 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.014
               Acetyltransf_10  29 gealllvaeeggkivGvielrdgsh 53 
                                    e+++  +++++ ivG+++lr+ s+
  gi|13541329|ref|NP_111017.1| 403 TEYFISYVTDDDHIVGFVRLRQPSE 427
                                   467777788999********99875 PP

  == domain 2  score: 19.7 bits;  conditional E-value: 1.4e-07
               Acetyltransf_10  61 peyrgqGigkaLleaveeeaekdgikl.eltvnaspyavpfYeklGFkavge 111
                                   +++++ G+g +L+e++e+ a +d+++l ++ v +    +++++k+G++++g+
  gi|13541329|ref|NP_111017.1| 458 KNWQHHGYGMRLMEEAERIA-RDDLGLdRILVISGIGVRQYFRKIGYEDLGP 508
                                   79*****************9.6668888********************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (515 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       567  (0.0316247); expected 358.6 (0.02)
Passed bias filter:                      512  (0.0285571); 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: 0.64u 0.26s 00:00:00.90 Elapsed: 00:00:00.47
# Mc/sec: 3283.19
//
Query:       gi|13541330|ref|NP_111018.1|  [L=585]
Description: potassium-transporting ATPase subunit A [Thermoplasma volcanium GSS1]
Scores for complete 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-168  560.2  31.3   4.7e-168  559.8  31.3    1.0  1  KdpA      Potassium-transporting ATPase A subunit


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 !  559.8  31.3  2.6e-172  4.7e-168       2     544 ..      29     571 ..      28     573 .. 0.98

  Alignments for each domain:
  == domain 1  score: 559.8 bits;  conditional E-value: 2.6e-172
                                   HHHHHHHHHHHHHHHHHHHHHTT-...--SS-SHHHHHHHHHHT---.----HHHHHHHHHHHHHHHHHHHHHHHHTTTTS CS
                          KdpA   2 lllllllllalplgkylakvfegektlldkllkpverllyrllgvdeeeemtwkeYalalllfnlvlllllylllrlqgvl 82 
                                   ++l ++ +++++l+ y+ak++++e t+l+kl+  v +++ +++g +e+++m++keY+++lllfn++  l+ +l++++q++l
  gi|13541330|ref|NP_111018.1|  29 IYLGITSIFSYVLSFYIAKIYRDEPTFLRKLTGSVISFFEKIIGESENHQMEFKEYFINLLLFNFFAGLISFLVIMYQKYL 109
                                   57889999************************************************************************* PP

                                   S--SS------HHHHHHHHHHHHTT-----S-HHHH--HHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHS-S-S----HHH CS
                          KdpA  83 plnpeglealspdlafntavSFvtntnlQhYsgestlsylsqmlgltvlnFvsaatGlavavalirglarketkelGnfyv 163
                                   p++    +++sp+l fnt+vSF+tntnlQhYs   +lsy+sq++++t l+F+sa tG+a+ +a++rgl+++   ++Gnfy+
  gi|13541330|ref|NP_111018.1| 110 PFS-YYATGMSPSLDFNTVVSFLTNTNLQHYSNPFRLSYFSQTFVITGLMFLSAGTGFAASMAFVRGLRTDV-GKIGNFYH 188
                                   **9.77899***********************************************************8775.******** PP

                                   HHHHHHHHTHHHHHHHHHHHHHHHT--------EEEE-.SSS-EEEE--SSHHHHHHHHHHTT----SSSSTTTSTTTS-S CS
                          KdpA 164 dlvrailrvLLPlslvvalllvaqGvpqtlsgkaevtt.legakqtialGpvAsleaIkqlGtnGGGffgaNsahpfenpt 243
                                   d++ +i+ ++LPls++v+++l+ +Gvp+t++   +vt  +++++ +i+lGpvA+leaIk++GtnGGGf+gaN+  pfenp+
  gi|13541330|ref|NP_111018.1| 189 DFLVSIFDLILPLSILVTIILILAGVPETIQRFISVTPfFTNNTVNIPLGPVATLEAIKNIGTNGGGFYGANAGFPFENPD 269
                                   *******************************999977516788************************************** PP

                                   HHHHHHHHHHHHHHHHHHHHHHHHHTS-THHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHH..-----TTB-SSS-HHH CS
                          KdpA 244 altnlleilaillipaalvftfGrmvkdkrqglailavmlvlflvllvvvvvaeaagnpalaeeqaggnmeGkEvrfGiaa 324
                                   ++tnlle++++++ip++ ++++G +++d++ g++++ v++++f++  +++++ e+ g p l+    +gnm GkE+ +G+++
  gi|13541330|ref|NP_111018.1| 270 WFTNLLEFVSFTIIPLGSLMALGIVFEDRKFGRMLYYVIMFFFVFDGLFAFFGEYVGVPFLHIGYYTGNMLGKETAIGVSQ 350
                                   ***************************************************************999*************** PP

                                   HHHHHHHHHHTT----SS-GGGS-HHHHHHHHHHHHTS-TT-TTTHHHHHHHHHHHHHHHHHHHHHTS--EETTEE--HHH CS
                          KdpA 325 salfavvttatstGavnamhdsltplgglvpllnmmlevvfGGvGvGllnllvfvilavFiagLmvGrtPeylgkkieare 405
                                   s++fav +t tstGa + ++ s+tp+g++  l+ ++l+  +GGvG+G+ln+++++i++vFi +LmvG+ Pe+++ +i+++e
  gi|13541330|ref|NP_111018.1| 351 SSIFAVGATLTSTGASDGALVSYTPAGIIGVLIGLLLNDPLGGVGTGVLNIFMYIIFTVFIGSLMVGKLPELMSLRIGSKE 431
                                   ********************************************************************************* PP

                                   HHHHHHHHHHHHHHHHHHHHHHTTSHHHTT.--S-THHHHHHHHHHHHHHHTT-----S-S---SHHHHHHHHHHHHHHHH CS
                          KdpA 406 vklaalaiLvhpllilvgtalalalpalas.lsnpgahglsevLYeftSaaanNGSafeGlgdntvfwnltlglamllgRf 485
                                   +k+++l++++hpll++++ +++l++p+l+s + np+   ++e+LYef+Saa+nNGS++ G+ +n++++n++ g++mllgR+
  gi|13541330|ref|NP_111018.1| 432 IKYSTLSLVTHPLLVVIPLGITLMIPHLSStFVNPNSSRITELLYEFASAASNNGSEMGGFLTNQPYFNYLDGVIMLLGRY 512
                                   **************************66655************************************************** PP

                                   HHHHHHHHHHHHHHTS------TT---SSHHHHHHHHHHHHHHHHHHHHHHHHHTTHHH CS
                          KdpA 486 lpiiavlaiAgslaakkkvpesagtlktdtplFvvllvgvilivgaLtFlPalaLGPia 544
                                   l + ++l+iA+s++ kk   +   +++t++ +F++ll+  +li+g L+++P+++LGP++
  gi|13541330|ref|NP_111018.1| 513 LLMGFQLVIAQSFSIKKAKVQYLRSIDTSNSVFALLLISAMLIIGLLSYFPIIVLGPLL 571
                                   *********************************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (585 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       697  (0.0388756); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.47
# Mc/sec: 3731.15
//
Query:       gi|13541331|ref|NP_111019.1|  [L=668]
Description: potassium-transporting ATPase subunit B [Thermoplasma volcanium GSS1]
Scores for 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  123.9   4.1      5e-36  123.9   4.1    3.2  3  E1-E2_ATPase     E1-E2 ATPase
    1.3e-26   94.3   0.4    1.9e-26   93.6   0.4    1.3  1  Hydrolase        haloacid dehalogenase-like hydrolase
    3.9e-07   30.1   8.3    1.8e-05   24.6   2.7    2.8  3  Hydrolase_3      haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.033   14.6   0.0       0.13   12.6   0.0    2.0  1  HAD              haloacid dehalogenase-like hydrolase
      0.034   14.6   0.0       0.11   13.0   0.0    1.9  1  CBS              CBS domain


Domain annotation for each model (and alignments):
>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.7     0.051   1.8e+02     121     156 ..      32      70 ..      21      91 .. 0.68
   2 !  123.9   4.1   1.4e-39     5e-36       6     179 ..     103     274 ..      99     276 .. 0.96
   3 ?    0.7   1.9     0.088   3.2e+02     115     164 ..     567     622 ..     557     631 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.051
                                   HHHHHHHHHHHHHHHS-STTTSSTT...HHHHHHHHHHH CS
                  E1-E2_ATPase 121 vlvpvvlliallvflialllgksla...eallralallv 156
                                   +l+ v+l+++++++++  + g + +   ++++ a+++l+
  gi|13541331|ref|NP_111019.1|  32 FLTEVSLFVSIFIYIFPSFFGVPYTgtyRSFYVAVVVLL 70 
                                   666777777777777777777666665555555555554 PP

  == domain 2  score: 123.9 bits;  conditional E-value: 1.4e-39
                                   EEEEE-TTS-EEEEGGG--TTSEEEEETT-B--SEEEEEEE-SEEE-TTTS---S-EE-G-TTEE-TT-EEEE-EEEEEEE CS
                  E1-E2_ATPase   6 takvirdgteeeidakelvpGDivllkagdrvpaDgrivegsaevdesaLTGEslpvekekgdmvfsGtvvvsgeakavVt 86 
                                    a+v +dg++++++++el+ +Di+++ + ++vp+Dg+++egs  vdes +TGEs++v k  gd+v+++t  v +++k+++t
  gi|13541331|ref|NP_111019.1| 103 IAHVQKDGNIVDVRSNELKKNDIIIIYKDEIVPIDGEVIEGSGYVDESNVTGESRAVMKVIGDTVTGSTRLVTDKLKIRAT 183
                                   68999**************************************************************************** PP

                                   E-TTTSTTTTTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTTHHHHHHHHHHHHHS-TTHHHHH CS
                  E1-E2_ATPase  87 atgedtelgkiarlveeakskktplqkkldklgkvlvpvvlliallvflialllgkslaeallralallvaaiPcaLplav 167
                                   a   +t+++k+++lve+++++ktp +  l+ + + l+++ l+i++ +f+i  + g++    ++  ++ll+a iP  +++++
  gi|13541331|ref|NP_111019.1| 184 ADPGSTFIDKMIELVEKSTREKTPNEISLTVFLSGLTLIFLVITASIFAISHYFGRT--ANIVMLIVLLIALIPTTIGALL 262
                                   ***************************************************998888..589999**************** PP

                                   HHHHHHHHHHHH CS
                  E1-E2_ATPase 168 plalalgarrla 179
                                   p + ++++++ +
  gi|13541331|ref|NP_111019.1| 263 PAIGIAAINKVS 274
                                   ******999875 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.088
                                   HHHHHHH..HHHHHHHHHHHHHHS-STTTSSTT....HHHHHHHHHHHHHS-TTHH CS
                  E1-E2_ATPase 115 ldklgkv..lvpvvlliallvflialllgksla....eallralallvaaiPcaLp 164
                                   ++ ++k+  ++p+++ ++  + l+++l   +++     al++   ++v  iP aL+
  gi|13541331|ref|NP_111019.1| 567 ANDISKYfvIIPAIFYMFPSLSLVNILDLTDPIvavtSALIFNTIIIVFLIPLALG 622
                                   56666663355678888888888888888888788988888889999999999997 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.6   0.4   5.4e-30   1.9e-26       1     210 []     292     516 ..     292     516 .. 0.77

  Alignments for each domain:
  == domain 1  score: 93.6 bits;  conditional E-value: 5.4e-30
                                   SSEEEEESBTTTBCHHHHHHHHHHHH...CHHHHHHHHHH...HHCHHHHHHHHHHHHH.............HHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxx...xxxxxxxxxxxxxxxx.............xxxxxxxxx RF
                     Hydrolase   1 iktvvfDkdGTLttgepsvedvivsa...alalaaaletg...sehpigkalvaaakar.............sgaltgfat 62 
                                   i+t+++Dk+GT+t ge+  +++++     +++ a+  +++    ++  g  + + ak+                       
  gi|13541331|ref|NP_111019.1| 292 IDTIILDKTGTITIGERKAVKFYPNKgisDVEFAKLAAMSsyyDQTKEGLSIFELAKKQgaeiskddlkgyeF-------- 364
                                   79************************77755555555555668666666666555555544444223333222........ PP

                                   ETTTE................HHHHTHHHHHHHH..HCHHHHHHHHHHHHHHCHHHHHH..TTHHHHHHHHHHTHHBHTTH CS
                                   xxxxx................xxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxx RF
                     Hydrolase  63 figrg................ayaigkpewltal..dippdlgaaigsaqsqgrtvall..qaralavftiadplkvkpea 123
                                                        ++ +g+ + l++      +  +a   +   +g t++ +  +++  +v++++d   +kp++
  gi|13541331|ref|NP_111019.1| 365 ----IpfssetkfsgiqspsdTVIKGSLKALKEKfqVADEFIEALCKEISMRGGTAIPVvhNGKFAGVIELQDL--IKPGI 439
                                   ....0222344555666999999999999999997756666666666666666666555669************..***** PP

                                   HHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTTGGGESEEEEHHCESSTTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hydrolase 124 aeavasLkaagievvlltgdnpetaeraanqlGddyfdaviasdietvakpspegkvaaireLqgkpeevamVGDgvnDaa 204
                                   +e + ++k + i++v++tgd++ ta+ +  q+G          ++e +a  +p +k  ++ + ++  + vamVGDg nDa+
  gi|13541331|ref|NP_111019.1| 440 KERISEIKNMDIKTVMCTGDDEVTAQYISAQAG----------IDEYIANSKPVDKYNVVIREKEGQRMVAMVGDGTNDAP 510
                                   *********************************..........5666******9999888888766668************ PP

                                   HHHHTT CS
                                   xxxxxx RF
                     Hydrolase 205 alaaAg 210
                                   ala+A+
  gi|13541331|ref|NP_111019.1| 511 ALAKAD 516
                                   ****98 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       1.4   4.9e+03       4      32 ..     291     319 ..     289     320 .. 0.89
   2 !    7.5   0.0   0.00085         3      16      60 ..     435     479 ..     429     490 .. 0.91
   3 !   24.6   2.7     5e-09   1.8e-05     204     242 ..     497     535 ..     491     542 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.4
                                   EIIIIIS-TTS---HHHHHHHHHHHHTTS CS
                   Hydrolase_3   4 DlDGTLlnsdkkisektkeaikklkekgi 32 
                                   D+D  +l+++++i+   ++a+k + +kgi
  gi|13541331|ref|NP_111019.1| 291 DIDTIILDKTGTITIGERKAVKFYPNKGI 319
                                   999999********999999999999987 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.00085
                                   --HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCCSEEEE CS
                   Hydrolase_3  16 isektkeaikklkekgikvviATGRslravlpvleelgldlpvia 60 
                                   i++ +ke i ++k+ +ik v +TG   ++++++  + g+d ++ +
  gi|13541331|ref|NP_111019.1| 435 IKPGIKERISEIKNMDIKTVMCTGDDEVTAQYISAQAGIDEYIAN 479
                                   678899**********************************88865 PP

  == domain 3  score: 24.6 bits;  conditional E-value: 5e-09
                                   GGEEEEESSGGGHHHHHHSSEEEEETTS-HHHHHHSSEE CS
                   Hydrolase_3 204 eeviafGDgeNDieMLeaaglgvAmgnaseevkkaAdyv 242
                                    +v+ +GDg ND + L +a++g Am+n+++ +k+aA+++
  gi|13541331|ref|NP_111019.1| 497 RMVAMVGDGTNDAPALAKADVGLAMNNGTQAAKEAANMI 535
                                   67999*******************************998 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   3.7e-05      0.13      84     187 ..     433     512 ..     420     513 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.7e-05
                           HAD  84 klldpgalellaahraaGdrvvvvSgglrplvepllaelgadevlatelevddrltgelglegkpvrgegkvaalrewlaa 164
                                    l++pg++e++++ +   +++v+++g  +  ++ + a+ g+de +a+        ++ +  ++ ++r+    ++ ++    
  gi|13541331|ref|NP_111019.1| 433 DLIKPGIKERISEIKNMDIKTVMCTGDDEVTAQYISAQAGIDEYIAN--------SKPVDKYNVVIRE----KEGQR---- 497
                                   4789********9999999*********************9999999........4554445555555....44444.... PP

                           HAD 165 egegidleevvay.GDspsDlpll 187
                                            +va  GD+ +D p+l
  gi|13541331|ref|NP_111019.1| 498 ---------MVAMvGDGTNDAPAL 512
                                   .........444448888887776 PP

>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0     3e-05      0.11      23      53 ..     408     436 ..     397     436 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3e-05
                                   HH.HHHHTSSEEEEEETTTBEEEEEEHHHHHH CS
                           CBS  23 el.mrekgvsrlPVVdedgklvGivtlrDllr 53 
                                   e+ m + g  ++PVV  +gk+ G++ l Dl++
  gi|13541331|ref|NP_111019.1| 408 EIsM-RGGT-AIPVV-HNGKFAGVIELQDLIK 436
                                   4445.6665.*****.8*************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (668 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1212  (0.0676); 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:                        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: 0.71u 0.30s 00:00:01.01 Elapsed: 00:00:00.47
# Mc/sec: 4252.80
//
Query:       gi|13541332|ref|NP_111020.1|  [L=209]
Description: potassium-transporting ATPase subunit C [Thermoplasma volcanium GSS1]
Scores for complete 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-44  151.4   0.0    2.6e-44  151.2   0.0    1.0  1  KdpC      K+-transporting ATPase, c chain
  ------ inclusion threshold ------
       0.16   12.0   1.1       0.43   10.6   1.1    1.7  1  LisH      LisH


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 !  151.2   0.0   2.9e-48   2.6e-44       3     180 ..       7     191 ..       5     193 .. 0.96

  Alignments for each domain:
  == domain 1  score: 151.2 bits;  conditional E-value: 2.9e-48
                                   HHHHHHHHHHHHHHTHHHHHHHHHHHHH-HHHHTT-EEE.ETEEEEETTT------SSS--------ST-TTT-------S CS
                          KdpC   3 kalrlllvltvllgliYplavtgiaqllfpeqAnGslieadgkvvGseligqeftsdkYfhgRpsavnynaaasggsnlgp 83 
                                   kal++ lv++ +lg+++p+++ +i++ ++p+q++G+ i+ dgkv+Gs l++++f+s+ +fh+Rpsa++yn + sg+  ++ 
  gi|13541332|ref|NP_111020.1|   7 KALVISLVFLFVLGFLFPTVTSLITEKALPNQSEGQPIKIDGKVYGSYLLAEAFNSSIFFHPRPSAIGYNLSESGSYPYSL 87 
                                   799****************************************************************************** PP

                                   S-HHHHHHHHHHHHHHHHH-TTS..-SB-HHHHS-BSSS---EE-HHHHHHTHHHHHHH........HT--HHHHHHHHHH CS
                          KdpC  84 snpellerveervaalraenpekkkeevPadlvtaSgSGLDPhIspeaAelQvarvaka........rglseeeveklvae 156
                                    npe+l+ +e+ ++++ ++np  +++++P  ++  S+SGLDP+I ++ A +Q++r++ a         +l e+ +++lv++
  gi|13541332|ref|NP_111020.1|  88 GNPEVLNLTEKYLDEFLKDNPGINASQIPYAMLSYSASGLDPNIPLQGALIQIPRISIAlhsitnnsVSLWENYLNDLVNK 168
                                   *********************************************************99888888777888999******* PP

                                   TEE--SSTTT---EEEHHHHHHHH CS
                          KdpC 157 ntegrllgilGeprVnVlklNlaL 180
                                   +t+++ + ++G+ +Vn++ lN+++
  gi|13541332|ref|NP_111020.1| 169 YTTQN-FPFFGSYYVNIMYLNVNI 191
                                   *9985.79*************975 PP

>> LisH  LisH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   1.1   4.8e-05      0.43       3      19 ..     187     203 ..     187     204 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 4.8e-05
                                   HHHHHHHHHHHCT-HHH CS
                          LisH   3 LNrLIydYLvkeGyeet 19 
                                   LN  I++YL+++Gy ++
  gi|13541332|ref|NP_111020.1| 187 LNVNILEYLMNNGYIKS 203
                                   7888**********765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       706  (0.0393775); expected 358.6 (0.02)
Passed bias filter:                      528  (0.0294495); 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 0.34s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1284.09
//
Query:       gi|13541333|ref|NP_111021.1|  [L=272]
Description: nucleotide-binding protein (UspA-related) [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.6e-11   43.1   2.5    3.4e-09   37.3   0.5    3.3  3  Usp       Universal stress protein family


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.3   0.5   1.9e-13   3.4e-09       4     140 ..      14     137 ..      11     138 .. 0.89
   2 ?   -1.6   0.0      0.19   3.5e+03       2      35 ..     146     179 ..     145     189 .. 0.85
   3 ?    2.0   0.0     0.016   2.8e+02      92     130 ..     223     260 ..     208     269 .. 0.77

  Alignments for each domain:
  == domain 1  score: 37.3 bits;  conditional E-value: 1.9e-13
                                   EEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCTTCEEEE CS
                           Usp   4 rIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaeaggvkvev 84 
                                   +I V++ +  +s+++l+ A +la  +g+e+ +++v d   + ++ +    +  + +e  ++              +++   
  gi|13541333|ref|NP_111021.1|  14 KIAVPMAEGRSSRRVLHIAMALADVFGSEISAVTVRDQAKDIMWTNKINVVTNAYKEGLAR-------------NIKIIPK 81 
                                   899********************************99998888887666555555555443.............5799*** PP

                                   EEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEE CS
                           Usp  85 vveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvV 140
                                   ++++ d++ +++ + +++++dl++++s +rs + r+  G vs++v+++a+ p+ +V
  gi|13541333|ref|NP_111021.1|  82 IITSSDVKSALINEINRHSYDLVIIASEKRSIITRITSGPVSNQVIKKAESPTALV 137
                                   ****************************************************9988 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.19
                                   -SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEE CS
                           Usp   2 ykrIlVavDgseeskkAlewAlelakargaelil 35 
                                   yk I +++ ++ +++ A+ ++l l k  ga+ +l
  gi|13541333|ref|NP_111021.1| 146 YKSIYIPLSETINTRSAVAFGLTLKKVMGAKAVL 179
                                   8899999999999999999999999988888766 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.016
                                   HHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHH CS
                           Usp  92 aeeilevaeeedadliVvGsrgrsglsrlllGSvseyvl 130
                                   +e+ l  a + +ad +V+G +  +   ++ + S  + ++
  gi|13541333|ref|NP_111021.1| 223 KESVLNGAASTGADAVVLGVKA-GENGKIRVNSIIKDLM 260
                                   66777779999********998.6666666777666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.51
# Mc/sec: 1604.28
//
Query:       gi|13541334|ref|NP_111022.1|  [L=164]
Description: hypothetical protein TVN0503 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.21s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1261.39
//
Query:       gi|13541335|ref|NP_111023.1|  [L=329]
Description: kinase related to galactokinase and mevalonate kinase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.1e-08   32.7   1.9    1.4e-07   31.8   0.0    2.2  2  GHMP_kinases_C  GHMP kinases C terminal
    1.6e-07   31.5   0.0    3.5e-07   30.4   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 ?   -1.2   0.7       0.3   2.7e+03      54      64 ..      97     107 ..      69     120 .. 0.73
   2 !   31.8   0.0   1.5e-11   1.4e-07       1      80 [.     229     308 ..     229     311 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.3
                GHMP_kinases_C  54 sGaGgGptvfa 64 
                                   +G+G+G++ +a
  gi|13541335|ref|NP_111023.1|  97 PGSGLGSSSAA 107
                                   57888877666 PP

  == domain 2  score: 31.8 bits;  conditional E-value: 1.5e-11
                GHMP_kinases_C   1 llealergdlellgellnlsqrselkavvgilppeleellealselGalgaklsGaGgGptvfalfkdkdeaeqvaral.r 80 
                                   l++a+  +d++++ +++n +++ +++   +  ++++++++e+++++Ga +a+l G G+ +++ +l   + + ++++ra+ +
  gi|13541335|ref|NP_111023.1| 229 LRKAVIDNDYSEFDQAINYGWEIKKTLGQKTTNRRVDTIIESALKNGASAARLMGGGSQGFILVLS-RPGKINELQRAMmN 308
                                   5789999****************5555**************************************9.99999999999955 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 !   30.4   0.0   3.9e-11   3.5e-07       1      66 []      88     156 ..      88     156 .. 0.85

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 3.9e-11
                                   EEEEEESSHTTSSSCHHHHHHHHHHHHHHHHTTEH..HHH.HHHHHHHH.HHHHHHHHHSHHHHHHHHSS CS
                GHMP_kinases_N   1 divikseiPvgaGLGSSAAlavalvaAllallgls..lee.aklaleae.rlaqggngsggDvaasvyGg 66 
                                   +i +++++P+g+GLGSS+A+  alv         +  +e  a+ ++++e ++++  + + +D +a+++Gg
  gi|13541335|ref|NP_111023.1|  88 RIIMSGDVPPGSGLGSSSAAMSALVNLTSIIRKTKynWESiARESYNIEkNYFH-IVLGLQDPYAIALGG 156
                                   58899**********************877776554354469999999977778.888999999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (329 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       654  (0.0364772); expected 358.6 (0.02)
Passed bias filter:                      540  (0.0301188); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.47
# Mc/sec: 2097.19
//
Query:       gi|13541336|ref|NP_111024.1|  [L=291]
Description: nucleoside-diphosphate sugar epimerase [Thermoplasma volcanium GSS1]
Scores for complete 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   53.6   0.0    3.1e-14   53.0   0.0    1.2  1  Epimerase      NAD dependent epimerase/dehydratase family
    3.6e-14   52.3   0.0    5.5e-14   51.7   0.0    1.3  1  DUF1731        Domain of unknown function (DUF1731)
      2e-06   27.5   0.0     0.0023   17.4   0.0    2.5  3  GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase


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 !   53.0   0.0   5.2e-18   3.1e-14       1     228 [.       3     204 ..       3     213 .. 0.85

  Alignments for each domain:
  == domain 1  score: 53.0 bits;  conditional E-value: 5.2e-18
                                   EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE-.-S.---HHH CS
                     Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfkeeqpdavihl.Aa.vggvaa 79 
                                   +++ G+tG+iG+a+   l    ++   ++r  ++++          ++ +   ++++++ k  ++d+vi+l +  +++ ++
  gi|13541336|ref|NP_111024.1|   3 VVIFGGTGLIGRAIYSSLP---HDFYIVSRSAKGQE----G-----QAHIIGLDEIDKI-K--ECDVVINLsGYsIASKRW 68 
                                   6899************998...56677777733332....2.....5566666677775.3..69******66699***** PP

                                   HHHSHHHHHHHHTHHHHHHHHHHHHHTCT..EEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHHHHHHHHHHHH CS
                     Epimerase  80 ssedpadfieknlqgtlnlleaarkagvk..rllflsSsevYGkdaeqpkeettltgplkpnspYaaaKlageklveayaa 158
                                   + + +++++++ +  t+ +++ +r  + k   +l  s    YG +++   +e t+++p+   s +  a la  +  ea++a
  gi|13541336|ref|NP_111024.1|  69 NRKVKEEIVRSRIDTTRLVVNFIRNLEKKpsAFLSGSAIGFYGHNTN---KELTEEDPF--GSGFL-ADLARSWEEEAMQA 143
                                   ************************98777558888888899**8888...677767788..56665.99************ PP

                                   HHT-EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHHHHHHHHH CS
                     Epimerase 159 qyglnaiilrlfnlyGprngegevsrvipalirkilegkqevtllgdgtalRdflyveDvaeaillvleh 228
                                   ++ ++++ lr  n  +p        ++++ali+   + k +v ++gdg++   +++  D+++a+ +v+e+
  gi|13541336|ref|NP_111024.1| 144 DGICRTVLLRTANFLSPK------GGFLSALINP--KSK-NVMYFGDGRQPVSWMHYADYVKAVEFVIEN 204
                                   *****************9......*********7..556.9****************************9 PP

>> DUF1731  Domain of unknown function (DUF1731)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.7   0.0   9.3e-18   5.5e-14       1      45 [.     239     284 ..     239     286 .. 0.96

  Alignments for each domain:
  == domain 1  score: 51.7 bits;  conditional E-value: 9.3e-18
                       DUF1731   1 vPafalklllG.emaellLegqrVlPkrLleaGFqFrypdleeALr 45 
                                   +P+f+ k++lG em + l++gq+V+Pk+L +aGF+F +pd+++A  
  gi|13541336|ref|NP_111024.1| 239 IPEFLGKIALGsEMYRELMSGQKVIPKKLIQAGFKFDFPDINTAAS 284
                                   7*****************************************9976 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 ?   -1.8   0.1      0.27   1.6e+03       2      20 ..       5      23 ..       4      35 .. 0.78
   2 !    7.2   0.0   0.00048       2.9      74     147 ..      50     124 ..      42     128 .. 0.85
   3 !   17.4   0.0   3.8e-07    0.0023     204     271 ..     169     237 ..     151     257 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.27
                                  EETTTSHHHHHHHHHHHHC CS
                 GDP_Man_Dehyd  2 iTGiaGfiGsylaelLlek 20
                                  i G++G iG  +   L + 
  gi|13541336|ref|NP_111024.1|  5 IFGGTGLIGRAIYSSLPHD 23
                                  89*******9988777655 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.00048
                                   HT-SEEEE--S---HHHHTTS..HHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB-TTS-- CS
                 GDP_Man_Dehyd  74 vqpdevynLAAqshVdvsfek..PeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpqtEttpf 147
                                    ++d v+nL + s  ++ ++    e+ ++  +  t  +++ ir+l+  k   f+  S    YG+ ++   tE+ pf
  gi|13541336|ref|NP_111024.1|  50 KECDVVINLSGYSIASKRWNRkvKEEIVRSRIDTTRLVVNFIRNLEK-KPSAFLSGSAIGFYGHNTNKELTEEDPF 124
                                   47899*********9999976224778888888888889*****985.6789**********************99 PP

  == domain 3  score: 17.4 bits;  conditional E-value: 3.8e-07
                                   HHTTS-C-EECTTTT-EEEEEEHHHHHHHHHHHHHCSS.---EEE-TT-EEECHHCHHCCHHCCCHHHH CS
                 GDP_Man_Dehyd 204 ialgkqevlylGnldakRdwghvkDyveamwlmlqqdk.pedyviatgethsvrefvelaflelgktie 271
                                   i+ + ++v+y+G++++  +w h  Dyv+a+  ++++ + +  +++++ + ++ +ef+e+  ++lg +i 
  gi|13541336|ref|NP_111024.1| 169 INPKSKNVMYFGDGRQPVSWMHYADYVKAVEFVIENASiAGPVNMSSPQPVTFKEFAEAFSKSLGSHIR 237
                                   66677899**************************9966267888999999*******998888887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       366  (0.0204139); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); 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 0.26s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1996.23
//
Query:       gi|13541337|ref|NP_111025.1|  [L=312]
Description: tRNA-modifying enzyme [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.1e-21   75.1   0.0    1.6e-20   74.2   0.0    1.5  1  Radical_SAM   Radical SAM superfamily
    5.2e-20   71.6   0.1      2e-19   69.7   0.0    2.0  2  Wyosine_form  Wyosine base formation
     0.0031   17.8   0.0     0.0059   16.9   0.0    1.5  1  Fer4_12       4Fe-4S single cluster domain
  ------ inclusion threshold ------
      0.031   14.6   0.0      0.045   14.0   0.0    1.3  1  Hydrolase     haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.2   0.0   3.5e-24   1.6e-20       3     166 ..      58     236 ..      56     236 .. 0.93

  Alignments for each domain:
  == domain 1  score: 74.2 bits;  conditional E-value: 3.5e-24
                                   EESEESS--TTTSCCTT.....HHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEE.................SSTGGGS CS
                                   xxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxx.................xxxxxxx RF
                   Radical_SAM   3 vtrgCnlrCsfCarpet.....vrregrgrslsveeileevkelkaekg.vkevilg.................ggeplly 60 
                                    +++C+ +C fC+r +       ++e++++++  e+i++++k ++   g +++  ++                  gep+ly
  gi|13541337|ref|NP_111025.1|  58 ALNACTENCAFCWRFQGfdsmhISDEDDPEFILEESIKQHLKLIS---GfKGNPKVSkeiweeathpkhmaislTGEPTLY 135
                                   6799****************************************8...55888888888888999999999999******* PP

                                   TTHHHHHHHHHHTCCCTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHH...HHHHHHTCTSHHHHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  61 pdfvellerlaklavpgiritvetngtlpdeeklerllelgvdrvslgleaadde...kvlklmnrghtfeevlealeklr 138
                                   +++ el+++++k+   gi+++++tngtl  + +le+l++l+ +++++++ a+++    + l++   g+++e + ++le+l 
  gi|13541337|ref|NP_111025.1| 136 SRLGELIAAAKKR---GISTFLVTNGTL--PMVLEKLDPLP-TQLYVTVAAPNKQifnQLLQPS-IGNGWENLNKTLELLP 209
                                   ************8...************..59*********.*************777666666.99************** PP

                                   HTTSETEEEEEEEBTTTSHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM 139 eagikrvvdrivglpGendeeleellel 166
                                   +++ +  v+r+++++ +n+  +ee+++l
  gi|13541337|ref|NP_111025.1| 210 SLNTR-KVIRHTLVRDVNMPYVEEYAKL 236
                                   **999.8****************99875 PP

>> Wyosine_form  Wyosine base formation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.91   4.1e+03      26      34 ..     226     234 ..     223     236 .. 0.83
   2 !   69.7   0.0   4.5e-23     2e-19       1      63 []     239     300 ..     239     300 .. 0.98

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.91
                                   ----HHHHH CS
                  Wyosine_form  26 nvPwheeva 34 
                                   n+P+ ee a
  gi|13541337|ref|NP_111025.1| 226 NMPYVEEYA 234
                                   9****9965 PP

  == domain 2  score: 69.7 bits;  conditional E-value: 4.5e-23
                                   HHT-SEEEEEE------------------HHHHHHHHHHHHTSSS.EEEEEEETTTTEEEEEE CS
                  Wyosine_form   1 kaepdFvEvKaytyvGssrsrLtmknvPwheevadfakrlegsaedYellaehrhSrvvllar 63 
                                   k++pdF+E K+y +vG+s s+L+ +n+P h+e+++f++ l+++++ Y+++a++ +Srv+++a+
  gi|13541337|ref|NP_111025.1| 239 KGDPDFIEAKGYVHVGYSISKLSTNNMPPHSEILEFSHSLSEKLG-YQFVADRVESRVAMIAK 300
                                   69*******************************************.***************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 !   16.9   0.0   1.3e-06    0.0059      13     115 ..      60     178 ..      49     188 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.3e-06
                       Fer4_12  13 sgCnlsCkgCfnketwsfk.......................sgkeftkelleeiiedlkkesiegltllGGEPllpenae 70 
                                   + C+ +C++C   +  +                         sg + + ++ +ei+e++ +++   ++l+ GEP l   ++
  gi|13541337|ref|NP_111025.1|  60 NACTENCAFCWRFQGFDSMhisdeddpefileesikqhlkliSGFKGNPKVSKEIWEEATHPKHMAISLT-GEPTL---YS 136
                                   679999999986666533356666667777777777777777999999**********************.5****...99 PP

                       Fer4_12  71 allelvkevkeekpekdiwlytgytleelskkekeellkeidvlv 115
                                    l el+   k++++  + ++++g+    l+  + ++l  ++ v+v
  gi|13541337|ref|NP_111025.1| 137 RLGELIAAAKKRGI-STFLVTNGTLPMVLE--KLDPLPTQLYVTV 178
                                   9*************.488888887655554..3566666666666 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   9.9e-06     0.045     111     184 ..     126     191 ..      40     194 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 9.9e-06
                                   HHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTTGGGESEEEEHHCESSTTTSHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hydrolase 111 ftiadplkvkpeaaeavasLkaagievvlltgdnpetaeraanqlGddyfdaviasdietvakpspegkvaair 184
                                   + +  + +++  + e++a+ k++gi ++l+t++   ++ + ++ l         ++  +tva p++++++++++
  gi|13541337|ref|NP_111025.1| 126 ISLTGEPTLYSRLGELIAAAKKRGISTFLVTNGTLPMVLEKLDPLP--------TQLYVTVAAPNKQIFNQLLQ 191
                                   5556667899999*************************99999988........66777899999999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); 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:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.43
# Mc/sec: 2200.98
//
Query:       gi|13541338|ref|NP_111026.1|  [L=544]
Description: chaperonin GroEL [Thermoplasma volcanium GSS1]
Scores for complete 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-177  591.0  17.8   1.8e-177  590.9  17.8    1.0  1  Cpn60_TCP1  TCP-1/cpn60 chaperonin family
  ------ inclusion threshold ------
      0.078   12.7   3.4       0.26   11.0   0.1    2.5  2  Phage_tube  Phage tail tube protein FII


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 !  590.9  17.8  2.1e-181  1.8e-177       1     490 [.      33     523 ..      33     524 .. 0.98

  Alignments for each domain:
  == domain 1  score: 590.9 bits;  conditional E-value: 2.1e-181
                                   HHHHHHCCSSTTXXEEEEEETTSEEEEEXSHHHHHHCSXXXSHHHHHHHHHHHHCCCCCTTCHHHHHHHHHHHHHHHHHHH CS
                    Cpn60_TCP1   1 ladivkttlGPkGmdKmlvnkggkvvvTnDGatilkeleiehPaakllveaaesqdeevGDGTttvviLageLleeaekli 81 
                                   +++ v+++lGP+GmdKmlv++ g++v+TnDG+tilke+++ehPaak++ve++++qd+ vGDGTtt+vi+ag Ll++ae li
  gi|13541338|ref|NP_111026.1|  33 ISNSVRSSLGPRGMDKMLVDSLGDIVITNDGVTILKEMDVEHPAAKMMVEVSKTQDSFVGDGTTTAVIIAGGLLQQAEALI 113
                                   7899***************************************************************************** PP

                                   HCTXXHHHHHHHHHHHHHHHHHHHHHHXEEBXSCSTT.HHHHHHHHHHCTTSSXXSTHHHHHHHHHHHHHCHCCCS...EE CS
                    Cpn60_TCP1  82 aagvhpttiiegyekalekaleaLkeiaveisseekdreeLlkvartslsskltskeaeelsklvvdAvklieene...ke 159
                                   +++vhpt+i egy++a e+a ++++ei+ +i   ++++e L+k+a+tsl+sk  s  +++l+++  +Avk++ e +   + 
  gi|13541338|ref|NP_111026.1| 114 NQNVHPTVISEGYRMASEEAKRIIDEISTKI--GKDEKELLIKLAQTSLNSKSASVAKDKLAEISYEAVKSVAELRdgkYY 192
                                   ***************************5555..56689*******************************65555555999* PP

                                   CSCCCEECCCCEECECTTSEEESEEEESS--SSTTSSCEEECEEEEEESS-BS--HHCCHHHCCCCSCCHHHHHHHHHHHH CS
                    Cpn60_TCP1 160 ldlgrikvvkieggsledselveGlvldkgvlspdmpkklenakvllldvsLeiektetkttvvlsdaeeleklekaeekq 240
                                   +d+++i+vvk++gg ++d+ l++G+++dk+ ++p mp  ++nak++lld +Lei+k+e +t+++++d++ ++k++ +ee++
  gi|13541338|ref|NP_111026.1| 193 VDFDNIQVVKKQGGAIDDTALINGIIVDKEKVHPGMPDVVKNAKIALLDAPLEIKKPEFDTNLRIEDPSMIQKFLAQEENM 273
                                   ********************************************************************************* PP

                                   HHHHHHHHHHTTECEEEESS-B-HHHHHHHHHCT-EEE-S--HHHHHHHHHHHT--EBSCGGGGGCGC-EEEEEEEECCET CS
                    Cpn60_TCP1 241 leellekiiksgvnvvvcqkgiddlalhflakngilalrrvkkkdlerlakatGatavssledltpeelGtakkveeekig 321
                                   l+e++eki++ g+nvv++qkgidd+a+h+l k+gi a+rrvkk+d+++lakatGat+vs++++++ ++lG+a++ve+ k+g
  gi|13541338|ref|NP_111026.1| 274 LREMVEKIKSVGANVVITQKGIDDMAQHYLSKEGIYAVRRVKKSDMDKLAKATGATVVSTIDEISASDLGSADRVEQVKVG 354
                                   ********************************************************************************* PP

                                   TCCEEEEECESSSSXEEEEEEESTCCCHHHHHHHHHHHHHHHHHHHHHHEEEETTTCHHHHHHHHHHCCCCTSXCCHHHHH CS
                    Cpn60_TCP1 322 sekttiieevksgkiatillrgatdtvldeieraiedAlnvvknaiedekvvpGGGatelelakklkeyaksvsgeeqlai 402
                                   ++++t+++++k++k++++l+rg t++v+de+er+i d+l+vv++a+ed+ + +GGGat  e+a +l++ya+++ g++qlai
  gi|13541338|ref|NP_111026.1| 355 DDYMTFVTGCKNPKAVSVLVRGETEHVVDEMERSITDSLHVVASALEDGAYTAGGGATAAEIAVRLRSYAQKIGGRQQLAI 435
                                   ********************************************************************************* PP

                                   HHHHHHHTHHHHHHHHHCTSXHHHHHHHHHHHHHTTXTTEEEETTTTCEEECCCCTXEEEHHHHHHHHHHHHHHHHHHHCE CS
                    Cpn60_TCP1 403 eafakALevipktLaeNaGldpievlaklraahnkgekelgidvesgeiidlveagvvDplkvkrqalksAteaastiLri 483
                                   e+fa+A+e++p++LaeNaGldpi+++ klra+h+kg+k +g++v sgei+d+v++gv++p++v +qa++sAteaa +iLri
  gi|13541338|ref|NP_111026.1| 436 EKFADAIEEVPRALAENAGLDPIDIILKLRAEHAKGNKYAGVNVFSGEIEDMVNNGVIEPIRVGKQAIESATEAAIMILRI 516
                                   ********************************************************************************* PP

                                   EEEEXXX CS
                    Cpn60_TCP1 484 deiikak 490
                                   d++i +k
  gi|13541338|ref|NP_111026.1| 517 DDVIATK 523
                                   ****987 PP

>> Phage_tube  Phage tail tube protein FII
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.6     0.021   1.9e+02      98     154 ..     149     206 ..      53     209 .. 0.70
   2 ?   11.0   0.1   2.9e-05      0.26      74     147 ..     365     439 ..     347     445 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.021
                    Phage_tube  98 vevvvrgrvkeidlGkakagektetkvtla.vtyykltvdGkelleiDvlnmiykvnG 154
                                    e  ++   ++++  +a  +++  ++++++ v+++ +  dGk  +++D ++ + k +G
  gi|13541338|ref|NP_111026.1| 149 KELLIKLAQTSLNSKSASVAKDKLAEISYEaVKSVAELRDGKYYVDFDNIQVVKKQGG 206
                                   455556666777777777777777888887799999999*********9999999888 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 2.9e-05
                    Phage_tube  74 akgkavqlrfrgalqredtaeekavevvvrgrvkeidlGkaka.gektetkvtlavtyykltvdGkelleiDvln 147
                                   +++kav++ +rg+ ++  ++ e++++  +++  + ++ G + a g  t +++++ +++y + ++G++ l i +++
  gi|13541338|ref|NP_111026.1| 365 KNPKAVSVLVRGETEHVVDEMERSITDSLHVVASALEDGAYTAgGGATAAEIAVRLRSYAQKIGGRQQLAIEKFA 439
                                   6789999*********99999********************961578999*********************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (544 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       749  (0.0417759); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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 0.29s 00:00:00.83 Elapsed: 00:00:00.43
# Mc/sec: 3780.13
//
Query:       gi|13541339|ref|NP_111027.1|  [L=211]
Description: thiamine-phosphate pyrophosphorylase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.2e-49  167.2   0.0      3e-49  166.8   0.0    1.2  1  TMP-TENI   Thiamine monophosphate synthase
     0.0021   17.8   0.1     0.0073   16.1   0.0    1.9  2  QRPTase_C  Quinolinate phosphoribosyl transferase, C-terminal
     0.0026   17.6   0.2     0.0062   16.4   0.2    1.6  1  YqbF       YqbF, hypothetical protein domain
  ------ inclusion threshold ------
      0.023   15.4   0.3          5    7.9   0.1    3.1  3  PTS_IIB    PTS system, Lactose/Cellobiose specific IIB subuni


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 !  166.8   0.0   6.6e-53     3e-49       1     181 []       9     186 ..       9     186 .. 0.98

  Alignments for each domain:
  == domain 1  score: 166.8 bits;  conditional E-value: 6.6e-53
                      TMP-TENI   1 lylvtdskldkneellevveealkggvtlvqlRekeldarellelaeklaalcrkygvpliindrvdlalavgadgvHlgq 81 
                                   lylvt +     +e+ e + +a++ggv+++q+R+k+   +  l++a+kl  ++++yg+p++++d+ +la+++gadgvH+g 
  gi|13541339|ref|NP_111027.1|   9 LYLVTYDYYG--AEFYEKIIDAIEGGVDILQYRDKTNAYSVKLQVARKLTSIAADYGIPFFVDDDPKLAKEAGADGVHIGR 87 
                                   7999996666..9******************************************************************** PP

                      TMP-TENI  82 ddlpvaearellgpdliiGlSvhslee.aeeaealgadYigvGpifpTdtKkdaeplgleglkelaealeiPvvaiGGitl 161
                                   dd p++++r +++   +iG+S+++  e a eae++ga+Y+++G++f+TdtKkda   +++ l+++++ ++iP+++iGGi+l
  gi|13541339|ref|NP_111027.1|  88 DDPPIEQVRDVFN--GLIGVSTYGNLElATEAEKKGASYVAFGSFFHTDTKKDAGIYDIKILEKARHFVKIPIFVIGGINL 166
                                   ************5..9*******99999***************************************************** PP

                      TMP-TENI 162 envaevleagadgvavvsai 181
                                   e++ +   + +dg+avvsai
  gi|13541339|ref|NP_111027.1| 167 ETITKFCGYSIDGIAVVSAI 186
                                   *******************8 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 ?   -2.2   0.0      0.67     3e+03      88     111 ..      20      44 ..      19      59 .. 0.66
   2 !   16.1   0.0   1.6e-06    0.0073      89     162 ..     110     190 ..      92     194 .. 0.67

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.67
                                   SSHHHHHHHHHHT-SEEEE.ES--H CS
                     QRPTase_C  88 esleeleevleaeadiimL.Dnfsv 111
                                   e++e++  ++e ++di +  D+ ++
  gi|13541339|ref|NP_111027.1|  20 EFYEKIIDAIEGGVDILQYrDKTNA 44 
                                   5678888888888888764355544 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 1.6e-06
                                   SHHHHHHHHHHT-SEEEEES--HHHHHHHHHHHHHHSTT.......SEEEEESS--TTTHHHHHCTT-SEEEECHHCHTB- CS
                     QRPTase_C  89 sleeleevleaeadiimLDnfsveelkkaveelkeknkr.......vlievSGgvtlenveeyaksgvdvisvgalthsvk 162
                                   +le ++e+ + +a+ + +  f  +++kk + + + k  +       + i+v Gg++le++++++ + +d i+v +++  ++
  gi|13541339|ref|NP_111027.1| 110 NLELATEAEKKGASYVAFGSFFHTDTKKDAGIYDIKILEkarhfvkIPIFVIGGINLETITKFCGYSIDGIAVVSAILAAE 190
                                   445555555666777777777665555544332211111123345599***********************9998887665 PP

>> YqbF  YqbF, hypothetical protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.2   1.4e-06    0.0062       1      35 [.     119     153 ..     119     154 .. 0.95

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.4e-06
                                   SS-SEEEETTEEEEBT-EEEE-HHHHHHHHHSTTE CS
                          YqbF   1 ikGktYtalGhtFklgveedVekeiynYLqdnefF 35 
                                   +kG++Y+a+G  F  + ++d      ++L ++++F
  gi|13541339|ref|NP_111027.1| 119 KKGASYVAFGSFFHTDTKKDAGIYDIKILEKARHF 153
                                   59******************99999999******9 PP

>> PTS_IIB  PTS system, Lactose/Cellobiose specific IIB subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0     0.062   2.8e+02      14      58 ..      49      90 ..      44     112 .. 0.75
   2 ?    1.8   0.0     0.088     4e+02      37      76 ..     110     147 ..      93     171 .. 0.66
   3 ?    7.9   0.1    0.0011         5      11      30 ..     183     204 ..     179     210 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.062
                                  HHHHHHHHHHHHHCTEEEEETTEEGGGHHHHHHT-SEEEEEESSG CS
                       PTS_IIB 14 lmaaeklekaakelgieaegeagveleaeeiaddaDlvllapqvr 58
                                  l +a kl ++a + gi   ++  +  + +++a  aD v ++ + +
  gi|13541339|ref|NP_111027.1| 49 LQVARKLTSIAADYGIPFFVDDDP--KLAKEAG-ADGVHIGRDDP 90
                                  57899**********999999999..4444444.88888877655 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.088
                                   E.GGGHHHHHHT-SEEEEEESSGGCTHHHHTTSEEEEECTT CS
                       PTS_IIB  37 v.eleaeeiaddaDlvllapqvrvkdlarfagkpvavinik 76 
                                     el  e++++ a +v  +  +   d++++ag  ++ i+i 
  gi|13541339|ref|NP_111027.1| 110 NlELATEAEKKGASYVAFGSFFH-TDTKKDAG--IYDIKIL 147
                                   34556666667777777777666.47777777..5555543 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0011
                                   HHHHHHHHHHHHHHHHCT..EE CS
                       PTS_IIB  11 atSlmaaeklekaakelg..ie 30 
                                    + ++aae+++kaakel   +e
  gi|13541339|ref|NP_111027.1| 183 VSAILAAENVKKAAKELKekVE 204
                                   5789************995555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       911  (0.0508115); expected 358.6 (0.02)
Passed bias filter:                      775  (0.0432261); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 1431.82
//
Query:       gi|13541340|ref|NP_111028.1|  [L=351]
Description: hydrogenase maturation factor [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.3e-25   87.6   0.0    1.5e-24   86.9   0.0    1.3  1  AIRS_C    AIR synthase related protein, C-terminal domain
    7.7e-10   39.3   0.1    1.5e-09   38.4   0.1    1.4  1  AIRS      AIR synthase related protein, N-terminal domain


Domain annotation for each model (and alignments):
>> AIRS_C  AIR synthase related protein, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.9   0.0   1.7e-28   1.5e-24       1     150 [.     162     319 ..     162     323 .. 0.85

  Alignments for each domain:
  == domain 1  score: 86.9 bits;  conditional E-value: 1.7e-28
                                   STTEEEEEEETSSCTCCHHHHHHHCHHHCTSHTT...TSEHHHHHHHHHHHHHHHHHHHH..HTTECEEEE--TTHHHHHH CS
                        AIRS_C   1 kpGdvliltgslGlggagtslkrkileeegldds...avqlgdvlleptliyvkralaal..kglvkaahDvTgGGLlgal 76 
                                   +pGd  i+t++ G+ +a+ +l r   ++ + ++     +   +++++   ++++  ++++  ++ ++++hD T+GGLlga+
  gi|13541340|ref|NP_111028.1| 162 RPGDIMIMTKTAGIEAAS-LLTRIFPNHVKKNLGedkYRYGFELFRKLSTVDEAIQAIEFgtRKAITSMHDATEGGLLGAV 241
                                   79****************.88786666666555565333344555555556666666666********************* PP

                                   HHHHHTTTEEEEEECGTHHHHHHHH.....HHHHHHHCSTTTEEEEEEEHGGHHHHHHHHHHTTCCCEEEEEEEEESSS CS
                        AIRS_C  77 aemapasgvgaeidldkvpifdele.....splemllsensGrllvavppeeadavlaileeeglpeaavIGevtakee 150
                                    e+a+asg g+ id +++ + d ++     +++++l+s ++G ll++++pe ad++++ l++ g+ + +vIG++t k+e
  gi|13541340|ref|NP_111028.1| 242 YEVAEASGNGVSIDKEAIHVDDYVKeihslFGIDPLRSISEGTLLMTIDPEYADEFMKRLTKSGI-DSYVIGKMTTKDE 319
                                   ****************99999988888999***********************************.8********9986 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 !   38.4   0.1   1.7e-13   1.5e-09       5      92 ..      52     148 ..      38     150 .. 0.89

  Alignments for each domain:
  == domain 1  score: 38.4 bits;  conditional E-value: 1.7e-13
                                   EEEEEEEEE.EECCTCCCC...HHHHHHHHHHHHHHTTTEEEEEEEEEEEEC......HHHHHHHHHHHHHHHTT-EEEEE CS
                          AIRS   5 vvvttdshnrpvlvepvhf...iGakavavnlsDlaamGArPlalllslalp......wleevvrglaeaaeelgvplvgG 76 
                                   ++vttd    p++ +pv +    ++ a +  +sD+ + G  P ++++ l+lp      +++++ + ++e a ++++++++G
  gi|13541340|ref|NP_111028.1|  52 MAVTTD----PFYFDPVFGyedSAWFAYHILASDITTAGVYPEYMTVDLNLPisisneEIARMWKTVHEEAYKYKTSIITG 128
                                   4899**....*******99************************************************************** PP

                                   EEEEESS....EEEEEEEEE CS
                          AIRS  77 dtsfsne....ptisvtavG 92 
                                   +t+++ +    ++  +t++G
  gi|13541340|ref|NP_111028.1| 129 HTARYANtgfpMVGGATMFG 148
                                   *****666895555566776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (351 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       382  (0.0213063); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 2313.60
//
Query:       gi|13541341|ref|NP_111029.1|  [L=517]
Description: amino acid transporter [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-25   90.2  50.3    1.6e-25   89.9  50.3    1.1  1  AA_permease_2  Amino acid permease
    6.7e-22   77.7  54.0    1.1e-21   77.0  54.0    1.3  1  AA_permease    Amino acid permease
  ------ inclusion threshold ------
      0.013   14.8   0.0      0.026   13.9   0.0    1.4  1  THF_DHG_CYH_C  Tetrahydrofolate dehydrogenase/cyclohydrolase,


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 !   89.9  50.3   2.6e-29   1.6e-25       3     420 ..      19     487 ..      17     494 .. 0.72

  Alignments for each domain:
  == domain 1  score: 89.9 bits;  conditional E-value: 2.6e-29
                 AA_permease_2   3 llsafalvigsvigsgifvknlaasggpalilwvwiavligs......lavllvyaElssalprsgGiyvytkaafgkkva 77 
                                   +++a+a  i++++ +  +v+     +  a+++ ++++ l+++      +  + ++  ls ++ + gG y+y + a g + a
  gi|13541341|ref|NP_111029.1|  19 TWGAIAEEISAMAPACDTVA----FMTSAAMFAYVLTPLAFLiatltmYLEVNTLYHLSKHHASAGGYYGYISTALGARSA 95 
                                   55555555666633222222....122334444444444444000000555555555677799****************** PP

                 AA_permease_2  78 flsawfnwfayvpvlasilsvaasyl.....lnalgpdlqgntwltyliaiaililvalinirgikesakiqnilgilkil 153
                                    ls++++++ +++++a+i +++a+ l      ++++ +l    w+++ +++++++  +++ i+gi+   k+ ++  i+ + 
  gi|13541341|ref|NP_111029.1|  96 VLSGFLYVMYQAVSTAAIPVYVAGILlpgimSYFFHITL--PIWIWIPFIAVFIVAPIILAILGIRPQMKYVKYASIFEVA 174
                                   ******************999888884443233333333..367888888********************99999999995 PP

                 AA_permease_2 154 lpliiliilglitvdgggfssl....stetdt....ffpngwpgvllglli..vlwsfdGfesaanvseevkk.kdvpkai 223
                                       +l +lgli++ ++  + +    ++++++    f p g p+  lgl++   l sf+G+ ++a   eevk  + + +a+
  gi|13541341|ref|NP_111029.1| 175 ----FLGVLGLIIILRSPDNTIqvfnPFAWSSyyseFKPIGGPFAGLGLGMifGLTSFIGYGGSAPLGEEVKVhRSITRAL 251
                                   ....56666666665544442222336666663333444455555666666447******************77******* PP

                 AA_permease_2 224 figllivlvlyllvniaflgvvpddeianlsnlgsvaalffeavggkvvaiivvilialsllgaintavigssrvlealar 304
                                   ++glliv+ + + v+ a++ + +  ++a+ +++  ++ +++ ++ g ++  +++++++ s++    +  + + rv++a+ar
  gi|13541341|ref|NP_111029.1| 252 VLGLLIVGAILTEVAYALTVGWGTTNMATFATSAIPGVIVATMYAGITGGLLLSLVAFNSAFSDSVAMQANAGRVYFAMAR 332
                                   *********9999988888888889999999987789999999887788888887777788888888888999******** PP

                 AA_permease_2 305 dgvlPrffakvn.kfgspiraiiltaivslillllfl.........................lassaaynfllsvsslgli 359
                                   d+v+P+ f+k++ +fgsp++a+i++a+vs++ ++l+                          +  + ++++l++++ +gli
  gi|13541341|ref|NP_111029.1| 333 DRVIPEKFSKISkRFGSPYVALIFIAVVSIATAMLIPflvevamgyaplylitshniekvnlIL-EYSFDLLSTMALVGLI 412
                                   ************99***************8887777799***********99999999998633.77899*********** PP

                 AA_permease_2 360 isyllliigalilrkkrphl....kr....pgkilvaiigalfllfllvalffppkgpatqss...liyt...ii 420
                                   ++ lll ++++ l ++ +++     +    +  +l+  +++ +++f+l+  ++pp+ p tq     + y    ii
  gi|13541341|ref|NP_111029.1| 413 SVHLLLNTSVMTLFRRLKEKhyglHKithpIEHYLLPSVATGIFVFVLYESIIPPVFPITQAVeaiVVYIvfmII 487
                                   ******988887777666443244335555333555555666666666555555555554443221333333233 PP

>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.0  54.0   1.8e-25   1.1e-21      18     466 ..      38     491 ..      21     503 .. 0.81

  Alignments for each domain:
  == domain 1  score: 77.0 bits;  conditional E-value: 1.8e-25
                   AA_permease  18 glgvvlsqaGplgallayllagvviflvmlslgeiatngpksggfytyasrflgpelGfviGlny.lfswitvlaleltaa 97 
                                   +    ++    + + la+l+a++ ++l +++l+ ++ +  ++gg+y y+s  lg + ++  G++y +++ + ++a+ + +a
  gi|13541341|ref|NP_111029.1|  38 AFMTSAAMFAYVLTPLAFLIATLTMYLEVNTLYHLSKHHASAGGYYGYISTALGARSAVLSGFLYvMYQAVSTAAIPVYVA 118
                                   55556667778899**************************************************62666778999999999 PP

                   AA_permease  98 sili.qfwelvtdl.pkawvt...gavflvvlliinlvgvkvygeaefilalikiiaiiafiivg..iillaggkpnkgag 171
                                   +il+ ++++++ ++ + +w++   +avf+v+ +i+ ++g++   +    +  ++ i  +af+ v+  ii+l + +++ +  
  gi|13541341|ref|NP_111029.1| 119 GILLpGIMSYFFHItLPIWIWipfIAVFIVAPIILAILGIRPQMK----YVKYASIFEVAFLGVLglIIILRSPDNTIQV- 194
                                   999856777755541447888********************9999....8888888888888777788888888888883. PP

                   AA_permease 172 frflgdngsifknnlppgfakeeegafknfisvfvivvfaftGielvaiiagEvkdPeksiPkailqvviritifYvlsll 252
                                     f  +++s  +  + p      +g f++   ++++ + +f G++  a +++Evk   +si +a    +++++ + + +++
  gi|13541341|ref|NP_111029.1| 195 --FNPFAWSSYYSEFKPI-----GGPFAGLGLGMIFGLTSFIGYGGSAPLGEEVKV-HRSITRALVLGLLIVGAILTEVAY 267
                                   ..2233333223344444.....899*****************************9.78********************** PP

                   AA_permease 253 ligllvprndlgllndsasaaspfvifikesgvsvlaplinaviltaalssansslysasRvlyslakdglaP.kvlkkvs 332
                                   ++++++++++   ++ sa +  +++++++++g+ + + l+ +v + +a+s ++++ + a Rv++++a+d+++P k+ k ++
  gi|13541341|ref|NP_111029.1| 268 ALTVGWGTTNMATFATSAIP--GVIVATMYAGITG-GLLLSLVAFNSAFSDSVAMQANAGRVYFAMARDRVIPeKFSKISK 345
                                   ***************99977..9999999999987.89***********************************99999999 PP

                   AA_permease 333 krgvPlraillsmiisllal......................llaslnlaapivfnfllaisaliglivwlliilsylrfR 391
                                   + g+P++a+++ +++s +                         ++++nl++++ f+ l++++ +  ++v+ll ++s + + 
  gi|13541341|ref|NP_111029.1| 346 RFGSPYVALIFIAVVSIATAmlipflvevamgyaplylitshNIEKVNLILEYSFDLLSTMALVGLISVHLLLNTSVMTLF 426
                                   99**************999999***************99888888999999999************************555 PP

                   AA_permease 392 kalkyqgrsieelgfkaallplgvilvlaaliiillilalyayltvkkgpkdwgaasfaaaylivllfliilvgv 466
                                   + lk++       g +  + p   +l   + + i++++ +  +++ +     +  +  ++a++ +++f+ii+++ 
  gi|13541341|ref|NP_111029.1| 427 RRLKEKHY-----GLHKITHPIEHYLLPSVATGIFVFVLYESIIP-P----VFPITQAVEAIVVYIVFMIIYIVF 491
                                   55444444.....33333333333344444444444444444444.2....222334566777777777777655 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 ?   13.9   0.0   4.3e-06     0.026     106     153 ..       2      50 ..       1      54 [. 0.89

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.3e-06
                                   E---EEC-TTEEE-SB-H.HHHCTTSSEE--TTTSCHHHHHHHHHHHHH CS
                 THF_DHG_CYH_C 106 DvGinrvekgklvGDvdf.eevkevasaitPvpgGVGpmTvamllkntl 153
                                   +vG ++ e+++l GDv++  +++e +sa++P  + V  mT a +++ +l
  gi|13541341|ref|NP_111029.1|   2 NVGNTTYESKRLHGDVSTwGAIAEEISAMAPACDTVAFMTSAAMFAYVL 50 
                                   79999999********86368999******************9998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (517 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1026  (0.0572257); 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:                         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 0.33s 00:00:00.97 Elapsed: 00:00:00.50
# Mc/sec: 3139.02
//
Query:       gi|13541342|ref|NP_111030.1|  [L=306]
Description: ABC-type peptide transport system, ATPase component [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-20   73.6   0.1    2.9e-20   73.2   0.1    1.2  1  ABC_tran         ABC transporter
    3.8e-05   23.6   4.6     0.0095   15.8   0.1    2.1  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    0.00011   22.6   0.1    0.00019   21.8   0.1    1.4  1  oligo_HPY        Oligopeptide/dipeptide transporter, C-termin
    0.00051   20.0   2.3     0.0023   17.9   2.3    1.9  1  ATPase_2         ATPase domain predominantly from Archaea
    0.00054   20.3   0.0    0.00087   19.6   0.0    1.4  1  AAA_22           AAA domain
    0.00076   19.1   0.2     0.0013   18.4   0.2    1.3  1  cobW             CobW/HypB/UreG, nucleotide-binding domain
     0.0022   18.5   2.4     0.0026   18.3   1.7    1.4  1  AAA_23           AAA domain
     0.0023   17.6   0.2     0.0041   16.8   0.2    1.4  1  AAA_29           P-loop containing region of AAA domain
      0.003   18.1   0.0     0.0065   17.0   0.0    1.6  1  AAA_18           AAA domain
     0.0042   17.1   1.2      0.038   14.0   0.1    2.2  2  AAA_14           AAA domain
     0.0084   15.6   3.1      0.067   12.6   3.1    1.9  1  SMC_N            RecF/RecN/SMC N terminal domain
  ------ inclusion threshold ------
      0.011   16.1   0.0      0.016   15.6   0.0    1.3  1  AAA_16           AAA ATPase domain
      0.013   15.4   0.2      0.029   14.3   0.2    1.5  1  RsgA_GTPase      RsgA GTPase
      0.022   14.2   1.2      0.067   12.6   0.9    1.9  1  Pox_A32          Poxvirus A32 protein
      0.023   13.7   0.1      0.034   13.1   0.1    1.2  1  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
      0.037   13.9   0.5      0.069   13.1   0.5    1.4  1  MobB             Molybdopterin guanine dinucleotide synthesis
      0.043   14.0   0.0       0.14   12.4   0.0    1.8  2  AAA_33           AAA domain
      0.054   12.5   0.4      0.089   11.8   0.4    1.3  1  T2SSE            Type II/IV secretion system protein
      0.065   12.2   0.1      0.091   11.7   0.1    1.2  1  DUF463           YcjX-like family, DUF463
      0.072   12.8   0.0       0.12   12.1   0.0    1.2  1  AAA_30           AAA domain
      0.077   12.2   4.2       0.13   11.4   4.2    1.5  1  NB-ARC           NB-ARC domain
      0.083   12.8   0.8       0.14   12.1   0.8    1.3  1  NACHT            NACHT domain
      0.089   12.5   0.3        0.3   10.8   0.1    1.8  2  Viral_helicase1  Viral (Superfamily 1) RNA helicase
      0.097   11.4   2.7        2.4    6.8   0.0    2.3  2  ABC_ATPase       Predicted ATPase of the ABC class


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.2   0.1   3.9e-23   2.9e-20       2     136 ..      29     175 ..      28     176 .. 0.82

  Alignments for each domain:
  == domain 1  score: 73.2 bits;  conditional E-value: 3.9e-23
                                   EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS..--S-TTSBHHHH. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxx. RF
                      ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe..pqlfpeltvren. 79 
                                   +n++++l++g++v+i+G +G+GK+tLlk ++ +++ ++Gei ++gk++   +++ +r+++ ++pq+  ++l+    ++++ 
  gi|13541342|ref|NP_111030.1|  29 HNINIELNRGKIVGITGLSGSGKTTLLKSILLETHIKSGEIIFNGKPIMPGDTKNYRRSVIYVPQNslDSLDIIWPIEDQv 109
                                   89****************************************************************543333333355557 PP

                                   .......HHHTC...HHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHH.HHHTSS.EEEEESTT CS
                                   .......xxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx.xxxxxxxx RF
                      ABC_tran  80 .......esdee...iekalsklglkelkdtvvksspssLSgGqkqrvalara.llkkpk.llllDEpt 136
                                          +       i+k+ +  +l++l+ + +k +  ++S+G + +++l ++ l+ k++ ++l+DEpt
  gi|13541342|ref|NP_111030.1| 110 kkilkqhN---VvydINKVSEIAKLIDLDISMLKLKSFEVSYGTRHKIVLLMSiLMAKRDlVVLMDEPT 175
                                   77664333...24558888888889999999999999*********9987665144455426788***9 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   1.3    0.0011      0.83       2      21 ..      41      60 ..      40      87 .. 0.74
   2 !   15.8   0.1   1.3e-05    0.0095     167     296 ..      87     205 ..      72     209 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0011
                        AAA_21  2 nvliGpNgsGKSnLLdaldl 21
                                   +++G  gsGK++LL+ + l
  gi|13541342|ref|NP_111030.1| 41 VGITGLSGSGKTTLLKSILL 60
                                  689*************9944 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 1.3e-05
                        AAA_21 167 gllnifadyfgfakekrllqrlvrslklveielsdlgegeeliasvderlrergvvflengdgqelparelSdGtkrllal 247
                                   ++   +++ +   ++++ +++ v++++++++ ++d+++++e  +++d+++              +l ++e+S Gt++ + l
  gi|13541342|ref|NP_111030.1|  87 SVIYVPQNSLDSLDIIWPIEDQVKKILKQHNVVYDINKVSEIAKLIDLDISM-----------LKLKSFEVSYGTRHKIVL 156
                                   5555666777777888889999999999999999999999999999999866...........999*************** PP

                        AAA_21 248 ltallralkkgsllliDEpEngLHPkllrrllell.kelsrngaQviltT 296
                                   l ++l a     ++l DEp ++ +    + +l ++ k++++ g+ +i+++
  gi|13541342|ref|NP_111030.1| 157 LMSILMAKRD-LVVLMDEPTLSQDAITAEGILNIIvKLAKDYGSSFIIVS 205
                                   *****99999.9*******9986665556666555444444666665555 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 !   21.8   0.1   2.6e-07   0.00019       1      65 []     227     286 ..     227     286 .. 0.94

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 2.6e-07
                     oligo_HPY   1 vErgpssklfdeplHPYTkaLlrsvprldrekdklekikgeapslerldeGCpFapRCpfaleeC 65 
                                   vE g+ ++l + p+HP T   ++ +p  + +++       + p +e  ++GCp++  C+ + + C
  gi|13541342|ref|NP_111030.1| 227 VENGTPNDLSKWPKHPFTYEFINMLPAHKTRDR-----FPKFPMTEFSENGCPYSIYCKNKIKGC 286
                                   8***************************99999.....777888889999**********99999 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   2.3   3.1e-06    0.0023      15     166 ..      33     207 ..      22     219 .. 0.65

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 3.1e-06
                      ATPase_2  15 lerepneiyfiYGpegsGKtaLlkeiienledkdkyviyy.ialreesiskldefie................eeeekkkl 78 
                                   +e ++ +i+ i+G  gsGKt+Llk i+ + + k+ ++i+   ++   +++++++++                 e ++kk l
  gi|13541342|ref|NP_111030.1|  33 IELNRGKIVGITGLSGSGKTTLLKSILLETHIKSGEIIFNgKPIMPGDTKNYRRSVIyvpqnsldsldiiwpiEDQVKKIL 113
                                   56778899******************9988777777777536778888888888766787777778888888655555544 PP

                      ATPase_2  79 ekal....................giavpkaeleeilkeksklvfkaielllekikkkgkkiiiiiDelqklidlglngae 139
                                   +++                     + +++++       e s   ++    ll++i   ++ +++++De        l +++
  gi|13541342|ref|NP_111030.1| 114 KQHNvvydinkvseiaklidldisMLKLKSF-------EVSYG-TRHKIVLLMSILMAKRDLVVLMDEPT------LSQDA 180
                                   4444666655555544422222111111111.......11122.22222344444455555777777743......33678 PP

                      ATPase_2 140 llvkeLlnliesltkekhlcvviclsS 166
                                      + +ln+i++l k++   ++i++sS
  gi|13541342|ref|NP_111030.1| 181 ITAEGILNIIVKLAKDYGSSFIIVSSS 207
                                   888999****************99999 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   1.2e-06   0.00087       5      70 ..      38     115 ..      34     206 .. 0.69

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.2e-06
                        AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaee...............erpevvfvtlpsstsskdllrellralglelka 70 
                                    +i+ +tG sG+GKTtll+ +l + ++     e                r++v++v  +s+  s d+   +  +++  lk 
  gi|13541342|ref|NP_111030.1|  38 GKIVGITGLSGSGKTTLLKSILLETHIK--SGEiifngkpimpgdtknYRRSVIYVPQNSLD-SLDIIWPIEDQVKKILKQ 115
                                   577889*****************99654..44466999999999998666666666555555.778888888877766666 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.2   1.7e-06    0.0013       2      34 ..      40      72 ..      39      85 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.7e-06
                                  EEEEEESTTCCHHHHHHHHHCT--SS-EEEEES CS
                          cobW  2 vtvltGflGsGKTtLlnhllenraglklavivN 34
                                  ++++tG  GsGKTtLl+++l +++ ++  +i N
  gi|13541342|ref|NP_111030.1| 40 IVGITGLSGSGKTTLLKSILLETHIKSGEIIFN 72
                                  578*****************9988888888887 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   1.7   3.5e-06    0.0026       7      40 ..      25      59 ..      23      62 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 3.5e-06
                        AAA_23  7 frsfrdqeidFsk.gltlItGpNGaGKTTildAik 40
                                  ++ +++ +i++++ +++ ItG  G+GKTT+l  i 
  gi|13541342|ref|NP_111030.1| 25 IGIIHNINIELNRgKIVGITGLSGSGKTTLLKSIL 59
                                  56678999***7758****************9885 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.2   5.4e-06    0.0041      13      41 ..      29      57 ..      16      72 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 5.4e-06
                        AAA_29 13 dghtieidlkg.atlltGpsGsGKSTllDA 41
                                  ++  ie+++ g ++ +tG sGsGK+Tll +
  gi|13541342|ref|NP_111030.1| 29 HNINIELNR-GkIVGITGLSGSGKTTLLKS 57
                                  444455554.35999************955 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   8.7e-06    0.0065       1      63 [.      41      98 ..      41     143 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 8.7e-06
                        AAA_18  1 IlltGtpGvGKttlakeLskrlgfgvnlrdvakenglllevdpealdeskrldedkldkllda 63
                                  +++tG +G+GKttl k +  ++  +++++++++++ +  + d +   +++r ++ + ++ ld 
  gi|13541342|ref|NP_111030.1| 41 VGITGLSGSGKTTLLKSILLET--HIKSGEIIFNGKPIMPGDTK---NYRRSVIYVPQNSLDS 98
                                  78**************995555..99999999999988888877...4444444444444444 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.1     5e-05     0.038       2      34 ..      38      70 ..      37      93 .. 0.88
   2 ?    1.9   0.1      0.28   2.1e+02      53      99 ..     154     205 ..     106     213 .. 0.60

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5e-05
                        AAA_14  2 rkilvitGaRrvGKTtllkqlikellvkkesil 34
                                  +ki+ itG+  +GKTtllk ++ e  +k+ +i+
  gi|13541342|ref|NP_111030.1| 38 GKIVGITGLSGSGKTTLLKSILLETHIKSGEII 70
                                  699*****************9877766666665 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.28
                        AAA_14  53 lelileklkeekktylflDEiqev...pewekalkslvd...egknldvivtG 99 
                                   + l+++ l+++++ ++++DE   +    ++e +l+ +v+   ++    +i+  
  gi|13541342|ref|NP_111030.1| 154 IVLLMSILMAKRDLVVLMDEPTLSqdaITAEGILNIIVKlakDYGS-SFIIVS 205
                                   34556665556889999***76662234455556666653213323.333333 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   3.1     9e-05     0.067      25     207 ..      39     216 ..      27     224 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 9e-05
                                   SEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--.....BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N  25 sftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihk.....skekasvkkaeveitfdnedkklkiekeevsis 100
                                   ++  i+G  GSGK+ ll +i  +L  +   +++s    ++i++       + ++  +  + +  +n+ ++l i  +     
  gi|13541342|ref|NP_111030.1|  39 KIVGITGLSGSGKTTLLKSI--LLE-T---HIKS---GEIIFNgkpimPGDTKNYRRSVIYVP-QNSLDSLDIIWPIEDQV 109
                                   56789***************..454.3...4554...45677766443344455555444443.44444434433333333 PP

                                   EEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 101 rrvkrkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvae 181
                                   +++ ++ +  y in+ +   k +   +++ ++++ + S G +    + Ll++i ++k+  ++l+De     D+   + + +
  gi|13541342|ref|NP_111030.1| 110 KKILKQHNVVYDINKVSEIAKLIDLDISMLKLKSFEVSYGTRH--KIVLLMSILMAKRDLVVLMDEPTLSQDAITAEGILN 188
                                   4556667779****999999999999**************986..78899******************************* PP

                                   HHHHHCTT..SEEEEE-SSHHHCCC-SC CS
                                   xxxxxxxx..xxxxxxxxxxxxxxxxxx RF
                         SMC_N 182 llkekskn..aQfivislreemlekadk 207
                                   ++ +  k+  + fi++s + e +  a+ 
  gi|13541342|ref|NP_111030.1| 189 IIVKLAKDygSSFIIVSSSPEPVFYASD 216
                                   **99998877899999987766555544 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   2.2e-05     0.016      23      46 ..      37      61 ..      28     137 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.2e-05
                        AAA_16 23 rpelvllsGesGvGKsslvrell.r 46
                                  r+ +v ++G sG+GK++l++++l +
  gi|13541342|ref|NP_111030.1| 37 RGKIVGITGLSGSGKTTLLKSILlE 61
                                  568999*************988733 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.2   3.8e-05     0.029      91     130 ..      29      69 ..      12      74 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.8e-05
                                   HHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT-----S-- CS
                   RsgA_GTPase  91 eelkellkd.ktsvlvGqSGvGKStLinallpelelktgev 130
                                   ++++ +l+  k++ + G SG GK+tL++++l e+++k ge+
  gi|13541342|ref|NP_111030.1|  29 HNINIELNRgKIVGITGLSGSGKTTLLKSILLETHIKSGEI 69 
                                   5666667666999*******************999999987 PP

>> Pox_A32  Poxvirus A32 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.9     9e-05     0.067      17      80 ..      42     125 ..      35     146 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 9e-05
                       Pox_A32  17 alvGgsGsGktvyLlsLl.rtlvkkykhifLltp...............vknseYdk..yvwP..dhinkvtseeeleYsL 77 
                                    ++G sGsGkt+ L+s+l +t +k    if   p               v +++ d+   +wP  d ++k+  ++++ Y +
  gi|13541342|ref|NP_111030.1|  42 GITGLSGSGKTTLLKSILlETHIKSGEIIFNGKPimpgdtknyrrsviyVPQNSLDSldIIWPieDQVKKILKQHNVVYDI 122
                                   4899************65166677778888777655577777777776655666554225777667777777777777776 PP

                       Pox_A32  78 sat 80 
                                    ++
  gi|13541342|ref|NP_111030.1| 123 NKV 125
                                   665 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   4.6e-05     0.034      18      52 ..      27      61 ..      20      70 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.6e-05
                                  HHHHHGGG-S-SEEEEEEE-TTSSHHHHHHHHHHH CS
                          MeaB 18 llerllakaGraqvvGltGvPGaGkstlvealgle 52
                                  +++++  +  r + vG+tG+ G+Gk tl++ + le
  gi|13541342|ref|NP_111030.1| 27 IIHNINIELNRGKIVGITGLSGSGKTTLLKSILLE 61
                                  566777778899****************9886544 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.5   9.2e-05     0.069       1      22 [.      40      61 ..      40      69 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 9.2e-05
                          MobB  1 vlgivgksgsGKTtLleklipe 22
                                  ++gi+g sgsGKTtLl+ ++ e
  gi|13541342|ref|NP_111030.1| 40 IVGITGLSGSGKTTLLKSILLE 61
                                  789*************998755 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00018      0.14       4      22 ..      43      61 ..      40      99 .. 0.88
   2 ?   -1.4   0.0       3.2   2.4e+03      69     102 ..     163     204 ..     147     210 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00018
                        AAA_33  4 lvGlpGsGKstlaerllkk 22
                                  + Gl+GsGK+tl++++l +
  gi|13541342|ref|NP_111030.1| 43 ITGLSGSGKTTLLKSILLE 61
                                  67***********998744 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 3.2
                        AAA_33  69 agrnvil..datnlsrrer......arflklarrlgvpvriv 102
                                   a+r++++  d + ls+++         ++kla+++g+ + iv
  gi|13541342|ref|NP_111030.1| 163 AKRDLVVlmDEPTLSQDAItaegilNIIVKLAKDYGSSFIIV 204
                                   444433334777666666555555566777788777666665 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.4   0.00012     0.089     126     158 ..      35      67 ..       7      72 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00012
                         T2SSE 126 vrerglilvsGgTgsGKttllyallkeinksde 158
                                   +++ +++ ++G  gsGKttll ++l e + ++ 
  gi|13541342|ref|NP_111030.1|  35 LNRGKIVGITGLSGSGKTTLLKSILLETHIKSG 67 
                                   344455569************999987665545 PP

>> DUF463  YcjX-like family, DUF463
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   0.00012     0.091       3      21 ..      41      59 ..      40      90 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00012
                        DUF463  3 lavTGLsraGKtvfitsLv 21
                                  +++TGLs++GKt+++ s+ 
  gi|13541342|ref|NP_111030.1| 41 VGITGLSGSGKTTLLKSIL 59
                                  69*************9986 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00016      0.12      18      44 ..      38      65 ..      32      77 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00016
                        AAA_30 18 drvavltGpAGtGKttalkal.reawea 44
                                   +++ +tG  G+GKtt+lk++  e++ +
  gi|13541342|ref|NP_111030.1| 38 GKIVGITGLSGSGKTTLLKSIlLETHIK 65
                                  45899**************985555544 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   4.2   0.00018      0.13      21      44 ..      39      62 ..      25     173 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00018
                                  EEEEEEESTTSSHHHHHHHHCCSH CS
                        NB-ARC 21 lvvalvGmgGvGKttlakqilnks 44
                                   +v++ G  G+GKttl+k+il + 
  gi|13541342|ref|NP_111030.1| 39 KIVGITGLSGSGKTTLLKSILLET 62
                                  59******************9873 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.8   0.00018      0.14       3      23 ..      41      61 ..      39      67 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00018
                                  EEEEC-TTTCHHHHHHHHHHH CS
                         NACHT  3 vilqGeaGsGKTtLlqklala 23
                                  v ++G +GsGKTtLl+++ l+
  gi|13541342|ref|NP_111030.1| 41 VGITGLSGSGKTTLLKSILLE 61
                                  6699*************9875 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 ?   10.8   0.1    0.0004       0.3       3      22 ..      43      62 ..      41      89 .. 0.78
   2 ?   -0.9   0.0       1.5   1.1e+03      32      75 ..     139     178 ..     122     191 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0004
               Viral_helicase1  3 vhGvpGcGKStlirkllrts 22
                                  + G  G+GK+tl++++l + 
  gi|13541342|ref|NP_111030.1| 43 ITGLSGSGKTTLLKSILLET 62
                                  78999************882 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.5
               Viral_helicase1  32 aelltegkpklpnlsvrtvdsflmalvkstkgkililDEylllh 75 
                                    +l +  +++ +++++  ++s+lma+ +     ++++DE +l +
  gi|13541342|ref|NP_111030.1| 139 LKLKSFEVSYGTRHKIVLLMSILMAKRD----LVVLMDEPTLSQ 178
                                   5666666788888999999999999876....499999988876 PP

>> ABC_ATPase  Predicted ATPase of the ABC class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.7     0.022        17     243     264 ..      36      58 ..      31      64 .. 0.87
   2 ?    6.8   0.0    0.0033       2.4     372     411 ..     182     221 ..     166     226 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.022
                                   -SS.EEEEEE-TTSSHHHHHHHH CS
                    ABC_ATPase 243 pkG.vtlIvGggfhGKsTLLeAl 264
                                    +G ++ I+G    GK+TLL+++
  gi|13541342|ref|NP_111030.1|  36 NRGkIVGITGLSGSGKTTLLKSI 58 
                                   5666999**************98 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0033
                                   -B--HHHCHHHHHHHH--EEEEEESS-GCCTTT-SEEEEE CS
                    ABC_ATPase 372 pitplvdrvrelykklgvstilvvggsgdyldvAdtvilm 411
                                   + + +++ + +l k++g s i+v+++ +  +  +d +  m
  gi|13541342|ref|NP_111030.1| 182 TAEGILNIIVKLAKDYGSSFIIVSSSPEPVFYASDFIYIM 221
                                   4456899999*************************99887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       594  (0.0331307); expected 358.6 (0.02)
Passed bias filter:                      499  (0.027832); expected 358.6 (0.02)
Passed Vit filter:                       106  (0.00591221); expected 17.9 (0.001)
Passed Fwd filter:                        24  (0.00133861); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              24  [number of targets reported over threshold]
# CPU time: 0.64u 0.35s 00:00:00.99 Elapsed: 00:00:00.53
# Mc/sec: 1750.46
//
Query:       gi|13541343|ref|NP_111031.1|  [L=257]
Description: ABC-type peptide transporter, ATPase component [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.8e-25   88.4   0.0    9.2e-25   87.8   0.0    1.3  1  ABC_tran      ABC transporter
    0.00017   21.1   0.2      0.019   14.4   0.2    2.2  1  SMC_N         RecF/RecN/SMC N terminal domain
    0.00025   21.0   2.2      0.097   12.5   0.0    2.2  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
     0.0037   17.5   0.1       0.13   12.5   0.1    2.3  1  SbcCD_C       Putative exonuclease SbcCD, C subunit
     0.0044   17.3   0.1      0.027   14.8   0.1    2.1  1  AAA_22        AAA domain
  ------ inclusion threshold ------
      0.012   15.3   0.0      0.027   14.2   0.0    1.6  1  AAA_29        P-loop containing region of AAA domain
      0.025   14.0   0.3       0.72    9.3   0.0    2.1  2  PhoH          PhoH-like protein
      0.031   14.2   0.2      0.057   13.3   0.2    1.8  1  ATPase_2      ATPase domain predominantly from Archaea
      0.053   14.0   0.1      0.053   14.0   0.1    1.4  1  AAA_23        AAA domain
      0.086   13.2   0.0       0.16   12.4   0.0    1.5  1  AAA_16        AAA ATPase domain
      0.087   13.2   0.2       0.29   11.5   0.0    1.9  2  RNA_helicase  RNA helicase
        0.1   12.8   0.1       0.14   12.3   0.1    1.4  1  AAA_33        AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.8   0.0   6.1e-28   9.2e-25       1     136 [.      27     174 ..      27     175 .. 0.92

  Alignments for each domain:
  == domain 1  score: 87.8 bits;  conditional E-value: 6.1e-28
                                   EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG...B-HHHCCHCEEEE-SS..--S-TTSBH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxx..xxxxxxxxx RF
                      ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke...qeleslrkeigvlpqe..pqlfpeltv 76 
                                   lkn+s ++ eg++++++G++G+GK+tL+++     +p++G++ + +k++++    +l+s+   +++++q+  ++l p  tv
  gi|13541343|ref|NP_111031.1|  27 LKNISYEFDEGTIYGVIGPSGSGKTTLANISVLYDRPDSGSVYYGNKEVTRmkpADLKSYAGIVRYVFQDpyTSLEPLRTV 107
                                   79***********************************************99999****************98899999999 PP

                                   HHH.........HHHTCHHHHHHHSTTGG..TTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                   xxx.........xxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  77 ren.........esdeeiekalsklglke..lkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                   + +           +ee+ k+++ lg++e   +d++     + LSgGq+qr+a   a++ +p +++lDEp+
  gi|13541343|ref|NP_111031.1| 108 GWHidtaaqsihIVQEEAWKIATYLGMPEsrYRDSI----VEDLSGGQRQRLAFIIAMIADPAIIILDEPF 174
                                   9999999999888888899*******9993334444....4*****************************7 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.2   1.3e-05     0.019     135     193 ..     116     199 ..      25     220 .. 0.59

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.3e-05
                                   T.............................CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHH CS
                                   x.............................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 135 e.............................lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkek 186
                                   +                              LSgG+++   la++  i ++   ++ +lDe  + LD  n   + ++l+ +
  gi|13541343|ref|NP_111031.1| 116 QsihivqeeawkiatylgmpesryrdsiveDLSGGQRQ--RLAFI--IAMIADPAIIILDEPFSMLDSYNSMFLLNYLRMN 192
                                   0333333344444444444444444444448******7..67777..5567778899**********************98 PP

                                   CTTSEEE CS
                                   xxxxxxx RF
                         SMC_N 187 sknaQfi 193
                                   +k   +i
  gi|13541343|ref|NP_111031.1| 193 KKGRVII 199
                                   8654433 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.7    0.0016       2.3       2      15 ..      40      53 ..      39      59 .. 0.90
   2 !   12.5   0.0   6.5e-05     0.097     234     279 ..     144     186 ..      95     199 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0016
                        AAA_21  2 nvliGpNgsGKSnL 15
                                   ++iGp gsGK++L
  gi|13541343|ref|NP_111031.1| 40 YGVIGPSGSGKTTL 53
                                  689**********9 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 6.5e-05
                        AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrll 279
                                   + +lS G+++ la++ a+++++   +++++DEp + L+      ll
  gi|13541343|ref|NP_111031.1| 144 VEDLSGGQRQRLAFIIAMIADP---AIIILDEPFSMLDSYNSMFLL 186
                                   5688****************99...********9988765555555 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 !   12.5   0.1     9e-05      0.13      31      89 ..     145     190 ..     133     191 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 9e-05
                       SbcCD_C  31 gtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllelle 89 
                                   + lSGG++q la ++ +      +        ++++++LDE Fs lD+ ++  ll++l+
  gi|13541343|ref|NP_111031.1| 145 EDLSGGQRQRLAFIIAM------IA-------DPAIIILDEPFSMLDSYNSMFLLNYLR 190
                                   56677777655554433......22.......489*************99999999886 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.1   1.8e-05     0.027       6      61 ..      38      94 ..      33     209 .. 0.60

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.8e-05
                        AAA_22  6 gilvvtGesGtGKTtllrrlleqldeeakaee.....erpevvfvtlpsstsskdllrell 61
                                  +i  v+G+sG+GKTtl++  +  +  +           ++ev +++++ ++s + + r ++
  gi|13541343|ref|NP_111031.1| 38 TIYGVIGPSGSGKTTLANISVLYDRPD----SgsvyyGNKEVTRMKPADLKSYAGIVRYVF 94
                                  67779***********98766654221....122334455555555555555555555554 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 ?   14.2   0.0   1.8e-05     0.027      16      38 ..      31      53 ..      15      63 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.8e-05
                        AAA_29 16 tieidlkg.atlltGpsGsGKSTl 38
                                  ++e+d+ g ++ ++GpsGsGK+Tl
  gi|13541343|ref|NP_111031.1| 31 SYEFDE-GtIYGVIGPSGSGKTTL 53
                                  456664.44889***********9 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   0.00048      0.72      18      37 ..      36      55 ..      26      60 .. 0.81
   2 ?    2.7   0.0     0.049        73     120     154 ..     165     202 ..     159     218 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00048
                                  H-SEEEEE--TTSSTTHHHH CS
                          PhoH 18 kndivfaiGpaGtGKtylav 37
                                  + +i  +iGp+G+GKt la 
  gi|13541343|ref|NP_111031.1| 36 EGTIYGVIGPSGSGKTTLAN 55
                                  5678999***********95 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.049
                                   SEEEEE-SGGG--HHHHHHHH...TTB-TT-EEEEEE- CS
                          PhoH 120 dafvilDEAQnttkeqmkmfl...tRlGenskvvvtGd 154
                                    a++ilDE  ++  +   mfl    R+ ++ +v++  d
  gi|13541343|ref|NP_111031.1| 165 PAIIILDEPFSMLDSYNSMFLlnyLRMNKKGRVIIYID 202
                                   589***********999999844459******999876 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.2   3.8e-05     0.057      16      57 ..      33      73 ..      23     208 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.8e-05
                      ATPase_2 16 erepneiyfiYGpegsGKtaLlkeiienledkdkyviyyial 57
                                  e ++ +iy + Gp gsGKt+L + ++   +  d   +yy + 
  gi|13541343|ref|NP_111031.1| 33 EFDEGTIYGVIGPSGSGKTTLANISVLYDRP-DSGSVYYGNK 73
                                  5667899**************9988766544.4566777655 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   3.5e-05     0.053      11      37 ..      28      55 ..       2     253 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.5e-05
                        AAA_23 11 rdqeidF.skgltlItGpNGaGKTTild 37
                                  ++ + +F +  ++ ++Gp G+GKTT+ +
  gi|13541343|ref|NP_111031.1| 28 KNISYEFdEGTIYGVIGPSGSGKTTLAN 55
                                  45555774447999***********986 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0    0.0001      0.16      27      42 ..      40      55 ..      33     173 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.0001
                        AAA_16 27 vllsGesGvGKsslvr 42
                                    ++G+sG+GK++l++
  gi|13541343|ref|NP_111031.1| 40 YGVIGPSGSGKTTLAN 55
                                  5699**********95 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00019      0.29       3      41 ..      42      75 ..      40      85 .. 0.84
   2 ?   -2.3   0.0       3.9   5.9e+03      51      76 ..     166     191 ..     158     220 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00019
                  RNA_helicase  3 lyGpsgeGKStlakeLakallkklklkkkdsvysrnped 41
                                  + Gpsg GK+tla+    ++l  ++ + ++svy++n+e 
  gi|13541343|ref|NP_111031.1| 42 VIGPSGSGKTTLANI---SVL--YDRPDSGSVYYGNKEV 75
                                  68************9...555..4778999999999886 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 3.9
                  RNA_helicase  51 evvvidDfgqvkdeenpsdlaelirl 76 
                                   ++++ d+  ++ d++n + l + +r+
  gi|13541343|ref|NP_111031.1| 166 AIIILDEPFSMLDSYNSMFLLNYLRM 191
                                   56666666666666444444444444 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   9.2e-05      0.14       4      17 ..      42      55 ..      40     176 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 9.2e-05
                        AAA_33  4 lvGlpGsGKstlae 17
                                  ++G++GsGK+tla 
  gi|13541343|ref|NP_111031.1| 42 VIGPSGSGKTTLAN 55
                                  69**********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       572  (0.0319036); expected 358.6 (0.02)
Passed bias filter:                      528  (0.0294495); expected 358.6 (0.02)
Passed Vit filter:                        91  (0.00507558); 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 0.32s 00:00:00.90 Elapsed: 00:00:00.49
# Mc/sec: 1582.43
//
Query:       gi|13541344|ref|NP_111032.1|  [L=266]
Description: phosphomethylpyrimidine kinase [Thermoplasma volcanium GSS1]
Scores for 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-88  294.2   0.0    7.9e-88  294.0   0.0    1.0  1  Phos_pyr_kin  Phosphomethylpyrimidine kinase
    5.2e-10   39.1   0.0    8.6e-10   38.4   0.0    1.3  1  PfkB          pfkB family carbohydrate kinase
    3.1e-05   23.6   0.0    8.1e-05   22.2   0.0    1.7  2  Carb_kinase   Carbohydrate kinase
  ------ inclusion threshold ------
       0.04   13.3   0.0        0.1   12.0   0.0    1.6  1  HK            Hydroxyethylthiazole kinase family


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 !  294.0   0.0   1.8e-91   7.9e-88       1     244 [.      13     254 ..      13     256 .. 0.98

  Alignments for each domain:
  == domain 1  score: 294.0 bits;  conditional E-value: 1.8e-91
                                   ETTSSSHHHHHHHHHHHTTEEEEEEEEEEEEEETTCEEEEEE--HHHHHHHHHHHHHTS--SEEEE-S--SHHHHHHHHHH CS
                  Phos_pyr_kin   1 DssGGAGiqADlktfsalgvygmsvitaltaqntkgvkevhplpaelveaqleavledvkvdavKiGmlasaeiievvaek 81 
                                   Ds+GGAGiqADlktf++l+v+gmsvita+taqn+ +v+++ p+p+e+v+ q+++v++d+kvd +K+Gml+s+eii+vv+  
  gi|13541344|ref|NP_111032.1|  13 DSGGGAGIQADLKTFNSLSVFGMSVITAVTAQNSYEVSGILPVPPEFVKLQIDTVAKDIKVDGAKTGMLFSSEIIKVVTGS 93 
                                   9******************************************************************************** PP

                                   HHHTTS.SEEEE---SSCTSSSBSSHHHHHHHHHHTGGG-SEEE-BHHHHHHHHT---SSHHHHHHHHHHHHHTT-SEEEE CS
                  Phos_pyr_kin  82 lkkykv.pvVlDPVmvaksgselleeeavealkeeLlplatvitPNlpEaeaLlgekikteedmkeaakkllklgakaVli 161
                                   +k y++ pv++DPVmv+ks+++ll+e+a+e+l + Llp++t++tPN+pEae L++++i+t edmk+aa+k+      +Vl+
  gi|13541344|ref|NP_111032.1|  94 IKDYSIkPVIVDPVMVSKSNARLLREDAIESLIKYLLPESTIVTPNIPEAEILASMSISTIEDMKAAAEKIGTEIGLKVLV 174
                                   *************************************************************************88889*** PP

                                   EEGGS-SSSEEEEEEEETSSEEEEEEEE----S--BTHHHHHHHHHHHHHHCTSSHHHHHHHHHHHHHHHHHCG-BSTSSS CS
                  Phos_pyr_kin 162 kGghlegeeavvtdvlydgeeveeleaerietknthGtGCtlssaiaaelakgesleeAvkkAkeyvteaikealelgkga 242
                                   kGgh +g     +d++ydg+++ ++e+ r+etknthGtG+tlssai + l kg++ +eA++ +keyv+ +i++++  g+g 
  gi|13541344|ref|NP_111032.1| 175 KGGHFNG-PP--IDIYYDGSNILKFEGTRYETKNTHGTGDTLSSAILSFLIKGYREQEAIALGKEYVEGSIRNSFPTGSGF 252
                                   ****844.34..5******************************************************************99 PP

                                   -B CS
                  Phos_pyr_kin 243 gp 244
                                   g+
  gi|13541344|ref|NP_111032.1| 253 GS 254
                                   87 PP

>> PfkB  pfkB family carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.4   0.0   1.9e-13   8.6e-10     172     283 ..     115     235 ..      93     242 .. 0.83

  Alignments for each domain:
  == domain 1  score: 38.4 bits;  conditional E-value: 1.9e-13
                                   H......HHHHHHHHHCTESEEEEEHHHHHHHHTSCTHSHHHHHHHHHHHHHTTSSEEEEEEGG...GEE.EEEETTEEEE CS
                          PfkB 172 q......fkeallellaladllkpneeElealtgekledieealaalhklkakgaktvvvtlGk...eGa.lvvekdgelk 242
                                            + ++ ll+ +++++pn  E+e+l+++++ +ie+ +aa++k+ ++   +v+v+ G     +  +++++++ lk
  gi|13541344|ref|NP_111032.1| 115 RllredaIESLIKYLLPESTIVTPNIPEAEILASMSISTIEDMKAAAEKIGTEIGLKVLVKGGHfngPPIdIYYDGSNILK 195
                                   3433343346778888*********************************99998899***999631133425666****** PP

                                   EEE.SSSS-SBGTTHHHHHHHHHHHHHHTTHHHHHHHHHHH CS
                          PfkB 243 vpavpkvkvvDttGAGDsfvggflaallegksleealrfan 283
                                   ++     +  +t G+GD+  +++l+ l +g + +ea++++ 
  gi|13541344|ref|NP_111032.1| 196 FEG-TRYETKNTHGTGDTLSSAILSFLIKGYREQEAIALGK 235
                                   ***.679*******************************996 PP

>> Carb_kinase  Carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1      0.39   1.8e+03       2      28 ..       7      35 ..       6      67 .. 0.67
   2 !   22.2   0.0   1.8e-08   8.1e-05     117     213 ..     131     233 ..      98     254 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.39
                                  EEEE-BTTCHHHHHHHHHHHHCTT..-SE CS
                   Carb_kinase  2 lvigGsedytGAallaalaalrlg..agl 28
                                  l i+Gs+   GA++ a l + ++    g+
  gi|13541344|ref|NP_111032.1|  7 LTIAGSDSGGGAGIQADLKTFNSLsvFGM 35
                                  56899999999999887776654321343 PP

  == domain 2  score: 22.2 bits;  conditional E-value: 1.8e-08
                                   TSSEEEE--HHHHHHHCTTTCHHCCSHHHHHHHHHHHHTTEEEEESTT.....SEEEECTTEEEEE-.---GGG-STTHHH CS
                   Carb_kinase 117 kaeviLTPhkkEfkrLlkaivkkeddrlelarelaqklnavvllkgek.....dvivspegevlins.tgssalakGGsGD 191
                                    + +i TP++ E + L+ +++   +d   +a+++  +++  vl+kg +       i + + ++l+ + t    + + G+GD
  gi|13541344|ref|NP_111032.1| 131 PESTIVTPNIPEAEILASMSISTIEDMKAAAEKIGTEIGLKVLVKGGHfngppIDIYYDGSNILKFEgTRYETKNTHGTGD 211
                                   5789*****************9999999******************9843332235555555555441445667789**** PP

                                   HHHHHHHHHHHCTSSHHHHHHH CS
                   Carb_kinase 192 vLaGligalLaqneasyeaaia 213
                                   +L+ +i+++L   +   ea + 
  gi|13541344|ref|NP_111032.1| 212 TLSSAILSFLIKGYREQEAIAL 233
                                   **********999977666554 PP

>> HK  Hydroxyethylthiazole kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   2.2e-05       0.1      67     198 ..      89     221 ..      76     234 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.2e-05
                                   HHHHHHHHHHHTT--EEEE-TTBTTBH...HHHHHHHHHHHHS..--SEEEEEHHHHHHHHTSSCCSCSSSSSS-SHHHHH CS
                            HK  67 alkaAvksakevnrPvvlDPVgvgAte...lRrelalellkev..klavikGNasEilslaglelkvkGvDskeaataava 142
                                   +++  +k +  + +Pv++DPV v+ ++   lR++ +++l+k+   +  ++  N  E   la ++         ++ +++ a
  gi|13541344|ref|NP_111032.1|  89 VVTGSIKDY--SIKPVIVDPVMVSKSNarlLREDAIESLIKYLlpESTIVTPNIPEAEILASMS--------ISTIEDMKA 159
                                   444444443..458*******9986651116789999999997334568888887777777664........344445556 PP

                                   HHHHHHHHHTSEEEEESS......SEEEEESSEEEEEE-S-GGGGGSTTHHHHHHHHHHHHH CS
                            HK 143 avqkvAqklrvvvvvtGe......vDvvsdgkkvyklknGtellgkitasGCllgsvvaafl 198
                                   a++k+ +++++ v+v G       +D+  dg++++k ++      +  ++G +l+s++ +fl
  gi|13541344|ref|NP_111032.1| 160 AAEKIGTEIGLKVLVKGGhfngppIDIYYDGSNILKFEGTRYETKNTHGTGDTLSSAILSFL 221
                                   77777788877776666323333368888888888887555555556688888888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       430  (0.0239835); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); 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: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 1607.78
//
Query:       gi|13541345|ref|NP_111033.1|  [L=226]
Description: transcription regulator [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.3e-07   30.2   0.0    8.3e-07   29.0   0.0    1.7  1  HTH_3     Helix-turn-helix
    2.2e-05   24.7   0.0      4e-05   23.9   0.0    1.4  1  HTH_31    Helix-turn-helix domain
    9.1e-05   22.4   0.0    0.00019   21.4   0.0    1.5  1  HTH_19    Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   0.0   1.4e-10   8.3e-07       1      48 [.      23      71 ..      23      76 .. 0.95

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 1.4e-10
                                  HHHHHHHTTHHHHHHHHHHTSSHHHHHHHHTT..SSCSBHHHHHHHHHHH CS
                         HTH_3  1 lkelRkqlglsqeeLAeklGvsrstisriEnG..ernPsletlkklakaL 48
                                  ++++R++ + sq eL+  l+ s+s is++E G  +  Ps+  + k+ +aL
  gi|13541345|ref|NP_111033.1| 23 IRKWREEFKVSQLELSNFLNQSPSVISDYETGrrKF-PSIASVRKIVDAL 71
                                  89******************************9666.*********9998 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.0   6.6e-09     4e-05       4      54 ..      21      71 ..      20      78 .. 0.94

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 6.6e-09
                        HTH_31  4 alLralReraGLsqeevAerlgvsestlsrlEqGrrgrpspavlealaral 54
                                  ++ r +Re+  +sq e+   l+ s+s +s++E+Grr  ps a ++++++al
  gi|13541345|ref|NP_111033.1| 21 ETIRKWREEFKVSQLELSNFLNQSPSVISDYETGRRKFPSIASVRKIVDAL 71
                                  6789*********************************************98 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   3.1e-08   0.00019       2      49 ..      21      68 ..      20      72 .. 0.90

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 3.1e-08
                        HTH_19  2 erLkeaReelgltqeelaerlgisrskisaiEngkkdvpsaelllkia 49
                                  e +++ Ree++ +q el++ l  s+s is +E+g+++ ps+  ++ki+
  gi|13541345|ref|NP_111033.1| 21 ETIRKWREEFKVSQLELSNFLNQSPSVISDYETGRRKFPSIASVRKIV 68
                                  679****************99999**********999**999888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1523.56
//
Query:       gi|13541346|ref|NP_111034.1|  [L=418]
Description: metal-dependent hydrolase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.5e-61  207.1   0.3    5.4e-61  206.8   0.3    1.0  1  Amidohydro_1  Amidohydrolase family
    4.4e-19   69.3   0.4    3.6e-15   56.4   0.0    2.2  2  Amidohydro_3  Amidohydrolase family
      5e-05   22.8   0.0    7.6e-05   22.2   0.0    1.4  1  TatD_DNase    TatD related DNase
  ------ inclusion threshold ------
      0.037   14.1   0.1       0.34   11.0   0.0    2.4  2  a_DG1_N2      Alpha-Dystroglycan N-terminal domain 2


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 !  206.8   0.3   1.2e-64   5.4e-61       1     343 [.      51     397 ..      51     398 .. 0.90

  Alignments for each domain:
  == domain 1  score: 206.8 bits;  conditional E-value: 1.2e-64
                                   EEEE-EEEEEEECETTECSSS....GHHHHH.........STTHHHHHHHHHHHHHHHHTTEEEEEEEEHSSTHHHHHHHH CS
                  Amidohydro_1   1 ivlPGlIDaHvHleqsllrga....tledwl.........vppetaaealesgiktalksGtttvadmgattstgiealle 68 
                                   +++PGlI++H H+ +s+++g     +l+++l          +   +   ++ g+ +++++G+t + d ++    + + +++
  gi|13541346|ref|NP_111034.1|  51 VLMPGLINTHAHVGMSASKGLfddvDLDSFLkktfeydsdRTSTGIFNSAKLGMYEMIGNGITAFVDLYY----SEDIIAK 127
                                   58****************999****************88777777889999*******************....99***** PP

                                   HHHTSSSEEEEEEESSEGGS......GCCCSHHHHHHHHHHHHHHHHHHCTTTCEEEEEEECGTCCSHHHHHHHHHHHHHH CS
                  Amidohydro_1  69 aaeelplglrilggkvsldr......gsaetskasreklkagaaetikgkadgvvkvalapheapafsdeelkealkeakk 143
                                   aaee+  g+r+++++v ld+      g         ++ ++ +  +    +++ v + ++  + + + d++ + a+++a+k
  gi|13541346|ref|NP_111034.1| 128 AAEEI--GIRAFLSWVTLDKelttqiG-------DPVENAENF--IRNHVGNKYVVPSVGVQGIYVANDDTFRRAMDLAEK 197
                                   ****8..************65554331.......333333333..22234678888************************* PP

                                   HTTEEEEEETSSCHHHHHHHHHHTTTEEEETTTTSTCCHHTTTHCCEEEHCTCEEEHHHHHHHHHHHHHHCEEHHHHHHHH CS
                  Amidohydro_1 144 rdlpvaiHaletkgevedaeaafgetiehgthlevaeslglldeiklilahgvhltpteaellkerlkeagvahcpfsnsi 224
                                   +++ +++H++et++ev da+++ g   e+  + e ++ +g+l++ ++++ah+v+ t +e++ll ++  +++v+    sn +
  gi|13541346|ref|NP_111034.1| 198 YGTILHMHLSETRKEVYDAVKKLG---ER--PIEHLHNIGILNK-RVLAAHCVWATYHEVRLLSKD--GVNVSWNSISNFK 270
                                   ************************...88..9999999******.*********************..9999988999999 PP

                                   SEH.HHHHHHHHHHHTSCEEEEEECTTSSCCGGHHHHHHHHHHHHHHCCTT.TTHCHCHHHHHHHHHTHHHHHHTT-TTTS CS
                  Amidohydro_1 225 lrs.grealrkaldeGvkvglgtDgaasgnslnlleelrlalklqrgllye.deegglslkealrmaTingAkalglddkv 303
                                   l++ g++++ ++++e+v+v++gtD+++s+nsl++++ +++ + +   ++y+ d +  +++ e+l+maT n+A+al l  ++
  gi|13541346|ref|NP_111034.1| 271 LGTgGIPPIPEMMRENVNVTIGTDSNGSNNSLDMFQAMKFSAISV--KNYRwD-ASLMKAQEILDMATRNAARALQL--NA 346
                                   88736999**********************************444..477767.555********************..** PP

                                   SSS-TTSB--EEEECCCT...........CGGGTTTCTSEEEEEEEETTEE CS
                  Amidohydro_1 304 GsievGkdADlvvvdldi...........laafvglkkdgnvkkvivkGkl 343
                                   GsievGk AD v++d +i            +++v+++++ nv++vi++G++
  gi|13541346|ref|NP_111034.1| 347 GSIEVGKLADVVLLDATIpsmiptneanaVSNIVYSSSPQNVDTVIIDGEI 397
                                   ****************5556788899999********************87 PP

>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.3   5.1e-05      0.23       3      21 ..      45      63 ..      44      77 .. 0.86
   2 !   56.4   0.0   8.1e-19   3.6e-15     261     471 ..     184     397 ..     159     398 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 5.1e-05
                  Amidohydro_3  3 iDakGrlvlPGFvDsHtHl 21
                                  iD ++++++PG++  H+H+
  gi|13541346|ref|NP_111034.1| 45 IDGTNKVLMPGLINTHAHV 63
                                  899***************4 PP

  == domain 2  score: 56.4 bits;  conditional E-value: 8.1e-19
                  Amidohydro_3 261 edealaelvaaadergldvaihaigdaavd.dvldafeaa....aekngnqdrr.rlehaegvtesqiervaalqvaagvq 335
                                    d+++++ +++a ++g  +++h  ++ +   d+++ + ++     ++ g   +r  ++h+ + t+++++ + + +v  ++ 
  gi|13541346|ref|NP_111034.1| 184 NDDTFRRAMDLAEKYGTILHMHLSETRKEVyDAVKKLGERpiehLHNIGILNKRvLAAHCVWATYHEVRLLSKDGVNVSWN 264
                                   4677999999999999999999999998888888888888777744444444444999*********************** PP

                  Amidohydro_3 336 pvfnfedelldsrlgperargstpvkellnagvkvalgsDapvgpfdpwprigaavmrktrrggevlrpdeelsleealal 416
                                    ++nf          +  + g++p+ e+++ +v+v+ g+D++ g+ +++  ++a+  +    + +++++   +  +e+l++
  gi|13541346|ref|NP_111034.1| 265 SISNF----------KLGTGGIPPIPEMMRENVNVTIGTDSN-GSNNSLDMFQAMKFSAISVK-NYRWDASLMKAQEILDM 333
                                   *****..........4456688******************44.45566666666666665544.8**************** PP

                  Amidohydro_3 417 yTrgpAkalgledrkGtLevGadADlvvldadpldvdppelaear...........vrltvvdGrv 471
                                    Tr++A+al l    G++evG+ AD+v+lda +  + p++ a+a+           v  +++dG++
  gi|13541346|ref|NP_111034.1| 334 ATRNAARALQLNA--GSIEVGKLADVVLLDATIPSMIPTNEANAVsnivyssspqnVDTVIIDGEI 397
                                   *************..***************99999999999999999999999999*****99987 PP

>> TatD_DNase  TatD related DNase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   1.7e-08   7.6e-05     110     187 ..     185     274 ..     169     343 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 1.7e-08
                                   HHHHHHHHHHHHHTTEEEEEEEES-HHHHHHHHHHCGGCCS............EEEETT--S-HHHHHHHHHTTEEEEE-G CS
                    TatD_DNase 110 eevFeeqlrlAkelklplviHlrkaeedlleilkeaaeaka............kvvlHsfsgsaeeakkflklgyyislsg 178
                                    + F++ ++lA++++ +l +Hl ++ +++++++k+++e+++                H+   +++e++ ++k g+ +s + 
  gi|13541346|ref|NP_111034.1| 185 DDTFRRAMDLAEKYGTILHMHLSETRKEVYDAVKKLGERPIehlhnigilnkrVLAAHCVWATYHEVRLLSKDGVNVSWNS 265
                                   578**********************************99977777777777644446889999999999999999999999 PP

                                   GGGTTTTHH CS
                    TatD_DNase 179 lltfknake 187
                                   +++fk ++ 
  gi|13541346|ref|NP_111034.1| 266 ISNFKLGTG 274
                                   999986655 PP

>> a_DG1_N2  Alpha-Dystroglycan N-terminal domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   7.5e-05      0.34      23      80 ..     207     264 ..     200     296 .. 0.88
   2 ?   -0.1   0.0      0.21   9.3e+02       5      24 ..     384     403 ..     380     405 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 7.5e-05
                      a_DG1_N2  23 skerlellakmkkfskvplellkllpvvnnrlldmsafmaGpGnakkvvenGallswk 80 
                                   s+ r e+ + +kk  + p+e+l+ + + n+r+l +    a   +++   ++G+ +sw+
  gi|13541346|ref|NP_111034.1| 207 SETRKEVYDAVKKLGERPIEHLHNIGILNKRVLAAHCVWATYHEVRLLSKDGVNVSWN 264
                                   56778889999**********************************************7 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.21
                      a_DG1_N2   5 epvtvltvildadltklssk 24 
                                    p  v tvi+d +++k++ k
  gi|13541346|ref|NP_111034.1| 384 SPQNVDTVIIDGEIKKINGK 403
                                   577889*********99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (418 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       584  (0.0325729); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 2572.85
//
Query:       gi|13541347|ref|NP_111035.1|  [L=155]
Description: transcription regulator [Thermoplasma volcanium GSS1]
Scores for complete 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   0.9      1e-06   28.6   0.3    1.6  2  PadR             Transcriptional regulator PadR-like family
    8.4e-05   22.9   0.0    0.00013   22.3   0.0    1.3  1  Penicillinase_R  Penicillinase repressor
    0.00036   20.3   0.1    0.00046   20.0   0.1    1.3  1  DUF4364          Domain of unknown function (DUF4364)
    0.00047   20.0   0.2     0.0013   18.6   0.1    1.8  2  TrmB             Sugar-specific transcriptional regulator Trm
    0.00053   19.9   0.3    0.00092   19.2   0.3    1.5  1  HTH_45           Winged helix-turn-helix
  ------ inclusion threshold ------
      0.052   13.8   0.1      0.072   13.3   0.1    1.2  1  STN1_2           CST, Suppressor of cdc thirteen homolog, com
       0.14   12.1   0.0       0.31   11.0   0.0    1.6  1  MarR             MarR family


Domain annotation for each model (and alignments):
>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.3   4.1e-10     1e-06       1      73 [.       8      71 ..       8      73 .. 0.92
   2 ?   -2.9   0.0       2.6   6.7e+03      12      25 ..      78      91 ..      75      96 .. 0.62

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 4.1e-10
                                  HHHHHCCS-EEHHHHHHHHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCHHH CS
                          PadR  1 iLalleeqpsyGyeiikeleelsegllelseGslYpaLkrLekeglveseweesgegpprkyYrlTdaGrrel 73
                                  iL ll+ +++  yei k+++ +     ++s+G+++p+ k+L + g+++ ++e      ++k+Y  T++G++++
  gi|13541347|ref|NP_111035.1|  8 ILILLSGREMTLYEISKRVDLY--S--TVSHGTVFPVIKKLLDGGFIKYRMEG-----NKKLYYATEKGQNYV 71
                                  7899999**************9..3..89*********************885.....8***********986 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.6
                                  HHHHHHHHHCCSTT CS
                          PadR 12 Gyeiikeleelseg 25
                                  G e+++++ e s g
  gi|13541347|ref|NP_111035.1| 78 GRELKEKIMEKSMG 91
                                  55666666665444 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   5.1e-08   0.00013      16     113 ..      15     113 ..       8     114 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 5.1e-08
                                   S-EEHHHHHHT--GGG---HHHHHHHHHHHHHTTS-EEEEETTEEEEE----XXXXX...XXXXXXXXXXXXXXXXXXXXX CS
               Penicillinase_R  16 geatvkevveeleeekelaysTVktllrrLvkKgllsrekegrafiYsplvseeeav...asavkqlldklfegsvkelva 93 
                                    e+t  e+ ++++  ++++  TV  ++++L++ g+++ + eg++ +Y+++ + +++v   ++  ++l +k++e+s+ +++ 
  gi|13541347|ref|NP_111035.1|  15 REMTLYEISKRVDLYSTVSHGTVFPVIKKLLDGGFIKYRMEGNKKLYYATEKGQNYVtniQNIGRELKEKIMEKSMGNALF 95 
                                   56899999999999999**********************************999998222456789999999999999885 PP

                                   XXXXXXXXXXXXXXXXXXXX CS
               Penicillinase_R  94 afveeeklseddleeLrell 113
                                    +      s++d+e+Lr+++
  gi|13541347|ref|NP_111035.1|  96 YLNLL--SSDEDAEALRTAI 113
                                   54333..5788888888765 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.1   1.8e-07   0.00046      38      88 ..      39      88 ..      14     108 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1.8e-07
                       DUF4364 38 qalseLvesglieeeekenktlykiTekGketlelfenripksirekidey 88
                                   ++++L++ g+i+ + + nk+ly  TekG++ +  ++n i  +++eki+e 
  gi|13541347|ref|NP_111035.1| 39 PVIKKLLDGGFIKYRMEGNKKLYYATEKGQNYVTNIQN-IGRELKEKIMEK 88
                                  6899***************************9998875.788888887765 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.1     5e-07    0.0013      16      65 ..      10      64 ..       5      66 .. 0.85
   2 ?   -2.5   0.0       1.9   4.9e+03      13      22 ..      95     104 ..      92     115 .. 0.69

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 5e-07
                                  HHHHHCCCHHCHHCCCTT....SSCHCHHHHHHHHHHCTSEEEES.STTTEEEE- CS
                          TrmB 16 aLlklgpatadeiaeelg....vprskvYevLrsLedkGlVerek.grpklYrav 65
                                   Ll+  ++t +ei+++++    v++ +v  v+++L+d G+++ +  g++klY a+
  gi|13541347|ref|NP_111035.1| 10 ILLSGREMTLYEISKRVDlystVSHGTVFPVIKKLLDGGFIKYRMeGNKKLYYAT 64
                                  79999**********9764444899****************866537899**997 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.9
                                   HCHHHHHHCC CS
                          TrmB  13 vYlaLlklgp 22 
                                    Yl Ll++++
  gi|13541347|ref|NP_111035.1|  95 FYLNLLSSDE 104
                                   6899996544 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.3   3.6e-07   0.00092      38      75 ..      39      80 ..       7      82 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 3.6e-07
                        HTH_45 38 kYLdmLvekgli....kkskekYvlTekGlelleklkeleel 75
                                    +++L++ g+i    + +k+ Y+ TekG++++ +++++ + 
  gi|13541347|ref|NP_111035.1| 39 PVIKKLLDGGFIkyrmEGNKKLYYATEKGQNYVTNIQNIGRE 80
                                  56899*******8887779******************98765 PP

>> STN1_2  CST, Suppressor of cdc thirteen homolog, complex subunit STN1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   2.8e-05     0.072     112     159 ..      39      84 ..      11      91 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.8e-05
                                   HHHHHHHHCTSEE-SSSSSTTEEEEGCCSHHHHHHHHHHHHTGGGXXT CS
                        STN1_2 112 ealqllqeeGlvfqkkksqdelyqvteqdkdLlkaildiiredcrrek 159
                                    +++ l + G++  +++ +++ly++te+ ++  ++i++i re   +ek
  gi|13541347|ref|NP_111035.1|  39 PVIKKLLDGGFIKYRMEGNKKLYYATEKGQNYVTNIQNIGRE--LKEK 84 
                                   57999*********************************9888..3455 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   0.00012      0.31      27      48 ..      30      51 ..       7      59 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00012
                                  HTS-HHHHHHHHHHHHHTTSEE CS
                          MarR 27 lgvskstvtrvldrLekkGlie 48
                                  + vs +tv  v+++L + G+i+
  gi|13541347|ref|NP_111035.1| 30 STVSHGTVFPVIKKLLDGGFIK 51
                                  56899***************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       649  (0.0361983); expected 358.6 (0.02)
Passed bias filter:                      526  (0.0293379); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1103.33
//
Query:       gi|13541348|ref|NP_111036.1|  [L=481]
Description: multidrug efflux permease [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-46  159.0  42.3    1.4e-46  159.0  42.3    2.6  2  MFS_1          Major Facilitator Superfamily
    3.7e-07   29.4   8.2    3.7e-07   29.4   8.2    4.4  4  Sugar_tr       Sugar (and other) transporter
    6.5e-05   21.6  12.9    6.5e-05   21.6  12.9    1.8  2  TRI12          Fungal trichothecene efflux pump (TRI12)
     0.0017   17.0   6.3     0.0017   17.0   6.3    4.5  4  MFS_2          MFS/sugar transport protein
  ------ inclusion threshold ------
       0.45   10.4   3.1       0.61   10.0   0.3    2.4  2  DUF412         Protein of unknown function, DUF412
        5.2    5.2  10.4       0.18   10.0   0.2    3.0  3  OATP           Organic Anion Transporter Polypeptide (OATP) f


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 !  159.0  42.3   4.8e-50   1.4e-46       2     353 .]      15     407 ..      14     407 .. 0.92
   2 ?   -1.9   5.2      0.39   1.2e+03     130     172 ..     429     468 ..     415     479 .. 0.57

  Alignments for each domain:
  == domain 1  score: 159.0 bits;  conditional E-value: 4.8e-50
                         MFS_1   2 llaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfa 82 
                                   ++a++l+++  ++++palp +l + +  + + +++++t+y +   ++s ++Grl+d +G +r++++ + ++++++ ++ fa
  gi|13541348|ref|NP_111036.1|  15 AFAGLLVTYVETMITPALP-ILVTFFDTNYDKLSWVITAYIISGTISSAIFGRLADMYGKKRIFIVLAGVYSIAVSFGGFA 94 
                                   78999**************.9*****************************************************6666696 PP

                         MFS_1  83 sslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsll 163
                                    +l  l++ r +qGlg+ ++fp++ ali d +pk++ ++a g++s++fs Ga++g +lg+++++++gW++++    +v+l+
  gi|13541348|ref|NP_111036.1|  95 KTLEELIIIRTVQGLGM-GMFPVSFALINDQVPKNRLALAQGIVSSTFSGGAAIGLVLGAWITQNYGWQWSYHSSIPVALI 174
                                   5555************8.9************************************************************** PP

                         MFS_1 164 afvlfllllpeepperkrkspkeee............................................kgtgpaplvpaw 200
                                   ++ +++++l +e ++rk   +                                                +++ p p+++ +
  gi|13541348|ref|NP_111036.1| 175 LLAVAAIYLHDESSRRKSTVDFIGVsmlaialvslilglsegeywgwssasiislfalslilvfafvylEQRSPEPFIN-L 254
                                   *998888888888888888777777******************************************************.* PP

                         MFS_1 201 kallkdpvlwillialllfffgfsglltllplylqe..vlgls.glllaglllallalvgailallagrlsdrlgrrrrll 278
                                   ++l++++vl++ +++l+ + +g+++l++ +p +lq+    g++ + +++gl+l  +a++++++a+la++l +  g++++++
  gi|13541348|ref|NP_111036.1| 255 SLLKTRNVLLANIAGLFAM-AGMFFLFYSVPPLLQDpePAGFGvTIVESGLILLPAAVLNMVFAPLAAKLTTNRGPKTAII 334
                                   *********9555555555.48888999999987762223444658*************************999******* PP

                         MFS_1 279 lallllllaalglallavtssavllllvlvliGfglgfvfpsllalasdlappeeagtasglfntagslggalgp 353
                                   ++l++l+++++gl++   +   v++l    ++G+g +f+f+ +++++  ++p+e+ag  +g + +++++g++l+p
  gi|13541348|ref|NP_111036.1| 335 VGLIILFFSYFGLYYNRSS--IVAILEDASIMGMGISFIFVGIINILLVSVPREKAGESTGMNVVFRNIGTSLAP 407
                                   ***************9999..44444477779*****************************************98 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.39
                         MFS_1 130 fslGailgpllggllasslgWravfyilaivsllafvlfllll 172
                                   + +G  + p+++++ + s+ + +++++  i+ ++a+vl    +
  gi|13541348|ref|NP_111036.1| 429 NFAGLGFIPIFSSFPS-SAAYDSIYMVGMIFVVVALVL--SMF 468
                                   4445555555555555.334666666666666666554..333 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   8.2   1.2e-10   3.7e-07       4     119 ..      13     114 ..      10     120 .. 0.81
   2 !    8.3   0.3    0.0003       0.9      40      81 ..     126     167 ..     114     174 .. 0.81
   3 !    4.9   0.5    0.0034        10     301     363 ..     174     242 ..     168     255 .. 0.64
   4 ?   -1.9   4.2      0.38   1.1e+03     296     356 ..     309     374 ..     295     383 .. 0.73

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 1.2e-10
                                   HHHHHHHHHHHHHHCGGGTHHHHHHHHTSTT--SHHHHHH...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHH CS
                      Sugar_tr   4 vaalggllfgYdtgvigafltllkfaknfglsksksskeessvlsglivsiflvGaiiGslfagllgdrfGRkkslliaav 84 
                                   +aa++gll  Y   +i ++l +l +++    +++++        ++++  ++++ ++i+s ++g l+d++G+k ++++ a 
  gi|13541348|ref|NP_111036.1|  13 IAAFAGLLVTYVETMITPALPILVTFF----DTNYD-------KLSWVITAYIISGTISSAIFGRLADMYGKKRIFIVLAG 82 
                                   566666666666666666666666222....22332.......2479********************************** PP

                                   HHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHH CS
                      Sugar_tr  85 lfvigavlqaaakgknsvevlivgRvlvGigvGla 119
                                   +++i+    ++ak   ++e li+ R + G+g+G++
  gi|13541348|ref|NP_111036.1|  83 VYSIAVSFGGFAK---TLEELIIIRTVQGLGMGMF 114
                                   *************...9****************86 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0003
                                   HHHH...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHH CS
                      Sugar_tr  40 skeessvlsglivsiflvGaiiGslfagllgdrfGRkkslli 81 
                                   +k+++++ +g++ s f+ Ga+iG +++ ++++ +G ++s+  
  gi|13541348|ref|NP_111036.1| 126 PKNRLALAQGIVSSTFSGGAAIGLVLGAWITQNYGWQWSYHS 167
                                   455567889****************************99865 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.0034
                                   HHHHHHHHHHHHHS-SHHHHH..HHHHHHHHHHHHHH..HHHHTTSS..........CHHHHHHHHHHHHHH CS
                      Sugar_tr 301 fvatfvaiflvdrfGRRtlll..lGaagmaicfvilgivalllvaks.......kaasivaivfialfialf 363
                                   ++  ++ai+l d  +RR+  +  +G+++ ai++v l    l l++++       + +s  a+ +i++f++++
  gi|13541348|ref|NP_111036.1| 174 ILLAVAAIYLHDESSRRKSTVdfIGVSMLAIALVSL---ILGLSEGEywgwssaSIISLFALSLILVFAFVY 242
                                   5667889**********8654327766666666655...344444445555111555555566666777666 PP

  == domain 4  score: -1.9 bits;  conditional E-value: 0.38
                                   HHHHHHHHHHHHHHHHHHS-SHHHHHHHHHHHHHHHHHHH......HHHHTTSS....CHHHHHHH CS
                      Sugar_tr 296 vgvvnfvatfvaiflvdrfGRRtllllGaagmaicfvilg....ivalllvaks.kaasivaivfi 356
                                     v+n+v+   a+ l    G +t  ++G+++ ++  + l      ++++l+++s  +++i +i+  
  gi|13541348|ref|NP_111036.1| 309 AAVLNMVFAPLAAKLTTNRGPKTAIIVGLIILFFSYFGLYynrsSIVAILEDASiMGMGISFIFVG 374
                                   679999999999999999999999999999888888777666776666666665455555555444 PP

>> TRI12  Fungal trichothecene efflux pump (TRI12)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6  12.9   2.2e-08   6.5e-05      59     309 ..      24     260 ..       2     282 .. 0.76
   2 ?   -2.4   0.9      0.39   1.2e+03     529     555 ..     445     471 ..     439     474 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 2.2e-08
                         TRI12  59 vlqasasalpnilqdvgq.sensslfstlwttgqavsilvmgrltdrfgrrp.fvilthilglvgaivgctatkfntllaa 137
                                   v    + alp ++       ++ s + t + +  ++s  ++grl+d +g++  f++l+ +   +    g  a+ ++ l+  
  gi|13541348|ref|NP_111036.1|  24 VETMITPALPILVTFFDTnYDKLSWVITAYIISGTISSAIFGRLADMYGKKRiFIVLAGVY-SIAVSFGGFAKTLEELIII 103
                                   33444567776655444303455677889999999**************866155555555.566677889999******* PP

                         TRI12 138 mtllgvaagpagasplfvgelmsnktkflgllivsipvvvtsglspylgqrlaiqgswrwifyiyiitsaiavllivvwyy 218
                                    t+ g+  g    s  ++ + + ++   l   ivs      ++++  lg  ++ +  w+w ++     s+i v li++   
  gi|13541348|ref|NP_111036.1| 104 RTVQGLGMGMFPVSFALINDQVPKNRLALAQGIVSSTFSGGAAIGLVLGAWITQNYGWQWSYH-----SSIPVALILLAV- 178
                                   *******************9999999999999***99999999*****************986.....666677766543. PP

                         TRI12 219 ppsfaqlhgkkvrkreelakldwigiilvivgvslfllgvswggkpnspwnsakviglissglgslvvfalyevygkpvrp 299
                                     +   lh    r++   + +d+ig+ ++++    ++lg+s g      w sa +i l++     ++vfa+  +  +  +p
  gi|13541348|ref|NP_111036.1| 179 --AAIYLHDESSRRK---STVDFIGVSMLAIALVSLILGLSEGEY--WGWSSASIISLFAL--SLILVFAFVYLEQRSPEP 250
                                   ..3445777666554...579*****888777777789***9975..68*********975..557899988888899999 PP

                         TRI12 300 ivppalfkdt 309
                                   ++  +l+k  
  gi|13541348|ref|NP_111036.1| 251 FINLSLLKTR 260
                                   **99999854 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.39
                         TRI12 529 tasyanvyyfamalgvipiiaslcmrd 555
                                   +a+y  +y + m + v+ ++ s+ m++
  gi|13541348|ref|NP_111036.1| 445 SAAYDSIYMVGMIFVVVALVLSMFMKN 471
                                   589999****************99987 PP

>> MFS_2  MFS/sugar transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   6.3   5.5e-07    0.0017     226     327 ..      12     113 ..       1     126 [. 0.69
   2 ?    1.4   2.7     0.031        93     264     310 ..     137     189 ..     128     210 .. 0.76
   3 ?   -0.5  15.3      0.12   3.5e+02     149     330 ..     198     370 ..     184     409 .. 0.72
   4 ?   -0.9   3.1      0.16   4.7e+02     269     312 ..     429     471 ..     407     477 .. 0.67

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 5.5e-07
                         MFS_2 226 flillllfllaalalgvlnglllYyltyvlgngsaasvfllvvtisallgiplwqplakrlgkkntyllgalltivllvlv 306
                                   +++ +++ l++++ ++++ +l +  +t++  n+++ s++ ++ +is++++++++ +la  +gkk+++++ a ++ +   + 
  gi|13541348|ref|NP_111036.1|  12 AIAAFAGLLVTYVETMITPALPI-LVTFFDTNYDKLSWVITAYIISGTISSAIFGRLADMYGKKRIFIVLAGVYSIAVSFG 91 
                                   56667777777777777777666.5677778*************************************9988775555444 PP

                         MFS_2 307 lll.qpsnlllflvllviagfg 327
                                    ++ + + l++  +++ +++  
  gi|13541348|ref|NP_111036.1|  92 GFAkTLEELIIIRTVQGLGMGM 113
                                   4441334444444444443333 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.031
                         MFS_2 264 fllvvtisallgiplwqplakrlgkkntyllgalltivllvlvlll......q 310
                                   ++ ++  +a++g++l +++++ +g + +y +++ ++++ll+++ +       +
  gi|13541348|ref|NP_111036.1| 137 VSSTFSGGAAIGLVLGAWITQNYGWQWSYHSSIPVALILLAVAAIYlhdessR 189
                                   4555667889***************************9999988776555542 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.12
                         MFS_2 149 laailafllvlilgglkserkgylifaliialLmllgviivvlgtkervemrkkekteqkeklslleqlkevfrnraflil 229
                                   ++++la++lv    g  se + + +  + i  L++l+ i+v++++  +          q+++ ++++   ++++ r  l+ 
  gi|13541348|ref|NP_111036.1| 198 GVSMLAIALVSLILG-LSEGEYWGWSSASIISLFALSLILVFAFVYLE----------QRSPEPFINL--SLLKTRNVLLA 265
                                   334444444444444.45668888889999999999999999999844..........5555555554..45566668888 PP

                         MFS_2 230 lllfllaalalgvlnglllYyltyvlgngsaasvfl.lvvtisal....lgiplwqplakrlgkkntyllgalltivllvl 305
                                    +++l+a++++++l+  +   l++   +g+ ++++  +++ ++a+    +++pl+++l++  g k+++++g++++++ +++
  gi|13541348|ref|NP_111036.1| 266 NIAGLFAMAGMFFLFYSVPPLLQDPEPAGFGVTIVEsGLILLPAAvlnmVFAPLAAKLTTNRGPKTAIIVGLIILFFSYFG 346
                                   8999*******************999999999987413334444444448888888888888999**************** PP

                         MFS_2 306 vlllqpsnlllflvllviagfgvgv 330
                                   ++    s++++ l  + i g+g+ +
  gi|13541348|ref|NP_111036.1| 347 LYYN-RSSIVAILEDASIMGMGISF 370
                                   9999.66666655433333333222 PP

  == domain 4  score: -0.9 bits;  conditional E-value: 0.16
                         MFS_2 269 tisallgiplwqplakrlgkkntyllgalltivllvlvlllqps 312
                                     ++l +ip+++ + +      +y++g+++++v lvl +++ ++
  gi|13541348|ref|NP_111036.1| 429 NFAGLGFIPIFSSFPSSAAYDSIYMVGMIFVVVALVLSMFM-KN 471
                                   44455666777777777777778888888888888888888.44 PP

>> DUF412  Protein of unknown function, DUF412
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.3    0.0002      0.61      29      89 ..     189     250 ..     165     267 .. 0.86
   2 ?   -0.1   0.2      0.26   7.9e+02      41      81 ..     307     349 ..     296     359 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0002
                        DUF412  29 rvikatrfaikvmpalavltlvlqlylagsealpqailtalfllsLPl.QGlywlGkraktp 89 
                                   r  +++ f    m a+a+++l+l l  +++  +++a +++lf+lsL l  ++++l +r+ +p
  gi|13541348|ref|NP_111036.1| 189 RRKSTVDFIGVSMLAIALVSLILGLSEGEYWGWSSASIISLFALSLILvFAFVYLEQRSPEP 250
                                   6667778888899****************99**************97527999****99876 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.26
                        DUF412  41 mpalavltlvlqlylagse..alpqailtalfllsLPlQGlyw 81 
                                   +pa ++ +++  l+ + ++     +ai+++l++l     Gly+
  gi|13541348|ref|NP_111036.1| 307 LPAAVLNMVFAPLAAKLTTnrGPKTAIIVGLIILFFSYFGLYY 349
                                   454443333333332222233788999******9999999997 PP

>> OATP  Organic Anion Transporter Polypeptide (OATP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.2   6.1e-05      0.18     141     195 ..     106     159 ..      93     170 .. 0.87
   2 ?    0.0   1.0     0.066     2e+02      51      79 ..     337     367 ..     331     380 .. 0.74
   3 ?   -1.8   1.3      0.23     7e+02     155     198 ..     377     420 ..     354     470 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 6.1e-05
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          OATP 141 llGiGatpiytlGisYidDnvkkknsplylgilyalrilGpalGfllGslllkly 195
                                   ++G+G   ++++  + i D v k++ +l  gi++++   G a+G +lG+ +++ y
  gi|13541348|ref|NP_111036.1| 106 VQGLGMG-MFPVSFALINDQVPKNRLALAQGIVSSTFSGGAAIGLVLGAWITQNY 159
                                   5566644.589999************************************99988 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.066
                                   xxxxxxxxxxxxxxxxxxxxxx..xxxxxxx RF
                          OATP  51 llilfvsYfggrghrPrwigig..allmalg 79 
                                   l+ilf sYfg   +r  +++i   a +m++g
  gi|13541348|ref|NP_111036.1| 337 LIILFFSYFGLYYNRSSIVAILedASIMGMG 367
                                   689999****999999999984334444444 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 0.23
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          OATP 155 sYidDnvkkknsplylgilyalrilGpalGfllGslllklyvdi 198
                                     +  +v ++++    g+  ++r +G  l+ ++G+++  +yv+ 
  gi|13541348|ref|NP_111036.1| 377 NILLVSVPREKAGESTGMNVVFRNIGTSLAPAIGGVFETMYVTY 420
                                   44444455555555556666667777777777777777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (481 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       977  (0.0544927); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                        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: 0.71u 0.30s 00:00:01.01 Elapsed: 00:00:00.46
# Mc/sec: 3170.68
//
Query:       gi|13541349|ref|NP_111037.1|  [L=524]
Description: hypothetical protein TVN0518 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.6e-08   34.7   0.3      0.028   14.7   0.1    4.1  3  NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosi
    0.00069   19.8   4.4        7.8    6.8   0.1    3.9  3  CARDB        CARDB
  ------ inclusion threshold ------
       0.11   12.4   0.7         14    5.6   0.9    2.7  2  ECSCR        Endothelial cell-specific chemotaxis regulator


Domain annotation for each model (and alignments):
>> NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0     0.033     2e+02      44      71 ..      92     119 ..      87     124 .. 0.89
   2 !   14.7   0.1   4.7e-06     0.028       8      69 ..     173     233 ..     170     242 .. 0.88
   3 !   12.1   0.0   2.9e-05      0.17      42      78 ..     422     458 ..     371     459 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.033
                   NPCBM_assoc  44 aaslapGetveatvkVtppagaaaGdye 71 
                                   ++ l++G+ v+   +V ++++a  G y+
  gi|13541349|ref|NP_111037.1|  92 FSYLPAGKPVTLVQMVNVNPNASDGLYR 119
                                   5679*********************995 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 4.7e-06
                   NPCBM_assoc   8 tltltvtndgtaaatnvslslslPeGWtvvevspasaaslapGetveatvkVtppagaaaGd 69 
                                    lt+ + n+g+  ++nvs+s  +P+G     ++ +++a ++pGe+v +t+ V++ ++a +G 
  gi|13541349|ref|NP_111037.1| 173 PLTVMLENNGNVYTQNVSISY-VPQGPIYGYTQNTTLAVIPPGEAVPVTFIVSVKNNATNGV 233
                                   5789999************96.8999887889999***********************9996 PP

  == domain 3  score: 12.1 bits;  conditional E-value: 2.9e-05
                   NPCBM_assoc  42 asaaslapGetveatvkVtppagaaaGdyevtakarl 78 
                                    ++a+l pG+++ + + V  ++ a  G+y++++ a++
  gi|13541349|ref|NP_111037.1| 422 ITIARLVPGQSFLVVFVVDTSSAAHSGQYPIQLYASW 458
                                   4677****************************99987 PP

>> CARDB  CARDB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.9   0.2    0.0026        15      22      72 ..     173     226 ..     160     260 .. 0.87
   2 !    6.5   0.0    0.0017       9.9      17      60 ..     276     321 ..     263     343 .. 0.78
   3 !    6.8   0.1    0.0013       7.8      19      83 ..     375     455 ..     360     462 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0026
                                   EEEEEEEE-SSS-EEEEEEEEEETTEEE...EEEEESEE-CTEEEEEEEEEE-S CS
                         CARDB  22 titvtvkNqGtaasgatkvalyldgelv...gtvtvpsLaagesttvsftwtte 72 
                                    +tv ++N+G+ + ++++++++  g      +++t++ + +ge + v+f + ++
  gi|13541349|ref|NP_111037.1| 173 PLTVMLENNGNVYTQNVSISYVPQGPIYgytQNTTLAVIPPGEAVPVTFIVSVK 226
                                   679999****************9999988889999*************999887 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0017
                                   TTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEE..EEEEESEE-CT CS
                         CARDB  17 vgeentitvtvkNqGtaasgatkvalyldgelv..gtvtvpsLaag 60 
                                   +++ +++++ ++N+G+ ++++t++ ++ ++ +v     +v+ L +g
  gi|13541349|ref|NP_111037.1| 276 NEKFISLKIGIQNSGNTYAKNTSIFITSSDFTVlsHGYNVSYLPSG 321
                                   555689999**************99999988887766777766665 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.0013
                                   SEEEEEEEEEE-SSS-EEEEEEEEEETTEEE..............EEEEESEE-CTEEEEEEEEEE-S..-S-CEEEEEEE CS
                         CARDB  19 eentitvtvkNqGtaasgatkvalyldgelv..............gtvtvpsLaagesttvsftwtte..ategevtltvv 83 
                                   ++++++++++N+G+ + ++++v l     l+              +++t++ L +g+s  v f + t+  a++g++ ++++
  gi|13541349|ref|NP_111037.1| 375 DKSSLYFNITNEGNRTMYDINVHLLYPAILTihtpssnpllaltaNNITIARLVPGQSFLVVFVVDTSsaAHSGQYPIQLY 455
                                   568899*****************9988877777776666666666666668888888888777777776777777777665 PP

>> ECSCR  Endothelial cell-specific chemotaxis regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0     0.012        73      82     100 ..     101     119 ..      95     121 .. 0.88
   2 ?    5.6   0.9    0.0023        14       9      53 ..     474     519 ..     469     523 .. 0.70

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.012
                         ECSCR  82 itlismkninsnnskgsyt 100
                                   +tl+ m n+n n s g y 
  gi|13541349|ref|NP_111037.1| 101 VTLVQMVNVNPNASDGLYR 119
                                   8**************9886 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0023
                         ECSCR   9 tilpsptsetvlt.vaafgvisfivilvvvviilvsvvslrfkcrk 53 
                                   ++  spt e  l+   +f  ++  v+ v+vv+++   v    k rk
  gi|13541349|ref|NP_111037.1| 474 SVRISPTVEQQLSdFFTFNYVTVAVLAVIVVVVVGIAVYAGVKSRK 519
                                   5666888888775256788888888777777777666777777777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (524 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       850  (0.0474092); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); 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: 00:00:00.43
# Mc/sec: 3639.34
//
Query:       gi|13541350|ref|NP_111038.1|  [L=220]
Description: winged helix-turn-helix domain-containing protein/riboflavin kinase [Thermoplasma volcanium GSS1]
Scores for complete 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  137.9   0.1    2.4e-40  137.4   0.1    1.2  1  CTP-dep_RFKase  Domain of unknown function DUF120
    1.4e-06   28.1   0.1      3e-06   27.1   0.1    1.5  1  HTH_Crp_2       Crp-like helix-turn-helix domain
    1.4e-05   25.0   0.2    2.8e-05   23.9   0.2    1.5  1  MarR            MarR family
    1.5e-05   24.8   0.0    2.8e-05   23.9   0.0    1.4  1  MarR_2          MarR family
    0.00023   20.7   0.1    0.00047   19.7   0.1    1.5  1  HTH_24          Winged helix-turn-helix DNA-binding
    0.00042   20.7   0.1      0.001   19.5   0.1    1.7  1  HTH_27          Winged helix DNA-binding domain
     0.0009   19.4   0.5     0.0031   17.7   0.2    2.0  2  HTH_34          Winged helix DNA-binding domain
      0.001   19.0   0.2     0.0022   17.9   0.2    1.6  1  HTH_36          Helix-turn-helix domain
     0.0085   16.3   0.7      0.023   14.9   0.2    2.1  2  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
  ------ inclusion threshold ------
      0.011   15.6   0.2      0.023   14.7   0.2    1.6  1  HTH_45          Winged helix-turn-helix
      0.014   15.4   2.5      0.036   14.0   0.5    2.6  3  HTH_11          HTH domain
      0.014   15.2   0.0      0.029   14.2   0.0    1.5  1  HTH_IclR        IclR helix-turn-helix domain
      0.032   14.6   0.1      0.054   13.8   0.1    1.4  1  Rrf2            Transcriptional regulator
       0.14   11.9   0.0       0.29   10.9   0.0    1.5  1  HTH_Tnp_4       Helix-turn-helix of DDE superfamily endonucle


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 !  137.4   0.1   1.9e-43   2.4e-40       1     121 []      99     218 ..      99     218 .. 0.99

  Alignments for each domain:
  == domain 1  score: 137.4 bits;  conditional E-value: 1.9e-43
                                   EE--SSHHHHHHCSHHHHHHHHHHHSS---SS-EEEEESCCGHHHHCHHHHS--EEE--EEETTEEE--EEEEEEEECCEE CS
                CTP-dep_RFKase   1 VvsGlgeGkyyvslegykeqfeeklgfepypGTLNvkldeeslelrkaleklkgieiegfedeertfgavkvypakiekik 81 
                                   Vv G+geGkyy+s+++y  qf+eklg+ py GTLN+k+d +s+ + ++l+ ++gi+iegf++e+rtfg+vk++++k ++++
  gi|13541350|ref|NP_111038.1|  99 VVPGMGEGKYYISRKQYIIQFQEKLGIIPYLGTLNIKVDPSSIPELRKLRGFTGIHIEGFRTEDRTFGSVKAFRCKTNGVP 179
                                   899****************************************************************************** PP

                                   EEEEEESS-SS.TTEEEEE-SS-HHHHTT--TT-EEEEEE CS
                CTP-dep_RFKase  82 aavvvperthyeedvlEiiapekLReklelkdgdevevev 121
                                     +++pert y +dv+Eii+++ LR++l+lkdgdev++ev
  gi|13541350|ref|NP_111038.1| 180 SFLIMPERTVY-TDVVEIISDKYLRNELNLKDGDEVTIEV 218
                                   ***********.9*************************97 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.1   2.4e-09     3e-06      21      59 ..      25      68 ..      10      73 .. 0.80

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 2.4e-09
                                  EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE.E..TEE..EEE CS
                     HTH_Crp_2 21 pltqeelAsmlGltretvsrilseLkreglis.r..grr..iri 59
                                   lt   lA+mlGl++++ sri+ +L++ g+i+ +  +r+  ++i
  gi|13541350|ref|NP_111038.1| 25 YLTSSKLANMLGLSQQSASRIIIDLEKLGYITrTvsKRGqlLTI 68
                                  589999**************************524323235555 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.2   2.2e-08   2.8e-05      18      52 ..      26      60 ..      11      62 .. 0.91

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 2.2e-08
                                  EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEE CS
                          MarR 18 lsvseLakklgvskstvtrvldrLekkGlieRsks 52
                                  l+ s+La++lg+s+ +++r++  Lek G+i+R+ s
  gi|13541350|ref|NP_111038.1| 26 LTSSKLANMLGLSQQSASRIIIDLEKLGYITRTVS 60
                                  6788****************************865 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.0   2.2e-08   2.8e-05      22      56 ..      26      60 ..      17      63 .. 0.90

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 2.2e-08
                                  EEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEES CS
                        MarR_2 22 ltvgelarrlglsksavsrilkrLvaaGLverrpg 56
                                  lt + la  lgls++++sri+ +L++ G+++r+ +
  gi|13541350|ref|NP_111038.1| 26 LTSSKLANMLGLSQQSASRIIIDLEKLGYITRTVS 60
                                  78899*************************99855 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.1   3.7e-07   0.00047      15      48 .]      23      56 ..      21      56 .. 0.94

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 3.7e-07
                        HTH_24 15 nprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                  ++ ++ + LA +lglS++  +r +  Le+ G+I+
  gi|13541350|ref|NP_111038.1| 23 KAYLTSSKLANMLGLSQQSASRIIIDLEKLGYIT 56
                                  67899****************************6 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.1     8e-07     0.001      21      68 .]      28      72 ..      22      72 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 8e-07
                        HTH_27 21 ladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68
                                   + l+ +l ++++++s ++  L++ G+++rt ++   r  ++++T+kG
  gi|13541350|ref|NP_111038.1| 28 SSKLANMLGLSQQSASRIIIDLEKLGYITRTVSK---RGQLLTITEKG 72
                                  678999**********************999776...**********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 !   17.7   0.2   2.4e-06    0.0031      18      80 .]      29      87 ..      20      87 .. 0.89
   2 ?   -1.9   0.0         3   3.9e+03      15      29 ..     197     211 ..     191     212 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2.4e-06
                        HTH_34 18 velkealeatdgnLsvhlkkLekagYievdkefkgkkprtllriTpeGreafkkyvkaLksll 80
                                  ++l + l++++   s  +  Lek gYi+++ +++g+    ll+iT++G++    ++++L+++l
  gi|13541350|ref|NP_111038.1| 29 SKLANMLGLSQQSASRIIIDLEKLGYITRTVSKRGQ----LLTITEKGLDLLYTEFAELSRIL 87
                                  67778888888899999999**********999999....******************99985 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3
                        HTH_34  15 adfvelkealeatdg 29 
                                   ++ ++l+++l++ dg
  gi|13541350|ref|NP_111038.1| 197 ISDKYLRNELNLKDG 211
                                   556789999999998 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.2   1.7e-06    0.0022      18      55 .]      18      55 ..       9      55 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.7e-06
                        HTH_36 18 anknggcfpsqetlakrlglsknTvsraikeLeqlGyi 55
                                  +++ + ++ + + la+ lgls +++sr+i  Le+lGyi
  gi|13541350|ref|NP_111038.1| 18 SDSSNKAYLTSSKLANMLGLSQQSASRIIIDLEKLGYI 55
                                  66778899999**************************9 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.2   1.8e-05     0.023      16      53 ..      17      56 ..       1      63 [. 0.78
   2 ?   -3.4   0.0       9.3   1.2e+04      32      41 ..     134     143 ..     133     147 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.8e-05
                                  HHH..HHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                Fe_dep_repress 16 lse..ekkvvktkdlaerLnvspssVsemlkkLekdGyve 53
                                  +s+  +k++ + ++la  L+ s  s+s  +  Lek Gy+ 
  gi|13541350|ref|NP_111038.1| 17 ASDssNKAYLTSSKLANMLGLSQQSASRIIIDLEKLGYIT 56
                                  444335789999**************************85 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 9.3
                                   HTS-HHHHHH CS
                Fe_dep_repress  32 LnvspssVse 41 
                                   ++v pss+ e
  gi|13541350|ref|NP_111038.1| 134 IKVDPSSIPE 143
                                   6899999755 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.2   1.8e-05     0.023      21      67 ..      27      77 ..      14      88 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.8e-05
                        HTH_45 21 kkTkimykanLsykllnkYLdmLvekgli....kkskekYvlTekGlelle 67
                                  + +k+     Ls + +++ +  L + g+i    +k+++  ++TekGl+ll 
  gi|13541350|ref|NP_111038.1| 27 TSSKLANMLGLSQQSASRIIIDLEKLGYItrtvSKRGQLLTITEKGLDLLY 77
                                  56778888899*****************9888899*************984 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       2.3     3e+03      33      42 ..       8      17 ..       8      20 .. 0.86
   2 ?   14.0   0.5   2.8e-05     0.036      12      46 ..      22      56 ..      11      64 .. 0.83
   3 ?   -0.7   0.1       1.1   1.5e+03      30      39 ..     187     196 ..     186     201 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 2.3
                        HTH_11 33 rrdIkaLeel 42
                                  +r Ik+++e+
  gi|13541350|ref|NP_111038.1|  8 YRAIKKIKEA 17
                                  799***9986 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 2.8e-05
                        HTH_11 12 argpisgeeLAeeLnvSrrtvrrdIkaLeelgvpI 46
                                  ++ ++++++LA  L++S +   r I +Le+lg+  
  gi|13541350|ref|NP_111038.1| 22 NKAYLTSSKLANMLGLSQQSASRIIIDLEKLGYIT 56
                                  4555****************************653 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 1.1
                        HTH_11  30 rtvrrdIkaL 39 
                                   rtv+ d+ ++
  gi|13541350|ref|NP_111038.1| 187 RTVYTDVVEI 196
                                   9*****9776 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 ?   14.2   0.0   2.2e-05     0.029      19      50 ..      26      57 ..      15      58 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.2e-05
                                  -BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                      HTH_IclR 19 ltlselArrtglpkStvhRlLqtLvelGyveq 50
                                  lt s lA+ +gl+  +++R++  L++lGy+++
  gi|13541350|ref|NP_111038.1| 26 LTSSKLANMLGLSQQSASRIIIDLEKLGYITR 57
                                  67899************************987 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   4.2e-05     0.054      17      56 ..      17      56 ..       1      65 [. 0.77

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.2e-05
                                  HHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          Rrf2 17 LakeeeeepvsseeiaerqnispsylekilakLrkaglvk 56
                                   +  +++  ++s+++a++ ++s++ +++i+  L+k g+++
  gi|13541350|ref|NP_111038.1| 17 ASDSSNKAYLTSSKLANMLGLSQQSASRIIIDLEKLGYIT 56
                                  4555666669****************************97 PP

>> HTH_Tnp_4  Helix-turn-helix of DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00023      0.29      17      46 ..      23      52 ..      22      56 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00023
                     HTH_Tnp_4 17 RlnltyqdLayrFgvsestvsrifhkwvdl 46
                                  + +lt + La   g s+ ++sri+  +++l
  gi|13541350|ref|NP_111038.1| 23 KAYLTSSKLANMLGLSQQSASRIIIDLEKL 52
                                  78*********************9777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       544  (0.0303419); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 1392.98
//
Query:       gi|13541351|ref|NP_111039.1|  [L=80]
Description: hypothetical protein TVN0520 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       876  (0.0488594); expected 358.6 (0.02)
Passed bias filter:                      619  (0.0345251); 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: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 549.86
//
Query:       gi|13541352|ref|NP_111040.1|  [L=759]
Description: phosphoribosylformylglycinamidine synthase II [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.2e-49  166.4   0.5      4e-36  124.5   0.5    2.3  2  AIRS_C          AIR synthase related protein, C-terminal doma
    2.2e-40  137.2   0.2      2e-22   79.6   0.2    2.4  2  AIRS            AIR synthase related protein, N-terminal doma
    2.8e-18   66.2   0.0    7.5e-17   61.6   0.0    2.6  2  FGAR-AT_linker  Formylglycinamide ribonucleotide amidotransfe
  ------ inclusion threshold ------
      0.093   13.0   0.2       0.29   11.4   0.2    1.8  1  DUF1884         Domain of unknown function (DUF1884)


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 !  124.5   0.5   8.9e-40     4e-36       1     155 [.     221     376 ..     221     377 .. 0.97
   2 !   39.7   0.0   1.1e-13   5.1e-10      58     148 ..     645     728 ..     599     733 .. 0.80

  Alignments for each domain:
  == domain 1  score: 124.5 bits;  conditional E-value: 8.9e-40
                                   STTEEEEEEET....SSCTCCHHHHHHHCHHHCTSHTTTSEHHHHHHHHHHHHHHHHHHHHHTTECEEEE--TTHHHHHHH CS
                        AIRS_C   1 kpGdvliltgs....lGlggagtslkrkileeeglddsavqlgdvlleptliyvkralaalkglvkaahDvTgGGLlgala 77 
                                   k+Gd+l+l+g+    +G++g++ ++++++ + ++  ++a qlg+++ e+ ++++++++ +l g +ka++D++gGGL++a+ 
  gi|13541352|ref|NP_111040.1| 221 KAGDKLLLVGGktgrDGIHGVN-FASATLTRISKSSRNAIQLGNPIVEHPMMRAVLEANEL-GIIKAMKDLGGGGLSSAAT 299
                                   69********************.888899999999988**********************9.******************* PP

                                   HHHHTTTEEEEEECGTHHHHHHHHHHHHHHHCSTTTEEEEEEEHGGHHHHHHHHHHTTCCCEEEEEEEEESSSEEEEE CS
                        AIRS_C  78 emapasgvgaeidldkvpifdelesplemllsensGrllvavppeeadavlaileeeglpeaavIGevtakeelsviv 155
                                   em++a+g+gaei+ld++++ d  +s++e+++se+++r+lv v pe+ ++ ++i+e++ l +++++G+v+++++ +v++
  gi|13541352|ref|NP_111040.1| 300 EMVFAGGFGAEISLDDIKLKDTDMSGWEIWISESQERMLVEVLPEDVEKMKEIAEKWSL-DFSILGTVVEGKKITVRY 376
                                   **********************************************************9.8***********999876 PP

  == domain 2  score: 39.7 bits;  conditional E-value: 1.1e-13
                                   HTTECEEEE--TTHHHHHHHHHHHTTTEEEEEECGTHHHHHHHHHHHHHHHCSTTTEEEEEEEHGGHHHHHHHHHHTTCCC CS
                        AIRS_C  58 kglvkaahDvTgGGLlgalaemapasgvgaeidldkvpifdelesplemllsensGrllvavppeeadavlaileeeglpe 138
                                   +  + +ahDv++GGL  alaem ++sg+g++idl +v +       +  l+se     ++ ++p ++++++a++++    +
  gi|13541352|ref|NP_111040.1| 645 SPYILSAHDVSDGGLFMALAEMSFGSGIGFNIDLGNVSASRS----SVKLFSECGNQIVLEIDPIHEEEFTAEFKDL---K 718
                                   46799******************************7777776....689**************************96...4 PP

                                   EEEEEEEEES CS
                        AIRS_C 139 aavIGevtak 148
                                     +IGe+ ++
  gi|13541352|ref|NP_111040.1| 719 IVRIGETGGD 728
                                   789**99876 PP

>> AIRS  AIR synthase related protein, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.6   0.2   4.5e-26     2e-22       1      94 []      89     209 ..      89     209 .. 0.94
   2 !   55.3   0.0   1.7e-18   7.8e-15       5      94 .]     478     582 ..     463     582 .. 0.92

  Alignments for each domain:
  == domain 1  score: 79.6 bits;  conditional E-value: 4.5e-26
                                   SSSEE.........EEEEEEEE.EECCTCCCCHHHHHHHHHHHHHHTTTEEEEEEEEEEEEC...............HHHH CS
                          AIRS   1 dDaav.........vvttdshnrpvlvepvhfiGakavavnlsDlaamGArPlalllslalp...............wlee 57 
                                   dDa+v         v++++shn+p++vep+ + +a++++++++D+++mGA+P+al++sl ++               ++++
  gi|13541352|ref|NP_111040.1|  89 DDAGVvefdkdyayVLKMESHNHPSAVEPYGG-AATGIGGIVRDVVCMGAQPIALVDSLFMGdvasqkydallspryIFQG 168
                                   677755555555559*****************.************************************************ PP

                                   HHHHHHHHHHHTT-EEEEEEEEEESS....EEEEEEEEEEE CS
                          AIRS  58 vvrglaeaaeelgvplvgGdtsfsne....ptisvtavGlv 94 
                                   vv g++++++++gvp v G + f+++    p+++++++G+v
  gi|13541352|ref|NP_111040.1| 169 VVGGIRDYGNRIGVPNVAGSVYFDQSynsnPLVNAGCIGIV 209
                                   ***********************988999**********97 PP

  == domain 2  score: 55.3 bits;  conditional E-value: 1.7e-18
                                   EEEEEEEEE.EECCTCCCCHHHHHHHHHHHHHHTTTEEEEEEEEEEEEC.........HHHHHHHHHHHHHHHTT-EEEEE CS
                          AIRS   5 vvvttdshnrpvlvepvhfiGakavavnlsDlaamGArPlalllslalp.........wleevvrglaeaaeelgvplvgG 76 
                                   +++t  s ++ v ++p+++ +  ++ +++++++++G++P  ++++l+++         ++ e vr +++ ++++  p+v G
  gi|13541352|ref|NP_111040.1| 478 LLITSGSRPNFVSIDPYNG-TLETLSEAVRNIVSTGGKPNSVVDALNFGnperqdimgQFVESVRAIGDFCRKFSLPVVAG 557
                                   4788888899999******.************************************************************* PP

                                   EEEEESS.......EEEEEEEEEEE CS
                          AIRS  77 dtsfsne.......ptisvtavGlv 94 
                                   ++sf+ne       pt+++++vG++
  gi|13541352|ref|NP_111040.1| 558 NVSFYNEfrnkdimPTPTIMMVGII 582
                                   ***********************96 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 !   61.6   0.0   1.7e-20   7.5e-17       3      50 .]      18      65 ..      16      65 .. 0.95
   2 ?    1.4   0.0      0.11   4.8e+02      12      37 ..     610     635 ..     609     636 .. 0.92

  Alignments for each domain:
  == domain 1  score: 61.6 bits;  conditional E-value: 1.7e-20
                FGAR-AT_linker  3 eankelglaLsdeEidylqeafeklgrnPtdvElemfaqvwSEHCrHK 50
                                  + +k++gl+Ls++E+++++++f k gr+P d+E+  +aq wSEHC++K
  gi|13541352|ref|NP_111040.1| 18 NMSKRHGLSLSLDEMKAVRDYFIKEGRDPIDAEIHAIAQSWSEHCSYK 65
                                  568999****************99***********************9 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.11
                FGAR-AT_linker  12 LsdeEidylqeafeklgrnPtdvEle 37 
                                   Ls +E+ +++++f +    P+  El+
  gi|13541352|ref|NP_111040.1| 610 LSGSEYARMNNIFDGFLPAPNLSELQ 635
                                   8999*********999999*****97 PP

>> DUF1884  Domain of unknown function (DUF1884)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2   6.4e-05      0.29      47      75 ..     706     734 ..     693     742 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 6.4e-05
                                   T------EETTEEEEE-GGGTTEEEEE-T CS
                       DUF1884  47 eeeeevtelsnlkveileeLGgDavvvDs 75 
                                   +eee   e  +lk+ ++ e GgD +++D 
  gi|13541352|ref|NP_111040.1| 706 HEEEFTAEFKDLKIVRIGETGGDRIIIDE 734
                                   567777899*******************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (759 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       469  (0.0261587); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); 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: 0.66u 0.27s 00:00:00.93 Elapsed: 00:00:00.45
# Mc/sec: 5114.52
//
Query:       gi|13541353|ref|NP_111041.1|  [L=362]
Description: glycosyltransferase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.4e-24   85.4   0.0    8.2e-24   84.5   0.0    1.4  1  Glyco_transf_4   Glycosyltransferase Family 4
    1.3e-21   76.9   0.1    2.1e-21   76.2   0.1    1.4  1  Glycos_transf_1  Glycosyl transferases group 1
    4.5e-17   62.7   0.0    1.6e-16   61.0   0.0    1.9  3  Glyco_trans_1_4  Glycosyl transferases group 1
    9.6e-11   42.4   0.0    1.4e-10   41.9   0.0    1.2  1  Glyco_trans_4_4  Glycosyl transferase 4-like domain
    1.2e-08   35.1   0.0    2.9e-08   33.8   0.0    1.7  2  Glyco_trans_4_2  Glycosyl transferase 4-like
    0.00018   21.9   0.0    0.00032   21.0   0.0    1.4  1  Glyco_trans_1_2  Glycosyl transferases group 1
  ------ inclusion threshold ------
      0.041   13.5   0.0         16    5.2   0.0    3.4  3  STAS             STAS domain
       0.11   12.6   0.2        1.1    9.5   0.0    2.4  2  UPF0180          Uncharacterised protein family (UPF0180)


Domain annotation for each model (and alignments):
>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.5   0.0   3.7e-27   8.2e-24       2     170 .]      15     180 ..      14     180 .. 0.77

  Alignments for each domain:
  == domain 1  score: 84.5 bits;  conditional E-value: 3.7e-27
                Glyco_transf_4   2 GGverhvleLaraLarrGheVtvvtpgddgpleeevelvvrvprvplpllk..rllrslaflrrlrrllkrekpDvvHahs 80 
                                    Gv +++ ++ r+L +rGheV++++ ++d+++ +       ++ vp+p++   r ++++ ++r ++ +++   pDv+H h+
  gi|13541353|ref|NP_111041.1|  15 DGVSTYLKDVKRGLEKRGHEVYIFSLTGDPHEKNV----FIPRTVPFPPYDqyRMPLIPFPFREFKTAVD-IMPDVIHLHN 90 
                                   6************************9999998888....3333333333330033334444445555555.8********* PP

                Glyco_transf_4  81 paalgaallalrrrlgiplVltvHglyekrllkarlkplsrllralerrl....lrradrviavSeatadelrerygvppe 157
                                   ++++  ++   +rrlg++ + t+H+  + +  ++ + p+s l++ l +r     +r+++ v+a+S +++++l++ +g+++ 
  gi|13541353|ref|NP_111041.1|  91 AFYMSSVGYLVARRLGKKPISTFHTDID-KMRESIRLPFSDLIFDLGKRYsiylYRKCKFVLAPSCQVKAYLER-CGLKN- 168
                                   99987655555556*************5.6666666777777777777766777********************.**987. PP

                Glyco_transf_4 158 kitVipnGvDler 170
                                    i+++p  vD+++
  gi|13541353|ref|NP_111041.1| 169 -IVTVPLFVDTDE 180
                                   .**********95 PP

>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.2   0.1   9.5e-25   2.1e-21       9     129 ..     185     300 ..     176     328 .. 0.91

  Alignments for each domain:
  == domain 1  score: 76.2 bits;  conditional E-value: 9.5e-25
                                   TTTTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSSSHHHH CS
               Glycos_transf_1   9 lgknekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsredleel 89 
                                   ++  +k+ iil++grl+k Kgv ++++++ + k      +k++iaG g+e++++k+ ++e  +  nv++lg+v+++++++l
  gi|13541353|ref|NP_111041.1| 185 KAS-NKQDIILYLGRLTKDKGVYRVLELANEMK---GTGYKFIIAGVGPELERMKAYVKENDI-SNVNILGYVKEDEKKQL 260
                                   444.7999**********************986...89*************************.89*************** PP

                                   HHCESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCH CS
               Glycos_transf_1  90 lknadifvlpsisEgfGivllEAmaaglpviasnaggpae 129
                                   ++ ++ f++ps  + fGi++ EA++ glp+i+s+  +++e
  gi|13541353|ref|NP_111041.1| 261 MEVSKFFIYPSSADTFGISVFEALSMGLPAIVSKEFPVKE 300
                                   *********************************9666554 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       6.3   1.4e+04      11      38 ..      11      42 ..       3      49 .. 0.60
   2 ?   -2.4   0.0       2.6   5.9e+03      69      83 ..     143     164 ..     140     181 .. 0.62
   3 !   61.0   0.0   6.9e-20   1.6e-16       2     129 ..     191     321 ..     190     325 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 6.3
                                  -GG.GTHHHHHHHH.HHHH.H.H..EEEEEES CS
               Glyco_trans_1_4 11 eenvkgvdllleav.pllrkk.d..vrlvivG 38
                                  ++  +gv   l+ v   l k+ +  + + + G
  gi|13541353|ref|NP_111041.1| 11 YPTPDGVSTYLKDVkRGLEKRgHevYIFSLTG 42
                                  55448888888888444554442455566666 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.6
                                   HHHH-SEEEE--.......--- CS
               Glyco_trans_1_4  69 llaaadvfvaPs.......egf 83 
                                   l+++++ ++aPs       e +
  gi|13541353|ref|NP_111041.1| 143 LYRKCKFVLAPScqvkaylERC 164
                                   5777777777776554444333 PP

  == domain 3  score: 61.0 bits;  conditional E-value: 6.9e-20
                                   EEEEEES---GG.GTHHHHHHHHHHHH.HHEEEEEES---...HHHHHHHT..T-T.TEEEE---..THHHHHHHH-SEEE CS
               Glyco_trans_1_4   2 pvilfvGrleenvkgvdllleavpllrkkdvrlvivGdgp.rpeeleelaa..gleerveftGfv..edlaellaaadvfv 77 
                                    +il++Grl+ + kgv  +le + +++   ++++i+G gp   e+++++++  ++ ++v ++G+v  +++++l++ ++ f+
  gi|13541353|ref|NP_111041.1| 191 DIILYLGRLT-KDKGVYRVLELANEMKGTGYKFIIAGVGPeL-ERMKAYVKenDI-SNVNILGYVkeDEKKQLMEVSKFFI 268
                                   589******5.55**************888*********965.599998876677.69*******9555************ PP

                                   E--..---SHHHHHHHHTT-EEEE-TGGGTTT--TTSSEE--TT-.HHHHHHHHH CS
               Glyco_trans_1_4  78 aPs..egfglkllEamaaglpvVatdvggiaevvgengllvppgd.pealaeail 129
                                    Ps   +fg+++ Ea+++glp ++++   ++e   +n+++ ++ +  + +a+++l
  gi|13541353|ref|NP_111041.1| 269 YPSsaDTFGISVFEALSMGLPAIVSKEFPVKE--DTNAIVYEDFSnIKHIANKLL 321
                                   ***987*******************8866788..777777763323666666655 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 !   41.9   0.0   6.1e-14   1.4e-10       2     158 ..      16     173 ..      15     174 .. 0.73

  Alignments for each domain:
  == domain 1  score: 41.9 bits;  conditional E-value: 6.1e-14
               Glyco_trans_4_4   2 GigryvaelaraLaarGheVtvltpapapgapeleedgvrvh.rlpvprrpspladlaal...ralrrllrqrrerpdvvh 78 
                                   G+++y  ++ r+L++rGheV ++  +++p +       v +   +p+p+  +  +++  +   r ++ ++   +  pdv+h
  gi|13541353|ref|NP_111041.1|  16 GVSTYLKDVKRGLEKRGHEVYIFSLTGDPHEK-----NVFIPrTVPFPPYDQ-YRMPLIPfpfREFKTAV---DIMPDVIH 87 
                                   99**********************96655555.....555541579999975.56666551224455566...******** PP

               Glyco_trans_4_4  79 ahs..ptaglaarlarrrrgiplvvtlhglllrrg....sgavrrlyraler...rllrradavlvvseaeaeelralgvp 150
                                   +h+  ++++   ++ar r g + + t+h++    +     +++  +++   r   +l+r +  vl++s ++ ++l+++g+ 
  gi|13541353|ref|NP_111041.1|  88 LHNafYMSSVGYLVAR-RLGKKPISTFHTDIDKMResirLPFSDLIFDLGKRysiYLYRKCKFVLAPSCQVKAYLERCGLK 167
                                   ***8445666556666.99*********855443323544455445544444445*************************9 PP

               Glyco_trans_4_4 151 adrvvvvp 158
                                     ++v+vp
  gi|13541353|ref|NP_111041.1| 168 --NIVTVP 173
                                   ..888888 PP

>> Glyco_trans_4_2  Glycosyl transferase 4-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.8   0.0   1.3e-11   2.9e-08      10     111 ..      18     117 ..       2     145 .. 0.75
   2 ?   -3.4   0.0         4     9e+03      13      32 ..     208     227 ..     194     244 .. 0.69

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 1.3e-11
               Glyco_trans_4_2  10 svhtlrlakeLakrgyeVhvitp.kkgakdeleaegihvhrlkvdrkgpleylk.afklkklikkikPDvvhahyakpygl 88 
                                   s++++ + ++L krg+eV+++++ +++++++ + +  +  +++   ++ + ++   f+ +k   +i PDv+h+h+a  +  
  gi|13541353|ref|NP_111041.1|  18 STYLKDVKRGLEKRGHEVYIFSLtGDPHEKNVFIP--RTVPFPPYDQYRMPLIPfPFREFKTAVDIMPDVIHLHNAFYMSS 96 
                                   7789999999*************555554433333..55666633567999998678999999*************99999 PP

               Glyco_trans_4_2  89 lgslaarlsgvipvvlsvwGldv 111
                                   +g+l+ar++g ++ + +++ +d+
  gi|13541353|ref|NP_111041.1|  97 VGYLVARRLG-KKPISTFH-TDI 117
                                   9*********.55558888.777 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 4
               Glyco_trans_4_2  13 tlrlakeLakrgyeVhvitp 32 
                                   +l+la+e++  gy+  ++  
  gi|13541353|ref|NP_111041.1| 208 VLELANEMKGTGYKFIIAGV 227
                                   56677777777777666554 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 !   21.0   0.0   1.4e-07   0.00032       4      91 ..     269     353 ..     266     354 .. 0.91

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.4e-07
               Glyco_trans_1_2   4 npsrsespnlrlfEaaacGafaltddaegleel.ftpgkevilfedleelaekirylla.npeerraiaeaarervlaeht 82 
                                    ps ++++   +fEa+ +G +a++++     e+ +++++ +i++ed  ++    ++ll+ + + ++++++ ar  + ++++
  gi|13541353|ref|NP_111041.1| 269 YPSSADTFGISVFEALSMGLPAIVSK-----EFpVKEDTNAIVYEDFSNIKHIANKLLNiDQATYSEMSTSARTLAISKYS 344
                                   5888999999***************4.....443788889***************************************** PP

               Glyco_trans_1_2  83 ydhraeqll 91 
                                    d+ ++qll
  gi|13541353|ref|NP_111041.1| 345 IDRHIDQLL 353
                                   *******98 PP

>> STAS  STAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0     0.007        16      69      95 ..      21      47 ..      16      53 .. 0.91
   2 ?    2.8   0.0     0.038        85      87     108 ..     152     172 ..     135     181 .. 0.77
   3 ?    0.9   0.0      0.15   3.5e+02      70      95 ..     209     234 ..     203     262 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.007
                                  HHHHHHHHHHTT-EEEEES--HHHHHH CS
                          STAS 69 Lkeilkelkrigvevvlvnikpevrek 95
                                  Lk++++ l+++g ev++ +++++ +ek
  gi|13541353|ref|NP_111041.1| 21 LKDVKRGLEKRGHEVYIFSLTGDPHEK 47
                                  9********************999987 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.038
                                   S--HHHHHHHHHTTCGGCC..S CS
                          STAS  87 nikpevreklektgffdeveee 108
                                    ++ +v+  le++g+ ++v + 
  gi|13541353|ref|NP_111041.1| 152 APSCQVKAYLERCGLKNIV-TV 172
                                   5899************999.44 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.15
                                   HHHHHHHHHTT-EEEEES--HHHHHH CS
                          STAS  70 keilkelkrigvevvlvnikpevrek 95 
                                    e+ +e+k  g +++++++ pe++++
  gi|13541353|ref|NP_111041.1| 209 LELANEMKGTGYKFIIAGVGPELERM 234
                                   6788999999***********99987 PP

>> UPF0180  Uncharacterised protein family (UPF0180)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0   0.00049       1.1       4      25 ..      16      37 ..      16      49 .. 0.86
   2 ?   -0.1   0.1      0.47     1e+03      12      41 ..     211     240 ..     201     262 .. 0.47

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00049
                       UPF0180  4 aVeegLsnvkeaLrekGYeVvd 25
                                  +V+  L++vk+ L+++G+eV  
  gi|13541353|ref|NP_111041.1| 16 GVSTYLKDVKRGLEKRGHEVYI 37
                                  58889***************75 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.47
                       UPF0180  12 vkeaLrekGYeVvdleteedaqsvdaiVvt 41 
                                   ++++++  GY+ +  +   + ++++a V +
  gi|13541353|ref|NP_111041.1| 211 LANEMKGTGYKFIIAGVGPELERMKAYVKE 240
                                   333444444444433333334444444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (362 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       511  (0.0285013); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.31s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 2284.15
//
Query:       gi|13541354|ref|NP_111042.1|  [L=348]
Description: hypothetical protein TVN0523 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      5e-47  160.5   0.1    5.5e-47  160.4   0.1    1.0  1  NAD_kinase  ATP-NAD kinase
    9.8e-05   22.0   0.0    0.00038   20.1   0.0    2.0  2  DAGK_cat    Diacylglycerol kinase catalytic domain
  ------ inclusion threshold ------
      0.019   14.5   0.0      0.036   13.7   0.0    1.4  1  AIRC        AIR carboxylase


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 !  160.4   0.1   9.2e-51   5.5e-47       2     292 .]       3     346 ..       2     346 .. 0.90

  Alignments for each domain:
  == domain 1  score: 160.4 bits;  conditional E-value: 9.2e-51
                                   EEEEESSC..................GGTCSHHHHHHHHHHHCT-...EEEEECCGGCCSSSTT--HHHHTTTT--..... CS
                    NAD_kinase   2 vgivvnpi..................kkeaieraeevarwLldals.rvlevtveeklgeslaeaaefrsevisvlkkvkt 63 
                                   +++v np                   + + +   ++  r+L++  +    ++++++ +ges+++  ++++ vi+++ ++ t
  gi|13541354|ref|NP_111042.1|   3 IAFVINPVaglgatlnlkgsdglaleDVSKSISIVRSHRFLKKLDFnGLHFFVPSGCMGESEVSIYTKEYDVIYTPSSPTT 83 
                                   566666666666666666666666652223333345567777775535556677788************************ PP

                                   ..EEECCC-TTTTTSSSEEEEEE-HHHHHHHHHHHHHCT-EEEEEESSS--SS-SE..EGGGHHHHHHHHHHT-SEEEEEE CS
                    NAD_kinase  64 tddtrkaleafadagvdliivvGGDGTaldvarllqkaeiPvlgvnaGvkgfltef..epeaaaellekllegeirvekre 142
                                   ++dt++ ++    +++dl+++vGGDGTa+d+    +  + Pv+gv+aGvk+++++f  +pe aa + +++ +g++r++k+e
  gi|13541354|ref|NP_111042.1|  84 RQDTINFVKSI--ESADLLVFVGGDGTARDILNSRN--DLPVIGVPAGVKMYSSVFaiSPERAADAVNQVAKGNYRIDKAE 160
                                   *********99..9*******************999..8****************************************** PP

                                   EEE.........................EEEEETTE............EEEEEEESSEEEEEESSSSS-EE..EEEEETTE CS
                    NAD_kinase 143 vld.........................avimrskgee......diadiviensvlnevviirgpgstlie..lelyvdte 190
                                   v+d                          ++ +sk+e+      dia++vie++   ++++i+gpg+t+++   e++++ +
  gi|13541354|ref|NP_111042.1| 161 VVDideelyrkgilsvkrygqlkvpeaqYIVENSKAEYdiagaeDIAEYVIEHM--ADETYIIGPGNTCKTieEEMGIKSN 239
                                   ***************************77777888888***************5..788999*********999******* PP

                                   EEEEEEESEE.....................EEE-TGGGGTHHHHTT--EE-TT---EEEEEESESSS----EEE-TT-EE CS
                    NAD_kinase 191 lleadqldgl.....................ivstPtGstayslsaGgplisPgvlailivpicPhslssrpiVvsssskl 250
                                   +l+ d+l+++                     +v++P G+++++l++G+++is ++l+         +  + +iVvss+s  
  gi|13541354|ref|NP_111042.1| 240 VLGFDILRNKklikedaseseiyeacsdkcmLVISPVGGQNFLLGRGNKQISDRILE--------RVGEENLIVVSSPS-- 310
                                   *********************************************************........**************.. PP

                                   EEEE-SS--EEEEETTTEEEEE-TT-EEEEEEESSEEEEEE. CS
                    NAD_kinase 251 rirvasrseallaldGseelelspgdevrvtasdkkfklirl 292
                                         ++e l  ++ + ++ l+ +++v+v +++  +kl+++
  gi|13541354|ref|NP_111042.1| 311 ------KAEHLKYVYIDTQIPLWSNGYVKVLVGYGRYKLVKV 346
                                   ......6778888899999********************986 PP

>> DAGK_cat  Diacylglycerol kinase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.42   2.5e+03       3      15 ..       4      16 ..       2      26 .. 0.80
   2 !   20.1   0.0   6.4e-08   0.00038      30     116 ..      73     152 ..      62     161 .. 0.70

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.42
                                  EEEE-TTCTTTTH CS
                      DAGK_cat  3 lvivNpksGkgkg 15
                                   +++Np +G g++
  gi|13541354|ref|NP_111042.1|  4 AFVINPVAGLGAT 16
                                  689*****98776 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 6.4e-08
                                   TCEEEEEE--STTHHHHHHHHHHHCC-SEEEEEESHHHHHHHHHHHCTHHCTTSEEEEEE-SS--HHHHHCT--S.SHHHH CS
                      DAGK_cat  30 gvelelieteepgdakelakeakeegvdlivvaGGDGtvsevlnglleelatkpplgiiPlGtgNdlaralgigk.dieea 109
                                    v ++    + ++d  +++k+++++  dl+v +GGDGt++ +ln+  +     +p+  +P+G     +  + i+   + +a
  gi|13541354|ref|NP_111042.1|  73 DVIYTPSSPTTRQDTINFVKSIESA--DLLVFVGGDGTARDILNSRND-----LPVIGVPAGVKM-YSSVFAISPeRAADA 145
                                   455555666678899999****996..****************97555.....777777888543.333333333366666 PP

                                   HHCHHCT CS
                      DAGK_cat 110 lesiikg 116
                                   +++++kg
  gi|13541354|ref|NP_111042.1| 146 VNQVAKG 152
                                   6666555 PP

>> AIRC  AIR carboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0     6e-06     0.036      38      88 ..      82     129 ..      64     151 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6e-06
                                   TSHHHHHHHHHHCHTTTEEEEEEEEESS--HHHHHHHHSSS-EEEEEE--S CS
                          AIRC  38 rtpeelleyaeeaeerglkviIagAGgaahLpgvvaslttlPVigvPvksk 88 
                                    t ++++++++++e+ +l v++ g G a +   ++ s  +lPVigvP   k
  gi|13541354|ref|NP_111042.1|  82 TTRQDTINFVKSIESADLLVFVGGDGTARD---ILNSRNDLPVIGVPAGVK 129
                                   5788999*******************9987...689***********8774 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (348 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       369  (0.0205812); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); 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: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 2184.73
//
Query:       gi|13541355|ref|NP_111043.1|  [L=399]
Description: multidrug efflux permease [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.5e-13   48.6  35.9    1.6e-06   27.3  17.1    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 !   27.3  17.1   8.9e-11   1.6e-06      12     182 ..      28     210 ..      19     232 .. 0.74
   2 !   26.8  11.4   1.3e-10   2.3e-06       7     148 ..     232     373 ..     226     397 .. 0.83

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 8.9e-11
                         MFS_1  12 rsilgpalpl.alaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfasslw.lllv 90 
                                   ++i+++al+l ++   l++s   ig+++++ al+ + +sl +G l+dr+G +  l+lg l  ++++++l+f+  +  l+++
  gi|13541355|ref|NP_111043.1|  28 IGIIFVALSLpLYLLILHVSIVNIGIIYVGTALVNVSFSLGIGMLGDRIGYKYSLMLGELPALVATTFLAFS-KSVdLIVI 107
                                   456777777778899**************************************************8999995.44445444 PP

                         MFS_1  91 lrv......lqGlgagalfpagaaliadwfpk.eergraigllsagfslGailg...pllggllasslg....Wravfyil 157
                                   + +       +G + g++  ++  +ia+++++ +er + +++++  +s+++i g       ++++ ++g    +++++ + 
  gi|13541355|ref|NP_111043.1| 108 ATIvsgsvgASGGMRGSFSVGITPYIARIWKDqSERISKMAYITFVASISSIGGslmLYSHAYVSKYFGnagaFELLYKLS 188
                                   4444666667888889999*************8888888877777666655555110555558888888777777777777 PP

                         MFS_1 158 aivsllafvlfllllpeepperkrk 182
                                    ++ l++f+    l + ++  +++k
  gi|13541355|ref|NP_111043.1| 189 FLLILVSFL---SLSLIKYDGKQNK 210
                                   777777766...3333333333333 PP

  == domain 2  score: 26.8 bits;  conditional E-value: 1.3e-10
                         MFS_1   7 lsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrr.vlllglllfalglllllfa.ssl 85 
                                   +++ a+++ +++++ +    +g+sps igl++t+ ++++a++s+++G++  ++ r++ v+l +++  a glll+++a s+l
  gi|13541355|ref|NP_111043.1| 232 INGSAIGFSMALITAWFEIRYGASPSRIGLIFTISYITTALGSYVAGHI--KIERKSaVYLGSATRIAQGLLLIAMAlSPL 310
                                   444444444444444556689****************************..*******************77777777999 PP

                         MFS_1  86 w.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllassl 148
                                   + l  +  ++  + ag+++p+ +++  + + +e+ g a ++ +a + ++     +++g+l++++
  gi|13541355|ref|NP_111043.1| 311 FyLASAIYIVRTIVAGFGTPIRNVVNIQGVREEDLGTASSIQGAPSRIAQSTS-GIAGFLMDYY 373
                                   98888899999999999****************************99999877.7888888665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (399 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       667  (0.0372023); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.26s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 2501.64
//
Query:       gi|13541356|ref|NP_111044.1|  [L=203]
Description: MarC family integral membrane protein [Thermoplasma volcanium GSS1]
Scores for complete 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-42  143.0  17.4    8.7e-42  142.8  17.4    1.0  1  MarC      MarC family integral membrane protein
  ------ inclusion threshold ------
      0.026   14.7   2.0      0.026   14.7   2.0    2.6  2  TMEM238   TMEM238 protein family


Domain annotation for each model (and alignments):
>> MarC  MarC family integral membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  142.8  17.4   9.8e-46   8.7e-42       3     202 ..       6     199 ..       4     200 .. 0.93

  Alignments for each domain:
  == domain 1  score: 142.8 bits;  conditional E-value: 9.8e-46
                          MarC   3 aiikafvsLlaiinplgnvpvflslleevskeerkrialkasilallillvfllfGelilklfgisidalkiaGgillfli 83 
                                   +++k+f+ L+++i+p+g++ +f s+++++++ e+ r ++ a++++ +il++f+l+G+ i+ +fgisi+al +aGg++l+l+
  gi|13541356|ref|NP_111044.1|   6 EFLKVFIPLFIVIDPFGSLVLFTSMTYNFNEGEKMRATKDAVVYGGIILVMFALAGQFIIYFFGISIEALEMAGGVILLLM 86 
                                   6899***************************************************************************** PP

                          MarC  84 aidmlkakqkkekkkkseeeeseekdeiavvPLAlPliaGPgaittvlvlaseassivekvavvlaillaalitllillls 164
                                   a++m+   ++  k++ se     +  +i +vP A+Pl+aGPgai+ v++l++      +k+ ++++i ++ l+++++++ +
  gi|13541356|ref|NP_111044.1|  87 AVEMIMEGNRP-KTSGSEVT---TDLDIGIVPFATPLLAGPGAISLVIILMKGPL--IDKIFTFVSIGIIFLMVYIFFKEA 161
                                   ****9877773.44444444...4679***********************98654..49********************** PP

                          MarC 165 slilrllgktginaleRlmGllLvalavqlivdGikei 202
                                   s++++ +g++ ++a++R++GllL+  a+q ++d++  +
  gi|13541356|ref|NP_111044.1| 162 SIVSKFIGNKAMKAVSRIFGLLLAGFAIQYFIDAVTAL 199
                                   *********************************99866 PP

>> TMEM238  TMEM238 protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   2.0   2.9e-06     0.026       4      60 ..       9      72 ..       8      78 .. 0.90
   2 ?   -0.9   0.2      0.22     2e+03      13      27 ..     144     158 ..     140     168 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.9e-06
                       TMEM238  4 kvflalavvfdvvGlvlLlvGifael.......lfgDllvytGaliiflSLlwwvlWYtgniev 60
                                  kvf+ l +v+d +G ++L++ +  ++         +D +vy G ++++++L++ ++ Y   i++
  gi|13541356|ref|NP_111044.1|  9 KVFIPLFIVIDPFGSLVLFTSMTYNFnegekmrATKDAVVYGGIILVMFALAGQFIIYFFGISI 72
                                  56778889***********************9999*****************999999887775 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.22
                       TMEM238  13 fdvvGlvlLlvGifa 27 
                                   f  +G++ L+v if 
  gi|13541356|ref|NP_111044.1| 144 FVSIGIIFLMVYIFF 158
                                   455677777777664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       932  (0.0519828); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 1333.04
//
Query:       gi|13541357|ref|NP_111045.1|  [L=241]
Description: ABC-type multidrug transport system, permease component [Thermoplasma volcanium GSS1]
Scores for complete 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-06   26.6  27.4    3.5e-06   26.6  27.4    1.9  2  ABC2_membrane    ABC-2 type transporter
  ------ inclusion threshold ------
       0.01   14.0   7.3      0.011   13.9   7.3    1.2  1  UPF0182          Uncharacterised protein family (UPF0182)


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 !   26.6  27.4     4e-10   3.5e-06       7     206 ..      11     204 ..       8     208 .. 0.77
   2 ?    0.7   1.2     0.034     3e+02      96     126 ..     207     238 ..     198     240 .. 0.56

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 4e-10
                 ABC2_membrane   7 lkreflqrwrdpslgllwrliqplllalvfgtvfgnlgnsedgl.nrpgllffsvlflafsaltsvapvferergvlerel 86 
                                   + + f+  +r ps++ ++ + +pl l++++  +        + l +++ + +f+ l  ++s+ ++  + f r +  ++ ++
  gi|13541357|ref|NP_111045.1|  11 WYYGFRAVKRGPSYL-ISAMSTPLALLFLIFIISR------GKLlDYALVGGFIGLVSSVSLSSAGDAAFLRLQLRIQDLF 84 
                                   56779999****999.9999999999998888888......3443664444444444443333333345555555557777 PP

                 ABC2_membrane  87 vsplyslsayvlakvlvelpvsllqalifllivyflvgldlsrf..flflllllltalaasslgllisalapsfedasqla 165
                                   v+   s+ +y+++ +l+++++s+   ++++++ +++  ++   +  + ++++l+l+++ +ss+++++s l ++++++  +a
  gi|13541357|ref|NP_111045.1|  85 VATSISPTDYMFGLTLSYFVFSIPGLVVYVILGIIFHVFTF--IgvLVLVAVLILLTISTSSISFIVSGLISHVRNVWGIA 163
                                   77777*****************9888888886666533333..1349999999999************************* PP

                 ABC2_membrane 166 slvllpllllsGffipidsmpkwlqwiaylnPltyavealr 206
                                   +++ +++++l + f+p+  +pk + +   ++P + a  +++
  gi|13541357|ref|NP_111045.1| 164 GILSVVMTVLPPTFYPYYIIPKAFLYALSVSPAASAAVIVQ 204
                                   ********************988888889999987776665 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.034
                 ABC2_membrane  96 yvlakvlvelpvsllqalifll.ivyflvgld 126
                                   + l+ +l+++++++++ +i+ + +  +++ ++
  gi|13541357|ref|NP_111045.1| 207 FGLSPILMQMLYIFILETIIYAfLGRVMIKWH 238
                                   45556666655554444444433777777665 PP

>> UPF0182  Uncharacterised protein family (UPF0182)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   7.3   1.2e-06     0.011     103     197 ..      71     165 ..      26     235 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.2e-06
                       UPF0182 103 lvassqwekvllflnstsfgvkDpifgkDisFYvFklPflel..llslllalvllaliavllvyllsgeslgirl.....k 176
                                   +++ +   +++ ++ +ts+  +D +fg  +s++vF++P l +  +l++++ ++ ++ ++vl++ l+  ++    +      
  gi|13541357|ref|NP_111045.1|  71 AAFLRLQLRIQDLFVATSISPTDYMFGLTLSYFVFSIPGLVVyvILGIIFHVFTFIGVLVLVAVLILLTIS---TssisfI 148
                                   333334457888999***********************776511555555555554444444444444333...2212233 PP

                       UPF0182 177 faelskaarrhlsvllallll 197
                                   +++l +++r+      ++  +
  gi|13541357|ref|NP_111045.1| 149 VSGLISHVRNV----WGIAGI 165
                                   33444433333....333322 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1122  (0.0625802); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); 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):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.34s 00:00:00.92 Elapsed: 00:00:00.50
# Mc/sec: 1463.08
//
Query:       gi|13541358|ref|NP_111046.1|  [L=279]
Description: ABC-type daunorubicin transport system, ATPase component [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.9e-24   86.8   0.0    2.6e-24   86.3   0.0    1.2  1  ABC_tran    ABC transporter
    4.2e-11   43.2   0.1    1.8e-06   28.0   0.0    2.1  2  AAA_21      AAA domain, putative AbiEii toxin, Type IV TA sys
      2e-05   24.5   0.0    0.00046   20.0   0.2    2.1  2  AAA_15      AAA ATPase domain
    2.6e-05   23.8   0.6     0.0018   17.8   0.6    2.2  1  SMC_N       RecF/RecN/SMC N terminal domain
     0.0003   21.4   0.1    0.00045   20.8   0.1    1.2  1  AAA_23      AAA domain
     0.0079   15.9   0.3      0.014   15.1   0.3    1.3  1  AAA_29      P-loop containing region of AAA domain
     0.0086   15.9   0.1      0.014   15.2   0.1    1.3  1  MukB        MukB N-terminal
  ------ inclusion threshold ------
      0.012   15.9   0.0      0.026   14.8   0.0    1.5  1  AAA_22      AAA domain
      0.029   14.8   0.1       0.21   12.0   0.0    2.2  3  AAA         ATPase family associated with various cellular ac
      0.035   12.8   0.2       0.21   10.2   0.1    1.9  2  AAA_13      AAA domain
      0.044   13.5   0.5       0.24   11.1   0.2    2.1  2  AAA_30      AAA domain
      0.057   13.8   0.0      0.069   13.5   0.0    1.3  1  AAA_16      AAA ATPase domain
      0.078   12.2   0.0       0.13   11.5   0.0    1.3  1  Zeta_toxin  Zeta toxin
      0.085   13.1   0.0        1.2    9.4   0.0    2.3  1  SbcCD_C     Putative exonuclease SbcCD, C subunit
       0.12    9.9   0.1       0.17    9.4   0.1    1.1  1  DUF3584     Protein of unknown function (DUF3584)
       0.13   12.0   0.1         11    5.7   0.1    2.1  2  AAA_24      AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.3   0.0   2.3e-27   2.6e-24       1     136 [.      18     160 ..      18     161 .. 0.95

  Alignments for each domain:
  == domain 1  score: 86.3 bits;  conditional E-value: 2.3e-27
                                   EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                      ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren.. 79 
                                   lk++sl++  g ++ ++G+nGaGK+t++++++ +l+pt+G+++++g d+ + e +++rk i  +pqe++    lt  e+  
  gi|13541358|ref|NP_111046.1|  18 LKDISLDIGSG-ITSVIGRNGAGKTTMMRIFSTQLRPTSGSVTINGYDVVK-ESNKVRKIICSIPQEASPIGVLTPLEQvk 96 
                                   68999999988.78899********************************99.999************9999999988888* PP

                                   ...........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                   ...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  80 ...........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                               +d+e+  als++gl+e  + ++     +LSgG+k++v +a+al  ++++++lDEpt
  gi|13541358|ref|NP_111046.1|  97 mylvarglsisSADREARIALSSVGLEESMKAPA----DTLSGGMKRKVFVAMALSANADIVFLDEPT 160
                                   **********999999************888888....*****************************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 !   13.3   0.0   4.7e-05     0.053       1      21 [.      29      49 ..      29      81 .. 0.82
   2 !   28.0   0.0   1.6e-09   1.8e-06     232     297 ..     128     187 ..     100     191 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.7e-05
                        AAA_21  1 lnvliGpNgsGKSnLLdaldl 21
                                  ++ +iG+Ng+GK++ +++++ 
  gi|13541358|ref|NP_111046.1| 29 ITSVIGRNGAGKTTMMRIFST 49
                                  6889*************9964 PP

  == domain 2  score: 28.0 bits;  conditional E-value: 1.6e-09
                        AAA_21 232 lparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTH 297
                                    pa+ lS G+kr  +++ al + +   +++++DEp +gL+P    +++ l+++l++    ++ltTH
  gi|13541358|ref|NP_111046.1| 128 APADTLSGGMKRKVFVAMALSANA---DIVFLDEPTTGLDPMSRLEVWSLIRNLRS---DIVLTTH 187
                                   578899*******88888888877...9*************888888899999966...******* PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.2   4.1e-07   0.00046      13      44 ..      17      48 ..      16      86 .. 0.80
   2 ?    2.6   0.0     0.079        89     287     364 ..     116     187 ..      60     188 .. 0.73

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 4.1e-07
                        AAA_15 13 slkdveidlseeltvliGkNnsGKSsileald 44
                                  +lkd+++d+ + +t +iG+N++GK++ ++++ 
  gi|13541358|ref|NP_111046.1| 17 ALKDISLDIGSGITSVIGRNGAGKTTMMRIFS 48
                                  589************************99885 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.079
                        AAA_15 287 k.......ddeelplnknGsGvqrllllillileaekkdekeeknvilliEEPEahLHpqaqkvlikllkelandnktQvi 360
                                           + ++ p++  + G++r +++++ +  +          +i++++EP + L p    +++ l+++l +d     +
  gi|13541358|ref|NP_111046.1| 116 AlssvgleESMKAPADTLSGGMKRKVFVAMALSANA---------DIVFLDEPTTGLDPMSRLEVWSLIRNLRSDI----V 183
                                   155666667788888888888888888877654444.........47**********9999999999999987665....7 PP

                        AAA_15 361 itTH 364
                                   +tTH
  gi|13541358|ref|NP_111046.1| 184 LTTH 187
                                   8888 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.6   1.6e-06    0.0018      16     200 ..      19     190 ..       7     208 .. 0.65

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.6e-06
                                   EEEEEETTSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--...BTTCSSTTEEEEEEEEEETTEESSSS CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N  16 ktvilpfsksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihk...skekasvkkaeveitfdnedkklkie 93 
                                   k ++l++ +++t+++G+NG+GK+ ++       +    ++lr ++ s  i+     ke+++v   ++   + +e + + + 
  gi|13541358|ref|NP_111046.1|  19 KDISLDIGSGITSVIGRNGAGKTTMMRIF----S----TQLRPTSGSVTINGydvVKESNKVR--KIICSIPQEASPIGVL 89 
                                   67899999****************99754....4....4788888888888732222222222..2222223333333444 PP

                                   SSCEEEEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N  94 keevsisrrvkrkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDek 174
                                   ++  +++  ++  g s    +++         l es++   ++LSgG k  v +a+ ++      a +++lDe    LD +
  gi|13541358|ref|NP_111046.1|  90 TPLEQVKMYLVARGLSISSADREARIALSSVGLEESMKAPADTLSGGMKRKVFVAMALS----ANADIVFLDEPTTGLDPM 166
                                   44455666666666655555555554455555556667777899999998887777665....456789999999999999 PP

                                   HHHHHHHHHHHHCTTSEEEEE-SSHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 175 nvkkvaellkeksknaQfivislree 200
                                    + +v +l+++ +  + ++ +++  e
  gi|13541358|ref|NP_111046.1| 167 SRLEVWSLIRNLR--SDIVLTTHYME 190
                                   9999999999998..66666665443 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.1     4e-07   0.00045       9      38 ..      17      46 ..      10      73 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 4e-07
                        AAA_23  9 sfrdqeidFskgltlItGpNGaGKTTildA 38
                                   ++d ++d ++g+t ++G NGaGKTT ++ 
  gi|13541358|ref|NP_111046.1| 17 ALKDISLDIGSGITSVIGRNGAGKTTMMRI 46
                                  567888999*****************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 !   15.1   0.3   1.3e-05     0.014      16      50 ..      20      55 ..      10      62 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.3e-05
                        AAA_29 16 tieidlkg.atlltGpsGsGKSTllDAiqalLvpak 50
                                  +i++d  + +t ++G++G+GK+T++  +++ L p++
  gi|13541358|ref|NP_111046.1| 20 DISLDIGSgITSVIGRNGAGKTTMMRIFSTQLRPTS 55
                                  5555655559**************976666666665 PP

>> MukB  MukB N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   1.3e-05     0.014       7      53 ..       5      54 ..       2      63 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.3e-05
                                  EEEEEEEETTEEE...EEE-HHHHHHHHHS--SHHHHHHHHHHHHHHS-- CS
                          MukB  7 ksltlinWnGffa...rtfdldelvttlsGgnGaGksttmaafvtaliPd 53
                                  +slt +  nG  a      d+ + +t++ G nGaGk+t+m  f t l P 
  gi|13541358|ref|NP_111046.1|  5 RSLTKVYKNGNNAlkdISLDIGSGITSVIGRNGAGKTTMMRIFSTQLRPT 54
                                  677777766655421134678899*******************9999886 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   2.3e-05     0.026       5      30 ..      27      52 ..      24      96 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.3e-05
                        AAA_22  5 agilvvtGesGtGKTtllrrlleqld 30
                                   gi+ v+G  G+GKTt +r +  ql 
  gi|13541358|ref|NP_111046.1| 27 SGITSVIGRNGAGKTTMMRIFSTQLR 52
                                  5899*****************99993 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00019      0.21       3      57 ..      32      83 ..      30      95 .. 0.81
   2 ?   -0.4   0.0       1.3   1.4e+03      50      66 ..     142     158 ..     100     160 .. 0.74
   3 ?   -2.7   0.0       6.4   7.2e+03      82      95 ..     209     222 ..     185     228 .. 0.57

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00019
                                  EESSTTSSHHHHHHHHHHHHT..HEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS CS
                           AAA  3 lyGppGtGKTllakavakelg..vefleisgsellskyvgesekkirelfkeakeka 57
                                  ++G  G GKT++++   ++l   +  ++i+g +++     + ++k+r+++ ++ ++a
  gi|13541358|ref|NP_111046.1| 32 VIGRNGAGKTTMMRIFSTQLRptSGSVTINGYDVV-----KESNKVRKIICSIPQEA 83
                                  6899****************644778*********.....67888888887776666 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.3
                                   HHHHHHTSTSEEEEEET CS
                           AAA  50 fkeakekakpsilfiDE 66 
                                   f ++  +a+  i+f+DE
  gi|13541358|ref|NP_111046.1| 142 FVAMALSANADIVFLDE 158
                                   333222224599***99 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 6.4
                                   HHHHHHHHHHHHHH CS
                           AAA  82 eervvnqLlteldg 95 
                                   +e ++++Ll+e+dg
  gi|13541358|ref|NP_111046.1| 209 KEGTLKELLSEFDG 222
                                   33456666666665 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1   0.00019      0.21      23      39 ..      34      50 ..      28      74 .. 0.82
   2 ?    0.2   0.0       0.2   2.2e+02     527     565 ..     151     183 ..     145     195 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00019
                        AAA_13 23 GwNGaGKTtLSrllrsl 39
                                  G+NGaGKTt+ r+++ +
  gi|13541358|ref|NP_111046.1| 34 GRNGAGKTTMMRIFSTQ 50
                                  9*************985 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.2
                        AAA_13 527 dkivviDDPvSSLDsnslfivfsliksrllkkkkakQlf 565
                                     iv++D P   LD  s   v sli++        + + 
  gi|13541358|ref|NP_111046.1| 151 ADIVFLDEPTTGLDPMSRLEVWSLIRNLR------SDIV 183
                                   679***********************985......4444 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.2   0.00022      0.24      20      44 ..      29      53 ..      17      67 .. 0.79
   2 ?   -0.3   0.0      0.69   7.7e+02      60      96 ..     120     158 ..      96     184 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00022
                        AAA_30 20 vavltGpAGtGKttalkalreawea 44
                                  ++ + G+ G+GKtt+++     ++ 
  gi|13541358|ref|NP_111046.1| 29 ITSVIGRNGAGKTTMMRIFSTQLRP 53
                                  78899************98665554 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.69
                        AAA_30  60 kvLaeelgieastiakllkrlk..grarlepg.tllivDE 96 
                                     L+e++ ++a+t+   +kr    + ++l+++ +++  DE
  gi|13541358|ref|NP_111046.1| 120 VGLEESMKAPADTLSGGMKRKVfvA-MALSANaDIVFLDE 158
                                   4588999999999999998887953.55555559999998 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   6.1e-05     0.069      24      66 ..      26      70 ..      15     219 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.1e-05
                        AAA_16 24 p.elvllsGesGvGKsslvrellralekdg.giflrgkcdqlesa 66
                                  + +++ ++G  G GK++++r + ++l+ +   ++++g  +  es+
  gi|13541358|ref|NP_111046.1| 26 GsGITSVIGRNGAGKTTMMRIFSTQLRPTSgSVTINGYDVVKESN 70
                                  348999*********************996255577766655544 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00012      0.13      23      53 ..      34      64 ..      29      86 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00012
                    Zeta_toxin 23 GqpGAGKselaellkdelerqgnvvrldpDd 53
                                  G  GAGK+++++ + ++l+++++ v++++ d
  gi|13541358|ref|NP_111046.1| 34 GRNGAGKTTMMRIFSTQLRPTSGSVTINGYD 64
                                  889************************9744 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0    0.0011       1.2      23      89 ..     123     176 ..     107     177 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0011
                       SbcCD_C  23 ekelsrssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllelle 89 
                                   e+++++ + tlSGG k++   + +a+al+a            ++vfLDE   +lD+ s+ ++ +l++
  gi|13541358|ref|NP_111046.1| 123 EESMKAPADTLSGGMKRK---VFVAMALSAN----------ADIVFLDEPTTGLDPMSRLEVWSLIR 176
                                   556788888888888833...3334444433..........35799999999999999888887776 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.1   0.00015      0.17      17      36 ..      27      46 ..      20      47 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00015
                       DUF3584 17 dghtnieGtNaaGKTtLlrL 36
                                  +g t + G N+aGKTt++r+
  gi|13541358|ref|NP_111046.1| 27 SGITSVIGRNGAGKTTMMRI 46
                                  57899*************96 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.1    0.0099        11       7      22 ..      32      47 ..      29      61 .. 0.87
   2 ?    4.2   0.0     0.027        30     117     173 ..     174     229 ..     168     256 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0099
                        AAA_24  7 iyGpsgiGKTtlakel 22
                                  ++G +g+GKTt+++ +
  gi|13541358|ref|NP_111046.1| 32 VIGRNGAGKTTMMRIF 47
                                  79**********9977 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.027
                        AAA_24 117 klqelrknvifiahektrkdedpegeakytrlepklgkktanelkeevDlvlranlk 173
                                    +++lr +++++ h  ++     +     +   + ++++t +el +e+D ++r++ +
  gi|13541358|ref|NP_111046.1| 174 LIRNLRSDIVLTTHYMEEAASLSKYI-IMVDHGTVIKEGTLKELLSEFDGLIRVESR 229
                                   5789999*************999666.66777788899999********99998864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.60u 0.31s 00:00:00.90 Elapsed: 00:00:00.50
# Mc/sec: 1686.96
//
Query:       gi|13541359|ref|NP_111047.1|  [L=390]
Description: nucleoside-diphosphate-sugar epimerase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      7e-22   78.1   0.0      1e-21   77.5   0.0    1.2  1  Epimerase        NAD dependent epimerase/dehydratase family
    6.6e-19   68.5   0.0    1.1e-14   54.6   0.0    2.4  2  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
     0.0015   18.1   0.0     0.0025   17.4   0.0    1.3  1  UDPG_MGDP_dh_N   UDP-glucose/GDP-mannose dehydrogenase family
  ------ inclusion threshold ------
      0.016   14.3   0.0      0.079   12.0   0.0    2.1  2  RmlD_sub_bind    RmlD substrate binding domain
      0.049   12.6   0.5      0.077   12.0   0.5    1.2  1  SDH_sah          Serine dehydrogenase proteinase
      0.078   12.1   0.0       0.16   11.0   0.0    1.4  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
       0.13   11.8   0.0       0.22   11.1   0.0    1.3  1  RanGAP1_C        RanGAP1 C-terminal domain


Domain annotation for each model (and alignments):
>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.5   0.0     4e-25     1e-21       1     239 [.       3     290 ..       3     290 .. 0.84

  Alignments for each domain:
  == domain 1  score: 77.5 bits;  conditional E-value: 4e-25
                                   EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC.......................EEEE--TT-HHHHHH CS
                     Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledl.......................elveldltdrsaler 58 
                                   il++G+ G+iG  l+ +ll++g++v g+d+  ++++ ++                            + ++d t+++ + r
  gi|13541359|ref|NP_111047.1|   3 ILIMGVDGYIGFPLALRLLTRGHDVYGIDNFITRKRVQKVGSDsalpissfafrnsvikkkfgkgiGFFYGDATNPKFIYR 83 
                                   89*****************************76666655544499************************************ PP

                                   HHHHHT-SEEEE--S---HHHHH...HSHHHHHHHHTHHHHHHHHHHHHHTCT.EEEEEEEGGGGTSCSS.SS........ CS
                     Epimerase  59 lfkeeqpdavihlAavggvaass...edpadfieknlqgtlnlleaarkagvk.rllflsSsevYGkdae.qp........ 126
                                   +++e++pda++hlA + + + s+   +++++++ kn++ tlnl+ a+++  ++  +l l++   YG ++  +p        
  gi|13541359|ref|NP_111047.1|  84 VINEVRPDAIVHLAEQRSAPYSMiglKEANETMVKNIVSTLNLIYAVKDITPEaHILKLGTMGEYGTPNIdIPegffeiey 164
                                   ***************777777762336899********************9998************777755777775554 PP

                                   ..BSTCSTTS--..--SSHHHHHHHHHHHHHHHHHHHHT-EEEEEEESEEESTT........S-TTS.TTSHHHHHHHHHH CS
                     Epimerase 127 ..keettltgpl..kpnspYaaaKlageklveayaaqyglnaiilrlfnlyGpr........ngege.vsrvipalirkil 194
                                     +++++   p+  + +s Y  +K++  + +  +++  g++++ ++   +yG r         ++++  + v+  +++++ 
  gi|13541359|ref|NP_111047.1| 165 hgRKDVL---PFprNASSWYHWTKVHDSNNLMFANKVWGTKVTDVMQGVVYGTRteeiektgLYTRFdIDEVYGTALNRFT 242
                                   4344555...77889***********999999999999****************555554443444444455555555555 PP

                                   TTS...SSEEEETTST-EEEEEEHHHHHHHHHHHHHHHTT-STTEEEE CS
                     Epimerase 195 egk...qevtllgdgtalRdflyveDvaeaillvlehvdagdkgeiyn 239
                                   ++    +++t +g+g + R fl  +D +e++ l+le++ +  + +++n
  gi|13541359|ref|NP_111047.1| 243 AEAiinEPITPYGKGGQTRGFLSLNDSIECLTLALENPPEFGEYRVFN 290
                                   5445555******************************88777777766 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 !   54.6   0.0   4.4e-18   1.1e-14       1     137 [.       4     152 ..       4     185 .. 0.82
   2 !   11.5   0.0   5.7e-05      0.15     202     306 ..     243     342 ..     225     356 .. 0.69

  Alignments for each domain:
  == domain 1  score: 54.6 bits;  conditional E-value: 4.4e-18
                                   EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHH...........HCTTT...TTGCCEEEEE--TT-HHHHHHH CS
                 GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgrie...........hlakdpkeeleenlklhkgDltDssslerl 70 
                                   Li G+ G+iG  la +Ll++g++v+gi++  +  +++++               +  k++  + + +++gD t+ + + r+
  gi|13541359|ref|NP_111047.1|   4 LIMGVDGYIGFPLALRLLTRGHDVYGIDNFITRKRVQKVGsdsalpissfaFRNSVIKKKFGKGIGFFYGDATNPKFIYRV 84 
                                   89*************************996666655544322222222221111122333445688*************** PP

                                   HHHHT-SEEEE--S---HHHHT...TSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-S CS
                 GDP_Man_Dehyd  71 laevqpdevynLAAqshVdvsf...ekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvq 137
                                   ++ev+pd++++LA q   ++s+   +++ +t+  n++ tl+L+ a++++   ++++++  +t   YG+++
  gi|13541359|ref|NP_111047.1|  85 INEVRPDAIVHLAEQRSAPYSMiglKEANETMVKNIVSTLNLIYAVKDIT--PEAHILKLGTMGEYGTPN 152
                                   *********************766689********************975..789999999999999875 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 5.7e-05
                                   HHHHTTS-C-EECTTTT-EEEEEEHHHHHHHHHHHHHC.SS---EE..E-TT-EEECHHCHHCCHHCCCHHHHHH...... CS
                 GDP_Man_Dehyd 202 arialgkqevlylGnldakRdwghvkDyveamwlmlqq.dkpedyv..iatgethsvrefvelaflelgktiewegkgeee 279
                                   a++  + ++++ +G++ ++R ++  +D +e++ l+l++  +  +y    +  e++sv++++e+   +l k+    gk+  e
  gi|13541359|ref|NP_111047.1| 243 AEAIIN-EPITPYGKGGQTRGFLSLNDSIECLTLALENpPEFGEYRvfNQFDEKYSVNQLAEMV-RDLYKEKF--GKE-PE 318
                                   555554.48889************************9943334443114557889999888864.44444322..222.22 PP

                                   ......TTGGCCCEECGG--SS--SB- CS
                 GDP_Man_Dehyd 280 vgrakesgkvvvevdpkyfrpgevdll 306
                                      + +  + +ve +++y+ p++++l 
  gi|13541359|ref|NP_111047.1| 319 ---IVHVDNPRVEKEEHYYNPEHEKLK 342
                                   ...234556788888888888887654 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   9.9e-07    0.0025       1      43 [.       1      46 [.       1      75 [. 0.84

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 9.9e-07
                                  SEEEEE--.STTHHHHHHHHHHCTSEEEEE-..S-HHHHHHHCTTS CS
                UDPG_MGDP_dh_N  1 mkisviGl.GYvGlvtaavlaeighevigvD..ideekvdklnsgk 43
                                  mki ++G  GY+G + a+ l  +gh+v g+D  i +++v+k+ s++
  gi|13541359|ref|NP_111047.1|  1 MKILIMGVdGYIGFPLALRLLTRGHDVYGIDnfITRKRVQKVGSDS 46
                                  8999***77**********************666889999887664 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   3.1e-05     0.079       1      59 [.       1      97 [.       1     102 [. 0.96
   2 ?   -1.8   0.0      0.51   1.3e+03     207     230 ..     178     201 ..     173     221 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.1e-05
                                  EEEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT......................................T--TTSHHHHHH CS
                 RmlD_sub_bind  1 mkilvtGanGqlGseLakqlaeeglevlaltre......................................eldltdaeavae 45
                                  mkil++G +G +G  La +l  +g++v+++++                                         d t+++ + +
  gi|13541359|ref|NP_111047.1|  1 MKILIMGVDGYIGFPLALRLLTRGHDVYGIDNFitrkrvqkvgsdsalpissfafrnsvikkkfgkgigffYGDATNPKFIYR 83
                                  89***************************97778888**********************************9*********** PP

                                  HHHHH--SEEEE-- CS
                 RmlD_sub_bind 46 llkeakpdvvvnaA 59
                                  +++e++pd++v++A
  gi|13541359|ref|NP_111047.1| 84 VINEVRPDAIVHLA 97
                                  ************99 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.51
                                   -EEEE---BS-EEHHHHHHHHHHH CS
                 RmlD_sub_bind 207 agvyHlanegetswlefArailke 230
                                   ++ yH++     + l fA+++  +
  gi|13541359|ref|NP_111047.1| 178 SSWYHWTKVHDSNNLMFANKVWGT 201
                                   6789*************9999754 PP

>> SDH_sah  Serine dehydrogenase proteinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.5     3e-05     0.077     192     257 ..     296     361 ..     288     387 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3e-05
                       SDH_sah 192 kaikqveefvyellkdkydeekakeiakklteGrwthdypltveelkelGlevntnvpeevyelle 257
                                    +++q+ e+v +l k+k+++e      ++    +  h y    e+lk lG +   ++  e+y+ ++
  gi|13541359|ref|NP_111047.1| 296 YSVNQLAEMVRDLYKEKFGKEPEIVHVDNPRVEKEEHYYNPEHEKLKALGYKRTKDIKSEIYDAID 361
                                   579*****************9877666777778899**************************9775 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   6.4e-05      0.16      57     117 ..      69     132 ..      38     140 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 6.4e-05
                                   ...E--TT-HHHHHHHTT..T-SEEEE------HHHHH...HSHHHHHHHHHHHHHHHHHHHHH CS
               Polysacc_synt_2  57 vpvigdvrdkerlekaleelkvdvvfhaAAlKhVPlve...enpleaiktNvlgtenvieaaie 117
                                     + gd ++ + + ++++e+++d+++h A  +  P      +++ e++  N+++t n+i a ++
  gi|13541359|ref|NP_111047.1|  69 GFFYGDATNPKFIYRVINEVRPDAIVHLAEQRSAPYSMiglKEANETMVKNIVSTLNLIYAVKD 132
                                   4557999****************************765112456677889********998766 PP

>> RanGAP1_C  RanGAP1 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   8.7e-05      0.22      24      73 ..     326     377 ..     307     388 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 8.7e-05
                     RanGAP1_C  24 pvdvssFlafPspeKLlkLGakraelieqqv..dvsdaekvveaflkissvy 73 
                                    v+ ++    P  eKL +LG kr++ i+ ++   + d +k  e ++ +  v+
  gi|13541359|ref|NP_111047.1| 326 RVEKEEHYYNPEHEKLKALGYKRTKDIKSEIydAIDDLNKFKERLMNLRNVI 377
                                   4666777889*********************966788999999999887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (390 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       610  (0.0340231); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); 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: 0.58u 0.32s 00:00:00.89 Elapsed: 00:00:00.50
# Mc/sec: 2354.33
//
Query:       gi|13541360|ref|NP_111048.1|  [L=246]
Description: dTDP-glucose pyrophosphorylase [Thermoplasma volcanium GSS1]
Scores for complete sequence (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   77.2   0.0    1.7e-21   77.0   0.0    1.1  1  NTP_transferase  Nucleotidyl transferase
      6e-06   26.7   0.0    6.8e-06   26.5   0.0    1.1  1  NTP_transf_3     MobA-like NTP transferase domain
  ------ inclusion threshold ------
      0.027   14.3   0.1      0.039   13.8   0.1    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 !   77.0   0.0   2.8e-25   1.7e-21      31     242 ..      40     232 ..       4     237 .. 0.80

  Alignments for each domain:
  == domain 1  score: 77.0 bits;  conditional E-value: 2.8e-25
                                   TETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEEEEESS--BGGHHHHHTHHHHTTSSE..EEEEETT CS
               NTP_transferase  31 erliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevlialepegkgtAdAvalaaelledeksdelvlvLgg 111
                                    ++i+ ++ r+  sgi++iivvl   + +  +++++  +    +v+ia+++e++g  dAv  a+++++  +    +l  g+
  gi|13541360|ref|NP_111048.1|  40 RPIIDCVIYRMKISGIDDIIVVLD-PKDEVTKKYIELSY---PDVQIAYQTEKRGYGDAVHSALQFIHGPF----LLNAGD 112
                                   289***************666666.55556677777665...47************************877....777888 PP

                                   EEEEST.THHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEEEECTTSBEEEEECS-SSHSHCSEECCSEEEEETTHHHHHH CS
               NTP_transferase 112 Dhlikd.ayeeavkkaiekaakgtvtfgivpveeateyGvieadeegrverfvEKPkeakaselassGiYvfnsevllfla 191
                                    +l++d + +++v++ ++ ++     +++ +v+++++yGv+e+de+g++  ++EKP+ +k s+la + iY+ +++vl ++ 
  gi|13541360|ref|NP_111048.1| 113 GVLFDDnTEKRIVDSYKSGNR-----LIAFKVDDPRRYGVVEMDENGNIAGLEEKPNLPK-SNLALAAIYILDKSVLNEI- 186
                                   888888444556666666666.....7788999***************************.*******************. PP

                                   HCCHHHTTSSCHHHHHHHHHHHTTEEEEEECSTTEE-EEEXSSHHHHHHHH CS
               NTP_transferase 192 kdleelkrgedeitdilpkaleegkvalaflfkdaeyWsDvGtldsllean 242
                                       +  + + e+td++ + +++g v+ ++++ d + W  vG  d + ++ 
  gi|13541360|ref|NP_111048.1| 187 ----DTGKANVELTDAIDRTIKKG-VKSDVIEIDRSEWISVGLADRYADVV 232
                                   ....7899***************8.555889999889*****999988875 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 !   26.5   0.0   1.1e-09   6.8e-06       1     124 [.       5     140 ..       5     202 .. 0.82

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 1.1e-09
                                   EEEEEESS-TTTTT....THHHHCC....CCC....CHHHHHHHHHCTT.-CEEEEECSH.CHHHH...HHTTCTS-EEE- CS
                  NTP_transf_3   1 aviLAGGrSsRmgg....dKallpl....ggk....pllervldalraagvdevvvvggd.eevla...alarlgvrvved 65 
                                   ++i A+G ++R g      K +  +    +gk    p+++ v+ +++ +g+d+++vv ++ +ev++   +l  ++v+++++
  gi|13541360|ref|NP_111048.1|   5 GLITAAGLGTRSGAsqfyRKEMFSIydarDGKvvirPIIDCVIYRMKISGIDDIIVVLDPkDEVTKkyiELSYPDVQIAYQ 85 
                                   6789*********556889***99975444449999*********************988677877333344557888888 PP

                                   TTSS-SHHHHHHHHHHHH.SSSCEEEEETT-TT--HHHHHHHHHCHHHHTSSEEEEESS CS
                  NTP_transf_3  66 edpgkgplaslaaalraaadadavlvlacDmPlltpelverllaaaaasgadvvvptye 124
                                   + + +g + ++++al+ +    ++l+ a+D +l++ ++ +r++++++ sg++ ++++ +
  gi|13541360|ref|NP_111048.1|  86 T-EKRGYGDAVHSALQFI--HGPFLLNAGDGVLFDDNTEKRIVDSYK-SGNRLIAFKVD 140
                                   7.589***********98..79**********************986.55555555544 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 ?   13.8   0.1   6.6e-06     0.039      27     113 ..      54     137 ..      32     172 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6.6e-06
                                   CEEEEEEEEES-SSCHHHHHGGGCH.C-TTEEEEEESSS-HHHHHHHHHHHH--SSEEEEEESSEEE-TTHHHHHHHHHHH CS
               Glycos_transf_2  27 pdfeiivvDDgStDetveileelak.edprvrvirreenvGkagalnaglraatgdyilflDaDdepdpdwleklvealek 106
                                     ++iivv D       e+ +++ + ++p+v +  ++e++G++ a+  +l+   g ++l   + + +d+++ +++v+ ++ 
  gi|13541360|ref|NP_111048.1|  54 GIDDIIVVLDPK----DEVTKKYIElSYPDVQIAYQTEKRGYGDAVHSALQFIHGPFLLNAGDGVLFDDNTEKRIVDSYKS 130
                                   567899999999....566666666679********************************999999999999999999999 PP

                                   .TTCEEE CS
               Glycos_transf_2 107 dgadvvl 113
                                   +++ +++
  gi|13541360|ref|NP_111048.1| 131 GNRLIAF 137
                                   6664444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1698.38
//
Query:       gi|13541361|ref|NP_111049.1|  [L=408]
Description: phosphoglycerate kinase [Thermoplasma volcanium GSS1]
Scores for complete 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-103  344.8   0.2   6.5e-103  344.6   0.2    1.0  1  PGK       Phosphoglycerate kinase


Domain annotation for each model (and alignments):
>> PGK  Phosphoglycerate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  344.6   0.2  3.6e-107  6.5e-103       2     377 ..       8     390 ..       7     391 .. 0.92

  Alignments for each domain:
  == domain 1  score: 344.6 bits;  conditional E-value: 3.6e-107
                                   GGS--TT-EEEEEE-----EECT.TEES--HHHHHHHHHHHHHHHTT-EEEEEE--S--TTS-GGG-SHHHHHHHHHHHTT CS
                           PGK   2 kdldlkgkrvlvRvDfNvplkke.gkitddtriraalpTikyllekgakvvllsHlgrpkgekeklslkpvaerLsellgk 81 
                                   + +dl+g+++ +RvD+N+p++   g+i  + r+ra+++Ti++l  ++ kvv+++H++rp g+++ +sl+++a+ +s++l+k
  gi|13541361|ref|NP_111049.1|   8 DSFDLAGRTIYLRVDINSPVNPVtGEIMGTDRFRAHVETIRKL--RDSKVVIVAHQSRP-GKDDFTSLRQHAQVMSRILNK 85 
                                   6789****************9778*******************..77899*********.89******************* PP

                                   -EEEESSTTSHHHHHHHHT-TTT-EEEES-GGGSTTTTTT-H.......HHHHHHHHT-SEEEE--GGGTTS--TTTTHHH CS
                           PGK  82 eVkfvedvvgeeveeaiaelkegevllLeNvrfykeEeknde.......elakklasladvyVnDAFgtahrahaStvgia 155
                                   +V fv++++g+ v++++++++eg++++LeN rfy+eE + ++       +++k l+ l+d+y+ DAF+++hra++++vg+ 
  gi|13541361|ref|NP_111049.1|  86 KVMFVDQLFGSLVNKTVESMNEGDIVMLENARFYSEEVDLTTlesmensNIVKGLSTLFDYYIIDAFAAIHRAQTTLVGFR 166
                                   *************************************5322222233347******************************* PP

                                   HCSEEEE-HHHHHHHHHHHHHHHS--SSEEEEEEES-HHHCHHHHHHHTTT-..SEEEEETCHHHHHHHHTT-B-TTSS-- CS
                           PGK 156 kvlsaaaGllmekElealskvlenperplvailGGakvsdkikvienLlekv..dkliigGgmantFlkaqgleigkslve 234
                                   ++ +++aG l+ekE+++++++ + +e p +ailGGak++d i+v en l++   dk+++gG++an+Fl a+g++igk+  +
  gi|13541361|ref|NP_111049.1| 167 RIKPNIAGALIEKEVTMIDRFRHLNESPKIAILGGAKIDDSIAVSENFLKSGfvDKILTGGVVANAFLWAKGIDIGKKNRD 247
                                   ***88********************************************98666**********************99884 PP

                                   G.........GGHHHHHHHHHHHHHHT-EEE--SEEEEESSSSTTS.EEEECCG--TT-EEEEE-HHHHHHHHHHHCC-SE CS
                           PGK 235 e.........dklelakellekakkkgvkillpvDvvvakeeaekeakvveveaipedemalDigpktielfaeaikeakt 306
                                             + +  +k ll+++   g++il+p D++++     + ++v ++ +ip+d+   Dig +t+ +++e+i++ak 
  gi|13541361|ref|NP_111049.1| 248 FiiknngdyeKLIAKCKGLLSEF---GDRILVPSDFILSP----SGERVSANGKIPDDQILADIGLDTVVEYSEIIDKAKA 321
                                   44444443323478888888877...59***********7....235888999**************************** PP

                                   EEEES-SS-TTSGCCCHHHHHHHHHHHHHCHTSEEEEESHHHHHHHHHTT-GGGSSEEESSSHHHHHHHCT CS
                           PGK 307 vvwnGpmGvfeiekfakGTkaiakalaeatkgalsivGGgdsaaaveklgladkvshvStGGgAsLelLeg 377
                                   +++nGpmG++eie++++GT++i + +a+++  a+si+GGg++++a++klgl+++++h StGGgA++++L+g
  gi|13541361|ref|NP_111049.1| 322 IFMNGPMGIYEIEAYSSGTREIFSSVAKSE--AFSIAGGGHTLSALDKLGLTNRIDHASTGGGALISYLSG 390
                                   ****************************84..6************************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (408 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       485  (0.0270511); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.22s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 3039.16
//
Query:       gi|13541362|ref|NP_111050.1|  [L=130]
Description: prefoldin subunit alpha [Thermoplasma volcanium GSS1]
Scores for complete 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-20   71.6   1.7    5.9e-20   71.4   1.7    1.0  1  Prefoldin     Prefoldin subunit
    2.3e-05   24.3   0.6      0.022   14.7   0.1    2.2  2  Prefoldin_2   Prefoldin subunit
    4.7e-05   23.7   7.2      0.039   14.3   0.8    2.2  2  FlaC_arch     Flagella accessory protein C (FlaC)
    0.00015   22.3   2.5      0.027   15.1   0.1    2.2  2  SlyX          SlyX
    0.00073   19.7   5.0      0.035   14.4   0.6    2.4  2  Osmo_CC       Osmosensory transporter coiled coil
      0.002   18.3   1.7       0.17   12.2   0.1    2.1  2  DUF948        Bacterial protein of unknown function (DUF948)
     0.0068   16.5   0.2      0.017   15.3   0.2    1.6  1  Mod_r         Modifier of rudimentary (Mod(r)) protein
     0.0076   16.0   3.5      0.023   14.5   0.4    2.2  2  SKA2          Spindle and kinetochore-associated protein 2
  ------ inclusion threshold ------
      0.014   15.1   2.8      0.076   12.8   0.1    2.2  2  DivIC         Septum formation initiator
       0.02   14.5   0.1      0.022   14.4   0.1    1.2  1  HAUS-augmin3  HAUS augmin-like complex subunit 3
      0.021   14.3   4.3       0.25   10.7   3.6    2.0  2  DUF4618       Domain of unknown function (DUF4618)
      0.022   14.8   0.5        5.7    7.0   0.0    2.3  2  DUF2443       Protein of unknown function (DUF2443)
      0.023   14.7   3.8       0.57   10.2   0.1    2.2  2  FlxA          FlxA-like protein
      0.044   14.2   1.5        7.4    7.0   0.0    2.1  2  DUF3232       Protein of unknown function (DUF3232)
      0.044   13.7   2.4       0.31   10.9   2.4    1.9  1  STAT_alpha    STAT protein, all-alpha domain
      0.046   14.2   5.4          2    8.9   1.0    2.1  2  DUF16         Protein of unknown function DUF16
      0.047   13.2   2.2       0.64    9.5   0.2    2.0  2  Vps5          Vps5 C terminal like
      0.049   13.7   1.7        2.4    8.3   0.3    2.4  2  Med9          RNA polymerase II transcription mediator comple
      0.053   13.1   3.9       0.88    9.1   0.8    2.0  2  PspA_IM30     PspA/IM30 family
       0.07   13.6   5.2        0.9   10.0   0.9    2.1  2  NPV_P10       Nucleopolyhedrovirus P10 protein
      0.091   12.1   3.6       0.12   11.6   3.6    1.2  1  CorA          CorA-like Mg2+ transporter protein
       0.12   12.7   2.6       0.13   12.6   0.5    2.0  2  TSC22         TSC-22/dip/bun family
       0.19   11.7   4.5        3.7    7.5   0.8    2.1  2  MIP-T3_C      Microtubule-binding protein MIP-T3 C-terminal r
       0.24   11.6   1.6       0.68   10.2   0.1    2.1  2  HALZ          Homeobox associated leucine zipper
       0.27   11.9   2.5        2.8    8.7   0.5    2.1  2  YabA          Initiation control protein YabA
       0.29   11.8   2.3        3.9    8.2   0.1    2.1  2  DUF4665       Domain of unknown function (DUF4665)
       0.33   11.3   5.6       0.23   11.8   1.4    2.2  2  Csm1_N        Csm1 N-terminal domain
       0.34   10.9   5.8        4.2    7.4   0.8    2.1  2  Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C
       0.38   10.9   6.5          6    7.0   1.6    2.1  2  Fib_alpha     Fibrinogen alpha/beta chain family
       0.44   10.6   3.3       0.43   10.6   0.5    2.1  2  DASH_Dad4     DASH complex subunit Dad4
       0.81   10.2   6.8        0.4   11.2   1.8    2.3  2  ZapB          Cell division protein ZapB
          1    9.7   7.8       0.59   10.4   1.1    2.1  2  DUF5082       Domain of unknown function (DUF5082)


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 !   71.4   1.7     1e-22   5.9e-20       2     119 ..      13     129 ..      12     130 .] 0.97

  Alignments for each domain:
  == domain 1  score: 71.4 bits;  conditional E-value: 1e-22
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT.-TT-EEEEEEETTEEEEEE--STTEEEEEEETTEEEEEEHHHHHHHH CS
                     Prefoldin   2 keeleslqaelaqlkeaieelektletlktlkkedegkevlvplgaglyvkaevkdtdkvlvdlGagyyveksleeAiell 82 
                                   ++ ++s+ a+++++++   e+++t+++l++ +   ++ke l+ +g+g++++++++ +++++v +G+g+y+  +  e ie l
  gi|13541362|ref|NP_111050.1|  13 ESLISSVDAQIDAINKMVLEVQTTIQILSSDEL-RQSKERLISVGSGIFANGNLDLDSDLIVPIGSGVYIAEKRSETIERL 92 
                                   7889*************************9999.9********************************************** PP

                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     Prefoldin  83 kkkleelekqlekleeeleklkdqittleanlaqlyq 119
                                   k ++e+l+++++kl ++ + l dq++t+  + a++ +
  gi|13541362|ref|NP_111050.1|  93 KANIENLKESIQKLMDQRRTLVDQYNTVYTTEATRNI 129
                                   *****************************99998765 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.1    0.0042       2.3      66     102 ..       4      40 ..       1      44 [. 0.91
   2 !   14.7   0.1   3.8e-05     0.022      53      94 ..      78     119 ..      64     123 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0042
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC CS
                   Prefoldin_2  66 eLeerketlekeiktlekqleklekeleelkeelqkk 102
                                   ++e++++++e  i+++  q++ ++k + e+++++q++
  gi|13541362|ref|NP_111050.1|   4 DVEAQLNYIESLISSVDAQIDAINKMVLEVQTTIQIL 40 
                                   7999******************************987 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 3.8e-05
                                   TEEEEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                   Prefoldin_2  53 dvlvkqdkeevkeeLeerketlekeiktlekqleklekelee 94 
                                   +v + +++ e++e+L++++e+l++ i++l +q ++l  +++ 
  gi|13541362|ref|NP_111050.1|  78 GVYIAEKRSETIERLKANIENLKESIQKLMDQRRTLVDQYNT 119
                                   578888999************************999888775 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.8   0.00019      0.11       4      38 ..       4      38 ..       2      53 .. 0.93
   2 !   14.3   0.8     7e-05     0.039      12      47 ..      85     120 ..      82     123 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00019
                     FlaC_arch  4 elEnklsklsteletvkkeneelsksveelkenVk 38
                                  ++E +l+ +++ +++v ++++ ++k v e++ +++
  gi|13541362|ref|NP_111050.1|  4 DVEAQLNYIESLISSVDAQIDAINKMVLEVQTTIQ 38
                                  68*****************************9997 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 7e-05
                     FlaC_arch  12 lsteletvkkeneelsksveelkenVkdllsLYEvV 47 
                                    s ++e +k+++e+l++s+++l ++ + l++ Y +V
  gi|13541362|ref|NP_111050.1|  85 RSETIERLKANIENLKESIQKLMDQRRTLVDQYNTV 120
                                   567899999999999999999999999999999998 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1   4.9e-05     0.027       2      47 ..       6      52 ..       5      64 .. 0.86
   2 ?    7.5   0.4     0.011       6.3      32      54 ..      88     110 ..      82     127 .. 0.56

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 4.9e-05
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHT- CS
                          SlyX  2 eerleeLEiklafqedtieeLndvvaeqqqqidrlq.rqlrllaerl 47
                                  e++l+ +E+ ++  + +i++ n++v e q +i+ l   +lr+ +erl
  gi|13541362|ref|NP_111050.1|  6 EAQLNYIESLISSVDAQIDAINKMVLEVQTTIQILSsDELRQSKERL 52
                                  788999***************************99625788888887 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.011
                                   HHHHHHHHHHHHHHT-XXXXXXX CS
                          SlyX  32 qidrlqrqlrllaerlkeleess 54 
                                   +i+rl++ ++ l+e +++l ++ 
  gi|13541362|ref|NP_111050.1|  88 TIERLKANIENLKESIQKLMDQR 110
                                   45555555555555555444443 PP

>> Osmo_CC  Osmosensory transporter coiled coil
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.3    0.0098       5.5      15      33 ..      10      28 ..       5      54 .. 0.80
   2 !   14.4   0.6   6.2e-05     0.035      19      41 ..      94     116 ..      83     119 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0098
                                  THHHHHHHHHHHHHHHHHH CS
                       Osmo_CC 15 dnIEqkvedideeIaaLee 33
                                  ++IE  +  +d++I a+++
  gi|13541362|ref|NP_111050.1| 10 NYIESLISSVDAQIDAINK 28
                                  78************99877 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 6.2e-05
                                   HHHHHHHHHHHHHHHHHHHHHHH CS
                       Osmo_CC  19 qkvedideeIaaLeekRqrLvdq 41 
                                    ++e++ e I++L+ +R +Lvdq
  gi|13541362|ref|NP_111050.1|  94 ANIENLKESIQKLMDQRRTLVDQ 116
                                   589*******************9 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.2      0.03        17      47      80 ..       3      36 ..       1      42 [. 0.79
   2 !   12.2   0.1    0.0003      0.17      18      59 ..      79     120 ..      71     127 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.03
                        DUF948 47 kevedllakvnelledvneklekvdplteavadl 80
                                  ++ve+ l+ ++ l + v  +++++++++ +v+++
  gi|13541362|ref|NP_111050.1|  3 RDVEAQLNYIESLISSVDAQIDAINKMVLEVQTT 36
                                  5778888888889999999999999999999876 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.0003
                        DUF948  18 ivvllklkktldeaaatieelekqvdpilkevedllakvnel 59 
                                   +++  k ++t+++++a ie+l++ +++++++ ++l+++ n++
  gi|13541362|ref|NP_111050.1|  79 VYIAEKRSETIERLKANIENLKESIQKLMDQRRTLVDQYNTV 120
                                   56666778999***********************99999985 PP

>> Mod_r  Modifier of rudimentary (Mod(r)) protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.2     3e-05     0.017      38      93 ..      45     119 ..       2     125 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3e-05
                         Mod_r  38 llaenesla........eknlslep..........eleelrselqekle.elkelekefeekeqeldellqkfsp 93 
                                   l+++ e+l         + nl+l             + e+rse++e+l+ ++++l+++ +++  +  +l+++++ 
  gi|13541362|ref|NP_111050.1|  45 LRQSKERLIsvgsgifaNGNLDLDSdlivpigsgvYIAEKRSETIERLKaNIENLKESIQKLMDQRRTLVDQYNT 119
                                   2222222224444444488888844599999999999************88*******************99986 PP

>> SKA2  Spindle and kinetochore-associated protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.2      0.23   1.3e+02      70      99 ..      14      43 ..       2      53 .. 0.69
   2 !   14.5   0.4     4e-05     0.023      45      78 ..      87     120 ..      85     129 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.23
                          SKA2 70 elidkirttlvanrellqqLqasaelppls 99
                                   li+++ +++ a  +++ + q ++++ + +
  gi|13541362|ref|NP_111050.1| 14 SLISSVDAQIDAINKMVLEVQTTIQILSSD 43
                                  567777888888888887777777665544 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 4e-05
                          SKA2  45 erlkkvkeelqaLkeqceellaekkelidkirtt 78 
                                   e ++++k+ +++Lke +++l  +++ l+d+ +t 
  gi|13541362|ref|NP_111050.1|  87 ETIERLKANIENLKESIQKLMDQRRTLVDQYNTV 120
                                   5799*************************99886 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.3      0.17        97      19      45 ..      16      42 ..       7      52 .. 0.78
   2 ?   12.8   0.1   0.00014     0.076      10      46 ..      80     116 ..      71     128 .. 0.53

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.17
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         DivIC 19 ykqlkqeiaalqaelaklkaeneeLea 45
                                  +++++++i+a+++ + +++ +++ L +
  gi|13541362|ref|NP_111050.1| 16 ISSVDAQIDAINKMVLEVQTTIQILSS 42
                                  567888888888888888888888765 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00014
                                   XXXXXXXXHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         DivIC  10 ifgkkgllaykqlkqeiaalqaelaklkaeneeLeae 46 
                                   ++ +k   ++ +lk++i+ l++ ++kl ++++ L ++
  gi|13541362|ref|NP_111050.1|  80 YIAEKRSETIERLKANIENLKESIQKLMDQRRTLVDQ 116
                                   4444444455555555555555555555555555444 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 ?   14.4   0.1   3.9e-05     0.022      24     105 ..      39     121 ..       9     129 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.9e-05
                  HAUS-augmin3  24 VLseeelqay.eeLkksGkpiLegeaLeeaLktiepsdlkqedvellevileeeeesleaLeqelqeLqkekalklkrlnk 103
                                   +Ls  el++  e L   G  i    +L+   + i p  +     e+ ++++e +++++e+L++ +q+L  +++ +  ++n 
  gi|13541362|ref|NP_111050.1|  39 ILSSDELRQSkERLISVGSGIFANGNLDLDSDLIVPIGSGVYIAEKRSETIERLKANIENLKESIQKLMDQRRTLVDQYNT 119
                                   6777777654155778888888888888888888888888888889999*******************************8 PP

                  HAUS-augmin3 104 Lq 105
                                     
  gi|13541362|ref|NP_111050.1| 120 VY 121
                                   65 PP

>> DUF4618  Domain of unknown function (DUF4618)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.1     0.051        29      73     108 ..       6      41 ..       1      45 [. 0.82
   2 ?   10.7   3.6   0.00045      0.25     193     224 ..      80     111 ..      12     123 .. 0.65

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.051
                       DUF4618  73 qeweekeekklekLeqqleqlnakvqklqeelnvLs 108
                                   +   + +e+ +++ + q++++n++v ++q+ +++Ls
  gi|13541362|ref|NP_111050.1|   6 EAQLNYIESLISSVDAQIDAINKMVLEVQTTIQILS 41 
                                   55556678889999999***********99999998 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00045
                       DUF4618 193 keiekfrefieeleeeipeLkaeveqLqaqae 224
                                   +  ek  e ie+l+ +i++Lk+++++L+ q++
  gi|13541362|ref|NP_111050.1|  80 YIAEKRSETIERLKANIENLKESIQKLMDQRR 111
                                   445677789*******************9987 PP

>> DUF2443  Protein of unknown function (DUF2443)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.1     0.021        12      50      76 ..       7      33 ..       3      36 .. 0.85
   2 ?    7.0   0.0      0.01       5.7      57      71 ..      87     101 ..      68     115 .. 0.61

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.021
                                  HHHHHHHHHHHHHHHHHHHHHHHHGGG CS
                       DUF2443 50 afltqideevekLkeaidaLnkikkel 76
                                  a l+ i+  ++ + ++ida+nk+  e+
  gi|13541362|ref|NP_111050.1|  7 AQLNYIESLISSVDAQIDAINKMVLEV 33
                                  5678899999************97765 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.01
                                   HHHHHHHHHHHHHHH CS
                       DUF2443  57 eevekLkeaidaLnk 71 
                                   e +e+Lk++i+ L  
  gi|13541362|ref|NP_111050.1|  87 ETIERLKANIENLKE 101
                                   555555555554433 PP

>> FlxA  FlxA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.8     0.032        18      19      50 ..      16      48 ..       4      54 .. 0.53
   2 ?   10.2   0.1     0.001      0.57      15      39 ..      85     109 ..      78     121 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.032
                          FlxA 19 iasLqkQiknlqkqLkelses.deltkeekkkq 50
                                  i+s   Qi+ ++k + e++++ + l+ +e ++ 
  gi|13541362|ref|NP_111050.1| 16 ISSVDAQIDAINKMVLEVQTTiQILSSDELRQS 48
                                  555555555555555555555444444444433 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.001
                          FlxA  15 sasqiasLqkQiknlqkqLkelses 39 
                                    ++ i++L+  i+nl++++++l ++
  gi|13541362|ref|NP_111050.1|  85 RSETIERLKANIENLKESIQKLMDQ 109
                                   5678999999999999999999988 PP

>> DUF3232  Protein of unknown function (DUF3232)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.3     0.017       9.7      24      70 ..       6      52 ..       1      55 [. 0.85
   2 ?    7.0   0.0     0.013       7.4      47      77 ..      82     114 ..      74     123 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.017
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCTS-HHHHHHHHHHH CS
                       DUF3232 24 evalelledlidaatrYvkkvvemearlasarfrleaeelkelveel 70
                                  e  l+ +e li ++   +  +++m   +++    l ++el++  e l
  gi|13541362|ref|NP_111050.1|  6 EAQLNYIESLISSVDAQIDAINKMVLEVQTTIQILSSDELRQSKERL 52
                                  345899*******************9999999999*****9987765 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.013
                                   HHHHH.HHHCCTS-HHHHHHHHHHH.HHHHHHH CS
                       DUF3232  47 mearl.asarfrleaeelkelveel.DrsRrla 77 
                                    e+r  ++ r++ + e+lke +++l D+ R+l+
  gi|13541362|ref|NP_111050.1|  82 AEKRSeTIERLKANIENLKESIQKLmDQRRTLV 114
                                   5555415679************98626666655 PP

>> STAT_alpha  STAT protein, all-alpha domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   2.4   0.00056      0.31       4      83 ..      19     121 ..       2     128 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00056
                    STAT_alpha   4 ieqrleelrskvqeteqdirkLedeqeeFdfqyqelqkl.....................................eqera 47 
                                   ++++++ ++++v e++ +i+ L               +                                       +e++
  gi|13541362|ref|NP_111050.1|  19 VDAQIDAINKMVLEVQTTIQILS--------------SDelrqskerlisvgsgifangnldldsdlivpigsgvyIAEKR 85 
                                   33444444444444444444444..............33444444444556777777777777777888889999855555 PP

                    STAT_alpha  48 esekkelkkqkellqqmlnaLdqkRkelvdklkell 83 
                                   + + ++lk + e+l++++++L+++R  lvd+ + + 
  gi|13541362|ref|NP_111050.1|  86 SETIERLKANIENLKESIQKLMDQRRTLVDQYNTVY 121
                                   555666999999999999999999999999988765 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.6    0.0071         4      56      89 ..       4      41 ..       1      57 [. 0.48
   2 ?    8.9   1.0    0.0037         2      45      84 ..      84     123 ..      43     128 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0071
                                  HHHHHHHHHHHHHHHHHHHHH...........HHHHHH CS
                         DUF16 56 kvekqgekikelkveqkaqgeeln....kvdetlelil 89
                                   ve+q + i+ l   ++aq +++n    +v+ t++++ 
  gi|13541362|ref|NP_111050.1|  4 DVEAQLNYIESLISSVDAQIDAINkmvlEVQTTIQILS 41
                                  45555555666666666666666633333333333332 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0037
                                   ...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.......H CS
                         DUF16  45 klgeqinkleqkvekqgekikelkveqkaqgeelnkvdet 84 
                                   k+ e i++l+ ++e++ e i++l  +  +  ++ n+v  t
  gi|13541362|ref|NP_111050.1|  84 KRSETIERLKANIENLKESIQKLMDQRRTLVDQYNTVYTT 123
                                   6778899999999999999999998888888887766555 PP

>> Vps5  Vps5 C terminal like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.1     0.071        40      35      82 ..       4      51 ..       2      59 .. 0.89
   2 ?    9.5   0.2    0.0011      0.64      28      62 ..      84     118 ..      79     125 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.071
                          Vps5 35 slesqLkkLykaiellvsqrkelasataelakslesLaslelskslsr 82
                                  ++e+qL  +++ i+++++q   + +++ e+ ++++ L+s el +s  r
  gi|13541362|ref|NP_111050.1|  4 DVEAQLNYIESLISSVDAQIDAINKMVLEVQTTIQILSSDELRQSKER 51
                                  5799***********************************999987655 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0011
                          Vps5  28 dkkqeldslesqLkkLykaiellvsqrkelasata 62 
                                   ++ ++++ l +++ +L ++i+ l +qr++l+   +
  gi|13541362|ref|NP_111050.1|  84 KRSETIERLKANIENLKESIQKLMDQRRTLVDQYN 118
                                   45678*************************97665 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 ?    4.5   0.0     0.068        38      48      75 ..       1      28 [.       1      33 [. 0.86
   2 ?    8.3   0.3    0.0042       2.4      50      69 ..      87     106 ..      80     127 .. 0.57

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.068
                          Med9 48 idrsveeqeaeieeleeqlakKrelLkk 75
                                  + r ve q+++ie+l  +++++ + ++k
  gi|13541362|ref|NP_111050.1|  1 MARDVEAQLNYIESLISSVDAQIDAINK 28
                                  57899**********9999998888776 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0042
                          Med9  50 rsveeqeaeieeleeqlakK 69 
                                   +++e  +a ie+l+e+++k 
  gi|13541362|ref|NP_111050.1|  87 ETIERLKANIENLKESIQKL 106
                                   44444444444444444432 PP

>> PspA_IM30  PspA/IM30 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.1     0.024        14      86     125 ..       2      41 ..       1      57 [. 0.73
   2 ?    9.1   0.8    0.0016      0.88     109     141 ..      84     116 ..      81     127 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.024
                     PspA_IM30  86 Arealaeikslekqaealetqlaqqrsaveqlrkqleale 125
                                   Ar + a++ + e+ +   ++q +  +++v ++++ ++ l 
  gi|13541362|ref|NP_111050.1|   2 ARDVEAQLNYIESLISSVDAQIDAINKMVLEVQTTIQILS 41 
                                   7777788888888888888888888888888888887664 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0016
                     PspA_IM30 109 qqrsaveqlrkqlealetkieelkakkellkar 141
                                   +  +++e l++++e+l+  i++l +++++l  +
  gi|13541362|ref|NP_111050.1|  84 KRSETIERLKANIENLKESIQKLMDQRRTLVDQ 116
                                   556889999999999999999999999998655 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.9    0.0016       0.9      30      67 ..       5      42 ..       2      55 .. 0.60
   2 ?    5.7   0.2     0.037        21      26      58 ..      88     120 ..      82     128 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0016
                       NPV_P10 30 vqenlpdvtelnekLdaqsaqLaeletkvenIqdiLnp 67
                                  v+++l+ ++ l + +daq ++++++  +v++  +iL++
  gi|13541362|ref|NP_111050.1|  5 VEAQLNYIESLISSVDAQIDAINKMVLEVQTTIQILSS 42
                                  55555555555555555555555555555555555554 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.037
                       NPV_P10  26 qvddvqenlpdvtelnekLdaqsaqLaeletkv 58 
                                    ++++++n+++++e  +kL +q  +L +  ++v
  gi|13541362|ref|NP_111050.1|  88 TIERLKANIENLKESIQKLMDQRRTLVDQYNTV 120
                                   577888888888888888888888777665555 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   3.6   0.00022      0.12     119     233 ..       8     128 ..       2     130 .] 0.84

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00022
                          CorA 119 ivdrlfellekleeeldeledel...edstkkeilrelaqlrrrlvklrralapnrevlk..rlla.kaddkllddedkey 193
                                    +++++ l++ +++++d + +++   ++ ++    +el q ++rl+ + + +++n ++    +l+   + +  + ++++e 
  gi|13541362|ref|NP_111050.1|   8 QLNYIESLISSVDAQIDAINKMVlevQTTIQILSSDELRQSKERLISVGSGIFANGNLDLdsDLIVpIGSGVYIAEKRSET 88 
                                   5677888999999999999999996677777777789999999*****9998887666544477778899999******** PP

                          CorA 194 lrdlldelerllemlealrerleslqdtyssllserlNrv 233
                                   +++l  ++e+l e ++ l ++ + l d+y+++ + +  r+
  gi|13541362|ref|NP_111050.1|  89 IERLKANIENLKESIQKLMDQRRTLVDQYNTVYTTEATRN 128
                                   ******************************9987766555 PP

>> TSC22  TSC-22/dip/bun family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1       3.6     2e+03      29      53 ..      25      49 ..      11      52 .. 0.67
   2 ?   12.6   0.5   0.00023      0.13      15      34 ..      95     114 ..      86     129 .. 0.54

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 3.6
                         TSC22 29 rnseleeENslLkalaspeqleqls 53
                                   ++++  E ++  +++s++ l q +
  gi|13541362|ref|NP_111050.1| 25 AINKMVLEVQTTIQILSSDELRQSK 49
                                  4556666666666777777777765 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00023
                         TSC22  15 eVevLkekIkeLeernsele 34 
                                    +e+Lke I+ L+++ ++l 
  gi|13541362|ref|NP_111050.1|  95 NIENLKESIQKLMDQRRTLV 114
                                   35666666666666655543 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 ?    7.5   0.8    0.0066       3.7     114     151 ..       4      41 ..       1      44 [. 0.91
   2 ?    5.9   0.2      0.02        11     110     128 ..      87     105 ..      78     119 .. 0.65

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0066
                      MIP-T3_C 114 plkaqlaeleeaIkdqkekisnvrakilkNeakiqkll 151
                                   +++aql+ +e+ I+    +i+++ + +l+ +  iq l 
  gi|13541362|ref|NP_111050.1|   4 DVEAQLNYIESLISSVDAQIDAINKMVLEVQTTIQILS 41 
                                   6899******************************9875 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.02
                      MIP-T3_C 110 ealeplkaqlaeleeaIkd 128
                                   e++e+lka++++l+e+I+ 
  gi|13541362|ref|NP_111050.1|  87 ETIERLKANIENLKESIQK 105
                                   4556666666666666653 PP

>> HALZ  Homeobox associated leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.1       1.9   1.1e+03      22      32 ..      43      53 ..      40      54 .. 0.82
   2 ?   10.2   0.1    0.0012      0.68       9      34 ..      91     116 ..      89     120 .. 0.67

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 1.9
                          HALZ 22 dsLkkenekLk 32
                                  d L++ +e+L 
  gi|13541362|ref|NP_111050.1| 43 DELRQSKERLI 53
                                  89999999997 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0012
                          HALZ   9 vLKasYdaLksdydsLkkenekLkae 34 
                                    LKa+ ++Lk + + L +++++L  +
  gi|13541362|ref|NP_111050.1|  91 RLKANIENLKESIQKLMDQRRTLVDQ 116
                                   57777777777777777777777665 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.1      0.21   1.2e+02       5      42 ..       4      41 ..       1      62 [. 0.67
   2 ?    8.7   0.5    0.0049       2.8      14      43 ..      86     115 ..      81     128 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.21
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          YabA  5 elfdkleeleeqleelleeleelkeelaelleenaeLe 42
                                  ++ ++l+ +e+ ++++ ++++++++ + e+    + L+
  gi|13541362|ref|NP_111050.1|  4 DVEAQLNYIESLISSVDAQIDAINKMVLEVQTTIQILS 41
                                  56677777777777777777777777766665555554 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0049
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          YabA  14 eeqleelleeleelkeelaelleenaeLel 43 
                                   +e++e+l++++e+lke++++l+++ ++L  
  gi|13541362|ref|NP_111050.1|  86 SETIERLKANIENLKESIQKLMDQRRTLVD 115
                                   567888888888888888888888877754 PP

>> DUF4665  Domain of unknown function (DUF4665)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.1    0.0069       3.9      29      74 ..       2      50 ..       1      57 [. 0.78
   2 ?    3.7   0.4      0.17        93      39      78 ..      81     120 ..      79     130 .] 0.74

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0069
                       DUF4665 29 AkpVttnLKkinav...kkekvenldkalvdiqkdlkslskklkletkk 74
                                  A+ V+ +L  i+      + ++  ++k+  ++q  ++ ls++   ++k+
  gi|13541362|ref|NP_111050.1|  2 ARDVEAQLNYIESLissVDAQIDAINKMVLEVQTTIQILSSDELRQSKE 50
                                  677888888877665557899*****************99966555554 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.17
                       DUF4665  39 inavkkekvenldkalvdiqkdlkslskklkletkkkekv 78 
                                   i  +++e +e+l   ++++++++++l  + ++   + ++v
  gi|13541362|ref|NP_111050.1|  81 IAEKRSETIERLKANIENLKESIQKLMDQRRTLVDQYNTV 120
                                   5567889999999999999999999888766665555554 PP

>> Csm1_N  Csm1 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.2      0.89     5e+02      43      60 ..      16      33 ..       4      51 .. 0.58
   2 ?   11.8   1.4   0.00042      0.23      37      66 ..      83     112 ..      81     116 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.89
                        Csm1_N 43 iesLkeqlaeleekvkel 60
                                  i+s+ +q++++++ v e 
  gi|13541362|ref|NP_111050.1| 16 ISSVDAQIDAINKMVLEV 33
                                  444455555554444433 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00042
                        Csm1_N  37 etkdqeiesLkeqlaeleekvkeleerrkk 66 
                                   e++++ ie+Lk+++++l+e +++l ++r++
  gi|13541362|ref|NP_111050.1|  83 EKRSETIERLKANIENLKESIQKLMDQRRT 112
                                   789999*****************9999876 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.8    0.0075       4.2      83     128 ..       5      50 ..       1      62 [. 0.63
   2 ?    6.4   0.3     0.015       8.4      62      92 ..      89     119 ..      74     127 .. 0.66

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0075
                  Baculo_PEP_C  83 lrneLtnlnsiltnLlssvtNinstLnnllqalnnldlgalsqele 128
                                   ++ +L+ ++s +++  +++  in+ +  + ++++ l +++l q  e
  gi|13541362|ref|NP_111050.1|   5 VEAQLNYIESLISSVDAQIDAINKMVLEVQTTIQILSSDELRQSKE 50 
                                   5556666666666666666666666666666666666666666554 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.015
                  Baculo_PEP_C  62 dtrldtlltnLtdalnalqdtlrneLtnlns 92 
                                    +rl+++++nL++++++l d+ r+  +  n+
  gi|13541362|ref|NP_111050.1|  89 IERLKANIENLKESIQKLMDQRRTLVDQYNT 119
                                   3467777777777777777666666555555 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   1.6     0.011         6      84     126 ..       3      45 ..       1      51 [. 0.77
   2 ?    6.8   0.2     0.013       7.1     101     124 ..      85     109 ..      79     125 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.011
                                   HHHHHCCCHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     Fib_alpha  84 keleeeilrlketidaqesnirvLqnvlesneqkiqkLeqdid 126
                                   +++e + ++++  i++   +i ++ +++ + +  iq L +d  
  gi|13541362|ref|NP_111050.1|   3 RDVEAQLNYIESLISSVDAQIDAINKMVLEVQTTIQILSSDEL 45 
                                   5778888888888888888888888888888888888877655 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.013
                                   H.HHHHHHHHHHHHHHHHHHHHHHH CS
                     Fib_alpha 101 e.snirvLqnvlesneqkiqkLeqd 124
                                     ++i+ L+ ++e+++++iqkL  +
  gi|13541362|ref|NP_111050.1|  85 RsETIERLKANIENLKESIQKLMDQ 109
                                   3377888888888888888888655 PP

>> DASH_Dad4  DASH complex subunit Dad4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.1       1.2   6.6e+02      31      47 ..      20      36 ..       6      45 .. 0.50
   2 ?   10.6   0.5   0.00078      0.43       7      34 ..      83     110 ..      81     127 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 1.2
                     DASH_Dad4 31 nkeleeinkkNknvelv 47
                                  + ++  ink   +v+++
  gi|13541362|ref|NP_111050.1| 20 DAQIDAINKMVLEVQTT 36
                                  33344444443333333 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00078
                     DASH_Dad4   7 eqqsalLsRIiknvekLnesvvelnkel 34 
                                   e+ s  ++R+ +n+e+L es+++l  + 
  gi|13541362|ref|NP_111050.1|  83 EKRSETIERLKANIENLKESIQKLMDQR 110
                                   6778899**************9986554 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.2      0.63   3.5e+02       6      28 ..      12      34 ..       7      55 .. 0.76
   2 ?   11.2   1.8   0.00071       0.4      18      47 ..      87     116 ..      83     128 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.63
                          ZapB  6 LeqLEskiqkaidtitlLqmeie 28
                                   e L s++++ id i ++  e++
  gi|13541362|ref|NP_111050.1| 12 IESLISSVDAQIDAINKMVLEVQ 34
                                  56777889999999999887776 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00071
                          ZapB  18 dtitlLqmeieeLkeeneelkeenreleee 47 
                                   +ti++L+  ie Lke  ++l ++ r l  +
  gi|13541362|ref|NP_111050.1|  87 ETIERLKANIENLKESIQKLMDQRRTLVDQ 116
                                   89*******************999998754 PP

>> DUF5082  Domain of unknown function (DUF5082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.8      0.16        91      84     116 ..      10      42 ..       1      51 [. 0.74
   2 ?   10.4   1.1    0.0011      0.59       8      47 ..      85     124 ..      81     129 .. 0.71

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.16
                       DUF5082  84 dkldelidaieeEIerLenqiseaqgvldtlqs 116
                                     +++li++++  I  + + + e q+ ++ l+s
  gi|13541362|ref|NP_111050.1|  10 NYIESLISSVDAQIDAINKMVLEVQTTIQILSS 42 
                                   457778888888888888888888888777665 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0011
                       DUF5082   8 lqaqiaelrseiaaleekIerLkeaktklsdekeslkqkk 47 
                                   + + i+ l+++i+ l e I++L   +++l+d+ +++++++
  gi|13541362|ref|NP_111050.1|  85 RSETIERLKANIENLKESIQKLMDQRRTLVDQYNTVYTTE 124
                                   4556777788888888888888888888888777776654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2059  (0.114842); expected 358.6 (0.02)
Passed bias filter:                     1145  (0.063863); expected 358.6 (0.02)
Passed Vit filter:                       172  (0.0095934); expected 17.9 (0.001)
Passed Fwd filter:                        32  (0.00178482); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              32  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 927.12
//
Query:       gi|13541363|ref|NP_111051.1|  [L=287]
Description: Signal recognition particle GTPase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-77  259.8   0.4    1.7e-77  259.5   0.4    1.1  1  SRP54            SRP54-type protein, GTPase domain
    1.4e-06   28.8   0.3    2.5e-06   28.0   0.3    1.4  1  AAA_17           AAA domain
    4.6e-06   26.8   0.8    1.3e-05   25.3   0.8    1.8  1  SRP54_N          SRP54-type protein, helical bundle domain
    5.6e-06   26.2   0.4      1e-05   25.3   0.3    1.4  1  AAA_30           AAA domain
    1.2e-05   24.9   0.3    1.9e-05   24.4   0.3    1.2  1  cobW             CobW/HypB/UreG, nucleotide-binding domain
    0.00049   19.4   0.2    0.00064   19.1   0.2    1.1  1  DUF2075          Uncharacterized conserved protein (DUF2075)
    0.00085   19.0   0.3     0.0028   17.4   0.2    1.9  2  Thymidylate_kin  Thymidylate kinase
     0.0015   18.4   0.1     0.0033   17.3   0.1    1.6  1  APS_kinase       Adenylylsulphate kinase
     0.0016   17.8   0.1     0.0027   17.0   0.1    1.4  1  Zeta_toxin       Zeta toxin
      0.002   18.3   0.1     0.0037   17.4   0.1    1.5  1  AAA_33           AAA domain
     0.0024   18.3   1.1     0.0043   17.5   1.1    1.5  1  AAA              ATPase family associated with various cellul
     0.0029   16.8   0.0     0.0041   16.3   0.0    1.1  1  PIF1             PIF1-like helicase
     0.0046   17.0   2.4      0.021   14.9   2.4    2.0  1  MMR_HSR1         50S ribosome-binding GTPase
     0.0049   16.4   0.6     0.0074   15.8   0.6    1.3  1  GTP_EFTU         Elongation factor Tu GTP binding domain
  ------ inclusion threshold ------
      0.013   15.8   0.2      0.056   13.8   0.2    2.0  1  AAA_19           AAA domain
      0.015   15.0   0.1      0.044   13.4   0.1    1.7  1  Peripla_BP_6     Periplasmic binding protein
      0.029   13.9   0.1       0.05   13.1   0.1    1.3  1  KdpD             Osmosensitive K+ channel His kinase sensor d
      0.035   14.0   0.1       0.07   13.0   0.1    1.4  1  Helicase_RecD    Helicase
      0.036   13.4   0.2      0.059   12.7   0.2    1.4  1  6PF2K            6-phosphofructo-2-kinase
      0.037   13.9   4.2       0.17   11.8   1.2    2.4  2  NTPase_1         NTPase
       0.05   13.9   0.0      0.094   13.0   0.0    1.4  1  AAA_22           AAA domain
      0.051   13.1   0.1       0.15   11.5   0.1    1.7  2  AAA_7            P-loop containing dynein motor region
      0.052   13.5   4.0       0.28   11.1   0.7    2.3  2  MobB             Molybdopterin guanine dinucleotide synthesis
      0.053   13.9   0.0      0.093   13.1   0.0    1.4  1  AAA_16           AAA ATPase domain
      0.054   13.6   2.7        0.2   11.7   2.7    2.0  1  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
      0.054   12.5   1.3       0.11   11.5   0.5    2.0  2  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
      0.056   13.7   0.1       0.13   12.5   0.1    1.6  1  PyrI             Aspartate carbamoyltransferase regulatory ch
       0.06   13.5   1.5       0.22   11.7   0.7    2.1  2  DUF4075          Domain of unknown function (DUF4075)
      0.087   12.6   0.7       0.75    9.5   0.4    2.1  2  ATP_bind_1       Conserved hypothetical ATP binding protein
      0.087   12.9   0.1       0.24   11.4   0.1    1.8  1  AAA_14           AAA domain
      0.092   12.5   0.7          9    6.0   0.0    2.3  2  PduV-EutP        Ethanolamine utilisation - propanediol utili
       0.14   12.1   1.1       0.42   10.6   1.2    1.8  1  ResIII           Type III restriction enzyme, res subunit


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 !  259.5   0.4   3.1e-80   1.7e-77       1     195 [.      87     281 ..      87     282 .. 0.99

  Alignments for each domain:
  == domain 1  score: 259.5 bits;  conditional E-value: 3.1e-80
                                   SEEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSSTTHHHHHHHHHHHTTEEEEESSTTSCHHHHHHHHHHHHHH CS
                         SRP54   1 pnvillvGlqGaGKTttlaKLaallkkegkkvllvaaDtfRaaAveQLktlaeklgvpvikkkeeadpaavakeavekake 81 
                                   p vi+++G++G+GKTtt++K+a++lk++gk+v+l a DtfRa+A+eQL+++++++gv+vik+++++dp +va++a+++ak+
  gi|13541363|ref|NP_111051.1|  87 PFVIMFLGINGTGKTTTIGKVAKYLKSKGKSVVLSASDTFRAGAIEQLSMIGKEIGVEVIKHEKGSDPSSVAFDAIQHAKA 167
                                   579****************************************************************************** PP

                                   TTSSEEEEEE--SSTTHHHHHHHHHHHHHHHSSSEEEEEEETTBHTHHHHHHHHHHHHSSCSEEEEESTTSSSSTTHHHHH CS
                         SRP54  82 ekidvvlvDTaGrlqndkelmeelkkikkvvkpdevllvldattgqeavkqakaFkeavgitgviltklDgdakgGaalsi 162
                                   ++id+vlvDTaGr++++k+lm+e+kkik+v +pd +llvlda++gq+ ++qa++F+e+vg+++vi+tklD+da+gG++lsi
  gi|13541363|ref|NP_111051.1| 168 RNIDYVLVDTAGRMNTNKNLMDEMKKIKRVSNPDITLLVLDAVAGQDSINQARTFHENVGFDAVIVTKLDTDARGGSILSI 248
                                   ********************************************************************************* PP

                                   HHHHTS-EEEEE-SSSTTGEEE--HHHHHHHHH CS
                         SRP54 163 aaelklPikfigvGekiedleefdperlvsrll 195
                                    + l +P+ f  vG+ ++d+ +fd+++++++l+
  gi|13541363|ref|NP_111051.1| 249 YHDLRKPVLFACVGQGLDDIMQFDADWYIEKLM 281
                                   ******************************997 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.3   4.4e-09   2.5e-06       1     108 [.      93     206 ..      93     220 .. 0.79

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 4.4e-09
                                   EE-TTSSHHHHHHHHHHHH....TEEEEEHHHHHHHHHHTTTSHSSHHHHC..TSHHHHHHHHHHHHHHHHHHHHHSSE.. CS
                        AAA_17   1 lGgPGsGKgtqceklveky....gfthlsaGdllreeakrgglakardemr..klpleekkelqkeaaekiaeeakkkg.. 73 
                                   lG+ G GK+t + k+++ +    +  +lsa+d +r+ a ++ l++  +e+     ++e+  +    a ++i+++++++   
  gi|13541363|ref|NP_111051.1|  93 LGINGTGKTTTIGKVAKYLkskgKSVVLSASDTFRAGAIEQ-LSMIGKEIGveVIKHEKGSDPSSVAFDAIQHAKARNIdy 172
                                   79*************98776666899*********998665.345555555435677788888888888888877443344 PP

                                   EEEEE-SEEEETTEEEESSHHHHHHHH..SEEEEE CS
                        AAA_17  74 vlvdghprikeqagfldglpkevleelkpdaiill 108
                                   vlvd+  r+++++ ++d+++k +++  +pd+ +l+
  gi|13541363|ref|NP_111051.1| 173 VLVDTAGRMNTNKNLMDEMKK-IKRVSNPDITLLV 206
                                   9*************9999986.8999999997774 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 !   25.3   0.8   2.4e-08   1.3e-05       2      60 ..       6      56 ..       2      74 .. 0.77

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 2.4e-08
                                  HHHHHHHHHHHCCSSCGHHHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHCTTS CS
                       SRP54_N  2 gkklnsalkklsgkskideedleealkeleeaLleaDVgvkvvkklienvkkkavgekk 60
                                  +kkl ++++    ++kid +   e   e+   L+eaDV+v++++ l + v++ +++ ++
  gi|13541363|ref|NP_111051.1|  6 KKKLVEIFS----RKKIDPDEAAE---EIPLKLIEADVSVETAEYLGNLVRN-KLKDRD 56
                                  677888886....57888776555...6**********************98.777554 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.3   1.9e-08     1e-05      20     104 ..      89     185 ..      82     206 .. 0.75

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 1.9e-08
                        AAA_30  20 vavltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLaeelgieastiakllkrlk.............grarle 87 
                                   v +  G  GtGKtt+++++++ ++++g++v++ A+    A ++++ l + ++ i   + +++             ++a+ +
  gi|13541363|ref|NP_111051.1|  89 VIMFLGINGTGKTTTIGKVAKYLKSKGKSVVLSASDTFRAGAIEQ-LSMIGKEIGVEVIKHEkgsdpssvafdaiQHAKAR 168
                                   6677899****************************9999999994.33333333333333333444566889887556666 PP

                        AAA_30  88 pgtllivDEagmvdtkq 104
                                   + + ++vD ag ++t++
  gi|13541363|ref|NP_111051.1| 169 NIDYVLVDTAGRMNTNK 185
                                   7799****999997754 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 !   24.4   0.3   3.3e-08   1.9e-05       2     152 ..      89     238 ..      88     253 .. 0.79

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 3.3e-08
                                   EEEEEESTTCCHHHHHHHHH..CT--SS-EEEEESS-SS.CHCCCCCCHCC..CT.EEEETTTTECCHCTT-HHHHHHHHH CS
                          cobW   2 vtvltGflGsGKTtLlnhll..enraglklavivNefge.vsiDaellret..gveivelenGciCctlredllkeleale 77 
                                   v+++ G  G+GKTt + ++    +++g+++ +   +     +i++  +  +  gve+++ e+G  + +++ d++++++a  
  gi|13541363|ref|NP_111051.1|  89 VIMFLGINGTGKTTTIGKVAkyLKSKGKSVVLSASDTFRaGAIEQLSMIGKeiGVEVIKHEKGSDPSSVAFDAIQHAKA-- 167
                                   67788999************766666666666666755425677755544336999**********9977777665543.. PP

                                   HHHTT-SEEEEEECTTTTHHHH.HTTSHHHHHCCCECEEEEEEETTTH.CCHCCHHHHHHHHHHTSSEEEEE-HHH CS
                          cobW  78 ereerldviliEttGlaePapv.afteeelksdltldavvavvDaknleaeeekieekaedqlaaadllvlnKtDl 152
                                    r  ++d++l+ t G ++ +   + + +++k+  + d+++ v+Da +  +++ ++++++++ + + d ++++K D+
  gi|13541363|ref|NP_111051.1| 168 -R--NIDYVLVDTAGRMNTNKNlMDEMKKIKRVSNPDITLLVLDAVAG-QDSINQARTFHENVGF-DAVIVTKLDT 238
                                   .4..59*********5555555266699*****************776.899999999****998.99999**996 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.2   1.2e-06   0.00064       6     131 ..      92     208 ..      87     240 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.2e-06
                       DUF2075   6 VtGvaGtGKtvvllnllaeleddeeertavylsvNhplvlvlrealakkeekkkkkeafeklssfinnlsefkkaeekkee 86 
                                     G  GtGKt    +++  l   +++ ++v+ls +  +++   e+l+     k+++ ++ k ++   + s   +a+++++ 
  gi|13541363|ref|NP_111051.1|  92 FLGINGTGKTTTIGKVAKYL---KSKGKSVVLSASDTFRAGAIEQLSMIG--KEIGVEVIKHEKGSDPSSVAFDAIQHAKA 167
                                   56999**************9...8899999****************6655..9999999999999999997799******* PP

                       DUF2075  87 pkedvvivDEAhrlltksdqaekqseenqlkelmkrakvvvalvD 131
                                   +++d v+vD A r++t+++    + e + +k++ +  +++++++D
  gi|13541363|ref|NP_111051.1| 168 RNIDYVLVDTAGRMNTNKNL---MDEMKKIKRVSN-PDITLLVLD 208
                                   ****************5554...334455555444.445555555 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.2   4.9e-06    0.0028       3      31 ..      94     122 ..      92     139 .. 0.91
   2 ?   -2.4   0.0       5.6   3.1e+03     104     124 ..     188     206 ..     182     219 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 4.9e-06
                                   ESTTSSHHHHHHHHHHHHHHTTE.EEEES CS
               Thymidylate_kin   3 GlDGaGKttqaellkerlkeegikvvltr 31 
                                   G++G+GKtt + +++++lk++g++vvl+ 
  gi|13541363|ref|NP_111051.1|  94 GINGTGKTTTIGKVAKYLKSKGKSVVLSA 122
                                   9*********************9999875 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 5.6
                                   CHHHHHHGGGTTSE-SEEEEE CS
               Thymidylate_kin 104 ldlvlslnedvllkPdltfll 124
                                   +d ++++++     Pd+t+l+
  gi|13541363|ref|NP_111051.1| 188 MDEMKKIKRVS--NPDITLLV 206
                                   55555555543..89999986 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.1   5.9e-06    0.0033       1      50 [.      86     135 ..      86     145 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 5.9e-06
                                   S-EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTTTTTTT-- CS
                    APS_kinase   1 rgvvvwltGlsgsGKstianalekkLvekgisvylLdGdnvRhgLnkdLg 50 
                                   +++v+++ G+ g+GK+t   +++k+L++kg+sv+l   d+ R g  ++L+
  gi|13541363|ref|NP_111051.1|  86 KPFVIMFLGINGTGKTTTIGKVAKYLKSKGKSVVLSASDTFRAGAIEQLS 135
                                   589***************************************99888886 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.1   4.8e-06    0.0027      13      56 ..      84     128 ..      77     197 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 4.8e-06
                    Zeta_toxin  13 qerPklillgGqpGAGKselaellkdelerqgnvvrld.pDdlRe 56 
                                   +++P +i+  G  G GK++++ +++++l+++g+ v+l+  D++R+
  gi|13541363|ref|NP_111051.1|  84 NKKPFVIMFLGINGTGKTTTIGKVAKYLKSKGKSVVLSaSDTFRA 128
                                   489**************************7777777762689997 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.1   6.6e-06    0.0037       1      90 [.      89     193 ..      89     230 .. 0.61

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 6.6e-06
                        AAA_33   1 lvllvGlpGsGKstlaerllkklg.....avllssdtlrr.rlfgtdqqskt......dytrvldrlyqilnelarkalsa 69 
                                   ++++ G +G+GK+t + +++k l+     +vl +sdt+r  +++      k+      +  + +d      ++ ++ a ++
  gi|13541363|ref|NP_111051.1|  89 VIMFLGINGTGKTTTIGKVAKYLKskgksVVLSASDTFRAgAIEQLSMIGKEigveviKHEKGSDPS-SVAFDAIQHAKAR 168
                                   89****************9988888889555555666655444442222333222222111122222.2344666666666 PP

                        AAA_33  70 grnvildat....nlsrrerarflk 90 
                                   +++++l  t    n++++ ++++ k
  gi|13541363|ref|NP_111051.1| 169 NIDYVLVDTagrmNTNKNLMDEMKK 193
                                   6666665555555555555555555 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   1.1   7.7e-06    0.0043       1      97 [.      90     195 ..      90     226 .. 0.61

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 7.7e-06
                                   EEEESSTTSSHHHHHHHHHHHHT..HEEEEEETTTCSSSSTTHHHHHHHHHHHHH.....HHTS..TSEEEEEETGGGHHH CS
                           AAA   1 vllyGppGtGKTllakavakelg..vefleisgsellskyvgesekkirelfkea.....keka..kpsilfiDEidalak 72 
                                   +++ G  GtGKT+++  vak l+   + + +s+s+ +     e+ + i    ke+     k+++  +ps + +D i     
  gi|13541363|ref|NP_111051.1|  90 IMFLGINGTGKTTTIGKVAKYLKskGKSVVLSASDTFRAGAIEQLSMI---GKEIgveviKHEKgsDPSSVAFDAIQHAKA 167
                                   5899*****************973356788888888844333322222...222211111333344566666666665544 PP

                                   HH...TTCCCHHHHHHHHHHHHHHHHTT CS
                           AAA  73 sr...sgseseeeervvnqLlteldgvk 97 
                                   ++      ++  ++++ + L+ e+++ k
  gi|13541363|ref|NP_111051.1| 168 RNidyVLVDTAGRMNTNKNLMDEMKKIK 195
                                   4454433445555555555555555555 PP

>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   7.4e-06    0.0041      18     122 ..      83     191 ..      78     201 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 7.4e-06
                                   ..HCTS-EEEEESTTSSCHHHHHHHHHHCHCTCCCEEEEESSHHHHHCC.TSEECHHHHT-TTSSS-HHHH..HHHTSCCC CS
                          PIF1  18 lnekgklfFvtGsgGtgKtflwkallkklrsegkivlavAssGvAalllegGrtahsrfkiplekdeestc..kikrgskl 96 
                                   +n+k+ ++ + G  GtgKt    ++ k+l+s+gk v+  As    a  +e+   +    ++++ k+e+ +   +++ +  +
  gi|13541363|ref|NP_111051.1|  83 VNKKPFVIMFLGINGTGKTTTIGKVAKYLKSKGKSVVLSASDTFRAGAIEQLSMIGKEIGVEVIKHEKGSDpsSVAFDAIQ 163
                                   57899999*********************************9999999988888888888888777765544477777777 PP

                                   HHHHHC-SEEEEECGGGS..BHHHHHHH CS
                          PIF1  97 aellkktsliiwDEapmv..erecfeal 122
                                     +  +++ +++D a  +  ++++++++
  gi|13541363|ref|NP_111051.1| 164 HAKARNIDYVLVDTAGRMntNKNLMDEM 191
                                   7777888888888775431145556655 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   2.4   3.7e-05     0.021       3      94 ..      91     220 ..      89     235 .. 0.51

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.7e-05
                                   EEEESTTSSHHHHHHHHHT.......STEEESSSTTSSSSEEEEEEEETTEE............................. CS
                      MMR_HSR1   3 aivGrpNvGKStLinaltg.......ekaivsdkpgtTrdinegrvklkgke............................. 47 
                                   +++G   +GK+t i +  +       +++  ++  +    i++  +   gke                             
  gi|13541363|ref|NP_111051.1|  91 MFLGINGTGKTTTIGKVAKylkskgkSVVLSASDTFRAGAIEQLSMI--GKEigvevikhekgsdpssvafdaiqhakarn 169
                                   66666667777777666653332222122222222222222222222..11123333333334444555555555555555 PP

                                   ..EEEEECGGCSSHHHHHHHHHHHHHHHHCTSEEEEEEETT..TTCSHHHH CS
                      MMR_HSR1  48 ..ielvDtpGliegaseekglgkaflaleeadlillvvdas..eeklkpld 94 
                                     ++lvDt+G ++++++  ++ k+++++ + d+ llv+da   ++++++ +
  gi|13541363|ref|NP_111051.1| 170 idYVLVDTAGRMNTNKNLMDEMKKIKRVSNPDITLLVLDAVagQDSINQAR 220
                                   55********555333333666666666667********886544454443 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.6   1.3e-05    0.0074       6     109 ..      90     215 ..      85     254 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.3e-05
                                   EEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEE.................TTCSS CS
                      GTP_EFTU   6 igiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaisle.................ketkk 69 
                                   i+++g   +GKtT+++++ ++++   k+     ++ +    + E+   i  ++ +  ++                 ++ ++
  gi|13541363|ref|NP_111051.1|  90 IMFLGINGTGKTTTIGKVAKYLKSKGKSVVLSASD-TFRAGAIEQLSMIGKEIGVEVIKhekgsdpssvafdaiqhAKARN 169
                                   566677779**************999955555433.333333333333333333222225577777777777765449999 PP

                                   EEEEEEEESSSGGGHHHHHHH......HHT-SEEEEEEETTTBSTH CS
                      GTP_EFTU  70 ylinliDtPGHvdFskevirg......lrvlDgavlvvdaveGvep 109
                                     + l+Dt G ++ +k+          ++  D+ +lv+dav G  +
  gi|13541363|ref|NP_111051.1| 170 IDYVLVDTAGRMNTNKNLMDEmkkikrVSNPDITLLVLDAVAGQDS 215
                                   **********998777665543333557889**********99543 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.2    0.0001     0.056      12      69 ..      89     195 ..      79     256 .. 0.59

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 0.0001
                        AAA_19  12 vllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrA..akelrerlaalgae...................... 68 
                                   v++ ++  GtGKT+++ ++ ++l++ g+     +l ++ t rA   ++l+      g+e                      
  gi|13541363|ref|NP_111051.1|  89 VIMFLGINGTGKTTTIGKVAKYLKSKGKS---VVLSASDTFRAgaIEQLSMI----GKEigvevikhekgsdpssvafdai 162
                                   55667999********9999999998843...45555555554104444433....3333333666666666666666666 PP

                        AAA_19  69 ................................a 69 
                                                                    
  gi|13541363|ref|NP_111051.1| 163 qhakarnidyvlvdtagrmntnknlmdemkkiK 195
                                   666644444444444444444444444444440 PP

>> Peripla_BP_6  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   7.8e-05     0.044     109     204 ..      87     183 ..      66     241 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7.8e-05
                                   TTEEESS--HHHHHHHHHHHHHHHTT..SCEEEEEEESSHHHHHHHHHHHHHHHCCTEEEEEEEEE-TTHHHHHHHHHHHH CS
                  Peripla_BP_6 109 pyvfslgpsysaqasalveylakelg..gkkvalvyadyafgregiaalkaaakaaGgevvgeepvplgttdfsaqvlqik 187
                                   p v+ +++ + +  +++++ +ak l+  g k ++++a + f + +i++l    k+ G+ev+ +e+ + +++    +++ +k
  gi|13541363|ref|NP_111051.1|  87 PFVIMFLGINGTGKTTTIGKVAKYLKskG-KSVVLSASDTFRAGAIEQLSMIGKEIGVEVIKHEKGSDPSSVAFDAIQHAK 166
                                   55555555555555666666777776425.5555555566********************988888888888888999999 PP

                                   TTT-SEEEEESSHHHHH CS
                  Peripla_BP_6 188 aagadavllagtgadla 204
                                   a + d+vl+ ++g +++
  gi|13541363|ref|NP_111051.1| 167 ARNIDYVLVDTAGRMNT 183
                                   99***999988888876 PP

>> KdpD  Osmosensitive K+ channel His kinase sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   8.9e-05      0.05       8      98 ..      92     185 ..      87     209 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 8.9e-05
                          KdpD   8 flGaapGvGktyamLeeaqelkeegvdvviglvethgrketeallegleviprkevey.kgkeleeld...ldailarkpe 84 
                                   flG ++G Gkt ++ + a+ lk++g+ vv+++ +t +   +e+l    + i  + +++ kg+  + +    ++++ ar+ +
  gi|13541363|ref|NP_111051.1|  92 FLG-INGTGKTTTIGKVAKYLKSKGKSVVLSASDTFRAGAIEQLSMIGKEIGVEVIKHeKGSDPSSVAfdaIQHAKARNID 171
                                   566.58****************************99999999887544444444444313444455540024555678899 PP

                          KdpD  85 vvlvDelahtnapg 98 
                                    vlvD  +  n+++
  gi|13541363|ref|NP_111051.1| 172 YVLVDTAGRMNTNK 185
                                   9****999988654 PP

>> Helicase_RecD  Helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   0.00013      0.07       6     102 ..      96     181 ..      92     198 .. 0.55

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00013
                 Helicase_RecD   6 RGRGKSaalGlalaaliaegksnilvtapskenvktlfeflakglealglkeeekkkkaekaelrvrkqrieyiapdellk 86 
                                    G+GK++++G++++ l ++gks ++++a +   +   +e+l    +++g++  +++k +       + +++ + a +++++
  gi|13541363|ref|NP_111051.1|  96 NGTGKTTTIGKVAKYLKSKGKS-VVLSASDTFRA-GAIEQLSMIGKEIGVEVIKHEKGS-------DPSSVAFDAIQHAKA 167
                                   59*****************984.44444443332.333333344444554442222222.......244455555554444 PP

                 Helicase_RecD  87 lkeqadllvvDEAAai 102
                                   ++   d ++vD A  +
  gi|13541363|ref|NP_111051.1| 168 RN--IDYVLVDTAGRM 181
                                   32..355555544433 PP

>> 6PF2K  6-phosphofructo-2-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.2   0.00011     0.059       8      42 ..      82     116 ..      77     167 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00011
                                   HT..S-EEEEEESSTTSSHHHHHHHHHHHHHHTT- CS
                         6PF2K   8 nlknsklvivlvGLpargKtyiskkltrylkwlgv 42 
                                   n +++++vi+++G+  +gKt++  k+ +ylk  g 
  gi|13541363|ref|NP_111051.1|  82 NVNKKPFVIMFLGINGTGKTTTIGKVAKYLKSKGK 116
                                   668899************************95543 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   1.2    0.0003      0.17       6      30 ..      94     118 ..      89     129 .. 0.90
   2 ?    2.7   0.1      0.18     1e+02      82     121 ..     155     194 ..     127     241 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0003
                                   --TTSSHHHHHHHHHHHH...GGGE CS
                      NTPase_1   6 GppGvGKtTlvkkvlellkssgvkv 30 
                                   G  G+GKtT + kv++ lks+g +v
  gi|13541363|ref|NP_111051.1|  94 GINGTGKTTTIGKVAKYLKSKGKSV 118
                                   889******************9887 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.18
                                   HHHHHHHHHHHH.HHH-EEEE---STTGGG-HHHHHHHHHH CS
                      NTPase_1  82 eelalealrkal.seadviviDEiGkmElkskkfkeaveev 121
                                   +++a +a+++a  ++ d +++D  G+m  + + + e ++++
  gi|13541363|ref|NP_111051.1| 155 SSVAFDAIQHAKaRNIDYVLVDTAGRMNTNKNLMDE-MKKI 194
                                   56888999999889999**********887665543.3333 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   0.00017     0.094       8     117 ..      90     199 ..      84     217 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00017
                        AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevv.fvtlpsstsskdllrellralglelka..erlsseellealeqa 85 
                                   ++  G  GtGKTt++ ++++ l+        +++vv +   +   +  + l+++ +++g+e  +  ++ + + +     q+
  gi|13541363|ref|NP_111051.1|  90 IMFLGINGTGKTTTIGKVAKYLKSK------GKSVVlSASDTFRAGAIEQLSMIGKEIGVEVIKheKGSDPSSVAFDAIQH 164
                                   677899**************99543......44444344444444777778999999999999966555555555555555 PP

                        AAA_22  86 lraravielliiDEaqhlr.s...eealeeLrslln 117
                                   ++ar     +++D a +++ +   ++ ++++++ +n
  gi|13541363|ref|NP_111051.1| 165 AKARNI-DYVLVDTAGRMNtNknlMDEMKKIKRVSN 199
                                   566666.9**********863467777777777777 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00027      0.15      35      71 ..      89     124 ..      79     136 .. 0.76
   2 ?   -2.3   0.0       4.8   2.7e+03       4      38 ..     223     258 ..     221     262 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00027
                         AAA_7  35 pvllvGptGtGKtviikdllkkldkekylsltinfsa 71 
                                    +++ G  GtGKt++i ++ k l+ +k +s++++ s 
  gi|13541363|ref|NP_111051.1|  89 VIMFLGINGTGKTTTIGKVAKYLK-SKGKSVVLSASD 124
                                   579***************999998.666666665555 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 4.8
                         AAA_7   4 deeakfseilVptvdt.vrysyllelllknkkpvll 38 
                                   +e++ f+ ++V   dt +r   +l+ + + +kpvl+
  gi|13541363|ref|NP_111051.1| 223 HENVGFDAVIVTKLDTdARGGSILSIYHDLRKPVLF 258
                                   577889999999999867888999999999999998 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.7   0.00051      0.28       1      30 [.      89     118 ..      89     126 .. 0.92
   2 ?    3.3   0.1      0.12        69      25      88 ..     138     197 ..     125     207 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00051
                          MobB   1 vlgivgksgsGKTtLleklipelkarglrv 30 
                                   v+ + g +g+GKTt + k+ + lk++g +v
  gi|13541363|ref|NP_111051.1|  89 VIMFLGINGTGKTTTIGKVAKYLKSKGKSV 118
                                   68999*********************9887 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.12
                          MobB  25 arglrvgtiKhahhgfdvdkpgkDsyrhrkAGA.kevlvaskerlalikeleeaelsleellarl 88 
                                    +++ v +iKh++ g d  +   D+ +h+kA   + vlv +  r+   k+l +     ++ ++r+
  gi|13541363|ref|NP_111051.1| 138 GKEIGVEVIKHEK-GSDPSSVAFDAIQHAKARNiDYVLVDTAGRMNTNKNLMD----EMKKIKRV 197
                                   3456677899975.778999999999999996526778888888877777633....23444444 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   0.00017     0.093      27      88 ..      90     152 ..      82     222 .. 0.57

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00017
                        AAA_16  27 vllsGesGvGKsslvrellralekdggiflrgkcdql..esaipysalaqalareellrqllde 88 
                                   +++ G  G+GK++ + +++++l+ +g  ++    d +  ++   +s++ + +   e+++ ++  
  gi|13541363|ref|NP_111051.1|  90 IMFLGINGTGKTTTIGKVAKYLKSKGKSVVLSASDTFraGAIEQLSMIGKEI-GVEVIKHEKGS 152
                                   778999*****************99744444444444112223335555555.33444444333 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   2.7   0.00037       0.2       9     101 ..      97     195 ..      94     244 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00037
                                   TSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCH....HTTEB-HHHH..........CCHCCCHHHHHHCHCHHHH.. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxx..........xxxxxxxxxxxxxxxxxxxxx RF
                          CbiA   9 GvGKTtlaanLaralarrglrVllvDaDpqannlai....leglendiep..........dlkrllellealgkkkalllk 75 
                                   G+GKTt+  + a++l+ +g+ V+l   D+ +   ai         + + +          + +  +  + a+++ ka   +
  gi|13541363|ref|NP_111051.1|  97 GTGKTTTIGKVAKYLKSKGKSVVLSASDTFRAG-AIeqlsM----IGK-EigvevikhekGSDPSSVAFDAIQHAKA--RN 169
                                   9**********************9877766322.2212221....111.1234445555555554455555555544..45 PP

                                   EEEEEEEEESS...-TTCHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          CbiA  76 iagvvlnrvdgeneetllkealeelk 101
                                   i  v++   +  n++++l++ ++++k
  gi|13541363|ref|NP_111051.1| 170 IDYVLVDTAGRMNTNKNLMDEMKKIK 195
                                   55555555555555566666666555 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   0.5   0.00019      0.11      30      66 ..      88     124 ..      78     192 .. 0.87
   2 ?   -1.5   0.0       1.8   9.9e+02     116     128 ..     222     234 ..     212     269 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00019
                                   EEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE- CS
                          MeaB  30 qvvGltGvPGaGkstlvealglelrrrGkrvavlavD 66 
                                    v+ + G+ G+Gk t++ +++  l+++Gk v + a D
  gi|13541363|ref|NP_111051.1|  88 FVIMFLGINGTGKTTTIGKVAKYLKSKGKSVVLSASD 124
                                   577889************************9887766 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.8
                                   HHHHTT-SEEEEE CS
                          MeaB 116 lleaaGfDvvlie 128
                                   + e +GfD v++ 
  gi|13541363|ref|NP_111051.1| 222 FHENVGFDAVIVT 234
                                   5678899999985 PP

>> PyrI  Aspartate carbamoyltransferase regulatory chain, allosteric domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   0.00024      0.13      20      86 ..      86     150 ..      79     157 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00024
                                   HHHHHHHCT--T...TS-EEEEEEEEETTTEEEEEEEEET----HHHHHHHCCC-TT-EEEEEETTE CS
                          PyrI  20 alkvlklLkldklkseekvaiiknvkskklgkKdiikiegkelseeeldklaliapnatiniIkdge 86 
                                   +  v+ +L++++  ++++ +i+k +k  k + K ++  ++ +++   +++l++i +++ +++Ik ++
  gi|13541363|ref|NP_111051.1|  86 KPFVIMFLGING--TGKTTTIGKVAKYLKSKGKSVVLSASDTFRAGAIEQLSMIGKEIGVEVIKHEK 150
                                   556888999996..555799***999999999*****9999**********************9876 PP

>> DUF4075  Domain of unknown function (DUF4075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.7   0.00039      0.22       3      28 ..       9      34 ..       7      42 .. 0.82
   2 ?   -0.7   0.0       2.9   1.7e+03      24      42 ..      73      90 ..      68      97 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00039
                       DUF4075  3 tkeifskkkvepeekpetieiqavsp 28
                                    eifs+kk++p+e  e i ++ +  
  gi|13541363|ref|NP_111051.1|  9 LVEIFSRKKIDPDEAAEEIPLKLIEA 34
                                  569**************998877655 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 2.9
                       DUF4075 24 qavspkvdelkveeepiva 42
                                   a+ pk d l v+++p v 
  gi|13541363|ref|NP_111051.1| 73 LAI-PKPDILNVNKKPFVI 90
                                  444.999*******99985 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.4    0.0013      0.75       2      27 ..      93     118 ..      92     124 .. 0.91
   2 ?    1.0   0.0      0.54   3.1e+02      89     126 ..     168     206 ..     155     239 .. 0.56

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0013
                    ATP_bind_1   2 vGpaGsGKttfvgalseilelrgrsv 27 
                                   +G  G GKtt +g+++++l+++g+sv
  gi|13541363|ref|NP_111051.1|  93 LGINGTGKTTTIGKVAKYLKSKGKSV 118
                                   7999******************9887 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.54
                    ATP_bind_1  89 eeddyllfDtPGQielfthseslakiveeLes.efalvv 126
                                   ++ dy+l+Dt G + + + + +  k +++ ++ +++l v
  gi|13541363|ref|NP_111051.1| 168 RNIDYVLVDTAGRMNTNKNLMDEMKKIKRVSNpDITLLV 206
                                   244999999999988776554444333333333333333 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00044      0.24       4      77 ..      89     166 ..      85     219 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00044
                        AAA_14   4 ilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpe....kllelileklkeekktylflDEiqevp 77 
                                   +++  G+  +GKTt + +++k l  k +s++  + d+ r  ++++ +    ++  ++ ++ k+++ + + +D iq+++
  gi|13541363|ref|NP_111051.1|  89 VIMFLGINGTGKTTTIGKVAKYLKSKGKSVVLSASDTFRAGAIEQLSmigkEIGVEVIKHEKGSDPSSVAFDAIQHAK 166
                                   56778***************8888666666666666666655554432333333333333334677889999999984 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.1     0.044        24       4      19 ..      90     105 ..      87     125 .. 0.86
   2 ?    6.0   0.0     0.016         9      33     103 ..     167     240 ..     155     254 .. 0.71

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.044
                     PduV-EutP   4 illiGkvgsGKttLtq 19 
                                   i+++G  g+GKtt   
  gi|13541363|ref|NP_111051.1|  90 IMFLGINGTGKTTTIG 105
                                   9***********9655 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.016
                     PduV-EutP  33 aiefsdeviDtPGeylenrklysalivt..saeadvialvqdateeesvfpp..gfasvfnkeviGiitkidlae 103
                                   a ++   ++Dt G    n++l+  ++ +    + d+  lv+da++ +  + +  +f + +  + + i+tk+d+  
  gi|13541363|ref|NP_111051.1| 167 ARNIDYVLVDTAGRMNTNKNLMDEMKKIkrVSNPDITLLVLDAVAGQDSINQarTFHENVGFDAV-IVTKLDTDA 240
                                   44555678**************999766225788*********9998887651134444444444.888888765 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 ?   10.6   1.2   0.00076      0.42      22      60 ..      85     120 ..      48     209 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00076
                                   .TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEE CS
                        ResIII  22 krdkrglikmaTGtGKTlvaaklierllkkgkeekflfl 60 
                                   k+   +++    GtGKT ++ k++++l++kgk    ++l
  gi|13541363|ref|NP_111051.1|  85 KKPFVIMFLGINGTGKTTTIGKVAKYLKSKGK---SVVL 120
                                   444566677788****************9966...3444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       632  (0.0352502); expected 358.6 (0.02)
Passed bias filter:                      523  (0.0291706); expected 358.6 (0.02)
Passed Vit filter:                       100  (0.00557756); expected 17.9 (0.001)
Passed Fwd filter:                        32  (0.00178482); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              32  [number of targets reported over threshold]
# CPU time: 0.67u 0.30s 00:00:00.97 Elapsed: 00:00:00.52
# Mc/sec: 1651.34
//
Query:       gi|13541364|ref|NP_111052.1|  [L=107]
Description: nucleic acid binding protein [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    6.1e-26   90.4   0.2    6.9e-26   90.2   0.2    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 !   90.2   0.2   3.9e-30   6.9e-26       1      96 []      13     105 ..      13     105 .. 0.98

  Alignments for each domain:
  == domain 1  score: 90.2 bits;  conditional E-value: 3.9e-30
                                   EEEEEEEEEEEETTSSTEEEEEEEESSSSEEEEEESCTTTSTHHHHTTEEEEEETTSESEEETTEEESSEE-EEECCESSC CS
                     tRNA_bind   1 lrvGkvleaeehpnadkLlvlkvdvGeeeprqivsgaknvyepeelvakkvvvvanlkpkklrGveSeGMilsaeeldeke 81 
                                   +r +kv+++e+++++++Ll++ vd+G+++ +qi+s ++++y+p +l++k +++++nlkp+k++G eS+GM+l+++  +e+ 
  gi|13541364|ref|NP_111052.1|  13 IRAAKVVSCEKVEKSRSLLRIVVDLGDQQ-KQIISSIADYYNPSDLIGKTIIILNNLKPAKFMGLESQGMLLAVD--NEEG 90 
                                   6889*************************.*********************************************..79** PP

                                   EEEEEESST--TTCE CS
                     tRNA_bind  82 vgilelpadveaGek 96 
                                   v++l+++++v++G+k
  gi|13541364|ref|NP_111052.1|  91 VKLLTVDGEVKPGSK 105
                                   *************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       334  (0.018629); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); 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 0.27s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 736.25
//
Query:       gi|13541365|ref|NP_111053.1|  [L=420]
Description: replication factor C large subunit [Thermoplasma volcanium GSS1]
Scores for complete 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   50.5   0.1    1.4e-12   48.2   0.0    2.1  2  AAA       ATPase family associated with various cellular acti
    1.8e-07   31.3   0.8    1.6e-05   24.9   0.0    3.0  3  Rad17     Rad17 P-loop domain
    0.00073   20.0   0.0     0.0017   18.8   0.0    1.7  1  AAA_16    AAA ATPase domain
    0.00079   19.5   0.0     0.0023   18.0   0.0    1.8  1  AAA_14    AAA domain
    0.00085   19.1   0.0     0.0015   18.3   0.0    1.4  1  RuvB_N    Holliday junction DNA helicase RuvB P-loop domain
     0.0013   18.1   0.0     0.0022   17.3   0.0    1.3  1  TIP49     TIP49 P-loop domain
     0.0019   18.5   0.1       0.18   12.1   0.1    2.5  1  AAA_22    AAA domain
     0.0078   16.2   0.0       0.02   14.9   0.0    1.7  2  AAA_5     AAA domain (dynein-related subfamily)
  ------ inclusion threshold ------
      0.039   13.1   0.0      0.082   12.1   0.0    1.6  1  DUF815    Protein of unknown function (DUF815)
      0.054   12.7   0.1        1.6    7.9   0.0    2.4  2  DUF2075   Uncharacterized conserved protein (DUF2075)
       0.12   11.6   0.1        0.6    9.4   0.1    2.0  2  ATPase    KaiC


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 !   48.2   0.0   8.3e-16   1.4e-12       1     108 [.      42     146 ..      42     167 .. 0.82
   2 ?   -1.2   0.0       1.5   2.5e+03      63      90 ..     223     250 ..     202     262 .. 0.59

  Alignments for each domain:
  == domain 1  score: 48.2 bits;  conditional E-value: 8.3e-16
                                   EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS..TS.EEEEEETGGGHHHHHTTCC CS
                           AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakeka..kp.silfiDEidalaksrsgse 78 
                                   ++lyG  G GKT++a a+a ++g +++e+++se ++    ++ + ++ l +++ ++   kp ++++iDE+d++++s+ + +
  gi|13541365|ref|NP_111053.1|  42 LILYGVQGSGKTSAAYAIAGTFGLPVVEMNASEQRNRESMKATALMASLYADLGASDfrKPsKVILIDEADNIFESN-NPK 121
                                   58*********************************888888888888888887776689899**************9.566 PP

                                   CHHHHHHHHHHHHHHHHTTTSSSTEEEEEE CS
                           AAA  79 seeeervvnqLlteldgvkkkeskviviga 108
                                   ++ ++  v +L + +++ ++      vi++
  gi|13541365|ref|NP_111053.1| 122 RGGDTGGVYELSKIVKETRN-----PVIIT 146
                                   66777777777777777766.....34444 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.5
                                   EEETGGGHHHHHTTCCCHHHHHHHHHHH CS
                           AAA  63 fiDEidalaksrsgseseeeervvnqLl 90 
                                   +i +++a a s+s+ ++++++++v+  +
  gi|13541365|ref|NP_111053.1| 223 IINDVEAAAVSQSSISQNNDRDTVESVY 250
                                   4566666666665555555555555555 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.0   9.6e-09   1.6e-05       8      75 ..       2      69 ..       1      84 [. 0.89
   2 ?    3.8   0.0     0.029        48     101     148 ..      73     118 ..      65     123 .. 0.82
   3 ?   -0.2   0.1      0.51   8.3e+02      64     106 ..     131     169 ..     118     206 .. 0.60

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 9.6e-09
                         Rad17  8 lWfekykPekaeelavhkkkieevkewlkadvLesrkkriLLisGPsGCgkstvvkvLskelgiklre 75
                                  +W +ky+P+  e+l v  +  ++++ w++a    s kkr L++ G  G gk+ +   ++  +g  + e
  gi|13541365|ref|NP_111053.1|  2 EWADKYRPKRIEDLIVSEEIRQKIQSWIDAWEEGSPKKRALILYGVQGSGKTSAAYAIAGTFGLPVVE 69
                                  6******************99********************************999998888877766 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.029
                         Rad17 101 rflsqiesfkeleLkdakylklqklGddlrtdkklilvedlPnkfyrd 148
                                   + +   es k   L+++ y  l     d r   k+il+++  n f+ +
  gi|13541365|ref|NP_111053.1|  73 SEQRNRESMKATALMASLYADLG--ASDFRKPSKVILIDEADNIFESN 118
                                   45666788889999*****7777..899*************9999865 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.51
                         Rad17  64 vLskelgiklrewlnpvslkepdn...qksdfkgltekesrflsqi 106
                                   +Lsk+    ++e  npv +   d+   +k+++ + ++ +s+    i
  gi|13541365|ref|NP_111053.1| 131 ELSKI----VKETRNPVIITMNDFyefRKKNYSSEVINNSES---I 169
                                   45554....678888888877776666888888888887732...2 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0     1e-06    0.0017       6      45 ..      19      60 ..      14     150 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1e-06
                        AAA_16  6 eeeleqLlsalervrsgrp..elvllsGesGvGKsslvrell 45
                                  ee +++++s ++++ +g+p  ++++l+G +G+GK+s + +++
  gi|13541365|ref|NP_111053.1| 19 EEIRQKIQSWIDAWEEGSPkkRALILYGVQGSGKTSAAYAIA 60
                                  788999*****************************9886666 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   1.4e-06    0.0023       2      76 ..      39     114 ..      38     173 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.4e-06
                        AAA_14   2 rkilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklke....ekktylflDEiqev 76 
                                   +++l++ G+  +GKT  ++ ++ +       ++++n  ++r++++ + + l+  + + l +    +  +++++DE+ ++
  gi|13541365|ref|NP_111053.1|  39 KRALILYGVQGSGKTSAAYAIAGTFG---LPVVEMNASEQRNRESMKATALMASLYADLGAsdfrKPSKVILIDEADNI 114
                                   6899******************9988...99***********9988776555444444222457778999*****9988 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 !   18.3   0.0     9e-07    0.0015       2      62 ..       8      68 ..       7     114 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 9e-07
                        RuvB_N  2 rPksleeyigqekvkeklkifieaakkreealdhvllyGpPGlGkttlakiiakelgvklk 62
                                  rPk++e+ i  e++++k++  i+a ++ + +   ++lyG  G Gkt+ a  ia  +g  + 
  gi|13541365|ref|NP_111053.1|  8 RPKRIEDLIVSEEIRQKIQSWIDAWEEGSPKKRALILYGVQGSGKTSAAYAIAGTFGLPVV 68
                                  9****************************************************98886554 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   1.4e-06    0.0022      32     103 ..      21      90 ..       5     115 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.4e-06
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                         TIP49  32 areaagvivelikekklaGravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkktevltqal 103
                                    r+     ++  +e+    ra++l G +g+Gkt+ a ai+  +g  +p v +++se    e  k+ +l+  l
  gi|13541365|ref|NP_111053.1|  21 IRQKIQSWIDAWEEGSPKKRALILYGVQGSGKTSAAYAIAGTFG--LPVVEMNASEQRNRESMKATALMASL 90 
                                   55555555666666666779***********************9..9*****************99999876 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.1   0.00011      0.18       5     104 ..      39     115 ..      36     148 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00011
                        AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdl.lrellralglelkaerlsseellealeq 84 
                                   ++ l+++G  G+GKT  +  ++ ++         + +vv+++++++ +++++ +++l   l               ++ + 
  gi|13541365|ref|NP_111053.1|  39 KRALILYGVQGSGKTSAAYAIAGTF---------GLPVVEMNASEQRNRESMkATALMASLYA-------------DLGAS 97 
                                   6788999999999999999999999.........89999999988886666633333333322.............33345 PP

                        AAA_22  85 alraravielliiDEaqhlr 104
                                    +r+ ++  +++iDEa++++
  gi|13541365|ref|NP_111053.1|  98 DFRKPSK--VILIDEADNIF 115
                                   5555555..77777777765 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   1.2e-05      0.02       2      77 ..      42     114 ..      41     122 .. 0.88
   2 ?   -3.5   0.0       5.9   9.6e+03     116     125 ..     143     153 ..     124     164 .. 0.57

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.2e-05
                                   EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------G-SEEEEESGGG- CS
                         AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraaregeilvlDEvera 77 
                                   ++L G +G+gK++ a  +a  ++ +v++++ +++ ++e +k    +      + d  + +  + ++++++DE +++
  gi|13541365|ref|NP_111053.1|  42 LILYGVQGSGKTSAAYAIAGTFGLPVVEMNASEQRNRESMKATALM---ASLYADLGASDFRKPSKVILIDEADNI 114
                                   89***************************************99998...666666666666689999999998865 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 5.9
                                   EEEEESS--.. CS
                         AAA_5 116 viatanpld.r 125
                                   vi t+n+ + +
  gi|13541365|ref|NP_111053.1| 143 VIITMNDFYeF 153
                                   56666665553 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0     5e-05     0.082      21      77 ..       6      63 ..       1      84 [. 0.84

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5e-05
                        DUF815 21 evdevklddLvgidkqkealventeqfleglpannvL.LwGarGtGKSslvkallney 77
                                  ++++ +++dL+  ++ ++++++ + ++ eg p + +L L+G +G+GK s   a+  ++
  gi|13541365|ref|NP_111053.1|  6 KYRPKRIEDLIVSEEIRQKIQSWIDAWEEGSPKKRALiLYGVQGSGKTSAAYAIAGTF 63
                                  56677899***********************99887549**********988887655 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0     0.001       1.6       2      55 ..      40      98 ..      39     106 .. 0.88
   2 ?    5.9   0.0     0.004       6.5      68     131 ..      84     149 ..      73     289 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.001
                       DUF2075  2 avvlVtGvaGtGKtvvllnllael.....eddeeertavylsvNhplvlvlrealakke 55
                                  + ++  Gv G+GKt  + +++ +      e++++e+++   ++  +l++ l+ +l  ++
  gi|13541365|ref|NP_111053.1| 40 RALILYGVQGSGKTSAAYAIAGTFglpvvEMNASEQRNRESMKATALMASLYADLGASD 98
                                  667889***********************9999999999999***********999887 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.004
                       DUF2075  68 ssfinnlsefkkaeekkeepkedvvivDEAhrlltksdq..aekqseenqlkelmkrak..vvvalvD 131
                                   ++++ +l    +  +++ +++ +v+++DEA  + +++++    ++ +  +l +++k+ +  v++ + D
  gi|13541365|ref|NP_111053.1|  84 TALMASLY--ADLGASDFRKPSKVILIDEADNIFESNNPkrGGDTGGVYELSKIVKETRnpVIITMND 149
                                   44444444..577788889999************9665522556666888999999855567776655 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.1   0.00037       0.6      13      61 ..      33      79 ..      21     141 .. 0.74
   2 ?    1.1   0.0      0.13   2.1e+02      88     163 ..      72     148 ..      65     162 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00037
                        ATPase 13 kgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepa..e 61
                                  ++G p++r+  ++G+ G+GKt  ++ ++i g  ++g p+v     e+   e
  gi|13541365|ref|NP_111053.1| 33 EEGSPKKRALILYGVQGSGKT--SAAYAIAG--TFGLPVVEMNASEQRnrE 79
                                  6899****************9..67788988..668888866666655443 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.13
                        ATPase  88 asesaeesaee.kdkedleelieelaeaikeikakrvviDsitglayeekeavaRei..lrqlvrvlkklgvTailvse 163
                                   ase++++ + + k ++ + +l ++l     ++  k ++iD  +++ ++++++   ++  + +l +++k+++   i++++
  gi|13541365|ref|NP_111053.1|  72 ASEQRNR-E-SmKATALMASLYADLGASDFRKPSKVILIDEADNIFESNNPKRGGDTggVYELSKIVKETRNPVIITMN 148
                                   3333332.2.2366777777777777777778889*********98888888877654488888888888888887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (420 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1004  (0.0559987); expected 358.6 (0.02)
Passed bias filter:                      648  (0.0361426); expected 358.6 (0.02)
Passed Vit filter:                        79  (0.00440627); 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: 0.70u 0.31s 00:00:01.01 Elapsed: 00:00:00.51
# Mc/sec: 2480.48
//
Query:       gi|13541366|ref|NP_111054.1|  [L=197]
Description: 50S ribosomal protein L15e [Thermoplasma volcanium GSS1]
Scores for 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-76  256.0   4.3    2.2e-76  255.8   4.3    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 !  255.8   4.3   1.3e-80   2.2e-76       2     191 .]       6     192 ..       5     192 .. 0.98

  Alignments for each domain:
  == domain 1  score: 255.8 bits;  conditional E-value: 1.3e-80
                                   SHHHHHHHTTSTTSHHHHHHHHHHHHHHTTS-SEEEESS-SSHHHHHHHT--SSTTEEEEEEEEE-SS---..---SS--- CS
                Ribosomal_L15e   2 aykylrelwkkkqsdvlrellrerlweyrqepavvrverptrldrArrLGYkakqGivvvrvrvrrGgrkkkvskgktgrk 82 
                                   +y+ +re wk+ +++++  + + r++ +r+ p+vvr+++ptr+drAr+LGYk+k+G++vvr rvrrGg+++  +k++ gr+
  gi|13541366|ref|NP_111054.1|   6 LYQEIREEWKSLKKSEIYDVEKSRMIGWRHGPSVVRLDHPTRIDRARALGYKSKDGFIVVRSRVRRGGSNR--EKIMGGRR 84 
                                   6999*******************************************************************..******** PP

                                   GGGG-SSS---SS-HHHHHHHHHHHHSTTSEEEEEEEEEEESSEEEEEEEEE-TTSHHHHT-TTTGGGGSGGGTTGGGGT- CS
                Ribosomal_L15e  83 pkrqgvnklkpakslqaiaeervgrklpnlrvLnSYwvgeDgtykyyEvilvDpshkairndkkinwickkvhkhRelrGl 163
                                   p+r ++nkl+++ksl+ iaeer+++k+pnl+vLnSY+vgeDg ykyyEvilvD+sh++i nd++i+wi ++++++R++rGl
  gi|13541366|ref|NP_111054.1|  85 PRRLAYNKLTRKKSLKLIAEERAADKYPNLEVLNSYYVGEDGLYKYYEVILVDKSHPNIYNDPHISWISEPQNTGRVYRGL 165
                                   ********************************************************************************* PP

                                   SHHHHHHTT-S-SS.TT-TTTSS-TGGG CS
                Ribosomal_L15e 164 tsagkksRGlrkkglkgaekirgsrran 191
                                   tsag k RGlr+ + kg++k r+s+ran
  gi|13541366|ref|NP_111054.1| 166 TSAGYKVRGLRTGR-KGSSKSRPSIRAN 192
                                   **********6655.***********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       407  (0.0227007); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1348.56
//
Query:       gi|13541367|ref|NP_111055.1|  [L=299]
Description: polysaccharide deacetylase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.7e-14   52.7   0.0    5.5e-14   52.1   0.0    1.3  1  Polysacc_deac_1  Polysaccharide deacetylase
  ------ inclusion threshold ------
       0.04   13.1   0.0      0.062   12.5   0.0    1.3  1  Glyco_hydro_57   Glycosyl hydrolase family 57
      0.094   12.4   0.9        0.2   11.3   0.3    1.8  2  DUF2334          Uncharacterized protein conserved in bacteri


Domain annotation for each model (and alignments):
>> Polysacc_deac_1  Polysaccharide deacetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.1   0.0   9.3e-18   5.5e-14      20     123 ..      41     144 ..      27     145 .. 0.96

  Alignments for each domain:
  == domain 1  score: 52.1 bits;  conditional E-value: 9.3e-18
                                   CHHHHHHHHHHCT--EEEEE-HHHHCH-HHHHHHHHHTTEEEEE--SS--EGGGSHHHHHHHHHHHHHHHHHHHHS----E CS
               Polysacc_deac_1  20 ntteilpvLkkykvkatffvigglvedypdevremaasGveignHtinhsnlkrlseeevrreierakdalrkalgreprl 100
                                   + +++l +++k  +k  ++v g  +e+ pdevr+++a+G+e+g H++ h++  ++s ++++r i+++ + +++++g++p  
  gi|13541367|ref|NP_111055.1|  41 GIPRLLRMFRKFCIKSSWYVPGIVMETFPDEVRAIYADGHELGTHGYLHEYAPSMSYDQEERVIAKTAELVKDITGHNPYG 121
                                   5799***************************************************************************** PP

                                   EE-GGGEE-HHHHHHHHHTT.EE CS
               Polysacc_deac_1 101 fryPygsasatvlevarelgfay 123
                                     +   + s ++ +++ ++g++y
  gi|13541367|ref|NP_111055.1| 122 HLPSQWEESVNTMRILMNHGYKY 144
                                   *********************98 PP

>> Glyco_hydro_57  Glycosyl hydrolase family 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0     1e-05     0.062     130     198 ..      78     145 ..      46     165 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1e-05
                                   TSEEEEEE-TT-B-GGG-S-HHHHHHHHHHHHHHHHHHHSS--SBEE-GGG-B--SHHHHHHHTT--EE CS
                Glyco_hydro_57 130 gqvElltspyyHpllpllpdsedieaqvkkarelyeeyfgqePrgfwlpElavspeileilaelGfeyl 198
                                   +  El t +y H ++p +++ ++ e+ + k  el++++ g +P g  ++    s  +++il + G++y 
  gi|13541367|ref|NP_111055.1|  78 DGHELGTHGYLHEYAPSMSY-DQEERVIAKTAELVKDITGHNPYGHLPSQWEESVNTMRILMNHGYKYA 145
                                   556999**************.889999****************************************96 PP

>> DUF2334  Uncharacterized protein conserved in bacteria (DUF2334)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.3   3.4e-05       0.2      57      90 ..      68      98 ..      63     184 .. 0.71
   2 ?   -1.6   0.0       0.3   1.8e+03      15      44 ..     221     248 ..     214     273 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 3.4e-05
                       DUF2334 57 fvevLkylqakGgeialHGYtHqygtvksevsge 90
                                  f + ++ + a+G+e++ HGY H+y     + s +
  gi|13541367|ref|NP_111055.1| 68 FPDEVRAIYADGHELGTHGYLHEYAP---SMSYD 98
                                  5567788889**************83...22222 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.3
                       DUF2334  15 leklkeiadyldkegipfsvavIPrykdp.k 44 
                                   le++k+  dy+++e   +  a+ P++++p +
  gi|13541367|ref|NP_111055.1| 221 LENWKAAFDYVYRE---YEYAIFPVNIHPdT 248
                                   56677777777765...66666677777732 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 2129.48
//
Query:       gi|13541368|ref|NP_111056.1|  [L=129]
Description: translation initiation factor IF-5A [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.2e-05   23.9   0.0    6.8e-05   22.9   0.0    1.5  1  eIF-5a    Eukaryotic elongation factor 5A hypusine, DNA-bindi
    5.2e-05   23.2   0.1    0.00013   21.9   0.0    1.7  2  EFP_N     Elongation factor P (EF-P) KOW-like domain
  ------ inclusion threshold ------
      0.051   12.7   0.0      0.069   12.3   0.0    1.1  1  URO-D     Uroporphyrinogen decarboxylase (URO-D)
      0.066   13.3   0.0       0.11   12.6   0.0    1.4  1  EFP       Elongation factor P (EF-P) OB domain


Domain annotation for each model (and alignments):
>> eIF-5a  Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0   1.5e-08   6.8e-05       1      66 [.      69     126 ..      69     127 .. 0.88

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 1.5e-08
                                   --EEEEEEEEEE-SS.EEEEEE.TT--EEE.EEGG..GB-HHHHTT--TT-E..EEEEEETTEEEEE CS
                        eIF-5a   1 nVkrkeyqLidIqdDgflsLmd.ddgetkeDlklpegelgkqikekfeegkdvlVtVlsamGeekii 66 
                                   ++++k +q+++++++   +Lmd ++ et     lp   l+ +i +k ++g +  V +++amG  ki+
  gi|13541368|ref|NP_111056.1|  69 IIEKKNAQVLSVMNN-EAQLMDsETFET---FVLP---LDPEIADKVKPGME--VPYWEAMGVRKIM 126
                                   599*********977.9****9666666...5599...999999999*****..********99997 PP

>> EFP_N  Elongation factor P (EF-P) KOW-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   2.9e-08   0.00013       3      32 ..       9      38 ..       7      40 .. 0.93
   2 ?   -3.1   0.0       1.9   8.7e+03      25      30 ..     107     112 ..     104     113 .. 0.65

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 2.9e-08
                                  GG--TT-EEEETTEEEEEEEEEEEEETTS- CS
                         EFP_N  3 selkkGlvieidgklyvVlefehvkpGkGq 32
                                   elk G  i id+ +++++e+  +kpGk +
  gi|13541368|ref|NP_111056.1|  9 RELKVGRYILIDDVPCKIVEITMSKPGKHG 38
                                  69**************************86 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1.9
                                   EEEETT CS
                         EFP_N  25 hvkpGk 30 
                                    vkpG+
  gi|13541368|ref|NP_111056.1| 107 KVKPGM 112
                                   577775 PP

>> URO-D  Uroporphyrinogen decarboxylase (URO-D)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   1.5e-05     0.069     196     239 ..      73     115 ..      68     119 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.5e-05
                                   TT-SEEEEEETTGGGS-HHHHHHHTHHHHHHHHHHHHH.H--S- CS
                         URO-D 196 agAdaiqifDswagllspedfeefvlpylkrivdevkaegpkvp 239
                                     A+++ + +  a+l++ e fe+fvlp   +i+d+vk    +vp
  gi|13541368|ref|NP_111056.1|  73 KNAQVLSVMNNEAQLMDSETFETFVLPLDPEIADKVKPGM-EVP 115
                                   679*********************************9854.455 PP

>> EFP  Elongation factor P (EF-P) OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   2.4e-05      0.11       6      35 ..      78     108 ..      73     115 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.4e-05
                                   EEEETTEEEEEETTT--EEEEEHH.HHTTGC CS
                           EFP   6 lYkdgdeyvFMdnetYeqielpke.qlgdaa 35 
                                   l   ++e  +Md+et+e + lp +  + d++
  gi|13541368|ref|NP_111056.1|  78 LSVMNNEAQLMDSETFETFVLPLDpEIADKV 108
                                   5556677889************986666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       546  (0.0304535); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 882.10
//
Query:       gi|13541369|ref|NP_111057.1|  [L=303]
Description: agmatinase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-69  235.0   0.0    1.4e-69  234.7   0.0    1.0  1  Arginase  Arginase family


Domain annotation for each model (and alignments):
>> Arginase  Arginase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  234.7   0.0   7.7e-74   1.4e-69       2     276 ..      34     290 ..      33     293 .. 0.94

  Alignments for each domain:
  == domain 1  score: 234.7 bits;  conditional E-value: 7.7e-74
                                   EEEEEEEE--TTTSSSGGGGGHHHHHHHHHHTSBTHCHEETTTTE.SCCSEEEEEEEEE--SSCHHHHHHHHHHHHHHHHH CS
                      Arginase   2 dvallGvPfdaagsgrpGarfGPraireasarleealeynlelgv.leelkivdlgdvavtpvdneevleqieeavaeilk 81 
                                   + +++G+Pfd + s+r+G++ +P++ir a  +le+   y+ + g+ l    ++dlgd++ +  d e v++++e+ v+++++
  gi|13541369|ref|NP_111057.1|  34 KYVVFGIPFDNTSSYRRGSKYAPDSIRGAYVNLES---YEYSYGIdLLASGMADLGDMEESE-DVEYVIDTVESVVSAVMS 110
                                   689*******************************8...5555566677899*******9986.9999************** PP

                                   TTCEEEEEESSGGGHHHHHHHHHHHHSTTEEEEEESSS----SSCTTTBSSSTTSHHHHHHHHTSECGCEEEEEEE-STCS CS
                      Arginase  82 agklpivlGGDHsialgilralaekygkplgvihfDAHaDlrtpetegsgnshGtpfrraaeegllkpkklvqiGirsvdn 162
                                   +gk+pi+lGG+Hsi++g++ral +    ++ ++ +DAH D+r ++  g++++h+++ rra+  +ll + +++ iGirsv++
  gi|13541369|ref|NP_111057.1| 111 DGKIPIMLGGEHSITVGAVRALPK----DVDLVIVDAHSDFRSSY-MGNKYNHACVTRRAL--DLLGEGRITSIGIRSVSR 184
                                   ********************9986....588**************.9**************..99**************** PP

                                   HHHHHHHHTTSEEEEHHHHHHHHHHHHHHHHHHHHTCTTSEEEEEEEGGGBBTTTSTSSSS-BSS-B-HHHHHHHHHHHHC CS
                      Arginase 163 eeyelakelgirvitmreidelglkavveeilervgaeedpvylSfDiDvlDpavaPGtGtpepgGltlrellallrelae 243
                                   ee+e+ +  ++ +i+  +++++g+++ +ee++++ +     vy+S+D+D++Dpa+aP++Gtpep Gl   ++++l+++l+ 
  gi|13541369|ref|NP_111057.1| 185 EEFEDPDFRKVSFISSFDVKKNGIDKYIEEVDRKSR----RVYISVDMDGIDPAYAPAVGTPEPFGLADTDVRRLIERLSY 261
                                   ******999****************99999998884....8**************************************66 PP

                                   HSEEEEEEEE-B-GGGSSTTTHHHHHHHHHHHH CS
                      Arginase 244 klnlvgaDvvEvnPaldteaeqtarlaarlvre 276
                                     + vg+D+vE++P +d+ + +t++laa+l++ 
  gi|13541369|ref|NP_111057.1| 262 --KAVGFDIVEFSPLYDN-G-NTSMLAAKLLQV 290
                                   ..88*************9.5.8*******9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (303 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       440  (0.0245412); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.31s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 1874.72
//
Query:       gi|13541370|ref|NP_111058.1|  [L=176]
Description: 50S ribosomal protein L10e [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.9e-30  104.2   0.1    5.8e-30  104.0   0.1    1.0  1  Ribosomal_L16  Ribosomal protein L16p/L10e


Domain annotation for each model (and alignments):
>> Ribosomal_L16  Ribosomal protein L16p/L10e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.0   0.1   3.2e-34   5.8e-30       4     132 .]      15     163 ..      12     163 .. 0.94

  Alignments for each domain:
  == domain 1  score: 104.0 bits;  conditional E-value: 3.2e-34
                                   SXXBSSSXXSSTSXX.XSXXXXXESX........EEEEESSXEEEEHHHHHHHHHHHCTCCCCTSXC...EEXXSXXXXEE CS
                 Ribosomal_L16   4 kkyrKsrkryirgvs.tkgtklefgd........ygLvalekgqltaealeaariainrylkkkrgk...klwirvfphhp 72 
                                   ++y++++  ++ gv+ +k+t++  g+        ++L+a+e++q++++aleaar+ +nr++++  g     l++  +phh+
  gi|13541370|ref|NP_111058.1|  15 PAYTRKE--FMGGVPyPKITTFVQGNqkrdfpieMQLIAMESCQVRHTALEAARVSVNRRMTEAAGLdnfYLKVVPYPHHV 93 
                                   6899999..99***************************************************8777798899999****** PP

                                   EEE-.....SS-TTTSSSS....XEEEEEEEEEXSSCEEEEE.TTXXXSHHHHHHHHHHHHTSSSXEEEE CS
                 Ribosomal_L16  73 vtkk.....agedRmgkGk....Gkpegwvarvkigqiifei.kagvneeiakealrraasKlpiktkiv 132
                                   ++++     ag+dR+++G+    G+p g++arv+ +++i+    ++ ++   k al++aa Klp+++k+v
  gi|13541370|ref|NP_111058.1|  94 LREHkmatgAGADRISSGMraafGRPVGTAARVYQNDVIMIGrTDEAHAHELKIALKKAAIKLPTPCKVV 163
                                   ****************************************996444588899****************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       304  (0.0169558); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1229.46
//
Query:       gi|13541371|ref|NP_111059.1|  [L=80]
Description: hypothetical protein TVN0540 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       280  (0.0156172); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 551.95
//
Query:       gi|13541372|ref|NP_111060.1|  [L=641]
Description: DNA gyrase subunit B [Thermoplasma volcanium GSS1]
Scores for complete 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-52  176.6   0.1    6.7e-52  175.5   0.1    1.6  1  DNA_gyraseB    DNA gyrase B
    2.4e-31  107.7   0.2    4.7e-31  106.8   0.2    1.4  1  DNA_gyraseB_C  DNA gyrase B subunit, carboxyl terminus
    9.8e-20   70.7   0.1    3.8e-19   68.8   0.0    2.1  2  Toprim         Toprim domain
    5.7e-19   68.7   0.2    1.9e-18   67.0   0.2    2.0  1  HATPase_c      Histidine kinase-, DNA gyrase B-, and HSP90-li
  ------ inclusion threshold ------
      0.013   15.3   0.0      0.027   14.3   0.0    1.5  1  HATPase_c_3    Histidine kinase-, DNA gyrase B-, and HSP90-li
      0.042   14.3   0.1       0.14   12.6   0.1    2.0  1  Toprim_4       Toprim domain


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 !  175.5   0.1   2.2e-55   6.7e-52       1     173 [.     232     399 ..     232     400 .. 0.97

  Alignments for each domain:
  == domain 1  score: 175.5 bits;  conditional E-value: 2.2e-55
                   DNA_gyraseB   1 GlkdfveelnkdkkelikevlsvegekaveevievevalqwtssysenilsFvNniatpeGGtHvdgfksaltktlneyak 81 
                                   G+ + v++l+++ k+li ++l+ ++e   +    ve+a+ +t++ +e ++s+vNni+tpeGGtHv+gf ++l +++++ya+
  gi|13541372|ref|NP_111060.1| 232 GIVELVKHLSEG-KNLIVDPLYWREEV--DH-YIVEFAFTYTTDVQEILQSYVNNISTPEGGTHVAGFHQGLSRAIQDYAR 308
                                   899*********.777777******99..77.9************************************************ PP

                   DNA_gyraseB  82 kkkllkkkeekisgediregltavvsvkipepqFeGQTKekLgnsevksivekvvseeleafleenkeeakkilekaveaa 162
                                   +++++k  + +i+g+d++eg++av+++k+++pqFeGQTK kLgns+v++iv++++s+ ++ fle n+ +a+ il+++++aa
  gi|13541372|ref|NP_111060.1| 309 SNGKIKGVD-DITGDDVKEGVIAVLHIKMQDPQFEGQTKAKLGNSKVRGIVQSITSKFVKTFLETNPHIADLILSRVLSAA 388
                                   ****99987.*********************************************************************** PP

                   DNA_gyraseB 163 kareaarkare 173
                                    area+rka+e
  gi|13541372|ref|NP_111060.1| 389 AAREASRKAKE 399
                                   *********98 PP

>> DNA_gyraseB_C  DNA gyrase B subunit, carboxyl terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.8   0.2   1.6e-34   4.7e-31       5      63 .]     572     630 ..     569     630 .. 0.97

  Alignments for each domain:
  == domain 1  score: 106.8 bits;  conditional E-value: 1.6e-34
                 DNA_gyraseB_C   5 eiqRfKGLGEmnpeqLweTTmdpetRrLlqvtiedaeeadelfstLmGkkvepRrefie 63 
                                    iqRfKGLGEmnpeqLw+TTm+p+tR+L+qvti+daeea+++fs+LmG+kvepRr+fie
  gi|13541372|ref|NP_111060.1| 572 IIQRFKGLGEMNPEQLWDTTMNPKTRKLVQVTIQDAEEAERIFSILMGEKVEPRRRFIE 630
                                   69********************************************************8 PP

>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       4.2   1.3e+04      16      37 ..     124     145 ..     120     166 .. 0.72
   2 !   68.8   0.0   1.3e-22   3.8e-19       1     102 [.     428     539 ..     428     540 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 4.2
                                   HTHTSTEEEEEEESSSSEEEHS CS
                        Toprim  16 kalgsgfqavtaslGhildlet 37 
                                   +al+s+  av+   Ghi+  ++
  gi|13541372|ref|NP_111060.1| 124 NALSSKLIAVVKRDGHIYYEVF 145
                                   5666777888888888876665 PP

  == domain 2  score: 68.8 bits;  conditional E-value: 1.3e-22
                                   EEEEESSHHHHHHHHHTHTSTEEEEEEESSSSEEEHSTTEEEEE.....ECTTTHHHHHH.....HHHHHHHHSEEEEECS CS
                        Toprim   1 elvivEgpsdaktiakalgsgfqavtaslGhildletefkpvye.....eiedkkkvlka.....lkelakradeiilatD 71 
                                   el+ivEg+s+ +++++a+++++qav++++G+il++e+     ++     +i+d   ++++     ++++++r+ +ii++tD
  gi|13541372|ref|NP_111060.1| 428 ELYIVEGDSAGGSAKQARNRQYQAVLPLRGKILNVEK--ASDMKvveneIIKDLVVAIGTgvkedINPRKLRYGKIIIMTD 506
                                   69***********************************..33333444555555555555588889**************** PP

                                   SSHHHHHHHHHHHHHHT....HHHTTTEEEEEESS CS
                        Toprim  72 pDreGeaiawellevlk....ellenkigrvefse 102
                                   +D++G +i+++ll+++      l+en  g+v+f+e
  gi|13541372|ref|NP_111060.1| 507 ADVDGAHIRTLLLTFFFryarSLIEN--GNVYFAE 539
                                   **************999455455555..9999998 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.0   0.2   6.4e-22   1.9e-18       1     111 [.      31     186 ..      31     187 .. 0.79

  Alignments for each domain:
  == domain 1  score: 67.0 bits;  conditional E-value: 6.4e-22
                                   EHHHHHHHHHHHHHHHHHHH..HSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHT..............GTCSTTCHHC CS
                     HATPase_c   1 gdekrLrqiisnlvdNavkf..atkageieveikaseddlvisveDnGiGipkedlk..............klfekfsqdd 65 
                                   +d ++L++++ ++vdN+v++  a+ +++i v+i   + d ++ veD+G+Gip+++++              ++++kf++ +
  gi|13541372|ref|NP_111060.1|  31 TDTRGLHHLVYEVVDNSVDEsvAGFCSNIYVKIG--K-DGSVLVEDDGRGIPVDIHPkynrpgleivltelHSGAKFDK-K 107
                                   5899****************8777**********..7.9******************************888888****.* PP

                                   STCHTSTSSSHHHHHHHHHHH.H.....TTTEEEE...........................EEETTTEEEEEEEEESS CS
                     HATPase_c  66 stkrggggtGlGlsivkklve.l.....mgGeiwv...........................esepgrGttftftlple 111
                                    +k++gg +G+G+ +v++l++ l      +G+i++                           ++ pg+Gt + f+++ e
  gi|13541372|ref|NP_111060.1| 108 VYKITGGLHGVGVHVVNALSSkLiavvkRDGHIYYevfekgipkeglktvedksvlekfgidIKYPGHGTIIKFYPDPE 186
                                   ****************886663545544225666565655555555555544444444443333368899999999876 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0     9e-06     0.027       7      46 ..      40      79 ..      35     134 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 9e-06
                   HATPase_c_3  7 laelvdNsld....AdaenvkievnknrgktgeivieDdGkGms 46
                                  + e+vdNs+d    + + n+++++ k+    g++ +eDdG G++
  gi|13541372|ref|NP_111060.1| 40 VYEVVDNSVDesvaGFCSNIYVKIGKD----GSVLVEDDGRGIP 79
                                  88********85544455677777775....7**********97 PP

>> Toprim_4  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   4.8e-05      0.14       6      69 ..     462     513 ..     457     524 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.8e-05
                      Toprim_4   6 VEgyaDvlalekagiknvvavlggalspldgirpeklktenlveaekkvkevilaldgDaeGea 69 
                                   VE   D+  +e+  ik +v   g+ +  ++ i+p kl++           ++i+++d+D++G  
  gi|13541372|ref|NP_111060.1| 462 VEKASDMKVVENEIIKDLVVAIGTGV--KEDINPRKLRY----------GKIIIMTDADVDGAH 513
                                   999***********************..9**********..........9***********975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (641 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       516  (0.0287802); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.55u 0.23s 00:00:00.78 Elapsed: 00:00:00.40
# Mc/sec: 4860.76
//
Query:       gi|13541373|ref|NP_111061.1|  [L=792]
Description: DNA gyrase subunit A [Thermoplasma volcanium GSS1]
Scores for complete 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-154  514.2   0.8   3.5e-154  513.8   0.8    1.1  1  DNA_topoisoIV    DNA gyrase/topoisomerase IV, subunit A
    5.3e-61  201.9  14.0    2.9e-11   42.6   0.1    6.8  7  DNA_gyraseA_C    DNA gyrase C-terminal domain, beta-propeller
  ------ inclusion threshold ------
      0.011   15.4   8.5       0.96    9.1   0.3    2.5  2  GrpE             GrpE
      0.026   14.3   1.5      0.072   12.9   1.5    1.7  1  DivIC            Septum formation initiator
      0.027   15.0   5.1      0.048   14.2   5.1    1.3  1  APG6_N           Apg6 coiled-coil region
      0.034   14.6   2.7      0.089   13.3   2.7    1.7  1  DUF4890          Domain of unknown function (DUF4890)
      0.054   13.2   0.4        0.1   12.2   0.4    1.4  1  Retrotran_gag_2  gag-polypeptide of LTR copia-type
      0.099   12.9   6.1       0.17   12.2   6.1    1.3  1  zf-C4H2          Zinc finger-containing protein
       0.26   11.4   2.4       0.62   10.2   2.4    1.6  1  Fib_alpha        Fibrinogen alpha/beta chain family
       0.27    9.9   6.1       0.38    9.3   6.1    1.1  1  AAA_13           AAA domain
        0.3   10.7   2.8       0.75    9.4   2.8    1.7  1  TPD52            Tumour protein D52 family
       0.33   11.1   3.2       0.32   11.1   0.3    2.5  2  Mst1_SARAH       C terminal SARAH domain of Mst1
        0.4   10.9   3.6       0.88    9.8   3.2    1.8  1  FliJ             Flagellar FliJ protein
        1.2    8.5   6.3        1.1    8.6   4.0    2.0  2  DUF4349          Domain of unknown function (DUF4349)
        6.3    7.4   8.0        6.1    7.5   4.4    2.8  2  Syntaxin-6_N     Syntaxin 6, N-terminal


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 !  513.8   0.8  2.9e-157  3.5e-154       1     416 [.      25     448 ..      25     461 .. 0.98

  Alignments for each domain:
  == domain 1  score: 513.8 bits;  conditional E-value: 2.9e-157
                 DNA_topoisoIV   1 RaiPsvrDGlKPvqRriLyamfkl.lnldkkekKvaqlvGevlgkYhPHGdaslydaivrlaqdfvgniplldpqGnfGsi 80 
                                   RaiP++rDGlKPvqRr+Lyam +l  ++dk++kK+a++vGe++gkYhPHGd+++yda+vr+aqdf++++pl+d+qGnfGsi
  gi|13541373|ref|NP_111061.1|  25 RAIPDARDGLKPVQRRVLYAMRELnVTHDKPYKKCARIVGETMGKYHPHGDMAIYDALVRMAQDFSLRYPLVDGQGNFGSI 105
                                   9******************************************************************************** PP

                 DNA_topoisoIV  81 ldgdkdAaaRYietrLskiarellkeidketvdyqenyDgsekEPevlppiiPnlLvnGaeGIavGmatkipphnlkeiid 161
                                    dgd++Aa+RY+e+rL+++a++++++id+etv+++ n+Dg+  EPe+lp+++PnlLvnG++GIavGmat++ phnl+ei d
  gi|13541373|ref|NP_111061.1| 106 -DGDSPAAMRYTEARLTQFAEDMMEDIDEETVNFRLNFDGTLPEPEYLPSKVPNLLVNGSSGIAVGMATNMVPHNLSEISD 185
                                   .******************************************************************************** PP

                 DNA_topoisoIV 162 aliallkgeea...ellelvlgPdfptgggiigkeeikeayetgrGkikvrakveiee.ktivitElPigvntskliekie 238
                                   a+++ l+++++   +ll++v+gPdfp+gg++  ++++ eay+tg+Gk+ v+++v+++e ++i+i+ lP+gvn+s l+e+i+
  gi|13541373|ref|NP_111061.1| 186 AIKYELRNRSCsvdDLLKIVKGPDFPGGGIVFYSKDLIEAYRTGKGKVIVQGEVDTSEeRRIIIKSLPYGVNKSVLVESIA 266
                                   *********99*********************99*********************9988********************** PP

                 DNA_topoisoIV 239 elvkkkkik.isdirdesdr.gvrivielkrgaseekvleklykktkLessisvnnlvlfdkkpkylslkeilkeflevrl 317
                                   +l k++ ik i+di+desdr g+rivi ++++  +  v+++ly++t+Le++i + nlvl+ ++pk+l+lk++l++f+++rl
  gi|13541373|ref|NP_111061.1| 267 NLAKNGIIKdITDIKDESDRnGIRIVIRVRDEDLKPLVMNQLYEHTDLETTIGIINLVLVGNQPKLLNLKQLLDQFIDHRL 347
                                   *****************9999************************************************************ PP

                 DNA_topoisoIV 318 evyerrkeyllekleerleilegllkalnkidevievirkskkekkakkeLiee..lseeqaeyllemrlrrLtkeevekl 396
                                   +v+ +r++y+lek +er ++l+g+l+a+++id+v+e++r+s++ +ka+++L ++  l+++q++++lemrl+rL ++e+e++
  gi|13541373|ref|NP_111061.1| 348 DVILKRSRYRLEKKNERHDVLSGVLTAIDNIDRVVEIVRGSDDVQKASETLKKTfnLNDRQVKAILEMRLQRLVHMERESV 428
                                   ******************************************************99************************* PP

                 DNA_topoisoIV 397 ekeieelekeikelekllak 416
                                    +e++++ekei++l++++++
  gi|13541373|ref|NP_111061.1| 429 VNELKSIEKEIADLKEIIES 448
                                   *****************998 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 ?   -4.0   0.0       8.8   1.1e+04      25      32 ..     227     234 ..     220     241 .. 0.73
   2 !   26.7   0.1   2.4e-09   2.8e-06       2      36 ..     494     529 ..     493     540 .. 0.84
   3 !   29.4   0.0   3.3e-10     4e-07       1      45 [.     542     589 ..     542     592 .. 0.93
   4 !   34.2   0.0   1.1e-11   1.3e-08       2      47 ..     598     641 ..     597     642 .. 0.94
   5 !   40.8   0.2   9.1e-14   1.1e-10       4      48 .]     648     692 ..     645     692 .. 0.96
   6 !   32.6   0.0   3.3e-11   3.9e-08       1      47 [.     695     742 ..     695     743 .. 0.93
   7 !   42.6   0.1   2.4e-14   2.9e-11       1      46 [.     746     791 ..     746     792 .] 0.97

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 8.8
                                   TTSCTEEG CS
                 DNA_gyraseA_C  25 RgakGvkg 32 
                                   R++kG+ +
  gi|13541373|ref|NP_111061.1| 227 RTGKGKVI 234
                                   77888766 PP

  == domain 2  score: 26.7 bits;  conditional E-value: 2.4e-09
                                   EEEEEETTSEEEEEEGGGS-BT-TTSCTEEGS.ETT CS
                 DNA_gyraseA_C   2 ellliTsnGyvkrfplselpeqgRgakGvkgi.klk 36 
                                    +++ +  G vkr+p++e+++q+Rg+kGv    k++
  gi|13541373|ref|NP_111061.1| 494 SVIMLSYGGLVKRVPIDEYRSQRRGGKGVNTSmKIS 529
                                   57888889*********************7665655 PP

  == domain 3  score: 29.4 bits;  conditional E-value: 3.3e-10
                                   SEEEEEETTSEEEEEEGGGS-BT-TTSCTEEGS...ETTTTSSEEEEE CS
                 DNA_gyraseA_C   1 dellliTsnGyvkrfplselpeqgRgakGvkgi...klkegdklvsvl 45 
                                   d + ++Ts G+v++++++e+p ++R++ Gv +    kl  +++++ v+
  gi|13541373|ref|NP_111061.1| 542 DTIYFFTSGGRVFKIKAYEIPKKSRTSLGVSAGaflKLQQNERVTEVM 589
                                   6799****************************9*********999876 PP

  == domain 4  score: 34.2 bits;  conditional E-value: 1.1e-11
                                   EEEEEETTSEEEEEEGGGS-BT-TTSCTEEGSETTTTSSEEEEEEE CS
                 DNA_gyraseA_C   2 ellliTsnGyvkrfplselpeqgRgakGvkgiklkegdklvsvlvv 47 
                                   +l+l+T+nG+vk++p++ +   +  ++G k+i+l+ +d+lvs+  +
  gi|13541373|ref|NP_111061.1| 598 HLVLVTRNGFVKKTPADPVFDAK--SSGLKIITLDGDDELVSASTI 641
                                   89*********************..77***************9876 PP

  == domain 5  score: 40.8 bits;  conditional E-value: 9.1e-14
                                   EEEETTSEEEEEEGGGS-BT-TTSCTEEGSETTTTSSEEEEEEES CS
                 DNA_gyraseA_C   4 lliTsnGyvkrfplselpeqgRgakGvkgiklkegdklvsvlvvs 48 
                                   ++ +s+G++  f+ se++e+gR ++Gv+ ++l e+d +v+++vv+
  gi|13541373|ref|NP_111061.1| 648 FVLSSKGKGSVFNTSEVRETGRSSMGVRSMRLGEEDYVVTAFVVK 692
                                   789****************************************96 PP

  == domain 6  score: 32.6 bits;  conditional E-value: 3.3e-11
                                   SEEEEEETTSEEEEEEGGGS-BT-TTSCTEEGSETTTT.SSEEEEEEE CS
                 DNA_gyraseA_C   1 dellliTsnGyvkrfplselpeqgRgakGvkgiklkeg.dklvsvlvv 47 
                                   +++l i+++G++kr++lse+p+ +Rg+ Gv +++ +e+ +k+  +++v
  gi|13541373|ref|NP_111061.1| 695 QDILSISEKGFGKRTNLSEFPVHHRGSGGVLVYRDTERtGKISQAIPV 742
                                   589*****************************9888888**9999988 PP

  == domain 7  score: 42.6 bits;  conditional E-value: 2.4e-14
                                   SEEEEEETTSEEEEEEGGGS-BT-TTSCTEEGSETTTTSSEEEEEE CS
                 DNA_gyraseA_C   1 dellliTsnGyvkrfplselpeqgRgakGvkgiklkegdklvsvlv 46 
                                   de+++++ n + +r+++se+pe++R ++Gvk+i+l++gd++ +v+v
  gi|13541373|ref|NP_111061.1| 746 DEVIIVSMNEKTIRIKASEIPETSRVTSGVKLIDLEDGDRIMAVAV 791
                                   89*****************************************987 PP

>> GrpE  GrpE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.3    0.0008      0.96      56     107 ..     359     414 ..     332     418 .. 0.76
   2 ?    9.1   2.8   0.00083      0.99      12      60 ..     430     478 ..     418     494 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0008
                                   HHHHHHHHHHHHHHHHHHHHHHHHHC......HHH-HH....HHHHHHHHHHHHHHHHHH CS
                          GrpE  56 akkfaiekfakdLLpvlDnleralksak....eneeek....slleGvemtlkqllkiLe 107
                                    kk +  +++   L  +Dn++r+++ ++         +     l++ ++++ +q + iLe
  gi|13541373|ref|NP_111061.1| 359 EKKNERHDVLSGVLTAIDNIDRVVEIVRgsddV----QkaseTLKKTFNLNDRQVKAILE 414
                                   4566677888889***************64444....43555999999999999999997 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00083
                                   HHHCCCCCCTTCHHHCTTSCCCCCCTTTTTTTTHHHHHHHHHHHHHHHH CS
                          GrpE  12 deeeeleeeleelekevkelkekllrllaefenlrkrtekekeeakkfa 60 
                                   +e+++ e+e+++l++ +++ +++++ l+ e+++++kr+ +++    kf+
  gi|13541373|ref|NP_111061.1| 430 NELKSIEKEIADLKEIIESEQKRIEVLEGEIDEIKKRYGDKRRTKIKFK 478
                                   6777788888888888888888888888888888888865555555443 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   1.5     6e-05     0.072      16      52 ..     429     465 ..     425     473 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6e-05
                                   XXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XX CS
                         DivIC  16 llaykqlkqeiaalqaelaklkaeneeLeaevkdLks 52 
                                   ++ +k++++eia+l++ +++ ++++e Le e+++ k+
  gi|13541373|ref|NP_111061.1| 429 VNELKSIEKEIADLKEIIESEQKRIEVLEGEIDEIKK 465
                                   577899***************************9976 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   5.1     4e-05     0.048      29     117 ..     392     479 ..     356     486 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4e-05
                        APG6_N  29 eeflkklkkekkeeekqdeeleeleeelek.lekeeeelleeLkelekereeleaelaaleeelealeeeeerfwreynel 108
                                   ++  ++lkk+ + +  +++  + le +l++ ++ e+e+ ++eLk +eke ++l++ +++ ++  e le e ++  ++y ++
  gi|13541373|ref|NP_111061.1| 392 QKASETLKKTFNLN--DRQVKAILEMRLQRlVHMERESVVNELKSIEKEIADLKEIIESEQKRIEVLEGEIDEIKKRYGDK 470
                                   44445555553332..355666778888884577889999***************************************** PP

                        APG6_N 109 qlellelee 117
                                   ++++++++e
  gi|13541373|ref|NP_111061.1| 471 RRTKIKFKE 479
                                   ***999987 PP

>> DUF4890  Domain of unknown function (DUF4890)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   2.7   7.4e-05     0.089      18      95 ..     392     468 ..     384     483 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 7.4e-05
                       DUF4890  18 ermTermvkeYsLnetqkkqLlElNlalvekmgdrpmrlkrdakrkkdkrdrkkaqatkkeerekkrkemkaareaYe 95 
                                   ++  e + k+++Ln+ q k +lE+ l+++ +m+     +++ +  +k+  d k+ ++ +++  e+   e+++ ++ Y 
  gi|13541373|ref|NP_111061.1| 392 QKASETLKKTFNLNDRQVKAILEMRLQRLVHMERES-VVNELKSIEKEIADLKEIIESEQKRIEVLEGEIDEIKKRYG 468
                                   78889999***********************97664.44444444455467777777777777777777777766664 PP

>> Retrotran_gag_2  gag-polypeptide of LTR copia-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.4   8.7e-05       0.1      18      88 ..     379     446 ..     364     457 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 8.7e-05
               Retrotran_gag_2  18 dsllelvkeektakevWdkLkelyekksaankltlrkklfslkmkegesvadhinkleelvneLsalgvki 88 
                                   d+++e v++++++ ++ ++Lk++++ ++++ k+ l  +l +l   e esv + ++ +e+ + +L++    i
  gi|13541373|ref|NP_111061.1| 379 DRVVEIVRGSDDVQKASETLKKTFNLNDRQVKAILEMRLQRLVHMERESVVNELKSIEKEIADLKE---II 446
                                   67889999***************************************9886666666655555554...44 PP

>> zf-C4H2  Zinc finger-containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   6.1   0.00014      0.17       4      96 ..     383     473 ..     380     517 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00014
                       zf-C4H2   4 eirektleleklknklakevealekeekcleeykkelelLeqEkmaHveeLrlIhaDinalEsvikeaeeekekslekakk 84 
                                   ei + +++++k ++ l+k +++ +++ k + e++    l+++E+++ v+eL+ I++ i +l ++i++ ++  e  + ++ +
  gi|13541373|ref|NP_111061.1| 383 EIVRGSDDVQKASETLKKTFNLNDRQVKAILEMRL-QRLVHMERESVVNELKSIEKEIADLKEIIESEQKRIEVLEGEIDE 462
                                   5666789999**********************975.57999***********************98777665554444544 PP

                       zf-C4H2  85 lyeeykklkeev 96 
                                   + + y   k+++
  gi|13541373|ref|NP_111061.1| 463 IKKRYGD-KRRT 473
                                   4444432.2223 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 ?   10.2   2.4   0.00052      0.62      45     115 ..     396     464 ..     369     469 .. 0.55

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00052
                                   CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHHHHHH CS
                     Fib_alpha  45 eeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesnirvLqnvlesne 115
                                   e+++++ +  ++ vk+i ++  ++  + +  ++v++++++ +e+ei++lke i ++ ++i+vL + +++ +
  gi|13541373|ref|NP_111061.1| 396 ETLKKTFNLNDRQVKAILEMRLQRLVHME-RESVVNELKS-IEKEIADLKEIIESEQKRIEVLEGEIDEIK 464
                                   22233333333334444444444444443.3666666654.555777777777777777777776666655 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   6.1   0.00032      0.38     364     459 ..     384     473 ..     330     480 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00032
                        AAA_13 364 iesikklvaeineliakhNekvanleeekeeakkklelhlveeleseldeykkkykklekaieklekelkeeeaelkklee 444
                                   i++++++v+++ e+ +    k+ nl++++ +a  +++l+++ ++e e     +++k++ek+i +l++ ++ e+++++ le+
  gi|13541373|ref|NP_111061.1| 384 IVRGSDDVQKASETLK----KTFNLNDRQVKAILEMRLQRLVHMERE--SVVNELKSIEKEIADLKEIIESEQKRIEVLEG 458
                                   2566777777777665....588999999999999999999999888..4678899************************* PP

                        AAA_13 445 eikeLekqlrdekpa 459
                                   ei e++k+  d++++
  gi|13541373|ref|NP_111061.1| 459 EIDEIKKRYGDKRRT 473
                                   *******99998875 PP

>> TPD52  Tumour protein D52 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   2.8   0.00063      0.75      17      59 ..     415     455 ..     383     476 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00063
                         TPD52  17 vsaseptlteeereeLkseLakleeeivtLrqvLaakekhlae 59 
                                   ++++   l   ere + +eL  +e+ei+ L++++ + +k++  
  gi|13541373|ref|NP_111061.1| 415 MRLQ--RLVHMERESVVNELKSIEKEIADLKEIIESEQKRIEV 455
                                   3333..59999**************************999754 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 ?   -2.4   0.2       4.5   5.4e+03      22      31 ..     434     443 ..     416     453 .. 0.78
   2 ?   11.1   0.3   0.00027      0.32      23      39 ..     456     472 ..     451     473 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 4.5
                    Mst1_SARAH  22 eMEqEieelr 31 
                                    +E+Ei +l+
  gi|13541373|ref|NP_111061.1| 434 SIEKEIADLK 443
                                   5688888776 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00027
                    Mst1_SARAH  23 MEqEieelrkrYqaKRq 39 
                                   +E Ei+e++krY  KR+
  gi|13541373|ref|NP_111061.1| 456 LEGEIDEIKKRYGDKRR 472
                                   899*************7 PP

>> FliJ  Flagellar FliJ protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   3.2   0.00074      0.88      19      99 ..     407     484 ..     388     493 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00074
                          FliJ  19 ekleeleqyrqeyqkqlsgeaqglsaaelrnyqafisaldeaiaqqkqelaqaekqvekareewqearqerkklekLkere 99 
                                    ++ ++ + r +    ++ e+    ++el+ +++ i+ l+e i++ ++ ++ +e ++++ ++++  +r+ + k++ + er 
  gi|13541373|ref|NP_111061.1| 407 RQVKAILEMRLQRLVHMERES---VVNELKSIEKEIADLKEIIESEQKRIEVLEGEIDEIKKRYGDKRRTKIKFKEIGERS 484
                                   444444444444444444444...689******************************************999998887775 PP

>> DUF4349  Domain of unknown function (DUF4349)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.2      0.91   1.1e+03      94     146 ..     357     409 ..     355     419 .. 0.90
   2 ?    8.6   4.0   0.00094       1.1     102     147 ..     414     461 ..     406     462 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.91
                       DUF4349  94 RlkaleasedrllallekaksvedlleiereLsevqaeieslegqlryLdnqv 146
                                   Rl+ +++  d l  +l   ++++ ++ei r   +vq+  e l+++++  d+qv
  gi|13541373|ref|NP_111061.1| 357 RLEKKNERHDVLSGVLTAIDNIDRVVEIVRGSDDVQKASETLKKTFNLNDRQV 409
                                   89999999999999999999********9999999999999999998888887 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00094
                       DUF4349 102 edrllal..lekaksvedlleiereLsevqaeieslegqlryLdnqva 147
                                   e rl+ l  +e+ + v++l +ie+e+++ ++ ies +++++ L+++++
  gi|13541373|ref|NP_111061.1| 414 EMRLQRLvhMERESVVNELKSIEKEIADLKEIIESEQKRIEVLEGEID 461
                                   45666652269999*****************************99886 PP

>> Syntaxin-6_N  Syntaxin 6, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.2      0.55   6.6e+02      34      72 ..     352     390 ..     329     412 .. 0.61
   2 ?    7.5   4.4    0.0051       6.1       8      83 ..     389     462 ..     385     483 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.55
                  Syntaxin-6_N  34 stseeldetrteLrkalrsiewdledLeetvriveknps 72 
                                   ++s    e ++e +  l+ + + +++++++v+iv+ + +
  gi|13541373|ref|NP_111061.1| 352 KRSRYRLEKKNERHDVLSGVLTAIDNIDRVVEIVRGSDD 390
                                   456666778888899999999999999999999965322 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0051
                  Syntaxin-6_N   8 eeVqkslnkaeslyrrwerlledtss.stseeldetrteLrkalrsiewdledLeetvriveknpskfkidekelsr 83 
                                   ++Vqk+ ++++++++   r  +   + + +  ++  r+ + ++l+sie+++ dL+e +   e+++++ ++ e e+++
  gi|13541373|ref|NP_111061.1| 389 DDVQKASETLKKTFNLNDRQVKAILEmRLQRLVHMERESVVNELKSIEKEIADLKEII---ESEQKRIEVLEGEIDE 462
                                   68888888888888888653444334355566666777899*****************...7777777777766654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (792 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1259  (0.0702214); expected 358.6 (0.02)
Passed bias filter:                      766  (0.0427241); expected 358.6 (0.02)
Passed Vit filter:                       116  (0.00646996); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.85u 0.37s 00:00:01.22 Elapsed: 00:00:00.53
# Mc/sec: 4536.38
//
Query:       gi|13541374|ref|NP_111062.1|  [L=208]
Description: nicotinamidase-like amidase [Thermoplasma volcanium GSS1]
Scores for complete 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-39  133.7   0.0    8.6e-39  133.5   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 !  133.5   0.0   4.8e-43   8.6e-39       1     172 [.      18     195 ..      18     198 .. 0.94

  Alignments for each domain:
  == domain 1  score: 133.5 bits;  conditional E-value: 4.8e-43
               Isochorismatase   1 talvviDmqndfveegvkeseeisavveninkllkaarkagipviftrdvhe...........leevkgdlderkaaphfk 70 
                                   t+lv +D+qn++v    +++ + ++++  ++ ++++ark+g++vi+t+ ++             ++ ++  ++  + + ++
  gi|13541374|ref|NP_111062.1|  18 TVLVAWDVQNGLV----NSIFNKNEFLGVVKNVIQSARKKGVKVIYTKITPMppgfesgyrlySMMKRYGVSDPDKVRFME 94 
                                   689**********....**********************************9**********777777777777788999* PP

               Isochorismatase  71 pgttgaelvpelaplegdvvvdKtrfsafagtdldeiLkelgiktivlaGiatdvCVeatardaldlGyevvvvsDAvaal 151
                                   pg+++ae++ elap +gd+v++K++ + f gt+++ +L+++gi+ti+++Giat++++e++ar+a ++G+ +vv++D+v++ 
  gi|13541374|ref|NP_111062.1|  95 PGSPEAEIYSELAPEQGDIVINKNTADLFIGTNVELMLRNAGIDTILFTGIATEFGIESSARSAGNRGFYPVVIQDGVSSP 175
                                   ********************************************************************************* PP

               Isochorismatase 152 spelhdaalkrlkqafatvit 172
                                   +++ h+aalk l+   a  i+
  gi|13541374|ref|NP_111062.1| 176 NKDMHEAALKILA-TQAITIK 195
                                   **********999.4455554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       604  (0.0336884); expected 358.6 (0.02)
Passed bias filter:                      547  (0.0305092); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1357.59
//
Query:       gi|13541375|ref|NP_111063.1|  [L=389]
Description: ABC-type molybdate transport system, solute-binding component [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    5.2e-14   52.5   0.0    9.5e-14   51.7   0.0    1.5  1  SBP_bac_11  Bacterial extracellular solute-binding protein
  ------ inclusion threshold ------
       0.11   12.9   0.2       0.36   11.2   0.1    2.0  2  ArgoL2      Argonaute linker 2 domain
        1.1    8.9   3.8        2.4    7.8   3.8    1.5  1  DUF3149     Protein of unknown function (DUF3149)


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 !   51.7   0.0   1.6e-17   9.5e-14       2     187 ..      44     277 ..      43     350 .. 0.72

  Alignments for each domain:
  == domain 1  score: 51.7 bits;  conditional E-value: 1.6e-17
                                   EEEE-SSTHHHHH.HHHHHHHHHH---EEEEESSHHHHHHHHHHH..-SEEEESSH.HHHH.HHHHGGGGGGG-EEEEEEE CS
                    SBP_bac_11   2 tvaaagslaaalr.elaaaFeahtgvkvevsaggsgklarqiadgarpDvwipassawlel.laaaglvqaesavplassp 80 
                                   + +aagsl+ al  + +++F + tg+kv +++ gs   a+ +++g+++ v+++as+  l + l+++ + + ++  ++  + 
  gi|13541375|ref|NP_111063.1|  44 NTFAAGSLKYALGnDFNPEFNNLTGIKVGMTFSGSISGAKEVQAGKQYSVFVSASAPVLYQnLINNTHYA-SWQIVFSANE 123
                                   66899******9889****************************************666555265554444.6********* PP

                                   EEEEESTT-....TT---SHHHHHHSS--EEEE--T-TTTTHH.HHHHGGG--............................ CS
                    SBP_bac_11  81 lviavpkgn....pkkikgwadLlkpglklavadPttspsGlaalalleaaga............................ 129
                                   ++i    ++    p  ++++++++k+++ +a ++ + +psG +a+++++ ag                             
  gi|13541375|ref|NP_111063.1| 124 MAITWTNSKyainPSWPYWFENITKNSTIVAASNASLDPSGFQAIETMKLAGIlytnwsdpfvqmafnhneslflqynkay 204
                                   ******99966666668899*****************************99544444445555555555555555554445 PP

                                   ..............HHHHHHHHHTEEEEESSHHHHHHH.......HHTTT-SEEEEEHHHHH..HSTTSSEEEE--TTT CS
                    SBP_bac_11 130 ..............qellkalekkvvklgessrqllta.......veageadagivyeseakaaengdkleavylpegl 187
                                                  +l+++++ +   + + ++ l+t        + +g ad++++y s+a+     ++l+++    g 
  gi|13541375|ref|NP_111063.1| 205 ntwfeklgykandsLALYHQIFISK--YLNHTTKLTTVeigldgyLTSGAADYALTYVSQAI----NQNLSYYKSATGG 277
                                   4444445555566644444444222..222223344335577778****************8....4444444444333 PP

>> ArgoL2  Argonaute linker 2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       1.8   1.1e+04      18      29 ..      60      72 ..      44      75 .. 0.58
   2 ?   11.2   0.1     6e-05      0.36       6      44 ..     341     381 ..     339     383 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1.8
                        ArgoL2 18 dpyl.rafGisid 29
                                  +p + +  Gi+++
  gi|13541375|ref|NP_111063.1| 60 NPEFnNLTGIKVG 72
                                  3555466688887 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 6e-05
                        ArgoL2   6 Ile.gvkvlgydd.dpylrafGisidpqmttVpGRvLppPt 44 
                                   I++ g + l  +  dp  + fGi+i++ + + ++ v ppP+
  gi|13541375|ref|NP_111063.1| 341 ITQmGQHYLAMSRfDPLSQPFGINISNMPKQLQAVVTPPPS 381
                                   777776667776668888****************9999995 PP

>> DUF3149  Protein of unknown function (DUF3149)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   3.8   0.00041       2.4      11      28 ..      12      29 ..      12      30 .. 0.93

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00041
                       DUF3149 11 LlSliVIvftigmgaffi 28
                                  +lS++VI+++ig+++ f+
  gi|13541375|ref|NP_111063.1| 12 WLSIAVILLVIGLVVGFA 29
                                  79*************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       700  (0.0390429); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 2614.87
//
Query:       gi|13541376|ref|NP_111064.1|  [L=264]
Description: ABC-type molybdate transport system, permease component [Thermoplasma volcanium GSS1]
Scores for complete 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-06   26.3  14.5    5.2e-06   26.3  14.5    2.6  2  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   6.9      0.12   2.2e+03      28      71 ..       8      73 ..       3      77 .. 0.58
   2 !   26.3  14.5   2.9e-10   5.2e-06      14     180 ..      78     258 ..      67     260 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.12
                  BPD_transp_1 28 lslPsfv..laillvlvf..................vilsilg.hlilp.viillllsaapyvrli 71
                                  l +P+f+  ++i+lv ++                  ++ si + ++i + v++l++l+++py ++i
  gi|13541376|ref|NP_111064.1|  8 LFFPIFLlyILIILVPIIraltyssigeitadlssgILPSIEYtYAICGvVAFLAVLFSLPYSYVI 73
                                  445666622444444444888888888888877776444444435555566777777777777766 PP

  == domain 2  score: 26.3 bits;  conditional E-value: 2.9e-10
                  BPD_transp_1  14 kkldkllrpliivllslPsfvlaillvlvf............vilsilghlilp.viillllsaapyvrlirraalrslpk 81 
                                   ++  k+ + l++++ ++P+ v++i+++  f            +i ++  ++ l  vii+l++ + +y ++ +  a +   +
  gi|13541376|ref|NP_111064.1|  78 GPAYKAADSLVEIPIMIPHSVVGIIMLITFeptmpighllakYIPGYSFDGTLFaVIITLFFLSSAYSIREIGIAYQKDVM 158
                                   667789999******************999*********999666666666666455555566666655555555566668 PP

                  BPD_transp_1  82 dlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydyseis...nggvl 159
                                   +++++a++lG+++   f+ + ++++l+p++ g++l++++++ +  ++++++ +  +   ++     + ys+++    g+++
  gi|13541376|ref|NP_111064.1| 159 EYENVAKTLGLGETLSFVIISMRLLLRPMMKGFLLSWARSVSEVGAILIVAYY--IFPSFVKLAGVFIYSQWLgygLGPAA 237
                                   ********************************************999999966..55555555555666666667767777 PP

                  BPD_transp_1 160 alviavlllnlvadilqrlld 180
                                   a  +++++  +++  + ++++
  gi|13541376|ref|NP_111064.1| 238 ASSAILIITGIAVTGIFKMVE 258
                                   777777777777777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       773  (0.0431145); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1666.51
//
Query:       gi|13541377|ref|NP_111065.1|  [L=300]
Description: ABC-type molybdate transporter, ATPase component [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.4e-32  110.4   0.0    1.7e-31  109.5   0.0    1.4  1  ABC_tran      ABC transporter
    2.1e-06   27.8   2.7    0.00065   19.6   0.4    2.5  3  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    5.6e-05   22.7   1.7     0.0024   17.4   0.2    2.1  2  SMC_N         RecF/RecN/SMC N terminal domain
    0.00015   21.5   0.2    0.00033   20.3   0.1    1.6  1  AAA_29        P-loop containing region of AAA domain
    0.00086   19.1   2.1     0.0059   16.4   2.1    2.2  1  AAA_15        AAA ATPase domain
     0.0012   19.4   0.6     0.0025   18.4   0.6    1.5  1  AAA_23        AAA domain
     0.0034   17.6   0.1      0.078   13.2   0.1    2.3  1  SbcCD_C       Putative exonuclease SbcCD, C subunit
     0.0056   15.4   0.3      0.008   14.9   0.0    1.4  2  AAA_13        AAA domain
      0.007   16.8   0.0      0.017   15.6   0.0    1.5  1  AAA           ATPase family associated with various cellular 
  ------ inclusion threshold ------
      0.012   15.0   0.0       0.02   14.3   0.0    1.3  1  Mg_chelatase  Magnesium chelatase, subunit ChlI
      0.021   14.2   0.2      0.093   12.1   0.1    1.9  2  FtsK_SpoIIIE  FtsK/SpoIIIE family
      0.022   14.7   0.1      0.056   13.4   0.0    1.6  2  NACHT         NACHT domain
      0.029   14.1   0.0      0.042   13.6   0.0    1.4  1  AAA_24        AAA domain
      0.083   13.0   0.2       0.22   11.6   0.1    1.7  2  DUF87         Helicase HerA, central domain
       0.12   11.6   0.0       0.27   10.4   0.0    1.5  2  DUF815        Protein of unknown function (DUF815)
       0.16   12.2   0.3          1    9.6   0.0    2.0  2  AAA_22        AAA domain
       0.17   11.8   0.1        0.3   11.0   0.1    1.4  1  RsgA_GTPase   RsgA GTPase


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.5   0.0   1.6e-34   1.7e-31      11     136 ..      25     153 ..      18     154 .. 0.91

  Alignments for each domain:
  == domain 1  score: 109.5 bits;  conditional E-value: 1.6e-34
                                   TSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.........HHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxx RF
                      ABC_tran  11 gekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren.........esd 82 
                                   g+   i+GenG+GKSt+lk++agl +p +G+i +dg+d+++  ++ ++++i+++pq+  lfp+++v +n          + 
  gi|13541377|ref|NP_111065.1|  25 GRHNFIMGENGSGKSTFLKTIAGLIDPISGRIDIDGNDITN--MPPWKRHIAYIPQNLLLFPQYKVMDNiaisikygqGDP 103
                                   66778***********************************9..***************************99997654444 PP

                                   TCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  83 eeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                   e ++++++ + l++l ++++    ++LSgGq+qrva+ara+++ p++ll+DEp+
  gi|13541377|ref|NP_111065.1| 104 EIFKEVVKVMHLEDLLERNI----YQLSGGQQQRVAVARAIVSMPRILLMDEPF 153
                                   44888888888888888888....*****************************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 !   19.6   0.4   6.2e-07   0.00065       2      25 ..      28      51 ..      28     108 .. 0.81
   2 !    8.0   0.0    0.0021       2.2     220     266 ..     109     152 ..      72     154 .. 0.83
   3 ?   -2.4   0.1       3.1   3.3e+03      13      31 ..     166     185 ..     157     237 .. 0.55

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 6.2e-07
                        AAA_21  2 nvliGpNgsGKSnLLdaldllarl 25
                                  n++ G NgsGKS++L+++ +l + 
  gi|13541377|ref|NP_111065.1| 28 NFIMGENGSGKSTFLKTIAGLIDP 51
                                  7899***************99542 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0021
                        AAA_21 220 gvvflengdgqelparelSdGtkrllalltallralkkgsllliDEp 266
                                    v  ++ +d  e+++++lS G+++  a++ a+ + +   ++ll DEp
  gi|13541377|ref|NP_111065.1| 109 VVKVMHLEDLLERNIYQLSGGQQQRVAVARAIVSMP---RILLMDEP 152
                                   56678889999**************9********99...*******9 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 3.1
                        AAA_21  13 SnLLdaldllarl..drdveg 31 
                                   SnLLd++d    +  +   ++
  gi|13541377|ref|NP_111065.1| 166 SNLLDLIDRYE-IdyIYVTHN 185
                                   55555555442.123222223 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.2   2.2e-06    0.0024      19      44 ..      20      45 ..       5      49 .. 0.86
   2 ?    4.7   0.1     0.017        18     116     205 ..     108     192 ..      85     205 .. 0.62

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2.2e-06
                                  EEETTSSEEEEEESTTSSHHHHHHHH CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 19 ilpfsksftaivGpNGSGKsnlldAi 44
                                  +l +s ++++i+G+NGSGKs +l  i
  gi|13541377|ref|NP_111065.1| 20 ELSLSGRHNFIMGENGSGKSTFLKTI 45
                                  6678899***************9988 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.017
                                   EEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHH.HHHHHHHH.HHCTTSEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxx.xxxxxxxxxx RF
                         SMC_N 116 kevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknv.kkvaellk.eksknaQfiv 194
                                   + v+   +++lle+   ++ +LSgG+++ va+a   Ai ++    + l+De  +  De+ + + +++ll+  ++ +  +i 
  gi|13541377|ref|NP_111065.1| 108 EVVKVMHLEDLLER---NIYQLSGGQQQRVAVAR--AIVSM--PRILLMDEPFSMQDERSRmSLISNLLDlIDRYEIDYIY 181
                                   44444555555554...2348******9998874..44433..33677888777777654415556666643445577777 PP

                                   E-SSHHHCCC- CS
                                   xxxxxxxxxxx RF
                         SMC_N 195 islreemleka 205
                                   ++++++ le  
  gi|13541377|ref|NP_111065.1| 182 VTHNSRDLELG 192
                                   77777766655 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.1   3.1e-07   0.00033      17      48 ..      19      51 ..       9      58 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 3.1e-07
                        AAA_29 17 ieidlkg.atlltGpsGsGKSTllDAiqalLvp 48
                                   e++l+g   +++G++GsGKST+l  i+ l+ p
  gi|13541377|ref|NP_111065.1| 19 KELSLSGrHNFIMGENGSGKSTFLKTIAGLIDP 51
                                  5667778889*************9888877666 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   2.1   5.6e-06    0.0059      18      66 ..      20      64 ..      10     238 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 5.6e-06
                        AAA_15 18 eidlseeltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedle 66
                                  e++ls   +++ G+N+sGKS++l+ +  +++      +  i+i+ +d+ 
  gi|13541377|ref|NP_111065.1| 20 ELSLSGRHNFIMGENGSGKSTFLKTIAGLIDPI----SGRIDIDGNDIT 64
                                  344444589*****************9999877....455555555554 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.6   2.3e-06    0.0025      13      39 ..      19      45 ..      10      49 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 2.3e-06
                        AAA_23 13 qeidFskgltlItGpNGaGKTTildAi 39
                                  +e+ +s   + I G+NG+GK+T+l  i
  gi|13541377|ref|NP_111065.1| 19 KELSLSGRHNFIMGENGSGKSTFLKTI 45
                                  578889999**************9877 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.1   7.4e-05     0.078      26      86 ..     119     166 ..     107     170 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7.4e-05
                       SbcCD_C  26 lsrssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatlle 86 
                                   l+r++ +lSGG++q    +a+a     ++       + +r++++DE Fs  De+s+ +l++
  gi|13541377|ref|NP_111065.1| 119 LERNIYQLSGGQQQR---VAVA----RAIV------SMPRILLMDEPFSMQDERSRMSLIS 166
                                   566777777777743...2222....2222......35899**************999886 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   7.6e-06     0.008       8      39 ..      17      48 ..      10      97 .. 0.80
   2 ?   -3.2   0.1       2.2   2.3e+03     527     570 ..     144     185 ..     139     187 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 7.6e-06
                        AAA_13  8 rgaeledfkriNliYGwNGaGKTtLSrllrsl 39
                                  + +el+  +r N+i G NG+GK+t+ + ++ l
  gi|13541377|ref|NP_111065.1| 17 SIKELSLSGRHNFIMGENGSGKSTFLKTIAGL 48
                                  5566666789***************9999887 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 2.2
                        AAA_13 527 dkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHn 570
                                    +i  +D P S  D  s ++ +s + + + ++ ++  +++ THn
  gi|13541377|ref|NP_111065.1| 144 PRILLMDEPFSMQDERSRMSLISNLLDLI-DRYEIDYIYV-THN 185
                                   67888999999999999888888887777.7777777776.887 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.6e-05     0.017       3      99 ..      30     178 ..      29     193 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.6e-05
                                   EESSTTSSHHHHHHHHHHHHT..HEEEEEETTTCSSS............................................ CS
                           AAA   3 lyGppGtGKTllakavakelg..vefleisgsellsk............................................ 37 
                                   ++G  G GK+++ k +a  ++  +  + i+g +++++                                            
  gi|13541377|ref|NP_111065.1|  30 IMGENGSGKSTFLKTIAGLIDpiSGRIDIDGNDITNMppwkrhiayipqnlllfpqykvmdniaisikygqgdpeifkevv 110
                                   689****************9776667999******9999****************************************** PP

                                   .............STTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTS CS
                           AAA  38 .............yvgesekkirelfkeakekakpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkk 99 
                                                y+  + ++ r  +++a  +  p il++DE  ++  +r      +++++++ Ll  +d+++ +
  gi|13541377|ref|NP_111065.1| 111 kvmhledllerniYQLSGGQQQRVAVARAIVSM-PRILLMDEPFSMQDER------SRMSLISNLLDLIDRYEID 178
                                   ****99999999999999999999999988887.9***********9999......999***********99874 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   1.9e-05      0.02      16      57 ..      20      60 ..       9      84 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.9e-05
                  Mg_chelatase 16 eiaaaGgHnlllvGppGsGKtmlakrlpsllpplseeealev 57
                                  e++ +G+Hn+++ G  GsGK+   k +++l+ p+s +  ++ 
  gi|13541377|ref|NP_111065.1| 20 ELSLSGRHNFIM-GENGSGKSTFLKTIAGLIDPISGRIDIDG 60
                                  78899****987.*****************999887665555 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   8.8e-05     0.093      40      59 ..      26      45 ..       8      49 .. 0.83
   2 ?   -0.6   0.0      0.64   6.8e+02       6      38 ..     127     160 ..     122     169 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 8.8e-05
                                  .SEEEE--TTSSHHHHHHHH CS
                  FtsK_SpoIIIE 40 shllvaGatgsGKStalntL 59
                                   h  ++G  gsGKSt+l+t+
  gi|13541377|ref|NP_111065.1| 26 RHNFIMGENGSGKSTFLKTI 45
                                  6999*************996 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.64
                                   HTSHHHHT---TTEEEEEEET.TS-EEEEEGGGS CS
                  FtsK_SpoIIIE   6 leskkfrtessqlpvalgkei.sgnplvldlkkm 38 
                                     +++ r++ ++++v++++   +++p+ ++   +
  gi|13541377|ref|NP_111065.1| 127 SGGQQQRVAVARAIVSMPRILlMDEPFSMQDERS 160
                                   56788899999***************99886655 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   5.3e-05     0.056       4      22 ..      29      47 ..      26      50 .. 0.88
   2 ?   -2.2   0.0       3.2   3.4e+03      53      81 ..     114     145 ..     106     176 .. 0.55

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.3e-05
                                  EEEC-TTTCHHHHHHHHHH CS
                         NACHT  4 ilqGeaGsGKTtLlqklal 22
                                  ++ Ge+GsGK+t+l+ +a 
  gi|13541377|ref|NP_111065.1| 29 FIMGENGSGKSTFLKTIAG 47
                                  799*************985 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 3.2
                                   -HCHHHCCCCTS--SSS-C...CHHHHCCSCC CS
                         NACHT  53 sladllfsqlpepaapvse...vwavllelpe 81 
                                   +l dll ++  ++++ +++   v   +++ p+
  gi|13541377|ref|NP_111065.1| 114 HLEDLLERNIYQLSGGQQQrvaVARAIVSMPR 145
                                   56667766666666666663333333333333 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0     4e-05     0.042       6      58 ..      29      78 ..      24     133 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4e-05
                        AAA_24  6 liyGpsgiGKTtlakelgpkplfidtekGlksldadkfpdieswedfldevve 58
                                  +i+G++g+GK+t++k++   + +id   G  ++d++++ +++ w+  + ++ +
  gi|13541377|ref|NP_111065.1| 29 FIMGENGSGKSTFLKTI---AGLIDPISGRIDIDGNDITNMPPWKRHIAYIPQ 78
                                  79***************...677777777778888888888888776666655 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   0.1   0.00021      0.22      21      43 ..      23      45 ..      10      56 .. 0.86
   2 ?   -1.5   0.0       2.1   2.2e+03     119     179 ..     117     175 ..      77     215 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00021
                         DUF87 21 lvtrHlAilgsTGsGKSntvavL 43
                                  l  rH  i+g+ GsGKS++ + +
  gi|13541377|ref|NP_111065.1| 23 LSGRHNFIMGENGSGKSTFLKTI 45
                                  5679***************9998 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.1
                         DUF87 119 svleealdqakakeekeklssdepveklleelkkekeelrklknqaiarlldkledllrkg 179
                                   ++le+ + q+  + +++++ +++ + ++   l  ++e+ + ++++++++l++ l dl++++
  gi|13541377|ref|NP_111065.1| 117 DLLERNIYQLS-GGQQQRVAVARAIVSMPRILL-MDEPFSMQDERSRMSLISNLLDLIDRY 175
                                   34444444443.344444444444444444444.444445555555555555555555554 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00025      0.27      54     112 ..      26      83 ..      16      91 .. 0.89
   2 ?   -3.5   0.0       4.3   4.5e+03     144     154 ..     179     189 ..     153     189 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00025
                        DUF815  54 nnvLLwGarGtGKSslvkallneyaeegLrlievekedlkelpklvellrerperfilf 112
                                   ++ +++G+ G+GKS+ +k++   +   + r i+++ +d++++p   ++++  p++++lf
  gi|13541377|ref|NP_111065.1|  26 RHNFIMGENGSGKSTFLKTIAGLIDPISGR-IDIDGNDITNMPPWKRHIAYIPQNLLLF 83 
                                   577899*************99888777766.8********************9999998 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 4.3
                        DUF815 144 liyaTsNrRhL 154
                                    iy+T N R+L
  gi|13541377|ref|NP_111065.1| 179 YIYVTHNSRDL 189
                                   47777777765 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00097         1       7      26 ..      27      46 ..      23      53 .. 0.86
   2 ?    0.1   0.1      0.82   8.7e+02      91     128 ..     132     182 ..     101     188 .. 0.65

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00097
                        AAA_22  7 ilvvtGesGtGKTtllrrll 26
                                  + +++Ge G+GK+t l++++
  gi|13541377|ref|NP_111065.1| 27 HNFIMGENGSGKSTFLKTIA 46
                                  6689************9876 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.82
                        AAA_22  91 v...........ielliiDEaqhlr...s.eealeeLrsllnlsrkgvqliLv 128
                                               +++l+ DE   +    s + ++++L +l +  r+ +  i+v
  gi|13541377|ref|NP_111065.1| 132 QrvavaraivsmPRILLMDEPFSMQderSrMSLISNLLDLID--RYEIDYIYV 182
                                   333333344666779999998777554425778888877777..777766665 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00029       0.3      96     121 ..      22      47 ..       4      60 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00029
                                   HCTTSEEEEECSTTSSHHHHHHHHCT CS
                   RsgA_GTPase  96 llkdktsvlvGqSGvGKStLinallp 121
                                    l+++  +++G+ G GKSt+++++++
  gi|13541377|ref|NP_111065.1|  22 SLSGRHNFIMGENGSGKSTFLKTIAG 47 
                                   5788999***************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       498  (0.0277762); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        92  (0.00513135); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 2053.70
//
Query:       gi|13541378|ref|NP_111066.1|  [L=250]
Description: cell wall biosynthesis glycosyltransferase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-23   83.1   0.1    2.6e-23   82.7   0.1    1.2  1  Glycos_transf_2  Glycosyl transferase family 2
    4.4e-12   46.4   0.0    1.4e-09   38.2   0.0    2.1  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
      2e-10   40.6   2.6    1.8e-05   24.3   0.4    2.3  2  Glyco_tranf_2_2  Glycosyltransferase like family 2
    1.3e-05   25.6   0.0    2.3e-05   24.8   0.0    1.4  1  Glyco_tranf_2_4  Glycosyl transferase family 2
    1.3e-05   25.2   0.0    2.2e-05   24.5   0.0    1.4  1  Glyco_trans_2_3  Glycosyl transferase family group 2


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.7   0.1   7.3e-27   2.6e-23       1     132 [.       7     130 ..       7     165 .. 0.90

  Alignments for each domain:
  == domain 1  score: 82.7 bits;  conditional E-value: 7.3e-27
                                   EEEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH--SS CS
               Glycos_transf_2   1 svviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglraatgd 81 
                                   svvi++ Ne+k+++++l+sl ++ +y++fe++vvDD S+D+t+ i++++    ++v++ir       + ++n g+ +++ +
  gi|13541378|ref|NP_111066.1|   7 SVVITIKNEAKNIQKLLDSLFNN-DYEHFEVVVVDDMSNDGTEGIVKKY----DKVKYIRTRCS--RGEGRNIGAMNSSFE 80 
                                   8**********************.*************************....79*******99..678899********* PP

                                   EEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SS CS
               Glycos_transf_2  82 yilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrv 132
                                    ilf D D +++ +w+  +v  l++ g  +++g++++++++++   r k +
  gi|13541378|ref|NP_111066.1|  81 NILFTDGDAIVSNGWIGGMVSVLNN-GFEIAIGKTVYTGKKRYIQDRVKIY 130
                                   *************************.999**********999988888775 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 !   38.2   0.0   3.8e-13   1.4e-09       5     223 ..       7     201 ..       4     207 .. 0.84

  Alignments for each domain:
  == domain 1  score: 38.2 bits;  conditional E-value: 3.8e-13
               Glyco_tranf_2_3   5 avlVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksralnealra 85 
                                   +v+++  ne++ + ++l+sl +++y  +evvvv+d+s ++t   ++    ++++  v+++ ++r  +s+g  r  n +  +
  gi|13541378|ref|NP_111066.1|   7 SVVITIKNEAKNIQKLLDSLFNNDYEHFEVVVVDDMSNDGTEGIVK----KYDK--VKYI-RTR--CSRGEGR--NIGAMN 76 
                                   89**************************************988776....5866..6988.445..6666666..999999 PP

               Glyco_tranf_2_3  86 vksdlvllvDdDtvvePdtlkrllqffltpkvgavgtpvfllnrstlvsalgalefaerhlrflaarralgvltlnGsgsl 166
                                    +++ +l+ D+D++v+ + +  ++ ++   + +++ ++      +++++   +++f+   +         +++      ++
  gi|13541378|ref|NP_111066.1|  77 SSFENILFTDGDAIVSNGWIGGMVSVL-NNGFEIAIGKTVYTGKKRYIQDRVKIYFNGIEI---------TAPS---VNLA 144
                                   9*************************9.888888877665555555666444445444443.........4544...7799 PP

               Glyco_tranf_2_3 167 irrevlkelegldplflltdDyelglrlrragfrtayvpgaavrevfpsslkayikq 223
                                   +  + +  l+g+d++f++++D++l lr+ + gf+  ++++ +v+   ++s+  + kq
  gi|13541378|ref|NP_111066.1| 145 YKKRAFFSLGGFDKRFVTAEDIDLNLRAAMSGFKFGFCNECVVYAKVRDSFISFLKQ 201
                                   9******************************************99998888877777 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 !   24.3   0.4   5.1e-09   1.8e-05       1     105 [.       7     102 ..       7     138 .. 0.80
   2 !   16.2   0.2   1.6e-06    0.0057     163     206 ..     138     179 ..     117     207 .. 0.75

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 5.1e-09
               Glyco_tranf_2_2   1 svviplraseerhyieerv..lqkakyydeeielivvddgSsekfleevssiidlnllv.ylkdeddkayslaaarNrGas 78 
                                   svvi ++++ ++  i+  +  l ++ y  e++e++vvdd S + +   v++      +v y++       s +  rN Ga 
  gi|13541378|ref|NP_111066.1|   7 SVVITIKNEAKN--IQKLLdsLFNNDY--EHFEVVVVDDMSNDGTEGIVKKY----DKVkYIRT----RCSRGEGRNIGAM 75 
                                   89**********..8877765556666..99*************66555544....44425333....58*********** PP

               Glyco_tranf_2_2  79 kaesdlvlFlDaDcfissDkfekilkl 105
                                   ++  + +lF D+D  +s   +  ++++
  gi|13541378|ref|NP_111066.1|  76 NSSFENILFTDGDAIVSNGWIGGMVSV 102
                                   ***************999887777774 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 1.6e-06
               Glyco_tranf_2_2 163 pssssilinrraflevGGyDErfrGhgaEDfdlllRlakaiksl 206
                                     s ++  ++raf  +GG+D rf   +aED dl lR a+   ++
  gi|13541378|ref|NP_111066.1| 138 APSVNLAYKKRAFFSLGGFDKRF--VTAEDIDLNLRAAMSGFKF 179
                                   345567789**************..99*******9988765555 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 !   24.8   0.0   6.4e-09   2.3e-05       1      57 [.      13      70 ..      13      91 .. 0.86

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 6.4e-09
               Glyco_tranf_2_4  1 rneadiLpeflahhlalgfdr..ilvydndstDgtrailkelpevkllhvdksyederr 57
                                  +nea+ +++ l+ + ++++++  ++v+d++s Dgt  i+k++++vk +++++s  +  r
  gi|13541378|ref|NP_111066.1| 13 KNEAKNIQKLLDSLFNNDYEHfeVVVVDDMSNDGTEGIVKKYDKVKYIRTRCSRGE-GR 70
                                  79*****************987799************************9998643.34 PP

>> Glyco_trans_2_3  Glycosyl transferase family group 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.0     6e-09   2.2e-05      75     137 ..     141     202 ..     128     245 .. 0.91

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 6e-09
               Glyco_trans_2_3  75 sgaflrrsalqevggwdgdessvsEDfdmglrlqrkGyrvrfvpeslvkekspltlraalrQr 137
                                   ++ +   +a+ ++gg+d + + ++ED d+ lr+++ G+++ f++e +v+ k+++++  +l+Q+
  gi|13541378|ref|NP_111066.1| 141 VNLAYKKRAFFSLGGFD-KRFVTAEDIDLNLRAAMSGFKFGFCNECVVYAKVRDSFISFLKQA 202
                                   67788889999******.7799***************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       663  (0.0369792); expected 358.6 (0.02)
Passed bias filter:                      548  (0.030565); 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: 0.56u 0.33s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 1522.74
//
Query:       gi|13541379|ref|NP_111067.1|  [L=62]
Description: hypothetical protein TVN0548 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      0.009   16.1   1.3      0.011   15.9   1.3    1.1  1  E3_UbLigase_RBR  E3 Ubiquitin Ligase RBR C-terminal 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 !   15.9   1.3   5.9e-07     0.011      29      77 ..       9      57 ..       1      60 [. 0.71

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 5.9e-07
               E3_UbLigase_RBR 29 kCkVleqketkegvkdeaCgkdvaegqaglCelHYkEyLvelinenkld 77
                                  +C+   +k +++ ++ ++   ++ + +  lC+ HYkEy  +  +e ++d
  gi|13541379|ref|NP_111067.1|  9 ECSNERFKTVPAELAKKVFSLKTDKTKVHLCKEHYKEYKKKTKEERDVD 57
                                  35555566777777888888888999999*********87776666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (62 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1706  (0.0951531); expected 358.6 (0.02)
Passed bias filter:                      640  (0.0356964); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.29s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 430.42
//
Query:       gi|13541380|ref|NP_111068.1|  [L=320]
Description: hypothetical protein TVN0549 [Thermoplasma volcanium GSS1]
Scores for complete 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-11   42.5   0.0      2e-10   40.7   0.0    1.7  1  Esterase       Putative esterase
    1.9e-05   24.5   0.0    2.7e-05   23.9   0.0    1.3  1  Abhydrolase_1  alpha/beta hydrolase fold
    0.00045   19.5   0.0    0.00066   19.0   0.0    1.2  1  Hydrolase_4    Serine aminopeptidase, S33
  ------ inclusion threshold ------
       0.19   11.9   0.0       0.34   11.0   0.0    1.4  1  GP3_package    DNA-packaging protein gp3


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 !   40.7   0.0   4.5e-14     2e-10      13     198 ..      30     272 ..      20     305 .. 0.84

  Alignments for each domain:
  == domain 1  score: 40.7 bits;  conditional E-value: 4.5e-14
                                   EE.CC.GGTTTEEEEEEE--T........THHCCHHHHHCHHCCCCHCCT.EEEEEECCCSS-TTTTTSBTTSBB.TTEEE CS
                      Esterase  13 yLPedyspgrkypvvylldGl........tgwdqnfrakelleslaregeiaeviivvvprggessfysdwdlgarfyena 85 
                                       d+s++ + p ++ l G+        + ++ ++   ++le+ a++    + +i+ +p+  +s  y          ++ 
  gi|13541380|ref|NP_111068.1|  30 I---DHSRNDRSPILIGLQGFfgtnrsfmNRYFNKVDFISVLEKIAEK-AENDGFIIALPDTMTS-LYG---------NQY 96 
                                   4...55999999999999999999999999999999999999876666.5678889999999988.344.........444 PP

                                   TTCCCCCCHCHHHHTHHHHHHHHHCSEECCCEEEEEETHHHHHHHHHHHCSTTTCCEEEEES--S-CC............. CS
                      Esterase  86 tegpgaeayetfltqeLlplldanfrtapdgravaGqSmGGlgALilalkhpdrFgsvssfSpivnps............. 153
                                    + p   +ye+f+ + +l +l +++ ++p    ++G S GG+gA +la++hpd+       S++v+               
  gi|13541380|ref|NP_111068.1|  97 INSPAVGNYEDFIVSDVLEYLFKRYGKRPV--GLFGKSSGGFGAYTLAVRHPDKI------SGFVDVAgdsgfeycylpdf 169
                                   5689999**********************9..9********************94......5555555555555567**** PP

                                   ................................................................HCHHHCTTCCHHHCC-C CS
                      Esterase 154 ................................................................namWgqeekeawqendp 170
                                                                                                      W++     w + dp
  gi|13541380|ref|NP_111068.1| 170 paaikyfrrygvlewytyvkskmnmspedmkvvnvlamsafyspdqeaemgiglpfdtrtgllkYDVWDK-----WRRLDP 245
                                   ***********************************************99999999999999998889966.....****** PP

                                   CCCHCHHCHTTSEEEEEEEECTTBCCCH CS
                      Esterase 171 vllakelsaslkalriyldvGtseddlg 198
                                   +++++++++ lk+  ++++vG+++d+ +
  gi|13541380|ref|NP_111068.1| 246 AFNISNNIDVLKDMAVFMQVGSRDDF-H 272
                                   ************************94.3 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.0   6.1e-09   2.7e-05      16     106 ..      64     157 ..      39     185 .. 0.81

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 6.1e-09
                                   GTTGHHHHHHHHT....TSEEEEEEETTSTTSSSTTTGB..CHHSHHHHHHHHHHHHHHCTTSSEEEEEETHHHHHHHHHH CS
                 Abhydrolase_1  16 waerglapaLakd....gfdvillDlrGvgySspapacin.ddygtasvaddldrildalgddkltlvGhSmGGmialaya 91 
                                   ++   + + +a++    gf + l+D + + y+   ++++   +y+++ v d+l+++  ++g +++ l G S GG+ a ++a
  gi|13541380|ref|NP_111068.1|  64 FIS--VLEKIAEKaendGFIIALPDTMTSLYGNQYINSPAvGNYEDFIVSDVLEYLFKRYGKRPVGLFGKSSGGFGAYTLA 142
                                   555..566666666667********************999*9999999********************************* PP

                                   HHHGGGEEEEEEESE CS
                 Abhydrolase_1  92 aeyperVkalvllga 106
                                    ++p++++++v +++
  gi|13541380|ref|NP_111068.1| 143 VRHPDKISGFVDVAG 157
                                   *********998777 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   1.5e-07   0.00066      64     108 ..     112     156 ..     102     213 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.5e-07
                   Hydrolase_4  64 afvekvkeehpelplfllGhSmGGliallyllrypdkvaglilsa 108
                                    ++e + ++++++p+ l+G S GG+ a +++ r+pdk++g++ +a
  gi|13541380|ref|NP_111068.1| 112 DVLEYLFKRYGKRPVGLFGKSSGGFGAYTLAVRHPDKISGFVDVA 156
                                   457788899*******************************99776 PP

>> GP3_package  DNA-packaging protein gp3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   7.7e-05      0.34      39      90 ..      35      85 ..      17      95 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 7.7e-05
                                  E-----HHHHHHHHT--HHHHHHHGG..SHHHHHHHHHHHHHHHHHHHHHHT CS
                   GP3_package 39 gdraptvtGLalyLgisrstlkeyekrkrefsetierikqivenqqiegala 90
                                   dr+p + GL  + g  rs +++y ++  +f  ++e+i +  en  +  al 
  gi|13541380|ref|NP_111068.1| 35 NDRSPILIGLQGFFGTNRSFMNRYFNKV-DFISVLEKIAEKAENDGFIIALP 85
                                  58999999******************76.**********9999987666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); 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:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 1963.04
//
Query:       gi|13541381|ref|NP_111069.1|  [L=111]
Description: nucleic acid binding protein [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.3e-12   46.8   0.0    2.6e-12   46.7   0.0    1.0  1  tRNA_bind  Putative tRNA binding domain


Domain annotation for each model (and alignments):
>> tRNA_bind  Putative tRNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.7   0.0   1.5e-16   2.6e-12       1      95 [.      15     108 ..      15     109 .. 0.95

  Alignments for each domain:
  == domain 1  score: 46.7 bits;  conditional E-value: 1.5e-16
                                   EEEEEEEEEEEETTSST.EEEEEEEESSSS.EEEEEESCTTTSTHHHHTTEEEEEETTSESEEETTEEESSEE-EEECCES CS
                     tRNA_bind   1 lrvGkvleaeehpnadk.LlvlkvdvGeee.prqivsgaknvyepeelvakkvvvvanlkpkklrGveSeGMilsaeelde 79 
                                   +r+G+++++  +p+a+k  ++lk+ +G+ + +++  ++++n+ + e+l+++ vv+v+n+ pk++  + S+ ++l++    +
  gi|13541381|ref|NP_111069.1|  15 IRIGRIISVDSFPEARKpAYKLKIYFGDDIgILNSSAQITNYKP-EDLLGRLVVAVVNFPPKRVANFISQVLVLGSI--TK 92 
                                   79****************************88999999999888.********************************..79 PP

                                   SCEEEEEESST--TTC CS
                     tRNA_bind  80 kevgilelpadveaGe 95 
                                   + v++l++++ + +G+
  gi|13541381|ref|NP_111069.1|  93 DGVKLLSVDEGAVPGD 108
                                   999*******999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       221  (0.0123264); expected 358.6 (0.02)
Passed bias filter:                      213  (0.0118802); 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: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 711.41
//
Query:       gi|13541382|ref|NP_111070.1|  [L=74]
Description: phosphoribosylformylglycinamidine synthase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      4e-19   68.5   0.2    4.9e-19   68.3   0.2    1.1  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 !   68.3   0.2   2.7e-23   4.9e-19       1      76 [.       2      71 ..       2      72 .. 0.94

  Alignments for each domain:
  == domain 1  score: 68.3 bits;  conditional E-value: 2.7e-23
                                  EEEEEEEE-TTS--HHHHHHHHHHHHTTHTTEEEEEEEEEEEEEEE-SSHHHHHHHHHHHHHHTTS-TTTEEEEEE CS
                          PurS  1 kakveVtlKkgvlDpqGkavkkalkslgyeevedvrvgkyieleleaedeeeaeeeveemceklLaNpviedyeie 76
                                  k+kveV++K+gv Dp++ ++ k+l+ lgy+e+++v++ k++ ++    +    eeev+++++k+L Npvi++y++e
  gi|13541382|ref|NP_111070.1|  2 KFKVEVSYKPGVEDPEALTLLKNLNILGYHEISNVSISKVYYFDAG--N----EEEVKQVADKILSNPVIHSYKVE 71
                                  689***************************************9987..3....468******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       500  (0.0278878); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 496.07
//
Query:       gi|13541383|ref|NP_111071.1|  [L=575]
Description: hypothetical protein TVN0552 [Thermoplasma volcanium GSS1]
Scores for complete 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-127  424.9  12.9   4.3e-127  424.8  12.9    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 !  424.8  12.9  2.4e-131  4.3e-127      16     563 ..      25     567 ..      11     568 .. 0.95

  Alignments for each domain:
  == domain 1  score: 424.8 bits;  conditional E-value: 2.4e-131
                       DUF2070  16 vsllliillalligllaflssklfgillfglpalvaflltlpvlrilggrltykrslflalltelivviisllaillsall 96 
                                     +++ i +++++++l   ++ ++++ l+  ++l+a++l+  + +++++++++krs++l++++++i+++++++  ++ a  
  gi|13541383|ref|NP_111071.1|  25 KYFIFPIATIAALDYLILKNI-YISVSLVVGTYLLAIFLDVIFSKFSRIIFPVKRSAYLNFVSLVIWSVFFWILFVIHA-- 102
                                   6788999999999***99999.8999999999***************999************************99998.. PP

                       DUF2070  97 qalvllalvlslalvfalrllvlvavsdesllkavlpaliqpllailllvlyfspesf..llllllslifalavylfivvv 175
                                   ++ +  +l+l++++++ +r+l+++++  ++ +k ++p++++ ++++l+++++f+++++  ++++l+sli+al +y++i+  
  gi|13541383|ref|NP_111071.1| 103 YRDIDVSLLLAVSSTTLFRFLIFYVFYPNDSIKELIPSMNYVYSMLLVFLFFFKNQYIlvVPFILSSLIYALSAYFLIRRS 183
                                   779999**********************************************77776511679****************** PP

                       DUF2070 176 drplkrnlgvsaldllsaFlahilegskel..Eeffeei.geeadvpvkvlsfrredg.ekallvvPniHPGPlgeiGGsn 252
                                   +  + ++++ s+ ++l++Fl++  + ++++   +ff++i   e+++pvk++ +r+++g  k+++v+P+iHPGP+g++G+sn
  gi|13541383|ref|NP_111071.1| 184 TNSFVKKYKASPSKILEFFLNSGKRLESNIsvKHFFDHIyRIERKIPVKIIQVRKKNGdIKVTMVFPYIHPGPFGTLGSSN 264
                                   ********************999888444445*******99**************************************** PP

                       DUF2070 253 Lpkilaerldel..vlvlHgtatHdfNlvserevekiveavkealeeleysskaskpvrvesgdvkllgqrfgdslllvit 331
                                   Lp +l++rl+e+  ++v+H+t+++d+N+  ++++++i+ a++ a +++ +++++s++++v  g++ ++ qrfg++ + +i 
  gi|13541383|ref|NP_111071.1| 265 LPARLSQRLPEFgdLMVFHTTTSNDNNCRGDEDIDNIAAAIRAASQKMIFTDRISRARKVVAGKYVVYLQRFGNFGFGAIV 345
                                   ********************************************************************************* PP

                       DUF2070 332 rapegiDDiplsvglsimaeakaegfedvllVDaHNsfseeagevlpgsedaeeliraaekalekleaaeeselkvgvars 412
                                   +++ ++DD+ l+ gl+++++ k++g++d++++Da+N+f+++a e     ++++  i+a+e+ +   +++++++ +vg+ars
  gi|13541383|ref|NP_111071.1| 346 PEKTPFDDVSLEEGLKVISHLKKSGADDFAVIDAQNNFTKKAPE----LKNCSTTIKAFEREFL--RNDPKYPARVGYARS 420
                                   **************************************999666....9************987..**************9 PP

                       DUF2070 413 etpkltpeeglGdlgiqvlvlevdgqktayvliDgNNmepglreeirealke.vdlevevmTTDtHvvngvslgynpvGek 492
                                     +      gl +lgiq++v+++ +   a+vl+D+NN++++l  + re++k+ v+ ++e++TTD+H+vn+  l+  p+G++
  gi|13541383|ref|NP_111071.1| 421 YREV----PGLAELGIQAIVFQTADRFDAVVLTDSNNVTTELIGKSREKVKNvVS-NLEIYTTDNHYVNASVLDVFPLGSR 496
                                   9997....9******************************************9888.**************888******** PP

                       DUF2070 493 vskdelielvlelvekAiadlepvevgyatervevkvfgedrfeelvstvnsvvsvakilaaallllaill 563
                                    s +e+ + ++++v++A +d+e+v+++++te + v++ ++++f++lvstv s+v++ak++a++++ +ai+ 
  gi|13541383|ref|NP_111071.1| 497 GSIEEISDIIADTVKRAKEDVEDVQIAMGTEYALVRMGEKNNFQNLVSTVFSSVKTAKYTALYTIPAAIAA 567
                                   ********************************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (575 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       975  (0.0543812); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.69u 0.31s 00:00:01.00 Elapsed: 00:00:00.51
# Mc/sec: 3371.43
//
Query:       gi|13541384|ref|NP_111072.1|  [L=229]
Description: hypothetical protein TVN0553 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score 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   13.9   0.6      0.039   13.9   0.6    1.7  2  DUF1706      Protein of unknown function (DUF1706)
      0.051   14.0   0.4       0.12   12.8   0.4    1.9  1  DUF234       Archaea bacterial proteins of unknown function
       0.59    8.7   5.9       0.67    8.6   5.9    1.1  1  Baculo_Y142  Baculovirus Y142 protein


Domain annotation for each model (and alignments):
>> DUF1706  Protein of unknown function (DUF1706)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.6   6.5e-06     0.039      88     161 ..      15      88 ..      11      91 .. 0.95
   2 ?   -2.3   0.1      0.63   3.8e+03      12      36 ..     117     141 ..     112     151 .. 0.59

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.5e-06
                                   HHHHHHHHHCTTS-HHHHHHHHHHHHHHHHHHHHHS-HHHHHSTTS-HHHS---HHHHHHHCTHHHHHHHHHHH CS
                       DUF1706  88 elnqkfyekyqdlsleelleelkesheellalieslsdeeLfekkgrkWtgkwtlgkyiqsntsspYknarkki 161
                                   +l  ++y++ +++++  + + l ++++e+++ ++   d++L +++  ++++++ l + i+s   s++++ ++ki
  gi|13541384|ref|NP_111072.1|  15 DLRSAMYAEQSHRKIMAIDQALYRRVREVIKELQVEADQQLKKQDIQEYMKTTRLIETIKSDFRSFFQRRYEKI 88 
                                   678899**************************************************************999998 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.63
                                   HHHHHHHHHHHHTTTTS-GGGT... CS
                       DUF1706  12 eaieknfekLiklidsipeeekkap 36 
                                   + i ++++++   +++i  ee +++
  gi|13541384|ref|NP_111072.1| 117 NLIMSEYDSFLPTLKDIAVEENQDQ 141
                                   5566666666666666666665444 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 ?   12.8   0.4     2e-05      0.12      10      49 ..      59      98 ..      49     147 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2e-05
                        DUF234 10 seielgeseevlekikeelneyvgkvFEelvrelllelnk 49
                                  +  e  +++ ++e+ik+++ ++++ ++E++v +++++ n+
  gi|13541384|ref|NP_111072.1| 59 DIQEYMKTTRLIETIKSDFRSFFQRRYEKIVSKAIYDINS 98
                                  444556677788********************99987665 PP

>> Baculo_Y142  Baculovirus Y142 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   5.9   0.00011      0.67     209     352 ..      82     227 ..      28     229 .] 0.66

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00011
                   Baculo_Y142 209 kavyrnvlskkvfttkiydvfdavekelktk.istiklvqrdyifd.atfPedLaelL.keyiskssiykvitkfvvee.l 285
                                   ++       +k++++ iyd+ +++   l  +   +i+ +    + +   f ++L+++  +e + +++   v +  v+ e +
  gi|13541384|ref|NP_111072.1|  82 QR-----RYEKIVSKAIYDINSEIISVLTEEeRGFIEKIHNLIMSEyDSFLPTLKDIAvEENQDQTTTTEVEKPMVISEpS 157
                                   22.....34677777777776655444433303344444433333346777799999879999999999999999999964 PP

                   Baculo_Y142 286 eel.knklvvdrytvdk..frklkikleiteqfpvmtdaessyifvpkeflqvketlnaffapklgvviL 352
                                   +   ++k + d+   +k  ++k  + + it+++p + +a  +yi+ +++++ + e +  ++  +   +iL
  gi|13541384|ref|NP_111072.1| 158 NPTsQEKPIKDQAQTEKkeIEKKDVLVMITQDLPPIAQADRNYILHANDLVYLSEDIARILEKRNSAIIL 227
                                   44414567788876665226777788999*****99***************9999887777666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1822  (0.101623); expected 358.6 (0.02)
Passed bias filter:                      538  (0.0300073); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.51
# Mc/sec: 1354.69
//
Query:       gi|13541385|ref|NP_111073.1|  [L=119]
Description: hypothetical protein TVN0554 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.9e-11   43.1   0.0    4.9e-11   42.8   0.0    1.1  1  Nitro_FeMo-Co  Dinitrogenase iron-molybdenum cofactor


Domain annotation for each model (and alignments):
>> Nitro_FeMo-Co  Dinitrogenase iron-molybdenum cofactor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.8   0.0   2.7e-15   4.9e-11      10      94 ..      16      99 ..       9     100 .. 0.96

  Alignments for each domain:
  == domain 1  score: 42.8 bits;  conditional E-value: 2.7e-15
                                  CC-SEEEEEEESSSCEEEEEEEE.GCCCTSSCSSTHHHHHHHHTT-SEEEESSSCHHHHHHHCTTTSEEEES-SSBHHHHHHH CS
                 Nitro_FeMo-Co 10 GrapyFaiyeveegevkivenrveeaadaegggggklaqllaeegvdvvivgkiGpralakleaagievykgaggtveealke 92
                                  G+++y +iy+v++g++ ++e+ +++a +a   +g ++ +++ ++gvd++i ++ G++ +  l+++ i+vy +++ +ve a+k+
  gi|13541385|ref|NP_111073.1| 16 GESQYVYIYDVKDGNADLLEKYENPAMHAYRAKGLQMLASAISRGVDAIILSELGRPGYSYLKDR-IKVYITPEVEVERAIKD 97
                                  899*******************999999999**********************************.****************9 PP

                                  HH CS
                 Nitro_FeMo-Co 93 vl 94
                                  v+
  gi|13541385|ref|NP_111073.1| 98 VI 99
                                  86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       322  (0.0179597); expected 358.6 (0.02)
Passed bias filter:                      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: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 756.73
//
Query:       gi|13541386|ref|NP_111074.1|  [L=127]
Description: 30S ribosomal protein S8e [Thermoplasma volcanium GSS1]
Scores for complete 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-35  121.6   4.9    2.8e-35  121.5   4.9    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 !  121.5   4.9   1.6e-39   2.8e-35       6     137 .]       5     126 ..       1     126 [. 0.97

  Alignments for each domain:
  == domain 1  score: 121.5 bits;  conditional E-value: 1.6e-39
                                   XCCCSEESSTEEXXXSSXXXCCSBXXXXXXXEES.SHEEEEEEETTCEEEEEEESESEEEEEETTTTEEEEEEEEEEECSS CS
                 Ribosomal_S8e   6 dskhkrkltGgkakllrkkrkielgrkekatklg.aervkvvrvrgGkrkkralrlkkanvthpeekvtkklkIlgVkknp 85 
                                   ++k+ +k tGg  k+ +kkr++elgr+++ tklg +   kv+r++gG++k  +  +++anv++  ek+ kk+kI++Vk+np
  gi|13541386|ref|NP_111074.1|   5 QGKSGKKPTGGNLKQAKKKRRFELGREPTLTKLGtKVERKVIRTMGGNSKAILFTADTANVYDIHEKKIKKVKIITVKENP 85 
                                   78999****************************967789****************************************** PP

                                   STCHHHHTTC--TTEEEEEESHHHHHHHHTTEEEEEEESEHHHHSSEEEEEE CS
                 Ribosomal_S8e  86 snneyvrlgvltKgaiievdvseLgevtqsgkvvAqvtsrPgqdGcvnavlL 137
                                   +n++yv+++++ Kg+ii+++++e           A vtsrPgqdG++na lL
  gi|13541386|ref|NP_111074.1|  86 ANSHYVQRNIINKGTIISTEIGE-----------AIVTSRPGQDGVINAKLL 126
                                   ***********************...........***************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       743  (0.0414412); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.22s 00:00:00.56 Elapsed: 00:00:00.38
# Mc/sec: 998.87
//
Query:       gi|13541387|ref|NP_111075.1|  [L=84]
Description: Signal recognition particle 19 kDa protein [Thermoplasma volcanium GSS1]
Scores for complete 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-07   30.0   0.1    9.6e-07   29.7   0.1    1.2  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 !   29.7   0.1   5.4e-11   9.6e-07       2      85 ..       5      77 ..       4      84 .] 0.82

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 5.4e-11
                                  EECCCCBTTS-CCCT--S-CCCSBSS--HHHHHHHHHHCTSCEEEEEEECTTSSTTCCEEEEEC-..........SS-CHHHH CS
                         SRP19  2 iYPvYldskktrkeGRrvpkelavenPtaqeiaealkalglevvvepeksyPrdwanpGrVrvklkedgkevnekiknkkell 84
                                  +Y +Y++++  r++GRr+pk+   +n t + ++ +l++ +++++v  e +yPr  ++p    v  +           +k+++l
  gi|13541387|ref|NP_111075.1|  5 LYLQYFNKDLPRSKGRRLPKKI-LQNFTEERLRSILEEARISYEVR-ECRYPRVPWQPSKMYVLDS---------NLKKTSIL 76
                                  799****************975.89********************9.9******999988877643.........23444444 PP

                                  H CS
                         SRP19 85 k 85
                                  k
  gi|13541387|ref|NP_111075.1| 77 K 77
                                  4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (84 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); 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: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 591.12
//
Query:       gi|13541388|ref|NP_111076.1|  [L=327]
Description: DNA primase large subunit [Thermoplasma volcanium GSS1]
Scores for complete 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-35  120.3   0.5    2.6e-34  118.8   0.5    1.7  1  DNA_primase_lrg  Eukaryotic and archaeal DNA primase, large s


Domain annotation for each model (and alignments):
>> DNA_primase_lrg  Eukaryotic and archaeal DNA primase, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.8   0.5   1.5e-38   2.6e-34       3     266 .]     117     319 ..     115     319 .. 0.86

  Alignments for each domain:
  == domain 1  score: 118.8 bits;  conditional E-value: 1.5e-38
                                   EEEEHHHHHHHTT-G........GS-EETTEEEE-HHHHHHHHHHHHHHHHHH..........HHGGGSSS---HHHHHHH CS
               DNA_primase_lrg   3 ykvpfedvldlvkrr........rvllkkGyaylpkeeleslllekfrkrlekalestkeslpeleeeikederekleell 75 
                                   + + + d++++++r         ++ + kG++y +k+ ++++l+e f +++ k ++s+++ +++    + +d+ + + el 
  gi|13541388|ref|NP_111076.1| 117 FEIGVFDFVKYASRVtgsqyrlsNQSVIKGIVYCQKDVAIKILRESFVSNMFKVIDSIDQTTASP---VLSDQTDSINELR 194
                                   5677778888888445577889999999********************************99966...5677775566666 PP

                                   CT--.............TTSSTTGGSHHHHTT--HHHHCCHHHHCCCSS--CHHHHHHHHHHHHCT--CHHHHCCCHCHST CS
               DNA_primase_lrg  76 ealsesyvaedvqeeedskisaknidklakesfPpCmrelleglkknghlkhegrlqltlFlkdiglsldeilelwkeaft 156
                                   e  +            +s   + +i++   ++fPpCm+e++++l ++ + +h grl++++Fl+++g+++dei+e++++a  
  gi|13541388|ref|NP_111076.1| 195 EFYK------------KSVYAKLTIGRGNTKAFPPCMKEIIRNLHEGINVPHMGRLAIASFLHKVGYTEDEIVEYFRNA-- 261
                                   6655............3334444579999*************************************************9.. PP

                                   ..HHHHHH.HTHCHCHHHCC-STT--------HHHHHHS....TT---S-HHHH.HHHHHHHHHHTT..HHHHHHHHHHHH CS
               DNA_primase_lrg 157 rteekFdk.eyrynirhnyGkegkrtnyspysCekiltkpppgkgdahgCpfrhdpdklktlLqeyglseediedilesvk 236
                                      ++Fd+  +ry+i+h  G e ++++ysp++Ce++          +h C++  d+dkl                      
  gi|13541388|ref|NP_111076.1| 262 ---PDFDEsITRYQIKHLSG-EISGVEYSPPKCETM--------RSNHLCFM--DDDKL---------------------- 306
                                   ...*****9***********.***************........56777*77..99999...................... PP

                                   TT.HHHHHHHHHHHHHS-TTT-SSCHHHCC CS
               DNA_primase_lrg 237 egeyqvaCtkvFelthkcerdeikhPlqYy 266
                                                    c++d +khPl+Yy
  gi|13541388|ref|NP_111076.1| 307 -----------------CHQDWMKHPLTYY 319
                                   .................8888888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       789  (0.0440069); expected 358.6 (0.02)
Passed bias filter:                      550  (0.0306766); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.64u 0.35s 00:00:00.99 Elapsed: 00:00:00.55
# Mc/sec: 1797.57
//
Query:       gi|13541389|ref|NP_111077.1|  [L=360]
Description: proline dipeptidase [Thermoplasma volcanium GSS1]
Scores for complete 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  236.9   0.1    2.3e-70  236.5   0.1    1.1  1  Peptidase_M24  Metallopeptidase family M24
    6.6e-11   43.0   0.0    1.2e-10   42.2   0.0    1.4  1  Creatinase_N   Creatinase/Prolidase N-terminal domain
  ------ inclusion threshold ------
      0.035   13.8   0.1      0.067   12.9   0.1    1.5  1  LUD_dom        LUD 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 !  236.5   0.1   3.8e-74   2.3e-70       2     208 ..     140     341 ..     139     342 .. 0.98

  Alignments for each domain:
  == domain 1  score: 236.5 bits;  conditional E-value: 3.8e-74
                                   HHHHHHHHHHHHHHHHHHHHHTTCBHHHHHHHHHHHHHHHTTTCEESSSSEEEEGGGGGSTTTBCSSSB--TTEEEEEEEE CS
                 Peptidase_M24   2 lirkaariasaaleavleaikpgvterelaaeieattlkrhgarglafppivasgenaavlhytpndrvlkegdlvlidag 82 
                                   ++++aa+i s++l  vl+ +k+gvte+e+a +i ++ + r+ga g++f++iva+g+na+++hy+p++ +lk+gd+vl+d+g
  gi|13541389|ref|NP_111077.1| 140 KLKEAAKIGSEILPDVLNDLKEGVTEYEVASKIVYY-MMRNGASGPSFDTIVAFGQNASMPHYSPGKAKLKKGDFVLMDYG 219
                                   789**************99***************99.7899**************************************** PP

                                   EEETTEEEEEEEEEECSSGSHHHHHHHHHHHHHHHHHHHC-STTSBHHHHHHHHHHHHHHTTBCCGBSSCSEEEESSSSSE CS
                 Peptidase_M24  83 aeydgyasDitrTvlvGkftpeqrelyeavleaqeaaikavkpGvtlseidaaarevlesaglakffphglGHgvGlevhd 163
                                   a+y+gy+sDitrTv++Gk ++eq+e+y +v++aqea+++a++ G++++++daaar+v+ s +++  f h+lGHgvGlevhd
  gi|13541389|ref|NP_111077.1| 220 AKYEGYCSDITRTVVFGKASEEQKEMYYTVKKAQEAGMNAIRSGANGKDVDAAARNVIDSTKYKGRFIHSLGHGVGLEVHD 300
                                   ************************************************************99*999*************** PP

                                   EEEEESSSTTCSSB--TTBEEEEEEEEEEETTTEEEEEBEEEEEE CS
                 Peptidase_M24 164 egpsvsresndgrkleeGmvftiEpgiyfapgeggvriedtvlvt 208
                                     p +s  ++ + +l+e mv+t+Epg+y +pg+ggvried+v+v+
  gi|13541389|ref|NP_111077.1| 301 H-PALS--PSLDLPLKESMVVTVEPGVY-VPGVGGVRIEDDVVVK 341
                                   9.**99..789*****************.9**************8 PP

>> Creatinase_N  Creatinase/Prolidase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.2   0.0     2e-14   1.2e-10      23     131 ..      28     131 ..      10     132 .. 0.84

  Alignments for each domain:
  == domain 1  score: 42.2 bits;  conditional E-value: 2e-14
                                   HHHHHHHSS...-SSSEEEEEEESSCEEEEEECTTHHHHHHHH.TTSEEEEESTHSSHHHHHHHHHHHHT-EEEE-TTSSB CS
                  Creatinase_N  23 enlrYltGfatetgsrglalvvtadgalllvdalryteaaeesatveevveyddpvealadllkellesekrvgveldalt 103
                                     + Y+t +++  ++  +++ v++d+a++++ +l+++ a+      ++v+ ++    +++++l++ll+++++vg++ ++l+
  gi|13541389|ref|NP_111077.1|  28 PTFTYITQTTKGIFEGSALI-VKKDKATIVTSQLEEEAARST---GMDVYIFKN-GTEFQNILRDLLKDVNTVGLNYNSLS 103
                                   6789*****55555555555.***********7776655555...599999998.9************************* PP

                                   HHHHHHHHHHCTTSEEEETHHHHHHHHS CS
                  Creatinase_N 104 vafyealkealpdaelvdaselieelRv 131
                                   +++y+++   +pd+e+ d+s+ i e R 
  gi|13541389|ref|NP_111077.1| 104 LSSYKMFLRIIPDKEFLDVSASILEARK 131
                                   **********************999996 PP

>> LUD_dom  LUD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   1.1e-05     0.067       5      64 ..      62     139 ..      59     169 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.1e-05
                       LUD_dom   5 ienleangaevyyaktaeealelilellkeksv.vseggstdlgeigl.................apalhsgreevld 64 
                                   +e++++ g++vy++k++ e ++++++llk+ ++ ++   s +l  + +                  +a + ++ee l+
  gi|13541389|ref|NP_111077.1|  62 EEAARSTGMDVYIFKNGTEFQNILRDLLKDVNTvGLNYNSLSLSSYKMflriipdkefldvsasiLEARKVKNEEELK 139
                                   578999************************977577888888888888656556555555554444444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       651  (0.0363099); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.51
# Mc/sec: 2139.09
//
Query:       gi|13541390|ref|NP_111078.1|  [L=233]
Description: DNA repair and recombination protein RadB [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-23   82.8   0.1    2.9e-23   82.4   0.1    1.1  1  Rad51     Rad51
      3e-08   33.5   0.2    4.3e-08   32.9   0.2    1.3  1  RecA      recA bacterial DNA recombination protein
    5.3e-07   29.2   2.6    0.00048   19.6   0.3    2.1  2  ATPase    KaiC
    8.9e-06   25.4   0.0    1.3e-05   24.9   0.0    1.2  1  AAA_25    AAA domain
     0.0072   16.0   0.0       0.01   15.5   0.0    1.2  1  Zot       Zonular occludens toxin (Zot)
  ------ inclusion threshold ------
      0.014   15.5   0.0      0.021   14.9   0.0    1.4  1  CbiA      CobQ/CobB/MinD/ParA nucleotide binding domain
      0.018   14.8   0.0      0.032   14.0   0.0    1.3  1  AAA_24    AAA domain
      0.025   15.1   0.0      0.043   14.4   0.0    1.5  1  AAA_18    AAA domain
      0.028   14.3   0.0      0.048   13.6   0.0    1.3  1  AAA_31    AAA domain
      0.041   12.8   0.0      0.056   12.4   0.0    1.1  1  AAA_10    AAA-like domain
      0.076   12.8   0.0        0.1   12.4   0.0    1.3  1  CLP1_P    mRNA cleavage and polyadenylation factor CLP1 P-loo
      0.094   12.0   0.0       0.14   11.5   0.0    1.3  1  MipZ      ATPase MipZ
       0.11   12.4   0.2       0.19   11.6   0.2    1.3  1  NACHT     NACHT domain
       0.12   12.4   0.1       0.89    9.6   0.0    2.0  2  DUF87     Helicase HerA, central domain
       0.15   11.5   0.0       0.22   10.9   0.0    1.2  1  ParA      NUBPL iron-transfer P-loop NTPase


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 !   82.4   0.1   2.4e-26   2.9e-23      13     253 ..       7     226 ..       1     228 [. 0.87

  Alignments for each domain:
  == domain 1  score: 82.4 bits;  conditional E-value: 2.4e-26
                                   HHSS-EE--S-HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHHHHHHTTS-TTTS--SSEEEEEESSS---GGGGHHHHH CS
                         Rad51  13 rsellqlttGskklDelLgGGietgsiteifGefrsGktqlchtlcvtvqlplelgGgegkavyidtegtfrperlveiae 93 
                                   ++++ +l  G   +D l +GG+e+g iteifGe +sGk+ +c+  +    l        +k+v+id+eg f +er ++i +
  gi|13541390|ref|NP_111078.1|   7 QEKIEKLPLGVACIDGLTNGGLEAGIITEIFGEGGSGKSNVCML-AACSALR-----LGKKVVFIDSEG-FSSERFLSICK 80 
                                   677888999999******************************95.4444454.....359*******96.9********84 PP

                                   HTT--HHHHGGGEEEEE--STTHHHHHHHHTHHHHHHS.-EEEEEEETTTGGGCH-------THHHHHHHHHHHHHHHHHH CS
                         Rad51  94 rykldkeevlenvayaRaytiehqeellqqaaallaed.kfallivDsvtalyRtdfsgrgelakRqqklgkllrtLrkla 173
                                      +d+    ++ ++ R+++ ++qe  +++ ++ + +d  ++l i+Ds    +R + +g  +  +R   + + l+ L+ +a
  gi|13541390|ref|NP_111078.1|  81 ---ADN----SKLKVIRVFSLDDQEVAITKFSKIIEKDaSYGLFILDSFSEFFRLERTG--DNQSRVIDFQRQLSLLSSIA 152
                                   ...555....466788*************99999987637**************99776..5579**************** PP

                                   HHH--EEEEEEE-------.------------HHHHHHHH-SEEEEEEE-STTEEEEEEES-SSS-S-E.EEEEEETTEEE CS
                         Rad51 174 defevavvitnqvvaqvdgqaalfsadpkkPigGlvlahasttRlalrkgkgeeRivkvvdsPnlpele.avfaigeeGie 253
                                    + ++ v+itnq+ +++        +    P gG v+ h ++    l +  + +R + v++  ++ e + + f i ++Gi 
  gi|13541390|ref|NP_111078.1| 153 AKRKIPVLITNQIYQDIAN------G-DILPFGGYVVDHIMKAIYRLERLPDGRRKMTVMKHRSVKEGNsVEFRIVQDGIS 226
                                   *************999877......4.468************999999999999999999999998865278999999995 PP

>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.9   0.2   3.6e-11   4.3e-08      28     194 ..       7     170 ..       2     233 .] 0.71

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 3.6e-11
                                   -----EE--S-HHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHTT--EEEEESS----HHHHHHTT--GGG- CS
                          RecA  28 klkvetissGslaldialGiGGlpkGriieiyGpessGkttlalhaiaeaqkkggvaafidaehaldpkyakklGvdidel 108
                                   ++k+e ++ G   +d  l  GGl  G i+ei+G   sGk+ +++ a ++a + g+ ++fid+e     ++      d  +l
  gi|13541390|ref|NP_111078.1|   7 QEKIEKLPLGVACIDG-LTNGGLEAGIITEIFGEGGSGKSNVCMLAACSALRLGKKVVFIDSEGFSSERFLSICKADNSKL 86 
                                   5789999999999995.777*******************************************988888877777777766 PP

                                   EE...E--SSHHHHHHHHHHHHT.TT--SEEEEE-TTT---STT-----------HHHHHHHHHHHHHHHHHTTT--EEEE CS
                          RecA 109 lv...sqpdtGeqaleiadalvr.sgaidlivvdsvaalvpkaeieGemgdskvglqarlmsqalrkltgaisksntvvif 185
                                    v      d  e a+    ++++  ++  l ++ds + +  + e  G+ +   +  q +l       l++  +k ++ v+ 
  gi|13541390|ref|NP_111078.1|  87 KVirvFSLDDQEVAITKFSKIIEkDASYGLFILDSFSEFF-RLERTGDNQSRVIDFQRQL-----SLLSSIAAKRKIPVLI 161
                                   54111557888999887777775157789******99875.8899999988888887554.....4567777788888888 PP

                                   EEE------ CS
                          RecA 186 inqirekiG 194
                                    nqi + i 
  gi|13541390|ref|NP_111078.1| 162 TNQIYQDIA 170
                                   888888775 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.3     4e-07   0.00048       2      57 ..      14      68 ..      13      80 .. 0.88
   2 !    9.9   0.1   0.00037      0.44     140     225 ..     141     226 ..      95     231 .. 0.73

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 4e-07
                        ATPase  2 ktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtve 57
                                  + g+  +D +++gG+  g ++ i Ge G+GK+ +++  + +   + g+++vf+  e
  gi|13541390|ref|NP_111078.1| 14 PLGVACIDGLTNGGLEAGIITEIFGEGGSGKSNVCMLAACSA-LRLGKKVVFIDSE 68
                                  568999*****************************9877766.666******9665 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00037
                        ATPase 140 aReilrqlvrvlkklgvTailvsekssseeaaggygveefivdgvivLdlkeiee.elvRtleivkmRgtkhskkehpfeI 219
                                   + ++l  l ++ +k+++  ++++++ ++  +        ++vd +++  +++++  + +R + ++k R+ k   + ++f I
  gi|13541390|ref|NP_111078.1| 141 FQRQLSLLSSIAAKRKIPVLITNQIYQDIANGDILPFGGYVVDHIMKAIYRLERLpDGRRKMTVMKHRSVKEG-NSVEFRI 220
                                   44566667777799999999999998855555555556677777777777776667999**********9965.5678999 PP

                        ATPase 220 teegik 225
                                    ++gi+
  gi|13541390|ref|NP_111078.1| 221 VQDGIS 226
                                   999986 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.0   1.1e-08   1.3e-05      23     186 ..      21     162 ..       6     165 .. 0.79

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 1.1e-08
                        AAA_25  23 rwlvkgllpagelallaGapgtGKttlaldlalava.tGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgealrddar 102
                                   + l  g l ag ++ ++G +g+GK+ +++  a++ + +Gk           kV++++ E+      +R+  +++a  d+++
  gi|13541390|ref|NP_111078.1|  21 DGLTNGGLEAGIITEIFGEGGSGKSNVCMLAACSALrLGK-----------KVVFIDSEGFS---SERFLSICKA--DNSK 85 
                                   566777889999***************9999999995655...........9**********...9999999988..4677 PP

                        AAA_25 103 llvldlagveslpLfakdrggtlltadvdaleaaieevegvrlvviDplsralggdensnsd...v..galvealeriarr 178
                                   l v+         +f++d+++ ++t +     + ie+ + ++l ++D++s++++ + + +++   +  ++ ++ l +ia++
  gi|13541390|ref|NP_111078.1|  86 LKVIR--------VFSLDDQEVAITKF----SKIIEKDASYGLFILDSFSEFFRLERTGDNQsrvIdfQRQLSLLSSIAAK 154
                                   77765........47778888778765....5666666779**************66666554442458888888888888 PP

                        AAA_25 179 tgaavllv 186
                                    ++ vl++
  gi|13541390|ref|NP_111078.1| 155 RKIPVLIT 162
                                   87777765 PP

>> Zot  Zonular occludens toxin (Zot)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   8.7e-06      0.01       7     106 ..      38     138 ..      33     170 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 8.7e-06
                           Zot   7 GapGsgKtsgavkkdllpalkegRkiit.nidGlrlerieqvlgekvstarlirid.npegaetlkefakwatid.kgall 84 
                                   G++GsgK+ + +   +  al+ g+k+++ + +G+  er+  + + + s  ++ir+    +++  + +f k    d   +l 
  gi|13541390|ref|NP_111078.1|  38 GEGGSGKSNVCMLA-ACSALRLGKKVVFiDSEGFSSERFLSICKADNSKLKVIRVFsLDDQEVAITKFSKIIEKDaSYGLF 117
                                   99******988877.88899988777776************99999998889998867778888889988888777889** PP

                           Zot  85 viDEcqeifpvrakegrkdpev 106
                                   ++D   e+f  +++ g ++  v
  gi|13541390|ref|NP_111078.1| 118 ILDSFSEFFRLERT-GDNQSRV 138
                                   **********9999.4544433 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 ?   14.9   0.0   1.8e-05     0.021       6      69 ..      38     154 ..      33     173 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.8e-05
                                   SSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCH..HTTEB-HHHH.............................. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxx.............................. RF
                          CbiA   6 tkGGvGKTtlaanLaralarrglrVllvDaDpqannlai..leglendiep.............................. 54 
                                   + GG+GK+ ++   a++  r g++V+ +D    ++  ++        + ++                              
  gi|13541390|ref|NP_111078.1|  38 GEGGSGKSNVCMLAACSALRLGKKVVFIDSEGFSSERFLsiC-----KADNsklkvirvfslddqevaitkfskiiekdas 113
                                   78**********99999999*********7766665553321.....1111234456677777777777777777777777 PP

                                   ..........................CCHCCCHHHHHHCHC CS
                                   ..........................xxxxxxxxxxxxxxx RF
                          CbiA  55 ..........................dlkrllellealgkk 69 
                                                             d +r l ll+++  k
  gi|13541390|ref|NP_111078.1| 114 yglfildsfseffrlertgdnqsrviDFQRQLSLLSSIAAK 154
                                   77777777777777777777777777777777777777766 PP

>> AAA_24  AAA 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     0.032       7      80 ..      36     128 ..      31     140 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.6e-05
                        AAA_24   7 iyGpsgiGKTtlakel.......gpkplfidtek.Glksldadkfpdie.............swedfldevvelaaelady 66 
                                   i+G+ g+GK+ ++  +       g+k++fid e+ ++ +     + ++                e  + ++ ++ +++a y
  gi|13541390|ref|NP_111078.1|  36 IFGEGGSGKSNVCMLAacsalrlGKKVVFIDSEGfSSERFL--SICKADnsklkvirvfsldDQEVAITKFSKIIEKDASY 114
                                   89*********999999999************996554422..22222233466777885555555666666669999*** PP

                        AAA_24  67 ktlviDtideleel 80 
                                      ++D+ +e+ +l
  gi|13541390|ref|NP_111078.1| 115 GLFILDSFSEFFRL 128
                                   *********99886 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   3.6e-05     0.043       3      95 ..      36     135 ..      35     171 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.6e-05
                        AAA_18   3 ltGtpGvGKttlakeLskrlgf..gvnlrdvakenglllevdpe......aldeskrldedkldklldaleenssaleegk 75 
                                   + G  G+GK+ ++   + +  +  g ++ ++ +e+ +++ +         +l+  +++  d ++++++++ +++++ ++ +
  gi|13541390|ref|NP_111078.1|  36 IFGEGGSGKSNVCMLAACSA-LrlGKKVVFIDSEGFSSERFLSIckadnsKLKVIRVFSLDDQEVAITKFSKIIEKDASYG 115
                                   66777*********996664.344666666666555555555555555599************************99**** PP

                        AAA_18  76 nlvidghlaeleseaakdik 95 
                                     ++d++ + ++ e+  d++
  gi|13541390|ref|NP_111078.1| 116 LFILDSFSEFFRLERTGDNQ 135
                                   *********99999877766 PP

>> AAA_31  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     0.048       9      85 ..      38     120 ..      31     147 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4e-05
                        AAA_31   9 qKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQanattglgiekneiektlyevl......ieeknikeaiiktkvenldl 83 
                                     GG GK+  ++  a++  +lgkkv  +D    ++  +   ++ ++ + ++++v+      +  ++ +++i k+ +  l +
  gi|13541390|ref|NP_111078.1|  38 GEGGSGKSNVCMLAACSALRLGKKVVFIDSEGFSSERFLSICKADNSKLKVIRVFslddqeVAITKFSKIIEKDASYGLFI 118
                                   57*****987765555556**********9988777775544666666777777543332233344445555554555555 PP

                        AAA_31  84 ip 85 
                                   + 
  gi|13541390|ref|NP_111078.1| 119 LD 120
                                   55 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   4.6e-05     0.056      25      88 ..      35      99 ..      23     120 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.6e-05
                        AAA_10 25 liiGdlGnGKSvlakllvlyisllggkaliiDpkke.rekfketlpeiakkinvvtLdseeeneg 88
                                   i G+ G GKS +  l+   ++ lg+k+++iD      e+f    ++  +k++v+++ s +++e+
  gi|13541390|ref|NP_111078.1| 35 EIFGEGGSGKSNVCMLAACSALRLGKKVVFIDSEGFsSERFLSICKADNSKLKVIRVFSLDDQEV 99
                                  689*****************************998756668888888788888888866666655 PP

>> CLP1_P  mRNA cleavage and polyadenylation factor CLP1 P-loop
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   8.6e-05       0.1       1      30 [.      38      67 ..      38     110 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 8.6e-05
                        CLP1_P  1 GpkdsGKSTlarlLlNyalrkgrkpvyvDl 30
                                  G+  sGKS ++ l +  alr g+k+v++D 
  gi|13541390|ref|NP_111078.1| 38 GEGGSGKSNVCMLAACSALRLGKKVVFIDS 67
                                  6778*************************6 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00011      0.14       9      38 ..      39      68 ..      33     120 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00011
                                  STTSSHHHHHHHHHHHHHTTT--EEEEE-- CS
                          MipZ  9 kGGsGksttavhvavaLlkkGarvaaidld 38
                                   GGsGks +++  a + l+ G++v  id +
  gi|13541390|ref|NP_111078.1| 39 EGGSGKSNVCMLAACSALRLGKKVVFIDSE 68
                                  59**********************988743 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.2   0.00016      0.19       6     124 ..      37     160 ..      33     165 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00016
                                   EC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEE....EETTTTTTS-.....-HCHHHCCCCTS--SSS-CCHHHHCCSC CS
                         NACHT   6 qGeaGsGKTtLlqklalawaegklpqgafklvFf....lslrelsrsgna..rsladllfsqlpepaapvsevwavllelp 80 
                                    Ge GsGK+     +++++a + l  g+ k+vF     +s+ ++  +++a    l+ + +  l++ + +++++ +++ + +
  gi|13541390|ref|NP_111078.1|  37 FGEGGSGKS----NVCMLAACSALRLGK-KVVFIdsegFSSERFLSICKAdnSKLKVIRVFSLDDQEVAITKFSKIIEKDA 112
                                   588899998....467777777777775.777765555667777777777866777777788999999999999999999* PP

                                   CCEEEEEE-STT-SS-TCH................HHHHHCTTTTT--EEE CS
                         NACHT  81 erlLlilDglDelvtdlgq.......kekqpvrtlLselirkkllpeasll 124
                                      L+ilD++ e+ +  +         + q+   lLs++  k   ++ ++l
  gi|13541390|ref|NP_111078.1| 113 SYGLFILDSFSEFFRLERTgdnqsrvIDFQRQLSLLSSIAAK---RKIPVL 160
                                   *************99766677776665566666666655555...555555 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00074      0.89      28      62 ..      36      69 ..      34     102 .. 0.82
   2 ?    0.3   0.0      0.53   6.3e+02      47      83 ..     107     143 ..     101     161 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00074
                         DUF87 28 ilgsTGsGKSntvavLleellekkgatililDpHG 62
                                  i+g+ GsGKSn   +   ++l + g +++ +D  G
  gi|13541390|ref|NP_111078.1| 36 IFGEGGSGKSNVCMLAACSAL-RLGKKVVFIDSEG 69
                                  9***********999999999.9999999999877 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.53
                         DUF87  47 lle.kkgatililDpHGEYgkalekllsekvkvitpsp 83 
                                   ++e + ++ + ilD  +E++++  +++ ++ +vi+ ++
  gi|13541390|ref|NP_111078.1| 107 IIEkDASYGLFILDSFSEFFRLE-RTGDNQSRVIDFQR 143
                                   55423344899999999999999.88888888888764 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 ?   10.9   0.0   0.00019      0.22       9      57 ..      36      82 ..      30     113 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00019
                          ParA  9 lSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgveeek 57
                                  + g GG GKS v +  A++  + g+kv  +D    G+s  r+l + +++
  gi|13541390|ref|NP_111078.1| 36 IFGEGGSGKSNVCMLAACSALRLGKKVVFIDS--EGFSSERFLSICKAD 82
                                  5699***********************99886..588888888876654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 1451.52
//
Query:       gi|13541391|ref|NP_111079.1|  [L=335]
Description: flap endonuclease-1 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    6.1e-26   90.6   0.0    1.3e-25   89.6   0.0    1.6  1  XPG_I       XPG I-region
    3.3e-19   69.2   0.0    7.3e-19   68.1   0.0    1.5  1  XPG_N       XPG N-terminal domain
     0.0002   21.9   0.3     0.0002   21.9   0.3    1.9  2  5_3_exonuc  5'-3' exonuclease, C-terminal SAM fold
  ------ inclusion threshold ------
       0.13   11.7   0.0       0.24   10.8   0.0    1.4  1  DUF5321     Family of unknown function (DUF5321)


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 !   89.6   0.0   2.8e-29   1.3e-25       2      94 .]     140     234 ..     139     234 .. 0.92

  Alignments for each domain:
  == domain 1  score: 89.6 bits;  conditional E-value: 2.8e-29
                                   HHT--EEE-SS-HHHHHHHHHHTTSSSEEE-SSSHHHHTT-SEEEESTT..ECECTT....EEECEEEEEEHHHHHHHHT- CS
                         XPG_I   2 lmgipyvvApgEAEAqcayLqkkglvdaviseDsDlllFGapkvlrnls.kkkskkk..kekekkkvevidlekvlkelgl 79 
                                    mgipyv+Ap+E+EAq++y+++k ++d+vis+D+D+llFGa+k+lrn+   +++k    + ++++++e++ l++vlk+ g+
  gi|13541391|ref|NP_111079.1| 140 YMGIPYVDAPSEGEAQASYMTRK-DADGVISQDYDCLLFGAKKILRNFAiYGRRKVPrkNVYRTVYPEYVMLDEVLKKNGI 219
                                   69******************987.79**********************96555444477889999**************** PP

                                   -HHHHHHHHHHHCET CS
                         XPG_I  80 treqlidlaillgcD 94 
                                   +++qli++ il+g+D
  gi|13541391|ref|NP_111079.1| 220 NQDQLIEIGILVGTD 234
                                   *************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 !   68.1   0.0   1.6e-22   7.3e-19      17     100 ..      12     100 ..       4     101 .. 0.93

  Alignments for each domain:
  == domain 1  score: 68.1 bits;  conditional E-value: 1.6e-22
                                   EEEEGGGGTTEEEEEEHHHHHHHHHHHSE.ETTEE-BS.....-HHHHHHHHHHHHHHHTTEEEEEEE--S--GGGHHHHH CS
                         XPG_N  17 rsvsiealegkklaiDaslwlyrfliavreqlgnalen.....tshlmglfsrllrlldfgikPifVFdgkapdlkkeele 92 
                                   ++ s++   +++ aiD +  ly++l +vr+ +g+ l+      tshl g+f+r++ l+++gikPifVFdgk+ +lk+ +le
  gi|13541391|ref|NP_111079.1|  12 HQTSLKDQANQVFAIDTYNILYQLLSNVRQYDGTPLMDssgnvTSHLYGIFYRTVNLVENGIKPIFVFDGKPSPLKNRTLE 92 
                                   4678899999************************99999999*************************************** PP

                                   HHHHHHHH CS
                         XPG_N  93 krserrqe 100
                                    r+ ++++
  gi|13541391|ref|NP_111079.1|  93 IRQLAKEK 100
                                   **998876 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 ?   -2.7   0.1         2   9.1e+03      52      63 ..      97     108 ..      88     124 .. 0.51
   2 !   21.9   0.3   4.5e-08    0.0002       4      50 ..     222     266 ..     219     282 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2
                    5_3_exonuc  52 kekklkekLeen 63 
                                   +++k+k++Lee+
  gi|13541391|ref|NP_111079.1|  97 AKEKAKAELEEA 108
                                   333333333332 PP

  == domain 2  score: 21.9 bits;  conditional E-value: 4.5e-08
                    5_3_exonuc   4 eqiidlkaLvGDssDnipGvpgiGektAakLlkeygsleeilenlde 50 
                                   +q+i++  LvG   D  +G++giG+k+A +L+k+ g+++++l+++ +
  gi|13541391|ref|NP_111079.1| 222 DQLIEIGILVGT--DFNEGIKGIGAKKALALIKKEGNIKAVLNKIGK 266
                                   677777778885..5558*************************9863 PP

>> DUF5321  Family of unknown function (DUF5321)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   5.5e-05      0.24      60     128 ..     247     315 ..     239     329 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 5.5e-05
                       DUF5321  60 airmialknefaaytrkadakielLreviekvqrGEevdveklLGtGdeekEreWeevLkeieeedall 128
                                   a+ +i+   +++a   k    ie L e+i+  ++   vdv+ + G  d++k +e+  v+++  ++  l 
  gi|13541391|ref|NP_111079.1| 247 ALALIKKEGNIKAVLNKIGKNIENLDEIIDFFKNPPVVDVKYVFGKPDPKKIEEFLCVVHDFSRDRILE 315
                                   677777777888899999999*******************************99999999988876655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1019  (0.0568353); expected 358.6 (0.02)
Passed bias filter:                      770  (0.0429472); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 2046.91
//
Query:       gi|13541392|ref|NP_111080.1|  [L=415]
Description: major facilitator superfamily permease [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.1e-27   95.0  61.3      4e-16   58.9  30.8    2.0  2  MFS_1            Major Facilitator Superfamily
    3.8e-09   35.6  39.4    3.8e-09   35.6  39.4    1.9  2  MFS_2            MFS/sugar transport protein
    0.00084   19.4   2.4    0.00084   19.4   2.4    5.1  6  Phage_holin_3_6  Putative Actinobacterial Holin-X, holin supe
  ------ inclusion threshold ------
      0.036   12.9  32.5      0.022   13.7  30.3    1.7  1  MFS_1_like       MFS_1 like family
       0.24   12.0   0.1       0.89   10.2   0.0    1.9  2  Sas10_Utp3       Sas10/Utp3/C1D 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 !   58.9  30.8   1.1e-19     4e-16       2     233 ..      20     249 ..      19     255 .. 0.80
   2 !   42.4  22.3   1.2e-14   4.2e-11      32     173 ..     258     401 ..     255     415 .] 0.79

  Alignments for each domain:
  == domain 1  score: 58.9 bits;  conditional E-value: 1.1e-19
                         MFS_1   2 llaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrr.vlllglllfalglllll. 80 
                                   +l++f + +++ +++++++ ++ + +gis + +g ++ +y + ++++s p+Gr +d+  + r +++lg+++++++ l+l+ 
  gi|13541392|ref|NP_111080.1|  20 SLGHFTNDFNILLFSVLIT-YYHRYFGISLALLGAIAIIYNIISGFLSTPIGRYADKTRAYRgLMMLGIFILGVS-LFLFg 98 
                                   5788999999999999999.*************************************999999************.44444 PP

                         MFS_1  81 fa...ss..lwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyi 156
                                   f+   +s  +w++l++ ++ G+g++++ p+g++++   + + + ++a+g+ +a+ s+G    p++   l+ ++g  ++ ++
  gi|13541392|ref|NP_111080.1|  99 FSflsASfvIWIMLIAVIFLGIGQAFYHPLGGSILNVTYGE-RAASALGINGAFGSIGRSALPVILVPLILLVGKAYALFV 178
                                   644444444889****************************9.*****************99988877777799*9999999 PP

                         MFS_1 157 laivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsglltllply 233
                                   ++  +++a+v++++ l   ++++ +++++e       +++ +  ++l+ + vl i+++++++ +++++g++t++  +
  gi|13541392|ref|NP_111080.1| 179 AGTYMFVAGVVIYAGLSFLKKREIPNRSREA-----SSAANK-ETYLRYRGVLAIIVAMIFIRAMFLTGTTTYISQF 249
                                   9999999999533333333333333333333.....233333.5677888877678888888888888888888776 PP

  == domain 2  score: 42.4 bits;  conditional E-value: 1.2e-14
                         MFS_1  32 seigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll.fa...sslw.lllvlrvlqGlgagalfpaga 107
                                     ++ +lt+ +l+a+++++++Grl++++G ++ + ++ +l+ l+ ++++ ++   + l  + +++ v++++++   fp+ +
  gi|13541392|ref|NP_111080.1| 258 ILMSYILTISFLTAVIGQPVFGRLTEKYGGKWSISITTILSTLF-FIFFmLSgdnAVLDtVTYAAFVFMAFTG---FPVLM 334
                                   56899***************************888888888888.4444244443222235888888888885...***** PP

                         MFS_1 108 aliadwfpkeergraigl.lsagfslGailgpllgglla.sslgWravfyilaivsllafvlfllllp 173
                                    ++ +++p +  + a+gl +++g+ +G  +g ++ ++++  ++  ++v++i+ i++++++  f+ l+p
  gi|13541392|ref|NP_111080.1| 335 GYVNQIVPNNISTTANGLvWGLGNTVGGGIGIAVMSIFLnLHFTLTSVMWIMIIFGVISAF-FIPLIP 401
                                   ****************963789*********8888888879*****************955.233333 PP

>> MFS_2  MFS/sugar transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.6  39.4   1.1e-12   3.8e-09      10     338 ..      27     336 ..      19     376 .. 0.69
   2 ?   -2.5   3.2      0.39   1.4e+03     297     327 ..     367     396 ..     359     411 .. 0.50

  Alignments for each domain:
  == domain 1  score: 35.6 bits;  conditional E-value: 1.1e-12
                         MFS_2  10 nilsvllatylliFytdvlglsaalvglvllvarlvDaitDpivGtlidktstrwGrrrPwlllsaiilavsiillftppe 90 
                                   ++  +l++ +l ++y   +g+s al+g++++++++++ +    +G ++dkt++    +r +++l+  il+vs++l+ +++ 
  gi|13541392|ref|NP_111080.1|  27 DFNILLFS-VLITYYHRYFGISLALLGAIAIIYNIISGFLSTPIGRYADKTRA----YRGLMMLGIFILGVSLFLFGFSFL 102
                                   44445555.6778999999**********************************....999************999977655 PP

                         MFS_2  91 lsqsakfiwllvtyillrilytlfeipyvslvpvltkdydeRtsltsvrsflsvlggvlaailafllvlilgglkserkgy 171
                                      ++ +iw++++++++     +f+ p +  + + t+     + l     f s++ ++l  il++l++l+ ++       y
  gi|13541392|ref|NP_111080.1| 103 --SASFVIWIMLIAVIFLGIGQAFYHPLGGSILNVTYGERAASALGINGAFGSIGRSALPVILVPLILLVGKA-------Y 174
                                   ..46999*********977777788888888888877776667777777788877788888887777666555.......6 PP

                         MFS_2 172 lifaliialLmllgviivvlgtkervemrkkekteqkeklslleqlkevfrnraflillllfllaalalgvlnglllYylt 252
                                    +f++   + ++++vi++ l + +++e      ++++e+ s+ ++   +     + i++++++++a+ l+ + +    ++ 
  gi|13541392|ref|NP_111080.1| 175 ALFVAGTYMFVAGVVIYAGLSFLKKREI----PNRSREASSAANKETYLRYRGVLAIIVAMIFIRAMFLTGTTTYISQFVL 251
                                   6666555555555555555666666555....3444444444444444444444555666666666666666666666666 PP

                         MFS_2 253 yvlgngsaasvfllvvtisallgiplwqplakrlgkkntyllgalltivllvlvlllqpsnlllflvllviagfgvgvaal 333
                                   + ++++  +s++l++ ++ a++g p++ +l+ ++g k ++ + ++l  +++++++l    n +l +v ++++ f + + + 
  gi|13541392|ref|NP_111080.1| 252 DRVKSEILMSYILTISFLTAVIGQPVFGRLTEKYGGKWSISITTILSTLFFIFFMLS-GDNAVLDTVTYAAFVFMAFTGFP 331
                                   7778888899999999*********************88888887777777777776.55544444444444444333333 PP

                         MFS_2 334 lpwsm 338
                                   +++  
  gi|13541392|ref|NP_111080.1| 332 VLMGY 336
                                   33333 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.39
                         MFS_2 297 lltivllvlvlllqpsnlllflvllviagfg 327
                                   +++ ++l l + l +s +++++++ vi+ f+
  gi|13541392|ref|NP_111080.1| 367 AVMSIFLNLHFTL-TSVMWIMIIFGVISAFF 396
                                   3333333333333.33333333333333333 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 ?   -2.8   0.3       1.8   6.5e+03      37      43 ..      48      54 ..      29      66 .. 0.47
   2 !    6.5   6.8    0.0022         8      30      80 ..      78     121 ..      73     126 .. 0.73
   3 !   19.4   2.4   2.3e-07   0.00084      31     103 ..     139     208 ..     136     213 .. 0.91
   4 ?   -1.2   1.4      0.57     2e+03      38      65 ..     225     257 ..     211     275 .. 0.45
   5 ?   -0.9   2.0      0.44   1.6e+03      54      85 ..     299     333 ..     287     349 .. 0.49
   6 ?   -8.7  12.3         5   1.8e+04      36      77 ..     351     387 ..     311     403 .. 0.55

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.8
               Phage_holin_3_6 37 agllgaa 43
                                  ++llga 
  gi|13541392|ref|NP_111080.1| 48 LALLGAI 54
                                  2222221 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0022
               Phage_holin_3_6  30 akragsgagllgaagvlallalllllvalalalaalwlaalivaavllvla 80 
                                   a r + ++g++++++ l l+++ +l++ +++++       +++a+++l ++
  gi|13541392|ref|NP_111080.1|  78 AYRGLMMLGIFILGVSLFLFGFSFLSASFVIWI-------MLIAVIFLGIG 121
                                   345556666677899999999999999998888.......55678888776 PP

  == domain 3  score: 19.4 bits;  conditional E-value: 2.3e-07
               Phage_holin_3_6  31 kragsgagllgaagvlallalllllvalalalaalwlaalivaavllvlagvlalvglkklkkakplpertie 103
                                   +ra+s++g+ ga g ++  al+++lv l+l++    + al va+ ++ +agv++++gl+ lkk++  p r++e
  gi|13541392|ref|NP_111080.1| 139 ERAASALGINGAFGSIGRSALPVILVPLILLV--GKAYALFVAGTYMFVAGVVIYAGLSFLKKREI-PNRSRE 208
                                   7999************************9888..7899999**********************775.999987 PP

  == domain 4  score: -1.2 bits;  conditional E-value: 0.57
               Phage_holin_3_6  38 gllgaagvlallalllllvala..lala.a..l 65 
                                   +++++a+++   ++l+ + + +  ++l+ +   
  gi|13541392|ref|NP_111080.1| 225 LAIIVAMIFIRAMFLTGTTTYIsqFVLDrVksE 257
                                   333333333333333333332233444433443 PP

  == domain 5  score: -0.9 bits;  conditional E-value: 0.44
               Phage_holin_3_6  54 llvalalala.a.lwlaali.vaavllvlagvlal 85 
                                    l++++++l+   + l ++   a v+++ +g  +l
  gi|13541392|ref|NP_111080.1| 299 TLFFIFFMLSgDnAVLDTVTyAAFVFMAFTGFPVL 333
                                   33333333332222222222122333333333333 PP

  == domain 6  score: -8.7 bits;  conditional E-value: 5
               Phage_holin_3_6  36 gagllgaagvlallalllllval..alalaalwlaalivaavll 77 
                                   g+++ ++  v + +++++++++l   + l+ +      v+ +++
  gi|13541392|ref|NP_111080.1| 351 GLVWGLGNTVGGGIGIAVMSIFLnlHFTLT-S------VMWIMI 387
                                   333333333444444444444442112221.1......222222 PP

>> MFS_1_like  MFS_1 like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7  30.3     6e-06     0.022      22     368 ..      37     367 ..      33     380 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6e-06
                    MFS_1_like  22 ltiylkskglkaseigiitlilplts.ilsppiwgvlaDrfgkrkkvvilslllsavlfl..sllfippskerqeesklev 99 
                                   +t y +  g++ +  g i  i  ++s +ls pi g  aD+++++  +++l++++  v+++  ++ f++             
  gi|13541392|ref|NP_111080.1|  37 ITYYHRYFGISLALLGAIAIIYNIISgFLSTPI-GRYADKTRAYRGLMMLGIFILGVSLFlfGFSFLS------------- 103
                                   677888889999999999999999984666665.999************9999887766612444555............. PP

                    MFS_1_like 100 svaqdvdaektfwilfllvvlasfflaailvlldaatlkel.gedrkd.yGrqrlfGsvGyaifafitGilidhysvnllp 178
                                          a+  +wi+++ v++  + +a   +l  ++ l+ + ge++    G    fGs+G     +i+  li  +  ++  
  gi|13541392|ref|NP_111080.1| 104 -------ASFVIWIMLIAVIFLGIGQAFYHPLGGSI-LNVTyGERAASaLGINGAFGSIGRSALPVILVPLILLVGKAYAL 176
                                   .......66666666666555555555555555555.555547776666************99999999999999988766 PP

                    MFS_1_like 179 ysallyvlaa.llvisllvvlilnetekesklkvtkslqvllnilknpeviifl.lvalilgmswgiienFlflYLkelga 257
                                   ++a  y++ a +++ + l++l+  e    s  +      +    l+ + v++++ ++++i  m+     ++++ +  +   
  gi|13541392|ref|NP_111080.1| 177 FVAGTYMFVAgVVIYAGLSFLKKREIPNRSREASS--AANKETYLRYRGVLAIIvAMIFIRAMFLTGTTTYISQFVLDRVK 255
                                   66777766551555555555555555444444444..3444556666666555505556778999999********99999 PP

                    MFS_1_like 258 sntllGslvalgvvaeiplfffaeklleklGhvklliiallayilrfllyaii.enawlvlpievLhgisfgllwaaavey 337
                                   s++l++ ++++  +  ++   +  +l+ek+G  + + i+ ++ +l f+   +  +na+l  ++ +   +   + + +++ y
  gi|13541392|ref|NP_111080.1| 256 SEILMSYILTISFLTAVIGQPVFGRLTEKYGGKWSISITTILSTLFFIFFMLSgDNAVLDTVTYAAFVFMAFTGFPVLMGY 336
                                   ******************************9776655554444444444333348887766666666666667789***** PP

                    MFS_1_like 338 vskiapksleatgqgllsglyfglGralGsl 368
                                   v++i+p+++ +t  gl+ gl   +G+++G  
  gi|13541392|ref|NP_111080.1| 337 VNQIVPNNISTTANGLVWGLGNTVGGGIGIA 367
                                   *****************99999999999954 PP

>> Sas10_Utp3  Sas10/Utp3/C1D family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00025      0.89      41      79 ..     251     282 ..     242     283 .. 0.83
   2 ?   -2.3   0.0         2   7.2e+03      53      66 ..     296     309 ..     288     317 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00025
                    Sas10_Utp3  41 llslKnelllaYllnlllylllklsgvelkdhpvvkeLv 79 
                                   l+++K e+l++Y+l+++++   ++ g+     pv+ +L+
  gi|13541392|ref|NP_111080.1| 251 LDRVKSEILMSYILTISFL--TAVIGQ-----PVFGRLT 282
                                   899****************..665553.....7777776 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2
                    Sas10_Utp3  53 llnlllylllklsg 66 
                                   +l+ l+++++ lsg
  gi|13541392|ref|NP_111080.1| 296 ILSTLFFIFFMLSG 309
                                   77889999999999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (415 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1233  (0.0687713); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); 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 0.35s 00:00:01.10 Elapsed: 00:00:00.52
# Mc/sec: 2406.03
//
Query:       gi|13541393|ref|NP_111081.1|  [L=171]
Description: 30S ribosomal protein S13P [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      3e-37  127.9   0.6    3.8e-37  127.6   0.6    1.1  1  Ribosomal_S13  Ribosomal protein S13/S18
     0.0041   17.6   0.4       0.53   10.8   0.1    2.3  2  Cucumo_2B      Cucumovirus protein 2B
  ------ inclusion threshold ------
      0.089   12.8   0.1       0.22   11.5   0.1    1.6  1  Sdh5           Flavinator of succinate dehydrogenase


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 !  127.6   0.6   6.3e-41   3.8e-37       1     128 []      33     160 ..      33     160 .. 0.99

  Alignments for each domain:
  == domain 1  score: 127.6 bits;  conditional E-value: 6.3e-41
                 Ribosomal_S13   1 RilgtdidgkkkveialtaikGiGrrkakiilkkadvdedkrigelteeeiekieeivenkaqykipnwi.nrqkdikdGk 80 
                                   Ri++ d++g++ + +al  +kGiG r   +i+++++++ +k+igel+e+eiek++e+ven ++y  p+w+ n++++  +Gk
  gi|13541393|ref|NP_111081.1|  33 RIANKDLNGERPIPLALSDLKGIGLRLGYAIAERLNLQPTKKIGELKEDEIEKLKEYVEN-KEYDLPDWLlNHRREPVTGK 112
                                   9***********************************************************.8999999999********** PP

                 Ribosomal_S13  81 dshvvendlrrklredieRlkkirsyrGlRHkrGlkvRGQrTkttgRt 128
                                   +  +v++dl+ +++edi+ +kkirsy+G+RH++G kvRGQrT+++gR+
  gi|13541393|ref|NP_111081.1| 113 NLNLVTTDLDVQVQEDINLMKKIRSYKGIRHEKGKKVRGQRTRSNGRR 160
                                   ***********************************************7 PP

>> Cucumo_2B  Cucumovirus protein 2B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.7   0.0     0.007        42      69      96 ..      75     102 ..      67     107 .. 0.90
   2 !   10.8   0.1   8.8e-05      0.53       5      45 ..     120     159 ..     117     165 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.007
                     Cucumo_2B  69 vaelpeseasrlelsaedhdfddtdwfa 96 
                                   + el e e  +l+   e++++d  dw+ 
  gi|13541393|ref|NP_111081.1|  75 IGELKEDEIEKLKEYVENKEYDLPDWLL 102
                                   789***********************85 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 8.8e-05
                     Cucumo_2B   5 nvelqlarmveakkqrrrshkqnrrerghkspserarsnlr 45 
                                   ++++q+   ++  k + rs+k  r+e+g+k   +r+rsn r
  gi|13541393|ref|NP_111081.1| 120 DLDVQVQEDINLMK-KIRSYKGIRHEKGKKVRGQRTRSNGR 159
                                   55666666666555.568*********************77 PP

>> Sdh5  Flavinator of succinate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   3.6e-05      0.22      26      66 ..      73     113 ..      72     123 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.6e-05
                                   HHTTT--HHHHHHHHHHHTS--HHHHHHHHT-.---S-HHH CS
                          Sdh5  26 khlatlseeeldaferLLdleDpdLldwltgrkeepedael 66 
                                   k++ +l+e+e++++++ ++ ++ dL dwl++++ ep + ++
  gi|13541393|ref|NP_111081.1|  73 KKIGELKEDEIEKLKEYVENKEYDLPDWLLNHRREPVTGKN 113
                                   567899**************************999976665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       687  (0.0383178); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1294.77
//
Query:       gi|13541394|ref|NP_111082.1|  [L=200]
Description: 30S ribosomal protein S4P [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.1e-14   52.9   0.5    7.8e-14   51.1   0.1    2.2  2  S4            S4 domain
    3.3e-05   24.7   3.0    7.8e-05   23.5   0.5    2.5  3  Ribosomal_S4  Ribosomal protein S4/S9 N-terminal domain


Domain annotation for each model (and alignments):
>> S4  S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0      0.47   4.2e+03      16      22 ..      52      58 ..      45      58 .. 0.72
   2 !   51.1   0.1   8.7e-18   7.8e-14       1      44 [.     106     149 ..     106     153 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.47
                                  HHHHHHH CS
                            S4 16 rreArql 22
                                  r++Ar l
  gi|13541394|ref|NP_111082.1| 52 RSQARYL 58
                                  99**965 PP

  == domain 2  score: 51.1 bits;  conditional E-value: 8.7e-18
                                   EEHHHHHHHTTSSSSHHHHHHHHHTTTEEETTEEE--TT-EE-T CS
                            S4   1 rRLdkvlarlglassrreArqlIehGrVlVNGkvvkdpsyrVkp 44 
                                   rRL+++++++ la s ++ArqlI hG+++VNG++v+ p++ V++
  gi|13541394|ref|NP_111082.1| 106 RRLQTIVFKKNLALSEKQARQLITHGHITVNGRRVTVPGMLVEA 149
                                   8***************************************9986 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 !   23.5   0.5   8.7e-09   7.8e-05      31      80 ..       9      60 ..       2      63 .. 0.84
   2 ?   -1.0   0.1      0.38   3.4e+03      58      73 ..      71      85 ..      67      91 .. 0.53
   3 ?   -0.4   0.0      0.24   2.2e+03      10      27 ..     105     144 ..     101     162 .. 0.65

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 8.7e-09
                                  TS.-----CHCH.HHHHHHHHHHHHT-S.HHHHHHHHHHHHHCCSHHHHHHHH CS
                  Ribosomal_S4 31 kr.rkklseYgk.qlrekqklkrrYgll.ekqfrryfkearrirGktgenLlq 80
                                  k+ ++   +++k +++e+ k+  +Ygl+ +++++r   ++++ir ++++ L +
  gi|13541394|ref|NP_111082.1|  9 KKySTPRHPWEKdRIDEENKILVKYGLKnKREIWRSEAMLSSIR-SQARYLRA 60
                                  333666679***********************************.99998865 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.38
                                  HHHHHHHHHHHHCCSH CS
                  Ribosomal_S4 58 kqfrryfkearrirGk 73
                                  kq+ r+ k+++r++  
  gi|13541394|ref|NP_111082.1| 71 KQLERMIKRLSRYK-I 85
                                  45555555555544.3 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.24
                                   HCHCTS-STSSS......................S-S-SS CS
                  Ribosomal_S4  10 lRrvgfklflkg......................reyppG 27 
                                    Rr+++ +f+k+                      r + pG
  gi|13541394|ref|NP_111082.1| 105 DRRLQTIVFKKNlalsekqarqlithghitvngrRVTVPG 144
                                   5777777777777776666655555555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1122  (0.0625802); expected 358.6 (0.02)
Passed bias filter:                      570  (0.0317921); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1272.05
//
Query:       gi|13541395|ref|NP_111083.1|  [L=132]
Description: 30S ribosomal protein S11P [Thermoplasma volcanium GSS1]
Scores for complete 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-42  142.2   2.1    9.7e-42  141.8   2.1    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 !  141.8   2.1   5.4e-46   9.7e-42       1     110 []      10     128 ..      10     128 .. 0.99

  Alignments for each domain:
  == domain 1  score: 141.8 bits;  conditional E-value: 5.4e-46
                 Ribosomal_S11   1 GvahiqasfnntiititdlkGaevlvksaGglgvkasr.kssPyaaqlaaekaaekvldkGikavevkvkg........pG 72 
                                   G+ahi+as+nntii++td +Gae+++  +Gg++vk++r ++sPyaa++aa+ + e+++++ i+ + +kv++        pG
  gi|13541395|ref|NP_111083.1|  10 GIAHIYASQNNTIIHVTDPTGAETIAMVSGGMVVKNDRdQASPYAAMKAADMVSETLKEHEITDLIIKVRApggnkskiPG 90 
                                   9*************************************9****************************************** PP

                 Ribosomal_S11  73 pGreaalralaraGlkigriedvtPiPhdgirrpkkrr 110
                                   pG++aa+ral raGlki rie+vtPiPhdg+++++++r
  gi|13541395|ref|NP_111083.1|  91 PGAQAAIRALSRAGLKIVRIEEVTPIPHDGTKKKGGKR 128
                                   *********************************99887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       618  (0.0344693); expected 358.6 (0.02)
Passed bias filter:                      509  (0.0283898); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 860.35
//
Query:       gi|13541396|ref|NP_111084.1|  [L=271]
Description: DNA-directed RNA polymerase subunit D [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.7e-21   75.0   0.0    1.7e-20   73.5   0.0    1.7  2  RNA_pol_A_bac  RNA polymerase Rpb3/RpoA insert domain
    5.5e-18   64.2   0.0      7e-18   63.8   0.0    1.1  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 !   73.5   0.0   1.9e-24   1.7e-20       5     112 .]      60     164 ..      57     164 .. 0.90
   2 ?   -1.6   0.0      0.38   3.4e+03      57      68 ..     191     202 ..     170     249 .. 0.62

  Alignments for each domain:
  == domain 1  score: 73.5 bits;  conditional E-value: 1.9e-24
                                   ECTSSS.HHHHHCHHHCSTCBSSCHHHHHHHHCTT-ETSSSSTTCSEEEEEEEEESSECEEGGGCBES.SSSCEESSTTSE CS
                 RNA_pol_A_bac   5 entsvlqDEvvaHrlgliplvsedvleillnlkelveeeeegeeeksvelkLnvkgpgevtagdlkle.dadveivnpdil 84 
                                   + +  l DE+vaHrlglipl+++  l   +++ ++ +   +g++ ++v+ ++n+ gp  v++gd++   ++d  +v+pdi+
  gi|13541396|ref|NP_111084.1|  60 DSSLPLFDEMVAHRLGLIPLKTDLSL---NFRDQC-SCGGKGCSLCTVTYSINKIGPASVMSGDIQAIsHPDLVPVDPDIP 136
                                   5556789**************66654...599999.44679************************976599********** PP

                                   EEEEETT-EEEEEEEEEEESSEECTTT- CS
                 RNA_pol_A_bac  85 IakLrkgqeleleakvkkGiGkehakfs 112
                                   I+kL  +q + ++a++  G++kehak++
  gi|13541396|ref|NP_111084.1| 137 IVKLGAKQAILITAEAILGTAKEHAKWQ 164
                                   ***************************6 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.38
                                   EEESSECEEGGG CS
                 RNA_pol_A_bac  57 nvkgpgevtagd 68 
                                   + ++p+ v ++d
  gi|13541396|ref|NP_111084.1| 191 KERCPKSVLSED 202
                                   445555555554 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 !   63.8   0.0   7.8e-22     7e-18       1      67 [.      14     260 ..      14     262 .. 0.83

  Alignments for each domain:
  == domain 1  score: 63.8 bits;  conditional E-value: 7.8e-22
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................................................... RF
                     RNA_pol_L   1 efllrgvdhtlgNaLRrillsevpgvaiea................................................... 30 
                                   +f+++g++++ +NaLRr+l++++p++aie+                                                   
  gi|13541396|ref|NP_111084.1|  14 SFEIDGITPSQANALRRTLINDIPKLAIENvtfhhgeirdaegnvydsslplfdemvahrlgliplktdlslnfrdqcscg 94 
                                   69************************************************9999999999999999999999999999999 PP

                                   .........................................xx...................................... RF
                     RNA_pol_L  31 .........................................pv...................................... 32 
                                                                            p+                                      
  gi|13541396|ref|NP_111084.1|  95 gkgcslctvtysinkigpasvmsgdiqaishpdlvpvdpdiPIvklgakqailitaeailgtakehakwqvtsgvaykyhr 175
                                   999999999999999998888888888888888886666661155555555555555556666666666666666666666 PP

                                   ..................................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     RNA_pol_L  33 ..................................................vkvntdkdklilevetdgslkPeealkeAlk 63 
                                                                                     v++++d++++i+  etdgsl++ee l++Al+
  gi|13541396|ref|NP_111084.1| 176 efevnkklfedwakikercpksvlsedentivftddygcndlsilfesdgVQIKEDDSRFIFHFETDGSLTAEETLSYALN 256
                                   66666677777777777777788888888888888888888888999999999**************************** PP

                                   xxxx RF
                     RNA_pol_L  64 iLke 67 
                                    L++
  gi|13541396|ref|NP_111084.1| 257 RLMD 260
                                   **98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       402  (0.0224218); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 1765.77
//
Query:       gi|13541397|ref|NP_111085.1|  [L=396]
Description: molybdopterin biosynthesis protein [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.1e-33  114.1   0.0    7.8e-33  113.5   0.0    1.3  1  MoeA_N         MoeA N-terminal region (domain I and II)
    6.4e-23   81.0   0.1      1e-22   80.3   0.1    1.3  1  MoCF_biosynth  Probable molybdopterin binding domain
    4.3e-19   68.5   0.0    9.4e-19   67.4   0.0    1.6  1  MoeA_C         MoeA C-terminal region (domain IV)


Domain annotation for each model (and alignments):
>> MoeA_N  MoeA N-terminal region (domain I and II)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.5   0.0   1.3e-36   7.8e-33      18     156 ..      25     170 ..       6     171 .. 0.83

  Alignments for each domain:
  == domain 1  score: 113.5 bits;  conditional E-value: 1.3e-36
                                   EEEEEGGCG-TT-BBSS-EE-SS-BSSS-EESSSEEEEEEBTTB--....................-S---TT-EEEE-TT CS
                        MoeA_N  18 eeevplaaealgrvlaedvvApedvPpfdnSamDGYAvraeagsgaseeep.........saageeperllpggavrimTG 89 
                                    +ev     ++g+ +a ++ +p d+P++d+Sa+DG+Avr e+  +a  ++p         + +++++ r  ++++++i+TG
  gi|13541397|ref|NP_111085.1|  25 MKEVRS-DISAGMYSAIPILSPSDFPQYDRSAVDGFAVRYEDVLSAGLNNPislklvgsiHVGDANNIRIGKNQCAEIFTG 104
                                   333444.3346***********************************99999********767777777777777******* PP

                                   SB--TT--EEEEGGGE..E....EETTE.S--STTTTEE-TTSSB-TTSEEE-TTBB--CCCHHHHHHC CS
                        MoeA_N  90 aplPegadaVvpvEdte.eeeaketvev.kavkpgenvrraGedikaGevllragtrltpaeigllasv 156
                                   a +PegadaVv++Ed+e e    e v + ++vk+ +n+ r+Ged+k G+ ++ +g+r+ p++i +    
  gi|13541397|ref|NP_111085.1| 105 AEVPEGADAVVMQEDAEiEG---EYVAIfRKVKKFQNIGRKGEDLKTGDKIIDRGQRIMPWHIPAFIET 170
                                   ***************96543...333336899*******************************887665 PP

>> MoCF_biosynth  Probable molybdopterin binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.3   0.1   1.7e-26     1e-22       1     142 [.     183     309 ..     183     311 .. 0.93

  Alignments for each domain:
  == domain 1  score: 80.3 bits;  conditional E-value: 1.7e-26
                                   EEEEE-HHHHTTSSGBHHHHHHHHHHHTTSEEEEEEEEE-SSHHHHHHHHHHHHHTSSEEEEESS-SSSTT--HHHHHHHH CS
                 MoCF_biosynth   1 avitvGdellsgkieDtngpllaellkelgvevskytvvpDdeeeikeallaaleeadviittGGtGptpdDvtpealakl 81 
                                   +v+++Gde++sgk++++++p+l++l+ + g++   ++ v D+ e+i++ + +++e+ d++i+tGG Gp++ D++  +l++l
  gi|13541397|ref|NP_111085.1| 183 GVLSTGDEIVSGKVKNASAPMLQSLIVRDGFNSVFLGNVEDNVEKISNVI-RSFEG-DLLIVTGGSGPSSTDLMDSILQNL 261
                                   69************************************************.55477.************************ PP

                                   HSEE-HHHHHHHHHHHHHHCCTTSHGGGGGGE.EETTEEEEE-SSHHHHHHHHHHHHHGGH CS
                 MoCF_biosynth  82 fekelegfeeafrrvslkpgkpvgvapgailsravgktiigLPGspkavkealeeillpal 142
                                   ++       ++f+++++kpg+   ++ +a ++++   +i+++ G p+a+  a e++++p +
  gi|13541397|ref|NP_111085.1| 262 GQ-------IIFHGIRMKPGR---TTGLALVNDK---PIFTISGLPVAALIAYENVIRPLI 309
                                   *9.......9***********...6666666875...9*******************9987 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 !   67.4   0.0   1.6e-22   9.4e-19       2      71 ..     325     394 ..     324     395 .. 0.97

  Alignments for each domain:
  == domain 1  score: 67.4 bits;  conditional E-value: 1.6e-22
                                   EEESS-EE--SSS-EEEEEEEES-S-EEEEEE-S---TT-GGGCTT--EEEEE-TT--EE-TT-EEEEEE CS
                        MoeA_C   2 arlaedlksdpgrreflRvilteedgeyvaeptgkqgSglLsslaeAnglivipegtegleaGeeVevil 71 
                                   ++l++++  ++ ++ f+Rv+l+++dg++++ p++++gSg++ s  +A+g+++i+e++eg+++G+ Vev l
  gi|13541397|ref|NP_111085.1| 325 GELTRSIFNNEAMKMFVRVRLSNKDGKIYVDPLRTTGSGIINSVINADGYLIIDENVEGYQEGQLVEVKL 394
                                   6899****************************************************************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       430  (0.0239835); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.50
# Mc/sec: 2399.82
//
Query:       gi|13541398|ref|NP_111086.1|  [L=626]
Description: molybdopterin biosynthesis protein MoeA/LysR substrate binding-domain-containing protein [Thermoplasma volcanium GSS1]
Scores for 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  140.7   0.1    5.1e-41  139.9   0.1    1.3  1  PBP_like       PBP superfamily domain
    3.8e-41  140.5   0.2    5.9e-41  139.8   0.2    1.3  1  MoeA_N         MoeA N-terminal region (domain I and II)
    4.6e-20   71.7   0.0    1.1e-19   70.6   0.0    1.6  1  MoCF_biosynth  Probable molybdopterin binding domain
    4.9e-07   29.8   0.0      4e-06   26.9   0.0    2.4  2  MoeA_C         MoeA C-terminal region (domain IV)
  ------ inclusion threshold ------
      0.055   13.4   0.0       0.14   12.1   0.0    1.6  1  Herpes_pp38    Herpesvirus pp38 phosphoprotein


Domain annotation for each model (and alignments):
>> PBP_like  PBP superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.9   0.1   1.4e-44   5.1e-41      12     192 ..     430     602 ..     425     603 .. 0.96

  Alignments for each domain:
  == domain 1  score: 139.9 bits;  conditional E-value: 1.4e-44
                                   EEEEEES-HHHHHHHHHTTS-SEEEESS---CCCHHCCCCCEEEEEEEEEEEE-CC-HCHCCCCHCCHHHS--BGGGC-S- CS
                      PBP_like  12 rvavanvGsggGlkalrageadiagshlldketeeynapalrkaldgievvlvnlarreqglvvakgnpkkitnwkdlada 92 
                                   ++++ nvG  gG++a++agead++g+h+l+   + yn++ + + l +    lv+++ r+ g+v + g    +++++++ d+
  gi|13541398|ref|NP_111086.1| 430 SAKIVNVGAWGGISAIKAGEADVSGIHILKN--GVYNISVYDNDLRN-VSYLVRGYLRNRGFVSKTG----VSSFQEILDK 503
                                   577899************************7..99***********9.579****************....********** PP

                                   B-EEEEE-TTSHHHHHHHHHHC-CEECTE-SSTTSEEESSHHHHHCCHCCETTCCECCCGG-HCCCCCCECTTCE-EEEEE CS
                      PBP_like  93 plrlvnRetGSGtrdlfdellkkegiskssikgyaqearshlavaaaVaagradvgvgieavaeelkgldfvplaeerydl 173
                                   ++++vnR++GSGtrdl++el+ +++  ++++kgy  e +++  va+aV++grad+g+++e  a +l gl+++ +++e yd+
  gi|13541398|ref|NP_111086.1| 504 GMVFVNRNKGSGTRDLIEELIGNNESIRKNMKGYLWETNTEAGVARAVEQGRADAGITLEYYAIKL-GLKYTHINKENYDI 583
                                   ***************************************************************998.************** PP

                                   EEECTCCCSHHHHHHHHHH CS
                      PBP_like 174 vvrkealddpevqaflefl 192
                                   +++ke +d++  qaf++ l
  gi|13541398|ref|NP_111086.1| 584 LISKEFYDSEYGQAFIKNL 602
                                   ****************976 PP

>> MoeA_N  MoeA N-terminal region (domain I and II)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.8   0.2   1.7e-44   5.9e-41       2     157 .]       9     173 ..       8     173 .. 0.90

  Alignments for each domain:
  == domain 1  score: 139.8 bits;  conditional E-value: 1.7e-44
                                   -HHHHHHHHHHH-.HH-EEE.EEGGCG-TT-BBSS-EE-SS-BSSS-EESSSEEEEEEBTTB--................. CS
                        MoeA_N   2 sveealaiilaal.eleeee.vplaaealgrvlaedvvApedvPpfdnSamDGYAvraeagsgaseeep........saag 72 
                                   s +ea +ii++++ +    e  ++ ++++g v+aedv ++ d+Ppfd+S +DGYAv  ++ +g +e++p        +aag
  gi|13541398|ref|NP_111086.1|   9 SSDEAKEIISQEIsKRIVFEdRKI-SDSAGYVSAEDVFSKYDIPPFDRSEVDGYAVFHSDVEGSEEDNPhrlkligsVAAG 88 
                                   678999999999965544444888.8999***********************************99999********8888 PP

                                   ..-S---TT-.EEEE-TTSB--TT--EEEEGGGE..E....EETTE.S--STTTTEE-TTSSB-TTSEEE-TTBB--CCCH CS
                        MoeA_N  73 eeperllpgg.avrimTGaplPegadaVvpvEdte.eeeaketvev.kavkpgenvrraGedikaGevllragtrltpaei 150
                                   ++++++l  g +v+++TGa +P+gadaVv+vEdt+ +    +tvev ++v pgen+   G di+ G+++l+agtr++p  i
  gi|13541398|ref|NP_111086.1|  89 DRSAPSLGTGsCVYVATGAIIPRGADAVVMVEDTRaS---GQTVEVfRSVYPGENISYSGTDISLGDLILKAGTRISPEAI 166
                                   88888888888***********************642...45566679********************************* PP

                                   HHHHHCT CS
                        MoeA_N 151 gllasvG 157
                                   g+la++G
  gi|13541398|ref|NP_111086.1| 167 GALAAAG 173
                                   *****98 PP

>> MoCF_biosynth  Probable molybdopterin binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.6   0.0     3e-23   1.1e-19       1     140 [.     186     321 ..     186     324 .. 0.94

  Alignments for each domain:
  == domain 1  score: 70.6 bits;  conditional E-value: 3e-23
                                   EEEEE-HHHH.......TTSSGBHHHHHHHHHHHTTSE.EEEEEEEE-SSHHHHHHHHHHHHHTSSEEEEESS-SSSTT-- CS
                 MoCF_biosynth   1 avitvGdell.......sgkieDtngpllaellkelgv.evskytvvpDdeeeikeallaaleeadviittGGtGptpdDv 73 
                                   a++++G+e++        g+i Dtn+ +++++l+  g+ + + +++ +D+e+e+++ + + l+++d+i  +G t+++ +D+
  gi|13541398|ref|NP_111086.1| 186 AILSTGNEVIepgnelkYGEIFDTNSNYFVAKLATTGLiDPEFIGIARDNEDELSKLVNDGLKKYDAIMASGSTSAGFYDM 266
                                   68999999999999999********************99**********************9******************* PP

                                   HHHHHHHHHSEE-HHHHHHHHHHHHHHCCTTSHGGGGGGE.EETTEEEEE-SSHHHHHHHHHHHHHG CS
                 MoCF_biosynth  74 tpealaklfekelegfeeafrrvslkpgkpvgvapgailsravgktiigLPGspkavkealeeillp 140
                                    ++++++l+++      ++f++++ kpgkp+ ++ +   s+   ++++g+PG+p +++++l  i++p
  gi|13541398|ref|NP_111086.1| 267 LYKIVEELGGE------ILFHGINIKPGKPTFFGLI---SG---HPFFGMPGFPLSSAVVLNYIVIP 321
                                   **********8......*************998888...65...48**************9999866 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 ?   -0.8   0.1      0.49   1.8e+03      47      69 ..     112     131 ..     111     132 .. 0.85
   2 !   26.9   0.0   1.1e-09     4e-06       2      72 .]     337     403 ..     336     403 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.49
                                   T--EEEEE-TT--EE-TT-EEEE CS
                        MoeA_C  47 eAnglivipegtegleaGeeVev 69 
                                   +A++ ++++  ++   +G++Vev
  gi|13541398|ref|NP_111086.1| 112 GADAVVMVEDTRA---SGQTVEV 131
                                   7999999998886...9999998 PP

  == domain 2  score: 26.9 bits;  conditional E-value: 1.1e-09
                                   EEESS-EE--SSS-EEEEEEEES-S-EEEEEE-S---TT-GGGCTT--EEEEE-TT--EE-TT-EEEEEE- CS
                        MoeA_C   2 arlaedlksdpgrreflRvilteedgeyvaeptgkqgSglLsslaeAnglivipegtegleaGeeVevill 72 
                                   ++  +++++++ +++ ++++lt    + +  p+ +++Sg +s +  A+gl+vip ++++++  e+V+++ +
  gi|13541398|ref|NP_111086.1| 337 VKVPFRINAEKLQETIYPAVLT---KKGYGFPI-MGNSGSISRMLYADGLMVIPGDEKYVSRDEKVKFYKF 403
                                   677899999*************...67799***.********************************99875 PP

>> Herpes_pp38  Herpesvirus pp38 phosphoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   3.9e-05      0.14      16      47 ..      91     122 ..      86     124 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.9e-05
                   Herpes_pp38  16 sakiLllGsCisFaaGtLvGktadvkvPlcds 47 
                                   sa +L  GsC+  a+G ++ ++ad  v + d+
  gi|13541398|ref|NP_111086.1|  91 SAPSLGTGSCVYVATGAIIPRGADAVVMVEDT 122
                                   8899999*****************98888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (626 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       480  (0.0267723); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:01.22
# Mc/sec: 1554.38
//
Query:       gi|13541399|ref|NP_111087.1|  [L=263]
Description: hypothetical protein TVN0568 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    0.00017   20.8   0.0     0.0018   17.4   0.0    1.9  2  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 !    1.3   0.0    0.0084   1.5e+02       2      57 ..      13      68 ..      12      76 .. 0.80
   2 !   17.4   0.0     1e-07    0.0018      95     233 ..      91     218 ..      88     236 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.0084
                                  EEEEESTTSHHHHHHHHHCTTTSEEEEEE..-TTT--TTSHHHHHHHHHHH--SEEEE CS
                 RmlD_sub_bind  2 kilvtGanGqlGseLakqlaeeglevlal..treeldltdaeavaellkeakpdvvvn 57
                                  + l+t an+  G +L k+l eeg++v a+  ++++ +l  +e v +  k+   d++vn
  gi|13541399|ref|NP_111087.1| 13 RALITVANNVAGFNLWKRLVEEGYDVDAIlpSEDKYNLLLSELVSRKNKK--YDFIVN 68
                                  568999******************99998656668888888888775444..666776 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 1e-07
                                   EEEEEEEGGGS-S-TTS-B-TTS----SSHHHHHHHHHHHHHHHH-SSEEEEEE-SEESSSSS-HHHHHHHHHHH-SEEEE CS
                 RmlD_sub_bind  95 lLihvStDyVFdGekkrpYeeddetsPlnvYGrtKlaGEqavlaagkkalivRtswvygekgknfvktmlrlakereelkv 175
                                   ++i++S+D V++ +   + +e+d+  P ++ G+  l+ E a    ++  l++R++ v g+   n +++ ++l + + ++++
  gi|13541399|ref|NP_111087.1|  91 KIIFISSDLVYEPRP-GKKKENDNAYPPTMEGKYFLEAESALD--VNSDLVLRVGLVTGRCVPNILTNTINLSRANMSIDL 168
                                   589*********994.44699********************97..7788******************************** PP

                                   ESS-EE--EEHHHHHHHHHHHHHHCHH.GGG-EEEE---BS-EEHHHHHHHHHHHHCH CS
                 RmlD_sub_bind 176 vaDqlgsPTsardlAevllqllekaaeekelagvyHlanegetswlefArailkeaga 233
                                       +++  s +dl+e+++ ll+k        g+y ++++  ++  +fA +  +++++
  gi|13541399|ref|NP_111087.1| 169 SGAVVRNFISNADLSEYIIRLLDKN-------GIYNASAKS-MTPRDFALELCAKINV 218
                                   ******************9999874.......678777766.7777888777777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       607  (0.0338558); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 1574.70
//
Query:       gi|13541400|ref|NP_111088.1|  [L=90]
Description: molybdopterin converting factor, small subunit [Thermoplasma volcanium GSS1]
Scores for complete sequence (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   60.8   0.0    1.8e-16   60.6   0.0    1.1  1  ThiS            ThiS family
  ------ inclusion threshold ------
       0.14   11.5   0.0       0.15   11.3   0.0    1.1  1  BsuBI_PstI_RE   BsuBI/PstI restriction endonuclease domain
       0.14   12.3   0.1       0.29   11.3   0.0    1.5  2  Lipoprotein_21  LppP/LprE lipoprotein


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 !   60.6   0.0     3e-20   1.8e-16       1      77 []      15      90 .]      15      90 .] 0.99

  Alignments for each domain:
  == domain 1  score: 60.6 bits;  conditional E-value: 3e-20
                                  EEETTCCHHHHT..CEEEEESSTSBHHHHHHHHHHHTCHHGTTTTEEEEETTEEEGCCTTTSB--TTCEEEEEESTTC- CS
                          ThiS  1 vllfaelrelag..eeelelaegstvaelleaLgerypelalerrvavavNgeivprlwldtelkdgDevailppVaGG 77
                                  v++fa  +e++g  ee +el+ gs+v+ l++++ ++y+++++++   +avN ++v++   ++ +++gD+vai+p V+GG
  gi|13541400|ref|NP_111088.1| 15 VRYFAYFKEKVGkdEEYFELSPGSNVGTLINEVMKKYKNIFNPKDTLIAVNYKYVDQ---NYNIAEGDTVAIMPHVSGG 90
                                  89*******************************************************...******************9 PP

>> BsuBI_PstI_RE  BsuBI/PstI restriction endonuclease domain
   #    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       7      43 ..      28      65 ..      23      83 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 2.6e-05
                 BsuBI_PstI_RE  7 ngeeiklspGks.nllikavieefaprFlkeaevlyvg 43
                                  ++e ++lspG +  +li++v++++++ F +++++++v+
  gi|13541400|ref|NP_111088.1| 28 DEEYFELSPGSNvGTLINEVMKKYKNIFNPKDTLIAVN 65
                                  567899****86479*******************9986 PP

>> Lipoprotein_21  LppP/LprE lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0      0.92   5.5e+03      57      65 ..      12      20 ..       9      26 .. 0.77
   2 ?   11.3   0.0   4.8e-05      0.29      33      68 ..      37      72 ..      35      84 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.92
                Lipoprotein_21 57 tVtVeYrwy 65
                                  +V+V+Y  y
  gi|13541400|ref|NP_111088.1| 12 KVRVRYFAY 20
                                  699999766 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 4.8e-05
                Lipoprotein_21 33 geflGtatpepyasiprvlrsdddtVtVeYrwykpd 68
                                  g  +Gt   e +++ +++ + +d+ ++V+Y++++++
  gi|13541400|ref|NP_111088.1| 37 GSNVGTLINEVMKKYKNIFNPKDTLIAVNYKYVDQN 72
                                  566999999***9999***************88765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       575  (0.0320709); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 612.47
//
Query:       gi|13541401|ref|NP_111089.1|  [L=224]
Description: transcription initiation factor IIB [Thermoplasma volcanium GSS1]
Scores for complete 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   56.2   0.2      2e-06   27.8   0.0    2.4  2  TFIIB       Transcription factor TFIIB repeat
    3.1e-06   27.3   0.1    6.8e-06   26.2   0.0    1.6  2  Cyclin_C    Cyclin, C-terminal domain
    9.9e-05   22.1   0.3     0.0024   17.6   0.1    2.2  2  Cyclin_N    Cyclin, N-terminal domain
  ------ inclusion threshold ------
      0.057   13.4   0.1        2.8    8.0   0.0    2.5  2  TFIIB_C_1   Transcription factor IIB C-terminal module 1
      0.084   13.3   0.0       0.21   12.0   0.1    1.7  2  Cyclin_C_2  Cyclin C-terminal 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 !   27.8   0.0   5.5e-10     2e-06       9      66 ..      51     108 ..      49     113 .. 0.92
   2 !   26.3   0.1   1.6e-09   5.6e-06       1      71 []     137     207 ..     137     207 .. 0.97

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 5.5e-10
                                   T--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS- CS
                         TFIIB   9 eLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqV 66 
                                   e+p +V ++A +++   ++ ++  Gr  ++++AAc+++A+r +    t++ +s  l++
  gi|13541401|ref|NP_111089.1|  51 EIPLEVMKNALNIYLDNVSHGISRGRGCTAVLAACILVASRSSPSPVTLRYVSRALKI 108
                                   68999*************************************9999999988888877 PP

  == domain 2  score: 26.3 bits;  conditional E-value: 1.6e-09
                                   HHHHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHHH CS
                         TFIIB   1 ikrfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekti 71 
                                   i+r a+ l+  + V+d+A  l ++ +++  l  +sp +ia ++ly+A+ ++  k  q+ + + + ++e+t+
  gi|13541401|ref|NP_111089.1| 137 IERYAESLNVDDDVRDEAIALTNKIASQVSLMRKSPSTIAISALYLASILKDRKLVQRYVTKKTGITEVTL 207
                                   7899***************************************************************9996 PP

>> Cyclin_C  Cyclin, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       1.7     6e+03       1       1 [.      96      96 ..      80     118 .. 0.52
   2 !   26.2   0.0   1.9e-09   6.8e-06       2      91 ..     132     219 ..     131     224 .] 0.91

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.7
                                  - CS
                      Cyclin_C  1 p 1 
                                  p
  gi|13541401|ref|NP_111089.1| 96 P 96
                                  2 PP

  == domain 2  score: 26.2 bits;  conditional E-value: 1.9e-09
                                   -HHHHHHHHHCCSSHT.-HCCHHCHHCHHHHHHCSCCHCCS-HHHHHHHHHHHCCHHHHS--S-HHHHHHC---HHHHHHH CS
                      Cyclin_C   2 tplsFlrrflkaadasedselrtlakylleltlldydflsyppSliAaaalllarstlnspewtetlehytgyskedlkpc 82 
                                    p++F++r+  + +   d ++r  a  l   ++ ++++++ +pS+iA +al+la+   +++  ++ +++ tg+++  l   
  gi|13541401|ref|NP_111089.1| 132 RPIDFIERYAESLNV--DDDVRDEAIALTNKIASQVSLMRKSPSTIAISALYLASILKDRKLVQRYVTKKTGITEVTLIRT 210
                                   59*******999555..448*************************************999********************* PP

                                   HHHHHHHHH CS
                      Cyclin_C  83 velilells 91 
                                   ++ i ++l+
  gi|13541401|ref|NP_111089.1| 211 YKEIYSYLT 219
                                   ****99984 PP

>> Cyclin_N  Cyclin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0     0.023        83      75     118 ..      80     120 ..      60     126 .. 0.71
   2 !   17.6   0.1   6.7e-07    0.0024      32      91 ..     131     190 ..     115     221 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.023
                                   HHHHHHHHHHHHHHSSS---HHHHHHHTTTSS-HHHHHHHHHHH CS
                      Cyclin_N  75 lvgatcLllAaKveeisppkledlvyitdeafteeeilemErli 118
                                    v a+c+l+A++    sp++l+ +  +    ++ + i + E l+
  gi|13541401|ref|NP_111089.1|  80 AVLAACILVASRSS-PSPVTLRYVSRAL--KIDPSRIWRTESLV 120
                                   6899*******983.3366655554443..46666666666666 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 6.7e-07
                                   HHHHHHHHHHHHHTT--TTHHHHHHHHHHHHHHHS---CCCHHHHHHHHHHHHHHHHSSS CS
                      Cyclin_N  32 ailidwlvevaekfkltpetlflavnyldRflskksvpkdklqlvgatcLllAaKveeis 91 
                                      id++ + ae+++++ ++   a+ + ++  s+ s+ ++   ++++++L+lA+ +++ +
  gi|13541401|ref|NP_111089.1| 131 VRPIDFIERYAESLNVDDDVRDEAIALTNKIASQVSLMRKSPSTIAISALYLASILKDRK 190
                                   4449**************************************************887764 PP

>> TFIIB_C_1  Transcription factor IIB C-terminal module 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.0   0.00079       2.8      22      71 ..      56     102 ..      34     123 .. 0.77
   2 ?    3.2   0.0     0.025        88       8      33 ..     136     161 ..     131     198 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00079
                     TFIIB_C_1  22 vleealelakrfvGkrrergervekqeevaaaclmlaaerlrqPvPLael 71 
                                   v+++al++    v +   rg+     + v aac+++a+     Pv L  +
  gi|13541401|ref|NP_111089.1|  56 VMKNALNIYLDNVSHGISRGRG---CTAVLAACILVASRSSPSPVTLRYV 102
                                   6666666666666666666553...5789************999998655 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.025
                     TFIIB_C_1   8 alevllklsrrdeavleealelakrf 33 
                                    +e + ++ ++d++v++ea++l ++ 
  gi|13541401|ref|NP_111089.1| 136 FIERYAESLNVDDDVRDEAIALTNKI 161
                                   67788899999**********98765 PP

>> Cyclin_C_2  Cyclin C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       2.3   8.1e+03      63      75 ..      95     107 ..      81     124 .. 0.58
   2 ?   12.0   0.1   5.8e-05      0.21      48      77 ..     170     203 ..     134     219 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2.3
                    Cyclin_C_2  63 eklaerYleeklg 75 
                                   ++++ rY+++ l+
  gi|13541401|ref|NP_111089.1|  95 SPVTLRYVSRALK 107
                                   3334667666654 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 5.8e-05
                    Cyclin_C_2  48 ytPsqIalaal....lladeklaerYleeklgke 77 
                                    +Ps Ia++al    +l+d+kl++rY+++k g +
  gi|13541401|ref|NP_111089.1| 170 KSPSTIAISALylasILKDRKLVQRYVTKKTGIT 203
                                   58*********55556679**********99765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       481  (0.026828); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1597.85
//
Query:       gi|13541402|ref|NP_111090.1|  [L=380]
Description: aminotransferase [Thermoplasma volcanium GSS1]
Scores for complete 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   93.1   0.0    2.3e-26   92.7   0.0    1.0  1  Aminotran_5  Aminotransferase class-V


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 !   92.7   0.0   1.3e-30   2.3e-26      33     340 ..      25     323 ..      11     343 .. 0.84

  Alignments for each domain:
  == domain 1  score: 92.7 bits;  conditional E-value: 1.3e-30
                                   SSSHHHHHHHHHHHHHHHHHHHHHT-STGGGEEEESSHHH.HHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHH CS
                   Aminotran_5  33 svhhlgkeatkaveearekvaelinaeseeeiiftsGtte.ainlvalslarslkpgdeivvteaehhanlvpwqelakrt 112
                                   +v+ ++ e+ +a+++  e ++ +++a++++    + G+++ a++ v       l ++ +++v +++  +n+  w+ + +++
  gi|13541402|ref|NP_111090.1|  25 NVGFASPEFLEAMRNSLEGLRIVVGADNSYLPFILPGSGTvAMESVTSI----LPRKGKVLVASNGVFGNR--WKPILDAH 99 
                                   56667789999999999**********9888777788774455554444....6899**************..******** PP

                                   TEEEEEEEBETTSCBEGGGHHHH--.TTEEEEEEESBETTTTEB--HHHHHHHHHHTT-EEEEE-TTTTTTS---HHHHTE CS
                   Aminotran_5 113 gakvkvipldeegeldldeleklln.ektklvaithvsnvtGtiqpveeigklakkkgalvlvDaaqavghipidvkklgv 192
                                    ++ +v+++++++++d+  ++++l+  + + + +thv+++tG+  ++eei++ a+     ++vD++++vg   ++vk++g+
  gi|13541402|ref|NP_111090.1| 100 RMEYEVLEAEPGKSVDPASIKDKLSsGNFASLVFTHVETSTGVRADIEEICRKARPLVDRIVVDGVASVGGETLKVKEWGI 180
                                   ************************7699****************************888999******************* PP

                                   SEEEEETTT.TTSSTT-EEEEEEHHHHHTS..SS.STTSEEEEET.TEEEEHCTTGGGS.S...S--HHHHHHHHHHHHHH CS
                   Aminotran_5 193 DflafsghK.llgPtGiGvlyvrkellekleplllggemveevsl.eettfaeapskfeaG...Tpnvagiiglgaaleyl 268
                                   D +   ++K l  P+G  +l+v k+ l++     + g+ ++ ++  e      +  k e G   T++v  +++l+ +++ +
  gi|13541402|ref|NP_111090.1| 181 DAIITASQKgLASPPGAALLVVAKDSLNNT---AGDGYFFDLKNWvEPMN---TYLKGENGylsTEPVGVVMALSHVFNDI 255
                                   ************************999988...66676666555533222...33333333333***************** PP

                                   HCHHHHHHHHHHHHHHHHHHHHHCTSTTEEEES.-B-CTCBSEEEEEETTCSHHHHHHHHHHTTEEEEEE-T CS
                   Aminotran_5 269 eeigleaiekhekelaeyllerlkslpgvrlygpdkaerrasivsfnfkgvhaedvatlLdeegIavrsGhh 340
                                   ++ gle+  k+++  +e+l e+l++++   l  +d+++ ++++++++ ++  ++d++++  + gI+  +G h
  gi|13541402|ref|NP_111090.1| 256 RAEGLENTIKRHRVFSEALNEGLEEIGLKVL--ADREHWSNTVTAVVAER--SDDIVKFALSMGIEFATGVH 323
                                   **************************99988..45666666666666654..67888888888999999977 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (380 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.34s 00:00:00.95 Elapsed: 00:00:00.55
# Mc/sec: 2091.84
//
Query:       gi|13541403|ref|NP_111091.1|  [L=410]
Description: hypothetical protein TVN0572 [Thermoplasma volcanium GSS1]
Scores for complete 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-65  220.0   0.0    5.6e-63  213.0   0.0    2.0  1  DUF790    Protein of unknown function (DUF790)


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 !  213.0   0.0   3.1e-67   5.6e-63       1     268 [.       1     261 [.       1     344 [. 0.94

  Alignments for each domain:
  == domain 1  score: 213.0 bits;  conditional E-value: 3.1e-67
                        DUF790   1 MLpsdllrvrr.rggkivpkflkeenlelaaelielfeehvGekrgeleeelkeleeeatdyklvrGLakllereaefete 80 
                                   M+p +ll++++ ++g+i+p ++ +++   a+++i++f++++G kr+el e++k++e +a+++k vr +a ller ++f+ +
  gi|13541403|ref|NP_111091.1|   1 MFPLELLVAKKtENGSIRPIVIPPDSKWPAENVIDTFRSSIGLKRRELYERIKDIEYQAKNPKTVRSMALLLERISKFRDS 81 
                                   9******9988699******************************************************************* PP

                        DUF790  81 spldpeelReevFeaaaeavvseeereevleevaeelgvspeeveealyadleenkiLtefeeitpeeLlkrYNlslvqtl 161
                                    +++++e+R+ +F+ ++  +v +eer++ +e +a++++v ++e+e aly+d+e +++L ++++itp++L+++YNl++++tl
  gi|13541403|ref|NP_111091.1|  82 FQVPSSEVRRFLFSLGP--AVRPEERHTLVEMAAKHFSVGKQEIEDALYGDIEPEQRLISVPDITPDWLVRNYNLEQIETL 160
                                   *****************..9************************************************************* PP

                        DUF790 162 LfkatelrirvsdaeykelfravkllgLmyeieedaeegleitvdGPaslfkaterYGlalAkllpallkvekWeleAeik 242
                                   ++ka ++ ++  + ++  ++ a+k lgLm+e+ +++  gl++ +dGP+s+f  ++rYG alA+    l+ +++W+++A+++
  gi|13541403|ref|NP_111091.1| 161 IYKAKSMVVKKLS-NWLPFIDAIKELGLMFEALNEE--GLTVIIDGPNSIFGGMDRYGSALAQAFSLLAGSSSWSISATVS 238
                                   *************.9*****************9988..9****************************************** PP

                        DUF790 243 drdkkkrelrfeldsedsglvshyee 268
                                    ++   ++++++ld++ + ++++++e
  gi|13541403|ref|NP_111091.1| 239 IGG---KDYSVQLDQSLNYYLPEKRE 261
                                   **9...9********88777776554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (410 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       576  (0.0321267); expected 358.6 (0.02)
Passed bias filter:                      543  (0.0302861); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 2577.03
//
Query:       gi|13541404|ref|NP_111092.1|  [L=455]
Description: DNA helicase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.5e-22   79.7   0.3    6.5e-22   78.3   0.1    1.8  2  ResIII         Type III restriction enzyme, res subunit
      1e-20   74.0   0.0    2.2e-20   73.0   0.0    1.4  1  ERCC3_RAD25_C  ERCC3/RAD25/XPB C-terminal helicase
    1.9e-16   60.3   0.2    3.7e-14   53.0   0.0    2.4  2  Helicase_C     Helicase conserved C-terminal domain
    2.7e-11   43.2   0.0    1.7e-10   40.6   0.0    2.4  2  XPB_DRD        Xeroderma pigmentosum group B helicase damage 
    6.6e-06   26.0   0.2    1.9e-05   24.5   0.2    1.8  1  DEAD           DEAD/DEAH box helicase
      0.005   15.6   0.1      0.019   13.7   0.1    1.9  1  SNF2_N         SNF2 family N-terminal 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 !   78.3   0.1   2.2e-25   6.5e-22       2     171 .]      71     210 ..      70     210 .. 0.93
   2 ?   -2.1   0.0       1.1   3.3e+03      48      61 ..     321     334 ..     289     376 .. 0.56

  Alignments for each domain:
  == domain 1  score: 78.3 bits;  conditional E-value: 2.2e-25
                                   -EE-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG.. CS
                        ResIII   2 lelreyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseay 82 
                                   ++lr+yQ +a+++++       + rg i+++T +GKT + +++i r +k     k+++lvp+++ll q+++++k++l+ + 
  gi|13541404|ref|NP_111092.1|  71 IKLRPYQSDALDKWA-----SSNMRGTIVLPTAAGKTHIGIEAINRTKK-----KTIILVPTIDLLTQWKQKIKELLNLD- 140
                                   79************9.....6789***********************99.....7**********************987. PP

                                   ..GEEEESSS-B--.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.TTTHHHHHT---SEEE CS
                        ResIII  83 keigkkvsgdkkkakekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakkswreilekfkeavll 163
                                     +g++  g+k+++        +i+v+t++s++           e+  ++fd+ii DE+H+l++ ++ r i+ ++ + ++l
  gi|13541404|ref|NP_111092.1| 141 --AGQIGGGEKEER--------EITVSTYDSAYLMA--------EKYGNHFDLIIADEVHHLAS-EKLRMIAMMYTARYRL 202
                                   ..677777777666........************99........9999****************.**************** PP

                                   EEESS-S- CS
                        ResIII 164 glTATper 171
                                   glTAT er
  gi|13541404|ref|NP_111092.1| 203 GLTATYER 210
                                   *****875 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.1
                                   H-S.....-EEEEE CS
                        ResIII  48 llkkgkeekflflv 61 
                                   l  ++k+e+++++ 
  gi|13541404|ref|NP_111092.1| 321 LVAQHKNERIIIFS 334
                                   22222233333333 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 !   73.0   0.0   7.2e-24   2.2e-20      35     183 ..     303     443 ..     295     445 .. 0.91

  Alignments for each domain:
  == domain 1  score: 73.0 bits;  conditional E-value: 7.2e-24
                 ERCC3_RAD25_C  35 kkllyvmnpn.kfracefLikyhekrgDkiivfsDnvfaLkeyakklkkpyiyGetseaerlkilqkfkknpkvntiflsk 114
                                   k+  ++mnp  k++++  L+  h  ++++ii+fs++  +  +++k++  p i+  ts+ er++i + fk+  k+n+i  s+
  gi|13541404|ref|NP_111092.1| 303 KSREIAMNPAgKIEMARTLVAQH--KNERIIIFSEDTETTYRISKEFLIPAITYMTSKDERSEIPELFKTG-KYNVIATSR 380
                                   5556788986599******9988..5789***************************************986.89******* PP

                 ERCC3_RAD25_C 115 vgDtsiDlPeanvliqisshfgsrrqeaqrlGriLrakkksneeefnaffYsLvskDtkemaystkrqq 183
                                   v D+ +D+P+a+v i +s   gs rq  qrlGriLr+  +     ++a  Y Lv + t e   s++r++
  gi|13541404|ref|NP_111092.1| 381 VLDEGVDFPDASVAIVMS-GSGSTRQFRQRLGRILRPSYG-----KKAVMYELVTSQTAEFGASRRRRK 443
                                   **************9665.679***************887.....79***************9999985 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.1   0.0    0.0091        27      13      58 ..     110     155 ..     101     179 .. 0.69
   2 !   53.0   0.0   1.3e-17   3.7e-14       3     109 ..     315     415 ..     313     417 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0091
                                   TTTTSEEEEEESSHHHHHH.HHHHHHHTTSTEEEESTTSTHHHHHHH CS
                    Helicase_C  13 eeeggkilifvntidrlek.vklllekkgikvavlhgelpqnereei 58 
                                   ++ ++k++i v+tid l +  + ++e  ++ +  + g  +++ere +
  gi|13541404|ref|NP_111092.1| 110 NRTKKKTIILVPTIDLLTQwKQKIKELLNLDAGQIGG-GEKEEREIT 155
                                   57899**********7766655554444566655555.455555544 PP

  == domain 2  score: 53.0 bits;  conditional E-value: 1.3e-17
                                   HHHHHHHHHHTTTTSEEEEEESSHHHHHHHHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTST CS
                    Helicase_C   3 leallellkleeeggkilifvntidrlekvklllekkgikvavlhgelpqnereeileqfnkgesdvLiatdvaerGidip 83 
                                   +e+   l+  ++++++i+if++ +++ +  ++    k++ + +++  ++++er ei e f+ g+++v+ +++v+ +G+d+p
  gi|13541404|ref|NP_111092.1| 315 IEMARTLV-AQHKNERIIIFSEDTETTY--RIS---KEFLIPAITYMTSKDERSEIPELFKTGKYNVIATSRVLDEGVDFP 389
                                   55666666.899*************997..666...446666777889********************************* PP

                                   TESEEEESSSSSSHHHHHHHHTTSSS CS
                    Helicase_C  84 kvnlVinfdlprnvtsyiqriGRtgR 109
                                   ++++ i ++   +++++ qr GR+ R
  gi|13541404|ref|NP_111092.1| 390 DASVAIVMSGSGSTRQFRQRLGRILR 415
                                   ************************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 !   40.6   0.0   5.6e-14   1.7e-10       1      57 []       4      59 ..       4      59 .. 0.94
   2 ?   -1.8   0.0      0.96   2.9e+03       5      14 ..      90      99 ..      89     111 .. 0.80

  Alignments for each domain:
  == domain 1  score: 40.6 bits;  conditional E-value: 5.6e-14
                                  EEEETTEEEECSSSTT...-C..T.EEETTTTEEEEEGGGHHHHHHHHHCTT--EEEES CS
                       XPB_DRD  1 LrYdrGTllidgdprgkaslp..fvewDeRvekyRapAlrYrdlveaLraagiefeDrv 57
                                  L+Y  G +li g++ +   lp   + +D R+ +yRa++++Y ++ e+L+ +g ef+D+v
  gi|13541404|ref|NP_111092.1|  4 LTYSGGSILIRGYEGE---LPpdIAIFDNRIMCYRALGMNYEKVAEYLKSKGKEFTDNV 59
                                  89************98...4445999*******************************98 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.96
                                  TTEEEECSSS CS
                       XPB_DRD  5 rGTllidgdp 14
                                  rGT+++ + +
  gi|13541404|ref|NP_111092.1| 90 RGTIVLPTAA 99
                                  8****98766 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.2   6.4e-09   1.9e-05       2     139 ..      75     190 ..      74     212 .. 0.70

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 6.4e-09
                                   HHHHHHHHHHH.TTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEE CS
                                   xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD   2 diQaeaiplil.gggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvlli 81 
                                   ++Q+ a++    ++    +  +T++GKT +  i ++       ++t++k++i++Pt  L  q  +++k++++   l +  i
  gi|13541404|ref|NP_111092.1|  75 PYQSDALDKWAsSNMRGTIVLPTAAGKTHI-GIEAI-------NRTKKKTIILVPTIDLLTQWKQKIKELLN---LDAGQI 144
                                   567777766663444667899*******99.66666.......58899************************...556555 PP

                                   ETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD  82 iggvaardqlskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfs 139
                                    gg++++          +i+v+t +    + + ++   +++ +++ DE++ l +++ +
  gi|13541404|ref|NP_111092.1| 145 GGGEKEE---------REITVSTYDSAYLMAE-KY--GNHFDLIIADEVHHLASEKLR 190
                                   5554443.........3567777777765554.44..578899999999999998433 PP

>> SNF2_N  SNF2 family N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.1   6.4e-06     0.019      93     214 ..     110     207 ..      43     208 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.4e-06
                                   ....S-EEEE--H.HHHHHHHHHHHHH-TTS-EEE--SSHHHH-----------------EEEE-HHHHHHHT......TT CS
                                   xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        SNF2_N  93 dtlagptLivvPa.slldqWeneierhvsssalrvlvyggqkkmkkkntkvapklladydvvittYdvlsreaelqkkrsv 172
                                   ++ ++ t+i+vP+ +ll+qW+++i++ ++ +a      gg++              ++ ++ + tYd     a       +
  gi|13541404|ref|NP_111092.1| 110 NRTKKKTIILVPTiDLLTQWKQKIKELLNLDAG---QIGGGE-------------KEEREITVSTYDSAYLMA-------E 167
                                   3444559*******************9999964...333332.............36899*******988666.......4 PP

                                   S-S-S-SEEEES-GGGT--TTSHHHHHHHH---S-EEEE-S- CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        SNF2_N 173 lkqvewkrvvlDEghtlknstskaaeavskLstsnrwiltGT 214
                                       + + ++ DE h l +++ ++  ++    +++r+ lt+T
  gi|13541404|ref|NP_111092.1| 168 KYGNHFDLIIADEVHHLASEKLRMIAMMY--TARYRLGLTAT 207
                                   4688999***********99766655555..899**999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (455 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       516  (0.0287802); 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:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 3196.60
//
Query:       gi|13541405|ref|NP_111093.1|  [L=381]
Description: SAM-dependent methyltransferase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score 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   15.1   0.0      0.021   14.4   0.0    1.3  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
      0.023   14.7   0.0      0.051   13.6   0.0    1.6  1  Frankia_peptide  Ribosomally synthesized peptide prototyped b


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 ?   14.4   0.0   2.3e-06     0.021       4      60 ..      91     144 ..      88     190 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.3e-06
               Methyltransf_15   4 ilDlfsGaGGnviqfalvfekviaieinleklacaqhNaevYgvsdkitlvlgdvfe 60 
                                   +lD+ sGaG ++i f l++    +ie+++++  ++  N  +Y    k  +v  d+ +
  gi|13541405|ref|NP_111093.1|  91 VLDVGSGAGMQCIMFGLEY-GCKGIEVDRSRYLMSLLNSIAY--RCKSEFVNSDFYK 144
                                   89****************9.89********************..5555666777665 PP

>> Frankia_peptide  Ribosomally synthesized peptide prototyped by Frankia Franean1_4349.
   #    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       2      23 ..       5      26 ..       4      34 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.7e-06
               Frankia_peptide  2 verlIgrAvtDeaFRqrLladp 23
                                  +e+++ rAv DeaFR +L    
  gi|13541405|ref|NP_111093.1|  5 LEKILERAVYDEAFRNKLNSQI 26
                                  79**************996655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (381 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.34s 00:00:00.93 Elapsed: 00:00:00.52
# Mc/sec: 2203.12
//
Query:       gi|13541406|ref|NP_111094.1|  [L=195]
Description: GTP cyclohydrolase II [Thermoplasma volcanium GSS1]
Scores for complete 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  196.8   0.0      2e-58  196.6   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 !  196.6   0.0   1.1e-62     2e-58       5     163 .]       7     168 ..       3     168 .. 0.96

  Alignments for each domain:
  == domain 1  score: 196.6 bits;  conditional E-value: 1.1e-62
                                   EEEEEETTEEEEEEEE--.....EEEEEE-.........EEEEEE--HHHHHS-B--TTTTTHHHHHHHHHHHH-.EEEEE CS
               GTP_cyclohydro2   5 eaklptrfgefrliayedkvdgkehlalvkgdi....pvlvRvHsecltgDvlgslrcdcgeqldealeliaeegrGvlvy 81 
                                   +aklpt+fg fr++++ ++ + k h ++v gd+    +v+ R+HsecltgDvlgslrcdc++ql ++l+++ +++ G+l+y
  gi|13541406|ref|NP_111094.1|   7 NAKLPTEFGLFRIYTFVNDEN-KDHAVIVRGDPrgkeNVPLRIHSECLTGDVLGSLRCDCRDQLIQSLRYLGRQEYGMLIY 86 
                                   689*************88755.99************9999*******************************77999***** PP

                                   E--TTTTTHHHHHHHHHHHHHCT--HHHHHHHHT--S-----HHHHHHHHHTT--EEEEE-S-HHHHHHHCTT....SEEE CS
               GTP_cyclohydro2  82 lrqegrgigllnklkayalqdeglDTveanlalglpadardygiaaqILkdlgvkkirLlTnnpekveaLegfgievverv 162
                                   lrqegrgigllnk+kay+lqd+g+DTveanl+lglp d r+y+ aa++L+ +++k+i ++Tnnpek+++L + gi+v+ r+
  gi|13541406|ref|NP_111094.1|  87 LRQEGRGIGLLNKIKAYSLQDMGADTVEANLKLGLPVDSRNYSFAAEVLRYFEIKSIYIMTNNPEKIKSLIESGINVKGRI 167
                                   *******************************************************************************99 PP

                                   E CS
               GTP_cyclohydro2 163 p 163
                                   p
  gi|13541406|ref|NP_111094.1| 168 P 168
                                   7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       379  (0.0211389); 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: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1239.37
//
Query:       gi|13541407|ref|NP_111095.1|  [L=194]
Description: indolepyruvate oxidoreductase subunit beta [Thermoplasma volcanium GSS1]
Scores for complete 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   1.1    3.9e-34  118.3   1.1    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 !  118.3   1.1   2.2e-38   3.9e-34       1     176 [.      12     182 ..      12     183 .. 0.93

  Alignments for each domain:
  == domain 1  score: 118.3 bits;  conditional E-value: 2.2e-38
                                   CTSTHHHHHHHHHHHHHHTT-EEEEEEEEESSSSSSCEEEEEEEESS.-SSS--TTSEEEEEESSHHHHHHHGGGEEEEEE CS
                           POR   1 GGqGvvtagkilakaaaraGyyvqanreygseirGghsyshvrisdepivpsievgeadllvaldaetlsehldglkpggi 81 
                                   GGqG++t+gk+la+aa+ aG +v  ++++g ++rGg++ +hvr+++    p ie+g+ad++++l+a+++ ++l++  p++ 
  gi|13541407|ref|NP_111095.1|  12 GGQGIITMGKMLATAADLAGVKVIVSETHGLSQRGGSVAVHVRMGNV-YAPLIERGKADYIIGLEASEAVRNLSYAGPNTK 91 
                                   9********************************************98.99****************9999*********** PP

                                   EEEECTCGTT-CCHHHCTS-HHHHHHH.T-EEEEE-HHHHHHHCCC.CCHHHHHHHHHHHHHHTS-HHHHHHHHHCCS-CH CS
                           POR  82 iiynseelkpdelkkakeeerelkerl.gvrvygvdatkiakeiggneraaNtvmlGalaallglplealeeaikkrfpkk 161
                                   +i+n++ +kp   k  +   +e+ e+l +++vy +da+ ia e+g+ ++  N+v+lG+++ +    + +l+  +++ ++  
  gi|13541407|ref|NP_111095.1|  92 FIINKNLIKPVLPKVMPATLDEVFEALkDYQVYHIDAETIAAESGN-RKGSNAVLLGYMYSINA--FRTLKISVNNFLQA- 168
                                   ************************999****************888.************99954..45666677666665. PP

                                   .HHHHHHHHHHHHHH CS
                           POR 162 keviekNlkafragy 176
                                     v e N+++frag+
  gi|13541407|ref|NP_111095.1| 169 -MVSESNKACFRAGI 182
                                   .58899999999995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        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: 00:00:00.44
# Mc/sec: 1327.20
//
Query:       gi|13541408|ref|NP_111096.1|  [L=604]
Description: indolepyruvate:ferredoxin oxidoreductase, alpha and beta subunits [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.4e-21   74.4   0.1    1.7e-20   73.4   0.1    1.5  1  TPP_enzyme_C     Thiamine pyrophosphate enzyme, C-terminal TP
    1.7e-15   57.4   0.0    2.9e-15   56.7   0.0    1.3  1  POR_N            Pyruvate flavodoxin/ferredoxin oxidoreductas
    6.9e-12   44.7  13.2    6.6e-09   35.2   4.8    2.6  2  Fer4             4Fe-4S binding domain
    2.3e-08   33.8  18.3    4.2e-07   29.8   3.7    2.9  3  Fer4_6           4Fe-4S binding domain
      1e-07   31.9  20.7    3.7e-05   23.8  11.0    2.4  2  Fer4_10          4Fe-4S dicluster domain
      1e-07   31.7   0.2     0.0065   16.1   0.0    2.3  2  TPP_enzyme_N     Thiamine pyrophosphate enzyme, N-terminal TP
    1.8e-07   31.6   7.8      4e-05   24.1   1.3    2.6  2  Fer4_7           4Fe-4S dicluster domain
    3.1e-07   30.1  16.2    6.5e-05   22.8   1.9    2.7  2  Fer4_2           4Fe-4S binding domain
      4e-06   26.9  11.2    6.7e-05   22.9  10.7    2.4  2  Fer4_21          4Fe-4S dicluster domain
      5e-06   26.6  19.7    0.00023   21.3   9.7    2.4  3  Fer4_9           4Fe-4S dicluster domain
    5.2e-06   26.9   2.8     0.0029   18.1   0.1    2.5  2  Fer4_17          4Fe-4S dicluster domain
    2.8e-05   24.3  11.6     0.0027   18.1   3.5    2.5  2  Fer4_4           4Fe-4S binding domain
      7e-05   23.7   8.1    0.00039   21.3   1.3    2.6  2  Fer4_16          4Fe-4S double cluster binding domain
    0.00075   20.0  10.3      0.051   14.1   3.7    3.0  2  Fer4_13          4Fe-4S single cluster domain of Ferredoxin I
    0.00079   20.2   6.0    0.00079   20.2   6.0    2.6  2  Fer4_3           4Fe-4S binding domain
    0.00084   19.2   0.0     0.0021   17.9   0.0    1.7  1  Transketolase_C  Transketolase, C-terminal domain
     0.0016   18.7   0.0     0.0046   17.2   0.0    1.8  1  PFOR_II          Pyruvate:ferredoxin oxidoreductase core doma
     0.0063   16.2   0.4       0.18   11.5   0.2    2.7  2  Transket_pyr     Transketolase, pyrimidine binding domain
     0.0067   16.8  11.1       0.11   13.0   2.9    2.6  2  Fer4_8           4Fe-4S dicluster domain
     0.0083   16.9   4.6       0.28   12.1   0.7    2.5  2  Fer4_22          4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.012   16.3   7.0       0.29   11.9   0.9    2.9  2  Fer4_15          4Fe-4S single cluster domain
      0.014   14.4   0.1      0.024   13.6   0.1    1.3  1  E1_dh            Dehydrogenase E1 component
        3.5    7.9   8.0       0.32   11.2   1.4    1.9  1  Fer4_18          4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.4   0.1   2.1e-23   1.7e-20       1     152 [.     382     517 ..     382     518 .. 0.93

  Alignments for each domain:
  == domain 1  score: 73.4 bits;  conditional E-value: 2.1e-23
                                   ESSHHHHHHHHHHTTSSSSEEECETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHT.GGGHHHHHHTT-SEEEEEE CS
                  TPP_enzyme_C   1 diGcltlwaarllkvkrprsyltsgglgtmGyglpaAiGaklakpdrevvaivGDGgflmi.lqelatavrrnlpitvvvl 80 
                                   diGc+tl      ++ +p + ++    + mG +++++ G+ +a  ++  v+i+GD++f+++ lq +a+av+++ p +++vl
  gi|13541408|ref|NP_111096.1| 382 DIGCYTL------GALPPFNEQD--SATNMGSSVGISNGVFRA-TGQIPVSIIGDSTFFHSgLQGVANAVYNGTPEIIIVL 453
                                   89****9......8888877777..89***************8.5679********************************* PP

                                   E-SBCCCHHHHHHHHTCCTTTTSBB.BS----HHHHHHHTTSE.EEEESSH.HHHHHHHHHHHH....CSSSEEEEE CS
                  TPP_enzyme_C  81 nNegygmtggqqepfggkrksgpagkdlkpvdfaklaealGak.garvekadveeleealkeal....ekkgpalie 152
                                   +N++++mtg+q++p ++             ++++++a+a+G++ + + ++ dv+e  +a+++a     e+k+pali+
  gi|13541408|ref|NP_111096.1| 454 DNRSTAMTGQQPSPSTH-------------ISIENVARAMGIDfVDTFDPFDVKEGSDAVQKAAeyvkENKKPALIV 517
                                   ************99874.............8999*********555*****************99999999***996 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 !   56.7   0.0   3.7e-18   2.9e-15       2     195 ..      16     198 ..      15     227 .. 0.89

  Alignments for each domain:
  == domain 1  score: 56.7 bits;  conditional E-value: 3.7e-18
                                   HHHHCTEEEEEE--BTTTCCHHHHHCHCCCCCTTEE.EEEE-SSHHHHHHHHHHHHCTT-EEEEEEECCHHHHCCCCHHHH CS
                         POR_N   2 aaiaagvdviaaYPITPsseiaeelaellakgevgdvevvqmesEigaisaviGAaaaGaraaTaTSgqGllLmienlgla 82 
                                   +a++agv+v+a+YP TPs+ei+e+l+ l ++++          +E  a +++ GAa+ G++a+ a    G+  + + l+  
  gi|13541408|ref|NP_111096.1|  16 GALKAGVEVAAGYPGTPSTEIIETLKGLNDSVYA-----EWSINEKVALETAYGAAMMGSKALAAMKHVGMNVAADPLFSS 91 
                                   789***********************99988886.....35569************************************* PP

                                   HHTT--EEEEEEEEE-STTBEEEEE--TTCHHHHS---EEEE-SSHHHHHHHHHHHHHHHHHCTSEEEEEEEHHHH.HEEE CS
                         POR_N  83 ageelPvvivvvaRalpstglsirtdqsDlmaardtglivlasenvqeafdlalvAfnlAekvrvPvivlfDgfllsheve 163
                                   + + +   +v+v    ps  +s +++q   ++ +   + v+ + + q a+dl+++Af ++ek+r Pvi+ +   ++ h ++
  gi|13541408|ref|NP_111096.1|  92 SYTGVDGALVIVSADDPSM-WSSQNEQDNRYYGLHALIPVIEPYDPQSAYDLTIKAFEISEKLRHPVILRTTTRVG-HVRS 170
                                   ************9999**9.***************************************************99999.**** PP

                                   EEEC-SGG.GS-----SBXXXXXXXXSXXXBX CS
                         POR_N 164 kvelpdeedelklikekleeyerkeyaldpek 195
                                   +v+++ +      +++k  e+++ +y + pe+
  gi|13541408|ref|NP_111096.1| 171 QVNFERDG----QKEKKGIEKNPGKYVMAPEN 198
                                   *****999....55555556666666566555 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   1.2   4.7e-05     0.036       2      16 ..     538     552 ..     537     553 .. 0.90
   2 !   35.2   4.8   8.5e-12   6.6e-09       4      24 .]     569     589 ..     567     589 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.7e-05
                                   EEETTTSSS-THHHH CS
                          Fer4   2 videekCigCGaCve 16 
                                   ++d ekC+gC +C++
  gi|13541408|ref|NP_111096.1| 538 EVDLEKCTGCSICYD 552
                                   79***********86 PP

  == domain 2  score: 35.2 bits;  conditional E-value: 8.5e-12
                                   ETTTSSS-THHHHHSTTTEEE CS
                          Fer4   4 deekCigCGaCvevCPvgAIt 24 
                                   + + CigCGaCvevCP++AI+
  gi|13541408|ref|NP_111096.1| 569 IDDSCIGCGACVEVCPFNAIK 589
                                   6799****************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 ?   -1.9   0.4       5.4   4.2e+03       6      12 ..     350     356 ..     350     356 .. 0.86
   2 !   14.0   1.2     5e-05     0.039       1      20 [.     536     557 ..     536     560 .. 0.83
   3 !   29.8   3.7   5.4e-10   4.2e-07       3      24 .]     567     588 ..     565     588 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 5.4
                        Fer4_6   6 pdkCigC 12 
                                   p +C gC
  gi|13541408|ref|NP_111096.1| 350 PALCPGC 356
                                   679**** PP

  == domain 2  score: 14.0 bits;  conditional E-value: 5e-05
                        Fer4_6   1 vveidpdkCigCgdCvrv..CP 20 
                                   ++e+d +kC+gC  C++   CP
  gi|13541408|ref|NP_111096.1| 536 KAEVDLEKCTGCSICYDFftCP 557
                                   689************7644477 PP

  == domain 3  score: 29.8 bits;  conditional E-value: 5.4e-10
                        Fer4_6   3 eidpdkCigCgdCvrvCPegai 24 
                                   ++ +d+CigCg+Cv vCP++ai
  gi|13541408|ref|NP_111096.1| 567 AFIDDSCIGCGACVEVCPFNAI 588
                                   5899*****************8 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8  11.0   4.7e-08   3.7e-05       2      56 .]     537     584 ..     536     584 .. 0.88
   2 !   22.2   2.1   1.5e-07   0.00012       5      27 ..     569     591 ..     565     601 .. 0.77

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 4.7e-08
                       Fer4_10   2 vvidddtCirCgkCvka..CPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                   +++d ++C++C  C ++  CP+         +   ++++    ++C+gcgaCve+CP
  gi|13541408|ref|NP_111096.1| 537 AEVDLEKCTGCSICYDFftCPS---------ILPLSNKKAFIDDSCIGCGACVEVCP 584
                                   67899***********556***.........8888888888899************9 PP

  == domain 2  score: 22.2 bits;  conditional E-value: 1.5e-07
                       Fer4_10   5 dddtCirCgkCvkaCPadltsvg 27 
                                    dd+Ci+Cg+Cv++CP+++ +v+
  gi|13541408|ref|NP_111096.1| 569 IDDSCIGCGACVEVCPFNAIKVK 591
                                   579**************664444 PP

>> TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   8.3e-06    0.0065      10     106 ..      17     113 ..       8     166 .. 0.70
   2 !   13.5   0.0   5.2e-05      0.04      50     159 ..     405     518 ..     398     529 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 8.3e-06
                                   HHHHCT--EEEE---CCCHHHHCCHHCT..TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHHHHCHHHHHHHHHH CS
                  TPP_enzyme_N  10 aLkalgvehvfgvpGsrilplldalseeq.girvvlarhEqgaafaAdgyaratgkpgvvlvtsgpGatnaltalaeAkvd 89 
                                   aLk +gve++ g+pG+ ++++++ l+  + ++    + +E +a   A g a++  k  +++ ++g ++  a   l++ +++
  gi|13541408|ref|NP_111096.1|  17 ALK-AGVEVAAGYPGTPSTEIIETLKGLNdSVYAEWSINEKVALETAYGAAMMGSKALAAMKHVGMNV--AADPLFSSSYT 94 
                                   455.5**********************9988888889*****************99999999997655..45555555555 PP

                                   T-..-EEEEEEE--CCCHH CS
                  TPP_enzyme_N  90 ri..Pllvlsgdrptslrg 106
                                   ++   l+++s+d p+   +
  gi|13541408|ref|NP_111096.1|  95 GVdgALVIVSADDPSMWSS 113
                                   5522355566666655555 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 5.2e-05
                                   HHHHHHHHHHHHHTS-EEEEE-CHHHHHHCHHHHHHHHHHT--EEEEEEE--CCCHH..S..TC--T-CCHHHCCCSSE.. CS
                  TPP_enzyme_N  50 gaafaAdgyaratgkpgvvlvtsgpGatnaltalaeAkvdriPllvlsgdrptslrg..qgvlqqeldqlalfrpvtky.. 126
                                   + +++  g++ratg++ v +    + + ++l ++a+A ++++P ++++ d+ ++     q+ +   +++++++r +  +  
  gi|13541408|ref|NP_111096.1| 405 SSVGISNGVFRATGQIPVSIIGDSTFFHSGLQGVANAVYNGTPEIIIVLDNRSTAMTgqQPSPSTHISIENVARAMGIDfv 485
                                   66788899*************9999***********************998777666454444444566666664443322 PP

                                   .EEE-SSGGGHHHHHHHHHHHHHSSS--EEEEEE CS
                  TPP_enzyme_N 127 .aervtspeelpealrrAirtalsgrpgPvylel 159
                                    ++ + +++e   a+++A +   ++++ P++++ 
  gi|13541408|ref|NP_111096.1| 486 dTFDPFDVKEGSDAVQKAAEYV-KENKKPALIVA 518
                                   2666666666677777777777.78888888765 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.7   0.00094      0.74      27      49 ..     533     557 ..     498     559 .. 0.72
   2 !   24.1   1.3   5.1e-08     4e-05       1      21 [.     572     592 ..     571     601 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00094
                        Fer4_7  27 gtekveidpekClgCgaCva..vCP 49 
                                    t+k+e+d ekC+gC  C +  +CP
  gi|13541408|ref|NP_111096.1| 533 YTMKAEVDLEKCTGCSICYDffTCP 557
                                   458899************9877787 PP

  == domain 2  score: 24.1 bits;  conditional E-value: 5.1e-08
                        Fer4_7   1 rCigCgaCvaaCpvkaielde 21 
                                   +CigCgaCv++Cp +ai+++ 
  gi|13541408|ref|NP_111096.1| 572 SCIGCGACVEVCPFNAIKVKG 592
                                   5***************99865 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   1.1   3.8e-06    0.0029       3      21 ..     537     557 ..     535     558 .. 0.86
   2 !   22.8   1.9   8.4e-08   6.5e-05       6      21 ..     569     584 ..     565     585 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 3.8e-06
                        Fer4_2   3 vvvdtdrCigCgaCvsa..CP 21 
                                   ++vd ++C+gC++C++   CP
  gi|13541408|ref|NP_111096.1| 537 AEVDLEKCTGCSICYDFftCP 557
                                   689***********9666799 PP

  == domain 2  score: 22.8 bits;  conditional E-value: 8.4e-08
                        Fer4_2   6 dtdrCigCgaCvsaCP 21 
                                     d+CigCgaCv +CP
  gi|13541408|ref|NP_111096.1| 569 IDDSCIGCGACVEVCP 584
                                   4589************ PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   1.7   0.00062      0.49      31      52 ..     534     557 ..     519     560 .. 0.70
   2 !   22.9  10.7   8.6e-08   6.7e-05       1      58 [.     537     589 ..     537     590 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00062
                       Fer4_21  31 ktvlkvvedeCvGCnlCss..vCP 52 
                                     +++v  ++C+GC +C++   CP
  gi|13541408|ref|NP_111096.1| 534 TMKAEVDLEKCTGCSICYDffTCP 557
                                   34567889*********8633577 PP

  == domain 2  score: 22.9 bits;  conditional E-value: 8.6e-08
                       Fer4_21   1 AridedkCigCgkCl..iaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedcie 58 
                                   A +d +kC gC  C+   +C+      + +++k+  + ++d+C+GC  C++vCP  ++i+
  gi|13541408|ref|NP_111096.1| 537 AEVDLEKCTGCSICYdfFTCP----SILPLSNKK--AFIDDSCIGCGACVEVCPF-NAIK 589
                                   78999*********8335677....344554444..589***************7.8887 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   2.1     0.015        12      33      44 ..     535     552 ..     498     560 .. 0.67
   2 !   21.3   9.7   2.9e-07   0.00023       1      51 []     543     588 ..     543     588 .. 0.86
   3 !   19.3   2.4   1.2e-06   0.00091       2      22 ..     573     593 ..     572     602 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.015
                        Fer4_9  33 e......eaCigCgaCve 44 
                                   +      e+C+gC  C++
  gi|13541408|ref|NP_111096.1| 535 MkaevdlEKCTGCSICYD 552
                                   033344478999999986 PP

  == domain 2  score: 21.3 bits;  conditional E-value: 2.9e-07
                        Fer4_9   1 kCtgCgaCvea..CpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51 
                                   kCtgC  C +   Cp+ +    +++ ++         CigCgaCve+Cp +ai
  gi|13541408|ref|NP_111096.1| 543 KCTGCSICYDFftCPSILPLSNKKAFIDDS-------CIGCGACVEVCPFNAI 588
                                   7*******77666**999988887777774.......************9987 PP

  == domain 3  score: 19.3 bits;  conditional E-value: 1.2e-06
                        Fer4_9   2 CtgCgaCveaCpagvvvedaa 22 
                                   C+gCgaCve+Cp+++++ + +
  gi|13541408|ref|NP_111096.1| 573 CIGCGACVEVCPFNAIKVKGN 593
                                   999999999999999977655 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.4    0.0039         3      35      58 ..     532     558 ..     503     566 .. 0.61
   2 !   18.1   0.1   3.7e-06    0.0029       2      30 ..     573     603 ..     572     604 .] 0.86

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0039
                       Fer4_17  35 eeaekee.kaslCieCgeCe..rkCPq 58 
                                   ++++k e   ++C++C  C     CP+
  gi|13541408|ref|NP_111096.1| 532 DYTMKAEvDLEKCTGCSICYdfFTCPS 558
                                   444444436778888888876667776 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 3.7e-06
                       Fer4_17   2 CiqCgyClpeCpsyea..ydnepkkllraak 30 
                                   Ci+Cg+C+++Cp++++   +n pk +++a++
  gi|13541408|ref|NP_111096.1| 573 CIGCGACVEVCPFNAIkvKGNAPKGWIEAWN 603
                                   ************9888778889999999886 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   1.1   0.00097      0.75       2      15 ..     542     557 ..     541     562 .. 0.93
   2 !   18.1   3.5   3.4e-06    0.0027       2      17 .]     571     586 ..     570     586 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00097
                        Fer4_4   2 erCigCgsCvaa..CP 15 
                                   e+C+gC  C+++  CP
  gi|13541408|ref|NP_111096.1| 542 EKCTGCSICYDFftCP 557
                                   89**********9999 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 3.4e-06
                        Fer4_4   2 erCigCgsCvaaCPqg 17 
                                   ++CigCg+Cv +CP++
  gi|13541408|ref|NP_111096.1| 571 DSCIGCGACVEVCPFN 586
                                   79************86 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.8     0.042        33      43      62 ..     535     552 ..     501     558 .. 0.66
   2 !   21.3   1.3     5e-07   0.00039       2      20 ..     573     591 ..     572     600 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.042
                       Fer4_16  43 edeekckkqeaitgCdiCqd 62 
                                    ++e     e++tgC iC d
  gi|13541408|ref|NP_111096.1| 535 MKAEV--DLEKCTGCSICYD 552
                                   33333..4589999999976 PP

  == domain 2  score: 21.3 bits;  conditional E-value: 5e-07
                       Fer4_16   2 CgtCgkCaevCPtnaikek 20 
                                   C++Cg+C+evCP naik k
  gi|13541408|ref|NP_111096.1| 573 CIGCGACVEVCPFNAIKVK 591
                                   ****************987 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.5    0.0032       2.5       1      18 [.     539     558 ..     539     567 .. 0.81
   2 !   14.1   3.7   6.5e-05     0.051       1      17 [.     569     584 ..     569     586 .. 0.95

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0032
                       Fer4_13   1 VDrdtCiacgaCve..laPd 18 
                                   VD ++C++c +C++  ++P 
  gi|13541408|ref|NP_111096.1| 539 VDLEKCTGCSICYDffTCPS 558
                                   89**********98334665 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 6.5e-05
                       Fer4_13   1 VDrdtCiacgaCvelaP 17 
                                   +D d+Ci+cgaCve++P
  gi|13541408|ref|NP_111096.1| 569 ID-DSCIGCGACVEVCP 584
                                   79.*************9 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   3.2       4.9   3.8e+03       1       7 [.     544     550 ..     544     557 .. 0.84
   2 !   20.2   6.0     1e-06   0.00079       1      15 []     573     587 ..     573     587 .. 0.98

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 4.9
                        Fer4_3   1 CtgCgaC 7  
                                   CtgC+ C
  gi|13541408|ref|NP_111096.1| 544 CTGCSIC 550
                                   ****977 PP

  == domain 2  score: 20.2 bits;  conditional E-value: 1e-06
                        Fer4_3   1 CtgCgaCvevCPvgA 15 
                                   C+gCgaCvevCP +A
  gi|13541408|ref|NP_111096.1| 573 CIGCGACVEVCPFNA 587
                                   ************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 !   17.9   0.0   2.8e-06    0.0021       7      72 ..     224     287 ..     219     309 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.8e-06
                                   ET.TSSEEEEEETTHHHHHHHHHHHHHTTTTCEEEEE-SEEESHHHHHHHHHHHHHSEEEEEEEEES CS
               Transketolase_C   7 re.gkdvtlvayGsmveealeAaeeLekegisaeVvdlrtvkplDketilesvkktgrlvvveeavk 72 
                                    + g++ +++a G   + + e+    e+eg++a +  l t  p+ ++ il+s+ + ++++vvee+ +
  gi|13541408|ref|NP_111096.1| 224 EDnGSNTLIIASGIAYPYVKEIT---EEEGLNANIFRLVTPVPIPEKSILDSMTRVKKVLVVEENDP 287
                                   44499999******999998887...789***********************************976 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 !   17.2   0.0   5.9e-06    0.0046       5      62 ..     232     286 ..     228     317 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 5.9e-06
                                   EEE-STHHHHHHHHHHHHHHTT--EEEEEES--BS--HHHHHHHSTT-SEEEEEE-S- CS
                       PFOR_II   5 ivamGsvagtaksavdelReegikvGllrlrtlrPFPeeelkellkkvkkvvvldrni 62 
                                   i+a G++   +k++     eeg+++ ++rl t  P Pe+ + + + +vkkv+v++ n 
  gi|13541408|ref|NP_111096.1| 232 IIASGIAYPYVKEI---TEEEGLNANIFRLVTPVPIPEKSILDSMTRVKKVLVVEEND 286
                                   56666665555554...5689**********************************997 PP

>> Transket_pyr  Transketolase, pyrimidine binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.2   0.00023      0.18      23     171 ..       6     162 ..       2     166 .. 0.71
   2 ?    0.1   0.0       0.7   5.5e+02     120     172 ..     466     520 ..     454     523 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00023
                                   EEEEESSTHHHHTTCHCCHHEGGT...............TEGEEE--S-HHHHHHHHHHHHHHCTTEEEEEEEEHHHHGGG CS
                  Transket_pyr  23 vvligaDvaggtfsvrkgllhdqg...............egrvidsgisEqavlgfavGaalagpllviveaqFgdFangA 88 
                                   v+++ +++a g +++  ++    +               +  + + +i E+ +l +a+Gaa+ g   +   a+  + +n  
  gi|13541408|ref|NP_111096.1|   6 VLMGNQAIAFGALKAGVEVAAGYPgtpsteiietlkglnDSVYAEWSINEKVALETAYGAAMMG--SKALAAMKHVGMN-- 82 
                                   5555555555555544444444445555555555666656688999******************..6888888888888.. PP

                                   HHGGHHHHH..CHHHHHT--EEEEESBSGGGSTTGTTTSBSSHHHHHHTSTTEEEE--SSHHHHHHHHHHHHHS..SS.SE CS
                  Transket_pyr  89 qiyadqair..sgeakgklkvgvvtrlpigvgedGpehqsaeleaflrlipglkvvrPsdpaetkhllrrairr..edrkP 165
                                     +a + ++  s+    ++ v+v   +p        + q  ++ +++ l + + v+ P+dp+ ++ l  +a +   + r+P
  gi|13541408|ref|NP_111096.1|  83 --VAADPLFssSYTGVDGALVIVSADDPS-----MWSSQNEQDNRYYGLHALIPVIEPYDPQSAYDLTIKAFEIseKLRHP 156
                                   ..555544400444445555555555555.....56777888999999999999****************9998778899* PP

                                   EEEEE- CS
                  Transket_pyr 166 vvlrlp 171
                                   v+lr++
  gi|13541408|ref|NP_111096.1| 157 VILRTT 162
                                   **9987 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.7
                                   TGTTTSBSSHHHHHHTSTTEEEE--SSHHHHHHHHHHHHHS..SS.SEEEEEE-S CS
                  Transket_pyr 120 dGpehqsaeleaflrlipglkvvrPsdpaetkhllrrairr..edrkPvvlrlpk 172
                                   +  +h s+e +a    i+ + ++ P d  e   ++++a+++  e++kP  ++ ++
  gi|13541408|ref|NP_111096.1| 466 SPSTHISIENVARAMGIDFVDTFDPFDVKEGSDAVQKAAEYvkENKKPALIVAKR 520
                                   55689999999999999999********************997778888887766 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   1.2    0.0048       3.7       2      19 ..     541     560 ..     540     569 .. 0.80
   2 !   13.0   2.9   0.00014      0.11       4      17 ..     572     585 ..     569     597 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0048
                        Fer4_8   2 lekCieCgaCq..saCpvlr 19 
                                   lekC++C+ C    +Cp++ 
  gi|13541408|ref|NP_111096.1| 541 LEKCTGCSICYdfFTCPSIL 560
                                   89*********7778*9876 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.00014
                        Fer4_8   4 kCieCgaCqsaCpv 17 
                                   +Ci+CgaC + Cp+
  gi|13541408|ref|NP_111096.1| 572 SCIGCGACVEVCPF 585
                                   56666666666663 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.2     0.027        21      65      91 ..     525     553 ..     500     560 .. 0.71
   2 !   12.1   0.7   0.00036      0.28      76      94 ..     567     585 ..     562     587 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.027
                       Fer4_22  65 rllhkls..efkekfgesgCvGCgRCiea 91 
                                    +l+k+   ++k++++ ++C+GC  C + 
  gi|13541408|ref|NP_111096.1| 525 EVLEKVGdyTMKAEVDLEKCTGCSICYDF 553
                                   566777611345566999********874 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00036
                       Fer4_22  76 kfgesgCvGCgRCieacpv 94 
                                    f   +C+GCg C+e+cp 
  gi|13541408|ref|NP_111096.1| 567 AFIDDSCIGCGACVEVCPF 585
                                   566789***********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 ?    6.5   0.6     0.018        14       3      16 ..     539     552 ..     538     562 .. 0.89
   2 ?   11.9   0.9   0.00037      0.29       6      19 ..     571     584 ..     568     594 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.018
                       Fer4_15   3 vDrdaCigcglCva 16 
                                   vD ++C+gc  C++
  gi|13541408|ref|NP_111096.1| 539 VDLEKCTGCSICYD 552
                                   9***********86 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00037
                       Fer4_15   6 daCigcglCvaeap 19 
                                   d Cigcg+Cv+++p
  gi|13541408|ref|NP_111096.1| 571 DSCIGCGACVEVCP 584
                                   89***********8 PP

>> E1_dh  Dehydrogenase E1 component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   3.1e-05     0.024     154     220 ..     449     516 ..     409     519 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.1e-05
                                   EEEEEEEESEETTEEHHHH-S---GGG..TTTTS-EEEEETTSHHHHHH...HHHHHHHHHHTTT--EEE CS
                         E1_dh 154 vifvveNNkygisTeaekasaskeladrargvgipglrVdgnDplavye...AvkfAaeraregkgplli 220
                                   +i v  N   +++ ++   s   ++ ++ar++gi    Vd  Dp+ v+e   Av+ Aae+ +e+k+p+li
  gi|13541408|ref|NP_111096.1| 449 IIIVLDNRSTAMTGQQPSPSTHISIENVARAMGIDF--VDTFDPFDVKEgsdAVQKAAEYVKENKKPALI 516
                                   57888888999999999999999999*99*999997..678888888654449****************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 ?   11.2   1.4   0.00041      0.32      57      74 ..     569     586 ..     557     594 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00041
                       Fer4_18  57 gagdcidcescvkvcPtg 74 
                                    +  ci c++cv+vcP +
  gi|13541408|ref|NP_111096.1| 569 IDDSCIGCGACVEVCPFN 586
                                   5678************75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (604 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       533  (0.0297284); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); 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: 0.66u 0.32s 00:00:00.98 Elapsed: 00:00:00.49
# Mc/sec: 3674.26
//
Query:       gi|13541409|ref|NP_111097.1|  [L=268]
Description: FKBP-type peptidyl-prolyl cis-trans isomerase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.9e-07   30.7   0.9    5.2e-06   26.7   0.1    2.5  2  FKBP_C    FKBP-type peptidyl-prolyl cis-trans isomerase
    0.00028   20.7   2.6       0.26   11.3   0.2    3.6  3  RsgI_N    Anti-sigma factor N-terminus
     0.0021   18.1   0.2     0.0051   16.9   0.2    1.6  1  FKBP26_C  FKBP26_C-terminal


Domain annotation for each model (and alignments):
>> FKBP_C  FKBP-type peptidyl-prolyl cis-trans isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.1   8.6e-10   5.2e-06       6      74 ..      11      93 ..       7     124 .. 0.85
   2 ?    2.0   0.0     0.045   2.7e+02      10      70 ..     135     196 ..     127     238 .. 0.58

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 8.6e-10
                                  -TTCEEEEEEEEEET.TSSEEEEH.............CCHTSEEEEETTSSSSCHHHHHHHTTSBTT-EEEEEEEGGGTTTTT CS
                        FKBP_C  6 kegdtVtvhykgkle.dgkvfdss.............rsrakplefkvGsgqvikGfeealegmkvGekrtltippelaYgek 74
                                  ++gd+++++y+ ++  d+k++++s              +++ ++ + vG++ + k + e  ++ +vG++ +++ippe a+g++
  gi|13541409|ref|NP_111097.1| 11 NTGDFIKIEYEMRVGdDKKLVATSkeelakenniydeKQKYGDIVVIVGQEGLFKEINESFKNAQVGQELEVEIPPEDAFGQR 93
                                  78************878888888899999988885544499999*************************************95 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.045
                                   EEEEEEEEEETTSSEEEEHCCHTSEEEEETTSSSSCH..HHHHHHTTSBTT-EEEEEEEGGGT CS
                        FKBP_C  10 tVtvhykgkledgkvfdssrsrakplefkvGsgqvik..GfeealegmkvGekrtltippela 70 
                                   +V v+y+ k++++kv  +  + +  ++ + ++ + i     +    +++v++  +++ip +++
  gi|13541409|ref|NP_111097.1| 135 RVLVDYNHKWAGKKVYYKY-KINGTITDTAEKVKAIIanNYDPEGFNVSVDDSIRIEIPENAK 196
                                   6777777777444444433.5444444444443322201222222334455555555555544 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 ?    3.6   0.0      0.01        61      13      30 ..      11      26 ..      10      40 .. 0.78
   2 !   11.3   0.2   4.3e-05      0.26       6      40 ..      53      90 ..      50      94 .. 0.86
   3 ?    3.6   0.1      0.01        61      25      36 ..     112     123 ..     105     125 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.01
                        RsgI_N 13 pdGeFikikrkggmkvGe 30
                                  + G+Fiki +  +m+vG+
  gi|13541409|ref|NP_111097.1| 11 NTGDFIKIEY--EMRVGD 26
                                  5799999876..677777 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 4.3e-05
                        RsgI_N  6 kkaivlTpdGeFikikrk.ggmkvGe..Eiefpekdii 40
                                  + ++++  +G F++i+   +  +vG+  E+e+p++d++
  gi|13541409|ref|NP_111097.1| 53 DIVVIVGQEGLFKEINESfKNAQVGQelEVEIPPEDAF 90
                                  567888889*******99566**************986 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.01
                        RsgI_N  25 gmkvGeEiefpe 36 
                                   +++vG+E+e++ 
  gi|13541409|ref|NP_111097.1| 112 DPRVGMEVEINR 123
                                   489******996 PP

>> FKBP26_C  FKBP26_C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.2   8.5e-07    0.0051       2      62 ..     163     219 ..     162     223 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 8.5e-07
                                   HHHHHHHHHHH-TT--..--EEEEETTEEEEE--TTGGGSTTHHHHHHHHHHHHHHH-TTE CS
                      FKBP26_C   2 kekikelIkryiPnidlekfkieiedktvtIelpeeakFieniqlaklrIAkdilkrieev 62 
                                    ek+k++I     n d e f+++++d+ ++Ie+pe+akF      ak +I++ ++k+i++ 
  gi|13541409|ref|NP_111097.1| 163 AEKVKAIIAN---NYDPEGFNVSVDDS-IRIEIPENAKFSVAWLDAKYTIVNTARKYIPGL 219
                                   59******99...778899*****886.7**********8888889***********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1155  (0.0644208); expected 358.6 (0.02)
Passed bias filter:                      599  (0.0334096); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 1922.17
//
Query:       gi|13541410|ref|NP_111098.1|  [L=250]
Description: rRNA methylase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-32  112.0   0.0    3.2e-32  111.6   0.0    1.2  1  SpoU_methylase   SpoU rRNA Methylase family
  ------ inclusion threshold ------
      0.013   15.4   0.0      0.037   13.9   0.0    1.7  2  Methyltrn_RNA_4  SAM-dependent RNA methyltransferase


Domain annotation for each model (and alignments):
>> SpoU_methylase  SpoU rRNA Methylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.6   0.0   3.6e-36   3.2e-32       2     142 .]      11     160 ..      10     160 .. 0.83

  Alignments for each domain:
  == domain 1  score: 111.6 bits;  conditional E-value: 3.6e-36
                                   EEEEEES-SSHHHHHHHHHHHHHTT-SEEEEESGSSCTCGSHHHHHHCTTHHHHHH.EEEESSHHHHHHHHCCCTEEEEEE CS
                SpoU_methylase   2 livvlveiedpgNlGaiaRtakafgaselvlvkprsadllnpeakraaagalevle.lkvvdsleealkelkeegfalvat 81 
                                   + vvlv+++++gN+Ga+aR++k+ g+s+l++v++r     ++ea + ++g +++le +++vdslee++++++ +  +  ++
  gi|13541410|ref|NP_111098.1|  11 IWVVLVQPKYQGNIGAVARSMKNSGLSKLIIVGNRP----DDEAFARSMGGRQILEnAEIVDSLEEIVHRFTIVAGTSSTA 87 
                                   579*****************************9544....57888889************************994333333 PP

                                   STT-SEGCCS.......HHH......TTEEEEEEBTTTBS-HHHHCTSSEEEE----TTSSS--HHHHHHHHHH CS
                SpoU_methylase  82 slkgkslsei.......dlk......ekvalvfGnEdkGlsnelleladrlvkIpmsgeveSLNvavAvailly 142
                                   s++ k+++++         k      +kvalvfG+Ed+Gl+ne+l+l++++++Ip +++++  N+++Avai+ly
  gi|13541410|ref|NP_111098.1|  88 SSNLKRFRRLpvdpetfW-KqmesqtGKVALVFGREDDGLRNEELDLCNYFIYIPGNPDYPVYNLSHAVAIVLY 160
                                   345555553333444440.1445667***********************************************9 PP

>> Methyltrn_RNA_4  SAM-dependent RNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.29   2.6e+03      30      58 ..      26      54 ..      23      58 .. 0.83
   2 ?   13.9   0.0   4.1e-06     0.037      77     177 ..      59     159 ..      47     163 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.29
                                  HHHHHHHHTT-SEEEEE---HHHHHHHHH CS
               Methyltrn_RNA_4 30 DiaRsartygvkkyyvvtpleaqrelver 58
                                   +aRs +  g++k+ +v +  + ++++++
  gi|13541410|ref|NP_111098.1| 26 AVARSMKNSGLSKLIIVGNRPDDEAFARS 54
                                  58999999999**9999999888887765 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 4.1e-06
                                   HHHTTEEEESSHHHHHHHHHHHHSS--EEEE--SS--SS-B-HHHHHHHHHH--S-EEEEE--.TT---HHHHTT-SEEB- CS
               Methyltrn_RNA_4  77 ealslvkvvesleealeeiekeegkkplvvatsArkkentvsyeelrelleeeekpvlllfGt.gwGlaeevlekadyiLe 156
                                   + l++ ++v+slee++++++   g++ +      r ++  v+ e++ +++e+++ +v l+fG    Gl +e l+ ++y++ 
  gi|13541410|ref|NP_111098.1|  59 QILENAEIVDSLEEIVHRFTIVAGTSSTASSNLKRFRRLPVDPETFWKQMESQTGKVALVFGReDDGLRNEELDLCNYFIY 139
                                   679999******************99999999999999999*********************7257************995 PP

                                   -TTTTSS-----HHHHHHHHH CS
               Methyltrn_RNA_4 157 pirgaseynHLsvrsAvaiil 177
                                    i g+ +y       Avai+l
  gi|13541410|ref|NP_111098.1| 140 -IPGNPDYPVYNLSHAVAIVL 159
                                   .99999*99999999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 1910.15
//
Query:       gi|13541411|ref|NP_111099.1|  [L=107]
Description: hypothetical protein TVN0580 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.1e-11   43.3   0.0    4.8e-11   43.1   0.0    1.2  1  DrsE         DsrE/DsrF-like family
  ------ inclusion threshold ------
      0.063   13.6   0.0      0.085   13.1   0.0    1.2  1  RNA_binding  RNA binding


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 !   43.1   0.0   5.3e-15   4.8e-11      23     116 ..      21     106 ..       1     107 [] 0.80

  Alignments for each domain:
  == domain 1  score: 43.1 bits;  conditional E-value: 5.3e-15
                                   HHHHHHTTT....-EEEEEE-GGGGGGGBS---TGGGTS---GGGGGGCGGGT-EEEEEHHHHHHTT--GGGE-.T--EEE CS
                          DrsE  23 lalaaaalg....hevsvffygdGvllllkgqtanpadeknlaellkalkeygvklyvCgqaakargldededl.gvgvev 98 
                                   ++l+          ev+v+f+ d++++l + + +        ++ + al ++g+ +++C++++ a g+d+d+++ gv+v+ 
  gi|13541411|ref|NP_111099.1|  21 MNLL----RedpsIEVEVVFHVDAITVLSA-ESE--------NKDVYALLKNGINVVACRNSMIAKGMDSDSLIlGVTVVN 88 
                                   3333....245559****************.222........24567778889****************99877899**** PP

                                   E-HHHHHHHHHH-SEEEE CS
                          DrsE  99 sglgelaelqnegdrvit 116
                                   +g+ el+++++eg+ +i+
  gi|13541411|ref|NP_111099.1|  89 AGIYELVKKISEGWIYIR 106
                                   **************9996 PP

>> RNA_binding  RNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   9.5e-06     0.085      13      68 ..       9      64 ..       2      83 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 9.5e-06
                                  -HHHHHHHHHTTSTTSE---EEEEEE-CCC-EEEEEEEEESSHHHHHHHHHHHHHH CS
                   RNA_binding 13 deekVlealsnllpeeeveieeeeaeGhygnpitileaelekkkakkvlkkllell 68
                                  d +kV + ++nl++  +++ ++e     + + it+l+ae e+k+  ++lk+ ++ +
  gi|13541411|ref|NP_111099.1|  9 DPSKVGQVVRNLMNLLREDPSIEVEVVFHVDAITVLSAESENKDVYALLKNGINVV 64
                                  7889999999998877555666666778899***********99999999866655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       475  (0.0264934); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.35u 0.21s 00:00:00.55 Elapsed: 00:00:00.35
# Mc/sec: 907.81
//
Query:       gi|13541412|ref|NP_111100.1|  [L=529]
Description: Fe-S oxidoreductase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.1e-17   63.5   0.2    8.6e-17   62.0   0.0    1.9  3  Radical_SAM  Radical SAM superfamily
    5.5e-17   61.9   0.1    2.1e-16   60.0   0.0    2.0  2  B12-binding  B12 binding domain
  ------ inclusion threshold ------
       0.03   14.4   0.0      0.088   13.0   0.0    1.7  1  MCD_N        Malonyl-CoA decarboxylase N-terminal domain
       0.13   12.4   0.1       0.34   11.1   0.1    1.6  1  Fer4_14      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       2.3     1e+04      83     112 ..      50      78 ..      29      87 .. 0.71
   2 ?   -3.5   0.0       2.6   1.2e+04     150     165 ..     120     135 ..     114     139 .. 0.76
   3 !   62.0   0.0   1.9e-20   8.6e-17       2     166 ..     199     363 ..     198     364 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 2.3
                                   EECSSCHGHHHHHHHHHTT-SEEEEEEBSS CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  83 etngtlpdeeklerllelgvdrvslgleaa 112
                                   e+ ++++  e+++ +++ ++d++ ++l+a+
  gi|13541412|ref|NP_111100.1|  50 EADELTL-NEMVAYIDRWRPDVIGITLHAT 78 
                                   4455555.6777777777788888887765 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 2.6
                                   EEBTTTSHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxx RF
                   Radical_SAM 150 vglpGendeeleelle 165
                                   v++ Ge de+++e+l+
  gi|13541412|ref|NP_111100.1| 120 VIVLGEGDETFREILK 135
                                   5667888888888775 PP

  == domain 3  score: 62.0 bits;  conditional E-value: 1.9e-20
                                   EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTC..CCTEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxx RF
                   Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlakla..vpgiri 80 
                                   +++rgC+++C fC+++ t  ++ ++r++s e+i+ee++++ +  g k v+++ +  ++yp+  +  +   ++   + g+++
  gi|13541412|ref|NP_111100.1| 199 ETSRGCPYACDFCSVTPT--WGNKWRNKSNERIMEELRII-KQLGYKWVFFTDDIFIVYPNVKQREDLFNRIIeeDLGLKF 276
                                   689**************8..********************.6999*******99999996655554444444433355555 PP

                                   EEEECSSCHG..HHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHHH CS
                                   xxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  81 tvetngtlpd..eeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglpGendee 159
                                    v   + +    ++ +++ +++g++   lg+e++++e vlk m++g   +  ++a++ l e+++ +   +++g p e  ++
  gi|13541412|ref|NP_111100.1| 277 IVQMRADVTAknPDLIKKAAQAGLTIAFLGIESGSEE-VLKAMHKGIITDSSIRAVKVLEENNVVVLGGMMLGAPYERISD 356
                                   55555555446699***********************.*************************999999999********* PP

                                   HHHHHHH CS
                                   xxxxxxx RF
                   Radical_SAM 160 leellel 166
                                   +++++++
  gi|13541412|ref|NP_111100.1| 357 IRKTIKF 363
                                   *999987 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.0   0.0   4.7e-20   2.1e-16       5     120 ..      17     133 ..      13     134 .. 0.92
   2 ?   -2.0   0.0       0.8   3.6e+03      22      47 ..     294     318 ..     276     322 .. 0.72

  Alignments for each domain:
  == domain 1  score: 60.0 bits;  conditional E-value: 4.7e-20
                   B12-binding   5 latvggdlhplGlavlaaalrdagf.eVqllganven...edivaairaekpdvvglSalltsqleavkelvellkrirpr 81 
                                    +++g+   plGl  la+  r  g+ +V++++++++     ++va i +++pdv+g++++ t+ +++ ++l+ ++k+i + 
  gi|13541412|ref|NP_111100.1|  17 TTKFGFLPTPLGLEDLAGEARVVGIkDVKIVDMEADEltlNEMVAYIDRWRPDVIGITLHATAAHSFSQQLATQVKSIYN- 96 
                                   566777778888888888888888889***************************************************76. PP

                   B12-binding  82 vkvvvGGahpsldpeetleaklgiddvvvgegedaleal 120
                                     +v+GG+ +++ p ++l   +g+d++v+geg+++++++
  gi|13541412|ref|NP_111100.1|  97 PLIVAGGHQATFVPNQLLD--NGFDVIVLGEGDETFREI 133
                                   79**************998..9**************998 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.8
                   B12-binding  22 aalrdagfeVqllganvenedivaai 47 
                                    a ++ g  + +lg++   e++++a+
  gi|13541412|ref|NP_111100.1| 294 KAAQA-GLTIAFLGIESGSEEVLKAM 318
                                   44444.88888888888888887765 PP

>> MCD_N  Malonyl-CoA decarboxylase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0     2e-05     0.088      35      62 ..     259     286 ..     256     297 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2e-05
                                   HHHHHHHHHTTSTTHHHHHHHHHHHHHH CS
                         MCD_N  35 rrqeLlrrlnlapgGvkfLVdmRadlla 62 
                                   +r  L+ r+ +   G+kf+V+mRad+ a
  gi|13541412|ref|NP_111100.1| 259 QREDLFNRIIEEDLGLKFIVQMRADVTA 286
                                   7999*********************965 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 ?   11.1   0.1   7.5e-05      0.34       7      36 ..     203     232 ..     200     247 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 7.5e-05
                       Fer4_14   7 gCnlsCkgCdnketwkselgkpqteelleq 36 
                                   gC+ +C +C  + tw +++ ++++e+++e+
  gi|13541412|ref|NP_111100.1| 203 GCPYACDFCSVTPTWGNKWRNKSNERIMEE 232
                                   9**********************9999864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (529 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       685  (0.0382063); expected 358.6 (0.02)
Passed bias filter:                      605  (0.0337442); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.68u 0.27s 00:00:00.95 Elapsed: 00:00:00.49
# Mc/sec: 3235.93
//
Query:       gi|13541413|ref|NP_111101.1|  [L=277]
Description: hypothetical protein TVN0582 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      5e-06   26.9   0.0      0.014   15.7   0.0    2.3  2  VWA       von Willebrand factor type A domain
    0.00024   21.7   0.0       0.17   12.5   0.0    2.3  2  VWA_2     von Willebrand factor type A domain


Domain annotation for each model (and alignments):
>> VWA  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.0   0.00018       1.6       4      48 ..      16      74 ..      15     117 .. 0.84
   2 !   15.7   0.0   1.5e-06     0.014      77     128 ..     130     181 ..     124     186 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00018
                                  EEEE-STTS.......CHHHHHHHHHHHHHHHHHHTB...TTTTEE....EEEEEESSS CS
                           VWA  4 fvlDgSgsm.......geenfekvkefikklveklev...gpegtr....vglvqfsse 48
                                  f++D+S sm       +e++ +++ ++i++ +++l+    +++g+r    vg++ +++e
  gi|13541413|ref|NP_111101.1| 16 FLVDQSRSMvrkiaggSESKAKEAADAINRQIGELIMrctKNDGVRdyfyVGVIGYGGE 74
                                  9************999999999************9956678888888888999999987 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 1.5e-06
                                   SSC-HHHHHHHHHHHHHHHHGTSSTTSEEEEEEEESS--CSSHTHHHHHHHH CS
                           VWA  77 gttntgkalkyaleklfkssagaRenakkviilltdGksndgdpkeaaneak 128
                                   ++t + ka++ a e + k  ++  + ++ +ii +tdG+s+dgdp ++a+++ 
  gi|13541413|ref|NP_111101.1| 130 SDTPMVKAMNMAKEAVEKWVSEHPSSYPPIIINVTDGQSTDGDPYPVARNIM 181
                                   4555899***************999***********************9986 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 !   12.5   0.0   1.9e-05      0.17       2      47 ..      15      73 ..      14      89 .. 0.78
   2 !    6.9   0.0    0.0011       9.6      74     107 .]     130     167 ..     122     167 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.9e-05
                         VWA_2  2 vfvlDtSgSmrng.dy.gptrleaakdaveallksl........pgd....rvglvtfsd 47
                                  +f++D S Sm ++ +  ++++   a+da+++ +++l          +     vg++ +++
  gi|13541413|ref|NP_111101.1| 15 LFLVDQSRSMVRKiAGgSESKAKEAADAINRQIGELimrctkndG-VrdyfYVGVIGYGG 73
                                  8*********77743336999999999999999977778886541.25577899999987 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0011
                         VWA_2  74 ggtnlaaaLqlarkalkkrr.....kgekrvivlitDge 107
                                    +t + +a+++a++a++k +     ++++ +i+ +tDg+
  gi|13541413|ref|NP_111101.1| 130 SDTPMVKAMNMAKEAVEK-WvsehpSSYPPIIINVTDGQ 167
                                   678999999999999963.3466679***********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       333  (0.0185733); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 2025.59
//
Query:       gi|13541414|ref|NP_111102.1|  [L=232]
Description: hypothetical protein TVN0583 [Thermoplasma volcanium GSS1]
Scores for complete 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   18.3   0.0     0.0019   17.9   0.0    1.2  1  PP2C_2    Protein phosphatase 2C


Domain annotation for each model (and alignments):
>> PP2C_2  Protein phosphatase 2C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   1.1e-07    0.0019      27     176 ..      32     182 ..      14     213 .. 0.65

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.1e-07
                        PP2C_2  27 laVaDGaGSakrSerGariaveavvealaelleseeeeeeallraleaailadv..lkeeaeaqdaelkdyatTllaavvt 105
                                   +a+aDG     +S +   +a  +v e+++    +   ++++l++++ +++++++   + +   + + +    +T l +vv+
  gi|13541414|ref|NP_111102.1|  32 FAMADGSSESVFSNI---WAKALVDEFVS---GDYILKIDTLVEKAASKWQSKLpwKEMKWFVKNKIMMGALSTFLGLVVS 106
                                   466777666666655...33333333333...2334568999*********888754444444555778888********* PP

                        PP2C_2 106 pdeivalqiGDGaivvrdrdgevqllgepdsgeyanq..ttfltsedaeeelrirrlk....ledgdalllmTDGla 176
                                   ++++ a+ +GD+++ ++ + g ++++   +  ++ n    +   ++   ++++i+ ++     +dg  l+++TD l+
  gi|13541414|ref|NP_111102.1| 107 DEKFSAVAVGDTCL-FVFSSGGYRSFPITKLSDFGNSpkLVWTGNPVLRARRQIKWVNflegQTDGVVLVMATDSLS 182
                                   **************.66889999999998888888884433333333333333333335444466777777777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       505  (0.0281667); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 1485.48
//
Query:       gi|13541415|ref|NP_111103.1|  [L=401]
Description: Serine/threonine protein kinase [Thermoplasma volcanium GSS1]
Scores for complete 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   36.5   0.1    5.2e-09   35.9   0.1    1.2  1  Pkinase      Protein kinase domain
    4.9e-06   26.3   0.1    1.3e-05   24.9   0.1    1.6  1  RIO1         RIO1 family
    0.00011   21.6   0.0    0.00016   21.1   0.0    1.2  1  Pkinase_Tyr  Protein tyrosine kinase
  ------ inclusion threshold ------
       0.01   15.7   0.0      0.019   14.9   0.0    1.4  1  APH          Phosphotransferase enzyme family
      0.051   12.0   0.0      0.076   11.5   0.0    1.1  1  AceK         Isocitrate dehydrogenase kinase/phosphatase (Ace


Domain annotation for each model (and alignments):
>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.9   0.1   1.4e-12   5.2e-09       9     190 ..     146     327 ..     143     343 .. 0.81

  Alignments for each domain:
  == domain 1  score: 35.9 bits;  conditional E-value: 1.4e-12
                                   EESSEEEEEEEETTTTEEEEEEEEECHCHCHHHHHHHHHHHHHHHHHS.CTTB--EEEEEEE......SSEEE..EEEE-- CS
                       Pkinase   9 eGsfGkVykaveketgkivAvKkikkekakkkkekkvlrEikilkklk.hpnivrlyevfee......kdely..lvleyv 80 
                                   +G++G ++k+   +++k +A+K++ k ++ +k+      Ei  + k++  + iv++ +          ++ +y  l ++++
  gi|13541415|ref|NP_111103.1| 146 SGNYGLIFKIE--KESKYYAIKCFTKGSDLHKRY----YEIGKHIKSRnLSCIVNFEYLEAGvrtmkdPSIYYpvLKMDWI 220
                                   699******98..799***********9998776....455444333335556655433222555553555557799**** PP

                                   TTEBHHHHHHHHSS--HHHHHHHHHHHHHHHHHHHHTTEE-SS-SGGGEEEETTTEEEE-SGTTSEESSSSCSBCTTTSCG CS
                       Pkinase  81 eggeladllerkgslseeeakkiakqilegleylHskgiiHrDlKpeNiLidekgelKitDFGlakelessskltsfvgts 161
                                   eg++l ++++r    + +e+++ia++ ++++  l +++i H Dl ++Ni+i+ +g++  +D++     + +   +++ g +
  gi|13541415|ref|NP_111103.1| 221 EGDSLYTYIKR-NLDDGKEIRRIANEFAKSVILLKKNHIAHGDLSSDNIMIS-NGKVIFVDYDGMYVPSLKDLPSNENGHE 299
                                   *********85.556788**********************************.*********9888877777799999999 PP

                                   GGS-HHHHTTSCBSHHHHHHHHHHHHHHH CS
                       Pkinase 162 eYlAPEvlkeneyskkvDvWslGvilyel 190
                                   ++  P   ++++y++ +D +s+ vi  +l
  gi|13541415|ref|NP_111103.1| 300 NFQHPSR-RSSDYGEDMDNFSALVIYTSL 327
                                   9999988.588999999999987776555 PP

>> RIO1  RIO1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.1   3.5e-09   1.3e-05      81     149 ..     213     280 ..     196     288 .. 0.82

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 3.5e-09
                                   TEEEEE--EETTEEGGBHHHCG-HHHHHHHHHHHHHHHHHHHHTSTEEESS-STTSEEEETTEEEE--G CS
                          RIO1  81 hvlvmefigedgvaapklkdveeeeeaeelyeevleemrklykeaglvHaDLSeyNvlvdedkvviIDv 149
                                    vl m++i+ d +  +  +++++ +e++++++e  ++  +l+k++++ H+DLS  N++++++kv+++D 
  gi|13541415|ref|NP_111103.1| 213 PVLKMDWIEGDSLYTYIKRNLDDGKEIRRIANEFAKS-VILLKKNHIAHGDLSSDNIMISNGKVIFVDY 280
                                   58899999966555555555556889*******9996.67778*************************6 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   4.5e-08   0.00016      68     144 ..     201     278 ..     142     298 .. 0.72

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 4.5e-08
                                   EEEESSSS....EEEEEE--TTEBHHHHHHHTCTTTSBHHHHHHHHHHHHHHHHHHHHTTEEEST-SGGGEEEEETTEEEE CS
                   Pkinase_Tyr  68 gvctkeep....llivteyvkgGdLlkfLrkkekekltlkdllsfalqvAkGmeyLeskklvHrdlaarNvLlsenkvvki 144
                                   gv t ++p     ++ +++++g +L ++++++     + k++ ++a + Ak +  L+++++ H dl++ N+++s++kv+ +
  gi|13541415|ref|NP_111103.1| 201 GVRTMKDPsiyyPVLKMDWIEGDSLYTYIKRN---LDDGKEIRRIANEFAKSVILLKKNHIAHGDLSSDNIMISNGKVIFV 278
                                   4445444444445667999************9...4456788899*****************************9998865 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   5.3e-06     0.019     139     194 ..     231     281 ..     204     285 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 5.3e-06
                                   CCTCCHHHHHHHHHHHHHHHH--SSS-EEEE-SS-SGGGEEEC..TTEEEEE---T CS
                           APH 139 selldlleeleeqvlaalaallpgelptvllHgDlhpgNllvdpddgrvtGviDfe 194
                                   ++l+d   e+++ +++++a+ +    +  + HgDl+++N+++   +g+v  ++D +
  gi|13541415|ref|NP_111103.1| 231 RNLDD-GKEIRR-IANEFAKSVILLKKNHIAHGDLSSDNIMIS--NGKV-IFVDYD 281
                                   55555.456666.777777777778889999************..6665.488876 PP

>> AceK  Isocitrate dehydrogenase kinase/phosphatase (AceK)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   2.1e-05     0.076     424     473 ..     235     283 ..     224     306 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.1e-05
                          AceK 424 deeeleaaveeyGnaikqlaaaniFpgDmllkNFGvtrhgrvvfYDYDei 473
                                   d +e+++  +e+++++  l +++i  gD+   N  ++ +g+v+f DYD +
  gi|13541415|ref|NP_111103.1| 235 DGKEIRRIANEFAKSVILLKKNHIAHGDLSSDNIMIS-NGKVIFVDYDGM 283
                                   5689999***************************887.69********75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (401 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       648  (0.0361426); expected 358.6 (0.02)
Passed bias filter:                      503  (0.0280551); 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: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.48
# Mc/sec: 2488.18
//
Query:       gi|13541416|ref|NP_111104.1|  [L=257]
Description: competence damage-inducible protein A [Thermoplasma volcanium GSS1]
Scores for complete 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  105.6   0.3    2.8e-30  104.9   0.1    1.4  2  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 !  104.9   0.1   1.6e-34   2.8e-30       2     137 ..       7     163 ..       6     168 .. 0.96
   2 ?   -3.2   0.0      0.34   6.1e+03      73      83 ..     228     238 ..     223     251 .. 0.50

  Alignments for each domain:
  == domain 1  score: 104.9 bits;  conditional E-value: 1.6e-34
                                   EEEE-HHHHTTSSGBHHHHHHHHHHHTTSEEEEEEEEE-SSHHHHHHHHHHHHHTSSEEEEESS-SSSTT--HHHHHHHHH CS
                 MoCF_biosynth   2 vitvGdellsgkieDtngpllaellkelgvevskytvvpDdeeeikeallaaleeadviittGGtGptpdDvtpealaklf 82 
                                   vitvG+e+l+g++++tn++++ + l+ +g++v+   +v Dd e+i+ a+++a+++ dvi+++GG+Gpt dD+t+e  ak++
  gi|13541416|ref|NP_111104.1|   7 VITVGNEVLKGRTVNTNASFIGNFLTYQGYRVKLGLTVMDDLEDISWAFKTAMDRGDVIVSSGGLGPTFDDMTVEGFAKAI 87 
                                   8************************************************9999**************************** PP

                                   SEE-HHHHHHHHHHHHHHCC......................TTSHGGGGGGE.EETTEEEEE-SSHHHHHHHHHHH CS
                 MoCF_biosynth  83 ekelegfeeafrrvslkpgk......................pvgvapgailsravgktiigLPGspkavkealeei 137
                                   +   ++++ a+ +++ k+++                      pvg+apg   s + gk++++LPG+p ++++ le +
  gi|13541416|ref|NP_111104.1|  88 GSDNKLNQDALAMIEEKYKNieitperkkmammpevckpirnPVGTAPGLLCSVG-GKKVVILPGVPMEMQALLESM 163
                                   ******************99*****************************888754.888*************99975 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 0.34
                                   -HHHHHHHHHS CS
                 MoCF_biosynth  73 vtpealaklfe 83 
                                   v +ea +k  +
  gi|13541416|ref|NP_111104.1| 228 VSQEAARKKVK 238
                                   44444433332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       659  (0.0367561); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 1808.63
//
Query:       gi|13541417|ref|NP_111105.1|  [L=227]
Description: uridylate kinase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.5e-25   89.5   1.1    5.9e-24   85.0   1.1    2.1  1  AA_kinase  Amino acid kinase family
  ------ inclusion threshold ------
       0.13   12.3   0.1         10    6.2   0.0    2.2  2  DUF218     DUF218 domain
       0.16   10.8   0.0       0.24   10.3   0.0    1.3  1  mTERF      mTERF


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 !   85.0   1.1   9.9e-28   5.9e-24       3     241 .]       5     203 ..       3     203 .. 0.86

  Alignments for each domain:
  == domain 1  score: 85.0 bits;  conditional E-value: 9.9e-28
                                   EEEEE-TTCCC.CTCC.HHHHHHHHHHHHHHHHTTEEEEEE--HHHHHHHHHH..TCCCCCHHHC....E..HHHHHHHHH CS
                     AA_kinase   3 vVvKlGGsslt.dkee.aslrrlaeqiaalkesgnklvvVhGggsftdgllal..ksglssgelaaglrstleeagevatr 79 
                                   +V+ lGGs+++ d+ + ++l+++a+++a    + +++ +V+Ggg++++ +++l    g+++++l                 
  gi|13541417|ref|NP_111105.1|   5 IVISLGGSVISgDPIDaDYLQSFAKILASS--KFKRIGIVTGGGKTARSYISLlrSLGINENML----------------- 66 
                                   8**********77777**************..56799****************88888888888................. PP

                                   HHHHHHHHHHHHHHHHTTHGEEEE-GGGTCEECCCE..HHHTTTCEEECCHHHHHHHTT-EEEEESEEEEETTTEEEEE-H CS
                     AA_kinase  80 dalaslgerlvaallaaglpavglsaaaldateagrdegsdgnvesvdaeaieelleagvvpvltgfigldeegelgrgss 160
                                   d++++ ++r++a  la++l      a+++ +++               +ea+ +l+++   +v++g    +e+g+    ++
  gi|13541417|ref|NP_111105.1|  67 DEIGIYATRMNALSLASLL----KGANPIIPSTV--------------EEAV-NLMSEYRFVVMGG----TEPGH----TT 120
                                   8******************....33444444432..............2344.4555545666666....58998....9* PP

                                   HHHHHHHHHHCTSSEEEEEESSSSCESSTTTTCCTTCECCEEEHHHCHH..CSSS.TTTHHHHCHHHHHHHHHCTT-EEEE CS
                     AA_kinase 161 DtiaallAealgAdkliiltdVdGVydadpkkvpdarllpeisvdeaee..saselatgGmkvkhpaalaaarrggipvvI 239
                                   Dt+aall+e  + d+li++t+VdGVyd dp+k +dar+++++ ++ea    + s  + g    ++  al +a+r++i+v++
  gi|13541417|ref|NP_111105.1| 121 DTVAALLCERSDTDTLINITSVDGVYDLDPNKYKDARRFDTLGYREAITlsTGSSVGAGPNVFMDITALSIAMRSKIKVIV 201
                                   **************************************************8888888888888*****************9 PP

                                   EE CS
                     AA_kinase 240 tn 241
                                   ++
  gi|13541417|ref|NP_111105.1| 202 AS 203
                                   85 PP

>> DUF218  DUF218 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0    0.0017        10      11      83 ..      18      88 ..       4      95 .. 0.70
   2 ?    4.7   0.0    0.0048        29      15      50 ..      94     127 ..      87     143 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0017
                        DUF218 11 pllaeRldeaaelyrag..k..iivsGggadedvseaeamaeylrelgvpeeailledrsrnTeenarfskell.ker 83
                                  p +a+ l+  a+++     k   iv+Ggg     + a+ +  +lr+lg++e ++l e     T+ na+ ++ ll + +
  gi|13541417|ref|NP_111105.1| 18 PIDADYLQSFAKILASSkfKriGIVTGGG-----KTARSYISLLRSLGINE-NMLDEIGIYATRMNALSLASLLkG-A 88
                                  55566666666666666442456888875.....57999***********7.899899999999999999999953.3 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0048
                        DUF218  15 eRldeaaelyragkiivsGggadedvseaeamaeyl 50 
                                   + ++ea++l+ +++++v Gg+  e+    + +a++l
  gi|13541417|ref|NP_111105.1|  94 STVEEAVNLMSEYRFVVMGGT--EPGHTTDTVAALL 127
                                   6689**************994..3444444455544 PP

>> mTERF  mTERF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   4.1e-05      0.24     102     158 ..      46     108 ..      21     129 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 4.1e-05
                         mTERF 102 enkiknlvevLrelGvpkkllarllisrpqvlaldlekkvk......pkeieekVevlkelgl 158
                                   +++ ++ ++ Lr+lG+++++l ++ i + +++al+l   +k      p ++ee V+++ e+ +
  gi|13541417|ref|NP_111105.1|  46 GKTARSYISLLRSLGINENMLDEIGIYATRMNALSLASLLKganpiiPSTVEEAVNLMSEYRF 108
                                   4556899****************************9998885555556788888888888766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.49
# Mc/sec: 1405.39
//
Query:       gi|13541418|ref|NP_111106.1|  [L=206]
Description: transposase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       647  (0.0360868); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1553.47
//
Query:       gi|13541419|ref|NP_111107.1|  [L=415]
Description: peptide chain release factor 1 [Thermoplasma volcanium GSS1]
Scores for complete 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-45  153.2   0.1    7.8e-45  152.5   0.1    1.4  1  eRF1_2          eRF1 domain 2
    1.9e-31  108.9   0.0    5.8e-31  107.3   0.0    1.9  1  eRF1_3          eRF1 domain 3
    5.7e-16   59.0   0.0    3.8e-15   56.3   0.0    2.0  2  acVLRF1         Actinobacteria/chloroflexi VLRF1 release fact
    1.8e-15   57.1   0.0    3.2e-15   56.3   0.0    1.4  1  eRF1_1          eRF1 domain 1
    8.7e-15   55.2   0.0    1.5e-14   54.4   0.0    1.4  1  baeRF_family10  Bacterial archaeo-eukaryotic release factor f
  ------ inclusion threshold ------
      0.062   12.8   0.0       0.13   11.7   0.0    1.5  1  T4_baseplate    T4 bacteriophage base plate protein
       0.17   11.8   0.0       0.46   10.4   0.0    1.7  1  UME             UME (NUC010) domain
       0.26   11.3   0.7       0.76    9.8   0.7    1.8  1  ADK_lid         Adenylate kinase, active site lid
       0.86    9.8   3.2        1.4    9.1   0.8    2.4  2  Zn-ribbon_8     Zinc ribbon domain


Domain annotation for each model (and alignments):
>> eRF1_2  eRF1 domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  152.5   0.1   3.9e-48   7.8e-45       2     133 .]     141     271 ..     140     271 .. 0.98

  Alignments for each domain:
  == domain 1  score: 152.5 bits;  conditional E-value: 3.9e-48
                                   EEEEEEETTEEEEEEEESSCEEEEEEEE------BSTTBSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCHTTTESEEEE CS
                        eRF1_2   2 vglivldegeAtigllkgsrtevlkkievsvPkKhkrGgqsarrfeRlreekleeflkkvaeaankafllvdkdklkgiil 82 
                                   +gliv+d++eAt+g+l+g+r+ev+++++++vP Kh++Ggqs+rrfeRl+e +++ef+kkv+e an+af+   ++++++i+l
  gi|13541419|ref|NP_111107.1| 141 YGLIVIDRKEATVGFLNGTRIEVVENVQSQVPSKHHQGGQSSRRFERLIEIAANEFFKKVGEIANNAFI-PRIKEIRAIFL 220
                                   89*******************************************************************.58********* PP

                                   EESSTHHHHHHHHHHHHHHHHTCCEEEEE-S-TSCHHHHHHHHCCHHHHCC CS
                        eRF1_2  83 agpgfvkeefldkdlldaelkkkviklvdvsyggesglnevlekaaevlkd 133
                                   +gpg +ke f++kd+l++e k+k+ +l+dv+y++esgl+e++eka+e++kd
  gi|13541419|ref|NP_111107.1| 221 GGPGATKEYFFEKDYLRNEVKDKIKDLFDVGYTDESGLRELVEKASESIKD 271
                                   ***********************************************9987 PP

>> eRF1_3  eRF1 domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.3   0.0   2.9e-34   5.8e-31       1     111 [.     274     405 ..     274     407 .. 0.98

  Alignments for each domain:
  == domain 1  score: 107.3 bits;  conditional E-value: 2.9e-34
                                   HHHHHHHHHHHHHHHHC.TCSSEEESHHHHHHHHHTT-EEEEEEEHCHHTSSSHHHHHS.................-HHH- CS
                        eRF1_3   1 liqekklleefleelak.dtgkavYGveevlkalemgAvetLLvseelersrdtlkekv.................ketge 63 
                                   +++ek+l+++fl+e++k d+g+avYG++ +++ale ++v+ LL+se ++r ++t+k+++                 +++g+
  gi|13541419|ref|NP_111107.1| 274 ISREKDLMDRFLREVKKpDGGLAVYGEKAIRDALEQKMVDLLLISEGIRRVKYTYKCPTcgeektfseepsewpvcDKDGT 354
                                   579****************************************************99999********************* PP

                                   HHHHHH...HHHHHHHHHHHTT-EEEEE-TTSHHHHHHHHHTTTEEEEESS CS
                        eRF1_3  64 elelve...lieelvenveesgakveiisseseeGeqlvkafgGiaaiLRy 111
                                    lel+    +ie+l++ ++esga+veiis++s+eG+ l++afgG+aa+LR+
  gi|13541419|ref|NP_111107.1| 355 PLELIGeddMIEDLYKLAKESGAQVEIISDQSDEGKLLKQAFGGLAAVLRF 405
                                   *****99*******************************************9 PP

>> acVLRF1  Actinobacteria/chloroflexi VLRF1 release factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.3   0.0   1.9e-18   3.8e-15       4     125 ..     143     266 ..     140     269 .. 0.89
   2 ?    1.4   0.1      0.19   3.7e+02      57      92 ..     260     310 ..     254     325 .. 0.69

  Alignments for each domain:
  == domain 1  score: 56.3 bits;  conditional E-value: 1.9e-18
                       acVLRF1   4 gvllvrrggfavgvveggelvaskvgtrdvqgrtaaGGwSqqRfaRrrenqadalleavaeaaarllaeesae...vvlgG 81 
                                   +++++r+ + +vg ++g++++ +++ +++v +++ +GG+S +Rf+R +e  a++ +++v e a++ + ++ +e   ++lgG
  gi|13541419|ref|NP_111107.1| 143 LIVIDRKEA-TVGFLNGTRIEVVENVQSQVPSKHHQGGQSSRRFERLIEIAANEFFKKVGEIANNAFIPRIKEiraIFLGG 222
                                   456677777.**************************************************************9******** PP

                       acVLRF1  82 drslvaevledarlaplatlareelldvpdprravLedavrrar 125
                                   + ++ + + e+  l++  + + ++l+dv+  +++ L++ v++a 
  gi|13541419|ref|NP_111107.1| 223 PGATKEYFFEKDYLRNEVKDKIKDLFDVGYTDESGLRELVEKAS 266
                                   ********9997755544444445999**99*****99999875 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.19
                       acVLRF1  57 alleavaeaaarllaeesae...............vvlgGdrslvaevled 92 
                                   +l+e++ e ++++  +++++               +++ G+++++++++++
  gi|13541419|ref|NP_111107.1| 260 ELVEKASESIKDMKISREKDlmdrflrevkkpdggLAVYGEKAIRDALEQK 310
                                   56666666666666444444444444455556788**********999886 PP

>> eRF1_1  eRF1 domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.3   0.0   1.6e-18   3.2e-15       2     128 ..      14     134 ..      13     135 .. 0.95

  Alignments for each domain:
  == domain 1  score: 56.3 bits;  conditional E-value: 1.6e-18
                                   EEEEE..CTBTTSCCEEEEEE-SCHHHHHHHHHCHTTHEEEEEEEECHHH.......--CEEEEEEEEEEEEEEECTT... CS
                        eRF1_1   2 kllkr..dlekdgsgsvtLipeddedlwhlynliapgdsvrastvrkvqresstgsreservklkLtikvekvdfdkd... 77 
                                   + l++  +l+++g+++++L+++++++++++  ++++++s+++++++k +r         ++v+ ++++ + +++++     
  gi|13541419|ref|NP_111107.1|  14 RALEElsKLHGRGTELISLYIPPEKQISDVVAYLRDEYSTSSNIKSKSTR---------KNVLAAIESIMSRLKYYRFppp 85 
                                   5666666899**************************************99.........9******************99* PP

                                   SSEEEEEEEEEEGGGG--TTSEEEEEE-TTSEEEEEECE.ESHHHHHHHHHH CS
                        eRF1_1  78 agvlrisGkvieenehvklgafhtldlelkrpftiikee.wdsfalerLkea 128
                                   +g++ + G +++  +   ++++ t  +e+++p+t++ ++ +++f++e+Lk +
  gi|13541419|ref|NP_111107.1|  86 NGLVFFVGHIATRGD---QTEMYTKIIEPPEPITTFMYKcDSEFHTEMLKAM 134
                                   ***************...8999***************888*********987 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 !   54.4   0.0   7.5e-18   1.5e-14       5     136 ..     130     266 ..     127     270 .. 0.88

  Alignments for each domain:
  == domain 1  score: 54.4 bits;  conditional E-value: 7.5e-18
                baeRF_family10   5 pLlealdeyerygvvlvdreraRlfevylgeleeveevegevpgrtktggwksqdrfqrreeeqaerhlkevAellaklle 85 
                                    L + lde e yg++++dr++a + +  + ++e ve v+++vp ++++gg+ s +rf+r  e  a +++k+v+e++++++ 
  gi|13541419|ref|NP_111107.1| 130 MLKAMLDEKEIYGLIVIDRKEATVGFLNGTRIEVVENVQSQVPSKHHQGGQ-SSRRFERLIEIAANEFFKKVGEIANNAFI 209
                                   67889**********************************************.****************************9 PP

                baeRF_family10  86 erg..verlvlgGdeeetaal..ldrlpkalrarvvgtlplpvda..saaaVlekae 136
                                   +r   +++++lgG+ + ++ +  +d l +++++++ + ++++ ++    ++++eka 
  gi|13541419|ref|NP_111107.1| 210 PRIkeIRAIFLGGPGATKEYFfeKDYLRNEVKDKIKDLFDVGYTDesGLRELVEKAS 266
                                   98767*********8888877445668889999988888888855466777777776 PP

>> T4_baseplate  T4 bacteriophage base plate protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   6.4e-05      0.13      59      99 ..     308     348 ..     296     365 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 6.4e-05
                  T4_baseplate  59 eylflkvlakSlgkekvevkitCpdcgkevkvslnldqikl 99 
                                   e+ ++ +l  S g   v+ +++Cp+cg+e+++s ++++  +
  gi|13541419|ref|NP_111107.1| 308 EQKMVDLLLISEGIRRVKYTYKCPTCGEEKTFSEEPSEWPV 348
                                   6677889999999999****************998888877 PP

>> UME  UME (NUC010) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00023      0.46       4      45 ..      38      79 ..      37      96 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00023
                           UME  4 qhilgiltrlseklndshgkkslaekkraikaleeliklags 45
                                  ++i  ++++l ++ ++s++ ks +++k+++ a+e +++ ++ 
  gi|13541419|ref|NP_111107.1| 38 KQISDVVAYLRDEYSTSSNIKSKSTRKNVLAAIESIMSRLKY 79
                                  678889*******************************98876 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 ?    9.8   0.7   0.00038      0.76       4      31 ..     330     356 ..     328     358 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00038
                                   -TTT--..EEETTTB--SSTTB-TTT--.- CS
                       ADK_lid   4 CpkCGr..sYhvvfnpPkveglCDkCGepL 31 
                                   Cp CG+  +++     P +  +CDk+G pL
  gi|13541419|ref|NP_111107.1| 330 CPTCGEekTFS---EEPSEWPVCDKDGTPL 356
                                   9****988999...66************99 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1      0.75   1.5e+03       4      21 ..     118     134 ..     117     140 .. 0.52
   2 ?    9.1   0.8   0.00071       1.4       4      16 ..     326     338 ..     325     357 .. 0.71

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.75
                   Zn-ribbon_8   4 YeYrCeeCghefevlqsi 21 
                                   + Y+C++     e l ++
  gi|13541419|ref|NP_111107.1| 118 FMYKCDS-EFHTEMLKAM 134
                                   5688877.3333444444 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00071
                   Zn-ribbon_8   4 YeYrCeeCghefe 16 
                                   Y Y+C  Cg+e +
  gi|13541419|ref|NP_111107.1| 326 YTYKCPTCGEEKT 338
                                   99*******7766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (415 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       982  (0.0547716); expected 358.6 (0.02)
Passed bias filter:                      830  (0.0462937); expected 358.6 (0.02)
Passed Vit filter:                        98  (0.005466); 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 0.29s 00:00:00.86 Elapsed: 00:00:00.44
# Mc/sec: 2855.55
//
Query:       gi|13541420|ref|NP_111108.1|  [L=309]
Description: cysteine synthase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-52  178.8   0.0      2e-52  178.4   0.0    1.1  1  PALP      Pyridoxal-phosphate dependent enzyme


Domain annotation for each model (and alignments):
>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  178.4   0.0   1.1e-56     2e-52       3     280 ..      21     278 ..      19     289 .. 0.91

  Alignments for each domain:
  == domain 1  score: 178.4 bits;  conditional E-value: 1.1e-56
                                   GCSSS--EEEECCTCCCCCCEEEEEEGGGSTTSBTTHHHHHHHHHHHHTT..TTTSEEEEEBSSHHHHHHHHHHHHHT-EE CS
                          PALP   3 lgigpTPlvrlprlskelgvplflKlEslnptgSfKdRgaeyllarlkeg..tgaktvveassGNhgralAaaaallGlkv 81 
                                    +ig+TP+ ++++     ++++++K E+ n +gS+KdR a +++ +lk +   ++k +veassGN+g+a++ ++++lGl++
  gi|13541420|ref|NP_111108.1|  21 AHIGNTPVEEIDA-----NGNIYAKIEWENRFGSIKDRPAFFIMDYLKSKgvLEGKAIVEASSGNTGLAISTISSMLGLQS 96 
                                   589*****99998.....669*************************99999****************************** PP

                                   EEEEETTS-HHHHHHHHHTT-EEEEECCH..HHHHHHHHHHHHHHSTTCEE--TTTSHHHHHH.HHTHHHHHHHHTTTTEE CS
                          PALP  82 tivvpadaspekvallrllGaevvevggd..ydeavaaaaelaaegegaylvsqfdnptvieg.ygtiglEileqlggkpd 159
                                    iv+p++as++ ++ + + G ++++++ d  ++ + ++a+ la++ +++y+++q++np++ +  y ++++E+l+q g  p+
  gi|13541420|ref|NP_111108.1|  97 CIVLPENASQATKKIIVENGSQLILTPPDlgTEGSIEKARSLASS-GSFYWINQHSNPLNSDVhYYSTAPELLDQEG-MPE 175
                                   **************************7774477777779******.**************************98886.*** PP

                                   EEEEE-SSSHHHHHHHHHHHHHSTT-EEEEEEECTTCGGTTCCS..S.SS..B.SSS.CCSTCS.CGTTCCHHHHSEEEEE CS
                          PALP 160 avvvpvGgGgliaGiaaglkerrpdvrvigvepegsdalarslragrrvtvpvsdtiadglavg.spselafelldrlvde 239
                                   a+v++vG+Gg+i+Gia+++ker+p+v+vigv+p+  + + + +                  +++ ++    ++l+  ++d+
  gi|13541420|ref|NP_111108.1| 176 AIVAGVGTGGTITGIARYFKERDPSVKVIGVQPSLYSHIPGLR------------------DIKkTSNKGLIDLYGSYIDD 238
                                   **********************************777777777..................22245677799********* PP

                                   EEEEEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHHHHHHHH CS
                          PALP 240 ivtvsdeealeamrllarregivvepssaaalaalklreag 280
                                   +  v++ +a++ +   + ++g +++ ss+a+l a   +  +
  gi|13541420|ref|NP_111108.1| 239 FLYVKESDAIAEVFDHYVNTGELIGISSGANLYAS-KQLSS 278
                                   *********999999999**************999.44444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 2416.79
//
Query:       gi|13541421|ref|NP_111109.1|  [L=407]
Description: glutamyl-tRNA reductase [Thermoplasma volcanium GSS1]
Scores for 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-28   98.4   0.1    1.2e-27   96.5   0.1    2.0  1  GlutR_N          Glutamyl-tRNAGlu reductase, N-terminal domai
    1.6e-24   86.5   0.1    4.4e-24   85.1   0.0    1.8  2  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
    4.4e-12   46.3   0.1      1e-11   45.1   0.1    1.6  1  GlutR_dimer      Glutamyl-tRNAGlu reductase, dimerisation dom
    0.00079   18.4   0.0     0.0016   17.5   0.0    1.4  1  OCD_Mu_crystall  Ornithine cyclodeaminase/mu-crystallin famil
  ------ inclusion threshold ------
      0.091   12.6   0.1       0.31   10.9   0.1    1.9  1  DUF3081          Protein of unknown function (DUF3081)
        0.1   13.1   0.2        5.3    7.5   0.2    2.9  3  AAA              ATPase family associated with various cellul


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 !   96.5   0.1     4e-31   1.2e-27      31     146 .]      35     134 ..      13     134 .. 0.86

  Alignments for each domain:
  == domain 1  score: 96.5 bits;  conditional E-value: 4e-31
                       GlutR_N  31 eekvkeaviLsTCNRtEiylsaeeeeeaseellellaevsleelkeklyvlegeeavrHlfrVasGLdSlvlGEdqIlgQv 111
                                   +++v+++viL TCNR+E+y + +                  +  ++  ++ +++ a++Hlf+Va+GLdS+ +GE+++l+Qv
  gi|13541421|ref|NP_111109.1|  35 DHGVEKYVILLTCNRVELYYRGDPF----------------DVQEKGYNIISDDMAINHLFHVAAGLDSMSIGENEVLKQV 99 
                                   348899*************533221................2223567899****************************** PP

                       GlutR_N 112 keayelakeagtlgkvLerlfqkaikvakrvrtet 146
                                   k+aye+++++g ++k+L+ +fq+ai+v+k vr++t
  gi|13541421|ref|NP_111109.1| 100 KQAYEKSSSMGKSDKFLSLIFQRAISVGKLVRSKT 134
                                   ********************************997 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.1   0.0   1.5e-27   4.4e-24       8     138 .]     152     265 ..     145     265 .. 0.92
   2 ?   -3.5   0.0       3.2   9.6e+03      61      78 ..     317     334 ..     308     348 .. 0.62

  Alignments for each domain:
  == domain 1  score: 85.1 bits;  conditional E-value: 1.5e-27
                                   S..TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEEEE-SSSSS- CS
                  Shikimate_DH   8 eslkekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeiealkleelkellaeadvvisataseep 88 
                                    +  ++k+ll+G+G++a+++a +++  ++k v+va+R++++++++ae++   e+e++ ++++++l++++dv+i+at+s++p
  gi|13541421|ref|NP_111109.1| 152 RKNGGNKILLVGNGMLASEIAPYFSYPQYK-VTVAGRNIDHVRAFAEKY---EYEYVLINDIDSLIKNNDVIITATSSKTP 228
                                   556689***********************9.******************...677************************** PP

                                   SB-HHHHHCCHHH.S..EEEEE--SS-SB-TTGGGSTTCCCEEHHHHHHH CS
                  Shikimate_DH  89 ilekeeveealkkrkkplllvDiavPRdvepevaeledvrlytvDdLkev 138
                                   i+e+++++  +       l++D+++P ++e      ++++++t+D+++e+
  gi|13541421|ref|NP_111109.1| 229 IVEERSLMPGK-------LFIDLGNPPNIE------RGNNVITLDEIYEI 265
                                   ******99776.......9***********......67888899988875 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 3.2
                                   -EEEEGCGHHHHHHT-SE CS
                  Shikimate_DH  61 iealkleelkellaeadv 78 
                                   +e++k+ +++  ++e+d+
  gi|13541421|ref|NP_111109.1| 317 MEIQKFRKMHPEVNENDL 334
                                   456666666666666665 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 !   45.1   0.1   3.4e-15     1e-11       1      85 [.     279     362 ..     279     377 .. 0.84

  Alignments for each domain:
  == domain 1  score: 45.1 bits;  conditional E-value: 3.4e-15
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-S..--------TTHHHHHHHHHHHHHHHHHHSS. CS
                   GlutR_dimer   1 kAeaiIeeeveefeawlkslevvptIkalrekaeeireeeleralkklaldgedreelekltrslvnkllheptarLkea. 80 
                                   +Ae +Ie e+++ ++++k l ++++ +++++ a+ ++  e+++++k  +  + +++ le+l++s++nk+l+ p+++Lk+  
  gi|13541421|ref|NP_111109.1| 279 QAEILIENEMKATMNKIKDLMIDDIFSQFYRFASVVQTMEIQKFRKMHP--EVNENDLEALAHSIINKILNVPVTTLKAVs 357
                                   79*******************************************9887..445555**********************96 PP

                                   -TTTT CS
                   GlutR_dimer  81 edeee 85 
                                   +++++
  gi|13541421|ref|NP_111109.1| 358 RSQGN 362
                                   33332 PP

>> OCD_Mu_crystall  Ornithine cyclodeaminase/mu-crystallin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   5.2e-07    0.0016     134     221 ..     161     243 ..     146     263 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 5.2e-07
                                   EE--SHHHHHHHHHHCCCS--SEEEEE-SSHHHHHHHHHHCCS.CTT-EEECSCHHHHTTSSEEEE----SS-SB-GGGS- CS
               OCD_Mu_crystall 134 iiGaGvqaetqlealkavldikevriydrdeeaaekfaenlqefefevsackseeeavegadivvtvTaakapilkaewvk 214
                                   ++G+G+ a  ++  ++   +  +v + +r+     +fae+   +e e +  ++    +++ d+++t+T +k pi+ +  + 
  gi|13541421|ref|NP_111109.1| 161 LVGNGMLASEIAPYFS--YPQYKVTVAGRNIDHVRAFAEK---YEYEYVLINDIDSLIKNNDVIITATSSKTPIVEERSLM 236
                                   6777777777666664..4556677777776666666665...56799999****************************** PP

                                   TT-EEEE CS
               OCD_Mu_crystall 215 pGahina 221
                                   pG +   
  gi|13541421|ref|NP_111109.1| 237 PGKLFID 243
                                   **98665 PP

>> DUF3081  Protein of unknown function (DUF3081)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00011      0.31       9      72 ..     147     214 ..     145     219 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00011
                       DUF3081   9 vfekvktkGekt....eneyklegieatedfDGYtvfLadkdvsltlgFHnkyhfeyekeeqldeFlk 72 
                                   v++ v+++G ++    +n++  ++i  + ++  Y v++a+++++    F +ky+ ey   + +d+ +k
  gi|13541421|ref|NP_111109.1| 147 VYDIVRKNGGNKillvGNGMLASEIAPYFSYPQYKVTVAGRNIDHVRAFAEKYEYEYVLINDIDSLIK 214
                                   9*******99988999*****************************************76666666655 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0       5.4   1.6e+04      97     113 ..      37      51 ..      31      53 .. 0.70
   2 ?    2.2   0.0     0.078   2.3e+02      47      74 ..     190     216 ..     137     237 .. 0.72
   3 ?    7.5   0.2    0.0018       5.3      59      98 ..     254     297 ..     239     325 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 5.4
                                   TTSSSTEEEEEEESSGG CS
                           AAA  97 kkkeskvivigatnrpd 113
                                       +k ++++++nr++
  gi|13541421|ref|NP_111109.1|  37 GV--EKYVILLTCNRVE 51 
                                   44..4689999999976 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.078
                                   HHHHHHHHHTSTSEEEEEETGGGHHHHH CS
                           AAA  47 relfkeakekakpsilfiDEidalaksr 74 
                                    ++ + a++ +    ++i +id+l+k++
  gi|13541421|ref|NP_111109.1| 190 DHVRAFAEKYE-YEYVLINDIDSLIKNN 216
                                   33333344443.4668999999999887 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0018
                                   SEEEEEETGGGHHHHH....TTCCCHHHHHHHHHHHHHHHHTTT CS
                           AAA  59 psilfiDEidalaksr....sgseseeeervvnqLlteldgvkk 98 
                                     ++ +DEi+++ k++    +++ ++ e  + n++ + +++ k+
  gi|13541421|ref|NP_111109.1| 254 NNVITLDEIYEISKKNemlrEEKINQAEILIENEMKATMNKIKD 297
                                   389***********999987777888888999999999988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (407 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1068  (0.0595683); expected 358.6 (0.02)
Passed bias filter:                      521  (0.0290591); 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: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 2534.57
//
Query:       gi|13541422|ref|NP_111110.1|  [L=249]
Description: ICC-like phosphoesterase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.3e-07   29.7   5.7    1.5e-06   28.9   5.5    1.3  1  Metallophos    Calcineurin-like phosphoesterase
    2.2e-05   24.7   0.1    3.8e-05   24.0   0.1    1.4  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d


Domain annotation for each model (and alignments):
>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   5.5   1.7e-10   1.5e-06       4      90 ..      26     122 ..      23     164 .. 0.71

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 1.7e-10
                                   EEEESBTB...........TTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSS......HHHHHHHHHHHHHHHHTSEE CS
                   Metallophos   4 lvigDlHl...........algggqlddllkllddllreekpdlvllaGDlvdrg......dlekellellaalvkypipv 67 
                                   +v++DlHl            l   q d +  ++d++ ++ +p  ++++GD+ ++       +++  +++++++  +    +
  gi|13541422|ref|NP_111110.1|  26 VVVSDLHLgyeeemnlhglFLPRMQRDHVTHIMDKIVERYDPEKIIINGDFKQEFsknlpsEWDD-IIYFINRYDD--RDL 103
                                   89*******999999999988889999999************************88966666666.6666666666..699 PP

                                   EEEC-TTS.....CHHHHHHHHHHHHHH CS
                   Metallophos  68 ylllGNHe.....gfeeellnkygylgi 90 
                                   ++++GNH+                ++++
  gi|13541422|ref|NP_111110.1| 104 IFVRGNHDnylatI---------LSKKN 122
                                   ********433331.........22221 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 !   24.0   0.1   4.2e-09   3.8e-05       4      98 ..      26     153 ..      23     175 .. 0.68

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 4.2e-09
                 Metallophos_2   4 aiiSDlH................snldaleavlealke.vgvdaiihaGDl....eeeep......evleellela...pv 54 
                                   +++SDlH                 ++d + ++++++ e  ++++ii  GD+               + +  +++++   ++
  gi|13541422|ref|NP_111110.1|  26 VVVSDLHlgyeeemnlhglflprMQRDHVTHIMDKIVErYDPEKIIINGDFkqefS---KnlpsewDDIIYFINRYddrDL 103
                                   79*****999999999999998866777777777666548999*******964322...23344443333344444899** PP

                 Metallophos_2  55 laVrGNnDeevveedvlreaaelgtdlpeeaelelagek.......vlliH 98 
                                   + VrGN+D ++++  ++++++el +++++++ +   g+k         l H
  gi|13541422|ref|NP_111110.1| 104 IFVRGNHD-NYLATILSKKNKELLDYYEDDRYFIYHGDKdlstkkiTILGH 153
                                   ********.667778888888888888655555544444344444333344 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       486  (0.0271069); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); 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 0.29s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1633.80
//
Query:       gi|13541423|ref|NP_111111.1|  [L=381]
Description: hypothetical protein TVN0592 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-47  161.5   0.2    2.4e-47  161.1   0.2    1.2  1  LUD_dom   LUD domain
    3.6e-09   36.9   1.2    7.8e-09   35.9   1.2    1.6  1  Fer4_8    4Fe-4S dicluster domain
    1.1e-07   31.8   1.7     0.0055   16.8   0.2    2.4  2  Fer4_10   4Fe-4S dicluster domain
    5.8e-06   26.8   5.0     0.0001   22.7   6.0    2.3  2  Fer4_17   4Fe-4S dicluster domain
    4.4e-05   24.0   2.7    9.4e-05   22.9   2.7    1.6  1  Fer4_7    4Fe-4S dicluster domain
     0.0012   18.9   8.7       0.01   15.9   1.9    2.3  2  Fer4_6    4Fe-4S binding domain
     0.0013   18.5   4.2       0.17   11.7   0.6    2.4  2  Fer4_20   Dihydroprymidine dehydrogenase domain II, 4Fe-4S cl
     0.0017   18.5   3.9      0.013   15.7   4.4    2.0  2  Fer4_9    4Fe-4S dicluster domain
      0.005   17.8   5.1      0.021   15.8   5.1    2.1  1  Fer4_16   4Fe-4S double cluster binding domain
      0.008   16.4   0.5        1.5    9.0   0.0    2.5  2  Fer4_18   4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.014   15.2   9.9      0.014   15.2   2.2    2.4  2  Fer4      4Fe-4S binding domain
      0.033   15.0   2.6        1.5    9.7   0.3    2.4  2  Fer4_22   4Fe-4S dicluster domain
      0.055   13.6   8.4        0.6   10.3   8.4    2.2  1  Fer4_21   4Fe-4S dicluster domain
      0.095   12.8   0.0       0.43   10.7   0.0    2.0  2  Rsbr_N    Rsbr N terminal
      0.097   13.2   6.3        0.3   11.7   0.4    2.2  2  Fer4_4    4Fe-4S binding domain
        0.5   10.6   8.5      0.097   12.8   1.1    2.3  2  Fer4_2    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 !  161.1   0.2   2.1e-50   2.4e-47       2     189 .]      51     280 ..      50     280 .. 0.97

  Alignments for each domain:
  == domain 1  score: 161.1 bits;  conditional E-value: 2.1e-50
                       LUD_dom   2 eefienleangaevyyaktaeealelilellkeksv.....................vseggstdlgeigl.......... 51 
                                   +++++++e+ g+++y+ak+++ea+++i +l+ ek++                       e+++tdlge+ +          
  gi|13541423|ref|NP_111111.1|  51 KRTMDSVEKLGGHAYLAKDKDEARKIIGDLVGEKKTvvfsktnvayeiglreflqerNNEVWETDLGEYLVqisrgwpthi 131
                                   799*******************************999******************************************** PP

                       LUD_dom  52 .apalhsgreevldlfeekl............treareelrekfltadvgitganfaiAetGtlvlvdnegnrraltflpk 119
                                    apal+++ree ++  ++              +++ r+ l+ k  +advgitgan++ A++G++ lv+negn r  t++p+
  gi|13541423|ref|NP_111111.1| 132 vAPALDMTREEAAKAVKKIDpsinenskiediVAAVRKFLMSKYVKADVGITGANAVAADSGSVALVENEGNIRIDTVMPP 212
                                   ****************9999************************************************************* PP

                       LUD_dom 120 vhivvvginkivpdledavkrlktaprnatrlqkktpyvsfisgpsrtadielvlvygvhgpkrihvilv 189
                                    hi+v+gi+kivp++ da++ +    + a      ++y+++ sgps+tadiel  v+ + gpk++h++l+
  gi|13541423|ref|NP_111111.1| 213 MHIAVTGIDKIVPTMRDALDEVMV--QAAYAGIFPPTYINVTSGPSSTADIELRRVSPATGPKDFHLVLI 280
                                   ************************..444445689*********************************97 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.9   1.2     7e-12   7.8e-09       3      65 .]     297     362 ..     295     362 .. 0.75

  Alignments for each domain:
  == domain 1  score: 35.9 bits;  conditional E-value: 7e-12
                        Fer4_8   3 ekCieCgaCqsaCpvlrrtkkhlldargeaae.......dvqeeqvleeeealwsCttcgaCtevCpvgi 65 
                                     Ci+Cg+C  +Cp++r+ +k+  +++   ++       +  ++    +   + +C++ g C+evCp++i
  gi|13541423|ref|NP_111111.1| 297 LLCIKCGRCYFSCPIYRTLGKEWISTKSPYNGptgvmwnYITNK----DPWPASYCVHSGGCKEVCPMKI 362
                                   56****************99766666666555555544422222....25678**************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 !   16.8   0.2   4.9e-06    0.0055       7      23 ..     297     313 ..     292     335 .. 0.76
   2 !   14.0   0.1   3.7e-05     0.041       6      28 ..     345     367 ..     340     381 .] 0.70

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 4.9e-06
                       Fer4_10   7 dtCirCgkCvkaCPadl 23 
                                     Ci+Cg+C  +CP + 
  gi|13541423|ref|NP_111111.1| 297 LLCIKCGRCYFSCPIYR 313
                                   57************943 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 3.7e-05
                       Fer4_10   6 ddtCirCgkCvkaCPadltsvga 28 
                                   ++ C++ g C+++CP++++  ++
  gi|13541423|ref|NP_111111.1| 345 ASYCVHSGGCKEVCPMKINIPEV 367
                                   578*************7733333 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   1.1   3.1e-05     0.034      34      57 ..     285     310 ..     264     313 .. 0.79
   2 !   22.7   6.0   9.2e-08    0.0001       2      61 .]     299     363 ..     298     363 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.1e-05
                       Fer4_17  34 leeaeke..ekaslCieCgeCerkCP 57 
                                   le+ ++e  ++a lCi+Cg+C  +CP
  gi|13541423|ref|NP_111111.1| 285 LEASKNEdlKEALLCIKCGRCYFSCP 310
                                   444433345799*************9 PP

  == domain 2  score: 22.7 bits;  conditional E-value: 9.2e-08
                       Fer4_17   2 CiqCgyClpeCpsyeaydne......pkkllraaklglleeaekeekaslCieCgeCerkCPqgld 61 
                                   Ci+Cg C  +Cp y+  ++e      p +    ++++ +++ ++   as C++ g+C+++CP++++
  gi|13541423|ref|NP_111111.1| 299 CIKCGRCYFSCPIYRTLGKEwistksPYNGPTGVMWNYITN-KDPWPASYCVHSGGCKEVCPMKIN 363
                                   ***************95553332111333333333332222.233489***************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 !   22.9   2.7   8.4e-08   9.4e-05       2      51 ..     299     361 ..     298     362 .. 0.59

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 8.4e-08
                        Fer4_7   2 CigCgaCvaaCpvkaield.......eeenekgt...ekveidpe...kClgCgaCvavCPtg 51 
                                   Ci+Cg+C   Cp +    +       +++ + g+     ++ dp+   +C++ g C +vCP +
  gi|13541423|ref|NP_111111.1| 299 CIKCGRCYFSCPIYRTLGKewistksPYNGPTGVmwnYITNKDPWpasYCVHSGGCKEVCPMK 361
                                   ************55555541222112223333323323335555433379999********76 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   1.9   9.2e-06      0.01       8      20 ..     298     310 ..     296     314 .. 0.92
   2 !    6.7   0.7    0.0073       8.2       7      22 ..     346     361 ..     345     364 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 9.2e-06
                        Fer4_6   8 kCigCgdCvrvCP 20 
                                   +Ci Cg+C+  CP
  gi|13541423|ref|NP_111111.1| 298 LCIKCGRCYFSCP 310
                                   7************ PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0073
                        Fer4_6   7 dkCigCgdCvrvCPeg 22 
                                   + C++ g C  vCP++
  gi|13541423|ref|NP_111111.1| 346 SYCVHSGGCKEVCPMK 361
                                   56************86 PP

>> Fer4_20  Dihydroprymidine dehydrogenase domain II, 4Fe-4S cluster
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.5    0.0027         3      11      47 ..     286     321 ..     280     348 .. 0.80
   2 !   11.7   0.6   0.00015      0.17      27      50 ..     348     372 ..     338     379 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0027
                                   ---HHHHHHHHTT----TT-HHHHCSTT---H.HHHHH CS
                       Fer4_20  11 glteeealeeAsRClqCkkapcvkgCPveidi.pefik 47 
                                   + +++e l+eA  C++C    c  +CP+  +  +e+i+
  gi|13541423|ref|NP_111111.1| 286 EASKNEDLKEALLCIKC--GRCYFSCPIYRTLgKEWIS 321
                                   56788899*********..78999***98765356776 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00015
                                   -T.T-HHHHCSTT---HHHHHHHHH CS
                       Fer4_20  27 Ck.kapcvkgCPveidipefikkia 50 
                                   C  +  c++ CP++i+ipe ik i+
  gi|13541423|ref|NP_111111.1| 348 CVhSGGCKEVCPMKINIPEVIKYIK 372
                                   541356**************99987 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   1.5   0.00044       0.5      34      47 ..     297     310 ..     278     314 .. 0.70
   2 !   15.7   4.4   1.1e-05     0.013       2      49 ..     299     361 ..     298     363 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00044
                        Fer4_9  34 eaCigCgaCveaCp 47 
                                     Ci+Cg+C+  Cp
  gi|13541423|ref|NP_111111.1| 297 LLCIKCGRCYFSCP 310
                                   46888888888887 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 1.1e-05
                        Fer4_9   2 CtgCgaCveaC...............pagvvvedaaerkarlraase..............eaCigCgaCveaCpkg 49 
                                   C++Cg+C  +C               p++  +                             + C++ g C e+Cp +
  gi|13541423|ref|NP_111111.1| 299 CIKCGRCYFSCpiyrtlgkewistksPYNGPT--------------GvmwnyitnkdpwpaSYCVHSGGCKEVCPMK 361
                                   ***********666666544444333222222..............23444466666677789************97 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   5.1   1.9e-05     0.021       2      66 ..     299     360 ..     298     361 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.9e-05
                       Fer4_16   2 CgtCgkCaevCPtnaikekkekeiearecisyntaekkdlaedeekck.kqeaitgCdiCqdvCPa 66 
                                   C++Cg+C  +CP     +k   e+ + ++  +  +    ++  ++k+   +  +   + C++vCP+
  gi|13541423|ref|NP_111111.1| 299 CIKCGRCYFSCPIYRTLGK---EWISTKSPYN-GPTGVMWNYITNKDPwPASYCVHSGGCKEVCPM 360
                                   *************999999...7777776554.34433333333333324566677789******8 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.1     0.025        28      54      73 ..     292     311 ..     280     318 .. 0.73
   2 !    9.0   0.0    0.0014       1.5      57      79 ..     344     366 ..     329     375 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.025
                       Fer4_18  54 kekgagdcidcescvkvcPt 73 
                                     k+a  ci+c+ c   cP+
  gi|13541423|ref|NP_111111.1| 292 DLKEALLCIKCGRCYFSCPI 311
                                   44566679999999999996 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0014
                       Fer4_18  57 gagdcidcescvkvcPtgidirk 79 
                                   +a+ c++ + c +vcP++i+i +
  gi|13541423|ref|NP_111111.1| 344 PASYCVHSGGCKEVCPMKINIPE 366
                                   5678****************976 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   2.2   1.3e-05     0.014       7      19 ..     298     310 ..     295     312 .. 0.93
   2 ?    4.4   1.0     0.032        35       7      20 ..     347     360 ..     342     362 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.3e-05
                                   TSSS-THHHHHST CS
                          Fer4   7 kCigCGaCvevCP 19 
                                   +Ci+CG+C+  CP
  gi|13541423|ref|NP_111111.1| 298 LCIKCGRCYFSCP 310
                                   7************ PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.032
                                   TSSS-THHHHHSTT CS
                          Fer4   7 kCigCGaCvevCPv 20 
                                    C++ G C evCP 
  gi|13541423|ref|NP_111111.1| 347 YCVHSGGCKEVCPM 360
                                   6777799******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 ?    9.7   0.3    0.0013       1.5      78      93 ..     295     310 ..     284     313 .. 0.73
   2 ?    4.9   0.1     0.041        46      79      96 .]     345     362 ..     330     362 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0013
                       Fer4_22  78 gesgCvGCgRCieacp 93 
                                   ++  C+ CgRC  +cp
  gi|13541423|ref|NP_111111.1| 295 EALLCIKCGRCYFSCP 310
                                   5667888888888887 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.041
                       Fer4_22  79 esgCvGCgRCieacpvki 96 
                                   +s Cv  g C+e+cp+ki
  gi|13541423|ref|NP_111111.1| 345 ASYCVHSGGCKEVCPMKI 362
                                   678999999999999876 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   8.4   0.00054       0.6       7      54 ..     298     361 ..     294     365 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00054
                       Fer4_21   7 kCigCgkCliaCe...dtshqai.........eidaktvl..........kvvedeCvGCnlCssvCPve 54 
                                    Ci+Cg+C+ +C+   + + + i         +                 +  ++ Cv    C +vCP++
  gi|13541423|ref|NP_111111.1| 298 LCIKCGRCYFSCPiyrTLGKEWIstkspyngpT------GvmwnyitnkdPWPASYCVHSGGCKEVCPMK 361
                                   5***********822234555565444332221......02334444444556899************84 PP

>> Rsbr_N  Rsbr N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.1      0.25   2.9e+02      49     121 ..      36     111 ..      19     114 .. 0.68
   2 ?   10.7   0.0   0.00038      0.43      31     115 ..      87     172 ..      42     177 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.25
                                   S.-SSTTHHHHHHHHHHHHHTT--H...HHHHHHHHHHHHHHHHHHHH..T--TT--HHHHHHHHHHHHHHHHHHH CS
                        Rsbr_N  49 eegneeleekleefaerlvqlGwpL...kyltkgLqefrkvvlellseeddvvkeeqslelleeieewidpivnel 121
                                   +e++ ++ ++l+++++r +     L   +yl+k   e rk++ +l+ e++ vv ++  + +   ++e++++ +ne+
  gi|13541423|ref|NP_111111.1|  36 REQKLKVIANLDTYVKRTMDSVEKLgghAYLAKDKDEARKIIGDLVGEKKTVVFSKTNVAYEIGLREFLQERNNEV 111
                                   5555666666666666655433333222688888888888888888888888888887777778888888888876 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00038
                                   HHHHHHHHHHHHHHHH-SS..-SSTTHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHHHHH...T--TT--HHHHHHH CS
                        Rsbr_N  31 evyektskefvdlilssve.egneeleekleefaerlvqlGwpLkyltkgLqefrkvvlellseed.dvvkeeqslellee 109
                                    v+ kt+  +   + + ++ ++ne  e +l e+  + +  Gwp + ++ +L + r+   +++++ d +  ++++  ++++ 
  gi|13541423|ref|NP_111111.1|  87 VVFSKTNVAYEIGLREFLQeRNNEVWETDLGEYLVQ-ISRGWPTHIVAPALDMTREEAAKAVKKIDpSINENSKIEDIVAA 166
                                   566666666655555555624455556677777655.578**************************8888889999***** PP

                                   HHHHHH CS
                        Rsbr_N 110 ieewid 115
                                   +++++ 
  gi|13541423|ref|NP_111111.1| 167 VRKFLM 172
                                   *99975 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.4   0.00027       0.3       4      15 ..     299     310 ..     291     326 .. 0.90
   2 ?    4.1   0.9     0.073        81       3      16 ..     347     360 ..     345     361 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00027
                        Fer4_4   4 CigCgsCvaaCP 15 
                                   Ci Cg+C+ +CP
  gi|13541423|ref|NP_111111.1| 299 CIKCGRCYFSCP 310
                                   ***********9 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.073
                        Fer4_4   3 rCigCgsCvaaCPq 16 
                                    C++ g C  +CP+
  gi|13541423|ref|NP_111111.1| 347 YCVHSGGCKEVCPM 360
                                   699999*******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 ?   12.8   1.1   8.6e-05     0.097       8      21 ..     297     310 ..     292     310 .. 0.89
   2 ?    1.4   1.2      0.38   4.2e+02      10      21 ..     348     359 ..     344     360 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 8.6e-05
                        Fer4_2   8 drCigCgaCvsaCP 21 
                                     Ci Cg C+ +CP
  gi|13541423|ref|NP_111111.1| 297 LLCIKCGRCYFSCP 310
                                   57***********9 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.38
                        Fer4_2  10 CigCgaCvsaCP 21 
                                   C++ g C  +CP
  gi|13541423|ref|NP_111111.1| 348 CVHSGGCKEVCP 359
                                   888899*****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (381 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       724  (0.0403815); expected 358.6 (0.02)
Passed bias filter:                      599  (0.0334096); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.63u 0.31s 00:00:00.94 Elapsed: 00:00:00.50
# Mc/sec: 2280.41
//
Query:       gi|13541424|ref|NP_111112.1|  [L=300]
Description: Fe-S oxidoreductase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.9e-08   32.3   0.0    2.5e-05   24.4   0.0    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 !    5.7   0.0   0.00096        17      42      83 ..     130     171 ..      99     173 .. 0.80
   2 !   24.4   0.0   1.4e-09   2.5e-05       3      84 ..     203     286 ..     201     287 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.00096
                           CCG  42 GagggrsgkeelaealakrnvetaeetgadaivtacpgCllq 83 
                                   G+  +  g+ +++++++k+ +e +++ ++  i+t++p+ +++
  gi|13541424|ref|NP_111112.1| 130 GSLLYELGFMDEFKEYGKKVFELFKQHKVSNIITIDPHTTNT 171
                                   777778889999***********************9986655 PP

  == domain 2  score: 24.4 bits;  conditional E-value: 1.4e-09
                           CCG   3 yfdgChllraa..ypevrkalkkllealgveleel...ekesCCGagggrsgkeelaealakrnvetaeetgadaivtacp 78 
                                   ++d+C + r    y+  r  ++   ++++ve ++        CCG + g   +++l++++ak ++et+ +++ d +++acp
  gi|13541424|ref|NP_111112.1| 203 LHDSCLYSRFLgmYESIRTTIRSA-GVELVEDPTVtgkGAGFCCGGPVG-PLNDKLSNEIAKARAETLTSVNKD-VLVACP 280
                                   799994444448877777766666.66666544432224478*******.556669**************9777.8999** PP

                           CCG  79 gCllql 84 
                                    C+++l
  gi|13541424|ref|NP_111112.1| 281 LCYANL 286
                                   ***987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       668  (0.0372581); expected 358.6 (0.02)
Passed bias filter:                      565  (0.0315132); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 1870.43
//
Query:       gi|13541425|ref|NP_111113.1|  [L=403]
Description: major facilitator superfamily permease [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-34  119.2  42.8    1.8e-34  119.2  42.8    1.8  2  MFS_1     Major Facilitator Superfamily
    1.4e-23   83.5  31.5    1.6e-20   73.4  11.9    2.4  2  Sugar_tr  Sugar (and other) transporter
    0.00093   17.6   1.5     0.0023   16.3   1.5    1.7  1  OATP      Organic Anion Transporter Polypeptide (OATP) family
  ------ inclusion threshold ------
      0.072   13.1   0.0      0.072   13.1   0.0    3.9  3  FixQ      Cbb3-type cytochrome oxidase component FixQ


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 !  119.2  42.8   4.1e-38   1.8e-34       6     348 ..      12     348 ..       7     353 .. 0.84
   2 ?   -0.0   0.4     0.072   3.2e+02     138     173 ..     357     389 ..     346     402 .. 0.61

  Alignments for each domain:
  == domain 1  score: 119.2 bits;  conditional E-value: 4.1e-38
                         MFS_1   6 flsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalg.lllllfassl 85 
                                    l a++++++++++  a+a++++++  ++ l +tl     +++sl++G+++d++Gr+ +++++ll++a++ +l+++ ++++
  gi|13541425|ref|NP_111113.1|  12 SLDAFDFFLITFVML-AIAKTFNVALIVVTLSITLTLSMRFIGSLFFGPIGDKYGRKITMIISLLFLAFFdTLVAF-SPTI 90 
                                   57899999******9.*************99999999999******************************555555.7888 PP

                         MFS_1  86 wlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllafv 166
                                   +++l+lr+l G+g+g+ + +g al+ +  p + rg + gl+++g+  G++l++++  +++  +gWr +f+++a+ ++ ++ 
  gi|13541425|ref|NP_111113.1|  91 TIFLILRALYGFGMGGEWGSGFALAMESLPAKARGWVSGLIQGGYPTGYLLAAVVYLAIYPRFGWRPMFFFAALPAIAVIY 171
                                   8*****************************************************************************955 PP

                         MFS_1 167 lfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsglltllplylqevlgls...gll 244
                                   +  +l ++e p  +  +++      +++ l++ +++ +k  v   l i l+++ f+  ++  l p++l  +l++s   +  
  gi|13541425|ref|NP_111113.1| 172 I--MLTTRESPVYAEYKERAS----FKKTLTT-IGKNWKLFVY--LSILLIGMNFVSHSTQDLYPTFLEHQLKFSptyA-A 242
                                   3..566555555555555555....5666666.4444444433..66666666667777****************6643.5 PP

                         MFS_1 245 laglllallalvgailallagrls..drlgrrrrlllallllllaalglallavtssavllllvlvl...iGfglgfvfps 320
                                   ++++++ ++a+vg   ++l+g +s  +rlgr++  + +l+++++++ ++a+  ++ +++l++++++    + f +  ++++
  gi|13541425|ref|NP_111113.1| 243 SIAIAYNAAAIVG---GILSGIISqnTRLGRKWNAVAFLAVGIVISPLWAFPQLFGHSSLIYMAFLApvvMQFIVQGAWAM 320
                                   5555566666666...999****96556***************************88888887444444488866667*** PP

                         MFS_1 321 llalasdlappeeagtasglfntagslg 348
                                     +++++  p+e+++t+ g++ ++g  +
  gi|13541425|ref|NP_111113.1| 321 PGVYMNERSPAEARATIPGVAYMVGVMV 348
                                   **********************998665 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.072
                         MFS_1 138 pllggllasslgWravfyilaivsllafvlfllllp 173
                                    +++++++++++++++ ++l ++ l ++    + l 
  gi|13541425|ref|NP_111113.1| 357 VAVSSMFSDNYSYSLLLLVLIVFPLTMVA---WALG 389
                                   56777777777777777776666666633...4444 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.4  11.9   3.6e-24   1.6e-20      50     205 ..      41     190 ..      27     204 .. 0.91
   2 !   16.0  10.8   9.4e-07    0.0042      43     188 ..     232     387 ..     206     393 .. 0.74

  Alignments for each domain:
  == domain 1  score: 73.4 bits;  conditional E-value: 3.6e-24
                                   HHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHHHHHHTT CS
                      Sugar_tr  50 livsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlvPmyisEi 130
                                   l+  ++l  ++iGslf+g++gd++GRk +++i+ +++     l a+++   ++ ++++ R l G+g+G++ +    ++ E 
  gi|13541425|ref|NP_111113.1|  41 LSITLTLSMRFIGSLFFGPIGDKYGRKITMIISLLFLAFFDTLVAFSP---TITIFLILRALYGFGMGGEWGSGFALAMES 118
                                   44555566789*************************************...9***************************** PP

                                   S-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-TTHHHHHHHCCHHHHHHHHHHGGGS---HHHHHHTT-HH CS
                      Sugar_tr 131 ApkklRgalvslyqlaitfGilvaaifglglnktsnadgwrillglqlvpallllilllflPESPrylvekgkee 205
                                    p+k Rg + +l q ++ +G l+aa+++l++    +   wr +++++++pa+++++++l+ +ESP y   k++ +
  gi|13541425|ref|NP_111113.1| 119 LPAKARGWVSGLIQGGYPTGYLLAAVVYLAIYPRFG---WRPMFFFAALPAIAVIYIMLTTRESPVYAEYKERAS 190
                                   ****************************99877777...****************************98887665 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 9.4e-07
                                   H.......HHHHHHHTHHHHHHHHHHHHHHHHH..HTTHHHHHHHHHHHHHHHHHHHH-TTTT...SS-TGGGGGHHHHHH CS
                      Sugar_tr  43 e....ssvlsglivsiflvGaiiGslfagllgd..rfGRkkslliaavlfvigavlqaaakgk...nsvevlivgRvlvGi 114
                                        s ++   i+ ++++ ai+G++++g++++  r+GRk+  +++ ++ ++ + l a+ +     + +++ +++ v++ +
  gi|13541425|ref|NP_111113.1| 232 HqlkfSPTYAASIAIAYNAAAIVGGILSGIISQntRLGRKWNAVAFLAVGIVISPLWAFPQLFghsSLIYMAFLAPVVMQF 312
                                   14444445667799999*************995449*****88776666666666666666335557899999******** PP

                                   HHHHHHHHHHHHHHTTS-SCCHHHH.HHHHHHHHHHHHHHHHHHHHHHHTSS-TTHHHHHHHCCHHHHHHHHHHG CS
                      Sugar_tr 115 gvGlasvlvPmyisEiApkklRgal.vslyqlaitfGilvaaifglglnktsnadgwrillglqlvpallllill 188
                                    v +a ++  +y++E +p++ R ++ ++ y +++ +    a+i  ++ +++s++  + +ll + +v++l+++++ 
  gi|13541425|ref|NP_111113.1| 313 IVQGAWAMPGVYMNERSPAEARATIpGVAYMVGVMVTSTAASIEVAVSSMFSDNYSYSLLLLVLIVFPLTMVAWA 387
                                   **********************7662555566666666556666666688888999************9998875 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 !   16.3   1.5   5.1e-07    0.0023     277     385 ..     185     294 ..     173     319 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 5.1e-07
                                   xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          OATP 277 lkslkdfpkalkrllkn.pifllvilssvfeillvaGfitFlpkylEtqFslsaseAnlltGvvvipgaalGillgGllvk 356
                                    k+ ++f k+l  + kn ++f+++++  + + ++        p +lE+q + s+++A+ + +++   +a++G +l+G++ +
  gi|13541425|ref|NP_111113.1| 185 YKERASFKKTLTTIGKNwKLFVYLSILLIGMNFVSHSTQDLYPTFLEHQLKFSPTYAASI-AIAYNAAAIVGGILSGIISQ 264
                                   4566788899999999966899999999999999999999*****************998.7888889999999******* PP

                                   xxxxxxxx.xxxxxxxxxxxxxxxxxxxxx RF
                          OATP 357 klklsakk.laklvlvvsllsllllllllf 385
                                     +l  k  ++++ +v  ++s l  ++ lf
  gi|13541425|ref|NP_111113.1| 265 NTRLGRKWnAVAFLAVGIVISPLWAFPQLF 294
                                   ****99872555555556666666666655 PP

>> FixQ  Cbb3-type cytochrome oxidase component FixQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   1.4       2.2     1e+04       3      23 ..      80     100 ..      72     102 .. 0.68
   2 ?    1.7   0.3     0.059   2.6e+02      15      43 ..     158     187 ..     158     189 .. 0.83
   3 ?   13.1   0.0   1.6e-05     0.072       9      35 ..     367     393 ..     365     398 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 2.2
                          FixQ   3 yealrgfadswgllflvllfy 23 
                                   +++l++f+ ++ +++ +  +y
  gi|13541425|ref|NP_111113.1|  80 FDTLVAFSPTITIFLILRALY 100
                                   567777777776666655555 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.059
                          FixQ  15 llflvllfygvviyafrpgn.rkdfedaAn 43 
                                   ++f+++l +++viy++   +  + ++++++
  gi|13541425|ref|NP_111113.1| 158 MFFFAALPAIAVIYIMLTTReSPVYAEYKE 187
                                   58999*********9988885599988875 PP

  == domain 3  score: 13.1 bits;  conditional E-value: 1.6e-05
                          FixQ   9 fadswgllflvllfygvviyafrpgnr 35 
                                   +++s++ll+l+++ + +v++a+ ++++
  gi|13541425|ref|NP_111113.1| 367 YSYSLLLLVLIVFPLTMVAWALGKESK 393
                                   89**********************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (403 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       949  (0.052931); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.65u 0.31s 00:00:00.96 Elapsed: 00:00:00.49
# Mc/sec: 2450.90
//
Query:       gi|13541426|ref|NP_111114.1|  [L=378]
Description: Fe-S oxidoreductase [Thermoplasma volcanium GSS1]
Scores for complete 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   39.3   2.1    1.5e-09   38.2   2.1    1.6  1  Fer4_8    4Fe-4S dicluster domain
      2e-08   34.7   7.3    6.1e-08   33.1   7.3    1.9  1  Fer4_7    4Fe-4S dicluster domain
    1.5e-07   31.5   0.0    0.00012   22.2   0.5    3.3  2  CCG       Cysteine-rich domain
    2.9e-06   27.3  18.5    1.4e-05   25.2   8.1    2.4  3  Fer4_9    4Fe-4S dicluster domain
    3.8e-06   26.5  20.6     0.0003   20.5   3.2    2.7  2  Fer4      4Fe-4S binding domain
    9.4e-06   25.7  20.3    0.00021   21.4  11.3    2.6  3  Fer4_10   4Fe-4S dicluster domain
    1.7e-05   24.6  18.4    0.00052   19.9   1.7    3.0  3  Fer4_2    4Fe-4S binding domain
    1.8e-05   24.8  17.3     0.0074   16.7   2.4    3.0  3  Fer4_4    4Fe-4S binding domain
    2.5e-05   24.4   6.4     0.0091   16.2   0.4    2.4  2  Fer4_18   4Fe-4S dicluster domain
    3.5e-05   24.3   5.9    3.5e-05   24.3   5.9    2.5  3  Fer4_17   4Fe-4S dicluster domain
    4.4e-05   23.4  23.8     0.0028   17.7   6.5    2.8  2  Fer4_6    4Fe-4S binding domain
    0.00032   20.8   8.3        0.1   12.7   1.4    2.5  2  Fer4_21   4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.055   14.4  15.0        0.6   11.1  13.7    2.6  2  Fer4_16   4Fe-4S double cluster binding domain
        0.4   10.5   7.0        7.1    6.4   6.6    2.3  2  Fer4_20   Dihydroprymidine dehydrogenase domain II, 4Fe-4S cl
        1.3   10.1  23.5       0.63   11.1   6.5    2.9  2  Fer4_3    4Fe-4S binding domain
        3.5    8.2  12.9        8.7    7.0   1.7    2.6  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I


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 !   38.2   2.1   1.3e-12   1.5e-09       2      65 .]       8      75 ..       7      75 .. 0.80

  Alignments for each domain:
  == domain 1  score: 38.2 bits;  conditional E-value: 1.3e-12
                        Fer4_8  2 lekCieCgaCqsaCpvlrrtk.khlldargeaae....dvqeeqvlee....eealwsCttcgaCtevCpvgi 65
                                  + kC++Cg+C+s Cp+l ++    +  arg++      +    ++  +     ++++sC+ c aC+ vCp g+
  gi|13541426|ref|NP_111114.1|  8 AGKCVNCGFCESVCPTLPASSfIASIGARGRVDIakfvY----KN-GTvidpSTSFYSCVDCYACVAVCPAGV 75
                                  679*****************9778888888888744332....22.22466799****************986 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.1   7.3   5.5e-11   6.1e-08       1      52 []      10      75 ..      10      75 .. 0.62

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 5.5e-11
                        Fer4_7  1 rCigCgaCvaaC.............pvkaieldeeenekgt.ekveidpekClgCgaCvavCPtga 52
                                  +C++Cg+C+++C               + +++ ++ +++gt  ++  +  +C++C+aCvavCP+g+
  gi|13541426|ref|NP_111114.1| 10 KCVNCGFCESVCptlpassfiasigARGRVDIAKFVYKNGTvIDPSTSFYSCVDCYACVAVCPAGV 75
                                  7***********444333333333333333344444444432344555668************996 PP

>> CCG  Cysteine-rich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0     0.058        65      18      79 ..     194     255 ..     184     257 .. 0.82
   2 !   22.2   0.5   1.1e-07   0.00012      29      84 ..     311     365 ..     290     366 .. 0.72

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.058
                           CCG  18 rkalkkllealgveleel.ekesCCGagggrsgkeelaealakrnvetaeetgadaivtacpg 79 
                                   r+++ + l+++g+++ +l e+e   G  ++  g+ + + ++a+   + ++e g++ i+t +p+
  gi|13541426|ref|NP_111114.1| 194 RNIVNA-LKKAGIKFGYLgEEEPYPGTFIYDLGFMDDFVSYAQYVSNLFREHGVERIITVDPH 255
                                   444444.48889999999888888899999999999999********************9986 PP

  == domain 2  score: 22.2 bits;  conditional E-value: 1.1e-07
                           CCG  29 gveleel.ekesCCGagggrsgkeelaealakrnvetaeetgadaivtacpgCllql 84 
                                   ++++ +   + +CCG +      + ++e++ +r++++++  +  +i+tacp C+++l
  gi|13541426|ref|NP_111114.1| 311 FIDVSPDtGQTKCCGGPDELLFPQ-ISENISQRRFSELKA-EGLPIITACPICYANL 365
                                   445555556899*****9977666.9**************.5889*********987 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   2.8   0.00043      0.48      35      48 ..      10      23 ..       4      26 .. 0.66
   2 !   25.2   8.1   1.2e-08   1.4e-05       1      49 [.      10      74 ..      10      76 .. 0.80
   3 !   15.6   2.6   1.2e-05     0.013       2      23 ..      61      82 ..      60      92 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00043
                        Fer4_9 35 aCigCgaCveaCpk 48
                                  +C+ Cg C+ +Cp+
  gi|13541426|ref|NP_111114.1| 10 KCVNCGFCESVCPT 23
                                  46666666666664 PP

  == domain 2  score: 25.2 bits;  conditional E-value: 1.2e-08
                        Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraase................eaCigCgaCveaCpkg 49
                                  kC++Cg C+++Cp+  ++   a   ar r + +                 +C++C aCv++Cp g
  gi|13541426|ref|NP_111114.1| 10 KCVNCGFCESVCPTLPASSFIASIGARGRVDIAkfvykngtvidpstsfYSCVDCYACVAVCPAG 74
                                  7***********766666666666666555444667899999999999999************87 PP

  == domain 3  score: 15.6 bits;  conditional E-value: 1.2e-05
                        Fer4_9  2 CtgCgaCveaCpagvvvedaae 23
                                  C++C aCv++Cpagv+ ++ +e
  gi|13541426|ref|NP_111114.1| 61 CVDCYACVAVCPAGVNAGKVSE 82
                                  9999999999999888776655 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   3.2   2.7e-07    0.0003       6      20 ..       9      23 ..       5      24 .. 0.92
   2 !   15.7   4.6   8.7e-06    0.0098       7      21 ..      60      74 ..      57      75 .. 0.91

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 2.7e-07
                                  TTSSS-THHHHHSTT CS
                          Fer4  6 ekCigCGaCvevCPv 20
                                   kC++CG C++vCP+
  gi|13541426|ref|NP_111114.1|  9 GKCVNCGFCESVCPT 23
                                  69************8 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 8.7e-06
                                  TSSS-THHHHHSTTT CS
                          Fer4  7 kCigCGaCvevCPvg 21
                                   C+ C aCv vCP g
  gi|13541426|ref|NP_111114.1| 60 SCVDCYACVAVCPAG 74
                                  5************98 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4  11.3   1.8e-07   0.00021       4      56 .]       6      72 ..       3      72 .. 0.83
   2 !   17.4   1.5   3.2e-06    0.0036       8      29 ..      60      81 ..      50     100 .. 0.68
   3 ?   -2.8   0.0       6.7   7.5e+03      17      21 ..     356     360 ..     344     368 .. 0.74

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.8e-07
                       Fer4_10  4 idddtCirCgkCvkaCPadl...............tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                   ++ +C++Cg C ++CP+ l               +  +  +++      ++  ++C +c aCv++CP
  gi|13541426|ref|NP_111114.1|  6 QEAGKCVNCGFCESVCPT-LpassfiasigargrvDIAKFVYKNGTVIDPSTSFYSCVDCYACVAVCP 72
                                  56789*************.77***********8885555555555556667789*************9 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 3.2e-06
                       Fer4_10  8 tCirCgkCvkaCPadltsvgak 29
                                  +C+ C +Cv++CPa +++ +++
  gi|13541426|ref|NP_111114.1| 60 SCVDCYACVAVCPAGVNAGKVS 81
                                  6999999999999955333333 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 6.7
                       Fer4_10  17 kaCPa 21 
                                   +aCP 
  gi|13541426|ref|NP_111114.1| 356 TACPI 360
                                   45554 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   1.7   4.7e-07   0.00052       7      22 .]       8      23 ..       3      23 .. 0.88
   2 !   14.7   3.2   2.2e-05     0.024       9      22 .]      60      73 ..      51      73 .. 0.87
   3 ?   -2.5   0.4       6.4   7.2e+03      18      21 ..     356     359 ..     355     362 .. 0.71

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 4.7e-07
                        Fer4_2  7 tdrCigCgaCvsaCPa 22
                                  + +C++Cg C s+CP+
  gi|13541426|ref|NP_111114.1|  8 AGKCVNCGFCESVCPT 23
                                  569************7 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 2.2e-05
                        Fer4_2  9 rCigCgaCvsaCPa 22
                                  +C+ C aCv +CPa
  gi|13541426|ref|NP_111114.1| 60 SCVDCYACVAVCPA 73
                                  7************8 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 6.4
                        Fer4_2  18 saCP 21 
                                   +aCP
  gi|13541426|ref|NP_111114.1| 356 TACP 359
                                   6777 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   2.4   6.6e-06    0.0074       3      16 ..      10      23 ..       8      29 .. 0.93
   2 !   16.7   2.5   6.8e-06    0.0077       3      17 .]      60      74 ..      58      78 .. 0.91
   3 ?   -1.4   0.2       4.2   4.7e+03       6      12 ..     357     363 ..     356     363 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 6.6e-06
                        Fer4_4  3 rCigCgsCvaaCPq 16
                                  +C++Cg C+++CP+
  gi|13541426|ref|NP_111114.1| 10 KCVNCGFCESVCPT 23
                                  8************5 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 6.8e-06
                        Fer4_4  3 rCigCgsCvaaCPqg 17
                                  +C++C +Cva+CP g
  gi|13541426|ref|NP_111114.1| 60 SCVDCYACVAVCPAG 74
                                  7************65 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 4.2
                        Fer4_4   6 gCgsCva 12 
                                    C+ C+a
  gi|13541426|ref|NP_111114.1| 357 ACPICYA 363
                                   6999985 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   1.0   0.00039      0.44      56      73 ..       6      23 ..       2      25 .. 0.91
   2 !   16.2   0.4   8.1e-06    0.0091      58      77 ..      58      77 ..      39      87 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00039
                       Fer4_18 56 kgagdcidcescvkvcPt 73
                                  ++ag+c++c++c +vcPt
  gi|13541426|ref|NP_111114.1|  6 QEAGKCVNCGFCESVCPT 23
                                  6789*************8 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 8.1e-06
                       Fer4_18 58 agdcidcescvkvcPtgidi 77
                                     c+dc +cv+vcP g++ 
  gi|13541426|ref|NP_111114.1| 58 FYSCVDCYACVAVCPAGVNA 77
                                  568**************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 !   11.1   2.5   0.00039      0.44      42      57 ..       7      22 ..       5      24 .. 0.83
   2 !   24.3   5.9   3.1e-08   3.5e-05       1      61 []      10      76 ..      10      76 .. 0.68
   3 ?   -2.9   0.1       9.4   1.1e+04      11      20 ..     357     366 ..     355     372 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00039
                       Fer4_17 42 kaslCieCgeCerkCP 57
                                  +a++C++Cg Ce++CP
  gi|13541426|ref|NP_111114.1|  7 EAGKCVNCGFCESVCP 22
                                  5788999999999999 PP

  == domain 2  score: 24.3 bits;  conditional E-value: 3.1e-08
                       Fer4_17  1 rCiqCgyClpeCpsyeaydnepk.kllraakl....glleeaeke.ekaslCieCgeCerkCPqgld 61
                                  +C +Cg+C+ +Cp++ a ++      + ++ +     +++++++  + + +C+ C  C+++CP+g++
  gi|13541426|ref|NP_111114.1| 10 KCVNCGFCESVCPTLPASSFIASiGARGRVDIakfvYKNGTVIDPsTSFYSCVDCYACVAVCPAGVN 76
                                  6************98886653221344444442233234445444379***************9985 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 9.4
                       Fer4_17  11 eCpsyeaydn 20 
                                   +Cp ++a+  
  gi|13541426|ref|NP_111114.1| 357 ACPICYANLA 366
                                   5888887654 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   2.7   4.5e-06    0.0051       8      21 ..      10      23 ..       7      27 .. 0.92
   2 !   17.7   6.5   2.5e-06    0.0028       8      23 ..      60      75 ..      60      76 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 4.5e-06
                        Fer4_6  8 kCigCgdCvrvCPe 21
                                  kC+ Cg C++vCP+
  gi|13541426|ref|NP_111114.1| 10 KCVNCGFCESVCPT 23
                                  9************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|13541426|ref|NP_111114.1| 60 SCVDCYACVAVCPAGV 75
                                  6*************97 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   1.4   9.2e-05       0.1      39      53 ..       9      23 ..       3      29 .. 0.83
   2 !   11.2   0.8   0.00027       0.3      40      53 ..      60      73 ..      41      78 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 9.2e-05
                       Fer4_21 39 deCvGCnlCssvCPv 53
                                   +Cv C  C svCP+
  gi|13541426|ref|NP_111114.1|  9 GKCVNCGFCESVCPT 23
                                  589999999999996 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00027
                       Fer4_21 40 eCvGCnlCssvCPv 53
                                  +Cv C  C++vCP 
  gi|13541426|ref|NP_111114.1| 60 SCVDCYACVAVCPA 73
                                  69999999999994 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1  13.7   0.00053       0.6       1      66 [.      10      73 ..      10      74 .. 0.71
   2 ?   10.6   2.7   0.00075      0.84       2      16 ..      61      75 ..      60      91 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00053
                       Fer4_16  1 rCgtCgkCaevCPtnaikekkekeiearecisy..ntaekkdlaedeekckkqeaitgCdiCqdvCPa 66
                                  +C++Cg C +vCPt   ++   ++i ar  ++    + ++ ++++ + +    + +  C +C++vCPa
  gi|13541426|ref|NP_111114.1| 10 KCVNCGFCESVCPTLPASSF-IASIGARGRVDIakFVYKNGTVIDPSTSF---YSCVDCYACVAVCPA 73
                                  5*************888887.56666666555511444444455555544...59************8 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00075
                       Fer4_16  2 CgtCgkCaevCPtna 16
                                  C++C +C+ vCP+++
  gi|13541426|ref|NP_111114.1| 61 CVDCYACVAVCPAGV 75
                                  ************986 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 ?    6.4   6.6    0.0063       7.1      17      88 ..       4      74 ..       1      85 [. 0.69
   2 ?    2.9   1.2     0.078        88      24      43 ..      61      78 ..      38     108 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0063
                                  HHHHHTT----TT-HHHHCSTT---HHHHHHHHHTT-HHHHHHHHHHH-S-..HHHHHHHS-GGGTGCCS-GGG CS
                       Fer4_20 17 aleeAsRClqCkkapcvkgCPveidipefikkiaegnleeaakiiketnsl..pavcgrvCpqeelCegaCvle 88
                                   ++eA +C++C    c++ CP+ +   +fi +i ++   + ak + ++ ++  p++    C     C + C  +
  gi|13541426|ref|NP_111114.1|  4 LIQEAGKCVNC--GFCESVCPT-LPASSFIASIGARGRVDIAKFVYKNGTVidPSTSFYSCVDCYACVAVCPAG 74
                                  689********..89******8.67899***9977665555555555444324555556677777777777665 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.078
                                  ----TT-HHHHCSTT---HH CS
                       Fer4_20 24 ClqCkkapcvkgCPveidip 43
                                  C++C    cv+ CP+ ++  
  gi|13541426|ref|NP_111114.1| 61 CVDC--YACVAVCPAGVNAG 78
                                  8888..67*******99864 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   5.4    0.0073       8.1       1      13 [.      11      23 ..      11      24 .. 0.95
   2 ?   11.1   6.5   0.00056      0.63       1      14 [.      61      74 ..      61      77 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0073
                        Fer4_3  1 CtgCgaCvevCPv 13
                                  C++Cg C+ vCP+
  gi|13541426|ref|NP_111114.1| 11 CVNCGFCESVCPT 23
                                  ************6 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00056
                        Fer4_3  1 CtgCgaCvevCPvg 14
                                  C+ C+aCv vCP g
  gi|13541426|ref|NP_111114.1| 61 CVDCYACVAVCPAG 74
                                  999*********44 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   1.7    0.0077       8.7       5      18 ..      10      23 ..       7      24 .. 0.89
   2 ?    5.7   3.9      0.02        22       5      18 ..      60      73 ..      59      74 .. 0.92

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0077
                       Fer4_13  5 tCiacgaCvelaPd 18
                                  +C++cg C +++P 
  gi|13541426|ref|NP_111114.1| 10 KCVNCGFCESVCPT 23
                                  8************6 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.02
                       Fer4_13  5 tCiacgaCvelaPd 18
                                  +C++c aCv+++P 
  gi|13541426|ref|NP_111114.1| 60 SCVDCYACVAVCPA 73
                                  6************5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (378 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       662  (0.0369234); expected 358.6 (0.02)
Passed bias filter:                      511  (0.0285013); 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):              16  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.41
# Mc/sec: 2735.71
//
Query:       gi|13541427|ref|NP_111115.1|  [L=459]
Description: FAD/FMN-containing dehydrogenase [Thermoplasma volcanium GSS1]
Scores for complete 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-60  202.5   0.0    1.2e-59  201.9   0.0    1.2  1  FAD-oxidase_C  FAD linked oxidases, C-terminal domain
    2.5e-43  147.2   0.0    3.9e-43  146.5   0.0    1.3  1  FAD_binding_4  FAD binding domain
  ------ inclusion threshold ------
       0.16   12.1   0.0       0.56   10.3   0.0    1.9  2  DNA_pol_D_N    DNA polymerase delta subunit OB-fold domain


Domain annotation for each model (and alignments):
>> FAD-oxidase_C  FAD linked oxidases, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  201.9   0.0   2.1e-63   1.2e-59       1     250 []     212     457 ..     212     457 .. 0.98

  Alignments for each domain:
  == domain 1  score: 201.9 bits;  conditional E-value: 2.1e-63
                                   --SEEEEEEEEESSHHHHHHHHHHHHHHT---SEEEEE-HHHHHHHHHTS-SSTTS-TTT-EEEEEEEEE-HHHHHHHHHH CS
                 FAD-oxidase_C   1 lpearavalvafpsfeaavkavreiaqagiipaalelmdkkaldlveatkgakkglpdeeealllvefegddeeeaeeele 81 
                                   +p+++a ++++++++e+a +av e++ +  ip + e++dk++ld v + +      p++++++l++ ++g+  e + ++ +
  gi|13541427|ref|NP_111115.1| 212 KPQKVARLVAFYQDIESAGRAVNELKVS-TIPEMAEFLDKISLDSVPEAITY----PPGTKYALIIDVSGPP-ELLGKKKT 286
                                   69999***********************.***********************....****************.77777777 PP

                                   HHHHHTTT-EEEEE..........ETGGGGGGGGHHHHHHHHHCTTEEEEEEEEEEEHHHHHHHHHHHHHHHHHHHEEEEE CS
                 FAD-oxidase_C  82 alveaileatgaadvlvaqdeaeaealwkaRkaalpylrdallkagvavlseDtsvPvsrladlvrdikalldkyglevvl 162
                                    + e++l+  ++++   ++d+ae+e++++aRk++++ + ++ + ++ ++++ D++vPvs+l++ +++i++  d+ g+++++
  gi|13541427|ref|NP_111115.1| 287 -ETEELLKRYAIST-KSTTDPAEMEKIYRARKGLYASILKLRKSEKEYIVIGDIVVPVSELPTSLKEIEKKRDEDGVRAAI 365
                                   .8***********9.****************************************************************** PP

                                   EEEEETTEEEEEEEEEEE..--TT--THHHHHHHHHHHHTT---------------....--------THHHHHHHHHHHH CS
                 FAD-oxidase_C 163 fgHagdgnlhlyilfdladeaeeeraeklvdevvdlavelgGsisgEHGvGldkka....ylerekgeeglalmrriKaal 239
                                   fgH+gdgn+h +i  dl d  +++++++++ +++++av++gGs+s+EHG+G++kk+    ++++ ++ ++l++m++iK+++
  gi|13541427|ref|NP_111115.1| 366 FGHIGDGNIHANIFADLGDNSAMDKVNRFMMDLAMVAVKHGGSVSAEHGIGIEKKQllieEMKYNNNLRTLDIMKAIKQVF 446
                                   ********************************************************9999********************* PP

                                   -TT--BSTT-- CS
                 FAD-oxidase_C 240 DPkgiLNPgkv 250
                                   DPk+iLN g++
  gi|13541427|ref|NP_111115.1| 447 DPKNILNRGNI 457
                                   ********975 PP

>> FAD_binding_4  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  146.5   0.0   6.5e-47   3.9e-43       1     138 [.      37     175 ..      37     176 .. 0.99

  Alignments for each domain:
  == domain 1  score: 146.5 bits;  conditional E-value: 6.5e-47
                                   EEEEEEESSHHHHHHHHHHHHHCTSCEEEESSSTTEESTTC.SCCEEEEEETTS--EEEEETTTTEEEEETTSBHHHHHHH CS
                 FAD_binding_4   1 paavvrpeseeevaaalrlaneaglpvlvrGgGssllgqav.atggvvldlsrlnrileideeegtatveaGvtlgdlvea 80 
                                   p+avv p+s+e+v++++rla +++ pv+v GgGssl+g+++ +++g+v+++ r+nril+i+ +++ +tve+G +l+dl+ +
  gi|13541427|ref|NP_111115.1|  37 PEAVVLPGSAEDVQTIMRLAYKYEKPVVVKGGGSSLTGSSIlKESGIVMSMLRMNRILDINLNDKCVTVEPGLRLNDLQLY 117
                                   89**************************************99*************************************** PP

                                   HHHHTTECSSGGGTTCGSBHHHTTTTT-EETTEEGG--HHGTEEEEEEEETTSEEEEE CS
                 FAD_binding_4  81 laakglllglepgsgipgtvGGaiatnagGygsekyGlirdnvlglevvladGevvrl 138
                                   l+++g +++++p+s   +tvGG i+tnagG +   yG ++d++lgl+vvladG++v++
  gi|13541427|ref|NP_111115.1| 118 LDKYGHFYPPDPASSMAATVGGSISTNAGGLRGVAYGVTKDWILGLDVVLADGTMVKF 175
                                   *******************************************************987 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 ?   -1.3   0.0      0.36   2.2e+03      30      47 ..      88     105 ..      49     106 .. 0.82
   2 ?   10.3   0.0   9.4e-05      0.56      31      69 ..     312     357 ..     216     397 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.36
                   DNA_pol_D_N  30 lkvnrildlkegeecivv 47 
                                   l++nrild++ +++c+ v
  gi|13541427|ref|NP_111115.1|  88 LRMNRILDINLNDKCVTV 105
                                   56899***9999999975 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 9.4e-05
                   DNA_pol_D_N  31 k......vnrildlkeg.eecivvGtiykemklkpsvlkeiakede 69 
                                          + +il+l+++ +e iv+G i++ +++ p+ lkei+k+++
  gi|13541427|ref|NP_111115.1| 312 YrarkglYASILKLRKSeKEYIVIGDIVVPVSELPTSLKEIEKKRD 357
                                   04444447788888777588999*******************8543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (459 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.46
# Mc/sec: 2984.87
//
Query:       gi|13541428|ref|NP_111116.1|  [L=1134]
Description: hypothetical protein TVN0597 [Thermoplasma volcanium GSS1]
Scores for complete 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   16.3   5.6        7.7    6.9   0.0    5.7  6  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
  ------ inclusion threshold ------
       0.52   10.9   4.0         12    6.5   0.1    4.9  3  DUF4369          Domain of unknown function (DUF4369)


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 ?    1.6   0.0     0.037   3.3e+02      39      57 ..     502     519 ..     479     544 .. 0.77
   2 ?   -1.3   0.0       0.3   2.7e+03      44      70 ..     679     704 ..     674     715 .. 0.69
   3 ?    2.1   0.0     0.026   2.3e+02      45      81 ..     750     785 ..     746     786 .. 0.75
   4 ?    0.2   0.1      0.11   9.6e+02      36      70 ..     824     849 ..     815     870 .. 0.52
   5 ?    0.9   0.0     0.062   5.5e+02      46      79 ..     965     995 ..     957     998 .. 0.74
   6 !    6.9   0.0   0.00086       7.7      44      69 ..    1032    1056 ..    1023    1067 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.037
               CarboxypepD_reg  39 afrlrglppgtysvtvsap 57 
                                   +f l ++ pg+y+v+v+ +
  gi|13541428|ref|NP_111116.1| 502 RFYL-NVDPGSYDVVVTVN 519
                                   4555.799*******9865 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.3
               CarboxypepD_reg  44 glppgtysvtvsapGyatatreevtlt 70 
                                    lp gty + + ++   + +++  t +
  gi|13541428|ref|NP_111116.1| 679 YLPNGTYALAIWHDSAYSLNYT-HTFS 704
                                   4899999999999988888875.4444 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.026
               CarboxypepD_reg  45 lppgtysvtvsa.pGyatatreevtltagqtttlditL 81 
                                   l+ g+y ++vsa +Gy  +t++ + ++ g+++ + itL
  gi|13541428|ref|NP_111116.1| 750 LQNGSYALHVSAvKGYYNTTIS-FNIS-GRQKIVMITL 785
                                   889*******873689999985.8888.6666666766 PP

  == domain 4  score: 0.2 bits;  conditional E-value: 0.11
               CarboxypepD_reg  36 adGafrlrglppgtysvtvsapGyatatreevtlt 70 
                                   ++G++++ gl   +y+ t+         + +vtl+
  gi|13541428|ref|NP_111116.1| 824 STGTYKIIGLGNANYTSTF---------FDTVTLS 849
                                   3455555555555555544.........4434443 PP

  == domain 5  score: 0.9 bits;  conditional E-value: 0.062
               CarboxypepD_reg  46 ppgtysvtvsapGyatatreevtltagqtttldi 79 
                                   + gty   + apGy++ ++  ++++   ++ l+ 
  gi|13541428|ref|NP_111116.1| 965 QNGTYYALAYAPGYRPLSI-LIEVNG--SESLNY 995
                                   679*************997.466554..444444 PP

  == domain 6  score: 6.9 bits;  conditional E-value: 0.00086
               CarboxypepD_reg   44 glppgtysvtvsapGyatatreevtl 69  
                                    +lp gty+ ++++ Gya+++++ + +
  gi|13541428|ref|NP_111116.1| 1032 DLPNGTYTAVFEKRGYAQSSIR-IIV 1056
                                    59****************9986.544 PP

>> DUF4369  Domain of unknown function (DUF4369)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1      0.21   1.9e+03      25      75 ..      39     104 ..      19     117 .. 0.56
   2 ?    6.5   0.1    0.0014        12      56      90 ..     465     500 ..     438     501 .. 0.82
   3 ?    0.6   0.0     0.091   8.2e+02      59      77 ..     909     934 ..     889     958 .. 0.69

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.21
                       DUF4369  25 vvklDsavvknGkFtfkgkvdeprlaylliddkgg...............alpfflengtititid 75 
                                   v+   +  + n +F f g+   + +   li ++                 +  +fl ng i ++++
  gi|13541428|ref|NP_111116.1|  39 VNANSTLDIINENFYFFGQSIRIYGKLTLISSTIYsqeanlsvidgtldiYSSVFLMNGSIYVYGS 104
                                   555555566666666666444322222222222222444555555555677778888887777766 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0014
                       DUF4369  56 dkggalpfflengtititiddgss.akvtGsptnde 90 
                                   +++ +l++++en+t+++ i++++  +  +G++ n+ 
  gi|13541428|ref|NP_111116.1| 465 SRNVSLNLYIENKTTNVLIASKEGvYIGSGTEKNET 500
                                   334489***************997877888888875 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.091
                       DUF4369  59 g.......alpfflengtititiddg 77 
                                   +        + ++ en ti i+++  
  gi|13541428|ref|NP_111116.1| 909 NfyflhseTVELYTENATIYINASAY 934
                                   24444444488999999999988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       572  (0.0319036); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.68u 0.29s 00:00:00.97 Elapsed: 00:00:00.46
# Mc/sec: 7381.75
//
Query:       gi|13541429|ref|NP_111117.1|  [L=157]
Description: phosphatase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.3e-09   37.2   0.0    3.9e-09   36.4   0.0    1.5  1  PNK3P           Polynucleotide kinase 3 phosphatase
    0.00015   21.8   0.0    0.00021   21.3   0.0    1.3  1  Hydrolase_like  HAD-hyrolase-like
    0.00068   19.8   0.0        0.2   11.7   0.0    2.2  2  HAD_2           Haloacid dehalogenase-like hydrolase
     0.0032   17.6   0.0     0.0044   17.1   0.0    1.3  1  Hydrolase_6     Haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.024   14.0   0.0       0.03   13.7   0.0    1.1  1  Spermine_synth  Spermine/spermidine synthase domain
       0.03   14.6   0.0       0.67   10.2   0.0    2.4  2  Hydrolase       haloacid dehalogenase-like hydrolase
       0.11   12.9   0.0       0.22   11.9   0.0    1.6  1  HAD             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 !   36.4   0.0   1.5e-12   3.9e-09      24     126 ..      33     136 ..      13     154 .. 0.75

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 1.5e-12
                         PNK3P  24 addwkllsesvlekLkklkeegykivifsNqggvvek.ktkkslekfkekieallkeldvp..llvyaatkkd...kyRKP 98 
                                   ++d  ++++  ++ L++ +++g+ i+i++Nq+g+ +   t++++++f + +++ lke ++    + y+  k +     RKP
  gi|13541429|ref|NP_111117.1|  33 PSDL-FIYPDAVDLLQRYQDDGFRIIIVTNQSGIGRGyFTESQFKEFSDFMNDKLKENGIVisAIYYCPHKPEdscNCRKP 112
                                   5553.566778899*********************9767777788888877777776544421445555553246689*** PP

                         PNK3P  99 etGmweelkkdleekleidkeksfyvGD 126
                                   etG+++e+ +d++     d  +s+ vGD
  gi|13541429|ref|NP_111117.1| 113 ETGLFSEVLEDYKV----DIPSSIVVGD 136
                                   ********999876....6666788888 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   8.2e-08   0.00021       2      45 ..     109     152 ..     108     157 .] 0.93

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 8.2e-08
                                   .STTSSHHHHHHHHHH---GGGEEEEES-TTTHHHHHHHCT-EE CS
                Hydrolase_like   2 lgKPepemydfalevlgsdpeevlmiGDrlatDiagAnnaGwks 45 
                                   ++KPe +++ + le++++d   ++++GDr + D ++A+++++ +
  gi|13541429|ref|NP_111117.1| 109 CRKPETGLFSEVLEDYKVDIPSSIVVGDRNEIDGEFARRIKLPF 152
                                   89*************************************99876 PP

>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.4   0.0    0.0034       8.6      77     105 ..      35      63 ..       3      83 .. 0.85
   2 !   11.7   0.0   7.7e-05       0.2     129     172 ..     105     149 ..      81     154 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0034
                         HAD_2  77 evkpydgvkelLeeLkeagyklgivTsks 105
                                    + +y+++ +lL+  ++ g+++ ivT++s
  gi|13541429|ref|NP_111117.1|  35 DLFIYPDAVDLLQRYQDDGFRIIIVTNQS 63 
                                   4789**********************986 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 7.7e-05
                         HAD_2 129 edvekkKPdpeviekaleklklkkeeviyvGDsp.tDieaakkag 172
                                   + ++ +KP++ ++ ++le +k++  + i+vGD +  D e a+++ 
  gi|13541429|ref|NP_111117.1| 105 DSCNCRKPETGLFSEVLEDYKVDIPSSIVVGDRNeIDGEFARRIK 149
                                   566778**************************9989999999876 PP

>> Hydrolase_6  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   1.7e-06    0.0044       3      47 ..      17      70 ..      15     102 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.7e-06
                                  EESTTTSE.........ETTEE-TTHHHHHHHHHHTT-EEEEEE---SS-HHHH CS
                   Hydrolase_6  3 fDidGvLw.........rgdkaipgaaealnalraagkpvvllTNnsskseeey 47
                                  +D dG++           +  ++p a+++l++ ++ g +++++TN+s+  +  +
  gi|13541429|ref|NP_111117.1| 17 IDRDGTINkdcpychnpSDLFIYPDAVDLLQRYQDDGFRIIIVTNQSGIGRGYF 70
                                  67777777444444333345579***********************99875544 PP

>> Spermine_synth  Spermine/spermidine synthase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.2e-05      0.03      79     166 ..      39     129 ..      20     133 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.2e-05
                                   ESTCHHHHCTCSS.-EEEEEEECCSTTCS..SCGCSSHHHHHHHHHTEEEEEEEEEEEEETTTCHHHHHHHHHHHHTTSSC CS
                Spermine_synth  79 lgdgfkflkayek.kfdvvivdsldpvgp..aenlFskeffdllkkvlkedGviilqaekpelekelvinvdksgkqvfal 156
                                     d++ +l++y++  f ++iv     +g     +   kef+d ++++lke+G++i+    +  + e+++n +k    +f+ 
  gi|13541429|ref|NP_111117.1|  39 YPDAVDLLQRYQDdGFRIIIVTNQSGIGRgyFTESQFKEFSDFMNDKLKENGIVISAIYYCPHKPEDSCNCRKPETGLFSE 119
                                   569999*******99999998887755541144444478****************99877777888888888877777776 PP

                                   EEEEEEEETT CS
                Spermine_synth 157 qvepsavlvP 166
                                   + e + v +P
  gi|13541429|ref|NP_111117.1| 120 VLEDYKVDIP 129
                                   7666666666 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.1     0.095   2.4e+02       1      12 [.      12      23 ..      12      33 .. 0.89
   2 ?   10.2   0.0   0.00026      0.67     118     199 ..      37     137 ..      32     148 .. 0.58

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.095
                                  SSEEEEESBTTT CS
                                  xxxxxxxxxxxx RF
                     Hydrolase  1 iktvvfDkdGTL 12
                                  +kt+++D dGT+
  gi|13541429|ref|NP_111117.1| 12 MKTLFIDRDGTI 23
                                  79*********9 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00026
                                   HBHTTHHHHHHHHHHTTEEEEEEESSEH...............HHHHHHHHHTTGGGESEEEEHHCES..........STT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxx...............xxxxxxxxxxxxxxxxxxxxxxxxx..........xxx RF
                     Hydrolase 118 kvkpeaaeavasLkaagievvlltgdnp...............etaeraanqlGddyfdaviasdiet..........vak 173
                                   +++p+a++++++ ++ g++++++t+++                 + +  +++ G      ++ s i            + k
  gi|13541429|ref|NP_111117.1|  37 FIYPDAVDLLQRYQDDGFRIIIVTNQSGigrgyftesqfkefsDFMNDKLKENG------IVISAIYYcphkpedscnCRK 111
                                   68**********************987644444433333322222222222222......111111113233445555666 PP

                                   TSHHHHHHHHHHHTSTGGGEEEEESS CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hydrolase 174 pspegkvaaireLqgkpeevamVGDg 199
                                   p+   + ++++ +++++   ++VGD+
  gi|13541429|ref|NP_111117.1| 112 PETGLFSEVLEDYKVDIPSSIVVGDR 137
                                   66666666666666666666666665 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   8.4e-05      0.22      85     111 ..      37      63 ..      27     139 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 8.4e-05
                           HAD  85 lldpgalellaahraaGdrvvvvSggl 111
                                   +++p+a++ll++ ++ G+r+++v++  
  gi|13541429|ref|NP_111117.1|  37 FIYPDAVDLLQRYQDDGFRIIIVTNQS 63 
                                   467*********************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       755  (0.0421105); expected 358.6 (0.02)
Passed bias filter:                      604  (0.0336884); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.52u 0.31s 00:00:00.83 Elapsed: 00:00:00.51
# Mc/sec: 934.35
//
Query:       gi|13541430|ref|NP_111118.1|  [L=437]
Description: DNA-binding protein [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.7e-25   88.7   0.0    1.2e-24   86.6   0.0    2.0  2  DUF1743       Domain of unknown function (DUF1743)
  ------ inclusion threshold ------
      0.035   14.1   0.1      0.063   13.3   0.1    1.4  1  HypA          Hydrogenase/urease nickel incorporation, metall
      0.047   13.4   1.0      0.089   12.5   1.0    1.4  1  Rep_fac-A_C   Replication factor-A C terminal domain
       0.17   12.0   1.6       0.41   10.8   1.6    1.6  1  zf-Mss51      Zinc-finger of mitochondrial splicing suppresso
       0.29   11.0   3.0       0.53   10.1   3.0    1.4  1  zf-RING_4     RING/Ubox like zinc-binding domain
       0.41   10.2   3.0        1.2    8.7   3.0    1.7  1  TF_Zn_Ribbon  TFIIB zinc-binding
        1.4    9.9   4.9        2.2    9.3   0.4    2.8  2  zf-C2H2_4     C2H2-type zinc finger


Domain annotation for each model (and alignments):
>> DUF1743  Domain of unknown function (DUF1743)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.71   1.8e+03      74     102 ..      74     105 ..      66     113 .. 0.72
   2 !   86.6   0.0   4.7e-28   1.2e-24       1     116 []     155     268 ..     155     268 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.71
                                   SEEEEEE...ES-HHHHHHHHHCSEE..S-EE CS
                       DUF1743  74 pvlfGir...gedpeallkaakeilskeeese 102
                                   ++l+G     +e+ e++l ++k++ +k++e +
  gi|13541430|ref|NP_111118.1|  74 KILYGYAegeDEYDENVLYVMKDLVEKYSELD 105
                                   67777641114555999999999999888766 PP

  == domain 2  score: 86.6 bits;  conditional E-value: 4.7e-28
                                   TTHHHHHHHHHH-..-TTS-EEEEEEEE-GGGTT---EEHHHHHHHHHHHTTCECTSEBTTTTCECCS-STTSSEEEEEEE CS
                       DUF1743   1 grgiiGAtaalganialedstyEllaYreperwgerevdeesvieadektypetfdnvDlshklvvlvPhtpdpvlfGirg 81 
                                   grgiiG+ aa+++     + tyE+laY++p+   e e ++++ + + ++t+  tf+nvD+++k+++++P+ ++pv+fGirg
  gi|13541430|ref|NP_111118.1| 155 GRGIIGSGAAISWPAT--RTTYEILAYKYPHPE-EIETEKKMRLSILADTFRGTFNNVDIANKYPAIFPNPKTPVIFGIRG 232
                                   89***********555..69***********98.888889999999999******************************** PP

                                   S-HHHHHHHHHCSEE..S-EEC.EEEEEESTTS-TT CS
                       DUF1743  82 edpeallkaakeilskeeesee.mavfrtnqgtdah 116
                                    +p  l +aak++  + +   +  + + tnq+td+h
  gi|13541430|ref|NP_111118.1| 233 LYPSVLANAAKKVIDDGSINYDsTVTYLTNQATDDH 268
                                   *************9987776667************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 ?   13.3   0.1   2.5e-05     0.063      68      95 ..     362     390 ..     327     398 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.5e-05
                                   --EEEETTTS-EEECHHH.HHS-TTTSSS CS
                          HypA  68 pvkvrCreCgkefeleek.alrCpkCgsa 95 
                                   +v+  C+ C+++++++ k ++rCpkCg++
  gi|13541430|ref|NP_111118.1| 362 RVTPLCKFCNTRTKSKGKnDFRCPKCGRR 390
                                   45567*********888669******985 PP

>> Rep_fac-A_C  Replication factor-A C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   1.0   3.5e-05     0.089      21      53 ..     367     397 ..     354     400 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.5e-05
                                   --STT---B-EEETTTEEEETTTTEEESS--EE CS
                   Rep_fac-A_C  21 CpsedCnkKvveeedgewrCekCdkeveepkyr 53 
                                   C+   Cn +  +++++ +rC kC +++++p+y 
  gi|13541430|ref|NP_111118.1| 367 CK--FCNTRTKSKGKNDFRCPKCGRRYNTPDYH 397
                                   77..8*************************996 PP

>> zf-Mss51  Zinc-finger of mitochondrial splicing suppressor 51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   1.6   0.00016      0.41       1      24 [.     366     389 ..     366     397 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00016
                      zf-Mss51   1 lCPvpkhkqtapkhvdfeCpdCGi 24 
                                   lC +++++ +++ + df Cp+CG 
  gi|13541430|ref|NP_111118.1| 366 LCKFCNTRTKSKGKNDFRCPKCGR 389
                                   5999999999*************5 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 ?   10.1   3.0   0.00021      0.53      24      48 .]     366     392 ..     365     392 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00021
                     zf-RING_4  24 iClfCyhrile..eeegrCPaCreeYk 48 
                                   +C fC +r ++  ++++rCP+C ++Y+
  gi|13541430|ref|NP_111118.1| 366 LCKFCNTRTKSkgKNDFRCPKCGRRYN 392
                                   6******999965579******99995 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   3.0   0.00046       1.2       3      26 ..     367     388 ..     366     390 .. 0.94

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00046
                                   ETTTTCEECHEETSTTCEEESSSS CS
                  TF_Zn_Ribbon   3 CPnCgstnlveDpergelvCtdCG 26 
                                   C+ C+++  +     ++++C++CG
  gi|13541430|ref|NP_111118.1| 367 CKFCNTR--TKSKGKNDFRCPKCG 388
                                   *****98..799***********9 PP

>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.5      0.29   7.5e+02       3      13 ..     367     377 ..     365     379 .. 0.79
   2 ?    9.3   0.4   0.00086       2.2       1      14 [.     382     395 ..     382     400 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.29
                     zf-C2H2_4   3 CpiCgksFssk 13 
                                   C++C+++ +sk
  gi|13541430|ref|NP_111118.1| 367 CKFCNTRTKSK 377
                                   ****9887776 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00086
                     zf-C2H2_4   1 fkCpiCgksFsskk 14 
                                   f+Cp Cg+++++++
  gi|13541430|ref|NP_111118.1| 382 FRCPKCGRRYNTPD 395
                                   89********9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (437 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       511  (0.0285013); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        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):               7  [number of targets reported over threshold]
# CPU time: 0.63u 0.34s 00:00:00.97 Elapsed: 00:00:00.55
# Mc/sec: 2392.58
//
Query:       gi|13541431|ref|NP_111119.1|  [L=258]
Description: undecaprenyl pyrophosphate synthase [Thermoplasma volcanium GSS1]
Scores for complete 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-79  264.3   0.0    9.3e-79  264.1   0.0    1.0  1  Prenyltransf  Putative undecaprenyl diphosphate synthase
  ------ inclusion threshold ------
      0.013   15.6   0.0      0.023   14.8   0.0    1.4  1  HBD           Helical bundle domain


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 !  264.1   0.0     1e-82   9.3e-79       1     224 []      35     257 ..      35     257 .. 0.94

  Alignments for each domain:
  == domain 1  score: 264.1 bits;  conditional E-value: 1e-82
                                   EE--HHHHHHHTT.S-HHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEEEGGGGGS-HHHHHHHHHHHH...HHHHHHHHHH CS
                  Prenyltransf   1 imDGNrRwAkkrgleereeGhkaGaealkeilelclelgvkvvtvYafSteNfkRskeevdalmellk...eellkeelke 78 
                                   i DGNrR+A+  g+ e+e Gh +G ++++e+l++c+el++k+vt+YafSteNfkRs+eevd+l++l++    +llk+e  +
  gi|13541431|ref|NP_111119.1|  35 ITDGNRRYARIVGIPENE-GHVKGKNKVEEVLDWCMELDIKIVTFYAFSTENFKRSPEEVDFLFHLINdafISLLKDE--R 112
                                   89***********76666.************************************************95554455555..9 PP

                                   HHHTTEEEEEESSGGGS-HHHHHHHHHHHHHHT.TTTSEEEEEEEEE-HHHHHHHHHHHHHHTT..SSSG.GGHSHHHHHC CS
                  Prenyltransf  79 llkegvrvrviGdlellpedvlealekaeeatkknnkklvlniavnYgsrdeiveavrelvkekseekkk.eeideetlek 158
                                   + k++++v+viG+ ++lpe ++e+++ +ee+tk n +++++n+a+ Yg+r+ei++a+++++++ ++ k + +eide+++++
  gi|13541431|ref|NP_111119.1| 113 VYKNKINVKVIGNVSMLPEYLRETIKITEETTK-NFSNYHMNLAIGYGGREEILDAIKRIARDAIAGKINvDEIDESKFRN 192
                                   9999*****************************.6666************************99988887567799***** PP

                                   TSTT..TSSS-SEEEEESS--S-TTSSTTTTTT-EEEEESSSGGG--HHHHHHHHHHHHHCHHHTT CS
                  Prenyltransf 159 hlytakalpdpDlliRtsGeeRlSnFllwqlayselyfldvlWPdfskedllealleyqkrerrfg 224
                                   +ly   +lpdpDl++RtsGeeR+SnFllwq+ayselyf+dv+WP+fsk d+l+a+ +yq+r+rrfg
  gi|13541431|ref|NP_111119.1| 193 YLYD-GNLPDPDLILRTSGEERISNFLLWQSAYSELYFSDVYWPEFSKLDFLRAIYSYQRRQRRFG 257
                                   ***6.678********************************************************98 PP

>> HBD  Helical bundle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   2.6e-06     0.023       5      59 ..      99     153 ..      95     163 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.6e-06
                                   HHHHHHHHHHHTSSSSS-SHHHHHHHHHHHHHHHHHT-SS--HHHHHHHHHHHHH CS
                           HBD   5 ylleeYleeLekvkqkddklkstRlsvvkrlaeYLneqtelteevkekiatYvkk 59 
                                    + + +++ L+  +  ++k++   ++ v  l eYL+e   +tee +++ + Y  +
  gi|13541431|ref|NP_111119.1|  99 LINDAFISLLKDERVYKNKINVKVIGNVSMLPEYLRETIKITEETTKNFSNYHMN 153
                                   5667899999999999*********************************999665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       653  (0.0364214); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1605.53
//
Query:       gi|13541432|ref|NP_111120.1|  [L=152]
Description: hypothetical protein TVN0601 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.041   14.2   0.6       0.26   11.7   0.1    2.1  2  Phage_int_SAM_5  Phage integrase SAM-like domain


Domain annotation for each model (and alignments):
>> 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 ?    0.9   0.1     0.033   5.9e+02      12      55 ..       9      52 ..       2      66 .. 0.70
   2 ?   11.7   0.1   1.4e-05      0.26      20      69 ..      78     139 ..      58     150 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.033
                                  HHHTTS-HHHHHHHHHHHHHTTTS-..S---TTT--HHHHHHHH CS
               Phage_int_SAM_5 12 kkkkkgskgtlrnykstlkhlkkFlkkkditfeeidkefleeFe 55
                                  +++kk + + +   + ++k++++  k++  t+ ei+ +  + F+
  gi|13541432|ref|NP_111120.1|  9 EETKKITISVKGIRDDLYKNVTDLAKHTGKTIGEITNDAYRTFI 52
                                  44444466666677777888888887778888888888777775 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 1.4e-05
                                   HHHHHHHHHHHHTTTS-........S---TTT--HHHHHHHHHHH......HHTS---HHHH CS
               Phage_int_SAM_5  20 gtlrnykstlkhlkkFl.....kk.kditfeeidkefleeFedYL......kkkkglsenti 69 
                                    ++++++ t + lk+F      ++ +++tf++++ e ++++ +++      +  k+++++ti
  gi|13541432|ref|NP_111120.1|  78 DNFKKLEVTAEDLKDFGqkvafRNiDELTFKNVTDEDIQKYVAFIdgvkilRIPKTVKKSTI 139
                                   567778888899999997777744477******************77777755566666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       868  (0.0484132); expected 358.6 (0.02)
Passed bias filter:                      529  (0.0295053); 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: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1013.17
//
Query:       gi|13541433|ref|NP_111121.1|  [L=131]
Description: hypothetical protein TVN0602 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       525  (0.0292822); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 00:00:00.50
# Mc/sec: 783.48
//
Query:       gi|13541434|ref|NP_111122.1|  [L=327]
Description: transcription regulator (HTH) [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-06   28.1   0.1    3.3e-06   26.9   0.1    1.5  1  MarR             MarR family
    5.9e-06   26.1   0.0    1.1e-05   25.2   0.0    1.4  1  MarR_2           MarR family
      7e-05   22.7   0.1    0.00014   21.8   0.1    1.5  1  HTH_Crp_2        Crp-like helix-turn-helix domain
    0.00016   21.3   0.0    0.00044   19.8   0.0    1.8  1  GntR             Bacterial regulatory proteins, gntR family
    0.00022   20.7   0.0    0.00057   19.4   0.0    1.8  1  HTH_24           Winged helix-turn-helix DNA-binding
    0.00035   20.5   0.0     0.0044   17.0   0.0    2.4  2  HTH_36           Helix-turn-helix domain
    0.00077   19.3   0.0      0.002   18.0   0.0    1.7  1  TrmB             Sugar-specific transcriptional regulator Trm
     0.0016   18.3   0.0      0.004   17.0   0.0    1.7  1  HTH_5            Bacterial regulatory protein, arsR family
     0.0068   16.2   0.1      0.046   13.5   0.0    2.1  2  LexA_DNA_bind    LexA DNA binding domain
      0.009   15.5   0.0      0.021   14.3   0.0    1.6  1  RepL             Firmicute plasmid replication protein (RepL)
       0.01   15.8   0.9      0.024   14.6   0.1    2.1  2  HTH_11           HTH domain
  ------ inclusion threshold ------
       0.01   16.0   0.9      0.031   14.5   0.0    2.4  1  Fe_dep_repress   Iron dependent repressor, N-terminal DNA bin
      0.012   15.1   0.0      0.026   14.0   0.0    1.5  1  HTH_CodY         CodY helix-turn-helix domain
      0.016   15.8   0.0      0.054   14.1   0.0    1.9  1  Phage_rep_O      Bacteriophage replication protein O
      0.035   14.1   0.0       0.12   12.4   0.0    1.9  1  HTH_29           Winged helix-turn helix
      0.041   14.2   0.0       0.21   11.9   0.0    2.0  2  Penicillinase_R  Penicillinase repressor
      0.052   14.0   0.0       0.12   12.8   0.0    1.6  1  HTH_27           Winged helix DNA-binding domain
       0.11   12.5   0.0       0.48   10.4   0.0    2.0  2  Cdc6_C           CDC6, C terminal winged helix domain
       0.12   12.2   0.1       0.32   10.8   0.1    1.7  1  UBA_3            Fungal ubiquitin-associated domain
       0.12   12.3   0.1       0.29   11.1   0.1    1.6  1  TBPIP            TBPIP/Hop2 winged helix domain
       0.16   12.1   0.0        0.3   11.2   0.0    1.4  1  HTH_20           Helix-turn-helix domain
       0.18   11.2   0.1       0.31   10.4   0.1    1.3  1  RNA_pol_Rpc34    RNA polymerase Rpc34 subunit
       0.18   11.6   0.0       0.38   10.6   0.0    1.6  1  HTH_IclR         IclR helix-turn-helix domain
       0.22   11.3   1.5        3.9    7.3   0.1    2.5  2  HTH_DeoR         DeoR-like 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 !   26.9   0.1   4.4e-09   3.3e-06       8      50 ..       7      51 ..       6      53 .. 0.94

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 4.4e-09
                                  HHHHHHHSTTEEHH..HHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                          MarR  8 iLrilyeqgplsvs..eLakklgvskstvtrvldrLekkGlieRs 50
                                  +Lr l++  +l +   ++ +++g skstv+++l+ Le+kG i+R+
  gi|13541434|ref|NP_111122.1|  7 LLRELKRARGLGIDqfQIEEMMGFSKSTVSEALKDLEEKGIIKRR 51
                                  8999******999999****************************8 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.0   1.5e-08   1.1e-05      10      55 ..       7      52 ..       6      55 .. 0.90

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 1.5e-08
                                  HHHHHHCTTTSEE..EHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                        MarR_2 10 vLaaLgrrpgrdl..tvgelarrlglsksavsrilkrLvaaGLverrp 55
                                  +L +L r+ g  l   + ++++ +g sks+vs +lk+L+++G + rr+
  gi|13541434|ref|NP_111122.1|  7 LLRELKRARG--LgiDQFQIEEMMGFSKSTVSEALKDLEEKGIIKRRT 52
                                  6888888888..555999***************************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 !   21.8   0.1   1.9e-07   0.00014      16      55 ..      16      52 ..       3      59 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1.9e-07
                                  CEEEEEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEETE CS
                     HTH_Crp_2 16 geielpltqeelAsmlGltretvsrilseLkreglisrgr 55
                                  g   l + q ++ +m+G + +tvs +l++L+++g+i+r++
  gi|13541434|ref|NP_111122.1| 16 G---LGIDQFQIEEMMGFSKSTVSEALKDLEEKGIIKRRT 52
                                  3...7778888889***********************764 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0     6e-07   0.00044      30      58 ..      24      52 ..      20      56 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 6e-07
                                  HHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
                          GntR 30 LaaefgVsrttvReALrrLeaeglverrq 58
                                  + +++g+s++tv eAL+ Le++g++ rr 
  gi|13541434|ref|NP_111122.1| 24 IEEMMGFSKSTVSEALKDLEEKGIIKRRT 52
                                  7799**********************997 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   7.6e-07   0.00057      19      48 .]      20      49 ..       7      49 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 7.6e-07
                        HTH_24 19 sqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                   q ++ e+ g S+stv++ lk Lee+G+Ik
  gi|13541434|ref|NP_111122.1| 20 DQFQIEEMMGFSKSTVSEALKDLEEKGIIK 49
                                  5666668899*******************8 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   5.9e-06    0.0044      31      55 .]      24      48 ..      20      48 .. 0.91
   2 ?    0.7   0.0      0.69   5.1e+02      28      46 ..     272     290 ..     225     292 .. 0.66

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 5.9e-06
                        HTH_36 31 lakrlglsknTvsraikeLeqlGyi 55
                                  + + +g sk+Tvs a+k Le++G+i
  gi|13541434|ref|NP_111122.1| 24 IEEMMGFSKSTVSEALKDLEEKGII 48
                                  66779******************98 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.69
                        HTH_36  28 qetlakrlglsknTvsrai 46 
                                    + +ak + +s +T+   +
  gi|13541434|ref|NP_111122.1| 272 IDIFAKSTSVSPKTAKASL 290
                                   6779999999999987665 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   2.6e-06     0.002      27      57 ..      23      53 ..      20      69 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.6e-06
                                  HHCCCTTSSCHCHHHHHHHHHHCTSEEEESS CS
                          TrmB 27 eiaeelgvprskvYevLrsLedkGlVerekg 57
                                  +i e+ g ++s+v e+L+ Le+kG+++r+  
  gi|13541434|ref|NP_111122.1| 23 QIEEMMGFSKSTVSEALKDLEEKGIIKRRTI 53
                                  599************************9974 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   5.4e-06     0.004      20      46 ..      23      49 ..      22      50 .. 0.95

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 5.4e-06
                                  HHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                         HTH_5 20 elaeelglsqstvShHLkkLreaGLVe 46
                                  ++ e++g s+stvS+ Lk L+e G+++
  gi|13541434|ref|NP_111122.1| 23 QIEEMMGFSKSTVSEALKDLEEKGIIK 49
                                  7999*********************96 PP

>> LexA_DNA_bind  LexA DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.0   6.2e-05     0.046      30      58 ..      23      50 ..      18      54 .. 0.91
   2 ?   -0.6   0.0       1.6   1.2e+03      15      32 ..     304     320 ..     303     323 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.2e-05
                                  HHHHHHTS-.HHHHHHHHHHHHHTTSEE- CS
                 LexA_DNA_bind 30 eiaralglkSpsaveehLkaLerKGyier 58
                                  +i + +g++  s+v e Lk Le KG+i+r
  gi|13541434|ref|NP_111122.1| 23 QIEEMMGFS-KSTVSEALKDLEEKGIIKR 50
                                  788999997.9****************98 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.6
                                   HHHHHHHHSS---HHHHH CS
                 LexA_DNA_bind  15 ikasieetgypPsireia 32 
                                   +k+++e  gypP i ei 
  gi|13541434|ref|NP_111122.1| 304 LKKYLEFIGYPP-IEEII 320
                                   68899999***9.55665 PP

>> RepL  Firmicute plasmid replication protein (RepL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   2.8e-05     0.021      64     111 ..       7      54 ..       2      57 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.8e-05
                          RepL  64 lidnlnsnntliatnRelaeetgislktvsetlkileeanilkkkanG 111
                                   l+ +l++   l + + ++ e  g s  tvse lk lee +i+k+++ G
  gi|13541434|ref|NP_111122.1|   7 LLRELKRARGLGIDQFQIEEMMGFSKSTVSEALKDLEEKGIIKRRTIG 54 
                                   566666667777778889999************************977 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.1   3.2e-05     0.024       5      44 ..       7      47 ..       4      55 .. 0.91
   2 ?   -2.8   0.1       8.9   6.6e+03      16      36 ..     251     271 ..     246     274 .. 0.62

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.2e-05
                        HTH_11  5 ilelLleargp.isgeeLAeeLnvSrrtvrrdIkaLeelgv 44
                                  +l+ L++arg  i   ++ e ++ S++tv   +k+Lee+g+
  gi|13541434|ref|NP_111122.1|  7 LLRELKRARGLgIDQFQIEEMMGFSKSTVSEALKDLEEKGI 47
                                  7899************************************3 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 8.9
                        HTH_11  16 isgeeLAeeLnvSrrtvrrdI 36 
                                    +  e+ +  ++Sr t r d+
  gi|13541434|ref|NP_111122.1| 251 RTLIEIVRLYKRSRFTAREDV 271
                                   555555566667777777765 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   4.2e-05     0.031      27      53 ..      23      49 ..      18      55 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.2e-05
                                  HHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                Fe_dep_repress 27 dlaerLnvspssVsemlkkLekdGyve 53
                                  ++ e ++ s+s+Vse lk Le++G ++
  gi|13541434|ref|NP_111122.1| 23 QIEEMMGFSKSTVSEALKDLEEKGIIK 49
                                  78899******************9765 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 ?   14.0   0.0   3.5e-05     0.026      10      42 ..      24      56 ..      20      62 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.5e-05
                      HTH_CodY 10 iaDriGitrsvivnaLrkLesaGiiesrsLGmk 42
                                  i + +G  +s +  aL+ Le  Gii  r +G k
  gi|13541434|ref|NP_111122.1| 24 IEEMMGFSKSTVSEALKDLEEKGIIKRRTIGGK 56
                                  67789*************************977 PP

>> Phage_rep_O  Bacteriophage replication protein O
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   7.2e-05     0.054      50      83 ..      19      52 ..      14      61 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 7.2e-05
                   Phage_rep_O 50 isnsqlveltgisrtkvskalkeLirekviikeg 83
                                  i + q+ e++g s++ vs+alk L ++++i+++ 
  gi|13541434|ref|NP_111122.1| 19 IDQFQIEEMMGFSKSTVSEALKDLEEKGIIKRRT 52
                                  7789**************************9865 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00016      0.12      13      46 ..      18      49 ..       9      59 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00016
                        HTH_29 13 s.tvsqiAkllglsrrtvyrwlkrfeegGlaalld 46
                                  +    qi +++g s++tv  +lk+ ee+G+   ++
  gi|13541434|ref|NP_111122.1| 18 GiDQFQIEEMMGFSKSTVSEALKDLEEKGI---IK 49
                                  444778999********************6...33 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00028      0.21      27      61 ..      24      58 ..      19      73 .. 0.84
   2 ?   -1.0   0.0         3   2.2e+03      14      41 ..     261     289 ..     254     292 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00028
                                  --GGG---HHHHHHHHHHHHHTTS-EEEEETTEEE CS
               Penicillinase_R 27 leeekelaysTVktllrrLvkKgllsrekegrafi 61
                                  +ee +  ++sTV   l+ L++Kg+++r++ g ++ 
  gi|13541434|ref|NP_111122.1| 24 IEEMMGFSKSTVSEALKDLEEKGIIKRRTIGGKIK 58
                                  56678899*******************99987654 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 3
                                   HHS-.EEHHHHHHT--GGG---HHHHHHH CS
               Penicillinase_R  14 ekge.atvkevveeleeekelaysTVktl 41 
                                   ++++ +  ++v++ +++ ++++++T k  
  gi|13541434|ref|NP_111122.1| 261 KRSRfTAREDVIDIFAKSTSVSPKTAKAS 289
                                   44552445678999999888888887765 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00017      0.12      23      51 ..      23      51 ..       5      62 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00017
                        HTH_27 23 dlcgrlnvedshisyslkkLtekGLvert 51
                                  ++ +++ +++s++s++lk L+ekG ++r 
  gi|13541434|ref|NP_111122.1| 23 QIEEMMGFSKSTVSEALKDLEEKGIIKRR 51
                                  5778999*****************99665 PP

>> Cdc6_C  CDC6, C terminal winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00065      0.48      38      74 ..      31      62 ..      24      65 .. 0.84
   2 ?   -2.7   0.0       7.8   5.8e+03      41      68 ..     228     251 ..     225     261 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00065
                                  -HHHHHHHHHHHHHTTSEEEEEEE-CC.C-EEEEEEE CS
                        Cdc6_C 38 tqrevsdllseLemlgileleksskGrregrtrkisL 74
                                  + ++vs+ l++Le +gi+++++      +g+ ++++L
  gi|13541434|ref|NP_111122.1| 31 SKSTVSEALKDLEEKGIIKRRTI-----GGKIKHVWL 62
                                  7899******************9.....477777766 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 7.8
                                   HHHHHHHHHHHTTSEEEEEEE-CC.C-E CS
                        Cdc6_C  41 evsdllseLemlgileleksskGrregr 68 
                                   ++sd+l+    +gi  +e++    re r
  gi|13541434|ref|NP_111122.1| 228 SFSDVLDSFPCCGISVSENN----RENR 251
                                   67788877777777777777....4444 PP

>> UBA_3  Fungal ubiquitin-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00043      0.32       6      38 ..      17      47 ..      13      54 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00043
                                  ---SHHHHHHHHHHT--HHHHHHHHHHS--SS- CS
                         UBA_3  6 yGidrdlVdefvsqGFekdkvievLkrLgiksl 38
                                  +Gid+  ++e+  +GF k  v e+Lk L+ k++
  gi|13541434|ref|NP_111122.1| 17 LGIDQFQIEEM--MGFSKSTVSEALKDLEEKGI 47
                                  68888888875..9**************98876 PP

>> TBPIP  TBPIP/Hop2 winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00039      0.29      29      54 ..      29      54 ..      21      64 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00039
                         TBPIP 29 klgKtavqkaLdeLvdegkiieKeyG 54
                                  +++K +v +aL  L+++g i+ +++G
  gi|13541434|ref|NP_111122.1| 29 GFSKSTVSEALKDLEEKGIIKRRTIG 54
                                  689*********************97 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0    0.0004       0.3      29      60 ..      23      54 ..       6      55 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0004
                                  HHHHHHTS-HHHHHHHHHHHHHCTTEEEECTE CS
                        HTH_20 29 elaerldlskntlsyHLrvLeeagLvevvreg 60
                                  ++ e ++ sk+t+s  L+ Lee g++++++ g
  gi|13541434|ref|NP_111122.1| 23 QIEEMMGFSKSTVSEALKDLEEKGIIKRRTIG 54
                                  56666789********************9865 PP

>> RNA_pol_Rpc34  RNA polymerase Rpc34 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   0.00042      0.31     102     135 ..      18      51 ..       7      57 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00042
                                   XEEHHHHHHTTGXXHHHHHHHHHHHHHTTXXEEE CS
                 RNA_pol_Rpc34 102 GIwsrtiksklnLhksvvkkcLksLeskkyiksv 135
                                   GI++ +i++ ++  ks v   Lk Le k+ ik +
  gi|13541434|ref|NP_111122.1|  18 GIDQFQIEEMMGFSKSTVSEALKDLEEKGIIKRR 51 
                                   9******************************975 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0    0.0005      0.38      24      50 ..      24      50 ..       7      52 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0005
                                  HHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                      HTH_IclR 24 lArrtglpkStvhRlLqtLvelGyveq 50
                                  + +  g +kStv+  L+ L+e G++++
  gi|13541434|ref|NP_111122.1| 24 IEEMMGFSKSTVSEALKDLEEKGIIKR 50
                                  6677899*****************998 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 ?    7.3   0.1    0.0052       3.9      19      49 ..      23      54 ..       4      57 .. 0.75
   2 ?    2.6   0.2      0.16   1.2e+02      16      36 ..     252     272 ..     246     279 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0052
                      HTH_DeoR 19 elvellgvSeaTiRRDLneLeeqglltR.thG 49
                                  ++ e  g S+ T+   L+ Lee+g+++R t G
  gi|13541434|ref|NP_111122.1| 23 QIEEMMGFSKSTVSEALKDLEEKGIIKRrTIG 54
                                  46688999*****************8761555 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.16
                      HTH_DeoR  16 sveelvellgvSeaTiRRDLn 36 
                                   ++ e+v l++ S  T+R D  
  gi|13541434|ref|NP_111122.1| 252 TLIEIVRLYKRSRFTAREDVI 272
                                   7889**************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       736  (0.0410508); expected 358.6 (0.02)
Passed bias filter:                      601  (0.0335211); expected 358.6 (0.02)
Passed Vit filter:                        83  (0.00462937); expected 17.9 (0.001)
Passed Fwd filter:                        24  (0.00133861); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              24  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 2154.82
//
Query:       gi|13541435|ref|NP_111123.1|  [L=107]
Description: transcription regulator [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.5e-06   25.4   1.2      2e-05   24.3   0.1    2.1  3  RHH_1           Ribbon-helix-helix protein, copG family
  ------ inclusion threshold ------
      0.069   13.6   0.1       0.16   12.4   0.0    1.7  2  ParD_antitoxin  Bacterial antitoxin of ParD toxin-antitoxin t


Domain annotation for each model (and alignments):
>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.1   2.3e-09     2e-05       1      33 [.       6      39 ..       6      42 .. 0.98
   2 ?   -1.8   0.0      0.38   3.4e+03       2       8 ..      73      79 ..      73      81 .. 0.86
   3 ?   -2.7   0.0      0.75   6.7e+03      29      34 ..      93      98 ..      90     101 .. 0.69

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 2.3e-09
                                  EEEEEEEHHHHHHHHHHHHHHT.SSHHHHHHHHH CS
                         RHH_1  1 rvsirldeellerLdelarrrg.rSrSelIReAl 33
                                  r+++rl+ +l+++++ l++ ++  S+S+++R+Al
  gi|13541435|ref|NP_111123.1|  6 RITVRLPLSLVDEIQNLVDTGEfESMSDVVRRAL 39
                                  8********************************8 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.38
                                  EEEEEEH CS
                         RHH_1  2 vsirlde 8 
                                  +si+ld+
  gi|13541435|ref|NP_111123.1| 73 TSITLDD 79
                                  6999997 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 0.75
                                  HHHHHH CS
                         RHH_1 29 IReAlr 34
                                   R+A++
  gi|13541435|ref|NP_111123.1| 93 ARDAIK 98
                                  578875 PP

>> ParD_antitoxin  Bacterial antitoxin of ParD toxin-antitoxin type II system and RHH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   1.7e-05      0.16      17      46 ..      19      48 ..      13      68 .. 0.82
   2 ?   -2.1   0.0      0.61   5.4e+03       5      11 ..      73      79 ..      70      94 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.7e-05
                                  HHHHHCTTS-SSHHHHHHHHHHHHHHHHHH CS
                ParD_antitoxin 17 idsqvaaGrYgsaseviraaLrLLeeretk 46
                                  i+  v +G + s s+v+r aL  L e  t 
  gi|13541435|ref|NP_111123.1| 19 IQNLVDTGEFESMSDVVRRALVYLTESRTA 48
                                  5667999**************988776553 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.61
                                  EEE---H CS
                ParD_antitoxin  5 tsvvLge 11
                                  ts++L++
  gi|13541435|ref|NP_111123.1| 73 TSITLDD 79
                                  7888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       478  (0.0266607); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 725.03
//
Query:       gi|13541436|ref|NP_111124.1|  [L=537]
Description: phenylalanyl-tRNA synthetase subunit beta [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.4e-36  123.4   0.0    1.6e-35  122.5   0.0    1.5  1  tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM 
    4.4e-09   36.2   0.0    7.2e-09   35.6   0.0    1.2  1  B3_4             B3/4 domain
      1e-08   35.4   0.0    2.8e-08   34.0   0.0    1.8  2  B5               tRNA synthetase B5 domain
  ------ inclusion threshold ------
      0.039   14.1   0.3       0.13   12.4   0.0    2.1  2  SapB_2           Saposin-like type B, region 2


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 !  122.5   0.0   3.6e-39   1.6e-35      11     214 .]     350     529 ..     344     529 .. 0.96

  Alignments for each domain:
  == domain 1  score: 122.5 bits;  conditional E-value: 3.6e-39
               tRNA_synthFbeta  11 tegelnkeqklrrklrdllagaGlnEvitysfvsekeldklleddderkavelanPlsedqsvlRtsLlpglLevlarNla 91 
                                   t g++n  +++++k+rd+++g+G++Ev+t+ ++ +   +++      +  v+++nP sed+sv+R  L  +lL+ larN +
  gi|13541436|ref|NP_111124.1| 350 TIGSPNIFNEIKEKIRDVVVGLGFQEVMTFVLTGKYYQEDF------QGEVRIENPKSEDYSVIRDRLYLNLLDLLARNKK 424
                                   55667888999******************************......799******************************* PP

               tRNA_synthFbeta  92 rgnedvrlFEigkvflkdseeelpeeerhlaivltgkreeeswsekaravdfydlkgivealleslgiekvefepaehpal 172
                                   + ++  r+FEig+v+         ++e+hl++++  +r            ++ + k i+ ++l+++   + +++ ++    
  gi|13541436|ref|NP_111124.1| 425 HPLP-QRIFEIGDVIVHG------KQETHLCVMVEDNR-----------SGVSTSKSILTSFLKRFSDHESKISGKKIYGC 487
                                   ****.*************......9*************...........*******************9************ PP

               tRNA_synthFbeta 173 hpgrsAeikvdgkevGvlGelhpevleafdlkqrvyvfEldl 214
                                     grs ei + gk +Gv+Ge+hp++le+f+l +++++fE+++
  gi|13541436|ref|NP_111124.1| 488 IEGRSGEIFLSGKSIGVIGEVHPSTLENFGLVNPISFFEINI 529
                                   ****************************************96 PP

>> B3_4  B3/4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.6   0.0   1.6e-12   7.2e-09      35     133 ..     109     232 ..      93     248 .. 0.92

  Alignments for each domain:
  == domain 1  score: 35.6 bits;  conditional E-value: 1.6e-12
                                   --HHHHHHHHHHHHHT-.....-EEEEEGGGTBTEEEEEE--TTEEEEBTTS-EEEE-T...................TSE CS
                          B3_4  35 innvVDitNyvmlelgq.....PlhafDldkiqgdivvrlakegeklvtldgkerelde...................edl 91 
                                   ++ ++D ++ +++ +g+      ++++Dldk +++++  +  + e++ t d  e ++++                   + +
  gi|13541436|ref|NP_111124.1| 109 LDDLIDYQEIIHQTVGKerkkvSIGIHDLDKTEPPFRYTTISKLERMKTYDSFEGTIEDvlqkhpkgmayssllpdsrRVP 189
                                   5679*****************************9**9999999999999998788887778889***************** PP

                                   EEETEEEEE.EETTTEEBTTTB--TT--EEEEEEEE--HHHHH CS
                          B3_4  92 viadsekpv.slagvmggeeskvsedTknvfleaaafdpvsir 133
                                    i d+++ + s++++++g  +k++ +T++ f+ ++++d+ s++
  gi|13541436|ref|NP_111124.1| 190 AILDKNGGIlSVPPIVNGIMTKIEPETRKFFVDITGMDSNSVK 232
                                   *******999***************************998886 PP

>> B5  tRNA synthetase B5 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       3.1   1.4e+04      11      24 ..      29      42 ..      24      51 .. 0.58
   2 !   34.0   0.0   6.2e-12   2.8e-08       3      66 ..     275     337 ..     273     338 .. 0.95

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 3.1
                                  HHTS---HHHHHHH CS
                                  xxxxxxxxxxxxxx RF
                            B5 11 llGidlseeeiiki 24
                                  ++G ++++ee iki
  gi|13541436|ref|NP_111124.1| 29 VIGYSFEDEEEIKI 42
                                  55655555554443 PP

  == domain 2  score: 34.0 bits;  conditional E-value: 6.2e-12
                                   EEHHHHHHHHTS---HHHHHHHHHHTT-E.EESSTTCEEEE--TT-TT--SHHHHHHHHHHHH- CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            B5   3 lrvekinkllGidlseeeiikiLkrlgceriekdkdlllVtvPswRsDlereeDliEEvaRlyG 66 
                                   l++++++++lG ++see++i  L+++g+   e +  ++ V vP +R+D+   +D+iE+ +  yG
  gi|13541436|ref|NP_111124.1| 275 LNLKYVSRYLGDKVSEENVILNLRKMGYV-AEPGYPEVMVYVPGFRVDVMGLVDIIEDFIKSYG 337
                                   7899************************7.59*******************************9 PP

>> SapB_2  Saposin-like type B, region 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0     3e-05      0.13       4      21 ..       9      26 ..       9      28 .. 0.90
   2 ?   -2.2   0.1       1.1   4.7e+03      12      26 ..     202     216 ..     201     216 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3e-05
                                  HHHHHHHHHHHHCCHCTT CS
                        SapB_2  4 kslVdqYgpliiqlLlse 21
                                  +slVd+Yg +i++lL+s+
  gi|13541436|ref|NP_111124.1|  9 QSLVDEYGKEIYSLLKSF 26
                                  689************997 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.1
                                   HHHHCCHCTT--HHH CS
                        SapB_2  12 pliiqlLlseldPke 26 
                                   p i++ ++ +++P++
  gi|13541436|ref|NP_111124.1| 202 PPIVNGIMTKIEPET 216
                                   899*******99985 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:                      498  (0.0277762); 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: 0.68u 0.31s 00:00:00.99 Elapsed: 00:00:00.53
# Mc/sec: 3063.42
//
Query:       gi|13541437|ref|NP_111125.1|  [L=169]
Description: acetyltransferase [Thermoplasma volcanium GSS1]
Scores for complete 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   62.3  20.8    1.9e-08   33.7   3.4    4.2  4  Hexapep     Bacterial transferase hexapeptide (six repeats)
      2e-08   33.8  12.8    1.1e-05   25.1   4.7    4.5  4  Hexapep_2   Hexapeptide repeat of succinyl-transferase
  ------ inclusion threshold ------
      0.056   12.4   0.0      0.075   12.0   0.0    1.4  1  Fucokinase  L-fucokinase
       0.64    8.1   6.7        1.2    7.1   5.8    1.9  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 !   17.3   0.3   6.5e-07    0.0029       3      28 ..       2      27 ..       1      35 [. 0.92
   2 !   10.0   0.3   0.00013      0.56      20      35 ..      40      55 ..      37      56 .. 0.83
   3 !   19.7   0.8   1.1e-07   0.00049       2      29 ..      62      88 ..      61      88 .. 0.95
   4 !   33.7   3.4   4.2e-12   1.9e-08       1      36 []      78     113 ..      78     113 .. 0.96

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 6.5e-07
                                  EEETTEEE-TTEEEETTEEE-TTEEE CS
                       Hexapep  3 vIGsnvlIgpfaviggnVkIGdnvkI 28
                                  +IG+nv+I   av+ g+V I d+v I
  gi|13541437|ref|NP_111125.1|  2 RIGKNVYIAETAVVIGDVDIADGVSI 27
                                  6***********************98 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00013
                                  EEE-TTEEEETTEEEE CS
                       Hexapep 20 VkIGdnvkIgagvvig 35
                                  ++IG+n+ I  +v+i+
  gi|13541437|ref|NP_111125.1| 40 IIIGENTNIQDNVTIH 55
                                  7899999999999996 PP

  == domain 3  score: 19.7 bits;  conditional E-value: 1.1e-07
                                  EEEETTEEE-TTEEEETTEEE-TTEEEE CS
                       Hexapep  2 tvIGsnvlIgpfaviggnVkIGdnvkIg 29
                                  t+IG+ v Ig++av+ +++++ d v Ig
  gi|13541437|ref|NP_111125.1| 62 TRIGKYVSIGHNAVV-HGCTVEDEVLIG 88
                                  89*************.*********998 PP

  == domain 4  score: 33.7 bits;  conditional E-value: 4.2e-12
                                   TEEEETTEEE-TTEEEETTEEE-TTEEEETTEEEES CS
                       Hexapep   1 stvIGsnvlIgpfaviggnVkIGdnvkIgagvvigg 36 
                                   ++++++ vlIg++a+i+++++IG ++++gag+v+++
  gi|13541437|ref|NP_111125.1|  78 GCTVEDEVLIGMGAIIMNGAQIGHGSIVGAGAVVTK 113
                                   6899******************************86 PP

>> Hexapep_2  Hexapeptide repeat of succinyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.7   0.3    0.0055        25       3      24 ..       2      25 ..       1      33 [. 0.69
   2 !    7.2   2.5   0.00094       4.2       4      26 ..      48      76 ..      39      78 .. 0.64
   3 !   20.3   1.1   7.4e-08   0.00033       1      32 [.      61      93 ..      61      95 .. 0.96
   4 !   25.1   4.7   2.5e-09   1.1e-05       3      34 .]      80     113 ..      78     113 .. 0.96

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0055
                                  EE-TT-EE-TT-E.ES.EEE-TT- CS
                     Hexapep_2  3 iIGdnCliGanag.iG.vslGdnc 24
                                  +IG+n+ i   a+ iG v++ d++
  gi|13541437|ref|NP_111125.1|  2 RIGKNVYIAETAVvIGdVDIADGV 25
                                  577777776667744447777765 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.00094
                                  E-TT-EE-TT-E....ES..EEE-TT-EE CS
                     Hexapep_2  4 IGdnCliGanag....iG..vslGdncvv 26
                                  I dn+ i+ + g    iG  vs+G n+vv
  gi|13541437|ref|NP_111125.1| 48 IQDNVTIHTDVGyptrIGkyVSIGHNAVV 76
                                  44666677776655555677777777776 PP

  == domain 3  score: 20.3 bits;  conditional E-value: 7.4e-08
                                  .EEE-TT-EE-TT-EE.SEEE-TT-EE-TT-EE CS
                     Hexapep_2  1 pviIGdnCliGanagi.GvslGdncvvgaGvvi 32
                                  p++IG+ + iG na++ G +++d++ +g+G +i
  gi|13541437|ref|NP_111125.1| 61 PTRIGKYVSIGHNAVVhGCTVEDEVLIGMGAII 93
                                  89*************99*************987 PP

  == domain 4  score: 25.1 bits;  conditional E-value: 2.5e-09
                                   EE-TT-EE-TT-EE..SEEE-TT-EE-TT-EE-S CS
                     Hexapep_2   3 iIGdnCliGanagi..GvslGdncvvgaGvvita 34 
                                   +++d +liG  a+i  G ++G +++vgaG v+t+
  gi|13541437|ref|NP_111125.1|  80 TVEDEVLIGMGAIImnGAQIGHGSIVGAGAVVTK 113
                                   69***********99******************7 PP

>> Fucokinase  L-fucokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   1.7e-05     0.075     279     336 ..      62     129 ..       7     153 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.7e-05
                    Fucokinase 279 Svlessvsvgegsviehsslkgnvsigsnsivsglelessee..........slelpddtilqtlslk 336
                                   + + ++vs+g ++v+  ++++++v ig + i+ +     + +           ++ p+++++ +l+ k
  gi|13541437|ref|NP_111125.1|  62 TRIGKYVSIGHNAVVHGCTVEDEVLIGMGAIIMNGAQIGHGSivgagavvtkGFKAPEYSVILGLPAK 129
                                   56889999********************9999764443333346666666666666666666666555 PP

>> DUF4954  Domain of unknown function (DUF4954)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   5.8   0.00028       1.2     176     257 ..      21     102 ..       8     121 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.00028
                       DUF4954 176 igekvkilnaglikNvkigdyatiegasklengtinSskeapveiGegViledfiissGskikdgavi.srcfvGqavklk 255
                                   i + v+i ++ +++ + ++++   e+++  +n ti+     p++iG+ V +    + +G++++d ++i + +++ ++ +++
  gi|13541437|ref|NP_111125.1|  21 IADGVSIFDSAVLR-ADLEKIIIGENTNIQDNVTIHTDVGYPTRIGKYVSIGHNAVVHGCTVEDEVLIgMGAIIMNGAQIG 100
                                   55666777766655.4666677778888889****************9999999999999999999883457777777777 PP

                       DUF4954 256 kq 257
                                   ++
  gi|13541437|ref|NP_111125.1| 101 HG 102
                                   75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       316  (0.0176251); expected 358.6 (0.02)
Passed bias filter:                      237  (0.0132188); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.35u 0.26s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 1270.03
//
Query:       gi|13541438|ref|NP_111126.1|  [L=247]
Description: flagellin [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.8e-50  171.3  13.8    2.2e-50  171.0  13.8    1.1  1  Arch_flagellin  Archaebacterial flagellin


Domain annotation for each model (and alignments):
>> Arch_flagellin  Archaebacterial flagellin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  171.0  13.8   1.2e-54   2.2e-50       1     164 []      20     233 ..      20     233 .. 0.99

  Alignments for each domain:
  == domain 1  score: 171.0 bits;  conditional E-value: 1.2e-54
                                   X--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT--EEEEEEE.....EEE-SSSSSEEEEEEE-- CS
                Arch_flagellin   1 GfvgigtlIvfIAmVlVAAvaagvlintagflqqkaqstgeesteqvssgleitgdvg.....dsatngtineitiyvkln 76 
                                   +++gigtlIvfIAmVlVAAvaa+vl++tag+lqqka+stg+++t+qvs+g+++ +++g       +t+g i++++i++  +
  gi|13541438|ref|NP_111126.1|  20 AETGIGTLIVFIAMVLVAAVAATVLVHTAGTLQQKATSTGSQTTQQVSTGIQVNSIYGldsnkSVPTHGVIEWLAIQISIT 100
                                   78***********************************************************99999*************** PP

                                   TTS--EEGGG-EEEEEESS--EE--E....................................................... CS
                Arch_flagellin  77 aGsspidlnkttisvtddgqetlltad............................................efgivvisdt 113
                                   aGsspi+l+++tis+t++g++++lt++                                            +f i v+sd 
  gi|13541438|ref|NP_111126.1| 101 AGSSPINLANVTISLTYHGVSASLTYVglenignatvtndvygfnsavggtnnvfnssyfktingasngskHFAILVLSDP 181
                                   *******************999999999***************************************************** PP

                                   .......T-EE-TT-EEEEEEE--.TTT---TT-EEEEEEE-SSS--EEEEE CS
                Arch_flagellin 114 dgsltngdevlekgekvelevnvn.eddgitagdevsvevvpenGasttief 164
                                   ++s+t++++v++++++v+l vnv+ ++ git+g++vs+ev+++ G++++i+f
  gi|13541438|ref|NP_111126.1| 182 TNSMTAQYPVISYEDQVDLLVNVSaVFGGITEGQAVSGEVQAPVGSPGVIQF 233
                                   **************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1058  (0.0590105); expected 358.6 (0.02)
Passed bias filter:                      527  (0.0293937); 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: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1788.97
//
Query:       gi|13541439|ref|NP_111127.1|  [L=154]
Description: flagellar protein C [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      3e-19   69.1   5.0      2e-17   63.3   1.7    2.6  2  FlaC_arch       Flagella accessory protein C (FlaC)
    7.3e-05   22.6   0.6    0.00012   21.8   0.4    1.6  1  LXG             LXG domain of WXG superfamily
    0.00054   20.4   0.4    0.00054   20.4   0.4    1.6  1  Spectrin        Spectrin repeat
    0.00073   20.0   1.3       0.04   14.4   0.1    2.4  2  NPV_P10         Nucleopolyhedrovirus P10 protein
    0.00086   18.7   2.8    0.00095   18.5   2.8    1.2  1  MPS2            Monopolar spindle protein 2
     0.0012   18.8   2.1      0.049   13.5   1.5    2.3  2  Bacillus_HBL    Bacillus haemolytic enterotoxin (HBL)
     0.0014   18.6   2.6     0.0074   16.3   2.6    2.0  1  Laminin_II      Laminin Domain II
     0.0019   16.9   1.9     0.0023   16.7   1.9    1.1  1  DUF4455         Domain of unknown function (DUF4455)
     0.0021   18.3   2.2       0.59   10.4   1.1    2.5  2  DUF948          Bacterial protein of unknown function (DUF948
     0.0032   17.7   2.5      0.009   16.2   2.5    1.7  1  BORCS6          BLOC-1-related complex sub-unit 6
     0.0033   17.5   1.0       0.28   11.2   0.3    2.2  2  Baculo_PEP_C    Baculovirus polyhedron envelope protein, PEP,
     0.0047   17.2   0.2      0.065   13.5   0.2    2.3  2  KxDL            Uncharacterized conserved protein
     0.0088   16.2   3.9      0.011   15.9   1.7    2.1  2  Fib_alpha       Fibrinogen alpha/beta chain family
     0.0098   15.1   3.2      0.015   14.6   1.2    1.9  2  DLP_helical     Dynamin-like helical domain
  ------ inclusion threshold ------
       0.01   15.0   3.7      0.011   14.9   3.7    1.1  1  Tmemb_cc2       Predicted transmembrane and coiled-coil 2 pro
      0.011   15.8   3.5       0.13   12.3   0.9    2.3  2  DUF1664         Protein of unknown function (DUF1664)
      0.012   15.5   5.4       0.17   11.7   0.3    2.6  3  CdvA            CdvA-like coiled-coil domain
      0.013   15.8   3.3       0.19   12.0   0.8    2.2  2  DUF5082         Domain of unknown function (DUF5082)
      0.021   15.0   0.3         19    5.6   0.1    3.2  3  WXG100          Proteins of 100 residues with WXG
       0.03   14.7   0.5      0.044   14.2   0.4    1.4  1  MitMem_reg      Maintenance of mitochondrial structure and fu
      0.031   14.3   1.5        7.8    6.7   0.0    3.1  2  YojJ            Bacterial membrane-spanning protein N-terminu
      0.032   12.2   2.2      0.058   11.3   2.3    1.4  1  Prominin        Prominin
      0.037   14.0   0.5        1.6    8.8   0.0    2.6  2  DUF4298         Domain of unknown function (DUF4298)
      0.037   13.4   6.6       0.18   11.2   3.2    2.1  2  DUF4618         Domain of unknown function (DUF4618)
      0.039   13.2   1.9      0.067   12.5   1.9    1.4  1  DUF3450         Protein of unknown function (DUF3450)
      0.044   14.2   1.8       0.26   11.7   0.5    2.1  2  TBCC_N          Tubulin-specific chaperone C N-terminal domai
      0.044   13.7   0.1      0.058   13.3   0.1    1.1  1  GP41            Retroviral envelope protein
      0.055   14.0   1.5       0.99   10.0   0.1    2.4  2  Syntaxin-6_N    Syntaxin 6, N-terminal
      0.055   13.6   3.2      0.076   13.1   3.2    1.3  1  UPF0242         Uncharacterised protein family (UPF0242) N-te
      0.069   12.8   6.9          1    8.9   6.8    2.2  1  DUF4795         Domain of unknown function (DUF4795)
      0.076   13.1   2.4        8.6    6.5   0.2    2.7  2  TolA_bind_tri   TolA binding protein trimerisation
      0.091   11.8   1.4       0.11   11.6   1.4    1.2  1  Atg14           Vacuolar sorting 38 and autophagy-related sub
      0.099   11.5   4.8       0.18   10.7   4.7    1.4  1  Spc7            Spc7 kinetochore protein
       0.15   12.1   2.0          2    8.5   0.5    2.4  2  COG2            COG (conserved oligomeric Golgi) complex comp
       0.17   11.8   5.4          1    9.3   2.6    2.2  2  Cauli_AT        Aphid transmission protein
       0.18   11.0   1.4       0.23   10.7   1.4    1.4  1  TMPIT           TMPIT-like protein
       0.19   11.2   1.9        1.3    8.6   0.3    2.1  2  Fzo_mitofusin   fzo-like conserved region
       0.28   11.2   8.2       0.53   10.3   6.7    2.0  1  CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein C
       0.28   11.8   5.7       0.54   10.9   2.8    2.1  2  HIP1_clath_bdg  Clathrin-binding domain of Huntingtin-interac
       0.36   11.3   5.8         21    5.7   3.8    2.4  2  DUF16           Protein of unknown function DUF16
       0.61   10.7   3.8        4.6    7.9   0.1    2.7  3  SlyX            SlyX
       0.67   10.3   7.0        2.6    8.4   3.4    2.7  2  BLOC1_2         Biogenesis of lysosome-related organelles com
        1.5    8.5   9.5        6.7    6.3   9.5    1.9  1  YkyA            Putative cell-wall binding lipoprotein
        7.1    7.3   7.6        1.6    9.4   3.0    2.3  1  YabA            Initiation control protein YabA


Domain annotation for each model (and alignments):
>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.3   1.7   4.8e-20     2e-17       1      55 []      49     103 ..      49     103 .. 0.99
   2 ?    6.5   0.1     0.028        11      20      44 ..     111     139 ..     105     141 .. 0.82

  Alignments for each domain:
  == domain 1  score: 63.3 bits;  conditional E-value: 4.8e-20
                     FlaC_arch   1 ridelEnklsklsteletvkkeneelsksveelkenVkdllsLYEvVsnqvNPFv 55 
                                   r+ ++En l+k+  ele  kk+++++++++e +kenVk+++sLYE Vs+++NPF+
  gi|13541439|ref|NP_111127.1|  49 RMTKIENNLGKMTAELEGQKKSLSDMKNELEGIKENVKMVVSLYELVSRDFNPFM 103
                                   899***************************************************7 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.028
                     FlaC_arch  20 kkeneelsksveelkenV....kdllsLY 44 
                                   +   eels+++++lk+ V    kdl +LY
  gi|13541439|ref|NP_111127.1| 111 RGITEELSDQINNLKRLVesaiKDLRELY 139
                                   556799********999988888998888 PP

>> LXG  LXG domain of WXG superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.4     3e-07   0.00012     105     182 ..      61     138 ..      41     150 .. 0.93

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 3e-07
                           LXG 105 englkkakevteelkdeinkilasvsdivslpelddsevkdslqkakkkvqetiekledfdqeqksalanlesdlkal 182
                                     +l+  k++++++k+e++ i+++v+ +vsl el +++++  ++k  +++  ++e l d  +++k++++++  dl++l
  gi|13541439|ref|NP_111127.1|  61 TAELEGQKKSLSDMKNELEGIKENVKMVVSLYELVSRDFNPFMDKTPEEIRGITEELSDQINNLKRLVESAIKDLREL 138
                                   56778899***************************************************************9999876 PP

>> Spectrin  Spectrin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.4   1.3e-06   0.00054      16     105 .]      45     137 ..      41     137 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 1.3e-06
                                   HHHHHHHHHCCSSCSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHTT...HTTHHHHHHHHHHHHHHHHHH CS
                      Spectrin  16 Wieekeellssedlgkdleevqallkkhkaleaelaaqqervkalnelaekl.ldeg...hsaseeieerleelnerWeeL 92 
                                    ++e ++++ +++lgk+ +e++ + k + ++++el+  +e+vk +  l e +  d +   ++++eei+  +eel ++  +L
  gi|13541439|ref|NP_111127.1|  45 AMNERMTKI-ENNLGKMTAELEGQKKSLSDMKNELEGIKENVKMVVSLYELVsRDFNpfmDKTPEEIRGITEELSDQINNL 124
                                   456666666.6666********************************888777555446668899***************** PP

                                   HHHHHHHHHHHHH CS
                      Spectrin  93 kelaaerkqkLee 105
                                   k+l+++  + L+e
  gi|13541439|ref|NP_111127.1| 125 KRLVESAIKDLRE 137
                                   *****99999976 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.1   9.9e-05      0.04      17      63 ..      39      83 ..      29      88 .. 0.87
   2 ?    4.1   0.1      0.16        65      40      73 ..     110     144 ..     100     146 .. 0.49

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 9.9e-05
                       NPV_P10 17 ddkV.dalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqd 63
                                  d kV da++++++++++nl +   ++++L++q ++L ++++++e I++
  gi|13541439|ref|NP_111127.1| 39 DPKViDAMNERMTKIENNLGK---MTAELEGQKKSLSDMKNELEGIKE 83
                                  5564499************99...77******************9986 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.16
                       NPV_P10  40 lnekLdaqsaqLaeletkven.IqdiLnpde..vPdl 73 
                                   +    +++s+q+++l+  ve+ I+d+       vPd+
  gi|13541439|ref|NP_111127.1| 110 IRGITEELSDQINNLKRLVESaIKDLRE--LygVPDI 144
                                   3333445555555555555431333222..1236666 PP

>> MPS2  Monopolar spindle protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   2.8   2.3e-06   0.00095     115     213 ..       7     105 ..       1     138 [. 0.80

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2.3e-06
                          MPS2 115 vkrlvvlssknsekdslstprkkilldllkkqesPeklrrsnrklkaLevrveslkdELeakdevlrekeRelleLkkrls 195
                                    k+lv++++    ++++++  k++ +    +  +P+    +n+++ ++e  + ++  ELe +++ l +   el  +k++++
  gi|13541439|ref|NP_111127.1|   7 MKKLVKKEAT-ATPQQSISEEKQVQAIHVTNGIDPKVIDAMNERMTKIENNLGKMTAELEGQKKSLSDMKNELEGIKENVK 86 
                                   4445544444.44555666667767777788899*********************************************** PP

                          MPS2 196 eykekYellqrefs.lyka 213
                                        Yel++r+f+ +  +
  gi|13541439|ref|NP_111127.1|  87 MVVSLYELVSRDFNpFMDK 105
                                   *************964433 PP

>> Bacillus_HBL  Bacillus haemolytic enterotoxin (HBL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   1.5   0.00012     0.049     133     175 ..      44      86 ..       4      87 .. 0.84
   2 ?    4.0   0.0       0.1        41     104     131 ..     111     138 ..      91     146 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00012
                  Bacillus_HBL 133 lklakdsknFktdvdeltsilagdsgvisqlqneiedlqgkik 175
                                   +++++  ++ ++++ ++t+ l+g+++ +s+++ne+e +++++k
  gi|13541439|ref|NP_111127.1|  44 DAMNERMTKIENNLGKMTAELEGQKKSLSDMKNELEGIKENVK 86 
                                   6788899999****************************99987 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.1
                  Bacillus_HBL 104 lellekLqeeiqqnqkevkqlikeLkkl 131
                                       e+L+++i++ +  v++ ik+L++l
  gi|13541439|ref|NP_111127.1| 111 RGITEELSDQINNLKRLVESAIKDLREL 138
                                   4445677777777777788888777776 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   2.6   1.8e-05    0.0074       4     102 ..      42     131 ..      40     138 .. 0.64

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.8e-05
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH CS
                    Laminin_II   4 laaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleea 84 
                                   ++++ ne ++++++ l ++ ++le  k++ls +++++e ++e+vk      ++++r       + p   +   e++   e+
  gi|13541439|ref|NP_111127.1|  42 VIDAMNERMTKIENNLGKMTAELEGQKKSLSDMKNELEGIKENVKMVVSLYELVSRDFNPFMDKTP---E---EIRGITEE 116
                                   566777777777777777777777777777777777777777776665555555554444333333...2...22333333 PP

                                   ...HHHHHHHHHHHHHHH CS
                    Laminin_II  85 ssslsdniseikelIaqA 102
                                      lsd+i+++k l++ A
  gi|13541439|ref|NP_111127.1| 117 ---LSDQINNLKRLVESA 131
                                   ...888888888888877 PP

>> DUF4455  Domain of unknown function (DUF4455)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   1.9   5.5e-06    0.0023     285     412 ..      18     148 ..       5     153 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 5.5e-06
                       DUF4455 285 klkkeLldlkvcseeeaeklvneellplvgklqrkaeeelekldksleelake...teaqsesLfkffqeaaqlwevheak 362
                                   + ++++++ k ++   + + ++++++ +++++  k e++l k++  le ++k    +++++e + + ++ ++ l+e   + 
  gi|13541439|ref|NP_111127.1|  18 TPQQSISEEKQVQAIHVTNGIDPKVIDAMNERMTKIENNLGKMTAELEGQKKSlsdMKNELEGIKENVKMVVSLYELVSRD 98 
                                   556777777778888888899*****************************98622267789999999************** PP

                       DUF4455 363 lekqeeelekkleqlrqkhdeenqakeaeLdklldklrqasteekLketl 412
                                   ++   ++  +++  ++++ ++++++ +   ++++++lr+    ++++++ 
  gi|13541439|ref|NP_111127.1|  99 FNPFMDKTPEEIRGITEELSDQINNLKRLVESAIKDLRELYGVPDIDQVI 148
                                   **************************************998888888765 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   1.1    0.0015      0.59      26      74 ..      41      89 ..       3     100 .. 0.84
   2 !    7.7   0.0      0.01       4.1      30      65 ..      98     133 ..      85     149 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0015
                        DUF948 26 ktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplt 74
                                  k++d+++++++++e+++++++ e+e+  +   ++ +++++  e+v+ ++
  gi|13541439|ref|NP_111127.1| 41 KVIDAMNERMTKIENNLGKMTAELEGQKKSLSDMKNELEGIKENVKMVV 89
                                  8999*******************99887777777776666666666555 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.01
                        DUF948  30 eaaatieelekqvdpilkevedllakvnelledvne 65 
                                    ++ +++++ +++++i++e+ d +++ ++l+e   +
  gi|13541439|ref|NP_111127.1|  98 DFNPFMDKTPEEIRGITEELSDQINNLKRLVESAIK 133
                                   556677777788888888888888888877765544 PP

>> BORCS6  BLOC-1-related complex sub-unit 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   2.5   2.2e-05     0.009      31     147 ..      13     129 ..       3     133 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.2e-05
                        BORCS6  31 lsesstpsasls..kqllaaq.ipeidpnvlsdlereaqkvaasvdnllenlssklhsisaltvgnietykdavdklgdav 108
                                    + ++tp +s+s  kq +a +  + idp+v++ ++++ +k+ +++ +++ +l+++ +s+s +  + +e  k+ v+ +    
  gi|13541439|ref|NP_111127.1|  13 KEATATPQQSISeeKQVQAIHvTNGIDPKVIDAMNERMTKIENNLGKMTAELEGQKKSLSDMK-NELEGIKENVKMVVSLY 92 
                                   3444444444443355666662456************************************97.67888999998888888 PP

                        BORCS6 109 DssiksmYqLlAkaEElskamkPveklakqikeikrlld 147
                                       +     + k+ E  + +  +e+l++qi+++krl++
  gi|13541439|ref|NP_111127.1|  93 ELVSRDFNPFMDKTPEEIRGI--TEELSDQINNLKRLVE 129
                                   888888889999985544555..6899********9997 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.3    0.0007      0.28      81     121 ..      44      84 ..       3      91 .. 0.65
   2 ?    5.1   0.0     0.052        21      55      85 ..     100     130 ..      83     139 .. 0.49

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0007
                  Baculo_PEP_C  81 dtlrneLtnlnsiltnLlssvtNinstLnnllqalnnldlg 121
                                   d++++++t ++++l  +++++ + +++L+ + + l++++++
  gi|13541439|ref|NP_111127.1|  44 DAMNERMTKIENNLGKMTAELEGQKKSLSDMKNELEGIKEN 84 
                                   56666666666666666666666666666666666666543 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.052
                  Baculo_PEP_C  55 ksllaeldtrldtlltnLtdalnalqdtlrn 85 
                                   +  + +  +++   +++L+d++n+l+  +++
  gi|13541439|ref|NP_111127.1| 100 NPFMDKTPEEIRGITEELSDQINNLKRLVES 130
                                   3333333344444444444444444433333 PP

>> KxDL  Uncharacterized conserved protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.2   0.00016     0.065      36      72 ..      50      86 ..      41      93 .. 0.89
   2 ?    1.0   0.0       1.3   5.2e+02      27      59 ..     105     137 ..      97     140 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00016
                          KxDL 36 nalsqerlaklrarfkqgtkllkevkkdLesifkkir 72
                                  +++ ++ l k++a+++ ++k l+++k++Le i+++++
  gi|13541439|ref|NP_111127.1| 50 MTKIENNLGKMTAELEGQKKSLSDMKNELEGIKENVK 86
                                  5688999**************************9997 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 1.3
                          KxDL  27 kknreLlelnalsqerlaklrarfkqgtkllke 59 
                                   k+ +e+  + ++++ + ++l+  +++ +k+l+e
  gi|13541439|ref|NP_111127.1| 105 KTPEEIRGITEELSDQINNLKRLVESAIKDLRE 137
                                   555555566666666666666666666555555 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 ?    6.6   2.0     0.021       8.4      22      64 ..      42      84 ..       3      86 .. 0.86
   2 !   15.9   1.7   2.7e-05     0.011      26     109 ..      46     140 ..      40     152 .. 0.54

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.021
                                  HHHCCCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHH CS
                     Fib_alpha 22 lqdlllkyekdvkkdlekleneleeisnstkeaeelvkeikds 64
                                  + d++++  ++++++l k++ ele  ++s +++++  + ik+ 
  gi|13541439|ref|NP_111127.1| 42 VIDAMNERMTKIENNLGKMTAELEGQKKSLSDMKNELEGIKEN 84
                                  5578888999999999999999999999999998888888876 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 2.7e-05
                                   CCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH..........H.HHHHHHHHHHHHHCCCHHHH CS
                     Fib_alpha  26 llkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkd..........n.dnvikksskeleeeilrlke 95 
                                   +++  ++++++l k++ ele  ++s +++++  + ik+ ++   + ++           +  + i+ +++el ++i++lk+
  gi|13541439|ref|NP_111127.1|  46 MNERMTKIENNLGKMTAELEGQKKSLSDMKNELEGIKENVKMVVSLYELvsrdfnpfmdKtPEEIRGITEELSDQINNLKR 126
                                   555555555555555555555555555555555544444444433333311112112111245777777888888888888 PP

                                   HHHCCHHHHHHHHH CS
                     Fib_alpha  96 tidaqesnirvLqn 109
                                    + + ++ +r+L +
  gi|13541439|ref|NP_111127.1| 127 LVESAIKDLRELYG 140
                                   88777777777765 PP

>> DLP_helical  Dynamin-like helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   1.2   3.6e-05     0.015      68     113 ..      42      87 ..      13     106 .. 0.84
   2 ?    0.7   0.0       0.6   2.5e+02      92     119 ..     109     136 ..      92     141 .. 0.54

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.6e-05
                   DLP_helical  68 irdvlerqlpeaeerleelekevekleesakriekelaelkkeiee 113
                                   + d +++++ ++e++l ++++e+e +++s++++++el+ +k++++ 
  gi|13541439|ref|NP_111127.1|  42 VIDAMNERMTKIENNLGKMTAELEGQKKSLSDMKNELEGIKENVKM 87 
                                   4599**************************************9975 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.6
                   DLP_helical  92 kleesakriekelaelkkeieearielr 119
                                   + +   +++++++++lk+ +e a ++lr
  gi|13541439|ref|NP_111127.1| 109 EIRGITEELSDQINNLKRLVESAIKDLR 136
                                   3334444444555555555555544444 PP

>> Tmemb_cc2  Predicted transmembrane and coiled-coil 2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   3.7   2.8e-05     0.011     181     289 ..      20     137 ..       3     153 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.8e-05
                     Tmemb_cc2 181 sddesssssvesssadsnsnseestasasksaesesqeklekileelqeikeeqerleeelerlkeqlkkel......... 252
                                   ++  s++++v+++++ + + ++    +a +++ ++ +++l k++ el+  k++ + +++ele +ke++k+ +         
  gi|13541439|ref|NP_111127.1|  20 QQSISEEKQVQAIHVTNGIDPK--VIDAMNERMTKIENNLGKMTAELEGQKKSLSDMKNELEGIKENVKMVVslyelvsrd 98 
                                   2222222232223333333333..33336677888899999****************************999999999999 PP

                     Tmemb_cc2 253 ..kllkqaLqeeryryerLEeqlndlteLhqnEienLKq 289
                                      ++ ++ +e r  +e+L +q+n+l  L    i+ L++
  gi|13541439|ref|NP_111127.1|  99 fnPFMDKTPEEIRGITEELSDQINNLKRLVESAIKDLRE 137
                                   998999999999*************99998888888775 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.9   0.00031      0.13      52     100 ..      41      89 ..      27     100 .. 0.74
   2 ?    4.0   0.0      0.12        50      51     100 ..     104     132 ..      98     153 .. 0.55

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00031
                       DUF1664  52 qvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseig 100
                                   +v +++++   ++++++ ++ ++l+ qk+  +++k+e++ ++e+++ + 
  gi|13541439|ref|NP_111127.1|  41 KVIDAMNERMTKIENNLGKMTAELEGQKKSLSDMKNELEGIKENVKMVV 89 
                                   5777778888888888888888888888888888888888888887665 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.12
                       DUF1664  51 eqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseig 100
                                   ++  e+++   ++Ls++i+++ +                      +++  
  gi|13541439|ref|NP_111127.1| 104 DKTPEEIRGITEELSDQINNLKR---------------------LVESAI 132
                                   33334444444444444444443.....................333333 PP

>> CdvA  CdvA-like coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.5     0.085        35      39      60 ..      40      61 ..       5      64 .. 0.78
   2 ?    8.8   1.1    0.0034       1.4      29      61 ..      41      73 ..      36      79 .. 0.86
   3 ?   11.7   0.3   0.00041      0.17       3      63 ..      68     128 ..      66     133 .. 0.95

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.085
                          CdvA 39 kelkeklkkrlkeledqiksle 60
                                   ++++ +++r++++e+++ +++
  gi|13541439|ref|NP_111127.1| 40 PKVIDAMNERMTKIENNLGKMT 61
                                  5899999999999999988776 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0034
                          CdvA 29 ealkklkekakelkeklkkrlkeledqikslek 61
                                  + +++++e++ ++ ++l k ++ele q ksl+ 
  gi|13541439|ref|NP_111127.1| 41 KVIDAMNERMTKIENNLGKMTAELEGQKKSLSD 73
                                  568899999999999999999999999999875 PP

  == domain 3  score: 11.7 bits;  conditional E-value: 0.00041
                          CdvA   3 kkALeeLvsegdipkstyeeikekleealkklkekakelkeklkkrlkeledqikslekal 63 
                                   kk L ++ +e ++ k+ ++++   +e  +++ +  +++  e+++  ++el dqi++l++++
  gi|13541439|ref|NP_111127.1|  68 KKSLSDMKNELEGIKENVKMVVSLYELVSRDFNPFMDKTPEEIRGITEELSDQINNLKRLV 128
                                   799******************************************************9975 PP

>> DUF5082  Domain of unknown function (DUF5082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.8   0.00048      0.19      81     123 .]      33      76 ..       2      76 .. 0.77
   2 ?    4.4   0.1       0.1        42      84     108 ..     108     132 ..      77     139 .. 0.55

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00048
                       DUF5082  81 tyvdkld.elidaieeEIerLenqiseaqgvldtlqsqlnslkn 123
                                   ++   +d ++ida++e  +++en + +++  l+ ++++l+++kn
  gi|13541439|ref|NP_111127.1|  33 HVTNGIDpKVIDAMNERMTKIENNLGKMTAELEGQKKSLSDMKN 76 
                                   5556677579********************************97 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.1
                       DUF5082  84 dkldelidaieeEIerLenqiseaq 108
                                   ++++ +  ++++ I++L+  +++a 
  gi|13541439|ref|NP_111127.1| 108 EEIRGITEELSDQINNLKRLVESAI 132
                                   3444444444444444444444443 PP

>> WXG100  Proteins of 100 residues with WXG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.1     0.067        27      54      82 ..      44      72 ..      40      74 .. 0.74
   2 ?    5.6   0.1     0.046        19      52      82 ..      63      93 ..      59      95 .. 0.82
   3 ?    3.5   0.0       0.2        82      12      36 ..     106     130 ..     102     134 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.067
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        WXG100 54 eewkqaaqklvdaLeeisealkqaanafe 82
                                  + +++ ++k+ ++L +++ +l+  +++++
  gi|13541439|ref|NP_111127.1| 44 DAMNERMTKIENNLGKMTAELEGQKKSLS 72
                                  66788888888888888888887777765 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.046
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        WXG100 52 efeewkqaaqklvdaLeeisealkqaanafe 82
                                  e+e  k+++ +++++Le+i e++k++ + +e
  gi|13541439|ref|NP_111127.1| 63 ELEGQKKSLSDMKNELEGIKENVKMVVSLYE 93
                                  5566688999999******999999888776 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.2
                                   HHHHHHHHHHHHHHHHHHHHHHHHH CS
                        WXG100  12 aaarfqkqaeeledelqrlkaevda 36 
                                   +  +++++ eel+d++++lk+ v++
  gi|13541439|ref|NP_111127.1| 106 TPEEIRGITEELSDQINNLKRLVES 130
                                   5557788889999999999988875 PP

>> MitMem_reg  Maintenance of mitochondrial structure and function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.4   0.00011     0.044      15      78 ..      53     130 ..      25     150 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 0.00011
                    MitMem_reg  15 iqdas...stlstglnrqyyslkilqerldlikdYlkkve.............egelpvnhe.ilrnlqkllnllPhlete 78 
                                   i   +   ++++++l+ q +sl+ +++ l+ ik+ +k v+              +++p + + i+++l++++n l  l ++
  gi|13541439|ref|NP_111127.1|  53 I---EnnlGKMTAELEGQKKSLSDMKNELEGIKENVKMVVslyelvsrdfnpfMDKTPEEIRgITEELSDQINNLKRLVES 130
                                   3...234799******************************77777666666663345555555999999999999877764 PP

>> YojJ  Bacterial membrane-spanning protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.6     0.079        32      15      48 ..      47      83 ..      41      92 .. 0.54
   2 ?    6.7   0.0     0.019       7.8       6      34 ..      98     126 ..      94     139 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.079
                          YojJ 15 keeLeqiekeleevlkaldeedeCl...Lcelesire 48
                                   e + +ie++l ++ ++l+ + + l     ele i+e
  gi|13541439|ref|NP_111127.1| 47 NERMTKIENNLGKMTAELEGQKKSLsdmKNELEGIKE 83
                                  5666667777777777766665542111233333333 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.019
                          YojJ   6 leeelkeklkeeLeqiekeleevlkalde 34 
                                   +++++  k+ ee++ i++el++ +++l+ 
  gi|13541439|ref|NP_111127.1|  98 DFNPFMDKTPEEIRGITEELSDQINNLKR 126
                                   6789999999***************9986 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   2.3   0.00014     0.058     241     326 ..      43     130 ..       5     139 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00014
                      Prominin 241 lerllenlkeakeqLeqvnklekeLrksgsqLrdglrgvkrdlnqalsn.lCqseeCskilssleiekldtskcl.dqlpn 319
                                   ++++ e +++++++L ++ + ++  +ks s++++ l+g+k++++ ++s  +  s++ + +++++  e+    ++l dq++n
  gi|13541439|ref|NP_111127.1|  43 IDAMNERMTKIENNLGKMTAELEGQKKSLSDMKNELEGIKENVKMVVSLyELVSRDFNPFMDKTPEEIRGITEELsDQINN 123
                                   7889999*************99999*****************999998876667999999999999999999999999999 PP

                      Prominin 320 vdevlea 326
                                   +++++e+
  gi|13541439|ref|NP_111127.1| 124 LKRLVES 130
                                   9998874 PP

>> DUF4298  Domain of unknown function (DUF4298)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.3      0.26     1e+02       7      32 ..      49      74 ..      41      93 .. 0.50
   2 ?    8.8   0.0    0.0038       1.6       4      53 ..     103     153 ..     101     154 .] 0.85

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.26
                                  HHHHHHHHHHHHHHHHHHHHHTHHHH CS
                       DUF4298  7 ildeisallqqLeealeqwkklqkkl 32
                                   + +i++ l ++   le  kk+ +++
  gi|13541439|ref|NP_111127.1| 49 RMTKIENNLGKMTAELEGQKKSLSDM 74
                                  44444444444444443333333332 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0038
                                   HHHHHHHHHHHHHHHHHHHHHHHHTH.HHHHHHHHHHTSHHHHHHHTS--S CS
                       DUF4298   4 mekildeisallqqLeealeqwkklq.kklakLdeYYqseqwredleasnk 53 
                                   m+k+ +ei  ++++L++ ++++k+l  + +++L+e Y+  +  +  ++ +k
  gi|13541439|ref|NP_111127.1| 103 MDKTPEEIRGITEELSDQINNLKRLVeSAIKDLRELYGVPDIDQVIQMEEK 153
                                   899999*****************98625799******98888888777666 PP

>> DUF4618  Domain of unknown function (DUF4618)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   3.2   0.00043      0.18     150     218 ..      19      87 ..       4      99 .. 0.88
   2 ?    4.0   0.1     0.072        29     191     221 ..     103     133 ..      90     139 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00043
                       DUF4618 150 vleklskkiqkkkekllkslaektlkatqeaLlqktlenqvlkkeiekfrefieeleeeipeLkaeveq 218
                                     +++s++ q +  ++++ +  k+++a++e +++   +  ++  e+e +++  +++++e++ +k++v+ 
  gi|13541439|ref|NP_111127.1|  19 PQQSISEEKQVQAIHVTNGIDPKVIDAMNERMTKIENNLGKMTAELEGQKKSLSDMKNELEGIKENVKM 87 
                                   4688999999999999************************************************99985 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.072
                       DUF4618 191 lkkeiekfrefieeleeeipeLkaeveqLqa 221
                                   + k  e+ r + eel  +i++Lk+ ve   +
  gi|13541439|ref|NP_111127.1| 103 MDKTPEEIRGITEELSDQINNLKRLVESAIK 133
                                   7777888889999999999999988876544 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   1.9   0.00016     0.067      63     138 ..      43     131 ..       4     141 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00016
                       DUF3450  63 levyneqlerlvasqeqeiasleeqieeieeierelvplle..kmidrLeqfveldlPf...........lleeRqarlak 130
                                   +++ ne+++++ +++ +  a+le q+++++ +++el+ + e  km+ +L ++v  d+ +             ee  +++++
  gi|13541439|ref|NP_111127.1|  43 IDAMNERMTKIENNLGKMTAELEGQKKSLSDMKNELEGIKEnvKMVVSLYELVSRDFNPfmdktpeeirgITEELSDQINN 123
                                   344555555555555555555555555555555555555442268999999999998553666555555555566666666 PP

                       DUF3450 131 Lkelmdra 138
                                   Lk l+++a
  gi|13541439|ref|NP_111127.1| 124 LKRLVESA 131
                                   66666555 PP

>> TBCC_N  Tubulin-specific chaperone C N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.5   0.00064      0.26      27      78 ..      25      84 ..       4      96 .. 0.68
   2 ?    1.8   0.0      0.78   3.2e+02      57      82 ..     106     131 ..      90     137 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00064
                        TBCC_N 27 eeekvds..........FlkaFteekaaieellesveesadksklkqkldeitaeiqeLqkl 78
                                  ee++v++            +a +e+  +ie++l +++  a+ + +k++l ++++e++ +++ 
  gi|13541439|ref|NP_111127.1| 25 EEKQVQAihvtngidpkVIDAMNERMTKIENNLGKMT--AELEGQKKSLSDMKNELEGIKEN 84
                                  22222224444445556999*****************..88888999999999998887765 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.78
                        TBCC_N  57 dksklkqkldeitaeiqeLqkllaes 82 
                                    +++ +   +e++ +i++L++l+  +
  gi|13541439|ref|NP_111127.1| 106 TPEEIRGITEELSDQINNLKRLVESA 131
                                   55666666778888888888887665 PP

>> GP41  Retroviral envelope protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   0.00014     0.058       5     116 ..      24     135 ..      20     148 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00014
                                   XXXXTHHHHHHHHHHHHHHHHHHHHH.HHH...HHHHHHHHHCHHHH..........HHHHHHHHS..TTSCCHHHHHCHH CS
                          GP41   5 sltksvqaatlvdglqrnvlkvleeq.qel...dkkleaRlsAleevvrvlgedvaslktrmklqChanykliCvtkvPyn 81 
                                   s  k+vqa ++ +g++ +v+++++e   ++     k+ a l+  ++ + ++ ++++ +k+  k+   + y+l+     P+ 
  gi|13541439|ref|NP_111127.1|  24 SEEKQVQAIHVTNGIDPKVIDAMNERmTKIennLGKMTAELEGQKKSLSDMKNELEGIKENVKMVV-SLYELVSRDFNPF- 102
                                   55689******************8762466444446677788888888999999******999998.89***********. PP

                                   H..HH..HHHHHHHHHHHH..HHHHHHHHHHHHHHHH CS
                          GP41  82 asdsWdkvkksLegiWnnt..evsydlaelhnliedi 116
                                        dk+ ++++gi ++   ++++    +++ i+d 
  gi|13541439|ref|NP_111127.1| 103 ----MDKTPEEIRGITEELsdQINNLKRLVESAIKDL 135
                                   ....689999999999887778999988888888886 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   0.3      0.16        67      35      62 ..      53      83 ..       3      91 .. 0.56
   2 ?   10.0   0.1    0.0024      0.99       7      61 ..      82     139 ..      78     153 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.16
                  Syntaxin-6_N 35 tseeldetrteL...rkalrsiewdledLee 62
                                   +++l + + eL   +k+l++++++le ++e
  gi|13541439|ref|NP_111127.1| 53 IENNLGKMTAELegqKKSLSDMKNELEGIKE 83
                                  3334444444441112344444444444444 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0024
                  Syntaxin-6_N   7 keeVqkslnkaeslyrrwerlledtsss...tseeldetrteLrkalrsiewdledLe 61 
                                   ke+V+  ++  e + r ++  +++t+++    +eel+++ ++L++ ++s+ +dl++L 
  gi|13541439|ref|NP_111127.1|  82 KENVKMVVSLYELVSRDFNPFMDKTPEEirgITEELSDQINNLKRLVESAIKDLRELY 139
                                   4555555555555555666666666663456899999999999999999999999985 PP

>> UPF0242  Uncharacterised protein family (UPF0242) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   3.2   0.00019     0.076      63     157 ..       9     123 ..       1     139 [. 0.69

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00019
                       UPF0242  63 eklekskleekeaklteld....................eglktkeealeelqeeeeeLkeeldakeeelerlkeenqqLq 123
                                   + ++k+ +++ ++ ++e++                    e ++++e++l ++++e e  k+ l+ +++ele  ke+ + + 
  gi|13541439|ref|NP_111127.1|   9 KLVKKEATATPQQSISEEKqvqaihvtngidpkvidamnERMTKIENNLGKMTAELEGQKKSLSDMKNELEGIKENVKMVV 89 
                                   333444444444444444444444455688888888888999999999999999999999999999999999998888877 PP

                       UPF0242 124 ekleaiaedfeelkleleeqLaekqellqeyqet 157
                                   +  e +++df+ +  +  e+++  +e l++  ++
  gi|13541439|ref|NP_111127.1|  90 SLYELVSRDFNPFMDKTPEEIRGITEELSDQINN 123
                                   7788888999988888888887665555444333 PP

>> DUF4795  Domain of unknown function (DUF4795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   6.8    0.0025         1      86     146 ..      46     136 ..       4     152 .. 0.57

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0025
                       DUF4795  86 fDeakkeLekmleellekleeqeealkkaldtLq............................eelkekld..rlelepLke 136
                                   + e+++++e++l ++   le+q ++l  + ++L+                            ee+    +   +++++Lk 
  gi|13541439|ref|NP_111127.1|  46 MNERMTKIENNLGKMTAELEGQKKSLSDMKNELEgikenvkmvvslyelvsrdfnpfmdktpEEIRGITEelSDQINNLKR 126
                                   333344444444555555555555555555555555555555555555555444444444445555555555556666666 PP

                       DUF4795 137 qleerlkelq 146
                                    +e+ +k l+
  gi|13541439|ref|NP_111127.1| 127 LVESAIKDLR 136
                                   6666666665 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 ?    5.7   0.2     0.038        16       2      34 ..      53      85 ..      45      91 .. 0.68
   2 ?    6.5   0.2     0.021       8.6      36      53 ..     109     126 ..     107     153 .. 0.69

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.038
                 TolA_bind_tri  2 ledrvarLErilearsqlllelqqqlealqqel 34
                                  +e+ + ++   le+++++l ++ ++le  ++ +
  gi|13541439|ref|NP_111127.1| 53 IENNLGKMTAELEGQKKSLSDMKNELEGIKENV 85
                                  355555666666666688888888888777665 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.021
                 TolA_bind_tri  36 eLRGqiEelqyqleqlee 53 
                                   e+RG +Eel+ q+++l++
  gi|13541439|ref|NP_111127.1| 109 EIRGITEELSDQINNLKR 126
                                   678888888888887765 PP

>> Atg14  Vacuolar sorting 38 and autophagy-related subunit 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   1.4   0.00027      0.11      36     140 ..      10     132 ..       3     153 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00027
                         Atg14  36 sekeslkkkiekalegkeeaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkklaklsdklk.... 112
                                   + k++     ++ ++++++++        + + ++ +  ++ +++++l ++ + l+ +kk++ + k++l++ ++++k    
  gi|13541439|ref|NP_111127.1|  10 LVKKEATATPQQSISEEKQVQAIHVTNGIDPKVIDAMNERMTKIENNLGKMTAELEGQKKSLSDMKNELEGIKENVKmvvs 90 
                                   455555556667777777777777888889999********************************************7777 PP

                         Atg14 113 ..............kRrsdleslqneleerrkkqiaklqdai 140
                                                 k  ++++ +++el+   +++ + + +ai
  gi|13541439|ref|NP_111127.1|  91 lyelvsrdfnpfmdKTPEEIRGITEELSDQINNLKRLVESAI 132
                                   777777777777765555555555555554444444444444 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   4.7   0.00044      0.18     172     276 ..      11     118 ..       2     150 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00044
                          Spc7 172 leeekaeleee.leklqe..aaeelesidkeeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqkseleee 249
                                   +++e ++  ++ + ++++  a +  + id++ + ++ e+++++++++ +  +el+  ++ l + ++++e +ke+ + + + 
  gi|13541439|ref|NP_111127.1|  11 VKKEATATPQQsISEEKQvqAIHVTNGIDPKVIDAMNERMTKIENNLGKMTAELEGQKKSLSDMKNELEGIKENVKMVVSL 91 
                                   444444333330333333212233345999999999999999999999999999999999999999999999999999988 PP

                          Spc7 250 iaeaervleeckgwsesevsrlkeevk 276
                                    +   r  +   + + +e++ ++ee++
  gi|13541439|ref|NP_111127.1|  92 YELVSRDFNPFMDKTPEEIRGITEELS 118
                                   888888888888888888876666554 PP

>> COG2  COG (conserved oligomeric Golgi) complex component, COG2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.5    0.0049         2      67     105 ..      46      84 ..      41      97 .. 0.71
   2 ?    2.7   0.0       0.3   1.2e+02      82     106 ..     107     131 ..      90     141 .. 0.61

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0049
                          COG2  67 lqeeleevesplaaarkkvesvreklsereeevesklee 105
                                   ++e++ ++e +l +++ ++e  +++ls++++e+e+  e+
  gi|13541439|ref|NP_111127.1|  46 MNERMTKIENNLGKMTAELEGQKKSLSDMKNELEGIKEN 84 
                                   677777777777777777777777777777777765444 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.3
                          COG2  82 rkkvesvreklsereeeveskleea 106
                                    ++++ ++e+ls+++++++  +e a
  gi|13541439|ref|NP_111127.1| 107 PEEIRGITEELSDQINNLKRLVESA 131
                                   4555555555555555555555443 PP

>> Cauli_AT  Aphid transmission protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   2.6    0.0025         1     111     162 ..      41      89 ..      13      90 .. 0.81
   2 ?    3.1   0.0       0.2        83     121     149 ..     108     137 ..      98     148 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0025
                      Cauli_AT 111 etLkeaqnrikkleeetkklaekivtekllkeevkdlderlseirdslkaii 162
                                   +++  +++r++k+e++  k++ +++ +   k+ + d++++l+ i++++k ++
  gi|13541439|ref|NP_111127.1|  41 KVIDAMNERMTKIENNLGKMTAELEGQ---KKSLSDMKNELEGIKENVKMVV 89 
                                   567778889999999999999999876...578999999**********998 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.2
                      Cauli_AT 121 kkleeetkklaekivt.ekllkeevkdlde 149
                                   +++   t++l+++i+  ++l+++ +kdl e
  gi|13541439|ref|NP_111127.1| 108 EEIRGITEELSDQINNlKRLVESAIKDLRE 137
                                   567777889999976537789999999976 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   1.4   0.00056      0.23       6      85 ..      45     127 ..       4     141 .. 0.59

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00056
                         TMPIT   6 elekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvk.................eeeeeeve 69 
                                    +++++ ++e++  +++++le  +k+ s++++e++  k+++              k                 +++ ee++
  gi|13541439|ref|NP_111127.1|  45 AMNERMTKIENNLGKMTAELEGQKKSLSDMKNELEGIKENV--------------KmvvslyelvsrdfnpfmDKTPEEIR 111
                                   34444444444444444444444444444444444444444..............44444444444444477766666666 PP

                         TMPIT  70 elkeelkerkkvlkev 85 
                                    ++eel+++ ++lk++
  gi|13541439|ref|NP_111127.1| 112 GITEELSDQINNLKRL 127
                                   6666666665555543 PP

>> Fzo_mitofusin  fzo-like conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.3    0.0032       1.3      89     148 ..      36      95 ..      21     106 .. 0.78
   2 ?    2.4   0.0      0.24        98     115     136 ..     108     129 ..      95     141 .. 0.52

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0032
                 Fzo_mitofusin  89 ancshqvqqelsstfarlcqqvdetekeleeeikelekeiekleevqkkakllrnkasll 148
                                   + ++ +v   +++ + +++++  ++++ele + k+l+   ++le ++++ k++    +l+
  gi|13541439|ref|NP_111127.1|  36 NGIDPKVIDAMNERMTKIENNLGKMTAELEGQKKSLSDMKNELEGIKENVKMVVSLYELV 95 
                                   556778888999999999999999999999999999999999999999998876555555 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.24
                 Fzo_mitofusin 115 keleeeikelekeiekleevqk 136
                                   +e++  ++el+ +i++l+++ +
  gi|13541439|ref|NP_111127.1| 108 EEIRGITEELSDQINNLKRLVE 129
                                   4444444444444444444322 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 ?   10.3   6.7    0.0013      0.53      26      79 ..      43      96 ..      40     138 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0013
                CENP-F_leu_zip 26 venLerelemseenqekvileaEtskaevetlkeeieelaeelreleldLvalr 79
                                  +++++  +  +e+n+ k++ e E +k+ ++ +k+e+e ++e+ +   +  + ++
  gi|13541439|ref|NP_111127.1| 43 IDAMNERMTKIENNLGKMTAELEGQKKSLSDMKNELEGIKENVKMVVSLYELVS 96
                                  778889999999999999999999999999999999999999886654433333 PP

>> HIP1_clath_bdg  Clathrin-binding domain of Huntingtin-interacting protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   2.8    0.0013      0.54       4      79 ..      10      82 ..       8      96 .. 0.74
   2 ?    1.4   0.1       1.2   4.8e+02      40      68 ..     107     135 ..      93     141 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0013
                HIP1_clath_bdg  4 LLrKnAevtkqlsvarqaqeeverekkeleeelerlkeeaerkleeqkeelekLkreleakraelarlkssLesse 79
                                  L++K+A  t q s + ++q +   + + ++ ++ ++ +e+  k+e+   +l k+ +ele +++ l+ +k+ Le  +
  gi|13541439|ref|NP_111127.1| 10 LVKKEATATPQQSISEEKQVQAIHVTNGIDPKVIDAMNERMTKIEN---NLGKMTAELEGQKKSLSDMKNELEGIK 82
                                  899************9999999999999999988888777777764...455556677777777777776666433 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 1.2
                HIP1_clath_bdg  40 keeaerkleeqkeelekLkreleakrael 68 
                                    ee +  +ee + ++++Lkr +e+  ++l
  gi|13541439|ref|NP_111127.1| 107 PEEIRGITEELSDQINNLKRLVESAIKDL 135
                                   44444455555566666666555555555 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   3.8     0.052        21      47      92 ..      40      85 ..       2      95 .. 0.61
   2 ?    5.4   0.0     0.062        25      23      64 ..      97     135 ..      92     150 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.052
                                  .HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.......HHHHHHHHH CS
                         DUF16 47 geqinkleqkvekqgekikelkveqkaqgeelnkvdetleliletL 92
                                   + i+++++ ++k ++++ ++++e + q+++l  +++ le i e +
  gi|13541439|ref|NP_111127.1| 40 PKVIDAMNERMTKIENNLGKMTAELEGQKKSLSDMKNELEGIKENV 85
                                  3456666666666666666666666666666666666666655544 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.062
                                   HHHHHB-..BHHHHHHHHHHHH...HHHHHHHHHHHHHHHHH CS
                         DUF16  23 kqlnefkdsnkqrLkkieakvdklgeqinkleqkvekqgeki 64 
                                   +++n f d + ++++ i ++++    qin+l+  ve   + +
  gi|13541439|ref|NP_111127.1|  97 RDFNPFMDKTPEEIRGITEELS---DQINNLKRLVESAIKDL 135
                                   78999**99**99999999998...56666666665555444 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1       9.3   3.8e+03      39      58 ..       6      25 ..       3      31 .. 0.62
   2 ?    7.9   0.1     0.011       4.6      18      55 ..      42      79 ..      39      88 .. 0.81
   3 ?    3.2   0.1      0.34   1.4e+02      20      43 ..     115     138 ..     102     152 .. 0.63

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 9.3
                                  HHHHHHHT-XXXXXXXXXXX CS
                          SlyX 39 qlrllaerlkeleessgase 58
                                   +++l+++ +++ ++++ se
  gi|13541439|ref|NP_111127.1|  6 NMKKLVKKEATATPQQSISE 25
                                  46667777766666665443 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.011
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXXX CS
                          SlyX 18 tieeLndvvaeqqqqidrlqrqlrllaerlkeleessg 55
                                  +i+++n+ +++ +  + +++++l+  ++ l++++++ +
  gi|13541439|ref|NP_111127.1| 42 VIDAMNERMTKIENNLGKMTAELEGQKKSLSDMKNELE 79
                                  68999999999999999999999999999988887765 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.34
                                   HHHHHHHHHHHHHHHHHHHHHHHH CS
                          SlyX  20 eeLndvvaeqqqqidrlqrqlrll 43 
                                   eeL+d++ +  + ++   + lr+l
  gi|13541439|ref|NP_111127.1| 115 EELSDQINNLKRLVESAIKDLREL 138
                                   455555555555555555555554 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 ?    8.4   3.4    0.0064       2.6      24      74 ..      42      85 ..       2      97 .. 0.61
   2 ?    3.7   0.3      0.19        75      16      64 ..      86     135 ..      81     153 .. 0.63

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0064
                       BLOC1_2 24 lLeklNeaasekykklkdvaaslekkleklnekyeelqpylqqidqiekqv 74
                                  ++ ++Ne++++  ++l +++a+le + + l+ +++el+        i+++v
  gi|13541439|ref|NP_111127.1| 42 VIDAMNERMTKIENNLGKMTAELEGQKKSLSDMKNELEG-------IKENV 85
                                  455555555544444444444444444433333333333.......33333 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.19
                       BLOC1_2  16 eatvedyklLe.klNeaasekykklkdvaaslekkleklnekyeelqpyl 64 
                                   +++v+ y+l+    N  + +  ++++ ++++l++++++l+++ e+  + l
  gi|13541439|ref|NP_111127.1|  86 KMVVSLYELVSrDFNPFMDKTPEEIRGITEELSDQINNLKRLVESAIKDL 135
                                   55555565554135555666667888888888888888888766544444 PP

>> YkyA  Putative cell-wall binding lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   9.5     0.017       6.7       8      93 ..       5      87 ..       2     140 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.017
                          YkyA  8 ealeeavelEkefeeqqekLtelekkeqelyeeiielgmdefdkikklsdealenveeReellekekesieeakeefekikee 90
                                  ++++++v++E + + qq+ ++  e+k+ +    ++  + +  d++++   +  +n+ + + +le +k+s+++ k+e+e ike+
  gi|13541439|ref|NP_111127.1|  5 NNMKKLVKKEATATPQQS-IS--EEKQVQAIHVTNGIDPKVIDAMNERMTKIENNLGKMTAELEGQKKSLSDMKNELEGIKEN 84
                                  677888888877766654.43..455555556666667888999999999999999999999999999999999999999999 PP

                          YkyA 91 iee 93
                                  ++ 
  gi|13541439|ref|NP_111127.1| 85 VKM 87
                                  875 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   3.0     0.004       1.6       6      77 ..      46     128 ..      43     141 .. 0.65

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.004
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH............XXXXXXXXXXXXXXXXXXXXXX CS
                          YabA   6 lfdkleeleeqleelleeleelkeelaelleenaeLeleneklrerl............eeeekkekekkkelsegkenLa 74 
                                   + ++++++e++l+++++ele  k++l+++ +e + ++ + + + + l            +++ ++ +  ++els+  +nL+
  gi|13541439|ref|NP_111127.1|  46 MNERMTKIENNLGKMTAELEGQKKSLSDMKNELEGIKENVKMVVS-LyelvsrdfnpfmDKTPEEIRGITEELSDQINNLK 125
                                   567888888888888888888888888887777666644333333.23666666777765555555556666666666666 PP

                                   XXX CS
                          YabA  75 rlY 77 
                                   rl 
  gi|13541439|ref|NP_111127.1| 126 RLV 128
                                   664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1875  (0.104579); expected 358.6 (0.02)
Passed bias filter:                      950  (0.0529868); expected 358.6 (0.02)
Passed Vit filter:                       154  (0.00858944); expected 17.9 (0.001)
Passed Fwd filter:                        45  (0.0025099); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              44  [number of targets reported over threshold]
# CPU time: 0.71u 0.34s 00:00:01.05 Elapsed: 00:00:00.50
# Mc/sec: 935.48
//
Query:       gi|13541440|ref|NP_111128.1|  [L=217]
Description: flagellar protein E [Thermoplasma volcanium GSS1]
Scores for complete sequence (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   95.4   0.1    2.5e-27   94.6   0.1    1.5  1  Arch_fla_DE  Archaeal flagella protein
  ------ inclusion threshold ------
      0.019   15.1   0.1       0.31   11.2   0.0    2.1  2  DUF2959      Protein of unknown function (DUF2959)


Domain annotation for each model (and alignments):
>> Arch_fla_DE  Archaeal flagella protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.6   0.1   2.8e-31   2.5e-27       2      95 .]      98     189 ..      97     189 .. 0.95

  Alignments for each domain:
  == domain 1  score: 94.6 bits;  conditional E-value: 2.8e-31
                   Arch_fla_DE   2 ekpyLeelpedyaaelvvleWlefLvervgvenaaealdyYeeigWiseevreeLlkylkgikledeekeelkkseltved 82 
                                   +k++Le++ +d+++ +v l+WlefL++++g+en++++ldyYe++gWis++v+e+++ky+k++++  ++ +e+k  + +++d
  gi|13541440|ref|NP_111128.1|  98 KKAKLEAIGDDVVSIMVSLRWLEFLLDNYGPENTLDVLDYYESLGWISSTVKEQMMKYAKMTGV-MNPAQEYK-IKPSIQD 176
                                   789************************************************************9.88888886.78***** PP

                   Arch_fla_DE  83 HvkSllyieklag 95 
                                   H+  +l+iekl+g
  gi|13541440|ref|NP_111128.1| 177 HIINMLFIEKLRG 189
                                   ***********86 PP

>> DUF2959  Protein of unknown function (DUF2959)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0     0.025   2.3e+02      42      70 ..      35      63 ..       7      87 .. 0.63
   2 ?   11.2   0.0   3.4e-05      0.31     112     172 ..     149     214 ..     140     216 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.025
                       DUF2959 42 kavvefdggeLekeyeklnkeyeesekaa 70
                                  ++ ++f ++++++   +l k+ye++++++
  gi|13541440|ref|NP_111128.1| 35 SSPIQFGKSDIDDLVANLLKRYEQTKENS 63
                                  34568889999999999999999988754 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 3.4e-05
                       DUF2959 112 ketrkkykellkamkka.ekkmePvlaalkdqvlfLK....hnlNaqaiaalkgelselekdvskl 172
                                   ke   ky++++  m+ a e k++P ++    ++lf+      ++N   i+al+ e+++++k v++l
  gi|13541440|ref|NP_111128.1| 149 KEQMMKYAKMTGVMNPAqEYKIKPSIQDHIINMLFIEklrgEEINRDLIEALEREFRTIRKGVDEL 214
                                   666789*********883569*****999999***862333589*******************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       737  (0.0411066); expected 358.6 (0.02)
Passed bias filter:                      504  (0.0281109); 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: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 1355.66
//
Query:       gi|13541441|ref|NP_111129.1|  [L=137]
Description: flagellar protein F [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      0.003   17.8   3.0     0.0033   17.6   3.0    1.1  1  Arch_flagellin  Archaebacterial flagellin
  ------ inclusion threshold ------
      0.043   14.3   2.1      0.072   13.6   2.1    1.4  1  DUF4179         Domain of unknown function (DUF4179)
       0.21   11.3   0.1       0.38   10.4   0.1    1.5  1  SH3-RhoG_link   SH3-RhoGEF linking unstructured region


Domain annotation for each model (and alignments):
>> Arch_flagellin  Archaebacterial flagellin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   3.0   5.5e-07    0.0033       5     119 ..       7     114 ..       2     131 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 5.5e-07
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT--EEEEEEEEEE-SSSSSEEEEEEE--TTS--EEGG CS
                Arch_flagellin   5 igtlIvfIAmVlVAAvaagvlintagflqqkaqstgeesteqvssgleitgdvgdsatngtineitiyvklnaGsspidln 85 
                                   ++++I++ + ++   ++++  +++ + ++++ q+  +++ +  ++++ei++ +++s++++     ++ v+   Gs++ +l+
  gi|13541441|ref|NP_111129.1|   7 VAAVIMLSSTLIFFGIVYSSYVQSNTSITNANQKLIKNIYNLENTKIEIVSYYYNSSSST----FYVNVT-DNGSTSFNLS 82 
                                   678899999999999999************************************888887....888888.89*******9 PP

                                   G-EEEEEESS--EE--E................. CS
                Arch_flagellin  86 kttisvtddgqetlltadefgivvisdtdgsltn 119
                                   ++ +++ +     +++ ++  i+ +++ + s+++
  gi|13541441|ref|NP_111129.1|  83 ESNVILNGT--LISFNESNQYIFPLETITISFKA 114
                                   999885443..35555555556666666666655 PP

>> DUF4179  Domain of unknown function (DUF4179)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   2.1   1.2e-05     0.072      10      68 ..       6      77 ..       3      94 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.2e-05
                                  XXXXXXXXXX..XXXXXXXXXXXXXXX.......--SS-HHHHT--SS-.....HHHHSEEEEEEEEETTEE CS
                       DUF4179 10 aaaaaalvll..llssrllspalAsal.....n.pvigslfeklsdskg.....eqeyvkpvnksaednGit 68
                                  ++aa++++    ++++++ s+ + s+      n ++i++++++++++ +     ++  ++     ++dnG t
  gi|13541441|ref|NP_111129.1|  6 TVAAVIMLSStlIFFGIVYSSYVQSNTsitnaNqKLIKNIYNLENTKIEivsyyYNSSSSTFYVNVTDNGST 77
                                  3333333332543333333333333446999999************999*9999888888899999***965 PP

>> SH3-RhoG_link  SH3-RhoGEF linking unstructured region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   6.3e-05      0.38     188     234 ..      26      84 ..      14     100 .. 0.55

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 6.3e-05
                 SH3-RhoG_link 188 setPsaaelvsaieelvkskmaledrp............sslivdtgdsssPsfnlsdn 234
                                   s + s + + +a ++l+k  + le+              s++ v+ +d +s sfnls++
  gi|13541441|ref|NP_111129.1|  26 SYVQSNTSITNANQKLIKNIYNLENTKieivsyyynsssSTFYVNVTDNGSTSFNLSES 84 
                                   55556666666666666666666655500000001111144555566666666666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1130  (0.0630264); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 918.46
//
Query:       gi|13541442|ref|NP_111130.1|  [L=147]
Description: flagellar protein G [Thermoplasma volcanium GSS1]
Scores for complete 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   46.5   7.8    5.5e-12   46.2   7.8    1.1  1  Arch_flagellin  Archaebacterial flagellin
  ------ inclusion threshold ------
       0.15   11.8   0.0       0.24   11.2   0.0    1.3  1  Secapin         Honey bee peptides


Domain annotation for each model (and alignments):
>> Arch_flagellin  Archaebacterial flagellin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.2   7.8   6.2e-16   5.5e-12       1     158 [.       2     139 ..       2     145 .. 0.85

  Alignments for each domain:
  == domain 1  score: 46.2 bits;  conditional E-value: 6.2e-16
                                   X--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT--EEEEEEEEEE-SSSSSEEEEEEE--TTS-- CS
                Arch_flagellin   1 GfvgigtlIvfIAmVlVAAvaagvlintagflqqkaqstgeesteqvssgleitgdvgdsatngtineitiyvklnaGssp 81 
                                   +++ +++l+ fI+ +l+ A a+ vl + +  +   +qs  +++t+ ++++++i++ + ++++++    + +y+k n+Gs  
  gi|13541442|ref|NP_111130.1|   2 ASTAVSELVFFIVTLLITASAVAVLSDQTIHIVYGMQSSSQRTTDMIQENFAIINNPDQIPYDN---GYVFYIK-NTGSVG 78 
                                   67899*****************************************************998885...69*****.****** PP

                                   EEGGG-EEEEEESS--EE--E..................T-EE-TT-EEEEEEE--TTT---TT-EEEEEEE-SSS- CS
                Arch_flagellin  82 idlnkttisvtddgqetlltadefgivvisdtdgsltngdevlekgekvelevnvneddgitagdevsvevvpenGa 158
                                     +++t+isv++dg          + v+ +  +  + +++ +l +g+++e++vn       t +++ s+++   +G+
  gi|13541442|ref|NP_111130.1|  79 FAFDNTSISVLVDG----------SAVTGKYVKFISLENSSILVPGQVGEIVVNE------TLSGYNSITISLGTGV 139
                                   **************..........6667777777778888999999999999996......3444444444555555 PP

>> Secapin  Honey bee peptides
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   2.7e-05      0.24       5      32 ..      37      64 ..      33      77 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 2.7e-05
                       Secapin  5 mqPLearsaDLvqePrYiidvPPrCPPG 32
                                  mq    r  D++qe   ii+ P + P  
  gi|13541442|ref|NP_111130.1| 37 MQSSSQRTTDMIQENFAIINNPDQIPYD 64
                                  999999****************999854 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       629  (0.0350828); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 951.84
//
Query:       gi|13541443|ref|NP_111131.1|  [L=223]
Description: flagellar accessory protein FlaH [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.7e-07   30.8   0.0    3.1e-07   30.0   0.0    1.4  1  ATPase     KaiC
     0.0033   16.8   0.0      0.027   13.8   0.0    2.0  2  DnaB_C     DnaB-like helicase C terminal domain
     0.0069   15.9   0.0      0.011   15.2   0.0    1.3  1  RecA       recA bacterial DNA recombination protein
     0.0075   15.6   0.1      0.029   13.6   0.1    1.8  2  Rad51      Rad51
  ------ inclusion threshold ------
      0.037   13.8   0.1        1.1    9.0   0.0    2.1  2  IstB_IS21  IstB-like ATP binding protein
       0.12   11.7   0.0       0.31   10.3   0.0    1.7  2  Thi4       Thi4 family


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 !   30.0   0.0     1e-10   3.1e-07       7     224 ..      11     215 ..       7     221 .. 0.78

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 1e-10
                        ATPase   7 glDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdlekleeegklaiid 87 
                                   +lD+ + gG++ g+   i G+   GKt+++l+ ++  +++ g  + +v+   p ++++    +lG  + +   +g ++++ 
  gi|13541443|ref|NP_111131.1|  11 ELDKRMGGGVYVGQLFTILGDNSEGKTLLSLRLAYGFLKN-GTSVAYVSSQMPVREFISFSDALGYPVLNEIISGTFMFVT 90 
                                   699*****************************99988777.**************************99999999999998 PP

                        ATPase  88 asesaeesaeekdkedleelieelaeaikeikakrvviDsitgl.ayeekeavaReilrqlvrvlkklgvTailvseksss 167
                                    +   ++     +k+ l+ l+++  e i+e++   ++iDs+++   y+ + +   +++ +l ++ +++  + il++  +ss
  gi|13541443|ref|NP_111131.1|  91 PVFILRK----PKKARLDDLLNN--EKIREKN--VLIIDSLNPAmFYDFDIN---TYMEKLRKF-SEN-RVVILTAS-PSS 157
                                   8877654....346666666664..5566554..689*****9944444444...444444333.333.34577776.788 PP

                        ATPase 168 eeaaggygveefivdgvivLdlkeieeelvRtleivkmRgtkhs.kkehpfeIte.egi 224
                                    + a++ ++++ +++ ++ L+ ke  +  +  ++ vk+ +   s ++ +pf +++ +g 
  gi|13541443|ref|NP_111131.1| 158 LDDATTLRINQ-LSTTIVTLHSKELGGMKRHFIDLVKYPMVVRSiQQSIPFRVEPgRGL 215
                                   8999999***9.9999999**99999999999999999876655144567777776555 PP

>> DnaB_C  DnaB-like helicase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.0     9e-06     0.027       8      62 ..      11      65 ..       6      69 .. 0.86
   2 ?    0.7   0.0     0.088   2.6e+02      90     136 ..     141     190 ..     108     203 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 9e-06
                                  HHH.HHCTSBXTTXEEEEEEXTTSSHHHHHHHHHHHHHHCSTSEEEEEESSSXHHH CS
                                  xxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        DnaB_C  8 dLD.kltsGlqkgdliiiAarpsmGktalalniaenaavkeklpvavfslemsaeq 62
                                  +LD ++ +G+  g+l+ i +  s Gkt l l +a    + + ++va++s  m+ ++
  gi|13541443|ref|NP_111131.1| 11 ELDkRMGGGVYVGQLFTILGDNSEGKTLLSLRLAYGFLK-NGTSVAYVSSQMPVRE 65
                                  78834567899************************9885.6789********9776 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.088
                                   HHHHH.HHHHHHHSEEEEEEXSSXCHHHHHHHHHHHHHH..TTEEEEEEE CS
                                   xxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxx RF
                        DnaB_C  90 eklte.aieelseaklfiddtpaltvseirskarrlkke..kglgliviD 136
                                   +k++e ++  l+ ++  +dd ++l ++++ + +  l+++  +g++  +iD
  gi|13541443|ref|NP_111131.1| 141 RKFSEnRVVILTASPSSLDDATTLRINQLSTTIVTLHSKelGGMKRHFID 190
                                   44444235667777788888888888888888877766555555555555 PP

>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   3.6e-06     0.011      41      93 ..      12      63 ..       5      85 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3.6e-06
                                  HHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHTT--EEEEESS--- CS
                          RecA 41 ldialGiGGlpkGriieiyGpessGkttlalhaiaeaqkkggvaafidaehal 93
                                  ld  +G GG+  G++  i G +s Gkt l+l++     k+g  +a++ ++  +
  gi|13541443|ref|NP_111131.1| 12 LDKRMG-GGVYVGQLFTILGDNSEGKTLLSLRLAYGFLKNGTSVAYVSSQMPV 63
                                  888999.9**************************************9887655 PP

>> Rad51  Rad51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.1   9.7e-06     0.029      24      58 ..      10      44 ..       5      48 .. 0.93
   2 ?   -0.9   0.0      0.27   8.1e+02     222     247 ..     141     166 ..     106     172 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 9.7e-06
                                  HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHHHH CS
                         Rad51 24 kklDelLgGGietgsiteifGefrsGktqlchtlc 58
                                   +lD+ +gGG+ +g++  i+G++  Gkt l+  l+
  gi|13541443|ref|NP_111131.1| 10 DELDKRMGGGVYVGQLFTILGDNSEGKTLLSLRLA 44
                                  58****************************99987 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.27
                                   E-STTEEEEEEES-SSS-S-EEEEEE CS
                         Rad51 222 kgkgeeRivkvvdsPnlpeleavfai 247
                                   ++  e+R+v ++ sP++ +  +++ i
  gi|13541443|ref|NP_111131.1| 141 RKFSENRVVILTASPSSLDDATTLRI 166
                                   22347777777777777666655555 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0   0.00036       1.1      49      84 ..      25      60 ..      20      70 .. 0.89
   2 ?    2.9   0.0     0.026        77      87     148 ..      95     154 ..      68     174 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00036
                     IstB_IS21 49 nivllGpsGvGKshlaialgveavraglsvlfvrve 84
                                   + +lG    GK+ l+  l++   ++g+sv +v+ +
  gi|13541443|ref|NP_111131.1| 25 LFTILGDNSEGKTLLSLRLAYGFLKNGTSVAYVSSQ 60
                                  57899***************************9865 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.026
                     IstB_IS21  87 veelkrarrdgklaralkrllkvdllilDdlgllpldqaeaellfeviekryerrsiiitsn 148
                                   +++ k+ar d+ l++  +++ + ++li+D l    + + + ++ +e + k  e+r +i+t+ 
  gi|13541443|ref|NP_111131.1|  95 LRKPKKARLDDLLNN--EKIREKNVLIIDSLNPAMFYDFDINTYMEKLRKFSENRVVILTAS 154
                                   455555555555543..5778889*******9999999999999999999999999999985 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0      0.83   2.5e+03      53      77 ..      16      39 ..      12      56 .. 0.75
   2 ?   10.3   0.0    0.0001      0.31       6      55 ..     134     182 ..     132     200 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.83
                                  --TTTTTTSTTBSEEEEETTTHHHH CS
                          Thi4 53 pGGGawlGGqlfsaivvrkpakelL 77
                                  +GGG++  Gqlf+ +  + ++k lL
  gi|13541443|ref|NP_111131.1| 16 MGGGVYV-GQLFTILGDNSEGKTLL 39
                                  6888876.58998777666666666 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0001
                                   HHHHHHHHHHTEEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--T CS
                          Thi4   6 eryfedllkyaesDvvivGaGssGLtaayylakkpdlkvailersvspGG 55 
                                   ++y+e+l k+ e  vvi  a +s L  a +l  + +l ++i+  +    G
  gi|13541443|ref|NP_111131.1| 134 NTYMEKLRKFSENRVVILTASPSSLDDATTLRIN-QLSTTIVTLHSKELG 182
                                   78***************************99998.888887765554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       376  (0.0209716); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-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: 00:00:00.38
# Mc/sec: 1769.10
//
Query:       gi|13541444|ref|NP_111132.1|  [L=535]
Description: ATPase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.5e-47  161.2   0.0    3.3e-47  160.8   0.0    1.1  1  T2SSE      Type II/IV secretion system protein
     0.0055   17.2   0.0      0.013   16.0   0.0    1.6  1  ABC_tran   ABC transporter
  ------ inclusion threshold ------
      0.047   13.5   0.0       0.11   12.3   0.0    1.5  1  DEAD       DEAD/DEAH box helicase
      0.048   13.4   0.0       0.14   11.9   0.0    1.8  1  AAA_29     P-loop containing region of AAA domain
      0.059   13.4   0.0      0.099   12.7   0.0    1.5  1  Dynamin_N  Dynamin family
      0.082   13.3   0.0       0.23   11.8   0.0    1.6  1  AAA_16     AAA ATPase domain
        0.1   12.1   0.0       0.51    9.8   0.0    1.9  2  AAA_7      P-loop containing dynein motor region
       0.15   12.3   0.0       0.35   11.1   0.0    1.6  1  AAA_22     AAA domain


Domain annotation for each model (and alignments):
>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  160.8   0.0   1.5e-50   3.3e-47       3     244 ..     158     403 ..     156     426 .. 0.94

  Alignments for each domain:
  == domain 1  score: 160.8 bits;  conditional E-value: 1.5e-50
                         T2SSE   3 illeallddekvsdihvekper.vkvrervdgielreveelekaalerlisriaalakldiseerplqdarlpekgvrlrv 82 
                                    +le+l++d+++ di    p++ ++v++  ++ +  ++ + + + l+ + +r+   +++ +s++rp++da+lp +g rl +
  gi|13541444|ref|NP_111132.1| 158 GPLEPLIRDSHIEDISGIGPDDvYIVHKIFGS-MATDITFGSMERLMVFSKRLSERVGRPVSDKRPIVDATLP-DGSRLSL 236
                                   578999**********9999998899888888.99**************************************.8888888 PP

                         T2SSE  83 vllPvvag..ealviRkksakeltlddlgaeealkekiaevlrkavrerglilvsGgTgsGKttllyallkeinksderiv 161
                                   v    + +  ++++iRk s+  l++ +l++ ++++ + a+ l  a++  +++ v G T sGKtt+++a++ +i  +  +i 
  gi|13541444|ref|NP_111132.1| 237 VYSTDISQrgPSFTIRKFSEVPLSIINLIKYNTMSYEEAAYLWLALEYGQSVFVCGETASGKTTVVNAIIPFIRPE-SKIY 316
                                   77766665569****************************************************************9.**** PP

                         T2SSE 162 tvEDpvEiqleganqvqlnak.....kakvtfadllraaLRlrPDrimvGEiRdketleilkAvnTGHlgslsTlHansaa 237
                                    +ED+ Ei+  ++   ql+++     + +v + dllr+aLR rP  i+vGEiR++e + + +A++TGH++ +sT Ha s++
  gi|13541444|ref|NP_111132.1| 317 SAEDTPEIRAPQKAWQQLVTResgseESRVSLYDLLRTALRSRPNYIIVGEIRGAEGAMAFQAMQTGHPV-ISTFHASSVK 396
                                   ********************999**999******************************************.********** PP

                         T2SSE 238 galerLe 244
                                   + ++r  
  gi|13541444|ref|NP_111132.1| 397 KMIQRFT 403
                                   ****986 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   5.8e-06     0.013       6      42 ..     280     316 ..     277     355 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 5.8e-06
                                   EEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran   6 lklkegekvaivGenGaGKStLlkllagllkpteGei 42 
                                   l l+ g+ v + Ge+ +GK+t++++++   +p++   
  gi|13541444|ref|NP_111132.1| 280 LALEYGQSVFVCGETASGKTTVVNAIIPFIRPESKIY 316
                                   67999***********************999965433 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   4.7e-05      0.11      11      36 ..     282     309 ..     272     336 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.7e-05
                                   HHTTCEEEEEESTTSSHHHH..HHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxx..xxxxxx RF
                          DEAD  11 ilgggdvlvaaeTGsGKTla..flipvl 36 
                                   +  g++v+v++eT+sGKT++  ++ip +
  gi|13541444|ref|NP_111132.1| 282 LEYGQSVFVCGETASGKTTVvnAIIPFI 309
                                   33799**************955566665 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   6.3e-05      0.14      24      50 ..     287     313 ..     269     317 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 6.3e-05
                        AAA_29  24 atlltGpsGsGKSTllDAiqalLvpak 50 
                                   ++++ G++ sGK+T++ Ai+  + p++
  gi|13541444|ref|NP_111132.1| 287 SVFVCGETASGKTTVVNAIIPFIRPES 313
                                   7899***************98888876 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   4.4e-05     0.099       1      75 [.     288     359 ..     288     422 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.4e-05
                                   EEEEEBTTTTHHHHHHHHHTS--S---SSS---S-EEEEECCT---CCS...SSEEEET-EB--CHHHHHHHHHH CS
                     Dynamin_N   1 iavvGsqSsGKSSvlnaLlgedilprgpnptTrrplelqlgeeeeaseravkeelkekekkledfsevreeieke 75 
                                   + v+G++ sGK++v+na++     p +++     + e++  ++    ++ v+ e +++e++ + ++ +r++++++
  gi|13541444|ref|NP_111132.1| 288 VFVCGETASGKTTVVNAIIPFI-RPESKIYSAEDTPEIRAPQKAW--QQLVTRESGSEESRVSLYDLLRTALRSR 359
                                   68****************9875.7888888888888888887777..3466677777777666666666666655 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    0.0001      0.23      25      52 ..     286     313 ..     280     382 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0001
                        AAA_16  25 elvllsGesGvGKsslvrellralekdg 52 
                                   ++v++ Ge ++GK+++v+++   ++ + 
  gi|13541444|ref|NP_111132.1| 286 QSVFVCGETASGKTTVVNAIIPFIRPES 313
                                   79*****************997777763 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00023      0.51      26      54 ..     278     306 ..     257     318 .. 0.81
   2 ?   -0.9   0.0      0.46     1e+03      67     112 ..     375     420 ..     372     425 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00023
                         AAA_7  26 lelllknkkpvllvGptGtGKtviikdll 54 
                                   l l l+ +++v+++G+t +GKt++++ ++
  gi|13541444|ref|NP_111132.1| 278 LWLALEYGQSVFVCGETASGKTTVVNAII 306
                                   45678999*****************9876 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.46
                         AAA_7  67 infsaqtsanqlqdiiesklekrrkgvygPpggkklvvFvDDlnmp 112
                                   + f+a+ + + + ++++++  k+  + +   + +  v+F+D+ln+ 
  gi|13541444|ref|NP_111132.1| 375 MAFQAMQTGHPVISTFHASSVKKMIQRFTGNPINIPVTFMDNLNIV 420
                                   667777777777777877777888888888888888999****986 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00016      0.35       4      29 ..     284     309 ..     282     382 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00016
                        AAA_22   4 tagilvvtGesGtGKTtllrrlleql 29 
                                   + ++++v+Ge+ +GKTt+++ +    
  gi|13541444|ref|NP_111132.1| 284 YGQSVFVCGETASGKTTVVNAIIPFI 309
                                   568999*************9987776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (535 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       737  (0.0411066); expected 358.6 (0.02)
Passed bias filter:                      671  (0.0374254); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.43
# Mc/sec: 3709.70
//
Query:       gi|13541445|ref|NP_111133.1|  [L=552]
Description: flagellar assembly protein J [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-10   41.5   0.1    1.1e-10   41.5   0.1    3.5  5  T2SSF     Type II secretion system (T2SS), protein F


Domain annotation for each model (and alignments):
>> T2SSF  Type II secretion system (T2SS), protein F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.3   1.5      0.95   1.7e+04     105     121 ..      44      60 ..      42      61 .. 0.77
   2 !   41.5   0.1   6.3e-15   1.1e-10       1     123 [.      81     208 ..      81     213 .. 0.93
   3 ?   -5.2   1.3         1   1.8e+04     105     116 ..     223     234 ..     219     243 .. 0.48
   4 !   11.3   0.1   1.4e-05      0.25       1     120 [.     329     452 ..     329     458 .. 0.73
   5 ?   -5.2   1.8         1   1.8e+04     107     121 ..     527     541 ..     525     544 .. 0.53

  Alignments for each domain:
  == domain 1  score: -4.3 bits;  conditional E-value: 0.95
                                   TXXXXXXXXXXXXXXXX CS
                         T2SSF 105 pllllvvallvllilla 121
                                   ++++l++al++++++++
  gi|13541445|ref|NP_111133.1|  44 VAAVLFLALAIGAAFFF 60 
                                   57788899999988886 PP

  == domain 2  score: 41.5 bits;  conditional E-value: 6.3e-15
                                   HHHHHHHHHHTT--HHHHHHHHHHHHSSHHHHHHHHHHHHHHHTTS.SHHHHHC....T-TT.TS-HHHHHHHHHHHHHT- CS
                         T2SSF   1 flrqlatllsaGvplveaLellaeeaengplaeelkriarrlraGg.slseale....rtpssefpelvvqlirageeggn 76 
                                   f++ +++l+ + +++ ++L ll++  + g l+ e+++i++ ++++g  l+ea+     +tps+ f+++++++++a+++g++
  gi|13541445|ref|NP_111133.1|  81 FITAFSSLVTSDANIIDVLILLSKKEKLGYLRVEIEKILNLVKNWGmGLAEAINfvakKTPSDLFSDFLTRFSHAIDSGQD 161
                                   8999****************************************99899******************************** PP

                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHTTXXXXXXXXXXXXXXXXXX CS
                         T2SSF  77 LaevLerlaeyleeerelrrkllaallepllllvvallvllillail 123
                                   L+e+ +      ++ +e+++ +++ ++     ++v ll+++++l+ +
  gi|13541445|ref|NP_111133.1| 162 LEEFTRSEVFSTMNSFETAYVSALYSFDLYRDIYVSLLLSFAFLITF 208
                                   ****9999999999999999999999999999999988888887654 PP

  == domain 3  score: -5.2 bits;  conditional E-value: 1
                                   TXXXXXXXXXXX CS
                         T2SSF 105 pllllvvallvl 116
                                   +l+l +++++++
  gi|13541445|ref|NP_111133.1| 223 VLMLSLIMVALG 234
                                   333333333333 PP

  == domain 4  score: 11.3 bits;  conditional E-value: 1.4e-05
                                   HHHHHHHHHHTT--H.HHHHHHHHHHHSSHHHHHHHHHHHHHHHTTSSHHHHHC....T-TT.TS-HHHHHHHHHHHHHT- CS
                         T2SSF   1 flrqlatllsaGvpl.veaLellaeeaengplaeelkriarrlraGgslseale....rtpssefpelvvqlirageeggn 76 
                                   f+r+l+   sa  +l  +aL+++  ++ +g l++ +++++rrl + ++  +a++     t+s  +     ++ ++++ g +
  gi|13541445|ref|NP_111133.1| 329 FIRSLSGSASARGNLlIDALKAIVMHD-FGILSKDVNKLYRRLLYRINSLKAWKmfsaDTGSHLIEIYSETYAESIDLGAD 408
                                   78888888887777526**********.**************************999866654446666666666666666 PP

                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHTTXXXXXXXXXXXXXXX CS
                         T2SSF  77 LaevLerlaeyleeerelrrkllaallepllllvvallvllill 120
                                     +  + ++e++e+   lr+++ ++ ++ + +++ + + l++ l
  gi|13541445|ref|NP_111133.1| 409 ALKSGMVISENFEKIVGLRKRKHSSVTSFVGIMYGITAGLAFSL 452
                                   66666666666666666666666666666666665555554444 PP

  == domain 5  score: -5.2 bits;  conditional E-value: 1
                                   XXXXXXXXXXXXXXX CS
                         T2SSF 107 lllvvallvllilla 121
                                   l+++++++v+   + 
  gi|13541445|ref|NP_111133.1| 527 LMIWIVSFVVYGTMY 541
                                   455555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (552 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       902  (0.0503096); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.67u 0.32s 00:00:00.99 Elapsed: 00:00:00.54
# Mc/sec: 3092.38
//
Query:       gi|13541446|ref|NP_111134.1|  [L=1202]
Description: TPR repeat-containing protein [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.1e-24   82.7   5.2      0.016   16.0   0.0   12.0 11  TPR_14       Tetratricopeptide repeat
    3.4e-23   81.9   5.5    8.6e-05   23.0   0.1    9.1  9  TPR_19       Tetratricopeptide repeat
    3.1e-16   59.7   0.7    1.9e-05   25.2   0.0    7.3  7  TPR_16       Tetratricopeptide repeat
    3.2e-12   46.5   8.2      0.058   13.6   0.1    6.9  7  ANAPC3       Anaphase-promoting complex, cyclosome, subunit 3
    1.6e-09   37.4   2.6      0.013   14.8   0.0    5.3  5  TPR_15       Tetratricopeptide repeat
    4.3e-09   35.8  28.7      0.016   15.3   0.0    9.4  9  TPR_2        Tetratricopeptide repeat
    6.1e-09   36.0   7.5        1.2    9.5   0.0    7.0  7  TPR_12       Tetratricopeptide repeat
    1.2e-05   25.6  14.4     0.0057   17.2   0.0    8.3  7  TPR_6        Tetratricopeptide repeat
      8e-05   22.3  13.9       0.19   11.6   0.0    6.6  6  TPR_1        Tetratricopeptide repeat
    9.5e-05   22.3  21.4     0.0052   16.7   0.3    7.9  7  Clathrin     Region in Clathrin and VPS
    0.00031   20.4   2.4        2.6    7.8   0.0    5.0  4  TPR_11       TPR repeat
    0.00039   20.4  26.9      0.075   13.3   0.1    8.4  8  TPR_8        Tetratricopeptide repeat
    0.00046   20.2   0.0       0.46   10.4   0.0    3.8  4  Wzy_C_2      Virulence factor membrane-bound polymerase, C-te
    0.00048   20.0   0.9        3.3    8.0   0.0    5.7  4  TPR_7        Tetratricopeptide repeat
     0.0013   19.2   0.0      0.016   15.7   0.0    2.8  2  BTAD         Bacterial transcriptional activator domain
     0.0032   17.2   1.0        0.4   10.4   0.3    3.6  3  TPR_21       Tetratricopeptide repeat-like domain
     0.0049   17.0   9.8         54    4.3   0.0    9.1  8  PPR          PPR repeat
  ------ inclusion threshold ------
       0.01   15.1   0.3       0.15   11.2   0.0    2.7  3  FAT          FAT domain
      0.025   13.9   0.0        5.6    6.2   0.1    3.6  3  TPR_MalT     MalT-like TPR region
       0.04   14.0   0.1       0.22   11.6   0.1    2.3  1  TPR_18       Tetratricopeptide repeat
      0.043   13.8   3.7          1    9.4   0.3    4.3  3  Mad3_BUB1_I  Mad3/BUB1 homology region 1
       0.11   13.3   0.4        2.2    9.1   0.1    3.3  2  DUF3349      Protein of unknown function (DUF3349)
       0.25   11.8   3.9       0.99    9.9   0.1    4.2  2  TPR_17       Tetratricopeptide repeat
       0.55   10.0   4.0         23    4.8   0.0    4.3  4  PPR_1        PPR repeat
        0.6   10.4   2.9        8.1    6.8   0.2    3.9  3  PqqD         Coenzyme PQQ synthesis protein D (PqqD)


Domain annotation for each model (and alignments):
>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       8.8   6.3e+03       5      27 ..     132     155 ..     129     166 .. 0.64
   2 ?    3.9   0.0      0.16   1.2e+02       3      42 ..     228     267 ..     226     269 .. 0.87
   3 !   12.9   0.0   0.00022      0.16       6      43 ..     265     302 ..     260     303 .. 0.88
   4 !   16.0   0.0   2.2e-05     0.016       5      44 .]     331     370 ..     327     370 .. 0.93
   5 ?    5.9   0.0     0.039        28       4      29 ..     575     600 ..     572     605 .. 0.82
   6 !   13.9   0.0   0.00011     0.077       4      33 ..     607     636 ..     604     644 .. 0.90
   7 ?   -0.6   0.0       4.7   3.4e+03       9      39 ..     705     735 ..     698     737 .. 0.80
   8 ?    4.4   0.0      0.12        84       6      32 ..     767     793 ..     763     799 .. 0.83
   9 !    8.8   0.1    0.0045       3.2       8      37 ..     890     919 ..     887     926 .. 0.89
  10 ?    3.5   0.2      0.22   1.6e+02      10      33 ..     926     949 ..     922     961 .. 0.89
  11 ?    0.2   0.0       2.7   1.9e+03      11      25 ..     995    1009 ..     991    1044 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 8.8
                        TPR_14   5 lalaeallalGdpde.Aiallrra 27 
                                    a+a +l   G+++e  ++++ ++
  gi|13541446|ref|NP_111134.1| 132 DAAALYLSKCGRYEEkIVQMYAER 155
                                   455666678899975377787776 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.16
                        TPR_14   3 allalaeallalGdpdeAiallrralalaPddaeawllla 42 
                                   + ++l++a l lG++    +l++  l+l P+d ++   la
  gi|13541446|ref|NP_111134.1| 228 LIKKLVQAALSLGEYTIGKELAKNGLKLKPADKDLMKWLA 267
                                   56799*************************9987766665 PP

  == domain 3  score: 12.9 bits;  conditional E-value: 0.00022
                        TPR_14   6 alaeallalGdpdeAiallrralalaPddaeawlllaq 43 
                                    la  l  +G++ eAi+ ++++l  +Pdd +a + l++
  gi|13541446|ref|NP_111134.1| 265 WLALCLSKSGNYGEAIETYKDLLTSYPDDIDATIDLMD 302
                                   56777899***********************9998876 PP

  == domain 4  score: 16.0 bits;  conditional E-value: 2.2e-05
                        TPR_14   5 lalaeallalGdpdeAiallrralalaPddaeawlllaql 44 
                                    +l +++ a+Gd  +A++l+++a +++P+++++ +++a++
  gi|13541446|ref|NP_111134.1| 331 IRLIQLMKASGDIGKAVELAKEAYKKFPSEDDVIIEYARI 370
                                   579999*******************************995 PP

  == domain 5  score: 5.9 bits;  conditional E-value: 0.039
                        TPR_14   4 llalaeallalGdpdeAiallrrala 29 
                                   l++  + +  +G++d+A +ll+r+ +
  gi|13541446|ref|NP_111134.1| 575 LYCFSSTFIDAGKLDDAYKLLQRYEK 600
                                   6677788999*************965 PP

  == domain 6  score: 13.9 bits;  conditional E-value: 0.00011
                        TPR_14   4 llalaeallalGdpdeAiallrralalaPd 33 
                                   +  +a++l+ +G+ +eA ++ ++a++l+P+
  gi|13541446|ref|NP_111134.1| 607 YFTYAKLLWKSGRNKEASRMVEKAIELFPN 636
                                   5679*************************7 PP

  == domain 7  score: -0.6 bits;  conditional E-value: 4.7
                        TPR_14   9 eallalGdpdeAiallrralalaPddaeawl 39 
                                   +++l + d  +A+++  r++++  +++++ +
  gi|13541446|ref|NP_111134.1| 705 DVYLKNKDIGDALKVSSRIISQSSESRDIAI 735
                                   48999***************99887777665 PP

  == domain 8  score: 4.4 bits;  conditional E-value: 0.12
                        TPR_14   6 alaeallalGdpdeAiallrralalaP 32 
                                   +++e+++  +++++Ai ++r+a++l+ 
  gi|13541446|ref|NP_111134.1| 767 EAGELMYSKRKYEDAISAFRKAIRLGV 793
                                   6788999999*************9865 PP

  == domain 9  score: 8.8 bits;  conditional E-value: 0.0045
                        TPR_14   8 aeallalGdpdeAiallrralalaPddaea 37 
                                   a+ ll+  ++deA+++lr++ +++ +daea
  gi|13541446|ref|NP_111134.1| 890 AKRLLNENKLDEALEILRQIHDTDESDAEA 919
                                   77789999********************98 PP

  == domain 10  score: 3.5 bits;  conditional E-value: 0.22
                        TPR_14  10 allalGdpdeAiallrralalaPd 33 
                                   +l+++G++ eA +++  a a++ d
  gi|13541446|ref|NP_111134.1| 926 VLRRQGKLTEAYEIAASAAAQCSD 949
                                   89***************9999865 PP

  == domain 11  score: 0.2 bits;  conditional E-value: 2.7
                        TPR_14   11 llalGdpdeAiallr 25  
                                    + +l ++d+A+++l 
  gi|13541446|ref|NP_111134.1|  995 MVELKQFDDAEEVLS 1009
                                    5678999***99996 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.1       1.4   9.7e+02      13      42 ..     214     243 ..     212     248 .. 0.85
   2 !   23.0   0.1   1.2e-07   8.6e-05      12      59 ..     247     294 ..     236     304 .. 0.88
   3 !    8.2   0.0    0.0051       3.6       3      35 ..     339     371 ..     338     379 .. 0.90
   4 !   17.0   0.0   8.8e-06    0.0063       2      57 ..     583     636 ..     582     643 .. 0.83
   5 ?   -0.3   0.0       2.2   1.5e+03       2      31 ..     708     737 ..     707     742 .. 0.86
   6 ?    0.9   0.0      0.92   6.6e+02       6      49 ..     744     786 ..     739     796 .. 0.70
   7 ?    2.8   0.0      0.24   1.8e+02       5      48 ..     776     818 ..     765     825 .. 0.74
   8 !   15.5   0.7   2.5e-05     0.018       1      51 [.     893     943 ..     893     950 .. 0.91
   9 ?    4.6   0.0     0.063        46       5      49 ..     968    1009 ..     964    1012 .. 0.69

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 1.4
                        TPR_19  13 lleqalqedpknaearllLAeallalgqld 42 
                                   +l  al+ d  +a++   L++a l+lg+++
  gi|13541446|ref|NP_111134.1| 214 ALDFALKIDISDADLIKKLVQAALSLGEYT 243
                                   5666788888899***************96 PP

  == domain 2  score: 23.0 bits;  conditional E-value: 1.2e-07
                        TPR_19  12 alleqalqedpknaearllLAeallalgqldeAealLdalpeedpdda 59 
                                   +l ++ l+ +p + ++  +LA +l ++g++ eA+++ ++l+ ++pdd 
  gi|13541446|ref|NP_111134.1| 247 ELAKNGLKLKPADKDLMKWLALCLSKSGNYGEAIETYKDLLTSYPDDI 294
                                   6788999***************************************84 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.0051
                        TPR_19   3 aegdyaeAlalleqalqedpknaearllLAeal 35 
                                   a+gd   A++l ++a+++ p  +++ + +A++ 
  gi|13541446|ref|NP_111134.1| 339 ASGDIGKAVELAKEAYKKFPSEDDVIIEYARIV 371
                                   68****************************975 PP

  == domain 4  score: 17.0 bits;  conditional E-value: 8.8e-06
                        TPR_19   2 laegdyaeAlalleqalqedpknaearl..lLAeallalgqldeAealLdalpeedpd 57 
                                   +++g++++A +ll++    + k  +  +   +A++l+++g+ +eA ++++++ e +p+
  gi|13541446|ref|NP_111134.1| 583 IDAGKLDDAYKLLQR----YEKEVDPFYyfTYAKLLWKSGRNKEASRMVEKAIELFPN 636
                                   799************....5555555553556**********************9998 PP

  == domain 5  score: -0.3 bits;  conditional E-value: 2.2
                        TPR_19   2 laegdyaeAlalleqalqedpknaearllL 31 
                                   l+++d  +Al+  +++++++ ++ ++++ +
  gi|13541446|ref|NP_111134.1| 708 LKNKDIGDALKVSSRIISQSSESRDIAIHY 737
                                   7899**************999998888765 PP

  == domain 6  score: 0.9 bits;  conditional E-value: 0.92
                        TPR_19   6 dyaeAlalleqalqedpknaearllLAeallalgqldeAealLd 49 
                                   d+++Ala++++ ++  ++ +e+     e++++   +++A+ +  
  gi|13541446|ref|NP_111134.1| 744 DLDAALAFMKNNIDTFNGKEELIE-AGELMYSKRKYEDAISAFR 786
                                   788888888886677666666666.6777777777777776554 PP

  == domain 7  score: 2.8 bits;  conditional E-value: 0.24
                        TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAealL 48 
                                    +y++A++++++a+     n+     + + l+++g ++eAe+l+
  gi|13541446|ref|NP_111134.1| 776 RKYEDAISAFRKAIRLGV-NPLSIPHYLDSLIETGSYAEAEDLV 818
                                   489999999999876644.3333334779999999999999886 PP

  == domain 8  score: 15.5 bits;  conditional E-value: 2.5e-05
                        TPR_19   1 llaegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdal 51 
                                   ll e++++eAl++l+q+ + d  +aea +   ++l  +g l+eA ++ + +
  gi|13541446|ref|NP_111134.1| 893 LLNENKLDEALEILRQIHDTDESDAEASIMTTDVLRRQGKLTEAYEIAASA 943
                                   567899***********************99*************9997766 PP

  == domain 9  score: 4.6 bits;  conditional E-value: 0.063
                        TPR_19    5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAealLd 49  
                                    g y + ++++++  +e+ +n       ++ +++l+q+d+Ae++L+
  gi|13541446|ref|NP_111134.1|  968 GMYSQIVKIFKK-RKEKDNNVIPY--VVKSMVELKQFDDAEEVLS 1009
                                    566667777777.33333333333..488899***********97 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.0   2.7e-08   1.9e-05       3      67 ..     232     293 ..     230     294 .. 0.97
   2 ?    2.1   0.0      0.45   3.2e+02      10      30 ..     340     360 ..     336     384 .. 0.83
   3 ?    6.4   0.1     0.021        15       7      61 ..     582     631 ..     580     636 .. 0.81
   4 ?   -1.8   0.0       7.2   5.2e+03       6      36 ..     706     736 ..     705     740 .. 0.77
   5 ?    6.6   0.0     0.017        12       9      27 ..     774     792 ..     767     821 .. 0.68
   6 !    9.0   0.0    0.0031       2.2       4      62 ..     890     946 ..     888     951 .. 0.85
   7 ?   -1.4   0.0       5.3   3.8e+03       9      22 ..     997    1010 ..     996    1039 .. 0.61

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 2.7e-08
                        TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67 
                                   l +aal +g+y+   ++++  lk+    P++ + + +l++++ + g++ eA++ y+ +l+ +pd+
  gi|13541446|ref|NP_111134.1| 232 LVQAALSLGEYTIGKELAKNGLKLK---PADKDLMKWLALCLSKSGNYGEAIETYKDLLTSYPDD 293
                                   7899*********************...***********************************98 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.45
                        TPR_16  10 agdyddAaaaleaalkrdpss 30 
                                   +gd  +A++++++a k++ps+
  gi|13541446|ref|NP_111134.1| 340 SGDIGKAVELAKEAYKKFPSE 360
                                   688889999999999999554 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.021
                        TPR_16   7 alragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraal 61 
                                   +++ag+ ddA ++l+++ k    +P+    ++ ++ ++++ gr +eA   +++a+
  gi|13541446|ref|NP_111134.1| 582 FIDAGKLDDAYKLLQRYEKEV--DPF---YYFTYAKLLWKSGRNKEASRMVEKAI 631
                                   57999************9999..688...99999999999999999855555555 PP

  == domain 4  score: -1.8 bits;  conditional E-value: 7.2
                        TPR_16   6 aalragdyddAaaaleaalkrdpssPdaaeA 36 
                                    +l+++d  dA+++  + + + ++s d a  
  gi|13541446|ref|NP_111134.1| 706 VYLKNKDIGDALKVSSRIISQSSESRDIAIH 736
                                   69999*******9988888888777665555 PP

  == domain 5  score: 6.6 bits;  conditional E-value: 0.017
                        TPR_16   9 ragdyddAaaaleaalkrd 27 
                                     ++y+dA+ a++ a++++
  gi|13541446|ref|NP_111134.1| 774 SKRKYEDAISAFRKAIRLG 792
                                   3456************998 PP

  == domain 6  score: 9.0 bits;  conditional E-value: 0.0031
                        TPR_16   4 araalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAa.alyraalr 62 
                                   a+ +l+ ++ d+A++ l++  + d     +aeA+    d++ rqg l+eA   +  aa++
  gi|13541446|ref|NP_111134.1| 890 AKRLLNENKLDEALEILRQIHDTD---ESDAEASIMTTDVLRRQGKLTEAYeIAASAAAQ 946
                                   7889999*******9999999999...999********************9555555544 PP

  == domain 7  score: -1.4 bits;  conditional E-value: 5.3
                        TPR_16    9 ragdyddAaaalea 22  
                                    +++++ddA+++l  
  gi|13541446|ref|NP_111134.1|  997 ELKQFDDAEEVLSS 1010
                                    56778888876643 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 ?   -2.4   0.0       7.9   5.7e+03      33      81 ..      92     140 ..      90     141 .. 0.77
   2 !   10.3   0.1   0.00089      0.64      19      53 ..     256     291 ..     230     320 .. 0.69
   3 !   11.7   0.1   0.00032      0.23      22      81 ..     571     629 ..     564     630 .. 0.91
   4 ?   -2.0   0.0       6.2   4.5e+03      32      54 ..     706     729 ..     705     738 .. 0.65
   5 !    7.0   0.0    0.0092       6.6      30      80 ..     769     819 ..     748     821 .. 0.86
   6 !   13.6   0.1     8e-05     0.058       2      58 ..     896     952 ..     895     961 .. 0.92
   7 ?    1.3   0.0      0.58   4.2e+02      33      80 ..     964    1009 ..     962    1011 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 7.9
                                   HHHTT-HHHHHHHHHCTSHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                        ANAPC3  33 lylngqykrAyellrkaklnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                   ly+ng y+   +++ + +  ++   +  l+  ++  +++y+ A   L+k
  gi|13541446|ref|NP_111134.1|  92 LYKNGYYDDVVKIITSDNYFCSIDSIISLLVSSSGHIERYDAAALYLSK 140
                                   7999999999999998888888888887777777788888877766665 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00089
                                   HH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHH CS
                        ANAPC3  19 etespedayllAlclylngqykrAyellrka.klns 53 
                                   ++ + +   +lAlcl ++g+y +A+e ++++  +++
  gi|13541446|ref|NP_111134.1| 256 KPADKDLMKWLALCLSKSGNYGEAIETYKDLlTSYP 291
                                   445555556899999999999999998888755555 PP

  == domain 3  score: 11.7 bits;  conditional E-value: 0.00032
                                   -HHHHHHHHHHHHHTT-HHHHHHHHHCTSHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                        ANAPC3  22 spedayllAlclylngqykrAyellrkaklnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                   +p  +y ++ ++  +g+ + Ay+ll+++ +++ ++ + +++A+ l k ++ +eA +  ek
  gi|13541446|ref|NP_111134.1| 571 RPRYLYCFSSTFIDAGKLDDAYKLLQRY-EKEVDPFYYFTYAKLLWKSGRNKEASRMVEK 629
                                   566778889999****************.889999*******************999887 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 6.2
                                   HHHHTT-HHHHHHHHHCT.SHHHC CS
                        ANAPC3  32 clylngqykrAyellrka.klnsk 54 
                                   ++++n++   A+++ ++   + s+
  gi|13541446|ref|NP_111134.1| 706 VYLKNKDIGDALKVSSRIiSQSSE 729
                                   688888888888888777333333 PP

  == domain 5  score: 7.0 bits;  conditional E-value: 0.0092
                                   HHHHHHTT-HHHHHHHHHCTSHHHC-HHHHHHHHHHHHHTT-HHHHHHHH- CS
                        ANAPC3  30 AlclylngqykrAyellrkaklnskslgcrylfAqcllkLkkyeeAiaaLe 80 
                                   ++ +y+  +y+ A+  +rka   + ++ +   +  +l++ ++y eA+++ +
  gi|13541446|ref|NP_111134.1| 769 GELMYSKRKYEDAISAFRKAIRLGVNPLSIPHYLDSLIETGSYAEAEDLVG 819
                                   7889****************66666677889999*************9987 PP

  == domain 6  score: 13.6 bits;  conditional E-value: 8e-05
                                   TT-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCTSHHHC-HHH CS
                        ANAPC3   2 qnnyknAiflaerllaaetespedayllAlclylngqykrAyellrkaklnskslgc 58 
                                    n++++A+ ++  ++ ++  ++e++ +   +l ++g+ ++Aye++ +a  ++++ +c
  gi|13541446|ref|NP_111134.1| 896 ENKLDEALEILRQIHDTDESDAEASIMTTDVLRRQGKLTEAYEIAASAAAQCSDTEC 952
                                   57899**********99999****************************888888887 PP

  == domain 7  score: 1.3 bits;  conditional E-value: 0.58
                                    HHHTT-HHHHHHHHHCTSHHHC-HHHHHHHHHHHHHTT-HHHHHHHH- CS
                        ANAPC3   33 lylngqykrAyellrkaklnskslgcrylfAqcllkLkkyeeAiaaLe 80  
                                    +y +g y +  ++++k k+  k+ ++     ++ ++Lk++++A+ +L+
  gi|13541446|ref|NP_111134.1|  964 MYDLGMYSQIVKIFKKRKE--KDNNVIPYVVKSMVELKQFDDAEEVLS 1009
                                    5777788888888888833..333334444589999*******99997 PP

>> TPR_15  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   1.8e-05     0.013     106     265 ..     155     311 ..     120     316 .. 0.88
   2 ?    4.1   0.0     0.031        22      75     109 ..     324     359 ..     317     397 .. 0.85
   3 !    9.3   0.0   0.00081      0.58     133     178 ..     595     636 ..     563     650 .. 0.79
   4 ?   -0.3   0.0       0.7     5e+02      14     174 ..     768     790 ..     737     821 .. 0.51
   5 ?    3.5   0.3     0.048        34      58     138 ..     894     982 ..     844    1008 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.8e-05
                        TPR_15 106 rfrsprlLssalellerakdydriaellksleeeeaaeqsaafllaraelyrqegqtdaAlrdyreAlalapdsselraal 186
                                   r r+p+  ++ +e + + +  +   +++ ++++    eqs+++l  +++   +++++d    ++  Al+ +  +++l+++l
  gi|13541446|ref|NP_111134.1| 155 RNRNPDTTKAIIEGYVNGNHCEMAIKFIMEIMS---REQSELYLGPLINCSIKTDDKDGMRAALDFALKIDISDADLIKKL 232
                                   666777777777777776666666566655554...479****************************************** PP

                        TPR_15 187 lWlliDlgrraeLrellkawkaraesdasLwgplaaAlllLgrpkkALeylrkqakenrkdplwllaYADaleqagrad 265
                                   + + + lg+++  +el k+  + + +d++L++ la  l++ g++ +A e ++  + + ++d+   +   D l+  g+a 
  gi|13541446|ref|NP_111134.1| 233 VQAALSLGEYTIGKELAKNGLKLKPADKDLMKWLALCLSKSGNYGEAIETYKDLLTSYPDDIDATIDLMDLLYEHGKAS 311
                                   ***********99******99999******************************************9999999999875 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.031
                        TPR_15  75 karaedyerliel.lydaepkeaarlaekgwrrfrs 109
                                   + r+ dy rli+l     +  +a++la +++++f s
  gi|13541446|ref|NP_111134.1| 324 QLRPLDYIRLIQLmKASGDIGKAVELAKEAYKKFPS 359
                                   557889999999977888999999999999998865 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.00081
                        TPR_15 133 lksleeeeaaeqsaafllaraelyrqegqtdaAlrdyreAlalapd 178
                                   l++     + e ++++++ +a+l  + g++++A r++++A++l+p+
  gi|13541446|ref|NP_111134.1| 595 LQR----YEKEVDPFYYFTYAKLLWKSGRNKEASRMVEKAIELFPN 636
                                   433....3445799****************************9997 PP

  == domain 4  score: -0.3 bits;  conditional E-value: 0.7
                        TPR_15  14 latllykqgdvkkAlevLkeaaqkaapskdteyWrtladLAwalqqedearkAyrqLlasgkaraedyerliellydaepk 94 
                                   + +l+y ++++                                                                      
  gi|13541446|ref|NP_111134.1| 768 AGELMYSKRKY---------------------------------------------------------------------- 778
                                   33333333333...................................................................... PP

                        TPR_15  95 eaarlaekgwrrfrsprlLssalellerakdydriaellksleeeeaaeqsaafllaraelyrqegqtdaAlrdyreAla 174
                                                                                                       ++A+ ++r+A++
  gi|13541446|ref|NP_111134.1| 779 --------------------------------------------------------------------EDAISAFRKAIR 790
                                   ....................................................................333333333333 PP

  == domain 5  score: 3.5 bits;  conditional E-value: 0.048
                        TPR_15  58 qqedearkAyrqLlasgkaraedyerlie...l.lydaepkeaarlaekgwrrfrsprl...Lssale.llerakdydria 130
                                    +e++ ++A++ L ++ + +++d+e+ i      +++ +  ea+++a ++  +  +++    L++ ++ ++++++ y++i+
  gi|13541446|ref|NP_111134.1| 894 LNENKLDEALEILRQIHDTDESDAEASIMttdVlRRQGKLTEAYEIAASAAAQCSDTECekeLYRRIYsIMYDLGMYSQIV 974
                                   455556666666666666666666655431124357888888999988888888776532225555551568888888888 PP

                        TPR_15 131 ellkslee 138
                                   +++k+ +e
  gi|13541446|ref|NP_111134.1| 975 KIFKKRKE 982
                                   88888554 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       8.6   6.2e+03      10      33 ..     235     258 ..     234     259 .. 0.84
   2 !   15.1   0.0   2.6e-05     0.018       5      34 .]     264     293 ..     261     293 .. 0.92
   3 ?    2.9   0.0      0.21   1.5e+02      13      32 ..     339     358 ..     335     360 .. 0.88
   4 ?   -0.4   0.1       2.4   1.7e+03       3      26 ..     574     597 ..     572     600 .. 0.78
   5 !   15.3   0.0   2.2e-05     0.016       2      33 ..     605     636 ..     604     637 .. 0.95
   6 !   14.7   0.2   3.5e-05     0.025       4      30 ..     765     791 ..     763     792 .. 0.91
   7 ?    0.7   0.0         1   7.4e+02       8      27 ..     890     909 ..     888     916 .. 0.80
   8 ?   -1.9   0.1       6.8   4.9e+03      10      22 ..     926     938 ..     925     946 .. 0.83
   9 ?   -0.7   0.2         3   2.2e+03       3      18 ..    1024    1039 ..    1023    1040 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 8.6
                         TPR_2  10 ayyklgdyeeAleafekAleldPn 33 
                                   a++ lg+y   +e+ +  l+l P 
  gi|13541446|ref|NP_111134.1| 235 AALSLGEYTIGKELAKNGLKLKPA 258
                                   678899999999999999999996 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 2.6e-05
                         TPR_2   5 ynlGlayyklgdyeeAleafekAleldPnn 34 
                                    +l+l++ k+g+y eA+e ++  l  +P++
  gi|13541446|ref|NP_111134.1| 264 KWLALCLSKSGNYGEAIETYKDLLTSYPDD 293
                                   68**********************999986 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.21
                         TPR_2  13 klgdyeeAleafekAleldP 32 
                                   ++gd  +A+e+ ++A +  P
  gi|13541446|ref|NP_111134.1| 339 ASGDIGKAVELAKEAYKKFP 358
                                   689**************999 PP

  == domain 4  score: -0.4 bits;  conditional E-value: 2.4
                         TPR_2   3 alynlGlayyklgdyeeAleafek 26 
                                   +ly+     + +g++++A +++++
  gi|13541446|ref|NP_111134.1| 574 YLYCFSSTFIDAGKLDDAYKLLQR 597
                                   566666777889999999999987 PP

  == domain 5  score: 15.3 bits;  conditional E-value: 2.2e-05
                         TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPn 33 
                                    +++  +++++k+g+ +eA +  ekA+el Pn
  gi|13541446|ref|NP_111134.1| 605 FYYFTYAKLLWKSGRNKEASRMVEKAIELFPN 636
                                   68*****************************8 PP

  == domain 6  score: 14.7 bits;  conditional E-value: 3.5e-05
                         TPR_2   4 lynlGlayyklgdyeeAleafekAlel 30 
                                   l + G++ y + +ye+A+ af+kA++l
  gi|13541446|ref|NP_111134.1| 765 LIEAGELMYSKRKYEDAISAFRKAIRL 791
                                   77889********************98 PP

  == domain 7  score: 0.7 bits;  conditional E-value: 1
                         TPR_2   8 GlayyklgdyeeAleafekA 27 
                                   ++ +++ ++++eAle +++ 
  gi|13541446|ref|NP_111134.1| 890 AKRLLNENKLDEALEILRQI 909
                                   66788999******998876 PP

  == domain 8  score: -1.9 bits;  conditional E-value: 6.8
                         TPR_2  10 ayyklgdyeeAle 22 
                                   +++++g++ eA e
  gi|13541446|ref|NP_111134.1| 926 VLRRQGKLTEAYE 938
                                   6899*****9976 PP

  == domain 9  score: -0.7 bits;  conditional E-value: 3
                         TPR_2    3 alynlGlayyklgdye 18  
                                     + n+G+ + +l++y+
  gi|13541446|ref|NP_111134.1| 1024 SYINQGRYLDRLNKYA 1039
                                    6888899999998886 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.0    0.0025       1.8      51      73 ..     266     288 ..     260     298 .. 0.64
   2 ?   -0.4   0.0       1.9   1.4e+03      56      73 ..     338     355 ..     332     359 .. 0.84
   3 !    9.5   0.0    0.0016       1.2      47      76 ..     606     635 ..     585     636 .. 0.84
   4 ?    3.7   0.1      0.11        78      51      74 ..     768     791 ..     764     792 .. 0.76
   5 !    8.6   0.4    0.0031       2.2      26      71 ..     899     943 ..     896     949 .. 0.86
   6 ?    5.3   0.1     0.033        23      12      47 ..     926     960 ..     925     979 .. 0.74
   7 ?    1.2   0.0      0.65   4.6e+02      43      62 ..    1020    1039 ..     997    1040 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0025
                        TPR_12  51 LgrlyralgryeeAlelleeala 73 
                                   L+ +++++g+y eA+e +++ l 
  gi|13541446|ref|NP_111134.1| 266 LALCLSKSGNYGEAIETYKDLLT 288
                                   45555566666666666555554 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.9
                        TPR_12  56 ralgryeeAlelleeala 73 
                                    a+g+  +A+el +ea++
  gi|13541446|ref|NP_111134.1| 338 KASGDIGKAVELAKEAYK 355
                                   578999999999999986 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.0016
                        TPR_12  47 tlrnLgrlyralgryeeAlelleealaiae 76 
                                   ++++++ l++++gr +eA ++ e+a+++++
  gi|13541446|ref|NP_111134.1| 606 YYFTYAKLLWKSGRNKEASRMVEKAIELFP 635
                                   6999**********************9976 PP

  == domain 4  score: 3.7 bits;  conditional E-value: 0.11
                        TPR_12  51 LgrlyralgryeeAlelleealai 74 
                                    g+l +   +ye+A++++++a+++
  gi|13541446|ref|NP_111134.1| 768 AGELMYSKRKYEDAISAFRKAIRL 791
                                   577766666999999999999875 PP

  == domain 5  score: 8.6 bits;  conditional E-value: 0.0031
                        TPR_12  26 lekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleea 71 
                                   l++alei r+++++d +  a++ +   +++r++g++ eA e+   a
  gi|13541446|ref|NP_111134.1| 899 LDEALEILRQIHDTD-ESDAEASIMTTDVLRRQGKLTEAYEIAASA 943
                                   789********9876.599*******************97776665 PP

  == domain 6  score: 5.3 bits;  conditional E-value: 0.033
                        TPR_12  12 vlrrlgrydeAlellekaleiarrllGpdhpltatt 47 
                                   vlrr+g+++eA e+   a ++++ + +++++l+ ++
  gi|13541446|ref|NP_111134.1| 926 VLRRQGKLTEAYEIAASAAAQCSDT-ECEKELYRRI 960
                                   89******************99655.4554444444 PP

  == domain 7  score: 1.2 bits;  conditional E-value: 0.65
                        TPR_12   43 ltattlrnLgrlyralgrye 62  
                                    +++++++n gr++++l++y+
  gi|13541446|ref|NP_111134.1| 1020 NALESYINQGRYLDRLNKYA 1039
                                    6899*************996 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   7.9e-06    0.0057       5      32 ..     265     292 ..     265     293 .. 0.95
   2 ?    1.3   0.0      0.94   6.8e+02       9      31 ..     336     358 ..     319     360 .. 0.76
   3 ?   -1.4   0.1       6.7   4.8e+03      13      26 ..     585     598 ..     580     601 .. 0.81
   4 ?   -0.4   0.0       3.2   2.3e+03       7      32 ..     611     636 ..     607     636 .. 0.71
   5 ?   -0.2   0.0       2.8     2e+03      22      32 ..     670     680 ..     661     680 .. 0.91
   6 ?    5.7   0.1     0.038        27       6      28 ..     768     790 ..     765     791 .. 0.88
   7 ?    1.5   0.0      0.83     6e+02      12      27 ..     895     910 ..     876     913 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 7.9e-06
                                   HHHHHHHHHHHHHHHHHHHHHHHHH-TT CS
                         TPR_6   5 klalsyrklgdtdkAlealerlikeYPd 32 
                                   +lal++ k g++ +A+e++++l+++YPd
  gi|13541446|ref|NP_111134.1| 265 WLALCLSKSGNYGEAIETYKDLLTSYPD 292
                                   79******77*****************9 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.94
                                   HHHHHHHHHHHHHHHHHHHHH-T CS
                         TPR_6   9 syrklgdtdkAlealerlikeYP 31 
                                   ++++ gd  kA+e+ ++  k++P
  gi|13541446|ref|NP_111134.1| 336 LMKASGDIGKAVELAKEAYKKFP 358
                                   44444788999999999999998 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 6.7
                                   HHHHHHHHHHHHHH CS
                         TPR_6  13 lgdtdkAlealerl 26 
                                   +g+ d+A ++l+r 
  gi|13541446|ref|NP_111134.1| 585 AGKLDDAYKLLQRY 598
                                   68999******996 PP

  == domain 4  score: -0.4 bits;  conditional E-value: 3.2
                                   HHHHHHHHHHHHHHHHHHHHHHH-TT CS
                         TPR_6   7 alsyrklgdtdkAlealerlikeYPd 32 
                                   a+++ k g+  +A ++ e+ i+ +P+
  gi|13541446|ref|NP_111134.1| 611 AKLLWKSGRNKEASRMVEKAIELFPN 636
                                   66666655777888888888888886 PP

  == domain 5  score: -0.2 bits;  conditional E-value: 2.8
                                   HHHHHHHH-TT CS
                         TPR_6  22 alerlikeYPd 32 
                                    l++li+++Pd
  gi|13541446|ref|NP_111134.1| 670 VLQSLIEDHPD 680
                                   79********8 PP

  == domain 6  score: 5.7 bits;  conditional E-value: 0.038
                                   HHHHHHHHHHHHHHHHHHHHHHH CS
                         TPR_6   6 lalsyrklgdtdkAlealerlik 28 
                                   +++++++  ++++A+ a+++ i+
  gi|13541446|ref|NP_111134.1| 768 AGELMYSKRKYEDAISAFRKAIR 790
                                   699999966***********996 PP

  == domain 7  score: 1.5 bits;  conditional E-value: 0.83
                                   HHHHHHHHHHHHHHHH CS
                         TPR_6  12 klgdtdkAlealerli 27 
                                   + ++ d+Ale+l+++ 
  gi|13541446|ref|NP_111134.1| 895 NENKLDEALEILRQIH 910
                                   3468899999999876 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.0   0.00027      0.19       6      29 ..     265     288 ..     261     293 .. 0.82
   2 ?   -2.4   0.2       7.2   5.1e+03      15      26 ..     586     597 ..     582     600 .. 0.58
   3 ?    4.6   0.0     0.045        32      10      33 ..     613     636 ..     611     637 .. 0.89
   4 !   10.4   0.0   0.00064      0.46      12      30 ..     773     791 ..     769     792 .. 0.91
   5 ?   -1.3   0.0       3.1   2.2e+03      12      24 ..     894     906 ..     893     915 .. 0.77
   6 ?   -2.8   0.1       9.8     7e+03      14      22 ..     998    1006 ..     997    1007 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00027
                                   HHHHHHHHTT-HHHHHHHHHHHHH CS
                         TPR_1   6 nlGnayfklgkydeAleyyekALe 29 
                                    l++++ k g+y eA+e y+  L+
  gi|13541446|ref|NP_111134.1| 265 WLALCLSKSGNYGEAIETYKDLLT 288
                                   69*****************96655 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 7.2
                                   T-HHHHHHHHHH CS
                         TPR_1  15 gkydeAleyyek 26 
                                   gk+d+A +  ++
  gi|13541446|ref|NP_111134.1| 586 GKLDDAYKLLQR 597
                                   566666555544 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.045
                                   HHHHTT-HHHHHHHHHHHHHHSTT CS
                         TPR_1  10 ayfklgkydeAleyyekALelnPn 33 
                                   ++ k g+ +eA    ekA+el Pn
  gi|13541446|ref|NP_111134.1| 613 LLWKSGRNKEASRMVEKAIELFPN 636
                                   67899999***************8 PP

  == domain 4  score: 10.4 bits;  conditional E-value: 0.00064
                                   HHTT-HHHHHHHHHHHHHH CS
                         TPR_1  12 fklgkydeAleyyekALel 30 
                                   +++ ky++A+ +++kA++l
  gi|13541446|ref|NP_111134.1| 773 YSKRKYEDAISAFRKAIRL 791
                                   5788*************87 PP

  == domain 5  score: -1.3 bits;  conditional E-value: 3.1
                                   HHTT-HHHHHHHH CS
                         TPR_1  12 fklgkydeAleyy 24 
                                   ++ +k+deAle  
  gi|13541446|ref|NP_111134.1| 894 LNENKLDEALEIL 906
                                   567999***9955 PP

  == domain 6  score: -2.8 bits;  conditional E-value: 9.8
                                    TT-HHHHHH CS
                         TPR_1   14 lgkydeAle 22  
                                    l+++d+A+e
  gi|13541446|ref|NP_111134.1|  998 LKQFDDAEE 1006
                                    89*****97 PP

>> Clathrin  Region in Clathrin and VPS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.3   7.2e-06    0.0052      10     137 ..      54     184 ..      52     190 .. 0.74
   2 ?   -0.0   0.0         1   7.4e+02       3      57 ..     155     207 ..     153     215 .. 0.80
   3 !    7.0   0.3    0.0068       4.9       3     100 ..     222     324 ..     220     356 .. 0.74
   4 ?    3.0   0.2      0.12        85      59     133 ..     407     480 ..     397     486 .. 0.77
   5 ?   -0.5   0.0       1.5   1.1e+03      17      66 ..     582     628 ..     580     638 .. 0.81
   6 ?    1.9   0.3      0.26   1.8e+02      76      96 ..     889     909 ..     827     951 .. 0.60
   7 ?    1.4   1.2      0.37   2.7e+02      63      63 ..     929     929 ..     877    1033 .. 0.54

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 7.2e-06
                                   CCCCHHHHHCTT-HHHHCHHHCCHHHCHTS--HHHHHHHHHHHHHTT-HHHHHHTTSS---.S-TTHHHHHH.HT-S...S CS
                      Clathrin  10 lsrvvklfeeaglleelleyLekvlkedskenpalqtallelyakyddpqeleeflkknnn.ydlekvaklc.ekad...l 85 
                                   +s +v++++++++l+el+ +L +++   +++   l+t++++ly     ++++ +++++ n+ + ++++++l+ +  +    
  gi|13541446|ref|NP_111134.1|  54 VSVLVRNVSDENQLRELITLLDSIV---PQNKGLLETKVVDLYKNGY-YDDVVKIITSDNYfCSIDSIISLLvSSSGhieR 130
                                   789**********************...8999***********7776.99*******88887*********9633331225 PP

                                   HHHHHHHHHTTXTHSSHSS.X.SSSSHCSCHHHHTTTTTXXSHHHHHHHHHHHS CS
                      Clathrin  86 yeeavilykkinefkkais.l.lkklkdfddaieyaakvsnpelwekllealld 137
                                   y+ a + ++k +++++ i+ + ++++ ++d    +++   n +  e ++++ ++
  gi|13541446|ref|NP_111134.1| 131 YDAAALYLSKCGRYEEKIVqMyAERNRNPDTTKAIIEGYVNGNHCEMAIKFIME 184
                                   566666666666666655557777777766655555555555555555555555 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 1
                                   CCCTTS-CCCCHHHHHCTT-HHHHCHHHCCHHHCHTS--HHHH.HHHHHHHHHTT- CS
                      Clathrin   3 eltdpidlsrvvklfeeaglleelleyLekvlkedskenpalq.tallelyakydd 57 
                                    +++p+  +++++ + + ++ e+++++  +++   s+e+++l+   l+ + +k+dd
  gi|13541446|ref|NP_111134.1| 155 RNRNPDTTKAIIEGYVNGNHCEMAIKFIMEIM---SREQSELYlGPLINCSIKTDD 207
                                   689999999***********************...666666663568888888887 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.0068
                                   CCCTTS-CCCCHHHHHCTT-HHHHCHHHCCHHHCHTS--HHHHHHHHHHHHHTT-HHHHHHTTS.S---....S-.TTHHH CS
                      Clathrin   3 eltdpidlsrvvklfeeaglleelleyLekvlkedskenpalqtallelyakyddpqeleeflk.knnn....yd.lekva 77 
                                   +++d++ ++++v+++ + g ++  +e+ +++lk  ++++++l   l+ ++ k++++ e+ e  k  +++    +d ++ + 
  gi|13541446|ref|NP_111134.1| 222 DISDADLIKKLVQAALSLGEYTIGKELAKNGLK-LKPADKDLMKWLALCLSKSGNYGEAIETYKdLLTSypddIDaTIDLM 301
                                   5788999999**********************5.66788**************8888888777764444232544356888 PP

                                   HHHHT-SSHHHHHHHHHTTXTHS CS
                      Clathrin  78 klcekadlyeeavilykkinefk 100
                                   +l+ ++++  e++++  ki++++
  gi|13541446|ref|NP_111134.1| 302 DLLYEHGKASEYLYVVEKIGRNQ 324
                                   9999****99*999999977653 PP

  == domain 4  score: 3.0 bits;  conditional E-value: 0.12
                                   HHHHHTTSS---S-TTHHHHHHHT-SSHHHHHHHHHTTXTHSSHSSXSSSSHCSCHHH.HTTTTTXXSHHHHHHHH CS
                      Clathrin  59 qeleeflkknnnydlekvaklcekadlyeeavilykkinefkkaisllkklkdfddai.eyaakvsnpelweklle 133
                                   ++ eef+k++++ d e v +   k +l   +++ +  +++f+k+++  k+l d +d +  ++ kv+++e++e l +
  gi|13541446|ref|NP_111134.1| 407 ERYEEFVKRFESSDNEDVKDEF-KGKLA-ASFVYLGFFDNFNKLVKENKNLLDDPDTVdSVFYKVRDKEALEILNS 480
                                   6889999999999999999974.44455.78888888******999445555555555999999999999998776 PP

  == domain 5  score: -0.5 bits;  conditional E-value: 1.5
                                   HHCTT-HHHHCHHHCCHHHCHTS--HHHHHHHHHHHHHTT-HHHHHHTTS CS
                      Clathrin  17 feeaglleelleyLekvlkedskenpalqtallelyakyddpqeleeflk 66 
                                   f +ag+l+ ++++L+      ++ +p ++  +++l+ k+++ +e+ ++++
  gi|13541446|ref|NP_111134.1| 582 FIDAGKLDDAYKLLQRYE---KEVDPFYYFTYAKLLWKSGRNKEASRMVE 628
                                   778899999999999999...45569999999999999988777776665 PP

  == domain 6  score: 1.9 bits;  conditional E-value: 0.26
                                   HHHHHHT-SSHHHHHHHHHTT CS
                      Clathrin  76 vaklcekadlyeeavilykki 96 
                                   +ak++ ++++ +ea+++++ i
  gi|13541446|ref|NP_111134.1| 889 IAKRLLNENKLDEALEILRQI 909
                                   333333333333333333333 PP

  == domain 7  score: 1.4 bits;  conditional E-value: 0.37
                                   H CS
                      Clathrin  63 e 63 
                                   +
  gi|13541446|ref|NP_111134.1| 929 R 929
                                   1 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.0    0.0041       2.9       6      30 ..     272     296 ..     270     308 .. 0.84
   2 !    7.8   0.0    0.0037       2.6       1      23 [.     769     791 ..     769     792 .. 0.88
   3 ?   -1.6   0.0       3.2   2.3e+03       7      19 ..     896     908 ..     891     919 .. 0.71
   4 ?   -0.5   0.0       1.4     1e+03       2      13 ..     925     936 ..     925     938 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0041
                        TPR_11   6 eqGkyeeAieaYkkAlkldPdnaea 30 
                                   + G+y eAie Yk  l   Pd+ +a
  gi|13541446|ref|NP_111134.1| 272 KSGNYGEAIETYKDLLTSYPDDIDA 296
                                   57***********999999998887 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0037
                        TPR_11   1 GdayyeqGkyeeAieaYkkAlkl 23 
                                   G + y++ kye+Ai a++kA++l
  gi|13541446|ref|NP_111134.1| 769 GELMYSKRKYEDAISAFRKAIRL 791
                                   55668999*************98 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 3.2
                        TPR_11   7 qGkyeeAieaYkk 19 
                                    +k++eA+e +++
  gi|13541446|ref|NP_111134.1| 896 ENKLDEALEILRQ 908
                                   689****997776 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 1.4
                        TPR_11   2 dayyeqGkyeeA 13 
                                   d+++ qGk++eA
  gi|13541446|ref|NP_111134.1| 925 DVLRRQGKLTEA 936
                                   7899*******9 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.2       6.8   4.9e+03       4      19 ..     131     146 ..     128     147 .. 0.55
   2 ?   -0.2   0.1       2.3   1.6e+03       7      34 .]     232     259 ..     231     259 .. 0.88
   3 !   12.1   0.0   0.00024      0.17       7      34 .]     266     293 ..     265     293 .. 0.93
   4 ?   -1.8   0.1       7.3   5.2e+03      18      25 ..     348     355 ..     339     356 .. 0.59
   5 !   13.3   0.1    0.0001     0.075       3      33 ..     606     636 ..     606     637 .. 0.95
   6 !    7.4   0.2    0.0083       5.9      13      30 ..     774     791 ..     766     791 .. 0.87
   7 ?   -1.6   0.0       6.1   4.3e+03      12      26 ..     894     908 ..     889     909 .. 0.86
   8 ?   -0.1   0.1       2.1   1.5e+03       2      18 ..    1023    1039 ..    1022    1042 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 6.8
                                   HHHHHHHHHHTT-HHH CS
                         TPR_8   4 yynlgsiylklgdyee 19 
                                   y   ++ ++k g+yee
  gi|13541446|ref|NP_111134.1| 131 YDAAALYLSKCGRYEE 146
                                   3334445566666665 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 2.3
                                   HHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                         TPR_8   7 lgsiylklgdyeeAkeyyekaleldpdn 34 
                                   l ++ l+lg+y   ke  +  l+l+p++
  gi|13541446|ref|NP_111134.1| 232 LVQAALSLGEYTIGKELAKNGLKLKPAD 259
                                   5678899******************985 PP

  == domain 3  score: 12.1 bits;  conditional E-value: 0.00024
                                   HHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                         TPR_8   7 lgsiylklgdyeeAkeyyekaleldpdn 34 
                                   l+++++k g+y eA+e+y+  l+  pd+
  gi|13541446|ref|NP_111134.1| 266 LALCLSKSGNYGEAIETYKDLLTSYPDD 293
                                   899*******************999985 PP

  == domain 4  score: -1.8 bits;  conditional E-value: 7.3
                                   HHHHHHHH CS
                         TPR_8  18 eeAkeyye 25 
                                   e Ake+y+
  gi|13541446|ref|NP_111134.1| 348 ELAKEAYK 355
                                   45666665 PP

  == domain 5  score: 13.3 bits;  conditional E-value: 0.0001
                                   HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                         TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                   +y+  +++++k g+ +eA    eka+el p+
  gi|13541446|ref|NP_111134.1| 606 YYFTYAKLLWKSGRNKEASRMVEKAIELFPN 636
                                   699*************************997 PP

  == domain 6  score: 7.4 bits;  conditional E-value: 0.0083
                                   HTT-HHHHHHHHHHHHHH CS
                         TPR_8  13 klgdyeeAkeyyekalel 30 
                                   ++ +ye A+++++ka++l
  gi|13541446|ref|NP_111134.1| 774 SKRKYEDAISAFRKAIRL 791
                                   6889************86 PP

  == domain 7  score: -1.6 bits;  conditional E-value: 6.1
                                   HHTT-HHHHHHHHHH CS
                         TPR_8  12 lklgdyeeAkeyyek 26 
                                   l+ ++++eA e +++
  gi|13541446|ref|NP_111134.1| 894 LNENKLDEALEILRQ 908
                                   68899******9987 PP

  == domain 8  score: -0.1 bits;  conditional E-value: 2.1
                                    CHHHHHHHHHHHTT-HH CS
                         TPR_8    2 eayynlgsiylklgdye 18  
                                    e+y n g+ ++ l++y 
  gi|13541446|ref|NP_111134.1| 1023 ESYINQGRYLDRLNKYA 1039
                                    899**********9997 PP

>> Wzy_C_2  Virulence factor membrane-bound polymerase, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0       1.3   9.1e+02     132     179 ..     248     296 ..     244     301 .. 0.80
   2 ?   -0.1   0.0         1   7.3e+02     127     179 ..     311     363 ..     306     370 .. 0.79
   3 !   10.4   0.0   0.00064      0.46     145     179 ..     606     640 ..     595     646 .. 0.89
   4 ?    3.2   0.0     0.099        71     107     168 ..     759     820 ..     746     830 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1.3
                       Wzy_C_2 132 larklihlsPepa.vierlilslallGdedeAeqilararalfpeedak 179
                                   la++ ++l+P  + +++ l+l+l  +G   eA  +++ +   +p++  +
  gi|13541446|ref|NP_111134.1| 248 LAKNGLKLKPADKdLMKWLALCLSKSGNYGEAIETYKDLLTSYPDDIDA 296
                                   566667777765415667899***********************98655 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1
                       Wzy_C_2 127 aaklalarklihlsPepavierlilslallGdedeAeqilararalfpeedak 179
                                    ++l + +k+ +++ +p  + rli++  ++Gd  +A    ++a + fp ed  
  gi|13541446|ref|NP_111134.1| 311 SEYLYVVEKIGRNQLRPLDYIRLIQLMKASGDIGKAVELAKEAYKKFPSEDDV 363
                                   55666666666666677788999********************99**999865 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.00064
                       Wzy_C_2 145 vierlilslallGdedeAeqilararalfpeedak 179
                                    +  ++ +l+ +G+ +eA +++++a+ lfp+ d++
  gi|13541446|ref|NP_111134.1| 606 YYFTYAKLLWKSGRNKEASRMVEKAIELFPNIDFH 640
                                   5668999***********************99876 PP

  == domain 4  score: 3.2 bits;  conditional E-value: 0.099
                       Wzy_C_2 107 frayadllelgllplspenlaaklalarklihlsPepavierlilslallGdedeAeqilar 168
                                   f+   +l e+g l+ s+ ++++ +++ rk+i+l   p  i  + +sl  +G  +eAe+ + r
  gi|13541446|ref|NP_111134.1| 759 FNGKEELIEAGELMYSKRKYEDAISAFRKAIRLGVNPLSIPHYLDSLIETGSYAEAEDLVGR 820
                                   78889999*************************************************98766 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.0    0.0046       3.3       5      26 ..     266     287 ..     266     295 .. 0.84
   2 ?    4.3   0.0     0.068        49      12      28 ..     775     791 ..     768     798 .. 0.76
   3 ?   -1.1   0.1       3.6   2.6e+03      11      33 ..     895     915 ..     893     918 .. 0.73
   4 ?   -1.8   0.0       6.1   4.3e+03      11      32 ..     966     985 ..     962     988 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0046
                         TPR_7   5 LarlysrlGdyeeAielyeqsL 26 
                                   La + s+ G+y eAie y+ +L
  gi|13541446|ref|NP_111134.1| 266 LALCLSKSGNYGEAIETYKDLL 287
                                   78999*************9854 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.068
                         TPR_7  12 lGdyeeAielyeqsLal 28 
                                    ++ye+Ai+ ++++++l
  gi|13541446|ref|NP_111134.1| 775 KRKYEDAISAFRKAIRL 791
                                   489**********5544 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 3.6
                         TPR_7  11 rlGdyeeAielyeqsLaltkdpe 33 
                                   ++++ +eA+e+++q    + d++
  gi|13541446|ref|NP_111134.1| 895 NENKLDEALEILRQ--IHDTDES 915
                                   578899******99..5555555 PP

  == domain 4  score: -1.8 bits;  conditional E-value: 6.1
                         TPR_7  11 rlGdyeeAielyeqsLaltkdp 32 
                                   +lG y++ ++++++  + +kd 
  gi|13541446|ref|NP_111134.1| 966 DLGMYSQIVKIFKK--RKEKDN 985
                                   699**********9..777765 PP

>> BTAD  Bacterial transcriptional activator domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   2.2e-05     0.016      63     125 ..     227     289 ..     196     299 .. 0.89
   2 ?   -1.5   0.0       4.4   3.2e+03      68     122 ..     333     387 ..     324     389 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.2e-05
                                   HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                          BTAD  63 ealealaeaelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrrl 125
                                   + +++l++a l+lG++    + +++ ++++P + +l++ l ++l +sG+ +eA+e+Y++l  +
  gi|13541446|ref|NP_111134.1| 227 DLIKKLVQAALSLGEYTIGKELAKNGLKLKPADKDLMKWLALCLSKSGNYGEAIETYKDLLTS 289
                                   667899****************************************************99765 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 4.4
                                   HHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                          BTAD  68 laeaelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerl 122
                                   l+++  + G++ +a++ ++++ ++ P  ++   +  r     G+++e   +Y +l
  gi|13541446|ref|NP_111134.1| 333 LIQLMKASGDIGKAVELAKEAYKKFPSEDDVIIEYARIVDEIGNKGESFDAYSKL 387
                                   5666668899999999999999999999999999999999999999999999765 PP

>> TPR_21  Tetratricopeptide repeat-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.76   5.5e+02      95     137 ..     310     351 ..     306     361 .. 0.77
   2 ?    1.6   0.0      0.27     2e+02     126     174 ..     742     790 ..     735     797 .. 0.80
   3 !   10.4   0.3   0.00055       0.4     119     173 ..     889     944 ..     865     960 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.76
                        TPR_21  95 AkaqLewvlekakdeelkalarlRLarvllaekkydeAlktLe 137
                                   A++ L  v+ek   ++l+ l  +RL +++ a +++ +A+++ +
  gi|13541446|ref|NP_111134.1| 310 ASEYL-YVVEKIGRNQLRPLDYIRLIQLMKASGDIGKAVELAK 351
                                   55555.5666777778*******************99987544 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.27
                        TPR_21 126 ekkydeAlktLeakkeeafaalvael.rGDilvaqgkldeAraaYqaAla 174
                                   e ++d+Al+ ++++  ++f+++ + +  G++++++ k ++A +a+++A++
  gi|13541446|ref|NP_111134.1| 742 EIDLDAALAFMKNNI-DTFNGKEELIeAGELMYSKRKYEDAISAFRKAIR 790
                                   567888888887654.578887776635*******************986 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.00055
                        TPR_21 119 LarvllaekkydeAlktLeakke.eafaalvaelrGDilvaqgkldeAraaYqaAl 173
                                   +a+ ll+e+k+deAl+ L + ++ ++ +a+++ +  D+l +qgkl+eA +    A 
  gi|13541446|ref|NP_111134.1| 889 IAKRLLNENKLDEALEILRQIHDtDESDAEASIMTTDVLRRQGKLTEAYEIAASAA 944
                                   4566799***********9988626789999999************9976544444 PP

>> PPR  PPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.1      0.13        90       5      28 ..     164     187 ..     161     189 .. 0.89
   2 ?    4.3   0.0     0.076        54       9      26 ..     269     286 ..     266     289 .. 0.89
   3 ?   -1.6   0.0         6   4.3e+03      17      28 ..     521     532 ..     512     533 .. 0.80
   4 ?    0.6   0.0       1.2   8.4e+02      13      25 ..     585     597 ..     581     601 .. 0.85
   5 ?   -0.6   0.0       2.9   2.1e+03      14      23 ..     625     634 ..     616     634 .. 0.85
   6 ?   -2.2   0.0         9   6.5e+03       8      22 ..     705     719 ..     705     719 .. 0.89
   7 ?    0.4   0.0       1.3   9.6e+02      13      31 .]     775     793 ..     772     793 .. 0.88
   8 ?    1.3   0.0      0.69   4.9e+02      13      26 ..     896     909 ..     891     911 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.13
                           PPR   5 slIsgycknGkleeAlelfkeMke 28 
                                   ++I gy+  + +e+A++++ e+ +
  gi|13541446|ref|NP_111134.1| 164 AIIEGYVNGNHCEMAIKFIMEIMS 187
                                   78****************999876 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.076
                           PPR   9 gycknGkleeAlelfkeM 26 
                                   +++k+G++ eA+e +k++
  gi|13541446|ref|NP_111134.1| 269 CLSKSGNYGEAIETYKDL 286
                                   799************987 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 6
                           PPR  17 eeAlelfkeMke 28 
                                     A+ +f++M++
  gi|13541446|ref|NP_111134.1| 521 ISAETYFRRMIS 532
                                   67999*****86 PP

  == domain 4  score: 0.6 bits;  conditional E-value: 1.2
                           PPR  13 nGkleeAlelfke 25 
                                   +Gkl++A +l+++
  gi|13541446|ref|NP_111134.1| 585 AGKLDDAYKLLQR 597
                                   7*********987 PP

  == domain 5  score: -0.6 bits;  conditional E-value: 2.9
                           PPR  14 GkleeAlelf 23 
                                   +++e+A+elf
  gi|13541446|ref|NP_111134.1| 625 RMVEKAIELF 634
                                   6899999998 PP

  == domain 6  score: -2.2 bits;  conditional E-value: 9
                           PPR   8 sgycknGkleeAlel 22 
                                   ++y kn ++ +Al++
  gi|13541446|ref|NP_111134.1| 705 DVYLKNKDIGDALKV 719
                                   579*********986 PP

  == domain 7  score: 0.4 bits;  conditional E-value: 1.3
                           PPR  13 nGkleeAlelfkeMkekGi 31 
                                   ++k+e+A++ f++ ++ G+
  gi|13541446|ref|NP_111134.1| 775 KRKYEDAISAFRKAIRLGV 793
                                   689**********999986 PP

  == domain 8  score: 1.3 bits;  conditional E-value: 0.69
                           PPR  13 nGkleeAlelfkeM 26 
                                   ++kl+eAle+++++
  gi|13541446|ref|NP_111134.1| 896 ENKLDEALEILRQI 909
                                   789*******9976 PP

>> FAT  FAT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       4.4   3.2e+03     185     250 ..     359     438 ..     331     454 .. 0.62
   2 ?   11.2   0.0   0.00021      0.15     157     215 ..     582     632 ..     575     657 .. 0.84
   3 ?    0.2   0.2      0.49   3.5e+02      42      92 ..     929     978 ..     895    1041 .. 0.74

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 4.4
                                   T.TSSCCCHHHHHHHCCH...HHHHSSCC........HHHHCCTSSCCC...SS-SS---............HHHHCCCT CS
                           FAT 185 appevvyaylKylwssge...qkealqkL........reftsellekke...elqsgleaqkeptnleeftkllarcylk 250
                                     ++v+++y+++  + g+   + +a++kL        + f+ ++l + e   e  + +e +++ + + ef+ +la  +  
  gi|13541446|ref|NP_111134.1| 359 SEDDVIIEYARIVDEIGNkgeSFDAYSKLfdkggkeaQSFILNYLFSREryeEFVKRFESSDNEDVKDEFKGKLAASFVY 438
                                   33478888888888777722245566666888888888888888888775555555555554444455555555655555 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00021
                                   HCHHHHCCSTTHHCCCCCHCTT.....TT.TSSCCCHHHHHHHCCHHHHHSSCCHHHHC CS
                           FAT 157 arksgrlslAekaLkelleedpeewlprappevvyaylKylwssgeqkealqkLrefts 215
                                     ++g+l+ A+k+L++ ++e +        p ++++y+K+lw+sg+ kea  ++++ ++
  gi|13541446|ref|NP_111134.1| 582 FIDAGKLDDAYKLLQRYEKEVD--------PFYYFTYAKLLWKSGRNKEASRMVEKAIE 632
                                   567899999********88888........9**********************999887 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.49
                                   H.--CCHCHHCCCH.CCCCCCCCCTS---SCCCCCHHHHHCCCCCHHHCHHCC CS
                           FAT  42 r.nqfdeakeliek.arqlldtelsalvgesynraygvlvrvQmlaEleeiiq 92 
                                   r  +++ea e++   a q+ dt   ++ +e+y+r y+++ ++ m++ + +i +
  gi|13541446|ref|NP_111134.1| 929 RqGKLTEAYEIAASaAAQCSDT---ECEKELYRRIYSIMYDLGMYSQIVKIFK 978
                                   3456666666654413444554...4678999999999999999887766654 PP

>> TPR_MalT  MalT-like TPR region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.92   6.6e+02       9      35 ..     335     361 ..     331     366 .. 0.86
   2 ?    2.4   0.0      0.11        82     123     191 ..     605     634 ..     581     653 .. 0.57
   3 ?    6.2   0.1    0.0078       5.6      62     114 ..     898     951 ..     888     965 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.92
                      TPR_MalT   9 llaiasgdaeralelArqALallpedd 35 
                                   +l  asgd+++a+elA++A + +p++d
  gi|13541446|ref|NP_111134.1| 335 QLMKASGDIGKAVELAKEAYKKFPSED 361
                                   677899*************98888876 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.11
                      TPR_MalT 123 fllvlladllyEwndLeeAeqhlqeGielleqlepeaaldayvllarialaqGdleeAetllekaeela 191
                                   f++  +a+ll+  ++ +eA ++++++iel                                        
  gi|13541446|ref|NP_111134.1| 605 FYYFTYAKLLWKSGRNKEASRMVEKAIEL---------------------------------------F 634
                                   33444444555555555555555555544.......................................4 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.0078
                      TPR_MalT  62 alqeaeklarqadslhva.llallqqaeilvaqGrLheAletyeqalqlateqg 114
                                    l ea +++rq++ ++ + + a +  +++l+ qG+L eA+e+   a ++  +++
  gi|13541446|ref|NP_111134.1| 898 KLDEALEILRQIHDTDESdAEASIMTTDVLRRQGKLTEAYEIAASAAAQCSDTE 951
                                   567888889999999775588888899**************9988877666654 PP

>> TPR_18  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00031      0.22      22      72 ..     272     322 ..     267     337 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00031
                        TPR_18  22 degnyltaieqLealdtryPfGaYaeqaqLDLiYakykskdyelavasidr 72 
                                   ++gny +aie  ++l t yP    a    +DL+Y + k ++y  +v +i r
  gi|13541446|ref|NP_111134.1| 272 KSGNYGEAIETYKDLLTSYPDDIDATIDLMDLLYEHGKASEYLYVVEKIGR 322
                                   589***************************************999988877 PP

>> Mad3_BUB1_I  Mad3/BUB1 homology region 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.62   4.5e+02      10      59 ..      18      66 ..      10      75 .. 0.84
   2 ?    9.4   0.3    0.0014         1      56     124 .]     564     631 ..     503     631 .. 0.89
   3 ?    0.4   0.0      0.83     6e+02      53      77 ..    1017    1042 ..     966    1053 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.62
                                  HHTG....-THHHHHHHHHHHHHH-TT-T.TT-HHHHHHHHHHHTTTSGG CS
                   Mad3_BUB1_I 10 leeaeegdDpLelwlryikwieesypqsskesgllellerclkkfkdder 59
                                  ++e +++d +L+  ++ i+ + ++ p + +++++ +++  +++++ d+++
  gi|13541446|ref|NP_111134.1| 18 IAE-KDQDKKLQRIDDLISLLRNTNPDDIDKKEIDPFVSVLVRNVSDENQ 66
                                  555.78899******************88899999999999988888776 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0014
                                   TSGGGTT-HHHHHHHHHHHTTSS-HHHHHHHHHHHTTSTTBHHHHHHHHHHHHHTT-HHHHHHHHHHH. CS
                   Mad3_BUB1_I  56 dderYknDpRylklwlkyadlveepreifkflaskkiGtklalfYeewAellekkgrfkeAeevyelGi 124
                                   ++  Y++ pRyl ++        +  + +k l++ +  +    +Y ++A+ll k+gr keA+++ e++i
  gi|13541446|ref|NP_111134.1| 564 NSGIYEDRPRYLYCFSSTFIDAGKLDDAYKLLQRYEK-EVDPFYYFTYAKLLWKSGRNKEASRMVEKAI 631
                                   5667999999999999888888999999999988775.44578999*******************9987 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.83
                                    HTTTS.GGGTT-HHHHHHHHHHHTTS CS
                   Mad3_BUB1_I   53 kfkdd.erYknDpRylklwlkyadlv 77  
                                    ++k+  e Y n  Ryl+   kya+ v
  gi|13541446|ref|NP_111134.1| 1017 AVKNAlESYINQGRYLDRLNKYASRV 1042
                                    44443489999999999999999855 PP

>> DUF3349  Protein of unknown function (DUF3349)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.1     0.003       2.2       4      44 ..      31      72 ..      28      95 .. 0.83
   2 ?   -0.8   0.0       3.9   2.8e+03      12      51 ..     288     330 ..     284     375 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.003
                                  HHHHHHHHHH-TT-B-HHHHHHHHHHHCTT--HH.HHHHHHH CS
                       DUF3349  4 asileWLragYPegvPeqdyvpLlalLrrrLsde.evkevae 44
                                  +++++ Lr+  P+++++++  p +++L r++sde +++e+++
  gi|13541446|ref|NP_111134.1| 31 DDLISLLRNTNPDDIDKKEIDPFVSVLVRNVSDEnQLRELIT 72
                                  67899**************************98725666655 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 3.9
                                   HH-TT-B-HHHHHHHHHHHCTT--HHHHHHHHHHHHHH-.....- CS
                       DUF3349  12 agYPegvPeqdyvpLlalLrrrLsdeevkevaeelvaea.....a 51 
                                   + YP+++++  ++ L+ lL ++ +  e   v+e++ +++      
  gi|13541446|ref|NP_111134.1| 288 TSYPDDIDA--TIDLMDLLYEHGKASEYLYVVEKIGRNQlrpldY 330
                                   568888876..4778888888877777777777777766444330 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.1    0.0014      0.99       2      34 .]     249     281 ..     248     281 .. 0.92
   2 ?   -0.9   0.0         4   2.8e+03       3      11 ..     628     636 ..     626     643 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0014
                        TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                    ++ l+l P + d++  LA +l+k G++++A++
  gi|13541446|ref|NP_111134.1| 249 AKNGLKLKPADKDLMKWLALCLSKSGNYGEAIE 281
                                   678899*************************86 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 4
                        TPR_17   3 lkaleldPn 11 
                                   +ka+el Pn
  gi|13541446|ref|NP_111134.1| 628 EKAIELFPN 636
                                   8*******9 PP

>> PPR_1  PPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.031        23      20      31 ..     585     596 ..     584     597 .. 0.90
   2 ?    0.2   0.0       0.9   6.5e+02      19      32 ..     616     629 ..     616     634 .. 0.76
   3 ?    2.5   0.0      0.17   1.2e+02      20      32 ..     896     908 ..     895     909 .. 0.90
   4 ?   -2.7   0.0       6.9   4.9e+03      19      28 ..     929     938 ..     929     939 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.031
                                   TS-HHHHHHHHH CS
                         PPR_1  20 aGrvdeAfelfd 31 
                                   aG++d+A++l+ 
  gi|13541446|ref|NP_111134.1| 585 AGKLDDAYKLLQ 596
                                   8*********95 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.9
                                   HTS-HHHHHHHHHH CS
                         PPR_1  19 kaGrvdeAfelfde 32 
                                   k Gr +eA +++++
  gi|13541446|ref|NP_111134.1| 616 KSGRNKEASRMVEK 629
                                   67888888888876 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.17
                                   TS-HHHHHHHHHH CS
                         PPR_1  20 aGrvdeAfelfde 32 
                                   ++++deA+e++++
  gi|13541446|ref|NP_111134.1| 896 ENKLDEALEILRQ 908
                                   79*********97 PP

  == domain 4  score: -2.7 bits;  conditional E-value: 6.9
                                   HTS-HHHHHH CS
                         PPR_1  19 kaGrvdeAfe 28 
                                   ++G++ eA+e
  gi|13541446|ref|NP_111134.1| 929 RQGKLTEAYE 938
                                   79******98 PP

>> PqqD  Coenzyme PQQ synthesis protein D (PqqD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.2     0.011       8.1      17      54 ..     884     921 ..     883     931 .. 0.89
   2 ?    1.0   0.1      0.74   5.3e+02      31      61 ..     934     967 ..     924     970 .. 0.83
   3 ?   -2.5   0.0       9.4   6.7e+03      43      59 ..    1062    1077 ..    1056    1078 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.011
                                   CHHHHHHHH-SSSS-HHHHHHHHHHHCT--HHHHHHHH CS
                          PqqD  17 etgafiWklldgersveeivaalaeeydvdeeeaeadv 54 
                                   e+g+ i k+l  e++++e  ++l+++ d de  aea +
  gi|13541446|ref|NP_111134.1| 884 EIGKVIAKRLLNENKLDEALEILRQIHDTDESDAEASI 921
                                   7889999999777*****************99999876 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.74
                                   -.HHHHHHHHHHHC.T--.HHHHHHHHHHHHHHH CS
                          PqqD  31 s.veeivaalaeey.dvd.eeeaeadvlafldqL 61 
                                   +   ei+a  a++  d + e+e+++++ + +++L
  gi|13541446|ref|NP_111134.1| 934 TeAYEIAASAAAQCsDTEcEKELYRRIYSIMYDL 967
                                   4567999999999989998899*******99998 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 9.4
                                    CT--HHHHHHHHHHHHH CS
                          PqqD   43 ydvdeeeaeadvlafld 59  
                                     dv+ e   +d+++fl+
  gi|13541446|ref|NP_111134.1| 1062 SDVP-EDMIQDIRDFLT 1077
                                    5788.8999******95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       918  (0.051202); expected 358.6 (0.02)
Passed bias filter:                      592  (0.0330191); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); expected 17.9 (0.001)
Passed Fwd filter:                        26  (0.00145016); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              25  [number of targets reported over threshold]
# CPU time: 0.96u 0.34s 00:00:01.30 Elapsed: 00:00:00.55
# Mc/sec: 6623.25
//
Query:       gi|13541447|ref|NP_111135.1|  [L=192]
Description: Zn-dependent protease [Thermoplasma volcanium GSS1]
Scores for 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-06   27.3  14.5    5.2e-05   22.6   1.0    3.2  3  Peptidase_M50  Peptidase family M50


Domain annotation for each model (and alignments):
>> Peptidase_M50  Peptidase family M50
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.9   0.7   0.00036       6.5       7      25 ..      48      66 ..      37      71 .. 0.70
   2 !    7.3   0.6   0.00014       2.6      89     107 ..     110     128 ..     104     134 .. 0.88
   3 !   22.6   1.0   2.9e-09   5.2e-05     191     220 ..     141     170 ..     129     179 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.00036
                                  XXXXXXXXXXXXXXXXXXX CS
                                  xxxxxxxxxxxxxxxxxxx RF
                 Peptidase_M50  7 gilvvvHElGHflvAklcg 25
                                  +   ++HEl+H +vA+  g
  gi|13541447|ref|NP_111135.1| 48 VTAFLMHELAHRYVARSYG 66
                                  223468*********9876 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.00014
                                   XXXXXXXXXXXXXXXXXXX CS
                                   xxxxxxxxxxxxxxxxxxx RF
                 Peptidase_M50  89 livlAGplanfilailvfv 107
                                    ++lAGp++n+ l+il++ 
  gi|13541447|ref|NP_111135.1| 110 KTALAGPAMNIFLGILFYG 128
                                   579*************996 PP

  == domain 3  score: 22.6 bits;  conditional E-value: 2.9e-09
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Peptidase_M50 191 flqllalisvnLgilNLlPipvLDGghllf 220
                                   ++ ++a +++ +g++NLlPip+LDG ++++
  gi|13541447|ref|NP_111135.1| 141 IFGYVAAMNFWFGFFNLLPIPPLDGYKVMN 170
                                   68899********************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1023  (0.0570584); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); 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):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.32s 00:00:00.88 Elapsed: 00:00:00.51
# Mc/sec: 1130.49
//
Query:       gi|13541448|ref|NP_111136.1|  [L=356]
Description: glycosyltransferase [Thermoplasma volcanium GSS1]
Scores for complete 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   61.7   0.0    8.6e-17   61.1   0.0    1.2  1  Glyco_transf_21  Glycosyl transferase family 21
    1.1e-07   31.9   0.0    2.4e-07   30.7   0.0    1.6  2  Glycos_transf_2  Glycosyl transferase family 2
    1.3e-05   25.3   0.0    0.00021   21.3   0.0    2.0  1  Glyco_tranf_2_3  Glycosyltransferase like family 2


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 !   61.1   0.0   1.4e-20   8.6e-17      13     165 ..     100     247 ..      89     255 .. 0.88

  Alignments for each domain:
  == domain 1  score: 61.1 bits;  conditional E-value: 1.4e-20
               Glyco_transf_21  13 vgvnpKvnnllqalea.akydllvisDsdvrvkpdyLeellaaledpkvglVtslpvgsdakglaaaleaaflntlagvlq 92 
                                   ++++ Kv ++++a+++   yd  vi+Dsd+r +++ Le+l+ +l  ++vgl t +p+ ++  gla++++a+  + ++ ++ 
  gi|13541448|ref|NP_111136.1| 100 EKCSGKVKAIATAIKKyTDYDAYVIADSDIRPNSNWLEDLVSPLCNDRVGLSTTFPYFVPIGGLASKVKAVWGTVGQSLME 180
                                   56888*******************************************************************9******** PP

               Glyco_transf_21  93 aklsglgfavGksmalrreaLeaiGGfealadeLAeDyalgkllraaGlkvvlspapiaqtsvprrsslrall 165
                                   +  + ++f++G s+a+ ++ + +   +  +  ++ +D al+++ +++ l ++ ++++  ++++ +++ + +++
  gi|13541448|ref|NP_111136.1| 181 S--KLTRFGWGGSLAFEKSLISDK--MDYFTSNISDDSALTAICKSKKLDIAYVKEA--RPAIYTAENFPQFW 247
                                   *..7889**************998..778889*****************99999885..33333333444444 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 !   30.7   0.0   4.1e-11   2.4e-07       2     114 ..      42     153 ..      41     199 .. 0.87
   2 ?   -2.0   0.0      0.47   2.8e+03     104     166 ..     250     312 ..     237     314 .. 0.65

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 4.1e-11
                                   EEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH.--SS CS
               Glycos_transf_2   2 vviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglra.atgd 81 
                                   v+ip+      l+  l+++ +q +y++ + + v D+ +De+v++le+    +  +  ++ e+  Gk +a+ +++++ ++ d
  gi|13541448|ref|NP_111136.1|  42 VIIPCKGLDLGLEDNLKAITKQ-NYDRADYLGVVDSLQDESVSVLEKVG-INYIISDYTCEKCSGKVKAIATAIKKyTDYD 120
                                   8999999999999*********.999999999999999**********6.59999*******************9945666 PP

                                   EEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEE CS
               Glycos_transf_2  82 yilflDaDdepdpdwleklvealekdgadvvlg 114
                                     ++ D+D  p+ +wle+lv +l +d++++   
  gi|13541448|ref|NP_111136.1| 121 AYVIADSDIRPNSNWLEDLVSPLCNDRVGLSTT 153
                                   ************************987765544 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.47
                                   HHH.TTCEEEEEEEEEECCCCCCCHC-SSEEEECCHCCCCHCCCCCCSTTCSTCCCEEEEHHH CS
               Glycos_transf_2 104 lekdgadvvlgqrprifgetdeiernkrvgenerlyfkerkrslkgnlsfeigsaallrreal 166
                                   +++  a  + ++++++ ++  +++   + ++   l + +   + +  +++ ig ++++ r+++
  gi|13541448|ref|NP_111136.1| 250 ANRQTALSINASPRVFTYGIIFYSLYIFEFFSAVLLTSISLAFVYLFIPVAIGVYRVYERSVI 312
                                   555444444455555555555555555557777777788888888888899999999999887 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 !   21.3   0.0   3.5e-08   0.00021       2     138 ..      39     169 ..      38     257 .. 0.71

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 3.5e-08
               Glyco_tranf_2_3   2 rdlavlVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvn..arnlgstgksraln 80 
                                     ++v++p+ + +  l++ l ++ +q y+r ++  vvd  ++e ++v+e        v++++++   +++ +s gk+ a++
  gi|13541448|ref|NP_111136.1|  39 K-TLVIIPCKGLDLGLEDNLKAITKQNYDRADYLGVVDSLQDESVSVLEK-------VGINYIISdyTCEKCS-GKVKAIA 110
                                   4.89*****99999*****************************9**9986.......7999999966688886.******* PP

               Glyco_tranf_2_3  81 ealravk.sdlvllvDdDtvvePdtlkrllqffltpkvgavgtpvfllnrstlvsalga 138
                                    a++ ++ +d  ++ D+D +   + l+ l+  +  ++vg  +t  ++     l s + a
  gi|13541448|ref|NP_111136.1| 111 TAIKKYTdYDAYVIADSDIRPNSNWLEDLVSPLCNDRVGLSTTFPYFVPIGGLASKVKA 169
                                   ****99989******************99999977778887776665555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (356 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       701  (0.0390987); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.48
# Mc/sec: 2209.86
//
Query:       gi|13541449|ref|NP_111137.1|  [L=91]
Description: elongation factor 1-beta [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.8e-15   55.8   2.9    4.2e-15   55.7   2.9    1.0  1  EF1_GNE   EF-1 guanine nucleotide exchange domain
  ------ inclusion threshold ------
      0.051   12.4   0.1      0.057   12.2   0.1    1.0  1  DLIC      Dynein light intermediate chain (DLIC)
      0.096   11.4   0.3       0.11   11.2   0.3    1.1  1  Bul1_N    Bul1 N terminus


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 !   55.7   2.9     7e-19   4.2e-15       2      88 ..       9      89 ..       8      91 .] 0.94

  Alignments for each domain:
  == domain 1  score: 55.7 bits;  conditional E-value: 7e-19
                                  EEEEEEESSS---HHHHHHHHHH.HS-T.SEE--.--EEE-SSS-EEEEEEEEESSS-GGGGHHHHHHTTS-S.....SEEEE CS
                       EF1_GNE  2 vvlevkPeddetdleelekkvksikleg.lvwgeasklepiafGlkkLqiscvieddkvstdeleekieeiegeledlVqsve 83
                                  v ++  P+d+++d + +e +vk+ kl+g ++++ ++++++i+fGlk +++++++ed+++++d++e+ ++ ++g     V++++
  gi|13541449|ref|NP_111137.1|  9 VSFKLLPSDSDVDTSVMESEVKE-KLNGvCKIN-NIEEKDIGFGLKYIHLEVIVEDKEGEVDRIEKVLSMVKG-----VGEIN 84
                                  67899******************.****99999.6**********************************9999.....99999 PP

                                  EEEEE CS
                       EF1_GNE 84 ivsfn 88
                                  +++++
  gi|13541449|ref|NP_111137.1| 85 TENVS 89
                                  98886 PP

>> DLIC  Dynein light intermediate chain (DLIC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   9.6e-06     0.057      22      71 ..      14      65 ..       7      78 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 9.6e-06
                          DLIC 22 lPsgksv..lvlGedgsGkttliaklqGveeekkGrGleylyldvkdedrdd 71
                                  lPs+ +v   v+  +   k   ++k+  +ee+  G Gl y++l+v  ed++ 
  gi|13541449|ref|NP_111137.1| 14 LPSDSDVdtSVMESEVKEKLNGVCKINNIEEKDIGFGLKYIHLEVIVEDKEG 65
                                  6776665336888888999999***********************9888764 PP

>> Bul1_N  Bul1 N terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.3   1.8e-05      0.11     159     222 ..      19      76 ..       7      79 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 1.8e-05
                        Bul1_N 159 elesilkeytsGDlinGyviieNkssepvkFemfyvtLegtisvidkksakkkkkrtvkrfLrM 222
                                   ++++++ e    + +nG + i+N  ++++ F++ y+ Le ++   dk    + +   +++ L M
  gi|13541449|ref|NP_111137.1|  19 DVDTSVMESEVKEKLNGVCKINNIEEKDIGFGLKYIHLEVIVE--DK----EGEVDRIEKVLSM 76 
                                   67888899999999*************************6554..33....3344455666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       512  (0.0285571); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); 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: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 625.75
//
Query:       gi|13541450|ref|NP_111138.1|  [L=55]
Description: RNA-binding protein involved in translation [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-09   37.7   5.7    1.5e-09   37.7   5.7    2.3  2  DUF1610         Domain of unknown function (DUF1610)
     0.0082   15.8  17.3       0.29   10.9   4.8    3.4  3  zinc_ribbon_2   zinc-ribbon domain
  ------ inclusion threshold ------
       0.01   15.8  12.0       0.11   12.6   6.3    2.3  2  DZR             Double zinc ribbon
      0.011   15.5  18.6      0.066   12.9   0.4    3.9  3  Rubredoxin_2    Rubredoxin metal binding domain
      0.017   15.0  10.9      0.028   14.4   1.2    3.1  2  PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
      0.021   15.1  10.5      0.024   14.9   3.0    2.1  2  C1_2            C1 domain
      0.035   13.5  13.2        1.2    8.6   3.1    3.4  3  zf-ribbon_3     zinc-ribbon domain
      0.045   14.2   8.4       0.81   10.2   8.1    2.0  1  zf-CHY          CHY zinc finger
       0.12   12.2  11.2       0.65    9.9   4.0    3.0  3  zf-HIT          HIT zinc finger
       0.14   12.3   0.7       0.14   12.3   0.7    2.6  2  Auto_anti-p27   Sjogren's syndrome/scleroderma autoantigen 1 
       0.16    9.8   5.1       0.18    9.6   5.1    1.0  1  PolC_DP2        DNA polymerase II large subunit DP2
       0.25   11.6  10.0          2    8.6  10.0    2.2  1  zf-UBR          Putative zinc finger in N-recognin (UBR box)
       0.42   10.9   6.6        7.5    6.9   2.5    2.9  2  Chordopox_RPO7  Chordopoxvirus DNA-directed RNA polymerase 7 
       0.46   10.6  11.5          5    7.3   3.4    2.8  2  DUF1272         Protein of unknown function (DUF1272)
       0.91    9.7  11.0        1.3    9.2   7.0    2.6  2  zf-B_box        B-box zinc finger
          1    9.4   8.7        1.6    8.8   0.1    2.1  2  HypA            Hydrogenase/urease nickel incorporation, meta
          1    9.6   7.2        2.5    8.3   0.2    1.8  1  FYVE_2          FYVE-type zinc finger
        1.4    8.8   0.1        1.4    8.8   0.1    3.6  3  A2L_zn_ribbon   A2L zinc ribbon domain
        2.3    8.2  10.9       0.62   10.0   4.7    2.2  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
        3.4    7.7  13.8         12    5.9   0.2    3.6  3  YhfH            YhfH-like protein
        4.1    7.7  13.2        9.6    6.5   3.9    2.8  2  zf-AN1          AN1-like Zinc finger
        4.1    7.1  14.4        2.4    7.8   0.1    3.6  4  zf_UBZ          Ubiquitin-Binding Zinc Finger
        5.6    7.1   9.4         29    4.8   9.4    2.1  1  Zn_Tnp_IS91     Transposase zinc-binding domain
        5.9    6.5  19.6        7.9    6.1  11.1    3.1  2  TF_Zn_Ribbon    TFIIB zinc-binding
        6.5    6.8  14.9         20    5.2   8.8    3.2  2  Nudix_N_2       Nudix N-terminal
        7.5    6.8  12.1        3.2    8.0   5.9    2.3  2  NOB1_Zn_bind    Nin one binding (NOB1) Zn-ribbon like
        8.9    6.3  17.1         16    5.5  10.5    3.3  2  Zn_ribbon_SprT  SprT-like zinc ribbon domain


Domain annotation for each model (and alignments):
>> DUF1610  Domain of unknown function (DUF1610)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.7   5.7   2.2e-12   1.5e-09       1      24 []       7      29 ..       7      29 .. 0.99
   2 ?    3.3   3.0      0.12        80      11      23 ..      39      51 ..      35      51 .. 0.95

  Alignments for each domain:
  == domain 1  score: 37.7 bits;  conditional E-value: 2.2e-12
                       DUF1610  1 CtSCGaelaprEravvFpCPNCGE 24
                                  CtSCG++l++++  ++F+CPNCG+
  gi|13541450|ref|NP_111138.1|  7 CTSCGVGLIDEG-FSIFLCPNCGN 29
                                  ************.**********7 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.12
                       DUF1610 11 rEravvFpCPNCG 23
                                  rE+++ + C +CG
  gi|13541450|ref|NP_111138.1| 39 REHSTPYVCSKCG 51
                                  8***********9 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.1     0.025        16       2       6 ..       7      11 ..       6      18 .. 0.75
   2 !   10.9   4.8   0.00044      0.29       2      16 ..      24      38 ..      23      40 .. 0.85
   3 ?    2.7   6.2      0.16   1.1e+02      16      22 ..      47      53 ..      34      54 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.025
                 zinc_ribbon_2  2 CpnCG 6 
                                  C++CG
  gi|13541450|ref|NP_111138.1|  7 CTSCG 11
                                  88888 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00044
                 zinc_ribbon_2  2 CpnCGaelqdnakFC 16
                                  CpnCG+e+  + k C
  gi|13541450|ref|NP_111138.1| 24 CPNCGNEIIGRCKTC 38
                                  *******98887777 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.16
                 zinc_ribbon_2 16 CpyCGtp 22
                                  C++CG++
  gi|13541450|ref|NP_111138.1| 47 CSKCGFE 53
                                  8888875 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   6.3   0.00016      0.11      13      46 ..       5      39 ..       3      40 .. 0.80
   2 ?    9.7   9.1    0.0013      0.87      15      49 .]      24      51 ..      24      54 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00016
                           DZR 13 rfCseCgtklkavaa.edrCpsCgekvdpearfCp 46
                                  ++C  Cg  l  +      Cp+Cg ++  ++++C 
  gi|13541450|ref|NP_111138.1|  5 ETCTSCGVGLIDEGFsIFLCPNCGNEIIGRCKTCR 39
                                  58999999998655567789999999999999996 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0013
                           DZR 15 CseCgtklkavaaedrCpsCgekvdpearfCpeCG 49
                                  C++Cg+++       rC  C e  +p   +C +CG
  gi|13541450|ref|NP_111138.1| 24 CPNCGNEII-----GRCKTCREHSTPY--VCSKCG 51
                                  777777776.....6777777776666..677776 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.5      0.27   1.8e+02       3       7 ..       7      11 ..       6      13 .. 0.71
   2 ?    6.9   5.5     0.008       5.3       1      23 [.      22      41 ..      22      43 .. 0.81
   3 ?   12.9   0.4    0.0001     0.066       1      10 [.      45      54 ..      45      55 .] 0.90

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.27
                  Rubredoxin_2  3 CsqCG 7 
                                  C +CG
  gi|13541450|ref|NP_111138.1|  7 CTSCG 11
                                  77787 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.008
                  Rubredoxin_2  1 YvCsqCGfesakwfGrCpsCgsW 23
                                  + C +CG+e     GrC+ C++ 
  gi|13541450|ref|NP_111138.1| 22 FLCPNCGNE---IIGRCKTCREH 41
                                  669999986...78******985 PP

  == domain 3  score: 12.9 bits;  conditional E-value: 0.0001
                  Rubredoxin_2  1 YvCsqCGfes 10
                                  YvCs+CGfe 
  gi|13541450|ref|NP_111138.1| 45 YVCSKCGFEG 54
                                  9*******96 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   1.2   4.3e-05     0.028      18      29 ..      20      31 ..       3      32 .. 0.90
   2 ?    6.7   0.2      0.01       6.8      20      28 ..      45      53 ..      40      53 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.3e-05
                PhnA_Zn_Ribbon 18 allvCpeCahEw 29
                                  ++++Cp+C++E+
  gi|13541450|ref|NP_111138.1| 20 SIFLCPNCGNEI 31
                                  69*********9 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.01
                PhnA_Zn_Ribbon 20 lvCpeCahE 28
                                  +vC++C+ E
  gi|13541450|ref|NP_111138.1| 45 YVCSKCGFE 53
                                  8*****987 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.6     0.026        17      19      38 ..       5      27 ..       3      32 .. 0.76
   2 ?   14.9   3.0   3.6e-05     0.024      17      40 ..      31      52 ..      28      53 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.026
                          C1_2 19 fnCsaCgrk..idgff.YsCseC 38
                                   +C  Cg     +gf  + C+ C
  gi|13541450|ref|NP_111138.1|  5 ETCTSCGVGliDEGFSiFLCPNC 27
                                  57999999984445559999999 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 3.6e-05
                          C1_2 17 esfnCsaCgrkidgffYsCseCdf 40
                                  + ++C++C++ +  + Y Cs+C f
  gi|13541450|ref|NP_111138.1| 31 IIGRCKTCREHS--TPYVCSKCGF 52
                                  6789*******6..55******98 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.1     0.014       9.3      18      25 ..       6      13 ..       4      18 .. 0.77
   2 ?    8.6   3.1    0.0018       1.2       5      11 ..      24      31 ..      23      39 .. 0.73
   3 ?    5.2   0.3     0.022        14      18      23 ..      46      51 ..      45      53 .. 0.58

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.014
                   zf-ribbon_3 18 vCpyCGtk 25
                                  +C++CG  
  gi|13541450|ref|NP_111138.1|  6 TCTSCGVG 13
                                  69999865 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0018
                   zf-ribbon_3  5 CPnCGa.p 11
                                  CPnCG+ +
  gi|13541450|ref|NP_111138.1| 24 CPNCGNeI 31
                                  77777655 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.022
                   zf-ribbon_3 18 vCpyCG 23
                                  vC +CG
  gi|13541450|ref|NP_111138.1| 46 VCSKCG 51
                                  455555 PP

>> zf-CHY  CHY zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   8.1    0.0012      0.81      42      73 ..      22      51 ..       6      53 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0012
                        zf-CHY 42 vlcllCeteqekavlCkkCkkefaeyfCpiCk 73
                                  +lc +C +e  +   Ck+C+++ + y+C++C 
  gi|13541450|ref|NP_111138.1| 22 FLCPNCGNE--IIGRCKTCREHSTPYVCSKCG 51
                                  678899886..8889****************7 PP

>> zf-HIT  HIT zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.2      0.32   2.2e+02      15      21 ..       6      12 ..       3      14 .. 0.75
   2 ?    4.3   0.0     0.055        37      16      21 ..      24      29 ..      16      31 .. 0.82
   3 ?    9.9   4.0   0.00098      0.65       4      20 ..      34      51 ..      32      53 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.32
                                  E-TTT-- CS
                        zf-HIT 15 kCpkCnt 21
                                  +C  C++
  gi|13541450|ref|NP_111138.1|  6 TCTSCGV 12
                                  6888875 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.055
                                  -TTT-- CS
                        zf-HIT 16 CpkCnt 21
                                  Cp+C+ 
  gi|13541450|ref|NP_111138.1| 24 CPNCGN 29
                                  999985 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.00098
                                  B-TTT-S.B-SEE-TTT- CS
                        zf-HIT  4 lCgvCgf.pakYkCpkCn 20
                                   C  C +    Y C+kC+
  gi|13541450|ref|NP_111138.1| 34 RCKTCREhSTPYVCSKCG 51
                                  7****************8 PP

>> Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.7   0.00022      0.14      16      40 .]       5      28 ..       2      28 .. 0.91
   2 ?   -0.6   4.1       2.4   1.6e+03      19      29 ..      36      49 ..      32      53 .. 0.52

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00022
                 Auto_anti-p27 16 etCpvCgvPLmrdrkggkvyCvaCd 40
                                  etC  Cgv L  + +    +C++C+
  gi|13541450|ref|NP_111138.1|  5 ETCTSCGVGLIDE-GFSIFLCPNCG 28
                                  89**********9.6789******6 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 2.4
                 Auto_anti-p27 19 pvC...gvPLmrdr 29
                                  ++C   ++P + ++
  gi|13541450|ref|NP_111138.1| 36 KTCrehSTPYVCSK 49
                                  55544444444333 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 ?    9.6   5.1   0.00027      0.18     616     650 ..      19      51 ..       2      54 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00027
                      PolC_DP2 616 iarrkCkkCgketlearCeeCgekteeklvCkkce 650
                                   ++   C++Cg+e    rC++C e+ ++ +vC+kc+
  gi|13541450|ref|NP_111138.1|  19 FSIFLCPNCGNEI-IGRCKTCREHSTP-YVCSKCG 51 
                                   4455677777664.4567777777777.7777775 PP

>> zf-UBR  Putative zinc finger in N-recognin (UBR box)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6  10.0     0.003         2       9      31 ..      29      51 ..       2      55 .] 0.88

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.003
                        zf-UBR  9 gevvyrCltCsldetsviCeeCf 31
                                  +e++ rC+tC+ ++t ++C++C 
  gi|13541450|ref|NP_111138.1| 29 NEIIGRCKTCREHSTPYVCSKCG 51
                                  48999*****************6 PP

>> Chordopox_RPO7  Chordopoxvirus DNA-directed RNA polymerase 7 kDa polypeptide (RPO7)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   2.5     0.011       7.5       1      22 [.       1      22 [.       1      39 [. 0.86
   2 ?    4.7   0.1     0.053        35       4      12 ..      44      52 ..      42      53 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.011
                Chordopox_RPO7  1 mvfplvCstCGrDlseeryrLl 22
                                  mv++  C++CG  l +e + + 
  gi|13541450|ref|NP_111138.1|  1 MVYKETCTSCGVGLIDEGFSIF 22
                                  99***********999988765 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.053
                Chordopox_RPO7  4 plvCstCGr 12
                                  p vCs CG+
  gi|13541450|ref|NP_111138.1| 44 PYVCSKCGF 52
                                  57******7 PP

>> DUF1272  Protein of unknown function (DUF1272)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   3.4    0.0075         5      42      54 ..      22      34 ..       2      34 .. 0.64
   2 ?    6.2   1.5     0.016        11      32      48 ..      35      51 ..      33      53 .. 0.93

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0075
                       DUF1272 42 nvCPncgGelvkR 54
                                    CPncg e++ R
  gi|13541450|ref|NP_111138.1| 22 FLCPNCGNEIIGR 34
                                  47*****999876 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.016
                       DUF1272 32 CaeCaeevlenvCPncg 48
                                  C++C e+    vC  cg
  gi|13541450|ref|NP_111138.1| 35 CKTCREHSTPYVCSKCG 51
                                  ****************9 PP

>> zf-B_box  B-box zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.1       0.6     4e+02      18      22 ..       7      11 ..       2      14 .. 0.68
   2 ?    9.2   7.0     0.002       1.3       5      29 ..      23      50 ..      20      54 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.6
                      zf-B_box 18 CedCq 22
                                  C++C+
  gi|13541450|ref|NP_111138.1|  7 CTSCG 11
                                  77776 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.002
                      zf-B_box  5 kCpeHknkpatlfCedCqq....plCeeC 29
                                   Cp+++ ++++  C++C++    ++C++C
  gi|13541450|ref|NP_111138.1| 23 LCPNCG-NEIIGRCKTCREhstpYVCSKC 50
                                  6*****.**********985555688888 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.1    0.0024       1.6      72      95 ..       6      30 ..       2      33 .. 0.75
   2 ?    4.5   3.8     0.053        35      69      93 ..      31      51 ..      29      54 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0024
                                  EETTTS-EEECHHH.HHS-TTTSSS CS
                          HypA 72 rCreCgkefeleek.alrCpkCgsa 95
                                  +C++Cg     e    + Cp+Cg++
  gi|13541450|ref|NP_111138.1|  6 TCTSCGVGLIDEGFsIFLCPNCGNE 30
                                  7*****666655534779****985 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.053
                                  -EEEETTTS-EEECHHHHHS-TTTS CS
                          HypA 69 vkvrCreCgkefeleekalrCpkCg 93
                                  +  rC++C+++ +     + C kCg
  gi|13541450|ref|NP_111138.1| 31 IIGRCKTCREHSTP----YVCSKCG 51
                                  5679****976664....47****8 PP

>> FYVE_2  FYVE-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.2    0.0037       2.5      79     102 ..       4      29 ..       1      32 [. 0.85

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0037
                        FYVE_2  79 lnvCkkCsve..nkkekvwlCkiCse 102
                                   +++C++C+v   ++  +++lC +C +
  gi|13541450|ref|NP_111138.1|   4 KETCTSCGVGliDEGFSIFLCPNCGN 29 
                                   689*****987788889*******65 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   5.8      0.38   2.5e+02      20      29 ..      20      29 ..       4      31 .. 0.71
   2 ?   -1.3   0.4       2.9   1.9e+03       6      10 ..      35      39 ..      34      40 .. 0.68
   3 ?    8.8   0.1     0.002       1.4       4      29 ..      45      52 ..      42      55 .] 0.56

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.38
                 A2L_zn_ribbon 20 gylvCieCga 29
                                  ++  C++Cg+
  gi|13541450|ref|NP_111138.1| 20 SIFLCPNCGN 29
                                  667899**98 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.9
                 A2L_zn_ribbon  6 CsvCg 10
                                  C+ C+
  gi|13541450|ref|NP_111138.1| 35 CKTCR 39
                                  77775 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.002
                 A2L_zn_ribbon  4 kvCsvCggngilnseqgylvCieCga 29
                                  +vCs+C                  g+
  gi|13541450|ref|NP_111138.1| 45 YVCSKC------------------GF 52
                                  555555..................54 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.7    0.0028       1.9      30      55 ..       6      30 ..       4      34 .. 0.86
   2 ?   10.0   4.7   0.00094      0.62      30      55 ..      23      53 ..      12      54 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0028
                OrfB_Zn_ribbon 30 tCseCgsknkealsgrtfkCpnCgfe 55
                                  tC  Cg  + +      f CpnCg e
  gi|13541450|ref|NP_111138.1|  6 TCTSCGVGLID-EGFSIFLCPNCGNE 30
                                  89999999999.8889999****987 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00094
                OrfB_Zn_ribbon 30 tCseCgsknke.....alsgrtfkCpnCgfe 55
                                   C++Cg +        + ++  ++C++Cgfe
  gi|13541450|ref|NP_111138.1| 23 LCPNCGNEIIGrcktcREHSTPYVCSKCGFE 53
                                  7*****988777888999***********97 PP

>> YhfH  YhfH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.2     0.019        12      15      21 ..       6      12 ..       2      18 .. 0.69
   2 ?    4.7   3.6     0.045        30      16      24 ..      24      32 ..      23      41 .. 0.85
   3 ?    2.9   0.2      0.16   1.1e+02      15      20 ..      46      51 ..      43      53 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.019
                          YhfH 15 kCteCGk 21
                                  +Ct+CG 
  gi|13541450|ref|NP_111138.1|  6 TCTSCGV 12
                                  6888886 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.045
                          YhfH 16 CteCGkeie 24
                                  C++CG+ei 
  gi|13541450|ref|NP_111138.1| 24 CPNCGNEII 32
                                  *******96 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.16
                          YhfH 15 kCteCG 20
                                  +C++CG
  gi|13541450|ref|NP_111138.1| 46 VCSKCG 51
                                  699**9 PP

>> zf-AN1  AN1-like Zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   7.6      0.48   3.2e+02       1      20 [.      24      39 ..       6      41 .. 0.59
   2 ?    6.5   3.9     0.014       9.6       1      20 [.      35      51 ..      34      53 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.48
                        zf-AN1  1 CsfksCkkkdflpfkCryCg 20
                                  C   +C++++   ++C++C+
  gi|13541450|ref|NP_111138.1| 24 CP--NCGNEII--GRCKTCR 39
                                  22..4555555..5666665 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.014
                        zf-AN1  1 CsfksCkkkdflpfkCryCg 20
                                  C+  +C+++ + p+ C++Cg
  gi|13541450|ref|NP_111138.1| 35 CK--TCREHST-PYVCSKCG 51
                                  54..7999987.*******8 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.2       1.1   7.6e+02       4       9 ..       6      11 ..       4      13 .. 0.86
   2 ?    7.7   0.2    0.0039       2.6       3      12 ..      22      31 ..      20      34 .. 0.89
   3 ?   -0.2   0.7       1.2     8e+02       5      11 ..      35      41 ..      33      42 .. 0.74
   4 ?    7.8   0.1    0.0037       2.4       3      10 ..      45      52 ..      43      55 .] 0.84

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 1.1
                        zf_UBZ  4 lCerCg 9 
                                  +C  Cg
  gi|13541450|ref|NP_111138.1|  6 TCTSCG 11
                                  8*9998 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0039
                        zf_UBZ  3 ylCerCgkei 12
                                  +lC+ Cg ei
  gi|13541450|ref|NP_111138.1| 22 FLCPNCGNEI 31
                                  89*****998 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 1.2
                        zf_UBZ  5 CerCgke 11
                                  C+ C ++
  gi|13541450|ref|NP_111138.1| 35 CKTCREH 41
                                  8888765 PP

  == domain 4  score: 7.8 bits;  conditional E-value: 0.0037
                        zf_UBZ  3 ylCerCgk 10
                                  y+C++Cg 
  gi|13541450|ref|NP_111138.1| 45 YVCSKCGF 52
                                  9*****96 PP

>> Zn_Tnp_IS91  Transposase zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   9.4     0.044        29      33      64 ..      15      51 ..       3      54 .. 0.72

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.044
                   Zn_Tnp_IS91 33 aalGfaryeCeeCghe.kivyfsCksrh....CpsCq 64
                                   + Gf+ + C++Cg+e    + +C++ +    C++C+
  gi|13541450|ref|NP_111138.1| 15 IDEGFSIFLCPNCGNEiIGRCKTCREHStpyvCSKCG 51
                                  467**********977466899999875344588886 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   1.3      0.04        26      21      27 ..       6      12 ..       4      22 .. 0.78
   2 ?    6.1  11.1     0.012       7.9       3      26 ..      24      51 ..      22      52 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.04
                                  EESSSSB CS
                  TF_Zn_Ribbon 21 vCtdCGl 27
                                  +Ct+CG+
  gi|13541450|ref|NP_111138.1|  6 TCTSCGV 12
                                  7****86 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.012
                                  ETTTTCEEC....HEETSTTCEEESSSS CS
                  TF_Zn_Ribbon  3 CPnCgstnl....veDpergelvCtdCG 26
                                  CPnCg++ +    +  + ++ +vC++CG
  gi|13541450|ref|NP_111138.1| 24 CPNCGNEIIgrckTCREHSTPYVCSKCG 51
                                  *****98569999888999********9 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.4     0.091        61      24      29 ..       6      11 ..       5      14 .. 0.74
   2 ?    5.2   8.8      0.03        20       3      30 ..      24      52 ..      23      52 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.091
                                  EETTTT CS
                     Nudix_N_2 24 vCpaCg 29
                                  +C++Cg
  gi|13541450|ref|NP_111138.1|  6 TCTSCG 11
                                  588887 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.03
                                  -TTT--B-EEE--.TT-SS-EEEETTTTE CS
                     Nudix_N_2  3 CsqCGtpvelrip.dgDnreRlvCpaCgt 30
                                  C++CG+++  r     ++ + +vC++Cg+
  gi|13541450|ref|NP_111138.1| 24 CPNCGNEIIGRCKtCREHSTPYVCSKCGF 52
                                  *******98777746899999******96 PP

>> NOB1_Zn_bind  Nin one binding (NOB1) Zn-ribbon like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   5.9    0.0049       3.2       9      39 ..       5      37 ..       2      42 .. 0.72
   2 ?    2.7   3.2      0.21   1.4e+02      10      30 ..      34      51 ..      31      53 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0049
                  NOB1_Zn_bind  9 lrChaCfkvt.kd.mtkkFCpkCGnktLkrvav 39
                                    C++C      +  +   Cp+CGn+ + r+++
  gi|13541450|ref|NP_111138.1|  5 ETCTSCGVGLiDEgFSIFLCPNCGNEIIGRCKT 37
                                  5799997644144255566*********99976 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.21
                  NOB1_Zn_bind 10 rChaCfkvtkdmtkkFCpkCG 30
                                  rC +C    +++t   C+kCG
  gi|13541450|ref|NP_111138.1| 34 RCKTCR---EHSTPYVCSKCG 51
                                  555554...4677888****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 ?    3.6   0.5     0.092        61       6      11 ..       6      11 ..       2      13 .. 0.86
   2 ?    5.5  10.5     0.024        16       7      32 ..      24      52 ..      21      54 .. 0.92

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.092
                Zn_ribbon_SprT  6 rCtgCg 11
                                  +Ct+Cg
  gi|13541450|ref|NP_111138.1|  6 TCTSCG 11
                                  6****9 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.024
                Zn_ribbon_SprT  7 CtgCgreythhlsi.rrhn..YrCrrCkg 32
                                  C++Cg+e+  + +  r h+  Y C +C+ 
  gi|13541450|ref|NP_111138.1| 24 CPNCGNEIIGRCKTcREHStpYVCSKCGF 52
                                  **************99999********85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (55 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       742  (0.0413855); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
Passed Fwd filter:                        50  (0.00278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              27  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 338.71
//
Query:       gi|13541451|ref|NP_111139.1|  [L=447]
Description: phosphomannomutase [Thermoplasma volcanium GSS1]
Scores for complete 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-40  135.5   0.2    7.5e-39  132.6   0.1    2.4  3  PGM_PMM_I    Phosphoglucomutase/phosphomannomutase, alpha/bet
    1.9e-28   98.9   0.1    3.4e-28   98.1   0.1    1.4  1  PGM_PMM_III  Phosphoglucomutase/phosphomannomutase, alpha/bet
    2.4e-25   89.1   0.0    5.7e-25   87.9   0.0    1.7  1  PGM_PMM_II   Phosphoglucomutase/phosphomannomutase, alpha/bet
    8.6e-12   45.1   0.0    2.5e-11   43.6   0.0    1.8  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 !  132.6   0.1   1.7e-42   7.5e-39       2     135 ..       5     131 ..       4     134 .. 0.94
   2 ?   -2.9   0.0       1.1     5e+03      52      70 ..     162     180 ..     160     199 .. 0.79
   3 ?   -0.6   0.0      0.22     1e+03     106     133 ..     393     421 ..     390     424 .. 0.76

  Alignments for each domain:
  == domain 1  score: 132.6 bits;  conditional E-value: 1.7e-42
                                   GGBBTTCEEEECCHCTBSCCHHHHHHHHHHHHCHHCSTS-EEEEEE-S-TTHHHHHHHHHHHHHCCT-CEEEEEEB-HHHH CS
                     PGM_PMM_I   2 qkfgtsGlRgkvgegeltpelveklgqaiaeylkaeakkkkvvvGrDtRvssrelaealaaglaanGvevillgllptPav 82 
                                   ++fgt+G+Rg+ + + + p+++ ++g+ai++y++      +++ G DtR +++++++a++ag++++G++vi+lg+lptPa+
  gi|13541451|ref|NP_111139.1|   5 RLFGTNGIRGIPN-DDMSPDFAMSVGKAIGTYVSG-----EIAFGTDTRLTGDMIKNAVIAGILSTGISVIDLGVLPTPAI 79 
                                   68********998.77******************7.....7**************************************** PP

                                   HHHHHHCCECEEEEE--TTS-TTCCCEEEEETTTCE--CHHHHHHHHHHCCT- CS
                     PGM_PMM_I  83 sfairklkadagimitaSHnppeyngiKvylsnGgpispeveekIeaiiekee 135
                                   +++ +k++   +++itaSHnpp+yngiKv++++G +++++ eekIe+i+ ++ 
  gi|13541451|ref|NP_111139.1|  80 QYYSKKHG-IYAVVITASHNPPQYNGIKVIDKDGTELERPGEEKIEEIFYSKA 131
                                   ******76.555***********************************997765 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.1
                                   THHHHHHHHHHHHHCCT-C CS
                     PGM_PMM_I  52 ssrelaealaaglaanGve 70 
                                    s+ +++ ++++la +G  
  gi|13541451|ref|NP_111139.1| 162 DSDNIKSHAFKVLADAGNG 180
                                   5788888999999988854 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.22
                                   CCCEEEEETTTCE--CHH.HHHHHHHHCC CS
                     PGM_PMM_I 106 yngiKvylsnGgpispev.eekIeaiiek 133
                                     giK++  +G  + ++  +ekI +i+++
  gi|13541451|ref|NP_111139.1| 393 TDGIKILKDDGWILIRPSgTEKILRIYAH 421
                                   689********755544449999998876 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 !   98.1   0.1   7.6e-32   3.4e-28       1     111 [.     256     362 ..     256     365 .. 0.95

  Alignments for each domain:
  == domain 1  score: 98.1 bits;  conditional E-value: 7.6e-32
                                   HHHHHHHHHHHHHHCHCSTTTCEEEEETTS-THHHHHHHHTT-EEEEESSSCHHHHHHHHHTTECEEEETTCEEEETTTBS CS
                   PGM_PMM_III   1 dgdqllallakylleeklkpgagvvktvmtslalervakklgiklvetkvGdkyvleemkeegavlGgEeSghiifldeat 81 
                                   dgd++lal++ky+++   +++  vv++v++s+ + +++++ g+kl++tkvG   v+++m ++ga++GgEe+g++i++++++
  gi|13541451|ref|NP_111139.1| 256 DGDRMLALITKYIAK---AGDV-VVTPVSSSDTIADICNAIGAKLIRTKVGAPIVARAMIDNGATIGGEENGGVIYGKHQY 332
                                   79***********77...4565.********************************************************** PP

                                   S--HHHHHHHHHHHHHHHTS-HHHHHHHHH CS
                   PGM_PMM_III  82 tkDGilaallvleilaetgkslselleell 111
                                   ++DG++++ lvl+++a t+k+lsel++el+
  gi|13541451|ref|NP_111139.1| 333 CRDGAMTVSLVLNLMASTNKKLSELISELP 362
                                   **************************8876 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 !   87.9   0.0   1.3e-28   5.7e-25       2     103 .]     152     252 ..     151     252 .. 0.98

  Alignments for each domain:
  == domain 1  score: 87.9 bits;  conditional E-value: 1.3e-28
                                   HHHHHGGGTS-HHHHHHHT-EEEEE-TT-TTHHHHHHHHHHTT-EEEES-----TT-TTSS----TT-TTTTHHHHGGGGG CS
                    PGM_PMM_II   2 aYiealkekvdseaikksglkvvidplhGaggeilkellkelgvdvvelnaepdpdfptkapnpeekealkllielvkkeg 82 
                                    Yi+++ ++vds+ ik+  +kv++d+++Ga+   +++ll++lg+ +++lna+pd+ f  ++++p + e+l  li l+k+ +
  gi|13541451|ref|NP_111139.1| 152 IYINGVISNVDSDNIKSHAFKVLADAGNGAAYYSTPKLLEKLGCSITTLNANPDGRFTARNAEPVP-ENLVNLISLMKSGR 231
                                   6*****************************************************************.************** PP

                                   -SEEEEE-TTS-BEEEEETTE CS
                    PGM_PMM_II  83 adlglafDgDaDRlgvvderG 103
                                   +dlg+a+DgDaDR +++de+G
  gi|13541451|ref|NP_111139.1| 232 FDLGIAHDGDADRAVFIDEKG 252
                                   *******************98 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 !   43.6   0.0   5.5e-15   2.5e-11       1      72 [.     366     438 ..     366     440 .. 0.80

  Alignments for each domain:
  == domain 1  score: 43.6 bits;  conditional E-value: 5.5e-15
                                   CCCCCHCC-TT..EECCCCCTTH...HCCCCCCCCGCCEEEE.EEEETTCCEEEEEEEESSHHHHHHHHHHHHHH CS
                    PGM_PMM_IV   1 linvrveekakvvaalaallkva...sikeglkilledGrrlavRpSGTepllrvyvEaksdeelarlaeevael 72 
                                   li+ +ve+  + +  la+ lk++   ++ +g+kil+ dG++l +RpSGTe  lr+y+++++ e+++++ e+ +++
  gi|13541451|ref|NP_111139.1| 366 LIKKKVERRVD-WPSLARELKKGervDETDGIKILKDDGWIL-IRPSGTEKILRIYAHSSDFELANKYCEQYIRK 438
                                   57777777655.3344444444456699**************.***********************999987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (447 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       430  (0.0239835); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 2648.87
//
Query:       gi|13541452|ref|NP_111140.1|  [L=199]
Description: phosphatidylglycerophosphate synthase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.2e-13   50.2   0.8    3.2e-13   50.2   0.8    2.5  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 !   50.2   0.8   1.8e-17   3.2e-13       2      66 .]      24      87 ..      23      87 .. 0.93
   2 ?    0.4   1.4     0.065   1.2e+03      26      35 ..     123     153 ..      95     193 .. 0.59

  Alignments for each domain:
  == domain 1  score: 50.2 bits;  conditional E-value: 1.8e-17
                                  -HHHHHHHHHHHHHHHHHGGGS-H..HHHHHHHHHHHHHTTHHHHHHHHTT---HHHHHHHHHHH CS
               CDP-OH_P_transf  2 lPnaiTllrlllsvlailllltyyplvlailllliasltDalDGklARrlnqvstlGkllDslaD 66
                                   Pn+i++++l+++ l+  +++++++l+l +l+l+i++l+Da+DGklAR  +++s+ G+++D+  D
  gi|13541452|ref|NP_111140.1| 24 SPNTISIISLISAGLTG-IFFYLNYLYLSLLFLIISALFDAVDGKLARIQGKSSKRGDFIDHSFD 87
                                  6**********999999.5679999***************************899*******877 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.065
                                   .......................HHHHHHHH CS
               CDP-OH_P_transf  26 p.....................lvlaillll 35 
                                   +                     lvl+++++ 
  gi|13541452|ref|NP_111140.1| 123 GtqaqalglnrlyagimgradrLVLMVIFIA 153
                                   3445555555555555555555444444442 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       625  (0.0348597); expected 358.6 (0.02)
Passed bias filter:                      234  (0.0130515); 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: 0.48u 0.31s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 1220.54
//
Query:       gi|13541453|ref|NP_111141.1|  [L=153]
Description: nucleotide kinase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.7e-14   53.4   0.3    5.9e-12   46.3   0.3    2.1  1  AAA_18           AAA domain
    3.2e-05   23.7   0.0      0.033   13.9   0.0    2.1  2  CoaE             Dephospho-CoA kinase
    0.00012   22.4   0.0    0.00025   21.3   0.0    1.5  1  AAA_28           AAA domain
    0.00031   21.2   0.7     0.0012   19.3   0.1    2.1  2  AAA_17           AAA domain
     0.0008   19.7   0.2     0.0017   18.6   0.1    1.6  1  AAA_22           AAA domain
    0.00097   18.9   0.0       0.46   10.1   0.0    2.2  2  Thymidylate_kin  Thymidylate kinase
     0.0031   17.4   0.1     0.0093   15.9   0.0    1.7  2  NTPase_1         NTPase
     0.0047   16.8   0.5        1.4    8.8   0.0    2.2  2  dNK              Deoxynucleoside kinase
  ------ inclusion threshold ------
      0.014   15.2   0.0      0.019   14.7   0.0    1.2  1  AAA_30           AAA domain
      0.015   15.1   0.1      0.033   13.9   0.0    1.6  2  ATP_bind_1       Conserved hypothetical ATP binding protein
      0.016   15.6   0.0      0.018   15.4   0.0    1.4  1  AAA_16           AAA ATPase domain
      0.018   14.8   0.0        1.7    8.3   0.0    2.2  2  PRK              Phosphoribulokinase / Uridine kinase family
       0.02   15.4   0.0      0.038   14.5   0.0    1.7  1  ABC_tran         ABC transporter
      0.026   14.2   0.1      0.045   13.5   0.1    1.4  1  AAA_24           AAA domain
      0.027   14.6   0.2       0.68   10.1   0.1    2.2  2  AAA_33           AAA domain
      0.042   13.9   1.1        0.3   11.2   0.1    2.4  2  ADK              Adenylate kinase
      0.054   12.5   0.1        0.1   11.6   0.0    1.4  2  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
      0.067   12.8   0.0       0.11   12.0   0.0    1.4  1  cobW             CobW/HypB/UreG, nucleotide-binding domain
      0.068   13.1   0.2      0.086   12.8   0.2    1.5  1  Rad17            Rad17 P-loop domain
      0.075   12.8   0.1       0.13   12.1   0.1    1.3  1  AAA_29           P-loop containing region of AAA domain
      0.076   12.7   0.1      0.084   12.6   0.1    1.4  1  Cytidylate_kin   Cytidylate kinase
        0.1   11.8   0.0        0.1   11.8   0.0    1.2  1  DUF2075          Uncharacterized conserved protein (DUF2075)
       0.13   12.7   1.0       0.36   11.3   1.0    2.1  1  AAA              ATPase family associated with various cellul
       0.14   12.6   0.0       0.27   11.6   0.0    1.5  1  RNA_helicase     RNA helicase
       0.27   10.8   0.1       0.49    9.9   0.1    1.4  1  AAA_25           AAA domain


Domain annotation for each model (and alignments):
>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.3   0.3   8.2e-15   5.9e-12       2     127 ..       6     109 ..       6     111 .. 0.76

  Alignments for each domain:
  == domain 1  score: 46.3 bits;  conditional E-value: 8.2e-15
                        AAA_18   2 lltGtpGvGKttlakeLskrlgf.gvnlrdvakenglllevdpealdeskrldedkldklldaleenssaleegknlvidg 81 
                                   ++tG+pG+GK+t++  L++  g+   + +++ake g+l++++ +   e+++++      + d +++           +i +
  gi|13541453|ref|NP_111141.1|   6 CITGPPGAGKSTVCSKLREY-GYnCKEGNELAKEYGCLFDEEVD--VECLEEKL-----AEDRFDG-----------IICS 67 
                                   79***************998.45566678899999999999888..33322222.....2244444...........5555 PP

                        AAA_18  82 hlaeleseaakdikkvvLtaspeelleRlekRgyeeakikeneeae 127
                                   h ++l+  + +    ++L+a+ + l++R+++Rgy+e ki+en e +
  gi|13541453|ref|NP_111141.1|  68 HYSHLLGCSTV----FILEADLNDLIDRMRARGYSEEKIQENIETQ 109
                                   55665555555....9**************************9976 PP

>> CoaE  Dephospho-CoA kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   4.6e-05     0.033       4      36 ..       6      38 ..       3      47 .. 0.90
   2 !    7.9   0.0    0.0032       2.3     122     160 ..      75     112 ..      66     118 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.6e-05
                                  EEEESTTSSHHHHHHHHHHTT-EEEEHHHHHHH CS
                          CoaE  4 gltGgiasGKstvanlfadlgvpivDaDlvArq 36
                                   +tG  ++GKstv++ ++++g++      +A++
  gi|13541453|ref|NP_111141.1|  6 CITGPPGAGKSTVCSKLREYGYNCKEGNELAKE 38
                                  69********************99888888876 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0032
                                   SSEEEEEE--HHHHHHHHHHCCTSTHHHHHHHHHHS--H CS
                          CoaE 122 iervlvvdvelelqveRlvardgvseeevkaiiaaQlse 160
                                   +++v++++++l+  ++R+ ar g see++++ i+ Q+s+
  gi|13541453|ref|NP_111141.1|  75 CSTVFILEADLNDLIDRMRAR-GYSEEKIQENIETQMSS 112
                                   7899999**********7666.99*************95 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   3.5e-07   0.00025       3      34 ..       6      39 ..       4      58 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 3.5e-07
                        AAA_28  3 vitGgestGKTtlleaLaargypvv..pEaarei 34
                                  +itG++++GK+t++++L + gy++    E a e+
  gi|13541453|ref|NP_111141.1|  6 CITGPPGAGKSTVCSKLREYGYNCKegNELAKEY 39
                                  8*******************99987666766665 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.1   1.7e-06    0.0012       1      22 [.       8      28 ..       8      57 .. 0.84
   2 ?    0.1   0.0       1.4   9.7e+02     103     132 ..      76     106 ..      52     109 .. 0.72

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.7e-06
                                  EE-TTSSHHHHHHHHHHHHTEE CS
                        AAA_17  1 lGgPGsGKgtqceklvekygft 22
                                  +G+PG+GK+t+c+kl  +yg+ 
  gi|13541453|ref|NP_111141.1|  8 TGPPGAGKSTVCSKLR-EYGYN 28
                                  7***********9995.56654 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1.4
                                   SEEEEEE--HHHHHHHHHHH.TTST-TS-SH CS
                        AAA_17 103 daiilleadpeeilerrlkd.rtrgrdddne 132
                                   +++++lead  ++++r+  +  +++   +n+
  gi|13541453|ref|NP_111141.1|  76 STVFILEADLNDLIDRMRARgYSEEKIQENI 106
                                   6788899999999998877623333344455 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.1   2.4e-06    0.0017       6      27 ..       3      24 ..       2      54 .. 0.92

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2.4e-06
                        AAA_22  6 gilvvtGesGtGKTtllrrlle 27
                                  +i ++tG++G+GK+t++ +l+e
  gi|13541453|ref|NP_111141.1|  3 KIACITGPPGAGKSTVCSKLRE 24
                                  6899**************9986 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.0    0.0055         4       3      19 ..       9      25 ..       7      39 .. 0.86
   2 !   10.1   0.0   0.00064      0.46     120     180 ..      77     137 ..      56     142 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0055
                                  ESTTSSHHHHHHHHHHH CS
               Thymidylate_kin  3 GlDGaGKttqaellker 19
                                  G  GaGK+t++ +l+e+
  gi|13541453|ref|NP_111141.1|  9 GPPGAGKSTVCSKLREY 25
                                  788***********986 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00064
                                   EEEEEESSHHHHHTSCCTTSSTTTSHHHHHHHHHHHHHHHHHHHH.TTSTEEEEETTS-HHH CS
               Thymidylate_kin 120 ltflldvdpevalkRlakrdeldeeeeeqldflrkvrerylelak.ederiliidasksiee 180
                                    +f+l+ d +  + R+++r+ ++e+++e+++++ +   +y +l +   +ri+++  + +i+e
  gi|13541453|ref|NP_111141.1|  77 TVFILEADLNDLIDRMRARGYSEEKIQENIETQMSSIFYYESLERlPANRIFTL-YNGNIDE 137
                                   689999***************99******9999888877777777777788777.4555555 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   1.3e-05    0.0093       3      21 ..       6      24 ..       4      31 .. 0.90
   2 ?   -1.7   0.0       3.3   2.3e+03     140     167 ..     115     142 ..      99     143 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.3e-05
                                  EEE--TTSSHHHHHHHHHH CS
                      NTPase_1  3 fiTGppGvGKtTlvkkvle 21
                                  +iTGppG GK+T+++k+ e
  gi|13541453|ref|NP_111141.1|  6 CITGPPGAGKSTVCSKLRE 24
                                  69**************976 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 3.3
                                   HHHHHHT-TT-EEEE--TTTTTTHHHHH CS
                      NTPase_1 140 lveeirerkdvkvfevteenrdalleei 167
                                    +e++++    ++f++ + n d+++++i
  gi|13541453|ref|NP_111141.1| 115 YYESLERLPANRIFTLYNGNIDETAKRI 142
                                   4677788888889999999988888877 PP

>> dNK  Deoxynucleoside kinase
   #    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      31 ..       6      36 ..       5      53 .. 0.79
   2 !    6.8   0.2    0.0077       5.5     125     160 ..      77     120 ..      53     147 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0019
                                  EEEESTTSSHHHHHHHHHCCST.CEEEE-HH CS
                           dNK  2 vveGnIgaGKstlvklLskklg.vkvfeEpv 31
                                  ++ G+ gaGKst+ + L++     k  +E+ 
  gi|13541453|ref|NP_111141.1|  6 CITGPPGAGKSTVCSKLREYGYnCKEGNELA 36
                                  99*************9998642255555555 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0077
                                   EEEEEE--HHHHHHHHHHCTTCCCT...TS-HH.....HHHHHH CS
                           dNK 125 lliYLkasletclerikkRgreeek...kield.....YlekLh 160
                                    +  L+a+l+ +  r++ Rg +eek   +ie++     Y+e+L+
  gi|13541453|ref|NP_111141.1|  77 TVFILEADLNDLIDRMRARGYSEEKiqeNIETQmssifYYESLE 120
                                   445599******************99885554323333777776 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   2.7e-05     0.019      19      40 ..       3      24 ..       1      33 [. 0.89

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.7e-05
                        AAA_30 19 rvavltGpAGtGKttalkalre 40
                                  ++a++tGp+G+GK+t+ ++lre
  gi|13541453|ref|NP_111141.1|  3 KIACITGPPGAGKSTVCSKLRE 24
                                  4789*************99998 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   4.7e-05     0.033       1      21 [.       7      27 ..       7      34 .. 0.86
   2 ?   -1.8   0.0       3.1   2.2e+03     195     203 ..     104     112 ..      64     149 .. 0.53

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.7e-05
                    ATP_bind_1  1 vvGpaGsGKttfvgalseile 21
                                  ++Gp+G+GK+t +++l e+  
  gi|13541453|ref|NP_111141.1|  7 ITGPPGAGKSTVCSKLREYGY 27
                                  68**************99855 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 3.1
                    ATP_bind_1 195 ekykklaea 203
                                   e  ++++++
  gi|13541453|ref|NP_111141.1| 104 ENIETQMSS 112
                                   333333333 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.0   2.5e-05     0.018      26      48 ..       4      25 ..       1     148 [. 0.69

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.5e-05
                        AAA_16 26 lvllsGesGvGKsslvrellral 48
                                  +  ++G++G GKs++  +l++ +
  gi|13541453|ref|NP_111141.1|  4 IACITGPPGAGKSTVCSKLRE-Y 25
                                  6679***************96.3 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0    0.0024       1.7       3      21 ..       6      24 ..       4      71 .. 0.88
   2 ?    4.8   0.0     0.029        21     152     172 ..      92     112 ..      77     118 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0024
                           PRK  3 gvagsSGaGkttvarklek 21
                                   ++g+ GaGk+tv  kl++
  gi|13541453|ref|NP_111141.1|  6 CITGPPGAGKSTVCSKLRE 24
                                  69*************9987 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.029
                           PRK 152 iaeRGrsleavldsilrrkpd 172
                                   + +RG+s e + ++i+ ++ +
  gi|13541453|ref|NP_111141.1|  92 MRARGYSEEKIQENIETQMSS 112
                                   789*************99976 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   5.3e-05     0.038      11      32 ..       2      23 ..       1     114 [. 0.86

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 5.3e-05
                                  TSEEEEEESTTSSHHHHHHHHT CS
                                  xxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran 11 gekvaivGenGaGKStLlklla 32
                                  g++  i+G+ GaGKSt+++ l 
  gi|13541453|ref|NP_111141.1|  2 GKIACITGPPGAGKSTVCSKLR 23
                                  88999***********997765 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   6.3e-05     0.045       2      22 ..       2      22 ..       1      35 [. 0.85

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.3e-05
                        AAA_24  2 klkiliyGpsgiGKTtlakel 22
                                  ++  +i+Gp+g+GK+t++++l
  gi|13541453|ref|NP_111141.1|  2 GKIACITGPPGAGKSTVCSKL 22
                                  56689*************998 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1   0.00094      0.68       4      19 ..       7      22 ..       4      37 .. 0.85
   2 ?    2.8   0.0      0.17   1.2e+02     100     136 ..      77     109 ..      34     117 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00094
                        AAA_33  4 lvGlpGsGKstlaerl 19
                                  + G+pG+GKst+  +l
  gi|13541453|ref|NP_111141.1|  7 ITGPPGAGKSTVCSKL 22
                                  57*********99886 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.17
                        AAA_33 100 rivvvetdeetlkeRlakRaangddrsevpeealdrq 136
                                   ++ ++e+d   l +R ++R  +++      +e++++q
  gi|13541453|ref|NP_111141.1|  77 TVFILEADLNDLIDRMRARGYSEE----KIQENIETQ 109
                                   577899999999999999999754....345555554 PP

>> ADK  Adenylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00042       0.3       1      18 [.       7      24 ..       7      33 .. 0.86
   2 ?    1.4   0.1      0.44   3.2e+02     103     132 ..      75     106 ..      28     121 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00042
                                  EEESTTSSHHHHHHHHHH CS
                                  xxxxxxxxxxxxxxxxxx RF
                           ADK  1 llGaPgaGKGtqaeklvk 18
                                  + G+PgaGK t+++kl +
  gi|13541453|ref|NP_111141.1|  7 ITGPPGAGKSTVCSKLRE 24
                                  67*************975 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.44
                                   ESEEEEEE--HHHHHHHHHT..GSHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxx..xxxxxxxxxx RF
                           ADK 103 ldlvleldvpeevlveRltg..DneetvkkRl 132
                                   + +v+ l+++ + l++R+     +ee++++ +
  gi|13541453|ref|NP_111141.1|  75 CSTVFILEADLNDLIDRMRArgYSEEKIQENI 106
                                   33444444444445555443334555555444 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00014       0.1      33      50 ..       6      23 ..       2      34 .. 0.87
   2 ?   -3.5   0.0       5.7   4.1e+03     229     250 ..      89     110 ..      81     121 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00014
                                  EEEE-TTSSHHHHHHHHH CS
                          MeaB 33 GltGvPGaGkstlvealg 50
                                   +tG PGaGkst+ ++l 
  gi|13541453|ref|NP_111141.1|  6 CITGPPGAGKSTVCSKLR 23
                                  69************9986 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 5.7
                                   HHHHHHTTHHHHHHHHHHHHHH CS
                          MeaB 229 revlkktGllekrrrerakeel 250
                                    + +++ G  e++ +e+ ++++
  gi|13541453|ref|NP_111141.1|  89 IDRMRARGYSEEKIQENIETQM 110
                                   5556666666666665555544 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00016      0.11       3      31 ..       5      37 ..       3      73 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00016
                                  EEEEESTTCCHHHHHHHHH....CT--SS-EEE CS
                          cobW  3 tvltGflGsGKTtLlnhll....enraglklav 31
                                    +tG++G+GK+t+ ++l     ++++g++la 
  gi|13541453|ref|NP_111141.1|  5 ACITGPPGAGKSTVCSKLReygyNCKEGNELAK 37
                                  679***********9999888888888888875 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.2   0.00012     0.086      46      75 ..       3      31 ..       1     114 [. 0.85

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00012
                         Rad17 46 riLLisGPsGCgkstvvkvLskelgiklre 75
                                  +i  i+GP+G gkstv   L +e+g++ +e
  gi|13541453|ref|NP_111141.1|  3 KIACITGPPGAGKSTVCSKL-REYGYNCKE 31
                                  5778************9998.577887776 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   0.00018      0.13      24      38 ..       4      18 ..       1      19 [. 0.86

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00018
                        AAA_29 24 atlltGpsGsGKSTl 38
                                  +  +tGp G+GKST+
  gi|13541453|ref|NP_111141.1|  4 IACITGPPGAGKSTV 18
                                  678***********7 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   0.00012     0.084       3      26 ..       7      29 ..       4     109 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00012
                                  EE-STTSSHHHHHHHHHHHHT-EE CS
                Cytidylate_kin  3 iDGPagsGKssvaralaeklglky 26
                                  i GP g+GKs+v+ +l  + g+++
  gi|13541453|ref|NP_111141.1|  7 ITGPPGAGKSTVCSKLR-EYGYNC 29
                                  88***********9994.455555 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00014       0.1       2      55 ..       3      60 ..       2     106 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00014
                       DUF2075  2 avvlVtGvaGtGKtvvllnllael....eddeeertavylsvNhplvlvlrealakke 55
                                  ++  +tG +G+GK+ v ++l        e +e+ ++   l   +  v+ l+e+la+++
  gi|13541453|ref|NP_111141.1|  3 KIACITGPPGAGKSTVCSKLREYGynckEGNELAKEYGCLFDEEVDVECLEEKLAEDR 60
                                  5788**************9987666655555566666666666666667777777766 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   1.0    0.0005      0.36       2      20 ..       6      24 ..       5     153 .] 0.77

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0005
                                  EEESSTTSSHHHHHHHHHH CS
                           AAA  2 llyGppGtGKTllakavak 20
                                  +++GppG GK+++++ + +
  gi|13541453|ref|NP_111141.1|  6 CITGPPGAGKSTVCSKLRE 24
                                  789***********98755 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00038      0.27       2      19 ..       6      23 ..       5      37 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00038
                  RNA_helicase  2 wlyGpsgeGKStlakeLa 19
                                  +++Gp+g GKSt++ +L 
  gi|13541453|ref|NP_111141.1|  6 CITGPPGAGKSTVCSKLR 23
                                  799***********9974 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.1   0.00069      0.49      33      53 ..       2      22 ..       1      23 [. 0.88

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00069
                        AAA_25 33 gelallaGapgtGKttlaldl 53
                                  g++a ++G+pg+GK+t+++ l
  gi|13541453|ref|NP_111141.1|  2 GKIACITGPPGAGKSTVCSKL 22
                                  778999**********99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       781  (0.0435607); expected 358.6 (0.02)
Passed bias filter:                      628  (0.0350271); expected 358.6 (0.02)
Passed Vit filter:                       114  (0.00635841); 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: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1032.90
//
Query:       gi|13541454|ref|NP_111142.1|  [L=445]
Description: purine-cytosine permease [Thermoplasma volcanium GSS1]
Scores for complete 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-18   64.9  44.4    1.7e-17   63.3  44.4    1.7  1  Transp_cyt_pur   Permease for cytosine/purines, uracil, thiam


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 !   63.3  44.4   9.6e-22   1.7e-17      10     439 ..      28     422 ..      23     423 .. 0.79

  Alignments for each domain:
  == domain 1  score: 63.3 bits;  conditional E-value: 9.6e-22
                Transp_cyt_pur  10 ktlnlfsiWlganlnintwvigalglalgLnwwqsvlviivgnligaifvallglaGakyGlpfpilsRasfGirgsllpl 90 
                                   ++  +f+iW+++nl +  +++g +++ lgL+   ++l+ ++g+l g+i++a +++ G+  ++p++ +    fG +g  + +
  gi|13541454|ref|NP_111142.1|  28 NPSSMFYIWFASNLTVGDFALGFIPVYLGLSESYAILSMVLGTLAGGILLAYMSMLGSINHMPQMEMGKGPFGRIGGSFLA 108
                                   56779********************************************************************55555556 PP

                Transp_cyt_pur  91 llrvviaivwfgvqawiGsealllmlgkifgkwleiggailgtsltelvtffifwvvslvivllgvskirkffviaallvp 171
                                   ll +    +w +v++++ s al+ +l++ +              +++++ +++   + +++  lg  +ir+++ + +++++
  gi|13541454|ref|NP_111142.1| 109 LLQWGNTAGWLTVNVILSSFALYEVLKIPY--------------YFIILLIAV---IVALTAALGYRAIRALERYMSYVLG 172
                                   66799*********************9993..............445555444...4445566889999999999****** PP

                Transp_cyt_pur 172 vaafgfliwalvkaegGpvldkavklgkselflsavagvlagfatlilnapDFtryaktkkssvkiqlvavpllftlllli 252
                                   ++++++ i+++ + +   +++ ++++++  +f  + a++ +  +++ + a+D++r   ++kss k++l ++ + +  ++++
  gi|13541454|ref|NP_111142.1| 173 ILFIVIIIFMVLR-HYTLIYSGSSSVSFIPAFGITFASAFSYIMSWGPYASDYSRHQYSPKSSRKVFLFTLGGSALATVFA 252
                                   **88888887655.5558888776666555677777777777777888888********************9999999998 PP

                Transp_cyt_pur 253 gilvaaaakaayganawspldilakfdetagvl.lililvalaqlgvnisanllsagldlaallPkkinikrgsliaavia 332
                                    i++  +a    g +  +p     +   ++g++ l+ ++ ++ +    ++ nl+s  l + a+ + k  + +g++ia + +
  gi|13541454|ref|NP_111142.1| 253 EIVGMFVAIG-SGNPSGNPA---TDLELVMGSFaLAGMISLFLGGISANAINLYSNSLSFIAMGF-KTRRITGVIIATLFS 328
                                   8877666544.555555555...233333555513445555555556667899999999999999.666666777766666 PP

                Transp_cyt_pur 333 lvivpwkllsssskl..ftaflsllavflspvagviiadyfvvrrgylklaalytrrrgsaYwyrkgvNwravaayivGia 411
                                   ++  +    + + ++    +fl++l++ ++p++gv+ia++f v      +++              + N++ v++y+++i+
  gi|13541454|ref|NP_111142.1| 329 VILGIF---GFTRFYgfYETFLFVLDYWITPWIGVMIAHFFLVHPNTSTMNN-------------TKLNMAGVLSYLISIL 393
                                   666666...55555552668*********************99876655544.............466************* PP

                Transp_cyt_pur 412 aglvgvagsvg..ikvvkgaeklfdlsylv 439
                                   +++++++ + g   ++++ +  + d+sy+v
  gi|13541454|ref|NP_111142.1| 394 ISIPFMS-PAGlfNMPIASILGGVDISYFV 422
                                   *****77.455588899999999*****99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (445 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1020  (0.0568911); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); 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):               1  [number of targets reported over threshold]
# CPU time: 0.69u 0.32s 00:00:01.01 Elapsed: 00:00:00.50
# Mc/sec: 2667.68
//
Query:       gi|13541455|ref|NP_111143.1|  [L=163]
Description: transcription regulator [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-23   83.0   0.7      2e-23   82.8   0.7    1.0  1  SMC_ScpB  Segregation and condensation complex subunit ScpB
  ------ inclusion threshold ------
      0.016   15.0   0.1      0.026   14.4   0.1    1.4  1  HTH_5     Bacterial regulatory protein, arsR family
      0.026   14.4   0.1      0.075   12.9   0.1    1.7  2  MarR_2    MarR family
       0.86    9.8   5.5       0.28   11.4   2.1    1.9  2  DUF3896   Protein of unknown function (DUF3896)


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 !   82.8   0.7   4.5e-27     2e-23       2     157 ..       6     152 ..       5     155 .. 0.95

  Alignments for each domain:
  == domain 1  score: 82.8 bits;  conditional E-value: 4.5e-27
                      SMC_ScpB   2 iiEAiLfvageplsleeLakilelskeeveealeeLkeeyeeedrglelvevaggyrlvtkpelaevvkklvkekkktrLs 82 
                                   ++EAiL++  +pls+++++ il+++  ++++++++L+ ey+++++ le+ +++++yr+++k+e+ +++ ++++     +Ls
  gi|13541455|ref|NP_111143.1|   6 KVEAILYATRNPLSVRSISLILGIEAGAISRIIKKLRLEYKKRNTSLEIAKIGNKYRIQLKKEYYDFAYRVMEP----ELS 82 
                                   79************************************************************************....*** PP

                      SMC_ScpB  83 qaaletLaiIaykqpvtraeieeiRGvnsdsvvrtLlerglieekgrkeepgrpilYgtTekFleyfglksleeL 157
                                   + +   La +a+++  + +   +  G+++d+++++L  + li+ ++    +g+ +   + e+F + fg+++ e L
  gi|13541455|ref|NP_111143.1|  83 KYETGFLATVALNEGASLSFFRKRYGSRTDDMISKLKTMSLIRTSK----KGNGTAIYLGENFEKVFGITKKE-L 152
                                   *********************************************9....5666777789*********9844.4 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   5.9e-06     0.026       1      40 [.       3      42 ..       3      44 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 5.9e-06
                                  SHHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHH CS
                         HTH_5  1 dptRlkILklLaegelcvcelaeelglsqstvShHLkkLr 40
                                  d+t+++ + +  +++l+v  ++ +lg+  +++S+  kkLr
  gi|13541455|ref|NP_111143.1|  3 DETKVEAILYATRNPLSVRSISLILGIEAGAISRIIKKLR 42
                                  7899999999999*********************999998 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   1.7e-05     0.075      16      45 ..      15      41 ..       7      42 .. 0.87
   2 ?   -3.5   0.0       2.3     1e+04      42      54 ..     115     127 ..     113     130 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.7e-05
                                  CTTTSEEEHHHHHHHHTSSHHHHHHHHHHH CS
                        MarR_2 16 rrpgrdltvgelarrlglsksavsrilkrL 45
                                  r+p   l+v+ +   lg++ +a+sri+k+L
  gi|13541455|ref|NP_111143.1| 15 RNP---LSVRSISLILGIEAGAISRIIKKL 41
                                  444...9**********************9 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 2.3
                                   HHHHHHTTSEEEE CS
                        MarR_2  42 lkrLvaaGLverr 54 
                                   + +L    L++++
  gi|13541455|ref|NP_111143.1| 115 ISKLKTMSLIRTS 127
                                   6678888899887 PP

>> DUF3896  Protein of unknown function (DUF3896)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   2.1   6.3e-05      0.28      11      61 .]      40      88 ..      36      88 .. 0.86
   2 ?   -1.2   0.1      0.54   2.4e+03      20      32 ..     113     125 ..     104     155 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 6.3e-05
                       DUF3896 11 kkyleekkqqlCkklssltlskkereqlkleidnyeyilnlvemnhyerGf 61
                                  k  le kk++    l+  ++ +k r qlk+e  ++ y +   e+  ye Gf
  gi|13541455|ref|NP_111143.1| 40 KLRLEYKKRNT--SLEIAKIGNKYRIQLKKEYYDFAYRVMEPELSKYETGF 88
                                  44689999986..56667889****************99999********9 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.54
                       DUF3896  20 qlCkklssltlsk 32 
                                   ++  kl+++ l +
  gi|13541455|ref|NP_111143.1| 113 DMISKLKTMSLIR 125
                                   5666777776633 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       674  (0.0375927); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 1285.28
//
Query:       gi|13541456|ref|NP_111144.1|  [L=435]
Description: phosphoribosylamine--glycine ligase [Thermoplasma volcanium GSS1]
Scores for complete 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-53  180.0   0.2    5.8e-53  179.6   0.2    1.2  1  GARS_A        Phosphoribosylglycinamide synthetase, ATP-grasp
    1.3e-16   61.2   0.0    2.9e-16   60.0   0.0    1.6  1  GARS_N        Phosphoribosylglycinamide synthetase, N domain
    1.5e-06   28.4   0.0    4.8e-06   26.8   0.0    1.9  1  GARS_C        Phosphoribosylglycinamide synthetase, C domain
     0.0057   17.5   0.0      0.011   16.5   0.0    1.5  1  GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fol
  ------ inclusion threshold ------
      0.053   13.6   0.0      0.091   12.8   0.0    1.4  1  Shikimate_DH  Shikimate / quinate 5-dehydrogenase
       0.11   11.9   0.1       0.21   11.0   0.1    1.4  1  GSH-S_ATP     Prokaryotic glutathione synthetase, ATP-grasp d
       0.15   11.2   0.1       0.31   10.3   0.1    1.5  1  ATPgrasp_ST   Sugar-transfer associated ATP-grasp


Domain annotation for each model (and alignments):
>> GARS_A  Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  179.6   0.2   2.3e-56   5.8e-53       1     193 [.     104     297 ..     104     298 .. 0.95

  Alignments for each domain:
  == domain 1  score: 179.6 bits;  conditional E-value: 2.3e-56
                                   HBHHHHHHHHHHTT--B-.-EEEESSHHHHHHHHHHHSSSEEEEEESC-GGGT-EEEE....SSHHHHHHHHHHHCTS-TT CS
                        GARS_A   1 asKsfakdllkkagipta.eyeaftdpeeakeyieeatakalVvKadglaagKgviva....kseeealkavkeilekkkf 76 
                                   +sK f++dll+++ ip+  +y++  + +e+k+++++ ++++  vK+ gl++gKgv+v+    ks+ ea++++ e+l+  + 
  gi|13541456|ref|NP_111144.1| 104 TSKMFMRDLLTRHSIPGNiNYKKCFSEQEVKDFFDKNKKDV-AVKPIGLTGGKGVKVMgeqlKSQGEAINYAIEVLQ--RD 181
                                   79***************99******************9999.9**************999999999**********7..44 PP

                                   CCCCSSEEEEE---SEEEEEEEEECTTEEEE---BEEEEEEECCCEEEEECECEEEE....S-TTS-HHHHHHHHHHTHHH CS
                        GARS_A  77 GeagekvviEelleGeEvsllalvdgktvkplplaqdhkrvlegDkgpnTGGmGays....papvvteellekikeeilep 153
                                   G     v+iE+++ GeE+sl+a++dgk++  +p++qd+kr++egD+gpnTGGmG++s     +p++++++ e++++ i++ 
  gi|13541456|ref|NP_111144.1| 182 G----VVLIEDRMIGEEFSLQAFTDGKNTSFMPIVQDYKRAFEGDTGPNTGGMGSISdvnfSLPFLSKKAPEDARH-IIND 257
                                   4....89**************************************************8877789999999999887.**** PP

                                   HHHHHHCTT---EEEEEEEEEEETTEEEEEEEESS--TTC CS
                        GARS_A 154 tveglkkegipfkGvLyaglmlvedgpkvlefnvRfgDpe 193
                                   +v ++ +e+ipfkGv+y+++m ++dg kv+e+n+Rf+Dpe
  gi|13541456|ref|NP_111144.1| 258 VVRAMYDENIPFKGVMYGQFMDTPDGVKVIEINARFADPE 297
                                   ***************************************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 !   60.0   0.0   1.1e-19   2.9e-16       2      90 .]       4     103 ..       3     103 .. 0.91

  Alignments for each domain:
  == domain 1  score: 60.0 bits;  conditional E-value: 1.1e-19
                                   EEEEEESSHHHHHHHHHHTTSTTESEEEEEE..--CGG............TTHHHHHHHHHHCTESEEEE-SHHHHHTTHH CS
                        GARS_N   2 kvLvvGsGGRehalawklaqspkvekvyvap..gNagt............edlealvefakeekidlvvvGpeapLvaGva 68 
                                   +vL++GsGGRe a+a+++++s    k++ +   +N+++            +d++++ +fa + ++d+v+vGp+  L + ++
  gi|13541456|ref|NP_111144.1|   4 RVLLIGSGGREDAIARAIKRSGA--KLFSVIghENPSIkrlsekyligdeKDYKSIEDFALSSSVDIVFVGPDPVLETPLV 82 
                                   79******************954..566555348999999999999999888899************************** PP

                                   HHHHHHHT-EEES--CCCCHHH CS
                        GARS_N  69 daleeekgikvfGpskeaAqlE 90 
                                   ++l ++ gi+v +p+ eaAq+E
  gi|13541456|ref|NP_111144.1|  83 NNLLKR-GIAVASPTMEAAQIE 103
                                   ***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 !   26.8   0.0   1.9e-09   4.8e-06       2      80 .]     333     420 ..     332     420 .. 0.83

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 1.9e-09
                                   EEEEEEETTT.....TSS--ST-EEBSTTEEEEESSEE.....EEE-SSEEEEEEEEESSHHHHHHHHHHHHTTCB-TTEE CS
                        GARS_C   2 vgvvlaskGY.....Pgsyekgkeitgegvkvfhagtk.....lvtsGGRvlavvavgetleeArakayeavkkikfeglf 72 
                                   v  ++++ GY     Pg+ + + ei++ ++++++a ++     + +s++R la+ + ++++ eA + + +a+k ++  + +
  gi|13541456|ref|NP_111144.1| 333 VLKYIVPPGYgqaplPGDLHIDPEIEKLDTELYYAAVSgtlydVKMSSSRSLAILGKADNIPEASEMVDSALKYVHG-SYY 412
                                   66788999995555556666666776666779999887888999******************************985.799 PP

                                   --STTTHH CS
                        GARS_C  73 yRkDIGar 80 
                                   +R+DIG++
  gi|13541456|ref|NP_111144.1| 413 VRRDIGKK 420
                                   9*****85 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 !   16.5   0.0   4.4e-06     0.011       2      89 ..       4      92 ..       3      94 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 4.4e-06
                                  EEEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHE...EESSHHHHHTCTTESEEEE-S-GGGHHHHHHH CS
                  GFO_IDH_MocA  2 rvaiiGaGkigskhlrplnesqrleevvalldpdaeraeavaesfgve...aysdleelladpeidavivatpngtheelaka 81
                                  rv++iG+G   +  +r++++s  ++++  ++  ++++ ++++e++ +     y+++e+ + ++ +d+v+v+  + +   l+ +
  gi|13541456|ref|NP_111144.1|  4 RVLLIGSGGREDAIARAIKRS--GAKLFSVIGHENPSIKRLSEKYLIGdekDYKSIEDFALSSSVDIVFVGPDPVLETPLVNN 84
                                  7999***88877778777777..99********************9998899******99999******************** PP

                                  HHHTT-EE CS
                  GFO_IDH_MocA 82 aleagkhv 89
                                  +l++g++v
  gi|13541456|ref|NP_111144.1| 85 LLKRGIAV 92
                                  ******98 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   3.5e-05     0.091      13      82 ..       3      72 ..       1     104 [. 0.87

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.5e-05
                                  -EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHH.T.ET-EEEEGCGHHHHHHT-SEEEE- CS
                  Shikimate_DH 13 kkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeel.kgeeiealkleelkellaeadvvisa 82
                                  ++vlliG G     +a+++ ++g+k   v++ +    k+l e++  g+e  ++++e+   l +++d+v++ 
  gi|13541456|ref|NP_111144.1|  3 SRVLLIGSGGREDAIARAIKRSGAKLFSVIGHENPSIKRLSEKYlIGDEKDYKSIEDFA-LSSSVDIVFVG 72
                                  68*****************************************9878889999999997.78899999974 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 ?   11.0   0.1   8.1e-05      0.21      21      56 ..     130     166 ..     122     192 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 8.1e-05
                                   HHHHHHHHHHHSS.EEEEESS--TTTT-EEE-TT-TT CS
                     GSH-S_ATP  21 keeirafleeqgd.vilKPldgkgGegvfrvkksdpn 56 
                                   ++e+++f +++++ v +KP++ +gG+gv  + ++ ++
  gi|13541456|ref|NP_111144.1| 130 EQEVKDFFDKNKKdVAVKPIGLTGGKGVKVMGEQLKS 166
                                   68899988776544**************887666333 PP

>> ATPgrasp_ST  Sugar-transfer associated ATP-grasp
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   0.00012      0.31      28      92 ..     112     168 ..      95     187 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00012
                   ATPgrasp_ST  28 lalraglkvpkllgvikeqaeiseleafvkeleegvviKpakgsgGkGilviteredqdylkssg 92 
                                   l+ r+ ++ +  +  +    + +e+++f  + +++v++Kp+   gGkG+ v+ e      lks+g
  gi|13541456|ref|NP_111144.1| 112 LLTRHSIPGNINYKKCF---SEQEVKDFFDKNKKDVAVKPIGLTGGKGVKVMGE-----QLKSQG 168
                                   44444444444333333...345667778888899****************966.....334444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (435 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       365  (0.0203581); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 2880.35
//
Query:       gi|13541457|ref|NP_111145.1|  [L=89]
Description: hypothetical protein TVN0626 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-32  111.9   0.1    1.2e-32  111.8   0.1    1.0  1  UPF0147   Uncharacterised protein family (UPF0147)
     0.0071   16.6   0.1        4.7    7.6   0.0    2.2  2  UPF0253   Uncharacterised protein family (UPF0253)
  ------ inclusion threshold ------
      0.069   13.3   0.0        0.1   12.7   0.0    1.5  1  Abi_C     Abortive infection C-terminus


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 !  111.8   0.1     2e-36   1.2e-32       2      80 ..       7      85 ..       6      86 .. 0.97

  Alignments for each domain:
  == domain 1  score: 111.8 bits;  conditional E-value: 2e-36
                                  HHHHHHHHHHHHHHHT-TTS-HHHHHHHHHHHHHHT-TTS-HHHHHHHHHHHHHHHHT-TTS-HHHHHHHHHHHHHHHH CS
                       UPF0147  2 eekikevielLeeiiedtsvPrniRraakeakekLkdekeslavraataisiLdeisnDpnmPlhaRtliwevvskLEt 80
                                  ++ ++ev++lL+e+++dt+vP+n+R++a+++k+kL++e+esl++r+at++s+Lde++nDpn+P+h Rt +++++skLE+
  gi|13541457|ref|NP_111145.1|  7 QNLFNEVMYLLDELSQDTTVPKNVRKVAQDSKTKLSQENESLDLRCATVLSMLDEMANDPNVPSHGRTDLYTIISKLEA 85
                                  6789**************************************************************************8 PP

>> UPF0253  Uncharacterised protein family (UPF0253)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.0    0.0011       6.7      30      51 ..      13      34 ..       6      37 .. 0.89
   2 !    7.6   0.0   0.00079       4.7      29      48 ..      54      73 ..      48      76 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0011
                       UPF0253 30 alktLdevaanealpeevrekA 51
                                  ++  Lde+ ++  +p++vr  A
  gi|13541457|ref|NP_111145.1| 13 VMYLLDELSQDTTVPKNVRKVA 34
                                  7889***************876 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.00079
                       UPF0253 29 calktLdevaanealpeevr 48
                                   +l  Lde+a++ ++p++ r
  gi|13541457|ref|NP_111145.1| 54 TVLSMLDEMANDPNVPSHGR 73
                                  6899************8765 PP

>> Abi_C  Abortive infection C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   1.7e-05       0.1      22      67 ..      39      85 ..       7      87 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.7e-05
                         Abi_C 22 apgakeikqilsglasivqglgeLRNk.ggtaHGrdskrkklsprhA 67
                                   + ++e +++   +a++++ l e+ N+    +HGr++ ++ +s+ +A
  gi|13541457|ref|NP_111145.1| 39 TKLSQENESLDLRCATVLSMLDEMANDpNVPSHGRTDLYTIISKLEA 85
                                  556666667777899*****************************999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       753  (0.041999); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 622.07
//
Query:       gi|13541458|ref|NP_111146.1|  [L=120]
Description: ArsR family transcriptional regulator [Thermoplasma volcanium GSS1]
Scores for 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-06   25.4   0.0    1.2e-05   25.0   0.0    1.2  1  SMC_ScpB   Segregation and condensation complex subunit ScpB
    5.8e-05   22.9   0.0    8.2e-05   22.4   0.0    1.3  1  MarR_2     MarR family
     0.0034   17.2   0.1      0.011   15.6   0.0    1.8  2  TrmB       Sugar-specific transcriptional regulator TrmB
  ------ inclusion threshold ------
      0.019   15.1   0.1      0.035   14.3   0.1    1.4  1  DUF2582    Winged helix-turn-helix domain (DUF2582)
      0.037   13.6   0.1      0.072   12.7   0.1    1.4  1  DUF3918    Protein of unknown function (DUF3918)
      0.042   14.2   0.0        0.1   13.0   0.0    1.7  1  Rrf2       Transcriptional regulator
      0.075   13.0   0.0       0.17   11.9   0.0    1.7  1  HTH_Crp_2  Crp-like helix-turn-helix domain
      0.098   12.9   0.0       0.14   12.3   0.0    1.3  1  HTH_34     Winged helix DNA-binding 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 !   25.0   0.0   5.2e-09   1.2e-05      68     149 ..      12      94 ..       2     109 .. 0.80

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 5.2e-09
                      SMC_ScpB  68 vvkklvkekkktrLsqaaletLaiIaykqpvtraeiee...iRGvnsdsvvrtLlerglieekgrkee.pgrpil.YgtTe 143
                                   ++k l+     +++ ++   tL +I  k+ vt+ eie+   +R  +++ +++ L ++g+i++++ k+e +grpi  Y++++
  gi|13541458|ref|NP_111146.1|  12 LAKYLMI----ADIPRSVAYTLVYIRDKDEVTSVEIERetgLRQPEVSIAMQWLRRKGWITKRNMKKEgKGRPIHgYRLSK 88 
                                   3333333....488999999****************9755577888999***********999876666*****99***** PP

                      SMC_ScpB 144 kFleyf 149
                                    F e +
  gi|13541458|ref|NP_111146.1|  89 SFSEIL 94 
                                   **9876 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   3.7e-08   8.2e-05       2      54 ..      20      70 ..      19      79 .. 0.91

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 3.7e-08
                                  T--HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                        MarR_2  2 gltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                  +++++ a  L ++++ ++  +t  e++r++gl ++ vs + + L ++G++++r
  gi|13541458|ref|NP_111146.1| 20 DIPRSVAYTLVYIRDKDE--VTSVEIERETGLRQPEVSIAMQWLRRKGWITKR 70
                                  678889999*********..******************************998 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.54   1.2e+03      31      41 ..      18      28 ..       5      31 .. 0.74
   2 !   15.6   0.0     5e-06     0.011      19      58 ..      34      73 ..      24      86 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.54
                                  CTTSSCHCHHH CS
                          TrmB 31 elgvprskvYe 41
                                  ++++prs +Y 
  gi|13541458|ref|NP_111146.1| 18 IADIPRSVAYT 28
                                  46899999996 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 5e-06
                                  HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                          TrmB 19 klgpatadeiaeelgvprskvYevLrsLedkGlVerekgr 58
                                   +++ t  ei +e+g+ ++ v  +++ L +kG+++++  +
  gi|13541458|ref|NP_111146.1| 34 DKDEVTSVEIERETGLRQPEVSIAMQWLRRKGWITKRNMK 73
                                  57789999***************************99876 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 ?   14.3   0.1   1.6e-05     0.035      19      55 ..      34      70 ..      30      77 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.6e-05
                                  CSSSEEHHHHHHHCT-SCHHHHHHHHHHHCTTSEEEE CS
                       DUF2582 19 engeislkelkrktglsdkelalAiGWLaREdKivie 55
                                  +++e++  e++r+tgl + e+  A+ WL R + i  +
  gi|13541458|ref|NP_111146.1| 34 DKDEVTSVEIERETGLRQPEVSIAMQWLRRKGWITKR 70
                                  6789999***********************8877655 PP

>> DUF3918  Protein of unknown function (DUF3918)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   3.2e-05     0.072      17      37 ..      57      77 ..      55      78 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.2e-05
                       DUF3918 17 ayqmaqkndmmskRnMKKlrk 37
                                  a q  ++++ ++kRnMKK +k
  gi|13541458|ref|NP_111146.1| 57 AMQWLRRKGWITKRNMKKEGK 77
                                  789999************766 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   4.5e-05       0.1      14      74 ..      29      93 ..      23     101 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.5e-05
                                  HHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE....TTT-T...CEEESSHCCCS CS
                          Rrf2 14 llyLakeeeeepvsseeiaerqnispsylekilakLrkaglvksv....rGkgG...GyrLakppeeI 74
                                  l+y+  ++e   v+s ei +++++ ++ ++  ++ Lr++g+++ +    +Gkg    GyrL+k+ +eI
  gi|13541458|ref|NP_111146.1| 29 LVYIRDKDE---VTSVEIERETGLRQPEVSIAMQWLRRKGWITKRnmkkEGKGRpihGYRLSKSFSEI 93
                                  445444444...9*****************************97522225654244478888877777 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   7.5e-05      0.17      21      55 ..      37      71 ..      10      75 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 7.5e-05
                                  EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEETE CS
                     HTH_Crp_2 21 pltqeelAsmlGltretvsrilseLkreglisrgr 55
                                   +t  e+ +  Gl++  vs +++ L+r+g+i++++
  gi|13541458|ref|NP_111146.1| 37 EVTSVEIERETGLRQPEVSIAMQWLRRKGWITKRN 71
                                  56777777889*********************653 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   6.3e-05      0.14       6      54 ..      29      77 ..      27     105 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.3e-05
                        HTH_34  6 lsyLasvdeadfvelkealeatdgnLsvhlkkLekagYievdkefkgkk 54
                                  l y  ++de++ ve+  ++++ + + s+ ++ L  +g+i+ +  +k++k
  gi|13541458|ref|NP_111146.1| 29 LVYIRDKDEVTSVEIERETGLRQPEVSIAMQWLRRKGWITKRNMKKEGK 77
                                  5677889********************************9766555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1156  (0.0644765); expected 358.6 (0.02)
Passed bias filter:                      698  (0.0389313); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 761.27
//
Query:       gi|13541459|ref|NP_111147.1|  [L=666]
Description: hypothetical protein TVN0628 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        1.3    7.9  49.2    1.8e+02    0.8  49.2    2.9  1  STT3      Oligosaccharyl transferase STT3 subunit


Domain annotation for each model (and alignments):
>> STT3  Oligosaccharyl transferase STT3 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8  49.2      0.01   1.8e+02      76     329 ..      63     348 ..      53     470 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.01
                                   TTCCHCCC.CHHHHHHCCHHCHHHHHHHHCCHHHHHHHHCHHHHHHHHHH.S-CCCHHHHHHHCCC-CCCCCTTSTT--ST CS
                          STT3  76 ygplivlLamlasaiinhsldvsirevclwlpallgsLlaIpiyflvrel.ksdiaGllAAlllaiaPgYlsrtvaGfyDt 155
                                   yg++ +++ ++++ +i++++ ++      ++p+++g+L++ +iyf+++e+ k+++ ++l+A++la+ P+  ++t   +   
  gi|13541459|ref|NP_111147.1|  63 YGSF-PVM-YWVISVIYFFTGIKWVYLLKFVPPVFGGLTVTIIYFIAKEItKDERVAFLSAIFLAVDPVQAYQTSISSI-- 139
                                   5544.555.8***********99999999******************99725779**************9888888775.. PP

                                   CCCCHHHHHHHHHHHHHHHHCCSTTCHHHHHHHHHHHHHHTTSCCGGHHHHCCHHHHHHHHHCTTT.............S- CS
                          STT3 156 dmfeivlllfvlffflkaiktksnkislaviaaliiflivlaWggyailiyallllfilalLiigr.............fe 223
                                    +f  ++ l+++ +fl +  + +    ++v a ++  l+v++     +++y l +l ila+   +r             f+
  gi|13541459|ref|NP_111147.1| 140 LVFGHFFGLLTILTFLTSFRNTK----YFVSATVFSVLLVMSHQLS-TFMYLLEMLGILAYYKLSRgsiglyhkiyieaFS 215
                                   68999******************....***************9997.9****99999999999999888888777777744 PP

                                   CCHHHHH................HHHHHHHHHH..CCCCCCCTTCHHHSTTTCHHCCCCHHHHHHHHCCCHHC..CCCCCH CS
                          STT3 224 lklkiav................tfsviiaflviaiivllflgfqvvavseiigalgifgllqlvafgsvvvlvaelkfyq 288
                                   +++ +                  +++  i ++ + +++ lf+ + ++ +s ++ a     ++      +++vl++ +    
  gi|13541459|ref|NP_111147.1| 216 SFMFLYWiinvkhtlgfisggslGIPWYITISIYFVLLTLFISLPKKYTSSLLWAIKKLRPINYKHTTKLAVLLSFVIPLA 296
                                   433222245777777777788886666666666666777777777666666666666666666555556666655555555 PP

                                   HCCCHHTT.HHHHTT--GGGHHHHHHHHHHHHC............CCCCCTS- CS
                          STT3 289 fislfqpgilsevlgligevvtalavlglialw............lgilysll 329
                                    i+l++   +++++g +  v  ++ +++ ia++            lg+l  ll
  gi|13541459|ref|NP_111147.1| 297 GIVLMRRY-ITNITGYTFAVFIPILLTVSIASVgyivawkkypvlLGMLALLL 348
                                   55566666.78888887777777777777777755555555555534433333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (666 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1003  (0.0559429); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.69u 0.28s 00:00:00.97 Elapsed: 00:00:00.46
# Mc/sec: 4318.07
//
Query:       gi|13541460|ref|NP_111148.1|  [L=233]
Description: SAM-dependent methyltransfera [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-05   25.5   0.0    5.1e-05   23.9   0.0    1.8  2  Methyltransf_25  Methyltransferase domain
     0.0001   22.9   0.0    0.00035   21.1   0.0    1.9  2  Methyltransf_11  Methyltransferase domain
    0.00021   21.2   0.0    0.00031   20.6   0.0    1.5  1  Methyltransf_23  Methyltransferase domain
    0.00084   18.8   0.0     0.0013   18.2   0.0    1.3  1  TehB             Tellurite resistance protein TehB
     0.0033   17.2   0.0     0.0055   16.5   0.0    1.5  1  Methyltransf_31  Methyltransferase domain
  ------ inclusion threshold ------
      0.063   13.2   0.0        0.1   12.5   0.0    1.3  1  Clat_adaptor_s   Clathrin adaptor complex small chain


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 ?   -2.1   0.0       2.2   6.6e+03      54      73 ..      23      42 ..      11      56 .. 0.60
   2 !   23.9   0.0   1.7e-08   5.1e-05       1      76 [.      64     130 ..      64     146 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 2.2
                                  BCCGBSSSTTTEEEEEEEST CS
               Methyltransf_25 54 daedlpfedgsfDlvvssga 73
                                  + e ++  dg++D+  +s+ 
  gi|13541460|ref|NP_111148.1| 23 SYEMIETSDGKIDVTSISYY 42
                                  33455566666666666543 PP

  == domain 2  score: 23.9 bits;  conditional E-value: 1.7e-08
                                   EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEEST.GGG CS
               Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssga.lhh 76 
                                   ++d+G+G Gr++l+l k++  ++v  +Dis++++  +++r         + ++++ +l++ d sfD  ++ g+ + +
  gi|13541460|ref|NP_111148.1|  64 IVDAGAGAGRHSLYLRKKG--YQVFPFDISPGAVSVMKKRG--------LDNASIMSLEEFDMSFDTLLLLGNnFGL 130
                                   89****************5..*******************9........5567777777777777777776655554 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       1.6   4.7e+03      49      74 ..      21      46 ..       6      54 .. 0.74
   2 !   21.1   0.0   1.2e-07   0.00035       1      63 [.      65     119 ..      65     135 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.6
                                  TEECCCTSS-TT-EEEEEEES-CCC- CS
               Methyltransf_11 49 vadaeklpfednsfDlvvssevlhhv 74
                                  +++ e +   d+++D+  +s  + + 
  gi|13541460|ref|NP_111148.1| 21 HCSYEMIETSDGKIDVTSISYYFKNY 46
                                  55667778889999988888777665 PP

  == domain 2  score: 21.1 bits;  conditional E-value: 1.2e-07
                                   EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EE CS
               Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfD 63 
                                   +d+G+G+Gr++ +l k+g++v+ +D+s+ ++ + k+++ ++        +++e+    d sfD
  gi|13541460|ref|NP_111148.1|  65 VDAGAGAGRHSLYLRKKGYQVFPFDISPGAVSVMKKRGLDNA-----SIMSLEE---FDMSFD 119
                                   599****************************99999987765.....3333333...244555 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0     1e-07   0.00031      22     115 ..      60     154 ..      40     213 .. 0.72

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 1e-07
               Methyltransf_23  22 aggrvLdiGcGtGillevlrengfsvtgvDlspeaveiaekakkaqkdqfdeqeaaepqgkfdlIvl....revlehvpdp 98 
                                   a+g ++d G+G G+ + +lr++g++v  +D+sp av+     kk   d++  ++ +e + +fd+  l    + +l + +  
  gi|13541460|ref|NP_111148.1|  60 AKGIIVDAGAGAGRHSLYLRKKGYQVFPFDISPGAVSVM---KKRGLDNASIMSLEEFDMSFDTLLLlgnnFGLLRSYKKA 137
                                   577899***************************999976...555555555556666666666665422224556666666 PP

               Methyltransf_23  99 pellrqiatllkpgGyl 115
                                   p +lr++++  ++ + +
  gi|13541460|ref|NP_111148.1| 138 PIYLRKLYEKSSDHAMI 154
                                   66666666655555555 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   4.2e-07    0.0013       8      69 ..      41      99 ..      35     122 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 4.2e-07
                                  HHHHHHT-----HHHHHHCCCS-S-EEEEES-TTSHHHHHHHHTT-EEEEEES-HHHHHHHH CS
                          TehB  8 yfskkynltathsevveavkivkpgkvldlgcgqgrnslylsllgydvtawdknensiafle 69
                                  y+ k y+  +   +  +a++    g ++d g g gr slyl  +gy+v  +d    +++ ++
  gi|13541460|ref|NP_111148.1| 41 YYFKNYDQWPLMEQ--KAIEYA-KGIIVDAGAGAGRHSLYLRKKGYQVFPFDISPGAVSVMK 99
                                  55555555554332..334433.35689********************99998777766554 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   1.9e-06    0.0055       7      62 ..      64     112 ..      58     151 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.9e-06
               Methyltransf_31   7 vlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgd 62 
                                   ++D+G+G+G+ ++ l ++   + +v+ +Dis+ a+++++++    gldn++    +
  gi|13541460|ref|NP_111148.1|  64 IVDAGAGAGRHSLYLRKK---GYQVFPFDISPGAVSVMKKR----GLDNASIMSLE 112
                                   79**************66...567***************97....88877655444 PP

>> Clat_adaptor_s  Clathrin adaptor complex small chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   3.5e-05       0.1      10      76 ..     135     201 ..     129     219 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.5e-05
                                   TTS-EEEEEESSSS-CHHHHHHHHHHHHHHHTT-SSS-SEEEETT..EEEEEEEETTEEEEEEEETTS- CS
                Clat_adaptor_s  10 kkgkvrlakfytavddkkkqklieevyelvsaRdsklsniveled..lkviYkryasLYFvvivdeqen 76 
                                   kk+ + l k y +++d  ++ +i e +  vs+R +   + +e  d  ++v+Yk+y + +F  ++ ++e+
  gi|13541460|ref|NP_111148.1| 135 KKAPIYLRKLYEKSSD--HAMIIGETTDPVSTRFASNDSGLEAGDltIRVVYKEYKTPWFEYMLASKEK 201
                                   5667788999988776..5789***********8887778888888899***********888877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1546.53
//
Query:       gi|13541461|ref|NP_111149.1|  [L=614]
Description: Mg-chelatase, I and D subunits [Thermoplasma volcanium GSS1]
Scores for complete 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   48.3   0.1    1.7e-12   47.0   0.1    1.7  1  AAA_lid_2        AAA lid domain
    5.4e-12   45.5   0.0    8.6e-11   41.6   0.0    2.3  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
    1.8e-10   41.4   0.9    3.1e-09   37.4   0.1    2.8  3  VWA_2            von Willebrand factor type A domain
    7.2e-09   35.8   0.0    4.9e-05   23.4   0.0    2.5  2  AAA_5            AAA domain (dynein-related subfamily)
    2.4e-05   24.7   0.0    6.6e-05   23.2   0.0    1.7  1  VWA              von Willebrand factor type A domain
    5.1e-05   22.5   0.1    0.00038   19.6   0.0    2.3  2  MCM              MCM P-loop domain
    0.00027   20.4   0.4     0.0005   19.5   0.4    1.4  1  VWA_CoxE         VWA domain containing CoxE-like protein
      0.001   19.5   0.0     0.0035   17.8   0.0    1.9  1  AAA_16           AAA ATPase domain
     0.0023   17.6   0.0        0.3   10.8   0.0    2.3  2  Sigma54_activat  Sigma-54 interaction domain
  ------ inclusion threshold ------
      0.015   15.7   0.0      0.077   13.4   0.0    2.2  1  AAA              ATPase family associated with various cellul
      0.092   12.8   0.0        0.3   11.2   0.0    2.1  1  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
       0.16   12.1   0.5       0.49   10.6   0.5    1.9  1  TIP49_C          TIP49 AAA-lid domain
       0.16   12.1   0.5         17    5.6   0.0    2.8  3  YadA_anchor      YadA-like membrane anchor domain
        0.2   12.3   4.2       0.11   13.1   1.1    2.2  2  Mg_chelatase_C   Magnesium chelatase, subunit ChlI C-terminal


Domain annotation for each model (and alignments):
>> AAA_lid_2  AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.0   0.1   1.3e-15   1.7e-12       4      60 ..     267     322 ..     264     333 .. 0.85

  Alignments for each domain:
  == domain 1  score: 47.0 bits;  conditional E-value: 1.3e-15
                     AAA_lid_2   4 rahlaielgvsgrRadlallraArAlAalegrdyVtpeDvkeaaplVLaHRlrrepe 60 
                                   +a+  i+l++  r a +++++a++A+Aal+gr++V+ eDv++a  l L HR++ +  
  gi|13541461|ref|NP_111149.1| 267 IANVVIKLNAGNR-AMITAIKASKAIAALAGRKKVNIEDVERALYLTLKHRVQDKSM 322
                                   6667788888777.*************************************995544 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.6   0.0   6.7e-14   8.6e-11       2     159 ..       8     188 ..       7     198 .. 0.80

  Alignments for each domain:
  == domain 1  score: 41.6 bits;  conditional E-value: 6.7e-14
                  Mg_chelatase   2 lkdvkGqeeakraleiaaaGgH..nlllvGppGsGKtmlakrlpsllpplseee....alevakiasvag....kkeeekl 72 
                                   ++ v+G+++ k+al i a       +l+ Gp G  K+ +a+ l  +lp+++  +      +    +s+++    k e+ ++
  gi|13541461|ref|NP_111149.1|   8 FSAVVGEDDLKEALLINAVNPRigGVLIRGPKGVAKSTIARSLIDILPEIDVVKdcpfKCDPDDYESMCDecriKYEKGQI 88 
                                   67899***********9987542279***********************98765122223445667776533223444455 PP

                  Mg_chelatase  73 lkrr...pfraphhsaskaalvGg.........gs.kpkpGeislahnGvLfLDElpefkrkvlevLRePledgevtisra 140
                                   ++ r   pf++   sa+   ++G+         g    +pG ++ a++G++++DE+  ++ +v++++ +   +g  +++r 
  gi|13541461|ref|NP_111149.1|  89 VRDRrkmPFVDLPVSATIDRVIGSidiskavneGIkALQPGLLADANRGIIYIDEVNLLDDSVIDAILDAAASGINVVERE 169
                                   54333349***99****9999997666555544333789****************************************** PP

                  Mg_chelatase 141 kakvefparfqlvaamNpc 159
                                     ++ +pa+f l+ +mNp 
  gi|13541461|ref|NP_111149.1| 170 GVSIVHPAKFILIGTMNPE 188
                                   *****************95 PP

>> VWA_2  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       2.2   2.8e+03      49      91 ..     268     315 ..     252     323 .. 0.65
   2 ?    0.5   0.0      0.73   9.4e+02      55      94 ..     382     421 ..     372     430 .. 0.73
   3 !   37.4   0.1   2.4e-12   3.1e-09       1     106 [.     440     541 ..     440     542 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 2.2
                         VWA_2  49 pevlipltkdkakilnalrnleak.....gggtnlaaaLqlarkalkk 91 
                                   ++v+i+l+ +++++ +a+++ +a      +++ n+++  + +  +lk+
  gi|13541461|ref|NP_111149.1| 268 ANVVIKLNAGNRAMITAIKASKAIaalagRKKVNIEDVERALYLTLKH 315
                                   466777777777777777777666666655666666655555555555 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.73
                         VWA_2  55 ltkdkakilnalrnleakgggtnlaaaLqlarkalkkrrk 94 
                                    t+++a + +++rnl++ + gt ++a   l++ al+++++
  gi|13541461|ref|NP_111149.1| 382 STSGRAGVADIIRNLDYNRTGTVFNAYETLVKMALNHDNR 421
                                   478899999*******988888777776666677887763 PP

  == domain 3  score: 37.4 bits;  conditional E-value: 2.4e-12
                         VWA_2   1 lvfvlDtSgSmrngdygptrleaakdaveallksl.p.gdrvglvtfsd.gpevlipltkdkakilnalrnleakgggtnl 78 
                                   +++ lD S Sm++     +r+++a+ +++++lks  + +++++ +tfs+ +  v + +t+d ++i++++  + ak g+t l
  gi|13541461|ref|NP_111149.1| 440 VILALDASRSMETM----KRIAIARGIARDFLKSAyRmRVKMSYLTFSGsDTAVRVEMTRDIGRIEEEIMHTVAK-GKTPL 515
                                   6899*********9....6**************6546688*********889*********************97.***** PP

                         VWA_2  79 aaaLqlarkalkkrrkgekrvivlitDg 106
                                    +aL+++ ++ ++ r  ++ v +litDg
  gi|13541461|ref|NP_111149.1| 516 PSALKKMYEISSRYR--KRTVSILITDG 541
                                   ************987..99999*****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 !    9.8   0.0   0.00059      0.75       2      23 ..      33      54 ..      32      68 .. 0.88
   2 !   23.4   0.0   3.8e-08   4.9e-05      33     138 .]     101     200 ..      87     200 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00059
                                  EEEE--SSSSHHHHHHHGGGGB CS
                         AAA_5  2 vlLvGppGtgKselaerlaaal 23
                                  vl+ Gp+G++Ks++a++l   l
  gi|13541461|ref|NP_111149.1| 33 VLIRGPKGVAKSTIARSLIDIL 54
                                  899*************998766 PP

  == domain 2  score: 23.4 bits;  conditional E-value: 3.8e-08
                                   -TT--HHHHH--B--.............--------G-SEEEEESGGG--HHHHHHHHHHHHSSEEE..-SSSEEE---.. CS
                         AAA_5  33 trdtteedlkgrreik....ngttslvdsplvraaregeilvlDEveraesevlnsLlslleerrllleeggelvkakndd 109
                                   + + t + ++g+++i+    +g ++l+++ l +a  +  i+++DEv+ ++++v+++ l         +e  g  + ++++ 
  gi|13541461|ref|NP_111149.1| 101 PVSATIDRVIGSIDISkavnEGIKALQPGLLADA--NRGIIYIDEVNLLDDSVIDAILDAAASGINVVEREGVSIVHPAK- 178
                                   5567889999999999998888888888888844..557*****************999999988888877777777775. PP

                                   ....-EEEEEESS--.-TT-TTHHHHTT- CS
                         AAA_5 110 llerfrviatanpldrslnelspalrsRf 138
                                       f +i+t+np +    +l p+lr+Rf
  gi|13541461|ref|NP_111149.1| 179 ----FILIGTMNPEE---GDLRPQLRDRF 200
                                   ....**********9...77889*****9 PP

>> VWA  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   5.2e-08   6.6e-05       2     117 ..     440     545 ..     440     561 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 5.2e-08
                                   EEEEEE-STTS.CHHHHHHHHHHHHHHHHHHTBTTTTEEEEEEEESSS.EEEEEETTSHCHHHHHHHHHHTGSGGGGSSC- CS
                           VWA   2 ivfvlDgSgsm.geenfekvkefikklveklevgpegtrvglvqfsse.vktefslndysskeellsalnnlkysgggttn 80 
                                   ++++lD+S sm + +++  ++ ++ +++++ +  + +++++ ++fs++ + + + ++++     + +++ + +++ g+t  
  gi|13541461|ref|NP_111149.1| 440 VILALDASRSMeTMKRIAIARGIARDFLKSAY--RMRVKMSYLTFSGSdTAVRVEMTRDI--GRIEEEIMH-TVAKGKTP- 514
                                   6899*******666777799999999999999..************87688889999966..899999999.56666666. PP

                                   HHHHHHHHHHHHHHHHGTSSTTSEEEEEEEESS--CS CS
                           VWA  81 tgkalkyaleklfkssagaRenakkviilltdGksnd 117
                                   + +alk+++e + ++ ++     + v il+tdG+ n 
  gi|13541461|ref|NP_111149.1| 515 LPSALKKMYE-ISSRYRK-----RTVSILITDGRANV 545
                                   ******9999.4444444.....88*********987 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.46   5.9e+02      60      81 ..      33      54 ..       8      60 .. 0.60
   2 !   19.6   0.0     3e-07   0.00038     108     178 ..     122     192 ..     111     204 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.46
                                  EEEEESSTSTHHHHHHHHHHHS CS
                           MCM 60 vllvgdpgtaKsqlLkyvekla 81
                                  vl+ g  g+aKs++ +++ +++
  gi|13541461|ref|NP_111149.1| 33 VLIRGPKGVAKSTIARSLIDIL 54
                                  6666777777777766666655 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 3e-07
                                   SSEEEEETHHHHTTTSEEEEESGGGSTCHHHHHHHHHHHHSEEEEESSSCEEEEE--EEEEEEE--SSSSC CS
                           MCM 108 gefvleaGalvladkGvcciDefdkmkeedrsalhEamEqqtisiaKaGivatLnartsvlaAanpkagry 178
                                   g  +l+ G l  a++G+++iDe++  +++  +a+++a  +    + + G+ ++ +a+  ++  +np++g  
  gi|13541461|ref|NP_111149.1| 122 GIKALQPGLLADANRGIIYIDEVNLLDDSVIDAILDAAASGINVVEREGVSIVHPAKFILIGTMNPEEGDL 192
                                   456899************************************9************************9975 PP

>> VWA_CoxE  VWA domain containing CoxE-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.4   3.9e-07    0.0005      38     170 ..     416     551 ..     377     556 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 3.9e-07
                      VWA_CoxE  38 lrhgge..lvelvrrkprerkprelvllvDvSgSmaaysaifla......llhAllqqlprtevfaFdtrlvdlTralrer 110
                                   l+h  +  ++++v  k+ +r++ +++l +D S+Sm++  +i +a      +l+++ + + +++ ++F+ + + +  ++  r
  gi|13541461|ref|NP_111149.1| 416 LNHDNRikPEDVVMTKATSRSSLPVILALDASRSMETMKRIAIArgiardFLKSAYRMRVKMSYLTFSGSDTAVRVEMT-R 495
                                   44444466899999999999999**************988766433222245555555557788***988887777776.5 PP

                      VWA_CoxE 111 DpaeaLarvsaavedlgGgTrigaalaeflelvtrpaLsrravvvlvsDglergdreell 170
                                   D  +  +++    +  +G T + +al+++ e  +r    +r+v +l++Dg    ++++++
  gi|13541461|ref|NP_111149.1| 496 DIGRIEEEIM--HTVAKGKTPLPSALKKMYEISSRYR--KRTVSILITDGRANVPINRSV 551
                                   6555555554..23379**************999777..9**********8777777665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   2.7e-06    0.0035      18     160 ..      24     161 ..      14     174 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.7e-06
                        AAA_16  18 rvrsgrpelvllsGesGvGKsslvrellralekdggif.lrgkcdqlesaipysa.laqalareellrqlldeaesaelea 96 
                                   ++  +r + vl++G++Gv Ks+++r+l + l + +++     kcd  + +   +   +++  + +++r+   +       +
  gi|13541461|ref|NP_111149.1|  24 NAVNPRIGGVLIRGPKGVAKSTIARSLIDILPEIDVVKdCPFKCDPDDYESMCDEcRIKYE-KGQIVRDRRKM--PFVDLP 101
                                   566677799*******************877666655577777777733433344344444.43666666655..224666 PP

                        AAA_16  97 wrekleealaavpelagaeasrllellkrll.allsrderplvlvlDdlqwadeaslql.laaLlr 160
                                    +++++++++     + +++++++e +k+l   ll+  +   ++ +D++  +d++  ++ l+a ++
  gi|13541461|ref|NP_111149.1| 102 VSATIDRVIG-----SIDISKAVNEGIKALQpGLLAD-ANRGIIYIDEVNLLDDSVIDAiLDAAAS 161
                                   6666777777.....5556699999999999888887.5559999999999999888886766665 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.022        28      23      43 ..      31      51 ..      15      65 .. 0.82
   2 !   10.8   0.0   0.00024       0.3      47     117 ..      91     159 ..      82     195 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.022
                                  S-EEEECSTTSSHHHHHHHHH CS
               Sigma54_activat 23 lsvlitGesGtGKellaraih 43
                                    vli+G +G+ K+++ar++ 
  gi|13541461|ref|NP_111149.1| 31 GGVLIRGPKGVAKSTIARSLI 51
                                  569**************9875 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00024
                                   TTTTS-EEEEETTTS-TTCHHHHHHEBSSSSSTTTSS-BEHHHHHTTTSEEEEETGGGS-HHHHHHHHHHH CS
               Sigma54_activat  47 krkekpfvavncaaipeelleseLFGhekGaFtGAekekkGlfekadgGtlfLDeigelplelQekLlrvl 117
                                   +r++ pfv + ++a+ ++++ s    ++k    G ++ + Gl+  a+ G++++De++ l+ ++   +l + 
  gi|13541461|ref|NP_111149.1|  91 DRRKMPFVDLPVSATIDRVIGS--IDISKAVNEGIKALQPGLLADANRGIIYIDEVNLLDDSVIDAILDAA 159
                                   5667777777777777777777..5667777788999999*****************99988877777655 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0     6e-05     0.077       1     125 [.      33     201 ..      33     206 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6e-05
                                   EEEESSTTSSHHHHHHHHHHHH............THE............................EEEEETTTCSSSSTT. CS
                           AAA   1 vllyGppGtGKTllakavakel............gve............................fleisgsellskyvg. 40 
                                   vl+ Gp+G+ K+++a++++  l              +                            f+ + +s  ++ ++g 
  gi|13541461|ref|NP_111149.1|  33 VLIRGPKGVAKSTIARSLIDILpeidvvkdcpfkC-DpddyesmcdecrikyekgqivrdrrkmpFVDLPVSATIDRVIGs 112
                                   6899*****************76555554444440.044444444444444455555555555558888888888775552 PP

                                   .HHHHHHHHHHHHHHHTS....TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTS......SSTEEEEEEES CS
                           AAA  41 .esekkirelfkeakeka....kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkk......eskvivigatn 110
                                    + +k ++e +k+++       +  i+ iDE+  l  s         + ++++  + ++ v+++       +k+i+ig+ n
  gi|13541461|ref|NP_111149.1| 113 iDISKAVNEGIKALQPGLladaNRGIIYIDEVNLLDDSV-------IDAILDAAASGINVVEREgvsivhPAKFILIGTMN 186
                                   245666666666665555777556********9996555.......333333333333333333666777788******99 PP

                                   S.GGGSTHHHHSTTSS CS
                           AAA 111 r.pdkldpallrgRfd 125
                                     + +l p+l+ +Rf 
  gi|13541461|ref|NP_111149.1| 187 PeEGDLRPQLR-DRFG 201
                                   98999999999.9996 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 ?   11.2   0.0   0.00023       0.3       9      92 ..      40     321 ..      33     546 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00023
                                   TSSHHHHHHHHHHHHHH.TT--EEEEEEEESSCCCCH....HTTEB-HHHH.............................. CS
                                   xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxx....xxxxxxxxxx.............................. RF
                          CbiA   9 GvGKTtlaanLaralar.rglrVllvDaDpqannlai....leglendiep.............................. 54 
                                   Gv K+t+a +L+ +l + +  +  ++++Dp+   ++     ++  +++i +                              
  gi|13541461|ref|NP_111149.1|  40 GVAKSTIARSLIDILPEiDVVKDCPFKCDPDDYESMCdecrIKYEKGQIVRdrrkmpfvdlpvsatidrvigsidiskavn 120
                                   8****************8889999*******888887666644444444448889**********9999999999999999 PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                          CbiA  55 ................................................................................. 54 
                                                                                                                    
  gi|13541461|ref|NP_111149.1| 121 egikalqpglladanrgiiyidevnllddsvidaildaaasginvveregvsivhpakfiligtmnpeegdlrpqlrdrfg 201
                                   999999999999999999999999999999999999999999999999999999999999999999999999999999999 PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                          CbiA  55 ................................................................................. 54 
                                                                                                                    
  gi|13541461|ref|NP_111149.1| 202 lsvdavqpdspdelitisdrveeydanprafaekyrrdqeklrasviearrilpevtisndlkryianvviklnagnrami 282
                                   999999999999999999999999999999999999999999999999999999999999999999999999999888888 PP

                                   CCHCCCHHHHHHCHCHHHH.....EEEEEEEEESS...-TT CS
                                   xxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxx RF
                          CbiA  55 dlkrllellealgkkkall...lkiagvvlnrvdgeneetl 92 
                                   ++++ ++ ++al ++k+++   ++ a ++  +++ +  +++
  gi|13541461|ref|NP_111149.1| 283 TAIKASKAIAALAGRKKVNiedVERALYLTLKHRVQ--DKS 321
                                   777777777777777777765544444444444444..444 PP

>> TIP49_C  TIP49 AAA-lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.5   0.00038      0.49      10      61 ..     256     309 ..     247     313 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00038
                       TIP49_C  10 gvkldeeAldlLak..igtetSLRYaiqLltpasilakkrkkkevevedveeve 61 
                                   +v ++++ + ++a+  i  + + R  i  +++++ +a + ++k+v++edve++ 
  gi|13541461|ref|NP_111149.1| 256 EVTISNDLKRYIANvvIKLNAGNRAMITAIKASKAIAALAGRKKVNIEDVERAL 309
                                   566666666666552234455667788889**********************85 PP

>> YadA_anchor  YadA-like membrane anchor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       5.5     7e+03      29      42 ..     314     327 ..     311     328 .. 0.86
   2 ?    3.6   0.1     0.057        72      39      56 ..     372     389 ..     364     390 .. 0.85
   3 ?    5.6   0.0     0.014        17      23      54 ..     457     491 ..     454     494 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 5.5
                   YadA_anchor  29 sarsngnlvvklgv 42 
                                   ++r+ ++ ++k+++
  gi|13541461|ref|NP_111149.1| 314 KHRVQDKSMIKGTI 327
                                   799********986 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.057
                   YadA_anchor  39 klgvavssggsvgggvGv 56 
                                   +++++++ +gs++g++Gv
  gi|13541461|ref|NP_111149.1| 372 RVSASFNESGSTSGRAGV 389
                                   6789999**********8 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.014
                   YadA_anchor  23 AvAvGasars.ngnlvvklgvav..ssggsvgggv 54 
                                   A+A G+++ +    ++++++ ++  +sg+++ ++v
  gi|13541461|ref|NP_111149.1| 457 AIARGIARDFlKSAYRMRVKMSYltFSGSDTAVRV 491
                                   99*****************************9998 PP

>> Mg_chelatase_C  Magnesium chelatase, subunit ChlI C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   1.1   8.9e-05      0.11      25      91 ..     241     310 ..     218     312 .. 0.83
   2 ?   -1.5   0.1       3.1     4e+03       6      26 ..     451     486 ..     446     536 .. 0.47

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 8.9e-05
                Mg_chelatase_C  25 e...naelsgeelrevceldeeaeelleeaierlglsaRaydrilkvArTiADLegseeieeehlaeAlq 91 
                                   e    + ++++ +   ++++++ ++ + +++ +l+   Ra+   +k ++ iA L+g+++++ e++++Al 
  gi|13541461|ref|NP_111149.1| 241 EklrASVIEARRILPEVTISNDLKRYIANVVIKLNAGNRAMITAIKASKAIAALAGRKKVNIEDVERALY 310
                                   23556677788888889999***********************************************985 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 3.1
                Mg_chelatase_C   6 evrerVaaAreiqkeRfake...............n 26 
                                   e  +r+a Ar i+++ ++++               +
  gi|13541461|ref|NP_111149.1| 451 ETMKRIAIARGIARDFLKSAyrmrvkmsyltfsgsD 486
                                   555566666665555443333333334444444441 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (614 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       667  (0.0372023); expected 358.6 (0.02)
Passed bias filter:                      546  (0.0304535); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.70u 0.31s 00:00:01.01 Elapsed: 00:00:00.48
# Mc/sec: 3857.93
//
Query:       gi|13541462|ref|NP_111150.1|  [L=305]
Description: aspartate carbamoyltransferase catalytic subunit [Thermoplasma volcanium GSS1]
Scores for 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  158.6   0.0    3.2e-46  157.0   0.1    1.7  2  OTCace_N  Aspartate/ornithine carbamoyltransferase, carbamoyl
    8.9e-29  100.6   0.0    1.5e-28   99.8   0.0    1.4  1  OTCace    Aspartate/ornithine carbamoyltransferase, Asp/Orn b


Domain annotation for each model (and alignments):
>> OTCace_N  Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  157.0   0.1   3.5e-50   3.2e-46       1     147 [.       5     146 ..       5     147 .. 0.94
   2 ?   -1.9   0.0      0.34   3.1e+03      37      72 ..     152     187 ..     148     197 .. 0.81

  Alignments for each domain:
  == domain 1  score: 157.0 bits;  conditional E-value: 3.5e-50
                                   S-BSSGGGS-HHHHHHHHHHHHHHHHHHHTTT-STTTTT-EEEEEESS--HHHHHHHHHHHHHTTSEEEEEESTTTSCTTT CS
                      OTCace_N   1 rhllsledlskeeieelldlaaelkekvkkekkekllkgktlallFeepStRTrvSfevAakrlGgkvlslseaediqlss 81 
                                   ++++s++d++++++ e++dl++++ ++++++ + +ll +k++a+lF+epStRTr+Sfe+A++rlGg+v+++s+   +++ss
  gi|13541462|ref|NP_111150.1|   5 KSVVSIDDVQNDDLFEIFDLSESMLKTIESKGNAPLLTNKIMATLFYEPSTRTRLSFESAMHRLGGSVITVSD---TKTSS 82 
                                   5789*******************************************************************95...57899 PP

                                   GGSTTSSCHHHHHHHHHHHTSEEEEEES..SHHHHHHHHHHHSSEEEEEEETSSB-HHHHHHHHHHHH CS
                      OTCace_N  82 vskgrkEsleDtarvlsryvdaiviRhp..gaeeleelakyasvpviNagdgdgeHPtQaLaDlltir 147
                                   ++kg  E+l+Dt+r+ s+y+d+iviRhp  ga  ++   ++ s p+iNagdg+g+HPtQ+++Dl+ti+
  gi|13541462|ref|NP_111150.1|  83 AAKG--ETLADTVRMASSYSDIIVIRHPleGA--ARLASRFTSKPIINAGDGSGQHPTQTILDLFTIK 146
                                   99**..**********************8766..66556677************************97 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.34
                                   TTT-EEEEEESS--HHHHHHHHHHHHHTTSEEEEEE CS
                      OTCace_N  37 lkgktlallFeepStRTrvSfevAakrlGgkvlsls 72 
                                   ++gk+++++   +  RT  S  +A +r   kv  +s
  gi|13541462|ref|NP_111150.1| 152 IDGKVITMVGDLRYGRTIHSLIIALSRFDVKVNLVS 187
                                   578899999999999999999999999888766555 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 !   99.8   0.0   1.7e-32   1.5e-28       1     155 [.     153     300 ..     153     302 .. 0.90

  Alignments for each domain:
  == domain 1  score: 99.8 bits;  conditional E-value: 1.7e-32
                                   CC.EEEEESS.TTSHHHHHHHHHHHHCT-EEEEES-TTSSH-HHHHHHHHHHHHHHT-EEEEESSCHHHHTT-SEEEE--S CS
                        OTCace   1 kglkiafvGd.kknnvanslikllarlgmdvvlvaPkglepdkevleeakknakksggsititedleeavkgaDvvytdvw 80 
                                   +g+ i++vGd  ++++++sli++l+r++++v+lv+P+ l+  + v++++ +      + ++  +dlee++ ++Dv+y +++
  gi|13541462|ref|NP_111150.1| 153 DGKVITMVGDlRYGRTIHSLIIALSRFDVKVNLVSPEILRLPEYVYSMLPD-----RNYVKEYNDLEEVIGETDVLYVTRI 228
                                   5899**********************************9996677755554.....5788899****************** PP

                                   SETTCCGGHH...HHHHHHCC.CSB-HHHHHHS-TT-EEEE-S---BTTTB-HHHHTSTTBHHHHHHHHHHHHHHHHHH CS
                        OTCace  81 vsmgeekere...erlkklkd.yqvteellklakkdaivlHcLPakrgeEvtdeVfdsprsvvfeqaeNrlhtikAllv 155
                                   +     ker+   ++++++ + y +++e ++++kk+ +++H+LP  r +E++ +V++ p++++f+qa +++ +++Al++
  gi|13541462|ref|NP_111150.1| 229 Q-----KERFsdqNEYQSVIGsYSINSETVEKMKKKSVIMHPLP--RVDEISPDVDNMPQAAYFRQAYYGVPVRMALIY 300
                                   *.....5555444677777777**********************..*******************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       513  (0.0286129); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 1956.37
//
Query:       gi|13541463|ref|NP_111151.1|  [L=152]
Description: aspartate carbamoyltransferase regulatory subunit [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-32  112.1   2.7    1.6e-32  111.6   2.7    1.3  1  PyrI      Aspartate carbamoyltransferase regulatory chain, al
    7.1e-17   61.0   2.9    7.1e-17   61.0   2.9    1.7  2  PyrI_C    Aspartate carbamoyltransferase regulatory chain, me
  ------ inclusion threshold ------
      0.021   14.0   0.0      0.023   13.8   0.0    1.0  1  DREV      DREV methyltransferase


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 !  111.6   2.7   2.7e-36   1.6e-32       1      94 []       6      98 ..       6      98 .. 0.98

  Alignments for each domain:
  == domain 1  score: 111.6 bits;  conditional E-value: 2.7e-36
                                  X-----SCEEEEEEEETT-HHHHHHHCT--T...TS-EEEEEEEEETTTEEEEEEEEET----HHHHHHHCCC-TT-EEEEEE CS
                          PyrI  1 lkvkkienGiViDHIkagkalkvlklLkldklkseekvaiiknvkskklgkKdiikiegkelseeeldklaliapnatiniIk 83
                                  lk++ki++G+ViDHI++gkal+vl++L++++ + + +v+++++v+s+k++ Kd+ikie+++l+++eld+++l apnati+iIk
  gi|13541463|ref|NP_111151.1|  6 LKISKIKDGTVIDHIPSGKALRVLSILGIRD-DVDYTVSVGMHVPSSKMEYKDVIKIENRSLDKNELDMISLTAPNATISIIK 87
                                  69****************************8.9999*********************************************** PP

                                  TTEEEEEE--. CS
                          PyrI 84 dgevveKkkve 94
                                  ++e+ eK+kve
  gi|13541463|ref|NP_111151.1| 88 NYEISEKFKVE 98
                                  ********985 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 ?   -2.6   0.0      0.89   5.3e+03      19      26 ..      90      97 ..      84      99 .. 0.72
   2 !   61.0   2.9   1.2e-20   7.1e-17       2      48 .]     103     150 ..     102     150 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.89
                                  S-.-EEEE CS
                        PyrI_C 19 pveskFkv 26
                                  ++++kFkv
  gi|13541463|ref|NP_111151.1| 90 EISEKFKV 97
                                  68889987 PP

  == domain 2  score: 61.0 bits;  conditional E-value: 1.2e-20
                                   EESSS--S-TTBGGGT.TS-.-EEEEEETTTTEEEETTT--EEEHHHH CS
                        PyrI_C   2 iegvlkCpNpnCItnn.epveskFkvedkekvklkCkYCekeiseeei 48 
                                   ++g++kC+N+nCItn+ epv+++F+++++++++l+C YC ++++e+++
  gi|13541463|ref|NP_111151.1| 103 LIGIIKCKNQNCITNTrEPVKPEFEIVSRHPLVLRCVYCQRTMNERDV 150
                                   78**************99**************************9986 PP

>> DREV  DREV methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   3.9e-06     0.023      42     168 ..      19     142 ..       3     150 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.9e-06
                          DREV  42 qlyhalassilslfmsktdinGllgrGsmfvlseeqfrkllaiekespasdqedkklldlGaGdGeitkrvaptfeevyat 122
                                   ++    a  +ls++  + d++  +  G     s+  ++ +++ie+ s   d+++  ++ l a +  i+ + +  ++e +  
  gi|13541463|ref|NP_111151.1|  19 HIPSGKALRVLSILGIRDDVDYTVSVGMHVPSSKMEYKDVIKIENRSL--DKNELDMISLTAPNATISIIKNYEISEKFKV 97 
                                   555556678999999999999999999777778889********6555..569999************************* PP

                          DREV 123 elsetmrdrlkkkkynvlsalelqetdvkldlilclnlldrcfdpl 168
                                   el  +++  +k k+ n +++      + ++++++   l+ rc    
  gi|13541463|ref|NP_111151.1|  98 ELPPKLIGIIKCKNQNCITNTREP-VKPEFEIVSRHPLVLRCVYCQ 142
                                   ******************987644.678999999999988887655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       628  (0.0350271); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 1016.35
//
Query:       gi|13541464|ref|NP_111152.1|  [L=232]
Description: uroporphyrinogen-III synthase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.5e-25   89.9   0.0      2e-25   89.5   0.0    1.1  1  HEM4        Uroporphyrinogen-III synthase HemD
     0.0092   15.7   0.8      0.056   13.2   0.0    2.3  3  MAF_flag10  Protein of unknown function DUF115


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 !   89.5   0.0   2.2e-29     2e-25      17     220 ..      29     209 ..      23     213 .. 0.91

  Alignments for each domain:
  == domain 1  score: 89.5 bits;  conditional E-value: 2.2e-29
                                   ---EECCECCHHHHHHHHH.T.....--SEEEE--HHHHHHHHHHHHHTT---HHHHHCSEEESSHHHHHHHHHTT---SE CS
                          HEM4  17 lPlieiepaedraelraal.ddleagkydwliftSanavealfealkreeedvkalaslkvaavGpaTaraLeelglrvdl 96 
                                   +P+ +  p      l+  + + l++++ d+++ftS+ +v+ +f +++         +  ++  +G+aT + ++++g +  l
  gi|13541464|ref|NP_111152.1|  29 IPVTRLMP------LDINIeKILKESAADCIVFTSTFGVDLFFSRVN--------MKGFTILGIGKATCERVQAYGHKC-L 94 
                                   67777777......5555523333889*******************9........77899****************999.7 PP

                                   E-..SSSHHHHGGGS-.---EEEEEE-SS.S--HHHHHHHHHTTEEEEEE-SEEEEE-HHHHHHHHHHHHTT--SEEEESS CS
                          HEM4  97 vpseegtaegLaeelaeslagkrvlllrgeiarddlaegLeergaevdevevYetvpaeeepeelkealkagevdavvftS 177
                                   +p+   ++egLa+++ ++ ++k++l+lr+++a++ l e+L+e g++  e  +Y+    +++ ++++++ k++++ +v++tS
  gi|13541464|ref|NP_111152.1|  95 YPE-NMDSEGLANLIISKCKDKKILILRSKKANEVLTEKLKEEGIDFLEFRIYDA---VPDTKDFEKHYKDQNCLGVIITS 171
                                   **9.9999********99999**********************************...77899****************** PP

                                   HHHHHHHHHH-S-HHHHHCTSEEEEESHHHHHHHHHTT---SE CS
                          HEM4 178 pstvrnllellkdegdelkevkvaaiGptTaealkklglkvdv 220
                                   + +++ ++ +lk+     ++  v++iG tT+++l ++g+ +d+
  gi|13541464|ref|NP_111152.1| 172 SMEAEIVIPFLKE-----DKKMVFSIGVTTTNTLMSHGIMPDI 209
                                   ***********95.....6899****************99887 PP

>> MAF_flag10  Protein of unknown function DUF115
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.1      0.61   5.5e+03      37      55 ..      37      56 ..      37      58 .. 0.79
   2 ?    1.1   0.0     0.031   2.8e+02      82     130 ..     105     156 ..      97     174 .. 0.67
   3 !   13.2   0.0   6.2e-06     0.056      41      78 ..     179     215 ..     143     227 .. 0.72

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 0.61
                    MAF_flag10 37 Leknlell.kelrdkaviia 55
                                  L+ n+e++ ke + ++++++
  gi|13541464|ref|NP_111152.1| 37 LDINIEKIlKESAADCIVFT 56
                                  67788888899998888887 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.031
                    MAF_flag10  82 syevfkeaekkgdiplvfasgvnpellkkykgpki.flvtgstqa...lelle 130
                                      +++++++k +i+++ +  +n+ l +k+k++ i fl  + + a   ++ +e
  gi|13541464|ref|NP_111152.1| 105 ANLIISKCKDK-KILILRSKKANEVLTEKLKEEGIdFLEFRIYDAvpdTKDFE 156
                                   44567888888.99999999999999999999988654433333355544554 PP

  == domain 3  score: 13.2 bits;  conditional E-value: 6.2e-06
                    MAF_flag10  41 lellkelrdkaviiaad.talkaLlkegIkPDivvslDp 78 
                                   +++lk  +dk ++++++ t++++L+++gI PDi  + D 
  gi|13541464|ref|NP_111152.1| 179 IPFLK--EDKKMVFSIGvTTTNTLMSHGIMPDITGNSDF 215
                                   78888..677778887757899***********877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       512  (0.0285571); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); 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 0.32s 00:00:00.83 Elapsed: 00:00:00.50
# Mc/sec: 1392.21
//
Query:       gi|13541465|ref|NP_111153.1|  [L=297]
Description: porphobilinogen deaminase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      6e-65  218.6   0.3    7.7e-65  218.2   0.3    1.1  1  Porphobil_deam   Porphobilinogen deaminase, dipyromethane cof
    0.00058   20.2   0.1     0.0054   17.1   0.0    2.6  4  Porphobil_deamC  Porphobilinogen deaminase, C-terminal domain
  ------ inclusion threshold ------
       0.04   12.9   0.0       0.86    8.5   0.0    2.2  2  SBP_bac_5        Bacterial extracellular solute-binding prote


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 !  218.2   0.3   1.3e-68   7.7e-65       1     198 [.       3     200 ..       3     205 .. 0.96

  Alignments for each domain:
  == domain 1  score: 218.2 bits;  conditional E-value: 1.3e-68
                Porphobil_deam   1 irigtRkSkLAlaqaelvaeaLke.eeeveivtiktkGDkildkpLakiggkglFtkeleeaLlegeidlaVhSlKDlpte 80 
                                   i+igtR S+LA+aqa++va++L++   ++eiv+ ++ GD ++++p+++ig++g+F+++l++ +l+geid+aVhS+KD+p+e
  gi|13541465|ref|NP_111153.1|   3 IKIGTRPSNLAVAQANMVASSLEAiGIDTEIVKHRSAGDIDTKNPIYSIGKTGVFVQDLNNMILRGEIDVAVHSAKDIPSE 83 
                                   89********************6656668**************************************************** PP

                Porphobil_deam  81 lpeglelaavlkredprDvlvvkssleelpegavvgTsSlRRkaqlkklrpdlevkdlRGnvdtRlrkldegeydaiiLAa 161
                                   ++++l++aa+lkr + +D+lv k +l++lp  a+vgTsS+RR  qlk +r+dl+++++RGn++tR++k++e  +dai++A+
  gi|13541465|ref|NP_111153.1|  84 IENRLTIAATLKRGSFNDALVSKYDLRSLPISAKVGTSSIRRIFQLKYARQDLKFENIRGNIETRIAKMSELGLDAIVMAE 164
                                   *********************6669*********************************************999******** PP

                Porphobil_deam 162 AGLkRlgleerisevlspeellpavgQGalavevrke 198
                                   A+++Rlgl+ + s+ l++++++pa+ QG++av  +ke
  gi|13541465|ref|NP_111153.1| 165 AAIQRLGLNVEYSK-LDENKFVPAPNQGIIAVVSKKE 200
                                   *******9888888.*****************99887 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 ?   -2.2   0.0      0.94   5.6e+03      45      73 ..      61      88 ..      54      89 .. 0.68
   2 ?   -2.1   0.0      0.88   5.3e+03      30      43 ..     151     164 ..     143     181 .. 0.72
   3 ?   -2.4   0.0       1.1   6.5e+03      36      49 ..     192     205 ..     189     215 .. 0.63
   4 !   17.1   0.0     9e-07    0.0054       3      52 ..     218     266 ..     216     285 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.94
                                  S..S-EEEEEEEE-GGGHHHHHHHHHHHH CS
               Porphobil_deamC 45 glksaveeaeakgeleeaeelGkklaeel 73
                                    ++++ + e+  ++  a++++ ++ ++l
  gi|13541465|ref|NP_111153.1| 61 L-NNMILRGEIDVAVHSAKDIPSEIENRL 88
                                  4.347777788888888888888777665 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.88
                                   TTE.EEEEEEEE-T CS
               Porphobil_deamC  30 aneelkLkglvlsl 43 
                                   + +el L+++v++ 
  gi|13541465|ref|NP_111153.1| 151 KMSELGLDAIVMAE 164
                                   34468888888765 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 1.1
                                   EEEEEE-TTS..S- CS
               Porphobil_deamC  36 Lkglvlsldglksa 49 
                                   ++++v +++g++  
  gi|13541465|ref|NP_111153.1| 192 IIAVVSKKEGTVRK 205
                                   56788888887622 PP

  == domain 4  score: 17.1 bits;  conditional E-value: 9e-07
                                   HHHHHHHHHHHTT--TTSSEEEEEEEE.TTE.EEEEEEEE-TTS..S-EEE CS
               Porphobil_deamC   3 evlaERallkeLeGGCsvPiGvyaeve.aneelkLkglvlsldglksavee 52 
                                   e+  ER++ ++L  GCs+P+G  ++ + ++   k+++ + s  g +  v+e
  gi|13541465|ref|NP_111153.1| 218 EMQIERSVVQQLKLGCSTPVGILSRPSgKGH--KIIAQFFSMQGDDVSVFE 266
                                   6778******************999886555..666666666665555555 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 ?    8.5   0.0   0.00014      0.86     307     336 ..      10      39 ..       3      92 .. 0.76
   2 ?    2.3   0.0     0.011        65     296     346 ..     142     191 ..     111     201 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00014
                                   SHHHHHHHHHHHHHHHHTTEEEEEEEECHH CS
                     SBP_bac_5 307 spaekaiaeliqqqlkkiGikvevktvdwa 336
                                   s+++ a a++++++l++iGi++e+    +a
  gi|13541465|ref|NP_111153.1|  10 SNLAVAQANMVASSLEAIGIDTEIVKHRSA 39 
                                   6677899****************9887664 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.011
                                   EEEEEEEEETTSHHHHHHHHHHHHHHHHTTEEEEEEEECHHHHHHHHHHCT CS
                     SBP_bac_5 296 klkltlllasgspaekaiaeliqqqlkkiGikvevktvdwaatylervkdg 346
                                   + ++ + +a  s++  ++  +  ++ +++G++ve   +d  +++ ++ ++g
  gi|13541465|ref|NP_111153.1| 142 RGNIETRIAKMSELGLDAIVMAEAAIQRLGLNVEYSKLDE-NKFVPAPNQG 191
                                   44578888888999999999******************99.8887777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       541  (0.0301746); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1999.97
//
Query:       gi|13541466|ref|NP_111154.1|  [L=420]
Description: glutamate-1-semialdehyde aminotransferase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.5e-67  226.8   0.0    4.2e-67  226.6   0.0    1.0  1  Aminotran_3  Aminotransferase class-III
  ------ inclusion threshold ------
       0.15   12.1   0.1        5.9    6.9   0.1    2.7  3  DUF1870      Domain of unknown function (DUF1870)


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 !  226.6   0.0   4.7e-71   4.2e-67      10     405 ..      29     415 ..      22     416 .. 0.89

  Alignments for each domain:
  == domain 1  score: 226.6 bits;  conditional E-value: 4.7e-71
                                   CEEEEEEEBTEEEETTS-EEEESSHHHHTTTT-BT-HHHHHHHHHHHTT-S---TTTCEEHHHHHHHHHHHHHCT-..SEE CS
                   Aminotran_3  10 llvitkaeGvyltdvdgkrylDlvssiavvnlGhahPkvvkavkeqaaklshvsfgaltnepalklaekllklapkgldkv 90 
                                   ++ +++++G+ + dvdg++y+D   ++ +++lGh++P+v+ av eqa+k   + fg   +e+ +klae + +   + ++++
  gi|13541466|ref|NP_111154.1|  29 PFYVKEGKGSTILDVDGNKYIDYCLGYGPLILGHSDPDVTRAVIEQAEKG--LLFGE-PSENEIKLAEMIKETSKN-IEMM 105
                                   4789**********************************************..44444.556678899877666555.**** PP

                                   EEESSHHHHHHHHHHHHHHHHHHTSHCTT-EEEEETTT---SSHHHHHHSS--TTTTTTCTTB-TSEEEE-TTBGGGTB-H CS
                   Aminotran_3  91 flansGseAvetAlKlarkyarekkatektkiiafkgafHGrtlgalsvtgskkkyktlfgpflpevvrlkypdeevlken 171
                                    + nsG+eA++ A++lar+       t ++ i++++g+fHG   ++l  +gs  +  t   p++p+++   ++  +v k+n
  gi|13541466|ref|NP_111154.1| 106 RFTNSGTEATMHAIRLARA------ITGRKLIVKMEGGFHGAHDYSLIKSGS--GTLTFGSPSSPGIPDEVAQTVIVGKYN 178
                                   *******************......9**************************..889999999*****9999999999999 PP

                                   HHHHHHHHHHHHHHHCHTCCCEEEEEE-SCETTTTSEB--CCHHHHHHHHHHHHT-EEEEE-TTTTTTTTSSSSGGGGCTS CS
                   Aminotran_3 172 eeeeaalleelealekkkkdevaAvivEpiqgegGvvvaspeflaklrelckkhdvllivDEvqtGfGrTGklfAlehagv 252
                                   +      ++ ++++ +k  d++aAvi+Epi g++Gv+ ++++fl+ lr++++kh+ lli+DEv tG       f  + + +
  gi|13541466|ref|NP_111154.1| 179 D------ENNIKEIFQKYGDKIAAVITEPIMGNAGVILPKQGFLEFLRDITQKHGSLLIFDEVITGYRFAFSPF-QDIMRI 252
                                   9......6679999999***********************************************9985554444.34569* PP

                                   --SEEEE-GGGGTTSS-EEEEEEHHHHTTS-TTS...B--TTTT-HHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHH CS
                   Aminotran_3 253 spDlmtlaKaltgGlplsavlataevmqalapgs...hgsTfgGnplacavalavleiieeekllenaqelgaalkegLee 330
                                    pD++t++K ++gGlp+  + + +e+m+ ++p++    ++Tf+Gnp+ +a+  a++e + ++++    ++  ++l +g  +
  gi|13541466|ref|NP_111154.1| 253 DPDITTMGKIIGGGLPIGLFGGSEEIMKNISPSGnvyEAGTFSGNPMSMAAGYAAMEKLSKQDYSI-LKKRTQKLVSGIDD 332
                                   *******************************999999************************99975.566678899***** PP

                                   HCTT-TTEEEEEEETTEEEEEEBCCCETTC...........HHHHHHHHHCTEE-EEETTTEEEE---TT--HHHHHHHHH CS
                   Aminotran_3 331 lqkkyevikevRgkGlmiaielkeeaevke...........keilkkakekGvlilsaGdnvirllppliitdeeidelle 400
                                   + ++++  ++++  G+m+ + + +++++              +++k++ ++Gv++ ++  +    + ++  +d +id+ l 
  gi|13541466|ref|NP_111154.1| 333 ILDRKHITHTIKYYGTMFQVFFADHVNN-YddalkarkevyFKLFKALSKNGVYLPPSQYE--TNFVSFAHSDSDIDATLA 410
                                   ****9999************66666664.3599****9999889**********8887743..334566677888888888 PP

                                   HHHHH CS
                   Aminotran_3 401 ilkka 405
                                   +++ka
  gi|13541466|ref|NP_111154.1| 411 AFEKA 415
                                   88776 PP

>> DUF1870  Domain of unknown function (DUF1870)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0      0.52   4.6e+03      75      95 ..      19      39 ..       7      42 .. 0.75
   2 ?    1.7   0.0     0.028   2.5e+02      42      73 ..     163     194 ..     156     199 .. 0.89
   3 ?    6.9   0.1   0.00066       5.9      48      85 ..     312     350 ..     302     376 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.52
                                  --EEE--SSHHHHHTTSTT-- CS
                       DUF1870 75 nstlryystlteflkvypead 95
                                  ns +ry++++  + k  + ++
  gi|13541466|ref|NP_111154.1| 19 NSPVRYFKDYPFYVKEGKGST 39
                                  6789***99988877655555 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.028
                                   ---HHHHHHHHHHHHHHHHHHHHHHHHHCCS- CS
                       DUF1870  42 pipdeivaelkelkklrkkkieeiveklndri 73 
                                    ipde+ +++   k   +++i+ei++k  d+i
  gi|13541466|ref|NP_111154.1| 163 GIPDEVAQTVIVGKYNDENNIKEIFQKYGDKI 194
                                   59********9999999**********99998 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.00066
                                   HHHHHHHHHHHHHHHHHHHHHHCCS-S--.EEE--SSHH CS
                       DUF1870  48 vaelkelkklrkkkieeiveklndrigns.tlryystlt 85 
                                    ++ +++ k+r++k+   ++++ dr   + t++yy+t+ 
  gi|13541466|ref|NP_111154.1| 312 SKQDYSILKKRTQKLVSGIDDILDRKHIThTIKYYGTMF 350
                                   555577889999999999999999876444******974 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (420 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       751  (0.0418874); expected 358.6 (0.02)
Passed bias filter:                      633  (0.0353059); 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: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.44
# Mc/sec: 2868.09
//
Query:       gi|13541467|ref|NP_111155.1|  [L=157]
Description: deoxycytidine triphosphate deaminase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.3e-16   58.8   0.0    5.2e-16   58.5   0.0    1.1  1  dUTPase   dUTPase
    6.7e-06   25.1   0.0    0.00017   20.5   0.0    2.1  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 !   58.5   0.0   5.8e-20   5.2e-16      22     125 ..      47     149 ..      31     152 .. 0.94

  Alignments for each domain:
  == domain 1  score: 58.5 bits;  conditional E-value: 5.8e-20
                                   SSEEEETTEEEEEEEEEEEE--TTEEEEEEE-HHHHHHHEEEEEEEEETTBTSEEEEEEEE-SSS-EEE-TT-EEEEEEEE CS
                       dUTPase  22 kdltvkpgetvlvptdisiklpdglaalilpRSglaakglivvpgvidsdyrGevkvvlfnltkkdvkikkgdRiAqLifa 102
                                   ++++v  +++ lv+t   + lp+++ a i  RS+ a++g+i   g id+ y G + +++fn +  d  i +gdRiAq+if 
  gi|13541467|ref|NP_111155.1|  47 DETIVGTMKHFLVSTLEVLRLPENVIANIWIRSSYARRGVIGSFGTIDAGYHGSLTLSFFNAGP-DLHISRGDRIAQVIFL 126
                                   6788889**********************************999*******************9.**************** PP

                                   EBECGEEEEESSTTTESSBTTXT CS
                       dUTPase 103 riltaeleevetlkatergeggf 125
                                   ++++ + + +e  +  ++ ++g+
  gi|13541467|ref|NP_111155.1| 127 EMKEKSSMSYEMRSGHYQHSRGV 149
                                   ****9999999889998888887 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 !    2.8   0.0    0.0045        41       4      39 ..       2      36 ..       1      41 [. 0.87
   2 !   20.5   0.0   1.9e-08   0.00017      79     177 ..      52     143 ..      41     157 .] 0.80

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.0045
                           DCD  4 ilpdqeiealieegaikaeepleeeqiqPaslDLrL 39
                                  +l d++i++++e+g +  +e++++  + P+  D+r+
  gi|13541467|ref|NP_111155.1|  2 VLNDNQIQKMVEQGFL-ISENFSDACLTPNGYDVRV 36
                                  7999**********99.5667999999999999997 PP

  == domain 2  score: 20.5 bits;  conditional E-value: 1.9e-08
                           DCD  79 ekgcvYivplleslaLpadlsaaanpksstGRlDvftRvitdkgeefdeveagYkGplyleisprsFsilvrkGsrLsqir 159
                                    +   ++v  le l+Lp+++ a+   +ss  R  v+         +f +++agY+G l l  +     + +++G+r++q+ 
  gi|13541467|ref|NP_111155.1|  52 GTMKHFLVSTLEVLRLPENVIANIWIRSSYARRGVI--------GSFGTIDAGYHGSLTLSFFNAGPDLHISRGDRIAQVI 124
                                   5566789999**********************8876........48**********************************9 PP

                           DCD 160 frrgeakls.deelkelha 177
                                   f + ++k s + e+++ h 
  gi|13541467|ref|NP_111155.1| 125 FLEMKEKSSmSYEMRSGHY 143
                                   9866555431455555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 1071.87
//
Query:       gi|13541468|ref|NP_111156.1|  [L=165]
Description: Acyl-CoA hydrolase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-16   60.4   0.0    2.1e-16   60.1   0.0    1.2  1  4HBT      Thioesterase superfamily


Domain annotation for each model (and alignments):
>> 4HBT  Thioesterase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.1   0.0   1.1e-20   2.1e-16       3      77 ..      27     100 ..      25     102 .. 0.96

  Alignments for each domain:
  == domain 1  score: 60.1 bits;  conditional E-value: 1.1e-20
                                   SB-HHHHHHHHHHHHHHHHHHTTSTTEEEEEEEEEEEESS-BBTTCEEEEEEEEEEEESSEEEEEEEEEETTSCE CS
                          4HBT   3 vvhgGvylallDeaagaalrslggrgilvvvvelsidflrpvrlgdeltvearvlrlgrtsavvevevrdedgrl 77 
                                   +++gG++++++D +a++++++++++ + v+++ +s+ fl p++lgd +++++ ++++ ++++++e++v +++g +
  gi|13541468|ref|NP_111156.1|  27 YLYGGRLMEWIDNCASIVATKHCRK-RTVTGSIDSLFFLLPIHLGDMVLLHGYINYTTKSTMEIEIDVIKQEGLT 100
                                   79**********************8.*********************************************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1238  (0.0690501); expected 358.6 (0.02)
Passed bias filter:                      817  (0.0455686); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 1199.48
//
Query:       gi|13541469|ref|NP_111157.1|  [L=304]
Description: hypothetical protein TVN0638 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       972  (0.0542138); expected 358.6 (0.02)
Passed bias filter:                      229  (0.0127726); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2202.49
//
Query:       gi|13541470|ref|NP_111158.1|  [L=664]
Description: ATPase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.7e-11   42.6   0.0    4.5e-06   25.8   0.1    2.4  2  AAA_10        AAA-like domain
    2.2e-07   31.2   0.5    1.6e-06   28.4   0.0    2.4  3  DUF87         Helicase HerA, central domain
    0.00012   22.4   0.0    0.00038   20.8   0.0    1.8  2  AAA_22        AAA domain
     0.0011   18.1   0.0      0.002   17.3   0.0    1.3  1  T2SSE         Type II/IV secretion system protein
     0.0037   16.7   0.0     0.0071   15.7   0.0    1.4  1  FtsK_SpoIIIE  FtsK/SpoIIIE family
     0.0086   15.6   0.0        1.4    8.4   0.0    2.6  2  Pox_A32       Poxvirus A32 protein
  ------ inclusion threshold ------
      0.019   14.3   0.5       0.07   12.5   0.5    1.9  1  ATPase        KaiC
      0.027   14.2   0.0       0.36   10.6   0.0    2.4  2  IstB_IS21     IstB-like ATP binding protein
      0.042   13.6   0.0      0.085   12.6   0.0    1.5  1  DEAD          DEAD/DEAH box helicase
      0.077   13.4   0.0          1    9.8   0.0    2.6  2  RNA_helicase  RNA helicase
       0.11   12.0   0.0       0.25   10.8   0.0    1.5  1  PhoH          PhoH-like protein
       0.14   12.2   0.3       0.91    9.6   0.0    2.6  3  CbiA          CobQ/CobB/MinD/ParA nucleotide binding 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 !   14.1   0.0   1.1e-05     0.017      23      60 ..     441     479 ..     436     501 .. 0.86
   2 !   25.8   0.1     3e-09   4.5e-06     237     313 ..     545     622 ..     529     630 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.1e-05
                        AAA_10  23 asliiGdlGnGKSvlakll.vlyisllggkaliiDpkke 60 
                                   + +++G++G GKS+++++l + ++  ++  ++i+Dp  e
  gi|13541470|ref|NP_111158.1| 441 NIIVTGETGSGKSYFSRILaISFVEDMDRSVVILDPLDE 479
                                   6799************98725688999999******988 PP

  == domain 2  score: 25.8 bits;  conditional E-value: 3e-09
                        AAA_10 237 dkkefkvvifDEawiftssaeGkkllkelvRiGRsynaavylvtqsadDv.lkeelknniglklaFretdkeeikkvL 313
                                   + +  k+v + Ea i+ +  e   ll++l R+ R +n+ v++v+qs +Dv +   + +n  + ++Fr + k  ++ vL
  gi|13541470|ref|NP_111158.1| 545 SVDGLKMVLIEEASILSKDREIGLLLENLTRQSRHFNTSVVIVSQSINDVkERYAIFENSVHSFMFRTKIKPTANTVL 622
                                   556678999************99***************************44556999999******77666666655 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.1       5.7   8.5e+03     159     190 ..      76     107 ..      69     133 .. 0.52
   2 !   28.4   0.0   1.1e-09   1.6e-06      28      65 ..     444     481 ..     439     504 .. 0.92
   3 ?   -1.2   0.0       1.2   1.8e+03     192     223 ..     508     539 ..     486     542 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 5.7
                         DUF87 159 klknqaiarlldkledllrkggsfsnsstdli 190
                                   k++n+ ++ l +  e++l++ ++ s++s + +
  gi|13541470|ref|NP_111158.1|  76 KPSNRVKQYLTKYTEKILQRLRKSSKTSVSRN 107
                                   45555555555555555555544433333333 PP

  == domain 2  score: 28.4 bits;  conditional E-value: 1.1e-09
                         DUF87  28 ilgsTGsGKSntvavLleellekkgatililDpHGEYg 65 
                                   + g+TGsGKS++ ++L  + +e+++ +++ilDp  EY+
  gi|13541470|ref|NP_111158.1| 444 VTGETGSGKSYFSRILAISFVEDMDRSVVILDPLDEYS 481
                                   78***********************************7 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 1.2
                         DUF87 192 llleklekegkitiidlsgvdelaqqlvvsvi 223
                                   +++e +++  k++ii + g d++++ +++ +i
  gi|13541470|ref|NP_111158.1| 508 NYEEGKSSRTKVVIIKFEGRDKNKLSSIMDYI 539
                                   56667889999********9999999888776 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       8.2   1.2e+04      56      90 ..      65      97 ..      52     109 .. 0.54
   2 !   20.8   0.0   2.5e-07   0.00038       7     128 ..     441     587 ..     438     592 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 8.2
                        AAA_22 56 llrellralglelkaerlsseell.ealeqalrara 90
                                  +l  ++ +++++ ++   + +++l ++ e+ l++ +
  gi|13541470|ref|NP_111158.1| 65 FLIPVVVEINRKPSN---RVKQYLtKYTEKILQRLR 97
                                  555555555555555...333333244444444443 PP

  == domain 2  score: 20.8 bits;  conditional E-value: 2.5e-07
                        AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaeeerpevv........fvtlpsst.sskdllrellr.alglelka....... 70 
                                    ++vtGe+G+GK++  r l+ +++e+     ++++vv        ++++ + + s  dl++ ++  al+ ++++       
  gi|13541470|ref|NP_111158.1| 441 NIIVTGETGSGKSYFSRILAISFVED-----MDRSVVildpldeySCDCFNAScSVLDLRKSIFLdALKTGGNYeegkssr 516
                                   689********************765.....5666666788887788998888899999998865145555555999**** PP

                        AAA_22  71 ...........erlsseellealeqalraravielliiDEaqhlrs.....eealeeLrsllnlsrkgvqliLv 128
                                                ++++ ++++++ ++r+ +  ++++i+Ea  l s       +le+L + +   ++++++++v
  gi|13541470|ref|NP_111158.1| 517 tkvviikfegrDKNKLSSIMDYIQAYFRSVDGLKMVLIEEASIL-SkdreiGLLLENLTRQSR--HFNTSVVIV 587
                                   *******98877778888888888888888889***********.445678889999999999..999999987 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 !   17.3   0.0   1.3e-06     0.002     129     173 ..     439     484 ..     419     504 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.3e-06
                         T2SSE 129 rglilvsGgTgsGKttllyal.lkeinksderivtvEDp.vEiqleg 173
                                    ++i+v+G TgsGK+ +  +l ++++++  +r v++ Dp  E+ ++ 
  gi|13541470|ref|NP_111158.1| 439 SYNIIVTGETGSGKSYFSRILaISFVEDM-DRSVVILDPlDEYSCDC 484
                                   689**************977615666666.55555555515787765 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   4.8e-06    0.0071      10      63 ..     409     463 ..     402     469 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 4.8e-06
                                   HHHT---TTEEEEEEETTS-EEEEEGGGS-..SEEEE--TTSSHHHHHHHHHHHH CS
                  FtsK_SpoIIIE  10 kfrtessqlpvalgkeisgnplvldlkkma.shllvaGatgsGKStalntLilSl 63 
                                   +f +e+ ++++  + e  g+p+ +d  +++  +++v G tgsGKS + + L +S 
  gi|13541470|ref|NP_111158.1| 409 YFSKEETKGIFIGFNEANGKPFFFDPFSAPsYNIIVTGETGSGKSYFSRILAISF 463
                                   567777777777788889************89*************9998887775 PP

>> Pox_A32  Poxvirus A32 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.0   0.00091       1.4       5      51 ..     431     478 ..     428     486 .. 0.81
   2 ?    4.3   0.0     0.016        24     116     141 ..     569     594 ..     529     606 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00091
                       Pox_A32   5 dresLlkkpFrlalvGgsGsGktvyLlsLlrtlvkky.khifLltpvk 51 
                                     +   +  ++++++G++GsGk  + + L  ++v+   + + +l p+ 
  gi|13541470|ref|NP_111158.1| 431 FFDPFSAPSYNIIVTGETGSGKSYFSRILAISFVEDMdRSVVILDPLD 478
                                   5566677889***************99999999998878888877765 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.016
                       Pox_A32 116 tLlellnvgRhlnvsiilLcqtykhv 141
                                    L +l+  +Rh n+s++++ q  + v
  gi|13541470|ref|NP_111158.1| 569 LLENLTRQSRHFNTSVVIVSQSINDV 594
                                   4779999************9998776 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.5   4.7e-05      0.07      22     178 ..     442     602 ..     437     620 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.7e-05
                        ATPase  22 vlitGepGtGKtifalqFlikgaekygepgvfv.tveepa.edlrenakslGwdlekleeegklaiidasesaeesaee.. 98 
                                   + +tGe+G+GK+ f+   +i+ +e++++ +v+   ++e +   +  +++ l  dl+k    + l     +e+++ s ++  
  gi|13541470|ref|NP_111158.1| 442 IIVTGETGSGKSYFSRILAISFVEDMDRSVVILdPLDEYScDCFNASCSVL--DLRKSIFLDALKTGGNYEEGKSSRTKvv 520
                                   789************************999988347777742233333333..3333222222333333333333222256 PP

                        ATPase  99 ......kdkedleelieelaeaikeika.krvviDsitglayeekeavaReilrqlvrvlkklgvTailvsekssseeaag 172
                                         +dk++l+++++ ++ + +++   k v+i   + l   +k+ ++   l +l+r+ ++ ++  ++vs+  +  + ++
  gi|13541470|ref|NP_111158.1| 521 iikfegRDKNKLSSIMDYIQAYFRSVDGlKMVLIEEASIL---SKDREIGLLLENLTRQSRHFNTSVVIVSQSIN--DVKE 596
                                   66666778999**************987688889888888...99999999********************9544..3333 PP

                        ATPase 173 gygvee 178
                                   +y++ e
  gi|13541470|ref|NP_111158.1| 597 RYAIFE 602
                                   444333 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 ?    0.3   0.0      0.33   4.9e+02     128     155 ..     196     224 ..     193     259 .. 0.75
   2 ?   10.6   0.0   0.00024      0.36      47      74 ..     439     466 ..     432     474 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.33
                     IstB_IS21 128 ellfeviekryerr.siiitsnlpfaewd 155
                                   ellf++i+k   r+ si + +nl+ +e++
  gi|13541470|ref|NP_111158.1| 196 ELLFDIINKSQHRSsSIKLDANLSSEEFG 224
                                   67888888877765146688888887775 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00024
                     IstB_IS21  47 kenivllGpsGvGKshlaialgveavra 74 
                                   + ni+++G +G GKs+++  l+ + v++
  gi|13541470|ref|NP_111158.1| 439 SYNIIVTGETGSGKSYFSRILAISFVED 466
                                   569***************9999988874 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   5.7e-05     0.085      16     136 ..     441     563 ..     434     596 .. 0.58

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.7e-05
                                   EEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTST.SEEE.EEETTSSHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx.xxxxxxxxxxxxxxx RF
                          DEAD  16 dvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyid.lrvl.liiggvaardqlskl 94 
                                   +++v +eTGsGK+    i +++ v    ++    ++i+ P+ e   +++n   ++++  + + +  l +gg+ ++ + s+ 
  gi|13541470|ref|NP_111158.1| 441 NIIVTGETGSGKSYFSRILAISFV----EDMDRSVVILDPLDEYSCDCFNASCSVLDLRKsIFLDaLKTGGNYEEGKSSR- 516
                                   799******************888....578889*******999999888877777732211122122333332222222. PP

                                   HTTCSEEE.EEHHHHHHHH.......HCTSSH.CTTEEEEEEETHHHHHHT CS
                                   xxxxxxxx.xxxxxxxxxx.......xxxxxx.xxxxxxxxxxxxxxxxxx RF
                          DEAD  95 dngvdivv.gtpgrlddll.......stgkln.lsqvrflVlDEadrlldq 136
                                      +++v+    gr  + l       +  +++ ++ ++++ + Ea  l+++
  gi|13541470|ref|NP_111158.1| 517 ---TKVVIiKFEGRDKNKLssimdyiQ-AYFRsVDGLKMVLIEEASILSKD 563
                                   ...233330333333332223334422.22223667777777777666665 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00068         1       1      26 [.     442     467 ..     442     493 .. 0.79
   2 ?    0.4   0.0      0.56   8.4e+02       5      57 ..     507     556 ..     505     588 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00068
                  RNA_helicase   1 iwlyGpsgeGKStlakeLakallkkl 26 
                                   i+++G++g GKS++++ La ++ +++
  gi|13541470|ref|NP_111158.1| 442 IIVTGETGSGKSYFSRILAISFVEDM 467
                                   689***************99998777 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.56
                  RNA_helicase   5 GpsgeGKStlakeLakallkklklkkkdsvys.rnpeddfwdgYtgqevvvidD 57 
                                   G+  eGKS+ +k ++ +++++   +k +++ s     + ++ + +g ++v+i++
  gi|13541470|ref|NP_111158.1| 507 GNYEEGKSSRTKVVIIKFEGR---DK-NKLSSiMDYIQAYFRSVDGLKMVLIEE 556
                                   556899999999987777733...22.333333566666666666666666665 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   0.00017      0.25      22      53 ..     442     473 ..     437     477 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00017
                                   EEEE--TTSSTTHHHHHHHHHHHHTTS-SEEE CS
                          PhoH  22 vfaiGpaGtGKtylavalavealkkkkvkrii 53 
                                   ++++G++G+GK+y++  la++ +++ + + +i
  gi|13541470|ref|NP_111158.1| 442 IIVTGETGSGKSYFSRILAISFVEDMDRSVVI 473
                                   5789*******************998766666 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 ?   -3.5   0.0       6.8     1e+04      82     113 ..      74      97 ..      64     107 .. 0.54
   2 ?   -3.4   0.0       6.5   9.7e+03      87     121 ..     133     167 ..     125     172 .. 0.59
   3 ?    9.6   0.0   0.00061      0.91       2     104 ..     442     542 ..     441     570 .. 0.61

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 6.8
                                   EEESS...-TTCHHHHHHHHHHCTS-EEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          CbiA  82 nrvdgeneetllkealeelkqrygvpvlgvip 113
                                   nr  +++ ++ l +  e+++qr        ++
  gi|13541470|ref|NP_111158.1|  74 NRKPSNRVKQYLTKYTEKILQR--------LR 97 
                                   4444444444444444444444........33 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 6.5
                                   ...-TTCHHHHHHHHHHC.TS-EEEEEE--CCHCCC CS
                                   xxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxx RF
                          CbiA  87 eneetllkealeelkqry.gvpvlgviprdeavaea 121
                                   e+++++l++ ++ l + + +   +  ip++++v ++
  gi|13541470|ref|NP_111158.1| 133 EASFNKLSKEIASLFKGIeASLTFYAIPEKVDV-RI 167
                                   556677777777766544322223367777776.55 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.00061
                                   EEEESSTTSSHHHHHHHHHHHHHH.TT--EEEEE.EEESSCCCCHHTTEB-HHHH....CCHCCCHHHHHHCHCHHHH..E CS
                                   xxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx.xxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxx RF
                          CbiA   2 aiastkGGvGKTtlaanLaralar.rglrVllvD.aDpqannlaileglendiep....dlkrllellealgkkkalllki 76 
                                   +i+ +  G+GK+ ++  La+++ +   + V+ +D +D  +   + +  ++ d+++    d+ + ++  e+ +         
  gi|13541470|ref|NP_111158.1| 442 IIVTGETGSGKSYFSRILAISFVEdMDRSVVILDpLDEYSCDCFNASCSVLDLRKsiflDALKTGGNYEEGK------SSR 516
                                   689999*****************9668889999977766555542222222222233333333333333333......446 PP

                                   EEEEEEEESS...-TTCHHHHHHHHHHC CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          CbiA  77 agvvlnrvdgeneetllkealeelkqry 104
                                     vv+ +++g+  +++  +++ +++q+y
  gi|13541470|ref|NP_111158.1| 517 TKVVIIKFEGR--DKNKLSSIMDYIQAY 542
                                   77777777777..444444444445555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (664 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1008  (0.0562218); expected 358.6 (0.02)
Passed bias filter:                      728  (0.0406046); 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):              12  [number of targets reported over threshold]
# CPU time: 0.69u 0.29s 00:00:00.98 Elapsed: 00:00:00.98
# Mc/sec: 2055.42
//
Query:       gi|13541471|ref|NP_111159.1|  [L=63]
Description: hypothetical protein TVN0640 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0018   17.9   1.2     0.0019   17.8   1.2    1.0  1  DUF1189          Protein of unknown function (DUF1189)
  ------ inclusion threshold ------
       0.12   12.6   0.2       0.21   11.8   0.2    1.4  1  MWFE             NADH-ubiquinone oxidoreductase MWFE subunit
       0.18   11.9   2.9        0.2   11.7   2.9    1.0  1  Phage_holin_3_6  Putative Actinobacterial Holin-X, holin supe
       0.67    9.0   5.2       0.75    8.8   5.2    1.0  1  FUSC-like        FUSC-like inner membrane protein yccS
        6.6    6.0   5.8          7    6.0   5.8    1.0  1  TMEM43           Transmembrane protein 43


Domain annotation for each model (and alignments):
>> DUF1189  Protein of unknown function (DUF1189)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   1.2   5.3e-07    0.0019     174     226 ..       4      56 ..       1      61 [. 0.94

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 5.3e-07
                       DUF1189 174 lidalilaliglilarilkiklsYkqlfkisvyalTlPtilnaileilnftvp 226
                                   +i +l +a++ + +a+ l+ ++ Y   f i++y++T+ ++++ il i+ +tv+
  gi|13541471|ref|NP_111159.1|   4 FIRVLGFAMLFIGVAFYLGWSIMYDTWFDIGLYSFTIVLVVFGILGIMLTTVK 56 
                                   899********************************************998886 PP

>> MWFE  NADH-ubiquinone oxidoreductase MWFE subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.2     6e-05      0.21       5      26 ..      35      56 ..      30      58 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 6e-05
                          MWFE  5 LlpygImiamfgitgaglskir 26
                                  L ++ I++++fgi g++l+ ++
  gi|13541471|ref|NP_111159.1| 35 LYSFTIVLVVFGILGIMLTTVK 56
                                  899***************9886 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 ?   11.7   2.9   5.5e-05       0.2      49      88 ..       8      53 ..       4      62 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5.5e-05
               Phage_holin_3_6 49 lalllllvala..lala.a..lwlaali.vaavllvlagvlalvgl 88
                                  l++++l++++a  l+ + +   w+   +  + ++lv+ g+l+++  
  gi|13541471|ref|NP_111159.1|  8 LGFAMLFIGVAfyLGWSiMydTWFDIGLySFTIVLVVFGILGIMLT 53
                                  4555555555411555544786666666566777777777776654 PP

>> FUSC-like  FUSC-like inner membrane protein yccS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   5.2   0.00021      0.75       5      45 ..      10      50 ..       6      56 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00021
                     FUSC-like  5 tllcfalaslivqlllpypwlfvlglllstflftmlgalGq 45
                                    ++f+ +++  + +++y+ +f +gl  +t++++++g+lG 
  gi|13541471|ref|NP_111159.1| 10 FAMLFIGVAFYLGWSIMYDTWFDIGLYSFTIVLVVFGILGI 50
                                  5678999********************************96 PP

>> TMEM43  Transmembrane protein 43
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   5.8    0.0019         7     188     239 ..       4      54 ..       1      56 [. 0.73

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0019
                        TMEM43 188 llRllGfllmflglllllsplsvlvslipllgelvglgla.lvalllslslsl 239
                                   ++R+lGf ++f+g++++l    +   ++ +  +l ++++  +v  +l+++l++
  gi|13541471|ref|NP_111159.1|   4 FIRVLGFAMLFIGVAFYLGWSIMYDTWFDI--GLYSFTIVlVVFGILGIMLTT 54 
                                   79***************9986555568888..555555442666677777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       942  (0.0525406); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-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 0.30s 00:00:00.75 Elapsed: 00:00:00.48
# Mc/sec: 392.29
//
Query:       gi|13541472|ref|NP_111160.1|  [L=326]
Description: HSP70 class molecular chaperone involved in cell morphogenesis [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-21   77.6   0.0    1.5e-21   77.1   0.0    1.2  1  ALP_N     Actin like proteins N terminal domain
      0.003   16.2   0.1     0.0074   14.9   0.1    1.5  2  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 !   77.1   0.0   1.7e-25   1.5e-21       1     147 []       5     154 ..       5     154 .. 0.87

  Alignments for each domain:
  == domain 1  score: 77.1 bits;  conditional E-value: 1.7e-25
                                   EEEE-SSEEEEE-GGG-EEEEES-EEEE--..SS-EETTT..EEEBBSSTTSEEEGGG--..SSSEB--SSTT-TTSTTTH CS
                         ALP_N   1 GiDiGygntKavsgeletvifPSvvapaeerslssligeg.dglrvevdgekyfvGelaerqgssasrsldddkaasedyk 80 
                                   G+D+Gyg+tK++  +++++ifPS +a  e+  +s++ig++  +l  + ++ k++ G+ a+  g++ +    d ++as+++ 
  gi|13541472|ref|NP_111160.1|   5 GLDVGYGDTKVIGIDGKRIIFPSRWAVTET--ESWGIGGKiPVLSTDGGQTKFIYGRYAS--GNNIRVPQGDGRLASKEAF 81 
                                   89****************************..55555555224444445555*******5..77777778*********** PP

                                   HHHHHHHHHH..---....EEEEEEEEE-GGGHHHHHHHHHHHHTTEEEEEE.GGGEEEEEEEEEEEEEETTHH CS
                         ALP_N  81 alllaalall..gke....eevvLvtGLPveqykkqkealkkrlkgehevvs.vngkersvevekvrvipQplG 147
                                    l++aal+    + +    +++v+ +G+P+++++ + +a k++l+++  +v+  +g+ r+ +v+++ + pQ++G
  gi|13541472|ref|NP_111160.1|  82 PLIAAALWESgiH-NdgspVDLVIGSGTPLGTFDLEVKAAKEALENKILTVTgPEGEVRQYNVTRLIMRPQGVG 154
                                   **********662.24666999999***********************9999*********************9 PP

>> MutL  MutL protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.03   2.7e+02     381     419 ..      98     136 ..      89     153 .. 0.79
   2 !   14.9   0.1   8.3e-07    0.0074     204     284 ..     125     197 ..     114     223 .. 0.69

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.03
                          MutL 381 tavkliigtGGvLthaprpeqilkalldakeeevllPee 419
                                   + v+l+ig+G  L   + + +++k++l++k  +v  Pe+
  gi|13541472|ref|NP_111160.1|  98 SPVDLVIGSGTPLGTFDLEVKAAKEALENKILTVTGPEG 136
                                   6799**********9999999999999987777777754 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 8.3e-07
                          MutL 204 lehivkakgls.kleelvsaeimpTPaAvlkavellae...eeekglgdllvvDvGGaTTdvhsvaegspekekvllklpe 280
                                   +++i+ + g + +++++  + ++  P+ v+ a+ ll++   e++   g  +v+DvG+ TTdv ++        +++    e
  gi|13541472|ref|NP_111160.1| 125 ENKILTVTGPEgEVRQYNVTRLIMRPQGVGAALYLLNQgiiEQQ--PGYGVVIDVGSRTTDVLTI--------NLM--DME 193
                                   5556655555425667777788889*************965544..5888************999........222..234 PP

                          MutL 281 prak 284
                                   p+++
  gi|13541472|ref|NP_111160.1| 194 PVVE 197
                                   5555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       324  (0.0180713); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 2140.53
//
Query:       gi|13541473|ref|NP_111161.1|  [L=106]
Description: hypothetical protein TVN0642 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0016   18.3   2.0     0.0017   18.2   2.0    1.1  1  DUF5105   Domain of unknown function (DUF5105)
     0.0029   16.9   0.1     0.0032   16.7   0.1    1.0  1  ERO1      Endoplasmic Reticulum Oxidoreductin 1 (ERO1)
     0.0038   17.5   2.8     0.0051   17.0   2.2    1.6  1  DUF2683   Protein of unknown function (DUF2683)
     0.0076   16.5   0.1      0.037   14.3   0.0    1.9  2  PerC      PerC transcriptional activator


Domain annotation for each model (and alignments):
>> DUF5105  Domain of unknown function (DUF5105)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   2.0   3.8e-07    0.0017      47     113 ..      24      94 ..       5     104 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 3.8e-07
                                   HHHHHHHHHHHTT--G.GGGGSHHHHHHHHHHHHHHHHH-EEEEEEEEEETTEEEEEEEEE...-EE-TTH CS
                       DUF5105  47 eesfkksfkralgyss.ssvtdkeldnlfkalkealkekakvetkvvsisgdkAeVevtvk...pidlsel 113
                                    e   +++kr ++ ++ +++ ++++d+l+++l    ke+ k     ++ s++kA+V++ vk   p+d+ +l
  gi|13541473|ref|NP_111161.1|  24 GETYVDTIKRIINNYFeYQLVKEAVDKLYDKLGVNEKENRKNDGDEKQVSKEKAQVKIPVKtgnPVDADKL 94 
                                   5667789999999999999***************************************9983334665555 PP

>> ERO1  Endoplasmic Reticulum Oxidoreductin 1 (ERO1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.1   7.1e-07    0.0032     198     264 ..      30      91 ..      17     105 .. 0.63

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 7.1e-07
                          ERO1 198 hperlenlYfnyalvlrAvaklapyleelefstgeeeedeetkellkeelakellsalsskekafde 264
                                     +r+ n Yf+y+lv  Av kl + l   e ++ +++ de  k+  ke+    ++++  ++ +  d 
  gi|13541473|ref|NP_111161.1|  30 TIKRIINNYFEYQLVKEAVDKLYDKLGVNEKENRKNDGDE--KQVSKEKA---QVKIPVKTGNPVDA 91 
                                   458999*******************998665544444444..33322222...22333333344444 PP

>> DUF2683  Protein of unknown function (DUF2683)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   2.2   1.1e-06    0.0051       2      47 ..       3      46 ..       2      75 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.1e-06
                       DUF2683  2 vqaivdisDesnriieivKakydlkdksaAidllieqyaeyllEaE 47
                                  v++++d+sD+++rii++++ + +       i+ +i++y ey l +E
  gi|13541473|ref|NP_111161.1|  3 VRIVLDLSDDEKRIIDLIRVQGETY--VDTIKRIINNYFEYQLVKE 46
                                  78999**************998765..56899******99988766 PP

>> PerC  PerC transcriptional activator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   8.3e-06     0.037      26      81 ..       5      62 ..       2      68 .. 0.78
   2 ?    0.6   0.0      0.15   6.9e+02      47      68 ..      81     102 ..      62     106 .] 0.65

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 8.3e-06
                          PerC 26 vmvlletdaeRklvalk..RaeClrkasrpplpalnlseikkavdrtykelGlatvse 81
                                  +++ l++d++R + +++      +  ++r   +  ++  +k+avd++y +lG++ +++
  gi|13541473|ref|NP_111161.1|  5 IVLDLSDDEKRIIDLIRvqGETYVDTIKRIINNYFEYQLVKEAVDKLYDKLGVNEKEN 62
                                  778889999996555441145677888888888999*****************77665 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.15
                          PerC  47 lrkasrpplpalnlseikkavd 68 
                                   +   + +p++a+ l+e kk  +
  gi|13541473|ref|NP_111161.1|  81 IPVKTGNPVDADKLAEFKKNLE 102
                                   4445568899999999998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1178  (0.0657036); expected 358.6 (0.02)
Passed bias filter:                      508  (0.028334); 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: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 767.79
//
Query:       gi|13541474|ref|NP_111162.1|  [L=115]
Description: hypothetical protein TVN0643 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.7e-12   46.6   0.2    4.5e-12   46.4   0.2    1.0  1  DrsE      DsrE/DsrF-like family
     0.0032   17.4   0.7     0.0038   17.1   0.7    1.2  1  DrsE_2    DsrE/DsrF/DrsH-like family


Domain annotation for each model (and alignments):
>> DrsE  DsrE/DsrF-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.4   0.2     5e-16   4.5e-12       2     117 .]       5     115 .]       4     115 .] 0.86

  Alignments for each domain:
  == domain 1  score: 46.4 bits;  conditional E-value: 5e-16
                                   EEEEEE-S-TTTBSHHHHHHHHHHHHHTTT-EEEEEE-GGGGGGGBS---TGGGTS---GGGGGGCGGGT-EEEEEHHHHH CS
                          DrsE   2 kvfilvtggpygseaarealelalaaaalghevsvffygdGvllllkgqtanpadeknlaellkalkeygvklyvCgqaak 82 
                                    v++++ +   ++e+   ++ ++ + +a+   v++ f g Gv ++lk    n++++  + +++++++  g++l vC  ++k
  gi|13541474|ref|NP_111162.1|   5 LVMVITGKENINTEMVAFNFAINSVQNAKA-TVEMLFLGRGVEAILK----NQNNSDTFLAQINKARSLGIRLTVCSVSMK 80 
                                   567777777778888888888888888777.****************....778889************************ PP

                                   HTT--GGGE-.T--EEEE-HHHHHHHHHH-SEEEE- CS
                          DrsE  83 argldededl.gvgvevsglgelaelqnegdrvitf 117
                                     g++ d+ + +   +v+g  e   ++ eg++vitf
  gi|13541474|ref|NP_111162.1|  81 SLGIE-DSMIfENIEKVMGGVETNAKIEEGYSVITF 115
                                   *****.666634466788999**************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 !   17.1   0.7   4.2e-07    0.0038      90     140 ..      33     101 ..       1     111 [. 0.65

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 4.2e-07
                                   H.................HHCT---HHHHHHHHHHTT-EEEEEHHHHHHHT--GGGB-TT-.EEE-HHH CS
                        DrsE_2  90 m.................kekgvasleeLleaakeagvklvaCqmtmdlmglkkeelidgv.eiagaat 140
                                                     ++++ ++    +++a+  g++l+ C ++m  +g++   +++++ +++g  +
  gi|13541474|ref|NP_111162.1|  33 KatvemlflgrgveailkNQNNSDTFLAQINKARSLGIRLTVCSVSMKSLGIEDSMIFENIeKVMGGVE 101
                                   023344444445555554667778888889*******************************87776554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       559  (0.0311785); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 738.69
//
Query:       gi|13541475|ref|NP_111163.1|  [L=278]
Description: permease [Thermoplasma volcanium GSS1]
Scores for complete 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-54  183.9  29.6    4.4e-54  183.6  29.6    1.0  1  TauE      Sulfite exporter TauE/SafE
  ------ inclusion threshold ------
       0.65   10.0  14.8        1.9    8.5   0.7    3.5  3  DUF1304   Protein of unknown function (DUF1304)
        1.2    7.7  11.4       0.03   13.0   4.3    1.9  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 !  183.6  29.6   7.3e-58   4.4e-54       2     236 .]      12     269 ..      11     269 .. 0.94

  Alignments for each domain:
  == domain 1  score: 183.6 bits;  conditional E-value: 7.3e-58
                          TauE   2 llagllaGfvagllGiGggliavPlLllll...ppavavatsllavvatslsgalahrrrgnvdwrlllllllgsliGall 79 
                                   ++ g+l+Gf  gl+G+Gg+++a+PlL++++   +p+++++t++lav++++l+++++h+r++nv+++++  ++++++iG+l+
  gi|13541475|ref|NP_111163.1|  12 IISGVLVGFSLGLIGGGGSILAIPLLIYFVgirDPHLVIGTTALAVGINALINVYSHLRKKNVNFKIGTAFTVFGVIGVLI 92 
                                   689*************************74568************************************************ PP

                          TauE  80 Gallllllpsellkllfgvlllllallmllrkkr....................srak..grerrptaillvligglvGll 138
                                   G+ l l +p+  l++lf++l+++++l+m+l+k r                          + +++ +   + ++g+l+G++
  gi|13541475|ref|NP_111163.1|  93 GTTLGLITPGGELLFLFSFLMIAIGLYMFLTKCRtcknfdalpkddppdppddpV--HfsNIRKKFGQFKVYIFGLLAGFA 171
                                   ****************************996666699999999988877665551..05567788889999999999**** PP

                          TauE 139 sGllGiGgGfllvpllllllglplkkavatslllilvislagalgyalagavdwpllllllpgallGallGarlarrlser 219
                                   sG++GiGgGfl+vp+ll+   +++  av+tsll + +++l++al y +ag v +p++ll+++g+++G++ Gar+++ +++ 
  gi|13541475|ref|NP_111163.1| 172 SGYFGIGGGFLIVPALLYSADITMNIAVGTSLLSVGTFGLVTALRYGIAGEVLVPIALLYVLGGIFGGFAGARVSTSMKRS 252
                                   ********************************************************************************* PP

                          TauE 220 tlrrlfallllvlgvkl 236
                                   tlrr+f ++++v+g+++
  gi|13541475|ref|NP_111163.1| 253 TLRRFFSIIIVVVGIYM 269
                                   ***************98 PP

>> DUF1304  Protein of unknown function (DUF1304)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.7   0.00032       1.9      53      92 ..      87     126 ..      54     135 .. 0.84
   2 ?    0.8   1.9     0.079   4.7e+02      67     104 ..     191     228 ..     167     233 .. 0.74
   3 ?    8.3   0.8   0.00037       2.2      58      90 ..     241     273 ..     228     278 .] 0.78

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00032
                       DUF1304  53 Aagliwglllgseavglalvlfflgcvvvaglygaltask 92 
                                    +g+++g+ lg  + g +l+++f + +++ gly++lt+ +
  gi|13541475|ref|NP_111163.1|  87 VIGVLIGTTLGLITPGGELLFLFSFLMIAIGLYMFLTKCR 126
                                   57888888887777899********************855 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.079
                       DUF1304  67 vglalvlfflgcvvvaglygaltaskkillvQglpall 104
                                   +  ++ +++ ++ + +g +g++ta + ++    l+++ 
  gi|13541475|ref|NP_111163.1| 191 ADITMNIAVGTSLLSVGTFGLVTALRYGIAGEVLVPIA 228
                                   357888889999999*********99888888887764 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.00037
                       DUF1304  58 wglllgseavglalvlfflgcvvvaglygalta 90 
                                   +g+ ++++   ++l  ff +++vv+g+y+a+ +
  gi|13541475|ref|NP_111163.1| 241 AGARVSTSMKRSTLRRFFSIIIVVVGIYMAIES 273
                                   44444566678899***************9976 PP

>> EMP70  Endomembrane protein 70
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.7      0.24   1.4e+03     323     323 ..      99      99 ..      48     126 .. 0.49
   2 ?   13.0   4.3     5e-06      0.03     272     347 ..     197     271 ..     185     276 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.24
                         EMP70 323 t 323
                                    
  gi|13541475|ref|NP_111163.1|  99 I 99 
                                   1 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 5e-06
                         EMP70 272 vqlllmalvtlllallgflspsnrgslltvalllyvllgliaGYvsarlyktfggekwkkntlltalllpgllflv 347
                                   + + + +l++ ++ l+  l +   g++l  + llyvl g+++G+++ar+  +++ ++  + ++   +++ g+ +++
  gi|13541475|ref|NP_111163.1| 197 IAVGTSLLSVGTFGLVTALRYGIAGEVLVPIALLYVLGGIFGGFAGARVSTSMK-RSTLRRFFSIIIVVVGIYMAI 271
                                   44555667777788888899999******************************9.788888888888888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       796  (0.0443973); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.32s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 1692.06
//
Query:       gi|13541476|ref|NP_111164.1|  [L=1713]
Description: helicase (Lhr-related) [Thermoplasma volcanium GSS1]
Scores for complete 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  164.9   0.0      5e-48  163.4   0.0    1.8  2  DEAD_assoc   DEAD/H associated
    5.3e-27   94.7   0.0    1.6e-26   93.2   0.0    1.8  2  DEAD         DEAD/DEAH box helicase
    5.8e-16   58.8   0.1    3.3e-15   56.4   0.1    2.4  1  Helicase_C   Helicase conserved C-terminal domain
    4.1e-09   36.7   0.0    1.3e-08   35.0   0.0    1.9  1  ResIII       Type III restriction enzyme, res subunit
    4.2e-05   23.3   5.7        1.9    8.4   0.0    5.3  4  TrmB         Sugar-specific transcriptional regulator TrmB
      0.001   18.9   6.1        0.1   12.5   0.1    4.2  4  TFIIE_alpha  TFIIE alpha subunit
     0.0018   18.6   0.0      0.019   15.3   0.0    2.6  3  AAA_19       AAA domain
  ------ inclusion threshold ------
      0.038   14.1   0.3      0.079   13.0   0.3    1.5  1  RepB         RepB plasmid partitioning protein
      0.048   13.4   0.3       0.95    9.2   0.3    3.1  2  DUF4116      Domain of unknown function (DUF4116)
      0.073   12.6   1.3       0.19   11.3   1.3    1.8  1  GerE         Bacterial regulatory proteins, luxR family
       0.18   12.2   0.2          2    8.8   0.2    2.6  1  AAA          ATPase family associated with various cellular a


Domain annotation for each model (and alignments):
>> DEAD_assoc  DEAD/H associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0       5.8   9.4e+03       4      22 ..     600     619 ..     599     621 .. 0.80
   2 !  163.4   0.0   3.1e-51     5e-48       1     191 []     630     816 ..     630     816 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 5.8
                    DEAD_assoc   4 drtllvErf.rdelgdwrlv 22 
                                   ++++l+Er+  de g + ++
  gi|13541476|ref|NP_111164.1| 600 PTRMLIERYhVDENGARSII 619
                                   6799*****98998888776 PP

  == domain 2  score: 163.4 bits;  conditional E-value: 3.1e-51
                    DEAD_assoc   1 lPtdrtllvErfrdelgdwrlvvhspfGrrvnealalllaarlsrrfgidvqvaanDdgivlllpleerlpllldellell 81 
                                   +Pt+++l vE  ++  g    v+h p+Gr+vn+al++ +a  +s++++++ +++++Ddg++++++  +++p  l e+++l+
  gi|13541476|ref|NP_111164.1| 630 IPTEDHLFVEGLEEPDGVFGAVFHVPLGRKVNDALSRSYALAISNKYQTNTRITVTDDGFIIYSE--NKIP--LGEAVKLI 706
                                   7************99***********************************************664..5888..56899*** PP

                    DEAD_assoc  82 spdeleedleaalnaselfkrrFrevAaralllprrypgkrkplwqqrlraaqLldvareypdfpllleavrevledqlDl 162
                                   ++++le+ +++a+ ++elfk rFr++Aar+l+++r+y+g   ++ +q+lr+++Ll+ +++++df +++e++re++ed +D+
  gi|13541476|ref|NP_111164.1| 707 NSENLEDYVRRAISNTELFKQRFRHCAARSLMILRSYKGYDISVARQQLRSDKLLNELQKHQDFSIIKETYREIMEDIMDV 787
                                   ********************************************************************************* PP

                    DEAD_assoc 163 erlaellrr.iaageirvvevetprpSpfA 191
                                   +r+ e++++ i +g+ +++   +++ Spf+
  gi|13541476|ref|NP_111164.1| 788 PRAIEYVKDvIDRGAYTIRP-YSRETSPFS 816
                                   *********44555666666.899999996 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.2   0.0   9.7e-30   1.6e-26       1     170 [.      33     216 ..      33     221 .. 0.84
   2 ?   -3.7   0.0       5.3   8.6e+03      48     103 ..     282     338 ..     271     341 .. 0.72

  Alignments for each domain:
  == domain 1  score: 93.2 bits;  conditional E-value: 9.7e-30
                                   -HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHS....TTSTS-EEEEEESSHHHHHHHHHHHHHHTTTST.. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                          DEAD   1 tdiQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyet....kgktgpkalivePtreLaeqtlnnlkkfkkyid.. 75 
                                   t+ Q+ aip i +g++vlv+ +TG+GKTl +++ ++++++      k +++  +++++P+++La+++ +nl+  ++ i   
  gi|13541476|ref|NP_111164.1|  33 TEPQKYAIPFIHEGRNVLVSSPTGTGKTLTAFLSIINELFMLarsgKLEDKIYCVYISPLKALANDVNKNLRAPLEGIYki 113
                                   577*********************************9998889999******************************64445 PP

                                   ..........SEEEEEETTSSHHHHHHHHHTT.CSEEEEEHHHHHHHHHCTSSH..CTTEEEEEEETHHHHHHTTTHHHHH CS
                                   ..........xxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD  76 ..........lrvlliiggvaardqlskldng.vdivvgtpgrlddllstgkln..lsqvrflVlDEadrlldqgfsdfin 143
                                             +rv++  +g++ + +++k+ ++ ++i+++tp+ +   ls+ +++  l++v+++++DE++++++ +++  ++
  gi|13541476|ref|NP_111164.1| 114 adedginlpkIRVSVR-SGDTSEGERQKMARKpPHILITTPESFSLTLSSPRMRenLRDVKYVIIDEIHEISSTKRGSLLS 193
                                   5788888877777655.5666666666665556************98854443333************************* PP

                                   HHHHHSHHHCTTSTTTSEEEEEESSBS CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD 144 rilnqlpqitcdgklqrqvivlSATlp 170
                                   + +++l+            i lSAT +
  gi|13541476|ref|NP_111164.1| 194 ANMERLEALRPGIL----RIGLSATQS 216
                                   ******54444433....899***975 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 5.3
                                   -EEEEEESSHHHHHHHHHHHHHHTTTSTSEEE.EEETTSSHHHHHHHHHTT.CSEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx.xxxxxx RF
                          DEAD  48 pkalivePtreLaeqtlnnlkkfkkyidlrvl.liiggvaardqlskldng.vdivvg 103
                                     +li + tr+ +e ++ +l++++ + +l+++ + +g++++ +  +kl+ng +++v++
  gi|13541476|ref|NP_111164.1| 282 RTTLIFTNTRSGTEHVALRLRSRGIE-SLEAHhSSMGKEQRVEVENKLKNGeLKCVIT 338
                                   56788888888888888888888886.3455546778888888888888777777776 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.4   0.1     2e-18   3.3e-15       6     108 ..     270     374 ..     266     376 .. 0.87

  Alignments for each domain:
  == domain 1  score: 56.4 bits;  conditional E-value: 2e-18
                                   HHHHH.HHTTTTSEEEEEESSHHHHHHHHHHHHHTTSTEE.EESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTSTT CS
                    Helicase_C   6 llell.kleeeggkilifvntidrlekvklllekkgikva.vlhgelpqnereeileqfnkgesdvLiatdvaerGidipk 84 
                                   +++++ +l ++ +++lif+nt++  e+v l l+++gi+++ ++h+++ +++r e+ ++ ++ge +++i+++ +e G+di  
  gi|13541476|ref|NP_111164.1| 270 MYDIIaDLVKQYRTTLIFTNTRSGTEHVALRLRSRGIESLeAHHSSMGKEQRVEVENKLKNGELKCVITSTSLELGVDIGY 350
                                   56665567799999*********88766666777787765167779*********************************** PP

                                   ESEEEESSSSSSHHHHHHHHTTSS CS
                    Helicase_C  85 vnlVinfdlprnvtsyiqriGRtg 108
                                   ++lVi+++ p++v++  qriGR g
  gi|13541476|ref|NP_111164.1| 351 IDLVIQIGSPKSVSKGLQRIGRSG 374
                                   **********************87 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.0   0.0   8.1e-12   1.3e-08      22     168 ..      44     214 ..      24     217 .. 0.75

  Alignments for each domain:
  == domain 1  score: 35.0 bits;  conditional E-value: 8.1e-12
                                   .TTSEEEEEESTTSTHHHHH.HHHHHHH-S...........-EEEEESSHHHHHHHHHHGGGGTGG............... CS
                        ResIII  22 krdkrglikmaTGtGKTlva.aklierllkkgkee......kflflvprkslleqtleefkkflseayke........... 84 
                                   ++ +++l+  +TGtGKTl+a +++i +l+  ++         ++ + p k+l +   ++++  l+  yk            
  gi|13541476|ref|NP_111164.1|  44 HEGRNVLVSSPTGTGKTLTAfLSIINELFMLARSGkledkiYCVYISPLKALANDVNKNLRAPLEGIYKIadedginlpki 124
                                   4567899*************999***999765554688988899999*************999999988766666665554 PP

                                   ...GEEEESSS-B--.........-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.T.......TTHHH CS
                        ResIII  85 ...igkkvsgdkkka..kekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakk.......swrei 153
                                      +    sgd+ +   ++ +++  +il+tt +s++  +   ++ + +      +++iiDE H +++ k       +++++
  gi|13541476|ref|NP_111164.1| 125 rvsV---RSGDTSEGerQKMARKPPHILITTPESFSLTL---SSPRMRENLRDVKYVIIDEIHEISSTKrgsllsaNMERL 199
                                   3320...333333335455688999**************...4444444444555************85566666688885 PP

                                   HHT---SEEEEEESS CS
                        ResIII 154 lekfkeavllglTAT 168
                                       +  +++gl+AT
  gi|13541476|ref|NP_111164.1| 200 EALRPGILRIGLSAT 214
                                   4444559*******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 !    8.4   0.0    0.0012       1.9      12      53 ..    1022    1064 ..    1017    1076 .. 0.89
   2 !    7.5   0.3    0.0024       3.8      20      57 ..    1184    1221 ..    1167    1231 .. 0.82
   3 ?    1.3   0.1      0.19   3.2e+02       1      62 [.    1480    1541 ..    1480    1543 .. 0.88
   4 ?    3.9   0.0      0.03        50      25      48 ..    1568    1591 ..    1564    1593 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0012
                                    CHCHHHH.HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEE CS
                          TrmB   12 kvYlaLl.klgpatadeiaeelgvprskvYevLrsLedkGlVe 53  
                                    +  ++Ll ++gp+t +ei  ++  ++ ++ ++L  L++ G V 
  gi|13541476|ref|NP_111164.1| 1022 RLLIKLLgSYGPSTLEEIEIKIPFDEDTIKSALDALISSGQVV 1064
                                    6678999********************************9886 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0024
                                    HCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESS CS
                          TrmB   20 lgpatadeiaeelgvprskvYevLrsLedkGlVerekg 57  
                                    +   t ++i+e+l+ ++  v +++rsLe k +V ++++
  gi|13541476|ref|NP_111164.1| 1184 KSGYTEEKISEKLNMEKRIVRQIIRSLEYKMMVGKSDS 1221
                                    5677999***********************99988765 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.19
                                    HHHCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEE CS
                          TrmB    1 LqklGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpklY 62  
                                    L+ + L++ E +v + ++  ++at +ei +  g++ + v  +  +L +  +  r+ +r+++Y
  gi|13541476|ref|NP_111164.1| 1480 LRSYQLTKEEQQVIKFIMGVDSATEREIERGCGLESAVVKAATDRLFKYRILARNFERKYFY 1541
                                    6678899999999999999********************99999999888777777777777 PP

  == domain 4  score: 3.9 bits;  conditional E-value: 0.03
                                    HCHHCCCTTSSCHCHHHHHHHHHH CS
                          TrmB   25 adeiaeelgvprskvYevLrsLed 48  
                                     +  + ++gvp+s +Y++ +sL++
  gi|13541476|ref|NP_111164.1| 1568 PSRMSTMIGVPESEIYSIASSLKN 1591
                                    5677899***********999975 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.1     0.011        17      32      60 ..     969     997 ..     958    1010 .. 0.89
   2 ?    0.9   0.1      0.26   4.2e+02      17      96 ..    1023    1103 ..    1012    1108 .. 0.69
   3 !   12.5   0.1   6.2e-05       0.1      16      53 ..    1177    1212 ..    1165    1219 .. 0.83
   4 ?   -2.3   0.0       2.4   3.9e+03      14      56 ..    1488    1530 ..    1484    1538 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.011
                                   HHHHHHTS-HHHHHHHHHHHHHCTSEEEE CS
                   TFIIE_alpha  32 dlakelkidlnelrklLnrLyearlvkyk 60 
                                   +l  ++k+  +elrk++ rL +a l++ k
  gi|13541476|ref|NP_111164.1| 969 ELRDLTKMGEEELRKVIGRLESAFLIERK 997
                                   78999******************999865 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.26
                                    HHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEEE.TTTEEEEEEEEEECCCHCCCHHHHHHHHHH CS
                   TFIIE_alpha   17 lvldvLlekgevteedlakelkidlnelrklLnrLyearlvkykrrrd.eekswykyywrinyeklvdvvkrkleevvk 94  
                                    l ++ L + g  t e+++ ++ +d   ++++L +L + + v y       +k+ +         k  dvv ++ +++ k
  gi|13541476|ref|NP_111164.1| 1023 LLIKLLGSYGPSTLEEIEIKIPFDEDTIKSALDALISSGQVVYDYITPvYSKQYMLSSDIEAMTKTKDVVPWRFSKITK 1101
                                    5667788888888899999999999999999999999988877655443333333333333445666777777777777 PP

                                    HH CS
                   TFIIE_alpha   95 kL 96  
                                    k+
  gi|13541476|ref|NP_111164.1| 1102 KV 1103
                                    66 PP

  == domain 3  score: 12.5 bits;  conditional E-value: 6.2e-05
                                    HHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHH CS
                   TFIIE_alpha   16 vlvldvLlekgevteedlakelkidlnelrklLnrLye 53  
                                      vl+++  k+  tee ++++l++++ ++r+++  L  
  gi|13541476|ref|NP_111164.1| 1177 EAVLEAI--KSGYTEEKISEKLNMEKRIVRQIIRSLEY 1212
                                    5567765..5999********************99965 PP

  == domain 4  score: -2.3 bits;  conditional E-value: 2.4
                                    HHHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTS CS
                   TFIIE_alpha   14 eavlvldvLlekgevteedlakelkidlnelrklLnrLyearl 56  
                                    e  +v++ ++     te ++++  +++  +++ +  rL++ r+
  gi|13541476|ref|NP_111164.1| 1488 EEQQVIKFIMGVDSATEREIERGCGLESAVVKAATDRLFKYRI 1530
                                    567899999988999999****99*999999999999998876 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.2e-05     0.019       1     127 [.      36     197 ..      36     210 .. 0.71
   2 ?   -0.9   0.0       1.1   1.8e+03      50      92 ..     425     465 ..     396     513 .. 0.67
   3 ?   -2.9   0.0       4.8   7.8e+03     108     132 ..     831     854 ..     824     862 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.2e-05
                        AAA_19   1 qreave.alkekvllvtaGpGtGKTrv..lkhivallvelggvkp...eeillvaftgrAakelrerlaalgaeatTiHrl 75 
                                   q+ a+   ++ +++lv  + GtGKT +  l  i +l+  +++ k+     ++ +++ +  a+ ++++l    a+ + i ++
  gi|13541476|ref|NP_111164.1|  36 QKYAIPfIHEGRNVLVSSPTGTGKTLTafLSIINELFMLARSGKLedkIYCVYISPLKALANDVNKNL---RAPLEGIYKI 113
                                   67788558999*************976433333333322222222212556667888899999**999...8898888888 PP

                        AAA_19  76 al..................................ldfddlltealelle..........eaeeekklqeeellivDEfq 112
                                   a                                   +                        + + +++l++ +++i+DE+ 
  gi|13541476|ref|NP_111164.1| 114 ADedginlpkirvsvrsgdtsegerqkmarkpphilI-------------TtpesfsltlsSPRMRENLRDVKYVIIDEIH 181
                                   7788889999999988888888777777776666532.............02223333333567788998888******** PP

                        AAA_19 113 dvd.elqyrLlkallg 127
                                   +++     +Ll+a ++
  gi|13541476|ref|NP_111164.1| 182 EISsTKRGSLLSANME 197
                                   ***9999999998774 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.1
                        AAA_19  50 ftgrAakelrerla..algaeatTiHrlalldfddlltealelle 92 
                                   + g A++++ ++ +  +++++ +T+H l    +dd +  +le+l 
  gi|13541476|ref|NP_111164.1| 425 LVGMAVERVWDAKEayEVLRSSYTFHTL---SWDDYV-LTLEYLS 465
                                   4555666665543300445669****99...455544.3444443 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 4.8
                        AAA_19 108 vDEfqdvdelqyrLlkallgekkkl 132
                                    D + +++elq r+l++++g++  +
  gi|13541476|ref|NP_111164.1| 831 EDRSKMLKELQGRMLEKIYGTTS-I 854
                                   57889999********9997664.4 PP

>> RepB  RepB plasmid partitioning protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.3   4.8e-05     0.079       3      81 ..    1168    1238 ..    1166    1241 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.8e-05
                          RepB    3 adlsfierarfaarleerGvdreeiasalgldkqtvskmvaraipegicaeevaLLkdvetgiaaiglakkigrarwve 81  
                                    +d+ +++  + +  ++++G+++e+i+ +l + k+ v     r+i+ ++   e +++ +++    +i  a++igr++ +e
  gi|13541476|ref|NP_111164.1| 1168 RDHEVSQNEEAVLEAIKSGYTEEKISEKLNMEKRIV-----RQIIRSL---EYKMMVGKSDSELVITDARDIGRGKALE 1238
                                    79999*******************************.....9999999...8888888888888899999999998776 PP

>> DUF4116  Domain of unknown function (DUF4116)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.66   1.1e+03      16      43 ..     258     287 ..     253     289 .. 0.87
   2 ?    9.2   0.3   0.00058      0.95       1      36 [.    1175    1209 ..    1175    1212 .. 0.95

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.66
                       DUF4116  16 lkylseeLknDk..eivlkAvkqngtalsy 43 
                                   l+++s e  nD+  +i+   vkq+ t l +
  gi|13541476|ref|NP_111164.1| 258 LTKVSYEVANDRmyDIIADLVKQYRTTLIF 287
                                   678999999***9999999*****998866 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00058
                       DUF4116    1 DrEivleavkkngsalkylseeLknDkeivlkAvkq 36  
                                    ++E vlea+k+ g+  +++se+L   k iv +++++
  gi|13541476|ref|NP_111164.1| 1175 NEEAVLEAIKS-GYTEEKISEKLNMEKRIVRQIIRS 1209
                                    7899*******.9********************985 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   1.3   0.00012      0.19       4      54 ..    1173    1224 ..    1170    1226 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00012
                                    -HHHHHHHHHHCTTS-HHHHHHHHTS-HHHHHHHHHHHHHHHT-.SSHHHHH CS
                          GerE    4 skRErevLrllaeGksnkeIAeelniSekTVkvhksnimkKLnv.ksrvelv 54  
                                    s+ E  vL+ + +G++ ++I+e+ln  ++ V+  ++++  K+ v ks++elv
  gi|13541476|ref|NP_111164.1| 1173 SQNEEAVLEAIKSGYTEEKISEKLNMEKRIVRQIIRSLEYKMMVgKSDSELV 1224
                                    78899*********************************99999855666665 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.2    0.0012         2       1      75 [.      49     188 ..      49     222 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0012
                                   EEEESSTTSSHHHHH.HHHHHHH...........THEEEEEETTTCS.SS............................... CS
                           AAA   1 vllyGppGtGKTlla.kavakel...........gvefleisgsell.sk............................... 37 
                                   vl++ p GtGKTl+a  ++++el           +++++ is  + l ++                               
  gi|13541476|ref|NP_111164.1|  49 VLVSSPTGTGKTLTAfLSIINELfmlarsgkledKIYCVYISPLKALaNDvnknlraplegiykiadedginlpkirvsvr 129
                                   68999*******998468999976667766666557778888777773448888888888888888888888888888888 PP

                                   ..................STTHHHHHHHHHHHHHHHTS...TSEEEEEETGGGHHHHHT CS
                           AAA  38 ..................yvgesekkirelfkeakeka...kpsilfiDEidalaksrs 75 
                                                     ++  ++++++ ++++ +  +   + + ++iDEi+++ ++++
  gi|13541476|ref|NP_111164.1| 130 sgdtsegerqkmarkpphILITTPESFSLTLSSPRMREnlrDVKYVIIDEIHEISSTKR 188
                                   88888888888888888866666666666666633333345558889999999988873 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1713 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       876  (0.0488594); expected 358.6 (0.02)
Passed bias filter:                      671  (0.0374254); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); 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: 1.08u 0.31s 00:00:01.39 Elapsed: 00:00:00.51
# Mc/sec: 10189.41
//
Query:       gi|13541477|ref|NP_111165.1|  [L=150]
Description: nucleotide-binding protein (UspA-related) [Thermoplasma volcanium GSS1]
Scores for complete 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-20   73.5   0.0    3.1e-20   73.1   0.0    1.1  1  Usp       Universal stress protein family


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.1   0.0   1.7e-24   3.1e-20       4     140 ..       3     142 ..       1     143 [. 0.81

  Alignments for each domain:
  == domain 1  score: 73.1 bits;  conditional E-value: 1.7e-24
                                   EEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHH..HHHHHHCTTCEE CS
                           Usp   4 rIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleada..akaaaeaggvkv 82 
                                   + l+a+Dgse+++ Ale+Al++ k+  ++ +++++i+ +  g+++++d  ++e+  e+++++ e+    ak++   + v+ 
  gi|13541477|ref|NP_111165.1|   3 KALIAYDGSETADCALEYALNFRKSI-DKYFVIYIIP-QIIGTTPTYDTYVPESMFEDQRKKGEEIIerAKKLVSNESVDL 81 
                                   789******************98885.6899999997.5667777777777777777777777766677555555555555 PP

                                   EEEEE...ESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEE CS
                           Usp  83 evvve...egdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvV 140
                                   e++++    + +a++ +evaee+++d+i++Gsr ++gls+++lGSvs+ +++ +++pVlv+
  gi|13541477|ref|NP_111165.1|  82 EFEIVdsgTKTVAHKAVEVAEEKGVDIIITGSRNLKGLSKIILGSVSSEIIKLSSVPVLVC 142
                                   5555411167889999*******************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       659  (0.0367561); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.31s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 967.16
//
Query:       gi|13541478|ref|NP_111166.1|  [L=75]
Description: 30S ribosomal protein S17e [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.7e-11   42.2   0.6    7.6e-11   42.0   0.6    1.0  1  Ribosomal_S17e  Ribosomal S17
      0.002   18.0   1.6     0.0023   17.9   1.6    1.0  1  EC042_2821      EC042_2821-lke REase


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 !   42.0   0.6   8.4e-15   7.6e-11       1      69 [.       1      69 [.       1      74 [. 0.94

  Alignments for each domain:
  == domain 1  score: 42.0 bits;  conditional E-value: 8.4e-15
                                  XX----HHHHHHHHHHHHS-TTT--S-HHHHHHHHHHHS----SHHHHHHHHHHHHHHHHTTSS--SS- CS
                Ribosomal_S17e  1 mgrvrtktvKkaarviiekyyskltndFhtnkkvceevaiipskklrnkiaGyvthlmkriqkgpvrgi 69
                                  mg +r   vK++a++i eky s +t+ F++nk+ +e++    sk+  n i+Gy t+++ + +++  r i
  gi|13541478|ref|NP_111166.1|  1 MGSIRPFNVKRTAEEIAEKYPSLFTEKFEENKRKLEKMMPDVSKRTINIISGYLTRYVVKKKEKAEREI 69
                                  89999999*************************************************999999888887 PP

>> EC042_2821  EC042_2821-lke REase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   1.6   2.5e-07    0.0023      24      77 ..      13      67 ..       7      74 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.5e-07
                    EC042_2821 24 edeikakyskeiaekllkfaneikelieetesdk.faigidvnlqivKkkekadl 77
                                   +ei +ky++   ek+++ ++++++++ ++++     i+   + ++vKkkeka  
  gi|13541478|ref|NP_111166.1| 13 AEEIAEKYPSLFTEKFEENKRKLEKMMPDVSKRTiNIISGYLTRYVVKKKEKAER 67
                                  5789*************************99998444555678899*****9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1202  (0.0670422); expected 358.6 (0.02)
Passed bias filter:                      537  (0.0299515); 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: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 484.59
//
Query:       gi|13541479|ref|NP_111167.1|  [L=131]
Description: hypothetical protein TVN0648 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score 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   14.5   0.1        1.6    9.0   0.1    2.2  2  RILP             Rab interacting lysosomal protein
      0.034   14.1   0.0      0.062   13.3   0.0    1.4  1  tRNA_anti-codon  OB-fold nucleic acid binding domain
       0.12   12.9   0.1       0.25   11.9   0.1    1.5  1  DUF4236          Protein of unknown function (DUF4236)


Domain annotation for each model (and alignments):
>> RILP  Rab interacting lysosomal protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.1   0.00026       1.6       3      17 ..      54      68 ..      53      70 .. 0.90
   2 ?    3.3   0.0     0.016        95      19      32 ..      85      98 ..      83     109 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00026
                          RILP  3 qELrdVLqERNeLKa 17
                                   E++d+L ER  LK 
  gi|13541479|ref|NP_111167.1| 54 SEIKDILAEREILKD 68
                                  59************6 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.016
                          RILP 19 lfllqEELayYkse 32
                                  l l +EE+ yY+s 
  gi|13541479|ref|NP_111167.1| 85 LTLWNEEICYYRSM 98
                                  56789*******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 ?   13.3   0.0     1e-05     0.062      29      69 ..      82     122 ..      78     125 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1e-05
                                   EEEEEEETHHHHHHHTTS-TTSEEEEE.EEEEECTTSSEEEE CS
               tRNA_anti-codon  29 riqvvlfreeatklaenlkeGdvvrvt.Grvkrrpggelelk 69 
                                   +++++l++ee  ++ + +k+G+ ++   +rv++++ g +e++
  gi|13541479|ref|NP_111167.1|  82 EMTLTLWNEEICYYRSMIKVGKKIKFVnCRVNFTRYG-VEVS 122
                                   5789******************************999.8886 PP

>> DUF4236  Protein of unknown function (DUF4236)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   4.2e-05      0.25       5      31 ..     103     128 ..      95     130 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.2e-05
                       DUF4236   5 ksikigPgvrlNlSksGiSvSvGvrga 31 
                                   k ik++   r+N+++ G+ vS+G rg+
  gi|13541479|ref|NP_111167.1| 103 KKIKFVN-CRVNFTRYGVEVSLGDRGF 128
                                   8899999.*****************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       682  (0.0380389); expected 358.6 (0.02)
Passed bias filter:                      516  (0.0287802); 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: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 939.27
//
Query:       gi|13541480|ref|NP_111168.1|  [L=388]
Description: acetyl-CoA acetyltransferase [Thermoplasma volcanium GSS1]
Scores for complete 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-80  269.8   0.3    2.7e-80  269.5   0.3    1.1  1  Thiolase_N     Thiolase, N-terminal domain
    5.6e-37  126.1   1.0      9e-37  125.5   0.0    1.9  3  Thiolase_C     Thiolase, C-terminal domain
      4e-06   26.6   1.1    2.7e-05   23.9   0.6    2.2  2  ketoacyl-synt  Beta-ketoacyl synthase, N-terminal domain


Domain annotation for each model (and alignments):
>> Thiolase_N  Thiolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  269.5   0.3   4.5e-84   2.7e-80       1     259 [.       4     256 ..       4     257 .. 0.97

  Alignments for each domain:
  == domain 1  score: 269.5 bits;  conditional E-value: 4.5e-84
                                   EEEEEEEEE--EETTSTTTTS-HHHHHHHHHHHHHHHHTS-GGGCCEEEEEHSSCTTSTSCHHHHHHHHTTS-TTSEEEEE CS
                    Thiolase_N   1 vvivsaartpigkfggslkdlsaeeLlaealkallekagvdpeevdevivGnvlqagegqniarqaalkagipeevpavtv 81 
                                   v+ivsa+rt+igkfg s+++++a +L+ +a+ka++e+ g+d+++++evi+Gnv+qag gqn+a qaa +ag+++e++  tv
  gi|13541480|ref|NP_111168.1|   4 VYIVSAKRTAIGKFGRSFSKIPAPQLGGAAIKAVIEDSGIDKSAIQEVIMGNVIQAGVGQNPAGQAARAAGLADEITKYTV 84 
                                   89******************************************************************************* PP

                                   EHGGGHHHHHHHHHHHHHHTTSHSEEEEEEEEESTTS-EEETCTTT...TGGSSSSEEEEEHHHHHHTEETTTTSEHHHHH CS
                    Thiolase_N  82 nkvcsSglkavalaaqsiaageadvvvagGvEsmsnaptaestdvr...sglklgdekakdllipdgladafneehmGlta 159
                                   n vc+Sg+ av  aa++i+ ge ++v+agG+E+msnap   ++d+r   ++l +++ k+ d ++ dgl+daf  ehmG++a
  gi|13541480|ref|NP_111168.1|  85 NVVCASGMLAVESAAREIKLGEREIVIAGGMENMSNAPFLLPSDLRwgpKHLLHKNYKIDDAMLVDGLTDAFYFEHMGVSA 165
                                   **********************************************777788899************************** PP

                                   HHHHHHHT--HHHHHHHHHHHHHHHHHHHHTTTTTTTBE-EEEEESSSEEEE-S-TTS-TT--HHHHHTS-BSSSTTSS-B CS
                    Thiolase_N 160 enlakkykisReeqdefAvkshqkaaaaqkagkFkdeivPvkvkgkkgkktvdkdeairsevtaekLaklkpaFkkeGtvt 240
                                   e++akky+i+Re+ de+ v+s+++a  a++ g+F++ei   +v +      +++de+ir+ +t+e Lakl paF+k+G  t
  gi|13541480|ref|NP_111168.1| 166 ERTAKKYGITREMADEYSVQSYERAIRATNTGEFSKEI---TVFS-----NLSQDEGIRK-TTMEDLAKLPPAFDKNGILT 237
                                   **************************************...3322.....579******9.******************** PP

                                   TTSB--BEEEEEEEEEEEH CS
                    Thiolase_N 241 AgnasqisDGaaavllmse 259
                                   Agn+ q+sDG +a+ll+se
  gi|13541480|ref|NP_111168.1| 238 AGNSAQLSDGGSALLLASE 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 ?   -3.7   0.0       1.5   9.2e+03      27      42 ..      33      48 ..      31      52 .. 0.79
   2 ?   -3.7   0.1       1.5   8.7e+03      97     114 ..      75      92 ..      70      98 .. 0.72
   3 !  125.5   0.0   1.5e-40     9e-37       1     122 [.     264     385 ..     264     386 .. 0.98

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 1.5
                                  HHHHHHHHHT--GGGE CS
                    Thiolase_C 27 aikkvlkkagltvedi 42
                                  aik+v+++ g++ + i
  gi|13541480|ref|NP_111168.1| 33 AIKAVIEDSGIDKSAI 48
                                  8899999999987766 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 1.5
                                   HHHCTTSEEEEEEEETTT CS
                    Thiolase_C  97 lkkeggklgvaalCiggg 114
                                   l  e +k++v  +C++g 
  gi|13541480|ref|NP_111168.1|  75 LADEITKYTVNVVCASGM 92 
                                   555667888888998764 PP

  == domain 3  score: 125.5 bits;  conditional E-value: 1.5e-40
                                   ---SEEEEEEEEEE--GGGGGGHHHHHHHHHHHHHT--GGGESEEEE--SBHHHHHHHHHHHT--GGGBSTT--HHHH-B- CS
                    Thiolase_C   1 lkplakirsyaevgvdpeilglgPayaikkvlkkagltvedidlfEinEAFaaqaLavakaldldlekvNvnGGaialGHP 81 
                                   lkp+aki+ y +++  p ++  +P++a++k+l+++g +++  d++E nEAF+   + v  +l++d e++NvnGGa+a+GHP
  gi|13541480|ref|NP_111168.1| 264 LKPIAKITGYESASLAPLDFVEAPIPATRKLLERQGKSIDYYDIVEHNEAFSIASIIVRDQLHIDNERFNVNGGAVAIGHP 344
                                   589****************************************************************************** PP

                                   TTTHHHHHHHHHHHHHHHCTTSEEEEEEEETTTEEEEEEEE CS
                    Thiolase_C  82 lGasGaRivvtllselkkeggklgvaalCigggqgvalvie 122
                                   +G sG+Ri+vtl+++lk+++ k+g+a+lC ggg +++l +e
  gi|13541480|ref|NP_111168.1| 345 IGNSGSRIIVTLINALKERHMKTGLATLCHGGGGAHTLTLE 385
                                   ***********************************998876 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 ?    0.3   0.0     0.073   4.3e+02      91     131 ..      29      69 ..      24      81 .. 0.77
   2 !   23.9   0.6   4.5e-09   2.7e-05     169     206 ..      82     119 ..      66     124 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.073
                                   HHHHHHHHHHHHHTS-HHTCTTGGEEEEEEESSTHHHHHHH CS
                 ketoacyl-synt  91 llleaawealedagltpeeldgsrvgvfiGvgagdyaalaa 131
                                   l   a +  +ed+g+++ ++++  +g++i +g g++ a +a
  gi|13541480|ref|NP_111168.1|  29 LGGAAIKAVIEDSGIDKSAIQEVIMGNVIQAGVGQNPAGQA 69 
                                   5667788899*******999999999999888887744443 PP

  == domain 2  score: 23.9 bits;  conditional E-value: 4.5e-09
                                   EEEESGGGHHHHHHHHHHHHHHTTS-SEEEEEEEE--- CS
                 ketoacyl-synt 169 vtvdtACsSslvavhaavqslrsgeadvalaGGvelll 206
                                   +tv   C+S+  av+ a ++++ ge ++++aGG+e + 
  gi|13541480|ref|NP_111168.1|  82 YTVNVVCASGMLAVESAAREIKLGEREIVIAGGMENMS 119
                                   789999****************************9776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (388 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); 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: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 2617.81
//
Query:       gi|13541481|ref|NP_111169.1|  [L=417]
Description: glycine oxidase (deaminating) [Thermoplasma volcanium GSS1]
Scores for complete 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-48  164.5   0.0    5.5e-48  164.3   0.0    1.0  1  DAO            FAD dependent oxidoreductase
    5.4e-08   32.4   0.0     0.0062   15.8   0.0    2.6  3  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    2.9e-06   26.7   0.0    4.6e-06   26.0   0.0    1.3  1  Thi4           Thi4 family
      4e-05   23.7   0.1    0.00016   21.9   0.0    2.0  2  NAD_binding_8  NAD(P)-binding Rossmann-like domain
     0.0002   20.6   0.0     0.0081   15.3   0.0    2.1  2  FAD_binding_2  FAD binding domain
     0.0017   18.4   0.0     0.0054   16.7   0.0    1.8  2  NAD_binding_9  FAD-NAD(P)-binding
     0.0021   18.6   0.2        9.5    6.9   0.0    3.6  4  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
     0.0069   15.5   0.0      0.011   14.8   0.0    1.4  1  Lycopene_cycl  Lycopene cyclase protein
     0.0084   14.9   0.0       0.28    9.9   0.0    2.2  2  HI0933_like    HI0933-like protein
  ------ inclusion threshold ------
      0.014   14.0   0.0      0.021   13.4   0.0    1.2  1  Mqo            Malate:quinone oxidoreductase (Mqo)
      0.039   13.1   0.0      0.066   12.3   0.0    1.3  1  K_oxygenase    L-lysine 6-monooxygenase (NADPH-requiring)
       0.09   12.0   0.0       0.17   11.1   0.0    1.4  1  FAD_binding_3  FAD binding domain


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 !  164.3   0.0   3.7e-51   5.5e-48       1     351 [.       4     382 ..       4     383 .. 0.79

  Alignments for each domain:
  == domain 1  score: 164.3 bits;  conditional E-value: 3.7e-51
                                   EEEEECTSHHHHHHHHHHHHTT....EEEEESSSSTTSSGGGSSEEEEESSSSTHHSTHHHHHHHHHHHHHHHHHHHHHSS CS
                           DAO   1 dvviiGGGiiGlstAyeLarrg....VtllekgdiagsgaSgrnsgllhsglrylpeaselarlslealeelreleeelgi 77 
                                   dv+iiG+Gi+Gls+A++L++++    +++l+k +  ++g +g++++ ++  +++  +    ++ls  ++++++++++ lgi
  gi|13541481|ref|NP_111169.1|   4 DVAIIGAGIVGLSAAFHLSEENpdlkILVLDKFHTYAQGNTGKSAAGFRDVFSSDIS----YKLSSSSIKFYDHVQNALGI 80 
                                   8******************885589*************************7753333....3******************* PP

                                   TTSEEEEEEEEEESSHHHHHHHHHHHHHH...........HHTTTTEEE.EEHHHHHHHSTTSTTTSEEEEETTEEEEEHH CS
                           DAO  78 didyrrtGllslaadeeelealdkllall...........leagldael.ldaeevrelepalpgllgalfypdtgqvdpa 146
                                   d++ +  G+l+l +de++   l +++++            +  +   ++ +d+e ++++   +++++ a+  +++g+++p 
  gi|13541481|ref|NP_111169.1|  81 DLGMHYVGYLFLLDDEKNAGVL-EKIGKKtsisevdldslN--DMGISIkVDEE-TKKVMG-ISDIKSAYIGKNCGIMEPD 156
                                   ************9887655556.555555588776666433..33444336665.888886.569**************** PP

                                   HHHHHHHHHHHHTT-EEEESECEEEEEEEE.............TCEEEEE....EECT.EEEEEEEEEEE--GGGHH.HHH CS
                           DAO 147 kltaalaraaealGveilegtevtgleeed.............gkvwgve....rttp.gendaadavVnaaGawsd.llg 208
                                   k +a++++++ ++Gve+++ t+v++l+ e                    +    +tt+ g + +ad+ V+a+ +w++ l++
  gi|13541481|ref|NP_111169.1| 157 KIAAFYYKECLKRGVEFHFDTNVQKLNLEPkeplnfpgepfiwQ----DKyiksVTTDkGDI-EADTFVLATDVWTNfLTD 232
                                   *************************9552234666666644431....33555768888986.5699**********5554 PP

                                   TTCTT..TSEEEEEEEEEEEEEECCTHSTGSG.CSEEEEE.EEETTTTEEEEEETTSEEEEEESSE....EETTCSSTSCS CS
                           DAO 209 llkel..dlpispvrgqvlvlkplseklvspa.ailpvpe.tdddgrgvyvtprkdgrvlvGgtad....eesgdddpevd 281
                                   +   +  d  i+p + q + +k+   + v ++  i ++ +  +   +gvy++p ++ ++   g ad    ++s  +dpe++
  gi|13541481|ref|NP_111169.1| 233 R---IgvDSHIRPKKRQLFKIKNEFIASVVSKsFIGTESFpFTVFPKGVYIRPAPSEKTFWAGVADdigrDFSFSEDPEAE 310
                                   4...3447799**********77766555554355555559888899******9888877766665588533333335777 PP

                                   HHHHHH.HHHHHHHHSGGG..CGEEEEEEEEEE..ETTSSEEEEEEETEEEEEEEEECTTTHHHHHHHHHHHHHH CS
                           DAO 282 eedide.llealrklfPql..gdvlrkwaGlrp..lpdglpligetpgvkglylatGhsghGltlapatGkllae 351
                                   e+ + + +++ l++++ ql  ++++  waG++   + dg+p+i ++    ++++atG sg+G++ + a+G++++ 
  gi|13541481|ref|NP_111169.1| 311 EQFYTYnVYQVLQAYMKQLssSSISGMWAGYYSynTIDGNPYIFRS---LNMIIATGTSGSGIMKGDAIGRVVSS 382
                                   7777779***********75566999*******7447******994...6*********************9976 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 !   15.8   0.0   4.2e-06    0.0062       1      79 [.       3      81 ..       3      99 .. 0.66
   2 ?   -2.5   0.0       1.5   2.3e+03     184     213 ..     110     139 ..     100     150 .. 0.76
   3 !   13.6   0.0   1.9e-05     0.029     182     235 ..     155     223 ..     145     238 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 4.2e-06
                                  CSEEEE--SHHHHHHHHHHHH..HTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHHHHHHCHHHH.CCCCHCCT.CEEEE CS
                                  xxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxx.xxxxx RF
                   Pyr_redox_2  1 kdvvviGgGpAGlaaaltlaq..agakvtlvelegtclnggcllskallgvaedaeiasevvkklnqg.ielllgee.vvkid 79
                                  +dv++iG+G+ Gl+aa +l++    +k++++  ++ + + +    k ++g+++  +       kl+++ i+++  ++ +++id
  gi|13541481|ref|NP_111169.1|  3 YDVAIIGAGIVGLSAAFHLSEenPDLKILVL--DKFHTYAQGNTGKSAAGFRDVFSSDI--SYKLSSSsIKFYDHVQnALGID 81
                                  69*******************5336777666..66666666666666666666655333..2233333355555544455555 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.5
                                   HHHHHHHHHHHHTTEEEEESCEEEEEEETT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2 184 elsaaleealekeGvevklgtsvkeidgng 213
                                   ++s+   + l+++G+ +k+ ++ k++ g +
  gi|13541481|ref|NP_111169.1| 110 SISEVDLDSLNDMGISIKVDEETKKVMGIS 139
                                   566666788999999999999999887655 PP

  == domain 3  score: 13.6 bits;  conditional E-value: 1.9e-05
                                   -HHHHHHHHHHHHHTTEEEEESCEEEEEEETTE...............EEEEEETTSCEEEESEEEE-S CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...............xxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2 182 dkelsaaleealekeGvevklgtsvkeidgnge...............klevvledgeeidadlvvvav 235
                                   +++++a++ ++  k+Gve+++ t+v++++ +++                ++ v++d+  i+ad+ v+a+
  gi|13541481|ref|NP_111169.1| 155 PDKIAAFYYKECLKRGVEFHFDTNVQKLNLEPKeplnfpgepfiwqdkYIKSVTTDKGDIEADTFVLAT 223
                                   68999************************999999*********98755559999999********997 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.0   3.1e-09   4.6e-06      17      53 ..       2      39 ..       1      69 [. 0.85

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 3.1e-09
                                  EEEEEEE--SHHHHHHHHHHHHC.TTS-EEEEESSSS- CS
                          Thi4 17 esDvvivGaGssGLtaayylakk.pdlkvailersvsp 53
                                    Dv+i+GaG  GL+aa+ l+++ pdlk+++l++  ++
  gi|13541481|ref|NP_111169.1|  2 RYDVAIIGAGIVGLSAAFHLSEEnPDLKILVLDKFHTY 39
                                  57*******************999********985544 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 !   21.9   0.0     1e-07   0.00016       1      27 [.       7      35 ..       7      49 .. 0.91
   2 ?   -3.0   0.0       6.2   9.2e+03      42      51 ..      76      86 ..      63      87 .. 0.67

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1e-07
                                  EE--SHHHHHHHHHHHCC..TEEEEEE-S CS
                 NAD_binding_8  1 IvGaGlsGlvaAylLaka..gfdvlllek 27
                                  I+GaG+ Gl+aA +L+++  ++++l+l+k
  gi|13541481|ref|NP_111169.1|  7 IIGAGIVGLSAAFHLSEEnpDLKILVLDK 35
                                  9****************87899******9 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 6.2
                                  T.CEECTS--- CS
                 NAD_binding_8 42 g.vrvdygahi 51
                                  +   +d+g+h+
  gi|13541481|ref|NP_111169.1| 76 NaLGIDLGMHY 86
                                  24778999998 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   5.4e-06    0.0081       1      44 [.       4      50 ..       4      78 .. 0.78
   2 ?    3.3   0.0     0.024        36     141     171 ..     156     186 ..     141     230 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 5.4e-06
                                  SEEEE--SHHHHHHHHHHHH..TTT-EEEEESSS.GGGSGGGG--S- CS
                 FAD_binding_2  1 DviViGsGlAGLaAAleaae..aGlkvavvekeq.efggatawsqGg 44
                                  Dv +iG+G+ GL+AA  ++e    lk++v++k + + +g+t  s +g
  gi|13541481|ref|NP_111169.1|  4 DVAIIGAGIVGLSAAFHLSEenPDLKILVLDKFHtYAQGNTGKSAAG 50
                                  9******************9533459***999651455666666544 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.024
                                   HHHHHHHHHHHHTCTEEEEESEEEEEEEECT CS
                 FAD_binding_2 141 hallarlvesarkagvdfqerteadeLived 171
                                    +++a  +++++k+gv+f++ t++++L+ e 
  gi|13541481|ref|NP_111169.1| 156 DKIAAFYYKECLKRGVEFHFDTNVQKLNLEP 186
                                   57899999*******************9986 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 !   16.7   0.0   3.6e-06    0.0054       1      38 [.       6      41 ..       6      61 .. 0.87
   2 ?   -1.9   0.0       1.9   2.8e+03     135     153 ..     205     223 ..     199     223 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 3.6e-06
                 NAD_binding_9  1 aivGaGprGlavlerLlarakkkspleitlfdp.sepga 38
                                  ai+GaG+ Gl+++ +L ++     +l+i + d+ +++ +
  gi|13541481|ref|NP_111169.1|  6 AIIGAGIVGLSAAFHLSEE---NPDLKILVLDKfHTYAQ 41
                                  8******************...59*********444443 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.9
                 NAD_binding_9 135 avlladgaslaadaVvLAl 153
                                   + +++d+  ++ad  vLA+
  gi|13541481|ref|NP_111169.1| 205 KSVTTDKGDIEADTFVLAT 223
                                   66799999*********97 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0     0.011        17       2      20 ..       5      23 ..       4      35 .. 0.83
   2 ?   -1.0   0.0       1.8   2.7e+03      15      29 ..      99     113 ..      98     134 .. 0.64
   3 ?    0.6   0.0      0.59   8.9e+02      44      71 ..     113     140 ..     108     144 .. 0.81
   4 !    6.9   0.0    0.0063       9.5      38      71 ..     154     187 ..     148     191 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.011
                                  EEEECSSHHHHHHHHHHHH CS
                     Pyr_redox  2 vvvvGgGyiglElAgalae 20
                                  v+++G+G +gl +A  l+e
  gi|13541481|ref|NP_111169.1|  5 VAIIGAGIVGLSAAFHLSE 23
                                  89**********9988776 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.8
                                   HHHHHHTTSEEEEEE CS
                     Pyr_redox  15 AgalaelgkkVtvve 29 
                                   Ag+l ++gkk+++ e
  gi|13541481|ref|NP_111169.1|  99 AGVLEKIGKKTSISE 113
                                   667777777766644 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.59
                                   HHHHHHHHHTTEEEECSEEEEEEEEETT CS
                     Pyr_redox  44 kilqeklekngievllntkveeiegsed 71 
                                   ++  ++l ++gi +  +++++++ g +d
  gi|13541481|ref|NP_111169.1| 113 EVDLDSLNDMGISIKVDEETKKVMGISD 140
                                   55578999***********999987766 PP

  == domain 4  score: 6.9 bits;  conditional E-value: 0.0063
                                   SSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETT CS
                     Pyr_redox  38 lDeeaskilqeklekngievllntkveeiegsed 71 
                                   +++++++   ++  k+g+e++++t+v++++ +++
  gi|13541481|ref|NP_111169.1| 154 EPDKIAAFYYKECLKRGVEFHFDTNVQKLNLEPK 187
                                   56778888889999**************987766 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   7.7e-06     0.011       1      32 [.       4      35 ..       4      79 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 7.7e-06
                 Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvliea 32
                                  Dv++iGaG  gls A +l e++p+lk+++++ 
  gi|13541481|ref|NP_111169.1|  4 DVAIIGAGIVGLSAAFHLSEENPDLKILVLDK 35
                                  9***************************9985 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.0   0.00019      0.28       1      33 [.       3      37 ..       3      41 .. 0.85
   2 ?    2.6   0.0     0.029        44     109     162 ..     156     223 ..     150     225 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00019
                                  -SEEEE--SHHHHHHHHHH..HHTT--EEEE-SSS CS
                   HI0933_like  1 kdviviGgGaAGlmaAisa..akrgkrVlllekak 33
                                  +dv++iG+G  Gl aA ++  ++ + ++l+l+k +
  gi|13541481|ref|NP_111169.1|  3 YDVAIIGAGIVGLSAAFHLseENPDLKILVLDKFH 37
                                  59****************95556789999999865 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.029
                                   HHHHHHHHHHHHHHT-EEE-S--EEEE...............ECETTE.EEEEE.TTEEEEESEEEE-- CS
                   HI0933_like 109 edivdallkelkeagvklrletevksv...............ekeedgkfrvktkseeeleadklvlAt 162
                                    +i  ++ ke+ ++gv+++ +t+v+++                 +++ + +v+t +++ +ead+ vlAt
  gi|13541481|ref|NP_111169.1| 156 DKIAAFYYKECLKRGVEFHFDTNVQKLnlepkeplnfpgepfIWQDKYIKSVTT-DKGDIEADTFVLAT 223
                                   57888999******************9777777777777766555555556666.77777777777775 PP

>> Mqo  Malate:quinone oxidoreductase (Mqo)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   1.4e-05     0.021       2      44 ..       2      44 ..       1      53 [. 0.91

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.4e-05
                           Mqo  2 kvdvvliGaGimsatlgvllkelepelsievlerldkvaeess 44
                                  ++dv +iGaGi+  + +  l+e +p+l+i vl++ ++ a+ ++
  gi|13541481|ref|NP_111169.1|  2 RYDVAIIGAGIVGLSAAFHLSEENPDLKILVLDKFHTYAQGNT 44
                                  58**********************************9999765 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 ?   12.3   0.0   4.4e-05     0.066       3      37 ..       3      37 ..       1      40 [. 0.92

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.4e-05
                   K_oxygenase  3 lDligiGiGpsnLsLailleevkkelkalflerqp 37
                                  +D+++iG+G   Ls a +l+e + +lk+l+l++ +
  gi|13541481|ref|NP_111169.1|  3 YDVAIIGAGIVGLSAAFHLSEENPDLKILVLDKFH 37
                                  9*******************************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 ?   11.1   0.0   0.00011      0.17       2      23 ..       3      24 ..       2      47 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00011
                                  EEEEEE--SHHHHHHHHHHHHT CS
                 FAD_binding_3  2 tdVlIVGaGpaGlmlallLsea 23
                                  +dV+I+GaG +Gl++a  Lse 
  gi|13541481|ref|NP_111169.1|  3 YDVAIIGAGIVGLSAAFHLSEE 24
                                  79*****************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (417 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       526  (0.0293379); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); 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: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.43
# Mc/sec: 2906.07
//
Query:       gi|13541482|ref|NP_111170.1|  [L=261]
Description: hypothetical protein TVN0651 [Thermoplasma volcanium GSS1]
Scores for 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   82.6   8.5      3e-23   82.6   8.5    2.6  3  SNARE_assoc      SNARE associated Golgi protein


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 !    3.0   0.2    0.0075   1.3e+02      57     110 ..      12      59 ..       2      66 .. 0.67
   2 !   82.6   8.5   1.7e-27     3e-23       1     119 [.      86     212 ..      86     213 .. 0.96
   3 ?   -3.7   0.1      0.92   1.6e+04      32      42 ..     241     251 ..     236     256 .. 0.50

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.0075
                   SNARE_assoc  57 kalerlverygflallllrllpivPrdlvnyvaGltrvsfkrFflatfiGsipw 110
                                   + ++r+++ yg++++ +l  ++ +       ++ +++++f ++f++  i+si  
  gi|13541482|ref|NP_111170.1|  12 NNYDRYFNIYGVVIAAVLAAIAAI------EIFEIFELPFEKYFAGIDIASIFS 59 
                                   456677766666666666666554......456678889999998888887765 PP

  == domain 2  score: 82.6 bits;  conditional E-value: 1.7e-27
                   SNARE_assoc   1 lPsevllvaaGvlf.....glllgtlvtslgallGaslayllgrylgr....kalrrkllsekrvkalerlverygflall 72 
                                   +Psev+l + G+l+     ++ +++  t++++++G+++ y+lg ylgr    k+l    +se+ + ++e ++++ g++ ++
  gi|13541482|ref|NP_111170.1|  86 IPSEVILPLSGFLVyqgsfNFAVVLADTIIASMVGSFIDYFLGLYLGRpiivKILSYFSISEDSLSRAETWIDKMGSFSVF 166
                                   799****99999999998899999999********************99999999999999999999************** PP

                   SNARE_assoc  73 llrllpivPrdlvnyvaGltrvsfkrFflatfiGsipwalvyaylGs 119
                                   l+r++p++ r+l++++aG+++++ + F+l+tf+Gs++w++ ++ylG+
  gi|13541482|ref|NP_111170.1| 167 LARFIPGI-RSLISLPAGMLKMKMWLFALMTFLGSFIWSFSLIYLGY 212
                                   ********.*************************************8 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 0.92
                   SNARE_assoc  32 slayllgrylg 42 
                                   slay++ ++++
  gi|13541482|ref|NP_111170.1| 241 SLAYIFYYIFL 251
                                   34444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       834  (0.0465168); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.34s 00:00:00.90 Elapsed: 00:00:00.52
# Mc/sec: 1505.55
//
Query:       gi|13541483|ref|NP_111171.1|  [L=98]
Description: hypothetical protein TVN0652 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.4e-11   43.1   0.0    3.9e-11   42.9   0.0    1.1  1  ABM       Antibiotic biosynthesis monooxygenase
    0.00063   18.7   0.8        0.1   11.4   0.1    2.0  2  SOR       Sulphur oxygenase reductase
  ------ inclusion threshold ------
      0.052   14.2   0.2      0.064   13.9   0.2    1.0  1  Dabb      Stress responsive A/B Barrel Domain
      0.073   13.1   0.1       0.08   13.0   0.1    1.2  1  rhaM      L-rhamnose mutarotase
      0.082   13.6   0.0       0.14   12.9   0.0    1.4  1  DUF4936   Domain of unknown function (DUF4936)
       0.31    9.4   0.0       0.31    9.4   0.0    1.0  1  MFS_3     Transmembrane secretion effector


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 !   42.9   0.0   1.3e-14   3.9e-11       1      75 [.       1      75 [.       1      78 [. 0.95

  Alignments for each domain:
  == domain 1  score: 42.9 bits;  conditional E-value: 1.3e-14
                                  CEEEEEEEEESTTGHHHHHHHHHHHHHHHHHTSTTEEEEEEEEEETSTTEEEEEEEESSHHHHHHHHTSHHHHHH CS
                           ABM  1 mviviaeirvkpgqaeafldafaeavesllaeepGclgyellrstedpdevvvieeWeseaaleahlksphfkaa 75
                                  m+ v  +++vk+g++e+f++ f ++ + l  +  G  ++ l+++ +d+ ++++++eWes ++++++ +s  fk++
  gi|13541483|ref|NP_111171.1|  1 MINVGLYYKVKKGHEEEFERTFNQVMQMLKTSSSGIKDVKLYQDVNDKQQYMIFTEWESLESFKNFIASRPFKET 75
                                  8889999********************99999**************************************99985 PP

>> SOR  Sulphur oxygenase reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.1   3.5e-05       0.1     164     191 ..       8      36 ..       2      45 .. 0.87
   2 !    6.3   0.0    0.0013       3.9     239     260 ..      44      65 ..      38      76 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.5e-05
                           SOR 164 htvkeGkekeFeegavetlellke.apGl 191
                                   ++vk+G+e+eFe +  +++++lk  ++G+
  gi|13541483|ref|NP_111171.1|   8 YKVKKGHEEEFERTFNQVMQMLKTsSSGI 36 
                                   58*********************966665 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0013
                           SOR 239 aaetPkeylvhveWesleaaqf 260
                                     +  ++y++ +eWesle+ + 
  gi|13541483|ref|NP_111171.1|  44 DVNDKQQYMIFTEWESLESFKN 65 
                                   567789**********998775 PP

>> Dabb  Stress responsive A/B Barrel Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.2   2.2e-05     0.064       8      89 ..       9      85 ..       6      91 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.2e-05
                                  EESSTTTHHHHHHHHHHHHHHHHGSTTTSEEEEEEESSSSSTSTT-SEEEEEEESSHHHHHHHHTSHHHHHHHHHHHHTEEE CS
                          Dabb  8 klkdevteeekaevlealeaLkdkipgiksievgrnvspeklakgydvvliseFeseedlkaYlehpahvefvelvkplvek 89
                                  k+k++ +ee ++++ + ++ Lk+  +gik+++  ++v++++     ++++++e es+e  k + +   ++e+++  k+++e+
  gi|13541483|ref|NP_111171.1|  9 KVKKGHEEEFERTFNQVMQMLKTSSSGIKDVKLYQDVNDKQ-----QYMIFTEWESLESFKNFIASRPFKETTDYGKSILED 85
                                  789999999999999999999*******************9.....9******************99999999999999986 PP

>> rhaM  L-rhamnose mutarotase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   2.7e-05      0.08       3      70 ..       5      70 ..       3      94 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.7e-05
                          rhaM  3 aqvlklkpeaieeYkklHaevwpevlealkeagirnysIyldeegntLfailevgddeeadaaaaaad 70
                                  ++  k+k++++ee+++  ++v + +++  +++gi++ ++y d ++++  +i++  ++ e++++ +a+ 
  gi|13541483|ref|NP_111171.1|  5 GLYYKVKKGHEEEFERTFNQVMQMLKT--SSSGIKDVKLYQDVNDKQQYMIFTEWESLESFKNFIASR 70
                                  67789999*******999999988765..589********9988887777765424777777766644 PP

>> DUF4936  Domain of unknown function (DUF4936)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   4.7e-05      0.14       2      45 ..       6      50 ..       6      75 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.7e-05
                       DUF4936  2 vYYrvaeadaaaalaavralqaal.aartgva.grLlrrlddpesq 45
                                  +YY+v++++++++  + ++++++l +   g++ ++L + ++d  +q
  gi|13541483|ref|NP_111171.1|  6 LYYKVKKGHEEEFERTFNQVMQMLkTSSSGIKdVKLYQDVNDK-QQ 50
                                  5***********************7778888624455554444.33 PP

>> MFS_3  Transmembrane secretion effector
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0    0.0001      0.31     424     484 ..       1      66 [.       1      84 [. 0.79

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0001
                         MFS_3 424 pvlvkieYkieeedieaFlkalaelrrv..rrrdGArkWtlvrdlenpevw...vEtflvetWley 484
                                   ++ v + Yk+++ ++e+F ++ +++ ++   +  G ++  l +d+++++++   +E+   e++ ++
  gi|13541483|ref|NP_111171.1|   1 MINVGLYYKVKKGHEEEFERTFNQVMQMlkTSSSGIKDVKLYQDVNDKQQYmifTEWESLESFKNF 66 
                                   6889999****************999983345789********99998875111566666665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1053  (0.0587317); expected 358.6 (0.02)
Passed bias filter:                      543  (0.0302861); 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: 0.52u 0.33s 00:00:00.85 Elapsed: 00:00:00.52
# Mc/sec: 569.75
//
Query:       gi|13541484|ref|NP_111172.1|  [L=515]
Description: NAD-dependent aldehyde dehydrogenase [Thermoplasma volcanium GSS1]
Scores for complete 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-128  427.1   0.0   8.9e-128  426.7   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 !  426.7   0.0    5e-132  8.9e-128       6     458 ..      51     507 ..      48     510 .. 0.94

  Alignments for each domain:
  == domain 1  score: 426.7 bits;  conditional E-value: 5e-132
                                   SSEEEEEETTTCEEEEEEE-B-HHHHHHHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHTHHHHHHHHHHHH---HHHH CS
                        Aldedh   6 setievinPatgeviakvpaataedvdaavaaAkeafkawaklpaeeRaeiLrkaadlleerkeelaeletletGkplaea 86 
                                   s++i+ i+P++g++ia+++ a+ + vd+av+   + +kaw +l  ++Ra i+ kaad+l e+k ++a+++t e+Gk+  ea
  gi|13541484|ref|NP_111172.1|  51 SKKIKDISPIDGKEIATFQLASDSSVDKAVDMLYKSYKAWYSLGYMKRALIFLKAADMLSEQKFKFAAILTYENGKNRYEA 131
                                   467****************************************************************************** PP

                                   HHHHHHHHHHHHHHHHHHHHHSE.EEEEEC..TTEEEEEEEEE-SEEEEEE-SSSCCHHHHHHHHHHHHTT-EEEEEE-TT CS
                        Aldedh  87 raeveeaidvlryyaelaekleg.evlpss..egklalvrrePlGvvgaItPWNfPlllaawklapalaaGNtvvlKPaee 164
                                    ++v+eaid++ryya  + + +g   ++ +  +++++++  +P+Gv g+I+P+Nf +++ +++  + l++GN+v+lKP+++
  gi|13541484|ref|NP_111172.1| 132 IGDVDEAIDFMRYYAMNLIENQGfIRFTGKayRNEESISIMKPYGVFGVISPFNF-FSIGVGMSSAPLVTGNAVILKPSSD 211
                                   ********************9994333333579**********************.78888888999************** PP

                                   SHHHHHHHHHHHHHTTS-TTSEEE--SSTCCHHHHHHH-TTESEEEEES-HHHHHHHHHH.HHCTTSEEEEEE---EEEEE CS
                        Aldedh 165 tplsalllaelfeeaglPkgvlnvvtgsgsevgealvehpevdkvsftGstevgrkiaka.aaknlkrvtlElGGknpliv 244
                                    pls +l ++l++eag+Pk+vl +v+gsg  vg+++ve+++v+ + ftGs++vg +i+++  ++  k v+ E+GGk+++iv
  gi|13541484|ref|NP_111172.1| 212 IPLSLYLWVRLMHEAGVPKNVLAFVSGSGGLVGRHIVENKKVAGIVFTGSRDVGLDIQRKsIDNGPKVVITEMGGKDAIIV 292
                                   ************************************************************55555688999********** PP

                                   -TTSHHHHHHHHHHHHHHGGGGTSTTSEEEEEEEHHHHHHHHHHHHHHHHT--BS-TTSTT-SB---SSHHHHHHHHHHHH CS
                        Aldedh 245 ledaDldkaveaivkgafgnaGQvCiaasrllvqesiydefveklveaakklkvgdpldedtdvGPliseaqlekvekyve 325
                                    ++aD+dkave++v++afg+aGQ+C+a+s l+v+++iydef+++l+++++++k  dp+++dt + P+i++++++k+ k+  
  gi|13541484|ref|NP_111172.1| 293 SNKADMDKAVEGVVRAAFGFAGQKCSACSLLYVHKDIYDEFMKRLKARTEAIKPDDPRKKDTFLNPIINKEAYDKFIKLKP 373
                                   ******************************************************************************955 PP

                                   HHHHTTSEEEE-TTE.SB-SSSTTEE--EEEES-TTTSHHHHS---SSEEEEEEESSHHHHHHHHHSSSEESEEEEE-SBH CS
                        Aldedh 326 eakeegaklllGgereeaglekgyfvePtvlanvtpdmriaqeEiFGPVlsvikfkdeeeaieiaNdteyGLaagvftkdl 406
                                   e  +   k+l+Gg   ++ ++ g++vePt+++++++d+ ia++EiF PVlsv+k++++eea++  N+ +yGL++g+ft+d+
  gi|13541484|ref|NP_111172.1| 374 EFNK--GKILTGG---HELNKPGFYVEPTIVTDLPKDAYIARNEIFLPVLSVFKCNSIEEAVDDINSMDYGLTGGIFTEDP 449
                                   5544..5******...78899************************************************************ PP

                                   HHHHHHHHHS-SSEEEESSS...ST--TTT.SEB--CGGGEES.-BSH.HHHHHHTEE CS
                        Aldedh 407 eraervaerleaGnvyiNds...ttgaaea.lpfgGvkqSglG.regg.kegleeyte 458
                                   ++++++ +++e+G +y N++   +tg++   +pf G+k Sg+  + +g  ++l+++++
  gi|13541484|ref|NP_111172.1| 450 KEIQYYFDNIEVGVIYANRKsggSTGSMVGsQPFVGWKLSGVSgKGTGsFYYLQQFLR 507
                                   *******************977788889999**********98544444888998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (515 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       621  (0.0346366); expected 358.6 (0.02)
Passed bias filter:                      520  (0.0290033); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.68u 0.35s 00:00:01.03 Elapsed: 00:00:00.55
# Mc/sec: 2815.53
//
Query:       gi|13541485|ref|NP_111173.1|  [L=514]
Description: O-antigen and teichoic acid export protein [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.4e-13   49.6  22.9    3.4e-13   49.6  22.9    3.1  2  Polysacc_synt    Polysaccharide biosynthesis protein
     0.0046   17.0  22.4     0.0046   17.0  22.4    4.7  4  Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domai
  ------ inclusion threshold ------
       0.94    9.6  10.9      0.026   14.6   1.9    2.9  3  GWT1             GWT1
        5.9    6.6  14.2       0.41   10.4   1.2    3.2  3  SPC25            Microsomal signal peptidase 25 kDa subunit (


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 !   49.6  22.9   7.6e-17   3.4e-13       2     246 ..       3     259 ..       2     285 .. 0.77
   2 ?  -15.3  20.3         4   1.8e+04     175     194 ..     401     420 ..     300     500 .. 0.47

  Alignments for each domain:
  == domain 1  score: 49.6 bits;  conditional E-value: 7.6e-17
                 Polysacc_synt   2 lkgvivlllsqlitkllafvtlvylarilgpegfGlvalalaivtllviltdlGlnaalvreiakyrekkelvslillnvl 82 
                                   +k++ +l++ ++i+++++++ l+ ++r++g +  G va+ + +++++++ t+lG++ a ++ i++ ++  e+ ++++ +v 
  gi|13541485|ref|NP_111173.1|   3 TKKSPILVTQNIINAIAGYIGLFFITRYVGITIWGFVAFGMGFTGIFSLATELGFSSAYTKSISEGKDV-EEATNTFFAVK 82 
                                   57778999***********************************************************95.66666666666 PP

                 Polysacc_synt  83 lvllvlvllfllllliaa.......flglpelavlylilalmll..llvgvasfrrglfqglermkyaavsqvveq.lsrv 153
                                   lvl v +++ +l+ l++        f +  e+ v++ ++ +++   ll +  s++++ f   +   +  v+ ++++ l+++
  gi|13541485|ref|NP_111173.1|  83 LVLAVIFVILALSALFFWtdvlhrgFQNPVEFWVIIALIPYYFFgtLLSIPKSYYSSTFSSYRQVLPSIVEAISRNgLFVA 163
                                   666666665555555555577777777777787777777777666888888899999999999999999998887725555 PP

                 Polysacc_synt 154 ilvliavflfldivaavlgavlaalvggivslavlrkkf.rprfvils..lklvrellsfsapltisslaillytyidsil 231
                                   i v+   +lf  +  a l++v++++ ++ +  ++++  + +++ +  +  +++ + +   ++pl +ss +++++ +id i+
  gi|13541485|ref|NP_111173.1| 164 IGVIYEYRLFR-FPDADLAIVIGSVYSITYTVYYIYMMYlGRPWHLGRpnKEMLKYFAIIALPLAASSGISTINGNIDKII 243
                                   55555555555.999*********************999644444433337777777789********************* PP

                 Polysacc_synt 232 lglllgaea.vGiYna 246
                                    +++  a+a  + Y+ 
  gi|13541485|ref|NP_111173.1| 244 VQFYWHADAtSALYTS 259
                                   ****999996677764 PP

  == domain 2  score: -15.3 bits;  conditional E-value: 4
                 Polysacc_synt 175 laalvggivslavlrkkfrp 194
                                   +a+l+ +i+ ++v++ ++ +
  gi|13541485|ref|NP_111173.1| 401 FASLIVAIGDYIVYKYIYSK 420
                                   22222222223333322222 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 ?   -1.7   5.5      0.61   2.7e+03      68     139 ..      18      94 ..       8     100 .. 0.49
   2 ?   -5.2   7.8         4   1.8e+04      60      86 ..     180     210 ..     114     278 .. 0.64
   3 ?    0.4   3.8      0.14   6.4e+02      61     137 ..     270     345 ..     255     348 .. 0.55
   4 !   17.0  22.4     1e-06    0.0046       2     142 ..     334     477 ..     333     478 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.61
               Polysacc_synt_C  68 vvavlnlyalrrllgiklellrrllkpllaalvmgivvylllllllglllla..............alalllav.lvgalv 133
                                   ++ ++ l+++ r++gi +      +   ++a++mg    ++++l  +l +++              a ++++av lv a++
  gi|13541485|ref|NP_111173.1|  18 IAGYIGLFFITRYVGITI------WG--FVAFGMGFT--GIFSLATELGFSSaytksisegkdveeATNTFFAVkLVLAVI 88 
                                   444555666666666666......21..122222222..222222222222233445555677776557777773355555 PP

               Polysacc_synt_C 134 Ylllll 139
                                   +++l+l
  gi|13541485|ref|NP_111173.1|  89 FVILAL 94 
                                   555443 PP

  == domain 2  score: -5.2 bits;  conditional E-value: 4
               Polysacc_synt_C  60 iatvlallvvavlnlyalrr.llgikl...e 86 
                                   +a+v++ + ++ + +y+++  +lg ++    
  gi|13541485|ref|NP_111173.1| 180 LAIVIGSVYSITYTVYYIYMmYLGRPWhlgR 210
                                   4555555555555555555423333334442 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.14
               Polysacc_synt_C  61 atvlallvvavlnlyalrrllgikl....ellrrllkpllaalvmgivvylllllllgllllaalalllavlvgalvYlll 137
                                   + +++ ++v vl     ++ + +       ++  ++ p+++al ++ v y+l+ +  g +++     l+ v+v+   Y+++
  gi|13541485|ref|NP_111173.1| 270 SGAISGFFVPVLSRKEKSKDIMYEApdleRFISLFILPFVIALSVFSV-YFLNIFSAGYRPYY----LILVFVALGNYIGI 345
                                   555666666666666666666666663333333444555555555555.44555555555544....55555555555554 PP

  == domain 4  score: 17.0 bits;  conditional E-value: 1e-06
               Polysacc_synt_C   2 LailalsiiflslstvlssiLqglgrqkialkalvigalvklilnlllip.........lfgivGaaiatvl.allvvavl 72 
                                   L+++al+  +  ++ ++ s +++ g+++ ++k++  +++++++ln++++p         ++g++G a+a+++ a   ++v+
  gi|13541485|ref|NP_111173.1| 334 LVFVALGNYIGIITGPYVSQIIASGKTWNIAKITTPSIIANIALNFIFVPpslfgythlSMGYTGTAFASLIvAIGDYIVY 414
                                   67777788888889999999*****************************66744444444556995555555055557777 PP

               Polysacc_synt_C  73 nlyalrrllgiklellrrllkpllaalvmgivvylllllllgllllaalalllavlvgalvYlllllllr 142
                                    +++ ++ ++i + +lr+   p +a ++ g +   ll+++ + ++   ++lll  l+++++++++ ++++
  gi|13541485|ref|NP_111173.1| 415 KYIYSKNVMHIGYRILRQA-IPSFAEILYGYI---LLMYIHPYSF---FVLLLVSLAAVFIFFGISIAIG 477
                                   7999999999999767777.678888888888...6666665555...3555555599999999988876 PP

>> GWT1  GWT1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   1.9   5.9e-06     0.026       9     137 ..      18     162 ..      15     164 .. 0.66
   2 ?   -1.2   0.1      0.43   1.9e+03      61      63 ..     307     309 ..     215     381 .. 0.68
   3 ?   -1.0   0.2      0.37   1.7e+03      96     104 ..     455     463 ..     386     506 .. 0.62

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 5.9e-06
                          GWT1   9 liGylaiyllgvslgkyvlkrekeae......................eeekkkkkkkkesketlkllikllllsilllll 67 
                                   + Gy+ ++++  ++g  +                              + ++ ++ k  e+ + +  ++kl+l++i+++l+
  gi|13541485|ref|NP_111173.1|  18 IAGYIGLFFITRYVGITIWGF----VafgmgftgifslatelgfssayT-KSISEGKDVEEATNTFFAVKLVLAVIFVILA 93 
                                   667777777777777666622....123456666666655555543321.1333334455556666777888888888888 PP

                          GWT1  68 llllelyvefvSRrlaN.lpYvlwvvalnltllllflliellfvekeeekerkekatstvleainrngLlv 137
                                   l +l +++++  R + N +++ ++++ +  +++  +l i +     +++ +++++  + ++eai+rngL+v
  gi|13541485|ref|NP_111173.1|  94 LSALFFWTDVLHRGFQNpVEFWVIIALIPYYFFGTLLSIPK--SYYSSTFSSYRQVLPSIVEAISRNGLFV 162
                                   88899999999999999445666666666666666666666..2457888999999*************97 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.43
                          GWT1  61 sil 63 
                                    ++
  gi|13541485|ref|NP_111173.1| 307 PFV 309
                                   222 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.37
                          GWT1  96 ltllllfll 104
                                   +++lll+ l
  gi|13541485|ref|NP_111173.1| 455 FFVLLLVSL 463
                                   222222222 PP

>> SPC25  Microsomal signal peptidase 25 kDa subunit (SPC25)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   1.2   9.1e-05      0.41      22      79 ..      75     136 ..      62     145 .. 0.82
   2 ?    3.9   0.2    0.0096        43      38      81 ..     161     203 ..     155     213 .. 0.77
   3 ?   -0.5   1.1      0.22   9.7e+02      27      62 ..     389     426 ..     365     458 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 9.1e-05
                         SPC25  22 shtltdvrLalGylavaiaava.flydykv..eFees.kpvlaiavvlYfilsgiltlystf 79 
                                    +t+  v+L+l ++ v++a+ a f+++ ++  +F++    +++ia++ Y+++ ++l + + +
  gi|13541485|ref|NP_111173.1|  75 TNTFFAVKLVLAVIFVILALSAlFFWTDVLhrGFQNPvEFWVIIALIPYYFFGTLLSIPKSY 136
                                   5677889*****99999998651555555589**998469*************999987766 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.0096
                         SPC25  38 aiaavaflydykveFeeskpvlaiavvlYfilsgiltlystfve 81 
                                   ++a+++ +   ++ F++   +++i+  +Y i  +++++y++++ 
  gi|13541485|ref|NP_111173.1| 161 FVAIGVIYEYRLFRFPDADLAIVIG-SVYSITYTVYYIYMMYLG 203
                                   4566665555556999987665555.68***********99975 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.22
                         SPC25  27 dvrLalGylavaiaava.flydykv.eFeeskpvlaia 62 
                                    ++L +Gy+ +a+a ++  + dy v ++  sk+v+ i+
  gi|13541485|ref|NP_111173.1| 389 YTHLSMGYTGTAFASLIvAIGDYIVyKYIYSKNVMHIG 426
                                   57899999999998665145566666777777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (514 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1065  (0.059401); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); 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):               4  [number of targets reported over threshold]
# CPU time: 0.72u 0.30s 00:00:01.02 Elapsed: 00:00:00.52
# Mc/sec: 2955.48
//
Query:       gi|13541486|ref|NP_111174.1|  [L=208]
Description: translation initiation factor IF-2 subunit beta [Thermoplasma volcanium GSS1]
Scores for 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  118.0   1.5    2.2e-34  117.8   0.5    1.5  2  eIF-5_eIF-2B     Domain found in IF2B/IF5
    4.7e-11   42.5   2.5    8.6e-11   41.7   2.5    1.4  1  TRAM             TRAM domain
  ------ inclusion threshold ------
      0.019   15.0   3.8      0.023   14.8   0.7    2.1  2  Elf1             Transcription elongation factor Elf1 like
      0.026   14.5   0.3      0.056   13.4   0.3    1.5  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
      0.042   14.0   0.4       0.09   12.9   0.4    1.5  1  Zn-ribbon_8      Zinc ribbon domain
      0.081   13.3   1.5       0.83   10.1   1.5    2.2  1  Lar_restr_allev  Restriction alleviation protein Lar
       0.19   12.1   3.7        4.6    7.6   1.3    2.5  2  S1               S1 RNA binding domain


Domain annotation for each model (and alignments):
>> eIF-5_eIF-2B  Domain found in IF2B/IF5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.8   0.5   8.7e-38   2.2e-34       5     117 .]      20     130 ..      17     130 .. 0.96
   2 ?   -3.1   0.0       2.7   6.9e+03      26      39 ..     189     202 ..     176     206 .. 0.53

  Alignments for each domain:
  == domain 1  score: 117.8 bits;  conditional E-value: 8.7e-38
                                   CSSSS--SSTT--EEEETT.EEEETTHHHHHHHHTTSHHHHHHHHHHHHTSEEEESETTEEEESSSSSCCHHHHHHHHHHH CS
                  eIF-5_eIF-2B   5 edkkerykmpklqvkvegkkktvivNfeeiakaLnrdpehvlkyllkelgtqgsidengrlilngkfeakkleklldkyie 85 
                                   +++ +r+k+p++++ +egk  t+i+Nf++i + +nrdp++v+k+l++elgt+    +++rli+n+k++ ++l++++++yi+
  gi|13541486|ref|NP_111174.1|  20 TKNIDRLKIPEPEIIREGK-ATIIRNFQDIIDIINRDPDQVIKFLTRELGTNIVQ-NGRRLIINKKVTLEELQEKMNEYIN 98 
                                   56778**************.********************************987.999********************** PP

                                   HHTSTSSSTSTCEEECCSSSCEEEEESSSTCE CS
                  eIF-5_eIF-2B  86 eyVlCkeCkspetelekeerllvlkCkaCgak 117
                                   +yV C+eC+s +te++k++r+++l CkaCga+
  gi|13541486|ref|NP_111174.1|  99 TYVRCYECGSLDTEIQKSGRVSLLVCKACGAQ 130
                                   ******************************85 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2.7
                                   EEETTHHHHHHHHT CS
                  eIF-5_eIF-2B  26 tvivNfeeiakaLn 39 
                                     i+N   ia+ ++
  gi|13541486|ref|NP_111174.1| 189 KKIKNDVAIAEVVS 202
                                   23455555555555 PP

>> TRAM  TRAM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.7   2.5   3.4e-14   8.6e-11       3      62 .]     146     201 ..     145     201 .. 0.97

  Alignments for each domain:
  == domain 1  score: 41.7 bits;  conditional E-value: 3.4e-14
                                   XXXXEEEEEEEEE-.TTSEEEEEET.TEEEEETT--T..TEEEEEEEEEE-SSEEEEEEE CS
                          TRAM   3 yvGstqeVlveglsksegegiGrtdngkvvfvpgdlpgIGdfVeVkItkvkrqyLrGell 62 
                                   ++G++++V++++++ s geg + +  g+++fvpg+++  G++V+VkI+k k+ ++ +e++
  gi|13541486|ref|NP_111174.1| 146 EEGKEYTVEISEVG-SSGEGRASFR-GFTIFVPGTKK--GETVKVKIKKIKNDVAIAEVV 201
                                   58************.**********.***********..******************997 PP

>> Elf1  Transcription elongation factor Elf1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.7   8.8e-06     0.023       8      57 ..      87     133 ..      80     143 .. 0.81
   2 ?    0.5   0.1      0.25   6.4e+02      30      44 ..     181     196 ..     175     202 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 8.8e-06
                          Elf1   8 kkrkkkkkkklptkFdCpfCnheksvevkldkkekiaevsCkvCgesfet 57 
                                   ++ ++k +++++t+ +C  C++    + +++k+ ++  + Ck Cg++  +
  gi|13541486|ref|NP_111174.1|  87 EELQEKMNEYINTYVRCYECGSL---DTEIQKSGRVSLLVCKACGAQHPI 133
                                   4556777888**********987...99*****************98764 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.25
                          Elf1  30 eksvevkldkkek.ia 44 
                                    ++v+vk++k ++ +a
  gi|13541486|ref|NP_111174.1| 181 GETVKVKIKKIKNdVA 196
                                   5799999999877433 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   0.3   2.2e-05     0.056      20      56 ..      91     131 ..      76     132 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.2e-05
                OrfB_Zn_ribbon  20 eevnpay.TSktCseCgsknke...alsgrtfkCpnCgfea 56 
                                   e++n++  T  +C eCgs ++e   +    +++C++Cg+++
  gi|13541486|ref|NP_111174.1|  91 EKMNEYInTYVRCYECGSLDTEiqkSGRVSLLVCKACGAQH 131
                                   67788878999***********9766777789******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 ?   12.9   0.4   3.5e-05      0.09       7      34 ..     102     129 ..      99     132 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.5e-05
                   Zn-ribbon_8   7 rCeeCghefevlqsisdapltaCPeCgs 34 
                                   rC eCg+  +++q++ + +l +C++Cg+
  gi|13541486|ref|NP_111174.1| 102 RCYECGSLDTEIQKSGRVSLLVCKACGA 129
                                   8*****8888***999999********8 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   1.5   0.00033      0.83       6      47 ..     103     145 ..      80     155 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00033
               Lar_restr_allev   6 CPfCggravlersqrvvaeigqcvyCadCga.....stpwfkiaede 47 
                                   C  Cg+ ++ ++  ++v+       C+ Cga       ++fk++e  
  gi|13541486|ref|NP_111174.1| 103 CYECGSLDTEIQKSGRVS----LLVCKACGAqhpihTVKEFKEEEGI 145
                                   666999888888888888....99*******6655544555555555 PP

>> S1  S1 RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.025        63      38      63 ..     134     158 ..     128     167 .. 0.83
   2 ?    7.6   1.3    0.0018       4.6      51      68 ..     179     196 ..     177     200 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.025
                                   SSSCEESCHHHCEETTEEEEEEEEEE CS
                            S1  38 srdarvedpdevlkvGdevkvkvlkv 63 
                                   +   + ++++e + +G+e+ v++ +v
  gi|13541486|ref|NP_111174.1| 134 HTV-KEFKEEEGIEEGKEYTVEISEV 158
                                   444.77899**************998 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0018
                                   ETTEEEEEEEEEEETTTT CS
                            S1  51 kvGdevkvkvlkvdkdrr 68 
                                   k+G++vkvk+ k+++d +
  gi|13541486|ref|NP_111174.1| 179 KKGETVKVKIKKIKNDVA 196
                                   89**********999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1311  (0.0731218); expected 358.6 (0.02)
Passed bias filter:                      843  (0.0470188); expected 358.6 (0.02)
Passed Vit filter:                       107  (0.00596798); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-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 0.27s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 1293.15
//
Query:       gi|13541487|ref|NP_111175.1|  [L=138]
Description: hypothetical protein TVN0656 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0057   16.8   0.1        1.8    8.8   0.0    2.2  2  RHH_8          Ribbon-Helix-Helix transcriptional regulator f
     0.0097   15.8   2.9        0.2   11.7   0.1    3.2  4  RHH_1          Ribbon-helix-helix protein, copG family
  ------ inclusion threshold ------
       0.15   12.1   0.4        3.8    7.6   0.0    2.1  2  TPK_catalytic  Thiamin pyrophosphokinase, catalytic domain


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 !    8.8   0.0    0.0003       1.8       5      48 ..       7      51 ..       3      70 .. 0.75
   2 !    6.2   0.0    0.0018        11      21      45 ..      77     101 ..      70     129 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0003
                         RHH_8  5 kvtinlgvvDLgqiD.lLveeGfYsnRtDlirtairaqLakhdda 48
                                  k+t+ ++  ++ +iD +L  +  +++R+++ir+a+ + +++++ +
  gi|13541487|ref|NP_111175.1|  7 KLTLRISEEEINEIDeFLNLNPEFGSRSEFIRHAVMQYISSKRIS 51
                                  888889999999998445557789***********9988776543 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0018
                         RHH_8  21 LveeGfYsnRtDlirtairaqLakh 45 
                                    +e+Gf+ +  Dli + +r+ L+  
  gi|13541487|ref|NP_111175.1|  77 AIENGFFKDENDLISAVLRESLEPF 101
                                   5789999999999999999998765 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 ?    2.5   0.1     0.026   1.6e+02       2      16 ..       8      22 ..       7      23 .. 0.93
   2 !   11.7   0.1   3.3e-05       0.2      24      37 ..      32      45 ..      31      46 .. 0.95
   3 ?   -3.1   0.0       1.5   8.8e+03      26      33 ..      91      98 ..      90     100 .. 0.74
   4 ?   -0.5   0.0      0.23   1.4e+03      23      34 ..     111     122 ..     106     124 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.026
                                  EEEEEEHHHHHHHHH CS
                         RHH_1  2 vsirldeellerLde 16
                                  +++r++ee++ ++de
  gi|13541487|ref|NP_111175.1|  8 LTLRISEEEINEIDE 22
                                  799**********98 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 3.3e-05
                                  SHHHHHHHHHHHHH CS
                         RHH_1 24 SrSelIReAlreyl 37
                                  SrSe+IR A+++y+
  gi|13541487|ref|NP_111175.1| 32 SRSEFIRHAVMQYI 45
                                  9***********97 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 1.5
                                  HHHHHHHH CS
                         RHH_1 26 SelIReAl 33
                                  S+++Re l
  gi|13541487|ref|NP_111175.1| 91 SAVLRESL 98
                                  78888876 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 0.23
                                   SSHHHHHHHHHH CS
                         RHH_1  23 rSrSelIReAlr 34 
                                   +++S+l+++++ 
  gi|13541487|ref|NP_111175.1| 111 KNMSDLMKALAS 122
                                   789999998875 PP

>> TPK_catalytic  Thiamin pyrophosphokinase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.1     0.018   1.1e+02      43      66 ..      37      60 ..      34      65 .. 0.87
   2 ?    7.6   0.0   0.00064       3.8      48      81 ..      95     128 ..      75     135 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.018
                 TPK_catalytic 43 irpevkefyeskgteivkkpdqds 66
                                  ir +v+++++sk + +vk++ q +
  gi|13541487|ref|NP_111175.1| 37 IRHAVMQYISSKRISVVKDDLQKT 60
                                  7899**************997765 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.00064
                 TPK_catalytic  48 kefyeskgteivkkpdqdstDlekaialvlekek 81 
                                   +e +e    ++vkk++++ +Dl+ka+a  ++ ++
  gi|13541487|ref|NP_111175.1|  95 RESLEPFVLKFVKKKSKNMSDLMKALASFENFKQ 128
                                   555566678999**************98887775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       707  (0.0394333); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 943.52
//
Query:       gi|13541488|ref|NP_111176.1|  [L=244]
Description: cell division GTPase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-05   25.7   0.1     0.0001   22.6   0.1    2.1  2  Tubulin   Tubulin/FtsZ family, GTPase domain
  ------ inclusion threshold ------
       0.13   12.2   0.0       0.26   11.2   0.0    1.5  1  FAD_syn   FAD synthetase
       0.22   11.4   0.0       0.32   10.9   0.0    1.2  1  DUF418    Protein of unknown function (DUF418)


Domain annotation for each model (and alignments):
>> Tubulin  Tubulin/FtsZ family, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0     0.088   5.2e+02       1      20 [.      31      50 ..      31      86 .. 0.83
   2 !   22.6   0.1   1.7e-08    0.0001     111     192 ..     124     199 ..     107     202 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.088
                                  EEEEEEEHHHHHHHHHHHHH CS
                       Tubulin  1 eiivigvGqcGnqignelwe 20
                                  +++v+ +G +G +i+ ++  
  gi|13541488|ref|NP_111176.1| 31 NVVVVSFGNAGFRILRKMNP 50
                                  5899**********999865 PP

  == domain 2  score: 22.6 bits;  conditional E-value: 1.7e-08
                                   TT-SE.SEEEEEEETTSSHHHHHHHHHHHHHHHTSTTSEEEEEEEE--GG.G-HHHHHHHHHHHHHHHHT-SEEEEEEHHH CS
                       Tubulin 111 ekcdslqgffitaslgGGTGSGlgpvilevlkeeypkalvvtvvvlPsefsevvvepynailalkelieesdavividNda 191
                                   +++    +f++++++gG +   + ++ le+l++   ++  ++++v+Ps+   +  + ++ai a++ l+   + ++v+dNd+
  gi|13541488|ref|NP_111176.1| 124 KSTGI--SFVLVSGFGGSFAQYAHSKFLEILNKS--GREALSIIVVPSSK--EGNRREKAISAINDLRATGNNIVVFDNDK 198
                                   55555..89*************************..9***********76..567899**********************8 PP

                                   H CS
                       Tubulin 192 L 192
                                   +
  gi|13541488|ref|NP_111176.1| 199 F 199
                                   6 PP

>> FAD_syn  FAD synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   4.3e-05      0.26      69     135 ..     120     186 ..      97     203 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 4.3e-05
                       FAD_syn  69 lelleelgvdavlvvdFtkefaelsaeeFiekllveklkvkavvvGfdfrfGkkregdvellkelga 135
                                   +++l+++g+ +vlv  F  +fa++   +F+e l ++  ++  ++v    + G++re  ++ +++l a
  gi|13541488|ref|NP_111176.1| 120 AQKLKSTGISFVLVSGFGGSFAQYAHSKFLEILNKSGREALSIIVVPSSKEGNRREKAISAINDLRA 186
                                   689***************************9988888888899999999999999998888888775 PP

>> DUF418  Protein of unknown function (DUF418)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   5.3e-05      0.32      47      97 ..     112     162 ..      97     167 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 5.3e-05
                        DUF418  47 llelllsvlrylaglllalgyvalillllakekrrrllralaavGRmALTn 97 
                                   + e +l++ + l +  +++++v++++  +a+ +++++l+ l++ GR AL+ 
  gi|13541488|ref|NP_111176.1| 112 TEEDALYAAQKLKSTGISFVLVSGFGGSFAQYAHSKFLEILNKSGREALSI 162
                                   566778889999999**********************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       713  (0.039768); expected 358.6 (0.02)
Passed bias filter:                      552  (0.0307881); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.46
# Mc/sec: 1591.28
//
Query:       gi|13541489|ref|NP_111177.1|  [L=143]
Description: transcription regulator [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.7e-15   55.0   0.0      8e-15   54.6   0.0    1.3  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain
    5.6e-11   41.8   0.5    8.3e-09   34.9   0.3    2.2  2  HTH_24          Winged helix-turn-helix DNA-binding
    4.2e-08   32.9   0.3    9.4e-08   31.8   0.1    1.7  2  HTH_AsnC-type   AsnC-type helix-turn-helix domain
    1.2e-06   28.3   0.0    2.3e-06   27.4   0.0    1.5  1  TrmB            Sugar-specific transcriptional regulator TrmB
    0.00048   19.9   0.0    0.00083   19.1   0.0    1.3  1  HTH_IclR        IclR helix-turn-helix domain
      0.004   17.0   0.0     0.0066   16.3   0.0    1.4  1  HTH_5           Bacterial regulatory protein, arsR family
  ------ inclusion threshold ------
      0.018   14.8   0.0      0.058   13.2   0.0    1.9  2  HTH_8           Bacterial regulatory protein, Fis family
      0.019   15.0   0.1      0.041   14.0   0.1    1.5  2  DUF2250         Uncharacterized protein conserved in archaea 
       0.14   12.6   0.0       0.26   11.8   0.0    1.4  1  HTH_27          Winged helix DNA-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 !   54.6   0.0     4e-18     8e-15      12      74 ..      78     140 ..      67     141 .. 0.92

  Alignments for each domain:
  == domain 1  score: 54.6 bits;  conditional E-value: 4e-18
                                   HHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEEE CS
                AsnC_trans_reg  12 qleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivle 74 
                                   + +++++++a+++eV+ +y ++G++d+l+kv+  ++ea+ +f+ +kl+++pg++r +t  v++
  gi|13541489|ref|NP_111177.1|  78 SQRDLAAKIATFKEVENVYIIAGEWDLLIKVRESSTEAIGNFVLDKLREMPGIERAQTITVFS 140
                                   67899*******************************************************997 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.9   0.3   4.2e-12   8.3e-09       1      48 []       1      48 [.       1      48 [. 0.99
   2 !    5.1   0.0    0.0082        16      16      27 ..      75      86 ..      68      87 .. 0.90

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 4.2e-12
                        HTH_24  1 ldetdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                  +de+d++IL++L++n+r  +++ ++ l++++ t+ +r+++++++G+Ik
  gi|13541489|ref|NP_111177.1|  1 MDEKDLQILNYLMENGRDKISDMSRTLDIPRVTIYERMQNMIKSGIIK 48
                                  8**********************************************8 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0082
                        HTH_24 16 prisqreLAerl 27
                                   +isqr+LA ++
  gi|13541489|ref|NP_111177.1| 75 DGISQRDLAAKI 86
                                  69*******986 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.8   0.1   4.7e-11   9.4e-08       1      41 [.       1      41 [.       1      42 [. 0.98
   2 ?   -2.0   0.0       1.7   3.4e+03      18      27 ..      77      86 ..      77      87 .. 0.81

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 4.7e-11
                 HTH_AsnC-type  1 LDeiDrkILeaLqedaRisyaeLAervGlSestvlrRvrrL 41
                                  +De D++IL+ L+e++R   +++++ + + + t+ +R++ +
  gi|13541489|ref|NP_111177.1|  1 MDEKDLQILNYLMENGRDKISDMSRTLDIPRVTIYERMQNM 41
                                  9*************************************987 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.7
                 HTH_AsnC-type 18 isyaeLAerv 27
                                  is ++LA+++
  gi|13541489|ref|NP_111177.1| 77 ISQRDLAAKI 86
                                  6899999875 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.0   1.2e-09   2.3e-06       8      55 ..       3      50 ..       1      59 [. 0.92

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 1.2e-09
                                  HHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEE CS
                          TrmB  8 eyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVere 55
                                  e + ++  +L+++g+ ++++ ++ l++pr ++Ye ++++++ G++++ 
  gi|13541489|ref|NP_111177.1|  3 EKDLQILNYLMENGRDKISDMSRTLDIPRVTIYERMQNMIKSGIIKKF 50
                                  7899999*************************************9975 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   4.2e-07   0.00083       6      49 ..       6      48 ..       3      49 .. 0.94

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 4.2e-07
                                  HHHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                      HTH_IclR  6 laiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyve 49
                                  l+iL++l e +++ ++s+++r +++p+ t +  +q +++ G+++
  gi|13541489|ref|NP_111177.1|  6 LQILNYLMENGRD-KISDMSRTLDIPRVTIYERMQNMIKSGIIK 48
                                  8************.************************999987 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   3.3e-06    0.0066       1      47 []       2      49 ..       2      49 .. 0.94

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 3.3e-06
                                  SHHHHHHHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                         HTH_5  1 dptRlkILklLae.gelcvcelaeelglsqstvShHLkkLreaGLVek 47
                                  d++ l+IL++L+e g  ++++ ++ l++++ t+ +    + ++G+++k
  gi|13541489|ref|NP_111177.1|  2 DEKDLQILNYLMEnGRDKISDMSRTLDIPRVTIYERMQNMIKSGIIKK 49
                                  56779********999*****************************986 PP

>> HTH_8  Bacterial regulatory protein, Fis family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   2.9e-05     0.058      20      40 ..      19      39 ..       9      41 .. 0.89
   2 ?   -2.7   0.0       2.7   5.4e+03       3      12 ..      90      99 ..      88      99 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.9e-05
                                  -HHHHHHHHTS-HHHHHHHHH CS
                         HTH_8 20 nkskAArlLGisRrtLyrKLk 40
                                   +s+++r L+i R t+y +++
  gi|13541489|ref|NP_111177.1| 19 KISDMSRTLDIPRVTIYERMQ 39
                                  5899****************8 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.7
                                  HHHHHHHHHH CS
                         HTH_8  3 eevEkelIea 12
                                  +evE  +I+a
  gi|13541489|ref|NP_111177.1| 90 KEVENVYIIA 99
                                  7999999986 PP

>> DUF2250  Uncharacterized protein conserved in archaea (DUF2250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   2.1e-05     0.041       7      55 ..       2      50 ..       1      53 [. 0.95
   2 ?   -3.1   0.0       4.4   8.7e+03      42      56 ..     120     134 ..     109     138 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.1e-05
                       DUF2250  7 delalkvlkhlkkanvdYaksiakeleipleevrellkkLeelGLlerv 55
                                  de++l++l++l + + d    +++ l+ip+  + e ++++ + G++++ 
  gi|13541489|ref|NP_111177.1|  2 DEKDLQILNYLMENGRDKISDMSRTLDIPRVTIYERMQNMIKSGIIKKF 50
                                  6789******************************************986 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 4.4
                       DUF2250  42 llkkLeelGLlerve 56 
                                   +l+kL+e+  +er +
  gi|13541489|ref|NP_111177.1| 120 VLDKLREMPGIERAQ 134
                                   467777777677665 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00013      0.26       5      50 ..       5      49 ..       1      52 [. 0.90

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00013
                        HTH_27  5 qalvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLver 50
                                  + ++L+ ++ +++r+k++d +++l++   +i + +  +++ G +++
  gi|13541489|ref|NP_111177.1|  5 DLQILNYLM-ENGRDKISDMSRTLDIPRVTIYERMQNMIKSGIIKK 49
                                  778999999.****************************99998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       495  (0.0276089); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 910.82
//
Query:       gi|13541490|ref|NP_111178.1|  [L=314]
Description: asparagine synthetase A [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.3e-51  174.2   0.1    4.1e-51  173.9   0.1    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 !  173.9   0.1   2.3e-55   4.1e-51      13     313 ..      17     308 ..      10     309 .. 0.89

  Alignments for each domain:
  == domain 1  score: 173.9 bits;  conditional E-value: 2.3e-55
                                   CCSHHHHHHHHHHHHHHHHHHHHHHHTT-EE----SEESS--SSSS--EEEEETTT.TEEE-E-S-SHHHHHHHHHCTHSE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   tRNA-synt_2  13 lrtekvskvlrlrstvtkavrkyleengfieietPiLsksdteegarlFkvksrekekeffaLtqspqlylellivagidr 93 
                                   l ++++++ l++ s+v +++ +yl+ +gfie+ +P++++  t     +   ++    +  + +t s+ +++ +l    +++
  gi|13541490|ref|NP_111178.1|  17 LEKPELQRALKIESSVRSYLSDYLKGRGFIEV-PPVIISVLTDPLNHPVYDPTIDYYGYKYSITKSMIFHKHILTKH-FGK 95 
                                   68999***************************.66777664554444433334444443347***************.*** PP

                                   EEEEEEEE--S--B...TTB-S-CEEEEEEEEET-SCHHHHHHHHHHHHHHHHHHHHCSCCCCCHTTTTTSEE-SSS-EEE CS
                                   xxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   tRNA-synt_2  94 vfqiaraFRaEdsr...tdrhlaEFtqieaemsfieeedimqvleelikslvkevlessakdiefvirrnskdlkkpfkrl 171
                                   +f+++++ R E+ +   t rhl+EFtq+++e+  ++ ed+m++ ee+i +l++++++++ +d++f  r     +kkpf+r+
  gi|13541490|ref|NP_111178.1|  96 IFTFSPNIRLEEEDkaeTGRHLSEFTQLDLEIRDATREDVMSLGEEMIVELFSKIKKTHSDDLKFFGRDLR-IPKKPFERI 175
                                   *********9986655599********************************************99999975.67889**** PP

                                   EHHHHHHHHHTS-SS--HHHHHHHHHHS--SEEEEEEEBGGGSTTCBBBSTTSTTBBSEEEEEET.TE.EEEEEEEB--SH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx.xxxxxxxxxxxx RF
                   tRNA-synt_2 172 tykeaieklneigkdldkaderalvkkeknepvfvtdfPaelkpFyarkeeddkkltesyDllin.gv.ElvgGslRiedp 250
                                    yk+a ++     ++    d    + kek+ep++++d P e + Fy r++ +++ +   +Dl+++ g+ E ++G  R+ + 
  gi|13541490|ref|NP_111178.1| 176 RYKDAEKE-----YGG---DFESILSKEKKEPFWIIDIPLEKREFYDREDPQRPGILVDMDLVYPeGFgEALSGGEREYKL 248
                                   ******99.....543...3445666799***********************************9788************* PP

                                   HHHHHHHHHCCHHSSSGGGGHHHHHHHHCT--SEEEEEEEHHHHHHHHCT-SSGGGCSSS-XX CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   tRNA-synt_2 251 eeleeklkskgldeeaeekfswylealeyGapphgGlglGldRlvmlllgsesIrdviaFPkl 313
                                   ++  e++++k  +   ee+f+wy+e  + G+ p +G+g+G++Rl+ +++g++ I dv +FPk+
  gi|13541490|ref|NP_111178.1| 249 DRIIERIHKKRQT---EEQFKWYIEFAKDGLYPSAGFGIGIERLTRYICGLSRIEDVHPFPKV 308
                                   **********999...*********************************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       580  (0.0323498); expected 358.6 (0.02)
Passed bias filter:                      494  (0.0275531); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.25s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 2043.27
//
Query:       gi|13541491|ref|NP_111179.1|  [L=200]
Description: DNA polymerase elongation subunit [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.5e-11   41.9   1.4    7.9e-09   35.1   1.4    2.2  1  DNA_pol_B_exo1  DNA polymerase family B, exonuclease domain
    1.6e-05   25.0   0.2    2.2e-05   24.5   0.2    1.4  1  RNase_H_2       RNase_H superfamily
    3.7e-05   23.5   0.1    6.3e-05   22.7   0.1    1.4  1  DNA_pol_B_exo2  Predicted 3'-5' exonuclease related to the ex
  ------ inclusion threshold ------
       0.14   11.9   0.0       0.25   11.1   0.0    1.5  2  XTBD            XRN-Two Binding Domain, XTBD


Domain annotation for each model (and alignments):
>> 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 !   35.1   1.4   1.8e-12   7.9e-09     157     282 ..      17     108 ..       4     115 .. 0.84

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 1.8e-12
                                   S-EEEEEEEEEETEETTSEETTTT..--EEEEEEEECCTC.SS.SEEEEEEECCCTSS----EE--SSTCSTTEEEEEESS CS
                DNA_pol_B_exo1 157 pplrvlsFDIeckskkgkfpdaensedpiiqIscvldglgekepearklftlrecaseeeedfeltpkpeypgvkvlefds 237
                                    + +++sFDIe+  ++gkf + en    ii+Is+   +l+       ++f+ +                        ++ +
  gi|13541491|ref|NP_111179.1|  17 KKSELISFDIETLVEDGKFLNNEN----IIAISYCTGDLN------CNVFVAE------------------------SEGE 63 
                                   66789*******************....******998877......2333333........................3457 PP

                                   HHHHHHHHHHHHHHH--SEEEESSTTTTHHHHHHHHHHHCCTCCH CS
                DNA_pol_B_exo1 238 EkelLqaflefikqydPdvitgYNidnFDlpYilnRakelykvkl 282
                                   E ++Lq+f  ++ +++P +i+gYN   +D+p i  ++++ + +k+
  gi|13541491|ref|NP_111179.1|  64 EETILQNFDLLLGNVKPAIILGYNHTGYDIPLISYKIRNFKDYKF 108
                                   9*********************************99998777665 PP

>> RNase_H_2  RNase_H superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.2     5e-09   2.2e-05       3     109 ..      24     139 ..      22     196 .. 0.74

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 5e-09
                     RNase_H_2   3 fDiEttGlspkk....nliyliGvldvdekeiekltqllaeepeeekailelflellekkka..lvtfngksFDvpflkrl 77 
                                   fDiEt  ++++k    + i+ i+++  d + ++    ++ae + ee+ il+ f  ll + k+  ++ +n +++D+p+++++
  gi|13541491|ref|NP_111179.1|  24 FDIETL-VEDGKflnnENIIAISYCTGDLNCNV----FVAESEGEEETILQNFDLLLGNVKPaiILGYNHTGYDIPLISYK 99 
                                   999996.55443231166788888865555444....567999999999999*55555554412677*************9 PP

                     RNase_H_2  78 f...kkyklde.....eefrhiDLlkelrkkklesysLks 109
                                   +   k+yk+ +      + +++D+++ +++ + + ++L++
  gi|13541491|ref|NP_111179.1| 100 IrnfKDYKFWNireyfGSAYTLDVMYLVKNLTGKIMKLED 139
                                   9877777776677555555889999988866655555544 PP

>> DNA_pol_B_exo2  Predicted 3'-5' exonuclease related to the exonuclease domain of PolB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.1   1.4e-08   6.3e-05      10     174 ..      40     197 ..      34     199 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 1.4e-08
                DNA_pol_B_exo2  10 rvvaisvvkarkdekfkvkslgeeessekelikkffegvekkkpqlV.sfngrgfDlpvleyralkhgvsapkyfdegded 89 
                                   +++ais +  + d + +v+   e+e +e++++++f   + + kp ++ ++n  g+D+p++ y+  +++ +  k+++  +  
  gi|13541491|ref|NP_111179.1|  40 NIIAISYC--TGDLNCNVFV-AESEGEEETILQNFDLLLGNVKPAIIlGYNHTGYDIPLISYK--IRNFKDYKFWNIREY- 114
                                   68888888..4555555554.5667789999****999*****987549*************9..79999*****99994. PP

                DNA_pol_B_exo2  90 rekkwn...nylsrystr.hlDLmdllseygaranakLdelakllglPGKlgvdGskVaelyqegklkeireYcetDvlnT 166
                                       ++    yl +  t   + L d +s y ++++ + + + +l g+ GK    G+++  l+++ + k+ + Y   D ++T
  gi|13541491|ref|NP_111179.1| 115 FGSAYTldvMYLVKNLTGkIMKLEDAISLYLGKSELEAKMIPSLNGM-GK----GEAIKYLWKN-ERKKFETYSLNDSIST 189
                                   444454446677776666599*********99988888877777776.54....8888888876.56899*********** PP

                DNA_pol_B_exo2 167 Ylvylrle 174
                                     ++ +++
  gi|13541491|ref|NP_111179.1| 190 LKIFYKIM 197
                                   *9999986 PP

>> XTBD  XRN-Two Binding Domain, XTBD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0         2   8.8e+03      18      35 ..      10      23 ..       8      26 .. 0.63
   2 ?   11.1   0.0   5.5e-05      0.25      40      73 ..     109     141 ..      63     153 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 2
                                  HHHHHHHGGGS-HHHHHH CS
                          XTBD 18 reFilrnkekfeedrLls 35
                                  r+F+ + k+    ++L+s
  gi|13541491|ref|NP_111179.1| 10 RAFVKQIKK----SELIS 23
                                  677766666....55555 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 5.5e-05
                                   HHHHHTT--B--HHHHHHHHHHHTTTTXXXXXXX CS
                          XTBD  40 fanlvflGcrYprevmekvkelaegiaaeveeak 73 
                                   +   +++G  Y  +vm  vk+l  +i+ + e+a 
  gi|13541491|ref|NP_111179.1| 109 WNIREYFGSAYTLDVMYLVKNLTGKIM-KLEDAI 141
                                   33349*********************8.777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       622  (0.0346924); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.69
# Mc/sec: 871.65
//
Query:       gi|13541492|ref|NP_111180.1|  [L=473]
Description: multidrug efflux permease [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      5e-39  134.2  64.7    6.1e-28   97.8  33.9    2.7  2  MFS_1     Major Facilitator Superfamily
    4.4e-06   25.8  24.3    3.2e-05   23.0   8.1    3.2  3  Sugar_tr  Sugar (and other) transporter
    3.2e-05   22.5   5.7    9.7e-05   21.0   5.7    1.8  1  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 !   97.8  33.9     1e-31   6.1e-28       2     232 ..      14     238 ..      13     245 .. 0.80
   2 !   41.2  22.8   1.6e-14   9.3e-11       2     140 ..     263     402 ..     262     470 .. 0.78

  Alignments for each domain:
  == domain 1  score: 97.8 bits;  conditional E-value: 1e-31
                         MFS_1   2 llaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfa 82 
                                   +++ fl+ ++++ l+++lp +++ +l+ +  +i ++l++y l++ ++s+++Gr sd +Gr+ ++ lg+++f +g+ll++ +
  gi|13541492|ref|NP_111180.1|  14 SIGSFLAVINSTSLLISLP-TIMISLHTTFLFIIWVLVIYPLVMTIGSPIFGRYSDFIGRKQLYGLGYIFFTIGSLLAS-S 92 
                                   6899***************.9999**************************************************66666.3 PP

                         MFS_1  83 .sslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsl 162
                                    +++ +l+++r++qGlg+++lf++++a+iad f ++e   aig  s+ +++++++gpl+gg+l+  l+Wr+vf+++ ++++
  gi|13541492|ref|NP_111180.1|  93 sINIDMLIAARAIQGLGGSLLFSNSLAIIADAFRQDELKWAIGTNSLIIGFATAIGPLVGGILT-VLNWRYVFVFNVPFGI 172
                                   477779**********************************************************.99************** PP

                         MFS_1 163 lafvlfllllpeepperkrkspkeeekgtgpaplvp......awkallkdpvlw......illialllfffgfsg.lltll 230
                                    +     + l   + e++ ++ +++     p+ +++      ++ + +++p  w      +          ++s+ +++ l
  gi|13541492|ref|NP_111180.1| 173 AGYF---MSLKIHDIEKRQVKAAKL-----PSVFFSifiillIIYMTFAPPNNWisfsglA---------YIISIaVSFIL 236
                                   *955...444455555555555444.....4444444545665666666665564443321.........22333222222 PP

                         MFS_1 231 pl 232
                                   ++
  gi|13541492|ref|NP_111180.1| 237 FI 238
                                   22 PP

  == domain 2  score: 41.2 bits;  conditional E-value: 1.6e-14
                         MFS_1   2 llaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrr.vlllglllfalglllllf 81 
                                   ++++fl++++r+ +++++ ++l+  l +sp + +l++  ya++ ++as+++Gr+  + G    ++ +gl+l+++g+++l+f
  gi|13541492|ref|NP_111180.1| 263 AISTFLNSITRYSILLIAIIMLQGPLSLSPLTSSLMVMPYAVALSLASYFVGRVHRK-GMEDhLIYAGLFLSFFGSFMLFF 342
                                   58999*****9999999999**********************************877.65555888888888888788888 PP

                         MFS_1  82 a..sslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpll 140
                                   +  +sl +++++  l G+g g++++ ++a++   +p+++rg+a gl ++  +lG+++g+  
  gi|13541492|ref|NP_111180.1| 343 VrdASL-PFYIGITLVGFGIGIFYTPSNAILMSTAPPNKRGSAAGLRTVILNLGSVIGMSM 402
                                   875555.5**************************************************543 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   8.1   5.3e-09   3.2e-05      47     115 ..      44     109 ..       8     117 .. 0.86
   2 ?   -3.9  11.6      0.74   4.4e+03     348     436 ..     151     241 ..     132     243 .. 0.84
   3 !   16.8   8.2     4e-07    0.0024      45     158 ..     292     403 ..     255     420 .. 0.85

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 5.3e-09
                                   HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHH CS
                      Sugar_tr  47 lsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGig 115
                                    + +++ i+ ++ +iGs ++g  +d++GRk+ +  + ++f ig++l   +    ++ +li++R + G+g
  gi|13541492|ref|NP_111180.1|  44 FIIWVLVIYPLVMTIGSPIFGRYSDFIGRKQLYGLGYIFFTIGSLLASSSI---NIDMLIAARAIQGLG 109
                                   578999*********************************************...9************98 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 0.74
                                   .CHHHHHHHHHHHHHHHTTTTHHHHHH...HHHHSHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHT-HHHHHHHHH CS
                      Sugar_tr 348 asivaivfialfialfalgwgpvpwvl...vsElfpqsvRskalaiavavnwlanflisllfpiiteaigggyvflvfagl 425
                                    +++++v+   ++++f++ +g   +++   + ++   +v+++ l  ++++ +++ ++i ++f    + i+ +   ++  ++
  gi|13541492|ref|NP_111180.1| 151 VGGILTVLNWRYVFVFNVPFGIAGYFMslkIHDIEKRQVKAAKLPSVFFSIFIILLIIYMTFAPPNNWIS-FSGLAYIISI 230
                                   588999999999****998888877773336899999*********************************.7777777889 PP

                                   HHHHHHHHHHH CS
                      Sugar_tr 426 avlfiifvfff 436
                                   av fi+f++f+
  gi|13541492|ref|NP_111180.1| 231 AVSFILFIYFT 241
                                   99999999996 PP

  == domain 3  score: 16.8 bits;  conditional E-value: 4e-07
                                   ..HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHH.HHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHH CS
                      Sugar_tr  45 svlsglivsiflvGaiiGslfagllgdrfGRkkslli.aavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlvP 124
                                    ++s+l+v  + v   + s+f+g  ++r G  + l+  + +l++ g+++ ++     +   +++g  lvG+g+G++++ + 
  gi|13541492|ref|NP_111180.1| 292 PLTSSLMVMPYAVALSLASYFVG-RVHRKGMEDHLIYaGLFLSFFGSFMLFFVR--DASLPFYIGITLVGFGIGIFYTPSN 369
                                   56788899999999999999999.567778888888747788899999999999..5688899999*************** PP

                                   HHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHH CS
                      Sugar_tr 125 myisEiApkklRgalvslyqlaitfGilvaaifg 158
                                     +   Ap+++Rg   +l  + + +G +++  + 
  gi|13541492|ref|NP_111180.1| 370 AILMSTAPPNKRGSAAGLRTVILNLGSVIGMSMV 403
                                   ****************************997665 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   5.7   1.6e-08   9.7e-05      36     200 ..      34     196 ..       7     204 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.6e-08
                         MFS_3  36 lmtdisasplmvAlvqaaatLPifllsilaGalaDnfdrRkvllavqlllalvsvlltvlaalgllspwlllaltlligiG 116
                                   +m +++++ l +  v +   L + + s + G  +D + r+++   ++++  ++s+l+ ++     ++  +l+a   + g+G
  gi|13541492|ref|NP_111180.1|  34 IMISLHTTFLFIIWVLVIYPLVMTIGSPIFGRYSDFIGRKQLYGLGYIFFTIGSLLASSS-----INIDMLIAARAIQGLG 109
                                   466667777777777777777777778888889999999999888999998888776655.....456689********** PP

                         MFS_3 117 aalndPaWqAsvgelvkrrdvpaAvaLnsvginiaRsvGPAlgGvlvaa.vGaalafav..nalsylalivallrwkrevr 194
                                    +l      A++ +  ++++++ A+  ns+ i  a ++GP +gG+l  +    +++f v      y++ + +    kr+v+
  gi|13541492|ref|NP_111180.1| 110 GSLLFSNSLAIIADAFRQDELKWAIGTNSLIIGFATAIGPLVGGILTVLnWRYVFVFNVpfGIAGYFMSLKIHDIEKRQVK 190
                                   ********************************************9854413445555541135789999999999999999 PP

                         MFS_3 195 ksslpr 200
                                   + +lp+
  gi|13541492|ref|NP_111180.1| 191 AAKLPS 196
                                   999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (473 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       913  (0.0509231); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.69u 0.29s 00:00:00.98 Elapsed: 00:00:00.47
# Mc/sec: 3030.51
//
Query:       gi|13541493|ref|NP_111181.1|  [L=140]
Description: CBS domain-containing protein [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.3e-26   91.1   1.2      8e-17   61.4   0.2    2.5  3  CBS       CBS domain


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.0   1.1e-10     2e-06       1      55 [.       5      58 ..       5      60 .. 0.86
   2 !   61.4   0.2   4.5e-21     8e-17       1      56 [.      70     124 ..      70     125 .. 0.94
   3 ?   -2.1   0.0      0.31   5.5e+03      17      25 ..     129     137 ..     127     139 .. 0.66

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 1.1e-10
                                  HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEE.ETTTBEEEEEEHHHHHHHH CS
                           CBS  1 VgdimtrdvvtvppdttleealelmrekgvsrlPVV.dedgklvGivtlrDllral 55
                                  ++dim++   t++pdtt  ea+  m++ +v ++++V de g + G+vt+ D ++++
  gi|13541493|ref|NP_111181.1|  5 ASDIMRKYTKTFRPDTTAYEAAVVMAQDHV-GFLIVeDETG-IRGMVTEWDYINKI 58
                                  589**********************87779.6669956666.*********88876 PP

  == domain 2  score: 61.4 bits;  conditional E-value: 4.5e-21
                                   HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                           CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                                   V++im++++++++pdt+  +++e+m ++g++rlPV+ e +klvG+vt rD+lra +
  gi|13541493|ref|NP_111181.1|  70 VEEIMNSPIISITPDTPTFKVAEIMSKNGIRRLPVM-EKNKLVGVVTSRDILRAFK 124
                                   89***********************8788*******.7888************976 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 0.31
                                   BHHHHHHHH CS
                           CBS  17 tleealelm 25 
                                   ++++++ ++
  gi|13541493|ref|NP_111181.1| 129 SISDIISRF 137
                                   677777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.22s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 993.52
//
Query:       gi|13541494|ref|NP_111182.1|  [L=211]
Description: proteasome protease subunit beta [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.7e-51  174.4   1.0      2e-51  174.2   1.0    1.0  1  Proteasome  Proteasome subunit


Domain annotation for each model (and alignments):
>> Proteasome  Proteasome subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  174.2   1.0   1.1e-55     2e-51       2     190 .]       6     186 ..       5     186 .. 0.97

  Alignments for each domain:
  == domain 1  score: 174.2 bits;  conditional E-value: 1.1e-55
                                   HHS-EEEEEEETTEEEEEEEEEEEETTEEEESSSSTSEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHSSGTCHH CS
                    Proteasome   2 kkGttvvGikgkdgvvlaadkratagskllskstveKifkiddhigvafaGlaaDartlvrraraeaqlyrlrygrpipve 82 
                                   ++Gtt+vGi+ +d v++a+++r+t+++ ++ k+  +K+f+id ++g+++aGl++Da++lvr+++ae++lyrl+   ++p+e
  gi|13541494|ref|NP_111182.1|   6 ETGTTTVGITLTDAVIMATERRVTMENFIMHKN-GKKLFQIDTYTGMTIAGLVGDAQVLVRYMKAELELYRLQRRVNMPIE 85 
                                   69***************************8888.7********************************************** PP

                                   HHHHHHHHHHHHHHHHCTTTTTSEEEEEEEEETTTEEEEEEEETTSEEEEESSEEEESTTHHHHHHHHHHHHSTTBSHHHH CS
                    Proteasome  83 rlvarvaaklqaytqrsgrrpfgvslliagvdeeggpeLyqidpsGsyieekdavaiGsgseaaktalekeykedltleea 163
                                       +va++l++++ + +  p++v+ll++g+d +  p++++id +G ++e+  ++++Gsgs +++++le++y+e+l+ +e+
  gi|13541494|ref|NP_111182.1|  86 ----AVATLLSNMLNQVKYMPYMVQLLVGGID-TS-PHVFSIDAAGGSVED-IYASTGSGSPFVYGVLESQYNEKLSIDEG 159
                                   ....999999999999999*************.65.***************.6**************************** PP

                                   HHHHHHHHHHHHHHBTTSCSSEEEEEE CS
                    Proteasome 164 velavkalkealerdklsgknievavi 190
                                   v+l+++a+++a +rd++sg+ i+vavi
  gi|13541494|ref|NP_111182.1| 160 VDLVIRAISAAKQRDSASGGMIDVAVI 186
                                   *************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       655  (0.036533); expected 358.6 (0.02)
Passed bias filter:                      528  (0.0294495); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 1408.85
//
Query:       gi|13541495|ref|NP_111183.1|  [L=639]
Description: metal-dependent RNase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.2e-31  107.1   5.4    6.6e-25   86.9   0.6    3.6  3  KH_7           KH domain
    1.4e-25   89.7   0.0    5.1e-25   87.9   0.0    2.0  2  Beta-Casp      Beta-Casp domain
    3.3e-14   53.4   0.4    2.8e-13   50.3   0.4    2.4  1  Lactamase_B    Metallo-beta-lactamase superfamily
    1.2e-12   47.5   0.1    3.8e-12   46.0   0.0    2.0  2  RMMBL          Zn-dependent metallo-hydrolase RNA specificity
    2.8e-12   46.5   0.0    6.1e-12   45.4   0.0    1.5  1  Lactamase_B_6  Metallo-beta-lactamase superfamily domain
    1.5e-06   27.9   0.0    3.2e-06   26.8   0.0    1.6  1  Lactamase_B_2  Beta-lactamase superfamily domain
  ------ inclusion threshold ------
       0.02   14.8   0.0      0.042   13.7   0.0    1.5  1  Lactamase_B_3  Beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> KH_7  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.9   0.6   2.6e-28   6.6e-25       2      68 .]       5      70 ..       4      70 .. 0.97
   2 !   18.8   0.5   4.5e-07    0.0011       5      51 ..      74     123 ..      71     128 .. 0.87
   3 ?    0.9   0.0      0.17   4.4e+02      45      65 ..     459     479 ..     445     482 .. 0.81

  Alignments for each domain:
  == domain 1  score: 86.9 bits;  conditional E-value: 2.6e-28
                          KH_7  2 evleelkekieeklPkevkitdveFEGPelViYtknpklfaengdlirklAkelrkRiviRpDpsvl 68
                                  ++l e+++ +++ +P++ kit++++EGP++V+Ytk+p+lfa+++dl r++A+e+r+Ri+iRpDps+l
  gi|13541495|ref|NP_111183.1|  5 DYLAETRQIFDRLYPDN-KITEIDYEGPTIVVYTKDPELFAKRDDLARQIAQEIRRRIAIRPDPSIL 70
                                  7899***********99.***********************************************97 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 4.5e-07
                          KH_7   5 eelkekieeklPkevkitdveFEG..PelViYtknpklfa.engdlirkl 51 
                                   ++ +++ie+ +Pke+ + d+ FEG   e+Vi +++p++++  n+++++++
  gi|13541495|ref|NP_111183.1|  74 DQARAEIEKIIPKEAGLEDIYFEGdtGEVVIEVDEPSIITaRNTEYVQEI 123
                                   67899*******************5559*********9875888999887 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.17
                          KH_7  45 gdlirklAkelrkRiviRpDp 65 
                                     + + l kelr  i++R ++
  gi|13541495|ref|NP_111183.1| 459 AAYPEYLNKELREAIMVRKEN 479
                                   55667799**********876 PP

>> Beta-Casp  Beta-Casp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       1.5   3.9e+03      65      68 ..     131     134 ..      78     215 .. 0.56
   2 !   87.9   0.0     2e-28   5.1e-25       2     110 .]     425     549 ..     424     549 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.5
                                   SEEE CS
                     Beta-Casp  65 pkvi 68 
                                   p ++
  gi|13541495|ref|NP_111183.1| 131 PRIV 134
                                   2222 PP

  == domain 2  score: 87.9 bits;  conditional E-value: 2e-28
                                   HHHHHHH..HCTT..TTS-S-EEEEE-HHHHHHHHHGGGGGG.........................E-SHH....HHHH. CS
                     Beta-Casp   2 qellylLeelwkekkledlklpiyldsplaskatevYkeyae.........................veakslewmeskke 57 
                                   qe++++Le+++++++  ++++++yld+ ++ +at+++ +y+e                         ve+++      ++e
  gi|13541495|ref|NP_111183.1| 425 QEVMIVLEDAMRNGR--IPQMNVYLDG-MIMEATAIHAAYPEylnkelreaimvrkenpflsqifkkVETRE------QRE 496
                                   9************55..7889******.*****************999999999999998877764444444......233 PP

                                   .HHHS-SSEEEEES-TTSSSSHHHHHHHHHTTSTTSEEEESS---TTSHHHHH CS
                     Beta-Casp  58 elnsskgpkvilassgmlegGrsrellkklledprntvilvgyqaegTlgrkl 110
                                   +++++++ kv+la+sgm++gG++ e++k+++++p++t+++vgyqa gT+g+++
  gi|13541495|ref|NP_111183.1| 497 DIAEDPESKVVLATSGMMNGGPVMEYFKAWAGNPKHTLVFVGYQADGTMGKRI 549
                                   57788999******************************************997 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.3   0.4   1.1e-16   2.8e-13       4     162 ..     191     367 ..     188     410 .. 0.78

  Alignments for each domain:
  == domain 1  score: 50.3 bits;  conditional E-value: 1.1e-16
                                   CSSEEEEEEETTCEEEES--SCHHHHHHHH......HHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHH CS
                   Lactamase_B   4 dpvnsyliegdggviLiDtGtsteaaraal......elaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaee 78 
                                   ++ +++l+ ++++ +LiD+G+ +  ++a        ++  +  ++  +davilTH+HlDH G l+ l +     +++    
  gi|13541495|ref|NP_111183.1| 191 VGRSATLVSTKNSKVLIDCGMMNVGPDADPwdaapyLYVPEVQPLSSIDAVILTHAHLDHSGLLPLLFKYGYDGPVYMTQP 271
                                   67899******************999998899***9********************************9999999999888 PP

                                   HHCCHCHHHHHHHHHCCHH............TTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEE CS
                   Lactamase_B  79 apalfmeeaddaasrkgll............lagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlf 147
                                   ++ l     dd+      +             +  + +     e  + + ++   ++ + ++ g+ ++h+++++g  +v++
  gi|13541495|ref|NP_111183.1| 272 TRDLAVLLQDDYIKVARMEggkvpyeskyirEELKHTITLRYGETTDITRDMRLTFYNAGHILGSASVHLHIGDGLYNVVL 352
                                   8888888887776666666888****997743333333334444444445555555667788999**************** PP

                                   ECTTTSSHHCCCCCC CS
                   Lactamase_B 148 tGDallagetgridl 162
                                   +GD+ ++  ++  + 
  gi|13541495|ref|NP_111183.1| 353 SGDVKFEKTWLFNPA 367
                                   ****99776666555 PP

>> RMMBL  Zn-dependent metallo-hydrolase RNA specificity domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.1       4.9   1.3e+04      13      23 ..     244     254 ..     239     257 .. 0.74
   2 !   46.0   0.0   1.5e-15   3.8e-12       2      60 ..     567     628 ..     566     630 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 4.9
                         RMMBL  13 fSgHadknell 23 
                                     +H d+++ll
  gi|13541495|ref|NP_111183.1| 244 THAHLDHSGLL 254
                                   67899999887 PP

  == domain 2  score: 46.0 bits;  conditional E-value: 1.5e-15
                         RMMBL   2 ipvkarieeid.fSgHadknellelirklkprn..vilvHGeeeatsalarllkeeegidvf 60 
                                   + +++ +e+ + fSgH+ k +ll +i++++p++  + ++HG+  +t+++arl ++ ++i+ +
  gi|13541495|ref|NP_111183.1| 567 YQINMDVETAEgFSGHSTKKQLLAYIATMQPKPkkILVNHGDNGKTAEFARLVRQRFNIESY 628
                                   789*******************************99999**************888888866 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 !   45.4   0.0   2.4e-15   6.1e-12       2     149 ..     198     341 ..     197     369 .. 0.75

  Alignments for each domain:
  == domain 1  score: 45.4 bits;  conditional E-value: 2.4e-15
                 Lactamase_B_6   2 LeldnvkiLlDvGwdeskvslesalkelekvi........ptvdliLLshatlehlGayallyakfksklllnipvyatlp 74 
                                   ++  n k+L+D+G+ +   +++   ++   ++        +++d+++L+ha l+h G ++ll++     ++ + pvy t+p
  gi|13541495|ref|NP_111183.1| 198 VSTKNSKVLIDCGMMNVGPDAD--PWDAAPYLyvpevqplSSIDAVILTHAHLDHSGLLPLLFK-----YGYDGPVYMTQP 271
                                   667799*******997754432..222222212223333399***************7776653.....67899******* PP

                 Lactamase_B_6  75 vvkLGrvslldlyaskgllgpedseeleledideafdkiktlkYsQklelkskldgltitaynaGhtlGGtiWki 149
                                   +  L+ ++  d+++ ++++g +     e + i+e  ++ +tl+Y  +++++    ++ +t ynaGh lG +  ++
  gi|13541495|ref|NP_111183.1| 272 TRDLAVLLQDDYIKVARMEGGKV--PYESKYIREELKHTITLRYGETTDITR---DMRLTFYNAGHILGSASVHL 341
                                   *****888888888888887543..3466789999*************9995...799***********886544 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 !   26.8   0.0   1.2e-09   3.2e-06       3      68 ..     205     274 ..     203     400 .. 0.73

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 1.2e-09
                                   EEES--TTHHHH......HTCGG.S--SSS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHH CS
                 Lactamase_B_2   3 iLiDagpdlrqq......alral.qPvelrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvla 68 
                                   +LiD+g   +++      a+++l  P   ++ l++idaV+lthaH DH  gll l   ++ + p+y ++ +++
  gi|13541495|ref|NP_111183.1| 205 VLIDCGMMNVGPdadpwdAAPYLyVP--EVQPLSSIDAVILTHAHLDHS-GLLPLLFKYGYDGPVYMTQPTRD 274
                                   78999888666665456666666445..5677789**************.88777775555678998877766 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 ?   13.7   0.0   1.6e-05     0.042       6      52 ..     192     253 ..     190     310 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.6e-05
                 Lactamase_B_3   6 ghnsflletagarilvDPfkanlgyeppa...............eeaDlvlisqaledHahl 52 
                                   g ++ l++t++ ++l+D +  n+g ++++                ++D+v++++a+ dH  l
  gi|13541495|ref|NP_111183.1| 192 GRSATLVSTKNSKVLIDCGMMNVGPDADPwdaapylyvpevqplSSIDAVILTHAHLDHSGL 253
                                   77889999999999999986666555544577778888888888***************765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (639 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       671  (0.0374254); expected 358.6 (0.02)
Passed bias filter:                      605  (0.0337442); 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: 0.70u 0.34s 00:00:01.04 Elapsed: 00:00:00.66
# Mc/sec: 2906.11
//
Query:       gi|13541496|ref|NP_111184.1|  [L=561]
Description: hypothetical protein TVN0665 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (561 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1005  (0.0560544); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); 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):               0  [number of targets reported over threshold]
# CPU time: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.48
# Mc/sec: 3514.20
//
Query:       gi|13541497|ref|NP_111185.1|  [L=223]
Description: translaldolase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-61  208.5   0.6    3.1e-61  207.3   0.6    1.5  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 !  207.3   0.6   1.7e-65   3.1e-61       1     244 [.       3     207 ..       3     219 .. 0.95

  Alignments for each domain:
  == domain 1  score: 207.3 bits;  conditional E-value: 1.7e-65
                                   EEEE---HHHHHHHHHTT---EEE--HHHHHH..TTS.-HHHHHHHHHHH........................H-S-EEE CS
                       TAL_FSA   1 lvlDtadrelikklleekgiqgvTtNPsliekaikykalydeaieeikkegkkvkeaydkLavedilealdllgadgrvsl 81 
                                   ++lDta++++ik+ ++ + ++gvTtNP+li+k++ +++ y e i+ei k+                      +  dg+vs+
  gi|13541497|ref|NP_111185.1|   3 IFLDTANISEIKEGIDLGLVDGVTTNPTLISKEAGGSKKYAEIIKEILKI----------------------V--DGPVSV 59 
                                   79***********************************9999999999988......................6..****** PP

                                   E-S-...-SHHHHHHHHHHHHTT-T..TEEEEEESSHHHHHHHHHHHHTT--EEEEEE-SHHHHHHHHHHT-SEEEEBHHH CS
                       TAL_FSA  82 EVdarlsddteatieeArrlialyerenvlIKiPateeGikAikeLkkeGinvnvTliFsleqalaaaeagasviSpFvgR 162
                                   EV++   ++ ++++eeAr+++al +  n ++KiP+t eG+kAi++L++e+i++n+Tl+F++ qal+aa++ga+++SpFvgR
  gi|13541497|ref|NP_111185.1|  60 EVVS---TKSDGMVEEARKIHALGD--NAVVKIPMTDEGLKAIRKLSQENIETNCTLVFNPIQALLAAKSGATYVSPFVGR 135
                                   ****...******************..****************************************************** PP

                                   HHTTT............S-HHHHHHHHHHHHHHHT-S-EEEEBS--SHHHHH..HHHT-SEEEE-HHHHHHHT--HHH... CS
                       TAL_FSA 163 iddllkkleekdklkgkddgvalvkeiynyykklgysTkvmaasfrnveeve..elagcdtvTippkllealakhgktsek 241
                                   +dd++            +dg++ + ei ++++++ ++T+++ as+rn+ +v+  + +g+d+vTip ++l+ l kh+kt+e 
  gi|13541497|ref|NP_111185.1| 136 LDDIG------------QDGMQIIDEIKTIFNNYIIKTQILVASVRNPIHVLraAIIGADVVTIPFSVLKLLIKHPKTDEG 204
                                   *****............7****************99*****************9************************555 PP

                                   ... CS
                       TAL_FSA 242 lee 244
                                   l+ 
  gi|13541497|ref|NP_111185.1| 205 LTR 207
                                   444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       496  (0.0276647); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.48
# Mc/sec: 1392.76
//
Query:       gi|13541498|ref|NP_111186.1|  [L=316]
Description: transketolase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      8e-37  126.6   0.0    1.1e-36  126.2   0.0    1.2  1  Transket_pyr     Transketolase, pyrimidine binding domain
    6.5e-31  106.8   0.1      1e-30  106.2   0.1    1.3  1  Transketolase_C  Transketolase, C-terminal domain
     0.0046   16.6   0.1      0.012   15.3   0.0    1.7  2  MoCF_biosynth    Probable molybdopterin binding domain
     0.0068   16.7   0.2       0.12   12.7   0.1    2.6  3  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 !  126.2   0.0   2.4e-40   1.1e-36       5     175 ..       6     166 ..       2     168 .. 0.96

  Alignments for each domain:
  == domain 1  score: 126.2 bits;  conditional E-value: 2.4e-40
                                   HHHHHHHHHHHHHCTTTTEEEEESSTHHHHTTCHCCHHEGGTTEGEEE--S-HHHHHHHHHHHHHHCTTEEEEEEEEHHHH CS
                  Transket_pyr   5 wrkaeaealaellkedpevvligaDvaggtfsvrkgllhdqgegrvidsgisEqavlgfavGaalagpllviveaqFgdFa 85 
                                    r+ +++ l el+++dp++v+++aD++ +t +  +++++++   r++++gisEq ++++a+G+a++g  +++++ +F+ F+
  gi|13541498|ref|NP_111186.1|   6 LRDTYGKELVELGRKDPDIVVLDADLSSSTKTGYFAKEFPE---RFFNMGISEQSMVTTAAGLAISG--KKPFVSTFAIFL 81 
                                   688999***********************************...***********************..9*********** PP

                                   GGGHHGGHHHHHCHHHHHT--EE.EEESBSGGGSTTGTTTSBSSHHHHHHTSTTEEEE--SSHHHHHHHHHHHHHSSS.SE CS
                  Transket_pyr  86 ngAqiyadqairsgeakgklkvg.vvtrlpigvgedGpehqsaeleaflrlipglkvvrPsdpaetkhllrrairredrkP 165
                                   +    +++++ir+      ++v  vvt+ +i vgedG++hq +e++ ++  +p+++v++Psd +etk ++    +   ++P
  gi|13541498|ref|NP_111186.1|  82 M----RTYEQIRQSICYNDVPVRfVVTHGGITVGEDGATHQIVEDVGIMSGLPNMSVIVPSDSVETKSVIDYLEN--IKHP 156
                                   *....****************************************************************998877..557* PP

                                   EEEEE-SSEE CS
                  Transket_pyr 166 vvlrlpksll 175
                                    ++rl++++ 
  gi|13541498|ref|NP_111186.1| 157 HYVRLSREKF 166
                                   ******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 !  106.2   0.1   2.3e-34     1e-30       1     124 []     179     299 ..     179     299 .. 0.98

  Alignments for each domain:
  == domain 1  score: 106.2 bits;  conditional E-value: 2.3e-34
                                   TEEEEEETTSSEEEEEETTHHHHHHHHHHHHHTTTTCEEEEE-SEEESHHHHHHHHHHHHHSEEEEEEEEESTTSHHHHHH CS
               Transketolase_C   1 gkaeilregkdvtlvayGsmveealeAaeeLekegisaeVvdlrtvkplDketilesvkktgrlvvveeavkrgGigseva 81 
                                   g++ ++++g+d t++a G mv+ aleAa++L+++gi+ +++++++vkp+Dk+ i +++++tgr+++ ee+++  G+gs v+
  gi|13541498|ref|NP_111186.1| 179 GRGYVVKDGSDATVIANGIMVSKALEAANALKDKGIDLRIINMPSVKPIDKDIIIKAARETGRIITAEEHSIYNGLGSRVS 259
                                   6678999************************************************************************** PP

                                   HHHHHCCCTTCSSEEEEEEE-SS.SSSSGHHHHHHHTT-SHHHH CS
               Transketolase_C  82 aalaeeafdgldapvkrvggpdv.iepgsaeelekafgldaeki 124
                                   ++++e    + ++ vkr+g+ d+ +++g+a el  +f +d+++i
  gi|13541498|ref|NP_111186.1| 260 EVVSE----NYPVIVKRIGMRDTfGKSGKAMELFSYFHMDVKDI 299
                                   *****....99*****************************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 ?   -2.9   0.0       1.1   4.8e+03      88     115 ..      43      70 ..      38      80 .. 0.73
   2 !   15.3   0.0   2.7e-06     0.012      44     125 ..      86     223 ..      83     232 .. 0.70

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.1
                                   HHHHHHHHHHHHHCCTTSHGGGGGGE.E CS
                 MoCF_biosynth  88 gfeeafrrvslkpgkpvgvapgailsra 115
                                   +f+e f  ++  +++ v++a+g  +s++
  gi|13541498|ref|NP_111186.1|  43 EFPERFFNMGISEQSMVTTAAGLAISGK 70 
                                   6777777888888888888888888765 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 2.7e-06
                                   HHHHHHHHHHHHTSSEEEEESS-SSSTT--HHHHHHHHHSE.E-HHHHHHHHHHHHHHCC..................... CS
                 MoCF_biosynth  44 eeikeallaaleeadviittGGtGptpdDvtpealaklfek.elegfeeafrrvslkpgk..................... 102
                                   e+i+++++ +   +++++t GG+ +++d  t++++++++ +  l+ +++++   s + ++                     
  gi|13541498|ref|NP_111186.1|  86 EQIRQSICYNDVPVRFVVTHGGITVGEDGATHQIVEDVGIMsGLPNMSVIVPSDSVETKSvidylenikhphyvrlsrekf 166
                                   78888887775556***********************98651577777777766666555777777777777777777777 PP

                                   .......................TTSHGGGGGGE.EE...........TTEEEEE-S CS
                 MoCF_biosynth 103 .......................pvgvapgailsrav...........gktiigLPG 125
                                                           +++a g+++s+a            +  ii++P 
  gi|13541498|ref|NP_111186.1| 167 pvindlsyefkigrgyvvkdgsdATVIANGIMVSKALeaanalkdkgiDLRIINMPS 223
                                   777777777777777777777776666666666666566666655433333666665 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 ?    0.8   0.0      0.14   6.1e+02      44      89 ..      13      59 ..       6      72 .. 0.72
   2 ?   -2.7   0.0       1.7   7.6e+03      72      95 ..      86     108 ..      83     112 .. 0.69
   3 !   12.7   0.1   2.7e-05      0.12       2      79 ..     189     266 ..     188     283 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.14
                                  HHHHHSTT-SEEEEEE-S--TT-G.-HHHHHHHHHTGGGTSEEEEEE CS
                       PFOR_II 44 elkellkkvkkvvvldrnisfgse.Gqlveevkaalkkskvkvvnfv 89
                                  el el +k   +vvld + s +++ G  ++e  +   +  ++  ++v
  gi|13541498|ref|NP_111186.1| 13 ELVELGRKDPDIVVLDADLSSSTKtGYFAKEFPERFFNMGISEQSMV 59
                                  6777778888999*****99888899999998777766633333333 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.7
                                   HHHHHHTGGGTSEEEEEE--GGG- CS
                       PFOR_II  72 eevkaalkkskvkvvnfvaglgGr 95 
                                   e ++++++ +   +v+fv  +gG 
  gi|13541498|ref|NP_111186.1|  86 EQIRQSICYN-DVPVRFVVTHGGI 108
                                   6677776555.5778888888885 PP

  == domain 3  score: 12.7 bits;  conditional E-value: 2.7e-05
                                   SEEEEE-STHHHHHHHHHHHHHHTT--EEEEEES--BS--HHHHHHHSTT-SEEEEEE-S--TT-G-HHHHHHHHHTG CS
                       PFOR_II   2 evvivamGsvagtaksavdelReegikvGllrlrtlrPFPeeelkellkkvkkvvvldrnisfgseGqlveevkaalk 79 
                                   +  ++a G+++++a +a+++l+++gi++ ++ + ++ P  ++ + ++++++ ++++ +    +   G  v+ev +  +
  gi|13541498|ref|NP_111186.1| 189 DATVIANGIMVSKALEAANALKDKGIDLRIINMPSVKPIDKDIIIKAARETGRIITAEEHSIYNGLGSRVSEVVSENY 266
                                   6789*****************************************************999977777888888877655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (316 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       548  (0.030565); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); 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: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 2102.61
//
Query:       gi|13541499|ref|NP_111187.1|  [L=273]
Description: transketolase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-54  185.0   0.0    2.6e-54  184.4   0.0    1.2  1  Transketolase_N  Transketolase, thiamine diphosphate binding 
    4.6e-10   39.2   0.3    2.7e-06   26.8   0.1    2.9  2  DXP_synthase_N   1-deoxy-D-xylulose-5-phosphate synthase
    1.5e-07   30.6   0.1    2.1e-07   30.1   0.1    1.2  1  XFP_N            XFP N-terminal domain
    2.6e-07   30.5   0.4    4.2e-06   26.6   0.4    2.1  1  TPP_enzyme_C     Thiamine pyrophosphate enzyme, C-terminal TP
  ------ inclusion threshold ------
      0.018   14.0   0.0      0.024   13.6   0.0    1.2  1  E1_dh            Dehydrogenase E1 component
       0.13   11.9   0.2         14    5.3   0.1    2.2  2  GrpE             GrpE


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 !  184.4   0.0   8.8e-58   2.6e-54       8     268 ..      14     261 ..       9     272 .. 0.92

  Alignments for each domain:
  == domain 1  score: 184.4 bits;  conditional E-value: 8.8e-58
                                   HHHHHHHHHHHHHT-S--HHHHHHHHHHHHHHHHT--B-TTBTT-TTS-EEEESSGGGHHHHHHHHHHTTSS--HHHHTTT CS
               Transketolase_N   8 aiRvLavDavekaksGhPGaplgladiaevlfkkllkhnPndpkwidRDRfvLsnGhaslllYsllhLtGydlsledlksf 88 
                                    iR   + +v +a+sGhPG +l++ di +vl+ k ++ +Pn+pk  +RDR +Ls Ghas  lY+ l + G+ ++++dl  f
  gi|13541499|ref|NP_111187.1|  14 KIRREIIRMVYNAQSGHPGGSLSVTDILTVLYFKEMNIDPNKPKDPKRDRLILSKGHASPALYATLAIRGF-FPVSDLSGF 93 
                                   56777788999************************************************************.89******* PP

                                   TSTT-SS-SS--TTTSTT--S---STTHHHHHHHHHHHHHHHHHHHH-BTTB-S----EEEEEEHHHHHSHHHHHHHHHHH CS
               Transketolase_N  89 rqlgsktpGhPelghtagvevttGPLGqGianavglalaektlaatynkpgfdivdhytyvilgDgclmeGvsseasslag 169
                                   r+l+s+  Gh   ++ +gvev tG LGqG+   vg+ala +    +y           +yvilgDg ++eG   e+     
  gi|13541499|ref|NP_111187.1|  94 RKLDSHLEGHVT-REVPGVEVSTGSLGQGLGIGVGMALAGRLDGMQYR----------VYVILGDGEMEEGNVWESLMAGY 163
                                   **********98.99************************998877776..........9****************987777 PP

                                   HTT-TTEEEEEEESSEETTEEGGG.T--S-HHHHHHHTT-EEEEETTTT-HHHHHHHHHHHHH-TTS-EEEEEE--TTTTS CS
               Transketolase_N 170 tlkLgkLivlyDdnkisidGetei.sftedvakrfeaygWhvievedgedveaikaaieeakaekdkPsliklrtviGygs 249
                                   + +L+++ ++ D+n i +dG t+  +  +d+++  e++gW+vie  dg++  +i++a++++k++ d+P++i  +tv G g 
  gi|13541499|ref|NP_111187.1| 164 KYNLNNITAILDKNGIQLDGYTKDiMPMHDIKSMVESFGWNVIE-IDGHNYDQIHEAVQASKNS-DRPTFIIANTVKGKGV 242
                                   89******************997615689**************9.9************999988.**************** PP

                                   TTTTTSGGGTSS---HHHH CS
               Transketolase_N 250 pakagtedvhGapLgedev 268
                                      +++ + hG+p + +e+
  gi|13541499|ref|NP_111187.1| 243 DFMENNPKYHGSPPESKEL 261
                                   *************888876 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 !   26.8   0.1   8.9e-10   2.7e-06      14     172 ..       4     178 ..       1     185 [. 0.76
   2 !    8.7   0.0   0.00029      0.87     231     270 ..     195     233 ..     180     236 .. 0.81

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 8.9e-10
                DXP_synthase_N  14 skeeleelaeelrefliesv.sktggHlasnLgvveLtlalh.yvf........dtpkDklvwDvgHqa.YvhKiltgRk. 82 
                                   ++ +l+++a ++r+++i++v ++++gH + +L+v ++   l+ +          d ++D+l+   gH +   +  l+ R  
  gi|13541499|ref|NP_111187.1|   4 TQIDLSDIALKIRREIIRMVyNAQSGHPGGSLSVTDILTVLYfKEMnidpnkpkDPKRDRLILSKGHASpALYATLAIRGf 84 
                                   567899************995779***********976666523331222111145679********98423556666643 PP

                DXP_synthase_N  83 ...dkfktlrqkgG.lsgfpkrsEseyDafeagHsstsisaalGlavardlkgekkkvvaviGDgaltgGmafealnnige 159
                                      ++++  r+ +  l g+ +r E +   +++g  +  + +++G+a a +l+g +++v  ++GDg +  G  +e+l    +
  gi|13541499|ref|NP_111187.1|  85 fpvSDLSGFRKLDShLEGHVTR-EVPGVEVSTGSLGQGLGIGVGMALAGRLDGMQYRVYVILGDGEMEEGNVWESLMAGYK 164
                                   3447889999876527777665.677778899999****************************************987655 PP

                DXP_synthase_N 160 l.kkkllvilNdNe 172
                                      +++  il  N 
  gi|13541499|ref|NP_111187.1| 165 YnLNNITAILDKNG 178
                                   41567778888776 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00029
                DXP_synthase_N 231 gtlfeelgfkYlGpidGhdleelikvleevkklkgpvllh 270
                                   +++ e++g + +  idGh+++++ ++++  k+ ++p+++ 
  gi|13541499|ref|NP_111187.1| 195 KSMVESFGWNVI-EIDGHNYDQIHEAVQASKNSDRPTFII 233
                                   567888888877.6**********************9985 PP

>> XFP_N  XFP N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   0.1   7.1e-11   2.1e-07     124     245 ..     100     221 ..      84     250 .. 0.85

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 7.1e-11
                         XFP_N 124 ipshvaaetPGsiheGGelGyalshayGav....ldnPdlivacvvGdGeaetGPlatswhsnkflnPaedGavlPileln 200
                                   +  hv+ e+PG     G lG  l   +G +    ld  +  v  ++GdGe e G +  s  +    n      +  il+ n
  gi|13541499|ref|NP_111187.1| 100 LEGHVTREVPGVEVSTGSLGQGLGIGVGMAlagrLDGMQYRVYVILGDGEMEEGNVWESLMAGYKYN---LNNITAILDKN 177
                                   578*********99999999999888886522336899999*************9876666654444...45678899*** PP

                         XFP_N 201 GykisnptilarisdeelkklfeGlGyepafvededteslhklla 245
                                   G ++   t    ++ +++k++ e +G+++  ++++++ ++h+++ 
  gi|13541499|ref|NP_111187.1| 178 GIQLDGYT-KDIMPMHDIKSMVESFGWNVIEIDGHNYDQIHEAVQ 221
                                   ***99887.57899**************************99765 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 !   26.6   0.4   1.4e-09   4.2e-06      26     152 ..     114     233 ..     102     234 .. 0.79

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 1.4e-09
                                   TTS-TTTHHHHHHHHHHH...ST.TSEEEEEEEHHHHHHT..GGGHHHHHHTT-SEEEEEEE-SBCCCHHHHHHHHTCCTT CS
                  TPP_enzyme_C  26 glgtmGyglpaAiGakla...kp.drevvaivGDGgflmi..lqelatavrrnlpitvvvlnNegygmtggqqepfggkrk 100
                                    +g++G gl++++G++la   +  + +v++i GDG +      + l+   ++nl+ ++ +l+ +g ++ g  ++       
  gi|13541499|ref|NP_111187.1| 114 STGSLGQGLGIGVGMALAgrlDGmQYRVYVILGDGEMEEGnvWESLMAGYKYNLNNITAILDKNGIQLDGYTKD------- 187
                                   57999************644432357**********86443589999999****66666666665533333222....... PP

                                   TTSBB.BS----HHHHHHHTTSEEEEESSH.HHHHHHHHHHHHCSSSEEEEE CS
                  TPP_enzyme_C 101 sgpagkdlkpvdfaklaealGakgarvekadveeleealkealekkgpalie 152
                                         + +  d+  ++e++G +++ ++ ++ ++++ea+++  ++++p++i 
  gi|13541499|ref|NP_111187.1| 188 ------IMPMHDIKSMVESFGWNVIEIDGHNYDQIHEAVQASKNSDRPTFII 233
                                   ......245569**************************************96 PP

>> E1_dh  Dehydrogenase E1 component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   7.9e-06     0.024      95     204 ..     110     220 ..      78     233 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 7.9e-06
                                   .BEEE-SSTTTHHHHHHHHHHHHHHHTS---EEEEEEGGGTT-HHHHHHHHHHHHTT--EEEEE.EEESEETTEEHHHH-S CS
                         E1_dh  95 rilggngivgaqvplvaGialaakiegkkevailliGDgAanqGdvyealnlaalwklpvifvv.eNNkygisTeaekasa 174
                                    +    g +g    ++ G+ala++ +g +  + ++ GDg   +G+v+e+l     ++l  i  +   N++ +   ++    
  gi|13541499|ref|NP_111187.1| 110 GVEVSTGSLGQGLGIGVGMALAGRLDGMQYRVYVILGDGEMEEGNVWESLMAGYKYNLNNITAIlDKNGIQLDGYTKDIMP 190
                                   45555566666667999********************************97777777766654415566666555555555 PP

                                   ---GGG..TTTTS-EEEEETTSHHHHHHHH CS
                         E1_dh 175 skeladrargvgipglrVdgnDplavyeAv 204
                                   + ++      +g   +++dg     ++eAv
  gi|13541499|ref|NP_111187.1| 191 MHDIKSMVESFGWNVIEIDGHNYDQIHEAV 220
                                   555555555666666666666655555555 PP

>> GrpE  GrpE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0    0.0076        23      88     112 ..     156     180 ..     142     183 .. 0.81
   2 ?    5.3   0.1    0.0048        14     100     138 ..     192     229 ..     182     239 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.0076
                                   HHHHHHHHHHHHHHHHHHHHHTT-E CS
                          GrpE  88 ekslleGvemtlkqllkiLekhgve 112
                                    +sl+ G++ +l+++  iL+k+g++
  gi|13541499|ref|NP_111187.1| 156 WESLMAGYKYNLNNITAILDKNGIQ 180
                                   4589999999999999999999997 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0048
                                   HHHHHHHHHTT-EE---TTSB--TTTEEEEEEECSSC.. CS
                          GrpE 100 kqllkiLekhgvekiepkgepFDpnlheavstveddeke 138
                                     ++++ e++g ++ie  g  +D ++heav+  ++++ +
  gi|13541499|ref|NP_111187.1| 192 HDIKSMVESFGWNVIEIDGHNYD-QIHEAVQASKNSDRP 229
                                   568999****************9.69******9999844 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       353  (0.0196888); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 1703.55
//
Query:       gi|13541500|ref|NP_111188.1|  [L=288]
Description: dihydrodipicolinate synthase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-38  132.1   0.0      2e-38  131.8   0.0    1.0  1  DHDPS     Dihydrodipicolinate synthetase family


Domain annotation for each model (and alignments):
>> DHDPS  Dihydrodipicolinate synthetase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.8   0.0   1.1e-42     2e-38       6     281 ..       5     272 ..       2     278 .. 0.88

  Alignments for each domain:
  == domain 1  score: 131.8 bits;  conditional E-value: 1.1e-42
                                   EEE----B-TTSSB-HHHHHHHHHHHHHCT-SEEEESSCCCTGGGS-HHHHHHHHHHHHHHHTTSSEEEEE---SSHHHHH CS
                         DHDPS   6 italvtpfdedgkldkealrklieflinkgvdglvvaGttGEsatlsteekeqlveiaveaakgripviagvGsnstseai 86 
                                   i+++vtpf+ +gk+d e+  +    l+  gv+ +++ GttG  ++ls++e+++l++   ++a+     i +vGs +++++i
  gi|13541500|ref|NP_111188.1|   5 IVPVVTPFK-EGKIDGEKFIHHCMSLLSVGVNYVFISGTTGLGPSLSINERMDLIKLSSNFADK---AIMQVGSMNLEDSI 81 
                                   789*****7.6***************************************************96...579*********** PP

                                   HHHHCCCCCT-SEEEEE---SS---HHH.HHHHHHHHHHCHSS-EEEEE-HHHHSHHHHHHHHHHHHT.STTEEEEEE-SS CS
                         DHDPS  87 klakkaeeaGadgvlavtPYYnkpsqeg.lyqhfkaiieatdlpvilYnvpsrtgadlspetvkrLae.lenivgvKeavg 165
                                   kla+ a+e G+ g++a++PYY    +e+ l++++ +i +    p+ +Yn p+ tg d++     ++ +   ni+gvK+++ 
  gi|13541500|ref|NP_111188.1|  82 KLARMAKENGIYGISALPPYYFGGIPEEwLIKYYVEISKII--PTFIYNYPKFTGYDINSSLAIKINKaGGNIIGVKDTIA 160
                                   *********************9887666499******9888..******************9999999789********** PP

                                   -CTHHHHHHCCCSTTSEEEES-GGGHHHHHHTT-SEEEESCHHCHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHCCCC CS
                         DHDPS 166 dleevikikkevgkdlviysGddelllsalslGadGvisvtsniagermrqlikalkeGdlaeaaelnekllplikilfae 246
                                   d++++   +   g+d++i+sG  + + +al  G+dG ++++ n++++   +l ++ ++    + +++ + +l + +++ + 
  gi|13541500|ref|NP_111188.1| 161 DISHMLSYRDL-GNDFIILSGPSNSIYEALRSGVDGSVAAAGNFMPKTFIELADKFEAEASFKLQKYINSVLSIANEYGSW 240
                                   **999999887.********************************************9977777788888888888888777 PP

                                   .SCCHHHHHHHHCTTSSSBB.--TTS--S-HHHHHH CS
                         DHDPS 247 .pnvilvktalellGlvveatlrkPltpleeeekee 281
                                      ++l+k   ++   ++    r P+ pl+   +e+
  gi|13541500|ref|NP_111188.1| 241 sAYYSLIKILRRYSAGDS----RAPFYPLNALDEEK 272
                                   466777777666554444....44555544444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.50
# Mc/sec: 1737.40
//
Query:       gi|13541501|ref|NP_111189.1|  [L=417]
Description: Acyl-CoA dehydrogenase [Thermoplasma volcanium GSS1]
Scores for complete 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-37  127.0   0.8    9.4e-37  126.5   0.8    1.3  1  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
      2e-24   86.4   0.0    5.9e-24   84.9   0.0    1.9  1  Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
    1.9e-20   72.8   0.1    3.8e-20   71.9   0.1    1.5  1  Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
      2e-17   63.7   0.1    2.7e-17   63.3   0.1    1.2  1  Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
  ------ inclusion threshold ------
      0.034   13.2   0.1      0.061   12.4   0.1    1.3  1  HpaB           4-hydroxyphenylacetate 3-hydroxylase C termina


Domain annotation for each model (and alignments):
>> Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.5   0.8   2.6e-40   9.4e-37       1     147 [.     230     383 ..     230     386 .. 0.94

  Alignments for each domain:
  == domain 1  score: 126.5 bits;  conditional E-value: 2.6e-40
                                   TBHHHHHTTTT--S-----..-SHHHHHHHHHHHHHHHTSB-CC-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH---.. CS
                 Acyl-CoA_dh_1   1 gkGfrvametlnheRlavaaaalglarraleealeyarrrkafgkplidhqlvreklaemaaeleaarllvyraaeald.. 79 
                                   + G +v+ + +  eRl++aa++lg+  +al  a +ya +r+afg +li+h+ + +klae  + l++a +lvy+aa+a+d  
  gi|13541501|ref|NP_111189.1| 230 NGGYEVFNRMMIPERLTTAAGSLGVSTAALKVATDYALKREAFGSKLIEHEGINFKLAESLTLLQSASALVYTAAKAADly 310
                                   6799999999*****************************************************************966622 PP

                                   .-----....HHHHHHHHHHHHHHHHHHHHHHHHHHGGGTTSGGGHHHHHHHHTHHHHHSSS-HHHHHHHHHH CS
                 Acyl-CoA_dh_1  80 .agkpd....raeasmaKlfaselaqevadlamqllGgaGyleeypverlyrdarvlrigeGtseiqrniiar 147
                                    +g+ +    r+ +smaKl  +e++++++++amq++Gg Gy++ yp+erl+rd+r+  i+ G+se++++ii+ 
  gi|13541501|ref|NP_111189.1| 311 eKGQTTqsyaRKLVSMAKLHSTEAMWKIVNDAMQIMGGIGYTTVYPIERLLRDSRLGLIWTGSSEVMKMIIQH 383
                                   1555559****************************************************************86 PP

>> Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.9   0.0   1.7e-27   5.9e-24       1     112 [.       4     115 ..       4     116 .. 0.96

  Alignments for each domain:
  == domain 1  score: 84.9 bits;  conditional E-value: 1.7e-27
                                   THHHHHHHHHHHHHHHHHTHHHHHHHHHHT.SGHHHHHHHHHHTTCTSTTS-GGGTS--S-HHHHHHHHHHHHHH-HHHHH CS
                 Acyl-CoA_dh_N   1 teeqealrdtvrefaeeelaphaaewdeeg.efprelwkklaelGllgitvpeeygGagldyleaaivaeelaradaglal 80 
                                   +ee++++rd  r++++e   + ++++++e+ +fpre+++ + ++G++g+ +p+eygG g++++++a ++ee+++ +  l+ 
  gi|13541501|ref|NP_111189.1|   4 NEEEKQIRDLCRRVVKEVPHELIRKIEREEvTFPREFIDFITKNGVVGLRFPKEYGGKGASWVAEASAVEEMGYLGFTLSC 84 
                                   69***************9999******9999************************************************** PP

                                   HHHHHHHTTHHHHHHHS-HHHHHHHHHHHHTT CS
                 Acyl-CoA_dh_N  81 llgvhsslvapailrfGteeqkrryLpklasg 112
                                   ++++++ ++ ++++r+Gt eqk++yL+ + sg
  gi|13541501|ref|NP_111189.1|  85 MYSLGTIVG-EPMYRYGTNEQKEKYLKGITSG 115
                                   ****98555.89*****************999 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 !   71.9   0.1   1.1e-23   3.8e-20       3      96 ..     122     217 ..     120     218 .. 0.90

  Alignments for each domain:
  == domain 1  score: 71.9 bits;  conditional E-value: 1.1e-23
                                   E---SS-SS-GGG---EEEEETT.EEEEEEEEEEEETTTT-SEEEEEEE.TS---..----EEEEEEE..GGGEEE----- CS
                 Acyl-CoA_dh_M   3 alTEpqaGsdvasvkttaaerdggeyvlnGeKiwitnaaiatlalvlar.tekpd..rarglslflvprdapgvsvrriee 80 
                                   a+TEp++Gsd+ ++  t+a ++g++y+lnG+K++i +++ a++++++a     ++  r+rg+s f+v+rd+pg++v+ +  
  gi|13541501|ref|NP_111189.1| 122 AITEPSGGSDLFGMMKTTAVKKGNKYILNGQKRFIVGGKGADFFVTYAItD-PNAksRTRGISAFIVDRDTPGLKVETLYG 201
                                   8*********877776688888889************************53.333588*********************** PP

                                   BSS-TTS-EEEEEEE. CS
                 Acyl-CoA_dh_M  81 klGlrglptgelvfed 96 
                                    +G +g  t+++v++d
  gi|13541501|ref|NP_111189.1| 202 LMGNKGGGTARIVYKD 217
                                   *************998 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 !   63.3   0.1   7.5e-21   2.7e-17       2     128 ..     246     369 ..     245     375 .. 0.95

  Alignments for each domain:
  == domain 1  score: 63.3 bits;  conditional E-value: 7.5e-21
                                   HHHHHHHHHHHHHHHHHHHHHHHHHCTTT-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----HHHHHH CS
                 Acyl-CoA_dh_2   2 giaavalGaAraalaefvelarervrassgekladdpatqlalaeaaarldAAralleraaaraealaaagkevtvedrae 82 
                                   + aa  lG+  aal+ ++++a +r    +g kl +++ + ++lae+ + l++A al++ aa++  +l ++g+  +   r+ 
  gi|13541501|ref|NP_111189.1| 246 TTAAGSLGVSTAALKVATDYALKREA--FGSKLIEHEGINFKLAESLTLLQSASALVYTAAKA-ADLYEKGQTTQSYARKL 323
                                   678999********************..********************************999.78899999999****** PP

                                   HHHHHHHHHHHHHHHHHHHHHHCGGGGGBTT-HHHHHHHHHHHHCT CS
                 Acyl-CoA_dh_2  83 arraaalavelaiaavdalfeaaGgsalrkesplqRlwRDahaaaa 128
                                    ++a+++ +e   ++v+++++++Gg ++++ +p++Rl+RD + + +
  gi|13541501|ref|NP_111189.1| 324 VSMAKLHSTEAMWKIVNDAMQIMGGIGYTTVYPIERLLRDSRLGLI 369
                                   ****************************************997755 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 ?   12.4   0.1   1.7e-05     0.061      45     116 ..     279     352 ..     269     365 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.7e-05
                                   SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EE-TTS-..EE--HHHHHHHHHHHHHHHHHHHHHHHHHHGGGGT- CS
                          HpaB  45 fshvqeklgelialrellyalliaaeaeaekdpsGv..ylPdlllanaarvlvtrlypriveilqdiaGGglit 116
                                   + ++  kl+e ++l++   al+++a+  a   ++G       ++l  +a+++ t+++++iv+ + +i+GG+  t
  gi|13541501|ref|NP_111189.1| 279 HEGINFKLAESLTLLQSASALVYTAAKAADLYEKGQttQSYARKLVSMAKLHSTEAMWKIVNDAMQIMGGIGYT 352
                                   667888************************99999733556789**************************8665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (417 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       572  (0.0319036); expected 358.6 (0.02)
Passed bias filter:                      507  (0.0282782); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 2603.08
//
Query:       gi|13541502|ref|NP_111190.1|  [L=518]
Description: Acyl-CoA synthetase (AMP-forming) [Thermoplasma volcanium GSS1]
Scores for 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-66  224.4   0.0    2.4e-66  224.1   0.0    1.0  1  AMP-binding    AMP-binding enzyme
      9e-10   39.4   0.0    1.5e-09   38.7   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 !  224.1   0.0   2.7e-70   2.4e-66      17     422 ..      26     416 ..      13     417 .. 0.85

  Alignments for each domain:
  == domain 1  score: 224.1 bits;  conditional E-value: 2.7e-70
                                   CCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEETTS-HHHHHHHHHHHTESE CS
                   AMP-binding  17 sgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvplnptltaeelayiledseakv 97 
                                   +++++++TY+el e + rlA+gL s ++  g+r+a+l +ns+e+ +al++i  aG  + p+n +l+ e+++  ++ ++ ++
  gi|13541502|ref|NP_111190.1|  26 TEGQRKITYKELFEDSVRLANGLSSCDLS-GKRIAVLDWNSIEYAIALYGIPFAGSSIHPINVRLPLEQISRTIKTARDEA 105
                                   34899*******************97886.899************************************************ PP

                                   EEETCTCCC..HHHHHHHHSCC.-EECEEEEESCCS-HCCHCCCHCCCCSCTTS-TSCCCS-BTTSEEEEEEE--SSSS-E CS
                   AMP-binding  98 liatvdsel..leklleaaakl.eavklvivldadellkeeelkeeeeseekaekpeeeeelkpddlayiiYTSGTTGkPK 175
                                   li  v+++   +++ l++a+ l +++  +i +++d++++ e+l ++ e+         +++ ++d+ + i++TSGTTG+PK
  gi|13541502|ref|NP_111190.1| 106 LI--VSKDFlpIAEKLAEAGLLsKKKIFTINVSSDDFSRFEDLIDDGEEV-------FTPKFDEDTEMSILFTSGTTGMPK 177
                                   **..4444324444444444331444445556666777666666655333.......233789****************** PP

                                   EEEEEHHHHHHHHHHHH..HHHC...SCCTTT-EEEESS-TTSCHHHHHHHHHHHHTT-EEEE-TTCGCCHHHHHHHHHHH CS
                   AMP-binding 176 GVmlshrnlvanvaslk..letr...fklkeddvvlsilplahifglilelllallsGatvvllpkdaaldpkllleliek 251
                                   +V ++hr +v++++++   l+ +    +l+++d+v+   p++hi ++  +l+++ + G + +l  k+++ +    l+li+ 
  gi|13541502|ref|NP_111190.1| 178 AVSYTHRKTVTAIWAILtsLSAYqglARLNSGDTVFPLIPFYHIWSW-GSLFISTMIGTKYILGGKFDPIS---TLKLIKS 254
                                   ************9999887555544444666****************.***************99999844...48***** PP

                                   HT-SEEEEEHHHHHHHHHCCCHHCHHHHCCGTT-SEEEEESS-EBHHHHHHHHHHHTCEEEEEEEEGGGSSEC..EE.... CS
                   AMP-binding 252 lkvtviagvPrvleallesgalkaakkakdlsslrlvllggeplspellrffralfgeevlegYGlTEttgvv..tv.... 326
                                   +k+t ++ vP++l all++++++       ls++++ l+gg+p++  l++++r++ +e +  +YG T  +++   t+    
  gi|13541502|ref|NP_111190.1| 255 EKATWMNMVPTMLYALLANDNES------VLSGMKI-LIGGSPIPNGLVEEARKRKIE-LTSIYGFTDGLIASigTIneay 327
                                   ******************87777......9999**9.68****************876.************9976447888 PP

                                   ..CHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEEEEEEEETTS-SEBTT-HHHHHHHEEETCCEEEEEEEEEEE CS
                   AMP-binding 327 ..lpleedkkklgsvGkplpgvevkivDeetgepvpdgeeGellvrgpgvmkgYlkkpeataeafdsegrwlrTGDlgrld 405
                                     +++e++ +   ++ +p p +e+kiv  + g p       e+++r+p++  gY  ++ +t+ a++ e +w+r GD g++d
  gi|13541502|ref|NP_111190.1| 328 gkIEDERKYEISTKYSTPSPLAELKIVKAD-GAPP------EIFFRSPWLPDGYVSDETETKNAYV-E-GWFRPGDSGHID 399
                                   9867677777778889************98.5555......************************9.6.7*********** PP

                                   TTSEEEEEEECCCEEEE CS
                   AMP-binding 406 edGyleivgRkkdlikl 422
                                   e G+l i +R kdlik+
  gi|13541502|ref|NP_111190.1| 400 EMGNLCIDDRVKDLIKS 416
                                   ***************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 !   38.7   0.0   1.7e-13   1.5e-09       2      76 .]     426     505 ..     425     505 .. 0.81

  Alignments for each domain:
  == domain 1  score: 38.7 bits;  conditional E-value: 1.7e-13
                                   HHHHHHSSTTEEEEEEE-----TTS---EEEEEE------HHHHHHHHHHH.....HT-TTTS-SEEEE-S---B-TTS- CS
                 AMP-binding_C   2 vEsalvshpaVaeaaVvGvpdevkGealvafVvlkdgsealeeeLkahvrk.....elgpyavpkkvvfvdelpktrsGK 76 
                                   +Es ++ +p+V+ +aVv  +d+++ e++vafV  +++ + l +++k+   +     ++ +++ p++++ +d +p+t +GK
  gi|13541502|ref|NP_111190.1| 426 LESYISGVPGVEMVAVVPRKDDKWVERPVAFVKSNKDFDNLVRNIKDLFDSlvksgKISSWWIPDEFYRIDNMPLTGTGK 505
                                   699******************************95553333344444442233356***********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (518 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       447  (0.0249317); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); 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 0.25s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 3587.30
//
Query:       gi|13541503|ref|NP_111191.1|  [L=191]
Description: hypothetical protein TVN0672 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.061   12.0   2.0       0.08   11.7   2.0    1.2  1  Clostridium_P47  Clostridium P-47 protein


Domain annotation for each model (and alignments):
>> Clostridium_P47  Clostridium P-47 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   2.0   4.5e-06      0.08     343     409 ..      83     144 ..      57     157 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4.5e-06
               Clostridium_P47 343 eqtlaYevvreasaqhrthvatwviitevilgvivavigsvagavggkvkslvdkiiiaiivaiiag 409
                                   ++tl+Y vv++ s+++   +  +v  +++++  +v+ + sv g++    + +   ii+++i++i++ 
  gi|13541503|ref|NP_111191.1|  83 QETLTYIVVKKRSKRYAFYIGLGVSAVNIVV--LVLSLVSVIGKI---TQFVYLLIILNVITSILFH 144
                                   689***************9999999988875..666777999999...8888899*********985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1004  (0.0559987); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 1258.36
//
Query:       gi|13541504|ref|NP_111192.1|  [L=122]
Description: hypothetical protein TVN0673 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-36  125.7   2.5    1.2e-36  125.5   2.5    1.0  1  YbjQ_1    Putative heavy-metal-binding
  ------ inclusion threshold ------
      0.037   14.4   0.3       0.31   11.4   0.1    2.1  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 !  125.5   2.5   1.3e-40   1.2e-36       1     104 []       7     109 ..       7     109 .. 0.99

  Alignments for each domain:
  == domain 1  score: 125.5 bits;  conditional E-value: 1.3e-40
                        YbjQ_1   1 mivtttesiegkeivevlgivtgetvrsrnvlkdilaglrslvGGelkayeeeleeareeAlerlkeeAeelGAnAvvgvr 81 
                                   +i++tt++i+gk+i++++g+++g tvrsr ++ +i+aglrsl+GGe+k+y+++l+++r++A+erl++ Ae++GAnAv+ +r
  gi|13541504|ref|NP_111192.1|   7 IIMVTTNYIPGKKITRIIGTIWGITVRSRGLGGNIVAGLRSLAGGEIKEYSKMLSDTRNTAMERLRDAAEQVGANAVIELR 87 
                                   699****************************************************************************** PP

                        YbjQ_1  82 ldtseigekgmlevlayGTAVkv 104
                                   +d+s+ig+  m+e++ayGTAV+v
  gi|13541504|ref|NP_111192.1|  88 FDSSDIGQ-VMTEIVAYGTAVVV 109
                                   ******99.************96 PP

>> DUF4156  Domain of unknown function (DUF4156)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0     0.029   2.6e+02      57      75 ..      34      52 ..      12      66 .. 0.77
   2 ?   11.4   0.1   3.4e-05      0.31      43      68 ..      61      86 ..      48     108 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.029
                       DUF4156 57 AaalGgntivlvtstatet 75
                                     lGgn + ++ s a+ +
  gi|13541504|ref|NP_111192.1| 34 SRGLGGNIVAGLRSLAGGE 52
                                  5679*****9999886655 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 3.4e-05
                       DUF4156 43 kelvrgaandLrneAaalGgntivlv 68
                                  ++   +a++ Lr+ A+++G+n ++ +
  gi|13541504|ref|NP_111192.1| 61 SDTRNTAMERLRDAAEQVGANAVIEL 86
                                  556678999************99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       613  (0.0341904); expected 358.6 (0.02)
Passed bias filter:                      496  (0.0276647); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 773.12
//
Query:       gi|13541505|ref|NP_111193.1|  [L=506]
Description: MutS-like ATPase involved in mismatch repair, partial [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      3e-22   79.6   0.0    5.4e-22   78.7   0.0    1.4  1  MutS_V     MutS domain V
     0.0038   17.2   0.4        2.9    7.9   0.0    3.3  3  Mor        Mor transcription activator family
     0.0087   16.6   1.6      0.025   15.1   0.1    2.2  2  AAA_23     AAA domain
  ------ inclusion threshold ------
       0.01   15.6   0.2        0.8    9.4   0.0    2.3  2  IstB_IS21  IstB-like ATP binding protein
      0.036   14.6   1.3       0.45   11.0   0.7    2.5  2  DUF2779    Domain of unknown function(DUF2779)
      0.041   14.4   0.0        2.4    8.7   0.0    2.5  2  AAA_18     AAA domain
      0.044   13.8   0.5       0.18   11.8   0.1    2.3  2  AAA_14     AAA domain
      0.076   12.6   0.0       0.16   11.5   0.0    1.5  1  AAA_27     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 !   78.7   0.0   2.4e-25   5.4e-22       1     137 [.     329     464 ..     329     503 .. 0.93

  Alignments for each domain:
  == domain 1  score: 78.7 bits;  conditional E-value: 2.4e-25
                                   EEEE-STTSSHHHHHHHHHHHHHHHHHT--BSSSEEEEE--SEEEEEE--------SS-HHHHHHHHHHHHHTT--TTSEE CS
                        MutS_V   1 llitGpnmaGkstylrqvalivllaqiGsfvpaekaeisivdkiftRvgasDdlakgkstFmvEmlEtasilknatekslv 81 
                                   +++tGpn +Gk t+ r+++ +  la +G  +p +ka++  vd+i+t    s+dl++ +     ++  + +il++ate+sl+
  gi|13541505|ref|NP_111193.1| 329 IVVTGPNSGGKTTFARSIGQVFFLAMLGLPIPGSKAKLFQVDNIYTHFEKSEDLENLRGKLEDDLIRMRKILDSATERSLI 409
                                   589****************************************************************************** PP

                                   EEESTS-SS-HHHHHHHHHHHHHHHHHTT--EEEEEES-GGGGGHHHHSTTEEEEE CS
                        MutS_V  82 ilDElGRGtstydGlaialavaeyllekikaktlfatHyheltklaekleevknlh 137
                                   i++E+   t++ d ++i + +++ + + +++ +++ t + el++++  ++ v++++
  gi|13541505|ref|NP_111193.1| 410 IINEMLSSTASKDAISIGTKIIDLINK-KNSICVYVTFFEELARIRGVISMVSQVD 464
                                   **********************97776.7899*************99988888765 PP

>> Mor  Mor transcription activator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.0    0.0013       2.9      57     105 ..      56     104 ..      47     107 .. 0.83
   2 ?    4.5   0.0     0.015        33      64      93 ..     195     226 ..     189     236 .. 0.82
   3 ?    0.4   0.0      0.28   6.2e+02      77      97 ..     488     505 ..     474     506 .] 0.74

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0013
                                   HHHHHHHHHHHHH--SS-HHHHHHHHT--HHHHHHHHHHHHH--XXXXX CS
                           Mor  57 lelelrdreifnefkGnnvaeLarkYglseqwiykiikrvrkeeiarrq 105
                                   l++ +  +eif++  +++v +L +++   +++iyk +  +++    ++q
  gi|13541505|ref|NP_111193.1|  56 LDTVKYRQEIFKDLLNSEVFALMKDFSEKMNTIYKWVSTADRLGGYQKQ 104
                                   555666789****************************999988766666 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.015
                                   HHHHHH--SS-H..HHHHHHHT--HHHHHHHH CS
                           Mor  64 reifnefkGnnv..aeLarkYglseqwiykii 93 
                                   +++f++f+++n   ++L r Y+ s++++   +
  gi|13541505|ref|NP_111193.1| 195 KKLFDKFTNRNAtsKSLKRFYETSMNQVEAAV 226
                                   689*****9987336899********997766 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.28
                                   HHHHHHT--HHHHHHHHHHHH CS
                           Mor  77 eLarkYglseqwiykiikrvr 97 
                                   ++a++Ygl++++   ii+rvr
  gi|13541505|ref|NP_111193.1| 488 AIAERYGLTYKK---IIERVR 505
                                   68999***9986...566665 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.1      0.44   9.8e+02      82     123 ..     184     217 ..     125     277 .. 0.54
   2 !   15.1   0.1   1.1e-05     0.025      16      47 ..     319     354 ..     312     450 .. 0.72

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.44
                        AAA_23  82 kdgry.trsiererelskkkgkttkkaklelleideleqfise 123
                                   ++g++ + +i  + + + ++ + t+         + l++f ++
  gi|13541505|ref|NP_111193.1| 184 DKGKDdYNEIVKKLFDKFTNRNATS---------KSLKRFYET 217
                                   1111111111112221111111111.........222222222 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 1.1e-05
                        AAA_23  16 dF....skgltlItGpNGaGKTTildAiklaLyget 47 
                                   dF    + ++ ++tGpN  GKTT+ + i  +++   
  gi|13541505|ref|NP_111193.1| 319 DFrlsrNENIIVVTGPNSGGKTTFARSIGQVFFLAM 354
                                   455566889*******************99888655 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0   0.00036       0.8      40      69 ..     318     348 ..     291     354 .. 0.72
   2 ?    3.6   0.1     0.022        50      80     145 ..     376     442 ..     364     451 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00036
                     IstB_IS21  40 tlsfiekkeniv.llGpsGvGKshlaialgv 69 
                                   ++  ++++eni+ ++Gp   GK+ +a ++g+
  gi|13541505|ref|NP_111193.1| 318 NDFRLSRNENIIvVTGPNSGGKTTFARSIGQ 348
                                   333477888875268**************97 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.022
                     IstB_IS21  80 fvrvedLveel.krarrdgklaralkrllkvdllilDdlgllpldqaeaellfeviekryerrsiii 145
                                   f + edL +   k++++  ++ ++l++ ++ +l+i+ ++   + ++++ +   ++i+   +++si +
  gi|13541505|ref|NP_111193.1| 376 FEKSEDLENLRgKLEDDLIRMRKILDSATERSLIIINEMLSSTASKDAISIGTKIIDLINKKNSICV 442
                                   555555543321334444588999***********************99999999999888888876 PP

>> DUF2779  Domain of unknown function(DUF2779)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.7    0.0002      0.45      44     116 ..     180     260 ..     157     274 .. 0.80
   2 ?    1.3   0.0       0.2   4.6e+02      59      80 ..     428     449 ..     373     472 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0002
                       DUF2779  44 flaespntdpreelieeLikiieke........gsvvvynksfEksrlkelaqlfpeykeelkqiienlvDlldlfkksly 116
                                    +++++++d  +e +++L++   ++          + +  ++ E ++l+ +a+lfpe+ ++l++++en    +d+++ ++y
  gi|13541505|ref|NP_111193.1| 180 TIRRDKGKDDYNEIVKKLFDKFTNRnatskslkRFYETSMNQVEAAVLELIARLFPEEFKALSSFYENHKNFIDPTTAQMY 260
                                   4557778899999999999999666688877765566666789*************************9999998888544 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.2
                       DUF2779  59 eeLikiiekegsvvvynksfEk 80 
                                    ++i+ i+k++s+ vy   fE+
  gi|13541505|ref|NP_111193.1| 428 TKIIDLINKKNSICVYVTFFEE 449
                                   4677888999999999999986 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0     0.064   1.4e+02      37     114 ..     199     312 ..     160     320 .. 0.74
   2 ?    8.7   0.0    0.0011       2.4       1     109 [.     329     452 ..     329     455 .. 0.59

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.064
                        AAA_18  37 lllevdpe...aldeskrldedkldklldaleenss............aleegknlvidghlaeleseaakdikk...... 96 
                                     +++ ++    l+++ +  ++++++++ +l    +             +e++kn  id   a+++ e ++ + +      
  gi|13541505|ref|NP_111193.1| 199 DKFTNRNAtskSLKRFYETSMNQVEAAVLELI---ArlfpeefkalssFYENHKN-FIDPTTAQMYRELQFYLSYieyisp 275
                                   44555555333444444444444433333333...23456777777778899999.99**********9999888999999 PP

                        AAA_18  97 ...................vvLtaspeelleRlekRg 114
                                                      +++++ +  l++Rl + g
  gi|13541505|ref|NP_111193.1| 276 lektglkfcipevgtvrdiYCIECFDLALAQRLLQSG 312
                                   9999999999999999999999999999999998866 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0011
                        AAA_18   1 IlltGtpGvGKttlakeLskrlgf........gvnlrdvakenglllevdpealdeskrldedkldklldaleenssalee 73 
                                   I++tG+   GKtt+a+ + +   f             ++++ +++++ +++   ++ + l+ +  d l++  +  + + +e
  gi|13541505|ref|NP_111193.1| 329 IVVTGPNSGGKTTFARSIGQVF-FlamlglpiPGSKAKLFQVDNIYTHFEKS--EDLENLRGKLEDDLIRMRKILD-SATE 405
                                   89***************95542.23445556633334455555555555555..2222222222222222222222.2467 PP

                        AAA_18  74 gknlvidghlaeleseaakdikk...........vvLtaspeelleR 109
                                    + ++i   l+   s +a+ i++           +++++   e l R
  gi|13541505|ref|NP_111193.1| 406 RSLIIINEMLSSTASKDAISIGTkiidlinkknsICVYVTFFEELAR 452
                                   78888888888888888888888887777777777776666555555 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1      0.67   1.5e+03      69      90 ..     197     218 ..     136     253 .. 0.68
   2 ?   11.8   0.1     8e-05      0.18       2      76 ..     326     417 ..     325     445 .. 0.60

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.67
                        AAA_14  69 flDEiqevpewekalkslvdeg 90 
                                   ++D   + +  +k lk++++++
  gi|13541505|ref|NP_111193.1| 197 LFDKFTNRNATSKSLKRFYETS 218
                                   4555555555555666655544 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 8e-05
                        AAA_14   2 rkilvitGaRrvGKTtllkqlikell.......vkkesilyinldderd..kkladpe....kllelileklke......e 63 
                                   ++i+v+tG+   GKTt+++ + +  +       ++ ++   +++d+  +  +k++d e    kl++ + ++  +       
  gi|13541505|ref|NP_111193.1| 326 ENIIVVTGPNSGGKTTFARSIGQVFFlamlglpIPGSKAKLFQVDNIYThfEKSEDLEnlrgKLEDDLIRM--RkildsaT 404
                                   689****************9998887899999944444444444443332222222222223222222221..01222346 PP

                        AAA_14  64 kktylflDEiqev 76 
                                   +++++++ E+  +
  gi|13541505|ref|NP_111193.1| 405 ERSLIIINEMLSS 417
                                   7888888887655 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   7.1e-05      0.16      21      51 ..     322     351 ..     316     372 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 7.1e-05
                        AAA_27  21 fsaeeadlhliyGpNEAGKstalrAisdllf 51 
                                   +s  ++++ ++ GpN  GK+t  r+i +++f
  gi|13541505|ref|NP_111193.1| 322 LS-RNENIIVVTGPNSGGKTTFARSIGQVFF 351
                                   44.578899*******************999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (506 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       973  (0.0542696); expected 358.6 (0.02)
Passed bias filter:                      671  (0.0374254); expected 358.6 (0.02)
Passed Vit filter:                        86  (0.0047967); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.44
# Mc/sec: 3441.43
//
Query:       gi|13541506|ref|NP_111194.1|  [L=500]
Description: MutS-like ATPase involved in mismatch repair [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-20   73.1   1.1    5.1e-18   65.8   0.2    2.8  3  MutS_V    MutS domain V
     0.0002   21.4   0.0      0.059   13.3   0.0    2.6  2  ATPase_2  ATPase domain predominantly from Archaea
     0.0021   18.3   0.1     0.0089   16.3   0.0    2.0  2  AAA_28    AAA domain
     0.0024   17.9   0.8      0.038   14.0   0.0    2.9  3  AAA_14    AAA domain
     0.0086   16.6   0.1      0.035   14.6   0.0    1.9  2  AAA_23    AAA domain
  ------ inclusion threshold ------
      0.035   13.9   0.0      0.089   12.6   0.0    1.6  1  AAA_29    P-loop containing region of AAA domain
      0.057   13.9   0.0       0.12   12.9   0.0    1.6  1  ABC_tran  ABC transporter
      0.059   13.0   0.0       0.11   12.0   0.0    1.4  1  AAA_27    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 ?   -1.1   0.0      0.71   1.6e+03       8      25 ..      38      55 ..      35      65 .. 0.77
   2 ?    4.5   0.0     0.014        31      64      95 ..     236     267 ..     222     272 .. 0.89
   3 !   65.8   0.2   2.3e-21   5.1e-18       2     127 ..     327     451 ..     326     492 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.71
                                  TSSHHHHHHHHHHHHHHH CS
                        MutS_V  8 maGkstylrqvalivlla 25
                                  maGk ty+ +v+  ++l 
  gi|13541506|ref|NP_111194.1| 38 MAGKDTYVFDVCRRTILN 55
                                  899999988888777765 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.014
                                   HHHHHHHHHTT--TTSEEEEESTS-SS-HHHH CS
                        MutS_V  64 EmlEtasilknatekslvilDElGRGtstydG 95 
                                    + Eta+il++++++ l  +D +  G + y G
  gi|13541506|ref|NP_111194.1| 236 SIRETAAILTESAQNVLAFIDRIKEGVAFYLG 267
                                   578********************999988866 PP

  == domain 3  score: 65.8 bits;  conditional E-value: 2.3e-21
                                   EEE-STTSSHHHHHHHHHHHHHHHHHT--BSSSEEEEE--SEEEEEE--------SS-HHHHHHHHHHHHHTT--TTSEEE CS
                        MutS_V   2 litGpnmaGkstylrqvalivllaqiGsfvpaekaeisivdkiftRvgasDdlakgkstFmvEmlEtasilknatekslvi 82 
                                    itG+n +Gkst+lr ++ ++l+ q G fv+ae+ +  i+  ift    ++d   +      Em+ ++ i++++ +   + 
  gi|13541506|ref|NP_111194.1| 327 FITGANRGGKSTLLRAIGQAQLMMQCGMFVAAESFSAYIASGIFTHFKREEDSGMSMGKLEEEMNRMSLIIDHIKAGGRLF 407
                                   69**************************************************999************************** PP

                                   EESTS-SS-HHHHHHHHHHHHHHHHHTT--EEEEEES-GGGGGHH CS
                        MutS_V  83 lDElGRGtstydGlaialavaeyllekikaktlfatHyheltkla 127
                                   l+E    t++ +G  ia+ v++ ll+    k++f tH++el++  
  gi|13541506|ref|NP_111194.1| 408 LNESFSSTNVREGSEIAKQVINALLD-SGVKVIFVTHFNELAESY 451
                                   *************************9.79************9754 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.0   2.6e-05     0.059      13      42 ..     316     345 ..     313     380 .. 0.87
   2 !    5.2   0.0    0.0077        17      35      68 ..     422     455 ..     420     491 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.6e-05
                      ATPase_2  13 eilerepneiyfiYGpegsGKtaLlkeiie 42 
                                   + l+ e ++i+fi+G  + GK++Ll+ i +
  gi|13541506|ref|NP_111194.1| 316 NSLSAEHDSIIFITGANRGGKSTLLRAIGQ 345
                                   6688999*******************9865 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0077
                      ATPase_2  35 aLlkeiienledkdkyviyyialreesiskldef 68 
                                    + k++i+ l+d++ +vi+++ ++e ++s+l + 
  gi|13541506|ref|NP_111194.1| 422 EIAKQVINALLDSGVKVIFVTHFNELAESYLGSV 455
                                   6789*********************999988766 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       1.3   2.9e+03      51      80 ..     228     257 ..     206     269 .. 0.65
   2 !   16.3   0.0     4e-06    0.0089       2      57 ..     326     385 ..     325     411 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.3
                        AAA_28  51 dllafaervleeqleeeaaaaankvlfcDr 80 
                                   +l +++++ ++e ++ +++ a+n + f+Dr
  gi|13541506|ref|NP_111194.1| 228 ELADMRAKSIRETAAILTESAQNVLAFIDR 257
                                   455555555556666666668899999998 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 4e-06
                        AAA_28   2 ivitGgestGKTtlleaLaar......gypvvpEaareileeklakgedalpwvedllafae 57 
                                   i itG+  +GK+tll+a+ +       g+ v +E++  ++ ++ +++++  ++    + + +
  gi|13541506|ref|NP_111194.1| 326 IFITGANRGGKSTLLRAIGQAqlmmqcGMFVAAESFSAYIASGIFTHFKREED--SGMSMGK 385
                                   78*****************6657777899999**********99999874333..3444444 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.39   8.8e+02      13      59 ..      39      86 ..      38     101 .. 0.58
   2 ?   -0.3   0.1      0.44   9.9e+02      29      77 ..     210     262 ..     198     278 .. 0.52
   3 !   14.0   0.0   1.7e-05     0.038       3      31 ..     324     359 ..     322     443 .. 0.56

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.39
                        AAA_14 13 vGKTtllkqlikell...vkkesilyinldderdkkladpekllelilek 59
                                  +GK t+++++ ++ +   v+++s++ +  d  +d+ +++++ +++ i + 
  gi|13541506|ref|NP_111194.1| 39 AGKDTYVFDVCRRTIlnsVNDKSTIIYRQDVLKDA-IRNQN-IIRKIYST 86
                                  59999999999999899977777766666666663.34332.33333222 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.44
                        AAA_14  29 kkesilyinldderdkkladpekllelilek...lke.ekktylflDEiqevp 77 
                                   +++++ y+  d+++  +++  +   + i+e    l+e  ++ + f+D i+e  
  gi|13541506|ref|NP_111194.1| 210 RERHYTYVLPDRDEIGAQELADMRAKSIRETaaiLTEsAQNVLAFIDRIKEGV 262
                                   45555555555544422222221222222222212223577889999888755 PP

  == domain 3  score: 14.0 bits;  conditional E-value: 1.7e-05
                        AAA_14   3 kilvitGaRrvGKTtllkqlikell.......vkke 31 
                                    i++itGa r GK+tll+ + + +l       v +e
  gi|13541506|ref|NP_111194.1| 324 SIIFITGANRGGKSTLLRAIGQAQLmmqcgmfVAAE 359
                                   699******************999965555542222 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       1.5   3.3e+03     126     126 ..      58      58 ..       3     135 .. 0.45
   2 !   14.6   0.0   1.6e-05     0.035      20      42 ..     324     346 ..     313     354 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.5
                        AAA_23 126 g 126
                                   +
  gi|13541506|ref|NP_111194.1|  58 N 58 
                                   1 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 1.6e-05
                        AAA_23  20 gltlItGpNGaGKTTildAikla 42 
                                    +  ItG N  GK+T+l+Ai  a
  gi|13541506|ref|NP_111194.1| 324 SIIFITGANRGGKSTLLRAIGQA 346
                                   5889****************765 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0     4e-05     0.089      21      42 ..     322     343 ..     314     351 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4e-05
                        AAA_29  21 lkgatlltGpsGsGKSTllDAi 42 
                                    ++++++tG++  GKSTll Ai
  gi|13541506|ref|NP_111194.1| 322 HDSIIFITGANRGGKSTLLRAI 343
                                   344899*************887 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   5.5e-05      0.12       5      33 ..     317     345 ..     315     426 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.5e-05
                                   EEEEETTSEEEEEESTTSSHHHHHHHHTT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran   5 slklkegekvaivGenGaGKStLlkllag 33 
                                   sl+ ++++++ i+G n  GKStLl+++ +
  gi|13541506|ref|NP_111194.1| 317 SLSAEHDSIIFITGANRGGKSTLLRAIGQ 345
                                   7889999*******************965 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0     5e-05      0.11      21      48 ..     318     345 ..     315     350 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 5e-05
                        AAA_27  21 fsaeeadlhliyGpNEAGKstalrAisd 48 
                                   +sae++++ +i G+N  GKst+lrAi +
  gi|13541506|ref|NP_111194.1| 318 LSAEHDSIIFITGANRGGKSTLLRAIGQ 345
                                   667788999****************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (500 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       645  (0.0359752); expected 358.6 (0.02)
Passed bias filter:                      538  (0.0300073); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.66u 0.34s 00:00:01.00 Elapsed: 00:00:00.51
# Mc/sec: 2949.16
//
Query:       gi|13541507|ref|NP_111195.1|  [L=211]
Description: formylmethanofuran dehydrogenase subunit E [Thermoplasma volcanium GSS1]
Scores for complete sequence (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   0.0    1.5e-26   93.0   0.0    1.1  1  FmdE      FmdE, Molybdenum formylmethanofuran dehydrogenase o
  ------ inclusion threshold ------
      0.086   13.1   0.8       0.16   12.2   0.8    1.4  1  LIM       LIM domain


Domain annotation for each model (and alignments):
>> FmdE  FmdE, Molybdenum formylmethanofuran dehydrogenase operon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.0   0.0   1.6e-30   1.5e-26       1     121 [.      15     146 ..      15     154 .. 0.84

  Alignments for each domain:
  == domain 1  score: 93.0 bits;  conditional E-value: 1.6e-30
                                   HHSS--CHHHHHHHHHHHHHHCC....-TTSSSEEEEES-S.....TCHHHHHHHHCS--TTTTSEEE--SS-SEEEEEET CS
                          FmdE   1 fHGHlCpglvlGyrmakaalkelgpkeeegdeelvaivetd.....sCldDAiqvltgctlGkgnlivmdygkkaltfkkr 76 
                                   fHGH Cp++ lGyr++ +a+k l++++e++ ++  +++e++     +C++D++q++tgct+Gkg l +  ygk al ++++
  gi|13541507|ref|NP_111195.1|  15 FHGHKCPYMPLGYRAGLYAMKLLKIDREKD-HKTLIYSEMSekdlnGCFNDGLQAATGCTYGKGLLNLLGYGKLALILYRK 94 
                                   9************************87766.9999999999999********************************99987 PP

                                   TT-EEEEEEE-........CCTHHHHHHHCCT--GGGS-HHHHHHHHHHHHHH CS
                          FmdE  77 ktgkavrlklk........eelpelreklakgkakeekeeeeleeeleeaikk 121
                                   + + avr++++        +++ e+++ +++gk+++e  +e +   +++++ +
  gi|13541507|ref|NP_111195.1|  95 D-KGAVRVHVRdeimdelsSRATEFFSLRKSGKEPSEIPDEFIDPIINDWMPS 146
                                   5.669******999977777777777777777776666666666666666554 PP

>> LIM  LIM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.8   1.8e-05      0.16      28      56 ..     174     202 ..     174     204 .. 0.95

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.8e-05
                                   B-TTT-SB-CTT.CEEETTEEEEHHHHHH CS
                           LIM  28 tCsdCqkeLkegsfyekdgklyCkkdylk 56 
                                   +C +C++   e +++  +gkl Ck dy++
  gi|13541507|ref|NP_111195.1| 174 KCDQCHEYVYEIDLVPSEGKLICKPDYYN 202
                                   6**************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       622  (0.0346924); expected 358.6 (0.02)
Passed bias filter:                      520  (0.0290033); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.53
# Mc/sec: 1205.96
//
Query:       gi|13541508|ref|NP_111196.1|  [L=250]
Description: permease [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-32  112.3  37.6    3.3e-32  112.0  37.6    1.0  1  TauE      Sulfite exporter TauE/SafE


Domain annotation for each model (and alignments):
>> TauE  Sulfite exporter TauE/SafE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.0  37.6   1.8e-36   3.3e-32       2     235 ..       9     244 ..       6     245 .. 0.92

  Alignments for each domain:
  == domain 1  score: 112.0 bits;  conditional E-value: 1.8e-36
                          TauE   2 llagllaGfvagllGiGggliavPlLlll.lppavavatsllavvatslsgalahrrrgnvdwrlllllllgsliGallGa 81 
                                   +++  + +++ + +G+G +  ++P+ + + +p  +a+a+ ll++v++  s+++ + +r +v w+l++++l++++i a+ Ga
  gi|13541508|ref|NP_111196.1|   9 FIITWILSALFATAGVGAANTLIPIYYSMgIPFSIAAAAGLLLNVFSLSSATVNNGKRDRVLWKLGIIFLAPAVIMAPMGA 89 
                                   555666789999************9999769***************************99********************* PP

                          TauE  82 llllllpsellkllfgvlllllallmllrkkr.srakgrerrptaillvligglvGllsGllGiGgGfllvpllllllglp 161
                                   l+  ++p ++l+++f+ +l ++ + +++ k + ++ k + ++++++l vl+g+++G+l+GllG+GgG++++p+l l    +
  gi|13541508|ref|NP_111196.1|  90 LVGIHTPRKVLLWMFVMFLGYTLYNLIRGKAKgNSDKFSVNAKGYALGVLVGAIAGFLGGLLGVGGGMIILPVLAL-IEKD 169
                                   *******************99999999955543444468899999999999999*******************995.799* PP

                          TauE 162 lkkavatslllilvislagalgyal.agavdwpllllllpgallGallGarlarrlsertlrrlfallllvlgvk 235
                                    kk+ at+ +++l++s++g+++y++ +  ++++l+l++l+g++lG++ G++l++++++ +++  ++l+++++ +k
  gi|13541508|ref|NP_111196.1| 170 YKKVSATAGFIALFSSASGFTSYLFlLKGISYNLWLIILIGGILGGFTGSYLMNKMKTIYVKYTIILIIAFVLIK 244
                                   ***********************6669999**************************************9999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1091  (0.0608511); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); 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):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.32s 00:00:00.90 Elapsed: 00:00:00.49
# Mc/sec: 1543.79
//
Query:       gi|13541509|ref|NP_111197.1|  [L=438]
Description: integrase/recombinase [Thermoplasma volcanium GSS1]
Scores for complete 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   0.0      0.015   15.1   0.0    1.7  2  Phage_integrase  Phage integrase family


Domain annotation for each model (and alignments):
>> Phage_integrase  Phage integrase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0      0.26   4.7e+03      70      82 ..     124     136 ..      97     156 .. 0.52
   2 !   15.1   0.0   8.3e-07     0.015      38     158 ..     170     303 ..     164     312 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.26
                                   EECTHHHHHHHHH CS
               Phage_integrase  70 vplseealellke 82 
                                   vp +ee+ + l++
  gi|13541509|ref|NP_111197.1| 124 VPTKEELSKILRM 136
                                   4444444444443 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 8.3e-07
                                   HHHTT-BGGGEECTTTEEEEE..EEECSSSSEEEEECTHHHHHHHHHHHHHH...CHCCTTTSBSSBETTSSB--HHHHHH CS
               Phage_integrase  38 sEllsLrvkdldlengvilvh..eregKgskeravplseealellkellska...leeaeksellfaskrgkplsrqtvrk 113
                                   +++  L+++ l+++n  ++++  +  +K++ +    l++e + +lk++l+++    e  +k+++l+a     p + qt+ +
  gi|13541509|ref|NP_111197.1| 170 GDIEDLDIDTLTFKNVPAKINvrNGLSKTRLKYFTFLGQEGCGYLKDYLDHRkasGEILKKESALLAPD---PGNVQTAHG 247
                                   67788999999999988777744666788888899999**************66656666666666666...677777777 PP

                                   HHHHHHHHCT-S.......SC--TTHHHHHHHHHH....HHHCTSHHHHHHHHT-S CS
               Phage_integrase 114 afkraveeagie.......kpltpHtlRhsfataL....leagvdlrvvqkllGHs 158
                                   ++++a  + +i          ++p  lR +fataL     +  ++    q+++GH+
  gi|13541509|ref|NP_111197.1| 248 FLRTALIAREIRkairnsnLSMRPYVLRVYFATALdiaeSKGSISHPWRQYIMGHK 303
                                   777777776666666677777************99553333445666678888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (438 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       421  (0.0234815); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 2746.91
//
Query:       gi|13541510|ref|NP_111198.1|  [L=196]
Description: hypothetical protein TVN0679 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.016   14.4   0.3      0.039   13.2   0.2    1.4  1  HIGH_NTase1    HIGH Nucleotidyl Transferase
       0.02   15.3   3.8      0.041   14.3   3.8    1.5  1  V-ATPase_G_2   Vacuolar (H+)-ATPase G subunit
       0.07   13.3   0.0       0.11   12.7   0.0    1.3  1  Spuma_A9PTase  Spumavirus aspartic protease (A9)
       0.07   13.7   0.5       0.23   12.0   0.3    2.0  3  Acyl-CoA_ox_N  Acyl-coenzyme A oxidase N-terminal


Domain annotation for each model (and alignments):
>> HIGH_NTase1  HIGH Nucleotidyl Transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.2   8.6e-06     0.039     122     168 ..      31      77 ..      21     118 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 8.6e-06
                   HIGH_NTase1 122 peeykealkeelkkglsypkarekalkeykkeeelllsspNniLgie 168
                                   ++++ke l+++ k+g++yp+ +++al++ k+ +e+l  + N+ L++e
  gi|13541510|ref|NP_111198.1|  31 SNDFKEFLDHYKKSGMTYPEIVKDALEKGKRMSEILQAEANDKLALE 77 
                                   5789***********************977666769999******98 PP

>> V-ATPase_G_2  Vacuolar (H+)-ATPase G subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   3.8   9.1e-06     0.041      31      95 ..      64     127 ..      50     131 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 9.1e-06
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCSHHHHH CS
                  V-ATPase_G_2  31 eveaAeaeAarilreAeakakalqaeyeqelaeevarireeararaeaeaqavrkraearlqqAv 95 
                                   e+ +Aea+ ++++ e +a +ka + +y+++l++e a ++e +rar ++ + ++ + +++r+q+A+
  gi|13541510|ref|NP_111198.1|  64 EILQAEAN-DKLALEMDAFVKASDLAYKERLEKELATMEETIRARVKESVLSAIAISTERIQKAI 127
                                   34455554.3677799999********************************************98 PP

>> Spuma_A9PTase  Spumavirus aspartic protease (A9)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   2.4e-05      0.11      84     131 ..     111     158 ..      92     174 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.4e-05
                                   --XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                 Spuma_A9PTase  84 pleltikidleeqqetllkesalskegkeelkklfekydalwqkwenq 131
                                    +  +i i  e+ q+ +l++ a+ ++gk+ ++++fe+y   w++ e +
  gi|13541510|ref|NP_111198.1| 111 SVLSAIAISTERIQKAILNSFAFDEHGKQLIRRIFERYRFTWNSVEAK 158
                                   4555799999********************************999865 PP

>> Acyl-CoA_ox_N  Acyl-coenzyme A oxidase N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.3   5.1e-05      0.23      25      67 ..      29      72 ..      18     116 .. 0.80
   2 ?   -0.3   0.1      0.33   1.5e+03      37      58 ..      83     104 ..      73     136 .. 0.72
   3 ?   -2.5   0.0       1.5   6.9e+03      20      35 ..     121     136 ..     115     153 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 5.1e-05
                                  HHCT-G.GGS-SSTGGGS-HHHHHHHHHHHHHHHHHHHHHTTSB CS
                 Acyl-CoA_ox_N 25 llesdp.efddaedyyflsreeryeealrkatrllkklrelqie 67
                                  ll++d  ef d+ + + +++ e  ++al+k++r+ + l+   ++
  gi|13541510|ref|NP_111198.1| 29 LLSNDFkEFLDHYKKSGMTYPEIVKDALEKGKRMSEILQAEAND 72
                                  556665588899************************99985543 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.33
                                   TGGGS-HHHHHHHHHHHHHHHH CS
                 Acyl-CoA_ox_N  37 dyyflsreeryeealrkatrll 58 
                                   + + l ++er e+ l+ + + +
  gi|13541510|ref|NP_111198.1|  83 KASDLAYKERLEKELATMEETI 104
                                   5566777777777777665544 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 1.5
                                   HHHHHHHCT-GGGS-S CS
                 Acyl-CoA_ox_N  20 relesllesdpefdda 35 
                                   +++++++ +   fd++
  gi|13541510|ref|NP_111198.1| 121 ERIQKAILNSFAFDEH 136
                                   4677777777777763 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1164  (0.0649228); expected 358.6 (0.02)
Passed bias filter:                      673  (0.037537); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.32s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 1216.12
//
Query:       gi|13541511|ref|NP_111199.1|  [L=81]
Description: integrase/recombinase [Thermoplasma volcanium GSS1]
Scores for complete 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-07   30.5   0.1      3e-07   30.4   0.1    1.1  1  Phage_integrase  Phage integrase family
  ------ inclusion threshold ------
       0.14   12.3   0.0       0.15   12.1   0.0    1.1  1  DUF3785          Protein of unknown function (DUF3785)


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 !   30.4   0.1   3.3e-11     3e-07       2      52 ..       6      53 ..       5      69 .. 0.93

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 3.3e-11
                                  HHHHHHHHHHHHCCGCHHHHHHHHHHHHHHHHT--HHHHTT-BGGGEECTT CS
               Phage_integrase  2 vltedeverllaaleeslkirdklllellyetGlRisEllsLrvkdldlen 52
                                  ++te e++r+l+ l++    rd++++  ly++G Ri El++L+  d+++++
  gi|13541511|ref|NP_111199.1|  6 MITETEMQRILTVLKN---PRDRAFISSLYDSGCRIEELITLKNRDISFDQ 53
                                  5899************...9*****************************97 PP

>> DUF3785  Protein of unknown function (DUF3785)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   1.7e-05      0.15      25      80 ..       4      58 ..       1      66 [. 0.87

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.7e-05
                       DUF3785 25 eneveglsldkileilneseevdfskeyykekceeckegveekkksfafleyhfyi 80
                                  +n ++  ++++il +l++  + +f +  y++ c +  e +  k++  +f +y  y 
  gi|13541511|ref|NP_111199.1|  4 DNMITETEMQRILTVLKNPRDRAFISSLYDSGC-RIEELITLKNRDISFDQYGSYF 58
                                  799******************************.7778888888888888887775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       443  (0.0247086); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.49
# Mc/sec: 500.28
//
Query:       gi|13541512|ref|NP_111200.1|  [L=1007]
Description: Type II restriction enzyme, methylase subunit [Thermoplasma volcanium GSS1]
Scores for complete sequence (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   0.0     0.0025   17.1   0.0    3.4  3  N6_Mtase        N-6 DNA Methylase
      8e-08   32.7   0.1    2.8e-07   31.0   0.1    1.9  1  Eco57I          Eco57I restriction-modification methylase
  ------ inclusion threshold ------
       0.18   12.2   0.2       0.71   10.3   0.0    2.1  2  UDPG_MGDP_dh_C  UDP-glucose/GDP-mannose dehydrogenase family,
       0.22   11.2   0.0        9.5    5.8   0.0    2.3  2  UPF0020         Putative RNA methylase family UPF0020
        1.4    8.7   3.7        4.6    7.1   0.7    2.7  3  Apolipoprotein  Apolipoprotein A1/A4/E domain


Domain annotation for each model (and alignments):
>> N6_Mtase  N-6 DNA Methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.3   0.0    0.0029        10       5      40 ..     298     330 ..     295     347 .. 0.81
   2 !   17.1   0.0   7.1e-07    0.0025      48     101 ..     380     449 ..     368     456 .. 0.86
   3 !   11.1   0.0   4.8e-05      0.17     122     188 ..     537     603 ..     489     620 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0029
                      N6_Mtase   5 llGdvYEyllrkfaeeegksgGeffTPrevsklive 40 
                                   l+G v+E ll +    e  ++G f+TP++ +++i +
  gi|13541512|ref|NP_111200.1| 298 LIGTVFENLLLEK---ERGEKGTFYTPKDEISFICR 330
                                   6789999998764...66777*******98888876 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 7.1e-07
                      N6_Mtase  48 esvyDpacGsggllvqaekvlkee................dgktkelsiyGqeknettyrLakmNlllhg 101
                                     v+Dpa+Gsgg+lv + + + +                  +kt   +iyG +++++++++a++ + l  
  gi|13541512|ref|NP_111200.1| 380 VRVVDPAVGSGGFLVVMMQEIVSIvteadsiagwisdpyeYKKTIYGNIYGFDIEPEAVEIARLRMWLSM 449
                                   469************9998887667889********999888899999****************999865 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 4.8e-05
                      N6_Mtase 122 kdkkfdvvvaNppfnqkewkektlekderfreavapksnadla..fllhiieslkpkGraavvlangvL 188
                                   + + +d+vv Npp+  +  ++ + e+ +++ ++ +  ++ dl   f +  +  lkp+G ++ +  +  L
  gi|13541512|ref|NP_111200.1| 537 MVNPADIVVMNPPYVRQ--ESIKQERKKYYVSTYKLDKKSDLYvyFFMRSLWLLKPNGYVSAITSDKWL 603
                                   67899************..6666666667777644444444433499999********99988887666 PP

>> Eco57I  Eco57I restriction-modification methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   0.1   7.9e-11   2.8e-07       4      71 ..     542     617 ..     540     646 .. 0.81

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 7.9e-11
                        Eco57I   4 dviiGNPPYqeseakkelkaleek..........akdiyqkFvekalkle..dkylaliiparflasgkglkefrekllk 71 
                                   d+++ NPPY ++e++k+ ++   k          ++d+y++F+ ++l l   ++y++ i++ ++l + +++k+++++l +
  gi|13541512|ref|NP_111200.1| 542 DIVVMNPPYVRQESIKQERK---KyyvstykldkKSDLYVYFFMRSLWLLkpNGYVSAITSDKWL-ETSYGKKLQDFLKS 617
                                   9************8887763...234578999999*************998889***********.88888888776643 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 ?   10.3   0.0    0.0002      0.71      12      41 ..     359     388 ..     357     411 .. 0.90
   2 ?   -2.7   0.1       2.2     8e+03      30      61 ..     540     568 ..     531     579 .. 0.54

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0002
                                   S--TT-HHHHHHHHHHHCTSEEEEE-SSTH CS
                UDPG_MGDP_dh_C  12 dDlReSpaldiieeLleegaevkiyDPkvk 41 
                                   d+lR+S+ ld i++L+e+  +v+++DP v 
  gi|13541512|ref|NP_111200.1| 359 DELRKSKKLDEIRNLKERLLKVRVVDPAVG 388
                                   89*************************985 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.2
                                   TSEEEEE-S.STHHCCCCHHGGBTCCEEES-CH CS
                UDPG_MGDP_dh_C  30 gaevkiyDP.kvkeeaveaeleekgvevvdsle 61 
                                    a+++++ P +v++e +++e ++    ++ s +
  gi|13541512|ref|NP_111200.1| 540 PADIVVMNPpYVRQESIKQERKK----YYVSTY 568
                                   56655555438888888774442....222333 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0    0.0027       9.5      31      94 ..     381     443 ..     373     452 .. 0.73
   2 ?    2.7   0.0     0.025        89     120     145 ..     539     564 ..     512     573 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0027
                                   -EEETT-TTSHHHHHHHHHHTT--TTTT----SS..HHHHHHHHHHHH--EEEEES-HHHHHHHHH CS
                       UPF0020  31 pllDPmCGsGtilIEaallganiapgllrefvle..lkaeaeeearaelklygsDldrrvvqgare 94 
                                   + +DP  GsG++l+    + ++i+ + +    +   + +  e ++    ++yg+D+++++v+ ar 
  gi|13541512|ref|NP_111200.1| 381 RVVDPAVGSGGFLVV---MMQEIVSIVTEADSIAgwISDPYEYKKTIYGNIYGFDIEPEAVEIARL 443
                                   579**********95...55555544443333334466666666666666************9986 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.025
                                   S---EEEE----------HHHHHHHH CS
                       UPF0020 120 gevdvivtnpPYGerlgskkalekLY 145
                                   +  d++v npPY +  + k++ +k Y
  gi|13541512|ref|NP_111200.1| 539 NPADIVVMNPPYVRQESIKQERKKYY 564
                                   4689********98777777666666 PP

>> Apolipoprotein  Apolipoprotein A1/A4/E domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       0.3   1.1e+03     156     170 ..     168     182 ..     157     190 .. 0.66
   2 ?   -0.2   0.1      0.21   7.6e+02      71      95 ..     339     363 ..     337     379 .. 0.58
   3 ?    7.1   0.7    0.0013       4.6      45      95 ..     474     525 ..     471     532 .. 0.46

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.3
                                   HHHHHHTS-TTSHHH CS
                Apolipoprotein 156 veelrekleeqaeel 170
                                    +el++kl++++e+ 
  gi|13541512|ref|NP_111200.1| 168 FQELSDKLTPYLEDH 182
                                   566666666666664 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.21
                                   HHHHCCHHHHHHHHHHHHCHHCCHH CS
                Apolipoprotein  71 lrqrlapyteelrerlaadaeelqe 95 
                                   l+ r +p ++ l++ +++ ++el++
  gi|13541512|ref|NP_111200.1| 339 LQDRYTPDSRSLQDGIDLYLDELRK 363
                                   4555555555555555555555554 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.0013
                                   HHHHHHHHCCCCHHHHHHCCCHHHHHHHHHCC.HHHHHHHHHHHHCHHCCHH CS
                Apolipoprotein  45 eleevrarlepyrdevqeqlgqnleelrqrla.pyteelrerlaadaeelqe 95 
                                   el++v ++++p ++e +  +++ +e++ ++ + +  + l++r++  +e+l++
  gi|13541512|ref|NP_111200.1| 474 ELQSVQKKITPEIEEERDHVEKLIEQYSNEHDhENKKSLKKRIESHTENLRK 525
                                   4445555555555555555555555554442202233333333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1007 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1080  (0.0602376); expected 358.6 (0.02)
Passed bias filter:                      684  (0.0381505); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.91u 0.36s 00:00:01.27 Elapsed: 00:00:00.52
# Mc/sec: 5799.79
//
Query:       gi|13541513|ref|NP_111201.1|  [L=1043]
Description: helicase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      1e-13   51.6   0.1    3.1e-13   50.0   0.1    1.9  1  Helicase_C  Helicase conserved C-terminal domain
    3.6e-12   45.7   0.0    1.6e-08   33.7   0.0    2.6  2  SNF2_N      SNF2 family N-terminal domain
    1.4e-11   44.4   0.0    3.6e-11   43.1   0.0    1.8  1  PLDc_2      PLD-like domain
    4.5e-08   33.3   0.0     0.0017   18.4   0.0    2.7  2  ResIII      Type III restriction enzyme, res subunit
    1.2e-05   25.1   0.1       0.17   11.6   0.0    3.1  3  DEAD        DEAD/DEAH box helicase
     0.0085   16.4   0.0      0.044   14.1   0.0    2.3  2  AAA_22      AAA domain
  ------ inclusion threshold ------
      0.014   14.6   0.0      0.029   13.6   0.0    1.4  1  DUF2075     Uncharacterized conserved protein (DUF2075)
      0.017   14.9   0.1      0.095   12.4   0.1    2.1  1  IstB_IS21   IstB-like ATP binding protein
      0.071   12.6   0.1       0.21   11.0   0.0    1.7  1  PhoH        PhoH-like protein


Domain annotation for each model (and alignments):
>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.0   0.1   1.5e-16   3.1e-13      14     111 .]     645     749 ..     628     749 .. 0.83

  Alignments for each domain:
  == domain 1  score: 50.0 bits;  conditional E-value: 1.5e-16
                                   TTTSEEEEEESSHHHHHH.HHHHHHHTTSTEEEESTT.......STHHHHHHHHHHHHTTSSSEEEESGGGTSSSTSTTES CS
                    Helicase_C  14 eeggkilifvntidrlek.vklllekkgikvavlhge.......lpqnereeileqfnkgesdvLiatdvaerGidipkvn 86 
                                   + ++ +++f+++  ++e   + ++e+ + +v   +g+        +++++  ++++f  ++  +Li+tdv++++ ++++++
  gi|13541513|ref|NP_111201.1| 645 SGKNGVILFTQYFATAEYvYNHMKERIKDRVMLATGSvcrdrfgVSKRDKTPVIRDF-MKNGGILISTDVLSESQNLQNAQ 724
                                   55667899999999887666777777777777777777778888*************.55667****************** PP

                                   EEEESSSSSSHHHHHHHHTTSSSTT CS
                    Helicase_C  87 lVinfdlprnvtsyiqriGRtgRag 111
                                   +++n+d+p+n+  +iqr+GR+ R+g
  gi|13541513|ref|NP_111201.1| 725 YIVNYDFPWNPVVLIQRAGRIDRIG 749
                                   *********************9986 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 !    9.1   0.0   0.00023      0.47      55     120 ..     256     310 ..     236     322 .. 0.78
   2 !   33.7   0.0     8e-12   1.6e-08     171     270 ..     325     430 ..     310     470 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00023
                                   T--EEE---TTS--HHHHHHHHH...HHTTTS---.......S-EEEE--HHHHHHHHHHHHH.H-T CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxx RF
                        SNF2_N  55 vrGGiLaDemGLGKTvqvlalilaqrakeekdkekkrkdtlagptLivvPaslldqWeneier.hvs 120
                                    +G ++aD +GLGKT  ++ l               + +  ++p Li  +++l + W++e+++ hv+
  gi|13541513|ref|NP_111201.1| 256 YNGVVIADSTGLGKTRVAINLAV---M---------AINDGRNPLLIAPKSALETTWKDEMDKtHVH 310
                                   568899*************9998...2.........2233457777766669********9863555 PP

  == domain 2  score: 33.7 bits;  conditional E-value: 8e-12
                                   TTS-S-S.-SEEEES-GGGT--TTSHHHHHHHH--...-S-EEEE-S--SSS-HHHHHHHHHH.H-TTTT--.HHHHHHHT CS
                                   xxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxx.xxxxxxxx RF
                        SNF2_N 171 svlkqve.wkrvvlDEghtlknstskaaeavskLs...tsnrwiltGTPiqnsledlygLlkf.Lreepfge.kqtfdkll 245
                                   +++k+++  +++++DE+h +k+  s+ + ++++L    +++ ++lt+TPi nsl dly+Ll++ Lr ++ ++   + +  +
  gi|13541513|ref|NP_111201.1| 325 EAIKEIQgKDFIIVDEAHYFKSPGSNRYSVLRDLMaagQKQIVLLTATPINNSLMDLYSLLSLyLRDDSISDiSPSLKGYF 405
                                   55666664689*********************9875645666789***************985366666666444555555 PP

                                   HHHHHHHHHHHHHHHHTT-STTEE- CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxx RF
                        SNF2_N 246 qrpieaqaekgrsrLlqllqrlmlr 270
                                   +   +  +++    +  +l+r+++r
  gi|13541513|ref|NP_111201.1| 406 SMQQKLWRNDEPVDIDAILRRFVVR 430
                                   5555555555555555555555555 PP

>> PLDc_2  PLD-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.1   0.0   1.8e-14   3.6e-11      10     133 .]      24     185 ..      16     185 .. 0.76

  Alignments for each domain:
  == domain 1  score: 43.1 bits;  conditional E-value: 1.8e-14
                        PLDc_2  10 ksidiatyyfvsdreildallkaakrgvkvrilldskkd...................................dagavde 55 
                                   +++ ia+ yf  + e ++++ +  k++  +++ll+++ +                                   ++++   
  gi|13541513|ref|NP_111201.1|  24 EELAIASAYF--NLEGYRNIQEGLKNK-PLKLLLGREPSesikfeeeaiknlesydedfyseqkdvfasevlnnEDDVSYF 101
                                   5666666777..444455555533333.57777776444777777777777777777777777777777777764445555 PP

                        PLDc_2  56 aslkelkellleagvevrvfetllgslHaKlylidgk........tvivGSsNltkrgldlnlElnvviedkelakeleee 128
                                     l++  e+  + +ve+r  +   +++H K+y+  ++         +ivGSsN+t  gl++n+Eln+ ++d+e ++el ++
  gi|13541513|ref|NP_111201.1| 102 SALHNAVEFFKRPEVEIRRVKG--RFFHGKAYMGARTsfsnmvsgFAIVGSSNFTGGGLSGNRELNMLTTDREGVTELIKW 180
                                   678888889999*****99765..679*******97778889999************************************ PP

                        PLDc_2 129 Ferlw 133
                                   F +lw
  gi|13541513|ref|NP_111201.1| 181 FLELW 185
                                   ****9 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   8.4e-07    0.0017      22      78 ..     254     308 ..     235     333 .. 0.75
   2 !   12.8   0.0   4.6e-05     0.091     130     170 ..     330     374 ..     306     375 .. 0.64

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 8.4e-07
                                   .TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGT CS
                        ResIII  22 krdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkfl 78 
                                   k  + ++i+  TG GKT+va++l+    + g+  + l+++p+ +l   +++e+ k+ 
  gi|13541513|ref|NP_111201.1| 254 KTYNGVVIADSTGLGKTRVAINLAVMAINDGR--NPLLIAPKSALETTWKDEMDKTH 308
                                   5566778999*******************988..9****************996654 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 4.6e-05
                                   TTT-SEEEEETGGGTTS...TTTHHHHHT---..SEEEEEESS-S CS
                        ResIII 130 rdrfdviiiDEaHrlgak..kswreilekfke..avllglTATpe 170
                                    + +d+ii+DEaH +++   + +  + + + +  + ++ lTATp 
  gi|13541513|ref|NP_111201.1| 330 IQGKDFIIVDEAHYFKSPgsNRYSVLRDLMAAgqKQIVLLTATPI 374
                                   34566************75434444433332233778889***95 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.0   0.00017      0.34       3      76 ..     247     313 ..     245     333 .. 0.77
   2 !   11.6   0.0   8.5e-05      0.17     119     171 ..     330     376 ..     301     381 .. 0.70
   3 ?   -1.5   0.0      0.92   1.8e+03      49     104 ..     649     711 ..     628     727 .. 0.59

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00017
                                   HHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTS CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD   3 iQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidl 76 
                                   iQa+ i  +++g  v++a  TG GKT +++  ++ ++     ++g   l+++P  +L     +++ k   +id 
  gi|13541513|ref|NP_111201.1| 247 IQASRILKTYNG--VVIADSTGLGKTRVAINLAVMAI-----NDGRNPLLIAPKSALETTWKDEMDKTHVHIDS 313
                                   788888887755..9*************998888777.....677788999**999988888888777777664 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 8.5e-05
                                   CTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTTSTTTSEEEEEESSBS.H CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x RF
                          DEAD 119 lsqvrflVlDEadrlldqgfsdfinrilnqlpqitcdgklqrqvivlSATlp.k 171
                                   ++   f+++DEa+ + +   +    ++l+ l    +    q+q+++l+AT+  +
  gi|13541513|ref|NP_111201.1| 330 IQGKDFIIVDEAHYFKSP--GSNRYSVLRDL---MAA--GQKQIVLLTATPInN 376
                                   67779************9..34444556666...233..3456*******9844 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 0.92
                                   EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEEET.......TSSHHHHHHHHH...TTCSEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxx...xxxxxxxxx RF
                          DEAD  49 kalivePtreLaeqtlnnlkkfkkyidlrvlliig.......gvaardqlskld...ngvdivvgt 104
                                    +++ +   + ae ++n++k+++k    rv+l +g       gv++rd+  +++   ++  i+++t
  gi|13541513|ref|NP_111201.1| 649 GVILFTQYFATAEYVYNHMKERIKD---RVMLATGsvcrdrfGVSKRDKTPVIRdfmKNGGILIST 711
                                   4555666666788899999999994...55555553333555677777777664333445555555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0   2.2e-05     0.044      14     127 ..     265     368 ..     254     378 .. 0.70
   2 ?   -2.8   0.0       3.7   7.3e+03      38      72 ..     985    1024 ..     950    1040 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.2e-05
                        AAA_22  14 sGtGKTtllrrlleqldeeakaee.erpevvfvtlpsstsskdllrellralglelkaerlsseellealeqalraravie 93 
                                   +G GKT+++ +l+  +      ++ ++p ++  + + +t++kd + +    +++      ++se l ++  +a+++ + + 
  gi|13541513|ref|NP_111201.1| 265 TGLGKTRVAINLAVMAI-----NDgRNPLLIAPKSALETTWKDEMDKTHVHIDS------KRSEYLSQHPDEAIKEIQGKD 334
                                   68888888888888873.....22345555555555555777776666666663......57778889999999999999* PP

                        AAA_22  94 lliiDEaqhlrs..eealeeLrsllnlsrkgvqliL 127
                                   ++i+DEa+++ s   + ++ Lr+l+  ++k++  +L
  gi|13541513|ref|NP_111201.1| 335 FIIVDEAHYFKSpgSNRYSVLRDLMAAGQKQI--VL 368
                                   **********7256999999999999444444..44 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 3.7
                        AAA_22   38 erpevv..fvtlpsstsskdllrellralglelka...er 72  
                                    ++ +vv  ++++ + +++ + +re+l+a+++ +k+   e+
  gi|13541513|ref|NP_111201.1|  985 AKQTVVttLYNAMKRGGLLEKAREVLNAYESTGKEdinEP 1024
                                    4555556678888888888888888888888777655544 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   1.4e-05     0.029       9     129 ..     264     369 ..     258     371 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.4e-05
                       DUF2075   9 vaGtGKtvvllnllaeleddeeertavylsvNhplvlvlrealakkeekkkkkeafeklssfinnlsefkkaeekkeepke 89 
                                    +G GKt v++nl++ +   +++r+  ++    +l  + + +++k+   +  +   ++++ + +  +     e+ ke +  
  gi|13541513|ref|NP_111201.1| 264 STGLGKTRVAINLAVMA--INDGRNPLLIAPKSALETTWKDEMDKTH-VHIDS---KRSEYLSQHPD-----EAIKEIQGK 333
                                   6799************9..99**********************8888.33333...33333334444.....334777799 PP

                       DUF2075  90 dvvivDEAhrlltksdqaekqseenqlkelmkr.akvvval 129
                                   d++ivDEAh   + +++         l++lm++ +k +v+l
  gi|13541513|ref|NP_111201.1| 334 DFIIVDEAHYFKSPGSN-----RYSVLRDLMAAgQKQIVLL 369
                                   *********99994433.....3478889988877766665 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   0.1   4.8e-05     0.095      34      77 ..     243     286 ..     234     376 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.8e-05
                     IstB_IS21  34 kvkeLatlsfiekkenivllGpsGvGKshlaialgveavragls 77 
                                    ++++++   +++ +++v+   +G GK+ +ai l+v a+++g +
  gi|13541513|ref|NP_111201.1| 243 VLSTIQASRILKTYNGVVIADSTGLGKTRVAINLAVMAINDGRN 286
                                   5567778888899999************************9976 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0    0.0001      0.21      13      80 ..     250     319 ..     242     336 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0001
                                   HHHHHH-SEEEEE--TTSSTTHHHHHHHHHHHHTTS-SEEEEEE-S--T..T----SS---------TTT CS
                          PhoH  13 lealkkndivfaiGpaGtGKtylavalavealkkkkvkriiltrpavea..geelGflpgdleekvdpyl 80 
                                    ++lk+++ v+++ ++G GKt +a+ lav a+++++   +i  + a+e   ++e+  +   ++ k + yl
  gi|13541513|ref|NP_111201.1| 250 SRILKTYNGVVIADSTGLGKTRVAINLAVMAINDGRNPLLIAPKSALETtwKDEMDKTHVHIDSKRSEYL 319
                                   56788999999*************************9999999999987666666666666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1043 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1078  (0.0601261); expected 358.6 (0.02)
Passed bias filter:                      739  (0.0412181); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); 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: 0.84u 0.31s 00:00:01.14 Elapsed: 00:00:00.48
# Mc/sec: 6549.71
//
Query:       gi|13541514|ref|NP_111202.1|  [L=168]
Description: hypothetical protein TVN0683 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       864  (0.0481901); 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:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1089.46
//
Query:       gi|13541515|ref|NP_111203.1|  [L=146]
Description: hypothetical protein TVN0684 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.5e-09   37.0   0.0    3.4e-09   36.6   0.0    1.2  1  DDE_Tnp_IS66  Transposase IS66 family


Domain annotation for each model (and alignments):
>> DDE_Tnp_IS66  Transposase IS66 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.6   0.0   1.9e-13   3.4e-09     223     280 ..      31      89 ..       8      91 .. 0.87

  Alignments for each domain:
  == domain 1  score: 36.6 bits;  conditional E-value: 1.9e-13
                  DDE_Tnp_IS66 223 pksklgkairyll.krweallrfledgrvpidNNaaERaiRpvvlgRKnslfagseeGa 280
                                   +++k +k++++ll +r+e l+ f+  ++v+++NN+aERa++p v+  K+ ++++se+G 
  gi|13541515|ref|NP_111203.1|  31 EHTKSRKFVDNLLkRRKEWLFSFVVHKDVEPTNNRAERALKPSVIYTKTNGGTRSETGD 89 
                                   688999999999834567799***********************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       514  (0.0286686); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 972.42
//
Query:       gi|13541516|ref|NP_111204.1|  [L=481]
Description: Beta-galactosidase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.7e-64  215.4   9.1    1.3e-32  112.8   1.3    3.1  3  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 !   34.1   0.5   5.5e-13   9.9e-09       2      88 ..       3      93 ..       2     105 .. 0.88
   2 !   72.6   0.0   1.1e-24     2e-20      89     257 ..     118     297 ..     111     303 .. 0.85
   3 !  112.8   1.3   7.3e-37   1.3e-32     285     451 ..     305     461 ..     297     463 .. 0.91

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 5.5e-13
                                  GGGS-TT-EEEEE--HHHHH--TTSTT---BHHHHHHHHGGGSTTS--.-SS...TT-HHHHHHHHHHHHHHTT-SEEEEE-- CS
                 Glyco_hydro_1  2 ketfpedFlwgaataayqiEGawnedGkgesiwDtftetpgkvlegsn.gdv...acdsYhrykeDvallkelgvkayrfSis 80
                                  +++fpedF +g + + +q E ++++    +s w ++ + ++++ +g   gd+   +  +++ yk+  +  +++g+k+ r+ + 
  gi|13541516|ref|NP_111204.1|  3 ENNFPEDFKFGWSQSGFQSEMGYDNAMDDKSDWYVWVHDKENIQSGLVsGDMpenGPGYWNNYKSFHEAAQNMGLKMARIGVE 85
                                  579************************************99998776555551116679************************ PP

                                  HHHHSTTS CS
                 Glyco_hydro_1 81 WpRilPkG 88
                                  W+R++P++
  gi|13541516|ref|NP_111204.1| 86 WSRLFPEP 93
                                  ******98 PP

  == domain 2  score: 72.6 bits;  conditional E-value: 1.1e-24
                                   TT---HHHHHHHHHHHHHHHHTT-EEEEEEESS--BHHHHH.H....-......GGG-SHHHHHHHHHHHHHHHHHTTT-- CS
                 Glyco_hydro_1  89 egeinekGlayYerLidelleagieplvTlyHwdlPqaLqd.e....G......gwenrsiidafkeyaevvfkrfgdkvk 158
                                   +  +n++ l++Y ++++ +++++i  ++ +yHw lP +L d      G      gw n +i++ f  +++++  +++d   
  gi|13541516|ref|NP_111204.1| 118 DKYVNKDALNHYIEIFNDIKNRNIDLIINMYHWPLPVWLSDpVsvrkGiktersGWLNDRIVQLFALFSSYIVYKMEDLAV 198
                                   6789**********************************9864223332444444*************************** PP

                                   EEEEEE-HHHHHHHHHT..SS-STT-S-TTTHHHHHHHHHHHHHHHHHHHHHHHTTT-EEEEEEEEEEEEESSSSHHHHHH CS
                 Glyco_hydro_1 159 lwlTfnEpnvvallgyl..tgefaPgkkdleaayeaaHnlllaharavklykevaqkgkigivlnlslaeplseseedkea 237
                                   ++ T+nEpnvv   g++   + f+P   + e a +++ n+l+ah+ a++++k+++ +  +gi+++ ++ +pl+++++++ a
  gi|13541516|ref|NP_111204.1| 199 AFSTMNEPNVVYGNGFIniKSGFPPSYLSSEFASKVKNNILKAHSLAYDSMKKIT-DKPVGIIYANTYFTPLDPEKDND-A 277
                                   *************999722578****999999******************99875.668**************987665.5 PP

                                   HHHHHHHHTHHHHHHHHHSS CS
                 Glyco_hydro_1 238 aeraleflngwfldpvvkGd 257
                                    ++a++ ++  f+dp++kGd
  gi|13541516|ref|NP_111204.1| 278 IAKADSDAKWSFFDPLIKGD 297
                                   5555555555699****998 PP

  == domain 3  score: 112.8 bits;  conditional E-value: 7.3e-37
                                   T--SEEEEEEEEEEEEEE--...-STT---.SSGGGGG-SBSS-B-SSSS-B-HHHHHHHHHHHHHTS----EEEEE---- CS
                 Glyco_hydro_1 285 gkadflglnyYtsrlvknkeseeaslskte.ekkleeevdpslpktdigwiiepeglrkllellkkeYqklpiyiteNGlg 364
                                   +k d++g+nyYt+++ +++    +sl+    + + ++ ++ + p++digw+ +pegl ++++   ++Y+ lp+y+teNG++
  gi|13541516|ref|NP_111204.1| 305 NKLDWIGINYYTRTMLRKDGDGYISLKGYGhSGSPNTVTNDKRPTSDIGWEFYPEGLEYVIMNYWNRYK-LPMYVTENGIA 384
                                   689**************9997777776554045556667999**************************9.**********9 PP

                                   EE-BSSSHHH--HHHHHHHHHHHHHHHHHHHTT--EEEEEEE-SB----GGGTTSEE--SEEEETTTTTEEEE-HHHHHHH CS
                 Glyco_hydro_1 365 akdeieegkveDdkRidYlkehlnevkkaiedgvdlkgYvawsllDnfewaegyskrfGlvyvdrnetleRtpkkSakwyk 445
                                   ++         D++R +Yl +h+++v +ai++g+++kgY+ wsl+Dn+ewa g+s +fGl+  d  e+++ + + Sa  yk
  gi|13541516|ref|NP_111204.1| 385 DNG--------DYQRPYYLVSHIASVLRAINKGANVKGYLHWSLVDNYEWALGFSPKFGLIGYD--ENKKLYWRPSALVYK 455
                                   988........89***********************************************9888..9999*********** PP

                                   HHHH-S CS
                 Glyco_hydro_1 446 eviekn 451
                                   e+++kn
  gi|13541516|ref|NP_111204.1| 456 EIATKN 461
                                   ***998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (481 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); 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: 0.65u 0.31s 00:00:00.96 Elapsed: 00:00:00.50
# Mc/sec: 2916.60
//
Query:       gi|13541517|ref|NP_111205.1|  [L=109]
Description: hypothetical protein TVN0686 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00091   19.8   0.2     0.0017   19.0   0.2    1.5  1  zf-ISL3   zinc-finger of transposase IS204/IS1001/IS1096/IS11


Domain annotation for each model (and alignments):
>> 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 !   19.0   0.2   9.6e-08    0.0017       5      37 ..      45      77 ..      42      80 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 9.6e-08
                       zf-ISL3  5 CPnCgsk.tvvkhgkkerrvrhlpiggkrvyLrl 37
                                  CP C++  +v++h  +er +r+l+  ++  ++++
  gi|13541517|ref|NP_111205.1| 45 CPMCRKEcMVYDHL-RERVWRDLDSIEFMSFVHA 77
                                  *******999***9.6*******98777766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       551  (0.0307323); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 765.72
//
Query:       gi|13541518|ref|NP_111206.1|  [L=93]
Description: hypothetical protein TVN0687, partial [Thermoplasma volcanium GSS1]
Scores for complete 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-21   75.1   0.1    6.7e-21   75.1   0.1    1.0  1  DDE_Tnp_ISL3  Transposase
  ------ inclusion threshold ------
      0.093   12.7   0.6       0.31   11.0   0.2    1.8  2  REPA_OB_2     Replication protein A OB domain


Domain annotation for each model (and alignments):
>> DDE_Tnp_ISL3  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.1   0.1   7.4e-25   6.7e-21      26     108 ..       4      88 ..       1      93 [] 0.92

  Alignments for each domain:
  == domain 1  score: 75.1 bits;  conditional E-value: 7.4e-25
                  DDE_Tnp_ISL3  26 grlldilpgRkketlkafleslsekerekveavvmDmsaayksavkealPnAk..ivvDrFHvvklanealdevRrreqke 104
                                    ++ +i+ +Rkke l+++ ++l+ ++ ++++av++Dm+ +++s++ e++P+A+  iv+D FHv+k++ne +d++R+++ ke
  gi|13541518|ref|NP_111206.1|   4 NDVEYIAYDRKKESLDEYYRTLTGEDLSNITAVSIDMWDPFMSSTMEYVPDAQskIVFDLFHVMKHVNESVDTTRKQVNKE 84 
                                   67788999**************999**************************9877************************** PP

                  DDE_Tnp_ISL3 105 lree 108
                                   l+++
  gi|13541518|ref|NP_111206.1|  85 LQKS 88 
                                   9764 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 ?    0.6   0.0     0.058   5.2e+02      39      59 ..      22      43 ..       4      60 .. 0.67
   2 ?   11.0   0.2   3.4e-05      0.31       6      41 ..      54      89 ..      49      91 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.058
                     REPA_OB_2 39 kreltlvDesga.svevtlWgk 59
                                   r+lt  D s+  +v++ +W+ 
  gi|13541518|ref|NP_111206.1| 22 YRTLTGEDLSNItAVSIDMWDP 43
                                  4777777888764789999986 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 3.4e-05
                     REPA_OB_2  6 nvekdsivDvigvvksveevseitskstekelkkre 41
                                  +++++ + D+  v+k+v+e+ + t+k+ +kel+k  
  gi|13541518|ref|NP_111206.1| 54 DAQSKIVFDLFHVMKHVNESVDTTRKQVNKELQKSG 89
                                  56677789*************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       853  (0.0475766); expected 358.6 (0.02)
Passed bias filter:                      513  (0.0286129); 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: 0.34u 0.22s 00:00:00.56 Elapsed: 00:00:00.37
# Mc/sec: 748.51
//
Query:       gi|13541519|ref|NP_111207.1|  [L=71]
Description: hypothetical protein TVN0688, partial [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.7e-13   48.7   3.4    8.5e-13   48.6   3.4    1.0  1  DDE_Tnp_ISL3  Transposase
  ------ inclusion threshold ------
       0.05   13.9   0.0      0.057   13.7   0.0    1.1  1  DUF1884       Domain of unknown function (DUF1884)


Domain annotation for each model (and alignments):
>> DDE_Tnp_ISL3  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.6   3.4   9.5e-17   8.5e-13     192     240 .]       1      49 [.       1      49 [. 0.96

  Alignments for each domain:
  == domain 1  score: 48.6 bits;  conditional E-value: 9.5e-17
                  DDE_Tnp_ISL3 192 tlknhreeIlnyfdsrlsngpvEgiNnkikaikrrayGfrnfenfrlri 240
                                   ++k h ++Ilnyf+++++n+++EgiN++i +i+++ayG+rn  n+r+ i
  gi|13541519|ref|NP_111207.1|   1 MMKVHIRNILNYFNHKITNARAEGINSNIALIQKMAYGYRNRGNLRTAI 49 
                                   68899****************************************9976 PP

>> DUF1884  Domain of unknown function (DUF1884)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   6.3e-06     0.057       4      38 ..       6      40 ..       3      49 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.3e-06
                                  HHHHHHHHHHHHHHHHHTT----EEEE-HHHHHHH CS
                       DUF1884  4 lirilevieekineLkleGfePdiiLvGkeaiefl 38
                                  + +il+  ++ki + + eG++ +i L+ k a+ + 
  gi|13541519|ref|NP_111207.1|  6 IRNILNYFNHKITNARAEGINSNIALIQKMAYGYR 40
                                  5679999*************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       321  (0.017904); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.37u 0.30s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 506.31
//
Query:       gi|13541520|ref|NP_111208.1|  [L=110]
Description: hypothetical protein TVN0689 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       319  (0.0177924); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.48
# Mc/sec: 683.31
//
Query:       gi|13541521|ref|NP_111209.1|  [L=647]
Description: hypothetical protein TVN0690 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.7e-07   29.9   0.2    8.8e-07   28.6   0.2    1.5  1  Cellulase  Cellulase (glycosyl hydrolase family 5)
     0.0013   18.8   0.2     0.0025   17.9   0.2    1.4  1  DUF4434    Domain of unknown function (DUF4434)


Domain annotation for each model (and alignments):
>> Cellulase  Cellulase (glycosyl hydrolase family 5)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.2   9.8e-11   8.8e-07      11     278 ..      23     277 ..      11     279 .. 0.79

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 9.8e-11
                                   EEECET..TSCGGSHHHHHHHHHHHT-SEEEEEEECTGGTTSSTTTGCTHHHHHHHHHHHHHHHHTT-EEEEEE...ESS. CS
                     Cellulase  11 kglsts..wgnpyttkalidevkdagfntvRlpvswgelvenapdykvdenslerveevvkyakenglyvildi...Hse. 85 
                                   ++++++  w  ++ + + ++e+k+ g +++R+ +  +  v  +  ++++ +s++ ++ +++ + +  l+v++     H   
  gi|13541521|ref|NP_111209.1|  23 ANIKMWkeWN-EQEILDDLKEAKNIGCDFLRVFILDEDFV--NAYGEINVKSMAYMTRFLDMCSSLHLKVFITFivgHMSg 100
                                   5556656564.45788899999*************76777..555579**********************88762325559 PP

                                   TTT..CSSSSTTTTHHHHHHHHHHHHHHHHHHHTTTTTTEEEESSSS--STTCTCCTCHHHTTHHHHHHHHHHHHHHHHTT CS
                     Cellulase  86 egw..ltkadgnssedtaeeffkklwtqiAerykkndevvifelmNEPhgnntgaewtseeadevkayaeeaikaIRavgp 164
                                    +w   +  d n +e++a + f+k+++ + ++yk  + + ++ + NE   +++++     + ++ + +   ++ ++++ +p
  gi|13541521|ref|NP_111209.1| 101 RNWviPWAPDNNIYESKAIMNFSKFVEHFVNEYKTHPAIEGWLMSNEITLVKRPS-----SPEQAMVLESVFYGIVKNLDP 176
                                   666443344456677778888************9999999**********99984.....4588888999*********** PP

                                   SSEEEEECHHHHTBHHHHHCTSGSSSSTTEEEEEEEETTTHHHTGCGSHSCTHHHHHHHHHHHHHHHHHHTTS.EEEEEEE CS
                     Cellulase 165 nrliivegnswsgnldgavlndPndsqdnliysvHfYgpsdfaqtefgkdltdktnlaqrledaakylvekgi.pviigEf 244
                                   ++++  +       + +  ++ Pn  ++   + +H Y  +d                + ++ ++ + + + g  pv+++Ef
  gi|13541521|ref|NP_111209.1| 177 DHTVSSGD------VLSFLQQPPNIRNHSDYAGLHLYF-YDNDLLR----------QRYSYGSLLNIFSNDGSvPVFLEEF 240
                                   ***98777......55546668999899999999*998.5533333..........367788999999998888******* PP

                                   ESSTTSSHHHHHHHHHH.....HHHHHHTTTEEEEEEES CS
                     Cellulase 245 Ggsnadgdlakeeaekw.....ldylkekgiswiyWsln 278
                                   G s+++g  +++++ +      +++l++++++ ++W+++
  gi|13541521|ref|NP_111209.1| 241 GFSTNQG--TEKSQGEFiystlWTALANESMGGLVWCFS 277
                                   **99999..666666667788788889999999999876 PP

>> DUF4434  Domain of unknown function (DUF4434)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.2   2.8e-07    0.0025      15     136 ..      29     153 ..      17     177 .. 0.67

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.8e-07
                                   ----HHHHHHHHHHHHHTT--EEEES.....-SEETTEESS--HHHHTT----SB-HHHHHHHHHHHTT-EEEEE--B-SH CS
                       DUF4434  15 qnltdkqWkeklrelkelgmntlilq.....rvsykgkafypskllkekfekkakdlveaiLdaAdklgmkvflglnydee 90 
                                   +++++++   +l+e k++g++ l +       v++ g+++++s          + + ++++ ++  k  + +++g   +++
  gi|13541521|ref|NP_111209.1|  29 KEWNEQEILDDLKEAKNIGCDFLRVFildedFVNAYGEINVKSMA-------YMTRFLDMCSSLHLKVFITFIVGHM-SGR 101
                                   567777777788888888888764332344423333334444433.......3467788888888888888888876.556 PP

                                   HHH.HS-GGGGHHHHHH......HHHHHHHHTTT-TTEEEEEE----SS--T CS
                       DUF4434  91 wwdveedlsweielakr......vaeelakkYghhkafyGWYiseEidnank 136
                                    w +    +++i+++k       ++e  +++Y++h+a++GW +s+Ei   ++
  gi|13541521|ref|NP_111209.1| 102 NWVIPWAPDNNIYESKAimnfskFVEHFVNEYKTHPAIEGWLMSNEITLVKR 153
                                   6655544444444444444444599**********************98775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (647 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       513  (0.0286129); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.73u 0.28s 00:00:01.01 Elapsed: 00:00:00.51
# Mc/sec: 3817.48
//
Query:       gi|13541522|ref|NP_111210.1|  [L=70]
Description: transposase [Thermoplasma volcanium GSS1]
Scores for complete 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   32.3   0.0    1.2e-07   31.9   0.0    1.1  1  HTH_Tnp_1    Transposase
    0.00038   20.4   0.0    0.00045   20.2   0.0    1.1  1  HTH_29       Winged helix-turn helix
     0.0052   16.9   0.0     0.0065   16.6   0.0    1.2  1  HTH_28       Helix-turn-helix domain
  ------ inclusion threshold ------
       0.11   12.7   0.0       0.15   12.2   0.0    1.3  1  HTH_Tnp_1_2  Helix-turn-helix of insertion element transposas
       0.16   11.8   0.0       0.19   11.6   0.0    1.2  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 !   31.9   0.0   3.4e-11   1.2e-07       6      49 ..       7      49 ..       5      61 .. 0.89

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 3.4e-11
                     HTH_Tnp_1  6 rwsdefKariVreslepgksvsevArrhgvspnqLykWrrqyre 49
                                  ++++ +Ka+i  es  +  +++ ++rrhgvs + +ykWr ++ e
  gi|13541522|ref|NP_111210.1|  7 KFTADEKAAIAMES-FTAINIAGLCRRHGVSVSNFYKWRDKFIE 49
                                  8*************.6789*********************9864 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   1.2e-07   0.00045      14      51 ..      25      63 ..      13      67 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 1.2e-07
                        HTH_29 14 tvsqiAkllglsrrtvyrwlkrfeegGlaalld.rrrsg 51
                                  +++ +++++g+s + +y+w++ f e G ++    + ++g
  gi|13541522|ref|NP_111210.1| 25 NIAGLCRRHGVSVSNFYKWRDKFIESGKQGFYGsGVNNG 63
                                  67889***********************99987666666 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   1.8e-06    0.0065      14      43 ..      25      54 ..      12      56 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.8e-06
                        HTH_28 14 svreaArelgisrrtvyrWikryeegGiag 43
                                  +++ ++r++g+s +  y+W+ ++ e G +g
  gi|13541522|ref|NP_111210.1| 25 NIAGLCRRHGVSVSNFYKWRDKFIESGKQG 54
                                  56669********************99877 PP

>> HTH_Tnp_1_2  Helix-turn-helix of insertion element transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   4.2e-05      0.15      20      49 ..      17      46 ..       4      54 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4.2e-05
                                  HHHHH--S-HHHHHHHHTS-HHHHHHHHH- CS
                   HTH_Tnp_1_2 20 vendyekltldeiaeevgvsrsTlykWkkk 49
                                  + + +    ++ +++  gvs s +ykW++k
  gi|13541522|ref|NP_111210.1| 17 AMESFTAINIAGLCRRHGVSVSNFYKWRDK 46
                                  445677888999****************86 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   5.2e-05      0.19      22      45 ..      28      51 ..       9      57 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5.2e-05
                        HTH_23 22 eIAreLgvsrrTvyrwlkryreeG 45
                                    +r++gvs +  y+w+ ++ e+G
  gi|13541522|ref|NP_111210.1| 28 GLCRRHGVSVSNFYKWRDKFIESG 51
                                  569*****************7776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 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:                        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: 0.40u 0.30s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 464.29
//
Query:       gi|13541523|ref|NP_111211.1|  [L=106]
Description: hypothetical protein TVN0692 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-08   34.9   0.0    1.8e-08   34.6   0.0    1.1  1  rve            Integrase core domain
    6.9e-08   32.2   0.1    9.6e-08   31.7   0.1    1.2  1  rve_3          Integrase core domain
  ------ inclusion threshold ------
      0.022   15.0   0.0      0.026   14.8   0.0    1.1  1  DDE_Tnp_IS240  DDE domain


Domain annotation for each model (and alignments):
>> rve  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.6   0.0     3e-12   1.8e-08      67     118 ..      25      76 ..       9      77 .. 0.92

  Alignments for each domain:
  == domain 1  score: 34.6 bits;  conditional E-value: 3e-12
                           rve  67 pervlsDngseytskafrefladlgirvsftrpgrpqdnGkvErfhrtlkde 118
                                    +++++Dn ++y++k f+ +++ l+i +++  ++ p+dnG +E+fh  lk++
  gi|13541523|ref|NP_111211.1|  25 NLVLRTDNSPQYIAKGFKHTARLLNIPHEYIVKQTPDDNGDIESFHNSLKTD 76 
                                   5789*********************************************975 PP

>> rve_3  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.7   0.1   1.6e-11   9.6e-08       3      54 ..      50     101 ..      48     103 .. 0.95

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 1.6e-11
                         rve_3   3 ielsyiapgkPqqNglvEsfngtlrdellneelfrslaearekleawredYN 54 
                                   i ++yi   +P +Ng +Esf+++l++ ++  +  +s ++a+e++e +  +YN
  gi|13541523|ref|NP_111211.1|  50 IPHEYIVKQTPDDNGDIESFHNSLKTDYIRLNDLESYEDAKELIEYASNEYN 101
                                   77999*********************************************** PP

>> DDE_Tnp_IS240  DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   4.3e-06     0.026      57     129 ..      23      96 ..      14     104 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4.3e-06
                 DDE_Tnp_IS240  57 lepeeivtDkasay.asalkelkregelfdevshvqvkylnnriEsdhrtlKkrlrptrgfkslksaaktlagf 129
                                   l++ ++ tD ++ y a+++k+  r  +  +e    q++  n  iEs h+ lK  +   + ++s + a++ ++  
  gi|13541523|ref|NP_111211.1|  23 LNNLVLRTDNSPQYiAKGFKHTARLLNIPHEYIVKQTPDDNGDIESFHNSLKTDYIRLNDLESYEDAKELIEYA 96 
                                   6788899999998855778888887766677777788999****************************999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       378  (0.0210832); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.44
# Mc/sec: 730.84
//
Query:       gi|13541524|ref|NP_111212.1|  [L=83]
Description: hypothetical protein TVN0693 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    5.6e-06   26.2   1.0    6.9e-06   25.8   1.0    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 !   25.8   1.0   3.9e-10   6.9e-06     170     213 ..       6      49 ..       3      50 .. 0.95

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 3.9e-10
                     DDE_Tnp_1 170 lyrlRwqiErvFkwlkrkfgldrlryrglnrveaqllllllaln 213
                                   +y++Rw i  +F+++k+ +++d+l +r+ n +  q+++ ++a+ 
  gi|13541524|ref|NP_111212.1|   6 IYSQRWNIDIFFRTMKTYLKIDHLISRKINSIMVQIFTAMIAYI 49 
                                   8*****************************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       715  (0.0398795); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); 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 0.32s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 541.76
//
Query:       gi|13541525|ref|NP_111213.1|  [L=121]
Description: hypothetical protein TVN0694 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       579  (0.032294); expected 358.6 (0.02)
Passed bias filter:                      504  (0.0281109); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.48
# Mc/sec: 752.16
//
Query:       gi|13541526|ref|NP_111214.1|  [L=180]
Description: site-specific recombinase, DNA invertase Pin-related [Thermoplasma volcanium GSS1]
Scores for complete 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-35  120.5   0.0    7.4e-35  120.2   0.0    1.1  1  Resolvase  Resolvase, N terminal domain
  ------ inclusion threshold ------
       0.11   12.2   0.1       0.37   10.6   0.0    1.9  2  HTH_38     Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> Resolvase  Resolvase, N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.2   0.0   8.3e-39   7.4e-35      18     145 ..       2     128 ..       1     129 [. 0.96

  Alignments for each domain:
  == domain 1  score: 120.2 bits;  conditional E-value: 8.3e-39
                                   HHHHHHHHH-S--..SE...EEEE.S-TT-TT-HHHHHHHHHHTT-EE.EEEESSCCCC-S...S-HHHHHHHHHTT-EEE CS
                     Resolvase  18 rQkealrayakenglkivkefeDkgvSGakleRpglkrllaalregkgdvlvvekldRLaRsvrdlltlleelrekgvslv 98 
                                   rQ+ea+r+y + +g+++ ++feDk++SG++++Rp+++r+l+ l+  + +v++v k+dR+aRs++dll++le l  +g  ++
  gi|13541526|ref|NP_111214.1|   2 RQREAIRQYVEPRGYEL-EFFEDKAKSGKNTQRPEFERMLKSLEG-RPKVVIVSKVDRFARSLSDLLRILEFLGHNGTGFI 80 
                                   8**************99.88***********************99.448******************************** PP

                                   ESS...SS----HHHHHHHHHHHHHHHHHHHHHCT-TTHHHHHHHHHH CS
                     Resolvase  99 slde.gidtstpmgrlllqilaalaeferelirertkeglaaakakGk 145
                                   s+++ gidt+tp+grlllqil+a+ efer++i   tk+g+++a  kG+
  gi|13541526|ref|NP_111214.1|  81 SINDpGIDTTTPNGRLLLQILGAFEEFERNMINSFTKAGREKAMNKGV 128
                                   ***956**************************************9997 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0      0.48   4.3e+03       9      19 ..     108     118 ..     106     120 .. 0.73
   2 ?   10.6   0.0   4.2e-05      0.37      12      42 ..     147     177 ..     141     178 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.48
                        HTH_38   9 eReeIerllae 19 
                                   eR++I    ++
  gi|13541526|ref|NP_111214.1| 108 ERNMINSFTKA 118
                                   99999766655 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 4.2e-05
                        HTH_38  12 eIerllaeGlslreIArrLgrspsTIsRElk 42 
                                   +   l  +Gls r+IA+ + +s + I + lk
  gi|13541526|ref|NP_111214.1| 147 KVMELKGKGLSARAIAKSMECSITPILKILK 177
                                   55667779***********999887777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       388  (0.0216409); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.51
# Mc/sec: 1071.66
//
Query:       gi|13541527|ref|NP_111215.1|  [L=60]
Description: AAA ATPase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0074   15.7   0.0     0.0074   15.7   0.0    1.1  1  FtsK_SpoIIIE     FtsK/SpoIIIE family
  ------ inclusion threshold ------
      0.011   16.1   0.0      0.012   15.9   0.0    1.2  1  AAA_22           AAA domain
      0.014   15.3   0.0      0.014   15.3   0.0    1.1  1  ATPase_2         ATPase domain predominantly from Archaea
      0.019   15.3   0.0      0.021   15.2   0.0    1.1  1  AAA_16           AAA ATPase domain
      0.034   13.3   0.0      0.036   13.3   0.0    1.0  1  DAP3             Mitochondrial ribosomal death-associated pro
      0.034   13.0   0.0      0.041   12.8   0.0    1.1  1  TrwB_AAD_bind    Type IV secretion-system coupling protein DN
      0.046   13.4   0.0      0.048   13.4   0.0    1.0  1  Sigma54_activat  Sigma-54 interaction domain
      0.057   13.1   0.0      0.073   12.8   0.0    1.2  1  AAA_24           AAA domain
      0.069   12.3   0.0      0.073   12.2   0.0    1.0  1  DUF815           Protein of unknown function (DUF815)
      0.076   12.1   0.0      0.081   12.0   0.0    1.1  1  T2SSE            Type II/IV secretion system protein
       0.12   12.9   0.1       0.21   12.0   0.0    1.4  2  AAA              ATPase family associated with various cellul
       0.16   11.9   0.0       0.17   11.9   0.0    1.1  1  ResIII           Type III restriction enzyme, res subunit
       0.17   11.8   0.0       0.17   11.8   0.0    1.1  1  Microtub_bd      Microtubule binding
       0.18   11.5   0.0       0.19   11.4   0.0    1.1  1  SWI2_SNF2        SWI2/SNF2 ATPase
       0.21   10.3   0.0       0.24   10.1   0.0    1.0  1  RNA12            RNA12 protein


Domain annotation for each model (and alignments):
>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   6.2e-06    0.0074      33      61 ..      25      50 ..       3      57 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 6.2e-06
                                  EEGGGS-.SEEEE--TTSSHHHHHHHHHH CS
                  FtsK_SpoIIIE 33 ldlkkmashllvaGatgsGKStalntLil 61
                                  ++l   + h+++ G++gsGK+  l +Li+
  gi|13541527|ref|NP_111215.1| 25 VNLH-LPRHIIIYGSKGSGKT--LSALIM 50
                                  3333.337************8..556665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.9   0.0   9.7e-06     0.012       6      30 ..      31      55 ..      15      58 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 9.7e-06
                        AAA_22  6 gilvvtGesGtGKTtllrrlleqld 30
                                  ++++++G +G+GKT+++  ++e l+
  gi|13541527|ref|NP_111215.1| 31 RHIIIYGSKGSGKTLSALIMVEALK 55
                                  79**************998888775 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.0   1.2e-05     0.014       9      46 ..      19      56 ..      12      60 .] 0.82

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.2e-05
                      ATPase_2  9 keleeilerepneiyfiYGpegsGKtaLlkeiienled 46
                                  ++l e+++    + + iYG++gsGKt     ++e l++
  gi|13541527|ref|NP_111215.1| 19 NDLAEYVNLHLPRHIIIYGSKGSGKTLSALIMVEALKE 56
                                  678889999999999***********877777777654 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.0   1.8e-05     0.021       7      41 ..      12      47 ..      11      59 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.8e-05
                        AAA_16  7 eeleqL.lsalervrsgrpelvllsGesGvGKsslv 41
                                  +el+++ +++ e v+ + p+ ++++G +G+GK+  +
  gi|13541527|ref|NP_111215.1| 12 KELDKVtNDLAEYVNLHLPRHIIIYGSKGSGKTLSA 47
                                  6788886666778999999**************876 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 ?   13.3   0.0     3e-05     0.036       2      39 ..       9      46 ..       8      56 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3e-05
                                  ---SHHHHHHHHHTTS-SSS---EEEEE-SSSSSTTTT CS
                          DAP3  2 lvReetlelikklkkadkkkkvkrlvltGekgsGKSvl 39
                                  l+R+e  ++++ l +  + +    ++++G kgsGK+++
  gi|13541527|ref|NP_111215.1|  9 LIRKELDKVTNDLAEYVNLHLPRHIIIYGSKGSGKTLS 46
                                  7899999999999999999999**************86 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   3.4e-05     0.041      16      41 ..      31      56 ..      24      58 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.4e-05
                 TrwB_AAD_bind 16 qhilivGttGsGKtqalekllraira 41
                                  +hi+i G+ GsGKt  +  +++a+++
  gi|13541527|ref|NP_111215.1| 31 RHIIIYGSKGSGKTLSALIMVEALKE 56
                                  8*************999998888765 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0     4e-05     0.048       6      45 ..      12      53 ..       8      59 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4e-05
                                  HHHHHHHHHHHHHCTSS..S-EEEECSTTSSHHHHHHHHHHH CS
               Sigma54_activat  6 ealkelleqikkvaktd..lsvlitGesGtGKellaraihea 45
                                  ++l ++++ ++++++ +   +++i G +G+GK+l a  + ea
  gi|13541527|ref|NP_111215.1| 12 KELDKVTNDLAEYVNLHlpRHIIIYGSKGSGKTLSALIMVEA 53
                                  567777777777776654489*************99988775 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   6.1e-05     0.073       3      22 ..      31      50 ..      29      57 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.1e-05
                        AAA_24  3 lkiliyGpsgiGKTtlakel 22
                                  + i+iyG+ g+GKT +a+ +
  gi|13541527|ref|NP_111215.1| 31 RHIIIYGSKGSGKTLSALIM 50
                                  5799**********999877 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   6.1e-05     0.073      34      69 ..      11      46 ..       6      58 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 6.1e-05
                        DUF815 34 dkqkealventeqfleglpannvLLwGarGtGKSsl 69
                                   k+ ++++++ +++++ +  ++++++G++G+GK   
  gi|13541527|ref|NP_111215.1| 11 RKELDKVTNDLAEYVNLHLPRHIIIYGSKGSGKTLS 46
                                  5667889999999********************533 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   6.7e-05     0.081     119     155 ..      22      56 ..       3      58 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 6.7e-05
                         T2SSE 119 aevlrkavrerglilvsGgTgsGKttllyallkeink 155
                                   ae ++        i++ G  gsGKt ++ ++++ +++
  gi|13541527|ref|NP_111215.1|  22 AEYVNLH--LPRHIIIYGSKGSGKTLSALIMVEALKE 56 
                                   4444433..346799*************999999887 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       5.4   6.4e+03      63      71 ..      10      18 ..       4      25 .. 0.56
   2 ?   12.0   0.0   0.00017      0.21       1      23 [.      33      55 ..      33      59 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 5.4
                                  EEETGGGHH CS
                           AAA 63 fiDEidala 71
                                  +  E+d+++
  gi|13541527|ref|NP_111215.1| 10 IRKELDKVT 18
                                  444555543 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00017
                                  EEEESSTTSSHHHHHHHHHHHHT CS
                           AAA  1 vllyGppGtGKTllakavakelg 23
                                  +++yG +G GKTl a  +++ l+
  gi|13541527|ref|NP_111215.1| 33 IIIYGSKGSGKTLSALIMVEALK 55
                                  689************99988876 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00014      0.17      12      51 ..      18      57 ..       7      60 .] 0.76

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00014
                                  HHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S. CS
                        ResIII 12 ienlleklkskrdkrglikmaTGtGKTlvaaklierllkk 51
                                   ++l+e ++ +  ++++i    G+GKTl a+ ++e+l+++
  gi|13541527|ref|NP_111215.1| 18 TNDLAEYVNLHLPRHIIIYGSKGSGKTLSALIMVEALKES 57
                                  34444444448889****************9999999887 PP

>> Microtub_bd  Microtubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00014      0.17      62      98 ..      12      45 ..       1      57 [. 0.77

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00014
                                  THCCCCCCCCHHHHHHHHTT--EEEEEEES....... CS
                   Microtub_bd 62 seqeevfeeisqlvqsaldgynvcifaygqTGsGKty 98
                                  +e ++v+++++ +v+  l +    i+ yg+ GsGKt 
  gi|13541527|ref|NP_111215.1| 12 KELDKVTNDLAEYVNLHLPR---HIIIYGSKGSGKTL 45
                                  45578999999999999865...59**********96 PP

>> SWI2_SNF2  SWI2/SNF2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00016      0.19      16      44 ..      28      56 ..       8      59 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00016
                     SWI2_SNF2 16 gdrkgGviWHtqGSGKsltmvflakklle 44
                                  +  ++ +i+  +GSGK+l+ ++++++l+e
  gi|13541527|ref|NP_111215.1| 28 HLPRHIIIYGSKGSGKTLSALIMVEALKE 56
                                  556777999***************99987 PP

>> RNA12  RNA12 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0    0.0002      0.24       5      41 ..      14      56 ..      11      58 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0002
                         RNA12  5 iedlkewleEnvn....tFivvkGPrGSGkk..eLvldrvlkd 41
                                   +++ + l+E+vn      i++ G +GSGk+   L++ ++lk+
  gi|13541527|ref|NP_111215.1| 14 LDKVTNDLAEYVNlhlpRHIIIYGSKGSGKTlsALIMVEALKE 56
                                  5667777777776333357***********6448999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (60 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       508  (0.028334); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); expected 358.6 (0.02)
Passed Vit filter:                       103  (0.00574488); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 389.37
//
Query:       gi|13541528|ref|NP_111216.1|  [L=188]
Description: hypothetical protein TVN0697 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
       0.16   12.3   0.0       0.34   11.3   0.0    1.5  1  NADH-UOR_E  putative NADH-ubiquinone oxidoreductase chain E


Domain annotation for each model (and alignments):
>> NADH-UOR_E  putative NADH-ubiquinone oxidoreductase chain E
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   1.9e-05      0.34      10      55 ..      62     108 ..      58     115 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 1.9e-05
                                   TTTTHHHHHHHHHTTS-.TT-EEEEEE-SS--SHHHHHHHTT-TTT- CS
                    NADH-UOR_E  10 kdnllerlkelldkevk.egevaiflfevgdFsavqksadlikergd 55 
                                   ++n    l++ll +e++ ++e ++++f v+ Fs+v   + ++++rg+
  gi|13541528|ref|NP_111216.1|  62 HKNYWRPLGKLLGEEIDiTDEEIVLVFPVKMFSKVAEIVPFVRKRGQ 108
                                   55677778889988886367899999******************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1242.90
//
Query:       gi|13541529|ref|NP_111217.1|  [L=138]
Description: hypothetical protein TVN0698 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       235  (0.0131073); expected 358.6 (0.02)
Passed bias filter:                      229  (0.0127726); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 00:00:00.42
# Mc/sec: 997.64
//
Query:       gi|13541530|ref|NP_111218.1|  [L=378]
Description: hypothetical protein TVN0699 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (378 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       639  (0.0356406); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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 0.25s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 2530.26
//
Query:       gi|13541531|ref|NP_111219.1|  [L=117]
Description: hypothetical protein TVN0700 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score 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      0.032   14.5   0.1    1.7  1  D5_N      D5 N terminal like


Domain annotation for each model (and alignments):
>> D5_N  D5 N terminal like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   1.8e-06     0.032     100     135 ..      74     109 ..       3     116 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.8e-06
                          D5_N 100 lllafaNGvldlktgelrdhepedyltkitpvdydp 135
                                   + ++ + G l+l+t++ + h p++++t+ +p  y p
  gi|13541531|ref|NP_111219.1|  74 HTIPIEAGLLNLQTKTITAHTPDYFYTEYLPRRYVP 109
                                   579999*************************99976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       244  (0.0136092); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); 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 0.28s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 792.81
//
Query:       gi|13541532|ref|NP_111220.1|  [L=180]
Description: hypothetical protein TVN0701 [Thermoplasma volcanium GSS1]
Scores for 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   35.7   0.2      1e-08   35.7   0.2    1.6  2  Prim-Pol  Bifunctional DNA primase/polymerase, N-terminal


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 !   35.7   0.2   5.8e-13     1e-08      85     155 ..      23      90 ..       6      93 .. 0.75
   2 ?   -2.7   0.2      0.38   6.8e+03       9      32 ..     149     170 ..     134     177 .. 0.51

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 5.8e-13
                      Prim-Pol  85 etvtvttgstgggrhlyfraPdglalpnsagklapgldlrgeggyvvappsvhetgraYrwledp...reiael 155
                                   +       ++ +g h yfr+ ++l ++++++   + ++++ +++y ++pps h++g++Y+w ++     +++++
  gi|13541532|ref|NP_111220.1|  23 N------VRSVRGAHWYFRNTKNLPNESNKQTAVGIFEFHTTNKYALIPPSDHPSGTKYEWEKPLptiGDLPDA 90 
                                   3......45667*******77666666666666666**************************766544444444 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.38
                      Prim-Pol   9 wpvvPlppggKrPlgkkwekdatt 32 
                                   wpv  l++++  P++ + + +  t
  gi|13541532|ref|NP_111220.1| 149 WPVA-LSQNSMIPAR-ATQGRNRT 170
                                   4422.2344444444.34444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       291  (0.0162307); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1177.43
//
Query:       gi|13541533|ref|NP_111221.1|  [L=320]
Description: hypothetical protein TVN0702 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.024   14.7   0.0       0.19   11.8   0.0    2.1  2  HTH_20    Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0     1e-05      0.19      19      46 ..      19      47 ..       9      48 .. 0.86
   2 ?   -0.1   0.0     0.057     1e+03       9      31 ..     283     305 ..     282     313 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1e-05
                                  H.STCTTB-HHHHHHHHTS-HHHHHHHHH CS
                        HTH_20 19 L.araegltaselaerldlskntlsyHLr 46
                                  L   +e+++ +el er +ls+  l yHL+
  gi|13541533|ref|NP_111221.1| 19 LdDNPEPMSREELRERTGLSREDLKYHLK 47
                                  46779***********************8 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.057
                                   -HHHHHHHHHHSTCTTB-HHHHH CS
                        HTH_20   9 hPvRrrilraLaraegltasela 31 
                                   ++++ +i++aL+++ +l  + ++
  gi|13541533|ref|NP_111221.1| 283 DKTQTDIFKALKGKVPLGYEVIH 305
                                   78999******888877666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       727  (0.0405488); expected 358.6 (0.02)
Passed bias filter:                      594  (0.0331307); 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: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 2016.30
//
Query:       gi|13541534|ref|NP_111222.1|  [L=218]
Description: Serine/threonine protein phosphatase [Thermoplasma volcanium GSS1]
Scores for complete sequence (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   61.0   0.0    1.8e-16   60.5   0.0    1.1  1  PP2C_2     Protein phosphatase 2C
      6e-08   32.8   0.0    1.8e-07   31.3   0.0    1.8  1  SpoIIE     Stage II sporulation protein E (SpoIIE)
    2.7e-05   23.9   0.0    0.00012   21.9   0.0    1.9  2  PP2C       Protein phosphatase 2C
  ------ inclusion threshold ------
       0.12   12.0   0.0       0.16   11.5   0.0    1.2  1  ATP-grasp  ATP-grasp domain


Domain annotation for each model (and alignments):
>> PP2C_2  Protein phosphatase 2C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.5   0.0   3.9e-20   1.8e-16      11     192 ..      19     189 ..      15     197 .. 0.78

  Alignments for each domain:
  == domain 1  score: 60.5 bits;  conditional E-value: 3.9e-20
                        PP2C_2  11 pcqDalavwtdsggsllaVaDGaGSakrSerGariaveavvealaelleseeeeeeallraleaailadvlkeeaeaqdae 91 
                                    ++D++   ++++  l++VaDG+GS ++S+ ++r av+ + +  +e+ +     +e+l++++ +  +     e ++ +  +
  gi|13541534|ref|NP_111222.1|  19 ENEDSYS--VTDD--LFIVADGVGSYEGSKDASRYAVNYLSKMAKEIQS-----KEQLVEEIIKLSE-----EIKSIGIIS 85 
                                   5777775..4444..78*******************9998888887775.....4667787776666.....346788888 PP

                        PP2C_2  92 lkdyatTllaav.vtpdeivalqiGDGaivvrdrdgevqllgepds.geyanqttfltsedaeeelrirrlk..ledgdal 168
                                    + + +T + ++ ++ ++ + +++GD+ iv+  r g++  l  +ds +  +++ ++l +   + +  ++ ++  le+gd +
  gi|13541534|ref|NP_111222.1|  86 GRPLMSTTISVLkISTEKYITANVGDSPIVL-LRSGKLYKLYIDDSeRSSTGNRFALEQAFGWNHVIVHSFEgkLEKGDLF 165
                                   888888888888799**************65.6777777776666525556666666666667777777776769****** PP

                        PP2C_2 169 llmTDGlanslrdeerfaelleel 192
                                   +++TDG++++l+de+++ ++l+el
  gi|13541534|ref|NP_111222.1| 166 IICTDGVSDNLSDEYDLYSILREL 189
                                   ****************99999886 PP

>> SpoIIE  Stage II sporulation protein E (SpoIIE)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   0.0     4e-11   1.8e-07       7     191 ..      31     214 ..      26     216 .. 0.65

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 4e-11
                                   EEEEECSS...SSHHHHHHHHHHHHHHHHHHHTTTS.HHHHHHHHHHHCHCTTSTT.TTCEEEEEEEETTTTEEEEEEESS CS
                        SpoIIE   7 lvvgDvvG...hGleAalimgllrsalrelatagle.paevlkrlnralardleeeerfaTavlavydpstgkleyanaGh 83 
                                   ++v+D+vG    + +A+  ++  +s++ + ++++ + ++e++k  +++ +  + +   +++ ++ v+++st+k   an+G+
  gi|13541534|ref|NP_111222.1|  31 FIVADGVGsyeGSKDASRYAVNYLSKMAKEIQSKEQlVEEIIKLSEEIKSIGIISGRPLMSTTISVLKISTEKYITANVGD 111
                                   78999999553333444444444444444443333325555555555555555555788888888889************* PP

                                   SSEEEEETTS.....TEEEEE--SS--TTTSSS.....T-EEEEEEE--TTEEEEEESCCCCSSSHHHHHHCCCHHCHHHH CS
                        SpoIIE  84 pppllvrpdg.....gtklllastglplGilpe.....adyetaelelepgdtlllyTDGvtEardsdgelfgkerllall 154
                                   +p++l+r+ +            stg    + +        + + e +le+gd+ +++TDGv ++ +++  l        +l
  gi|13541534|ref|NP_111222.1| 112 SPIVLLRSGKlyklyIDDSERSSTGNRFALEQAfgwnhVIVHSFEGKLEKGDLFIICTDGVSDNLSDEYDL------YSIL 186
                                   ********66877773333344444444443336665599999999*****************99666665......4444 PP

                                   CT.....HCCHHHHHHHHHHHHTTSSSSS-EEEEEEE CS
                        SpoIIE 155 asaegesleelldalveellelgsgeleDDitllvlr 191
                                   +       e  ++++v+ +l+  +g + DD+t++ + 
  gi|13541534|ref|NP_111222.1| 187 R-------ELDAQTIVRLALN--KGIKPDDATIIKVY 214
                                   4.......2345555655555..45667777777665 PP

>> PP2C  Protein phosphatase 2C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   2.6e-08   0.00012      11     133 ..       7     123 ..       1     135 [. 0.65
   2 ?   -0.4   0.0      0.16   7.1e+02     206     223 ..     163     180 ..     152     206 .. 0.75

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 2.6e-08
                                   CCSSHHEEEECCCCTCTTCCCCCCEEEEEEEEESSSH....HHHHHHHHHHHHHHHHHHCHTTHHHHHHHHHHHHHHHHHH CS
                          PP2C  11 arksmedahislanlesssgkssvsffavfdghggse....aakyarehleeilksqksfeelekleqalrksfladtdee 87 
                                   +++s+   h++l+n    s   ++ +f v dg+g++e    a++ya + l +++k+ +s+e+l        + + + ++ee
  gi|13541534|ref|NP_111222.1|   7 FSDSSAVPHLHLENED--SYSVTDDLFIVADGVGSYEgskdASRYAVNYLSKMAKEIQSKEQL-------VEEIIK-LSEE 77 
                                   5556666666666443..566788889999998877611114445555555555555555555.......455555.5555 PP

                                   HHH..HHHHCHCCT-EEEEEEEEEETTEEEEEEESS-EEEEEETTEEE CS
                          PP2C  88 lks..skantepsksGstavvalirgtklyvAnvGDSravLcrkgnak 133
                                   +ks      +      +t +v  i+ +k ++AnvGDS +vL r+g+ +
  gi|13541534|ref|NP_111222.1|  78 IKSigI--ISGRPLMSTTISVLKISTEKYITANVGDSPIVLLRSGKLY 123
                                   665321..12345566899999999999***************99865 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.16
                                   EEEEEE-HHHHTTSHHHH CS
                          PP2C 206 efliLacdGlwdvlsdqe 223
                                   + +i+ +dG+ d lsd+ 
  gi|13541534|ref|NP_111222.1| 163 DLFIICTDGVSDNLSDEY 180
                                   56789999*999999984 PP

>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   3.6e-05      0.16      31      90 ..      31      90 ..      10     116 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.6e-05
                                  EEEEESSS-CTTTTEEEECTCCGHHCHHHHCGTTCEEEEE----SEEEEEEEEEETTC-E CS
                     ATP-grasp 31 vvvKarrlgydGkGqsvvrseedleqalealkeekvivEefvpfekElsvlvvrsaeGet 90
                                  ++v   +++y+G         + l+++++++++++ +vEe+++++ E+  +++ s +  +
  gi|13541534|ref|NP_111222.1| 31 FIVADGVGSYEGSKDASRYAVNYLSKMAKEIQSKEQLVEEIIKLSEEIKSIGIISGRPLM 90
                                  5666677888888888888888999999*********************99987665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       657  (0.0366445); expected 358.6 (0.02)
Passed bias filter:                      521  (0.0290591); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1457.17
//
Query:       gi|13541535|ref|NP_111223.1|  [L=216]
Description: sugar fermentation stimulation protein A [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-33  115.3   0.0    2.6e-33  114.8   0.0    1.2  1  SfsA      Sugar fermentation stimulation protein RE domain
    1.1e-14   54.3   0.2    1.8e-14   53.7   0.2    1.4  1  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 !  114.8   0.0   2.9e-37   2.6e-33      11     135 ..      79     197 ..      71     200 .. 0.88

  Alignments for each domain:
  == domain 1  score: 114.8 bits;  conditional E-value: 2.9e-37
                                   HEE...........EEES-EETTEE-SEEEE-S.SSEEEEEEEE--EE..EEEEE-SS--HHHHHHHHHHHHHHHTT-EEE CS
                          SfsA  11 lesgli.elagyeeikrevkygnsriDfllekeeeekcyvEVKsvtleeggialfPdapteRgqkhleeLaelvkegyrav 90 
                                   l+s++  ++   +e+k+evk+++ r+Df+++     ++++EVK++tl+ +g+a fPdapt Rg +hl+ L +l++eg+ a+
  gi|13541535|ref|NP_111223.1|  79 LHSQIAsHF-VSQECKPEVKIDDRRLDFACN-----DIFIEVKGCTLSIDGVAIFPDAPTLRGYEHLRLLERLAQEGKGAY 153
                                   444443222.34689**************55.....69***********99****************************** PP

                                   EEEEE-SSS--EEEE-TTT-HHHHHHHHHHHHHT-EEEEEEEEE- CS
                          SfsA  91 vlfvvqredarefkpnkeidpefaealreaaeaGVevlaydckvt 135
                                   vlf++  +da++f+pn+e+dp+f++ +++a ++GV++   +++++
  gi|13541535|ref|NP_111223.1| 154 VLFLIF-SDATSFRPNSETDPRFSDEFYKALKNGVKFSFKRFSFD 197
                                   *****9.69***************************998888776 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 !   53.7   0.2     2e-18   1.8e-14       1      63 []      12      75 ..      12      75 .. 0.89

  Alignments for each domain:
  == domain 1  score: 53.7 bits;  conditional E-value: 2e-18
                                  EEEEETTEEEEEEE.....EE----S--TTT--TT-EEEEE....ESSS-SEEEEEEEETTEEEE- CS
                        SfsA_N  1 lrRpnRFladveldg...tvHvpntGrlkelllpGarvllsksdnpkrKtkytleavekegtwvgi 63
                                  ++R+nRFl++v+l++   ++H++++Grlke+++ G++vl+++  + ++Kt y++    +e+++++i
  gi|13541535|ref|NP_111223.1| 12 VERVNRFLVNVKLNDkivEAHLHDPGRLKEIIYTGNKVLVRR--KSGKKTGYRITFGLREDQYILI 75
                                  79************75656**********************6..678******9988888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       310  (0.0172904); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 1444.79
//
Query:       gi|13541536|ref|NP_111224.1|  [L=288]
Description: small-conductance mechanosensitive channel protein [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.4e-20   73.0   6.7    2.4e-20   73.0   6.7    1.7  2  MS_channel  Mechanosensitive ion channel


Domain annotation for each model (and alignments):
>> MS_channel  Mechanosensitive ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.4   1.2      0.66   1.2e+04       7      19 ..      13      25 ..       9      34 .. 0.46
   2 !   73.0   6.7   1.3e-24   2.4e-20       4     142 ..      92     236 ..      90     286 .. 0.87

  Alignments for each domain:
  == domain 1  score: -4.4 bits;  conditional E-value: 0.66
                                  HHHHHHHHHHHHT CS
                    MS_channel  7 liivvgilivlsl 19
                                  ++i+++i i+l+ 
  gi|13541536|ref|NP_111224.1| 13 IAIILVISIALFI 25
                                  3333333333333 PP

  == domain 2  score: 73.0 bits;  conditional E-value: 1.3e-24
                                   HHHHHHHHHHHHHHHTTT--SCCHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHTT-SS-TT-EEESS......SEEEEEEE CS
                    MS_channel   4 lkiliivvgilivlsllgvnvsallavlGalglalglalkdlisnlvaGiillfekpfkiGDlveig......dieGtVed 78 
                                   +++ +++++i ++l++lg+n++  l++  +++l +g+al++++sn+++G+ ++   ++k G++v +g       i+G++++
  gi|13541536|ref|NP_111224.1|  92 ISFFMYTLIIAVILTSLGINLTGALVGGSVGALIIGIALQNIFSNIFSGFAVTSAGAIKPGEIVSMGswlfgsPITGEIVK 172
                                   78999**************************************************************************** PP

                                   E-SSEEEEEETTSEEEEEEHHHHHTS-E.EESSS.SSEEEEEEEEEE-TTS-...HHHHHHHHHH CS
                    MS_channel  79 iglrttkirtfdgrivtiPnsslvtsni.eNlsresgtrrikvsigvtyssdvkklekvleelke 142
                                   ++ ++t++++ +gri+ +Pns+++ ++i e ls+ +   + +v+++++ + +++++ek ++e++ 
  gi|13541536|ref|NP_111224.1| 173 VSYLFTDVKNSNGRIIKVPNSAFLGNTIfERLSG-ESDFSYNVQVTLPSDVPQSAIEKHIREINA 236
                                   ***********************98776155555.666666666666666666677777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       966  (0.0538792); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); 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 0.28s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2053.76
//
Query:       gi|13541537|ref|NP_111225.1|  [L=133]
Description: thioesterase [Thermoplasma volcanium GSS1]
Scores for complete 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   60.7   0.1    2.1e-16   60.5   0.1    1.0  1  4HBT_2       Thioesterase-like superfamily
    4.1e-15   55.9   0.0    5.2e-15   55.6   0.0    1.1  1  4HBT         Thioesterase superfamily
    5.4e-13   48.8   1.2    5.1e-06   25.9   0.5    2.0  2  Acyl-ACP_TE  Acyl-ACP thioesterase


Domain annotation for each model (and alignments):
>> 4HBT_2  Thioesterase-like superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.5   0.1   3.6e-20   2.1e-16       1     121 [.      13     126 ..      13     128 .. 0.95

  Alignments for each domain:
  == domain 1  score: 60.5 bits;  conditional E-value: 3.6e-20
                        4HBT_2   1 vrpndvDlnghlnnarylryleearvkflertglksrsiarrgiglilssahvryrrplkfpdrltvefrvididaktlii 81 
                                   vr nd+D  gh+nna y+ y+e++r++f+  +++  + ++   i  ++++a+ ++ +++ + d ++v++ ++++  +++ +
  gi|13541537|ref|NP_111225.1|  13 VRYNDLDTVGHVNNAIYFTYFEIGRIDFI--NKF-LWKFKSDEINFVIARAEADFIKSILLYDVVYVRTWISRVGNTSFDF 90 
                                   799**************************..899.9********************************************* PP

                        4HBT_2  82 ehrflsnadgkkaarveerivvmdygkrskkapvPpellk 121
                                    +r+ + +dgk+ a++++ +v+  +  + k++pvP+e+++
  gi|13541537|ref|NP_111225.1|  91 SYRLED-EDGKEYATGKTINVILSN--G-KPSPVPNEIKA 126
                                   ****99.66777*************..3.78****99975 PP

>> 4HBT  Thioesterase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.6   0.0   8.8e-19   5.2e-15       2      78 ..      22     102 ..      21     103 .. 0.97

  Alignments for each domain:
  == domain 1  score: 55.6 bits;  conditional E-value: 8.8e-19
                                   SSB-HHHHHHHHHHHHHHHHHHTTST....TEEEEEEEEEEEESS-BBTTCEEEEEEEEEEEESSEEEEEEEEEETTSCEE CS
                          4HBT   2 GvvhgGvylallDeaagaalrslggr....gilvvvvelsidflrpvrlgdeltvearvlrlgrtsavvevevrdedgrlv 78 
                                   G+v+++ y+++++ ++ +++++   +    +i +v+++ ++df++++ l d+++v+++++r+g+ts+ +++++ dedg++ 
  gi|13541537|ref|NP_111225.1|  22 GHVNNAIYFTYFEIGRIDFINKFLWKfksdEINFVIARAEADFIKSILLYDVVYVRTWISRVGNTSFDFSYRLEDEDGKEY 102
                                   9*********************999999*************************************************9976 PP

>> Acyl-ACP_TE  Acyl-ACP thioesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.5   8.6e-10   5.1e-06     153     180 ..       5      32 ..       2      47 .. 0.85
   2 !   22.3   0.0   1.1e-08   6.8e-05      49     133 ..      48     130 ..      34     133 .] 0.89

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 8.6e-10
                   Acyl-ACP_TE 153 eseekelkvrysDlDlnqHvNNvkYlew 180
                                   ++++++++vry DlD+ +HvNN+ Y+ +
  gi|13541537|ref|NP_111225.1|   5 AYSKTKIQVRYNDLDTVGHVNNAIYFTY 32 
                                   678899*******************986 PP

  == domain 2  score: 22.3 bits;  conditional E-value: 1.1e-08
                   Acyl-ACP_TE  49 lkklnlvWvvakyeieierlpefgdkveietwaesenklfcyrdfkvrdekgekiieaksvfvlmdqetrrlsrvtdeila 129
                                   +k  +   v+a+ e +  + + + d+v ++tw++  ++      ++++de+g++ ++ k + v++   + ++s v++ei a
  gi|13541537|ref|NP_111225.1|  48 FKSDEINFVIARAEADFIKSILLYDVVYVRTWISRVGNTSFDFSYRLEDEDGKEYATGKTINVILS--NGKPSPVPNEIKA 126
                                   78888999*************************************************999999985..5789999**9999 PP

                   Acyl-ACP_TE 130 eyee 133
                                    + e
  gi|13541537|ref|NP_111225.1| 127 LLME 130
                                   8844 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       340  (0.0189637); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); 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 0.27s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 939.19
//
Query:       gi|13541538|ref|NP_111226.1|  [L=96]
Description: coiled-coil protein [Thermoplasma volcanium GSS1]
Scores for complete 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   5.3      0.076   12.9   1.2    2.9  2  HSBP1            Heat shock factor binding protein 1
     0.0012   18.0   5.7     0.0015   17.7   5.7    1.0  1  TelA             Toxic anion resistance protein (TelA)
     0.0016   18.9   0.5     0.0018   18.7   0.5    1.1  1  DUF5063          Domain of unknown function (DUF5063)
     0.0039   17.1   2.8     0.0059   16.5   1.9    1.6  1  Apolipoprotein   Apolipoprotein A1/A4/E domain
     0.0095   16.4   1.2      0.018   15.5   1.2    1.5  1  NPV_P10          Nucleopolyhedrovirus P10 protein
  ------ inclusion threshold ------
      0.026   15.1   5.4       0.03   14.9   5.4    1.1  1  DUF2408          Protein of unknown function (DUF2408)
      0.026   14.5   0.1      0.045   13.8   0.1    1.4  1  FAS_N            N-terminal domain in fatty acid synthase sub
      0.029   14.6   6.3      0.079   13.2   1.2    2.3  2  XhlA             Haemolysin XhlA
      0.031   15.3   3.0      0.031   15.3   3.0    1.8  2  DUF4927          Domain of unknown function (DUF4927)
      0.032   14.3   7.7         12    6.0   7.7    2.7  1  DASH_Dad3        DASH complex subunit Dad3
      0.036   14.6   1.2      0.053   14.1   1.2    1.5  1  TipAS            TipAS antibiotic-recognition domain
      0.041   13.3   0.5      0.044   13.2   0.5    1.1  1  Chal_sti_synt_N  Chalcone and stilbene synthases, N-terminal 
      0.058   13.3   3.0        4.5    7.2   0.2    2.6  3  MtrG             Tetrahydromethanopterin S-methyltransferase,
      0.063   13.8   3.7      0.072   13.6   3.7    1.1  1  Carbpep_Y_N      Carboxypeptidase Y pro-peptide
      0.085   12.6   0.2      0.098   12.4   0.2    1.0  1  Peptidase_C26    Peptidase C26
      0.086   13.1   0.1       0.13   12.5   0.1    1.3  1  Retrotrans_gag   Retrotransposon gag protein
      0.087   12.9   1.5        3.4    7.8   0.1    2.4  2  DUF465           Protein of unknown function (DUF465)
      0.091   12.8   5.5       0.18   11.9   4.1    1.9  2  DUF1664          Protein of unknown function (DUF1664)
       0.11   12.8   3.1        2.5    8.4   0.4    2.9  2  Osmo_CC          Osmosensory transporter coiled coil
       0.45   11.0   6.0        2.6    8.5   1.2    2.3  2  LPP              Lipoprotein leucine-zipper
        0.6   10.2   4.3        6.6    6.9   0.2    2.4  2  YojJ             Bacterial membrane-spanning protein N-termin
          1    9.6   9.8        2.6    8.3   4.5    2.1  2  DUF5446          Family of unknown function (DUF5446)
        1.5    9.0   6.4        8.2    6.6   0.3    2.5  2  RapH_N           response regulator aspartate phosphatase H, 
        2.2    8.9   8.8        3.8    8.1   2.5    2.2  2  YtxH             YtxH-like protein
        3.3    7.9  11.4        9.4    6.4   4.0    2.6  2  bZIP_1           bZIP transcription factor


Domain annotation for each model (and alignments):
>> HSBP1  Heat shock factor binding protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   1.2   0.00011     0.076      25      46 ..       7      28 ..       2      32 .. 0.63
   2 !    8.9   0.2    0.0019       1.4       6      29 ..      33      56 ..      31      85 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00011
                         HSBP1 25 ilsriDdMssriDdLEksiadl 46
                                  +l++ +++ss+iD++Ek ++ l
  gi|13541538|ref|NP_111226.1|  7 VLDKHNEISSKIDNMEKKLDLL 28
                                  5666666677777777666544 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0019
                         HSBP1  6 vVenlLqqlqdkFqtmsdqilsri 29
                                  v+ +  +++++k++++s++++  +
  gi|13541538|ref|NP_111226.1| 33 VIKEYYSEMEKKMNSLSEEVVAGL 56
                                  66666789999*****99998632 PP

>> TelA  Toxic anion resistance protein (TelA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   5.7   2.1e-06    0.0015      89     167 ..       9      83 ..       3      91 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2.1e-06
                          TelA  89 akYekaeeqidkIvkeLekgqdellkdnaaLdqlyeknleyfkeLekyiaaG.ekkleeldekllpeleakaeasgdped 167
                                   +k ++++++id+  k+L     +ll dn+ +++ y ++ + ++ L++ ++aG  +kl+++ ++l +++e+ +++++d++ 
  gi|13541538|ref|NP_111226.1|   9 DKHNEISSKIDNMEKKL-----DLLSDNSVIKEYYSEMEKKMNSLSEEVVAGlSEKLDNIANELGKAVEKMESKNQDQTL 83 
                                   55555555555555544.....589***************************6678999999999999998887777743 PP

>> DUF5063  Domain of unknown function (DUF5063)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.5   2.6e-06    0.0018      86     135 ..      35      84 ..       4      88 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2.6e-06
                       DUF5063  86 ddYlevfdpdmkysdtpiaasisedLadIyqdlknglavyregneeemee 135
                                    +Y  ++++ m+   ++++a +se+L  I+ +l++ ++ ++ +n++++ +
  gi|13541538|ref|NP_111226.1|  35 KEYYSEMEKKMNSLSEEVVAGLSEKLDNIANELGKAVEKMESKNQDQTLQ 84 
                                   6899999999999889*************************999998544 PP

>> Apolipoprotein  Apolipoprotein A1/A4/E domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   1.9   8.3e-06    0.0059       9      64 ..      34      89 ..      26      93 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 8.3e-06
                                  HHHHHCCHHHCHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHCC CS
                Apolipoprotein  9 lkayaeeleeqlaplaqelrdrlskeleelrarlraeleevrarlepyrdevqeql 64
                                  +k+y +e+e+++++l++e+++ ls++l+++ ++l++ +e   ++ ++++ +++++ 
  gi|13541538|ref|NP_111226.1| 34 IKEYYSEMEKKMNSLSEEVVAGLSEKLDNIANELGKAVEKMESKNQDQTLQAEKKT 89
                                  789999****************************9999999999988888777765 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   1.2   2.5e-05     0.018      13      66 ..      11      68 ..       5      82 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.5e-05
                       NPV_P10 13 ikavddkVdalqqqvddvqenl...pdvtelnekLdaqsaq.LaeletkvenIqdiLn 66
                                   +++++k+d +++++d +++n+   +  +e+++k++++s++ +a l++k++nI + L 
  gi|13541538|ref|NP_111226.1| 11 HNEISSKIDNMEKKLDLLSDNSvikEYYSEMEKKMNSLSEEvVAGLSEKLDNIANELG 68
                                  5799************99999744345789********9872578********99886 PP

>> DUF2408  Protein of unknown function (DUF2408)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   5.4   4.2e-05      0.03      32     106 ..       6      81 ..       1      88 [. 0.79

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 4.2e-05
                       DUF2408  32 eeakeseevkeelkelkeeLkkieskrdeegkFkseegkevvekgqavlngLlddcfdlvedlkaqd..geekkvas 106
                                   +  ++++e+++++++++++L  + ++ + ++ + se +k++++ +++v++gL ++  +++++l +     e+k+ ++
  gi|13541538|ref|NP_111226.1|   6 DVLDKHNEISSKIDNMEKKLDLLSDNSVIKEYY-SEMEKKMNSLSEEVVAGLSEKLDNIANELGKAVekMESKNQDQ 81 
                                   445678889*******************96666.666669***********************88753334444444 PP

>> FAS_N  N-terminal domain in fatty acid synthase subunit beta
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   6.3e-05     0.045      89     124 ..       3      39 ..       1      43 [. 0.92

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6.3e-05
                         FAS_N  89 fessyL.kkndihalvsnLpsettllakkeviraYyk 124
                                   f+++ L k+n+i + + n++++  ll+ + vi+ Yy+
  gi|13541538|ref|NP_111226.1|   3 FKKDVLdKHNEISSKIDNMEKKLDLLSDNSVIKEYYS 39 
                                   8999998899************99************7 PP

>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   1.2   0.00011     0.079       1      40 [.      13      51 ..       6      53 .. 0.86
   2 ?    4.8   0.5     0.046        33       4      33 ..      51      77 ..      50      87 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00011
                          XhlA  1 eikerlerietkldnleervdkleekaaeaeekiknleed 40
                                  ei  ++  +e+kld l++  + ++e  +e+e+k  +l e+
  gi|13541538|ref|NP_111226.1| 13 EISSKIDNMEKKLDLLSDN-SVIKEYYSEMEKKMNSLSEE 51
                                  6788999999999999996.79999999999999998875 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.046
                          XhlA  4 erlerietkldnleervdkleekaaeaeek 33
                                  e ++ + +kldn+ ++   l +  +++e+k
  gi|13541538|ref|NP_111226.1| 51 EVVAGLSEKLDNIANE---LGKAVEKMESK 77
                                  6677788999999995...66777777665 PP

>> DUF4927  Domain of unknown function (DUF4927)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   3.0   4.3e-05     0.031      23      86 ..       5      67 ..       3      70 .. 0.89
   2 ?    0.4   0.2       1.9   1.4e+03      37      64 ..      71      83 ..      65      95 .. 0.53

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 4.3e-05
                       DUF4927 23 ddskdsllkdikPKlEeldskveqgsssklatsksekeeskiktedqdelpgdednLdeILgdL 86
                                   d  d+  ++i  K++++++k +  s ++++    ++ e k+++  ++ + g  ++Ld+I ++L
  gi|13541538|ref|NP_111226.1|  5 KDVLDK-HNEISSKIDNMEKKLDLLSDNSVIKEYYSEMEKKMNSLSEEVVAGLSEKLDNIANEL 67
                                  455554.799******************99999999*********999999999******9988 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1.9
                       DUF4927 37 lEeldskveqgsssklatsksekeeski 64
                                  +E+++sk +  +               +
  gi|13541538|ref|NP_111226.1| 71 VEKMESKNQDQT---------------L 83
                                  455555544433...............2 PP

>> DASH_Dad3  DASH complex subunit Dad3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   7.7     0.017        12       5      48 ..       4      45 ..       1      91 [. 0.74

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.017
                     DASH_Dad3  5 eqevLdeYerLaenlktLaselkeLasn........steeildgLReLErki 48
                                   ++vLd+ +++++++++++++l+ L++n        +          +E+k+
  gi|13541538|ref|NP_111226.1|  4 KKDVLDKHNEISSKIDNMEKKLDLLSDNsvikeyysE----------MEKKM 45
                                  6799999999999999999999999888444433330..........33333 PP

>> TipAS  TipAS antibiotic-recognition domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   1.2   7.4e-05     0.053      13      53 ..      36      76 ..      11      89 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 7.4e-05
                                  X.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..XXXX CS
                         TipAS 13 aayqeseekiaklskedweelkaelkelfaklaaalaagkd 53
                                  ++y+e+e+k+++ls+e ++ l ++l+++ ++l++a+++ ++
  gi|13541538|ref|NP_111226.1| 36 EYYSEMEKKMNSLSEEVVAGLSEKLDNIANELGKAVEKMES 76
                                  469999*****************************955443 PP

>> Chal_sti_synt_N  Chalcone and stilbene synthases, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.5   6.1e-05     0.044      43     111 ..      15      83 ..       3      95 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.1e-05
               Chal_sti_synt_N  43 sedlaelkeklerlcdkstvkkryivlteeileenPeltaemapsldarleivnaevlklgkeaalkal 111
                                   s ++ ++ +kl+ l d+s++k+ y  + + + +   e+ a  +  ld+  + + ++v k+  +   ++l
  gi|13541538|ref|NP_111226.1|  15 SSKIDNMEKKLDLLSDNSVIKEYYSEMEKKMNSLSEEVVAGLSEKLDNIANELGKAVEKMESKNQDQTL 83 
                                   55667899**********************999999999999999999888888899998766555444 PP

>> MtrG  Tetrahydromethanopterin S-methyltransferase, subunit G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.2    0.0063       4.5      10      29 ..       9      28 ..       6      35 .. 0.85
   2 ?    6.1   0.1     0.014        10       9      43 ..      35      69 ..      31      74 .. 0.85
   3 ?    2.2   0.1      0.23   1.6e+02      12      42 ..      60      90 ..      55      92 .. 0.67

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0063
                          MtrG 10 ddfnevkkrLdeieekvefv 29
                                  d  ne+ +++d++e+k++  
  gi|13541538|ref|NP_111226.1|  9 DKHNEISSKIDNMEKKLDLL 28
                                  5689************9965 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.014
                          MtrG  9 pddfnevkkrLdeieekvefvnsEiaqriGkkvGR 43
                                  ++ ++e++k+++ + e v    sE    i  ++G+
  gi|13541538|ref|NP_111226.1| 35 KEYYSEMEKKMNSLSEEVVAGLSEKLDNIANELGK 69
                                  567999***********999999999888888886 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.23
                          MtrG 12 fnevkkrLdeieekvefvnsEiaqriGkkvG 42
                                   +++ + L +  ek+e  n + + ++ kk+G
  gi|13541538|ref|NP_111226.1| 60 LDNIANELGKAVEKMESKNQDQTLQAEKKTG 90
                                  4566677777777777777777777777776 PP

>> Carbpep_Y_N  Carboxypeptidase Y pro-peptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   3.7    0.0001     0.072      23     104 ..      14      94 ..       6      96 .] 0.81

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.0001
                   Carbpep_Y_N  23 iqnplkdlQqalklelnyd.tkklskllee.eekknnvfekiskvlneplkeltseakkiWsemelkfPdavsklkfktkp 101
                                   i ++++++ ++l l +++      +++  e e+k n + e++   l+e+l+++ +e+ k+ + me k  d+  ++++kt++
  gi|13541538|ref|NP_111226.1|  14 ISSKIDNMEKKLDLLSDNSvI---KEYYSEmEKKMNSLSEEVVAGLSEKLDNIANELGKAVEKMESKNQDQTLQAEKKTGK 91 
                                   566778888888885555544...55555559999999****************************************988 PP

                   Carbpep_Y_N 102 kkk 104
                                   +k 
  gi|13541538|ref|NP_111226.1|  92 GKT 94 
                                   775 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.2   0.00014     0.098     144     207 ..      18      82 ..       3      85 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00014
                 Peptidase_C26 144 qsaashavkv.ekgsllaellgseeievnslHhqaikelaeelrveAvaeDgviEaieseeakaf 207
                                    +++++++++   +s+++e +++ e ++nsl +  +  l+e+l  +A      +E +es++++++
  gi|13541538|ref|NP_111226.1|  18 IDNMEKKLDLlSDNSVIKEYYSEMEKKMNSLSEEVVAGLSEKLDNIANELGKAVEKMESKNQDQT 82 
                                   367777777525899*********************************************99865 PP

>> Retrotrans_gag  Retrotransposon gag protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   0.00019      0.13      33      80 ..       5      52 ..       3      75 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00019
                Retrotrans_gag 33 kkaflktflpserkdqleeelsslrQgtesvreYvtrfktladqlde.v 80
                                  k+++ k+++ s++ d +e++l  l+  +  ++eY+ ++++ ++ l e v
  gi|13541538|ref|NP_111226.1|  5 KDVLDKHNEISSKIDNMEKKLDLLSD-NSVIKEYYSEMEKKMNSLSEeV 52
                                  67889999999***************.************9999998652 PP

>> DUF465  Protein of unknown function (DUF465)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.1    0.0048       3.4       6      22 ..       9      25 ..       6      36 .. 0.84
   2 ?    4.1   0.1     0.066        47       9      28 ..      65      84 ..      65      88 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0048
                                  HHHHHHHHHHHHHHTT- CS
                        DUF465  6 eeHeeLdkeIhalearp 22
                                  ++H+e+  +I+++e++ 
  gi|13541538|ref|NP_111226.1|  9 DKHNEISSKIDNMEKKL 25
                                  79************975 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.066
                                  HHHHHHHHHHHTT-.S-HHH CS
                        DUF465  9 eeLdkeIhalearpvtddle 28
                                  +eL k+++++e ++++  l+
  gi|13541538|ref|NP_111226.1| 65 NELGKAVEKMESKNQDQTLQ 84
                                  7999*********9865555 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   4.1   0.00025      0.18      55     123 ..       5      77 ..       2      79 .. 0.71
   2 ?    7.2   0.8    0.0067       4.8      39      79 ..      41      82 ..      38      92 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00025
                       DUF1664  55 eslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedv.....esvkeaveglesklerieek 123
                                   +++ +  +++ss+id+++kkld  ++ s  ike  +e+++++++++e+v     e+++++ ++l++ +e++e+k
  gi|13541538|ref|NP_111226.1|   5 KDVLDKHNEISSKIDNMEKKLDLLSDNS-VIKEYYSEMEKKMNSLSEEVvaglsEKLDNIANELGKAVEKMESK 77 
                                   667888999************9877643.566666666666666666653333367788888888888888876 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0067
                       DUF1664 39 lsdavesvskql.eqvseslaatkrhLssridrvdkkldeqk 79
                                  +++ ++s+s+++   +se+l +  ++L + ++++++k ++q+
  gi|13541538|ref|NP_111226.1| 41 MEKKMNSLSEEVvAGLSEKLDNIANELGKAVEKMESKNQDQT 82
                                  556666666553256777777777777777777776544443 PP

>> Osmo_CC  Osmosensory transporter coiled coil
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.1     0.081        58      13      29 ..      10      26 ..       5      32 .. 0.58
   2 ?    8.4   0.4    0.0035       2.5       9      36 ..      33      61 ..      30      85 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.081
                                  XXTHHHHHHHHHHHHHH CS
                       Osmo_CC 13 hYdnIEqkvedideeIa 29
                                  ++++I  k+++ ++ + 
  gi|13541538|ref|NP_111226.1| 10 KHNEISSKIDNMEKKLD 26
                                  45555555555555443 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0035
                                  XXXXXXTHHHHHHHHHHHHH.HHHHHHHH CS
                       Osmo_CC  9 lLqehYdnIEqkvedideeI.aaLeekRq 36
                                  + +e+Y + E+k + + ee+ a L ek +
  gi|13541538|ref|NP_111226.1| 33 VIKEYYSEMEKKMNSLSEEVvAGLSEKLD 61
                                  679***************96366777755 PP

>> LPP  Lipoprotein leucine-zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.2     0.045        33       2      22 ..      11      31 ..      10      43 .. 0.80
   2 ?    8.5   1.2    0.0036       2.6       1      30 [.      44      74 ..      44      87 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.045
                           LPP  2 ldeLssqVsqLkskvdqlssd 22
                                   +e+ss + ++++k d ls++
  gi|13541538|ref|NP_111226.1| 11 HNEISSKIDNMEKKLDLLSDN 31
                                  589999999999999999886 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0036
                           LPP  1 kldeLssqV.sqLkskvdqlssdvnsakaaa 30
                                  k++ Ls++V   L++k d++++++ +a + +
  gi|13541538|ref|NP_111226.1| 44 KMNSLSEEVvAGLSEKLDNIANELGKAVEKM 74
                                  899***997256**********954444333 PP

>> YojJ  Bacterial membrane-spanning protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.9     0.048        35       9      33 ..       2      26 ..       1      47 [. 0.78
   2 ?    6.9   0.2    0.0092       6.6       5      37 ..      47      79 ..      43      83 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.048
                          YojJ  9 elkeklkeeLeqiekeleevlkald 33
                                  ++k+++  + ++i+ +++++ k+ld
  gi|13541538|ref|NP_111226.1|  2 SFKKDVLDKHNEISSKIDNMEKKLD 26
                                  5899999999999999999999998 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0092
                          YojJ  5 cleeelkeklkeeLeqiekeleevlkaldeede 37
                                   l+ee    l e+L +i +el + +++++++++
  gi|13541538|ref|NP_111226.1| 47 SLSEEVVAGLSEKLDNIANELGKAVEKMESKNQ 79
                                  56777778899*****************99876 PP

>> DUF5446  Family of unknown function (DUF5446)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   4.5    0.0037       2.6       7      54 ..       4      52 ..       2      54 .. 0.86
   2 ?    4.4   0.2     0.058        41      19      42 ..      58      81 ..      53      87 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0037
                       DUF5446  7 KdsvLqlLeeiEeeltevEkelse.avneteaekeekeeerldllekEl 54
                                  K +vL    ei ++++++Ek+l + + n   +e  ++ e+ ++ l +E+
  gi|13541538|ref|NP_111226.1|  4 KKDVLDKHNEISSKIDNMEKKLDLlSDNSVIKEYYSEMEKKMNSLSEEV 52
                                  89999999**************862667777888899999999999998 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.058
                       DUF5446 19 eeltevEkelseavneteaekeek 42
                                  e+l+++ +el++av + e   + +
  gi|13541538|ref|NP_111226.1| 58 EKLDNIANELGKAVEKMESKNQDQ 81
                                  7999**********9999877654 PP

>> RapH_N  response regulator aspartate phosphatase H, N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.3     0.011       8.2      30      47 ..      11      28 ..       6      29 .. 0.88
   2 ?    5.0   0.2     0.037        26      10      41 ..      33      64 ..      31      68 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.011
                                  HHHHHHHHCTS---HHHH CS
                        RapH_N 30 keeikqeleemeedqdvl 47
                                  ++ei +++++me+  d+l
  gi|13541538|ref|NP_111226.1| 11 HNEISSKIDNMEKKLDLL 28
                                  58**********998887 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.037
                                  HHHHHHHHHHTT-HHHHHHHHHHHHHHHCTS- CS
                        RapH_N 10 klneWYsaIkkrsvekAeelkeeikqeleeme 41
                                   ++e+Ys++ k+  + +ee+ +   ++l+++ 
  gi|13541538|ref|NP_111226.1| 33 VIKEYYSEMEKKMNSLSEEVVAGLSEKLDNIA 64
                                  699*********99999999999999999986 PP

>> YtxH  YtxH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.7     0.026        18      29      73 ..       6      51 ..       2      55 .. 0.50
   2 ?    8.1   2.5    0.0053       3.8      25      63 ..      51      89 ..      49      96 .] 0.83

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.026
                          YtxH 29 dlkekaddlkekakelleeakeka.....kekaedlkekvkekadelkek 73
                                  d+ +k ++++ k+    +++++k      ++ ++++ +++++k ++l+e+
  gi|13541538|ref|NP_111226.1|  6 DVLDKHNEISSKI----DNMEKKLdllsdNSVIKEYYSEMEKKMNSLSEE 51
                                  4444444454444....333444466667555555555555555555554 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0053
                          YtxH 25 etRkdlkekaddlkekakelleeakekakekaedlkekv 63
                                  e+ + l+ek+d++++ + +++e++++k ++++ ++ +k 
  gi|13541538|ref|NP_111226.1| 51 EVVAGLSEKLDNIANELGKAVEKMESKNQDQTLQAEKKT 89
                                  777889******************999988877776665 PP

>> bZIP_1  bZIP transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.6     0.024        17      36      62 ..       6      30 ..       2      32 .. 0.83
   2 ?    6.4   4.0     0.013       9.4      25      63 ..      35      78 ..      34      79 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.024
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        bZIP_1 36 kaLekeNksLkseleelkkevekLksk 62
                                  ++L+k N+  +s++++++k+ + L+s+
  gi|13541538|ref|NP_111226.1|  6 DVLDKHNE-ISSKIDNMEKKLD-LLSD 30
                                  799****9.**********998.5554 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.013
                                  HHHHHHHHHHHHHHHHH.....HHHHHHHHHHHHHHHHHHHHHH CS
                        bZIP_1 25 qaeieeLerrvkaLeke.....NksLkseleelkkevekLkskv 63
                                  +++ +e e+++  L++e      ++L + ++el k vek++sk+
  gi|13541538|ref|NP_111226.1| 35 KEYYSEMEKKMNSLSEEvvaglSEKLDNIANELGKAVEKMESKN 78
                                  68999999999999988322223566667777888899999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2540  (0.14167); expected 358.6 (0.02)
Passed bias filter:                      786  (0.0438396); expected 358.6 (0.02)
Passed Vit filter:                       106  (0.00591221); expected 17.9 (0.001)
Passed Fwd filter:                        25  (0.00139439); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              25  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 691.47
//
Query:       gi|13541539|ref|NP_111227.1|  [L=547]
Description: amino acid transporter [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-26   93.2  58.3    1.5e-26   93.2  58.3    2.0  2  AA_permease_2  Amino acid permease
    6.7e-17   61.2  48.5    6.7e-17   61.2  48.5    2.1  2  AA_permease    Amino acid permease
  ------ inclusion threshold ------
        2.8    7.9   7.3         22    5.0   0.7    3.8  3  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 !   93.2  58.3   2.6e-30   1.5e-26       8     419 ..      37     487 ..      36     494 .. 0.82
   2 ?   -4.5   7.1       1.1   6.8e+03      85     132 ..     484     529 ..     466     534 .. 0.53

  Alignments for each domain:
  == domain 1  score: 93.2 bits;  conditional E-value: 2.6e-30
                 AA_permease_2   8 alvigsv..igsgifvkn..laasggpalilwvwiavligslavllvyaElssalprsgGiyvytkaafgkkvaflsawfn 84 
                                   +lvig++  +g+g ++++  +++ +gp++i+ ++i+++++ + v+++++Els + p  gG + y+ ++ g++   l+a++ 
  gi|13541539|ref|NP_111227.1|  37 MLVIGLIaaVGTGALFAPvaMVGVAGPSAIMGWIIGAIMY-TFVSFTFVELSKTYPEAGGPSRYSLYTHGRFTNALNAFAD 116
                                   58999998899*******999*******************.89*********99********************9999988 PP

                 AA_permease_2  85 wfayvpvlasilsv...aasyl.lnalgpdlqgntwltyliaiaililvalinirgikesakiqnilgilkillpliilii 161
                                   ++ y++  ++ + +   +++yl  +++++++ + t l  ++++++l+l+  +n++g+k  +k+  ++g +k+ + l+ ++ 
  gi|13541539|ref|NP_111227.1| 117 LIWYIFIPPIEALAtveGLQYLyPHFIASSGAP-TLLGAGLGVLVLALFLPLNYFGVKAFGKYSLYIGFVKLAVYLLAAFG 196
                                   666666555554440036666544445556555.6899**********************************999999999 PP

                 AA_permease_2 162 lglitvdgggfsslstetdtffpngwpgvllgllivlwsfdGfesaanvsee...vkk.kdvpkaifigllivlvlyllvn 238
                                     +++++++ f       + f+p g +g+l++++ ++++f+G+ ++  ++ee    k+ + + ++i++ ++  +++y+l++
  gi|13541539|ref|NP_111227.1| 197 MMFVFFKFDNFY---IYRGGFLPFGFSGILFAIPFAMFAFGGIRVVPDYAEEtteTKEnRFLGRTIIYTVIGQSLIYILFS 274
                                   999999999998...45666********************************765444466******************** PP

                 AA_permease_2 239 iaflgvvpddei.........anlsnlgsvaalffeavggkvvaiivvilialsllgaintavigssrvlealardgvlPr 310
                                   iaf++++ ++ i          +++ + +++  ++  +++ vv iiv ++ +l+ +  +  +v + +rvl a ar +++ +
  gi|13541539|ref|NP_111227.1| 275 IAFIAGLKWSAIsiapgawadVKSNITENPFVFLASSYHNYVVLIIVLVVSILGPFVTGYVYVGSGARVLLATARSKIMAS 355
                                   ************98998888633333455688888888888**************************************** PP

                 AA_permease_2 311 ffakvn.kfgspiraiiltaivslillllfllassaaynfllsvsslgliisyllliigalilrkkrphlkr......... 381
                                    ++k +  +  p+ ++i ++iv  i++++++ ++  ++++ll+ ++++ ++ + ++ +++++ r++   +k+         
  gi|13541539|ref|NP_111227.1| 356 SMKKLSeTYAVPYWSVIAFVIVGAIVAFISAPVP--DIYALLTDAVVAGYLGFSVTPVAMIVSRRQGATKKEdklpagtti 434
                                   ******99***************88887776665..899999999999999999999999999999887766667655565 PP

                 AA_permease_2 382 .............pgkil.vaiigalfllfllvalffppkgpatqssliyt.i 419
                                                +  ++ v   +++++l +lv+++++  + +  +s++y  +
  gi|13541539|ref|NP_111227.1| 435 aviafisssliafWSGWPsVPYAMFILALAMLVFGIVYKIKEHFLNSIWYIlY 487
                                   55555444444433335425555577777777777787777777777776643 PP

  == domain 2  score: -4.5 bits;  conditional E-value: 1.1
                 AA_permease_2  85 wfayvpvlasilsvaasyllnalgpdlqgntwltyliaiaililvali 132
                                    + y++++ ++++++    ln++ p+ + +t ++  i +ai+  + +i
  gi|13541539|ref|NP_111227.1| 484 YILYMAFILLMSYIGSDGALNLI-PF-TYSTLIVAAISAAIFFPWGII 529
                                   23344444455555555556655.32.234555555555555554444 PP

>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.2  48.5   1.1e-20   6.7e-17       2     418 ..      37     442 ..      36     449 .. 0.80
   2 ?   -7.8  15.2         3   1.8e+04      90     156 ..     434     523 ..     430     540 .. 0.47

  Alignments for each domain:
  == domain 1  score: 61.2 bits;  conditional E-value: 1.1e-20
                   AA_permease   2 vlvialggviGtglfvglgvvlsqaGplgallayllagvviflvmlslgeiatngpksggfytyasrflgpelGfviGlny 82 
                                   +lvi l  ++Gtg +++    ++ aGp +a+ +++++ +++++v  ++ e++  +p++gg + y+  ++g+      ++  
  gi|13541539|ref|NP_111227.1|  37 MLVIGLIAAVGTGALFAPVAMVGVAGP-SAIMGWIIGAIMYTFVSFTFVELSKTYPEAGGPSRYSLYTHGRFTNALNAFAD 116
                                   678899999******************.999***************************************99999999999 PP

                   AA_permease  83 lfswitvlaleltaasiliqfwelvtdlpkawvt........gavflvvlliinlvgvkvygeaefilalikiiaiiafii 155
                                   l+ +i+  ++e  a +  +q++  +++ +   +         g+++l+++l +n++gvk++g+ ++ + ++k+   +    
  gi|13541539|ref|NP_111227.1| 117 LIWYIFIPPIEALATVEGLQYL--YPHFIASSGAptllgaglGVLVLALFLPLNYFGVKAFGKYSLYIGFVKLAVYLLAAF 195
                                   9999******************..***99777779****************************888755554433333333 PP

                   AA_permease 156 vgiillaggkpnkgagfrflgdngsifknnlppgfakeeegafknfisvfvivvfaftGielvaiiagEvkdPeks..iPk 234
                                   + +++ ++ +        f+ + g+    +lp g        f+++++++++++faf Gi  v+  a+E+ + +++  + +
  gi|13541539|ref|NP_111227.1| 196 GMMFVFFKFD---N----FYIYRGG----FLPFG--------FSGILFAIPFAMFAFGGIRVVPDYAEETTETKENrfLGR 257
                                   3333334443...4....7899999....78888........****************************999876669** PP

                   AA_permease 235 ailqvviritifYvlsllligllvprndlgllndsasa.......aspfvifikesgvsvlaplinaviltaalssanssl 308
                                    i+++vi   ++Y+l++++ ++++ +++ ++  ++  a         pfv   ++  + v+  ++ +v+++  + ++  ++
  gi|13541539|ref|NP_111227.1| 258 TIIYTVIGQSLIYILFSIAFIAGLKWSAISIAPGAW-AdvksnitENPFVFLASSYHNYVVLIIVLVVSILGPFVTGYVYV 337
                                   ***************************977766433.24676666555555555544444444444444444555555666 PP

                   AA_permease 309 ysasRvlyslakdglaPkvlkkv.skrgvPlraillsmiisllalllaslnlaapivfnfllaisaliglivwlliilsyl 388
                                    s+ Rvl + a+++++++ +kk+ + + vP+ +++++ i+++++ ++++  ++   +++ l   + ++g + + ++ ++ +
  gi|13541539|ref|NP_111227.1| 338 GSGARVLLATARSKIMASSMKKLsETYAVPYWSVIAFVIVGAIVAFISAPVPD---IYALLTD-AVVAGYLGFSVTPVAMI 414
                                   7788*************66666516799**************99977666666...6666655.55677778888888888 PP

                   AA_permease 389 rfRkalkyqgrsieelgfkaallplgvilv 418
                                   + R++  +++   ++l++ +  ++  +i+ 
  gi|13541539|ref|NP_111227.1| 415 VSRRQGATKKE--DKLPAGTTIAVIAFISS 442
                                   88888777777..77887777777766654 PP

  == domain 2  score: -7.8 bits;  conditional E-value: 3
                   AA_permease  90 laleltaasiliqfwelvtdlpkawvt.......................gavflvvlliinlvgvkvygeaefilaliki 147
                                   +a+  +++s+li fw+  +++p+a  +                        ++ ++++l+++++g  +      ++ + +i
  gi|13541539|ref|NP_111227.1| 434 IAVIAFISSSLIAFWSGWPSVPYAMFIlalamlvfgivykikehflnsiwYILYMAFILLMSYIGSDGALNLIPFTYSTLI 514
                                   555566666666666666666633333222222222222222222222225555555555555555555554444444444 PP

                   AA_permease 148 iaiiafiiv 156
                                   +a+i+  i+
  gi|13541539|ref|NP_111227.1| 515 VAAISAAIF 523
                                   444444444 PP

>> Herpes_US9  Alphaherpesvirus tegument protein US9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0    0.0048        29      18      51 ..      19      52 ..      15      59 .. 0.77
   2 ?   -3.9   0.4       2.2   1.3e+04      43      56 ..     223     236 ..     222     237 .. 0.82
   3 ?    5.0   0.7    0.0038        22      35      56 ..     315     335 ..     311     337 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.0048
                    Herpes_US9 18 iGkyqsklrrRkkrtfCvitliivllvAvlsaa.F 51
                                  +  +q+ ++ +k  tf   +l+i l+ Av ++a F
  gi|13541539|ref|NP_111227.1| 19 MAEQQHEVKLKKALTFP-QMLVIGLIAAVGTGAlF 52
                                  6789*****99998886.67888889998555515 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 2.2
                    Herpes_US9  43 lvAvlsaaFalGal 56 
                                   l+A+  a Fa+G +
  gi|13541539|ref|NP_111227.1| 223 LFAIPFAMFAFGGI 236
                                   79999999999976 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.0038
                    Herpes_US9  35 vitliivllvAvlsaaFalGal 56 
                                   +++liivl+v +l+  F  G++
  gi|13541539|ref|NP_111227.1| 315 YVVLIIVLVVSILG-PFVTGYV 335
                                   899*********97.5778886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (547 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       928  (0.0517597); 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:                        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: 0.78u 0.36s 00:00:01.14 Elapsed: 00:00:00.53
# Mc/sec: 3118.20
//
Query:       gi|13541540|ref|NP_111228.1|  [L=141]
Description: hypothetical protein TVN0709 [Thermoplasma volcanium GSS1]
Scores for complete 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   20.9   0.3    0.00039   20.3   0.3    1.3  1  HTH_45    Winged helix-turn-helix
  ------ inclusion threshold ------
      0.063   13.0   0.1      0.091   12.5   0.1    1.2  1  DUF4364   Domain of unknown function (DUF4364)


Domain annotation for each model (and alignments):
>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.3   4.3e-08   0.00039      13      67 ..      66     123 ..      51     130 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 4.3e-08
                        HTH_45  13 eaisegeakkTkimykanLsykllnkYLdmLvekgli....kkskekYvlTekGlelle 67 
                                   ++i ++  +kT+i+ ++ L++++ ++ ++ + + gl+      + + Y+l e G  +l+
  gi|13541540|ref|NP_111228.1|  66 KNI-DKPMTKTEIINRSMLNFRRGENIINCMENTGLLdtniVGKRKYYSLSELGDLILN 123
                                   345.78889***************************64444789999*******98886 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1     1e-05     0.091       8      72 ..      64     124 ..      60     140 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1e-05
                       DUF4364   8 llkkvkfpltnsqlseiileneytnYfdlqqalseLvesglieeeekenktlykiTekGketlel 72 
                                   ++k++++p+t+++++    ++ ++n+   +++++ ++++gl++++   ++++y+++e G+ +l+ 
  gi|13541540|ref|NP_111228.1|  64 TMKNIDKPMTKTEII----NRSMLNFRRGENIINCMENTGLLDTNIVGKRKYYSLSELGDLILNV 124
                                   578999999999975....68899********************999************988874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 970.91
//
Query:       gi|13541541|ref|NP_111229.1|  [L=1376]
Description: hypothetical protein TVN0710 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.1e-16   59.3   0.0    1.1e-15   58.2   0.0    1.5  1  Pro-kuma_activ  Pro-kumamolisin, activation domain
  ------ inclusion threshold ------
      0.088   12.8   0.2       0.26   11.3   0.2    1.7  1  CMV_1a_C        Cucumber mosaic virus 1a protein C terminal
       0.22   12.0   5.4       0.56   10.6   0.0    3.3  4  LPP             Lipoprotein leucine-zipper
       0.28   11.2   3.9        1.2    9.1   0.2    2.3  2  Baculo_PEP_C    Baculovirus polyhedron envelope protein, PEP,


Domain annotation for each model (and alignments):
>> Pro-kuma_activ  Pro-kumamolisin, activation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.2   0.0   2.4e-19   1.1e-15       6     140 ..      69     222 ..      66     224 .. 0.89

  Alignments for each domain:
  == domain 1  score: 58.2 bits;  conditional E-value: 2.4e-19
                Pro-kuma_activ   6 rgraasstllpvrigLkqnnlekledflmdvsdpkspnygkhltaeevaelfapseeaidaVrnwLessgiaasrhsdtkg 86 
                                    ++ ++s +++v + Lk++    l+ +++ +  p+sp y+++lt++++ ++f+   +++ a  +++e +gi++   + t+ 
  gi|13541541|ref|NP_111229.1|  69 TSAYSPSAQISVFVSLKPQG--NLQGYVNSLYEPGSPYYHQFLTSSQIGNRFGLDAQTYGAFVSYFEGYGISVGT-TSTRL 146
                                   5678999*********9999..99************************************************999.9**** PP

                Pro-kuma_activ  87 wiafsatvaqverllktsfeaYshk............kgss............slarcdeyslPealknyvdyihptd 140
                                    ++++++v q+ ++++t+++a++ k            +  +            ++a ++  ++Pe+l++yv++i +++
  gi|13541541|ref|NP_111229.1| 147 SLSLTGSVYQFDQAFHTRIQAFQYKyvsngiwnplfgN--NsavpgsvsystpFFASTSDLKIPESLERYVSGISGLN 222
                                   *********************99446866777777652..04577777888879999999**************9985 PP

>> CMV_1a_C  Cucumber mosaic virus 1a protein C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.2   5.7e-05      0.26      24      54 ..     257     287 ..     246     293 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 5.7e-05
                      CMV_1a_C  24 yrrvddlvnvhladGrWlvPedfeysvGyne 54 
                                   y   +d+ n+ +a+  W +P+++ ++vGy  
  gi|13541541|ref|NP_111229.1| 257 YPSLNDIQNITYANYTWTYPQNVYFAVGYQT 287
                                   55678999*********************75 PP

>> LPP  Lipoprotein leucine-zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.2   0.0         4   1.8e+04       7      22 ..     987    1002 ..     985    1005 .. 0.81
   2 ?   -1.8   0.2      0.93   4.1e+03       7      23 ..    1229    1245 ..    1228    1248 .. 0.72
   3 ?   10.6   0.0   0.00012      0.56       8      37 ..    1259    1288 ..    1254    1289 .. 0.93
   4 ?    2.1   0.1     0.056   2.5e+02       2      25 ..    1316    1339 ..    1309    1344 .. 0.51

  Alignments for each domain:
  == domain 1  score: -4.2 bits;  conditional E-value: 4
                           LPP    7 sqVsqLkskvdqlssd 22  
                                    +qV qL +  d l+s+
  gi|13541541|ref|NP_111229.1|  987 TQVVQLRATYDGLTSN 1002
                                    7999999999999887 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.93
                           LPP    7 sqVsqLkskvdqlssdv 23  
                                    ++V +L++ ++++++ +
  gi|13541541|ref|NP_111229.1| 1229 NDVTNLQNSISSVQKAI 1245
                                    67888888888777665 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 0.00012
                           LPP    8 qVsqLkskvdqlssdvnsakaaaqaakeEA 37  
                                    ++s+L skv +ls++ n++ ++++ +k+EA
  gi|13541541|ref|NP_111229.1| 1259 NLSALRSKVYKLSEEYNQSVSDLNMIKAEA 1288
                                    689**************************9 PP

  == domain 4  score: 2.1 bits;  conditional E-value: 0.056
                           LPP    2 ldeLssqVsqLkskvdqlssdvns 25  
                                    ld+L  ++ ++ s++++++ ++++
  gi|13541541|ref|NP_111229.1| 1316 LDNLHGEIASMASQINAIAGNQKA 1339
                                    344444444444455544444444 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.2   0.00028       1.2      38     113 ..    1229    1306 ..    1226    1311 .. 0.86
   2 ?    2.6   0.5     0.029   1.3e+02      84     105 ..    1313    1334 ..    1308    1343 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00028
                  Baculo_PEP_C   38 tlldaietqLnalsedlksllaeldtrldtlltnLtdalnalq...dtlrneLtnlnsiltnLlssvtNinstLnnllq 113 
                                    ++++++++++++++++++ +    +t+ + +l++L +++ +l+   ++  ++L+ ++++  +L  s + instL nl++
  gi|13541541|ref|NP_111229.1| 1229 NDVTNLQNSISSVQKAISYSTGYPNTEYNGNLSALRSKVYKLSeeyNQSVSDLNMIKAEAGSLYES-GSINSTLYNLVE 1306
                                    7899***************9999999*****************55544456788888888889855.99********96 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.029
                  Baculo_PEP_C   84 rneLtnlnsiltnLlssvtNin 105 
                                    +neL+nl  ++++++s++  i 
  gi|13541541|ref|NP_111229.1| 1313 NNELDNLHGEIASMASQINAIA 1334
                                    7999999999999999987663 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1376 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       514  (0.0286686); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); 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: 0.84u 0.24s 00:00:01.08 Elapsed: 00:00:00.45
# Mc/sec: 9236.55
//
Query:       gi|13541542|ref|NP_111230.1|  [L=256]
Description: 3-oxoacyl-[acyl-carrier-protein] reductase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-45  155.8   0.0    1.6e-45  155.5   0.0    1.0  1  adh_short_C2    Enoyl-(Acyl carrier protein) reductase
      5e-39  133.8   0.1    5.8e-39  133.6   0.1    1.0  1  adh_short       short chain dehydrogenase
     0.0015   18.4   0.0     0.0029   17.5   0.0    1.3  1  NAD_binding_10  NAD(P)H-binding
     0.0019   18.1   0.0     0.0042   17.0   0.0    1.6  1  KR              KR domain
  ------ inclusion threshold ------
      0.034   13.5   0.0      0.052   12.9   0.0    1.2  1  DUF1776         Fungal family of unknown function (DUF1776)
      0.088   13.1   0.0          4    7.8   0.0    2.5  2  Syntaxin-18_N   SNARE-complex protein Syntaxin-18 N-terminus


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 !  155.5   0.0   5.5e-49   1.6e-45       3     234 .]      13     252 ..      12     252 .. 0.93

  Alignments for each domain:
  == domain 1  score: 155.5 bits;  conditional E-value: 5.5e-49
                                   T.TSHHHHHHHHHHHTT-EEEEEESSGGH.HHHHHHHHHHTTSEE..EE--TTSHHHHHHHHHHHHHHHSSEEEEEE---- CS
                  adh_short_C2   3 a.sgIGraiAkalaeeGaevvltdlneea.kkrveelaeelgaev..lecDVtdeeqvealveevvekfgklDilvnnagi 79 
                                   a  gIG++i+  l   G+++ +  ++e++ ++  ee++ ++g+e+  + +D + ++++e++v++ +ek+g++D lv n g 
  gi|13541542|ref|NP_111230.1|  13 AsAGIGKGIVAVLLGYGYNITAFSRDESKlRALKEEMKLKFGREIntVVADLSVRSDLENVVSNHREKYGSIDNLVVNYGD 93 
                                   559**************************888888888899999778*********************************9 PP

                                   -EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHH.HCTSC.CEEEEEEEGGGTSBSTTTTHHHHHHHHHHHHHHHHHHH CS
                  adh_short_C2  80 apklkgpfletsreefdraldvnlyslfllakaalp.lmkeg.gsivnlssvgaervvpnynaygaaKaalealtrylAve 158
                                    +   ++f+e+s+e++d a+++ l+s+++l+++al+ +++ + gsiv ++s+  +  +++ ++ +  + a+++l+++l +e
  gi|13541542|ref|NP_111230.1|  94 PKV--SSFIEISDEDWDYAISMMLKSTIYLTREALRdMIRTKhGSIVYVTSMTVREPIEGFSISASLRSAVISLAKTLTHE 172
                                   998..*******************************9666556************************************** PP

                                   HGGGTEEEEEEEE--BHCTGGGGSTT....HHHHHHHHHHHSTTSS-B-HHHHHHHHHHHCSGGGTT--SEEEEESTTGG CS
                  adh_short_C2 159 lgpkgiRvNavspgpikTlaasgikg....fdelleelearaplgrlgtpeevaeaalfLasdeasyitGqtlvvDgGlt 234
                                   + ++giRvN++++g+ +T+  ++i +    + + +++l+ ++pl+r+g+pee++e++ fL+s ++syi+G+++ +DgG+t
  gi|13541542|ref|NP_111230.1| 173 VSQNGIRVNTIAQGYFNTDRFRDIMKreidSLSGMKRLAGEIPLRRVGEPEEIGELVEFLLSSRSSYINGANIPIDGGIT 252
                                   *******************99998874422334788999***************************************97 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.6   0.1   1.9e-42   5.8e-39       3     191 ..       8     197 ..       6     201 .. 0.98

  Alignments for each domain:
  == domain 1  score: 133.6 bits;  conditional E-value: 1.9e-42
                                   EEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHT.TSEEEEEE-TTTSHHHHHHHHHHHHHHHSSESEEE CS
                     adh_short   3 vlvtGassGIGraiakelakeGakvvvvdrseekleevakelkee.gakalaiqvDvtdreevealvekavkklgkldvLv 82 
                                   v+v  as+GIG+ i+  l+  G+++++++r e+kl+++++e+k + g+++ ++ +D++ r+++e++v++ ++k+g++d Lv
  gi|13541542|ref|NP_111230.1|   8 VIVSAASAGIGKGIVAVLLGYGYNITAFSRDESKLRALKEEMKLKfGREINTVVADLSVRSDLENVVSNHREKYGSIDNLV 88 
                                   89*****************************************99************************************ PP

                                   E---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHHHHHHHHHHHH CS
                     adh_short  83 nNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsKaavagltrsl 163
                                    N G  ++++f e+s+e+w+  i++ l++++ ltr++l+ m++ + G+Iv v+S++ ++p +g++  ++   av++l+++l
  gi|13541542|ref|NP_111230.1|  89 VNYGDPKVSSFIEISDEDWDYAISMMLKSTIYLTREALRDMIRTKHGSIVYVTSMTVREPIEGFSISASLRSAVISLAKTL 169
                                   ******************************************************************9999*********** PP

                                   HHHHGGGTEEEEEEEESSBSSHHHHHHC CS
                     adh_short 164 akelaptgirvnavaPGlvdTdmakelr 191
                                    +e+++ girvn++a G+++Td  +++ 
  gi|13541542|ref|NP_111230.1| 170 THEVSQNGIRVNTIAQGYFNTDRFRDIM 197
                                   **********************988765 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   9.7e-07    0.0029       2     102 ..      13     146 ..      12     164 .. 0.67

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 9.7e-07
                                   TTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTT......TCEEEE--TT-CCHHHHHHT.......T-SEEEES-- CS
                NAD_binding_10   2 AtGkvGrllvkellargghevtalvRnpeklaeleaee......glevvegdvtdvedlaealk.......gadaVvsalg 69 
                                   A+ ++G+ +v+ ll   g+++ta+ R+++kl +l++e       ++++v++d++  +dl+++++        +d  v++ g
  gi|13541542|ref|NP_111230.1|  13 ASAGIGKGIVAVLLGY-GYNITAFSRDESKLRALKEEMklkfgrEINTVVADLSVRSDLENVVSnhrekygSIDNLVVNYG 92 
                                   7789************.5**************9987662333335668999999999999999844444444455555555 PP

                                   -TCC.......HHHH................HHHHHHHHHHCT--EEEEEEETTTT CS
                NAD_binding_10  70 gggk.......deeg................aknivdaakeagvkRfvlvsaigvg 102
                                     +        d                   ++ +++ + +++   +v+v+++ v+
  gi|13541542|ref|NP_111230.1|  93 DPKVssfieisD--EdwdyaismmlkstiylTREALRDMIRTKHGSIVYVTSMTVR 146
                                   555444444332..023445555555556666666666666666666666666666 PP

>> KR  KR 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    0.0042       3     120 ..       8     122 ..       6     169 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.4e-06
                                   EEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHT.T-EEEE----TT-HHHHHHHHHHHHHHSS-- CS
                            KR   3 ylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaeleal.gaevevvaaDvsdkdavealleeikaeeppi 82 
                                   +++  +  g+G+ ++  l+  g  ++  +sR+++   + +al +e++ + g e+++v aD+s ++++e+++++ +++ ++i
  gi|13541542|ref|NP_111230.1|   8 VIVSAASAGIGKGIVAVLLGYGY-NITAFSRDES---KLRALKEEMKLKfGREINTVVADLSVRSDLENVVSNHREKYGSI 84 
                                   56777888999999999999995.799*****43...4444556666656******************************* PP

                                   -EEEE---------TTT--HHHHHHHHTTTTHHHHHHH CS
                            KR  83 kGvihaAgvlrdklleemtaedleqvlapKvkGawnLh 120
                                      +   g  + + + e ++ed++ +++  +k +  L 
  gi|13541542|ref|NP_111230.1|  85 DNLVVNYGDPKVSSFIEISDEDWDYAISMMLKSTIYLT 122
                                   ***********************999998888887775 PP

>> DUF1776  Fungal family of unknown function (DUF1776)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   1.7e-05     0.052     108     202 ..      99     190 ..      90     209 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.7e-05
                       DUF1776 108 ietiplsswaselnerllspi.ltlqallplltsrakqkakiivvnpsissslnlpfhapEalvssalsalfevLkrelrp 187
                                   + +i+ + w  ++   l s+i lt +al   ++    +k   iv+ +s++    +   ++ a + sa+ +l+++L++e+++
  gi|13541542|ref|NP_111230.1|  99 FIEISDEDWDYAISMMLKSTIyLTREALRDMIR----TKHGSIVYVTSMTVREPIEGFSISASLRSAVISLAKTLTHEVSQ 175
                                   556888888888887777777566666666666....68888999999999999999************************ PP

                       DUF1776 188 hnidvtqikLGnldl 202
                                    +i v +i  G ++ 
  gi|13541542|ref|NP_111230.1| 176 NGIRVNTIAQGYFNT 190
                                   *********999985 PP

>> Syntaxin-18_N  SNARE-complex protein Syntaxin-18 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0     0.056   1.7e+02      56      74 ..      68      86 ..      35     105 .. 0.82
   2 ?    7.8   0.0    0.0013         4      54      72 ..     224     242 ..     223     248 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.056
                 Syntaxin-18_N 56 tkLrkfLleirkaYlnvrs 74
                                  ++L+++ +++r++Y ++ +
  gi|13541542|ref|NP_111230.1| 68 SDLENVVSNHREKYGSIDN 86
                                  589***********88755 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0013
                 Syntaxin-18_N  54 hItkLrkfLleirkaYlnv 72 
                                    I +L +fLl+ r++Y+n 
  gi|13541542|ref|NP_111230.1| 224 EIGELVEFLLSSRSSYING 242
                                   699**************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       652  (0.0363657); expected 358.6 (0.02)
Passed bias filter:                      564  (0.0314574); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.81
# Mc/sec: 958.64
//
Query:       gi|13541543|ref|NP_111231.1|  [L=129]
Description: hypothetical protein TVN0712 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-09   37.4   0.0    2.1e-09   36.7   0.0    1.4  1  HTH_OrfB_IS605  Helix-turn-helix domain
     0.0069   16.5   0.1      0.018   15.2   0.1    1.6  2  DUF1148         Protein of unknown function (DUF1148)


Domain annotation for each model (and alignments):
>> HTH_OrfB_IS605  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.7   0.0   2.3e-13   2.1e-09      10      47 .]       9      46 ..       1      46 [. 0.93

  Alignments for each domain:
  == domain 1  score: 36.7 bits;  conditional E-value: 2.3e-13
                HTH_OrfB_IS605 10 lyPTpeQeeklartfGcvRfVYNkaLaerkeayeeegk 47
                                  + P + Q+ ++a++fG   fV+N++L++r + y+e+ k
  gi|13541543|ref|NP_111231.1|  9 IDPRNDQAVLIAKHFGSTNFVWNYFLEQRVREYKENDK 46
                                  7899******************************9976 PP

>> DUF1148  Protein of unknown function (DUF1148)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1     2e-06     0.018      42      76 ..      31      65 ..      11      72 .. 0.84
   2 ?   -1.9   0.0      0.41   3.7e+03      32      54 ..      96     118 ..      81     124 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2e-06
                       DUF1148 42 gffletrlfqfessprflldvdmadclsrawnkwp 76
                                   +fle r+ +++ + +fl   dm  cl+   nk+ 
  gi|13541543|ref|NP_111231.1| 31 NYFLEQRVREYKENDKFLTAFDMMKCLTALKNKYA 65
                                  69***************************999986 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.41
                       DUF1148  32 lpalfspaeegffletrlfqfes 54 
                                   +p + s  ++ +f+  + f+f+ 
  gi|13541543|ref|NP_111231.1|  96 FPKFKSKKDKQYFIVPQHFKFKG 118
                                   56666777777787777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1042  (0.0581181); expected 358.6 (0.02)
Passed bias filter:                      556  (0.0310112); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 874.17
//
Query:       gi|13541544|ref|NP_111232.1|  [L=70]
Description: hypothetical protein TVN0713 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      9e-08   32.4   0.1    9.7e-08   32.3   0.1    1.1  1  OrfB_IS605  Probable transposase


Domain annotation for each model (and alignments):
>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.3   0.1   5.4e-12   9.7e-08      12      68 ..      16      69 ..       7      70 .] 0.92

  Alignments for each domain:
  == domain 1  score: 32.3 bits;  conditional E-value: 5.4e-12
                    OrfB_IS605 12 kpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksk 68
                                   +kgn+ +giDlG + +a+++++     + ++ ++k+++k+ ++ +++l++k+k+ k
  gi|13541544|ref|NP_111232.1| 16 LEKGNEIIGIDLGTEGFAALSNGI---RIEEPISIKREEKRIKRTQKKLAKKKKDGK 69
                                  6899********************...*************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       968  (0.0539907); 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: 0.37u 0.28s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 489.59
//
Query:       gi|13541545|ref|NP_111233.1|  [L=139]
Description: hypothetical protein TVN0714 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.2e-14   52.6   0.1    4.4e-14   52.2   0.1    1.2  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
  ------ inclusion threshold ------
       0.03   13.9   0.2      0.092   12.3   0.1    1.8  2  TF_Zn_Ribbon    TFIIB zinc-binding


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 !   52.2   0.1   4.9e-18   4.4e-14       1      67 [.      25      93 ..      25      95 .. 0.96

  Alignments for each domain:
  == domain 1  score: 52.2 bits;  conditional E-value: 4.9e-18
                OrfB_Zn_ribbon  1 frklkeqleykakeyGikveevnpay.TSktCseCgsknke.alsgrtfkCpnCgfeadrDvnAaiNil 67
                                  ++ +k++l+yka+   ++++e+ ++  +    s+Cg ++++ +ls+r f+C+nCg+++drD+n aiNi 
  gi|13541545|ref|NP_111233.1| 25 WYDFKQKLKYKAECGNMEFIEIGRFDpSFEIWSRCGWIDYNlKLSDRIFRCENCGLVIDRDLNTAINIS 93
                                  899***********************788999************************************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 ?   -2.2   0.0      0.35   3.2e+03      24      28 ..      37      41 ..      36      46 .. 0.63
   2 ?   12.3   0.1     1e-05     0.092      20      33 ..      73      86 ..      72      90 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.35
                                  SSSBE CS
                  TF_Zn_Ribbon 24 dCGlV 28
                                  +CG++
  gi|13541545|ref|NP_111233.1| 37 ECGNM 41
                                  56655 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 1e-05
                                  EEESSSSBEEEECC CS
                  TF_Zn_Ribbon 20 lvCtdCGlVledns 33
                                  ++C++CGlV++ + 
  gi|13541545|ref|NP_111233.1| 73 FRCENCGLVIDRDL 86
                                  79********9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 876.43
//
Query:       gi|13541546|ref|NP_111234.1|  [L=186]
Description: threonine efflux protein [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-12   47.6  13.8    1.9e-12   47.1  13.8    1.2  1  LysE      LysE type translocator
  ------ inclusion threshold ------
        8.1    6.7  10.1        1.2    9.4   4.0    2.3  2  DPM3      Dolichol-phosphate mannosyltransferase subunit 3 (D


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 !   47.1  13.8   2.1e-16   1.9e-12       1     190 [.      14     185 ..      14     186 .] 0.83

  Alignments for each domain:
  == domain 1  score: 47.1 bits;  conditional E-value: 2.1e-16
                          LysE   1 lslllspGpqnllvlkqgikrgfkggilvalgvligdavlillgllGlalLlkaapivlsilrllGgayLlwlgvlalrda 81 
                                   lsl ++pGp+n +++ +++++   +g  v++g++++d++++++++   + + k    +l  l ++G ++ +++++++l+++
  gi|13541546|ref|NP_111234.1|  14 LSLTAPPGPVNSIISVESVRSK-IHGSSVGAGAMTADIIFFIIVYSFGNIVPK---SALYALYIVGSIVMFYFAYSTLKKS 90 
                                   58999*************9999.999*************99998875555555...889999*****************99 PP

                          LysE  82 kekkveaeksveaslvkpflkglllslsNPkailfwlsvisallakaeqygdagrlilaaglvvasliwfsllaflaarls 162
                                    + k    ++        +  gll+ +sNP+ i++w+  +  +++       +g++ l+ g+v+ + i+ +++   a+r+ 
  gi|13541546|ref|NP_111234.1|  91 SRYKT---RR------GNYFVGLLVGISNPFQIIWWVTAGLFVVN---HMSLIGVFGLFSGVVLWITIFPFFVNKYAKRYE 159
                                   99984...33......44778****************99988888...677788887777777777777777777777777 PP

                          LysE 163 rrlsskkvlriinvvvgvlligfavkll 190
                                   ++++      ++ + +gv ++++++k++
  gi|13541546|ref|NP_111234.1| 160 KYVRIAS--SVVLISFGVYILIVGIKVI 185
                                   7777775..4677778888888888876 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 ?    0.6   0.4     0.071   6.3e+02      36      60 ..      61      85 ..      39      90 .. 0.78
   2 ?    9.4   4.0   0.00013       1.2      11      56 ..     134     180 ..     113     186 .] 0.76

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.071
                          DPM3 36 evvpvlPlwalvlfGayslatlgyg 60
                                  ++vp   l+al ++G+  ++   y+
  gi|13541546|ref|NP_111234.1| 61 NIVPKSALYALYIVGSIVMFYFAYS 85
                                  5677788888888888887776665 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00013
                          DPM3  11 allllal..wlalllrlvslplskvqdevvpvlPlwalvlfGayslat 56 
                                   + l++++  w++++   v+  + k ++++v +++ ++l++fG+y l++
  gi|13541546|ref|NP_111234.1| 134 FGLFSGVvlWITIFPFFVNK-YAKRYEKYVRIASSVVLISFGVYILIV 180
                                   44444441166655555533.59*********************9974 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       903  (0.0503653); 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 0.31s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1178.33
//
Query:       gi|13541547|ref|NP_111235.1|  [L=142]
Description: nucleotide-binding protein (UspA-related) [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.3e-23   83.3   0.0    2.6e-23   83.1   0.0    1.0  1  Usp            Universal stress protein family
  ------ inclusion threshold ------
      0.031   14.6   0.7      0.072   13.4   0.6    1.6  1  OmpH           Outer membrane protein (OmpH-like)
       0.15   11.8   0.1       0.24   11.1   0.1    1.3  1  Baculo_LEF5_C  Baculoviridae late expression factor 5 C-termi


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 !   83.1   0.0   4.3e-27   2.6e-23       4     141 .]       2     141 ..       1     141 [. 0.91

  Alignments for each domain:
  == domain 1  score: 83.1 bits;  conditional E-value: 4.3e-27
                                   EEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHH...HHHHHHCTTCE CS
                           Usp   4 rIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleada...akaaaeaggvk 81 
                                   r++Va+Dgs+ ++kA+ +Al l k++ ++ ++l+v+ + ++ +      + e+ e+++++a +  ++   + ++     ++
  gi|13541547|ref|NP_111235.1|   2 RVIVAYDGSPGADKAVGFALGL-KDSIDKYFILYVSRDITDLSGQLVYISDETVEQQERLADEIVNKaksLMTRSGVDYEV 81 
                                   99*******************7.667789*******************************999999966666666666677 PP

                                   EEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                           Usp  82 vevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                    +v+  + d + +i+++a+e+++d i +G+r+++gl++++lGS s+ +l+ ++cpV+vV+
  gi|13541547|ref|NP_111235.1|  82 MKVDSNGEDISKVIVKIAQEKGIDVIFTGTRKLRGLDKFFLGSISSGILALSSCPVIVVP 141
                                   777777889999***********************************************7 PP

>> OmpH  Outer membrane protein (OmpH-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.6   1.2e-05     0.072      93     116 ..      86     109 ..      45     119 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.2e-05
                                   HHHHHHHHHHHHHHHHTT-SEEEE CS
                          OmpH  93 pildkinkaikevakekgydlvld 116
                                   +  + i k+i ++a+ekg+d+++ 
  gi|13541547|ref|NP_111235.1|  86 SNGEDISKVIVKIAQEKGIDVIFT 109
                                   34599******************8 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 ?   11.1   0.1   4.1e-05      0.24      19      32 ..      53      66 ..      47      70 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 4.1e-05
                 Baculo_LEF5_C 19 tiEiQnRagDEivs 32
                                  t+E Q R  DEiv+
  gi|13541547|ref|NP_111235.1| 53 TVEQQERLADEIVN 66
                                  9************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       738  (0.0411624); expected 358.6 (0.02)
Passed bias filter:                      595  (0.0331865); 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: 0.46u 0.33s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 890.74
//
Query:       gi|13541548|ref|NP_111236.1|  [L=241]
Description: ribose-5-phosphate isomerase A [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.5e-55  186.3   0.1    4.5e-55  185.9   0.1    1.1  1  Rib_5-P_isom_A  Ribose 5-phosphate isomerase A (phosphoribois
    1.3e-07   31.7   0.2    5.5e-05   23.2   0.1    2.3  2  DeoRC           DeoR C terminal sensor domain
  ------ inclusion threshold ------
      0.021   13.9   0.0      0.034   13.3   0.0    1.3  1  Sugar-bind      Putative sugar-binding domain
      0.049   13.0   0.2       0.15   11.5   0.1    1.8  2  CoA_trans       Coenzyme A transferase
      0.073   11.7   0.0        0.1   11.2   0.0    1.2  1  Adenylate_cycl  Adenylate cyclase, class-I


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 !  185.9   0.1   1.3e-58   4.5e-55       2     173 .]      53     221 ..      52     221 .. 0.94

  Alignments for each domain:
  == domain 1  score: 185.9 bits;  conditional E-value: 1.3e-58
                                   EEESSHHHHHHHHHTT--BE-G.GCCSSEEEEEE--SEEETTS-EE--TTS-HHHHHHHHHTEEEEEEEEEGGGBESS.TT CS
                Rib_5-P_isom_A   2 gvptSeqteelaeelgipllsl.deveeidlaiDGaDevdedlnliKGgGgallrEKivaaaakkfiviadesKlvek.lg 80 
                                   gv tS+++eela+++gi++++  +++  idl+iDGaD+v+ + +liKGgGgallrEKiva+++k+++vi+d++K+ ++ +g
  gi|13541548|ref|NP_111236.1|  53 GVCTSKKSEELARAAGIEISENpEQI--IDLTIDGADQVNLHGTLIKGGGGALLREKIVAYNSKEMYVIVDSRKIDDEnFG 131
                                   89****************99985565..************************************************99999 PP

                                   SS-EEEEE-GGGHHHHHHHHHHTTT-EEEE-TETTTTEE-B-TTS-EEEEEESSSBSSSHHHHHHHHHTSTTEEEESEE-S CS
                Rib_5-P_isom_A  81 kfpvPveVlpfaleavarelekllggkpelReakgkdgpvvTdngnlilDvkfeekiedpeelekelksipGVvetGlFlg 161
                                   +fp+PveV+pf ++ ++++l+k +  +++lR+ ++++  ++Tdngn+i D+kf+ +i++ +elek++ksipGVv++GlF +
  gi|13541548|ref|NP_111236.1| 132 SFPLPVEVVPFLHRMTLENLRK-ICPSTDLRK-NSDGTLFITDNGNYIADMKFG-RIRETNELEKKIKSIPGVVDVGLFNN 209
                                   *********************6.58899***9.556899**************5.677*********************** PP

                                   --SEEEEEETTC CS
                Rib_5-P_isom_A 162 ladkvlvgkedg 173
                                   +adk++ g++dg
  gi|13541548|ref|NP_111236.1| 210 IADKIFEGNDDG 221
                                   ******999987 PP

>> DeoRC  DeoR C terminal sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.1   1.5e-08   5.5e-05       4      41 ..       6      43 ..       4      73 .. 0.87
   2 !    6.6   0.0    0.0019       6.9     120     146 ..     106     132 ..      76     138 .. 0.80

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 1.5e-08
                         DeoRC  4 eeKrrIAkaAaeliedgdtifldaGtTtlelaraLaek 41
                                  ++Kr+ A +Aa++++ g++i +++GtT+ +l+++L ++
  gi|13541548|ref|NP_111236.1|  6 KQKRNAAVEAASYVKTGMVIGIGTGTTARYLIEELGRR 43
                                  69********************************9876 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0019
                         DeoRC 120 kralieaarrvillaDssKfgkrafvr 146
                                   ++ ++ +++++++++Ds K++ ++f +
  gi|13541548|ref|NP_111236.1| 106 EKIVAYNSKEMYVIVDSRKIDDENFGS 132
                                   5667789**************998865 PP

>> Sugar-bind  Putative sugar-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   9.6e-06     0.034      42      80 ..      11      50 ..       2      66 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 9.6e-06
                                  HHHHHHHH--TTEEEEE-SSHHHHHHHHHTHH.CCHTCEE CS
                    Sugar-bind 42 aaqllesllkdgdvvgvgwGrtlsavaealtp.kslrdvk 80
                                  aa    s++k g+v+g+g+G+t + ++e+l +  s +++k
  gi|13541548|ref|NP_111236.1| 11 AAVEAASYVKTGMVIGIGTGTTARYLIEELGRrVSEENLK 50
                                  455556889*********************9965556655 PP

>> CoA_trans  Coenzyme A transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   4.1e-05      0.15       3      47 ..      11      51 ..       9      57 .. 0.83
   2 ?   -3.3   0.0       1.3   4.8e+03     187     209 ..     179     201 ..     172     202 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4.1e-05
                                  HHHHHHCTT--TTEEEEE-SBTTBT.HHHHHHHHHHHHTTTSEEEE CS
                     CoA_trans  3 taaeavakeikdGmtvavGGFglig.iPealiaalarsgvkdltvi 47
                                   a ea++ ++k Gm++ +G    +g ++ +li++l r+   ++  i
  gi|13541548|ref|NP_111236.1| 11 AAVEAAS-YVKTGMVIGIG----TGtTARYLIEELGRRVSEENLKI 51
                                  5678888.***********....8879********99987766666 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.3
                                   EEEEEEEECTTSSECCCESBTGG CS
                     CoA_trans 187 ileveeivekgkldpekvliPgv 209
                                   ++   +i e ++l ++  +iPgv
  gi|13541548|ref|NP_111236.1| 179 DMKFGRIRETNELEKKIKSIPGV 201
                                   55556778888888999999987 PP

>> Adenylate_cycl  Adenylate cyclase, class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   2.9e-05       0.1     494     543 ..     186     235 ..     169     240 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 2.9e-05
                Adenylate_cycl 494 praeleeeeklkvpeiidefasegllqfffedneegfnvYildeknelei 543
                                    +++  e++ +++p ++d  + + +   +fe n++g+n+Y++ ek+++e 
  gi|13541548|ref|NP_111236.1| 186 RETNELEKKIKSIPGVVDVGLFNNIADKIFEGNDDGCNIYVVSEKGRIEK 235
                                   444555689999***********************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       519  (0.0289475); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1645.55
//
Query:       gi|13541549|ref|NP_111237.1|  [L=476]
Description: amino acid transporter [Thermoplasma volcanium GSS1]
Scores for complete 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-35  121.4  54.0    5.6e-35  120.8  54.0    1.2  1  AA_permease    Amino acid permease
    1.4e-23   83.4  61.2    1.9e-23   83.0  61.2    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 !  120.8  54.0   6.3e-39   5.6e-35       5     473 ..      22     464 ..      16     469 .. 0.81

  Alignments for each domain:
  == domain 1  score: 120.8 bits;  conditional E-value: 6.3e-39
                   AA_permease   5 ialggviGtglfvglgvvlsqaGplgallayllagvviflvmlslgeiatngpksggfytyasrflgpelGfviGlnylfs 85 
                                   +a++ + ++g   ++    +++ ++++ layl+a++ +++ +++ ++ + ++ ++ggfyty ++  g+  G   G+ ++fs
  gi|13541549|ref|NP_111237.1|  22 QAIAMISPLGAVAATMTGSASIALGSLPLAYLIAIFAVLFWINTPYQYSKKIASAGGFYTYNRNGAGQYYGSISGYVLFFS 102
                                   5777777899999999999999999****************************************************9999 PP

                   AA_permease  86 witvlalelt..aasiliqfwel.vtdlpkawvt..gavflvvlliin.lvgvkvygeaefilalikiiaiiafiivg... 157
                                   + +++++++   +a+ + ++ e  +   ++aw++  +++ +++l++++ ++g++++ + +    l   i++ia+++++   
  gi|13541549|ref|NP_111237.1| 103 YYMTYTNAILfiTAVFIPGLFEIfFGITLTAWIWipVLIAIGLLVLLPaYLGIEGSTKYS----LASSIIQIALLVILslt 179
                                   999999986511444444666664777777888888888888888776378999998844....33333333333333322 PP

                   AA_permease 158 iillaggkpnkgagfrflgdngsifknnlppgfakeeegafknfisvfvivvfaftGielvaiiagEvkdPeksiPkailq 238
                                   ii++ g +++ +                ++p+      g f  ++++++ ++f+++G ++v+ +++E+k P+++i  a l 
  gi|13541549|ref|NP_111237.1| 180 IIVIKGPANTLE---------------PFTPK----PAGGFGPVFVGMILAIFSMSGSSAVVSLGEEAKQPKRNIRNALLI 241
                                   544444444444...............56666....4557***************************************** PP

                   AA_permease 239 vviritifYvlsllligllvprndlgllndsasa........aspfvifikesgvsvlaplinaviltaalssansslysa 311
                                    ++ +++++vl +++++++++ ++ + +++s+ a        +++++ ++k+ g++++   +++++  +++  +++ l sa
  gi|13541549|ref|NP_111237.1| 242 SFLVTGVVFVLTSYALTIGWGISNMNTFAQSNPAagltvgqgVPGIIEALKYMGMPMAIAMMIFAVN-SLYTGSLAPLNSA 321
                                   *****************************99988************************999999987.7889999****** PP

                   AA_permease 312 sRvlyslakdglaP.kvlkkvskrgvPlraillsmiisllalllaslnlaapivfnfllaisaliglivwlliilsylrfR 391
                                    R+++++++dg+aP  ++k ++k++ P++a+++ ++++ l+ l+a+l+ ++++ f +l+++sa++ +i ++++ +s+++  
  gi|13541549|ref|NP_111237.1| 322 ARMFFAMSRDGIAPkVFAKTHGKYKTPHVALVFIAFTGILVSLIAGLAMGPFNGFLYLVTASAVALFIGHIMTDISLPVAF 402
                                   **************6677889*********************************************************655 PP

                   AA_permease 392 kalkyqgrsieelgfkaallplgvilvlaaliiillilalyayltvkkgpkdwgaasfaaaylivllfliilvgvklhvkn 472
                                   k++++ +               +   vl a++++ll+ ++y+++  ++ p +      +a +  v+ ++++ +g++++ +n
  gi|13541549|ref|NP_111237.1| 403 KKFREFSV--------------LKHAVLPAISLVLLLIGIYYSFFPPTYPTN------IAIITAVIFMVAVAIGINVYLRN 463
                                   55555444..............334456666666666666655554555544......66666666666666666666666 PP

                   AA_permease 473 k 473
                                   +
  gi|13541549|ref|NP_111237.1| 464 G 464
                                   5 PP

>> AA_permease_2  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.0  61.2   2.1e-27   1.9e-23      11     424 ..      24     452 ..      14     460 .. 0.72

  Alignments for each domain:
  == domain 1  score: 83.0 bits;  conditional E-value: 2.1e-27
                 AA_permease_2  11 igsvigsgifvknlaasggpa...lilwvwiavligslavllvyaElssalprsgGiyvytkaafgkkvaflsawfnwfay 88 
                                   i  +  +g +++++++s+ +a   l l ++ia++++ l  + +  ++s ++ + gG y+y +++ g + +++s++ ++f+y
  gi|13541549|ref|NP_111237.1|  24 IAMISPLGAVAATMTGSASIAlgsLPLAYLIAIFAV-LFWINTPYQYSKKIASAGGFYTYNRNGAGQYYGSISGYVLFFSY 103
                                   444433455555444443333233666666666666.4455555678999***************9999999999888888 PP

                 AA_permease_2  89 vpvlasilsvaasyl.....lnalgp.dlqgntwltyliaiaililvalinirgikesakiqnilgilkillpliiliilg 163
                                     +  + +++++ +        ++++ +l+   w+++ + iai +lv l  ++gi +s k+     i+ i  +l+il ++ 
  gi|13541549|ref|NP_111237.1| 104 YMTY-TNAILFITAVfipglFEIFFGiTLT--AWIWIPVLIAIGLLVLLPAYLGIEGSTKYSLASSIIQIA-LLVILSLTI 180
                                   7754.3333333332222213333322454..55555555666666666778******************5.767777555 PP

                 AA_permease_2 164 litvdgggfsslstetdtffpn...gwpgvllgllivlwsfdGfesaanvseevkk..kdvpkaifigllivlvlyllvni 239
                                   +++ +g  ++      + f+p    g   v++g+  +++s++G +++++  ee+k+  ++++ a+ i++l+++v+++l++ 
  gi|13541549|ref|NP_111237.1| 181 IVI-KGPANT-----LEPFTPKpagGFGPVFVGMILAIFSMSGSSAVVSLGEEAKQpkRNIRNALLISFLVTGVVFVLTSY 255
                                   555.555555.....456777743344448***********************7766489********************* PP

                 AA_permease_2 240 aflgvvpddeianlsnlgsv............aalffeavggkvvaiivvilialsllgaintavigssrvlealardgvl 308
                                   a++++ +++++++ ++++ +            ++++  +  g  +ai+++i+++ sl  + ++ + +++r+++a++rdg+ 
  gi|13541549|ref|NP_111237.1| 256 ALTIGWGISNMNTFAQSNPAagltvgqgvpgiIEALKYM--GMPMAIAMMIFAVNSLYTGSLAPLNSAARMFFAMSRDGIA 334
                                   ***********7777777553333333333223333333..345666667777777777888888889************* PP

                 AA_permease_2 309 Prffakvn.kfgspiraiiltaivslillllfllas..saaynfllsvsslgliisyllliigalilrkkrphlkrpgkil 386
                                   P++fak++ k+++p +a++++a   ++++l+  la    + + +l+++s+++l+i  +++ i++ +  kk +++   + ++
  gi|13541549|ref|NP_111237.1| 335 PKVFAKTHgKYKTPHVALVFIAFTGILVSLIAGLAMgpFNGFLYLVTASAVALFIGHIMTDISLPVAFKKFREFSVLKHAV 415
                                   **********************999666666665533345566***************************99999988888 PP

                 AA_permease_2 387 vaiigalfllfllvalffppkgpatqssliytiiltva 424
                                   + +i++++ll+ ++  ffpp  p++   +i+++i++va
  gi|13541549|ref|NP_111237.1| 416 LPAISLVLLLIGIYYSFFPPTYPTN-IAIITAVIFMVA 452
                                   8888**************9877765.466666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (476 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1015  (0.0566122); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        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: 0.68u 0.31s 00:00:00.99 Elapsed: 00:00:00.46
# Mc/sec: 3077.56
//
Query:       gi|13541550|ref|NP_111238.1|  [L=186]
Description: hypothetical protein TVN0719 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.2e-36  123.9   0.0      4e-36  123.6   0.0    1.1  1  Macro     Macro domain


Domain annotation for each model (and alignments):
>> Macro  Macro domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.6   0.0   2.2e-40     4e-36       1     117 [.      27     143 ..      27     144 .. 0.96

  Alignments for each domain:
  == domain 1  score: 123.6 bits;  conditional E-value: 2.2e-40
                                   EEEEETTSS-CSHHHHHHHHHHHHHHHHHHHHHHHHHHS..--TTSEEEEE-TTSSSSEEEEEESE-TTTSTSTTHHHHHH CS
                         Macro   1 VnAaNsrllggggvagaihraagkalkeeckelekkqgg..cllGeavvtpaynlpakyvihtvgplftsskskeeeella 79 
                                   VnAaN +l+ggggv+gaih ++gk +  ec el++ + +  ++ Gea +t++++l+akyvihtvgp+++  +++e++e+l 
  gi|13541550|ref|NP_111238.1|  27 VNAANPSLMGGGGVDGAIHLKGGKTIDLECAELRRTKWPkgLPPGEADITSGGKLKAKYVIHTVGPIYR--GQEEDAETLY 105
                                   9********************************99876667***************************9..9********* PP

                                   HHHHHHHHHHHHTT-SEEEEE-TTSSTTSBTHHHHHHH CS
                         Macro  80 kayknalelaeekgiksvafPaistGifgvpweeaarv 117
                                   ++y ++le a+ +gik +afPaistGi+g+p+eea  +
  gi|13541550|ref|NP_111238.1| 106 SSYYRSLEIAKIHGIKCIAFPAISTGIYGYPFEEASVI 143
                                   **********************************9766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       280  (0.0156172); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1184.43
//
Query:       gi|13541551|ref|NP_111239.1|  [L=430]
Description: methyltransferase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.3e-09   35.5   5.2    9.8e-09   34.9   5.2    1.4  1  N6_Mtase         N-6 DNA Methylase
    0.00021   21.8   2.8    0.00028   21.4   0.5    2.4  2  Eco57I           Eco57I restriction-modification methylase
     0.0014   18.4   0.0     0.0027   17.5   0.0    1.4  1  Methyltransf_31  Methyltransferase domain
     0.0083   15.8   0.0      0.018   14.7   0.0    1.5  1  UPF0020          Putative RNA methylase family UPF0020


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 !   34.9   5.2   2.2e-12   9.8e-09     107     297 ..      93     286 ..      51     337 .. 0.83

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 2.2e-12
                      N6_Mtase 107 vkirlgdtlekpkfekdkkfdvvvaNppfnqkewkektlekderfrea.vapksnadlafllhiieslkpkGraavvlang 186
                                    +i+ +dtl++    + kk  + ++Npp+   ++  k++e+  ++ +     k+ +dl  + ++    ++  ++  +++++
  gi|13541551|ref|NP_111239.1|  93 KNIQVKDTLKEYPLLNVKKPIYHITNPPYLYIGYIAKHKENFGQLDYFtASLKGLQDLYQIALMNDLQNEINQMVYIIPSN 173
                                   368899999875555588888999**********77766666667776345577889999999999888999999****** PP

                      N6_Mtase 187 vLfrggkegkIrkalvekdlveavialpeklFyntsiptcilvlkkekaerkgkvlfidaseefkkkdrkknklteediek 267
                                    Lf  ++ + Ir++++    ++  i + +k+F nt+++++i ++++ +a +++++ f   + + + k +++ +l++++  +
  gi|13541551|ref|NP_111239.1| 174 FLFGHSVSNLIRRKFLPWYKINDAIIFEKKIFENTGVNVAICFFERTTA-KNSTIKFKATKINGEIK-EREYILSHKNDYR 252
                                   ************************************************6.78888887777777777.7999****99998 PP

                      N6_Mtase 268 ildtykek....skevdkfskvveleeiaendyn 297
                                     + +  +    +k++ k s+  + +ei +n  n
  gi|13541551|ref|NP_111239.1| 253 AGTEFDDYiksqEKNTLKISYYLTKKEIDNNPGN 286
                                   8888887755334444489999999999988655 PP

>> Eco57I  Eco57I restriction-modification methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.5   6.2e-08   0.00028       7     104 ..     116     221 ..     113     223 .. 0.86
   2 ?   -1.0   0.1      0.54   2.4e+03      47      58 ..     395     406 ..     314     428 .. 0.61

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 6.2e-08
                        Eco57I   7 iGNPPYqeseakkelkaleek.............akdiyqkFvekalkledkylaliiparflasgkglkefrekllkdkk 74 
                                   i NPPY  +  + + k+   +              +d+yq+ + + l+ e + ++ iip+ fl + ++ + +r+k+l   k
  gi|13541551|ref|NP_111239.1| 116 ITNPPYLYIGYIAKHKE---NfgqldyftaslkgLQDLYQIALMNDLQNEINQMVYIIPSNFLFGHSVSNLIRRKFLPWYK 193
                                   78****99885554442...224468899999999*****9999999999888889*******999999************ PP

                        Eco57I  75 lkklvefedskevFkdveikggilvflkdk 104
                                   ++  + fe++  +F+++ ++ +i++f + +
  gi|13541551|ref|NP_111239.1| 194 INDAIIFEKK--IFENTGVNVAICFFERTT 221
                                   *******975..6************98876 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.54
                        Eco57I  47 laliiparflas 58 
                                   + +++  ++ ++
  gi|13541551|ref|NP_111239.1| 395 SEFMTTYKYSNN 406
                                   234444444444 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0     6e-07    0.0027       7      53 ..      33      86 ..      29     133 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 6e-07
               Methyltransf_31  7 vlDlGCGtGeltfelaeelgpkae.......vvGiDiseeaielArenaqklgl 53
                                   +Dl +G+G+l++ + +++ ++++       ++++Di++e++e+A +na++  +
  gi|13541551|ref|NP_111239.1| 33 WVDLFAGEGNLILPILDLVPEEKRieffrdnIFLFDIQKEMVERAIKNAESYRI 86
                                  68**************966654446677788*****************997555 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0     4e-06     0.018      77     132 ..      62     122 ..      29     137 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4e-06
                                   --EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG.--....STTS---EEEE----- CS
                       UPF0020  77 lklygsDldrrvvqgareNaekagvgdliefsqadaak.Lr....lkegevdvivtnpPYG 132
                                    +++ +D+++++v++a +Nae++++   i+ ++ ++++ L+    l+ ++    +tnpPY 
  gi|13541551|ref|NP_111239.1|  62 DNIFLFDIQKEMVERAIKNAESYRIPRMIAEKNIQVKDtLKeyplLNVKKPIYHITNPPYL 122
                                   448889************************9999998734466642222334569999995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (430 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       650  (0.0362541); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 2764.37
//
Query:       gi|13541552|ref|NP_111240.1|  [L=301]
Description: major facilitator superfamily permease [Thermoplasma volcanium GSS1]
Scores for complete sequence (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   31.0  14.7    1.2e-07   31.0  14.7    1.7  2  MFS_1     Major Facilitator Superfamily
    0.00078   18.0   6.6      0.001   17.6   6.6    1.1  1  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 !   31.0  14.7   1.3e-11   1.2e-07     107     346 ..      25     249 ..       8     257 .. 0.75
   2 ?   -1.6   2.0      0.11     1e+03     266     294 ..     257     287 ..     242     300 .. 0.38

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 1.3e-11
                         MFS_1 107 aaliadwfpkeergraigllsagfslGailgpllggllasslg..Wravfyilaivsllafvlfllllpeepperkrkspk 185
                                    a+i +  ++e   +a++l  ++ s+ ++ g+++gg+++ +++  +  v++ + ++sll+++    ++  +++ +++ ++ 
  gi|13541552|ref|NP_111240.1|  25 SAIIKKFLKEESYKKAVSLNFLTGSVTSLTGAIIGGVFLIYFSdyFVDVMISAVLISLLSAI---PVIQKTQRVNENRNTF 102
                                   7999999********************************88885544455555555666655...6666666666666666 PP

                         MFS_1 186 eeekgtgpaplvpawkallkdp.vlwillialllfffgfsglltllplylqevlglsglllaglllallalvgailallag 265
                                            ++++  +++l++   +  ll+a++l+++++s+ ++ + l+ + vl+ + +++++     + +++ i++++++
  gi|13541552|ref|NP_111240.1| 103 SG-------EMKS-VGLFLRRIsGF--LLLAFFLNGLFISIDTYSSGLF-NLVLKANPAYYTA-----FNMAVPIGMMVGT 167
                                   55.......4555.33333333033..8888888886666666666665.8888888324444.....3333333355777 PP

                         MFS_1 266 rls.drlgrrrrlllallllllaalglallavtssavllllvlvliGfglgfvfpsllalasdlappeeagtasglfntag 345
                                    l+  r+ ++    ++ + ++++a +l++l++++ ++l ++  ++iG+ l +++++l++ + + +p +  g++s+++ ++ 
  gi|13541552|ref|NP_111240.1| 168 PLVnVRYFKMEEPAFISGMIFIFAPLLIILSLSKFPTLDIIDAFTIGLLLPLINIPLNSRLIKIIPGKIYGKISAVMRIFV 248
                                   777678888899999999999999999999999999****************************************99554 PP

                         MFS_1 346 s 346
                                   +
  gi|13541552|ref|NP_111240.1| 249 Q 249
                                   4 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.11
                         MFS_1 266 rlsdr..lgrrrrlllallllllaalglall 294
                                   +l +   +g    +++ +++ll++ l+l+ +
  gi|13541552|ref|NP_111240.1| 257 ALFNVlaIGISVKTVFLYVGLLVIPLALYGM 287
                                   3333322222222222222222222222222 PP

>> MFS_3  Transmembrane secretion effector
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   6.6   1.1e-07     0.001     109     381 ..       9     277 ..       2     293 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.1e-07
                         MFS_3 109 ltlligiGaalndPaWqAsvgelvkrrdvpaAvaLnsvginiaRsvGPAlgGvlvaavGaalafavnalsylalivallrw 189
                                   +t +   G++l++ +++A++  ++k +  ++Av Ln +   ++   G  +gGv +  +   ++  + +   + l+ a+  +
  gi|13541552|ref|NP_111240.1|   9 VTAVSIFGQTLKTDSFSAIIKKFLKEESYKKAVSLNFLTGSVTSLTGAIIGGVFLIYFSDYFVDVMISAVLISLLSAIPVI 89 
                                   56666789***************************************************9999888887788888888777 PP

                         MFS_3 190 krevrksslprEkllealra.glRftaasreikavlvRaalFglsasavlaLLPlvardqldgdalvyGillgalGvGAil 269
                                   +++ r ++  r+++ + ++  gl   ++s  +  ++    lF    +    L  lv    l+++++ y  +  a+ +G ++
  gi|13541552|ref|NP_111240.1|  90 QKTQRVNE-NRNTFSGEMKSvGLFLRRISGFLLLAFFLNGLFISIDTYSSGLFNLV----LKANPAYYTAFNMAVPIGMMV 165
                                   77666665.45667666654288888999999999988888888888888899998....678999*************** PP

                         MFS_3 270 galllsrLRerlsserlvllaavalAlvllslalasslwvavlvlllgGaaWitalstlnvavqlavPrWvvgRalavYlt 350
                                   g+ l++    ++++ ++++   + +A  l++l+l++   + ++     G    +    ln+    ++P  + g+  av   
  gi|13541552|ref|NP_111240.1| 166 GTPLVNVRYFKMEEPAFISGMIFIFAPLLIILSLSKFPTLDIIDAFTIGLLLPLINIPLNSRLIKIIPGKIYGKISAVMRI 246
                                   *99999888899**********************99888888877777777666677788888888899999998888888 PP

                         MFS_3 351 vlaGglaaGsllWGavaealsvtlaLlaaaa 381
                                    ++G+  a ++l+ ++a  +sv++  l  ++
  gi|13541552|ref|NP_111240.1| 247 FVQGAQPAMGALFNVLAIGISVKTVFLYVGL 277
                                   8888888888888888888888777666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       760  (0.0423894); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2111.40
//
Query:       gi|13541553|ref|NP_111241.1|  [L=224]
Description: restriction endonuclease, partial [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0036   17.4   0.3      0.043   14.0   0.3    2.3  1  HNH_2     HNH endonuclease


Domain annotation for each model (and alignments):
>> HNH_2  HNH endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.3   2.4e-06     0.043       1      71 [.     123     173 ..     123     174 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.4e-06
                         HNH_2   1 CvitgiddpslleaAHIiPwslssffndlilnrfeigrillekgstidspsNgllLspdiHklFdqflfaf 71 
                                   C ++gid + ll ++HI       +    +l            +++  +  N llL++ ++ +Fd+ l+++
  gi|13541553|ref|NP_111241.1| 123 CLLCGIDVDDLLVVSHIKD-----V----FLF-----------PEDAGNLYNTLLLCRLHDGMFDRKLISI 173
                                   7788877777778888877.....1....222...........25778899*****************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       544  (0.0303419); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1521.42
//
Query:       gi|13541554|ref|NP_111242.1|  [L=196]
Description: integrase/recombinase [Thermoplasma volcanium GSS1]
Scores for complete 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   82.3   0.0    5.6e-23   81.6   0.0    1.3  1  Phage_integrase  Phage integrase family
  ------ inclusion threshold ------
      0.051   13.4   0.0       0.15   11.9   0.0    1.8  2  HTH_23           Homeodomain-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 !   81.6   0.0   6.3e-27   5.6e-23      17     166 ..      37     178 ..      14     182 .. 0.85

  Alignments for each domain:
  == domain 1  score: 81.6 bits;  conditional E-value: 6.3e-27
                                   C....HHHHHHHHHHHHHHHHT--HHHHTT-BGGGEECTTTEEEEEEEECSSSSE.EEEECTHHHHHHHHHHHHHHCHCCT CS
               Phage_integrase  17 e....slkirdklllellyetGlRisEllsLrvkdldlengvilvheregKgske.ravplseealellkellskaleeae 92 
                                   +     lk+rd ll+  ++e G Ris++l+++vkd+d+ n+ +++  +++Kg+     +p+s+++l ++ + + +    + 
  gi|13541554|ref|NP_111242.1|  37 SkiipYLKARDVLLVNCMWELGGRISDILNIEVKDIDFMNKLVIL--KVKKGGGFiNKIPVSDNLLLAFSNFMREL---N- 111
                                   244545788999*********************************..777765544889**************999...3. PP

                                   TTSBSSBETTSSB--HHHHHHHHHHHHHHCT-SSC--TTHHHHHHHHHHHHHCTSHHHHHHHHT-SSCCHHHHH CS
               Phage_integrase  93 ksellfaskrgkplsrqtvrkafkraveeagiekpltpHtlRhsfataLleagvdlrvvqkllGHssisttqiY 166
                                          ++r  ++ rqt++k +k ++++ g++  l+pH++Rh +a  Ll +gv+++v+++ lGH++  t+ +Y
  gi|13541554|ref|NP_111242.1| 112 -----VSNRRLFKMDRQTAWKKIKGYGNKIGLN--LHPHMFRHGLAIYLLLKGVPIQVIARRLGHKNAMTILQY 178
                                   .....3344445678*****************9..********************************9998777 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       1.2   1.1e+04      25      33 ..     108     116 ..     108     119 .. 0.76
   2 ?   11.9   0.0   1.7e-05      0.15       6      34 ..     146     175 ..     142     179 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 1.2
                        HTH_23  25 reLgvsrrT 33 
                                   reL+vs r 
  gi|13541554|ref|NP_111242.1| 108 RELNVSNRR 116
                                   689999775 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 1.7e-05
                        HTH_23   6 eRlrillllaeGlsvreIAreLg.vsrrTv 34 
                                   ++ ++++ll++G +++ IAr+Lg  + +T+
  gi|13541554|ref|NP_111242.1| 146 RHGLAIYLLLKGVPIQVIARRLGhKNAMTI 175
                                   56789*****************64888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       685  (0.0382063); expected 358.6 (0.02)
Passed bias filter:                      543  (0.0302861); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1302.82
//
Query:       gi|13541555|ref|NP_111243.1|  [L=165]
Description: hypothetical protein TVN0724 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                      1155  (0.0644208); expected 358.6 (0.02)
Passed bias filter:                      582  (0.0324614); 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: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1120.29
//
Query:       gi|13541556|ref|NP_111244.1|  [L=102]
Description: Type II restriction enzyme, methylase subunit [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.9e-06   27.7   0.5      5e-06   27.0   0.5    1.4  1  Eco57I    Eco57I restriction-modification methylase
    0.00048   19.5   0.0    0.00058   19.2   0.0    1.0  1  N6_Mtase  N-6 DNA Methylase
  ------ inclusion threshold ------
       0.19   11.3   0.0         11    5.5   0.0    2.0  2  MTS       Methyltransferase small domain


Domain annotation for each model (and alignments):
>> Eco57I  Eco57I restriction-modification methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.5   8.3e-10     5e-06       3      61 ..      27      95 ..      22      99 .. 0.78

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 8.3e-10
                        Eco57I  3 fdviiGNPPYqeseakkelkaleek...........akdiyqkFvekalkle..dkylaliiparflasgkg 61
                                  f ++iGNPPY  ++   +l+++  k             + y  Fve+a +l    +y ++iip+  l ++++
  gi|13541556|ref|NP_111244.1| 27 FYIVIGNPPYVDIK---GLDPTIVKylfsnyttvenRMNPYSAFVERAANLLknYGYFGFIIPNSILYNESY 95
                                  89********9998...66655555677788888878899***********95556899****988865555 PP

>> N6_Mtase  N-6 DNA Methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   9.6e-08   0.00058     121     194 ..      22      96 ..       6      98 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 9.6e-08
                      N6_Mtase 121 ekdkkfdvvvaNppfnqkewkektlekderfrea..vapksnadlafllhiieslkpkGraavvlangvLfrggke 194
                                   +k+  f +v+ Npp+ + +  + t+ k   f+++  v ++ n   af+  + + lk+ G  +++++n +L++++ +
  gi|13541556|ref|NP_111244.1|  22 MKNGGFYIVIGNPPYVDIKGLDPTIVKYL-FSNYttVENRMNPYSAFVERAANLLKNYGYFGFIIPNSILYNESYK 96 
                                   4677899********88755566666665.7776657777777889*************************98766 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0    0.0018        11      93     123 ..      22      52 ..      10      57 .. 0.83
   2 ?    4.1   0.0     0.005        30     114     147 ..      60      93 ..      54      98 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0018
                                   STTS-EEEEEE---STTTCHCHHHHHHHHHH CS
                           MTS  93 veekkfdlivsNPPfhagkatelavaeelia 123
                                   ++++ f +++ NPP+ + k  + ++++ l+ 
  gi|13541556|ref|NP_111244.1|  22 MKNGGFYIVIGNPPYVDIKGLDPTIVKYLFS 52 
                                   56778999********999999999988875 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.005
                                   HHHHHHHHHHHHHHHEEEEEEEEEEEETTSCHHH CS
                           MTS 114 elavaeeliaeAkeaLkegGeLliVanrklgyes 147
                                   + +   ++++ A++ Lk+ G + +++ + + y++
  gi|13541556|ref|NP_111244.1|  60 RMNPYSAFVERAANLLKNYGYFGFIIPNSILYNE 93 
                                   5677889*************99888877776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       433  (0.0241508); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 668.11
//
Query:       gi|13541557|ref|NP_111245.1|  [L=123]
Description: integrase/recombinase, partial [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.5e-23   81.6   0.0      6e-23   81.5   0.0    1.0  1  Phage_integrase  Phage integrase family


Domain annotation for each model (and alignments):
>> Phage_integrase  Phage integrase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.5   0.0   3.4e-27     6e-23      30     157 ..       1     123 []       1     123 [] 0.97

  Alignments for each domain:
  == domain 1  score: 81.5 bits;  conditional E-value: 3.4e-27
                                   HHHHT--HHHHTT-BGGGEECTTTEEEEEEEECSSSSEEEEECTHHHHHHHHHHHHHH..CHCCTTTSBSSBETTSSB--H CS
               Phage_integrase  30 lyetGlRisEllsLrvkdldlengvilvheregKgskeravplseealellkellska..leeaeksellfaskrgkplsr 108
                                   ++++ lR +E++ L+++++   + +i+v    gKg+ker v l+ e  e+l ++l+++   ++ e+++++f  +  k+ls 
  gi|13541557|ref|NP_111245.1|   1 MFNCVLRLKEACDLKISNI--YDDTIKV---LGKGQKERLVYLPPETKEALMDYLKVRtpEKNLEDRDYVFTTASWKKLSY 76 
                                   67999*************9..8999***...9**************************9999999**************** PP

                                   HHHHHHHHHHHHHCT-SSC--TTHHHHHHHHHHHHHCTSHHHHHHHHT- CS
               Phage_integrase 109 qtvrkafkraveeagiekpltpHtlRhsfataLleagvdlrvvqkllGH 157
                                   + + k+ +++   ag++  ++pH+ Rh++at+L ++gv++  v++llGH
  gi|13541557|ref|NP_111245.1|  77 NYFTKICHEISIMAGVK--WHPHMVRHTYATELFKSGVNIYYVARLLGH 123
                                   *****************..****************************** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 830.99
//
Query:       gi|13541558|ref|NP_111246.1|  [L=305]
Description: esterase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-67  227.9   0.0    2.2e-67  227.0   0.0    1.4  2  Abhydrolase_3  alpha/beta hydrolase fold
    2.5e-08   33.2   0.0    2.9e-08   33.0   0.0    1.1  1  Say1_Mug180    Steryl acetyl hydrolase
    3.3e-06   26.3   0.1      3e-05   23.1   0.1    1.9  1  COesterase     Carboxylesterase family
  ------ inclusion threshold ------
      0.016   14.7   0.1      0.034   13.6   0.1    1.7  1  Peptidase_S9   Prolyl oligopeptidase family
       0.07   12.7   0.0        0.1   12.1   0.0    1.3  1  DUF2974        Protein of unknown function (DUF2974)


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 ?   -3.0   0.0       1.5   5.3e+03     161     190 ..      36      65 ..       8      69 .. 0.67
   2 !  227.0   0.0   6.2e-71   2.2e-67       1     210 [.      75     279 ..      75     280 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.5
                                   S-SST---EEEEEETT-TTHHHHHHHHHHH CS
                 Abhydrolase_3 161 edlsglpptlvvvaefDplrdegeayaerl 190
                                   +  sg+p++ + v e  +l  +++++ +rl
  gi|13541558|ref|NP_111246.1|  36 TPASGAPKVKISVVEDMILDTDAAKLPARL 65 
                                   347888888888888877777777666665 PP

  == domain 2  score: 227.0 bits;  conditional E-value: 6.2e-71
                                   EEEE--STTTS--TTTTHHHHHHHHHHHTSEEEEEE---TTTS-TTHHHHHHHHHHHHHHHTHHHHTETTCEEEEEEETHH CS
                 Abhydrolase_3   1 lvyfHGGGfvlgsldthdalcrelakelgavvvsvdYrlAPehpfPaavedalaalrwlaeqawelgadpsrivlaGdSaG 81 
                                   ++yfHGGGfv+gs++thd+lcr++ak +g  v+sv Yrl Pe++fP a  da++++ +++++++elg+d ++i+l+GdSaG
  gi|13541558|ref|NP_111246.1|  75 VLYFHGGGFVFGSIETHDSLCRRIAKYSGSKVISVGYRLGPENKFPVAQIDAFNSYLYVLKRSEELGVDSDKIALMGDSAG 155
                                   79************************************************************99***************** PP

                                   HHHHHHHHHHHHHTT---EEEEEEESE-SSTSSTTSHHHHHCHHTTTSSSSCHHHHHHHHHHHSS.GGGGGSTTTSGGGCS CS
                 Abhydrolase_3  82 GnlaaavalrardegepkvagqvliyPvtdlertesesikkaeeladgplltraaldlfwrlylp.eadrddplaspllae 161
                                   Gnlaa+++l+ard+g   ++ qvl+yP t + + +s+s+    e+++   lt++ l++f ++yl+  +d+ +p++sp+la 
  gi|13541558|ref|NP_111246.1| 156 GNLAAVASLMARDKGIKLPRLQVLVYPSTGP-DMTSKSY---LEYSS-IYLTKELLNWFSSQYLNsIEDALNPYFSPILA- 230
                                   **************9888*********9988.8889999...45555.889*************66999***********. PP

                                   -SST---EEEEEETT-TTHHHHHHHHHHHHHTT--EEEEEETTEETTGG CS
                 Abhydrolase_3 162 dlsglpptlvvvaefDplrdegeayaerlraagvevelieyegmvHgfa 210
                                   dlsglp+++vv+ e+Dpl ++ge y++ lr+ gv+v+ i+++gm+Hgf+
  gi|13541558|ref|NP_111246.1| 231 DLSGLPEAIVVTDEYDPLLEQGETYSATLRDSGVPVTSIRVNGMIHGFL 279
                                   ************************************************7 PP

>> Say1_Mug180  Steryl acetyl hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.0   0.0   8.1e-12   2.9e-08     118     237 ..      68     186 ..      12     229 .. 0.75

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 8.1e-12
                   Say1_Mug180 118 dPkvDpvllylHGGgfalklipvtlvfLsnlrklfpdmailvsDYtvtaakdqskkYplqvleslavydylvks...kgf. 194
                                   d ++D ++ly+HGGgf+++ i +  +    + k ++   ++ + Y +       +k+p    ++ + y y+ k    +g+ 
  gi|13541558|ref|NP_111246.1|  68 DSNSDSLVLYFHGGGFVFGSIETHDSLCRRIAK-YSGSKVISVGYRLGP----ENKFPVAQIDAFNSYLYVLKRseeLGVd 143
                                   6789******************99888777776.566677888999987....78999999*********98642223442 PP

                   Say1_Mug180 195 .knvvvlGdSaGGnlvLslllklsklnkvvlPkkaiaiSPWlnl 237
                                     ++ ++GdSaGGnl  +  l  ++ +   lP+  +++ P   +
  gi|13541558|ref|NP_111246.1| 144 sDKIALMGDSAGGNLAAVASLMARD-KGIKLPRLQVLVYPSTGP 186
                                   279***********86555444443.223478888887776554 PP

>> COesterase  Carboxylesterase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.1   8.2e-09     3e-05      99     206 ..      66     166 ..      53     176 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 8.2e-09
                                   SSTTSSEEEEEEE--STTTS-BGCGS-..THHHHHHHTSEEEEE----HHHHH-B-SSTTSBS-HHHHHHHHHHHHHHHHG CS
                    COesterase  99 keakkklPVlVwihGggfqtgsaseyd..gsaLaaegnvivVtinYRlGvlGFlstgdeeapGNvGllDqvlALrWVkenI 177
                                    + +++ + + ++hGggf++gs +++d  ++ +a++ +  v+++ YRlG+         ++   v+  D      +V +  
  gi|13541558|ref|NP_111246.1|  66 YDDSNSDSLVLYFHGGGFVFGSIETHDslCRRIAKYSGSKVISVGYRLGPEN-------KF--PVAQIDAFNSYLYVLKRS 137
                                   556667799**************996633799*****************833.......33..36789************* PP

                                   GGGTEEEEEEEEEEETHHHHHHHHHHHSG CS
                    COesterase 178 asFGGdpervtlfGesAGaasvsllllsp 206
                                   ++ G d++++ l+G+sAG+ ++++ +l  
  gi|13541558|ref|NP_111246.1| 138 EELGVDSDKIALMGDSAGGNLAAVASLMA 166
                                   *******************9988877654 PP

>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   9.5e-06     0.034      60      86 ..     141     167 ..     123     283 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 9.5e-06
                                   S--GGGEEEEEETHHHHHHHHHHHH-G CS
                  Peptidase_S9  60 yvdserlaitGgSyGGyltgaalnqrp 86 
                                    vds+++a++G S+GG l+++a  ++ 
  gi|13541558|ref|NP_111246.1| 141 GVDSDKIALMGDSAGGNLAAVASLMAR 167
                                   69*****************99987665 PP

>> DUF2974  Protein of unknown function (DUF2974)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   2.9e-05       0.1      82     108 ..     143     169 ..     119     220 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.9e-05
                       DUF2974  82 segkiylgGhSkGGnlAvyaamnaedd 108
                                    ++ki l G S GGnlA+ a+++a d+
  gi|13541558|ref|NP_111246.1| 143 DSDKIALMGDSAGGNLAAVASLMARDK 169
                                   3459****************9997765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       376  (0.0209716); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 1939.90
//
Query:       gi|13541559|ref|NP_111247.1|  [L=315]
Description: transcription regulator [Thermoplasma volcanium GSS1]
Scores for 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-67  225.8   0.3    9.8e-67  225.5   0.3    1.0  1  ROK          ROK family
     0.0015   18.1   0.0       0.15   11.5   0.0    2.2  2  BcrAD_BadFG  BadF/BadG/BcrA/BcrD ATPase 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 !  225.5   0.3   1.1e-70   9.8e-67       2     259 ..       6     281 ..       5     297 .. 0.91

  Alignments for each domain:
  == domain 1  score: 225.5 bits;  conditional E-value: 1.1e-70
                                   EEEEE-SSEEEEEEEETTS-EEEEEEEEEHCCH.....HCCHHHHHHHHHHCCCHCCHTEEEEEEEEESSEEETTCCEBSS CS
                           ROK   2 igidiGgtkialalvdeegeilarekvetptet.....teetlvdaiaelvdeaerkadeliavgigspGlisdksgkivs 77 
                                   +g d+Ggtki   +++++g+il++ +++t +       +ee+++   a+l+++  +k d    +gi+++G++++k+g ++ 
  gi|13541559|ref|NP_111247.1|   6 LGYDVGGTKISTVVGNDNGNILSNVRMPTVKHLgkkrlIEEMITMGDAALKKAGVDKPD---MIGIIFAGPVDNKKGVVIA 83 
                                   588************************77655411111666666677777777777777...9****************** PP

                                   GGCGCC.CCTTHHHHHHHHHTS-EEEEEHHHHHHHHHHHHCTTTTTS-EEEEEESSSEEEEEEETTEEE--TTS-TT-GGG CS
                           ROK  78 tpnitw.enfdlvekleerlnvpvevenDvnaaalaEavfgaskdvenviyvtvgtGvGaGviingklitGrnGvagelGH 157
                                    pni +  nf++ve +++ ++  +++enD+ aaa aE  fg  k+v+n++y+t++tG+G+G+ ingkl++G++G+agelGH
  gi|13541559|ref|NP_111247.1|  84 SPNIFGlSNFNIVEPIQKYYGAKTYLENDATAAAIAERLFGSGKNVDNFVYMTLSTGIGGGIFINGKLYKGAHGMAGELGH 164
                                   ******9************************************************************************** PP

                                   SBS-TTS-B-TTS-BSBHHHCCSHHHHHHCHTC..............CGTTS-HHHHHHHHCTT-HHHHHHHHHHHHHHHH CS
                           ROK 158 iqldpegekcgCGnqgClEtlasgralekraqq..............kgekleakeiiklaekgdevaeevverlaeylak 224
                                     +  +g+ cgCG++gClE+la g+a+++r+ +              ++ +++a+++++  +kgd  ++ ++e+  +yla 
  gi|13541559|ref|NP_111247.1| 165 SVIMVNGPTCGCGRRGCLEALAGGKAIARRVIEnlnavrdsnffsriRPTEITAEKVFEGKKKGDMFSQLILEETIYYLAV 245
                                   ******************************9999*********************************************** PP

                                   HHHHHHHHH--SEEEEEHCCCTSTTHH.HHHHHHHH CS
                           ROK 225 aiadlinlfdpqaivlgGgvseadkll.eairklvk 259
                                   +i+++in++dp+ +++gGg+s+a k l ++++ ++ 
  gi|13541559|ref|NP_111247.1| 246 GIVNIINILDPELVIIGGGISKAGKDLfDPLNDAIR 281
                                   *********************997644466555544 PP

>> BcrAD_BadFG  BadF/BadG/BcrA/BcrD ATPase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.0   1.7e-05      0.15       1      68 [.       6      71 ..       6     137 .. 0.77
   2 !    4.6   0.0    0.0022        20     177     242 ..     218     282 ..     213     295 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 1.7e-05
                                  EEEEE-SSEEEEEEEETTTEEEEEEEE--TTS-HHH.........HHHHHHHHHHT--GGGECEE..E CS
                   BcrAD_BadFG  1 vGiDgGsTttkavlmdekgevlgrgitnsanlesvrfeaaekvleealtealerageeeadieetylv 68
                                  +G D+G+T++ +v+ +++g++l +    ++ ++  +++   + + +  ++al++ag ++ d+  +++ 
  gi|13541559|ref|NP_111247.1|  6 LGYDVGGTKISTVVGNDNGNILSNVRM-PT-VKHLGKKRLIEEMITMGDAALKKAGVDKPDMIGIIFA 71
                                  799*****************8776543.22.3334444333333344457888888888887666544 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.0022
                                   HHHHHHHHHHTT--HHHHHHHHHHHHHHHHHHHHHTT---SS.EEEESGGGG-.HHHHHHH.....H CS
                   BcrAD_BadFG 177 aeaelrdalsggekaedIlaglhraialrvialisrsggvtdevtltGGvakn.eaavkelrklvke 242
                                   ae++++  ++g+  ++ Il+++  ++a  + ++i+ ++ +   v++ GG++k+ + +   l++ + e
  gi|13541559|ref|NP_111247.1| 218 AEKVFEGKKKGDMFSQLILEETIYYLAVGIVNIINILDPE--LVIIGGGISKAgKDLFDPLNDAIRE 282
                                   7899999**************************9999988..5899999998722233444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (315 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 1975.15
//
Query:       gi|13541560|ref|NP_111248.1|  [L=364]
Description: chorismate synthase [Thermoplasma volcanium GSS1]
Scores for complete 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-118  392.7   0.0     1e-117  392.5   0.0    1.0  1  Chorismate_synt  Chorismate synthase


Domain annotation for each model (and alignments):
>> Chorismate_synt  Chorismate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  392.5   0.0  5.6e-122    1e-117       1     327 []       8     347 ..       8     347 .. 0.96

  Alignments for each domain:
  == domain 1  score: 392.5 bits;  conditional E-value: 5.6e-122
                                   SEEEEE-SCCSSEEEEEEE---BT-B--HHHHHHHHHHHTCTSSSSSSHHHCS-EEEEESSEETTEE-SS-EEEEEE-TTS CS
               Chorismate_synt   1 lrvttfGeShgkalgavidgvpagleldeediqkeLdrRrpgqsklttqrkEkDeveilsGvfegktlGtpiallieNkdq 81 
                                   l+++ fG Shg+++g ++dg+p g ++  + iqk ++ Rrpg++ +t+qrkE+D v+i+sG+++g t G+pi+++ieNk++
  gi|13541560|ref|NP_111248.1|   8 LKLSLFGSSHGESVGSLVDGFPVGYKIPLDYIQKYMEYRRPGNTIITSQRKEEDVVKIISGMHNGFTDGSPITMIIENKNV 88 
                                   67899*************************************99************************************* PP

                                   -..SSSSSTSBE-TTSTCHHHHHHC.-S.STHCCCCCTHHCHHHHHHHHHHHHHHHHTTTEEEEEEEEEETTE.......C CS
               Chorismate_synt  82 rskdyeeikevpRpgHADltyalkY.girdlrgggrsSaReTaarvaaGavakklLkelgieivayvssigei.......e 154
                                    s+ yee+ke pRpgH+D+t  +kY  +r+++ggg  S+R Ta  vaaGa+ak++L++lgi+i++y++sige+       +
  gi|13541560|ref|NP_111248.1|  89 ISSYYEELKENPRPGHSDYTLYVKYgDFRNYEGGGFLSGRMTAPLVAAGALAKSYLDSLGIKITSYMKSIGEVtcdeirgD 169
                                   *************************999*******************************************8877655321 PP

                                   HHHHH.TT-BS-CCCHHHHHHHHHHHHHTT--B-EEEEEEEES--TT-SBTTTB-HHHHHHHHHHTSTTEEEEEETTGGGG CS
               Chorismate_synt 155 keaen.pvrcpdeeaaeemeeaieeakkegdslGgvvevvvkgvpaGlGepvfdkldakLakalmsipAvkgveiGsGfea 234
                                       n ++r+pd+e+++ +++++ +++k+gds+Gg + ++v+g+p+G+Gep+f+++++++++a++sipAvk++e+G+Gf+ 
  gi|13541560|ref|NP_111248.1| 170 --PYNfETRIPDPEKNSLATSLLVDIMKSGDSIGGRIDTIVEGLPPGVGEPFFNSVESEISRAMFSIPAVKAIEFGDGFTL 248
                                   ..445599************************************************************************* PP

                                   GGSBHHHHS--EE......EESS-TTTTEETTEEBSS-EEEEEEE--SS--SSEEEEEBTTS-E-EEEE--S-S-S-THHH CS
               Chorismate_synt 235 aelkGseanDeiv......lrktnnaGGieGGisnGepivvrvavKpipsiakeqktvdletkeevelevkgrhDpcvvpr 309
                                   +++kGseanD+++      l+ktn++GGi+GG+++G+p+ +++avKp+psi+k+q+t++l +ke+ e++vkgrhDpcv++r
  gi|13541560|ref|NP_111248.1| 249 SKMKGSEANDPFTvldghiLTKTNHNGGILGGMTTGMPVKFSIAVKPTPSIHKKQDTINLISKEKSEITVKGRHDPCVAIR 329
                                   *************77776655************************************************************ PP

                                   HHHHHHHHHHHHHHHHHH CS
               Chorismate_synt 310 avvvveamvalvladall 327
                                   av+vve+++a+vl+d+++
  gi|13541560|ref|NP_111248.1| 330 AVPVVECLTAFVLMDLMM 347
                                   ***************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (364 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       302  (0.0168442); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 2489.66
//
Query:       gi|13541561|ref|NP_111249.1|  [L=189]
Description: phosphoglycerate mutase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.4e-34  117.9   0.0    1.2e-33  116.5   0.0    1.6  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 !  116.5   0.0   6.4e-38   1.2e-33       2     185 ..       5     171 ..       4     176 .. 0.91

  Alignments for each domain:
  == domain 1  score: 116.5 bits;  conditional E-value: 6.4e-38
                                   EEEE---BTTB--....TT--.--B-HHHHHHHHHHHHHHTTS---EEEE-SSHHHHHHHHHHHHCTT--EEE-GGGS--- CS
                    His_Phos_1   2 yLvRHGetewnaegrlqgrtd.vpLteeGreqAealaerlagepidaiysSplkRarqTaeliaealglpveldegLrEid 81 
                                   +LvRHGe+e n  g+++   d  pLt+ Greq+  +a +la+ ++d i++Sp+ Ra+qTa++ia+++gl++ +d++ rE  
  gi|13541561|ref|NP_111249.1|   5 ILVRHGESETNLYGIISSDYDrYPLTQYGREQVTFIAPKLAELKFDGIITSPILRAVQTARIIANKCGLEILTDDRVRESG 85 
                                   7**************888877479********************************************************* PP

                                   -GGGTT-B.HHHHHH..HSHHHHHHHHH-GGG-BS-BHHHHHHHHHHHHHHHHHHTTTSEEEEEE-HHHHHHHHHHHHT-- CS
                    His_Phos_1  82 fGdweglttaeiaeeypeeleawlrdpadvrppggEsledvaaRvaaaleelaarhegetvlvVsHggvirallarllglp 162
                                   fG + +++ +ei  +        ++d       + E +e  ++R++++++e   +      ++VsH+ +i+al++++lg+ 
  gi|13541561|ref|NP_111249.1|  86 FGPYNNMHISEIPWK-------SREDM------KMEPWESHVKRMREVINEYDGS-----YIIVSHAYPIKALICDMLGMG 148
                                   *******88888777.......22232......3899*********999876544.....69******************* PP

                                   GGGGGGB---TT-EEEEEE-SS- CS
                    His_Phos_1 163 leelrrleldnaslsvlefdegg 185
                                    ++   +e++nas+s +++++g+
  gi|13541561|ref|NP_111249.1| 149 EDDCYSVEIKNASMSAIDVTNGR 171
                                   *******************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       367  (0.0204696); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.32s 00:00:00.88 Elapsed: 00:00:00.54
# Mc/sec: 1061.85
//
Query:       gi|13541562|ref|NP_111250.1|  [L=647]
Description: thioredoxin domain-containing protein [Thermoplasma volcanium GSS1]
Scores for complete 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  226.5   0.1    2.7e-67  225.8   0.1    1.3  1  Thioredox_DsbH   Protein of unknown function, DUF255
    5.6e-10   39.3   0.0    1.2e-09   38.2   0.0    1.6  1  Thioredoxin_7    Thioredoxin-like
      5e-05   22.0   0.0    0.00053   18.6   0.0    2.1  2  Glyco_hydro_127  Beta-L-arabinofuranosidase, GH127
    0.00041   19.4   0.2      0.088   11.7   0.0    2.6  3  Glyco_hydro_47   Glycosyl hydrolase family 47
    0.00059   19.5   0.2     0.0042   16.6   0.0    2.3  3  Glyco_hydro_76   Glycosyl hydrolase family 76
     0.0012   18.4   1.3       0.21   11.1   0.0    3.4  3  C5-epim_C        D-glucuronyl C5-epimerase C-terminus
      0.003   16.7   0.0      0.021   13.9   0.0    2.3  3  Glyco_hydro_88   Glycosyl Hydrolase Family 88
  ------ inclusion threshold ------
      0.068   13.4   0.1       0.86    9.9   0.0    2.8  2  PMBR             Pseudomurein-binding repeat


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 !  225.8   0.1   1.2e-70   2.7e-67       2     162 ..       3     163 ..       2     164 .. 0.98

  Alignments for each domain:
  == domain 1  score: 225.8 bits;  conditional E-value: 1.2e-70
                Thioredox_DsbH   2 nrlaeekspYllqhaknpvdWypwgeealekakeedkpillsiGysachWChvmekesfedeevaallnesfvsvkvDree 82 
                                   n+l +ekspYll+h+++p+dW+pw+e a++ka +e+++i+lsiGys+chWChv+++esf+d++va++ln+++v++kvDree
  gi|13541562|ref|NP_111250.1|   3 NELVHEKSPYLLMHSNDPIDWMPWSERAFSKAAAENRLIFLSIGYSTCHWCHVIHDESFSDKDVADILNKNYVCIKVDREE 83 
                                   99******************************************************************************* PP

                Thioredox_DsbH  83 rPdldkiymeavqaltgsggWPlnvfltpdlkpffggtYfpkeeregrpgflevlekiaelweeereeleeeaeelleal 162
                                   rPdld+++m+++ +++gsggWPlnv+l pd++p+f+ tY+pke+r g++g+++++++ia +w+++ +++e++a ++++a+
  gi|13541562|ref|NP_111250.1|  84 RPDLDSYFMNVSAVINGSGGWPLNVILLPDRRPVFAFTYVPKEDRRGMTGLKTLAQQIALIWKNDPQQFESQAVAVMDAV 163
                                   ************************************************************************99998876 PP

>> Thioredoxin_7  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.2   0.0   5.5e-13   1.2e-09       1      65 [.      22      86 ..      22     111 .. 0.93

  Alignments for each domain:
  == domain 1  score: 38.2 bits;  conditional E-value: 5.5e-13
                                  ---SSHHHHHHHHHHHT--EEEEE--TT-HHHHHHHHHHHH-HHHHH.HHHT-EEEEESS--S-G CS
                 Thioredoxin_7  1 ewlsdldealakaaergkpvlvffgaswcftCqalerdflsdeevkaalaekfvllrvdvterda 65
                                  +w+ + ++a++kaa++++ +++ +g s+c+ C+++ ++  sd++v+ +l++++v+ +vd +er +
  gi|13541562|ref|NP_111250.1| 22 DWMPWSERAFSKAAAENRLIFLSIGYSTCHWCHVIHDESFSDKDVADILNKNYVCIKVDREERPD 86
                                  7**********************************************************999865 PP

>> Glyco_hydro_127  Beta-L-arabinofuranosidase, GH127
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.1   0.0    0.0015       3.3     148     201 ..     388     442 ..     369     457 .. 0.73
   2 !   18.6   0.0   2.4e-07   0.00053     132     264 ..     423     562 ..     418     570 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0015
                                   HHHHHHHHHHHHHHCCS-CCHHHHHTTTHHCTHH.HHHHHHHHHHT-CHHHHHHH CS
               Glyco_hydro_127 148 dvatrladyleevleklgdeqlqkalvpehggie.ealvklyelTgdkrYldlAk 201
                                   d++ r  + l e+ +k ++ ++ k++ ++ +g+   +l + y++Tgdk++ld A 
  gi|13541562|ref|NP_111250.1| 388 DMLSRSIEKLREAEKKRKKPSVDKKILTDLNGLAiSSLSWAYRATGDKEFLDSAV 442
                                   55555555565666666677778888888888886899*************9885 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 2.4e-07
                                   HHHHHHHHHH--HHHHHHHHHHHHHHHHHHCCS-CCHHHHHTTT.........HHCTHHHHHHHHHHHHT-CHHHHHHHHC CS
               Glyco_hydro_127 132 egavayyqatgkeklldvatrladyleevleklgdeqlqkalvp.........ehggieealvklyelTgdkrYldlAkrf 203
                                   + +  +y+atg++++ld a+ + +++  + + +gd  l +  +          +   +  +l++ly++T d++Yl+ Ak++
  gi|13541562|ref|NP_111250.1| 423 SSLSWAYRATGDKEFLDSAVSVSEFI--IKNMIGDYLLHSFFEGsasvksslfDYAFLIRGLIDLYTITFDQKYLEEAKKL 501
                                   667779********************..66666776665544442222222223344557889999*************** PP

                                   CHHCCHCC....T-HCTTT-SSTCGCHHCHHCCHHHHHHHHHHHHHHHHHCTTHCCHHHHHHHHH CS
               Glyco_hydro_127 204 idergldp....eklaykqdelpvrhqntaigkavRatylysgladvyeetgddkllkaaerlwd 264
                                    de++        kl+++ d+ +  +++ + + a     +++ l d+  +t+d ++ ++a++  +
  gi|13541562|ref|NP_111250.1| 502 ADEAIKFLfdgkFKLSEEIDDPQIADSEVESPYAT----IVADLDDLSLLTEDLQYHQIADQALT 562
                                   ***9976676666799999*9999**999999999....999*************9999887555 PP

>> Glyco_hydro_47  Glycosyl hydrolase family 47
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       0.6   1.4e+03     156     181 ..     275     300 ..     267     319 .. 0.76
   2 !    4.3   0.0    0.0068        15     366     396 ..     421     451 ..     417     469 .. 0.89
   3 !   11.7   0.0   3.9e-05     0.088      86     203 ..     481     586 ..     461     597 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.6
                                   HHHHHHHHT-CHHHHHHHCCHHHHHC CS
                Glyco_hydro_47 156 ftrLsqlTgdkkYedlaervtkalee 181
                                   f+++  lT+d+ Y d++  + + ++e
  gi|13541562|ref|NP_111250.1| 275 FSKMFMLTRDNVYRDMIYDIKRFMDE 300
                                   55566778888888888777777766 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.0068
                                   HHHHHHHHHHHH--THHHHHHHHHHHHHHHH CS
                Glyco_hydro_47 366 aiESlfylYritgdekyrevgwemfealeka 396
                                   ai Sl  +Yr+tgd+++++ + ++ e + k+
  gi|13541562|ref|NP_111250.1| 421 AISSLSWAYRATGDKEFLDSAVSVSEFIIKN 451
                                   688999**************99988877765 PP

  == domain 3  score: 11.7 bits;  conditional E-value: 3.9e-05
                                   HHHHHHHHH.S-HHHHHHHHHHHHHH.HHGGGSSTTS---SEEETTT--EE-.STCGCEEEHHHHCSSHHHHHHHHHHHT- CS
                Glyco_hydro_47  86 GLlsaydlsekkedvllekAveladr.LlpAFdtpsglpvarvnlkkrkaskkerassesvlAelgslslEftrLsqlTgd 165
                                   GL+  y ++   ++ +le+A++lad  +   Fd        +++l  +++  + +   ++v +  ++++  +  Ls lT+d
  gi|13541562|ref|NP_111250.1| 481 GLIDLYTIT--FDQKYLEEAKKLADEaIKFLFD-------GKFKL--SEEIDDPQIADSEVESPYATIVADLDDLSLLTED 550
                                   899999999..999**********862555666.......56666..33344433333567799***************** PP

                                   CHHHHHHHCCHHHHHCHCC.HHHTTB-BSEEETTT--E CS
                Glyco_hydro_47 166 kkYedlaervtkaleelqektklpglvpikidastgkf 203
                                    +Y ++a+++ + + ++   +++p  +p+++   ++++
  gi|13541562|ref|NP_111250.1| 551 LQYHQIADQALTSVFDAV--SRFPSAFPSMVISAEKHI 586
                                   **********99999954..567888888776665555 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 ?   -1.7   0.3       0.7   1.6e+03      34      63 ..     264     293 ..     244     317 .. 0.70
   2 ?    2.0   0.0     0.055   1.2e+02     211     258 ..     408     455 ..     398     472 .. 0.78
   3 !   16.6   0.0   1.9e-06    0.0042     167     262 ..     429     516 ..     416     540 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.7
                                   GHHHHHHHHHHHHHHHHHCTTCCCHHHHHH CS
                Glyco_hydro_76  34 ywWeagalfgalidywrltgdstyndlitq 63 
                                   + +++ +l++ + ++  lt+d+ y+d+i++
  gi|13541562|ref|NP_111250.1| 264 MLYTQTQLMKLFSKMFMLTRDNVYRDMIYD 293
                                   567777888888888888888888888765 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.055
                                   EEE---HHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHCEEC CS
                Glyco_hydro_76 211 dinklqwtYnqGtylsgaaylynaTgdekWldrvkgllnatlstffpd 258
                                   +++k  +t  +G+ +s+    y+aTgd+++ld +  + + + + ++ d
  gi|13541562|ref|NP_111250.1| 408 SVDKKILTDLNGLAISSLSWAYRATGDKEFLDSAVSVSEFIIKNMIGD 455
                                   577888888899999999999999999999999988888776666555 PP

  == domain 3  score: 16.6 bits;  conditional E-value: 1.9e-06
                                   HHHH--CHHHHHHHHHHHHHHHHSCS.BTTTS-B-SEEETTTCCEEEE---HHHHHHHHHHHHHHHHHHH--HHHHHHHHH CS
                Glyco_hydro_76 167 arytgnetYlewAekvwdWvedvgli.ddedwlvyDgasvednctdinklqwtYnqGtylsgaaylynaTgdekWldrvkg 246
                                   +r+tg++++l+ A +v +++ + ++i d   ++++ g        +++       +++++ g + ly +T d+k+l+++k+
  gi|13541562|ref|NP_111250.1| 429 YRATGDKEFLDSAVSVSEFIIK-NMIgDYLLHSFFEGS------ASVKSSL--FDYAFLIRGLIDLYTITFDQKYLEEAKK 500
                                   8999999999999999999999.788233334444442......2233333..6789************************ PP

                                   HHHHHHHHCEECTTEE CS
                Glyco_hydro_76 247 llnatlstffpdgnil 262
                                   l++ + +++f+++  l
  gi|13541562|ref|NP_111250.1| 501 LADEAIKFLFDGKFKL 516
                                   **********994334 PP

>> C5-epim_C  D-glucuronyl C5-epimerase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.26   5.8e+02      30      51 ..     267     288 ..     263     299 .. 0.89
   2 !   11.1   0.0   9.3e-05      0.21      32      60 ..     419     447 ..     417     463 .. 0.88
   3 ?    3.1   0.1     0.027        60      34      59 ..     478     503 ..     469     512 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.26
                     C5-epim_C  30 aqgqaisvllrAYeltgdekYl 51 
                                   +q q+++++++ + lt d+ Y 
  gi|13541562|ref|NP_111250.1| 267 TQTQLMKLFSKMFMLTRDNVYR 288
                                   799***************9995 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 9.3e-05
                     C5-epim_C  32 gqaisvllrAYeltgdekYlkaakkalks 60 
                                   g ais l+ AY++tgd+++l++a  + ++
  gi|13541562|ref|NP_111250.1| 419 GLAISSLSWAYRATGDKEFLDSAVSVSEF 447
                                   889*******************9887665 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.027
                     C5-epim_C  34 aisvllrAYeltgdekYlkaakkalk 59 
                                   +i  l+  Y  t d+kYl+ akk+ +
  gi|13541562|ref|NP_111250.1| 478 LIRGLIDLYTITFDQKYLEEAKKLAD 503
                                   566788889************99865 PP

>> Glyco_hydro_88  Glycosyl Hydrolase Family 88
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.43   9.5e+02     144     167 ..     281     304 ..     218     318 .. 0.66
   2 !   13.9   0.0   9.5e-06     0.021      31     105 ..     418     506 ..     394     528 .. 0.83
   3 !    8.5   0.0   0.00042      0.94      29      63 ..     473     507 ..     454     572 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.43
                                   HHCGTHHHHHHHHHHHHHHHHHBE CS
                Glyco_hydro_88 144 vtgepkyldeaikqflltarhlfd 167
                                   +t ++ y+d++ +  + ++++l+ 
  gi|13541562|ref|NP_111250.1| 281 LTRDNVYRDMIYDIKRFMDENLYW 304
                                   344444444444444444444444 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 9.5e-06
                                   HHHHHHHHHHHHHHH--HHHHHHHHHHHHHCCCTTS-..............CTTSGGGTGHHHHHHHHHHHH-THHHHHHH CS
                Glyco_hydro_88  31 nGvflsglleayeatgdkeyldyakawadslideggk..............telelDdidigllllllyeltkderykeaa 97 
                                   nG+++s+l  ay atgdke+ld a +  +  i+++                ++   D++ +   l++ly +t d++y e a
  gi|13541562|ref|NP_111250.1| 418 NGLAISSLSWAYRATGDKEFLDSAVSVSEFIIKNMIGdyllhsffegsasvKSSLFDYAFLIRGLIDLYTITFDQKYLEEA 498
                                   899999********************888888888777888888888888888889999999999**************** PP

                                   HHHHHHHH CS
                Glyco_hydro_88  98 eeladyvl 105
                                   ++lad  +
  gi|13541562|ref|NP_111250.1| 499 KKLADEAI 506
                                   ***99554 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.00042
                                   HHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHCCC CS
                Glyco_hydro_88  29 wtnGvflsglleayeatgdkeyldyakawadslid 63 
                                   ++ +++++gl+++y +t d++yl+ ak+ ad+ i+
  gi|13541562|ref|NP_111250.1| 473 FDYAFLIRGLIDLYTITFDQKYLEEAKKLADEAIK 507
                                   6789999********************98887664 PP

>> PMBR  Pseudomurein-binding repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00039      0.86       8      24 ..     285     301 ..     284     307 .. 0.93
   2 ?   -1.1   0.0       1.2   2.6e+03       8      21 ..     435     448 ..     433     451 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00039
                          PMBR   8 eeyldmasrvlafiesn 24 
                                   + y+dm++++++f+++n
  gi|13541562|ref|NP_111250.1| 285 NVYRDMIYDIKRFMDEN 301
                                   57*************99 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.2
                          PMBR   8 eeyldmasrvlafi 21 
                                    e+ld a+ v  fi
  gi|13541562|ref|NP_111250.1| 435 KEFLDSAVSVSEFI 448
                                   69********9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (647 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       647  (0.0360868); expected 358.6 (0.02)
Passed bias filter:                      558  (0.0311228); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.71u 0.35s 00:00:01.06 Elapsed: 00:00:00.49
# Mc/sec: 3993.62
//
Query:       gi|13541563|ref|NP_111251.1|  [L=458]
Description: cytochrome bd-type quinol oxidase, subunit 1 [Thermoplasma volcanium GSS1]
Scores for complete 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-92  308.2  24.1    8.1e-92  308.0  24.1    1.0  1  Cyt_bd_oxida_I  Cytochrome bd terminal oxidase subunit I


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 !  308.0  24.1   4.5e-96   8.1e-92       3     417 ..       8     440 ..       6     441 .. 0.93

  Alignments for each domain:
  == domain 1  score: 308.0 bits;  conditional E-value: 4.5e-96
                Cyt_bd_oxida_I   3 RlqfaltavfHflfvpltlGlalllailetlylrtgdekykklakfwgklfainFavGvvtGivlefqfgtnWseysrfvG 83 
                                   Rl fa+++  H+l+v +++Gl+++l +le+++++ +d +y  l+++++k ++++FavG+++G v+++++  ++++++++++
  gi|13541563|ref|NP_111251.1|   8 RLLFAYSIGSHILIVLMSIGLSVILPVLEYIAIKYKDVYYDLLTRRVAKALVMFFAVGTASGAVMAVELIDLFPKFMTIIA 88 
                                   99******************************************************************************* PP

                Cyt_bd_oxida_I  84 difgapLaiEgllAFflEstflglmlfgwdrv.skklhllatwlvaigtllSalwIlaanswmqtPvGaelnpdtgraelt 163
                                    + ++p+++E ++AFflE ++l  +++ wd + ++  h+l+t+ va gtl+Sa++I+++n+wm+tP+G+++++ +++ +l 
  gi|13541563|ref|NP_111251.1|  89 VVGVLPFYYE-IFAFFLETIMLVSYYYYWDVFkNRMHHWLLTFGVAGGTLASAVFITMINAWMNTPNGFNISYYEKTGKLI 168
                                   **********.7********************677779********************************98776655664 PP

                Cyt_bd_oxida_I 164 ..dflavlfnpsalakflHtvlaalltaaffvagvsawyllr....rekefarkslkialvvalvaallqallGdlsgkev 238
                                     +++  +++ps+  +++H+v+ + +++ +++ + +a+++lr    + k ++ k lk+++ + +++++++ l+G l+++ +
  gi|13541563|ref|NP_111251.1| 169 dvNPFITALTPSTGREVFHVVIVTAFAGLMVLGAFFAYQYLRakteEAKTLYMKGLKVTFPMNMFLIIMAGLSGTLEMSGL 249
                                   34999999**********************************97644444******************************* PP

                Cyt_bd_oxida_I 239 aetqpaKlAAmeglwetee..aplslfgipdeeeekne..faieiPgllsllat.gsldgevkGlndlpkeevPpvalvfw 314
                                   +++qp+K+AA++ +    +  ap +lfg + e++ +      i+iP ++slla  g+l+++v+Gl+++p++++Pp + v+ 
  gi|13541563|ref|NP_111251.1| 250 LTYQPEKYAALDLNPYPIArdAPEHLFGTIVEKNGHYYvlGGIKIPFVQSLLAGnGNLNTPVPGLSQFPTSTWPP-LAVHD 329
                                   ************998655568********9998887764445**********985789****************9.899** PP

                Cyt_bd_oxida_I 315 sfrimvglgvlllllallalll..........rwllrllllaiplpfiaveaGWivtevGRqPWivygllrtadavspvsa 385
                                   +f++mv+ g+ll l++l +l+           + ++ + +l+++l +  ++ GW++ evGRqPWi+y+++++ +a+    +
  gi|13541563|ref|NP_111251.1| 330 TFDLMVIGGTLLGLFLLSVLIAwilkkkpyesKGFMVAQILFAILTIPIYIGGWVTDEVGRQPWIIYNVMTVYQAA--NYS 408
                                   ***********99988877644559*******88999999999999999**************************9..999 PP

                Cyt_bd_oxida_I 386 gevllslilflllylvLlvvevylllklikkg 417
                                   +++++  +l++++y++L+ + +++ ++l+k+g
  gi|13541563|ref|NP_111251.1| 409 PSIIVPGYLIMAFYTILMPFSYWYAFRLMKQG 440
                                   9****************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (458 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       775  (0.0432261); 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):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 2884.55
//
Query:       gi|13541564|ref|NP_111252.1|  [L=330]
Description: hypothetical protein TVN0733 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0044   16.4  36.7     0.0064   15.9  36.7    1.2  1  Cyt_bd_oxida_II  Cytochrome bd terminal oxidase subunit II
      0.007   16.2   1.5      0.007   16.2   1.5    2.3  2  Cortexin         Cortexin of kidney


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 !   15.9  36.7   7.2e-07    0.0064      27     300 ..      26     315 ..       2     319 .. 0.63

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 7.2e-07
               Cyt_bd_oxida_II  27 GillpllakkdeerrlllnsigpvWdgnevWLvtaggalfaaFPlayatlfsglylpllliLlglilRgvaf...efrska 104
                                   G++l++    ++  + ++++++p+W+++ ++L ++++ + a F  +   +  ++  +ll+ L+++i+R va+   ef + +
  gi|13541564|ref|NP_111252.1|  26 GFMLLF--DWKNSGQKIMTYVAPIWEVTGTFLAMFVVETDATFAGILIPAAFAFAALLLIFLILFIVRNVAIilgEFAGSR 104
                                   334444..223567789******************************************************9555555555 PP

               Cyt_bd_oxida_II 105 eskrwrklwdlaffigSllaalllGvalgnllqGvpfdadeyg.flsdll.........npfallvglllvalflllGaly 175
                                   +     +   ++++i+ ll+++++ +  +++++G  ++ d +g  +++ll         n+ ++l+g   +++++  + + 
  gi|13541564|ref|NP_111252.1| 105 KI-FTDRQLYYIYVIATLLISVVFLAFSSAIISGNGVKIDIAGnPVDSLLsvsnaeisfNLASWLAGPGDILFVVSAALIA 184
                                   43.366666778888888888888888899999777654422333333333334444446666666665555555444444 PP

               Cyt_bd_oxida_II 176 lalktegelqerarrlalvlalvllvllvvvllwtll......lvllllavlalllavlllrkkreglaflasaltvllvv 250
                                   + l       +r+ ++  + +++ ++l +v ++ + +      ++++++ + + +l  + l+k + ++  ++ ++++++ +
  gi|13541564|ref|NP_111252.1| 185 FGLSPVFYDVDRFSTYGVISSVIGFILGIVSFVQMGVhispiiIIPAIIIIGVPILYRIGLAK-KILTNKALFIVLLIVSI 264
                                   444444344456666666666444444444444444444443234433333333333333222.34445555556666667 PP

               Cyt_bd_oxida_II 251 lllavslfPyllpssltianaass.eytlkvmlivalillplvlaytawly 300
                                   + l ++++P+ +  +l + +  ++ +  + ++l  ++ +++l ++  +++y
  gi|13541564|ref|NP_111252.1| 265 YSLYFTVYPSAMNGKLPLSQIITTgPMVIGTILTTVVGFTLLAFMLSLYVY 315
                                   7778889********998887655155566666666666666666667766 PP

>> Cortexin  Cortexin of kidney
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   1.5   7.8e-07     0.007      25      49 ..      74      98 ..      57     103 .. 0.92
   2 ?   -1.9   0.1      0.33     3e+03      34      44 ..     255     265 ..     250     275 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 7.8e-07
                      Cortexin 25 vfafvilLlifLglLivrCfriLLD 49
                                  +faf  lLlifL l ivr + i+L 
  gi|13541564|ref|NP_111252.1| 74 AFAFAALLLIFLILFIVRNVAIILG 98
                                  8*********************996 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.33
                      Cortexin  34 ifLglLivrCf 44 
                                   +f++lLiv  +
  gi|13541564|ref|NP_111252.1| 255 LFIVLLIVSIY 265
                                   57777777655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1268  (0.0707234); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); 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):               2  [number of targets reported over threshold]
# CPU time: 0.70u 0.34s 00:00:01.04 Elapsed: 00:00:00.51
# Mc/sec: 1965.53
//
Query:       gi|13541565|ref|NP_111253.1|  [L=252]
Description: geranylgeranylglyceryl phosphate synthase-like protein [Thermoplasma volcanium GSS1]
Scores for complete 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-54  183.4   0.1    5.2e-54  183.1   0.1    1.0  1  PcrB             PcrB family
    2.9e-09   36.7   0.1    9.1e-09   35.1   0.0    1.7  2  His_biosynth     Histidine biosynthesis protein
    0.00013   21.2   0.3     0.0022   17.2   0.1    2.0  2  Dus              Dihydrouridine synthase (Dus)
    0.00019   20.4   0.3     0.0011   17.8   0.1    2.0  2  Trp_syntA        Tryptophan synthase alpha chain
     0.0011   18.4   0.9     0.0028   17.1   0.1    2.0  3  G3P_antiterm     Glycerol-3-phosphate responsive antiterminat
     0.0012   18.0   0.1       0.13   11.5   0.0    2.1  2  NanE             Putative N-acetylmannosamine-6-phosphate epi
     0.0017   17.7   0.1      0.041   13.2   0.0    2.2  2  TMP-TENI         Thiamine monophosphate synthase
     0.0018   17.6   0.3     0.0031   16.8   0.3    1.3  1  DHO_dh           Dihydroorotate dehydrogenase
     0.0065   15.5   0.7      0.086   11.8   0.1    2.0  2  IMPDH            IMP dehydrogenase / GMP reductase domain
  ------ inclusion threshold ------
      0.023   14.0   0.5      0.041   13.2   0.1    1.5  2  ThiG             Thiazole biosynthesis protein ThiG
      0.036   13.4   0.1      0.075   12.4   0.1    1.5  1  Ribul_P_3_epim   Ribulose-phosphate 3 epimerase family
        0.2   11.6   0.0       0.99    9.3   0.0    2.1  2  Glyco_tran_WecB  Glycosyl transferase WecB/TagA/CpsF 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 !  183.1   0.1   3.5e-57   5.2e-54       4     215 ..      12     230 ..       8     241 .. 0.89

  Alignments for each domain:
  == domain 1  score: 183.1 bits;  conditional E-value: 3.5e-57
                                   GGTS.EEEEE-TTSS-CHHHHHHH...HCTT-SEEEEECST...CHHHHHHHHHHHHHCTSSS-EEEEESSGGG--TTSSE CS
                          PcrB   4 leer.hltklDPeeenpdEiveiv...iesgtDavmigGsq...svtldntvrllkkvsriklPivlepsnvegvvryaDa 77 
                                    +e+ h+t++DP  + pdE ++i+      gtD +m+gGs+   +  +d+tv ++k++  ++l ++l+p+  + ++r+aDa
  gi|13541565|ref|NP_111253.1|  12 KNEKiHMTLIDPAAKSPDESAKIAkeaEMAGTDFIMVGGSTdidERLMDQTVSAIKEN--TNLKVILFPGSSNMISRHADA 90 
                                   45668*****************996644579*********95444457**********..9******************** PP

                                   EEEEEETTBSSTTTTTHHHHHHHHHHHHHHHCTEEEEEEEEEBTTTSHHHHHTTB-.B-TTHHHHHHHHHHHHHHTT-SEE CS
                          PcrB  78 lFvmsllnsanadWivgahalglkkvkklieseeilaegYlvvePdskvaavteak.vdlnkediaayallaakllglrli 157
                                   +F+msllns++ ++ivg + ++ k +  l   +e ++++Ylv  P+ +v++v++a+ +d    + a  + laa+++g++li
  gi|13541565|ref|NP_111253.1|  91 IFFMSLLNSSDREFIVGHQVKASKFLSLLG--IEKIPMAYLVFSPGMTVGRVGKANlIDSFDRETALSYSLAAQYMGFKLI 169
                                   *****************8888776666666..************************998766666666777********** PP

                                   EEE-.TTSSS-H.HHHHHHHHHHSSSEEEEESS--SHHHHHHHHCC.SSEEEE-CHHHHHH CS
                          PcrB 158 YlEa.sGaledv.eevialkkklekarlivGGGirsaEkAkevvea.ADvivvGnvveekd 215
                                   Y+Ea sGa+ +v e +i  +k   ++ livGGGir++E+A +++ a AD+iv+G + e+++
  gi|13541565|ref|NP_111253.1| 170 YFEAgSGAPRPVsEDTISYVKSKINIPLIVGGGIRDPETAMRIALAgADMIVTGSIAEKSN 230
                                   *******************************************************998876 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.75   1.1e+03      37      73 ..      34      71 ..       7      86 .. 0.52
   2 !   35.1   0.0   6.1e-12   9.1e-09      44     121 ..     167     242 ..     146     251 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.75
                                  HHHHHT-SEEEEEEHHHHCT.THHHHHHHHHHHHHH-S CS
                  His_biosynth 37 ryeeegadelhvvDldaake.greanldlveeiaeevf 73
                                    +e+++    ++++ ++ +  ++ + + v++i e+++
  gi|13541565|ref|NP_111253.1| 34 IAKEAEMAGTDFIMVGGSTDiDERLMDQTVSAIKENTN 71
                                  33333333333333333332023333344444444444 PP

  == domain 2  score: 35.1 bits;  conditional E-value: 6.1e-12
                                   SEEEEEEHHHHCTTHHHHHHHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH-THHHHHHHHHHCG CS
                  His_biosynth  44 delhvvDldaakegreanldlveeiaeevfipvqvGGGIrsledveelleagadkviigtaavknpelikelaekfgs 121
                                   + +++    ++ + r++  d ++ + ++++ip+ vGGGIr+ e++ ++  agad ++ g+ a k+ ++ + l + +g+
  gi|13541565|ref|NP_111253.1| 167 KLIYFEA--GSGAPRPVSEDTISYVKSKINIPLIVGGGIRDPETAMRIALAGADMIVTGSIAEKSNNVYSVLRNIIGK 242
                                   5555543..45568999**********************************************999998877777776 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0     0.057        85     135     186 ..      26      74 ..       2      77 .. 0.73
   2 !   17.2   0.1   1.5e-06    0.0022     173     218 ..     184     228 ..     175     244 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.057
                                   TTTC.HHHHHHHHHHCT-SEEEEESSECCCTT-CG--CHHHHHHHHH-SS-E CS
                           Dus 135 deeenalelakiveaaGaqaltvHgRtraqnyegtadweaIkevkqavsipv 186
                                   ++ +++ ++ak +e aG ++++v g t  +++      ++++++k++ ++ v
  gi|13541565|ref|NP_111253.1|  26 KSPDESAKIAKEAEMAGTDFIMVGGSTDIDERLMD---QTVSAIKENTNLKV 74 
                                   55677889999999999999999998877665443...55666666666555 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 1.5e-06
                                   HHHHHHHHH-SS-EEEESS--SHHHHHHHHHHH--SEEEESCHHCC CS
                           Dus 173 eaIkevkqavsipviaNGdIkdaedaqaileetGadgvmigrgalg 218
                                   ++I++vk +++ip+i+ G+I+d+e a +i    Gad ++ g  a++
  gi|13541565|ref|NP_111253.1| 184 DTISYVKSKINIPLIVGGGIRDPETAMRIALA-GADMIVTGSIAEK 228
                                   79**************************9887.9999999877765 PP

>> Trp_syntA  Tryptophan synthase alpha chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.17   2.5e+02       8      44 ..      13      49 ..       5      72 .. 0.68
   2 !   17.8   0.1   7.6e-07    0.0011     187     228 ..     183     225 ..     175     243 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.17
                                  TB-EEEEEEETTSS-HHHHHHHHHHHHHCT-SSEEEE CS
                     Trp_syntA  8 nraafvpyvtagdpdleqsleilkalekagadviElG 44
                                  n++  ++ +     + ++s++i k+ e ag+d i +G
  gi|13541565|ref|NP_111253.1| 13 NEKIHMTLIDPAAKSPDESAKIAKEAEMAGTDFIMVG 49
                                  4445555555555556677777777777777777655 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 7.6e-07
                                   HHHHHHHHHCTSS-EEEESSS-SHHHHHHHH.TT-SEEEE-HH CS
                     Trp_syntA 187 delverlkkltavPvavGFGistkeqvkqva.kvadGvivGSa 228
                                   +++++ +k+  + P+ vG Gi+++e++ ++a ++ad ++ GS 
  gi|13541565|ref|NP_111253.1| 183 EDTISYVKSKINIPLIVGGGIRDPETAMRIAlAGADMIVTGSI 225
                                   5678999************************9*********95 PP

>> G3P_antiterm  Glycerol-3-phosphate responsive antiterminator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       1.6   2.4e+03     109     137 ..       8      37 ..       3      72 .. 0.58
   2 ?   -1.7   0.0       1.1   1.7e+03     100     127 ..      54      81 ..      29      93 .. 0.68
   3 !   17.1   0.1   1.9e-06    0.0028     124     168 ..     178     223 ..     172     226 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.6
                                   HHHHHHHT-SEEEEESGGG.HHHHCTSTTS CS
                  G3P_antiterm 109 lkqiekskpdavevlPglv.pkvikeikke 137
                                   ++++++ k ++  + P+   p+  ++i ke
  gi|13541565|ref|NP_111253.1|   8 MRKLKNEKIHMTLIDPAAKsPDESAKIAKE 37 
                                   445555555555555555444444444444 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.1
                                   -SHHHHHHHHHHHHHHT-SEEEEESGGG CS
                  G3P_antiterm 100 iDssalekalkqiekskpdavevlPglv 127
                                   iD + +++++++i++++   v + Pg  
  gi|13541565|ref|NP_111253.1|  54 IDERLMDQTVSAIKENTNLKVILFPGSS 81 
                                   6777777777777777666666666655 PP

  == domain 3  score: 17.1 bits;  conditional E-value: 1.9e-06
                                   SGGG.HHHHCTSTTS...EEEEESS--SHHHHHHHCTT.SSEEEE- CS
                  G3P_antiterm 124 Pglv.pkvikeikkelkipiiaGGLietkedveealkaGaiavsts 168
                                   P  v  ++i+ +k++++ip+i GG i++ e+ +++  aGa+ + t+
  gi|13541565|ref|NP_111253.1| 178 PRPVsEDTISYVKSKINIPLIVGGGIRDPETAMRIALAGADMIVTG 223
                                   556667899**********************************997 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 ?    4.7   0.0      0.01        15     135     191 ..       6      67 ..       5      68 .. 0.74
   2 !   11.5   0.0   8.6e-05      0.13     141     184 ..     191     234 ..     150     242 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.01
                                   HHHHHHHHTT--.EEEES---SHHH....HHHHHTT--SEEEE-HHHH-HHHHHHHHHHHT- CS
                          NanE 135 alvkalseaglk.viaeGrintPek....akkaieiGvdavvvGsaitrleeiakkfveaik 191
                                   +++++l++++++ ++++   ++P++    ak+a   G d ++vG++    e+++++ v+aik
  gi|13541565|ref|NP_111253.1|   6 QMMRKLKNEKIHmTLIDPAAKSPDEsakiAKEAEMAGTDFIMVGGSTDIDERLMDQTVSAIK 67 
                                   68899999999867888888888762222445556799******998888888777777776 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 8.6e-05
                                   HHTT--EEEES---SHHHHHHHHTT--SEEEE-HHHH-HHHHHH CS
                          NanE 141 seaglkviaeGrintPekakkaieiGvdavvvGsaitrleeiak 184
                                   s+ ++ +i+ G i  Pe a ++   G+d++v Gs   + +++ +
  gi|13541565|ref|NP_111253.1| 191 SKINIPLIVGGGIRDPETAMRIALAGADMIVTGSIAEKSNNVYS 234
                                   456789***************************98877777765 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0      0.06        89     108     124 ..      33      50 ..      13      69 .. 0.83
   2 !   13.2   0.0   2.8e-05     0.041     114     176 ..     158     221 ..     148     226 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.06
                      TMP-TENI 108 e.aeeaealgadYigvGp 124
                                   + a+eae++g d+i+vG 
  gi|13541565|ref|NP_111253.1|  33 KiAKEAEMAGTDFIMVGG 50 
                                   25999**********995 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 2.8e-05
                      TMP-TENI 114 algadYigvGpifpTdtKkdaeplgleglkelaealeiPvvaiGGi.tlenvaevleagadgva 176
                                   +l+a Y+g+  i+  +    ++p+  ++++ ++++++iP+++ GGi ++e++ +++ agad++ 
  gi|13541565|ref|NP_111253.1| 158 SLAAQYMGFKLIYFEAGSGAPRPVSEDTISYVKSKINIPLIVGGGIrDPETAMRIALAGADMIV 221
                                   566777777777777777777999999*******************447888999999999986 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.3     2e-06    0.0031     222     282 ..     175     232 ..     163     246 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2e-06
                                   EEGGGHHHHHHHHHHHHHHTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHHHHHGTC CS
                        DHO_dh 222 sGkalkdialkvirelykrlkkeipiIgvGGiesgeDalekieaGAslvqvytalvfegpk 282
                                   sG++ ++++  +i +++++++  ip+I  GGi   e a+  + aGA ++  ++   +++ +
  gi|13541565|ref|NP_111253.1| 175 SGAP-RPVSEDTISYVKSKIN--IPLIVGGGIRDPETAMRIALAGADMIVTGSIAEKSNNV 232
                                   6666.89999***********..**************************999988766543 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.1     0.049        73     101     149 ..      27      75 ..       3      91 .. 0.70
   2 !   11.8   0.1   5.7e-05     0.086     187     238 ..     174     225 ..     170     241 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.049
                                   SSTTHHHHHHHHHHTT-SEEEEE-STSSSHHHH.HHHHHHHHHTTTSEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx RF
                         IMPDH 101 vkedalervkalveagvdvlvvdsahghsekvl.eavkeikkkveevevi 149
                                     +++ + +k+   ag d+++v  +    e+ + ++v++ik+++ +++vi
  gi|13541565|ref|NP_111253.1|  27 SPDESAKIAKEAEMAGTDFIMVGGSTDIDERLMdQTVSAIKENT-NLKVI 75 
                                   44456677778888999999998776666555416899999998.67776 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 5.7e-05
                                   SB---HHHHHHHHHHHHCTCT-EEEEES---SHHHHHHHHHTT-SEEEESCC CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         IMPDH 187 gvGvpqltAvaevaeaakkagvpviaDGGikysgdivkAlaaGadavmlGsl 238
                                   g G p+  +  +++ + +k ++p+i  GGi+  +  ++   aGad+++ Gs+
  gi|13541565|ref|NP_111253.1| 174 GSGAPRPVSEDTISYVKSKINIPLIVGGGIRDPETAMRIALAGADMIVTGSI 225
                                   6677777776777788899999999999999999888888889999999986 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0         2   2.9e+03      79      96 ..      32      48 ..       8      73 .. 0.60
   2 ?   13.2   0.1   2.7e-05     0.041     163     212 ..     182     230 ..     172     240 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2
                                  HHHHHHHHHTTS-SEEEE CS
                          ThiG 79 vriarlarevletdlikl 96
                                   +ia+ a e+++td+i +
  gi|13541565|ref|NP_111253.1| 32 AKIAKEA-EMAGTDFIMV 48
                                  3333322.3345555544 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 2.7e-05
                                   -HHHHHHHHHH-SS-BEEES---SHHHHHHHHHTT-SEEEESHHHHTSSS CS
                          ThiG 163 nkealkiiieeakvPvivDAGigspsdaaqamelGadavllntavaeakd 212
                                   ++ +++ + +++++P+iv  Gi+ p+ a+     Gad ++   ++ae ++
  gi|13541565|ref|NP_111253.1| 182 SEDTISYVKSKINIPLIVGGGIRDPETAMRIALAGADMIVTG-SIAEKSN 230
                                   56789999**********************999999987655.4555444 PP

>> Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1     5e-05     0.075     162     195 ..     190     224 ..     181     226 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5e-05
                                   HHT---EEEEESS--T.TTCHHHHHHT--EEEESH CS
                Ribul_P_3_epim 162 ekeldlkievDGGvkl.dnieqiaeagadvlVags 195
                                   +++ ++ + v GG+++ +++ +ia agad++V+gs
  gi|13541565|ref|NP_111253.1| 190 KSKINIPLIVGGGIRDpETAMRIALAGADMIVTGS 224
                                   446789999*****854899**************8 PP

>> Glyco_tran_WecB  Glycosyl transferase WecB/TagA/CpsF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0   0.00066      0.99      57     120 ..       4      66 ..       2     122 .. 0.80
   2 ?   -0.4   0.0      0.64   9.6e+02      84     104 ..     204     224 ..     158     243 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00066
               Glyco_tran_WecB  57 lekaaerlrekypglriagthdgy.keeeeeaiieainaskpdlllvglGapkqEkwiarlkeel 120
                                   l+++ ++l+++  ++++  + +   +++e+++i+++ + ++ d+++vg  +   E+++ +  +++
  gi|13541565|ref|NP_111253.1|   4 LKQMMRKLKNE--KIHMTLIDPAAkSPDESAKIAKEAEMAGTDFIMVGGSTDIDERLMDQTVSAI 66 
                                   66777777777..45555455554458******************************99987766 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.64
               Glyco_tran_WecB  84 eeeaiieainaskpdlllvgl 104
                                    +++ + +i+ +++d+++ g 
  gi|13541565|ref|NP_111253.1| 204 RDPETAMRIALAGADMIVTGS 224
                                   344555555566666665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       621  (0.0346366); expected 358.6 (0.02)
Passed bias filter:                      517  (0.028836); 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: 0.57u 0.32s 00:00:00.88 Elapsed: 00:00:00.50
# Mc/sec: 1530.18
//
Query:       gi|13541566|ref|NP_111254.1|  [L=269]
Description: (S)-2,3-di-O-geranylgeranylglyceryl phosphate synthase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.9e-32  111.2  14.2    6.1e-32  110.9  14.2    1.1  1  UbiA      UbiA prenyltransferase family
     0.0033   17.7   2.0     0.0087   16.3   0.1    2.1  2  Shisa     Wnt and FGF inhibitory regulator


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 !  110.9  14.2   6.8e-36   6.1e-32       6     243 ..      20     250 ..      16     263 .. 0.81

  Alignments for each domain:
  == domain 1  score: 110.9 bits;  conditional E-value: 6.8e-36
                          UbiA   6 lvg..lalaaggspdlllllllllgtllaaaaanalNdyfDreiDadmertpnRPlvsGrispkealifaivllilgllll 84 
                                   +++  +a++   +++ll + l+++ ++l+++++n++Nd++D++ D+   ++pnRPlv+G+i +  a+++a ++++++++l+
  gi|13541566|ref|NP_111254.1|  20 YISafIAIGYAVTSHLLPVTLAAFSVFLVTSGGNIINDIVDIDVDRV--NHPNRPLVTGEIRVSSAKFIASAMFAVAIVLS 98 
                                   444134444444445566888888999********************..******************************** PP

                          UbiA  85 alllnpltallgllalllyvvYtglrlKrrtllgtvvggiafglppllgwaavtgslsllalllalavflltwaialandl 165
                                    ll+++ + ++++la++l+++Y  l++K+++l g+ v+++  gl++++g   v+      +++l+++ f+  ++  +++d+
  gi|13541566|ref|NP_111254.1|  99 -LLISFIATGIVVLAIMLLIFYE-LYFKKTGLPGNTVISLLIGLIFVFGGISVSSY--GKMIFLFVLAFTSNMSREIIKDV 175
                                   .**********************.9****************************997..567777777799*********** PP

                          UbiA 166 rdregDrkagiktlpvvlGrkaarillalllavlllallllllalllllylllalllaalallraarlvrrrdakkaa 243
                                   +d++gD+   + t+p ++G k+a+  +  +++++l+++ +++++l  l +++l+++++a a+++ + ++ +r+++ ++
  gi|13541566|ref|NP_111254.1| 176 EDVNGDK--DRITFPKKYGVKKALL-VSDIIIGVLILVSFIPYLLKILSIYYLYVVIVADAIFILSGIFSSRNPSIGQ 250
                                   ******6..567************9.5556666666644455555555555555555555555556777777776555 PP

>> Shisa  Wnt and FGF inhibitory regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   9.7e-07    0.0087      75     119 ..      83     126 ..      64     137 .. 0.79
   2 ?    0.6   0.2     0.063   5.6e+02      87     108 ..     192     213 ..     165     240 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 9.7e-07
                         Shisa  75 alevpkdiyvpvlivktifivfvivgvvvivcccgclkkkqrekr 119
                                   a+ +  ++++ v+iv +++i+f+ +g+vv+ ++  +++ +  +k+
  gi|13541566|ref|NP_111254.1|  83 AKFI-ASAMFAVAIVLSLLISFIATGIVVLAIMLLIFYELYFKKT 126
                                   3333.357899***************************9988887 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.063
                         Shisa  87 livktifivfvivgvvvivccc 108
                                    + k ++++ +i+gv+++v  +
  gi|13541566|ref|NP_111254.1| 192 GVKKALLVSDIIIGVLILVSFI 213
                                   4445566666666666655443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1064  (0.0593452); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.33s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 1716.13
//
Query:       gi|13541567|ref|NP_111255.1|  [L=342]
Description: N(2),N(2)-dimethylguanosine tRNA methyltransferase [Thermoplasma volcanium GSS1]
Scores for complete 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-72  243.7   0.0    3.5e-71  240.4   0.0    2.0  1  TRM              N2,N2-dimethylguanosine tRNA methyltransfera
    1.5e-05   24.9   0.2     0.0001   22.2   0.0    2.0  2  Met_10           Met-10+ like-protein
    6.7e-05   22.6   0.0    0.00012   21.8   0.0    1.3  1  Cons_hypoth95    Conserved hypothetical protein 95
      0.007   16.1   0.1      0.014   15.2   0.1    1.4  1  Methyltransf_16  Lysine methyltransferase
  ------ inclusion threshold ------
      0.064   12.6   0.2        0.1   12.0   0.2    1.2  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
      0.071   12.7   0.0       0.12   11.9   0.0    1.3  1  MTS              Methyltransferase small domain
       0.14   12.5   0.0        0.3   11.4   0.0    1.5  1  DDE_Tnp_IS1      IS1 transposase


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 !  240.4   0.0   1.4e-74   3.5e-71       1     375 [.       6     336 ..       6     337 .. 0.90

  Alignments for each domain:
  == domain 1  score: 240.4 bits;  conditional E-value: 1.4e-74
                                   TTEEEEE----SS--TT--SS--GGGHHHHHHHHHH...HHHHHHHH-S-EEEEESS-TTSHHHHHHHHH-S-EEEEEEE- CS
                           TRM   1 GeakikvedkevtvskkeeVFYNPvqefnRDlsvlvirqlellkkklgekikvldaLsasGlRaiRfalEvpgvkevlaND 81 
                                   G+a i+v+++ +   ++++ FYN  q  nRDl++ +i   + ++ +     kvld++ +sG+R+iR +lE  ++ +v++ +
  gi|13541567|ref|NP_111255.1|   6 GSAVIEVPEAYSGPGRRSPGFYNADQVLNRDLTIDLI---NEFGVE-----KVLDGFGGSGVRGIRISLE--TKAKVVIAE 76 
                                   677788888877788899******************4...444555.....69*****************..66788889* PP

                                   S-HHHHHHHHHHHHHTT--.GGEEEE-S-HHHHHC--SS-EEEEEE--SS--GGGHHHHHHHEEEEEEEEEEE--HHHHTT CS
                           TRM  82 isekAvelikeNvklneve.eivvineddAnvllaekkkrfdviDlDPfGspapfldsavqsvkekglLlvTaTDtavLaG 161
                                   is+   e+ik+N+ +n+ e ++++      n+   + + +fd+iD+DP+Gsp+p+ld+a+  v+++g+L +TaTD ++L+G
  gi|13541567|ref|NP_111255.1|  77 ISPSSCEIIKQNIAINNAEaDLIHD-----NFQCVSSHIAFDYIDVDPYGSPVPYLDAAIMNVRKGGYLGITATDQSTLTG 152
                                   *****************99554433.....455568999****************************************** PP

                                   SSHHHHHHHHSSB---STTHHHHHHHHHHHHHHHHHHTTTEEEEEEEEEEETTEEEEEEEEEE-HHHHHHHHTTEEEEEEE CS
                           TRM 162 aspekclrkYgavalkselcHEvalRillkavareaakYekavepllslsadfYvrvfvkvktgaakvkkvleklglvlhC 242
                                   ++ +k  r+Yga+ ++  + HE+++R l++++ar+aa +++++ep ls+ +++Y+rvfvkv +g++ ++k++e++g++ + 
  gi|13541567|ref|NP_111255.1| 153 STLNKTRRRYGAYIVNDIYRHEMGIRTLIGYIARRAAAFDRYIEPQLSIWNHHYYRVFVKVGKGVNGADKMIENIGYLNK- 232
                                   *****************************************************************************998. PP

                                   TTT--EEEE--GGG--SB-TTT-SBEEEEEEEE-S-S--HHHHHHHHHHHCT..-TTS-HHHHHHHHHHHHHHS--SS-EE CS
                           TRM 243 sgClseekvkglakfkaecehcgaklhlaGPlwlgplkdkefveevleeaekekeeelkkrvkklLklikeElldaplyyd 323
                                       +    +++ +        + k    GP+wl +l+++e++e++ +            rv k +++ik++  +  l+ d
  gi|13541567|ref|NP_111255.1| 233 ----H----TTIDN--------SFKDVNEGPVWLSNLNNAELLEKIRDP-----------RVSKKIEMIKHD--NRLLFVD 284
                                   ....2....22222........2333457***********998887654...........555677899999..999**** PP

                                   HHHHHHHHT-SS---HHHHHHH....TT-EE-TTSTTEEE-SS-HHHHHHHH CS
                           TRM 324 lsqlasvlklsvpplkkvvsalkelgfevsrtHakpkaikTnapleavvevl 375
                                   l ++a++ +ls ppl kv++++ + g+e+ rt ++p++ikT+ p+ +v e+l
  gi|13541567|ref|NP_111255.1| 285 LTDIARKTSLSLPPLAKVMDEIMKHGYEAHRTSFSPTGIKTDCPYAEVSEIL 336
                                   *************************************************998 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   3.9e-08    0.0001     102     195 ..      48     138 ..      26     143 .. 0.81
   2 ?    0.4   0.0      0.18   4.7e+02     140     164 ..     258     282 ..     248     315 .. 0.74

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 3.9e-08
                                   -EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEEEEES-GGG---TT-EEEEEE--TTTGGG CS
                        Met_10 102 evVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekvvkpileDgrevireqladrvvmnlpksaie 182
                                   e V+d f G G   i i+  +kak v+a ++ P+s + +k+ni+ N+ e  +  i    + v  + ++d +  +   s + 
  gi|13541567|ref|NP_111255.1|  48 EKVLDGFGGSGVRGIRISLETKAKVVIA-EISPSSCEIIKQNIAINNAEADL--IHDNFQCVSSHIAFDYIDVDPYGSPVP 125
                                   78****************9999996665.9******************9988..555556666577777776777778888 PP

                                   GHHHHHHHEEEEE CS
                        Met_10 183 Fldkvlaalkdgg 195
                                   +ld+++  +++gg
  gi|13541567|ref|NP_111255.1| 126 YLDAAIMNVRKGG 138
                                   8888887777765 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.18
                                   HHHHHHHTT-TTCEEEEES-GGG-- CS
                        Met_10 140 lkeniklNkvekvvkpileDgrevi 164
                                   l e i+  +v+k+++ i++D+r + 
  gi|13541567|ref|NP_111255.1| 258 LLEKIRDPRVSKKIEMIKHDNRLLF 282
                                   567899999************9765 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   4.7e-08   0.00012      41     123 ..      46     120 ..      35     145 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 4.7e-08
                                   CC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-EEEEEEE-- CS
                 Cons_hypoth95  41 egarvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkleeetaelkedaleallklakkkeefdivflDP 121
                                     ++vLD f+GsG+ g+       +k+v+ e +++ ++i+k+n++  ++e   a l++d+++ ++++      fd++ +DP
  gi|13541567|ref|NP_111255.1|  46 GVEKVLDGFGGSGVRGIRISLETKAKVVIAEISPSSCEIIKQNIAINNAE---ADLIHDNFQCVSSH----IAFDYIDVDP 119
                                   45679************8766777899999**************988866...79999999999777....79*******8 PP

                                   SS CS
                 Cons_hypoth95 122 Py 123
                                    y
  gi|13541567|ref|NP_111255.1| 120 -Y 120
                                   .3 PP

>> Methyltransf_16  Lysine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   5.3e-06     0.014      49      94 ..      49      94 ..      31     105 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 5.3e-06
               Methyltransf_16 49 svlELGsGtGlvGlavaellpeakviltDlee.llellkknielnkn 94
                                  +vl+   G+G+ G+ + +  ++akv+++ ++   +e++k+ni++n++
  gi|13541567|ref|NP_111255.1| 49 KVLDGFGGSGVRGIRISLE-TKAKVVIAEISPsSCEIIKQNIAINNA 94
                                  66665679********999.9********98769**********884 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.2     4e-05       0.1     163     216 ..      48     100 ..      38     118 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4e-05
                          PrmA 163 eevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveakleva 216
                                   e+vlD   GSG+  i  ++   +kvv   i + + ++ k+N+++N+ ea l ++
  gi|13541567|ref|NP_111255.1|  48 EKVLDGFGGSGVRGIRISLETKAKVVIAEISPSSCEIIKQNIAINNAEADL-IH 100
                                   799**999***************************************9977.33 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   4.7e-05      0.12      32     101 ..      47     115 ..      24     119 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.7e-05
                                   CSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTSTTS-EEEE CS
                           MTS  32 sgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvleeveekkfdli 101
                                    +kvlD   G Gv g+ +  e++  +v++ +++  + e+ k+n++ n++e+++++ +     ++  fd+i
  gi|13541567|ref|NP_111255.1|  47 VEKVLDGFGGSGVRGIRISLETKA-KVVIAEISPSSCEIIKQNIAINNAEADLIHDNFQCVSSHIAFDYI 115
                                   468999999********9986655.9***************************99998766666667766 PP

>> DDE_Tnp_IS1  IS1 transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00012       0.3      59     115 ..     140     196 ..     129     208 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00012
                   DDE_Tnp_IS1  59 vviltsddwglyerelkkdkhliskiytqriernnltlrtrlkrlarkslsfsksve 115
                                   ++i  +d+ +l ++ l+k +   +    + i r+++ +rt +  +ar++ +f + +e
  gi|13541567|ref|NP_111255.1| 140 LGITATDQSTLTGSTLNKTRRRYGAYIVNDIYRHEMGIRTLIGYIARRAAAFDRYIE 196
                                   688999***********************************************9988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (342 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 2085.02
//
Query:       gi|13541568|ref|NP_111256.1|  [L=181]
Description: NTPase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.3e-44  150.4   2.7    4.8e-44  150.2   2.7    1.0  1  NTPase_1  NTPase
    5.1e-06   26.2   0.0      9e-06   25.4   0.0    1.3  1  DUF2478   Protein of unknown function (DUF2478)
  ------ inclusion threshold ------
      0.011   15.4   0.0      0.019   14.7   0.0    1.3  1  AAA_30    AAA domain
       0.13   12.3   0.1       0.28   11.2   0.1    1.5  1  AAA_5     AAA domain (dynein-related subfamily)


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 !  150.2   2.7   1.1e-47   4.8e-44       1     168 []       7     174 ..       7     174 .. 0.99

  Alignments for each domain:
  == domain 1  score: 150.2 bits;  conditional E-value: 1.1e-47
                                   EEEEE--TTSSHHHHHHHHHHHH...GGGEEEEEEEEE-------EEEEEET.T--EEEEEETT---SSEETTEEE-HHHH CS
                      NTPase_1   1 kvfiTGppGvGKtTlvkkvlellkssgvkvgGfyteevreggrrigFkivdlasgeegiLarveakreprvgkyvvdvesf 81 
                                   k+ iTGp G+ K   ++k++ +l+++g++v+G++ ++v ++g+ +g++i d+ ++++ +++ +++ ++++++k  vd+  +
  gi|13541568|ref|NP_111256.1|   7 KIGITGPVGSIKAEALQKIIGMLQNDGLNVQGVLISKVSDDGKLTGYTIEDILTKKKVQFCDEKFVSRVKIDKLGVDTRLL 87 
                                   589****************************************************************************** PP

                                   HHHHHHHHHHHHHHH-EEEE---STTGGG-HHHHHHHHHHHTTTSEEEEE--SS--SHHHHHHHT-TT-EEEE--TTTTTT CS
                      NTPase_1  82 eelalealrkalseadviviDEiGkmElkskkfkeaveevLksekpvlavihrrkdlalveeirerkdvkvfevteenrda 162
                                   ee+ +++l+ka ++advi+iDE+Gk+E ++kk+++++ee+Lk++kp+++++h+r+++++++ei++ ++v+vf++t+ n++ 
  gi|13541568|ref|NP_111256.1|  88 EEILIPSLQKARESADVIIIDEVGKLENTTKKIHSEIEETLKCGKPLIVTLHKRSRNPVLQEIKSLEGVRVFDITPINKNI 168
                                   ********************************************************************************* PP

                                   HHHHHH CS
                      NTPase_1 163 lleeil 168
                                   l+ +++
  gi|13541568|ref|NP_111256.1| 169 LPFKVM 174
                                   *99886 PP

>> DUF2478  Protein of unknown function (DUF2478)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.0     2e-09     9e-06      14     134 ..      20     142 ..      10     148 .. 0.87

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 2e-09
                       DUF2478  14 alLaafaerlraeGlrvaGvvqenaeeaegkkcdmeledlatgeririsqdlgsgs...qgCrLdpeaLaeaaaaverala 91 
                                   + L+++   l+++Gl+v Gv+ ++ ++ +gk +  ++ed+ t ++++ + +            +d+  L+e+     ++ +
  gi|13541568|ref|NP_111256.1|  20 EALQKIIGMLQNDGLNVQGVLISKVSD-DGKLTGYTIEDILTKKKVQFCDEKFVSRvkiDKLGVDTRLLEEILIPSLQKAR 99 
                                   679999999************888886.57778**************99886544301145668999************** PP

                       DUF2478  92 egadlvivnkFGkqEaeGrGlreeiaaalaagiPvltaVsekl 134
                                   e ad++i+   Gk+E + + + +ei++ l+ g P++++++++ 
  gi|13541568|ref|NP_111256.1| 100 ESADVIIIDEVGKLENTTKKIHSEIEETLKCGKPLIVTLHKRS 142
                                   *************************************999875 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   4.2e-06     0.019      23     103 ..      10     116 ..       4     131 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4.2e-06
                        AAA_30  23 ltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLaeelgieastiakllkrlk...................... 81 
                                   +tGp G+ K  al+++  +++++g +v g+        +++++  ++++ti+ +l++ k                      
  gi|13541568|ref|NP_111256.1|  10 ITGPVGSIKAEALQKIIGMLQNDGLNVQGV-----LISKVSDDGKLTGYTIEDILTKKKvqfcdekfvsrvkidklgvdtr 85 
                                   89*********************9777665.....5556777878888999999988888899999999999999999999 PP

                        AAA_30  82 ..........grarlepgtllivDEagmvdtk 103
                                             + ++ e+++++i+DE+g + ++
  gi|13541568|ref|NP_111256.1|  86 lleeilipslQ-KARESADVIIIDEVGKLENT 116
                                   99999998642.445566*********99654 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   6.2e-05      0.28       4      81 ..      10     117 ..       8     128 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 6.2e-05
                                   EE--SSSSHHHHHHHGGGGB...S--EEEEE--TT--HHHHH--B--............--------.............. CS
                         AAA_5   4 LvGppGtgKselaerlaaal...nreveyvqltrdtteedlkgrreik...ngttslvdsplvraar.............. 64 
                                   + Gp G+ K e  +++  +l   + +v+ v++++     +l+g +  +   +++ ++ d ++v  ++              
  gi|13541568|ref|NP_111256.1|  10 ITGPVGSIKAEALQKIIGMLqndGLNVQGVLISKVSDDGKLTGYTIEDiltKKKVQFCDEKFVSRVKidklgvdtrlleei 90 
                                   579*****************9888899999999998888888866644888999999******9999************** PP

                                   ..........G-SEEEEESGGG--HHH CS
                         AAA_5  65 ..........egeilvlDEveraesev 81 
                                             +++++++DEv ++e  +
  gi|13541568|ref|NP_111256.1|  91 lipslqkareSADVIIIDEVGKLENTT 117
                                   ********************9887544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       631  (0.0351944); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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 0.35s 00:00:00.91 Elapsed: 00:00:00.54
# Mc/sec: 1003.86
//
Query:       gi|13541569|ref|NP_111257.1|  [L=120]
Description: hypothetical protein TVN0738 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-41  141.7   0.1    1.2e-41  141.6   0.1    1.0  1  DHNA      Dihydroneopterin aldolase
  ------ inclusion threshold ------
      0.058   13.8   0.0       0.11   12.9   0.0    1.4  1  hSH3      Helically-extended SH3 domain


Domain annotation for each model (and alignments):
>> DHNA  Dihydroneopterin aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.6   0.1   1.3e-45   1.2e-41       1     108 []      12     119 ..      12     119 .. 0.98

  Alignments for each domain:
  == domain 1  score: 141.6 bits;  conditional E-value: 1.3e-45
                                   -HHHHHHHHHHHHHHHHHHHHTT-EESTTTHHHHHHHHHHHHHTSTTEEEEEEEE-S-..GGCC-STS-EE--TTTEEEEE CS
                          DHNA   1 tdrerAvFEagiklgalyHqfvGtPvseesaeslekaieesielQPfvedvkvkidrekleekleefgYteLtgemldvei 81 
                                   t+rerA+FEagiklg++yHq+vG+P+++++++slekai +si++QPfv +++vkid +  ++k   ++Y +L+gemldv +
  gi|13541569|ref|NP_111257.1|  12 TSRERAIFEAGIKLGTVYHQYVGIPLNQSNISSLEKAIRDSIMVQPFVVEAEVKIDPNVNNKKPGVYKYLTLSGEMLDVMV 92 
                                   789*******************************************************99999999*************** PP

                                   EEEETTEEEEEEEEEETTTTEEEEEEE CS
                          DHNA  82 tvkyeeaevkarleyieeldYplmkve 108
                                   +v+ye+  vkarl+y+ e+dYplm++e
  gi|13541569|ref|NP_111257.1|  93 KVDYEGSVVKARLRYVPEMDYPLMYIE 119
                                   *************************96 PP

>> hSH3  Helically-extended SH3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   1.3e-05      0.11      13      49 ..      60      96 ..      56     108 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.3e-05
                          hSH3 13 vlysvtvdpnlaskklggkdLpvkrgeildviqktdd 49
                                  v  +v++dpn+++kk g  +    +ge+ldv+ k d 
  gi|13541569|ref|NP_111257.1| 60 VEAEVKIDPNVNNKKPGVYKYLTLSGEMLDVMVKVDY 96
                                  67899************98888889*******99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); 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: 0.51u 0.33s 00:00:00.84 Elapsed: 00:00:00.53
# Mc/sec: 685.99
//
Query:       gi|13541570|ref|NP_111258.1|  [L=885]
Description: DNA helicase II [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-39  136.9   2.4      1e-39  136.9   2.4    2.4  2  UvrD-helicase    UvrD/REP helicase N-terminal domain
    1.7e-23   83.6   0.0    6.4e-23   81.7   0.0    2.1  2  AAA_19           AAA domain
    4.9e-17   62.3   3.0    4.8e-12   45.9   0.0    4.2  5  UvrD_C           UvrD-like helicase C-terminal domain
    1.1e-09   38.6   1.7    4.2e-09   36.7   1.7    1.9  1  PDDEXK_1         PD-(D/E)XK nuclease superfamily
    2.3e-06   27.5   2.0       0.55    9.9   0.2    4.1  3  Viral_helicase1  Viral (Superfamily 1) RNA helicase
    1.7e-05   24.6   0.0    0.00026   20.8   0.0    2.3  2  UvrD_C_2         UvrD-like helicase C-terminal domain
    4.3e-05   23.4   0.3    0.00011   22.0   0.0    1.8  2  AAA_11           AAA domain
    0.00011   22.0   0.0     0.0067   16.2   0.0    2.5  2  AAA_30           AAA domain
  ------ inclusion threshold ------
      0.024   14.7   6.8       0.17   11.9   1.4    3.7  3  AAA_14           AAA domain
      0.046   13.9   0.0         19    5.5   0.0    3.3  3  DUF5354          Family of unknown function (DUF5354)


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 !  136.9   2.4   5.7e-43     1e-39      15     309 ..       3     261 ..       1     267 [. 0.81
   2 ?   -1.6   0.6      0.83   1.5e+03     184     188 ..     776     780 ..     685     860 .. 0.51

  Alignments for each domain:
  == domain 1  score: 136.9 bits;  conditional E-value: 5.7e-43
                                   EEEEEE-TTSSHHHHHHHHHHHHHHTSSSTGGGEEEEESSHHHHHHHHHHHHHHHHHCCHHCTT-HHHHHHHHHCTTSEEE CS
                 UvrD-helicase  15 pilveAsAGsGKTfvlaerilrlikeeeiepdrilvvTFTnkAaeElkeRieealkkaeqessdderlrlalqnlseanis 95 
                                   ++lv+A++G+GKT+ l ++++ l+k + +++++il++TFTnkA + ++e i ++ + + +           + +l+++n+ 
  gi|13541570|ref|NP_111258.1|   3 TTLVSAGPGTGKTTSLSSKYVSLVKSG-VDQNDILCLTFTNKAVDNMREAILKTAQREGV-----------ELELHKLNVH 71 
                                   78*************************.*************************9999875...........5689****** PP

                                   EHHHHHHHHHHHHHGGTTSHTTTEEECHHHHHHCCHHHHHHHHHSCHSHTTTTHHHHHHHHHHHHHHCCCCCHHHH..CCC CS
                 UvrD-helicase  96 TlHsfcqkilkkeanrigldpnfrildeedeedlkqqellkelleksaddslnldkkkleklikelsksrnikkee..lsl 174
                                   T+Hsf+  ++k+  +r  +++nf  +   d  +l  + +++ +   +  d++  + +++      + ks ni  +e  ++ 
  gi|13541570|ref|NP_111258.1|  72 TFHSFAFHFVKNLGYRDIINHNFLRKLIYD--YLTNNHVFNYDRS-YIIDRMVPSIENAI----RYVKSYNIGRIEdpQNI 145
                                   ***********************7555555..4446666666664.55554444444433....34555555533311344 PP

                                   HHHHHCHHHHHHHHHHHTTCCTTHHCHSSTSCSHHHHHHHHHHHHHHHHHHHHTCEEHHHHHHHHHHHHHHCHHHHHHHHH CS
                 UvrD-helicase 175 skskaeelrelvskakekqlspkelkkafekasdlqkkiaeflkeyqeqkkeenalDfsdllhallelleeneelaealre 255
                                    +s+ e++  ++++ k ++l+  +       a+ +   ++++++ y+++k++++ +D++d+l+++++l+e+          
  gi|13541570|ref|NP_111258.1| 146 LNSVREDMDRVIKEKKIDKLTLDQ-------AEIFMTHFINIINLYEQEKENRKVIDYNDMLIKFINLSEK---------P 210
                                   556666666666555555555555.......55589*******************************9997.........6 PP

                                   HSSEEEESSGGG-BHHHHHHHHHHHTTTTTEEEEE-GGG--GGGGTB-THHHHH CS
                 UvrD-helicase 256 rykeiliDEyQDTnkiQyrilkllasgheelfmvGDpkQsIYgFRgAdielflk 309
                                   +yk++liDE QD +   ++i   +a++   +  vGD+kQsI+gF+g+ +++f +
  gi|13541570|ref|NP_111258.1| 211 HYKYVLIDELQDVSDLEAKIAGSVAEN---IYAVGDKKQSIFGFQGGGFSNFIS 261
                                   9********************999876...8****************9999976 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.83
                                   HHHHH CS
                 UvrD-helicase 184 elvsk 188
                                   +++++
  gi|13541570|ref|NP_111258.1| 776 KTTTR 780
                                   11111 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.7   0.0   3.6e-26   6.4e-23      12     145 ..       3     251 ..       1     252 [. 0.90
   2 ?   -2.4   0.0       3.1   5.5e+03     109     123 ..     532     546 ..     494     555 .. 0.55

  Alignments for each domain:
  == domain 1  score: 81.7 bits;  conditional E-value: 3.6e-26
                        AAA_19  12 vllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgae...........atTiHrlal.... 77 
                                   + lv aGpGtGKT+ l  +   lv+ g v+ ++il+++ft++A++++re++ +  ++            +T+H++a+    
  gi|13541570|ref|NP_111258.1|   3 TTLVSAGPGTGKTTSLSSKYVSLVKSG-VDQNDILCLTFTNKAVDNMREAILKTAQRegvelelhklnVHTFHSFAFhfvk 82 
                                   679**********************99.778******************996666669******************9**** PP

                        AAA_19  78 ................................................................................. 77 
                                                                                                                    
  gi|13541570|ref|NP_111258.1|  83 nlgyrdiinhnflrkliydyltnnhvfnydrsyiidrmvpsienairyvksynigriedpqnilnsvredmdrvikekkid 163
                                   ********************************************************************************* PP

                        AAA_19  78 ..............................ldfddlltealelleeaeeekklqeeellivDEfqdvdelqyrLlkallge 128
                                                                 +d++d l    ++++    ++k  + +++++DE qdv++l+ ++   ++  
  gi|13541570|ref|NP_111258.1| 164 kltldqaeifmthfiniinlyeqekenrkvIDYNDML---IKFIN---LSEKP-HYKYVLIDELQDVSDLEAKIAGSVA-- 235
                                   *999999999999999988888887776666666655...44433...22222.456*********************9.. PP

                        AAA_19 129 kkklllvGDpdQliyvf 145
                                    +++ +vGD++Q+i+ f
  gi|13541570|ref|NP_111258.1| 236 -ENIYAVGDKKQSIFGF 251
                                   .669**********998 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 3.1
                        AAA_19 109 DEfqdvdelqyrLlk 123
                                   D f+ vd  +y+L++
  gi|13541570|ref|NP_111258.1| 532 DNFSVVDLCAYELIR 546
                                   455555555555555 PP

>> UvrD_C  UvrD-like helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.5      0.42   7.6e+02     219     259 ..     144     192 ..      16     218 .. 0.53
   2 !   11.4   0.0   8.5e-05      0.15       3     130 ..     271     390 ..     269     435 .. 0.70
   3 !   45.9   0.0   2.7e-15   4.8e-12     264     346 ..     484     580 ..     462     582 .. 0.77
   4 ?   -2.9   0.0       1.8   3.3e+03     183     223 ..     680     721 ..     626     778 .. 0.57
   5 ?    0.9   0.1      0.13   2.4e+02      93     122 ..     786     815 ..     767     821 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.42
                                   xxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxxxxxxxxx RF
                        UvrD_C 219 eklaelkekseskrkkee........klenlreLysllkelekkeeeee 259
                                   + l++++e  ++  k+++         +  +  ++++++ +e+++e+ +
  gi|13541570|ref|NP_111258.1| 144 NILNSVREDMDRVIKEKKidkltldqAEIFMTHFINIINLYEQEKENRK 192
                                   3333333333333322222223112122233444444444444333333 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 8.5e-05
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        UvrD_C   3 LekNyRStksLlkaankflenilnrrale.kek.ktvekgekivvleaeteeeEaekiaatikallekneklediavLvRs 81 
                                   L++ +R  k +lk a++f+++ ++   +e  ek ++v++ +       e  e  +++i + + +++     + ++ ++ R+
  gi|13541570|ref|NP_111258.1| 271 LTEDHRNGKAILKYAKEFFKKSTKGGLDEdLEKlTSVRDHD----GYVEVIEGSYSDILSVLDRFP-----RGSVGIIART 342
                                   78899999999*99999998888884444344456666655....223445666777777777777.....9********* PP

                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        UvrD_C  82 nkdadkiskaLkkegipfnvvdeekfFkreeikdilaylkllankqdki 130
                                   n++  +isk L ++gi++   + ++  +     d+l +l++++ ++d+ 
  gi|13541570|ref|NP_111258.1| 343 NAQVINISKVLDSHGIKYS-SSATSSNSEMAKNDVLDFLRMILFDDDDF 390
                                   *****************98.44555555555567777777776665554 PP

  == domain 3  score: 45.9 bits;  conditional E-value: 2.7e-15
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx.............xxxxxx....xxxxxx RF
                        UvrD_C 264 lneileiatLseseleeskkkekipiiTiHqAKGlEFdvVf.lagleegtfP.............syrskk....ekrleE 326
                                    +++l++    ++el es++ e+i ++T+H+AKGlEFd V+ l + + ++f              +    k     +  +E
  gi|13541570|ref|NP_111258.1| 484 RQDLLNYLEVCDQELTESSNTERISVLTVHKAKGLEFDHVIyLPKTTRDNFSvvdlcayelirekT----KrdisTELEDE 560
                                   345555555668999899888*****************9964889999999999999887666443....0445577789* PP

                                   xxxxxxxxxxxxxxxxxxxx RF
                        UvrD_C 327 EkRlfYVaiTRAkkrLfisy 346
                                   + R+ +VaiTR+   L+i++
  gi|13541570|ref|NP_111258.1| 561 DTRVDFVAITRPVHTLIIIT 580
                                   *****************986 PP

  == domain 4  score: -2.9 bits;  conditional E-value: 1.8
                                   xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        UvrD_C 183 aleeknlelllkk.iektaeerqalvskyadlfkelaeklae 223
                                   a++++ + + l + + k++    ++  +y++++ ++ + + +
  gi|13541570|ref|NP_111258.1| 680 AMKQGSEIHTLAElLFKKESTELEIPPNYRPQYDNILKVIDD 721
                                   222222222333334444444444455555555555544444 PP

  == domain 5  score: 0.9 bits;  conditional E-value: 0.13
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        UvrD_C  93 kkegipfnvvdeekfFkreeikdilaylkl 122
                                   k++++  +++++ + ++r++ik+++ay+ l
  gi|13541570|ref|NP_111258.1| 786 KQLHFYKTIYSKSQSLDRSKIKTLIAYISL 815
                                   5555666789999999***********986 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 !   36.7   1.7   2.4e-12   4.2e-09      14     204 ..     663     832 ..     652     865 .. 0.70

  Alignments for each domain:
  == domain 1  score: 36.7 bits;  conditional E-value: 2.4e-12
                      PDDEXK_1  14 plrfflryllglreeeeleapdlGtlvHaaleefyewkkldkedleelleeaveelwpellleeeilessarlrylaeklk 94 
                                   p++f  +++lgl  ++++ a+  G+ +H ++e +++       + ++ l     e+ p+  ++        ++  + +   
  gi|13541570|ref|NP_111258.1| 663 PFQFLKEHILGL--KYKVPAMKQGSEIHTLAELLFK-------KESTEL-----EIPPN--YRP-------QYDNILKVID 720
                                   9***********..788888888*************.......777777.....55566..333.......3477888888 PP

                      PDDEXK_1  95 evleklve.rlaeeleakrgfrpvale.lefggekvrLkGriDrvddkegelriiDyKtgsappkskelaelkeglQlllY 173
                                   ++ +++   ++++e+e   + +++  e  +f      L G++D v + +++++i+DyKt +   ++++  + ++  Ql +Y
  gi|13541570|ref|NP_111258.1| 721 DMQKRYGAvQISAEEEVTLPGQYLLPEaKSFI-----LYGKLDAVFQSGDYYYIVDYKTDK---TTTR--QKEHTKQLHFY 791
                                   88888865566665555555788888867999.....********99999********999...4444..334555***** PP

                      PDDEXK_1 174 llalaegeelkeege.pagalylrleepkvk..........d 204
                                     ++ + + l    + +  ++y++l+ p  +          d
  gi|13541570|ref|NP_111258.1| 792 KTIYSKSQSLDRS-KiKTLIAYISLRTPVNTgkvdyrleevD 832
                                   *****99554433.2588888888866655544433333330 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 ?    4.8   0.0     0.011        20       2      21 ..       5      24 ..       4      83 .. 0.72
   2 !    9.4   0.0   0.00045      0.81      48     104 ..     198     251 ..     166     313 .. 0.72
   3 !    9.9   0.2   0.00031      0.55     173     208 ..     495     532 ..     465     580 .. 0.71

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.011
               Viral_helicase1  2 vvhGvpGcGKStlirkllrt 21
                                  +v++ pG GK+t++ + + +
  gi|13541570|ref|NP_111258.1|  5 LVSAGPGTGKTTSLSSKYVS 24
                                  79999*******99888766 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00045
               Viral_helicase1  48 rtvdsflmalvkstkgkililDEylllhaGyilllaalskaklvilfGDplQipfhs 104
                                    ++ +f +   k+ ++k++++DE + +    +++ +a s a++++++GD +Q+ f  
  gi|13541570|ref|NP_111258.1| 198 DMLIKFINLSEKP-HYKYVLIDELQDVSD--LEAKIAGSVAENIYAVGDKKQSIFGF 251
                                   4445566666666.7***********995..88888889999**********86653 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.00031
               Viral_helicase1 173 tqalkealgvr..evttvhevqGltfdkVtlvllketd 208
                                    q+l+e+ + +  +v+tvh + Gl+fd+V+ + +++ d
  gi|13541570|ref|NP_111258.1| 495 DQELTESSNTEriSVLTVHKAKGLEFDHVIYLPKTTRD 532
                                   34444444444677***************988775554 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 !   20.8   0.0   1.4e-07   0.00026       4      20 ..     509     525 ..     507     542 .. 0.84
   2 ?    0.9   0.0      0.23   4.2e+02      34      51 ..     561     578 ..     551     579 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 1.4e-07
                      UvrD_C_2   4 altihkaQGsefpaViv 20 
                                   +lt+hka+G+ef++Vi 
  gi|13541570|ref|NP_111258.1| 509 VLTVHKAKGLEFDHVIY 525
                                   89*************97 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.23
                      UvrD_C_2  34 rrrlLYtavTRAreklil 51 
                                     r  ++a+TR  + li+
  gi|13541570|ref|NP_111258.1| 561 DTRVDFVAITRPVHTLII 578
                                   577789*****8888887 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   6.4e-08   0.00011      19      80 ..       3      57 ..       1      76 [. 0.86
   2 ?   -2.4   0.1       1.8   3.2e+03     131     131 ..     191     191 ..     114     246 .. 0.52

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 6.4e-08
                        AAA_11 19 itliqGPPGtgKTktivellsqllsrrkseeeksakpriLvCapSNaAvDellerllrglld 80
                                   tl++  PGtgKT+ + + + +l      ++++  ++ iL  + +N+AvD++ e +l+   +
  gi|13541570|ref|NP_111258.1|  3 TTLVSAGPGTGKTTSLSSKYVSL------VKSGVDQNDILCLTFTNKAVDNMREAILK-TAQ 57
                                  5899**************99999......678***********************999.333 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.8
                        AAA_11 131 k 131
                                   +
  gi|13541570|ref|NP_111258.1| 191 R 191
                                   0 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   3.7e-06    0.0067      21      70 ..       4      56 ..       1      89 [. 0.78
   2 ?    3.1   0.0     0.039        70      89     160 ..     211     280 ..     180     314 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 3.7e-06
                        AAA_30 21 avltGpAGtGKttalkal.reaweaag...grviglAptgkaAkvLaeelgiea 70
                                  +++ +++GtGKtt+l++  + ++++ g    +++ l+ t+ka ++++e++  +a
  gi|13541570|ref|NP_111258.1|  4 TLVSAGPGTGKTTSLSSKyVSLVKS-GvdqNDILCLTFTNKAVDNMREAILKTA 56
                                  6899***********9873666666.435699***************8764433 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.039
                        AAA_30  89 g.tllivDEagmvdtkqlaallkaaekagakvilvGDerQlasVeaGgvlrdlvea.agigtaeLtevvRqkes 160
                                   + + +++DE   v+  +++   + ae+    +  vGD++Q     +Gg ++  +++  +++   Lte +R  ++
  gi|13541570|ref|NP_111258.1| 211 HyKYVLIDELQDVSDLEAKIAGSVAEN----IYAVGDKKQSIFGFQGGGFSNFISNfPNHQLKYLTEDHRNGKA 280
                                   457899999988887776655555555....*********8887888888888765347778888888888543 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0     0.049        88      13      49 ..      12      51 ..       9      69 .. 0.82
   2 ?   11.9   1.4   9.6e-05      0.17      33      89 ..     178     236 ..     153     245 .. 0.65
   3 ?   -3.6   0.1       5.8     1e+04      92     111 ..     359     378 ..     349     381 .. 0.72

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.049
                        AAA_14 13 vGKTtllkqlikell...vkkesilyinldderdkkladp 49
                                  +GKTt l   + +l    v++++il +++ ++  +++++ 
  gi|13541570|ref|NP_111258.1| 12 TGKTTSLSSKYVSLVksgVDQNDILCLTFTNKAVDNMREA 51
                                  7******9998888899**************999887754 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 9.6e-05
                        AAA_14  33 ilyinldderdkkla..dpekllelileklkeekktylflDEiqevpewekalkslvde 89 
                                   i  inl ++++++++  d++++l  + ++ ++++ +y+++DE q v+++e  + + v e
  gi|13541570|ref|NP_111258.1| 178 INIINLYEQEKENRKviDYNDMLIKFINLSEKPHYKYVLIDELQDVSDLEAKIAGSVAE 236
                                   3334444444433332244444544455433358999*************999887765 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 5.8
                        AAA_14  92 nldvivtGSnskllskeiat 111
                                   ++   +t Sns + ++++ +
  gi|13541570|ref|NP_111258.1| 359 KYSSSATSSNSEMAKNDVLD 378
                                   55667899999999988766 PP

>> DUF5354  Family of unknown function (DUF5354)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0     0.024        43      43      92 ..     499     549 ..     484     557 .. 0.78
   2 ?   -2.9   0.0       4.2   7.5e+03      38      72 ..     592     627 ..     588     656 .. 0.69
   3 ?    5.5   0.0     0.011        19      61      91 ..     710     740 ..     702     749 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.024
                       DUF5354  43 pdpkdlekfyvnGvdee.sddyenvlklfeeteekyavlnvClqEalqlkk 92 
                                   ++++++e++ v  v +    ++++v+ l ++t ++++v+ +C+ E +  k+
  gi|13541570|ref|NP_111258.1| 499 TESSNTERISVLTVHKAkGLEFDHVIYLPKTTRDNFSVVDLCAYELIREKT 549
                                   56777777778777654145899*********************9887554 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 4.2
                       DUF5354  38 lcsympdpkdlekfyvnGvdeesddyenvlk.lfee 72 
                                   + s  p++ ++e++ +  vd + + y+ +++  f++
  gi|13541570|ref|NP_111258.1| 592 IKSGKPTAPSTEHYSITSVDPNIEAYSAFINgRFDQ 627
                                   555566666777788888888888888766523544 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.011
                       DUF5354  61 ddyenvlklfeeteekyavlnvClqEalqlk 91 
                                    +y+n+lk+ ++ +++y+++++ ++E ++l 
  gi|13541570|ref|NP_111258.1| 710 PQYDNILKVIDDMQKRYGAVQISAEEEVTLP 740
                                   58************************98875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (885 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       783  (0.0436723); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.81u 0.34s 00:00:01.15 Elapsed: 00:00:00.58
# Mc/sec: 4575.86
//
Query:       gi|13541571|ref|NP_111259.1|  [L=396]
Description: metal-dependent carboxypeptidase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.7e-35  121.5   0.1    5.4e-35  121.0   0.1    1.2  1  Peptidase_M20   Peptidase family M20/M25/M40
    3.2e-13   49.5   0.0    7.6e-13   48.3   0.0    1.5  1  M20_dimer       Peptidase dimerisation domain
  ------ inclusion threshold ------
       0.11   12.0   0.0       0.16   11.5   0.0    1.2  1  vATP-synt_AC39  ATP synthase (C/AC39) subunit


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 !  121.0   0.1   9.1e-39   5.4e-35       2     195 ..      76     378 ..      75     389 .. 0.91

  Alignments for each domain:
  == domain 1  score: 121.0 bits;  conditional E-value: 9.1e-39
                                   EEEES-BSS.TTCGGGSSSTTSEEETTTEEESTTTTTTHHHHHHHHHHHHHHHHHTTT-SSEEEEEEESTTS.STTTHHHH CS
                                   xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxx RF
                 Peptidase_M20   2 lgsHlDvVp.eeetdgwttpfslteedGklyGrGaddmkggvlaalealralkdegikpkgtivllfqpdEE.ggrgGaka 80 
                                   l++++D++p +e+t g   pf++++  G+++++G+d + +++++a+++l ++ de    +g++++lfqp+EE ggrgGa  
  gi|13541571|ref|NP_111259.1|  76 LRADMDALPvQEQT-GL--PFASKNS-GVMHACGHDSHVAMLIGAAYVLSKHGDEL---DGNVKFLFQPAEEdGGRGGALP 149
                                   89*******77777.55..*****88.************************99998...*************6666***** PP

                                   HHH.HHHTTTCESEEEEEEEESSSBTCHSTETEEEE............................................. CS
                                   xxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................................. RF
                 Peptidase_M20  81 lle.gleerekvdavfelhieepgileagklaigvv............................................. 115
                                   ++e g++e+ +vd+vf+lh+  ++ +  g +ai+ +                                             
  gi|13541571|ref|NP_111259.1| 150 MIEdGALENPHVDHVFGLHVL-GDFPA-GYFAIRGGpimaapdsfkievhgrgghgsapwdtvdpifvssqiiqalygmrs 228
                                   ***877799***********9.99998.8988888899******************************************* PP

                                   ...............................................................EEEEEEEEEESHEEECCH CS
                                   ...............................................................xxxxxxxxxxxxxxxxxx RF
                 Peptidase_M20 116 ...............................................................kvevelleggapvtlnds 133
                                                                                                  k++v+++e+++pvt+nd+
  gi|13541571|ref|NP_111259.1| 229 rnvdqrdplvisvcsvhsgtkdniipdnallegtlrtldedvradmkkkisntaeavagafgaKADVSFIENAYPVTYNDP 309
                                   **************************************************************88****99*********** PP

                                   HHHHHHHHHHHHHHTSCEEEE.EES.SSBHTHHHH.TTTE.EEEEEE.SSG..GCTTS.TTTEEE.HHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxx.xxx.xxxxxxxxx.xxxx.xxxxxx.xxx..xxxxx.xxxxxx.xxxxx RF
                 Peptidase_M20 134 plvkalaeaaeelfgekveli.vsg.pggtdarff.agip.tvmifg.pgs..glaHs.pnEyvd.ledle 195
                                   ++++ ++++++++ g  ++++ +++  gg+d + f ++ p t++++g +++  g+++  +  ++  +ed+ 
  gi|13541571|ref|NP_111259.1| 310 AITEEVKSILSSIKG--MKTMeTKPlLGGEDVSRFlQRAPgTYYFLGtRNEkkGIIYPnHSSKFTvDEDYL 378
                                   ************879..5666567789********6666989999**777457777777999988544544 PP

>> M20_dimer  Peptidase dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.3   0.0   1.3e-16   7.6e-13       8     105 ..     191     286 ..     190     289 .. 0.96

  Alignments for each domain:
  == domain 1  score: 48.3 bits;  conditional E-value: 1.3e-16
                                   EEEEEEE-B-EEGG-TTTTB-HHHHHHHHHHCSCTTEEC.....TCCTCCCCCEECCE-CCCCEESSEEEEEEEEEHHHHH CS
                     M20_dimer   8 ggkitvkgkagHsgapgagaNAieklarllaeledeegdiaeerslprttlnvtgiegGsaknvipdeaeakidiRllpge 88 
                                   ++ki+v+g++gH++ap + +++i   ++++++l   ++++    +  +  ++v+++++G++ n+ipd a ++ ++R+l+++
  gi|13541571|ref|NP_111259.1| 191 SFKIEVHGRGGHGSAPWDTVDPIFVSSQIIQALYGMRSRNV--DQRDPLVISVCSVHSGTKDNIIPDNALLEGTLRTLDED 269
                                   69**********************************99977..89999********************************* PP

                                   HHHHHHHHHHHHHTSCC CS
                     M20_dimer  89 dpeevleeieeilekea 105
                                    +++ +++i + +e++a
  gi|13541571|ref|NP_111259.1| 270 VRADMKKKISNTAEAVA 286
                                   **********9999887 PP

>> 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 ?   11.5   0.0   2.7e-05      0.16     179     261 ..     269     351 ..     242     378 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.7e-05
                                   HHHHHHHTSS-HH...HHHHHHHHHHHHHHHHHHHTTTSS......T...--SS-S--HHHHHHHHTT-G.....GG.GGS CS
                vATP-synt_AC39 179 dllkfckklggetaeilreilgfeiDlrniniilrskkygelskedrkkllipggslypeglealaeaedveellaalkyt 259
                                   d+ +  kk+ ++tae ++ ++g+++D+  i +++ +      + e++k+ l ++  +++ +++ l+  edv+++l+    t
  gi|13541571|ref|NP_111259.1| 269 DVRADMKKKISNTAEAVAGAFGAKADVSFIENAYPVTYNDPAITEEVKSILSSIKGMKTMETKPLLGGEDVSRFLQRAPGT 349
                                   33333454457899***********************977889999*******************************8888 PP

                                   ST CS
                vATP-synt_AC39 260 ey 261
                                   +y
  gi|13541571|ref|NP_111259.1| 350 YY 351
                                   87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.62u 0.36s 00:00:00.98 Elapsed: 00:00:00.54
# Mc/sec: 2210.51
//
Query:       gi|13541572|ref|NP_111260.1|  [L=217]
Description: hypothetical protein TVN0741 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.8e-08   31.6   3.9    8.8e-08   31.6   3.9    1.9  2  zinc_ribbon_2    zinc-ribbon domain
    1.1e-06   27.9   4.2    1.6e-06   27.3   4.2    1.3  1  zf-ribbon_3      zinc-ribbon domain
    2.1e-06   27.7   3.0    3.3e-06   27.0   3.0    1.3  1  UPF0547          Uncharacterised protein family UPF0547
    3.9e-05   23.6   0.6    6.7e-05   22.8   0.6    1.3  1  DZR              Double zinc ribbon
    4.3e-05   24.2   1.9    7.1e-05   23.5   1.9    1.5  1  zinc_ribbon_15   zinc-ribbon family
  ------ inclusion threshold ------
      0.023   14.9   0.0      0.042   14.0   0.0    1.6  1  Vps36_ESCRT-II   Vacuolar protein sorting protein 36 Vps36
      0.024   14.2   0.0      0.031   13.8   0.0    1.1  1  Peptidase_M64    IgA Peptidase M64
      0.041   13.9   0.2      0.081   12.9   0.2    1.5  1  HypA             Hydrogenase/urease nickel incorporation, met
      0.097   12.9   2.1         11    6.3   0.1    2.5  2  zf-RING_7        C4-type zinc ribbon domain
       0.11   11.9   0.0       0.16   11.5   0.0    1.2  1  T4BSS_DotI_IcmL  Type-IV b secretion system, inner-membrane c
        0.2   11.7   1.1       0.42   10.6   1.1    1.5  1  DUF2116          Uncharacterized protein containing a Zn-ribb
        2.6    8.1   5.8        7.8    6.6   5.1    2.1  2  YhfH             YhfH-like protein
        4.2    7.5   7.9        1.3    9.1   0.2    2.9  2  Rubredoxin       Rubredoxin
        7.7    6.6   6.2         12    6.0   0.7    2.6  2  Zn_Tnp_IS1595    Transposase 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 ?   -2.0   0.2       2.5   3.2e+03       6      12 ..     159     165 ..     159     166 .. 0.82
   2 !   31.6   3.9   6.9e-11   8.8e-08       1      22 [.     194     215 ..     194     216 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 2.5
                 zinc_ribbon_2   6 Gaelqdn 12 
                                   Gae+q++
  gi|13541572|ref|NP_111260.1| 159 GAENQNK 165
                                   99**986 PP

  == domain 2  score: 31.6 bits;  conditional E-value: 6.9e-11
                 zinc_ribbon_2   1 fCpnCGaelqdnakFCpyCGtp 22 
                                   +CpnCG+ ++ ++++CpyCG++
  gi|13541572|ref|NP_111260.1| 194 RCPNCGKDIPIDSVYCPYCGFK 215
                                   6*******************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 !   27.3   4.2   1.3e-09   1.6e-06       2      25 ..     192     215 ..     191     216 .. 0.92

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 1.3e-09
                   zf-ribbon_3   2 tvrCPnCGa.plssddnvCpyCGtk 25 
                                   t+rCPnCG+ +   d + CpyCG k
  gi|13541572|ref|NP_111260.1| 192 TKRCPNCGKdI-PIDSVYCPYCGFK 215
                                   89*******77.***********87 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   3.0   2.6e-09   3.3e-06       1      22 [.     193     214 ..     193     215 .. 0.97

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 2.6e-09
                       UPF0547   1 KvCPeCeakvPvaaqfCphCGy 22 
                                   K+CP C   +P++ + Cp+CG+
  gi|13541572|ref|NP_111260.1| 193 KRCPNCGKDIPIDSVYCPYCGF 214
                                   99*******************9 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.6   5.2e-08   6.7e-05      23      49 .]     187     213 ..     173     213 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 5.2e-08
                           DZR  23 kavaaedrCpsCgekvdpearfCpeCG 49 
                                   ka ++ +rCp+Cg++++ ++ +Cp+CG
  gi|13541572|ref|NP_111260.1| 187 KALPKTKRCPNCGKDIPIDSVYCPYCG 213
                                   444558999999999999999999998 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   1.9   5.6e-08   7.1e-05      54      86 .]     177     213 ..     113     213 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 5.6e-08
                zinc_ribbon_15  54 gkeiekkesse....kkeCknCgkeveeefkyCpkCg 86 
                                    +++ek+e+++    +k+C+nCgk +  ++ yCp+Cg
  gi|13541572|ref|NP_111260.1| 177 PERLEKGEETKalpkTKRCPNCGKDIPIDSVYCPYCG 213
                                   334444444447777*********************9 PP

>> Vps36_ESCRT-II  Vacuolar protein sorting protein 36 Vps36
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   3.3e-05     0.042      30      52 ..      24      42 ..       1      80 [. 0.73

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.3e-05
                Vps36_ESCRT-II 30 eKilnrqnGrlyLTthriiyvds 52
                                  +    + +G+lyLT +r+iy ++
  gi|13541572|ref|NP_111260.1| 24 Q----YFKGTLYLTDKRLIYEEK 42
                                  3....459************655 PP

>> Peptidase_M64  IgA Peptidase M64
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   2.4e-05     0.031      21     107 ..     103     194 ..      87     207 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.4e-05
                                   S--GGGHHHHHHHHHHHHHHHTTSTTTTTTGGGEEEEEE----SSSS-.....BBGGGTB----TT--BSSBTTBTTB-B- CS
                 Peptidase_M64  21 GYtaaerekfekdArklvealfsaepfkeykadfnvwavkapseesGv.....srpltgverrsalgstydafdseRyllv 96 
                                   G  ++e++++++dA++  e+  + +  +e ++++++ + kap+++ G+     ++   + +++ ++++t+   + eR+   
  gi|13541572|ref|NP_111260.1| 103 GKWQSEMMRWTTDAKRRHEQEEKIKSEEEKRREIELARAKAPTANIGMyinagKKEGAENQNKNFIETTFSEINPERLEKG 183
                                   66789******************************************9875322222345567899*****9999999888 PP

                                   --HHHHHHHHT CS
                 Peptidase_M64  97 venrakrdaas 107
                                   +e +a+ ++++
  gi|13541572|ref|NP_111260.1| 184 EETKALPKTKR 194
                                   88887777665 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.2   6.3e-05     0.081      44      93 ..     168     213 ..     151     216 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.3e-05
                                   HHHHHHHHHCC.TTTT-EEEEEEE--EEEETTTS-EEECHHHHHS-TTTS CS
                          HypA  44 LefafellaegtvlegaeLeieevpvkvrCreCgkefeleekalrCpkCg 93 
                                   +e++f+ ++ + + +g   e +  p + rC +Cgk++ +++  + Cp Cg
  gi|13541572|ref|NP_111260.1| 168 IETTFSEINPERLEKGE--ETKALPKTKRCPNCGKDIPIDS--VYCPYCG 213
                                   55555555555554444..467889999**********994..57****9 PP

>> zf-RING_7  C4-type zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.1    0.0085        11      24      30 ..     193     199 ..     172     200 .. 0.77
   2 ?    5.8   0.4     0.013        16      24      30 ..     207     213 ..     204     213 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0085
                                   EE-TTT- CS
                     zf-RING_7  24 vtCpeCG 30 
                                    +Cp+CG
  gi|13541572|ref|NP_111260.1| 193 KRCPNCG 199
                                   59****9 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.013
                                   EE-TTT- CS
                     zf-RING_7  24 vtCpeCG 30 
                                   v+Cp+CG
  gi|13541572|ref|NP_111260.1| 207 VYCPYCG 213
                                   89****9 PP

>> T4BSS_DotI_IcmL  Type-IV b secretion system, inner-membrane complex component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00012      0.16       4      60 ..      62     117 ..      59     120 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00012
               T4BSS_DotI_IcmL   4 slvlnvllvvalvyllakpPepkyfattadGrirelvpldkPvlsdsellaWaakav 60 
                                    lv+n+ ++v  + l +k+      +tt++G  r  ++l++P + +se+++W+++a 
  gi|13541572|ref|NP_111260.1|  62 YLVVNISIAVPKIKLGTKKTLSVE-FTTEKGDDRATFVLKDPGKWQSEMMRWTTDAK 117
                                   567788888888876666555544.45669************************986 PP

>> DUF2116  Uncharacterized protein containing a Zn-ribbon (DUF2116)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   1.1   0.00033      0.42       4      20 ..     193     209 ..     190     213 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00033
                       DUF2116   4 kHCivCGkaIpldesfC 20 
                                   k C++CGk Ip d + C
  gi|13541572|ref|NP_111260.1| 193 KRCPNCGKDIPIDSVYC 209
                                   78*************99 PP

>> YhfH  YhfH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   5.1    0.0061       7.8       9      23 ..     187     202 ..     183     212 .. 0.86
   2 ?   -1.0   0.2       1.5   1.9e+03      15      20 ..     208     213 ..     204     215 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0061
                          YhfH   9 rnLPk.KkCteCGkei 23 
                                   + LPk K C++CGk+i
  gi|13541572|ref|NP_111260.1| 187 KALPKtKRCPNCGKDI 202
                                   567755********98 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.5
                          YhfH  15 kCteCG 20 
                                    C+ CG
  gi|13541572|ref|NP_111260.1| 208 YCPYCG 213
                                   5****9 PP

>> Rubredoxin  Rubredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.2     0.001       1.3      28      41 ..     186     199 ..     176     202 .. 0.83
   2 ?    3.1   0.3     0.079     1e+02      30      43 ..     201     215 ..     200     217 .] 0.71

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.001
                                   GGGS-TT-BBTTTB CS
                    Rubredoxin  28 FedlPddWvCPdCg 41 
                                    ++lP++ +CP+Cg
  gi|13541572|ref|NP_111260.1| 186 TKALPKTKRCPNCG 199
                                   579**********8 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.079
                                   GS-.TT-BBTTTB-B CS
                    Rubredoxin  30 dlP.ddWvCPdCgve 43 
                                   d+P d   CP Cg +
  gi|13541572|ref|NP_111260.1| 201 DIPiDSVYCPYCGFK 215
                                   77744567****975 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 ?    6.0   0.7    0.0093        12      16      27 ..     190     201 ..     185     207 .. 0.79
   2 ?    3.2   0.5     0.068        87      19      26 ..     207     214 ..     204     217 .] 0.77

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0093
                 Zn_Tnp_IS1595  16 pngfvCPhCgsr 27 
                                   p + +CP+Cg++
  gi|13541572|ref|NP_111260.1| 190 PKTKRCPNCGKD 201
                                   56678*****75 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.068
                 Zn_Tnp_IS1595  19 fvCPhCgs 26 
                                   + CP+Cg 
  gi|13541572|ref|NP_111260.1| 207 VYCPYCGF 214
                                   45****95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1148  (0.0640303); expected 358.6 (0.02)
Passed bias filter:                      635  (0.0354175); expected 358.6 (0.02)
Passed Vit filter:                        96  (0.00535445); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.62u 0.32s 00:00:00.94 Elapsed: 00:00:00.55
# Mc/sec: 1184.53
//
Query:       gi|13541573|ref|NP_111261.1|  [L=100]
Description: DNA-directed RNA polymerase subunit M [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-18   66.4   2.8    1.4e-18   66.4   2.8    3.1  3  TFIIS_C          Transcription factor S-II (TFIIS)
    5.2e-07   29.1  11.6    9.5e-05   21.8   1.5    2.9  2  TF_Zn_Ribbon     TFIIB zinc-binding
    6.2e-07   29.2   1.8    6.2e-07   29.2   1.8    2.7  2  RNA_POL_M_15KD   RNA polymerases M/15 Kd subunit
    1.5e-06   28.1  10.6    4.5e-05   23.4   1.1    2.6  2  DZR              Double zinc ribbon
    1.7e-06   27.5  12.7       0.27   11.0   0.3    4.3  4  zinc_ribbon_2    zinc-ribbon domain
    1.1e-05   25.3  14.2    0.00058   19.8   1.7    3.1  3  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
      9e-05   22.3  12.0       0.28   11.2   2.9    4.0  3  PhnA_Zn_Ribbon   PhnA Zinc-Ribbon
    0.00014   21.7  10.6      0.013   15.4   1.1    2.4  2  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
    0.00032   20.7   9.2       0.11   12.7   1.9    2.4  2  zf-Mss51         Zinc-finger of mitochondrial splicing suppre
     0.0004   20.0   0.5     0.0004   20.0   0.5    3.2  3  zf-RRN7          Zinc-finger of RNA-polymerase I-specific TFI
    0.00074   19.5   7.5      0.022   14.7   0.2    2.9  2  zinc-ribbons_6   zinc-ribbons
     0.0017   18.3   6.3       0.96    9.5   2.2    3.5  3  DNA_ligase_ZBD   NAD-dependent DNA ligase C4 zinc finger doma
     0.0018   18.5  11.2      0.027   14.7   0.3    4.0  4  zinc_ribbon_9    zinc-ribbon
     0.0045   16.6  12.4        5.9    6.6   0.1    4.2  4  zf_UBZ           Ubiquitin-Binding Zinc Finger
     0.0046   16.7   5.8       0.83    9.3   0.6    2.1  1  TackOD1          Thaumarchaeal output domain 1
     0.0055   16.7   7.6       0.12   12.4   2.9    2.6  2  HypA             Hydrogenase/urease nickel incorporation, met
     0.0069   16.3  14.7       0.11   12.5   4.5    4.1  3  Nudix_N_2        Nudix N-terminal
      0.007   16.5  16.2        3.8    7.7   4.7    4.2  3  Zn-ribbon_8      Zinc ribbon domain
     0.0099   16.3   3.4        1.9    9.0   0.6    2.3  2  zf-C4pol         C4-type zinc-finger of DNA polymerase delta
  ------ inclusion threshold ------
      0.011   15.4   3.6      0.011   15.4   3.6    3.8  3  zf-NADH-PPase    NADH pyrophosphatase zinc ribbon domain
      0.017   14.9  14.4       0.29   10.9   0.1    4.0  3  zf-C4_Topoisom   Topoisomerase DNA binding C4 zinc finger
       0.02   14.9   0.4       0.02   14.9   0.4    2.3  3  zf-C2HC5         Putative zinc finger motif, C2HC5-type
      0.023   15.4  12.3        1.8    9.3   0.1    4.1  4  zf-ISL3          zinc-finger of transposase IS204/IS1001/IS10
      0.024   14.8   2.9       0.17   12.1   2.9    2.1  1  FYVE             FYVE zinc finger
      0.032   14.0  11.9        3.2    7.6   0.1    4.3  4  A2L_zn_ribbon    A2L zinc ribbon domain
      0.032   14.6   7.8        2.1    8.8   0.8    3.2  3  Lar_restr_allev  Restriction alleviation protein Lar
      0.036   14.3   5.4      0.096   13.0   0.6    3.0  3  Ribosomal_L32p   Ribosomal L32p protein family
      0.051   13.2   3.0        0.2   11.3   0.7    2.0  2  zf-SNAP50_C      snRNA-activating protein of 50kDa MW C termi
      0.063   12.7   6.4       0.69    9.3   0.5    2.5  3  NMD3             NMD3 family
      0.063   13.7  11.6        1.1    9.7   0.1    4.2  5  zf-IS66          zinc-finger binding domain of transposase IS
      0.078   13.0   5.9        5.5    7.1   0.1    3.9  4  ADK_lid          Adenylate kinase, active site lid
      0.098   12.8   2.0      0.098   12.8   2.0    2.7  3  Ribosomal_S27    Ribosomal protein S27a
      0.098   12.8  19.7          1    9.5   0.6    4.2  4  UPF0547          Uncharacterised protein family UPF0547
        0.1   12.3   4.6        5.4    6.7   0.1    3.7  3  GATA             GATA zinc finger
       0.11   11.9  18.7       0.76    9.3   7.6    4.1  3  zf-ribbon_3      zinc-ribbon domain
       0.13   12.1   0.1       0.22   11.4   0.1    1.3  1  hemP             Hemin uptake protein hemP
       0.16   11.7  13.7          2    8.2   2.9    3.4  2  zinc_ribbon_10   Predicted integral membrane zinc-ribbon meta
       0.16   12.2   3.5       0.78   10.0   1.1    2.2  2  PHF5             PHF5-like protein
       0.24   11.8  11.0        7.1    7.1   0.1    3.7  4  GFA              Glutathione-dependent formaldehyde-activatin
       0.26   11.8   8.5        3.7    8.1   2.5    2.6  2  zf-CHY           CHY zinc finger
        0.3   11.1  12.3        0.4   10.7   1.4    3.7  3  CpXC             CpXC protein
       0.35   11.3   6.5          1    9.8   0.7    2.3  2  DnaJ_CXXCXGXG    DnaJ central domain
        0.4   10.9  11.1       0.55   10.4   3.6    3.1  3  Auto_anti-p27    Sjogren's syndrome/scleroderma autoantigen 1
        0.4   10.9  10.1        5.2    7.3   0.1    4.0  4  zf-RING_7        C4-type zinc ribbon domain
       0.48   10.1  13.4        6.2    6.6   0.4    4.1  4  DNA_RNApol_7kD   DNA directed RNA polymerase, 7 kDa subunit
       0.52   10.3   5.1       0.44   10.5   0.5    2.5  2  DUF4428          Domain of unknown function (DUF4428)
       0.79    9.9  10.2       0.96    9.7   1.0    3.2  3  Ribosomal_L37e   Ribosomal protein L37e
       0.79    9.2   4.1         23    4.5   0.2    3.2  3  Mu-like_Com      Mu-like prophage protein Com
        1.1    9.1  21.4        1.6    8.6   0.5    4.1  4  Rubredoxin_2     Rubredoxin metal binding domain
        1.2    9.0   7.5       0.44   10.4   0.2    2.6  2  zf-ZPR1          ZPR1 zinc-finger domain
        1.4    9.0  14.2        4.4    7.5   0.3    4.2  4  zf-ACC           Acetyl-coA carboxylase zinc finger domain
        1.4    7.3   6.9         46    2.4   6.9    2.3  1  Terminase_GpA    Phage terminase large subunit (GpA)
        1.8    8.4  13.1        2.1    8.2   0.1    3.6  3  zf-RING_4        RING/Ubox like zinc-binding domain
          2    8.0  11.4        9.3    5.9   0.2    3.8  4  zf_C2H2_10       C2H2 type zinc-finger
          2    8.3  12.6         17    5.4   0.1    4.0  4  DUF35_N          Rubredoxin-like zinc ribbon domain (DUF35_N)
        2.7    8.0   8.6        2.6    8.0   1.8    3.2  3  Prok-RING_1      Prokaryotic RING finger family 1
        2.9    8.5  17.2        1.3    9.6   0.2    3.8  3  zf-H2C2_2        Zinc-finger double domain
        2.9    8.1  12.0       0.43   10.8   1.8    3.0  2  zf-Dof           Dof domain, zinc finger
        3.1    8.2  10.3    3.6e+02    1.5  10.3    3.2  1  Rpr2             RNAse P Rpr2/Rpp21/SNM1 subunit domain
        3.9    7.5  14.1         72    3.4   0.1    4.1  3  zinc_ribbon_4    zinc-ribbon domain
        4.5    8.1  13.9         22    5.9   1.5    3.1  2  zinc_ribbon_15   zinc-ribbon family
        4.6    7.1   9.0       0.68    9.8   0.8    3.1  3  Cys_rich_CPCC    Cysteine-rich CPCC
        5.8    6.8   9.9         11    5.9   0.4    3.3  3  Cys_rich_KTR     Cysteine-rich KTR
        6.1    6.8  18.1         22    5.1   0.8    3.9  3  zf-HIT           HIT zinc finger
        6.1    6.9  10.0         33    4.6   0.1    3.5  3  YhfH             YhfH-like protein
        6.2    6.2  16.0         15    5.1   4.0    3.5  3  zf-TFIIB         Transcription factor zinc-finger
        6.3    6.9  15.9        6.4    6.9   0.5    4.2  4  Rubredoxin       Rubredoxin
        6.3    6.8  15.2         12    5.9   3.4    4.0  3  zf_CopZ          Zinc binding domain
        6.8    7.1  12.2        5.1    7.5   0.8    2.9  2  C1_2             C1 domain
        9.1    6.3  16.8          7    6.7   6.6    3.8  3  Zn_ribbon_SprT   SprT-like zinc ribbon domain
        9.2    6.9  13.2        8.9    7.0   0.1    3.9  4  zf-C2H2          Zinc finger, C2H2 type
        9.4    6.3  16.5        5.5    7.0   0.4    4.1  4  DUF1936          Domain of unknown function (DUF1936)


Domain annotation for each model (and alignments):
>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.5      0.17        43       2       8 ..       2       8 ..       1      14 [. 0.85
   2 ?    4.3   0.3      0.15        38      29      36 ..      17      24 ..      11      26 .. 0.76
   3 !   66.4   2.8   5.8e-21   1.4e-18       2      39 .]      61      98 ..      60      98 .. 0.98

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.17
                       TFIIS_C 2 kCpkCgs 8
                                  CpkCgs
  gi|13541573|ref|NP_111261.1| 2 FCPKCGS 8
                                 5****97 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.15
                       TFIIS_C 29 ykCtkCgh 36
                                  y+C +Cg+
  gi|13541573|ref|NP_111261.1| 17 YVCPSCGY 24
                                  77888876 PP

  == domain 3  score: 66.4 bits;  conditional E-value: 5.8e-21
                       TFIIS_C  2 kCpkCgsreayffqlQtRsaDEpmtvfykCtkCghrWr 39
                                   Cp+C+++ a ++ +QtRsaDEp+t fy+C +Cg+rWr
  gi|13541573|ref|NP_111261.1| 61 ICPRCHHKGARYVLKQTRSADEPETKFYTCEECGYRWR 98
                                  6************************************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 !   21.8   1.5   3.8e-07   9.5e-05       1      29 [.       1      26 [.       1      36 [. 0.90
   2 !   11.2   3.0   0.00082       0.2       2      27 ..      61      95 ..      60      99 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 3.8e-07
                                  EEETTTTCEECHEETSTTCEEESSSSBEE CS
                  TF_Zn_Ribbon  1 ykCPnCgstnlveDpergelvCtdCGlVl 29
                                  + CP+Cgs   +  p +g +vC++CG+ +
  gi|13541573|ref|NP_111261.1|  1 MFCPKCGS---LMTPVNGRYVCPSCGYEV 26
                                  68******...788999*********977 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00082
                                  EETTTTCEE.C........HEETSTTCEEESSSSB CS
                  TF_Zn_Ribbon  2 kCPnCgstn.l........veDpergelvCtdCGl 27
                                  +CP C+++             +pe+  ++C++CG+
  gi|13541573|ref|NP_111261.1| 61 ICPRCHHKGaRyvlkqtrsADEPETKFYTCEECGY 95
                                  6999999774478899996666999999******7 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   1.8   2.5e-09   6.2e-07       3      30 ..       2      25 ..       1      31 [. 0.95
   2 ?    6.0   0.4     0.045        11      18      29 ..      84      95 ..      78      97 .. 0.74

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 2.5e-09
                                  BESTTTSBEEEEECSCCCEEEESSSS-E CS
                RNA_POL_M_15KD  3 FCpkCgNlLlpkedkegknfeCrqCgYe 30
                                  FCpkCg+l+ p +++ +    C +CgYe
  gi|13541573|ref|NP_111261.1|  2 FCPKCGSLMTPVNGRYV----CPSCGYE 25
                                  *****************....******9 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.045
                                  CCCEEEESSSS- CS
                RNA_POL_M_15KD 18 egknfeCrqCgY 29
                                  e+k + C  CgY
  gi|13541573|ref|NP_111261.1| 84 ETKFYTCEECGY 95
                                  455599****** PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   1.1   1.8e-07   4.5e-05      14      41 ..       2      29 ..       1      31 [. 0.93
   2 !    8.9   2.7    0.0062       1.5      14      37 ..      61      96 ..      53     100 .] 0.55

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 1.8e-07
                           DZR 14 fCseCgtklkavaaedrCpsCgekvdpe 41
                                  fC++Cg+ + +v+  ++CpsCg++v+++
  gi|13541573|ref|NP_111261.1|  2 FCPKCGSLMTPVNGRYVCPSCGYEVSKK 29
                                  9***********************9987 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0062
                           DZR 14 fCseCgtk.....lkavaa.......edrCpsCgek 37
                                   C++C +k     lk++ +        ++C +Cg+ 
  gi|13541573|ref|NP_111261.1| 61 ICPRCHHKgaryvLKQTRSadepetkFYTCEECGYR 96
                                  566666664444433222255666666666666654 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.2    0.0012      0.31      15      20 ..       2       7 ..       1      10 [. 0.74
   2 !   11.0   0.3    0.0011      0.27       2      11 ..      19      28 ..      18      31 .. 0.83
   3 ?    5.9   0.1     0.042        11      14      22 ..      60      68 ..      56      69 .. 0.61
   4 ?    6.6   0.3     0.027       6.6      12      21 ..      84      95 ..      82      97 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0012
                 zinc_ribbon_2 15 FCpyCG 20
                                  FCp+CG
  gi|13541573|ref|NP_111261.1|  2 FCPKCG 7 
                                  788887 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.0011
                 zinc_ribbon_2  2 CpnCGaelqd 11
                                  Cp+CG+e+++
  gi|13541573|ref|NP_111261.1| 19 CPSCGYEVSK 28
                                  9****99975 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.042
                 zinc_ribbon_2 14 kFCpyCGtp 22
                                    Cp+C ++
  gi|13541573|ref|NP_111261.1| 60 AICPRCHHK 68
                                  556666654 PP

  == domain 4  score: 6.6 bits;  conditional E-value: 0.027
                 zinc_ribbon_2 12 nakF..CpyCGt 21
                                  + kF  C++CG+
  gi|13541573|ref|NP_111261.1| 84 ETKFytCEECGY 95
                                  567777****98 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   5.2     0.032       7.9      21      45 ..       3      24 ..       1      25 [. 0.70
   2 !    8.5   0.4    0.0078       1.9      18      27 ..      16      25 ..      12      32 .. 0.78
   3 !   19.8   1.7   2.3e-06   0.00058      19      45 ..      60      95 ..      55      96 .. 0.91

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.032
                 Zn_Tnp_IS1595 21 CPhCgsrkayriktrglfqCkeCrk 45
                                  CP+Cg  ++ +  + g++ C +C++
  gi|13541573|ref|NP_111261.1|  3 CPKCG--SLMTPVN-GRYVCPSCGY 24
                                  99999..3333333.6999999987 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0078
                 Zn_Tnp_IS1595 18 gfvCPhCgsr 27
                                  + vCP Cg++
  gi|13541573|ref|NP_111261.1| 16 RYVCPSCGYE 25
                                  578*****87 PP

  == domain 3  score: 19.8 bits;  conditional E-value: 2.3e-06
                 Zn_Tnp_IS1595 19 fvCPhCgsr.kayrikt........rglfqCkeCrk 45
                                   +CP+C+++   y +k+         + + C+eC++
  gi|13541573|ref|NP_111261.1| 60 AICPRCHHKgARYVLKQtrsadepeTKFYTCEECGY 95
                                  57*******9999999999***************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 !   11.2   2.9    0.0011      0.28       5      28 ..       3      25 ..       2      27 .. 0.88
   2 ?    5.6   0.7     0.064        16      21      27 ..      61      67 ..      60      68 .. 0.93
   3 ?    7.9   0.0     0.012       2.9      17      29 ..      85      97 ..      70      98 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0011
                PhnA_Zn_Ribbon  5 CplCaSeytYedgallvCpeCahE 28
                                  Cp+C+S  t   +  +vCp C++E
  gi|13541573|ref|NP_111261.1|  3 CPKCGSLMT-PVNGRYVCPSCGYE 25
                                  999999888.77888********9 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.064
                PhnA_Zn_Ribbon 21 vCpeCah 27
                                  +Cp C+h
  gi|13541573|ref|NP_111261.1| 61 ICPRCHH 67
                                  9*****9 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.012
                PhnA_Zn_Ribbon 17 gallvCpeCahEw 29
                                  +  + C+eC++ w
  gi|13541573|ref|NP_111261.1| 85 TKFYTCEECGYRW 97
                                  56788*****988 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   1.1   5.2e-05     0.013      31      55 ..       3      25 ..       2      29 .. 0.94
   2 !   10.9   2.7    0.0013      0.33      25      56 ..      56      97 ..      48      99 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 5.2e-05
                OrfB_Zn_ribbon 31 CseCgsknkealsgrtfkCpnCgfe 55
                                  C++Cgs +++   + +++Cp+Cg+e
  gi|13541573|ref|NP_111261.1|  3 CPKCGSLMTP--VNGRYVCPSCGYE 25
                                  **********..99*********98 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.0013
                OrfB_Zn_ribbon 25 ayTSktCseCgsknke..........alsgrtfkCpnCgfea 56
                                    +   C++C +k+ +          +++++ ++C++Cg+++
  gi|13541573|ref|NP_111261.1| 56 LDSDAICPRCHHKGARyvlkqtrsadEPETKFYTCEECGYRW 97
                                  556678*********99*****9999999999*******986 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 !   12.7   1.9   0.00042      0.11       2      32 ..       3      32 ..       2      49 .. 0.85
   2 !   12.3   0.8   0.00056      0.14       2      24 ..      62      95 ..      61      97 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00042
                      zf-Mss51  2 CPvpkhkqtapkhvdfeCpdCGiptycseeh 32
                                  CP + + + +p + ++ Cp CG+ +   +e 
  gi|13541573|ref|NP_111261.1|  3 CPKCGSLM-TPVNGRYVCPSCGYEVSKKKED 32
                                  9***7666.7999**********99888775 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00056
                      zf-Mss51  2 CPvpkhkqt...........apkhvdfeCpdCGi 24
                                  CP ++hk +           +p+   ++C +CG+
  gi|13541573|ref|NP_111261.1| 62 CPRCHHKGAryvlkqtrsadEPETKFYTCEECGY 95
                                  ****99999************************7 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 !   20.0   0.5   1.6e-06    0.0004       7      28 ..       3      23 ..       1      24 [. 0.96
   2 ?    5.2   0.7     0.067        17      23      30 ..      61      68 ..      61      68 .. 0.89
   3 ?    2.3   1.4      0.54   1.3e+02      21      28 ..      87      94 ..      87      97 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1.6e-06
                       zf-RRN7  7 CgvCgcrsftlddGfyyCrrCh 28
                                  C+ Cg+ + t+ +G+y+C +C+
  gi|13541573|ref|NP_111261.1|  3 CPKCGS-LMTPVNGRYVCPSCG 23
                                  ******.**************9 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.067
                       zf-RRN7 23 yCrrChtq 30
                                  +C rCh++
  gi|13541573|ref|NP_111261.1| 61 ICPRCHHK 68
                                  7*****95 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.54
                       zf-RRN7 21 fyyCrrCh 28
                                  fy C +C+
  gi|13541573|ref|NP_111261.1| 87 FYTCEECG 94
                                  79999998 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.2     9e-05     0.022       3      29 ..       3      29 ..       1      35 [. 0.88
   2 ?    5.4   2.8     0.072        18       2      23 ..      61      94 ..      60      99 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 9e-05
                                  -SSS-S--EE-SSEEE-TTT--EEEEE CS
                zinc-ribbons_6  3 CpeCqqelekrgeqyhCeaCqedlkke 29
                                  Cp+C + ++  + +y C +C  +++k+
  gi|13541573|ref|NP_111261.1|  3 CPKCGSLMTPVNGRYVCPSCGYEVSKK 29
                                  *********9999*******9988765 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.072
                                  --SSS-S--EE-S............SEEE-TTT- CS
                zinc-ribbons_6  2 kCpeCqqelekrg............eqyhCeaCq 23
                                  +Cp+C+++  +              + y+Ce+C 
  gi|13541573|ref|NP_111261.1| 61 ICPRCHHKGARYVlkqtrsadepetKFYTCEECG 94
                                  6999999987665555677777776677777775 PP

>> DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.1     0.029       7.3       2       7 ..       3       8 ..       2      10 .. 0.91
   2 !    9.5   2.2    0.0038      0.96       2      15 ..      19      32 ..      18      66 .. 0.67
   3 ?    2.7   0.2      0.51   1.3e+02       2       8 ..      62      68 ..      61      72 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.029
                DNA_ligase_ZBD 2 CPvCGs 7
                                 CP CGs
  gi|13541573|ref|NP_111261.1| 3 CPKCGS 8
                                 *****9 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0038
                DNA_ligase_ZBD  2 CPvCGsavvReege 15
                                  CP+CG +v ++ ++
  gi|13541573|ref|NP_111261.1| 19 CPSCGYEVSKKKED 32
                                  *********65532 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.51
                DNA_ligase_ZBD  2 CPvCGsa 8 
                                  CP C+++
  gi|13541573|ref|NP_111261.1| 62 CPRCHHK 68
                                  ****976 PP

>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.2       0.5   1.2e+02      23      29 ..       2       8 ..       1       9 [. 0.87
   2 ?    4.7   0.1      0.15        38      19      28 ..      15      23 ..      10      25 .. 0.74
   3 !   14.7   0.3   0.00011     0.027      10      29 ..      49      67 ..      48      69 .. 0.75
   4 ?    1.4   0.1       1.6   3.9e+02      17      28 ..      83      94 ..      75      96 .. 0.61

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.5
                 zinc_ribbon_9 23 lCPhCgg 29
                                  +CP Cg+
  gi|13541573|ref|NP_111261.1|  2 FCPKCGS 8 
                                  5****97 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.15
                 zinc_ribbon_9 19 dsdvlCPhCg 28
                                   + v CP+Cg
  gi|13541573|ref|NP_111261.1| 15 GRYV-CPSCG 23
                                  5567.****8 PP

  == domain 3  score: 14.7 bits;  conditional E-value: 0.00011
                 zinc_ribbon_9 10 rfVsvspdedsdvlCPhCgg 29
                                   +Vs++p +++++ CP+C+ 
  gi|13541573|ref|NP_111261.1| 49 EEVSAEPLDSDAI-CPRCHH 67
                                  6799988755555.****85 PP

  == domain 4  score: 1.4 bits;  conditional E-value: 1.6
                 zinc_ribbon_9 17 dedsdv..lCPhCg 28
                                  +e+  +  +C +Cg
  gi|13541573|ref|NP_111261.1| 83 PET--KfyTCEECG 94
                                  222..2448****7 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.1     0.053        13       4      12 ..       2      10 ..       1      13 [. 0.84
   2 ?    6.6   0.1     0.024       5.9       2      14 ..      16      28 ..      15      32 .. 0.82
   3 ?    5.1   0.2     0.069        17       4      10 ..      61      67 ..      58      69 .. 0.84
   4 ?    6.0   0.6     0.037       9.2       3       9 ..      88      94 ..      86      96 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.053
                        zf_UBZ  4 lCerCgkei 12
                                  +C++Cg+ +
  gi|13541573|ref|NP_111261.1|  2 FCPKCGSLM 10
                                  7*****876 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.024
                        zf_UBZ  2 tylCerCgkeipe 14
                                   y+C+ Cg e++ 
  gi|13541573|ref|NP_111261.1| 16 RYVCPSCGYEVSK 28
                                  69******98876 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.069
                        zf_UBZ  4 lCerCgk 10
                                  +C+rC++
  gi|13541573|ref|NP_111261.1| 61 ICPRCHH 67
                                  7****97 PP

  == domain 4  score: 6.0 bits;  conditional E-value: 0.037
                        zf_UBZ  3 ylCerCg 9 
                                  y+Ce+Cg
  gi|13541573|ref|NP_111261.1| 88 YTCEECG 94
                                  9*****8 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.6    0.0033      0.83      62     111 ..      48      95 ..      25      99 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0033
                       TackOD1  62 rglleeelvdrirlCpsCksghlnvrevCpkCkSidieeqelihhftCgn 111
                                   r+ + +e +d+  +Cp+C+++    r+v ++ +S+d  e+++  + +Cg+
  gi|13541573|ref|NP_111261.1|  48 REEVSAEPLDSDAICPRCHHKGA--RYVLKQTRSADEPETKFYTCEECGY 95 
                                   45566788899999****98865..5566899999999999999999997 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 !    9.4   1.1    0.0041         1      72      95 ..       2      25 ..       1      37 [. 0.74
   2 !   12.4   2.9   0.00049      0.12      67      98 ..      13      71 ..      10     100 .] 0.79

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0041
                                  EETTTS-EEECHHHHHS-TTTSSS CS
                          HypA 72 rCreCgkefeleekalrCpkCgsa 95
                                   C +Cg+ ++  + ++ Cp+Cg +
  gi|13541573|ref|NP_111261.1|  2 FCPKCGSLMTPVNGRYVCPSCGYE 25
                                  699999998866546889999975 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00049
                                  E--EEEETTTS-EEECHHHHH...........................S-TTTSSS-EE CS
                          HypA 67 vpvkvrCreCgkefeleekal...........................rCpkCgsadve 98
                                  v+ ++ C +Cg+e+++++++l                            Cp+C++++ +
  gi|13541573|ref|NP_111261.1| 13 VNGRYVCPSCGYEVSKKKEDLkivnksndketimireevsaepldsdaICPRCHHKGAR 71
                                  66788899999999977643345788899999999999999999999989999887655 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   4.5   0.00043      0.11       2      30 ..       2      24 ..       1      24 [. 0.84
   2 ?    2.7   0.6      0.48   1.2e+02      23      30 ..      60      67 ..      60      67 .. 0.85
   3 ?    3.0   0.1       0.4     1e+02      24      30 ..      89      95 ..      77      97 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00043
                                  B-TTT--B-EEE--TT-SS-EEEETTTTE CS
                     Nudix_N_2  2 FCsqCGtpvelripdgDnreRlvCpaCgt 30
                                  FC++CG+ ++          R+vCp+Cg+
  gi|13541573|ref|NP_111261.1|  2 FCPKCGSLMTPV------NGRYVCPSCGY 24
                                  9*****986654......47*******97 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.48
                                  EEETTTTE CS
                     Nudix_N_2 23 lvCpaCgt 30
                                  ++Cp+C++
  gi|13541573|ref|NP_111261.1| 60 AICPRCHH 67
                                  58****97 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.4
                                  EETTTTE CS
                     Nudix_N_2 24 vCpaCgt 30
                                  +C+ Cg+
  gi|13541573|ref|NP_111261.1| 89 TCEECGY 95
                                  6777775 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.4     0.074        18      29      34 ..       3       8 ..       1      13 [. 0.81
   2 ?    7.7   4.7     0.015       3.8       6      35 ..      17      68 ..      16      74 .. 0.65
   3 ?    5.7   0.2     0.066        17       6      14 ..      88      96 ..      76      99 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.074
                   Zn-ribbon_8 29 CPeCgs 34
                                  CP+Cgs
  gi|13541573|ref|NP_111261.1|  3 CPKCGS 8 
                                  *****9 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.015
                   Zn-ribbon_8  6 YrCeeCghefe.......vlqsis.dap...............ltaCPeCgse 35
                                  Y C +Cg e         + +  s d++               +  CP+C+++
  gi|13541573|ref|NP_111261.1| 17 YVCPSCGYEVSkkkedlkI-VNKSnDKEtimireevsaepldsDAICPRCHHK 68
                                  9999999888889998862.333324445666666666667745559999984 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.066
                   Zn-ribbon_8  6 YrCeeCghe 14
                                  Y CeeCg +
  gi|13541573|ref|NP_111261.1| 88 YTCEECGYR 96
                                  889999865 PP

>> zf-C4pol  C4-type zinc-finger of DNA polymerase delta
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.1     0.012       2.9       1      35 [.       3      43 ..       3      54 .. 0.69
   2 !    9.0   0.6    0.0078       1.9      10      43 ..      59      92 ..      45      99 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.012
                      zf-C4pol  1 ClvCkeklk....kalCkkCr..sdkqesllkllsrlkele 35
                                  C  C++ ++    + +C +C    +k+++ lk++++ ++ e
  gi|13541573|ref|NP_111261.1|  3 CPKCGSLMTpvngRYVCPSCGyeVSKKKEDLKIVNKSNDKE 43
                                  999**766678899******632333333666666666655 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0078
                      zf-C4pol 10 kalCkkCrsdkqesllkllsrlkelekklnelet 43
                                  +a+C +C+++ ++ +lk+ ++  e e+k+  +e+
  gi|13541573|ref|NP_111261.1| 59 DAICPRCHHKGARYVLKQTRSADEPETKFYTCEE 92
                                  689****866666688888888888888876544 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 ?   15.4   3.6   4.3e-05     0.011       5      31 ..       2      26 ..       1      26 [. 0.94
   2 ?    1.2   0.3       1.2   3.1e+02       6       9 ..      62      65 ..      60      68 .. 0.73
   3 ?    1.0   0.3       1.4   3.4e+02      24      30 ..      90      96 ..      89      96 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 4.3e-05
                 zf-NADH-PPase  5 FCgrCGaptepaeggwarvCpaCgleh 31
                                  FC++CG+ + p+ g    vCp+Cg+e+
  gi|13541573|ref|NP_111261.1|  2 FCPKCGSLMTPVNG--RYVCPSCGYEV 26
                                  **************..77******986 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 1.2
                 zf-NADH-PPase  6 CgrC 9 
                                  C+rC
  gi|13541573|ref|NP_111261.1| 62 CPRC 65
                                  7777 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 1.4
                 zf-NADH-PPase 24 CpaCgle 30
                                  C+ Cg++
  gi|13541573|ref|NP_111261.1| 90 CEECGYR 96
                                  9****87 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 ?   10.9   0.1    0.0012      0.29       4      18 ..       3      17 ..       2      18 .. 0.91
   2 ?    6.6   0.3     0.026       6.6       4      15 ..      19      30 ..      16      34 .. 0.85
   3 ?    2.3   4.2       0.6   1.5e+02       3      25 ..      61      91 ..      59      96 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0012
                                  -SSS--EEEEEE-SS CS
                zf-C4_Topoisom  4 CPkCggdLvlkrgkk 18
                                  CPkCg+ +   +g++
  gi|13541573|ref|NP_111261.1|  3 CPKCGSLMTPVNGRY 17
                                  ********9998886 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.026
                                  -SSS--EEEEEE CS
                zf-C4_Topoisom  4 CPkCggdLvlkr 15
                                  CP+Cg ++ +k+
  gi|13541573|ref|NP_111261.1| 19 CPSCGYEVSKKK 30
                                  *****9988886 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.6
                                  E-SSS...--EEEEEE-SSS.....EEEEES CS
                zf-C4_Topoisom  3 kCPkC...ggdLvlkrgkkG.....kFvGCs 25
                                   CP C   g+  vlk+++       kF+ C 
  gi|13541573|ref|NP_111261.1| 61 ICPRChhkGARYVLKQTRSAdepetKFYTCE 91
                                  6999955447788888887777777888886 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 ?   14.9   0.4   7.9e-05      0.02      19      53 ..       2      35 ..       1      36 [. 0.91
   2 ?   -0.9   0.0       6.6   1.7e+03      36      42 ..      61      67 ..      53      77 .. 0.74
   3 ?   -1.2   0.1       8.7   2.2e+03      19      24 ..      89      94 ..      84      95 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 7.9e-05
                      zf-C2HC5 19 nClnCGkiiCakeglskpCsfCgspllsseerqel 53
                                   C +CG  +   +g    C++Cg ++ +++e  ++
  gi|13541573|ref|NP_111261.1|  2 FCPKCGSLMTPVNGR-YVCPSCGYEVSKKKEDLKI 35
                                  599************.*********9999998777 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 6.6
                      zf-C2HC5 36 pCsfCgs 42
                                   C+ C++
  gi|13541573|ref|NP_111261.1| 61 ICPRCHH 67
                                  4666654 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 8.7
                      zf-C2HC5 19 nClnCG 24
                                   C +CG
  gi|13541573|ref|NP_111261.1| 89 TCEECG 94
                                  577887 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 ?    9.3   0.1    0.0071       1.8       4      19 ..       2      17 ..       1      18 [. 0.86
   2 ?    6.4   0.2     0.056        14       4      14 ..      18      38 ..      16      51 .. 0.63
   3 ?    5.2   0.2      0.14        35       4      14 ..      61      71 ..      59      81 .. 0.70
   4 ?    1.4   0.2       2.1   5.3e+02       4      10 ..      89      95 ..      88     100 .] 0.73

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0071
                       zf-ISL3  4 rCPnCgsktvvkhgkk 19
                                   CP+Cgs +  ++g++
  gi|13541573|ref|NP_111261.1|  2 FCPKCGSLMTPVNGRY 17
                                  7*******99999976 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.056
                       zf-ISL3  4 rCPnCgsk.tv.........v 14
                                  +CP Cg   ++         +
  gi|13541573|ref|NP_111261.1| 18 VCPSCGYEvSKkkedlkivnK 38
                                  6*****995333455555555 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.14
                       zf-ISL3  4 rCPnCgsktvv 14
                                   CP+C+ k ++
  gi|13541573|ref|NP_111261.1| 61 ICPRCHHKGAR 71
                                  6*****99443 PP

  == domain 4  score: 1.4 bits;  conditional E-value: 2.1
                       zf-ISL3  4 rCPnCgs 10
                                  +C +Cg 
  gi|13541573|ref|NP_111261.1| 89 TCEECGY 95
                                  6888876 PP

>> FYVE  FYVE zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   2.9   0.00067      0.17      12      65 ..       3      68 ..       1      99 [. 0.64

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00067
                                  -TTT--B--SSS--EE-TTT--EE-STTS-EEE.EE.........GGGTEEEEE..........EE-HHHHHH CS
                          FYVE 12 CeiCakkFsllrrrhhCrlCGkvvCekCssklvall.........ekeaeeksv..........rvCkeClae 65
                                  C++C +  + ++ r+ C  CG  v +k  + ++ +                              +C +C+++
  gi|13541573|ref|NP_111261.1|  3 CPKCGSLMTPVNGRYVCPSCGYEVSKKKEDLKIVNKsndketimiR-------EevsaepldsdAICPRCHHK 68
                                  9***********************9887766664443333333331.......04444444555556555543 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 ?    7.6   0.1     0.013       3.2      22      29 ..       1       8 [.       1      11 [. 0.90
   2 ?    7.5   0.2     0.014       3.4      20      30 ..      15      25 ..      14      27 .. 0.86
   3 ?    1.4   0.1       1.1   2.9e+02      20      27 ..      58      65 ..      57      69 .. 0.51
   4 ?    3.0   0.2      0.34        85      22      29 ..      88      95 ..      85      96 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.013
                 A2L_zn_ribbon 22 lvCieCga 29
                                  ++C++Cg+
  gi|13541573|ref|NP_111261.1|  1 MFCPKCGS 8 
                                  8******7 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.014
                 A2L_zn_ribbon 20 gylvCieCgas 30
                                  g +vC+ Cg++
  gi|13541573|ref|NP_111261.1| 15 GRYVCPSCGYE 25
                                  569******95 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 1.1
                 A2L_zn_ribbon 20 gylvCieC 27
                                  ++ +C+ C
  gi|13541573|ref|NP_111261.1| 58 SDAICPRC 65
                                  44455555 PP

  == domain 4  score: 3.0 bits;  conditional E-value: 0.34
                 A2L_zn_ribbon 22 lvCieCga 29
                                  + C eCg+
  gi|13541573|ref|NP_111261.1| 88 YTCEECGY 95
                                  56888886 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.4      0.75   1.9e+02       6      11 ..       3       8 ..       2      13 .. 0.87
   2 ?    6.6   0.0     0.041        10       4      21 ..      17      34 ..      14      56 .. 0.85
   3 ?    8.8   0.8    0.0085       2.1       6      36 ..      62      95 ..      57     100 .] 0.66

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.75
               Lar_restr_allev  6 CPfCgg 11
                                  CP Cg+
  gi|13541573|ref|NP_111261.1|  3 CPKCGS 8 
                                  999997 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.041
               Lar_restr_allev  4 kpCPfCggravlersqrv 21
                                  + CP Cg +  ++++ ++
  gi|13541573|ref|NP_111261.1| 17 YVCPSCGYEVSKKKEDLK 34
                                  57*****99999988765 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.0085
               Lar_restr_allev  6 CPfC...ggravlersqrvvaeigq.cvyCadCga 36
                                  CP C   g r vl+++ + ++   + + +C++Cg+
  gi|13541573|ref|NP_111261.1| 62 CPRChhkGARYVLKQTRSADEPE-TkFYTCEECGY 95
                                  99994434445555555555444.36********9 PP

>> Ribosomal_L32p  Ribosomal L32p protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.6   0.00039     0.096      29      52 ..       3      29 ..       1      33 [. 0.80
   2 ?    2.2   0.0      0.91   2.3e+02      41      50 ..      61      69 ..      48      76 .. 0.72
   3 ?   -0.4   0.1       5.7   1.4e+03      41      47 ..      89      95 ..      82      98 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00039
                                  ETTTCCEECT...TC-BTTTTBSSSBX CS
                Ribosomal_L32p 29 cpncgelklp...HrvcpscGyYkgre 52
                                  cp+cg+l  p   + vcpscGy   ++
  gi|13541573|ref|NP_111261.1|  3 CPKCGSLMTPvngRYVCPSCGYEVSKK 29
                                  *****888766669*******976555 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.91
                                  -BTTTTBSSS CS
                Ribosomal_L32p 41 vcpscGyYkg 50
                                  +cp c + kg
  gi|13541573|ref|NP_111261.1| 61 ICPRC-HHKG 69
                                  67777.4444 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 5.7
                                  -BTTTTB CS
                Ribosomal_L32p 41 vcpscGy 47
                                   c +cGy
  gi|13541573|ref|NP_111261.1| 89 TCEECGY 95
                                  4677766 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 ?    2.2   0.1      0.48   1.2e+02     165     191 ..       9      35 ..       5      46 .. 0.74
   2 ?   11.3   0.7   0.00079       0.2     145     178 ..      58      93 ..      50      99 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.48
                   zf-SNAP50_C 165 kllpedpsyfCdkCfrslhydkngekl 191
                                    ++p +  y+C +C  ++  +k+  k+
  gi|13541573|ref|NP_111261.1|   9 LMTPVNGRYVCPSCGYEVSKKKEDLKI 35 
                                   5788899999*9998887776666655 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00079
                   zf-SNAP50_C 145 rrkkCkvCekfsakwvvlndkll..pedpsyfCdkC 178
                                       C  C+++ a++v+ + + +  pe+++y C++C
  gi|13541573|ref|NP_111261.1|  58 SDAICPRCHHKGARYVLKQTRSAdePETKFYTCEEC 93 
                                   5678*************99555522889******** PP

>> NMD3  NMD3 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.5    0.0028      0.69       1      22 [.       3      25 ..       3      40 .. 0.84
   2 ?    5.3   0.1     0.047        12     105     143 ..      33      71 ..      24      77 .. 0.77
   3 ?    5.6   0.7     0.037       9.2      13      44 ..      59      96 ..      48     100 .] 0.66

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0028
                          NMD3  1 CcrCGkeieeling..lCedCllk 22
                                  C++CG+ ++ ++ng  +C++C  +
  gi|13541573|ref|NP_111261.1|  3 CPKCGSLMT-PVNGryVCPSCGYE 25
                                  ********7.77999******654 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.047
                          NMD3 105 vtvqgevrgenetilqqevevevkvkrqqCprCsriagg 143
                                   +++ ++ ++++++++++ev+ e   +  +CprC+ + ++
  gi|13541573|ref|NP_111261.1|  33 LKIVNKSNDKETIMIREEVSAEPLDSDAICPRCHHKGAR 71 
                                   555566656678889999999999999******987665 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.037
                          NMD3 13 nglCedCllkevdite......giekievevCkeCgry 44
                                  +++C++C  k  + +        +++ ++  C+eCg  
  gi|13541573|ref|NP_111261.1| 59 DAICPRCHHKGARYVLkqtrsaDEPETKFYTCEECGYR 96
                                  4599999999877777333333334466999****965 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 ?    9.7   0.1    0.0044       1.1       4      17 ..       3      16 ..       2      18 .. 0.85
   2 ?    3.7   0.7      0.32        80      39      46 .]      16      23 ..      15      23 .. 0.81
   3 ?    4.4   0.3      0.21        52       3      13 ..      18      28 ..      17      34 .. 0.65
   4 ?    3.4   0.0      0.41     1e+02       3      10 ..      61      68 ..      59      81 .. 0.78
   5 ?    1.7   0.2       1.4   3.5e+02       3       8 ..      89      94 ..      87      98 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0044
                       zf-IS66  4 CpcCGgllkpiged 17
                                  Cp+CG+l++p+ ++
  gi|13541573|ref|NP_111261.1|  3 CPKCGSLMTPVNGR 16
                                  ********999776 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.32
                       zf-IS66 39 kyaCpcCe 46
                                  +y Cp+C+
  gi|13541573|ref|NP_111261.1| 16 RYVCPSCG 23
                                  68999996 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.21
                       zf-IS66  3 tCpcCGgllkp 13
                                  +Cp CG ++++
  gi|13541573|ref|NP_111261.1| 18 VCPSCGYEVSK 28
                                  58888866555 PP

  == domain 4  score: 3.4 bits;  conditional E-value: 0.41
                       zf-IS66  3 tCpcCGgl 10
                                  +Cp C+++
  gi|13541573|ref|NP_111261.1| 61 ICPRCHHK 68
                                  79999985 PP

  == domain 5  score: 1.7 bits;  conditional E-value: 1.4
                       zf-IS66  3 tCpcCG 8 
                                  tC +CG
  gi|13541573|ref|NP_111261.1| 89 TCEECG 94
                                  455555 PP

>> ADK_lid  Adenylate kinase, active site lid
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.1      0.12        30       3      29 ..       2       8 ..       1      11 [. 0.54
   2 ?    7.1   0.1     0.022       5.5       1       8 [.      16      23 ..      16      34 .. 0.94
   3 ?    0.7   0.1       2.1   5.3e+02      22      28 ..      60      66 ..      37      68 .. 0.78
   4 ?    0.9   0.1       1.9   4.8e+02       3       8 ..      89      94 ..      86      96 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.12
                                  E-TTT--EEETTTB--SSTTB-TTT-- CS
                       ADK_lid  3 vCpkCGrsYhvvfnpPkveglCDkCGe 29
                                   CpkCG                    +
  gi|13541573|ref|NP_111261.1|  2 FCPKCG--------------------S 8 
                                  355555....................4 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.022
                                  EEE-TTT- CS
                       ADK_lid  1 RrvCpkCG 8 
                                  R vCp+CG
  gi|13541573|ref|NP_111261.1| 16 RYVCPSCG 23
                                  99*****9 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 2.1
                                  TB-TTT- CS
                       ADK_lid 22 glCDkCG 28
                                   +C  C+
  gi|13541573|ref|NP_111261.1| 60 AICPRCH 66
                                  4555554 PP

  == domain 4  score: 0.9 bits;  conditional E-value: 1.9
                                  E-TTT- CS
                       ADK_lid  3 vCpkCG 8 
                                  +C+ CG
  gi|13541573|ref|NP_111261.1| 89 TCEECG 94
                                  677776 PP

>> Ribosomal_S27  Ribosomal protein S27a
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   2.0   0.00039     0.098      20      44 ..       3      24 ..       1      25 [. 0.94
   2 ?   -0.1   0.2       4.3   1.1e+03      20      43 ..      62      66 ..      59      72 .. 0.67
   3 ?   -0.9   0.5       7.7   1.9e+03      38      44 ..      89      95 ..      86      96 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00039
                                  -SS-S-TTSBEEECTTEEEESSTTT CS
                 Ribosomal_S27 20 CpreCGaGvfMAehkdRkyCGkCgl 44
                                  Cp+ C  G  M   ++R+ C +Cg+
  gi|13541573|ref|NP_111261.1|  3 CPK-C--GSLMTPVNGRYVCPSCGY 24
                                  ***.*..*****************8 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 4.3
                                  -SS-S-TTSBEEECTTEEEESSTT CS
                 Ribosomal_S27 20 CpreCGaGvfMAehkdRkyCGkCg 43
                                  Cpr C                  +
  gi|13541573|ref|NP_111261.1| 62 CPR-C------------------H 66
                                  666.6..................3 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 7.7
                                  EESSTTT CS
                 Ribosomal_S27 38 yCGkCgl 44
                                  +C  Cg+
  gi|13541573|ref|NP_111261.1| 89 TCEECGY 95
                                  6888876 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.6      0.21        53      16      21 ..       2       7 ..       1       8 [. 0.86
   2 ?    8.0   0.5     0.012         3      16      23 ..      18      25 ..      17      28 .. 0.77
   3 ?    3.6   0.5      0.28        70       3       9 ..      62      68 ..      61      68 .. 0.83
   4 ?    9.5   0.6     0.004         1      17      25 ..      90      98 ..      88      99 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.21
                       UPF0547 16 fCphCG 21
                                  fCp CG
  gi|13541573|ref|NP_111261.1|  2 FCPKCG 7 
                                  899998 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.012
                       UPF0547 16 fCphCGyv 23
                                  +Cp CGy+
  gi|13541573|ref|NP_111261.1| 18 VCPSCGYE 25
                                  58888886 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.28
                       UPF0547  3 CPeCeak 9 
                                  CP+C +k
  gi|13541573|ref|NP_111261.1| 62 CPRCHHK 68
                                  9999875 PP

  == domain 4  score: 9.5 bits;  conditional E-value: 0.004
                       UPF0547 17 CphCGyvFq 25
                                  C +CGy++ 
  gi|13541573|ref|NP_111261.1| 90 CEECGYRWR 98
                                  9*******6 PP

>> GATA  GATA zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.5      0.13        33      17      32 ..      14      28 ..       3      32 .. 0.60
   2 ?   -0.3   0.0       3.4   8.5e+02       7      26 ..      42      65 ..      40      69 .. 0.54
   3 ?    6.7   0.1     0.022       5.4      23      33 ..      90     100 .]      78     100 .] 0.88

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.13
                          GATA 17 dgnksLCnaCGlyykk 32
                                  +g + +C +CG    k
  gi|13541573|ref|NP_111261.1| 14 NGRY-VCPSCGYEVSK 28
                                  5666.88888866555 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 3.4
                          GATA  7 tkTplWRrg....pdgnksLCnaC 26
                                  ++T + R++    p  +   C  C
  gi|13541573|ref|NP_111261.1| 42 KETIMIREEvsaePLDSDAICPRC 65
                                  567777766444444444445444 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.022
                          GATA  23 CnaCGlyykkk 33 
                                   C+ CG +++ +
  gi|13541573|ref|NP_111261.1|  90 CEECGYRWREY 100
                                   ********975 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   7.6    0.0031      0.76       4      25 ..       2      25 ..       1      26 [. 0.83
   2 ?    4.3   0.2      0.11        27      15      22 ..      58      65 ..      53      68 .. 0.72
   3 ?    2.1   0.4      0.54   1.3e+02      18      24 ..      89      95 ..      88      96 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0031
                   zf-ribbon_3  4 rCPnCGa.p.lssddnvCpyCGtk 25
                                  +CP+CG+   +  +  vCp+CG++
  gi|13541573|ref|NP_111261.1|  2 FCPKCGSlMtPVNGRYVCPSCGYE 25
                                  6******555556999******85 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.11
                   zf-ribbon_3 15 ddnvCpyC 22
                                  +d +Cp C
  gi|13541573|ref|NP_111261.1| 58 SDAICPRC 65
                                  67778877 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.54
                   zf-ribbon_3 18 vCpyCGt 24
                                  +C  CG+
  gi|13541573|ref|NP_111261.1| 89 TCEECGY 95
                                  5889998 PP

>> hemP  Hemin uptake protein hemP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00087      0.22      17      30 ..      66      79 ..      64      80 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00087
                                  EETTEEEEEEE-TT CS
                          hemP 17 eHgGetYrLRiTrn 30
                                  +H+G++Y+L++Tr 
  gi|13541573|ref|NP_111261.1| 66 HHKGARYVLKQTRS 79
                                  6***********95 PP

>> zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   3.2     0.048        12      39      52 ..      11      24 ..       1      26 [. 0.74
   2 ?    8.2   2.9    0.0081         2      24      52 ..      61      95 ..      45      97 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.048
                zinc_ribbon_10 39 eleevkyrCpkCga 52
                                  ++ + +y+Cp+Cg 
  gi|13541573|ref|NP_111261.1| 11 TPVNGRYVCPSCGY 24
                                  456779******96 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0081
                zinc_ribbon_10 24 ICskChshnGlap......keeleevkyrCpkCga 52
                                  IC+ Ch++   +        +e+e+  y C +Cg 
  gi|13541573|ref|NP_111261.1| 61 ICPRCHHKGARYVlkqtrsADEPETKFYTCEECGY 95
                                  9*****99988877777655666666899****96 PP

>> PHF5  PHF5-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   1.1    0.0031      0.78      30      87 ..       3      64 ..       2      76 .. 0.64
   2 ?    3.1   0.4      0.43   1.1e+02      37      51 ..      79      95 ..      57      99 .. 0.51

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0031
                          PHF5 30 cpicdslvkpatkvricdecsfgkleek..ciicgs.kgvsdayyclecvrlekdrdG.cpr 87
                                  cp c sl++p++   +c +c +  +++k    i ++ + +++    +e ++   d d  cpr
  gi|13541573|ref|NP_111261.1|  3 CPKCGSLMTPVNGRYVCPSCGYEVSKKKedLKIVNKsNDKETIMIREEVSAEPLDSDAiCPR 64
                                  999*****************987664431134444414444444444444444555533666 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.43
                          PHF5 37 v..kpatkvricdecsf 51
                                     +p+tk   c+ec +
  gi|13541573|ref|NP_111261.1| 79 SadEPETKFYTCEECGY 95
                                  23367777788888876 PP

>> GFA  Glutathione-dependent formaldehyde-activating enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.3      0.12        31      50      60 ..       1      11 [.       1      16 [. 0.85
   2 ?    7.1   0.1     0.028       7.1      49      64 ..      16      31 ..      10      48 .. 0.78
   3 ?    1.9   0.1       1.2   2.9e+02      41      57 ..      50      67 ..      27      77 .. 0.59
   4 ?    5.5   0.2     0.086        21      39      58 ..      76      96 ..      66      99 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.12
                           GFA 50 sfCpeCgsply 60
                                  +fCp+Cgs ++
  gi|13541573|ref|NP_111261.1|  1 MFCPKCGSLMT 11
                                  5******9876 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.028
                           GFA 49 rsfCpeCgsplysees 64
                                  r++Cp+Cg ++  +++
  gi|13541573|ref|NP_111261.1| 16 RYVCPSCGYEVSKKKE 31
                                  79*******9996433 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 1.2
                           GFA 41 adsgnkvtr.sfCpeCgs 57
                                  + s ++++   +Cp+C  
  gi|13541573|ref|NP_111261.1| 50 EVSAEPLDSdAICPRCHH 67
                                  445566666589999975 PP

  == domain 4  score: 5.5 bits;  conditional E-value: 0.086
                           GFA 39 kt.adsgnkvtrsfCpeCgsp 58
                                  +t ++ + + + + C+eCg +
  gi|13541573|ref|NP_111261.1| 76 QTrSADEPETKFYTCEECGYR 96
                                  333667777888******976 PP

>> zf-CHY  CHY zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.4     0.064        16      56      73 ..       2      23 ..       1      25 [. 0.82
   2 ?    8.1   2.5     0.015       3.7      22      67 ..      62     100 .]      48     100 .] 0.67

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.064
                        zf-CHY 56 lCkkCkk....efaeyfCpiCk 73
                                   C kC++      ++y+Cp C 
  gi|13541573|ref|NP_111261.1|  2 FCPKCGSlmtpVNGRYVCPSCG 23
                                  6999999887767899*****6 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.015
                        zf-CHY  22 CreCHeeledhelerlevkevlcllCeteqekavlCkkCkkefaey 67 
                                   C +CH++ ++  l++++         ++ ++k  +C++C+ + +ey
  gi|13541573|ref|NP_111261.1|  62 CPRCHHKGARYVLKQTRS-------ADEPETKFYTCEECGYRWREY 100
                                   999997444333333333.......355666778888888777776 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.2      0.52   1.3e+02      40      48 ..       3      11 ..       1      16 [. 0.76
   2 ?   10.7   1.4    0.0016       0.4       3      47 ..      19      69 ..      17      73 .. 0.69
   3 ?    3.1   0.3      0.38        94      37      46 ..      87      96 ..      82      99 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.52
                          CpXC 40 CpkCgatak 48
                                  CpkCg   +
  gi|13541573|ref|NP_111261.1|  3 CPKCGSLMT 11
                                  999987765 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.0016
                          CpXC  3 CpaCgkef.....eaeiwtsidadedpelkeklldgslf.eatCpkCgata 47
                                  Cp+Cg e      + +i++  + +e+  ++e++ ++ l  +a Cp+C++++
  gi|13541573|ref|NP_111261.1| 19 CPSCGYEVskkkeDLKIVNKSNDKETIMIREEVSAEPLDsDAICPRCHHKG 69
                                  9***976611111455555556666667999**9999962699****9986 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.38
                          CpXC 37 eatCpkCgat 46
                                   +tC++Cg++
  gi|13541573|ref|NP_111261.1| 87 FYTCEECGYR 96
                                  589*****87 PP

>> DnaJ_CXXCXGXG  DnaJ central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   3.1      0.26        65       1      25 [.       3      27 ..       3      71 .. 0.38
   2 ?    9.8   0.7     0.004         1      14      48 ..      59      94 ..      48      96 .. 0.64

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.26
                 DnaJ_CXXCXGXG  1 CkkCkGsgakkgkkktCktCkGsGv 25
                                  C+kC    +  + +  C++C+ + +
  gi|13541573|ref|NP_111261.1|  3 CPKCGSLMTPVNGRYVCPSCGYEVS 27
                                  6666555543233566777754442 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.004
                 DnaJ_CXXCXGXG 14 kktCktCkGsG.vvreeqktlgpfvqqsqstCpeCe 48
                                     C++C+ +G + + +q++ +   +++  tC+eC+
  gi|13541573|ref|NP_111261.1| 59 DAICPRCHHKGaRYVLKQTRSADEPETKFYTCEECG 94
                                  456999999995545555432223334456999995 PP

>> Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   3.6    0.0022      0.55      18      40 .]       3      23 ..       2      23 .. 0.87
   2 ?    3.5   0.0      0.33        82      32      39 ..      58      65 ..      43      77 .. 0.74
   3 ?    0.1   0.2       3.7   9.2e+02      17      22 ..      89      94 ..      88      96 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0022
                 Auto_anti-p27 18 CpvCgvPLmrdrkggkvyCvaCd 40
                                  Cp+Cg+ +     +g+++C++C+
  gi|13541573|ref|NP_111261.1|  3 CPKCGSLMTP--VNGRYVCPSCG 23
                                  *****97777..679*******6 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.33
                 Auto_anti-p27 32 gkvyCvaC 39
                                   + +C++C
  gi|13541573|ref|NP_111261.1| 58 SDAICPRC 65
                                  55667777 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 3.7
                 Auto_anti-p27 17 tCpvCg 22
                                  tC++Cg
  gi|13541573|ref|NP_111261.1| 89 TCEECG 94
                                  8****8 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 ?    4.2   0.1      0.19        48      25      32 ..       2       9 ..       1      10 [. 0.84
   2 ?    2.6   0.7      0.65   1.6e+02      26      30 ..      19      23 ..      17      23 .. 0.90
   3 ?    0.6   0.1       2.7   6.7e+02      24      30 ..      60      66 ..      46      66 .. 0.82
   4 ?    7.3   0.1     0.021       5.2      22      30 ..      86      94 ..      73      94 .. 0.65

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.19
                                  E-TTT--E CS
                     zf-RING_7 25 tCpeCGRI 32
                                  +Cp CG +
  gi|13541573|ref|NP_111261.1|  2 FCPKCGSL 9 
                                  8*****76 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.65
                                  -TTT- CS
                     zf-RING_7 26 CpeCG 30
                                  Cp+CG
  gi|13541573|ref|NP_111261.1| 19 CPSCG 23
                                  ****9 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 2.7
                                  EE-TTT- CS
                     zf-RING_7 24 vtCpeCG 30
                                  + Cp C+
  gi|13541573|ref|NP_111261.1| 60 AICPRCH 66
                                  6799996 PP

  == domain 4  score: 7.3 bits;  conditional E-value: 0.021
                                  B-EE-TTT- CS
                     zf-RING_7 22 evvtCpeCG 30
                                  +  tC+eCG
  gi|13541573|ref|NP_111261.1| 86 KFYTCEECG 94
                                  379*****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 ?    1.0   0.1       1.4   3.6e+02      20      25 ..       3       8 ..       2      10 .. 0.82
   2 ?    6.6   0.4     0.025       6.2       1      16 [.      17      32 ..      17      33 .. 0.88
   3 ?    2.9   0.1      0.35        86      19      30 ..      64      75 ..      56      77 .. 0.72
   4 ?    6.4   0.4     0.029       7.1      20      26 ..      90      96 ..      88      97 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 1.4
                                  -SSS-- CS
                DNA_RNApol_7kD 20 CkeCGh 25
                                  C +CG+
  gi|13541573|ref|NP_111261.1|  3 CPKCGS 8 
                                  888985 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.025
                                  -B-SSS--B----SSS CS
                DNA_RNApol_7kD  1 YiCgeCgaevslkkgd 16
                                  Y C  Cg evs kk+d
  gi|13541573|ref|NP_111261.1| 17 YVCPSCGYEVSKKKED 32
                                  99999**999988887 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.35
                                  --SSS-----B- CS
                DNA_RNApol_7kD 19 RCkeCGhRilYK 30
                                  RC + G R + K
  gi|13541573|ref|NP_111261.1| 64 RCHHKGARYVLK 75
                                  677777777777 PP

  == domain 4  score: 6.4 bits;  conditional E-value: 0.029
                                  -SSS--- CS
                DNA_RNApol_7kD 20 CkeCGhR 26
                                  C eCG+R
  gi|13541573|ref|NP_111261.1| 90 CEECGYR 96
                                  9999998 PP

>> DUF4428  Domain of unknown function (DUF4428)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.5    0.0018      0.44      11      41 ..       9      37 ..       3      45 .. 0.74
   2 ?    1.5   0.4       1.1   2.8e+02      21      29 ..      60      68 ..      54      94 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0018
                       DUF4428 11 llkrlkleDgyvCkdClkKlseflsdvkikk 41
                                  l++   ++  yvC++C  + s  ++d ki +
  gi|13541573|ref|NP_111261.1|  9 LMT--PVNGRYVCPSCGYEVSKKKEDLKIVN 37
                                  455..56666*******99988888888765 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 1.1
                       DUF4428 21 yvCkdClkK 29
                                   +C+ C  K
  gi|13541573|ref|NP_111261.1| 60 AICPRCHHK 68
                                  699999888 PP

>> Ribosomal_L37e  Ribosomal protein L37e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   1.0    0.0039      0.96      18      45 ..       2      30 ..       1      39 [. 0.74
   2 ?    1.2   0.1       1.7   4.1e+02      17      25 ..      60      68 ..      57      81 .. 0.76
   3 ?    4.2   0.3      0.19        48      33      40 ..      89      96 ..      84     100 .] 0.77

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0039
                Ribosomal_L37e 18 lCrrCgkrsyhvq.kktCascGypsaklr 45
                                  +C +Cg+    v+ + +C scGy  +k++
  gi|13541573|ref|NP_111261.1|  2 FCPKCGSLMTPVNgRYVCPSCGYEVSKKK 30
                                  69999998777762557******665554 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 1.7
                Ribosomal_L37e 17 ilCrrCgkr 25
                                   +C rC ++
  gi|13541573|ref|NP_111261.1| 60 AICPRCHHK 68
                                  579999876 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.19
                Ribosomal_L37e 33 tCascGyp 40
                                  tC +cGy+
  gi|13541573|ref|NP_111261.1| 89 TCEECGYR 96
                                  89999996 PP

>> Mu-like_Com  Mu-like prophage protein Com
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.2     0.093        23      27      33 ..       3       9 ..       1      15 [. 0.89
   2 ?    0.4   0.1       1.9   4.6e+02      27      31 ..      19      23 ..      16      30 .. 0.90
   3 ?    4.1   0.0      0.13        31      17      30 ..      53      65 ..      48      81 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.093
                   Mu-like_Com 27 CPRCGtL 33
                                  CP+CG L
  gi|13541573|ref|NP_111261.1|  3 CPKCGSL 9 
                                  *****98 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1.9
                   Mu-like_Com 27 CPRCG 31
                                  CP CG
  gi|13541573|ref|NP_111261.1| 19 CPSCG 23
                                  ****9 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.13
                   Mu-like_Com 17 aeAlDeltiKCPRC 30
                                  ae lD     CPRC
  gi|13541573|ref|NP_111261.1| 53 AEPLD-SDAICPRC 65
                                  66777.5566**** PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.3      0.39        97      17      22 ..       3       8 ..       2       9 .. 0.84
   2 ?    8.6   0.5    0.0062       1.6       1      11 [.      17      27 ..      17      28 .. 0.86
   3 ?    3.4   0.9      0.25        62      17      22 ..      62      67 ..      61      69 .. 0.89
   4 ?    7.3   1.9     0.016       3.9       1       9 [.      88      96 ..      88     100 .] 0.87

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.39
                  Rubredoxin_2 17 CpsCgs 22
                                  Cp Cgs
  gi|13541573|ref|NP_111261.1|  3 CPKCGS 8 
                                  999986 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0062
                  Rubredoxin_2  1 YvCsqCGfesa 11
                                  YvC +CG+e +
  gi|13541573|ref|NP_111261.1| 17 YVCPSCGYEVS 27
                                  9*******865 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.25
                  Rubredoxin_2 17 CpsCgs 22
                                  Cp C++
  gi|13541573|ref|NP_111261.1| 62 CPRCHH 67
                                  ****97 PP

  == domain 4  score: 7.3 bits;  conditional E-value: 0.016
                  Rubredoxin_2  1 YvCsqCGfe 9 
                                  Y C++CG++
  gi|13541573|ref|NP_111261.1| 88 YTCEECGYR 96
                                  99*****97 PP

>> zf-ZPR1  ZPR1 zinc-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   2.3       1.3   3.3e+02      31      44 ..      17      30 ..       1      54 [. 0.70
   2 ?   10.4   0.2    0.0018      0.44       2      42 ..      61      99 ..      60     100 .] 0.69

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 1.3
                       zf-ZPR1 31 feCehCgyknnevk 44
                                  ++C++Cgy+ ++ k
  gi|13541573|ref|NP_111261.1| 17 YVCPSCGYEVSKKK 30
                                  56888887655443 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0018
                       zf-ZPR1  2 lCpsCgkengetrllltkiPyfkeviimsfeCehCgyknne 42
                                   Cp+C+ ++g  ++l  +     e     ++Ce+Cgy+ +e
  gi|13541573|ref|NP_111261.1| 61 ICPRCH-HKGARYVL-KQTRSADEPETKFYTCEECGYRWRE 99
                                  6****8.55544443.344456666778899******9776 PP

>> zf-ACC  Acetyl-coA carboxylase zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.2     0.081        20       4      10 ..       3       9 ..       2      10 .. 0.82
   2 ?    7.5   0.3     0.018       4.4      21      26 .]      17      22 ..      14      29 .. 0.84
   3 ?    1.2   0.3       1.7   4.1e+02      23      26 .]      62      65 ..      60      67 .. 0.67
   4 ?    2.7   0.2      0.56   1.4e+02       3       8 ..      89      94 ..      84      94 .. 0.65

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.081
                        zf-ACC  4 CpsCgem 10
                                  Cp+Cg++
  gi|13541573|ref|NP_111261.1|  3 CPKCGSL 9 
                                  9999986 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.018
                        zf-ACC 21 yVCPkC 26
                                  yVCP+C
  gi|13541573|ref|NP_111261.1| 17 YVCPSC 22
                                  888888 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 1.7
                        zf-ACC 23 CPkC 26
                                  CP C
  gi|13541573|ref|NP_111261.1| 62 CPRC 65
                                  5555 PP

  == domain 4  score: 2.7 bits;  conditional E-value: 0.56
                        zf-ACC  3 KCpsCg 8 
                                   C++Cg
  gi|13541573|ref|NP_111261.1| 89 TCEECG 94
                                  466665 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 ?    2.4   6.9      0.19        46     201     239 ..      62      99 ..       1     100 [] 0.79

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.19
                 Terminase_GpA 201 CphCgelqels.ferlkwpegeaeekaryvCphcgsliee 239
                                   Cp+C +       ++ + +++ ++e+  y+C++cg  + e
  gi|13541573|ref|NP_111261.1|  62 CPRCHHKGARYvLKQTR-SAD-EPETKFYTCEECGYRWRE 99 
                                   77777666533244433.444.899999999999988765 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 ?   -0.4   4.3         4   9.9e+02      25      43 ..       3      22 ..       1      27 [. 0.53
   2 ?    4.8   0.1     0.099        25      35      45 ..      57      67 ..      47      68 .. 0.80
   3 ?    8.2   0.1    0.0084       2.1       7      23 ..      79      96 ..      75      99 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 4
                     zf-RING_4 25 ClfCyhrile..eeegrCPaC 43
                                  C  C + +++  +   +CP C
  gi|13541573|ref|NP_111261.1|  3 CPKCGS-LMTpvNGRYVCPSC 22
                                  444532.33324455667777 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.099
                     zf-RING_4 35 eeegrCPaCre 45
                                  +++++CP C +
  gi|13541573|ref|NP_111261.1| 57 DSDAICPRCHH 67
                                  56899****86 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.0084
                     zf-RING_4  7 eldetdkdlkpC.eCgyq 23
                                   +de +++++ C eCgy+
  gi|13541573|ref|NP_111261.1| 79 SADEPETKFYTCeECGYR 96
                                  57999*******99***8 PP

>> zf_C2H2_10  C2H2 type zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.2     0.037       9.3       5       9 ..       3       7 ..       1      11 [. 0.86
   2 ?    5.3   0.1     0.057        14       3      11 ..      17      25 ..      16      27 .. 0.85
   3 ?    2.8   0.2      0.36        88       5      10 ..      62      67 ..      59      69 .. 0.83
   4 ?   -1.0   0.1       5.4   1.3e+03       3      10 ..      88      95 ..      87      97 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.037
                    zf_C2H2_10 5 CPKCq 9
                                 CPKC+
  gi|13541573|ref|NP_111261.1| 3 CPKCG 7
                                 ****8 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.057
                    zf_C2H2_10  3 fsCPKCqek 11
                                  + CP C++ 
  gi|13541573|ref|NP_111261.1| 17 YVCPSCGYE 25
                                  78*****96 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.36
                    zf_C2H2_10  5 CPKCqe 10
                                  CP+C  
  gi|13541573|ref|NP_111261.1| 62 CPRCHH 67
                                  ****86 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 5.4
                    zf_C2H2_10  3 fsCPKCqe 10
                                  + C  C++
  gi|13541573|ref|NP_111261.1| 88 YTCEECGY 95
                                  67999998 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.1     0.069        17      27      33 ..       2       8 ..       1      11 [. 0.82
   2 ?    3.7   0.4      0.23        58      26      32 ..      17      23 ..      16      24 .. 0.70
   3 ?    4.0   0.6      0.19        48      26      32 ..      60      66 ..      58      70 .. 0.84
   4 ?    1.5   0.0       1.1   2.8e+02       5      18 ..      81      94 ..      79      96 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.069
                       DUF35_N 27 vCphCgs 33
                                  +Cp+Cgs
  gi|13541573|ref|NP_111261.1|  2 FCPKCGS 8 
                                  6999987 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.23
                       DUF35_N 26 avCphCg 32
                                   vCp Cg
  gi|13541573|ref|NP_111261.1| 17 YVCPSCG 23
                                  6788886 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.19
                       DUF35_N 26 avCphCg 32
                                  a+Cp+C+
  gi|13541573|ref|NP_111261.1| 60 AICPRCH 66
                                  79****6 PP

  == domain 4  score: 1.5 bits;  conditional E-value: 1.1
                       DUF35_N  5 aegrLvgqrCpdCG 18
                                  +e++  +  C  CG
  gi|13541573|ref|NP_111261.1| 81 DEPETKFYTCEECG 94
                                  66677777899998 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 ?    8.0   1.8      0.01       2.6       7      27 ..       3      23 ..       1      29 [. 0.93
   2 ?    2.0   0.1      0.79     2e+02      22      26 ..      61      65 ..      49      72 .. 0.73
   3 ?    0.1   0.1       3.1   7.6e+02      22      27 ..      89      94 ..      83      97 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.01
                   Prok-RING_1  7 CpvCgkelkeedDiVvCpeCg 27
                                  Cp Cg  +++ +   vCp Cg
  gi|13541573|ref|NP_111261.1|  3 CPKCGSLMTPVNGRYVCPSCG 23
                                  ********************9 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.79
                   Prok-RING_1 22 vCpeC 26
                                  +Cp C
  gi|13541573|ref|NP_111261.1| 61 ICPRC 65
                                  56666 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 3.1
                   Prok-RING_1 22 vCpeCg 27
                                  +C eCg
  gi|13541573|ref|NP_111261.1| 89 TCEECG 94
                                  588887 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 ?    1.5   0.5       1.8   4.6e+02      17      21 ..       3       7 ..       2      10 .. 0.88
   2 ?    8.4   0.3     0.012         3      14      23 ..      16      25 ..       8      28 .. 0.77
   3 ?    9.6   0.2    0.0051       1.3      13      22 ..      86      95 ..      74      96 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 1.8
                     zf-H2C2_2 17 CplCd 21
                                  Cp+C+
  gi|13541573|ref|NP_111261.1|  3 CPKCG 7 
                                  ****7 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.012
                     zf-H2C2_2 14 pyeCplCdka 23
                                  +y Cp+C++ 
  gi|13541573|ref|NP_111261.1| 16 RYVCPSCGYE 25
                                  69******95 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.0051
                     zf-H2C2_2 13 kpyeCplCdk 22
                                  k+y+C++C++
  gi|13541573|ref|NP_111261.1| 86 KFYTCEECGY 95
                                  56*******9 PP

>> zf-Dof  Dof domain, zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   2.8       2.6   6.5e+02       6      14 ..       3      11 ..       1      28 [. 0.66
   2 ?   10.8   1.8    0.0017      0.43       4      38 ..      60      97 ..      57      99 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 2.6
                        zf-Dof  6 CprCestnt 14
                                  Cp+C s  t
  gi|13541573|ref|NP_111261.1|  3 CPKCGSLMT 11
                                  777766544 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.0017
                        zf-Dof  4 lkCprCestntkFcYyNNyslsqPR...yfCkaCrryW 38
                                    CprC+ +  ++      s + P    y+C +C   W
  gi|13541573|ref|NP_111261.1| 60 AICPRCHHKGARYVLKQTRSADEPEtkfYTCEECGYRW 97
                                  57*******************999656699****9999 PP

>> Rpr2  RNAse P Rpr2/Rpp21/SNM1 subunit domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5  10.3       1.4   3.6e+02      47      90 .]       2      94 ..       1      94 [. 0.59

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 1.4
                                  B-TTT--B--CTTTEEEEE.......E-SSS-E.................................................. CS
                          Rpr2 47 vCkkCgsvlipgvtcsvrv.......enkskkkkkkkkka........................................... 79
                                  +C kCgs+++p  + +           +k++                                                    
  gi|13541573|ref|NP_111261.1|  2 FCPKCGSLMTPV-NGRYVCpscgyevSKKKE--------Dlkivnksndketimireevsaepldsdaicprchhkgaryvlk 75
                                  788888888874.333333222222222121........12233344466667777778888888888888888777777777 PP

                                  ..........EEEEETTTT CS
                          Rpr2 80 ........dvlvvtClaCg 90
                                           +  +tC +Cg
  gi|13541573|ref|NP_111261.1| 76 qtrsadepETKFYTCEECG 94
                                  7777777744459999996 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.1      0.29        72      28      33 ..       3       8 ..       1      11 [. 0.70
   2 ?    3.2   0.2      0.33        82       4       9 ..      18      23 ..      16      30 .. 0.79
   3 ?    3.1   5.2      0.37        92       4      36 .]      61      98 ..      59      98 .. 0.67

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.29
                 zinc_ribbon_4 28 CskCgh 33
                                  C+kCg 
  gi|13541573|ref|NP_111261.1|  3 CPKCGS 8 
                                  777775 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.33
                 zinc_ribbon_4  4 tCpsCk 9 
                                  +CpsC+
  gi|13541573|ref|NP_111261.1| 18 VCPSCG 23
                                  699996 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.37
                 zinc_ribbon_4  4 tCpsCk...akyeiddeklp..akgvkvrCskCghvFr 36
                                   Cp+C+   a+y +   + +  ++++  +C  Cg  +r
  gi|13541573|ref|NP_111261.1| 61 ICPRCHhkgARYVLKQTRSAdePETKFYTCEECGYRWR 98
                                  68999744466888877744356666778888888885 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   8.7      0.42     1e+02      38      73 ..      17      67 ..       1      72 [. 0.66
   2 ?    5.9   1.5     0.087        22      39      73 ..      61      95 ..      60      99 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.42
                zinc_ribbon_15 38 lacskCkslleaskelgkeiekkesse...............kkeCknCgk 73
                                  ++c +C++ ++++ke  k ++k++++e                 +C++C++
  gi|13541573|ref|NP_111261.1| 17 YVCPSCGYEVSKKKEDLKIVNKSNDKEtimireevsaepldsDAICPRCHH 67
                                  457777777777776666666655555667777777777777999999987 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.087
                zinc_ribbon_15 39 acskCkslleaskelgkeiekkessekkeCknCgk 73
                                   c +C+++ +    ++++  ++ +++ ++C++Cg 
  gi|13541573|ref|NP_111261.1| 61 ICPRCHHKGARYVLKQTRSADEPETKFYTCEECGY 95
                                  58888888888877777777777777999999986 PP

>> Cys_rich_CPCC  Cysteine-rich CPCC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.8    0.0027      0.68       3      32 ..       3      30 ..       1      50 [. 0.68
   2 ?    1.2   0.1       1.3   3.2e+02      18      27 ..      59      68 ..      44      87 .. 0.73
   3 ?   -0.1   0.3       3.5   8.6e+02       1       9 [.      88      96 ..      88      99 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0027
                 Cys_rich_CPCC  3 CpcCgyltleeeegsydiCpvCfWedDlvq 32
                                  Cp Cg l+ + + g y +Cp C +e  + +
  gi|13541573|ref|NP_111261.1|  3 CPKCGSLMTPVN-GRY-VCPSCGYEVSKKK 30
                                  888888888777.777.8888887755443 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 1.3
                 Cys_rich_CPCC 18 ydiCpvCfWe 27
                                    iCp C+ +
  gi|13541573|ref|NP_111261.1| 59 DAICPRCHHK 68
                                  5678888754 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 3.5
                 Cys_rich_CPCC  1 yqCpcCgyl 9 
                                  y+C  Cgy+
  gi|13541573|ref|NP_111261.1| 88 YTCEECGYR 96
                                  68999**96 PP

>> Cys_rich_KTR  Cysteine-rich KTR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.4     0.044        11      28      33 ..       1       6 [.       1      10 [. 0.87
   2 ?    2.1   0.1       0.7   1.7e+02       6      36 ..      19      25 ..      16      41 .. 0.61
   3 ?    3.6   0.9      0.23        56       5      21 ..      61      77 ..      59      93 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.044
                  Cys_rich_KTR 28 LfCPKC 33
                                  +fCPKC
  gi|13541573|ref|NP_111261.1|  1 MFCPKC 6 
                                  7***** PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.7
                  Cys_rich_KTR  6 cPvCgnkTRlkiredTvLknfpLfCPKCkqe 36
                                  cP Cg                         e
  gi|13541573|ref|NP_111261.1| 19 CPSCGY------------------------E 25
                                  666654........................3 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.23
                  Cys_rich_KTR  5 lcPvCgnkTRlkiredT 21
                                  +cP C+ k    + ++T
  gi|13541573|ref|NP_111261.1| 61 ICPRCHHKGARYVLKQT 77
                                  69999888766666666 PP

>> zf-HIT  HIT zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   5.3      0.11        26       5      20 ..       3      23 ..       2      26 .. 0.75
   2 ?    2.7   0.2      0.49   1.2e+02      16      20 ..      62      66 ..      61      72 .. 0.84
   3 ?    5.1   0.8     0.086        22      14      22 ..      88      96 ..      83     100 .] 0.81

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.11
                                  -TTT-S.....B-SEE-TTT- CS
                        zf-HIT  5 CgvCgf.....pakYkCpkCn 20
                                  C  Cg       ++Y Cp C+
  gi|13541573|ref|NP_111261.1|  3 CPKCGSlmtpvNGRYVCPSCG 23
                                  6667666666689*******8 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.49
                                  -TTT- CS
                        zf-HIT 16 CpkCn 20
                                  Cp+C+
  gi|13541573|ref|NP_111261.1| 62 CPRCH 66
                                  ****7 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.086
                                  EE-TTT--E CS
                        zf-HIT 14 YkCpkCntr 22
                                  Y+C  C+ r
  gi|13541573|ref|NP_111261.1| 88 YTCEECGYR 96
                                  999999976 PP

>> YhfH  YhfH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.1       0.2        51      16      23 ..       3      10 ..       2      13 .. 0.87
   2 ?    4.6   0.1      0.13        33      15      27 ..      18      30 ..      15      31 .. 0.81
   3 ?    3.7   0.1      0.26        64      15      21 ..      89      95 ..      85      99 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.2
                          YhfH 16 CteCGkei 23
                                  C++CG+ +
  gi|13541573|ref|NP_111261.1|  3 CPKCGSLM 10
                                  *****977 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.13
                          YhfH 15 kCteCGkeieEqa 27
                                  +C++CG e   ++
  gi|13541573|ref|NP_111261.1| 18 VCPSCGYEVSKKK 30
                                  6*****9987665 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.26
                          YhfH 15 kCteCGk 21
                                  +C eCG 
  gi|13541573|ref|NP_111261.1| 89 TCEECGY 95
                                  6999995 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   4.4      0.22        55       2      25 ..       3      22 ..       2      23 .. 0.73
   2 ?    1.7   0.6      0.64   1.6e+02       2       6 ..      19      23 ..      18      29 .. 0.76
   3 ?    5.1   4.0     0.059        15       2      26 ..      62      94 ..      61      97 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.22
                      zf-TFIIB  2 CPkCqdeleeserggveidyCpqC 25
                                  CPkC++ +++++ +     +Cp+C
  gi|13541573|ref|NP_111261.1|  3 CPKCGSLMTPVNGRY----VCPSC 22
                                  9****9999887553....56665 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.64
                      zf-TFIIB  2 CPkCq 6 
                                  CP+C+
  gi|13541573|ref|NP_111261.1| 19 CPSCG 23
                                  77776 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.059
                      zf-TFIIB  2 CPkCqdele.....eser...ggveidyCpqCr 26
                                  CP+C++        ++++    + ++++C++C+
  gi|13541573|ref|NP_111261.1| 62 CPRCHHKGAryvlkQTRSadePETKFYTCEECG 94
                                  ****99755577754444776889999999997 PP

>> Rubredoxin  Rubredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.7       1.1   2.9e+02      37      41 ..       3       7 ..       1      12 [. 0.84
   2 ?    6.9   0.5     0.026       6.4      35      43 ..      17      25 ..      11      32 .. 0.67
   3 ?    3.5   0.0       0.3        73      33      43 ..      58      68 ..      47      72 .. 0.78
   4 ?    3.9   0.8      0.22        54       2      11 ..      88      97 ..      82     100 .] 0.87

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 1.1
                                  BTTTB CS
                    Rubredoxin 37 CPdCg 41
                                  CP+Cg
  gi|13541573|ref|NP_111261.1|  3 CPKCG 7 
                                  ****8 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.026
                                  -BBTTTB-B CS
                    Rubredoxin 35 WvCPdCgve 43
                                  +vCP+Cg e
  gi|13541573|ref|NP_111261.1| 17 YVCPSCGYE 25
                                  677777543 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.3
                                  TT-BBTTTB-B CS
                    Rubredoxin 33 ddWvCPdCgve 43
                                   d +CP C  +
  gi|13541573|ref|NP_111261.1| 58 SDAICPRCHHK 68
                                  5778****765 PP

  == domain 4  score: 3.9 bits;  conditional E-value: 0.22
                                  EEETTT-BEE CS
                    Rubredoxin  2 yeCkvCgyvY 11
                                  y C+ Cgy +
  gi|13541573|ref|NP_111261.1| 88 YTCEECGYRW 97
                                  89*****976 PP

>> zf_CopZ  Zinc binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.2      0.18        44       3      15 ..       2      14 ..       1      18 [. 0.81
   2 ?    2.2   0.3       0.7   1.7e+02       3      10 ..      18      25 ..      16      32 .. 0.81
   3 ?    5.9   3.4     0.049        12       2      13 ..      60      71 ..      59      94 .. 0.65

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.18
                                  B-TTT--B-EEE- CS
                       zf_CopZ  3 kCPvCgkkGkkVk 15
                                   CP+Cg+  ++V+
  gi|13541573|ref|NP_111261.1|  2 FCPKCGSLMTPVN 14
                                  6*****9988887 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.7
                                  B-TTT--B CS
                       zf_CopZ  3 kCPvCgkk 10
                                   CP+Cg +
  gi|13541573|ref|NP_111261.1| 18 VCPSCGYE 25
                                  6****987 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.049
                                  -B-TTT--B-EE CS
                       zf_CopZ  2 kkCPvCgkkGkk 13
                                  + CP+C++kG +
  gi|13541573|ref|NP_111261.1| 60 AICPRCHHKGAR 71
                                  57********75 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.8     0.021       5.1      20      42 ..       2      26 ..       1      29 [. 0.82
   2 ?    3.2   4.7      0.44   1.1e+02      30      40 ..      85      95 ..      46      98 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.021
                          C1_2 20 nCsaCgrkidgff..YsCseCdfsl 42
                                   C  Cg  +++ +  Y C+ C + +
  gi|13541573|ref|NP_111261.1|  2 FCPKCGSLMTPVNgrYVCPSCGYEV 26
                                  688899998888888******9865 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.44
                          C1_2 30 gffYsCseCdf 40
                                   +fY+C+eC +
  gi|13541573|ref|NP_111261.1| 85 TKFYTCEECGY 95
                                  456****9*87 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.1      0.59   1.5e+02       7      11 ..       3       7 ..       1      12 [. 0.71
   2 ?    6.7   6.6     0.028         7       5      32 ..      17      67 ..      16      71 .. 0.75
   3 ?   -0.0   0.5       3.4   8.4e+02       5      11 ..      88      94 ..      84      97 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.59
                Zn_ribbon_SprT  7 CtgCg 11
                                  C+ Cg
  gi|13541573|ref|NP_111261.1|  3 CPKCG 7 
                                  77776 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.028
                Zn_ribbon_SprT  5 YrCtgCgreythhlsirrhn...........................YrCrrCkg 32
                                  Y+C++Cg    ++ s++ +                             +C+rC+ 
  gi|13541573|ref|NP_111261.1| 17 YVCPSCG----YEVSKKKEDlkivnksndketimireevsaepldsdAICPRCHH 67
                                  *******....55555555555777888888888888888888888888888875 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 3.4
                Zn_ribbon_SprT  5 YrCtgCg 11
                                  Y+C  Cg
  gi|13541573|ref|NP_111261.1| 88 YTCEECG 94
                                  8999999 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.2       2.9   7.1e+02       3       7 ..       3       7 ..       2      11 .. 0.87
   2 ?    7.0   0.1     0.036       8.9       1      16 [.      17      33 ..      17      35 .. 0.73
   3 ?    0.5   0.1         4   9.9e+02       3       8 ..      62      67 ..      61      74 .. 0.76
   4 ?    5.0   0.6      0.16        39       1       8 [.      88      95 ..      88      97 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 2.9
                                 ETTTT CS
                       zf-C2H2 3 CpdCg 7
                                 Cp+Cg
  gi|13541573|ref|NP_111261.1| 3 CPKCG 7
                                 99998 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.036
                                  EEETTTT.EEESSHHHH CS
                       zf-C2H2  1 ykCpdCg.ksFkrksnL 16
                                  y+Cp Cg ++ k k++L
  gi|13541573|ref|NP_111261.1| 17 YVCPSCGyEVSKKKEDL 33
                                  9******6666666665 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 4
                                  ETTTTE CS
                       zf-C2H2  3 CpdCgk 8 
                                  Cp C+ 
  gi|13541573|ref|NP_111261.1| 62 CPRCHH 67
                                  999986 PP

  == domain 4  score: 5.0 bits;  conditional E-value: 0.16
                                  EEETTTTE CS
                       zf-C2H2  1 ykCpdCgk 8 
                                  y+C++Cg+
  gi|13541573|ref|NP_111261.1| 88 YTCEECGY 95
                                  9*****96 PP

>> DUF1936  Domain of unknown function (DUF1936)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.4     0.022       5.5       2       7 ..       3       8 ..       2      14 .. 0.84
   2 ?    1.9   0.4      0.89   2.2e+02       2       6 ..      19      23 ..      18      26 .. 0.67
   3 ?    2.4   0.3      0.59   1.5e+02       1       6 [.      61      66 ..      61      70 .. 0.88
   4 ?    4.7   0.4      0.11        29      16      32 ..      81      95 ..      79      96 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.022
                                 -TTTSS CS
                       DUF1936 2 CPKCnv 7
                                 CPKC++
  gi|13541573|ref|NP_111261.1| 3 CPKCGS 8
                                 ****98 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.89
                                  -TTTS CS
                       DUF1936  2 CPKCn 6 
                                  CP C+
  gi|13541573|ref|NP_111261.1| 19 CPSCG 23
                                  77776 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.59
                                  B-TTTS CS
                       DUF1936  1 lCPKCn 6 
                                  +CP+C 
  gi|13541573|ref|NP_111261.1| 61 ICPRCH 66
                                  8****5 PP

  == domain 4  score: 4.7 bits;  conditional E-value: 0.11
                                  TTS-EEEEEES-TT--- CS
                       DUF1936 16 ekGEIKvFRCdredCdY 32
                                  ++ E K++ C  e+C+Y
  gi|13541573|ref|NP_111261.1| 81 DEPETKFYTC--EECGY 95
                                  56799*****..68999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1008  (0.0562218); expected 358.6 (0.02)
Passed bias filter:                      632  (0.0352502); expected 358.6 (0.02)
Passed Vit filter:                       122  (0.00680462); expected 17.9 (0.001)
Passed Fwd filter:                        86  (0.0047967); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              72  [number of targets reported over threshold]
# CPU time: 0.71u 0.34s 00:00:01.05 Elapsed: 00:00:00.60
# Mc/sec: 498.19
//
Query:       gi|13541574|ref|NP_111262.1|  [L=134]
Description: CoA-binding protein [Thermoplasma volcanium GSS1]
Scores for 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-39  134.7   0.4    2.3e-39  134.5   0.4    1.0  1  CoA_binding_2   CoA binding domain
    1.2e-06   29.1   0.0    2.2e-06   28.3   0.0    1.4  1  CoA_binding     CoA binding domain
  ------ inclusion threshold ------
      0.097   11.9   0.0       0.15   11.2   0.0    1.4  2  Glyco_hydro_57  Glycosyl hydrolase family 57


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 !  134.5   0.4   3.8e-43   2.3e-39       1     115 [.      12     126 ..      12     127 .. 0.98

  Alignments for each domain:
  == domain 1  score: 134.5 bits;  conditional E-value: 3.8e-43
                                   --EEEET--S-TTSHHHHHHHHHHHHT--EEEESSS-SEETTEES----T....T--EEEE-S-HHHHGGGHHHHHHH--S CS
                 CoA_binding_2   1 rtiaVvGasdnpgkfgykvlryllehglpvvpVnpkeeeilgekvyaslaedpepvdlvdvftppeatpeivkealalgak 81 
                                   +++aVvG s+np+k +y+v++yl ehg++v+pVnp+ ++ +g k+y+s+++ + +v++vdvf++pea++e+v++al++ +k
  gi|13541574|ref|NP_111262.1|  12 KNVAVVGISSNPEKDSYRVAKYLMEHGFRVIPVNPNLSSWEGLKAYPSVSAIEDKVEIVDVFRKPEAVLEVVDDALKVSPK 92 
                                   689***********************************************8579*************************** PP

                                   EEEE-TT---HHHHHHHHHTT-EEE.ES-HHHHH CS
                 CoA_binding_2  82 avwlqpgsedeeaaelaeeagirvvgdrCilveg 115
                                   ++w+q+g+++eea +lae++gi+vv+d+C++ e+
  gi|13541574|ref|NP_111262.1|  93 VIWMQEGVVNEEARQLAEKHGINVVMDKCMMKEH 126
                                   *******************************987 PP

>> CoA_binding  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   0.0   3.6e-10   2.2e-06       4      92 ..      12      96 ..       9      99 .. 0.94

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 3.6e-10
                                  EEEEEETTTSHHHHHHHHHHHHHHECEEEEEEC-TTTTTCEETTEEEESCHHHHHHHCTTTEEEEES-HHHHHHHHHHHHHTT CS
                   CoA_binding  4 tkviviGagglgiaglyhfkeklkygikavfgvnprkvgtevlglpvyksvdeleektevdvavitvPaesaqeavdelveag 86
                                  ++v+v+G++ +  +  y++++ l  +   v++vnp+   +  +gl++y+sv+ +e+k  v++  ++  +e++ e+vd++++ +
  gi|13541574|ref|NP_111262.1| 12 KNVAVVGISSNPEKDSYRVAKYLMEHGFRVIPVNPN--LSSWEGLKAYPSVSAIEDK--VEIVDVFRKPEAVLEVVDDALKVS 90
                                  79*****************999999999********..999****************..88888899**************99 PP

                                  -SEEEE CS
                   CoA_binding 87 ikgivi 92
                                   k+i++
  gi|13541574|ref|NP_111262.1| 91 PKVIWM 96
                                  999985 PP

>> Glyco_hydro_57  Glycosyl hydrolase family 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0      0.57   3.4e+03     184     198 ..      28      42 ..      24      55 .. 0.77
   2 ?   11.2   0.0   2.6e-05      0.15     162     199 ..      81     118 ..      60     131 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 0.57
                                   -SHHHHHHHTT--EE CS
                Glyco_hydro_57 184 peileilaelGfeyl 198
                                   ++++++l e Gf+++
  gi|13541574|ref|NP_111262.1|  28 YRVAKYLMEHGFRVI 42 
                                   677888888888776 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 2.6e-05
                                   HHHHHHHSS--SBEE-GGG-B--SHHHHHHHTT--EEE CS
                Glyco_hydro_57 162 elyeeyfgqePrgfwlpElavspeileilaelGfeylf 199
                                   e++ + + ++P+++w  E +v++e  ++ ++ G+++++
  gi|13541574|ref|NP_111262.1|  81 EVVDDALKVSPKVIWMQEGVVNEEARQLAEKHGINVVM 118
                                   56778899**************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       504  (0.0281109); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); 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 0.29s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 836.61
//
Query:       gi|13541575|ref|NP_111263.1|  [L=123]
Description: succinate dehydrogenase, hydrophobic anchor subunit [Thermoplasma volcanium GSS1]
Scores for complete 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   43.1   7.8    4.8e-11   42.8   7.8    1.3  1  Sdh_cyt         Succinate dehydrogenase/Fumarate reductase tr
      0.009   16.1   4.3      0.016   15.3   4.4    1.5  1  Fumarate_red_D  Fumarate reductase subunit D
  ------ inclusion threshold ------
      0.014   15.4   2.4      0.014   15.4   2.4    2.0  2  Colicin_V       Colicin V production protein
      0.031   14.0   1.6      0.043   13.5   1.6    1.3  1  DUF5083         Domain of unknown function (DUF5083)


Domain annotation for each model (and alignments):
>> Sdh_cyt  Succinate dehydrogenase/Fumarate reductase transmembrane subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.8   7.8   1.1e-14   4.8e-11      24     120 ..      15     105 ..       3     121 .. 0.79

  Alignments for each domain:
  == domain 1  score: 42.8 bits;  conditional E-value: 1.1e-14
                       Sdh_cyt  24 ilhritGvallvglllllvwlllalslsspesfarvvallaspiklilllllllallyHllnGiRhllwDlglglelesar 104
                                    ++  tG++l++ +l +++++   +++   + f  vv+ l++p++l+  l++++++ yH++nG+ h++ D+ +     s++
  gi|13541575|ref|NP_111263.1|  15 FVQAATGLFLVF-FLGVHLYVAHINFGNPVALFGSVVNQLHNPWWLAFFLIFVYIVTYHGINGLSHVIDDTSI-----SDK 89 
                                   57899*******.666666666778888999***************************************833.....334 PP

                       Sdh_cyt 105 ksalavlalavalvlv 120
                                   +++++ +al+v+ v++
  gi|13541575|ref|NP_111263.1|  90 SKKYIGIALMVIYVIT 105
                                   4444444555544443 PP

>> Fumarate_red_D  Fumarate reductase subunit D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   4.4   3.7e-06     0.016      28     111 ..      24     108 ..      14     116 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3.7e-06
                Fumarate_red_D  28 lililglllplGl..ldsdalsyekvlafaqswigklvllvviilplwhalhrihhglhdlkihvkkaaklifYglAalls 106
                                   l++ lg+ l ++   +++ ++ + +v++ +++++  ++ l+ + ++++h+++ + h+++d  i  k ++k+i  +l +++ 
  gi|13541575|ref|NP_111263.1|  24 LVFFLGVHLYVAHinFGNPVALFGSVVNQLHNPWWLAFFLIFVYIVTYHGINGLSHVIDDTSISDK-SKKYIGIALMVIYV 103
                                   555566555555422444566778888889999999999999**********************99.88988888877777 PP

                Fumarate_red_D 107 vvali 111
                                   +++++
  gi|13541575|ref|NP_111263.1| 104 ITIIY 108
                                   66654 PP

>> Colicin_V  Colicin V production protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.6      0.11   4.9e+02      61      74 ..      19      33 ..       5      55 .. 0.59
   2 ?   15.4   2.4   3.1e-06     0.014      29      86 ..      61     120 ..      57     123 .] 0.88

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.11
                     Colicin_V 61 iiaf.lllfllvlli 74
                                  + +  l+ fl+v l 
  gi|13541575|ref|NP_111263.1| 19 ATGLfLVFFLGVHLY 33
                                  333313333333333 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 3.1e-06
                     Colicin_V  29 lgwvvafvvasllypslaellae..lilspalaaiiaflllfllvllivsllgallsklv 86 
                                    +++++++v+++  + l++ + +  ++ +++ + +ia +++++++++ +++l++l+s+++
  gi|13541575|ref|NP_111263.1|  61 FFLIFVYIVTYHGINGLSHVIDDtsISDKSKKYIGIALMVIYVITIIYGTILAVLVSRMT 120
                                   57899******************88667778888999999*****************986 PP

>> DUF5083  Domain of unknown function (DUF5083)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   1.6   9.6e-06     0.043      19      72 ..      57     113 ..      44     120 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 9.6e-06
                       DUF5083  19 fimtvllafapllaellnnrlqygrd...fsdkvalysyisimvvyvitilleiify 72 
                                   + +  +l+f  +++    n l +  d   +sdk   y  i++mv+yviti+   i+ 
  gi|13541575|ref|NP_111263.1|  57 WWLAFFLIFVYIVTYHGINGLSHVIDdtsISDKSKKYIGIALMVIYVITIIYGTILA 113
                                   5566667777777766555555544333389*******************9988865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1102  (0.0614647); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); 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):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 762.83
//
Query:       gi|13541576|ref|NP_111264.1|  [L=140]
Description: succinate dehydrogenase, subunit C [Thermoplasma volcanium GSS1]
Scores for complete 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   46.7   3.8    3.6e-12   46.4   3.8    1.1  1  Sdh_cyt     Succinate dehydrogenase/Fumarate reductase transm
  ------ inclusion threshold ------
       0.58    9.0   3.2       0.33    9.8   0.7    1.7  2  Baculo_p48  Baculovirus P48 protein


Domain annotation for each model (and alignments):
>> Sdh_cyt  Succinate dehydrogenase/Fumarate reductase transmembrane subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.4   3.8     4e-16   3.6e-12      13     104 ..      18     111 ..       9     128 .. 0.70

  Alignments for each domain:
  == domain 1  score: 46.4 bits;  conditional E-value: 4e-16
                       Sdh_cyt  13 lyrlplgawlsilhritGvallv.glllllvwlllalsls.spe..sfarvvallas...piklilllllllallyHllnG 86 
                                    yr+  + +++ +hri+G+++l+ ++l+ +   +l+++l+ +p   +++++v++++      +l+l +ll+l+ +yH++nG
  gi|13541576|ref|NP_111264.1|  18 FYRKGWDYFAFTMHRISGIVILFyLYLHYI---VLSNLLHpGPNgiDYNKIVTSITVgpyDSFLVLDFLLALVIFYHGANG 95 
                                   578889999**************5555555...44565664555336777766666664435666669************* PP

                       Sdh_cyt  87 iRhllwDlglglelesar 104
                                   +R+ l  +g+gl++  ++
  gi|13541576|ref|NP_111264.1|  96 VRLALNEFGIGLNK--NK 111
                                   ********998832..22 PP

>> Baculo_p48  Baculovirus P48 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.7   3.7e-05      0.33     146     170 ..      18      45 ..       6      79 .. 0.73
   2 ?   -0.9   0.1     0.069   6.1e+02     254     285 ..      97     128 ..      90     134 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 3.7e-05
                    Baculo_p48 146 slqeGWdiflrpil...glilllyvllk 170
                                     ++GWd+f+++++   g+++l+y+ l+
  gi|13541576|ref|NP_111264.1|  18 FYRKGWDYFAFTMHrisGIVILFYLYLH 45 
                                   5679********9955567888888766 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.069
                    Baculo_p48 254 llplkqfmvdieknfkkkkvdklasklliGly 285
                                    l l +f + ++kn     + +++s++l Gl+
  gi|13541576|ref|NP_111264.1|  97 RLALNEFGIGLNKNKALFIIFEVISMILLGLF 128
                                   56788999999999999999999999*99998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); expected 358.6 (0.02)
Passed bias filter:                      213  (0.0118802); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 910.66
//
Query:       gi|13541577|ref|NP_111265.1|  [L=240]
Description: succinate dehydrogenase iron-sulfur subunit [Thermoplasma volcanium GSS1]
Scores for 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  117.9   0.0      2e-34  117.9   0.0    1.9  2  Fer2_3           2Fe-2S iron-sulfur cluster binding domain
    5.6e-10   39.5   1.7    5.6e-10   39.5   1.7    2.0  2  Fer4_8           4Fe-4S dicluster domain
    1.2e-08   35.0   3.4    1.2e-08   35.0   3.4    2.0  2  Fer4_10          4Fe-4S dicluster domain
    2.4e-07   31.2  16.5    7.7e-06   26.4   6.9    2.8  3  Fer4_7           4Fe-4S dicluster domain
    2.8e-07   31.0   1.8    2.8e-07   31.0   1.8    2.1  2  Fer4_17          4Fe-4S dicluster domain
    6.3e-07   29.5  14.5    7.6e-06   26.0   5.4    2.6  3  Fer4_9           4Fe-4S dicluster domain
     0.0001   21.9   3.0     0.0001   21.9   3.0    3.2  3  Fer4             4Fe-4S binding domain
    0.00062   19.7   2.0     0.0017   18.3   0.1    2.5  3  Fer2             2Fe-2S iron-sulfur cluster binding domain
    0.00089   19.2   2.1    0.00089   19.2   2.1    3.1  2  Fer4_6           4Fe-4S binding domain
     0.0012   19.0   4.1       0.14   12.3   0.1    2.7  3  Fer4_18          4Fe-4S dicluster domain
     0.0018   18.3   7.0      0.005   16.9   0.5    3.1  3  Fer4_21          4Fe-4S dicluster domain
     0.0033   17.4   1.6     0.0033   17.4   1.6    3.4  3  Fer4_2           4Fe-4S binding domain
     0.0033   16.9   0.0     0.0047   16.4   0.0    1.1  1  Ribosomal_L27_C  Ribosomal L27 protein C-terminal domain
     0.0066   17.3   5.8      0.065   14.1   1.6    2.6  2  Fer4_22          4Fe-4S dicluster domain
  ------ inclusion threshold ------
       0.01   16.3   0.6       0.01   16.3   0.6    3.1  2  Fer4_4           4Fe-4S binding domain
      0.028   15.3   3.5      0.028   15.3   3.5    3.0  2  Fer4_3           4Fe-4S binding domain
      0.051   14.5   8.7      0.051   14.5   8.7    2.8  4  Fer4_16          4Fe-4S double cluster binding domain
        1.3    9.6   7.0        6.5    7.4   3.8    3.2  3  Fer4_13          4Fe-4S single cluster domain of Ferredoxin I
        7.1    6.4   9.2        5.4    6.8   0.5    2.6  3  Fer4_20          Dihydroprymidine dehydrogenase domain II, 4F


Domain annotation for each model (and alignments):
>> Fer2_3  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.9   0.0   2.1e-37     2e-34       2     108 ..       7     108 ..       6     109 .. 0.95
   2 ?   -2.1   0.0         4   3.8e+03      38      74 ..     178     214 ..     171     236 .. 0.63

  Alignments for each domain:
  == domain 1  score: 117.9 bits;  conditional E-value: 2.1e-37
                        Fer2_3   2 lkvkRfdprrdrgkqkvqeyeveaeeedtvldaLlkikeevdptlafrasCregiCGscavainGkptlaCtatikdlakq 82 
                                   +++kR d    +gk+++q+y+v++++  tvl+ Ll+ike++d+tl+fr+sCr +iCGsc+++i Gkp++aC++ i+dl+++
  gi|13541577|ref|NP_111265.1|   7 FEIKRKDG---SGKTYFQKYNVPKDKVSTVLEGLLYIKENLDQTLSFRYSCRMEICGSCGMEIQGKPRMACSTIIEDLKSD 84 
                                   67788777...679***************************************************************9987 PP

                        Fer2_3  83 kseieleplpkfpvirDLvvDideml 108
                                   k  i++epl++++virDLvvDid+++
  gi|13541577|ref|NP_111265.1|  85 K--IRIEPLKHYKVIRDLVVDIDPFF 108
                                   6..********************997 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 4
                        Fer2_3  38 ikeevdptlafrasCregiCGscavainGkptlaCta 74 
                                   i ++ d+  ++r +   g  G+      G+ t +C +
  gi|13541577|ref|NP_111265.1| 178 IADNRDKGAKYRVEVVDGENGTARCHFAGECTEVCPK 214
                                   5555666666666666666666666666666666654 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1       2.3   2.2e+03      53      57 ..      58      62 ..      22      76 .. 0.79
   2 !   39.5   1.7     6e-13   5.6e-10       4      65 .]     145     216 ..     142     216 .. 0.71

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 2.3
                        Fer4_8 53 tcgaC 57
                                  +cg+C
  gi|13541577|ref|NP_111265.1| 58 ICGSC 62
                                  34444 PP

  == domain 2  score: 39.5 bits;  conditional E-value: 6e-13
                        Fer4_8   4 kCieCgaCqsaCp...........vlrrtk.khlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvgi 65 
                                    Ci+Cg+C++aCp           +  + + + + d+r++ a+   + +v+++e++  +C+  g+CtevCp+g+
  gi|13541577|ref|NP_111265.1| 145 MCIKCGLCMAACPiegsdpsylgpAPLAAAwRYIADNRDKGAK--YRVEVVDGENGTARCHFAGECTEVCPKGV 216
                                   7***********7555555555442233334666777777666..33344456999***************986 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.4       3.1   2.9e+03       8      51 ..      58      62 ..      42      74 .. 0.72
   2 !   35.0   3.4   1.2e-11   1.2e-08       4      56 .]     141     213 ..     138     213 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 3.1
                       Fer4_10  8 tCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaC 51
                                                                          cg+C
  gi|13541577|ref|NP_111265.1| 58 I---------------------------------------CGSC 62
                                  3.......................................3333 PP

  == domain 2  score: 35.0 bits;  conditional E-value: 1.2e-11
                       Fer4_10   4 idddtCirCgkCvkaCPadl....................tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                    +   Ci+Cg C++aCP                       +++++ +++ e    + +  +C++ g+C+e+CP
  gi|13541577|ref|NP_111265.1| 141 ANYAMCIKCGLCMAACPIEGsdpsylgpaplaaawryiadNRDKGAKYRVEVVDGENGTARCHFAGECTEVCP 213
                                   56788*************88******************8877788888888888888***************9 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.1         1   9.6e+02      29      42 ..      50      63 ..      18      77 .. 0.70
   2 !   17.5   2.0   5.1e-06    0.0048      25      49 ..     133     157 ..     101     160 .. 0.77
   3 !   26.4   6.9   8.2e-09   7.7e-06       2      52 .]     146     216 ..     145     216 .. 0.57

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 1
                        Fer4_7 29 ekveidpekClgCg 42
                                   ++  ++e C +Cg
  gi|13541577|ref|NP_111265.1| 50 FRYSCRMEICGSCG 63
                                  55667778888886 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 5.1e-06
                        Fer4_7  25 ekgtekveidpekClgCgaCvavCP 49 
                                    +++ + + ++ +C+ Cg C+a+CP
  gi|13541577|ref|NP_111265.1| 133 TPEQFHEYANYAMCIKCGLCMAACP 157
                                   3455666778899999999999999 PP

  == domain 3  score: 26.4 bits;  conditional E-value: 8.2e-09
                        Fer4_7   2 CigCgaCvaaC...............pvkaieldeeenekgt....ekv..eidpekClgCgaCvavCPtga 52 
                                   Ci+Cg C+aaC                + ++++ + +++kg     e v  e    +C + g+C +vCP+g+
  gi|13541577|ref|NP_111265.1| 146 CIKCGLCMAACpiegsdpsylgpaplAAAWRYIAD-NRDKGAkyrvEVVdgENGTARCHFAGECTEVCPKGV 216
                                   ***********444444444444422233333333.333332222222322444568************996 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1       2.1     2e+03      41      50 ..      54      63 ..      19      79 .. 0.76
   2 !   31.0   1.8   2.9e-10   2.8e-07       2      61 .]     146     217 ..     135     217 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 2.1
                       Fer4_17 41 ekaslCieCg 50
                                  ++++ C +Cg
  gi|13541577|ref|NP_111265.1| 54 CRMEICGSCG 63
                                  4555555554 PP

  == domain 2  score: 31.0 bits;  conditional E-value: 2.9e-10
                       Fer4_17   2 CiqCgyClpeCpsyeaydne..pkkllraakl..........glleeaekeekaslCieCgeCerkCPqgld 61 
                                   Ci+Cg C+++Cp     +++  p+ l++a+++           ++e +  e+   +C+  geC+++CP+g++
  gi|13541577|ref|NP_111265.1| 146 CIKCGLCMAACPIEGSDPSYlgPAPLAAAWRYiadnrdkgakYRVEVVDGENGTARCHFAGECTEVCPKGVN 217
                                   *************9998876558888888877766555443223333444589****************985 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.2       1.5   1.4e+03      39      42 ..      59      62 ..      35      77 .. 0.65
   2 !   15.9   1.7   1.1e-05     0.011      33      47 ..     135     157 ..     117     161 .. 0.68
   3 !   26.0   5.4     8e-09   7.6e-06       2      49 ..     146     215 ..     145     216 .. 0.94

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 1.5
                        Fer4_9 39 CgaC 42
                                  Cg+C
  gi|13541577|ref|NP_111265.1| 59 CGSC 62
                                  4444 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 1.1e-05
                        Fer4_9  33 e........eaCigCgaCveaCp 47 
                                   e          Ci+Cg C++aCp
  gi|13541577|ref|NP_111265.1| 135 EqfheyanyAMCIKCGLCMAACP 157
                                   12333333466999999999999 PP

  == domain 3  score: 26.0 bits;  conditional E-value: 8e-09
                        Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraase......................eaCigCgaCveaCpkg 49 
                                   C++Cg C++aCp +   ++  +      a+++                       +C++ g+C+e+Cpkg
  gi|13541577|ref|NP_111265.1| 146 CIKCGLCMAACPIEGSDPSYLGPAPLAAAWRYiadnrdkgakyrvevvdgengtARCHFAGECTEVCPKG 215
                                   ***********99999999999999999999999999999999***********9*************98 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.8       1.7   1.6e+03       8      12 ..      59      63 ..      56      64 .. 0.59
   2 !   21.9   3.0   1.1e-07    0.0001       4      20 ..     142     158 ..     139     159 .. 0.89
   3 !    8.1   1.3    0.0025       2.4       8      21 ..     202     215 ..     199     216 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.7
                                  SSS-T CS
                          Fer4  8 CigCG 12
                                  C  CG
  gi|13541577|ref|NP_111265.1| 59 CGSCG 63
                                  66665 PP

  == domain 2  score: 21.9 bits;  conditional E-value: 1.1e-07
                                   ETTTSSS-THHHHHSTT CS
                          Fer4   4 deekCigCGaCvevCPv 20 
                                   ++ +Ci+CG+C+ +CP 
  gi|13541577|ref|NP_111265.1| 142 NYAMCIKCGLCMAACPI 158
                                   7889************6 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.0025
                                   SSS-THHHHHSTTT CS
                          Fer4   8 CigCGaCvevCPvg 21 
                                   C + G+C evCP g
  gi|13541577|ref|NP_111265.1| 202 CHFAGECTEVCPKG 215
                                   55559*******88 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 !   18.3   0.1   1.8e-06    0.0017      19      77 ..      37      78 ..      21      83 .. 0.76
   2 ?   -0.5   0.1       1.3   1.2e+03      39      47 ..     148     156 ..     138     177 .. 0.73
   3 ?   -2.3   0.0       4.7   4.4e+03       4      17 ..     184     197 ..     181     203 .. 0.71

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.8e-06
                                  HHHHHHH.TTTTTSTTSSSSSSSSTTEEEEEESCECTTSSSSTHHHHHTTEEEEGGGSEE CS
                          Fer2 19 lldaaee.nggidipysCggggCgtClvevlegevqsdetelegeeldegklrlaCqtiv 77
                                  ll + e+ ++ + ++ysC++  Cg+C  e+             g++      r+aC ti+
  gi|13541577|ref|NP_111265.1| 37 LLYIKENlDQTLSFRYSCRMEICGSCGMEIQ------------GKP------RMACSTII 78
                                  455556666699***************9987............665......68888775 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.3
                                   SSSTTEEEE CS
                          Fer2  39 gCgtClvev 47 
                                   +Cg C++ +
  gi|13541577|ref|NP_111265.1| 148 KCGLCMAAC 156
                                   499999754 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 4.7
                                   TTEEEEEEEETTTH CS
                          Fer2   4 dgkevevevadget 17 
                                   +g +++vev+dge+
  gi|13541577|ref|NP_111265.1| 184 KGAKYRVEVVDGEN 197
                                   56677777777775 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   2.1   9.4e-07   0.00089       5      20 ..     142     157 ..     140     161 .. 0.87
   2 !    6.8   0.6    0.0081       7.6      13      23 ..     206     216 ..     201     220 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 9.4e-07
                        Fer4_6   5 dpdkCigCgdCvrvCP 20 
                                   ++  Ci Cg C+++CP
  gi|13541577|ref|NP_111265.1| 142 NYAMCIKCGLCMAACP 157
                                   6789************ PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0081
                        Fer4_6  13 gdCvrvCPega 23 
                                   g+C+ vCP g+
  gi|13541577|ref|NP_111265.1| 206 GECTEVCPKGV 216
                                   89******876 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.2       4.3     4e+03      94     105 ..      73      84 ..      51      89 .. 0.65
   2 !   12.3   0.1   0.00015      0.14      44      73 ..     128     158 ..      91     161 .. 0.64
   3 !    7.7   0.0    0.0042         4      52      76 ..     193     217 ..     175     225 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 4.3
                       Fer4_18  94 acdkvmeklgkp 105
                                   ac++++e l+ +
  gi|13541577|ref|NP_111265.1|  73 ACSTIIEDLKSD 84 
                                   788888888766 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00015
                       Fer4_18  44 kkalkekee.rkekgagdcidcescvkvcPt 73 
                                   k+  ++ e+ ++ ++ + ci+c+ c++ cP+
  gi|13541577|ref|NP_111265.1| 128 KELSQTPEQfHEYANYAMCIKCGLCMAACPI 158
                                   333344444144567899************7 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0042
                       Fer4_18  52 erkekgagdcidcescvkvcPtgid 76 
                                      e+g++ c   + c +vcP g++
  gi|13541577|ref|NP_111265.1| 193 VDGENGTARCHFAGECTEVCPKGVN 217
                                   345688999*************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 ?   -0.1   0.1       1.1     1e+03      14      39 ..      74      99 ..      57     103 .. 0.77
   2 !   16.9   0.5   5.3e-06     0.005       6      54 ..     144     159 ..     129     163 .. 0.61
   3 ?    3.3   0.1     0.096        91      40      52 ..     201     213 ..     181     225 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 1.1
                       Fer4_21 14 CliaCedtshqaieidaktvlkvved 39
                                  C +  ed   + i+i++ +++kv+ d
  gi|13541577|ref|NP_111265.1| 74 CSTIIEDLKSDKIRIEPLKHYKVIRD 99
                                  66666777788888888888888876 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 5.3e-06
                       Fer4_21   6 dkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPve 54 
                                   ++Ci+Cg+C+ aC                                 P+e
  gi|13541577|ref|NP_111265.1| 144 AMCIKCGLCMAAC---------------------------------PIE 159
                                   4555555555555.................................554 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.096
                       Fer4_21  40 eCvGCnlCssvCP 52 
                                   +C     C++vCP
  gi|13541577|ref|NP_111265.1| 201 RCHFAGECTEVCP 213
                                   5666667999999 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   1.6       1.2   1.2e+03       8      14 ..      57      63 ..      52      76 .. 0.71
   2 !   17.4   1.6   3.5e-06    0.0033       4      21 ..     140     157 ..     138     157 .. 0.92
   3 ?    4.7   1.2     0.038        36      13      21 ..     202     213 ..     199     214 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 1.2
                        Fer4_2  8 drCigCg 14
                                  ++C +Cg
  gi|13541577|ref|NP_111265.1| 57 EICGSCG 63
                                  4566665 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 3.5e-06
                        Fer4_2   4 vvdtdrCigCgaCvsaCP 21 
                                   +++ ++Ci Cg C  aCP
  gi|13541577|ref|NP_111265.1| 140 YANYAMCIKCGLCMAACP 157
                                   68999************9 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.038
                        Fer4_2  13 C...gaCvsaCP 21 
                                   C   g C+ +CP
  gi|13541577|ref|NP_111265.1| 202 ChfaGECTEVCP 213
                                   655579*****9 PP

>> Ribosomal_L27_C  Ribosomal L27 protein C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0     5e-06    0.0047      99     188 ..      21     115 ..      15     120 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 5e-06
               Ribosomal_L27_C  99 kreelskekleeklkelkevtekldksvsf..dnklelikyiseeek...qelknellkkLkekaseiltkkdkkevkelf 174
                                   ++ ++ k+k+++ l+ l  + e+ld+++sf  ++++e++ +   e +   +  ++ ++++Lk+   +i+  k  k +++l+
  gi|13541577|ref|NP_111265.1|  21 QKYNVPKDKVSTVLEGLLYIKENLDQTLSFrySCRMEICGSCGMEIQgkpRMACSTIIEDLKSDKIRIEPLKHYKVIRDLV 101
                                   6778889**********************96679*****99887755112557899******9977*************** PP

               Ribosomal_L27_C 175 kdasefltlseevk 188
                                    d + f+++ +evk
  gi|13541577|ref|NP_111265.1| 102 VDIDPFFDKYKEVK 115
                                   *********99996 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   1.6   6.9e-05     0.065      41      94 ..     107     158 ..      53     159 .. 0.65
   2 ?    4.4   0.1     0.071        67      77      94 ..     197     214 ..     179     218 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 6.9e-05
                       Fer4_22  41 lleeftkvaggenvrkekkerlrqrllhklsefkekfgesgCvGCgRCieacpv 94 
                                   +++++++v+    v ++   ++ + l +  ++f+e  +  +C+ Cg C++acp 
  gi|13541577|ref|NP_111265.1| 107 FFDKYKEVKPY--VIRDDDGKYDKELSQTPEQFHEYANYAMCIKCGLCMAACPI 158
                                   44455554444..445566788899999999999999***************95 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.071
                       Fer4_22  77 fgesgCvGCgRCieacpv 94 
                                    g+  C   g C+e+cp+
  gi|13541577|ref|NP_111265.1| 197 NGTARCHFAGECTEVCPK 214
                                   566666666667777665 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   16.3   0.6   1.1e-05      0.01       3      15 ..     145     157 ..     143     174 .. 0.90
   2 ?    3.4   0.5      0.14   1.4e+02       8      16 ..     206     214 ..     200     220 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.1e-05
                        Fer4_4   3 rCigCgsCvaaCP 15 
                                    Ci Cg C+aaCP
  gi|13541577|ref|NP_111265.1| 145 MCIKCGLCMAACP 157
                                   6***********9 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.14
                        Fer4_4   8 gsCvaaCPq 16 
                                   g C+ +CP 
  gi|13541577|ref|NP_111265.1| 206 GECTEVCPK 214
                                   57******6 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   3.5     3e-05     0.028       1      13 [.     146     158 ..     146     161 .. 0.89
   2 ?    9.8   1.4    0.0018       1.7       5      14 ..     206     215 ..     200     216 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3e-05
                        Fer4_3   1 CtgCgaCvevCPv 13 
                                   C+ Cg+C+ +CP 
  gi|13541577|ref|NP_111265.1| 146 CIKCGLCMAACPI 158
                                   ************4 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0018
                        Fer4_3   5 gaCvevCPvg 14 
                                   g C evCP+g
  gi|13541577|ref|NP_111265.1| 206 GECTEVCPKG 215
                                   58******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 ?   -2.3   0.2       9.3   8.8e+03      57      60 ..      59      62 ..      42      64 .. 0.69
   2 ?   11.9   2.6   0.00035      0.33      53      66 ..     145     158 ..     109     159 .. 0.62
   3 ?   14.5   8.7   5.4e-05     0.051       2      66 ..     146     214 ..     145     215 .. 0.61
   4 ?    7.1   0.9     0.011        11       2      15 ..     202     215 ..     201     227 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 9.3
                       Fer4_16 57 CdiC 60
                                  C+ C
  gi|13541577|ref|NP_111265.1| 59 CGSC 62
                                  4444 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00035
                       Fer4_16  53 aitgCdiCqdvCPa 66 
                                    ++ C+ C+++CP+
  gi|13541577|ref|NP_111265.1| 145 MCIKCGLCMAACPI 158
                                   45677777777764 PP

  == domain 3  score: 14.5 bits;  conditional E-value: 5.4e-05
                       Fer4_16   2 CgtCgkCaevCPtnaikek...kekeiearecisyntaekkdlaede.ekckkqeaitgCdiCqdvCPa 66 
                                   C++Cg C+ +CP +  +      ++ ++a + i+ n ++  +++ +    ++   ++++ + C++vCP 
  gi|13541577|ref|NP_111265.1| 146 CIKCGLCMAACPIEGSDPSylgPAPLAAAWRYIADNRDKGAKYRVEVvDGENGTARCHFAGECTEVCPK 214
                                   ************9887766222234444444444433333333333313333447889999*******6 PP

  == domain 4  score: 7.1 bits;  conditional E-value: 0.011
                       Fer4_16   2 CgtCgkCaevCPtn 15 
                                   C+  g+C+evCP +
  gi|13541577|ref|NP_111265.1| 202 CHFAGECTEVCPKG 215
                                   77777888888876 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       3.7   3.5e+03      22      46 ..      11      35 ..       9      38 .. 0.75
   2 ?    7.4   3.8    0.0069       6.5       5      17 ..     145     157 ..     142     158 .. 0.92
   3 ?    0.9   0.1      0.73   6.9e+02       5      18 ..     201     214 ..     183     215 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 3.7
                       Fer4_13 22 eddeggasvvaeqptseeekadaee 46
                                  ++d  g+ ++++ ++++++ + + e
  gi|13541577|ref|NP_111265.1| 11 RKDGSGKTYFQKYNVPKDKVSTVLE 35
                                  5677789999999998887776665 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0069
                       Fer4_13   5 tCiacgaCvelaP 17 
                                    Ci cg+C +++P
  gi|13541577|ref|NP_111265.1| 145 MCIKCGLCMAACP 157
                                   5***********9 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.73
                       Fer4_13   5 tCiacgaCvelaPd 18 
                                   +C   g C e++P+
  gi|13541577|ref|NP_111265.1| 201 RCHFAGECTEVCPK 214
                                   57777889999995 PP

>> Fer4_20  Dihydroprymidine dehydrogenase domain II, 4Fe-4S cluster
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.2       4.2   3.9e+03      83     103 ..      72      94 ..      51      97 .. 0.52
   2 ?    6.8   0.5    0.0058       5.4      19      46 ..     141     166 ..     125     183 .. 0.77
   3 ?    5.3   0.2     0.017        16      22      55 ..     200     231 ..     180     238 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 4.2
                                   CS-GG..GTTB.----HHHHHHH CS
                       Fer4_20  83 gaCvl..ekkgkepvaigklerf 103
                                   +aC++  e+ ++++++i+ l+++
  gi|13541577|ref|NP_111265.1|  72 MACSTiiEDLKSDKIRIEPLKHY 94 
                                   34544112223456666666665 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0058
                                   HHHTT----TT-HHHHCSTT---HHHHH CS
                       Fer4_20  19 eeAsRClqCkkapcvkgCPveidipefi 46 
                                   ++ + C++C    c+++CP+e + p+++
  gi|13541577|ref|NP_111265.1| 141 ANYAMCIKC--GLCMAACPIEGSDPSYL 166
                                   4445799**..89*******99988886 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.017
                                   TT----TT-HHHHCSTT---HHHHHHHHHTT-HH CS
                       Fer4_20  22 sRClqCkkapcvkgCPveidipefikkiaegnle 55 
                                   +RC      +c++ CP  ++    i+k+++  l+
  gi|13541577|ref|NP_111265.1| 200 ARCHFA--GECTEVCPKGVNPSFAIQKLRKTALK 231
                                   455544..68*********999889999887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       595  (0.0331865); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); 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 0.30s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 1479.81
//
Query:       gi|13541578|ref|NP_111266.1|  [L=567]
Description: succinate dehydrogenase flavoprotein subunit [Thermoplasma volcanium GSS1]
Scores for complete 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-94  315.8   0.1      6e-94  315.5   0.1    1.1  1  FAD_binding_2   FAD binding domain
    6.3e-43  145.8   0.0    9.8e-43  145.2   0.0    1.3  1  Succ_DH_flav_C  Fumarate reductase flavoprotein C-term
    0.00014   21.2   1.1      0.012   14.9   0.2    3.0  3  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    0.00015   21.3   2.3      0.031   13.6   2.0    2.7  3  FAD_oxidored    FAD dependent oxidoreductase
     0.0055   15.8   0.4      0.017   14.3   0.4    1.8  1  GIDA            Glucose inhibited division protein A
  ------ inclusion threshold ------
      0.013   14.8   2.7       0.24   10.7   0.6    2.2  2  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
      0.029   13.1   0.8      0.051   12.3   0.8    1.4  1  HI0933_like     HI0933-like protein
      0.078   12.2   0.3       0.67    9.2   0.1    2.3  2  Thi4            Thi4 family
      0.099   11.7   0.2      0.099   11.7   0.2    1.5  2  Lycopene_cycl   Lycopene cyclase protein


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 !  315.5   0.1     3e-97     6e-94       1     416 [.       7     386 ..       7     387 .. 0.97

  Alignments for each domain:
  == domain 1  score: 315.5 bits;  conditional E-value: 3e-97
                                   SEEEE--SHHHHHHHHHHHHTTT..-EEEEESSSGGGSGGGG--S-EE-TT..SSGGSTC.CHHHHHHHHHHHHTTT-S-H CS
                 FAD_binding_2   1 DviViGsGlAGLaAAleaaeaGl..kvavvekeqefggatawsqGgidavlspeqkkagikdspelhrtdtlkaldeladq 79 
                                   DviV G+G+AGL+AA++aae ++  +v vv+k  + +++++ ++Gg  avl+        kds +lh++dt+k++d+ladq
  gi|13541578|ref|NP_111266.1|   7 DVIVLGGGMAGLRAAVAAAEYNKniSVGVVSKLYPLRSHSVSAEGGTSAVLN-------PKDSFDLHAYDTIKGSDYLADQ 80 
                                   9*******************555469*************************3.......359******************* PP

                                   HHHHHHHHTHHHHHHHHHHTT----BCCTSSB-EEE-TT-SSTEEEE-.STT-......HHHHHHHHHHHHHHTCT.EEEE CS
                 FAD_binding_2  80 plveafveaapeavdeLeelgvpfsrtedgpvdvrelGglsatartlhdaadarretlvtghallarlvesarkag.vdfq 159
                                   ++ve fv+ +pe +    ++g+p+sr++dg++ +r++G+ls + r  + aad+      tg++++ +l+ +a++++ ++f+
  gi|13541578|ref|NP_111266.1|  81 DAVEEFVRLVPEQIYTTDHWGCPWSRNPDGTISQRDFGALSFP-RATF-AADK------TGFHVMQTLFSRALRYEnIHFY 153
                                   *******************************************.9999.****......********************** PP

                                   ESEEEEEEEECTTEEEEEEEEETTTTCEEEEEESEEEE-----GG..........GSSSBSSGTT-S-HHHHHHHCTTSSE CS
                 FAD_binding_2 160 erteadeLivedgrvtGavvenpesgrevrirakavvlatgGfgrallkellgaaaeaettnapavtGdglalalragaal 240
                                   ++++a+++  ++gr++  +  n+++g  v +++ka + a+gG+gr           ++ +t a+ v+Gdg+a+a+rag++l
  gi|13541578|ref|NP_111266.1| 154 NEYFATSMFLDNGRMNSLTTINLRTGDFVVFQSKAFIFAAGGAGR----------LYQFSTYAHSVSGDGDAIAYRAGIPL 224
                                   *********************************************..........************************** PP

                                   ES..TT-EEEEEEEET....TTTBB--THHHHTT-EEE-TTSSBTH.......GGGS-HHHHHHHHH.HHHHTTTS..... CS
                 FAD_binding_2 241 nddrmeevqfhPtslvpirdgsgiLitealrgeGgilvdkdGrrFm.......nelasrdvvsrailekeiaeggs..... 309
                                   +d  me++qfhPt+lv    +sgiLite++r +Gg+l++ + +rFm        e asrdvvsrai+  ei+ g++     
  gi|13541578|ref|NP_111266.1| 225 KD--MEFIQFHPTGLV----PSGILITEGARADGGYLLNGENKRFMqayapnkLEKASRDVVSRAIM-WEIEAGRGvkgey 298
                                   **..************....*******************************998999**********.999999999**** PP

                                   ..CCBEEEE-TT.SSHHHHHHHSHHHHHHHHHCCT......S-TTTSEEE.......EEEEEEEES-EEEBETTSBESTTE CS
                 FAD_binding_2 310 ..eanvyldashgldaegleatleaineeaangldkdfgrgidpadrpipgpfyavkvvpaqhytmgGvetdengrvldad 388
                                      ++v+ld++h   a+ l+++l+ i e+a+++ +      id+ ++ ip       v+pa+hytmgG+  + ++ +    
  gi|13541578|ref|NP_111266.1| 299 gdMEYVWLDLRH--MADVLDERLPMITEIAKKFNG------IDAHTELIP-------VHPATHYTMGGIDSNVRTTT---- 360
                                   *988********..999***************999......*********.......***********988888888.... PP

                                   EESSBTEEE-STCEESSSSTTS--TTHH CS
                 FAD_binding_2 389 gqpipGLYAaGevaaggvhganrlgGns 416
                                       +G +AaGe a++++hganrlg+ns
  gi|13541578|ref|NP_111266.1| 361 --DYSGIFAAGENACVSIHGANRLGSNS 386
                                   ..*************************8 PP

>> Succ_DH_flav_C  Fumarate reductase flavoprotein C-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  145.2   0.0   4.9e-46   9.8e-43       1     128 []     442     567 .]     442     567 .] 0.97

  Alignments for each domain:
  == domain 1  score: 145.2 bits;  conditional E-value: 4.9e-46
                                   .HHHHHHHHHHSSSSB-HHHHHHHHHHHHHHHHHHTTB--S---SSS-HHHHHHHHHHHHHHHHHHHHHHHHH--S-BTTB CS
                Succ_DH_flav_C   1 rkeLgkimqkkvgvfRteegLkealkelkelrerlknvkvtdkskvaNqelvealelanllelAeaiaksAlaRkESrGaH 81 
                                   r++L+  m+k+vg+fR+e+gL++ lk++k+l+er++n++++dks+++N el+ ale+  +l++Ae+i+++Al RkESrGaH
  gi|13541578|ref|NP_111266.1| 442 REDLRINMDKNVGIFRDENGLNTSLKNIKQLKERYNNISIQDKSSTFNMELEWALEVGFMLDIAEVITTGALLRKESRGAH 522
                                   6789999************************************************************************** PP

                                   EBTTS-SEETTT-SEEEEE...TT-SS-EEEEEE--GGG--S---SS CS
                Succ_DH_flav_C  82 aredfperdDenwlkhtlasldaakeeveleyepveletlkpkeRsY 128
                                   +r+d+p+rdDen+lkht+a+++  k+ ++++y+pv +++ +p+ R+Y
  gi|13541578|ref|NP_111266.1| 523 YRKDYPNRDDENYLKHTIATYT--KDGPRITYKPVVITKWQPTVRTY 567
                                   *******************666..569*******************9 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.2     6e-06     0.012       2      28 ..       7      35 ..       6      60 .. 0.80
   2 ?    1.3   0.0     0.083   1.7e+02     256     278 ..     350     372 ..     329     387 .. 0.69
   3 ?    1.8   0.0     0.057   1.1e+02       8      71 ..     394     483 ..     394     513 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 6e-06
                                  SEEEE--SHHHHHHHHHHHH..HTS-EEE CS
                                  xxxxxxxxxxxxxxxxxxxx..xxxxxxx RF
                   Pyr_redox_2  2 dvvviGgGpAGlaaaltlaq..agakvtl 28
                                  dv+v+GgG+AGl+aa  +a+  +++ v +
  gi|13541578|ref|NP_111266.1|  7 DVIVLGGGMAGLRAAVAAAEynKNISVGV 35
                                  8*******************444555555 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.083
                                   TEEE--TTSBESSTTEEE-GGGC CS
                                   xxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2 256 ggivvdeflrtnvpgiyaiGDva 278
                                   ggi  + +  t   gi+a+G  a
  gi|13541578|ref|NP_111266.1| 350 GGIDSNVRTTTDYSGIFAAGENA 372
                                   6666666666679*******877 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.057
                                   -SHHHHHHHHHHHHHTS-EEEEE...TTHCHHHCSHHHHCHHHHHHHHHHHHH.......................HHHHC CS
                                   xxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxx.......................xxxxx RF
                   Pyr_redox_2   8 gGpAGlaaaltlaqagakvtlve...legtclnggcllskallgvaedaeias.......................evvkk 62 
                                   g++AG++aa+++ ++ +  ++v+    e+   +++ l  +  ++va+ +e ++                       +++k+
  gi|13541578|ref|NP_111266.1| 394 GNVAGVSAAKYAMEHDIPDLVVSnveNEEKRIWDDLLKRNGGENVAKIREDLRinmdknvgifrdenglntslkniKQLKE 474
                                   678999999999998666555533437888888888888888888888887778888888877777766666655544444 PP

                                   HHHHCCCCH CS
                                   xxxxxxxxx RF
                   Pyr_redox_2  63 lnqgielll 71 
                                     ++i    
  gi|13541578|ref|NP_111266.1| 475 RYNNISIQD 483
                                   444444444 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   2.0   1.6e-05     0.031       1      23 [.       7      29 ..       7      38 .. 0.90
   2 !    4.8   0.0    0.0074        15      86     156 ..     134     207 ..      82     307 .. 0.84
   3 ?   -1.2   0.0      0.51     1e+03     400     419 ..     390     410 ..     376     421 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.6e-05
                  FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGa 23
                                  Dv+V GGg+aG+ AA+aAa+  +
  gi|13541578|ref|NP_111266.1|  7 DVIVLGGGMAGLRAAVAAAEYNK 29
                                  9******************8776 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.0074
                  FAD_oxidored  86 pevakavleemlaeagvtvllntrlvevekegkriesvtveske.g.rktirAkvfiDAT.gdGdlaalaGvpy 156
                                    +v+++++   l+ ++++ + + +++++  +++r++s+t+ + + g   ++++k fi A  g G l  ++   +
  gi|13541578|ref|NP_111266.1| 134 FHVMQTLFSRALRYENIHFYNEYFATSMFLDNGRMNSLTTINLRtGdFVVFQSKAFIFAAgGAGRLYQFSTYAH 207
                                   5899**************************999******99999999999******965514566666555555 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.51
                  FAD_oxidored 400 cmalGqAaGv.aAalaleegv 419
                                   c+alG  aGv aA +a+e+++
  gi|13541578|ref|NP_111266.1| 390 CLALGNVAGVsAAKYAMEHDI 410
                                   899999999934556777666 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.4   8.3e-06     0.017       1      24 [.       7      30 ..       7      51 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 8.3e-06
                                  CEEEE-SSHHHHHHHHHHHHTT-- CS
                          GIDA  1 dviViGgGhAGceAAlaaarlGak 24
                                  dviV+GgG+AG+ AA+aaa+ + +
  gi|13541578|ref|NP_111266.1|  7 DVIVLGGGMAGLRAAVAAAEYNKN 30
                                  8******************87655 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.6   0.00012      0.24      30      55 ..       7      32 ..       3      40 .. 0.87
   2 ?    3.7   0.1     0.016        31       3      31 ..     376     404 ..     374     406 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00012
                                  EEEEESTSHHHHHHHHHHHHTT-EEE CS
                   AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVt 55
                                   v+v+GgG+aGl A+ +a++ + ++ 
  gi|13541578|ref|NP_111266.1|  7 DVIVLGGGMAGLRAAVAAAEYNKNIS 32
                                  69***************998887765 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.016
                                   HHHHHHCSCGCTSEEETTCEETCB---EE CS
                   AlaDh_PNT_C   3 leaakalekffggkgtlaGgvpgvepakv 31 
                                   +++a+ l   ++ + +++G v gv++ak 
  gi|13541578|ref|NP_111266.1| 376 IHGANRLGSNSTNECLALGNVAGVSAAKY 404
                                   689************************96 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.8   2.5e-05     0.051       2      28 ..       7      33 ..       6      39 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.5e-05
                                  SEEEE--SHHHHHHHHHHHHTT--EEE CS
                   HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVll 28
                                  dviv+GgG AGl aA++aa+ +k++ +
  gi|13541578|ref|NP_111266.1|  7 DVIVLGGGMAGLRAAVAAAEYNKNISV 33
                                  8******************99988765 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.1   0.00034      0.67      16      47 ..       4      36 ..       1      53 [. 0.83
   2 ?    0.0   0.0      0.21   4.1e+02     208     233 ..     358     384 ..     319     385 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00034
                                  TEEEEEEE--SHHHHHHHHHHHHC.TTS-EEEE CS
                          Thi4 16 aesDvvivGaGssGLtaayylakk.pdlkvail 47
                                  ++ Dv++ G+G +GL aa   a+   ++ v ++
  gi|13541578|ref|NP_111266.1|  4 IKEDVIVLGGGMAGLRAAVAAAEYnKNISVGVV 36
                                  578***************999987567776665 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.21
                                   ECEEETTEEE-THH.HHHHHT-EB--S CS
                          Thi4 208 trevvpnlyvaGme.vaevdganRmGp 233
                                   t   + ++++aG +    ++ganR+G+
  gi|13541578|ref|NP_111266.1| 358 TTTDYSGIFAAGENaCVSIHGANRLGS 384
                                   45568999*9997515689******96 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.2     5e-05     0.099       1      30 [.       7      36 ..       7      47 .. 0.91
   2 ?   -4.2   0.1       3.2   6.4e+03     268     276 ..     341     349 ..     338     362 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5e-05
                 Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvli 30
                                  Dv+v G+G Agl+ A   +e +++++v+++
  gi|13541578|ref|NP_111266.1|  7 DVIVLGGGMAGLRAAVAAAEYNKNISVGVV 36
                                  9***************************99 PP

  == domain 2  score: -4.2 bits;  conditional E-value: 3.2
                 Lycopene_cycl 268 vhPaTGYsv 276
                                   vhPaT Y++
  gi|13541578|ref|NP_111266.1| 341 VHPATHYTM 349
                                   89***9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (567 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); 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: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 3540.93
//
Query:       gi|13541579|ref|NP_111267.1|  [L=280]
Description: DMT family permease [Thermoplasma volcanium GSS1]
Scores for complete 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  118.6  35.2    9.7e-19   67.9  16.1    2.1  2  EamA       EamA-like transporter family
  ------ inclusion threshold ------
        4.7    7.2  16.9       0.89    9.5   1.8    3.4  3  RseC_MucC  Positive regulator of sigma(E), RseC/MucC


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 !   57.0  11.1   2.5e-19   2.3e-15       6     134 ..       6     124 ..       1     127 [. 0.90
   2 !   67.9  16.1   1.1e-22   9.7e-19       2     135 ..     136     266 ..     135     268 .. 0.97

  Alignments for each domain:
  == domain 1  score: 57.0 bits;  conditional E-value: 2.5e-19
                          EamA   6 lallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegklaklslkdwllllllgllgtvlafllffyal 86 
                                   +++  ++f ++++ ++k ++++vsp  + ++r+l++g++ll++a   ++++          ++ll+++ ++ +  ++ y+l
  gi|13541579|ref|NP_111267.1|   6 YLIPYVIFTSFSYYFAKNGVEQVSPSLFMGIRYLLSGLILLPFAKKLRITK---------NIILLAIMTSTST-AFWAYGL 76 
                                   5666789***************************************99999.........5566665544444.68***** PP

                          EamA  87 kktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvll 134
                                    ++s+++ +++++ +P+f+l +++l   e++++ +++giv+++ Gv++
  gi|13541579|ref|NP_111267.1|  77 LYVSPAESAVLSYSMPIFSLPIAFLMVSERPSKVEIIGIVIGFTGVII 124
                                   **********************************************97 PP

  == domain 2  score: 67.9 bits;  conditional E-value: 1.1e-22
                          EamA   2 lgillallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegklaklslkdwllllllgllgtvlafllf 82 
                                   +g++l +  a+fwa+ +v+ ++ l++ +p+++++++fli++++l+++ +l  + +  +sl+    ++ +++lg++l f+l+
  gi|13541579|ref|NP_111267.1| 136 FGAVLTISNAVFWASFTVFYRK-LKEEDPFSTNAMQFLIGSLFLFALVPLDPSHN--FSLSFAVDVIWMATLGGALQFILW 213
                                   6999******************.7*********************9999998888..************************ PP

                          EamA  83 fyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvlli 135
                                   +  +k + + +++++ + +P+ft+il+v+l +e ++ + ++g+++++ G+++ 
  gi|13541579|ref|NP_111267.1| 214 NFMVKISAVNRITVLAFAVPIFTTILGVILSHEIPSGLAIAGVIIMFTGIFVS 266
                                   **************************************************986 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 ?   -1.2   0.1       0.2   1.8e+03      71     117 ..       6      51 ..       4      65 .. 0.55
   2 ?    6.4   2.1   0.00089         8      65     109 ..      83     127 ..      61     137 .. 0.88
   3 ?    9.5   1.8    0.0001      0.89      61     110 ..     220     265 ..     214     272 .. 0.72

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.2
                     RseC_MucC  71 YllPllllilgallgsallgssellaalgallglvlgflivrllskr 117
                                   Yl+P +++  +   +    g +++   l++ +  +l+ li+  ++k+
  gi|13541579|ref|NP_111267.1|   6 YLIPYVIFTSFSYYFAKN-GVEQVSPSLFMGIRYLLSGLILLPFAKK 51 
                                   788877776666555555.3444444444444444444444444444 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.00089
                     RseC_MucC  65 kaallvYllPllllilgallgsallgssellaalgallglvlgfl 109
                                   ++a+l Y +P++ l ++ l++s    + e++ +++++ g++++ +
  gi|13541579|ref|NP_111267.1|  83 ESAVLSYSMPIFSLPIAFLMVSERPSKVEIIGIVIGFTGVIIYGI 127
                                   6899*********977777777666899***********999865 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.0001
                     RseC_MucC  61 ksllkaallvYllPllllilgallgsallgssellaalgallglvlgfli 110
                                   +++ + ++l++++P+++ ilg++l + +    ++la+ +++++++ g+++
  gi|13541579|ref|NP_111267.1| 220 SAVNRITVLAFAVPIFTTILGVILSHEIP---SGLAI-AGVIIMFTGIFV 265
                                   6788999*********************4...44444.344444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       683  (0.0380947); expected 358.6 (0.02)
Passed bias filter:                      218  (0.0121591); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.35s 00:00:00.96 Elapsed: 00:00:00.56
# Mc/sec: 1516.70
//
Query:       gi|161760541|ref|NP_111268.2|  [L=150]
Description: molybdenum cofactor biosynthesis protein MoaC [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-41  140.8   0.6    3.2e-41  140.6   0.6    1.0  1  MoaC      MoaC family


Domain annotation for each model (and alignments):
>> MoaC  MoaC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  140.6   0.6   1.8e-45   3.2e-41       1     135 [.       8     147 ..       8     148 .. 0.98

  Alignments for each domain:
  == domain 1  score: 140.6 bits;  conditional E-value: 1.8e-45
                                    E---TTS--EEEEEEEEEEEEE-HHHHHHHHTTSSTTB-HHHHHHHHHHHHHHHHHHHSTT-----EEEEEEEEEEETTT CS
                           MoaC   1 mvdvsekeetkrtAvAegrvklseetlelikekklkkGdvlavariagimaaKktseliplcHplpltkveveleleeee 80 
                                    m+++s+k++++r+A+A gr++l++et+++ik++++kkG+v++++r  g+m aK+t   ip+cH++p++ v+v+++l   e
  gi|161760541|ref|NP_111268.2|   8 MINISRKDVVARKATAVGRIYLRKETITAIKNNQVKKGNVIEISRAVGTMYAKNTFLQIPYCHNIPIEGVDVDFSLG--E 85 
                                    99************************************************************************987..7 PP

                                    TEEEEEEEEEEEESS--HHHHHHHHHHHHHHHHHHHTTTHTT.......-EEEEEEEEEEES CS
                           MoaC  81 esveieatvktegktGvemEALtavsvaaltvyDmvKavdke.......mvieevrlveKsg 135
                                    + ve++++++t+ ktG+emEA+ +v+ a+l+++DmvK ++k+       ++ie v++++K++
  gi|161760541|ref|NP_111268.2|  86 NYVEVTCSTTTSYKTGIEMEAINCVNGALLNIWDMVKYLEKDetgnypeTRIEGVHVIKKTK 147
                                    9****************************************99*****************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       520  (0.0290033); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 965.64
//
Query:       gi|13541581|ref|NP_111269.1|  [L=77]
Description: hypothetical protein TVN0750, partial [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-14   54.4   0.4    1.3e-14   54.3   0.4    1.0  1  Y1_Tnp    Transposase IS200 like


Domain annotation for each model (and alignments):
>> Y1_Tnp  Transposase IS200 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.3   0.4   7.3e-19   1.3e-14      45     120 ..       1      73 [.       1      74 [. 0.96

  Alignments for each domain:
  == domain 1  score: 54.3 bits;  conditional E-value: 7.3e-19
                        Y1_Tnp  45 lelmpDHvHllvelppklsiskivkalkgassrlinkefpelkkkklkkeslWqrgYfvstvgeasletvkrYIen 120
                                   +e+m+D v l+++++pk+ +  +v+++kg+ s+ ++ ef+el++k     +lW ++ f+s+vg+++l++vk+YIe+
  gi|13541581|ref|NP_111269.1|   1 MEIMQDNVYLILDVNPKMGVYYVVNRIKGYVSYTLRVEFHELRRKLS---TLWIHSKFISSVGSVTLDAVKKYIEE 73 
                                   79*****************************************8864...6***********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       525  (0.0292822); 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: 0.33u 0.24s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 593.46
//
Query:       gi|13541582|ref|NP_111270.1|  [L=162]
Description: molybdopterin biosynthesis protein [Thermoplasma volcanium GSS1]
Scores for complete 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   76.4   0.0    2.1e-21   76.1   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 !   76.1   0.0   1.2e-25   2.1e-21       2     143 ..      18     153 ..      17     154 .. 0.87

  Alignments for each domain:
  == domain 1  score: 76.1 bits;  conditional E-value: 1.2e-25
                                   EEEE-HHHHTTSSGBHHHHHHHHHHHTTSEEEEEEEEE-SSHHHHHHHHHHHHHTSSEEEEESS-SSSTT--HHHHHHHHH CS
                 MoCF_biosynth   2 vitvGdellsgkieDtngpllaellkelgvevskytvvpDdeeeikeallaaleeadviittGGtGptpdDvtpealaklf 82 
                                   v+tv++++  +  +D++g++l e+l   g++ + ++vv+Dd+ +i +a+ +++++ d+ ++ GGtG++++Dvt  +l+++ 
  gi|13541582|ref|NP_111270.1|  18 VVTVSSTRNIN--NDESGKILEEKL---GFHNISREVVRDDPVRILSAIFSKWDDFDAFVLNGGTGISKYDVTTNTLRRIA 93 
                                   56666666666..799999998876...599999***************777799************************** PP

                                   SEE-HHHHHHHHHHHHHHCCTTSHGGGGGGE.EE.....TTEEEEE-SSHHHHHHHHHHHHHGGHH CS
                 MoCF_biosynth  83 ekelegfeeafrrvslkpgkpvgvapgailsrav.....gktiigLPGspkavkealeeillpale 143
                                   +ke++gf+e+frr++         + + +ls+a      gk+i+ LPG p+a   ++ +il ++l+
  gi|13541582|ref|NP_111270.1|  94 DKEIPGFGELFRRMGESD-----AGVFSYLSGAGmfivyGKPIFSLPGAPSAQPIGASLIL-DILD 153
                                   *****************8.....6777778887789999999*********9888888887.6665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1108.10
//
Query:       gi|13541583|ref|NP_111271.1|  [L=340]
Description: threonine synthase [Thermoplasma volcanium GSS1]
Scores for complete 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-51  175.5   0.0    1.9e-51  175.3   0.0    1.0  1  PALP             Pyridoxal-phosphate dependent enzyme
  ------ inclusion threshold ------
      0.063   13.1   0.2      0.099   12.5   0.2    1.3  1  DFP              DNA / pantothenate metabolism flavoprotein
       0.46   10.1   4.8        1.2    8.8   4.8    1.7  1  RecR             RecR protein
        0.8    9.5   3.0        1.6    8.5   3.0    1.5  1  zinc_ribbon_2    zinc-ribbon domain
        5.8    6.6   6.3          3    7.6   0.3    2.4  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 !  175.3   0.0   5.2e-55   1.9e-51       4     294 .]      54     334 ..      51     334 .. 0.88

  Alignments for each domain:
  == domain 1  score: 175.3 bits;  conditional E-value: 5.2e-55
                                   CSSS--EEEECCTCCCCCCEEEEEEGGGSTTSBTTHHHHHHHHHH...HHTTTTTSEEEEEBSSHHHHHHHHHHHHHT-EE CS
                          PALP   4 gigpTPlvrlprlskelgvplflKlEslnptgSfKdRgaeyllar...lkegtgaktvveassGNhgralAaaaallGlkv 81 
                                   g+ +TP+v            + +K ++ +pt S+KdRg   l+++   +++ +   t+ e ssGN+g+++Aa++a++Glkv
  gi|13541583|ref|NP_111271.1|  54 GEVETPIVNYGE--------VKFKIDYYQPTFSYKDRGSKVLISHirdITPSQNISTISEDSSGNAGASIAAYGAAAGLKV 126
                                   555666666655........669**********************655555599*************************** PP

                                   EEEEETTS-HHHHHHHHHTT-EEEEECCHHHHHHHHHHHHHHHSTTCEE--TTTSHHHHHHHHTHHHHHHHHTTTTEEEEE CS
                          PALP  82 tivvpadaspekvallrllGaevvevggdydeavaaaaelaaegegaylvsqfdnptviegygtiglEileqlggkpdavv 162
                                    ++vp+++s +k +++  +Gae v+++g+ ++      ++aae+ g+y++s+   p   +g  ++++Ei  q+ + pd+++
  gi|13541583|ref|NP_111271.1| 127 KVYVPKTVSGQKFKQILVYGAEAVKIDGNREDV-----QIAAENSGYYYASHVLRPEFRDGIRSLAYEIFMQTEKMPDHIF 202
                                   **************************8855554.....4455559************************************ PP

                                   EE-SSSHHHHHHHHHHHH..HSTT......-EEEEEEECTTCGGTTCCS..S.SS..B.SSS.CCSTCS..CGTTCCHHHH CS
                          PALP 163 vpvGgGgliaGiaaglke..rrpd......vrvigvepegsdalarslragrrvtvpvsdtiadglavg..spselafell 233
                                    pv+ G l+ G++ g+ +  r  +      +++++v++e ++++ + l   + ++ + +++iad+l  +     e+ +++ 
  gi|13541583|ref|NP_111271.1| 203 IPVSAGTLLIGLYSGFEHlfR--SgeiekiPNIVAVQAEAVSPVCAKLNGEQFDENSNATSIADALVSKkpILLEKMLSI- 280
                                   ******************763..3337789******************88888888889**********84444555555. PP

                                   SEEEEEEEEEEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHHHHHHHHCCTTCEEEEEEE-B CS
                          PALP 234 drlvdeivtvsdeealeamrllarregivvepssaaalaalklreagelkegdrvvviltg 294
                                    r +++++ vsd+e++ea ++la   gi +e ss +++aa+   ++++l+++   +++ltg
  gi|13541583|ref|NP_111271.1| 281 LRENGKCIRVSDNEIIEARKELA-LKGIYAEYSSSTVFAAY---KKKKLENS---LLVLTG 334
                                   566777*****************.*****************...99999999...888887 PP

>> DFP  DNA / pantothenate metabolism flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2   2.8e-05     0.099      19      52 ..      99     132 ..      82     164 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.8e-05
                                   TTEEEEE----HHHHHHHHHHHHTT-EEEEEE-S CS
                           DFP  19 pVRfisNrSSGkmGyalAeaaaarGaeVtlvsgp 52 
                                   ++ +is  SSG  G+++A+  aa+G +V++   +
  gi|13541583|ref|NP_111271.1|  99 NISTISEDSSGNAGASIAAYGAAAGLKVKVYVPK 132
                                   6779************************974443 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   4.8   0.00032       1.2      16      36 ..       4      26 ..       3      28 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00032
                                  -EE-TTT--EESSS..S-CCCCS CS
                          RecR 16 vrhCsrCgnlteed..lCaICsd 36
                                  + +C rCgn+  ++   C++C +
  gi|13541583|ref|NP_111271.1|  4 IVRCIRCGNVRKNEelRCPVCGN 26
                                  678*******7776435****65 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   3.0   0.00045       1.6       1      20 [.       6      25 ..       6      26 .. 0.94

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00045
                 zinc_ribbon_2  1 fCpnCGaelqdnakFCpyCG 20
                                  +C +CG+  ++++  Cp CG
  gi|13541583|ref|NP_111271.1|  6 RCIRCGNVRKNEELRCPVCG 25
                                  699****************9 PP

>> Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   1.5     0.067   2.4e+02       8      15 ..       6      13 ..       3      15 .. 0.88
   2 ?    7.6   0.3   0.00083         3       3      18 ..      15      30 ..      13      32 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.067
                                  E-TTT--E CS
               Desulfoferrod_N  8 kCevCGni 15
                                  +C  CGn+
  gi|13541583|ref|NP_111271.1|  6 RCIRCGNV 13
                                  9******8 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.00083
                                  TT-EEE-TTT--EEEE CS
               Desulfoferrod_N  3 klevYkCevCGniVeV 18
                                  k+e  +C vCGn  e+
  gi|13541583|ref|NP_111271.1| 15 KNEELRCPVCGNLYEI 30
                                  67778*******8776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (340 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       570  (0.0317921); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 2323.38
//
Query:       gi|13541584|ref|NP_111272.1|  [L=150]
Description: hypothetical protein TVN0753 [Thermoplasma volcanium GSS1]
Scores for complete sequence (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   32.2   0.8      3e-07   31.2   0.8    1.7  1  Pilin_N    Archaeal Type IV pilin, N-terminal
  ------ inclusion threshold ------
       0.05   13.0   0.0       0.08   12.3   0.0    1.4  1  Flp1_like  Putative Flagellin, Flp1-like, domain


Domain annotation for each model (and alignments):
>> Pilin_N  Archaeal Type IV pilin, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   0.8   3.4e-11     3e-07       1      59 [.       4      63 ..       4     112 .. 0.87

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 3.4e-11
                       Pilin_N  1 eAVSpViGviLmvaitvIlaAviaafvlgl.asneekapqasievkidssastgknavsl 59
                                  +AVSp+i  iL++aitv laA + + v+ +  + +  +pqa  +v   s++s+ ++ +++
  gi|13541584|ref|NP_111272.1|  4 KAVSPIIATILLIAITVALAATFYTEVTPYfTEAQYYTPQAVTDVMNVSNGSSFSYDIYI 63
                                  69**************************99999********9988755555544444555 PP

>> Flp1_like  Putative Flagellin, Flp1-like, domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0     9e-06      0.08      11      33 ..       9      31 ..       1      37 [. 0.85

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 9e-06
                     Flp1_like 11 vVEiiLIivVligLvliFKkqit 33
                                  +++ iL+i++ ++L+  F +++t
  gi|13541584|ref|NP_111272.1|  9 IIATILLIAITVALAATFYTEVT 31
                                  89**************9988877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       667  (0.0372023); 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:                         2  (0.000111551); expected 0.2 (1e-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: 1096.32
//
Query:       gi|13541585|ref|NP_111273.1|  [L=366]
Description: hypothetical protein TVN0754 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score 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   11.5   0.5       0.26   11.0   0.5    1.2  1  zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
        0.2   11.7   0.6       0.32   11.0   0.6    1.3  1  Zn_Tnp_IS1595  Transposase zinc-ribbon domain
        0.2   11.6   1.3        2.5    8.1   0.0    2.2  2  Nudix_N_2      Nudix N-terminal
        1.9    8.2   6.1         18    5.1   6.1    2.1  1  zf-RRN7        Zinc-finger of RNA-polymerase I-specific TFIIB


Domain annotation for each model (and alignments):
>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.5   5.9e-05      0.26       6      29 ..     310     333 ..     308     335 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 5.9e-05
                 zf-NADH-PPase   6 CgrCGaptepaeggwarvCpaCgl 29 
                                   C+ CG+ +  ++ ++++ C++C +
  gi|13541585|ref|NP_111273.1| 310 CPECGGVVFHVKEDMSLECDHCHH 333
                                   **********************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 ?   11.0   0.6   7.2e-05      0.32      19      45 ..     308     333 ..     306     334 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 7.2e-05
                 Zn_Tnp_IS1595  19 fvCPhCgsrkayriktrglfqCkeCrk 45 
                                    vCP Cg+  ++  ++   ++C +C++
  gi|13541585|ref|NP_111273.1| 308 SVCPECGGVVFHVKED-MSLECDHCHH 333
                                   58*****766555555.9*******98 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.0   0.00055       2.5      20      31 ..     305     316 ..     295     319 .. 0.83
   2 ?    1.9   0.5      0.05   2.2e+02      25      31 ..     328     334 ..     326     335 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00055
                                   S-EEEETTTTEE CS
                     Nudix_N_2  20 reRlvCpaCgti 31 
                                     R vCp Cg +
  gi|13541585|ref|NP_111273.1| 305 FIRSVCPECGGV 316
                                   57*******987 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.05
                                   ETTTTEE CS
                     Nudix_N_2  25 CpaCgti 31 
                                   C++C+++
  gi|13541585|ref|NP_111273.1| 328 CDHCHHV 334
                                   *****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 ?    5.1   6.1     0.004        18       6      30 ..     309     334 ..     306     335 .. 0.93

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.004
                       zf-RRN7   6 pCgvCgcrsftl.ddGfyyCrrChtq 30 
                                   +C++Cg++ f+  +d    C++Ch++
  gi|13541585|ref|NP_111273.1| 309 VCPECGGVVFHVkEDMSLECDHCHHV 334
                                   8**************9999*****98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1265  (0.0705561); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); 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):               4  [number of targets reported over threshold]
# CPU time: 0.59u 0.26s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 2426.34
//
Query:       gi|13541586|ref|NP_111274.1|  [L=59]
Description: metal-binding protein [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-14   53.9   0.0    1.8e-14   53.7   0.0    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 !   53.7   0.0   9.9e-19   1.8e-14       2      56 .]       3      57 ..       2      57 .. 0.97

  Alignments for each domain:
  == domain 1  score: 53.7 bits;  conditional E-value: 9.9e-19
                       DUF1059  2 kefkCgDvgpdCgfeitaeteeEvlrkvaeHakaaHglteippelvekiksaIkd 56
                                  + f+C+D g+dC+++ + e +e++ + v+ H ++aHg+ + ++e+++k+ s Ik+
  gi|13541586|ref|NP_111274.1|  3 YVFRCRDYGFDCSYTLEEERKEDIPPMVKMHLRYAHGIYDFTDEVRDKVLSVIKE 57
                                  79************************************************99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       381  (0.0212505); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 392.29
//
Query:       gi|13541587|ref|NP_111275.1|  [L=236]
Description: metal-dependent hydrolase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     0.0018   16.9   0.4      0.003   16.1   0.1    1.4  2  tRNA-synt_2c  tRNA synthetases class II (A)
     0.0052   15.2   0.0      0.006   15.0   0.0    1.1  1  Birna_RdRp    Birnavirus RNA dependent RNA polymerase (VP1)
  ------ inclusion threshold ------
       0.12   12.5   0.1       0.36   10.9   0.1    1.8  1  BCL_N         BCL7, N-terminal conserver region


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 !   16.1   0.1     5e-07     0.003     489     551 ..      30      92 ..      22      93 .. 0.92
   2 ?   -2.8   0.0      0.27   1.6e+03     103     135 ..     147     181 ..     139     227 .. 0.57

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 5e-07
                                   ESEEXXXXSSSSCSXXXEEEEESSEEEEESEEEEETTEEEEEXSS.XSXXXTTSEEEEEEXHH CS
                  tRNA-synt_2c 489 LdrTpfYaesGGqigDeGliekegaefrvkdvqkakgvvlhkgkleegklkvgdkvkaevdee 551
                                   +d++ fY++  G  +D+G++  eg+e +++d+   ++++  +   ++ +  vg++vk ++d+e
  gi|13541587|ref|NP_111275.1|  30 VDKSIFYPTLFGEPNDTGKVIIEGKEYQIVDTIYDGEYIHLISMDTYPQGLVGKSVKQVIDWE 92 
                                   599*****************************9999988888888889999**********97 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.27
                                   HHHHHHHHHTTTT--GGGEEEEEETTEH..HHHHH CS
                  tRNA-synt_2c 103 iefawelltkelgldkerlyvtvfeedd..eavei 135
                                   ++ a+e+++++l+++ + + + +f + d  + ++i
  gi|13541587|ref|NP_111275.1| 147 MSKANEMVKQNLEISFSYISMDEFLNRDdlKKMSI 181
                                   44555666666666666666655544442333333 PP

>> Birna_RdRp  Birnavirus RNA dependent RNA polymerase (VP1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0     1e-06     0.006     591     659 ..      69     139 ..      47     191 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1e-06
                                   HHHHHHHS---S-SHHHHTSTTHHHHHHHHHH.HHHHHTTGGGSHHHHHHHHHH.HHHHHHHHHHHT---H CS
                    Birna_RdRp 591 rllasaaypkGlenkalkskpGaeiaykivry.ealrlvGGwnypllekalkan.asaarkrleakGvpld 659
                                    l++  +yp+Gl  k++k+ +  e+ y  +r+  alrl+ G  y l   +++ n + + r  ++    +++
  gi|13541587|ref|NP_111275.1|  69 HLISMDTYPQGLVGKSVKQVIDWEKRYVHMRFrTALRLISGLSYKLWGVSCRVNeTYDDRAWIDIEKPDIT 139
                                   689999**********************9998359***************986526788876655444443 PP

>> BCL_N  BCL7, N-terminal conserver region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   6.1e-05      0.36      19      42 ..      81     105 ..      79     107 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 6.1e-05
                         BCL_N  19 vikslekVrkWEKkWVtvk.dtslk 42 
                                   v ks+++V  WEK++V ++  t l+
  gi|13541587|ref|NP_111275.1|  81 VGKSVKQVIDWEKRYVHMRfRTALR 105
                                   56899***********998677776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       775  (0.0432261); expected 358.6 (0.02)
Passed bias filter:                      524  (0.0292264); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 1536.50
//
Query:       gi|13541588|ref|NP_111276.1|  [L=428]
Description: folylpolyglutamate synthase [Thermoplasma volcanium GSS1]
Scores for complete 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-18   64.8   0.0    1.4e-17   64.3   0.0    1.2  1  Mur_ligase_M  Mur ligase middle domain
    5.5e-08   33.0   0.0    2.3e-07   31.0   0.0    2.1  2  Mur_ligase_C  Mur ligase family, glutamate ligase domain


Domain annotation for each model (and alignments):
>> Mur_ligase_M  Mur ligase middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.3   0.0   1.6e-21   1.4e-17       1     191 [.      42     264 ..      42     265 .. 0.86

  Alignments for each domain:
  == domain 1  score: 64.3 bits;  conditional E-value: 1.6e-21
                                   EESSS-HHHHHHHHHHHHHCT..EEEEETTC........................................SS-THHHHHH CS
                  Mur_ligase_M   1 vTGtnGKTTtteliaaileka..gkvigtvg........................................ttnneiglpk 39 
                                   +TG+nGK +t+ +i++il+++  ++v+++                                           t  e+++  
  gi|13541588|ref|NP_111276.1|  42 ITGSNGKGSTSAFIYSILRQKfsVGVYTSPHlerfneriivdneevpdeyidgfiekyrpkfdelskvnrnPTFFEVTTMM 122
                                   8*****************9997666777777*************************************9985566777777 PP

                                   HHHHHHHTT-SEEEEE--HCHHHCTTTCCHCBESEEEE---TSTTHHHH.SSHHHHHHHHHHHHHTSETTCEEEEETTSC. CS
                  Mur_ligase_M  40 tlaemekkeaeyavlEvsshglgekrlegllkpdvavitnispdHldfh.gtlenyaeaKaelferlkeegiavinaddpy 119
                                   +++ +++ +++ya +Ev+    g     +++ p+v vi  ++ +H d +  +l  +a++Ka ++++ +     v+  d+p 
  gi|13541588|ref|NP_111276.1| 123 AFQYFKDRKVDYASVEVGLG--GRLDATNIIMPEVSVIAQVGYEHADKLgCSLTSIAYEKAGIIKEGR---PIVLQDDKPE 198
                                   78888889************..44444555*****************9955899**********9655...4555555543 PP

                                   ...CHHHHHCTCCTCEEEEESSSTSECEEEEEEEEETTEEEEEEEEETTEEEEEEESSCSCHHHHHHHHHHHH CS
                  Mur_ligase_M 120 .akelikklkkakvkvvtfglekeaedlraknieeksegteiellevkggeleieipllGkhnvyNalaaiaa 191
                                    ++e+++ ++ +++ ++t + +k +      n++++++gt++++    +++++i+++l+G++++ Na+ ai+a
  gi|13541588|ref|NP_111276.1| 199 vVNEVRRIAQVKHSPLITLDRNKIK------NLHVDENGTDFDFD-GTNDTYHIHTSLIGDYQALNAATAILA 264
                                   3788888888888889999888865......9**********998.56999*******************987 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 ?   -3.2   0.0       1.2   1.1e+04      57      80 ..     196     219 ..     190     221 .. 0.65
   2 !   31.0   0.0   2.5e-11   2.3e-07       1      66 [.     286     346 ..     286     366 .. 0.76

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 1.2
                                   CHCTHHHHHHHHCCHSSE.EEEEES CS
                  Mur_ligase_C  57 trtfhdefgrlasalads.lvvlgd 80 
                                     +  +e+ r+a+  + s l++l+ 
  gi|13541588|ref|NP_111276.1| 196 KPEVVNEVRRIAQV-KHSpLITLDR 219
                                   55566788888885.7777777765 PP

  == domain 2  score: 31.0 bits;  conditional E-value: 2.5e-11
                                   CTTSSEEEEETTTEEEEEET--SHHHHHHHHHHHHHHSSSSEEEEEEEESTT.CCSCHCTHHHHHH CS
                  Mur_ligase_C   1 vkgRlevvgeadgvtvidDyahnpdslsaalkalreiapdkrlilvfgpggelgertrtfhdefgr 66 
                                   ++gRle++++  +++vi+D ahnp ++++ +++++++++ ++  +v+g + +  +++++f+  + +
  gi|13541588|ref|NP_111276.1| 286 WPGRLEIIDR--SPLVIIDAAHNPPAANKMVRTVKKVFN-REPTIVAGILSD--KDAYSFFSVLRQ 346
                                   79********..9************************97.899999998877..333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (428 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       565  (0.0315132); expected 358.6 (0.02)
Passed bias filter:                      496  (0.0276647); 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: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 2688.88
//
Query:       gi|13541589|ref|NP_111277.1|  [L=404]
Description: cell division control protein 6 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.2e-18   64.2   0.1    2.4e-17   62.7   0.1    1.9  1  Cdc6_C           CDC6, C terminal winged helix domain
    1.2e-11   45.0   0.0    7.2e-11   42.5   0.0    2.1  2  AAA_22           AAA domain
    1.1e-10   42.1   0.2    4.2e-10   40.2   0.2    2.0  1  AAA              ATPase family associated with various cellul
      6e-10   39.8   0.0      1e-06   29.2   0.0    2.5  2  AAA_16           AAA ATPase domain
    1.4e-05   24.6   0.2    7.4e-05   22.2   0.2    2.0  1  TniB             Bacterial TniB protein
    1.6e-05   25.0   1.0    0.00031   20.7   0.3    2.5  2  ATPase_2         ATPase domain predominantly from Archaea
     0.0001   22.1   0.4        4.5    7.0   0.0    3.8  4  DEAD             DEAD/DEAH box helicase
     0.0013   18.4   0.0     0.0036   17.0   0.0    1.7  1  Sigma54_activat  Sigma-54 interaction domain
     0.0017   17.9   0.1     0.0076   15.8   0.1    2.1  2  AAA_7            P-loop containing dynein motor region
     0.0025   17.7   2.0       0.22   11.4   0.0    2.6  3  Bac_DnaA         Bacterial dnaA  protein
     0.0026   17.0   0.0     0.0048   16.1   0.0    1.4  1  DUF815           Protein of unknown function (DUF815)
     0.0034   16.5   0.0     0.0079   15.3   0.0    1.6  1  T2SSE            Type II/IV secretion system protein
     0.0045   16.9   0.2      0.019   14.9   0.1    2.0  2  Microtub_bd      Microtubule binding
     0.0053   16.7   0.0      0.024   14.6   0.0    2.2  1  AAA_5            AAA domain (dynein-related subfamily)
     0.0092   16.5   0.1      0.058   13.9   0.0    2.3  2  AAA_18           AAA domain
  ------ inclusion threshold ------
      0.011   16.1   0.3      0.054   13.9   0.0    2.2  2  RNA_helicase     RNA helicase
      0.016   15.6   0.1        0.1   12.9   0.0    2.2  2  AAA_19           AAA domain
      0.025   13.9   0.0      0.042   13.1   0.0    1.3  1  Zeta_toxin       Zeta toxin
      0.032   13.5   0.2        1.2    8.3   0.0    2.4  2  KAP_NTPase       KAP family P-loop domain
       0.04   13.4   0.7      0.097   12.1   0.0    1.8  2  Fer4_NifH        4Fe-4S iron sulfur cluster binding proteins,
      0.048   12.8   0.0       0.18   10.9   0.1    1.9  2  PIF1             PIF1-like helicase
      0.051   13.6   0.0        0.5   10.3   0.0    2.3  2  ResIII           Type III restriction enzyme, res subunit
      0.058   13.5   0.1       0.25   11.4   0.1    2.0  1  AAA_2            AAA domain (Cdc48 subfamily)
       0.08   12.6   0.0        0.4   10.4   0.0    2.0  2  AAA_30           AAA domain
        0.1   12.3   0.8       0.29   10.9   0.8    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 !   62.7   0.1   3.4e-20   2.4e-17       4      82 ..     303     379 ..     300     381 .. 0.88

  Alignments for each domain:
  == domain 1  score: 62.7 bits;  conditional E-value: 3.4e-20
                                   HHHHHCHCSSS-EEHHHHHHHHHHHHHHTT-----HHHHHHHHHHHHHTTSEEEEEEE-CC.C-EEEEEEESSSCHHHH CS
                        Cdc6_C   4 lvlllrksgkeevttgevyevYkslCesegvdpltqrevsdllseLemlgileleksskGrregrtrkisLnvdpddvl 82 
                                   ++   +  + ++v tge+ye Y+++Ce++g++plt r++sdll+eL+++g++ + +++ G+ +grtr +s+  + ++++
  gi|13541589|ref|NP_111277.1| 303 AIVTQE-IEPNSVITGEIYENYRRICEDLGFTPLTPRRISDLLTELSDYGLIVVDERNMGK-YGRTRGFSVVKEIETIK 379
                                   333334.6889*************************************************8.*****999987777776 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.5   0.0     1e-13   7.2e-11       4     131 ..      52     178 ..      48     201 .. 0.81
   2 ?   -0.5   0.0       1.9   1.4e+03      59      99 ..     318     357 ..     280     360 .. 0.76

  Alignments for each domain:
  == domain 1  score: 42.5 bits;  conditional E-value: 1e-13
                        AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka.erlsseelleale 83 
                                   + + ++v+G +GtGKT + + +++ l+e+      ++ev++v++    s+ ++l  ++++ g e+    +   +++++   
  gi|13541589|ref|NP_111277.1|  52 RPSNIIVYGKTGTGKTSTTKYVTRMLQEAT----SNVEVIYVNCEIYDSPYSILVYVANFAGGEKIPeLGWPVDRIYREAV 128
                                   67889*********************7644....5***************************9999943333444445555 PP

                        AAA_22  84 qalraravielliiDEaqhlr..s..eealeeLrsllnlsrkgvqliLvGtp 131
                                   + ++ +++  ++++DE+++l+  s  + ++  L+ + +    +v++ ++G +
  gi|13541589|ref|NP_111277.1| 129 DRINGTGKFFVIVLDEMDRLIkkSggDSLYVLLKLMTD--VENVKVSMIGIT 178
                                   5555555589*********9987364555556677788..889999888865 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.9
                        AAA_22  59 ellralglelkaerlsseell.ealeqalraravielliiDE 99 
                                   e+ +++ + +++  l    l  +++ + l + ++ +l+++DE
  gi|13541589|ref|NP_111277.1| 318 EIYENYRRICED--LGFTPLTpRRISDLLTELSDYGLIVVDE 357
                                   555555555555..6666777788888888888889999998 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.2   0.2   5.8e-13   4.2e-10       1     125 [.      56     196 ..      56     201 .. 0.71

  Alignments for each domain:
  == domain 1  score: 40.2 bits;  conditional E-value: 5.8e-13
                                   EEEESSTTSSHHHHHHHHHHHH.....THEEEEEETTTCSSS..................STTHHHHHHHHHHHHHHHTST CS
                           AAA   1 vllyGppGtGKTllakavakel.....gvefleisgsellsk..................yvgesekkirelfkeakekak 58 
                                   +++yG  GtGKT++ k v + l     +ve++ +++    s                   +     +  re ++++    k
  gi|13541589|ref|NP_111277.1|  56 IIVYGKTGTGKTSTTKYVTRMLqeatsNVEVIYVNCEIYDSPysilvyvanfaggekipeLGWPVDRIYREAVDRINGTGK 136
                                   689******************844444466666666544444666666666644443332444444555666666655545 PP

                                   SEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESS...GGGSTHHHHSTTSS CS
                           AAA  59 psilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnr...pdkldpallrgRfd 125
                                     ++++DE+d+l+k++       + + + +Ll+ + +v++   kv +ig+tn+    ++ld+ +  +R++
  gi|13541589|ref|NP_111277.1| 137 FFVIVLDEMDRLIKKS-------GGDSLYVLLKLMTDVENV--KVSMIGITNDttlLENLDSRIK-SRLN 196
                                   5***************.......8999*************5..8*********555555555555.6665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   0.0   1.4e-09     1e-06       2      73 ..      30     102 ..      29     115 .. 0.83
   2 !    8.0   0.0    0.0049       3.5     123     164 ..     124     166 ..     108     175 .. 0.72

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 1.4e-09
                        AAA_16   2 lvGReeeleqLlsale.rvrsgrpelvllsGesGvGKsslvrellralekd..ggiflrgkcdqlesaipysala 73 
                                   ++ Re++++ + ++l+   r +rp++++++G  G+GK+s  + + r l+++  ++ +++ +c+ +  + pys+l+
  gi|13541589|ref|NP_111277.1|  30 FPHREKQINDMVTILSsIMRNSRPSNIIVYGKTGTGKTSTTKYVTRMLQEAtsNVEVIYVNCEIY--DSPYSILV 102
                                   889********9999944555666*****************999987777765588899999999..88997754 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0049
                        AAA_16 123 lkrllallsrderplvlvlDdlq.wadeaslqllaaLlrlles 164
                                    +++++++  +++ +v+vlD+++  ++ +  + l+ Ll+l+++
  gi|13541589|ref|NP_111277.1| 124 YREAVDRINGTGKFFVIVLDEMDrLIKKSGGDSLYVLLKLMTD 166
                                   56777777777999*********54455566667777777665 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.2     1e-07   7.4e-05      15     183 ..      33     199 ..      29     202 .. 0.73

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 1e-07
                          TniB  15 rakeilerLeeLleypkrkrmpnlllvGdsnnGKtmivekFarlhppekdedaekvpvlvvqap..pkpdekrlyaaiLea 93 
                                   r k+i ++   L +  +++r++n++++G++ +GKt+  +  +r+ ++++    ++v+v++v++   ++p     y a ++ 
  gi|13541589|ref|NP_111277.1|  33 REKQINDMVTILSSIMRNSRPSNIIVYGKTGTGKTSTTKYVTRMLQEAT----SNVEVIYVNCEiyDSPYSILVYVANFAG 109
                                   5678888888899999********************9988887766554....7889999986611566666667766666 PP

                          TniB  94 lgaplkararvskleqqvlrllr.elkvrvLiiDEihnllagsarkqreflnalksLgnelkipivlvGteealral.rtD 172
                                    ++  +  + v++++++++  ++ + k  v+++DE+++l++ s  +   +  +lk +++  ++ + ++G+++ +++l + D
  gi|13541589|ref|NP_111277.1| 110 GEKIPELGWPVDRIYREAVDRINgTGKFFVIVLDEMDRLIKKSGGDS--LYVLLKLMTDVENVKVSMIGITNDTTLLeNLD 188
                                   666667788999999888877762567899**********7666655..55556666665555555556555444442789 PP

                          TniB 173 pqlasRFepia 183
                                   + ++sR++++ 
  gi|13541589|ref|NP_111277.1| 189 SRIKSRLNQES 199
                                   99**9998865 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 !   20.7   0.3   4.3e-07   0.00031       2     172 ..      31     185 ..      30     199 .. 0.68
   2 ?   -3.2   0.0       9.2   6.6e+03       6      19 ..     373     386 ..     342     391 .. 0.57

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 4.3e-07
                      ATPase_2   2 fdRekelkeleeil....erepneiyfiYGpegsGKtaLlkeiienledkdk..yviyyialreesiskldefieeeeekk 76 
                                     Rek ++++ +il    ++++ + + +YG  g GKt+  k +   l++     +viy++  + +++ +        ++++
  gi|13541589|ref|NP_111277.1|  31 PHREKQINDMVTILssimRNSRPSNIIVYGKTGTGKTSTTKYVTRMLQEATSnvEVIYVN-CEIYDSPYSILV----YVAN 106
                                   569999998766551111556667799*****************9996655533666654.555555444444....4444 PP

                      ATPase_2  77 klekal.giavpkaeleeilkeksklvfkaielllekikkkgkkiiiiiDelqklidlglngaellvkeLlnliesltkek 156
                                        + g+++p+             v++   ++ + i+ +gk  +i++De+ +li  + ++ ++ ++ Ll+l+ +   e+
  gi|13541589|ref|NP_111277.1| 107 ----FAgGEKIPELG---------WPVDRIYREAVDRINGTGKFFVIVLDEMDRLI--K-KSGGDSLYVLLKLMTD--VEN 169
                                   ....33256677744.........589999*************************9..4.4556667778888877..344 PP

                      ATPase_2 157 hlcvviclsSeglfie 172
                                    ++  i  + ++ ++e
  gi|13541589|ref|NP_111277.1| 170 VKVSMIGITNDTTLLE 185
                                   4444455566666666 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 9.2
                      ATPase_2   6 kelkeleeilerep 19 
                                   ke++ ++++l +++
  gi|13541589|ref|NP_111277.1| 373 KEIETIKKYLMEDE 386
                                   44444444444433 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   0.0    0.0062       4.5      14      39 ..      53      80 ..      38     102 .. 0.74
   2 !    6.7   0.0     0.008       5.7     123     150 ..     138     165 ..     122     179 .. 0.79
   3 ?   -1.7   0.0       3.1   2.2e+03     141     172 ..     281     308 ..     271     311 .. 0.69
   4 ?    3.7   0.0     0.064        46      98     130 ..     330     358 ..     305     381 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0062
                                  TCEEEEEESTTSSHHHH..HHHHHHHHH CS
                                  xxxxxxxxxxxxxxxxx..xxxxxxxxx RF
                          DEAD 14 ggdvlvaaeTGsGKTla..flipvlqiv 39
                                    +++v ++TG+GKT    ++  +lq+ 
  gi|13541589|ref|NP_111277.1| 53 PSNIIVYGKTGTGKTSTtkYVTRMLQEA 80
                                  4799**********98744666666655 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.008
                                   EEEEEETHHHHHHTTTHHHHHHHHHHSH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD 123 rflVlDEadrlldqgfsdfinrilnqlp 150
                                    ++VlDE+drl +++ +d +  +l+ + 
  gi|13541589|ref|NP_111277.1| 138 FVIVLDEMDRLIKKSGGDSLYVLLKLMT 165
                                   579***********99999988887773 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 3.1
                                   HHHHHHHHSHHHCTTSTTTSEEEEEESSBSHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD 141 finrilnqlpqitcdgklqrqvivlSATlpkd 172
                                   ++n ++++++    + + ++++++lSA ++++
  gi|13541589|ref|NP_111277.1| 281 EMNVMHEAIN----TLPIHSKIVLLSAIVTQE 308
                                   4666777773....445445699999977765 PP

  == domain 4  score: 3.7 bits;  conditional E-value: 0.064
                                   CSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD  98 vdivvgtpgrlddllstgklnlsqvrflVlDEa 130
                                   + ++  tp r+ dll+    +ls+  ++V+DE 
  gi|13541589|ref|NP_111277.1| 330 LGFTPLTPRRISDLLT----ELSDYGLIVVDER 358
                                   5666679******995....49**********5 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   5.1e-06    0.0036       5      61 ..      34      94 ..      31     103 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 5.1e-06
                                  SHHHHHHHHHHHHHCTSS..S-EEEECSTTSSHHHHHHHHHH..HSTTTTS-EEEEETTTS CS
               Sigma54_activat  5 sealkelleqikkvaktd..lsvlitGesGtGKellaraihe..askrkekpfvavncaai 61
                                  +++++++++ ++++++++  +++++ G++GtGK+   + + +  ++  ++ +++ vnc  +
  gi|13541589|ref|NP_111277.1| 34 EKQINDMVTILSSIMRNSrpSNIIVYGKTGTGKTSTTKYVTRmlQEATSNVEVIYVNCEIY 94
                                  567778888888887665569*******************99444455677899****754 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 !   15.8   0.1   1.1e-05    0.0076      27      69 ..      45      91 ..      36     102 .. 0.69
   2 ?   -1.6   0.0       2.2   1.6e+03      74      88 ..     206     220 ..     159     232 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.1e-05
                         AAA_7 27 elllknkk..pvllvGptGtGKtviikdllkkld..kekylsltinf 69
                                  + +++n++  +++++G+tGtGKt+++k +++ l+  ++++ ++ +n+
  gi|13541589|ref|NP_111277.1| 45 SSIMRNSRpsNIIVYGKTGTGKTSTTKYVTRMLQeaTSNVEVIYVNC 91
                                  55555554116899*************99999992234444444444 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.2
                         AAA_7  74 sanqlqdiiesklek 88 
                                   +a++++dii s+lek
  gi|13541589|ref|NP_111277.1| 206 NATEIRDIIASRLEK 220
                                   566777777777776 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.0    0.0003      0.22      37      74 ..      56      93 ..      36      99 .. 0.90
   2 ?    5.3   0.1     0.022        16     100     158 ..     139     198 ..     129     234 .. 0.75
   3 ?   -2.8   0.2       6.2   4.5e+03     161     191 ..     255     285 ..     252     293 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0003
                                  EEEE-SSSSSHHHHHHHHHHHHHHHSSSS-EEEEEHHH CS
                      Bac_DnaA 37 lfiygevGlGktHLlkaignevlenapelrvvYltaee 74
                                  +++yg++G Gkt   k ++  ++e +++  v+Y++ e 
  gi|13541589|ref|NP_111277.1| 56 IIVYGKTGTGKTSTTKYVTRMLQEATSNVEVIYVNCEI 93
                                  789*******************************9986 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.022
                                   EEEEE-GGGGTT-HHHHHHHHHHHHHH..HTTT-EEEEEESS-TTT-SS--HHHHHHHHSS CS
                      Bac_DnaA 100 vLliDDiqflagkektqeelfhtfnal..leegkqvvlssDrsPkeleeledrlrsrfeaG 158
                                   v+++D++  l +k++ +  l+ ++  +  +e+ k  ++      + le+l++r++sr+++ 
  gi|13541589|ref|NP_111277.1| 139 VIVLDEMDRLIKKSGGD-SLYVLLKLMtdVENVKVSMIGITNDTTLLENLDSRIKSRLNQE 198
                                   67889999999999654.5555555551134555556777788899************975 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 6.2
                                   EE-----HHHHHHHHHHHHHHTT----TTHH CS
                      Bac_DnaA 161 vdieppdletrlailkkkieaeklevpeevl 191
                                   ++ie + +e rl++ +k++ +++ +   +v+
  gi|13541589|ref|NP_111277.1| 255 IAIEIAIRENRLKVTEKEVYEARDKYEMNVM 285
                                   6777777888999999998866655444433 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   6.7e-06    0.0048      34      87 ..      34      89 ..      23     105 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 6.7e-06
                        DUF815 34 dkqkealventeqfleglpannvLLwGarGtGKSslvkallneyaeeg..Lrliev 87
                                  +kq +++v+  +  +++ + +n++++G+ GtGK s+ k +++ ++e++  + +i v
  gi|13541589|ref|NP_111277.1| 34 EKQINDMVTILSSIMRNSRPSNIIVYGKTGTGKTSTTKYVTRMLQEATsnVEVIYV 89
                                  788899999999999************************99998887655666666 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.1e-05    0.0079     118     161 ..      44      85 ..      24      96 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.1e-05
                         T2SSE 118 iaevlrkavrerglilvsGgTgsGKttllyallkeinksderiv 161
                                   +++++r++  +  +i+v G Tg+GKt ++  +  ++++ + ++ 
  gi|13541589|ref|NP_111277.1|  44 LSSIMRNS--RPSNIIVYGKTGTGKTSTTKYVTRMLQEATSNVE 85 
                                   34455555..778****************999999988877664 PP

>> Microtub_bd  Microtubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.1   2.6e-05     0.019      68     115 ..      37      85 ..      24     103 .. 0.72
   2 ?   -1.9   0.0         4   2.9e+03      67      91 ..     371     395 ..     367     399 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.6e-05
                                   CCCCHHHHHHHH.TT--EEEEEEES................ST-HCHHH CS
                   Microtub_bd  68 feeisqlvqsal.dgynvcifaygqTGsGKtyTmegeeeeagmiprave 115
                                   ++++  ++ s + +    +i+ yg+TG GKt T +  ++  +  ++ ve
  gi|13541589|ref|NP_111277.1|  37 INDMVTILSSIMrNSRPSNIIVYGKTGTGKTSTTKYVTRMLQEATSNVE 85 
                                   556666667777688889**************99885544444444444 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 4
                                   CCCCCHHHHHHHHTT--EEEEEEES CS
                   Microtub_bd  67 vfeeisqlvqsaldgynvcifaygq 91 
                                   v++ei+ + +  +++ n ++f +++
  gi|13541589|ref|NP_111277.1| 371 VVKEIETIKKYLMEDENLSMFKTSK 395
                                   8899999999999999999998876 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   3.4e-05     0.024       1      77 [.      55     148 ..      55     195 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.4e-05
                                   EEEEE--SSSSHHHHHHHGGGGB.....S--EEEEE--.TT--HHHHH--B--..............--------...... CS
                         AAA_5   1 dvlLvGppGtgKselaerlaaal.....nreveyvqlt.rdtteedlkgrreik.....ngttslvdsplvraar...... 64 
                                   ++++ G++GtgK++ ++++ ++l     n ev yv++   d +++ l++  +++     ++  + vd ++ +a+       
  gi|13541589|ref|NP_111277.1|  55 NIIVYGKTGTGKTSTTKYVTRMLqeatsNVEVIYVNCEiYDSPYSILVYVANFAggekiPELGWPVDRIYREAVDringtg 135
                                   5899*******************9998888888888873467777788888887444433333444555555554777766 PP

                                   G-SEEEEESGGG- CS
                         AAA_5  65 egeilvlDEvera 77 
                                   +  ++vlDE +r+
  gi|13541589|ref|NP_111277.1| 136 KFFVIVLDEMDRL 148
                                   6667777777765 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   8.1e-05     0.058       1      26 [.      56      87 ..      56     136 .. 0.81
   2 ?   -0.7   0.0       2.7   1.9e+03      34      70 ..     263     306 ..     246     325 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 8.1e-05
                        AAA_18  1 IlltGtpGvGKttlakeLskrl.gf.....gv 26
                                  I++ G+ G+GKt+ +k++ ++l +      ++
  gi|13541589|ref|NP_111277.1| 56 IIVYGKTGTGKTSTTKYVTRMLqEAtsnveVI 87
                                  9*****************98874444555544 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 2.7
                        AAA_18  34 englllevdpealdeskrldedkldklldaleenss........a 70 
                                   en+l  ++ +  ++  ++ +++++++++++l  +s+        +
  gi|13541589|ref|NP_111277.1| 263 ENRLKVTEKEV-YEARDKYEMNVMHEAINTLPIHSKivllsaivT 306
                                   45555555555.777888888888888888888875444444443 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   7.6e-05     0.054       1      30 [.      56      83 ..      56      99 .. 0.77
   2 ?   -2.0   0.0       6.4   4.6e+03      52      92 ..     139     180 ..     132     185 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 7.6e-05
                  RNA_helicase  1 iwlyGpsgeGKStlakeLakallkklklkk 30
                                  i++yG++g+GK++++k++++ l+++    +
  gi|13541589|ref|NP_111277.1| 56 IIVYGKTGTGKTSTTKYVTRMLQEAT--SN 83
                                  789**************888888555..33 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 6.4
                  RNA_helicase  52 vvvidDfgqvkdee.npsdlaelirlvsstpyplnmasleek 92 
                                   v+v d++ +  +++  +s +  l  + +  ++++ m  + + 
  gi|13541589|ref|NP_111277.1| 139 VIVLDEMDRLIKKSgGDSLYVLLKLMTDVENVKVSMIGITND 180
                                   678888888888887888888888888888889988888775 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00014       0.1       7      39 ..      50      82 ..      45      91 .. 0.80
   2 ?   -0.5   0.0         2   1.4e+03      99     113 ..     346     360 ..     266     383 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00014
                        AAA_19  7 alkekvllvtaGpGtGKTrvlkhivallvelgg 39
                                  +++ ++++v +  GtGKT ++k + ++l+e+++
  gi|13541589|ref|NP_111277.1| 50 NSRPSNIIVYGKTGTGKTSTTKYVTRMLQEATS 82
                                  6778899****************9999998874 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 2
                        AAA_19  99 klqeee.llivDEfqd 113
                                   +l + + l++vDE  +
  gi|13541589|ref|NP_111277.1| 346 EL-SDYgLIVVDERNM 360
                                   45.4455999999887 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   5.8e-05     0.042      10      49 ..      47      86 ..      38      90 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.8e-05
                    Zeta_toxin 10 ypsqerPklillgGqpGAGKselaellkdelerqgnvvrl 49
                                  + +++rP  i++ G +G GK+++ +++++ l+++ + v++
  gi|13541589|ref|NP_111277.1| 47 IMRNSRPSNIIVYGKTGTGKTSTTKYVTRMLQEATSNVEV 86
                                  45789**************************966665554 PP

>> KAP_NTPase  KAP family P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0    0.0017       1.2       2      57 ..      34      90 ..      33      99 .. 0.79
   2 ?    2.7   0.1     0.083        60     157     205 ..     120     169 ..     105     202 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0017
                    KAP_NTPase  2 dlyasaladilseptl..atpivvgLygkWGsGKssllnkledelkefakpvrflfae 57
                                  ++ ++ +++ils+  +  ++p+ + +ygk G+GK+s  + + + l+e   +v+++ ++
  gi|13541589|ref|NP_111277.1| 34 EKQINDMVTILSSI-MrnSRPSNIIVYGKTGTGKTSTTKYVTRMLQEATSNVEVIYVN 90
                                  56777777888754.34699*******************9999999996666666554 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.083
                    KAP_NTPase 157 veelladmektLdalqkrlVvviDdLDrcetee.vlqlleavkllfslkp 205
                                   v+ ++ ++++ +    k  V+v+D++Dr+ ++    +l  ++kl+ ++++
  gi|13541589|ref|NP_111277.1| 120 VDRIYREAVDRINGTGKFFVIVLDEMDRLIKKSgGDSLYVLLKLMTDVEN 169
                                   5566667777777788889*********8554314455555566666644 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 ?   12.1   0.0   0.00013     0.097       2      36 ..      55      91 ..      54     103 .. 0.81
   2 ?   -1.4   0.1       1.8   1.3e+03     190     246 ..     274     328 ..     247     349 .. 0.52

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00013
                     Fer4_NifH  2 kiaiyGkGGiGksttsqnlsaalaemgkk..vlivGC 36
                                  +i +yGk G Gk+ t++ ++ +l+e      v+ v C
  gi|13541589|ref|NP_111277.1| 55 NIIVYGKTGTGKTSTTKYVTRMLQEATSNveVIYVNC 91
                                  589********************99876511555666 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.8
                     Fer4_NifH 190 reliekfaeelgtkvlevvPrdeivrkaelrkktvieyapeseqakeyrelarkile 246
                                    e  +k+  ++  + ++++P + ++        ++ e +p+s ++ e  e  r+i e
  gi|13541589|ref|NP_111277.1| 274 YEARDKYEMNVMHEAINTLPIHSKIVLL--SAIVTQEIEPNSVITGEIYENYRRICE 328
                                   3555677777778888888877665432..222333333333333222222333333 PP

>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00025      0.18      11      54 ..      41      85 ..      33      90 .. 0.80
   2 ?   -2.1   0.0       2.2   1.6e+03      91     113 ..     338     360 ..     333     363 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00025
                                  HHH.......HCTS-EEEEESTTSSCHHHHHHHHHHCHCTCCCEE CS
                          PIF1 11 daiieavln.ekgklfFvtGsgGtgKtflwkallkklrsegkivl 54
                                   +i+ ++++ +++ ++ v+G  GtgKt   k ++ +l++  ++v 
  gi|13541589|ref|NP_111277.1| 41 VTILSSIMRnSRPSNIIVYGKTGTGKTSTTKYVTRMLQEATSNVE 85
                                  467777775489****************99999999998777764 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.2
                                   HTSCCCHHHHHC-SEEEEECGGG CS
                          PIF1  91 krgsklaellkktsliiwDEapm 113
                                   +r s+l  +l++  li++DE  m
  gi|13541589|ref|NP_111277.1| 338 RRISDLLTELSDYGLIVVDERNM 360
                                   566788899999********998 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 ?   10.3   0.0    0.0007       0.5       5      57 ..      33      86 ..      29      96 .. 0.69
   2 ?    0.2   0.0      0.94   6.7e+02     129     147 ..     133     151 ..     120     187 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0007
                                  -HHHHHHHHHHT.......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-E CS
                        ResIII  5 reyQeeaienlleklks.krdkrglikmaTGtGKTlvaaklierllkkgkeekf 57
                                  re Q++ +  +l+++    r  ++++   TGtGKT +   +++ l+++ ++ ++
  gi|13541589|ref|NP_111277.1| 33 REKQINDMVTILSSIMRnSRPSNIIVYGKTGTGKTSTTKYVTRMLQEATSNVEV 86
                                  5666666666666665435666889999********997777777776654444 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.94
                                   HTTT-SEEEEETGGGTTS. CS
                        ResIII 129 lrdrfdviiiDEaHrlgak 147
                                   + ++f vi+ DE  rl +k
  gi|13541589|ref|NP_111277.1| 133 GTGKFFVIVLDEMDRLIKK 151
                                   4566667777777666654 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00035      0.25       4     101 ..      54     162 ..      51     174 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00035
                                   --EEEE--TTSSHHHHHHHHHHHTT-.....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS............. CS
                         AAA_2   4 isilllgptgvGktelakalaellfv.kkekkliradaselleeeevehlvsrligappgyvgaeegG............. 70 
                                   ++i++ g+tg+Gkt ++k + ++l+  +++ ++i +++  +        ++   + +  g  +  e G             
  gi|13541589|ref|NP_111277.1|  54 SNIIVYGKTGTGKTSTTKYVTRMLQEaTSNVEVIYVNCEIYDS----PYSILVYVANFAGGEKIPELGwpvdriyreavdr 130
                                   799*******************999434455555556655555....8888888888888888888888888888888899 PP

                                   ........EEEEETGGG-------------HHHHHHHHH CS
                         AAA_2  71 ........ivllDEidKihpkessgadvSregVqrdLLq 101
                                           ++ lDE+d+  +        S+ + + +LL+
  gi|13541589|ref|NP_111277.1| 131 ingtgkffVIVLDEMDRLIK-------KSGGDSLYVLLK 162
                                   99999999999999999888.......455555555555 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00055       0.4      21      50 ..      56      85 ..      43      92 .. 0.82
   2 ?   -1.7   0.0       2.8     2e+03      86      99 ..     347     360 ..     324     376 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00055
                        AAA_30 21 avltGpAGtGKttalkalreaweaaggrvi 50
                                   ++ G  GtGKt + k +++++++a  +v 
  gi|13541589|ref|NP_111277.1| 56 IIVYGKTGTGKTSTTKYVTRMLQEATSNVE 85
                                  6889****************9999976654 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.8
                        AAA_30  86 lepgtllivDEagm 99 
                                   l++  l++vDE  m
  gi|13541589|ref|NP_111277.1| 347 LSDYGLIVVDERNM 360
                                   3445799****888 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.8    0.0004      0.29       3      24 ..      54      74 ..      52     155 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0004
                        AAA_24  3 lkiliyGpsgiGKTtlakelgp 24
                                   +i++yG+ g+GKT++ k    
  gi|13541589|ref|NP_111277.1| 54 SNIIVYGKTGTGKTSTTKYV-T 74
                                  589*************9987.3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (404 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       861  (0.0480228); expected 358.6 (0.02)
Passed bias filter:                      626  (0.0349155); expected 358.6 (0.02)
Passed Vit filter:                       104  (0.00580066); expected 17.9 (0.001)
Passed Fwd filter:                        25  (0.00139439); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              25  [number of targets reported over threshold]
# CPU time: 0.68u 0.34s 00:00:01.02 Elapsed: 00:00:00.52
# Mc/sec: 2347.64
//
Query:       gi|13541590|ref|NP_111278.1|  [L=435]
Description: glutamate dehydrogenase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.4e-73  245.7   0.1    7.9e-73  245.2   0.1    1.2  1  ELFV_dehydrog    Glutamate/Leucine/Phenylalanine/Valine dehyd
    3.6e-57  191.9   0.0    6.5e-57  191.0   0.0    1.5  1  ELFV_dehydrog_N  Glu/Leu/Phe/Val dehydrogenase, dimerisation 
    0.00039   19.8   0.1    0.00072   19.0   0.1    1.4  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
  ------ inclusion threshold ------
      0.016   15.6   0.0      0.037   14.3   0.0    1.7  1  Gp_dh_N          Glyceraldehyde 3-phosphate dehydrogenase, NA


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 !  245.2   0.1   1.8e-76   7.9e-73       1     243 []     200     433 ..     200     433 .. 0.98

  Alignments for each domain:
  == domain 1  score: 245.2 bits;  conditional E-value: 1.8e-76
                                   T--TTTTTHHHHHHHHHHHHHHHHTTTS-STTEEEEEE--SHHHHHHHHHHHHC.T-EEEEEEESSEEEEETTEE-HHHHH CS
                 ELFV_dehydrog   1 GGsldrpeaTglGvvyyveemlkklkldslegkrvaisGsGnvgsyaallltel.gakvvavsDssGviydpeGldieell 80 
                                   GGsl+r ++Tg G +++++e +kk++ld l+++rva++G+Gnvg++a+++++e+ gakvvavsD +G iy+++G+++++ll
  gi|13541590|ref|NP_111278.1| 200 GGSLGRFDSTGKGGMFVLREGAKKIGLD-LSKARVAVQGFGNVGQFAVKFVQEMfGAKVVAVSDIKGGIYSENGFKFDDLL 279
                                   9***********************9999.************************99************************** PP

                                   HHHHCSSSSTTHSHHSTSTSEEESHHSHHHHSS-SEEEE-SSTTSB-HHHHTHTHHTT-SEEE-SSSS-B-HHHHHHHHHT CS
                 ELFV_dehydrog  81 elkeerksvkeykkssekkaeyieneeellelkvdilvPcAtqneideenakalikngvklvvEgANlpttqeAkeileea 161
                                   ++ ++ +sv  ++     + + i+ne elle +vd+l+P+A++++i+e+na+ +ik  +k+++E AN+ptt+eA+eil ++
  gi|13541590|ref|NP_111278.1| 280 AWSKKIGSVVGFP-----GSKPITNE-ELLESDVDVLIPAAIEEQITEKNAD-KIK--AKIILELANGPTTPEADEILYKK 351
                                   *************.....3478***7.*************************.999..*********************** PP

                                   T-EEE-HHHHTTHHHHHHHHHHHHHHCT----HHHHHHHHHHHHHHHHHHHHHHHHHCT-THHHHHHHHHHHHHHHHHHHC CS
                 ELFV_dehydrog 162 gvlvvpdkaaNaGGVtvSslEmlqnlarlswteeevdeklkkimkeifkavveeaeeykqelvkganiagfekvaeamkaq 242
                                   g lv+pd+++N+GGV+vS++E++qn+ + +wt+eev +kl+++ +++ ++v++++++y+++ +++a++++++kva+amk +
  gi|13541590|ref|NP_111278.1| 352 GKLVLPDVLSNSGGVIVSYFEWVQNNYGEYWTTEEVYDKLDQKITKAARQVLDTMDKYHVDPRTAAYVIAVKKVADAMKVR 432
                                   *******************************************************************************99 PP

                                   T CS
                 ELFV_dehydrog 243 G 243
                                   G
  gi|13541590|ref|NP_111278.1| 433 G 433
                                   8 PP

>> ELFV_dehydrog_N  Glu/Leu/Phe/Val dehydrogenase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  191.0   0.0   1.4e-60   6.5e-57       1     129 [.      54     181 ..      54     182 .. 0.99

  Alignments for each domain:
  == domain 1  score: 191.0 bits;  conditional E-value: 1.4e-60
                                   -SEEEEEEEEEE-TTSBEEEEEEEEEEEE-TTSSEEEEEEEETT--HHHHHHHHHHHHHHHHHTTSS-EEEEEEEES-GGG CS
               ELFV_dehydrog_N   1 pervlqvtvpvkrdnGelevikgyraqhssalgPakGGiRfhpsvnldevkaLaalmtyKnalvdlpfGGakggvkidpkk 81 
                                   p+++lqv++pvk+d+G+++v++g+r+ h+ a+gPakGGiR+hp+ +l++vkaL+++mt+K+a++d+p+GGakgg+++dp++
  gi|13541590|ref|NP_111278.1|  54 PQKILQVSIPVKMDDGKVRVFTGFRVRHNIARGPAKGGIRYHPQETLSTVKALSMWMTWKCAIADIPYGGAKGGIICDPST 134
                                   789****************************************************************************** PP

                                   S-HHHHHHHHHHHHHHHG.GG-BTTTEEEEBBTTB-HHHHHHHHHHHH CS
               ELFV_dehydrog_N  82 lseeeleritrrfvrelakkfiGpgiDvpApDvgtgaremawladeyk 129
                                   ls+ eler+ r ++r++a +fiGp++DvpApDv+t+++ maw++dey+
  gi|13541590|ref|NP_111278.1| 135 LSQGELERLSRGYIRAIA-DFIGPEVDVPAPDVNTNPQIMAWMMDEYE 181
                                   ******************.****************************7 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.1   1.6e-07   0.00072      24      93 ..     218     283 ..     201     304 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.6e-07
                                   HTTCCGSBS-GTTSEEEEES-SHHHHHHHHHHH.HTT-EEEEESSSHHHHHCHHHHTCEECSHHHHHHH-S CS
                  2-Hacid_dh_C  24 ksekallgkelsgktvGiiGlGrIGqavakrlk.afgmkviaydrskkkeeeeeelgvelvsleellaesD 93 
                                   ++ ++  g +ls+ +v++ G+G++Gq + k ++  fg+kv+a++  k      +e+g+   ++++lla+s 
  gi|13541590|ref|NP_111278.1| 218 REGAKKIGLDLSKARVAVQGFGNVGQFAVKFVQeMFGAKVVAVSDIKG--GIYSENGF---KFDDLLAWSK 283
                                   556778899*********************99989********99855..33566666...5666666665 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 ?   14.3   0.0   8.4e-06     0.037       2      47 ..     232     277 ..     231     332 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 8.4e-06
                                   EEEEESTSHHHHHHHHHHHHHTTCEEEEEE-TS-HHHHHHHHHEET CS
                       Gp_dh_N   2 kvainGfGRIGrlvlralleekelevvaindltdletlayllkyDs 47 
                                   +va+ GfG +G+ +++ + e    +vva+ d+    + +  +k+D 
  gi|13541590|ref|NP_111278.1| 232 RVAVQGFGNVGQFAVKFVQEMFGAKVVAVSDIKGGIYSENGFKFDD 277
                                   89*****************************988878888888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (435 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       595  (0.0331865); 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:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 2822.36
//
Query:       gi|13541591|ref|NP_111279.1|  [L=416]
Description: glutamate dehydrogenase [Thermoplasma volcanium GSS1]
Scores for complete 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-73  245.7   0.6    7.8e-73  245.2   0.6    1.2  1  ELFV_dehydrog    Glutamate/Leucine/Phenylalanine/Valine dehyd
    5.3e-57  191.3   0.0    9.2e-57  190.5   0.0    1.4  1  ELFV_dehydrog_N  Glu/Leu/Phe/Val dehydrogenase, dimerisation 
     0.0013   18.2   0.3     0.0024   17.2   0.3    1.4  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas


Domain annotation for each model (and alignments):
>> ELFV_dehydrog  Glutamate/Leucine/Phenylalanine/Valine dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  245.2   0.6   1.3e-76   7.8e-73       1     243 []     181     414 ..     181     414 .. 0.99

  Alignments for each domain:
  == domain 1  score: 245.2 bits;  conditional E-value: 1.3e-76
                                   T--TTTTTHHHHHHHHHHHHHHHHTTTS-STTEEEEEE--SHHHHHHHHHHHHC.T-EEEEEEESSEEEEETTEE-HHHHH CS
                 ELFV_dehydrog   1 GGsldrpeaTglGvvyyveemlkklkldslegkrvaisGsGnvgsyaallltel.gakvvavsDssGviydpeGldieell 80 
                                   GGs++r +aT+ G +y+++e +k+++ld l++++va++G+Gn g++a+++++e+ gakvvavsD +G i++++G++ e+ll
  gi|13541591|ref|NP_111279.1| 181 GGSEGRGDATAKGGMYVLREGAKRVGLD-LSKATVAVQGFGNAGQFAVKFVQEMfGAKVVAVSDTKGGIFKSDGINYEALL 260
                                   9***********************9999.************************99************************** PP

                                   HHHHCSSSSTTHSHHSTSTSEEESHHSHHHHSS-SEEEE-SSTTSB-HHHHTHTHHTT-SEEE-SSSS-B-HHHHHHHHHT CS
                 ELFV_dehydrog  81 elkeerksvkeykkssekkaeyieneeellelkvdilvPcAtqneideenakalikngvklvvEgANlpttqeAkeileea 161
                                   ++k++++sv  ++     + + i+ne elle +vd+l+P+A++++i+e+na+ +ik  +k+++E AN+ptt+eA+eil ++
  gi|13541591|ref|NP_111279.1| 261 DHKRKTGSVVGFP-----GSKPITNE-ELLESDVDVLIPAAIEEQITEKNAD-KIK--AKIILELANGPTTPEADEILYKK 332
                                   *************.....3478***7.*************************.999..*********************** PP

                                   T-EEE-HHHHTTHHHHHHHHHHHHHHCT----HHHHHHHHHHHHHHHHHHHHHHHHHCT-THHHHHHHHHHHHHHHHHHHC CS
                 ELFV_dehydrog 162 gvlvvpdkaaNaGGVtvSslEmlqnlarlswteeevdeklkkimkeifkavveeaeeykqelvkganiagfekvaeamkaq 242
                                   g l +pd+++N+GGVtvS++E++qn+ + +wt+eev ekl+k+m+++ ++v +++++yk + +++a++++++kva+amka+
  gi|13541591|ref|NP_111279.1| 333 GRLDLPDFLSNSGGVTVSYFEWVQNNYGEYWTAEEVYEKLDKKMTKAAHEVFDAMDKYKINPRTAAYVISVKKVADAMKAR 413
                                   ********************************************************************************9 PP

                                   T CS
                 ELFV_dehydrog 243 G 243
                                   G
  gi|13541591|ref|NP_111279.1| 414 G 414
                                   9 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 !  190.5   0.0   1.5e-60   9.2e-57       1     129 [.      35     162 ..      35     163 .. 0.99

  Alignments for each domain:
  == domain 1  score: 190.5 bits;  conditional E-value: 1.5e-60
                                   -SEEEEEEEEEE-TTSBEEEEEEEEEEEE-TTSSEEEEEEEETT--HHHHHHHHHHHHHHHHHTTSS-EEEEEEEES-GGG CS
               ELFV_dehydrog_N   1 pervlqvtvpvkrdnGelevikgyraqhssalgPakGGiRfhpsvnldevkaLaalmtyKnalvdlpfGGakggvkidpkk 81 
                                   pe++lqv++pv++dnG+++v++g+r+ +++a+gP kGGiR+hp+ +l++vkaLa++mt+K+a++d+p+GGakgg+++dpk+
  gi|13541591|ref|NP_111279.1|  35 PEKILQVSIPVRMDNGKIKVFTGFRVRYNTARGPGKGGIRYHPDETLSTVKALASWMTWKCAIADIPYGGAKGGIICDPKS 115
                                   899****************************************************************************** PP

                                   S-HHHHHHHHHHHHHHHG.GG-BTTTEEEEBBTTB-HHHHHHHHHHHH CS
               ELFV_dehydrog_N  82 lseeeleritrrfvrelakkfiGpgiDvpApDvgtgaremawladeyk 129
                                   +s+ eler+ r ++r++a +fiGp++DvpApDv+t+++ maw++dey+
  gi|13541591|ref|NP_111279.1| 116 MSQGELERLSRGYIRAIA-DFIGPEVDVPAPDVYTNPQIMAWMMDEYE 162
                                   ******************.****************************7 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 !   17.2   0.3   4.1e-07    0.0024      23      70 ..     196     246 ..     185     270 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 4.1e-07
                                   C..HTTCCGSBS-GTTSEEEEES-SHHHHHHHHHHH.HTT-EEEEESSSHH CS
                  2-Hacid_dh_C  23 w..ksekallgkelsgktvGiiGlGrIGqavakrlk.afgmkviaydrskk 70 
                                   +  ++ ++  g +ls+ tv++ G+G+ Gq + k ++  fg+kv+a++ +k 
  gi|13541591|ref|NP_111279.1| 196 YvlREGAKRVGLDLSKATVAVQGFGNAGQFAVKFVQeMFGAKVVAVSDTKG 246
                                   455666788999*********************99989********99854 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (416 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       801  (0.0446762); expected 358.6 (0.02)
Passed bias filter:                      675  (0.0376485); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 2800.18
//
Query:       gi|13541592|ref|NP_111280.1|  [L=910]
Description: leucyl-tRNA synthetase [Thermoplasma volcanium GSS1]
Scores for 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  205.7   0.8    3.5e-60  203.9   0.8    1.8  1  tRNA-synt_1    tRNA synthetases class I (I, L, M and V)
    5.6e-23   81.3   2.9    1.1e-10   40.8   0.0    3.4  3  tRNA-synt_1g   tRNA synthetases class I (M)
    8.7e-13   48.5   0.2    2.5e-12   47.0   0.2    1.8  1  Anticodon_1    Anticodon-binding domain of tRNA
    3.2e-12   46.4   0.1    8.4e-12   45.0   0.1    1.7  1  tRNA-synt_1_2  Leucyl-tRNA synthetase, Domain 2
    2.8e-09   36.8   0.6    0.00025   20.5   0.0    3.8  4  tRNA-synt_1e   tRNA synthetases class I (C) catalytic domain
    0.00077   18.5   0.0     0.0025   16.8   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 !  203.9   0.8   1.2e-63   3.5e-60       1     601 [.      22     650 ..      22     651 .. 0.81

  Alignments for each domain:
  == domain 1  score: 203.9 bits;  conditional E-value: 1.2e-63
                   tRNA-synt_1   1 klyekWeeedvfkkelekekekkefilvdgPPyvtGslHiGhalaktlkdivirykrmkGkevlyvpGwDhaGlaieakve 81 
                                   k+++ We + vf+++    +e+k+f+++++ Py +GslH+Gh  + tl di+ rykr + ++vl+ +G+   G +i a  e
  gi|13541592|ref|NP_111280.1|  22 KWQNAWERDHVFEPK---IDERKKFMITVPWPYTNGSLHVGHGRTYTLGDIIARYKRSRNYNVLFPMGFHQSGTPILAFSE 99 
                                   58899*********9...677899*************************************************99977666 PP

                   tRNA-synt_1  82 kklgake......kkerkklgreefr...ekv...rewkaeyaeeirkqvkrlGvsvDfdreylTldkeleeavkevfvrl 150
                                   +  + +       ++   ++g++++    ek    r++++++++ i +++k+lG s+D+ r+    d+ +++ vk+ f +l
  gi|13541592|ref|NP_111280.1| 100 RIRAGDAstialyRSYLSEYGEKDIDgwlEKFkdpRNIADYFSNAIINDFKHLGYSIDWTRKFTSADEFYQNVVKWQFHKL 180
                                   54322220111114456788887654111333222678999*********************99999999*********** PP

                   tRNA-synt_1 151 adkgliyrgkklvnwstklktalselEveykdkkdalihvafpl..adkeevklviaTTtPeTllgdtavavnpeldyv.. 227
                                    +kgli + k+++ +s +   a+ e +++  d++ ++++ ++ +   ++++ +l++a  +PeTl+g t + +np  +yv  
  gi|13541592|ref|NP_111280.1| 181 NEKGLIKQDKYPILYSIDDDNAVGEDDIKDGDTDKVSVE-EYTAvfFESNSYSLIAASLRPETLFGVTNIWINPTGEYVki 260
                                   ****************************99999988876.4443355566669**************************99 PP

                   tRNA-synt_1 228 .itkeklilaeallkslvkkesekkiledergkeLegkevelplvnrkipiiaddyvdkeaGtGvVkiaPahdedDyevgk 307
                                    i ++  ++ +  +++l  ++++  +   + +++++ k+++ p+ ++++p+ + d+vd+++GtGvV   P h   D+   +
  gi|13541592|ref|NP_111280.1| 261 kIGDKIAVVSKEAVDKLKYQRNDVSVIGPISAESIQRKKFTTPF-GKEVPVYKADFVDTDNGTGVVYSVPSHSVYDFVYYR 340
                                   8889999999999****9999**********************9.689*****************************9988 PP

                   tRNA-synt_1 308 kynl.evinildedgtlteea...............................aefeglkvfdarkkvveelkekglllkae 356
                                   + +  ++++++++  ++ e                                 +e++gl+v dar+k+ ++l   g+ +   
  gi|13541592|ref|NP_111280.1| 341 RKKSgQTPVVIEAPLKMPEVEikfdlnskegldeatkelyksefyygklvnsGEYTGLTVRDAREKIKKDLIGSGKAIIFY 421
                                   877756666666666666555788888888999999***********************************9999876655 PP

                   tRNA-synt_1 357 kiehsvpfcerskkpiiyrateqWfvrvke..ladaalkavekvqfvpkskekryaswleniqdWciSRqrwWGhripl.. 433
                                   +++ +  ++  + k+i+  + +qWf+  ++  l++ + + ++++ ++p+++++ +++ +   ++    R r  G+++p+  
  gi|13541592|ref|NP_111280.1| 422 ETSRKA-VTRGGSKVIVAVLPDQWFIDYSAdwLKKLSHDMLNRMMIYPEMYRNVMNDAIDWLKERPCARRRGLGTKLPFdd 501
                                   544443.333455677788999****98877799999999999999998755555444444444458999********622 PP

                   tRNA-synt_1 434 .fvsketeevvvreelkelvagreeeeaekkalekeakdklkkekgelekdedvlDvWFsSgswpfstlgypeedteelkk 513
                                    +v +         +l++ +      ++ ++ ++    +kl +e+g+l  de+ +   F+ g +++       + ++e++ 
  gi|13541592|ref|NP_111280.1| 502 rWVIE---------SLSDSTI---YPAVYTTSIQ---MRKL-YENGKL--DENAIERIFDGGEVQNDEER---TARNEFSY 561
                                   22222.........2222222...2222222222...2344.344444..78899999****99998777...6688**** PP

                   tRNA-synt_1 514 ffpadmlleGlDiirgWvarlillslaltgsePf.kevlvhglvrdeeGrKmSKslgNvidpldvikkygadalRltli.l 592
                                    +p d+ l+ +  i   ++  ++   a++  e +   ++++glv+ ++G K+SKs+gNv++ l++ kky+ad+ Rl+++ +
  gi|13541592|ref|NP_111280.1| 562 WYPVDIRLTAVPHISNHLSFYVMNHAAIFPPEKWpSGLIISGLVV-SNGAKISKSKGNVVSLLEITKKYSADIYRLYVAvQ 641
                                   ****************99999999999987776615688999998.68*******************************99 PP

                   tRNA-synt_1 593 sdvgrdinl 601
                                   +dv++ +++
  gi|13541592|ref|NP_111280.1| 642 ADVSSTMDW 650
                                   999887776 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 !   40.8   0.0   3.8e-14   1.1e-10       2      54 ..      44      96 ..      43     114 .. 0.93
   2 !   11.0   0.2   4.2e-05      0.13      61     133 ..     132     206 ..     117     213 .. 0.82
   3 !   27.8   0.1   3.3e-10   9.9e-07     307     375 ..     591     659 ..     545     665 .. 0.76

  Alignments for each domain:
  == domain 1  score: 40.8 bits;  conditional E-value: 3.8e-14
                                  EEEE--B--SS---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHH CS
                  tRNA-synt_1g  2 lvttalpYangklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpiel 54
                                  ++t+++pY+ng+lH+Gh +++  +Di+aRykr r+++vlf  g  + Gtpi  
  gi|13541592|ref|NP_111280.1| 44 MITVPWPYTNGSLHVGHGRTYTLGDIIARYKRSRNYNVLFPMGFHQSGTPILA 96
                                  89************************************************975 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 4.2e-05
                                   S-HHHHHHHHHHHHHHHHHHTT---SEEEETTS..HHHHHHHHHHHHHHHHTT-EEEEEEEEEEETTTTEEE-GG CS
                  tRNA-synt_1g  61 vtpeelvekvheeikelfkklnisfdkygrtts..eehkelvqeifkklkekgliyekeieqlycpkderflpdr 133
                                    +p+++++ ++++i ++fk+l+ s d   + ts  e  +++v+  f+kl+ekgli++ ++  ly+ +d++   + 
  gi|13541592|ref|NP_111280.1| 132 KDPRNIADYFSNAIINDFKHLGYSIDWTRKFTSadEFYQNVVKWQFHKLNEKGLIKQDKYPILYSIDDDNAVGED 206
                                   679999**************999998655544311456899999*********************9998776665 PP

  == domain 3  score: 27.8 bits;  conditional E-value: 3.3e-10
                                   TT----S-EEEE--EEE--------------HHHHHHHH-HHHHHHHHHHHS-TTS-EEE-HHHHHHHH CS
                  tRNA-synt_1g 307 aelklpkkvvaheyltvegkKlSkSrgvvvkakealerldadllRYylaaeapekkDldfswedfverv 375
                                      k p+ ++ ++ +  +g+K+SkS+g+vv   e++++++ad+ R y+a++a+ ++ +d++++d+ + v
  gi|13541592|ref|NP_111280.1| 591 PPEKWPSGLIISGLVVSNGAKISKSKGNVVSLLEITKKYSADIYRLYVAVQADVSSTMDWNENDLSNIV 659
                                   3456799999*************************************************9999887654 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 !   47.0   0.2   8.2e-16   2.5e-12       2     147 ..     684     822 ..     683     827 .. 0.80

  Alignments for each domain:
  == domain 1  score: 47.0 bits;  conditional E-value: 8.2e-16
                   Anticodon_1   2 rwilselnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedkraaqevllevletllrllaPfmP 82 
                                    w++s++++ +k++ + ++ +++++a+ ++++ ++ndl     + + +r +s++        + l+ ++  +lr l P++ 
  gi|13541592|ref|NP_111280.1| 684 TWFVSRFAERLKQFMDQMDGFQIRDAYINIFYGTLNDL-----KYAVNRGASQN--------RSLASIIADWLRALMPVIS 751
                                   6***********************************99.....33334443332........67***************** PP

                   Anticodon_1  83 fitEelwqreeeelgkkesimlaewpe.kaeelekel.e.........eeevellkeivkairklrselkikpsse 147
                                   + +Ee w    +++ +++ ++ +++ +  a e ++ l +          + +++++ i++ i+++ s  +i p+s 
  gi|13541592|ref|NP_111280.1| 752 HHAEEYW----HRYVSNTYVSINPFDDnFA-EKYERLaKvyglstsefYQVMDYVEHIIQDINNIISVTGIEPKSV 822
                                   *******....7777888899999985322.222222335567777889999999999999999999999998864 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 !   45.0   0.1   2.8e-15   8.4e-12      29     184 ..     239     411 ..     226     412 .. 0.79

  Alignments for each domain:
  == domain 1  score: 45.0 bits;  conditional E-value: 2.8e-15
                 tRNA-synt_1_2  29 rpdtlfGvtfvalapehplvekl.aekkkel.aafieevkkksesereletkekeGvftglkaihPitgekipiwvanyvl 107
                                   rp+tlfGvt + + p  + v+    +k + + ++ ++++k +++  + +   + e ++ + k + P+ g+++p++ a++v 
  gi|13541592|ref|NP_111280.1| 239 RPETLFGVTNIWINPTGEYVKIKiGDKIAVVsKEAVDKLKYQRNDVSVIGPISAESIQRK-KFTTPF-GKEVPVYKADFVD 317
                                   9****************9998653444444425788999999999999999988888766.567798.789********** PP

                 tRNA-synt_1_2 108 meygtgavmavPahdqrDfeFakkynlpikqvikpedee.kklee.............seeayte...egilvnsgefdgl 171
                                   ++ gtg+v +vP+h   Df + ++ +   ++v+ ++  +  ++e+             ++e y++    g+lvnsge++gl
  gi|13541592|ref|NP_111280.1| 318 TDNGTGVVYSVPSHSVYDFVYYRRKKSGQTPVVIEAPLKmPEVEIkfdlnskegldeaTKELYKSefyYGKLVNSGEYTGL 398
                                   ********************99988876666655333333555544556677777777666666534579*********** PP

                 tRNA-synt_1_2 172 kskeakekiakkl 184
                                   ++++a+eki k l
  gi|13541592|ref|NP_111280.1| 399 TVRDAREKIKKDL 411
                                   *********9875 PP

>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.0     4e-05      0.12      20      50 ..      53      83 ..      36     173 .. 0.91
   2 ?   -1.6   0.0      0.45   1.4e+03     128     171 ..     519     562 ..     412     565 .. 0.79
   3 !   20.5   0.0   8.4e-08   0.00025     229     298 ..     586     657 ..     569     660 .. 0.81
   4 ?   -1.2   0.0      0.33     1e+03      77     117 ..     774     813 ..     761     844 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4e-05
                                  TS--BHHHHHHHHHHHHHHHHHHHTT-EEEE CS
                  tRNA-synt_1e 20 ydashlGhaRslvafDilrrilqalgYdvqf 50
                                      h+Gh+R++   Di++r+ ++++Y+v f
  gi|13541592|ref|NP_111280.1| 53 NGSLHVGHGRTYTLGDIIARYKRSRNYNVLF 83
                                  5679*************************98 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.45
                                   -EEE-GGG-TTTTTTTT--HHHHHHT----S--S-SSTT-EEEE CS
                  tRNA-synt_1e 128 dvyfdvskkeeYgklskqnleelelgaegevseekkdkkDfaLW 171
                                   ++  +++k  e gkl+++ +e + +g e+++ ee+  +++f  W
  gi|13541592|ref|NP_111280.1| 519 TTSIQMRKLYENGKLDENAIERIFDGGEVQNDEERTARNEFSYW 562
                                   55566677778889999999999888888888888888999888 PP

  == domain 3  score: 20.5 bits;  conditional E-value: 8.4e-08
                                   HHHHSS.S--EEEEEEE--EEETTBE--TTTT---BHHHHHTTS-HHHHHHHHH.SS-TTS-EEE-HHHHHH CS
                  tRNA-synt_1e 229 seaafd.kqlvkyflhnghlkiegekmsksLknfitikdvlkkfdprqlRllll.sahyrsqldfkeellee 298
                                   + a f  +++    + +g +  +g k+sks +n++++ ++ kk+++ + Rl+++ +a+  s++d++e++l++
  gi|13541592|ref|NP_111280.1| 586 HAAIFPpEKWPSGLIISGLVVSNGAKISKSKGNVVSLLEITKKYSADIYRLYVAvQADVSSTMDWNENDLSN 657
                                   455565567777888899********************************99862678999*******9987 PP

  == domain 4  score: -1.2 bits;  conditional E-value: 0.33
                                   HHHHHHHHHHHHHTT----SB--BGGGGHHHHHHHHHHHHH CS
                  tRNA-synt_1e  77 ekfieefkkdleaLnvlkptleprvsekvdeiielveklie 117
                                   ++f e++++  +  ++  ++   +v+++v++ii+ ++++i+
  gi|13541592|ref|NP_111280.1| 774 DNFAEKYERLAKVYGLS-TSEFYQVMDYVEHIIQDINNIIS 813
                                   45555555544444443.35556888888888888888875 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 !   16.8   0.0   8.2e-07    0.0025     266     340 ..     596     670 ..     574     711 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 8.2e-07
                  tRNA-synt_1f 266 PekvvYelillkggekmssSkGnvltledwlevaepevlrflilr.rkPkkakkldldleilrlvdeYdklerkyf 340
                                   P +++   + +++g+k+s+SkGnv++l ++++ ++ ++ r++++  +   + ++ + + ++ ++v  +++++ ++ 
  gi|13541592|ref|NP_111280.1| 596 PSGLIISGLVVSNGAKISKSKGNVVSLLEITKKYSADIYRLYVAVqADVSSTMDWNEN-DLSNIVRRFNEFKTIMD 670
                                   666666667889999*************************988750445555555555.78888877777776664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (910 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       621  (0.0346366); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); 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: 0.84u 0.29s 00:00:01.12 Elapsed: 00:00:00.54
# Mc/sec: 5086.32
//
Query:       gi|13541593|ref|NP_111281.1|  [L=182]
Description: pyruvoyl-dependent arginine decarboxylase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-58  197.1   0.1    1.8e-58  196.9   0.1    1.0  1  PvlArgDC  Pyruvoyl-dependent arginine decarboxylase (PvlArgDC


Domain annotation for each model (and alignments):
>> PvlArgDC  Pyruvoyl-dependent arginine decarboxylase (PvlArgDC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  196.9   0.1     1e-62   1.8e-58       1     162 []       5     180 ..       5     180 .. 0.99

  Alignments for each domain:
  == domain 1  score: 196.9 bits;  conditional E-value: 1e-62
                      PvlArgDC   1 vPkkvfltkGvgeskeelasFdlALldAgIenfNLvkvSSilPpeaeivsveeglkelppGsivevvmarassnepgrlia 81 
                                   vP+++f+t+Gvg+++++l+sF++AL+dAgI++fNL ++SSi+Pp+a++vs+eeglk+l+pG+i+++v+ar++sne +r+i+
  gi|13541593|ref|NP_111281.1|   5 VPSEIFFTRGVGRGETQLESFEAALRDAGIAQFNLSSISSIFPPHAKMVSKEEGLKKLSPGQILFTVLARNTSNELNRMIS 85 
                                   79******************************************************************************* PP

                      PvlArgDC  82 aavgvaipkdekkgGyiaEysgfgeseeeaeeeaeelaaemlattrgl..............leekiietkeievaaveak 148
                                   aa+g+aip+d++k+Gy++E+++fge+e+ a++ ae+laaeml++t g               le+ki++t +i+++av+  
  gi|13541593|ref|NP_111281.1|  86 AAIGYAIPRDKSKWGYLSEHHSFGETEKVAGSFAEKLAAEMLSSTFGStsqliydkekeeyvLEDKILTTGNISATAVVLS 166
                                   ********************************************9999*************9899**************** PP

                      PvlArgDC 149 vekygtvlaaavfv 162
                                   +++++tv+aaav++
  gi|13541593|ref|NP_111281.1| 167 HDEWTTVVAAAVLI 180
                                   ************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1150.42
//
Query:       gi|13541594|ref|NP_111282.1|  [L=486]
Description: amino acid transporter [Thermoplasma volcanium GSS1]
Scores for complete 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  121.0  55.5    5.5e-35  121.0  55.5    1.9  2  AA_permease_2  Amino acid permease
    1.5e-23   83.2  49.1    1.5e-23   83.2  49.1    1.8  2  AA_permease    Amino acid permease
  ------ inclusion threshold ------
       0.75   10.6   0.1       0.75   10.6   0.1    5.5  6  DUF751         Protein of unknown function (DUF751)


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 !  121.0  55.5   9.2e-39   5.5e-35       2     406 ..      19     435 ..      18     444 .. 0.83
   2 ?    0.1   1.6     0.046   2.8e+02     157     206 ..     440     485 ..     436     486 .] 0.55

  Alignments for each domain:
  == domain 1  score: 121.0 bits;  conditional E-value: 9.2e-39
                 AA_permease_2   2 sllsafalvigsvigsgifvkn...laasggpalilwvwiavligslavllvyaElssalprsgGiyvytkaafgkkvafl 79 
                                   sl+ +++l +  +igsg +++    + ++g   +i++++++ +i+   v+l+++E+ssa+p  gG    ++ afgk+ +f+
  gi|13541594|ref|NP_111282.1|  19 SLFNLVMLNSMGMIGSGWLFAAlytSSYAGSFGSIVSWILGGVIV-ALVALTFMEVSSAFPLAGGSTPMGEFAFGKLGGFI 98 
                                   6666666666667****9999877655557777***********9.58********999********************** PP

                 AA_permease_2  80 sawfnwfayvpvlasilsvaasyllnalgpdlqgntw...ltyliaiaililvalinirgikesakiqnilgilkillpli 157
                                   ++w +w++ + + ++ +++++ yl +++++ ++++ +   l yl++i++li+++lin+ ++k  +++++ ++i+k+ +p +
  gi|13541594|ref|NP_111282.1|  99 AGWGAWISDIMTPPIEAVAMVTYLSFFVKGLITPSGIllpLGYLVVIIVLIVIFLINLQAVKVFGNVTSGIMIWKWAVPAL 179
                                   ***************************999777775533377**********************************99954 PP

                 AA_permease_2 158 iliilglitvdgggfsslstetdtffpngwpg.vllgllivlwsfdGfesaanvseevkkkd.vpkaifigllivlvlyll 236
                                    +i   li + ++ ++++  + + f ++ + + ++l+l++v++sf Gf +a+n++ e +++d + k  +i++++vl lyl 
  gi|13541594|ref|NP_111282.1| 180 AVI--TLISLAFHPSNFA--IAGRFYQGYSGIfYALVLGGVVFSFEGFRGAINMAAESQHRDyIWKSVIIAVGVVLALYLA 256
                                   444..4444445555432..455555554443379999**********************988****************** PP

                 AA_permease_2 237 vniaflgvvpddei.......anlsnlgsv......aalffeavg...gkvvaiivvilialsllgaintavigssrvlea 301
                                   +++af+g++ +++               s+       ++f+e +     +++  i+ i +++s  ga++++ ++ +r++++
  gi|13541594|ref|NP_111282.1| 257 IQVAFIGALDWNKAgvslgdwG------SLstsvllSGPFAEEAKfvxLGWLVFILLIDAVVSPGGAGLSYAAYPARIFQS 331
                                   ***********99964444441......4344555566666666544478******************************* PP

                 AA_permease_2 302 lardgvlPrffakvnkfgspiraiiltaivslillllfllassaaynfllsvsslgliisyllliigalilrkkrphlkrp 382
                                   +a+ g+ P++f+  +k++ p ra+il + v l++l  f +      ++ll + +  l+i y +  ++  ilrk+ p+ +r+
  gi|13541594|ref|NP_111282.1| 332 MAEFGYAPKWFKELSKKKVPARALILGFFVGLVFLYEFPG-----WDLLLGILTSTLVIGYVMGPASINILRKHAPNVERM 407
                                   *******************************998877776.....59*********************************6 PP

                 AA_permease_2 383 gk....ilvaiigalfllfllvalffpp 406
                                    +      +a i+++f+ +++++  +p+
  gi|13541594|ref|NP_111282.1| 408 FMlrgsSFIAPIAFIFSSLIIYWSGWPL 435
                                   5544545667777777777776666665 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.046
                 AA_permease_2 157 iiliilglitvdgggfsslstetdtffpngwpgv.llgllivlwsfdGfes 206
                                   ++++i+gl+++  ++f+   + +d  + ++ +g+ l++ll v+ +++G+++
  gi|13541594|ref|NP_111282.1| 440 VVAVIAGLFMF--SYFT---HVNDFDWVEIRSGMwLVALLFVIAVLSGYDF 485
                                   45566666665..3333...2245556666666634456666777777665 PP

>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.2  49.1   2.5e-27   1.5e-23       3     382 ..      24     389 ..      22     429 .. 0.83
   2 ?   -4.3   4.4      0.86   5.1e+03      80     127 ..     427     477 ..     412     482 .. 0.63

  Alignments for each domain:
  == domain 1  score: 83.2 bits;  conditional E-value: 2.5e-27
                   AA_permease   3 lvialggviGtglfvglgvvlsqaGplgallayllagvviflvmlslgeiatngpksggfytyasrflgpelGfviGlnyl 83 
                                   ++ +  g+iG g +++  ++ s aG  g +++++l+gv+++lv+l++ e+++++p +gg + + +   g+  Gf  G+  +
  gi|13541594|ref|NP_111282.1|  24 VMLNSMGMIGSGWLFAALYTSSYAGSFGSIVSWILGGVIVALVALTFMEVSSAFPLAGGSTPMGEFAFGKLGGFIAGWGAW 104
                                   66777789************************************************************************* PP

                   AA_permease  84 fswitvlaleltaasiliqfwelvtdlpkawvt........gavflvvlliinlvgvkvygeaefi.lalikiiaiiafii 155
                                   +s+i++ ++e +a++ +++f   v+ l++  ++        ++++l+v+++inl +vkv+g +    +++ + + ++a+i 
  gi|13541594|ref|NP_111282.1| 105 ISDIMTPPIEAVAMVTYLSFF--VKGLITPSGIllplgylvVIIVLIVIFLINLQAVKVFGNVTSGiMIWKWAVPALAVIT 183
                                   *********************..99999999999******9999999999***********97555155555555555555 PP

                   AA_permease 156 vgiillaggkpnkga.gfrflgdngsifknnlppgfakeeegafknfisvfvivvfaftGielvaiiagEvkdPeksiPka 235
                                   +    +   +p+++a  +rf++  ++if++ + +g                  vvf+f G+   +++a+E++  +  i k+
  gi|13541594|ref|NP_111282.1| 184 LI---SLAFHPSNFAiAGRFYQGYSGIFYALVLGG------------------VVFSFEGFRGAINMAAESQH-RDYIWKS 242
                                   44...566777788444555555555455444444..................99***************986.99***** PP

                   AA_permease 236 ilqvviritifYvlsllligllvprndlgllndsasa.......aspfvifikesgvsvlaplinaviltaalssanssly 309
                                   ++ +v  ++ +Y+ + ++ +  +++n  g+  +           ++pf    k+  +  l +++ +   ++  ++++s+ +
  gi|13541594|ref|NP_111282.1| 243 VIIAVGVVLALYLAIQVAFIGALDWNKAGVSLGDWGSlstsvllSGPFAEEAKFVXLGWLVFILLIDAVVSPGGAGLSYAA 323
                                   **************************98875533222577889999*999888888877777777777889999******* PP

                   AA_permease 310 sasRvlyslakdglaPkvlkkvskrgvPlraillsmiisllal....llaslnlaapivfnfllaisaliglivwll 382
                                      R+++s+a+ g+aPk++k +sk++vP+ra++l ++++l++l                ++ ll i +   +i +++
  gi|13541594|ref|NP_111282.1| 324 YPARIFQSMAEFGYAPKWFKELSKKKVPARALILGFFVGLVFLyefpG-----------WDLLLGILTSTLVIGYVM 389
                                   ******************************************934330...........444444444444444444 PP

  == domain 2  score: -4.3 bits;  conditional E-value: 0.86
                   AA_permease  80 lnylfswitvlaleltaasiliqfwelvtdlpkawvt.....gavflvvllii 127
                                   ++y++ w +   + +++++ l+ f  ++t+++  + +     g+ ++++l++i
  gi|13541594|ref|NP_111282.1| 427 IIYWSGWPLSGEVVVAVIAGLFMFS-YFTHVN-DFDWveirsGMWLVALLFVI 477
                                   3477777777777777777777777.788888.77777777744444444444 PP

>> DUF751  Protein of unknown function (DUF751)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.3       2.8   1.7e+04      16      19 ..      57      60 ..      46      70 .. 0.51
   2 ?   -0.2   0.2      0.29   1.7e+03      18      44 ..      96     122 ..      88     131 .. 0.73
   3 ?   -3.9   4.1         3   1.8e+04      16      52 ..     146     183 ..     139     189 .. 0.54
   4 ?   -3.0   0.2       2.2   1.3e+04      41      53 ..     243     255 ..     240     259 .. 0.61
   5 ?   10.6   0.1   0.00013      0.75      25      52 ..     340     367 ..     332     369 .. 0.90
   6 ?    3.0   1.6     0.028   1.7e+02      15      54 ..     415     454 ..     413     455 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 2.8
                        DUF751 16 llGi 19
                                  +lG 
  gi|13541594|ref|NP_111282.1| 57 ILGG 60
                                  2222 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.29
                        DUF751  18 Giflalfeplkpllknpvtaialigll 44 
                                   G++     ++  ++  p+ a+a++  l
  gi|13541594|ref|NP_111282.1|  96 GFIAGWGAWISDIMTPPIEAVAMVTYL 122
                                   455556679999999999999998765 PP

  == domain 3  score: -3.9 bits;  conditional E-value: 3
                        DUF751  16 llGiflalfe.plkpllknpvtaialigllvgglafly 52 
                                   ++ i+++l++ + ++++ n ++ i++    v +la+++
  gi|13541594|ref|NP_111282.1| 146 IVLIVIFLINlQAVKVFGNVTSGIMIWKWAVPALAVIT 183
                                   33333333221455667777777776666666666555 PP

  == domain 4  score: -3.0 bits;  conditional E-value: 2.2
                        DUF751  41 igllvgglaflyf 53 
                                   +++ vg+++ ly+
  gi|13541594|ref|NP_111282.1| 243 VIIAVGVVLALYL 255
                                   4556666666665 PP

  == domain 5  score: 10.6 bits;  conditional E-value: 0.00013
                        DUF751  25 eplkpllknpvtaialigllvgglafly 52 
                                   +++k+l k++v a ali+++  gl+fly
  gi|13541594|ref|NP_111282.1| 340 KWFKELSKKKVPARALILGFFVGLVFLY 367
                                   8*************99999999999997 PP

  == domain 6  score: 3.0 bits;  conditional E-value: 0.028
                        DUF751  15 illGiflalfeplkpllknpvtaialigllvgglaflyft 54 
                                   ++  i++++ + ++ +   p++  +++ +++g+++f yft
  gi|13541594|ref|NP_111282.1| 415 FIAPIAFIFSSLIIYWSGWPLSGEVVVAVIAGLFMFSYFT 454
                                   5666777777778888888999999**************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (486 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       965  (0.0538234); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                        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: 0.77u 0.31s 00:00:01.08 Elapsed: 00:00:00.49
# Mc/sec: 2956.76
//
Query:       gi|13541595|ref|NP_111283.1|  [L=416]
Description: transposase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.9e-20   71.3   1.0    1.4e-19   70.5   1.0    1.4  1  OrfB_IS605      Probable transposase
    7.8e-09   35.3   0.0    2.5e-08   33.7   0.0    1.9  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
     0.0012   18.2   0.4     0.0019   17.6   0.4    1.3  1  Glyco_hydro_97  Glycoside hydrolase 97
  ------ inclusion threshold ------
       0.16   12.3   0.4       0.55   10.6   0.1    2.0  2  RuvX            Holliday junction resolvase


Domain annotation for each model (and alignments):
>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.5   1.0   3.1e-23   1.4e-19       2     117 ..     172     289 ..     171     292 .. 0.94

  Alignments for each domain:
  == domain 1  score: 70.5 bits;  conditional E-value: 3.1e-23
                    OrfB_IS605   2 ipveveve.lpkpkgnkaagiDlGinnLatvvtedgtw.flykgrrlksdykylakeiaelqsklkksknykkasrklarl 80 
                                   i++e e+   p +k++++ giD+G++nL+t  ++  ++ +  k+  lks ++y++ke a+  s+ + ++n +k++ k+++l
  gi|13541595|ref|NP_111283.1| 172 IVYEKETAdIPITKPKRVMGIDIGVRNLVTIGNNIHERgIAVKAGLLKSINQYFNKELARYRSINDLQGNERKQTVKIRKL 252
                                   67887776699************************9988778889************************************ PP

                    OrfB_IS605  81 hrkrsrrrkhllhklathliktlkevgvetLnvgnmk 117
                                   ++kr+r++k+ +hk++++++++ k ++++t+++g+  
  gi|13541595|ref|NP_111283.1| 253 FMKRNRKVKDIMHKVSKSIVEYAKIMNIDTIVIGHNN 289
                                   *********************************9876 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 !   33.7   0.0   5.5e-12   2.5e-08       1      69 []     310     384 ..     310     384 .. 0.84

  Alignments for each domain:
  == domain 1  score: 33.7 bits;  conditional E-value: 5.5e-12
                OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknke.......alsgrtfkCpnCgfeadrDvnAaiNilkr 69 
                                   f+ l+ q++yka+e Gi+v+  n+ yTSk Cs    ++ e       ++ +r    ++ g  +++D+ +++Ni+k+
  gi|13541595|ref|NP_111283.1| 310 FNMLISQIKYKAEEIGITVIMQNEDYTSK-CSFLDNESIEhhgtymgKRIHRGIFQSATGKLIHADLQSSYNIIKK 384
                                   78899***********************8.5544444444477888878888888888***************996 PP

>> Glyco_hydro_97  Glycoside hydrolase 97
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.4   4.2e-07    0.0019      30     110 ..     261     340 ..     237     391 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 4.2e-07
                Glyco_hydro_97  30 hgantetvkryiDfAaengleyvlvegwdegWee..kkkkekefdftkpypdfdleelvaYakekgvgvelwlhsetsgnv 108
                                   + +  +  k  +++A+ ++++++++ g ++ W++  ++ k+++++f++   ++ + ++   a+e g  +++++++e ++++
  gi|13541595|ref|NP_111283.1| 261 KDIMHKVSKSIVEYAKIMNIDTIVI-GHNNRWKDssNMGKKNNQNFVQLPFNMLISQIKYKAEEIG--ITVIMQNEDYTSK 338
                                   5566777899***************.*******998888999999999999999999877777777..7777777665554 PP

                Glyco_hydro_97 109 an 110
                                    +
  gi|13541595|ref|NP_111283.1| 339 CS 340
                                   43 PP

>> RuvX  Holliday junction resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.73   3.3e+03       2      12 ..     188     198 ..     187     238 .. 0.74
   2 ?   10.6   0.1   0.00012      0.55      37     101 ..     265     339 ..     239     357 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.73
                                   -EEEEEESSSE CS
                          RuvX   2 rilglDvGtkr 12 
                                   r++g+D+G ++
  gi|13541595|ref|NP_111283.1| 188 RVMGIDIGVRN 198
                                   89999999764 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00012
                                   HHHHHHHHHHHHHTT--EEEEE------SSS---SSTTHHHHHHHHHT............T-EEEEE--S----X CS
                          RuvX  37 ekdleelkelvkeeeveeiVvGlPlnldgsegesakkvrkfaeeLakrl..........kklpvelvDErlttve 101
                                   +k  + + e++k  ++++iV+G   + ++s++   k+ ++f++   + l           +++v++ +E +t++ 
  gi|13541595|ref|NP_111283.1| 265 HKVSKSIVEYAKIMNIDTIVIGHNNRWKDSSNMGKKNNQNFVQLPFNMLisqikykaeeIGITVIMQNEDYTSKC 339
                                   45567788888888**********888888888888888888765444456667777777889*********985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (416 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1134  (0.0632495); expected 358.6 (0.02)
Passed bias filter:                      531  (0.0296168); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.49
# Mc/sec: 2556.53
//
Query:       gi|13541596|ref|NP_111284.1|  [L=137]
Description: site-specific integrase-resolvase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.3e-05   24.0   0.0    8.5e-05   22.7   0.0    1.7  2  HTH_17        Helix-turn-helix domain
     0.0003   20.9   0.1    0.00045   20.3   0.1    1.4  1  Resolvase     Resolvase, N terminal domain
     0.0087   16.1   0.3      0.018   15.1   0.3    1.5  1  MerR_1        MerR HTH family regulatory protein
  ------ inclusion threshold ------
       0.03   14.5   0.4      0.051   13.8   0.4    1.3  1  Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain


Domain annotation for each model (and alignments):
>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.0   1.9e-08   8.5e-05       2      49 ..       1      49 [.       1      51 [. 0.89
   2 ?   -2.1   0.0         1   4.5e+03      30      43 ..      83      97 ..      67      97 .. 0.60

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 1.9e-08
                        HTH_17  2 ltveEaAelLgvsrstvyrlirrgelpaa.kiGrrwriprsdleewlek 49
                                  ++ eE+ +lL +sr+t++ + ++g+++++   ++r+ + ++d+ + l+k
  gi|13541596|ref|NP_111284.1|  1 MKAEEVLNLLQISRKTLHVYSKDGRIRYTvMPNKRYNYNEEDVYKILNK 49
                                  789***********************999636677*******9999987 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1
                        HTH_17 30 a.kiGrrwriprsdl 43
                                  + +i ++  +++s++
  gi|13541596|ref|NP_111284.1| 83 YeRIYNKCTFTCSEV 97
                                  246777778888875 PP

>> Resolvase  Resolvase, N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.1     1e-07   0.00045       2      41 ..      56      97 ..      55     129 .. 0.72

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 1e-07
                                  EEEEEES-----THHHHHHHHHHHH-S--..SE.......EEEE CS
                     Resolvase  2 igYaRvSteeqddslerQkealrayakenglkivk....efeDk 41
                                  ++Y RvSt++q+++l++Q+++ +++   +  +i +    + ++ 
  gi|13541596|ref|NP_111284.1| 56 VLYERVSTAKQKNDLQNQIDQMKQVVFYE--RIYNkctfTCSEV 97
                                  79**********************99887..6544452333444 PP

>> MerR_1  MerR HTH family regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.3     4e-06     0.018       1      46 [.       1      46 [.       1      48 [. 0.91

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 4e-06
                                  EEHHHHHHHHTS-HHHHHHHHHHTT-S-EE-TTS-EEEEHHHHHHH CS
                        MerR_1  1 ysigevakilgvtthtlrywekegllkpkrteggrryYtdedierL 46
                                  ++  ev ++l+++ +tl+ + k g ++     + r+ Y++ed+  +
  gi|13541596|ref|NP_111284.1|  1 MKAEEVLNLLQISRKTLHVYSKDGRIRYTVMPNKRYNYNEEDVYKI 46
                                  6678999***********************88888*******9876 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 ?   13.8   0.4   1.1e-05     0.051      23      64 ..      38      79 ..      31      90 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.1e-05
                                  CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC CS
                  Seryl_tRNA_N 23 edkadvdelleldekrrelqveleelqaerNelskeIgkakk 64
                                    ++dv ++l  d kr+++  e  +  +++N l+++I ++k+
  gi|13541596|ref|NP_111284.1| 38 YNEEDVYKILNKDVKRKTVLYERVSTAKQKNDLQNQIDQMKQ 79
                                  5689***********************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1432  (0.0798706); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 934.64
//
Query:       gi|13541597|ref|NP_111285.1|  [L=67]
Description: hypothetical protein TVN0766 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.053   14.0   1.6      0.063   13.7   1.6    1.1  1  DUF202    Domain of unknown function (DUF202)


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 ?   13.7   1.6   3.5e-06     0.063      16      65 ..      12      64 ..       8      67 .] 0.73

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.5e-06
                        DUF202 16 tslalialglallrffltgepsal...gkilglilivlgiltllvglvrylrr 65
                                   slal +++++l+ +  +++ + +    ++  ++l++l++++++v ++ y+  
  gi|13541597|ref|NP_111285.1| 12 SSLALSIIAFLLALILMQPNSAGYpevPAVPTYVLFGLSAASFAVFIYEYFTA 64
                                  5788888888888776666666652214666899********99999999965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (67 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       682  (0.0380389); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 451.51
//
Query:       gi|13541598|ref|NP_111286.1|  [L=301]
Description: acetyltransferase [Thermoplasma volcanium GSS1]
Scores for complete 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-13   49.1   0.0    1.5e-12   47.8   0.0    1.8  2  Acetyltransf_1   Acetyltransferase (GNAT) family
    1.2e-12   47.9   0.0    3.2e-12   46.5   0.0    1.7  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    3.3e-10   40.3   0.0    6.7e-10   39.3   0.0    1.6  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    1.6e-07   31.1   0.0    8.6e-07   28.8   0.0    2.0  2  FR47             FR47-like protein
    7.9e-06   26.1   0.6    0.00024   21.3   0.2    2.3  2  Acetyltransf_4   Acetyltransferase (GNAT) domain
     0.0016   18.4   0.0     0.0032   17.4   0.0    1.5  1  Acetyltransf_13  ESCO1/2 acetyl-transferase
     0.0063   16.6   0.0      0.016   15.3   0.0    1.8  1  Acetyltransf_9   Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
      0.017   15.0   0.1        4.5    7.1   0.0    2.7  2  Acetyltransf_18  Acetyltransferase (GNAT) domain
      0.022   14.9   0.0      0.091   12.9   0.0    2.1  1  Acetyltransf_CG  GCN5-related N-acetyl-transferase
       0.13   12.0   0.0       0.21   11.3   0.0    1.3  1  UNC-93           Ion channel regulatory protein UNC-93


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 ?   -2.9   0.0       4.3   7.7e+03      34      48 ..      45      59 ..      16      77 .. 0.56
   2 !   47.8   0.0   8.2e-16   1.5e-12      41     117 .]     206     282 ..     143     282 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 4.3
                                  EEEEEEETTEEEEEE CS
                Acetyltransf_1 34 gllvaeedgeliGfi 48
                                     v  +++e+ G++
  gi|13541598|ref|NP_111286.1| 45 KNRVLIHGDEVMGYA 59
                                  222333556666666 PP

  == domain 2  score: 47.8 bits;  conditional E-value: 8.2e-16
                                   T...TEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTESEEEEEEETTEHHHHHHHHHTTE CS
                Acetyltransf_1  41 d...geliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeerareegikkivlaveedndaairlYeklGF 117
                                   +   +++ G +   k+    +g+++i +l+Vs+e r+kG+++aLl+++++ +r+  i+ + l v+e n +ai lY+k+GF
  gi|13541598|ref|NP_111286.1| 206 IygsEKIQGGLITVKYL--GTGEYFISDLFVSKEQRNKGIATALLNEAAKALRNLKIEDVSLIVSEGN-PAIDLYKKMGF 282
                                   34446666666444443..58*****************************99999**99999898877.******88**9 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.5   0.0   1.8e-15   3.2e-12      52     113 ..     224     289 ..     187     295 .. 0.84

  Alignments for each domain:
  == domain 1  score: 46.5 bits;  conditional E-value: 1.8e-15
               Acetyltransf_10  52 s...hisllfVdpeyrgqGigkaLleaveeeaekdgikl.eltvnaspyavpfYeklGFkavgeeq 113
                                        is lfV++e+r +Gi++aLl+++ +++++ +i+  +l v + + a+++Y+k+GF+  g+ +
  gi|13541598|ref|NP_111286.1| 224 TgeyFISDLFVSKEQRNKGIATALLNEAAKALRNLKIEDvSLIVSEGNPAIDLYKKMGFEYSGQRK 289
                                   244689*****************************************************9887765 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.3   0.0   3.8e-13   6.7e-10      21      75 ..     220     283 ..     183     284 .. 0.67

  Alignments for each domain:
  == domain 1  score: 39.3 bits;  conditional E-value: 3.8e-13
                                   EEES...TCTEEEEE-GGGTTSSHHHHHHH.HTT...SEEEEEEEEE..THH..HHHHHHHHTTEE CS
                Acetyltransf_7  21 slld...aeitrlaVdpeyrgkGiGraLle.aae...kgiileqlel..nae..kaikfYeklGFe 75 
                                   + l+   + i  l+V++e r+kGi++aLl+ a +   +++++e + l  + e  +ai++Y+k+GFe
  gi|13541598|ref|NP_111286.1| 220 KYLGtgeYFISDLFVSKEQRNKGIATALLNeA-AkalRNLKIEDVSLivS-EgnPAIDLYKKMGFE 283
                                   222243334444*****************943.22455544443344442.2349**********8 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.97   1.7e+03      64      80 ..     111     127 ..     105     131 .. 0.83
   2 !   28.8   0.0   4.8e-10   8.6e-07      23      83 ..     228     288 ..     218     291 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.97
                                   T-HHHHHHHHHHT-EEE CS
                          FR47  64 sNtpsirlyeklGfeki 80 
                                   +N++   ++ klG+ k 
  gi|13541598|ref|NP_111286.1| 111 ANDECDDILAKLGYSKV 127
                                   788889999*****987 PP

  == domain 2  score: 28.8 bits;  conditional E-value: 4.8e-10
                                   SEEEEEE-GGG-SSSHHHHHHHHHHHHHHHS-S-EEEEEETT-HHHHHHHHHHT-EEEEEE CS
                          FR47  23 elgalqvlpehrrrGlgsrlvkalakeiaergktvllvvvasNtpsirlyeklGfekieet 83 
                                   +++ l v +e r++G ++ l ++ ak++++  ++ + ++v + +p+i ly+k+Gfe   ++
  gi|13541598|ref|NP_111286.1| 228 FISDLFVSKEQRNKGIATALLNEAAKALRNLKIEDVSLIVSEGNPAIDLYKKMGFEYSGQR 288
                                   578899************************77777777777778***********987555 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0     0.052        93      98     146 ..      87     136 ..      29     141 .. 0.82
   2 !   21.3   0.2   1.4e-07   0.00024      47     146 ..     202     294 ..     155     296 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.052
                Acetyltransf_4  98 lidaleqvl.keqnienllaeiaspnensiqfhkalGFelvgifkkcikk 146
                                   l ++le +     +++ +l ei+ +n++  +++++lG+++v + k  +k 
  gi|13541598|ref|NP_111286.1|  87 LKNLLEWIHvNSGGLRVFLDEIFNANDECDDILAKLGYSKVTRIKLTAKT 136
                                   5555555554667888899999999***************9988766665 PP

  == domain 2  score: 21.3 bits;  conditional E-value: 1.4e-07
                Acetyltransf_4  47 ekeyvflvae.sdrivGyaylgqfkkrakdwkaelsvylaerdnnkeglgrelidaleqvlkeqnienllaeiaspnensi 126
                                   e +++++ ++ ++ ++   ylg  ++       +   ++  + ++++g++ +l++   + l++  ie     i+s+  ++i
  gi|13541598|ref|NP_111286.1| 202 EASFIYGSEKiQGGLITVKYLGTGEY------FISDLFVS-KEQRNKGIATALLNEAAKALRNLKIEDV-SLIVSEGNPAI 274
                                   45888888888888888888886666......77777775.89*************************7.57888999*** PP

                Acetyltransf_4 127 qfhkalGFelvgifkkcikk 146
                                   +++k++GFe  g+ k +i++
  gi|13541598|ref|NP_111286.1| 275 DLYKKMGFEYSGQRKYVIYI 294
                                   ************99988886 PP

>> Acetyltransf_13  ESCO1/2 acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   1.8e-06    0.0032       7      32 ..     229     254 ..     227     265 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.8e-06
               Acetyltransf_13   7 isriWvssshRrkgiAtkLldaaren 32 
                                   is ++vs++ R+kgiAt+Ll+ a++ 
  gi|13541598|ref|NP_111286.1| 229 ISDLFVSKEQRNKGIATALLNEAAKA 254
                                   899******************99875 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   9.1e-06     0.016      75     127 ..     228     284 ..     148     285 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 9.1e-06
                                   EEEEEEE-CCGTTS-HHHHHHHHHHHHHHHT...T--EEEE--.SSHHHHHTTT-EE CS
                Acetyltransf_9  75 gvtgVavapehrgrgvlskLlaraleemree...gqplsllfP.ssipiYrrfGyei 127
                                    +++  v  e+r++g++++Ll++a + +r     +++l++  +  +i++Y+++G+e+
  gi|13541598|ref|NP_111286.1| 228 FISDLFVSKEQRNKGIATALLNEAAKALRNLkieDVSLIVSEGnPAIDLYKKMGFEY 284
                                   5788899**************98766666651004555554445458********97 PP

>> Acetyltransf_18  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.0    0.0025       4.5      12     106 ..      30     131 ..      27     147 .. 0.66
   2 ?    5.0   0.0     0.012        21      59     110 ..     240     293 ..     238     301 .] 0.74

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0025
               Acetyltransf_18  12 dRskfLkrrlkqaeqklvvveedgeivGyglarktrkglk.iGPlvAeneeiA.....eaLlkalvanaegkkvrid.vpe 85 
                                   +R ++L + l+  e+k  v   ++e+ Gy+++++ + g + iG +   +++       ++Ll+ +  n +g  v +d + +
  gi|13541598|ref|NP_111286.1|  30 KRFNILIEKLTNNEIKNRVLIHGDEVMGYAFMINSMYGDRsIGNIGFMKKDYCndirlKNLLEWIHVNSGGLRVFLDeIFN 110
                                   6889999999999999999999999********999987778877544443331111134444444445554455553444 PP

               Acetyltransf_18  86 enkalielleklgfkevfeca 106
                                    n++  ++l+klg+++v++ +
  gi|13541598|ref|NP_111286.1| 111 ANDECDDILAKLGYSKVTRIK 131
                                   467777777777777776655 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.012
               Acetyltransf_18  59 neeiAeaLlkalvanaeg...kkvridvpeenkalielleklgfkevfecarmvk 110
                                   n+ iA aLl+++++  ++   + v + v+e n+ +i+l +k+gf+   + ++ ++
  gi|13541598|ref|NP_111286.1| 240 NKGIATALLNEAAKALRNlkiEDVSLIVSEGNP-AIDLYKKMGFEYSGQRKYVIY 293
                                   6678899998877665553337799****9765.689********9998877766 PP

>> Acetyltransf_CG  GCN5-related N-acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   5.1e-05     0.091      17      54 ..     219     256 ..     167     261 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.1e-05
               Acetyltransf_CG  17 YevrkegvldfthTeVpeelrGkGiAkkLvkaalddar 54 
                                    +  ++g++ +   +V++e r kGiA +L ++a +  r
  gi|13541598|ref|NP_111286.1| 219 VKYLGTGEYFISDLFVSKEQRNKGIATALLNEAAKALR 256
                                   3446889999**********************998877 PP

>> UNC-93  Ion channel regulatory protein UNC-93
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00012      0.21      87     135 ..     201     249 ..     196     252 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00012
                        UNC-93  87 lnkyylyissallGvgaallwtgqGsyLsenstretiernssilwallk 135
                                   +   ++y s  + G   ++ + g G+y ++     + +rn +i +all+
  gi|13541598|ref|NP_111286.1| 201 PEASFIYGSEKIQGGLITVKYLGTGEYFISDLFVSKEQRNKGIATALLN 249
                                   66789*****************************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       773  (0.0431145); expected 358.6 (0.02)
Passed bias filter:                      509  (0.0283898); 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: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2168.62
//
Query:       gi|13541599|ref|NP_111287.1|  [L=448]
Description: malate oxidoreductase (malic enzyme) [Thermoplasma volcanium GSS1]
Scores for 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   82.1   0.0    8.4e-16   58.3   0.1    3.2  3  malic     Malic enzyme, N-terminal domain
    2.7e-22   79.3   0.9    1.3e-21   77.1   0.9    1.9  1  Malic_M   Malic enzyme, NAD binding domain


Domain annotation for each model (and alignments):
>> malic  Malic enzyme, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.3   0.1   9.4e-20   8.4e-16       2     118 ..      25     120 ..      24     123 .. 0.92
   2 !   20.3   0.0   4.3e-08   0.00039     147     181 ..     122     156 ..     118     157 .. 0.92
   3 ?   -3.5   0.0      0.88   7.9e+03      55      80 ..     238     262 ..     232     264 .. 0.67

  Alignments for each domain:
  == domain 1  score: 58.3 bits;  conditional E-value: 9.4e-20
                                   TTECCCCCCHHCCCHHHHHHHHSTTCHHHHHHHHHHHGGCHHSCCCEGGGETCHHHHHTTSS.SS..EEEEE-SSSBTTTB CS
                         malic   2 eknetlfykllkekleellpivYtPtvgeacqeyseeyrkarglylsikdkekikeilknlpeedvkvivvtdgeriLGlG 82 
                                   +k++t+ + ++++   ++++i+YtP+v+++ ++++++++    +++ + ++                +++ tdg+r+LGlG
  gi|13541599|ref|NP_111287.1|  25 GKIQTMSKVPVRSL--DDFSIWYTPGVAAVSRKIATDHDLSF-ELTGRWNT----------------IAILTDGTRVLGLG 86 
                                   67888888888888..9*********************9999.99999999................9************* PP

                                   S-G.HHHHHHHHHHHHHHHHHHS-EGGGEEEEEECS- CS
                         malic  83 dlG.vagvgimvGKlaLytalagidPekvlpvvldvg 118
                                   ++G  a++++m+GK+ +++ l+g++   ++pv + v+
  gi|13541599|ref|NP_111287.1|  87 NIGpEAAMPVMEGKALIFNYLGGVN---AIPVPIRVS 120
                                   *************************...888877665 PP

  == domain 2  score: 20.3 bits;  conditional E-value: 4.3e-08
                                   HHHHHHHHHHHHGCTSEEEE-S--CCHHHHHHHHH CS
                         malic 147 vdefveavkelfppkaliqfEDfkaknafeilery 181
                                    +efv+++k+l+p++++i++ED++++++f +le +
  gi|13541599|ref|NP_111287.1| 122 REEFVSVAKSLEPSFGGINLEDIESPKCFFLLETL 156
                                   589****************************9976 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 0.88
                                   HHHHHTTSS.SS..EEEEE-SSSBTT CS
                         malic  55 ikeilknlpeedvkvivvtdgeriLG 80 
                                   +++++ n p  + ++++ t+ger+ G
  gi|13541599|ref|NP_111287.1| 238 MDSLMLNNPW-KYQLAIETNGERVKG 262
                                   4555555442.367899999999965 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 !   77.1   0.9   1.4e-25   1.3e-21       3     242 ..     171     385 ..     170     401 .. 0.80

  Alignments for each domain:
  == domain 1  score: 77.1 bits;  conditional E-value: 1.4e-25
                                   HHHHHHHHHHHHHHHHH-S-GGG--EEEEC-SHHHHHHHHHHHHHHHTTTS-HHHHHTTEEEEETTEE-BTT-S---TT.. CS
                       Malic_M   3 gTaavalagllaalkitgkklseqkivvlGaGsagiGiaeqivealvkeGlseeeakkkiylvDrkGLltedrekleee.. 81 
                                   gTa+++lag++++++i gkk++e k+v+ GaG+a i  a +      ++G ++    ++i lvD+kG+l  +r+++++   
  gi|13541599|ref|NP_111287.1| 171 GTASITLAGIINSIRIVGKKIEEVKVVFNGAGAANIAAAYLFK----AAGFKK----ENIILVDSKGVLQPERQDMDSLml 243
                                   9*********************************998776654....456655....589*************99965411 PP

                                   TGGGSBS.--SS--S....SHHHHHHHH--SEEEE-SSS.SS-S-HHHHHHHHHHSSS-EEEE--SSGGGSSS-HHHHHHH CS
                       Malic_M  82 kkpfakk.keelkeakdkltLeevvkkvkptvliGlsgv.agafteeivremaksterPiilplSNPtskaEataedvlkw 160
                                   ++p+  + + e++  + k +L+e++k   +++li ++   + + + + v+em    + Pi++ l NP    E  +e++ + 
  gi|13541599|ref|NP_111287.1| 244 NNPWKYQlAIETNGERVKGDLKEALKG--ADILISAAKSgPDTVDAKLVKEMN---NDPIVFVLANPIP--EMWPEEAKE- 316
                                   444433312334444467899999997..689998765426889999999985...68*********97..678999875. PP

                                   TTT-SEEEESS----EEETSEEE--EE--GGGTHHHHHHHHHHTT-SS--HHHHHHHHHHHHTT--HHHHHTT-SS--GGG CS
                       Malic_M 161 tdgkalvasGsPfkpvelngktyeigQaNNayifPglglgvivarakritdemllaaaealaelvseeelkegsllPelse 241
                                    +g+ +va+G          +   ++Q NN+++fPg+  gv+ arak ++ ++++aa+ ++a++v+e +++  ++ P+++e
  gi|13541599|ref|NP_111287.1| 317 -NGAKIVATG----------RSDFPNQINNSLVFPGVFRGVLDARAKGVNFDVMVAASYEIANFVEEPTAE--KIVPTMEE 384
                                   .99******8..........456799***************************************998875..88888876 PP

                                   H CS
                       Malic_M 242 i 242
                                    
  gi|13541599|ref|NP_111287.1| 385 W 385
                                   4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (448 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       382  (0.0213063); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.65u 0.31s 00:00:00.96 Elapsed: 00:00:00.54
# Mc/sec: 2502.21
//
Query:       gi|13541600|ref|NP_111288.1|  [L=156]
Description: acetyltransferase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-13   51.3   0.0    1.4e-13   51.1   0.0    1.1  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    3.4e-13   49.8   0.1    5.4e-13   49.2   0.1    1.3  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    6.2e-13   48.8   0.0    8.9e-13   48.3   0.0    1.2  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
      9e-12   45.4   0.8      1e-11   45.2   0.8    1.0  1  Acetyltransf_4   Acetyltransferase (GNAT) domain
    4.1e-09   36.3   0.0    3.1e-07   30.2   0.0    2.1  2  FR47             FR47-like protein
    0.00011   22.2   0.1    0.00071   19.7   0.1    2.2  1  Acetyltransf_9   Acetyltransferase (GNAT) domain
     0.0024   17.8   0.0     0.0047   16.9   0.0    1.4  1  Acetyltransf_13  ESCO1/2 acetyl-transferase
     0.0053   16.5   0.0     0.0087   15.8   0.0    1.5  1  PanZ             Acetyltransferase (GNAT) domain, PanZ
     0.0053   16.7   0.9     0.0091   15.9   0.9    1.4  1  LMP              LMP repeated region
  ------ inclusion threshold ------
      0.028   14.5   0.0      0.043   13.9   0.0    1.3  1  Acetyltransf_CG  GCN5-related N-acetyl-transferase
      0.033   13.7   1.1      0.056   12.9   1.0    1.5  1  Acetyltransf_15  Putative acetyl-transferase
      0.049   13.4   0.0       0.13   12.1   0.0    1.7  2  Acetyltransf_16  GNAT acetyltransferase, Mec-17


Domain annotation for each model (and alignments):
>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.1   0.0   9.7e-17   1.4e-13       8     117 .]      30     145 ..      22     145 .. 0.75

  Alignments for each domain:
  == domain 1  score: 51.1 bits;  conditional E-value: 9.7e-17
                                   HHHHTHHHHHHHHHHH...HHHHHHSTTCEEEEEEETTEEEEEE....EEEEEET...TSTTEEEEEEEEESGGGTTSSHH CS
                Acetyltransf_1   8 lvesffppnedaseee...feesfsleaegllvaeedgeliGfi....sllkipd...ekggvayieslaVspeyrgkGlG 78 
                                   + ++ f + e++  ++     ++   ++  llvae d+++ G +              e + +a i++++V peyr++G+G
  gi|13541600|ref|NP_111288.1|  30 EFDCIFNVSEQSKADIekyINKIMNSDDHVLLVAELDNKITGILfadiL----FRiyyEPKYEARIREFYVMPEYRRNGIG 106
                                   455555444444444433333333334447888**********966633....3344468999****************** PP

                                   HHHHHHHHHHHHHTTESEEEEEEETTEHHHHHHHHHTTE CS
                Acetyltransf_1  79 saLlealeerareegikkivlaveedndaairlYeklGF 117
                                   ++L++al +++  +gi+ i ++  + n  a+++Y+k G+
  gi|13541600|ref|NP_111288.1| 107 KKLIDALKRELDPKGITFITAEFPALNLIAQNFYKKIGY 145
                                   ****************9999988777********88998 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.2   0.1   3.6e-16   5.4e-13       2      76 .]      57     147 ..      56     147 .. 0.72

  Alignments for each domain:
  == domain 1  score: 49.2 bits;  conditional E-value: 3.6e-16
                                   TEEEEEEEETTEEEEEEEEEEES.........TCTEEEEE-GGGTTSSHHHHHHHH..TT...SEEE...EEEEEETHH.. CS
                Acetyltransf_7   2 kgevfVaeddgkivGfialslld.........aeitrlaVdpeyrgkGiGraLlea..ae...kgii...leqlelnae.. 63 
                                   ++ ++Vae d+ki G + + +l          a i +++V peyr++GiG++L++a  +e   kgi+       e   +  
  gi|13541600|ref|NP_111288.1|  57 DHVLLVAELDNKITGILFADILFriyyepkyeARIREFYVMPEYRRNGIGKKLIDAlkREldpKGITfitA---EF--Pal 132
                                   566789*******996665555599888866555555******************8542267778543221...22..122 PP

                                   ..HHHHHHHHTTEEE CS
                Acetyltransf_7  64 ..kaikfYeklGFee 76 
                                      a++fY+k G++e
  gi|13541600|ref|NP_111288.1| 133 nlIAQNFYKKIGYRE 147
                                   3489*********86 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.3   0.0     6e-16   8.9e-13      21     109 ..      48     148 ..      32     153 .. 0.87

  Alignments for each domain:
  == domain 1  score: 48.3 bits;  conditional E-value: 6e-16
               Acetyltransf_10  21 alrerieegealllvaeeggkivGvi......el.rdgs...hisllfVdpeyrgqGigkaLleaveeeaekdgikl.elt 90 
                                    +++ +++ +++llvae ++ki G++      ++ ++ +   +i  ++V peyr++Gigk+L++a+++e++ +gi   + +
  gi|13541600|ref|NP_111288.1|  48 YINKIMNSDDHVLLVAELDNKITGILfadilfRIyYEPKyeaRIREFYVMPEYRRNGIGKKLIDALKRELDPKGITFiTAE 128
                                   35566689*****************98888887766666999********************************9988899 PP

               Acetyltransf_10  91 vnasp.yavpfYeklGFkav 109
                                     a +  a++fY+k+G++++
  gi|13541600|ref|NP_111288.1| 129 FPALNlIAQNFYKKIGYREI 148
                                   999999***********987 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.2   0.8   6.9e-15     1e-11       1     135 [.       6     146 ..       6     155 .. 0.84

  Alignments for each domain:
  == domain 1  score: 45.2 bits;  conditional E-value: 6.9e-15
                Acetyltransf_4   1 iraateeDakeilaiy.aeyvvntaitfeyev..ssveefekflealdsekeyvflvae.sdrivGyaylgqfkkr.akdw 76 
                                   ir +++eD+++  + +   +++n +++++ +v  +s+ ++ek ++++      v+lvae + +i G++ +  + +r +++ 
  gi|13541600|ref|NP_111288.1|   6 IRRMKKEDMESVMDQLlRLKRLNSEFDCIFNVseQSKADIEKYINKIMNSDDHVLLVAElDNKITGILFAD-ILFRiYYEP 85 
                                   8999******98765548889******65555338888999******777799999***9********998.555557766 PP

                Acetyltransf_4  77 kael...svylaerdnnkeglgrelidaleqvlkeqnienllaeiaspnensiqfhkalGFe 135
                                   k e    ++y+     + +g+g++lidal+  l   +i+ ++ae  + n ++++f+k++G++
  gi|13541600|ref|NP_111288.1|  86 KYEArirEFYVM-PEYRRNGIGKKLIDALKRELDPKGITFITAEFPALNLIAQNFYKKIGYR 146
                                   655422289**8.689*****************************99**************8 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.025        38      47      80 ..      49      82 ..      45      88 .. 0.87
   2 !   30.2   0.0   2.1e-10   3.1e-07      22      81 ..      89     149 ..      83     152 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.025
                                  HHHHHHS-S-EEEEEETT-HHHHHHHHHHT-EEE CS
                          FR47 47 akeiaergktvllvvvasNtpsirlyeklGfeki 80
                                  +++i++ +++vllv+  +N+    l+  + f+ +
  gi|13541600|ref|NP_111288.1| 49 INKIMNSDDHVLLVAELDNKITGILFADILFRIY 82
                                  679999**************99999999988876 PP

  == domain 2  score: 30.2 bits;  conditional E-value: 2.1e-10
                                   SSEEEEEE-GGG-SSSHHHHHHHHHHHHHHHS-S-.EEEEEETT-HHHHHHHHHHT-EEEE CS
                          FR47  22 gelgalqvlpehrrrGlgsrlvkalakeiaergkt.vllvvvasNtpsirlyeklGfekie 81 
                                     +   +v pe rr G g++l+ al +e+  +g+t +++   a N  ++++y+k+G+++i 
  gi|13541600|ref|NP_111288.1|  89 ARIREFYVMPEYRRNGIGKKLIDALKRELDPKGITfITAEFPALNLIAQNFYKKIGYREIV 149
                                   6677889***************************9457889999**************984 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.1   4.7e-07   0.00071      20     127 ..      34     147 ..       5     148 .. 0.72

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 4.7e-07
                                   HTT----H...HHHHHHHHHHTTSEE.EEEEE.TTEEEEEEEEEEEEEEETTEEEEEEEEEEEEE-CCGTTS-HHHHHHHH CS
                Acetyltransf_9  20 aFqdeesple.eireyfrklleesrv.lgaed.ngelvgqlallplelnvpGktlkaagvtgVavapehrgrgvlskLlar 97 
                                    F+++e+  + +i++y +k+++++++ l++ + ++++ g l + +  ++++ +    a +    v pe+r++g+ +kL+++
  gi|13541600|ref|NP_111288.1|  34 IFNVSEQS-KaDIEKYINKIMNSDDHvLLVAElDNKITGIL-FADILFRIYYEPKYEARIREFYVMPEYRRNGIGKKLIDA 112
                                   56666666.44788888888886544033333477777765.4455555544444446788899***************** PP

                                   HHHHHHHTT--EEEE.--....SSHHHHHTTT-EE CS
                Acetyltransf_9  98 aleemreegqplsll.fP....ssipiYrrfGyei 127
                                   + +e++ +g+++++  fP    ++ ++Y++ Gy+ 
  gi|13541600|ref|NP_111288.1| 113 LKRELDPKGITFITAeFPalnlIAQNFYKKIGYRE 147
                                   ***********98653889988889********86 PP

>> Acetyltransf_13  ESCO1/2 acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   3.2e-06    0.0047       7      32 ..      91     116 ..      89     122 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 3.2e-06
               Acetyltransf_13   7 isriWvssshRrkgiAtkLldaaren 32 
                                   i+  +v++++Rr+gi +kL+da+ ++
  gi|13541600|ref|NP_111288.1|  91 IREFYVMPEYRRNGIGKKLIDALKRE 116
                                   7889*****************99865 PP

>> PanZ  Acetyltransferase (GNAT) domain, PanZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   5.8e-06    0.0087      10      92 ..      37     120 ..      22     152 .. 0.62

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 5.8e-06
                          PanZ  10 lsaqdkiDLakIy....paqsaealeaalteegalfaarFNdRlLgAvkveledk.eaelsdlcVRevTRrRGVgsyLlee 85 
                                   +s+q k D++k       + ++  l   ++ ++++    F d l    ++ +e k ea+++++ V  + Rr G+g++L++ 
  gi|13541600|ref|NP_111288.1|  37 VSEQSKADIEKYInkimNSDDHVLLV--AELDNKITGILFADILF---RIYYEPKyEARIREFYVMPEYRRNGIGKKLIDA 112
                                   55666666554332321333333333..34444555556666553...5556544489*********************** PP

                          PanZ  86 arrqa.Pe 92 
                                    +r++ P+
  gi|13541600|ref|NP_111288.1| 113 LKRELdPK 120
                                   **998443 PP

>> LMP  LMP repeated region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.9   6.1e-06    0.0091      57     104 ..      21      68 ..       3      71 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 6.1e-06
                           LMP  57 tkkLekFnkdkeakFkeLeqtRkdieeFlkdvknnpnYaelvkdLtsk 104
                                     +L++ n + +  F+  eq + die++++++ n++ +  lv +L++k
  gi|13541600|ref|NP_111288.1|  21 LLRLKRLNSEFDCIFNVSEQSKADIEKYINKIMNSDDHVLLVAELDNK 68 
                                   4578999**************************************997 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 ?   13.9   0.0   2.9e-05     0.043      20      49 ..      84     113 ..      64     125 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.9e-05
               Acetyltransf_CG  20 rkegvldfthTeVpeelrGkGiAkkLvkaa 49 
                                   +++ +  +   +V +e+r+ Gi+kkL++a 
  gi|13541600|ref|NP_111288.1|  84 EPKYEARIREFYVMPEYRRNGIGKKLIDAL 113
                                   46667889999****************986 PP

>> Acetyltransf_15  Putative acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   1.0   3.7e-05     0.056      10     100 ..      25     116 ..      15     150 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.7e-05
               Acetyltransf_15  10 kdilkevkkeFrnkrdeeeaitknenkydivqykkkeeLva..svfivkkkyyslvssilie.knvleiYtlyvsekyrgk 87 
                                   k +  e    F+ +++++ +i+k++nk  i+++ ++  Lva    +i    + ++   i  e k    i ++yv ++yr+ 
  gi|13541600|ref|NP_111288.1|  25 KRLNSEFDCIFNVSEQSKADIEKYINK--IMNSDDHVLLVAelDNKITGILFADILFRIYYEpKYEARIREFYVMPEYRRN 103
                                   5566667777999999999*****999..99*99*99999944447888888887654443314445899999******** PP

               Acetyltransf_15  88 GlakklLeeslke 100
                                   G+ kkl+    +e
  gi|13541600|ref|NP_111288.1| 104 GIGKKLIDALKRE 116
                                   *****99766555 PP

>> Acetyltransf_16  GNAT acetyltransferase, Mec-17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0         1   1.6e+03      54      65 ..      49      60 ..       5      75 .. 0.57
   2 ?   12.1   0.0   8.4e-05      0.13     106     128 ..      91     113 ..      82     142 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1
                                  HHHHHHS-EEEE CS
               Acetyltransf_16 54 aeklqssdhvlY 65
                                  ++k+++sd+++ 
  gi|13541600|ref|NP_111288.1| 49 INKIMNSDDHVL 60
                                  234444443333 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 8.4e-05
                                   EEEEEE-GGGTTSSHHHHHHHHH CS
               Acetyltransf_16 106 vldFyvheseqrkGlGkklfeam 128
                                   + +Fyv+ +  r+G+Gkkl++a+
  gi|13541600|ref|NP_111288.1|  91 IREFYVMPEYRRNGIGKKLIDAL 113
                                   568*****************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1117  (0.0623013); expected 358.6 (0.02)
Passed bias filter:                      790  (0.0440627); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1146.00
//
Query:       gi|13541601|ref|NP_111289.1|  [L=249]
Description: hypothetical protein TVN0770 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.4e-26   90.6   0.5    1.4e-25   89.0   0.1    2.1  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
  ------ inclusion threshold ------
      0.013   14.9   0.5      0.018   14.5   0.5    1.2  1  RNase_E_G       Ribonuclease E/G family
      0.046   14.0   0.4      0.094   13.0   0.4    1.5  1  C1_2            C1 domain
      0.082   12.9   0.1       0.17   11.9   0.1    1.5  1  HypA            Hydrogenase/urease nickel incorporation, meta
      0.084   12.9   1.2       0.15   12.1   1.2    1.3  1  DZR             Double zinc ribbon
       0.92    9.6   3.3        2.6    8.2   0.4    2.2  2  UPF0547         Uncharacterised protein family UPF0547


Domain annotation for each model (and alignments):
>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       1.5   4.5e+03       6      21 ..     115     132 ..     111     142 .. 0.60
   2 !   89.0   0.1   4.6e-29   1.4e-25       1      69 []     154     220 ..     154     220 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.5
                OrfB_Zn_ribbon   6 eqleykakey..Gikvee 21 
                                   +++ + ak+   Gik+e+
  gi|13541601|ref|NP_111289.1| 115 KKIVQEAKQNgmGIKLEY 132
                                   556566666522555555 PP

  == domain 2  score: 89.0 bits;  conditional E-value: 4.6e-29
                OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNilkr 69 
                                   f+++++++eyka+  Gi+v++v+p++TSk+Cs+Cg k+++  sg++fkCp Cg++ ++D nA++Ni+ r
  gi|13541601|ref|NP_111289.1| 154 FYQIEKMIEYKARLLGIPVVYVDPYNTSKECSRCGLKGNR--SGKEFKCPGCGHVDNADANASFNIALR 220
                                   7899************************************..************************976 PP

>> RNase_E_G  Ribonuclease E/G family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.5     6e-06     0.018      57     154 ..      66     162 ..      38     166 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 6e-06
                     RNase_E_G  57 eelekdleelkkkweeilekakkrkapsllyeeedlllrvlrdllnedieeivvddkelyeeik.eyleevapeleekvel 136
                                    +l+k +e++++k+++i+++ +k+ +++++ +++d  +r+ +d+ ++  ++iv + k+    ik eyl+ +++ ++++   
  gi|13541601|ref|NP_111289.1|  66 LKLRKSAEHIHRKYKNIRKHLQKKGKYRMVKKAKDRENRIEKDVNHKVSKKIVQEAKQNGMGIKlEYLNGIRNAKSSRNFR 146
                                   579999****************9********************99999999999988877666526667777766665444 PP

                     RNase_E_G 137 yeeeeplfelysiekqie 154
                                   y    +  + y+iek ie
  gi|13541601|ref|NP_111289.1| 147 Y--PLNSWSFYQIEKMIE 162
                                   4..234566677776665 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.4   3.2e-05     0.094      13      39 ..     176     204 ..     162     208 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.2e-05
                          C1_2  13 edssesfnCsaCgrkidgff..YsCseCd 39 
                                   ++++ s++Cs Cg k++ +   ++C+ C 
  gi|13541601|ref|NP_111289.1| 176 DPYNTSKECSRCGLKGNRSGkeFKCPGCG 204
                                   578899*********7666677***9995 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 ?   11.9   0.1   5.8e-05      0.17      67      96 ..     178     207 ..     150     217 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 5.8e-05
                                   E--EEEETTTS-EEECHHHHHS-TTTSSS- CS
                          HypA  67 vpvkvrCreCgkefeleekalrCpkCgsad 96 
                                    + + +C++Cg +++ + k+++Cp Cg+ d
  gi|13541601|ref|NP_111289.1| 178 YNTSKECSRCGLKGNRSGKEFKCPGCGHVD 207
                                   567789********9887799*****9864 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   1.2   5.2e-05      0.15      11      43 ..     180     212 ..     176     216 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5.2e-05
                           DZR  11 darfCseCgtklkavaaedrCpsCgekvdpear 43 
                                    ++ Cs+Cg k ++  +e +Cp Cg+  +++a+
  gi|13541601|ref|NP_111289.1| 180 TSKECSRCGLKGNRSGKEFKCPGCGHVDNADAN 212
                                   6788*******999999********98555544 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.1     0.084   2.5e+02      15      21 ..     182     188 ..     180     189 .. 0.88
   2 ?    8.2   0.4   0.00086       2.6      16      26 .]     199     209 ..     198     209 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.084
                       UPF0547  15 qfCphCG 21 
                                   ++C+ CG
  gi|13541601|ref|NP_111289.1| 182 KECSRCG 188
                                   89*99*9 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.00086
                       UPF0547  16 fCphCGyvFqa 26 
                                   +Cp CG+v++a
  gi|13541601|ref|NP_111289.1| 199 KCPGCGHVDNA 209
                                   6******9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1834  (0.102292); expected 358.6 (0.02)
Passed bias filter:                      882  (0.049194); expected 358.6 (0.02)
Passed Vit filter:                       112  (0.00624686); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-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: 00:00:00.46
# Mc/sec: 1619.53
//
Query:       gi|13541602|ref|NP_111290.1|  [L=175]
Description: nicotinamidase-like amidase [Thermoplasma volcanium GSS1]
Scores for complete 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  146.7   0.0    8.4e-43  146.6   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 !  146.6   0.0   4.7e-47   8.4e-43       2     160 ..       4     158 ..       3     170 .. 0.94

  Alignments for each domain:
  == domain 1  score: 146.6 bits;  conditional E-value: 4.7e-47
               Isochorismatase   2 alvviDmqndfveegvkeseeisavveninkllkaarkagipviftrdvheleevkgdlderkaaphfkpgttgaelvpel 82 
                                    lvviDm ndfv +g+ ++ e   +v  ++ +l+a+rk+g+p++ft+d h     k d++ + +  h  +g++ga++++el
  gi|13541602|ref|NP_111290.1|   4 GLVVIDMLNDFV-HGTLKTQESLSTVIPARNVLEAFRKKGLPIFFTNDAHY----KEDPEMKIWGSHAMKGSWGAQIIEEL 79 
                                   69**********.999999999999**************************....************************** PP

               Isochorismatase  83 aplegdvvvdKtrfsafagtdldeiLkelgiktivlaGiatdvCVeatardaldlGyevvvvsDAvaalspel.hdaal 160
                                   +ple+++v++K+ +saf+gt+ld+iL+++g++++ l G+ +d+CV++ta dal ++y ++vv+DAvaa+   + +d+ +
  gi|13541602|ref|NP_111290.1|  80 KPLESEFVIEKHAYSAFYGTNLDQILRARGVTELFLIGLDADICVRHTAADALYRNYAITVVEDAVAARIDKNwKDYFI 158
                                   *******************************************************************997776455555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       356  (0.0198561); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1276.00
//
Query:       gi|13541603|ref|NP_111291.1|  [L=565]
Description: methylmalonyl-CoA mutase, alpha subunit [Thermoplasma volcanium GSS1]
Scores for complete 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-227  754.5   0.0   5.8e-227  754.3   0.0    1.0  1  MM_CoA_mutase  Methylmalonyl-CoA mutase
  ------ inclusion threshold ------
      0.032   14.2   0.3       0.15   12.0   0.0    2.2  3  DUF4833        Domain of unknown function (DUF4833)


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 !  754.3   0.0  6.5e-231  5.8e-227       3     513 .]      46     557 ..      44     557 .. 0.98

  Alignments for each domain:
  == domain 1  score: 754.3 bits;  conditional E-value: 6.5e-231
                 MM_CoA_mutase   3 aegievkplYtaedl.eekklgeslPGefPftRGvkatmyrgrpWtirqyagfstaeetnerykklLeaGqtglsvafdlp 82 
                                   +++i++k++Yt+ed+ +  + +  +PGe+PftRG++++myrg+ Wt+r++ gf+t+e+tn+r+++l+e+G tgls+afd+p
  gi|13541603|ref|NP_111291.1|  46 SSEIKLKEVYTKEDVpDL-ESRLGMPGEYPFTRGIYPNMYRGKLWTMRMFSGFGTPEDTNRRLHYLIENGETGLSIAFDMP 125
                                   689************522.55566********************************************************* PP

                 MM_CoA_mutase  83 tlrgyDsdhpraegevGkaGvaidsledmetlldgidldkvsvsmtinaaalpllamylaaaeeqgvdleklsgtiqnDiL 163
                                   tl+gyD+d++r+ege+Gk+Gv++++l+dme++++gidl+kvs+smtina+a++l+amyla+a++qgv+ +++sgt+q+DiL
  gi|13541603|ref|NP_111291.1| 126 TLYGYDADSERSEGEIGKCGVNVSTLKDMEVIFKGIDLSKVSTSMTINAPAAILTAMYLAIAKKQGVPFDQVSGTVQADIL 206
                                   ********************************************************************************* PP

                 MM_CoA_mutase 164 kellargtyiyppepslrliadiieyaakevpkfntisvsgyhireaGatavqElAftladGveYvralleaGldvdefap 244
                                   ke++a+++++yppe ++r+i d++ y++k+vpk+n is+sgyhireaG++avqElAftladG+ Yv+ +++aGldvd+fap
  gi|13541603|ref|NP_111291.1| 207 KEYIAQKEWMYPPEAHIRIIRDMMVYCTKNVPKWNYISISGYHIREAGSSAVQELAFTLADGFYYVDLGIKAGLDVDSFAP 287
                                   ********************************************************************************* PP

                 MM_CoA_mutase 245 rlsFffaigsdffeeiAklRAaRrlWarivkekfgakeekslklrvhaqTsgvsltaqdpyvNilRttlealaAvlggtqs 325
                                   rlsFff+ + +ffeeiAklRAaRr+Wa+++kek+gak+++s++lr+h+qTsg++lt q+p +Ni+Rtt+ea+aAvlggtqs
  gi|13541603|ref|NP_111291.1| 288 RLSFFFNSSINFFEEIAKLRAARRIWATVMKEKYGAKNPRSMMLRFHTQTSGYTLTWQQPLNNIIRTTIEAMAAVLGGTQS 368
                                   ********************************************************************************* PP

                 MM_CoA_mutase 326 lhtnsfDealalPtefsariArntqlilaeEsgvakvvDPlgGSyyvEaLTdelaekawklfqeieeaGGmlkaiesGlvq 406
                                   lhtns+Dea+alP+++++++A++tq+i+aeEsg+ +v+DPlgGSyyvE+LTd+++e+a k+f++ie++GG+l+ai+ G++q
  gi|13541603|ref|NP_111291.1| 369 LHTNSYDEAWALPSDQAVKVALRTQQIIAEESGIPDVIDPLGGSYYVEWLTDRMEEEAYKYFDRIESMGGILEAIKRGYIQ 449
                                   ********************************************************************************* PP

                 MM_CoA_mutase 407 eeiaesaarrqkaiesrkevivGvNkfrpneeekelevlkideeveerqaerlealraerdeaavkaaLaalgeaarse.. 485
                                   +eia+++++rqk++e+++ev+vGvNk+  +e e++++ lkid+++ee q +rl++++++rde++v++aL++l++a+ +e  
  gi|13541603|ref|NP_111291.1| 450 KEIADTSYKRQKKLETGQEVMVGVNKY-IEEGEEPINYLKIDKKAEEMQRNRLKEVKKTRDESKVREALDELRKAMLNEne 529
                                   ***************************.89999*****************************************9987789 PP

                 MM_CoA_mutase 486 nllaraveaaralatlGeisdaleevfg 513
                                   nl+++ ++a++a+at+ eisd+ ++vfg
  gi|13541603|ref|NP_111291.1| 530 NLMPYYIKAVEAYATIQEISDVGRDVFG 557
                                   **************************98 PP

>> DUF4833  Domain of unknown function (DUF4833)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.1       1.5   1.4e+04      89     107 ..      38      56 ..      33      58 .. 0.72
   2 ?   12.0   0.0   1.7e-05      0.15      53     114 ..     126     191 ..     112     202 .. 0.87
   3 ?   -2.5   0.0      0.53   4.8e+03     115     130 ..     236     251 ..     225     255 .. 0.78

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 1.5
                       DUF4833  89 yvvytkingkkaiLekvfv 107
                                   y+ ++  n+ ++ L++v+ 
  gi|13541603|ref|NP_111291.1|  38 YKERVYQNSSEIKLKEVYT 56 
                                   6666777888999999996 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 1.7e-05
                       DUF4833  53 laYGvkvkkvskn....eyevslvalkkrplyLkkdkkgkyvvytkingkkaiLekvfvkieetsl 114
                                   + YG++ ++++++    ++ v++  lk++++  k  +  k+ + ++in   aiL  +++ i + + 
  gi|13541603|ref|NP_111291.1| 126 TLYGYDADSERSEgeigKCGVNVSTLKDMEVIFKGIDLSKVSTSMTINAPAAILTAMYLAIAKKQG 191
                                   56****999966666777****************999999********************966554 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 0.53
                       DUF4833 115 wvpkveyielkGvdla 130
                                    vpk +yi ++G ++ 
  gi|13541603|ref|NP_111291.1| 236 NVPKWNYISISGYHIR 251
                                   57999*****998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (565 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       996  (0.0555525); expected 358.6 (0.02)
Passed bias filter:                      538  (0.0300073); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.71u 0.31s 00:00:01.02 Elapsed: 00:00:00.48
# Mc/sec: 3518.01
//
Query:       gi|13541604|ref|NP_111292.1|  [L=148]
Description: methylmalonyl-CoA mutase, cobalamin-binding subunit [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.6e-21   76.6   0.2    1.9e-21   76.3   0.2    1.1  1  B12-binding  B12 binding domain


Domain annotation for each model (and alignments):
>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.3   0.2   1.1e-25   1.9e-21       1     105 [.      15     118 ..      15     131 .. 0.91

  Alignments for each domain:
  == domain 1  score: 76.3 bits;  conditional E-value: 1.1e-25
                   B12-binding   1 ikvllatvggdlhplGlavlaaalrdagfeVqllganvenedivaairaekpdvvglSalltsqleavkelvel..lkrir 79 
                                   ikvlla+ + d h++G+ vla+alrdag++V++ g+  ++e++v+ +++e++dv+glS+l +++++a+k++v+l  +k+i 
  gi|13541604|ref|NP_111292.1|  15 IKVLLAKPAIDGHDRGIFVLARALRDAGMDVIYAGLLPTPEQVVDIAISEDVDVIGLSLLNGAHMTAFKKVVDLlhEKGI- 94 
                                   5899**********************************************************************999999. PP

                   B12-binding  80 prvkvvvGGahpsldpeetleaklgi 105
                                   +++ vv GG++p  d  + le+ +gi
  gi|13541604|ref|NP_111292.1|  95 DDIAVVGGGIIPDDDKPL-LEK-IGI 118
                                   679999999999988888.554.664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       373  (0.0208043); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.50
# Mc/sec: 898.96
//
Query:       gi|13541605|ref|NP_111293.1|  [L=315]
Description: GTPase [Thermoplasma volcanium GSS1]
Scores for complete 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-80  268.6   0.1    5.4e-80  268.2   0.1    1.1  1  MeaB           Methylmalonyl Co-A mutase-associated GTPase Me
    2.5e-06   27.5   0.0     0.0014   18.5   0.0    2.9  2  ATP_bind_1     Conserved hypothetical ATP binding protein
    3.3e-05   23.7   0.0    6.4e-05   22.8   0.0    1.4  1  AAA_30         AAA domain
    3.9e-05   23.3   0.5    0.00024   20.8   0.5    2.1  1  cobW           CobW/HypB/UreG, nucleotide-binding domain
    8.3e-05   23.1   2.7    9.8e-05   22.9   0.3    2.4  2  AAA_18         AAA domain
    0.00018   21.5   0.2    0.00034   20.6   0.2    1.6  1  NTPase_1       NTPase
    0.00038   20.2   0.1     0.0015   18.2   0.1    2.0  1  SRP54          SRP54-type protein, GTPase domain
    0.00064   19.7   0.0      0.001   19.0   0.0    1.3  1  Rad17          Rad17 P-loop domain
     0.0012   18.9   0.0     0.0021   18.1   0.0    1.5  1  CbiA           CobQ/CobB/MinD/ParA nucleotide binding domain
     0.0016   19.0   0.3     0.0038   17.7   0.3    1.7  1  ABC_tran       ABC transporter
     0.0031   17.8   0.0     0.0083   16.4   0.0    1.7  1  AAA_22         AAA domain
     0.0038   16.8   0.1      0.071   12.6   0.1    2.3  1  GTP_EFTU       Elongation factor Tu GTP binding domain
     0.0042   17.0   0.0       0.11   12.4   0.0    2.3  2  RsgA_GTPase    RsgA GTPase
     0.0042   16.6   0.1     0.0042   16.6   0.1    1.6  2  ParA           NUBPL iron-transfer P-loop NTPase
     0.0062   15.8   0.0      0.011   15.0   0.0    1.3  1  KAP_NTPase     KAP family P-loop domain
  ------ inclusion threshold ------
      0.019   15.4   0.0      0.041   14.3   0.0    1.7  1  AAA            ATPase family associated with various cellular
      0.019   15.3   0.0       0.04   14.3   0.0    1.6  1  RNA_helicase   RNA helicase
       0.02   14.4   0.1      0.039   13.4   0.1    1.6  1  Fer4_NifH      4Fe-4S iron sulfur cluster binding proteins, N
       0.02   14.8   1.5      0.091   12.7   0.1    2.2  2  AAA_31         AAA domain
       0.02   14.9   0.1      0.054   13.6   0.1    1.9  1  MMR_HSR1       50S ribosome-binding GTPase
      0.032   14.2   0.0      0.069   13.1   0.0    1.6  1  AAA_5          AAA domain (dynein-related subfamily)
      0.032   13.7   0.1      0.032   13.7   0.1    1.7  2  KTI12          Chromatin associated protein KTI12
       0.04   13.7   0.1      0.097   12.4   0.1    1.6  1  AAA_29         P-loop containing region of AAA domain
       0.04   13.8   0.0      0.071   13.0   0.0    1.4  1  APS_kinase     Adenylylsulphate kinase
      0.048   12.8   0.5      0.091   11.9   0.5    1.4  1  ArsA_ATPase    Anion-transporting ATPase
      0.052   13.9   0.1       0.11   12.9   0.1    1.6  1  AAA_16         AAA ATPase domain
      0.052   13.3   0.2       0.16   11.7   0.1    1.8  2  RuvB_N         Holliday junction DNA helicase RuvB P-loop dom
      0.066   13.1   0.2       0.33   10.8   0.1    1.9  2  Helicase_RecD  Helicase
      0.087   12.6   0.0       0.19   11.4   0.0    1.5  1  IstB_IS21      IstB-like ATP binding protein
        0.1   12.9   0.1       0.21   11.9   0.1    1.5  1  AAA_19         AAA domain
       0.12   11.7   0.2       0.19   11.1   0.2    1.3  1  Mg_chelatase   Magnesium chelatase, subunit ChlI


Domain annotation for each model (and alignments):
>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  268.2   0.1   9.3e-83   5.4e-80       1     255 [.      18     265 ..      18     276 .. 0.92

  Alignments for each domain:
  == domain 1  score: 268.2 bits;  conditional E-value: 9.3e-83
                                   HHHHHHHHH--SHHHHHHHHHHGGG-S-SEEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE---------------- CS
                          MeaB   1 LaraitlveserpeakellerllakaGraqvvGltGvPGaGkstlvealglelrrrGkrvavlavDPsspftGGsilGDkl 81 
                                   +arai lve+++  + el++++ +++G+a+ +G+tG PG+Gkst++  l   l ++Gk+v++lavD sspf+GG++lG+++
  gi|13541605|ref|NP_111293.1|  18 IARAISLVEEDNDYSYELIREIYPYTGKAHIIGITGPPGVGKSTMIGILSKMLSEHGKKVSILAVDASSPFSGGTLLGNRI 98 
                                   59******************************************************************************* PP

                                   --HCCCTSTTEEEEEE-----HHHHHHHHHHHHHHHHHTT-SEEEEEEESSTTHHHHHHTT-SEEEEEEESSTTTTTTT-- CS
                          MeaB  82 RleelavdegvfiRslpsrGalGGlaaktrevvllleaaGfDvvlietvGvGqsevdvaevvdtfvvlllpeaGDelqgik 162
                                   R++e+  + g+++Rs++ rG  GGl++ t ++v++l+a G D ++ietvG+Gqs++d++ ++dt++v l p+ GD +q+ik
  gi|13541605|ref|NP_111293.1|  99 RMQEILSKYGIYMRSVANRGFTGGLSRSTWNIVKVLDASGSDYIIIETVGAGQSDIDIVYLADTVIVTLAPGLGDSIQAIK 179
                                   ********************************************************************************* PP

                                   CCCHHH-SEEEEE---HHHHHHHHHHHHHHHHHCSTTBTTB--EEEEEBCCCTBSHHHHHHHHHHHHHHHHHTTHHHHHHH CS
                          MeaB 163 kGileiaDiivvnkaDkkeaekaarelraaleleeekekeWrpkvlktsavegeGidelvdaieehrevlkktGllekrrr 243
                                    G++ei+Di+v+nk D++++  a ++++        ++++W+p+v+ t +++geG d+l++ai ehr++ +++G++++ r 
  gi|13541605|ref|NP_111293.1| 180 SGMMEIGDIFVINKMDREGSFFALKDIMDN----VYEHNGWNPRVVGTNSLKGEGYDKLLEAIDEHRKYSEASGNKKEIRY 256
                                   ****************99988877665543....34579**********************************99887766 PP

                                   HHHHHHHHHHHH CS
                          MeaB 244 erakeelrelve 255
                                   + + +     ++
  gi|13541605|ref|NP_111293.1| 257 KEEIR---LAIS 265
                                   44433...3333 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 !   18.5   0.0   2.3e-06    0.0014       1      34 [.      51      84 ..      51      88 .. 0.93
   2 ?    5.2   0.0     0.027        16     196     238 ..     199     241 ..     135     244 .. 0.70

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2.3e-06
                    ATP_bind_1  1 vvGpaGsGKttfvgalseilelrgrsvavvNLDP 34
                                  ++Gp+G+GK+t++g ls++l++ g++v ++  D 
  gi|13541605|ref|NP_111293.1| 51 ITGPPGVGKSTMIGILSKMLSEHGKKVSILAVDA 84
                                  68**************************999886 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.027
                    ATP_bind_1 196 kykklaeaiaelleefalvlrflplssekeesiedllslidea 238
                                    +  l+  + ++ e  + ++r++  +s k+e++++ll++ide+
  gi|13541605|ref|NP_111293.1| 199 SFFALKDIMDNVYEHNGWNPRVVGTNSLKGEGYDKLLEAIDEH 241
                                   4444555666666777778889999999999999999999886 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0   1.1e-07   6.4e-05      16      56 ..      44      84 ..      35      86 .. 0.89

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 1.1e-07
                        AAA_30 16 sgdrvavltGpAGtGKttalkalreaweaaggrviglAptg 56
                                  +++ +  +tGp+G GK+t+++ l +++ ++g++v +lA  +
  gi|13541605|ref|NP_111293.1| 44 GKAHIIGITGPPGVGKSTMIGILSKMLSEHGKKVSILAVDA 84
                                  45568889*****************************9865 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.5   4.1e-07   0.00024       2     156 ..      48     200 ..      47     215 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 4.1e-07
                                   EEEEEESTTCCHHHHHHHHH..CT--SS-EEEEESS-SSCHCCCCCCHCCCT...........EEEETTTTECCHCTT-HH CS
                          cobW   2 vtvltGflGsGKTtLlnhll..enraglklavivNefgevsiDaellretgve..........ivelenGciCctlredll 70 
                                   ++++tG++G GK+t++  l     ++g+k+ ++  + ++    ++ll ++  +          + +++n +    l+    
  gi|13541605|ref|NP_111293.1|  48 IIGITGPPGVGKSTMIGILSkmLSEHGKKVSILAVDASSPFSGGTLLGNRIRMqeilskygiyMRSVANRGFTGGLSRSTW 128
                                   679************9877766788*************8777788885553333456777777999999888888888887 PP

                                   HHHHHHHHHHTT-SEEEEEECTTTTHHHHHTTSHHHHHCCCECEEEEEEETTTH.CCHCCHHHHHHHHHHTSSEEEEE-HH CS
                          cobW  71 kelealeereerldviliEttGlaePapvafteeelksdltldavvavvDaknleaeeekieekaedqlaaadllvlnKtD 151
                                   + ++ l +     d+i+iEt+G  +              + +d+v++ +        +++i+     +++  d++v+nK+D
  gi|13541605|ref|NP_111293.1| 129 NIVKVLDASG--SDYIIIETVGAGQSDID--------IVYLADTVIVTLAP----GLGDSIQAIKSGMMEIGDIFVINKMD 195
                                   7777777777..8*********7765543........47888888888887....6799********************** PP

                                   HHCHC CS
                          cobW 152 lldee 156
                                      + 
  gi|13541605|ref|NP_111293.1| 196 REGSF 200
                                   87665 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.3   1.7e-07   9.8e-05       1      24 [.      49      73 ..      49     149 .. 0.85
   2 ?   -0.9   0.1       3.8   2.2e+03      76      76 ..     253     253 ..     191     311 .. 0.57

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 1.7e-07
                        AAA_18  1 IlltGtpGvGKttlakeLskrl.gf 24
                                  I++tG+pGvGK+t+   Lsk+l + 
  gi|13541605|ref|NP_111293.1| 49 IGITGPPGVGKSTMIGILSKMLsEH 73
                                  89*******************8333 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 3.8
                        AAA_18  76 n 76 
                                    
  gi|13541605|ref|NP_111293.1| 253 E 253
                                   1 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.2   5.8e-07   0.00034       2      31 ..      49      78 ..      48     148 .. 0.93

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 5.8e-07
                                  EEEE--TTSSHHHHHHHHHHHH...GGGEE CS
                      NTPase_1  2 vfiTGppGvGKtTlvkkvlellkssgvkvg 31
                                  + iTGppGvGK+T++  ++++l+++g kv+
  gi|13541605|ref|NP_111293.1| 49 IGITGPPGVGKSTMIGILSKMLSEHGKKVS 78
                                  67***********************99986 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.1   2.6e-06    0.0015       3      39 ..      48      84 ..      46     169 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2.6e-06
                                  EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEEST CS
                         SRP54  3 villvGlqGaGKTttlaKLaallkkegkkvllvaaDt 39
                                  +i + G+ G+GK t ++ L+++l+++gkkv + a+D 
  gi|13541605|ref|NP_111293.1| 48 IIGITGPPGVGKSTMIGILSKMLSEHGKKVSILAVDA 84
                                  5678999****************************96 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   1.8e-06     0.001      45      72 ..      46      73 ..      37     110 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.8e-06
                         Rad17 45 kriLLisGPsGCgkstvvkvLskelgik 72
                                   +i+ i+GP+G gkst++ +Lsk l+ +
  gi|13541605|ref|NP_111293.1| 46 AHIIGITGPPGVGKSTMIGILSKMLSEH 73
                                  56999******************88654 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   3.7e-06    0.0021       9      91 ..      56     233 ..      48     269 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 3.7e-06
                                   TSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCH.HTTEB-HHHH.................................. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx.................................. RF
                          CbiA   9 GvGKTtlaanLaralarrglrVllvDaDpqannlai.leglendiep.................................. 54 
                                   GvGK+t+   L + l+++g++V  + +D  ++ +   l g++++ ++                                  
  gi|13541605|ref|NP_111293.1|  56 GVGKSTMIGILSKMLSEHGKKVSILAVDASSPFSGGtLLGNRIRMQEilskygiymrsvanrgftgglsrstwnivkvlda 136
                                   9*************************9999999874566666666669999999999999999999999999999999999 PP

                                   ..........................................................CCHCCCHHHHHHCHCHHHH.... CS
                                   ..........................................................xxxxxxxxxxxxxxxxxxx..xx RF
                          CbiA  55 ..........................................................dlkrllellealgkkkall..lk 75 
                                                                                             d++     l+++  ++  +   +
  gi|13541605|ref|NP_111293.1| 137 sgsdyiiietvgagqsdidivyladtvivtlapglgdsiqaiksgmmeigdifvinkmDREGSFFALKDIMDNVYEHngWN 217
                                   999999999999999999999999999999888888766666666666666666665544333333344433332223566 PP

                                   EEEEEEEEESS...-T CS
                                   xxxxxxxxxxxxxxxx RF
                          CbiA  76 iagvvlnrvdgeneet 91 
                                   +  v+ n  +ge +++
  gi|13541605|ref|NP_111293.1| 218 PRVVGTNSLKGEGYDK 233
                                   6666666666664444 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.3   6.6e-06    0.0038      12      44 ..      47      79 ..      42     132 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 6.6e-06
                                  SEEEEEESTTSSHHHHHHHHTTSS--SEEEEEE CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran 12 ekvaivGenGaGKStLlkllagllkpteGeill 44
                                  ++++i+G+ G GKSt++ +l+++l+    ++ +
  gi|13541605|ref|NP_111293.1| 47 HIIGITGPPGVGKSTMIGILSKMLSEHGKKVSI 79
                                  789********************9987777755 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   1.4e-05    0.0083       5      56 ..      46      93 ..      42     108 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.4e-05
                        AAA_22  5 agilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdl 56
                                  a i+ +tG++G+GK+t +  l + l e+ k    +++++ v+++s+ s  +l
  gi|13541605|ref|NP_111293.1| 46 AHIIGITGPPGVGKSTMIGILSKMLSEHGK----KVSILAVDASSPFSGGTL 93
                                  67889*******************977654....899999999998865555 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.1   0.00012     0.071     120     191 ..     182     241 ..      45     243 .. 0.54

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00012
                                   HTTTEEEEEEESCGST..HHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTBTHHHHHHHHHHH CS
                      GTP_EFTU 120 kegvpiivfiNKmDrl..kaelkeiveevkqklsrkeeklekygekgekevpvvfgSalkgegvktllealvel 191
                                    +++  i++iNKmDr      lk i ++v+++           g +      vv + +lkgeg+++llea++e+
  gi|13541605|ref|NP_111293.1| 182 MMEIGDIFVINKMDREgsFFALKDIMDNVYEHN----------GWNP----RVVGTNSLKGEGYDKLLEAIDEH 241
                                   3445589********954455566666666444..........5555....599999*************9997 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.0   0.00019      0.11      90     130 ..      36      77 ..       3      82 .. 0.78
   2 ?    2.1   0.0      0.28   1.6e+02      48      99 ..     186     240 ..     178     246 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00019
                                   HHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT-----S-- CS
                   RsgA_GTPase  90 leelkellkd.ktsvlvGqSGvGKStLinallpelelktgev 130
                                   ++e+ ++  + +++ + G+ GvGKSt+i  l   l+ + ++v
  gi|13541605|ref|NP_111293.1|  36 IREIYPYTGKaHIIGITGPPGVGKSTMIGILSKMLSEHGKKV 77 
                                   5566666655588899************99987766555555 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.28
                                   EEEEEEE-GGG--HHHHHHHHHH...HHHHTTSEEEE--TTTHTTHHHHHHHCTT CS
                   RsgA_GTPase  48 epvivlnKiDlleeeeeleelke...elealgyevllvsaktkegleelkellkd 99 
                                     + v+nK+D   +  +l+++++   e + ++ +v+ +++ ++eg+++l e++++
  gi|13541605|ref|NP_111293.1| 186 GDIFVINKMDREGSFFALKDIMDnvyEHNGWNPRVVGTNSLKGEGYDKLLEAIDE 240
                                   5678999999877766555444311155678889999999999*****9999877 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 !   16.6   0.1   7.3e-06    0.0042       9      45 ..      51      87 ..      45     112 .. 0.82
   2 ?   -2.9   0.2       6.5   3.8e+03     113     130 ..     161     178 ..     152     191 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 7.3e-06
                          ParA  9 lSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGp 45
                                  + g  GVGKSt+   l+ +L+++g+kv++l +D   p
  gi|13541605|ref|NP_111293.1| 51 ITGPPGVGKSTMIGILSKMLSEHGKKVSILAVDASSP 87
                                  45777***************************97665 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 6.5
                          ParA 113 DyLiiDlPPGtgDeqltv 130
                                   D +i+ l PG gD   ++
  gi|13541605|ref|NP_111293.1| 161 DTVIVTLAPGLGDSIQAI 178
                                   788899999999976555 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 !   15.0   0.0   1.9e-05     0.011      18      59 ..      44      85 ..      29      94 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.9e-05
                    KAP_NTPase 18 atpivvgLygkWGsGKssllnkledelkefakpvrflfaefn 59
                                  ++  ++g++g+ G+GKs+++  l + l+e+ k+v++l ++++
  gi|13541605|ref|NP_111293.1| 44 GKAHIIGITGPPGVGKSTMIGILSKMLSEHGKKVSILAVDAS 85
                                  66779*************************999999888876 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   7.1e-05     0.041       3      35 ..      51      88 ..      49     155 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 7.1e-05
                                  EESSTTSSHHHHHHHHHHHH.....THEEEEEETTTCS CS
                           AAA  3 lyGppGtGKTllakavakel.....gvefleisgsell 35
                                  ++GppG+GK++++  + k l     +v++l +++s+ +
  gi|13541605|ref|NP_111293.1| 51 ITGPPGVGKSTMIGILSKMLsehgkKVSILAVDASSPF 88
                                  68*****************9554444667777776654 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0     7e-05      0.04       3      26 ..      51      74 ..      49     119 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 7e-05
                  RNA_helicase  3 lyGpsgeGKStlakeLakallkkl 26
                                  ++Gp+g+GKSt++  L+k l+++ 
  gi|13541605|ref|NP_111293.1| 51 ITGPPGVGKSTMIGILSKMLSEHG 74
                                  89***************9999776 PP

>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   6.8e-05     0.039       3      40 ..      49      86 ..      47     121 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.8e-05
                     Fer4_NifH  3 iaiyGkGGiGksttsqnlsaalaemgkkvlivGCDPka 40
                                  i i G  G+Gkst +  ls++l+e+gkkv i+  D  +
  gi|13541605|ref|NP_111293.1| 49 IGITGPPGVGKSTMIGILSKMLSEHGKKVSILAVDASS 86
                                  7889999**********************999988654 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   0.00016     0.091      12      41 ..      56      85 ..      48     115 .. 0.84
   2 ?    0.6   0.1      0.77   4.5e+02     119     150 ..     140     170 ..     104     188 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00016
                        AAA_31 12 GvGKTTtsvnlaaalaklgkkvLlvDlDpQ 41
                                  GvGK+T    l+++l++ gkkv +  +D+ 
  gi|13541605|ref|NP_111293.1| 56 GVGKSTMIGILSKMLSEHGKKVSILAVDAS 85
                                  9********************977777764 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.77
                        AAA_31 119 DyiiiDcpPsLglltenaLvasdsviipvqae 150
                                   Dyiii +  + g   + +++ +d+vi+ + + 
  gi|13541605|ref|NP_111293.1| 140 DYIIIETVGA-GQSDIDIVYLADTVIVTLAPG 170
                                   8899988865.777888999999999999875 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   9.4e-05     0.054       2      41 ..      49     100 ..      48     193 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 9.4e-05
                                   EEEEESTTSSHHHHHHHHHT............STEEESSSTTSSSSEEEEEE CS
                      MMR_HSR1   2 vaivGrpNvGKStLinaltg............ekaivsdkpgtTrdinegrv 41 
                                   ++i G p vGKSt+i  l++            ++   s + g T+  n++r+
  gi|13541605|ref|NP_111293.1|  49 IGITGPPGVGKSTMIGILSKmlsehgkkvsilAVDASSPFSGGTLLGNRIRM 100
                                   89*************9999755444443322223344555555555555555 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   0.00012     0.069       4      32 ..      51      82 ..      49     119 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00012
                                  EE--SSSSHHHHHHHGGGGB...S--EEEEE- CS
                         AAA_5  4 LvGppGtgKselaerlaaal...nreveyvql 32
                                  + GppG+gKs+++  l+++l   +++v + + 
  gi|13541605|ref|NP_111293.1| 51 ITGPPGVGKSTMIGILSKMLsehGKKVSILAV 82
                                  58******************887666555544 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   5.6e-05     0.032       4      38 ..      49      83 ..      47      94 .. 0.87
   2 ?   -2.7   0.3       5.6   3.2e+03      49      71 ..     249     271 ..     232     273 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.6e-05
                                  EEEE--TTSSHHHHHHHHHHHHHHTT--EEEE-TH CS
                         KTI12  4 vvltGlPssGKstrakeLakaleeekrsvvvidde 38
                                  + +tG P +GKst+   L+k l+e++++v ++  +
  gi|13541605|ref|NP_111293.1| 49 IGITGPPGVGKSTMIGILSKMLSEHGKKVSILAVD 83
                                  559**************************998744 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 5.6
                                   -GGGHHHHHHHHHHHHHHHHTT. CS
                         KTI12  49 dsakekalRsslrsavkrdLske 71 
                                    ++ke + ++++r a++r+++k+
  gi|13541605|ref|NP_111293.1| 249 GNKKEIRYKEEIRLAISREIEKK 271
                                   23444555677888888888774 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   0.00017     0.097      26      39 ..      50      63 ..      37      77 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00017
                        AAA_29 26 lltGpsGsGKSTll 39
                                   +tGp G+GKST++
  gi|13541605|ref|NP_111293.1| 50 GITGPPGVGKSTMI 63
                                  59***********9 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   0.00012     0.071       3      39 ..      47      83 ..      45      85 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00012
                                  EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHH CS
                    APS_kinase  3 vvvwltGlsgsGKstianalekkLvekgisvylLdGd 39
                                   ++ +tG  g GKst+   l+k+L e+g++v +L  d
  gi|13541605|ref|NP_111293.1| 47 HIIGITGPPGVGKSTMIGILSKMLSEHGKKVSILAVD 83
                                  67889**************************999755 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.5   0.00016     0.091       3      39 ..      48      84 ..      46      90 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00016
                                  EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-ST CS
                   ArsA_ATPase  3 vilvgGKGGVGKttvsaatavklsekgkkvllistDP 39
                                  +i ++G  GVGK+t+   ++  lse+gkkv ++++D 
  gi|13541605|ref|NP_111293.1| 48 IIGITGPPGVGKSTMIGILSKMLSEHGKKVSILAVDA 84
                                  78899****************************9995 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   0.00019      0.11      22      51 ..      44      73 ..      34     100 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00019
                        AAA_16 22 grpelvllsGesGvGKsslvrellralekd 51
                                  g  +++ ++G++GvGKs+++  l + l+++
  gi|13541605|ref|NP_111293.1| 44 GKAHIIGITGPPGVGKSTMIGILSKMLSEH 73
                                  4557889************98888776666 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 ?   11.7   0.1   0.00027      0.16      35      70 ..      47      83 ..      43     104 .. 0.82
   2 ?   -2.4   0.0         6   3.5e+03      34      47 ..     161     174 ..     158     202 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00027
                        RuvB_N 35 hvl.lyGpPGlGkttlakiiakelgvklkitsgPvle 70
                                  h++ ++GpPG+Gk+t+  i++k l  + k  s  +++
  gi|13541605|ref|NP_111293.1| 47 HIIgITGPPGVGKSTMIGILSKMLSEHGKKVSILAVD 83
                                  554489***************9999888877766655 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 6
                        RuvB_N  34 dhvllyGpPGlGkt 47 
                                   d v+++ +PGlG +
  gi|13541605|ref|NP_111293.1| 161 DTVIVTLAPGLGDS 174
                                   77888888999865 PP

>> Helicase_RecD  Helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00058      0.33       2      33 ..      51      81 ..      50     104 .. 0.82
   2 ?   -0.2   0.0       1.4   7.9e+02     146     173 ..     248     275 ..     227     277 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00058
                 Helicase_RecD  2 ltAdRGRGKSaalGlalaaliaegksnilvta 33
                                  +t+ +G GKS+++G++ + l ++gk ++ + a
  gi|13541605|ref|NP_111293.1| 51 ITGPPGVGKSTMIGILSKMLSEHGK-KVSILA 81
                                  899**************99999998.444443 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.4
                 Helicase_RecD 146 krelreleleepiRyaegdplEkwlndl 173
                                   + + +e++ +e iR a   ++Ek +n +
  gi|13541605|ref|NP_111293.1| 248 SGNKKEIRYKEEIRLAISREIEKKVNGA 275
                                   3356788888888888888888887765 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00034      0.19      43      81 ..      42      80 ..      27      84 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00034
                     IstB_IS21 43 fiekkenivllGpsGvGKshlaialgveavraglsvlfv 81
                                  ++ k++ i ++Gp+GvGKs +   l++   ++g++v+ +
  gi|13541605|ref|NP_111293.1| 42 YTGKAHIIGITGPPGVGKSTMIGILSKMLSEHGKKVSIL 80
                                  667788899*****************99999*9999865 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   0.00037      0.21       9      47 ..      45      81 ..      37      86 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00037
                        AAA_19  9 kekvllvtaGpGtGKTrvlkhivallvelggvkpeeill 47
                                  k++++ +t++pG GK++++    ++l e g+    +il+
  gi|13541605|ref|NP_111293.1| 45 KAHIIGITGPPGVGKSTMIGILSKMLSEHGKK--VSILA 81
                                  677899*************9999888888743..44544 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.2   0.00033      0.19      22      53 ..      46      77 ..      41     105 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00033
                  Mg_chelatase 22 gHnlllvGppGsGKtmlakrlpsllpplseee 53
                                   H + ++GppG GK+ ++  l+++l++  ++ 
  gi|13541605|ref|NP_111293.1| 46 AHIIGITGPPGVGKSTMIGILSKMLSEHGKKV 77
                                  4667799******************9987664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (315 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       648  (0.0361426); expected 358.6 (0.02)
Passed bias filter:                      562  (0.0313459); expected 358.6 (0.02)
Passed Vit filter:                       110  (0.00613531); 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: 0.63u 0.32s 00:00:00.95 Elapsed: 00:00:00.50
# Mc/sec: 1908.11
//
Query:       gi|13541606|ref|NP_111294.1|  [L=124]
Description: molecular chaperone (small heat shock protein, hsp20-related) [Thermoplasma volcanium GSS1]
Scores for complete 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-13   50.1   1.5    2.7e-13   49.9   1.5    1.1  1  HSP20       Hsp20/alpha crystallin family
    1.5e-09   37.3   0.0    2.5e-09   36.5   0.0    1.4  1  ArsA_HSP20  HSP20-like domain found in ArsA
     0.0089   15.4   2.1       0.01   15.2   2.1    1.1  1  DUF4097     Putative adhesin


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 !   49.9   1.5   4.5e-17   2.7e-13       5      89 ..      36     117 ..      32     124 .] 0.86

  Alignments for each domain:
  == domain 1  score: 49.9 bits;  conditional E-value: 4.5e-17
                                   SEEEEEEEEE-TT--CCCEEEEEETTEEEEEEE--..---TT----SS---EEEEEE--STTB-TTT-EEEEETTEEEEEE CS
                         HSP20   5 eeeefevkldvpglkkeelkvkvednrvlvkgeheeeeedekglikerssrkFsrkftLPenvdadkvkaslkdGvLtvtv 85 
                                   + +   ++++++g++k+++kv+v++n++++++e++  +e ++++i +r + k  + ++LP ++++++++a++++G+Ltv +
  gi|13541606|ref|NP_111294.1|  36 DSSDLVLEAEMAGFDKKNIKVSVNKNVLTISAERK--REYSTVYIDQR-VDKVYKVVKLPVEIEQQDISAKYSEGILTVRM 113
                                   56677899***************************..89999999955.55555799**********************99 PP

                                   EBSS CS
                         HSP20  86 pkke 89 
                                   + k+
  gi|13541606|ref|NP_111294.1| 114 KTKN 117
                                   8765 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 !   36.5   0.0   4.3e-13   2.5e-09       4      63 .]      40     113 ..      37     113 .. 0.96

  Alignments for each domain:
  == domain 1  score: 36.5 bits;  conditional E-value: 4.3e-13
                    ArsA_HSP20   4 yvlkldLPfvdkeeidlsrsgdeLtIkig...............nfrRqitLPsvlarkevtsAkfedgvLeIrF 63 
                                    vl +++ ++dk++i++s + + LtI+++               +  +++ LP  + ++++ sAk+ +g L++r+
  gi|13541606|ref|NP_111294.1|  40 LVLEAEMAGFDKKNIKVSVNKNVLTISAErkreystvyidqrvdKVYKVVKLPVEIEQQDI-SAKYSEGILTVRM 113
                                   799*************************************999999999************.***********98 PP

>> DUF4097  Putative adhesin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   2.1   1.7e-06      0.01      33     104 ..      50     116 ..      31     124 .] 0.77

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.7e-06
                       DUF4097  33 lkkqkve.etggtLsitqkekngvstgfikelssgekskitiylPkktkledlqvkassGdlsvekatklkae 104
                                   +kk+ +  ++ + L+i+ ++k+++st  i   +  +k + +++lP + + +d+++k s G l+v     +k++
  gi|13541606|ref|NP_111294.1|  50 DKKNIKVsVNKNVLTISAERKREYSTVYI--DQRVDKVYKVVKLPVEIEQQDISAKYSEGILTVR----MKTK 116
                                   34444444*******************99..8999*************9***********98866....2222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       909  (0.0507); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 845.46
//
Query:       gi|13541607|ref|NP_111295.1|  [L=510]
Description: protein kinase [Thermoplasma volcanium GSS1]
Scores for complete 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-25   88.1   0.0      1e-24   87.0   0.0    1.6  1  ABC1      ABC1 family
    5.7e-05   22.6   1.2    9.3e-05   21.9   1.2    1.4  1  Pkinase   Protein kinase domain
     0.0001   22.0   6.0    0.00028   20.5   0.3    2.4  3  RIO1      RIO1 family
  ------ inclusion threshold ------
      0.012   15.5   0.4        0.1   12.5   0.1    2.5  3  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 !   87.0   0.0   2.3e-28     1e-24       6     118 ..     105     217 ..     101     218 .. 0.96

  Alignments for each domain:
  == domain 1  score: 87.0 bits;  conditional E-value: 2.3e-28
                          ABC1   6 kleeiFaefdeePiAaASiaqVhrAklksgeeVavKvqrpgvkkriksDlellkllakllkkflkelr.ldleelvdefsk 85 
                                   k++++F+efde++i  AS++qV+rA+ k g+ V+vKv r ++++r+ksDl  +++l+k +k  ++++  l++e+++ +f+k
  gi|13541607|ref|NP_111295.1| 105 KIDQVFDEFDENAISGASLGQVYRATYK-GRLVVVKVNRFNIEDRLKSDLIAIRRLLKHAKGRIENFLyLSIENVIMDFNK 184
                                   799**********************875.9*******************************999999989*********** PP

                          ABC1  86 slleEldferEAknaekfrenfaklkevkvPkv 118
                                   +++ E+d+++E +n++ +r+n++++++v +P+v
  gi|13541607|ref|NP_111295.1| 185 RIFDEIDYRKEVSNMNLIRSNLHEDDRVIIPQV 217
                                   ********************************9 PP

>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   1.2   2.1e-08   9.3e-05      39     150 ..     180     301 ..     123     309 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 2.1e-08
                                   HHHHHHHHHHHHHHHHHSCTTB--EEEEEEE...........SSEEEEEEE--TTEBHHHHHH.HHSS--HHHHHHHHHHH CS
                       Pkinase  39 kkkekkvlrEikilkklkhpnivrlyevfee...........kdelylvleyveggeladlle.rkgslseeeakkiakqi 107
                                    + +k+++ Ei + k+++ +n++r      +           +++ +lv+ey++g++++++   ++++++ +e+   + ++
  gi|13541607|ref|NP_111295.1| 180 MDFNKRIFDEIDYRKEVSNMNLIRSNLHEDDrviipqvieglSSKEVLVMEYISGTKIDNVQIlKEKNIDTKELALRVDTV 260
                                   4556899****************9877766699999***99999999*********9988766577888888888888888 PP

                                   HHHHHHHHHTTEE-SS-SGGGEEEETTTEEEE-SGTTSEESSS CS
                       Pkinase 108 legleylHskgiiHrDlKpeNiLidekgelKitDFGlakeles 150
                                   +  ++ l +  i+H D  p Ni + ++g + + DFG++  ++ 
  gi|13541607|ref|NP_111295.1| 261 F--MRMLLKDTIFHADPHPGNISVADDGSIILYDFGMVGFIND 301
                                   7..78999*****************************988876 PP

>> RIO1  RIO1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.1       1.8     8e+03      12      35 ..      11      34 ..       5      43 .. 0.65
   2 !    5.1   0.2    0.0034        15     115     186 ..     123     193 ..      94     195 .. 0.78
   3 !   20.5   0.3   6.3e-08   0.00028      56     149 ..     193     293 ..     190     297 .. 0.72

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 1.8
                                  EEEEEEE-S---SS-HHHHCTTTS CS
                          RIO1 12 evaiKiyktstteFkkrkkyvsge 35
                                  ++ +K+y + ++  k+rk+ ++++
  gi|13541607|ref|NP_111295.1| 11 HILLKLYPVFRRYLKDRKRAKEND 34
                                  456677777777777776665554 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0034
                                   HHHHHHHHHTSTEEESS-STTSEEEETTEEEE--GTTEEETTSTTHHHHHHHHHHHHHHHHHTTC-----HH CS
                          RIO1 115 leemrklykeaglvHaDLSeyNvlvdedkvviIDvsQaveldhpnalefLerDveniikfFrrkgvekvdee 186
                                   l ++ ++  + +lv   ++ +N + d+ k  +I +   +++++ + ++fL   +en+i  F+++  +++d++
  gi|13541607|ref|NP_111295.1| 123 LGQVYRATYKGRLVVVKVNRFN-IEDRLKSDLIAIRRLLKHAKGRIENFLYLSIENVIMDFNKRIFDEIDYR 193
                                   4455555558899999999999.45555999999999***************************99998887 PP

  == domain 3  score: 20.5 bits;  conditional E-value: 6.3e-08
                                   HHHHHHHHHH....HHTT.--S--EEE..EETTEEEEE--EETTEEGGBHHHCG.-HHHHHHHHHHHHHHHHHHHHTSTEE CS
                          RIO1  56 ekEfrnLkrl....eeag.vpvPkpie..lkrhvlvmefigedgvaapklkdve.eeeeaeelyeevleemrklykeaglv 128
                                   +kE++n++ +    +e + v +P++ie    ++vlvme+i+  g+++ +++ ++ ++ +++el+  v     +++ + ++ 
  gi|13541607|ref|NP_111295.1| 193 RKEVSNMNLIrsnlHEDDrVIIPQVIEglSSKEVLVMEYIS--GTKIDNVQILKeKNIDTKELALRVDTVFMRMLLKDTIF 271
                                   5777777654111134335899***97446899********..6666666666633566677776666666677779**** PP

                                   ESS-STTSEEEETT.EEEE--G CS
                          RIO1 129 HaDLSeyNvlvded.kvviIDv 149
                                   HaD    N+ v +d  +++ D+
  gi|13541607|ref|NP_111295.1| 272 HADPHPGNISVADDgSIILYDF 293
                                   *********9999978888887 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.53   2.4e+03     114     157 ..      68     114 ..      56     126 .. 0.75
   2 ?   -0.4   0.0      0.19   8.6e+02      53      84 ..     213     239 ..     114     250 .. 0.52
   3 ?   12.5   0.1   2.2e-05       0.1     153     198 ..     258     298 ..     241     300 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.53
                                   TB-SHHCHTCCHHHHHHCHHHCCCGCCTCC....HHHHHHHHHHHHHH CS
                           APH 114 pladflaqdlellrqlesatarllaselld....lleeleeqvlaala 157
                                   +++ +++ +l+ +r+l ++  +++ +++++     l ++++ v ++++
  gi|13541607|ref|NP_111295.1|  68 RPDLMPKEYLAAFRKLQDQVDPDPFPLVKQiierNLGKIDQ-VFDEFD 114
                                   55667778888889999998888888888866655566666.666665 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.19
                                   B--B-CTTBS-EEETTEEEEEEE----EE-SS CS
                           APH  53 pvPevlagdtddeeigllfalieyvpgrsllr 84 
                                    +P+v+      + +  +++++ey+ g+ +++
  gi|13541607|ref|NP_111295.1| 213 IIPQVIE-----GLSSKEVLVMEYISGTKIDN 239
                                   2455555.....44445666677776666665 PP

  == domain 3  score: 12.5 bits;  conditional E-value: 2.2e-05
                                   HHHHHHH--SSS-EEEE-SS-SGGGEEEC..TTEEEEE---TT-EE CS
                           APH 153 laalaallpgelptvllHgDlhpgNllvdpddgrvtGviDfedagl 198
                                      + + l+   + ++ H D+hpgN+ v +d+  +  + Df+++g 
  gi|13541607|ref|NP_111295.1| 258 DTVFMRMLL---KDTIFHADPHPGNISVADDGSII--LYDFGMVGF 298
                                   444444444...799**************665555..89**99975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (510 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       682  (0.0380389); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.64u 0.31s 00:00:00.95 Elapsed: 00:00:00.49
# Mc/sec: 3122.77
//
Query:       gi|13541608|ref|NP_111296.1|  [L=110]
Description: thioredoxin [Thermoplasma volcanium GSS1]
Scores for complete sequence (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   70.0   0.3    1.5e-19   69.9   0.3    1.0  1  Thioredoxin    Thioredoxin
    9.6e-07   29.1   0.5     0.0021   18.3   0.0    2.1  2  Thioredoxin_8  Thioredoxin-like
    5.4e-05   22.7   0.0    5.7e-05   22.6   0.0    1.1  1  OST3_OST6      OST3 / OST6 family, transporter family
     0.0011   18.9   0.1     0.0013   18.7   0.1    1.2  1  AhpC-TSA       AhpC/TSA family
     0.0012   18.8   0.1     0.0017   18.4   0.1    1.3  1  Thioredoxin_3  Thioredoxin domain
     0.0048   17.3   0.3        0.1   13.0   0.3    2.0  1  Thioredoxin_2  Thioredoxin-like domain
  ------ inclusion threshold ------
      0.018   14.8   0.2      0.021   14.6   0.2    1.1  1  Thioredoxin_9  Thioredoxin
      0.064   13.0   0.0       0.08   12.7   0.0    1.3  1  Redoxin        Redoxin


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 !   69.9   0.3   6.7e-23   1.5e-19       2     100 ..       4     100 ..       3     103 .. 0.94

  Alignments for each domain:
  == domain 1  score: 69.9 bits;  conditional E-value: 6.7e-23
                                   EEESSHHHHHHHHTTTSSEEEEEEE-TTSHHHHCHHHHHHHHHHHCTTTSEEEEEETTTSHHHHHHTT-SSSSEEEEEETT CS
                   Thioredoxin   2 vlvltkenFeeevakekklvlveFyApwCghCkalaPeleklaeelkdkvklakvdvdenedlakkyevegiPtlklfkng 82 
                                   v++++ e+++e +   +k +++e +A+wC +Ck + P le+++e+l+    + +++vd+n+++ +++++++iP ++lf ng
  gi|13541608|ref|NP_111296.1|   4 VKEINYEEYKELIGT-SKSFILELWAEWCHPCKIMMPYLEEACEKLN-ACYFFRINVDKNPKIIDELNINSIPRIILFVNG 82 
                                   56788999***9999.99*****************************.9******************************** PP

                                   EEEEEEESS-HHHHHHHH CS
                   Thioredoxin  83 kevkkyegarekeklaaf 100
                                   ++  +++g ++ + +++ 
  gi|13541608|ref|NP_111296.1|  83 EKTGEIKGFQKSDVIIEE 100
                                   *********999988875 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   9.6e-07    0.0021       2      31 ..      20      49 ..      19      50 .. 0.93
   2 !   10.7   0.1   0.00023      0.51      57      89 ..      49      79 ..      47      85 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 9.6e-07
                                  SEEEEEE--SSSHHHHHHHHHHHHHHHHHH CS
                 Thioredoxin_8  2 kvvlLyfgaswcppckaftpklkelyeklk 31
                                  k ++L  +a+wc+pck ++p l e  ekl+
  gi|13541608|ref|NP_111296.1| 20 KSFILELWAEWCHPCKIMMPYLEEACEKLN 49
                                  678999*********************998 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00023
                                  S-TTSEE.EE-TT-HHHHTT-S--TT-SEEEEE CS
                 Thioredoxin_8 57 nkkpwlsvpfddkkrnklkkkynvkaiPtlvvl 89
                                  n  ++++++ + +k+ k+++++n+++iP++++ 
  gi|13541608|ref|NP_111296.1| 49 N--ACYFFRINVDKNPKIIDELNINSIPRIILF 79
                                  4..89************************9986 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 !   22.6   0.0   2.6e-08   5.7e-05      70     109 ..      47      86 ..      19     104 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 2.6e-08
                     OST3_OST6  70 kskklfFakvdfdegkdvFqklglnsaPhlllfppkkgpk 109
                                   k +  +F+++++d+++++  +l++ns+P+++lf   ++  
  gi|13541608|ref|NP_111296.1|  47 KLNACYFFRINVDKNPKIIDELNINSIPRIILFVNGEKTG 86 
                                   56789****************************9855444 PP

>> AhpC-TSA  AhpC/TSA 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    0.0013      25      75 ..      17      66 ..       4      98 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 5.6e-07
                                  T..SEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCHHHHH CS
                      AhpC-TSA 25 g..kpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvdspeshkk 75
                                  g  k  +l  +++ wc +C+  +p l++++e++    +  + ++vd+  ++ +
  gi|13541608|ref|NP_111296.1| 17 GtsKSFILELWAE-WCHPCKIMMPYLEEACEKLN--ACYFFRINVDKNPKIID 66
                                  344889*******.*******************9..89999999999887655 PP

>> Thioredoxin_3  Thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.1   7.4e-07    0.0017      10      58 ..      31      83 ..      24     101 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 7.4e-07
                                  STTCHHHHHHHHHHCHCCT.CECEEECCTTHHHH.HHCT-SSSSEE..ECTTC CS
                 Thioredoxin_3 10 CakCpklekavkeaaaekg.ikaevekvtdfeei.ekygVmsvPal..vidgk 58
                                  C+ C+ ++  ++ea ++++  ++  ++v ++++i ++ ++ s+P +  +++g+
  gi|13541608|ref|NP_111296.1| 31 CHPCKIMMPYLEEACEKLNaCYFFRINVDKNPKIiDELNINSIPRIilFVNGE 83
                                  ******************96888999999999999**********97788987 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.3   4.6e-05       0.1       4     103 ..      18      95 ..      15     100 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.6e-05
                 Thioredoxin_2   4 ngkpvlvvftdpdCpyCkklkkelkel.ddvtvrvllfplkpsfepkavaiwcakekkkafkdieenvelarkygvrgtPt 83 
                                   + k +++  ++++C  Ck ++  l+e  ++++ +            ++++i  +k++k             +++++++ P 
  gi|13541608|ref|NP_111296.1|  18 TSKSFILELWAEWCHPCKIMMPYLEEAcEKLNAC------------YFFRINVDKNPK-----------IIDELNINSIPR 75 
                                   6677777788888888888888888885555555............677777777776...........9999******** PP

                 Thioredoxin_2  84 iv.fldgkeivarlpGyvpae 103
                                   i+ f +g+ +  +++G+ +++
  gi|13541608|ref|NP_111296.1|  76 IIlFVNGE-KTGEIKGFQKSD 95 
                                   77699999.667899988776 PP

>> Thioredoxin_9  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.2   9.3e-06     0.021      43     107 ..      21      82 ..       5      99 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 9.3e-06
                                   EEEEEE--TT-HHHHHHHHHHHHHHHH-TTEEEEEE-HHHHHHHTTTTTT-SS--SSEEEEE-TT CS
                 Thioredoxin_9  43 lkilvltedwCgDaavnvPvlakiaelnpnievkillrdenlelmdqyltngaraiPtliildee 107
                                     il l ++wC  + +++P+l+++ e  +   +  +  d+n++++d+      ++iP +i++ ++
  gi|13541608|ref|NP_111296.1|  21 SFILELWAEWCHPCKIMMPYLEEACEKLNACYFFRINVDKNPKIIDELNI---NSIPRIILFVNG 82 
                                   556778899***************99998888888889********9965...899988877654 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   3.6e-05      0.08      29      74 ..      20      62 ..      10      84 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.6e-05
                                  SEEEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEEEEESSSH CS
                       Redoxin 29 kkvvvnfvpgafcPtCsaehpyleklaellkekgvdvvavvadnda 74
                                  k+ ++  ++  +c +C+  +pyle+  e+   ++  ++ +++d+++
  gi|13541608|ref|NP_111296.1| 20 KSFILELWAE-WCHPCKIMMPYLEEACEK--LNACYFFRINVDKNP 62
                                  6778899999.**************9776..455556666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 748.26
//
Query:       gi|13541609|ref|NP_111297.1|  [L=107]
Description: hypothetical protein TVN0778 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      237  (0.0132188); 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: 00:00:00.41
# Mc/sec: 775.02
//
Query:       gi|13541610|ref|NP_111298.1|  [L=242]
Description: TPR repeat-containing protein [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    0.00042   20.2   2.7        8.7    6.7   0.0    4.5  5  TPR_2         Tetratricopeptide repeat
     0.0013   18.9   2.7         14    6.1   0.0    4.0  5  TPR_12        Tetratricopeptide repeat
     0.0025   17.8   0.8       0.16   12.1   0.0    3.2  3  ANAPC5        Anaphase-promoting complex subunit 5
  ------ inclusion threshold ------
      0.035   13.2   0.4      0.043   12.9   0.4    1.3  1  ANF_receptor  Receptor family ligand binding region
      0.046   13.8   0.0        2.3    8.4   0.1    2.4  2  Hormone_3     Pancreatic hormone peptide
       0.14   12.0   3.9        2.3    8.0   3.8    2.2  1  IPK           Inositol polyphosphate kinase
       0.24   11.8   1.9        4.5    7.7   0.1    2.7  2  DUF1871       Domain of unknown function (DUF1871)
        3.9    6.9   6.9        7.5    6.0   0.3    2.3  2  Z1            Z1 domain


Domain annotation for each model (and alignments):
>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.6   0.1    0.0044       9.9       8      30 ..      11      33 ..       4      37 .. 0.80
   2 ?   -1.5   0.0       1.6   3.7e+03       2      16 ..      42      56 ..      41      73 .. 0.69
   3 !    6.7   0.0    0.0039       8.7       4      31 ..      86     113 ..      83     116 .. 0.91
   4 ?   -1.9   0.1       2.2     5e+03      16      29 ..     137     150 ..     137     154 .. 0.77
   5 ?    3.6   0.0     0.038        85       4      25 ..     215     236 ..     212     240 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0044
                         TPR_2  8 GlayyklgdyeeAleafekAlel 30
                                  ++  +++ +y +Al+++ +A+e 
  gi|13541610|ref|NP_111298.1| 11 ADRNFEKEKYIDALRDYLAAIEK 33
                                  66678999*************96 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.6
                         TPR_2  2 ealynlGlayyklgd 16
                                  e+ y   ++y +l++
  gi|13541610|ref|NP_111298.1| 42 EIAYKVSQIYHYLQK 56
                                  555666677766654 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.0039
                         TPR_2   4 lynlGlayyklgdyeeAleafekAleld 31 
                                   l n+G +++ +g+ e+  + +++A+e +
  gi|13541610|ref|NP_111298.1|  86 LINIGTILIDSGKKEDGMRKLDEAIEKA 113
                                   789**********************987 PP

  == domain 4  score: -1.9 bits;  conditional E-value: 2.2
                         TPR_2  16 dyeeAleafekAle 29 
                                   d++eA + ++ + e
  gi|13541610|ref|NP_111298.1| 137 DPDEAFKIYQDVAE 150
                                   67999999987766 PP

  == domain 5  score: 3.6 bits;  conditional E-value: 0.038
                         TPR_2   4 lynlGlayyklgdyeeAleafe 25 
                                   +    +++++l++ e+A+e  +
  gi|13541610|ref|NP_111298.1| 215 YDTASDIAMALDNVEDAIEIAK 236
                                   666778999********99665 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.1   0.3    0.0062        14      15      62 ..      16      59 ..       5      60 .. 0.78
   2 ?   -0.3   0.0      0.58   1.3e+03      29      62 ..      69     100 ..      60     115 .. 0.59
   3 ?    3.0   0.0     0.055   1.2e+02       8      70 ..      88     147 ..      82     148 .. 0.72
   4 !    6.1   0.0    0.0061        14      18      51 ..     137     168 ..     132     193 .. 0.79
   5 ?    3.0   0.0     0.056   1.2e+02      55      76 ..     215     236 ..     210     240 .. 0.61

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0062
                        TPR_12 15 rlgrydeAlellekaleiarrllGpdhpltattlrnLgrly.ralgrye 62
                                  + ++y +Al+ + +a+e +      d +l a++ +  +++y +++++ +
  gi|13541610|ref|NP_111298.1| 16 EKEKYIDALRDYLAAIEKV-----QDDDLKAEIAYKVSQIYhYLQKDSD 59
                                  678999*********5555.....45568***********934666665 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.58
                        TPR_12  29 aleiarrllGpdhpltattlrnLgrlyralgrye 62 
                                   al i+++   ++ +l +  l+n+g+++  +g+ e
  gi|13541610|ref|NP_111298.1|  69 ALKIHEEK--GEMDLQVLDLINIGTILIDSGKKE 100
                                   55666555..444455666666666666666554 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.055
                        TPR_12   8 nlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlellee 70 
                                   n++++l   g+ ++  + l++a+e a+++   d +l  ++l   + + + + +++eA +++++
  gi|13541610|ref|NP_111298.1|  88 NIGTILIDSGKKEDGMRKLDEAIEKAKET--NDDELIMISLTSKAGIISDS-DPDEAFKIYQD 147
                                   78888888888888888899999999888..55556666666666664555.89999888886 PP

  == domain 4  score: 6.1 bits;  conditional E-value: 0.0061
                        TPR_12  18 rydeAlellekaleiarrllGpdhpltattlrnL 51 
                                   + deA+++++ + e  +++  +d++++  +l +L
  gi|13541610|ref|NP_111298.1| 137 DPDEAFKIYQDVAEKSEKI--EDWEDYFDALSGL 168
                                   789****************..9999999999887 PP

  == domain 5  score: 3.0 bits;  conditional E-value: 0.056
                        TPR_12  55 yralgryeeAlelleealaiae 76 
                                   y+ + + + Al+  e+a++ia+
  gi|13541610|ref|NP_111298.1| 215 YDTASDIAMALDNVEDAIEIAK 236
                                   5555566666666666666655 PP

>> ANAPC5  Anaphase-promoting complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.0   7.1e-05      0.16      39      86 ..      80     128 ..      25     136 .. 0.77
   2 ?    1.1   0.0      0.19   4.2e+02      56      91 ..     157     192 ..     148     195 .. 0.76
   3 ?    1.3   0.1      0.16   3.7e+02      57      76 ..     221     240 ..     202     242 .] 0.81

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7.1e-05
                        ANAPC5  39 syqya.lLnlaslhadfghneeAvkaleeairlArenkDkscLalalaw 86 
                                    +q+  l+n  ++  d g++e+ ++ l eai+ A+e++D++ + + l++
  gi|13541610|ref|NP_111298.1|  80 DLQVLdLINIGTILIDSGKKEDGMRKLDEAIEKAKETNDDELIMISLTS 128
                                   44444477888888888***********************988777665 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.19
                        ANAPC5  56 hneeAvkaleeairlArenkDkscLalalawlarll 91 
                                   ++e+  +al+  i++ r++ + +  ++a+  + +l+
  gi|13541610|ref|NP_111298.1| 157 DWEDYFDALSGLINITRKKDEGKAFQMAMDAIDKLE 192
                                   556667888888999999999888888888776665 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.16
                        ANAPC5  57 neeAvkaleeairlArenkD 76 
                                    + A++ +e+ai++A+  ++
  gi|13541610|ref|NP_111298.1| 221 IAMALDNVEDAIEIAKRLQN 240
                                   5679999********97665 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 ?   12.9   0.4   1.9e-05     0.043     218     294 ..     152     229 ..      47     241 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.9e-05
                                   CTTS-CC..HHHHHTT-EEEEE--B-HHHHHHHHH...ST--CCCSSSTCCGSTTCCHHHHH...HHHHHHHHHHHHHHH CS
                  ANF_receptor 218 lvldkpeltgleaaegvlgfrlkdpnspkfsefld...kreklsdekqnyenegkeqisyqaalmYdaVyllaeAlnkll 294
                                   ++  +++ ++++a+ g++ ++ k  + + f+  +d   k ek+s+  + +++ +++++  ++ ++Yd+   +a+Al+++ 
  gi|13541610|ref|NP_111298.1| 152 SEKIEDWEDYFDALSGLINITRKKDEGKAFQMAMDaidKLEKISA--TIKSKKERKEFIESFSYLYDTASDIAMALDNVE 229
                                   22223336799************************7765555553..556666666777777788************997 PP

>> Hormone_3  Pancreatic hormone peptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.1     0.001       2.3      17      29 ..      18      30 ..      16      31 .. 0.86
   2 ?    2.8   0.0     0.056   1.3e+02      12      28 ..     154     170 ..     151     174 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.001
                                  HHHHHHHHHHHHH CS
                     Hormone_3 17 akYyaaLrhYlnl 29
                                   kY++aLr+Yl+ 
  gi|13541610|ref|NP_111298.1| 18 EKYIDALRDYLAA 30
                                  59*********86 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.056
                                   -HHHHHHHHHHHHHHHH CS
                     Hormone_3  12 spEeLakYyaaLrhYln 28 
                                    +E++  Y++aL   +n
  gi|13541610|ref|NP_111298.1| 154 KIEDWEDYFDALSGLIN 170
                                   58**********87666 PP

>> IPK  Inositol polyphosphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   3.8     0.001       2.3      67     123 ..       4      59 ..       1     222 [. 0.83

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.001
                                   EEEEEHHHHCT-SHHHHHHHHHHCCCSSSSCCHHHHHHHCHHHHHHHHHHHHHCSHS CS
                           IPK  67 yltvdkkygrslskeevkealkkFlsngkslrkdakaaskllerLqelkqvlesqes 123
                                   ++t  k+  r+++ke+  +al+++l++ ++++ d  +  +++ ++ ++++ l++ + 
  gi|13541610|ref|NP_111298.1|   4 VETLIKNADRNFEKEKYIDALRDYLAAIEKVQDDD-LKAEIAYKVSQIYHYLQKDSD 59 
                                   66778999******************887666555.6666***********998654 PP

>> DUF1871  Domain of unknown function (DUF1871)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.2     0.067   1.5e+02      26      49 ..      30      53 ..       7      75 .. 0.74
   2 ?    7.7   0.1     0.002       4.5      19      45 ..     215     240 ..     210     241 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.067
                                  HHHHHTT-S-HHHHHHHHHHHHHH CS
                       DUF1871 26 vvqavyelddpkklakkiqeiyev 49
                                  +++ v++ d   ++a k+ +iy++
  gi|13541610|ref|NP_111298.1| 30 AIEKVQDDDLKAEIAYKVSQIYHY 53
                                  3444555555678999******86 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.002
                                   GHHHHHHHHHHHTT-S-HHHHHHHHHH CS
                       DUF1871  19 YetEaadvvqavyelddpkklakkiqe 45 
                                   Y+t a+d+  a+ +++d+ ++ak++q+
  gi|13541610|ref|NP_111298.1| 215 YDT-ASDIAMALDNVEDAIEIAKRLQN 240
                                   666.79******************996 PP

>> Z1  Z1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   1.0     0.014        32      29     106 ..       7      79 ..       2     104 .. 0.73
   2 ?    6.0   0.3    0.0033       7.5      26      89 ..     165     228 ..     149     242 .] 0.65

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.014
                            Z1  29 Lvhvsrfkdeqekvaelieelleelkkelkesaeekkeellkeleklwekektstkseeeelsfeevkeelkealeki 106
                                   L+  + ++ e+ek+ ++++++l +++k  +   +  k+e+  +++++++    +++s+e++++f e++ +++e   ++
  gi|13541610|ref|NP_111298.1|   7 LIKNADRNFEKEKYIDALRDYLAAIEKVQD---DDLKAEIAYKVSQIYHYL--QKDSDENSMKFAEIALKIHEEKGEM 79 
                                   666666677777777888888887766533...357788888888888877..5667888889999988888776555 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0033
                            Z1  26 nsmLvhvsrfkdeqekvaelieel..leelkkelkesaeekkeellkeleklwekektstkseeee 89 
                                    s L++++r+kde + ++ +++++  le+++ ++k++  ++++e+++ ++ l+++ +  + + ++ 
  gi|13541610|ref|NP_111298.1| 165 LSGLINITRKKDEGKAFQMAMDAIdkLEKISATIKSK--KERKEFIESFSYLYDTASDIAMALDNV 228
                                   677999***9999887776665441166666666666..899999999999999982222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1599  (0.0891851); expected 358.6 (0.02)
Passed bias filter:                      590  (0.0329076); 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: 0.55u 0.32s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 1484.40
//
Query:       gi|13541611|ref|NP_111299.1|  [L=159]
Description: hypothetical protein TVN0780 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-37  128.9   1.8    1.2e-37  128.8   1.8    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 !  128.8   1.8   6.6e-42   1.2e-37       3     143 ..       6     151 ..       4     152 .. 0.95

  Alignments for each domain:
  == domain 1  score: 128.8 bits;  conditional E-value: 6.6e-42
                       DUF2240   3 kiavaapfkk..krkdklsesdfvfalsldrkwlspdqakklldraeeegLlekkdgdlvpnfdvaeveiPlgFkpdeell 81 
                                   +++++a +++  k+ ++ + +df++++s++rk+l pd++k+++d+a +e Ll kk+++ +pnf+++++ +Pl+F+++e+ l
  gi|13541611|ref|NP_111299.1|   6 ARKLIAMVAAdtKKVESFGLQDFINVISFRRKLLAPDTVKRFVDEAVKENLLVKKGERFAPNFSTSGIVVPLDFTVSEKDL 86 
                                   5677777776568999*************************************************************9888 PP

                       DUF2240  82 ....kekstferildaiaastgiekkevvaeinelqeelkglvdveaaalvvakkegvdvddliee 143
                                       k+k+ ++rilda++as++++kke++ae++e +e+lk l+++++a+l++ +++g+d++d+++e
  gi|13541611|ref|NP_111299.1|  87 fsasKDKPLIDRILDAATASGKLTKKEAIAEAHEFMENLK-LITFQTALLAIMNEHGIDISDFLRE 151
                                   8***************************************.**********************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       624  (0.0348039); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); 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 0.21s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 1279.66
//
Query:       gi|13541612|ref|NP_111300.1|  [L=321]
Description: bifunctional methylated DNA-protein cysteine methyltransferase/deoxyinosine 3'endonuclease [Thermoplasma volcanium GSS1]
Scores for 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-27   95.2   0.1    1.7e-26   93.1   0.1    1.9  1  Endonuclease_5  Endonuclease V
    2.1e-17   63.0   0.0    5.8e-17   61.6   0.0    1.7  1  DNA_binding_1   6-O-methylguanine DNA methyltransferase, DNA 


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 !   93.1   0.1   1.9e-30   1.7e-26      12     182 ..     133     280 ..     120     294 .. 0.75

  Alignments for each domain:
  == domain 1  score: 93.1 bits;  conditional E-value: 1.9e-30
                                   --SGG-SEEEEEEEEEEECTCEEEEEEEEEEETTTTEEEEEEEEEEE--S-SSTT-CHHHCHHHHHHHHCC-SS--SEEEE CS
                Endonuclease_5  12 klkeklklvaGvDvsfvkeekkeavaalvvldlpslevvekavavvklsfpYipgfLaFRElpvllkaleklkqkpdvllv 92 
                                   + + +l+++a++Dvs+   ++++ +a+ vv++  + ++    v  ++  fpYipg+LaF+E++++ ++++    +  ++l+
  gi|13541612|ref|NP_111300.1| 133 RNDYSLDTIAAFDVSY---KETRGYASKVVYN--KGKIG-AYVYSSDSMFPYIPGYLAFKEFKFIRALYD----NETMILI 203
                                   3333489*********...3334499999987..55544.455567789************998776665....4569*** PP

                                   EC-SSSSTTS--HHHHHHHHHTS-EEEEESS-SSSBE----SSTTEEEEEEETTEEEEEEEESSTTS--EEEEEECSS-HH CS
                Endonuclease_5  93 DGnGiaHprrlGlAshlGvlldlptiGvaKsllvgkveepekekgsvvplvsegevigaalrtkknvkpiyvSvGhrisle 173
                                   DGnGi+Hpr +GlA+h Gv l++++iG+aK+l   +v+         ++l+ +g v g ++         +vS+G+ri++e
  gi|13541612|ref|NP_111300.1| 204 DGNGILHPRFAGLATHAGVSLKTASIGIAKHLINCTVKG--------SDLLISGVVAGKMIGH-----HTIVSPGNRINVE 271
                                   ******************************998765442........3444347777777764.....458********** PP

                                   HHHHHHHHC CS
                Endonuclease_5 174 talelvlal 182
                                   +a +l+++ 
  gi|13541612|ref|NP_111300.1| 272 EAGRLIEQR 280
                                   **9999876 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 !   61.6   0.0   6.5e-21   5.8e-17       7      78 ..      16      89 ..      13      92 .. 0.87

  Alignments for each domain:
  == domain 1  score: 61.6 bits;  conditional E-value: 6.5e-21
                                  HHHHTTS-TT-BEEHHHHHHHTT.TSCHHHHHHHHHTSSBTTTSGGGGEEBTTSBCCTTTT..CHHHHHHHHHH CS
                 DNA_binding_1  7 wellrqIpyGkvttYgeiAkllgkpkaaraVgqalaanplailvPcHRVvgadgklggyag..glerkralLea 78
                                  ++l+rqIp G v tYg++A++lg+p aar Vg +l  n+ +  +Pc++Vv  dg++g+y++  g ++k + L +
  gi|13541612|ref|NP_111300.1| 16 YNLVRQIPDGMVSTYGDLAEALGDPVAARSVGFMLSINKEPDYIPCYKVVPHDGSVGNYTHplGSAEKMRRLIR 89
                                  89*********************************************************554555555555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 2284.11
//
Query:       gi|13541613|ref|NP_111301.1|  [L=359]
Description: mevalonate pyrophosphate decarboxylase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.016   15.1   0.0      0.029   14.3   0.0    1.4  1  WH1             WH1 domain
      0.022   15.0   2.3      0.054   13.7   2.3    1.7  1  GHMP_kinases_N  GHMP kinases N terminal domain


Domain annotation for each model (and alignments):
>> WH1  WH1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   3.2e-06     0.029      38      78 ..     255     295 ..     219     329 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.2e-06
                                   EEEEEETTTTEEEEEEEETTT-SEEEEEEE-SS---B-SSS CS
                           WH1  38 vslvkdstqnsyflrlvklqdakvvieqeiyknleynqarq 78 
                                   +++++++t n+y + +v +  +k++++q+  + +  +++  
  gi|13541613|ref|NP_111301.1| 255 AQIIENATTNTYLMHSVLISTGKLLWNQDTLRAMGIVEDMR 295
                                   6899************************9999998776654 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 ?   13.7   2.3   6.1e-06     0.054      11      47 ..     129     168 ..     119     179 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.1e-06
                                   TSSSCHHHHHHHHHHHHHHH.HTTEH.HHH.HHHHHHHHH CS
                GHMP_kinases_N  11 gaGLGSSAAlavalvaAlla.llgls.lee.aklaleaer 47 
                                   ++GLG SAA+a+a+ + l + l++++ l++ + ++++a  
  gi|13541613|ref|NP_111301.1| 129 AKGLGESAAVAAAASRSLVSaLFEKEaLKDsNFISIVARL 168
                                   56***************96626666666555555655554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (359 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       338  (0.0188521); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 2351.63
//
Query:       gi|13541614|ref|NP_111302.1|  [L=420]
Description: glycerate kinase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-54  184.7   0.0    2.6e-54  184.2   0.0    1.2  1  DUF4147   Domain of unknown function (DUF4147)
    2.5e-28   98.4   0.2    4.1e-28   97.7   0.2    1.4  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 !  184.2   0.0   2.9e-58   2.6e-54       7     204 ..      25     221 ..      20     241 .. 0.89

  Alignments for each domain:
  == domain 1  score: 184.2 bits;  conditional E-value: 2.9e-58
                                   HHHHHTTSHHHHHHTTHHHH--.......-SEEEEEESTTHHHHHHHHH....HHHG.EEEEEEETT-----TT-EEEEE- CS
                       DUF4147   7 eaaveavdpeklvkralslkeeeldlskkkrvvvvgaGKAaaamaaalee...ealk.sgvvvvkkghaeekerievleaa 83 
                                   ++  +  +p+k++++a+    +e+dl+k+  v+v+g+GKAa +m   ++e   ++lk  g+++   ++ +   ++++l+++
  gi|13541614|ref|NP_111302.1|  25 NEVFKDFEPNKVTEKAV----NEIDLNKYAGVYVIGFGKAAYEMYLGVREhvkRKLKyAGIIIPSDQEVQYLPELDILRGT 101
                                   5667888999**99999....3599********************77774355445578888888788889999******* PP

                                   SSS--HHHHHHHHHHHHHHSS--TT-EEEEEE-TTHHHHS--B-TT--HHHHHHHHHHHHHCT--HHHHHHHHHTTBSSTT CS
                       DUF4147  84 hplPdeesveaarkilelaeklkeddlvlvliSGGgSAllaaPaegitledkqaltkaLlasGasIqelNtVRkhlsaikG 164
                                   hpl +  sv++++k+l+ a+  +++dlvlvliSGGgS+l++ P+egit+++++++++a++ + a+I elNt+R++ls++kG
  gi|13541614|ref|NP_111302.1| 102 HPLTSTLSVTSSKKLLSKAR-PSANDLVLVLISGGGSSLFEIPQEGITIDQMASISRAMMDHSANIYELNTIRSALSSVKG 181
                                   ******************99.7999******************************************************** PP

                                   THHHHHHTTSEEEEEEE--STT--TTTGGG-TTS-----H CS
                       DUF4147 165 GrLaraaaparvvsLilSDVvgddldvIASGPtvpdsstf 204
                                   G+Lar+++pa++++Li+SDV+gdd+++IASGP + ++ + 
  gi|13541614|ref|NP_111302.1| 182 GKLARILYPATIIALIISDVPGDDISIIASGPLAENKLDP 221
                                   *********************************9865444 PP

>> MOFRL  MOFRL family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.7   0.2   4.6e-32   4.1e-28       3     109 .]     311     411 ..     309     411 .. 0.94

  Alignments for each domain:
  == domain 1  score: 97.7 bits;  conditional E-value: 4.6e-32
                                   EEEEE--B----S-----HHHHHHHHHHH...HTTT-TTEEEEEEETTS--SSSS--EEEEETTHHHHHHHTT--HHHHHH CS
                         MOFRL   3 llsgGEttvtvkgkGkGGrnqelalalalelkelegaeevvllsagtDGiDGptdaaGaivdaetleraeaagldakeaLa 83 
                                   +++gGEttv+vkg+G GGrn elal++++ l+   + +++ +ls+gtDGiDG + aaG+iv++++  ++++  ++++e+L+
  gi|13541614|ref|NP_111302.1| 311 FVAGGETTVNVKGNGIGGRNLELALRFMK-LA---NFSDFLFLSIGTDGIDGVSPAAGGIVSSDMKLKISS--QELEETLD 385
                                   799*************************9.44...4589*************************9988887..699***** PP

                                   TT-HHHHHHHTT-EE-----S----E CS
                         MOFRL  84 nndsyeffeklgallktgpTgtNVnD 109
                                   +nd+++++++ + +++tg Tg+NV+D
  gi|13541614|ref|NP_111302.1| 386 RNDAFTLLSAYHGAIMTGRTGNNVSD 411
                                   ************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (420 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       561  (0.0312901); 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: 0.64u 0.29s 00:00:00.93 Elapsed: 00:00:00.51
# Mc/sec: 2493.56
//
Query:       gi|13541615|ref|NP_111303.1|  [L=500]
Description: benzoylformate decarboxylase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.9e-37  127.9   0.0    5.5e-37  127.0   0.0    1.4  1  TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP b
    3.4e-17   62.6   0.0      9e-17   61.3   0.0    1.7  2  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b
    9.3e-12   44.9   0.0    1.8e-11   43.9   0.0    1.5  1  TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
  ------ inclusion threshold ------
      0.033   14.6   0.0       0.12   12.8   0.0    2.0  1  FtsA          Cell division protein FtsA


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 !  127.0   0.0   1.2e-40   5.5e-37       1     169 [.       1     163 [.       1     165 [. 0.95

  Alignments for each domain:
  == domain 1  score: 127.0 bits;  conditional E-value: 1.2e-40
                                   EEHHHHHHHHHHHCT--EEEE---CCCHHHHCCHHCT.TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHHHHCHH CS
                  TPP_enzyme_N   1 mtvaealvraLkalgvehvfgvpGsrilplldalseeqgirvvlarhEqgaafaAdgyaratgkpgvvlvtsgpGatnalt 81 
                                   m+++e+++++L+++    v+g+pG+++ p+l  +++ +     l++h    +++Ad++++ +g+p+vv+++s pG+ n + 
  gi|13541615|ref|NP_111303.1|   1 MKASEIFAKTLEEHELYPVYGNPGTTEIPMLSFVKDYR-----LTLHDSISVAMADAVSQYSGRPAVVNLHSLPGISNSMA 76 
                                   789****************************9999996.....99************************************ PP

                                   HHHHHHHHT--EEEEEEE--CCCHHS..TC--T..-CCHHHCCCSSEEEE-SSGGGHHHHHHHHHHHHHSSS--EEEEEEE CS
                  TPP_enzyme_N  82 alaeAkvdriPllvlsgdrptslrgqgvlqqel..dqlalfrpvtkyaervtspeelpealrrAirtalsgrpgPvylelp 160
                                    +++A+++++P+++ +g++++++       + l  dq++++ p++kya++v+ p+e+pea++rA+++a++++ gPv+l++p
  gi|13541615|ref|NP_111303.1|  77 FIYSAFKNNSPIIITAGQQDRRHLI---YDPLLsgDQVDMVSPYVKYAYEVRMPSEIPEAMKRAYEIAMTPPYGPVFLSFP 154
                                   ********************99998...4433356********************************************** PP

                                   HHHCC-EEE CS
                  TPP_enzyme_N 161 kdvlleevd 169
                                   +d+++e+++
  gi|13541615|ref|NP_111303.1| 155 MDLMDEDAE 163
                                   *****9875 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 ?   -3.6   0.0         2   8.8e+03     126     143 ..     123     138 ..     108     145 .. 0.71
   2 !   61.3   0.0     2e-20     9e-17      12     137 ..     361     481 ..     351     492 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 2
                                   EESSH.HHHHHHHHHHHH CS
                  TPP_enzyme_C 126 rvekadveeleealkeal 143
                                      ++ ++e+ ea+k+a 
  gi|13541615|ref|NP_111303.1| 123 E--VRMPSEIPEAMKRAY 138
                                   3..444488999999886 PP

  == domain 2  score: 61.3 bits;  conditional E-value: 2e-20
                                   HHTTSSSSEEECETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHTGGGHHHHHHTT-SEEEEEEE-SBCCCHHHHH CS
                  TPP_enzyme_C  12 llkvkrprsyltsgglgtmGyglpaAiGaklakpdrevvaivGDGgflmilqelatavrrnlpitvvvlnNegygmtggqq 92 
                                   +  +  p+sy+ts   g +G+g +a +G+++++  ++   i+GDG+f++++q l+ta r++ p ++vvl N++y+  +  +
  gi|13541615|ref|NP_111303.1| 361 Y-FADGPKSYYTSR-GGPLGWGDAATVGISALQ--ERTLGIIGDGAFMYTVQSLWTASRYGMPSKFVVLRNNAYNILRSYS 437
                                   4.345589999975.69**************84..69******************************************** PP

                                   HHHTCCTTTTSBB.BS----HHHHHHHTTSEEE.EESSH.HHHHHH CS
                  TPP_enzyme_C  93 epfggkrksgpagkdlkpvdfaklaealGakga.rvekadveelee 137
                                   + fg + + ++    + + d++k+ e+lG+++  + + +d++ l+e
  gi|13541615|ref|NP_111303.1| 438 KAFGYGIEDADF--LKLEYDPVKVSEGLGVEARvYASIDDIKWLKE 481
                                   ****98887766..68899************543444444455544 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 !   43.9   0.0     4e-15   1.8e-11       2     118 ..     183     296 ..     182     309 .. 0.82

  Alignments for each domain:
  == domain 1  score: 43.9 bits;  conditional E-value: 4e-15
                                   HHHHHHHHH-SSEEEEE-CHHCHTTGHHHHHHHHHHHT-EEEEEGGGTTSS-TTSTTEEEESGGGSCHHHHHHHHH-SEEE CS
                  TPP_enzyme_M   2 ekaaellkaakrpvilvGggvarsgaseelrelaeklgiPvvttlmgkgvipedhplylgmlglhgskaanealeeaDlvl 82 
                                   + +++++++a++++i+ G +v+  ga + +re++ kl++Pv++ +  +g+   ++++++  l  +  +a +++l   Dlvl
  gi|13541615|ref|NP_111303.1| 183 KSIMDRVNSARKVAIVYGYEVDLYGAMDLAREFSTKLNVPVFSEPWSQGSCCYRDQNFVRDLPPA-MAAIDAILSTFDLVL 262
                                   678899******************************************************99998.99************* PP

                                   EES-SSSTCCCTTTTT.TTTTT-EEEEEESSCCCCTT CS
                  TPP_enzyme_M  83 alGarfddirttgsep.efapeakiihididpaeigk 118
                                   ++G   +di+++ + p e  ++ +   i + p+++  
  gi|13541615|ref|NP_111303.1| 263 FIG---SDIFVYPYTPaEALRNVEAYFISTRPTHFAG 296
                                   ***...6667777666444444355555555555554 PP

>> FtsA  Cell division protein FtsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   2.6e-05      0.12      23      71 ..     167     275 ..     157     409 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.6e-05
                                   EEEES--HHHHHHHHHHHHT--HHHHHHHHHHH--S--.......EEEEEHHHHH.......................... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxx.......................... RF
                          FtsA  23 lrvigvggngitkdiakalrtaveeAerikikyGsala.......ekeigrkels.......................... 70 
                                   ++   ++g  i++di+k++   v++A +++i yG+ +         +e++  +l+                          
  gi|13541615|ref|NP_111303.1| 167 SEFYSTPGIAIDEDIVKSIMDRVNSARKVAIVYGYEVDlygamdlAREFS-TKLNvpvfsepwsqgsccyrdqnfvrdlpp 246
                                   56677899**************************9888888777755555.344455555666666666665555555555 PP

                                   ............................G CS
                                   ............................x RF
                          FtsA  71 ............................g 71 
                                                                
  gi|13541615|ref|NP_111303.1| 247 amaaidailstfdlvlfigsdifvypytP 275
                                   55555555555555555555555555552 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (500 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       466  (0.0259914); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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 0.29s 00:00:00.94 Elapsed: 00:00:00.49
# Mc/sec: 3038.69
//
Query:       gi|13541616|ref|NP_111304.1|  [L=166]
Description: Rossmann fold nucleotide-binding protein [Thermoplasma volcanium GSS1]
Scores for complete sequence (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   0.4    1.5e-40  138.4   0.4    1.0  1  LDcluster4       SLOG cluster4 family
     0.0003   20.1   0.0       0.18   11.0   0.0    2.1  2  DNA_processg_A   DNA recombination-mediator protein A
     0.0075   16.4   0.0      0.012   15.7   0.0    1.3  1  Lysine_decarbox  Possible lysine decarboxylase


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   0.4   2.5e-44   1.5e-40       2     157 .]       4     149 ..       3     149 .. 0.93

  Alignments for each domain:
  == domain 1  score: 138.4 bits;  conditional E-value: 2.5e-44
                    LDcluster4   2 lkigVmGsaeteakeealelaeelGrliAkegavlltGgrtGvmeaaskGakeagGltvGilpassekehsnkyvdiiiyT 82 
                                   l+i+V+G ++  +++e+ +l +++Gr++Ak ++v+++Gg tGvme++skG++e +G++vGilp+ + +e +n+yv+i ++T
  gi|13541616|ref|NP_111304.1|   4 LNIAVIGGSR--VSQEVCTLSYNVGRILAKYNVVVFCGGLTGVMECVSKGVSEGNGIVVGILPGYDPSE-ANDYVTIKVPT 81 
                                   68*****999..8999************************************************66665.7778******* PP

                    LDcluster4  83 GlglagRnlilvlssdvviaiggrsGTlsEialaleegkpvivlkgtdellseiiekkekderkvivaespkelv 157
                                   G+g++ Rn++++++s++vi i+g++GTlsE ++a++egk v+ l       +  i +k+++e++v+v+ +p+++v
  gi|13541616|ref|NP_111304.1|  82 GMGYM-RNFLIIRASQAVISIDGSAGTLSEASFAISEGKDVVSLF------ELNIPRKKEKEGHVYVEPDPEKAV 149
                                   *****.**************************************9......567788888888899999999986 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 !   11.0   0.0   3.1e-05      0.18      44     103 ..       5      64 ..       1      72 [. 0.94
   2 !    7.4   0.0   0.00038       2.3     145     185 ..      86     124 ..      78     148 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 3.1e-05
                DNA_processg_A  44 avaiVGtRkaseygkevakklakelaeagitivSGlAlGiDaaahraaleaggktvavlg 103
                                   ++a++G  ++s++  ++  ++ + la+ ++++  G+  G+ ++  ++  e +g  v++l+
  gi|13541616|ref|NP_111304.1|   5 NIAVIGGSRVSQEVCTLSYNVGRILAKYNVVVFCGGLTGVMECVSKGVSEGNGIVVGILP 64 
                                   79**********************************************999999999997 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.00038
                DNA_processg_A 145 eRnriiaglseavlvveaaekSGalitaelAlelgrevfav 185
                                   +Rn +i   s+av+ +  +   G+l  a++A+++g++v+ +
  gi|13541616|ref|NP_111304.1|  86 MRNFLIIRASQAVISI--DGSAGTLSEASFAISEGKDVVSL 124
                                   6888998889987665..5678****************985 PP

>> Lysine_decarbox  Possible lysine decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   2.1e-06     0.012       1      69 [.      45     111 ..      45     119 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.1e-06
                                   HHHHHHHHHHTTS-EEEEEECCHHHHHCCTTT-SEEEEESSHHHHHHHHHHHESEEEE-S-SHHHHHHH CS
               Lysine_decarbox   1 meavakgaleaggrviGiipkillaeeapneevnelvivedmeeRkealveladafvilPGGiGTleEl 69 
                                   me v+kg+ e +g v+Gi p    +e  +n++v+  v +    +R+  +++ ++a++ + G +GTl E+
  gi|13541616|ref|NP_111304.1|  45 MECVSKGVSEGNGIVVGILPGYDPSE--ANDYVTIKVPTGMGYMRNFLIIRASQAVISIDGSAGTLSEA 111
                                   999***************77766544..5889987777777889**********************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       480  (0.0267723); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1087.28
//
Query:       gi|13541617|ref|NP_111305.1|  [L=131]
Description: hypothetical protein TVN0786 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.3e-05   23.8   3.6    4.3e-05   23.8   3.6    1.8  2  PsiE      Phosphate-starvation-inducible E
  ------ inclusion threshold ------
       0.16   12.3   1.5       0.18   12.2   0.1    1.6  2  DUF4396   Domain of unknown function (DUF4396)
        3.9    7.5   7.2        9.9    6.1   1.2    2.3  2  TRIQK     Triple QxxK/R motif-containing protein family


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 ?   -2.3   0.3      0.99   5.9e+03       4       7 ..      19      22 ..      13      28 .. 0.48
   2 !   23.8   3.6   7.1e-09   4.3e-05       2      68 .]      52     119 ..      51     119 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.99
                          PsiE  4 iLll 7 
                                  iL+l
  gi|13541617|ref|NP_111305.1| 19 ILIL 22
                                  2222 PP

  == domain 2  score: 23.8 bits;  conditional E-value: 7.1e-09
                          PsiE   2 gdiLllLillEllrtivaylkehriavrlvieaaiiavaRklIildlkdggylt.llglaaailaLgl 68 
                                   g+ +  L+llEl++ + + +      +r v+ea++  ++R++Ii+    +  ++ l +la++i+aL++
  gi|13541617|ref|NP_111305.1|  52 GNAFFALVLLELFEGVHDFIVKSPQGLRHVVEAGLSYIIREIIIDISTGIKDIYsLSALAIVIIALSV 119
                                   678889**********9999999888*******************66666666658888888998875 PP

>> DUF4396  Domain of unknown function (DUF4396)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1     3e-05      0.18      45      98 ..      19      72 ..       8      88 .. 0.86
   2 ?   -1.0   0.1      0.35   2.1e+03      42      55 ..     109     122 ..      79     128 .. 0.58

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3e-05
                       DUF4396 45 svvlalllgllletalllrekglslaealktAlkadtlSmlamevgmnlvmlll 98
                                   ++la+++ l + ++ l   ++++l e +  A++  ++ ++  e+ + + ++++
  gi|13541617|ref|NP_111305.1| 19 ILILAIVFDLCFSIYQLIILRSSGLEELVYSAVGNAFFALVLLELFEGVHDFIV 72
                                  5789*********999999999************************99999988 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.35
                       DUF4396  42 milsvvlalllgll 55 
                                   ++  v++al ++l+
  gi|13541617|ref|NP_111305.1| 109 ALAIVIIALSVSLY 122
                                   22333333333333 PP

>> TRIQK  Triple QxxK/R motif-containing protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   1.2    0.0016       9.9      48      74 ..      15      41 ..       9      46 .. 0.86
   2 ?    4.6   0.5    0.0048        29      46      76 ..      99     129 ..      94     131 .] 0.75

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0016
                         TRIQK 48 ikevllvlvailvlllalYalfflnls 74
                                  i e++l+l+ ++ l +++Y l+ l+ s
  gi|13541617|ref|NP_111305.1| 15 IIEAILILAIVFDLCFSIYQLIILRSS 41
                                  668999***************988755 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.0048
                         TRIQK  46 sgikevllv.lvailvlllalYalfflnlske 76 
                                   +gik++  +  +ai+++ l++ +l+fl l+k+
  gi|13541617|ref|NP_111305.1|  99 TGIKDIYSLsALAIVIIALSV-SLYFLVLTKN 129
                                   689999877577777777766.7889999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       798  (0.0445089); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 888.85
//
Query:       gi|13541618|ref|NP_111306.1|  [L=582]
Description: amino acid transporter [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (582 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1118  (0.0623571); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.78u 0.36s 00:00:01.14 Elapsed: 00:00:00.50
# Mc/sec: 3489.74
//
Query:       gi|13541619|ref|NP_111307.1|  [L=147]
Description: hypothetical protein TVN0788 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.14   12.1   4.6        3.3    7.6   2.5    2.0  2  Fig1      Ca2+ regulator and membrane fusion protein Fig1


Domain annotation for each model (and alignments):
>> Fig1  Ca2+ regulator and membrane fusion protein Fig1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.1   0.00044       7.9      48      92 ..      28      72 ..      13      78 .. 0.80
   2 ?    7.6   2.5   0.00018       3.3     120     180 ..      72     132 ..      66     140 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.00044
                          Fig1 48 lslsssssskstsdplnlvelakkfsdnvvhpyllmvaiiLtlll 92
                                  +s++++  + +ts+++nl e ++ + ++  h+ l+++ai  ++l+
  gi|13541619|ref|NP_111307.1| 28 TSINRIRRTFQTSKDQNLMEFRQIVGQQENHNDLIYAAIGEFFLS 72
                                  45577888888999************************9755554 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.00018
                          Fig1 120 lvlsflllllwlvgalwqhvassaastlveeasmgivkskvGkkaealgWfafaflllvcl 180
                                    ++++ll+++++v +l++ v+++ + +++++ ++++vk +  + +e+++ +a+af++l++ 
  gi|13541619|ref|NP_111307.1|  72 SAFMILLSVIMMVPSLFSFVNTQLSYNYLRSFALNVVKFNTAGYIEIIATLAIAFTILFLA 132
                                   5789999*******************************************99999777543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1116  (0.0622455); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.44
# Mc/sec: 1001.76
//
Query:       gi|13541620|ref|NP_111308.1|  [L=339]
Description: hypothetical protein TVN0789 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (339 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1192  (0.0664845); expected 358.6 (0.02)
Passed bias filter:                      628  (0.0350271); 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: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 2242.63
//
Query:       gi|13541621|ref|NP_111309.1|  [L=476]
Description: thiamine biosynthesis protein ThiI [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.1e-50  172.0   0.0    2.3e-49  167.7   0.0    2.2  2  ThiI       Thiamine biosynthesis protein (ThiI)
    7.9e-18   64.9   2.3    2.7e-17   63.2   0.2    2.4  2  THUMP      THUMP domain
    0.00011   22.6   0.0    0.00032   21.2   0.0    1.7  1  Rhodanese  Rhodanese-like domain
     0.0034   16.9   0.0        1.1    8.7   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 !  167.7   0.0   5.1e-53   2.3e-49       1     196 [.     166     358 ..     166     359 .. 0.94
   2 ?    2.0   0.0      0.03   1.3e+02       2      38 ..     425     461 ..     424     475 .. 0.79

  Alignments for each domain:
  == domain 1  score: 167.7 bits;  conditional E-value: 5.1e-53
                          ThiI   1 gtqgkvlaLlSgGiDSpVaaylllkRG..crvvlvhlknepgtseeaiekveklaellaeyqtslevklvvvdfkevlkei 79 
                                   g++gk ++++SgGiDSpVa++l++kRG  c + ++ l  +p+ +++  e  +kl+e ++ y    + ++++ d +++++++
  gi|13541621|ref|NP_111309.1| 166 GSEGKLISMVSGGIDSPVATWLMMKRGspCDIFFCSL-ADPIDTQAFLEIAKKLVERWSPYR---DGNVFIADCRDLIRDM 242
                                   789************************7778888888.5999999****************9...699************* PP

                          ThiI  80 lekvkekltivllkrkmlriAekvaeeegakalvtGesLgqVaSqtleNlrvisavvnllilrPLigldKeeiiklAkeig 160
                                   + + k +   v +k+ ++r+Ae++ae++++  +vtGesLgqV+Sqt eNl  i++ +n +i rPLigldK+ei ++A++ig
  gi|13541621|ref|NP_111309.1| 243 VIEKKTNFNNVTFKKVLYRLAERLAEKYRYLGIVTGESLGQVSSQTAENLLSIEHGINFPIYRPLIGLDKDEITAIARDIG 323
                                   ********************************************************************************* PP

                          ThiI 161 tyeisiekedkCsvlakhPttkakleevekaeeklk 196
                                   t+    +  + Cs++++hP+t++k e++e+  +k++
  gi|13541621|ref|NP_111309.1| 324 TFPE-KNVGEFCSLFSAHPVTRSKWEDIEEDVKKID 358
                                   *974.34459*******************9988876 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.03
                          ThiI   2 tqgkvlaLlSgGiDSpVaaylllkRGcrvvlvhlkne 38 
                                   t+ k +   S G+ S   a++l +RG+++ + ++++ 
  gi|13541621|ref|NP_111309.1| 425 TSKKYVFYCSMGLQSAYVASVLRERGIEAYFTTFSKL 461
                                   567888889**********************999643 PP

>> THUMP  THUMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.2   0.2   6.1e-21   2.7e-17      14     141 ..      33     153 ..      20     155 .. 0.84
   2 ?    0.9   0.1     0.096   4.3e+02      61      89 ..     344     370 ..     330     395 .. 0.74

  Alignments for each domain:
  == domain 1  score: 63.2 bits;  conditional E-value: 6.1e-21
                                   -SEEEEETTEEEEECTEEEEEETHHHHHHHHHTSTTECEEEEEEEEEESSHHHHHHHHHHHHHHHHHHCT-EEEEEEEESS CS
                         THUMP  14 verveagkgrivvelkgekpeedeellkealekargiqrvipvcevceadledileaakeivkkkfeeeketFaVrvkrrg 94 
                                   + ++++   r+++  + + ++e+e+ +  +l+k++gi++ +   ++++++ edi ++++++ ++k +++  tF Vr++r g
  gi|13541621|ref|NP_111309.1|  33 YYKKIGYEARCQLLAG-RLLVEAENDI--PLSKVFGIKSYSECIRIKFENQEDIVKKVHALYEEKVKGK--TFGVRCRRTG 108
                                   5555555555555543.4456677777..899999*******************************999..********** PP

                                   STSSSHHHHHHHHHHHHHHCCTT-EE-SSS-SEEEEEEEETTEEEEE CS
                         THUMP  95 khfeftsreinrevGkaivektglkVdlenPdivvrveiikdkayis 141
                                    h +fts ++++++G+a+ +  +  Vdl++P++ ++v+i ++ a+i+
  gi|13541621|ref|NP_111309.1| 109 TH-SFTSIDMEKAIGDALYSISN-GVDLKSPEVWIHVDIVGKDALIY 153
                                   **.*****************777.*****************999986 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.096
                                   ESSHHHHHHHHHHHHHHHHHHCT-EEEEE CS
                         THUMP  61 eadledileaakeivkkkfeeeketFaVr 89 
                                   + + edi+e +k+i+ +kf+e     a++
  gi|13541621|ref|NP_111309.1| 344 RSKWEDIEEDVKKIDIEKFIERV--TAIK 370
                                   56678899999999888888873..3333 PP

>> Rhodanese  Rhodanese-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   7.1e-08   0.00032       7      90 ..     387     450 ..     381     465 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 7.1e-08
                     Rhodanese   7 ellekgkvallDvRppeeYekghIpgAvnvskdtlsrakkseapllelpeellelgidnkktvvvycdgggraaaaaallk 87 
                                   ++le+   +++D R ++ Yek+h +gA+++                +l ++l+    d  k+ v+yc+ g ++a +a  l+
  gi|13541621|ref|NP_111309.1| 387 KNLEDA--VFIDLRKKDLYEKSHYQGARHL----------------DLEQALAIN--DTSKKYVFYCSMGLQSAYVASVLR 447
                                   444333..4*********************................555556665..77*************999999999 PP

                     Rhodanese  88 klG 90 
                                   + G
  gi|13541621|ref|NP_111309.1| 448 ERG 450
                                   766 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.0   0.00024       1.1       3      29 ..     172     198 ..     170     334 .. 0.51
   2 ?   -2.6   0.1      0.73   3.3e+03       3      32 ..     430     459 ..     428     468 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00024
                                   EEE--SSHHHHHHHHHHHHH-SEEEEE CS
                          QueC   3 vvllSGGlDSttvlalakkegkeveal 29 
                                   + ++SGG+DS ++++l++k+g  + + 
  gi|13541621|ref|NP_111309.1| 172 ISMVSGGIDSPVATWLMMKRGSPCDIF 198
                                   667777777777777777776654443 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.73
                                   EEE--SSHHHHHHHHHHHHH-SEEEEEEEE CS
                          QueC   3 vvllSGGlDSttvlalakkegkevealtfd 32 
                                   v   S Gl S+ v+ + +++g e +  tf+
  gi|13541621|ref|NP_111309.1| 430 VFYCSMGLQSAYVASVLRERGIEAYFTTFS 459
                                   667789999999999999999999988886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (476 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       564  (0.0314574); 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: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 3086.65
//
Query:       gi|13541622|ref|NP_111310.1|  [L=223]
Description: hypothetical protein TVN0791 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-44  152.0   0.0    1.7e-44  151.8   0.0    1.0  1  Chlor_dismutase  Chlorite dismutase
  ------ inclusion threshold ------
       0.12   12.3   0.0         14    5.5   0.0    2.1  2  MHC_I_2          Class I Histocompatibility antigen, NKG2D li


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 !  151.8   0.0   1.8e-48   1.7e-44       5     193 ..      28     211 ..      24     212 .. 0.93

  Alignments for each domain:
  == domain 1  score: 151.8 bits;  conditional E-value: 1.8e-48
                                   HHHHHHHHHHTTSCEEEEEEEETSTTTT-SEEEEEEESSHHHHHHHHHHHHHSTGGGGEEEEEEEEEEEEEESSSSS-GGG CS
               Chlor_dismutase   5 veelealleeaeegvlralysvlGlradaDlmlwllretleelqeaerelrrtalgkvlepaysyvsvtelseYkeedeen 85 
                                   +++l+++l++a+++ +++l ++ ++r d+Dl++w+ ++t++++ e+++++   +l  +++ +ys +s++ +s Y    +++
  gi|13541622|ref|NP_111310.1|  28 LNKLSSILRDAKSK-MINLHTYRSFRYDSDLVFWFSSRTPDDILELKEKIGF-TLLPYANATYSSISIYDESPY----NAM 102
                                   57788999999999.***********************************98.899******************....566 PP

                                   HHHCHHHHS----SSSEEEEEEEEE-EEGGGS-HHHHHHHHHHHHHHHHGCTT...EEEEEEE-TTTSSSSEEEEEEESST CS
               Chlor_dismutase  86 kshvearlapelpkkkyvcvYPmsksreWYllpeeeRrelmaeHgeigrkYgk...VrqiitgsfGldDyEwgvaleaddl 163
                                   ++++e  l+   ++ +y+++YPmsk+ eWYllp++eR+e+m+eH++++ k+++   +r+++t+sfG++D+E++v +e +d+
  gi|13541622|ref|NP_111310.1| 103 NKKLEDSLKL--KPLDYFVAYPMSKDPEWYLLPFDERKEIMREHIDTALKHPDekgIRSYTTYSFGIGDQEFVVLYELPDI 181
                                   6777666654..5699***********************************66689************************* PP

                                   HHHHHHHHHHCTSHHHHHHEEE-S-EEEEE CS
               Chlor_dismutase 164 eefkdlvyelRfdeasakvaeegpfyvGrr 193
                                   +++ ++ ++lR+ +a++++ +e+p+++Gr+
  gi|13541622|ref|NP_111310.1| 182 AAWSRVTEKLREVKARKWIVKETPIILGRL 211
                                   ****************************86 PP

>> MHC_I_2  Class I Histocompatibility antigen, NKG2D ligand, domains 1 and 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0    0.0026        23      61     159 ..      24     121 ..      16     131 .. 0.70
   2 ?    5.5   0.0    0.0016        14      86     124 ..     139     177 ..     132     203 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0026
                                   HHHHHHHHHHHHHHHHHCS.---TTTT-SS--EEEEEEES-TT-SSS--EEEEEETTTEEEEEETT.TTEEEESCHHHHH. CS
                       MHC_I_2  61 ltqpvndlcqklrdkvsnt.kvdthktngyphlqvtmiypqsqgqtpsatwefnisdsyfftfyte.nmswrsandesgv. 138
                                   + +p+n l   lrd  s+  ++ t+++  y   +  +++  s  +tp    e++    + +  y++   s  s  des   
  gi|13541622|ref|NP_111310.1|  24 VKEPLNKLSSILRDAKSKMiNLHTYRSFRY---DSDLVFWFS-SRTPDDILELKEKIGFTLLPYANaTYSSISIYDESPYn 100
                                   567999999999997765313444444444...344555544.57999999988777776666665156788899999753 PP

                                   HHHHHTT-HHHHHHHHTHHHH CS
                       MHC_I_2 139 imnkwnddgdlvqrlkyfipe 159
                                    mnk  +d   ++ l yf+  
  gi|13541622|ref|NP_111310.1| 101 AMNKKLEDSLKLKPLDYFVAY 121
                                   89**9999999999***9965 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0016
                                   T-SS--EEEEEEES-TT-SSS--EEEEEETTTEEEEEET CS
                       MHC_I_2  86 tngyphlqvtmiypqsqgqtpsatwefnisdsyfftfyt 124
                                        h++ ++ +p+ +g    +t+ f i d  f+ +y 
  gi|13541622|ref|NP_111310.1| 139 EIMREHIDTALKHPDEKGIRSYTTYSFGIGDQEFVVLYE 177
                                   5556799999*************************9995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       389  (0.0216967); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        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 0.33s 00:00:00.83 Elapsed: 00:00:00.54
# Mc/sec: 1247.21
//
Query:       gi|13541623|ref|NP_111311.1|  [L=345]
Description: cell division protein FtsZ [Thermoplasma volcanium GSS1]
Scores for 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-41  140.6   0.1    1.3e-40  139.7   0.1    1.5  1  Tubulin    Tubulin/FtsZ family, GTPase domain
    2.9e-25   88.4   1.4    8.5e-25   86.9   1.4    1.9  1  FtsZ_C     FtsZ family, C-terminal domain
  ------ inclusion threshold ------
       0.39    9.8   3.0       0.71    9.0   0.9    2.2  2  Tubulin_2  Tubulin like


Domain annotation for each model (and alignments):
>> Tubulin  Tubulin/FtsZ family, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.7   0.1   2.2e-44   1.3e-40       1     194 [.      28     186 ..      28     189 .. 0.97

  Alignments for each domain:
  == domain 1  score: 139.7 bits;  conditional E-value: 2.2e-44
                                   EEEEEEEHHHHHHHHHHHHH...HHHCH....HHHT.....TTEEEEE....EEESBHHHHHTS-GS......EEEE--CC CS
                       Tubulin   1 eiivigvGqcGnqignelwellakehgiqsdgdslesfFsesgkveyiprsvaidtdpqvlneikagselfnpnklllgke 81 
                                   +i+v+g+G++G++++n+l++    e ++             sg v++i    a++td+ +l +i+a+      +k+llgk+
  gi|13541623|ref|NP_111311.1|  28 RIKVFGFGGSGSNTINRLMR----E-NL-------------SG-VKLI----ACNTDAAHLLRIRAH------SKILLGKN 79 
                                   599*****************....7.88.............78.9999....***************......******** PP

                                   CCTTC--TT-HHHHHHHHHHTHHHHHHHHTT-SE.SEEEEEEETTSSHHHHHHHHHHHHHHHTSTTSEEEEEEEE--GG.G CS
                       Tubulin  82 gagnngaggypevgkeaaeeileeirkevekcdslqgffitaslgGGTGSGlgpvilevlkeeypkalvvtvvvlPsefse 162
                                    ++++gag++p+vg+ aa+e++ ei k+++++     +fita+lgGGTG+G++p++++++k++  +al++++ +lP+++ e
  gi|13541623|ref|NP_111311.1|  80 LTRGLGAGADPSVGEMAAKESESEILKQIDETSI---VFITAGLGGGTGTGAAPYVAKLAKDR--GALTISFATLPFST-E 154
                                   **********************************...**************************..************99.* PP

                                   -HHHHHHHHHHHHHHHHT-SEEEEEEHHHHHC CS
                       Tubulin 163 vvvepynailalkelieesdavividNdaLlk 194
                                   + v+++na +++++l+++sda ++i+Nd+L++
  gi|13541623|ref|NP_111311.1| 155 GFVRMKNAYEGVRKLVKNSDAAVIIPNDKLIE 186
                                   ******************************87 PP

>> FtsZ_C  FtsZ family, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.9   1.4   1.4e-28   8.5e-25       1      95 []     236     332 ..     236     332 .. 0.96

  Alignments for each domain:
  == domain 1  score: 86.9 bits;  conditional E-value: 1.4e-28
                                   EEEEEEEEEEES..TTHHHHHHHHHHTSGGGT--GGG-SEEEEEEEE-TT--HHHHHHHHHHHHHHS-TTSEEEEEEEE-T CS
                        FtsZ_C   1 GvAmmgvGeasg..edraeeaaeaaisspLLdvdlsgAkgvlvnitggsdltlkEveevaetireevdeeanvivGavide 79 
                                   G   +g+G++s   +dr  ea e+a+ sp +dvd+s Akg+++n+tgg+dl+l+E++++a+ +++++  +a++++G+v+de
  gi|13541623|ref|NP_111311.1| 236 GYSAIGMGSSSQavNDRIVEALEKALDSPFMDVDISKAKGAIINVTGGRDLQLQEAQQAADILKKKIARDATIMWGTVVDE 316
                                   677899999887679****************************************************************** PP

                                   T--SEEEEEEEEES-X CS
                        FtsZ_C  80 eledeirvtvvatglk 95 
                                   +++ ++++ v+++g+k
  gi|13541623|ref|NP_111311.1| 317 SIRSSVKILVIVAGVK 332
                                   **************96 PP

>> Tubulin_2  Tubulin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0     0.081   4.8e+02       4      19 ..      33      48 ..      31      73 .. 0.89
   2 ?    9.0   0.9   0.00012      0.71     152     178 ..     107     134 ..      68     141 .. 0.72

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.081
                     Tubulin_2  4 GLGGtGgkvlaelrrr 19
                                  G GG+G++++++l+r 
  gi|13541623|ref|NP_111311.1| 33 GFGGSGSNTINRLMRE 48
                                  99**********9985 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00012
                     Tubulin_2 152 e.eeglnvfVvgSLaGGTGSGiflDvay 178
                                   + +e   vf+  +L GGTG G +  va 
  gi|13541623|ref|NP_111311.1| 107 QiDETSIVFITAGLGGGTGTGAAPYVAK 134
                                   2234478**************8876665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       529  (0.0295053); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.32s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 2058.67
//
Query:       gi|13541624|ref|NP_111312.1|  [L=217]
Description: hypothetical protein TVN0793 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.8e-37  128.2   1.2    4.3e-37  128.1   1.2    1.0  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 !  128.1   1.2   2.4e-41   4.3e-37       2     191 ..      18     202 ..      17     203 .. 0.96

  Alignments for each domain:
  == domain 1  score: 128.1 bits;  conditional E-value: 2.4e-41
                          CbiZ   2 feeprrvlssavlngGlrelravlnhqvpegyeredpeeyleeyleelglppektvgllTaadmenaaiaeeefedlevta 82 
                                   f+ + r  ssa++ngG+++++a++n++v+ +y++e   e  +e+l++ +++++ tv+ lTa+d++ +++a++  +  +  +
  gi|13541624|ref|NP_111312.1|  18 FHSEARKFSSAPFNGGVGRAKAYINRTVNLDYNEEVISET-KEFLARNKIEENGTVCTLTAVDVNTHVVAKKYLDTNSLIV 97 
                                   788999******************************9777.**************************************** PP

                          CbiZ  83 vvTaGvesnavragdedeeaekpGTINiivlinaaLtdaalvralitatEAKtaalqdlgvrsryseg.atGTgTDaiava 162
                                   ++TaG+  n v++g+    +  +GTINi++l++ +L+da ++++++t++E K++ ++d+ v +r +++  +GT+TD++ v+
  gi|13541624|ref|NP_111312.1|  98 YITAGF-DNTVSIGNV---KGMHGTINIALLTDFPLSDAGVLNLFQTIVESKAQFMNDAHVTDRATGKvGPGTSTDTVSVF 174
                                   ******.********4...6899********************************************************** PP

                          CbiZ 163 adkegeeeltyaGkhtklGeliaraVyeA 191
                                     ++++ +++yaG  t +G+  + +Vy++
  gi|13541624|ref|NP_111312.1| 175 VFNDEK-TINYAGRITAIGHEASLMVYNS 202
                                   **6666.6*****************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); 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: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1479.11
//
Query:       gi|13541625|ref|NP_111313.1|  [L=91]
Description: molybdopterin converting factor, small subunit [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.2e-19   68.2   0.0    8.2e-19   68.0   0.0    1.0  1  ThiS      ThiS family
     0.0002   21.6   0.0    0.00022   21.5   0.0    1.1  1  Urm1      Urm1 (Ubiquitin related modifier)


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 !   68.0   0.0   9.2e-23   8.2e-19       1      77 []       5      91 .]       5      91 .] 0.98

  Alignments for each domain:
  == domain 1  score: 68.0 bits;  conditional E-value: 9.2e-23
                                  EEETTCCHHHHTCEEEEESSTSBHHHHHHHHHHHTCHHG.........TTTTEEEEETTEEEGC.CTTTSB--TTCEEEEEES CS
                          ThiS  1 vllfaelrelageeelelaegstvaelleaLgerypela.........lerrvavavNgeivpr.lwldtelkdgDevailpp 73
                                  v+++a+lr ++g++ +e++  +++++l+  L+++y+e +         l ++v++++Ng+++++ ++l+t+lkdgD ++++pp
  gi|13541625|ref|NP_111313.1|  5 VRYYANLRSVTGKKLEEFDGIKNIDDLISLLNQEYGEKFrklmyngneLYPNVIILLNGNNINSiEGLKTPLKDGDNIDVFPP 87
                                  89*********************************9999*********99********************************* PP

                                  TTC- CS
                          ThiS 74 VaGG 77
                                  VaGG
  gi|13541625|ref|NP_111313.1| 88 VAGG 91
                                  ***9 PP

>> Urm1  Urm1 (Ubiquitin related modifier)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   2.4e-08   0.00022      23      95 ..      18      90 ..       3      91 .] 0.85

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 2.4e-08
                                  EE-SSSSS-BHHHHHHHHCCCC-SSGHHHCBSTTSB-TTEEEEETTCEHHHCTCCCSB--TTEEEEEEETTT- CS
                          Urm1 23 eleieseevnleeliayikknlikerkevFlekdkvrPGilvLindaDwellgekdyelkdkDkivFistlhG 95
                                  +le  +   n+++li+ ++++  ++ +++  +++++ P +++L+n  +++ ++ +++ lkd+D+i     + G
  gi|13541625|ref|NP_111313.1| 18 KLEEFDGIKNIDDLISLLNQEYGEKFRKLMYNGNELYPNVIILLNGNNINSIEGLKTPLKDGDNIDVFPPVAG 90
                                  55655667799*************9889999*********************************976666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       470  (0.0262145); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 611.40
//
Query:       gi|13541626|ref|NP_111314.1|  [L=603]
Description: aldehyde:ferredoxin oxidoreductase [Thermoplasma volcanium GSS1]
Scores for complete 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-134  447.2   0.0   5.9e-134  446.8   0.0    1.1  1  AFOR_C    Aldehyde ferredoxin oxidoreductase, domains 2 & 3
      6e-84  280.8   0.3    1.2e-83  279.9   0.3    1.5  2  AFOR_N    Aldehyde ferredoxin oxidoreductase, N-terminal doma


Domain annotation for each model (and alignments):
>> AFOR_C  Aldehyde ferredoxin oxidoreductase, domains 2 & 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  446.8   0.0  6.6e-138  5.9e-134       5     382 .]     223     598 ..     220     598 .. 0.98

  Alignments for each domain:
  == domain 1  score: 446.8 bits;  conditional E-value: 6.6e-138
                                   HHHHHHHHSH.HHHHHHHH-GGGHHHHHHHTT---BTTTTB.S--TTGGGGSHHHHHHHTEEEE.E-TT-SS--EEEEE.. CS
                        AFOR_C   5 kiqkeiksspqvtaelrkyGTaelvnianetgalptknfqe.gtfekaekisgealeekylvknegCfsCpiaCgrevkve 84 
                                   k+ k+ik++p+++++l+++GT +lvni+n++g+++ kn +e g  + a+++sge+l+e+yl +n+ Cf+Cpi Cgr+v+ +
  gi|13541626|ref|NP_111314.1| 223 KMLKKIKENPVTSQGLTQFGTEVLVNIINKSGIYSNKNLTEsGDDPLADDVSGETLAETYLLHNQPCFACPIGCGRVVRYN 303
                                   6789******9999***************************8889999****************99*************98 PP

                                   ....ETEE---HHHHHHHTGGGT---HHHHHHHHHHHHHHTB-HHHHHHHHHHHHHHHHTTSS-HHHHTS----TT-THHH CS
                        AFOR_C  85 egkkvkvegpeyetlaalGsnlgiddleailklnelcdelGlDtisaGntiafamelyekGllkkedtdglelefgdaeal 165
                                   e +   +egpeye+++alG+n+gi+dl +i+ +n+ +d+lG DtisaG t++ amelye+G + ++d++  + +fg++ al
  gi|13541626|ref|NP_111314.1| 304 ERE---SEGPEYESTWALGPNTGIHDLYTIIAANDNADRLGYDTISAGLTMSAAMELYENGKIPDKDVGPTKPKFGNQSAL 381
                                   888...59************************************************************************* PP

                                   HHHHHHHHTT-TTHHHHTT-HHHHHHCTT-GGG--EETTEE--SS-GGG-HHHHHHHHH-TTSS-SGGG-THHHH.....S CS
                        AFOR_C 166 lellekiAkregigdllAeGvkrlaeklgaeelamhvkGlelpaydprgakgmalaYatsnrGacHlrayliale.....e 241
                                   le+  k A+r+++g  lAeG+k+l+e +g + ++m+vkG+e++aydprg++gmal+Yatsn G++H+ray+i+ e      
  gi|13541626|ref|NP_111314.1| 382 LEMSVKLAYRKDFGSKLAEGSKKLSEMYGDPSVSMSVKGQEIAAYDPRGVWGMALEYATSNIGGSHMRAYTISNEilgveP 462
                                   ******************************************************************************986 PP

                                   ---TT--HHHHHHHHHHHHHHHHHHHHT--GGGG-HHH......HHHHHHHHHT----HHHHHHHHHHHHHHHHHHHHHHT CS
                        AFOR_C 242 kvdpletegkaelvkwfqdltalvdslglCkftseaeerldlelyakllsavtGidvteeellkaGeRiynleRlfnlreG 322
                                     dpl+ egkaelvk+ qd+t+++d+ glC+f+s     l+l++y +l++avtG+++t+ee++ka+eR++nleRlfnl++G
  gi|13541626|ref|NP_111314.1| 463 VSDPLKLEGKAELVKYVQDFTEVMDCSGLCQFPS---FALNLDDYLELVNAVTGFNYTKEEIMKAAERVWNLERLFNLKAG 540
                                   6799999***************************...6789**************************************** PP

                                   --HHHS---HHHHHS---SSTTTT---..-HHHHHHHHHHHHT--TTS---HHHHHHCT- CS
                        AFOR_C 323 ltrkddtlperlleeplkegpakgkvledeleemldeyYelrGWdetGvPtketlkrLgL 382
                                   ++++dd+lper+l++p+++gp+kg+++   +e+++++yY++rGW+e+G Pt+e+lk+LgL
  gi|13541626|ref|NP_111314.1| 541 IKPEDDKLPERFLKDPIPKGPKKGNTV--PFEKLIKDYYKVRGWTENGYPTPEKLKELGL 598
                                   ***********************9998..7*****************************8 PP

>> AFOR_N  Aldehyde ferredoxin oxidoreductase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  279.9   0.3   1.3e-87   1.2e-83       1     197 [.       7     205 ..       7     206 .. 0.97
   2 ?   -3.4   0.0      0.84   7.6e+03      23      48 ..     439     463 ..     435     469 .. 0.69

  Alignments for each domain:
  == domain 1  score: 279.9 bits;  conditional E-value: 1.3e-87
                                   SEEEEEETTTTEEEEEE--HHHHHHH-SCHHHHHHHHHHHS-TTS-TTSTTS-EEEEE-TTTTSSSTTB-EEEEEEE-TTT CS
                        AFOR_N   1 gkilrvdLstgkieveelpeelaekylGgrglaakllldevppgvdplspenplvfatGpltgtpapgsgrlvvvaksPlt 81 
                                   gkilr+dLs gk ++e+++  +a++y+Gg+gla+++  +ev+p++dp++pen l++a+Gpltgt+ap+++r+++v+ksPlt
  gi|13541626|ref|NP_111314.1|   7 GKILRIDLSAGKLSIENTNMTWAKDYIGGQGLATRYYVEEVDPKIDPYDPENELIIAPGPLTGTSAPTAARYMAVTKSPLT 87 
                                   79******************************************************************************* PP

                                   SSEEEEEEETCHHHHHHHCT-SEEEEES--SS-EEEEEETTEEEEEE-TTTTTS-HHHHHHHHHHHHTS..EEEEE-HHHH CS
                        AFOR_N  82 gtlgesnaGgrfgaelkraGydaivieGkaekpvylvieddkveiedaedlwgldtyettealkeelgd..kvaviGpaGe 160
                                   gt+++sn+Gg+fga+lk+aG+d+i+++Gk++kpvyl+++++k+e++da+dlwg+d++ett+ l ++     +va+iGpaGe
  gi|13541626|ref|NP_111314.1|  88 GTITRSNSGGYFGAKLKHAGFDMIIFKGKSKKPVYLYVDNGKAELRDASDLWGKDVFETTDILTSRISGnvSVACIGPAGE 168
                                   ****************************************************************9776657899******* PP

                                   TT-TTB-E.EETTEEE-SSSHHHHHHHTTEEEEEEE- CS
                        AFOR_N 161 nlvrfAsisvddgraagrgGlGavmgsKnlkaivvrg 197
                                   nlv+fAsi+ d++raagr G+GavmgsKnlkaiv+ g
  gi|13541626|ref|NP_111314.1| 169 NLVKFASIMNDKHRAAGRNGVGAVMGSKNLKAIVAGG 205
                                   ********666999********************987 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 0.84
                                   HHHH-SCHHHHHHHHHHHS-TTS-TT CS
                        AFOR_N  23 aekylGgrglaakllldevppgvdpl 48 
                                   a + +Gg+ + a+ + +e+  gv+p+
  gi|13541626|ref|NP_111314.1| 439 ATSNIGGSHMRAYTISNEI-LGVEPV 463
                                   4566899999999999977.445544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (603 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       317  (0.0176809); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.23s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 4029.52
//
Query:       gi|13541627|ref|NP_111315.1|  [L=387]
Description: glycine hydroxymethyltransferase [Thermoplasma volcanium GSS1]
Scores for complete 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-44  151.7   0.0    3.6e-44  151.0   0.0    1.3  1  SHMT             Serine hydroxymethyltransferase
    6.3e-06   25.7   0.0    9.4e-06   25.1   0.0    1.2  1  Beta_elim_lyase  Beta-eliminating lyase
     0.0021   17.5   0.0      0.003   16.9   0.0    1.2  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
  ------ inclusion threshold ------
      0.036   13.1   0.0      0.058   12.4   0.0    1.3  1  SelA             L-seryl-tRNA selenium transferase


Domain annotation for each model (and alignments):
>> SHMT  Serine hydroxymethyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  151.0   0.0   7.9e-48   3.6e-44       8     384 ..       4     347 ..       2     360 .. 0.84

  Alignments for each domain:
  == domain 1  score: 151.0 bits;  conditional E-value: 7.9e-48
                                   HHHHHHHHHHHHHHSEE-STT-----HHHHHHHTSGGGG----EETTEESSST-HHHHHHHHHHHHHHHHHCT-STTTEEE CS
                          SHMT   8 vaeiikkekerqkeeieliasenftskavlealGsvltnkyaeGyPGkryyGGcefvdeveelaqdrakelfkldpakwgv 88 
                                   + +i+++    +++ i+l asen++s++v  al s +  +y+    G   yGG+++ +e+ee +++ a e+f+ +    ++
  gi|13541627|ref|NP_111315.1|   4 ILSIVQDADIYRSSVINLQASENVISPNVRRALASDFASRYSHKENGVNDYGGTKYAEELEESVNELASEVFNFK----YA 80 
                                   778888888888899************************************************************....** PP

                                   E---SSHHHHHHHHHHHHT-TT-EEEEESCTTTSTGGGT-BTSS-B-SHHHHHSEEEEE-B-TTTSSB-HHHHHHHHHHH- CS
                          SHMT  89 nvqplsGsqanlavytallepgdrilgldladGGhlthGakveskkisassklfesveykvdketglidydelekkakefk 169
                                   + +plsG  a  +v +al++ g+ i+ +   +GG+   G+         s + f+s    ++  ++ id+++ ek+   ++
  gi|13541627|ref|NP_111315.1|  81 DAKPLSGHVAAETVLAALVKRGESIMKIPERNGGYQ--GYLNGY---LPSLMGFRSYDIPMK-PDQAIDFESFEKTIDYIR 155
                                   **********************************84..665555...223345666666666.6899************** PP

                                   -SEEEEE-SST-S---HHHHHHHHHHTT-EEEEE-GGGHHHHHTTSS--GCCTSSEEEEESSSTT-S-S-EEEEEC-SEEE CS
                          SHMT 170 PklivaGtsaysrlidyarlreiadevgayllvdmahiaGlvaagvipsPfeyadvvtttthktlrGprgglillrkgvks 250
                                   Pk+++ G+s + + +d  ++re++++vg++ll d +h+ Gl+a+g +   +  +dvv   thkt+ Gp+gg+il++     
  gi|13541627|ref|NP_111315.1| 156 PKVVILGQSVFVKSYDIPKVRELCNSVGSMLLYDASHVMGLIAGGTFQKDIGLCDVVFGSTHKTFFGPQGGIILTN----- 231
                                   ****************************************************************************..... PP

                                   EETTTEEEEHHHHHHHHHHHTTTT-SS--HHHHHHHHHHHHHCTSHHHHHHHHHHHHHHHHHHHHHH.HTT-EEGGGS-SS CS
                          SHMT 251 vdktgkevleelekkinsavfPglqGGPlnhviaakavalkealepefkvyqkqvlknakalaealk.ekgyklvsgGtdn 330
                                         ev + +ekki    +           +a++ val+e+ +   ++y+++v+knak la++l  +  +k     t++
  gi|13541627|ref|NP_111315.1| 232 ----EAEVFDRIEKKITWITM----DNFNISRMAGVGVALEETKK-FGREYASRVVKNAKDLAKELDgKLPIKYSPWFTES 303
                                   ....34556666666655544....445677899******98644.459*****************735578888999*** PP

                                   SEEEEEGGGGTS-HHHHHHHHHHTTEE-EEE--TTSSTTTT-SEEEEESHHHHH CS
                          SHMT 331 hlvlvdlrekgldGkraekvlekvnitankntvPgdksalvtsGlrlGtpalts 384
                                   h vl+d +  + dG ++ k  e      +kn++  d+        r+Gt+ +t+
  gi|13541627|ref|NP_111315.1| 304 HQVLIDEEGLKKDGYDTIKFSED----LEKNGIIVDRIG------RIGTAEITR 347
                                   ******88888888776555544....456776666543......666666665 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.0   2.1e-09   9.4e-06      24     252 ..      50     281 ..      38     310 .. 0.78

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 2.1e-09
                                   --CCCT--HHHHHHHHHHHH....HTT-SEEEE.ES-HHHHHHHHHHHH--TTEEEEE..ETT-HHHHSSTTHHHHCC--E CS
               Beta_elim_lyase  24 GdesYgedktvnrLedavae....lfgkeaalf.vpqGtaAnsillkillqrgeeviv..tepahihfdetgaiaelagvk 97 
                                   G + Yg+ k  ++Le+ v+e    +f +++a     +G  A +  l++l++rge+++   ++++ +  + +g +  l g +
  gi|13541627|ref|NP_111315.1|  50 GVNDYGGTKYAEELEESVNElaseVFNFKYADAkPLSGHVAAETVLAALVKRGESIMKipERNGGYQGYLNGYLPSLMGFR 130
                                   66789***********999955555566655443559*99999999******9998541144566667777********** PP

                                   EEEE-EBTTTBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEETTHHHHHHHH CS
               Beta_elim_lyase  98 lrdlknkeaGkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgARfanaaksl 178
                                     d++ k +  +d+e++e+ i+   +   ++k+++l + +       v+   + +v++++++ g  l++D+  ++    + 
  gi|13541627|ref|NP_111315.1| 131 SYDIPMKPDQAIDFESFEKTIDY--I---RPKVVILGQSVF------VKSYDIPKVRELCNSVGSMLLYDASHVMGLI-AG 199
                                   ***********************..6...99*****99988......6888999******************999866.44 PP

                                   TS-CHHHHTTSSEEEEESSSTT--SS-EEEEE-HH....HHHHHHHHHHHHT---S.STHHHHH..........HHHHHHH CS
               Beta_elim_lyase 179 geivkemfsyvDsvtmslkKdllanvGgvlafrddeledylaerveqrkylggglr.qagvlaa........leagirale 250
                                   g + ++ +  +D+v  s  K  + + Gg+++++++e +d +++ +++  +   +++  agv +a        +e++ r+++
  gi|13541627|ref|NP_111315.1| 200 G-TFQKDIGLCDVVFGSTHKTFFGPQGGIILTNEAEVFDRIEKKITWITMDNFNISrMAGVGVAleetkkfgREYASRVVK 279
                                   4.55555689*******************************9999997765444432344444433555555444444444 PP

                                   HS CS
               Beta_elim_lyase 251 eg 252
                                   + 
  gi|13541627|ref|NP_111315.1| 280 NA 281
                                   44 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 !   16.9   0.0   6.7e-07     0.003      98     195 ..     141     240 ..     133     273 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 6.7e-07
                                   SB-GGGCGGG--TTE..EEEEEB-GGGB---HHHHHHHHHHCT-EEEEE-TT-TT-EETTEECCCSSSEEEEE-BTTSSS- CS
               DegT_DnrJ_EryC1  98 nidpaaieaaitert..kaIlpVhlyGqvadmdalkaiaakhglkvieDaAhAlGatykgkkvGalgdaavfSFyptKnlt 176
                                    id ++ e+ i   +    Il   ++ ++ d++++++++++ g +++ Da+h +G    g    ++g + v+     K++ 
  gi|13541627|ref|NP_111315.1| 141 AIDFESFEKTIDYIRpkVVILGQSVFVKSYDIPKVRELCNSVGSMLLYDASHVMGLIAGGTFQKDIGLCDVVFGSTHKTFF 221
                                   567777777777655533455567888999******************************666666666666556678999 PP

                                   SSS-EEEEESTHHHHHHHH CS
               DegT_DnrJ_EryC1 177 tGeGGavvtndeelaekar 195
                                      GG+++tn++e+ ++++
  gi|13541627|ref|NP_111315.1| 222 GPQGGIILTNEAEVFDRIE 240
                                   99************99997 PP

>> SelA  L-seryl-tRNA selenium transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   1.3e-05     0.058     174     236 ..     179     242 ..     164     282 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.3e-05
                                   EEEEES-B-S-GGG.GT-----BHHHHHHTT-SEEEEETTSTT-SSS-EEEEE-H.HHHHHHHHS CS
                          SelA 174 leDlGsGllvdlse.yglskePtvqealaeGvdlvsfsGDkllGgpqaGiivGkk.elieklkkn 236
                                   ++ +Gs ll d s+ +gl    t+q+ +   +d+v  s  k + gpq Gii+ +  e+ ++++k+
  gi|13541627|ref|NP_111315.1| 179 CNSVGSMLLYDASHvMGLIAGGTFQKDIGL-CDVVFGSTHKTFFGPQGGIILTNEaEVFDRIEKK 242
                                   45679999999986369***********99.********************98752677888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (387 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       540  (0.0301188); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.57u 0.33s 00:00:00.89 Elapsed: 00:00:00.47
# Mc/sec: 2456.40
//
Query:       gi|13541628|ref|NP_111316.1|  [L=361]
Description: CBS domain-containing protein [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.2e-49  166.6  12.4    2.3e-13   50.3   0.1    4.2  4  CBS         CBS domain
  ------ inclusion threshold ------
      0.026   15.1   0.0        6.1    7.5   0.0    3.3  2  GAF         GAF domain
       0.17   12.0   0.3         61    3.7   0.0    3.6  4  sCache_3_2  Single cache domain 3


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.3   0.1   3.9e-17   2.3e-13       1      54 [.       3      55 ..       3      57 .. 0.94
   2 !   43.8   0.1   4.2e-15   2.5e-11      10      56 ..      72     117 ..      62     118 .. 0.92
   3 !   44.7   0.2   2.3e-15   1.4e-11       3      53 ..     129     179 ..     126     182 .. 0.92
   4 !   33.7   0.7   6.1e-12   3.7e-08       3      55 ..     205     255 ..     203     257 .. 0.85

  Alignments for each domain:
  == domain 1  score: 50.3 bits;  conditional E-value: 3.9e-17
                                  HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHH CS
                           CBS  1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllra 54
                                  V+++mt+d+vtv  d+t ++++ +m e+g+++lPV+d  +++ G++t +Dll++
  gi|13541628|ref|NP_111316.1|  3 VRELMTPDPVTVGVDDTFSKVMSKMNETGIHQLPVMD-GNRYAGMITYSDLLKK 55
                                  89***********************9999*******6.666***********96 PP

  == domain 2  score: 43.8 bits;  conditional E-value: 4.2e-15
                                   EEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                           CBS  10 vtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                                   +t++ d+++ ea++l++++g+s+lPV  + gklvGi++++D+++ + 
  gi|13541628|ref|NP_111316.1|  72 PTLSADDDVLEAVRLIKDTGLSALPVF-DKGKLVGIISRTDIIKRID 117
                                   79**************99*********.6**************9985 PP

  == domain 3  score: 44.7 bits;  conditional E-value: 2.3e-15
                                   HHSBSSCEEEETTSBHHHHHHHHHHHT.SSEEEEEETTTBEEEEEEHHHHHH CS
                           CBS   3 dimtrdvvtvppdttleealelmrekg.vsrlPVVdedgklvGivtlrDllr 53 
                                   +im++d+v v++d+++eea++ +r+ + v  +PVVd++++lvGiv l D+l 
  gi|13541628|ref|NP_111316.1| 129 QIMSPDPVAVSEDDSIEEAFDSLRQLNeV-EIPVVDNEERLVGIVKLNDILG 179
                                   79*********************987779.*****9999***********96 PP

  == domain 4  score: 33.7 bits;  conditional E-value: 6.1e-12
                                   HHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                           CBS   3 dimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                   ++m + +++v+  ++++ ++++m +++++ +P+V ++gklvGi+  +Dl++ +
  gi|13541628|ref|NP_111316.1| 205 SVMDP-PISVDRYADVKTVVDEMMKNELHIMPIV-DSGKLVGIIDFSDLINII 255
                                   67755.55**************757779777***.6**************877 PP

>> GAF  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0     0.017     1e+02      80     105 ..      79     107 ..       4     114 .. 0.67
   2 ?    7.5   0.0     0.001       6.1      72     109 ..     215     250 ..     127     264 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.017
                                   HHHHHTTES...EEEEEEEEETTEEEEEE CS
                           GAF  80 dllenmgir...sslvvPlvndgelwGll 105
                                   d+le+   +    + ++P++++g+l+G++
  gi|13541628|ref|NP_111316.1|  79 DVLEAVRLIkdtGLSALPVFDKGKLVGII 107
                                   33334444444445689999999999997 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.001
                                   THHTTHHHHHHHHTTESEEEEEEEEETTEEEEEEEEEE CS
                           GAF  72 rfaqynrrdllenmgirsslvvPlvndgelwGllvlhn 109
                                   r+a+   + ++++m  + +  +P+v+ g+l+G++++ +
  gi|13541628|ref|NP_111316.1| 215 RYAD--VKTVVDEMMKNELHIMPIVDSGKLVGIIDFSD 250
                                   4555..556777777778889*************9876 PP

>> sCache_3_2  Single cache domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.41   2.5e+03     108     122 ..      34      47 ..      23      49 .. 0.86
   2 ?    3.7   0.0      0.01        61     108     123 ..      94     108 ..      67     109 .. 0.81
   3 ?    1.6   0.0     0.046   2.7e+02     106     123 ..     156     173 ..     131     174 .. 0.89
   4 ?    1.4   0.1     0.052   3.1e+02     109     122 ..     234     246 ..     231     248 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.41
                    sCache_3_2 108 klPvfdadgrviGiv 122
                                   +lPv+d ++r +G++
  gi|13541628|ref|NP_111316.1|  34 QLPVMD-GNRYAGMI 47 
                                   789999.89999998 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.01
                    sCache_3_2 108 klPvfdadgrviGivs 123
                                   +lPvfd  g+++Gi+s
  gi|13541628|ref|NP_111316.1|  94 ALPVFD-KGKLVGIIS 108
                                   79****.9******97 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.046
                    sCache_3_2 106 rvklPvfdadgrviGivs 123
                                   +v  Pv+d++ r++Giv 
  gi|13541628|ref|NP_111316.1| 156 EVEIPVVDNEERLVGIVK 173
                                   6889************95 PP

  == domain 4  score: 1.4 bits;  conditional E-value: 0.052
                    sCache_3_2 109 lPvfdadgrviGiv 122
                                   +P++d +g+++Gi+
  gi|13541628|ref|NP_111316.1| 234 MPIVD-SGKLVGII 246
                                   8****.9*****98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (361 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); 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: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 2471.89
//
Query:       gi|13541629|ref|NP_111317.1|  [L=436]
Description: Zn-dependent protease [Thermoplasma volcanium GSS1]
Scores for complete 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-45  154.3   2.4    7.3e-45  154.0   2.4    1.1  1  PmbA_TldD  Putative modulator of DNA gyrase
  ------ inclusion threshold ------
      0.082   13.1   0.1        0.2   11.9   0.1    1.6  1  SRP54_N    SRP54-type protein, helical bundle domain


Domain annotation for each model (and alignments):
>> PmbA_TldD  Putative modulator of DNA gyrase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  154.0   2.4   8.2e-49   7.3e-45      10     275 ..       4     286 ..       1     290 [. 0.80

  Alignments for each domain:
  == domain 1  score: 154.0 bits;  conditional E-value: 8.2e-49
                                   EEEEEEEETTEEEEEEEEEEEEEEEEEEETTEEEEEE...ESSHHHHHHHHHHHHHHCCS---TT-............... CS
                     PmbA_TldD  10 estsvrfengevetnsssedsglgvrvikggrlgfastldtsdealeeaveraveiaklapedpea............... 75 
                                   +s+  +++nge + +sss+ sg+++rv+ + ++++a++++ + e +++ +++a++ +++ ++ +                 
  gi|13541629|ref|NP_111317.1|   4 TSRGAFYRNGEFDGSSSSRGSGYAIRVVND-SIAIAYSNSDDWERVKKRIDEALDRSRKIGKSKIFtgrdvrsswtklgnk 83 
                                   678889********************9965.55555544444458888888888888777777777899999999888888 PP

                                   ..GGS-HHHHHHHHHHHHHH.CHCSTTEEEEEEEEEE......EEE.EEEEEEETTSEEEEEEEEEEEEEEEEEE...STC CS
                     PmbA_TldD  76 ..eevsaeekielleelekalrsadpkienskgarisgvsaslsaskeeklianSeGldveqtrtrvslslsvia.d.dgg 152
                                      + + +e +++l+e++ a+ +       ++++ri+    s+s++  + +++n+eG++v+ +++r+++++ + + + + +
  gi|13541629|ref|NP_111317.1|  84 kvLDTDFNEIVDILKEADTAASN-------VAQLRIN----SISDKIVKEYYMNTEGSEVHGEYSRIYFQYLIGVvEsG-N 152
                                   77777777777888888877544.......4457999....669999*************9999999987777776633.2 PP

                                   S....ET.EEEEEEEESSHHHS..SSHHHHHHHHHHCTTT.-..B---SEEEEEEE-HHHHHHHHHGHHHHHTBHHHHH.. CS
                     PmbA_TldD 153 s....gd.gmgggsgyedleeedleeiaeeaaekalasle.a..kplppgkypVvlspeavgsllheavghaleadavl.. 223
                                   +    +  g  gg++     ++dl +iaee +e a+++ e a   +++pgk++V+++pe  g   he+ gh++e+d+++  
  gi|13541629|ref|NP_111317.1| 153 YeqssEEyGYTGGYE-----TFDLGRIAEEEREDAVKLREiAlaPSVEPGKFDVIIGPEISGIVAHESAGHPTEYDRIAgr 228
                                   233342222233333.....34455588888888888876553255*********************************** PP

                                   ....TT--TTTT.-TTSB-S-TT--EEEETT-......-SB-TTSBB---EEEEETTE CS
                     PmbA_TldD 224 ....egrSflkd.klGekvaselltivddpts.gglgsypfDdEGvptqrtvlIenGv 275
                                       +g Sfl++ k+  k++sel+++vddpt  +++g+y +DdEGvp+++++l ++G 
  gi|13541629|ref|NP_111317.1| 229 eavlAGESFLSGkKFPYKIGSELVNVVDDPTVeNSFGYYLYDDEGVPARKRYLYKDGM 286
                                   99999*****9866999**************99************************7 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 ?   11.9   0.1   2.3e-05       0.2       3      58 ..      71     122 ..      69     133 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.3e-05
                                   HHHHHHHHHHCCSSCGHHHHHHHHHHHHHHHHHHTT--HHHHHHH.HHHHHHHHHCT CS
                       SRP54_N   3 kklnsalkklsgkskideedleealkeleeaLleaDVgvkvvkkl.ienvkkkavge 58 
                                   + ++s ++kl +k+++ + d++e    + ++L eaD + + v +l i+++ +k v+e
  gi|13541629|ref|NP_111317.1|  71 RDVRSSWTKLGNKKVL-DTDFNE----IVDILKEADTAASNVAQLrINSISDKIVKE 122
                                   6678999998888766.5889**....************999999458888888874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (436 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       429  (0.0239277); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.46
# Mc/sec: 2819.01
//
Query:       gi|13541630|ref|NP_111318.1|  [L=431]
Description: Zn-dependent protease [Thermoplasma volcanium GSS1]
Scores for complete sequence (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  120.6   5.1    1.7e-34  120.0   5.1    1.3  1  PmbA_TldD  Putative modulator of DNA gyrase
  ------ inclusion threshold ------
      0.057   14.0   0.0       0.81   10.3   0.0    2.4  2  LGFP       LGFP repeat


Domain annotation for each model (and alignments):
>> PmbA_TldD  Putative modulator of DNA gyrase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.0   5.1   1.9e-38   1.7e-34       4     279 .]      23     294 ..      20     294 .. 0.70

  Alignments for each domain:
  == domain 1  score: 120.0 bits;  conditional E-value: 1.9e-38
                                   EEEEEEEEEEEEEETTEEEEEEEEEEEEEEEEEEETTEEEE..EE...ESS.....HHHHHHHHHHHHHHCCS---TT-.. CS
                     PmbA_TldD   4 vrleesestsvrfengevetnsssedsglgvrvikggrlgf..astldtsd.....ealeeaveraveiaklapedpea.. 75 
                                   v  e  + t+vrf+n++++ ++ ++++g+ + v +g ++++  +++  +++     + l++++ ++ e++ + + ++++  
  gi|13541630|ref|NP_111318.1|  23 VKQEYASDTQVRFSNSKLDLTNIWDEYGIDIFVSSGRKTASiaVHS--PDEgiskiDYLQKVLSNSPENSIYEGINDKKqi 101
                                   66788999****************************9**9976332..333334465666777766666655544444466 PP

                                   .GGS-HHHHHHHHHHHH..HH.CHCSTTEEEEEEEEEE......EEE.EEEEEEETTSE.EEEEEEEEEE.EEEEEEE.S. CS
                     PmbA_TldD  76 .eevsaeekielleele..kalrsadpkienskgarisgvsaslsaskeeklianSeGl.dveqtrtrvs.lslsviadd. 150
                                    + v++++  + +++++  + + + d+        ++  vs+ +          +Se + + ++++++++ +++++ +++ 
  gi|13541630|ref|NP_111318.1| 102 yRAVDYKDDEKDVQDMAvaAISSAEDE--------GARRVSGLIYKR-------SSEESiFTRYNTYSAHkYGIEAAVRSf 167
                                   645555554444555553122222222........555554555555.......444333444444444336666666222 PP

                                   .TCS.....ETEEEEEEEESSHHHS..SSHHHHHHHHHHCTTT-B---SEEEEEEE-HHHHHHHHHGHHHHHTBHHHHHTT CS
                     PmbA_TldD 151 .ggs.....gdgmgggsgyedleeedleeiaeeaaekalasleakplppgkypVvlspeavgsllheavghaleadavleg 225
                                    g+s     +        y    ++d ee++++ ++ +l+   +++   gky+V++sp+a+g+++++     ++a ++  g
  gi|13541630|ref|NP_111318.1| 168 iGESsgqytA-------HYGPSSKADTEEVGKRSVRSILKVD-SVKGNEGKYRVIFSPMAFGNIISYGS-YLFSAYSIISG 239
                                   2222221121.......1122223789999*99999988877.7777899****************866.699******** PP

                                   --TTTT-TTSB-S-TT--EEEETT-......-SB-TTSBB---EEEEETTEE--- CS
                     PmbA_TldD 226 rSflkdklGekvaselltivddpts.gglgsypfDdEGvptqrtvlIenGvLkny 279
                                   +S l++++G++va+e +++vddpt+ +g+g+  fDdE ++t+r+++Ie+G+Lk+y
  gi|13541630|ref|NP_111318.1| 240 MSYLEGRIGKEVANESFSLVDDPTDtKGIGFEYFDDEATATKRNTIIERGILKTY 294
                                   ****88******************99****************************9 PP

>> LGFP  LGFP repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0     0.095   8.6e+02      25      44 ..     121     140 ..     113     143 .. 0.81
   2 ?   10.3   0.0     9e-05      0.81      17      47 ..     351     382 ..     351     387 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.095
                          LGFP  25 siyWspatGahavkgaIrdk 44 
                                   +i    + Ga+ v g I+++
  gi|13541630|ref|NP_111318.1| 121 AISSAEDEGARRVSGLIYKR 140
                                   55556678*********986 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 9e-05
                          LGFP  17 ryqhFegGsiyWspatG.ahavkgaIrdkWaa 47 
                                   r+q++++G++   p+ G  h vkg+I + W+ 
  gi|13541630|ref|NP_111318.1| 351 RFQDYRNGVFSTVPRDGiYHIVKGEIKESWSG 382
                                   89**************989999********75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (431 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 2775.07
//
Query:       gi|13541631|ref|NP_111319.1|  [L=779]
Description: aminopeptidase N [Thermoplasma volcanium GSS1]
Scores for complete 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-81  272.4   0.1    5.7e-81  271.2   0.1    1.7  1  Peptidase_M1    Peptidase family M1 domain
    1.6e-36  126.2   0.1    7.2e-36  124.1   0.0    2.0  2  Peptidase_M1_N  Peptidase M1 N-terminal domain
    1.3e-25   90.7   0.0    1.8e-25   90.2   0.0    1.2  1  ERAP1_C         ERAP1-like C-terminal domain


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 !  271.2   0.1   9.5e-85   5.7e-81       1     218 []     195     411 ..     195     411 .. 0.98

  Alignments for each domain:
  == domain 1  score: 271.2 bits;  conditional E-value: 9.5e-85
                                   HHHHHHHHHHHHHHHHHTS--SSSEEEEEEESSTTSSEEEETTEEEEEGGGC-SSTTTS-HHHHHHHHHHHHHHHHHHHBT CS
                  Peptidase_M1   1 yalevtkkllefleeyfkvpYplpkldlvalpdfsagAMEnwglityreelllvdpenssesdkrsvaeviaHElaHqWfG 81 
                                   y ++++k+ +ef+e yf++pY+lpk++l+ +p+f agAMEnwg+it+re +l +  +ns++s+ r  a+viaHE+aHqWfG
  gi|13541631|ref|NP_111319.1| 195 YPIDIAKRSIEFYEGYFGIPYALPKMHLISVPEFGAGAMENWGAITFREIYLDIA-DNSAASTLRLSANVIAHEIAHQWFG 274
                                   56899**********************************************9887.78999999***************** PP

                                   TTEEESSGGGGHHHHHHHHHHHHHHHHHHSCCCHCHHHHHHHCHHHHHHHHTSTTHHHSSGG-GSHHHHHHTSSHHHHHHH CS
                  Peptidase_M1  82 nlVtmkwWddlwLnEGfatyleylildklepewevseqllleeveealsedaldeshpitqevekpseidevFdsiaYeKG 162
                                   +lVtmkwW+dlwLnE+fat+++y+ +d ++pew+++ ++ +++++ al +d+l+++hpi++ v++p+ei+++Fd+i+Y KG
  gi|13541631|ref|NP_111319.1| 275 DLVTMKWWNDLWLNESFATFMSYKTMDTIHPEWQFWGDFFVSRTSGALRSDSLKNTHPIEVDVKDPDEISQIFDEISYGKG 355
                                   ********************************************************************************* PP

                                   HHHHHHHHHHCTHHHHHHHHHHHHHHCTTEEE-HHHHHHHHHHCCCSCHHTHHHHH CS
                  Peptidase_M1 163 asllrmlekllgeevFqkglksYlkefkyknaetedlwdaleealnkdisevmdtw 218
                                   as+lrm+e+++g e+F+kg+++Ylke++y+nae +dlw+a+e++++k ++++m+ w
  gi|13541631|ref|NP_111319.1| 356 ASILRMIEDYVGAEDFRKGISKYLKEHAYGNAEGSDLWNAIETESGKPVNRIMEAW 411
                                   ******************************************************99 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   0.0   1.2e-39   7.2e-36       4     186 .]       5     163 ..       3     163 .. 0.88
   2 ?   -1.1   0.0      0.32   1.9e+03      95     111 ..     478     494 ..     452     501 .. 0.76

  Alignments for each domain:
  == domain 1  score: 124.1 bits;  conditional E-value: 1.2e-39
                                   EEEEEEEEETTTTEEEEEEEEEEEESS-ECEEEEEESSEEEECEEEEECTTCTCEEEEEEEECTTTTCEEEEECCEEETTC CS
                Peptidase_M1_N   4 hYdldlkidlkektfkGsvtitlqlkeatseivldakdlkiksvslsaevksesvkidfkieqkdeelltiklkeslqqts 84 
                                   +Ydl+l++dl++ktf+G+ ti+ +      + vlda  ++i+ +      k ++++++    ++d++ll i+  e+ q   
  gi|13541631|ref|NP_111319.1|   5 EYDLTLDLDLQSKTFHGTETISASSG----DFVLDAVGFNIEWI------KVNGSDAK---FEYDGNLLKINGLETAQ--- 69 
                                   7*******************998776....9**********444......44455555...5699*****99999666... PP

                                   EEEEEEEEEEE-BSSSSEEEEEEEEETSCEEEEEEEE-TTTTGGGTS-B--STTSEBEEEEEEEEETTSEEEESSECCCEE CS
                Peptidase_M1_N  85 kytLeieyegelndklaGlykstYtdkgekkvvvvTqfeatdARsafPCfDePsvKAtftisikapkeetalSnmpeeese 165
                                     ++ei y+g+++d+l G+y        e++ +v+T+featdAR++fPC+D P++KA f+i++  +k++ a+Snmp++++e
  gi|13541631|ref|NP_111319.1|  70 --KVEISYSGKISDSLSGIYFAG----RESNGMVTTHFEATDARRMFPCIDHPAYKAVFSITLVIDKDYDAISNMPIKKVE 144
                                   ..99****************733....455789*********************************************777 PP

                                   EETTCEEEEEEEEEESBEGGG CS
                Peptidase_M1_N 166 klengqkiteFeqtpkmstYL 186
                                   +   ++ki+eFe+tp+mstYL
  gi|13541631|ref|NP_111319.1| 145 TS--DRKIVEFEKTPRMSTYL 163
                                   66..589*************9 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.32
                                   E-BSSSSEEEEEEEEET CS
                Peptidase_M1_N  95 elndklaGlykstYtdk 111
                                   +ln +  G+y+ +Y d+
  gi|13541631|ref|NP_111319.1| 478 KLNADNLGFYRVNYDDE 494
                                   67888889999999875 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 !   90.2   0.0     3e-29   1.8e-25       2     302 ..     477     760 ..     476     769 .. 0.82

  Alignments for each domain:
  == domain 1  score: 90.2 bits;  conditional E-value: 3e-29
                                   EEESGGG-SSSEEEE-HHHHHHHHHHHHGGGS-HHHHHHHHHHHHHHHHTTSS-HHHHHHGGG.GGGG--SHHHHHHHHHH CS
                       ERAP1_C   2 vllNdddtGyyrVnYdeeslaalleqllskklspldRaglisdafalaragelsaadlldlllgylanEtdylvwsqalsq 82 
                                   ++lN+d +G+yrVnYd+e + +++e +++k l+pldR+gl++d+fa+  ag ++ +++ + ++++  n++d  v s + +q
  gi|13541631|ref|NP_111319.1| 477 IKLNADNLGFYRVNYDDETFSKIIE-NMDK-LTPLDRVGLVDDLFAFLMAGVITPDTYKNRIKSF-FNDKDANVISNIVNQ 554
                                   8************************.6666.********************************88.59************* PP

                                   HHHHHHHHTTSTTHHHHHHHHHHHHHHHHHHHHHT.TTS-HHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHCSTT-S-H CS
                       ERAP1_C  83 latlksllsadplyaalkaflrklleplaeklgwepgeshldaqlrslllsaacaagdpevveearklfkawlegddlipp 163
                                    ++l+ +  +      ++a +r++l  +++ l     ++++ +    ++ ++++ ++++ + e ++ +f ++ ++     p
  gi|13541631|ref|NP_111319.1| 555 FEYLRIIT-H-----YFDADAREFLGTAIRYLES--ADDENLKIAYGKASRLLALLDEAYC-ETLAPRFSNFEQQ----TP 622
                                   ***98776.4.....788999*********9964..3455777777888888877776655.55666*****665....8* PP

                                   HHHHHHHHHHHHHS-HHHHHHHHHHHHC-SSHHHHHHHHHHHCC-S-HHHHHHHHHHCTTT..S-GGGHHHH.HHHH.HST CS
                       ERAP1_C 164 dlrwavycalaanggeaewdallerykdtsapsekeaalralaatpdpellerllnfvlesdevrnqdlral.laglannp 243
                                   +l++a+ +a a   +  +++ + e+y++ +  + k ++++  +  +++  l  +  ++ e++e+++qd+ +  l++l ++ 
  gi|13541631|ref|NP_111319.1| 623 ELKSAIATAYAL--STGDVKGMVEKYRSLDRDEDKVKIISGFGKLKSSTDLSVVSGMI-EKGEIKKQDMLSFyLSAL-ETM 699
                                   *******99974..46677889999965553378*******************99999.799********9944555.669 PP

                                   THHHHHHHHHHHCHCCHHH....HTSSTSCHHHHHHHHHT..T--SHHHHHHHHHHHCHTT--GG CS
                       ERAP1_C 244 egrellwefvkenwdalak....rwsggeildrivkgllp..gftseeelaeieaffadkdtpgl 302
                                   +gre    ++ +n ++++k    +++g+ +++r v+ +lp  g+t ++ +  ie+  ++++t gl
  gi|13541631|ref|NP_111319.1| 700 AGRE----YIYSNLENIVKnvirYFTGNRTASRTVEQILPviGLTHPDAASIIERIGSKNTTMGL 760
                                   9998....566666666653332667666***********7777788887777776666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (779 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       556  (0.0310112); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); 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: 0.70u 0.33s 00:00:01.03 Elapsed: 00:00:00.48
# Mc/sec: 4832.55
//
Query:       gi|13541632|ref|NP_111320.1|  [L=464]
Description: multidrug efflux permease [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.5e-42  144.6  63.6    3.5e-42  144.6  63.6    2.9  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 !  144.6  63.6     2e-46   3.5e-42       2     352 ..      11     399 ..      10     400 .. 0.92
   2 ?   -1.1   5.4     0.039   7.1e+02     136     165 ..     416     454 ..     401     462 .. 0.58

  Alignments for each domain:
  == domain 1  score: 144.6 bits;  conditional E-value: 2e-46
                         MFS_1   2 llaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfa 82 
                                   +++ f++ + +s++++a+p  +a  ++++ + ++l+  +  +  a ++++lGrl+d +Gr  ++ +g+l+f++++++++f+
  gi|13541632|ref|NP_111320.1|  11 SIGSFVTPFFSSVVSFAVP-KIALFYHLNFQDASLIPLIILIPLASTMILLGRLADSIGRTFIFRIGFLIFSVSAFIGAFS 90 
                                   6899***************.999999************************************************9999996 PP

                         MFS_1  83 sslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsll 163
                                    s+++l v+ +++G+g++al +++ ali  +f++++rg+a+g+ ++++ lG  ++p lgg+l++ +gW+++fy+ a+++l+
  gi|13541632|ref|NP_111320.1|  91 KSFPILTVALFFSGFGSAALSTNSTALIGYIFAGDKRGSALGINAMAVYLGLTMAPFLGGILIEFVGWQSIFYLTAPLALI 171
                                   6666***************************************************************************** PP

                         MFS_1 164 afvlfllllpeepperkrkspkeee............................................kgtgpaplvpaw 200
                                   +  l++ + + + +e k     + +                                            +++++++l+p  
  gi|13541632|ref|NP_111320.1| 172 G--LAVSFATLKGVEAKGRMNSDYLsavffstalfslafflalgyvynfeqflplliigvaflylffhrNKRVETQLIP-A 249
                                   *..5557776666666666666666788*****************************************9999999999.8 PP

                         MFS_1 201 kallkdpvlwillialllfffgfsglltllplylqevlglsglllaglllallalvgailallagrlsdrlgrrrrlllal 281
                                    ++++++ +++  +++ll+ + ++++++ + +ylq  l+ s  ++agl +    ++++il+++agr+sdr+g+r     ++
  gi|13541632|ref|NP_111320.1| 250 NLFKSNRTFLFSNVTALLNYLSTFSIVFVFSIYLQVILKVS-PFQAGLSILPEPVFMVILSPIAGRISDRIGSRYLASAGM 329
                                   88999998877889999999999******************.8****999999********************77777777 PP

                         MFS_1 282 lllllaalglallavtssavllllvlvliGfglgfvfpsllalasdlappeeagtasglfntagslggalg 352
                                   +++ l++l+l++++ + s +l++++l +iG+g+gf++++ ++ ++ +ap+e++g asg+ +t++ +g +l+
  gi|13541632|ref|NP_111320.1| 330 AIIGLSFLFLYVFPKI-SVFLVMVFLSFIGIGFGFFSAPNTNSVMGSAPREMSGIASGFLGTMRFVGQFLS 399
                                   7777777777777777.66666668888***************************************9986 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.039
                         MFS_1 136 lgpllggllasslg.........Wravfyilaivsllaf 165
                                   +  +++g++++            +r+v++i a++s++++
  gi|13541632|ref|NP_111320.1| 416 VVGIFSGIFVTISQayydsfvsgFRLVMLISAVLSFIGA 454
                                   333455544433334455555557777777777777764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (464 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       811  (0.045234); expected 358.6 (0.02)
Passed bias filter:                      229  (0.0127726); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.69u 0.27s 00:00:00.96 Elapsed: 00:00:00.49
# Mc/sec: 2856.98
//
Query:       gi|13541633|ref|NP_111321.1|  [L=345]
Description: carbamoyl phosphate synthase small subunit [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-40  138.3   0.1    1.8e-40  137.7   0.1    1.3  1  CPSase_sm_chain  Carbamoyl-phosphate synthase small chain, CP
    3.7e-37  128.0   0.0    5.8e-37  127.3   0.0    1.3  1  GATase           Glutamine amidotransferase class-I
    1.9e-08   34.4   0.3    0.00057   19.7   0.1    2.2  2  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 !  137.7   0.1   3.1e-44   1.8e-40       2     126 ..       3     128 ..       2     130 .. 0.97

  Alignments for each domain:
  == domain 1  score: 137.7 bits;  conditional E-value: 3.1e-44
               CPSase_sm_chain   2 avLvLedGtvfeGksfg.akeavGEvvfnTgmtGYqeiltDpsYagqilvltypliGnyGvneedvesekikvaglvvrel 81 
                                   ++Lv+edGtv++G+++g  kea+GE+vf+T+mtGY e+ltDpsY gq+lv++ p+i ny ++  ++es+ +kv++l+ +++
  gi|13541633|ref|NP_111321.1|   3 KYLVMEDGTVLSGQGYGsYKEAYGELVFTTSMTGYLETLTDPSYVGQMLVFASPTIANYALEMGKMESNGVKVSALITKDA 83 
                                   79***************77************************************************************** PP

               CPSase_sm_chain  82 seepsnwraeesLsewlkeekipgisgvDTRaLtkklrekgamkg 126
                                   + e ++    ++++e+lke++ipgi g+DTR+L++k+r++g++++
  gi|13541633|ref|NP_111321.1|  84 HIELKKGGYGREFDEFLKEQGIPGIDGIDTRMLVRKIRANGVLRS 128
                                   *****************************************9876 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.3   0.0   9.7e-41   5.8e-37       4     186 ..     173     337 ..     170     340 .. 0.92

  Alignments for each domain:
  == domain 1  score: 127.3 bits;  conditional E-value: 9.7e-41
                                   ESSTSTHHHHHHHHHHTT-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTT...TTTHHHHHHHHCTSTS-EEEETHHH CS
                        GATase   4 DnydsvtenlvhalvelgvkvevvpidasaeeilellknpdgilvsgGpgspg...vegkieaikearenkiPiLGICLGm 81 
                                   D +   ++n +++l+  ++++ vv  +++ +ei    +++d+i+vs+Gpg+p+     + i+++++ ++  +P++GIC+G+
  gi|13541633|ref|NP_111321.1| 173 DLG---SKNTLKELMLQNFSLIVVDKQTNLDEI----EGYDAIFVSNGPGDPShpsLSNVIKFLSHNIG-VKPLFGICFGL 245
                                   555...78999999999***********99999....59**************8888888888888888.99********* PP

                                   HHHHHHTTTEEEEEECEEEEEEEEEEEETTTCGGTTTTSEEEEEEEEEEEEESGCHHHTTEEEEEEEETTEEEEEEEEETT CS
                        GATase  82 QllaiefgrkvvkekekehhggtmrlgddetallyglknevierhrHryevnpkelepaglevtakseddeelmeiiekkn 162
                                   Q++ +++g+k++k+k ++h+g ++ ++d       g+  ++ ++h+H+y+v+   +  ++++v++++++d+  +eiie ++
  gi|13541633|ref|NP_111321.1| 246 QAISLAYGAKTYKMK-FGHRGSNHAVTD-------GT-HSYVTTHNHGYAVDG--STVKDFKVIGWDANDG-TVEIIEGDD 314
                                   ***************.************.......87.8999**********9..56777**********6.99******9 PP

                                   TEEEESSBTTSTTSTTHHHHHHHH CS
                        GATase 163 pfvgvQFHPEststpegpellfnf 186
                                    +++vQFHPE++++p++++++f +
  gi|13541633|ref|NP_111321.1| 315 -MFAVQFHPEASPGPHDTRWFFGE 337
                                   .9*****************99976 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.1   9.3e-06     0.056     106     129 ..     236     259 ..     226     282 .. 0.81
   2 !   19.7   0.1   9.5e-08   0.00057     166     216 .]     275     323 ..     263     323 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 9.3e-06
                 Peptidase_C26 106 vPilgiCrGlqllnvalGGtlyqd 129
                                   +P++giC Glq +  a+G ++y+ 
  gi|13541633|ref|NP_111321.1| 236 KPLFGICFGLQAISLAYGAKTYKM 259
                                   7*****************999975 PP

  == domain 2  score: 19.7 bits;  conditional E-value: 9.5e-08
                 Peptidase_C26 166 eeievnslHhqaike.laeelrveAvae.DgviEaieseeakafvlgvQwHPE 216
                                   ++  ++  H  a++    ++++v+ +++ Dg++E ie  +    +++vQ+HPE
  gi|13541633|ref|NP_111321.1| 275 HSYVTTHNHGYAVDGsTVKDFKVIGWDAnDGTVEIIEGDD----MFAVQFHPE 323
                                   4556667799999864789*******999********999....79******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       274  (0.0152825); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.23s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2465.60
//
Query:       gi|13541634|ref|NP_111322.1|  [L=1044]
Description: carbamoyl phosphate synthase large subunit [Thermoplasma volcanium GSS1]
Scores for complete 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-80  268.0   0.7    2.5e-58  197.0   0.0    2.2  2  CPSase_L_D2      Carbamoyl-phosphate synthase L chain, ATP bi
      1e-28  100.1   0.0    6.9e-28   97.5   0.0    2.3  2  CPSase_L_D3      Carbamoyl-phosphate synthetase large chain, 
    8.5e-19   67.5   0.0    7.9e-18   64.4   0.0    2.6  2  MGS              MGS-like domain
    6.6e-14   51.8   0.0    1.9e-05   24.4   0.0    2.9  2  ATPgrasp_Ter     ATP-grasp in the biosynthetic pathway with T
    5.3e-13   48.9   0.4    3.4e-06   26.8   0.2    2.4  2  ATP-grasp        ATP-grasp domain
    3.1e-11   43.6   2.1      7e-05   22.9   0.2    2.7  2  ATP-grasp_3      ATP-grasp domain
      4e-07   29.8   5.3     0.0035   16.9   0.1    3.1  3  Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
  ------ inclusion threshold ------
      0.094   12.2   0.1        1.7    8.0   0.0    2.4  2  ATP-grasp_5      ATP-grasp domain


Domain annotation for each model (and alignments):
>> CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  197.0   0.0   1.1e-61   2.5e-58       2     210 ..     129     331 ..     128     332 .. 0.88
   2 !   69.5   0.2   1.2e-22   2.8e-19       1     201 [.     660     851 ..     660     861 .. 0.89

  Alignments for each domain:
  == domain 1  score: 197.0 bits;  conditional E-value: 1.1e-61
                                   HHHHHHHHHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEETTCCTTTTEEEESSHHHHHHHHHHHHHHHHHHHSTS- CS
                   CPSase_L_D2   2 kesakealkkinvpvvpssaapvetleealaiakeigyPviikaafglGGkGmrvarneeelaelvkkalaeakaafgnkq 82 
                                   ++++++ l  i+++  +      ++ +e  +i k    Pvi++++f+lGG+G+ +++++eel++ +++ ++       ++ 
  gi|13541634|ref|NP_111322.1| 129 RQKFHDFLISIGERDPERYRISRSNYKE--EIEKIPFMPVIVRTSFSLGGSGGNIVKTKEELKAYAEELFRGI----DEDY 203
                                   5555555555655555555552222222..23333346***************************99999888....5999 PP

                                   EEEEE--SSSEEEEEEEEEETTS-EEEEEEEEECCEC..TCCCCEEEES-SS--HHHHHHHHHHHHHHHHHHT-EEEEEEE CS
                   CPSase_L_D2  83 vlvekslkgpkeiEvevlrDakgnvitvcerenslql..rtqkvievAPsqtLtdeerqalreaavkvvrevgvvgagtve 161
                                   + v++sl+g ke+E+e++rD+ gn+itvc++en++++  +t+++i+v PsqtL+d ++++lr aa+k+v+ +g+vga++++
  gi|13541634|ref|NP_111322.1| 204 IEVNRSLAGLKELEYEMIRDSIGNCITVCNMENLDPMgvHTGESIVVTPSQTLSDIQYHMLRDAAIKIVSGLGIVGACNIQ 284
                                   ********************************************************************************* PP

                                   EEEETTTTEEEEEEEESS--CCHHHHHHHHS--HHHHHHHHHTT--GCG CS
                   CPSase_L_D2 162 flldpkskeyyviEvNtRlsvesalaekaTGldlvkeaakialgekLee 210
                                   f+ld   ++yyv+EvN+R s++sala+kaTG++++ +aakia+g++L e
  gi|13541634|ref|NP_111322.1| 285 FALD--GNDYYVVEVNPRTSRSSALASKATGYPIARIAAKIAVGYNLTE 331
                                   ****..59***************************************87 PP

  == domain 2  score: 69.5 bits;  conditional E-value: 1.2e-22
                                   SHHHHHHHHHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEETTCCTTTTEEEESSHHHHHHHHHHHHHHHHHHHSTS CS
                   CPSase_L_D2   1 DkesakealkkinvpvvpssaapvetleealaiakeigyPviikaafglGGkGmrvarneeelaelvkkalaeakaafgnk 81 
                                   D++ +++ l++++++  + + a  +++eea++ +  +g Pvi++a+  +GG+ m ++++ + l+e  ++ +++       +
  gi|13541634|ref|NP_111322.1| 660 DRSLFSKRLEAMGIDQPKFEVA--TNAEEAINKSLALGLPVILRASHVIGGRAMDIIYDYDFLVERSREVFENV------N 732
                                   8999999999999998776666..99****************************************99999999......8 PP

                                   -EEEEE--SSSEEEEEEEEEETTS-EEE..EEEEEECCECTCCCCEEEES-SS--HHHHHHHHHHHHHHHHHHT-EEEEEE CS
                   CPSase_L_D2  82 qvlvekslkgpkeiEvevlrDakgnvit..vcerenslqlrtqkvievAPsqtLtdeerqalreaavkvvrevgvvgagtv 160
                                   +vlv k+l++  ei+v+ ++  ++  i   + ++e    ++ ++   +   + + +++ +++++   k+vre +++g  ++
  gi|13541634|ref|NP_111322.1| 733 SVLVSKYLENAVEIDVDFVSNGEDFQICgiLVHIEE-AGVHSGDATMIFGPKIVPQAAEEKIKSIVGKLVREFNLIGISNL 812
                                   ********************9999877511444443.3459999999888899**************************** PP

                                   EEEEETTTTEEEEEEEESS--CCHHHHHHHHS--HHHHHHH CS
                   CPSase_L_D2 161 eflldpkskeyyviEvNtRlsvesalaekaTGldlvkeaak 201
                                   + +++  ++e yviE+N+R s++ +  +kaTG++ v+ a+ 
  gi|13541634|ref|NP_111322.1| 813 QAAIK--DDEVYVIELNARSSRSIPFISKATGYNWVELAVS 851
                                   ****9..59*************************9988775 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 ?   -0.8   0.0      0.86   1.9e+03      26      80 ..      59     116 ..      52     136 .. 0.65
   2 !   97.5   0.0   3.1e-31   6.9e-28       3     122 .]     418     533 ..     416     533 .. 0.96

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.86
                   CPSase_L_D3  26 eiheltkidpwFLekleelvelekelkkkkk...eldeellreakklGfsDkqiaell 80 
                                   ei++   i+p  +e +e +++ e+  + + +   ++  +l+ ++kk+G+ Dk+  +++
  gi|13541634|ref|NP_111322.1|  59 EIADRVYIEPITVEAVETIIRKEEIDAIEPHmggQTALNLVVSLKKMGIIDKYGIKII 116
                                   66677777777778888888777653333335666777789999****9999755554 PP

  == domain 2  score: 97.5 bits;  conditional E-value: 3.1e-31
                   CPSase_L_D3   3 lkeptdeRifaiaealrrglsveeiheltkidpwFLekleelvelekelkkkkkeldeellreakklGfsDkqiaelleee 83 
                                   +++p+d+Rifai+eal r++ v++i e +++d++F+ek++++v++ k+l+  +    +e l ++kklG+sD+ i + ++  
  gi|13541634|ref|NP_111322.1| 418 VRTPNDRRIFAIFEALFRDFPVDRIMEESMYDRYFIEKMQNIVDYLKTLEFGH---IPENLISLKKLGISDEIIGRTCG-I 494
                                   789*********************************************99876...79999**************9976.7 PP

                   CPSase_L_D3  84 eeeevrelrkklgilpvykrvDtcAaeFeaetpYlYstY 122
                                   + +e++++r   +ilpv+k++Dtc++eFe   pYlYstY
  gi|13541634|ref|NP_111322.1| 495 DPDEITRYRITNRILPVFKEIDTCSGEFEVIAPYLYSTY 533
                                   8889**********************************9 PP

>> MGS  MGS-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.99   2.2e+03      65      93 ..     294     327 ..     262     328 .. 0.70
   2 !   64.4   0.0   3.5e-21   7.9e-18       2      95 .]     931    1018 ..     930    1018 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.99
                                   EEE--THHHHHH.....CHHHHHHHHHHHTTSHE CS
                           MGS  65 intlypfkatva.....kdgykirraaenidIpl 93 
                                   ++ ++p++++ +       gy i+r+a +i +++
  gi|13541634|ref|NP_111322.1| 294 VVEVNPRTSRSSalaskATGYPIARIAAKIAVGY 327
                                   3344444443333466678999*******99986 PP

  == domain 2  score: 64.4 bits;  conditional E-value: 3.5e-21
                                    HHHHHHHHHHTTCEEEEEHHHHHHHHHTT--EEECCCCHSTGSGGTHCHHHHHHHHTTSCCEEEEE--THHHHHHCHHH CS
                           MGS    2 lvelakklkelgfellATgGTakllkeagipvtevvektgegerlggrveildaikngeidlvintlypfkatvakdgy 80  
                                    ++e a  +k++g +++AT GT ++l+e gi+ +e v +++++ ++     i d+i +g idlvint++ ++  v+ dg+
  gi|13541634|ref|NP_111322.1|  931 IIEAASIMKQNGLKIYATMGTSRYLRERGIE-CETVYRIKDERKPR----IYDMILAGYIDLVINTPEMNAGSVR-DGF 1003
                                    7899999************************.77777777777999....************************9.*** PP

                                    HHHHHHHHTTSHEES CS
                           MGS   81 kirraaenidIplpt 95  
                                    kirr+++  +Ipl+t
  gi|13541634|ref|NP_111322.1| 1004 KIRRLCVRKGIPLVT 1018
                                    *************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 !   24.1   0.0   1.1e-08   2.4e-05      49     125 ..     264     341 ..     253     346 .. 0.85
   2 !   24.4   0.0   8.7e-09   1.9e-05      45     120 ..     789     865 ..     730     874 .. 0.76

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 1.1e-08
                  ATPgrasp_Ter  49 lielaerlaeefgldglvnvQvrededgpkLLEiNpRasGGlg.ysalaGvnlpylalklllgleteeveepeeglrv 125
                                   l ++a +++  +g+ g  n+Q+  d++ +++ E+NpR s      s ++G  ++++a+k + g + +e+++p ++ ++
  gi|13541634|ref|NP_111322.1| 264 LRDAAIKIVSGLGIVGACNIQFALDGNDYYVVEVNPRTSRSSAlASKATGYPIARIAAKIAVGYNLTEIRNPITKNTF 341
                                   568999********************************96555156777**************988888888776655 PP

  == domain 2  score: 24.4 bits;  conditional E-value: 8.7e-09
                  ATPgrasp_Ter  45 kdeelielaerlaeefgldglvnvQvrededgpkLLEiNpRasGGlg.ysalaGvnlpylalklllgleteeveepe 120
                                   ++e++ +++ +l++ef+l g+ n+Q   ++d+ +++E N+R s  +  +s ++G n ++la+ +++  + e+v    
  gi|13541634|ref|NP_111322.1| 789 AEEKIKSIVGKLVREFNLIGISNLQAAIKDDEVYVIELNARSSRSIPfISKATGYNWVELAVSAIMTGKLEKVSVSS 865
                                   5677888999************************************8357888*********999887655555444 PP

>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   2.1e-07   0.00048      18     161 ..     152     302 ..     144     310 .. 0.81
   2 !   26.8   0.2   1.5e-09   3.4e-06       2     159 ..     669     829 ..     668     833 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 2.1e-07
                                   HHHHHHHHHH-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHC....GTTCEEEEE----SEEEEEEEEEETTC-EEE-- CS
                     ATP-grasp  18 eeleeaaeelglpvvvKarrlgydGkGqsvvrseedleqaleal....keekvivEefvpfekElsvlvvrsaeGetafyp 94 
                                   ++ +e +e++ +  v+ +   +  G G  +v+ +e+l+  +e+l    +e  + v       kEl   ++r+  G+  ++ 
  gi|13541634|ref|NP_111322.1| 152 SNYKEEIEKIPFMPVIVRTSFSLGGSGGNIVKTKEELKAYAEELfrgiDEDYIEVNRSLAGLKELEYEMIRDSIGNCITVC 232
                                   46788889998877777799***********************97765555566666677778899999************ PP

                                   EEEEEEETTEEE...EEEECEE-SCH.HHHHHHHHHHHHHHHHTSSEEEEEEEEEETTCTEEEEEEESS-- CS
                     ATP-grasp  95 vvetvqedgilr...lsvapaevsek.aqkkaeeiakkiveeLggvGvfavElFvledgellvnElapRpH 161
                                    +e++   g+     ++v p++  ++ + +  ++ a kiv+ Lg+vG   +  F l+ ++ +v E+ pR+ 
  gi|13541634|ref|NP_111322.1| 233 NMENLDPMGVHTgesIVVTPSQTLSDiQYHMLRDAAIKIVSGLGIVGACNIQ-FALDGNDYYVVEVNPRTS 302
                                   ******9999753337889988877725566778888**************8.5663555*********85 PP

  == domain 2  score: 26.8 bits;  conditional E-value: 1.5e-09
                                   HTTT--B-EEEEECCHHHHHHHHHHH-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHC..GTTCEEEEE----SEEEEE CS
                     ATP-grasp   2 eklglpvprflaveskeeleeaaeelglpvvvKarrlgydGkGqsvvrseedleqaleal..keekvivEefvpfekElsv 80 
                                   e++g+  p+f +++++ee+ +   +lglpv+++ + +   G+   ++ + + l +  +++  + ++v+v ++ +  +E+ v
  gi|13541634|ref|NP_111322.1| 669 EAMGIDQPKFEVATNAEEAINKSLALGLPVILR-ASHVIGGRAMDIIYDYDFLVERSREVfeNVNSVLVSKYLENAVEIDV 748
                                   678999***************************.88999**********99888888877777799*************** PP

                                   EEEEETTC-EEE--EEEEEEETTE....EEEEEECEE-SCHHHHHHHHHHHHHHHHHTSSEEEEEEEEEETTCTEEEEEEE CS
                     ATP-grasp  81 lvvrsaeGetafypvvetvqedgi....lrlsvapaevsekaqkkaeeiakkiveeLggvGvfavElFvledgellvnEla 157
                                     v + e  ++++ +  +++e g+      + + p+ v+++a++k+++i+ k+v+e++ +G+  +   ++ d+e++v El 
  gi|13541634|ref|NP_111322.1| 749 DFVSNGED-FQICGILVHIEEAGVhsgdATMIFGPKIVPQAAEEKIKSIVGKLVREFNLIGISNLQAAIK-DDEVYVIELN 827
                                   ***98776.999999999987655111168999*********************************9998.8889999998 PP

                                   SS CS
                     ATP-grasp 158 pR 159
                                    R
  gi|13541634|ref|NP_111322.1| 828 AR 829
                                   88 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.1   3.2e-07   0.00072      21     158 ..     153     301 ..     128     304 .. 0.74
   2 !   22.9   0.2   3.1e-08     7e-05       3     158 ..     660     830 ..     658     833 .. 0.66

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 3.2e-07
                                   ...-EESS--SSSEEEEESS-------B--SS--TTE.........EEEE---S.......EEEEEEEEE.SSSEEEEEEE CS
                   ATP-grasp_3  21 kleaeeleeeekklvvKprdGaggesvrvveekeeaeaaieeve..lvqefieG.......kplSvsllsdgekvlvlavn 92 
                                   ++++e  +    +++v  + + gg++  +v+ kee++a  ee+   +  ++ie        k+l  +++ d   + + ++n
  gi|13541634|ref|NP_111322.1| 153 NYKEEIEKIPFMPVIVRTSFSLGGSGGNIVKTKEELKAYAEELFrgIDEDYIEVnrslaglKELEYEMIRDSIGNCITVCN 233
                                   556666666688999999999999999999999999988888778866666664111111245566677777777777777 PP

                                   EEEEET....TEEEEE...EES----H...HHHHHHHHHHHHTTSTT--EEEEEEEEESS.SEEEEEEESS- CS
                   ATP-grasp_3  93 rqliekaekefvyaGn...vtpietel...keevvelaeevvekleglaGyvGvDlvlkdeepyviEvNPRl 158
                                    + ++      v +G+   vtp++t      + ++++a ++v+ l g++G   + + l  ++ yv+EvNPR 
  gi|13541634|ref|NP_111322.1| 234 MENLDPM---GVHTGEsivVTPSQTLSdiqYHMLRDAAIKIVSGL-GIVGACNIQFALDGNDYYVVEVNPRT 301
                                   7777653...66666632257777765453567789999999999.*************************6 PP

  == domain 2  score: 22.9 bits;  conditional E-value: 3.1e-08
                                   SHHHHHHHHTTT.S---.........-EESS--.......SSSEEEEESS-------B--SS--TTE.............E CS
                   ATP-grasp_3   3 dKlktykkLkeagvkvP.....tkleaeeleee.......ekklvvKprdGaggesvrvveekeeaeaaieeve......l 65 
                                   d   + k+L++ g+  P     t++e+     +         ++++  +   gg ++ ++ + + + +   ev       l
  gi|13541634|ref|NP_111322.1| 660 DRSLFSKRLEAMGIDQPkfevaTNAEE-----AinkslalGLPVILRASHVIGGRAMDIIYDYDFLVERSREVFenvnsvL 735
                                   666777888888888886654322222.....1222345577888888888888887777666544433333223344779 PP

                                   EEE---.SEEEEEEEEE.SSSEEEEEEEEEEEET........TEEEEEEES----HHHHHHHHHHHHHTTSTT--EEEEEE CS
                   ATP-grasp_3  66 vqefie.GkplSvsllsdgekvlvlavnrqliekaeke....fvyaGnvtpietelkeevvelaeevvekleglaGyvGvD 141
                                   v++++e   ++ v+++s+ge++++  +   + e + ++    +++  +++p     +e++ +++ ++v+++ +l G+    
  gi|13541634|ref|NP_111322.1| 736 VSKYLEnAVEIDVDFVSNGEDFQICGILVHIEEAGVHSgdatMIFGPKIVPQ--AAEEKIKSIVGKLVREF-NLIGISNLQ 813
                                   9999993579*********877665544433333222244423333344444..46999************.********* PP

                                   EEESS.SEEEEEEESS- CS
                   ATP-grasp_3 142 lvlkdeepyviEvNPRl 158
                                     +kd+e yviE N+R 
  gi|13541634|ref|NP_111322.1| 814 AAIKDDEVYVIELNARS 830
                                   ***************95 PP

>> Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.1   1.6e-06    0.0035      22     174 ..     149     299 ..     142     305 .. 0.79
   2 !   13.3   0.7     2e-05     0.046       3     174 ..     669     828 ..     668     831 .. 0.90
   3 ?   -1.3   0.0      0.59   1.3e+03      82     143 ..     915     981 ..     905     989 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.6e-06
                                   H-H-HHHHHHHHHC-SSEEEEES.SSSTTTTEEEESSGGGHHHHHHHHHT.T-SC.EEEEE--.ESEEEEEEEEETSSCEE CS
               Dala_Dala_lig_C  22 eekkellekveeelgypvfVKpa.reGSSvGvskveseeelkeaieeafk.ydek.vlvEeai.egreievavlgneklev 98 
                                    +++++ e++e+   +pv+V+ +  +G S G + v+++eelk++ ee f+  de+ + v + +   +e+e  ++ +   ++
  gi|13541634|ref|NP_111322.1| 149 ISRSNYKEEIEKIPFMPVIVRTSfSLGGS-GGNIVKTKEELKAYAEELFRgIDEDyIEVNRSLaGLKELEYEMIRDSIGNC 228
                                   5566778888888899*****98345666.779****************944554255777787789********555555 PP

                                   EEEEEEE-SSSSS-HHHHHC.TT-EEESS----HHHHHHHHHHHHHHHHHTT--SEEEEEEEEETTTEEEEEEEES CS
               Dala_Dala_lig_C  99 sevgeivvkkgfydyeakysddkaqlevpaklekeveekiqelalkaykaldlrGlaRvDfflteegeivlnEvNt 174
                                    +v ++       d    ++++++ ++   +l++ +++ ++++a+k+ + l++ G + + f l+  ++ ++ EvN+
  gi|13541634|ref|NP_111322.1| 229 ITVCNME----NLDPMGVHTGESIVVTPSQTLSDIQYHMLRDAAIKIVSGLGIVGACNIQFALD-GNDYYVVEVNP 299
                                   5544443....345555666788888888999*******************************9.7789999**96 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 2e-05
                                   HHTT--B--EEEEETTHHCH-H-HHHHHHHHHC-SSEEEEESSSSTTTTEEEESSGGGHHHHHHHHHTT-SCEEEEE--.E CS
               Dala_Dala_lig_C   3 kaaGlpvvpyvvlekeeakeekkellekveeelgypvfVKpareGSSvGvskveseeelkeaieeafkydekvlvEeai.e 82 
                                   +a+G+ +++++v +++e   +k         +lg+pv+ ++++      +  +   + l e  +e f+  ++vlv +++ +
  gi|13541634|ref|NP_111322.1| 669 EAMGIDQPKFEVATNAEEAINK-------SLALGLPVILRASHVIGGRAMDIIYDYDFLVERSREVFENVNSVLVSKYLeN 742
                                   6789999999998888887777.......679**********99888889999999***********************99 PP

                                   SEEEEEEEEETSS.CEEEEEEEEE-SSSSS-HHHHHC.TT-EEESS----HHHHHHHHHHHHHHHHHTT--SEEEEEEEEE CS
               Dala_Dala_lig_C  83 greievavlgnek.levsevgeivvkkgfydyeakysddkaqlevpaklekeveekiqelalkaykaldlrGlaRvDfflt 162
                                   + ei+v  + n++ +++  +  ++ + g+       s+d+++++ p  ++++ eeki+ ++ k  +  +l G++ +   ++
  gi|13541634|ref|NP_111322.1| 743 AVEIDVDFVSNGEdFQICGILVHIEEAGVH------SGDATMIFGPKIVPQAAEEKIKSIVGKLVREFNLIGISNLQAAIK 817
                                   ******999876549999999999998885......679999***********************************9998 PP

                                   TTTEEEEEEEES CS
               Dala_Dala_lig_C 163 eegeivlnEvNt 174
                                    ++e+++ E+N 
  gi|13541634|ref|NP_111322.1| 818 -DDEVYVIELNA 828
                                   .9999**9*996 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 0.59
                                   ESEEEEEEEEETSSCEEEEEEEEE-SSSSS-HHH....HHC..TT-EEESS----HHHHHHHHHHHH CS
               Dala_Dala_lig_C  82 egreievavlgneklevsevgeivvkkgfydyea....kysd.dkaqlevpaklekeveekiqelal 143
                                   +++ + ++v +++k+++ e+  i++++g+  y++    +y     +++e   ++++e++ +i ++ l
  gi|13541634|ref|NP_111322.1| 915 DIKSVFISVRDDDKPRIIEAASIMKQNGLKIYATmgtsRYLReRGIECETVYRIKDERKPRIYDMIL 981
                                   56778899999************99995544443112266433666666666777777776666655 PP

>> ATP-grasp_5  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0     0.094   2.1e+02      86     143 ..     608     662 ..     571     667 .. 0.79
   2 ?    8.0   0.0   0.00076       1.7      19      54 ..     668     703 ..     664     706 .. 0.93

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.094
                   ATP-grasp_5  86 ervkekspeariegvlVqemakrggrElivgvteDpvFGpvilfGlGGtavevlkdva 143
                                   e+v++  ++a+++g++Vq   +  g+   +    ++v G  +++G++   ++ ++d++
  gi|13541634|ref|NP_111322.1| 608 EHVSNILAKANLRGLIVQFSGQ-TGQN--IARRIENVLGSSVVMGTSSESIDRIEDRS 662
                                   6677777999********9977.4554..55667789999999999999999999987 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00076
                   ATP-grasp_5  19 leaygipvvetrlassaeeaveaaeeigypvvlKiv 54 
                                   lea+gi+ +++ +a++aeea++   ++g pv l+  
  gi|13541634|ref|NP_111322.1| 668 LEAMGIDQPKFEVATNAEEAINKSLALGLPVILRAS 703
                                   89*****************************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1044 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       557  (0.031067); expected 358.6 (0.02)
Passed bias filter:                      501  (0.0279436); 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: 0.82u 0.34s 00:00:01.15 Elapsed: 00:00:00.49
# Mc/sec: 6413.02
//
Query:       gi|13541635|ref|NP_111323.1|  [L=215]
Description: endonuclease III [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-21   76.6   0.0    2.6e-21   76.1   0.0    1.3  1  HhH-GPD        HhH-GPD superfamily base excision DNA repair p
    1.1e-08   34.5   0.0    3.4e-08   32.9   0.0    1.9  1  HHH            Helix-hairpin-helix motif
      1e-05   26.0   1.2      0.075   13.7   0.1    2.5  2  HHH_5          Helix-hairpin-helix domain
     0.0072   16.4   0.0          2    8.6   0.0    2.8  2  HHH_2          Helix-hairpin-helix motif
  ------ inclusion threshold ------
       0.12   12.7   3.3       0.19   12.1   3.3    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 !   76.1   0.0   7.2e-25   2.6e-21       1     107 [.      35     169 ..      35     170 .. 0.96

  Alignments for each domain:
  == domain 1  score: 76.1 bits;  conditional E-value: 7.2e-25
                                   HHHHHHTTS-HHHHHHHHHHHHHHHSHCSHHHHHHSHHHHHHHHHTTSTTHHHHHHHHHHHHHHHH............... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............... RF
                       HhH-GPD   1 vsailsqqtsderanriierlferfgfptpedladadeekLrelirelGfyrrKakyikelArilv............... 66 
                                   + ++lsq+t+de++ ++   l+er+   t e la+ad +++ ++i+++Gf+r Kak i+ +A+i+                
  gi|13541635|ref|NP_111323.1|  35 ITTVLSQRTKDETTDQAALALYERYR--TIEGLASADVSDVGSIISKVGFWRVKAKKIIMIAQIIRdeygskvpasmdqll 113
                                   5689********************97..***************************************************** PP

                                   ..................S-SSS--TTSHHHHHHHHHHTTSSSSTTHHHHHHHHHHHHH CS
                                   ..................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       HhH-GPD  67 ..................gkpdvlivvDvhvrrilkrlrsikekktkkkvekkleelle 107
                                                     g   ++i+vD+hv ri +r+++ +  kt+++++++l+++++
  gi|13541635|ref|NP_111323.1| 114 slpgvgvktasvvlaeglG--IPMIAVDTHVFRISHRIGWSSS-KTPEQTAQDLMQIIP 169
                                   ***************9655..79*******************9.6*********99987 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.9   0.0   9.5e-12   3.4e-08       2      29 ..     101     128 ..     100     129 .. 0.94

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 9.5e-12
                                   HHHHHTSSHHHHHTSTT-SHHHHHHHHH CS
                           HHH   2 leglipasreeLlalPGVGpktAeaIls 29 
                                   +++ +pas+++Ll+lPGVG ktA ++l+
  gi|13541635|ref|NP_111323.1| 101 YGSKVPASMDQLLSLPGVGVKTASVVLA 128
                                   8999*********************996 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.1   2.1e-05     0.075      14      55 ..      51      94 ..      48      95 .. 0.85
   2 !   10.8   0.1   0.00016      0.57       3      22 ..     111     130 ..     108     136 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.1e-05
                                  HHHHHHTTT--SHHHHHHS-HHH....HHTSTTS-HHHHHHHHHHH CS
                         HHH_5 14 tAlallsaGiesvedlaaadvee....LakipGiGkktAeriilel 55
                                   Alal++  ++++e la+adv +    ++k+ G+   +A++ii+ +
  gi|13541635|ref|NP_111323.1| 51 AALALYER-YRTIEGLASADVSDvgsiISKV-GFWRVKAKKIIMIA 94
                                  79******.**********998866666666.99999999999865 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00016
                                   HHHTSTT--HHHHHHHHTTT CS
                         HHH_5   3 eLlsvsGiGpktAlallsaG 22 
                                   +Lls++G+G ktA  +l  G
  gi|13541635|ref|NP_111323.1| 111 QLLSLPGVGVKTASVVLAEG 130
                                   68888888888887777765 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.0   0.00056         2      14      39 ..      50      75 ..      49      82 .. 0.86
   2 !    4.7   0.0    0.0093        33      32      51 ..     107     126 ..     105     128 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00056
                         HHH_2 14 ktAklLakrFksldaLkkasleeLle 39
                                  ++A +L +r+++++ L++a++ +  +
  gi|13541635|ref|NP_111323.1| 50 QAALALYERYRTIEGLASADVSDVGS 75
                                  68999***************988755 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0093
                         HHH_2  32 asleeLlevddiGeeiAqsi 51 
                                   as+++Ll+++++G ++A+ +
  gi|13541635|ref|NP_111323.1| 107 ASMDQLLSLPGVGVKTASVV 126
                                   78888999999998888766 PP

>> EndIII_4Fe-2S  Iron-sulfur binding domain of endonuclease III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   3.3   5.4e-05      0.19       1      17 []     188     204 ..     188     204 .. 0.98

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5.4e-05
                 EndIII_4Fe-2S   1 CTARkPkCeaCPLaDlC 17 
                                   C + +PkC  C ++++C
  gi|13541635|ref|NP_111323.1| 188 CRPVSPKCSMCRINEFC 204
                                   99*************** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       507  (0.0282782); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1465.11
//
Query:       gi|13541636|ref|NP_111324.1|  [L=590]
Description: amino acid transporter [Thermoplasma volcanium GSS1]
Scores for complete 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-36  123.5  65.5    9.7e-36  123.5  65.5    2.5  2  AA_permease_2  Amino acid permease
    6.6e-32  110.7  44.7    6.6e-32  110.7  44.7    2.1  2  AA_permease    Amino acid permease
  ------ inclusion threshold ------
        2.2    8.3   5.6        6.3    6.8   1.9    3.2  2  TNFR_16_TM     Tumor necrosis factor receptor member 16 trans


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 !  123.5  65.5   1.6e-39   9.7e-36       5     397 ..      20     433 ..      16     513 .. 0.85
   2 ?   -3.2   5.5      0.45   2.7e+03       5      46 ..     525     566 ..     521     574 .. 0.64

  Alignments for each domain:
  == domain 1  score: 123.5 bits;  conditional E-value: 1.6e-39
                 AA_permease_2   5 safalvigsvigsgifvkn..laasggpalilwvwiavligslavllvyaElssalprsgGiyvytkaafgkkvaflsawf 83 
                                   ++f+l+++ +igsg +++    a ++gp +i++++ia+l + +  +l++aElss +p sg i+ + ++  g    f+ +w+
  gi|13541636|ref|NP_111324.1|  20 DLFFLAVTGMIGSGWLFAAldTASYVGPGSIFTWMIAALFF-FVIALAFAELSSIIPYSGSIVRFNQYSHGSISNFMIGWA 99 
                                   68************99999955555**************99.79***********************99999999****** PP

                 AA_permease_2  84 nwfayvpvlasilsvaasyllnalgpdlqgn.....twltyliaiaililvalinirgikesakiqnilgilkillpliil 159
                                   +++++v ++++ +++++ y  + + p+l+++     t l +++ i++++++++i+ +g++ ++k++++l+++ki +p+i++
  gi|13541636|ref|NP_111324.1| 100 YLIGAVSTVTVEAISLVTYTSTYM-PQLYNSsvgvlTPLGIIVSIFLILFFFFIQFMGVNVYGKLNTVLTTWKIAIPVITV 179
                                   *******99998888999888866.666665676668899***************************************** PP

                 AA_permease_2 160 iilglitvdgggfsslstetdtffpngwpgvllglli..vlwsfdGfesaanvseevkk..kdvpkaifigllivlvlyll 236
                                   ++l  + +++g f       + f+p g + ++++l    v+++f Gf   + ++ e+k+  +dvp+ ++ +ll+++ +y+ 
  gi|13541636|ref|NP_111324.1| 180 VLLMSFSFHPGNFK----VAHGFLPYGTSAIFAALIPsgVVYAFEGFRQGIEYAGEAKNpqRDVPMSLIAALLVTIAIYVA 256
                                   *******9999998....4788****99998888855469****************888779******************* PP

                 AA_permease_2 237 vniaflgvvpddei.......anlsnlgsv.......aalffeavggkvvaiivvilial.....sllgaintavi.gssr 297
                                   ++iaf+g + ++ +       +       +        ++f+ a+  + vai+++++i++     ++ +a ++++  +s+r
  gi|13541636|ref|NP_111324.1| 257 LQIAFIGSIRWSDLslspgdwT-------LlskstwaSGPFYYATKYSGVAILAIFAIVIlidafISPLASLGVYEgTSAR 330
                                   **************55555543.......123334437999999986644444443333334444444455555541578* PP

                 AA_permease_2 298 vlealardgvlPrffakvn.kfgspiraiiltaivslillllfllassaaynfllsvsslgliisyllliigalilrkkrp 377
                                    ++ l+r +vlP+ff +++ kf +p++++i+t+i+s+++l  f      + ++++ + + + +  yl + ++  +lrk  p
  gi|13541636|ref|NP_111324.1| 331 SFYGLSRLNVLPEFFGSIHpKFRTPWVGLIFTLIISSLFLAPFP-----SWYLIVGINASFTVYAYLSAGTTNSVLRKLAP 406
                                   ************************************99986664.....589***************************** PP

                 AA_permease_2 378 hlkrpgk.......ilvaiigalfllf 397
                                   +l+rp k        +va+++a +l++
  gi|13541636|ref|NP_111324.1| 407 DLNRPFKlpfatvlSPVAFVAASMLVY 433
                                   ****76645556655666666666655 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 0.45
                 AA_permease_2   5 safalvigsvigsgifvknlaasggpalilwvwiavligsla 46 
                                   s+ ++v++s++g+ +++ +l ++++++   ++++a+l +++ 
  gi|13541636|ref|NP_111324.1| 525 SVWIIVYNSILGTMSYFGSLGTNAIAYPYDYLIFAALSFFIF 566
                                   566778888888888888644455555555566666665432 PP

>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.7  44.7   1.1e-35   6.6e-32       2     374 ..      21     398 ..      20     402 .. 0.87
   2 ?   -4.6  12.2         1     6e+03     107     210 ..     439     569 ..     415     579 .. 0.57

  Alignments for each domain:
  == domain 1  score: 110.7 bits;  conditional E-value: 1.1e-35
                   AA_permease   2 vlvialggviGtglfvglgvvlsqaGplgallayllagvviflvmlslgeiatngpksggfytyasrflgpelGfviGlny 82 
                                   +++ a+ g+iG g +++   ++s +Gp g +  +++a +++f ++l+++e+++++p sg++  + + ++g+   f+iG+ y
  gi|13541636|ref|NP_111324.1|  21 LFFLAVTGMIGSGWLFAALDTASYVGP-GSIFTWMIAALFFFVIALAFAELSSIIPYSGSIVRFNQYSHGSISNFMIGWAY 100
                                   678999*********************.777************************************************** PP

                   AA_permease  83 lfswitvlaleltaasiliqfwel.vtdlpkawvt............gavflvvlliinlvgvkvygeaefilalikiiai 150
                                   l+  + ++++e   a++l+++ ++ +++l                  ++ +++++++i+++gv vyg+  ++l+  ki + 
  gi|13541636|ref|NP_111324.1| 101 LIGAVSTVTVE---AISLVTYTSTyMPQLY-N--SsvgvltplgiivSIFLILFFFFIQFMGVNVYGKLNTVLTTWKIAIP 175
                                   ***********...7788888844244444.3..344799***99944445566789************************ PP

                   AA_permease 151 iafiivgiillaggkpnkgagfrflgdngsifknnlppgfakeeegafknfisvfv..ivvfaftGielvaiiagEvkdPe 229
                                   +++++++  ++++ +p ++        +++    +lp g        +++++++++   vv af G+  ++  agE+k+P+
  gi|13541636|ref|NP_111324.1| 176 VITVVLL--MSFSFHPGNF--------KVA--HGFLPYG--------TSAIFAALIpsGVVYAFEGFRQGIEYAGEAKNPQ 236
                                   *999999..5666666666........222..3347777........666666664337899******************* PP

                   AA_permease 230 ksiPkailqvviritifYvlsllligllvprndlgllndsasa.......aspfvifikesgvsvlaplinaviltaalss 303
                                   +++P + + +++ ++ +Yv + ++ +  + ++dl+l  +  +        ++pf +++k+sgv++la ++++vil+ a+ s
  gi|13541636|ref|NP_111324.1| 237 RDVPMSLIAALLVTIAIYVALQIAFIGSIRWSDLSLSPGDWTLlskstwaSGPFYYATKYSGVAILA-IFAIVILIDAFIS 316
                                   *********************************98888666669999999*************9998.6899999999999 PP

                   AA_permease 304 anssly....sasRvlyslakdglaP.kvlkkvskrgvPlraillsmiisllal.......llaslnlaapivfnfllais 372
                                    ++sl     ++ R +y l++ +++P ++++ + k + P++++++++iis l+l       l+ ++n++ ++v+++l+a +
  gi|13541636|ref|NP_111324.1| 317 PLASLGvyegTSARSFYGLSRLNVLPeFFGSIHPKFRTPWVGLIFTLIISSLFLapfpswyLIVGINAS-FTVYAYLSAGT 396
                                   9998852233578*************99999**************************************.9******9988 PP

                   AA_permease 373 al 374
                                   + 
  gi|13541636|ref|NP_111324.1| 397 TN 398
                                   75 PP

  == domain 2  score: -4.6 bits;  conditional E-value: 1
                   AA_permease 107 vtdlpkawvt.............................gavflvvlliinlvgvkvygeaefilalikiiaiiafiivgi 158
                                   + d +    +                             +av +++l+i+ ++g   y  +e+   ++  i +i f  + i
  gi|13541636|ref|NP_111324.1| 439 IIDFL----IlivyaglpllilskfreslditsreaialSAVYWILLSIVGYFGYISYIPFEVYWPILNSIPAITFAFLYI 515
                                   22222....1222356666666666666666666666789***********************998888888888877774 PP

                   AA_permease 159 illaggkpnkga.........gfrflgdngsifknnlppgfakeeegafknfisvfvivvf 210
                                    + +++  +            +++++g+ g+    n +++   +  + + + +s+f+++v 
  gi|13541636|ref|NP_111324.1| 516 RSRSNEVVSSVWiivynsilgTMSYFGSLGT----NAIAY--PY-DYLIFAALSFFIFFVS 569
                                   4444433333334444443455566666666....44444..22.2233333444444443 PP

>> TNFR_16_TM  Tumor necrosis factor receptor member 16 trans-membrane domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   1.9    0.0011       6.3      12      28 ..     242     258 ..     239     260 .. 0.90
   2 ?    0.9   0.1     0.078   4.7e+02       7      17 ..     528     538 ..     525     539 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0011
                    TNFR_16_TM  12 SILaaVvvgLlaYvifK 28 
                                   S++aa +v++++Yv++ 
  gi|13541636|ref|NP_111324.1| 242 SLIAALLVTIAIYVALQ 258
                                   9*************975 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.078
                    TNFR_16_TM   7 IPiYcSILaaV 17 
                                   I +Y SIL+++
  gi|13541636|ref|NP_111324.1| 528 IIVYNSILGTM 538
                                   669******86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (590 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       887  (0.0494729); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.82u 0.33s 00:00:01.14 Elapsed: 00:00:00.55
# Mc/sec: 3234.64
//
Query:       gi|13541637|ref|NP_111325.1|  [L=409]
Description: diaminopimelate decarboxylase [Thermoplasma volcanium GSS1]
Scores for complete 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-42  143.1   0.0    1.2e-41  142.7   0.0    1.1  1  Orn_Arg_deC_N    Pyridoxal-dependent decarboxylase, pyridoxal
    1.7e-12   47.4   0.0    2.3e-12   47.0   0.0    1.4  1  Orn_DAP_Arg_deC  Pyridoxal-dependent decarboxylase, C-termina
     0.0066   16.1   0.0      0.011   15.4   0.0    1.3  1  Ala_racemase_N   Alanine racemase, N-terminal domain


Domain annotation for each model (and alignments):
>> Orn_Arg_deC_N  Pyridoxal-dependent decarboxylase, pyridoxal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  142.7   0.0   2.1e-45   1.2e-41       6     247 .]      42     277 ..      38     277 .. 0.93

  Alignments for each domain:
  == domain 1  score: 142.7 bits;  conditional E-value: 2.1e-45
                                   HHHHHHHHHCT.CCEEEEEGGG---HHHHHHHHHTTEEEEESSHHHHHHHHHCTTTGGGEEEEESS--HHHHHHHHHCTHT CS
                 Orn_Arg_deC_N   6 rklkrwkkalp.rikvfYavKansdlavlellaelGlgldcaSkaElelvlaagvsperiifanpckqreelryalekgvk 85 
                                   +++++   a+p   k fY vKans++++++l+ ++G+g ++ S +E+++++   ++p++i f+ ++ ++ee+  al++g+k
  gi|13541637|ref|NP_111325.1|  42 KNVSSLFGAMPkVTKCFYSVKANSNPNLVRLIGRQGCGSEVTSLGEIQIAMISSIDPDDILFTPNNVSKEEMDFALDRGIK 122
                                   55555556666556899**************************************************************** PP

                                   EEEESSHHHHHHHHHHHCCEEEEEEEE-SCCSSSSTCCCSSSTTSSSSEEHCHHHHHHHHHHHHTTEEEEEEE---BSSC- CS
                 Orn_Arg_deC_N  86 vvtvdnveeleklaklapeakvllRiktdvsaatcelistggessKFGaaleeavealleaakeenlqlvGvsfHvGSgvs 166
                                    +t+++  + e +++ ++ea    Ri++++ +++++ ++tgg+ sKFG++  e++  l   ake+++   G+++ vGS  +
  gi|13541637|ref|NP_111325.1| 123 -ITFNSPGQFELVSNRVEEA--TFRINPGIGHGEHPGTTTGGHGSKFGIDP-ETALKLYTRAKELGIRKFGIHMMVGSNNT 199
                                   .*************999987..58***************************.8888888999******************* PP

                                   SCHHHHHHHHHHHHHHHHHH.HHT---SEEE--S-BS-HCSTTSSSSTHHHHHHHHHHHHHHHHHTSSS-EEEE--SHHHH CS
                 Orn_Arg_deC_N 167 dleafvkavekalklfdela.elGvklkiLdvGGGfgveyeeeeeplkleeiaekirealeeafpgdkevtiiaEpGRalv 246
                                   d+  +++  +k + + +e++    ++   +d+GGGfgv y++e+  l++++  + ++e ++++  g +  ++ +EpGR++v
  gi|13541637|ref|NP_111325.1| 200 DADLMLTFYKKFFDMASEIEkTAHLQFSYIDIGGGFGVPYNDEQRSLDIKKLGSGLKELVDQY--GIE--RLFIEPGRYIV 276
                                   ********************44556***********************************999..445..9*********9 PP

                                   G CS
                 Orn_Arg_deC_N 247 a 247
                                   a
  gi|13541637|ref|NP_111325.1| 277 A 277
                                   8 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 !   47.0   0.0   3.8e-16   2.3e-12       2      98 .]     274     359 ..      58     359 .. 0.84

  Alignments for each domain:
  == domain 1  score: 47.0 bits;  conditional E-value: 3.8e-16
                                   EEEEGGEEEEEEEEEEEEETCEEEEEES--TTTS-HHHHCTT-S-E.ESBTT-SCEEC.EEEEEEEE-SSSSTT-EEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
               Orn_DAP_Arg_deC   2 yvydeagvLvtrViavkesekkkfvivdaGmndllrpalygsfhei.pvkeeeaekeeeeeeevdvvGptCesgDvlakdr 81 
                                   y++ +ag+Lv +V +v     + fv +d Gmn ++r alyg+ h++ +++       +++e e+ v G++Ce +Dv +  r
  gi|13541637|ref|NP_111325.1| 274 YIVADAGILVGKVYDVY----NGFVGTDIGMNINIRHALYGAEHRFyALT------GRSDEAEYIVTGQICENTDVTG--R 342
                                   45559************....35***********************6664......2345678***************..8 PP

                                   EEEE--TT-EEEESS-S CS
                                   xxxxxxxxxxxxxxxxx RF
               Orn_DAP_Arg_deC  82 elpelevGdllafedaG 98 
                                      ++++Gdl+a+ daG
  gi|13541637|ref|NP_111325.1| 343 LTGKVQIGDLVAMYDAG 359
                                   8888***********98 PP

>> Ala_racemase_N  Alanine racemase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.8e-06     0.011       5     189 ..      39     228 ..      36     255 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.8e-06
                                   HHHHHHHHHHHHSCTTSEEEEE-HHHHHTTHHHHHHHHHHHTTESEEEESSHHHHHHHHHTTSCSEEEEESC.STGGGHHH CS
                Ala_racemase_N   5 alrhNlrrlralagpgaklmavvKanayghgavevaralaeggadgfgvatleEalelreagitapilvleg.fspeelaa 84 
                                   ++ +N++ l  ++++++k++  vKan  +  +  + r     +++ +g+ +++   ++ +     +il     +s+ee++ 
  gi|13541637|ref|NP_111325.1|  39 RIVKNVSSLFGAMPKVTKCFYSVKANSNPNLVRLIGRQGCGSEVTSLGEIQIAMISSIDPD----DILFTPNnVSKEEMDF 115
                                   57788999999997899********888888877777556556777777777766677777....786666689******* PP

                                   HHHTTEEEEESSHHHHHHHHHHHHH......TTS-EEEEEEBESSSS..SSSBSCHHHHHHHHHHHHTTTEEEEEEE-S-S CS
                Ala_racemase_N  85 laeydltvtvdsleqlealaaaare......agkplrvhlkidtgmg..RlGftpeeleellealaalpglrleglmtHfa 157
                                   ++++++++t +s+ q e +++  +e       g  +  h    tg++  + G++pe + +l+ ++++l  +r  g+    +
  gi|13541637|ref|NP_111325.1| 116 ALDRGIKITFNSPGQFELVSNRVEEatfrinPGIGHGEHPGTTTGGHgsKFGIDPETALKLYTRAKELG-IRKFGIHMMVG 195
                                   **********************9986666665555555667789988******************9985.44444444333 PP

                                   ST.TSTSHHHHHHHHHHHHHHHHHHHTT.GGGSE CS
                Ala_racemase_N 158 sa.depdeeteaqlarfeealeelekag.lrppv 189
                                   s   + d  + +  ++f ++++e+ek++ l+  +
  gi|13541637|ref|NP_111325.1| 196 SNnTDAD-LMLTFYKKFFDMASEIEKTAhLQFSY 228
                                   3313333.55555666666666666555465555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (409 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       441  (0.024597); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); 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: 0.51u 0.33s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 2467.06
//
Query:       gi|13541638|ref|NP_111326.1|  [L=1141]
Description: chromosome segregation ATPase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.1e-42  143.3  51.9    1.3e-28  100.0   0.4    4.2  3  SMC_N         RecF/RecN/SMC N terminal domain
    3.2e-25   88.7   0.0    1.4e-24   86.6   0.0    2.2  2  SMC_hinge     SMC proteins Flexible Hinge Domain
    6.1e-15   56.3  18.1    6.1e-15   56.3  18.1    7.0  3  AAA_23        AAA domain
    1.3e-09   38.3  86.4    1.9e-08   34.4  26.8    4.4  2  AAA_15        AAA ATPase domain
    7.7e-06   25.6   0.0    1.6e-05   24.6   0.0    1.5  1  AAA_29        P-loop containing region of AAA domain
      7e-05   22.8  29.9    0.00055   19.8   0.3    4.7  3  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
     0.0038   17.3  30.6      0.077   13.0   1.0    6.6  7  Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C
     0.0045   16.1  17.9     0.0045   16.1  17.9    6.6  4  Atg14         Vacuolar sorting 38 and autophagy-related subun
  ------ inclusion threshold ------
      0.028   14.7   3.5       0.16   12.2   1.0    3.8  2  VPS11_C       Vacuolar protein sorting protein 11 C terminal
       0.11   12.4   0.9       0.55   10.2   0.1    2.7  3  DUF4322       Domain of unknown function (DUF4322)
       0.15   12.3   2.0       0.21   11.8   0.1    2.4  2  SbcCD_C       Putative exonuclease SbcCD, C subunit
       0.29   10.9  98.1      0.034   13.9  17.3    7.8  7  DUF4201       Domain of unknown function (DUF4201)
       0.81    8.2 105.4      0.028   13.1  16.9    5.8  5  AAA_13        AAA domain
        3.1    6.6 120.6       0.16   10.8  10.7    7.8  7  Spc7          Spc7 kinetochore protein
        7.2    6.6  43.2      0.074   13.1   3.2    6.8  6  DUF1043       Protein of unknown function (DUF1043)
        7.5    6.7  96.4      0.099   12.9  14.2    7.8  8  ATG16         Autophagy protein 16 (ATG16)


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 !  100.0   0.4   1.1e-31   1.3e-28       1     133 [.       4     127 ..       4     149 .. 0.93
   2 ?    0.3   1.4      0.34   3.8e+02      92     141 ..     234     283 ..     184     318 .. 0.73
   3 !   49.0  37.0   4.4e-16   4.9e-13      61     217 ..     361    1121 ..     353    1124 .. 0.81

  Alignments for each domain:
  == domain 1  score: 100.0 bits;  conditional E-value: 1.1e-31
                                   EEEEEEEESETTEECEEEEEETTSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N   1 vlkrleienFksyagktvilpfsksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaevei 81 
                                   +++r+e  nFks++ k++++ fs+++++i GpNGSGKsn+ d +lFvLG++s +++r++klsdli+k    +s + ++v +
  gi|13541638|ref|NP_111326.1|   4 YIERIEAYNFKSFR-KKKTIYFSRGLNVISGPNGSGKSNIGDMLLFVLGTKSIHSVRADKLSDLISK----DSGNTCYVIV 79 
                                   799**********8.9999***********************************************9....77899***** PP

                                   EEEETTEESSSSSSCEEEEEEEETTSE..EEEEETTEEE-HHHHHHHHHCTT-S CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N  82 tfdnedkklkiekeevsisrrvkrkge..seykingkevtkkevsellesagis 133
                                   tf+n++ k      +++isrr++ ++e  s y++ng+++++++v++ l+  gi+
  gi|13541638|ref|NP_111326.1|  80 TFKNDEGK------SLEISRRLVIEDEpkSYYYVNGTKARQSDVEDALSAFGIN 127
                                   ***99998......677887777666656*********************9997 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.34
                                   SSSSCEEEEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N  92 iekeevsisrrvkrkgeseykingkevtkkevsellesagiskelLSgGe 141
                                   i++ + ++    k+ ++s++ i + + +++ +++ll+++  + + L  Ge
  gi|13541638|ref|NP_111326.1| 234 IQAIDRQVDSIEKEIEKSKVLISDLNLRYHSIEQLLSEETKKLNDLTSGE 283
                                   33333333333344456999****************99998888888887 PP

  == domain 3  score: 49.0 bits;  conditional E-value: 4.4e-16
                                    CCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STT.... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.... RF
                         SMC_N   61 lsdlihkskekasvkkaeveitfdnedkklkiekeevsisrrvkrkgeseykingkevtkkevsellesagiske.... 135 
                                    +++l+ + +++++ ++a+  +  + +d ++ki+k + +i+  +++  e +++i+gk  + +e++e +e+ g++ +    
  gi|13541638|ref|NP_111326.1|  361 YNKLVAE-AQEKEKENATSRV--KTKDYQVKISKLNDEINSLKEKLAEINMAIKGKIDRITELEERMEDIGLKVKadew 436 
                                    5666666.4444445554444..34566666777777777777777777777777777777777777777777777777 PP

                                    ............................................................................... CS
                                    ............................................................................... RF
                         SMC_N  136 ............................................................................... 135 
                                                                                                                   
  gi|13541638|ref|NP_111326.1|  437 klsqnaedlskyrdryyklkseydeiqekisklssqisaaeatarasvprqidrasqveeikknisgvvgqirdlisyg 515 
                                    7777777777777777777777777777777777777777777777777777777777777777777777777777777 PP

                                    ............................................................................... CS
                                    ............................................................................... RF
                         SMC_N  136 ............................................................................... 135 
                                                                                                                   
  gi|13541638|ref|NP_111326.1|  516 eryaiavesaasarlnavvvdtdvtakrcieylrekkispmtflplnkmramsnlsepdilsrdagflgflidfidfdd 594 
                                    7777777777777777777777777777777777777777777777777777777777777777777777777777777 PP

                                    ............................................................................... CS
                                    ............................................................................... RF
                         SMC_N  136 ............................................................................... 135 
                                                                                                                   
  gi|13541638|ref|NP_111326.1|  595 kyrnavfwvfrdtglvsdidagrrlmgsirlvsldgdvfdpsgsitggfrrqvrqparspsedldsmkkelaflqseka 673 
                                    7777777777777777777777777777777777777777777777777777777777777777777777777777777 PP

                                    ............................................................................... CS
                                    ............................................................................... RF
                         SMC_N  136 ............................................................................... 135 
                                                                                                                   
  gi|13541638|ref|NP_111326.1|  674 kikkeldealqsmsdaskktgeiekerqiinddlaknkqilkdiaselsklkqeiaenkeekealekdisdrqldlhky 752 
                                    7777777777777777777777777777777777777777777777777777777777777777777777777777777 PP

                                    ............................................................................... CS
                                    ............................................................................... RF
                         SMC_N  136 ............................................................................... 135 
                                                                                                                   
  gi|13541638|ref|NP_111326.1|  753 qealndiyddlgqsiidtiensmrkledyrkkisaitadievkekrvsfldkesnnivqqnieleiqrkavedeihnie 831 
                                    7777777777777777777777777777777777777777777777777777777777777777777777777777777 PP

                                    ............................................................................... CS
                                    ............................................................................... RF
                         SMC_N  136 ............................................................................... 135 
                                                                                                                   
  gi|13541638|ref|NP_111326.1|  832 iqkrsmeeelkkhelflkqlesshsdiaskikdmenemkeirskieeinsdveikrsilselkvkrsvvadrnsaieae 910 
                                    7777777777777777777888899****************************************************** PP

                                    ............................................................................... CS
                                    ............................................................................... RF
                         SMC_N  136 ............................................................................... 135 
                                                                                                                   
  gi|13541638|ref|NP_111326.1|  911 mqsipeptmiegdivlekrkceadisalgdinngaiqeyeesvkaynelkdkknrlelerrslqdltdslnkkkkevfv 989 
                                    ******************************************************************************* PP

                                    ...................................................CS-HHHHHHHHHHHHHHHHCCS--SEEE CS
                                    ...................................................xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N  136 ...................................................lLSgGektLvalaLlfAiqkvkpaplyl 163 
                                                                                       +LSgGek+++a++++ A+q+  p+++y+
  gi|13541638|ref|NP_111326.1|  990 stfekinekmnyvygtinggtaslvlkgddplesavevsvtpkdkatvkiqALSGGEKSIAAMSFITAVQMLMPSSIYF 1068
                                    ******************************************************************************* PP

                                    ECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-SCEEEEEEEETT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N  164 lDeidaaLDeknvkkvaellkeksknaQfivislreemlekadklvgvtkveng 217 
                                    lDe+d+ LD+ n + + +l++ek  +aQ i isl+  ++e a + +g+t+ +ng
  gi|13541638|ref|NP_111326.1| 1069 LDEVDMYLDAYNAESMIRLIREKAGEAQTILISLKVSVFEYAANAIGITS-RNG 1121
                                    *************************************************9.555 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 !   86.6   0.0   1.3e-27   1.4e-24       2     116 ..     502     619 ..     501     620 .. 0.96
   2 ?   -2.7   0.0       6.1   6.9e+03      40      61 ..    1080    1100 ..    1077    1112 .. 0.75

  Alignments for each domain:
  == domain 1  score: 86.6 bits;  conditional E-value: 1.3e-27
                     SMC_hinge   2 kgvlGrladlievdegyekAveaalgnrlqalvvedeetakkiieflkkknagratflpldrikqknkadgandkns...g 79 
                                   +gv+G++ dli+  e+y +Ave a+ +rl+a+vv+++ tak++ie+l++k+   +tflpl++++  ++ ++++   +   +
  gi|13541638|ref|NP_111326.1| 502 SGVVGQIRDLISYGERYAIAVESAASARLNAVVVDTDVTAKRCIEYLREKKISPMTFLPLNKMRAMSNLSEPDILSRdagF 582
                                   79************************************************************999999999987766999* PP

                     SMC_hinge  80 avplidlvevddelrkalryllgdtlvvdsldeAeel 116
                                    ++lid++++dd++r+a+  +++dt +v+++d++++l
  gi|13541638|ref|NP_111326.1| 583 LGFLIDFIDFDDKYRNAVFWVFRDTGLVSDIDAGRRL 619
                                   *********************************9987 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 6.1
                     SMC_hinge   40 takkiieflkkknagratflpl 61  
                                     a+++i+ +++k ag a+ + +
  gi|13541638|ref|NP_111326.1| 1080 NAESMIRLIREK-AGEAQTILI 1100
                                    68899999**99.777776665 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.3  18.1   5.5e-18   6.1e-15       5     192 ..      11     269 ..       7     298 .. 0.73
   2 ?   -2.5  20.3       5.3     6e+03      98     200 .]     775     884 ..     759     884 .. 0.54
   3 ?    4.9   1.6     0.029        32     137     191 ..     948     998 ..     893    1004 .. 0.58

  Alignments for each domain:
  == domain 1  score: 56.3 bits;  conditional E-value: 5.5e-18
                        AAA_23   5 enfrsf.rdqeidFskgltlItGpNGaGKTTildAiklaLygetprlsrksgrgfeksdveiesegkvkayveltfenkdg 84 
                                    nf+sf ++++i Fs+gl++I+GpNG+GK+ i d + ++L+ ++    r ++     sd  i+++  +  yv +tf+n+ g
  gi|13541638|ref|NP_111326.1|  11 YNFKSFrKKKTIYFSRGLNVISGPNGSGKSNIGDMLLFVLGTKSIHSVRADK----LSDL-ISKDSGNTCYVIVTFKNDEG 86 
                                   5*****66688*****************************997655555442....3333.33333444558888888877 PP

                        AAA_23  85 ry...................................................trsiererelskkkgkttkkaklellei 114
                                   ++                                                   ++++  +  +++k  +++ +++ + +e 
  gi|13541638|ref|NP_111326.1|  87 KSleisrrlviedepksyyyvngtkarqsdvedalsafginfgtysfvlqgdiNDFVGMSGVERRKLIERIAGTEQFDVEL 167
                                   77888888888888888899999999999********************9999999999********************** PP

                        AAA_23 115 deleqfisellgskkiilnlilflgqerfeefelkdkke............rleelekeleeledekkllekl....eqek 179
                                   ++ ++ i+e  ++ +i +++i+++gqe ++   +k+kke            r  el+k++e +   ++ ++++    e+e 
  gi|13541638|ref|NP_111326.1| 168 EKARNDIEEVGKNLDILSSMIDIKGQEVEKLRIEKEKKErydilskrlrdiRFTELSKAKEANDRSIQAIDRQvdsiEKEI 248
                                   ********9888888888**********98888888888677777777777555555555555555555555565543333 PP

                        AAA_23 180 ekek........eleeleeel 192
                                   ek k        +++ +e+ l
  gi|13541638|ref|NP_111326.1| 249 EKSKvlisdlnlRYHSIEQLL 269
                                   333345555555222222222 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 5.3
                        AAA_23  98 kkkgkttkkaklelleideleqfisellgskkiilnlilflgqer....feefelkdkke...........rleelekele 163
                                     k + ++k++  ++ +              +   ++++fl++e+    ++++el+ + +           + +++e+el+
  gi|13541638|ref|NP_111326.1| 775 MRKLEDYRKKISAITAD-------------IEVKEKRVSFLDKESnnivQQNIELEIQRKavedeihnieiQKRSMEEELK 842
                                   33333333333333322.............222223333333333233322222222222222344444456677777777 PP

                        AAA_23 164 eledekkllekl.....eqekekekeleeleeeleeilkele 200
                                   + e + k+le        ++k+ e+e +e+++++eei++++e
  gi|13541638|ref|NP_111326.1| 843 KHELFLKQLESShsdiaSKIKDMENEMKEIRSKIEEINSDVE 884
                                   7777777777779999989999999************99875 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.029
                        AAA_23 137 flgqerfeefelkdkkerleelekeleeledekkllekleqekekek...eleeleee 191
                                    + ++ ++++elkdkk+rle  +++l++l+d        +++k+ke    ++e+++e+
  gi|13541638|ref|NP_111326.1| 948 EYEESVKAYNELKDKKNRLELERRSLQDLTDS-------LNKKKKEVfvsTFEKINEK 998
                                   23333333344444444433333333333333.......4333333344455555555 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.4  26.8   1.7e-11   1.9e-08       2     275 ..       4     397 ..       4     465 .. 0.58
   2 !   11.0  23.0   0.00022      0.24      74     360 ..     787    1098 ..     776    1101 .. 0.61

  Alignments for each domain:
  == domain 1  score: 34.4 bits;  conditional E-value: 1.7e-11
                        AAA_15   2 kIkkikikNFRslkd.veidlseeltvliGkNnsGKSsilealdlFlnnkekkn.....................kkviki 60 
                                   +I++i+  NF+s+++  +i +s  l+v+ G+N+sGKS+i ++l + l +k+ ++                     +     
  gi|13541638|ref|NP_111326.1|   4 YIERIEAYNFKSFRKkKTIYFSRGLNVISGPNGSGKSNIGDMLLFVLGTKSIHSvradklsdliskdsgntcyviV----- 79 
                                   699***********999*********************************77776666666666666665544441..... PP

                        AAA_15  61 ekedleifeniseskdikIdvef.......................................................... 83 
                                                        +f                                                          
  gi|13541638|ref|NP_111326.1|  80 ---------------------TFkndegksleisrrlviedepksyyyvngtkarqsdvedalsafginfgtysfvlqgdi 139
                                   .....................333344444444444444445566666777777777777777777777777899999999 PP

                        AAA_15  84 .................................................aekekakeyektlkskekkkadlllkkkesdl 115
                                                                                    + k+++ e ++++k+k+++++          l
  gi|13541638|ref|NP_111326.1| 140 ndfvgmsgverrklieriagteqfdvelekarndieevgknldilssmiDIKGQEVEKLRIEKEKKERYDI---------L 211
                                   99999999999999888888888888777777776666555555544432223444444444444444443.........4 PP

                        AAA_15 116 kktikdkklklkknelsdekisvekkkskkelpkekeeklekekeelkidkedlkklikkleeslkkee............ 184
                                   +k+++d  +   ++ +  +  s++ +   ++  +++ ek++  + +l +   +++ l+++ +++l+               
  gi|13541638|ref|NP_111326.1| 212 SKRLRDIRFTELSKAKEANDRSIQAIDRQVDSIEKEIEKSKVLISDLNLRYHSIEQLLSEETKKLNDLTsgeirtvqeklr 292
                                   555555555555555555555555555555555555555555555555555555555554444444444433333333333 PP

                        AAA_15 185 .......elknvlksaiiklllisakRnvsdedsekkssllgklkekileealqekl.................eeeltek 241
                                          +                     +++ sekk  + + +k++ +++a +ek                  +++l+e+
  gi|13541638|ref|NP_111326.1| 293 sleisiaS--------------------LDSKISEKKLRMQDMAKQEAIDDARREKYeaeaeeirksleserreRDKLQEE 353
                                   33333331....................44444444444444444444444444444333333344444444444455555 PP

                        AAA_15 242 lkeiqeklkeidkklaeelk.........kilkkkidkik.kfn 275
                                   +   +++++++  + +e++k         k+++ ki+k++  +n
  gi|13541638|ref|NP_111326.1| 354 FIAAEDEYNKLVAEAQEKEKenatsrvktKDYQVKISKLNdEIN 397
                                   55555555555555444444555555555444444444432222 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00022
                        AAA_15   74 skdikIdvefaekekakeyektlkskekkkadlllkkkesdlkktikdkklklkknelsdekisvekkks.......kk 145 
                                     ++ +I+v++       +++++l+++  +  +  ++ +++++    + ++++++              k        k 
  gi|13541638|ref|NP_111326.1|  787 AITADIEVKE-------KRVSFLDKESNNIVQQNIELEIQRKAVEDEIHNIEIQ--------------KRsmeeelkKH 844 
                                    4444444444.......2222222222222222222222222222222222221..............11222222122 PP

                        AAA_15  146 elpkekeeklekekeelkid..kedlkklikkleeslkkee.........................elknvlksaiikl 197 
                                    el+ ++ e++ +++   ki+   +++k++ +k+ee+ +  e                         e++++ +  +i+ 
  gi|13541638|ref|NP_111326.1|  845 ELFLKQLESS-HSDIASKIKdmENEMKEIRSKIEEINSDVEikrsilselkvkrsvvadrnsaieaEMQSIPEPTMIEG 922 
                                    2222222222.22222222223344444444444444333333344444444444555777777777777778888888 PP

                        AAA_15  198 llisakRnvsdedsekkssllgklkekileealqekleeeltek.lkeiqeklkeidkklaeelkkilkkkidkik.kf 274 
                                    ++  +kR+ + + s   + + g+++e   +  ++ + e++++++ l+    +l+++ + l++++k+++ + ++ki+ k+
  gi|13541638|ref|NP_111326.1|  923 DIVLEKRKCEADISALGDINNGAIQEYEES--VKAYNELKDKKNrLELERRSLQDLTDSLNKKKKEVFVSTFEKINeKM 999 
                                    888888888887777644444444443332..333334444444044456799************99999999999999 PP

                        AAA_15  275 nykgkkneeieik....................ddeelplnknGsGvqrllllillileaekkdekeeknvilliEEPE 333 
                                    ny + + + ++ +                    d+  +++   + G +++  +++  +  +       ++ i++++E +
  gi|13541638|ref|NP_111326.1| 1000 NYVYGTINGGTASlvlkgddplesavevsvtpkDKATVKIQALSGGEKSIAAMSFITAVQMLM-----PSSIYFLDEVD 1073
                                    99999999999999*******************************************999999.....*********** PP

                        AAA_15  334 ahLHpqaqkvlikllkelandnktQvi 360 
                                     +L   + +++i+l++e a +   Q+i
  gi|13541638|ref|NP_111326.1| 1074 MYLDAYNAESMIRLIREKAGEA--QTI 1098
                                    ****************988887..666 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.0   1.4e-08   1.6e-05       2      47 ..       6      51 ..       5      58 .. 0.90

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 1.4e-08
                        AAA_29  2 krlqlvNWgtfdg.htieidlkgatlltGpsGsGKSTllDAiqalLv 47
                                  +r++ +N  +f++ +ti ++ +g  +++Gp+GsGKS + D + ++L 
  gi|13541638|ref|NP_111326.1|  6 ERIEAYNFKSFRKkKTIYFS-RGLNVISGPNGSGKSNIGDMLLFVLG 51
                                  799**********9999999.788**************999999885 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.3   4.9e-07   0.00055       1      36 [.      28      67 ..      28     134 .. 0.67
   2 ?   -3.1   5.7       4.7   5.2e+03      42     138 ..     154     250 ..     141     352 .. 0.71
   3 !   15.7   6.9   8.7e-06    0.0097     219     296 ..     984    1101 ..     623    1101 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 4.9e-07
                        AAA_21  1 lnvliGpNgsGKSnLLdaldllarl....drdvegltdel 36
                                  lnv+ GpNgsGKSn+ d l ++ ++       ++ l d  
  gi|13541638|ref|NP_111326.1| 28 LNVISGPNGSGKSNIGDMLLFVLGTksihSVRADKLSDLI 67
                                  79*******************9886665533333333333 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 4.7
                        AAA_21  42 irkipslldlydpeipfefeieeflsqgvryryglrlersqveeklssvetllesgllldkrsleeedvfnpeargirggv 122
                                   i  i++   ++ + ++++  iee++++    +  ++++ + ve   +++e++++  +l++++ ++++ + +  ++ ++  +
  gi|13541638|ref|NP_111326.1| 154 IERIAGTEQFDVELEKARNDIEEVGKNLDILSSMIDIKGQEVEKLRIEKEKKERYDILSKRLRDIRFTELSKAKEANDRSI 234
                                   555666666666667777777766666667777777777777777777788888888888877777777777777777777 PP

                        AAA_21 123 svfslkelsvsepndl 138
                                   +   ++  s+++++++
  gi|13541638|ref|NP_111326.1| 235 QAIDRQVDSIEKEIEK 250
                                   7777776666655444 PP

  == domain 3  score: 15.7 bits;  conditional E-value: 8.7e-06
                        AAA_21  219 r........................................gvvflengdgqelparelSdGtkrll..alltallral 255 
                                    +                                          v + ++d   + +  lS G k+++   ++ta+  + 
  gi|13541638|ref|NP_111326.1|  984 KkevfvstfekinekmnyvygtinggtaslvlkgddplesaVEVSVTPKDKATVKIQALSGGEKSIAamSFITAVQMLM 1062
                                    1222333333344447777777777777777777777777889999999*****************9899********* PP

                        AAA_21  256 kkgsllliDEpEngLHPkllrrllellkelsrngaQviltT 296 
                                    ++ s++++DE++  L+    ++ ++l++e++   aQ il +
  gi|13541638|ref|NP_111326.1| 1063 PS-SIYFLDEVDMYLDAYNAESMIRLIREKAG-EAQTILIS 1101
                                    99.************************99988.88988765 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   1.0   6.9e-05     0.077      34     108 ..     228     305 ..     207     317 .. 0.60
   2 ?    4.1   0.3     0.039        43      43     110 ..     350     412 ..     344     435 .. 0.48
   3 !    7.1   0.4    0.0048       5.4      18     107 ..     392     479 ..     375     485 .. 0.59
   4 ?    2.4   0.0      0.13   1.5e+02      44      97 ..     456     511 ..     436     514 .. 0.56
   5 !    6.9   2.1    0.0054         6      27      97 ..     708     781 ..     700     793 .. 0.72
   6 ?    4.1   1.5      0.04        45      34      94 ..     821     883 ..     802     893 .. 0.59
   7 ?    0.2   0.0      0.64   7.2e+02      33      95 ..     932    1000 ..     922    1013 .. 0.52

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.9e-05
                  Baculo_PEP_C  34 aqlatlldaietqLnalsedlks...llaeldtrldtlltnLtdalnalqdtlrneLtnlnsiltnLlssvtNinstL 108
                                    +  + ++ai++q++++++++++   l+++l+ r ++  + L++  ++l+d  + e+ +++ +l +L  s++ + s +
  gi|13541638|ref|NP_111326.1| 228 EANDRSIQAIDRQVDSIEKEIEKskvLISDLNLRYHSIEQLLSEETKKLNDLTSGEIRTVQEKLRSLEISIASLDSKI 305
                                   344456777777777777777663335566666666666666666666666666666666666666666665554443 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.039
                  Baculo_PEP_C  43 ietqLnalsedlksllaeldt.rldtlltnLtdalnalqdtlrneLtnlnsiltnLlssvtNinstLnn 110
                                   +++++ a +++ ++l+ae ++ + ++++++++++  +++      +  ln ++++L  +++ in ++++
  gi|13541638|ref|NP_111326.1| 350 LQEEFIAAEDEYNKLVAEAQEkEKENATSRVKTKDYQVK------ISKLNDEINSLKEKLAEINMAIKG 412
                                   555555556666666665555322222333333333333......333333333333333333333333 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.0048
                  Baculo_PEP_C  18 LtnvLnairlqnvqilaqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalqdtlrneLtnlnsiltnLl 98 
                                   L++ +n+++ ++++i  +++  +d i + L++  ed+   +++ + +l+++++ L++   +   +l++e + ++ +++ L 
  gi|13541638|ref|NP_111326.1| 392 LNDEINSLKEKLAEINMAIKGKIDRITE-LEERMEDIGLKVKADEWKLSQNAEDLSKYRDRY-YKLKSEYDEIQEKISKLS 470
                                   3333444444444444444444443332.333333333333333336666666665555555.489999999999999999 PP

                  Baculo_PEP_C  99 ssvtNinst 107
                                   s++   ++t
  gi|13541638|ref|NP_111326.1| 471 SQISAAEAT 479
                                   999876665 PP

  == domain 4  score: 2.4 bits;  conditional E-value: 0.13
                  Baculo_PEP_C  44 etqLnalsedlksllaeldtrldtlltnLtdalnalq..dtlrneLtnlnsiltnL 97 
                                   +++ ++++e++++l+++++++ +t+ + + +++ + +  +++++++ ++  ++ +L
  gi|13541638|ref|NP_111326.1| 456 KSEYDEIQEKISKLSSQISAAEATARASVPRQIDRASqvEEIKKNISGVVGQIRDL 511
                                   44444555555555555555555555555555555554555555555555555555 PP

  == domain 5  score: 6.9 bits;  conditional E-value: 0.0054
                  Baculo_PEP_C  27 lqnvqilaqlatlldaietqLnalsedlksllaeldt...rldtlltnLtdalnalqdtlrneLtnlnsiltnL 97 
                                   ++n qil ++a+ l ++++++ + +e+ ++l +++++   +l++  ++L+d    l +++   ++n   +l + 
  gi|13541638|ref|NP_111326.1| 708 AKNKQILKDIASELSKLKQEIAENKEEKEALEKDISDrqlDLHKYQEALNDIYDDLGQSIIDTIENSMRKLEDY 781
                                   677888888888888888888887777777666666666699999*******9999977766666666555555 PP

  == domain 6  score: 4.1 bits;  conditional E-value: 0.04
                  Baculo_PEP_C  34 aqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalq...dtlrneLtnlnsil 94 
                                    +++  + +ie q  +++e+lk+  + + ++l+++ + + ++++ ++   +++r++++ +ns++
  gi|13541638|ref|NP_111326.1| 821 KAVEDEIHNIEIQKRSMEEELKK-HELFLKQLESSHSDIASKIKDMEnemKEIRSKIEEINSDV 883
                                   34444455555555555555554.2223336666666666666666655557788888888776 PP

  == domain 7  score: 0.2 bits;  conditional E-value: 0.64
                  Baculo_PEP_C   33 laqlatlldaietqLnalsedlksllaeldt...rldtlltnLtdalnalq....dtlrneLtnlnsilt 95  
                                     a++++l d  ++ +++ +e++k+  +el++   rl+     L+d   +l+    + + +  + +n +++
  gi|13541638|ref|NP_111326.1|  932 EADISALGDINNGAIQEYEESVKA-YNELKDkknRLELERRSLQDLTDSLNkkkkEVFVSTFEKINEKMN 1000
                                    566666667777777777777765.333333333444333333333333333335444444444444444 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 ?    1.3   7.8      0.13   1.5e+02      59     156 ..     150     250 ..     130     267 .. 0.70
   2 !    5.4  11.0    0.0072       8.1      29     113 ..     345     422 ..     334     433 .. 0.55
   3 !    6.8   2.5    0.0028       3.2      21      72 ..     442     497 ..     431     514 .. 0.62
   4 !   16.1  17.9     4e-06    0.0045      18     153 ..     652     784 ..     644     796 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.13
                         Atg14  59 edkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkklaklsdklkkRrsdleslqneleerrkkqiaklqda 139
                                   ++k+  + a  e+   + ++ r+ ++e+ + l+ l + i++k ++++kl+ + k+++++ + l+++l+  r ++++k  +a
  gi|13541638|ref|NP_111326.1| 150 RRKLIERIAGTEQFDVELEKARNDIEEVGKNLDILSSMIDIKGQEVEKLRIE-KEKKERYDILSKRLRDIRFTELSKAKEA 229
                                   5667777777888888888888999999999999999999999999999988.6888888888888888888888887654 PP

                         Atg14 140 ik....rieqklsslssktle 156
                                          i+++ +s+++++ +
  gi|13541638|ref|NP_111326.1| 230 NDrsiqAIDRQVDSIEKEIEK 250
                                   431111444444444443333 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0072
                         Atg14  29 erlaklksekeslkkkiekalegkeeaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkklaklsd 109
                                    +  kl++e  +                  ed+  ++ a ++e+ ++ a +r +++  + k+s+l++ei+  k+kla+ + 
  gi|13541638|ref|NP_111326.1| 345 RERDKLQEEFIAA-----------------EDEYNKLVAEAQEKEKENATSRVKTKDYQVKISKLNDEINSLKEKLAEINM 408
                                   3333333333333.................344455566667777777777777777777777777777777777777777 PP

                         Atg14 110 klk..........k 113
                                   ++k          +
  gi|13541638|ref|NP_111326.1| 409 AIKgkidriteleE 422
                                   77643333333333 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.0028
                         Atg14  21 perlyelrerlaklksekeslkkkiekalegke....eaeqledkiknkkakleel 72 
                                    e+l ++r r++klkse +++++ki+k+ ++ +     a  +  +   ++ ++ee+
  gi|13541638|ref|NP_111326.1| 442 AEDLSKYRDRYYKLKSEYDEIQEKISKLSSQISaaeaTARASVPRQIDRASQVEEI 497
                                   57888899999999999999999999887777732221111122222233333333 PP

  == domain 4  score: 16.1 bits;  conditional E-value: 4e-06
                         Atg14  18 rngperlyelrerlaklksekeslkkkiekalegkeeaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeie 98 
                                   r+ +e+l + +++la l+sek+ +kk++++al++ +   ++++k     +  + +  + a+ ++ l+ +   ls+lk+ei+
  gi|13541638|ref|NP_111326.1| 652 RSPSEDLDSMKKELAFLQSEKAKIKKELDEALQSMS---DASKKTGEIEKERQIINDDLAKNKQILKDIASELSKLKQEIA 729
                                   56689*******************************...666666666777777788888888889*************** PP

                         Atg14  99 ekkkklaklsdklkkRrsdleslqneleerrkkqiaklqdaikrieqklsslssk 153
                                   e k++ ++l +++++R+ dl + q+ l+    ++ +++ d+i ++ +kl++ ++k
  gi|13541638|ref|NP_111326.1| 730 ENKEEKEALEKDISDRQLDLHKYQEALNDIYDDLGQSIIDTIENSMRKLEDYRKK 784
                                   *****************************99999999999999888887776665 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 ?   -1.4   0.1       2.5   2.8e+03       9      27 ..     199     217 ..     196     219 .. 0.83
   2 ?   12.2   1.0   0.00014      0.16       4      30 ..     830     857 ..     827     858 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 2.5
                       VPS11_C   9 raQeesadrhdlFkaaLee 27 
                                   r  +e ++r+d++ + L++
  gi|13541638|ref|NP_111326.1| 199 RIEKEKKERYDILSKRLRD 217
                                   667899*******999875 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00014
                       VPS11_C   4 irelrraQeesadrhdlFkaaLees.eD 30 
                                   i+  +r+ ee  ++h+lF ++Le+s +D
  gi|13541638|ref|NP_111326.1| 830 IEIQKRSMEEELKKHELFLKQLESShSD 857
                                   7778999*****************9787 PP

>> DUF4322  Domain of unknown function (DUF4322)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1   0.00049      0.55       8      31 ..     171     197 ..     167     200 .. 0.84
   2 ?   -3.0   0.0       6.2   6.9e+03      31      48 ..     249     267 ..     245     270 .. 0.69
   3 ?   -3.5   0.0       9.1     1e+04      20      38 ..    1083    1101 ..    1079    1104 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00049
                       DUF4322   8 qnnvqqiGykL...LsmldfkGkkaee 31 
                                   +n+++++G  L    sm+d kG+ +e 
  gi|13541638|ref|NP_111326.1| 171 RNDIEEVGKNLdilSSMIDIKGQEVEK 197
                                   8*******98544269********997 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 6.2
                       DUF4322  31 evakvLvsa.aLlndsien 48 
                                   e +kvL+s   L   sie+
  gi|13541638|ref|NP_111326.1| 249 EKSKVLISDlNLRYHSIEQ 267
                                   6799***972466677775 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 9.1
                       DUF4322   20 smldfkGkkaeevakvLvs 38  
                                    sm+    +ka e   +L+s
  gi|13541638|ref|NP_111326.1| 1083 SMIRLIREKAGEAQTILIS 1101
                                    89999999****9999998 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 ?   -2.9   0.1       7.4   8.2e+03       6      43 ..     445     483 ..     441     486 .. 0.61
   2 ?   11.8   0.1   0.00019      0.21      26      89 ..    1035    1089 ..    1021    1090 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 7.4
                       SbcCD_C   6 yRnylsfevevr.dedgkekelsrssgtlSGGekqflay 43 
                                     +y + +++ + + d+ ++++s+ s++ S  e+   a+
  gi|13541638|ref|NP_111326.1| 445 LSKYRDRYYKLKsEYDEIQEKISKLSSQISAAEATARAS 483
                                   445555555555345555566888888889888866655 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00019
                       SbcCD_C   26 lsrssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllelle 89  
                                       ++++lSGGek  +a++ +  a+ +l+ s        ++ fLDE    lD+ +++++++l++
  gi|13541638|ref|NP_111326.1| 1035 ATVKIQALSGGEK-SIAAMSFITAVQMLMPS--------SIYFLDEVDMYLDAYNAESMIRLIR 1089
                                    456899*******.66666666677777777........599*******************987 PP

>> DUF4201  Domain of unknown function (DUF4201)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   9.8     0.023        26      46     129 ..     236     320 ..     230     340 .. 0.77
   2 ?   13.9  17.3     3e-05     0.034       2     136 ..     341     474 ..     340     480 .. 0.92
   3 ?    4.7   5.4      0.02        23      79     130 ..     658     709 ..     646     712 .. 0.78
   4 ?    9.2   9.2   0.00081      0.91      79     161 ..     707     785 ..     705     788 .. 0.88
   5 ?    6.9   5.0    0.0042       4.7      71     138 ..     770     837 ..     765     841 .. 0.93
   6 ?    6.9   3.4    0.0042       4.7      81     140 ..     857     916 ..     838     932 .. 0.87
   7 ?    1.9   3.8      0.14   1.6e+02      94     151 ..     943     999 ..     925    1005 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.023
                       DUF4201  46 qlqienqalnkkIeernkeLkrlkkkttktvhalthlkeklhmles.elselkkelkekeerlaklrkelykvklerdklr 125
                                    + +++ + +k+Ie  +  ++ l +++++  + l+++ +kl+ l+s e ++ +++l+++e  +a+l+ ++++ kl+ + + 
  gi|13541638|ref|NP_111326.1| 236 AIDRQVDSIEKEIEKSKVLISDLNLRYHSIEQLLSEETKKLNDLTSgEIRTVQEKLRSLEISIASLDSKISEKKLRMQDMA 316
                                   57789999**********************************444337777777777777777777777777777766666 PP

                       DUF4201 126 kqne 129
                                   kq +
  gi|13541638|ref|NP_111326.1| 317 KQEA 320
                                   6654 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 3e-05
                       DUF4201   2 rkkrnelsklrlklislkhqlaki..qeklekkeelgegLtlidFeqlqienqalnkkIeernkeLkrlkkkttktvhalt 80 
                                   +++r+e +kl+ + i+++  + k+  +++ ++ke+ +  ++++d+   q ++ +ln++I++ +++L ++   ++ ++ ++t
  gi|13541638|ref|NP_111326.1| 341 ESERRERDKLQEEFIAAEDEYNKLvaEAQEKEKENATSRVKTKDY---QVKISKLNDEINSLKEKLAEINMAIKGKIDRIT 418
                                   57899999************999833556678899*********9...67889**************************** PP

                       DUF4201  81 hlkeklhmleselselkkelkekeerlaklrkelykvklerdklrkqneklkqqgg 136
                                   +l e++  +  ++++ + +l++  e+l k+r++ yk+k e d ++++ +kl++q  
  gi|13541638|ref|NP_111326.1| 419 ELEERMEDIGLKVKADEWKLSQNAEDLSKYRDRYYKLKSEYDEIQEKISKLSSQIS 474
                                   ***************************************************99966 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.02
                       DUF4201  79 lthlkeklhmleselselkkelkekeerlaklrkelykvklerdklrkqnek 130
                                   l  +k+ l +l+se ++ kkel+e  +   +  k++ + ++er+ + ++ +k
  gi|13541638|ref|NP_111326.1| 658 LDSMKKELAFLQSEKAKIKKELDEALQSMSDASKKTGEIEKERQIINDDLAK 709
                                   6677888888888888888888888888888888888888888888877766 PP

  == domain 4  score: 9.2 bits;  conditional E-value: 0.00081
                       DUF4201  79 lthlkeklhmleselselkkelkekeerlaklrkelykvklerdklrkqneklkqqggllrvPaLlkDYdktkekveekrk 159
                                   l+ +k+ l+ ++sels+lk+e+ e +e++++l+k ++  +l+ +k+++  +++ +++g+    ++    ++ + k+e+ rk
  gi|13541638|ref|NP_111326.1| 707 LAKNKQILKDIASELSKLKQEIAENKEEKEALEKDISDRQLDLHKYQEALNDIYDDLGQ----SIIDTIENSMRKLEDYRK 783
                                   7899***************************************************9999....555556667777777777 PP

                       DUF4201 160 sv 161
                                   ++
  gi|13541638|ref|NP_111326.1| 784 KI 785
                                   76 PP

  == domain 5  score: 6.9 bits;  conditional E-value: 0.0042
                       DUF4201  71 kttktvhalthlkeklhmleselselkkelkekeerlaklrkelykvklerdklrkqneklkqqggll 138
                                   ++ +++ +l+++++k +++++  + ++k+ + ++++ + + ++  +++ +r+ ++++ ++++ q+  +
  gi|13541638|ref|NP_111326.1| 770 TIENSMRKLEDYRKKISAITADIEVKEKRVSFLDKESNNIVQQNIELEIQRKAVEDEIHNIEIQKRSM 837
                                   68899*******************************************************99988766 PP

  == domain 6  score: 6.9 bits;  conditional E-value: 0.0042
                       DUF4201  81 hlkeklhmleselselkkelkekeerlaklrkelykvklerdklrkqneklkqqggllrv 140
                                   ++  k + +e+e++e +++++e++ + +  r  l+++k +r+ + ++n+ ++++ + +  
  gi|13541638|ref|NP_111326.1| 857 DIASKIKDMENEMKEIRSKIEEINSDVEIKRSILSELKVKRSVVADRNSAIEAEMQSIPE 916
                                   566788999***************************************999988776655 PP

  == domain 7  score: 1.9 bits;  conditional E-value: 0.14
                       DUF4201  94 selkkelkekeerlaklrkelykvklerdklrkqneklkqqggllrvPaLlkDYdktk 151
                                   + + +e++e  +  ++l+++ ++++ler  l++  + l++++ +++v    k   +++
  gi|13541638|ref|NP_111326.1| 943 NGAIQEYEESVKAYNELKDKKNRLELERRSLQDLTDSLNKKKKEVFVSTFEK-INEKM 999
                                   5667899999999999*****************9999999999998866655.55555 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.2     0.016        18      14      36 ..      23      46 ..      10      64 .. 0.76
   2 ?    4.2  23.0     0.012        14     283     466 ..     162     353 ..     148     357 .. 0.77
   3 ?   13.1  16.9   2.5e-05     0.028     320     478 ..     344     513 ..     338     529 .. 0.74
   4 ?    4.5  37.3    0.0099        11     292     467 ..     672     883 ..     656     900 .. 0.65
   5 ?    1.5   2.4     0.082        92     310     363 ..     946     998 ..     921    1042 .. 0.70

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.016
                        AAA_13 14 dfkr.iNliYGwNGaGKTtLSrll 36
                                   f+r  N+i G NG+GK+ +  +l
  gi|13541638|ref|NP_111326.1| 23 YFSRgLNVISGPNGSGKSNIGDML 46
                                  455548************987665 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.012
                        AAA_13 283 ekqerLekliekveskkselleklkavsdeasensafeedkeelkaeaealeeqLkglqraleaKrkepfksvelesvkak 363
                                   ++  +Lek+ +++e+  +  l+ l +++d + ++ +  +  +e k++ + l+++L+ ++     K ke     +++ ++ +
  gi|13541638|ref|NP_111326.1| 162 QFDVELEKARNDIEEVGK-NLDILSSMIDIKGQEVEKLRIEKEKKERYDILSKRLRDIRFTELSKAKEAND-RSIQAIDRQ 240
                                   444566666666666664.34778888887665555555566667778**********9999999999877.99******* PP

                        AAA_13 364 iesikklvaeineliakhNekvanleeekeeakkklelhlv..........eeleseldeykkkykklekaieklekelke 434
                                   ++si+k++++ + li++ N + +++e+  +e +kkl                +le  +  +++k+++ +  ++++ k+ + 
  gi|13541638|ref|NP_111326.1| 241 VDSIEKEIEKSKVLISDLNLRYHSIEQLLSEETKKLNDLTSgeirtvqeklRSLEISIASLDSKISEKKLRMQDMAKQEAI 321
                                   ***************************999999999987655666666666666666666777777777777788888888 PP

                        AAA_13 435 eeaelkkleeeikeLekqlrdekpaaeeinke 466
                                   + a+ +k+e+e++e++k+l++e++  +++ +e
  gi|13541638|ref|NP_111326.1| 322 DDARREKYEAEAEEIRKSLESERRERDKLQEE 353
                                   88888999999999999999998887777665 PP

  == domain 3  score: 13.1 bits;  conditional E-value: 2.5e-05
                        AAA_13 320 eedkeelkaeaealeeqLkglqraleaKrkepfk.svelesvkakie.......sikklvaeineliakhNekvanleeek 392
                                   ++++++l++e+ a e++ ++l  + ++K ke ++ +v++++++ ki+       s+k+++aein  i+    ++++lee+ 
  gi|13541638|ref|NP_111326.1| 344 RRERDKLQEEFIAAEDEYNKLVAEAQEKEKENATsRVKTKDYQVKISklndeinSLKEKLAEINMAIKGKIDRITELEERM 424
                                   455666777777777777777777777776666546667777777742222222777777777777777778888889999 PP

                        AAA_13 393 eeakkklelhl..veeleseldeykkkykklekaieklekelkeeeaelkkleeeikeLekqlrdekpaaeeinkeLkaf. 470
                                   e++  k+++++  +++  ++l++y + y kl+ +  + ++++++ ++++ ++e+ +++   +  d    +eei k ++ + 
  gi|13541638|ref|NP_111326.1| 425 EDIGLKVKADEwkLSQNAEDLSKYRDRYYKLKSEYDEIQEKISKLSSQISAAEATARASVPRQIDRASQVEEIKKNISGVv 505
                                   988888888884458899999999999999999999999999999999999999999999999999999999999999888 PP

                        AAA_13 471 GlgeleLk 478
                                   G  ++ ++
  gi|13541638|ref|NP_111326.1| 506 GQIRDLIS 513
                                   87666555 PP

  == domain 4  score: 4.5 bits;  conditional E-value: 0.0099
                        AAA_13 292 iekveskkselleklkavsde....asensafeed.......keelkaeaealeeqLkglqraleaKrkepfk.svelesv 360
                                   ++k++++ +e+l+++ ++s++    ++e+++ ++d        +++ +e+++l++++ +++++ ea  k+++  +++l+++
  gi|13541638|ref|NP_111326.1| 672 KAKIKKELDEALQSMSDASKKtgeiEKERQIINDDlaknkqiLKDIASELSKLKQEIAENKEEKEALEKDISDrQLDLHKY 752
                                   444444444443333333333333322222222222222233344444444444444444444444444444434444444 PP

                        AAA_13 361 kakie......................sikklvaeineliakhNekvanleeekee.akkklelhl.veeleseldeykkk 417
                                   ++ ++                         k++++i + i+   ++v+ l++e ++ +++++el +  + +e+e+++ + +
  gi|13541638|ref|NP_111326.1| 753 QEALNdiyddlgqsiidtiensmrkleDYRKKISAITADIEVKEKRVSFLDKESNNiVQQNIELEIqRKAVEDEIHNIEIQ 833
                                   4444444455555555555555555559999999999999999999999988776515677888774577899******** PP

                        AAA_13 418 ykklekaieklekelkeeeaelkkleeeikeLekqlrdekpaaeeinkeL 467
                                   ++++e++++k e  lk+ e+    ++ +ik++e+++++++  +eein+ +
  gi|13541638|ref|NP_111326.1| 834 KRSMEEELKKHELFLKQLESSHSDIASKIKDMENEMKEIRSKIEEINSDV 883
                                   ***********************************************865 PP

  == domain 5  score: 1.5 bits;  conditional E-value: 0.082
                        AAA_13 310 sdeasensafeedkeelkaeaealeeqLkglqraleaKrkepfksvelesvkak 363
                                   ++e++e  ++ ++ ++ k+++e  + +L+ l + l++K+ke+f   + e++++k
  gi|13541638|ref|NP_111326.1| 946 IQEYEESVKAYNELKDKKNRLELERRSLQDLTDSLNKKKKEVFV-STFEKINEK 998
                                   33444444555555555666666667788888888888888886.444444444 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   6.2      0.54     6e+02     194     281 ..     161     247 ..     148     249 .. 0.59
   2 ?    6.4  19.8    0.0031       3.5     140     258 ..     226     348 ..     217     352 .. 0.72
   3 ?    4.1  15.0     0.016        18     146     238 ..     338     433 ..     334     440 .. 0.58
   4 ?   10.8  10.7   0.00015      0.16     157     263 ..     388     501 ..     383     505 .. 0.66
   5 ?    9.7  19.5   0.00032      0.36     146     251 ..     656     757 ..     645     763 .. 0.77
   6 ?   10.0  18.4   0.00025      0.28     145     263 ..     765     889 ..     756     899 .. 0.84
   7 ?   -0.3   3.7      0.34   3.8e+02     154     217 ..     934     997 ..     918    1003 .. 0.56

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.54
                          Spc7 194 esidkeeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqkseleeeiaeaerv..leeckgwsesevsrlk 272
                                   e+ d  eLe++r++++e+ ++++ ++ +++ + +++e+l+ + e+ ke+++ l ++++   r+  l + k+ ++  ++++ 
  gi|13541638|ref|NP_111326.1| 161 EQFD-VELEKARNDIEEVGKNLDILSSMIDIKGQEVEKLRIEKEK-KERYDILSKRLRD-IRFteLSKAKEANDRSIQAID 238
                                   4433.4788888888888888888888888777777777665533.3444444444443.333013455556666677777 PP

                          Spc7 273 eevkaleel 281
                                    +v+++e++
  gi|13541638|ref|NP_111326.1| 239 RQVDSIEKE 247
                                   777777765 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0031
                          Spc7 140 LkegleenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeeles....idkeeLeelreelaelkaeie 216
                                    ke  ++ +++++++ + +ek+ e+ + l  +l+ ++ ++e+ l ++ ++ ++l+s      +e+L++l  ++a+l+++i+
  gi|13541638|ref|NP_111326.1| 226 AKEANDRSIQAIDRQVDSIEKEIEKSKVLISDLNLRYHSIEQLLSEETKKLNDLTSgeirTVQEKLRSLEISIASLDSKIS 306
                                   577778899999999999999999999999999999999999999988876666665543446677777777777777777 PP

                          Spc7 217 ekkkelaelqeqleeleekieelkeqkseleeeiaeaervle 258
                                   ekk +++++ +q +  +++ e+ +++ +e+++ +++++r ++
  gi|13541638|ref|NP_111326.1| 307 EKKLRMQDMAKQEAIDDARREKYEAEAEEIRKSLESERRERD 348
                                   777777777777776677777777777777766666666555 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.016
                          Spc7 146 enlegleedkelLekqeeeldellpeleeekaeleeeleklqe..aaeelesid.keeLeelreelaelkaeieekkkela 223
                                   + le+ ++++++L+++   +++ +++l++e +e e+e ++ +   +  +++ ++ ++e+++l+e+lae++  i+ k ++++
  gi|13541638|ref|NP_111326.1| 338 KSLESERRERDKLQEEFIAAEDEYNKLVAEAQEKEKENATSRVktKDYQVKISKlNDEINSLKEKLAEINMAIKGKIDRIT 418
                                   444444455555555555555555555555555444444333311333333345578888888888888888888888888 PP

                          Spc7 224 elqeqleeleekiee 238
                                   el+e++e++  k+++
  gi|13541638|ref|NP_111326.1| 419 ELEERMEDIGLKVKA 433
                                   888888887777665 PP

  == domain 4  score: 10.8 bits;  conditional E-value: 0.00015
                          Spc7 157 lLekqeeeldellpeleeekaeleeeleklqeaaeeles......idkeeLeelreelaelkaeieekkkelaelqeqlee 231
                                   +++k ++e+++l+++l e   +++ +++++ e +e +e+       d+ +L +  e+l++    + ++k e++e qe++ +
  gi|13541638|ref|NP_111326.1| 388 KISKLNDEINSLKEKLAEINMAIKGKIDRITELEERMEDiglkvkADEWKLSQNAEDLSKYRDRYYKLKSEYDEIQEKISK 468
                                   577788888888888888888888888888888888888555544556666666666666666666666666666666666 PP

                          Spc7 232 leekieelke.qkseleeeiaeaervleeckgw 263
                                   l+++i+++++  ++++  +i +a +v e +k++
  gi|13541638|ref|NP_111326.1| 469 LSSQISAAEAtARASVPRQIDRASQVEEIKKNI 501
                                   666666665413556666777777777766665 PP

  == domain 5  score: 9.7 bits;  conditional E-value: 0.00032
                          Spc7 146 enlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelq 226
                                   e l++++++ + L+++++++++ l+e  +  ++ +++  +++++     +i +++L++ ++ l+++ +e++++k+e+ae +
  gi|13541638|ref|NP_111326.1| 656 EDLDSMKKELAFLQSEKAKIKKELDEALQSMSDASKKTGEIEKE----RQIINDDLAKNKQILKDIASELSKLKQEIAENK 732
                                   56677777777777777777666666666666666666665553....457788999999999999999999999999999 PP

                          Spc7 227 eqleeleekieelkeqkseleeeia 251
                                   e++e+le++i++ +   ++++e+++
  gi|13541638|ref|NP_111326.1| 733 EEKEALEKDISDRQLDLHKYQEALN 757
                                   9999999999999999999998876 PP

  == domain 6  score: 10.0 bits;  conditional E-value: 0.00025
                          Spc7 145 eenlegleedkelLekqeeeldellpeleeeka...eleeeleklqeaaeeles..id.keeLeelreelaelkaeieekk 219
                                   +++++++e+  ++Le+ +++++++  ++e +++    l +e +++ +++ ele      ++e++++  + ++ ++e+++++
  gi|13541638|ref|NP_111326.1| 765 QSIIDTIENSMRKLEDYRKKISAITADIEVKEKrvsFLDKESNNIVQQNIELEIqrKAvEDEIHNIEIQKRSMEEELKKHE 845
                                   5678889999999999999999999988766662235789999988866666543333499******************** PP

                          Spc7 220 kelaelqeqleeleekieelkeqkseleeeiaeaervleeckgw 263
                                     l++l++   ++++ki++++++++e++++i+e ++ +e ++++
  gi|13541638|ref|NP_111326.1| 846 LFLKQLESSHSDIASKIKDMENEMKEIRSKIEEINSDVEIKRSI 889
                                   ***************************************99986 PP

  == domain 7  score: -0.3 bits;  conditional E-value: 0.34
                          Spc7 154 dkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelree.laelkaeiee 217
                                   d + L + ++ + + ++e ++ ++el+++ ++l+ ++++l++++  +L++ ++e +++  ++i+e
  gi|13541638|ref|NP_111326.1| 934 DISALGDINNGAIQEYEESVKAYNELKDKKNRLELERRSLQDLTD-SLNKKKKEvFVSTFEKINE 997
                                   555555555555555666666666666666666666666655543.3333333313444455554 PP

>> DUF1043  Protein of unknown function (DUF1043)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   4.5    0.0024       2.6      27      99 ..     224     326 ..     210     395 .. 0.78
   2 ?   -0.3   1.1      0.89     1e+03      59      79 ..     453     473 ..     376     501 .. 0.56
   3 ?   13.1   3.2   6.6e-05     0.074      30      77 ..     686     733 ..     667     735 .. 0.84
   4 ?    3.6   1.5     0.058        65      24      74 ..     733     784 ..     730     813 .. 0.80
   5 ?    1.7   4.1      0.22   2.5e+02      24      80 ..     811     879 ..     800     917 .. 0.69
   6 ?   -0.1   0.1       0.8     9e+02      24      49 ..     950     975 ..     945    1036 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0024
                       DUF1043  27 kklekelekakaeleeqkqeledHfaqsaelLetlaedyqkLyqhlaksseeL............................ 79 
                                   +k ++  +++ +++++q + +e+ +++s+ l+++l+ +y+ + q l++++++L                            
  gi|13541638|ref|NP_111326.1| 224 SKAKEANDRSIQAIDRQVDSIEKEIEKSKVLISDLNLRYHSIEQLLSEETKKLndltsgeirtvqeklrsleisiasldsk 304
                                   677888889999*****************************************9999998888888888887777666666 PP

                       DUF1043  80 .......lpeleeqelfqqkkleekka 99 
                                          +     q++++q+ +  +++
  gi|13541638|ref|NP_111326.1| 305 isekklrM-----QDMAKQEAIDDARR 326
                                   54333332.....33333333333333 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.89
                       DUF1043  59 etlaedyqkLyqhlaksseeL 79 
                                    +l+++y++++++++k s+++
  gi|13541638|ref|NP_111326.1| 453 YKLKSEYDEIQEKISKLSSQI 473
                                   233444444444444444444 PP

  == domain 3  score: 13.1 bits;  conditional E-value: 6.6e-05
                       DUF1043  30 ekelekakaeleeqkqeledHfaqsaelLetlaedyqkLyqhlaksse 77 
                                     +  k++ e+e+ +q ++d +a+++++L+++a++ +kL+q +a+++e
  gi|13541638|ref|NP_111326.1| 686 MSDASKKTGEIEKERQIINDDLAKNKQILKDIASELSKLKQEIAENKE 733
                                   4456677889**********************************9987 PP

  == domain 4  score: 3.6 bits;  conditional E-value: 0.058
                       DUF1043  24 kkqkklekelekakaeleeqkqeledHfaqs.aelLetlaedyqkLyqhlak 74 
                                   ++++ lek++ + +  l+++++ l+d  +   +++++t++++++kL ++ +k
  gi|13541638|ref|NP_111326.1| 733 EEKEALEKDISDRQLDLHKYQEALNDIYDDLgQSIIDTIENSMRKLEDYRKK 784
                                   57889*********************9988615689*********9877555 PP

  == domain 5  score: 1.7 bits;  conditional E-value: 0.22
                       DUF1043  24 kkqkklekelekakae...leeqkqeledHfaqsaelLetlaedyqkLyqhlaksseeL.........l 80 
                                   +++ +le + ++ ++e   +e qk+ +e+ +++    L++l+++ +++ ++++  ++e+         +
  gi|13541638|ref|NP_111326.1| 811 QQNIELEIQRKAVEDEihnIEIQKRSMEEELKKHELFLKQLESSHSDIASKIKDMENEMkeirskieeI 879
                                   555556555555554411167899999999*999999*****999999999999999985544443330 PP

  == domain 6  score: -0.1 bits;  conditional E-value: 0.8
                       DUF1043  24 kkqkklekelekakaeleeqkqeled 49 
                                   +++ k  +el+++k++le  ++ l+d
  gi|13541638|ref|NP_111326.1| 950 EESVKAYNELKDKKNRLELERRSLQD 975
                                   56667777888888888777776665 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   4.9       1.4   1.6e+03      26     148 ..     152     278 ..     149     283 .. 0.60
   2 ?   12.9  14.2   8.9e-05     0.099     100     183 ..     287     370 ..     283     370 .. 0.97
   3 ?    6.3   4.1     0.009        10     107     175 ..     371     439 ..     369     444 .. 0.80
   4 ?    3.2   1.5     0.082        92      71     135 ..     440     504 ..     432     511 .. 0.71
   5 ?    5.7  16.0     0.014        15      71     175 ..     653     757 ..     635     765 .. 0.62
   6 ?    3.4   7.1     0.068        76     104     177 ..     771     844 ..     765     846 .. 0.94
   7 ?    6.2   6.0    0.0095        11      77     140 ..     835     898 ..     833     914 .. 0.76
   8 ?    6.3   0.2     0.009        10      15      50 ..     947     982 ..     935    1000 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1.4
                         ATG16  26 rLldrtsaleaenaklekaaasaks........sksskksakekeasasqsnskqsakiqsleqklaqlreelaelyksrg 98 
                                   +L++r++  e+   +leka ++ ++        s s+   + ++ ++ +  +++++++   l+++l  +r   +el k+++
  gi|13541638|ref|NP_111326.1| 152 KLIERIAGTEQFDVELEKARNDIEEvgknldilS-SMIDIKGQEVEKLRI-EKEKKERYDILSKRLRDIR--FTELSKAKE 228
                                   5666666666666666666666666655554421.111222222222222.3334444444444444444..688888888 PP

                         ATG16  99 elaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelre 148
                                    +  ++++   +++  e+++++ +  + +l+ +  ++e+ l++ +++l++
  gi|13541638|ref|NP_111326.1| 229 ANDRSIQAIDRQVDSIEKEIEKSKVLISDLNLRYHSIEQLLSEETKKLND 278
                                   88888888888888888888888888888888777777777777766655 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 8.9e-05
                         ATG16 100 laqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekeklvqdlqDElsaLqlqlnqaEeklrklekE 180
                                    +++l++l+ +++ l++k++e++ r++++ ++ a    ++++ e+e +e +k ++  + E + Lq ++  aE++++kl +E
  gi|13541638|ref|NP_111326.1| 287 VQEKLRSLEISIASLDSKISEKKLRMQDMAKQEAIDDARREKYEAEAEEIRKSLESERRERDKLQEEFIAAEDEYNKLVAE 367
                                   6899***************************************************************************** PP

                         ATG16 181 Nke 183
                                   ++e
  gi|13541638|ref|NP_111326.1| 368 AQE 370
                                   986 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.009
                         ATG16 107 lneelqkleeklkedeerlaeleaeraaletklkdreeelrekeklvqdlqDElsaLqlqlnqaEeklr 175
                                   +++e ++ + k+k  + ++ +l++e+++l++kl++ ++++++k   + +l + ++   l+++  E kl 
  gi|13541638|ref|NP_111326.1| 371 KEKENATSRVKTKDYQVKISKLNDEINSLKEKLAEINMAIKGKIDRITELEERMEDIGLKVKADEWKLS 439
                                   678888888999999999999999999999999999999999998888888888887777777776665 PP

  == domain 4  score: 3.2 bits;  conditional E-value: 0.082
                         ATG16  71 kqsakiqsleqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraal 135
                                   ++++++++  ++ ++l++e  e + + ++l++++ +++++ ++   +   ++++++e++++++ +
  gi|13541638|ref|NP_111326.1| 440 QNAEDLSKYRDRYYKLKSEYDEIQEKISKLSSQISAAEATARASVPRQIDRASQVEEIKKNISGV 504
                                   45566777777778888888888888888888888888888887777777777777777766655 PP

  == domain 5  score: 5.7 bits;  conditional E-value: 0.014
                         ATG16  71 kqsakiqsleqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekek 151
                                   + s+++ s++++la l++e a+  k+  e  q+  +++++  + e++ +  +  la+ ++  +++  +l+++++e++e ++
  gi|13541638|ref|NP_111326.1| 653 SPSEDLDSMKKELAFLQSEKAKIKKELDEALQSMSDASKKTGEIEKERQIINDDLAKNKQILKDIASELSKLKQEIAENKE 733
                                   234566666666666666666666666666666666666666666666666666666666666666666666666666666 PP

                         ATG16 152 lvqdlqDElsaLqlqlnqaEeklr 175
                                     ++l  ++s  ql l +  e+l+
  gi|13541638|ref|NP_111326.1| 734 EKEALEKDISDRQLDLHKYQEALN 757
                                   666666666666666666666555 PP

  == domain 6  score: 3.4 bits;  conditional E-value: 0.068
                         ATG16 104 llelneelqkleeklkedeerlaeleaeraaletklkdreeelrekeklvqdlqDElsaLqlqlnqaEeklrkl 177
                                   + + + +l++ ++k+++ ++ ++  e++++ l ++ ++  ++  e+e   +++ DE+   ++q  ++Ee+l+k 
  gi|13541638|ref|NP_111326.1| 771 IENSMRKLEDYRKKISAITADIEVKEKRVSFLDKESNNIVQQNIELEIQRKAVEDEIHNIEIQKRSMEEELKKH 844
                                   6778899****************************************************************986 PP

  == domain 7  score: 6.2 bits;  conditional E-value: 0.0095
                         ATG16  77 qsleqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklk 140
                                    s+e++l+++   l++l  s+++ a++++++++e+++ ++k++e ++ ++  ++  ++l+ k++
  gi|13541638|ref|NP_111326.1| 835 RSMEEELKKHELFLKQLESSHSDIASKIKDMENEMKEIRSKIEEINSDVEIKRSILSELKVKRS 898
                                   6789999999999999999999999999999999999999998888888777777776666654 PP

  == domain 8  score: 6.3 bits;  conditional E-value: 0.009
                         ATG16  15 kafaeliqaynrLldrtsaleaenaklekaaasaks 50 
                                   + ++e ++ayn+L d+ + le e+++l+  + s ++
  gi|13541638|ref|NP_111326.1| 947 QEYEESVKAYNELKDKKNRLELERRSLQDLTDSLNK 982
                                   567889999999999999999999999665544443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2876  (0.160411); expected 358.6 (0.02)
Passed bias filter:                      571  (0.0318478); expected 358.6 (0.02)
Passed Vit filter:                       182  (0.0101512); expected 17.9 (0.001)
Passed Fwd filter:                       124  (0.00691617); 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: 3.21u 0.45s 00:00:03.66 Elapsed: 00:00:00.81
# Mc/sec: 4249.84
//
Query:       gi|13541639|ref|NP_111327.1|  [L=250]
Description: hypothetical protein TVN0808 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
     0.0037   16.5   0.0     0.0087   15.3   0.0    1.7  1  Rad21_Rec8  Conserved region of Rad21 / Rec8 like protein
  ------ inclusion threshold ------
       0.11   12.7   0.0       0.17   12.0   0.0    1.3  1  DUF3333     Domain of unknown function (DUF3333)


Domain annotation for each model (and alignments):
>> Rad21_Rec8  Conserved region of Rad21 / Rec8 like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   9.7e-07    0.0087       3      50 ..     200     246 ..     198     249 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 9.7e-07
                                   HHHTT----------HHHHHHHHHHHHHHHHTSEEEEESSTT--EEEE CS
                    Rad21_Rec8   3 kekdslsllpagktRkeAArlFyelLvLatkgvIkvkQeaPYgdIlit 50 
                                   k+k++ s++  g+tR+e A  F     L   g I+++Qe+P gdIli 
  gi|13541639|ref|NP_111327.1| 200 KQKVFMSEIW-GNTRRERAVFFLYSMFLFRDGRISLSQEEPNGDILIE 246
                                   7889988886.5666666667778899*******************97 PP

>> DUF3333  Domain of unknown function (DUF3333)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   1.9e-05      0.17      32      93 ..     150     209 ..     145     225 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.9e-05
                       DUF3333  32 LlvsIvskGltA.Ftqteitleveldaeeidpkgkaeeskklatanyeklirdalkaklp.eve 93 
                                   L+ +I +k +++ ++++++ + +e+d ++++p+     s+++ +  y+++i++  ++ +  e+ 
  gi|13541639|ref|NP_111327.1| 150 LIDEIRRKMYSSrLQKKKVDVHIEFDSSKLNPDR----SEEMIEKTYRAIIESGKQKVFMsEIW 209
                                   555666666665367889***************9....6899**********999988875444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       592  (0.0330191); expected 358.6 (0.02)
Passed bias filter:                      478  (0.0266607); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 1693.12
//
Query:       gi|13541640|ref|NP_111328.1|  [L=197]
Description: hypothetical protein TVN0809 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-18   67.5  12.0    1.3e-18   67.2  12.0    1.0  1  DUF998    Protein of unknown function (DUF998)
  ------ inclusion threshold ------
       0.02   15.1   1.1       0.02   15.1   1.1    2.9  3  DUF3784   Domain of unknown function (DUF3784)


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 !   67.2  12.0   1.5e-22   1.3e-18       1     184 [.      15     187 ..      15     188 .. 0.85

  Alignments for each domain:
  == domain 1  score: 67.2 bits;  conditional E-value: 1.5e-22
                        DUF998   1 vaaallalavilaaallrpgydplrhaiSeLgaeggpggwlfnaglvllgllvlalavgllraargragragrlllavagl 81 
                                   ++++++a++++ +++++ p + + ++a+S+Lg    p g+lfn g ++ g+l ++++ +l    +  +++  ++ll+++g+
  gi|13541640|ref|NP_111328.1|  15 IVGPIFAISLVFIDVAVSPWFTWQHNALSDLGV--HPYGYLFNLGIIVEGFLNVLFVMAL---FEIGLKKRIGALLIISGI 90 
                                   4677777777*******9999************..***********************99...567788888888899*** PP

                        DUF998  82 glvlagvfptdpgggspslsglvHglasavaflalavavllla..saarrrawallrlvggvallllvaalvwllaaaldg 160
                                   +l+l+gvf++d  +         H +++++ fl++++++++++  + +      +  l+++++l+ +++++++++  +  +
  gi|13541640|ref|NP_111328.1|  91 ALALVGVFNEDHPP--------YHLIFALIYFLLFPIGIIVASipRLFPFYVKLYSMLASILSLIDIFIGIGFVFKFISIK 163
                                   ***********997........*********************544444444444455555555556677777777799** PP

                        DUF998 161 slllGlaerllvlaitawllalal 184
                                   + +l ++e++ +l+   w +++++
  gi|13541640|ref|NP_111328.1| 164 NVGLSIPEIIEALLLGSWSVLVSV 187
                                   ********************9987 PP

>> DUF3784  Domain of unknown function (DUF3784)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.3      0.49   4.4e+03      56      59 ..      19      22 ..       4      37 .. 0.47
   2 ?   15.1   1.1   2.3e-06      0.02      40      89 ..      75     124 ..      71     128 .. 0.83
   3 ?    0.5   2.6      0.08   7.2e+02      41      89 ..     135     188 ..     133     192 .. 0.55

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.49
                       DUF3784 56 lfll 59
                                  +f++
  gi|13541640|ref|NP_111328.1| 19 IFAI 22
                                  1111 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 2.3e-06
                       DUF3784  40 kklsrfmgivllligilflllgllsaiesealliialiviiiiviylivy 89 
                                    +l +++g +l++ gi+++l g+++  +  + li+ali ++++ i++iv 
  gi|13541640|ref|NP_111328.1|  75 IGLKKRIGALLIISGIALALVGVFNEDHPPYHLIFALIYFLLFPIGIIVA 124
                                   5899********************88888888888888777777777765 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.08
                       DUF3784  41 klsrfmgivllligilflllgll......saiesealliialiviiiiviylivy 89 
                                   kl+ +   +l li  +f+ +g++      ++++ +   ii  +++  +++++ vy
  gi|13541640|ref|NP_111328.1| 135 KLYSMLASILSLID-IFIGIGFVfkfisiKNVGLSIPEIIEALLLGSWSVLVSVY 188
                                   56666777777777.5555555545444544445555555555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       719  (0.0401026); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.33s 00:00:00.90 Elapsed: 00:00:00.55
# Mc/sec: 1070.50
//
Query:       gi|13541641|ref|NP_111329.1|  [L=429]
Description: major facilitator superfamily permease [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-31  108.7  30.7    2.4e-19   69.5  14.0    2.0  2  Sugar_tr  Sugar (and other) transporter
    8.2e-26   90.7  49.7    2.1e-15   56.5  26.6    2.1  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 !   69.5  14.0   2.7e-23   2.4e-19       5     204 ..      19     223 ..      16     243 .. 0.91
   2 !   45.7   8.5   4.5e-16     4e-12     273     446 ..     258     423 ..     223     428 .. 0.76

  Alignments for each domain:
  == domain 1  score: 69.5 bits;  conditional E-value: 2.7e-23
                                   HHHHH.HHHHHHHHCGGGTHHHHHHHHTSTT--SHHHHHH...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHH CS
                      Sugar_tr   5 aalgg.llfgYdtgvigafltllkfaknfglsksksskeessvlsglivsiflvGaiiGslfagllgdrfGRkkslliaav 84 
                                   a++ g ++++Y +++ ++ +  ++ a+  ++sks++       l+ l++++ +v + +G++++g  gdr+GRk+ lli+ +
  gi|13541641|ref|NP_111329.1|  19 ASMIGtIIEWYGIFIFSSGAIYIADAFYPTVSKSVGIL-----LTLLTFALGFVTRPVGAFVFGHYGDRLGRKNMLLITLL 94 
                                   55555599**********99999988888888888744.....679*********************************** PP

                                   HHHHHHHHHH-TTTT.....SS-TGGGGGHHHHHHHHHHHHHHHHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Sugar_tr  85 lfvigavlqaaakgk.....nsvevlivgRvlvGigvGlasvlvPmyisEiApkklRgalvslyqlaitfGilvaaifglg 160
                                   ++ i++ l+++++++     +++ +l+v R+++G+g+G++ + + +++ E+  k++Rg+  s+ q+ + +G +++ +  l+
  gi|13541641|ref|NP_111329.1|  95 ISGISTGLTGVIPDYvsigiWAIILLVVLRLILGFGLGGERGGAMLLTLENF-KSKRGFWASFVQSTVGIGLILGVVAFLV 174
                                   *************99**999******************************95.789*******************999998 PP

                                   HHTSS-.....TTHHHHHHHCCHHHHHHHHHHGGGS---HHHHHHTT-H CS
                      Sugar_tr 161 lnktsn.....adgwrillglqlvpallllilllflPESPrylvekgke 204
                                   l+         + gwri++ l++v+ ++ l++++ + E+P +   k+++
  gi|13541641|ref|NP_111329.1| 175 LEFLLPssamySYGWRIPFLLSFVIVVIGLLIRYRIKETPIFEAAKREK 223
                                   876666677999******************************9888765 PP

  == domain 2  score: 45.7 bits;  conditional E-value: 4.5e-16
                                   HHHHTTTHHHHSS-THH...HHHHHHHHHHHHHHHHHHHHHHHHS-SHHHHHHHHHHHHHHHHHHH..HHHHTTSS...CH CS
                      Sugar_tr 273 imyysptifenlglsks...llvtiivgvvnfvatfvaiflvdrfGRRtllllGaagmaicfvilgivalllvakskaasi 350
                                    + + p+ife++ + +    l++t+i+ v  ++++fv+  ++dr GRR++ll+  a++++++       + lv+      i
  gi|13541641|ref|NP_111329.1| 258 AIGLLPVIFESTKVITIdegLVATFIFAVADIIFVFVGGIVSDRYGRRPILLMANAIALVLLYPA----IYLVSP-----I 329
                                   44567999999988776678*******************************99877766655444....344444.....4 PP

                                   HHHHHHHHHHHHHHTTTTHHHHHHHHHHSHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHT-HHHHHHHHHHHHHHH CS
                      Sugar_tr 351 vaivfialfialfalgwgpvpwvlvsElfpqsvRskalaiavavnwlanflisllfpiiteaigggyvflvfaglavlfii 431
                                    + + +alf  +++l+  p+ +++ sE+fp++vR+++ +++++   + n +i+   p++ + +g  +++ ++ ++ ++fii
  gi|13541641|ref|NP_111329.1| 330 EFSAILALFGLAHGLSYSPLGALI-SEIFPTNVRYSGNSMSYQ---FGNAFIGGPAPYASDLLG-SVFYPLYPVFTLIFII 405
                                   56778899999*********9655.*************99887...56889*************.6666666666666666 PP

                                   H...HHHHS--STT--CC CS
                      Sugar_tr 432 f...vfffvpetkgrtle 446
                                   +   v ++  etk+ +le
  gi|13541641|ref|NP_111329.1| 406 IafgVIVKSKETKNNSLE 423
                                   611155667788888887 PP

>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.5  26.6   2.4e-19   2.1e-15       3     232 ..      22     264 ..      20     272 .. 0.73
   2 !   40.0  15.2   2.5e-14   2.2e-10      37     172 ..     280     410 ..     272     426 .. 0.76

  Alignments for each domain:
  == domain 1  score: 56.5 bits;  conditional E-value: 2.4e-19
                         MFS_1   3 laaflsalarsilgpalplalaedlgispse.igllltl..yalga...avaslplGrlsdrfGrrrvlllglllfalg.l 76 
                                   +++++  ++++i+++ +  ++a+++  ++s  +g+lltl  +alg+    v+++++G+ +dr+Gr+ +ll++ll+++++ +
  gi|13541641|ref|NP_111329.1|  22 IGTIIEWYGIFIFSSGAI-YIADAFYPTVSKsVGILLTLltFALGFvtrPVGAFVFGHYGDRLGRKNMLLITLLISGIStG 101
                                   677788888888888887.8999988666656777777766666555569*****************************44 PP

                         MFS_1  77 llllfa....sslw.l..llvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllgg........ 142
                                   l ++++    +++w +  l+vlr++ G+g g+   +++ l+ + f+  +rg+  +++++++++G ilg ++          
  gi|13541641|ref|NP_111329.1| 102 LTGVIPdyvsIGIWaIilLVVLRLILGFGLGGERGGAMLLTLENFKS-KRGFWASFVQSTVGIGLILGVVAFLvlefllps 181
                                   444442444677775577****************************9.********************8877767766666 PP

                         MFS_1 143 .llasslgWravfyilaivsllafvlfllllpeepperkrkspkeeekgtgpaplvp....awkallkdpvlwillialll 218
                                    +++ s+gWr +f++  ++ ++++++   +   e p  +  + +++     + p+++     wk++ +      +l+++ +
  gi|13541641|ref|NP_111329.1| 182 sAMY-SYGWRIPFLLSFVIVVIGLLI--RYRIKETPIFEAAKREKQ---ISGLPAKQlfkrNWKEVIAGT----ILAGSSG 252
                                   5555.777***************774..555333333333333333...334444441223455555555....7777777 PP

                         MFS_1 219 fffgfsglltllpl 232
                                   +f  f+++  llp+
  gi|13541641|ref|NP_111329.1| 253 NF--FYFAIGLLPV 264
                                   74..4445555554 PP

  == domain 2  score: 40.0 bits;  conditional E-value: 2.5e-14
                         MFS_1  37 lltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll..fasslwlllvlrvlqGlgagalfpagaaliadwfp 115
                                   ++ ++a++ +++++++G +sdr+Grr++ll++ ++ ++  l+++  ++s++  + +  +l Gl+ g++++  +ali+++fp
  gi|13541641|ref|NP_111329.1| 280 ATFIFAVADIIFVFVGGIVSDRYGRRPILLMANAIALVL-LYPAiyLVSPI-EFSAILALFGLAHGLSYSPLGALISEIFP 358
                                   345599999******************999999999999.77775334444.5**************************** PP

                         MFS_1 116 keergraigllsagfslGailgpllggllasslg......Wravfyilaivsllafvlfllll 172
                                       +  ++  s+++++G ++  + +++ +++lg      +        +v+ l f+++++ +
  gi|13541641|ref|NP_111329.1| 359 T---NVRYSGNSMSYQFGNAFIGGPAPYASDLLGsvfyplY--------PVFTLIFIIIAFGV 410
                                   9...777888899******9999999999999996654432........33333323222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (429 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       698  (0.0389313); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.68u 0.34s 00:00:01.02 Elapsed: 00:00:00.53
# Mc/sec: 2456.88
//
Query:       gi|13541642|ref|NP_111330.1|  [L=533]
Description: N-methylhydaintoinase B [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   1.3e-165  551.8   0.0   1.4e-165  551.6   0.0    1.0  1  Hydantoinase_B  Hydantoinase B/oxoprolinase


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 !  551.6   0.0  7.9e-170  1.4e-165       5     516 .]       4     518 ..       1     518 [. 0.96

  Alignments for each domain:
  == domain 1  score: 551.6 bits;  conditional E-value: 7.9e-170
                Hydantoinase_B   5 levfrnrlmsiaeemgrtlqrtaiSpnikerlDfscalfdadgelvaqaphipvhlgsmseavkavlekfeg.e..lkpGD 82 
                                    e+++++ + +aeemg++l+r+aiSpni+er+D sca++d+dg++vaqa+hipvhlgs+   +++++  +++ +  l++GD
  gi|13541642|ref|NP_111330.1|   4 SEIISKATQYVAEEMGAALKRSAISPNIRERMDHSCAVLDSDGRIVAQAEHIPVHLGSFRVGARNIMSWLQAhNliLEDGD 84 
                                   69***************************************************************9954433334599*** PP

                Hydantoinase_B  83 vlltNdPyaggtHlpDitvitPvfhegelvffvasraHhaDiGGitpGsmppdateifeEGlrippvklveegeleedvle 163
                                   +l+tNdPy  gtHl+D+t+++Pv++eg+l+++v ++aH +D+GG + Gs++p+a+++f+EGl+ippv+l ++g l+ dv++
  gi|13541642|ref|NP_111330.1|  85 MLITNDPYISGTHLNDVTLMAPVYYEGKLLAYVINKAHNVDVGGPVFGSLNPHAKNLFQEGLIIPPVRLLKKGILDPDVFS 165
                                   ********************************************************************************* PP

                Hydantoinase_B 164 lllanvRtpednlgDlkAqiaanqvgerrlkelieeyGldtveaamdeildnaeravraalaelpdgtyeaedylddg... 241
                                   ++++n + p+   gD++Aqiaan++g++r++e++e++G +     ++++++ ++  +  a++ +++g++  edyl+++   
  gi|13541642|ref|NP_111330.1| 166 FIVNNFKDPDTANGDINAQIAANKRGISRVREIFERFGPEDTISSWNQLIKGSRDIAIFAISGWKKGKFYSEDYLETDygt 246
                                   ***************************************************************************764346 PP

                Hydantoinase_B 242 ipikvtvtidgdeatvDftgtspqvkgniNaplavtlsaviyvlrclvdediplNeGclrpievklpegsllnpsepaavv 322
                                     ik +++++++ + vDf+gtspq++ +iNa++ vt sa+ +++r+ +d d+p+NeG++++i+v++ +gsllnp++p +v+
  gi|13541642|ref|NP_111330.1| 247 AVIKAALEVKNNGILVDFSGTSPQLEYPINAVPGVTFSATAFAIRSALDIDVPTNEGFYSMIDVRADQGSLLNPDRPHPVS 327
                                   6999999999*********************************************************************** PP

                Hydantoinase_B 323 ggnvetsqrvvdvvlkalaqalpervaAasqgtmnnltfggvderggeffgyyetiagGaGArpgkdGasavhvhmtntrn 403
                                   ggnvet+qr++dvvl al++++p  +++as+gtm n+++gg +  +g++++yyeti+gG GA++ + G+s+vh++mtnt n
  gi|13541642|ref|NP_111330.1| 328 GGNVETTQRIADVVLHALSDCIPGAIPSASSGTMFNIMLGGDRG-NGTYWTYYETIGGGNGASRIRPGVSGVHSNMTNTLN 407
                                   ****************************************8765.58899******************************* PP

                Hydantoinase_B 404 tdvEilErryPvlverfelrpdsgGaGkyrGGdGvvreieflepevtvsilserrvfapwGlaGGepGargrvvlnllvrg 484
                                   t++E+ Er+yP+ ++++ lr++sgG+G ++GGdG++r++++l+p  t+s++++r +++p+ l+GG+ G++g++++     g
  gi|13541642|ref|NP_111330.1| 408 TPIEVAEREYPLFFTSYTLRRGSGGKGLMKGGDGIIRSFRVLKP-STLSVIADRFKIPPYALMGGGTGKTGALFI-VHSDG 486
                                   *******************************************9.***************************775.22338 PP

                Hydantoinase_B 485 eeenlggkatvelkagdvlvietpGGGGyGdp 516
                                   ++++ ++k+ vel+++d ++ +tpGG GyG p
  gi|13541642|ref|NP_111330.1| 487 KRVKCPSKCIVELNENDEVIAMTPGGSGYGAP 518
                                   99999*************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (533 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); 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: 0.65u 0.31s 00:00:00.96 Elapsed: 00:00:00.50
# Mc/sec: 3230.25
//
Query:       gi|13541643|ref|NP_111331.1|  [L=656]
Description: N-methylhydaintoinase A [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-94  316.9   1.1      1e-91  307.2   0.2    2.2  2  Hydantoinase_A  Hydantoinase/oxoprolinase
    1.9e-47  161.3   0.0    3.9e-47  160.3   0.0    1.6  1  Hydant_A_N      Hydantoinase/oxoprolinase N-terminal region
  ------ inclusion threshold ------
      0.024   15.0   0.0      0.058   13.8   0.0    1.7  1  FtsA            Cell division protein FtsA
      0.024   13.2   1.3        6.9    5.1   0.1    2.9  3  MutL            MutL protein
      0.094   12.9   0.2        3.9    7.6   0.0    2.3  2  Cass2           Integron-associated effector binding 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 !    8.4   0.0   0.00031       1.1      81     105 ..       6      30 ..       2      51 .. 0.87
   2 !  307.2   0.2   2.8e-95     1e-91       1     289 [.     199     489 ..     199     491 .. 0.98

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00031
                Hydantoinase_A  81 vItfDmGGTstDvslikdgevevsl 105
                                    I +D+GGT tDv ++++ ++e ++
  gi|13541643|ref|NP_111331.1|   6 SISVDIGGTFTDVVVMRNSKIEKVF 30 
                                   599**************99998655 PP

  == domain 2  score: 307.2 bits;  conditional E-value: 2.8e-95
                Hydantoinase_A   1 rtetavvnAylspilreylesvekslekrgakarlmvmqsdGglvsadearkkpvetilSGPaaGvvgaaatsklagekkv 81 
                                   rt t+vvnA+l p+++eyl+++e+sl ++  k+ + vm+s Gglvs++ea+ kpv +i+SGPaaGv++a++++++ + +++
  gi|13541643|ref|NP_111331.1| 199 RTATTVVNAALVPVVSEYLRKLEASLYEK-YKPSMSVMSSAGGLVSFSEAKSKPVSIIESGPAAGVIAANEFARQIKISNI 278
                                   899*************************5.78************************************************* PP

                Hydantoinase_A  82 ItfDmGGTstDvslikdgevevsletei............agvkvrlpaldirtvgagGgsilvvdeggklrvgpesagad 150
                                   + fDmGGT++++ ++  ++ve+++e e+            +g+++r+p++d+++v+agGg+i+++d++g++++gp sag+d
  gi|13541643|ref|NP_111331.1| 279 LSFDMGGTTAKAGTVLGNNVEITSEFEVggtshhgrivkgSGYPIRFPFVDLAEVSAGGGTIVWKDKSGAINIGPMSAGSD 359
                                   ********************************************************************************* PP

                Hydantoinase_A 151 pgpacyrkGgteltvTDanlvLGrlqpedflsgpdgdqkldvelarrafeelakelnlkveevAegilsvavenmanavrk 231
                                   pgp++y++Gg e+t+TDanl+LG ++++ ++   + d kl+++la +a+++l++++     evA ++l++a  +ma+a+r 
  gi|13541643|ref|NP_111331.1| 360 PGPVSYDRGGREPTITDANLILGIINEK-MS---GSDFKLRKDLAIEAMSKLGEPY-----EVASKALKLADLEMARAIRL 431
                                   ***************************9.88...88******************99.....******************** PP

                Hydantoinase_A 232 lsvergldpkeltlvvfGGaGaqhaaalaeelgvkkvivppyagvlsalGmalAdvre 289
                                   ++vergldp+ ++l++fGGaG+qhaa++a e+++k+vi+pp +gv+salG++++d++ 
  gi|13541643|ref|NP_111331.1| 432 VTVERGLDPESFVLMGFGGAGPQHAARVASEVNIKRVIIPPNPGVFSALGLLFSDWKY 489
                                   *****************************************************99876 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 !  160.3   0.0   1.1e-50   3.9e-47       2     176 ..       7     179 ..       6     181 .. 0.96

  Alignments for each domain:
  == domain 1  score: 160.3 bits;  conditional E-value: 1.1e-50
                    Hydant_A_N   2 igIDvGGTfTDavaldekeeevavlKllstpdavaegirealeevleesiprtskidvvrmGTTvatNallerkg...erv 79 
                                   i +D+GGTfTD+v++++  +  +v+K+++tp++++ g+++ +e +      + ++++  +++TT+atN ll + g   +++
  gi|13541643|ref|NP_111331.1|   7 ISVDIGGTFTDVVVMRNS-KIEKVFKVPTTPRNPEIGVLNGIEIA------KLTELNEFVHATTIATNSLLGQYGlnlPKI 80 
                                   78**************66.99**********************98......3789************************** PP

                    Hydant_A_N  80 aLittkgfrdlleigrqnrpdlfelrik..kplvlyeevvevderveadgevlkpldeeevrealkalkaagvesiavvll 158
                                   aLittkgf+d++eigrqnrp l++l+++  k lv +++++e+der+++dge++kp+d+ + ++ +  + +++ +s+av++l
  gi|13541643|ref|NP_111331.1|  81 ALITTKGFKDIIEIGRQNRPSLYDLNFVrpKALVSRNMRFEIDERTNVDGEIIKPVDQVSAKKLADLIEKKKPQSVAVSFL 161
                                   **************************998888999********************************************** PP

                    Hydant_A_N 159 hSylnpehElrvaeiare 176
                                   hSy+n+++E+++ e++++
  gi|13541643|ref|NP_111331.1| 162 HSYINDNNERQILELFKD 179
                                   ************998875 PP

>> FtsA  Cell division protein FtsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   1.6e-05     0.058       2      60 ..       8      78 ..       7     217 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.6e-05
                                  EEEE-SSSEEEEEEETTEEEEEEEES-....-HHHHHHHHHHHHT--HHH...HHHHHH.....HH--S-- CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxx...xxxxxx.....xxxxxxx RF
                          FtsA  2 lvDiGagktdvavaedgalvhlrvigv....ggngitkdiakalrtavee...Aeriki.....kyGsala 60
                                   vDiG++ tdv+v++++++ ++  +++    +  g+ ++i++a  t ++e   A  i++     +yG  l+
  gi|13541643|ref|NP_111331.1|  8 SVDIGGTFTDVVVMRNSKIEKVFKVPTtprnPEIGVLNGIEIAKLTELNEfvhATTIATnsllgQYGLNLP 78
                                  69******************988888888888888989877776655544222555554444444555555 PP

>> MutL  MutL protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0    0.0027       9.7       3      37 ..       8      38 ..       6      74 .. 0.59
   2 ?    0.6   0.0     0.047   1.7e+02      30      72 ..     199     241 ..     186     245 .. 0.85
   3 ?    5.1   0.1    0.0019       6.9     224     273 ..     255     302 ..     242     319 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0027
                          MutL  3 viDiGSttTkvtlvdlekvderllgqaeapTtvee 37
                                   +DiG t+T v++++++k    +    + pTt  +
  gi|13541643|ref|NP_111331.1|  8 SVDIGGTFTDVVVMRNSK----IEKVFKVPTTPRN 38
                                  567777777776666633....4444445555543 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.047
                          MutL  30 eapTtveeedvleGleealeeleeklgktevdevlatSSAaGg 72 
                                   ++ Ttv ++ ++  ++e l++le++l ++ +  + + SSA+G 
  gi|13541643|ref|NP_111331.1| 199 RTATTVVNAALVPVVSEYLRKLEASLYEKYKPSMSVMSSAGGL 241
                                   5678888899999999*********998888899999999885 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.0019
                          MutL 224 impTPaAvlkavellaeeeekglgdllvvDvGGaTTdvhsvaegspekek 273
                                   i   PaA + a++ +a+  + ++ ++l +D+GG+T    +v+ ++ e+++
  gi|13541643|ref|NP_111331.1| 255 IESGPAAGVIAANEFAR--QIKISNILSFDMGGTTAKAGTVLGNNVEITS 302
                                   55668887778888888..57799***********999998766666555 PP

>> Cass2  Integron-associated effector binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0     0.036   1.3e+02      14      63 ..     119     170 ..     116     177 .. 0.77
   2 ?    7.6   0.0    0.0011       3.9      29      89 ..     497     557 ..     483     560 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.036
                                   EEETTCCCCH...HHHHHHHHHHHHH..HHCTT.SBSTEEEEEEEC-TT-CCG CS
                         Cass2  14 ryegskeeedlnkeigklwreflekg..rlkki.kkdkrvfgiyhdyeseenk 63 
                                   r+e++++ +  + ei k+ +++++k+  +l +  k+++ ++++ h+y + +n+
  gi|13541643|ref|NP_111331.1| 119 RFEIDERTN-VDGEIIKPVDQVSAKKlaDLIEKkKPQSVAVSFLHSYINDNNE 170
                                   566667766.6999**********99885555526669999999999886665 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0011
                                   HHHHHHHHHHHHHCTTSBSTEEEEEEEC-TT-CCGEEEEEEEEE-TTSSS-TT-EEEEE-- CS
                         Cass2  29 gklwreflekgrlkkikkdkrvfgiyhdyeseenkfsyyagvevpsdsevpeglvkkeiPg 89 
                                   ++l ++f e + + + k+ +  f++y+d+ + +++ +  + v+vp++  ++ ++ k ++++
  gi|13541643|ref|NP_111331.1| 497 KNLEDDFEELKSILSAKHGDAKFSMYADCRYVGQGSELTVPVTVPDKRVIESDFEKLHFEA 557
                                   4566666666667777777************************************999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (656 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.67u 0.30s 00:00:00.97 Elapsed: 00:00:00.50
# Mc/sec: 3923.61
//
Query:       gi|13541644|ref|NP_111332.1|  [L=290]
Description: phospholipase D [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.5e-30  105.8   0.3    1.9e-15   56.9   0.0    2.1  2  PLDc_2       PLD-like domain
    6.2e-05   22.5   0.4     0.0091   15.5   0.0    2.4  2  PP_kinase_C  Polyphosphate kinase C-terminal domain 2
     0.0012   19.0   0.5        1.9    8.8   0.0    3.2  3  PLDc         Phospholipase D Active site motif


Domain annotation for each model (and alignments):
>> PLDc_2  PLD-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.9   0.0   3.2e-19   1.9e-15       1     133 []      14     143 ..      14     143 .. 0.78
   2 !   47.3   0.0     3e-16   1.8e-12      28     133 .]     187     284 ..     169     284 .. 0.82

  Alignments for each domain:
  == domain 1  score: 56.9 bits;  conditional E-value: 3.2e-19
                        PLDc_2   1 liqliksAkksidiatyyfvsdreildallkaakrgvkvrilldskkddagavdeaslkelkellleagvevrvfet.... 77 
                                   +i+ i++ +k+i +  y +  d+ i++++++a+krgv+vri++d    +++++  +s+   kel  ++ + v+++ +    
  gi|13541644|ref|NP_111332.1|  14 IIKFIRRVRKKIFMNFYLI-DDDRIINEIREAKKRGVDVRIIVDG---KPYGMG-QSKVDVKEL-SSTCASVKLSPPrfda 88 
                                   6778999888888877777.*************************...444433.444444454.4444555554423333 PP

                        PLDc_2  78 llgslHaKlylidgktvivGSsNltkrgldlnlElnvviedkelakeleeeFerlw 133
                                    + + HaK+++  +k+  +G++N+t++++++n+E + + +++++ k l + F ++w
  gi|13541644|ref|NP_111332.1|  89 SDVFDHAKYMVS-EKYFEIGTANMTEASFSRNREYIYIGKNRKIRKCLMSLFISDW 143
                                   22555***9998.799************************************9999 PP

  == domain 2  score: 47.3 bits;  conditional E-value: 3e-16
                        PLDc_2  28 allkaakrgvkvrilldskkddagavdeaslkelkellleagvevrvfetllgslHaKlylidgktvivGSsNltkrgldl 108
                                    +  +++r +k++i+++s++   + +     +++k+l +e gv+ r++ ++   +HaK++l+ +++v++GS+N+t  +l++
  gi|13541644|ref|NP_111332.1| 187 IIETLSSRRRKLKIVIPSSA---SQN---DIANMKKL-RERGVKARLMPPDRLYMHAKAVLF-KDYVFIGSQNFTSTSLNR 259
                                   445589999********933...333...34678888.999*****98754478********.68**************** PP

                        PLDc_2 109 nlElnvviedkelakeleeeFerlw 133
                                   n+E++++i +     ++++++ ++w
  gi|13541644|ref|NP_111332.1| 260 NREVGIIIRSLSDRRKIKRIMVADW 284
                                   *********9988888888877777 PP

>> PP_kinase_C  Polyphosphate kinase C-terminal domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   1.5e-06    0.0091      29      63 ..      23      57 ..      13     147 .. 0.89
   2 !    5.5   0.1    0.0018        11     101     144 ..     242     285 ..     212     290 .] 0.84

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.5e-06
                   PP_kinase_C 29 akiilklNsledkeiidkLyeAsqaGVkiklivrg 63
                                   ki++    ++d +ii+++ eA + GV++++iv g
  gi|13541644|ref|NP_111332.1| 23 KKIFMNFYLIDDDRIINEIREAKKRGVDVRIIVDG 57
                                  478899999************************87 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0018
                   PP_kinase_C 101 eeevyisSaDlmtRnldrRvevlvpvedeklkkelkeilelqlk 144
                                   ++ v+i+S  +++ +l+r  ev + + + + ++++k+i+ + +k
  gi|13541644|ref|NP_111332.1| 242 KDYVFIGSQNFTSTSLNRNREVGIIIRSLSDRRKIKRIMVADWK 285
                                   6789*********************************9987776 PP

>> PLDc  Phospholipase D Active site motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1         1   6.2e+03       9      16 ..      29      36 ..      27      38 .. 0.72
   2 !    8.8   0.0   0.00032       1.9       5      26 ..      93     113 ..      90     115 .. 0.82
   3 !    6.8   0.0    0.0014       8.1       5      27 ..     234     255 ..     232     256 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1
                                  EEEETTTE CS
                          PLDc  9 ivivDdrv 16
                                  ++ +Dd++
  gi|13541644|ref|NP_111332.1| 29 FYLIDDDR 36
                                  77899986 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00032
                                   E---EEEETTTEEEEE---SSH CS
                          PLDc   5 hHqKivivDdrvafvGgaNLcd 26 
                                    H+K +++ ++ + +G+aN++ 
  gi|13541644|ref|NP_111332.1|  93 DHAKYMVSEKY-FEIGTANMTE 113
                                   69999887777.********97 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.0014
                                   E---EEEETTTEEEEE---SSHH CS
                          PLDc   5 hHqKivivDdrvafvGgaNLcdg 27 
                                   +H+K v + d+ +f+G+ N++  
  gi|13541644|ref|NP_111332.1| 234 MHAKAVLFKDY-VFIGSQNFTST 255
                                   68888888777.*******9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       466  (0.0259914); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 1758.10
//
Query:       gi|13541645|ref|NP_111333.1|  [L=674]
Description: ski2-like helicase [Thermoplasma volcanium GSS1]
Scores for complete 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-28   98.2   0.0      1e-24   87.3   0.0    2.5  2  DEAD        DEAD/DEAH box helicase
    7.8e-12   45.5   0.0    1.6e-10   41.3   0.0    2.9  2  Helicase_C  Helicase conserved C-terminal domain
    4.7e-10   39.7   0.0    7.9e-10   39.0   0.0    1.4  1  ResIII      Type III restriction enzyme, res subunit
    1.4e-05   25.6   0.0      4e-05   24.1   0.0    1.8  1  HHH_5       Helix-hairpin-helix domain
     0.0023   18.1   0.0     0.0074   16.5   0.0    1.9  1  Cdd1        Pathogenicity locus
  ------ inclusion threshold ------
      0.022   13.8   0.0      0.057   12.5   0.0    1.7  1  T2SSE       Type II/IV secretion system protein
        0.2   11.9   0.0       0.52   10.6   0.0    1.6  1  DUF4332     Domain of unknown function (DUF4332)


Domain annotation for each model (and alignments):
>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.3   0.0   3.9e-28     1e-24       2     170 ..      25     180 ..      24     185 .. 0.92
   2 !    8.4   0.0   0.00066       1.7      43      80 ..     232     270 ..     223     324 .. 0.81

  Alignments for each domain:
  == domain 1  score: 87.3 bits;  conditional E-value: 3.9e-28
                                   HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD   2 diQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvllii 82 
                                   d Q+ ai+++ +g++++v+ +T++GKTl++  ++++++     k++ k ++++P+r+La + +++l+++ + +++rv+l i
  gi|13541645|ref|NP_111333.1|  25 DHQRMAIEQFRKGKNIMVSVPTAAGKTLIAYSAIYETF-----KKKLKSIYIVPLRSLAMEKYEELSRLRE-LGMRVKLSI 99 
                                   79*********************************999.....8899********************9999.899***999 PP

                                   TTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTTSTTTSEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD  83 ggvaardqlskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqitcdgklqrqvi 163
                                   g+  ++d  + + +++d+v+ t ++ d+l++     +++v ++V+DE++++ d+ +++++++++++ +  + +     ++i
  gi|13541645|ref|NP_111333.1| 100 GN--YDDTPDFI-KRYDVVILTSEKADSLMHHDPYMMEEVGLMVIDEIHMIGDEYRGPTLETVITTARYVNPE----TRII 173
                                   95..77888899.99***************999999*******************************655444....45** PP

                                   EEESSBS CS
                                   xxxxxxx RF
                          DEAD 164 vlSATlp 170
                                   +lSAT++
  gi|13541645|ref|NP_111333.1| 174 ALSATVS 180
                                   *****98 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00066
                                   TTSTS-EEEEEESSHHHHHHHHHHHHHHTTTST.SEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxx RF
                          DEAD  43 kgktgpkalivePtreLaeqtlnnlkkfkkyid.lrvll 80 
                                   + ++g ++li + +r+ ae++++nl++++++i+ l+v++
  gi|13541645|ref|NP_111333.1| 232 TVDDGGQVLIFVSSRKRAEDMAKNLSQLFDPINdLKVSS 270
                                   567889************************965477764 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 ?    0.0   0.0      0.42   1.1e+03      54      72 ..      26      43 ..      24      76 .. 0.79
   2 !   41.3   0.0   6.2e-14   1.6e-10      10     111 .]     228     364 ..     224     364 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.42
                                  HHHHHHHHHHTTSSSEEEE CS
                    Helicase_C 54 ereeileqfnkgesdvLia 72
                                  +++ ++eqf+kg+   +++
  gi|13541645|ref|NP_111333.1| 26 HQRMAIEQFRKGKNI-MVS 43
                                  678899999999854.333 PP

  == domain 2  score: 41.3 bits;  conditional E-value: 6.2e-14
                                   H..HHTTTTSEEEEEESSHHHHHH.....HHHH....................HHHT..TSTEEEESTTSTHHHHHHHHHH CS
                    Helicase_C  10 l..kleeeggkilifvntidrlek.....vkll....................lekk..gikvavlhgelpqnereeileq 61 
                                   l  ++  +gg++lifv +++r+e+      +l+                    +  +     v  +h+ l++++r  i ++
  gi|13541645|ref|NP_111333.1| 228 LvkETVDDGGQVLIFVSSRKRAEDmaknlSQLFdpindlkvssedanvyddllN--EmlPHGVSFHHAGLSNEQRSFIEKA 306
                                   344567899***********8866644443333666666666555555554323..256788888**************** PP

                                   HHTTSSSEEEESGGGTSSSTSTTESEEEESSSS.........SSHHHHHHHHTTSSSTT CS
                    Helicase_C  62 fnkgesdvLiatdvaerGidipkvnlVinfdlp.........rnvtsyiqriGRtgRag 111
                                   f++ + +v++at  ++ G+++p ++lVi  d+           +  +++q+iGR+gR g
  gi|13541645|ref|NP_111333.1| 307 FRHRKLKVIVATPTLAAGVNLP-ARLVIVKDVTrygdlgityLSNMEVKQMIGRAGRPG 364
                                   *********************9.9****999997665555544459***********75 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.0   0.0   3.1e-13   7.9e-10       2     169 ..      21     179 ..      20     181 .. 0.83

  Alignments for each domain:
  == domain 1  score: 39.0 bits;  conditional E-value: 3.1e-13
                                   -EE-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG.. CS
                        ResIII   2 lelreyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseay 82 
                                   +el+++Q  aie+++      + k++++  +T +GKTl+a+++i++ +kk+   k + +vp +sl    +ee++++ +   
  gi|13541645|ref|NP_111333.1|  21 FELYDHQRMAIEQFR------KGKNIMVSVPTAAGKTLIAYSAIYETFKKKL--KSIYIVPLRSLAMEKYEELSRLRELGM 93 
                                   7899********996......7899************************966..9*****************999999875 PP

                                   ..GEEEESSS-B--.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS....TTTHHH...HHT- CS
                        ResIII  83 keigkkvsgdkkkakekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgak...kswrei...lekf 157
                                     ++ ++ +  ++    +++  ++++ t +++d+ +     +++ +  ++  +++iDE H +g++    + + +   ++++
  gi|13541645|ref|NP_111333.1|  94 R-VKLSIGNYDDT--PDFIKRYDVVILTSEKADSLM-----HHDPYMMEEVGLMVIDEIHMIGDEyrgPTLETVittARYV 166
                                   3.33333333333..3689*****************.....9999*******************76553666653444554 PP

                                   .--SEEEEEESS- CS
                        ResIII 158 .keavllglTATp 169
                                    +e  +++l+AT 
  gi|13541645|ref|NP_111333.1| 167 nPETRIIALSATV 179
                                   266999******7 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.0   1.6e-08     4e-05       6      56 ..     616     666 ..     609     667 .. 0.91

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 1.6e-08
                                   TSTT--HHHHHHHHTTT--SHHHHHHS-HHHHHTSTTS-HHHHHHHHHHHH CS
                         HHH_5   6 svsGiGpktAlallsaGiesvedlaaadveeLakipGiGkktAeriilelk 56 
                                    ++ iG+++A++l++aGi  v++la  d+ ++  + G++  +A  ++  +k
  gi|13541645|ref|NP_111333.1| 616 LIPAIGRVRARRLYEAGIHNVQELAFSDPSRIKMLYGFSDTLANAVVKRAK 666
                                   4899***************************************99998887 PP

>> Cdd1  Pathogenicity locus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   2.9e-06    0.0074       2      40 ..     608     646 ..     607     652 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.9e-06
                          Cdd1   2 rkalkelqdiPniGkalaedlvelGirsveelkgedpee 40 
                                   r++l +l  iP iG+  a+ l+e Gi++v+el+ +dp +
  gi|13541645|ref|NP_111333.1| 608 REELMDLVLIPAIGRVRARRLYEAGIHNVQELAFSDPSR 646
                                   578899999***************************986 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   2.2e-05     0.057     104     156 ..       2      64 ..       1      72 [. 0.75

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.2e-05
                         T2SSE 104 tlddlgaeealk...........ekiaevlrkavrerglilvsGgTgsGKttllyallkeinks 156
                                   +++dlg++e++            ++++ ++++  r+ ++i+vs +T  GKt ++y+++ e  k+
  gi|13541645|ref|NP_111333.1|   2 KISDLGYDESFLdlfegndfelyDHQRMAIEQF-RKGKNIMVSVPTAAGKTLIAYSAIYETFKK 64 
                                   566777777776777777777777888888888.999*****************9887664443 PP

>> DUF4332  Domain of unknown function (DUF4332)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0    0.0002      0.52      52      87 ..     611     646 ..     595     650 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0002
                       DUF4332  52 lAdLarikgigeeyaeLLeaaGvdsvaeLaqrnpan 87 
                                   l dL+ i+ ig+  a  L +aG+  v+eLa + p++
  gi|13541645|ref|NP_111333.1| 611 LMDLVLIPAIGRVRARRLYEAGIHNVQELAFSDPSR 646
                                   679***************************999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (674 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       706  (0.0393775); 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:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.75u 0.31s 00:00:01.06 Elapsed: 00:00:00.49
# Mc/sec: 4167.07
//
Query:       gi|13541646|ref|NP_111334.1|  [L=307]
Description: methyltransferase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-47  161.9   0.0      2e-47  161.5   0.0    1.1  1  Met_10           Met-10+ like-protein
    3.3e-10   39.7   0.0    7.5e-10   38.5   0.0    1.6  1  Trm5_N           tRNA methyltransferase 5 N-terminal domain
    1.5e-06   28.8   0.0    1.3e-05   25.8   0.0    2.2  2  Methyltransf_25  Methyltransferase domain
    2.4e-06   27.2   0.0    4.3e-06   26.4   0.0    1.3  1  MTS              Methyltransferase small domain
    3.7e-05   23.4   0.0    5.6e-05   22.8   0.0    1.4  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
    0.00012   21.9   0.1    0.00066   19.5   0.0    2.0  2  Methyltransf_31  Methyltransferase domain
     0.0014   18.3   0.0     0.0028   17.3   0.0    1.5  2  Cons_hypoth95    Conserved hypothetical protein 95
     0.0016   17.9   0.0     0.0026   17.2   0.0    1.2  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
     0.0034   16.6   0.0      0.027   13.6   0.0    1.9  2  TRM              N2,N2-dimethylguanosine tRNA methyltransfera
  ------ inclusion threshold ------
       0.01   15.8   0.1      0.022   14.7   0.0    1.6  2  Methyltransf_18  Methyltransferase domain
      0.013   15.2   0.0      0.034   13.9   0.0    1.7  1  N6_N4_Mtase      DNA methylase
      0.028   14.1   0.3       0.75    9.4   0.3    2.2  1  UPF0020          Putative RNA methylase family UPF0020
       0.09   12.4   0.0       0.17   11.5   0.0    1.6  1  MethyltransfD12  D12 class N6 adenine-specific DNA methyltran


Domain annotation for each model (and alignments):
>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  161.5   0.0   1.5e-50     2e-47       2     199 .]      69     260 ..      68     261 .. 0.93

  Alignments for each domain:
  == domain 1  score: 161.5 bits;  conditional E-value: 1.5e-50
                                   EEEEETTEEEEEB-TTSSHHHHHHHHHHHHHSS-SCEEEE-S-SBTTTTB--EEEEEES-.SEEEEEETTEEEEEETTTS- CS
                        Met_10   2 kfeiiGdvvilnlreelkeykkvigevildktkvktvlrkvsevegefRtfelevlaGsdstetihkEngcrfklDvskvy 82 
                                   +f+iiG ++i ++++   e++k+i ++    +++k+v+ +++  +g+ R ++l +laG dst+   +Engc fk+Dvsk y
  gi|13541646|ref|NP_111334.1|  69 SFDIIGTIAITKKDD--VEFAKEILKT---HKNIKSVYLDKGV-KGKERIRDLVLLAGIDSTVALYRENGCIFKIDVSKSY 143
                                   699999999977554..5666666555...55******99875.************************************* PP

                                   --GGGHHHHHHHHTT--TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEEEEES-GGG- CS
                        Met_10  83 fsskleaErerlaklveegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekvvkpileDgrev 163
                                   fs++l++Er+rl+  + +ge +vd+fAG Gp +i +ak  + +++++id+n ++++ l+e ++lN +  +++pi++D+r++
  gi|13541646|ref|NP_111334.1| 144 FSPRLATERRRLVDSILDGEFIVDMFAGSGPISIEVAK-KRRVKIISIDINCAAIESLQESMRLNSLLGTITPICGDARQL 223
                                   *************************************9.88899************************************* PP

                                   --.TT-EEEEEE--TTTGGGGHHHHHHHEEEEEEEEE CS
                        Met_10 164 ir.eqladrvvmnlpksaieFldkvlaalkdggvihy 199
                                   i+  + adr++mn+p+ a +Fl ++l+alk gg i y
  gi|13541646|ref|NP_111334.1| 224 IKdIHDADRIIMNHPTDAFSFLPCALEALKYGGHINY 260
                                   *98899***********************99876655 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 !   38.5   0.0   5.5e-13   7.5e-10       2      43 ..       7      48 ..       7      52 .. 0.95

  Alignments for each domain:
  == domain 1  score: 38.5 bits;  conditional E-value: 5.5e-13
                                  EEEEGGGHHHHHHHHHHTT-B-TTS--EEETTEEEEEB-S-- CS
                        Trm5_N  2 ikVpkkegEkvRkkLlekglLdrnyKIksdddylyIPvkeep 43
                                  +kV+++++ +++k L + g +d +y I++++dy++IPvk+ +
  gi|13541646|ref|NP_111334.1|  7 VKVERRMADRTIKMLQSRGYFDSDYEIRHEGDYVLIPVKDGF 48
                                  8**************************************986 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0       0.9   1.2e+03      50      90 ..      52      91 ..      45      96 .. 0.66
   2 !   25.8   0.0   9.4e-09   1.3e-05       1      96 [.     165     255 ..     165     256 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.9
                                  EEESBCCGBS...SSTTTEEEEEEESTGGGSSHHHHHHHHHHHH CS
               Methyltransf_25 50 fvqgdaedlp...fedgsfDlvvssgalhhlsdedlekalkeia 90
                                  +v++dae+ p    ++gsfD++  + a   ++++d  ++ kei 
  gi|13541646|ref|NP_111334.1| 52 VVVKDAEKKPkviPASGSFDIIGTI-A---ITKKDDVEFAKEIL 91
                                  57788888764435899***99884.3...34445556777665 PP

  == domain 2  score: 25.8 bits;  conditional E-value: 9.4e-09
                                   EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCGBSSSTTTEEEEEEESTGGGSSH CS
               Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl..nvefvqgdaedlpfedgsfDlvvssgalhhlsd 79 
                                   ++d+ +G+G +++++ak+  + k++ +Di+ +++e  +e ++ ++l   ++ ++gda++l  + +  D ++++    h  +
  gi|13541646|ref|NP_111334.1| 165 IVDMFAGSGPISIEVAKK-RRVKIISIDINCAAIESLQESMRLNSLlgTITPICGDARQLIKDIHDADRIIMN----H--P 238
                                   799***************.58********************999999**************9999******95....2..2 PP

                                   HHHHHHHHHHHHHEEEE CS
               Methyltransf_25  80 edlekalkeiarvLkpg 96 
                                    d+  +l  + ++Lk g
  gi|13541646|ref|NP_111334.1| 239 TDAFSFLPCALEALKYG 255
                                   34445666666666655 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.0   3.1e-09   4.3e-06      33     106 ..     163     238 ..     143     245 .. 0.85

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 3.1e-09
                                   SEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC..EEEEE-STTTTSTT.S-EEEEEE--- CS
                           MTS  33 gkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle..vevvasdvleevee.kkfdlivsNPP 106
                                   + ++D+ +G G++++++ak+  ++++  +d++ +A+es +e ++ n l   ++ +  d+ + +++ ++ d i++N P
  gi|13541646|ref|NP_111334.1| 163 EFIVDMFAGSGPISIEVAKKR-RVKIISIDINCAAIESLQESMRLNSLLgtITPICGDARQLIKDiHDADRIIMNHP 238
                                   449***************976.55999********************9967777788888888854689******88 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 !   22.8   0.0   4.1e-08   5.6e-05       3      67 ..     164     229 ..     162     279 .. 0.90

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 4.1e-08
               Methyltransf_15   3 vilDlfsGaGGnviqfalv.fekviaieinleklacaqhNaevYgvsdkitlvlgdvfellaklkl 67 
                                    i+D+f+G+G  +i+ a++   k+i+i+in   ++  q+  ++      it+++gd  +l++ ++ 
  gi|13541646|ref|NP_111334.1| 164 FIVDMFAGSGPISIEVAKKrRVKIISIDINCAAIESLQESMRLNSLLGTITPICGDARQLIKDIHD 229
                                   79***************986679************************************9987654 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      0.52   7.2e+02      60      96 ..      54      96 ..      51     113 .. 0.69
   2 !   19.5   0.0   4.8e-07   0.00066       7      96 ..     165     251 ..     159     288 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.52
               Methyltransf_31 60 qgdieelekl.ledekfDlilsnevl..naladpdkile...e 96
                                  + d+e+++k   +  +fD+i + ++   +++ + ++il+   +
  gi|13541646|ref|NP_111334.1| 54 VKDAEKKPKViPASGSFDIIGTIAITkkDDVEFAKEILKthkN 96
                                  5688888887766799999877655566666666666664444 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 4.8e-07
               Methyltransf_31   7 vlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeqgdieeleklledekfDlilsnevlna 86 
                                   ++D  +G+G +++e a++   + ++++iDi++ aie+ +e  + + l   ++   gd+ +l k+++d   D i+ n + +a
  gi|13541646|ref|NP_111334.1| 165 IVDMFAGSGPISIEVAKK--RRVKIISIDINCAAIESLQESMRLNSLLgTITPICGDARQLIKDIHD--ADRIIMNHPTDA 241
                                   79**************64..4799*************999666555544999999***996655676..999****99999 PP

               Methyltransf_31  87 ladpdkilee 96 
                                   +++++++le 
  gi|13541646|ref|NP_111334.1| 242 FSFLPCALEA 251
                                   9999999985 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       5.3   7.4e+03      93     120 ..      76     103 ..      68     103 .. 0.71
   2 !   17.3   0.0     2e-06    0.0028      40     106 ..     160     226 ..     148     288 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 5.3
                                   TEEEEES-HHHHCTS--SS-EEEEEEE- CS
                 Cons_hypoth95  93 taelkedaleallklakkkeefdivflD 120
                                   +a+ k+d++e +++  k+++++  v+lD
  gi|13541646|ref|NP_111334.1|  76 IAITKKDDVEFAKEILKTHKNIKSVYLD 103
                                   5666777777777777777888888887 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 2e-06
                                   HCC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCT CS
                 Cons_hypoth95  40 iegarvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkleeetaelkedaleallk 106
                                   ++g+ ++D+faGsG +++E +     k++ ++ + +a++ l+e ++   l ++++ +  da + ++ 
  gi|13541646|ref|NP_111334.1| 160 LDGEFIVDMFAGSGPISIEVAKKRRVKIISIDINCAAIESLQESMRLNSLLGTITPICGDARQLIKD 226
                                   6778899**************99999*****************999888887777777777666654 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   1.9e-06    0.0026     160     263 ..     160     265 ..     152     285 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.9e-06
                          PrmA 160 kegeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveakleva..lseellk.eekadvivaNILae 237
                                     ge ++D+ +GSG ++i +ak    k++ +Di+  A+++ +e ++lN++   ++ +   +++l+k  + ad i+ N   +
  gi|13541646|ref|NP_111334.1| 160 LDGEFIVDMFAGSGPISIEVAKKRRVKIISIDINCAAIESLQESMRLNSLLGTITPIcgDARQLIKdIHDADRIIMNHPTD 240
                                   5678899*****************************************998877432112333333456789999998777 PP

                          PrmA 238 vlielaedikklvkeggllilSGilk 263
                                   +  ++++ + +++k gg++    il+
  gi|13541646|ref|NP_111334.1| 241 AF-SFLPCALEALKYGGHINYYEILN 265
                                   64.57778888888888877766665 PP

>> TRM  N2,N2-dimethylguanosine tRNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.13   1.8e+02     258     304 ..      60     106 ..       6     141 .. 0.79
   2 !   13.6   0.0     2e-05     0.027      53     122 ..     165     232 ..     138     259 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.13
                                   -SB-TTT-SBEEEEEEEE-S-S--HHHHHHHHHHHCT..-TTS-HHH CS
                           TRM 258 kaecehcgaklhlaGPlwlgplkdkefveevleeaekekeeelkkrv 304
                                   k + +  + +++++G + + +  d ef +e+l++ ++ k+  l k v
  gi|13541646|ref|NP_111334.1|  60 KPKVIPASGSFDIIGTIAITKKDDVEFAKEILKTHKNIKSVYLDKGV 106
                                   56677778899999******************999997644443333 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 2e-05
                                   EEESS-TTSHHHHHHHHH-S-EEEEEEE-S-HHHHHHHHHHHHHTT--GGEEEE-S-HHHHHC--SS-EE CS
                           TRM  53 vldaLsasGlRaiRfalEvpgvkevlaNDisekAvelikeNvklneveeivvineddAnvllaekkkrfd 122
                                   ++d +++sG  +i  a+      +++  Di+  A+e+++e ++ln+   ++++  +dA+ l++ ++ +  
  gi|13541646|ref|NP_111334.1| 165 IVDMFAGSGPISIEVAKK--RRVKIISIDINCAAIESLQESMRLNSLLGTITPICGDARQLIKDIHDADR 232
                                   7899*****999999998..66678889********************99999999*****987776544 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       5.3   7.3e+03      68      90 ..      99     120 ..      81     124 .. 0.52
   2 ?   14.7   0.0   1.6e-05     0.022       9      88 ..     156     235 ..     145     236 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 5.3
               Methyltransf_18  68 evrlsdGleklkeeevdtvviaG 90 
                                   +v+l +G++  + +  d v++aG
  gi|13541646|ref|NP_111334.1|  99 SVYLDKGVKGKE-RIRDLVLLAG 120
                                   344555555443.2245555555 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 1.6e-05
               Methyltransf_18   9 aslvekgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievrlsdGleklkeee.vdtvvi 88 
                                   ++ + +g+ ++D  +  g ++i+++k++++ k+i +Din  ++e+ +e+++ ++l   i+ +++d  + +k+ + +d +++
  gi|13541646|ref|NP_111334.1| 156 VDSILDGEFIVDMFAGSGPISIEVAKKRRV-KIISIDINCAAIESLQESMRLNSLLGTITPICGDARQLIKDIHdADRIIM 235
                                   5556679999999999*********98888.9************************************9996555998876 PP

>> N6_N4_Mtase  DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   2.4e-05     0.034     183     229 ..     153     200 ..       6     202 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.4e-05
                                   HHHHHHS-TT-EEEETT-TTTHHHHHHHHTT-.EEEEEESSHHHHHHH CS
                   N6_N4_Mtase 183 rlIklstkkgdivlDpFaGSGtTavaakelgr.kfiGieieeeyvela 229
                                   r +  s  +g+ ++D FaGSG + +++++  r k i+i+i+  ++e+ 
  gi|13541646|ref|NP_111334.1| 153 RRLVDSILDGEFIVDMFAGSGPISIEVAKKRRvKIISIDINCAAIESL 200
                                   445567788************9977666555527889***98888765 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.3   0.00055      0.75      29     130 ..     162     238 ..     144     239 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00055
                                   TS-EEETT-TTSHHHHHHHHHHTT--TTTT----SSHHHHHHHHHHHH--EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE CS
                       UPF0020  29 gepllDPmCGsGtilIEaallganiapgllrefvlelkaeaeeearaelklygsDldrrvvqgareNaekagvgdliefsq 109
                                   ge ++D + GsG i IE a                          ++++k++ +D++ ++++  +e  +   + ++i+  +
  gi|13541646|ref|NP_111334.1| 162 GEFIVDMFAGSGPISIEVAK-------------------------KRRVKIISIDINCAAIESLQESMRLNSLLGTITPIC 217
                                   55566666666666666553.........................344567888888888888888888888888888888 PP

                                   --GGG--STTS---EEEE--- CS
                       UPF0020 110 adaakLrlkegevdvivtnpP 130
                                    da++L ++ ++ d i+ n P
  gi|13541646|ref|NP_111334.1| 218 GDARQLIKDIHDADRIIMNHP 238
                                   888888867778888888877 PP

>> MethyltransfD12  D12 class N6 adenine-specific DNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00012      0.17      20      63 ..     161     205 ..     148     294 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00012
                                   --SEEEETT-TTSCCHHCS....SSCEEEEES-HHHHHHHHHHCC CS
               MethyltransfD12  20 kgktfvepFaGggaVffeakk.qgkkvlinDinedlinlykalik 63 
                                   +g+ +v+ FaG+g +++e+ k +  k+++ Din   i   +  ++
  gi|13541646|ref|NP_111334.1| 161 DGEFIVDMFAGSGPISIEVAKkRRVKIISIDINCAAIESLQESMR 205
                                   66779**************9989999*******988877776555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 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:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 2172.93
//
Query:       gi|13541647|ref|NP_111335.1|  [L=435]
Description: NAD(FAD)-dependent dehydrogenase [Thermoplasma volcanium GSS1]
Scores for complete sequence (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  182.3   1.8    1.6e-53  181.9   1.8    1.1  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    1.8e-21   76.4   3.3    1.6e-14   54.2   0.1    3.4  3  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    1.6e-20   73.6   1.3    2.1e-15   56.8   0.1    2.3  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    1.3e-18   67.3   0.0    8.1e-18   64.7   0.0    2.1  2  Pyr_redox_dim   Pyridine nucleotide-disulphide oxidoreductase
    2.8e-10   39.5   2.5    0.00057   18.7   0.6    4.2  4  HI0933_like     HI0933-like protein
    2.6e-09   37.1   3.3      0.017   14.7   0.3    4.0  4  DAO             FAD dependent oxidoreductase
    4.8e-08   32.5   3.9    8.8e-05   21.8   0.1    3.1  3  FAD_binding_2   FAD binding domain
    2.9e-07   29.9   4.4      0.013   14.6   0.5    3.7  5  GIDA            Glucose inhibited division protein A
    7.5e-07   28.7   2.2      0.014   14.7   0.1    2.4  2  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
      3e-06   27.3   0.9    5.6e-06   26.3   0.0    1.8  2  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
    4.7e-06   26.7   2.5       0.02   15.1   0.2    2.5  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    1.6e-05   25.1   2.2     0.0074   16.5   0.3    2.7  2  TrkA_N          TrkA-N domain
    6.5e-05   22.2   2.2      0.017   14.2   0.1    2.3  2  Lycopene_cycl   Lycopene cyclase protein
    7.4e-05   22.2   2.2     0.0012   18.1   0.1    2.2  2  FAD_binding_3   FAD binding domain
    0.00017   20.9   2.1       0.15   11.3   0.3    2.3  2  Thi4            Thi4 family
    0.00024   21.5   0.4       0.02   15.3   0.1    2.5  2  NAD_binding_7   Putative NAD(P)-binding
     0.0012   18.9   1.6        2.1    8.3   0.0    4.0  4  NAD_binding_9   FAD-NAD(P)-binding
      0.003   16.8   1.4      0.015   14.5   0.1    2.5  3  K_oxygenase     L-lysine 6-monooxygenase (NADPH-requiring)
     0.0093   16.5   0.1        1.2    9.7   0.0    2.8  2  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
  ------ inclusion threshold ------
       0.01   15.8   0.2      0.049   13.6   0.0    2.0  2  NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogen
      0.024   13.5   1.4        0.1   11.5   0.2    2.2  2  Trp_halogenase  Tryptophan halogenase
      0.029   13.7   6.9       0.12   11.7   0.7    2.6  3  FAD_oxidored    FAD dependent oxidoreductase
      0.045   13.3   1.3        0.1   12.2   0.1    2.1  2  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
       0.11   11.9   0.3       0.24   10.7   0.0    1.7  2  ThiF            ThiF family


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  181.9   1.8   2.1e-56   1.6e-53       2     294 .]       2     296 ..       1     296 [. 0.90

  Alignments for each domain:
  == domain 1  score: 181.9 bits;  conditional E-value: 2.1e-56
                                   SEEEE--SHHHHHHHHHHHH..HTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH.......HHHHCHHHHCCCCHCC CS
                                   xxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxx RF
                   Pyr_redox_2   2 dvvviGgGpAGlaaaltlaq..agakvtlvelegtclnggcllskallgvaedaeias.......evvkklnqgielllge 73 
                                   +++viGgG+AG++aa ++++     +v++ve++ ++ +  c +++ l gv ++ e ++             + gi++ll +
  gi|13541647|ref|NP_111335.1|   2 KIIVIGGGAAGMSAASKAKRvnPDSEVIVVESGSYVSYAECGIPYYLQGVVGHIEDLLhyplsefT----EKRGIKVLLHT 78 
                                   89******************8669*******************************999*9875441....3568******9 PP

                                   TCEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHHHHHHCCSS-T.SEEEEES-SHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx RF
                   Pyr_redox_2  74 evvkidpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGvaenvgklvrtldsaealklkllp.krivvvGgGyi 153
                                   +v++id+ +  v l     +++  ++yd+l++AtGs+p+ +++  +   ++ ++r+l+sa + +    + k++++vG+G+ 
  gi|13541647|ref|NP_111335.1|  79 TVTRIDTLHSSVLL-----NNGDVLKYDRLIIATGSRPKPIDVISD--RTI-SIRSLESAMRARNLIEKsKDVTIVGAGVL 151
                                   ******99999999.....56669****************988877..333.44888888887766655688********* PP

                                   HHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTEEEEEEETTSCEEEESEEEE- CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2 154 GvElAaalaklgkevtlveardrllraldkelsaaleealekeGvevklgtsvkeidgngeklevvledgeeidadlvvva 234
                                   GvElA++la+ gk+v ++   dr+l++ld++++++ +e++  + ++v+ ++s k ++++  +++ ++++ +  ++d v++a
  gi|13541647|ref|NP_111335.1| 152 GVELASVLAESGKNVKVISKYDRVLPQLDEDIGKIFHEYFSSR-IDVQKQSSLKSAEEDRGRVK-ITTSVDDHECDAVIYA 230
                                   *****************************************96.*************9999666.88888889******** PP

                                   S-EEES-HHCSHCCT-EEEETTEEE--TTSBESSTTEEE-GGGC.......TECCSS--HHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxx RF
                   Pyr_redox_2 235 vGvrpstelleeklglelderggivvdeflrtnvpgiyaiGDva.......ggkggpelaqaAvqqG 294
                                   +G+ p++e++  ++g+++ +r++i+++ +++t+ pg+ya+GDva       g ++ + laq A ++G
  gi|13541647|ref|NP_111335.1| 231 TGIIPNSEIA-VEAGIKTGDRNAILTNGHMETSEPGVYAAGDVAtvrnivtGLDEMMPLAQIANKAG 296
                                   **********.*********************************88888877777777887777665 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   0.2   0.00012      0.09       1      32 [.       2      35 ..       2      42 .. 0.90
   2 !    7.8   0.0    0.0066         5      50      71 ..      67      88 ..      59      95 .. 0.80
   3 !   54.2   0.1   2.1e-17   1.6e-14       2      77 ..     143     216 ..     142     222 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00012
                                  EEEEECSSHHHHHHHHHHHHTT..SEEEEEESSS CS
                     Pyr_redox  1 kvvvvGgGyiglElAgalaelg..kkVtvversd 32
                                  k++v+GgG  g+ +A+ +++ +  ++V vve ++
  gi|13541647|ref|NP_111335.1|  2 KIIVIGGGAAGMSAASKAKRVNpdSEVIVVESGS 35
                                  79******************99889999999876 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0066
                                  HHHTTEEEECSEEEEEEEEETT CS
                     Pyr_redox 50 lekngievllntkveeiegsed 71
                                   ek+gi+vll+t+v++i++  +
  gi|13541647|ref|NP_111335.1| 67 TEKRGIKVLLHTTVTRIDTLHS 88
                                  5889*************97655 PP

  == domain 3  score: 54.2 bits;  conditional E-value: 2.1e-17
                                   EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTSEEEEE CS
                     Pyr_redox   2 vvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekngievllntkveeiegsedgvesvk 77 
                                   v++vG+G++g+ElA++lae gk+V+v+   d++l++lDe+++ki++e+++ + i+v  ++++++ e++   v+ ++
  gi|13541647|ref|NP_111335.1| 143 VTIVGAGVLGVELASVLAESGKNVKVISKYDRVLPQLDEDIGKIFHEYFSSR-IDVQKQSSLKSAEEDRGRVK-IT 216
                                   89**************************************************.*************7776444.54 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 !   15.5   0.1     1e-05    0.0075       1      33 [.       4      37 ..       4      41 .. 0.88
   2 !   56.8   0.1   2.8e-18   2.1e-15      87     305 .]      63     270 ..      51     270 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1e-05
                   Pyr_redox_3  1 iIiGaGPaGlaaaielkkagl.edylilEkgnig 33
                                  i+iG+G+aG++aa ++k+++  ++++++E g+ +
  gi|13541647|ref|NP_111335.1|  4 IVIGGGAAGMSAASKAKRVNPdSEVIVVESGSYV 37
                                  89****************9984679999999876 PP

  == domain 2  score: 56.8 bits;  conditional E-value: 2.8e-18
                   Pyr_redox_3  87 lrevaksfelpiklfeeVesvkkedegfevetsketyeAkkviiAtGefdkPnklnipGeek..lvkhyskvkefhkya.g 164
                                   l+e +++  +++ l+++V++++  +++ ++  + ++++ +++iiAtG   +P+  ++            s +++ + ++  
  gi|13541647|ref|NP_111335.1|  63 LSEFTEKRGIKVLLHTTVTRIDTLHSS-VLLNNGDVLKYDRLIIATGS--RPKPIDVISDRTisIRSLESAMRARNLIEkS 140
                                   67889999**************98655.5556788************9..7777777777651133344444444444438 PP

                   Pyr_redox_3 165 qkvvViGgknSavDaAlelvrkgaeVtvvtrgseiekeesdpsyslkpdienrleelvkeekikvlfnaevkeikekeeey 245
                                   ++v+++G++  +v+ A  l++ g++V+v+ + +       ++  +l  di + ++e+ + ++i+v +++++k+ +e+  ++
  gi|13541647|ref|NP_111335.1| 141 KDVTIVGAGVLGVELASVLAESGKNVKVISKYD-------RVLPQLDEDIGKIFHEYFS-SRIDVQKQSSLKSAEEDRGRV 213
                                   99*****************************97.......4566799999999999998.55******************* PP

                   Pyr_redox_3 246 kvktedgkkvevkddvvlatGykpdlsflkkslfeldedgrpvlteeteetnvpglflaG 305
                                   k++t+     ++ d v++atG  p+ ++  ++++++  d+   lt+  +et  pg++ aG
  gi|13541647|ref|NP_111335.1| 214 KITTSVD-D-HECDAVIYATGIIPNSEIAVEAGIKT-GDRNAILTNGHMETSEPGVYAAG 270
                                   ***9994.3.45699*************999***99.999999***************99 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 ?   -0.8   0.0       2.5   1.9e+03      54      77 ..     137     160 ..     122     169 .. 0.80
   2 !   64.7   0.0   1.1e-20   8.1e-18       4     103 ..     319     419 ..     316     424 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 2.5
                                   EEETTTTBEEEEEEECTTHHHHHH CS
                 Pyr_redox_dim  54 vadaktgkvlGahivGpgageliq 77 
                                   + + k+  ++Ga ++G + +++++
  gi|13541647|ref|NP_111335.1| 137 IEKSKDVTIVGAGVLGVELASVLA 160
                                   5556889999**999988877665 PP

  == domain 2  score: 64.7 bits;  conditional E-value: 1.1e-20
                                   EEESSSEEEEEES-HHHHHHHHSGEEEEEEEEECGHHHCHTTH.TEEEEEEEEETTTTBEEEEEEECTTHHH.HHHHHHHH CS
                 Pyr_redox_dim   4 vvftdpevasvGlteeeAkaagieikvgkfpfkangralayae.tkgfvKlvadaktgkvlGahivGpgage.liqelava 82 
                                   v+++d+ev+++G++e  Aka g  i + k+ +ka +ra +y+  ++++vK+++ ++++++lGa+++G + +  +++ +a+a
  gi|13541647|ref|NP_111335.1| 319 VKVFDYEVGFTGINESRAKALG--IPYEKTLIKAKSRANYYPGkQDIYVKIIYGKNDKRLLGAQVIGTDGAAwRLNTIATA 397
                                   7899******************..8888999***********99***********************655555******** PP

                                   HHTTSBHH.HHHTSBSSSSSTG CS
                 Pyr_redox_dim  83 ikagltve.dladtihihPtls 103
                                   i  g +v+ ++ d++++ P++ 
  gi|13541647|ref|NP_111335.1| 398 IFGGFKVSdLFYDDLGYTPPFG 419
                                   ********66*********997 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   0.6   7.6e-07   0.00057       2      33 ..       2      35 ..       1      38 [. 0.85
   2 !    6.6   0.0    0.0035       2.6     119     165 ..      67     110 ..      56     127 .. 0.83
   3 !    7.2   0.0    0.0024       1.8       2      35 ..     142     175 ..     141     180 .. 0.91
   4 ?    3.4   0.0     0.035        26     121     163 ..     192     232 ..     182     237 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 7.6e-07
                                  SEEEE--SHHHHHHHHHH..HHTT--EEEE-SSS CS
                   HI0933_like  2 dviviGgGaAGlmaAisa..akrgkrVlllekak 33
                                  ++iviGgGaAG+ aA +a   + +++V+++e+++
  gi|13541647|ref|NP_111335.1|  2 KIIVIGGGAAGMSAASKAkrVNPDSEVIVVESGS 35
                                  79****************5556889999999875 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0035
                                   HHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE----S CS
                   HI0933_like 119 lkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtGGl 165
                                    +++g+k+ l+t+v+++++ +++   v +++++ l+ d+l++AtG+ 
  gi|13541647|ref|NP_111335.1|  67 TEKRGIKVLLHTTVTRIDTLHSS---VLLNNGDVLKYDRLIIATGSR 110
                                   5789*************665444...666789************986 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.0024
                                   SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS CS
                   HI0933_like   2 dviviGgGaAGlmaAisaakrgkrVlllekakkl 35 
                                   dv ++G+G  G+  A  +a+ gk+V ++ k +++
  gi|13541647|ref|NP_111335.1| 142 DVTIVGAGVLGVELASVLAESGKNVKVISKYDRV 175
                                   89**************************998776 PP

  == domain 4  score: 3.4 bits;  conditional E-value: 0.035
                                   HHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE--- CS
                   HI0933_like 121 eagvklrletevksvekeedgkfrvktkseeeleadklvlAtG 163
                                   +++++++ ++++ks+e++  g+++++t s +  e+d+++ AtG
  gi|13541647|ref|NP_111335.1| 192 SSRIDVQKQSSLKSAEED-RGRVKITT-SVDDHECDAVIYATG 232
                                   567899999999999765.55599999.99************9 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.3   2.3e-05     0.017       1      32 [.       2      37 ..       2      44 .. 0.85
   2 !    9.7   0.0   0.00078      0.59     138     202 ..      47     109 ..      39     126 .. 0.76
   3 !    9.4   0.1   0.00096      0.72       1      30 [.     142     173 ..     142     178 .. 0.92
   4 ?    1.1   0.0      0.31   2.3e+02     164     203 ..     198     234 ..     186     266 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.3e-05
                                  EEEEECTSHHHHHHHHHHHHT..T...EEEEESSSST CS
                           DAO  1 dvviiGGGiiGlstAyeLarr..g...Vtllekgdia 32
                                  ++++iGGG +G+s+A  + +r  +   V+++e+g+ +
  gi|13541647|ref|NP_111335.1|  2 KIIVIGGGAAGMSAASKA-KRvnPdseVIVVESGSYV 37
                                  59****************.6655378******99765 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00078
                                   TTEEEE.EHHHHHHHHHHH.HHHTT-EEEESECEEEEEEEETCEEEEEEECTEEEEEEEEEEE--GG CS
                           DAO 138 pdtgqv.dpakltaalara.aealGveilegtevtgleeedgkvwgverttpgendaadavVnaaGa 202
                                   + +g+v + + l+++ +++  e++G+++l++t+vt+++      + v   ++g + ++d +++a+G 
  gi|13541647|ref|NP_111335.1|  47 YLQGVVgHIEDLLHYPLSEfTEKRGIKVLLHTTVTRIDTL---HSSVL-LNNGDVLKYDRLIIATGS 109
                                   445788899999999999945999*************553...45553.33377645799*****95 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.00096
                                   EEEEECTSHHHHHHHHHHHHTT..EEEEESSS CS
                           DAO   1 dvviiGGGiiGlstAyeLarrg..Vtllekgd 30 
                                   dv i+G+G+ G+  A  La+ g  V ++ k d
  gi|13541647|ref|NP_111335.1| 142 DVTIVGAGVLGVELASVLAESGknVKVISKYD 173
                                   89******************999**9999875 PP

  == domain 4  score: 1.1 bits;  conditional E-value: 0.31
                                   EESECEEEEEEEETCEEEEEEECT.EEEEEEEEEEE--GGG CS
                           DAO 164 legtevtgleeedgkvwgverttp.gendaadavVnaaGaw 203
                                    +++  ++ ee++g+ +++  tt+    +++dav+ a+G+ 
  gi|13541647|ref|NP_111335.1| 198 QKQSSLKSAEEDRGR-VKI--TTSvDD-HECDAVIYATGII 234
                                   555556666665566.445..454332.568********64 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.1   1.2e-07   8.8e-05       2      34 ..       3      37 ..       2      82 .. 0.90
   2 !    8.3   0.5    0.0014       1.1       1      31 [.     142     172 ..     142     176 .. 0.94
   3 ?    2.2   0.0     0.099        74     378     403 ..     255     276 ..     195     291 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1.2e-07
                                  EEEE--SHHHHHHHHHHHH.TTT.-EEEEESSSGG CS
                 FAD_binding_2  2 viViGsGlAGLaAAleaae.aGl.kvavvekeqef 34
                                  +iViG+G+AG++AA +a++ +   +v+vve ++++
  gi|13541647|ref|NP_111335.1|  3 IIVIGGGAAGMSAASKAKRvNPDsEVIVVESGSYV 37
                                  79****************985556******99984 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0014
                                   SEEEE--SHHHHHHHHHHHHTTT-EEEEESS CS
                 FAD_binding_2   1 DviViGsGlAGLaAAleaaeaGlkvavveke 31 
                                   Dv ++G+G+ G   A  +ae G++v v++k 
  gi|13541647|ref|NP_111335.1| 142 DVTIVGAGVLGVELASVLAESGKNVKVISKY 172
                                   899**************************96 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.099
                                   BETTSBESTTEEESSBTEEE-STCE..E CS
                 FAD_binding_2 378 tdengrvldadgqpipGLYAaGeva..a 403
                                   t+ ++++        pG YAaG va   
  gi|13541647|ref|NP_111335.1| 255 TNGHMET------SEPGVYAAGDVAtvR 276
                                   5555555......889********9553 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   0.5   1.8e-05     0.013       1      25 [.       2      26 ..       2      43 .. 0.81
   2 ?    4.6   0.0     0.019        14     114     150 ..      76     109 ..      64     140 .. 0.73
   3 !    9.8   0.0    0.0005      0.37       1      32 [.     142     172 ..     142     188 .. 0.87
   4 ?   -2.9   0.0       3.6   2.7e+03     134     161 ..     217     244 ..     194     262 .. 0.64
   5 ?   -2.8   0.0       3.4   2.5e+03     346     364 ..     254     272 ..     250     276 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.8e-05
                                  CEEEE-SSHHHHHHHHHHHHTT--E CS
                          GIDA  1 dviViGgGhAGceAAlaaarlGakv 25
                                  ++iViGgG AG+ AA +a+r + + 
  gi|13541647|ref|NP_111335.1|  2 KIIVIGGGAAGMSAASKAKRVNPDS 26
                                  69*****************987655 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.019
                                   EES-EEEEEECTTEEEEEEETTS-EEEECEEEE--TT CS
                          GIDA 114 ieeeveeliveekkvkgvvtedgetikakavviatGt 150
                                   ++ +v+++++     + v++++g ++k +  +iatG+
  gi|13541647|ref|NP_111335.1|  76 LHTTVTRIDT---LHSSVLLNNGDVLKYDRLIIATGS 109
                                   4566777755...5667*******************9 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.0005
                                   CEEEE-SSHHHHHHHHHHHHTT--EEEEES-G CS
                          GIDA   1 dviViGgGhAGceAAlaaarlGakvlLithkl 32 
                                   dv+++G+G  G+e A  +a++G +v+ i  k+
  gi|13541647|ref|NP_111335.1| 142 DVTIVGAGVLGVELASVLAESGKNVKVI-SKY 172
                                   79***********************999.444 PP

  == domain 4  score: -2.9 bits;  conditional E-value: 3.6
                                   TTS-EEEECEEEE--TT-BT-EEEETTE CS
                          GIDA 134 edgetikakavviatGtflkgkihigek 161
                                   ++    +++av+ atG   +++i +   
  gi|13541647|ref|NP_111335.1| 217 TSVDDHECDAVIYATGIIPNSEIAVEAG 244
                                   4445566788999999877777776444 PP

  == domain 5  score: -2.8 bits;  conditional E-value: 3.4
                                   B-T.TSBBSSSBTEEE-CGG CS
                          GIDA 346 lln.tLetkkvkgLflAGqi 364
                                   l+n ++et+  +g+++AG++
  gi|13541647|ref|NP_111335.1| 254 LTNgHMETS-EPGVYAAGDV 272
                                   567789998.99******98 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.5   5.4e-05     0.041      30      53 ..       2      25 ..       1      38 [. 0.85
   2 !   14.7   0.1   1.8e-05     0.014      29      78 ..     141     195 ..     125     234 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.4e-05
                                  EEEEESTSHHHHHHHHHHHHTT-E CS
                   AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgak 53
                                  k++viGgG aG++A++ ak+++ +
  gi|13541647|ref|NP_111335.1|  2 KIIVIGGGAAGMSAASKAKRVNPD 25
                                  899****************98755 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 1.8e-05
                                   -EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHH.TTTCECEE....H CS
                   AlaDh_PNT_C  29 akvlviGgGvaGlqAiatakglgakVtvlDvrparleqles.lgakfvev....l 78 
                                     v+++G+Gv G++ +++ ++ g +V+v+ +  ++l ql++ +g+ f e     +
  gi|13541647|ref|NP_111335.1| 141 KDVTIVGAGVLGVELASVLAESGKNVKVISKYDRVLPQLDEdIGKIFHEYfssrI 195
                                   579*************************************976666555444441 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 ?   -2.0   0.2       3.9   2.9e+03       1      18 [.       2      19 ..       2      33 .. 0.75
   2 !   26.3   0.0   7.6e-09   5.6e-06       2      83 ..     143     228 ..     142     235 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 3.9
                                  EEEEE--SCCHHHHHHHH CS
                       3HCDH_N  1 kvaviGaGtmGagiaavf 18
                                  k+ viG G  G + a+ +
  gi|13541647|ref|NP_111335.1|  2 KIIVIGGGAAGMSAASKA 19
                                  5789****9999988765 PP

  == domain 2  score: 26.3 bits;  conditional E-value: 7.6e-09
                                   EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTT.TSS-....HHHHCCCHHCEEEES-HHHHH CS
                       3HCDH_N   2 vaviGaGtmGagiaavfasagleVvlvdiseealekalekieksleklvek.gklk....eeeveaalarisfttdleeav 77 
                                   v+++GaG++G ++a+v+a++g +V+++   ++ l +  e i k +++  ++   ++     +++e+   r+++tt++++  
  gi|13541647|ref|NP_111335.1| 143 VTIVGAGVLGVELASVLAESGKNVKVISKYDRVLPQLDEDIGKIFHEYFSSrIDVQkqssLKSAEEDRGRVKITTSVDDH- 222
                                   9****************************9999999999999955544332012222222567888999********999. PP

                                   C-SEEE CS
                       3HCDH_N  78 dadlvi 83 
                                   ++d vi
  gi|13541647|ref|NP_111335.1| 223 ECDAVI 228
                                   888887 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 !   15.1   0.2   2.7e-05      0.02       1      31 [.       5      37 ..       5      40 .. 0.88
   2 !   11.1   0.2   0.00048      0.36       1      30 [.     145     174 ..     145     175 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.7e-05
                                  EE--SHHHHHHHHHHHCC..TEEEEEE-SSSSS CS
                 NAD_binding_8  1 IvGaGlsGlvaAylLaka..gfdvlllekrdrl 31
                                  ++G+G++G++aA+ +++   + +v ++e+++++
  gi|13541647|ref|NP_111335.1|  5 VIGGGAAGMSAASKAKRVnpDSEVIVVESGSYV 37
                                  8***************95468899999999876 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00048
                                   EE--SHHHHHHHHHHHCCTEEEEEE-SSSS CS
                 NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrdr 30 
                                   IvGaG+ G  +A+ La+ g++v ++ k dr
  gi|13541647|ref|NP_111335.1| 145 IVGAGVLGVELASVLAESGKNVKVISKYDR 174
                                   9***********************988766 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.0    0.0061       4.5       1      29 [.       3      33 ..       3      66 .. 0.78
   2 !   16.5   0.3   9.9e-06    0.0074       2      93 ..     144     240 ..     143     256 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0061
                                  EEEES-SHHHHHHHHHHHH.TT.EEEEEEES CS
                        TrkA_N  1 iiiiGlGrvGrslaeeLse.gg.kdvvvidk 29
                                  ii+iG G  G+s a + ++ +  ++v+v+++
  gi|13541647|ref|NP_111335.1|  3 IIVIGGGAAGMSAASKAKRvNPdSEVIVVES 33
                                  89*****************665866999997 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 9.9e-06
                                   EEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTT...SE...EEES-TTSHHHHHHTTGGGESEEEE-SSSHHHH CS
                        TrkA_N   2 iiiGlGrvGrslaeeLseggkdvvvidkdeerveelreeg...le...vvvgdatdeevLeeagiekadaviaatgddean 76 
                                    i+G+G +G +la  L e+gk+v vi k ++++ +l e+    ++       d+ +++ L++a+ ++ + v ++t+ d+  
  gi|13541647|ref|NP_111335.1| 144 TIVGAGVLGVELASVLAESGKNVKVISKYDRVLPQLDEDIgkiFHeyfSSRIDVQKQSSLKSAEEDRGR-VKITTSVDDHE 223
                                   79****************6668**************877734433322333566666666666666665.44455566555 PP

                                   HHHHHHHHHHTSSSEEE CS
                        TrkA_N  77 ilavllakelnpkkkii 93 
                                     av +a  + p+ +i 
  gi|13541647|ref|NP_111335.1| 224 CDAVIYATGIIPNSEIA 240
                                   56666666666665555 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.1   2.2e-05     0.017       2      36 ..       3      37 ..       2      42 .. 0.91
   2 !    7.4   0.2    0.0026       1.9       1      28 [.     142     169 ..     142     176 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.2e-05
                 Lycopene_cycl  2 vvviGaGpAglslAarlteakpglkvvlieaspsl 36
                                  ++viG+G+Ag+s A +  + +p+ +v+++e++  +
  gi|13541647|ref|NP_111335.1|  3 IIVIGGGAAGMSAASKAKRVNPDSEVIVVESGSYV 37
                                  89****************************99876 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0026
                 Lycopene_cycl   1 DvvviGaGpAglslAarlteakpglkvv 28 
                                   Dv ++GaG  g+ lA  l+e+ +++kv+
  gi|13541647|ref|NP_111335.1| 142 DVTIVGAGVLGVELASVLAESGKNVKVI 169
                                   9*****************8888877775 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.2     0.039        29       3      18 ..       2      17 ..       1      31 [. 0.92
   2 !   18.1   0.1   1.7e-06    0.0012       3      35 ..     142     174 ..     140     179 .. 0.92

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.039
                                  EEEEE--SHHHHHHHH CS
                 FAD_binding_3  3 dVlIVGaGpaGlmlal 18
                                  +++++G+G aG+++a+
  gi|13541647|ref|NP_111335.1|  2 KIIVIGGGAAGMSAAS 17
                                  689***********96 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 1.7e-06
                                   EEEEE--SHHHHHHHHHHHHTTHHEEEEESSSS CS
                 FAD_binding_3   3 dVlIVGaGpaGlmlallLseaGvrvvlvekrst 35 
                                   dV IVGaG  G+ la++L+e G +v ++ k+++
  gi|13541647|ref|NP_111335.1| 142 DVTIVGAGVLGVELASVLAESGKNVKVISKYDR 174
                                   8*****************************986 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.3    0.0002      0.15      19      49 ..       2      33 ..       1      41 [. 0.90
   2 !    9.0   0.1   0.00098      0.73      17      45 ..     140     169 ..     126     176 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0002
                                  EEEEE--SHHHHHHHHHHHHC.TTS-EEEEES CS
                          Thi4 19 DvvivGaGssGLtaayylakk.pdlkvailer 49
                                   ++++G+G++G++aa    +  pd +v+++e+
  gi|13541647|ref|NP_111335.1|  2 KIIVIGGGAAGMSAASKAKRVnPDSEVIVVES 33
                                  69*************9988878********96 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00098
                                   EEEEEEE--SHHHHHHHHHHHHC.TTS-EE CS
                          Thi4  17 esDvvivGaGssGLtaayylakk.pdlkva 45 
                                     Dv ivGaG  G+  a +la++  ++kv+
  gi|13541647|ref|NP_111335.1| 140 SKDVTIVGAGVLGVELASVLAESgKNVKVI 169
                                   47********************96777764 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 ?    4.1   0.0     0.086        64       9      38 ..       2      33 ..       1     111 [. 0.69
   2 !   15.3   0.1   2.6e-05      0.02       7      51 ..     140     198 ..     136     253 .. 0.64

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.086
                 NAD_binding_7  9 kvlvvGgGevAarkvrklleag..akvtvvap 38
                                  k++v+GgG  +++ ++k  + +   +v+vv  
  gi|13541647|ref|NP_111335.1|  2 KIIVIGGGAAGMSAASKAKRVNpdSEVIVVES 33
                                  689*****998876666665442256666544 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 2.6e-05
                 NAD_binding_7   7 gkkvlvvGgGevAarkvrklleagakvtvvapev.....keele............elvkla 51 
                                    k v +vG+G ++ + ++ l+e+g++v+v+++           +            ++++++
  gi|13541647|ref|NP_111335.1| 140 SKDVTIVGAGVLGVELASVLAESGKNVKVISKYDrvlpqL---DedigkifheyfsSRIDVQ 198
                                   689****************************985443320...1334444444444333333 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 ?    2.5   0.0      0.17   1.3e+02       2      32 ..       5      32 ..       4      41 .. 0.75
   2 !    8.3   0.0    0.0028       2.1     108     155 ..      63     109 ..      51     110 .. 0.76
   3 ?    2.1   0.0      0.23   1.7e+02       2      20 ..     145     163 ..     144     174 .. 0.83
   4 ?    1.8   0.0      0.28   2.1e+02     118     154 ..     196     232 ..     187     234 .. 0.73

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.17
                 NAD_binding_9  2 ivGaGprGlavlerLlarakkkspleitlfd 32
                                  ++G+G++G++++ +  +      + e+ +++
  gi|13541647|ref|NP_111335.1|  5 VIGGGAAGMSAASKAKRV---NPDSEVIVVE 32
                                  8**********9886655...4556666666 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0028
                 NAD_binding_9 108 larlpegvtvevh.raevvdleeradgqavlladgaslaadaVvLAlGh 155
                                   l+++ e+  ++v+ +++v+++++ +++  vll++g+ l++d++++A+G 
  gi|13541647|ref|NP_111335.1|  63 LSEFTEKRGIKVLlHTTVTRIDTLHSS--VLLNNGDVLKYDRLIIATGS 109
                                   555545555555437899999999887..899***************95 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.23
                 NAD_binding_9   2 ivGaGprGlavlerLlara 20 
                                   ivGaG+ G+ ++  L+++ 
  gi|13541647|ref|NP_111335.1| 145 IVGAGVLGVELASVLAESG 163
                                   9***********9999884 PP

  == domain 4  score: 1.8 bits;  conditional E-value: 0.28
                 NAD_binding_9 118 evhraevvdleeradgqavlladgaslaadaVvLAlG 154
                                   +v +++ ++ +e+++g+  ++++ + +++daV+ A+G
  gi|13541647|ref|NP_111335.1| 196 DVQKQSSLKSAEEDRGRVKITTSVDDHECDAVIYATG 232
                                   55555555555666666666889999**********9 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1      0.89   6.7e+02     193     219 ..       2      28 ..       1      39 [. 0.63
   2 !   14.5   0.1     2e-05     0.015     144     242 ..      95     192 ..      47     218 .. 0.73
   3 ?    0.3   0.0       0.4     3e+02     294     339 ..     194     232 ..     179     233 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.89
                   K_oxygenase 193 riaVvGsGqSaaeifedllrrqkkvel 219
                                   +i+V+G+G  +   + ++ r ++++e+
  gi|13541647|ref|NP_111335.1|   2 KIIVIGGGAAGMSAASKAKRVNPDSEV 28 
                                   677888877776666666555555555 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 2e-05
                   K_oxygenase 144 eeelearnlvlgvGtepkiPevleklegkervvHsseylerkeellakkriaVvGsGqSaaeifedllrrqkkvelklvtr 224
                                    + l+  +l++++G++pk  +v+ + +    +   +++++ ++  +++k++++vG+G  + e++  l+++ k  ++k++++
  gi|13541647|ref|NP_111335.1|  95 GDVLKYDRLIIATGSRPKPIDVISDRT--ISIRSLESAMRARNLIEKSKDVTIVGAGVLGVELASVLAESGK--NVKVISK 171
                                   556667799******999778887755..34555555666666799**********************9988..5666666 PP

                   K_oxygenase 225 sealepldd...spfvneifs 242
                                    +++ p  d    ++  e+fs
  gi|13541647|ref|NP_111335.1| 172 YDRVLPQLDediGKIFHEYFS 192
                                   666655433011444455555 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.4
                   K_oxygenase 294 rlrllpnrevesaeaegkgeveltlrneesgeeetlevdavvlATG 339
                                   r+ ++++++++sae++  g+v++t++       + +e+dav++ATG
  gi|13541647|ref|NP_111335.1| 194 RIDVQKQSSLKSAEEDR-GRVKITTSV------DDHECDAVIYATG 232
                                   56677777777777776.467766655......77899*******9 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.1       0.1        78       1      33 [.       2      33 ..       2      42 .. 0.87
   2 !    9.7   0.0    0.0017       1.2       2      46 ..     143     183 ..     142     220 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.1
                                  EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEE CS
                 F420_oxidored  1 kigiiGaGnmgealasgllaagaqpheivvans 33
                                  ki +iG+G  g + as++ + + +++e++v+ s
  gi|13541647|ref|NP_111335.1|  2 KIIVIGGGAAGMSAASKAKRVN-PDSEVIVVES 33
                                  6889************999998.9999998855 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0017
                                   EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHH CS
                 F420_oxidored   2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeel 46 
                                   + i+GaG +g  las l+++g   +++ v+ s+    + +l e++
  gi|13541647|ref|NP_111335.1| 143 VTIVGAGVLGVELASVLAESG---KNVKVI-SKYDRVLPQLDEDI 183
                                   6899*****************...999988.66555555555555 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 ?   -0.8   0.1       1.7   1.3e+03       1      20 [.       2      21 ..       2      34 .. 0.77
   2 ?   13.6   0.0   6.6e-05     0.049       2      38 ..     143     179 ..     142     188 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.7
                                  -EEEE--SHHHHHHHHHHHT CS
                NAD_Gly3P_dh_N  1 kiavlGaGswGtalAkvlae 20
                                  ki v+G+G+ G + A   ++
  gi|13541647|ref|NP_111335.1|  2 KIIVIGGGAAGMSAASKAKR 21
                                  799******99998876555 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 6.6e-05
                                   EEEE--SHHHHHHHHHHHTTT--EEEE-S-HHHHHHH CS
                NAD_Gly3P_dh_N   2 iavlGaGswGtalAkvlaenghevrlwvreeelieei 38 
                                   ++++GaG  G  lA vlae g++v+++++ + ++ ++
  gi|13541647|ref|NP_111335.1| 143 VTIVGAGVLGVELASVLAESGKNVKVISKYDRVLPQL 179
                                   9************************998877666655 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.2   0.00013       0.1       1      34 [.       2      34 ..       2      43 .. 0.88
   2 ?    0.3   0.1      0.33   2.5e+02       1      31 [.     142     169 ..     142     179 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00013
                                  EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-S CS
                Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlvese 34
                                  ki+++GGG aG  aA+  +++   + ev +ves 
  gi|13541647|ref|NP_111335.1|  2 KIIVIGGGAAGMSAASKAKRVN-PDSEVIVVESG 34
                                  79*********99999999998.559*****995 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.33
                                   EEEEE--SHHHHHHHHHHHHHTTTSSEEEEE CS
                Trp_halogenase   1 kivivGGGtaGwlaAaalakalkgklevtlv 31 
                                   +++ivG+G  G   A++la+ +k+   v+++
  gi|13541647|ref|NP_111335.1| 142 DVTIVGAGVLGVELASVLAESGKN---VKVI 169
                                   599****************99944...5555 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.7   0.00016      0.12       2      31 ..       3      34 ..       2      37 .. 0.80
   2 ?   -2.5   0.0       3.3   2.4e+03      95     115 ..      65      85 ..      57      94 .. 0.82
   3 ?    4.9   0.5     0.019        14       1      33 [.     142     174 ..     142     175 .. 0.95

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00016
                  FAD_oxidored  2 vvVvGGgpaGvaAAiaAara..GakvlLveer 31
                                  ++V+GGg+aG+ AA  A+r   + +v++ve  
  gi|13541647|ref|NP_111335.1|  3 IIVIGGGAAGMSAASKAKRVnpDSEVIVVESG 34
                                  89****************96224578888765 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 3.3
                  FAD_oxidored  95 emlaeagvtvllntrlvevek 115
                                   e+ ++ g++vll+t+++++++
  gi|13541647|ref|NP_111335.1|  65 EFTEKRGIKVLLHTTVTRIDT 85 
                                   6668899*********98876 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.019
                  FAD_oxidored   1 DvvVvGGgpaGvaAAiaAaraGakvlLveergv 33 
                                   Dv +vG+g+ Gv  A   a++G++v +++++++
  gi|13541647|ref|NP_111335.1| 142 DVTIVGAGVLGVELASVLAESGKNVKVISKYDR 174
                                   9***************************99875 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 ?   -0.9   0.1       1.3     1e+03       2     120 ..       2      32 ..       1      42 [. 0.50
   2 ?   12.2   0.1   0.00013       0.1       2      53 ..     142     193 ..     141     237 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1.3
                                   EEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHHCTTS-SS--TTHHHHHHHHCHTTTEEEES-HHHHHHC-SEEEE CS
                UDPG_MGDP_dh_N   2 kisviGlGYvGlvtaavlaeighevigvDideekvdklnsgkipiyepgLeelvkkavesgrlsfttdvekaveeadvifi 82 
                                   ki viG G  G+  a                                                                  
  gi|13541647|ref|NP_111335.1|   2 KIIVIGGGAAGMSAAS----------------------------------------------------------------- 17 
                                   5556666555554443................................................................. PP

                                   -----B-TTTTCB-THHHHHHHHHHHHHHHCEEEEEE- CS
                UDPG_MGDP_dh_N  83 aVgTPskkkgkaaDlkyvesaarsiaealkkgkvvvvk 120
                                                          + +++  + +v+vv+
  gi|13541647|ref|NP_111335.1|  18 -----------------------KAKRVNPDSEVIVVE 32 
                                   .......................333333344444444 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00013
                                   EEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHHCTTS-SS--TTHHH CS
                UDPG_MGDP_dh_N   2 kisviGlGYvGlvtaavlaeighevigvDideekvdklnsgkipiyepgLee 53 
                                    ++++G+G +G+  a vlae g++v ++ + ++   +l ++  +i+++  ++
  gi|13541647|ref|NP_111335.1| 142 DVTIVGAGVLGVELASVLAESGKNVKVISKYDRVLPQLDEDIGKIFHEYFSS 193
                                   599*************************999999999999988888776554 PP

>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.1       9.4     7e+03      21      34 ..       3      16 ..       2      30 .. 0.59
   2 ?   10.7   0.0   0.00032      0.24      18      41 ..     140     163 ..     119     171 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 9.4
                                  EEEE--SHHHHHHH CS
                                  xxxxxxxxxxxxxx RF
                          ThiF 21 vllvGaGglGsell 34
                                  + ++G G+ G  ++
  gi|13541647|ref|NP_111335.1|  3 IIVIGGGAAGMSAA 16
                                  56666666665554 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00032
                                   TSEEEEE--SHHHHHHHHHHHHHT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxx RF
                          ThiF  18 dskvllvGaGglGsellknLalsG 41 
                                   ++ v +vGaG lG el+  La sG
  gi|13541647|ref|NP_111335.1| 140 SKDVTIVGAGVLGVELASVLAESG 163
                                   47899****************999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (435 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       388  (0.0216409); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                        24  (0.00133861); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              24  [number of targets reported over threshold]
# CPU time: 0.63u 0.30s 00:00:00.93 Elapsed: 00:00:00.47
# Mc/sec: 2789.69
//
Query:       gi|13541648|ref|NP_111336.1|  [L=894]
Description: Lhr-like helicase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      3e-32  111.8   0.0    2.5e-31  108.8   0.0    2.2  2  DEAD           DEAD/DEAH box helicase
    2.6e-19   69.6   0.0    1.3e-17   64.2   0.0    2.8  2  Helicase_C     Helicase conserved C-terminal domain
    1.3e-12   47.9   0.1    2.7e-11   43.6   0.0    2.4  2  DEAD_assoc     DEAD/H associated
    1.9e-08   34.5   0.0    2.1e-07   31.1   0.0    2.5  3  ResIII         Type III restriction enzyme, res subunit
  ------ inclusion threshold ------
      0.029   13.7   0.3       0.77    9.1   0.0    2.4  2  zf-RanBP       Zn-finger in Ran binding protein and others
      0.053   13.5   0.1       0.16   11.9   0.1    1.8  1  PUB            PUB domain
      0.097   12.7   0.0       0.29   11.1   0.0    1.8  1  NOGCT          NOGCT (NUC087) domain
        0.1   12.6   0.0       0.31   11.1   0.0    1.8  1  HypA           Hydrogenase/urease nickel incorporation, metal
        1.1    9.3   2.7       0.57   10.2   0.3    1.8  2  Zn_Tnp_IS1595  Transposase zinc-ribbon 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 !  108.8   0.0   1.3e-34   2.5e-31       1     172 [.      25     192 ..      25     198 .. 0.89
   2 ?   -0.2   0.0      0.36   7.1e+02      33      72 ..     372     409 ..     369     448 .. 0.75

  Alignments for each domain:
  == domain 1  score: 108.8 bits;  conditional E-value: 1.3e-34
                                   -HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD   1 tdiQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvlli 81 
                                   td Q+++ip+il+g++vl+  +TGsGKT+a+++p+++ +++ ++ ++  a++++P+r+L ++++ +l +++k ++++v++ 
  gi|13541648|ref|NP_111336.1|  25 TDPQERIIPEILDGKNVLLLSPTGSGKTEAAVMPIFDMILK-RHPDKIFAIYITPLRALNRDIVYRLVEYGKDLGIKVQVR 104
                                   788************************************99.99*****************************99999866 PP

                                   ETTSSHHHHHHHHHTT.CSEEEEEHHHHHHHHHCTSSH..CTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTTSTTT CS
                                   xxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD  82 iggvaardqlskldng.vdivvgtpgrlddllstgkln..lsqvrflVlDEadrlldqgfsdfinrilnqlpqitcdgklq 159
                                    ++ +  ++++++ ++ +divv+tp+ l+ ll+ ++l+  +s+v+++V+DE +   +++++ +++  l++l++   +    
  gi|13541648|ref|NP_111336.1| 105 HSDMTD-SDRKRMTADpPDIVVTTPESLQILLNGRNLSklISNVKIVVVDELHDAAENERGSQLSVALERLRDLAGN---- 180
                                   555555.5555554556***************88888888*******************************655444.... PP

                                   SEEEEEESSBSHH CS
                                   xxxxxxxxxxxxx RF
                          DEAD 160 rqvivlSATlpkd 172
                                    q i lSAT+  +
  gi|13541648|ref|NP_111336.1| 181 FQRIGLSATVG-N 192
                                   56*******96.4 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.36
                                   HHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD  33 ipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkk 72 
                                   i++++++ e  gk +p  ++   +  La+q+l+++++ k 
  gi|13541648|ref|NP_111336.1| 372 IAIVDSIKE--GKIEPVQIMRNSLSTLANQILSEVNSKKR 409
                                   666777754..888889999999999******99987776 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0      0.14   2.7e+02      39      60 ..      94     118 ..      58     136 .. 0.71
   2 !   64.2   0.0   6.3e-21   1.3e-17      13     106 ..     252     347 ..     243     350 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.14
                                   T...TSTEEEESTTSTHHHHHHHHH CS
                    Helicase_C  39 k...gikvavlhgelpqnereeile 60 
                                       gikv v h++++ ++r+++ +
  gi|13541648|ref|NP_111336.1|  94 GkdlGIKVQVRHSDMTDSDRKRMTA 118
                                   12459***************98766 PP

  == domain 2  score: 64.2 bits;  conditional E-value: 6.3e-21
                                   TTTTSEEEEEESSHHHHHH..HHHHHHHT.TSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTSTTESEEEE CS
                    Helicase_C  13 eeeggkilifvntidrlek..vklllekk.gikvavlhgelpqnereeileqfnkgesdvLiatdvaerGidipkvnlVin 90 
                                    +++  +l+fvn++  +e+  +  l+ k+ +i v+v+hg+l+ + re + ++f++g+++ Li+t+ +e Gidi  ++ Vi+
  gi|13541648|ref|NP_111336.1| 252 INRHAGSLVFVNRRFVAEDlaF-RLRLKFgDIPVLVHHGSLSRETRENAENSFKEGKVRALICTSSLELGIDIGTASAVIQ 331
                                   4777889********8876533.33445568************************************************** PP

                                   SSSSSSHHHHHHHHTT CS
                    Helicase_C  91 fdlprnvtsyiqriGR 106
                                   f+ pr++ ++iqriGR
  gi|13541648|ref|NP_111336.1| 332 FNSPRQINKMIQRIGR 347
                                   **************** PP

>> DEAD_assoc  DEAD/H associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0     0.099     2e+02     155     191 .]     361     397 ..     359     397 .. 0.90
   2 !   43.6   0.0   1.4e-14   2.7e-11       2     170 ..     580     732 ..     579     746 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.099
                    DEAD_assoc 155 vledqlDlerlaellrriaageirvvevetprpSpfA 191
                                   v +d++++e++ +++++i++g+i+ v++  ++ S +A
  gi|13541648|ref|NP_111336.1| 361 VCTDVIEMEEAIAIVDSIKEGKIEPVQIMRNSLSTLA 397
                                   6789********************9999888888876 PP

  == domain 2  score: 43.6 bits;  conditional E-value: 1.4e-14
                    DEAD_assoc   2 PtdrtllvErfrdelgdwrlvvhspfGrrvnealalllaarlsrrfgidvqvaanDdgivlllpleerlpllldellells 82 
                                    t ++++vE+++d     ++v+  ++G++ n a a +l+  ls+ +g +v+   +++ i l ++ +  +++  ++l+  + 
  gi|13541648|ref|NP_111336.1| 580 ATSDEVIVESYND-----EIVIQILLGTKGNFAVAEVLSNLLSSITGESVESDYSPYHIYLRTSRKIYADD-AKKLILDVF 654
                                   6899********9.....57*****************************************7643333333.344555566 PP

                    DEAD_assoc  83 pdeleedleaalnaselfkrrFrevAaralllprrypgkrkplwqqrlraaqLldvareypdfpllleavrevledqlDle 163
                                     ++e+ l a+  +s  fk+ F   A+++++++ + +         r+r ++++d++    d++l++  vr+ ++d++D++
  gi|13541648|ref|NP_111336.1| 655 GSDFEQYLAASAPRSRFFKSVFLYEARKFGVISAEADL-------DRIRIDKIMDAYM---DTVLYRDSVRKLINDYMDVD 725
                                   677********************************988.......9**********98...******************** PP

                    DEAD_assoc 164 rlaellr 170
                                   +l+ + +
  gi|13541648|ref|NP_111336.1| 726 ALRSFKA 732
                                   **98755 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.1   0.0   1.1e-10   2.1e-07      14     169 ..      34     190 ..      21     192 .. 0.71
   2 ?   -0.4   0.0      0.49   9.8e+02      70     118 ..     429     474 ..     399     499 .. 0.78
   3 ?   -3.5   0.0       4.6   9.1e+03      93     121 ..     623     648 ..     602     670 .. 0.71

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 1.1e-10
                                   HHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.......-EEEEESSH....HHHHHHHHHGGGGTGG....GEEE CS
                        ResIII  14 nlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkee..kflflvprk....slleqtleefkkflseaykeigkk 88 
                                   ++l      + k++l+  +TG+GKT  a+  i  +  k++ +   ++ + p +    +++ ++ e  k++  + + +++  
  gi|13541648|ref|NP_111336.1|  34 EIL------DGKNVLLLSPTGSGKTEAAVMPIFDMILKRHPDkiFAIYITPLRalnrDIVYRLVEYGKDLGIKVQVRHSDM 108
                                   444......5689999************66666666666666242345566552222445555555555555554445555 PP

                                   ESSS-B--.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.T.......TTHHHHHT---SEE CS
                        ResIII  89 vsgdkkkakekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakk.......swreilekfkeavl 162
                                   +++d+k+     ++  +i+vtt +sl+  +   +  + ++l ++ +++++DE H +++++       + +++ +   ++ +
  gi|13541648|ref|NP_111336.1| 109 TDSDRKRM---TADPPDIVVTTPESLQILL---NGRNLSKLISNVKIVVVDELHDAAENErgsqlsvALERLRDLAGNFQR 183
                                   55555555...9999***************...99***********************9556666667777777778899* PP

                                   EEEESS- CS
                        ResIII 163 lglTATp 169
                                   +gl+AT 
  gi|13541648|ref|NP_111336.1| 184 IGLSATV 190
                                   ******6 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.49
                                   HHHHGGGGTGG....GEEEESSS-B--.......-SEEEEEHHHHHHTH CS
                        ResIII  70 tleefkkflseaykeigkkvsgdkkkakekdstnkkilvttiqsldads 118
                                   t++e++++++  + +++k++ +dk +   k++++ ++++++i+++ +++
  gi|13541648|ref|NP_111336.1| 429 TYDEYMEVIHFLA-DTKKIWLEDKFIG--KRRNTLRYYIENISMIPSEK 474
                                   4455666666553.3888888888888..99999999999999998887 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 4.6
                                   -B--.......-SEEEEEHHHHHHTH... CS
                        ResIII  93 kkkakekdstnkkilvttiqsldadseee 121
                                   + +   +d +  +i++ t  +++ad  ++
  gi|13541648|ref|NP_111336.1| 623 SVE---SDYSPYHIYLRTSRKIYADDAKK 648
                                   333...47788899999999999998544 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 ?    9.1   0.0   0.00039      0.77      13      28 ..     778     793 ..     777     794 .. 0.93
   2 ?    2.0   0.1     0.064   1.3e+02      19      26 ..     803     810 ..     800     811 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00039
                                   EEESSSSB-TTT--BT CS
                      zf-RanBP  13 qNfawstkCvaCqapk 28 
                                   +N+  s++C++C++++
  gi|13541648|ref|NP_111336.1| 778 MNERVSLYCLSCGSVR 793
                                   8*************98 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.064
                                   SB-TTT-- CS
                      zf-RanBP  19 tkCvaCqa 26 
                                   +kC+aC++
  gi|13541648|ref|NP_111336.1| 803 PKCEACGS 810
                                   79****97 PP

>> PUB  PUB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1     8e-05      0.16       9      35 ..     458     484 ..     454     488 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 8e-05
                           PUB   9 ktLrkylnNilehpteekyrrIrleNk 35 
                                   +tLr y++Ni+  p+e++y+ I ++ k
  gi|13541648|ref|NP_111336.1| 458 NTLRYYIENISMIPSEKNYKVIDITGK 484
                                   8*********************88766 PP

>> NOGCT  NOGCT (NUC087) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00015      0.29      36      46 ..      31      41 ..      18      42 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00015
                         NOGCT 36 iiPEildGkNv 46
                                  iiPEildGkNv
  gi|13541648|ref|NP_111336.1| 31 IIPEILDGKNV 41
                                  8*********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 ?   11.1   0.0   0.00016      0.31      55      99 ..     768     815 ..     728     822 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00016
                                   .TTTT-EEEEEEE--EEEETTTS-EEECHH.H..HHS-TTTSSS-EEE CS
                          HypA  55 tvlegaeLeieevpvkvrCreCgkefelee.k..alrCpkCgsadvei 99 
                                    +le+ + +i +++v+++C +Cg+  + +  +    +C++Cgs+ v  
  gi|13541648|ref|NP_111336.1| 768 AILESVKNRIMNERVSLYCLSCGSVRSYRVrDlkVPKCEACGSRLVAA 815
                                   4567777789999**********7777554233345999999987765 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 ?   -2.9   0.1       3.6   7.1e+03      33      41 ..     569     577 ..     560     578 .. 0.61
   2 ?   10.2   0.3   0.00029      0.57      20      44 ..     785     809 ..     768     811 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 3.6
                 Zn_Tnp_IS1595  33 ktrglfqCk 41 
                                   ++ +++ C+
  gi|13541648|ref|NP_111336.1| 569 EKLRQWYCN 577
                                   445789998 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00029
                 Zn_Tnp_IS1595  20 vCPhCgsrkayriktrglfqCkeCr 44 
                                    C  Cgs ++yr+++ ++ +C++C+
  gi|13541648|ref|NP_111336.1| 785 YCLSCGSVRSYRVRDLKVPKCEACG 809
                                   499*********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (894 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       573  (0.0319594); expected 358.6 (0.02)
Passed bias filter:                      508  (0.028334); 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: 0.74u 0.29s 00:00:01.03 Elapsed: 00:00:00.46
# Mc/sec: 5805.95
//
Query:       gi|13541649|ref|NP_111337.1|  [L=560]
Description: membrane-associated Zn-dependent protease 1 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0009   18.6   0.8     0.0017   17.7   0.8    1.5  1  Peptidase_M50  Peptidase family M50


Domain annotation for each model (and alignments):
>> Peptidase_M50  Peptidase family M50
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.8   9.3e-08    0.0017     169     247 ..     217     293 ..     112     295 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 9.3e-08
                                   XXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                   xxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Peptidase_M50 169 tlggpisiaqlaseaa.eaglssflqllalisvnLgilNLlPipvLDGghllfalleairrkplserkeevanlvglall 247
                                    +g pi +  ++++ + ++g+ ++++++ +i+v++  + +lPi  LDGg + +all + +   +  +  +++ ++gl +l
  gi|13541649|ref|NP_111337.1| 217 LVGSPIVFQLVMGSIIpSNGILYPVAYAGWIGVIVSSFDALPIGYLDGGLVSSALLGKNS---IYLSYASIIAIIGLSIL 293
                                   5666776666665544267899*****************************999998776...88888888888888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (560 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       748  (0.0417201); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 3886.85
//
Query:       gi|13541650|ref|NP_111338.1|  [L=878]
Description: alanyl-tRNA synthetase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     1e-103  347.8   0.3   6.4e-103  345.2   0.3    2.1  1  tRNA-synt_2c  tRNA synthetases class II (A)
      2e-11   43.8   1.1    4.5e-11   42.6   1.1    1.7  1  tRNA_SAD      Threonyl and Alanyl tRNA synthetase second addi
  ------ inclusion threshold ------
       0.11   11.7   0.1       0.22   10.7   0.1    1.4  1  tRNA-synt_2e  Glycyl-tRNA synthetase alpha subunit


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 !  345.2   0.3  1.1e-106  6.4e-103       1     552 []      66     584 ..      66     584 .. 0.90

  Alignments for each domain:
  == domain 1  score: 345.2 bits;  conditional E-value: 1.1e-106
                                   HHHHHHHHHHHCTT-EEE----SS-SSSTTCSS--SGGGGGHHHHTTSSCGGSSSEEEEEEEEE-EETTEEGGGGTTTSSS CS
                  tRNA-synt_2c   1 eirekFldfFekkgHtvvksssvvpendptllfvnAgmaqfkpiflgkeakpklkravnsQkciRagGkhnDlenVGktar 81 
                                   e+r++F dfFek+gH+ ++ ++vvp++++++l+vnA++++f+p ++++  kp+ +++v sQ++iR++    D++ VG t+r
  gi|13541650|ref|NP_111338.1|  66 EMRKAFFDFFEKRGHKLLEPYPVVPRWREDVLLVNASIYDFQPHVTSGIVKPPGNPIVMSQPSIRMN----DVDLVGVTGR 142
                                   89*****************************************************************....********** PP

                                   --SEEEEEEEEESS.....SS-HHHHHHHHHHHHHTTTT--GGGEEEEEETTEH..HHHHHHHHTTTTEGGGEEEE-HHHH CS
                  tRNA-synt_2c  82 HhTfFeMlGnfsfg.....dYfkeeaiefawelltkelgldkerlyvtvfeedd..eaveiweklvgvpeerilrfgekdn 155
                                   H+T FeMl + +f+      Y+kee++ +++e+lt+ lg+d + +++++ ++ +  +a+++ e +v++ e ++l+f ++++
  gi|13541650|ref|NP_111338.1| 143 HLTSFEMLCHDAFNskndfVYWKEETVRYSYEFLTDGLGIDGSLITYKEKPWSGggNAGNALEVFVRGLEVATLVF-MDMK 222
                                   *****************999*********************************999*******************9.6655 PP

                                   EEESSSS......EEEEEEEEEEEECETTSHHCHCCCCTTCTCCHEEEEEEEEEEEEEESTTSHEEEEEEEEEEEEEEHHH CS
                  tRNA-synt_2c 156 fwemgdt......gpcgpcseiyydrgeeigkrkaaseveadddrvleiwnlvfmqfnreedgtlkpLpkksidtGmgler 230
                                     + g+       + +++++++++++g e+ ++ ++++++++++++ ei++ v+++  +e +++ + L    ++       
  gi|13541650|ref|NP_111338.1| 223 EDQEGEVeiegtrYTKMDMQIVDTGYGLERLTWLSQGTPTVYQAIYPEIIDYVLENSYVE-SIDNEFLSDVVRV------- 295
                                   5555555666666*******************************************9999.7777777654443....... PP

                                   HHHHHTTHSSGGGSCCTHHHHHHHHHHHT--TCSTCCHHHHHHHHHHHHHHHHHHHHTT--SSSSHHHHHHHHHHHHHHHH CS
                  tRNA-synt_2c 231 lvavLqevrsnydtdlfvpvieaieeisgatyedkdetdealrviaDHvralafaladGvvpsnegrgYvlRrllRravrh 311
                                     +v   +r+ yd+ ++++ + ++   + + +e++++   ++ v+ DH+r+l ++    v+psn++ gY++R+l+Rr++r 
  gi|13541650|ref|NP_111338.1| 296 --SV---MREPYDEAFVLSTLGEKYPNALERFEKAKK-VRDIFVLIDHARSLMHMFEAFVIPSNVKVGYLARLLIRRSIRA 370
                                   ..33...345666665554444433333335544444.56789************************************** PP

                                   HHHTT-SSTHHHHHHHHHHHHHTTTGCCHHCCHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCCSEEXHHHHHHHHH CS
                  tRNA-synt_2c 312 akkLglkekflaklvavvvevlgdvypelkekeekveeiieeEeerFakTlerGlklleelikklkkkkelsgedafkLyd 392
                                    k++g+k + l +l++   ++l+d+ + l    e+++++++ E +++++  +rG++++e+ +k+   kk ++ +d+  Lyd
  gi|13541650|ref|NP_111338.1| 371 QKNIGFKGS-LINLIERNYNELKDIVKPLP--IEFIKDVLSIEMQKYSELEKRGQQVIEKILKT---KKSIDIDDLVLLYD 445
                                   *********.889**************996..589***************************97...789*********** PP

                                   CHXXXHHHHHHHHHCTTXEEXHHHHHHHHHHHHHHHCCHHSXSSXXXXXXXXTTSHCHHCCTSTTTXXXXXXTSXXXXXXS CS
                  tRNA-synt_2c 393 tyGfPvdltkeiaeekglkvdiegfekameeqrerskkekkekklikkdvealkelkkteeflgyeeleaeakvlallkdk 473
                                   ++G+ +d+++ +a+ekglkv i+ +++am+ +r+++k++ k+++      +++ +++++   l+y++           +++
  gi|13541650|ref|NP_111338.1| 446 SHGISPDVVAAMAAEKGLKVMIPPNFHAMVISRHEKKSALKKSA------KVYPNIETR--TLYYDD----------STMR 508
                                   ************************************88888766......555555444..479999..........4458 PP

                                   EEEEEEEEEETTEEEESEEXXXXSSSSCSXXXEEEEESSEEEEESEEEEETTEEEEEXSS.XSXXXTTSEEEEEEXHHH CS
                  tRNA-synt_2c 474 efveeveegeevgvvLdrTpfYaesGGqigDeGliekegaefrvkdvqkakgvvlhkgkleegklkvgdkvkaevdeer 552
                                   ef+  v  ++ + v+Ld+T+fY+e+GGq +D+G+ e +g++++v dvqk ++ ++hk +    ++ +g +vk+++d+er
  gi|13541650|ref|NP_111338.1| 509 EFTGLVMYSKGNEVILDKTAFYPEGGGQPADHGYFEFKGKKINVLDVQKHGNAIVHKLDG---EIPEGVRVKGVIDWER 584
                                   999999999999********************************************9876...5************986 PP

>> tRNA_SAD  Threonyl and Alanyl tRNA synthetase second additional domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.6   1.1   7.6e-15   4.5e-11       1      43 [.     683     725 ..     683     726 .. 0.97

  Alignments for each domain:
  == domain 1  score: 42.6 bits;  conditional E-value: 7.6e-15
                                   EEEEEETT.EEEEESS---SBGGGC-SEEEECCECCCTCEEEE CS
                      tRNA_SAD   1 vrvvsiGdisvelCgGtHvpnTgeIgafkilseesiakglrRI 43 
                                   vrvv+i+ ++ e CgGtH++n++ Ig  ki + e+i+++++RI
  gi|13541650|ref|NP_111338.1| 683 VRVVEIEGVDAEGCGGTHLKNISSIGVLKIKKIEAIQENIYRI 725
                                   9*****779*********************************9 PP

>> tRNA-synt_2e  Glycyl-tRNA synthetase alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   3.7e-05      0.22     118     192 ..     197     283 ..     177     354 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 3.7e-05
                                   GTEEEEEEEEEETTCEEEEEEEEE....EETTEE-S........S--EEEEEEHHHHHHHHCT-SSGGG-ECCTTEEHHHH CS
                  tRNA-synt_2e 118 lGawGlGwevwldGmeitqftYfq....qvgglelk........pvsveityGleRlamylqevdnvydlewnekvtygdv 186
                                    G  G   ev++ G+e++ + +++    q g +e++        +  v+  yGleRl+   q++ +vy+  + e + y   
  gi|13541650|ref|NP_111338.1| 197 GGNAGNALEVFVRGLEVATLVFMDmkedQEGEVEIEgtrytkmdMQIVDTGYGLERLTWLSQGTPTVYQAIYPEIIDYVLE 277
                                   477888899999999999999985333355655543111111113456678*********************999988544 PP

                                   HHHHHH CS
                  tRNA-synt_2e 187 flqnev 192
                                    +  e 
  gi|13541650|ref|NP_111338.1| 278 NSYVES 283
                                   444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (878 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       609  (0.0339673); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); 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):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.25s 00:00:00.85 Elapsed: 00:00:00.41
# Mc/sec: 6396.47
//
Query:       gi|13541651|ref|NP_111339.1|  [L=140]
Description: GAF domain-containing protein [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.6e-09   37.1   0.0    3.9e-09   36.9   0.0    1.1  1  GAF_2     GAF domain
    5.3e-07   30.3   0.0    6.5e-07   30.0   0.0    1.1  1  GAF       GAF domain
    1.1e-05   25.7   0.0    1.4e-05   25.5   0.0    1.1  1  GAF_3     GAF domain


Domain annotation for each model (and alignments):
>> GAF_2  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.9   0.0   6.6e-13   3.9e-09       7     134 ..      10     132 ..       1     136 [. 0.74

  Alignments for each domain:
  == domain 1  score: 36.9 bits;  conditional E-value: 6.6e-13
                                   HHHHHHHHHHHS.S....EEEEEEE-TTS-EEEEEEEES-TTSTT-S-B---TTHHHHHHHHTS-EEES-GGG-S-HHHHH CS
                         GAF_2   7 lldlvldelvel.g.aa.lgyillvdddgglrlaawgeaeeefgaaldrplgeglvgealrtgrpvilndleedpdkkglp 84 
                                   +l++v++ l e     + +g++++  ++++l+l+a+ ++  e+       lg+gl+  a+ +++ v   d++++p    l 
  gi|13541651|ref|NP_111339.1|  10 VLQEVCRILKESnKkYDwVGVYVM--ENRKLKLEAFVGEKTEHEVIN---LGDGLCSLAVLKNEVVNEYDVKSNPK--YL- 82 
                                   566666666664224557777777..458888887776666665555...8****999999976333333555443..33. PP

                                   HHHHTT--EEEEEE-TTS---EEEEES......--HHHHHHHHHHHHHHH CS
                         GAF_2  85 aghaglrsflavPlisegrvvGvlnlyankppafdeedlelLeelaeqia 134
                                   a  +  +s+++vP++++g+++G + + ++ ++afd +d e+L+ +a++ia
  gi|13541651|ref|NP_111339.1|  83 ACFPSTQSEIVVPVRYGGKPIGEIDIDSDTKGAFDKADEEFLSKVADLIA 132
                                   366899999***************************************98 PP

>> GAF  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   0.0   1.1e-10   6.5e-07       5     130 ..      10     132 ..       2     134 .. 0.72

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 1.1e-10
                                   HHHHHHHHHH.HHHTESEEEEEE..EEETTEEECEEEEECCEEEETTSHHHHHHHHHSSSEEESTGGTSTTHHTTHHHHHH CS
                           GAF   5 lldtvveelr.ellgadrvalyl..pdydGlhydipqasrwlfmkngrgicgqvlatgqplvipdstpdprfaqynrrdll 82 
                                   +l++v++ l+ +  ++d+v +y   ++ + l++ + +  +   +  g+g+c  ++ ++++++  d++  p +++ +     
  gi|13541651|ref|NP_111339.1|  10 VLQEVCRILKeSNKKYDWVGVYVmeNRKLKLEAFVGEKTEHEVINLGDGLCSLAVLKNEVVNEYDVKSNPKYLA-C----- 84 
                                   44444444444444579999987442222333323333333444449999998888799999999999999988.3..... PP

                                   HHTTESEEEEEEEEETTEEEEEEEEEESSS.CSHHHHHHHHHHHHHHHH CS
                           GAF  83 enmgirsslvvPlvndgelwGllvlhnpsp.pftreelellqvladqva 130
                                     + ++s +vvP++ +g+ +G +++++ ++  f+++++e+l  +ad++a
  gi|13541651|ref|NP_111339.1|  85 -FPSTQSEIVVPVRYGGKPIGEIDIDSDTKgAFDKADEEFLSKVADLIA 132
                                   .3566699*******************65668**************997 PP

>> GAF_3  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.0   2.3e-09   1.4e-05      20     124 ..      26     132 ..       2     134 .. 0.75

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 2.3e-09
                         GAF_3  20 evgalllldedgnklqvaagw.dgkpalsesldedsalarralssgevvse...psfaee.dglp.draalavPLvagrqv 94 
                                   +++ +++ ++++ kl +  g+ ++    +e++  ++ l+++a+   evv e   +s ++   + p +++ ++vP++ g ++
  gi|13541651|ref|NP_111339.1|  26 DWVGVYVMENRKLKLEAFVGEkTE----HEVINLGDGLCSLAVLKNEVVNEydvKSNPKYlACFPsTQSEIVVPVRYGGKP 102
                                   456788889898888777777233....356777777788777778887775554444431344437999*********** PP

                         GAF_3  95 iGvlalastkprafdaedlelleslArqia 124
                                   iG + + s+ ++afd +d+e+l+ +A++ia
  gi|13541651|ref|NP_111339.1| 103 IGEIDIDSDTKGAFDKADEEFLSKVADLIA 132
                                   ****************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.52
# Mc/sec: 815.61
//
Query:       gi|13541652|ref|NP_111340.1|  [L=297]
Description: small-conductance mechanosensitive channel protein [Thermoplasma volcanium GSS1]
Scores for complete 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-20   71.0   5.6    9.5e-20   71.0   5.6    2.1  2  MS_channel  Mechanosensitive ion channel
  ------ inclusion threshold ------
       0.56    9.6   6.9       0.85    9.0   6.9    1.2  1  Ceramidase  Ceramidase


Domain annotation for each model (and alignments):
>> MS_channel  Mechanosensitive ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -6.4   6.5         2   1.8e+04       4      28 ..      17      41 ..      11      61 .. 0.64
   2 !   71.0   5.6   1.1e-23   9.5e-20       3     133 ..      83     238 ..      81     292 .. 0.83

  Alignments for each domain:
  == domain 1  score: -6.4 bits;  conditional E-value: 2
                                  HHHHHHHHHHHHHHHTTT--SCCHH CS
                    MS_channel  4 lkiliivvgilivlsllgvnvsall 28
                                  + ++i+++++l vlsl+++ + ++ 
  gi|13541652|ref|NP_111340.1| 17 IVLIIVLLALLYVLSLFHIVPIKFS 41
                                  5567777777777777777654443 PP

  == domain 2  score: 71.0 bits;  conditional E-value: 1.1e-23
                                   HHHHHHHHHHHHHHHHTTT--SCCHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHTT-SS-TT-EEESS............. CS
                    MS_channel   3 ilkiliivvgilivlsllgvnvsallavlGalglalglalkdlisnlvaGiillfekpfkiGDlveig............. 70 
                                   i+++l ++++ l+vl  lg++vs+++ + ++l++ +gla++++++n+++G++l++ +pfk+GD++ ++             
  gi|13541652|ref|NP_111340.1|  83 IISLLGYFIISLAVLAALGIDVSSVILGSAFLSAIIGLAAQSVLANVFGGLFLSIVRPFKLGDHIVVNtwqfpvsfpsypp 163
                                   788999*************************************************************************** PP

                                   ...........SEEEEEEEE-SSEEEEEETTSEEEEEEHHHHHTS-EEESSS.SSEEEEEEEE..EE-TTS-...H CS
                    MS_channel  71 ...........dieGtVediglrttkirtfdgrivtiPnsslvtsnieNlsresgtrrikvsi..gvtyssdvkkl 133
                                                +G+V di++  t+i   +g +v iPn+ +++++i+ l+++s t+++++++   ++++ + +k+
  gi|13541652|ref|NP_111340.1| 164 kyfsrdfiegsIYRGIVSDISINYTSIALESGDVVKIPNNIMIQAAIT-LRHGSVTVQARYEVpkYINFNDIYNKI 238
                                   *********98899**************************99988887.555344444443331145555553333 PP

>> Ceramidase  Ceramidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   6.9   9.4e-05      0.85     110     187 ..      17      91 ..       4      98 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 9.4e-05
                    Ceramidase 110 vllgvlltalavvvtllylvlkepvlhqvafalltvlvllrsiyliekkvdksdeaakkevkklallgliifllgfli 187
                                   ++l ++l+al  v++l+++v     +  +++a+++ lv++ ++ +++k v ++  + ++e k+l  + +ii llg++i
  gi|13541652|ref|NP_111340.1|  17 IVLIIVLLALLYVLSLFHIV--PIKFSRILYAVVIGLVIYAIVRIVTKYV-ERFISLHSEFKHLKYIVFIISLLGYFI 91 
                                   45556666777777777777..77999*******************9999.569999*******************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1242  (0.0692732); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); 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):               2  [number of targets reported over threshold]
# CPU time: 0.63u 0.31s 00:00:00.94 Elapsed: 00:00:00.49
# Mc/sec: 1822.63
//
Query:       gi|13541653|ref|NP_111341.1|  [L=430]
Description: major facilitator superfamily permease [Thermoplasma volcanium GSS1]
Scores for complete sequence (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   83.5  44.1    1.8e-15   56.7  18.0    2.1  2  MFS_1       Major Facilitator Superfamily
    1.1e-08   34.4  18.1     0.0007   18.6  14.5    2.2  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 !   32.4  18.7   5.2e-12   4.7e-08       5     181 ..      21     197 ..      17     224 .. 0.81
   2 !   56.7  18.0     2e-19   1.8e-15       2     182 ..     220     405 ..     219     413 .. 0.78

  Alignments for each domain:
  == domain 1  score: 32.4 bits;  conditional E-value: 5.2e-12
                         MFS_1   5 aflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll.fass 84 
                                   afl++++++++++ +   ++  lg+sp e+g+l ++   ++ +++l++Grlsdr G rr +++++ + ++  ++l+ f + 
  gi|13541653|ref|NP_111341.1|  21 AFLVSFGANTASSYIG-VYGVLLGSSPIEMGMLQAFSNSLSNAGQLFWGRLSDRTGYRRPWIFAASIALAINWILMaF-IR 99 
                                   6888888888888888.88889**************999*****************9995555555555554777767.78 PP

                         MFS_1  85 lw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslg...Wravfyilaivs 161
                                    +  l+++  +++l +++++ +  +l++d++    rg+ +++++  ++ G ++  l+  +l++ ++     ++f +  + +
  gi|13541653|ref|NP_111341.1| 100 TPyELIISYSIMSLISAMIAVNWFSLLTDISRYGSRGSFLSYINNISGTGNLISLLAMVFLLHGISrdqLVVPFSLGSVSY 180
                                   8879**************************************************999999997777887666666666666 PP

                         MFS_1 162 llafvlfllllpeepperkr 181
                                   + +++   l   +++++rk+
  gi|13541653|ref|NP_111341.1| 181 IASAI---LISKVKEVRRKT 197
                                   66666...555555555555 PP

  == domain 2  score: 56.7 bits;  conditional E-value: 2e-19
                         MFS_1   2 llaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalg.lllllf 81 
                                   ++a  + ++ +s+++p++p+++ +  ++s   ++ l+++  +++++ +  +G l+dr+ r +++++  +++++  l+++ f
  gi|13541653|ref|NP_111341.1| 220 FMAMNVQGFFWSMAWPIFPITIVSVMHFSLPMVSALTATNIVFTMLIQRAVGNLADRINRVPLIFANRIMLGFIpLMYGYF 300
                                   6788899***************************************************77777777666666664555558 PP

                         MFS_1  82 asslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsl 162
                                    s++  ++ + v +G+++g+ + ++++++ d++p+ +rg +i+++++++++ +  g + ggl++s++   ++  ++ ++++
  gi|13541653|ref|NP_111341.1| 301 -SNFLEFMGMEVYSGIASGLQNVVMNSYLMDIVPEGHRGEYISIINGFNGIIYFAGSMSGGLILSNFLGYLPLHAAVAITF 380
                                   .9999********************************************************99966663333333333333 PP

                         MFS_1 163 lafv.......lfllllpeepperkrk 182
                                     +        +  l+l  ++pe +r 
  gi|13541653|ref|NP_111341.1| 381 TIIAagrftssF--LFLGLKEPEARRG 405
                                   332212322322..4444444444443 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 !   17.4   0.2   1.8e-07    0.0016      18      86 ..      31      99 ..      16     118 .. 0.87
   2 !   18.6  14.5   7.8e-08    0.0007     156     374 ..     139     363 ..     102     369 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.8e-07
                    MFS_1_like 18 llPYltiylkskglkaseigiitlilpltsilsppiwgvlaDrfgkrkkvvilslllsavlflsllfip 86
                                     Y+++y    g ++ e g++ +    +s +++++wg l+Dr+g r + + +++++ a+ ++ + fi 
  gi|13541653|ref|NP_111341.1| 31 ASSYIGVYGVLLGSSPIEMGMLQAFSNSLSNAGQLFWGRLSDRTGYRRPWIFAASIALAINWILMAFIR 99
                                  3459********************************************************999888885 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 7.8e-08
                    MFS_1_like 156 vGyaifafitGilidhysvnllp.......ysallyvlaallvisllvvlilnetekesklkvtksl.qvllnilknpevi 228
                                   ++y+     tG li  + + +l        +++ + +  + +++s ++  i + +e  +k+ +tk+  + + +  +n+  +
  gi|13541653|ref|NP_111341.1| 139 LSYINNISGTGNLISLLAMVFLLhgisrdqLVVPFSLGSVSYIASAIL--ISKVKEVRRKTVLTKNIiRTVSEARNNRYFF 217
                                   567777778888888888877766876666545555555666666666..4444444555554443326677777788888 PP

                    MFS_1_like 229 ifllvalilgmswgiienFlflYL.kelgasntllGslvalgvvaeiplfffaeklleklGhvklliiallayilrfllya 308
                                     ++++ + g++w++++  + + + + + +s  ++++l+a   v ++ +     +l +++  v l+++  ++  +  l+y+
  gi|13541653|ref|NP_111341.1| 218 NYFMAMNVQGFFWSMAWPIFPITIvSVMHFSLPMVSALTATNIVFTMLIQRAVGNLADRINRVPLIFANRIMLGFIPLMYG 298
                                   89999***********998888777999***************************************************** PP

                    MFS_1_like 309 iienawlvlpievLhgisfgllwaaaveyvskiapksleatgqgllsglyfglGralGsliGGllw 374
                                   +++n+   + +ev +gi+ gl  +++ +y  +i+p+++++ ++++++g+  g+  + Gs+ GGl+ 
  gi|13541653|ref|NP_111341.1| 299 YFSNFLEFMGMEVYSGIASGLQNVVMNSYLMDIVPEGHRGEYISIINGF-NGIIYFAGSMSGGLIL 363
                                   ************************************************9.89***********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (430 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       539  (0.030063); expected 358.6 (0.02)
Passed bias filter:                      224  (0.0124937); 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: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 2734.01
//
Query:       gi|13541654|ref|NP_111342.1|  [L=798]
Description: DNA polymerase II [Thermoplasma volcanium GSS1]
Scores for complete 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-63  212.8   0.1    1.5e-62  211.8   0.1    1.5  1  DNA_pol_B       DNA polymerase family B
    1.3e-15   57.3   1.5    6.8e-12   45.2   0.1    2.6  2  DNA_pol_B_exo1  DNA polymerase family B, exonuclease domain
    0.00019   21.2   0.0     0.0004   20.1   0.0    1.4  1  DNA_pol_B_exo2  Predicted 3'-5' exonuclease related to the ex
    0.00043   20.0   0.0    0.00099   18.9   0.0    1.5  1  DNA_pol_A_exo1  3'-5' exonuclease
  ------ inclusion threshold ------
       0.44    9.3   7.1       0.13   11.1   1.9    2.6  3  DNA_pol_B_2     DNA polymerase type B, organellar and viral


Domain annotation for each model (and alignments):
>> DNA_pol_B  DNA polymerase family B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  211.8   0.1   4.2e-66   1.5e-62       5     457 ..     353     754 ..     349     756 .. 0.91

  Alignments for each domain:
  == domain 1  score: 211.8 bits;  conditional E-value: 4.2e-66
                                   HHHHS-HHHHHHHHHHHHHHHTTBE-B-----.--SS.-S----BE----EEESS-EEEEEETTHHHHHHHHTT-STTTCE CS
                     DNA_pol_B   5 rvledgqqirveslLlrlakeegfilpdrtekkgkeeegYqGatVlePkkglydkpvlvlDFaSLYPsiiqahNlcyttlv 85 
                                    v + g +  v s+L+r+a++e++ +p ++ ++ ke+ + qG+ V     gly+ +v+vlDF+S+YPs+i+++N+c+ttl+
  gi|13541654|ref|NP_111342.1| 353 DVANAGTSNYVDSILIRAADRENIGVP-MNAHNLKED-EIQGGYVHTIGAGLYS-NVIVLDFKSMYPSMIIKYNVCFTTLD 430
                                   5667899999*****************.888866666.8**************7.5899*********************9 PP

                                   -HCCHCCT--BTT...TEEE-TCC-EEE-TTS---HHHHHHHHHHHHHHHHHHHHHCS--HHHHHHHHHHHHHHHHHHHHH CS
                     DNA_pol_B  86 aseeeakeleaedeyleveveprlvefvkksvregllpklLkdllakRkaikkelkeekdefekalldkqQlalKvtaNsv 166
                                    + e               v+p + +f+++++++gl+p++L++l+a R  +kk++ke+k+e e+  +d  Q a+Kv++N++
  gi|13541654|ref|NP_111342.1| 431 PKGEI--------------VSPTGIRFLSPEKKKGLIPRILQELMADRDDVKKRMKEAKSEDERLFYDGIQNAIKVLMNTF 497
                                   98876..............5577899******************************************************* PP

                                   HHHHTSTTSTT--HHHHHHHHHHHHHHHHHHHHHHHHT...SSGGGT-SS.....T-EEEEEBSSEEEEE-S-SSHHHHHH CS
                     DNA_pol_B 167 YGftGvansrlpclalAasvTtiGRemLektkelvekkaellskllalpeeaeeeklkviYGDTDSvfielkvkdveellk 247
                                   YG++  +  r+   ++ + +T+  Re+++++ +++e+                  + +viYGDTDSvf+e +    e+++k
  gi|13541654|ref|NP_111342.1| 498 YGVLASSFYRFTDPKIGSAITAFARETIKHIIDVLESS-----------------GHRVIYGDTDSVFVESGDVRQEDAIK 561
                                   ************************************88.................99************************ PP

                                   HHHHHHHHHHT.TSTTT--EEEEEEEEEEEEE.ETTEEEEEEEEESSTTSEEEEESSGGGSTTS-HHHHHHHHHHHHHHSS CS
                     DNA_pol_B 248 igkelaeevseklfkkplklefekvykkllLi.sKKkYaglkvektskanklliKGvdlvRrdncklvkevikkvlelllk 327
                                   +gkel +++se   ++ l l+f  v+ +   + +KK+Yag  v  ++ +++++iKG ++ R d+ +l+++  +kv++ +l 
  gi|13541654|ref|NP_111342.1| 562 TGKELSQKLSE---EEGLTLDFQMVLDPFFSHgAKKRYAGKCVYPEDMKGEIIIKGYEVRRTDSFDLQSTALSKVIDFILD 639
                                   ***********...77789*********997747**********999999*****************************98 PP

                                   S....S-HHHHHHHHHHHHHHHHHHHHTT-S-GGGG-EEEEESS.CCCS..SGCCSHHHHHHHHHHHHCSS---TTCEEEE CS
                     DNA_pol_B 328 deteersleeglealksilkdvleeleenkvplekfvlskelskepeny..ksknlphlevakrlkkrneeapevgdrisY 406
                                         +++ ++++  +++k+v++   + ++++e +v+s++++   ++y  ++ +l+++ +a++l +r +e+  +g ++s+
  gi|13541654|ref|NP_111342.1| 640 R-----DVQGAINYADDLVKKVRN--GDPSIDIESLVISRTVKD-FSSYkaNTDSLANIRAARKLIER-GETFVPGMKVSW 711
                                   8.....9999**999999976665..47789***********99.56663667789**********99.79999******* PP

                                   EEBETSS.....SS-GGGTEEEHHHHHHCCSEB-HHHHHHTTHHHHHHHHT CS
                     DNA_pol_B 407 vivekkkevkkknllaseraedpeyvleknlpidieyYlsqllkevarlle 457
                                   ++++ kk        + + +e   y ++ + + d +yY ++l +++ r+++
  gi|13541654|ref|NP_111342.1| 712 IVTNGKK--------TPQEVEPYIYGSKLESKPDWDYYAKRLSETLNRVID 754
                                   *999975........445555558888888899999999999999999886 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 !   11.0   0.2   4.6e-05      0.17      71     194 ..      78     190 ..      24     198 .. 0.70
   2 !   45.2   0.1   1.9e-15   6.8e-12     235     298 ..     197     261 ..     189     275 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 4.6e-05
                                   EEEEEESSTCHHHHHHHHHHHCCCCCCCCSSS--HHHHHHHHCTS-TTCEEEEETEEEEGCC--C-.SEEEEEETTTSCEE CS
                DNA_pol_B_exo1  71 ylkvsvsnpnelkkirkelspleeivdvyeydvdylerflidnkivgfgwysvkkylvraegkisncdveidcdvddliak 151
                                   + ++++++p ++++ r++       ++v  +d++++ rf++d ++  +++ ++  ++++ ++   ++d+ +++d+ ++i++
  gi|13541654|ref|NP_111342.1|  78 VKRIYIRSPWKVPEYRRRC-----PFEVLAADIPFHHRFIYDFDL--GACVRITGEDISGTEGNFTTDLVLKIDKIENIPD 151
                                   6677777777777777777.....3889999**********9887..6678888777776666666677777777777773 PP

                                   TTTCCS-EEEEEEEEEETEETTSEETTTT..--EEEEEEEE.CC CS
                DNA_pol_B_exo1 152 pkesepplrvlsFDIeckskkgkfpdaensedpiiqIscvl.dg 194
                                       + +l+vlsFD e     ++  d+ +    +i  s+++ d 
  gi|13541654|ref|NP_111342.1| 152 F---NVNLKVLSFDVENEINRENVEDYGK--ILVIGYSIMFgDI 190
                                   3...369999*******999999999999..7888777777333 PP

  == domain 2  score: 45.2 bits;  conditional E-value: 1.9e-15
                                   ESSHHHHHHHHHHHHHHH--SEEEESSTTTTHHHHHHHHHHHCCT.CCHCG.SCCSCTCEECCCC CS
                DNA_pol_B_exo1 235 fdsEkelLqaflefikqydPdvitgYNidnFDlpYilnRakelyk.vklsklgrlnkggrskvse 298
                                   + +Eke+L +f+++i+ +dPdvitgYNid +D+ +i+ R++++ + ++l + g ++++   + ++
  gi|13541654|ref|NP_111342.1| 197 HGDEKEILYRFIDLIRAEDPDVITGYNIDGYDMLVIQRRMEQYGIhLNLGRDGSVPRRIMDQFWR 261
                                   569**************************************999757899988888666666555 PP

>> DNA_pol_B_exo2  Predicted 3'-5' exonuclease related to the exonuclease domain of PolB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   1.1e-07    0.0004      26     177 ..     189     338 ..     178     348 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 1.1e-07
                DNA_pol_B_exo2  26 kvkslgeeessekelikkffegvekkkpqlVs.fngrgfDlpvleyralkhgvsapkyfdegdedrekkwnnylsrystr. 104
                                   ++++ ge + +eke++ +f++ ++++ p +++ +n  g+D+ v++ r  ++g++ +   d +      +  + + r + r 
  gi|13541654|ref|NP_111342.1| 189 DIQKKGEIHGDEKEILYRFIDLIRAEDPDVITgYNIDGYDMLVIQRRMEQYGIHLNLGRDGSV---PRRIMDQFWRVHGRl 266
                                   55666778889*****************98855********************9876555544...788889999999998 PP

                DNA_pol_B_exo2 105 hlDLmdllseygaranakLdelakllglPGKlgvdGskVaelyqegklkeireYcetDvlnTYlvylrlellr 177
                                     D    + +    ++++Ld +a  l   GK  +d  ++ + +q+ +++e+ +Yc  D+  T  ++ +l++l+
  gi|13541654|ref|NP_111342.1| 267 ISDTWWNVKKILHPKHESLDYIAMKLLGEGKDSIDRLNIEAEWQK-RQDEVISYCIKDADLTLRIFEKLRVLE 338
                                   889999999999999********999889**************97.5688999*****999999998887765 PP

>> DNA_pol_A_exo1  3'-5' exonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   2.8e-07   0.00099     113     172 ..     278     335 ..     261     337 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 2.8e-07
                                   TTHSTTSSHHHHHHHHHS..B---GHCCTTSSTTTSSS-HHHHHHHHHHHHHTHHHHHHHHH CS
                DNA_pol_A_exo1 113 ldyershsLdsLaekylg..dleldkeeqiakwqkarplleeqllYAaeDadvllrlfkkLt 172
                                   l ++   sLd++a+k+lg  +  +d   + a wq +r   +e+++Y+ +Dad++lr+f+kL+
  gi|13541654|ref|NP_111342.1| 278 LHPKH-ESLDYIAMKLLGegKDSIDRLNIEAEWQ-KR--QDEVISYCIKDADLTLRIFEKLR 335
                                   44444.69**********999999999*******.55..69*******************97 PP

>> DNA_pol_B_2  DNA polymerase type B, organellar and viral
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   1.9   3.7e-05      0.13     212     247 ..     389     423 ..     290     429 .. 0.77
   2 ?   -2.2   0.0       0.4   1.4e+03     370     384 ..     486     500 ..     470     506 .. 0.76
   3 ?   -3.3   0.1      0.84     3e+03      21      73 ..     579     633 ..     576     685 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 3.7e-05
                   DNA_pol_B_2 212 ayrGGrcypsvlgiyeeniyvyDvnSlYPsamthyp 247
                                    + GG++  +  g +  n+ v D++S+YPs+  +y 
  gi|13541654|ref|NP_111342.1| 389 EIQGGYVHTIGAG-LYSNVIVLDFKSMYPSMIIKYN 423
                                   588****555455.55***************99875 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.4
                   DNA_pol_B_2 370 krsiaKlllNsLYGr 384
                                   +++ +K l+N+ YG 
  gi|13541654|ref|NP_111342.1| 486 IQNAIKVLMNTFYGV 500
                                   56789*********6 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 0.84
                   DNA_pol_B_2  21 dgnfilkslskkleikkiiwkngkilsldikyk....evkitvrDsllllptsLrkl 73 
                                   d++++l+ ++ ++   k +++ +++++ d+k +     +++  +Ds+ l +t L+k 
  gi|13541654|ref|NP_111342.1| 579 DFQMVLDPFFSHG--AKKRYAGKCVYPEDMKGEiiikGYEVRRTDSFDLQSTALSKV 633
                                   6777777777766..677777778888877777777788888899999999999984 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (798 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       611  (0.0340789); expected 358.6 (0.02)
Passed bias filter:                      519  (0.0289475); 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: 0.86u 0.37s 00:00:01.23 Elapsed: 00:00:00.59
# Mc/sec: 4075.14
//
Query:       gi|13541655|ref|NP_111343.1|  [L=301]
Description: ornithine cyclodeaminase [Thermoplasma volcanium GSS1]
Scores for complete 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  145.5   0.6    2.3e-42  145.1   0.6    1.1  1  OCD_Mu_crystall  Ornithine cyclodeaminase/mu-crystallin famil
    0.00016   22.2   0.1    0.00044   20.8   0.1    1.7  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
    0.00053   20.1   0.3      0.001   19.2   0.1    1.5  2  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
  ------ inclusion threshold ------
      0.076   13.3   0.1       0.18   12.1   0.1    1.6  1  Halo_GVPC        Halobacterial gas vesicle protein C (GVPC) r


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 !  145.1   0.6   5.1e-46   2.3e-42       7     306 ..       5     290 ..       1     298 [. 0.91

  Alignments for each domain:
  == domain 1  score: 145.1 bits;  conditional E-value: 5.1e-46
                                   -HHHHHCCH-HCCCHHHHHHHHHHHHCC-CE----EEEEECCGTEEEEEEEEEETTTTEEEEEEEEEETTTCCCTSSSEEE CS
               OCD_Mu_crystall   7 taveveeelllddlakaveeafrrlasgkvkkpprvalevkdsrgelevmpaylagrellgvKlvnshpenkksglptvta 87 
                                   t+ +v ++  ++++++av eaf+++ +g++    rv+ +++d  g+l+ mpa++++ +  g+K +        +g      
  gi|13541655|ref|NP_111343.1|   5 TEDDVDKNFDMKAAINAVREAFEEYGKGRAYSSTRVRTFSQD--GVLNTMPAAMEKYHISGLKSYYATR----NG---AKF 76 
                                   77899*************************************..************9999999885432....23...356 PP

                                   EEEEE-TTT--EEEEEE-HHHHHHHHHHHHHHHHHHHS-TT--EEEEE--SHHHHHHHHHHCCCS--SEEEEE-SSHHHHH CS
               OCD_Mu_crystall  88 lvvLndpetGvplalmdatlltalRTaAvsavaakyLarkdasvlaiiGaGvqaetqlealkavldikevriydrdeeaae 168
                                   +vvL+d+     la+++a+ l ++RT+Av a a+  L  k+ + +aiiG G qaetqle + +v++ +e+r+y r++e a 
  gi|13541655|ref|NP_111343.1|  77 VVVLFDTAADELLAIIEANRLGQIRTGAVTAYATSILH-KNVEIFAIIGSGFQAETQLEGMLKVANPTEIRVYSRNQEHAR 156
                                   89********************************9995.89**************************************** PP

                                   HHHHHCCS..CTT-EEECSCHHHHTTSSEEEE----SS-SB-GGGS-TT-EEEE-S--STT--SB-HHHHHCCEEEE.SHH CS
               OCD_Mu_crystall 169 kfaenlqe.fefevsackseeeavegadivvtvTaakapilkaewvkpGahinavgadapgkteLdddilkradifv.dse 247
                                    f e+ ++ f++ ++a++s+e a  gad ++t+T ++ pi+  ++++   hin+ g++  +++e + ++l  a+i+v +++
  gi|13541655|ref|NP_111343.1| 157 NFSERSSKkFGVSIRAVESAEAALIGADTITTITNSNVPIVYRKYLGDEYHINLAGSNYINRREAESAVLSDANIVVtEHL 237
                                   ******9989*******************************************************************9888 PP

                                   HHHHHC.CCCHCHHHTTSSTCGGEEEEHHHHHCTSS-..-STTSEEEEE----HHHHHHH CS
               OCD_Mu_crystall 248 aqaree.GeiqvaiekgvlaedakvaelgeviaGkkpGRtsdeeitlfdsvGlaveDvaa 306
                                   +q  +e  ei       v+   +   el +v   ++p R s+   t+f+s+G++ eD+  
  gi|13541655|ref|NP_111343.1| 238 EQSLIEsVEISE----YVKLGGK-PIELKDVA--VDPTRYSKFHRTVFKSMGIGLEDIIS 290
                                   887665156666....4444444.469***97..7999*******************965 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.1   9.8e-08   0.00044       2      60 ..     120     180 ..     119     195 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 9.8e-08
                                   EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC....-EEECECHHHHHH CS
                 F420_oxidored   2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg....vkvtavdneeaae 60 
                                   ++iiG+G ++e+ ++g+l+   +p+ei+v  srn+e a+ + e+ +    v++ av+ +eaa 
  gi|13541655|ref|NP_111343.1| 120 FAIIGSGFQAETQLEGMLKVA-NPTEIRVY-SRNQEHARNFSERSSkkfgVSIRAVESAEAAL 180
                                   69*****************96.9*****55.**********9887766666666666666654 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   0.1   2.2e-07     0.001      15      93 ..     120     200 ..     108     209 .. 0.86
   2 ?   -3.1   0.0       1.7   7.5e+03      74      98 ..     227     240 ..     220     265 .. 0.53

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 2.2e-07
                                   EEEES-SHHHHHHHHHHHC.CT-CEEEEEESSHHHHHHHHHHH.T.ET-EEEEGCGHHHHHHT-SEEEE-SSSSS-SB-HH CS
                  Shikimate_DH  15 vlliGaGemaelvakhLla.kgvkkvvvaNRtlerakelaeel.kgeeiealkleelkellaeadvvisataseepileke 93 
                                     +iG G  ae  ++ +l+ ++ +++ v  R++e+a+++ e+  k+  ++++++e+ +++l  ad + + t+s+ pi+ ++
  gi|13541655|ref|NP_111343.1| 120 FAIIGSGFQAETQLEGMLKvANPTEIRVYSRNQEHARNFSERSsKKFGVSIRAVESAEAALIGADTITTITNSNVPIVYRK 200
                                   469****999998886555169******************99956667899**************************9876 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1.7
                                   HT-SEEEE-SSSSS-SB-HHHHHCC CS
                  Shikimate_DH  74 aeadvvisataseepilekeeveea 98 
                                   ++a++v+            e++e++
  gi|13541655|ref|NP_111343.1| 227 SDANIVV-----------TEHLEQS 240
                                   3334433...........3333333 PP

>> Halo_GVPC  Halobacterial gas vesicle protein C (GVPC) repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1     4e-05      0.18      12      25 ..      16      29 ..      14      31 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4e-05
                     Halo_GVPC 12 reefdatqdaFeaY 25
                                  +++++a+++aFe+Y
  gi|13541655|ref|NP_111343.1| 16 KAAINAVREAFEEY 29
                                  689**********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       542  (0.0302304); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 1951.40
//
Query:       gi|13541656|ref|NP_111344.1|  [L=343]
Description: glucosamine 6-phosphate synthase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.9e-17   62.7   0.1    8.4e-10   38.6   0.0    2.5  2  SIS         SIS domain
     0.0018   18.4   0.2     0.0056   16.7   0.2    1.8  1  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 !   21.7   0.1   1.5e-08   0.00014       7     118 ..      45     153 ..      43     162 .. 0.83
   2 !   38.6   0.0   9.3e-14   8.4e-10       2      75 ..     195     268 ..     194     315 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 1.5e-08
                                   EEEEEESHHHHHHHHHHHHHHHHHHTSEEEEEEHHHHHHTGGGG-STTCEEEEEESSSHHHHHHHHHHHHHHTTSEEEEEE CS
                           SIS   7 riyvlGaGtsyaiakelalkleeiggivvevedaselkhgvlalideddlvilisfsgetkdlvaaaelakergakiiaIT 87 
                                    i ++G Gt y+++  ++  +e+ g     v++a+e    +l++++    +i is++g tk++v+a  +a+   +k+ +IT
  gi|13541656|ref|NP_111344.1|  45 DITFIGNGTAYHAGYIGSGIIEKYGL-RRRVVQAYE----YLNYLKYSSSFIGISHTGKTKSTVDAMLKARIT-GKTAGIT 119
                                   689**************999977765.566777888....799***********************9988765.6899*** PP

                                   SSTTSHHHHHSSEEEEEEEECHC...SSSHCHHH CS
                           SIS  88 dskgsplareadlalyinaepet...lvastksl 118
                                   +  +spl+++ d+ + i  e+++     a+++s 
  gi|13541656|ref|NP_111344.1| 120 HYRDSPLYNSVDVPILIEDEDKSlcnTKAFFNSA 153
                                   ************9999999999955545555544 PP

  == domain 2  score: 38.6 bits;  conditional E-value: 9.3e-14
                                   HCTSSEEEEEESHHHHHHHHHHHHHHHHHHTSEEEEEEHHHHHHTGGGG-STTCEEEEEESSSHHHHHHHHHHH CS
                           SIS   2 LakakriyvlGaGtsyaiakelalkleeiggivvevedaselkhgvlalideddlvilisfsgetkdlvaaael 75 
                                   L + k i+vlG+G ++++a+e+a k+ e +  ++e+ + +e+ hg  a++de++lvil+ + + + + ++ ++ 
  gi|13541656|ref|NP_111344.1| 195 LDNVKDIFVLGSGPNFPVAREAAQKIREATHLHAEGIELEEFNHGCTAVMDENTLVILVETERDKERANQIVRA 268
                                   67889******************************************************976666655555544 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 !   16.7   0.2   6.3e-07    0.0056       9     140 ..     192     321 ..     184     324 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 6.3e-07
                                   HHHHTT.SEEEEE-..TT-THHHHHHHHHHHHTT----B---.SSHHHHHHHTTSS-GGGGTTEEEEEESSHH........ CS
                    bact-PGI_C   9 Alelag.klpviygssellevaArRfknqlnenAKipafagvlpeanhneivgleaeeelkkrlrlvllrdeeehprvkkr 88 
                                     el + k   ++g s++  ++Ar +++++ e   ++a   +l e+nh   ++++      +++ ++l++ e++++r +++
  gi|13541656|ref|NP_111344.1| 192 SAELDNvKDIFVLG-SGPNFPVAREAAQKIREATHLHAEGIELEEFNHGCTAVMD------ENTLVILVETERDKERANQI 265
                                   55666666677899.9999***********************************4......45666666666666677776 PP

                                   HHHHH.....HHHTTTSSEEEEE---SSSHHHHHHHHHHHHHHHHHHHHHHCT---S CS
                    bact-PGI_C  89 aeivk.....elaeergvrvtevkaegesplerlaslillgDfvSvylAllrgvDPt 140
                                   +++ +     ++a +  ++++  +  +++ l+  ++++ l  + ++ylA+ rg++P 
  gi|13541656|ref|NP_111344.1| 266 VRASSyvgspTMAINGDAEISYYSDYQDEYLSPFVNMVPLY-YLAYYLAVRRGINPD 321
                                   66665222223344444666666667888888888888776.99***********95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (343 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       500  (0.0278878); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.63u 0.31s 00:00:00.94 Elapsed: 00:00:00.53
# Mc/sec: 1944.09
//
Query:       gi|13541657|ref|NP_111345.1|  [L=294]
Description: 3-hydroxyacyl-CoA dehydrogenase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-66  223.9   0.9    1.6e-66  223.6   0.9    1.1  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
    3.5e-24   85.2   0.0    1.4e-23   83.3   0.0    1.9  2  3HCDH            3-hydroxyacyl-CoA dehydrogenase, C-terminal 
    1.6e-07   31.7   1.0    3.1e-07   30.7   0.4    1.8  2  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
      3e-06   27.3   0.6    1.1e-05   25.5   0.6    2.0  1  NAD_Gly3P_dh_N   NAD-dependent glycerol-3-phosphate dehydroge
    9.7e-06   26.1   0.9    2.1e-05   25.0   0.9    1.6  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
    6.4e-05   22.3   0.2    0.00011   21.6   0.2    1.2  1  Pyr_redox_2      Pyridine nucleotide-disulphide oxidoreductas
    0.00015   22.3   0.4    0.00031   21.2   0.4    1.5  1  Pyr_redox        Pyridine nucleotide-disulphide oxidoreductas
    0.00016   21.3   1.5    0.00039   20.1   1.4    1.7  1  UDPG_MGDP_dh_N   UDP-glucose/GDP-mannose dehydrogenase family
     0.0029   17.0   0.4     0.0056   16.1   0.4    1.5  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
     0.0037   17.5   0.3      0.011   16.0   0.3    1.8  1  TrkA_N           TrkA-N domain
     0.0062   16.1   0.1      0.013   15.1   0.0    1.6  2  adh_short_C2     Enoyl-(Acyl carrier protein) reductase
     0.0062   16.2   0.0     0.0082   15.8   0.0    1.3  1  ApbA             Ketopantoate reductase PanE/ApbA
  ------ inclusion threshold ------
      0.014   15.6   0.1      0.069   13.4   0.1    2.0  2  NAD_binding_8    NAD(P)-binding Rossmann-like domain
      0.015   14.6   0.1      0.021   14.1   0.1    1.3  1  AlaDh_PNT_C      Alanine dehydrogenase/PNT, C-terminal domain
      0.019   15.2   0.1      0.062   13.6   0.1    1.9  1  Spidroin_MaSp    Major ampullate spidroin 1 and 2
       0.02   14.7   0.6      0.035   13.9   0.5    1.7  1  DFP              DNA / pantothenate metabolism flavoprotein
       0.02   15.3   0.0      0.044   14.2   0.0    1.7  1  NAD_binding_7    Putative NAD(P)-binding
      0.029   13.8   0.1      0.061   12.8   0.0    1.5  1  adh_short        short chain dehydrogenase
      0.052   13.8   0.1      0.081   13.2   0.1    1.4  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
      0.085   12.9   0.1       0.17   11.9   0.1    1.6  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
       0.14   12.6   0.0        0.2   12.1   0.0    1.3  1  XdhC_C           XdhC Rossmann 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 !  223.6   0.9   1.9e-69   1.6e-66       1     179 [.       5     186 ..       5     187 .. 0.99

  Alignments for each domain:
  == domain 1  score: 223.6 bits;  conditional E-value: 1.9e-69
                                   EEEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHH...HHHCCTTTTSS-HHHHCCCHHCEEEES-HHHHHC CS
                       3HCDH_N   1 kvaviGaGtmGagiaavfasagleVvlvdiseealekalekiek...sleklvekgklkeeeveaalarisfttdleeavd 78 
                                   +++v+G+G+mG+gia+vfa+ag++V++vd++e++le+al++i++    l++lv+kg+++e++ +++++ris++t++ ++ +
  gi|13541657|ref|NP_111345.1|   5 NIGVVGSGVMGQGIAQVFAKAGYKVTIVDVNEQILENALKAISDgkyGLRNLVNKGQISENDLNSIMSRISTSTEYTSLSS 85 
                                   69*****************************************99999********************************* PP

                                   -SEEEE-S-SSHHHHHHHHHHHHCCS-TTSEEEE--SSS-HHHHCCCSSSGGGEEEEEE-SSTTT--EEEEEE-TT--HHH CS
                       3HCDH_N  79 adlviEavvEnlelKrkvfaelekiakpdailasnTSslsiselaealkrperviglHFfnPpplmkLvEvvrgekTseet 159
                                   +d+++Eav+E+l++Kr+vfa+le+ +++d+ilasnTS+++i+e+++ l+ +er+ig+H+fnP+p+mkL+Evv+++ Tseet
  gi|13541657|ref|NP_111345.1|  86 CDFIVEAVPEDLRIKREVFAKLESNVSKDTILASNTSGIMIAEITSGLSYKERIIGMHWFNPAPVMKLIEVVKAQLTSEET 166
                                   ********************************************************************************* PP

                                   HHHHHHHHHHTT-EEEEECS CS
                       3HCDH_N 160 vatvvelakkigktpvvvkd 179
                                   ++t++elak+igk+p++v d
  gi|13541657|ref|NP_111345.1| 167 FNTTMELAKEIGKVPIKVAD 186
                                   ******************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 ?   -1.3   0.0         4   3.4e+03      52      85 ..      32      61 ..      13      72 .. 0.68
   2 !   83.3   0.0   1.6e-26   1.4e-23       1      92 [.     189     280 ..     189     284 .. 0.98

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 4
                                  HHHHHHHHHHHHHHTTTHGGHH-HHHHHHHHTT- CS
                         3HCDH 52 ldvakkilevlaeelgerayapsplleklveagr 85
                                  +dv+++ile   ++ ++ +y     l++lv++g+
  gi|13541657|ref|NP_111345.1| 32 VDVNEQILENALKAISDGKYG----LRNLVNKGQ 61
                                  566666666666666666666....555555555 PP

  == domain 2  score: 83.3 bits;  conditional E-value: 1.6e-26
                                   TTTHHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHHHHHHHTTTHGGHH-HHHHHHH CS
                         3HCDH   1 GFvvnRvlapllneavrlveegvaspediDaamrlglGlpmGpfelldlvgldvakkilevlaeelgerayapsplleklv 81 
                                   GF+++R +  +l  a+r +e+gva+ +diDa+++ ++G+pmGpfel+d +g+d++++i+ +l+ee+g++++ p+  l+++v
  gi|13541657|ref|NP_111345.1| 189 GFYTTRFIEGWLLSAIRSAEQGVATRKDIDAMTKMAFGFPMGPFELMDIIGIDTVYHIATYLYEETGDPQFIPPISLKQMV 269
                                   9******************************************************************************** PP

                                   HTT--BGGGTB CS
                         3HCDH  82 eagrlgrktgk 92 
                                    +g +g k+ k
  gi|13541657|ref|NP_111345.1| 270 LNGYIGDKKVK 280
                                   *******9875 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 !   30.7   0.4   3.6e-10   3.1e-07       1      89 [.       5     120 ..       5     141 .. 0.78
   2 ?   -3.0   0.0       8.5   7.2e+03      91     115 ..     164     188 ..     158     188 .. 0.74

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 3.6e-10
                                   EEEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT.........................EEE-SSHH.HHHHH CS
                 NAD_binding_2   1 kigfiGlGvMGsnmalnllkagykvavynrtkekveelvaeg.........................akaaesie.elvas 55 
                                   +ig++G GvMG+ +a+ ++kagykv++++++++ +e+++++                           ++ +s e   ++s
  gi|13541657|ref|NP_111345.1|   5 NIGVVGSGVMGQGIAQVFAKAGYKVTIVDVNEQILENALKAIsdgkyglrnlvnkgqisendlnsimSRISTSTEyTSLSS 85 
                                   69******************************9999888886566888999999998888888777533333333245566 PP

                                   CSEEEE-SSSHHHHHHHHHS.HCCC--TT-EEEE- CS
                 NAD_binding_2  56 ldvvitmvkagkavdevieg.llealkkgdilidg 89 
                                   +d+++  v+++  ++  ++  l ++++k++il   
  gi|13541657|ref|NP_111345.1|  86 CDFIVEAVPEDLRIKREVFAkLESNVSKDTILASN 120
                                   69999999998887655554488888888887655 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 8.5
                                   ---HHHHHHHHHHHHHTT-EEEEEE CS
                 NAD_binding_2  91 tsspedtrelakelkekglkfldaP 115
                                      +++t elake+ +  +k+ d+P
  gi|13541657|ref|NP_111345.1| 164 EETFNTTMELAKEIGKVPIKVADVP 188
                                   4567788888888888777777776 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.6   1.2e-08   1.1e-05       2     107 ..       6     128 ..       5     180 .. 0.75

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 1.2e-08
                                   EEEE--SHHHHHHHHHHHTTT--EEEE-S-H....HHHHHHHH......HSSBTTTBTT----TTEE...EES-HHHHHTT CS
                NAD_Gly3P_dh_N   2 iavlGaGswGtalAkvlaenghevrlwvree....elieeine......ehenvkyLpgiklpenlv...attdlaealkg 69 
                                   i+v+G+G  G  +A+v+a++g +v++   +e    + +++i++      +  n+  + + +l++ +     +t+  ++l+ 
  gi|13541657|ref|NP_111345.1|   6 IGVVGSGVMGQGIAQVFAKAGYKVTIVDVNEqileNALKAISDgkyglrNLVNKGQISENDLNSIMSrisTSTE-YTSLSS 85 
                                   99***************************997887455555541111113345555555555554431003333.357889 PP

                                   --EEEE---HH..HHHHHHHHHCCC--TT-EEEE---SE...E CS
                NAD_Gly3P_dh_N  70 adiivlvvPsq..alrevlkklkgllkkkailvsliKGi...e 107
                                   +d+iv +vP    + rev++kl+  ++k++il+s + Gi   e
  gi|13541657|ref|NP_111345.1|  86 CDFIVEAVPEDlrIKREVFAKLESNVSKDTILASNTSGImiaE 128
                                   *********9622579********************9995532 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.9   2.5e-08   2.1e-05       2      93 ..       6     119 ..       5     123 .. 0.88

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 2.5e-08
                                   EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC........................-EEECECHHHH CS
                 F420_oxidored   2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg........................vkvtavdneea 58 
                                   ig++G+G mg+++a+ +++ag   ++++++ + n++ +e + ++++                         ++++++  + 
  gi|13541657|ref|NP_111345.1|   6 IGVVGSGVMGQGIAQVFAKAG---YKVTIV-DVNEQILENALKAISdgkyglrnlvnkgqisendlnsimSRISTSTEYTS 82 
                                   9********************...****88.999999999999999999*******************9989999999999 PP

                                   HHH-SEEEE-S-..HHHHHHHHHHCGHHHHTTSEEEE CS
                 F420_oxidored  59 aeeadvvvlavk..pedveevlselakdalkgklvis 93 
                                   ++++d++v av+   +   ev ++l ++ +k++++ s
  gi|13541657|ref|NP_111345.1|  83 LSSCDFIVEAVPedLRIKREVFAKLESNVSKDTILAS 119
                                   99*********83334566788888888888887766 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.2   1.3e-07   0.00011     144     186 ..       5      47 ..       2      50 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 1.3e-07
                                   EEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2 144 rivvvGgGyiGvElAaalaklgkevtlveardrllraldkels 186
                                   +i vvG+G+ G  +A+++ak+g++vt+v+ ++++l++  k++s
  gi|13541657|ref|NP_111345.1|   5 NIGVVGSGVMGQGIAQVFAKAGYKVTIVDVNEQILENALKAIS 47 
                                   688********************************76666665 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.4   3.7e-07   0.00031       2      36 ..       6      40 ..       5      48 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 3.7e-07
                                  EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSST CS
                     Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkllr 36
                                  + vvG+G+ g   A+++a+ g kVt+v+ ++++l 
  gi|13541657|ref|NP_111345.1|  6 IGVVGSGVMGQGIAQVFAKAGYKVTIVDVNEQILE 40
                                  78*******************************92 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   1.4   4.5e-07   0.00039       2      57 ..       5      59 ..       4     101 .. 0.71

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 4.5e-07
                                  EEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHHCTTS-SS--TTHHHHHHH CS
                UDPG_MGDP_dh_N  2 kisviGlGYvGlvtaavlaeighevigvDideekvdklnsgkipiyepgLeelvkk 57
                                  +i v+G+G +G   a v+a++g +v++vD++e+  ++  +  i+    gL++lv+k
  gi|13541657|ref|NP_111345.1|  5 NIGVVGSGVMGQGIAQVFAKAGYKVTIVDVNEQILENALK-AISDGKYGLRNLVNK 59
                                  79*****************************986654332.333344555555554 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.4   6.6e-06    0.0056      37      73 ..       4      40 ..       1      62 [. 0.81

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 6.6e-06
                                  SEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHH CS
                  2-Hacid_dh_C 37 ktvGiiGlGrIGqavakrlkafgmkviaydrskkkee 73
                                  + +G++G G +Gq +a+++++ g kv+++d++++  e
  gi|13541657|ref|NP_111345.1|  4 SNIGVVGSGVMGQGIAQVFAKAGYKVTIVDVNEQILE 40
                                  579***************************9987444 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.3   1.3e-05     0.011       3      38 ..       8      43 ..       6      53 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.3e-05
                                  EES-SHHHHHHHHHHHH.TTEEEEEEESSHHHHHHHH CS
                        TrkA_N  3 iiGlGrvGrslaeeLse.ggkdvvvidkdeerveelr 38
                                  ++G G +G+ +a+ + + g+ +v+++d +e+ +e++ 
  gi|13541657|ref|NP_111345.1|  8 VVGSGVMGQGIAQVFAKaGY-KVTIVDVNEQILENAL 43
                                  9****************777.6*********999875 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 !   15.1   0.0   1.5e-05     0.013       6      39 ..      14      48 ..       7      86 .. 0.84
   2 ?   -3.3   0.0       6.3   5.4e+03      29      44 ..     164     180 ..     155     188 .. 0.46

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.5e-05
                                  HHHHHHHHHHHTT-EEEEEESSGGH.HHHHHHHHH CS
                  adh_short_C2  6 IGraiAkalaeeGaevvltdlneea.kkrveelae 39
                                  +G++iA+ +a++G++v ++d+ne+  +++++++ +
  gi|13541657|ref|NP_111345.1| 14 MGQGIAQVFAKAGYKVTIVDVNEQIlENALKAISD 48
                                  7***********************97777776654 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 6.3
                                   GH.HHHHHHHHHHTTSE CS
                  adh_short_C2  29 ea.kkrveelaeelgae 44 
                                   e+  +++ ela+e+g+ 
  gi|13541657|ref|NP_111345.1| 164 EEtFNTTMELAKEIGKV 180
                                   33344444555555433 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   9.6e-06    0.0082       1      61 [.       6      65 ..       6     141 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 9.6e-06
                                  EEEES-SHHHHHHHHHHHHHTHCEEEE-SCHHHHHHHHHCEEEEETT..CEEEEEECEEECCH CS
                          ApbA  1 iailGaGaiGsllaakLakagadvtlilrsrrlealkknGlrltseg..geeilrppealsae 61
                                  i ++G+G +G+ +a   akag++vt+++ ++   ++ +n l+  s+g  g ++l ++ ++s+ 
  gi|13541657|ref|NP_111345.1|  6 IGVVGSGVMGQGIAQVFAKAGYKVTIVDVNE---QILENALKAISDGkyGLRNLVNKGQISEN 65
                                  78*************************9988...56666666655555666666666655555 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   8.1e-05     0.069       1      31 [.       8      38 ..       8      58 .. 0.92
   2 ?   -0.9   0.0       2.4     2e+03      48      55 ..     141     148 ..     129     155 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 8.1e-05
                                  EE--SHHHHHHHHHHHCCTEEEEEE-SSSSS CS
                 NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrl 31
                                  +vG+G+ G  +A+  akag++v++++ ++++
  gi|13541657|ref|NP_111345.1|  8 VVGSGVMGQGIAQVFAKAGYKVTIVDVNEQI 38
                                  8************************988765 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 2.4
                                   S---EEET CS
                 NAD_binding_8  48 gahifhgs 55 
                                   g+h+f++ 
  gi|13541657|ref|NP_111345.1| 141 GMHWFNPA 148
                                   99***994 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 ?   14.1   0.1   2.5e-05     0.021      30      68 ..       5      43 ..       1      93 [. 0.86

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.5e-05
                                  EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHH CS
                   AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVtvlDvrparleqle 68
                                  ++ v+G Gv G+  +++ ++ g kVt++Dv+++ le+  
  gi|13541657|ref|NP_111345.1|  5 NIGVVGSGVMGQGIAQVFAKAGYKVTIVDVNEQILENAL 43
                                  678*****************************9999764 PP

>> Spidroin_MaSp  Major ampullate spidroin 1 and 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   7.2e-05     0.062      20      61 ..      54      93 ..      36      97 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 7.2e-05
                                  HHHCCCSS--TTCHHHHHHHHHHHHHCCSTTT-CCHHHHHHH CS
                 Spidroin_MaSp 20 sslvsagalnvaalsnvissvvsqvsasnpglsscdvlvqvL 61
                                   +lv++g+++ + l +++s ++++ +    +lsscd +v++ 
  gi|13541657|ref|NP_111345.1| 54 RNLVNKGQISENDLNSIMSRISTSTEYT--SLSSCDFIVEAV 93
                                  5789999999999999999998888877..7********985 PP

>> DFP  DNA / pantothenate metabolism flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.5   4.1e-05     0.035      23      54 ..       6      37 ..       2     143 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.1e-05
                                  EEE----HHHHHHHHHHHHTT-EEEEEE-S-S CS
                           DFP 23 isNrSSGkmGyalAeaaaarGaeVtlvsgpvs 54
                                  i+   SG mG  +A+ +a++G +Vt+v  + +
  gi|13541657|ref|NP_111345.1|  6 IGVVGSGVMGQGIAQVFAKAGYKVTIVDVNEQ 37
                                  55568**********************98854 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   5.1e-05     0.044       9      63 ..       5      87 ..       1     195 [. 0.64

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5.1e-05
                 NAD_binding_7  9 kvlvvGgGevAarkvrklleagakvtvvapevkeeleelvklaeee................................lekdl 59
                                  ++ vvG G +++  ++ +++ag kvt+v+ + +++le+ +k++++                                     l
  gi|13541657|ref|NP_111345.1|  5 NIGVVGSGVMGQGIAQVFAKAGYKVTIVDVN-EQILENALKAISDGkyglrnlvnkgqisendlnsimsriststeytS---L 83
                                  677************************9998.56667555544333333333333334333333333333333333220...3 PP

                 NAD_binding_7 60 egad 63
                                  +  d
  gi|13541657|ref|NP_111345.1| 84 SSCD 87
                                  3333 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   7.2e-05     0.061       9      46 ..      11      48 ..       6      78 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 7.2e-05
                                  TSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHH CS
                     adh_short  9 ssGIGraiakelakeGakvvvvdrseekleevakelke 46
                                  s+ +G+ ia+ +ak+G+kv++vd +e+ le+++k + +
  gi|13541657|ref|NP_111345.1| 11 SGVMGQGIAQVFAKAGYKVTIVDVNEQILENALKAISD 48
                                  4468***************************9999875 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 ?   13.2   0.1   9.5e-05     0.081       1      46 [.       6      48 ..       6      95 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 9.5e-05
                                  EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTT CS
               Sacchrp_dh_NADP  1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaakalg 46
                                  + ++G+G +Gq++a++ a+ + +  ++t++d +++ le+++++++ 
  gi|13541657|ref|NP_111345.1|  6 IGVVGSGVMGQGIAQVFAKAG-Y--KVTIVDVNEQILENALKAISD 48
                                  689****************97.6..8*********99999987733 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1    0.0002      0.17      13      52 ..       4      42 ..       1      90 [. 0.80

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0002
                                  -EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHH CS
                  Shikimate_DH 13 kkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakel 52
                                  +++ ++G G m++ +a+ ++++g+k v+++  + +  ++ 
  gi|13541657|ref|NP_111345.1|  4 SNIGVVGSGVMGQGIAQVFAKAGYK-VTIVDVNEQILENA 42
                                  6799********************9.99987666655555 PP

>> XdhC_C  XdhC Rossmann domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00024       0.2       3      34 ..       8      39 ..       6     111 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00024
                                  EE--STTHHHHHHHHHHHTEEEEEEES-GGGG CS
                        XdhC_C  3 ifGaghvaqalarlaaalgfrvtvvdpreefa 34
                                  ++G g ++q +a++ a++g++vt+vd +e++ 
  gi|13541657|ref|NP_111345.1|  8 VVGSGVMGQGIAQVFAKAGYKVTIVDVNEQIL 39
                                  89************************999765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (294 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       617  (0.0344135); expected 358.6 (0.02)
Passed bias filter:                      545  (0.0303977); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.47
# Mc/sec: 1889.07
//
Query:       gi|13541658|ref|NP_111346.1|  [L=227]
Description: Uracil-DNA glycosylase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.9e-34  118.9   0.0    2.2e-34  118.7   0.0    1.1  1  UDG             Uracil DNA glycosylase superfamily
  ------ inclusion threshold ------
       0.12   11.0   0.0       0.13   10.8   0.0    1.1  1  Fiji_64_capsid  Fijivirus 64 kDa capsid protein
       0.73   10.4   2.9          4    8.0   0.9    2.5  2  PQQ_3           PQQ-like 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 !  118.7   0.0   3.7e-38   2.2e-34       1     153 [.      49     220 ..      49     222 .. 0.94

  Alignments for each domain:
  == domain 1  score: 118.7 bits;  conditional E-value: 3.7e-38
                                   HHC-CTT-SEEEEESSTCHH.HHHHSSSS.-.STT--HHHHHHHCCCCCCCHHG........CTEEEEESSS....SECGC CS
                           UDG   1 pgegppdakvvivGeaPgae.edatglpFsg.ragnllrkllneaglkrdlese........qgvyitnvvkcrppgnrdt 71 
                                   pg+g+++ +++ivG aP a+ +++tg+ F+g ++++ l ++l eag++++++s+         + yit +vkc pp n+  
  gi|13541658|ref|NP_111346.1|  49 PGYGDISGRLLIVGLAPAATgGNRTGRVFTGdKSSDFLVSCLFEAGITNQPTSVsrgdglvyIDSYITAAVKCVPPDNK-- 127
                                   79*****************************9999***************9999***********************99.. PP

                                   TTCCCCTCCHHHHHHHHHHHH.SSEEEEESHHHHHH...........HHHHSCESCCCSCT..SEEEEES-SSTTTTTTTT CS
                           UDG  72 ptsaeikacaplleeeiellk.prlivllGktaakall.........geklgklrgklleak.irvlplphPsplnrnffk 141
                                   pt +eik+c p+l  e++++k  +++++lGk+a++++l          + +++++g ++++   +++p++hPsp+n+n++k
  gi|13541658|ref|NP_111346.1| 128 PTMDEIKNCMPYLIFEVKQMKnLKVVLALGKIAFDSVLdvlrsfgtnTKGMKFVHGNVYDTGtFKLVPSYHPSPRNVNTGK 208
                                   *********************9**************9888999987555777*********88***************999 PP

                                   SHHHHHHHHHHH CS
                           UDG 142 snpelkaeawed 153
                                    ++e+    +++
  gi|13541658|ref|NP_111346.1| 209 LKREDFVSLLQK 220
                                   999988877765 PP

>> Fiji_64_capsid  Fijivirus 64 kDa capsid protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   2.2e-05      0.13     150     220 ..      92     165 ..      84     210 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 2.2e-05
                Fiji_64_capsid 150 egnltlkpisa.dgvevvlddsyinavskvigpdvhklidkcckefp..ahvgtileevkyclilgklrlaggy 220
                                   e  +t +p s   g  +v  dsyi a  k + pd +  +d+  + +p        ++++k +l lgk+ +    
  gi|13541658|ref|NP_111346.1|  92 EAGITNQPTSVsRGDGLVYIDSYITAAVKCVPPDNKPTMDEIKNCMPylIFEVKQMKNLKVVLALGKIAFDSVL 165
                                   56678888875257789999******************997655555005555668999********9876655 PP

>> PQQ_3  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.9   0.00067         4       1      20 [.      40      69 ..      40      86 .. 0.63
   2 ?    1.4   0.0     0.084     5e+02      15      26 ..     100     111 ..      92     118 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00067
                         PQQ_3  1 GevlWsvqlpg..pvnssp........avd 20
                                  G++ Ws+++pg  ++ + +        a++
  gi|13541658|ref|NP_111346.1| 40 GQEYWSRPVPGygDISGRLlivglapaATG 69
                                  99********94455444465555554444 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.084
                         PQQ_3  15 sspavdgglvyv 26 
                                   +s+  ++glvy+
  gi|13541658|ref|NP_111346.1| 100 TSVSRGDGLVYI 111
                                   455778*****8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       380  (0.0211947); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1485.67
//
Query:       gi|13541659|ref|NP_111347.1|  [L=423]
Description: Mn2+ transporter [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-39  136.4  27.2    6.3e-38  130.7  27.2    2.1  1  Nramp     Natural resistance-associated macrophage protein


Domain annotation for each model (and alignments):
>> Nramp  Natural resistance-associated macrophage protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.7  27.2   3.5e-42   6.3e-38       3     355 ..      36     395 ..      34     398 .. 0.81

  Alignments for each domain:
  == domain 1  score: 130.7 bits;  conditional E-value: 3.5e-42
                         Nramp   3 tdlqaGaqfGykLlwvlllstllaillqelsarLGlvTgkglaelirerlpkkvsillwilaelaiiatdlaeviGaAial 83 
                                   t lq+Ga+fG++++ v+l+ ++ ++++q+ +  LG+ +g+g+ e+ir+r+++++++l++i +    i++ +ae  G+Ai+l
  gi|13541659|ref|NP_111347.1|  36 TGLQSGAEFGFHMIFVMLILIPPLFIVQNAAGYLGIYSGMGVGEAIRQRYGRRLALLAAIPMASTDILSYIAEYSGIAIGL 116
                                   789****************************************************************************** PP

                         Nramp  84 nllfgipllvgvlitavlvllllflekggyrklEaliialvlvialsFiaelflvkpdwgevlkglvvPslpg..keslll 162
                                   +++  ++ +++v+++ v+  l+++   + y ++E +++++ + ++l  i++++l+kp+w++v+   + P  p   +++ ++
  gi|13541659|ref|NP_111347.1| 117 YMVG-VSPYISVPVVFVIHNLIVL--MRRYGRIESILMIVSVGLVLFIIVSVALMKPSWHSVILTGLNPIQPYgnHDFDIM 194
                                   **97.7777777777777777777..699*******99999999888899*********99988778799998999***** PP

                         Nramp 163 avgilGatvmphnlflhsslvqerkitidrsekeealkyeriDtiialivaflinlailivaAavlysggkdvesledaae 243
                                   +++ lGa++mp ++f+++   +++        +  ++k +r +t+i+ iv+ +   +++iv A ++  g    ++ + +a+
  gi|13541659|ref|NP_111347.1| 195 IIANLGAIIMPFMIFYQAGASVQKSLLD----Q--DIKISRNETAIGSIVSEVL--MVMIVIAGTFIGGY--ATEPKMLAA 265
                                   *******************999999333....4..5***************996..56677799999444..478999999 PP

                         Nramp 244 aLepllGskaasvlFaigLlaaGlsStitgtlagqyvmegflglrislwlrrlitralafvpal..........ivillig 314
                                   aL p  G+ +a ++ a g + aG++++i+++la+++ ++++lg+++   +rr +    ++ +++          ++ l +g
  gi|13541659|ref|NP_111347.1| 266 ALLPF-GT-YAYYITAAGFVTAGFLALIVISLASSWGIAEALGWKLYSGRRRGMH-KAQMKGLTeersdcdrrkFIYLYMG 343
                                   99995.95.************************************9988888665.3333333222222222223344444 PP

                         Nramp 315 aele...........lvkllvlsqvllslllPfaliplllltsskklMGefk 355
                                   ++++           l+ l +   ++ +l+l ++ ++l ll+s++k+M  ++
  gi|13541659|ref|NP_111347.1| 344 ESIPaaaialsfsayLLPLVIDLMIVFVLVLAPVGVLLGLLVSDQKIMNGHR 395
                                   4444555556666554444444445666666666677777777777776666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (423 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       999  (0.0557198); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); 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):               1  [number of targets reported over threshold]
# CPU time: 0.63u 0.28s 00:00:00.91 Elapsed: 00:00:00.48
# Mc/sec: 2649.72
//
Query:       gi|13541660|ref|NP_111348.1|  [L=1028]
Description: isoleucyl-tRNA synthetase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   1.3e-168  562.0   0.0   1.7e-168  561.6   0.0    1.1  1  tRNA-synt_1    tRNA synthetases class I (I, L, M and V)
    2.4e-30  105.5   0.1    5.4e-30  104.4   0.1    1.6  1  Anticodon_1    Anticodon-binding domain of tRNA
    9.2e-18   64.1   5.5    1.2e-08   34.2   0.5    4.2  3  tRNA-synt_1g   tRNA synthetases class I (M)
    1.1e-06   27.8   1.6    1.2e-05   24.4   0.0    2.9  4  tRNA-synt_1f   tRNA synthetases class I (K)
    2.6e-05   23.7   0.1     0.0025   17.2   0.0    2.4  2  tRNA-synt_1e   tRNA synthetases class I (C) catalytic domain
  ------ inclusion threshold ------
      0.091   12.3   0.0       0.17   11.4   0.0    1.4  1  tRNA-synt_1_2  Leucyl-tRNA synthetase, Domain 2
        0.1   12.6   0.5          7    6.7   0.0    3.0  3  Zn_Tnp_IS1595  Transposase zinc-ribbon domain
        1.7    8.3   4.6         14    5.4   0.1    2.8  3  zf_UBZ         Ubiquitin-Binding Zinc Finger
        7.4    6.6   7.5       0.23   11.4   0.6    2.1  2  DUF1610        Domain of unknown function (DUF1610)


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 !  561.6   0.0  8.7e-172  1.7e-168       2     596 ..      22     624 ..      21     630 .. 0.94

  Alignments for each domain:
  == domain 1  score: 561.6 bits;  conditional E-value: 8.7e-172
                   tRNA-synt_1   2 lyekWeeedvfkkelekekekkefilvdgPPyvtGslHiGhalaktlkdivirykrmkGkevlyvp.GwDhaGlaieakve 81 
                                   ++  W+++ + +k   k++  k+f++  gPP ++G++HiGha+++t+kdiv ry++m+G++  ++  GwD++Gl++e + e
  gi|13541660|ref|NP_111348.1|  22 ILRYWNDHAINEKI-FKKEGTKKFVFLEGPPTANGRPHIGHAMTRTIKDIVLRYNTMTGHKIYRRYgGWDCHGLPVELEAE 101
                                   67889999998888.44556899**************************************9877537************* PP

                   tRNA-synt_1  82 kklgakekkerkklgreefrekvrewkaeyaeeirkqvkrlGvsvDfdreylTldkeleeavkevfvrladkgliyrgkkl 162
                                   k +g k k++  ++g+e+f+  +r+ + +y++e++   + +G s+D++ +y+Tl +e+ e+ + v++ ++++gl+y+   +
  gi|13541660|ref|NP_111348.1| 102 KYFGFKTKSDIINYGVEKFNSYCRDSVFRYIDEWKTVDQIIGFSIDHSGDYITLRNEYIESEWYVLKYIYENGLLYKDYTV 182
                                   ********************************************************************************* PP

                   tRNA-synt_1 163 vnwstklktalselEv..eykdkkdalihvafpladkeevklviaTTtPeTllgdtavavnpeldyv...itkeklilaea 238
                                   v+++++++t+ls  Ev   ykd+kd++++v+f+ +++e++++v++TTtP+Tl+++  ++vnp+++y+    ++ k+ +a++
  gi|13541660|ref|NP_111348.1| 183 VPYCPRCETSLSSHEVaqGYKDVKDPSVYVRFKEKGSENTYFVAWTTTPWTLPSNEFLVVNPDIEYSlieYNNAKYYVASS 263
                                   ****************988************************************************99889999999*99 PP

                   tRNA-synt_1 239 llkslvkkesekkiledergkeLegkevelpl.....vnrkipiiaddyvdkeaGtGvVkiaPahdedDyevgkkynlevi 314
                                   + + ++k   + k+l++++g eL gk +e++l        +++++++d+v+   G+G+V+ aPa+++dDy++gk+ n++++
  gi|13541660|ref|NP_111348.1| 264 RAQYIFK---DFKVLKKMKGFELAGKGYEQLLpfldpPAGALRVVTGDFVTDIDGSGIVHAAPAFGSDDYQIGKRENVPIL 341
                                   9998886...679***************9988888887899**************************************** PP

                   tRNA-synt_1 315 nildedgtlteeaaefeglkvfdarkkvveelkekglllkaekiehsvpfcerskkpiiyrateqWfvrvkeladaalkav 395
                                   n++d++g++++e   + g kv +a++ ++ +lk++gll+k+ek ehs+pfc r ++p++y+  ++Wf+rv++++d++++++
  gi|13541660|ref|NP_111348.1| 342 NPVDKNGRFSDERLPWYGKKVREANEDIIVYLKNNGLLIKSEKYEHSYPFCYRCDTPLLYYPLDAWFIRVSSVRDKLVENN 422
                                   ********************************************************************************* PP

                   tRNA-synt_1 396 ekvqfvpks.kekryaswleniqdWciSRqrwWGhriplfvsketeevvvreelkelvagreeeeaekkalekeakdkl.. 473
                                   ek++++p+  k+ r+ ++l +++dW++SR+r+WG+++p+++ +++  v +  + ke+++   + ++  ++l++  +d++  
  gi|13541660|ref|NP_111348.1| 423 EKIRWKPDYlKHGRFGNFLDEAKDWNLSRDRFWGTPLPVWRCRNNH-VRFIGSRKEIEE---MGATVPQDLHRPYIDEVkf 499
                                   ********98999****************************99965.888666666555...7777788888888888866 PP

                   tRNA-synt_1 474 ..kkekgelekdedvlDvWFsSgswpfstlgypeedteelkkffpadmlleGlDiirgWvarlillslaltgsePfkevlv 552
                                      +  +e+++++ v+D+WF+Sgs +++ ++yp+ed+ + ++  p ++++e +D++rgW++ l ++s+ +++++ + + l 
  gi|13541660|ref|NP_111348.1| 500 vcPDCGEEMRREPYVIDTWFDSGSATYAAMHYPFEDNFDPSSDLPVSFITEAIDQTRGWFYVLHVISTIMFNKNAYDSALS 580
                                   66667799************************************************************************* PP

                   tRNA-synt_1 553 hglvrdeeGrKmSKslgNvidpldvikkygadalRltlilsdvg 596
                                    ++++de+GrKmSKs+gN +  ld +k+++ d+lRl+ ++    
  gi|13541660|ref|NP_111348.1| 581 ISFILDEQGRKMSKSKGNSVFALDYLKQVAPDSLRLFFLYGAPW 624
                                   ************************************99866554 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 !  104.4   0.1   2.7e-33   5.4e-30       1     150 [.     674     820 ..     674     822 .. 0.92

  Alignments for each domain:
  == domain 1  score: 104.4 bits;  conditional E-value: 2.7e-33
                   Anticodon_1   1 drwilselnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedkra.aqevllevletllrllaPf 80 
                                   d+w++s++n ++ e ++ay++++f+++++  ++f +++l+++yl+l+++r++ e+ ++++  a+++l++++ t +++laP+
  gi|13541660|ref|NP_111348.1| 674 DKWLISKINTFIIESRRAYDDLDFHEVVRLSMDF-VDNLSNFYLRLSRRRFWAEDVTEDKLaAYSTLYTAIMTCSKVLAPI 753
                                   9********************************7.888******************99967699***************** PP

                   Anticodon_1  81 mPfitEelwqreeeel.gkkesimlaewpe.kaeelekeleeeevellkeivkairklrselkikpsselkv 150
                                   +Pf++++l+     +l g  esi+l ++pe + ++ + +l e+ ++ + ++++++r++r+e++ik ++++k 
  gi|13541660|ref|NP_111348.1| 754 VPFVSDYLY----LSLhGPYESIHLDSFPEpDTSKIDHDL-EKRMDQAYSVIETVRRIRQEINIKGRQPVKE 820
                                   *********....8886778*********85555545555.89*************************9876 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 !   34.2   0.5     6e-12   1.2e-08       9     144 ..      52     191 ..      49     205 .. 0.59
   2 !    6.8   0.0    0.0012       2.4     167     239 ..     390     464 ..     374     472 .. 0.77
   3 !   21.6   0.1   3.9e-08   7.9e-05     321     376 ..     585     638 ..     559     654 .. 0.72

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 6e-12
                                   --SS---HHHHHHHHHHHHHHHHHHHTT-EEE.EEEEE---SHHHHHHHHHT.TS-HHHHHHHHHHHHHHHHHH.TT---. CS
                  tRNA-synt_1g   9 YangklHlGhllevisaDifaRykrlrgeevl.fvcgtDehGtpielkAeke.gvtpeelvekvheeikelfkk.lnisf. 85 
                                    ang++H+Gh+++  + Di+ Ry+ ++g++++   +g D hG p+el+Aek  g + +  + ++  e  + +++     + 
  gi|13541660|ref|NP_111348.1|  52 TANGRPHIGHAMTRTIKDIVLRYNTMTGHKIYrRYGGWDCHGLPVELEAEKYfGFKTKSDIINYGVEKFNSYCRdSVFRYi 132
                                   58****************************7626899************98545554443333333333333320222221 PP

                                   SEEEETTSHHHHHHHHHHHHHHHHTT-EEEEEEEEEEETTTTEEE-GGG-EE....... CS
                  tRNA-synt_1g  86 dkygrttseehkelvqeifkklkekgliyekeieqlycpkderflpdryvegtCPkcks 144
                                   d++++ ++    ++ ++      ++++i+++ +   y  +++  + d  v   CP c++
  gi|13541660|ref|NP_111348.1| 133 DEWKTVDQIIGFSIDHSGDYITLRNEYIESEWYVLKYIYENGLLYKDYTVVPYCPRCET 191
                                   33333333333333333222233445555555555555555555555555555555543 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0012
                                   ..........EEE.EEEEEE-GGGGHHHHHHHH.HH-TTSHHHHHHHH.HHHHT----EE-ESS-SSS-EET...T CS
                  tRNA-synt_1g 167 pksaisgskpevketehlffklskfekklkewieeeekeleenvkkivkewlkegLkdlaisrdldwGipvP...g 239
                                   p +  +++   +   + +f ++s++++kl e  e+ + +     +    ++l+e  kd+++srd  wG p+P    
  gi|13541660|ref|NP_111348.1| 390 PFCYRCDTPLLYYPLDAWFIRVSSVRDKLVENNEKIRWKPDYLKHGRFGNFLDE-AKDWNLSRDRFWGTPLPvwrC 464
                                   667777777777778899999999999998877555544445555667788888.9***************95542 PP

  == domain 3  score: 21.6 bits;  conditional E-value: 3.9e-08
                                   EEE--------------HHHHHHHH-HHHHHHHHHHHS-TTS.-EEE-HHHHHHHHH CS
                  tRNA-synt_1g 321 ltvegkKlSkSrgvvvkakealerldadllRYylaaeapekk.DldfswedfvervN 376
                                   l  +g+K+SkS+g+ v+a ++l+++ +d lR ++++ ap k+ +ld   ++++++v 
  gi|13541660|ref|NP_111348.1| 585 LDEQGRKMSKSKGNSVFALDYLKQVAPDSLRLFFLYGAPWKSkNLD---RKIIDEVS 638
                                   56689**************************999997775540333...33333333 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 ?    0.8   0.0     0.091   1.8e+02       9      59 ..      33      79 ..      25      87 .. 0.67
   2 ?   -3.9   0.1       2.4   4.8e+03     171     183 ..     180     192 ..     167     222 .. 0.60
   3 ?   -3.7   0.0       2.1   4.3e+03     209     226 ..     414     431 ..     372     431 .. 0.75
   4 !   24.4   0.0     6e-09   1.2e-05     272     322 ..     582     632 ..     562     640 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.091
                  tRNA-synt_1f  9 eklieerkkkkaekdevvvesGispSGliHiGnlrevltadlvaralrkrg 59
                                  ek+    +kk+ +k+ v +e   ++ G++HiG +      d+v r  +  g
  gi|13541660|ref|NP_111348.1| 33 EKI----FKKEGTKKFVFLEGPPTANGRPHIGHAMTRTIKDIVLRYNTMTG 79
                                  333....3333355667777778999******9988888888877655555 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 2.4
                  tRNA-synt_1f 171 spylpvcekcgrv 183
                                   + + p+c++c+  
  gi|13541660|ref|NP_111348.1| 180 YTVVPYCPRCETS 192
                                   4566777777652 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 2.1
                  tRNA-synt_1f 209 eevdiregngKLqWkvdw 226
                                   ++ ++ e n K++Wk d+
  gi|13541660|ref|NP_111348.1| 414 VRDKLVENNEKIRWKPDY 431
                                   455677888999999997 PP

  == domain 4  score: 24.4 bits;  conditional E-value: 6e-09
                  tRNA-synt_1f 272 elillkggekmssSkGnvltledwlevaepevlrflilrrkPkkakkldld 322
                                    +il+++g+kms+SkGn +   d l+ + p++lr+++l   P k+k+ld +
  gi|13541660|ref|NP_111348.1| 582 SFILDEQGRKMSKSKGNSVFALDYLKQVAPDSLRLFFLYGAPWKSKNLDRK 632
                                   699*********************************************987 PP

>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.013        25      17      48 ..      51      82 ..      35      84 .. 0.83
   2 !   17.2   0.0   1.2e-06    0.0025     249     287 ..     587     626 ..     565     639 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.013
                                  EBTTS--BHHHHHHHHHHHHHHHHHHHTT-EE CS
                  tRNA-synt_1e 17 ptvydashlGhaRslvafDilrrilqalgYdv 48
                                  pt+    h+Gha +  + Di+ r+  ++g+++
  gi|13541660|ref|NP_111348.1| 51 PTANGRPHIGHAMTRTIKDIVLRYNTMTGHKI 82
                                  799999******************99998876 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 1.2e-06
                                   ETTBE--TTTT---BHHHHHTTS-HHHHHHHHHS.S-TTS CS
                  tRNA-synt_1e 249 iegekmsksLknfitikdvlkkfdprqlRlllls.ahyrs 287
                                    +g+kmsks +n ++  d lk++ p  lRl++l  a ++s
  gi|13541660|ref|NP_111348.1| 587 EQGRKMSKSKGNSVFALDYLKQVAPDSLRLFFLYgAPWKS 626
                                   4689*************************99875144554 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 ?   11.4   0.0   8.4e-05      0.17      11     144 ..     211     348 ..     206     386 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 8.4e-05
                 tRNA-synt_1_2  11 eiefkvees.eeklevfttrpdtlfGvtfvalapehplveklaekkkelaafieevkkksesereletkekeGv...ftgl 87 
                                    ++fk ++s ++ +  +tt p tl + +f+++ p+ +         ++ + ++++ + +   +  +  k+ +G+    +g 
  gi|13541660|ref|NP_111348.1| 211 YVRFKEKGSeNTYFVAWTTTPWTLPSNEFLVVNPDIEYSLIE---YNNAKYYVASSRAQYIFKDFKVLKKMKGFelaGKGY 288
                                   678888888445666799999999999999999986654322...222344555555555555544455555553222455 PP

                 tRNA-synt_1_2  88 kaihPit...gekipiwvanyvlmeygtgavmavPahdqrDfeFakkynlpikqvikped 144
                                   + + P+       + + + ++v    g+g v a Pa  + D++  k+ n+pi + + +++
  gi|13541660|ref|NP_111348.1| 289 EQLLPFLdppAGALRVVTGDFVTDIDGSGIVHAAPAFGSDDYQIGKRENVPILNPVDKNG 348
                                   55556552224469*************************************988777554 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 ?    2.4   0.0     0.079   1.6e+02      19      32 ..     184     198 ..     165     206 .. 0.75
   2 ?   -2.9   0.1       3.7   7.3e+03      13      32 ..     453     472 ..     442     476 .. 0.57
   3 ?    6.7   0.0    0.0035         7      18      33 ..     498     516 ..     495     523 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.079
                 Zn_Tnp_IS1595  19 fvCPhCgsr.kayri 32 
                                   + CP+C+ + +++++
  gi|13541660|ref|NP_111348.1| 184 PYCPRCETSlSSHEV 198
                                   67****988766655 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 3.7
                 Zn_Tnp_IS1595  13 lrWpng.fvCPhCgsrkayri 32 
                                   ++W++  +   +C + ++++i
  gi|13541660|ref|NP_111348.1| 453 RFWGTPlP-VWRCRNNHVRFI 472
                                   55666531.135777776666 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.0035
                 Zn_Tnp_IS1595  18 gfvCPhCgsr...kayrik 33 
                                   +fvCP Cg +   ++y i 
  gi|13541660|ref|NP_111348.1| 498 KFVCPDCGEEmrrEPYVID 516
                                   59******99888888776 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.1     0.017        34       5      17 ..     186     198 ..     185     200 .. 0.89
   2 ?   -2.8   0.1       2.6   5.1e+03       4      11 ..     391     398 ..     391     400 .. 0.79
   3 ?    5.4   0.1     0.007        14       3      12 ..     499     508 ..     497     511 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.017
                        zf_UBZ   5 CerCgkeipesel 17 
                                   C+rC ++++++e+
  gi|13541660|ref|NP_111348.1| 186 CPRCETSLSSHEV 198
                                   **********997 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2.6
                        zf_UBZ   4 lCerCgke 11 
                                   +C rC+++
  gi|13541660|ref|NP_111348.1| 391 FCYRCDTP 398
                                   699**986 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.007
                        zf_UBZ   3 ylCerCgkei 12 
                                   ++C++Cg+e+
  gi|13541660|ref|NP_111348.1| 499 FVCPDCGEEM 508
                                   9******997 PP

>> DUF1610  Domain of unknown function (DUF1610)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   1.2       4.5   8.9e+03      18      22 ..     185     189 ..     182     189 .. 0.85
   2 ?   11.4   0.6   0.00012      0.23      15      24 .]     497     506 ..     495     506 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 4.5
                       DUF1610  18 pCPNC 22 
                                   +CP C
  gi|13541660|ref|NP_111348.1| 185 YCPRC 189
                                   8**99 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00012
                       DUF1610  15 vvFpCPNCGE 24 
                                   v+F CP CGE
  gi|13541660|ref|NP_111348.1| 497 VKFVCPDCGE 506
                                   9********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1028 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       645  (0.0359752); expected 358.6 (0.02)
Passed bias filter:                      545  (0.0303977); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.79u 0.32s 00:00:01.11 Elapsed: 00:00:00.48
# Mc/sec: 6439.21
//
Query:       gi|13541661|ref|NP_111349.1|  [L=206]
Description: rhodanese-related protein [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.4e-15   56.5   0.1    7.8e-12   45.7   0.0    2.1  2  Rhodanese  Rhodanese-like domain


Domain annotation for each model (and alignments):
>> Rhodanese  Rhodanese-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.0    0.0001       1.9       4      62 ..      10      74 ..       7     101 .. 0.82
   2 !   45.7   0.0   4.4e-16   7.8e-12       2     106 ..     106     192 ..     105     193 .. 0.93

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0001
                     Rhodanese  4 elkellekgkvallDvRppeeYekghIpgAvnv.....skdtlsrakkseapllelpeellel.g 62
                                   +k+ l++++ +++D  p + Ye+ h p ++ +     s+++ls  +++ a +  +p+ l++l +
  gi|13541661|ref|NP_111349.1| 10 IVKQFLDDNNSVIVDFDPIDLYEAVHPPFSIRLsidriSAMPLSILRRRAAAFVSDPQTLSKLlN 74
                                  578888999999*********************99999999999999999999999999988842 PP

  == domain 2  score: 45.7 bits;  conditional E-value: 4.4e-16
                     Rhodanese   2 akelkellekgkvallDvRppeeYekghIpgAvnvskdtlsrakkseapllelpeellelgidnkktvvvycdgggraaaa 82 
                                   a++l+e++++    +lDvR+p e   g+I +++n+             p  el e+++ l   ++k+  v+c++g+r+aaa
  gi|13541661|ref|NP_111349.1| 106 AADLYENIKAYT--VLDVREPFELIFGSIANSINI-------------PISELREKWKIL--ERDKKYAVICAHGNRSAAA 169
                                   678899997776..9********888*********.............************..***************9999 PP

                     Rhodanese  83 aallkklGyknvsvldGGfkawke 106
                                     +l +lG  n+  ++GG+++w e
  gi|13541661|ref|NP_111349.1| 170 VEFLSQLG-LNIVDVEGGIQSWIE 192
                                   999999**.7************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       607  (0.0338558); expected 358.6 (0.02)
Passed bias filter:                      556  (0.0310112); 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: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 1249.66
//
Query:       gi|13541662|ref|NP_111350.1|  [L=117]
Description: hypothetical protein TVN0831 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score 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   14.1   0.0       0.11   12.5   0.0    1.9  1  DUF4250   Domain of unknown function (DUF4250)


Domain annotation for each model (and alignments):
>> DUF4250  Domain of unknown function (DUF4250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   6.2e-06      0.11      35      55 .]      93     113 ..      79     113 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.2e-06
                       DUF4250  35 eeleekLasigYeYdeeqnqF 55 
                                   ++l + L +igY+Yd++++ F
  gi|13541662|ref|NP_111350.1|  93 AALRDSLREIGYQYDAQSRGF 113
                                   68999***********98766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       711  (0.0396564); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 818.31
//
Query:       gi|13541663|ref|NP_111351.1|  [L=188]
Description: phosphoglycerate mutase [Thermoplasma volcanium GSS1]
Scores for complete 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   93.1   0.0    1.9e-26   93.0   0.0    1.0  1  His_Phos_1  Histidine phosphatase superfamily (branch 1)
  ------ inclusion threshold ------
      0.022   14.9   0.0      0.042   14.0   0.0    1.4  1  Skp1        Skp1 family, dimerisation domain
      0.084   13.5   0.0       0.29   11.7   0.0    1.8  2  QIL1        MICOS complex subunit MIC13, QIL1


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 !   93.0   0.0   3.2e-30   1.9e-26       1     179 [.       4     175 ..       4     186 .. 0.90

  Alignments for each domain:
  == domain 1  score: 93.0 bits;  conditional E-value: 3.2e-30
                                   EEEEE---BTTB--....TT----B-HHHHHHHHHHHHHHTTS---EEEE-SSHHHHHHHHHHHHCTT.--EEE-GGGS-- CS
                    His_Phos_1   1 lyLvRHGetewnaegrlqgrtdvpLteeGreqAealaerlagepidaiysSplkRarqTaeliaealg.lpveldegLrEi 80 
                                   +yLvRH++t +n+++r+qgr+d+++ +  +e      + +++e+i++iysS + Ra++ a+++a+ lg  ++ ld +++E+
  gi|13541663|ref|NP_111351.1|   4 VYLVRHAKTIMNYTNRWQGRSDSDILPGAIEKLLSSIKSIENEGINKIYSSCIGRAIKSAAAAANVLGlNSIFLDCRFNER 84 
                                   69******************************************************************889999******* PP

                                   --GGGTT-B.HHHHHH..HSHHHHHHHHH-GGG-BS-BHHHHHHHHHHHHHHHHHHTTTSEEEEEE-HHHHHHHHHHHHT- CS
                    His_Phos_1  81 dfGdweglttaeiaeeypeeleawlrdpadvrppggEsledvaaRvaaaleelaarhegetvlvVsHggvirallarllgl 161
                                   d+G +eg+t +ei+ ++  e+    +++  ++ p  Es+ d+++Rv + le l +    ++ l+++Hggv+ra++++l + 
  gi|13541663|ref|NP_111351.1|  85 DLGLLEGKTVDEIRTKFGIEFLYITSRDI-EKLPYVESWPDFVSRVFSGLESLPD----GRTLLITHGGVLRAVYNTLSH- 159
                                   **********************9999988.6999***************998865....458**************9764. PP

                                   -GGGGGGB---TT-EEEE CS
                    His_Phos_1 162 pleelrrleldnaslsvl 179
                                     ++ rr+ +dn  + vl
  gi|13541663|ref|NP_111351.1| 160 --SDERRVIFDNGDILVL 175
                                   ..4445566677777666 PP

>> Skp1  Skp1 family, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   7.1e-06     0.042      15      30 ..      89     104 ..      87     105 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 7.1e-06
                          Skp1  15 ikgktpeeiReiFnIe 30 
                                   ++gkt++eiR  F+Ie
  gi|13541663|ref|NP_111351.1|  89 LEGKTVDEIRTKFGIE 104
                                   79*************7 PP

>> QIL1  MICOS complex subunit MIC13, QIL1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       0.7   4.2e+03      45      63 ..      33      51 ..       8      56 .. 0.64
   2 ?   11.7   0.0   4.9e-05      0.29      28      72 ..      94     138 ..      91     139 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.7
                          QIL1 45 veevkfslveyWNkgVkkv 63
                                   e++ +s++++ N+g++k+
  gi|13541663|ref|NP_111351.1| 33 IEKLLSSIKSIENEGINKI 51
                                  4555556666666776665 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 4.9e-05
                          QIL1  28 vdevkkklclevpklpsveevkf.slveyWNkgVkkvfsflselPt 72 
                                   vde++ k+++e+    +++++++ + ve+W ++V  vfs+l++lP 
  gi|13541663|ref|NP_111351.1|  94 VDEIRTKFGIEFLYI-TSRDIEKlPYVESWPDFVSRVFSGLESLPD 138
                                   666777777773333.3355666688******************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1207.72
//
Query:       gi|13541664|ref|NP_111352.1|  [L=182]
Description: 2-oxoacid-ferredoxin oxidoreductase, gamma subunit [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.9e-36  124.2   0.3      7e-36  123.9   0.3    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 !  123.9   0.3   3.9e-40     7e-36       1     177 []      10     176 ..      10     176 .. 0.93

  Alignments for each domain:
  == domain 1  score: 123.9 bits;  conditional E-value: 3.9e-40
                                   CTSTHHHHHHHHHHHHHHTT-EEEEEEEEESSSSSSCEEEEEEEESS.-SSS--TTSEEEEEESSHHHHH..HHGGGEEEE CS
                           POR   1 GGqGvvtagkilakaaaraGyyvqanreygseirGghsyshvrisdepivpsievgeadllvaldaetls..ehldglkpg 79 
                                   GGqG+vta++ila+aa+ +G+y+++++++g e+rG+++++  ri++ +i+   +++++d++v+ld   l   ++ dglk g
  gi|13541664|ref|NP_111352.1|  10 GGQGAVTASRILAAAAFLEGKYAVSFPFFGTERRGAPVTAFTRIDENEIYVKSQIYDPDIIVVLDTYVLRtsNVTDGLKSG 90 
                                   9*********************************************879988888**********9999678********* PP

                                   EEEEEECTCGTT-CCHHHCTS-HHHHHHHT-EEEEE-HHHHHHHCCC....CCHHHHHHHHHHHHHHT.S-HHHHHHHHHC CS
                           POR  80 giiiynseelkpdelkkakeeerelkerlgvrvygvdatkiakeiggn...eraaNtvmlGalaallg.lplealeeaikk 156
                                   gi+++ns+ ++++   +ak             v +vda  ia ++g      +++Nt m+Ga+a+++g ++le++++  + 
  gi|13541664|ref|NP_111352.1|  91 GIAVINSPLPPESFNLNAK-------------VATVDAVGIAVKHGLGsraNPVINTSMIGAFAKATGlVSLESVLKSTET 158
                                   *******776666666655.............459********99988788999*************************** PP

                                   CS-CH.HHHHHHHHHHHHHHH CS
                           POR 157 rfpkkkeviekNlkafragye 177
                                   ++p+k   +++Nl+a++++ye
  gi|13541664|ref|NP_111352.1| 159 NVPGK---VKENLDAVKEAYE 176
                                   ****9...************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       333  (0.0185733); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 1195.30
//
Query:       gi|13541665|ref|NP_111353.1|  [L=94]
Description: 2-oxoisovalerate-ferredoxin oxidoreductase, subunit delta (vorD) [Thermoplasma volcanium GSS1]
Scores for complete sequence (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   47.2  20.0    1.4e-07   31.0   3.4    2.2  2  Fer4      4Fe-4S binding domain
    4.5e-09   36.0  17.5      2e-05   24.5   3.1    2.3  2  Fer4_6    4Fe-4S binding domain
    6.5e-09   35.8  11.0      1e-08   35.2  11.0    1.3  1  Fer4_21   4Fe-4S dicluster domain
    1.8e-08   34.4  24.0      2e-06   27.9  13.8    1.6  2  Fer4_9    4Fe-4S dicluster domain
    2.8e-08   34.2  27.8    4.1e-07   30.5  14.5    1.9  2  Fer4_7    4Fe-4S dicluster domain
    1.8e-07   32.0  12.6    0.00081   20.3   1.0    2.2  2  Fer4_16   4Fe-4S double cluster binding domain
    3.3e-07   30.0  10.5     0.0003   20.7   1.9    2.4  2  Fer4_2    4Fe-4S binding domain
    3.6e-06   27.0  15.1    1.8e-05   24.8  13.1    2.1  2  Fer4_10   4Fe-4S dicluster domain
    0.00067   20.2  12.9     0.0035   17.8   1.4    2.4  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
     0.0022   18.7   9.7       0.31   11.8   0.3    2.5  2  Fer4_15   4Fe-4S single cluster domain
     0.0031   17.9  12.6     0.0085   16.5  12.6    1.7  1  Fer4_8    4Fe-4S dicluster domain
     0.0045   17.4  14.5       0.02   15.3   1.6    2.5  2  Fer4_4    4Fe-4S binding domain
  ------ inclusion threshold ------
       0.01   16.4  15.3        0.3   11.7   2.5    2.1  2  Fer4_17   4Fe-4S dicluster domain
       0.26   12.2  11.5       0.23   12.3   2.5    2.2  3  Fer4_22   4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   3.4   1.1e-10   1.4e-07       1      24 []      22      45 ..      22      45 .. 0.94
   2 !   22.2   8.7   6.6e-08   8.5e-05       2      23 ..      65      86 ..      64      87 .. 0.93

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 1.1e-10
                                  EEEETTTSSS-THHHHHSTTTEEE CS
                          Fer4  1 vvideekCigCGaCvevCPvgAIt 24
                                  ++i ++kCi+C++C + CP +AI+
  gi|13541665|ref|NP_111353.1| 22 PTIQYDKCIRCMICWKYCPDNAIE 45
                                  5799*******************6 PP

  == domain 2  score: 22.2 bits;  conditional E-value: 6.6e-08
                                  EEETTTSSS-THHHHHSTTTEE CS
                          Fer4  2 videekCigCGaCvevCPvgAI 23
                                   id+  C gCG+C++ CP  +I
  gi|13541665|ref|NP_111353.1| 65 AIDYKFCKGCGICANECPEKCI 86
                                  69*****************999 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   3.1   1.5e-08     2e-05       1      24 []      21      44 ..      21      44 .. 0.96
   2 !   17.4   6.6   2.7e-06    0.0035       1      24 []      63      86 ..      63      87 .. 0.92

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 1.5e-08
                        Fer4_6  1 vveidpdkCigCgdCvrvCPegai 24
                                  +++i++dkCi C+ C + CP +ai
  gi|13541665|ref|NP_111353.1| 21 KPTIQYDKCIRCMICWKYCPDNAI 44
                                  69********************98 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 2.7e-06
                        Fer4_6  1 vveidpdkCigCgdCvrvCPegai 24
                                  +++id+  C gCg C++ CPe+ i
  gi|13541665|ref|NP_111353.1| 63 FPAIDYKFCKGCGICANECPEKCI 86
                                  6899****************9865 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.2  11.0   7.9e-12     1e-08       2      59 .]      23      88 ..      22      88 .. 0.76

  Alignments for each domain:
  == domain 1  score: 35.2 bits;  conditional E-value: 7.9e-12
                       Fer4_21  2 ridedkCigCgkCliaCedtshqaieidakt...vl......kvvedeCvGCnlCssvCPvedciem 59
                                  +i+ dkCi C  C + C+d++++  ++d+k+   ++      ++  + C GC +C++ CP e+ci+m
  gi|13541665|ref|NP_111353.1| 23 TIQYDKCIRCMICWKYCPDNAIEIKTGDEKApneRVakmefpAIDYKFCKGCGICANECP-EKCIDM 88
                                  5899***************99887755544322222344443445689************.8***98 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   2.5   1.9e-06    0.0024      33      51 .]      22      44 ..       5      44 .. 0.69
   2 !   27.9  13.8   1.6e-09     2e-06       1      51 []      28      86 ..      28      86 .. 0.95

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.9e-06
                        Fer4_9 33 e....eaCigCgaCveaCpkgai 51
                                       ++Ci C+ C + Cp +ai
  gi|13541665|ref|NP_111353.1| 22 PtiqyDKCIRCMICWKYCPDNAI 44
                                  1445579*************987 PP

  == domain 2  score: 27.9 bits;  conditional E-value: 1.6e-09
                        Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraase........eaCigCgaCveaCpkgai 51
                                  kC++C  C + Cp ++++ + + +ka +++  +        + C gCg C++ Cp+++i
  gi|13541665|ref|NP_111353.1| 28 KCIRCMICWKYCPDNAIEIKTGDEKAPNERVAKmefpaidyKFCKGCGICANECPEKCI 86
                                  7*************************99888879*******99************9987 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.5  14.5   3.2e-10   4.1e-07       1      50 [.      28      83 ..      28      85 .. 0.80
   2 !   15.4   5.3   1.6e-05     0.021       2      21 ..      71      90 ..      70      92 .. 0.91

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 3.2e-10
                        Fer4_7  1 rCigCgaCvaaCpvkaieldeeenekgtekv......eidpekClgCgaCvavCPt 50
                                  +Ci C  C ++Cp +aie++  ++++++e+v      +id+  C gCg C+++CP 
  gi|13541665|ref|NP_111353.1| 28 KCIRCMICWKYCPDNAIEIKTGDEKAPNERVakmefpAIDYKFCKGCGICANECPE 83
                                  7*****************99665555443333334459999**************7 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 1.6e-05
                        Fer4_7  2 CigCgaCvaaCpvkaielde 21
                                  C gCg C++ Cp k+i+++ 
  gi|13541665|ref|NP_111353.1| 71 CKGCGICANECPEKCIDMEF 90
                                  ****************9975 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   1.0   6.4e-07   0.00081       1      28 [.      28      55 ..      28      68 .. 0.77
   2 !   16.9   4.5   7.2e-06    0.0092       1      20 [.      70      89 ..      70      94 .] 0.89

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 6.4e-07
                       Fer4_16  1 rCgtCgkCaevCPtnaikekkekeiear 28
                                  +C++C  C + CP nai+ k+  e +++
  gi|13541665|ref|NP_111353.1| 28 KCIRCMICWKYCPDNAIEIKTGDEKAPN 55
                                  6****************98844444444 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 7.2e-06
                       Fer4_16  1 rCgtCgkCaevCPtnaikek 20
                                  +C++Cg Ca+ CP+++i+++
  gi|13541665|ref|NP_111353.1| 70 FCKGCGICANECPEKCIDME 89
                                  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 !   14.1   1.7   2.9e-05     0.037       4      21 ..      23      40 ..      20      41 .. 0.83
   2 !   20.7   1.9   2.3e-07    0.0003       3      22 .]      64      83 ..      62      83 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.9e-05
                        Fer4_2  4 vvdtdrCigCgaCvsaCP 21
                                   +  d+Ci+C +C + CP
  gi|13541665|ref|NP_111353.1| 23 TIQYDKCIRCMICWKYCP 40
                                  56679********87799 PP

  == domain 2  score: 20.7 bits;  conditional E-value: 2.3e-07
                        Fer4_2  3 vvvdtdrCigCgaCvsaCPa 22
                                  +++d   C gCg+C + CP+
  gi|13541665|ref|NP_111353.1| 64 PAIDYKFCKGCGICANECPE 83
                                  789****************5 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8  13.1   1.4e-08   1.8e-05       2      56 .]      22      82 ..      21      82 .. 0.79
   2 !   12.7   4.9   8.4e-05      0.11       3      21 ..      65      83 ..      63      92 .. 0.86

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 1.4e-08
                       Fer4_10  2 vvidddtCirCgkCvkaCPadl......tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                  + i+ d+CirC  C k CP ++      +++  ++   + e   ++++ C gcg C+ +CP
  gi|13541665|ref|NP_111353.1| 22 PTIQYDKCIRCMICWKYCPDNAieiktgDEKAPNERVAKMEFPAIDYKFCKGCGICANECP 82
                                  57999***************99999864444444444455556679**************9 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 8.4e-05
                       Fer4_10  3 vidddtCirCgkCvkaCPa 21
                                   id + C +Cg C + CP 
  gi|13541665|ref|NP_111353.1| 65 AIDYKFCKGCGICANECPE 83
                                  589999************8 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   1.4   2.7e-06    0.0035       4      18 ..      27      41 ..      24      49 .. 0.93
   2 !    7.5   4.3    0.0046       5.9       1      18 [.      66      83 ..      66      87 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.7e-06
                       Fer4_13  4 dtCiacgaCvelaPd 18
                                  d+Ci c++C++ +Pd
  gi|13541665|ref|NP_111353.1| 27 DKCIRCMICWKYCPD 41
                                  89************9 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0046
                       Fer4_13  1 VDrdtCiacgaCvelaPd 18
                                  +D + C +cg+C++ +P+
  gi|13541665|ref|NP_111353.1| 66 IDYKFCKGCGICANECPE 83
                                  67778************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 !   11.8   0.3   0.00024      0.31       3      24 ..      24      46 ..      23      64 .. 0.74
   2 !    9.9   4.2   0.00094       1.2       3      20 ..      66      83 ..      65      88 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00024
                       Fer4_15  3 vDrdaCigcglCvaeape.vfel 24
                                  +  d+Ci c  C++ +p+  +e+
  gi|13541665|ref|NP_111353.1| 24 IQYDKCIRCMICWKYCPDnAIEI 46
                                  6679************7514554 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00094
                       Fer4_15  3 vDrdaCigcglCvaeape 20
                                  +D + C gcg C+ e+pe
  gi|13541665|ref|NP_111353.1| 66 IDYKFCKGCGICANECPE 83
                                  89999***********97 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5  12.6   6.6e-06    0.0085       3      64 ..      27      84 ..      25      85 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 6.6e-06
                        Fer4_8  3 ekCieCgaCqsaCp..vlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64
                                  +kCi+C+ C + Cp  +++ +  + + +++++a+ ++           + C +cg C+++Cp++
  gi|13541665|ref|NP_111353.1| 27 DKCIRCMICWKYCPdnAIEIKTGDEKAPNERVAK-MEFPAI-----DYKFCKGCGICANECPEK 84
                                  79***********986555555666666666666.555444.....5799************97 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   1.6   1.6e-05      0.02       1      17 []      26      42 ..      26      48 .. 0.93
   2 !    8.7   3.6    0.0021       2.7       4      16 ..      71      83 ..      60      84 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.6e-05
                        Fer4_4  1 qerCigCgsCvaaCPqg 17
                                  +++Ci+C+ C  +CP++
  gi|13541665|ref|NP_111353.1| 26 YDKCIRCMICWKYCPDN 42
                                  59*************75 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0021
                        Fer4_4  4 CigCgsCvaaCPq 16
                                  C gCg C + CP 
  gi|13541665|ref|NP_111353.1| 71 CKGCGICANECPE 83
                                  99**********5 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   2.5   0.00023       0.3      41      59 ..      24      42 ..       5      44 .. 0.76
   2 ?   11.4  16.0   0.00028      0.35       1      59 [.      28      84 ..      28      87 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00023
                       Fer4_17 41 ekaslCieCgeCerkCPqg 59
                                   + ++Ci C  C ++CP +
  gi|13541665|ref|NP_111353.1| 24 IQYDKCIRCMICWKYCPDN 42
                                  3778999999999999976 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00028
                       Fer4_17  1 rCiqCgyClpeCpsyea..ydnepkkllraaklglleeaeke.ekaslCieCgeCerkCPqg 59
                                  +Ci+C  C + Cp +++     ++k + ++     + ++e      + C +Cg C+ +CP++
  gi|13541665|ref|NP_111353.1| 28 KCIRCMICWKYCPDNAIeiKTGDEKAPNER-----VAKMEFPaIDYKFCKGCGICANECPEK 84
                                  6************88775322334444443.....444444324789*************85 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   1.8     0.029        37      80      93 ..      27      40 ..       6      44 .. 0.66
   2 ?    4.9   1.9     0.037        47       1      14 [.      28      41 ..      28      63 .. 0.74
   3 ?   12.3   2.5   0.00018      0.23      76      95 ..      65      84 ..      45      85 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.029
                       Fer4_22 80 sgCvGCgRCieacp 93
                                   +C+ C  C + cp
  gi|13541665|ref|NP_111353.1| 27 DKCIRCMICWKYCP 40
                                  55666666666665 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.037
                       Fer4_22  1 rClsCgaCtlvCpt 14
                                  +C++C  C   Cp 
  gi|13541665|ref|NP_111353.1| 28 KCIRCMICWKYCPD 41
                                  79999999999995 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 0.00018
                       Fer4_22 76 kfgesgCvGCgRCieacpvk 95
                                   ++ + C GCg C + cp+k
  gi|13541665|ref|NP_111353.1| 65 AIDYKFCKGCGICANECPEK 84
                                  468999***********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       618  (0.0344693); expected 358.6 (0.02)
Passed bias filter:                      220  (0.0122706); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); 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: 0.43u 0.30s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 600.66
//
Query:       gi|13541666|ref|NP_111354.1|  [L=392]
Description: pyruvate:ferredoxin oxidoreductase, alpha subunit [Thermoplasma volcanium GSS1]
Scores for complete 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-63  212.0   0.1    1.3e-62  211.6   0.1    1.1  1  POR_N            Pyruvate flavodoxin/ferredoxin oxidoreductas
    3.9e-31  107.4   0.0    9.5e-31  106.1   0.0    1.7  1  PFOR_II          Pyruvate:ferredoxin oxidoreductase core doma
    0.00021   21.2   0.0    0.00049   20.0   0.0    1.6  1  Transketolase_C  Transketolase, C-terminal domain
     0.0089   15.5   0.6      0.033   13.6   0.1    1.9  2  ZnuA             Zinc-uptake complex component A periplasmic


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 !  211.6   0.1   2.8e-66   1.3e-62       2     228 ..      20     242 ..      19     245 .. 0.94

  Alignments for each domain:
  == domain 1  score: 211.6 bits;  conditional E-value: 2.8e-66
                                   HHHHCTEEEEEE--BTTTCCHHHHHCHCCCCCTTEE.EEEE-SSHHHHHHHHHHHHCTT-EEEEEEECCHHHHCCCCHHHH CS
                         POR_N   2 aaiaagvdviaaYPITPsseiaeelaellakgevgdvevvqmesEigaisaviGAaaaGaraaTaTSgqGllLmienlgla 82 
                                   +a+ a+v+ i+aYPITP+++i+e+la+++a+ e+ d+++v++esE++a ++v+ + +aG+r+ TaTS++Gll+m+e+l++a
  gi|13541666|ref|NP_111354.1|  20 GAKLARVKLISAYPITPQTTIVEKLASMIANDEL-DAKYVKVESEHSALATVVSSELAGVRSYTATSSHGLLYMHEMLHWA 99 
                                   7999*****************************9.9********************************************* PP

                                   HHTT--EEEEEEEEE-STTBEEEEE--TTCHHHHS---EEEE-SSHHHHHHHHHHHHHHHHH..CTSEEEEEEEHHHH.HE CS
                         POR_N  83 ageelPvvivvvaRalpstglsirtdqsDlmaardtglivlasenvqeafdlalvAfnlAek..vrvPvivlfDgfllshe 161
                                   +g++lP+v+ vv+Ra+  + ++i+ dqsD m   dtg+++++ e++qea d++++++++Ae+  v +P++ + D+f+lsh+
  gi|13541666|ref|NP_111354.1| 100 SGQRLPIVMSVVNRAIGPP-WNIWADQSDTMNQKDTGWMQVYCESNQEALDTIIMGYKIAENkdVLLPLMSMEDAFILSHT 179
                                   *******************.************************************************************* PP

                                   EEEEEC-SGG.GS-----SBXXXXXXXXSXXXBXXTXXTSSXXEE.ESBXBXTTSXBXXXXHHHHHHH CS
                         POR_N 162 vekvelpdeedelklikekleeyerkeyaldpekpiargtaanpd.tglehrekgneaedaaekvvee 228
                                    e+v++ d+e     ++e l++ +    +++ e+p+ +g +++pd  ++e ++++  ++++a+ ++e+
  gi|13541666|ref|NP_111354.1| 180 SEPVTIRDQE----SVNEYLPDLDL-PFKINEEHPMGYGSYDTPDgSFMELKKDMVDSMQKAKRIIED 242
                                   **********....67766666544.55899*************945689999999999999998876 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 !  106.1   0.0   2.1e-34   9.5e-31       1     102 []     267     369 ..     267     369 .. 0.99

  Alignments for each domain:
  == domain 1  score: 106.1 bits;  conditional E-value: 2.1e-34
                                   -SEEEEE-STHHHHHHHHHHHHHHTT--EEEEEES--BS--HHHHHHHSTT-SEEEEEE-S--TT-G-HHHHHHHHHTGGG CS
                       PFOR_II   1 AevvivamGsvagtaksavdelReegikvGllrlrtlrPFPeeelkellkkvkkvvvldrnisfgseGqlveevkaalkks 81 
                                   A+++i+a+G++a+ta+ +vd lR++g+kvGl+r+r++rPFP+ee+ + lk vk+  v+dr++sf+s G+ + e+ + l+++
  gi|13541666|ref|NP_111354.1| 267 ADYAIIATGTIASTARYVVDILRKKGEKVGLIRIRYFRPFPYEEILSSLKYVKAAGVIDRSVSFSSGGPTYVEIVQGLYGK 347
                                   9******************************************************************************** PP

                                   .TSEEEEEE--GGG----HHHH CS
                       PFOR_II  82 .kvkvvnfvaglgGrditvedi 102
                                    +v++ +f+ag+gGrd++++di
  gi|13541666|ref|NP_111354.1| 348 lNVPLSSFIAGIGGRDVRIQDI 369
                                   ********************97 PP

>> Transketolase_C  Transketolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   1.1e-07   0.00049       8      96 ..     265     352 ..     260     373 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1.1e-07
                                   TTSSEEEEEETTHHHHHHHHHHHHHTTTTCEEEEE-SEEESHHHHHHHHHHHHHSEEEEEEEEESTTSHHHHHHHHHHHCC CS
               Transketolase_C   8 egkdvtlvayGsmveealeAaeeLekegisaeVvdlrtvkplDketilesvkktgrlvvveeavkrgGigsevaaalaeea 88 
                                   e  d +++a+G+  ++a  +++ L+k+g ++ ++ +r ++p+  e il+s+k  +   v++  v + + g   +++++  +
  gi|13541666|ref|NP_111354.1| 265 EDADYAIIATGTIASTARYVVDILRKKGEKVGLIRIRYFRPFPYEEILSSLKYVKAAGVIDRSVSFSSGGPTYVEIVQG-L 344
                                   678999******************************************9999888777777776666666666666666.6 PP

                                   CTTCSSEE CS
               Transketolase_C  89 fdgldapv 96 
                                   + +l++p 
  gi|13541666|ref|NP_111354.1| 345 YGKLNVPL 352
                                   66666665 PP

>> ZnuA  Zinc-uptake complex component A periplasmic
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.1   7.4e-06     0.033     151     232 ..       5      88 ..       1      97 [. 0.83
   2 ?   -0.2   0.0      0.12   5.4e+02     161     246 ..     253     341 ..     222     348 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 7.4e-06
                                   GTEGEEEESSSTTHHHHHHTT-EEEEEESSSSSHHHHHHHHHHHHHTT-SEEEEET.TS-THHHHHHHHHH.T-EEEEE-S CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx.xxxxxxxxx RF
                          ZnuA 151 eekrklvtthdafgylarayglevagiagisteaaqiaalieeikeagvkaifvep.laspklaetlaeea.gvkvatlys 229
                                   +++r+++t +da++y a+   ++++++  i+++   +++l+ +i ++++ a +v+  ++ ++la+ + +e  gv+  t  s
  gi|13541666|ref|NP_111354.1|   5 QDYRTIMTGNDAVAYGAKLARVKLISAYPITPQTTIVEKLASMIANDELDAKYVKVeSEHSALATVVSSELaGVRSYTATS 85 
                                   4899**********************99*****999999999999999999999884557777777777887898776555 PP

                                   TSS CS
                                   xxx RF
                          ZnuA 230 lds 232
                                    ++
  gi|13541666|ref|NP_111354.1|  86 SHG 88 
                                   455 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.12
                                   STTHHHHHHTT-EEEEEESSSSS..HHHHHHHHHHHHHTT-SEEEEET.TS-THHHHHHHHHHT.-EE.EEE-STSSSTST CS
                                   xxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx.xxx.xxxxxxxxxxxx RF
                          ZnuA 161 dafgylarayglevagiagiste..aaqiaalieeikeagvkaifvep.laspklaetlaeeag.vkv.atlysldslgde 236
                                     +g l ++y +e a  a i t   a++ + +++ ++++g k+ ++    ++p   e++ +  + vk  ++++   s++ +
  gi|13541666|ref|NP_111354.1| 253 TEYGGLIEKYRMEDADYAIIATGtiASTARYVVDILRKKGEKVGLIRIrYFRPFPYEEILSSLKyVKAaGVIDRSVSFSSG 333
                                   457778889999999887777778999999999999998888766655355777777777777556652446665566666 PP

                                   TSTTSHHHHH CS
                                   xxxxxxxxxx RF
                          ZnuA 237 gsaetYidmm 246
                                   g  +tY++++
  gi|13541666|ref|NP_111354.1| 334 G--PTYVEIV 341
                                   5..7777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (392 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       571  (0.0318478); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 2491.66
//
Query:       gi|13541667|ref|NP_111355.1|  [L=295]
Description: 2-ketoisovalerate ferredoxin oxidoreductase subunit beta [Thermoplasma volcanium GSS1]
Scores for complete 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-22   77.7   0.8    1.4e-21   76.9   0.2    1.7  2  TPP_enzyme_C    Thiamine pyrophosphate enzyme, C-terminal TPP
  ------ inclusion threshold ------
      0.036   13.3   0.3       0.14   11.4   0.3    2.0  1  DXP_synthase_N  1-deoxy-D-xylulose-5-phosphate synthase


Domain annotation for each model (and alignments):
>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.26   2.3e+03      20      42 ..       9      31 ..       4      43 .. 0.64
   2 !   76.9   0.2   1.6e-25   1.4e-21      30     153 .]      63     206 ..      45     206 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.26
                                  EEECETTTS-TTTHHHHHHHHHH CS
                  TPP_enzyme_C 20 syltsgglgtmGyglpaAiGakl 42
                                  +++ +g ++++G g   A+   l
  gi|13541667|ref|NP_111355.1|  9 ELMEPGHTACHGCGATLAMRYVL 31
                                  45557778899999888875555 PP

  == domain 2  score: 76.9 bits;  conditional E-value: 1.6e-25
                                   TTTHHHHHHHHHH.....H.....STTSEEEEEEEHHHHHHT.GGGHHHHHHTT-SEEEEEEE-SBCCCHHHH...HHHHT CS
                  TPP_enzyme_C  30 mGyglpaAiGakl.....a.....kpdrevvaivGDGgflmi.lqelatavrrnlpitvvvlnNegygmtggq...qepfg 96 
                                   m y+  aA+Ga++     a     k+d +vv ++GDGg+++i lq l+ a++r++++ +++++Negy++tg q   ++p+g
  gi|13541667|ref|NP_111355.1|  63 MVYTPFAATGASIsglreAldiqgKEDYNVVGFAGDGGTADIgLQGLSGAMERGHNVFYIMYDNEGYMNTGVQrsgSTPYG 143
                                   5566668888888776652566557899***************************************************** PP

                                   CCTTTTSBB......BS----HHHHHHHTTSE.EEEESSH.HHHHHHHHHHHHCSSSEEEEEE CS
                  TPP_enzyme_C  97 gkrksgpagk.....dlkpvdfaklaealGak.garvekadveeleealkealekkgpaliev 153
                                   +k++++p gk      ++++ +a ++ a  ++ +a+ ++a++e++ +++++a+e +gp +i++
  gi|13541667|ref|NP_111355.1| 144 AKTTTTPVGKerdfkRENKKVVADMMIAQNVPyVATATVAYPEDIIKKIERAREINGPKFIQI 206
                                   ************99668888999999999***999999**********************986 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 ?   11.4   0.3   1.5e-05      0.14     119     177 ..      74     132 ..      63     208 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 1.5e-05
                DXP_synthase_N 119 aalGlavardlkg.ekkkvvaviGDgaltgGmafealnnigelkkkllvilNdNemsisk 177
                                    + Gl +a d++g e+++vv   GDg+ t+ + +++l  + e  ++++ i+ dNe  +++
  gi|13541667|ref|NP_111355.1|  74 SISGLREALDIQGkEDYNVVGFAGDGG-TADIGLQGLSGAMERGHNVFYIMYDNEGYMNT 132
                                   3579*******996789*********9.999***********************976655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       682  (0.0380389); expected 358.6 (0.02)
Passed bias filter:                      580  (0.0323498); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 1879.11
//
Query:       gi|13541668|ref|NP_111356.1|  [L=185]
Description: SAM-dependent methyltransferase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-21   77.3   0.0    2.9e-21   75.9   0.0    1.7  2  Methyltransf_11  Methyltransferase domain
    1.8e-19   70.2   0.0    1.3e-18   67.4   0.0    1.9  2  Methyltransf_25  Methyltransferase domain
      1e-13   51.4   0.0    2.1e-13   50.3   0.0    1.5  1  Methyltransf_31  Methyltransferase domain
    7.4e-13   48.4   0.0    1.1e-12   47.8   0.0    1.2  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    1.2e-11   45.2   0.0    1.9e-11   44.6   0.0    1.3  1  Methyltransf_12  Methyltransferase domain
    4.1e-05   22.8   0.0    5.9e-05   22.3   0.0    1.2  1  RrnaAD           Ribosomal RNA adenine dimethylase
    4.8e-05   23.3   0.0    5.5e-05   23.1   0.0    1.1  1  Methyltransf_23  Methyltransferase domain
    0.00018   21.5   0.0    0.00029   20.9   0.0    1.2  1  Methyltransf_32  Methyltransferase domain
     0.0012   19.0   0.0     0.0015   18.7   0.0    1.2  1  FtsJ             FtsJ-like methyltransferase
     0.0015   17.6   0.0     0.0018   17.5   0.0    1.1  1  DREV             DREV methyltransferase
     0.0017   17.5   0.0     0.0023   17.1   0.0    1.2  1  Fibrillarin      Fibrillarin
      0.002   17.7   0.0     0.0028   17.2   0.0    1.2  1  MTS              Methyltransferase small domain
     0.0024   17.5   0.0     0.0033   17.1   0.0    1.1  1  MetW             Methionine biosynthesis protein MetW
  ------ inclusion threshold ------
      0.013   14.8   0.0      0.021   14.1   0.0    1.3  1  Methyltransf_2   O-methyltransferase domain
      0.054   12.5   0.0      0.076   12.0   0.0    1.1  1  tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
      0.091   12.6   0.0       0.29   10.9   0.0    1.8  1  Methyltransf_8   Hypothetical 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 !   75.9   0.0   2.6e-24   2.9e-21       1      91 [.      38     128 ..      38     132 .. 0.95
   2 ?   -2.4   0.0       7.1     8e+03      24      38 ..     151     165 ..     140     172 .. 0.73

  Alignments for each domain:
  == domain 1  score: 75.9 bits;  conditional E-value: 2.6e-24
                                   EEET-TTSHHHHHHHHTT.SEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-CCHHHH CS
               Methyltransf_11   1 LdvGcGtGrlaealakrg.arvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhvedpeka 80 
                                   +d+GcG G ++ +l ++  ++v+++D s+em+++ k+++ ++ + +  ++a aek+p++d s Dlv++ ++ h ++d++++
  gi|13541668|ref|NP_111356.1|  38 VDLGCGPGFFTLPLSETTdGKVYAIDASQEMIDALKQRIDGRSN-IVTIKAPAEKIPLPDLSADLVFIANAYHDFDDRDEV 117
                                   59*************9999***********************96.888********************************* PP

                                   HHHHHHHEEEE CS
               Methyltransf_11  81 lkeiaRvLkpg 91 
                                   l+ei+R+L+ g
  gi|13541668|ref|NP_111356.1| 118 LSEIYRILRAG 128
                                   *********97 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 7.1
                                   EES-HHHHHHHHHHC CS
               Methyltransf_11  24 vDlskemlklakeka 38 
                                   +D  ++ml++a+++ 
  gi|13541668|ref|NP_111356.1| 151 IDKKEAMLEIASHNF 165
                                   666777777777665 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.4   0.0   1.2e-21   1.3e-18       1      96 [.      37     128 ..      37     128 .. 0.93
   2 ?    0.4   0.0      0.97   1.1e+03      27      42 ..     151     166 ..     148     176 .. 0.82

  Alignments for each domain:
  == domain 1  score: 67.4 bits;  conditional E-value: 1.2e-21
                                   EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGSSHHH CS
               Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhlsded 81 
                                   ++dlGcG+G +tl l++   ++kv+++D s+em++a ++r++ +  n+  +++ ae++p++d s Dlv++++a+h ++  d
  gi|13541668|ref|NP_111356.1|  37 IVDLGCGPGFFTLPLSETT-DGKVYAIDASQEMIDALKQRIDGR-SNIVTIKAPAEKIPLPDLSADLVFIANAYHDFD--D 113
                                   89****************7.8********************654.4************************99988888..6 PP

                                   HHHHHHHHHHHEEEE CS
               Methyltransf_25  82 lekalkeiarvLkpg 96 
                                   ++++l+ei+r+L+ g
  gi|13541668|ref|NP_111356.1| 114 RDEVLSEIYRILRAG 128
                                   67**********976 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.97
                                   EESSHHHHHHHHHHHH CS
               Methyltransf_25  27 vDiseemleaarerae 42 
                                   +D  e+mle+a ++++
  gi|13541668|ref|NP_111356.1| 151 IDKKEAMLEIASHNFD 166
                                   8999*******99984 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.3   0.0   1.9e-16   2.1e-13       3     109 ..      33     132 ..      31     164 .. 0.90

  Alignments for each domain:
  == domain 1  score: 50.3 bits;  conditional E-value: 1.9e-16
               Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsnev 83 
                                    +  ++DlGCG G++t+ l e+  ++++v+ iD s+e+i   +++ +  g +n+   ++++e+++  l d + Dl++  ++
  gi|13541668|ref|NP_111356.1|  33 PNFDIVDLGCGPGFFTLPLSET--TDGKVYAIDASQEMIDALKQRID--GRSNIVTIKAPAEKIP--LPDLSADLVFIANA 107
                                   57789***************44..79******************977..999*************..9************* PP

               Methyltransf_31  84 lnaladpdkileeiervlkpggilli 109
                                    +++ d d++l ei r l+  g++l+
  gi|13541668|ref|NP_111356.1| 108 YHDFDDRDEVLSEIYRILR-AGRFLV 132
                                   ******************9.566664 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.8   0.0   9.6e-16   1.1e-12      33     156 ..      17     138 ..       7     143 .. 0.88

  Alignments for each domain:
  == domain 1  score: 47.8 bits;  conditional E-value: 9.6e-16
                                   HHHHH..HHHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-T CS
               Ubie_methyltran  33 rlWkk..fveklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLp 111
                                   + W +  ++      ++  +++D+ +G g +++ ls++  + gkv  +D +++m++  ++++  +g +ni  ++a ae++p
  gi|13541668|ref|NP_111356.1|  17 KEWEDpeKIVSQIPIQPNFDIVDLGCGPGFFTLPLSET--TDGKVYAIDASQEMIDALKQRI--DGRSNIVTIKAPAEKIP 93 
                                   56776656666666677779***************997..579**************99998..5899************* PP

                                   TS-T-EEEEEEES-GGG-S-HHHHHHHHHHHEEEEEEEEEEEE-- CS
               Ubie_methyltran 112 feddsfDvvtvsfGlrnvtDklkaLkeayrvlkpGGrlvvlefsk 156
                                     d s D+v ++    ++ D++++L e+yr+l++G  lv ++  k
  gi|13541668|ref|NP_111356.1|  94 LPDLSADLVFIANAYHDFDDRDEVLSEIYRILRAGRFLVDIDWKK 138
                                   **********************************99888777665 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.6   0.0   1.7e-14   1.9e-11       1      96 [.      38     128 ..      38     131 .. 0.89

  Alignments for each domain:
  == domain 1  score: 44.6 bits;  conditional E-value: 1.7e-14
               Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhhlkd 81 
                                   +++GcG G ++ +l e   d +++++D s+++i++ k+++  r+n     ++  a+ +   d   s Dlv+++n+ h ++d
  gi|13541668|ref|NP_111356.1|  38 VDLGCGPGFFTLPLSET-TDGKVYAIDASQEMIDALKQRIDGRSN--IVTIKAPAEKIPLPDL--SADLVFIANAYHDFDD 113
                                   59************999.***************888888888885..6677777777766666..**************** PP

               Methyltransf_12  82 irevldnirklLkpg 96 
                                   ++evl++i++ L+ g
  gi|13541668|ref|NP_111356.1| 114 RDEVLSEIYRILRAG 128
                                   ************987 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   5.3e-08   5.9e-05      21      84 ..      24      88 ..      22     114 .. 0.88

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 5.3e-08
                                  HHHHHH-GGTTSEEEEES-TTTCCHHHHHCC-.SEEEEE-S-HHHHHHHHCHTTTCCCEEEE-S- CS
                        RrnaAD 21 eIldklnleekltvleigpGkGilTeeLakra.kqvvvlElderLakllqkklskdeklkvvhqD 84
                                  +I++++ ++++  ++++g G+G++T +L +    +v ++   ++++  l++++   +++  +++ 
  gi|13541668|ref|NP_111356.1| 24 KIVSQIPIQPNFDIVDLGCGPGFFTLPLSETTdGKVYAIDASQEMIDALKQRIDGRSNIVTIKAP 88
                                  8*******************************99*****************99988888777765 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0   4.9e-08   5.5e-05      21     115 ..      32     131 ..       6     161 .. 0.83

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 4.9e-08
               Methyltransf_23  21 raggrvLdiGcGtGillevlrengf.svtgvDlspeaveiae....kakkaqkdqfdeqeaaepqgkfdlIvlrevlehvp 96 
                                   +++  ++d+GcG G ++  l+e    +v+++D+s e+++ ++    ++++ +  ++++++++ p+ + dl+   +  + ++
  gi|13541668|ref|NP_111356.1|  32 QPNFDIVDLGCGPGFFTLPLSETTDgKVYAIDASQEMIDALKqridGRSNIVTIKAPAEKIPLPDLSADLVFIANAYHDFD 112
                                   4555899*******999999998778*************998888855555555555578888889*************** PP

               Methyltransf_23  97 dppellrqiatllkpgGyl 115
                                   d  e+l+ i+++l+ g  l
  gi|13541668|ref|NP_111356.1| 113 DRDEVLSEIYRILRAGRFL 131
                                   *************977655 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   2.6e-07   0.00029      24      71 ..      32      76 ..      21      91 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 2.6e-07
               Methyltransf_32 24 sgaltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekra 71
                                  ++++++vD+G+G g+ +  l+        kv++ida++e++++ ++r 
  gi|13541668|ref|NP_111356.1| 32 QPNFDIVDLGCGPGFFTLPLSE---TTDGKVYAIDASQEMIDALKQRI 76
                                  56789*****************...889************99988775 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   1.3e-06    0.0015      19      65 ..      31      78 ..      20     127 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.3e-06
                                  S-TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEES.SSS.....HHHTTEEE CS
                          FtsJ 19 fkpgktvvDlgaaPGgwsqvllqrlgakgkvvavDl.qpm.....aplpgvtt 65
                                  ++p+  +vDlg++PG ++  l++ +   gkv+a+D  q+m     +   ++  
  gi|13541668|ref|NP_111356.1| 31 IQPNFDIVDLGCGPGFFTLPLSETT-D-GKVYAIDAsQEMidalkQ---RIDG 78
                                  4566779*****************6.4.9*******9999854431...3332 PP

>> DREV  DREV methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   1.6e-06    0.0018      95     180 ..      34     127 ..      24     169 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.6e-06
                          DREV  95 dkklldlGaGdGeitkrvaptfee.vyatelsetmrdrlkkk...kynvlsalelqet....dvkldlilclnlldrcfdp 167
                                   +  ++dlG G G  t  +++t +  vya ++s++m+d lk++   + n++++   +e     d+  dl+   n     +d 
  gi|13541668|ref|NP_111356.1|  34 NFDIVDLGCGPGFFTLPLSETTDGkVYAIDASQEMIDALKQRidgRSNIVTIKAPAEKiplpDLSADLVFIANAYHDFDDR 114
                                   56799**************999744**************987444578888876444223338899999999999999999 PP

                          DREV 168 lklledirsalep 180
                                    ++l +i+ +l++
  gi|13541668|ref|NP_111356.1| 115 DEVLSEIYRILRA 127
                                   9999998887765 PP

>> Fibrillarin  Fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0     2e-06    0.0023      63     129 ..      26      90 ..      23     113 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2e-06
                                   -S--S--TTSEEEEESTTTSHHHHHHHHHHTTTSEEEEEESSHHHHHHHHHHHTTSTTEEEEES-TT CS
                   Fibrillarin  63 lkelpikkgskvLYlGaasGttvsHvsDivgeegvvyavefsprvlrelievakkRknivPileDAr 129
                                   ++++pi+++  ++ lG + G     +s+  +  g+vya++ s+ ++  l +  + R+niv i + A+
  gi|13541668|ref|NP_111356.1|  26 VSQIPIQPNFDIVDLGCGPGFFTLPLSETTD--GKVYAIDASQEMIDALKQRIDGRSNIVTIKAPAE 90 
                                   7899*******************9***9877..***************************9987775 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   2.5e-06    0.0028      25      76 ..      27      77 ..      23     109 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.5e-06
                                  HHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHH CS
                           MTS 25 etlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenle 76
                                  +++p + + +++DlGcG G+ ++ l + ++  +v ++d++ + +++ k+ + 
  gi|13541668|ref|NP_111356.1| 27 SQIPIQPNFDIVDLGCGPGFFTLPLSETTDG-KVYAIDASQEMIDALKQRID 77
                                  5666667778***************997776.8********99999988765 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   2.9e-06    0.0033      11     103 ..      31     126 ..      20     132 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.9e-06
                          MetW  11 ikpgsrvldlGcGdGellellkeekqvdgrGleldeegvaecvak..G.lsviqgdldkdlenfedksfdyvvlsqtlqat 88 
                                   i+p+  ++dlGcG G +   l e+ + + + ++ ++e + +  ++  G  +++   +  +    +d s d+v ++ +    
  gi|13541668|ref|NP_111356.1|  31 IQPNFDIVDLGCGPGFFTLPLSETTDGKVYAIDASQEMIDALKQRidGrSNIVTIKAPAEKIPLPDLSADLVFIANAYHDF 111
                                   788899***********999*****************999887774432578888888888999***************** PP

                          MetW  89 rnpkevldellrigr 103
                                    + +evl+e+ ri r
  gi|13541668|ref|NP_111356.1| 112 DDRDEVLSEIYRILR 126
                                   **********99965 PP

>> Methyltransf_2  O-methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   1.9e-05     0.021      54     161 ..      25     130 ..      17     148 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.9e-05
                                   HHHSS-GGG-SEEEEET-TTSHHHHHHHHH-TT-EEEEEE-HH.HHHHHHHHS-----TTEEEEES-TTTS---..--SEE CS
                Methyltransf_2  54 vleafdleglkslvDvGGGtGalakaivsayPtikvivfDlpe.VveaAkehlsageeervefvgGdffkdslP..eaDai 131
                                   ++ ++ +++   +vD+G G G +    +++    kv   D ++  + a k++   + ++++  ++    k +lP  +aD++
  gi|13541668|ref|NP_111356.1|  25 IVSQIPIQPNFDIVDLGCGPGFFTLPLSET-TDGKVYAIDASQeMIDALKQR--IDGRSNIVTIKAPAEKIPLPdlSADLV 102
                                   556666666677899999999887777665.456777778776144444555..55566666666667778999999**** PP

                                   EEESSGGGS-HHHHHHHHHHHHHH--TT-E CS
                Methyltransf_2 132 llkrvlhDwsdekcvklLkrvkkalpagGk 161
                                   ++++  hD++d +  ++L ++++ l+ag  
  gi|13541668|ref|NP_111356.1| 103 FIANAYHDFDDRD--EVLSEIYRILRAGRF 130
                                   ***********96..899*****9998754 PP

>> tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   6.7e-05     0.076     202     254 ..      34      85 ..      24      94 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 6.7e-05
               tRNA_U5-meth_tr 202 kgdllelycGnGnfslalarnfe.kvlateiakssveaaqyniaankidnvqii 254
                                   + d+++l cG G f+l+l+++   kv a + ++  ++a +  i+     n+  i
  gi|13541668|ref|NP_111356.1|  34 NFDIVDLGCGPGFFTLPLSETTDgKVYAIDASQEMIDALKQRIDGR--SNIVTI 85 
                                   5699***************987559***********9998888643..355445 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00026      0.29      75     154 ..      36     131 ..      15     170 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00026
                                   -EEEES-TT-HHH..HH--S-..EEEEE.....SS-SSTTE........EES-TTS-S--TT-EEEEEEES---S.S-HHH CS
                Methyltransf_8  75 vvadlGcGeakia..eavrekekvrsfd.....lvavnerv........vacdlakvPledesvdvavfclslmg.tnlad 139
                                    ++dlGcG    +   + +   kv ++d     + a+++r+        +     k+Pl d s+d++ +  +    ++  +
  gi|13541668|ref|NP_111356.1|  36 DIVDLGCGPGFFTlpLSETTDGKVYAIDasqemIDALKQRIdgrsnivtIKAPAEKIPLPDLSADLVFIANAYHDfDDRDE 116
                                   56677777665552233333345555552222222333332111111112233479*********9988888765256777 PP

                                   HHHHHHHHEEEEEEE CS
                Methyltransf_8 140 flkeanrvlkvGGll 154
                                    l e++r+l+ G +l
  gi|13541668|ref|NP_111356.1| 117 VLSEIYRILRAGRFL 131
                                   99*********9776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); 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 0.24s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 1155.42
//
Query:       gi|13541669|ref|NP_111357.1|  [L=369]
Description: coenzyme PQQ synthesis protein E [Thermoplasma volcanium GSS1]
Scores for complete 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-13   48.9   0.0    1.8e-12   48.0   0.0    1.5  1  Radical_SAM  Radical SAM superfamily
    1.4e-06   28.7   0.1    3.4e-06   27.5   0.1    1.7  1  SPASM        Iron-sulfur cluster-binding domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.0   0.0     2e-16   1.8e-12       2     166 ..      15     173 ..      14     174 .. 0.84

  Alignments for each domain:
  == domain 1  score: 48.0 bits;  conditional E-value: 2e-16
                                   EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHH.HHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelk.aekgvkevilgggepllypdfvellerlaklavpgirit 81 
                                   ++t++C l+C +C  +     e  + ++  +e ++ +  +k + k    vil+gg+ l  +++ ++++ l+     +i ++
  gi|13541669|ref|NP_111357.1|  15 ETTKACGLKCEHCRASAI--LEALPDEMNYDESIDFLSHIKeFGKPYPIVILTGGDMLRKRRINDIMKYLKDA---EIPFS 90 
                                   6899************97..99999999999999999999855556*********999999888888888887...66666 PP

                                   EEECSSCHG.HHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHHHH CS
                                   xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  82 vetngtlpd.eeklerllelgvdrvslgleaaddekvlklmn.rghtfeevlealeklreagikrvvdrivglpGendeel 160
                                   v+   t    +e ++ +le gv  vs++l+   d  v+++++  ++ f+++++++ekl + gi+   +++v+++  +  +l
  gi|13541669|ref|NP_111357.1|  91 VSPAVTEMLtDERIKSFLEFGVSSVSISLDGMKD--VHEKVRgVPGVFDDTVRVVEKLIKEGIP-MQINTVVMR-STVNDL 167
                                   6655555335************************..566665599*******************.999999998.666667 PP

                                   HHHHHH CS
                                   xxxxxx RF
                   Radical_SAM 161 eellel 166
                                    ++l+l
  gi|13541669|ref|NP_111357.1| 168 PKVLKL 173
                                   777666 PP

>> SPASM  Iron-sulfur cluster-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   0.1   3.8e-10   3.4e-06       5      67 ..     277     332 ..     274     338 .. 0.80

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 3.8e-10
                         SPASM   5 srslfInsdGdVvpCcvdkktyveelklGnireesleeIwnse.eyqefrkskkfplielCrnC 67 
                                   +  +f+ ++GdV+p  +       ++k+Gn++++s+ +I++++  ++++r+   ++l   C  C
  gi|13541669|ref|NP_111357.1| 277 YGIIFVGHNGDVYPSGFL------PYKVGNVKNQSIVDIYRKSeLLRKIRD--PDNLVGKCGFC 332
                                   6779***********333......6***************66648999**4..55555667666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); 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: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 2407.77
//
Query:       gi|13541670|ref|NP_111358.1|  [L=150]
Description: hypothetical protein TVN0839 [Thermoplasma volcanium GSS1]
Scores for complete 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-33  113.8   0.0    5.5e-33  113.7   0.0    1.0  1  COXG             Carbon monoxide dehydrogenase subunit G (Cox
     0.0027   18.0   0.0      0.015   15.6   0.0    1.8  1  Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid tra
     0.0038   17.5   0.2      0.031   14.6   0.1    2.5  2  Meis_PKNOX_N     N-terminal of Homeobox Meis and PKNOX1
  ------ inclusion threshold ------
       0.13   12.2   0.1       0.17   11.7   0.1    1.2  1  Endonuc_Holl     Endonuclease related to archaeal Holliday ju


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 !  113.7   0.0   1.2e-36   5.5e-33       1     140 []       5     148 ..       5     148 .. 0.95

  Alignments for each domain:
  == domain 1  score: 113.7 bits;  conditional E-value: 1.2e-36
                                   EEEEESS-HHHHHHHHT-HHHHGGGSTTEEEEEEETTEEEEEEEEESSSSEEEE....EEEEEEEEEETTTEEE..EEEEE CS
                          COXG   1 GefrvaapkeavwefLndpeklarciPGvksvekegdeykvkvklkvGplkgsf....karvelselekensttieikGkG 77 
                                   G+f v++++++v++f+ + e++ +c+PG++s++ +g+e+++ ++l++++l+ s+    ++++++    +e++  i+++G+G
  gi|13541670|ref|NP_111358.1|   5 GSFYVDRDPAEVKQFISNFENVVACLPGIDSYTNNGNEFECRIRLDISSLSNSYlkhiSGKMKFLF-VPERDNGISVNGSG 84 
                                   89******************************************************9988888864.4555556******* PP

                                   E-SSEEEEEEEEEEEEEETT.EEEEEEEEEEEEEHHHHS-HHHHHHHHHHHHHHHHHHHHHHHT CS
                          COXG  78 rgagvaidfalvvlveeggg.trlswsakvnvggllaslGsrlidsaarklinelfecissklg 140
                                   r+ag++++++++v ve++++  ++ wsa++++g +l+ +Gs++i++++ ++i++++ec++ k++
  gi|13541670|ref|NP_111358.1|  85 RIAGSSVSMNVKVFVEGSNEhAKVTWSAAIDYGLILKAMGSEKIKEVTDENIKRSIECLRGKIS 148
                                   ***********************************************************99885 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 !   15.6   0.0   3.3e-06     0.015       7     133 ..       6     138 ..       2     146 .. 0.61

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 3.3e-06
                                   EEEESS-HHHHHHHHTTTTGGGGT-TTEEEEECSESTSSSTTTEEEEECCCS.........SEEEEEEEEEETTTTEEEEE CS
               Polyketide_cyc2   7 svviaappekVwalvsdfenwprWhpevarveleggggpargvegtvrvggr.........gtvreelvevdpegrllsyr 78 
                                   s  ++++p++V  ++s+fen+ +  p++++++    +g+  + e ++r                +++++ v ++   +s +
  gi|13541670|ref|NP_111358.1|   6 SFYVDRDPAEVKQFISNFENVVACLPGIDSYTN---NGN--EFECRIRLDISslsnsylkhISGKMKFLFVPERDNGISVN 81 
                                   7789*************************8854...445..3446666444334556664422666666663345555555 PP

                                   EE.SSS-TSEEEEEEEEECC..ETEEEEEEEEEEEE--TT--HHHHHHHHHHHHHHH CS
               Polyketide_cyc2  79 ivkpvpvanyvatwtvtpdg..ggtrvtwtgefdagplggpfekpaaakavkgdlea 133
                                   + +   +++++ +++v  +g  +  +vtw++++d g + + +  + +++   +++++
  gi|13541670|ref|NP_111358.1|  82 GSGRIAGSSVSMNVKVFVEGsnEHAKVTWSAAIDYGLILKAMGSEKIKEVTDENIKR 138
                                   5323333444444444444422669999*9999984444444444444444444554 PP

>> Meis_PKNOX_N  N-terminal of Homeobox Meis and PKNOX1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0         1   4.5e+03      65      78 ..      56      69 ..      52      76 .. 0.73
   2 !   14.6   0.1     7e-06     0.031      51      77 ..     123     149 ..      82     150 .] 0.77

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1
                  Meis_PKNOX_N 65 eRYiacLkgkmpid 78
                                  + Y++ + gkm+  
  gi|13541670|ref|NP_111358.1| 56 NSYLKHISGKMKFL 69
                                  66889999999865 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 7e-06
                  Meis_PKNOX_N  51 lelekVhELCdnFceRYiacLkgkmpi 77 
                                   +  ek++E+ d+  +R i+cL+gk+ +
  gi|13541670|ref|NP_111358.1| 123 MGSEKIKEVTDENIKRSIECLRGKISM 149
                                   5689********************976 PP

>> Endonuc_Holl  Endonuclease related to archaeal Holliday junction resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   3.8e-05      0.17      46      85 ..     109     148 ..      93     150 .] 0.84

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.8e-05
                  Endonuc_Holl  46 eallkkeaevkleewkkkeekeiRedaikksksvilgkvt 85 
                                   + ++  ++ + l+   ++++ke+ ++ ik+s++ ++gk++
  gi|13541670|ref|NP_111358.1| 109 TWSAAIDYGLILKAMGSEKIKEVTDENIKRSIECLRGKIS 148
                                   5566777888899999**********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       475  (0.0264934); 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:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.49
# Mc/sec: 921.23
//
Query:       gi|13541671|ref|NP_111359.1|  [L=414]
Description: glycerol-3-phosphate dehydrogenase [Thermoplasma volcanium GSS1]
Scores for complete 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-47  161.6   0.0    4.5e-47  161.3   0.0    1.0  1  DAO             FAD dependent oxidoreductase
    1.1e-09   38.3   0.2      3e-09   37.0   0.2    1.8  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    0.00035   19.9   0.0     0.0035   16.6   0.0    2.1  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
     0.0051   15.6   0.0       0.01   14.6   0.0    1.5  1  HI0933_like     HI0933-like protein
     0.0083   16.7   0.3       0.17   12.4   0.2    2.5  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
  ------ inclusion threshold ------
      0.016   14.8   0.0      0.028   14.1   0.0    1.4  1  ApbA            Ketopantoate reductase PanE/ApbA
       0.02   14.8   0.4       0.13   12.2   0.1    2.1  2  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
      0.021   14.1   0.4      0.044   13.0   0.2    1.6  2  Thi4            Thi4 family
      0.031   13.8   0.1      0.072   12.7   0.1    1.6  1  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
      0.035   13.9   0.2       0.22   11.4   0.1    2.3  2  KH_1            KH domain
      0.048   12.9   0.0      0.076   12.2   0.0    1.2  1  FAD_binding_3   FAD binding domain
      0.055   12.6   0.3        0.1   11.7   0.3    1.4  1  FAD_binding_2   FAD binding domain


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 !  161.3   0.0     3e-50   4.5e-47       1     351 [.       3     349 ..       3     350 .. 0.84

  Alignments for each domain:
  == domain 1  score: 161.3 bits;  conditional E-value: 3e-50
                                   EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSGGGSSEEEEESSSSTHHSTHHHHHHHH.HHHHHHHHHHHHHSST CS
                           DAO   1 dvviiGGGiiGlstAyeLarrg..VtllekgdiagsgaSgrnsgllhsglrylpeaselarlsl.ealeelreleeelgid 78 
                                   +++++G+Gi+Gl+tAy+L++ g  V +++kgdia+ g+Sg+  g+lhsg ry+       ++s+ e++ e   +++  +  
  gi|13541671|ref|NP_111359.1|   3 KIAVVGAGITGLFTAYYLSASGfdVEVFDKGDIAS-GTSGKFHGMLHSGARYAVTD----KVSAsECISENNTISSF-A-R 76 
                                   59*****************************6655.**************988866....66665889999999975.4.3 PP

                                   TSEEEEEEEEEESSHHHHHHHHHHHHHHHHTTTTEEEEEHHHHHHHSTTSTTTSEEEEETTEEEEEHHHHHHHHHHHHHHT CS
                           DAO  79 idyrrtGllslaadeeelealdkllallleagldaelldaeevrelepalpgllgalfypdtgqvdpakltaalaraaeal 159
                                   +    tG +++ +++ee ++ d l +++++ag++++ +d +e +++ep+++++   +++pd  ++ ++++ aa+a++a  +
  gi|13541671|ref|NP_111359.1|  77 WFINDTGGYFVSSNREESDYGDTLTKACNDAGIPNYDIDVDEFKKIEPNVKNVDRVIHVPD-KVIRAYEFSAAVAAEAFMN 156
                                   ************999999999999999999****988***99******9879999******.9****************** PP

                                   T-EEEESECEEEEEEEE.TCEEEEEEECTEEEE..EEEEEEE--GGGHH.HHHTT..CTTTSEEEEEEEEEEEE.EECCTH CS
                           DAO 160 Gveilegtevtgleeed.gkvwgverttpgend..aadavVnaaGawsd.llgll..keldlpispvrgqvlvl.kplsek 233
                                   G +++++++v +++e++ + v g+  + +g+ +  ++d +Vna+G++s+ +l+l+  +    p++p  g ++v+ kp+ ++
  gi|13541671|ref|NP_111359.1| 157 GTKFRLYSPVASVSEKGgKYVLGI--ERNGSLHyeHFDLIVNATGPFSGeFLKLAgyG--GSPVMPSAGIMVVFsKPIVRS 233
                                   *************88762333333..2235542346788**********555666444..46************5555442 PP

                                   STGSGCSEEEEEEEETTTTEEEEEETTSEEEEEESSEEETTCSSTSCSHHHHHHHHHHHHHHSGGGCGEE..EEEEEEEE. CS
                           DAO 234 lvspaailpvpetdddgrgvyvtprkdgrvlvGgtadeesgdddpevdeedidellealrklfPqlgdvl..rkwaGlrp. 311
                                         i      +++++  +++p+ dg  ++G++a+  ++++++++d+ed+++++e ++ l+P +++v   r+++ +rp 
  gi|13541671|ref|NP_111359.1| 234 -----IINR---MREPSDADIMVPY-DGLSILGTSAVIVDDPENFSIDSEDVEAMIEDMSSLIPLIRNVNysRTYYSVRPl 305
                                   .....3333...77899999****9.7*9999****99999999*********************97766337999****5 PP

                                   ETTS..........SEEEEEEETEEEEEEEEECTTTHHHHHHHHHHHHHH CS
                           DAO 312 lpdg..........lpligetpgvkglylatGhsghGltlapatGkllae 351
                                   l d+          + +i +    +g++ + G     +t++ ++G+++a+
  gi|13541671|ref|NP_111359.1| 306 LEDEgddarkasrsFRIIKN---GEGVFTVVGG---KFTTGRLIGEHVAK 349
                                   34444667999997888877...48*****998...************95 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.0   0.2     2e-12     3e-09       1      36 [.       6      41 ..       6      74 .. 0.88

  Alignments for each domain:
  == domain 1  score: 37.0 bits;  conditional E-value: 2e-12
                                  EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG- CS
                 NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraa 36
                                  +vGaG++Gl +Ay+L+  gfdv++++k+d  +G + 
  gi|13541671|ref|NP_111359.1|  6 VVGAGITGLFTAYYLSASGFDVEVFDKGDIASGTSG 41
                                  8*****************************999654 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 !   16.6   0.0   2.4e-06    0.0035       2      58 ..       3     117 ..       2     210 .. 0.64

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.4e-06
                                   SEEEE--SHHHHHHHHHHHHHTS-EEEEE....TTHCHHHCSHHHHCHHHHHHHHHHHHH..................... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxx..................... RF
                   Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlve....legtclnggcllskallgvaedaeias..................... 57 
                                   +++v+G+G+ Gl +a +l+++g++v +++    + gt   ++ +l++ ++ +  d+  as                     
  gi|13541671|ref|NP_111359.1|   3 KIAVVGAGITGLFTAYYLSASGFDVEVFDkgdiASGTSGKFHGMLHSGARYAVTDKVSASecisenntissfarwfindtg 83 
                                   789999999999999999999999999965555444444555555555555555554444666666555555555555555 PP

                                   .................................H CS
                                   .................................x RF
                   Pyr_redox_2  58 .................................e 58 
                                                                    +
  gi|13541671|ref|NP_111359.1|  84 gyfvssnreesdygdtltkacndagipnydidvD 117
                                   5555555555555555555555555555555552 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   6.8e-06      0.01       2      33 ..       3      34 ..       2      83 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 6.8e-06
                                  SEEEE--SHHHHHHHHHHHHTT--EEEE-SSS CS
                   HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekak 33
                                  +++v+G+G  Gl++A  +++ g +V +++k++
  gi|13541671|ref|NP_111359.1|  3 KIAVVGAGITGLFTAYYLSASGFDVEVFDKGD 34
                                  799***************************86 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.2   0.00012      0.17       1      32 [.       3      34 ..       3      39 .. 0.93
   2 ?    1.5   0.0       0.3   4.4e+02      27      75 ..     132     179 ..     118     184 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00012
                                  EEEEECSSHHHHHHHHHHHHTTSEEEEEESSS CS
                     Pyr_redox  1 kvvvvGgGyiglElAgalaelgkkVtvversd 32
                                  k++vvG+G +gl  A +l++ g +V v++ +d
  gi|13541671|ref|NP_111359.1|  3 KIAVVGAGITGLFTAYYLSASGFDVEVFDKGD 34
                                  79*************************98876 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.3
                                   EEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTS.EEE CS
                     Pyr_redox  27 vversdkllrllDeeaskilqeklekngievllntkveeiegsedg.ves 75 
                                   v++  dk+ r++  e+s++++ +   ng +++l + v+++ +++ + v +
  gi|13541671|ref|NP_111359.1| 132 VIHVPDKVIRAY--EFSAAVAAEAFMNGTKFRLYSPVASVSEKGGKyVLG 179
                                   677777777555..588999999999**************9999886655 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   1.9e-05     0.028       1      35 [.       4      37 ..       4      75 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.9e-05
                                  EEEES-SHHHHHHHHHHHHHTHCEEEE-SCHHHHH CS
                          ApbA  1 iailGaGaiGsllaakLakagadvtlilrsrrlea 35
                                  ia++GaG  G + a++L++ g dv + ++++ +++
  gi|13541671|ref|NP_111359.1|  4 IAVVGAGITGLFTAYYLSASGFDVEVFDKGD-IAS 37
                                  89**********************9999988.554 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   8.6e-05      0.13       1      30 [.       3      32 ..       3      74 .. 0.84
   2 ?    0.3   0.0      0.37   5.6e+02      41      88 ..     365     412 ..     349     413 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 8.6e-05
                                  EEEEE--SCCHHHHHHHHHHTT-EEEEE-S CS
                       3HCDH_N  1 kvaviGaGtmGagiaavfasagleVvlvdi 30
                                  k+av+GaG+ G   a+ + ++g++V ++d 
  gi|13541671|ref|NP_111359.1|  3 KIAVVGAGITGLFTAYYLSASGFDVEVFDK 32
                                  69*************************997 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.37
                                   HHHHHHHCCTTTTSS-HHHHCCCHHCEEEES-HHHHHC-SEEEE-S-S CS
                       3HCDH_N  41 kieksleklvekgklkeeeveaalarisfttdleeavdadlviEavvE 88 
                                    +++++e+++ek   +++ +++a++ri + ++ ++++++ + i +++E
  gi|13541671|ref|NP_111359.1| 365 DLNSTYERFIEKYGRDDKYIAKAMSRIGTIDEENAMRSVAYAISTIIE 412
                                   5678899999999999999********999999888888888887776 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.2   2.9e-05     0.044      20      63 ..       4      47 ..       1      59 [. 0.83
   2 ?   -3.3   0.0       2.9   4.4e+03       1      39 [.     227     265 ..     227     267 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.9e-05
                                  EEEE--SHHHHHHHHHHHHCTTS-EEEEES.SSS--TTTTTTSTT CS
                          Thi4 20 vvivGaGssGLtaayylakkpdlkvailer.svspGGGawlGGql 63
                                  +++vGaG +GL +ayyl+ + ++ v ++++  ++ G      G+l
  gi|13541671|ref|NP_111359.1|  4 IAVVGAGITGLFTAYYLSAS-GFDVEVFDKgDIASGTSGKFHGML 47
                                  89*****************9.*****9987357777655556665 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2.9
                                   HHHHHHHHHHHHHHHTEEEEEEE--SHHHHHHHHHHHHC CS
                          Thi4   1 sraiveryfedllkyaesDvvivGaGssGLtaayylakk 39 
                                   s+ iv++ ++ + +  ++D+++   G s L ++ ++  +
  gi|13541671|ref|NP_111359.1| 227 SKPIVRSIINRMREPSDADIMVPYDGLSILGTSAVIVDD 265
                                   678999999999999999999998888888777776655 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   4.8e-05     0.072       2      31 ..       3      32 ..       2      68 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.8e-05
                                  EEEEE--STTHHHHHHHHHHCTSEEEEE-S CS
                UDPG_MGDP_dh_N  2 kisviGlGYvGlvtaavlaeighevigvDi 31
                                  ki+v+G+G  Gl ta  l++ g++v + D+
  gi|13541671|ref|NP_111359.1|  3 KIAVVGAGITGLFTAYYLSASGFDVEVFDK 32
                                  8************************99986 PP

>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.91   1.4e+03      20      36 ..     233     249 ..     232     280 .. 0.79
   2 ?   11.4   0.1   0.00015      0.22      23      64 ..     349     391 ..     339     393 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.91
                                   HHHHHHHHHHT-EEEEE CS
                          KH_1  20 snIkeIreetgakIkvp 36 
                                   s I+++re + a I vp
  gi|13541671|ref|NP_111359.1| 233 SIINRMREPSDADIMVP 249
                                   67999999889999987 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00015
                                   HHHHHHHT-EEEEESSTT....T.-EEEEEE.SHHHHHHHHHHH CS
                          KH_1  23 keIreetgakIkvpksedeg.sderevtisG.speavekAkeli 64 
                                   keI +etga I+++ ++d   + er ++  G + + ++kA+ +i
  gi|13541671|ref|NP_111359.1| 349 KEISKETGATIRIE-NPDLNsTYERFIEKYGrDDKYIAKAMSRI 391
                                   9***********87.55444799**9999997777688888776 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   5.1e-05     0.076       4      34 ..       4      34 ..       2      48 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 5.1e-05
                                  EEEE--SHHHHHHHHHHHHTTHHEEEEESSS CS
                 FAD_binding_3  4 VlIVGaGpaGlmlallLseaGvrvvlvekrs 34
                                  +++VGaG +Gl +a  Ls  G +v + +k +
  gi|13541671|ref|NP_111359.1|  4 IAVVGAGITGLFTAYYLSASGFDVEVFDKGD 34
                                  78**********************9999966 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.3   6.7e-05       0.1       2      39 ..       4      41 ..       3      54 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 6.7e-05
                                  EEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGG CS
                 FAD_binding_2  2 viViGsGlAGLaAAleaaeaGlkvavvekeqefggata 39
                                  + V+G+G+ GL  A+ ++  G +v v +k++  +g++ 
  gi|13541671|ref|NP_111359.1|  4 IAVVGAGITGLFTAYYLSASGFDVEVFDKGDIASGTSG 41
                                  67****************************99888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       586  (0.0326845); expected 358.6 (0.02)
Passed bias filter:                      529  (0.0295053); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.66u 0.30s 00:00:00.96 Elapsed: 00:00:00.48
# Mc/sec: 2578.50
//
Query:       gi|13541672|ref|NP_111360.1|  [L=196]
Description: glycerophosphoryl diester phosphodiesterase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00012   21.9   0.0      0.021   14.6   0.0    2.1  1  GDPD      Glycerophosphoryl diester phosphodiesterase family
  ------ inclusion threshold ------
       0.12   12.8   0.0       0.44   11.1   0.0    1.8  2  GDPD_2    Glycerophosphoryl diester phosphodiesterase family


Domain annotation for each model (and alignments):
>> GDPD  Glycerophosphoryl diester phosphodiesterase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   2.3e-06     0.021      89     255 ..      44     186 ..      19     190 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.3e-06
                                   C.....B...BHHHHHHHHHHCCSEEEEEEECCCCCCCHHHHHHTCHHHCCCCCSCHHTT..STTCSCEEEESTHHHHHHH CS
                          GDPD  89 e.....fpfptleevlkkpqnvglnieikipmlseakeeeelqivkeilksvdeilkkvlkkadkrkvifssfnpdilkll 164
                                          p+p l+evl++  +++  ieik++++++  ++  +      + +   +l       d   vi  sf+ +++ +l
  gi|13541672|ref|NP_111360.1|  44 VklisgGPIPSLSEVLERYSSMNYFIEIKVEHFDNKAARLVD---LVANNIYASRL------IDRSIVI--SFSGEAIDYL 113
                                   144555788999999988888888888888888887777773...22222222222......1344455..8888888888 PP

                                   HHTCTCTEEEEEEHHHHHHC-E.EECHCCCCCCCTCCCCHHCCCHCCCEB.CHHHHHHHTT-EEEEBSB-THSHHHHHHHH CS
                          GDPD 165 rekqpklpllflteggteaeadssleraakfakadallgevsavaeglgdpdlVkraksrglvvhvytvnnedeeemkrll 245
                                   +e  p+++  + ++++   e++          k   ll+  +++++      + + ++     v ++tv++   e    l+
  gi|13541672|ref|NP_111360.1| 114 TEHYPDIRSGLDFDDPGLLEDA--------QSKYGVLLPHYFLISQD-----FCRNLR---KPVIPWTVDDV--ELANKLK 176
                                   8888888888888877777776........44556667777777776.....444444...57999****99..8888999 PP

                                   CCC-SEEEES CS
                          GDPD 246 eagvdgvitD 255
                                   ++g++g+it+
  gi|13541672|ref|NP_111360.1| 177 KLGCKGIITN 186
                                   *******997 PP

>> GDPD_2  Glycerophosphoryl diester phosphodiesterase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       0.7   6.3e+03      13      23 ..      65      75 ..      63      75 .. 0.85
   2 ?   11.1   0.0   4.9e-05      0.44       5      28 ..     164     187 ..     161     188 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.7
                        GDPD_2 13 wrelvgaGVdg 23
                                  ++++++ +V +
  gi|13541672|ref|NP_111360.1| 65 MNYFIEIKVEH 75
                                  89***999975 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 4.9e-05
                        GDPD_2   5 WttddeavwrelvgaGVdgInTDd 28 
                                   Wt+dd  + + l ++G  gI+T++
  gi|13541672|ref|NP_111360.1| 164 WTVDDVELANKLKKLGCKGIITNV 187
                                   **********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       381  (0.0212505); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.32s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1225.39
//
Query:       gi|13541673|ref|NP_111361.1|  [L=434]
Description: transposase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-34  119.1   0.1    1.2e-34  119.1   0.1    1.6  2  OrfB_IS605      Probable transposase
    5.3e-17   61.5   0.0    1.1e-16   60.5   0.0    1.6  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
  ------ inclusion threshold ------
      0.011   16.2   0.0      0.026   14.9   0.0    1.6  1  RuvX            Holliday junction resolvase


Domain annotation for each model (and alignments):
>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.2       2.2   1.3e+04      71      89 ..      47      65 ..      37      75 .. 0.56
   2 !  119.1   0.1   2.1e-38   1.2e-34       1     119 [.     170     285 ..     170     286 .. 0.98

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 2.2
                    OrfB_IS605 71 kkasrklarlhrkrsrrrk 89
                                     s+ ++ +++k ++++k
  gi|13541673|ref|NP_111361.1| 47 VDFSKTEKEVYEKYKQILK 65
                                  4445555555555555554 PP

  == domain 2  score: 119.1 bits;  conditional E-value: 2.1e-38
                    OrfB_IS605   1 sipvevevelpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrklarlh 81 
                                   +ipvev++   k++ + +a+iDlGi nLatv++edg+w+++kg ++ s+y+y++k+i   q++l+++k  + +sr++++lh
  gi|13541673|ref|NP_111361.1| 170 YIPVEVQN-DVKAEDKLKASIDLGIINLATVYVEDGSWYIFKGGSVLSQYEYYSKRISVAQKTLARHK--QGRSREMKLLH 247
                                   589***98.89999******************************************************..*********** PP

                    OrfB_IS605  82 rkrsrrrkhllhklathliktlkevgvetLnvgnmkdi 119
                                   +kr+r++kh+l++++++++++ k++gv+++ +g++k+i
  gi|13541673|ref|NP_111361.1| 248 EKRKRFLKHALNSMVRKIMEEFKNKGVGEIAIGYPKEI 285
                                   ***********************************987 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.5   0.0   1.8e-20   1.1e-16       2      68 ..     301     368 ..     300     369 .. 0.95

  Alignments for each domain:
  == domain 1  score: 60.5 bits;  conditional E-value: 1.8e-20
                OrfB_Zn_ribbon   2 rklkeqleykakeyGikveevnpayTSktCseCgsknke.alsgrtfkCpnCgfeadrDvnAaiNilk 68 
                                   + ++++ e   +e G+kv++v++a+TSktCs Cg+ +++ + ++ +++C + g ++++D+n+aiNil+
  gi|13541673|ref|NP_111361.1| 301 GYIIRRFEGVGEELGVKVVKVDEAWTSKTCSLCGEAHDDgRIKRGLYRCLRIGKVINADLNGAINILH 368
                                   66788899999****************************9**************************96 PP

>> RuvX  Holliday junction resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   4.3e-06     0.026      30     103 ..     252     331 ..     223     344 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 4.3e-06
                                   EEE---HHHHHHHHHHHHHHTT--EEEEE------SSS---SS.TTHHHHHHHHHT........T-EEEEE--S----XXX CS
                          RuvX  30 tierkskekdleelkelvkeeeveeiVvGlPlnldgsegesak.kvrkfaeeLakrl......kklpvelvDErlttveae 103
                                    + +++ ++ ++++ e +k++ v ei +G+P+++++++g++   ++ ++   + +r+       +++v+ vDE  t+++ +
  gi|13541673|ref|NP_111361.1| 252 RFLKHALNSMVRKIMEEFKNKGVGEIAIGYPKEISKDHGNKLTvNFWNYGYII-RRFegvgeeLGVKVVKVDEAWTSKTCS 331
                                   33444448999**********************97776655441444443333.233233444488***********9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (434 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       924  (0.0515366); expected 358.6 (0.02)
Passed bias filter:                      528  (0.0294495); 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: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.46
# Mc/sec: 2853.34
//
Query:       gi|13541674|ref|NP_111362.1|  [L=134]
Description: hypothetical protein TVN0843 [Thermoplasma volcanium GSS1]
Scores for complete 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  134.2   0.3    2.6e-39  134.1   0.3    1.0  1  Y1_Tnp    Transposase IS200 like
  ------ inclusion threshold ------
       0.04   14.0   0.6         20    5.3   0.0    3.0  3  HTH_3     Helix-turn-helix


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 !  134.1   0.3   2.9e-43   2.6e-39       2     121 .]      11     126 ..      10     126 .. 0.96

  Alignments for each domain:
  == domain 1  score: 134.1 bits;  conditional E-value: 2.9e-43
                        Y1_Tnp   2 snlkyhivlvtkyRrkvltgeveerlkeiikeiaekkevkilelelmpDHvHllvelppklsiskivkalkgassrlinke 82 
                                   + ++yh  +++kyRr +lt+ev+e  ke++k+ia++ +++i++le+mpDH+Hl+v++pp++s+s + + +kg+s+rli k+
  gi|13541674|ref|NP_111362.1|  11 YLCNYHYLWIPKYRRAILTNEVAEYTKEVLKSIAKELGCEIIALEVMPDHIHLFVNCPPRYSPSYLTNYFKGKSARLILKK 91 
                                   78*****************************************************************************99 PP

                        Y1_Tnp  83 fpelkkkklkkeslWqrgYfvstvgeasletvkrYIenq 121
                                    pel++   k  +lW+r+Yfvst+g++s et+k+YIe+q
  gi|13541674|ref|NP_111362.1|  92 SPELRRY--K--KLWSRSYFVSTAGNVSSETIKKYIEEQ 126
                                   9998843..4..5************************98 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0    0.0024        21      37      52 ..      36      51 ..      28      54 .. 0.87
   2 ?    5.3   0.0    0.0023        20      22      34 ..      72      84 ..      70     101 .. 0.87
   3 ?    0.4   0.0     0.076   6.8e+02       8      30 ..     100     123 ..      94     126 .. 0.61

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0024
                                  BHHHHHHHHHHHTSEH CS
                         HTH_3 37 sletlkklakaLgvsl 52
                                  + e+lk +ak Lg+++
  gi|13541674|ref|NP_111362.1| 36 TKEVLKSIAKELGCEI 51
                                  789***********87 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0023
                                  SHHHHHHHHTTSS CS
                         HTH_3 22 srstisriEnGer 34
                                  s+s+++++++G++
  gi|13541674|ref|NP_111362.1| 72 SPSYLTNYFKGKS 84
                                  9**********76 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.076
                                   TTHHH.HHHHHHHTSSHHHHHHHH CS
                         HTH_3   8 lglsq.eeLAeklGvsrstisriE 30 
                                   + +s+   ++ + +vs  ti +++
  gi|13541674|ref|NP_111362.1| 100 KLWSRsYFVSTAGNVSSETIKKYI 123
                                   555553444555568888888885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       568  (0.0316805); 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: 0.34u 0.24s 00:00:00.58 Elapsed: 00:00:00.40
# Mc/sec: 1013.19
//
Query:       gi|13541675|ref|NP_111363.1|  [L=66]
Description: hypothetical protein TVN0844 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       203  (0.0113224); expected 358.6 (0.02)
Passed bias filter:                      187  (0.01043); 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 0.30s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 421.93
//
Query:       gi|13541676|ref|NP_111364.1|  [L=178]
Description: nicotinamide-nucleotide adenylyltransferase [Thermoplasma volcanium GSS1]
Scores for complete 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-13   49.5   0.1    8.2e-13   48.8   0.1    1.4  1  CTP_transf_like  Cytidylyltransferase-like
  ------ inclusion threshold ------
        0.1   12.3   0.0         14    5.3   0.0    2.4  3  Citrate_ly_lig   Citrate lyase ligase C-terminal domain
       0.11   12.4   0.1       0.15   11.9   0.1    1.3  1  FAD_syn          FAD synthetase


Domain annotation for each model (and alignments):
>> CTP_transf_like  Cytidylyltransferase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.8   0.1   1.4e-16   8.2e-13       2     142 ..      11     138 ..      10     139 .. 0.90

  Alignments for each domain:
  == domain 1  score: 48.8 bits;  conditional E-value: 1.4e-16
                                   EEE--TT--HHHHHHHHHHHHHSSESEEEEEESSTHCSST-SCSSTHHHHHHHHHHHTTCTTEEEEEEESEHHHHHHHTTT CS
               CTP_transf_like   2 agGtFDpiHlGHlrlleqakklleedlivgvpsdeppkkkkkplasaeeRlemlelakevdevisvdpweltrevlkklkp 82 
                                   + G+F+p+HlGHl+++++++++ +  +i+g+ s++ ++ +  ++++a eR  m+ +  e +    v  ++l++  +++ ++
  gi|13541676|ref|NP_111364.1|  11 LIGRFQPFHLGHLEIVKRILRENDS-IIIGIGSAQYSHTT-VNPFTAGERHLMISRTLEREH---VYNYYLVP--IEDVNA 84 
                                   68***********************.************99.**************9955555...77888887..667777 PP

                                   TEEEEEEEHHHHHHHHCHHHHHHHHHHHHHEEEEEEHTTCEEEEEEECCTTTCSHHHHHH CS
               CTP_transf_like  83 dklylvigadvledfsewkeleeilgnvklvvvsrpekqanvllkaekrtngiSstkire 142
                                   +   +v   ++l+      +++ +++n++lv + ++ek ++v  +++ ++++  +tkire
  gi|13541676|ref|NP_111364.1|  85 N-SLWVSHVEALAP-----KFDVVYTNNPLVRRLFTEKHYEVRSLPMVNRSEWTGTKIRE 138
                                   5.588888888888.....89**************************************8 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 ?    4.6   0.0    0.0039        23       9      36 ..      16      43 ..       9      50 .. 0.83
   2 ?    5.3   0.0    0.0023        14       8      32 ..      50      74 ..      47      87 .. 0.81
   3 ?   -2.7   0.0      0.69   4.1e+03     127     160 ..     107     138 ..      97     150 .. 0.52

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.0039
                Citrate_ly_lig  9 nPftlGhryLvekaakendvvhlfvvke 36
                                   Pf lGh  +v++  +end +++ + + 
  gi|13541676|ref|NP_111364.1| 16 QPFHLGHLEIVKRILRENDSIIIGIGSA 43
                                  7*******************99877655 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0023
                Citrate_ly_lig  8 anPftlGhryLvekaakendvvhlf 32
                                   nPft G r+L+   + e ++v+ +
  gi|13541676|ref|NP_111364.1| 50 VNPFTAGERHLMISRTLEREHVYNY 74
                                  6**********98888888888754 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 0.69
                Citrate_ly_lig 127 qalkevlekaeievveierkekeeelisaskvrk 160
                                     +++ +++++ ev  ++ ++++e     +k+r+
  gi|13541676|ref|NP_111364.1| 107 PLVRRLFTEKHYEVRSLPMVNRSEW--TGTKIRE 138
                                   4555556666666665555544432..3445553 PP

>> FAD_syn  FAD synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   2.6e-05      0.15       3      35 ..       3      35 ..       1      77 [. 0.73

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.6e-05
                       FAD_syn  3 eedegavvtlGnFDGvHlGHqallkkaveaake 35
                                  +++e+ +  +G F  +HlGH +++k+++++ ++
  gi|13541676|ref|NP_111364.1|  3 STKEHRAFLIGRFQPFHLGHLEIVKRILRENDS 35
                                  567788999*****************9988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       302  (0.0168442); 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: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1250.32
//
Query:       gi|13541677|ref|NP_111365.1|  [L=629]
Description: 2-oxoacid--ferredoxin oxidoreductase, alpha subunit [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.2e-56  190.3   0.0    7.4e-56  189.5   0.0    1.4  1  POR_N            Pyruvate flavodoxin/ferredoxin oxidoreductas
    1.5e-37  129.4   0.2    3.9e-36  124.8   0.1    2.4  2  POR              Pyruvate ferredoxin/flavodoxin oxidoreductas
    1.4e-08   35.0   0.0      1e-07   32.2   0.0    2.4  2  PFOR_II          Pyruvate:ferredoxin oxidoreductase core doma
    4.6e-06   26.5   0.0    1.2e-05   25.2   0.0    1.7  1  Transketolase_C  Transketolase, C-terminal domain
    0.00028   20.5   0.0     0.0006   19.5   0.0    1.5  1  TPP_enzyme_N     Thiamine pyrophosphate enzyme, N-terminal TP


Domain annotation for each model (and alignments):
>> POR_N  Pyruvate flavodoxin/ferredoxin oxidoreductase, thiamine diP-bdg
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  189.5   0.0   2.1e-59   7.4e-56       3     230 ..     243     487 ..     241     488 .. 0.86

  Alignments for each domain:
  == domain 1  score: 189.5 bits;  conditional E-value: 2.1e-59
                                   HHHCTEEEEEE--BTTTCC...HHHHHC..HCCCCCTT....EE.EEEE-SSHHHHHHHHHHHHCTT-EEEEEEECCHHHH CS
                         POR_N   3 aiaagvdviaaYPITPsse...iaeela..ellakgev....gdvevvqmesEigaisaviGAaaaGaraaTaTSgqGllL 74 
                                   ++ +g++++++YPITP+s+    +ee++  ++l+++      g v++vq+e+E++ai+++iG a++Gar+aTaTSg+G++L
  gi|13541677|ref|NP_111365.1| 243 KLLGGLRFQTYYPITPASDestTLEEHQniKWLKNEAEslkkGGVVIVQTEDELSAINMAIGGALTGARSATATSGPGFSL 323
                                   678899************966644444311344444447888779************************************ PP

                                   CCCCHHHHHHTT--EEEEEEEEE-STTBEEEEE--TTCHHHH.....S---EEEE-SSHHHHHHHHHHHHHHHHHCTSEEE CS
                         POR_N  75 mienlglaageelPvvivvvaRalpstglsirtdqsDlmaar.....dtglivlasenvqeafdlalvAfnlAekvrvPvi 150
                                   m e l +a+++e+P+v++ + R++pstgl++r+ qsDl++a+     +++ iv++s++v e+  +a++A+n+A k+++Pvi
  gi|13541677|ref|NP_111365.1| 324 MAEGLSFAGMDEVPLVVTFYERGGPSTGLPTRNGQSDLLFALnaghgEYPRIVFSSGTVDECIYDAVKALNYAAKYQMPVI 404
                                   ********************************************************************************* PP

                                   EEEEHHHH.HEEEEEEC-SGG..GS-----SBXXXXXXXXSXXXBX...XT.XXTSSXXEEESBXBXTTSXBXXXXHHHHH CS
                         POR_N 151 vlfDgfllshevekvelpdee.delklikekleeyerkeyaldpek...pi.argtaanpdtglehrekgneaedaaekvv 226
                                   +l+D+ l+ ++ + +   d + ++++ ++  +e  + k+y+l++++   p+ ++g   +++tg+eh+e g+ +ed  + ++
  gi|13541677|ref|NP_111365.1| 405 HLIDKNLA-NTLDLISKIDLDkVKIEKVELAKEGDDVKRYDLNTQNgvsPYaVMGRNIFWMTGDEHDELGHVTED-SDIRD 483
                                   ********.**999999999966666666666666777787776542224414577889**************99.77777 PP

                                   HHHH CS
                         POR_N 227 eeve 230
                                   +++e
  gi|13541677|ref|NP_111365.1| 484 RMME 487
                                   7776 PP

>> POR  Pyruvate ferredoxin/flavodoxin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.8   0.1   1.1e-39   3.9e-36       2     176 ..      12     209 ..       9     210 .. 0.92
   2 ?    2.0   0.0     0.053   1.9e+02      70      88 ..     276     294 ..     261     306 .. 0.82

  Alignments for each domain:
  == domain 1  score: 124.8 bits;  conditional E-value: 1.1e-39
                                   TSTHHHHHHHHHHHHHHTT-EEEEEEEEESSSSSSCEEEEEEEESS.-SSS--TTSEEEEEESSHHHHHHHGGGEEEEEEE CS
                           POR   2 GqGvvtagkilakaaaraGyyvqanreygseirGghsyshvrisdepivpsievgeadllvaldaetlsehldglkpggii 82 
                                   G G+ ta+++ +ka+a +Gy v++ rey+s+i+G+hsy+h+r+ ++ + +s++ +++++ vald++t++ehld++ + +i+
  gi|13541677|ref|NP_111365.1|  12 GGGIDTAANLVGKAVATSGYGVLSVREYHSNIKGRHSYTHMRVKED-QPRSLK-YPVNIFVALDPDTIFEHLDDVSEASIV 90 
                                   99*******************************************9.889999.*************************** PP

                                   EEECTCGTT-CCHHHCTS-HHHHHHH......................T-EEEEE-HHHHHHHCCC....CCHHHHHHHHH CS
                           POR  83 iynseelkpdelkkakeeerelkerl......................gvrvygvdatkiakeiggn...eraaNtvmlGa 138
                                   iy++++ + d  + +  + ++ ++ +                      g+++++v++ +ia+++  n   +r+ Nt++ ++
  gi|13541677|ref|NP_111365.1|  91 IYDKTTEDYDLQAARMIMRDTSAKIRsilqengfettirgalkymqkrGAKLLPVPFADIATQAVPNgtpSRYFNTIGAAI 171
                                   ***976555555544444444444448***********************************99999999*********** PP

                                   HHHHHTS-HHHHHHHHHCCS-CH.HHHHHHHHHHHHHH CS
                           POR 139 laallglplealeeaikkrfpkkkeviekNlkafragy 176
                                   ++a++g++++  ++ i+  f++k++v+e+N+k++++ y
  gi|13541677|ref|NP_111365.1| 172 ALAIIGIDEKFAKDSISYIFRGKQQVVEENVKVVEQSY 209
                                   **********************************9987 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.053
                                   HHHGGGEEEEEEEEEECTC CS
                           POR  70 sehldglkpggiiiynsee 88 
                                   ++ ++ lk+gg++i+++e+
  gi|13541677|ref|NP_111365.1| 276 KNEAESLKKGGVVIVQTED 294
                                   466788*********9965 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 ?   -1.1   0.0      0.64   2.3e+03      26      59 ..     242     276 ..     237     303 .. 0.71
   2 !   32.2   0.0   2.9e-11     1e-07       1      97 [.     514     603 ..     514     608 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.64
                                   T--EEEEEES--BS-.-HHHHHHHSTT-SEEEEEE CS
                       PFOR_II  26 gikvGllrlrtlrPF.Peeelkellkkvkkvvvld 59 
                                   g  +G lr +t++P  P+ + ++ l++ +++  l 
  gi|13541677|ref|NP_111365.1| 242 GKLLGGLRFQTYYPItPASDESTTLEEHQNIKWLK 276
                                   667899********548877777777777665555 PP

  == domain 2  score: 32.2 bits;  conditional E-value: 2.9e-11
                                   -SEEEEE-STHHHHHHHHHHHHHHTT--EEEEEES--BS--HHHHHHHSTT-SEEEEEE-S--TT-G-HHHHHHHHHTGGG CS
                       PFOR_II   1 AevvivamGsvagtaksavdelReegikvGllrlrtlrPFPeeelkellkkvkkvvvldrnisfgseGqlveevkaalkks 81 
                                   A++ +v+ Gs  g + ++++ l+++ i + ll l+++ PFP+e +k++l+k++ v++++ n++     q ++ +k  +   
  gi|13541677|ref|NP_111365.1| 514 ADITFVTWGSQKGPILDVIEDLKQDDITANLLYLKMFSPFPTEFVKSILSKAHLVIDVESNFT----AQAAQMIKLYT--G 588
                                   89***********************************************99999999999984....33333333332..1 PP

                                   TSEEEEEE--GGG--- CS
                       PFOR_II  82 kvkvvnfvaglgGrdi 97 
                                    +++ n + + +Gr +
  gi|13541677|ref|NP_111365.1| 589 -IEIENKILKYNGRHM 603
                                   .345555555555555 PP

>> Transketolase_C  Transketolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.0   3.3e-09   1.2e-05       7      70 ..     511     574 ..     504     603 .. 0.91

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 3.3e-09
                                   ETTSSEEEEEETTHHHHHHHHHHHHHTTTTCEEEEE-SEEESHHHHHHHHHHHHHSEEEEEEEE CS
               Transketolase_C   7 regkdvtlvayGsmveealeAaeeLekegisaeVvdlrtvkplDketilesvkktgrlvvveea 70 
                                    e  d+t+v++Gs+    l+++e+L+++ i+a ++ l  ++p+ +e +++++ k + ++ ve +
  gi|13541677|ref|NP_111365.1| 511 PEDADITFVTWGSQKGPILDVIEDLKQDDITANLLYLKMFSPFPTEFVKSILSKAHLVIDVESN 574
                                   4589*****************************************************9999876 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 !   19.5   0.0   1.7e-07    0.0006      33     147 ..     281     393 ..     269     412 .. 0.74

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.7e-07
                                   CHHCT.TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHHHHCHHHHHHHHHHT--EEEEEEE--CCCHHS..TC-- CS
                  TPP_enzyme_N  33 alseeqgirvvlarhEqgaafaAdgyaratgkpgvvlvtsgpGatnaltalaeAkvdriPllvlsgdrptslrgqgvlqqe 113
                                   +l++  g+ +v++ +E +a+++A g a     +  + +tsgpG+  +  +l  A  d +Pl+v   +r+  ++g ++ +++
  gi|13541677|ref|NP_111365.1| 281 SLKKG-GVVIVQTEDELSAINMAIGGALTGA-R-SATATSGPGFSLMAEGLSFAGMDEVPLVVTFYERGGPSTGLPTRNGQ 358
                                   44444.7999***************988754.4.455679***********************999998888884444433 PP

                                   T-.CCHHHCCCSSEEEE-SSGGGHHHHHHHHHHHH CS
                  TPP_enzyme_N 114 ld.qlalfrpvtkyaervtspeelpealrrAirta 147
                                    d   al + + +y + v s+ ++ e + +A++++
  gi|13541677|ref|NP_111365.1| 359 SDlLFALNAGHGEYPRIVFSSGTVDECIYDAVKAL 393
                                   43244555566666666666666666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (629 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       627  (0.0349713); expected 358.6 (0.02)
Passed bias filter:                      501  (0.0279436); 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: 0.66u 0.29s 00:00:00.95 Elapsed: 00:00:00.48
# Mc/sec: 3955.13
//
Query:       gi|13541678|ref|NP_111366.1|  [L=307]
Description: 2-oxoglutarate ferredoxin oxidoreductase subunit beta [Thermoplasma volcanium GSS1]
Scores for complete 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-27   94.3   0.3    8.8e-27   93.8   0.3    1.2  1  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b
    1.2e-26   92.6   1.5    2.3e-26   91.7   1.5    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 !   93.8   0.3   9.8e-31   8.8e-27       2     153 .]      46     193 ..      35     193 .. 0.92

  Alignments for each domain:
  == domain 1  score: 93.8 bits;  conditional E-value: 9.8e-31
                                   SSHHHHHHHHHHTTSSSSEEEC.ETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHT.GGGHHHHHHTT-SEEEEEE CS
                  TPP_enzyme_C   2 iGcltlwaarllkvkrprsylt.sgglgtmGyglpaAiGaklakpdrevvaivGDGgflmi.lqelatavrrnlpitvvvl 80 
                                   iGc+             ++y++ +g ++ +G+++p+A+G+kl +p+ +v+++ GDG+++ i   +l+   rrn  itv+++
  gi|13541678|ref|NP_111366.1|  46 IGCSGK----------TPHYVNaAGAHTLHGRAIPVAVGVKLTNPHLKVIVTGGDGDLMSIgAGHLVAEGRRNSGITVLMY 116
                                   566665..........789999899************************************99****************** PP

                                   E-SBCCCHHHH...HHHHTCCTTTTSBB.BS----HHHHHHHTTSE.EEEESSH.HHHHHHHHHHHHCSSSEEEEEE CS
                  TPP_enzyme_C  81 nNegygmtggq...qepfggkrksgpagkdlkpvdfaklaealGak.garvekadveeleealkealekkgpaliev 153
                                   +N++yg+t+gq   + + g ++ks   +++ + +++ +la + G + +ar  + ++++l++++k+a++  g+++i++
  gi|13541678|ref|NP_111366.1| 117 DNAVYGLTKGQaapTLKLGVQTKSLARPNIYDAINPIMLAISSGYSfVARGFSFEIAHLKNIIKQAIMFPGSSFIDI 193
                                   ***********9966666777777777779****************999999***********************97 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 !   91.7   1.5   2.5e-30   2.3e-26       1      64 [.     197     272 ..     197     274 .. 0.98

  Alignments for each domain:
  == domain 1  score: 91.7 bits;  conditional E-value: 2.5e-30
                                   XTTTXSSSXSXXXXX-EEEGGGS.T---EE..........HHHHHHHHT-----EEEEEEEE.TTS--HHHHHHT. CS
                    PFO_beta_C   1 CvtFNkvnTfdwYkervykleed.gyDpsd..........lekAlekalewgdkiplGifYk.eekptyeerleel 64 
                                   C+t+N++nT+dwYk+rvykl++d ++Dp            ++kA+ek++ewgdkip+G+fY  +++p+++erl+++
  gi|13541678|ref|NP_111366.1| 197 CPTYNNINTMDWYKKRVYKLDDDkSWDPVItendpkaeekYNKAIEKSFEWGDKIPIGVFYVnKKVPPFTERLKQY 272
                                   **********************99*****999*****************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       520  (0.0290033); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.49
# Mc/sec: 1896.53
//
Query:       gi|13541679|ref|NP_111367.1|  [L=386]
Description: aspartate aminotransferase [Thermoplasma volcanium GSS1]
Scores for complete 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-58  197.6   0.0    3.9e-58  197.4   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
    5.5e-07   28.8   0.0      9e-07   28.1   0.0    1.3  1  Alliinase_C      Allinase
    1.7e-06   26.8   0.0    2.6e-06   26.2   0.0    1.3  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
      0.002   18.0   0.0      0.003   17.4   0.0    1.2  1  DUF410           Protein of unknown function (DUF410)


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 !  197.4   0.0   8.6e-62   3.9e-58       2     360 ..      35     379 ..      34     382 .. 0.91

  Alignments for each domain:
  == domain 1  score: 197.4 bits;  conditional E-value: 8.6e-62
                                   EEEESSSSSTTSTTSSHHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHH CS
                 Aminotran_1_2   2 dvinLgsneylgdsgkptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGagalie 82 
                                   +v  L s+++++      +p+v++a k+  +  ++ + y++++g pel++a+a+ l r++k+k  +  +v+v++G   ++ 
  gi|13541679|ref|NP_111367.1|  35 KVYRLESGDPSFS----LPPHVKEAIKQ--AIENNKTHYTDSTGIPELRKAIAEKLVRKNKIKDATPENVIVSNGGMNALY 109
                                   67889********....*********99..77777788*******************99999988888************* PP

                                   HHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT-- CS
                 Aminotran_1_2  83 alifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilvesphNPtGt 163
                                   + ++ l l pgde+++pdp ++++ +i++l+ g  +r p+      ++ +e++++ ++++     k+k ++v+sphNPtG 
  gi|13541679|ref|NP_111367.1| 110 VTFRSL-LSPGDEVIIPDPMWTEIAEIIKLAEGVPIRLPV------ENYIEEMQK-YEDDD----KVKAVFVNSPHNPTGL 178
                                   ******.9*******************************4......467777666.55433....89************** PP

                                   B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEEEEE.EHHHHHHH CS
                 Aminotran_1_2 164 vatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKafGlaGeRvGyilg.naavvsql 243
                                   v+t++++  ++++a+++++++++DeaY++  f+  +    ++  ++++n++ + s+sK +++ G+R+Gy+   ++ + + +
  gi|13541679|ref|NP_111367.1| 179 VFTPKQIDGIISFAESKGIFIVSDEAYEDVIFDGRE---HVSPGSKYDNTISLFSMSKTYAMSGLRIGYAHTnSEILYDRM 256
                                   *********************************653...3889999999***********************556788*** PP

                                   HHHHHHHTS..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS.TEEEECCSCSSEEEEEETHH..CHHH CS
                 Aminotran_1_2 244 rklsrpfls..ssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLael.glkvlasqsgmflltdlsae..take 319
                                   +kl r  +    s++q+ ++aal  +++   ++ +mr+++qkrr+ ++++  +  +l+ +++ ++++l+  ++++  + k+
  gi|13541679|ref|NP_111367.1| 257 KKLLRCTINgvNSATQYGAVAALTGPQE---FVGQMRSEYQKRRDIIFNAVSKSrYLEPVKPGGTFYLWAKIKEYpkEVKD 334
                                   *****999899****************7...9*******************999********************9886666 PP

                                   HHHH...HHHTCTEEEEEGGGGTS..TTEEEEECTTS-HHHHHHHH CS
                 Aminotran_1_2 320 lskk...Lleevgvyvtpgtsftv..pgrlRitvAglteeeleelv 360
                                    +++   Ll++ gv  +pg  f+    g +R+ + + ++e ++e+ 
  gi|13541679|ref|NP_111367.1| 335 SWDMtyyLLDKTGVGSSPGPVFGPagDGYIRFAF-SADTEHVREAS 379
                                   6666888****************99999******.88888888875 PP

>> Alliinase_C  Allinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.0     2e-10     9e-07     140     240 ..     166     279 ..     148     309 .. 0.69

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 2e-10
                                   EEEEESS-TTT------.....--..-TT-EE.EEEE-TT-STTT.....S---S-B--SEEEEEHHHHHS-GGG-EEEEE CS
                   Alliinase_C 140 ielvtsPnnPdgllrea.....vv..kgseak.viyDlayYWPhy.....tpitskadedimLftlskltGhaGsrlGWal 207
                                     +v sP nP gl+  +     ++  ++s+++ ++ D ay    +         sk d+ i+Lf++sk+   +G r+G+a 
  gi|13541679|ref|NP_111367.1| 166 AVFVNSPHNPTGLVFTPkqidgIIsfAESKGIfIVSDEAYEDVIFdgrehVSPGSKYDNTISLFSMSKTYAMSGLRIGYAH 246
                                   347888888888774322222255554444442455777754333111003345789************************ PP

                                   ES-HHHHHHHHHHHHHHHSS--HHHHHHHHHHH CS
                   Alliinase_C 208 vkdkevakklveyieknsiGvskesqlrvlkil 240
                                      + +++++ + ++ +  Gv   +q  ++  l
  gi|13541679|ref|NP_111367.1| 247 TNSEILYDRMKKLLRCTINGVNSATQYGAVAAL 279
                                   **************************8877766 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 !   26.2   0.0   5.8e-10   2.6e-06      67     175 ..      93     204 ..      52     210 .. 0.81

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 5.8e-10
                                   -..SEEEEESSHHHHHHHHHHTTS-TTEEEEEESTSSHHHHHHHHHTHHHTTCEEEEESTTSHHHHHHHCCT.TEEEEEEE CS
               Cys_Met_Meta_PP  67 g..eaalavssGmaAiaaailallkaGdeivvsddlYggtqrllkkvlkklgievkfvdtsdleelekaike.ntklvylE 144
                                   +  e++++ + Gm A+ +++++ll+ Gde+++ d ++    +++k      g+ ++    + +ee++k  ++ ++k+v++ 
  gi|13541679|ref|NP_111367.1|  93 AtpENVIVSNGGMNALYVTFRSLLSPGDEVIIPDPMWTEIAEIIK---LAEGVPIRLPVENYIEEMQKYEDDdKVKAVFVN 170
                                   44478899999**************************88777665...3456777776666788888877655******** PP

                                   SS-TTTT---...-HHHHHHHHHHTT-EEEEEGT CS
               Cys_Met_Meta_PP 145 tptnpllkvv...DiekiaklakkagvlvvvDnt 175
                                   +p np+  v     i  i+++a ++g+ +v D +
  gi|13541679|ref|NP_111367.1| 171 SPHNPTGLVFtpkQIDGIISFAESKGIFIVSDEA 204
                                   *****9777533379999**********999976 PP

>> DUF410  Protein of unknown function (DUF410)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   6.8e-07     0.003      63     115 ..      42     101 ..      11     115 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 6.8e-07
                        DUF410  63 eep......erkkfikaaikwSakkgekkaGdpeLhhllaklllkegeleeAer.hlllg 115
                                    +p        k+ ik+ai+  +++ ++++G peL++++a++l++++++++A + + +++
  gi|13541679|ref|NP_111367.1|  42 GDPsfslppHVKEAIKQAIENNKTHYTDSTGIPELRKAIAEKLVRKNKIKDATPeNVIVS 101
                                   3445666668999**************************************875144444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (386 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       602  (0.0335769); expected 358.6 (0.02)
Passed bias filter:                      556  (0.0310112); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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 0.32s 00:00:00.94 Elapsed: 00:00:00.51
# Mc/sec: 2276.91
//
Query:       gi|13541680|ref|NP_111368.1|  [L=277]
Description: site-specific DNA methylase [Thermoplasma volcanium GSS1]
Scores for 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-59  199.6   0.3      8e-59  199.4   0.3    1.0  1  MethyltransfD12  D12 class N6 adenine-specific DNA methyltran
  ------ inclusion threshold ------
      0.035   13.9   0.0       0.06   13.2   0.0    1.3  1  CdvA             CdvA-like coiled-coil domain


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 !  199.4   0.3   8.9e-63     8e-59       1     260 []      14     259 ..      14     259 .. 0.96

  Alignments for each domain:
  == domain 1  score: 199.4 bits;  conditional E-value: 8.9e-63
                                   STTTSCTTHHHHHCCS-..--SEEEETT-TTSCCHHCS.....SSCEEEEES-HHHHHHHHHHCCHSHHHHHHHHH.TCTT CS
               MethyltransfD12   1 YiGgKrkllpeIkelipkdkgktfvepFaGggaVffeakk..qgkkvlinDinedlinlykaliknnveelikelekllek 79 
                                   ++GgKr+l+p I +++p+ + kt++epF Gg+aV +++ +  ++ k++++D+n dl+ lyk +++ ++ eli+ +++l ++
  gi|13541680|ref|NP_111368.1|  14 WAGGKRQLIPYIMRYVPE-RFKTYYEPFLGGAAVLIHLYSkgRISKAVVSDVNRDLYMLYKEIKE-RPIELISVMRSLNFQ 92 
                                   9****************9.779*************9998888*******************5555.7*********98888 PP

                                   GGC.TSHHHHHHHHHHHH...HHH-HHHHHHHHHHHHCCBGGG---B-TTS-B---B-S-SS-....HHHHHHHHHHHHHC CS
               MethyltransfD12  80 eelenereyfyelreefnkkidaireaeeaidflylnrllfsglervnkkgnfnvpygaykkpkkvaekelklrseklkna 160
                                       n+re +y+ r+ fn   ++ +++ ++++++yln+++++gl+r n+ g fnvp+g+ ++  + + +++ ++s++l + 
  gi|13541680|ref|NP_111368.1|  93 ----NKREDYYRARDLFN---ETSDYKLRSALLIYLNKHGYNGLYRLNSLGLFNVPFGRHRNTSFPSDQDILSLSNMLSSC 166
                                   ....89************...999***************************************999999************ PP

                                   CEEEC-CHHHHTT--TTE.EEEE--S-T.S...TS--GGGG.CS-HHHHHHHHHHHHHH.HHTT-EEEEEEESEESHHHHH CS
               MethyltransfD12 161 kiecgdfdavllkakieddivYlDPPYnprqytanytlyetlafsdedevrlaevlkslsskfgvkvllsnsfkdtklfre 241
                                   +i+++df+++ + a +++d+vY+DPPY p+++t+n+t+y++ +f+ +d+vrl++v+ +l s +gv v+ +ns  dt+ +r+
  gi|13541680|ref|NP_111368.1| 167 TILNEDFEKAVAGA-ESGDFVYFDPPYVPLSKTSNFTSYTESGFTHKDQVRLKDVFIEL-SNRGVFVMETNS--DTENVRD 243
                                   *************9.8888****************************************.6***********..******* PP

                                   HCTT...SEEEEECCCCHH CS
               MethyltransfD12 242 lyksYnnesileveelrai 260
                                   lyk    ++i+ v ++r+i
  gi|13541680|ref|NP_111368.1| 244 LYKA---FEIIGVPARRNI 259
                                   ****...***999998876 PP

>> CdvA  CdvA-like coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   6.7e-06      0.06       5      46 ..      46      87 ..      44      89 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.7e-06
                          CdvA  5 ALeeLvsegdipkstyeeikekleealkklkekakelkeklk 46
                                  +L  L+s+g+i+k++++++++ l   +k++ke+  el++ ++
  gi|13541680|ref|NP_111368.1| 46 VLIHLYSKGRISKAVVSDVNRDLYMLYKEIKERPIELISVMR 87
                                  6999*****************************999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1784.87
//
Query:       gi|13541681|ref|NP_111369.1|  [L=223]
Description: metal-dependent hydrolase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.9e-28   97.6   0.0    8.7e-28   97.3   0.0    1.1  1  Lactamase_B_3  Beta-lactamase superfamily domain
    1.8e-24   86.4   0.0    2.5e-24   85.9   0.0    1.2  1  Lactamase_B_2  Beta-lactamase superfamily domain
    1.2e-12   48.3   0.7    3.6e-12   46.7   0.7    1.7  1  Lactamase_B    Metallo-beta-lactamase superfamily
  ------ inclusion threshold ------
       0.13   12.5   0.0       0.23   11.7   0.0    1.4  1  DUF1884        Domain of unknown function (DUF1884)


Domain annotation for each model (and alignments):
>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.3   0.0   1.9e-31   8.7e-28       1     163 []       4     187 ..       4     187 .. 0.86

  Alignments for each domain:
  == domain 1  score: 97.3 bits;  conditional E-value: 1.9e-31
                 Lactamase_B_3   1 eltwlghnsflletagarilvDPfka...nlgyeppaeeaDlvlisqaledHahletlkqlaenvkvlee........... 67 
                                   ++ w+gh++f +e++ +++l+DPf      ++++++  ++D++l+++++ dHa+ +   +  + ++vl+            
  gi|13541681|ref|NP_111369.1|   4 KIIWHGHACFSIEGK-KNVLIDPFLTgnpMAKVKAEDLNPDIILVTHGHYDHAADAVSISKRTGAPVLSVfelseifkesg 83 
                                   588*********975.89******6544578888888***************99887666555555555566666666666 PP

                 Lactamase_B_3  68 ........geslevggleiravatshdav.ggsergenngflleqdgltiyhlGhlahelsseelkelgrvDvvltPvggp 139
                                           g+++e++g++i+a+ + h ++  g+  g+ +g++++  g +iyh G++++  ++e +    r+++ l+P+gg+
  gi|13541681|ref|NP_111369.1|  84 intidinpGGTVEFEGVSIKATIATHSSSyDGRYAGNPVGYVIDI-GRKIYHAGDTGYFKDMELIGSVDRPEISLLPIGGH 163
                                   666666669*************999987747999999******77.9***********99999999999************ PP

                 Lactamase_B_3 140 ltlgqeealelakrLkpklvlPmh 163
                                   +t++ + a+e++k+Lk+ + +Pmh
  gi|13541681|ref|NP_111369.1| 164 YTMDVDGAVEALKMLKSPIAIPMH 187
                                   ***********************9 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.9   0.0   5.7e-28   2.5e-24       2     201 .]      20     188 ..      19     188 .. 0.85

  Alignments for each domain:
  == domain 1  score: 85.9 bits;  conditional E-value: 5.7e-28
                                   EEEES--TTHHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHHHCHTT CS
                 Lactamase_B_2   2 riLiDagpdlrqqalralqPvelrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfvylaleee 82 
                                   ++LiD+++   +  ++   +v++ d     d +l+th+HyDH a++ ++ ++++        + vl+v e + ++    e 
  gi|13541681|ref|NP_111369.1|  20 NVLIDPFLT--G--NPMA-KVKAEDL--NPDIILVTHGHYDHAADAVSISKRTG--------APVLSVFELSEIFK---ES 82 
                                   89****999..3..4554.3334444..77*********************544........34555555554433...33 PP

                                   TTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S---.HHHHHHHCT-SEEEE CS
                 Lactamase_B_2  83 pavnvheldwgesfelgdggleitatparhksgrrldrnagdtlGlriegggkrvyyigDtgyip.eeigerlggadllll 162
                                    ++n+ ++++g+++e++  g++i+at a h+s   ++r ag  +G++i+  g+++y++gDtgy++  e+   ++ +++ ll
  gi|13541681|ref|NP_111369.1|  83 -GINTIDINPGGTVEFE--GVSIKATIATHSSSY-DGRYAGNPVGYVID-IGRKIYHAGDTGYFKdMELIGSVDRPEISLL 158
                                   .67799**********8..899************.9*************.8**************544667********** PP

                                   E-S-SSTTHHHHHHT---STSHHHHCTTSSSSEEEEESB CS
                 Lactamase_B_2 163 ditayeddemirhmgHltpeeaveaaadlgakrlvliHi 201
                                   +i+         +++++++++avea+++l+  +++++H+
  gi|13541681|ref|NP_111369.1| 159 PIG---------GHYTMDVDGAVEALKMLKSPIAIPMHY 188
                                   ***.........99************************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 !   46.7   0.7     8e-16   3.6e-12      14     183 ..      17     179 ..       7     187 .. 0.83

  Alignments for each domain:
  == domain 1  score: 46.7 bits;  conditional E-value: 8e-16
                                   TTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCHCHHHHHHHHHC CS
                   Lactamase_B  14 dggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalfmeeaddaasrk 94 
                                   +++++LiD+ +++  + +      ++ +++++d +++TH+H+DH++++  + ++t++pv  v e  + +++ + ++     
  gi|13541681|ref|NP_111369.1|  17 GKKNVLIDPFLTGNPMAK------VKAEDLNPDIILVTHGHYDHAADAVSISKRTGAPVLSVFELSEIFKESGINTI---- 87 
                                   899**************9......69************************************************773.... PP

                                   CHHTTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTSSHHCCCCCC..........TTC CS
                   Lactamase_B  95 glllagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDallagetgridl.........tlrg 166
                                         +  ++  v  e+  + a        + g   g+ +g v + g+k+  +GD+++  + ++i+          +++g
  gi|13541681|ref|NP_111369.1|  88 ------DINPGGTVEFEGVSIKATIATHSSSYDGRYAGNPVGYVIDIGRKIYHAGDTGYFKDMELIGSvdrpeisllPIGG 162
                                   ......3344444555555555555555677888899999999******************99999999999998888888 PP

                                   EEE-SHCHHHHHHHHHH CS
                   Lactamase_B 167 aevrdpsdaekyldsll 183
                                   ++++d ++a ++l+ l+
  gi|13541681|ref|NP_111369.1| 163 HYTMDVDGAVEALKMLK 179
                                   88888888777776554 PP

>> DUF1884  Domain of unknown function (DUF1884)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   5.2e-05      0.23      15      58 ..      32      75 ..      28      91 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5.2e-05
                                  HHHHHHTT----EEEE-HHHHHHHHHHHHHHHT------EETTE CS
                       DUF1884 15 ineLkleGfePdiiLvGkeaieflkealkkeleeeeevtelsnl 58
                                  +  +k e ++PdiiLv +  +++  +a+        +v+ + +l
  gi|13541681|ref|NP_111369.1| 32 MAKVKAEDLNPDIILVTHGHYDHAADAVSISKRTGAPVLSVFEL 75
                                  667899********************998666666666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       299  (0.0166769); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 1369.98
//
Query:       gi|13541682|ref|NP_111370.1|  [L=121]
Description: nucleic acid-binding protein [Thermoplasma volcanium GSS1]
Scores for complete 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-18   65.0   0.1    8.3e-18   64.8   0.1    1.0  1  PIN_9     PIN like domain
    7.4e-05   23.2   0.3     0.0063   17.0   0.2    2.0  2  PIN       PIN domain
     0.0016   18.8   0.0     0.0035   17.7   0.0    1.6  1  Fcf1      Fcf1
  ------ inclusion threshold ------
      0.012   15.9   0.0      0.026   14.8   0.0    1.6  1  PIN_4     PIN domain


Domain annotation for each model (and alignments):
>> PIN_9  PIN like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.8   0.1   1.8e-21   8.3e-18       1     115 [.       9     116 ..       9     117 .. 0.95

  Alignments for each domain:
  == domain 1  score: 64.8 bits;  conditional E-value: 1.8e-21
                         PIN_9   1 vilDtnaLmipvqfgvdifeelerllgsvelvvpkavleELerlakagkgkertaakvalsLaerceiveaeeekaDdail 81 
                                   ++lDtna++  ++ ++++ +++ ++ g  +  vp  v++EL  l      k++  a++a + a+++ei+e++ +++Dd ++
  gi|13541682|ref|NP_111370.1|   9 ILLDTNAIIYAIEKKIRLEDAVIEIPGVSRPAVPYCVIRELYGL-----AKKNVTARIAYQYAKKLEIIETD-KYGDDGVI 83 
                                   689*****************************************.....5677899****************.******** PP

                         PIN_9  82 elakeldaavlvTnDreLkkrllekgipvilLRq 115
                                   e a +++a vl TnD  L +rl+e gi+v ++ +
  gi|13541682|ref|NP_111370.1|  84 EAAMKTGAMVL-TNDERLSRRLRETGIKVAMISG 116
                                   *******9999.*****************98765 PP

>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.2   1.4e-06    0.0063       1      60 [.       9      61 ..       9      80 .. 0.78
   2 !    6.0   0.1    0.0037        17      80     118 ..      61     102 ..      57     106 .. 0.62

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.4e-06
                                  EEE-HHHHHHHHTTSHHHHHHHHHHHTSSEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHH CS
                           PIN  1 ivlDTsvliallrgeekaeaarklleeleelvtsalvlaEllyvlarrkskrekaaelve 60
                                  i+lDT+++i++++++ + e a+  + ++++ +++  v+ El+  +++       + + + 
  gi|13541682|ref|NP_111370.1|  9 ILLDTNAIIYAIEKKIRLEDAVIEIPGVSRPAVPYCVIRELYGLAKK-------NVTARI 61
                                  79***********************999************9988888.......222222 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0037
                                   HHHHHHHHHH.....SBHHHHHHHHHHHHHT-EEE.ESSTHHHH CS
                           PIN  80 eaaeialkyg.....llpnDaliaAtAkehgikliatfDedfrr 118
                                   +a+++a+k++     +   D + +  A ++g+ ++ t+De+++r
  gi|13541682|ref|NP_111370.1|  61 IAYQYAKKLEiietdKYGDDGV-IEAAMKTGAMVL-TNDERLSR 102
                                   5555555555555634444444.555566666588.*****987 PP

>> Fcf1  Fcf1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   7.8e-07    0.0035       8      82 ..      38     107 ..      33     120 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 7.8e-07
                                   EEEEEHHHHHHHHHCT.....-HHHHHHHTTSEEE----SS---HHHHHHHHH-BTB-TT-EEEE-S-HHHHHHHHTS CS
                          Fcf1   8 kpliTqCviaeleklgkk...lkealkiaktferlkCnhkkptsaddClvsvvkkkknkkryivAtqDkdlrrrlrki 82 
                                    p +  Cvi+el+ l kk    + a+++ak++e  + ++    + dd + +       k   +v t+D+ l rrlr+ 
  gi|13541682|ref|NP_111370.1|  38 RPAVPYCVIRELYGLAKKnvtARIAYQYAKKLEIIETDK----YGDDGVIEAAM----KTGAMVLTNDERLSRRLRET 107
                                   688999**********88555667777777777777666....88998888877....46789*************86 PP

>> PIN_4  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   5.7e-06     0.026       2      64 ..      10      79 ..       9     111 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 5.7e-06
                         PIN_4  2 VlDTnvlLhdpealksf.......keehdvviPitVleELdklKkgsserelarlarqanrlldelleke 64
                                   lDTn +++ +e   ++        +  +  +P+ V++EL +l k++ + ++a++  + +++++  +   
  gi|13541682|ref|NP_111370.1| 10 LLDTNAIIYAIEKKIRLedavieiPGVSRPAVPYCVIRELYGLAKKNVTARIAYQYAKKLEIIETDKYGD 79
                                  69******999876666777877777778899***********999999999999999999998765444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       523  (0.0291706); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); 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 0.29s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 825.88
//
Query:       gi|13541683|ref|NP_111371.1|  [L=203]
Description: 2-phosphoglycerate kinase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.5e-09   36.9   0.1    9.2e-09   35.9   0.1    1.5  1  AAA_18        AAA domain
    3.2e-06   27.6   0.1    1.7e-05   25.3   0.1    2.1  1  AAA_17        AAA domain
    3.9e-05   23.8   0.0     0.0003   21.0   0.0    2.1  1  AAA_33        AAA domain
    0.00027   20.3   0.1     0.0059   15.9   0.1    2.3  1  Zeta_toxin    Zeta toxin
     0.0041   17.5   0.0     0.0089   16.4   0.0    1.7  2  AAA           ATPase family associated with various cellular 
     0.0049   16.6   0.1      0.014   15.2   0.0    1.7  2  RuvB_N        Holliday junction DNA helicase RuvB P-loop doma
  ------ inclusion threshold ------
      0.014   14.6   1.4        0.2   10.8   0.2    2.3  2  ArsA_ATPase   Anion-transporting ATPase
      0.036   14.4   0.1      0.085   13.3   0.1    1.7  1  RNA_helicase  RNA helicase
      0.053   13.9   0.1      0.071   13.5   0.1    1.4  1  AAA_16        AAA ATPase domain
      0.077   13.2   0.7       0.85    9.9   0.7    2.4  2  Roc           Ras of Complex, Roc, domain of DAPkinase


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 !   35.9   0.1   5.2e-12   9.2e-09       1     120 [.       6     147 ..       6     162 .. 0.71

  Alignments for each domain:
  == domain 1  score: 35.9 bits;  conditional E-value: 5.2e-12
                        AAA_18   1 IlltGtpGvGKttlakeLskrlgf.....gvnlrdvakenglllevdpe.........aldeskrldedkldklldaleen 67 
                                   Il+ G+pGvGKt+++  L+++lg+     g+ lr+ ++      +  ++           +  + +++++ d++   + ++
  gi|13541683|ref|NP_111371.1|   6 ILIGGVPGVGKTSISGFLARELGIdimlsGDYLREFLRPLFGDNPLIQKsvydawqayGQKTDENIVKGYIDQAKIMMAGI 86 
                                   99********************99989994444444444333333333344456444444555555555555555555555 PP

                        AAA_18  68 ss....aleegknlvidg..hlaeleseaakdikk.vvLtasp.eelleRlekRgyeeaki 120
                                   ++    a e+g+nl+++   +l e++se+a+ ++  ++L+  + + +++Rl +R + ++k 
  gi|13541683|ref|NP_111371.1|  87 DRilirAIENGENLILETlyFLPEMLSEKARNNVHmFYLYIGDeKLHRDRLVDRINYTHKN 147
                                   5588888888*******7336899999999998889***9988455689*****9888885 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.1   9.3e-09   1.7e-05       2     123 ..      10     140 ..       9     151 .. 0.65

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 9.3e-09
                                   E-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTT.T................SHSSHHHHCTSHHHHHHHHHHHHHHHH CS
                        AAA_17   2 GgPGsGKgtqceklvekygfthlsaGdllreeakrg.g................lakardemrklpleekkelqkeaaeki 65 
                                   G+PG+GK+ ++  l++++g+ ++  Gd+lre  ++  g                 +k+++++ k+++++ k +++ + ++i
  gi|13541683|ref|NP_111371.1|  10 GVPGVGKTSISGFLARELGIDIMLSGDYLREFLRPLfGdnpliqksvydawqayGQKTDENIVKGYIDQAKIMMAGI-DRI 89 
                                   9******************************9988864556555555444444334444444455544444333222.333 PP

                                   HHHH..HSSEEEEEE-SEEEETTEEEESSHHHHHHHH..SEEEEEE--HHHHHHHHHHHT CS
                        AAA_17  66 aeea..kkkgvlvdghprikeqagfldglpkevleelkpdaiilleadpeeilerrlkdr 123
                                     +a  + +++++++ +       fl+++ +e  +  +  ++++l++ +e++++ rl dr
  gi|13541683|ref|NP_111371.1|  90 LIRAieNGENLILETLY-------FLPEMLSE--KARNNVHMFYLYIGDEKLHRDRLVDR 140
                                   33332234556666666.......56666665..33344788888888888888888765 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   1.7e-07    0.0003       2      48 ..       6      53 ..       5     200 .. 0.76

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.7e-07
                        AAA_33  2 vllvGlpGsGKstlaerllkklg.avllssdtlrrrlfgtdqqsktdy 48
                                  +l+ G+pG+GK+  +  l+++lg  + ls d+lr+ l++   +++  +
  gi|13541683|ref|NP_111371.1|  6 ILIGGVPGVGKTSISGFLARELGiDIMLSGDYLREFLRPLFGDNPLIQ 53
                                  7889********************9*******8887776333333322 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   3.3e-06    0.0059      17      58 ..       4      42 ..       2     165 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 3.3e-06
                    Zeta_toxin 17 klillgGqpGAGKselaellkdelerqgnvvrldpDdlRelh 58
                                  k+il+gG pG GK++++  l++el   g  + l++D lRe+ 
  gi|13541683|ref|NP_111371.1|  4 KIILIGGVPGVGKTSISGFLAREL---GIDIMLSGDYLREFL 42
                                  79*********************9...778999999999986 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0     5e-06    0.0089       1      46 [.       6      71 ..       6     122 .. 0.70
   2 ?   -2.0   0.0       2.4   4.4e+03      84     111 ..     152     184 ..     131     195 .. 0.57

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 5e-06
                                  EEEESSTTSSHHHHHHHHHHHHTHE....................EEEEETTTCSSSSTTHHHHHH CS
                           AAA  1 vllyGppGtGKTllakavakelgve....................fleisgsellskyvgesekki 46
                                  +l+ G pG+GKT++   +a+elg++                    +++ s+ + ++ y +++ ++i
  gi|13541683|ref|NP_111371.1|  6 ILIGGVPGVGKTSISGFLARELGIDimlsgdylreflrplfgdnpLIQKSVYDAWQAYGQKTDENI 71
                                  5788*****************987644444444444444444444666666666655555555544 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.4
                                   HHHHHHHHHHHHTTTS.....SSTEEEEEEESS CS
                           AAA  84 rvvnqLlteldgvkkk.....eskvivigatnr 111
                                   r++++L++  + ++ +     e +v +i ++n+
  gi|13541683|ref|NP_111371.1| 152 RLAEHLYEYRNIMEYSmmrssEYNVKIIDTSNY 184
                                   445555444333333333333445666666666 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   7.7e-06     0.014      36      63 ..       6      33 ..       2      40 .. 0.87
   2 ?   -2.4   0.0       1.9   3.4e+03      19      38 ..      72      91 ..      61     101 .. 0.54

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 7.7e-06
                        RuvB_N 36 vllyGpPGlGkttlakiiakelgvklki 63
                                  +l+ G PG+Gkt+++  +a+elg+++  
  gi|13541683|ref|NP_111371.1|  6 ILIGGVPGVGKTSISGFLARELGIDIML 33
                                  78899******************99865 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.9
                        RuvB_N 19 lkifieaakkreealdhvll 38
                                  +k +i+ ak     +d +l+
  gi|13541683|ref|NP_111371.1| 72 VKGYIDQAKIMMAGIDRILI 91
                                  44444444444444444443 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.2   0.00011       0.2       2      25 ..       4      27 ..       3      30 .. 0.89
   2 ?    2.6   0.0     0.035        62      92     133 ..     136     182 ..      90     191 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00011
                                  EEEEEEESTTSSHHHHHHHHHHHH CS
                   ArsA_ATPase  2 kvilvgGKGGVGKttvsaatavkl 25
                                  k+il+gG  GVGKt++s  +a +l
  gi|13541683|ref|NP_111371.1|  4 KIILIGGVPGVGKTSISGFLAREL 27
                                  89***************9888665 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.035
                                   HHHHHHHHHHTSSTTH...HHHHHHHHHHHH..HHCSSSSEEEEESB CS
                   ArsA_ATPase  92 eledvlaeelaslPGi...deilsfeellky..vkeeeydvvvlDta 133
                                    l d ++ + +  PG+   + +  + ++++y  ++++ey+v ++Dt+
  gi|13541683|ref|NP_111371.1| 136 RLVDRINYTHKNSPGTrlaEHLYEYRNIMEYsmMRSSEYNVKIIDTS 182
                                   44444444444448754446778888998873356**********96 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   4.7e-05     0.085       1      60 [.       6      88 ..       6     121 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.7e-05
                  RNA_helicase  1 iwlyGpsgeGKStlakeLakallkkl.......................klkkkdsvysrnpeddfwdgYtgqevvvidDfgq 60
                                  i++ G +g+GK++++  La++l  ++                           + + y +++++++++gY +q+ +++  + +
  gi|13541683|ref|NP_111371.1|  6 ILIGGVPGVGKTSISGFLARELGIDImlsgdylreflrplfgdnpliqkSVYDAWQAYGQKTDENIVKGYIDQAKIMMAGIDR 88
                                  5688999****************888899999*************99976666678888999999******999999876665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   3.9e-05     0.071      25      51 ..       4      30 ..       1     105 [. 0.79

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.9e-05
                        AAA_16 25 elvllsGesGvGKsslvrellralekd 51
                                   ++l+ G +GvGK+s+   l+r+l  d
  gi|13541683|ref|NP_111371.1|  4 KIILIGGVPGVGKTSISGFLARELGID 30
                                  689*************99999998877 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 ?    9.9   0.7   0.00047      0.85       1      88 [.       4      87 ..       4     104 .. 0.74
   2 ?   -1.4   0.0       1.5   2.6e+03      48      70 ..     167     188 ..     126     197 .. 0.59

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00047
                                  EEEEESS.TTSSHHHHHHCHCT-CCC-EEETTTTEEEEEEECGGSGGCTTBTTTTCEEEEEEEE-SGGCTTTT-HHHHCTSCE CS
                           Roc  1 KvvlvGd.sgvGKtsllkrfvedkfsekekstigvdfltkevtkikgvendkkvkkvklniWDtaGqerfrslhplylreaal 82
                                  K++l+G   gvGKts+   + + +     + +++ d+l++ +  + g  ++  ++k  ++ W   Gq+  +++ + y+ +a++
  gi|13541683|ref|NP_111371.1|  4 KIILIGGvPGVGKTSISGFLAR-EL--GIDIMLSGDYLREFLRPLFG--DNPLIQKSVYDAWQAYGQKTDENIVKGYIDQAKI 81
                                  7888864389*****9876663.33..34556677777766655555..3445777889***********************9 PP

                                  EEEEEE CS
                           Roc 83 ailvyd 88
                                  +++ +d
  gi|13541683|ref|NP_111371.1| 82 MMAGID 87
                                  998777 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.5
                                   TTBTTTTCEEEEEEEE-SGGCTT CS
                           Roc  48 endkkvkkvklniWDtaGqerfr 70 
                                   +   + ++++++i Dt+  e+ r
  gi|13541683|ref|NP_111371.1| 167 SMM-RSSEYNVKIIDTSNYEEAR 188
                                   222.2345666777776666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       714  (0.0398237); expected 358.6 (0.02)
Passed bias filter:                      538  (0.0300073); expected 358.6 (0.02)
Passed Vit filter:                        83  (0.00462937); 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 0.33s 00:00:00.89 Elapsed: 00:00:00.50
# Mc/sec: 1229.03
//
Query:       gi|13541684|ref|NP_111372.1|  [L=194]
Description: nicotinamidase-like amidase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.4e-11   43.6   0.0    4.8e-11   43.1   0.0    1.3  1  Isochorismatase  Isochorismatase family
  ------ inclusion threshold ------
      0.016   14.6   0.1      0.055   12.9   0.0    1.8  2  ZnuA             Zinc-uptake complex component A periplasmic


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 !   43.1   0.0   5.4e-15   4.8e-11       3     174 ..      16     185 ..      14     186 .. 0.73

  Alignments for each domain:
  == domain 1  score: 43.1 bits;  conditional E-value: 5.4e-15
               Isochorismatase   3 lvviDmqndfveegvkeseeisavveninkllkaarkagipviftrdvhe...leevkgdlderkaaphfkpgttgaelvp 80 
                                   lv+    ++ +    k++    +++   +   +a++  +ip +f++ +++   l++       +k+   + p++ ++e + 
  gi|13541684|ref|NP_111372.1|  16 LVIMNATEENF----KHIFSKLEFITSMKVIEDAMKLYNIPAVFIERNFRssrLSDYIARKYSQKMVSLMSPSSYDEEYIR 92 
                                   55555555555....444444444444444445556667888999999886665555555555566666666666666666 PP

               Isochorismatase  81 elaple..gdvvvdKtrfsafagtdldeiLkelgiktivlaGiatdvCVeatardaldlGyevvvvsDAvaalspelhdaa 159
                                   ++  l+      +     ++f+++ + ++++ +g +t+vlaG+ t+  +  +a++ l ++y ++v+sDA++++s+ ++  a
  gi|13541684|ref|NP_111372.1|  93 QFGELAipPGLSIG--SEDIFSDNTVRNMIEGSGKTTVVLAGFYTESDIYISAIESLLHDYYTFVISDATSTISERTYFEA 171
                                   66666644444444..459************************************************************** PP

               Isochorismatase 160 lkrlkqafatvitte 174
                                   l+ l+ + ++vi++ 
  gi|13541684|ref|NP_111372.1| 172 LDLLS-QHVEVIDSR 185
                                   ****9.677777765 PP

>> ZnuA  Zinc-uptake complex component A periplasmic
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   6.1e-06     0.055     184     243 ..      36      91 ..      12      98 .. 0.77
   2 ?   -0.7   0.0     0.088   7.8e+02     204     250 ..     107     148 ..     104     155 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.1e-06
                                   HHHHHHHHHHHHHTT-SEEEEETTS.-THHHHHHHHHHT-EEEEE-STSSSTSTTSTTSHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ZnuA 184 aaqiaalieeikeagvkaifvepla.spklaetlaeeagvkvatlysldslgdegsaetYi 243
                                      ++ + +++k  +++a+f+e ++ s++l + +a+++  k++ l s  s ++      Yi
  gi|13541684|ref|NP_111372.1|  36 ITSMKVIEDAMKLYNIPAVFIERNFrSSRLSDYIARKYSQKMVSLMSPSSYDE-----EYI 91 
                                   56788899999************998999**********99999887343332.....455 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.088
                                   EETTS-THHHHHHHHHHT-EEEEE-STSSSTSTTSTTSHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ZnuA 204 veplaspklaetlaeeagvkvatlysldslgdegsaetYidmmranl 250
                                   +e  +s++++++++e  g  +++l ++++  +    + Yi+ ++  l
  gi|13541684|ref|NP_111372.1| 107 SEDIFSDNTVRNMIEGSGKTTVVLAGFYT--ES---DIYISAIESLL 148
                                   57788999999999988866666666444..22...25777776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       579  (0.032294); 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: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 1341.26
//
Query:       gi|13541685|ref|NP_111373.1|  [L=247]
Description: dolichol-phosphate-mannosyltransferase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.1e-29  101.6   0.0    6.2e-29  101.0   0.0    1.3  1  Glycos_transf_2  Glycosyl transferase family 2
    2.2e-06   27.7   0.0    2.9e-06   27.3   0.0    1.2  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
      0.001   19.5   0.0     0.0023   18.4   0.0    1.5  1  Glyco_tranf_2_4  Glycosyl transferase family 2
  ------ inclusion threshold ------
      0.013   14.9   0.0      0.027   14.0   0.0    1.5  1  Glyco_transf_21  Glycosyl transferase family 21
      0.017   14.6   0.0      0.028   13.9   0.0    1.3  1  Glyco_tranf_2_2  Glycosyltransferase like family 2


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.0   0.0   1.7e-32   6.2e-29       1     133 [.       6     141 ..       6     175 .. 0.85

  Alignments for each domain:
  == domain 1  score: 101.0 bits;  conditional E-value: 1.7e-32
                                   EEEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH--SS CS
               Glycos_transf_2   1 svviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglraatgd 81 
                                   s v  t Ne  +++ +l+ + +   y++feii+vDD+S+D+t+e l e + +d++++vi ++ +vG  g+l  g+  a+g+
  gi|13541685|ref|NP_111373.1|   6 SLVAATLNEIGNIATFLDKVEKELIYYNFEIIIVDDNSSDGTKEYLAERSLKDKNLHVIENPYRVGMLGSLKMGINSAKGK 86 
                                   5677899******************************************99****************************** PP

                                   EEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SS....E CS
               Glycos_transf_2  82 yilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrv....g 133
                                   y +++DaD++++p+ +  ++e+l++ g d+v+g+r++++g+ + ++  +       
  gi|13541685|ref|NP_111373.1|  87 YCIVMDADLQHPPEAILSIIERLNH-GCDIVVGSRYVNGGSAGDRNSYRALlsigA 141
                                   *************************.************999887776554455543 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.0   8.1e-10   2.9e-06       8     132 ..       9     128 ..       3     189 .. 0.72

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 8.1e-10
               Glyco_tranf_2_3   8 Vptfneedvlgevlesllaqe.yprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksralnealravk 87 
                                    +t+ne   +   l+ + +   y ++e+++v+d+s+++t e + e  + l+d  ++v+ n+ +    g   +l+ +++ +k
  gi|13541685|ref|NP_111373.1|   9 AATLNEIGNIATFLDKVEKELiYYNFEIIIVDDNSSDGTKEYLAE--RSLKDKNLHVIENPYR---VGMLGSLKMGINSAK 84 
                                   5566666655556666665434789****************9976..99**99*****55543...46678899******* PP

               Glyco_tranf_2_3  88 sdlvllvDdDtvvePdtlkrllqffltpkvgavgtpvfllnrstl 132
                                   +++ +++D+D    P+++ ++   +  +++++v ++++++ +s+ 
  gi|13541685|ref|NP_111373.1|  85 GKYCIVMDADLQHPPEAILSIIERL-NHGCDIVVGSRYVNGGSAG 128
                                   ************************9.***********99865532 PP

>> Glyco_tranf_2_4  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   6.6e-07    0.0023      21      81 ..      35      94 ..      17      95 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 6.6e-07
               Glyco_tranf_2_4 21 rilvydndstDgtrailke..lpevkllhvdksyederrqve.llkallaryaeadwvlvvDaD 81
                                  +i+++d++s+Dgt ++l+e  l++ +l  ++++y+    ++   lk  +++ a++++++v+DaD
  gi|13541685|ref|NP_111373.1| 35 EIIIVDDNSSDGTKEYLAErsLKDKNLHVIENPYR---VGMLgSLKMGINS-AKGKYCIVMDAD 94
                                  69***************884458888888888886...4443244444444.589********9 PP

>> Glyco_transf_21  Glycosyl transferase family 21
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   7.5e-06     0.027      22      93 ..      76     146 ..      59     159 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 7.5e-06
               Glyco_transf_21  22 llqaleaakydllvisDsdvrvkpdyLeellaaledpkvglVtslpvgsdakglaaaleaaflntlagvlqa 93 
                                   l  ++++ak ++ ++ D+d   +p+++ ++ ++l + ++ +V++  ++ + +   ++  +a+l+++a++l++
  gi|13541685|ref|NP_111373.1|  76 LKMGINSAKGKYCIVMDADLQHPPEAILSIIERLNH-GCDIVVGSRYVNGGSAGDRNSYRALLSIGAQYLSY 146
                                   6678899****************************8.9*******999999988888888888877776666 PP

>> Glyco_tranf_2_2  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   7.9e-06     0.028      19      96 ..      25      99 ..      14     116 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 7.9e-06
               Glyco_tranf_2_2 19 vlqkakyydeeielivvddgSsekfleev..ssiidlnllvylkdeddkayslaaarNrGaskaesdlvlFlDaDcfiss 96
                                  v ++  y   ++e+i+vdd Ss+ + e +  +s++d+nl+v  ++      +   +   G++ a++ + + +DaD    +
  gi|13541685|ref|NP_111373.1| 25 VEKELIY--YNFEIIIVDDNSSDGTKEYLaeRSLKDKNLHVI-ENP--YRVGMLGSLKMGINSAKGKYCIVMDADLQHPP 99
                                  5555556..49*************9999844589*******8.333..4567778999****************976555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       516  (0.0287802); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-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 0.27s 00:00:00.84 Elapsed: 00:00:01.34
# Mc/sec: 559.47
//
Query:       gi|13541686|ref|NP_111374.1|  [L=107]
Description: hypothetical protein TVN0855 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        1.8    8.7   8.0        3.6    7.8   8.0    1.5  1  AT_hook   AT hook motif


Domain annotation for each model (and alignments):
>> AT_hook  AT hook motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   8.0    0.0002       3.6       1      12 [.      86      97 ..      86      98 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0002
                       AT_hook  1 kRkRGRPrKaat 12
                                  +RkRGRP+ +++
  gi|13541686|ref|NP_111374.1| 86 PRKRGRPKGSSK 97
                                  7*******9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       429  (0.0239277); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.46
# Mc/sec: 692.49
//
Query:       gi|13541687|ref|NP_111375.1|  [L=516]
Description: family X DNA polymerase [Thermoplasma volcanium GSS1]
Scores for complete sequence (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   70.1   0.0    2.6e-19   69.1   0.0    1.5  1  DNA_pol_B_thumb  DNA polymerase beta thumb
    5.8e-18   65.0   2.0    1.2e-16   60.9   0.8    2.9  3  HHH_8            Helix-hairpin-helix domain
    3.2e-11   43.6   2.1    3.1e-06   27.7   0.0    3.2  3  HHH_5            Helix-hairpin-helix domain
    5.3e-06   26.0   0.2      0.026   14.4   0.1    2.9  2  HHH              Helix-hairpin-helix motif
    9.6e-06   25.8   0.2    0.00055   20.1   0.0    2.9  2  HHH_3            Helix-hairpin-helix motif
     0.0012   19.0   0.0     0.0026   17.9   0.0    1.6  1  DNA_pol_B_palm   DNA polymerase beta palm
     0.0036   17.4   0.0       0.12   12.5   0.0    3.2  3  HHH_2            Helix-hairpin-helix motif
  ------ inclusion threshold ------
      0.035   14.5   0.7         20    5.8   0.0    3.8  3  IMS_HHH          IMS family HHH motif
      0.086   13.5   1.0        1.5    9.5   0.0    2.9  3  5_3_exonuc       5'-3' exonuclease, C-terminal SAM fold


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 !   69.1   0.0   1.3e-22   2.6e-19       1      70 []     258     319 ..     258     319 .. 0.95

  Alignments for each domain:
  == domain 1  score: 69.1 bits;  conditional E-value: 1.3e-22
                                   HHHHHHS-HHHHHHHHHHHHCTTEEEETTEEE.......ETCCCEEEC-SSHHHHHHHCTS----GGGTT CS
               DNA_pol_B_thumb   1 allyfTGsktFnrdlRrlakkkglkLnssglrdekgkaeddddgelvevetErdvfelLglpyipPeeRe 70 
                                   a++yfTGsk++n++lRrla  kg+kLn++gl+          d++ v +  E++v+e L+l yipPe+Re
  gi|13541687|ref|NP_111375.1| 258 AMQYFTGSKDHNIKLRRLAIGKGMKLNEYGLF--------SGDKNIVSGMPEEKVYETLDLAYIPPELRE 319
                                   799*****************************........677779999********************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 !   60.9   0.8   5.8e-20   1.2e-16       1      67 [.       3      76 ..       3      77 .. 0.93
   2 ?   -2.9   0.0       4.7   9.3e+03      49      61 ..      98     110 ..      89     117 .. 0.70
   3 ?    2.0   0.0      0.13   2.7e+02      33      61 ..     119     145 ..     115     151 .. 0.73

  Alignments for each domain:
  == domain 1  score: 60.9 bits;  conditional E-value: 5.8e-20
                                  HHHHHHHHHHHHHHHHHCT..--CCCHHHHHHHHCCCCC-SS-HHHH.TT....HCTTSTT--HHHHHHHHHHH CS
                         HHH_8  1 NkeiadaLeeladllelkg..edpfrvraYrrAaraiealpeeitsl.ee....eltklpgiGkkiaakieeil 67
                                  N++ia+++ e+a lle +g   ++f ++aY +A rai ++ e+++++ e+    +l ++pgiGk+ia+ki e++
  gi|13541687|ref|NP_111375.1|  3 NQDIARIFTEIAYLLEAAGeqKSQFEANAYLKASRAISSMQEDLETIyEKggkdALLSIPGIGKGIADKIVEYI 76
                                  9******************6666************************844589899****************97 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 4.7
                                   CTTSTT--HHHHH CS
                         HHH_8  49 ltklpgiGkkiaa 61 
                                   l k+ g+G+k  a
  gi|13541687|ref|NP_111375.1|  98 LMKIEGLGPKKLA 110
                                   7799999966444 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.13
                                   CCCCC-SS-HHHHTTHCTTSTT--HHHHH CS
                         HHH_8  33 raiealpeeitsleeeltklpgiGkkiaa 61 
                                   +++e+l  +i + ++ ++ +pg+G+k  +
  gi|13541687|ref|NP_111375.1| 119 TNVEELRNAILN-HK-VRGIPGFGEKSEN 145
                                   556666666666.55.9*******99765 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.1   2.6e-05     0.052      24      53 ..      44      74 ..      33      78 .. 0.77
   2 !   27.7   0.0   1.6e-09   3.1e-06       1      52 [.      95     148 ..      95     152 .. 0.91
   3 ?   -2.7   0.0       4.9   9.8e+03      17      45 ..     194     226 ..     192     230 .. 0.56

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.6e-05
                                  -SHHHHHHS.-HHHHHTSTTS-HHHHHHHHH CS
                         HHH_5 24 esvedlaaa.dveeLakipGiGkktAeriil 53
                                  e +e + ++  +++L +ipGiGk  A++i++
  gi|13541687|ref|NP_111375.1| 44 EDLETIYEKgGKDALLSIPGIGKGIADKIVE 74
                                  45677776635789***************97 PP

  == domain 2  score: 27.7 bits;  conditional E-value: 1.6e-09
                                   -HHHHTSTT--HHHHHHHHTT.T--SHHHHHHS-H.HHHHTSTTS-HHHHHHHH CS
                         HHH_5   1 feeLlsvsGiGpktAlallsa.Giesvedlaaadv.eeLakipGiGkktAerii 52 
                                   f +L++++G+Gpk    l+ a Gi+ ve+l +a   +++  ipG+G+k   +++
  gi|13541687|ref|NP_111375.1|  95 FISLMKIEGLGPKKLAVLYQAlGITNVEELRNAILnHKVRGIPGFGEKSENQLL 148
                                   779******************99***********8459999*******988775 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 4.9
                                   HHHTTT--SHHHHHHS-....H.HHHHTSTTS-H CS
                         HHH_5  17 allsaGiesvedlaaad....v.eeLakipGiGk 45 
                                   ++ ++ i+ ++ laa +      +++ ++ G++ 
  gi|13541687|ref|NP_111375.1| 194 RMKET-IGDIDILAASEypnaLmDKFVEMDGVSS 226
                                   56677.7777777765322222356666666665 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.1   1.3e-05     0.026      11      30 .]      56      75 ..      55      75 .. 0.92
   2 !    8.5   0.0   0.00097       1.9       3      23 ..      88     108 ..      86     114 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.3e-05
                                  HHHHTSTT-SHHHHHHHHHH CS
                           HHH 11 eeLlalPGVGpktAeaIlsy 30
                                  + Ll++PG+G+  A++I +y
  gi|13541687|ref|NP_111375.1| 56 DALLSIPGIGKGIADKIVEY 75
                                  569**************998 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00097
                                   HHHHTSSHHHHHTSTT-SHHH CS
                           HHH   3 eglipasreeLlalPGVGpkt 23 
                                   +   p ++  L++++G Gpk+
  gi|13541687|ref|NP_111375.1|  88 KKKYPIDFISLMKIEGLGPKK 108
                                   6678889999**********8 PP

>> HHH_3  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   2.8e-07   0.00055      14      52 ..      56      93 ..      54      95 .. 0.91
   2 ?    2.2   0.0      0.11   2.2e+02      46      58 ..      98     110 ..      94     116 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 2.8e-07
                         HHH_3 14 eeLqklpGlgpklAknIvayReknGpfksreeLlkvkgl 52
                                  + L  +pG+g+ +A++Iv+y  + G +++ e+L+k++ +
  gi|13541687|ref|NP_111375.1| 56 DALLSIPGIGKGIADKIVEYI-NSGSIQKYEDLKKKYPI 93
                                  57899****************.889**********9866 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.11
                         HHH_3  46 Llkvkglgpktfe 58 
                                   L+k++glgpk++ 
  gi|13541687|ref|NP_111375.1|  98 LMKIEGLGPKKLA 110
                                   8899999999875 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 !   17.9   0.0   1.3e-06    0.0026      13      50 ..     172     209 ..     160     256 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.3e-06
                                   HHHHHHHHH-TT-EEEE-HHHHTT-SEESSEEEEEEBT CS
                DNA_pol_B_palm  13 lvkkaakeldpevevivcGSYRRgaessGDvDvlitkk 50 
                                    +k+ +++    + v ++GS RR +e+ GD+D+l   +
  gi|13541687|ref|NP_111375.1| 172 RIKNYLESTGYALIVEIAGSTRRMKETIGDIDILAASE 209
                                   567777888888999******************97655 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.0     6e-05      0.12      34      61 ..      55      82 ..      34      84 .. 0.78
   2 ?    0.4   0.0      0.36   7.2e+02       4      51 ..     114     161 ..     111     170 .. 0.69
   3 ?   -2.5   0.0       2.8   5.6e+03      32      48 ..     213     229 ..     211     230 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6e-05
                         HHH_2 34 leeLlevddiGeeiAqsivefFeneknr 61
                                   + Ll++++iG+ iA++ive+ ++ + +
  gi|13541687|ref|NP_111375.1| 55 KDALLSIPGIGKGIADKIVEYINSGSIQ 82
                                  578******************9876665 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.36
                         HHH_2   4 faLGIrhVGektAklLakrFksldaLkkasleeLlevddiGeeiAqsi 51 
                                    aLGI +V e    +L ++ + +  + + s+++Ll+  + +e++++ i
  gi|13541687|ref|NP_111375.1| 114 QALGITNVEELRNAILNHKVRGIPGFGEKSENQLLKNIEMAERVSERI 161
                                   578888887777777777777777777777777777666666666665 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 2.8
                         HHH_2  32 asleeLlevddiGeeiA 48 
                                   a +++ +e d++  +iA
  gi|13541687|ref|NP_111375.1| 213 ALMDKFVEMDGVSSIIA 229
                                   44555666666666666 PP

>> IMS_HHH  IMS family HHH motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.035        71      15      27 ..      60      72 ..      60      75 .. 0.86
   2 ?   -0.4   0.0      0.91   1.8e+03      15      32 .]     100     118 ..      94     118 .. 0.78
   3 ?    5.8   0.0    0.0098        20       9      28 ..     129     149 ..     121     152 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.035
                       IMS_HHH 15 kipGiGgklgekL 27
                                  +ipGiG+  ++k+
  gi|13541687|ref|NP_111375.1| 60 SIPGIGKGIADKI 72
                                  69******99985 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.91
                       IMS_HHH  15 kipGiGgklgekLek.lGi 32 
                                   ki G+G+k  + L + lGi
  gi|13541687|ref|NP_111375.1| 100 KIEGLGPKKLAVLYQaLGI 118
                                   5669****99996655877 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.0098
                       IMS_HHH   9 wplpitkipGiGgklgek.Le 28 
                                    + +++ ipG+G k + + L+
  gi|13541687|ref|NP_111375.1| 129 LNHKVRGIPGFGEKSENQlLK 149
                                   57899*********9988665 PP

>> 5_3_exonuc  5'-3' exonuclease, C-terminal SAM fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       6.3   1.3e+04      54      75 ..      27      48 ..       6      52 .. 0.45
   2 ?    1.2   0.1      0.28   5.5e+02      18      40 ..      56      78 ..      54     117 .. 0.83
   3 ?    9.5   0.0   0.00074       1.5      19      50 ..     132     163 ..     130     188 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 6.3
                    5_3_exonuc 54 kklkekLeenkeearlskkLat 75
                                   ++++ L++++    + ++L t
  gi|13541687|ref|NP_111375.1| 27 FEANAYLKASRAISSMQEDLET 48
                                  2333334444444444444444 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.28
                    5_3_exonuc 18 DnipGvpgiGektAakLlkeygs 40
                                  D +  +pgiG+  A k+++ ++s
  gi|13541687|ref|NP_111375.1| 56 DALLSIPGIGKGIADKIVEYINS 78
                                  677789*****999999876654 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.00074
                    5_3_exonuc  19 nipGvpgiGektAakLlkeygsleeilenlde 50 
                                   ++ G+pg Gek   +Llk+++  e + e++  
  gi|13541687|ref|NP_111375.1| 132 KVRGIPGFGEKSENQLLKNIEMAERVSERIPI 163
                                   689*********************99998863 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (516 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       544  (0.0303419); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.71u 0.33s 00:00:01.04 Elapsed: 00:00:00.55
# Mc/sec: 2832.29
//
Query:       gi|13541688|ref|NP_111376.1|  [L=120]
Description: hypothetical protein TVN0857 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                      1011  (0.0563891); expected 358.6 (0.02)
Passed bias filter:                      517  (0.028836); 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):               0  [number of targets reported over threshold]
# CPU time: 0.56u 0.33s 00:00:00.89 Elapsed: 00:00:00.54
# Mc/sec: 664.18
//
Query:       gi|13541689|ref|NP_111377.1|  [L=218]
Description: metal-dependent hydrolase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-31  108.6   0.0    3.3e-31  108.3   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 !  108.3   0.0   1.8e-35   3.3e-31       2     135 ..       9     157 ..       8     158 .. 0.90

  Alignments for each domain:
  == domain 1  score: 108.3 bits;  conditional E-value: 1.8e-35
                       Cyclase   2 dLshplsedtpvwp.dp...................islsehtGTHlDapgHfae..ktidelpleelvgpavvldvsaka 60 
                                   dL++p+++ +pvwp +p                   i+ s+htGTH+Dap+H++e   t+d+l+l +l+g + +l v    
  gi|13541689|ref|NP_111377.1|   9 DLTAPIYPYMPVWPsNPpvelkpivtvpkdgylaeiIEASTHTGTHIDAPAHMIEggTTVDDLDLASLIGTGYCLKV--L- 86 
                                   9************7544678888999*****************************999*******************..5. PP

                       Cyclase  61 aaedyeiitaedleaalakqgveikpgdivlirTgwskrl..edkekyrnpglseeaaewlaekgvkavGvDtlsvD 135
                                     +d ++i   +l  a++ qg  i +++i+li Tgw k++  + + +y+ pglse+aa++l++k+vkavG+Dtl+++
  gi|13541689|ref|NP_111377.1|  87 --PDGHTIRSTHL--AEKWQG--IYNNSILLIETGWYKKRgyTREFQYDFPGLSEDAADFLIQKHVKAVGIDTLGIE 157
                                   ..67778899999..556688..88*************996544456699************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       206  (0.0114898); expected 358.6 (0.02)
Passed bias filter:                      201  (0.0112109); 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: 0.55u 0.25s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1363.91
//
Query:       gi|13541690|ref|NP_111378.1|  [L=78]
Description: nucleic-acid-binding protein (Zn-ribbon) [Thermoplasma volcanium GSS1]
Scores for complete 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   23.9   0.9      0.066   12.6   0.1    2.2  2  zf-ribbon_3      zinc-ribbon domain
      0.001   18.7   1.9       0.58    9.9   0.2    2.3  2  zinc_ribbon_2    zinc-ribbon domain
     0.0017   17.7   0.2        1.7    8.0   0.0    2.2  2  zf-TFIIB         Transcription factor zinc-finger
     0.0023   18.0   1.0      0.013   15.6   1.0    1.9  1  zinc_ribbon_13   Nucleic-acid-binding protein containing Zn-r
     0.0027   17.8   1.6        1.1    9.4   0.1    2.2  2  Zn-ribbon_8      Zinc ribbon domain
     0.0031   17.5   0.0      0.005   16.8   0.0    1.3  1  DZR              Double zinc ribbon
     0.0034   17.8   1.0       0.67   10.4   0.1    2.2  2  zf-IS66          zinc-finger binding domain of transposase IS
     0.0078   15.7   2.7          1    8.9   0.2    2.2  2  TF_Zn_Ribbon     TFIIB zinc-binding
     0.0079   16.2   1.8        1.2    9.2   0.4    2.4  2  YhfH             YhfH-like protein
  ------ inclusion threshold ------
      0.015   15.2   1.2        4.5    7.3   0.1    2.2  2  Nudix_N_2        Nudix N-terminal
      0.017   14.8   2.3       0.29   10.8   0.2    2.3  2  zf-RRN7          Zinc-finger of RNA-polymerase I-specific TFI
      0.019   15.0   0.1      0.024   14.6   0.1    1.2  1  HypA             Hydrogenase/urease nickel incorporation, met
      0.019   14.7   2.5       0.42   10.4   0.4    2.2  2  A2L_zn_ribbon    A2L zinc ribbon domain
      0.023   14.7   0.1        3.4    7.7   0.0    2.2  2  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
      0.023   14.6   2.1       0.38   10.6   0.2    2.1  2  zf-HIT           HIT zinc finger
      0.023   14.6   3.0       0.51   10.3   0.4    2.2  2  DUF35_N          Rubredoxin-like zinc ribbon domain (DUF35_N)
      0.025   14.9   1.0       0.31   11.4   1.0    2.0  1  GFA              Glutathione-dependent formaldehyde-activatin
      0.029   15.1   0.6        4.3    8.1   0.1    2.2  2  zf-ISL3          zinc-finger of transposase IS204/IS1001/IS10
      0.033   13.8   2.5        1.7    8.4   0.1    2.3  2  zf-NADH-PPase    NADH pyrophosphatase zinc ribbon domain
      0.035   13.7   2.0        2.3    7.9   0.2    2.2  2  zf_UBZ           Ubiquitin-Binding Zinc Finger
      0.058   13.3   0.5        6.9    6.7   0.1    2.1  2  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
      0.064   13.2   1.8       0.48   10.4   0.1    2.2  2  Zn_ribbon_SprT   SprT-like zinc ribbon domain
        0.1   12.3   1.5        2.1    8.1   0.1    2.3  2  Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
       0.14   12.4   1.5        1.3    9.3   0.0    2.1  2  zf-RING_7        C4-type zinc ribbon domain
       0.14   11.9   5.0        4.5    7.1   0.5    2.4  2  Rubredoxin_2     Rubredoxin metal binding domain
       0.16   11.6   3.2        4.8    6.9   0.2    2.2  2  zf-tcix          Putative treble-clef, zinc-finger, Zn-bindin
       0.16   12.0   0.8       0.81    9.7   0.0    1.9  2  DUF1451          Zinc-ribbon containing domain
       0.18   11.7   2.8        8.5    6.4   0.2    2.5  2  RNA_POL_M_15KD   RNA polymerases M/15 Kd subunit
        1.6    8.8   5.0         17    5.5   0.7    2.2  2  Ogr_Delta        Ogr/Delta-like zinc finger
          2    8.2   6.6         11    5.9   0.2    2.6  3  zf-C4_Topoisom   Topoisomerase DNA binding C4 zinc finger


Domain annotation for each model (and alignments):
>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.1   0.00069      0.41       2      10 ..       2      10 ..       1      18 [. 0.80
   2 !   12.6   0.1   0.00011     0.066       3      11 ..      49      57 ..      47      59 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00069
                   zf-ribbon_3  2 tvrCPnCGa 10
                                  +++C+nCG+
  gi|13541690|ref|NP_111378.1|  2 ERKCSNCGS 10
                                  678999997 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00011
                   zf-ribbon_3  3 vrCPnCGap 11
                                  +rCP+CG++
  gi|13541690|ref|NP_111378.1| 49 YRCPQCGKV 57
                                  89*****97 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.2   0.00098      0.58       1       9 [.       4      12 ..       4      16 .. 0.81
   2 !    8.3   0.1    0.0032       1.9       1       7 [.      50      56 ..      41      57 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00098
                 zinc_ribbon_2  1 fCpnCGael 9 
                                  +C+nCG e 
  gi|13541690|ref|NP_111378.1|  4 KCSNCGSEM 12
                                  799999886 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0032
                 zinc_ribbon_2  1 fCpnCGa 7 
                                  +Cp+CG+
  gi|13541690|ref|NP_111378.1| 50 RCPQCGK 56
                                  4666665 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.0    0.0036       2.2       1      11 [.       4      17 ..       4      27 .. 0.72
   2 !    8.0   0.0    0.0028       1.7      15      26 ..      44      55 ..      37      55 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0036
                      zf-TFIIB  1 kCPkCqdele...e 11
                                  kC +C++e+e   +
  gi|13541690|ref|NP_111378.1|  4 KCSNCGSEMEsvgD 17
                                  8********95552 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0028
                      zf-TFIIB 15 ggveidyCpqCr 26
                                  + + +++CpqC+
  gi|13541690|ref|NP_111378.1| 44 QTFSLYRCPQCG 55
                                  56889******7 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 !   15.6   1.0   2.2e-05     0.013       1      55 [.       4      68 ..       4      75 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.2e-05
                zinc_ribbon_13  1 kCpKCgnteaevkeva..atG......sglskifdv..qnkkfitvsCknCgYtelYkaetsegk 55
                                  kC+ Cg++  +v++++  + G       +l  + d+   +++f +  C +Cg +++Y++++ eg+
  gi|13541690|ref|NP_111378.1|  4 KCSNCGSEMESVGDMKfrVGGftgiggMFLGGWNDMmeSTQTFSLYRCPQCGKVDFYEPRSDEGS 68
                                  588888877666655411333300111344555576334678******************99987 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.2    0.0048       2.8       7      21 ..       4      18 ..       2      22 .. 0.77
   2 !    9.4   0.1    0.0019       1.1       6      34 ..      49      56 ..      38      70 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0048
                   Zn-ribbon_8  7 rCeeCghefevlqsi 21
                                  +C +Cg+e e +  +
  gi|13541690|ref|NP_111378.1|  4 KCSNCGSEMESVGDM 18
                                  799999999976555 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0019
                   Zn-ribbon_8  6 YrCeeCghefevlqsisdapltaCPeCgs 34
                                  YrC +Cg                     +
  gi|13541690|ref|NP_111378.1| 49 YRCPQCG---------------------K 56
                                  5566665.....................3 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   8.4e-06     0.005      13      36 ..       3      56 ..       1      61 [. 0.95

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 8.4e-06
                           DZR 13 rfCseCgtklkavaa..............................edrCpsCge 36
                                  r Cs+Cg+++++v +                               +rCp+Cg+
  gi|13541690|ref|NP_111378.1|  3 RKCSNCGSEMESVGDmkfrvggftgiggmflggwndmmestqtfsLYRCPQCGK 56
                                  67*********9999*************************************97 PP

>> zf-IS66  zinc-finger binding domain of transposase IS66
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.1    0.0011      0.67       1      16 [.       2      17 ..       2      21 .. 0.88
   2 ?    6.3   0.1     0.021        13      41      46 .]      50      55 ..      48      71 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0011
                       zf-IS66  1 prtCpcCGgllkpige 16
                                  +r+C++CG+++  +g+
  gi|13541690|ref|NP_111378.1|  2 ERKCSNCGSEMESVGD 17
                                  689********99997 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.021
                       zf-IS66 41 aCpcCe 46
                                  +Cp+C+
  gi|13541690|ref|NP_111378.1| 50 RCPQCG 55
                                  555554 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   0.2    0.0059       3.5       2      10 ..       4      12 ..       3      19 .. 0.67
   2 !    8.9   0.2    0.0017         1       1      14 [.      49      62 ..      49      69 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0059
                                  EETTTTCEE CS
                  TF_Zn_Ribbon  2 kCPnCgstn 10
                                  kC nCgs++
  gi|13541690|ref|NP_111378.1|  4 KCSNCGSEM 12
                                  677777654 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0017
                                  EEETTTTCEECHEE CS
                  TF_Zn_Ribbon  1 ykCPnCgstnlveD 14
                                  y+CP Cg  +++e+
  gi|13541690|ref|NP_111378.1| 49 YRCPQCGKVDFYEP 62
                                  78999999887665 PP

>> YhfH  YhfH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.4     0.002       1.2      15      24 ..       4      13 ..       2      17 .. 0.87
   2 ?    6.2   0.0     0.017        10      15      22 ..      50      57 ..      37      61 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.002
                          YhfH 15 kCteCGkeie 24
                                  kC++CG+e+e
  gi|13541690|ref|NP_111378.1|  4 KCSNCGSEME 13
                                  8********8 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.017
                          YhfH 15 kCteCGke 22
                                   C++CGk+
  gi|13541690|ref|NP_111378.1| 50 RCPQCGKV 57
                                  6*****95 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.1    0.0085       5.1       3      11 ..       5      13 ..       3      21 .. 0.89
   2 ?    7.3   0.1    0.0075       4.5      24      32 ..      50      58 ..      49      61 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0085
                                  -TTT--B-E CS
                     Nudix_N_2  3 CsqCGtpve 11
                                  Cs+CG+++e
  gi|13541690|ref|NP_111378.1|  5 CSNCGSEME 13
                                  ******987 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0075
                                  EETTTTEEE CS
                     Nudix_N_2 24 vCpaCgtih 32
                                  +Cp+Cg + 
  gi|13541690|ref|NP_111378.1| 50 RCPQCGKVD 58
                                  788888885 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 ?    3.9   0.1     0.075        45       6      12 ..       4      10 ..       1      17 [. 0.76
   2 ?   10.8   0.2   0.00049      0.29       6      17 ..      50      61 ..      50      64 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.075
                       zf-RRN7  6 pCgvCgc 12
                                   C  Cg+
  gi|13541690|ref|NP_111378.1|  4 KCSNCGS 10
                                  7999999 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00049
                       zf-RRN7  6 pCgvCgcrsftl 17
                                  +C++Cg ++f++
  gi|13541690|ref|NP_111378.1| 50 RCPQCGKVDFYE 61
                                  7*********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 ?   14.6   0.1     4e-05     0.024      71      97 ..       3      59 ..       1      69 [. 0.87

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4e-05
                                  EEETTTS-EEECHHH.HH.............................S-TTTSSS-E CS
                          HypA 71 vrCreCgkefeleek.al.............................rCpkCgsadv 97
                                   +C++Cg+e+e+  + ++                             rCp+Cg+ d+
  gi|13541690|ref|NP_111378.1|  3 RKCSNCGSEMESVGDmKFrvggftgiggmflggwndmmestqtfslyRCPQCGKVDF 59
                                  58*********7765444889********************************9876 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.4    0.0007      0.42       3      14 ..       2      13 ..       1      14 [. 0.90
   2 ?    4.4   0.1     0.054        32      18      28 ..      45      55 ..      37      59 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0007
                 A2L_zn_ribbon  3 lkvCsvCggngi 14
                                  +++Cs+Cg++++
  gi|13541690|ref|NP_111378.1|  2 ERKCSNCGSEME 13
                                  589*******96 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.054
                 A2L_zn_ribbon 18 eqgylvCieCg 28
                                  + + + C+ Cg
  gi|13541690|ref|NP_111378.1| 45 TFSLYRCPQCG 55
                                  557899****9 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.029        17      19      28 ..       3      13 ..       1      21 [. 0.79
   2 ?    7.7   0.0    0.0058       3.4      20      30 ..      50      60 ..      36      69 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.029
                 Zn_Tnp_IS1595 19 fvCPhCgsr.k 28
                                  + C +Cgs+ +
  gi|13541690|ref|NP_111378.1|  3 RKCSNCGSEmE 13
                                  67****99864 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0058
                 Zn_Tnp_IS1595 20 vCPhCgsrkay 30
                                  +CP Cg+  +y
  gi|13541690|ref|NP_111378.1| 50 RCPQCGKVDFY 60
                                  68999876666 PP

>> zf-HIT  HIT zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.1     0.087        52      15      20 ..       4       9 ..       1      13 [. 0.67
   2 ?   10.6   0.2   0.00064      0.38      11      20 ..      46      55 ..      43      57 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.087
                                  E-TTT- CS
                        zf-HIT 15 kCpkCn 20
                                  kC++C+
  gi|13541690|ref|NP_111378.1|  4 KCSNCG 9 
                                  566665 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00064
                                  B-SEE-TTT- CS
                        zf-HIT 11 pakYkCpkCn 20
                                  ++ Y+Cp+C+
  gi|13541690|ref|NP_111378.1| 46 FSLYRCPQCG 55
                                  678******8 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.1     0.039        23      13      33 ..       4      10 ..       2      13 .. 0.59
   2 ?   10.3   0.4   0.00086      0.51      12      23 ..      49      60 ..      44      64 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.039
                       DUF35_N 13 rCpdCGtvqfPPravCphCgs 33
                                  +              C++Cgs
  gi|13541690|ref|NP_111378.1|  4 K--------------CSNCGS 10
                                  4..............555554 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00086
                       DUF35_N 12 qrCpdCGtvqfP 23
                                   rCp CG+v f+
  gi|13541690|ref|NP_111378.1| 49 YRCPQCGKVDFY 60
                                  6********998 PP

>> GFA  Glutathione-dependent formaldehyde-activating enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   1.0   0.00052      0.31       5      64 ..       5      63 ..       4      71 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00052
                           GFA  5 CsdCrkasgsaftanavvkaealelleg.elkeykktadsgnkvtrsfCpeCgsplysees 64
                                  Cs+C     s     + ++   ++ + g  l  +++  +s+++++ + Cp+Cg   ++e++
  gi|13541690|ref|NP_111378.1|  5 CSNCGSEMESVGD--MKFRVGGFTGIGGmFLGGWNDMMESTQTFSLYRCPQCGKVDFYEPR 63
                                  5555554443333..3444557777777778899999****************98777644 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 ?    5.7   0.0     0.041        25       3      13 ..       3      13 ..       2      22 .. 0.79
   2 ?    8.1   0.1    0.0072       4.3       4      12 ..      50      58 ..      48      75 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.041
                       zf-ISL3  3 hrCPnCgsktv 13
                                  ++C nCgs + 
  gi|13541690|ref|NP_111378.1|  3 RKCSNCGSEME 13
                                  58*****9864 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0072
                       zf-ISL3  4 rCPnCgskt 12
                                  rCP+Cg++ 
  gi|13541690|ref|NP_111378.1| 50 RCPQCGKVD 58
                                  8*****984 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.1    0.0028       1.7       6      14 ..       5      13 ..       2      15 .. 0.81
   2 ?    5.3   0.4     0.025        15      23      28 ..      50      55 ..      49      57 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0028
                 zf-NADH-PPase  6 CgrCGapte 14
                                  C+ CG+++e
  gi|13541690|ref|NP_111378.1|  5 CSNCGSEME 13
                                  899999887 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.025
                 zf-NADH-PPase 23 vCpaCg 28
                                  +Cp+Cg
  gi|13541690|ref|NP_111378.1| 50 RCPQCG 55
                                  577776 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.1     0.021        13       4      14 ..       4      14 ..       2      18 .. 0.85
   2 ?    7.9   0.2    0.0038       2.3       2      10 ..      48      56 ..      47      57 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.021
                        zf_UBZ  4 lCerCgkeipe 14
                                   C+ Cg+e+++
  gi|13541690|ref|NP_111378.1|  4 KCSNCGSEMES 14
                                  6******9986 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0038
                        zf_UBZ  2 tylCerCgk 10
                                   y C++Cgk
  gi|13541690|ref|NP_111378.1| 48 LYRCPQCGK 56
                                  599*****9 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.1     0.011       6.9      30      40 ..       4      14 ..       3      26 .. 0.78
   2 ?    5.4   0.0     0.029        17      30      37 ..      50      57 ..      38      72 .. 0.69

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.011
                OrfB_Zn_ribbon 30 tCseCgsknke 40
                                  +Cs+Cgs+++ 
  gi|13541690|ref|NP_111378.1|  4 KCSNCGSEMES 14
                                  7*****99987 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.029
                OrfB_Zn_ribbon 30 tCseCgsk 37
                                  +C++Cg++
  gi|13541690|ref|NP_111378.1| 50 RCPQCGKV 57
                                  45555554 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.1      0.31   1.9e+02       6      13 ..       4      11 ..       4      13 .. 0.81
   2 ?   10.4   0.1    0.0008      0.48       4      11 ..      48      55 ..      44      59 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.31
                Zn_ribbon_SprT  6 rCtgCgre 13
                                  +C +Cg+e
  gi|13541690|ref|NP_111378.1|  4 KCSNCGSE 11
                                  699**976 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0008
                Zn_ribbon_SprT  4 vYrCtgCg 11
                                   YrC++Cg
  gi|13541690|ref|NP_111378.1| 48 LYRCPQCG 55
                                  69999999 PP

>> Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.2      0.12        70       8      16 ..       4      12 ..       3      16 .. 0.79
   2 ?    8.1   0.1    0.0035       2.1       3      15 ..      45      57 ..      43      58 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.12
                                  E-TTT--EE CS
               Desulfoferrod_N  8 kCevCGniV 16
                                  kC  CG + 
  gi|13541690|ref|NP_111378.1|  4 KCSNCGSEM 12
                                  899999765 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0035
                                  TT-EEE-TTT--E CS
               Desulfoferrod_N  3 klevYkCevCGni 15
                                  +   Y+C  CG +
  gi|13541690|ref|NP_111378.1| 45 TFSLYRCPQCGKV 57
                                  6678*******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 ?    1.9   0.5      0.43   2.6e+02      26      30 ..       5       9 ..       4      12 .. 0.70
   2 ?    9.3   0.0    0.0021       1.3      23      30 ..      48      55 ..      36      56 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.43
                                  -TTT- CS
                     zf-RING_7 26 CpeCG 30
                                  C +CG
  gi|13541690|ref|NP_111378.1|  5 CSNCG 9 
                                  77777 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0021
                                  -EE-TTT- CS
                     zf-RING_7 23 vvtCpeCG 30
                                  + +Cp+CG
  gi|13541690|ref|NP_111378.1| 48 LYRCPQCG 55
                                  78*****9 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.3    0.0097       5.8       3       9 ..       5      11 ..       4      15 .. 0.81
   2 ?    7.1   0.5    0.0076       4.5       1       7 [.      49      55 ..      49      58 .. 0.61

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0097
                  Rubredoxin_2  3 CsqCGfe 9 
                                  Cs+CG+e
  gi|13541690|ref|NP_111378.1|  5 CSNCGSE 11
                                  9999987 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0076
                  Rubredoxin_2  1 YvCsqCG 7 
                                  Y+C qCG
  gi|13541690|ref|NP_111378.1| 49 YRCPQCG 55
                                  5666665 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 ?    6.9   0.2     0.008       4.8      11      18 ..       3      10 ..       3      13 .. 0.90
   2 ?    5.2   0.2     0.026        16      12      17 ..      50      55 ..      47      57 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.008
                       zf-tcix 11 rkCpkCGt 18
                                  rkC++CG 
  gi|13541690|ref|NP_111378.1|  3 RKCSNCGS 10
                                  9******6 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.026
                       zf-tcix 12 kCpkCG 17
                                  +Cp+CG
  gi|13541690|ref|NP_111378.1| 50 RCPQCG 55
                                  7***** PP

>> DUF1451  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.2      0.66   3.9e+02     116     125 ..       4      13 ..       2      17 .. 0.80
   2 ?    9.7   0.0    0.0014      0.81     104     143 ..      20      59 ..      13      62 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.66
                       DUF1451 116 vCekCgkela 125
                                    C +Cg e++
  gi|13541690|ref|NP_111378.1|   4 KCSNCGSEME 13 
                                   5899998886 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0014
                       DUF1451 104 yqsGevvglGtlvCekCgkelalkkteeippCpkCgateF 143
                                   ++ G ++g+G +     + +++ ++t  + +Cp+Cg+  F
  gi|13541690|ref|NP_111378.1|  20 FRVGGFTGIGGMFLGGWNDMMESTQTFSLYRCPQCGKVDF 59 
                                   67788888888888888999****************9988 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.2     0.014       8.5      24      33 ..       5      14 ..       2      17 .. 0.80
   2 ?    5.3   0.3      0.03        18       8      28 ..      37      55 ..      37      66 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.014
                                  ESSSS-EEES CS
                RNA_POL_M_15KD 24 CrqCgYeepa 33
                                  C++Cg+e ++
  gi|13541690|ref|NP_111378.1|  5 CSNCGSEMES 14
                                  9999999875 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.03
                                  TSBEEEEECSCCCEEEESSSS CS
                RNA_POL_M_15KD  8 gNlLlpkedkegknfeCrqCg 28
                                  ++++++++  +   + C qCg
  gi|13541690|ref|NP_111378.1| 37 NDMMESTQTFSL--YRCPQCG 55
                                  788888887777..6699997 PP

>> Ogr_Delta  Ogr/Delta-like zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.2     0.035        21       1      10 [.       4      13 ..       4      14 .. 0.88
   2 ?    5.5   0.7     0.029        17       1       7 [.      50      56 ..      50      57 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.035
                     Ogr_Delta  1 rCPhCgapaa 10
                                  +C +Cg+++ 
  gi|13541690|ref|NP_111378.1|  4 KCSNCGSEME 13
                                  6******995 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.029
                     Ogr_Delta  1 rCPhCga 7 
                                  rCP+Cg+
  gi|13541690|ref|NP_111378.1| 50 RCPQCGK 56
                                  7****96 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 ?    5.9   0.2     0.018        11       2      11 ..       3      12 ..       2      17 .. 0.88
   2 ?   -2.3   0.1       6.8   4.1e+03      18      23 ..      29      34 ..      26      34 .. 0.78
   3 ?    5.9   0.1     0.018        11       4       9 ..      51      56 ..      49      67 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.018
                                  EE-SSS--EE CS
                zf-C4_Topoisom  2 ekCPkCggdL 11
                                  +kC  Cg+++
  gi|13541690|ref|NP_111378.1|  3 RKCSNCGSEM 12
                                  89******99 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 6.8
                                  SSEEEE CS
                zf-C4_Topoisom 18 kGkFvG 23
                                   G+F+G
  gi|13541690|ref|NP_111378.1| 29 GGMFLG 34
                                  68**98 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.018
                                  -SSS-- CS
                zf-C4_Topoisom  4 CPkCgg 9 
                                  CP+Cg+
  gi|13541690|ref|NP_111378.1| 51 CPQCGK 56
                                  ****94 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       681  (0.0379832); expected 358.6 (0.02)
Passed bias filter:                      542  (0.0302304); expected 358.6 (0.02)
Passed Vit filter:                        93  (0.00518713); expected 17.9 (0.001)
Passed Fwd filter:                        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: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 527.15
//
Query:       gi|13541691|ref|NP_111379.1|  [L=123]
Description: hypothetical protein TVN0860 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       907  (0.0505884); expected 358.6 (0.02)
Passed bias filter:                      525  (0.0292822); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 855.62
//
Query:       gi|13541692|ref|NP_111380.1|  [L=268]
Description: prephenate dehydratase [Thermoplasma volcanium GSS1]
Scores for complete 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-51  172.7   0.0    1.1e-50  172.0   0.0    1.3  1  PDT       Prephenate dehydratase
    3.6e-05   23.4   0.0    6.8e-05   22.6   0.0    1.5  1  ACT       ACT domain
     0.0024   16.8   0.1     0.0035   16.3   0.1    1.1  1  DUF711    Uncharacterised ACR (DUF711)
     0.0044   16.8   0.0        2.6    8.0   0.0    2.8  3  TusA      Sulfurtransferase TusA
  ------ inclusion threshold ------
      0.084   13.5   0.0       0.24   12.0   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 !  172.0   0.0     3e-54   1.1e-50       2     181 ..       4     174 ..       3     176 .. 0.96

  Alignments for each domain:
  == domain 1  score: 172.0 bits;  conditional E-value: 3e-54
                                   EEES-TTSHHHHHHCCCS.....EEEEES-HHHHHHHHCTTS-SEEEEEEEESSS-B-HHHHHHHHH.SSEEEEEEEEEE- CS
                           PDT   2 aylGpegtyshqAalkvfkaedvelipvasieevfeavekgeadyavvPiENsteGsVnetlDlLlkesdlkivgEvvlpi 82 
                                   +ylGp+ +ys  A++k+      + +p+++i ++f+avekg +d avvP+ENs+eG+V +tlDlL + +d++i++E++l++
  gi|13541692|ref|NP_111380.1|   4 GYLGPKMSYSFLATSKMG---YNDGVPFKTIFDLFDAVEKGGIDRAVVPVENSLEGQVGQTLDLLFS-KDVSIIEEYYLRV 80 
                                   69*************988...7789******************************************.99*********** PP

                                   --EEEE-TT--TTT--EEEE-HHHHHHTHHHHHH-.TTSEEEE-S-HHHHHHHHHHCT-TTEEEEE-HHHHHHTT-EEEEC CS
                           PDT  83 ehcLlakpktkleeikkvyShpqalgQcrkfLeehlpqvervavestaeAakkveassdkdaaaiasevaaelyglkvlee 163
                                    hc++a  +   +++k v+Shpqal Qc++++e+h  +  +++ +st++ ++k+ ++++k +a+i+se+aa++++l +l++
  gi|13541692|ref|NP_111380.1|  81 VHCIAATDN---ADVKIVHSHPQALMQCSNYIEKH--GYAVIEETSTTAGIEKLFNEQNKGHAVICSEEAASACKLTILDR 156
                                   ****77665...5**********************..******************************************** PP

                                   S-SS-S--EEEEEEEEET CS
                           PDT 164 niedkknntTRFlvlake 181
                                   +i ++++n+TRF+v++k+
  gi|13541692|ref|NP_111380.1| 157 DIGNEHDNFTRFFVITKK 174
                                   ***************987 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   1.9e-08   6.8e-05       3      37 ..     186     220 ..     184     247 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 1.9e-08
                                   EEEEEESSTTHHHHHHHHHHHTTSEEEEEEEEEES CS
                           ACT   3 lrvgvpDrPGlLarvfgaladrgiNidsieqrsse 37 
                                   + + + ++PG La +  +la++gi  ++ie+r+ +
  gi|13541692|ref|NP_111380.1| 186 IAFTLLNKPGSLASIVDVLAKYGIDMTKIESRPIK 220
                                   567889**************************985 PP

>> DUF711  Uncharacterised ACR (DUF711)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   9.7e-07    0.0035      32     151 ..      89     215 ..      78     218 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 9.7e-07
                        DUF711  32 kiyekiikkaaklvktveeieeeyGievvtkRisvtpisellaeasaeea....velakt.........ldelakevgvdf 99 
                                   +   ki+++  + + ++++  e++G+ v++   ++  i++l++e+++ +a         +         ld+   +   + 
  gi|13541692|ref|NP_111380.1|  89 NADVKIVHSHPQALMQCSNYIEKHGYAVIEETSTTAGIEKLFNEQNKGHAvicsE----EaasackltiLDRDIGNEHDN- 164
                                   45567889999999******************************99777755432....244467778899998888888. PP

                        DUF711 100 iggfsalvekgltkgdkeliesipealaetervcssvnvastkaginmdavr 151
                                      f+ +++kgl+k + + i++   +l++ + + s v v   k gi+m +++
  gi|13541692|ref|NP_111380.1| 165 FTRFFVITKKGLAKPQGDKISIAFTLLNKPGSLASIVDV-LAKYGIDMTKIE 215
                                   55688899*******************************.778*****9986 PP

>> TusA  Sulfurtransferase TusA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.0   0.00071       2.6      27      59 ..      89     121 ..      85     130 .. 0.84
   2 ?   -2.9   0.0       1.8   6.4e+03      48      62 ..     133     147 ..     133     153 .. 0.68
   3 !    5.7   0.0    0.0036        13      15      59 ..     170     216 ..     169     230 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00071
                                   T-EEEEEESSCHHHHHHHHHHHHHTEEEEEEE- CS
                          TusA  27 gevlevladdpaatediprfakklghelvevee 59 
                                   ++ ++++ ++p+a    +++ +k+g++++e + 
  gi|13541692|ref|NP_111380.1|  89 NADVKIVHSHPQALMQCSNYIEKHGYAVIEETS 121
                                   5678899********************999854 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.8
                                   HHHTEEEEEEE-GCC CS
                          TusA  48 kklghelveveeedg 62 
                                   +++gh+++  ee   
  gi|13541692|ref|NP_111380.1| 133 QNKGHAVICSEEAAS 147
                                   578999988877555 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.0036
                                   HHHHHHHCCCGCT-EEE...EEESSCHHHHHHHHHHHHHTEEEEEEE- CS
                          TusA  15 lklkkalekleegevle...vladdpaatediprfakklghelvevee 59 
                                   + +kk l+k + g+++     l++ p++   i   + k g +++++e 
  gi|13541692|ref|NP_111380.1| 170 VITKKGLAK-PQGDKISiafTLLNKPGSLASIVDVLAKYGIDMTKIES 216
                                   7899*****.9*****8777899*****************99999865 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   6.7e-05      0.24       8      43 ..     185     220 ..     182     232 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 6.7e-05
                         ACT_4   8 rleveaedrkglLaditqviseekanivsvnaktrk 43 
                                   ++  +  +++g La+i++v+++ ++++++++++  k
  gi|13541692|ref|NP_111380.1| 185 SIAFTLLNKPGSLASIVDVLAKYGIDMTKIESRPIK 220
                                   6788999***********************998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       590  (0.0329076); expected 358.6 (0.02)
Passed bias filter:                      494  (0.0275531); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-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: 00:00:00.48
# Mc/sec: 1688.67
//
Query:       gi|13541693|ref|NP_111381.1|  [L=314]
Description: cell wall biosynthesis glycosyltransferase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.1e-17   61.9   0.4      1e-16   61.2   0.4    1.4  1  Glycos_transf_2  Glycosyl transferase family 2
    9.7e-06   25.6   0.0    1.4e-05   25.1   0.0    1.2  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
  ------ inclusion threshold ------
      0.049   13.4   2.1        0.1   12.4   0.8    2.1  2  CdiI             CDI immunity 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 !   61.2   0.4   1.7e-20     1e-16       1     131 [.       7     132 ..       7     169 .. 0.86

  Alignments for each domain:
  == domain 1  score: 61.2 bits;  conditional E-value: 1.7e-20
                                   EEEEEESS-TTTHHHHHHHHHHH.GGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH--S CS
               Glycos_transf_2   1 svviptyNeektlletlesllaq.dpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglraatg 80 
                                   sv+i++yN+++ ll +++s+l+q  +++ +eiiv+++   D   ++++e      +++ i  e n+ ++g + ++l  ++g
  gi|13541693|ref|NP_111381.1|   7 SVIIIAYNRKEFLLDAIKSALDQtLDREYYEIIVIKNFQDDTIDNFIKEN-----NIKGIISE-NKSLGGKISEALYVSKG 81 
                                   8**********************9999************9999*******.....9*******.77*************** PP

                                   SEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-S CS
               Glycos_transf_2  81 dyilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkr 131
                                   +++ fl +Dd +d+++le +++ + ++ + v + ++  + +e++++  +++
  gi|13541693|ref|NP_111381.1|  82 EIVSFLEDDDMFDRQKLETVYKIFRRNTNVVYYHNVAEYIDESGKKLGRTN 132
                                   **************************7776666666666666655555444 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 !   25.1   0.0   2.3e-09   1.4e-05       1     112 [.       4     105 ..       4     155 .. 0.86

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 2.3e-09
               Glyco_tranf_2_3   1 prdlavlVptfneedvlgevlesllaqeypr..vevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksral 79 
                                   p+ ++v++ ++n+ + l++ + s+l q+ +r  +e++v+ +  d+   ++++e      +  ++ ++ ++  + +gk+   
  gi|13541693|ref|NP_111381.1|   4 PF-ISVIIIAYNRKEFLLDAIKSALDQTLDReyYEIIVIKNFQDDTIDNFIKE------N-NIKGIISEN-KSLGGKIS-- 73 
                                   67.9***********************986668******************99......3.466666655.45557765.. PP

               Glyco_tranf_2_3  80 nealravksdlvllvDdDtvvePdtlkrllqff 112
                                    eal   k+++v +++dD+  +   l+ +  +f
  gi|13541693|ref|NP_111381.1|  74 -EALYVSKGEIVSFLEDDDMFDRQKLETVYKIF 105
                                   .******************99888877777777 PP

>> CdiI  CDI immunity protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.8   1.7e-05       0.1      10      76 ..      34     103 ..      28     117 .. 0.80
   2 ?   -1.5   0.0      0.32   1.9e+03      83     103 ..     218     242 ..     204     247 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.7e-05
                                   S-EEEEEEEESSSEEE-TTS--EEE-TT--.HHHHHHHHHHHH..HT--B-SHHHH.HHH-HHHHHHHHH CS
                          CdiI  10 kfisissylesrlllldpkqslklLspdvs.dselGkairkaL..sksreiepedsddifdkekvkeryk 76 
                                   +++ i+ + +++ +  d+  + + ++  +s +++lG +i +aL  sk ++++  + dd+fd++k++  yk
  gi|13541693|ref|NP_111381.1|  34 EYYEIIVIKNFQDDTIDNFIKENNIKGIISeNKSLGGKISEALyvSKGEIVSFLEDDDMFDRQKLETVYK 103
                                   6888999999999999998888888877762678********944555677766778********99998 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.32
                                   HHHHT-S-HH....HHHTT-EEEEE CS
                          CdiI  83 meeygYkskk....alfkkmdflsv 103
                                    e y+Y skk    a+f  ++ +s+
  gi|13541693|ref|NP_111381.1| 218 TELYNYFSKKgtrrAIFNHIMEVSI 242
                                   5667776654222277777776666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       772  (0.0430587); 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:                         3  (0.000167327); expected 0.2 (1e-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: 2058.98
//
Query:       gi|13541694|ref|NP_111382.1|  [L=377]
Description: glycosyltransferase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-15   57.4   0.0    2.1e-15   56.7   0.0    1.3  1  Glycos_transf_1  Glycosyl transferases group 1
    3.5e-13   50.2   0.0    5.3e-13   49.6   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 !   56.7   0.0   2.4e-19   2.1e-15       4     127 ..     186     303 ..     184     342 .. 0.87

  Alignments for each domain:
  == domain 1  score: 56.7 bits;  conditional E-value: 2.4e-19
                                   HHHHHTTTTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSS CS
               Glycos_transf_1   4 kkrkklgknekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsre 84 
                                   + ++k +++++   +l+vgrle+ Kg+dl+i+++++++   n  vk+ + G+ge+     +++ + +   n++++g +s+ 
  gi|13541694|ref|NP_111382.1| 186 TSQFKPKARDNTVNVLFVGRLEYIKGIDLFIEVCKKFEG--NTGVKFNVSGGGEY-----SQILNDNKLPNLTYHGVLSEG 259
                                   66788888899999***********************85..7*********9999.....999999999************ PP

                                   SHHHHHHCESEEEEEESSBSS-HHHHHHHHTT--EEEET.TTTH CS
               Glycos_transf_1  85 dleellknadifvlpsisEgfGivllEAmaaglpviasn.aggp 127
                                   +l  l+ ++dif++p ++++ + v+ EA++ag  +i+s+ + g 
  gi|13541694|ref|NP_111382.1| 260 ELADLYGKCDIFLYPTRWDAQPSVIAEALSAGEYIITSQrIRGT 303
                                   **************************************976665 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.6   0.0   5.9e-17   5.3e-13       3     116 ..     199     314 ..     197     336 .. 0.77

  Alignments for each domain:
  == domain 1  score: 49.6 bits;  conditional E-value: 5.9e-17
                                   EEEEES---GG.GTHHHHHHHHHHHH.HH.EEEEEES---..HHHHHHHTT-T.TEEEE---..THHHHHHHH-SEEEE-- CS
               Glyco_trans_1_4   3 vilfvGrleenvkgvdllleavpllrkkd.vrlvivGdgprpeeleelaagleerveftGfv..edlaellaaadvfvaPs 80 
                                   ++lfvGrl e +kg+dl++e +++   +  v++ + G+g+ ++ l++  ++l ++ +++G +   +la+l+ ++d+f+ P+
  gi|13541694|ref|NP_111382.1| 199 NVLFVGRL-EYIKGIDLFIEVCKKFEGNTgVKFNVSGGGEYSQILND--NKL-PNLTYHGVLseGELADLYGKCDIFLYPT 275
                                   69******.899**************7746*******9975434542..366.9******996446*************** PP

                                   ..---SHHHHHHHHTT-EEEE-.TGGGTTT--TTSSEE- CS
               Glyco_trans_1_4  81 ..egfglkllEamaaglpvVat.dvggiaevvgengllv 116
                                        + ++ Ea++ag  ++++ ++ g+ + + e g+l 
  gi|13541694|ref|NP_111382.1| 276 rwDAQPSVIAEALSAGEYIITSqRIRGTYDDLSEKGFLE 314
                                   7669******************44557666445667664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (377 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 2511.60
//
Query:       gi|13541695|ref|NP_111383.1|  [L=367]
Description: glycosyltransferase [Thermoplasma volcanium GSS1]
Scores for complete 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   38.8   0.0    1.3e-09   37.9   0.0    1.4  1  Glycos_transf_1  Glycosyl transferases group 1
    4.6e-06   26.7   0.0    7.6e-06   26.0   0.0    1.3  1  Glyco_transf_4   Glycosyltransferase Family 4
    1.7e-05   25.3   0.0    3.8e-05   24.1   0.0    1.7  1  Glyco_trans_1_4  Glycosyl transferases group 1
    0.00017   21.9   0.0     0.0004   20.7   0.0    1.6  1  Glyco_trans_1_2  Glycosyl transferases group 1
  ------ inclusion threshold ------
       0.12   12.1   0.0       0.19   11.5   0.0    1.2  1  Vesiculo_matrix  Vesiculovirus matrix protein


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 !   37.9   0.0   3.5e-13   1.3e-09      74     162 ..     251     337 ..     246     345 .. 0.86

  Alignments for each domain:
  == domain 1  score: 37.9 bits;  conditional E-value: 3.5e-13
                                   GGGEEECCHSSSHHHHHHCESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHH CS
               Glycos_transf_1  74 nviflgevsredleellknadifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairk 154
                                    v+ lg+++++ + ++l+ a+++++   +E++G+ + E++a+g+pvi++n +gp+  ++ +e+  ++ ++  e+l +a rk
  gi|13541695|ref|NP_111383.1| 251 GVKNLGYLDENTMVKVLSGASATLFLYNYEALGLIPFESLACGTPVITYNKQGPSLELAGNENVTFISTY--EELLDACRK 329
                                   677899999999**************************************77777777777777777777..********* PP

                                   HHHSHHHH CS
               Glycos_transf_1 155 lledeelr 162
                                   +le e+++
  gi|13541695|ref|NP_111383.1| 330 ALEREKDN 337
                                   **998543 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.0   2.1e-09   7.6e-06       5     154 ..      16     188 ..      15     198 .. 0.71

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 2.1e-09
                Glyco_transf_4   5 erhvleLaraLarrGheVtvvtpgddgpleeev...........elvvrvprvplpllkrllrslaflrrlrrllkre... 71 
                                   +r ++ LaraL r+   Vt++ ++  +++ e v           + +++ + +  +++ ++++    ++ l++    +   
  gi|13541695|ref|NP_111383.1|  16 NRLAFSLARALSRL-NSVTLFIHTITQRTKESVedyirpaelkyIKIIDQGHFGVRFSLNYQFLRKKAKELAK----Fitd 91 
                                   577899********.9*****6666666666665555666554433333333333444444444444444555....4455 PP

                Glyco_transf_4  72 ..kpDvv.Hahspaalgaallalrr.rlgiplVltvHglye..........krllkarlkplsrllralerrllrradrvi 138
                                     ++D+v  + +++ ++  +++    ++ + lV  +H++            + l +   +p++ +l+ +er  +   d ++
  gi|13541695|ref|NP_111383.1|  92 ngEYDIVfVIANEGHWLPQYIKKNSrAKVLLLVMELHDHGVvsmerypeknSMLRNIVFSPFYGFLKFFERSRFEEFDGFF 172
                                   59*****877777888888877776556666677788888888999999887777888899999999999999******** PP

                Glyco_transf_4 139 avSeatadelrerygv 154
                                   a+S +t+  ++ +yg+
  gi|13541695|ref|NP_111383.1| 173 ANSTWTKTLFEYLYGL 188
                                   *********9999994 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 !   24.1   0.0     1e-08   3.8e-05      52     133 ..     248     332 ..     213     333 .. 0.78

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 1e-08
                                   T-T.TEEEE---.TH.HHHHHHH-SEEEE--..---SHHHHHHHHTT-EEEE-TGGGT.TT--.TTSSEE--TT-HHHHHH CS
               Glyco_trans_1_4  52 gleerveftGfv.ed.laellaaadvfvaPs..egfglkllEamaaglpvVatdvggi.aevv.gengllvppgdpealae 126
                                   +l e+v+ +G++ e+ + ++l+ a+ +++    e +gl   E++a+g+pv++ + +g+  e+  +en   ++    e+l +
  gi|13541695|ref|NP_111383.1| 248 NL-EGVKNLGYLdENtMVKVLSGASATLFLYnyEALGLIPFESLACGTPVITYNKQGPsLELAgNENVTFIS--TYEELLD 325
                                   44.6999*****6336*****999998888888*********************998435555434444555..6889999 PP

                                   HHHHHHH CS
               Glyco_trans_1_4 127 ailrLle 133
                                   a+ + le
  gi|13541695|ref|NP_111383.1| 326 ACRKALE 332
                                   9888775 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   1.1e-07    0.0004       2      65 ..     273     336 ..     272     353 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 1.1e-07
               Glyco_trans_1_2   2 vLnpsrsespnlrlfEaaacGafaltddaegleelftpgkevilfedleelaekiryllanpee 65 
                                   +L++ ++e + l  fE +acG++++t   +g+   +  ++ v ++++ eel+++ r++l+ +++
  gi|13541695|ref|NP_111383.1| 273 TLFLYNYEALGLIPFESLACGTPVITYNKQGPSLELAGNENVTFISTYEELLDACRKALEREKD 336
                                   67888888899999*************9999999887776777777*************97775 PP

>> Vesiculo_matrix  Vesiculovirus matrix protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   5.4e-05      0.19     151     192 ..      51      92 ..      32      97 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 5.4e-05
               Vesiculo_matrix 151 mldveikyrkylnislyketvelsytisddkskeaaknilDa 192
                                   ++  e ky k +  ++++   +l y++  +k+ke ak i D+
  gi|13541695|ref|NP_111383.1|  51 IRPAELKYIKIIDQGHFGVRFSLNYQFLRKKAKELAKFITDN 92 
                                   577899*********************************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (367 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       542  (0.0302304); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 2252.77
//
Query:       gi|13541696|ref|NP_111384.1|  [L=58]
Description: transposase, partial [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.4e-08   33.7   0.0    3.5e-08   33.6   0.0    1.0  1  HTH_Tnp_1  Transposase
     0.0012   18.9   0.0     0.0015   18.6   0.0    1.1  1  HTH_28     Helix-turn-helix domain
  ------ inclusion threshold ------
      0.036   14.2   0.0      0.038   14.1   0.0    1.1  1  DUF1153    Protein of unknown function (DUF1153)


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 !   33.6   0.0   5.9e-12   3.5e-08       3      47 ..       3      47 ..       1      57 [. 0.90

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 5.9e-12
                     HTH_Tnp_1  3 rrrrwsdefKariVreslepgksvsevArrhgvspnqLykWrrqy 47
                                   r+ + +e+K++iV + l++  svs+++r+++++ + +y W+ + 
  gi|13541696|ref|NP_111384.1|  3 ERKVYKPEEKLKIVLQGLSGTISVSDLCRKYDIKSARFYSWKEKL 47
                                  6899**************************************997 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   2.6e-07    0.0015       1      35 [.      11      46 ..      11      48 .. 0.95

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2.6e-07
                        HTH_28  1 qRleiikllaaGh.svreaArelgisrrtvyrWikr 35
                                  ++l+i+++ ++G  sv++++r++ i + + y+W  +
  gi|13541696|ref|NP_111384.1| 11 EKLKIVLQGLSGTiSVSDLCRKYDIKSARFYSWKEK 46
                                  69*******************************865 PP

>> DUF1153  Protein of unknown function (DUF1153)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   6.4e-06     0.038      35      73 ..      12      50 ..       2      55 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 6.4e-06
                                  HHHHHHHHHCTTS-HHHHHHCTTSSHHHHHHHHHHCCT- CS
                       DUF1153 35 KaevvaavrggLlsleealerYklseeEfasWqkaverh 73
                                  K ++v    +g +s+++ +++Y++ +  f sW++ + r+
  gi|13541696|ref|NP_111384.1| 12 KLKIVLQGLSGTISVSDLCRKYDIKSARFYSWKEKLMRS 50
                                  566666666899*********************988775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       359  (0.0200234); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.29s 00:00:00.71 Elapsed: 00:00:00.47
# Mc/sec: 372.73
//
Query:       gi|13541697|ref|NP_111385.1|  [L=121]
Description: hypothetical protein TVN0866 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.012   15.8   0.0      0.092   13.0   0.0    1.9  2  HTH_Tnp_Tc3_2  Transposase
      0.041   14.3   0.0      0.062   13.7   0.0    1.3  1  GP68           Phage protein Gp68
      0.043   14.4   0.0      0.066   13.8   0.0    1.3  1  HTH_32         Homeodomain-like domain


Domain annotation for each model (and alignments):
>> HTH_Tnp_Tc3_2  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.12     7e+02      32      50 ..      11      28 ..       9      38 .. 0.76
   2 ?   13.0   0.0   1.5e-05     0.092       6      45 ..      68     108 ..      65     117 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.12
                 HTH_Tnp_Tc3_2 32 reTirrrLrkaglkkrkpr 50
                                  ++T+ + + +ag+++   +
  gi|13541697|ref|NP_111385.1| 11 HRTVMNAMERAGYSGKA-T 28
                                  689*********99854.3 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 1.5e-05
                 HTH_Tnp_Tc3_2   6 rlvrkdPritlreLanelkee.GksvsreTirrrLrkaglk 45 
                                    + rk+P++++re+a  l +e  +  s + + r+L+k++l 
  gi|13541697|ref|NP_111385.1|  68 GYRRKQPEMSFREIAYTLIDEdLTYLSPQSVYRILKKHDLI 108
                                   5679****************988889************995 PP

>> GP68  Phage protein Gp68
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0     1e-05     0.062      22      40 ..      15      33 ..       3      44 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1e-05
                          GP68 22 vlrmrraGykGaailkllk 40
                                  +  m+raGy G+a+lk+l+
  gi|13541697|ref|NP_111385.1| 15 MNAMERAGYSGKATLKILR 33
                                  457**************97 PP

>> HTH_32  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   1.1e-05     0.066      31      73 .]      60     102 ..      50     102 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.1e-05
                        HTH_32  31 devrariiallreeprWsprqlaarlaeregvkvShstvyriL 73 
                                   ++ +  +i  +r++p++s r++a  l +++   +S+ +vyriL
  gi|13541697|ref|NP_111385.1|  60 EDDEWIVIGYRRKQPEMSFREIAYTLIDEDLTYLSPQSVYRIL 102
                                   66677788899899************7777666*********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       449  (0.0250432); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 764.90
//
Query:       gi|13541698|ref|NP_111386.1|  [L=156]
Description: hypothetical protein TVN0867 [Thermoplasma volcanium GSS1]
Scores for complete sequence (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    1.4e-16   60.8   0.0    1.1  1  rve            Integrase core domain
    0.00019   21.2   0.2    0.00052   19.7   0.1    1.8  2  rve_3          Integrase core domain
    0.00079   19.7   0.1      0.001   19.3   0.1    1.2  1  DDE_Tnp_IS240  DDE domain


Domain annotation for each model (and alignments):
>> rve  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.8   0.0   2.3e-20   1.4e-16      15     119 .]       3     107 ..       1     107 [. 0.94

  Alignments for each domain:
  == domain 1  score: 60.8 bits;  conditional E-value: 2.3e-20
                           rve  15 vripdgggkayllvvvddfsrlilaealsdemdastvlalleravarfggve..pervlsDngseytskafrefladlgir 93 
                                   ++   +g++ yll+++d +sr+i+ + l  +md +++    +ra++ + ++     +++sDngs++++ +f+ +l++++ +
  gi|13541698|ref|NP_111386.1|   3 IK--INGRFFYLLIFIDEYSRYIVHHSLLISMDVDSISMEAQRAIDTLRKSSlaEPVIQSDNGSSFIAMEFKHVLRENHLT 81 
                                   44..44668*****************************************9999889************************ PP

                           rve  94 vsftrpgrpqdnGkvErfhrtlkdei 119
                                   +++ rp+  + n++vEr+++t+++ +
  gi|13541698|ref|NP_111386.1|  82 QKLIRPHTQENNAIVERANKTMRESW 107
                                   **********************9976 PP

>> rve_3  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       1.4   8.2e+03      21      34 ..      43      56 ..      40      61 .. 0.63
   2 !   19.7   0.1   8.8e-08   0.00052       3      34 ..      80     111 ..      78     121 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 1.4
                         rve_3 21 sfngtlrdellnee 34
                                  + + tlr+  l e+
  gi|13541698|ref|NP_111386.1| 43 RAIDTLRKSSLAEP 56
                                  55667777666655 PP

  == domain 2  score: 19.7 bits;  conditional E-value: 8.8e-08
                         rve_3   3 ielsyiapgkPqqNglvEsfngtlrdellnee 34 
                                   +++++i+p++   N+ vE+ n+t+r+ ++ ++
  gi|13541698|ref|NP_111386.1|  80 LTQKLIRPHTQENNAIVERANKTMRESWYLSY 111
                                   6899***********************98765 PP

>> DDE_Tnp_IS240  DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.1   1.7e-07     0.001      10     110 ..       2     107 ..       1     128 [. 0.82

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.7e-07
                 DDE_Tnp_IS240  10 yvkikGkwaYlyravDkegr.ildflvskrRdtkaakaflrkalkkek...lepeeivtD.kasayasalkelkregelfd 85 
                                   y+ki+G+  Yl   +D+ +r i+   +    d+++     ++a++  +   l + +i  D ++s  a  +k++ re +l++
  gi|13541698|ref|NP_111386.1|   2 YIKINGRFFYLLIFIDEYSRyIVHHSLLISMDVDSISMEAQRAIDTLRkssLAEPVIQSDnGSSFIAMEFKHVLRENHLTQ 82 
                                   9***********************9999999999888777777776655445555566661555557789*******9999 PP

                 DDE_Tnp_IS240  86 evshvqvkylnnriEsdhrtlKkrl 110
                                   +  + +++ +n ++E+ ++t++++ 
  gi|13541698|ref|NP_111386.1|  83 KLIRPHTQENNAIVERANKTMRESW 107
                                   9999999999999*******99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       572  (0.0319036); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.32s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 948.28
//
Query:       gi|13541699|ref|NP_111387.1|  [L=183]
Description: hypothetical protein TVN0868, partial [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       481  (0.026828); 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:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.30s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1275.98
//
Query:       gi|13541700|ref|NP_111388.1|  [L=270]
Description: cell wall biosynthesis glycosyltransferase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-12   47.0   1.0    3.3e-12   46.5   0.9    1.3  1  Glycos_transf_2  Glycosyl transferase family 2
    0.00093   17.9   1.5     0.0013   17.4   1.5    1.2  1  Fiji_64_capsid   Fijivirus 64 kDa capsid 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 !   46.5   0.9   3.7e-16   3.3e-12       3     132 ..      10     136 ..       8     176 .. 0.80

  Alignments for each domain:
  == domain 1  score: 46.5 bits;  conditional E-value: 3.7e-16
                                   EEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCH..C-TTEEEEEESSS-HHHHHHHHHHHH--SS CS
               Glycos_transf_2   3 viptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelak..edprvrvirreenvGkagalnaglraatgd 81 
                                    i+tyN  k l e+l+ l +      + +++vD++S  + ++ + ++ +   + +  +i++e n G a aln+g+++   +
  gi|13541700|ref|NP_111388.1|  10 LIVTYNPDKRLIESLTKLEKL----VDFVVIVDNNS--N-KSPVLDYISnnIFNDRYLIQLEDNLGIAYALNTGIKYILEK 83 
                                   699******999999999999....9**********..4.444445544488899999********************999 PP

                                   ....EEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SS CS
               Glycos_transf_2  82 ....yilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrv 132
                                       yil+lD+D++p  d++++l+++++       +g +  i++++ +i+  + v
  gi|13541700|ref|NP_111388.1|  84 ghydYILTLDQDTVPLIDDIKELIKRANSIYS--NIGIIALISKMDPKIPEFTDV 136
                                   9999***********************99666..666666666666666665555 PP

>> Fiji_64_capsid  Fijivirus 64 kDa capsid protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   1.5   1.5e-07    0.0013      20      96 ..      29     108 ..       8     126 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.5e-07
                Fiji_64_capsid  20 rlsdtiil..ndkpkitllsyf.dnifteaniikapkehsvqstvniyvklellkrlydrlqsvdtstlpyisqikealr 96 
                                   +l d +++  n+  k  +l y+ +nif +  +i+   +  +  ++n  +k  l k  yd + ++d  t+p i +ike ++
  gi|13541700|ref|NP_111388.1|  29 KLVDFVVIvdNNSNKSPVLDYIsNNIFNDRYLIQLEDNLGIAYALNTGIKYILEKGHYDYILTLDQDTVPLIDDIKELIK 108
                                   56665444126778999***98458****************************************************876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       479  (0.0267165); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1703.40
//
Query:       gi|13541701|ref|NP_111389.1|  [L=72]
Description: hypothetical protein TVN0870, partial [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.9e-09   34.8   0.1    8.4e-09   34.8   0.1    1.0  1  Transposase_mut  Transposase, Mutator family


Domain annotation for each model (and alignments):
>> Transposase_mut  Transposase, Mutator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.8   0.1   4.7e-13   8.4e-09     230     300 ..       1      71 [.       1      72 [] 0.97

  Alignments for each domain:
  == domain 1  score: 34.8 bits;  conditional E-value: 4.7e-13
               Transposase_mut 230 lvvsDahkGLvkaisavfpeaavQrCrvHllrnllakvpkkkadkvaealksiykaedaeearealeefle 300
                                   ++v+D+ k L + + + +  ++ Q C++H+lr l + v kk+ad+++++  +++k  + eea  +++ef +
  gi|13541701|ref|NP_111389.1|   1 MIVADGIKNLDEEVMEIYNRSEFQLCTIHYLRGLKSDVRKKDADDITNDGDKMFKCDNKEEAIIKFNEFKN 71 
                                   689************************************************************99999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (72 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.29s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 488.88
//
Query:       gi|13541702|ref|NP_111390.1|  [L=170]
Description: cell wall biosynthesis glycosyltransferase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.015   15.1   0.0      0.021   14.7   0.0    1.3  1  Glycos_transf_2  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 ?   14.7   0.0   1.2e-06     0.021      66     122 ..       7      61 ..       2     100 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.2e-06
                                   HHHHHHHHHHHH--SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECC CS
               Glycos_transf_2  66 GkagalnaglraatgdyilflDaDdepdpdwleklvealekdgadvvlgqrprifge 122
                                    ++g +   l+ ++g+++ fl +Dd ++ ++le + + +++++a   +++     ++
  gi|13541702|ref|NP_111390.1|   7 SLSGKIYDTLKITNGNVVSFLEDDDLFTSNKLEIVFNLFKNENA--CYYHNASEIVD 61 
                                   5778888899*******************************776..33333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      234  (0.0130515); 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: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1160.95
//
Query:       gi|13541703|ref|NP_111391.1|  [L=150]
Description: glycosyltransferase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-23   82.7   0.0    2.8e-23   82.3   0.0    1.1  1  Glycos_transf_1  Glycosyl transferases group 1
    3.1e-15   56.8   0.0    3.7e-15   56.5   0.0    1.2  1  Glyco_trans_1_4  Glycosyl transferases group 1
    4.4e-09   36.6   0.0    6.4e-09   36.1   0.0    1.2  1  Glyco_trans_1_2  Glycosyl transferases group 1


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.3   0.0   4.6e-27   2.8e-23      70     169 ..      23     122 ..       7     125 .. 0.97

  Alignments for each domain:
  == domain 1  score: 82.3 bits;  conditional E-value: 4.6e-27
                                   CTTCGGGEEECCHSSSHHHHHHCESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHH CS
               Glycos_transf_1  70 elsdnviflgevsredleellknadifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealae 150
                                    +++++i++ ++sr+ l  l++++ ifvlpsi Eg++ ++lEAma+g++v+++++gg+ e++kdg +G++++  +   l +
  gi|13541703|ref|NP_111391.1|  23 DIRNEIIYYYRLSRKVLLGLYNKSIIFVLPSIVEGMPSPPLEAMACGCAVVVTDNGGVNEYIKDGLNGIVCPVRDSYCLYQ 103
                                   6899***************************************************************************** PP

                                   HHHHHHHSHHHHHHHHHHH CS
               Glycos_transf_1 151 airklledeelrerlgena 169
                                   +++ l++++ lre++++ +
  gi|13541703|ref|NP_111391.1| 104 KVILLINNKALREQMIQDG 122
                                   ***************9977 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 !   56.5   0.0   6.3e-19   3.7e-15      33     134 .]       8     111 ..       1     111 [. 0.81

  Alignments for each domain:
  == domain 1  score: 56.5 bits;  conditional E-value: 6.3e-19
                                   EEEEES---..HHHHHHHTT-T.TEEEE---..THHHHHHHH-SEEEE--..---SHHHHHHHHTT-EEEE-TGGGTTT-- CS
               Glyco_trans_1_4  33 rlvivGdgprpeeleelaagleerveftGfv..edlaellaaadvfvaPs..egfglkllEamaaglpvVatdvggiaevv 109
                                   +++  Gd + + e+ +   ++++++++  ++  + l  l++++ +fv+Ps  eg++   lEama+g++vV+td gg++e++
  gi|13541703|ref|NP_111391.1|   8 KITAFGDYKLD-EIPA---DIRNEIIYYYRLsrKVLLGLYNKSIIFVLPSivEGMPSPPLEAMACGCAVVVTDNGGVNEYI 84 
                                   55556654322.3432...44566777777754449999****************************************** PP

                                   ..TTSSEE--TT-HHHHHHHHHHHHH- CS
               Glyco_trans_1_4 110 ..gengllvppgdpealaeailrLled 134
                                     g ng+++p +d+  l ++++ L+++
  gi|13541703|ref|NP_111391.1|  85 kdGLNGIVCPVRDSYCLYQKVILLINN 111
                                   *99******************999986 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 !   36.1   0.0   1.1e-12   6.4e-09       2      87 ..      49     135 ..      43     140 .. 0.91

  Alignments for each domain:
  == domain 1  score: 36.1 bits;  conditional E-value: 1.1e-12
               Glyco_trans_1_2   2 vLnpsrsespnlrlfEaaacGafaltddaegleelftpgkevilfe..dleelaekiryllanpeerraiaeaarervlae 80 
                                   ++ ps  e++    +Ea+acG+ ++++d  g+ e++++g  +i+    d   l +k+  l++n ++r+++ + + e   +e
  gi|13541703|ref|NP_111391.1|  49 FVLPSIVEGMPSPPLEAMACGCAVVVTDNGGVNEYIKDGLNGIVCPvrDSYCLYQKVILLINNKALREQMIQDGLET-AKE 128
                                   55677888888899**************************99999999****************************9.899 PP

               Glyco_trans_1_2  81 htydhra 87 
                                   ++yd+  
  gi|13541703|ref|NP_111391.1| 129 FSYDNMN 135
                                   9999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.51
# Mc/sec: 891.30
//
Query:       gi|13541704|ref|NP_111392.1|  [L=291]
Description: SAM-dependent methyltransferase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.4e-11   43.5   0.2    7.2e-11   42.4   0.2    1.5  1  Methyltransf_21  Methyltransferase FkbM domain
    3.3e-05   23.7   2.1    0.00035   20.4   0.1    2.4  3  Met_10           Met-10+ like-protein
    3.5e-05   23.8   0.1    0.00094   19.1   0.0    2.3  2  Methyltransf_18  Methyltransferase domain
  ------ inclusion threshold ------
      0.015   14.9   0.1       0.03   13.9   0.1    1.6  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
      0.042   13.4   0.1       0.06   12.9   0.1    1.3  1  Methyltransf_22  Methyltransferase domain


Domain annotation for each model (and alignments):
>> Methyltransf_21  Methyltransferase FkbM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.4   0.2     2e-14   7.2e-11       1     172 [.     114     261 ..     114     262 .. 0.74

  Alignments for each domain:
  == domain 1  score: 42.4 bits;  conditional E-value: 2e-14
               Methyltransf_21   1 dvGanigvwdsfanltarlcggggevlaiEPvpnslpkfeklranlltlavgndvglyelivegksg..gkyfpfavgdtn 79 
                                   d+Ganig  ds ++++   +++ ++v+a+EP p+    ++    n     + n  +l + i+  ++g  ++ +   + d  
  gi|13541704|ref|NP_111392.1| 114 DIGANIG--DSSIYFA---LNNAKKVIALEPYPY---SYNIALKN-----IKNY-DLQDKIILLNAGygQDGTIKVDPDFK 180
                                   9******..9999996...779999*********...99999999.....4444.23333333333334445555555555 PP

               Methyltransf_21  80 gfstssvlggedaryievpvvtldsfleeikksrid..llkiDvEGaElevLeGaqkglkrcqpnlivvEvhkfkefetel 158
                                   + +t      + ++ +++  + l ++l ++    id  +lk+D+EG E++ L+ ++++lk+  +  i +E h         
  gi|13541704|ref|NP_111392.1| 181 NPGTINLR--SFTDGMDIKILSLKTLLSDY---QIDkaVLKMDCEGCEYNLLKEDNDTLKK--FERIEIEYHY-------G 247
                                   55555544..78999999999999999999...88888**************999999977..3335567775.......5 PP

               Methyltransf_21 159 fdeirqflrecgyr 172
                                    +++ ++l+e+g+ 
  gi|13541704|ref|NP_111392.1| 248 YEKLKDKLEEAGFT 261
                                   67788888888875 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0      0.85   3.1e+03     115     138 ..      55      76 ..      13      87 .. 0.55
   2 !   20.4   0.1   9.9e-08   0.00035      99     155 ..     107     162 ..      99     170 .. 0.90
   3 ?    2.6   0.1     0.028     1e+02       6      93 ..     193     281 ..     188     290 .. 0.69

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.85
                                   HHHCCHHTTSSEEEEEES-HHHHH CS
                        Met_10 115 aipiakyskakrvlaidlnPesvk 138
                                   ++      ++  ++ ++l+ +s+k
  gi|13541704|ref|NP_111392.1|  55 SVLFTT--RNDHIYNVNLEGNSIK 76 
                                   333332..4445555555555555 PP

  == domain 2  score: 20.4 bits;  conditional E-value: 9.9e-08
                                   -TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEEE CS
                        Met_10  99 eegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekvvkp 155
                                    e+e+V+d+ A iG  +i  a   +ak+v+a +  P+s++   +nik  ++++++  
  gi|13541704|ref|NP_111392.1| 107 VENETVIDIGANIGDSSIYFAL-NNAKKVIALEPYPYSYNIALKNIKNYDLQDKIIL 162
                                   589******************6.99**********************9999998855 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.028
                                   ETTEEEEEB-TTSSHHHHHHHHHHHHHSS-SCEEEE-S-.SBTTTTB--EEEEEES-.SEEEEEETTEEEEEETTTS---G CS
                        Met_10   6 iGdvvilnlreelkeykkvigevildktkvktvlrkvse.vegefRtfelevlaGsdstetihkEngcrfklDvskvyfss 85 
                                     d+ il l++ l++y+ + + + +d + ++  l k+++    +f + e+e  +G ++++ + +E g +        +f++
  gi|13541704|ref|NP_111392.1| 193 GMDIKILSLKTLLSDYQIDKAVLKMDCEGCEYNLLKEDNdTLKKFERIEIEYHYGYEKLKDKLEEAGFTVTYTKPVKLFNK 273
                                   558999999999999876655556666699987777776135678888999999999898888888877665444445665 PP

                                   GGHHHHHH CS
                        Met_10  86 kleaErer 93 
                                     ++  +r
  gi|13541704|ref|NP_111392.1| 274 DATEHNMR 281
                                   55555555 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   2.6e-07   0.00094      14      69 ..     108     162 ..     100     175 .. 0.87
   2 ?    2.2   0.0     0.044   1.6e+02      98     139 ..     225     266 ..     203     273 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 2.6e-07
               Methyltransf_18  14 kgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkiev 69 
                                   ++++v+DiG+  g  +iy +  ++akkvia +  + +++ a +ni++++l+dki +
  gi|13541704|ref|NP_111392.1| 108 ENETVIDIGANIGDSSIYFAL-NNAKKVIALEPYPYSYNIALKNIKNYDLQDKIIL 162
                                   4779***************96.5689**************************9976 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.044
               Methyltransf_18  98 eILeeakeklkkikklilqpnseaeelRkylvengfkiedEe 139
                                   ++L+e++++lkk++++ ++ +  +e+l++ l e gf+++  +
  gi|13541704|ref|NP_111392.1| 225 NLLKEDNDTLKKFERIEIEYHYGYEKLKDKLEEAGFTVTYTK 266
                                   678999999999999999999999999999999999987655 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   8.4e-06      0.03       2      59 ..     110     168 ..     109     246 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 8.4e-06
               Methyltransf_15   2 rvilDlfsGaGGnviqfalv.fekviaieinleklacaqhNaevYgvsdkitlvlgdvf 59 
                                   ++++D+ +  G  +i fal+  +kvia+e  +   ++a +N + Y+ +dki l  + + 
  gi|13541704|ref|NP_111392.1| 110 ETVIDIGANIGDSSIYFALNnAKKVIALEPYPYSYNIALKNIKNYDLQDKIILLNAGYG 168
                                   5789999999********87689****************************98876655 PP

>> Methyltransf_22  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   1.7e-05      0.06     168     240 ..     204     277 ..     148     286 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.7e-05
               Methyltransf_22 168 klghklrtidvlkidcekcewenykdwvevdi..rqilvevhglpskkaaplaasdffdafrkasyvrfskevnv 240
                                    l+  +    vlk+dce ce++  k+  ++    ++i +e h   +k +  l+ + f  +++k     f+k++  
  gi|13541704|ref|NP_111392.1| 204 LLSDYQIDKAVLKMDCEGCEYNLLKEDNDTLKkfERIEIEYHYGYEKLKDKLEEAGFTVTYTKPV-KLFNKDATE 277
                                   33333344469**********99987665433237888888876666665555555555554433.245555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       659  (0.0367561); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); 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: 0.59u 0.32s 00:00:00.90 Elapsed: 00:00:00.52
# Mc/sec: 1679.59
//
Query:       gi|13541705|ref|NP_111393.1|  [L=105]
Description: integrase/recombinase, partial [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      8e-09   35.5   0.0    8.7e-09   35.4   0.0    1.1  1  Phage_integrase  Phage integrase family


Domain annotation for each model (and alignments):
>> Phage_integrase  Phage integrase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.4   0.0   4.9e-13   8.7e-09       4      67 ..      23      82 ..      20     103 .. 0.78

  Alignments for each domain:
  == domain 1  score: 35.4 bits;  conditional E-value: 4.9e-13
                                  HHHHHHHHHHCCGCHHHHHHHHHHHHHHHHT--HHHHTT-BGGGEECTTTEEEEEEEECSSSSE CS
               Phage_integrase  4 tedeverllaaleeslkirdklllellyetGlRisEllsLrvkdldlengvilvheregKgske 67
                                  t   v++++ ++++   +rdk+++ +ly +G R+sE+lsL+++d+   +++  +   +gK++  
  gi|13541705|ref|NP_111393.1| 23 TRTGVDEIIRNCNN---ARDKAIISILYYSGCRVSEILSLKISDIVY-EEYCVISHFHGKTGNR 82
                                  56678999999999...****************************55.5555555666666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       320  (0.0178482); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); 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 0.27s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 704.46
//
Query:       gi|13541706|ref|NP_111394.1|  [L=57]
Description: aldo/keto reductase, partial [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.3e-14   52.8   0.0    3.4e-14   52.8   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 !   52.8   0.0   1.9e-18   3.4e-14      89     143 ..       3      56 ..       1      57 [] 0.95

  Alignments for each domain:
  == domain 1  score: 52.8 bits;  conditional E-value: 1.9e-18
                                   HHHHHHHHHT-S-EEEEEE-S--TTS-.HHHHHHHHHHHHHTTSEEEEEEES--H CS
                  Aldo_ket_red  89 sleeslkrLgtdyvDllllHrpdpslpsieevldaleelvkeGkiraiGvSnfsv 143
                                   + e+sl +Lg dy+Dl+++ +p+p++  i e+++a eel +eGki++iG+ nfs+
  gi|13541706|ref|NP_111394.1|   3 AREASLNKLGIDYLDLYQFNWPNPDVL-IGETMKATEELMDEGKIKNIGINNFSA 56 
                                   5689***********************.*************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (57 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       253  (0.0141112); expected 358.6 (0.02)
Passed bias filter:                      215  (0.0119917); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 385.03
//
Query:       gi|13541707|ref|NP_111395.1|  [L=351]
Description: cell wall biosynthesis glycosyltransferase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-16   60.5   1.4    2.8e-16   59.8   1.4    1.3  1  Glycos_transf_2  Glycosyl transferase family 2
    1.3e-06   28.5   0.0    1.7e-06   28.1   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 !   59.8   1.4   3.1e-20   2.8e-16       1     133 [.      10     145 ..      10     181 .. 0.82

  Alignments for each domain:
  == domain 1  score: 59.8 bits;  conditional E-value: 3.1e-20
                                   EEEEEESS-TTTHHHHHHHHHHH.GGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH--S CS
               Glycos_transf_2   1 svviptyNeektlletlesllaq.dpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglraatg 80 
                                   sv+i++yN+++ ll +++s+l+q  +++ +eiiv+++   D   ++++e      +++ i  e n+ ++g + ++l  ++g
  gi|13541707|ref|NP_111395.1|  10 SVIIIAYNRKEFLLDAIKSALNQtLDREYYEIIVIKNFQDDTIDNFIKEN-----NIKGIISE-NKSLGGKISEALYVSKG 84 
                                   8**********************9999************9999*******.....9*******.77*************** PP

                                   SEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SS.........E CS
               Glycos_transf_2  81 dyilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrv.........g 133
                                   +++ fl +Dd + p++l+++++ +   ++ +v+++  +i+ +++ +e  +           +
  gi|13541707|ref|NP_111395.1|  85 EIVSFLEDDDLFFPNKLREVYDIFIS-NPNLVYYHNNFIKTNNRLFEIDYSEnkknkkiflK 145
                                   **************************.66688888777777777776665533333333333 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 !   28.1   0.0   1.9e-10   1.7e-06       4     119 ..       9     114 ..       7     139 .. 0.84

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 1.9e-10
               Glyco_tranf_2_3   4 lavlVptfneedvlgevlesllaqeypr..vevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksralnea 82 
                                   ++v++ ++n+ + l++ + s+l+q+ +r  +e++v+ +  d+   ++++e      +  ++ ++ ++  + +gk+    ea
  gi|13541707|ref|NP_111395.1|   9 ISVIIIAYNRKEFLLDAIKSALNQTLDReyYEIIVIKNFQDDTIDNFIKE------N-NIKGIISEN-KSLGGKIS---EA 78 
                                   89**********************986668******************99......3.466666655.45557765...** PP

               Glyco_tranf_2_3  83 lravksdlvllvDdDtvvePdtlkrllqffltpkvga 119
                                   l   k+++v +++dD++  P+ l+ +  +f  +++  
  gi|13541707|ref|NP_111395.1|  79 LYVSKGEIVSFLEDDDLFFPNKLREVYDIF-ISNPNL 114
                                   ***********************9999988.444455 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (351 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       844  (0.0470746); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 2351.46
//
Query:       gi|13541708|ref|NP_111396.1|  [L=376]
Description: glycosyltransferase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-12   48.4   0.0    1.6e-12   47.8   0.0    1.3  1  Glyco_transf_4   Glycosyltransferase Family 4
    3.5e-10   39.7   0.0    6.7e-10   38.8   0.0    1.4  1  Glycos_transf_1  Glycosyl transferases group 1
    1.1e-08   35.6   0.0    1.6e-08   35.2   0.0    1.3  1  Glyco_trans_4_4  Glycosyl transferase 4-like domain
    6.7e-05   23.3   0.0    0.00015   22.2   0.0    1.5  1  Glyco_trans_1_4  Glycosyl transferases group 1
  ------ inclusion threshold ------
      0.026   14.7   0.0      0.056   13.6   0.0    1.5  1  Flavodoxin_1     Flavodoxin
       0.05   13.7   0.0       0.12   12.4   0.0    1.7  1  Glyco_transf_28  Glycosyltransferase family 28 N-terminal dom
      0.052   13.6   0.1       0.22   11.6   0.1    2.0  2  P_C10            Protein C10


Domain annotation for each model (and alignments):
>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.8   0.0   6.1e-16   1.6e-12       3     155 ..      14     182 ..      12     186 .. 0.81

  Alignments for each domain:
  == domain 1  score: 47.8 bits;  conditional E-value: 6.1e-16
                Glyco_transf_4   3 GverhvleLaraLarrGheVtvv...tpgddgpleeev...............elvvrvprvplpllkrllr..slaflrr 63 
                                   G++  +   a++L ++G++V +v   + ++++ l ++                +l+++++   + l++r     ++  + +
  gi|13541708|ref|NP_111396.1|  14 GAQKIAIAEAKQLTKMGYKVKLVflrATESGRNLLNKLedidyeifsgenykpKLIYSFITGLFMLDRRGEGtvDYNLINK 94 
                                   778888889**************8874444444444446999999**999999888888888887777766511667799* PP

                Glyco_transf_4  64 lrrllkrekpDvvHahspaalgaallalrrrlgiplVltvHglyekrllkarlkplsrllralerrllrradrviavSeat 144
                                   ++r +k+++ D + +h+ +a+ +a+l+++r+lgip+ + +H +      k++   l +++ ++er +l++ad+++av+e++
  gi|13541708|ref|NP_111396.1|  95 FARSVKKGDADYIICHDQWAG-LAGLKIKRKLGIPYSVMMHEHVN---GKYNVPVLGKIATKMERDVLKNADKIFAVTEKI 171
                                   *****************9987.555677777*************3...344444567888889****************** PP

                Glyco_transf_4 145 adelrerygvp 155
                                   a+++ + yg++
  gi|13541708|ref|NP_111396.1| 172 ANNVTSIYGFK 182
                                   ********987 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 !   38.8   0.0   2.6e-13   6.7e-10       8     159 ..     195     343 ..     191     361 .. 0.86

  Alignments for each domain:
  == domain 1  score: 38.8 bits;  conditional E-value: 2.6e-13
                                   HTTTTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES....STTHHHHHHHHHHHCTTCGGGEEECCHSSS CS
               Glycos_transf_1   8 klgknekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaG...ngeeekelkklaeelelsdnviflgevsred 85 
                                    +++ e+++iil  +   k   +d+ ++ ++       p++kl ++G    ++e++ +k+ + +++l+++vi+  ++++e+
  gi|13541708|ref|NP_111396.1| 195 TKNFHERDNIILATSTWGKDRSPDTYLDIIEA-----IPDFKLYFIGrwnLKSEFEDFKNNVYKRNLQEKVIINDNMPDEE 270
                                   56777999999999999999999999999996.....599*******99989999************************** PP

                                   HHHHHHCESEEEEEESS..BSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHSH CS
               Glycos_transf_1  86 leellknadifvlpsis..EgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairkllede 159
                                   l+el+ +++ ++    +   g+G++ + A++  +pvi+  + g++++++++  G++v++n   ++++ ++ +le++
  gi|13541708|ref|NP_111396.1| 271 LDELYASSKFVIRFGGTkeYGLGTATVFAISHLTPVIIDSTLGISDIITKYGGGYIVDKN---DINKISNFILENN 343
                                   *******99888776666669***************************************...6666666666666 PP

>> Glyco_trans_4_4  Glycosyl transferase 4-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.2   0.0   6.2e-12   1.6e-08      51     148 ..      83     180 ..      14     185 .. 0.86

  Alignments for each domain:
  == domain 1  score: 35.2 bits;  conditional E-value: 6.2e-12
               Glyco_trans_4_4  51 pspladlaalralrrllrqrrerpdvvhahsptaglaarlarrrrgiplvvtlhgll.lrrgsgavrrlyralerrllrra 130
                                   ++++ d+  +  ++r +  ++   d +++h+  agla++ ++r+ gip+ v +h++  + +  + ++ +++ +er +l++a
  gi|13541708|ref|NP_111396.1|  83 GEGTVDYNLINKFARSV--KKGDADYIICHDQWAGLAGLKIKRKLGIPYSVMMHEHVnGKYNVPVLGKIATKMERDVLKNA 161
                                   44555666678899999..9***********88*********899*********98756666******************* PP

               Glyco_trans_4_4 131 davlvvseaeaeelra.lg 148
                                   d +++v+e +a  ++  +g
  gi|13541708|ref|NP_111396.1| 162 DKIFAVTEKIANNVTSiYG 180
                                   **********998877555 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   5.9e-08   0.00015      20     126 ..     220     337 ..     202     342 .. 0.77

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 5.9e-08
                                   HHHHHHHHH.HHEEEEEES---.....HHHHHHHT..T-T.TEEEE---..THHHHHHHH-SEEEE--...-.--SHHHHH CS
               Glyco_trans_1_4  20 lleavpllrkkdvrlvivGdgp.rp..eeleelaa..gleerveftGfv..edlaellaaadvfvaPs...e.gfglkllE 89 
                                    l+ ++++   d++l+++G+ + ++  e++++ +   +l+e+v++   +  e+l+el+a+++ ++      e g+g +++ 
  gi|13541708|ref|NP_111396.1| 220 YLDIIEAIP--DFKLYFIGRWNlKSefEDFKNNVYkrNLQEKVIINDNMpdEELDELYASSKFVIRFGgtkEyGLGTATVF 298
                                   555556666..689*****777544344444444258999*********8666********988876687758******** PP

                                   HHHTT-EEEE-TGGGTTT--...TTSSEE--TT-HHHHHH CS
               Glyco_trans_1_4  90 amaaglpvVatdvggiaevv...gengllvppgdpealae 126
                                   a ++ +pv+  ++ gi++++   g  g++v+++d +++ +
  gi|13541708|ref|NP_111396.1| 299 AISHLTPVIIDSTLGISDIItkyG-GGYIVDKNDINKISN 337
                                   ***********999******8532.57***9999887766 PP

>> Flavodoxin_1  Flavodoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   2.2e-05     0.056      10      65 ..     168     220 ..     166     252 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.2e-05
                                   HHHHHHHHHHHHHHTTTEEEEEEEEGTTSCGGGGGTHSEEEEEEEEETTTBEEGGG CS
                  Flavodoxin_1  10 teklAkqlaeelgehgfnadvvslsdydeslseieeealllvvtsTfgnGdppeng 65 
                                   tek+A+ +  + g  + ++d+v +   +  ++++ e +++++ tsT+g++  p+++
  gi|13541708|ref|NP_111396.1| 168 TEKIANNVTSIYG-FKCEPDLVGMTLQK--TKNFHERDNIILATSTWGKDRSPDTY 220
                                   89**********9.8999*******999..58********************9875 PP

>> Glyco_transf_28  Glycosyltransferase family 28 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   4.8e-05      0.12       8      71 ..      12      77 ..       5      89 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.8e-05
                                  SHHHHHHHHHHHHHHHCTT-EEE..EEEETCCCHHHHHHCCT-EEEE---GHCTT..CHHHHCCHH CS
               Glyco_transf_28  8 TgGhvfPalAlakeLkkegheVr..ylgtkrgleerlveeaglefepiageklrrklspknlkeil 71
                                  T+G   +a+A ak+L k g++V+  +l +++  ++ l++ +++ +e ++ge ++ kl+ ++++ ++
  gi|13541708|ref|NP_111396.1| 12 TAGAQKIAIAEAKQLTKMGYKVKlvFLRATESGRNLLNKLEDIDYEIFSGENYKPKLIYSFITGLF 77
                                  7788889**************************************************999998776 PP

>> P_C10  Protein C10
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   8.5e-05      0.22      17      85 ..     137     205 ..     131     210 .. 0.85
   2 ?   -2.1   0.0       1.7   4.3e+03      43      60 ..     302     322 ..     293     355 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 8.5e-05
                         P_C10  17 leqpenaakleeakesagndmlkvmqlvlPvvvqiqmevikkyGFaedreGvvkfaqlvrelekedkev 85 
                                   ++ + n+  l ++ ++++ d+lk   +++ v  +i  +v + yGF  + + v   +q ++++++ d+ +
  gi|13541708|ref|NP_111396.1| 137 VNGKYNVPVLGKIATKMERDVLKNADKIFAVTEKIANNVTSIYGFKCEPDLVGMTLQKTKNFHERDNII 205
                                   56667778889999*******************************988888877888888888877755 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.7
                         P_C10  43 lvlPvvvqiq...mevikkyG 60 
                                   ++ Pv+++      ++i+kyG
  gi|13541708|ref|NP_111396.1| 302 HLTPVIIDSTlgiSDIITKYG 322
                                   566666654311147888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (376 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       687  (0.0383178); 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:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 2480.30
//
Query:       gi|13541709|ref|NP_111397.1|  [L=87]
Description: translation initiation factor IF-1 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.062   14.1   0.0       0.08   13.7   0.0    1.1  1  PCB_OB    Penicillin-binding protein OB-like domain
       0.12   12.4   0.0        0.2   11.7   0.0    1.6  1  NLPC_P60  NlpC/P60 family


Domain annotation for each model (and alignments):
>> PCB_OB  Penicillin-binding protein OB-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0     9e-06      0.08      71     106 ..      30      69 ..      24      71 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 9e-06
                                   TTTS-B---CCCHCCC--TTEEEEEEE-TT.....S-EEE CS
                        PCB_OB  71 lsdkkqgkapksasdvlkpGdvvlvrkeed....egewrL 106
                                   +++++  ++ k ++  l+pGdv++++ +++    + ewrL
  gi|13541709|ref|NP_111397.1|  30 NNKNHLCNKGKLMNVKLSPGDVIVIQTVDEfnhiGMEWRL 69 
                                   5566778899999****************87777777877 PP

>> NLPC_P60  NlpC/P60 family
   #    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      46      71 ..      40      65 ..       8      86 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.2e-05
                                  .EEGGG--TTEEEEESGTGGESEEEE CS
                      NLPC_P60 46 eiskselkrGDLvffktkkgisHvgi 71
                                  +  + +l++GD+++++t ++ +H+g+
  gi|13541709|ref|NP_111397.1| 40 KLMNVKLSPGDVIVIQTVDEFNHIGM 65
                                  56778899*****************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.49
# Mc/sec: 532.02
//
Query:       gi|13541710|ref|NP_111398.1|  [L=858]
Description: hypothetical protein TVN0879 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (858 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1421  (0.0792571); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); 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):               0  [number of targets reported over threshold]
# CPU time: 0.70u 0.31s 00:00:01.01 Elapsed: 00:00:00.50
# Mc/sec: 5156.04
//
Query:       gi|13541711|ref|NP_111399.1|  [L=353]
Description: glycosyltransferase [Thermoplasma volcanium GSS1]
Scores for complete 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-26   91.4   0.2    8.3e-26   90.5   0.2    1.4  1  Glycos_transf_1  Glycosyl transferases group 1
    1.9e-21   76.9   0.0    3.6e-21   76.0   0.0    1.4  1  Glyco_trans_1_4  Glycosyl transferases group 1
    3.6e-14   53.1   0.0    6.9e-14   52.2   0.0    1.5  1  Glyco_transf_4   Glycosyltransferase Family 4
    0.00011   22.6   0.0     0.0004   20.7   0.0    1.9  2  Glyco_trans_1_2  Glycosyl transferases group 1
  ------ inclusion threshold ------
      0.021   14.9   0.1      0.072   13.1   0.0    1.9  2  Glyco_trans_4_2  Glycosyl transferase 4-like
      0.051   12.1   0.0      0.077   11.5   0.0    1.2  1  Glycogen_syn     Glycogen synthase
       0.19   12.2   0.0       0.61   10.5   0.0    1.8  1  Glyco_trans_4_4  Glycosyl transferase 4-like domain


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.5   0.2   3.3e-29   8.3e-26       7     165 ..     176     326 ..     171     337 .. 0.92

  Alignments for each domain:
  == domain 1  score: 90.5 bits;  conditional E-value: 3.3e-29
                                   HHTTTTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSSSHH CS
               Glycos_transf_1   7 kklgknekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsredle 87 
                                   + +gk+++   +l+ g l+k+K+++++i+ ++ l k+  +n+kl+i+G+g  ++e+k++++  +   n+ f+g++++++l 
  gi|13541711|ref|NP_111399.1| 176 FHTGKKTDNVQLLYFGGLRKYKRPEYAITIYENLYKK-IDNLKLIIVGDGILLNEIKDKVKGKNY--NIVFTGKLEYDELA 253
                                   67899999**************************888.*********************999988..************** PP

                                   HHHHCESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHSHHHHHHH CS
               Glycos_transf_1  88 ellknadifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairklledeelrerl 165
                                   ++++ + + ++ s +Eg+G ++lEA a+g+p +a +++g+ +++ dg +G+lv +  + ++ ++i  ++++e   +++
  gi|13541711|ref|NP_111399.1| 254 KIIRESWVNLHFSVTEGWGYSILEASASGTPSVAFKVPGVVDTIIDGYNGFLVNN--INEFTDKILYIIKNE---DKF 326
                                   ****************************************************965..5*************9...333 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 !   76.0   0.0   1.4e-24   3.6e-21       3     134 .]     186     322 ..     184     322 .. 0.92

  Alignments for each domain:
  == domain 1  score: 76.0 bits;  conditional E-value: 1.4e-24
                                   EEEEES---GG.GTHHHHHHHHHHHH.H.H.EEEEEES---...HHHHHHHTT-T.TEEEE---..THHHHHHHH-SEEEE CS
               Glyco_trans_1_4   3 vilfvGrleenvkgvdllleavpllrkk.d.vrlvivGdgp.rpeeleelaagleerveftGfv..edlaellaaadvfva 78 
                                    +l++G l +++k+ ++ +   + l kk d ++l+ivGdg   + e++++++g + +++ftG++  ++la+++++++v + 
  gi|13541711|ref|NP_111399.1| 186 QLLYFGGL-RKYKRPEYAITIYENLYKKiDnLKLIIVGDGIlLN-EIKDKVKGKNYNIVFTGKLeyDELAKIIRESWVNLH 264
                                   589*****.677**********999888756*********9775.9**999976678*******9888************* PP

                                   --..---SHHHHHHHHTT-EEEE-TGGGTTT--..TTSSEE--TT-HHHHHHHHHHHHH- CS
               Glyco_trans_1_4  79 Ps..egfglkllEamaaglpvVatdvggiaevv..gengllvppgdpealaeailrLled 134
                                    s  eg+g+++lEa a+g+p Va++v+g+ +++  g ng+lv+  + ++++++il ++++
  gi|13541711|ref|NP_111399.1| 265 FSvtEGWGYSILEASASGTPSVAFKVPGVVDTIidGYNGFLVN--NINEFTDKILYIIKN 322
                                   ***9************************988888********9..9*********99876 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.2   0.0   2.7e-17   6.9e-14       1     169 [.      16     174 ..      16     175 .. 0.81

  Alignments for each domain:
  == domain 1  score: 52.2 bits;  conditional E-value: 2.7e-17
                Glyco_transf_4   1 vGGverhvleLaraLarrGheVtvvtpgddgpleeevelvvrvprvplpllkrllrslaflrrlrrllkrekpDvv..... 76 
                                   +GG+er ++e+ ++L ++++ V +vt +++  le+e         v   + +r + +++ ++++r+++k+ +pDv+     
  gi|13541711|ref|NP_111399.1|  16 AGGAERTIYEVGKRLSKLNIGVNLVTVNPGNLLEYE--------NVDGIIIYRIKGNIRTHLYVRKMIKKINPDVIiddmg 88 
                                   59**********************************........4445556689999*******************76655 PP

                Glyco_transf_4  77 HahspaalgaallalrrrlgiplVltvHglyekrllkarlkplsrllralerrl..lrradrviavSeatadelrerygvp 155
                                   Ha  +++ ++         +  +V+  H ++ k+l ++ + +l +++  +e+    + + + +++ S++  ++l++ +g++
  gi|13541711|ref|NP_111399.1|  89 HAVPWFSPWFT-------DKRVIVFFRHLHA-KSLPGQVNFFLAKIITLVEKLYpiIYKNNIFVTESDTSENDLID-LGIK 160
                                   55555555544.......3445555556666.55666666666666666666667789999***************.**** PP

                Glyco_transf_4 156 pekitVipnGvDle 169
                                   +++i+ ip+GvDl+
  gi|13541711|ref|NP_111399.1| 161 KDRIVRIPPGVDLN 174
                                   ************96 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       1.7   4.4e+03      36      61 ..      97     124 ..      92     125 .. 0.85
   2 !   20.7   0.0   1.6e-07    0.0004       1      87 [.     261     343 ..     261     348 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.7
               Glyco_trans_1_2  36 lftpgkevilfe..dleelaekirylla 61 
                                   +ft+++ +++f+    ++l  +++++la
  gi|13541711|ref|NP_111399.1|  97 WFTDKRVIVFFRhlHAKSLPGQVNFFLA 124
                                   7999999999999999999999999886 PP

  == domain 2  score: 20.7 bits;  conditional E-value: 1.6e-07
               Glyco_trans_1_2   1 ivLnpsrsespnlrlfEaaacGafaltddaegleelftpgkevilfedleelaekiryllanpeerraiaeaarervlaeh 81 
                                   ++L+ s  e+  + ++Ea a+G++ ++ + +g+ + + +g  ++l+ + +e+ +ki y ++n+++       + +++ +++
  gi|13541711|ref|NP_111399.1| 261 VNLHFSVTEGWGYSILEASASGTPSVAFKVPGVVDTIIDGYNGFLVNNINEFTDKILYIIKNEDKFI----LNSRKFAENF 337
                                   57889999999999***********************************************999843....4445556666 PP

               Glyco_trans_1_2  82 tydhra 87 
                                   t+++ a
  gi|13541711|ref|NP_111399.1| 338 TWEKTA 343
                                   666665 PP

>> Glyco_trans_4_2  Glycosyl transferase 4-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   2.8e-05     0.072      15      79 ..      25      84 ..      18      88 .. 0.89
   2 ?   -2.8   0.0       2.3   5.9e+03      44      81 ..     224     264 ..     214     293 .. 0.48

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.8e-05
               Glyco_trans_4_2 15 rlakeLakrgyeVhvitpkkga.kdeleaegihvhrlkvdrkgpleylk.afklkklikkikPDvvh 79
                                  ++ k L+k ++ V ++t ++g   ++++ +gi ++r+k       ++++  + ++k+ikki+PDv++
  gi|13541711|ref|NP_111399.1| 25 EVGKRLSKLNIGVNLVTVNPGNlLEYENVDGIIIYRIK-------GNIRtHLYVRKMIKKINPDVII 84
                                  567889999999******99999**************9.......777646689***********95 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2.3
               Glyco_trans_4_2  44 gihvhrlkvdrkgpleyl..ka.fklkklikkikPDvvhah 81 
                                   gi + ++k+++kg+  ++  +  +++ +l k i   +v++h
  gi|13541711|ref|NP_111399.1| 224 GILLNEIKDKVKGKNYNIvfTGkLEYDELAKIIRESWVNLH 264
                                   55555555555554444322211233444444444444444 PP

>> Glycogen_syn  Glycogen synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0     3e-05     0.077     460     527 ..     247     325 ..     225     342 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3e-05
                                   --HHHH...HHH-SEEE---SSBSS-HHHHHHHHTT--EEE........ETTBHHHHHHHHH-TTGGGGTEEEE--SSS CS
                  Glycogen_syn 460 ldyeef...vrGchlGvfpsyyepwGytpaectvmGipsvt........tnlsGfGcfmeeliedakdyGiyivdrrfk 527
                                   l+y+e+   +r + + +  s  e wGy+  e +  G psv+        t + G+  f+ + i++ +d+ +yi+    k
  gi|13541711|ref|NP_111399.1| 247 LEYDELakiIRESWVNLHFSVTEGWGYSILEASASGTPSVAfkvpgvvdTIIDGYNGFLVNNINEFTDKILYIIKNEDK 325
                                   5676642227899999999*******************986333333336778999*****************987655 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 ?   10.5   0.0   0.00024      0.61       1     160 []      17     170 ..      17     170 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00024
               Glyco_trans_4_4   1 gGigryvaelaraLaarGheVtvltpapapgapeleedgvrvhrlpvprrpspladlaalralrrllrqrrerpdvvhahs 81 
                                   gG++r ++e+ ++L ++   V ++t +p +  + ++ dg+ ++r++           +    +r ++  ++ +pdv++   
  gi|13541711|ref|NP_111399.1|  17 GGAERTIYEVGKRLSKLNIGVNLVTVNPGNLLEYENVDGIIIYRIKGN--------IRTHLYVRKMI--KKINPDVIIDDM 87 
                                   8*************************999999999*********9876........33345689999..999999999777 PP

               Glyco_trans_4_4  82 pt.aglaarlarrrrgiplvvtlhglllrrg.sgavrrlyraler..rllrradavlvvseaeaeelralgvpadrvvvvp 158
                                    +  +++  +   +r i ++ +lh+  l+++ + +++ +++ +e+   ++     +++ s+    +l++lg+  dr+v +p
  gi|13541711|ref|NP_111399.1|  88 GHaVPWFSPWFTDKRVIVFFRHLHAKSLPGQvNFFLAKIITLVEKlyPIIYKNNIFVTESDTSENDLIDLGIKKDRIVRIP 168
                                   442556666666588889999999877766678889999988877668999999999999999999******99**99999 PP

               Glyco_trans_4_4 159 ng 160
                                   +g
  gi|13541711|ref|NP_111399.1| 169 PG 170
                                   87 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:                      332  (0.0185175); 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: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 2219.05
//
Query:       gi|13541712|ref|NP_111400.1|  [L=223]
Description: SAM-dependent methyltransferase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.2e-09   35.7   0.0    8.1e-09   35.5   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
    4.4e-07   30.5   0.0    7.3e-07   29.7   0.0    1.4  1  Methyltransf_11  Methyltransferase domain
    7.2e-07   29.9   0.0    2.7e-06   28.0   0.0    2.0  2  Methyltransf_12  Methyltransferase domain
    1.2e-05   25.2   0.0    1.5e-05   24.8   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
    0.00048   20.8   0.0    0.00072   20.2   0.0    1.4  1  Methyltransf_25  Methyltransferase domain
     0.0024   17.3   0.2          3    7.4   0.0    2.7  3  Lipid_DES        Sphingolipid Delta4-desaturase (DES)
  ------ inclusion threshold ------
      0.093   12.1   0.1       0.13   11.6   0.1    1.1  1  XRN_N            XRN 5'-3' exonuclease N-terminus


Domain annotation for each model (and alignments):
>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.5   0.0   3.1e-12   8.1e-09      75     156 ..      90     181 ..      13     183 .. 0.78

  Alignments for each domain:
  == domain 1  score: 35.5 bits;  conditional E-value: 3.1e-12
               Methyltransf_23  75 eaaepqgkfdlIvlrevlehvp.dppellrqiatllkpgGylllseplaslkedrllld.......w.lylvpag..rhis 144
                                   + +ep+ kfdl++ +e+leh+  d + ++r+ia+ll+p+G ++l++p+a  +  ++++        w +y+  +g  +hi+
  gi|13541712|ref|NP_111400.1|  90 NNPEPNSKFDLVIISETLEHIFaDDEIVMRSIANLLRPNGIIYLTVPNAARH-INRIKLlfgknifWsKYDILNGgyGHIR 169
                                   3456999**************9899**********************99755.4443333566776556666666777777 PP

               Methyltransf_23 145 ffsarslkelle 156
                                    ++  ++k +le
  gi|13541712|ref|NP_111400.1| 170 EYTVIEVKSMLE 181
                                   777777776666 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.7   0.0   2.9e-10   7.3e-07      18      95 ..      56     132 ..      40     133 .. 0.82

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 2.9e-10
                                   TSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCT.SS-TT-EEEEEEES-CCC-.CCHHHHHHHHHHHEEEEEEEE CS
               Methyltransf_11  18 garvvgvDlskemlklakekaseeglkvefvvadaekl.pfednsfDlvvssevlhhv.edpekalkeiaRvLkpgGllv 95 
                                   g r+++  ++ e+lk + + +  e+   +++  d++k  p ++++fDlv++se+l+h+ +d e +++ ia +L+p+G+++
  gi|13541712|ref|NP_111400.1|  56 GDRYYCAVPNVEFLKSVDQLYISEQ---NIIYYDITKNnPEPNSKFDLVIISETLEHIfADDEIVMRSIANLLRPNGIIY 132
                                   3777777778888888877777776...3688899986699************************************997 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.0     1e-09   2.7e-06      54      99 .]      88     131 ..      40     131 .. 0.81
   2 ?   -1.1   0.0       1.3   3.3e+03      35      65 ..     137     182 ..     134     190 .. 0.61

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 1e-09
               Methyltransf_12  54 ealdlldldgg..ssfDlvvasnvlhhl.kdirevldnirklLkpgGrl 99 
                                   ++++      +  s+fDlv++s++l+h+ +d + v+++i++lL+p+G++
  gi|13541712|ref|NP_111400.1|  88 TKNN---P--EpnSKFDLVIISETLEHIfADDEIVMRSIANLLRPNGII 131
                                   2222...2..2449*********************************85 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.3
               Methyltransf_12  35 dakeklakrennnnnnvelealdlldldgg...............s 65 
                                   +a++++++++ ++ +n+ + + d+l+   g               +
  gi|13541712|ref|NP_111400.1| 137 NAARHINRIKLLFGKNIFWSKYDILNGGYGhireytvievksmleK 182
                                   6778888888888888888888877654445544444444444434 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0     6e-09   1.5e-05      62     114 ..      86     138 ..      65     181 .. 0.81

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 6e-09
               Methyltransf_31  62 diee.leklledekfDlilsnevl.naladpdkileeiervlkpggilliedprl 114
                                   di++  +     +kfDl++  e+l + +ad + ++++i ++l+p+gi+ ++ p++
  gi|13541712|ref|NP_111400.1|  86 DITKnNP--EPNSKFDLVIISETLeHIFADDEIVMRSIANLLRPNGIIYLTVPNA 138
                                   5666444..4569***********888899999999**************99993 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   2.8e-07   0.00072      49      97 .]      81     129 ..      40     129 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 2.8e-07
                                   EEEESBCCG.BSSSTTTEEEEEEESTGGG.SSHHHHHHHHHHHHHHEEEEE CS
               Methyltransf_25  49 efvqgdaed.lpfedgsfDlvvssgalhh.lsdedlekalkeiarvLkpgG 97 
                                   +++  d+++  p+++++fDlv++s +l+h + d+  e +++ ia++L+p+G
  gi|13541712|ref|NP_111400.1|  81 NIIYYDITKnNPEPNSKFDLVIISETLEHiFADD--EIVMRSIANLLRPNG 129
                                   5566677542789999*******999*9955544..678**********99 PP

>> Lipid_DES  Sphingolipid Delta4-desaturase (DES)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.0    0.0013       3.5      11      24 ..      15      28 ..      12      38 .. 0.80
   2 ?   -3.0   0.0       2.1   5.4e+03      28      35 ..     145     152 ..     143     153 .. 0.83
   3 !    7.4   0.0    0.0012         3      19      36 ..     177     194 ..     176     195 .. 0.93

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0013
                     Lipid_DES 11 dePHasRRkeILkk 24
                                  ++ Ha+R k +L +
  gi|13541712|ref|NP_111400.1| 15 EQTHAERHKLMLRD 28
                                  899*********75 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2.1
                     Lipid_DES  28 ikkLmGpd 35 
                                   ik L+G +
  gi|13541712|ref|NP_111400.1| 145 IKLLFGKN 152
                                   999**986 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.0012
                     Lipid_DES  19 keILkkhPeikkLmGpdp 36 
                                   k +L+k+ ++++ +G +p
  gi|13541712|ref|NP_111400.1| 177 KSMLEKYFDVRQIYGFNP 194
                                   78**************99 PP

>> XRN_N  XRN 5'-3' exonuclease N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   5.1e-05      0.13       9      92 ..      54     135 ..      43     141 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5.1e-05
                                   HHHHHSGGGEEE------SSSS-EEEEEEETHHHHHHHHS-SS...S-......--SSHHHHHHHHHHHHHHHHHHH-EEE CS
                         XRN_N   9 wlserypkivkevieeeeeeekefdnLYlDmNgiihkcshked...keekelskkpkteeeifkkifkyidrlvkivrprk 86 
                                   +l +ry  +v +v+       k++d+LY+   +ii+  + k++   +++++l+  ++t e+if +    ++++ +++rp+ 
  gi|13541712|ref|NP_111400.1|  54 YLGDRYYCAVPNVE-----FLKSVDQLYISEQNIIYYDITKNNpepNSKFDLVIISETLEHIFADDEIVMRSIANLLRPNG 129
                                   66666654444443.....2238*******99999988877666667778888999999999999999999********** PP

                                   EEEEE- CS
                         XRN_N  87 llylav 92 
                                   ++yl+v
  gi|13541712|ref|NP_111400.1| 130 IIYLTV 135
                                   ***987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-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: 00:00:00.49
# Mc/sec: 1370.54
//
Query:       gi|13541713|ref|NP_111401.1|  [L=139]
Description: hypothetical protein TVN0882 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score 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   14.9   0.0      0.015   14.7   0.0    1.1  1  DDE_5     DDE superfamily endonuclease


Domain annotation for each model (and alignments):
>> DDE_5  DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   8.2e-07     0.015      45     155 ..      15     121 ..       4     128 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 8.2e-07
                         DDE_5  45 qalqrflsrspwddaklrrrlarlvlpllapeaavlaiDdTgfpkdGkasvgvarqycgalgkadncqvavslglatervs 125
                                    ++ rfls++   d  + ++l  +++  +++ + +laiDd  + k Gk + + ++ ++++ g+++ + ++ +  l  +   
  gi|13541713|ref|NP_111401.1|  15 SSMNRFLSSNIDTDLMFMKTL--ENINSVED-DGILAIDD-IIKKTGKNIEAAGWIFDHSTGRTVWGIQFATSVLSGRYGI 91 
                                   566677766533333444444..33334433.347*****.789************************************* PP

                         DDE_5 126 apldwrlylpeswaqdlsarrrragvpddv 155
                                   +p++ + y+ ++  +d  + r + +++++v
  gi|13541713|ref|NP_111401.1|  92 YPISAEVYMIKESLDDENEYRSKIDIQKGV 121
                                   ******998766666657777777766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); 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: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 905.76
//
Query:       gi|13541714|ref|NP_111402.1|  [L=126]
Description: hypothetical protein TVN0883 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       449  (0.0250432); 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:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 850.33
//
Query:       gi|13541715|ref|NP_111403.1|  [L=264]
Description: cell wall biosynthesis glycosyltransferase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-17   63.8   0.0    2.2e-17   63.4   0.0    1.2  1  Glycos_transf_2  Glycosyl transferase family 2
    7.7e-06   26.0   0.0    8.9e-06   25.8   0.0    1.2  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
     0.0073   16.0   0.1      0.053   13.2   0.0    2.1  2  Glyco_transf_7N  N-terminal region of glycosyl transferase gr


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 !   63.4   0.0   3.7e-21   2.2e-17       1     168 [.      18     180 ..      18     182 .. 0.92

  Alignments for each domain:
  == domain 1  score: 63.4 bits;  conditional E-value: 3.7e-21
                                   EEEEEESS-TTTHHHHHHHHHHH..GGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH-- CS
               Glycos_transf_2   1 svviptyNeektlletlesllaq..dpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglraat 79 
                                   +v+ip+yNeek l  +l  l++    + +++++ v  Dg+ D+t++ ++  ++e+  + + + + + Gk++a+ +++  at
  gi|13541715|ref|NP_111403.1|  18 TVIIPAYNEEKRLMPVLYELCEYirSNSLEWKVMVSIDGD-DGTESNVKIMMQEYSFLSYSKGKGRGGKGAAIKRAITSAT 97 
                                   69**************************************.***********************999************** PP

                                   SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SSEEEECCHCCCCHCCCCCCSTTCSTCCCE CS
               Glycos_transf_2  80 gdyilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrvgenerlyfkerkrslkgnlsfeigsaal 160
                                   g++++++DaD  ++ + + k ++  +   +d+++  r+ ++g++ ++ r+    + +r+++k  + +l+ ++ +  +++ +
  gi|13541715|ref|NP_111403.1|  98 GEFVILMDADGSVPLKEIVKALDLTNY--YDLIIFDRYSNRGNRIPFIRR----FPSRGFNKLVRIFLGLKINDTQCGYKI 172
                                   *************97655555555444..788999999999999999998....89************************* PP

                                   EEEHHHHH CS
               Glycos_transf_2 161 lrrealee 168
                                   ++re++++
  gi|13541715|ref|NP_111403.1| 173 IKREYAQR 180
                                   ****9875 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 !   25.8   0.0   1.5e-09   8.9e-06       4     108 ..      17     118 ..      15     201 .. 0.84

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 1.5e-09
               Glyco_tranf_2_3   4 lavlVptfneedvlgevlesllaqey.prvevvvvv.desdaetlevaeelaaalpdvrvrvvvnarnlgstgksralnea 82 
                                    +v++p++nee++l  vl +l  + +  ++e  v+v   +d++t ++++ + ++++   +++   ++  g++gk  a+++a
  gi|13541715|ref|NP_111403.1|  17 STVIIPAYNEEKRLMPVLYELCEYIRsNSLEWKVMVsIDGDDGTESNVKIMMQEYSF--LSY---SKGKGRGGKGAAIKRA 92 
                                   58********************98653558888888656788888888888888866..453...454499********** PP

               Glyco_tranf_2_3  83 lravksdlvllvDdDtvvePdtlkrl 108
                                   +  +++++v+l+D+D  v    + ++
  gi|13541715|ref|NP_111403.1|  93 ITSATGEFVILMDADGSVPLKEIVKA 118
                                   ***************87765555555 PP

>> Glyco_transf_7N  N-terminal region of glycosyl transferase group 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.0   8.9e-06     0.053      42      99 ..      10      67 ..       5      78 .. 0.84
   2 ?   -0.0   0.1      0.11   6.3e+02      84     107 ..     173     196 ..     153     202 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 8.9e-06
               Glyco_transf_7N 42 dckarqkvaiiipyrnreehLkillkrLhpllqrQqldykiyvieqagnetFnrakll 99
                                  +  a q+ ++iip  n e++L+ +l++L + ++   l++k++v    ++ t    k++
  gi|13541715|ref|NP_111403.1| 10 NSIAYQRSTVIIPAYNEEKRLMPVLYELCEYIRSNSLEWKVMVSIDGDDGTESNVKIM 67
                                  5568899************************************887777766555555 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.11
               Glyco_transf_7N  84 vieqagnetFnrakllnvgfleal 107
                                   +     ++ Fn+ ++ n+ f  al
  gi|13541715|ref|NP_111403.1| 173 IKREYAQRAFNKITISNAFFDVAL 196
                                   334457889******999998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       549  (0.0306208); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.51
# Mc/sec: 1556.56
//
Query:       gi|13541716|ref|NP_111404.1|  [L=175]
Description: hypothetical protein TVN0885 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        4.7    7.1  15.2        1.3    8.9   8.7    2.2  2  DUF2975   Protein of unknown function (DUF2975)


Domain annotation for each model (and alignments):
>> DUF2975  Protein of unknown function (DUF2975)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.4    0.0087   1.6e+02      93     118 ..      15      40 ..       3      47 .. 0.68
   2 ?    8.9   8.7   7.5e-05       1.3      20     100 ..      71     148 ..      48     160 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.0087
                       DUF2975  93 vllllgvafaslvigllvlvlaella 118
                                   +  l+ + ++s+v+  ++lv +++++
  gi|13541716|ref|NP_111404.1|  15 MSYLVSLKYVSFVLISVILVFRKIIR 40 
                                   44555566677777777777777765 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 7.5e-05
                       DUF2975  20 vlllgvlallafvvalvqlwkLlrsirkgevFspanvrrLrriglaliaaalllaagivalallaelelapgvvllllgva 100
                                    ll +vl l+afv+++++ +   rsi     Fs+ n+ +++r g+++++++l +++ +    ++ ++  + ++vll+l   
  gi|13541716|ref|NP_111404.1|  71 SLLGIVLSLIAFVFGIYISFHTTRSI---VFFSKNNILYYKRPGWVVAIWSLAFLTRLALILFFPSFNGDLFTVLLFLASG 148
                                   68889999999999999999999888...69*******************9999998888888888766666666665443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       859  (0.0479112); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); 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):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1179.03
//
Query:       gi|13541717|ref|NP_111405.1|  [L=544]
Description: hypothetical protein TVN0886 [Thermoplasma volcanium GSS1]
Scores for complete 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-34  117.4  28.6    1.1e-33  116.8  28.6    1.4  1  DUF2079      Predicted membrane protein (DUF2079)
  ------ inclusion threshold ------
      0.035   14.2   0.3        0.2   11.8   0.0    2.6  2  ETRAMP       Malarial early transcribed membrane protein (ETR
        2.3    8.3   5.4         11    6.2   5.4    2.2  1  DUF1003      Protein of unknown function (DUF1003)


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 !  116.8  28.6   1.9e-37   1.1e-33      44     454 ..      58     452 ..      27     454 .. 0.84

  Alignments for each domain:
  == domain 1  score: 116.8 bits;  conditional E-value: 1.9e-37
                       DUF2079  44 apillllaplyalfPsvltLllvqalllslgglplyrlarerllsrrlalliallYllspvvinptlfdFhpevlaiPlll 124
                                   ++i++ll+p+y l P +  Ll++q +++slg++p+y + +++l+s+  ++++ +l+ll+  ++++ +fdFh + l+ P l+
  gi|13541717|ref|NP_111405.1|  58 KLIYFLLYPFYSLDPNPEYLLVFQDFFISLGSIPIYFISKKILNSEFFGFIFGILWLLYYPIYGVEWFDFHFMALF-PTLF 137
                                   5799************************************************************************.**** PP

                       DUF2079 125 lalllalrrrkwllllvlilllllvredlslvvvilglwlilre..rkrrkiglillllglawvilvtsvliPlfsstksq 203
                                   l ++ a++ +k   + +l ++l+++ ++++++++ + l+ +l +  r  ++   + l++ ++ v++++++  P++      
  gi|13541717|ref|NP_111405.1| 138 LTAV-AFLSYKKYRFSLLFMFLSAITDYMAPLIILMYLVVLLVKreRVPKY-YYASLVVPFFAVFVAVNIASPSYT----- 211
                                   ***9.*************************999999888888772333445.777888888888889999999992..... PP

                       DUF2079 204 vfgverysylgsSlleillnlitqpllvlqellspegdklkyllllflplgflpllsspawLlvalPllllnllsgyspql 284
                                               +l  +   +i++p ++ ++l+     k++y  ++ lpl++lp+    +  l+ +P+++l ++ +y+p+l
  gi|13541717|ref|NP_111405.1| 212 -----------LGLINYT-AIIKDPAIIASMLV--R--KIIYYPMIALPLALLPFG--SIDILMIIPYVGLSIVHNYTPYL 274
                                   ...........4666665.5899***9998888..5..9****************6..7888899**************97 PP

                       DUF2079 285 s.lgyqYsllvipflvlaaifglaklsssvelrrikriwsvalvlvlvltlflnparslsflvpdsesp.....vvylstl 359
                                     + yqY +l  + ++l+a+  ++k  ++++++++k i+ v+++l++++ l+++p+ +l + + + +s+     + + +t+
  gi|13541717|ref|NP_111405.1| 275 MpILYQYPALTSAPIFLGALSSISKCMKKISRKKVKSILIVIISLSIITFLLFTPYGNLLTDNNNHFSYvdyfvGGNYQTS 355
                                   5278*****************************************************************999996677777 PP

                       DUF2079 360 aqlqas......rellklIpsdasvlatsnLaPhlan.Rayvylfpeneelydleylleevdyvlldvafrgwasrkdrer 433
                                   +++ ++        +++++p++++++ ++n +P +++  + v+++  n++    ey + ++ +v+   ++   + + ++  
  gi|13541717|ref|NP_111405.1| 356 ERITETkydryiYSAVSYVPKGSTLAIQNN-MPQFTQdYRWVLPIN-NYSG-SPEYVITDPYSVWFY-NTTLSPGSYTNYV 432
                                   777777788779999*****9999999999.599999766666654.4443.234444444444444.3344445555555 PP

                       DUF2079 434 klidklrnsgrygviaeedgv 454
                                   k++++   sg yg++ e dg+
  gi|13541717|ref|NP_111405.1| 433 KFTNERLLSG-YGIYFECDGI 452
                                   5555555553.7777777776 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 ?   -2.8   0.4       1.1   6.7e+03      56      62 ..      14      20 ..       1      25 [. 0.54
   2 ?   11.8   0.0   3.3e-05       0.2       7      71 ..     194     328 ..     190     340 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.1
                        ETRAMP 56 iiistia 62
                                  i+isti+
  gi|13541717|ref|NP_111405.1| 14 IVISTIS 20
                                  3444444 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 3.3e-05
                        ETRAMP   7 llffafLlavnlltpeslcdevnkkk....................................................... 32 
                                   + ffa+++avn+++p++     n                                                          
  gi|13541717|ref|NP_111405.1| 194 VPFFAVFVAVNIASPSYTLGLINYTAiikdpaiiasmlvrkiiyypmialplallpfgsidilmiipyvglsivhnytpyl 274
                                   56999**********9999999976699999************************************************** PP

                        ETRAMP  33 ................ekakkaikkiddkiekkkkkkKliiistiatalallvas 71 
                                                     a+ +i k  +ki +kk k  li+i +++++  ll+ +
  gi|13541717|ref|NP_111405.1| 275 mpilyqypaltsapifLGALSSISKCMKKISRKKVKSILIVIISLSIITFLLF-T 328
                                   *************99999***************99999999999999988887.4 PP

>> DUF1003  Protein of unknown function (DUF1003)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   5.4    0.0018        11      27      56 ..     142     171 ..     104     174 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0018
                       DUF1003  27 glkpfDpypFillnlvlslqaalaaplIll 56 
                                      ++ +y F ll ++ls +  ++aplI+l
  gi|13541717|ref|NP_111405.1| 142 AFLSYKKYRFSLLFMFLSAITDYMAPLIIL 171
                                   5678899********************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (544 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       769  (0.0428914); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.67u 0.36s 00:00:01.03 Elapsed: 00:00:00.55
# Mc/sec: 2962.62
//
Query:       gi|13541718|ref|NP_111406.1|  [L=307]
Description: nucleoside-diphosphate-sugar epimerase [Thermoplasma volcanium GSS1]
Scores for complete 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  131.5   0.0    4.3e-38  131.1   0.0    1.1  1  Epimerase        NAD dependent epimerase/dehydratase family
    3.1e-31  109.0   0.6    9.2e-31  107.5   0.6    1.8  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    6.7e-08   31.9   0.0    2.4e-07   30.0   0.0    1.8  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    7.9e-05   21.9   0.1     0.0017   17.6   0.1    2.6  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
    0.00018   20.7   0.0    0.00025   20.2   0.0    1.3  1  RmlD_sub_bind    RmlD substrate binding domain
     0.0012   18.1   0.2       0.48    9.5   0.0    2.8  2  NAD_binding_4    Male sterility protein
  ------ inclusion threshold ------
      0.091   12.5   0.1       0.18   11.5   0.0    1.5  2  ELFV_dehydrog    Glutamate/Leucine/Phenylalanine/Valine dehyd


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 !  131.1   0.0   1.7e-41   4.3e-38       1     241 []       8     235 ..       8     235 .. 0.89

  Alignments for each domain:
  == domain 1  score: 131.1 bits;  conditional E-value: 1.7e-41
                                   EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE--S---HHHHH CS
                     Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfkeeqpdavihlAavggvaass 81 
                                   ilVtG++GfiGs+lv +l ek+ +v +ld+l+++s + +++ l+ ve     ++++ +++   +pd+++h++ +++ + + 
  gi|13541718|ref|NP_111406.1|   8 ILVTGGAGFIGSNLVARLSEKN-HVYVLDSLQTGSLH-NIDGLSNVEFIKDYAKNVSNYCI--NPDYIFHIGVYSSSPMYR 84 
                                   8******************998.7999****666654.45556666666666778888888..9*******9988888878 PP

                                   HSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSS.BSTCSTTS----SSHHHHHHHHHHHHHHHHHHHHT CS
                     Epimerase  82 edpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqp.keettltgplkpnspYaaaKlageklveayaaqyg 161
                                   ++p   + + ++ +  +le a+k++   ++f+s+s++Y  +++ p +e +t   pl  +  Y  a + +e++ e y + y+
  gi|13541718|ref|NP_111406.1|  85 SNPFL-VSEAIHDMIAILELAKKSKT-PVVFASTSSIYNGVKP-PhRENVT---PL-VSDYYTEARISMERISELYSKLYD 158
                                   88777.456999************99.****************.8566666...88.8899******************** PP

                                   -EEEEEEESEEESTTS-TTS.TTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHHHHHHHHHHTT-STTEEEEES CS
                     Epimerase 162 lnaiilrlfnlyGprngege.vsrvipalirkilegkqevtllgdgtalRdflyveDvaeaillvlehvdagdkgeiyniG 241
                                   +n+ ++r f++yG r+ +++  ++++++++  ++++k + +++gdg+++Rdf++v+Dv++a++l++e+    d  ++yn+G
  gi|13541718|ref|NP_111406.1| 159 INISAMRFFSIYGYREMKKRmYANLVSQFLWDMHSKK-SPIIYGDGEQRRDFVFVDDVVDALILAAEK---SDGFQVYNVG 235
                                   ***************777777****************.******************************...667889**99 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.5   0.6   3.6e-34   9.2e-31       1     331 [.       9     299 ..       9     300 .. 0.84

  Alignments for each domain:
  == domain 1  score: 107.5 bits;  conditional E-value: 3.6e-34
                                   EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-SEEEE CS
                 GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpdevyn 81 
                                   L+TG+aGfiGs+l+ +L ek++ v++++     ++tg+++++         +n++++k   ++ s+       ++pd +++
  gi|13541718|ref|NP_111406.1|   9 LVTGGAGFIGSNLVARLSEKNH-VYVLDS----LQTGSLHNIDG------LSNVEFIKDYAKNVSN-----YCINPDYIFH 73 
                                   9******************965.777653....35555555542......2367887755555443.....3479****** PP

                                   --S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB-TTS-----SHHHHHHHHHHH CS
                 GDP_Man_Dehyd  82 LAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpqtEttpfyPrsPYaaaKlyadw 162
                                    +  s  +   ++P  + e+ +  ++ +Le++++     k+ +++aSts +Y  v+  p +E+        Y  a+++ + 
  gi|13541718|ref|NP_111406.1|  74 IGVYSSSPMYRSNPFLVSEA-IHDMIAILELAKKS----KTPVVFASTSSIYNGVK-PPHRENVTPLVSDYYTEARISMER 148
                                   ***************99998.99*********985....578999*******9997.77777766666789********** PP

                                   HHHHHHHHH---EEEEEE-EEESTTS-T.TSCCCHHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHHHHHHHHHHHHC.SS CS
                 GDP_Man_Dehyd 163 ivvnyreayglfavngilfnhesprrge.tfvtrkitravarialgkqevlylGnldakRdwghvkDyveamwlmlqq.dk 241
                                   i + y + y++ ++  ++f  ++ r  + ++  +++++++  ++ +k + +++G+++++Rd+ +v+D+v+a+ l+ ++ d 
  gi|13541718|ref|NP_111406.1| 149 ISELYSKLYDINISAMRFFSIYGYREMKkRMYANLVSQFLWDMHSKKSP-IIYGDGEQRRDFVFVDDVVDALILAAEKsDG 228
                                   ***********************9977626999999*****99998865.569********************99987355 PP

                                   ---EEE-TT-EEECHHCHHCCHHCCCHHHHHH............TTGGCCCEECGG--SS--SB--B-THHHHHHH----S CS
                 GDP_Man_Dehyd 242 pedyviatgethsvrefvelaflelgktiewegkgeeevgrakesgkvvvevdpkyfrpgevdlllgdaskakeeLgWkpk 322
                                    + y+++tg ++s++e+v++ ++ lg +ie +                   + ++++ ++ v+++l+d++ka++ +g+++k
  gi|13541718|ref|NP_111406.1| 229 FQVYNVGTGVNYSLNELVQKLNKYLGSNIEPK-------------------YVENPMAKTYVHETLADTNKAEKMIGFRAK 290
                                   68999********************9987653...................34456666778999**************** PP

                                   S-HHHHHHH CS
                 GDP_Man_Dehyd 323 vsfeelvre 331
                                   +s++e++++
  gi|13541718|ref|NP_111406.1| 291 ISLDEGIKR 299
                                   ******997 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   0.0   9.4e-11   2.4e-07       1     231 [.       9     225 ..       9     232 .. 0.75

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 9.4e-11
                     3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkkviegDvtdkdkleealegvdvvihlaslvdvag 81 
                                   +vtGgaGF+G++lv +L + +   +v vlD  +  +l++    +nv+ +i+ D   ++++++ + + d ++h+ ++  +  
  gi|13541718|ref|NP_111406.1|   9 LVTGGAGFIGSNLVARLSEKN---HVYVLDSLQTGSLHNIDGLSNVE-FIK-DY--AKNVSNYCINPDYIFHI-GVYSSSP 81 
                                   69**************97776...6*****99999987776666776.554.43..5689*************.5555555 PP

                     3Beta_HSD  82 klted.eimkvnvkGTrnvleacvkagvrvlvYtSsaevvgpnslgeeilngdEeleyeslhqdaypesKalaEklvlkaN 161
                                   +++++  + +  ++    +le ++k+  + +v+ S+ ++  +    ++ +    ++++ +l +d y+e +   E++     
  gi|13541718|ref|NP_111406.1|  82 MYRSNpFLVSEAIHDMIAILELAKKSKTP-VVFASTSSIYNG---VKPPH----RENVTPLVSDYYTEARISMERISELY- 153
                                   5555515667789*********9998865.689999887666...44444....56778889999999987777754333. PP

                     3Beta_HSD 162 grtlknggrlyTcaLRpagiyGegd..kl.lvpllkql...aklglalfkigdeevlsdrvYvgNvawahilAara 231
                                     +l    +++  a+R   iyG ++  k+   +l+ q    ++++++ + +gd e+  d+v+v+ v++a ilAa +
  gi|13541718|ref|NP_111406.1| 154 S-KLY---DINISAMRFFSIYGYREmkKRmYANLVSQFlwdMHSKKSPIIYGDGEQRRDFVFVDDVVDALILAAEK 225
                                   3.344...56999*********6651133133444443222466778899***********************975 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.1   6.5e-07    0.0017       1     251 [.       8     257 ..       8     270 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 6.5e-07
                                   EEEETTTSHHHHHHHHHHHHHB-SEEEEEES.-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T-SE CS
               Polysacc_synt_2   1 vlvtGagGsiGselvrqilkkkpkkiiller.dElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelkvdv 80 
                                   +lvtG++G iGs+lv ++ +k+  ++++l++ +  +l++i+        +  +      +i d   ++++++ +   ++d+
  gi|13541718|ref|NP_111406.1|   8 ILVTGGAGFIGSNLVARLSEKN--HVYVLDSlQTGSLHNIDGLS-----N--V-----EFIKDY--AKNVSNYCI--NPDY 70 
                                   89***************98765..56666651444556665533.....2..2.....234443..345666666..8*** PP

                                   EEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEEG...GGSS--SHHHHHHHHHHHHHHHGGG--SS CS
               Polysacc_synt_2  81 vfhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkvvliStD...KAvnPtnvmGatKrlaekllqalakesee 158
                                   +fh   +   P+  +np+  ++  ++ +  ++e a++++   vv+ St      v+P     +t ++++ ++ a  + ++ 
  gi|13541718|ref|NP_111406.1|  71 IFHIGVYSSSPMYRSNPF-LVSEAIHDMIAILELAKKSKT-PVVFASTSsiyNGVKPPHRENVTPLVSDYYTEARISMERI 149
                                   *****************9.57889***********99986.5788888722257889999999999999999887777766 PP

                                   S-.......-EEEEEEE-EETTGT.......TSSHHHHHHHHHTT.SSEEES-TT-EEEEE-HHHHHHHHHHHHHH--SS- CS
               Polysacc_synt_2 159 kk.......tkfvvvRfGNVlgSr.......GSviplFkkqikeg.gpvtvTdpemtRyfmtieeavqLvlqalalakgge 224
                                   ++        ++++ Rf  + g r         ++  F   ++++ +p+   d e  R f+ +++ v+ ++ a+++++g +
  gi|13541718|ref|NP_111406.1| 150 SElysklydINISAMRFFSIYGYRemkkrmyANLVSQFLWDMHSKkSPIIYGDGEQRRDFVFVDDVVDALILAAEKSDGFQ 230
                                   667788888899999999988876333333346777777666655489999999999999999999999999999999999 PP

                                   EEEE--.-EEEHHHHHHHH........ CS
               Polysacc_synt_2 225 ifvldmGepvkivdlakalielsglee 251
                                   ++ +  G  +++ +l+++l ++ g + 
  gi|13541718|ref|NP_111406.1| 231 VYNVGTGVNYSLNELVQKLNKYLGSNI 257
                                   999999999999999999998888655 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 !   20.2   0.0   9.9e-08   0.00025       2     138 ..       7     152 ..       6     235 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 9.9e-08
                                   EEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT............T--TTSHHHHHHHH.....HHH--SEEEE------HH CS
                 RmlD_sub_bind   2 kilvtGanGqlGseLakqlaeeglevlaltre............eldltdaeavaell.....keakpdvvvnaAAytavD 65 
                                   +ilvtG+ G +Gs+L+++l+e++ +v+ l++             ++++ +               ++pd + + + y    
  gi|13541718|ref|NP_111406.1|   7 EILVTGGAGFIGSNLVARLSEKN-HVYVLDSLqtgslhnidglsNVEFIKDY-----AknvsnYCINPDYIFHIGVYSSSP 81 
                                   69*******************99.7777766556776654443333333322.....2333335579************99 PP

                                   HHHHSHHHHHHHHTHHHHHHHHHHHHCT-EEEEEEEGGGS-S-TTS-B-TTS----SSHHHHHHHHHHHHHHH CS
                 RmlD_sub_bind  66 kaEseeeaayavnaeavealAeaaaavgalLihvStDyVFdGekkrpYeeddetsPlnvYGrtKlaGEqavla 138
                                      s++ + +++  +   a+ e+a++ + ++++ St  +++G k+ p +e+ ++    +Y ++++ +E+  + 
  gi|13541718|ref|NP_111406.1|  82 MYRSNPFLVSEAIHDM-IAILELAKKSKTPVVFASTSSIYNGVKP-PHRENVTPLVSDYYTEARISMERISEL 152
                                   9999988877765554.467799*******************955.688888888889999999999986554 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.0   0.00019      0.48       1      28 [.      10      34 ..      10      41 .. 0.87
   2 !    5.5   0.0    0.0031         8     116     153 ..      98     133 ..      59     219 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00019
                                  EE-TTSHHHHHHHHHHHHHS-.TEEEEE CS
                 NAD_binding_4  1 lTGaTGFLGkvLlekLLrttpevkiyll 28
                                  +TG+ GF+G+ L+++L +++   ++y+l
  gi|13541718|ref|NP_111406.1| 10 VTGGAGFIGSNLVARLSEKN---HVYVL 34
                                  7**************98776...46665 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0031
                                   HHHHHHHTSSS--.-EEEEEE.GGGTTS-TTT--SSS-H CS
                 NAD_binding_4 116 revlelakklkklkvllhvST.ayvngeregeveekvye 153
                                     +lelakk k   ++++ ST ++ ng +    +e+v++
  gi|13541718|ref|NP_111406.1|  98 IAILELAKKSKT--PVVFASTsSIYNGVKP-PHRENVTP 133
                                   679999*97654..5999999777777776.34555554 PP

>> ELFV_dehydrog  Glutamate/Leucine/Phenylalanine/Valine dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   7.2e-05      0.18      33      87 ..       7      62 ..       1      76 [. 0.84
   2 ?   -3.6   0.0       2.8   7.1e+03      11      26 ..     235     250 ..     233     261 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 7.2e-05
                                  EEEEEE--SHHHHHHHHHHHHCT-EEEEEEESSEEEEETTEE.-HHHHHHHHHCSS CS
                 ELFV_dehydrog 33 krvaisGsGnvgsyaallltelgakvvavsDssGviydpeGl.dieellelkeerk 87
                                  + ++++G G +gs+ +  l+e+++ +v  s ++G +++ +Gl ++e +++++++  
  gi|13541718|ref|NP_111406.1|  7 EILVTGGAGFIGSNLVARLSEKNHVYVLDSLQTGSLHNIDGLsNVEFIKDYAKNVS 62
                                  34567788******************99999***********99999999977654 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 2.8
                                   HHHHHHHHHHHHHHTT CS
                 ELFV_dehydrog  11 glGvvyyveemlkklk 26 
                                   g Gv y ++e+++kl+
  gi|13541718|ref|NP_111406.1| 235 GTGVNYSLNELVQKLN 250
                                   5666666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       631  (0.0351944); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.61u 0.33s 00:00:00.94 Elapsed: 00:00:00.49
# Mc/sec: 1873.20
//
Query:       gi|13541719|ref|NP_111407.1|  [L=324]
Description: kinase related to galactokinase and mevalonate kinase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.3e-12   46.6   0.0    1.8e-11   44.2   0.0    2.2  3  GHMP_kinases_C  GHMP kinases C terminal
    8.3e-11   42.0   0.0    1.7e-10   41.0   0.0    1.5  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 ?   -2.5   0.0      0.77   6.9e+03      29      43 ..      65      79 ..      47      85 .. 0.76
   2 ?   -2.5   0.0      0.76   6.8e+03       6      21 ..     175     190 ..     173     222 .. 0.58
   3 !   44.2   0.0     2e-15   1.8e-11       2      79 ..     226     302 ..     225     306 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.77
                GHMP_kinases_C 29 vgilppeleelleal 43
                                   +i++p+++e l++l
  gi|13541719|ref|NP_111407.1| 65 EDIEHPSVRESLKLL 79
                                  568888888888877 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.76
                GHMP_kinases_C   6 ergdlellgellnlsq 21 
                                   ++++le ++++l l+ 
  gi|13541719|ref|NP_111407.1| 175 NAKSLEDFRNHLLLLY 190
                                   5566677777766443 PP

  == domain 3  score: 44.2 bits;  conditional E-value: 2e-15
                GHMP_kinases_C   2 lealergdlellgellnlsqrselkavvgilppeleellealselGalgaklsGaGgGptvfalfkdkdeaeqvaral 79 
                                   +ea+++  ++++g ++  ++ +++k + gi+++++++l e++++ Ga+g+kl GaGgG+++  ++ ++++ ++++ al
  gi|13541719|ref|NP_111407.1| 226 FEAVYKAEYPRIGAIMDANWKNKKKLTDGISNDIIDNLYELAMKKGAYGGKLIGAGGGGFLLFVC-EPSDSDDIIKAL 302
                                   5677777889************8888***************************************.999999999887 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 !   41.0   0.0   1.9e-14   1.7e-10       2      66 .]      87     155 ..      86     155 .. 0.87

  Alignments for each domain:
  == domain 1  score: 41.0 bits;  conditional E-value: 1.9e-14
                                   EEEEESSHT.TSSSCHHHHHHHHHHHHHHHHTTEHH...HH.HHHHHHHHHHHHHHHHHSHHHHHHHHSS CS
                GHMP_kinases_N   2 ivikseiPv.gaGLGSSAAlavalvaAllallglsl...ee.aklaleaerlaqggngsggDvaasvyGg 66 
                                   i + s+iP  g+GLGSS+++ v+l+ Al a+ g +l   ee a+ a+ +er++ +  g+ +D++ ++yGg
  gi|13541719|ref|NP_111407.1|  87 ILSISDIPSkGTGLGSSSTFLVGLLNALHAYKG-ELtsrEElAREAVLIEREILKEPGGKQDQYMAAYGG 155
                                   67789**99788***************988885.55444337***********9999************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (324 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       784  (0.043728); expected 358.6 (0.02)
Passed bias filter:                      504  (0.0281109); 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: 0.63u 0.30s 00:00:00.93 Elapsed: 00:00:00.51
# Mc/sec: 1921.03
//
Query:       gi|13541720|ref|NP_111408.1|  [L=506]
Description: O-antigen and teichoic acid export protein [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-21   77.4  23.5    1.1e-21   77.4  23.5    1.8  2  Polysacc_synt_3  Polysaccharide biosynthesis protein
    4.2e-15   56.1  16.5    4.2e-15   56.1  16.5    5.0  5  Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domai
    4.3e-11   42.7  50.5    7.1e-07   29.0  15.7    3.0  3  MatE             MatE
    8.7e-11   41.7  37.5    8.7e-11   41.7  37.5    2.4  2  Polysacc_synt    Polysaccharide biosynthesis protein
    1.1e-10   40.7  38.8    1.1e-10   40.7  38.8    1.5  1  MurJ             Lipid II flippase MurJ


Domain annotation for each model (and alignments):
>> Polysacc_synt_3  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.4  23.5     3e-25   1.1e-21       1     290 [.      32     335 ..      32     338 .. 0.84
   2 ?   -1.4   0.4       0.3   1.1e+03      50      87 ..     345     382 ..     334     447 .. 0.63

  Alignments for each domain:
  == domain 1  score: 77.4 bits;  conditional E-value: 3e-25
               Polysacc_synt_3   1 vLARLLspedFGvvaialvvislanlfvdmGlssaliqke..dltee....dlstvf...tfnlvlgllialvlfllapli 72 
                                   v+ R+ s +  G va+ +++i+l+nl+ ++Gl++a+ +     l ++      s vf    + ++++ +  + +f+la+ i
  gi|13541720|ref|NP_111408.1|  32 VIVRFFSASQVGAVALFIAIIGLFNLIFSFGLGTAVQHFAsyHLGRQeyatAKSIVFkilILGIIFSSIGLITMFYLAKPI 112
                                   678********************************8665422333332222334455111456788888889999999999 PP

               Polysacc_synt_3  73 as.fynqpelvtvlrvlalvlilsglssvqeallrrelkFkklfkitlvssvvgvivaivlAllglgvwALvigtllssll 152
                                   +  f   ++  +++++l++vl+   l+ + +        F +   ++++  + +   a+vlA+l+++++ +v+g+ +  +l
  gi|13541720|ref|NP_111408.1| 113 SItFMHTAQYTPIVKLLSIVLVGDVLFGLLNGSALGLQLFRASGLMNIIIWITYYSTALVLAFLLKSLYYVVVGWSVGIFL 193
                                   985778999****************99999988888889************************************999988 PP

               Polysacc_synt_3 153 slvllw.laskwrprlkfslkslke..lfsfglklllsnllnylarnldnlliGkvlssaaLGlYsvakrlaslpvaeits 230
                                    ++l++ l++k + + k + ++l++  lf+f++ +lls+++ y a+ +d ++++ +++ +aLG+Y+ a  +as+ +  i +
  gi|13541720|ref|NP_111408.1| 194 GVILYLyLIIKSTKNYKGRPRHLTPslLFQFSIPVLLSSIISYGATYIDRFIVAGLMTLSALGVYNFALLVASS-IGFIVA 273
                                   8877541444555555555555543339****************************************977766.67999* PP

               Polysacc_synt_3 231 viakVlfPalSrl..qddkkklrelylkvlrlialivlPiavglavvaellvkvllGsqWle 290
                                   +++++++P +S++    +++++++ +  ++ ++a + +P+a g+av++++++++l G+ ++e
  gi|13541720|ref|NP_111408.1| 274 PLNNIMLPKFSEFygEGNRENIKNRTAIATTVVAGVYVPAALGVAVLSKMIITLLAGKYYEE 335
                                   ************9334578889999999999**************************99876 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.3
               Polysacc_synt_3  50 vftfnlvlgllialvlfllapliasfynqpelvtvlrv 87 
                                   vf   +v++ +++ +++++++    +y ++       +
  gi|13541720|ref|NP_111408.1| 345 VFSALFVTSNVMTQLIAAVRETRVFIYSSAASLASNAI 382
                                   33444444444444444444333333333333333333 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 ?   -2.5  11.2       1.3   4.8e+03      53     140 ..      14     103 ..       6     108 .. 0.75
   2 ?   -6.9  18.4         5   1.8e+04      97     140 ..     154     204 ..     100     207 .. 0.70
   3 ?   -9.7  25.2         5   1.8e+04       5     133 ..     129     272 ..     125     276 .. 0.65
   4 ?   -1.2   6.2      0.54   1.9e+03      87     133 ..     221     272 ..     211     330 .. 0.73
   5 !   56.1  16.5   1.2e-18   4.2e-15       2     142 ..     340     475 ..     339     476 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.3
               Polysacc_synt_C  53 fgivGaaiatvlallvvavlnlyalrrllgiklellrrll.kpllaalvmgivvylllllllgllllaal.alllavlvga 131
                                   ++ +Ga +    + l+++v+  ++   ++g    ++  +    l++++++g +v +++++ lg   +a+  ++++++l+ +
  gi|13541720|ref|NP_111408.1|  14 YQFTGAGAQLFSGALFYTVIVRFFSASQVGAVALFIAIIGlFNLIFSFGLGTAVQHFASYHLGRQEYATAkSIVFKILILG 94 
                                   566788888888888888888888888888877334433357789999999999999999999998887789999999999 PP

               Polysacc_synt_C 132 lvYllllll 140
                                   +++  + l+
  gi|13541720|ref|NP_111408.1|  95 IIFSSIGLI 103
                                   998665554 PP

  == domain 2  score: -6.9 bits;  conditional E-value: 5
               Polysacc_synt_C  97 aalvmgiv...vylllllllglllla....alalllavlvgalvYllllll 140
                                   a+ +m i+   +y+ + l+l +ll +     +   +++++g+++Yl+l+++
  gi|13541720|ref|NP_111408.1| 154 ASGLMNIIiwiTYYSTALVLAFLLKSlyyvVVGWSVGIFLGVILYLYLIIK 204
                                   333333332223444444444444444443447778899********9997 PP

  == domain 3  score: -9.7 bits;  conditional E-value: 5
               Polysacc_synt_C   5 lalsiiflslstvlssiLqglgrqkialkalvigal....vklilnllli.plfgivGaaiatvlallvvavlnlyalrrl 80 
                                   l+++++  +l+ +l++   gl   ++  + ++i  +      l+l +ll   ++ +vG ++++ l+ +++++l++   +++
  gi|13541720|ref|NP_111408.1| 129 LSIVLVGDVLFGLLNGSALGLQLFRASGLMNIIIWItyysTALVLAFLLKsLYYVVVGWSVGIFLGVILYLYLIIKSTKNY 209
                                   555555556666655555555555555555555555232233444444443445679999999999999999888888888 PP

               Polysacc_synt_C  81 lgikl.....ellrrllkpllaalvmgivvylllllllglllla......alalllavlvgalv 133
                                    g +       l++  + +ll++++ ++++y + ++++  l+        ++all+a  +g +v
  gi|13541720|ref|NP_111408.1| 210 KGRPRhltpsLLFQFSIPVLLSSIISYGATY-IDRFIVAGLMTLsalgvyNFALLVASSIGFIV 272
                                   8877788886666666788888888888877.77776666665567766666777777787776 PP

  == domain 4  score: -1.2 bits;  conditional E-value: 0.54
               Polysacc_synt_C  87 llrrllkpllaalvmgivvylllllllglllla......alalllavlvgalv 133
                                   l++  + +ll++++ ++++y + ++++  l+        ++all+a  +g +v
  gi|13541720|ref|NP_111408.1| 221 LFQFSIPVLLSSIISYGATY-IDRFIVAGLMTLsalgvyNFALLVASSIGFIV 272
                                   46666677777777777766.55555555554456655555666666666665 PP

  == domain 5  score: 56.1 bits;  conditional E-value: 1.2e-18
               Polysacc_synt_C   2 LailalsiiflslstvlssiLqglgrqkialkalvigalvklilnllliplfgivGaaiatvlallvvavlnlyalrrllg 82 
                                   ++i+++   +++ s+v+++++ ++ +++ ++++++++++ + il+++lip+fgi Ga+i+    +++++++++ +++++  
  gi|13541720|ref|NP_111408.1| 340 ISIIMVFSALFVTSNVMTQLIAAVRETRVFIYSSAASLASNAILSIILIPHFGIEGASIGFSSIYAASFFVLYKYAKKTGF 420
                                   5677778888888999**************************************************************999 PP

               Polysacc_synt_C  83 iklellrrllkpllaalvmgivvylllllllgllllaal.alllavlvgalvYlllllllr 142
                                   ++   + +l k+  ++lvm+ vv+  + + +g++    +  l+  +l+ga+vYl+++  +r
  gi|13541720|ref|NP_111408.1| 421 YQA-NVYDLAKVWGSSLVMVFVVL-AFEVRFGTS----IdLLVPYILLGAVVYLGMIKSTR 475
                                   999.599999************55.555555554....447999999********997666 PP

>> MatE  MatE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4  19.6   2.5e-09     9e-06      11     148 ..      24     165 ..      20     177 .. 0.75
   2 !   29.0  15.7     2e-10   7.1e-07       1     160 [.     227     385 ..     227     386 .. 0.97
   3 ?   -3.1   0.1       1.5   5.3e+03     108     126 ..     426     444 ..     397     452 .. 0.52

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 2.5e-09
                          MatE  11 llslidtllvgrl.gskalAavsialsilsllfv.fllglstalttlvgqalGaknfkrakealrqglilllllsliiall 89 
                                   ++++++  ++ r+ +++ ++av++++ i+ l+ + f++gl+ta++ ++++ lG   +  ak +++++lil++++s i  + 
  gi|13541720|ref|NP_111408.1|  24 FSGALFYTVIVRFfSASQVGAVALFIAIIGLFNLiFSFGLGTAVQHFASYHLGRQEYATAKSIVFKILILGIIFSSIGLIT 104
                                   55555555666666******************999********************************************** PP

                          MatE  90 vllfseqilslftqdeevlelakrylrililgipalal.ql..vlsgilrgagktkvplyis 148
                                   ++ ++++i   f ++++ ++++k +l+i+++g ++++l +   +    +r+ g + ++  i+
  gi|13541720|ref|NP_111408.1| 105 MFYLAKPISITFMHTAQYTPIVK-LLSIVLVGDVLFGLlNGsaLGLQLFRASGLMNIIIWIT 165
                                   ************99998666555.55555555444443033112233455555555555555 PP

  == domain 2  score: 29.0 bits;  conditional E-value: 2e-10
                          MatE   1 Pialenllesllslidtllvgrl.gskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqglilll 80 
                                   P++l++++ +  + id ++v++l   +al+++++al ++s +++++  l++ + +  + ++G++n++++k+ + +++ +++
  gi|13541720|ref|NP_111408.1| 227 PVLLSSIISYGATYIDRFIVAGLmTLSALGVYNFALLVASSIGFIVAPLNNIMLPKFSEFYGEGNRENIKNRTAIATTVVA 307
                                   99******************************************************************************* PP

                          MatE  81 llsliiallvllfseqilslftqdeevlelakrylrililgipalalqlvlsgilrgagktkvplyislislllniplny 160
                                   ++++++al v ++s+ i+ l+  +    e +++ ++i+ ++  +++ ++v +    ++ +t+v  y s++sl  n++l+ 
  gi|13541720|ref|NP_111408.1| 308 GVYVPAALGVAVLSKMIITLLAGK--YYEEGSDAISIIMVFSALFVTSNVMTQLIAAVRETRVFIYSSAASLASNAILSI 385
                                   *********************655..69********************************************99999876 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 1.5
                          MatE 108 lelakrylrililgipala 126
                                     lak + + l+++ ++la
  gi|13541720|ref|NP_111408.1| 426 YDLAKVWGSSLVMVFVVLA 444
                                   4444444444444444433 PP

>> Polysacc_synt  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.7  37.5   2.4e-14   8.7e-11      19     273 ..      26     286 ..      11     287 .. 0.82
   2 ?   -6.0  14.2         5   1.8e+04      86     192 ..     316     419 ..     291     465 .. 0.73

  Alignments for each domain:
  == domain 1  score: 41.7 bits;  conditional E-value: 2.4e-14
                 Polysacc_synt  19 afvtlvylarilgpegfGlvalalaivtllviltdlGlnaalvreiakyrek..kelvslillnvllvllvlvllflllll 97 
                                   ++++++++ r+ ++ ++G val +ai++l+ +++++Gl++a+  + + +  +  + + ++i+ ++l++ ++++ + l++++
  gi|13541720|ref|NP_111408.1|  26 GALFYTVIVRFFSASQVGAVALFIAIIGLFNLIFSFGLGTAVQHFASYHLGRqeYATAKSIVFKILILGIIFSSIGLITMF 106
                                   789***********************************9987666666666588777777777777777776666555554 PP

                 Polysacc_synt  98 iaa......flglpelavlylilalmllllvgvasfrrglfqglermkyaavsqvveqlsrvilvliavflfldivaavlg 172
                                     a      f++  +++ ++ +l+++l+       + +g   gl+ +++  + +++  +++  + l++ fl ++++++v+g
  gi|13541720|ref|NP_111408.1| 107 YLAkpisitFMHTAQYTPIVKLLSIVLV-GDVLFGLLNGSALGLQLFRASGLMNIIIWITYYSTALVLAFLLKSLYYVVVG 186
                                   4446999978888888888888888877.777778888999999999999999999999999999999999999******* PP

                 Polysacc_synt 173 avlaalvggivslavlrkkfrprfvilslklv.rellsfsapltisslaillytyidsillglllgaeavGiYnaayqllv 252
                                    +++ ++g i++l+++ k  +  +  + ++l+   l+ fs+p+ +ss++++  tyid+++ + l   +a+G Yn+a  +++
  gi|13541720|ref|NP_111408.1| 187 WSVGIFLGVILYLYLIIKSTKNYKGRP-RHLTpSLLFQFSIPVLLSSIISYGATYIDRFIVAGLMTLSALGVYNFALLVAS 266
                                   ************999996665333333.3333056899*********************9999999***********9999 PP

                 Polysacc_synt 253 aisgllapivtaalfPvfsel 273
                                    i  ++ap ++  + P fse+
  gi|13541720|ref|NP_111408.1| 267 SIGFIVAPLNN-IMLPKFSEF 286
                                   99999999999.999999985 PP

  == domain 2  score: -6.0 bits;  conditional E-value: 5
                 Polysacc_synt  86 lvlvllfllllliaaflglpelavlylilalmllllvgvasfrrglfqglermkyaavsqvveqlsrvilvliavflfldi 166
                                   +v+vl   ++ l+a  ++++    + +i+ ++ l  + ++ + ++l  +++  + +  s+ ++  s +il++i++ +f+ i
  gi|13541720|ref|NP_111408.1| 316 GVAVLSKMIITLLAGKYYEEGSDAISIIMVFSAL--FVTSNVMTQLIAAVRETRVFIYSSAASLASNAILSIILIPHFG-I 393
                                   3333333444444445555555555555555555..566778899**********************************.9 PP

                 Polysacc_synt 167 vaavlgavlaalvggivslavlrkkf 192
                                    +a +g ++ + ++ +v++ + +k  
  gi|13541720|ref|NP_111408.1| 394 EGASIGFSSIYAASFFVLYKYAKKTG 419
                                   99999999999999888888877654 PP

>> MurJ  Lipid II flippase MurJ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.7  38.8   3.2e-14   1.1e-10      67     427 ..      94     444 ..      67     462 .. 0.79

  Alignments for each domain:
  == domain 1  score: 40.7 bits;  conditional E-value: 3.2e-14
                          MurJ  67 lllvtligilaapllirllatgfdeetlelavsllrillpylllvslsavfgavLnar....kkFfapafsPvllNvsvIl 143
                                    +++  ig++ + +l++ ++ +f  +t +++ +++++l  +++lv    v++++Ln +    + F a+++  ++  ++   
  gi|13541720|ref|NP_111408.1|  94 GIIFSSIGLITMFYLAKPISITF-MHTAQYT-PIVKLL--SIVLV--GDVLFGLLNGSalglQLFRASGLMNIIIWITYYS 168
                                   23344455666666666666666.5555555.455443..33333..3455555554422226799999999999999999 PP

                          MurJ 144 tllllanklgeeailaLaiGvliGgvlqllvqlpalkkaglllkprfafrdeglkkflklllptllgvsvsqlnllvdtal 224
                                   t+l+la  l+  + +++++G+ +G +l +++ l+ + k   + k r     +    +++  +p ll++ +s+ ++++d ++
  gi|13541720|ref|NP_111408.1| 169 TALVLAFLLK--SLYYVVVGWSVGIFLGVILYLYLIIKSTKNYKGRPRHLTP--SLLFQFSIPVLLSSIISYGATYIDRFI 245
                                   9999999999..9999************************999998887777..56899999******************* PP

                          MurJ 225 AsflaegsvsilayadrilqlPlglfgvsistvlLPrlSrsakekdedevrdllsqairltllllipvsfgllvlskpivs 305
                                      l++ s+  +++  +++   +g ++  + +++LP++S+ + e++ ++++++++ a+ +++ + +p++ g++vlsk i++
  gi|13541720|ref|NP_111408.1| 246 VAGLMTLSALGVYNFALLVASSIGFIVAPLNNIMLPKFSEFYGEGNRENIKNRTAIATTVVAGVYVPAALGVAVLSKMIIT 326
                                   999****************************************************************************** PP

                          MurJ 306 llferGnFseedveataevLaayalgLipyalvklllrvfYAredtktPvkislislvlnillsllllpplgvvglalats 386
                                   ll   G++ ee   a++ ++  +al + +  +++l++    A ++t+  ++ s  sl  n++ls++l+p +g  g +++ s
  gi|13541720|ref|NP_111408.1| 327 LLA--GKYYEEGSDAISIIMVFSALFVTSNVMTQLIA----AVRETRVFIYSSAASLASNAILSIILIPHFGIEGASIGFS 401
                                   **9..***********999888888777766666666....77******************************99888888 PP

                          MurJ 387 lsaliglvllyvllrkrlklteargiktflak...lvvllalaa 427
                                     + +++ +ly +++k  ++++a+++ +       lv++++++a
  gi|13541720|ref|NP_111408.1| 402 SIYAASFFVLYKYAKKT-GFYQANVYDLAKVWgssLVMVFVVLA 444
                                   88888888888887777.55555544332222222333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (506 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1026  (0.0572257); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.76u 0.31s 00:00:01.07 Elapsed: 00:00:00.51
# Mc/sec: 2995.32
//
Query:       gi|13541721|ref|NP_111409.1|  [L=581]
Description: acylaminoacyl-peptidase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-39  135.4   0.0    2.9e-39  134.8   0.0    1.3  1  Peptidase_S9   Prolyl oligopeptidase family
    8.5e-08   32.1   3.6    0.00014   21.6   2.4    2.3  2  Abhydrolase_1  alpha/beta hydrolase fold
    5.4e-07   29.1   0.5     0.0032   16.8   0.0    2.3  2  Hydrolase_4    Serine aminopeptidase, S33
    1.9e-06   27.3   0.2       0.28   10.3   0.0    3.1  3  DUF2920        Protein of unknown function (DUF2920)
    1.8e-05   24.5   0.0    0.00019   21.2   0.0    2.2  2  FSH1           Serine hydrolase (FSH1)
    0.00018   21.1   0.0    0.00029   20.4   0.0    1.3  1  DLH            Dienelactone hydrolase family
  ------ inclusion threshold ------
      0.041   13.5   0.0       0.25   10.9   0.0    2.0  2  Peptidase_S15  X-Pro dipeptidyl-peptidase (S15 family)
      0.042   14.4   0.0      0.063   13.9   0.0    1.3  1  Abhydrolase_6  Alpha/beta hydrolase family
       0.06   13.5   0.0       0.12   12.5   0.0    1.4  1  Abhydrolase_4  TAP-like protein
       0.16   11.7   0.0       0.53   10.1   0.0    1.7  2  Abhydrolase_2  Phospholipase/Carboxylesterase


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 !  134.8   0.0   1.6e-42   2.9e-39       6     209 ..     373     580 ..     368     581 .] 0.90

  Alignments for each domain:
  == domain 1  score: 134.8 bits;  conditional E-value: 1.6e-42
                                   HHHHHHCCT-EEEEE--TTSSTTHCHHHHTTSGGGGHHHHHHHHHHHHHHHHTT.S--GGGEEEEEETHHHHHHHHHHHH- CS
                  Peptidase_S9   6 elqlladrGyvvvvanirGsggyGeafhdagkrklgqnefdDfiaaaealakeg.yvdserlaitGgSyGGyltgaalnqr 85 
                                   e+++la++G+ v++ n++GsggyGe+f+ ++ +++g ++++ +i  ++ + +++ +   ++  +tGgSyGGy+t+ +++ +
  gi|13541721|ref|NP_111409.1| 373 EFNYLASNGFNVIFGNPHGSGGYGEDFAASVIGDWGGKDYEELISFVRDAKDKYgLF--DNFHVTGGSYGGYMTNHIVT-K 450
                                   7899**********************************************7766555..8999****************.* PP

                                   GGG-SEEEEESE---CCCHHCSTTS...THHHCCCC--TTT..CHHHHHHHHHH-CGGG-----EEEEEEETT-SSS-THH CS
                  Peptidase_S9  86 pdlFkaavaevpvvdvlrydsdtdl...lteeymewgnpee..neegykelspyspldnvkaypplLlihGlaDdrvppae 161
                                   +dlF+ av+e+++++ l++  ++d+   +++      +p+   n+   +++sp+ ++++  +++p+L+ihG++D+r+p+++
  gi|13541721|ref|NP_111409.1| 451 TDLFRSAVSERSISNFLSMCGTSDIgfwFNAIENAVKDPWIseNQITLMKMSPIYHVKR--VKTPILFIHGENDSRCPIEQ 529
                                   **************************875553333344543447888889999999999..99****************** PP

                                   HHHHHHHHH--S-SEEEEEETTS-S...STTSSHHHHHHHHHHHHHHHHHC CS
                  Peptidase_S9 162 alklvaaLqkkgknvlllifpdegH...gvgkprakveelarllaFlkeal 209
                                   a+++++aL+ +g++++l+   +  H   + g+p++ +++l+  l+++k++ 
  gi|13541721|ref|NP_111409.1| 530 AEQFYTALKINGVETKLVRSIGDSHehaRKGNPENMRKRLELKLEWFKSHS 580
                                   *************************988888999999**********9986 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   2.4   7.9e-08   0.00014       1      90 [.     353     447 ..     353     474 .. 0.76
   2 !    9.7   0.0   0.00034      0.61     187     240 ..     477     542 ..     455     555 .. 0.80

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 7.9e-08
                                   SEEEEE-STTTCGGG..GTTGHHHHHHHHTTSEEEEEEETTST...TSSSTTTGB.....CHHSHHHHHHHHHHHHHHCTT CS
                 Abhydrolase_1   1 pvlvilhGlpgssdv..waerglapaLakdgfdvillDlrGvg...ySspapacin....ddygtasvaddldrildalgd 72 
                                   p+++++hG+p  s+   ++    +++La +gf vi  ++ G+g   +  +a+        +dy+   +  +++ ++d++g+
  gi|13541721|ref|NP_111409.1| 353 PTILFVHGGPHASYGnaYYI--EFNYLASNGFNVIFGNPHGSGgygEDFAASVI-GdwggKDYEE--LISFVRDAKDKYGL 428
                                   789********877744555..9***************9887621044444444.2587777777..78888888888885 PP

                                   .SSEEEEEETHHHHHHHHH CS
                 Abhydrolase_1  73 .dkltlvGhSmGGmialay 90 
                                    d++++ G+S+GG +  + 
  gi|13541721|ref|NP_111409.1| 429 fDNFHVTGGSYGGYMTNHI 447
                                   59999********987665 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00034
                                   HHHHHHHHCCHHHHHHHHHC..........THHHHSEEEEEEETTCSSSCH.HHHHHHHHC.HTSE CS
                 Abhydrolase_1 187 ksieqwpttdsaklllrlre..........lknvlaptlvisgtsDplvpp.kaledlaql.lpkk 240
                                   ++++ +++  +++++ + ++          +k v+ p+l+i+g++D   p+ +a  ++++l ++++
  gi|13541721|ref|NP_111409.1| 477 FWFNAIENAVKDPWISENQItlmkmspiyhVKRVKTPILFIHGENDSRCPIeQAEQFYTALkINGV 542
                                   56677777777778877777999999*************************888888877777764 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.5   0.00022      0.39       4      96 ..     352     450 ..     349     459 .. 0.77
   2 !   16.8   0.0   1.8e-06    0.0032     187     227 ..     507     547 ..     496     553 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00022
                   Hydrolase_4   4 kavvvlvHGl..aehsgryaelaeaLaaqGfavyalDhrGhGrsegkrghvpsfddy.vdDlaafvekvkeehpel....p 77 
                                     ++++vHG   a++ ++y   +++La +Gf+v+  + +G G  + +    + + d+  +D +++++ v++ + +     +
  gi|13541721|ref|NP_111409.1| 352 NPTILFVHGGphASYGNAYYIEFNYLASNGFNVIFGNPHGSGGYG-EDFAASVIGDWgGKDYEELISFVRDAKDKYglfdN 431
                                   6799*****6437788999999**********************5.55445555554257888888888766666656789 PP

                   Hydrolase_4  78 lfllGhSmGGliallyllr 96 
                                   + + G S GG+++ +++++
  gi|13541721|ref|NP_111409.1| 432 FHVTGGSYGGYMTNHIVTK 450
                                   99*********99888766 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 1.8e-06
                   Hydrolase_4 187 aakitlPllllhGeaDkvvdpeasrelyerlgskdktlkly 227
                                   ++++++P+l++hGe+D  ++ e+++++y +l+ + ++ kl 
  gi|13541721|ref|NP_111409.1| 507 VKRVKTPILFIHGENDSRCPIEQAEQFYTALKINGVETKLV 547
                                   6899****************************999888875 PP

>> DUF2920  Protein of unknown function (DUF2920)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.0    0.0011       1.9     252     294 ..      53      95 ..      21     104 .. 0.86
   2 !   10.3   0.0   0.00016      0.28     163     199 ..     415     450 ..     411     465 .. 0.84
   3 !    5.7   0.0    0.0039       6.9     284     320 ..     511     546 ..     494     554 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0011
                       DUF2920 252 rkensprfFdneryliRtlleedllqlqsqknkntiyvsyHse 294
                                    +e+sp+f +++ y+iR+  + d+l++  + ++ t  +syH +
  gi|13541721|ref|NP_111409.1|  53 GRESSPKFINDDLYYIRSDENTDHLMVLRRYSEPTEIFSYHKI 95 
                                   5789***********************9999999999999975 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00016
                       DUF2920 163 iinalkdlvkrfpkeadlpviliGgsyGGYlal.LiaK 199
                                   +i  ++d++ +++ +   +  + GgsyGGY+++ +++K
  gi|13541721|ref|NP_111409.1| 415 LISFVRDAKDKYGLFD--NFHVTGGSYGGYMTNhIVTK 450
                                   678899*******998..9999*********8614455 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.0039
                       DUF2920 284 kntiyvsyHsekDklapaeeKiqlakilkklgfdvel 320
                                   k t  +++H e+D+  p+e+ +q++++lk+ g + +l
  gi|13541721|ref|NP_111409.1| 511 K-TPILFIHGENDSRCPIEQAEQFYTALKINGVETKL 546
                                   4.8899**************************99887 PP

>> FSH1  Serine hydrolase (FSH1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.25   4.5e+02     172     205 ..     295     327 ..     290     333 .. 0.89
   2 !   21.2   0.0     1e-07   0.00019      85     189 ..     411     539 ..     406     551 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.25
                          FSH1 172 DtvvdeerseaLaeafknsskvlkHpggHfvPnk 205
                                   D+ v+e+++ +++++f++ + +l + gg f Pn+
  gi|13541721|ref|NP_111409.1| 295 DFDVSENEMAYIYTNFEK-PSILSFRGGEFDPNN 327
                                   788999************.*********999986 PP

  == domain 2  score: 21.2 bits;  conditional E-value: 1e-07
                          FSH1  85 gleesldavkdyikengpfdG..iiGFSqGaalaallaslleellkeashpslkfailvsGfkleepk............. 150
                                   ++ee +++v+d+ ++ g fd   + G S G+ +++ ++++++  +   s+ s+  ++ ++G +  +               
  gi|13541721|ref|NP_111409.1| 411 DYEELISFVRDAKDKYGLFDNfhVTGGSYGGYMTNHIVTKTDLFRSAVSERSISNFLSMCGTSDIGFWfnaienavkdpwi 491
                                   6788999999999999999864489*****************999888999999999999977633335555677888999 PP

                          FSH1 151 .........yeeyyeedkiqtptLhvlGelDtvvdeerseaLaeafkn 189
                                            +++ y+ ++++tp+L+++Ge+D+  + e++e++++a k 
  gi|13541721|ref|NP_111409.1| 492 senqitlmkMSPIYHVKRVKTPILFIHGENDSRCPIEQAEQFYTALKI 539
                                   888888887778999999*************************99875 PP

>> DLH  Dienelactone hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   1.6e-07   0.00029     135     213 ..     502     576 ..     497     580 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 1.6e-07
                           DLH 135 keleeaakikapilalfgeeDefipadevekleealkaanvdlelkvYpgagHaFandsresyneeaaedawervlelf 213
                                   +++ +++++k+pil+++ge+D   p +++e++  alk ++v+ +l+   g  H  a++ +++   ++     e  le+f
  gi|13541721|ref|NP_111409.1| 502 SPIYHVKRVKTPILFIHGENDSRCPIEQAEQFYTALKINGVETKLVRSIGDSHEHARKGNPENMRKR----LELKLEWF 576
                                   6788899****************************************99999988888776544443....44444444 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 ?   -0.2   0.1      0.34   6.1e+02     103     136 ..     432     464 ..     349     471 .. 0.75
   2 ?   10.9   0.0   0.00014      0.25     220     261 ..     503     547 ..     472     554 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.34
                                   EEEEEECHHHHHHHHHCTT--TTEEEEEEECE-S CS
                 Peptidase_S15 103 VgmtGiSYlGttqllaaatgvpalkaivpeaais 136
                                     +tG SY+G++ + + + +++  + +v+e +is
  gi|13541721|ref|NP_111409.1| 432 FHVTGGSYGGYMTNHIVT-KTDLFRSAVSERSIS 464
                                   557999****99998888.666666666666666 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00014
                                   HHHHHCT--S-EEEEEECCSSTTC.CHHHHHHHHHCCTT-..EEE CS
                 Peptidase_S15 220 lsedadkvkapvllvgGwnDwnvk.ngaiklyealkapgv..kli 261
                                   +  ++++vk+p+l+++G nD     ++a ++y alk +gv  kl+
  gi|13541721|ref|NP_111409.1| 503 PIYHVKRVKTPILFIHGENDSRCPiEQAEQFYTALKINGVetKLV 547
                                   34478****************999************999877665 PP

>> Abhydrolase_6  Alpha/beta hydrolase 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     0.063       1      81 [.     355     446 ..     355     534 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.5e-05
                                   EEEE--GC.....G...CHHHHHHHHCCTCEEEEE--T....TST..S-GGCS--HHHCHHHHHHHCCTT........TTS CS
                 Abhydrolase_6   1 vlllHGagssassW...lvapLaallaagvhvlapDlp....GhG..rsdpppldledladlaalldelaa......gggp 66 
                                   +l++HG+++   s+   ++ ++ +l++ g+ v+ +  p    G+G  ++ +   d+    d+++l+  +++        ++
  gi|13541721|ref|NP_111409.1| 355 ILFVHGGPH--ASYgnaYYIEFNYLASNGFNVI-FGNPhgsgGYGedFAASVIGDWGG-KDYEELISFVRDakdkygLFDN 431
                                   89****888..66665436699999****7777.888866666663333445577777.8887777777666667777777 PP

                                   EEEEEETCHHHHHHH CS
                 Abhydrolase_6  67 vvlvGHSlGGalala 81 
                                   +++ G S+GG++  +
  gi|13541721|ref|NP_111409.1| 432 FHVTGGSYGGYMTNH 446
                                   8*********96655 PP

>> Abhydrolase_4  TAP-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   6.5e-05      0.12      31      80 ..     508     561 ..     495     565 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.5e-05
                 Abhydrolase_4  31 akgaapvLllqnerDpaTPyegakklakalgg.a...vlvtvegeGHgalaagn 80 
                                   +++++p+L++ +e+D  +P e+a+++  al+  +   +lv   g+ H+  ++gn
  gi|13541721|ref|NP_111409.1| 508 KRVKTPILFIHGENDSRCPIEQAEQFYTALKInGvetKLVRSIGDSHEHARKGN 561
                                   44579*********************9999864455577777777777766555 PP

>> Abhydrolase_2  Phospholipase/Carboxylesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       1.4   2.6e+03      11      22 ..     349     360 ..     347     380 .. 0.85
   2 ?   10.1   0.0   0.00029      0.53     153     201 ..     507     556 ..     495     566 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.4
                                   S---EEEEEE-- CS
                 Abhydrolase_2  11 dkaqavviflHG 22 
                                   dk++++++f+HG
  gi|13541721|ref|NP_111409.1| 349 DKNNPTILFVHG 360
                                   78899******9 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00029
                                   GG.GG-EEEEEEETT-SSS-HHHHHHHHHHHHTTS-GEEEEEETT--SS- CS
                 Abhydrolase_2 153 vt.kklpilqiHgeeDpvvplalgkaakevlkkllkkvelksyeglaHsi 201
                                   v  +k+pil iHge D   p+  +++++ +lk +  + +l+   g +H+ 
  gi|13541721|ref|NP_111409.1| 507 VKrVKTPILFIHGENDSRCPIEQAEQFYTALKINGVETKLVRSIGDSHEH 556
                                   44479*************************99888877777777777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (581 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.71u 0.28s 00:00:00.99 Elapsed: 00:00:00.49
# Mc/sec: 3546.14
//
Query:       gi|13541722|ref|NP_111410.1|  [L=341]
Description: glycosyltransferase [Thermoplasma volcanium GSS1]
Scores for complete 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-12   46.0   0.0    8.9e-12   44.9   0.0    1.6  1  Glycos_transf_1  Glycosyl transferases group 1
    1.2e-08   35.4   0.0    2.4e-08   34.5   0.0    1.5  1  Glyco_trans_1_4  Glycosyl transferases group 1


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.9   0.0     1e-15   8.9e-12       7     123 ..     172     280 ..     167     298 .. 0.87

  Alignments for each domain:
  == domain 1  score: 44.9 bits;  conditional E-value: 1e-15
                                   HHTTTTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSSSHH CS
               Glycos_transf_1   7 kklgknekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsredle 87 
                                   + ++ +e+ k+ils+g  + +K++dl+i+ + +l++    ++ ++ +G   ++ +l+ +  e + + + +++ ++s+++l+
  gi|13541722|ref|NP_111410.1| 172 EIKRVRETVKTILSIGSNDQRKRPDLVIDFLNSLPA----EYTFIRVG--GDLSTLHGK--EIKPKCKFEYYHNLSEDQLD 244
                                   566778999*************************74....57777777..466666655..888888999*********** PP

                                   HHHHCESEEEEEESSBSS-HHHHHHHHTT--EEEET CS
               Glycos_transf_1  88 ellknadifvlpsisEgfGivllEAmaaglpviasn 123
                                   +l+++adi+++ps++Eg+G++++EA+  ++pv++  
  gi|13541722|ref|NP_111410.1| 245 ALYNRADILFFPSEKEGLGLPIIEALIHRIPVLINS 280
                                   ********************************9865 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 !   34.5   0.0   2.7e-12   2.4e-08       2     101 ..     181     280 ..     180     304 .. 0.81

  Alignments for each domain:
  == domain 1  score: 34.5 bits;  conditional E-value: 2.7e-12
                                   EEEEEES---GG.GTHHHHHHHHHHHH.HHEEEEEES---..HHHHHHHTT-T.TEEEE---...TH.HHHHHHH-SEEEE CS
               Glyco_trans_1_4   2 pvilfvGrleenvkgvdllleavpllrkkdvrlvivGdgprpeeleelaagleerveftGfv...ed.laellaaadvfva 78 
                                   ++il +G+  +++k+ dl+++ +  l ++ ++++ vG g+ +  l+   ++++++++f  +    ed l++l+++ad++ +
  gi|13541722|ref|NP_111410.1| 181 KTILSIGSN-DQRKRPDLVIDFLNSLPAE-YTFIRVG-GDLS-TLHG--KEIKPKCKFEYYHnlsEDqLDALYNRADILFF 255
                                   689999*99.677************9955.9******.7554.5652..2567887777777778556************* PP

                                   --..---SHHHHHHHHTT-EEEE-T CS
               Glyco_trans_1_4  79 Ps..egfglkllEamaaglpvVatd 101
                                   Ps  eg+gl ++Ea+ + +pv   +
  gi|13541722|ref|NP_111410.1| 256 PSekEGLGLPIIEALIHRIPVLINS 280
                                   **888****************8764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        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 0.23s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 2543.29
//
Query:       gi|13541723|ref|NP_111411.1|  [L=340]
Description: cell wall biosynthesis glycosyltransferase [Thermoplasma volcanium GSS1]
Scores for complete 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   69.8   0.7      4e-19   69.0   0.7    1.3  1  Glycos_transf_2  Glycosyl transferase family 2
      5e-07   29.9   0.0    7.1e-07   29.3   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 !   69.0   0.7   4.5e-23     4e-19       1     166 [.       5     166 ..       5     169 .. 0.82

  Alignments for each domain:
  == domain 1  score: 69.0 bits;  conditional E-value: 4.5e-23
                                   EEEEEESS-TTTHHHHHHHHHHH.GGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH--S CS
               Glycos_transf_2   1 svviptyNeektlletlesllaq.dpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglraatg 80 
                                   sv+i++yN+++ ll +++s+l+q  +++ +eiiv+++  +D   ++++e      +++ i  e n+ ++g + ++l+a+ g
  gi|13541723|ref|NP_111411.1|   5 SVIITAYNRKEFLLDAIKSALNQtLDRKYYEIIVIKNFQEDTIDNFIKEN-----NIKGIISE-NKSLGGKISEALKASEG 79 
                                   8**********************9999***********************.....9*******.77*************** PP

                                   SEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SS..EEEECCHCCCCHCCCCCCSTTCSTCCC CS
               Glycos_transf_2  81 dyilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrv..generlyfkerkrslkgnlsfeigsaa 159
                                   +++ fl +Dd +d+++le +++++ + ++d+v+++   i  +++ +e +k+   +e+    ++ rk  l++n + +  s  
  gi|13541723|ref|NP_111411.1|  80 EIVSFLEDDDMFDRQKLETVYRKFRE-NPDIVYYHNNQIIIDENGKEIRKNGvlNERKLNSTEVRKSPLDINPMLFNMSSI 159
                                   **************************.777888877666666665555555446555555555555555555555555555 PP

                                   EEEEHHH CS
               Glycos_transf_2 160 llrreal 166
                                    +rr+++
  gi|13541723|ref|NP_111411.1| 160 SIRRSYY 166
                                   5566655 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 !   29.3   0.0     8e-11   7.1e-07       4     121 ..       4     111 ..       2     123 .. 0.84

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 8e-11
               Glyco_tranf_2_3   4 lavlVptfneedvlgevlesllaqeypr..vevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksralnea 82 
                                   ++v+++++n+ + l++ + s+l+q+ +r  +e++v+ +  ++   ++++e      +  ++ ++ ++  + +gk+    ea
  gi|13541723|ref|NP_111411.1|   4 ISVIITAYNRKEFLLDAIKSALNQTLDRkyYEIIVIKNFQEDTIDNFIKE------N-NIKGIISEN-KSLGGKIS---EA 73 
                                   79**********************986668*************9****99......3.466666655.45557765...** PP

               Glyco_tranf_2_3  83 lravksdlvllvDdDtvvePdtlkrllqffltpkvgavg 121
                                   l+a ++++v +++dD+  +   l+ + + f ++++++v+
  gi|13541723|ref|NP_111411.1|  74 LKASEGEIVSFLEDDDMFDRQKLETVYRKF-RENPDIVY 111
                                   ****************99888888777777.66666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (340 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       735  (0.040995); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 2159.08
//
Query:       gi|13541724|ref|NP_111412.1|  [L=504]
Description: gamma-glutamyltranspeptidase [Thermoplasma volcanium GSS1]
Scores for complete 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-105  351.2   0.0   6.5e-104  348.5   0.0    1.8  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 !  348.5   0.0  3.6e-108  6.5e-104       2     512 .]      25     499 ..      24     499 .. 0.91

  Alignments for each domain:
  == domain 1  score: 348.5 bits;  conditional E-value: 3.6e-108
                                   HHHHTT--HHHHHHHHHHHHHHHSTTT-STTSEEEEEEEETTSCEEEEEEE--BB-TT--TTTTTSCBCCHHHHSSGG.G- CS
               G_glu_transpept   2 evLrkGGnAvDAavAaalclgvvepqssGiGGGgfllvydaktkkvealdaretAPaaatkdmfdkegdsklsktgal.av 81 
                                   ++++kGGn +DAa+A++ +l+v++ + +G+GG++f+lv+ +++ k   +++++++ +++++ ++ + g s+++++g   a+
  gi|13541724|ref|NP_111412.1|  25 KIIEKGGNIFDAAIAVSSVLSVTQNNLCGLGGDAFALVRYNGRVKG--YNGSGKSSRNVNRGLYFELGYSRIPERGIYsAI 103
                                   799*************************************999988..7***************9***********9989* PP

                                   BB--HHHHHHHHHHHH-SS-HHHHHHHHHHHHHH-EE--HHHHHHHHHCHHHHHTSHHHHHHHEETTSE--TTSEE--HHH CS
               G_glu_transpept  82 gVPGevagleeahkkyGklpwadllepaiklareGfpvsealaralaeaeerlkkdpelaklFlpegevlkagellkqpal 162
                                   +VPG v+ +  ++ +y+++ ++dl+  aik+a+ Gf +++++++ l ++++ l ++ ++++ F+p g+++++g+l+ q++l
  gi|13541724|ref|NP_111412.1| 104 TVPGLVDLWNSLYLEYATMRFSDLISDAIKYAETGFYITRHYEESLIASSPILGQY-NWSNQFMPYGKIPAEGDLFIQKDL 183
                                   ***************************************************87777.999********************* PP

                                   HHHHHHHHHHTTHHHHSSHHHHHHHHHHHHTT-S--HHHHHH---EEES-EEEEETTCEEEEE-TTCSHHHHHHHHHHHHC CS
               G_glu_transpept 163 AktLerlaeeGaeaFYkGelAeklvaelqkagGiltaeDLanykvevreplsadyrggytvyepppssggivllqiLnile 243
                                   A tL+++aeeG+++FY+G l + + + ++k++ ++  +DL+++k+   +p++ +y  +y+v+e+ p+s+g+++  +L +le
  gi|13541724|ref|NP_111412.1| 184 AGTLREIAEEGPRSFYDGYLSDIIFKAMEKTNLLIDSKDLSDHKTLAANPVKSTY-MDYDVFETAPNSQGATVNYWLALLE 263
                                   *******************************************************.89*********************** PP

                                   TTTGGGCTTTCHHHHHHHHHHHHHHHHHHHHH-SSTTTSSSGHCHHHHHT-HHHHHHHHTT.BTTB..SGGGCSCGGCSCG CS
               G_glu_transpept 244 gfdlkslssnsaetlhllvEamklayadRsrylgDpdfvknptelveellskeyakeraklIkdkaatpsseyykaaeaae 324
                                   +  +++       +   +vE+   ay+ Rs ++gDp+ ++    +  +llsk              a p   yy++   +e
  gi|13541724|ref|NP_111412.1| 264 QKIQNK-----IPRPVDIVESGLEAYRWRSMFIGDPERMP----FNGDLLSK-------------GAGP---YYNNPRVPE 319
                                   *99443.....34456788888889999***********9....57899999.............3333...788888899 PP

                                   .TTEEEEEEEEETTS-EEEEEEEESSTTTTSEBETTTTEBE--GGGGSBSTS..TTSCSTTSTTB--TT----B----EEE CS
               G_glu_transpept 325 esggTthlsvvDregnaVSltstinllFGsgvvvpgtGilLnnemddfstgvenafgldpspanaiePgkRplssmaPtiv 405
                                   ++g+Tt++s+ D++gn +S++++++++FGsg++ +gtG++L+n+++ f+        ld ++ n +eP+kR+++++a +i+
  gi|13541724|ref|NP_111412.1| 320 DKGDTTYFSISDANGNSISMIQSNYMGFGSGIIPEGTGFVLQNRGSYFT--------LDDKHHNSLEPRKRTFHTLAACII 392
                                   9************************************************........************************ PP

                                   EETTEEEEEEEEESGGGHHHHHHHHHHHHHTT-S-HHHHHHS--EEE.....SSSSTEEEESTTS.HHHHHHHHHTTSEEE CS
               G_glu_transpept 406 lkdgkpvlvlGaaGGsriisavlqvlvnvldlgldlqeavdaprihh.....qllpdkvevEegfseevveeLearGhkvk 481
                                   +kdg+ v  lG++GG+ ++++++q+++  + ++l +qea+++pr+       + +p +++vE+    ++++e e    +++
  gi|13541724|ref|NP_111412.1| 393 EKDGELVYSLGTMGGDIQPQVQVQIITGLINQDLMPQEAIERPRWAFpatiyE-QPSVLNVED---TSLINENE-TRLRIN 468
                                   *********************************************99777742.577888886...33333322.223455 PP

                                   ESSSTCCCEEEEEEEETTTEEEEEE-TTTTT CS
               G_glu_transpept 482 evedsssvvaavavakekgvleaasDprkdg 512
                                     + sss+++a+++a  +g++ ++sDpr+dg
  gi|13541724|ref|NP_111412.1| 469 PMKYSSSFGTAQVTALLNGRVAGGSDPRGDG 499
                                   55666666666666669***********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (504 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.34s 00:00:00.95 Elapsed: 00:00:00.51
# Mc/sec: 2961.92
//
Query:       gi|13541725|ref|NP_111413.1|  [L=409]
Description: sugar transport permease [Thermoplasma volcanium GSS1]
Scores for complete 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-37  127.6  49.8    5.3e-37  127.6  49.8    1.6  2  MFS_1      Major Facilitator Superfamily
    4.6e-14   52.1  41.9    3.4e-10   39.4  15.1    2.3  2  Sugar_tr   Sugar (and other) transporter
    7.5e-05   21.3   6.8    7.5e-05   21.3   6.8    2.1  2  MFS_3      Transmembrane secretion effector
  ------ inclusion threshold ------
       0.28   11.4   4.7         18    5.6   0.2    3.6  3  DUF2530    Protein of unknown function (DUF2530)
       0.77    8.5  39.4      0.011   14.6   7.6    3.5  4  LacY_symp  LacY proton/sugar symporter
        6.2    5.3  42.9        1.1    7.8   9.4    2.8  2  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 !  127.6  49.8   1.8e-40   5.3e-37       6     353 .]      27     352 ..      13     352 .. 0.86
   2 !    7.9   0.6   0.00041       1.2     128     175 ..     342     388 ..     342     400 .. 0.75

  Alignments for each domain:
  == domain 1  score: 127.6 bits;  conditional E-value: 1.8e-40
                         MFS_1   6 flsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll.fassl 85 
                                   ++s ++ s+++ a+p ++ +   +    +g+l+++ya+g a++sl++G++ drf+++++++ ++llf+++ ++l+ + s+ 
  gi|13541725|ref|NP_111413.1|  27 LVSDFDGSAYTYAAP-YILSRISLPTFYFGILISGYAAGIAIFSLVGGFMFDRFSPKSTVVYSVLLFSIF-TILTgY-STN 104
                                   566777788888888.777777788888******************************************.888868.666 PP

                         MFS_1  86 w.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllaf 165
                                      l+++rvl G+g g++ +a+++++ d  p+  rg ++ ++++ ++lG+ ++p +   ++   ++r +f+i +i++++++
  gi|13541725|ref|NP_111413.1| 105 AiELVISRVLVGFGVGMFQSASVSFLGDANPE-TRGAGVMVWGVLAGLGTFIAPYIILPFL--PNYRIPFLISGILGFIVA 182
                                   769*************************9999.9999999*************88866666..589**************7 PP

                         MFS_1 166 vlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsglltllplylqevlglsgllla 246
                                    +  ++++++p+ +k ++ k              ++++l++  ++  ++++++f+f + gll +   +l +v g++   ++
  gi|13541725|ref|NP_111413.1| 183 AV--FYFVVPPVFKKEEKLKNP------------FRHVLNRYSVF-PMVSMFFFGFTLLGLLGYYSDFLSSVVGFG-KTSV 247
                                   74..777777777777665555............77777777554.55555555556666555555558*******.8*** PP

                         MFS_1 247 glllallalvgailallagrlsdrlgrrrrlllallllllaalglallavtssavllllvlvliGfglgfvfpsllalasd 327
                                   ++++++l+++g+i+++ ag +sd +gr++ l++a+ l++++ l++ +++     +l+ll+ + +G+g++++++++ a  +d
  gi|13541725|ref|NP_111413.1| 248 AIIISFLGVGGVIFGIPAGIFSDMVGRKIVLIIAITLISISMLAITYAPRD--LILFLLATLAFGTGWSIFSILSPATGQD 326
                                   ***************************888888888888888888888888..7777778888****************** PP

                         MFS_1 328 lappeeagtasglfntagslggalgp 353
                                   ++  e+ g++sg++ +++++gg++gp
  gi|13541725|ref|NP_111413.1| 327 MVRDEAVGSVSGAILMTFNIGGIIGP 352
                                   *************************9 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.00041
                         MFS_1 128 agfslGailgpllgglla.sslgWravfyilaivsllafvlfllllpee 175
                                   ++f++G i+gpl  gl++   +  ra f+ +  + +++++l  l +  +
  gi|13541725|ref|NP_111413.1| 342 MTFNIGGIIGPLMIGLILaKGFTLRAGFLYFIDIPAILALL--LTIAMK 388
                                   579*******9999988879999999999998888888775..444444 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.4  15.1   1.1e-13   3.4e-10      43     191 ..      44     188 ..      17     209 .. 0.86
   2 !   18.6  18.7   2.3e-07   0.00069      47     188 ..     246     387 ..     211     391 .. 0.89

  Alignments for each domain:
  == domain 1  score: 39.4 bits;  conditional E-value: 1.1e-13
                                   H........HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHH CS
                      Sugar_tr  43 e.....ssvlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGl 118
                                          + + g++ s + +G +i sl++g++ drf+ k++ + +++lf+i ++l++ ++   +   l+++RvlvG+gvG+
  gi|13541725|ref|NP_111413.1|  44 LsrislPTFYFGILISGYAAGIAIFSLVGGFMFDRFSPKSTVVYSVLLFSIFTILTGYST---NAIELVISRVLVGFGVGM 121
                                   15555578899*************************************************...8999************** PP

                                   HHHHHHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-TTHHHHHHHCCHHHHHHHHHHGGGS CS
                      Sugar_tr 119 asvlvPmyisEiApkklRgalvslyqlaitfGilvaaifglglnktsnadgwrillglqlvpallllilllfl 191
                                   ++  +  +++  A ++ Rga v+++ +   +G ++a  + l +    n   +ri++ ++ ++  +++++++f+
  gi|13541725|ref|NP_111413.1| 122 FQSASVSFLGD-ANPETRGAGVMVWGVLAGLGTFIAPYIILPF--LPN---YRIPFLISGILGFIVAAVFYFV 188
                                   ********996.78889*******************8877666..445...7899999999999888888775 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 2.3e-07
                                   HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHHHHH CS
                      Sugar_tr  47 lsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlvPmyi 127
                                    + +i s++ vG++i ++ ag+++d++GRk +l+ia++l +i+ + +  a+  + + +++++ +  G g+ ++s+l+P + 
  gi|13541725|ref|NP_111413.1| 246 SVAIIISFLGVGGVIFGIPAGIFSDMVGRKIVLIIAITLISISMLAITYAP--RDLILFLLATLAFGTGWSIFSILSPATG 324
                                   567999***************************************999999..68************************** PP

                                   HTTS-SCCHHHHHHHHHHHHHHHHHHH.HHHHHHHHTSS-.TTHHHHHHHCCHHHHHHHHHHG CS
                      Sugar_tr 128 sEiApkklRgalvslyqlaitfGilva.aifglglnktsn.adgwrillglqlvpallllill 188
                                   + +  ++  g + +   +   +G +++  ++gl+l+k    + g+ +++ + +++alll i++
  gi|13541725|ref|NP_111413.1| 325 QDMVRDEAVGSVSGAILMTFNIGGIIGpLMIGLILAKGFTlRAGFLYFIDIPAILALLLTIAM 387
                                   ****999999888877777777766663799****98888899*************9999876 PP

>> MFS_3  Transmembrane secretion effector
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   1.3     0.027        81     255     318 ..      53     116 ..      18     131 .. 0.63
   2 !   21.3   6.8   2.5e-08   7.5e-05      46     196 ..     246     395 ..     234     407 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.027
                         MFS_3 255 vyGillgalGvGAilgalllsrLRerlsserlvllaavalAlvllslalasslwvavlvlllgG 318
                                    +Gil+++  +G  + +l+  ++ +r+s +  v ++++ + +  + ++ ++++  +v+  +l G
  gi|13541725|ref|NP_111413.1|  53 YFGILISGYAAGIAIFSLVGGFMFDRFSPKSTVVYSVLLFSIFTILTGYSTNAIELVISRVLVG 116
                                   4566666666666666666666666666666666666666666666666666555555444444 PP

  == domain 2  score: 21.3 bits;  conditional E-value: 2.5e-08
                         MFS_3  46 mvAlvqaaatLPifllsilaGalaDnfdrRkvllavqlllalvsvlltvlaalgllspwlllaltlligiGaalndPaWqA 126
                                    vA++     +  +++ i+aG+ +D + r+ vl+++   l++ s+l+++ a  +l   +l l  tl  g G ++ +    A
  gi|13541725|ref|NP_111413.1| 246 SVAIIISFLGVGGVIFGIPAGIFSDMVGRKIVLIIAI-TLISISMLAITYAPRDL---ILFLLATLAFGTGWSIFSILSPA 322
                                   566666666666789************9776666655.55677888877777665...5778889999*****9999999* PP

                         MFS_3 127 svgelvkrrdvpaAvaLnsvginiaRsvGPAlgGvlvaa...vGaalafavnalsylalivallrwkrevrks 196
                                   + +++v+ + v +      + +ni   +GP + G+++a    + a + + ++  + lal+++++   ++  k+
  gi|13541725|ref|NP_111413.1| 323 TGQDMVRDEAVGSVSGAILMTFNIGGIIGPLMIGLILAKgftLRAGFLYFIDIPAILALLLTIAMKYPKNIKE 395
                                   *************99999*******************963223455667788888888888887655554444 PP

>> DUF2530  Protein of unknown function (DUF2530)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.2     0.006        18      13      54 ..      81     122 ..      78     129 .. 0.91
   2 ?    5.6   0.0    0.0063        19      14      36 ..     169     191 ..     161     199 .. 0.85
   3 ?   -2.9   0.2       2.8   8.3e+03      41      48 ..     299     306 ..     273     319 .. 0.45

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.006
                       DUF2530  13 prpvivvgtllWlvalvvllvvgdaleswlpvclaGlvvGll 54 
                                   p+  +v  +ll+ + ++++  +++a+e ++   l+G++vG++
  gi|13541725|ref|NP_111413.1|  81 PKSTVVYSVLLFSIFTILTGYSTNAIELVISRVLVGFGVGMF 122
                                   677899999*******************************86 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0063
                       DUF2530  14 rpvivvgtllWlvalvvllvvgd 36 
                                    p+++ g+l ++va+v  +vv +
  gi|13541725|ref|NP_111413.1| 169 IPFLISGILGFIVAAVFYFVVPP 191
                                   5899**************99854 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 2.8
                       DUF2530  41 wlpvclaG 48 
                                   ++ + la 
  gi|13541725|ref|NP_111413.1| 299 LILFLLAT 306
                                   33333333 PP

>> LacY_symp  LacY proton/sugar symporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   4.7   3.9e-06     0.012     215     327 ..       6     120 ..       1     133 [. 0.84
   2 ?   -2.1   4.0      0.42   1.3e+03      77     118 ..     144     186 ..     139     195 .. 0.75
   3 ?   14.6   7.6   3.6e-06     0.011       9      85 ..     210     287 ..     203     310 .. 0.80
   4 ?   -2.7   0.7      0.62   1.8e+03     101     121 ..     342     362 ..     337     370 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.9e-06
                     LacY_symp 215 elfkdrklwvfvlyvvGva.svydvfdqqfavffks.lfespeaGtrvfGyvttagellnalimfiaplivnriGaknall 293
                                   ++  ++k+w+++++vvG   ++   fd    ++ +  +++     t  fG + +      a+  ++  ++ +r  +k +++
  gi|13541725|ref|NP_111413.1|   6 NIVSNNKIWMLIIFVVGAIpALVSDFDGSAYTYAAPyILSRISLPTFYFGILISGYAAGIAIFSLVGGFMFDRFSPKSTVV 86 
                                   567789***********76256777998755555441556678889999***99999999999****************** PP

                     LacY_symp 294 iagvimsvrilgsafattalevvilkllhalevp 327
                                    ++++ s+  + + ++t+a+e+vi ++l  + v 
  gi|13541725|ref|NP_111413.1|  87 YSVLLFSIFTILTGYSTNAIELVISRVLVGFGVG 120
                                   ********99999*************99888775 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.42
                     LacY_symp  77 lw.vislllvlfapfliyvfepllqlnilvGalvGgvflGlvy 118
                                   +w v++ l  ++ap++i  f p  ++ +l+  ++G +   + y
  gi|13541725|ref|NP_111413.1| 144 VWgVLAGLGTFIAPYIILPFLPNYRIPFLISGILGFIVAAVFY 186
                                   5634567778999999999999999999888888877655555 PP

  == domain 3  score: 14.6 bits;  conditional E-value: 3.6e-06
                     LacY_symp   9 fylf.alffffyffimsayfplfpvwlkevlglsktetGivfsvislfsilfqplfGlisdklGlkkellwvislllv 85 
                                   + +f +++ ff+ f +     +++ +l+ v+g+ kt + i+ s + +  ++f    G+ sd +G k  l+ +i+l+ +
  gi|13541725|ref|NP_111413.1| 210 YSVFpMVSMFFFGFTLLGLLGYYSDFLSSVVGFGKTSVAIIISFLGVGGVIFGIPAGIFSDMVGRKIVLIIAITLISI 287
                                   444423344445566666789************************************************999988755 PP

  == domain 4  score: -2.7 bits;  conditional E-value: 0.62
                     LacY_symp 101 lnilvGalvGgvflGlvysag 121
                                   + + +G ++G + +Gl+ + g
  gi|13541725|ref|NP_111413.1| 342 MTFNIGGIIGPLMIGLILAKG 362
                                   678899*********998766 PP

>> MFS_2  MFS/sugar transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   9.4   0.00036       1.1     217     342 ..       4     133 ..       1     138 [. 0.78
   2 ?    5.7  21.7    0.0016       4.7     149     382 ..     151     360 ..     136     368 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00036
                         MFS_2 217 lkevfrnraflillllfllaalalg..vlnglllYyltyvlgngsaasvfllvvtisal....lgiplwqplakrlgkknt 291
                                   ++++ +n + ++l+++++ a+ al+  +  +++ Y + y+l   s  ++++++++ + +    +++++   +  r++ k t
  gi|13541725|ref|NP_111413.1|   4 TRNIVSNNKIWMLIIFVVGAIPALVsdFDGSAYTYAAPYILSRISLPTFYFGILISGYAagiaIFSLVGGFMFDRFSPKST 84 
                                   677777777666665555555554411566888888999999999999999988776665556888888899*****9999 PP

                         MFS_2 292 yllgalltivllvlvlllqpsnlllflvllviagfgvgvaallpwsmladv 342
                                   ++ + ll  ++++l+     +n + +++  v++gfgvg+++++  s+l+d+
  gi|13541725|ref|NP_111413.1|  85 VVYSVLLFSIFTILTGYS--TNAIELVISRVLVGFGVGMFQSASVSFLGDA 133
                                   988887777776666665..9999************************996 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0016
                         MFS_2 149 laailafllvlilgglkserkgylifaliialLmllgviivvlgtkervemrkkekteqkeklslleqlkevfrnraflil 229
                                   l++++a+ ++l +    + r  +li ++++ +++++ +++v  ++              k+  +l + +++v+ nr+ +  
  gi|13541725|ref|NP_111413.1| 151 LGTFIAPYIILPFLP--NYRIPFLISGILGFIVAAVFYFVVPPVF--------------KKEEKLKNPFRHVL-NRYSVFP 214
                                   344444444444443..3555555555555555554444443333..............33445566777777.5677788 PP

                         MFS_2 230 lllfllaalalgvlnglllYyltyvlg.ngsaasvfllvvtisallgiplwqplakrlgkkntyllgalltivllvlvlll 309
                                   +++ +++ ++l+ l g +  +l  v+g  ++ ++++  ++ ++++++ + +  +    g+k + ++ a+ +i++++l++  
  gi|13541725|ref|NP_111413.1| 215 MVSMFFFGFTLLGLLGYYSDFLSSVVGfGKTSVAIIISFLGVGGVIFGIPAGIFSDMVGRKIVLII-AITLISISMLAITY 294
                                   88888888888888888999999****777777777777777777666666666666666655555.55555555555555 PP

                         MFS_2 310 qpsnlllflvllviagfgvgvaallpwsmladvvDygelktGkrregvffavlsfisklatgiglgvsgllLs 382
                                    p++l+lfl++++++g+g  ++ +l +++  d+v + +        g++ ++ +++ ++++ ig +++gl+L+
  gi|13541725|ref|NP_111413.1| 295 APRDLILFLLATLAFGTGWSIFSILSPATGQDMVRDEA-------VGSVSGAILMTFNIGGIIGPLMIGLILA 360
                                   5*********************************8877.......8999999999999999999999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (409 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1004  (0.0559987); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.76u 0.37s 00:00:01.12 Elapsed: 00:00:00.56
# Mc/sec: 2218.52
//
Query:       gi|13541726|ref|NP_111414.1|  [L=1030]
Description: Tricorn protease [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.9e-23   82.3   0.0    6.1e-23   81.2   0.0    1.6  1  Peptidase_S41  Peptidase family S41
    9.8e-19   67.2   1.7    2.5e-18   65.9   1.7    1.7  1  Tricorn_C1     Tricorn protease C1 domain
    4.9e-18   64.9   0.0    1.3e-17   63.6   0.0    1.7  1  Tricorn_PDZ    Tricorn protease PDZ domain
    3.1e-06   26.9  11.6    0.00026   20.8   0.2    6.8  7  PD40           WD40-like Beta Propeller Repeat
     0.0001   21.7   6.7       0.11   11.7   0.2    3.2  3  DUF5050        Domain of unknown function (DUF5050)
  ------ inclusion threshold ------
      0.014   15.2   0.0      0.029   14.2   0.0    1.5  1  PDZ_6          PDZ domain
      0.096   13.0   0.1        3.4    8.0   0.0    3.0  3  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 !   81.2   0.0   2.4e-26   6.1e-23       1     165 [.     839     993 ..     839     994 .. 0.91

  Alignments for each domain:
  == domain 1  score: 81.2 bits;  conditional E-value: 2.4e-26
                                   EEEEEEES-BCCTHHHHHHHHHHHHHH.TTSSEEEEE-TTB-EBEHHHHHHHHHCCSSSSEEEEEECTTSEEEEEEHTCSS CS
                 Peptidase_S41   1 kiGyiripsfsektkeelakalkelkk.knvkglilDlRnNgGGlldeavelaslflddglivstrgrdgkkkkkskteka 80 
                                   +iGyi+ip++       l++++++  + ++ +gli+D+R+NgGG +++++    ++ + g+  ++rg+ + +         
  gi|13541726|ref|NP_111414.1| 839 RIGYIHIPDM---GIMGLNEFYRQYVTeASRNGLIVDVRFNGGGFVSQLILEKLYMKRLGYDNPRRGTLEPYP-------- 908
                                   69********...56677777776666579*****************************99999999998888........ PP

                                   -STT-BSSEEEEEE-TTBBTHHHHHHHHHHHTTSEEEEES-.-SB-EEEEEEEE-TTSSEEEEEEEEEEETTSBC.TTTTS CS
                 Peptidase_S41  81 seevqykgplvvLvnegsaSaseifagalkdngratlvGer.tfGkgtvqsvvelndgsalkltiakyltpdgrs.iekkG 159
                                      ++ +gp++ ++ne+  S+++if++ +k  +++tl+G+r ++G  +++  ++l dg++l+ +   ++ +  ++ +e+ G
  gi|13541726|ref|NP_111414.1| 909 --MNSIEGPMIAITNEYAGSDGDIFSYSFKALHLGTLIGTRtWGGVVGISPRRKLIDGTVLSQPEYAFWFKGSGFsVENYG 987
                                   ..24699**********************************999*******************9999999888888***** PP

                                   ---SEE CS
                 Peptidase_S41 160 vePdie 165
                                   v+Pd++
  gi|13541726|ref|NP_111414.1| 988 VDPDVV 993
                                   ****97 PP

>> Tricorn_C1  Tricorn protease C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.9   1.7   9.7e-22   2.5e-18       2      70 .]     644     712 ..     643     712 .. 0.96

  Alignments for each domain:
  == domain 1  score: 65.9 bits;  conditional E-value: 9.7e-22
                                   HHHHHHHHHHHHHHHHHSS-HHHHHHHHHHHHHHHHGGGGG--SHHHHHHHHHHHHHTT--S---EE-- CS
                    Tricorn_C1   2 aEwaqmfdeawrllrdkFydpdmhgvDWeavkerYepllprvatrdeladllsemlgeLntsHvyvsgg 70 
                                   +++a+m+deaw+l rd+++d++   +  e+++erY++l++r+ tr +l++l+ e++ge++tsH+y++gg
  gi|13541726|ref|NP_111414.1| 644 EDFAEMYDEAWKLARDNYWDKEHALTISEKIYERYRKLVERCVTRWDLSYLITEIQGEYRTSHSYEMGG 712
                                   6899*****************99999***************************************9875 PP

>> Tricorn_PDZ  Tricorn protease PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.6   0.0   4.9e-21   1.3e-17       1      85 [.     723     807 ..     723     810 .. 0.97

  Alignments for each domain:
  == domain 1  score: 63.6 bits;  conditional E-value: 4.9e-21
                                   -B-SEEEEEETTEEEEEEE-BS-TTSSS-B-GGGGGS---.TT-EEEEETTEE-BTTB-HHHHHHTTTTSEEEEEEE-STT CS
                   Tricorn_PDZ   1 GlLGadleldkgayriakilpGdswdeearSPLaepGvnvreGdlilavdgepvskekgiaelLvgkagkeveLtvkrkdg 81 
                                   G++++d+++++g y i  il Gd+++e+++SP+  + +++  Gd+++++dg p++k k+i+e+Lvgk++++v +++++kd+
  gi|13541726|ref|NP_111414.1| 723 GRIACDFKYSNGEYVISDILYGDPSNENEKSPFLLSTLDADIGDAVIEIDGIPIGKGKSIYEALVGKGNRSVLVKIRKKDN 803
                                   89******************************************************************************9 PP

                                   -EEE CS
                   Tricorn_PDZ  82 karr 85 
                                    +r+
  gi|13541726|ref|NP_111414.1| 804 SVRS 807
                                   9886 PP

>> PD40  WD40-like Beta Propeller Repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.0      0.36   9.3e+02      16      24 ..     102     110 ..     100     110 .. 0.85
   2 ?    2.1   0.0     0.078     2e+02       9      37 ..     190     215 ..     183     216 .. 0.78
   3 ?    1.1   0.0      0.16   4.2e+02      19      26 ..     241     248 ..     241     249 .. 0.96
   4 ?   -2.0   0.0       1.5   3.8e+03      17      24 ..     373     380 ..     372     380 .. 0.90
   5 ?    1.3   0.0      0.14   3.5e+02      13      26 ..     411     424 ..     405     424 .. 0.87
   6 !   20.8   0.2     1e-07   0.00026       4      32 ..     453     482 ..     452     485 .. 0.88
   7 ?    0.7   0.1      0.21   5.3e+02      16      27 ..     601     612 ..     598     617 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.36
                                   E-TTSSEEE CS
                          PD40  16 fSPDGkrla 24 
                                   fS+DG+ ++
  gi|13541726|ref|NP_111414.1| 102 FSKDGSIIV 110
                                   9****9986 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.078
                                   S.EEEEEE-TTSSEEEEEEECT.TCEEEE CS
                          PD40   9 gnegaPsfSPDGkrlaFsSdRgsGkpdIy 37 
                                    ++ +P + +D   ++F  d + G  +Iy
  gi|13541726|ref|NP_111414.1| 190 NHISCPVIVKDR--IYFITDID-GAGNIY 215
                                   567777777777..******99.999999 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.16
                                   TSSEEEEE CS
                          PD40  19 DGkrlaFs 26 
                                   DGk+++Fs
  gi|13541726|ref|NP_111414.1| 241 DGKTIVFS 248
                                   9******8 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 1.5
                                   -TTSSEEE CS
                          PD40  17 SPDGkrla 24 
                                   S DGk+l+
  gi|13541726|ref|NP_111414.1| 373 SADGKYLV 380
                                   89****96 PP

  == domain 5  score: 1.3 bits;  conditional E-value: 0.14
                                   EEEE-TTSSEEEEE CS
                          PD40  13 aPsfSPDGkrlaFs 26 
                                   ++++S+D + +a+s
  gi|13541726|ref|NP_111414.1| 411 DFAISKDSRFIAYS 424
                                   689*********97 PP

  == domain 6  score: 20.8 bits;  conditional E-value: 1e-07
                                   --SSSS.EEEEEE-TTSSEEEEEEECT..T CS
                          PD40   4 ltntpgnegaPsfSPDGkrlaFsSdRg.sG 32 
                                   +t+ ++n++aP+f+ D ++l++ S+R+ + 
  gi|13541726|ref|NP_111414.1| 453 VTTETANDFAPAFDADTNYLYYLSNRSlDP 482
                                   899***********************9544 PP

  == domain 7  score: 0.7 bits;  conditional E-value: 0.21
                                   E-TTSSEEEEEE CS
                          PD40  16 fSPDGkrlaFsS 27 
                                   +S DG++++Fs 
  gi|13541726|ref|NP_111414.1| 601 ISTDGSKIMFSK 612
                                   678*******95 PP

>> DUF5050  Domain of unknown function (DUF5050)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.2   4.3e-05      0.11     160     231 ..     173     249 ..     141     264 .. 0.77
   2 ?   -0.2   0.2      0.18   4.7e+02      30      67 ..     442     481 ..     435     497 .. 0.67
   3 !   11.4   0.1   5.3e-05      0.14     150     225 ..     569     645 ..     560     650 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4.3e-05
                                   EEEEETTTTEEEEEE.-S-EEEEEEEETTEEEE.EGGGTT-EEEE-SSS---EE-S-S-...EEEEEEETTEEEEEE CS
                       DUF5050 160 lykldtdgksiskvs.eenlyllvvegdyiYyi.dlsknyaLyrvklsgsekevltedk...vdnyNvtgnwiYyqk 231
                                   +++  ++++ ++ +  e+++ ++v++ d iY+i d++   ++y ++l+g++ ++ t+ +    +++N++g++i ++ 
  gi|13541726|ref|NP_111414.1| 173 IWSGTIEKGFKKIIDlENHISCPVIVKDRIYFItDIDGAGNIYSTNLDGNDLKKHTDFHeyyPRHLNTDGKTIVFSM 249
                                   55555555555555415666779999999999758899999*****9999988876554222577999999987765 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.18
                                   EEEEETTS-..S-EEEEEEEEEEEEE-SSEEEEEEE---- CS
                       DUF5050  30 LYkmnsdgs..nlkklsddsvsyinvagnyiYYvrnndkk 67 
                                   L+ m +d++    ++ ++d +    ++ ny+YY +n + +
  gi|13541726|ref|NP_111414.1| 442 LFDMLNDKHydVTTETANDFAPAFDADTNYLYYLSNRSLD 481
                                   6666555554234556677777888899999999887655 PP

  == domain 3  score: 11.4 bits;  conditional E-value: 5.3e-05
                                   EEE-T.TT--EEEEETTTTEEEEEE-S-EEE.EEEEETTEEEEEGGGTT-EEEE-SSS---EE-..S-S-EEEEEEETT CS
                       DUF5050 150 Yytgesedhslykldtdgksiskvseenlyl.lvvegdyiYyidlsknyaLyrvklsgsekevl..tedkvdnyNvtgn 225
                                   Yy+g+ e++ ++k++ ++k+++++++e + + ++ +g +i +   +++ +Ly  ++++ e+e+   ++  + + Nv+++
  gi|13541726|ref|NP_111414.1| 569 YYSGQPEKGIIVKFEFKDKKVKEIKKEVVDFkISTDGSKIMF--SKQDGKLYTFRMEKPEEEKSlnIDAITIVSNVKED 645
                                   ***************************999879999******..55888999888888877665214444455788875 PP

>> PDZ_6  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   1.2e-05     0.029      18      56 .]     764     800 ..     761     800 .. 0.96

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.2e-05
                         PDZ_6  18 vGDiilsvNGqpveglsladvaallrgsagesvvlvvrr 56 
                                   +GD +++++G+p+  ++ + + ++l g++++sv +++r+
  gi|13541726|ref|NP_111414.1| 764 IGDAVIEIDGIPI--GKGKSIYEALVGKGNRSVLVKIRK 800
                                   69***********..**********************96 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 ?   -1.1   0.0      0.94   2.4e+03      47      75 ..     331     360 ..     314     372 .. 0.78
   2 ?    8.0   0.0    0.0013       3.4      41      72 ..     367     398 ..     359     411 .. 0.85
   3 ?    0.3   0.0      0.34   8.7e+02      36      76 ..     591     631 ..     579     642 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.94
                   ANAPC4_WD40  47 kpdgklLavaysdg.evrlldaesgkvvhs 75 
                                   ++++  L+++ +dg ++ ++da +g++ ++
  gi|13541726|ref|NP_111414.1| 331 SKNEISLVIGDKDGdSIGVFDAGTGEMKRK 360
                                   45666799999**98899999999998765 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0013
                   ANAPC4_WD40  41 vrsLaWkpdgklLavaysdgevrlldaesgkv 72 
                                   + s++ + dgk L+v+ ++ ++ l+d+++g+v
  gi|13541726|ref|NP_111414.1| 367 IFSVKSSADGKYLVVGNDNFQILLIDVSNGTV 398
                                   66778889*********************986 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.34
                   ANAPC4_WD40  36 kedsevrsLaWkpdgklLavaysdgevrlldaesgkvvhsl 76 
                                   + ++ev +++ + dg+ ++++ +dg++  + +e+ +  +sl
  gi|13541726|ref|NP_111414.1| 591 EIKKEVVDFKISTDGSKIMFSKQDGKLYTFRMEKPEEEKSL 631
                                   557899999999*************9999888887665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1030 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       626  (0.0349155); expected 358.6 (0.02)
Passed bias filter:                      523  (0.0291706); 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: 0.78u 0.32s 00:00:01.10 Elapsed: 00:00:00.50
# Mc/sec: 6147.76
//
Query:       gi|13541727|ref|NP_111415.1|  [L=245]
Description: SAM-dependent methyltransferase [Thermoplasma volcanium GSS1]
Scores for complete 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-20   71.4   0.0    1.1e-19   70.9   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
    3.8e-19   69.0   0.3    7.3e-19   68.1   0.3    1.4  1  Methyltransf_31  Methyltransferase domain
    4.1e-19   69.0   0.0    8.1e-19   68.1   0.0    1.5  1  Methyltransf_11  Methyltransferase domain
    2.2e-17   63.6   0.1    4.2e-17   62.6   0.1    1.5  1  Methyltransf_25  Methyltransferase domain
    1.2e-13   51.6   0.0    2.6e-13   50.5   0.0    1.6  1  Methyltransf_12  Methyltransferase domain
    3.9e-11   42.7   0.4    9.5e-11   41.5   0.1    1.7  2  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    2.4e-08   33.7   0.0    3.5e-08   33.2   0.0    1.2  1  MTS              Methyltransferase small domain
    6.3e-07   29.1   0.0      8e-07   28.8   0.0    1.2  1  Methyltransf_PK  AdoMet dependent proline di-methyltransferas
    1.7e-06   27.6   0.0      2e-06   27.3   0.0    1.2  1  CMAS             Mycolic acid cyclopropane synthetase
    0.00014   21.3   0.0    0.00024   20.5   0.0    1.4  1  GidB             rRNA small subunit methyltransferase G
    0.00016   21.5   0.0    0.00032   20.5   0.0    1.4  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    0.00021   20.7   0.0    0.00028   20.3   0.0    1.1  1  Methyltransf_2   O-methyltransferase domain
    0.00078   18.6   0.0      0.002   17.2   0.0    1.6  2  RrnaAD           Ribosomal RNA adenine dimethylase
    0.00086   18.8   0.0       0.14   11.6   0.0    2.1  2  SAM_MT           Putative SAM-dependent methyltransferase
     0.0012   18.5   0.0     0.0019   17.9   0.0    1.3  1  NodS             Nodulation protein S (NodS)
     0.0086   15.6   0.1      0.019   14.4   0.1    1.6  1  CheR             CheR methyltransferase, SAM binding domain
  ------ inclusion threshold ------
       0.12   13.4   0.0        0.2   12.7   0.0    1.4  1  Methyltransf_24  Methyltransferase domain
       0.21   11.5   1.3       0.41   10.6   0.1    1.9  2  Methyltransf_18  Methyltransferase domain


Domain annotation for each model (and alignments):
>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.9   0.0   1.1e-22   1.1e-19      10     163 ..      24     181 ..      13     183 .. 0.86

  Alignments for each domain:
  == domain 1  score: 70.9 bits;  conditional E-value: 1.1e-22
               Methyltransf_23  10 sdklerllpklraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae......kakkaqkdqfdeqeaaepqgkfd 84 
                                   +d++e l+  +  +  +Ld+++GtG ++ ++++  ++vt+ D  ++++e a+         k++k    + ++++++gkfd
  gi|13541727|ref|NP_111415.1|  24 QDLTELLGLINTHRDTCLDVATGTGFTAASISQICAHVTALDETRAMIEQAQsliesrA-TKNVKFVL-STFEDFDDGKFD 102
                                   456666666699999*******************99****************9999852.33333333.467899****** PP

               Methyltransf_23  85 lIvlrevlehvpdppellrqiatllkpgGylllseplaslkedrllldwlylvpag.rhisffsarslkelleeaGlevv 163
                                   lI++r  l+h++d ++ +++++t+l+pgG l + +  ++ ++dr+   + ++++++ +hi     +++ +l+ee++++++
  gi|13541727|ref|NP_111415.1| 103 LITCRRALHHFKDKEAFFKKARTMLNPGGILAIADMVSP-ANDRKDNFNVLERIRDpTHIGALKVEEMIKLFEENNFQDI 181
                                   ***********************************9766.88888888899999999***99999************987 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.1   0.3   7.3e-22   7.3e-19       6     113 ..      39     139 ..      35     190 .. 0.82

  Alignments for each domain:
  == domain 1  score: 68.1 bits;  conditional E-value: 7.3e-22
               Methyltransf_31   6 rvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsnevlna 86 
                                   + lD+++GtG+ +  +  +++  a+v+ +D +  +ie+A++  ++   +nv+F  + +e+++    d kfDli+++ +l++
  gi|13541727|ref|NP_111415.1|  39 TCLDVATGTGFTAASIS-QIC--AHVTALDETRAMIEQAQSLIESRATKNVKFVLSTFEDFD----DGKFDLITCRRALHH 112
                                   679******99888888.666..8************************************88....8************** PP

               Methyltransf_31  87 ladpdkileeiervlkpggilliedpr 113
                                   ++d++++++++   l+pggil+i+d+ 
  gi|13541727|ref|NP_111415.1| 113 FKDKEAFFKKARTMLNPGGILAIADMV 139
                                   *************************99 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.1   0.0   8.1e-22   8.1e-19       1      96 []      41     135 ..      41     135 .. 0.98

  Alignments for each domain:
  == domain 1  score: 68.1 bits;  conditional E-value: 8.1e-22
                                   EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-.EEEETTEECCCTSS-TT-EEEEEEES-CCC-CCHHHH CS
               Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseegl.kvefvvadaeklpfednsfDlvvssevlhhvedpeka 80 
                                   Ldv++GtG  a+ + + +a+v+++D + +m+++a++ ++ +   +v+fv +++e+  f d++fDl++++ +lhh++d e++
  gi|13541727|ref|NP_111415.1|  41 LDVATGTGFTAASISQICAHVTALDETRAMIEQAQSLIESRATkNVKFVLSTFED--FDDGKFDLITCRRALHHFKDKEAF 119
                                   8****************************************999**********8..************************ PP

                                   HHHHHHHEEEEEEEEE CS
               Methyltransf_11  81 lkeiaRvLkpgGllvi 96 
                                   +k+++ +L pgG+l+i
  gi|13541727|ref|NP_111415.1| 120 FKKARTMLNPGGILAI 135
                                   *************986 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.6   0.1   4.3e-20   4.2e-17       2      97 .]      41     131 ..      40     131 .. 0.94

  Alignments for each domain:
  == domain 1  score: 62.6 bits;  conditional E-value: 4.3e-20
                                   EEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBSSSTTTEEEEEEESTGGGSSHHH CS
               Methyltransf_25   2 LdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl.nvefvqgdaedlpfedgsfDlvvssgalhhlsded 81 
                                   Ld+++GtG +++ +++ +  a+vt++D + +m+e+a++ +e++   nv+fv   +ed++  dg+fDl++++ alhh++  d
  gi|13541727|ref|NP_111415.1|  41 LDVATGTGFTAASISQIC--AHVTALDETRAMIEQAQSLIESRATkNVKFVLSTFEDFD--DGKFDLITCRRALHHFK--D 115
                                   9***************98..********************997668**********975..99*******999***98..6 PP

                                   HHHHHHHHHHHEEEEE CS
               Methyltransf_25  82 lekalkeiarvLkpgG 97 
                                    e+++k+++ +L+pgG
  gi|13541727|ref|NP_111415.1| 116 KEAFFKKARTMLNPGG 131
                                   67*************9 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.5   0.0   2.6e-16   2.6e-13       1      99 []      41     133 ..      41     133 .. 0.82

  Alignments for each domain:
  == domain 1  score: 50.5 bits;  conditional E-value: 2.6e-16
               Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhhlkd 81 
                                   L++ +GtG +++ + +    +++t++D  +++ie+a+  + +r  +n+++v l + +++d  + ++fDl+++  +lhh+kd
  gi|13541727|ref|NP_111415.1|  41 LDVATGTGFTAASISQI--CAHVTALDETRAMIEQAQSLIESRATKNVKFV-LSTFEDFD--D-GKFDLITCRRALHHFKD 115
                                   89************999..**************666666666555444444.44444333..2.3**************** PP

               Methyltransf_12  82 irevldnirklLkpgGrl 99 
                                   ++++++++r +L+pgG+l
  gi|13541727|ref|NP_111415.1| 116 KEAFFKKARTMLNPGGIL 133
                                   ****************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 !   41.5   0.1   9.6e-14   9.5e-11      48     157 ..      37     141 ..      11     151 .. 0.87
   2 ?   -1.7   0.0       1.4   1.4e+03     202     222 ..     167     187 ..     164     192 .. 0.84

  Alignments for each domain:
  == domain 1  score: 41.5 bits;  conditional E-value: 9.6e-14
                                   TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EEEEEEES-GGG CS
               Ubie_methyltran  48 gakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfeddsfDvvtvsfGlrn 128
                                     + lDva+Gtg  a+++s+      +v+ lD    m+++++  ++ ++++n++f+ +  e  +f+d+ fD++t    l  
  gi|13541727|ref|NP_111415.1|  37 RDTCLDVATGTGFTAASISQICA---HVTALDETRAMIEQAQSLIESRATKNVKFVLSTFE--DFDDGKFDLITCRRALHH 112
                                   4589*********9999998764...7999***************************9998..599*************** PP

                                   -S-HHHHHHHHHHHEEEEEEEEEEEE--- CS
               Ubie_methyltran 129 vtDklkaLkeayrvlkpGGrlvvlefskv 157
                                   + Dk+  +k+a+ +l pGG+l + ++  +
  gi|13541727|ref|NP_111415.1| 113 FKDKEAFFKKARTMLNPGGILAIADMVSP 141
                                   *********************98877655 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.4
                                   HHHHHHHHHTTEEEEEEEEEG CS
               Ubie_methyltran 202 etlkeliedaGfksveyeslt 222
                                   e++ +l+e+  f+ ++y+ +t
  gi|13541727|ref|NP_111415.1| 167 EEMIKLFEENNFQDIKYKIIT 187
                                   67889999********99777 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.2   0.0   3.5e-11   3.5e-08      27     137 ..      33     135 ..      20     155 .. 0.89

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 3.5e-11
                                   CHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTSTTS-EEEEEE---S CS
                           MTS  27 lpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvleeveekkfdlivsNPPf 107
                                   +++ ++++ lD+++G+G+ +a++ + + +  vt++d+  + +e a+  +e+ + +   +  + +e+++++kfdli +   +
  gi|13541727|ref|NP_111415.1|  33 INT-HRDTCLDVATGTGFTAASISQICAH--VTALDETRAMIEQAQSLIESRATKNVKFVLSTFEDFDDGKFDLITCRRAL 110
                                   444.7778*****************9999..9***********************66666678999***********9999 PP

                                   TTTCHCHHHHHHHHHHHHHHHEEEEEEEEE CS
                           MTS 108 hagkatelavaeeliaeAkeaLkegGeLli 137
                                   h+ k+      e+++++A+ +L++gG L i
  gi|13541727|ref|NP_111415.1| 111 HHFKD-----KEAFFKKARTMLNPGGILAI 135
                                   99998.....89**************9986 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 !   28.8   0.0   8.1e-10     8e-07      55     168 ..      36     144 ..      17     185 .. 0.87

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 8.1e-10
               Methyltransf_PK  55 evkvaldcGaGiGrvtknlLlkllskvDlvepvekflekakeelaeekkkvgkvyvvglqeftPeegrYdliWiqWcvghL 135
                                   + ++ ld+ +G G  t   + ++ ++v  ++ ++ ++e+a++ + +  +k  k+    +++f  ++g++dli ++  + h+
  gi|13541727|ref|NP_111415.1|  36 HRDTCLDVATGTGF-TAASISQICAHVTALDETRAMIEQAQSLIESRATKNVKFVLSTFEDF--DDGKFDLITCRRALHHF 113
                                   55678999999995.66778999******************999998888888999999998..79*************** PP

               Methyltransf_PK 136 tDedlvaflkrckkalkpnGlivvkenvakeek 168
                                    D++  af+k++ + l+p+G++ + + v+  + 
  gi|13541727|ref|NP_111415.1| 114 KDKE--AFFKKARTMLNPGGILAIADMVSPAND 144
                                   ***9..8******************99987663 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.0     2e-09     2e-06      64     175 ..      38     146 ..       7     192 .. 0.85

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 2e-09
                                   -EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG---.--SEEEEES-GGGTSGG CS
                          CMAS  64 mtlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvdeldlerkvevklldyedlde.kvdrvvsvgafehvgke 143
                                   +t Ld+ +G G ++  ++++  ++v +l   +   ++a+  ++++  +++v+  l+ +ed+d+ k+d +    a+ h++ +
  gi|13541727|ref|NP_111415.1|  38 DTCLDVATGTGFTAA-SISQICAHVTALDETRAMIEQAQSLIESRA-TKNVKFVLSTFEDFDDgKFDLITCRRALHHFKDK 116
                                   789*******98876.567779999999999999999999998887.56778889*******99**************877 PP

                                   GHHHHHHHHHHHS-TT-EEEEEEEEE--HHHH CS
                          CMAS 144 nydtffkklkkllkedGllllhtitslhkkel 175
                                     ++ffkk+ ++l+++G+l++  ++s+ ++ +
  gi|13541727|ref|NP_111415.1| 117 --EAFFKKARTMLNPGGILAIADMVSPANDRK 146
                                   ..79****************999888877765 PP

>> GidB  rRNA small subunit methyltransferase G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   2.4e-07   0.00024      39     142 ..      27     131 ..      21     149 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 2.4e-07
                                   HHHGGCS-CCC-.EEEETSTTTTTHHHHHHH-TTSEEEEEES-HHHHHHHHHHHHHCT-SSEEEEES-CCCTTTTT-EEEE CS
                          GidB  39 lsvlellkekrdkviDvGsGaGlPGipLaiarpelkltLleslekkiaFLeevkeelklenveivearaeekqeeekydvv 119
                                    ++l l++ +rd+++Dv +G G+ +  ++ +++  ++t l+ +   i+  + ++e  + +nv++v +  e+     k+d++
  gi|13541727|ref|NP_111415.1|  27 TELLGLINTHRDTCLDVATGTGFTAASISQICA--HVTALDETRAMIEQAQSLIESRATKNVKFVLSTFED-FDDGKFDLI 104
                                   5677788889989**********9988777765..5779********************************.67899**** PP

                                   EEC.-SSSHHHHHHHHCC...CEEEEE CS
                          GidB 120 tsR.Alaslnelteillk...llkegg 142
                                   t+R Al ++++  ++ +k   +l++gg
  gi|13541727|ref|NP_111415.1| 105 TCRrALHHFKDKEAFFKKartMLNPGG 131
                                   *95488887765444433221555555 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   3.2e-07   0.00032      65     130 ..      26      90 ..      11     100 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 3.2e-07
                                   HHHHTT-..-TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEE CS
                          PCMT  65 alellel..kkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvv 130
                                   ++ell l  ++ +  L+v +G+G+ +a ++++  +++   +++ ++ ++e+a+  ++  +++nv++v 
  gi|13541727|ref|NP_111415.1|  26 LTELLGLinTHRDTCLDVATGTGFTAASISQICAHVT---ALDETRAMIEQAQSLIESRATKNVKFVL 90 
                                   578888522566789******************9988...9***********************9986 PP

>> Methyltransf_2  O-methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   2.8e-07   0.00028      65     176 ..      39     147 ..       2     160 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 2.8e-07
                                   EEEEET-TTSHHHHHHHHH-TT-EEEEEE.-HHHHHHHHHHS-----TTEEEEES-TTTS-----SEEEEESSGGGS-HHH CS
                Methyltransf_2  65 slvDvGGGtGalakaivsayPtikvivfD.lpeVveaAkehlsageeervefvgGdffkdslPeaDaillkrvlhDwsdek 144
                                   + +Dv  GtG +a+ i++   +++   +D     +e+A++ +++ ++++v+fv   f +    + D+i   r lh ++d++
  gi|13541727|ref|NP_111415.1|  39 TCLDVATGTGFTAASISQICAHVT--ALDeTRAMIEQAQSLIESRATKNVKFVLSTFEDFDDGKFDLITCRRALHHFKDKE 117
                                   578***************987765..455156789*******************9999888889***************97 PP

                                   HHHHHHHHHHH--TT-EEEEEE----TTS--- CS
                Methyltransf_2 145 cvklLkrvkkalpagGkvivveavlgadpsge 176
                                      + k+ +  l++gG + ++++v +a+ +++
  gi|13541727|ref|NP_111415.1| 118 --AFFKKARTMLNPGGILAIADMVSPANDRKD 147
                                   ..589*******************99887765 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0     2e-06     0.002      30      89 ..      36      97 ..      22     122 .. 0.86
   2 ?   -1.7   0.0       1.2   1.2e+03     240     262 ..     152     175 ..     136     177 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2e-06
                                  TTSEEEEES-TTTCCHHHHHCC-SEEEEE-S-HHHHHHHHCHTT..TCCCEEEE-S-CCGHH CS
                        RrnaAD 30 ekltvleigpGkGilTeeLakrakqvvvlElderLakllqkkls..kdeklkvvhqDflkfe 89
                                    +t l++++G+G++ +++ +++ +v++l   +++++  q  ++    +++k v   f +f+
  gi|13541727|ref|NP_111415.1| 36 HRDTCLDVATGTGFTAASISQICAHVTALDETRAMIEQAQSLIEsrATKNVKFVLSTFEDFD 97
                                  67999************************************998878889998877776666 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.2
                                   ..T--TTTCCCCSGHHHHHHHHHH CS
                        RrnaAD 240 t.gindnalvkklsaeqtldifke 262
                                     +i d++ ++ l++e+++++f+e
  gi|13541727|ref|NP_111415.1| 152 LeRIRDPTHIGALKVEEMIKLFEE 175
                                   2489999***********999986 PP

>> SAM_MT  Putative SAM-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.013        13      46     102 ..      11      67 ..       6      89 .. 0.85
   2 !   11.6   0.0   0.00014      0.14     113     201 ..     152     240 ..     149     243 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.013
                        SAM_MT  46 aaahRrkfgggrgeaiakavglkkgvlptvlDaTaGlGrDafvlaslGckvtliErh 102
                                   a  + +++++ +g+ +   +gl +  + t lD  +G G  a+ ++++ ++vt ++  
  gi|13541727|ref|NP_111415.1|  11 AEDYAKSKSHEKGQDLTELLGLINTHRDTCLDVATGTGFTAASISQICAHVTALDET 67 
                                   5566778889999**************************************987654 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00014
                        SAM_MT 113 lkRakqdaeigel.laerlkLlaasslealakleeekpdvvYlDPmyPhkkksalvKKemrvfqqlvGadedadeLleaal 192
                                   l+R ++ ++ig+l ++e +kL+++++++ ++     + +  + + +yP  k s + KK ++++++l  ++ ++ +L +  l
  gi|13541727|ref|NP_111415.1| 152 LERIRDPTHIGALkVEEMIKLFEENNFQDIKYKII-TEELTFEEWLYPITKESEVGKKCLEFLNSLSTEELNQIRLDANRL 231
                                   78888888888751566779999999999998888.999****************************************** PP

                        SAM_MT 193 alakkRvvV 201
                                   +l+k+R+v+
  gi|13541727|ref|NP_111415.1| 232 TLSKQRIVI 240
                                   *******97 PP

>> NodS  Nodulation protein S (NodS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   1.9e-06    0.0019      42     136 ..      35     127 ..      14     146 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.9e-06
                          NodS  42 gsiadalevGcaaGalterlapyckrltvvdvveeaiararervke..sshiswivsdvqqfstdekfdlivvaevlyyie 120
                                    +    l+v   +G  +  ++ +c ++t +d     i++a+  ++   + +++++ s  + f+ d kfdli +   l++ +
  gi|13541727|ref|NP_111415.1|  35 THRDTCLDVATGTGFTAASISQICAHVTALDETRAMIEQAQSLIESraTKNVKFVLSTFEDFD-DGKFDLITCRRALHHFK 114
                                   334467999999999999***********************988652267899********98.689************** PP

                          NodS 121 dvaelraavrnlvsll 136
                                   d++++    r   ++l
  gi|13541727|ref|NP_111415.1| 115 DKEAFFKKAR---TML 127
                                   *987644333...444 PP

>> CheR  CheR methyltransferase, SAM 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     0.019     111     173 ..      75     135 ..      38     154 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.9e-05
                                   E..E-HHHHTTEEEEE--TTT-SGGG--EEEEEE-SSGGGC-CHHHHHHHHHHHCCEEEEEEEEE CS
                          CheR 111 k..vkkeikelvkFeklnllekksvlgklDvifcrnvliYfdeetqekvlerfaeklkpgglLll 173
                                   +  +++  +++vkF  +   +     gk+D+i+cr  l  f+  ++e+  ++ + +l+pgg+L +
  gi|13541727|ref|NP_111415.1|  75 QslIESRATKNVKFVLSTFED--FDDGKFDLITCRRALHHFK--DKEAFFKKARTMLNPGGILAI 135
                                   234888888899997665544..6789**************6..6899***************98 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0    0.0002       0.2      25     105 ..      60     137 ..      23     138 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.0002
               Methyltransf_24  25 rlvavdhdpgaeeaaalare..aglddrvrlikadseealaslaagsiDllfiD.gghaaeavledleallprlapggvvl 102
                                   +++a+d  +      a++++  + +++r++  ++   ++++++++g++Dl+ +  + h  ++  ++++ ++ +l+pgg++ 
  gi|13541727|ref|NP_111415.1|  60 HVTALDETR------AMIEQaqSLIESRATKNVKFVLSTFEDFDDGKFDLITCRrALHHFKDKEAFFKKARTMLNPGGILA 134
                                   344444444......333333334455555555555667777789*******97258899*******************98 PP

               Methyltransf_24 103 fdD 105
                                   + D
  gi|13541727|ref|NP_111415.1| 135 IAD 137
                                   766 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00041      0.41       7      73 ..      28      92 ..      24     106 .. 0.78
   2 ?   -0.9   0.2       1.4   1.4e+03     129     144 ..     179     194 ..     167     200 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00041
               Methyltransf_18  7 aiaslvekgs.rvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievrlsd 73
                                  ++  l+++++ +++D+ t  g+ ++ +   +++ +v+a D  +  +e+a++ ie+   +++++++ls 
  gi|13541727|ref|NP_111415.1| 28 ELLGLINTHRdTCLDVATGTGFTAASIS--QICAHVTALDETRAMIEQAQSLIESRA-TKNVKFVLST 92
                                  55667776555999*******9998886..7**********************9865.5779988874 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.4
               Methyltransf_18 129 vengfkiedEelvkee 144
                                   ++ ++ki+ Eel +ee
  gi|13541727|ref|NP_111415.1| 179 QDIKYKIITEELTFEE 194
                                   5678999999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       778  (0.0433934); expected 358.6 (0.02)
Passed bias filter:                      506  (0.0282224); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.52u 0.32s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 1488.11
//
Query:       gi|13541728|ref|NP_111416.1|  [L=186]
Description: hypothetical protein TVN0897 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.016   14.8   6.5      0.022   14.4   6.5    1.4  1  PMT_4TMC  C-terminal four TMM region of protein-O-mannosyltra


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 ?   14.4   6.5   1.2e-06     0.022      51     175 ..      62     185 ..      16     186 .] 0.80

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.2e-06
                      PMT_4TMC  51 iyllGNpvlwwlstiallvfvllllalllrrqrgvkdleeeetr....llnsglflllgwalhylPfflmgRvlflhhYlp 127
                                   i ++G+  + ++s+i+l+++ l++l++ +r+ r+ +++ ee++     +   +++++   a  y  +f+++  l    Y+ 
  gi|13541728|ref|NP_111416.1|  62 IAFIGSKYIRVASVIILVLVSLYILINSIRESREAREI-EETSLlvsaFPDPAFLPMAIIAYTYGTYFVISTGL---IYVA 138
                                   7899999999***************************9.333333556666677888899999*******9998...69** PP

                      PMT_4TMC 128 AllfailllaalldfllkslkkslkkkklvklivvvvllvlviavFif 175
                                   A+ +a+l++ +l+++ l ++ +sl k  +v +ivvvvll+ ++++++f
  gi|13541728|ref|NP_111416.1| 139 ASTIALLAVVFLVNIGLLRKLSSL-KPVTVDRIVVVVLLLTAAYIYFF 185
                                   ***************985544444.34677788887777777777654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1096  (0.06113); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.29s 00:00:00.87 Elapsed: 00:00:00.53
# Mc/sec: 1065.65
//
Query:       gi|13541729|ref|NP_111417.1|  [L=473]
Description: amino acid transporter [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.5e-26   91.9  54.5    4.6e-26   91.5  54.5    1.1  1  AA_permease    Amino acid permease
    6.5e-26   91.1  59.6    8.1e-26   90.8  59.6    1.0  1  AA_permease_2  Amino acid permease
  ------ inclusion threshold ------
        2.4    7.1  24.9       0.17   10.9  18.3    2.4  2  PHO4           Phosphate transporter family
        6.2    6.6   5.1        6.2    6.6   3.2    2.0  1  DUF3464        Photosynthesis affected mutant 68


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 !   91.5  54.5     1e-29   4.6e-26      18     431 ..      36     418 ..      18     453 .. 0.79

  Alignments for each domain:
  == domain 1  score: 91.5 bits;  conditional E-value: 1e-29
                   AA_permease  18 glgvvlsqaGplgallayllagvviflvmlslgeiatngpksggfytyasrflgpelGfviGlnylfswitvl.aleltaa 97 
                                    +gv+l + G   + l++ll++v+++++m+s ++++ +++++g++yt+a+++lgp+ G + ++n  f++i+++  +++ ++
  gi|13541729|ref|NP_111417.1|  36 LTGVALFALGA--TPLSILLGVVFYLFIMNSGYQFSKYISSAGSYYTFAAKSLGPKIGIFQAWNMIFYSILGYsSFGFLGL 114
                                   44555555555..9**************************************************999999876369***** PP

                   AA_permease  98 siliqfwelvtdlpkawvt..gavf.lvvlliinlvgvkvygeaefilalikiiaiiafiivg.iillaggkpnkgagfrf 174
                                   + +i+++  +++l+++ v+  +av   ++ ++++++g+k +      + ++ +++ ++++i+g i +++++++++      
  gi|13541729|ref|NP_111417.1| 115 AAFISMI--NPSLNSTAVWvtIAVAaATIAFLFTYFGIKTSTD----YQILGGVIEVSVLIIGsILIIISAGNSNT----- 184
                                   *******..6666666666334443145667889******999....66788888889999995545555555555..... PP

                   AA_permease 175 lgdngsifknnlppgfakeeegafknfisvfvivvfaftGielvaiiagEvkdPeksiPkailqvviritifYvlslllig 255
                                       +s+f    +pg      g  + f+s++  vv+ f  +++++ +a+E+k+P  ++ +a +++++  +i  +l++++ +
  gi|13541729|ref|NP_111417.1| 185 ----LSVFTTKYIPG------GLSQIFYSMIYSVVLFFGTTLSITSLAEEAKNPHIAVRRALISTIVVAGITLILVSYAFT 255
                                   ....34333333344......4566788999999999999***************************************** PP

                   AA_permease 256 llvprndlgllndsasaaspfvifikesgvsvlaplinaviltaalssansslysasRvlyslakdglaP...kvlkkvsk 333
                                   ++ + ++ g + +s ++     +++ ++ + +l  l++av+  + +++ +s + + +R++ys+a++g++    +  k +++
  gi|13541729|ref|NP_111417.1| 256 IGYGPTNMGAFIKSPDP----GLVMFKHVSYILYILLIAVTVNSFMGYNVSVSNANTRIYYSFARSGILFlprSLKKIHER 332
                                   ************99999....67788899999999999*****************************9755588888899* PP

                   AA_permease 334 rgvPlraillsmiisllalllaslnlaapivfnfllaisaliglivwlliilsylrfRkalkyqgrsieelgfkaallplg 414
                                   +g+P+++ ++++i+sl + l+ +++++++i   ++l ++++++   ++++++ ++ + k++        ++++  +l++ +
  gi|13541729|ref|NP_111417.1| 333 YGSPYNSAIFVFIVSLSVGLAFGFAFGPEIGGLVMLFANGYAAYTEHIVASIGLPFYAKKM-------GDFKVLQHLVFPI 406
                                   ***************************9999999*********************555554.......4444444444333 PP

                   AA_permease 415 vilvlaaliiillilal 431
                                     ++++a +i+     +
  gi|13541729|ref|NP_111417.1| 407 IAVGVLAAVIF-----F 418
                                   33333222222.....2 PP

>> AA_permease_2  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.8  59.6   1.8e-29   8.1e-26      24     416 ..      39     432 ..      13     442 .. 0.82

  Alignments for each domain:
  == domain 1  score: 90.8 bits;  conditional E-value: 1.8e-29
                 AA_permease_2  24 laasggpalilwvwiavligslavllvyaElssalprsgGiyvytkaafgkkvaflsawfnwfayvpvlasilsvaasyll 104
                                   +a+ +  a+ l+++++v+ +++++   y  +s  +++ g  y+++++  g+k++ + aw   f  +++ +s   +++++++
  gi|13541729|ref|NP_111417.1|  39 VALFALGATPLSILLGVVFYLFIMNSGYQ-FSKYISSAGSYYTFAAKSLGPKIGIFQAWNMIFYSILGYSSFGFLGLAAFI 118
                                   33336667888888999999899999988.8888*************************9999999999888899****** PP

                 AA_permease_2 105 nalgpdlqgntwltyliaiaililvalinirgikesakiqnilgilkillpliiliilglitvdgggfsslstetdtffpn 185
                                   ++++p+l+  t  ++ ia+a  ++ +l++++gik+s  +q  +g++ +  +lii  il +i + g+ ++ +++ t+++ ++
  gi|13541729|ref|NP_111417.1| 119 SMINPSLNS-TAVWVTIAVAAATIAFLFTYFGIKTSTDYQILGGVIEV-SVLIIGSILIIISA-GNSNTLSVFTTKYIPGG 196
                                   ******965.6799**********************************.78777777777775.55555556777777777 PP

                 AA_permease_2 186 gwpgvllgllivlwsfdGfesaanvseevkk..kdvpkaifigllivlvlyllvniaflgvvpddeianlsnlgsvaalff 264
                                    ++++ ++++ v++ f+   s+++ +ee+k+    v++a+++ ++++++  +lv+ af+++ ++ ++     +++++ ++f
  gi|13541729|ref|NP_111417.1| 197 LSQIFYSMIYSVVLFFGTTLSITSLAEEAKNphIAVRRALISTIVVAGITLILVSYAFTIGYGPTNMGAFIKSPDPGLVMF 277
                                   888899999*******************9997459********************************998999******** PP

                 AA_permease_2 265 eavggkvvaiivvilialsllgaintavigssrvlealardgvlP..rffakvn.kfgspiraiiltaivslillllflla 342
                                   + v   ++ i+++++++ s +g   +++ +++r+++++ar g+l   r ++k++ ++gsp+++ i+++ivsl ++l+f +a
  gi|13541729|ref|NP_111417.1| 278 KHVS-YILYILLIAVTVNSFMGYNVSVSNANTRIYYSFARSGILFlpRSLKKIHeRYGSPYNSAIFVFIVSLSVGLAFGFA 357
                                   **98.78888888888889***********************98888************************9999999875 PP

                 AA_permease_2 343 ssaayn......fllsvsslgliisyllliigalilrkkrphlkrpgkilvaiigalfllfllvalffppkgpatqssli 416
                                       +       ++l +  ++++   ++++ig+ ++ kk+ ++k      v  i+a+++l +++++ ++p+ pa + +++
  gi|13541729|ref|NP_111417.1| 358 ----FGpeigglVMLFANGYAAYTEHIVASIGLPFYAKKMGDFKVLQHL-VFPIIAVGVLAAVIFFTLYPAPPAYPYNIA 432
                                   ....334455559999999999999*****************9997655.444555555556655556666666666653 PP

>> PHO4  Phosphate transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.9      0.14   6.3e+02      88     143 ..       3      64 ..       2     107 .. 0.66
   2 ?   10.9  18.3   3.7e-05      0.17      58     174 ..     122     256 ..      81     447 .. 0.66

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.14
                          PHO4  88 StthslvGaliG.aalaaeggeavkw.....kklvkivlswvlsPllggiiaallfllvkrl 143
                                   S t +l  ++iG + l+ +++ a++        l+ ++l+ + +  l+++++++++l+++  
  gi|13541729|ref|NP_111417.1|   3 SNTYTLKEGVIGeFRLVWQAMGALSIaadasYLLTGVALFALGATPLSILLGVVFYLFIMNS 64 
                                   66666666777655555544444444334333677788899999999999999999988876 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 3.7e-05
                          PHO4  58 dpselm.lgmlaallgaavwlllatvlglPvStthslvGaliGaalaa.........eggeavkw..............kk 114
                                   +ps    ++ + ++++aa+  +l t++g+ +St   + G++i +++ +         +                     ++
  gi|13541729|ref|NP_111417.1| 122 NPSLNStAVWVTIAVAAATIAFLFTYFGIKTSTDYQILGGVIEVSVLIigsiliiisA------GnsntlsvfttkyipGG 196
                                   343333377888999999999**************************96666666551......03344444666766669 PP

                          PHO4 115 lvkivlswvlsPllggiiaallfllvkrlilvkeklknalralpvlvlvtiailalsilf 174
                                   l +i++s++ s++l +     ++ l + +   + ++++al ++ v++ +t++++++++++
  gi|13541729|ref|NP_111417.1| 197 LSQIFYSMIYSVVLFFGTTLSITSLAEEAKNPHIAVRRALISTIVVAGITLILVSYAFTI 256
                                   *************************99993332445555555555544443333333222 PP

>> DUF3464  Photosynthesis affected mutant 68
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   3.2    0.0014       6.2      71     119 ..      47      95 ..      35     111 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0014
                       DUF3464  71 lalGlatfvvfylivskelvdlptwvvllvslvlFglgvlGlsYGvlSa 119
                                   + l +++ vvfyl++ ++ +++++++  + s  +F++  lG   G++ a
  gi|13541729|ref|NP_111417.1|  47 TPLSILLGVVFYLFIMNSGYQFSKYISSAGSYYTFAAKSLGPKIGIFQA 95 
                                   4578999**********************************99999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (473 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       901  (0.0502538); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.44
# Mc/sec: 3209.38
//
Query:       gi|13541730|ref|NP_111418.1|  [L=349]
Description: dTDP-glucose pyrophosphorylase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-49  168.5   0.0    2.3e-49  168.2   0.0    1.1  1  NTP_transferase  Nucleotidyl transferase
    7.1e-07   29.7   0.0      9e-07   29.4   0.0    1.2  1  NTP_transf_3     MobA-like NTP transferase domain
    3.9e-05   23.2   2.4    0.00057   19.5   0.4    3.6  4  Hexapep          Bacterial transferase hexapeptide (six repea
    0.00093   18.2   0.1     0.0013   17.8   0.1    1.2  1  Fucokinase       L-fucokinase


Domain annotation for each model (and alignments):
>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  168.2   0.0   5.1e-53   2.3e-49       1     245 [.       2     234 ..       2     237 .. 0.96

  Alignments for each domain:
  == domain 1  score: 168.2 bits;  conditional E-value: 5.1e-53
                                   EEEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEEEEES CS
               NTP_transferase   1 kavILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevlialep 81 
                                   k++IL+GGsGtRL+PLt t  k+l+p++gk ++ ++ l++l++ gi++i +v+ +    +v++ +++gs+++v+++++++p
  gi|13541730|ref|NP_111418.1|   2 KGIILHGGSGTRLRPLTYTDVKQLLPIAGK-PISEYALENLIEIGIKNINIVIGSVGGLEVKKFYGDGSRWNVNISYTYQP 81 
                                   79****************************.************************************************** PP

                                   S--BGGHHHHHTHHHHTTSSE..EEEEETTEEEESTTHHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEEEECTTSBEEEE CS
               NTP_transferase  82 egkgtAdAvalaaelledeksdelvlvLggDhlikdayeeavkkaiekaakgtvtfgivpveeateyGvieadeegrverf 162
                                   e+ g+A+A+ l + ++++++    ++v+ gD + ++ ++++ ++++++++  +  +g+vpv++++++G++e+d+ g++ ++
  gi|13541730|ref|NP_111418.1|  82 EPLGIAHAIGLTKAFVGNDD----FVVFLGDNYLQNGISNLYEDFTNAGS--DGHLGLVPVDNPSQFGIAEVDN-GKISKL 155
                                   *****************999....788888999999**************..899******************9.8***** PP

                                   ECS-SSHSHCSEECCSEEEEETTHHHHHHHCCHHHTTSSCHHHHHHHHHHHTTEEEEEECSTTEE-EEEXSSHHHHHHHHH CS
               NTP_transferase 163 vEKPkeakaselassGiYvfnsevllflakdleelkrgedeitdilpkaleegkvalaflfkdaeyWsDvGtldslleane 243
                                   vEKPk+++ s+la  G+Y+ +++v++ + + l+++krge eit++ + ++++g +  + + +++   +D+Gt+d++l  n+
  gi|13541730|ref|NP_111418.1| 156 VEKPKTPT-SNLAIVGVYFLTPKVFESI-DRLKPSKRGEYEITEAYQDMIDRGLKISYSIISGW--FKDTGTVDDFLACNR 232
                                   ********.*******************.78**********************99999999994..59*********9988 PP

                                   HH CS
               NTP_transferase 244 kl 245
                                    +
  gi|13541730|ref|NP_111418.1| 233 LI 234
                                   66 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.0     2e-10     9e-07       1     107 [.       3     118 ..       3     198 .. 0.75

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 2e-10
                                   EEEEEESS-TTTT..T...THHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSH...CHHHHHHTTCTS-EEE-TTS..S.. CS
                  NTP_transf_3   1 aviLAGGrSsRmg..g...dKallplggkpllervldalraagvdevvvvggd...eevlaalarlgvrvvededp..g.. 69 
                                   ++iL GG ++R+   +    K+llp++gkp+ e++l++l + g++++ +v g+    ev++ + + g r+ ++  +  +  
  gi|13541730|ref|NP_111418.1|   3 GIILHGGSGTRLRplTytdVKQLLPIAGKPISEYALENLIEIGIKNINIVIGSvggLEVKK-FYGDGSRWNVNISYtyQpe 82 
                                   79**********85414569******************************98854335554.4455555555544421200 PP

                                   .-SHHHHHHHHHHHH.SSSCEEEEETT-TT--HHHHHHH CS
                  NTP_transf_3  70 .kgplaslaaalraaadadavlvlacDmPlltpelverl 107
                                     g+++++    + + ++d ++v+++D  l  ++ +  l
  gi|13541730|ref|NP_111418.1|  83 pLGIAHAIGLTKAFV-GNDDFVVFLGDNYL--QNGISNL 118
                                   134444443333444.89999999999755..3444444 PP

>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.6   0.0    0.0015       6.8       4      30 ..     253     279 ..     253     284 .. 0.79
   2 !   19.5   0.4   1.3e-07   0.00057       2      30 ..     269     296 ..     268     301 .. 0.94
   3 !   11.3   0.5   4.9e-05      0.22       2      22 ..     286     310 ..     285     311 .. 0.78
   4 ?   -0.4   0.0      0.23   1.1e+03       8      19 ..     321     332 ..     319     334 .. 0.56

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0015
                                   EETTEEE-TTEEEETTEEE-TTEEEET CS
                       Hexapep   4 IGsnvlIgpfaviggnVkIGdnvkIga 30 
                                   I+  v+I + + + g++ IG++++I++
  gi|13541730|ref|NP_111418.1| 253 IHPTVKISSDSEVVGPCFIGEGTRIEH 279
                                   667788888888999999999999975 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 1.3e-07
                                   EEEETTEEE-TTEEEETTEEE-TTEEEET CS
                       Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIga 30 
                                   ++IG+++ I   ++ig+ + IG+n++I +
  gi|13541730|ref|NP_111418.1| 269 CFIGEGTRIE-HSYIGPYTSIGSNCIIKN 296
                                   9*********.****************76 PP

  == domain 3  score: 11.3 bits;  conditional E-value: 4.9e-05
                                   EEEETTEEE-T....TEEEETTEEE CS
                       Hexapep   2 tvIGsnvlIgp....faviggnVkI 22 
                                   t IGsn++I +     ++i+++++I
  gi|13541730|ref|NP_111418.1| 286 TSIGSNCIIKNaeieDSIIMDGCEI 310
                                   78********777777777777766 PP

  == domain 4  score: -0.4 bits;  conditional E-value: 0.23
                                   EEE-TTEEEETT CS
                       Hexapep   8 vlIgpfaviggn 19 
                                   +l+gp++ + ++
  gi|13541730|ref|NP_111418.1| 321 SLLGPNVRVVSG 332
                                   556666666555 PP

>> Fucokinase  L-fucokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.1   2.9e-07    0.0013     278     318 ..     262     302 ..     231     338 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.9e-07
                    Fucokinase 278 nSvlessvsvgegsviehsslkgnvsigsnsivsgleless 318
                                   +S + + + +geg+ iehs +++ +sigsn+i+ + e+e s
  gi|13541730|ref|NP_111418.1| 262 DSEVVGPCFIGEGTRIEHSYIGPYTSIGSNCIIKNAEIEDS 302
                                   566778899************************99999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (349 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       225  (0.0125495); expected 358.6 (0.02)
Passed bias filter:                      216  (0.0120475); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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: 2603.33
//
Query:       gi|13541731|ref|NP_111419.1|  [L=280]
Description: dTDP-4-dehydrorhamnose reductase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.9e-57  193.2   0.0    6.2e-57  192.9   0.0    1.0  1  RmlD_sub_bind    RmlD substrate binding domain
    6.7e-18   65.0   0.3    2.4e-17   63.2   0.3    1.8  1  Epimerase        NAD dependent epimerase/dehydratase family
    2.1e-11   43.8   0.2    4.2e-11   42.8   0.0    1.5  2  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    5.6e-10   38.8   0.2    4.3e-09   35.9   0.0    2.3  2  Polysacc_synt_2  Polysaccharide biosynthesis protein
    1.5e-08   34.1   0.1      3e-08   33.1   0.1    1.6  1  NAD_binding_4    Male sterility protein
    5.7e-05   22.2   0.1    8.2e-05   21.7   0.1    1.2  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras


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 !  192.9   0.0   2.1e-60   6.2e-57       2     280 ..       3     269 ..       2     275 .. 0.93

  Alignments for each domain:
  == domain 1  score: 192.9 bits;  conditional E-value: 2.1e-60
                                   EEEEESTTSHHHHHHHHHCTTTSEEEEEE-TTT--TTSHHHHHHHHHHH--SEEEE------HHHHHHSHHHHHHHHTHHH CS
                 RmlD_sub_bind   2 kilvtGanGqlGseLakqlaeeglevlaltreeldltdaeavaellkeakpdvvvnaAAytavDkaEseeeaayavnaeav 82 
                                   +il++G +GqlG+eL k++ ++     +++ +++d+td +++a l+++a+pd+v+n AA+t+vD++E+e+e+ay vna +v
  gi|13541731|ref|NP_111419.1|   3 NILIFGHTGQLGRELLKLVPNA--ISGSINGKRVDITDYSEIALLFSQASPDIVINSAAFTNVDRCEKEREKAYLVNAIGV 81 
                                   69****************9954..45677889************************************************* PP

                                   HHHHHHHHHCT-EEEEEEEGGGS-S-TTS-B-TTS----SSHHHHHHHHHHHHHHHH-SSEEEEEE-SEESSSSS-HHHHH CS
                 RmlD_sub_bind  83 ealAeaaaavgalLihvStDyVFdGekkrpYeeddetsPlnvYGrtKlaGEqavlaagkkalivRtswvygekgknfvktm 163
                                   +++ +++ +++++Li++StDyVF+Ge+ + Y+edd ++P+n+YG tK  G    l +++++++vRts v+g+  +nf   +
  gi|13541731|ref|NP_111419.1|  82 RNIVKLCDKYNSKLIQISTDYVFNGERGN-YKEDDIPDPINYYGYTKSIGDAYAL-SSDNTIVVRTSGVFGN-ANNFPLFV 159
                                   **************************766.********************99888.78899**********9.89****** PP

                                   HHHHHH-SEEEEESS-EE--EEHHHHHHHHHHHHHHCHH.GGG-EEEE---BS-EEHHHHHHHHHHHHCHTTSEEEEE-CC CS
                 RmlD_sub_bind 164 lrlakereelkvvaDqlgsPTsardlAevllqllekaaeekelagvyHlanegetswlefArailkeagadseevkpista 244
                                    +++k   e++v++  + sP +a+ l+++l  l++k ++     g+  +a+++ +s++++A ai++++g d++ ++ ++  
  gi|13541731|ref|NP_111419.1| 160 YNRLKAGLEVDVIKG-YYSPIHANLLSKALYVLISKGTH----RGIINIAGQR-ISRFDLATAIANRFGFDQKLIREVPDL 234
                                   *************96.679*******************9....9*******99.************************765 PP

                                   CS--SS---SBE-B--HHHHHCCT----BHHHHHHH CS
                 RmlD_sub_bind 245 eyptpAkRPanSvLdtekleatfgiklrewrealke 280
                                   +    A+RP +S+Ld + +++ + +   + +++l++
  gi|13541731|ref|NP_111419.1| 235 K-EMVARRPFDSSLDISYAKKLIDFDFYTLESNLNS 269
                                   5.578***************9999888777777665 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.2   0.3   8.1e-21   2.4e-17       1     185 [.       4     162 ..       4     169 .. 0.87

  Alignments for each domain:
  == domain 1  score: 63.2 bits;  conditional E-value: 8.1e-21
                                   EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE--S---HHHHH CS
                     Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfkeeqpdavihlAavggvaass 81 
                                   il+ G+tG++G+ l+k + ++   + g  +                ++d+td s+++ lf++  pd+vi+ Aa  +v++  
  gi|13541731|ref|NP_111419.1|   4 ILIFGHTGQLGRELLKLVPNA---ISGSING--------------KRVDITDYSEIALLFSQASPDIVINSAAFTNVDRCE 67 
                                   89*************999986...5555555..............379********************************* PP

                                   HSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHHHHHHHHHHHHHHT- CS
                     Epimerase  82 edpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKlageklveayaaqygl 162
                                   +++++ +  n++g++n+++ + k++  +l+++s++ v+       ke+++      p + Y+++K  g+ ++ +       
  gi|13541731|ref|NP_111419.1|  68 KEREKAYLVNAIGVRNIVKLCDKYNS-KLIQISTDYVFNGERGNYKEDDI----PDPINYYGYTKSIGDAYALSS-----D 138
                                   **************************.***********977774344444....57*************999875.....3 PP

                                   EEEEEEESEEESTT.S-TTSTTSH CS
                     Epimerase 163 naiilrlfnlyGpr.ngegevsrv 185
                                   n+i++r + ++G   n++ +v + 
  gi|13541731|ref|NP_111419.1| 139 NTIVVRTSGVFGNAnNFPLFVYNR 162
                                   689999999999998888886555 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 ?   -2.1   0.0      0.66     2e+03       1      16 [.       5      20 ..       5      26 .. 0.87
   2 !   42.8   0.0   1.4e-14   4.2e-11      53     164 ..      28     134 ..      15     154 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.66
                                  EEETTTSHHHHHHHHH CS
                 GDP_Man_Dehyd  1 LiTGiaGfiGsylael 16
                                  Li G +G+ G  l++l
  gi|13541731|ref|NP_111419.1|  5 LIFGHTGQLGRELLKL 20
                                  89********988765 PP

  == domain 2  score: 42.8 bits;  conditional E-value: 1.4e-14
                                   CEEEEE--TT-HHHHHHHHHHHT-SEEEE--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG CS
                 GDP_Man_Dehyd  53 nlklhkgDltDssslerllaevqpdevynLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvY 133
                                   +++  ++D+tD s++  l++++ pd v+n AA   Vd+  ++ e+ + vn++G+ ++++++ +++     +++q+St+ v+
  gi|13541731|ref|NP_111419.1|  28 SINGKRVDITDYSEIALLFSQASPDIVINSAAFTNVDRCEKEREKAYLVNAIGVRNIVKLCDKYNS----KLIQISTDYVF 104
                                   5666789*******************************************************9974....8********** PP

                                   -S-SSSSB-TTS-----SHHHHHHHHHHHHH CS
                 GDP_Man_Dehyd 134 GkvqevpqtEttpfyPrsPYaaaKlyadwiv 164
                                    + ++  ++E+   +P + Y+ +K + d  +
  gi|13541731|ref|NP_111419.1| 105 -NGERGNYKEDDIPDPINYYGYTKSIGDAYA 134
                                   .3445789****************9998766 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.23     7e+02       1      18 [.       4      21 ..       4      29 .. 0.87
   2 !   35.9   0.0   1.5e-12   4.3e-09      61     155 ..      34     140 ..      12     154 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.23
                                  EEEETTTSHHHHHHHHHH CS
               Polysacc_synt_2  1 vlvtGagGsiGselvrqi 18
                                  +l+ G +G +G+el++ +
  gi|13541731|ref|NP_111419.1|  4 ILIFGHTGQLGRELLKLV 21
                                  799***********9865 PP

  == domain 2  score: 35.9 bits;  conditional E-value: 1.5e-12
                                   --TT-HHHHHHHTT..T-SEEEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEEGGGSS........ CS
               Polysacc_synt_2  61 gdvrdkerlekaleelkvdvvfhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkvvliStDKAvn........ 133
                                    d++d ++++ ++++ ++d+v+++AA+ +V  +e++  +a   N +g +n+++ + +++ +k++ iStD   n        
  gi|13541731|ref|NP_111419.1|  34 VDITDYSEIALLFSQASPDIVINSAAFTNVDRCEKEREKAYLVNAIGVRNIVKLCDKYN-SKLIQISTDYVFNgergnyke 113
                                   79*******************************************************98.689*****9776433444444 PP

                                   .....--SHHHHHHHHHHHHHHHGGG- CS
               Polysacc_synt_2 134 .....PtnvmGatKrlaekllqalake 155
                                        P+n +G tK + + ++ + +++
  gi|13541731|ref|NP_111419.1| 114 ddipdPINYYGYTKSIGDAYALSSDNT 140
                                   444449999999999999998887766 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.1   0.1     1e-11     3e-08      66     208 ..      26     150 ..       9     212 .. 0.72

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 1e-11
                                   E--TTSGGGG--HHHHHHH...HHH--EEEE--SS-S.ST...TSSEEHHHHHHHHHHHHHHHTSSS--.-EEEEEEGGGT CS
                 NAD_binding_4  66 eGDlseprlGLseedlqel...aeevdviihsaAtvnfde...pykellrvNveGtrevlelakklkklkvllhvSTayvn 140
                                   +G ++ +r+ + + +   l   +++ d++i+saA +n+d+   + ++++ vN  G+r++++l+ k +++  l+++ST yv 
  gi|13541731|ref|NP_111419.1|  26 SGSINGKRVDITDYSEIALlfsQASPDIVINSAAFTNVDRcekEREKAYLVNAIGVRNIVKLCDKYNSK--LIQISTDYVF 104
                                   555555555555544333334456779**********9984446667*****************99888..******6665 PP

                                   TS-TTT--SSS-H......HHH--EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEE- CS
                 NAD_binding_4 141 geregeveekvyeegekeekldederaklkglpntYeqsKalaEklvrearrrsglpvvivRpsiitg 208
                                   + ++g+                  ++++  +  n Y ++K +++    +       ++++vR s + g
  gi|13541731|ref|NP_111419.1| 105 NGERGNY-----------------KEDDIPDPINYYGYTKSIGDAYALSSD-----NTIVVRTSGVFG 150
                                   5555554.................455666777778888888877776666.....235677776666 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 !   21.7   0.1   2.7e-08   8.2e-05      51     196 ..      33     163 ..      16     181 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 2.7e-08
                     3Beta_HSD  51 egDvtdkdkleealegv..dvvihlaslvdvag.kltedeimkvnvkGTrnvleacvkagvrvlvYtSsaevvgpnslgee 128
                                    +D+td +++     ++  d+vi  a+ ++v   + ++++ + vn  G rn+++ c k +  +l+  S+ + v++   g  
  gi|13541731|ref|NP_111419.1|  33 RVDITDYSEIALLFSQAspDIVINSAAFTNVDRcEKEREKAYLVNAIGVRNIVKLCDKYN-SKLIQIST-DYVFN---G-- 106
                                   689999999988776653379999*******98799999*****************9998.56787776.77888...4.. PP

                     3Beta_HSD 129 ilngdEeleyeslhqdaypesKalaEklvlkaNgrtlknggrlyTcaLRpagiyGegdkllvpllkql 196
                                     +g+ ++   + + + y ++K++ +++ l++ +          T+ +R +g++G+ +++ + ++++l
  gi|13541731|ref|NP_111419.1| 107 -ERGNYKEDDIPDPINYYGYTKSIGDAYALSSDN----------TIVVRTSGVFGNANNFPLFVYNRL 163
                                   .468888888889999*****************9..........99**********999887777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       363  (0.0202465); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 1913.04
//
Query:       gi|13541732|ref|NP_111420.1|  [L=179]
Description: dTDP-4-dehydrorhamnose 3,5-epimerase [Thermoplasma volcanium GSS1]
Scores for complete 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-62  209.3   0.0    3.3e-62  209.1   0.0    1.0  1  dTDP_sugar_isom  dTDP-4-dehydrorhamnose 3,5-epimerase


Domain annotation for each model (and alignments):
>> dTDP_sugar_isom  dTDP-4-dehydrorhamnose 3,5-epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  209.1   0.0   1.8e-66   3.3e-62       1     167 [.       7     171 ..       7     173 .. 0.97

  Alignments for each domain:
  == domain 1  score: 209.1 bits;  conditional E-value: 1.8e-66
                                   E-SSTTCEEEEE-EEEETTEEEEEEEEHHHHHHHTS-----EEEEEEEETTBEEEEEEESSCS---EEEEEEESEEEEEEE CS
               dTDP_sugar_isom   1 eteiegvlliepkvfgDeRGfflesfneeefaeagleaefvqdnlsvskkgvlRGlHfqkepkaqaklvrvvrGevldvaV 81 
                                   etei++v+ i  ++++D+RG+f e ++++ef++  l+++fvqdn+s+s++gv+RGlHfq+ep aq+klv v++G+++dvaV
  gi|13541732|ref|NP_111420.1|   7 ETEIPDVIHIVCNRYEDNRGYFEERYKASEFDRI-LHVRFVQDNHSFSRRGVIRGLHFQREPMAQGKLVGVITGRIYDVAV 86 
                                   699*****************************87.6779****************************************** PP

                                   E-BTTSTTTT-EEEEEEETTT--EEEE-TTEEEEEEE-SSEEEEEEEESS---GGGEEEE-TT-TTTT---..SS.B--HH CS
               dTDP_sugar_isom  82 DlRkgSptfgkwvgveLsaenkrqlyipegfahGflvlsdeaevlYkvteyyapesergirwnDpelgidw..eelilSek 160
                                   DlRk+S tfgkwv   Ls  n+++l+ip+gfahGf++l+d ++v+Ykv++ +++++e gi +nDp+l+idw  +++i+Sek
  gi|13541732|ref|NP_111420.1|  87 DLRKDSVTFGKWVYRVLS--NNEMLWIPRGFAHGFQALED-SHVVYKVDNEFSRQHEDGIIFNDPDLAIDWpiKDPIVSEK 164
                                   ******************..9*****************98.899*****************************99****** PP

                                   HHT-B-H CS
               dTDP_sugar_isom 161 Dkaapsl 167
                                   D ++ ++
  gi|13541732|ref|NP_111420.1| 165 DIKLGTF 171
                                   *998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (179 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       317  (0.0176809); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 1172.98
//
Query:       gi|13541733|ref|NP_111421.1|  [L=318]
Description: dTDP-D-glucose 4,6-dehydratase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-83  280.6   0.0    2.3e-83  280.4   0.0    1.0  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    5.8e-60  202.7   0.1    7.3e-60  202.4   0.1    1.1  1  Epimerase        NAD dependent epimerase/dehydratase family
      1e-16   60.9   0.0    1.4e-16   60.4   0.0    1.2  1  RmlD_sub_bind    RmlD substrate binding domain
    3.5e-16   59.1   0.0    4.4e-16   58.7   0.0    1.1  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    3.2e-12   46.2   0.0    5.7e-11   42.1   0.0    2.2  1  NAD_binding_4    Male sterility protein
    1.6e-11   43.9   0.0    1.9e-10   40.4   0.0    2.2  2  Polysacc_synt_2  Polysaccharide biosynthesis protein
    1.3e-05   25.2   0.0    2.1e-05   24.5   0.0    1.3  1  NAD_binding_10   NAD(P)H-binding
    0.00038   20.0   0.0      0.002   17.6   0.0    1.9  1  adh_short        short chain dehydrogenase
     0.0032   17.7   0.0      0.006   16.8   0.0    1.4  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
     0.0085   15.7   0.1      0.068   12.7   0.0    2.1  2  NmrA             NmrA-like family
  ------ inclusion threshold ------
      0.025   14.7   0.0      0.088   12.9   0.0    1.9  2  DapB_N           Dihydrodipicolinate reductase, N-terminus
      0.031   14.2   0.0      0.059   13.3   0.0    1.4  1  KR               KR domain
      0.079   13.1   0.0       0.15   12.2   0.0    1.4  1  Ldh_1_N          lactate/malate dehydrogenase, NAD binding do


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 !  280.4   0.0   1.7e-86   2.3e-83       1     332 []       4     305 ..       4     305 .. 0.93

  Alignments for each domain:
  == domain 1  score: 280.4 bits;  conditional E-value: 1.7e-86
                                   EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-SEEEE CS
                 GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpdevyn 81 
                                   L+TG+aGfiGs++++++l+k+++   iv+ ++++++++ + + +   ++ +++++l+k+D+ +++++e+++++v  d v+n
  gi|13541733|ref|NP_111421.1|   4 LVTGGAGFIGSNFINYWLKKHQRD-SIVNVDKLTYAANPDYVDH---KSFSDRYELIKADIANAKQIESIIKDV--DCVVN 78 
                                   9*******************8877.689999******9998853...45789*********************9..9**** PP

                                   --S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-S...SSSB-TTS-----SHHHHHHHH CS
                 GDP_Man_Dehyd  82 LAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvq...evpqtEttpfyPrsPYaaaKly 159
                                   +AA+shVd+s+++Pe +++ n +G++++Lea+r++     +rf+q+St+Ev+G++    + +++E+ p+ Pr+PY+a+K++
  gi|13541733|ref|NP_111421.1|  79 FAAESHVDNSIKSPEPFIRSNYVGVYNILEAVRKYD----IRFHQISTDEVFGSLPldsSQKFDEHSPYAPRNPYSATKAA 155
                                   **********************************95....7*************9654366789***************** PP

                                   HHHHHHHHHHHH---EEEEEE-EEESTTS-TTSCCCHHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHHHHHHHHHHHHCS CS
                 GDP_Man_Dehyd 160 adwivvnyreayglfavngilfnhesprrgetfvtrkitravarialgkqevlylGnldakRdwghvkDyveamwlmlqqd 240
                                   ad++v++y ++yg+ a++++++n+++p ++    +++i+++v ++ ++   ++++G ++++Rdw hv D+++a+ ++l+++
  gi|13541733|ref|NP_111421.1| 156 ADMLVRSYINTYGIKATISNCSNNYGPNQH---REKLIPKTVYNAIHNF-RIPIYGSGRQIRDWIHVLDHCSAIEAILERG 232
                                   ****************************85...56*********99987.67889************************** PP

                                   S---EEE-TT-EEECHHCHHCCHHCCCHHHHHH............TTGGCCCEECGG--SS--SB--B-THHHHHHH---- CS
                 GDP_Man_Dehyd 241 kpedyviatgethsvrefvelaflelgktiewegkgeeevgrakesgkvvvevdpkyfrpgevdlllgdaskakeeLgWkp 321
                                   +        get+ v   +e  +++++k+i                gk++  ++++ +rpg++ ++++d++k+++eL+Wkp
  gi|13541733|ref|NP_111421.1| 233 R-------IGETYLVSARNEQHNIDVVKKILGI------------LGKDESLIEYVSDRPGHDVRYAIDPKKIENELDWKP 294
                                   9.......7******************998764............3567788999************************** PP

                                   SS-HHHHHHHH CS
                 GDP_Man_Dehyd 322 kvsfeelvrem 332
                                   ++ f+e++r++
  gi|13541733|ref|NP_111421.1| 295 SIPFDEGLRDT 305
                                   ********986 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  202.4   0.1   5.3e-63   7.3e-60       2     240 ..       4     240 ..       3     241 .. 0.95

  Alignments for each domain:
  == domain 1  score: 202.4 bits;  conditional E-value: 5.3e-63
                                   EEETTTSHHHHHHHHHHHHCT.SE.EEEEES-STTTTCHHCHHC......EEEE--TT-HHHHHHHHHHHT-SEEEE--S- CS
                     Epimerase   2 lVtGatGfiGsalvkallekg.ye.vigldrlssasntarledl......elveldltdrsalerlfkeeqpdavihlAav 74 
                                   lVtG++GfiGs++++++l+k+  + ++++d+l++a n    +++      el+++d+ +++++e ++k  ++d+v+++Aa+
  gi|13541733|ref|NP_111421.1|   4 LVTGGAGFIGSNFINYWLKKHqRDsIVNVDKLTYAANPDYVDHKsfsdryELIKADIANAKQIESIIK--DVDCVVNFAAE 82 
                                   9*******************96447****************999************************..89********* PP

                                   --HHHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHHHHHHHHH CS
                     Epimerase  75 ggvaassedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKlageklvea 155
                                   ++v++s+++p+ fi++n +g++n+lea+rk+++ r++++s++ev+G  +    ++  + +p++p++pY+a+K+a++ lv++
  gi|13541733|ref|NP_111421.1|  83 SHVDNSIKSPEPFIRSNYVGVYNILEAVRKYDI-RFHQISTDEVFGSLPLDSSQKFDEHSPYAPRNPYSATKAAADMLVRS 162
                                   *********************************.************98885567777778********************* PP

                                   HHHHHT-EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHHHHHHHHHHTT-STTE CS
                     Epimerase 156 yaaqyglnaiilrlfnlyGprngegevsrvipalirkilegkqevtllgdgtalRdflyveDvaeaillvlehvdagdkge 236
                                   y ++yg++a+i +++n+yGp+   ++++++ip+ + ++ ++   + ++g+g++ Rd+++v D++ ai ++le+   g+ ge
  gi|13541733|ref|NP_111421.1| 163 YINTYGIKATISNCSNNYGPN---QHREKLIPKTVYNAIHNF-RIPIYGSGRQIRDWIHVLDHCSAIEAILER---GRIGE 236
                                   *********************...99***********99999.9*****************************...88888 PP

                                   EEEE CS
                     Epimerase 237 iyni 240
                                   +y +
  gi|13541733|ref|NP_111421.1| 237 TYLV 240
                                   8765 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.4   0.0     1e-19   1.4e-16       1     143 [.       1     167 [.       1     187 [. 0.89

  Alignments for each domain:
  == domain 1  score: 60.4 bits;  conditional E-value: 1e-19
                                   EEEEEESTTSHHHHHHHHHCTTTSE..EEEEE-TT.....................T--TTSHHHHHHHHHHH--SEEEE- CS
                 RmlD_sub_bind   1 mkilvtGanGqlGseLakqlaeegl..evlaltre.....................eldltdaeavaellkeakpdvvvna 58 
                                   mk+lvtG+ G +Gs+ ++   +++   +++ +++                      ++d+++a+++++++k+   d+vvn 
  gi|13541733|ref|NP_111421.1|   1 MKLLVTGGAGFIGSNFINYWLKKHQrdSIVNVDKLtyaanpdyvdhksfsdryeliKADIANAKQIESIIKD--VDCVVNF 79 
                                   89*************998766654311344444448999*********************************..677**** PP

                                   -----HHHHHHSHHHHHHHHTHHHHHHHHHHHHCT-EEEEEEEGGGS-S-...TTS-B-TTS----SSHHHHHHHHHHHHH CS
                 RmlD_sub_bind  59 AAytavDkaEseeeaayavnaeavealAeaaaavgalLihvStDyVFdGe...kkrpYeeddetsPlnvYGrtKlaGEqav 136
                                   AA   vD+  + +e   + n  +v ++ ea +++++ + ++StD VF       ++++ e+++ +P+n Y +tK+a    v
  gi|13541733|ref|NP_111421.1|  80 AAESHVDNSIKSPEPFIRSNYVGVYNILEAVRKYDIRFHQISTDEVFGSLpldSSQKFDEHSPYAPRNPYSATKAAADMLV 160
                                   ***********************************************8867768899************************ PP

                                   HHH-SSE CS
                 RmlD_sub_bind 137 laagkka 143
                                   +++ +++
  gi|13541733|ref|NP_111421.1| 161 RSYINTY 167
                                   *977655 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.7   0.0   3.2e-19   4.4e-16       1     217 [.       4     217 ..       4     241 .. 0.78

  Alignments for each domain:
  == domain 1  score: 58.7 bits;  conditional E-value: 3.2e-19
                     3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlD...lrespelleelskvnvkkviegDvtdkdkleealegvdvvihlaslvd 78 
                                   +vtGgaGF+G++ ++  ++ ++   +  +D    + +p   ++ s +++ ++i++D+ +++++e  +++vd+v+  a+ + 
  gi|13541733|ref|NP_111421.1|   4 LVTGGAGFIGSNFINYWLKKHQRDSIVNVDkltYAANPDYVDHKSFSDRYELIKADIANAKQIESIIKDVDCVVNFAAESH 84 
                                   69*****************99999999999655677888889989999999****************************** PP

                     3Beta_HSD  79 vag.kltedeimkvnvkGTrnvleacvkagvrvlvYtSsaevvgpnslgeeilngdEeleyeslhqdaypesKalaEklvl 158
                                   v +   + + + + n+ G  n+lea +k ++r+    S+ ev ++    +  ++ dE+ +y   + ++y+ +Ka a+ lv 
  gi|13541733|ref|NP_111421.1|  85 VDNsIKSPEPFIRSNYVGVYNILEAVRKYDIRFH-QISTDEV-FGSLPLDSSQKFDEHSPYA--PRNPYSATKAAADMLVR 161
                                   *9846678889********************973.4555555.5558889999999*99996..689************98 PP

                     3Beta_HSD 159 kaNgrtlkngg.rlyTcaLRpagiyGegdkl..lvpllkqlaklglalfkigdeevlsdrvY 217
                                   +  +    +++ ++  c    +  yG+ +++  l p  +  a ++  +  +g+ +++ d++ 
  gi|13541733|ref|NP_111421.1| 162 SYIN--TYGIKaTISNC----SNNYGPNQHRekLIPKTVYNAIHNFRIPIYGSGRQIRDWIH 217
                                   7544..12222134444....35577665441133333333334555666666666666665 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.1   0.0   4.1e-14   5.7e-11       1     208 [.       5     181 ..       5     229 .. 0.81

  Alignments for each domain:
  == domain 1  score: 42.1 bits;  conditional E-value: 4.1e-14
                                   EE-TTSHHHHHHHHHHHHHS-.TEEEEEE-SSSHHHHHHHHHHHT-SS-HHHHHHHHHTTTEEEEE--TTSGGGG--HHHH CS
                 NAD_binding_4   1 lTGaTGFLGkvLlekLLrttpevkiyllvRaksgesaeeRleeelekkelfsallkelaerikvveGDlseprlGLseedl 81 
                                   +TG+ GF+G+ +++ +L+++++          ++    ++l+ +   + + ++     ++r + +++D+++ +      ++
  gi|13541733|ref|NP_111421.1|   5 VTGGAGFIGSNFINYWLKKHQR----------DSIVNVDKLTYAANPDYVDHKS---FSDRYELIKADIANAK------QI 66 
                                   7******************994..........3334456675666666666555...499**********765......9* PP

                                   HHHHHH--EEEE--SS-S.STTSSE...EHHHHHHHHHHHHHHHTSSS--.-EEEEEE.GGGTTS-TTT--SSS-H..... CS
                 NAD_binding_4  82 qelaeevdviihsaAtvnfdepyke...llrvNveGtrevlelakklkklkvllhvST.ayvngeregeveekvyeegeke 158
                                   + +++ vd++++ aA  ++d+++k    ++r N  G+ ++le  +k      ++++ST  ++     +             
  gi|13541733|ref|NP_111421.1|  67 ESIIKDVDCVVNFAAESHVDNSIKSpepFIRSNYVGVYNILEAVRKYDIR--FHQISTdEVFGSLPLD-S----------- 133
                                   *********************99887779*************99988666..******6555555553.3........... PP

                                   .HHH--EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEE- CS
                 NAD_binding_4 159 ekldederaklkglpntYeqsKalaEklvrearrrsglpvvivRpsiitg 208
                                      ++ ++ +     n Y+ +Ka+a++lvr++ +  g++++i  +s+ +g
  gi|13541733|ref|NP_111421.1| 134 --SQKFDEHSPYAPRNPYSATKAAADMLVRSYINTYGIKATISNCSNNYG 181
                                   ..5667778889999***************************99997666 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.4   0.0   1.4e-13   1.9e-10       1     130 [.       3     124 ..       3     132 .. 0.82
   2 ?    1.2   0.0      0.12   1.6e+02     134     169 ..     145     181 ..     141     278 .. 0.51

  Alignments for each domain:
  == domain 1  score: 40.4 bits;  conditional E-value: 1.4e-13
                                   EEEETTTSHHHHHHHHHHHHHB-SE.EEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T-SE CS
               Polysacc_synt_2   1 vlvtGagGsiGselvrqilkkkpkk.iillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelkvdv 80 
                                   +lvtG++G iGs++++  lkk+ +  i+ +++     y+ + ++   +++k+++ ++  + +d+++++++e++++  +vd+
  gi|13541733|ref|NP_111421.1|   3 LLVTGGAGFIGSNFINYWLKKHQRDsIVNVDKL---TYAANPDY---VDHKSFSDRYELIKADIANAKQIESIIK--DVDC 75 
                                   59*****************99665504444443...33444443...344444445556779*************..**** PP

                                   EEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEEGG CS
               Polysacc_synt_2  81 vfhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkvvliStDK 130
                                   v++ AA  hV    + p   i+ N +g  n++ea  ++++ ++  iStD 
  gi|13541733|ref|NP_111421.1|  76 VVNFAAESHVDNSIKSPEPFIRSNYVGVYNILEAVRKYDI-RFHQISTDE 124
                                   ***************************************9.5999***96 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.12
                                   --SHHHHHHHHHHHHHHHGGG--SSS-.-EEEEEEE- CS
               Polysacc_synt_2 134 PtnvmGatKrlaekllqalakeseekk.tkfvvvRfG 169
                                   P n + atK++a++l+ ++ ++ + k     +   +G
  gi|13541733|ref|NP_111421.1| 145 PRNPYSATKAAADMLVRSYINTYGIKAtISNCSNNYG 181
                                   7778888888888888776665544431333444444 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 !   24.5   0.0   1.5e-08   2.1e-05       1     133 [.       7     162 ..       7     173 .. 0.68

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 1.5e-08
                                   TTTSHHHHHHHHHHHHC-......T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES---TCCHH CS
                NAD_binding_10   1 GAtGkvGrllvkellarg......ghevtalvRnpeklaeleaeeglevvegdvtdvedlaealkgadaVvsalggggkde 75 
                                   G+ G +G+  ++  l+++      +++   ++ np+ +++ + +++ e++++d+ +++++++ +k++d Vv  ++ ++ d+
  gi|13541733|ref|NP_111421.1|   7 GGAGFIGSNFINYWLKKHqrdsivNVDKLTYAANPDYVDHKSFSDRYELIKADIANAKQIESIIKDVDCVVNFAAESHVDN 87 
                                   7778888888888877754333222222233556666654334589**********************8887777777666 PP

                                   HH.............HHHHHHHHHHCT--EEEEEEETTTTSG....CGCHHHHHHHHCCHHHHHH.HHHHHHHHHH CS
                NAD_binding_10  76 eg.............aknivdaakeagvkRfvlvsaigvgde....vpgefgewnkellkaylaa.kraaeellra 133
                                    +             + ni++a+++ ++ Rf  +s+  v  +    + ++f+e    + ++ + a k+aa+ l+r+
  gi|13541733|ref|NP_111421.1|  88 SIkspepfirsnyvgVYNILEAVRKYDI-RFHQISTDEVFGSlpldSSQKFDEHSPYAPRNPYSAtKAAADMLVRS 162
                                   666777788888899*************.******98887651111334455555556665565515566666654 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   1.5e-06     0.002       4     167 ..       4     167 ..       2     177 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.5e-06
                                   EEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHT..TSEEEEEE-TTTSHHHHHHHHHHHHHHHSSESEEE CS
                     adh_short   4 lvtGassGIGraiakelakeGakvvvvdrseekleevakelkee..gakalaiqvDvtdreevealvekavkklgkldvLv 82 
                                   lvtG+++ IG ++ +  +k+  +  +v+  + + ++  + +  +  ++++  i++D+++++++e +++++       d++v
  gi|13541733|ref|NP_111421.1|   4 LVTGGAGFIGSNFINYWLKKHQRDSIVNVDKLTYAANPDYVDHKsfSDRYELIKADIANAKQIESIIKDV-------DCVV 77 
                                   8***************999999999999998899889888888888999*********999999998876.......**** PP

                                   E---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHH.......HCTTEEEEEEEEGGG..TSB-TTBHHHHHHHH CS
                     adh_short  83 nNAGitgsgpfselseeewervievNltgvflltravlpaml.......kqssGrIvnvsSvag..kvpvagvaaYsAsKa 154
                                   n A+ +      + s +  e  i  N++gv+++ +av ++ +       ++  G+    sS+    + p+a   +YsA+Ka
  gi|13541733|ref|NP_111421.1|  78 NFAAES----HVDNSIKSPEPFIRSNYVGVYNILEAVRKYDIrfhqistDEVFGSLPLDSSQKFdeHSPYAPRNPYSATKA 154
                                   ***994....4455667788999**************9994467677778888999999999864467888899******* PP

                                   HHHHHHHHHHHHH CS
                     adh_short 155 avagltrslakel 167
                                   a ++l+rs  + +
  gi|13541733|ref|NP_111421.1| 155 AADMLVRSYINTY 167
                                   ******9976655 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   4.3e-06     0.006       5      78 ..       8      81 ..       3      90 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 4.3e-06
                                  --SHHHHHHHHHHHCTCCT-GEEEEEESSHHHH.HHHHCHH.TTTCEEEEE--TTTHHHHHHHHHTTSSEEEE-SS CS
               Sacchrp_dh_NADP  5 GaGsvGqavaellarhfdvdaeitvadrskekl.ealaaka.lgvrfeaialdaenyeavLaallkegdlvvnlsp 78
                                  GaG++G+ ++ + +++++ d  i+ +d+    +    ++++  + r e i+ d++n ++ +++++k+ d vvn + 
  gi|13541733|ref|NP_111421.1|  8 GAGFIGSNFINYWLKKHQRD-SIVNVDKLTYAAnPDYVDHKsFSDRYELIKADIANAKQ-IESIIKDVDCVVNFAA 81
                                  67*********999999876.777777643332033333335999**************.*************876 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.0   4.9e-05     0.068       2      73 ..       4      81 ..       3      91 .. 0.79
   2 ?    0.3   0.0      0.31   4.2e+02     123     142 ..     158     177 ..     134     197 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.9e-05
                                  EESSTTSHHHHHHHHHHHHHT-EEEEEES-S.......-SHHHHHHHHSTTEEEES-TT-HHHHHHHHTT-SEEEE--- CS
                          NmrA  2 lviGaTGrqGksvvrallkaghkvralvRdt.......kselakslkeaGvelvkgdlddkeslvealkgvdvvfsvtg 73
                                  lv+G++G +G+ ++++ lk+  +  ++  d        +    ks++++  el+k+d+ + + +++++k+vd v    +
  gi|13541733|ref|NP_111421.1|  4 LVTGGAGFIGSNFINYWLKKHQRDSIVNVDKltyaanpDYVDHKSFSDR-YELIKADIANAKQIESIIKDVDCVVNFAA 81
                                  8*****************955544444444445555669999999*998.8*********************9975554 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.31
                                   HHHHHHHHHCTS-EEEEEE- CS
                          NmrA 123 aeieeyvralgipytfvyag 142
                                   + ++ y+   gi +t+  + 
  gi|13541733|ref|NP_111421.1| 158 MLVRSYINTYGIKATISNCS 177
                                   4699999999*****98764 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   6.4e-05     0.088       1      84 [.       1      89 [.       1      92 [. 0.77
   2 ?   -1.5   0.0       1.9   2.7e+03      10      30 ..     232     253 ..     209     288 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.4e-05
                                  EEEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTC.....STTTTTBHHHHSSSS--S-BEBSSHHHHHHH-SEEEE-S-HH CS
                        DapB_N  1 ikvavvGasGrmGkevvkaveeaedlelvaavdrke.....selegkdagellglgklgvavtddleevlekadvliDFTtpe 78
                                  +k++v+G +G +G++ ++   ++ +      vd+ +       ++ k++++  +l k ++a  +++e++++++d+++ F + +
  gi|13541733|ref|NP_111421.1|  1 MKLLVTGGAGFIGSNFINYWLKKHQRDSIVNVDKLTyaanpDYVDHKSFSDRYELIKADIANAKQIESIIKDVDCVVNFAAES 83
                                  7999***********9999888755555544444332222255667777788888899**********************998 PP

                                  HHHHHH CS
                        DapB_N 79 avlenl 84
                                   v + +
  gi|13541733|ref|NP_111421.1| 84 HVDNSI 89
                                  887765 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.9
                                   SHHHHH.HHHHHHHSTTEEEEE CS
                        DapB_N  10 GrmGke.vvkaveeaedlelva 30 
                                   Gr+G++ +v+a +e+ ++ +v+
  gi|13541733|ref|NP_111421.1| 232 GRIGETyLVSARNEQHNIDVVK 253
                                   4555432333333333333333 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   4.3e-05     0.059       4      76 ..       4      74 ..       2      79 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.3e-05
                                  EEETTTSHHHHHHHH.HHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHH CS
                            KR  4 litGGlGgLGlelar.wlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeik 76
                                  l+tGG+G +G  +++ wl ++ + ++v + +   + +++       ++   + e+++aD+++++++e+++++++
  gi|13541733|ref|NP_111421.1|  4 LVTGGAGFIGSNFINyWLKKHQRDSIVNVDKL--TYAANP-DYVDHKSFSDRYELIKADIANAKQIESIIKDVD 74
                                  9**********998736666667778777777..333333.344467778899****************99875 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 ?   12.2   0.0   0.00011      0.15       1      78 [.       1      81 [.       1      86 [. 0.79

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00011
                                  EEEEEETTTSHHHHHHHHHHHHTTSSSEEEEE-SSHHHHHHHHHHHHHCH...CCSTS-EEEEESSGGGGTTESEEEE--S CS
                       Ldh_1_N  1 vkvavvGaaGgiGqslalllankkladelaLlDiakekleGvaldlshis...tflsvkvkvsekeeealkdadvvvitag 78
                                  +k+ v+G aG+iG+++    ++k+  d ++ +D  + +++ + +d +  s     +++++   ++ e+++kd+d+vv  a+
  gi|13541733|ref|NP_111421.1|  1 MKLLVTGGAGFIGSNFINYWLKKHQRDSIVNVDKLTYAANPDYVDHKSFSdryELIKADIANAKQIESIIKDVDCVVNFAA 81
                                  6999***********999888888888899999998999999999766541104445555556699**********98776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       562  (0.0313459); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); 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: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 2014.66
//
Query:       gi|13541734|ref|NP_111422.1|  [L=127]
Description: hypothetical protein TVN0903 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.1e-25   86.7   1.0    1.1e-24   86.1   1.0    1.3  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
     0.0031   17.0   0.5       0.58    9.7   0.1    2.3  2  TF_Zn_Ribbon     TFIIB zinc-binding
  ------ inclusion threshold ------
      0.021   14.6   4.0        1.2    8.9   0.2    2.3  2  Rubredoxin_2     Rubredoxin metal binding domain
      0.021   14.9   0.2      0.026   14.6   0.2    1.2  1  HypA             Hydrogenase/urease nickel incorporation, met
      0.026   14.8   1.3      0.037   14.4   1.3    1.2  1  C1_2             C1 domain
       0.05   13.1   1.1       0.05   13.1   1.1    2.3  2  zn-ribbon_14     Zinc-ribbon
      0.055   13.5   0.9      0.084   12.9   0.9    1.3  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
      0.069   13.2   0.1      0.079   13.0   0.1    1.2  1  zf-C3HC          C3HC zinc finger-like
      0.074   13.2   1.8        1.8    8.7   0.2    2.2  2  UPF0547          Uncharacterised protein family UPF0547
       0.11   12.0   0.0       0.18   11.4   0.0    1.3  1  BetaGal_dom3     Beta-galactosidase, domain 3
       0.12   12.1   3.2        0.4   10.4   3.3    1.9  2  DNA_RNApol_7kD   DNA directed RNA polymerase, 7 kDa subunit
       0.29   10.8   1.4        2.1    8.1   0.1    2.2  2  Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
       0.41   10.4   7.8        2.7    7.8   1.2    2.3  3  zinc_ribbon_2    zinc-ribbon domain
        1.7    8.1   5.3         39    3.8   5.3    2.2  1  zf-ribbon_3      zinc-ribbon domain


Domain annotation for each model (and alignments):
>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.1   1.0   8.8e-28   1.1e-24       3      66 ..      26      89 ..      24      91 .. 0.98

  Alignments for each domain:
  == domain 1  score: 86.1 bits;  conditional E-value: 8.8e-28
                OrfB_Zn_ribbon  3 klkeqleykakeyGikveevnpayTSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNi 66
                                  +l++++eyka+++G+kv+++np y+ ++Cs+Cg+++ke++++ +fkC+nCgfe+++D+nA++Ni
  gi|13541734|ref|NP_111422.1| 26 ELEKFIEYKAEDAGKKVIYINPKYSPQKCSRCGYVSKENRHDSVFKCKNCGFELNADLNASRNI 89
                                  6899***********************************************************9 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.1   0.00045      0.58      22      36 ..      54      68 ..      53      68 .. 0.93
   2 !    5.4   0.1      0.01        13       1       7 [.      70      76 ..      70      87 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00045
                                  ESSSSBEEEECCCCC CS
                  TF_Zn_Ribbon 22 CtdCGlVlednside 36
                                  C++CG+V  +n  d+
  gi|13541734|ref|NP_111422.1| 54 CSRCGYVSKENRHDS 68
                                  ***********9986 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.01
                                  EEETTTT CS
                  TF_Zn_Ribbon  1 ykCPnCg 7 
                                  +kC+nCg
  gi|13541734|ref|NP_111422.1| 70 FKCKNCG 76
                                  6899998 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.5    0.0041       5.2       3      11 ..      54      62 ..      53      64 .. 0.86
   2 ?    8.9   0.2   0.00097       1.2       1       9 [.      70      78 ..      70      81 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0041
                  Rubredoxin_2  3 CsqCGfesa 11
                                  Cs+CG++s 
  gi|13541734|ref|NP_111422.1| 54 CSRCGYVSK 62
                                  ******985 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00097
                  Rubredoxin_2  1 YvCsqCGfe 9 
                                  + C++CGfe
  gi|13541734|ref|NP_111422.1| 70 FKCKNCGFE 78
                                  89*****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 ?   14.6   0.2     2e-05     0.026      60     107 ..      41      91 ..       6      95 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2e-05
                                   -EEEEEEE--EEEETTTS-EEECHH.H.HHS-TTTSSS.-EEEEESSSEEE CS
                          HypA  60 aeLeieevpvkvrCreCgkefelee.k.alrCpkCgsa.dveivsGeellv 107
                                   +++ i+ +    +C++Cg+  ++++ +  ++C++Cg + + ++ + ++++v
  gi|13541734|ref|NP_111422.1|  41 KVIYINPKYSPQKCSRCGYVSKENRhDsVFKCKNCGFElNADLNASRNIEV 91 
                                   4555666667789*****999977644688*****9765777777777666 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   1.3   2.9e-05     0.037      13      43 ..      46      80 ..      31      82 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.9e-05
                          C1_2 13 edssesfnCsaCgrkidgff....YsCseCdfslh 43
                                  +++++  +Cs Cg  +++++    ++C+ C f l 
  gi|13541734|ref|NP_111422.1| 46 NPKYSPQKCSRCGYVSKENRhdsvFKCKNCGFELN 80
                                  5788899********888888999********986 PP

>> zn-ribbon_14  Zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   1.1   3.9e-05      0.05       1      11 [.      52      62 ..      52      64 .. 0.89
   2 ?    1.9   0.5      0.12   1.6e+02       2       8 ..      71      77 ..      70      78 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.9e-05
                  zn-ribbon_14  1 gkCerCGylSS 11
                                  +kC+rCGy+S 
  gi|13541734|ref|NP_111422.1| 52 QKCSRCGYVSK 62
                                  79*******96 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.12
                  zn-ribbon_14  2 kCerCGy 8 
                                  kC+ CG+
  gi|13541734|ref|NP_111422.1| 71 KCKNCGF 77
                                  7****96 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.9   6.6e-05     0.084      11      45 ..      40      77 ..      32      78 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.6e-05
                 Zn_Tnp_IS1595 11 ealrWpng....fvCPhCgsr.kayriktrglfqCkeCrk 45
                                  +++++ n     + C +Cg+  k  r  +  +f+Ck C+ 
  gi|13541734|ref|NP_111422.1| 40 KKVIYINPkyspQKCSRCGYVsKENRHDS--VFKCKNCGF 77
                                  55666666666577*****8867666666..*******86 PP

>> zf-C3HC  C3HC zinc finger-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   6.2e-05     0.079      24      59 ..      47      85 ..      22     108 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.2e-05
                       zf-C3HC 24 selselkcAkrGWkcvs...kdrlkCevCgaslvlklks 59
                                  ++ s+ kc++ G++  +      +kC+ Cg +l + l+ 
  gi|13541734|ref|NP_111422.1| 47 PKYSPQKCSRCGYVSKEnrhDSVFKCKNCGFELNADLNA 85
                                  567999********9775657889*********998633 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.2    0.0014       1.8      15      23 ..      52      60 ..      49      63 .. 0.90
   2 ?    3.9   0.1     0.045        58      16      23 ..      71      78 ..      68      81 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0014
                       UPF0547 15 qfCphCGyv 23
                                  q+C+ CGyv
  gi|13541734|ref|NP_111422.1| 52 QKCSRCGYV 60
                                  89******8 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.045
                       UPF0547 16 fCphCGyv 23
                                  +C  CG++
  gi|13541734|ref|NP_111422.1| 71 KCKNCGFE 78
                                  7999**97 PP

>> BetaGal_dom3  Beta-galactosidase, domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00014      0.18      36      66 ..      77     114 ..      68     118 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00014
                  BetaGal_dom3  36 LaltGDlnatttlevi.ap......ssvktltwNgkkl 66 
                                    +l++Dlna+ ++evi +       s  ++l +N  +l
  gi|13541734|ref|NP_111422.1|  77 FELNADLNASRNIEVIrVSeyfrllSASQSLLFNETPL 114
                                   689*************8777888877778888887776 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   0.4       0.1   1.3e+02      19      25 ..      53      59 ..      47      62 .. 0.81
   2 ?   10.4   3.3   0.00031       0.4       2      25 ..      53      77 ..      52      79 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.1
                                  --SSS-- CS
                DNA_RNApol_7kD 19 RCkeCGh 25
                                  +C  CG+
  gi|13541734|ref|NP_111422.1| 53 KCSRCGY 59
                                  7999997 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00031
                                  B-SSS--B----SSS--.--SSS-- CS
                DNA_RNApol_7kD  2 iCgeCgaevslkkgdpi.RCkeCGh 25
                                  +C +Cg   + ++ d++ +Ck+CG+
  gi|13541734|ref|NP_111422.1| 53 KCSRCGYVSKENRHDSVfKCKNCGF 77
                                  6999*9988855555544******8 PP

>> Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.1      0.18   2.4e+02       8      15 ..      53      60 ..      49      62 .. 0.87
   2 ?    8.1   0.1    0.0016       2.1       3      13 ..      66      76 ..      64      80 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.18
                                  E-TTT--E CS
               Desulfoferrod_N  8 kCevCGni 15
                                  kC  CG +
  gi|13541734|ref|NP_111422.1| 53 KCSRCGYV 60
                                  9*****65 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0016
                                  TT-EEE-TTT- CS
               Desulfoferrod_N  3 klevYkCevCG 13
                                  +  v+kC+ CG
  gi|13541734|ref|NP_111422.1| 66 HDSVFKCKNCG 76
                                  668*******9 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.6     0.016        21       1       6 [.      53      58 ..      46      61 .. 0.72
   2 ?    5.3   7.6     0.013        17       1      23 []      53      79 ..      53      79 .. 0.79
   3 ?    7.8   1.2    0.0021       2.7       1      10 [.      71      80 ..      71      82 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.016
                 zinc_ribbon_2  1 fCpnCG 6 
                                  +C++CG
  gi|13541734|ref|NP_111422.1| 53 KCSRCG 58
                                  466666 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.013
                 zinc_ribbon_2  1 fCpnCG...aelqdnakF.CpyCGtpl 23
                                  +C++CG   +e+  +++F C +CG++l
  gi|13541734|ref|NP_111422.1| 53 KCSRCGyvsKENRHDSVFkCKNCGFEL 79
                                  799999555577778888******987 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.0021
                 zinc_ribbon_2  1 fCpnCGaelq 10
                                  +C+nCG el 
  gi|13541734|ref|NP_111422.1| 71 KCKNCGFELN 80
                                  7*****9985 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   5.3     0.031        39       4      26 .]      53      79 ..      51      79 .. 0.65

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.031
                   zf-ribbon_3  4 rCPnCGaplssddnv.....CpyCGtkl 26
                                  +C++CG + s++ ++     C++CG +l
  gi|13541734|ref|NP_111422.1| 53 KCSRCGYV-SKENRHdsvfkCKNCGFEL 79
                                  68888876.6655533333399999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       884  (0.0493056); expected 358.6 (0.02)
Passed bias filter:                      579  (0.032294); expected 358.6 (0.02)
Passed Vit filter:                        98  (0.005466); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.48u 0.31s 00:00:00.79 Elapsed: 00:00:00.53
# Mc/sec: 726.61
//
Query:       gi|13541735|ref|NP_111423.1|  [L=325]
Description: cell wall biosynthesis glycosyltransferase [Thermoplasma volcanium GSS1]
Scores for complete 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   50.8   0.5    2.9e-13   50.0   0.5    1.4  1  Glycos_transf_2  Glycosyl transferase family 2
    9.9e-07   28.9   0.0    1.5e-06   28.3   0.0    1.3  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    0.00032   20.2   0.8     0.0005   19.6   0.8    1.2  1  Glyco_tranf_2_2  Glycosyltransferase like family 2
  ------ inclusion threshold ------
      0.063   12.7   0.0      0.093   12.1   0.0    1.2  1  Fringe           Fringe-like


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 !   50.0   0.5   6.5e-17   2.9e-13       1     129 [.       6     128 ..       6     167 .. 0.80

  Alignments for each domain:
  == domain 1  score: 50.0 bits;  conditional E-value: 6.5e-17
                                   EEEEEESS-TTTHHHHHHHHHHH.GGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH--S CS
               Glycos_transf_2   1 svviptyNeektlletlesllaq.dpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglraatg 80 
                                   sv+i ++ ++k++ ++++s+l+q   ++++eii+v++ S   + +++e+     +   v+       ++  + +g+ ++++
  gi|13541735|ref|NP_111423.1|   6 SVIISAHDRKKYVMNAIKSVLDQsVGRDKIEIILVKNFSDVALDNFCEKN----KIKNVLFFG-P-TLGEKMARGIMESSS 80 
                                   8**************************************66666666666....445555555.4.799************ PP

                                   SEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC CS
               Glycos_transf_2  81 dyilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiern 129
                                   ++i+flD+Dd ++p+++e +++a+++ ++ v + + +ri +e+++i   
  gi|13541735|ref|NP_111423.1|  81 EIICFLDDDDMFEPNKVENVLKAFNE-DDIVYYHNGVRIIDEDGRIVEK 128
                                   **************************.6657776666666666666554 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 !   28.3   0.0   3.3e-10   1.5e-06       4     115 ..       5     107 ..       3     175 .. 0.79

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 3.3e-10
               Glyco_tranf_2_3   4 lavlVptfneedvlgevlesllaqey..prvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksralnea 82 
                                   ++v++ + ++ +++ + + s+l q+   + +e+++v + sd +  +++e        ++++ v      g+ +  ++++++
  gi|13541735|ref|NP_111423.1|   5 VSVIISAHDRKKYVMNAIKSVLDQSVgrDKIEIILVKNFSDVALDNFCEK-------NKIKNV---LFFGP-TLGEKMARG 74 
                                   99**********************952366****************9986.......355544...32466.4448899** PP

               Glyco_tranf_2_3  83 lravksdlvllvDdDtvvePdtlkrllqffltp 115
                                   +   +s+++ ++DdD+  eP+ ++ +l +f+ +
  gi|13541735|ref|NP_111423.1|  75 IMESSSEIICFLDDDDMFEPNKVENVLKAFNED 107
                                   *****************************9433 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 !   19.6   0.8   1.1e-07    0.0005       4     105 ..       7     103 ..       4     115 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.1e-07
               Glyco_tranf_2_2   4 iplraseerhyieervlqkakyy..deeielivvddgSsekfleevssiidlnllvylkdeddkayslaaarNrGaskaes 82 
                                   + + a+++++y+++ ++    +    ++ie+i+v + S       + +++++n+   +        +l+    rG+ ++ s
  gi|13541735|ref|NP_111423.1|   7 VIISAHDRKKYVMNAIKSVLDQSvgRDKIEIILVKNFSDVA----LDNFCEKNKIKNVLFF---GPTLGEKMARGIMESSS 80 
                                   3457899999******554444444899*********9877....99****9986542222...3346777889******* PP

               Glyco_tranf_2_2  83 dlvlFlDaDcfissDkfekilkl 105
                                   +++ FlD D+++ ++k+e++lk 
  gi|13541735|ref|NP_111423.1|  81 EIICFLDDDDMFEPNKVENVLKA 103
                                   ********************994 PP

>> Fringe  Fringe-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   2.1e-05     0.093      82     119 ..      75     112 ..      52     138 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.1e-05
                        Fringe  82 fleskkkWfchvDDDnylnveaLlklLskynhtqdvyl 119
                                   ++es+++ +c +DDD +  ++++ ++L+++n+++ vy 
  gi|13541735|ref|NP_111423.1|  75 IMESSSEIICFLDDDDMFEPNKVENVLKAFNEDDIVYY 112
                                   68899999*************************99994 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       656  (0.0365888); 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:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.64u 0.37s 00:00:01.01 Elapsed: 00:00:01.04
# Mc/sec: 941.11
//
Query:       gi|13541736|ref|NP_111424.1|  [L=256]
Description: nucleoside-diphosphate-sugar epimerase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-29  103.2   0.4    1.3e-26   93.6   0.4    2.8  1  Epimerase        NAD dependent epimerase/dehydratase family
    4.6e-23   82.1   0.2      1e-17   64.6   0.0    3.0  2  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    3.5e-05   22.9   0.1      0.011   14.8   0.0    2.3  2  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    0.00018   20.7   0.0      0.075   12.1   0.0    2.5  2  RmlD_sub_bind    RmlD substrate binding domain
     0.0025   17.8   0.5        2.2    8.4   0.0    2.6  2  Nup35_RRM_2      Nup53/35/40-type RNA recognition motif
  ------ inclusion threshold ------
      0.044   12.9   0.0       0.14   11.2   0.0    1.8  2  Polysacc_synt_2  Polysaccharide biosynthesis protein
      0.086   12.4   0.0       0.15   11.6   0.0    1.4  2  NmrA             NmrA-like family
       0.13   11.4   0.1        1.9    7.6   0.0    2.4  3  NAD_binding_4    Male sterility 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 !   93.6   0.4   5.6e-30   1.3e-26       1     228 [.       3     180 ..       3     190 .. 0.89

  Alignments for each domain:
  == domain 1  score: 93.6 bits;  conditional E-value: 5.6e-30
                                   EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE--S---HHHHH CS
                     Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfkeeqpdavihlAavggvaass 81 
                                   ilVtG++GfiGs++  +++ +  ev g+d                            + +++ + d++ih+Aa g ++ s+
  gi|13541736|ref|NP_111424.1|   3 ILVTGHRGFIGSHIYSYFNGN-SEVYGFDIG--------------------------DKLEDRRYDVIIHMAARGLIRKSI 56 
                                   8******************86.599999988..........................2345569***************** PP

                                   HSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHHHHHHHHHHHHHHT- CS
                     Epimerase  82 edpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKlageklveayaaqygl 162
                                   e p d+++++l ++++ le ark++   ++f sS    G  ae             p++pY++aK  +e+ ++ y + ygl
  gi|13541736|ref|NP_111424.1|  57 EFPYDYFQDDLSLVVRFLELARKNDS-VFIFPSS----GSTAE-------------PTNPYSLAKKNAEEWIRLYGKLYGL 119
                                   ************************99.*******....65555.............77*********************** PP

                                   EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHHHHHHHHH CS
                     Epimerase 163 naiilrlfnlyGprngegevsrvipalirkilegkqevtllgdgtalRdflyveDvaeaillvleh 228
                                   ++ ilr fn+yG +      ++ +  + + +l+g+ e +++gdg++ Rdflyv Dv   i ++l++
  gi|13541736|ref|NP_111424.1| 120 KYYILRFFNIYGDG----AKKGAVYLFTKAALSGE-EAIVYGDGSHIRDFLYVGDVPITIERILNE 180
                                   **************....77777888999999999.*******************98877777777 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 !    9.8   0.2    0.0002      0.45       1      28 [.       4      30 ..       4      37 .. 0.82
   2 !   64.6   0.0   4.4e-21     1e-17      71     276 ..      35     218 ..      30     244 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0002
                                  EEETTTSHHHHHHHHHHHHCT-CCEEEE CS
                 GDP_Man_Dehyd  1 LiTGiaGfiGsylaelLlekgyevhgiv 28
                                  L+TG  GfiGs++  ++  +  ev+g++
  gi|13541736|ref|NP_111424.1|  4 LVTGHRGFIGSHIYSYFNGN-SEVYGFD 30
                                  9************9998765.7777765 PP

  == domain 2  score: 64.6 bits;  conditional E-value: 4.4e-21
                                   HHHHT-SEEEE--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB-TTS-----S CS
                 GDP_Man_Dehyd  71 laevqpdevynLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpqtEttpfyPrs 151
                                   l++ + d ++++AA   +++s+e P  +++ ++  ++r Le++r+     +  f++ S+    G++           +P++
  gi|13541736|ref|NP_111424.1|  35 LEDRRYDVIIHMAARGLIRKSIEFPYDYFQDDLSLVVRFLELARKN----DSVFIFPSS----GST----------AEPTN 97 
                                   567789**************************************95....457888887....555..........47*** PP

                                   HHHHHHHHHHHHHHHHHHHH---EEEEEE-EEESTTS-TTSCCCHHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHHHHHH CS
                 GDP_Man_Dehyd 152 PYaaaKlyadwivvnyreayglfavngilfnhesprrgetfvtrkitravarialgkqevlylGnldakRdwghvkDyvea 232
                                   PY+ aK  a+  ++ y + ygl   + ++fn ++   +    +  + ++   ++ g+ e +++G+++++Rd+++v D+   
  gi|13541736|ref|NP_111424.1|  98 PYSLAKKNAEEWIRLYGKLYGLKYYILRFFNIYGDGAK----KGAVYLFTKAALSGE-EAIVYGDGSHIRDFLYVGDVPIT 173
                                   **********************************9953....345566656666676.7788******************* PP

                                   HHHHHHC.SS---EEE-TT-EEECHHCHHCCHHCCCHHHHHH... CS
                 GDP_Man_Dehyd 233 mwlmlqq.dkpedyviatgethsvrefvelaflelgktiewegkg 276
                                   + ++l++  ++ +y +++g+ +sv++++ l  + +gk+i  + ++
  gi|13541736|ref|NP_111424.1| 174 IERILNEkYRTGEYEVGSGKGTSVNDLISLIEKVTGKKIRTRHED 218
                                   *****87246799****************9999999998877543 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 !    6.1   0.0    0.0022       4.9       1      30 [.       4      30 ..       4      57 .. 0.76
   2 !   14.8   0.0   4.8e-06     0.011     142     222 ..      95     171 ..      88     182 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0022
                     3Beta_HSD  1 vvtGgaGFlGralvkeLvrleelkevrvlD 30
                                  +vtG +GF+G+++ + +       ev  +D
  gi|13541736|ref|NP_111424.1|  4 LVTGHRGFIGSHIYSYFNGNS---EVYGFD 30
                                  69**********987653333...454444 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 4.8e-06
                     3Beta_HSD 142 hqdaypesKalaEklvlkaNgrtlknggrlyTcaLRpagiyGegdkl.lvpllkqlaklglalfkigdeevlsdrvYvgNv 221
                                   ++++y+  K+ aE+ +          g  l    LR   iyG+g k+  v l+ ++a +g++ + +gd + + d+ Yvg v
  gi|13541736|ref|NP_111424.1|  95 PTNPYSLAKKNAEEWIRLYGK---LYG--LKYYILRFFNIYGDGAKKgAVYLFTKAALSGEEAIVYGDGSHIRDFLYVGDV 170
                                   678899999999999987766...233..66678**********887256677899999********************99 PP

                     3Beta_HSD 222 a 222
                                    
  gi|13541736|ref|NP_111424.1| 171 P 171
                                   5 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.4   0.0    0.0018         4       1      30 [.       1      29 [.       1      52 [. 0.76
   2 !   12.1   0.0   3.4e-05     0.075     118     176 ..      92     155 ..      69     216 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0018
                                  EEEEEESTTSHHHHHHHHHCTTTSEEEEEE CS
                 RmlD_sub_bind  1 mkilvtGanGqlGseLakqlaeeglevlal 30
                                  m ilvtG +G +Gs+++  ++ +  ev+++
  gi|13541736|ref|NP_111424.1|  1 MMILVTGHRGFIGSHIYSYFNGNS-EVYGF 29
                                  78*****************99887.88877 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 3.4e-05
                                   ----SSHHHHHHHHHHHHHHH....H-SSEEEEEE-SEESS.SSS-HHHHHHHHHHH-SEEEEE CS
                 RmlD_sub_bind 118 etsPlnvYGrtKlaGEqavla....agkkalivRtswvyge.kgknfvktmlrlakereelkvv 176
                                   + +P n Y  +K + E++++     +g k++i+R+  +yg+  +k  v  + + a + ee  v 
  gi|13541736|ref|NP_111424.1|  92 TAEPTNPYSLAKKNAEEWIRLygklYGLKYYILRFFNIYGDgAKKGAVYLFTKAALSGEEAIVY 155
                                   679*****************955556679**********9846667777777777777766665 PP

>> Nup35_RRM_2  Nup53/35/40-type RNA recognition motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.0   0.00097       2.2       6      34 ..      26      64 ..      25      85 .. 0.79
   2 !    7.1   0.1    0.0024       5.4       2      25 ..     108     131 ..     107     133 .. 0.92

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00097
                   Nup35_RRM_2  6 VsGydteli.....elVlehFasfGeIvk.hyvp....k 34
                                  V+G+d +++     ++V+ h+a  G I k +++p    +
  gi|13541736|ref|NP_111424.1| 26 VYGFDIGDKledrrYDVIIHMAARGLIRKsIEFPydyfQ 64
                                  89999999999999*************998777766663 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0024
                   Nup35_RRM_2   2 twvaVsGydtelielVlehFasfG 25 
                                    w+  +G   +l++++l++F+ +G
  gi|13541736|ref|NP_111424.1| 108 EWIRLYGKLYGLKYYILRFFNIYG 131
                                   7999****************9887 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       0.3   6.8e+02       1      16 [.       3      18 ..       3      25 .. 0.87
   2 ?   11.2   0.0   6.4e-05      0.14      73     204 ..      35     165 ..      30     223 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.3
                                  EEEETTTSHHHHHHHH CS
               Polysacc_synt_2  1 vlvtGagGsiGselvr 16
                                  +lvtG  G iGs++ +
  gi|13541736|ref|NP_111424.1|  3 ILVTGHRGFIGSHIYS 18
                                  89**********9875 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 6.4e-05
                                   TT..T-SEEEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEEGGGSS--SHHHHHHHHHHHHHHHGG CS
               Polysacc_synt_2  73 leelkvdvvfhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkvvliStDKAvnPtnvmGatKrlaekllqala 153
                                   le+ + dv++h AA   +    e+p++ ++         +e a +++ + +++ S+   ++Ptn + ++K+ ae  +  + 
  gi|13541736|ref|NP_111424.1|  35 LEDRRYDVIIHMAARGLIRKSIEFPYDYFQDDLSLVVRFLELARKND-SVFIFPSSGSTAEPTNPYSLAKKNAEEWIRLYG 114
                                   6778899***********99999********************9987.689**************************9999 PP

                                   G--SSS--EEEEEEE-EETTG...TTSSHHHHHHHHHTT.SSEEES-TT-EEEEE CS
               Polysacc_synt_2 154 keseekktkfvvvRfGNVlgS...rGSviplFkkqikeg.gpvtvTdpemtRyfm 204
                                   k       k+++ Rf N+ g    +G v  lF+k   +g + +   d + +R f+
  gi|13541736|ref|NP_111424.1| 115 KLY---GLKYYILRFFNIYGDgakKGAV-YLFTKAALSGeEAIVYGDGSHIRDFL 165
                                   998...89*********99742224554.45555544442455555555555555 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       2.6   5.7e+03       1      16 [.       3      18 ..       3      21 .. 0.86
   2 ?   11.6   0.0   6.8e-05      0.15     159     230 ..     144     213 ..      88     216 .. 0.76

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 2.6
                                  EEESSTTSHHHHHHHH CS
                          NmrA  1 IlviGaTGrqGksvvr 16
                                  Ilv+G  G +G+++ +
  gi|13541736|ref|NP_111424.1|  3 ILVTGHRGFIGSHIYS 18
                                  8999999****99976 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 6.8e-05
                                   EE-TTS.-EEEEESS-TTS-EE-HHHHHHHHHHHHHHHHHHHTTEEEEE-SEEE-HHHHHHHHHHHHTS-EE CS
                          NmrA 159 dtappedkvtllgpgnpkavlldaeeDiGafvikilkdprklkgkriklagntlsgneivelfekkigktvk 230
                                   + a +++ +++ g+g+    +l  + D+   +  il +++   g++   +g+  s+n++++l+ek++gk+++
  gi|13541736|ref|NP_111424.1| 144 KAALSGEEAIVYGDGSHIRDFL-YVGDVPITIERIL-NEKYRTGEYEVGSGKGTSVNDLISLIEKVTGKKIR 213
                                   4445555788888888777777.8888855555555.54555999999*********************996 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.39   8.6e+02       1      12 [.       5      16 ..       5      18 .. 0.91
   2 ?    0.4   0.0      0.14     3e+02      87     110 ..      39      62 ..      33      95 .. 0.60
   3 ?    7.6   0.0   0.00086       1.9     170     209 ..      93     132 ..      87     147 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.39
                                  EE-TTSHHHHHH CS
                 NAD_binding_4  1 lTGaTGFLGkvL 12
                                  +TG  GF+G+++
  gi|13541736|ref|NP_111424.1|  5 VTGHRGFIGSHI 16
                                  7*********97 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.14
                                   H--EEEE--SS-S.STTSSEEHHH CS
                 NAD_binding_4  87 evdviihsaAtvnfdepykellrv 110
                                   + dviih+aA+  + ++++  ++ 
  gi|13541736|ref|NP_111424.1|  39 RYDVIIHMAARGLIRKSIEFPYDY 62 
                                   5799****9986666655554444 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.00086
                                   TTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEE-- CS
                 NAD_binding_4 170 kglpntYeqsKalaEklvrearrrsglpvvivRpsiitge 209
                                   ++ +n Y+  K  aE+ +r +++  gl+  i+R  +i+g+
  gi|13541736|ref|NP_111424.1|  93 AEPTNPYSLAKKNAEEWIRLYGKLYGLKYYILRFFNIYGD 132
                                   56789****************************9999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); 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:                         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: 00:00:00.52
# Mc/sec: 1491.23
//
Query:       gi|13541737|ref|NP_111425.1|  [L=216]
Description: DNA-binding protein [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-15   57.1   0.0    2.6e-15   55.9   0.0    1.6  2  HTH_10    HTH DNA binding domain
  ------ inclusion threshold ------
      0.067   12.8   0.0       0.21   11.2   0.0    1.9  2  HTH_24    Winged helix-turn-helix DNA-binding
        0.1   12.4   0.0       0.23   11.4   0.0    1.6  1  HTH_5     Bacterial regulatory protein, arsR family


Domain annotation for each model (and alignments):
>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       1.8   1.1e+04      38      46 ..      15      23 ..      12      25 .. 0.76
   2 !   55.9   0.0   4.3e-19   2.6e-15       1      53 []     159     211 ..     159     211 .. 0.99

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 1.8
                        HTH_10 38 stlsehLrk 46
                                  s++ ehL++
  gi|13541737|ref|NP_111425.1| 15 SAAAEHLQN 23
                                  577888875 PP

  == domain 2  score: 55.9 bits;  conditional E-value: 4.3e-19
                        HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaesklie 53 
                                   LT+ +++++   +++G+F +PR  +l +++ e+G++k+t+++h+r+ae+k++e
  gi|13541737|ref|NP_111425.1| 159 LTETERRIVNSSLRQGFFSWPRSYDLTSISREFGLTKPTILYHIRNAERKVME 211
                                   9**************************************************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 ?   -2.8   0.0      0.81   4.8e+03       1      10 [.     159     168 ..     159     169 .. 0.81
   2 ?   11.2   0.0   3.5e-05      0.21      22      44 ..     186     208 ..     183     208 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.81
                        HTH_24   1 ldetdrkILe 10 
                                   l et+r+I +
  gi|13541737|ref|NP_111425.1| 159 LTETERRIVN 168
                                   57999*9976 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 3.5e-05
                        HTH_24  22 eLAerlglSpstvnrrlkrLeee 44 
                                    ++++ gl+++t+++++++ e++
  gi|13541737|ref|NP_111425.1| 186 SISREFGLTKPTILYHIRNAERK 208
                                   69****************99875 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   3.8e-05      0.23      15      37 ..     181     203 ..     164     204 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.8e-05
                                   SEEHHHHHHHHTS-HHHHHHHHH CS
                         HTH_5  15 elcvcelaeelglsqstvShHLk 37 
                                   ++  + +++e+gl+++t+ +H +
  gi|13541737|ref|NP_111425.1| 181 SYDLTSISREFGLTKPTILYHIR 203
                                   566789***************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.31s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1387.43
//
Query:       gi|13541738|ref|NP_111426.1|  [L=455]
Description: major facilitator superfamily permease [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.4e-36  123.6  22.4    1.1e-35  123.4  22.4    1.0  1  Sugar_tr  Sugar (and other) transporter
    1.6e-26   93.0  39.2    1.2e-22   80.3  17.6    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 !  123.4  22.4   1.3e-39   1.1e-35      48     430 ..      64     436 ..      10     454 .. 0.80

  Alignments for each domain:
  == domain 1  score: 123.4 bits;  conditional E-value: 1.3e-39
                                   HHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHHHHHH CS
                      Sugar_tr  48 sglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlvPmyis 128
                                   + ++  +f++G+++Gs+f+g+lgd  GR+ ++l   ++f+ g ++ ++     +  ++++  ++ GigvG++  +v +++s
  gi|13541738|ref|NP_111426.1|  64 TLVVPTAFFLGEFVGSIFFGWLGDQRGRRTVFLYNLLVFSGGMIIAGLMS---TAILIAIFVFIGGIGVGGEFPIVDTFTS 141
                                   33445799*****************************************9...88999999******************** PP

                                   TTS-SCCH.HHHHHHHHHHHHHHHHHHHHHHHHHHTSS-.TTHHHHHHHCCHHHHHHHHHHGGGS---HHHHHHTT-HHHH CS
                      Sugar_tr 129 EiApkklR.galvslyqlaitfGilvaaifglglnktsn.adgwrillglqlvpallllilllflPESPrylvekgkeeea 207
                                   E+ p k R ++l ++y  a+t+G ++a+ +++ ++ +    + wril+++  +  +++ ++++ l+ESPr+l  +g+++ea
  gi|13541738|ref|NP_111426.1| 142 EMMPGKERgKRLATVYTIAVTAGPVIAF-LTYEMKIVAPpYVSWRILFWFMGIVGIAIWAVRTQLRESPRWLEVHGRYKEA 221
                                   ********778************99986.67888877778899************************************** PP

                                   HHHHHHHHHC...HHHHHHHHHHHHHHHHHHH.....HTTHHHHSH...HHHHHHHHHHHHHHTTHHH.HHHHTTTHHHHS CS
                      Sugar_tr 208 kevlaklrge...edadrelaeekdsleaeqeeekaswkellssktvrqrlligvvlqifqqltGina.imyysptifenl 284
                                   ++++++ ++    e+  ++l e k+++e +++  k  +k ++   + r+r+++++  q+fq  tGi++ ++ ++pt++   
  gi|13541738|ref|NP_111426.1| 222 DAIVKDWEQRvieEKHLQSLPEPKSETEVSER--KSRYKDIFAP-DLRRRTIMMLIFQFFQ--TGIFYgFTSLAPTFLLYK 297
                                   ******77775556666666666666666633..5677777777.6899999999999998..7888746789**987666 PP

                                   S-THH..HHHHHHHHHHHHHHHHHHHHHHHHS-SHHHHHHHHHHHHHHHHHHH..HHHHTTSS...CHHHHHHHHHHHHHH CS
                      Sugar_tr 285 glsks..llvtiivgvvnfvatfvaiflvdrfGRRtllllGaagmaicfvilgivalllvakskaasivaivfialfialf 363
                                   g++    l++++i++   f+ +++ +f++d++ R+   + +a+ + ++ +++g    ++++     +  +i++++  ++l 
  gi|13541738|ref|NP_111426.1| 298 GITLVhsLEFSFIIYSGFFFGSIFNVFIIDKVERKWGIIASAVLAGVFGTLFG----IIPNV----TATVIFGFITTFVLW 370
                                   6655555****************************555555555555555555....33333....223333333333344 PP

                                   HTTTTHHHHHHHHHHSHTTTHHHHHHHHHHHHHHH.HHHHHHHHHHHHCHHHT-HHHHHHHHHHHHHH CS
                      Sugar_tr 364 algwgpvpwvlvsElfpqsvRskalaiavavnwla.nflisllfpiiteaigggyvflvfaglavlfi 430
                                   +  +      + +E+fp++vR++a+  ++ v+ ++ ++l+ +++ +++ +   + ++l+++++a++++
  gi|13541738|ref|NP_111426.1| 371 N--FSNFYHTYQAEIFPTRVRPTAAGTVYSVSRIStSILVPFITAFFLPHGLLASFGLIWVFIAIVVF 436
                                   4..4566777889*************999999886267889999988877775666666666666654 PP

>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.3  17.6   1.4e-26   1.2e-22      17     260 ..      47     318 ..      37     321 .. 0.75
   2 !   16.3  19.0   3.9e-07    0.0035      43     166 ..     313     436 ..     300     454 .. 0.79

  Alignments for each domain:
  == domain 1  score: 80.3 bits;  conditional E-value: 1.4e-26
                         MFS_1  17 palplalaedlgispseigl.lltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll.fasslwlllvlrvlq 95 
                                   ++l  ++a+ l++s+  + l + t+++lg +v+s+++G+l+d  Grr v+l  ll+f+ g++++  + s+  l++++ ++ 
  gi|13541738|ref|NP_111426.1|  47 VILA-LVASVLHFSHVLATLvVPTAFFLGEFVGSIFFGWLGDQRGRRTVFLYNLLVFSGGMIIAGlM-STAILIAIFVFIG 125
                                   4444.66777999999999988899***********************************5555545.55559999***** PP

                         MFS_1  96 Glgagalfpagaaliadwfpkeergraigllsa.gfslGailgpllgg...lla.sslgWravfyilaivsllafvlflll 171
                                   G+g g+ fp++ ++++++ p++erg+ ++ +++ ++ +G++++ l      ++a  +++Wr +f++++iv++     +++ 
  gi|13541738|ref|NP_111426.1| 126 GIGVGGEFPIVDTFTSEMMPGKERGKRLATVYTiAVTAGPVIAFLT-YemkIVApPYVSWRILFWFMGIVGIAI---WAVR 202
                                   ****************************877773666666666333.347788889999*************97...4478 PP

                         MFS_1 172 lpeepperkrkspkeee..........................kgtgpaplvp......awkallkdpvlw....illial 216
                                      ++++r+ + + + +                          +       ++       +k ++++        +l++ +
  gi|13541738|ref|NP_111426.1| 203 TQLRESPRWLEVHGRYKeadaivkdweqrvieekhlqslpepkS------ETEvserksRYKDIFAPDLRRrtimMLIFQF 277
                                   88888888888888888889999888888888888775554432......2224445566666666663323444688888 PP

                         MFS_1 217 llfffgfsglltllplylqevlglsglllaglllallalvgail 260
                                   + ++ +f+g+++l p++     g++ l+ ++ ++ +++ +++++
  gi|13541738|ref|NP_111426.1| 278 FQTG-IFYGFTSLAPTF-LLYKGIT-LVHSLEFSFIIYSGFFFG 318
                                   8887.9**********9.7777777.444444444444444444 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 3.9e-07
                         MFS_1  43 lgaavaslplGrlsdrfGrrrvlllglllfalglllllfasslwlllvlrvlqGlgagalfpagaaliadwfpkeergrai 123
                                    g++++s++  +++d++ r++ ++++++l +++++l+ +++++++ +++ +++ +    +    +++ a++fp + r+ a 
  gi|13541738|ref|NP_111426.1| 313 SGFFFGSIFNVFIIDKVERKWGIIASAVLAGVFGTLFGIIPNVTATVIFGFITTFVLWNFSNFYHTYQAEIFPTRVRPTAA 393
                                   37899999*************99999999999967777449999************************************* PP

                         MFS_1 124 gllsagfslGa.ilgpllggllasslgWravfyilaivsllafv 166
                                   g +++ + +++ il p + ++++ + g  a+f ++ ++ ++++ 
  gi|13541738|ref|NP_111426.1| 394 GTVYSVSRISTsILVPFITAFFLPH-GLLASFGLIWVFIAIVVF 436
                                   ***********77778888877755.444444444444444422 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (455 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       815  (0.0454571); 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:                         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: 0.66u 0.31s 00:00:00.97 Elapsed: 00:00:00.49
# Mc/sec: 2783.93
//
Query:       gi|13541739|ref|NP_111427.1|  [L=372]
Description: carnitine dehydratase [Thermoplasma volcanium GSS1]
Scores for complete 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-85  286.4   0.0    3.9e-85  286.2   0.0    1.0  1  CoA_transf_3  CoA-transferase family III
  ------ inclusion threshold ------
       0.12   12.6   0.0       0.31   11.2   0.0    1.7  1  Death         Death domain


Domain annotation for each model (and alignments):
>> CoA_transf_3  CoA-transferase family III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  286.2   0.0   4.4e-89   3.9e-85       5     337 ..       2     326 ..       1     349 [. 0.94

  Alignments for each domain:
  == domain 1  score: 286.2 bits;  conditional E-value: 4.4e-89
                  CoA_transf_3   5 rVldlsqvlaGplatslLAdlGAeVIkvEppkkgDpaRkvgpseekgesayflavnrnKrsvalDlkseegrellkrLvak 85 
                                   r +++++++aGp+a+ lL+dlG eVIkvE+pk+gD aR ++      +s++f+ +nrnK+sv++D+k++egr++l +L+ +
  gi|13541739|ref|NP_111427.1|   2 RAIEIGHIVAGPTAGLLLSDLGFEVIKVERPKSGDIARSLTG----TSSGAFAFYNRNKKSVTIDFKQKEGRDVLMKLIGT 78 
                                   7799***********************************965....789******************************** PP

                  CoA_transf_3  86 ADVvieNfrpgvlerlglgyeelrainPrLiyasvsgyGqsGpkakrpgyDlvaqaasGlmsltgepdgpPvkvgvplgDi 166
                                   +DV+i+N+  g+le+ gl+y+e+++ nP Liy+s+ gyG +Gp++kr ++D  ++  sGl+++tg+ ++p ++vg +++D+
  gi|13541739|ref|NP_111427.1|  79 SDVLIDNLGYGALESAGLSYDEMKKHNPGLIYLSIRGYG-NGPYEKRKSLDFPIEIHSGLAYMTGTLEKP-MRVGASMIDM 157
                                   ***************************************.7************************98776.********** PP

                  CoA_transf_3 167 vtgllaavailaallarertGkGqvidvslleaalallapqlleylatgevperqgnrdpaaapygvyrtkdg.wvaiaaa 246
                                    +++++++a+l a+++re+tGkG+++ + ++e+al ++++++++y   g++ ++ +++ +a+ +y++++tkd+  v++a++
  gi|13541739|ref|NP_111427.1| 158 SAAMFGVIAVLDAIIEREKTGKGKQVTIGMFETALFFMGQHITTYQLIGKELKPINEDGFAWGIYDFFTTKDNkKVFVAVT 238
                                   *********************************************99999999999999********************** PP

                  CoA_transf_3 247 tdkqwaalckalgrpelaedprfatnasrlenraeldaelaewlaertaaewlellaaagvpaapvntleevlddpqlaar 327
                                   t++qw+++c+++        ++f tna r+ +r+ l   l+ ++ + + + ++e+l+ a++  a +n++ ++l+dp+  a+
  gi|13541739|ref|NP_111427.1| 239 TEDQWKKFCEVFSLSFC---DEFPTNAIRYSKRDTLIPMLQDVMGKFDSTGLVERLESANISYAVLNKPWDLLNDPHASAK 316
                                   *************9854...8999******************************************************999 PP

                  CoA_transf_3 328 glvvevddpd 337
                                    + +e+   +
  gi|13541739|ref|NP_111427.1| 317 MISEEYCGRK 326
                                   8887776555 PP

>> Death  Death domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   3.4e-05      0.31       8      38 ..     340     369 ..     336     370 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3.4e-05
                                   HCCSTCCSCCHHHHHHHTTSHHHHHHHHHHS CS
                         Death   8 ldhpdplgkdWkelarkLglseeeidrieke 38 
                                    d+p++ g   +e+ r+Lg+s++eid++e++
  gi|13541739|ref|NP_111427.1| 340 SDPPKL-GDYTREVLRELGYSDYEIDYMEHN 369
                                   566555.9*******************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (372 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 2675.22
//
Query:       gi|13541740|ref|NP_111428.1|  [L=344]
Description: isopropylmalate synthase [Thermoplasma volcanium GSS1]
Scores for complete 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-50  171.6   0.2    6.3e-50  170.2   0.2    1.6  1  HMGL-like      HMGL-like
  ------ inclusion threshold ------
      0.014   14.1   0.1      0.036   12.8   0.0    1.6  2  EPSP_synthase  EPSP synthase (3-phosphoshikimate 1-carboxyvin


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 !  170.2   0.2   7.1e-54   6.3e-50       4     263 ..       2     242 ..       1     243 [. 0.96

  Alignments for each domain:
  == domain 1  score: 170.2 bits;  conditional E-value: 7.1e-54
                                   EEE-TTTHHHHTSSS---HHHHHHHHHHHHHHT-SEE--TSGGGT.THHHHHHHS---TT-B..--EE-SSHHHHHHHHH. CS
                     HMGL-like   4 ivdttLRDGeqalkaalsveeklaiakaLdeagvdeiEvgfpaaseddfevvraiakavkkarilalvrarekdikaavea 84 
                                   ++d tLR+G qa++ a++++ek++ia+  ++ g++   v+ p+a e ++e+ r+i +     + ++l r+ ++d++  ++ 
  gi|13541740|ref|NP_111428.1|   2 LTDDTLREGMQAPGIAFTLDEKIRIAQSISKSGIKRALVSYPSAHESEVEAARKITDLHLFDDTYSLGRSIKEDVDSIIS- 81 
                                   6899****************************************************************************. PP

                                   ...TT-SEEEEEEES-HHHHHHHHSSTHHHHHHHHHHHHHHHHHTT-ETTT-BTTTBS--HHHHHHHHHHHHHHT-SEEEE CS
                     HMGL-like  85 lkgagakrvhvfiatselhlkaklkkdreevakkaeeavkaarslgkdvelsledasrtdleflaevveaaeeaGatrini 165
                                      +g  +v + ++  +            + ++k+ ++vk+a+++ ++ve+ + d  + + e++ ++++++ e Ga +++i
  gi|13541740|ref|NP_111428.1|  82 ---TGS-KVTLHLPFGD------------YDINKICDVVKYASDHSDSVEIAIVDMVKYEKEKIFDLAKKLWECGASIVQI 146
                                   ...664.4666777777............44889999******************************************** PP

                                   EETTS---HHHHHHHHHHHHHHS-.GGGEEEEEB-TTS-HHHHHHHHHHTT--EEEEBTTS--SSBBB-BHHHHHHHHHHT CS
                     HMGL-like 166 aDtvGvltPneaaelisalkervkdkvilsvHcHndlGlAvantlaAveaGadrvdgtvnGlGeraGnaaleelvaaleal 246
                                   +Dt G +tP+ +++++s++k+++k  v+++vHcHnd GlA+an++a++eaG+d vd+t++G+Ger+G a++  ++  le++
  gi|13541740|ref|NP_111428.1| 147 PDTTGRATPKRVHDVVSYIKQNLK--VKVEVHCHNDHGLAIANSIAGIEAGCDYVDTTIFGIGERNGIADTASIASYLEKA 225
                                   ************************..******************************************************* PP

                                   T-B----HHHHHHHHHH CS
                     HMGL-like 247 gvdtgldlqklrsiaal 263
                                   g++ +++++ lr++ +l
  gi|13541740|ref|NP_111428.1| 226 GYEDKINFEMLRKTYDL 242
                                   ***********998765 PP

>> 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 ?   -1.6   0.0     0.094   8.4e+02     156     188 ..      23      55 ..      19      91 .. 0.79
   2 ?   12.8   0.0     4e-06     0.036     334     396 ..     123     196 ..      58     207 .. 0.71

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.094
                                   EEEEETSSTTHHHHHHHHHHHTTSBSEEEEES- CS
                 EPSP_synthase 156 gveikaevsSqqvtsllllaallaegtteleel 188
                                   +++i+ ++s  +++ +l +++   e ++e    
  gi|13541740|ref|NP_111428.1|  23 KIRIAQSISKSGIKRALVSYPSAHESEVEAARK 55 
                                   789999999999999999999666667776554 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 4e-06
                                   GSSSTTCCHHHHHHHTTT-EEEEETTEEE..........EEEEEE.......EB-EEEE-TTSTTTTHHHHHHHHHSBS CS
                 EPSP_synthase 334 vketdrlaamateLrklGaeveeeedgli..........iipaek......qlkgaevesydDhRiamalalaglvaeg 396
                                     e ++++ +a+ L  +Ga + + +d+            +    +      ++k +ev++++Dh +a+a ++ag+ a +
  gi|13541740|ref|NP_111428.1| 123 KYEKEKIFDLAKKLWECGASIVQIPDTTGratpkrvhdvV----SyikqnlKVK-VEVHCHNDHGLAIANSIAGIEAGC 196
                                   45889********************987666666644430....2555532454.9******************76665 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:                        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: 0.64u 0.29s 00:00:00.93 Elapsed: 00:00:00.51
# Mc/sec: 2048.45
//
Query:       gi|13541741|ref|NP_111429.1|  [L=298]
Description: proline iminopeptidase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.9e-20   72.0   0.0    2.5e-19   69.9   0.0    1.8  1  Abhydrolase_1  alpha/beta hydrolase fold
    7.3e-20   71.3   0.0    3.6e-19   69.0   0.0    1.8  1  Hydrolase_4    Serine aminopeptidase, S33
      2e-11   45.0   0.0    2.5e-11   44.6   0.0    1.1  1  Abhydrolase_6  Alpha/beta hydrolase family
    3.3e-05   23.1   0.0    4.5e-05   22.6   0.0    1.2  1  DUF1057        Alpha/beta hydrolase of unknown function (DUF1
    0.00015   21.3   0.1     0.0019   17.7   0.0    2.2  2  Peptidase_S9   Prolyl oligopeptidase family
    0.00053   19.9   0.0      0.001   18.9   0.0    1.5  1  Abhydrolase_2  Phospholipase/Carboxylesterase
     0.0019   17.8   0.0      0.013   15.1   0.0    2.1  2  Peptidase_S15  X-Pro dipeptidyl-peptidase (S15 family)
     0.0036   17.2   0.0      0.012   15.4   0.0    1.8  2  Abhydrolase_3  alpha/beta hydrolase fold
  ------ inclusion threshold ------
      0.052   12.2   0.1        1.7    7.2   0.0    2.2  2  AXE1           Acetyl xylan esterase (AXE1)


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 !   69.9   0.0   1.3e-22   2.5e-19       5     256 ..      38     282 ..      36     283 .. 0.80

  Alignments for each domain:
  == domain 1  score: 69.9 bits;  conditional E-value: 1.3e-22
                                   EE-STTTCGGGGTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTTGB.CHHSHHHHHHHHHHH.HHHCTTSSEEEEEETHHH CS
                 Abhydrolase_1   5 ilhGlpgssdvwaerglapaLakdgfdvillDlrGvgySspapacinddygtasvaddldri.ldalgddkltlvGhSmGG 84 
                                    lhG+pg s+ +       +La++g +v+ +D+ G+g+S+ +     + ++++   +  +++ ++ +gddk+ l+G S+GG
  gi|13541741|ref|NP_111429.1|  38 TLHGGPGMSHDYLL--SLTDLAEKGITVLFYDQFGCGRSEEPEK---EKFTIDYGVEEAEAVkKNIFGDDKVFLMGSSYGG 113
                                   68*****9887666..78899999*******************9...89******************************** PP

                                   HHHHHHHHHHGGGEEEEEEESE.CSSCCHHHHHHHHHHHHHHCHHCHHHHHHHHHHHHHHHHCCSCHHHHHHHHHHHHHH. CS
                 Abhydrolase_1  85 mialayaaeyperVkalvllga.idpaaslieaqrqqaksfpdffdgyaadcarnpagplladelaaleqrhrlvdalkf. 163
                                   ++alaya +y+ + k+l+  g+ ++ +    e qr +++ + ++ + ++  +++         e+  +++++ l+ +  + 
  gi|13541741|ref|NP_111429.1| 114 ALALAYAVKYQAHLKGLIISGGlSSVPLTVKEMQRLIDELPEKYRNAIRKYGEVGDYQNPEYQEAVNYFYHQHLLRSE-Dw 193
                                   *****************************************************9999999999999999998876544.34 PP

                                   .HCHHHCCHHHHHHHCHHHHHHHHHHHHHHHHCCHHHHHHHHHCTHHHHSEEEEEEETTCSSSCHHHHHHHHHCHTSEEEE CS
                 Abhydrolase_1 164 .pdkskrfpssgsdnasslatgalksieqwpttdsaklllrlrelknvlaptlvisgtsDplvppkaledlaqllpkkrlv 243
                                    p  + +  +    ++++ ++++ + +    t       +++++   +++ptl+  g+ D ++  ++ e + +++ +++l+
  gi|13541741|ref|NP_111429.1| 194 pP-EVLKSLEYAEERNVYRTMNGPNEFTITGTIRDWDITDKIGI---ISVPTLITVGEFDEVTQ-NVAEVIHSKIDNSQLI 269
                                   52.22222222223333333333333333333333333444444...666*************7.6777777779****** PP

                                   EEETCSSSHHHHS CS
                 Abhydrolase_1 244 visdagHlafleg 256
                                   v+  + Hl  +e+
  gi|13541741|ref|NP_111429.1| 270 VFKACSHLTMWED 282
                                   ********99985 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.0   0.0   1.8e-22   3.6e-19       2     237 ..      31     281 ..      30     283 .. 0.77

  Alignments for each domain:
  == domain 1  score: 69.0 bits;  conditional E-value: 1.8e-22
                   Hydrolase_4   2 epkavvvlvHGlaehsgryaelaeaLaaqGfavyalDhrGhGrsegkrghvpsfddyvdDlaafvekvkeehpelplfllG 82 
                                   ++ka ++ +HG    s  y     +La++G+ v+ +D+ G Grse    +   +d  v+ ++a+ +++    ++ ++fl+G
  gi|13541741|ref|NP_111429.1|  31 NEKAKLMTLHGGPGMSHDYLLSLTDLAEKGITVLFYDQFGCGRSEEPEKEKFTIDYGVEEAEAVKKNI---FGDDKVFLMG 108
                                   6799****************************************977777788999999999987555...5888****** PP

                   Hydrolase_4  83 hSmGGliallyllrypdkvaglilsaPalkikaklkappllklllkllgkllpklqv...................snnlk 144
                                    S GG++al+y+ +y+++++gli+s+ + +++  +k  ++++l+ +l  k    ++                     ++++
  gi|13541741|ref|NP_111429.1| 109 SSYGGALALAYAVKYQAHLKGLIISGGLSSVPLTVK--EMQRLIDELPEKYRNAIRKygevgdyqnpeyqeavnyfYHQHL 187
                                   ********************************9864..4455544444444444444444799999999999999966667 PP

                   Hydrolase_4 145 adslsrdpevvaayeadplv.hgkitvrlllelldamkrleeraakit...lPllllhGeaDkvvdpeasrelyerlgskd 221
                                    +s    pev++++e  +     ++ ++     ++++ r ++ ++ki    +P+l+  Ge D+v+++ a + ++ ++   +
  gi|13541741|ref|NP_111429.1| 188 LRSEDWPPEVLKSLEYAEERnVYRTMNGPNEFTITGTIRDWDITDKIGiisVPTLITVGEFDEVTQNVA-EVIHSKID--N 265
                                   777777788888777777774444444444444555555444444444445*************99544.34444444..7 PP

                   Hydrolase_4 222 ktlklypglyHellnE 237
                                    +l +++ + H ++ E
  gi|13541741|ref|NP_111429.1| 266 SQLIVFKACSHLTMWE 281
                                   8999999999988766 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.6   0.0   1.3e-14   2.5e-11       4     219 ..      39     288 ..      36     289 .. 0.59

  Alignments for each domain:
  == domain 1  score: 44.6 bits;  conditional E-value: 1.3e-14
                                   E--GC.....G.CHHHHHHHHCCTCEEEEE--TTSTS-GGCS--HHHCHHH.HHHHCCTT.....TTSEEEEEETCHHHHH CS
                 Abhydrolase_6   4 lHGagssassW.lvapLaallaagvhvlapDlpGhGrsdpppldledladl.aalldelaa...gggpvvlvGHSlGGala 79 
                                   lHG+++ ++++ l  +L  l+ +g++vl +D  G+Grs+ p  +     d+ ++ ++++++   g+++v+l+G S+GGala
  gi|13541741|ref|NP_111429.1|  39 LHGGPGMSHDYlL--SLTDLAEKGITVLFYDQFGCGRSEEPEKEKFT-IDYgVEEAEAVKKnifGDDKVFLMGSSYGGALA 116
                                   8*****99***67..*********************88777744444.66664444444444448899************* PP

                                   HHHHHCC.......EEEEES-..----TTT...S----TTHHHHHHTT-C.........CCCHCCH.......S-HSCCCC CS
                 Abhydrolase_6  80 laaapla.....lvvgvlldppptalpagl...laaalelllallallrl.........lawlsre.......plprlfla 136
                                   la   +a      + g+++++   ++p++    ++ + el+++++ + r+         +     e       ++ +++l+
  gi|13541741|ref|NP_111429.1| 117 LA---YAvkyqaHLKGLIISGGLSSVPLTVkemQRLIDELPEKYRNAIRKygevgdyqnP-----EyqeavnyFYHQHLLR 189
                                   **...7777777445577777333333333443444444444444444443333222222.....1233334433334444 PP

                                   HHH......C...CCCHCHCCCGHHHHCCHHC......HTTCCHHTT-TTGCEEE.CTT-CHHHHCHHCCCH.STTEEETC CS
                 Abhydrolase_6 137 ded......a...daawrarlarlaallaglg......llpaaawadlpvpllvl.ggeDplvprllerlla.qagarlpv 200
                                    ed      +   +a+ r  ++++     +        +   + +  + vp+l+  g+ D++ +  +e ++  ++  +l +
  gi|13541741|ref|NP_111429.1| 190 SEDwppevlKsleYAEERNVYRTMNGPNEFTItgtirdWDITDKIGIISVPTLITvGEFDEVTQNVAEVIHSkIDNSQL-I 269
                                   44433222112222333333333332222111111121222444444444443323899**9999999999999*****.* PP

                                   E...SSS-HHHHSHHHHHH CS
                 Abhydrolase_6 201 vlpgaGHlphleepdevae 219
                                   v++ ++Hl + e+ de+++
  gi|13541741|ref|NP_111429.1| 270 VFKACSHLTMWEDRDEYNR 288
                                   *******999989899875 PP

>> DUF1057  Alpha/beta hydrolase of unknown function (DUF1057)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   2.3e-08   4.5e-05      19     140 ..      15     138 ..       1     172 [. 0.83

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 2.3e-08
                       DUF1057  19 veveav..YeDslasgsplGtvvalhGsPGshnDfkYirskleelkiRligvnyPGfefvtgylgqkytnaeRnsyskall 97 
                                   v+++    Y  +++  + +   ++lhG PG   D+      l e+ i ++  +  G    ++ +++k+t     + ++a+ 
  gi|13541741|ref|NP_111429.1|  15 VKIQGIyiYYKVCKAENEKAKLMTLHGGPGMSHDYLLSLTDLAEKGITVLFYDQFGCGRSEEPEKEKFTIDYGVEEAEAVK 95 
                                   5555441156899*****************99999999999*****************************99999****** PP

                       DUF1057  98 eelelkgklillghsRGcenaLqlavtleahGlvlinptGlrv 140
                                   +++  ++k+ l+g s G+  aL  av+++ah   li + Gl  
  gi|13541741|ref|NP_111429.1|  96 KNIFGDDKVFLMGSSYGGALALAYAVKYQAHLKGLIISGGLSS 138
                                   ****************************999888888888864 PP

>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   9.5e-07    0.0019      55     133 ..      93     180 ..      84     200 .. 0.62
   2 ?    1.3   0.0       0.1     2e+02     141     207 ..     235     296 ..     198     298 .] 0.64

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 9.5e-07
                                   HHHTTS--GGGEEEEEETHHHHHHHHHHHH-GGG-SEEEEESE---CCCHHCSTTS..........THH.HCCCC--TTTC CS
                  Peptidase_S9  55 lakegyvdserlaitGgSyGGyltgaalnqrpdlFkaavaevpvvdvlrydsdtdl..........lte.eymewgnpeen 124
                                   ++k+++   ++++++G SyGG l++a + + +   k+++++ + + v  + ++ +            +  +y e g+  +n
  gi|13541741|ref|NP_111429.1|  93 AVKKNIFGDDKVFLMGSSYGGALALAYAVKYQAHLKGLIISGGLSSVPLTVKEMQRlidelpekyrNAIrKYGEVGDY-QN 172
                                   567788889*******************99999999888777766665555543222222144422111233333333.34 PP

                                   HHHHHHHHH CS
                  Peptidase_S9 125 eegykelsp 133
                                   +e y+e+ +
  gi|13541741|ref|NP_111429.1| 173 PE-YQEAVN 180
                                   44.444444 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.1
                                   -.---EEEEEEETT-SSS-THHHHHHHHHHH--S-S.EEEEEETTS-SSTTSSHHHHHHHHHHHHHHHH CS
                  Peptidase_S9 141 k.aypplLlihGlaDdrvppaealklvaaLqkkgkn.vlllifpdegHgvgkprakveelarllaFlke 207
                                     +++p+L+++G+ D+ +      + va++   + + ++l +f+   H + + +++ e  + ll+F+++
  gi|13541741|ref|NP_111429.1| 235 GiISVPTLITVGEFDEVT------QNVAEVIHSKIDnSQLIVFKACSH-LTMWEDRDEYNRILLQFIEK 296
                                   356788999999999866......444444433333377778877777.44445555555566666665 PP

>> Abhydrolase_2  Phospholipase/Carboxylesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   5.2e-07     0.001     102     158 ..      99     154 ..      78     191 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 5.2e-07
                                   --GGGEEEEEETHHHHHHHHHHHT-SS--SEEEEES---TTGGGTTTTS-GGGGG-E CS
                 Abhydrolase_2 102 ipssriiigGFSqGaalalylaltlpkklggivafsgalplsqklessatavtkklp 158
                                      ++++++G S G+alal+ a++++  l+g ++ +g  + + ++++ + ++  +lp
  gi|13541741|ref|NP_111429.1|  99 FGDDKVFLMGSSYGGALALAYAVKYQAHLKGLIISGGLSSVPLTVKEMQRLID-ELP 154
                                   67899*********************************999999998776665.555 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 !   15.1   0.0   6.6e-06     0.013      52     137 ..      49     138 ..      21     143 .. 0.76
   2 ?    0.0   0.0      0.26   5.2e+02     223     249 ..     233     258 ..     170     278 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 6.6e-06
                                   H......HHHTT-EEEEEE-TTSTTS-S---TTTTTHHHHHHHHHHHHHHCTTEEEEEEEEEECHHHHHHHHHCTT--TTE CS
                 Peptidase_S15  52 v......fvarGYavVvqdvrGtggSeGeftvgdsdeaedgadvidWlakqpwsnGkVgmtGiSYlGttqllaaatgvpal 126
                                          ++++G +v+++d  G g Se e +   +  ++ g++  + + k+ + ++kV  +G+SY+G ++l+ a++ + +l
  gi|13541741|ref|NP_111429.1|  49 YllsltdLAEKGITVLFYDQFGCGRSE-EPEK-EKFTIDYGVEEAEAVKKNIFGDDKVFLMGSSYGGALALAYAVKYQAHL 127
                                   155555688999999999999999998.5555.445555677777777888999*************************** PP

                                   EEEEEECE-S- CS
                 Peptidase_S15 127 kaivpeaaisd 137
                                   k +++  ++s+
  gi|13541741|ref|NP_111429.1| 128 KGLIISGGLSS 138
                                   *9998877776 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.26
                                   HHCT--S-EEEEEECCSSTTCCHHHHH CS
                 Peptidase_S15 223 dadkvkapvllvgGwnDwnvkngaikl 249
                                   ++  + +p+l++ G +D +v++++ ++
  gi|13541741|ref|NP_111429.1| 233 KIGIISVPTLITVGEFD-EVTQNVAEV 258
                                   556688999********.888666554 PP

>> Abhydrolase_3  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   6.3e-06     0.012      68     109 ..      99     141 ..      77     186 .. 0.75
   2 ?   -1.5   0.0      0.94   1.9e+03     168     188 ..     240     257 ..     238     278 .. 0.64

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 6.3e-06
                                   ETTCEEEEEEETHHHHHHHHHHHHHHHTT---..EEEEEEESE- CS
                 Abhydrolase_3  68 adpsrivlaGdSaGGnlaaavalrardegepk..vagqvliyPv 109
                                      ++++l+G S GG la+a a++ +++ + +  ++g +   P+
  gi|13541741|ref|NP_111429.1|  99 FGDDKVFLMGSSYGGALALAYAVKYQAHLK-GliISGGLSSVPL 141
                                   55789*****************99988732.2346666666664 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.94
                                   -EEEEEETT-TTHHHHHHHHH CS
                 Abhydrolase_3 168 ptlvvvaefDplrdegeayae 188
                                   ptl+ v+efD   ++   +ae
  gi|13541741|ref|NP_111429.1| 240 PTLITVGEFDEVTQN---VAE 257
                                   899999999866544...344 PP

>> AXE1  Acetyl xylan esterase (AXE1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0   0.00086       1.7     173     192 ..     101     120 ..      87     133 .. 0.82
   2 ?    2.9   0.0     0.018        35     221     266 ..     173     221 ..     145     252 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.00086
                                   EEEEEEEEETHHHHHHHHHH CS
                          AXE1 173 eeRvavlGasqGGalalava 192
                                   +++v+ +G+s GGalala a
  gi|13541741|ref|NP_111429.1| 101 DDKVFLMGSSYGGALALAYA 120
                                   5789*************987 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.018
                                   TTCHHHHHHHHHSH-CCHHH...HHHHHHHTT-HHHHHCC--S-EEEEE CS
                          AXE1 221 eaYdEitrylkldperekee...evletLsYiDvknlAkrvkaevllsv 266
                                     Y+E ++y+  +   + e+   evl+ L Y +  n+ + ++++  +++
  gi|13541741|ref|NP_111429.1| 173 PEYQEAVNYFYHQHLLRSEDwppEVLKSLEYAEERNVYRTMNGPNEFTI 221
                                   469******984443333323338*************999999998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (298 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       614  (0.0342462); expected 358.6 (0.02)
Passed bias filter:                      505  (0.0281667); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2267.52
//
Query:       gi|13541742|ref|NP_111430.1|  [L=466]
Description: amino acid transporter [Thermoplasma volcanium GSS1]
Scores for complete 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-24   84.3  52.6      1e-23   83.7  52.6    1.3  1  AA_permease    Amino acid permease
    3.6e-23   82.1  56.0    4.7e-23   81.7  56.0    1.1  1  AA_permease_2  Amino acid permease
  ------ inclusion threshold ------
          1    9.2   7.6         11    5.9   5.2    2.6  2  DUF4774        Domain of unknown function (DUF4774)


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 !   83.7  52.6   1.7e-27     1e-23       2     445 ..      15     433 ..      14     451 .. 0.77

  Alignments for each domain:
  == domain 1  score: 83.7 bits;  conditional E-value: 1.7e-27
                   AA_permease   2 vlvialggviGtglfvglgvvlsqaGplgallayllagvviflvmlslgeiatngpksggfytyasrflgpelGfviGlny 82 
                                   vl++ ++   ++g  v++    ++  ++++ la ++a+v++fl +l++  i+t++   gg+y y++   g+e+G + G+ y
  gi|13541742|ref|NP_111430.1|  15 VLFQGVAASAPAGAAVATMTGSAAFALGSLPLAAAVAFVIVFLNALIIRRISTHVAGPGGYYDYIKTGFGKEVGIFSGWVY 95 
                                   78889999999999999999999999999**************************************************** PP

                   AA_permease  83 lfswitvlaleltaasiliqfwelvtdlpkawvtgavflvvlliinlvgvkvy..g.eaefilalikiiaiiafiivg..i 158
                                    +++i++la+    ++ ++  +  ++ +  + v g +++ +l++   +g  v+  g + ++ + ++ +   ia++++   +
  gi|13541742|ref|NP_111430.1|  96 ILYQIAALAFISLSIAVFVPAL--LSYIYGISVPGNLWIPLLIGAAAFGYLVSfsGiRGSLRYVSVMGSLEIAVVVFIglF 174
                                   *****98887755555555544..666666666655555555555555533321111223446666666665555555344 PP

                   AA_permease 159 illaggkpnkgagfrflgdngsifknnlppgfa.keeegafknfisvfvivvfaftGielvaiiagEvkdPeksiPkailq 238
                                   i+l+  + n                    + f+ k++++ +++++ +  +++ af+G++  + +++E+k+ +k i  a++ 
  gi|13541742|ref|NP_111430.1| 175 IILSHPAINTP------------------AVFTlKYDKFGVSGIALGVLFMYTAFSGFGGMTPLGEEAKNAKKLIGDAVII 237
                                   44433333333..................33444688999***************************************** PP

                   AA_permease 239 vviritifYvlsllligllvprndlgllndsasaaspfvifikesgvsvlaplinaviltaalssansslysasRvlysla 319
                                     +++++f+v+++++ +++++ ++  + +  +++  ++ ++++  g+ + a li+++ + ++l   + ++ s  R+  s++
  gi|13541742|ref|NP_111430.1| 238 SSVILGVFFVFAAYAFTVGWGPSSMESYANNLVP--GIKLAQVDIGLWA-AILITIFYINSILTDNVTFSNSVARITLSMS 315
                                   ************************9999988866..**********965.68999999999******************** PP

                   AA_permease 320 kdglaP.kvlkkvskrgvPlraillsmiisllalllaslnlaapivfnfllaisaliglivwlliilsylrf.Rkalkyqg 398
                                   +dg++P +  ++++kr+ P+ a l++ i+s+++ ll+   l+++  f f   +s+l++l+v++l++ls++++ +k+ ++ g
  gi|13541742|ref|NP_111430.1| 316 RDGVLPrFLSEVHEKRKTPHFAGLVMVIASVIIGLLSVEFLGPFGGFLFTGVLSTLAALLVHMLANLSLPVIiKKKANKVG 396
                                   ******7777899*********************999999999***************************55044433334 PP

                   AA_permease 399 rsieelgfkaallplgvilvlaaliiillilalyayltvkkgpkdwg 445
                                     +  l++          +v a+l+ ++  +++ ++++v +   ++g
  gi|13541742|ref|NP_111430.1| 397 VLNVALPV----------TVTAILVYVFYGTFVSISTPVVAASISFG 433
                                   43333333..........33344444444444444444333333333 PP

>> AA_permease_2  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.7  56.0   7.9e-27   4.7e-23      15     418 ..      26     437 ..      11     445 .. 0.76

  Alignments for each domain:
  == domain 1  score: 81.7 bits;  conditional E-value: 7.9e-27
                 AA_permease_2  15 igsgi.fvknlaasggpalilwvwiavligslavllvyaElssalprsgGiyvytkaafgkkvaflsawfnwfayvpvlas 94 
                                   +g+++ +++++aa +  +l l   +a +i+ +  +l++  +s++    gG y y k +fgk v+ +s+w + + ++++la+
  gi|13541742|ref|NP_111430.1|  26 AGAAVaTMTGSAAFALGSLPLAAAVAFVIV-FLNALIIRRISTHVAGPGGYYDYIKTGFGKEVGIFSGWVYILYQIAALAF 105
                                   443331222244445566777778888887.6899************************************7766666655 PP

                 AA_permease_2  95 il...svaasyllnalgp.dlqgntwltyliaiaililvalinirgikesakiqnilgilkillpliiliilglitvdggg 171
                                   i+   +v++ +ll+ +++ ++ gn w+ +li++a + +++  +  gi++s ++ +++g l i  ++ ++i l +i+ ++ +
  gi|13541742|ref|NP_111430.1| 106 ISlsiAVFVPALLSYIYGiSVPGNLWIPLLIGAAAFGYLV--SFSGIRGSLRYVSVMGSLEIA-VV-VFIGLFIILSHPAI 182
                                   4322166888888887755999999999999999888765..569*****************5.54.44435555555555 PP

                 AA_permease_2 172 fsslstetdtffpngwpgvllgllivlwsfdGfesaanvseevkk.kd.vpkaifigllivlvlyllvniaflgvvpddei 250
                                   ++ ++  t +  + g +g++lg l +  +f+Gf + +   ee+k+ k+ +  a +i+ +i +v++++ + af+ + +++++
  gi|13541742|ref|NP_111430.1| 183 NTPAV-FTLKYDKFGVSGIALGVLFMYTAFSGFGGMTPLGEEAKNaKKlIGDAVIISSVILGVFFVFAAYAFTVGWGPSSM 262
                                   55322.2223444599999999999*******************99766******************************** PP

                 AA_permease_2 251 anlsnlgsvaalffeavggkvvaiivvilialsllgaintavigssrvlealardgvlPrffakvn.kfgspiraiiltai 330
                                   ++ +n + ++ ++++   g ++ai++ i+ + s+l    t++ +++r+  +++rdgvlPrf++ v+ k+++p  a  + +i
  gi|13541742|ref|NP_111430.1| 263 ESYANNLVPGIKLAQVDIGLWAAILITIFYINSILTDNVTFSNSVARITLSMSRDGVLPRFLSEVHeKRKTPHFAGLVMVI 343
                                   77666333677777775567************************************************************* PP

                 AA_permease_2 331 vslillllfl..lassaaynfllsvsslgliisyllliigalilrkkrphl.krpgk.ilvaiigalfllfll.valffpp 406
                                    s+i++ll+   l++   + f   +s+l+++++ +l+ +++ ++ kk+ ++ +      +v+ +++l+ +f   ++ +  p
  gi|13541742|ref|NP_111430.1| 344 ASVIIGLLSVefLGPFGGFLFTGVLSTLAALLVHMLANLSLPVIIKKKANKvGVLNVaLPVTVTAILVYVFYGtFVSISTP 424
                                   **99998888885555679999***************99998888888876455554245666665555554313333222 PP

                 AA_permease_2 407 kgpa.tqssliyt 418
                                   +++a ++++ + t
  gi|13541742|ref|NP_111430.1| 425 VVAAsISFGAWAT 437
                                   2222244444444 PP

>> DUF4774  Domain of unknown function (DUF4774)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   5.2    0.0019        11      16      46 ..      18      50 ..      17      53 .. 0.76
   2 ?    2.8   0.0     0.018   1.1e+02       2      17 ..      59      74 ..      58      75 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0019
                       DUF4774 16 gGvAisaPvgtaivkkGkkglalaa....PdavAi 46
                                  +GvA+saP+g a++   ++g+a +a    P a+A+
  gi|13541742|ref|NP_111430.1| 18 QGVAASAPAGAAVA--TMTGSAAFAlgslPLAAAV 50
                                  5*************..8888887753334555555 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.018
                       DUF4774  2 slevkpvGkAvaGkgG 17
                                   l++++++  vaG+gG
  gi|13541742|ref|NP_111430.1| 59 ALIIRRISTHVAGPGG 74
                                  58999*********99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (466 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       897  (0.0500307); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); 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):               3  [number of targets reported over threshold]
# CPU time: 0.66u 0.34s 00:00:01.00 Elapsed: 00:00:00.51
# Mc/sec: 2765.99
//
Query:       gi|13541743|ref|NP_111431.1|  [L=592]
Description: acylaminoacyl-peptidase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-46  158.9   0.1    1.6e-46  158.4   0.1    1.2  1  Peptidase_S9   Prolyl oligopeptidase family
    9.3e-10   38.4   0.0    1.7e-09   37.5   0.0    1.4  1  DLH            Dienelactone hydrolase family
    2.4e-06   27.4   0.7     0.0054   16.4   1.0    2.5  3  Abhydrolase_1  alpha/beta hydrolase fold
    4.8e-06   26.5   0.3     0.0016   18.3   0.0    2.3  2  Abhydrolase_2  Phospholipase/Carboxylesterase
    7.4e-06   25.7   0.1       0.15   11.6   0.2    2.2  2  Peptidase_S15  X-Pro dipeptidyl-peptidase (S15 family)
      2e-05   24.0   0.4     0.0033   16.7   0.5    2.2  2  DUF2920        Protein of unknown function (DUF2920)
    7.4e-05   22.8   0.4      0.013   15.4   0.0    2.7  2  BAAT_C         BAAT / Acyl-CoA thioester hydrolase C terminal
    0.00017   20.9   0.1       0.11   11.7   0.0    2.2  2  Hydrolase_4    Serine aminopeptidase, S33
    0.00088   19.2   0.0       0.29   10.9   0.0    2.7  3  Abhydrolase_3  alpha/beta hydrolase fold
     0.0014   19.3   0.0      0.011   16.3   0.0    2.0  1  Abhydrolase_6  Alpha/beta hydrolase family
  ------ inclusion threshold ------
      0.016   14.6   0.2        0.5    9.6   0.0    2.2  2  LIP            Secretory lipase
      0.066   12.0   0.1      0.098   11.4   0.1    1.2  1  Peptidase_S28  Serine carboxypeptidase S28


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 !  158.4   0.1   1.1e-49   1.6e-46      10     210 ..     394     591 ..     386     592 .] 0.94

  Alignments for each domain:
  == domain 1  score: 158.4 bits;  conditional E-value: 1.1e-49
                                   HHCCT-EEEEE--TTSSTTHCHHHHTTSGGGGHHHHHHHHHHHHHHHHTTS--GGGEEEEEETHHHHHHHHHHHH-GGG-S CS
                  Peptidase_S9  10 ladrGyvvvvanirGsggyGeafhdagkrklgqnefdDfiaaaealakegyvdserlaitGgSyGGyltgaalnqrpdlFk 90 
                                       G+ v+++n+rGs g G++++++  ++lg  +f+D+i ++++l + g +d+++++itGgSyGGy+++ a++ ++d+F 
  gi|13541743|ref|NP_111431.1| 394 YLGYGFSVFMPNYRGSVGLGREYAESNIGDLGGMDFEDVISGIKYLQQSGKIDTKNIFITGGSYGGYMSALAVM-KTDIFN 473
                                   4478**********************************************************************.****** PP

                                   EEEEESE---CCCHHCSTTSTHH.HCCCC--TTTCHHHHHHHHHH-CGGG-----EEEEEEETT-SSS-THHHHHHHHHHH CS
                  Peptidase_S9  91 aavaevpvvdvlrydsdtdllte.eymewgnpeeneegykelspyspldnvkaypplLlihGlaDdrvppaealklvaaLq 170
                                   a v+  +++d+++++ +++l+++ +     +p ++ e+y++ sp++  ++   ++p+Ll+hG +D+ vp+ + +++++ L+
  gi|13541743|ref|NP_111431.1| 474 ASVSLFGISDWISFHGTSNLYEWdRIHLDADP-WSFEKYDRYSPIRIKRK--PKTPVLLMHGVNDKYVPIGQYYEFYRFLK 551
                                   *****************999999788887888.67777999999999888..***************************** PP

                                   --S-SEEEEEETTS-SSTTSSHHHHHHHHHHHHHHHHHCT CS
                  Peptidase_S9 171 kkgknvlllifpdegHgvgkprakveelarllaFlkealg 210
                                   ++g++v++ ++p egHg+ +  + +++++++ +F+k++l+
  gi|13541743|ref|NP_111431.1| 552 ENGDEVKMIVYPREGHGFTERAHIIRQYKETIDFFKSHLK 591
                                   *******************999999*************98 PP

>> DLH  Dienelactone hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.5   0.0   1.2e-12   1.7e-09      84     196 ..     434     578 ..     395     587 .. 0.91

  Alignments for each domain:
  == domain 1  score: 37.5 bits;  conditional E-value: 1.2e-12
                           DLH  84 aavaylksvpevstkkvgvvGfCmGGalalllaaevpevdaavafYG..............................lspe 134
                                     ++yl++ ++ +tk++ ++G   GG ++ l   + + ++a+v+ +G                                  
  gi|13541743|ref|NP_111431.1| 434 SGIKYLQQSGKIDTKNIFITGGSYGGYMSALAVMKTDIFNASVSLFGisdwisfhgtsnlyewdrihldadpwsfekYDRY 514
                                   4589***************************99999*************************************99887888 PP

                           DLH 135 keleeaakikapilalfgeeDefipadevekleealkaanvdlelkvYpgagHaFandsre..s 196
                                   +++   +k k+p+l ++g +D+ +p ++  ++   lk+++ ++++ vYp  gH+F+++ +   +
  gi|13541743|ref|NP_111431.1| 515 SPIRIKRKPKTPVLLMHGVNDKYVPIGQYYEFYRFLKENGDEVKMIVYPREGHGFTERAHIirQ 578
                                   99******************************************************99876444 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       4.4   6.6e+03     216     256 ..     219     260 ..     216     261 .. 0.83
   2 !   16.4   1.0   3.6e-06    0.0054       1     103 [.     370     477 ..     370     515 .. 0.64
   3 !    8.4   0.0     0.001       1.5     204     250 ..     520     567 ..     506     570 .. 0.78

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 4.4
                                   EEEETTCSSSCH.HHHHHHHHCHTSEEEEEEETCSSSHHHHS CS
                 Abhydrolase_1 216 visgtsDplvpp.kaledlaqllpkkrlvvisdagHlafleg 256
                                   + s++sD+ v   ++++ ++++ ++ ++  +s + H++f++g
  gi|13541743|ref|NP_111431.1| 219 IESTMSDRGVVSgDVIVLSDSDKKNLTEGNESSYSHIVFYDG 260
                                   667888888888888888888889999999999999999987 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 3.6e-06
                                   SEEEEE-STTTCGGGGTTGHHHHHHHHT......TSEEEEEEETTS.TTSSSTTTGB..CHHSHHHHHHHHH...HHHHHC CS
                 Abhydrolase_1   1 pvlvilhGlpgssdvwaerglapaLakd......gfdvillDlrGv.gySspapacin.ddygtasvaddld...rildal 70 
                                   p++v++hG+p s+   ++++l +    +      gf v++++ rG+ g ++   +  n  d g ++++d++    +++++ 
  gi|13541743|ref|NP_111431.1| 370 PLIVYVHGGPTSFS--YGAFLDR----TsvylgyGFSVFMPNYRGSvGLGREYAE-SNiGDLGGMDFEDVISgikYLQQSG 443
                                   789********996..4533444....4445589***********6255655555.4565555555555555443777777 PP

                                   TTSSEE..EEEETHHHHHHHHHHHHHGGGEEEEEE CS
                 Abhydrolase_1  71 gddklt..lvGhSmGGmialayaaeyperVkalvl 103
                                   ++d  +  + G+S+GG +++ +  +  +  +a v+
  gi|13541743|ref|NP_111431.1| 444 KIDTKNifITGGSYGGYMSALAVMKT-DIFNASVS 477
                                   7766555699********99988774.33444444 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.001
                                   HHCTHHHHSEEEEEEETTCSSSCH.HHHHHHHHCHTS...EEEEEEETCSS CS
                 Abhydrolase_1 204 lrelknvlaptlvisgtsDplvpp.kaledlaqllpk...krlvvisdagH 250
                                    r+    + p+l+++g +D++vp+ +++e+++ l  +   ++ +v++ +gH
  gi|13541743|ref|NP_111431.1| 520 KRK---PKTPVLLMHGVNDKYVPIgQYYEFYRFLKENgdeVKMIVYPREGH 567
                                   333...355***************999999999988888999999999999 PP

>> Abhydrolase_2  Phospholipase/Carboxylesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.8   0.2     0.007        10      93     125 ..     435     468 ..     427     491 .. 0.78
   2 !   18.3   0.0   1.1e-06    0.0016     156     202 ..     524     570 ..     515     582 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.007
                                   HHHHHHHTT.--GGGEEEEEETHHHHHHHHHHHT CS
                 Abhydrolase_2  93 lidaelkkg.ipssriiigGFSqGaalalylalt 125
                                    i++ ++ g i+ ++i+i G S G+ ++  ++++
  gi|13541743|ref|NP_111431.1| 435 GIKYLQQSGkIDTKNIFITGGSYGGYMSALAVMK 468
                                   5788888889***************997555444 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 1.1e-06
                                   G-EEEEEEETT-SSS-HHHHHHHHHHHHTTS-GEEEEEETT--SS-- CS
                 Abhydrolase_2 156 klpilqiHgeeDpvvplalgkaakevlkkllkkvelksyeglaHsid 202
                                   k+p+l++Hg  D++vp+   ++++ +lk++  +v++ +y+  +H   
  gi|13541743|ref|NP_111431.1| 524 KTPVLLMHGVNDKYVPIGQYYEFYRFLKENGDEVKMIVYPREGHGFT 570
                                   8***************************************9999765 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 !   11.6   0.2    0.0001      0.15      79     140 ..     425     486 ..     378     504 .. 0.79
   2 !   11.6   0.0    0.0001      0.15     225     264 ..     521     563 ..     496     567 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0001
                                   TTTHHHHHHHHHHHHHHC.TTEEEEEEEEEECHHHHHHHHHCTT--TTEEEEEEECE-S-TCC CS
                 Peptidase_S15  79 dsdeaedgadvidWlakq.pwsnGkVgmtGiSYlGttqllaaatgvpalkaivpeaaisdlyd 140
                                   +  + ed+ + i+ l++  +  + ++  tG SY+G+++ la + +++  +a v++++isd+  
  gi|13541743|ref|NP_111431.1| 425 GGMDFEDVISGIKYLQQSgKIDTKNIFITGGSYGGYMSALAVM-KTDIFNASVSLFGISDWIS 486
                                   556778888889999999999****************988877.99***************87 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.0001
                                   CT--S-EEEEEECCSSTTC.CHHHHHHHHHCCTT-..EEEEEC CS
                 Peptidase_S15 225 dkvkapvllvgGwnDwnvk.ngaiklyealkapgv..klilgp 264
                                   +k k+pvll++G nD+ v   + +++y+ lk++g   k+i+ p
  gi|13541743|ref|NP_111431.1| 521 RKPKTPVLLMHGVNDKYVPiGQYYEFYRFLKENGDevKMIVYP 563
                                   7899***********88889*************9988888755 PP

>> DUF2920  Protein of unknown function (DUF2920)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.5   2.2e-06    0.0033     156     197 ..     425     465 ..     417     488 .. 0.88
   2 !    5.2   0.0    0.0067        10     284     322 ..     523     561 ..     476     567 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 2.2e-06
                       DUF2920 156 GimaAlDiinalkdlvkrfpkeadlpviliGgsyGGYlalLi 197
                                   G m   D+i  +k+l +   +++ +++ + GgsyGGY++ L+
  gi|13541743|ref|NP_111431.1| 425 GGMDFEDVISGIKYLQQSGKIDT-KNIFITGGSYGGYMSALA 465
                                   6688889********99988888.9**************997 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0067
                       DUF2920 284 kntiyvsyHsekDklapaeeKiqlakilkklgfdvelel 322
                                    +t  + +H  +Dk++p+ +  ++++ lk+ g +v++++
  gi|13541743|ref|NP_111431.1| 523 PKTPVLLMHGVNDKYVPIGQYYEFYRFLKENGDEVKMIV 561
                                   3488999*****************************987 PP

>> BAAT_C  BAAT / Acyl-CoA thioester hydrolase C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0     9e-06     0.013     102     163 ..     510     569 ..     428     572 .. 0.90
   2 ?   -3.7   0.1       6.2   9.3e+03     200     211 ..     579     590 ..     576     591 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 9e-06
                                   GGGCCCB--GGG-.-SEEEEEEETT-SSS-HHHHHHHHHHHHHCTT--.--EEEEETTB-S-- CS
                        BAAT_C 102 klaekalipveka.kgpillvvgedDknwpSkesaekaserLkkagkkvevqlltYpkaGHli 163
                                   k ++ + i++ +  k+p+ll+ g++Dk +p  ++  +  + Lk++g +  v+++ Yp  GH +
  gi|13541743|ref|NP_111431.1| 510 KYDRYSPIRIKRKpKTPVLLMHGVNDKYVPIGQYY-EFYRFLKENGDE--VKMIVYPREGHGF 569
                                   55666778898888*******************99.89999*****99..9**********65 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 6.2
                                   HHHHHHHHHHH- CS
                        BAAT_C 200 WkkilkFlkkhl 211
                                    k+++ F+k hl
  gi|13541743|ref|NP_111431.1| 579 YKETIDFFKSHL 590
                                   589999***998 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.9   0.1    0.0022       3.3       7      97 ..     372     469 ..     366     479 .. 0.61
   2 !   11.7   0.0   7.3e-05      0.11     190     232 ..     523     567 ..     517     571 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0022
                   Hydrolase_4   7 vvlvHGlae..hsgryaelaeaLaaqGfavyalDhrGhGrsegkrghvpsfddyvdDlaafvekvk.eehpel....plfl 80 
                                   +v vHG     ++g++ + +      Gf+v++ ++rG    + + ++ +  d    D++ +++ +k  +++++    ++f+
  gi|13541743|ref|NP_111431.1| 372 IVYVHGGPTsfSYGAFLDRTSVYLGYGFSVFMPNYRGSVGLGREYAESNIGDLGGMDFEDVISGIKyLQQSGKidtkNIFI 452
                                   666666543113455555555556678999999999875554334433333333445555554444333333334679*** PP

                   Hydrolase_4  81 lGhSmGGliallyllry 97 
                                    G S GG++++l++ + 
  gi|13541743|ref|NP_111431.1| 453 TGGSYGGYMSALAVMKT 469
                                   **********9998665 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 7.3e-05
                   Hydrolase_4 190 itlPllllhGeaDkvvdpeasrelyerlgsk..dktlklypglyH 232
                                    ++P+ll+hG +Dk v+ ++  e+y+ l+ +  ++++ +yp   H
  gi|13541743|ref|NP_111431.1| 523 PKTPVLLMHGVNDKYVPIGQYYEFYRFLKENgdEVKMIVYPREGH 567
                                   579******************999999998865677777877666 PP

>> Abhydrolase_3  alpha/beta hydrolase fold
   #    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       1      26 [.     255     280 ..     255     282 .. 0.85
   2 !   10.9   0.0    0.0002      0.29      49      91 ..     429     468 ..     426     477 .. 0.87
   3 ?    5.3   0.0     0.011        16     186     210 ..     546     570 ..     511     571 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 3.9
                                   EEEE--STTTS--TTTTHHHHHHHHH CS
                 Abhydrolase_3   1 lvyfHGGGfvlgsldthdalcrelak 26 
                                   +v++ G  +vl++ +th ++++ l++
  gi|13541743|ref|NP_111431.1| 255 IVFYDGEIYVLENHETHFRVISLLTR 280
                                   68999************988888776 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.0002
                                   HHHHHHHHHHHHHTHHHHTETTCEEEEEEETHHHHHHHHHHHH CS
                 Abhydrolase_3  49 vedalaalrwlaeqawelgadpsrivlaGdSaGGnlaaavalr 91 
                                   +ed+++ +++l+++    ++d+++i++ G S GG ++a ++++
  gi|13541743|ref|NP_111431.1| 429 FEDVISGIKYLQQSG---KIDTKNIFITGGSYGGYMSALAVMK 468
                                   789999999999884...8*****************9987765 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.011
                                   HHHHHHHTT--EEEEEETTEETTGG CS
                 Abhydrolase_3 186 yaerlraagvevelieyegmvHgfa 210
                                   +++ l+++g ev++i+y+ + Hgf 
  gi|13541743|ref|NP_111431.1| 546 FYRFLKENGDEVKMIVYPREGHGFT 570
                                   56889******************96 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   7.4e-06     0.011       1      92 [.     372     472 ..     372     585 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 7.4e-06
                                   EEEE--GC.....G.CHHHH...HHHHCCTCEEEEE--TTS...TS-GGCS--HHHC..HHHHHHHCCTT.........TT CS
                 Abhydrolase_6   1 vlllHGagssassW.lvapL...aallaagvhvlapDlpGh...Grsdpppldledl..adlaalldelaa.......ggg 65 
                                   ++ +HG+++s   + + a+L     +l+ g+ v++p ++G    G ++ +  +  dl   d+++++ +++        +++
  gi|13541743|ref|NP_111431.1| 372 IVYVHGGPTS---FsYGAFLdrtSVYLGYGFSVFMPNYRGSvglG-REYAESNIGDLggMDFEDVISGIKYlqqsgkiDTK 448
                                   6889**9965...53233445446677888899******999444.555555555544455566666665566677789** PP

                                   SEEEEEETCHHHHHHHHHHCC..EEEE CS
                 Abhydrolase_6  66 pvvlvGHSlGGalalaaaplalvvgvl 92 
                                   ++++ G S+GG+++++a++ ++   ++
  gi|13541743|ref|NP_111431.1| 449 NIFITGGSYGGYMSALAVMKTD---IF 472
                                   ************9998666663...22 PP

>> LIP  Secretory lipase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.2      0.05        75      23      99 ..     395     476 ..     388     482 .. 0.66
   2 ?    9.6   0.0   0.00034       0.5     212     245 ..     521     554 ..     513     572 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.05
                           LIP  23 LkeGyyVvvpDyeGpks......tftvgrqsgkavLdsiraalksekvtgiksdakvalwGYSgGslAsawAaelqpeYAP 97 
                                   L  G+ V +p y G  +         +g   g    d i ++ k  + +g  ++ ++ + G S+G+  sa A      +  
  gi|13541743|ref|NP_111431.1| 395 LGYGFSVFMPNYRGSVGlgreyaESNIGDLGGMDFEDVISGI-KYLQQSGKIDTKNIFITGGSYGGYMSALAVMKTDIFNA 474
                                   677999999999887776664442234555554444444443.3555555558899**************99876665555 PP

                           LIP  98 el 99 
                                    +
  gi|13541743|ref|NP_111431.1| 475 SV 476
                                   55 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00034
                           LIP 212 avPqiPvlvyhgvidelipikdakklaknwcdkg 245
                                     P++Pvl++hgv d+ +pi +  + ++   ++g
  gi|13541743|ref|NP_111431.1| 521 RKPKTPVLLMHGVNDKYVPIGQYYEFYRFLKENG 554
                                   56*******************9998887665555 PP

>> Peptidase_S28  Serine carboxypeptidase S28
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   6.5e-05     0.098      94     130 ..     430     465 ..     427     477 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 6.5e-05
                 Peptidase_S28  94 aDlasfikalkqkfklsssskwitfGgSYsgsLaawa 130
                                   +D++s ik l+q  k+++++ + + GgSY+g ++a a
  gi|13541743|ref|NP_111431.1| 430 EDVISGIKYLQQSGKIDTKN-IFITGGSYGGYMSALA 465
                                   7**********999998888.5566**********87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (592 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.72u 0.34s 00:00:01.06 Elapsed: 00:00:00.51
# Mc/sec: 3493.83
//
Query:       gi|13541744|ref|NP_111432.1|  [L=115]
Description: hypothetical protein TVN0913 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       278  (0.0155056); expected 358.6 (0.02)
Passed bias filter:                      242  (0.0134977); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 795.05
//
Query:       gi|13541745|ref|NP_111433.1|  [L=461]
Description: metal-dependent hydrolase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.5e-49  168.2   0.0    5.8e-49  167.8   0.0    1.0  1  Amidohydro_3  Amidohydrolase family
      3e-16   59.7   0.1    3.2e-11   43.2   0.0    3.1  4  Amidohydro_1  Amidohydrolase family
  ------ inclusion threshold ------
       0.15   11.6   0.1       0.56    9.7   0.0    1.9  2  AbiJ_NTD3     AbiJ N-terminal domain 3


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 !  167.8   0.0   9.6e-53   5.8e-49       3     471 ..      42     458 ..      40     459 .. 0.85

  Alignments for each domain:
  == domain 1  score: 167.8 bits;  conditional E-value: 9.6e-53
                  Amidohydro_3   3 iDakGrlvlPGFvDsHtHlagggvnlrllrlpdarvtslegvltavrdqagttpkgrwivgeGwdeaqfaeerfpyalael 83 
                                   iD++G++v+PGF+DsH+Hl ++g  l  +rl+ ++ +s e+v ++++++ +    ++ ++++ wde+ +  ++   +  ++
  gi|13541745|ref|NP_111433.1|  42 IDLSGKIVFPGFIDSHAHLLSTG--LEDIRLNLYHTKSKEEVVERIAEYSKG---KEKVIAYRWDESMWKPQSSYLTSSDI 117
                                   9**********************..7777777777***************98...6778899*********99999***** PP

                  Amidohydro_3  84 devledapvllaaldtHaavrnsaaldlagiteatpdpaggeilrdangegatgllregafhlvldlaplareaeaaavaa 164
                                   + +    pv + ++d+H av+n++a+d   i+++++++    i+++++ e +++ l              ++++ ++a+ +
  gi|13541745|ref|NP_111433.1| 118 NGI--PVPVVAFRRDGHMAVANQKAMDV--IGTTRKEG----IFKEDDIE-LLEPLVKP-----------NEAEIRDALNT 178
                                   ***..9999999***************9..77667775....********.99999977...........*********** PP

                  Amidohydro_3 165 alaalasyGitsveagggnvsslddleplfeltaeeklplrviikelldaaerlglpls......pgseeltigavklfad 239
                                   a+ ++ s Gi++v    ++     d+ ++ e+++ +  pl++ +     + +      s      +g+   ++ ++k+f+d
  gi|13541745|ref|NP_111433.1| 179 AANRAISLGIVAV---RDM----VDISTYNEYKNIK-TPLKIYK-----VLY------SdsifdkFGTSSQNDWGIKAFLD 240
                                   *************...444....5888888887775.5666652.....222......123444478888999******** PP

                  Amidohydro_3 240 gvlgsrtalltepyftgwpdfedealaelvaaadergldvaihaigdaavddvldafeaaaekngnqdrrrlehaegvtes 320
                                   g+lgsrta+ +     +   +++ ++++ +++   + l++a+haig+ av+ +++ f    ++ g++   ++eh e v+++
  gi|13541745|ref|NP_111433.1| 241 GSLGSRTAAHKGW-DASNLKMDESKFENFAKQIWMHNLPLAVHAIGEVAVETAAKVF---YRNAGRNR-NSIEHFELVDDD 316
                                   ********98842.22333444445**************************666666...44444443.38******7777 PP

                  Amidohydro_3 321 qiervaalqvaagvqpvfnf...edelldsrlgperargstpvkellnagvkvalgsDapvgpfdpwprigaavmrktrrg 398
                                    ++ + +   +++ qp f     + +++++r+g e     +p++++++ g+++a+gsD    p+ p+++i++av+++    
  gi|13541745|ref|NP_111433.1| 317 VLDYITK-TTIISSQPNFLEwagKGGMYEDRVGGEWLYKNNPFRWMIDRGIHLAFGSD--SMPIGPMYGIYYAVNSEY--- 391
                                   7776666.56788998888899*999********************************..88999*********9888... PP

                  Amidohydro_3 399 gevlrpdeelsleealalyTrgpAkalgledrkGtLevGadADlvvldadpldvdppelaearvrltvvdGrv 471
                                         +++++leea++ y++g+ ++lg e   G+L+vG++AD +v+d ++l+     ++ a+++ t+++G++
  gi|13541745|ref|NP_111433.1| 392 -----QRQKITLEEAVRCYSEGGSYLLGTEGYMGMLRVGYSADMAVFDEKLLKDL-RGIKAAKPEITIINGKI 458
                                   .....7999***************************************6665543.45777889*******97 PP

>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.0   1.4e-05     0.082       1      28 [.      48      76 ..      48      92 .. 0.67
   2 ?   -0.5   0.0       0.1   6.2e+02     183     237 ..     139     196 ..     127     200 .. 0.60
   3 ?   -0.8   0.0      0.12   7.4e+02      32      59 ..     171     198 ..     150     309 .. 0.68
   4 !   43.2   0.0   5.3e-15   3.2e-11     230     343 ..     356     458 ..     354     459 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.4e-05
                                  EEEE-EEEEEEECETTECSSSGHHHHH......S CS
                  Amidohydro_1  1 ivlPGlIDaHvHleqsllrgatledwl......v 28
                                  iv+PG+ID+H Hl ++      led++       
  gi|13541745|ref|NP_111433.1| 48 IVFPGFIDSHAHLLST-----GLEDIRlnlyhtK 76
                                  79***********655.....4555554444443 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.1
                                   HTTTHCCEEEHCTCEEEHH..HHHHHHHHHHHHCEE..HHHHHHHHSEHHHHHHHHHHH CS
                  Amidohydro_1 183 glldeiklilahgvhltpt..eaellkerlkeagva..hcpfsnsilrsgrealrkald 237
                                   ++ d+i ++++ g++ +++   +e l +  +ea +   +  ++n+ ++ g+ a+r+++d
  gi|13541745|ref|NP_111433.1| 139 KAMDVIGTTRKEGIFKEDDieLLEPLVKP-NEAEIRdaLNTAANRAISLGIVAVRDMVD 196
                                   56667777777777777443333333333.33333355777788888888888887776 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.12
                                   HHHHHHHHHHHHHHHTTEEEEEEEEHSS CS
                  Amidohydro_1  32 taaealesgiktalksGtttvadmgatt 59 
                                   +++ al++++ +a++ G+  v+dm    
  gi|13541745|ref|NP_111433.1| 171 EIRDALNTAANRAISLGIVAVRDMVDIS 198
                                   5555666666666666666666665543 PP

  == domain 4  score: 43.2 bits;  conditional E-value: 5.3e-15
                                   HHHHHHHHHTSCEEEEEECTTSSCCGGHHHHHHHHHHHHHHCCTTTTHCHCHHHHHHHHHTHHHHHHTT-TTTSSSS-TTS CS
                  Amidohydro_1 230 ealrkaldeGvkvglgtDgaasgnslnlleelrlalklqrgllyedeegglslkealrmaTingAkalglddkvGsievGk 310
                                   +++r+++d+G++ ++g+D   s+  + +  ++ +a+      + e ++++++l+ea+r+++ +g   lg + + G + vG+
  gi|13541745|ref|NP_111433.1| 356 NPFRWMIDRGIHLAFGSD---SMPIGPM-YGIYYAV------NSEYQRQKITLEEAVRCYSEGGSYLLGTEGYMGMLRVGY 426
                                   579***************...8888888.5555555......666789********************************* PP

                                   B--EEEECCCTCGGGTTTCTSEEEEEEEETTEE CS
                  Amidohydro_1 311 dADlvvvdldilaafvglkkdgnvkkvivkGkl 343
                                    AD++v+d ++l+++ g+k   ++  +i++Gk+
  gi|13541745|ref|NP_111433.1| 427 SADMAVFDEKLLKDLRGIKA-AKPEITIINGKI 458
                                   ******************77.77********97 PP

>> AbiJ_NTD3  AbiJ N-terminal domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.26   1.6e+03      90     108 ..     159     177 ..     158     203 .. 0.79
   2 ?    9.7   0.0   9.3e-05      0.56      11      57 ..     222     275 ..     216     278 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.26
                     AbiJ_NTD3  90 elvhPdvrpdeeeqrrlve 108
                                   el+ P v+p+e+e+r+ ++
  gi|13541745|ref|NP_111433.1| 159 ELLEPLVKPNEAEIRDALN 177
                                   6899999999999887443 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 9.3e-05
                     AbiJ_NTD3  11 adaldle.......eeslfgeldeveflsrlwdldalpstdsrfsnarddiaqH 57 
                                   +d++ ++       +  l g+l+  +   + wd ++l+ ++s+f+n +++i++H
  gi|13541745|ref|NP_111433.1| 222 FDKFGTSsqndwgiKAFLDGSLGSRTAAHKGWDASNLKMDESKFENFAKQIWMH 275
                                   5555555444444455566677777788889*********************** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (461 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 3232.49
//
Query:       gi|13541746|ref|NP_111434.1|  [L=246]
Description: enoyl-CoA hydratase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-33  115.3   0.0    3.1e-33  115.1   0.0    1.0  1  ECH_1     Enoyl-CoA hydratase/isomerase
    1.6e-21   77.2   0.0    1.9e-21   77.0   0.0    1.1  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 !  115.1   0.0   3.5e-37   3.1e-33       5     245 ..      11     245 ..       7     246 .] 0.88

  Alignments for each domain:
  == domain 1  score: 115.1 bits;  conditional E-value: 3.5e-37
                                   TEEEEEE--CGCTTEE-HHHHHHHHHHHHHHHHSTTECEEEEEEBTSEEEEEB-HHHHHHHHC.HHHHHHHCCHHHHHHHH CS
                         ECH_1   5 gvaviklnrPeavNalsaelltEliqalekleddksvravvLtGgdkaFaaGadlkemaeeek.akqallkeevlelwtkl 84 
                                    +a +k+ r e++Na++     E+        +  ++++ ++tG ++aF++G d+++m++ e  a+ +++ +++++ ++kl
  gi|13541746|ref|NP_111434.1|  11 DIAILKFTRSEKLNAFDFDSWREFSSNVD---EASNYKGLIITGEGRAFSSGDDINAMYKFEDyAESKSFFKTLFDVLQKL 88 
                                   6999********************97655...55578**********************977669999************* PP

                                   HHSSSEEEEEE-SEEETHHHHHHHHSSEEEEETTTEEE-GGGGGTS--CTTCHHHHHHHHHHHHHHHHHHHT-EEEHHHHH CS
                         ECH_1  85 ytvpkpviaavnGaaigGGlelalacDiviaadnasfglnelklGlipgaggtqilarkvGkskAeeilllgkkisaqeal 165
                                   ++ p p+iaavnG a+gGG+e+ l+ D+v+  ++a f  +e+++Gl+p+  +t   +   G + +++++++  +++ +eal
  gi|13541746|ref|NP_111434.1|  89 MHYPHPIIAAVNGLAAGGGAEILLTLDYVVSVKDAWFWFPEARIGLYPP-ILTSLGVYVFGIKNVKKLAINMPRLTSEEAL 168
                                   ************************************************6.5677777899********************* PP

                                   HCTSSSEEESG.GGHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTSHHHHHHHHHHHTCSH CS
                         ECH_1 166 kvGlvdkvvpe.eqlleealelaeklaekspaalrqlkealnakledalaeqleaeaklfestfskddikeGlqaflEkrk 245
                                   + Glvd ++ + ++l e a++ +++l++ +  ++  +++ l   +  +l++      + + +t  +++ k++++ f+  rk
  gi|13541746|ref|NP_111434.1| 169 NLGLVDMIIEDkNKLTEIAVNKVRELNRVPTVSYTSMRKVLASIVLPHLKQ----SLDTLAETAVEEEAKRSMELFIKSRK 245
                                   *********99899*************888888877777766655555554....45566667777777788888877665 PP

>> ECH_2  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.0   0.0   2.1e-25   1.9e-21       2     202 ..      13     212 ..      12     243 .. 0.83

  Alignments for each domain:
  == domain 1  score: 77.0 bits;  conditional E-value: 2.1e-25
                                   EEEEE--GGGTT-B-HHHHHHHHHHHHHHCC-TT-SEEEEEESSSSECE--B--HHHHHHHHCS-THHHHHHHHHHHHHHH CS
                         ECH_2   2 gvitLnrpkalNaLslemvralkealkewekddevklvvlkgagekafCAGgDvralyeaakegkkeeeeffreeYklnyl 82 
                                   +++++ r ++lNa + +  r++++ ++e    ++ k ++++g+g +af++G D++a+y+ ++  ++  ++ff++ +++ + 
  gi|13541746|ref|NP_111434.1|  13 AILKFTRSEKLNAFDFDSWREFSSNVDE---ASNYKGLIITGEG-RAFSSGDDINAMYKFEDYAES--KSFFKTLFDVLQK 87 
                                   578899***************9999888...578999*****88.**************9998664..57*********** PP

                                   HHC-SS-EEEEE-BEEETHHHHHHTTSSEEEE-TT-EEE--GGGGT----TTHHHHHHCSSTTHHHHHHHH---B-HHHHH CS
                         ECH_2  83 iatypkpvvalmdGivmGgGvGlsvhgsfrvvtertvfAmPEtaIGlfPDvGgsyfLsrlpgelGlylalTGarlkgadal 163
                                   + +yp p++a ++G++ GgG+ + +   + v  +++ f  PE +IGl+P + +s        +  + la+   rl++++al
  gi|13541746|ref|NP_111434.1|  88 LMHYPHPIIAAVNGLAAGGGAEILLTLDYVVSVKDAWFWFPEARIGLYPPILTSLGVYVFGIKNVKKLAINMPRLTSEEAL 168
                                   *********************************************************99999999**************** PP

                                   HTTS--EE--GG.GHHHHH....HHHHTT........------- CS
                         ECH_2 164 aaglathyvpse.kleale....eaLaelessdeeaveevleel 202
                                   ++gl + +++++ kl +++    ++L ++ + + +++++vl+++
  gi|13541746|ref|NP_111434.1| 169 NLGLVDMIIEDKnKLTEIAvnkvRELNRVPTVSYTSMRKVLASI 212
                                   *********87614555543222333333333355555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       587  (0.0327403); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1619.85
//
Query:       gi|13541747|ref|NP_111435.1|  [L=574]
Description: cobalamin biosynthesis protein (CbiG-related)/precorrin-6Y methylase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.9e-35  120.7   0.0    1.8e-34  119.5   0.0    1.6  1  TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
    9.6e-17   60.8   0.2    2.1e-16   59.7   0.2    1.6  1  CbiG_N        Cobalamin synthesis G N-terminal
    2.8e-12   47.2   0.0      2e-11   44.4   0.0    2.1  2  CbiG_C        Cobalamin synthesis G C-terminus
  ------ inclusion threshold ------
      0.032   14.2   0.0       0.49   10.4   0.1    2.6  2  SIS_2         SIS domain
       0.17   12.0   0.0       0.35   11.0   0.0    1.5  1  CbiG_mid      Cobalamin biosynthesis central region


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 !  119.5   0.0   5.1e-38   1.8e-34       1     212 [.     356     555 ..     356     556 .. 0.85

  Alignments for each domain:
  == domain 1  score: 119.5 bits;  conditional E-value: 5.1e-38
                  TP_methylase   1 klylVGvGpGdpellTvrAlralktadvvlgddsraleilldllaeeleleapmgkekepleeayeeiaeal...aealra 78 
                                   k++++GvGp dp l+T++A++ +++ad+v+g++    +i+++++ +           ke+   +++++++ +   +++ ++
  gi|13541747|ref|NP_111435.1| 356 KIWFIGVGPSDPSLMTLAAIDRIAKADIVAGYE-MPMRIARNAIGK-----------KEQIVLHWKDQQKYVeriIDLYDK 424
                                   799******************************.999999988865...........555556655555555555****** PP

                  TP_methylase  79 gkdVvllvsGDPlvygtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvllpglakeeerelealla 159
                                   g ++++l++GD +++ +  el++++  r+++  +e+iPG+ss+qaa ar+g+pl+ + +++++++  +++++++ l+  l 
  gi|13541747|ref|NP_111435.1| 425 GYRIAFLFTGDSCFSES--ELIRRFIGRCRN--YEIIPGISSVQAASARSGMPLELTPVISFHVTGYIEDRKKEMLDS-LR 500
                                   ***************88..666555554543..*******************************55555556666666.56 PP

                  TP_methylase 160 ngdtlvllkapr..klaelaelLkea.lyddttpvavveragtedervvrgtleel 212
                                   ++++++++ +p    ++++a+ L+e  + + t +v+v+e ++ e+erv++ tle++
  gi|13541747|ref|NP_111435.1| 501 RNGRVLVIPRPYdfMPSKIADYLIENgISGST-EVTVMEYLTSENERVTHNTLEQI 555
                                   688999999999555***********999966.********************986 PP

>> CbiG_N  Cobalamin synthesis G N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.7   0.2   5.9e-20   2.1e-16       6      80 ..      64     138 ..      59     140 .. 0.95

  Alignments for each domain:
  == domain 1  score: 59.7 bits;  conditional E-value: 5.9e-20
                                   HCCC-SEEEEES-HHHHHHHHHHH---TTT--EEEEE-TT--EEEEEE-TT.TTHHHHHHHHHHHTT-EE-XXXX CS
                        CbiG_N   6 lfkeydalvfilaaGivvRliapllkdKktDpaVvvvdeagrfvisllsGhlggAnelAeeiaallgaepviTta 80 
                                    ++++d lv+++++G +vR+i +    K++  aV+vvd+ gr++i+++ Gh+g An +A+ i++l+g e +iT a
  gi|13541747|ref|NP_111435.1|  64 EVRKSDVLVLVMSLGGAVRIIEKASILKEEGIAVIVVDDYGRYAIPIVNGHSGSANVFARLISELIGSEYIITDA 138
                                   578899*******************************************************************88 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 ?   -0.0   0.0      0.35   1.3e+03      42      84 ..      19      65 ..      12      70 .. 0.66
   2 !   44.4   0.0   5.7e-15     2e-11       2     116 .]     229     347 ..     228     347 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.35
                                  CCSHHHHH..HHHHHHCTSTEEEE-HHHHHCHH..CSCT-CHHHCCC CS
                        CbiG_C 42 lKadepgl..lelaeklglplktfsaeeLaave..vpnpsefvkkev 84
                                  ++ +e +l   e  ++ gl +k++s+++L+ ++  + ++++fv +ev
  gi|13541747|ref|NP_111435.1| 19 KRGSETALeiSEKLSEKGLAVKCYSRSNLKGCNtyIGSTQNFVLSEV 65
                                  44444443113444555789*********999766667777877766 PP

  == domain 2  score: 44.4 bits;  conditional E-value: 5.7e-15
                                   EEEEEE-SS--HHHHHHHHHHHHHHCT--GGGEEEEEESSCCSHHHHHHHHHHHCTSTEEEE-HHHHHCHH...CSCT-CH CS
                        CbiG_C   2 vvGiGcrrgtsaeeieeaieealeeaglseeavaalatidlKadepgllelaeklglplktfsaeeLaave...vpnpsef 79 
                                    vGiG+  ++++ +i++ iee+l   gl  ++v++++++   +    l el+++ g +++tfsa++L++v+   + + se 
  gi|13541747|ref|NP_111435.1| 229 SVGIGFTGKADPYNIKKRIEEVLLSLGLGYDDVNCVSSLRYNK---FLSELIKDNGTEFRTFSADDLKSVDvslLSHISEE 306
                                   79************************************98765...9***********************87788899*** PP

                                   HHCCCSSS-HHHHHHHHHC....EECSCEEEE.TTEEEEEE CS
                        CbiG_C  80 vkkevGvpsVaEaaAllaa...arllvpKqak.ggvTvAia 116
                                   +++++G+p+ aE++All     +r++ p ++  + +T+++a
  gi|13541747|ref|NP_111435.1| 307 AEEKLGIPGSAEPSALLSLgpgSRIIYPFTKFdHSMTISVA 347
                                   ****************9853336999998766689999997 PP

>> SIS_2  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   0.00014      0.49      96     136 ..      60     100 ..      30     101 .. 0.86
   2 ?    0.2   0.0      0.19   6.9e+02      25      85 ..     415     474 ..     407     503 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00014
                                   HHHTT--TT-EEEEE-SS--SHHHHHHHHHHHHHT-EEEEE CS
                         SIS_2  96 lrlvrlkpgDvLlviSnsGnnavvveaaeaakergmkviAl 136
                                     l++++++DvL+ + + G    ++e a   ke g++vi++
  gi|13541747|ref|NP_111435.1|  60 FVLSEVRKSDVLVLVMSLGGAVRIIEKASILKEEGIAVIVV 100
                                   445789*********************************86 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.19
                                   HHHHHHHHHTT--EEEEESGGGHHHHHHTSSSTT-BTTEEEE--GGGSSSSST..THHHHH CS
                         SIS_2  25 aeliadslenggkvlvfGsGhSaalaeelaaragglaeferialpalalhtdaeatkssal 85 
                                   +e i d   +g ++  + +G S    +el+ r++g++  + i++    +++  +a++ + l
  gi|13541747|ref|NP_111435.1| 415 VERIIDLYDKGYRIAFLFTGDSCFSESELIRRFIGRCRNYEIIPGISSVQAA-SARSGMPL 474
                                   5667777888999999999******************999888654444433.35555555 PP

>> CbiG_mid  Cobalamin biosynthesis central region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   9.9e-05      0.35       3      71 ..     147     214 ..     145     224 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 9.9e-05
                      CbiG_mid   3 lDilgrpfGwriegegaltevsaalvngepvavlqdvrlegterlertlpehvdveyke.........kaliwitprq 71 
                                   +  + r++ ++i++ +++ +++ al+ng+pv              e+++ +h ++  k+         +a+i+it+r 
  gi|13541747|ref|NP_111435.1| 147 VEEMSRRLYCTIANPECVLKINTALANGDPVFARN----------ESSKRKHAFEMIKYpwktysrsdDAKIIITDRP 214
                                   666778999**********************8888..........23333333333332344445567*******985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (574 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       447  (0.0249317); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.68u 0.27s 00:00:00.95 Elapsed: 00:00:00.48
# Mc/sec: 3615.78
//
Query:       gi|13541748|ref|NP_111436.1|  [L=251]
Description: precorrin-4 methylase [Thermoplasma volcanium GSS1]
Scores for complete 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-50  170.9   0.0    4.3e-50  170.6   0.0    1.1  1  TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
     0.0068   16.8   0.1      0.037   14.4   0.1    2.1  1  Radical_SAM   Radical SAM superfamily


Domain annotation for each model (and alignments):
>> TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  170.6   0.0   4.8e-54   4.3e-50       3     212 ..       2     206 ..       1     207 [. 0.89

  Alignments for each domain:
  == domain 1  score: 170.6 bits;  conditional E-value: 4.8e-54
                  TP_methylase   3 ylVGvGpGdpellTvrAlralktadvvlgddsraleilldllaeeleleapmgkekepleeayeeiaealaealragkdVv 83 
                                   y+VG+GpGdpellT++A+++l++a vv++++s++   +l+++++        ++  +++e + ++i ++ + + ++gkdVv
  gi|13541748|ref|NP_111436.1|   2 YIVGAGPGDPELLTLKAYNILRKAGVVIYAGSLVNPEILKYANP-------SAEIYNSAEMDINKIMDISIILIAEGKDVV 75 
                                   9******************************9977777677643.......3444555555555555555*********** PP

                  TP_methylase  84 llvsGDPlvygtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvl....lpglakeeereleallan 160
                                   +l+sGDP +yg+ +e ++ lr+  +gi++eviPGvs l++aaa+lgi+lt+++ ++sv+      ++  +e++ + al+++
  gi|13541748|ref|NP_111436.1|  76 RLHSGDPHLYGALMEQLSLLRE--KGIDFEVIPGVSVLTSAAASLGIELTMDNISQSVIiargSLRIPVPEKQSILALSSH 154
                                   *****************99999..9***********************************999555566789999999*** PP

                  TP_methylase 161 gdtlvllkaprklaelaelLkea.lyddttpvavveragtedervvrgtleel 212
                                   + t+v+++a + +++++e+L++  +++ +tpv vv + +++de+v+rgtle++
  gi|13541748|ref|NP_111436.1| 155 QSTMVIFTAIHIIEKVVEDLLKGgYPK-DTPVGVVYHSTWKDEKVIRGTLEDI 206
                                   ***********************6666.55********************986 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.1   4.1e-06     0.037      22      75 ..      48     143 ..      36     236 .. 0.62

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.1e-06
                                   HHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTC............................ CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................ RF
                   Radical_SAM  22 regrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlakla............................ 74 
                                     + ++++++ +i+++  +l    g+++v l++g+p ly  + e l  l+++                             
  gi|13541748|ref|NP_111436.1|  48 EIYNSAEMDINKIMDISIIL-IAEGKDVVRLHSGDPHLYGALMEQLSLLREKGidfevipgvsvltsaaaslgieltmdni 127
                                   56778899************.7889**************999999999999866666655555555555555555555555 PP

                                   ...............C CS
                                   ...............x RF
                   Radical_SAM  75 ...............v 75 
                                                   
  gi|13541748|ref|NP_111436.1| 128 sqsviiargslripvP 143
                                   5555555555555541 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       532  (0.0296726); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 1753.08
//
Query:       gi|13541749|ref|NP_111437.1|  [L=229]
Description: precorrin-2 methylase [Thermoplasma volcanium GSS1]
Scores for complete 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  107.8   0.0    8.3e-31  107.6   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 !  107.6   0.0   4.6e-35   8.3e-31       1     206 [.       2     211 ..       2     216 .. 0.86

  Alignments for each domain:
  == domain 1  score: 107.6 bits;  conditional E-value: 4.6e-35
                  TP_methylase   1 klylVGvGpGdpellTvrAlralktadvvlgddsr.....aleilldllaeel........eleapmgkekepleeayeei 68 
                                   kly+VG+GpGdp l+T++Al+++ ++d+++ + s      a +il++l a +          le+pm+++ + +    e++
  gi|13541749|ref|NP_111437.1|   2 KLYVVGLGPGDPSLVTLKALDTVLKSDIIYVPCSGgehriARSILEKLFAGKNegslpqvkDLEFPMTRDHNYNKSFLEKN 82 
                                   79***************************7555223234666666666665559****************9999999**** PP

                  TP_methylase  69 aealaealragkdVvllvsGDPlvygtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvllpglake 149
                                   ++ ++ +l++ k   ++v+G P++y+t++++ + l++  +g+++e +PGv s++a+ ar+ i ++ g++++ v+   ++ +
  gi|13541749|ref|NP_111437.1|  83 VAEIISDLAKHKILSYAVIGSPTFYSTFGKIKQMLEE--KGVSIEYVPGVNSVDACSARSSINIASGDDSVLVT---TY-R 157
                                   *************************************..9**********************************...34.4 PP

                  TP_methylase 150 eereleallangdtlvllkaprk...laelaelLkealyddttpvavveragtedervvr 206
                                   +  e+  + +  dt+v++k p     l++++ l+     +d  + ++++r++++ e +++
  gi|13541749|ref|NP_111437.1| 158 KLLEIGSFEK-YDTVVIMKVPTGsfsLERIRNLM-----GDGMKYIYARRCTMDSEFITE 211
                                   4555555444.8******9999445588888877.....4558***********998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); 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: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1498.87
//
Query:       gi|13541750|ref|NP_111438.1|  [L=201]
Description: precorrin-6Y methylase [Thermoplasma volcanium GSS1]
Scores for complete 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-13   49.4   0.0    6.7e-13   48.7   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
      8e-13   48.6   0.0    1.5e-12   47.7   0.0    1.4  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    1.3e-10   41.8   0.0    4.7e-10   40.0   0.0    1.8  2  Methyltransf_25  Methyltransferase domain
    1.6e-09   37.5   0.0    2.1e-09   37.1   0.0    1.2  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    3.9e-09   36.3   0.0      3e-07   30.2   0.0    2.1  2  MTS              Methyltransferase small domain
    1.6e-07   31.9   0.0    2.8e-07   31.1   0.0    1.5  1  Methyltransf_11  Methyltransferase domain
    5.2e-07   29.3   0.1    6.7e-07   29.0   0.1    1.1  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    3.8e-06   26.8   0.0    5.3e-06   26.3   0.0    1.2  1  GCD14            tRNA methyltransferase complex GCD14 subunit
    1.7e-05   24.1   0.0    2.6e-05   23.5   0.0    1.3  1  Methyltransf_3   O-methyltransferase
    0.00013   21.9   0.0    0.00047   20.1   0.0    1.7  2  Methyltransf_18  Methyltransferase domain
    0.00014   21.4   0.1     0.0011   18.5   0.0    2.1  2  Methyltransf_4   Putative methyltransferase
    0.00015   22.5   0.1    0.00077   20.2   0.1    2.0  2  Methyltransf_12  Methyltransferase domain
    0.00021   21.0   0.0    0.00037   20.2   0.0    1.3  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
    0.00062   19.6   0.0    0.00094   19.1   0.0    1.3  1  Methyltransf_23  Methyltransferase domain
     0.0013   18.4   0.0      0.002   17.8   0.0    1.4  1  Cons_hypoth95    Conserved hypothetical protein 95
     0.0013   18.1   0.0     0.0019   17.6   0.0    1.3  1  GidB             rRNA small subunit methyltransferase G
     0.0052   16.3   0.0      0.015   14.9   0.0    1.6  2  Methyltransf_5   MraW methylase family
  ------ inclusion threshold ------
      0.015   14.6   0.0      0.019   14.3   0.0    1.3  1  CMAS             Mycolic acid cyclopropane synthetase
      0.037   13.7   0.0      0.078   12.6   0.0    1.8  1  UPF0020          Putative RNA methylase family UPF0020
       0.06   12.4   0.0       0.12   11.5   0.0    1.4  2  RrnaAD           Ribosomal RNA adenine dimethylase
      0.087   12.8   0.0       0.17   11.9   0.0    1.5  1  ADH_zinc_N       Zinc-binding dehydrogenase


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 !   48.7   0.0   7.8e-16   6.7e-13       4     127 ..      45     162 ..      43     190 .. 0.78

  Alignments for each domain:
  == domain 1  score: 48.7 bits;  conditional E-value: 7.8e-16
               Methyltransf_31   4 glrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklg.ldnveFeqgdiee.leklledekfDlilsne 82 
                                   g ++lD+G+GtG  +  + +++gp+++++ +D++e+ai+lAr n+++l  ++n+++  +d+ +  + +   ++fD i+  +
  gi|13541750|ref|NP_111438.1|  45 GGHFLDIGTGTGSVAVDMSRLAGPNGKIIALDRDEKAIKLARINLDRLSpYKNIQLVLADAYAySP-A---DSFDAIFIGG 121
                                   5679*****************************************9985388***********444.3...8******975 PP

               Methyltransf_31  83 vlnaladpdkileeiervlkpggilliedprllaelpakveeesk 127
                                         d+++   +    lk+g +++i+ ++  + l + ve+ + 
  gi|13541750|ref|NP_111438.1| 122 GT---GDLPNLVSKYVPFLKSGARVVINAIQ-VKTLNDAVESLEL 162
                                   54...55555555555588888888888888.5555555555444 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 !   47.7   0.0   1.8e-15   1.5e-12      66     172 ..      37     146 ..      27     174 .. 0.86

  Alignments for each domain:
  == domain 1  score: 47.7 bits;  conditional E-value: 1.8e-15
                                   HHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTC.SEEEEES-GGGTTGGG-SEEE CS
                          PCMT  66 lellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldle.nvivvvgDGrkGyeekaPYda 145
                                   l+ l +++g + L++G+G+G  ++ ++rl g++g++++++r ++ ++ a+ nl +l    n+++v +D +  y ++  +da
  gi|13541750|ref|NP_111438.1|  37 LNRLGVRNGGHFLDIGTGTGSVAVDMSRLAGPNGKIIALDRDEKAIKLARINLDRLSPYkNIQLVLADAY-AYSPADSFDA 116
                                   55677999**********************************************987544********75.6999999*** PP

                                   EEESSBBSS--H...HHHHTEEEEEEEEEE CS
                          PCMT 146 ihvgaaapeiPe...alidQLkeGGrlvvP 172
                                   i++g ++ ++P+   +++  Lk+G r+v+ 
  gi|13541750|ref|NP_111438.1| 117 IFIGGGTGDLPNlvsKYVPFLKSGARVVIN 146
                                   *******9999733367788******9985 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.0   0.0   5.6e-13   4.7e-10       2      71 ..      49     120 ..      48     144 .. 0.85
   2 ?    1.3   0.0      0.65   5.6e+02       4      52 ..     119     172 ..     119     189 .. 0.76

  Alignments for each domain:
  == domain 1  score: 40.0 bits;  conditional E-value: 5.6e-13
                                   EEET-TTSHHHHHHHCTST.SSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCGBSSSTTTEEEEEEE CS
               Methyltransf_25   2 LdlGcGtGrltlalakrlg.kakvtgvDiseemleaareraeeegl..nvefvqgdaedlpfedgsfDlvvss 71 
                                   Ld+G+GtG ++ ++++  g ++k++++D +e++++ ar ++++ ++  n+++v +da +++ +d sfD++++ 
  gi|13541750|ref|NP_111438.1|  49 LDIGTGTGSVAVDMSRLAGpNGKIIALDRDEKAIKLARINLDRLSPykNIQLVLADAYAYSPAD-SFDAIFIG 120
                                   9****************9669********************9988889************9776.*****994 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.65
                                   ET-TTSHHHHHHHCTS....TSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEE CS
               Methyltransf_25   4 lGcGtGrltlalakrl....gkakvtgvDiseemleaareraeeegl.nvefvq 52 
                                   +G GtG+l   ++k +    + a+v+   i+ + l+ a e +e +++ nv++++
  gi|13541750|ref|NP_111438.1| 119 IGGGTGDLPNLVSKYVpflkSGARVVINAIQVKTLNDAVESLELNNFrNVSVIE 172
                                   689999999998888766642588888888888888888888777777777665 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.1   0.0   2.4e-12   2.1e-09      42     150 ..      39     144 ..      30     169 .. 0.82

  Alignments for each domain:
  == domain 1  score: 37.1 bits;  conditional E-value: 2.4e-12
                                   H--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSS.TEEEEE--TTT-TTS-T-EEEEE CS
               Ubie_methyltran  42 lvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegki.nieflqanaeeLpfeddsfDvvt 121
                                   + +v++g ++lD+ +Gtg +a+++s+ +g +gk++ lD +e+ +k ++  l + + + ni+++ a+a +     dsfD + 
  gi|13541750|ref|NP_111438.1|  39 RLGVRNGGHFLDIGTGTGSVAVDMSRLAGPNGKIIALDRDEKAIKLARINLDRLSPYkNIQLVLADAYAYS-PADSFDAIF 118
                                   678999*********************************************9977555*********9986.5689***** PP

                                   EES-GGG-S-HHHHHHHHHHHEEEEEEEE CS
               Ubie_methyltran 122 vsfGlrnvtDklkaLkeayrvlkpGGrlv 150
                                   ++ G  +    ++ + +    lk G r+v
  gi|13541750|ref|NP_111438.1| 119 IGGGTGD---LPNLVSKYVPFLKSGARVV 144
                                   **99654...4444445555555555554 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   0.0   3.5e-10     3e-07      25     102 ..      38     118 ..      34     120 .. 0.89
   2 ?    4.5   0.0     0.026        22      56     109 ..     141     196 ..     117     200 .. 0.68

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 3.5e-10
                                   HHCHCCTCSEEEEET-TTSHHHHHHHHH.TTC.EEEEEESBHHHHHHHHHHHHHTTGC..EEEEE-STTTTSTTS-EEEEE CS
                           MTS  25 etlpkelsgkvlDlGcGaGvlgaalake.speaevtlvdvdarAlesakenleankle..vevvasdvleeveekkfdliv 102
                                   + l  +  g+ lD+G+G+G +++ + +   p+ ++ ++d d +A+++a+ nl +      +++v  d+++  + ++fd+i 
  gi|13541750|ref|NP_111438.1|  38 NRLGVRNGGHFLDIGTGTGSVAVDMSRLaGPNGKIIALDRDEKAIKLARINLDRLSPYknIQLVLADAYAYSPADSFDAIF 118
                                   5566678899**************9986268888******************99887778******************995 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.026
                                   .EEEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STTTTST.TS-EEEEEE---STT CS
                           MTS  56 aevtlvdvdarAlesakenleankle.vevvasdvleeve.ekkfdlivsNPPfha 109
                                   a+v++  ++ + l+ a e le n+++ v+v++ ++   ++   ++ +i  NP f  
  gi|13541750|ref|NP_111438.1| 141 ARVVINAIQVKTLNDAVESLELNNFRnVSVIEVQISVGMKtGSSYAMIARNPIFVV 196
                                   456666777777888888888888888778777777777634699*******8865 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.1   0.0   3.3e-10   2.8e-07       1      69 [.      49     121 ..      49     147 .. 0.85

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 3.3e-10
                                   EEET-TTSHHHHHHHHTT...SEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEECCCTSS-TT-EEEEEEES CS
               Methyltransf_11   1 LdvGcGtGrlaealakrg...arvvgvDlskemlklakekaseegl..kvefvvadaeklpfednsfDlvvsse 69 
                                   Ld+G+GtG++a ++ + +   ++++++D +++++kla+ +  +  +  ++++v ada     + +sfD++++  
  gi|13541750|ref|NP_111438.1|  49 LDIGTGTGSVAVDMSRLAgpnGKIIALDRDEKAIKLARINLDRLSPykNIQLVLADAYAYSPA-DSFDAIFIGG 121
                                   8**************777799*******************99999999**********97545.5*****9876 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   0.1   7.8e-10   6.7e-07     156     282 ..      38     170 ..      28     176 .. 0.79

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 7.8e-10
                          PrmA 156 ekl.vkegeevlDvGtGSGiLaiaaakLg..akkvvavDiDevAvkvakeNaelNkveaklevalseellk...eekadvi 230
                                   ++l v++g ++lD+GtG+G  a+  ++L+    k++a+D De A+k a+ N+++ +  +++++ l+ ++ +   + ++d i
  gi|13541750|ref|NP_111438.1|  38 NRLgVRNGGHFLDIGTGTGSVAVDMSRLAgpNGKIIALDRDEKAIKLARINLDRLSPYKNIQLVLA-DAYAyspADSFDAI 117
                                   5545788999******************844579*******************9999999988654.44432345788999 PP

                          PrmA 231 vaNILaevlielaedikklvkeggllilSGilkekaeevaeale.qgfeleev 282
                                   +       l +l+++   ++k+g+++++  i  +  ++  e le ++f+ ++v
  gi|13541750|ref|NP_111438.1| 118 FIGGGTGDLPNLVSKYVPFLKSGARVVINAIQVKTLNDAVESLElNNFRNVSV 170
                                   88888899999999999999999999999996666655555554257776665 PP

>> GCD14  tRNA methyltransferase complex GCD14 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.0   6.2e-09   5.3e-06      28     175 ..      31     176 ..      26     189 .. 0.83

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 6.2e-09
                         GCD14  28 Dislii.mkLelkpGsvvvesGtGsgslshaiartvaPtGhlftfefheqraekareefrehelsqlvtvthrDvckeGfd 107
                                   +i li   +L +++G   ++ GtG+gs++  ++r  +P G++ +++  e+ ++ ar ++ +    +++++   D+      
  gi|13541750|ref|NP_111438.1|  31 EIRLISlNRLGVRNGGHFLDIGTGTGSVAVDMSRLAGPNGKIIALDRDEKAIKLARINLDRLSPYKNIQLVLADAYAYS-- 109
                                   5667752579**********************************************99998888888888777776544.. PP

                         GCD14 108 eevsgkvDavfL.....DlPaPweaiphaakalkkeggrlCsfsPCieqvqrtceaLrelgfteietlevllr 175
                                       ++ Da+f+     DlP   + + + +  l k+g+r+   +  +  +  ++e L+  +f +++++ev++ 
  gi|13541750|ref|NP_111438.1| 110 --PADSFDAIFIgggtgDLP---NLVSKYVPFL-KSGARVVINAIQVKTLNDAVESLELNNFRNVSVIEVQIS 176
                                   ..46778****944333444...3577777777.889999999999999999999999999999999999875 PP

>> Methyltransf_3  O-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0     3e-08   2.6e-05      44     156 ..      41     146 ..      22     179 .. 0.86

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 3e-08
                                   HHHT--EEEEE--TTSHHHHHHHTTS-TT-EEEEEES-HHHHHHHHHHHHHTT-GGGEEEEES-HHHHHHHHHTSSS---E CS
                Methyltransf_3  44 klvnakrvleiGvftGyslLatalalPeDGkilaididreayeialkfiqkagvaekieliegdalkvLeelvkdkklpef 124
                                    + n  + l+iG+ tG  ++ ++    ++Gki+a+d d++a ++a+  +++ +  + i+l  +da +        ++  +f
  gi|13541750|ref|NP_111438.1|  41 GVRNGGHFLDIGTGTGSVAVDMSRLAGPNGKIIALDRDEKAIKLARINLDRLSPYKNIQLVLADAYAY-------SPADSF 114
                                   56777889****************99**********************************99999864.......45668* PP

                                   EEEEE-S-GGGHHHHHHHHHHTEEEEEEEEEE CS
                Methyltransf_3 125 DfifvDaDkssyvnyyeklleLvkvGgliaiD 156
                                   D if+     + +n   k + ++k G  ++i+
  gi|13541750|ref|NP_111438.1| 115 DAIFIGGGTGDLPNLVSKYVPFLKSGARVVIN 146
                                   ******99999999999999999999888775 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   5.5e-07   0.00047      12      93 ..      42     124 ..      31     147 .. 0.87
   2 ?   -0.4   0.0       1.2     1e+03      40      77 ..     142     181 ..     129     189 .. 0.74

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 5.5e-07
               Methyltransf_18  12 vekgsrvaDiGtDHgylpiylvk.egkakkviasDinegplekakeniekagledkievrlsdGleklkeeevdtvviaGm 91 
                                   v++g +++DiGt  g +++ + +  g   k+ia D  e++++ a+ n+++ +  ++i+++l+d  +   ++++d++ i G 
  gi|13541750|ref|NP_111438.1|  42 VRNGGHFLDIGTGTGSVAVDMSRlAGPNGKIIALDRDEKAIKLARINLDRLSPYKNIQLVLADAYAYSPADSFDAIFIGGG 122
                                   778899*************9986378999***********************************99887777****99885 PP

               Methyltransf_18  92 Gg 93 
                                    g
  gi|13541750|ref|NP_111438.1| 123 TG 124
                                   44 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.2
               Methyltransf_18  40 kviasDinegplekakeniekagled..kievrlsdGlek 77 
                                   +v+   i+ + l+ a e++e +++++   iev +s G+++
  gi|13541750|ref|NP_111438.1| 142 RVVINAIQVKTLNDAVESLELNNFRNvsVIEVQISVGMKT 181
                                   5666667888888999988888875533688888888765 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   1.2e-06    0.0011       4      62 ..      47     107 ..      44     120 .. 0.87
   2 ?    0.3   0.1      0.49   4.2e+02      36      54 ..     148     166 ..     117     175 .. 0.62

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.2e-06
                                   EEEEET-TTSHHHHHHHH.HSTTSEEEEEES-HHHHHHHHHHHHHC.TTSSEEEEES-CCC CS
                Methyltransf_4   4 vvleiGcGkGeflvalAk.knPdknflGiEirvkvvakvlkkieal.elkNlrilrgdalk 62 
                                    +l+iG+G G++ v+++  + P+ ++++++  +k ++ +  + ++l  +kN++++  da  
  gi|13541750|ref|NP_111438.1|  47 HFLDIGTGTGSVAVDMSRlAGPNGKIIALDRDEKAIKLARINLDRLsPYKNIQLVLADAYA 107
                                   589**************7478****************999999998789*********943 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.49
                                   HHHHHHHHHHHHCTTSSEE CS
                Methyltransf_4  36 kvvakvlkkiealelkNlr 54 
                                     v+++++++e lel+N+r
  gi|13541750|ref|NP_111438.1| 148 IQVKTLNDAVESLELNNFR 166
                                   4455555555555555544 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.1     9e-07   0.00077       1      73 [.      49     120 ..      49     129 .. 0.83
   2 ?    1.2   0.0      0.72   6.1e+02       3      48 ..     119     168 ..     118     185 .. 0.66

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 9e-07
               Methyltransf_12   1 LeiGcGtGsllrallekl.pdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvas 73 
                                   L+iG+GtGs++  + +   p+ +++++D +++ai+ a+  l + ++++  n++l   d+   ++ +sfD++++ 
  gi|13541750|ref|NP_111438.1|  49 LDIGTGTGSVAVDMSRLAgPNGKIIALDRDEKAIKLARINLDRLSPYK--NIQLVLADAYAYSPADSFDAIFIG 120
                                   8**********99999999***************77777777777655..6666666666667778****9875 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.72
               Methyltransf_12   3 iGcGtGsllrallekl....pdieytgvDispsaiedakeklakrennnn 48 
                                   iG+GtG+l   + ++     ++++++   i+ + ++da e l  ++ +n+
  gi|13541750|ref|NP_111438.1| 119 IGGGTGDLPNLVSKYVpflkSGARVVINAIQVKTLNDAVESLELNNFRNV 168
                                   89999999888888775555555555555555555555555555555555 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 !   20.2   0.0   4.4e-07   0.00037       4      83 ..      40     117 ..      37     121 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 4.4e-07
                                   H---TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT.--SEEEEES-CTCCHHHHCC..EEEE CS
               Methyltr_RsmB-F   4 LapqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLg.vtntivleaDarkidkvlggelfDri 83 
                                   L  +++ ++lD+ ++ G+    ++ l  ++g+++A+d++++ +k    nl rL+  +n++++ aDa  ++       fD i
  gi|13541750|ref|NP_111438.1|  40 LGVRNGGHFLDIGTGTGSVAVDMSRLAGPNGKIIALDRDEKAIKLARINLDRLSpYKNIQLVLADAYAYSPAD---SFDAI 117
                                   56789999*********************************************6367********98874332...46666 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   1.1e-06   0.00094      21      97 ..      43     128 ..      29     156 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.1e-06
               Methyltransf_23  21 raggrvLdiGcGtGillevl.rengf..svtgvDlspeaveiae......kakkaqkdqfdeqeaaepqgkfdlIvlrevl 92 
                                   r gg  LdiG+GtG+++  + r  g   ++++ D +++a+++a+      +++k+++       a  p+++fd I    ++
  gi|13541750|ref|NP_111438.1|  43 RNGGHFLDIGTGTGSVAVDMsRLAGPngKIIALDRDEKAIKLARinldrlSPYKNIQLVLADAYAYSPADSFDAIFIGGGT 123
                                   778899*********99999677788899*********************8888888888888899999999999887777 PP

               Methyltransf_23  93 ehvpd 97 
                                   + +p+
  gi|13541750|ref|NP_111438.1| 124 GDLPN 128
                                   77777 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   2.3e-06     0.002      34     119 ..      38     119 ..      23     175 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.3e-06
                                   HHHCCCHCC-EEEETT-TTSHHHHHHHHTT-...SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS CS
                 Cons_hypoth95  34 nilaaeiegarvLDlfaGsGalglEAlSRga...kkavlvekdkeavkilkenleelkleeetaelkedaleallklakkk 111
                                   n l+   +g ++LD+  G+G++++  +SR a    k++++++d++a+k+ + nl++l   ++++ +  da+   +      
  gi|13541750|ref|NP_111438.1|  38 NRLG-VRNGGHFLDIGTGTGSVAVD-MSRLAgpnGKIIALDRDEKAIKLARINLDRLSPYKNIQLVLADAYAYSPAD---- 112
                                   5555.346789*************8.79988333589*********************9988999888887766555.... PP

                                   -EEEEEEE CS
                 Cons_hypoth95 112 eefdivfl 119
                                    +fd +f+
  gi|13541750|ref|NP_111438.1| 113 -SFDAIFI 119
                                   .7999997 PP

>> GidB  rRNA small subunit methyltransferase G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   2.2e-06    0.0019      49     146 ..      46     145 ..      33     181 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2.2e-06
                                   C-.EEEETSTTTTTHHHHH.HH-TTSEEEEEES-HHHHHHHH.HHHHHCT-SSEEEEES-CCCTTTTT-EEEEEEC.-SSS CS
                          GidB  49 rdkviDvGsGaGlPGipLa.iarpelkltLleslekkiaFLe.evkeelklenveivearaeekqeeekydvvtsR.Alas 126
                                     +++D+G+G G  ++ ++ +a p+ k++ l+++ek i+  + ++ +    +n++ v a+a ++ + +++d++ +  + + 
  gi|13541750|ref|NP_111438.1|  46 G-HFLDIGTGTGSVAVDMSrLAGPNGKIIALDRDEKAIKLARiNLDRLSPYKNIQLVLADAYAYSPADSFDAIFIGgGTGD 125
                                   3.59************9965999****************887345556679**********************88526888 PP

                                   HHHHHHHHCCCEEEEEEEEE CS
                          GidB 127 lnelteillkllkegglila 146
                                   l +l++   ++lk+g ++++
  gi|13541750|ref|NP_111438.1| 126 LPNLVSKYVPFLKSGARVVI 145
                                   99999999998888877764 PP

>> Methyltransf_5  MraW methylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   1.7e-05     0.015      13      81 ..      37     102 ..      27     123 .. 0.76
   2 ?   -0.6   0.0      0.87   7.4e+02     217     266 ..     124     175 ..     105     199 .. 0.64

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.7e-05
                                   HHHT---TT-EEEES--TTSHHHHHHHTT--TT.EEEEEES-HHHHHHHTT.....---EEEEES-GGGH CS
                Methyltransf_5  13 vellepkedgvyiDaTlGaggHsealLeqlsel.rligidrDksalarakerLkefekrltlvkgnfkel 81 
                                   ++ l ++++g ++D   G+g  +  + +    + ++i++drD++a++ a+ +L +       +k+    l
  gi|13541750|ref|NP_111438.1|  37 LNRLGVRNGGHFLDIGTGTGSVAVDMSRLAGPNgKIIALDRDEKAIKLARINLDRLS----PYKNIQLVL 102
                                   5677889****************99998877777****************8765543....233333333 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.87
                                   HHHHHHHHHHHHHEEEEEEEEE..EESSHHHHHHHHHHHHHTT--------- CS
                Methyltransf_5 217 eeleelleaalellakggrlav..isFhSledrivkkvfkeaskkeevPagl 266
                                     l++l+++ +  l++g+r+++  i  + l+d +    +++  + + +  ++
  gi|13541750|ref|NP_111438.1| 124 GDLPNLVSKYVPFLKSGARVVInaIQVKTLNDAVESLELNNFRNVSVIEVQI 175
                                   5677788888888888888776446666777766555555555544444444 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   2.2e-05     0.019      53     101 ..      35      83 ..      19     158 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.2e-05
                                   HHHTTTT--TT-EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHH CS
                          CMAS  53 lileklelkpGmtlLdiGcGWGslvrraverydvkvvglTlSkeqakla 101
                                   + l++l++++G + LdiG+G Gs+++ + +  + +   + l +++++  
  gi|13541750|ref|NP_111438.1|  35 ISLNRLGVRNGGHFLDIGTGTGSVAVDMSRLAGPNGKIIALDRDEKAIK 83 
                                   46899********************999887666655555555554444 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   9.2e-05     0.078      75     125 ..      68     117 ..      29     180 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 9.2e-05
                                   HH--EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EE CS
                       UPF0020  75 aelklygsDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdvi 125
                                   ++ k++++D d+++++ ar N+ +    + i+++ ada +   + +++d+i
  gi|13541750|ref|NP_111438.1|  68 PNGKIIALDRDEKAIKLARINLDRLSPYKNIQLVLADAYAYS-PADSFDAI 117
                                   56679*********************************9999.88899988 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00014      0.12      27      90 ..      41     110 ..      32     129 .. 0.84
   2 ?   -3.0   0.1       3.5     3e+03      19      37 ..     153     173 ..     148     181 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00014
                                   -GGTTSEEEEES-TTTCCHHHHHCC-...SEEEEE-S-HHHHHHHHCHTT...TCCCEEEE-S-CCGHHH CS
                        RrnaAD  27 nleekltvleigpGkGilTeeLakra...kqvvvlElderLakllqkkls...kdeklkvvhqDflkfet 90 
                                    +++    l+ig+G+G   + +   a    +  +l  de+ +kl + +l    +++++++v +D++ ++ 
  gi|13541750|ref|NP_111438.1|  41 GVRNGGHFLDIGTGTGSVAVDMSRLAgpnGKIIALDRDEKAIKLARINLDrlsPYKNIQLVLADAYAYSP 110
                                   55667778**************999999999****999987777765554444*************9876 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 3.5
                                   HHHHHHHH-GG..TTSEEEEE CS
                        RrnaAD  19 ineIldklnle..ekltvlei 37 
                                   +n++++ l+l+   +  v+e+
  gi|13541750|ref|NP_111438.1| 153 LNDAVESLELNnfRNVSVIEV 173
                                   555666666554444444444 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0    0.0002      0.17       1      97 [.      54     160 ..      54     190 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0002
                                   HHHHHHHHHHHHTT-..EEEEEESSHHHHHHHHHTTESEEEETTTC.HHHHHHHHHTTTSSEEEEEESSC...SHHHHHHH CS
                    ADH_zinc_N   1 gvGlaavqlAkalGa..eviavdsseeklelakklGadevinykea.dlverikeltggegvdvvfecvG...sgatleaa 75 
                                   g G+ av + + +G   ++ia d++e+ ++la+ +  d++  yk+   + ++  +    + +d++f   G    +  ++ +
  gi|13541750|ref|NP_111438.1|  54 GTGSVAVDMSRLAGPngKIIALDRDEKAIKLAR-INLDRLSPYKNIqLVLADAYAYSPADSFDAIFIGGGtgdLPNLVSKY 133
                                   78*************9**********8666665.66899999966532333333333377888999888855667788899 PP

                                   HHCEEEEEEEEECSC.TSSEEE....E CS
                    ADH_zinc_N  76 lkllkpgGrlvvvGg.gkgeee....f 97 
                                   + +lk g r+v+ ++ +k  ++    +
  gi|13541750|ref|NP_111438.1| 134 VPFLKSGARVVINAIqVKTLNDavesL 160
                                   999999999999998755444454443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); 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: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.44
# Mc/sec: 1374.01
//
Query:       gi|13541751|ref|NP_111439.1|  [L=377]
Description: cobalt-precorrin-6A synthase [Thermoplasma volcanium GSS1]
Scores for complete 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-64  215.6   5.5    6.7e-64  215.6   5.5    1.5  2  CbiD          CbiD
     0.0016   17.9   0.0     0.0047   16.4   0.0    1.7  1  Sigma70_r4    Sigma-70, region 4
  ------ inclusion threshold ------
      0.018   14.4   0.0       0.06   12.8   0.0    1.8  2  HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family I
      0.063   13.5   0.1       0.34   11.1   0.0    2.3  2  NusG_add      NusG additional domain
       0.11   12.2   0.1       0.19   11.3   0.1    1.3  1  SMC_ScpB      Segregation and condensation complex subunit Sc


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 !  215.6   5.5   1.9e-67   6.7e-64       2     252 .]      14     272 ..      13     272 .. 0.94
   2 ?   -2.4   0.1      0.63   2.3e+03      14      33 ..     289     308 ..     283     344 .. 0.49

  Alignments for each domain:
  == domain 1  score: 215.6 bits;  conditional E-value: 1.9e-67
                          CbiD   2 rsGyTtGscAaAAakaAllallkgekleeveielpkgekleipiekvalleee...aavikdaGddpDvTngaeivaeve. 78 
                                   ++G+TtG +AaAAaka++l++lkg ++++v + +p g+++e+++ +  +++e+   a+ +k +Gd+pD  ng++i ++ + 
  gi|13541751|ref|NP_111439.1|  14 QYGITTGLTAAAAAKACTLTVLKG-VQNRVVVPTPIGIRIEVKVVESVRIDESsgyASAEKFSGDNPDQLNGITIRCHCKv 93 
                                   68*******************877.5799**************876666566669*********************99999 PP

                          CbiD  79 ........eeieiegGeGvGrvtkpgLevevgeaAInpvprkmieenveevleeakegvevtisvpeGeelAkkTlNprlG 151
                                           ++i+i+g  G+G+v k+gL +++ge+AI++ +rkmie++v+e++     +ve+ isvp+Gee Ak T+N+++G
  gi|13541751|ref|NP_111439.1|  94 vkkqengrSKITISGNAGIGVVEKDGLGIRPGEKAISQGARKMIEDAVREAAGG--YDVELSISVPNGEEFAKLTMNEKVG 172
                                   99******78******************************************87..57*********************** PP

                          CbiD 152 ivgGiSiLGTtGivepmSeeallesireelkvaaaeglkelvlvtGnkgeklakkklglpeealvkvsnfvgealeeaaek 232
                                   + gGiS+LGTtGi ep+S+e++  +++  +   + + +k +vl++Gn++ k+akk + lp++a+v +++ vg+a+++  e 
  gi|13541751|ref|NP_111439.1| 173 VFGGISVLGTTGIEEPVSTEEYELHLKYIVAAGR-CVSKIIVLCPGNTALKFAKKYFALPDKAFVLIGDKVGAAVSASIES 252
                                   **********************999987766655.4589****************99************************ PP

                          CbiD 233 gvkkvllvghiGKlvKlagG 252
                                    +++v+++g  GKlvK+a+G
  gi|13541751|ref|NP_111439.1| 253 AYDHVVIFGLPGKLVKIAAG 272
                                   ******************99 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.63
                          CbiD  14 AakaAllallkgekleevei 33 
                                   Aa aA++ + kg +++ +e 
  gi|13541751|ref|NP_111439.1| 289 AAVAAMYGISKGAVKRIMES 308
                                   55555555543332222221 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   1.3e-06    0.0047      18      41 ..     283     306 ..     276     309 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.3e-06
                                   TTT--HHHHHHHHTS-HHHHHHHH CS
                    Sigma70_r4  18 geglTleEIgerlgiSrerVrqie 41 
                                   g+  Tl+ +++++giS+++V++i+
  gi|13541751|ref|NP_111439.1| 283 GRMETLAAVAAMYGISKGAVKRIM 306
                                   6778*******************8 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   1.7e-05      0.06      27      49 ..     285     307 ..     283     309 .. 0.90
   2 ?   -3.3   0.0       1.8   6.4e+03      10      18 ..     333     341 ..     333     342 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.7e-05
                  HTH_Tnp_ISL3  27 srsvkavArqlgvSwtTVwrild 49 
                                   + + +avA+++g+S   V+ri+ 
  gi|13541751|ref|NP_111439.1| 285 METLAAVAAMYGISKGAVKRIME 307
                                   6799*****************96 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.8
                  HTH_Tnp_ISL3  10 sriTlrlea 18 
                                   sri++rl+a
  gi|13541751|ref|NP_111439.1| 333 SRISNRLKA 341
                                   799***986 PP

>> NusG_add  NusG additional domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   9.6e-05      0.34      27      75 ..     219     268 ..     186     274 .. 0.81
   2 ?   -1.5   0.0      0.78   2.8e+03      61      79 ..     310     328 ..     293     341 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 9.6e-05
                      NusG_add  27 vdrkylktyv.ipekaklvtGlkigarvkqGmplaadgeyiceldGkive 75 
                                      k++k+y+ +p+ka +  G k+ga v   +  a d  +i  l Gk+v+
  gi|13541751|ref|NP_111439.1| 219 TALKFAKKYFaLPDKAFVLIGDKVGAAVSASIESAYDHVVIFGLPGKLVK 268
                                   456999998659**********************************9997 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.78
                      NusG_add  61 adgeyiceldGkivevekl 79 
                                   + ge i+ ++ + + +e l
  gi|13541751|ref|NP_111439.1| 310 NTGEAISIIEQEGIVAEVL 328
                                   5555555444433333333 PP

>> SMC_ScpB  Segregation and condensation complex subunit ScpB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   5.3e-05      0.19      78     127 ..     277     327 ..     264     337 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 5.3e-05
                      SMC_ScpB  78 ktrLsqaaletLaiIaykqpvtraeieeiRGvn.sdsvvrtLlerglieek 127
                                   +++     +etLa +a    +++  +++i  ++ + ++++ + ++g++ e+
  gi|13541751|ref|NP_111439.1| 277 HSKVADGRMETLAAVAAMYGISKGAVKRIMESSnTGEAISIIEQEGIVAEV 327
                                   56777889**********************9887999********999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (377 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       565  (0.0315132); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 2412.35
//
Query:       gi|13541752|ref|NP_111440.1|  [L=251]
Description: precorrin-3B methylase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.9e-34  117.3   0.0      1e-33  117.1   0.0    1.0  1  TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
  ------ inclusion threshold ------
       0.05   13.3   0.2       0.56   10.0   0.0    2.7  3  DUF5488       Family of unknown function (DUF5488)


Domain annotation for each model (and alignments):
>> TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.1   0.0   1.1e-37     1e-33       2     210 ..       5     210 ..       4     213 .. 0.86

  Alignments for each domain:
  == domain 1  score: 117.1 bits;  conditional E-value: 1.1e-37
                  TP_methylase   2 lylVGvGpGdpellTvrAlralktadvvlgddsraleilldllaeeleleapmgkekepleeayeeiaealaealragkdV 82 
                                   l++VG+GpG+ +l+T+ A  a+++++ v+g   ++ + ++++ +        ++   ++  ++  e a++ +e++r+g++V
  gi|13541752|ref|NP_111440.1|   5 LFVVGIGPGSNDLMTPQASLAIERSEYVIGFS-LYVSFIKEKFP--------NKIYISNGMQGEIERAKKAIELARSGHNV 76 
                                   789*****************************.9*****98764........4555567777888889999********** PP

                  TP_methylase  83 vllvsGDPlvygtgselvealrareagie.veviPGvsslqaaaarlgiplteggevlsvl..lpglakeeereleallan 160
                                    +++sGD  +yg++++++e+l+  e +++ v v+PG+s+l+++a+ lg pl++++ vls++  l++++ ++  ++++++a 
  gi|13541752|ref|NP_111440.1|  77 SIISSGDAGIYGIAGAVFEILSTLEDNMPeVSVVPGISALSSCASLLGSPLSNDFMVLSLSdlLTPWEVIR--KRAEAAAI 155
                                   *******************99999999988********************************999999555..55555666 PP

                  TP_methylase 161 gdtlvllkapr..k....laelaelLkealyddttpvavveragtedervvrgtle 210
                                    d + ++++pr  +    l++++e  +++ +  +tpv +v++a ++d+    + l+
  gi|13541752|ref|NP_111440.1| 156 LDLVTVIYNPRgsRfpnnLEKVMEYFLKY-RSGDTPVGIVRNAYRPDQSAKIVQLK 210
                                   79*********655555566666666666.66677*************98877776 PP

>> DUF5488  Family of unknown function (DUF5488)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   6.3e-05      0.56      25      48 ..      64      87 ..      41      98 .. 0.81
   2 ?   -2.7   0.0      0.56     5e+03      43      61 ..     141     158 ..     139     163 .. 0.68
   3 ?   -0.6   0.0      0.13   1.1e+03      42      51 ..     188     197 ..     186     204 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 6.3e-05
                       DUF5488 25 ksmieisrssynvsvivntpiGvi 48
                                  k  ie++rs +nvs+i     G+ 
  gi|13541752|ref|NP_111440.1| 64 KKAIELARSGHNVSIISSGDAGIY 87
                                  789*************98888775 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.56
                       DUF5488  43 tpiGvitnaasmaayvndl 61 
                                   tp  vi   a  aa + dl
  gi|13541752|ref|NP_111440.1| 141 TPWEVIRKRAEAAAIL-DL 158
                                   7888998888877754.44 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.13
                       DUF5488  42 ntpiGvitna 51 
                                   +tp+G++ na
  gi|13541752|ref|NP_111440.1| 188 DTPVGIVRNA 197
                                   69*****998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.34s 00:00:00.89 Elapsed: 00:00:00.53
# Mc/sec: 1423.66
//
Query:       gi|13541753|ref|NP_111441.1|  [L=237]
Description: precorrin isomerase [Thermoplasma volcanium GSS1]
Scores for complete 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-56  189.4   0.2    7.1e-56  189.0   0.2    1.2  1  CbiC         Precorrin-8X methylmutase
  ------ inclusion threshold ------
       0.16   12.1   0.1        1.2    9.3   0.0    2.6  3  Lambda_CIII  Lambda Phage CIII


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 !  189.0   0.2   7.9e-60   7.1e-56       1     193 [.      40     231 ..      40     234 .. 0.96

  Alignments for each domain:
  == domain 1  score: 189.0 bits;  conditional E-value: 7.9e-60
                                   HHHHHHHHHHHCHC-TT.S-CHHHHHHHHHHHHHT-CCHHHHEEE-TTHHHHHHHHHHCT-EEEESSHHHHCCS-HHHHHT CS
                          CbiC   1 eIeaeSfaiideelgeeelseeeeevvrRvihatadfelaellrfspdaveaglealkagapivtDvemvkaGitkkrlek 81 
                                   +Ie+eS++ii+   + +  +++e+ + ++++ha++df l +l+r+sp++v++ +e l++g++iv+D++mvkaGi +k l  
  gi|13541753|ref|NP_111441.1|  40 KIEEESINIIETVTE-SIENARERYLFSKIVHAAGDFRLIDLIRMSPGFVDTVAEKLRDGCRIVVDAKMVKAGIYNKNLLD 119
                                   59********99886.557889999*************************************************9999888 PP

                                   TC-EEEECTC-HHHHHHHHHHTS-HHHHHHHHHHH.CTTTCEEEESS-HHHHHHHHHHHHHS..HTSEEEE----SCCHHH CS
                          CbiC  82 lgnevlclladpevaelakekgitrsaaamekaae.elegaivviGnAPtALlellelieegkvkpalvigvPvGFvgaae 161
                                    +++++ + +d++v +++k+ git+sa am+ a e   ++ai+viGnAPtAL+ell++++++k kp +vigvPvGFv+aa 
  gi|13541753|ref|NP_111441.1| 120 -RCRIMYYGDDERVDRISKQMGITKSASAMRIASEdGVRDAIFVIGNAPTALIELLNIVRDTKEKPPAVIGVPVGFVQAAR 199
                                   .7********************************98899****************************************** PP

                                   HHHHHHCSSS-EEEESSS---HHHHHHHHHHH CS
                          CbiC 162 sKealaesevpyitveGrkGGsavAaaivnaL 193
                                   +K  l +s+++y+t+ G++GGs++Aa+++na 
  gi|13541753|ref|NP_111441.1| 200 AKYSLVSSGIDYLTILGSRGGSPIAASVINAF 231
                                   ******************************95 PP

>> Lambda_CIII  Lambda Phage CIII
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0   0.00013       1.2      19      34 ..      89     104 ..      84     105 .. 0.87
   2 ?   -3.8   0.0       1.6   1.4e+04      10      20 ..     110     120 ..     109     121 .. 0.77
   3 ?   -3.1   0.2      0.94   8.4e+03      32      37 ..     170     175 ..     169     175 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00013
                   Lambda_CIII  19 dRitrklRegwkrlid 34 
                                   d +++klR+g++ ++d
  gi|13541753|ref|NP_111441.1|  89 DTVAEKLRDGCRIVVD 104
                                   789*********8887 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 1.6
                   Lambda_CIII  10 aGvpqESlLdR 20 
                                   aG+ +  lLdR
  gi|13541753|ref|NP_111441.1| 110 AGIYNKNLLDR 120
                                   67777889998 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 0.94
                   Lambda_CIII  32 lidiLN 37 
                                   li++LN
  gi|13541753|ref|NP_111441.1| 170 LIELLN 175
                                   8****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       591  (0.0329634); expected 358.6 (0.02)
Passed bias filter:                      520  (0.0290033); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 1504.11
//
Query:       gi|13541754|ref|NP_111442.1|  [L=252]
Description: uroporphyrinogen-III methylase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.5e-30  105.2   0.0    5.3e-30  104.9   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 !  104.9   0.0     3e-34   5.3e-30       1     204 [.       3     205 ..       3     212 .. 0.81

  Alignments for each domain:
  == domain 1  score: 104.9 bits;  conditional E-value: 3e-34
                  TP_methylase   1 klylVGvGpGdpellTvrAlralktadvvlgddsraleilldllaeeleleapmgke.kepleeayeeiaealaealragk 80 
                                   k+y+VG+GpG p+l+Tv +l+a+++++vv+ d+ ++++ l ++ + ++ ++ + g++   +++ + + i   ++e +++  
  gi|13541754|ref|NP_111442.1|   3 KFYIVGAGPGEPDLITVMGLEAIRESQVVFKDA-LVSDDLIEKYCTNK-VQVNVGHRqGTSSDVGLKIILNYIKENANNFD 81 
                                   79****************************999.76655555555443.44444444034455557777778888888888 PP

                  TP_methylase  81 dVvllvsGDPlvygtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvl......lpglakeeerele 155
                                    +v+l+sGDP ++++ se+++a++    g++v v+PG++s+  ++++ gipl+ +++++++        +  +k +++ l 
  gi|13541754|ref|NP_111442.1|  82 VAVHLKSGDPGIFSRLSEEIRAVST--LGFDVIVVPGITSAIGVPTFYGIPLSVKDVSRHIAivtasiSE--GKFNASSLG 158
                                   8999*********************..********************************999*9985433..467899999 PP

                  TP_methylase 156 allangdtlvllkaprklaelaelLkealyddttpvavveragtederv 204
                                   ++l+ +d +v+l++ r l+++a+ L+++      ++ +ve+++++  ++
  gi|13541754|ref|NP_111442.1| 159 DALKYADVVVVLMGSRFLKQIAR-LSQS-ILGHSDMLIVENGTLPSAKI 205
                                   99999*******99995555554.4455.244568********997665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.56
# Mc/sec: 1360.66
//
Query:       gi|13541755|ref|NP_111443.1|  [L=214]
Description: siroheme synthase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.5e-09   34.7   0.2    2.1e-08   33.5   0.2    1.7  1  Sirohm_synth_M  Sirohaem biosynthesis protein central
    0.00071   20.0   0.0     0.0027   18.1   0.0    1.8  2  NAD_binding_7   Putative NAD(P)-binding


Domain annotation for each model (and alignments):
>> Sirohm_synth_M  Sirohaem biosynthesis protein central
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.5   0.2   2.3e-12   2.1e-08       2      27 ..     115     140 ..     115     141 .. 0.96

  Alignments for each domain:
  == domain 1  score: 33.5 bits;  conditional E-value: 2.3e-12
                Sirohm_synth_M   2 GpLQIaiSTnGksPrLAaliRreier 27 
                                   Gp++Ia+ST GksP+++ +++++i++
  gi|13541755|ref|NP_111443.1| 115 GPIKIAVSTSGKSPAMTVMVKKRIAA 140
                                   9***********************97 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   3.1e-07    0.0027       4     100 ..       6     106 ..       3     110 .. 0.81
   2 ?   -0.8   0.0      0.23     2e+03      78      92 ..     156     170 ..     121     187 .. 0.55

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 3.1e-07
                 NAD_binding_7   4 dlkgkkvlvvGgGevAarkvrklleagakvtvvapevkeeleelvklaeeelekd...legad..lviaatddrelneria 79 
                                   +l++ + l +G G+    k++   ++  +v v++ ev  e  + +++++  +e++   +e ++  l+++ t+dr+l +++a
  gi|13541755|ref|NP_111443.1|   6 RLSKSTSLFIGHGKEFRDKFELYHSEFGTVYVISDEVLLEDANVIRVSS-SFEDSydaIESVKpfLAFISTEDRDLDTKLA 85 
                                   6788889999999999999999999999********8777667777654.355541224443355**************** PP

                 NAD_binding_7  80 eaakarrilvnvadkpelcdf 100
                                   + a++  +lv v d+ +l d+
  gi|13541755|ref|NP_111443.1|  86 YFARRHSKLVYVPDRNDLNDI 106
                                   ***************999887 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.23
                 NAD_binding_7  78 iaeaakarrilvnva 92 
                                   + + a++r++ +  +
  gi|13541755|ref|NP_111443.1| 156 VEAIARNREKIISSV 170
                                   222223333444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 1332.34
//
Query:       gi|13541756|ref|NP_111444.1|  [L=110]
Description: hypothetical protein TVN0925 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.21   11.6   0.1       0.33   11.0   0.1    1.2  1  DUF4245   Protein of unknown function (DUF4245)


Domain annotation for each model (and alignments):
>> DUF4245  Protein of unknown function (DUF4245)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   1.8e-05      0.33       9      39 ..       6      34 ..       3      40 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 1.8e-05
                       DUF4245  9 mvlSlavlvavvlvlvgltgrcsfnpgqvpe 39
                                  ++lS+++lvavvl++ g+++  s +p  v+e
  gi|13541756|ref|NP_111444.1|  6 LFLSILALVAVVLLVYGMIPPISSTP--VSE 34
                                  79*******************99999..655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       641  (0.0357521); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.32s 00:00:00.80 Elapsed: 00:00:00.50
# Mc/sec: 655.54
//
Query:       gi|13541757|ref|NP_111445.1|  [L=195]
Description: aspartokinase beta subunit [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.017   15.4   0.1       0.03   14.6   0.1    1.4  1  Peptidase_M3_N  Oligopeptidase F
      0.061   13.1   0.7       0.73    9.7   0.1    2.2  2  ACT_7           ACT domain
       0.13   12.7   0.1       0.22   12.0   0.1    1.3  1  Lipid_bd        Lipid-binding putative hydrolase


Domain annotation for each model (and alignments):
>> Peptidase_M3_N  Oligopeptidase F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1     5e-06      0.03       9      42 ..      56      88 ..      54      98 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 5e-06
                Peptidase_M3_N  9 kleellkeepelaeyrfyleeilrqkphtLseee 42
                                   l++ll++   +++yr+y +++lr+ + +L +++
  gi|13541757|ref|NP_111445.1| 56 SLQKLLQQ-AGFKDYRKYTDDLLRKSKIVLQDKV 88
                                  689****8.*********************9985 PP

>> ACT_7  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.1     0.034     2e+02      28      49 ..      89     111 ..      85     123 .. 0.82
   2 ?    9.7   0.1   0.00012      0.73       2      55 ..     129     183 ..     128     193 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.034
                                   HHHHHTTT---EEEE.-SS-EEE CS
                         ACT_7  28 aspLaeagIsifqiS.tyrtdyi 49 
                                   +   +++++ + ++S t+ td++
  gi|13541757|ref|NP_111445.1|  89 TVITSRHKVDVDYLSaTFLTDSV 111
                                   556689999************98 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00012
                                   EEEEEEEEEE-S-.---SS--HHHHHHHHHHTTT---EEEE..-SS-EEEEEEGGG CS
                         ACT_7   2 sedgwiklsvvgsglpfdvtGivaklaspLaeagIsifqiS..tyrtdyiLVpeed 55 
                                   ++++++ + + ++   ++++G++  +++     gI+i q+   +  t+++L + ed
  gi|13541757|ref|NP_111445.1| 129 VQRDVSLIHIFSPPEIVSTPGFALNVVERVYSMGINIIQLIscSNETMIVL-KRED 183
                                   677888888888866677*********************988555555555.5554 PP

>> Lipid_bd  Lipid-binding putative hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   3.7e-05      0.22      15      57 ..      79     122 ..      72     133 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.7e-05
                                   SSEEEEE-TTSSS--EEEEEEETTTTEEE-SSEEE.SSSSE... CS
                      Lipid_bd  15 adkmwlddkgnfwevkvkvnvdvesltFsgeeven.vaydsgat 57 
                                   ++k+ l+dk++    + kv+vd+ s tF +++v   +    ++t
  gi|13541757|ref|NP_111445.1|  79 KSKIVLQDKVTVITSRHKVDVDYLSATFLTDSVVYiIDESRTKT 122
                                   78999*************************99888333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       634  (0.0353617); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 1291.33
//
Query:       gi|13541758|ref|NP_111446.1|  [L=397]
Description: argininosuccinate synthase [Thermoplasma volcanium GSS1]
Scores for complete 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-125  418.1   0.0   4.9e-125  417.8   0.0    1.0  1  Arginosuc_synth  Arginosuccinate synthase
     0.0099   15.5   0.0      0.014   15.0   0.0    1.2  1  ThiI             Thiamine biosynthesis protein (ThiI)
  ------ inclusion threshold ------
      0.011   15.2   0.0       0.02   14.4   0.0    1.5  1  QueC             Queuosine biosynthesis protein QueC
        0.2   11.3   0.0       0.29   10.8   0.0    1.2  1  Asn_synthase     Asparagine synthase


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 !  417.8   0.0  1.1e-128  4.9e-125       2     380 ..       6     377 ..       5     383 .. 0.98

  Alignments for each domain:
  == domain 1  score: 417.8 bits;  conditional E-value: 1.1e-128
               Arginosuc_synth   2 LaysGGlDtsviikllkeklgeeviavavdvGqeeedldevkekalklgavksvvvDakeefvedyifpaikanalYedrY 82 
                                   L ysGGlDtsv+ik+++e+lg++v ++++d+G++  dl++++eka+++gav+++v D+ +ef  +yi ++i an+ Ye+ Y
  gi|13541758|ref|NP_111446.1|   6 LLYSGGLDTSVMIKWMNENLGYDVSTLTLDIGNN--DLKSIREKAEAIGAVETFVEDVXQEFSYEYISKSILANGSYEG-Y 83 
                                   78******************************99..*******************************************.* PP

               Arginosuc_synth  83 llgtalaRPliakklvevakkegaeavahGctGkGnDqvRfevsirslaPdlkviaPvReleltReeeieyakekgipvev 163
                                   +l+talaRPl+akk ve+a+k+g ea+ahG+tG+GnDqvRfe++i++l+P l+++aPvR++++ R+eeieyak+++i v++
  gi|13541758|ref|NP_111446.1|  84 PLSTALARPLMAKKAVELAEKHGFEAIAHGSTGRGNDQVRFELGIKALNPSLEMLAPVRDWNMLRSEEIEYAKKNNIIVPS 164
                                   ********************************************************************************9 PP

               Arginosuc_synth 164 tkkkpysiDenllgrsieagiLedpknappediyeltkdpakapdepeeveiefekGvPvaldgeelsvlelieklneiag 244
                                   +    ys+Denl+grsie++ +e+++   ped+ye+  +p +a    e++++ef +G+Pva++++ ++  +li +ln i+g
  gi|13541758|ref|NP_111446.1| 165 D--GKYSVDENLWGRSIEGSEIENMSLPVPEDAYEWLVPPWEAG-PGEVIKLEFSNGLPVAINDSDFELQNLIANLNIIGG 242
                                   8..66***********************************9998.899********************************* PP

               Arginosuc_synth 245 khGvGRiDivedRlvglksReiYeapaalvLikahkdlekltlerevakfkkiveekyaelvYkGlwfsPlkealdafiek 325
                                   ++ +G iD+vedR+ g+ksRe+Ye+paa ++  ah  le+l+l++++  +k+++++k+++ vY+Glw++P ++ l a  e 
  gi|13541758|ref|NP_111446.1| 243 RNSIGLIDHVEDRITGIKSREVYECPAAEIITYAHGYLESLILNKHEISIKSFLDSKFSQFVYNGLWYDPAMKPLIAGEEI 323
                                   ********************************************************************************* PP

               Arginosuc_synth 326 tqervtGtvrvklfkGsvvvlgReseeslYdeelasydeedefdqkeaeGfikih 380
                                    + +++G++ +kl+kG+++ +g + ++  Y++++a y  + efdqk+ +Gfi+i+
  gi|13541758|ref|NP_111446.1| 324 LNSEINGSISLKLYKGKIYFNGSKGANFSYNSNVANYS-TYEFDQKSSKGFIDIF 377
                                   *************************************9.999**********986 PP

>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   3.2e-06     0.014       6     116 ..       4     114 ..       1     122 [. 0.85

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.2e-06
                          ThiI   6 vlaLlSgGiDSpVa.aylllkRGcrvvlvhlknepgtseeaiekveklaellaeyqtslevklvvvdfkevlkeilekv.k 84 
                                    l+L SgG+D  V   ++  + G  v +++l+     +++  + +++ ae +   +t +e     ++++ + k+il +   
  gi|13541758|ref|NP_111446.1|   4 LLLLYSGGLDTSVMiKWMNENLGYDVSTLTLD----IGNNDLKSIREKAEAIGAVETFVEDVXQEFSYEYISKSILANGsY 80 
                                   58899*****999725666788*********7....677788999999999999999999999***********9876535 PP

                          ThiI  85 ekl..tivllkrkmlriAekvaeeegakalvtGe 116
                                   e++   + l +  m + A ++ae++g +a+  G+
  gi|13541758|ref|NP_111446.1|  81 EGYplSTALARPLMAKKAVELAEKHGFEAIAHGS 114
                                   55422789**********************9997 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   4.6e-06      0.02       3      51 ..       5      55 ..       3     116 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.6e-06
                                  EEE--SSHHHHHHHHHHHHH.-SEEEEEEEESS-T.TSHHHHHHHHHHHHT CS
                          QueC  3 vvllSGGlDSttvlalakke.gkevealtfdYgqr.hkkeleaakkiakel 51
                                  ++l SGGlD ++++ +++++ g+ v +lt+d g++  k+  e+a++i +  
  gi|13541758|ref|NP_111446.1|  5 LLLYSGGLDTSVMIKWMNENlGYDVSTLTLDIGNNdLKSIREKAEAIGAVE 55
                                  6799*********999987636***********993344444444443333 PP

>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   6.4e-05      0.29      22      77 ..       6      58 ..       2      94 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 6.4e-05
                  Asn_synthase 22 alLSGGlDSSliaalaarqsksplktFsigfeekgsdeakyakevaehlgtehtel 77
                                  +l SGGlD S+    +++ +  ++ t +++    g++++k  +e ae++g   t +
  gi|13541758|ref|NP_111446.1|  6 LLYSGGLDTSVMIKWMNENLGYDVSTLTLDI---GNNDLKSIREKAEAIGAVETFV 58
                                  566****************************...***************9876654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (397 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       450  (0.025099); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.49
# Mc/sec: 2444.53
//
Query:       gi|13541759|ref|NP_111447.1|  [L=437]
Description: argininosuccinate lyase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.9e-23   82.7   0.0    3.9e-23   82.3   0.0    1.1  1  Lyase_1          Lyase
  ------ inclusion threshold ------
       0.13   12.1   0.0       0.29   11.0   0.0    1.6  1  Acetyltransf_18  Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> Lyase_1  Lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.3   0.0   4.3e-27   3.9e-23      20     310 ..      27     292 ..      12     294 .. 0.86

  Alignments for each domain:
  == domain 1  score: 82.3 bits;  conditional E-value: 4.3e-27
                                   HHGGGHHHHHCHHHHHHHHHHHTTSSTHHHHHHHHHHHHHHHCHCHHCGGHHHBSSSSSHHHHHHHHHHHHHHHHTTHSSG CS
                       Lyase_1  20 enfrlseedikalaalkkaaakanvdlkeeaaaiikaldevleegklddqfvlkviqegsgtavnmnlnevigellgekve 100
                                    +  l++++i  l+a+   + k +++ +e  +  ++al +  e g    ++ ++v +e+ +ta++  ++ +         +
  gi|13541759|ref|NP_111447.1|  27 ADTILEKYEIINLMAYHYELIKIGIINEEDGKCLLNALIKAYE-G----KITIDVKDEDVHTAIENWVKGLCP-------K 95 
                                   5666677777778888888888888887777777777777777.4....566*************97776666.......8 PP

                                   IIIIITTT--HHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHTTT-EEEEEETTEEEEEEEHHHHHHHHHHHHHH CS
                       Lyase_1 101 pndkvhtgqSsnDqvpTalrlalkkalsekLlpaleqLidalkekakefkdvvkiGrThlqdAtPvtlgqelsayaealer 181
                                     + +    S+n+qv  ++ l l ++ ++      + +++ ++++   + +  ++G+Th q+A+P t+  ++ ++   ler
  gi|13541759|ref|NP_111447.1|  96 NWENLRLFLSRNEQVHADMILYLLDSFYK----MNKIFQSCIEKTIGVNGEGYLPGYTHFQQAMPFTFKSFMNSVLLLLER 172
                                   8899999********************54....67778899999999999******************************* PP

                                   HHHHHHHHHHHHTCEETTTTTTTSSTTTSCCTHHHHHHHHHHHHHCST.EESSSHHHHHHC-HHHHHHHHHHHHHHHHHHH CS
                       Lyase_1 182 drerlkellkrllvellgggtavgtglnadpefaelvakelakvtglp.vkapnsfeavsdrDavvellgalkllatsLsk 261
                                   ++ ++ +  ++++  + g g++ g ++ a+     ++ + l    gl    ++++f +      ++e+++ + ++++ Ls+
  gi|13541759|ref|NP_111447.1| 173 NILNVHDFFQKIRINVYGYGSGYGSPISAKFD---KMGELL----GLRyDHKNPIFLSSLYPQTLLEASQLIVTIMMPLSR 246
                                   ***************************99998...444444....5666777778877777889***************** PP

                                   HHHHHHHHTSTTTSSEEEEGCCTSSC-TTSTTTEBTHHHHHHHHHHHHH CS
                       Lyase_1 262 faeDlrllssgeaglvelslaesepGSSiMPgKvNPvqlElltgvagrv 310
                                   ++ D + + s   g++ + +  ++ GSS+MP K+NP+ lE+++g a+  
  gi|13541759|ref|NP_111447.1| 247 LSSDTINYYS--RGIMDIPDEFTT-GSSLMPNKRNPDYLEMIQGLAAES 292
                                   **********..9***********.*******************99865 PP

>> Acetyltransf_18  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   3.3e-05      0.29      59      93 ..      53      88 ..      49     105 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 3.3e-05
               Acetyltransf_18 59 neeiAeaLlkalvanaegkkvridvpee..nkaliel 93
                                  nee  ++Ll+al++ +egk ++idv++e  ++a++++
  gi|13541759|ref|NP_111447.1| 53 NEEDGKCLLNALIKAYEGK-ITIDVKDEdvHTAIENW 88
                                  78999*************9.******98444445555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (437 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); 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: 0.62u 0.26s 00:00:00.88 Elapsed: 00:00:00.50
# Mc/sec: 2647.44
//
Query:       gi|13541760|ref|NP_111448.1|  [L=282]
Description: gluconolactonase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-66  224.9   0.1    1.3e-66  224.7   0.1    1.0  1  SGL           SMP-30/Gluconolactonase/LRE-like region
     0.0024   17.8   0.5        1.1    9.3   0.0    3.6  3  SBBP          Beta-propeller repeat
     0.0051   17.0   0.0       0.55   10.5   0.0    2.9  3  Arylesterase  Arylesterase


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 !  224.7   0.1   2.1e-70   1.3e-66       1     245 [.      13     252 ..      13     253 .. 0.97

  Alignments for each domain:
  == domain 1  score: 224.7 bits;  conditional E-value: 2.1e-70
                           SGL   1 lgEGpvwdeeegaLlwvDilgqrihrldpatgketvldtpesvGaiaprkdgrlvvasksglalldlasgeletladeeed 81 
                                   lgEGp++d ++++++w+Di+g++ h ld+++g+   ++  +++++i+p++ + + ++  +g++ +d ++ + + l++   d
  gi|13541760|ref|NP_111448.1|  13 LGEGPTYDSKRNRVYWIDITGKKFHYLDLNDGSIYNFESVGMISSIVPTNIDLMAATIGHGFYSID-DQANHTLLFELK-D 91 
                                   79**********************************************555**************9.677899999995.6 PP

                           SGL  82 ekpllrfNDgvvdpdGrlwfGtmgdeeakgeevgalyrldpdgklervlddltipNGlawspdgktlYlaDsltrkiwayd 162
                                   e  ++rfNDg++dp+Gr+++Gtm+ +e+++   g+ly+++++  ++r+l++lti+NG+aw+   + +Y++D++trk+ ay+
  gi|13541760|ref|NP_111448.1|  92 ESNETRFNDGKADPEGRYVAGTMDLKESRPI--GSLYVFNGK-GVRRLLSNLTISNGIAWDTRRRIFYHIDTPTRKVRAYS 169
                                   66*****************************..********9.9************************************* PP

                           SGL 163 vdaeggklsnrrvfadlkkgegepDGlavDaeGnvwvAvwgggkvvrfdpd.GklieeiklpakrvtscaFgGpdlrtLyi 242
                                   +dae + + +++  +d+k+++g pDG+++D++Gn++vA+wgg+k++++dp+  + i+e++lpak++ts +F+G+ l+tLy+
  gi|13541760|ref|NP_111448.1| 170 FDAEMN-IISKDIAVDFKEEQGSPDGMTIDSDGNLFVAHWGGSKLSVWDPErKRKIDEYDLPAKNITSAVFAGKGLNTLYV 249
                                   ***999.8889999*************************************999*************************** PP

                           SGL 243 tsa 245
                                   +sa
  gi|13541760|ref|NP_111448.1| 250 SSA 252
                                   *98 PP

>> SBBP  Beta-propeller repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0      0.01        63      10      27 ..     138     155 ..     136     156 .. 0.89
   2 ?   -0.4   0.0      0.19   1.2e+03      13      22 ..     176     185 ..     174     186 .. 0.83
   3 !    9.3   0.0   0.00018       1.1      17      29 ..     194     206 ..     191     206 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.01
                          SBBP  10 gastygngIavDsnGNiY 27 
                                   ++ t+ ngIa D+   i+
  gi|13541760|ref|NP_111448.1| 138 SNLTISNGIAWDTRRRIF 155
                                   68899********99997 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.19
                          SBBP  13 tygngIavDs 22 
                                   ++ ++IavD 
  gi|13541760|ref|NP_111448.1| 176 IISKDIAVDF 185
                                   6789*****5 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.00018
                          SBBP  17 gIavDsnGNiYvt 29 
                                   g+++Ds+GN +v+
  gi|13541760|ref|NP_111448.1| 194 GMTIDSDGNLFVA 206
                                   99*********97 PP

>> Arylesterase  Arylesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0      0.02   1.2e+02      57      82 ..      15      40 ..       2      43 .. 0.84
   2 !   10.5   0.0   9.2e-05      0.55      36      78 ..     123     165 ..     111     173 .. 0.84
   3 ?   -1.7   0.0      0.56   3.4e+03      55      71 ..     191     206 ..     185     209 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.02
                  Arylesterase 57 nGInidadkkyiyvadilresihvmk 82
                                   G ++d+++  +y  di+ ++ h ++
  gi|13541760|ref|NP_111448.1| 15 EGPTYDSKRNRVYWIDITGKKFHYLD 40
                                  6889****************999875 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 9.2e-05
                  Arylesterase  36 tavvYyspsevkvvasglssanGInidadkkyiyvadilresi 78 
                                   ++ + ++++ v+   s l+ +nGI  d+ +++ y  d   +++
  gi|13541760|ref|NP_111448.1| 123 GSLYVFNGKGVRRLLSNLTISNGIAWDTRRRIFYHIDTPTRKV 165
                                   5667799**************************9777655555 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.56
                  Arylesterase  55 sanGInidadkkyiyva 71 
                                   s+ G++id+d   ++va
  gi|13541760|ref|NP_111448.1| 191 SPDGMTIDSDGN-LFVA 206
                                   899*****9975.5565 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       305  (0.0170115); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.48
# Mc/sec: 1776.73
//
Query:       gi|13541761|ref|NP_111449.1|  [L=312]
Description: Zn-dependent hydrolase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.5e-26   92.9   0.6    2.6e-25   89.6   0.6    2.0  1  Lactamase_B    Metallo-beta-lactamase superfamily
    9.6e-07   28.5   0.1    1.8e-06   27.6   0.1    1.5  1  Lactamase_B_2  Beta-lactamase superfamily domain
    0.00054   19.4   0.0    0.00093   18.7   0.0    1.3  1  Lactamase_B_6  Metallo-beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.6   0.6   4.4e-29   2.6e-25       5     197 .]      19     219 ..      15     219 .. 0.93

  Alignments for each domain:
  == domain 1  score: 89.6 bits;  conditional E-value: 4.4e-29
                                   SSEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCHCH CS
                   Lactamase_B   5 pvnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalfme 85 
                                    +n+y +  d+g iLiDtG+s++  ++      + ++ +d+ av+lTHlH+DH+Gg+  + e+ +vpv++++++    +  
  gi|13541761|ref|NP_111449.1|  19 TANIYRVPSDKGYILIDTGMSGDSVDQ------IVKESNDIQAVFLTHLHIDHVGGALRIHEELGVPVYMNSKDINLIRQV 93 
                                   57999999******************9......8*****************************************999999 PP

                                   HHHHHHHHCCHH....................TTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEE CS
                   Lactamase_B  86 eaddaasrkgll....................lagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvl 146
                                   + d++a  k+                      + +            +d+  +  ++l++++ pgh++g+  v  ++g + 
  gi|13541761|ref|NP_111449.1|  94 ANDKEAYIKKYVdifrgngvplsmqedlihmhPVINFYEYYSKLGFLQDISNLKLKELKFVPVPGHSPGSTAVITEDGYMM 174
                                   998877777777************99999998666666666677777888888999************************* PP

                                   EECTTTSSHHCCCCCC.TTCEEE-SHCHHHHHHHHHHHHHHHCHSEEEESS CS
                   Lactamase_B 147 ftGDallagetgridltlrgaevrdpsdaekyldsllklaglkaevlvpgH 197
                                   f+GD +l++ t+ i+        +  +d ++yl+sl+ +++l +++++pgH
  gi|13541761|ref|NP_111449.1| 175 FSGDHILERITPNISV------YGEEDDLGNYLKSLELVKKLSPKIIFPGH 219
                                   ****************......999************************** 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 !   27.6   0.1     3e-10   1.8e-06       3      64 ..      32      84 ..      31     128 .. 0.76

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 3e-10
                                  EEES--TTHHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEH CS
                 Lactamase_B_2  3 iLiDagpdlrqqalralqPvelrdelppidaVllthaHyDHlaglltlrelrpkklplyapk 64
                                  iLiD+g +  +   +     + ++e ++i+aV+lth H+DH+ g+l + e  +  +p+y + 
  gi|13541761|ref|NP_111449.1| 32 ILIDTGMS--GD--SVD---QIVKESNDIQAVFLTHLHIDHVGGALRIHEELG--VPVYMNS 84
                                  78888888..22..111...1245568*****************999999333..7888554 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 !   18.7   0.0   1.5e-07   0.00093       5     145 ..      28     164 ..      25     171 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.5e-07
                 Lactamase_B_6   5 dnvkiLlDvGwdeskvslesalkelekviptvdliLLshatlehlGayallyakfksklllnipvyatlpvvkLGrvsl.. 83 
                                   d+  iL+D G+++ +      ++++ k  ++++++ L+h  ++h+G+   l ++  ++  l +pvy +   ++L r +   
  gi|13541761|ref|NP_111449.1|  28 DKGYILIDTGMSGDS------VDQIVKESNDIQAVFLTHLHIDHVGGA--LRIH--EE--LGVPVYMNSKDINLIRQVAnd 96 
                                   6778********973......4566777889***************94..3332..33..569****99999999988867 PP

                 Lactamase_B_6  84 ........ldlyaskgllgpedseeleledideafdkiktlkYsQklelkskldgltitaynaGhtlGGt 145
                                           +d ++ +g+  +++++ ++++ + + ++  ++l + Q ++   kl++l +++   Gh++G t
  gi|13541761|ref|NP_111449.1|  97 keayikkyVDIFRGNGVPLSMQEDLIHMHPVINFYEYYSKLGFLQDISNL-KLKELKFVPVP-GHSPGST 164
                                   77777666677777888888888889999999999999999999987544.57888888874.8888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       598  (0.0333538); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 1897.16
//
Query:       gi|13541762|ref|NP_111450.1|  [L=426]
Description: tryptophan synthase subunit beta [Thermoplasma volcanium GSS1]
Scores for complete 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  132.7   0.0    2.1e-38  132.4   0.0    1.1  1  PALP      Pyridoxal-phosphate dependent enzyme


Domain annotation for each model (and alignments):
>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.4   0.0   1.2e-42   2.1e-38       3     294 .]      71     410 ..      69     410 .. 0.77

  Alignments for each domain:
  == domain 1  score: 132.4 bits;  conditional E-value: 1.2e-42
                                   GCSSS--EEEECCTCCCCCCE..EEEEEGGGSTTSBTTHHHHHHHHHHHHTTTTTSEEEEEBSSHHHHHHHHHHHHHT-EE CS
                          PALP   3 lgigpTPlvrlprlskelgvp..lflKlEslnptgSfKdRgaeyllarlkegtgaktvveassGNhgralAaaaallGlkv 81 
                                   ++ +pTP++r+++l++ lg++  ++lK+Es + +gS+K++ a   +  +k+ +++ + +e+++G++g a+A+a+al+G+++
  gi|13541762|ref|NP_111450.1|  71 QVGRPTPIIRAKNLEEFLGGNikIYLKMESYTYSGSHKINSALAHVFFAKQDNAKFVSTETGAGQWGSAVALASALFGVDS 151
                                   5789************************************************89999999999****************** PP

                                   EEEEETTS-...HHHHHHHHHTT-EEEEE..................CCHHHHHHHHHHHHHHHSTTCEE--TTTSHHHHH CS
                          PALP  82 tivvpadas...pekvallrllGaevvev..................ggdydeavaaaaelaaegegaylvsqfdnptvie 141
                                   +i++ +++    p+++ ++ ++Ga+ + +                  +g+   a + a  +a +++g y++ +  n+++  
  gi|13541762|ref|NP_111450.1| 152 HIFMVRTSFyakPYRKYMMYMYGAHPHPSpsefteygkevlkknpdtPGSLGLAISEAIHYALDNGGKYIAGSVINSDILF 232
                                   ***9999888889****************4444444444443333333333333333334444455555555555666555 PP

                                   HHHTHHHHHH...HHTTTTEEEEEEE-SSSHHHHHHHHHHHH...HSTT..-EEEEEEECTTCGGTTCC......S..S.S CS
                          PALP 142 gygtiglEil...eqlggkpdavvvpvGgGgliaGiaaglke...rrpd..vrvigvepegsdalarsl......ragrrv 208
                                     + +g+E +   e  g++pd+vv  vGgG++ a++a+++ +   + ++   + i+  ++++++++++       ++    
  gi|13541762|ref|NP_111450.1| 233 -KTIAGMEAKkqmEMAGEDPDYVVGVVGGGSNYAALAFPFLAdelQSGKvkRTYIASGSKEVPKMTEGEyrydypDT---- 308
                                   .6667899984555566*************************98855553233444455699999999954444444.... PP

                                   S..B...................SSS.CCSTCSCGTTCCHHHHSEEEEEEEEEEHHHHHHHHHHHHHHHSB-B-HHHHHHH CS
                          PALP 209 tvpvs..................dtiadglavgspselafelldrlvdeivtvsdeealeamrllarregivvepssaaal 271
                                       +                     a gl+ +++++    l+ + + ++   ++eea++++r + ++eg+++ p + +al
  gi|13541762|ref|NP_111450.1| 309 ----GkvlpllkmytigydfippAVYAGGLRYHAVAPTLSLLMNKGIVQARDYDQEEAFKWARIFSEKEGYIPAPETSHAL 385
                                   ....244466666*****777777777777777777777778899999********************************* PP

                                   HHH...HHHHHHCCTTCEEEEEEE-B CS
                          PALP 272 aal...klreagelkegdrvvviltg 294
                                     l      ++ge ++ ++v+v ++g
  gi|13541762|ref|NP_111450.1| 386 PILkeiADSNRGEREK-KTVLVSFSG 410
                                   ***9644444444444.477777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (426 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       441  (0.024597); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); 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: 0.58u 0.35s 00:00:00.93 Elapsed: 00:00:00.51
# Mc/sec: 2504.55
//
Query:       gi|13541763|ref|NP_111451.1|  [L=571]
Description: Fe-S oxidoreductase [Thermoplasma volcanium GSS1]
Scores for 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   77.1   0.0    4.1e-21   76.1   0.0    1.6  1  Radical_SAM  Radical SAM superfamily
    5.6e-08   32.9   1.2    5.2e-07   29.8   0.0    3.0  3  Fer4_14      4Fe-4S single cluster domain
    8.5e-06   26.1   0.1    3.3e-05   24.2   0.1    2.1  1  Fer4_12      4Fe-4S single cluster domain
  ------ inclusion threshold ------
      0.018   15.1   0.1      0.043   13.9   0.1    1.6  1  DUF2059      Uncharacterized protein conserved in bacteria (D


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.1   0.0   9.1e-25   4.1e-21       1     166 [.     113     271 ..     113     272 .. 0.93

  Alignments for each domain:
  == domain 1  score: 76.1 bits;  conditional E-value: 9.1e-25
                                   EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHH..HHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelk..aekgvkevilgggepllypdfvellerlaklavpgir 79 
                                   +vvt+ C l C++C ++ +   +++ ++ ++++i   ++++k  +  g++ v ++ggep++++d++++++ ++++     +
  gi|13541763|ref|NP_111451.1| 113 IVVTNRCDLSCWYCFFYAK--ENEPIYEPTQDQIRMMLRRMKneKPVGANAVQITGGEPTMRDDIIDIVRIAREE--GYDH 189
                                   689**************96..*********************845555***************************..9*** PP

                                   EEEEECSSCHG..HHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHH CS
                                   xxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  80 itvetngtlpd..eeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglpGende 158
                                   + + tn ++    ++++++ +e+g ++++ + + ++++      n+ ++f e+ +ale++++a +  vv + +++ G+nd 
  gi|13541763|ref|NP_111451.1| 190 VQLNTNSVRAAfdPDFVRKVREAGSNVIYTSFDGPTPR-----SNP-KNFWEIPDALENYKKAPLG-VVLVPTVIGGVNDM 263
                                   *********88**************************9.....545.7778888*********999.*************9 PP

                                   HHHHHHHH CS
                                   xxxxxxxx RF
                   Radical_SAM 159 eleellel 166
                                    l +++++
  gi|13541763|ref|NP_111451.1| 264 YLGDIIRF 271
                                   99999886 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.36   1.6e+03      12      23 ..      19      30 ..      16      43 .. 0.85
   2 ?   -2.0   0.6      0.83   3.7e+03       8      19 ..      94     105 ..      87     108 .. 0.80
   3 !   29.8   0.0   1.2e-10   5.2e-07       4      92 ..     115     199 ..     113     217 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.36
                       Fer4_14 12 CkgCdnketwks 23
                                  C+gC ++e++++
  gi|13541763|ref|NP_111451.1| 19 CPGCVDEEKFDQ 30
                                  *******99975 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.83
                       Fer4_14   8 CnlsCkgCdnke 19 
                                   C+ +C  C +++
  gi|13541763|ref|NP_111451.1|  94 CPTHCGLCVKHK 105
                                   ********9776 PP

  == domain 3  score: 29.8 bits;  conditional E-value: 1.2e-10
                       Fer4_14   4 rlsgCnlsCkgCdnketwkselgkp.qte.elleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeeypekk 82 
                                    +++C lsC  C+  ++ ++   +p q++ +++ +++  ++++ + ++ + +tGGeP +    ++++++v+  +ee+   +
  gi|13541763|ref|NP_111451.1| 115 VTNRCDLSCWYCFFYAKENEPIYEPtQDQiRMMLRRM--KNEKPVGANAVQITGGEPTMR---DDIIDIVRIAREEG-YDH 189
                                   49***********777777755444033313444555..88888999**********955...99***********9.678 PP

                       Fer4_14  83 iwletngtle 92 
                                   ++l+tn + +
  gi|13541763|ref|NP_111451.1| 190 VQLNTNSVRA 199
                                   9****98765 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.1   7.4e-09   3.3e-05       4      91 ..     108     194 ..      93     222 .. 0.77

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 7.4e-09
                       Fer4_12   4 eGvrlslfvsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesi...egltllGGEPllpenaeallelvkevke 81 
                                   +G+  ++ +++C+lsC +Cf   +++ +   e t++ ++ +++++k+e+    + + ++GGEP +   +++++++v+  +e
  gi|13541763|ref|NP_111451.1| 108 TGLGNIVVTNRCDLSCWYCFF-YAKENEPIYEPTQDQIRMMLRRMKNEKPvgaNAVQITGGEPTM---RDDIIDIVRIARE 184
                                   5666678899**********3.333333333335666667777776655567799**********...99*********** PP

                       Fer4_12  82 ekpekdiwly 91 
                                   e+++ + + +
  gi|13541763|ref|NP_111451.1| 185 EGYDHVQLNT 194
                                   *996444333 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 ?   13.9   0.1   9.7e-06     0.043      13      40 ..     526     553 ..     522     554 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 9.7e-06
                                   HHS-HHHHHHHHHHHHSHHHHHHHHHHH CS
                       DUF2059  13 ktfteaelkailaFYkSPlGkkllekep 40 
                                   ++++ ++ k+i+aFY+  +G+kl+e e+
  gi|13541763|ref|NP_111451.1| 526 REYSMEDKKRIIAFYERSIGRKLTEEEI 553
                                   67888999****************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (571 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       531  (0.0296168); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.68u 0.33s 00:00:01.01 Elapsed: 00:00:00.55
# Mc/sec: 3146.28
//
Query:       gi|13541764|ref|NP_111452.1|  [L=133]
Description: hypothetical protein TVN0933 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.1e-26   91.1   0.1    7.9e-26   90.9   0.1    1.0  1  Archease  Archease protein family (MTH1598/TM1083)


Domain annotation for each model (and alignments):
>> Archease  Archease protein family (MTH1598/TM1083)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.9   0.1   4.4e-30   7.9e-26       1     137 [.       3     132 ..       3     133 .] 0.93

  Alignments for each domain:
  == domain 1  score: 90.9 bits;  conditional E-value: 4.4e-30
                                   EEE---SSEEEEEEE-SSSHHHHHHHHHHHHHHHS--TT---S-EEEEEEEESSSHHHHHHHHHHHHHHHHHT--S----E CS
                      Archease   1 yeyldhtADviieawGksleeafesaalalfeymtdlskvepkeekeieveaedledlLfdfLdellylfdteyfvfkevk 81 
                                   ye+ldh++D++i ++G++ ee+f++a+ a+++++ d+ k+++k++ +  ++++  ed+++++L+ +l+++dt+y+++ ++ 
  gi|13541764|ref|NP_111452.1|   3 YEILDHESDIGIMVYGTTYEELFSNAVYAMADLILDVGKLKEKRKMHEIIRGNTPEDIMVNLLSRVLFYVDTYYTLYFRA- 82 
                                   9******************************************999999************************9999999. PP

                                   EEE.E-SSSEEEEEEEE----.-TT--------B--S---EEEEETTEEEEEEEEE CS
                      Archease  82 vdeeeeeeeleleaeargekfdkekhevqtevKAvTyhelrieeeddgweayvvvD 137
                                      + + e+ +l++ ++g ++ +e+ e+++ +KAvTy+e+ ++ ed    a+v++D
  gi|13541764|ref|NP_111452.1|  83 ---TCKYEDSTLDVYLYGSEI-PEEVEYRNVIKAVTYSEIAVKPED--GFARVIFD 132
                                   ...5566789***********.5557789***************99..67889998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       324  (0.0180713); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 812.08
//
Query:       gi|13541765|ref|NP_111453.1|  [L=151]
Description: transcription regulator [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    9.8e-15   54.3   0.0    1.8e-14   53.5   0.0    1.4  1  PadR         Transcriptional regulator PadR-like family
    5.9e-06   26.9   0.0    8.2e-06   26.4   0.0    1.4  1  RTP          Replication terminator protein
  ------ inclusion threshold ------
      0.019   15.1   0.3      0.037   14.2   0.3    1.5  1  T4_Rnl2_C    T4 RNA ligase 2 C-terminal
      0.026   14.2   0.1        7.5    6.3   0.0    2.4  2  SelB-wing_3  Elongation factor SelB, winged helix
      0.031   14.2   0.0       0.23   11.4   0.0    2.3  1  TrmB         Sugar-specific transcriptional regulator TrmB
      0.062   12.1   0.0      0.071   11.9   0.0    1.2  1  BChl_A       Bacteriochlorophyll A protein
       0.13   12.3   0.0       0.34   10.9   0.0    1.7  1  HTH_45       Winged helix-turn-helix
       0.15   12.1   0.0       0.26   11.3   0.0    1.4  1  BLACT_WH     Beta-lactamase associated winged helix 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 !   53.5   0.0   7.9e-18   1.8e-14       1      73 [.      18      82 ..      18      84 .. 0.95

  Alignments for each domain:
  == domain 1  score: 53.5 bits;  conditional E-value: 7.9e-18
                                  HHHHHCCS-EEHHHHHHHHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCHHH CS
                          PadR  1 iLalleeqpsyGyeiikeleelsegllelseGslYpaLkrLekeglveseweesgegpprkyYrlTdaGrrel 73
                                  iL+l++ +p+ G e+++e+e++s g++++s+Gs+YpaL++Le++glv ++++          Y+ T++G++el
  gi|13541765|ref|NP_111453.1| 18 ILYLVSTKPMNGAEVMDEIERHSFGMWRPSPGSVYPALEQLEADGLVIRNEDGR--------YAATEQGKEEL 82
                                  89*********************************************9998864........99*****9998 PP

>> RTP  Replication terminator protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.0   3.7e-09   8.2e-06       4      68 ..       8      71 ..       4     102 .. 0.88

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 3.7e-09
                                  --HHHHHHHHHHHHHHTT-EBCTCHHHHHHHHHTTTT.----HHHHHHHHHHHHHTTSEEEEEEEB CS
                           RTP  4 lkqrAFlklylitlvekkklyglklldelkkeFkelg.ykPnhseiyralhelvedgilkrrkelk 68
                                  +k+r  lk +++ lv +k++ g +++de+ +  +++g ++P++  +y al++l  dg++ r++  +
  gi|13541765|ref|NP_111453.1|  8 VKRRGNLKYWILYLVSTKPMNGAEVMDEIER--HSFGmWRPSPGSVYPALEQLEADGLVIRNEDGR 71
                                  789999**********************965..47777*********************9987766 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 ?   14.2   0.3   1.6e-05     0.037      18      38 ..     123     143 ..     120     149 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.6e-05
                                   --HHHHHHHHHTSS--STTTH CS
                     T4_Rnl2_C  18 vtenRLnNviSKigeitrknf 38 
                                   ++  RL+Nv+SKi e+  k  
  gi|13541765|ref|NP_111453.1| 123 LNVTRLENVVSKINELISKWS 143
                                   6899***********997755 PP

>> SelB-wing_3  Elongation factor SelB, winged helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0    0.0053        12      32      44 ..       2      14 ..       1      17 [. 0.90
   2 ?    6.3   0.0    0.0034       7.5      27      46 ..      53      72 ..      51      73 .. 0.92

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0053
                                  HHHCTSEEEETTE CS
                   SelB-wing_3 32 fDrigvTrRvgDk 44
                                  fD++ +++R+g+ 
  gi|13541765|ref|NP_111453.1|  2 FDKFNFVKRRGNL 14
                                  9**********97 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0034
                                  HHHHHHHHCTSEEEETTEEE CS
                   SelB-wing_3 27 plLEyfDrigvTrRvgDkRv 46
                                  p LE + + g+++R++D R 
  gi|13541765|ref|NP_111453.1| 53 PALEQLEADGLVIRNEDGRY 72
                                  78***************995 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0    0.0001      0.23      17      58 ..      21      70 ..      17      76 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0001
                                  HHHHCCCHHCHHCCCTTS........SCHCHHHHHHHHHHCTSEEEESST CS
                          TrmB 17 Llklgpatadeiaeelgv........prskvYevLrsLedkGlVerekgr 58
                                  L++ +p++  e+  e+++        +  +vY +L++Le  GlV r++  
  gi|13541765|ref|NP_111453.1| 21 LVSTKPMNGAEVMDEIERhsfgmwrpSPGSVYPALEQLEADGLVIRNEDG 70
                                  666666666666666665222222223469***************99865 PP

>> BChl_A  Bacteriochlorophyll A protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   3.2e-05     0.071     162     227 ..      41     107 ..      28     143 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.2e-05
                        BChl_A 162 fndyirdvwliGpaftaleegGqslsnievasigteeGgekarvgvsdfrfs...hggsGivdsisrwl 227
                                   f+ +      + pa + le  G  + n +  + +te+G  k ++g+++  fs   ++ sGivd i   +
  gi|13541765|ref|NP_111453.1|  41 FGMWRPSPGSVYPALEQLEADGLVIRNEDGRYAATEQG--KEELGITSAEFSrspKTVSGIVDEIESMV 107
                                   5555555556789999**********************..5556666666652125789****997543 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00015      0.34      40      66 ..      55      82 ..      50      88 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00015
                        HTH_45 40 LdmLvekgli.kkskekYvlTekGlell 66
                                  L++L   gl+ +++++ Y  Te+G+e l
  gi|13541765|ref|NP_111453.1| 55 LEQLEADGLViRNEDGRYAATEQGKEEL 82
                                  899******6699***********9865 PP

>> BLACT_WH  Beta-lactamase associated winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00012      0.26      18      45 ..      44      70 ..      42      74 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00012
                      BLACT_WH 18 hpaAergvlahLeKLeeeGkVkregdkg 45
                                  +++   +v+  Le Le++G+V r++d g
  gi|13541765|ref|NP_111453.1| 44 WRPSPGSVYPALEQLEADGLVIRNED-G 70
                                  66667799999************997.4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       546  (0.0304535); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.50u 0.31s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 959.54
//
Query:       gi|13541766|ref|NP_111454.1|  [L=339]
Description: ABC-type multidrug transport system, ATPase component [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.1e-28  100.4   0.0    2.6e-28   99.3   0.0    1.6  2  ABC_tran    ABC transporter
    4.6e-13   49.7   0.0    1.2e-12   48.4   0.0    1.7  1  DUF4162     Domain of unknown function (DUF4162)
      6e-09   36.1   0.2    5.1e-05   23.2   0.0    2.4  2  AAA_21      AAA domain, putative AbiEii toxin, Type IV TA sys
    0.00012   22.5   0.2     0.0023   18.4   0.2    2.6  1  AAA         ATPase family associated with various cellular ac
     0.0006   19.6   0.0      0.039   13.6   0.3    2.4  2  AAA_15      AAA ATPase domain
    0.00064   20.3   0.7      0.001   19.6   0.3    1.7  2  AAA_23      AAA domain
     0.0031   17.2   0.1       0.92    9.2   0.0    2.3  2  AAA_24      AAA domain
     0.0086   16.4   0.1      0.031   14.6   0.1    2.0  1  AAA_22      AAA domain
  ------ inclusion threshold ------
      0.026   14.2   0.3       0.08   12.7   0.1    1.9  2  AAA_29      P-loop containing region of AAA domain
      0.068   12.9   0.0       0.13   11.9   0.0    1.4  1  AAA_30      AAA domain
      0.078   12.6   0.4       0.31   10.6   0.5    1.8  2  SRP54       SRP54-type protein, GTPase domain
       0.15   11.3   0.0       0.28   10.4   0.0    1.4  1  Zeta_toxin  Zeta toxin


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.3   0.0   1.7e-31   2.6e-28       2     136 ..      31     173 ..      30     174 .. 0.97
   2 ?   -2.2   0.0       3.8   5.6e+03     107     119 ..     264     276 ..     203     301 .. 0.57

  Alignments for each domain:
  == domain 1  score: 99.3 bits;  conditional E-value: 1.7e-31
                                   EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx... RF
                      ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren... 79 
                                   ++++++++e e+++++G+nGaGK+t +k+l+   +pt+G+ ++ g dl + ++e+ r+ igv+pq+ + + +l+  en   
  gi|13541766|ref|NP_111454.1|  31 SDLNIEIEEAEIYGLLGKNGAGKTTTIKMLTTAIEPTSGNAKVAGYDLLK-DREKIRNIIGVVPQDLTTDADLKGIENlrm 110
                                   6899*********************************************9.9**********************88899** PP

                                   ..........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                   ..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  80 ..........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                              ++++i+++l+ ++l+++ ++ v    s++SgG+++r++l + l+++pk+l+lDEpt
  gi|13541766|ref|NP_111454.1| 111 iaafydipksVAESRINDLLNIVDLTDWGNKYV----SQYSGGMRKRLELICGLVNAPKILFLDEPT 173
                                   *******99888999******************....*****************************9 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 3.8
                                   GGS-HHHHHHHHH CS
                                   xxxxxxxxxxxxx RF
                      ABC_tran 107 ssLSgGqkqrval 119
                                   ss+Sg  k+r+++
  gi|13541766|ref|NP_111454.1| 264 SSISGEDKVRIKV 276
                                   4444444444443 PP

>> DUF4162  Domain of unknown function (DUF4162)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.4   0.0   7.9e-16   1.2e-12       1      81 []     228     315 ..     228     315 .. 0.85

  Alignments for each domain:
  == domain 1  score: 48.4 bits;  conditional E-value: 7.9e-16
                                   E-HHHHHTTS-SSEEEEE....-------..--.-EEEE-TTS-EEEEE--.-----------.----EEEEEEEE---HH CS
                       DUF4162   1 GtleeiKrsygknrieve....adaeelleepg.veeveeeggelelkled.eeaanellkal.tsgveirsFeeeePsLn 74 
                                   Gt++e+K+s+++++i+++    ++ae+++  p+ + +    ++++++k+e+ ++  +++l++l ++g++  ++++++PsL+
  gi|13541766|ref|NP_111454.1| 228 GTPDELKSSLKGDIITMQfsgsDEAEAARYYPNaLYSSISGEDKVRIKVENsDVELPKILSYLtQKGISPLTINVKKPSLD 308
                                   9*****************97743355555557766666555689******99***********77**************** PP

                                   HHHHHHH CS
                       DUF4162  75 dIFiekv 81 
                                   ++F+e++
  gi|13541766|ref|NP_111454.1| 309 EVFLEYT 315
                                   *****86 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.5   0.00039      0.58       2      19 ..      43      60 ..      42      84 .. 0.82
   2 !   23.2   0.0   3.4e-08   5.1e-05     235     300 ..     144     207 ..     128     210 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00039
                        AAA_21  2 nvliGpNgsGKSnLLdal 19
                                   +l G+Ng+GK++ ++ l
  gi|13541766|ref|NP_111454.1| 43 YGLLGKNGAGKTTTIKML 60
                                  689***********9988 PP

  == domain 2  score: 23.2 bits;  conditional E-value: 3.4e-08
                        AAA_21 235 relSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHSpl 300
                                   ++ S G+++ l l+  l  a+   ++l++DEp +gL+    ++ ++ +++ ++  g+ +ilt+H  +
  gi|13541766|ref|NP_111454.1| 144 SQYSGGMRKRLELICGLVNAP---KILFLDEPTLGLDVNTRAKMWKYIRDIQKeLGVTIILTSHYLE 207
                                   577999*9999*******999...9***********************6666669*********766 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.2   1.5e-06    0.0023       3     122 ..      45     217 ..      43     223 .. 0.70

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.5e-06
                                   EESSTTSSHHHHHHHHHHHHT..HEEEEEETTTCSSS............................................ CS
                           AAA   3 lyGppGtGKTllakavakelg..vefleisgsellsk............................................ 37 
                                   l G  G GKT+++k + + ++  +   ++ g +ll++                                            
  gi|13541766|ref|NP_111454.1|  45 LLGKNGAGKTTTIKMLTTAIEptSGNAKVAGYDLLKDrekirniigvvpqdlttdadlkgienlrmiaafydipksvaesr 125
                                   789****************85322234444444442234455555555555555555555555555555555666666666 PP

                                   ................STTHHHHHHHHHHHHHHHTS.TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSS CS
                           AAA  38 ................yvgesekkirelfkeakeka.kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkes 101
                                                   yv++ +  +r+ ++ +     +p+ilf+DE       +          + +++ + + + +k+ +
  gi|13541766|ref|NP_111454.1| 126 indllnivdltdwgnkYVSQYSGGMRKRLELICGLVnAPKILFLDEPTLGLDVN----------TRAKMWKYIRDIQKELG 196
                                   666666666666666699999999999998886655679*******77665555..........7899**********888 PP

                                   TEEEEEEESSGGGSTHHHHS.T CS
                           AAA 102 kvivigatnrpdkldpallr.g 122
                                    v++i+++++ +++d+   r +
  gi|13541766|ref|NP_111454.1| 197 -VTIILTSHYLEEVDELANRiS 217
                                   .************999887655 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.3   2.6e-05     0.039       5      44 ..      21      61 ..      18     136 .. 0.85
   2 ?    3.5   0.0     0.032        48     323     364 ..     163     204 ..     142     206 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.6e-05
                        AAA_15  5 kikikNFRslkdveidlsee.ltvliGkNnsGKSsileald 44
                                  ki   N ++ +d  i+++e  +  l GkN++GK++ +++l 
  gi|13541766|ref|NP_111454.1| 21 KIYSGNIKAVSDLNIEIEEAeIYGLLGKNGAGKTTTIKMLT 61
                                  55556889999*9****9988999**************995 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.032
                        AAA_15 323 knvilliEEPEahLHpqaqkvlikllkelandnktQviitTH 364
                                    ++il+++EP + L  +    ++k+++++ ++    +i+t+H
  gi|13541766|ref|NP_111454.1| 163 APKILFLDEPTLGLDVNTRAKMWKYIRDIQKELGVTIILTSH 204
                                   5789*****************************99******9 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.3     7e-07     0.001       6      45 ..      26      66 ..      21     220 .. 0.80
   2 ?   -2.2   0.0       3.3   4.9e+03      69      84 ..     266     281 ..     217     323 .. 0.57

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 7e-07
                        AAA_23  6 nfrsfrdqeidF.skgltlItGpNGaGKTTildAiklaLyg 45
                                  n++  +d +i+  +  ++ + G+NGaGKTT +  ++ a   
  gi|13541766|ref|NP_111454.1| 26 NIKAVSDLNIEIeEAEIYGLLGKNGAGKTTTIKMLTTAIEP 66
                                  888999999***777********************999755 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 3.3
                        AAA_23  69 gkvkayveltfenkdg 84 
                                    +++  v++++en d 
  gi|13541766|ref|NP_111454.1| 266 ISGEDKVRIKVENSDV 281
                                   3333344444444443 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.0   0.00062      0.92       6      22 ..      44      60 ..      40     151 .. 0.88
   2 !    6.1   0.0    0.0056       8.4     108     141 ..     181     215 ..     178     237 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00062
                        AAA_24  6 liyGpsgiGKTtlakel 22
                                   + G++g+GKTt++k+l
  gi|13541766|ref|NP_111454.1| 44 GLLGKNGAGKTTTIKML 60
                                  589************99 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0056
                        AAA_24 108 aeefrrllkklq.elrknvifiahektrkdedpeg 141
                                   +++++++++++q el+ ++i+++h  ++ de  ++
  gi|13541766|ref|NP_111454.1| 181 RAKMWKYIRDIQkELGVTIILTSHYLEEVDELANR 215
                                   6799******6527899********9999997754 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.1     2e-05     0.031       5     128 ..      40     202 ..      36     234 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2e-05
                        AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaee..............erpevvfvtlpsstsskdl..lrellralglelk 69 
                                   a i  + G  G+GKTt++++l+   +  +  ++              +  +vv  +l+ + ++k +  lr+++ +++ +++
  gi|13541766|ref|NP_111454.1|  40 AEIYGLLGKNGAGKTTTIKMLTTAIEPTSGNAKvagydllkdrekirNIIGVVPQDLTTDADLKGIenLRMIAAFYDIPKS 120
                                   5666688****************9865444444777777777644432222223333333344444445555555555555 PP

                        AAA_22  70 a......erlsseellealeqalrarav...............ielliiDEaqh.lr...seealeeLrsllnlsrkgvql 125
                                            l+  +l +  ++++++++                +++l +DE    l+   ++++++++r++++  + gv++
  gi|13541766|ref|NP_111454.1| 121 VaesrinDLLNIVDLTDWGNKYVSQYSGgmrkrlelicglvnaPKILFLDEPTLgLDvntRAKMWKYIRDIQK--ELGVTI 199
                                   5777777555555555555555555555556666666666777889999999999988755999999999999..888888 PP

                        AAA_22 126 iLv 128
                                   iL 
  gi|13541766|ref|NP_111454.1| 200 ILT 202
                                   885 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   5.3e-05      0.08      11      49 ..      29      67 ..      19      73 .. 0.77
   2 ?   -2.1   0.0       2.2   3.3e+03      20      38 ..     219     237 ..     213     238 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.3e-05
                        AAA_29 11 tfdghtieidlkgatlltGpsGsGKSTllDAiqalLvpa 49
                                    ++  iei++++++ l G++G+GK+T +  +++ + p+
  gi|13541766|ref|NP_111454.1| 29 AVSDLNIEIEEAEIYGLLGKNGAGKTTTIKMLTTAIEPT 67
                                  5566678999888999***********997777776665 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.2
                        AAA_29  20 dlkgatlltGpsGsGKSTl 38 
                                     +g +l+tG+    KS+l
  gi|13541766|ref|NP_111454.1| 219 IDHGKILVTGTPDELKSSL 237
                                   4467899999887777765 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     9e-05      0.13      20      47 ..      42      71 ..      34      96 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 9e-05
                        AAA_30 20 vavltGpAGtGKttalkalreaweaa.g.g 47
                                  +  l G  G+GKtt++k l+ a+e   g  
  gi|13541766|ref|NP_111454.1| 42 IYGLLGKNGAGKTTTIKMLTTAIEPTsGnA 71
                                  66789****************999774443 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.5   0.00021      0.31       5      35 ..      44      74 ..      40      80 .. 0.77
   2 ?   -1.2   0.0      0.91   1.4e+03      95     148 ..     150     202 ..     146     218 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00021
                                  EEEESTTSSHHHHHHHHHHHHHHTTS-EEEE CS
                         SRP54  5 llvGlqGaGKTttlaKLaallkkegkkvllv 35
                                   l+G +GaGKTtt+  L   ++    ++ ++
  gi|13541766|ref|NP_111454.1| 44 GLLGKNGAGKTTTIKMLTTAIEPTSGNAKVA 74
                                  589***********99998887765555555 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.91
                                   STTHHHHHHHHHHHHHHHSSSEEEEEEETTBHTHHHHHHHHHHHHSSCSEEEEE CS
                         SRP54  95 lqndkelmeelkkikkvvkpdevllvldattgqeavkqakaFkeavgitgvilt 148
                                   +++  el+  l +  k++  de  l ld +t  ++ k +++ ++++g+t +ilt
  gi|13541766|ref|NP_111454.1| 150 MRKRLELICGLVNAPKILFLDEPTLGLDVNTRAKMWKYIRDIQKELGVT-IILT 202
                                   5566677777777778888888888899999999999999999999886.5555 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   0.00019      0.28      19      46 ..      43      71 ..      29      90 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00019
                    Zeta_toxin 19 illgGqpGAGKselaellkdele.rqgnv 46
                                  + l G  GAGK++++++l++++e + gn+
  gi|13541766|ref|NP_111454.1| 43 YGLLGKNGAGKTTTIKMLTTAIEpTSGNA 71
                                  556799***************99555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (339 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       693  (0.0386525); expected 358.6 (0.02)
Passed bias filter:                      635  (0.0354175); expected 358.6 (0.02)
Passed Vit filter:                        79  (0.00440627); 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 0.32s 00:00:00.90 Elapsed: 00:00:00.46
# Mc/sec: 2220.36
//
Query:       gi|13541767|ref|NP_111455.1|  [L=267]
Description: ABC transporter permease [Thermoplasma volcanium GSS1]
Scores for complete 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  125.2  28.0    2.3e-36  125.2  28.0    1.9  2  ABC2_membrane    ABC-2 type transporter
    2.3e-14   53.3  37.9    2.3e-14   53.3  37.9    1.9  2  ABC2_membrane_3  ABC-2 family transporter protein
  ------ inclusion threshold ------
        0.1   11.9  31.9       0.66    9.2  31.9    1.9  1  ABC2_membrane_2  ABC-2 family transporter protein


Domain annotation for each model (and alignments):
>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.2  28.0   3.8e-40   2.3e-36       6     207 ..       7     224 ..       4     227 .. 0.90
   2 ?   -0.7   1.9      0.13   7.7e+02      99     122 ..     237     260 ..     228     265 .. 0.72

  Alignments for each domain:
  == domain 1  score: 125.2 bits;  conditional E-value: 3.8e-40
                 ABC2_membrane   6 llkreflqrwrdpslgllwrliqplllalvfgtvfgnlg....nsedglnr............pgllffsvlflafsalts 70 
                                   l+ re+++++r+p+++ ++ l+qp++++++fg++f   +      ++   +             g+l ++ lf++  ++++
  gi|13541767|ref|NP_111455.1|   7 LTAREIKKWYRNPVYL-IVGLLQPVFWIILFGSAFDISKfggpFVSS---FfngapdyitymiGGILTITGLFTG--MFSG 81 
                                   799**********999.99*****************75533322222...2556888888877777777777777..**** PP

                 ABC2_membrane  71 vapvferergvlerelvsplyslsayvlakvlvelpvsllqalifllivyflv.gldls.rf.....flflllllltalaa 144
                                   + ++++r+ g+l+r lvsp+ ++s++v++++l++++++++q++i+++i++++  gl++s +f     ++++ ++l++++++
  gi|13541767|ref|NP_111455.1|  82 INIIWDRRLGILQRFLVSPI-KRSSIVFSRILASVVRIIVQVIILIAIALVIPnGLRISnSFtvidaLIMVSTVLMISFIF 161
                                   ********************.******************************988*****97777888************** PP

                 ABC2_membrane 145 sslgllisalapsfedasqlaslvllpllllsGffipidsmpkwlqwiaylnPltyavealrs 207
                                   ss++ +i++ ++ +e+++ ++++v lpl++ s +++p+d m +wl  ia++nP+++  e++r 
  gi|13541767|ref|NP_111455.1| 162 SSIFSIIAIRMTRMETIMGITNMVNLPLMFASYALFPPDLMVSWLSTIAKYNPVSWSAESIRL 224
                                   *****************************************88*****************996 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.13
                 ABC2_membrane  99 akvlvelpvsllqalifllivyfl 122
                                   a++ ++l++ ++++++++++vyf+
  gi|13541767|ref|NP_111455.1| 237 AQLGTYLLYLFALTVAMIVLVYFV 260
                                   666677777777777777777776 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   2.4     0.042   2.5e+02     213     236 ..      21      45 ..      20      54 .. 0.72
   2 !   53.3  37.9   3.9e-18   2.3e-14     152     344 ..      53     258 ..      48     259 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.042
               ABC2_membrane_3 213 dflvyllqlllilll...afglgipfg 236
                                   +++v+llq +++++l   af+  i+ +
  gi|13541767|ref|NP_111455.1|  21 YLIVGLLQPVFWIILfgsAFD--ISKF 45 
                                   899*********997577777..5544 PP

  == domain 2  score: 53.3 bits;  conditional E-value: 3.9e-18
               ABC2_membrane_3 152 leeelsnvasflvgliliilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllilllafgl. 231
                                    ++ ++++  +++g il i  ++t++f   +i+ +++ +i+++ lvs+++++++++s+il++++  ++q+++++++a+ + 
  gi|13541767|ref|NP_111455.1|  53 FFNGAPDYITYMIGGILTITGLFTGMFSGINIIWDRRLGILQRFLVSPIKRSSIVFSRILASVVRIIVQVIILIAIALVIp 133
                                   588999999*****88888877888888889********************************************988866 PP

               ABC2_membrane_3 232 .......gipfgnlglllllfllfglayialgyllsslfknsetaqilifivilllsgffgglfpledlpsalkwifsiiP 305
                                          ++++ + ++++  +l+ ++++++++  +   ++++et ++++ +v+l+l++++++lfp + + s+l++i+ ++P
  gi|13541767|ref|NP_111455.1| 134 nglrisnSFTVIDALIMVSTVLMISFIFSSIFSIIAIRMTRMETIMGITNMVNLPLMFASYALFPPDLMVSWLSTIAKYNP 214
                                   756555444444555555555555777777788888889999*************************************** PP

               ABC2_membrane_3 306 ffapglgllrli.....tgdplweillsliilalfavvylllal 344
                                    ++ ++++  li     +  +++++++ l++l++++v++++l++
  gi|13541767|ref|NP_111455.1| 215 VSWSAESIRLLIiygslNSSQMAQLGTYLLYLFALTVAMIVLVY 258
                                   ********999887775333677799**************9986 PP

>> ABC2_membrane_2  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2  31.9   0.00011      0.66      80     281 ..      61     259 ..       5     261 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00011
               ABC2_membrane_2  80 imavlipvi......aalfgadaiagEkergTlkllLskPvsRdeillgKfigglaiglaiavallatvllalaiilalgi 154
                                   i++++++++        +f+   i  ++  g l + L +P+ R++i+++ ++++++ +++  v++l++  l +   l  ++
  gi|13541767|ref|NP_111455.1|  61 ITYMIGGILtitglfTGMFSGINIIWDRRLGILQRFLVSPIKRSSIVFSRILASVVRIIV-QVIILIAIALVIPNGLRISN 140
                                   45555555555555566777777777899999*************************444.33333332344555666667 PP

               ABC2_membrane_2 155 vlaledllllvvasvlllllvvflalglllSsvarssreaaalalglfvvlailvpivlygvaellagpavpqeindflsl 235
                                   ++++ d l+ +v++vl++     + ++  +S++a  + + ++   g+  + ++  + ++y++  + ++ +    +  ++  
  gi|13541767|ref|NP_111455.1| 141 SFTVIDALI-MVSTVLMIS----FIFSSIFSIIAI-RMTRMETIMGITNMVNLPLMFASYALFPPDLMVS----WLSTIAK 211
                                   777777654.455555666....345555666666.6778888888999999999999999888888444....6888888 PP

               ABC2_membrane_2 236 lsptsayntllneilagsdlna..lgstatnllilllllavllvlgyv 281
                                   ++p s+    ++ ++  ++ln+  +++ +t+ll+l +l+++++vl+y+
  gi|13541767|ref|NP_111455.1| 212 YNPVSWSAESIRLLIIYGSLNSsqMAQLGTYLLYLFALTVAMIVLVYF 259
                                   8999986655555554444555589999******************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1263  (0.0704445); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 1721.92
//
Query:       gi|13541768|ref|NP_111456.1|  [L=382]
Description: Fe-S oxidoreductase [Thermoplasma volcanium GSS1]
Scores for complete 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-13   49.2   0.0    1.4e-12   48.4   0.0    1.3  1  Radical_SAM  Radical SAM superfamily


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.4   0.0   7.6e-17   1.4e-12       6     150 ..     138     287 ..     134     305 .. 0.77

  Alignments for each domain:
  == domain 1  score: 48.4 bits;  conditional E-value: 7.6e-17
                                   EESS-.-TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHH..HHTT..SEEEEEESSTGGGSTTHHHHHHHHHHTC...CCTE CS
                                   xxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxx RF
                   Radical_SAM   6 gCnlr.CsfCarpetvrregrgrslsveeileevkelk..aekg..vkevilgggepllypdfvellerlakla...vpgi 78 
                                   gC+ + C+fC  ++     ++++++ ++e +e+v+++k  +  g  ++  +++g+   ++ +   ll  l  ++      +
  gi|13541768|ref|NP_111456.1| 138 GCSWNrCTFCKLYR----DRDYMVRLPDEFKEHVRQVKdyFGEGlsARKTVFLGDANAVNLEQKTLLSYLDLIKeefGLPV 214
                                   888777*******5....8******************87555566666777777777777666666666666656564444 PP

                                   EEEEEECSSCHG..HHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEE CS
                                   xxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  79 ritvetngtlpd..eeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdriv 150
                                     +v +  t  +  e + +++++ g+ rv+lgle++d+  vl+l+n++ +++e ++++  +++ag++  ++ + 
  gi|13541768|ref|NP_111456.1| 215 YAFVDAISTQKRksEMHFREMKDHGLKRVYLGLESGDPG-VLRLLNKMMNLSEAINLVNQIKDAGLNIGIILMA 287
                                   44444444443478*************************.***************************5333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (382 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       581  (0.0324056); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.48
# Mc/sec: 2374.97
//
Query:       gi|13541769|ref|NP_111457.1|  [L=216]
Description: metal-dependent transcription regulator [Thermoplasma volcanium GSS1]
Scores for complete 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   68.7   0.1    6.5e-19   67.8   0.1    1.5  1  Fe_dep_repr_C   Iron dependent repressor, metal binding and d
      1e-07   32.1   0.2    2.7e-07   30.8   0.0    1.8  2  FeoA            FeoA domain
      9e-06   25.5   0.1    1.4e-05   24.9   0.1    1.2  1  DUF4423         Domain of unknown function (DUF4423)
    0.00077   19.1   0.7     0.0013   18.4   0.7    1.3  1  DDRGK           DDRGK domain
     0.0012   19.0   0.3     0.0033   17.6   0.3    1.8  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
     0.0027   17.5   0.1     0.0058   16.5   0.1    1.5  1  TrmB            Sugar-specific transcriptional regulator TrmB
  ------ inclusion threshold ------
      0.014   15.4   0.0      0.023   14.6   0.0    1.4  1  HTH_36          Helix-turn-helix domain
      0.014   15.7   0.7      0.033   14.5   0.7    1.6  1  DUF4362         Domain of unknown function (DUF4362)
      0.044   13.7   0.7       0.91    9.5   0.3    2.7  3  HTH_11          HTH domain
      0.087   12.9   0.2       0.18   12.0   0.2    1.6  1  DUF2250         Uncharacterized protein conserved in archaea 
       0.09   12.7   0.0       0.26   11.2   0.0    1.7  1  MarR_2          MarR family
        0.1   12.6   0.1       0.96    9.5   0.0    2.4  3  HTH_Crp_2       Crp-like helix-turn-helix domain
       0.14   12.3   0.0       0.52   10.5   0.0    1.9  2  Mrr_N           Mrr N-terminal domain


Domain annotation for each model (and alignments):
>> Fe_dep_repr_C  Iron dependent repressor, metal binding and dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.8   0.1   4.7e-22   6.5e-19       1      69 [.      65     132 ..      65     133 .. 0.98

  Alignments for each domain:
  == domain 1  score: 67.8 bits;  conditional E-value: 4.7e-22
                                   -HHHHHHHHHHHHHHHHHHHHHHHHCT--CCCHHHHCCCCGGGS-HHHHHHHHHHCT-.SB-TTS-B-- CS
                 Fe_dep_repr_C   1 TekGrelAkrlvrrhrllerfLvdvlgvdweeaheeAerlEhalseelierldellgfpeecPhgdpip 69 
                                   T++G  +A+  +r+hr++e++L++ +g++w+ +++eA+ +Eh ++ee+i+r+ e ++  ++cPhg+pip
  gi|13541769|ref|NP_111457.1|  65 TDQGDIEANIFLRKHRTAEVLLSQCVGIEWDAVDREAMGIEHGMTEEIIHRVIERFNA-KRCPHGNPIP 132
                                   99******************************************************96.*********9 PP

>> FeoA  FeoA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1       4.7   6.5e+03      30      43 ..     101     114 ..     100     116 .. 0.78
   2 !   30.8   0.0   1.9e-10   2.7e-07       2      73 ..     145     213 ..     144     214 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 4.7
                                   HHT--TT-EEEEEE CS
                          FeoA  30 emGlvpGarievva 43 
                                   +mG+  G + e+++
  gi|13541769|ref|NP_111457.1| 101 AMGIEHGMTEEIIH 114
                                   89999998888776 PP

  == domain 2  score: 30.8 bits;  conditional E-value: 1.9e-10
                                   EGGG--TT-EEEEEEE-TT.SSHHHHHHHHT--TT-EEEEEEE-TTS-SEEEEETTEEEEE-HHHHTTEEEE CS
                          FeoA   2 pLsdlkeGergeiarisdedpellrrLremGlvpGarievvarapfggplvvrvgdtrvaLgreeAqaIlVe 73 
                                   + +dl+e   ++i+ri+ e +e+l++L +  + pGa+++++ r  f  pl+++ ++  ++L+ ++A+aI V 
  gi|13541769|ref|NP_111457.1| 145 RITDLNETGDVIISRIIYETDEILNYLYANQILPGAKVKII-RTGF--PLQIEKDGRLLSLDPSIAKAIRVS 213
                                   678999***********************************.5555..9********************996 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.1   9.9e-09   1.4e-05      17      81 ..       6      67 ..       2      87 .. 0.94

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 9.9e-09
                       DUF4423 17 yfssWyypvirellplkdfkadpeelakrlrpkisaeevekalefLlklgllkkdedgkyrqtek 81
                                  + ++ y  +i+el+  +d+ a+ + +ak l+  ++ + +++ ++ L +lg++kk   gky+ t++
  gi|13541769|ref|NP_111457.1|  6 VTEEDYLKIIQELVLYQDY-AQLSDIAKSLQ--VKRQSARDEINHLIDLGMVKKIDRGKYVLTDQ 67
                                  678999********99999.***********..****************************9986 PP

>> DDRGK  DDRGK domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.7   9.3e-07    0.0013     100     163 ..      11      72 ..       2      80 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 9.3e-07
                                   HHHHHHHHHHH-SEE-HHHHHHHH-S-HHHHHHHHHHHHHHSSS-EEE-TT--EEE---XXXXX CS
                         DDRGK 100 lleefinyikekKvvlleelavkfklktqevierikeLeeqgsltGvlDdrGkyiyitdeElea 163
                                    l+ + + +  + + +l ++a  +++k q +++ i++L + g+++ +  drGky+   + ++ea
  gi|13541769|ref|NP_111457.1|  11 YLKIIQELVLYQDYAQLSDIAKSLQVKRQSARDEINHLIDLGMVKKI--DRGKYVLTDQGDIEA 72 
                                   555556667778899******************************98..9*****999888887 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.3   2.4e-06    0.0033       6      53 ..       8      55 ..       5      64 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2.4e-06
                                  HHHHHHHHHHHHHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                Fe_dep_repress  6 tEdYLetIYtlseekkvvktkdlaerLnvspssVsemlkkLekdGyve 53
                                   EdYL+ I +l   +++++ +d+a+ L+v+  s+   ++ L + G v+
  gi|13541769|ref|NP_111457.1|  8 EEDYLKIIQELVLYQDYAQLSDIAKSLQVKRQSARDEINHLIDLGMVK 55
                                  69***********************************99999988886 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   0.1   4.2e-06    0.0058      18      60 ..      20      62 ..      12      66 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 4.2e-06
                                  HHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTT CS
                          TrmB 18 lklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpk 60
                                  l ++ a+ ++ia+ l v r+++ + ++ L+d G+V+++++ ++
  gi|13541769|ref|NP_111457.1| 20 LYQDYAQLSDIAKSLQVKRQSARDEINHLIDLGMVKKIDRGKY 62
                                  377788999****************************987765 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   1.7e-05     0.023      24      53 ..      23      52 ..      14      54 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.7e-05
                        HTH_36 24 cfpsqetlakrlglsknTvsraikeLeqlG 53
                                   +++ +++ak l +++++++  i+ L++lG
  gi|13541769|ref|NP_111457.1| 23 DYAQLSDIAKSLQVKRQSARDEINHLIDLG 52
                                  699**************************9 PP

>> DUF4362  Domain of unknown function (DUF4362)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.7   2.4e-05     0.033      27      56 ..     139     168 ..     136     175 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.4e-05
                       DUF4362  27 kkkdkirivsyTeeGdpiledleydgkklk 56 
                                   +k d +ri+++ e Gd+i++ ++y+ +++ 
  gi|13541769|ref|NP_111457.1| 139 EKIDDVRITDLNETGDVIISRIIYETDEIL 168
                                   578*********************998886 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.3   0.00066      0.91       3      44 ..      12      55 ..      11      61 .. 0.90
   2 ?   -2.4   0.0       3.5   4.9e+03      27      41 ..     108     122 ..     106     126 .. 0.74
   3 ?    0.9   0.0      0.31   4.3e+02      36      48 ..     146     158 ..     145     159 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00066
                        HTH_11  3 lqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelg..v 44
                                  l+i++ L   +++   +++A+ L v r+  r  I  L +lg   
  gi|13541769|ref|NP_111457.1| 12 LKIIQELVLYQDYAQLSDIAKSLQVKRQSARDEINHLIDLGmvK 55
                                  589**********************************9999543 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 3.5
                        HTH_11  27 vSrrtvrrdIkaLee 41 
                                   +++  ++r I++ ++
  gi|13541769|ref|NP_111457.1| 108 MTEEIIHRVIERFNA 122
                                   677889999988666 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.31
                        HTH_11  36 IkaLeelgvpIes 48 
                                   I +L+e+g+ I+s
  gi|13541769|ref|NP_111457.1| 146 ITDLNETGDVIIS 158
                                   899*****99998 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 ?   12.0   0.2   0.00013      0.18       7      56 ..       8      58 ..       3      81 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00013
                       DUF2250  7 delalkvlkhlkkanvdYaks..iakeleipleevrellkkLeelGLlerve 56
                                  +e++lk+++ l  +  dYa++  iak l+++++ +r+ +++L +lG++++ +
  gi|13541769|ref|NP_111457.1|  8 EEDYLKIIQELV-LYQDYAQLsdIAKSLQVKRQSARDEINHLIDLGMVKKID 58
                                  566889998885.678***86559*************************986 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00019      0.26      24      53 ..      27      56 ..      16      62 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00019
                                  HHHHHHHHTSSHHHHHHHHHHHHHTTSEEE CS
                        MarR_2 24 vgelarrlglsksavsrilkrLvaaGLver 53
                                   +++a+ l+++++++   ++ L + G+v +
  gi|13541769|ref|NP_111457.1| 27 LSDIAKSLQVKRQSARDEINHLIDLGMVKK 56
                                  58*************************986 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0   0.00069      0.96      25      61 ..      28      66 ..      24      72 .. 0.85
   2 ?   -0.0   0.0      0.65   8.9e+02      22      47 ..      97     122 ..      79     127 .. 0.71
   3 ?   -2.7   0.0       4.3   5.9e+03      48      63 ..     135     150 ..     133     151 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00069
                                  HHHHHHTTSSHHHHHHHHHHHHHTTSEE.ETEE.EEES- CS
                     HTH_Crp_2 25 eelAsmlGltretvsrilseLkreglis.rgrr.irild 61
                                   ++A  l + r++   ++++L + g+++   r+  +++d
  gi|13541769|ref|NP_111457.1| 28 SDIAKSLQVKRQSARDEINHLIDLGMVKkIDRGkYVLTD 66
                                  59**************************63433388877 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.65
                                   HHHHHHHHHTTSSHHHHHHHHHHHHH CS
                     HTH_Crp_2  22 ltqeelAsmlGltretvsrilseLkr 47 
                                   + +e ++   G+t e + r++ ++  
  gi|13541769|ref|NP_111457.1|  97 VDREAMGIEHGMTEEIIHRVIERFNA 122
                                   55666777779999999999998876 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 4.3
                                   TTSEE.ETEEEEES-HH CS
                     HTH_Crp_2  48 eglis.rgrririldle 63 
                                   eg+++     +ri+dl+
  gi|13541769|ref|NP_111457.1| 135 EGYVEkIDD-VRITDLN 150
                                   788884465.9999985 PP

>> Mrr_N  Mrr N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00038      0.52      53      81 ..      40      68 ..       9      70 .. 0.83
   2 ?   -1.6   0.0       2.2     3e+03      19      32 ..     109     121 ..     100     124 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00038
                         Mrr_N 53 rvgWartyLkkagllespkrgvwkiTekG 81
                                   ++  +++L   g++++ +rg++ +T++G
  gi|13541769|ref|NP_111457.1| 40 SARDEINHLIDLGMVKKIDRGKYVLTDQG 68
                                  55666889********************9 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.2
                         Mrr_N  19 rlkeirervaerfg 32 
                                   + +ei+ rv+erf+
  gi|13541769|ref|NP_111457.1| 109 T-EEIIHRVIERFN 121
                                   3.799999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       479  (0.0267165); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1569.60
//
Query:       gi|13541770|ref|NP_111458.1|  [L=487]
Description: amino acid transporter [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.1e-36  124.0  55.6      8e-36  123.6  55.6    1.1  1  AA_permease    Amino acid permease
    1.2e-25   90.3  57.7    1.7e-25   89.7  57.7    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 !  123.6  55.6   8.9e-40     8e-36       8     464 ..      27     473 ..      24     480 .. 0.81

  Alignments for each domain:
  == domain 1  score: 123.6 bits;  conditional E-value: 8.9e-40
                   AA_permease   8 ggviGtglfvglgvvlsqaGplgallayllagvviflvmlslgeiatngpksggfytyasrflgpelGfviGlnylfswit 88 
                                   + v Gt+ ++ + ++++  G  ++ l++ll+ vv++l+ +s++e++ + +++gg+yt++sr lg ++Gfv++l+y  ++i+
  gi|13541770|ref|NP_111458.1|  27 LYVAGTASIITSTFITHPFGSYAIPLILLLSLVVYALMSYSMYEFSRKLSSAGGYYTFVSRGLGNSAGFVTALSYITYEIL 107
                                   56899*********************************************************************9988888 PP

                   AA_permease  89 vlaleltaasiliqfwelvtdlpkawvt...........gavflvvlliinlvgvkvygeaefilalikiiaiiafiivg. 157
                                    ++   +++  +++f+  +   p++ +            + vf+++++++ ++g+k + +    + ++ + + +af+i++ 
  gi|13541770|ref|NP_111458.1| 108 SFTG--FGILGFLGFA--YAIFPSLGIAipdpeflwmpvAFVFIGLVSLLIYLGIKPSLR----FVSYTVFIEVAFLIFTs 180
                                   7753..4566666666..55555555556788888899*9*****************999....9***************7 PP

                   AA_permease 158 iillaggkpnkgagfrflgdngsifknnlppgfakeeegafknfisvfvivvfaftGielvaiiagEvkdPeksiPkailq 238
                                   + l++  +++           ++     ++p    + +   ++++++++ ++ af Gi+  + ia+E+k P++++P ail 
  gi|13541770|ref|NP_111458.1| 181 VALIVMHHTSVN---------LE----PFTPT---PMGNDPYAIFAMMIYAIGAFVGIGGSIPIAEETKKPKRNVPLAILV 245
                                   444444443333.........22....33333...3344489*************************************** PP

                   AA_permease 239 vviritifYvlsllligllvprndlgllndsasaaspfvifikesgvsvlapl..inaviltaalssansslysasRvlys 317
                                   ++  ++i  +l++++ ++ ++ n  +l+ +s ++++++ i+ +  g   +  +  i++++l + + + +s+ + a+Rv++s
  gi|13541770|ref|NP_111458.1| 246 TIAVLGITIILASYAQVVSWGLNRIDLFGSSSDPYPLLTIYHSAFGPLSIILFwaIIIIVLNSFFTATVSLGTNATRVIFS 326
                                   **********************************99999999998865555542377888999****************** PP

                   AA_permease 318 lakdglaPkvlkkvskr.gvPlraillsmiisllal...............llaslnlaapivfnfllaisaliglivwll 382
                                   +a++g++P++l+ ++++ g P +a+++ ++is +++               ++a l+++      fll +   i+ iv++l
  gi|13541770|ref|NP_111458.1| 327 MAREGALPSFLSEMNRNnGTPTMAMIVLTAISIAIVigvgagfeffghfspVNALLTSS-----VFLLILESPITYIVHIL 402
                                   ***************96379****************55555555555544444444444.....44444444455555555 PP

                   AA_permease 383 iilsylrfRkalkyqgrsieelgfkaallplgvilvlaaliiillilalyayltvkkgpkdwgaasfaaaylivllfliil 463
                                   +++s++ ++           + + k+    l+ +lv+ ++++++li+a++a + +    +d  +asfa+  +i++ +l++ 
  gi|13541770|ref|NP_111458.1| 403 TNTSLYSYM-----------KKRTKMKAKDLFKYLVIPSVSTVTLIAAIVAGIYFNLFLVDAIYASFALIAIIIISTLVMR 472
                                   555555333...........3456777888899999999999999999998888777778888999999999988888876 PP

                   AA_permease 464 v 464
                                    
  gi|13541770|ref|NP_111458.1| 473 A 473
                                   5 PP

>> AA_permease_2  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.7  57.7   1.9e-29   1.7e-25      14     407 ..      29     448 ..      14     476 .. 0.72

  Alignments for each domain:
  == domain 1  score: 89.7 bits;  conditional E-value: 1.9e-29
                 AA_permease_2  14 vigsgifvkn.laas..ggpalilwvwiavligslavllvyaElssalprsgGiyvytkaafgkkvaflsawfnwfayvpv 91 
                                   v+g+++++++  +++  g  a+ l+++++ +++   +++ + E+s +l++ gG y++++++ g+ ++f++a ++    +++
  gi|13541770|ref|NP_111458.1|  29 VAGTASIITStFITHpfGSYAIPLILLLSLVVY-ALMSYSMYEFSRKLSSAGGYYTFVSRGLGNSAGFVTALSYITYEILS 108
                                   366666666654444534444556666666666.68**************************************9999999 PP

                 AA_permease_2  92 lasilsvaasyllnalgpdlqgn....twltyliaiaililvalinirgikesakiqnilgilkillpliiliilglitvd 168
                                   +++  ++++  +++a++p+l        +l++ +a++++ lv l++++gik s ++ ++++ + +  +li+   ++li+ +
  gi|13541770|ref|NP_111458.1| 109 FTGFGILGFLGFAYAIFPSLGIAipdpEFLWMPVAFVFIGLVSLLIYLGIKPSLRFVSYTVFIEVA-FLIFTS-VALIVMH 187
                                   9999999***********55444555599************************************5.655555.5555554 PP

                 AA_permease_2 169 gggfsslstetdtffpn..gwpg..vllgllivlwsfdGfesaanvseevkk..kdvpkaifigllivlvlyllvniaflg 243
                                   ++  +      + f+p+  g++   +++++  ++ +f+G+ +++ ++ee kk  ++vp+ai + +++ ++  +l + a + 
  gi|13541770|ref|NP_111458.1| 188 HTSVN-----LEPFTPTpmGNDPyaIFAMMIYAIGAFVGIGGSIPIAEETKKpkRNVPLAILVTIAVLGITIILASYAQVV 263
                                   44444.....4566666669997435778888*****************8877579*****99999999999998777666 PP

                 AA_permease_2 244 vvpddei...anlsnlgsv.aalffeavggk...vvaiivvilialsllgaintavigssrvlealardgvlPrffakvn. 316
                                     + + i    ++s+ +++ ++++  a+g +   +++++++i++  s + a  ++ + ++rv++++ar+g+lP+f++ +n 
  gi|13541770|ref|NP_111458.1| 264 SWGLNRIdlfGSSSD-PYPlLTIYHSAFG-PlsiILFWAIIIIVLNSFFTATVSLGTNATRVIFSMAREGALPSFLSEMNr 342
                                   666666744333333.3342555555555.43368888888888889*********************************9 PP

                 AA_permease_2 317 kfgspiraiiltaivslillllfl........lassaayn.......fllsvsslgliisyllliigalilrkkrphlkr. 381
                                    +g+p+ a+i+   +s+++++ +         +   + +n       fll + s   +i+ +l+ +++  + kkr + k  
  gi|13541770|ref|NP_111458.1| 343 NNGTPTMAMIVLTAISIAIVIGVGagfeffghF---SPVNalltssvFLLILESPITYIVHILTNTSLYSYMKKRTKMKAk 420
                                   9***************88877777777776662...234422222224444444444555555555555554554444334 PP

                 AA_permease_2 382 ..pgkilvaiigalfllfllvalffppk 407
                                     +++ ++  +++++l+ ++va+++ + 
  gi|13541770|ref|NP_111458.1| 421 dlFKYLVIPSVSTVTLIAAIVAGIYFNL 448
                                   6755555666666666666666664422 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (487 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1114  (0.062134); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.76u 0.34s 00:00:01.10 Elapsed: 00:00:00.52
# Mc/sec: 2844.63
//
Query:       gi|13541771|ref|NP_111459.1|  [L=96]
Description: hypothetical protein TVN0940 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.7e-24   85.5   0.2    1.9e-24   85.4   0.2    1.0  1  Thiamine_BP  Thiamine-binding protein
  ------ inclusion threshold ------
       0.07   13.3   0.0      0.084   13.1   0.0    1.1  1  AAA_lid_1    AAA+ lid domain


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 !   85.4   0.2   2.1e-28   1.9e-24       1      91 [.       4      94 ..       4      95 .. 0.97

  Alignments for each domain:
  == domain 1  score: 85.4 bits;  conditional E-value: 2.1e-28
                                  EEEEEEECSSSSSGHHHHHHHHHHHHHTTSSEEEEETTEEEEEEE.HHHHHHHHHHHHHHHHCTTSSEEEEEEEEEEESSS-- CS
                   Thiamine_BP  1 veisviPlgtegesvskyVakvvevlkesglkyeltpmgTtiege.ldevmevvkkahealfeaGakRvstvikiddrrdkeq 82
                                  +ei+ iP+g  g+s skyV+++ +  k+ g+ ++ ++mgT+ie++ l++++e+vk+ +ea++++G+kRv t++kid+r d e+
  gi|13541771|ref|NP_111459.1|  4 AEITYIPIGE-GTSASKYVNAALAEFKKMGIAFYPNSMGTVIEAKdLETIFEAVKRGEEAIIQKGIKRVETYLKIDHRIDAEN 85
                                  689*****97.************************************************************************ PP

                                  -HHHHHHHH CS
                   Thiamine_BP 83 tleeKvksv 91
                                  ++++K++++
  gi|13541771|ref|NP_111459.1| 86 SVQKKISEL 94
                                  *****9875 PP

>> AAA_lid_1  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   9.4e-06     0.084       2      73 ..      21      90 ..      20      95 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 9.4e-06
                     AAA_lid_1  2 vaaalalhkkiaatflptaikfhyvfnlrdlsnifqgllfssaevlkapldlirlylheservygdkmveek 73
                                  v+aala  kk+  +f p ++    v++ +dl  if+ +      +++  +  +  yl+  +r+  +  v++k
  gi|13541771|ref|NP_111459.1| 21 VNAALAEFKKMGIAFYPNSM--GTVIEAKDLETIFEAVKRGEEAIIQKGIKRVETYLKIDHRIDAENSVQKK 90
                                  799**************997..579*************************************9999988877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       632  (0.0352502); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); 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 0.24s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 723.76
//
Query:       gi|13541772|ref|NP_111460.1|  [L=193]
Description: hypothetical protein TVN0941 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.028   14.8   1.4      0.057   13.8   1.4    1.5  1  Lipoprotein_17  Lipoprotein associated domain
        0.1   12.5   0.0       0.21   11.6   0.0    1.5  1  DUF5348         Domain of unknown function (DUF5348)


Domain annotation for each model (and alignments):
>> Lipoprotein_17  Lipoprotein associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   1.4   6.4e-06     0.057       5      66 ..     116     184 ..     109     191 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6.4e-06
                                   H.TT--BTTTEE...ETTSTT--GGGS-HHH....EEE-S..-TTTEEEEEEEE-THHHHHTEEEEEEEE CS
                Lipoprotein_17   5 i.knlelknnak...kntLPSevtnsnlknd....nfitfpntkngvsfsikivssanDeeGtLkvkvtl 66 
                                   + +n+++++n      +++PS++t+ n + +     ++++ +   g s+s+++++ +nD+ G   + +++
  gi|13541772|ref|NP_111460.1| 116 LfDNFTIEQNGSnmvLTVKPSNFTSGNTI-TvyanGNQKSGQLELGRSWSYEFTIVSNDSSGYAGIAISI 184
                                   45788888888889**************6.569*85566677777888888777778****988877754 PP

>> DUF5348  Domain of unknown function (DUF5348)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   2.3e-05      0.21       9      50 ..     126     163 ..     120     178 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.3e-05
                       DUF5348   9 grryvvrfgdgeeygLhcGeslevlvedeWvptriEmdngew 50 
                                   g  +v++  + +++  ++G ++ v+ ++  +++++E+++  w
  gi|13541772|ref|NP_111460.1| 126 GSNMVLTV-KPSNF--TSGNTITVYANGNQKSGQLELGR-SW 163
                                   55555553.33467..*********************96.44 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       530  (0.029561); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); 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 0.22s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1507.60
//
Query:       gi|13541773|ref|NP_111461.1|  [L=207]
Description: HAD superfamily hydrolase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.1e-31  108.4   0.1    8.1e-31  107.5   0.0    1.5  2  HAD_2           Haloacid dehalogenase-like hydrolase
    1.3e-16   61.5   0.7      1e-14   55.4   0.7    2.1  1  Hydrolase       haloacid dehalogenase-like hydrolase
    3.1e-08   33.6   0.0    5.8e-08   32.7   0.0    1.5  1  Hydrolase_like  HAD-hyrolase-like
    0.00039   20.9   0.7     0.0033   17.8   0.7    2.2  1  HAD             haloacid dehalogenase-like hydrolase
     0.0038   17.0   0.2        8.7    6.0   0.1    3.2  3  Hydrolase_3     haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
       0.17   12.1   0.2        0.5   10.6   0.1    1.8  2  DUF3861         Domain of Unknown Function with PDB structure


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 !  107.5   0.0   2.7e-34   8.1e-31       1     178 []       6     172 ..       6     172 .. 0.95
   2 ?   -2.8   0.0       1.9   5.7e+03      75      93 ..     184     202 ..     176     205 .. 0.65

  Alignments for each domain:
  == domain 1  score: 107.5 bits;  conditional E-value: 2.7e-34
                         HAD_2   1 iiFDlDgTlldteeliiqafnelleeyglselseeelrkliglslrellrklgeseeeeekieellrkyneekkkkevkpy 81 
                                   +iFD+DgTlld++++ i++++e+++++g+ +++++ ++ +ig +  +l rk+ ++     ++e l ++y  +k + +vk++
  gi|13541773|ref|NP_111461.1|   6 VIFDFDGTLLDSVDVRITSWQEAFKDFGV-NVPRDVIKPMIGYPGVDLARKFVNNPL---DVEMLQEDYFLKKID-SVKLF 81 
                                   7**************************99.9***********************988...9999*9********9.***** PP

                         HAD_2  82 dgvkelLeeLkeagyklgivTsksreaveekleqlgiesyFdvivtsedvekkKPdpeviekaleklklkkeeviyvGDsp 162
                                   ++v+ +++ Lk++g+k+ +vTs +r++++++    +     d++vt +dv+k KPdpe++  al+k+ ++++e+++vGD  
  gi|13541773|ref|NP_111461.1|  82 QDVIPTIHRLKDRGIKVSVVTSTRRSVMNRF----D--LPVDTVVTIDDVSKGKPDPEPYIIALKKMAVEPKECVVVGDIE 156
                                   **********************999887654....3..3678*************************************** PP

                         HAD_2 163 tDieaakkagikviav 178
                                   +D+  +kk+ ++++ v
  gi|13541773|ref|NP_111461.1| 157 NDLVPGKKIMCTTVLV 172
                                   ********99998865 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.9
                         HAD_2  75 kkevkpydgvkelLeeLke 93 
                                   ++e++ ++++++++ee+++
  gi|13541773|ref|NP_111461.1| 184 DYEIENISDLIKIIEEIES 202
                                   4567777777777777754 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.4   0.7   3.4e-18     1e-14       1     204 [.       3     160 ..       3     165 .. 0.86

  Alignments for each domain:
  == domain 1  score: 55.4 bits;  conditional E-value: 3.4e-18
                                   SSEEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHETTTEHHHHTHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hydrolase   1 iktvvfDkdGTLttgepsvedvivsaalalaaaletgsehpigkalvaaakarsgaltgfatfigrgayaigkpewltald 81 
                                   ik v+fD+dGTL+++  +  + ++                       +a+k+ + ++ +        + +ig p    a  
  gi|13541773|ref|NP_111461.1|   3 IKGVIFDFDGTLLDSVDVRITSWQ-----------------------EAFKDFGVNVPRDVI-----KPMIGYPGVDLAR- 54 
                                   799**********77744444444.......................669999999977777.....8999999977777. PP

                                   CHHHHHHHHHHHHHHCHHHHHHTTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTTGGGESE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hydrolase  82 ippdlgaaigsaqsqgrtvallqaralavftiadplkvkpeaaeavasLkaagievvlltgdnpetaeraanqlGddyfda 162
                                             +      +v +l  +++  ++  d+ k+++++  ++++Lk++gi+v ++t+  ++  +r    ++      
  gi|13541773|ref|NP_111461.1|  55 ----------KFVNNPLDVEML--QEDYFLKKIDSVKLFQDVIPTIHRLKDRGIKVSVVTSTRRSVMNRFDLPVD-----T 118
                                   ..........668888888888..888888888999**************************9999999888899.....8 PP

                                   EEEHHCESSTTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hydrolase 163 viasdietvakpspegkvaaireLqgkpeevamVGDgvnDaa 204
                                   v+++d++  +kp+pe +  a++++ ++p+e+++VGD  nD+ 
  gi|13541773|ref|NP_111461.1| 119 VVTIDDVSKGKPDPEPYIIALKKMAVEPKECVVVGDIENDLV 160
                                   88888888********************************85 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7   0.0     2e-11   5.8e-08       3      53 ..     128     177 ..     126     193 .. 0.91

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 2e-11
                                   STTSSHHHHHHHHHH---GGGEEEEES-TTTHHHHHHHCT-EEEEESSSSS CS
                Hydrolase_like   3 gKPepemydfalevlgsdpeevlmiGDrlatDiagAnnaGwksvLVltGvt 53 
                                   gKP pe y  al+++ ++p+e++++GD  + D+  ++++ +++vLV+ G  
  gi|13541773|ref|NP_111461.1| 128 GKPDPEPYIIALKKMAVEPKECVVVGDI-ENDLVPGKKIMCTTVLVKHGRD 177
                                   9***************************.*******************974 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.7   1.1e-06    0.0033       1     184 [.       6     159 ..       6     160 .. 0.56

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.1e-06
                           HAD   1 alfDfDgTLldg.dsle.....lllrfllrrgaprlwralreklllalfrellrldraglaelleallaglseelaaeler 75 
                                   ++fDfDgTLld+ d  +     ++ + ++ + +++  + +  ++  +l+r++  +  ++++ l+           ++++ +
  gi|13541773|ref|NP_111461.1|   6 VIFDFDGTLLDSvDVRItswqeAFKD-FGVNVPRDVIKPMIGYPGVDLARKFVNN-PLDVEMLQ-----------EDYFLK 73 
                                   79**********55555444422222.3333333334444444444443333333.33333333...........334444 PP

                           HAD  76 fvaevirpklldpgalellaahraaGdrvvvvSgglrplvepllaelgadevlatelevddrltgelglegkpvrgegkva 156
                                    +++v+   l+  ++   +++ +++G++v vv+++ r ++ ++   l     ++t +  d +++++   +++  +      
  gi|13541773|ref|NP_111461.1|  74 KIDSVK---LF-QDVIPTIHRLKDRGIKVSVVTSTRRSVMNRFD--LP----VDTVVTID-DVSKG--KPDPEPYI----I 137
                                   443333...44.45666666688*****************9998..88....55533334.44444..34444444....4 PP

                           HAD 157 alrewlaaegegidleevvayGDspsDl 184
                                   al++       + +++e+v++GD ++Dl
  gi|13541773|ref|NP_111461.1| 138 ALKK------MAVEPKECVVVGDIENDL 159
                                   6666......444556699999988887 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.0   0.1    0.0029       8.7       1      15 [.       6      20 ..       6      32 .. 0.75
   2 ?    2.2   0.0     0.041   1.2e+02      19      39 ..      83     103 ..      73     114 .. 0.83
   3 !    4.8   0.0    0.0066        20     196     216 ..     139     159 ..     135     160 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0029
                                  EEEEIIIIIS-TTS- CS
                   Hydrolase_3  1 ialDlDGTLlnsdkk 15
                                  +++D DGTLl+s   
  gi|13541773|ref|NP_111461.1|  6 VIFDFDGTLLDSVDV 20
                                  69********98655 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.041
                                   HHHHHHHHHHHTTSEEEEE-S CS
                   Hydrolase_3  19 ktkeaikklkekgikvviATG 39 
                                     + +i++lk++gikv + T 
  gi|13541773|ref|NP_111461.1|  83 DVIPTIHRLKDRGIKVSVVTS 103
                                   56779***********99986 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.0066
                                   HHHCT--GGGEEEEESSGGGH CS
                   Hydrolase_3 196 akelnisleeviafGDgeNDi 216
                                   +k++ ++++e++++GD eND+
  gi|13541773|ref|NP_111461.1| 139 LKKMAVEPKECVVVGDIENDL 159
                                   578899**************7 PP

>> DUF3861  Domain of Unknown Function with PDB structure (DUF3861)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       1.2   3.7e+03      57      65 ..      77      85 ..      63      92 .. 0.72
   2 ?   10.6   0.1   0.00017       0.5       9      45 ..     169     205 ..     164     207 .] 0.84

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.2
                       DUF3861 57 glkLlgevm 65
                                  ++kL+++v+
  gi|13541773|ref|NP_111461.1| 77 SVKLFQDVI 85
                                  577888776 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00017
                       DUF3861   9 eledadgeeseekpleFeaenhdDilkiverlkkked 45 
                                    +  ++g+ ++++  ++e+en  D++ki+e++++k++
  gi|13541773|ref|NP_111461.1| 169 TVLVKHGRDVHSPFADYEIENISDLIKIIEEIESKSQ 205
                                   555678889999999******************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       555  (0.0309554); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); 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: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1394.83
//
Query:       gi|13541774|ref|NP_111462.1|  [L=261]
Description: molybdopterin/thiamine biosynthesis dinucleotide-utilizing protein [Thermoplasma volcanium GSS1]
Scores for complete 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-57  193.6   0.2    4.1e-57  193.4   0.2    1.0  1  ThiF             ThiF family
    6.6e-05   23.0   0.1    0.00013   22.1   0.1    1.6  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
       0.01   15.2   0.1      0.042   13.2   0.0    1.9  2  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
  ------ inclusion threshold ------
      0.063   13.2   0.6       0.11   12.4   0.6    1.6  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
       0.16   12.2   1.4        0.7   10.2   1.5    2.0  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma


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 !  193.4   0.2   1.1e-60   4.1e-57       1     244 []       8     241 ..       8     241 .. 0.96

  Alignments for each domain:
  == domain 1  score: 193.4 bits;  conditional E-value: 1.1e-60
                                   THHHHHH..HHHHHHHHHHTSEEEEE--SHHHHHHHHHHHHHTTTEEEEEESSB--GGGGGTBTTS-GGGTTSBHHHHHHH CS
                                   xxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ThiF   1 ysrqlal..lgedgqekLrdskvllvGaGglGsellknLalsGvgkltlvDnDkielsNlnRqflfreediGkpKaevaae 79 
                                   y+rq+al  ++ d+++k+r+s v ++G+Gg+Gs ++ ++++sG++kl +vD D +  sNl Rq+l+ e+diG +Kae+a++
  gi|13541774|ref|NP_111462.1|   8 YARQIALrvFNADDLKKIRNSVVSVIGVGGVGSLIADLFVRSGIKKLIIVDRDYVTSSNLYRQVLYDENDIGDSKAEAAKR 88 
                                   789988886999********************************************************************* PP

                                   HHHHT-TTSEEEEEES-CCGCCS-HHHHTT-SEEEEESSSHHHHHHHHHHHHHHT-EEEEEEEETTEEEEEEEEECCS-EC CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ThiF  80 alqeinpdveveavteritdetvleellesvDlVvdalDniearrlvnracvkkgiplieagtlgfegqvvviipgktgcy 160
                                   +l+++n+dve+ea +e +++ + +e +++s Dl++d++Dn+++r+++n+a+vk+ +p+i a++ +++gqv +iip+kt+cy
  gi|13541774|ref|NP_111462.1|  89 RLSKVNSDVEIEARNETFDAGN-AERIVSSSDLIMDGTDNLTSRLILNDAAVKNMKPWIMASAIETYGQVKAIIPEKTSCY 168
                                   ********************66.69******************************************************** PP

                                   TSS-TGGS.EECCCCEEHHHHHHCTE-B-HHHHHHHHHHHHHHHHHHHTTBCGGGCCEEEECCTTTTEEEEECCEEEEEEC CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ThiF 161 eCldpsstedptekkvplctsiagnipaiatttavvaglaalellkllsgkeklenslltqvdllesrfenvelerakksk 241
                                   +C +       ++  +p+c + +g   ++++++++va++a +  +k+l gke   +sl+ ++d++++  +++ + r  +++
  gi|13541774|ref|NP_111462.1| 169 RCYF-----SGEPFAQPTC-AEVG---VLSSLVTMVASIAWTLGIKVLTGKE-VDGSLF-NIDAWTQEIDRIAIDRMDDCE 238
                                   ***8.....4666778***.9999...*********************9999.999999.9*****************999 PP

                                   -TT CS
                                   xxx RF
                          ThiF 242 clv 244
                                   c+v
  gi|13541774|ref|NP_111462.1| 239 CCV 241
                                   975 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.1   3.5e-08   0.00013       7      58 ..      22      75 ..      12     143 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 3.5e-08
                                  HS..TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHH..T. CS
                  Shikimate_DH  7 leslkekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeel..kg 58
                                  l++++++ v +iG G +++l+a  ++++g+kk++++ R++   ++l +++  ++
  gi|13541774|ref|NP_111462.1| 22 LKKIRNSVVSVIGVGGVGSLIADLFVRSGIKKLIIVDRDYVTSSNLYRQVlyDE 75
                                  557888999********************************9999999874344 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.0   1.2e-05     0.042      29      70 ..      20      62 ..       5      78 .. 0.81
   2 ?   -0.6   0.0       0.2   7.3e+02      74     119 ..     100     144 ..      81     147 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.2e-05
                                  GSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-.EEEEESSSHH CS
                  2-Hacid_dh_C 29 llgkelsgktvGiiGlGrIGqavakrlkafgm.kviaydrskk 70
                                     k+++++ v +iG+G +G+ +a+++   g+ k+i++dr   
  gi|13541774|ref|NP_111462.1| 20 DDLKKIRNSVVSVIGVGGVGSLIADLFVRSGIkKLIIVDRDYV 62
                                  556899*************************977888888655 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.2
                                   CHHHHTCEECSHHHHHHH-SEEEE-S--STTTTTSBSHHHHHCSTT CS
                  2-Hacid_dh_C  74 eeeelgvelvsleellaesDivslhlpltpetrhlinaeelakmkk 119
                                   e++++ ++  + e ++++sD ++  +  +   r ++n+++ + mk+
  gi|13541774|ref|NP_111462.1| 100 EARNETFDAGNAERIVSSSDLIMDGTD-NLTSRLILNDAAVKNMKP 144
                                   455566667788889999998865554.556677888888888886 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 ?   12.4   0.6   3.1e-05      0.11       2      72 ..      30      98 ..      29     167 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.1e-05
                                  EEEE--SCCHHHHHHHHHHTT-E.EEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS-HHHHCCCHHCEEEES- CS
                       3HCDH_N  2 vaviGaGtmGagiaavfasagle.Vvlvdiseealekalekieksleklvekgklkeeeveaalarisfttd 72
                                  v viG G +G+ ia +f+++g++   +vd++  +  +     ++ l      g  k+e ++++l++++ + +
  gi|13541774|ref|NP_111462.1| 30 VSVIGVGGVGSLIADLFVRSGIKkLIIVDRDYVTSSNL---YRQVLYDENDIGDSKAEAAKRRLSKVNSDVE 98
                                  89*******************97244455533322222...2223334444455555555555555554444 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   1.5   0.00019       0.7       2      40 ..      31      67 ..      30     143 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00019
                                  EEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHH CS
               Sacchrp_dh_NADP  2 liiGaGsvGqavaellarhfdvdaeitvadrskekleal 40
                                   +iG G+vG+ +a+l +r++    +++++dr+     +l
  gi|13541774|ref|NP_111462.1| 31 SVIGVGGVGSLIADLFVRSGIK--KLIIVDRDYVTSSNL 67
                                  69*****************966..9*****986555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       688  (0.0383736); expected 358.6 (0.02)
Passed bias filter:                      541  (0.0301746); 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: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 1660.93
//
Query:       gi|13541775|ref|NP_111463.1|  [L=335]
Description: alcohol dehydrogenase [Thermoplasma volcanium GSS1]
Scores for complete 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-30  104.6   0.0    5.2e-30  103.5   0.0    1.6  1  ADH_N           Alcohol dehydrogenase GroES-like domain
      3e-30  104.9   0.0      5e-30  104.1   0.0    1.4  1  ADH_zinc_N      Zinc-binding dehydrogenase
    3.2e-14   54.1   0.0    5.5e-14   53.4   0.0    1.4  1  ADH_zinc_N_2    Zinc-binding dehydrogenase
    5.8e-09   35.8   0.1    8.3e-09   35.2   0.1    1.1  1  Glu_dehyd_C     Glucose dehydrogenase C-terminus
    3.5e-05   23.2   0.5    6.2e-05   22.4   0.5    1.3  1  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
     0.0083   15.6   0.2      0.013   15.0   0.2    1.2  1  PALP            Pyridoxal-phosphate dependent enzyme
     0.0088   16.0   0.0      0.013   15.3   0.0    1.3  1  NAD_binding_10  NAD(P)H-binding
     0.0096   15.3   0.3      0.015   14.6   0.3    1.2  1  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
  ------ inclusion threshold ------
       0.01   15.3   0.6      0.027   13.9   0.6    1.8  1  adh_short       short chain dehydrogenase
      0.011   16.0   0.0      0.025   14.9   0.0    1.5  1  TrkA_N          TrkA-N domain
      0.014   15.1   0.3      0.024   14.4   0.3    1.3  1  ELFV_dehydrog   Glutamate/Leucine/Phenylalanine/Valine dehydr
      0.031   14.4   0.1      0.061   13.5   0.1    1.4  1  ACP_syn_III_C   3-Oxoacyl-[acyl-carrier-protein (ACP)] syntha


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 !  103.5   0.0   3.5e-33   5.2e-30       2     108 ..      26     131 ..      25     132 .. 0.97

  Alignments for each domain:
  == domain 1  score: 103.5 bits;  conditional E-value: 3.5e-33
                                   TEEEEEEEEEEE-HHHHHHHTTSTTTTSSSSEE---EEEEEEEEESTT-CS--TT-EEEE-SEEE-SSSHHHHTT-GGG-T CS
                         ADH_N   2 gevlikvkaagiCgsDlhilkggkelevklplilGHEivGeveevgpevkklkvGdrVvvepliscgeCaaCkegeenlCe 82 
                                   +evlik ++ag+C  Dl  ++g   ++ +lp+i GHEi G+v++vg++v+ ++ Gd+V   + i+cg+C+ C++g+enlC+
  gi|13541775|ref|NP_111463.1|  26 NEVLIKQEYAGVCYRDLLAATG-FFPRIALPMIQGHEIGGTVVKVGDKVEAFRPGDKVSSLIYIPCGKCEFCRSGNENLCP 105
                                   89********************.8********************************************************* PP

                                   TBEETTTSS-SSSBSEEEECGGGEEE CS
                         ADH_N  83 eakllgvsldGgfaeyvvvpekklvk 108
                                   ++k lg +++Ggf +yv +pe +lvk
  gi|13541775|ref|NP_111463.1| 106 YKKSLGEEVQGGFRQYVNIPEISLVK 131
                                   ********************988886 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.1   0.0   3.3e-33     5e-30       1     129 [.     175     298 ..     175     299 .. 0.97

  Alignments for each domain:
  == domain 1  score: 104.1 bits;  conditional E-value: 3.3e-33
                                   HHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTESEEEETTTCHHHHHHHHHTTTSSEEEEEESSCSHHHHHHHHHCEEE CS
                    ADH_zinc_N   1 gvGlaavqlAkalGaeviavdsseeklelakklGadevinykeadlverikeltggegvdvvfecvGsgatleaalkllkp 81 
                                   gvG++av++Aka+Ga+via   s+ekl+l++k+Gad++++ ++ +++e++k+l    g+d+v+ecvG   t+e++l++l+ 
  gi|13541775|ref|NP_111463.1| 175 GVGIHAVEMAKAFGATVIAETTSPEKLDLLEKIGADYIVDGNS-KFNEDVKKLG---GADIVLECVG-IYTFERSLRSLNN 250
                                   9****************************************77.**********...9*********.************* PP

                                   EEEEEECSC.TSSEEEEEHHHHHHTT-EEEEE-SSCHHHHHHHHHHHHH CS
                    ADH_zinc_N  82 gGrlvvvGg.gkgeeefdlrnlllkeksilGsllgslreefkealdlla 129
                                   gG++v++G    ++ +++l+ ++lk  +i+Gs+ ++ +++++eal++++
  gi|13541775|ref|NP_111463.1| 251 GGKMVIIGNvKPDPVSLPLGLIILKGNTIRGSISST-KKDVEEALNMVS 298
                                   ********98888888********************.9******99876 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 !   53.4   0.0   3.7e-17   5.5e-14       1     131 [.     207     331 ..     207     333 .. 0.78

  Alignments for each domain:
  == domain 1  score: 53.4 bits;  conditional E-value: 3.7e-17
                                   TT-SEEE..ETT.STTHHHHH-TT-EEEEEES-HHHHH.HHHHHHEEEEEEEEE----.S-EEE-CHHHCTTT-EEEE--G CS
                  ADH_zinc_N_2   1 lGAdevi..dyr.tedfeaatggegvDvvldtvggealleaslkvlpggGrlvsiggpplsaallkpakkrkgrsvkyefl 78 
                                   +GAd ++  +++ +ed+ +++  +g D+vl++vg  ++ e+sl+ l++gG++v ig+     +  ++++  +   +k +++
  gi|13541775|ref|NP_111463.1| 207 IGADYIVdgNSKfNEDV-KKL--GGADIVLECVGIYTF-ERSLRSLNNGGKMVIIGN----VKPDPVSLPLGLIILKGNTI 279
                                   59*****6666666666.355..679********9999.*******888*******6....34444444444444444444 PP

                                   GG...-.-HHHHHHHHHHHHHHH----EEEEEEGGGHHHHHHHHHSS--SSEE CS
                  ADH_zinc_N_2  79 fsmkasaqadileelaalieeGklrpvvdrvfpleeaaeAhrylesgrarGKi 131
                                       +s ++d  ee ++++++G ++p v+++ ++++++eA+++++ ++  G+i
  gi|13541775|ref|NP_111463.1| 280 RGSISSTKKD-VEEALNMVSKGMIKPIVGKEIDISQINEAYKLMKDKKSSGRI 331
                                   4433334777.****************************************98 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 !   35.2   0.1   5.6e-12   8.3e-09      31     202 ..     164     322 ..     151     333 .. 0.84

  Alignments for each domain:
  == domain 1  score: 35.2 bits;  conditional E-value: 5.6e-12
                   Glu_dehyd_C  31 pesalvlGaG.slGLLalalleaeerglervyvlgrrdrpdptidlveelGatYvdsretpvdeipeaseemdlvvEaTGs 110
                                    +++l++GaG  +G+ a+ + +    ++   +v++ +     ++dl+e++Ga Y+   +++ +e  +     d+v+E+ G 
  gi|13541775|ref|NP_111463.1| 164 GKKVLITGAGgGVGIHAVEMAK----AFG-ATVIAETTS-PEKLDLLEKIGADYIVDGNSKFNEDVKKLGGADIVLECVGI 238
                                   5789****97369998855554....576.456775444.5689**********999999998888999***********8 PP

                   Glu_dehyd_C 111 akhafeaiealapnGvaaLlGvpedsevevdggelhrelvleNkalvGsvNanrrhfeaavdtLaalpeslldelvtkvvd 191
                                         +++ l+  G ++++G  ++  v++  g     ++l+ + + Gs+ +  +  e+a++    +++ +++ +v k++d
  gi|13541775|ref|NP_111463.1| 239 YT-FERSLRSLNNGGKMVIIGNVKPDPVSLPLGL----IILKGNTIRGSISSTKKDVEEALNM---VSKGMIKPIVGKEID 311
                                   65.4579*******************9***9997....58999*************9998665...56789********** PP

                   Glu_dehyd_C 192 ldeleeAfedd 202
                                   +++++eA++  
  gi|13541775|ref|NP_111463.1| 312 ISQINEAYKLM 322
                                   ********854 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.5   4.1e-08   6.2e-05      28     100 ..     164     237 ..     144     242 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 4.1e-08
                                   --EEEEEST.SHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTTCECEEHCHHHHHHHHHHHH-SEEEE--- CS
                   AlaDh_PNT_C  28 pakvlviGg.GvaGlqAiatakglgakVtvlDvrparleqleslgakfvevlksqeellaeavkeadvvigtvl 100
                                     kvl+ G+ G +G++A+++ak++ga+V +  ++p++l  le++ga ++   +s+ ++  +++  ad+v  +v 
  gi|13541775|ref|NP_111463.1| 164 GKKVLITGAgGGVGIHAVEMAKAFGATVIAETTSPEKLDLLEKIGADYIVDGNSKFNEDVKKLGGADIVLECVG 237
                                   4589***972579**********************************887777777777777888999887665 PP

>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.2   8.6e-06     0.013      42     113 ..     151     221 ..     145     239 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 8.6e-06
                                   HHHHHHH.HHTTTTTSEEEEEBSSHHHHHHHHHHHHHT-EEEEEEETTS-HHHHHHHHHTT-EEEEECCH.HHH CS
                          PALP  42 aeyllar.lkegtgaktvveassGNhgralAaaaallGlkvtivvpadaspekvallrllGaevvevggd.yde 113
                                   ++++l+r  k g+g+k+++++ +G  g+ +  +a+++G     v+ +++spek++ll+  Ga+ ++ g++ ++e
  gi|13541775|ref|NP_111463.1| 151 LYHALKRmGKAGEGKKVLITGAGGGVGIHAVEMAKAFG---ATVIAETTSPEKLDLLEKIGADYIVDGNSkFNE 221
                                   3455555533447899**********************...7778899999***********988763333555 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0     9e-06     0.013       1      69 [.     171     237 ..     171     254 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 9e-06
                                   TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES-- CS
                NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtdvedlaealkgadaVvsalg 69 
                                   GA G+vG ++v+ + a  g +v a + +pekl+ le+  +  +v+g+    ed+++ l gad+V+ ++g
  gi|13541775|ref|NP_111463.1| 171 GAGGGVGIHAVEMAKAF-GATVIAETTSPEKLDLLEKIGADYIVDGNSKFNEDVKK-LGGADIVLECVG 237
                                   9****************.59*************88876666799999999999765.899999987775 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.3     1e-05     0.015      28      78 ..     156     207 ..     144     217 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1e-05
                                   CGSBS-GTTSEEEEES-S.HHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHH CS
                  2-Hacid_dh_C  28 allgkelsgktvGiiGlG.rIGqavakrlkafgmkviaydrskkkeeeeeel 78 
                                   + +gk  +gk+v i G+G  +G ++ +++kafg+ via  +s++k +  e+ 
  gi|13541775|ref|NP_111463.1| 156 KRMGKAGEGKKVLITGAGgGVGIHAVEMAKAFGATVIAETTSPEKLDLLEKI 207
                                   67888999********9637******************99998876655555 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.6   1.8e-05     0.027       1      46 [.     165     209 ..     165     244 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.8e-05
                                   SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHH CS
                     adh_short   1 kvvlvtGassGIGraiakelakeGakvvvvdrseekleevakelke 46 
                                   k vl+tGa++G+G   ++   + Ga+v++   s+ekl  +++++++
  gi|13541775|ref|NP_111463.1| 165 KKVLITGAGGGVGIHAVEMAKAFGATVIAETTSPEKL-DLLEKIGA 209
                                   789**************************99999999.67777765 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   1.7e-05     0.025      77     114 ..     178     213 ..     165     214 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.7e-05
                                   HHHHHHHHHHTSSSEEEEEESSGGGHHHHHHHTTSEEE CS
                        TrkA_N  77 ilavllakelnpkkkiiaraqdpehaellkklgadvvi 114
                                   i av++ak  ++ +++ia++ +pe+ +ll+k+gad+++
  gi|13541775|ref|NP_111463.1| 178 IHAVEMAKA-FG-ATVIAETTSPEKLDLLEKIGADYIV 213
                                   778999996.44.57*********************98 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 ?   14.4   0.3   1.6e-05     0.024      11      60 ..     140     193 ..     135     210 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.6e-05
                                   HHHHHHHHHHHHHHTTTS...-STTEEEEEE--.SHHHHHHHHHHHHCT-EEEE CS
                 ELFV_dehydrog  11 glGvvyyveemlkklkld...slegkrvaisGs.Gnvgsyaallltelgakvva 60 
                                   +l+++++v  ml ++  +     egk+v i G  G vg +a+++++  ga+v+a
  gi|13541775|ref|NP_111463.1| 140 SLSLAACVTGMLYHALKRmgkAGEGKKVLITGAgGGVGIHAVEMAKAFGATVIA 193
                                   667777777776663222444689****************************98 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 ?   13.5   0.1   4.1e-05     0.061      37      86 ..     131     181 ..     118     184 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.1e-05
                                   GB--THHHH-B-GGGHHHHHHHHHHHT.TSS-TT-EEEEEEEETTTEEEEE CS
                 ACP_syn_III_C  37 kvvvnldeyGntsaasiplaLdeavee.gklkpgdlvllvgfGaGltwgaa 86 
                                   k+++n+d      aa +  +L +a+++ gk  +g++vl++g+G+G+ + a+
  gi|13541775|ref|NP_111463.1| 131 KAPNNVDGASLSLAACVTGMLYHALKRmGKAGEGKKVLITGAGGGVGIHAV 181
                                   67777777777778888888877776527****************998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       712  (0.0397122); expected 358.6 (0.02)
Passed bias filter:                      603  (0.0336327); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.66u 0.32s 00:00:00.98 Elapsed: 00:00:00.53
# Mc/sec: 1895.73
//
Query:       gi|13541776|ref|NP_111464.1|  [L=132]
Description: metal-dependent transcription regulator [Thermoplasma volcanium GSS1]
Scores for 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-13   48.9   0.0    7.3e-13   48.4   0.0    1.2  1  Fe_dep_repr_C    Iron dependent repressor, metal binding and 
    5.9e-07   29.6   0.0    1.1e-06   28.7   0.0    1.5  1  Fe_dep_repress   Iron dependent repressor, N-terminal DNA bin
    9.5e-06   25.5   0.1    1.9e-05   24.5   0.0    1.5  2  HTH_Crp_2        Crp-like helix-turn-helix domain
    1.8e-05   24.6   0.0    3.5e-05   23.7   0.0    1.6  1  MarR             MarR family
    6.8e-05   22.3   0.0     0.0002   20.9   0.0    1.7  2  HTH_24           Winged helix-turn-helix DNA-binding
     0.0004   20.7   0.0    0.00052   20.3   0.0    1.2  1  Rrf2             Transcriptional regulator
    0.00041   20.1   0.1    0.00066   19.4   0.1    1.3  1  LexA_DNA_bind    LexA DNA binding domain
    0.00049   19.9   0.0     0.0015   18.4   0.0    1.7  2  MarR_2           MarR family
     0.0013   18.5   0.1     0.0033   17.3   0.0    1.7  2  TrmB             Sugar-specific transcriptional regulator Trm
     0.0017   18.8   0.0     0.0029   18.1   0.0    1.4  1  HTH_27           Winged helix DNA-binding domain
      0.008   16.1   0.4      0.013   15.4   0.1    1.5  2  HTH_45           Winged helix-turn-helix
     0.0083   16.3   0.0       0.01   16.0   0.0    1.4  1  B-block_TFIIIC   B-block binding subunit of TFIIIC
  ------ inclusion threshold ------
       0.02   14.8   0.0      0.036   14.0   0.0    1.5  1  PadR             Transcriptional regulator PadR-like family
      0.028   14.2   0.0       0.13   12.1   0.0    1.9  2  HTH_IclR         IclR helix-turn-helix domain
      0.041   14.2   0.0      0.091   13.1   0.0    1.5  2  Penicillinase_R  Penicillinase repressor
      0.079   12.8   0.0       0.18   11.7   0.0    1.5  1  HTH_10           HTH DNA binding domain
       0.16   12.0   0.0       0.27   11.2   0.0    1.5  1  HTH_36           Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> Fe_dep_repr_C  Iron dependent repressor, metal binding and dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.4   0.0   6.9e-16   7.3e-13       1      68 [.      64     130 ..      64     131 .. 0.97

  Alignments for each domain:
  == domain 1  score: 48.4 bits;  conditional E-value: 6.9e-16
                                   -HHHHHHHHHHHHHHHHHHHHHHHHCT--CCCHHHHCCCCGGGS-HHHHHHHHHHCT-.SB-TTS-B- CS
                 Fe_dep_repr_C   1 TekGrelAkrlvrrhrllerfLvdvlgvdweeaheeAerlEhalseelierldellgfpeecPhgdpi 68 
                                   T +G+e+ kr+v  hr+le++ ++  g+d++ea+++  +++  ++ + ++++ + lg+p++cPhg++i
  gi|13541776|ref|NP_111464.1|  64 TIDGEEEYKRIVTVHRTLEVLYSR-SGIDADEACKKIGNFDFLVDYDDAKKISNALGNPKKCPHGKEI 130
                                   568*******************77.*****************************************98 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.0   1.1e-09   1.1e-06      19      53 ..      21      55 ..       4      60 .. 0.86

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 1.1e-09
                                  HHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                Fe_dep_repress 19 ekkvvktkdlaerLnvspssVsemlkkLekdGyve 53
                                  +  +v+ kdl+  +n++p+sV e l++Le++G+++
  gi|13541776|ref|NP_111464.1| 21 SVFPVRLKDLSGMMNIKPPSVLEILNRLEEKGLIK 55
                                  6667999**************************86 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.0   1.8e-08   1.9e-05      18      57 ..      22      61 ..       7      67 .. 0.82
   2 ?   -3.1   0.0       7.7   8.1e+03      36      45 ..      75      84 ..      73      90 .. 0.71

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 1.8e-08
                                  EEEEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEETEE.E CS
                     HTH_Crp_2 18 ielpltqeelAsmlGltretvsrilseLkreglisrgrr.i 57
                                  + +p+  ++l+ m+++ + +v  il++L+++gli++ r+ i
  gi|13541776|ref|NP_111464.1| 22 V-FPVRLKDLSGMMNIKPPSVLEILNRLEEKGLIKKDRGmI 61
                                  3.89999****************************765534 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 7.7
                                  HHHHHHHHHH CS
                     HTH_Crp_2 36 etvsrilseL 45
                                  +tv r+l  L
  gi|13541776|ref|NP_111464.1| 75 VTVHRTLEVL 84
                                  6788887655 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0   3.3e-08   3.5e-05      17      49 ..      24      56 ..       4      59 .. 0.85

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 3.3e-08
                                  TEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                          MarR 17 plsvseLakklgvskstvtrvldrLekkGlieR 49
                                  p ++++L  ++++++++v ++l rLe+kGli++
  gi|13541776|ref|NP_111464.1| 24 PVRLKDLSGMMNIKPPSVLEILNRLEEKGLIKK 56
                                  57899**************************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 !   20.9   0.0   1.9e-07    0.0002      21      48 .]      28      55 ..      26      55 .. 0.96
   2 ?   -2.0   0.0       2.6   2.7e+03       7      28 ..      79     100 ..      76     100 .. 0.70

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 1.9e-07
                        HTH_24 21 reLAerlglSpstvnrrlkrLeeeGlIk 48
                                  ++L+ + ++ p+ v++ l+rLee+GlIk
  gi|13541776|ref|NP_111464.1| 28 KDLSGMMNIKPPSVLEILNRLEEKGLIK 55
                                  79*************************8 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.6
                        HTH_24   7 kILelLqknprisqreLAerlg 28 
                                   + Le+L+  ++i   e ++++g
  gi|13541776|ref|NP_111464.1|  79 RTLEVLYSRSGIDADEACKKIG 100
                                   5688888888887777777765 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   4.9e-07   0.00052      13      60 ..      11      59 ..       1      69 [. 0.87

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 4.9e-07
                                  HHHHHHHSSTCC-.B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETT CS
                          Rrf2 13 allyLakeeeeep.vsseeiaerqnispsylekilakLrkaglvksvrG 60
                                  +l+++++ +++   v++++++ ++ni+p+ +  il++L+++gl+k  rG
  gi|13541776|ref|NP_111464.1| 11 CLIMIKEFKNSVFpVRLKDLSGMMNIKPPSVLEILNRLEEKGLIKKDRG 59
                                  67777776666545**********************************9 PP

>> LexA_DNA_bind  LexA DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.1   6.3e-07   0.00066       1      60 [.       1      58 [.       1      60 [. 0.92

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 6.3e-07
                                  XX---HHHHHHHHHHHHHHHHHSS---HHHHHHHHTS-.HHHHHHHHHHHHHTTSEE-GG CS
                 LexA_DNA_bind  1 mkkLTerQrevldlikasieetgypPsireiaralglkSpsaveehLkaLerKGyierdp 60
                                  mk  T++ r+ l +ik++ ++  +p   ++++  +++k p +v e L++Le KG+i+ d 
  gi|13541776|ref|NP_111464.1|  1 MKTITKKERDCLIMIKEF-KNSVFPVRLKDLSGMMNIK-PPSVLEILNRLEEKGLIKKDR 58
                                  8999***********986.7789***************.999**************9876 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   1.4e-06    0.0015      21      54 ..      24      57 ..       4      60 .. 0.80
   2 ?   -1.3   0.0         2   2.1e+03       6      27 ..      76      95 ..      75     100 .. 0.64

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.4e-06
                                  EEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                        MarR_2 21 dltvgelarrlglsksavsrilkrLvaaGLverr 54
                                  +++ ++l   +++++++v  il+rL+++GL+ + 
  gi|13541776|ref|NP_111464.1| 24 PVRLKDLSGMMNIKPPSVLEILNRLEEKGLIKKD 57
                                  579999*************************875 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2
                                  HHHHHHHHHHCTTTSEEEHHHH CS
                        MarR_2  6 aqarvLaaLgrrpgrdltvgel 27
                                  + +r L +L+ r g  + + e 
  gi|13541776|ref|NP_111464.1| 76 TVHRTLEVLYSRSG--IDADEA 95
                                  45677777777777..666555 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   3.1e-06    0.0033      24      57 ..      26      59 ..      23      79 .. 0.85
   2 ?   -2.9   0.0       6.1   6.4e+03      25      36 ..     111     122 ..     109     123 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3.1e-06
                                  HHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESS CS
                          TrmB 24 tadeiaeelgvprskvYevLrsLedkGlVerekg 57
                                  + ++++ + ++  ++v e+L++Le+kGl+++ +g
  gi|13541776|ref|NP_111464.1| 26 RLKDLSGMMNIKPPSVLEILNRLEEKGLIKKDRG 59
                                  5689999***********************9987 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 6.1
                                   HCHHCCCTTSSC CS
                          TrmB  25 adeiaeelgvpr 36 
                                   a++i+++lg p+
  gi|13541776|ref|NP_111464.1| 111 AKKISNALGNPK 122
                                   788999998876 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   2.7e-06    0.0029      18      57 ..      24      58 ..      20      67 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2.7e-06
                        HTH_27 18 rkkladlcgrlnvedshisyslkkLtekGLvertgdeadr 57
                                  +++l+dl+g++n+   ++ ++l++L+ekGL+++     dr
  gi|13541776|ref|NP_111464.1| 24 PVRLKDLSGMMNIKPPSVLEILNRLEEKGLIKK-----DR 58
                                  6789***************************43.....33 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       7.8   8.2e+03      58      73 ..       4      19 ..       3      21 .. 0.72
   2 !   15.4   0.1   1.3e-05     0.013      38      75 ..      43      80 ..      32      82 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 7.8
                        HTH_45 58 lTekGlelleklkele 73
                                  +T+k ++ l  +ke++
  gi|13541776|ref|NP_111464.1|  4 ITKKERDCLIMIKEFK 19
                                  7888888887777776 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 1.3e-05
                        HTH_45 38 kYLdmLvekglikkskekYvlTekGlelleklkeleel 75
                                  + L+ L ekglikk+ ++  lT  G+e ++++ +++++
  gi|13541776|ref|NP_111464.1| 43 EILNRLEEKGLIKKDRGMIALTIDGEEEYKRIVTVHRT 80
                                  6799**************************99999886 PP

>> B-block_TFIIIC  B-block binding subunit of TFIIIC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   9.4e-06      0.01      22      52 ..      28      58 ..      25     115 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 9.4e-06
                B-block_TFIIIC 22 sdLakeskqdprslfyrlksLekkgLIvkqs 52
                                  +dL+  ++++p s+  +l+ Le+kgLI+k  
  gi|13541776|ref|NP_111464.1| 28 KDLSGMMNIKPPSVLEILNRLEEKGLIKKDR 58
                                  6999************************975 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   3.4e-05     0.036      18      51 ..      26      58 ..      24      73 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.4e-05
                                  HHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEE CS
                          PadR 18 eleelsegllelseGslYpaLkrLekeglvesew 51
                                  +l++l +g++++++ s+  +L+rLe++gl+++ +
  gi|13541776|ref|NP_111464.1| 26 RLKDL-SGMMNIKPPSVLEILNRLEEKGLIKKDR 58
                                  57888.599*********************9875 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00013      0.13      18      51 ..      24      57 ..      16      58 .. 0.92
   2 ?   -0.7   0.2       1.2   1.3e+03      34      42 ..      76      84 ..      76      87 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00013
                                  S-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE.. CS
                      HTH_IclR 18 eltlselArrtglpkStvhRlLqtLvelGyveqd 51
                                  +++l++l+    + +++v  +L+ L+e G++++d
  gi|13541776|ref|NP_111464.1| 24 PVRLKDLSGMMNIKPPSVLEILNRLEEKGLIKKD 57
                                  6799999999**********************98 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.2
                                  HHHHHHHHH CS
                      HTH_IclR 34 tvhRlLqtL 42
                                  tvhR L  L
  gi|13541776|ref|NP_111464.1| 76 TVHRTLEVL 84
                                  799988876 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   8.7e-05     0.091       2      55 ..       5      58 ..       4      63 .. 0.76
   2 ?   -1.8   0.0       3.7   3.9e+03      37      53 ..      76      92 ..      61     113 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 8.7e-05
                                  --S-SHHHHHHHHHS-EEHHHHHHT--GGG---HHHHHHHHHHHHHTTS-EEEE CS
               Penicillinase_R  2 gelEaevmeilwekgeatvkevveeleeekelaysTVktllrrLvkKgllsrek 55
                                  ++ E+  + ++ e ++       + l+  ++ ++ +V  +l+rL++Kgl+++++
  gi|13541776|ref|NP_111464.1|  5 TKKERDCLIMIKEFKNSVFPVRLKDLSGMMNIKPPSVLEILNRLEEKGLIKKDR 58
                                  56666666666666664444445678999999******************9876 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 3.7
                                  HHHHHHHHHHHTTS-EE CS
               Penicillinase_R 37 TVktllrrLvkKgllsr 53
                                  TV+ +l+ L+ +  +++
  gi|13541776|ref|NP_111464.1| 76 TVHRTLEVLYSRSGIDA 92
                                  66666666665555444 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00017      0.18      24      50 ..      25      51 ..      24      53 .. 0.95

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00017
                        HTH_10 24 vtlkeLAkelGIskstlsehLrkaesk 50
                                  v+lk+L+  ++I++++++e+L++ e+k
  gi|13541776|ref|NP_111464.1| 25 VRLKDLSGMMNIKPPSVLEILNRLEEK 51
                                  689********************9998 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00026      0.27      22      55 .]      20      54 ..       4      54 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00026
                        HTH_36 22 ggcfp.sqetlakrlglsknTvsraikeLeqlGyi 55
                                  + +fp   ++l+  ++++  +v  +++ Le++G+i
  gi|13541776|ref|NP_111464.1| 20 NSVFPvRLKDLSGMMNIKPPSVLEILNRLEEKGLI 54
                                  558999999************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       595  (0.0331865); expected 358.6 (0.02)
Passed bias filter:                      529  (0.0295053); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.41u 0.30s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 908.48
//
Query:       gi|13541777|ref|NP_111465.1|  [L=53]
Description: hypothetical protein TVN0946 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       370  (0.020637); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.45
# Mc/sec: 356.90
//
Query:       gi|13541778|ref|NP_111466.1|  [L=745]
Description: ATPase of the AAA+ class involved in cell division [Thermoplasma volcanium GSS1]
Scores for complete 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-100  332.4   0.0    4.7e-50  169.4   0.0    2.6  2  AAA              ATPase family associated with various cellul
    2.7e-31  107.1   0.0    4.3e-18   64.8   0.0    2.7  2  AAA_lid_3        AAA+ lid domain
    3.2e-25   88.1   2.6    1.3e-24   86.2   2.6    2.1  1  CDC48_N          Cell division protein 48 (CDC48), N-terminal
    3.7e-18   66.2   0.1    1.6e-07   31.6   0.0    3.0  3  AAA_2            AAA domain (Cdc48 subfamily)
    6.8e-16   58.4   0.0    8.9e-08   32.0   0.0    2.7  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    2.1e-13   51.0   0.0    4.1e-06   27.3   0.0    3.0  2  AAA_16           AAA ATPase domain
    1.2e-11   44.7   0.0    1.8e-05   24.8   0.0    2.5  2  AAA_14           AAA domain
    4.2e-11   43.0   0.5    0.00013   22.0   0.1    3.9  2  AAA_5            AAA domain (dynein-related subfamily)
    3.8e-10   40.2   0.6     0.0094   16.2   0.0    4.0  4  AAA_22           AAA domain
    1.3e-09   37.7   1.2     0.0012   18.1   0.0    3.2  3  TIP49            TIP49 P-loop domain
    1.1e-08   34.8   0.1    2.5e-08   33.6   0.1    1.7  1  CDC48_2          Cell division protein 48 (CDC48), domain 2
    2.1e-08   34.4   0.0     0.0011   19.2   0.0    2.5  2  AAA_33           AAA domain
    1.5e-07   31.3   0.0      0.014   15.1   0.0    2.5  2  IstB_IS21        IstB-like ATP binding protein
    1.7e-07   31.8   0.1      0.023   15.3   0.0    3.5  3  AAA_18           AAA domain
    8.8e-07   28.7   3.1          2    7.9   0.1    4.6  4  AAA_25           AAA domain
    1.1e-06   29.0   0.0      0.087   13.2   0.0    2.7  2  RNA_helicase     RNA helicase
    2.8e-06   27.2   0.0       0.11   12.2   0.0    2.6  2  AAA_24           AAA domain
    4.2e-06   26.3   0.1       0.12   11.8   0.0    2.4  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    9.2e-06   25.5   0.1       0.14   11.8   0.0    3.7  2  Sigma54_activat  Sigma-54 interaction domain
    1.7e-05   25.1   0.0      0.039   14.2   0.0    2.5  2  AAA_28           AAA domain
    3.3e-05   23.8   0.0       0.21   11.4   0.0    2.6  2  AAA_3            ATPase family associated with various cellul
    4.4e-05   23.5   0.0       0.19   11.8   0.0    2.4  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
    4.7e-05   23.9   0.1      0.087   13.3   0.0    2.7  2  ABC_tran         ABC transporter
    5.5e-05   22.6   0.0     0.0054   16.0   0.0    2.2  2  DUF2075          Uncharacterized conserved protein (DUF2075)
    6.5e-05   22.5   0.0       0.37   10.3   0.0    2.5  2  AAA_7            P-loop containing dynein motor region
    0.00014   22.3   0.0       0.71   10.3   0.0    2.9  2  AAA_17           AAA domain
    0.00036   20.5   1.2        1.4    8.8   0.1    3.5  3  ATPase_2         ATPase domain predominantly from Archaea
    0.00044   19.6   0.1        0.2   10.9   0.0    2.5  2  Zeta_toxin       Zeta toxin
    0.00056   19.1   0.0       0.69    9.0   0.0    2.4  2  DUF815           Protein of unknown function (DUF815)
    0.00071   18.8   0.0        1.4    8.0   0.0    2.8  2  NB-ARC           NB-ARC domain
    0.00082   19.3   0.5        1.2    9.1   0.0    3.0  2  Vps4_C           Vps4 C terminal oligomerisation domain
    0.00098   19.1   0.1        1.8    8.4   0.0    3.3  3  NACHT            NACHT domain
      0.001   18.5   5.8          3    7.1   0.0    4.3  5  ATPase           KaiC
     0.0041   16.2   0.1       0.55    9.3   0.0    2.2  2  Parvo_NS1        Parvovirus non-structural protein NS1
     0.0042   16.6   3.2       0.55    9.7   0.1    3.0  2  PhoH             PhoH-like protein
     0.0045   16.7   0.1        1.3    8.7   0.0    2.8  2  AAA_30           AAA domain
     0.0051   16.7   0.0        2.1    8.1   0.0    3.1  2  Bac_DnaA         Bacterial dnaA  protein
     0.0062   16.4   0.0        2.5    7.8   0.0    2.6  2  AAA_11           AAA domain
     0.0069   16.7   0.7        2.8    8.3   0.2    2.8  2  AAA_19           AAA domain
     0.0083   15.8   0.5         44    3.7   0.0    4.4  4  Guanylate_kin    Guanylate kinase
     0.0089   16.1   0.0          1    9.5   0.0    2.5  2  Sigma54_activ_2  Sigma-54 interaction domain
  ------ inclusion threshold ------
       0.02   14.8   3.8        4.8    7.1   0.0    4.0  4  NTPase_1         NTPase
      0.025   14.3   0.1        2.1    8.0   0.0    2.5  2  Cytidylate_kin   Cytidylate kinase
      0.025   14.7   0.0        8.8    6.4   0.0    2.8  2  SKI              Shikimate kinase
      0.054   12.7   0.0        3.5    6.7   0.0    2.2  2  DAP3             Mitochondrial ribosomal death-associated pro
      0.064   13.4   0.1          2    8.5   0.0    2.7  2  Cytidylate_kin2  Cytidylate kinase-like family
      0.065   12.1   0.1         19    4.0   0.0    3.0  3  AFG1_ATPase      AFG1-like ATPase
      0.069   13.4   0.2        1.3    9.3   0.0    2.5  2  Hydin_ADK        Hydin Adenylate kinase-like domain
      0.072   12.5   0.1        7.2    5.9   0.0    2.4  2  IPT              Isopentenyl transferase
      0.086   12.6   0.0        6.7    6.4   0.0    2.2  2  Viral_helicase1  Viral (Superfamily 1) RNA helicase


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  169.4   0.0   1.3e-52   4.7e-50       1     131 [.     227     356 ..     227     357 .. 0.98
   2 !  160.5   0.0   7.8e-50   2.8e-47       2     131 ..     505     634 ..     504     635 .. 0.97

  Alignments for each domain:
  == domain 1  score: 169.4 bits;  conditional E-value: 1.3e-52
                                   EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCHH CS
                           AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsgsesee 81 
                                   v+lyGppGtGKTl+a+ava+e+g++fl+i+g+e++sky g+se+k+re+f++a+e a psi+fiDEid++a++r++ + e+
  gi|13541778|ref|NP_111466.1| 227 VILYGPPGTGKTLIARAVANESGANFLSINGPEIMSKYYGQSEQKLREIFSKAEETA-PSIIFIDEIDSIAPKREEVQGEV 306
                                   79******************************************************9.*********************** PP

                                   HHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                           AAA  82 eervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                   e+rvv+qLlt +dg+k++ + vivigatnr+d +dpal+r gRfdr+iei+
  gi|13541778|ref|NP_111466.1| 307 ERRVVAQLLTLMDGMKERGH-VIVIGATNRIDAVDPALRRpGRFDREIEIG 356
                                   *****************866.***************************996 PP

  == domain 2  score: 160.5 bits;  conditional E-value: 7.8e-50
                                   EEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH.TTCCCHH CS
                           AAA   2 llyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr.sgsesee 81 
                                   llyGppG+GKTllakava+e++++f++i+g+e+lsk+vgesek ire+fk+ak+ a p i+f+DEid++a++r ++s+s++
  gi|13541778|ref|NP_111466.1| 505 LLYGPPGVGKTLLAKAVATESNANFISIKGPEVLSKWVGESEKAIREIFKKAKQVA-PAIVFLDEIDSIAPRRgTTSDSGV 584
                                   9******************************************************9.****************9999**** PP

                                   HHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                           AAA  82 eervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                   +er+vnqLlt ldg +  ++ v+ igatnrpd +dpallr gRfd+ i+i+
  gi|13541778|ref|NP_111466.1| 585 TERIVNQLLTSLDGIEVMNG-VVAIGATNRPDIMDPALLRaGRFDKLIYIP 634
                                   *****************755.***************************997 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.5   0.0   9.7e-13   3.5e-10       4      40 ..     387     423 ..     385     444 .. 0.78
   2 !   64.8   0.0   1.2e-20   4.3e-18       1      45 []     657     703 ..     657     703 .. 0.93

  Alignments for each domain:
  == domain 1  score: 39.5 bits;  conditional E-value: 9.7e-13
                     AAA_lid_3   4 lkeLAerTeGySGADlaalcreAallAlrrgikeitm 40 
                                   l+e A  T G++GADlaal+re+a++Alrr ++ei+ 
  gi|13541778|ref|NP_111466.1| 387 LEEMADYTYGFVGADLAALVRESAMNALRRYLPEIDL 423
                                   68999*************************6655543 PP

  == domain 2  score: 64.8 bits;  conditional E-value: 1.2e-20
                     AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrgik..eitmedfee 45 
                                   dvdl+ +A+rTeGy+GADl++lcreA+++A+r++ +  ++++++f++
  gi|13541778|ref|NP_111466.1| 657 DVDLDSIAQRTEGYVGADLENLCREAGMNAYRENPDatQVSQKNFID 703
                                   9********************************988635*****975 PP

>> CDC48_N  Cell division protein 48 (CDC48), N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.2   2.6   3.6e-27   1.3e-24       2      84 ..       9      91 ..       8      92 .. 0.98

  Alignments for each domain:
  == domain 1  score: 86.2 bits;  conditional E-value: 3.6e-27
                                  EEEECCSS-CSSTTEEEE-HHHHHHHTS-TTSEEEEECCCCEEEEEEEBSTTSTTTTEEEE-HHHHHHHT--TTEEEEEEEE- CS
                       CDC48_N  2 LrVaeapqedvgrgivridpedmeelglepgdvveiegkrkTvaivwpaepedegkgiIrmdgvtRknagvsiGdkVtVrkae 84
                                  LrVaea+++d g ++vr+d++  + l+ e gdvveie+ rkTv  v++a+pede+kgi+r+d+v+R+n+g+siGdkV+Vrk++
  gi|13541778|ref|NP_111466.1|  9 LRVAEANSTDPGMSRVRLDESSRRLLDAEIGDVVEIEKARKTVGRVYRARPEDENKGIVRIDSVMRNNCGASIGDKVRVRKVR 91
                                  9*******************************************************************************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 ?   -2.0   0.0       9.1   3.3e+03      36      76 ..      34      71 ..      21      74 .. 0.67
   2 !   31.6   0.0   4.5e-10   1.6e-07       6     105 ..     227     320 ..     223     334 .. 0.89
   3 !   31.1   0.0   6.6e-10   2.4e-07       4     108 ..     502     601 ..     499     610 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 9.1
                                  EEEEGGG-------THHHHHHHHHTTT-HHHHTTSEEEEET CS
                         AAA_2 36 iradaselleeeevehlvsrligappgyvgaeegGivllDE 76
                                    a+  ++ e e+++++v r   a+p   + e++Giv +D 
  gi|13541778|ref|NP_111466.1| 34 LDAEIGDVVEIEKARKTVGRVYRARP---EDENKGIVRIDS 71
                                  55555566666677777777766666...457888888885 PP

  == domain 2  score: 31.6 bits;  conditional E-value: 4.5e-10
                                   EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG----. CS
                         AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKihpk. 83 
                                   ++l gp g+Gkt++a+a+a+   +    ++  ++  e++     + + ++++  ++   +aee    i+++DEid i+pk 
  gi|13541778|ref|NP_111466.1| 227 VILYGPPGTGKTLIARAVANESGA----NFLSINGPEIMS----KYYGQSEQKLREIFSKAEETApsIIFIDEIDSIAPKr 299
                                   4677******************96....************....999999999999999999999**************97 PP

                                   ---------HHHHHHHHHHHH- CS
                         AAA_2  84 essgadvSregVqrdLLqileg 105
                                   e+ + +v r  V+  LL +++g
  gi|13541778|ref|NP_111466.1| 300 EEVQGEVER-RVVAQLLTLMDG 320
                                   677777766.577789999997 PP

  == domain 3  score: 31.1 bits;  conditional E-value: 6.6e-10
                                   --EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG--- CS
                         AAA_2   4 isilllgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKihp 82 
                                     +ll gp gvGkt+laka+a   ++    ++i +   e+l     + + ++++  ++  ++a++    iv+lDEid i+p
  gi|13541778|ref|NP_111466.1| 502 KGFLLYGPPGVGKTLLAKAVATESNA----NFISIKGPEVLS----KWVGESEKAIREIFKKAKQVApaIVFLDEIDSIAP 574
                                   5699********************96....************....66666677777777777777788************ PP

                                   ---------.-HHHHHHHHHHHH--EE CS
                         AAA_2  83 kessgadvS.regVqrdLLqileggtl 108
                                   ++ +++d    e +++ LL  l+g ++
  gi|13541778|ref|NP_111466.1| 575 RRGTTSDSGvTERIVNQLLTSLDGIEV 601
                                   955555544268899999999998766 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.0   0.0   2.5e-10   8.9e-08      35     103 ..     226     302 ..     218     350 .. 0.83
   2 !   23.4   0.0   1.2e-07   4.2e-05      36      96 ..     504     572 ..     495     580 .. 0.75

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 2.5e-10
                        RuvB_N  35 hvllyGpPGlGkttlakiiakelgvklkitsgPvl......ekagdlaalltnleek..dvlfideihrlsraveev 103
                                    v+lyGpPG Gkt +a+ +a+e g+++ +  gP +      + ++ l  ++++ ee+   ++fidei  ++++ eev
  gi|13541778|ref|NP_111466.1| 226 GVILYGPPGTGKTLIARAVANESGANFLSINGPEImskyygQSEQKLREIFSKAEETapSIIFIDEIDSIAPKREEV 302
                                   599******************************994333333457899999998876337*************9998 PP

  == domain 2  score: 23.4 bits;  conditional E-value: 1.2e-07
                        RuvB_N  36 vllyGpPGlGkttlakiiakelgvklkitsgPvl......ekagdlaalltnleek..dvlfideihrl 96 
                                    llyGpPG+Gkt lak +a+e ++++ +  gP +      e ++ +  ++++ ++    ++f+dei  +
  gi|13541778|ref|NP_111466.1| 504 FLLYGPPGVGKTLLAKAVATESNANFISIKGPEVlskwvgESEKAIREIFKKAKQVapAIVFLDEIDSI 572
                                   69*****************************96533222233455666666665532258888888766 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.0   1.1e-08   4.1e-06      16     142 ..     216     331 ..     212     345 .. 0.73
   2 !   19.9   0.0   2.1e-06   0.00076      25      86 ..     502     553 ..     491     599 .. 0.63

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 1.1e-08
                        AAA_16  16 lervrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesaelea 96 
                                   +er+    p  v+l+G++G+GK+ ++r+++++  ++   fl+ +  +  ++  y +  q l r    +    ++e+a    
  gi|13541778|ref|NP_111466.1| 216 FERLGITPPKGVILYGPPGTGKTLIARAVANESGAN---FLSINGPEI-MSKYYGQSEQKL-R----EIFSKAEETAPSII 287
                                   66666666799*******************866666...999999999.444444444444.4....44444444456666 PP

                        AAA_16  97 wrekleealaavpelagaeasrllellkrllallsrderplvlvlD 142
                                   + +++++ +    e+ g+ ++r+ ++l  l++ ++++++  v+v+ 
  gi|13541778|ref|NP_111466.1| 288 FIDEIDSIAPKREEVQGEVERRVVAQLLTLMDGMKERGH--VIVIG 331
                                   66777777777778888888***************9999..66665 PP

  == domain 2  score: 19.9 bits;  conditional E-value: 2.1e-06
                        AAA_16  25 elvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqll 86 
                                      ll+G++GvGK+ l+++++++ +++   f++ k  +      +s ++    + + +r++ 
  gi|13541778|ref|NP_111466.1| 502 KGFLLYGPPGVGKTLLAKAVATESNAN---FISIKGPEV-----LSKWVGES-E-KAIREIF 553
                                   789******************988888...777777777.....22233333.2.3333333 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0   4.9e-08   1.8e-05       5     104 ..     227     336 ..     224     355 .. 0.81
   2 !   17.1   0.0   1.1e-05    0.0041       5      76 ..     504     572 ..     501     600 .. 0.84

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 4.9e-08
                        AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqev......... 76 
                                   +++ G+  +GKT +++ +++e+     ++l in  +   k + ++e+ l++i++k++e   +++f+DEi  +         
  gi|13541778|ref|NP_111466.1| 227 VILYGPPGTGKTLIARAVANESG---ANFLSINGPEIMSKYYGQSEQKLREIFSKAEETAPSIIFIDEIDSIapkreevqg 304
                                   899****************9999...**********99988887775566666665555899**********999999998 PP

                        AAA_14  77 ...pewekalkslvd.egknldvivtGSnskl 104
                                      +++   l  l+d  +++++viv G  + +
  gi|13541778|ref|NP_111466.1| 305 eveRRVVAQLLTLMDgMKERGHVIVIGATNRI 336
                                   88888888888888854478899998887765 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 1.1e-05
                        AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqev 76 
                                    ++ G+  vGKT l+k ++ e+     +++ i+  +   k   ++ek +++i++k+k+    ++flDEi  +
  gi|13541778|ref|NP_111466.1| 504 FLLYGPPGVGKTLLAKAVATESN---ANFISIKGPEVLSKWVGESEKAIREIFKKAKQVAPAIVFLDEIDSI 572
                                   5789***************9888...8999999888888888888888888888866668899******876 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 !   22.0   0.1   3.6e-07   0.00013       1     136 [.     226     345 ..     226     346 .. 0.72
   2 !   16.2   0.1   2.2e-05    0.0078       2      78 ..     504     573 ..     503     623 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 3.6e-07
                                   EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGGG--. CS
                         AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEverae. 78 
                                   +v+L GppGtgK+ +a+ +a   +++++ +++++ +++   + +       ++l   ++  +a+   ++i+++DE++ +  
  gi|13541778|ref|NP_111466.1| 226 GVILYGPPGTGKTLIARAVANESGANFLSINGPEIMSKYYGQSE-------QKL--REIFSKAEetAPSIIFIDEIDSIAp 297
                                   59*******************************98776432222.......333..3333333334899********9973 PP

                                   ..HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TTHHHHT CS
                         AAA_5  79 ..sevlnsLlslleerrllleeggelvkaknddllerfrviatanpldrslnelspalrs 136
                                      ev++++ +    + l l++g ++ ++        + vi+++n+ d     ++palr+
  gi|13541778|ref|NP_111466.1| 298 krEEVQGEVERRVVAQLLTLMDGMKERGH--------VIVIGATNRID----AVDPALRR 345
                                   33467777766666666666666666655........88999999998....77888775 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 2.2e-05
                                   EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------.G-SEEEEESGGG-- CS
                         AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar.egeilvlDEverae 78 
                                   +lL GppG+gK+ la+ +a   n+++  + +++      ++ ++   ++ ++    ++++a +  ++i++lDE++ + 
  gi|13541778|ref|NP_111466.1| 504 FLLYGPPGVGKTLLAKAVATESNANFISIKGPE------VLSKWV--GESEKAIREIFKKAKQvAPAIVFLDEIDSIA 573
                                   89*****************99999999888887......555555..3333444444444444778888888887665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   2.6e-05    0.0094       8      58 ..     227     277 ..     223     281 .. 0.73
   2 ?    5.9   0.0      0.04        14      73     131 ..     267     333 ..     259     339 .. 0.70
   3 !   14.5   0.0   8.7e-05     0.031       9      41 ..     505     528 ..     499     556 .. 0.77
   4 ?   -0.5   0.0       3.9   1.4e+03      82     112 ..     549     592 ..     538     611 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.6e-05
                        AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevv.fvtlpsstsskdllr 58 
                                   ++++G++GtGKT+ +r ++++  + ++   ++pe++ +++ +s+ +++++++
  gi|13541778|ref|NP_111466.1| 227 VILYGPPGTGKTLIARAVANESGA-NFLSINGPEIMsKYYGQSEQKLREIFS 277
                                   689*****************9743.233335666666777777777777765 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.04
                        AAA_22  73 lsseellealeqalraravielliiDEaqhlr...s.......eealeeLrsllnlsrkgvqliLvGtp 131
                                   +s++ l+e + +a +++   +++ iDE++ +    +        +++ +L +l++  +   ++i++G +
  gi|13541778|ref|NP_111466.1| 267 QSEQKLREIFSKAEETAP--SIIFIDEIDSIApkrEevqgeveRRVVAQLLTLMDGMKERGHVIVIGAT 333
                                   455555555555544444..6**********88751566777788888888999987778888888877 PP

  == domain 3  score: 14.5 bits;  conditional E-value: 8.7e-05
                        AAA_22   9 vvtGesGtGKTtllrrlleqldeeakaeeerpe 41 
                                   +++G++G+GKT+l++ ++ +          ++ 
  gi|13541778|ref|NP_111466.1| 505 LLYGPPGVGKTLLAKAVATES---------NAN 528
                                   79***************9987.........333 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 3.9
                        AAA_22  82 leqalrarav..ielliiDEaqhlr....s.......eealeeL 112
                                   +++ +++++   ++++ +DE++ +     +       e+++++L
  gi|13541778|ref|NP_111466.1| 549 IREIFKKAKQvaPAIVFLDEIDSIAprrgTtsdsgvtERIVNQL 592
                                   44444555556779999*****9976544134445555555555 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1       2.2     8e+02     172     195 ..      37      60 ..      22     101 .. 0.82
   2 !   18.1   0.0   3.3e-06    0.0012      51     101 ..     225     274 ..     218     318 .. 0.88
   3 !   16.5   0.0   1.1e-05    0.0038      51     107 ..     502     557 ..     494     563 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 2.2
                                   -TT-EEEEETTT--EEE-SSS-SS CS
                         TIP49 172 kegDviviekesGkvkklGrsear 195
                                   + gDv+ iek++ +v ++ r++ +
  gi|13541778|ref|NP_111466.1|  37 EIGDVVEIEKARKTVGRVYRARPE 60 
                                   6799****9999999999887655 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 3.3e-06
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXX CS
                         TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkktev.ltq 101
                                   ++v+l Gp+gtGkt +a a+++e g    f +++g e+ s    ++e  l +
  gi|13541778|ref|NP_111466.1| 225 KGVILYGPPGTGKTLIARAVANESG--ANFLSINGPEIMSKYYGQSEQkLRE 274
                                   89*********************98..78**********9988887742444 PP

  == domain 3  score: 16.5 bits;  conditional E-value: 1.1e-05
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXX CS
                         TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkkte.vltqalrksi 107
                                   ++ Ll Gp+g Gkt la a++ e +    f++++g ev s  v  +e ++ + ++k+ 
  gi|13541778|ref|NP_111466.1| 502 KGFLLYGPPGVGKTLLAKAVATESN--ANFISIKGPEVLSKWVGESEkAIREIFKKAK 557
                                   899******************9965..89*************9998846777888875 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 !   33.6   0.1   6.9e-11   2.5e-08       3      63 ..     113     178 ..     111     179 .. 0.92

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 6.9e-11
                                   SCCCCHHHHCCCTTEEE-TTEEEEECCT....CCCEEEEEEEECCCC.SCEEECTSCCEEESTTCC CS
                       CDC48_2   3 dgdemaylkrqFlgrpvtkGdlvvfefk....gqeiklvVvstePkg.pvgitetTeielgtkpve 63 
                                    ++ ++y++r++  rp  + d + ++ +     + + ++Vv+t P   pv i e+T+ie++++p++
  gi|13541778|ref|NP_111466.1| 113 GEGIEEYVQRALIRRPMLEQDNISVPGLtlagQTGLLFKVVKTMPGKvPVEIGEETKIEIREEPAS 178
                                   556566*********************99999999*****************************97 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0     3e-06    0.0011       2      79 ..     227     334 ..     227     366 .. 0.72
   2 !   12.7   0.0   0.00031      0.11       3      44 ..     505     548 ..     504     595 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 3e-06
                        AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqskt............................dytrvl 52 
                                   v+l G+pG+GK+  a+ ++++ g  +  ++ ++++++++g+ +q+++                             + +v+
  gi|13541778|ref|NP_111466.1| 227 VILYGPPGTGKTLIARAVANESGanFLSINGPEIMSKYYGQSEQKLReifskaeetapsiifideidsiapkreeVQGEVE 307
                                   7899*******************7777789999999999966665555666666666666666666666665555444566 PP

                        AAA_33  53 drlyqilnelarkalsagrnvildatn 79 
                                    r+ ++l  l + + ++g  +++ atn
  gi|13541778|ref|NP_111466.1| 308 RRVVAQLLTLMDGMKERGHVIVIGATN 334
                                   666666666665555555555556665 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00031
                        AAA_33   3 llvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqs 44 
                                   ll G+pG+GK+ la+ ++ +    ++ +  ++++++ +g+ ++ 
  gi|13541778|ref|NP_111466.1| 505 LLYGPPGVGKTLLAKAVATESNanFISIKGPEVLSKWVGESEKA 548
                                   678***************99996777777777777776655544 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.0   0.00012     0.041      48      71 ..     225     248 ..     214     296 .. 0.88
   2 !   15.1   0.0     4e-05     0.014      45      73 ..     499     527 ..     472     569 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.00012
                     IstB_IS21  48 enivllGpsGvGKshlaialgvea 71 
                                   ++++l Gp+G+GK+ +a a++ e 
  gi|13541778|ref|NP_111466.1| 225 KGVILYGPPGTGKTLIARAVANES 248
                                   689****************99875 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 4e-05
                     IstB_IS21  45 ekkenivllGpsGvGKshlaialgveavr 73 
                                   + +++++l Gp+GvGK+ la a+++e  +
  gi|13541778|ref|NP_111466.1| 499 RPSKGFLLYGPPGVGKTLLAKAVATESNA 527
                                   567889*****************998755 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   6.3e-05     0.023       1      26 [.     227     270 ..     227     335 .. 0.58
   2 !   11.8   0.0   0.00076      0.27       2      22 ..     505     525 ..     505     606 .. 0.77
   3 ?   -0.5   0.0       4.6   1.7e+03      20      61 ..     665     706 ..     660     731 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 6.3e-05
                        AAA_18   1 IlltGtpGvGKttlakeLskrl.gf.................gv 26 
                                   ++l G+pG+GKt +a++++++  ++                  +
  gi|13541778|ref|NP_111466.1| 227 VILYGPPGTGKTLIARAVANESgANflsingpeimskyygqsEQ 270
                                   79****************88863335766666666666555533 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00076
                        AAA_18   2 lltGtpGvGKttlakeLskrl 22 
                                   ll G+pGvGKt lak+++ + 
  gi|13541778|ref|NP_111466.1| 505 LLYGPPGVGKTLLAKAVATES 525
                                   589**************7664 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 4.6
                        AAA_18  20 krl.gf.gvnlrdvakenglllevdpealdeskrldedkldkll 61 
                                   +r+ g+ g  l  +++e g+  +++++  d +++ ++++ d+l 
  gi|13541778|ref|NP_111466.1| 665 QRTeGYvGADLENLCREAGMNAYRENP--DATQVSQKNFIDALK 706
                                   45547789999999*********9999..655555555544443 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.1    0.0056         2      36      52 ..     227     243 ..     220     253 .. 0.87
   2 ?    5.4   0.0     0.035        12     128     177 ..     270     319 ..     252     334 .. 0.83
   3 !    7.7   0.1    0.0068       2.4      37      54 ..     505     522 ..     497     525 .. 0.84
   4 ?    4.3   0.0     0.073        26     128     172 ..     547     592 ..     537     599 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0056
                        AAA_25  36 allaGapgtGKttlald 52 
                                   ++l+G+pgtGKt +a  
  gi|13541778|ref|NP_111466.1| 227 VILYGPPGTGKTLIARA 243
                                   69**********99865 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.035
                        AAA_25 128 advdaleaaieevegvrlvviDplsralggdensnsdv.galvealeriar 177
                                   ++++++  ++ee++ +  + iD ++++ +  e+ + +v +++v++l  + +
  gi|13541778|ref|NP_111466.1| 270 QKLREIFSKAEETA-PSIIFIDEIDSIAPKREEVQGEVeRRVVAQLLTLMD 319
                                   66788888999955.**********************99****99988765 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0068
                        AAA_25  37 llaGapgtGKttlaldla 54 
                                   ll+G+pg+GKt la  +a
  gi|13541778|ref|NP_111466.1| 505 LLYGPPGVGKTLLAKAVA 522
                                   89***********97666 PP

  == domain 4  score: 4.3 bits;  conditional E-value: 0.073
                        AAA_25 128 advdaleaaieevegvrlvviDplsralgg.densnsdv.galveal 172
                                    +++++ +++++v+ ++ v +D ++++ +  + +s+s v +++v++l
  gi|13541778|ref|NP_111466.1| 547 KAIREIFKKAKQVA-PAIVFLDEIDSIAPRrGTTSDSGVtERIVNQL 592
                                   689999******87.***********999999999999999999997 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.0   0.00024     0.087       1      50 [.     227     267 ..     227     301 .. 0.67
   2 !   12.9   0.0   0.00031      0.11       2      30 ..     505     533 ..     504     575 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00024
                  RNA_helicase   1 iwlyGpsgeGKStlakeLakallkklklkkkdsvysrnpeddfwdgYtgq 50 
                                   ++lyGp+g+GK+++a+ +a++   ++ +++           +++++Y gq
  gi|13541778|ref|NP_111466.1| 227 VILYGPPGTGKTLIARAVANESGANFLSIN---------GPEIMSKYYGQ 267
                                   689**************7777665553333.........33344444444 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 0.00031
                  RNA_helicase   2 wlyGpsgeGKStlakeLakallkklklkk 30 
                                   +lyGp+g+GK++lak +a++   ++ ++k
  gi|13541778|ref|NP_111466.1| 505 LLYGPPGVGKTLLAKAVATESNANFISIK 533
                                   69**************9988776664444 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.0   0.00031      0.11       5      76 ..     227     294 ..     224     309 .. 0.64
   2 !   12.2   0.0   0.00032      0.11       5      29 ..     504     530 ..     501     579 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00031
                        AAA_24   5 iliyGpsgiGKTtlakel....gpkplfidtekGlksldadkfpdieswedfldevvelaaeladyktlviDtide 76 
                                   +++yGp+g+GKT +a+      g ++l i+  + + s +  +     s +++++ + + ++  +  ++++iD id 
  gi|13541778|ref|NP_111466.1| 227 VILYGPPGTGKTLIARAVanesGANFLSINGPEIM-SKYYGQ-----SEQKLREIFSKAEETAP--SIIFIDEIDS 294
                                   789************99987666666666555522.222222.....34555555555544444..5666666665 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00032
                        AAA_24   5 iliyGpsgiGKTtlakel..gpkplfi 29 
                                   +l+yGp+g+GKT lak    + ++ fi
  gi|13541778|ref|NP_111466.1| 504 FLLYGPPGVGKTLLAKAVatESNANFI 530
                                   69*************998775555555 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.0   0.00032      0.12      25      42 ..     227     244 ..     221     248 .. 0.90
   2 !   11.8   0.0   0.00032      0.12      25      43 ..     504     522 ..     498     528 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00032
                  Mg_chelatase  25 lllvGppGsGKtmlakrl 42 
                                   ++l+GppG+GKt++a+++
  gi|13541778|ref|NP_111466.1| 227 VILYGPPGTGKTLIARAV 244
                                   79*************987 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00032
                  Mg_chelatase  25 lllvGppGsGKtmlakrlp 43 
                                   +ll+GppG GKt+lak+++
  gi|13541778|ref|NP_111466.1| 504 FLLYGPPGVGKTLLAKAVA 522
                                   79*************9875 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.0    0.0004      0.14      24      61 ..     226     260 ..     215     336 .. 0.76
   2 !    8.3   0.0     0.005       1.8      25      54 ..     504     530 ..     492     579 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0004
                                   -EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS CS
               Sigma54_activat  24 svlitGesGtGKellaraiheaskrkekpfvavncaai 61 
                                    v++ G  GtGK+l+ara+ ++s    ++f+++n  +i
  gi|13541778|ref|NP_111466.1| 226 GVILYGPPGTGKTLIARAVANESG---ANFLSINGPEI 260
                                   699***************998776...77888886654 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.005
                                   EEEECSTTSSHHHHHHHHHHHSTTTTS-EE CS
               Sigma54_activat  25 vlitGesGtGKellaraiheaskrkekpfv 54 
                                    l+ G  G+GK+lla+a+ ++s+   ++f+
  gi|13541778|ref|NP_111466.1| 504 FLLYGPPGVGKTLLAKAVATESN---ANFI 530
                                   699**************988776...4455 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   0.00011     0.039       2      45 ..     227     275 ..     226     320 .. 0.65
   2 !    8.3   0.0     0.007       2.5       3      34 ..     505     541 ..     504     570 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 0.00011
                        AAA_28   2 ivitGgestGKTtlleaLaar.gypvv....pEaareileeklakgeda 45 
                                   +++ G+++tGKT +++a a++ g + +    pE++ +++ +  +k +++
  gi|13541778|ref|NP_111466.1| 227 VILYGPPGTGKTLIARAVANEsGANFLsingPEIMSKYYGQSEQKLREI 275
                                   789****************877655541156666666665554444433 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.007
                        AAA_28   3 vitGgestGKTtlleaLaar...gypvv..pEaarei 34 
                                    + G+++ GKT l++a a +   ++  +  pE+  + 
  gi|13541778|ref|NP_111466.1| 505 LLYGPPGVGKTLLAKAVATEsnaNFISIkgPEVLSKW 541
                                   689***************5543333333355555544 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.0    0.0019      0.69       2      77 ..     227     298 ..     226     337 .. 0.74
   2 !   11.4   0.0   0.00059      0.21       3      77 ..     505     575 ..     503     615 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0019
                         AAA_3   2 vllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeekekefefkkGpvfanllladeinrappk 77 
                                   v+l g PG++ktl+++a+a+  +++f  i   p+++     G++  e+k +e+  k+     ++++ dei+  +pk
  gi|13541778|ref|NP_111466.1| 227 VILYGPPGTGKTLIARAVANESGANFLSIN-GPEIMS-KYYGQS--EQKLREIFSKAEETAPSIIFIDEIDSIAPK 298
                                   7899********************999886.566663.344443..344445555555555666666666666665 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00059
                         AAA_3   3 llegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeekekefefkkGpvfanllladeinrappk 77 
                                   ll g PG++ktll+ka+a+  +++f  i+  p++l    +G +  e++ +e+  k+  v   +++ dei+  +p+
  gi|13541778|ref|NP_111466.1| 505 LLYGPPGVGKTLLAKAVATESNANFISIK-GPEVLSK-WVGES--EKAIREIFKKAKQVAPAIVFLDEIDSIAPR 575
                                   8999********************99987.5666644.44543..444455555666677777777887776665 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.0   0.00052      0.19      19      59 ..     224     264 ..     194     275 .. 0.77
   2 !    9.1   0.0    0.0035       1.2      19      49 ..     501     533 ..     478     537 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00052
                                   TEEEEEEESTTSSHHHHHHHHHHHTT--..----TTTTSEEEE CS
                          TsaE  19 gdvilLeGdLGaGKTtlvrglakalgve..evkSPTFtlveeY 59 
                                    + ++L+G+ G+GKT ++r++a++ g +  +++ P   ++++Y
  gi|13541778|ref|NP_111466.1| 224 PKGVILYGPPGTGKTLIARAVANESGANflSINGP--EIMSKY 264
                                   4459*********************9988888888..466665 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0035
                                   TEEEEEEESTTSSHHHHHHHHHHHTT--..--- CS
                          TsaE  19 gdvilLeGdLGaGKTtlvrglakalgve..evk 49 
                                   ++ +lL+G+ G+GKT l++++a + + +  ++k
  gi|13541778|ref|NP_111466.1| 501 SKGFLLYGPPGVGKTLLAKAVATESNANfiSIK 533
                                   44589****************998877655555 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0     0.013       4.8       8      64 ..     221     275 ..     218     336 .. 0.71
   2 !   13.3   0.0   0.00024     0.087       6      76 ..     496     565 ..     494     612 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.013
                                   EETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran   8 lkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvl 64 
                                   + + + v + G+ G+GK+ +++++a+++      + ++g ++ ++   +++++++ +
  gi|13541778|ref|NP_111466.1| 221 ITPPKGVILYGPPGTGKTLIARAVANESGA--NFLSINGPEIMSKYYGQSEQKLREI 275
                                   566677899***************999764..3344455555554444444444444 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 0.00024
                                   EEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS.--S-TTSBH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                      ABC_tran   6 lklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe.pqlfpeltv 76 
                                   l +++++   + G+ G GK+ L+k++a +++  +  i ++g ++ ++   +++k i+ ++++ +q+ p +  
  gi|13541778|ref|NP_111466.1| 496 LGIRPSKGFLLYGPPGVGKTLLAKAVATESN--ANFISIKGPEVLSKWVGESEKAIREIFKKaKQVAPAIVF 565
                                   6688888999*******************97..688889999999999999999999999987777777754 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   1.5e-05    0.0054       4      75 ..     227     293 ..     224     312 .. 0.69
   2 ?    4.4   0.0     0.053        19       4      25 ..     504     525 ..     501     567 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.5e-05
                       DUF2075   4 vlVtGvaGtGKtvvllnllaeleddeeertavylsvNhplvl.vlrealakkeekkkkkea.fekls.sfinnls 75 
                                   v+  G +GtGKt+++ ++++e         a++ls N+p+++ +++ + ++k  ++ +++a  + +s  fi +++
  gi|13541778|ref|NP_111466.1| 227 VILYGPPGTGKTLIARAVANES-------GANFLSINGPEIMsKYYGQSEQKL-REIFSKAeETAPSiIFIDEID 293
                                   6789*************99998.......99********98736777776666.333333303333313555555 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.053
                       DUF2075   4 vlVtGvaGtGKtvvllnllael 25 
                                   +l  G +G GKt+++ ++++e 
  gi|13541778|ref|NP_111466.1| 504 FLLYGPPGVGKTLLAKAVATES 525
                                   7889***********9999987 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.0     0.001      0.37      33      58 ..     224     249 ..     214     303 .. 0.82
   2 !    9.6   0.0    0.0017      0.62      30      61 ..     498     528 ..     488     535 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.001
                         AAA_7  33 kkpvllvGptGtGKtviikdllkkld 58 
                                    k v+l+Gp GtGKt+i++ + ++  
  gi|13541778|ref|NP_111466.1| 224 PKGVILYGPPGTGKTLIARAVANESG 249
                                   5789**************99888766 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0017
                         AAA_7  30 lknkkpvllvGptGtGKtviikdllkkldkek 61 
                                   ++ +k +ll+Gp G+GKt+++k + ++ +  +
  gi|13541778|ref|NP_111466.1| 498 IRPSKGFLLYGPPGVGKTLLAKAVATESN-AN 528
                                   6678899***************9887766.44 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.0    0.0054       1.9       1      27 [.     230     257 ..     230     310 .. 0.75
   2 !   10.3   0.0     0.002      0.71       1      27 [.     507     534 ..     507     582 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0054
                                   EE-TTSSHHHHHHHHHHHHTEEEEEH.H CS
                        AAA_17   1 lGgPGsGKgtqceklvekygfthlsa.G 27 
                                   +G+PG GK+ +++ ++ + g  +ls  G
  gi|13541778|ref|NP_111466.1| 230 YGPPGTGKTLIARAVANESGANFLSInG 257
                                   7****************99888877544 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.002
                                   EE-TTSSHHHHHHHHHHHHTEEEEEH.H CS
                        AAA_17   1 lGgPGsGKgtqceklvekygfthlsa.G 27 
                                   +G+PG+GK+ +++ ++ + +  ++s  G
  gi|13541778|ref|NP_111466.1| 507 YGPPGVGKTLLAKAVATESNANFISIkG 534
                                   7**************9998777776544 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.1    0.0039       1.4      21     121 ..     225     329 ..     214     332 .. 0.51
   2 !    7.7   0.0    0.0082       2.9      23      44 ..     504     525 ..     492     532 .. 0.83
   3 ?   -1.1   0.1       4.2   1.5e+03     107     130 ..     546     572 ..     525     581 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0039
                      ATPase_2  21 eiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefie..........eeeekkklekalgiavpkael 91 
                                   + + +YGp g GKt + + +++++   ++     i+  e+ ++++ ++ +          e+  +  + + + +  pk   
  gi|13541778|ref|NP_111466.1| 225 KGVILYGPPGTGKTLIARAVANES-GANF---LSINGPEIMSKYYGQSEQklreifskaeETAPSIIFIDEIDSIAPK--R 299
                                   55789********98888777776.3333...3344444444444444111111111111333333333333333333..3 PP

                      ATPase_2  92 eeilkeksklvfkaielllekikkkgkkii 121
                                   ee+  e  + v +++  l++ +k++g  i+
  gi|13541778|ref|NP_111466.1| 300 EEVQGEVERRVVAQLLTLMDGMKERGHVIV 329
                                   344446667777777777777777776555 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0082
                      ATPase_2  23 yfiYGpegsGKtaLlkeiienl 44 
                                    ++YGp g+GKt L k +++++
  gi|13541778|ref|NP_111466.1| 504 FLLYGPPGVGKTLLAKAVATES 525
                                   689************9998776 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 4.2
                      ATPase_2 107 elllekikkkgkk...iiiiiDelqkl 130
                                   e+++++i kk+k+    i+++De+  +
  gi|13541778|ref|NP_111466.1| 546 EKAIREIFKKAKQvapAIVFLDEIDSI 572
                                   556677777777777567888998776 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.0   0.00055       0.2      16      51 ..     224     257 ..     216     271 .. 0.90
   2 ?    5.8   0.0      0.02       7.2      20      50 ..     505     533 ..     495     537 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00055
                    Zeta_toxin  16 PklillgGqpGAGKselaellkdelerqgnvvrldp 51 
                                   Pk ++l G pG GK+ +a+++++e   + n++ +++
  gi|13541778|ref|NP_111466.1| 224 PKGVILYGPPGTGKTLIARAVANES--GANFLSING 257
                                   999*********************8..899999986 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.02
                    Zeta_toxin  20 llgGqpGAGKselaellkdelerqgnvvrld 50 
                                   ll G pG GK+ la+++++e   + n++ ++
  gi|13541778|ref|NP_111466.1| 505 LLYGPPGVGKTLLAKAVATES--NANFISIK 533
                                   7889****************8..99999887 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.0    0.0053       1.9      52      84 ..     223     255 ..     173     333 .. 0.77
   2 !    9.0   0.0    0.0019      0.69      22     102 ..     461     552 ..     443     570 .. 0.63

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0053
                        DUF815  52 pannvLLwGarGtGKSslvkallneyaeegLrl 84 
                                   p + v+L+G  GtGK  + +a+ ne  ++ L +
  gi|13541778|ref|NP_111466.1| 223 PPKGVILYGPPGTGKTLIARAVANESGANFLSI 255
                                   66789********************99988776 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0019
                        DUF815  22 vdevklddLvgidkqkealvente.........qfleglpannvLLwGarGtGKSslvkallneyaeeg..Lrlieveked 91 
                                   v +v++dd+ g+++ k++++e +e         + l  +p++  LL+G  G+GK  l ka+ +e +++   ++  ev  + 
  gi|13541778|ref|NP_111466.1| 461 VPNVHWDDIGGLEDVKREVKETVElpllkpdvfKRLGIRPSKGFLLYGPPGVGKTLLAKAVATESNANFisIKGPEVLSKW 541
                                   5566777777777777777666552222221112234578999********************999987333334666666 PP

                        DUF815  92 lkelpklvell 102
                                   + e +k ++++
  gi|13541778|ref|NP_111466.1| 542 VGESEKAIREI 552
                                   65555554444 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.0    0.0055         2      23      43 ..     227     247 ..     214     254 .. 0.88
   2 !    8.0   0.0    0.0039       1.4      24      44 ..     505     525 ..     491     554 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0055
                                   EEEEESTTSSHHHHHHHHCCS CS
                        NB-ARC  23 valvGmgGvGKttlakqilnk 43 
                                   v l+G +G GKt +a+ + n+
  gi|13541778|ref|NP_111466.1| 227 VILYGPPGTGKTLIARAVANE 247
                                   789***************998 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0039
                                   EEEESTTSSHHHHHHHHCCSH CS
                        NB-ARC  24 alvGmgGvGKttlakqilnks 44 
                                    l+G +GvGKt lak +  +s
  gi|13541778|ref|NP_111466.1| 505 LLYGPPGVGKTLLAKAVATES 525
                                   589************998874 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 ?    7.1   0.1     0.015       5.5      19      44 ..     427     452 ..     419     456 .. 0.79
   2 !    9.1   0.0    0.0035       1.2      28      54 ..     695     721 ..     691     728 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.015
                        Vps4_C  19 ipsdklleP.pvtlkDflkalkkarpt 44 
                                   ip+ ++le   vt +Df++alk+  p+
  gi|13541778|ref|NP_111466.1| 427 IPT-EILEKmVVTEEDFKNALKNIEPS 452
                                   454.45555499************998 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0035
                        Vps4_C  28 pvtlkDflkalkkarptVskeDLekhe 54 
                                   +v+ k f++alk+ rp++ +e ++ ++
  gi|13541778|ref|NP_111466.1| 695 QVSQKNFIDALKTIRPSIDEEVIKFYK 721
                                   68999***************9998775 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0     0.019       6.9       3      23 ..     227     247 ..     225     252 .. 0.89
   2 ?   -1.9   0.0       7.9   2.8e+03      63     105 ..     266     311 ..     259     342 .. 0.61
   3 !    8.4   0.0    0.0051       1.8       4      23 ..     505     524 ..     503     529 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.019
                                   EEEEC-TTTCHHHHHHHHHHH CS
                         NACHT   3 vilqGeaGsGKTtLlqklala 23 
                                   vil G++G GKT  ++ +a +
  gi|13541778|ref|NP_111466.1| 227 VILYGPPGTGKTLIARAVANE 247
                                   89*************999865 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 7.9
                                   TS--SSS-CCHHHHCCSCCCEEEEEE-STT-SS-TCH.......... CS
                         NACHT  63 pepaapvsevwavllelperlLlilDglDelvtdlgq....kekqpv 105
                                    +++++ +e+++   e + ++ + +D +D ++ + ++     e++ v
  gi|13541778|ref|NP_111466.1| 266 GQSEQKLREIFSKAEETAPSIIF-IDEIDSIAPKREEvqgeVERRVV 311
                                   55666666666666666666655.47777777766655553333333 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.0051
                                   EEEC-TTTCHHHHHHHHHHH CS
                         NACHT   4 ilqGeaGsGKTtLlqklala 23 
                                   +l G++G+GKT L++ +a++
  gi|13541778|ref|NP_111466.1| 505 LLYGPPGVGKTLLAKAVATE 524
                                   689************99986 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       8.7   3.1e+03     167     186 ..     107     126 ..      64     175 .. 0.65
   2 ?    6.8   0.1     0.011       3.8      15      37 ..     220     242 ..     213     254 .. 0.82
   3 ?    4.0   0.1     0.078        28     115     155 ..     279     322 ..     258     335 .. 0.67
   4 !    7.1   0.0    0.0085         3      15      43 ..     497     525 ..     487     556 .. 0.85
   5 ?   -1.3   0.0       3.2   1.1e+03     125     155 ..     569     600 ..     527     606 .. 0.69

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 8.7
                        ATPase 167 seeaaggygveefivdgviv 186
                                   +++ + g g+ee++    i+
  gi|13541778|ref|NP_111466.1| 107 DQRLKFGEGIEEYVQRALIR 126
                                   45555667777777766665 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.011
                        ATPase  15 GipegrvvlitGepGtGKtifal 37 
                                   Gi   + v ++G pGtGKt++a 
  gi|13541778|ref|NP_111466.1| 220 GITPPKGVILYGPPGTGKTLIAR 242
                                   6777778999**********986 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.078
                        ATPase 115 ikeikakrvviDsitgl...ayeekeavaReilrqlvrvlkklg 155
                                    +e+  + + iD i+++    +e + +v R+ + ql++ + +++
  gi|13541778|ref|NP_111466.1| 279 AEETAPSIIFIDEIDSIapkREEVQGEVERRVVAQLLTLMDGMK 322
                                   34444566777777777432556666789*******99996654 PP

  == domain 4  score: 7.1 bits;  conditional E-value: 0.0085
                        ATPase  15 GipegrvvlitGepGtGKtifalqFlikg 43 
                                   Gi   +  l++G pG GKt++a+  + ++
  gi|13541778|ref|NP_111466.1| 497 GIRPSKGFLLYGPPGVGKTLLAKAVATES 525
                                   88888999*************98766655 PP

  == domain 5  score: -1.3 bits;  conditional E-value: 3.2
                        ATPase 125 iDsitgl.ayeekeavaReilrqlvrvlkklg 155
                                   iDsi++   +++++ v+ +i+ ql++ l +++
  gi|13541778|ref|NP_111466.1| 569 IDSIAPRrGTTSDSGVTERIVNQLLTSLDGIE 600
                                   67777776677788888999999988887665 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 !    9.3   0.0    0.0015      0.55     117     137 ..     227     247 ..     221     251 .. 0.89
   2 ?    4.6   0.0     0.042        15     118     136 ..     505     523 ..     498     528 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0015
                     Parvo_NS1 117 vwfyGpantGktnlaeaIaka 137
                                   v +yGp+ tGkt +a+a a+ 
  gi|13541778|ref|NP_111466.1| 227 VILYGPPGTGKTLIARAVANE 247
                                   789**************9985 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.042
                     Parvo_NS1 118 wfyGpantGktnlaeaIak 136
                                   ++yGp+  Gkt la+a a+
  gi|13541778|ref|NP_111466.1| 505 LLYGPPGVGKTLLAKAVAT 523
                                   69**************997 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.1    0.0015      0.55      22      41 ..     227     246 ..     220     252 .. 0.87
   2 ?    6.2   0.0     0.018       6.3      23      42 ..     505     524 ..     497     531 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0015
                                   EEEE--TTSSTTHHHHHHHH CS
                          PhoH  22 vfaiGpaGtGKtylavalav 41 
                                   v+  Gp GtGKt++a a+a 
  gi|13541778|ref|NP_111466.1| 227 VILYGPPGTGKTLIARAVAN 246
                                   7899***********99985 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.018
                                   EEE--TTSSTTHHHHHHHHH CS
                          PhoH  23 faiGpaGtGKtylavalave 42 
                                      Gp G GKt+la a+a e
  gi|13541778|ref|NP_111466.1| 505 LLYGPPGVGKTLLAKAVATE 524
                                   568*************9976 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.0    0.0035       1.3      21      40 ..     227     246 ..     214     255 .. 0.85
   2 ?    4.7   0.0     0.061        22      22      40 ..     505     523 ..     493     534 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0035
                        AAA_30  21 avltGpAGtGKttalkalre 40 
                                   ++l Gp+GtGKt + +a+++
  gi|13541778|ref|NP_111466.1| 227 VILYGPPGTGKTLIARAVAN 246
                                   7899**********999865 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.061
                        AAA_30  22 vltGpAGtGKttalkalre 40 
                                   +l Gp+G GKt + ka++ 
  gi|13541778|ref|NP_111466.1| 505 LLYGPPGVGKTLLAKAVAT 523
                                   789**********999975 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.059        21      37     116 ..     227     303 ..     223     392 .. 0.62
   2 !    8.1   0.0    0.0059       2.1      37      65 ..     504     532 ..     499     672 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.059
                                   EEEE-SSSSSHHHHHHHHHHHHHHHSSSS-EEEEEHHHHHHHHHHHHHTT-HHHHHH.HHTT-SEEEEE-GGGGTT-.HHH CS
                      Bac_DnaA  37 lfiygevGlGktHLlkaignevlenapelrvvYltaeeFlnelvkalrdkkaeefke.klrkvDvLliDDiqflagk.ekt 115
                                   +++yg+ G Gkt + +a++ne  +n+     + +++ e +++     ++k  e f + +  +  ++ iD+i  +a k e++
  gi|13541778|ref|NP_111466.1| 227 VILYGPPGTGKTLIARAVANESGANF-----LSINGPEIMSKYYGQSEQKLREIFSKaEETAPSIIFIDEIDSIAPKrEEV 302
                                   689**********9999998766655.....44555555555555544444444533033455666677777776552344 PP

                                   H CS
                      Bac_DnaA 116 q 116
                                   q
  gi|13541778|ref|NP_111466.1| 303 Q 303
                                   4 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0059
                                   EEEE-SSSSSHHHHHHHHHHHHHHHSSSS CS
                      Bac_DnaA  37 lfiygevGlGktHLlkaignevlenapel 65 
                                   +++yg+ G+Gkt L ka++ e  +n+ + 
  gi|13541778|ref|NP_111466.1| 504 FLLYGPPGVGKTLLAKAVATESNANFISI 532
                                   699***************98877665443 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.0    0.0071       2.5      20      41 ..     227     248 ..     205     287 .. 0.81
   2 ?    5.6   0.0     0.033        12      20      72 ..     504     554 ..     495     566 .. 0.66

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0071
                        AAA_11  20 tliqGPPGtgKTktivellsql 41 
                                   +++ GPPGtgKT    ++ ++ 
  gi|13541778|ref|NP_111466.1| 227 VILYGPPGTGKTLIARAVANES 248
                                   5789********8887777765 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.033
                        AAA_11  20 tliqGPPGtgKTktivellsqllsrrkseeeksakpriL..vCapSNaAvDelle 72 
                                   +l+ GPPG gKT    ++  + +     +    ++p++L    ++S++A+ e+ +
  gi|13541778|ref|NP_111466.1| 504 FLLYGPPGVGKTLLAKAVATESNA----NFISIKGPEVLskWVGESEKAIREIFK 554
                                   699*********887777777732....234445555542235666666655555 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.2    0.0077       2.8      11      31 ..     225     245 ..     220     279 .. 0.86
   2 ?    5.5   0.0     0.054        19      10      31 ..     501     522 ..     497     573 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0077
                        AAA_19  11 kvllvtaGpGtGKTrvlkhiv 31 
                                   k +++ ++pGtGKT + +++ 
  gi|13541778|ref|NP_111466.1| 225 KGVILYGPPGTGKTLIARAVA 245
                                   66899*********9987765 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.054
                        AAA_19  10 ekvllvtaGpGtGKTrvlkhiv 31 
                                   +k +l+ ++pG GKT + k++ 
  gi|13541778|ref|NP_111466.1| 501 SKGFLLYGPPGVGKTLLAKAVA 522
                                   667899*********8877655 PP

>> Guanylate_kin  Guanylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0      0.12        44       3      30 ..     225     252 ..     224     259 .. 0.86
   2 ?    0.3   0.0       1.4     5e+02      75      95 ..     261     281 ..     253     302 .. 0.80
   3 ?    2.5   0.0      0.28        99       5      31 ..     504     530 ..     501     540 .. 0.85
   4 ?    2.9   0.0      0.22        78      76      99 ..     539     567 ..     532     576 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.12
                                   SEEEEESTTTSSHHHHHHHHHHHSTTTE CS
                 Guanylate_kin   3 rpvvlvgpsgaGksslkkaLlselpekf 30 
                                   + v+l gp g+Gk  +  a+ +e   +f
  gi|13541778|ref|NP_111466.1| 225 KGVILYGPPGTGKTLIARAVANESGANF 252
                                   569**************99999888777 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 1.4
                                   TTEEEEEEHHHHHHHHHTTSE CS
                 Guanylate_kin  75 sgnlygtsveaieevlekgki 95 
                                    +++yg+s ++ +e++ k+ +
  gi|13541778|ref|NP_111466.1| 261 MSKYYGQSEQKLREIFSKAEE 281
                                   6789***********998876 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.28
                                   EEEESTTTSSHHHHHHHHHHHSTTTEE CS
                 Guanylate_kin   5 vvlvgpsgaGksslkkaLlselpekfg 31 
                                     l gp g+Gk  l ka+ +e + +f 
  gi|13541778|ref|NP_111466.1| 504 FLLYGPPGVGKTLLAKAVATESNANFI 530
                                   6799**************999988884 PP

  == domain 4  score: 2.9 bits;  conditional E-value: 0.22
                                   TEEEEEEHHHHHHHHHTTSE.....EEEE CS
                 Guanylate_kin  76 gnlygtsveaieevlekgki.....viLD 99 
                                   ++  g+s +ai+e+++k+k+     v+LD
  gi|13541778|ref|NP_111466.1| 539 SKWVGESEKAIREIFKKAKQvapaiVFLD 567
                                   56779**************9666556666 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.0    0.0028         1      24      82 ..     227     296 ..     222     333 .. 0.71
   2 ?    3.9   0.0      0.15        55      25      80 ..     505     571 ..     499     577 .. 0.59

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0028
                                   EEEEEETT--HHHHHHCC--TTS-EE--SS.TTHHHH-H........HHHHHHT...TTSEEEEEE-TT-- CS
               Sigma54_activ_2  24 vfltGekGsgkelvArlLhknsgpwleifv.verlaklp........ldlleqa...kggtLylkdiadls 82 
                                   v l G++G+gk+l+Ar+ +++sg +    +  e  +k           +++ +a    + ++++ +i+++ 
  gi|13541778|ref|NP_111466.1| 227 VILYGPPGTGKTLIARAVANESGANFLSINgPEIMSK-YygqseqklREIFSKAeetAPSIIFIDEIDSIA 296
                                   7899****************99986433220222221.112222233556655533366777888877765 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.15
                                   EEEEETT--HHHHHHCC--TTS-E.E--SSTTHHHH-H.......HHHHHHT...TTSEEEEEE-TT CS
               Sigma54_activ_2  25 fltGekGsgkelvArlLhknsgpw.leifvverlaklp.......ldlleqa...kggtLylkdiad 80 
                                   +l G++G gk+l A++ + +s  + ++i+  e l+k          +++++a    +++ +l +i++
  gi|13541778|ref|NP_111466.1| 505 LLYGPPGVGKTLLAKAVATESNANfISIKGPEVLSKWVgesekaiREIFKKAkqvAPAIVFLDEIDS 571
                                   799*************988765531344333333321122223335555553222566666666665 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0     0.077        28       2      23 ..     227     248 ..     226     262 .. 0.81
   2 ?    1.3   0.1      0.79   2.8e+02      82     119 ..     269     307 ..     258     324 .. 0.72
   3 ?   -1.6   0.1       6.1   2.2e+03      89     119 ..     454     484 ..     432     492 .. 0.65
   4 ?    7.1   0.0     0.013       4.8       3      32 ..     505     534 ..     503     569 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.077
                                   EEEE--TTSSHHHHHHHHHHHH CS
                      NTPase_1   2 vfiTGppGvGKtTlvkkvlell 23 
                                   v++ GppG+GKt + + v+++ 
  gi|13541778|ref|NP_111466.1| 227 VILYGPPGTGKTLIARAVANES 248
                                   7899********9999998875 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.79
                                   HHHHHHHHHHHH.HHH-EEEE---STTGGG-HHHHHHHH CS
                      NTPase_1  82 eelalealrkal.seadviviDEiGkmElkskkfkeave 119
                                   e+   e+++ka  + + +i iDEi ++  k ++++ +ve
  gi|13541778|ref|NP_111466.1| 269 EQKLREIFSKAEeTAPSIIFIDEIDSIAPKREEVQGEVE 307
                                   55556666666634556*******888777777776665 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 6.1
                                   HHHHHHHH-EEEE---STTGGG-HHHHHHHH CS
                      NTPase_1  89 lrkalseadviviDEiGkmElkskkfkeave 119
                                   lr+ + e   +  D iG +E   +++ke+ve
  gi|13541778|ref|NP_111466.1| 454 LREVMVEVPNVHWDDIGGLEDVKREVKETVE 484
                                   4444444444556999999999999999987 PP

  == domain 4  score: 7.1 bits;  conditional E-value: 0.013
                                   EEE--TTSSHHHHHHHHHHHH...GGGEEE CS
                      NTPase_1   3 fiTGppGvGKtTlvkkvlellkssgvkvgG 32 
                                   ++ GppGvGKt l k v+ + + + ++++G
  gi|13541778|ref|NP_111466.1| 505 LLYGPPGVGKTLLAKAVATESNANFISIKG 534
                                   678**********99999887766666666 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.0    0.0058       2.1       3      28 ..     229     254 ..     227     257 .. 0.91
   2 ?    3.6   0.0      0.13        46       5      28 ..     508     531 ..     505     533 .. 0.92

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0058
                                   EE-STTSSHHHHHHHHHHHHT-EEEE CS
                Cytidylate_kin   3 iDGPagsGKssvaralaeklglkyld 28 
                                   + GP g+GK  +ara+a++ g+++l+
  gi|13541778|ref|NP_111466.1| 229 LYGPPGTGKTLIARAVANESGANFLS 254
                                   56********************9986 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.13
                                   -STTSSHHHHHHHHHHHHT-EEEE CS
                Cytidylate_kin   5 GPagsGKssvaralaeklglkyld 28 
                                   GP g GK  +a+a+a++ ++++++
  gi|13541778|ref|NP_111466.1| 508 GPPGVGKTLLAKAVATESNANFIS 531
                                   9******************99985 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0     0.025       8.8       1      24 [.     233     256 ..     233     283 .. 0.71
   2 ?    5.3   0.0     0.054        19       1      32 [.     510     543 ..     510     559 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.025
                                   TTSSHHHHHHHHHHHHTSEEEEHH CS
                           SKI   1 mGaGKstvGkllAkklglefiDlD 24 
                                   +G+GK+ +++++A++ g +f+ + 
  gi|13541778|ref|NP_111466.1| 233 PGTGKTLIARAVANESGANFLSIN 256
                                   69****************997654 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.054
                                   TTSSHHHHHHHHHHHHTSEEEEH..HHHHHHHHT CS
                           SKI   1 mGaGKstvGkllAkklglefiDl..Deliekrtg 32 
                                   +G+GK+ ++k++A + + +fi +   e+++k +g
  gi|13541778|ref|NP_111466.1| 510 PGVGKTLLAKAVATESNANFISIkgPEVLSKWVG 543
                                   69******************97633455555555 PP

>> DAP3  Mitochondrial ribosomal death-associated protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.086        31      22      39 ..     223     240 ..     214     261 .. 0.84
   2 ?    6.7   0.0    0.0096       3.5      21      60 ..     499     537 ..     480     557 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.086
                                   ---EEEEE-SSSSSTTTT CS
                          DAP3  22 kvkrlvltGekgsGKSvl 39 
                                   + k ++l+G +g+GK++ 
  gi|13541778|ref|NP_111466.1| 223 PPKGVILYGPPGTGKTLI 240
                                   56679**********974 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0096
                                   S---EEEEE-SSSSSTTTTHHHHHHHGGGS--EEEEES-G CS
                          DAP3  21 kkvkrlvltGekgsGKSvlLlqalayAlekgwvvlhvpea 60 
                                   ++ k ++l+G +g+GK++ L++a+a   +++++ ++ pe+
  gi|13541778|ref|NP_111466.1| 499 RPSKGFLLYGPPGVGKTL-LAKAVATESNANFISIKGPEV 537
                                   677889**********85.777777766667776666654 PP

>> Cytidylate_kin2  Cytidylate kinase-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.0    0.0057         2       8      53 ..     233     280 ..     229     331 .. 0.74
   2 ?    1.4   0.0      0.84     3e+02       9      52 ..     511     555 ..     507     596 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0057
               Cytidylate_kin2   8 yGsgGetigeaLAekLglpfydreiieevakelglseeev.eevde.r 53 
                                    G+g++ i++a+A++ g +f++ + +e ++k  g se+++ e +++ +
  gi|13541778|ref|NP_111466.1| 233 PGTGKTLIARAVANESGANFLSINGPEIMSKYYGQSEQKLrEIFSKaE 280
                                   59***********************************99964444432 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.84
               Cytidylate_kin2   9 GsgGetigeaLAekLglpfydreiieevakelglseeev.eevde 52 
                                   G g++ +++a+A++ + +f++ + +e ++k  g se+ + e +++
  gi|13541778|ref|NP_111466.1| 511 GVGKTLLAKAVATESNANFISIKGPEVLSKWVGESEKAIrEIFKK 555
                                   899******************999999999999999988444444 PP

>> AFG1_ATPase  AFG1-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.071        25      59      78 ..     221     240 ..     202     247 .. 0.86
   2 ?    4.0   0.0     0.053        19      57      79 ..     496     518 ..     475     525 .. 0.86
   3 ?    0.0   0.0      0.86   3.1e+02      16      67 ..     692     745 .]     683     745 .] 0.73

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.071
                   AFG1_ATPase  59 vepvrglYlwGgvGrGKtyl 78 
                                    +p++g+ l+G+ G GKt +
  gi|13541778|ref|NP_111466.1| 221 ITPPKGVILYGPPGTGKTLI 240
                                   689***************76 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.053
                   AFG1_ATPase  57 ksvepvrglYlwGgvGrGKtylm 79 
                                      +p +g  l+G+ G+GKt l 
  gi|13541778|ref|NP_111466.1| 496 LGIRPSKGFLLYGPPGVGKTLLA 518
                                   45679***************985 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 0.86
                   AFG1_ATPase  16 ivadaaqaeavealdrlteelaaqdlarks...salgklfgrkrksvepvrglYl 67 
                                     ++++q++ ++al+ +  +++ +     +   +++gk + +kr ++   +glYl
  gi|13541778|ref|NP_111466.1| 692 DATQVSQKNFIDALKTIRPSIDEEVIKFYKsisETMGKSVSEKR-KELQDQGLYL 745
                                   5677999*******999987666543222234488999999998.566899***8 PP

>> Hydin_ADK  Hydin Adenylate kinase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0    0.0036       1.3       2      31 ..     227     256 ..     226     283 .. 0.88
   2 ?    1.2   0.0       1.1   3.8e+02       4      30 ..     506     532 ..     504     540 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0036
                     Hydin_ADK   2 iivhGaPlsGKtatavtLakkYeaAlltiD 31 
                                   +i+ G+P +GKt +a ++a + +a +l+i 
  gi|13541778|ref|NP_111466.1| 227 VILYGPPGTGKTLIARAVANESGANFLSIN 256
                                   899*************************97 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 1.1
                     Hydin_ADK   4 vhGaPlsGKtatavtLakkYeaAllti 30 
                                   + G+P  GKt  a ++a + +a +++i
  gi|13541778|ref|NP_111466.1| 506 LYGPPGVGKTLLAKAVATESNANFISI 532
                                   67********************99998 PP

>> IPT  Isopentenyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0      0.02       7.2       5      31 ..     228     254 ..     225     257 .. 0.90
   2 ?    4.0   0.0     0.077        28       4      32 ..     504     532 ..     501     553 .. 0.92

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.02
                           IPT   5 lifGatttGKtaeaiklaketgapviv 31 
                                   +++G+ +tGKt  a ++a+e ga  ++
  gi|13541778|ref|NP_111466.1| 228 ILYGPPGTGKTLIARAVANESGANFLS 254
                                   68********************98776 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.077
                           IPT   4 ylifGatttGKtaeaiklaketgapvivl 32 
                                   +l++G+ ++GKt  a ++a e  a  i++
  gi|13541778|ref|NP_111466.1| 504 FLLYGPPGVGKTLLAKAVATESNANFISI 532
                                   69******************999988875 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 ?    3.8   0.0      0.11        41       5      71 ..     231     292 ..     227     297 .. 0.78
   2 ?    6.4   0.0     0.019       6.7       5      71 ..     508     569 ..     505     574 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.11
               Viral_helicase1   5 GvpGcGKStlirkllrts.liltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDEy 71 
                                   G pG GK+ + r ++++s  ++ +++   e+ ++   +++++  + + ++++++       i+++DE+
  gi|13541778|ref|NP_111466.1| 231 GPPGTGKTLIARAVANESgANFLSING-PEIMSKYYGQSEQKLREIFSKAEETAP-----SIIFIDEI 292
                                   88***************9966666666.688888877777777777787777654.....48999997 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.019
               Viral_helicase1   5 GvpGcGKStlirkllrts.liltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDEy 71 
                                   G pG GK+ l + ++ +s  ++ +++   e+l++++ ++++   + ++++ + +  +    i++lDE+
  gi|13541778|ref|NP_111466.1| 508 GPPGVGKTLLAKAVATESnANFISIKG-PEVLSKWVGESEKAIREIFKKAKQVA--P---AIVFLDEI 569
                                   77*************999*89989998.9*******888888777777655533..3...59999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (745 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       598  (0.0333538); expected 358.6 (0.02)
Passed bias filter:                      536  (0.0298957); expected 358.6 (0.02)
Passed Vit filter:                        91  (0.00507558); expected 17.9 (0.001)
Passed Fwd filter:                        50  (0.00278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              50  [number of targets reported over threshold]
# CPU time: 0.75u 0.29s 00:00:01.04 Elapsed: 00:00:00.46
# Mc/sec: 4892.62
//
Query:       gi|13541779|ref|NP_111467.1|  [L=162]
Description: hypothetical protein TVN0948 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-09   38.2   4.1    2.2e-09   38.1   3.0    1.7  2  Pilin_N   Archaeal Type IV pilin, N-terminal
    0.00059   20.1   1.5    0.00059   20.1   1.5    1.6  2  Wzz       Chain length determinant protein


Domain annotation for each model (and alignments):
>> Pilin_N  Archaeal Type IV pilin, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.1   3.0   2.4e-13   2.2e-09       1      60 [.       8      70 ..       8      96 .. 0.78
   2 ?   -2.4   0.0       1.1   9.8e+03      17      61 ..     122     127 ..     108     145 .. 0.65

  Alignments for each domain:
  == domain 1  score: 38.1 bits;  conditional E-value: 2.4e-13
                       Pilin_N  1 eAVSpViGviLmvaitvIlaAviaafvlgl.asneekapqasievkidssastgkna..vsle 60
                                  eAVSp+i  iL++ait++laA + +  +g+ +  ++ +p asi+++ ++s+++ +    +++ 
  gi|13541779|ref|NP_111467.1|  8 EAVSPIIATILLIAITIVLAATLYSLLGGYvSLISSPTPTASITITNETSSTSPDSIysIYVS 70
                                  69****************************9999999*****977755555443222445554 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.1
                       Pilin_N  17 vIlaAviaafvlglasneekapqasievkidssastgknavsleh 61 
                                   v                                       ++++ 
  gi|13541779|ref|NP_111467.1| 122 V---------------------------------------ITITS 127
                                   2.......................................44444 PP

>> Wzz  Chain length determinant protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   1.5   6.6e-08   0.00059      16      79 ..      21      86 ..      10      97 .. 0.85
   2 ?   -2.1   0.0      0.53   4.8e+03      42      55 ..     104     117 ..     101     143 .. 0.53

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 6.6e-08
                                  XXXXXXXXXXXXXXXXXXXXXXXX-EEEEEEEES--CHHH.HH.HHHHCCHHHHHHHHHHHHHHHH CS
                           Wzz 16 kklIilvtllfallaviyaflatpkYtataqilvpekkqv.ea.ssltaqdvqanlqlasteieil 79
                                   ++I+l + l  ll++ ++++++p+ ta+++i+ ++++   ++  s+++++v+an +l+    ei+
  gi|13541779|ref|NP_111467.1| 21 AITIVLAATLYSLLGGYVSLISSPTPTASITITNETSSTSpDSiYSIYVSSVNANVSLTDVKLEII 86
                                  57888889999999***********************9999778999999*****99887777776 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.53
                                   EEEEEEES--CHHH CS
                           Wzz  42 tataqilvpekkqv 55 
                                    ++  i+v+ ++  
  gi|13541779|ref|NP_111467.1| 104 ISDWAITVHGPDYL 117
                                   55566666655543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       857  (0.0477997); expected 358.6 (0.02)
Passed bias filter:                      512  (0.0285571); 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: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1227.58
//
Query:       gi|13541780|ref|NP_111468.1|  [L=253]
Description: translation initiation factor IF-2B subunit delta [Thermoplasma volcanium GSS1]
Scores for complete 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   0.0    2.8e-23   82.5   0.0    1.4  1  IF-2B           Initiation factor 2 subunit family
    0.00019   21.4   0.0    0.00022   21.3   0.0    1.2  1  PS_pyruv_trans  Polysaccharide pyruvyl transferase


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 !   82.5   0.0   3.2e-27   2.8e-23     111     276 ..      90     242 ..      64     248 .. 0.84

  Alignments for each domain:
  == domain 1  score: 82.5 bits;  conditional E-value: 3.2e-27
                                   EEEES--SHHHHHHHHHHHTTEEEEEEEEEXTTTTHHHTHHHHHHHTTXEEEEEEGGGHHHHHHCTESEEEEEXSEEETTS CS
                         IF-2B 111 ilTicnsktvlevlraaakekkkfkVivvEsrPrlqGrltakeLvqagipvtlitdsavayvmseevdkvivGAdrilenG 191
                                   + Ti+  +++ +++ + ++ +   + + +EsrP l+G  +akeL+  gi   ++td+++ +  ++  ++vivG d+il + 
  gi|13541780|ref|NP_111468.1|  90 VATISAGSMLKKFVTSSKSLD---TLYILESRPMLEGSAMAKELKSSGIRAIVLTDASMCVAVEN-ANAVIVGSDSILGDM 166
                                   455555555555555555544...899**************************************.*************** PP

                                   EEEEETTHHHHHHHHHHTTXEEEEEXXGGGBESTSSSGGGSSXXBEXTHHHHEETTEESSTTTEEEEEBSEEEEEGGGXSE CS
                         IF-2B 192 aiankiGTsslAvlAkefnipvlvvaeslkfservqldedifieerdpeellnitgeriaeeelkvvnpafDvtPpelItl 272
                                   +++ kiGT  lA++A++   p++    s+k +e++  +        +  +l  +++  iae  ++++n  fD tP++lI+ 
  gi|13541780|ref|NP_111468.1| 167 TLIHKIGTFPLALCARRLGKPFISLSISMKYEEKFTYNTY------PGFQLHSCNE--IAE-GIDCINKYFDKTPRDLIDY 238
                                   *******************************999888773......4445555554..544.9*****************9 PP

                                   EEET CS
                         IF-2B 273 iITe 276
                                   i+ e
  gi|13541780|ref|NP_111468.1| 239 IVME 242
                                   9977 PP

>> PS_pyruv_trans  Polysaccharide pyruvyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   2.4e-08   0.00022      61     130 ..     120     211 ..      30     218 .. 0.76

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 2.4e-08
                                   ..................................EEE--E......EEEETT-HHHHHHHHHHHHHS-SSEEEE-SEEE.. CS
                PS_pyruv_trans  61 i............................ddaddviivGgd..gtlgndgdlsrlpdalrllflakkagkpviilgqgiGp 111
                                                                 +++ ++ivG+d  ++++ +++   +   + l+++a+++gkp+i+l++++  
  gi|13541780|ref|NP_111468.1| 120 MlegsamakelkssgiraivltdasmcvaVENANAVIVGSDsiLGDMTLIHKIGT---FPLALCARRLGKPFISLSISM-- 195
                                   1444444455555555777777888888889999*******99777777777777...*********************.. PP

                                   -S-HHHHHHHHHHHHHTTE CS
                PS_pyruv_trans 112 flnealrkllkkilakadl 130
                                      +  +k+  + ++ + l
  gi|13541780|ref|NP_111468.1| 196 ---KYEEKFTYNTYPGFQL 211
                                   ...5555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       498  (0.0277762); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 1734.00
//
Query:       gi|13541781|ref|NP_111469.1|  [L=270]
Description: aldose 1-epimerase [Thermoplasma volcanium GSS1]
Scores for complete 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-44  149.9   0.0    1.2e-43  149.5   0.0    1.2  1  Aldose_epim  Aldose 1-epimerase
  ------ inclusion threshold ------
       0.01   15.6   0.0      0.016   15.0   0.0    1.3  1  PTEN_C2      C2 domain of PTEN tumour-suppressor protein


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 !  149.5   0.0   1.4e-47   1.2e-43       4     298 ..       4     264 ..       1     267 [. 0.92

  Alignments for each domain:
  == domain 1  score: 149.5 bits;  conditional E-value: 1.4e-47
                                   EEEETTEEEEEECTCTTEEEEEEETT.STEESB-B-STHHHHHHSCCSSCEECSS-SEEETTEEEETTEEEECCCCBTTTC CS
                   Aldose_epim   4 tlkngaglsakislyGAtllslkvpdkeqrevllgsddaeeylkdsyfgatlgrvanRianGeFeldGkpyqlpqneegkn 84 
                                   ++ ++    a+is +G++l +l+ ++   + +l  +dd  ++ +     a+l+++anR++nGeF+ldGk+y lp+ + ++n
  gi|13541781|ref|NP_111469.1|   4 SIGDD-SNGAVISIVGSHLDKLNLNG--TAILLERYDDSPTHFG----SAFLFPYANRVRNGEFTLDGKRYFLPKDD-ENN 76 
                                   56665.57799***************..5677777787545555....4****************************.*** PP

                                   EETBSGGGSB-EEEEEEETTEEEEEEEEEEETCHCSTSEEEEEEEEEEETTEEEEEEEEEEESS.S-EEEEEEEEEEEETS CS
                   Aldose_epim  85 plHGgargreWeveevkeddgvtvslvlkpdgeegypgdlevrvtytLnednelkieyeatndg.kptpfnltnHtYFnls 164
                                   ++HG++ +++++++e+ e ++vt++++  +d  e yp  +e+ +t+t++e + +++ ++a n g  + p+++++H+YF ++
  gi|13541781|ref|NP_111469.1|  77 SIHGLVLSKKFDLVEKIE-NSVTMRYIM-AD--ECYPSPIEIFITHTVSEGK-YTCRVKASNRGlTRAPVSAGFHPYFLYN 152
                                   ***************995.888888888.66..89***************77.**************************** PP

                                   SC...TCTGGEEEEEEEEEEEECTTSGEEEEEEECTTCCCCCCSSEEHCSSETEEEEEEEESSCSEEEEEETTTTEEEEEE CS
                   Aldose_epim 165 ge...sidshelqieadeylevdeeliptgelkdvkgtpfdfrqpkaigedlkglDhayllksklkaviidpdkksgikle 242
                                   g    + ++ ++++e d+++++ +                  +++  ++ed   + h++ ++       i++d +s+++  
  gi|13541781|ref|NP_111469.1| 153 GRwaiKKPRDTWKLEYDGQFPTGK------------------MDKFLFEED--SFMHEFDNQF-FADEDIVVDMGSHMIQI 212
                                   ************************..................889999999..5999999999.99999************ PP

                                   EETTSSEEEEEECTTTTSEECCEEESSECTCETCCCECHHHT-EEEHTTTEEEEEE CS
                   Aldose_epim 243 vsttepalvvytgnflkkylsreglaletqmlpdepnhpefpsivlkpGesysaet 298
                                    ++++p +v+y+g    ky   +++a+e++m  +++++++ ++ +++pGes+++ +
  gi|13541781|ref|NP_111469.1| 213 ERENMPFFVIYNG----KYSGGKSVAIEPMMSAVDAFNNGIGLRIVNPGESIEFAY 264
                                   *************....8999******************************99876 PP

>> PTEN_C2  C2 domain of PTEN tumour-suppressor protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   1.8e-06     0.016      23      92 ..     143     223 ..     128     226 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.8e-06
                                   SEE-EEEEEEETTEEEEE----GGGS--E.............EGGG--EEEEEEEEE-SEEEEEEEEEEEETTS-EEEEEE CS
                       PTEN_C2  23 ggckpkvkvyngkkkvfkelasykdstey.............raktfiieeskrvpveGDvlveflhkdskllkkekmfrv 90 
                                    g++p++  yng   + k++ +  +++ +             ++++f+ e++++++   D++v++ +  ++++++++ f v
  gi|13541781|ref|NP_111469.1| 143 AGFHPYFL-YNGRWAI-KKPRDTWKLEYDgqfptgkmdkflfEEDSFMHEFDNQFFADEDIVVDMGSHMIQIERENMPFFV 221
                                   46677776.8888888.5555555555556888888889999***********************9999999999999987 PP

                                   EE CS
                       PTEN_C2  91 wf 92 
                                     
  gi|13541781|ref|NP_111469.1| 222 IY 223
                                   65 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       283  (0.0157845); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); 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 0.26s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1900.24
//
Query:       gi|13541782|ref|NP_111470.1|  [L=117]
Description: hypothetical protein TVN0951 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.037   14.1   0.2       0.28   11.3   0.2    2.3  1  DUF2250   Uncharacterized protein conserved in archaea (DUF22


Domain annotation for each model (and alignments):
>> DUF2250  Uncharacterized protein conserved in archaea (DUF2250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.2   1.5e-05      0.28      11      88 ..      14     106 ..       4     111 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 1.5e-05
                       DUF2250  11 lkvlkhlkkanvdYaksiakel........eipleevrellkkLeelGLlervegktikrteaklKk.......ksevhkh 76 
                                    k+l h+ + ++d +k +a++l          + +e++e++kk+e+l L+   +g   +      K+       +   +  
  gi|13541782|ref|NP_111470.1|  14 EKILVHIYRYGPDSPKYMAHRLlgasgwapTYDEKEIKEKCKKMESLRLIRVFQGPLKRSPTSSVKPwikikarEINYKPA 94 
                                   589999************99975444444456789***********98876555443332233333211000003333445 PP

                       DUF2250  77 HtYYrltreGel 88 
                                     YY+lt++G+ 
  gi|13541782|ref|NP_111470.1|  95 GIYYELTKDGKR 106
                                   679999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 935.17
//
Query:       gi|13541783|ref|NP_111471.1|  [L=393]
Description: transposase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.6e-17   62.5   0.2    6.2e-17   61.3   0.2    1.7  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    0.00077   19.1   0.3     0.0013   18.4   0.3    1.4  1  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain
    0.00088   19.0   1.6       0.22   11.1   0.1    2.2  2  DUF2229         CoA enzyme activase uncharacterised domain (D
     0.0063   16.5   0.4     0.0063   16.5   0.4    1.6  2  PBECR5          phage-Barnase-EndoU-ColicinE5/D-RelE like nuc
  ------ inclusion threshold ------
      0.016   15.2   0.7      0.029   14.4   0.7    1.4  1  DZR             Double zinc ribbon
       0.04   13.6   2.2       0.13   12.0   2.2    1.9  1  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
       0.15   11.9   1.9       0.28   11.1   1.9    1.4  1  C1_1            Phorbol esters/diacylglycerol binding domain 
       0.15   12.0   0.5       0.31   11.0   0.5    1.5  1  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
       0.34   10.8   2.4       0.66    9.9   2.4    1.5  1  PHD             PHD-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 !   61.3   0.2   3.1e-20   6.2e-17       1      67 [.     288     356 ..     288     358 .. 0.89

  Alignments for each domain:
  == domain 1  score: 61.3 bits;  conditional E-value: 3.1e-20
                OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnp...ayTSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNil 67 
                                   ++ l  q+ yka ++G +v+e  +   ++TS  Cs+Cgs  +   +gr +kC++Cg+e+drDvnA+iNi+
  gi|13541783|ref|NP_111471.1| 288 YGMLASQVMYKASWEGLPVIELTRketRNTSRMCSVCGSLTRI-EHGRILKCDSCGLEIDRDVNACINIA 356
                                   5678899*************986522256**********9999.9************************8 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 !   18.4   0.3   6.4e-07    0.0013       2      30 ..     317     344 ..     316     345 .. 0.92

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 6.4e-07
                 zf-NADH-PPase   2 thrFCgrCGaptepaeggwarvCpaCgle 30 
                                   t+r C+ CG+ t+ ++g + + C++Cgle
  gi|13541783|ref|NP_111471.1| 317 TSRMCSVCGSLTRIEHG-RILKCDSCGLE 344
                                   6788*********9999.*********98 PP

>> DUF2229  CoA enzyme activase uncharacterised domain (DUF2229)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.1   0.00011      0.22     113     173 ..      34     103 ..      12     134 .. 0.63
   2 !    6.9   0.2    0.0021       4.3      90     179 ..     165     257 ..     156     260 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00011
                       DUF2229 113 llspvldle.dkke.....lakqlle...elgiskkeikkAvekAleaqkafkeelrkkgeelleeleee 173
                                   +++ ++++  +k+      + +++++   e++i      +A++kA++  k+++++l+kk++++++++e+ 
  gi|13541783|ref|NP_111471.1|  34 MVNFTINIMiEKNLtsrnsVSNEVYHklkEYEIPSYYYIEAINKAVALVKTYRKRLKKKQKATVPHVEKP 103
                                   3333333332222222222223333234488********************************9987774 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0021
                       DUF2229  90 eynCpivqglpeviknnleeeikllspvldledkkelakqlle...elgiskkeikkAv..ekAleaqkafkeelrkkgee 165
                                      C+ + g+  +++n++  ++++ ++++dl++  e+++++ +   +++++ ++i++ +  + + ++ +++k+ +++  ++
  gi|13541783|ref|NP_111471.1| 165 AIECTTTVGVDRNLRNAT-VGNEFHHEIYDLSNVVEIKQRYRKkesHFHRNDRRIREKIlsKYGKRERNRVKQIMHETSKA 244
                                   567***************.68899999999999999888888667788999999999873356888888888888888877 PP

                       DUF2229 166 lleeleeegkkgiv 179
                                   ++++++ ++k+ iv
  gi|13541783|ref|NP_111471.1| 245 IVSNAS-TRKEMIV 257
                                   777633.3334444 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 ?   -2.5   0.1         2   4.1e+03     133     176 ..      48      91 ..      29     101 .. 0.55
   2 !   16.5   0.4   3.2e-06    0.0063     132     228 ..     169     266 ..     142     281 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 2
                        PBECR5 133 tsegse.keLaekllndeavkaaYLadkGeevevayvekektfte 176
                                   ts +s+ +e   kl++ e   + Y+ +  ++v  ++   +k++++
  gi|13541783|ref|NP_111471.1|  48 TSRNSVsNEVYHKLKEYEIPSYYYIEAINKAVALVKTY-RKRLKK 91 
                                   44444313444555555555555555555555553333.234444 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 3.2e-06
                        PBECR5 132 ltsegsekeLaekllndeavkaaYLadkGeevevayvekektfteeqvevlekltdalgddeee.geelaekiieekaeia 211
                                    t+ g  ++L +   ++e  +++Y  ++  e++++y++ke +f  ++++  ek+  ++g+ e + ++++ +++++    +a
  gi|13541783|ref|NP_111471.1| 169 TTTVGVDRNLRNATVGNEFHHEIYDLSNVVEIKQRYRKKESHFHRNDRRIREKILSKYGKRERNrVKQIMHETSKAIVSNA 249
                                   4556778999999999********9999***********99*****************98777668899999999999999 PP

                        PBECR5 212 kseakdrketekdkmed 228
                                    ++ + ++ ++++ +++
  gi|13541783|ref|NP_111471.1| 250 STRKEMIVLENIRGINK 266
                                   88888888888777765 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.7   1.4e-05     0.029       7      46 ..     313     353 ..     311     354 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.4e-05
                           DZR   7 elppdarfCseCgtklkavaa..edrCpsCgekvdpearfCp 46 
                                   e+++ +r+Cs Cg+  +  ++    +C+sCg ++d + + C 
  gi|13541783|ref|NP_111471.1| 313 ETRNTSRMCSVCGSLTR-IEHgrILKCDSCGLEIDRDVNACI 353
                                   678899*******9876.4445799**************996 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   2.2   6.3e-05      0.13       3      25 ..     321     343 ..     320     345 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 6.3e-05
                                   -SSS--B----SSS----SSS-- CS
                DNA_RNApol_7kD   3 CgeCgaevslkkgdpiRCkeCGh 25 
                                   C  Cg+ +++++g +++C  CG 
  gi|13541783|ref|NP_111471.1| 321 CSVCGSLTRIEHGRILKCDSCGL 343
                                   999*******************7 PP

>> C1_1  Phorbol esters/diacylglycerol binding domain (C1 domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   1.9   0.00014      0.28       9      44 ..     316     354 ..     311     362 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00014
                                   SS--B-TTT-SB--SSSS-EEEETTT--EE-CC...CCT CS
                          C1_1   9 kqptfCkhCgeflwgkekqglkCswCkllvHkk...Che 44 
                                   + +  C+ Cg++ + +  ++lkC+ C+l ++ +   C++
  gi|13541783|ref|NP_111471.1| 316 NTSRMCSVCGSLTRIEHGRILKCDSCGLEIDRDvnaCIN 354
                                   56789********55*************99887667766 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 ?   11.0   0.5   0.00016      0.31      19      44 ..     319     342 ..     312     344 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00016
                 Zn_Tnp_IS1595  19 fvCPhCgsrkayriktrglfqCkeCr 44 
                                   + C  Cg  +++ri++ + ++C +C+
  gi|13541783|ref|NP_111471.1| 319 RMCSVCG--SLTRIEHGRILKCDSCG 342
                                   67*****..9***************7 PP

>> PHD  PHD-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   2.4   0.00033      0.66       1      22 [.     320     342 ..     320     356 .. 0.92

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00033
                                   SBTTTTS.TTSTTSCEEEETTTS CS
                           PHD   1 rCavCkk.ksdeeeelvqCdgCk 22 
                                   +C+vC++ +  e+++++ Cd+C+
  gi|13541783|ref|NP_111471.1| 320 MCSVCGSlTRIEHGRILKCDSCG 342
                                   5******98899**********7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1277  (0.0712254); expected 358.6 (0.02)
Passed bias filter:                      560  (0.0312343); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 2579.86
//
Query:       gi|13541784|ref|NP_111472.1|  [L=290]
Description: hypothetical protein TVN0953 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score 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   15.1   0.1      0.097   13.6   0.1    1.8  1  Pilin_N   Archaeal Type IV pilin, N-terminal


Domain annotation for each model (and alignments):
>> Pilin_N  Archaeal Type IV pilin, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   5.4e-06     0.097       1      21 [.       6      26 ..       6      45 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.4e-06
                       Pilin_N  1 eAVSpViGviLmvaitvIlaA 21
                                  +AVS++iG +++ ai+v l+ 
  gi|13541784|ref|NP_111472.1|  6 SAVSEIIGTVILFAIVVTLVT 26
                                  69**************98875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       796  (0.0443973); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); 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 0.29s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1934.42
//
Query:       gi|13541785|ref|NP_111473.1|  [L=404]
Description: glycosyltransferase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-15   57.9   0.1      3e-15   56.7   0.1    1.6  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    3.1e-12   46.8   1.2      5e-12   46.2   1.2    1.5  1  Glyco_trans_2_3  Glycosyl transferase family group 2
    2.5e-11   43.7   0.0    4.4e-11   42.9   0.0    1.4  1  Glycos_transf_2  Glycosyl transferase family 2
    1.8e-08   34.1   0.2    1.6e-07   31.0   0.2    2.0  1  Glyco_transf_21  Glycosyl transferase family 21
  ------ inclusion threshold ------
       0.77   10.3   6.1        4.3    7.9   0.8    2.5  2  DUF5489          Family of unknown function (DUF5489)


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 !   56.7   0.1   8.4e-19     3e-15      73     228 ..      95     258 ..      35     259 .. 0.87

  Alignments for each domain:
  == domain 1  score: 56.7 bits;  conditional E-value: 8.4e-19
               Glyco_tranf_2_3  73 tgksralnealravksdlvllvDdDtvvePdtlkrllqffltpkvgavgtpvfllnrstlvsalgalefaerhlrflaarr 153
                                    gk+  l++ ++ v++ lv +vD+Dtv+  +++  +l +f ++ vg vgt+   +   + vs +  +    r   f + ++
  gi|13541785|ref|NP_111473.1|  95 VGKRGVLSRSMQYVDTPLVMFVDSDTVLPQGAVLDMLKYF-DDHVGGVGTNITINKSGHPVSYSSEFVERVREVIFKSISK 174
                                   3788889999******************88888888****.999******************8877776777888899999 PP

               Glyco_tranf_2_3 154 algvltlnGsgslirrevlkele.........gldplflltdDyelglrlrragfrtayvpgaavrevfpsslkayikqrn 225
                                     +v+ l G++ ++r++++k l            ++++ l+dD  ++ +l r+g+rt+  + + vr+++ ss+k++++q  
  gi|13541785|ref|NP_111473.1| 175 NSSVMVLDGRCAMYRADLVKPLLtskefteniVMGRKSKLGDDRQITSYLIRQGYRTVKDYNVYVRTYQYSSFKKFFRQQV 255
                                   999*************************99866666999********************99999***************** PP

               Glyco_tranf_2_3 226 Rwv 228
                                   Rw 
  gi|13541785|ref|NP_111473.1| 256 RWG 258
                                   **6 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 !   46.2   1.2   1.4e-15     5e-12       2     185 ..     113     309 ..     112     395 .. 0.79

  Alignments for each domain:
  == domain 1  score: 46.2 bits;  conditional E-value: 1.4e-15
               Glyco_trans_2_3   2 illlDaDtvlppdclreiaaelaspevaivqgpvlvm.nvanwleelaalffaedhgkdilvrealgrvvpsvGsgaflrr 81 
                                   ++++D+Dtvlp+  +++ +  +++  v+ v ++++++  ++++ +    +++ + +++  ++  ++++v+ + G++a+ r+
  gi|13541785|ref|NP_111473.1| 113 VMFVDSDTVLPQGAVLDMLKYFDD-HVGGVGTNITINkSGHPVSYSSEFVERVREVIFKSIS--KNSSVMVLDGRCAMYRA 190
                                   899*******************97.7**********95567777777777777777776666..567799999******** PP

               Glyco_trans_2_3  82 salq.........evggwdgdessvsEDfdmglrlqrkGyrvrfvpeslvkekspltlraalrQrkRwayGc.....el.e 147
                                   ++++         e+    g+ s +++D  +   l r+Gyr++    + v+++  ++++ ++rQ  Rw +       ++ +
  gi|13541785|ref|NP_111473.1| 191 DLVKplltskeftEN-IVMGRKSKLGDDRQITSYLIRQGYRTVKDYNVYVRTYQYSSFKKFFRQQVRWGRVGwtyffKDiW 270
                                   ****66665555533.4445679*******************9887789999999999***********997443332244 PP

               Glyco_trans_2_3 148 klillvrllgylgsllwsalp.lhlallllfsllalalv 185
                                   + +++     y++ ll ++l+ l  ++  + sl++++  
  gi|13541785|ref|NP_111473.1| 271 NGTARKAGALYTFDLLYMYLLpLFTTIIAILSLIYILPH 309
                                   444455555777777777754233333333333333222 PP

>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.9   0.0   1.2e-14   4.4e-11       1     166 [.      39     193 ..      39     197 .. 0.83

  Alignments for each domain:
  == domain 1  score: 42.9 bits;  conditional E-value: 1.2e-14
                                   EEEEEESS-.TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH--S CS
               Glycos_transf_2   1 svviptyNe.ektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglraatg 80 
                                   ++v+p+yNe     +et +sl++q       ++ v   S D+  +++ e +    ++ +i+ ee vGk g l + ++++++
  gi|13541785|ref|NP_111473.1|  39 TIVVPVYNEeVGIFAETMKSLRNQ-----GAVVKVFGDSCDGVYKQIAESM----GFDFIKIEEHVGKRGVLSRSMQYVDT 110
                                   69*******99999**********.....6667777777678866666664....9************************* PP

                                   SEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SSEEEECCHCCCCHCCCCCCSTTCSTCCCEE CS
               Glycos_transf_2  81 dyilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrvgenerlyfkerkrslkgnlsfeigsaall 161
                                    +++f+D+D++ + + + ++++++++  +++v  ++  ++++       ++   +       +  s++ ++++  g +a++
  gi|13541785|ref|NP_111473.1| 111 PLVMFVDSDTVLPQGAVLDMLKYFDD-HVGGVGTNITINKSGHPVSYSSEF--VERVREVIFKSISKNSSVMVLDGRCAMY 188
                                   **************************.888888888777777777777765..4555555566667778999999999999 PP

                                   EEHHH CS
               Glycos_transf_2 162 rreal 166
                                   r +++
  gi|13541785|ref|NP_111473.1| 189 RADLV 193
                                   98876 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 !   31.0   0.2   4.5e-11   1.6e-07      20     173 .]      99     259 ..      92     259 .. 0.69

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 4.5e-11
               Glyco_transf_21  20 nnllqaleaakydllvisDsdvrvkpdyLeellaaledpkvglVtslpvgsdak...glaaaleaafl.ntlagvlqakls 96 
                                     l++ ++++ ++l+++ Dsd+++++ ++ ++l+++ d  vg V   +   +     +  ++++      ++  + +   s
  gi|13541785|ref|NP_111473.1|  99 GVLSRSMQYVDTPLVMFVDSDTVLPQGAVLDMLKYFDD-HVGGVGTNITINKSGhpvSYSSEFVERVReVIFKSISK--NS 176
                                   56778889999**************************9.78877544333333202244444433333122222222..35 PP

               Glyco_transf_21  97 glgfavGksmalrreaLeaiGGfeal........adeLAeDyalgkllraaGlkvvlspapiaqtsvprrsslrallaRql 169
                                    +    G + ++r + ++ +   +++        + +L +D +++ +l ++G+++v   ++ ++t  + +ss+++++++q+
  gi|13541785|ref|NP_111473.1| 177 SVMVLDGRCAMYRADLVKPLLTSKEFtenivmgrKSKLGDDRQITSYLIRQGYRTVKDYNVYVRTY-Q-YSSFKKFFRQQV 255
                                   666666777777777666666666652222222246899*********************988765.4.78********** PP

               Glyco_transf_21 170 rWar 173
                                   rW r
  gi|13541785|ref|NP_111473.1| 256 RWGR 259
                                   **75 PP

>> DUF5489  Family of unknown function (DUF5489)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.8    0.0012       4.3      42      68 ..     278     304 ..     261     308 .. 0.87
   2 ?    4.6   0.4     0.013        47      53      70 ..     335     352 ..     320     360 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0012
                       DUF5489  42 giasafvlmfmdflplfwgiaiifgli 68 
                                   g   +f l++m +lplf  i  i+ li
  gi|13541785|ref|NP_111473.1| 278 GALYTFDLLYMYLLPLFTTIIAILSLI 304
                                   5667899*************9999998 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.013
                       DUF5489  53 dflplfwgiaiifgliag 70 
                                    f+p+fw i  i g++  
  gi|13541785|ref|NP_111473.1| 335 SFIPIFWIIRTIVGFLNT 352
                                   59**********998754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (404 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       978  (0.0545485); expected 358.6 (0.02)
Passed bias filter:                      537  (0.0299515); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.63u 0.31s 00:00:00.94 Elapsed: 00:00:00.52
# Mc/sec: 2338.17
//
Query:       gi|13541786|ref|NP_111474.1|  [L=249]
Description: SAM-dependent methyltransferase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.9e-24   85.7   0.0    5.8e-24   85.1   0.0    1.3  1  GCD14            tRNA methyltransferase complex GCD14 subunit
    6.9e-07   29.2   0.0      1e-06   28.6   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    1.1e-06   28.6   0.0    1.4e-06   28.2   0.0    1.2  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    6.2e-05   23.6   0.0     0.0001   22.9   0.0    1.4  1  Methyltransf_25  Methyltransferase domain
     0.0025   18.5   0.0     0.0069   17.1   0.0    1.7  1  Methyltransf_12  Methyltransferase domain
  ------ inclusion threshold ------
      0.017   16.1   0.0      0.079   14.0   0.0    2.1  2  Methyltransf_24  Methyltransferase domain
      0.036   14.7   0.0      0.082   13.6   0.0    1.6  1  Methyltransf_11  Methyltransferase domain
      0.039   13.3   0.0      0.056   12.8   0.0    1.2  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
      0.076   12.6   0.0       0.11   12.0   0.0    1.2  1  MTS              Methyltransferase small domain
       0.11   11.7   0.0       0.15   11.2   0.0    1.2  1  Methyltransf_3   O-methyltransferase
       0.13   11.7   0.0       0.18   11.2   0.0    1.2  1  TehB             Tellurite resistance protein TehB
       0.13   11.5   0.0        0.2   11.0   0.0    1.2  1  GidB             rRNA small subunit methyltransferase G


Domain annotation for each model (and alignments):
>> GCD14  tRNA methyltransferase complex GCD14 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.1   0.0   3.9e-27   5.8e-24      17     184 ..      59     221 ..      46     238 .. 0.89

  Alignments for each domain:
  == domain 1  score: 85.1 bits;  conditional E-value: 3.9e-27
                         GCD14  17 LphrtqilytaDisliimkLelkpGsvvvesGtGsgslshaiartvaPtGhlftfefheqraekareefrehelsqlvtvt 97 
                                   ++ rtqi+  aD + iim+  l  G +++e G Gsg ls +i+ +++  Ghl  ++   + ++     f  ++ls++  ++
  gi|13541786|ref|NP_111474.1|  59 IKRRTQIISPADAAYIIMRTGLGIGMKAMEIGVGSGNLSAYILWAIGKEGHLTLVDREMESIQ-----FSLNNLSKFYDLE 134
                                   678*************************************************99986555554.....7778899999999 PP

                         GCD14  98 hrDvc.keGfdeevsgkvDavfLDlPaPweaiphaakalkkeggrlCsfsPCieqvqrtceaLrelgfteietlevllrty 177
                                   + D    +  + +v+++ Da+f+D+P+Pw+ +++++ +l k g++   + P  +qv +t+  L+e+gf+ +et e++ r+ 
  gi|13541786|ref|NP_111474.1| 135 NVDYViGDPSSLKVNNDYDALFVDIPNPWNYLENLKMVL-KPGSMAEFYLPNFDQVEKTVLGLEEHGFVHLETAEIQRRRL 214
                                   999653777799***********************9999.7888888999******************************* PP

                         GCD14 178 evrkskl 184
                                    vrk   
  gi|13541786|ref|NP_111474.1| 215 IVRKDAT 221
                                   9998765 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.0   6.9e-10     1e-06       4     105 ..      83     177 ..      81     206 .. 0.89

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 6.9e-10
               Methyltransf_31   4 glrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqkl.gldnveFeqgdieeleklledekfDlilsnev 83 
                                   g++ +++G G+G+l+  +   +g++++++++D++ e+i+++ +n++k   l+nv   +gd  +l+  ++ + +D ++    
  gi|13541786|ref|NP_111474.1|  83 GMKAMEIGVGSGNLSAYILWAIGKEGHLTLVDREMESIQFSLNNLSKFyDLENVDYVIGDPSSLK--VN-NDYDALFV--- 157
                                   5788999*******9888889**********************998652466*************..66.89999888... PP

               Methyltransf_31  84 lnaladpdkileeiervlkpgg 105
                                     ++++p ++le+++ vlkpg+
  gi|13541786|ref|NP_111474.1| 158 --DIPNPWNYLENLKMVLKPGS 177
                                   ..6*****************97 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2   0.0   9.3e-10   1.4e-06      27     149 ..      39     158 ..      18     177 .. 0.86

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 9.3e-10
                                   HS-GGGGSSCGGGGGTTSSS-EEEETTEEE--HHHHHHHHHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESB CS
                          PCMT  27 evdReefvpesfkekaYedaplsigynatiSaphmvalalellelkkgarvLevGsGsGyltavlarlvgekgrvvsieri 107
                                   +vd + f+ ++f  ++++   l i   + i +p   a+++    l  g++++e+G GsG l+a +   +g++g++  ++r 
  gi|13541786|ref|NP_111474.1|  39 SVDGQPFIVAKF--MPFNYGRL-IKRRTQIISPADAAYIIMRTGLGIGMKAMEIGVGSGNLSAYILWAIGKEGHLTLVDRE 116
                                   667777777766..56666666.778888889999999999999************************************* PP

                                   HHHHHHHHHHHHH.CTTCSEEEEES-GGGTTGGG-SEEEEEES CS
                          PCMT 108 kelveeakrnlkk.ldlenvivvvgDGrkGyeekaPYdaihvg 149
                                    e ++ + +nl k  dlenv  v+gD     + +  Yda++v 
  gi|13541786|ref|NP_111474.1| 117 MESIQFSLNNLSKfYDLENVDYVIGDPS-SLKVNNDYDALFVD 158
                                   ***********8846999********75.57778889998886 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     7e-08    0.0001       2      96 ..      87     176 ..      86     176 .. 0.87

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 7e-08
                                   EEET-TTSHHHHHHHCTST.SSEEEEEESSHHHHHHHHHHHHH.TTT.TEEEEESBCCGBSSSTTTEEEEEEESTGGGSSH CS
               Methyltransf_25   2 LdlGcGtGrltlalakrlg.kakvtgvDiseemleaareraee.egl.nvefvqgdaedlpfedgsfDlvvssgalhhlsd 79 
                                   +++G G+G+l+++++ ++g ++++t vD   e ++   +++++  +l nv++v gd ++l+ ++  +D+ ++      +  
  gi|13541786|ref|NP_111474.1|  87 MEIGVGSGNLSAYILWAIGkEGHLTLVDREMESIQFSLNNLSKfYDLeNVDYVIGDPSSLKVNN-DYDALFVD-----I-- 159
                                   69************9999669********************8865558*************875.9***9993.....2.. PP

                                   HHHHHHHHHHHHHEEEE CS
               Methyltransf_25  80 edlekalkeiarvLkpg 96 
                                   ++  ++l++++ vLkpg
  gi|13541786|ref|NP_111474.1| 160 PNPWNYLENLKMVLKPG 176
                                   34557999999999998 PP

>> Methyltransf_12  Methyltransferase 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    0.0069       1      96 [.      87     176 ..      87     179 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 4.6e-06
               Methyltransf_12   1 LeiGcGtGsllrallekl.pdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhhlk 80 
                                   +eiG G+G+l++++l ++ ++ ++t vD   ++i+   + l+k  +   +nv++   d ++l+ ++ +D+      +  ++
  gi|13541786|ref|NP_111474.1|  87 MEIGVGSGNLSAYILWAIgKEGHLTLVDREMESIQFSLNNLSKFYD--LENVDYVIGDPSSLKVNNDYDAL-----FVDIP 160
                                   69********************************999999999886..55777777787778778899985.....45678 PP

               Methyltransf_12  81 direvldnirklLkpg 96 
                                   ++  +l+n++ +Lkpg
  gi|13541786|ref|NP_111474.1| 161 NPWNYLENLKMVLKPG 176
                                   8888888888888887 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       3.5   5.2e+03      67      78 ..      32      43 ..      18      51 .. 0.80
   2 ?   14.0   0.0   5.3e-05     0.079       1      99 [.      87     177 ..      87     181 .. 0.70

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 3.5
               Methyltransf_24 67 agsiDllfiDgg 78
                                  a++ Dl+ +Dg+
  gi|13541786|ref|NP_111474.1| 32 ASPGDLISVDGQ 43
                                  678899999987 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 5.3e-05
               Methyltransf_24   1 vEiGvysGvstlwllralrrngagrlvavdhdpgaeeaaalare...aglddrvrlikadseealaslaagsiDllfiDgg 78 
                                   +EiGv sG+ ++++l a+ + g  +l+ vd +   e  +  +++    +  ++v+ + +d +++  +++  ++D lf+D +
  gi|13541786|ref|NP_111474.1|  87 MEIGVGSGNLSAYILWAIGKEG--HLTLVDREM--ESIQFSLNNlskFYDLENVDYVIGDPSSL--KVN-NDYDALFVDIP 160
                                   59***************99998..6******99..34455554432122223455555544444..445.79*******98 PP

               Methyltransf_24  79 haaeavledleallprlapgg 99 
                                          ++le+l  +l+pg+
  gi|13541786|ref|NP_111474.1| 161 ----NPWNYLENLKMVLKPGS 177
                                   ....67778888888888876 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   5.5e-05     0.082       2      93 ..      88     178 ..      87     181 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.5e-05
                                   EET-TTSHHHHHHH.HTT..SEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEECCCTSS-TT-EEEEEEES-CCC-CCH CS
               Methyltransf_11   2 dvGcGtGrlaeala.krg..arvvgvDlskemlklakekaseegl..kvefvvadaeklpfednsfDlvvssevlhhvedp 77 
                                   ++G+G+G l++++    g  ++++ vD   e ++ + ++ s+ +   +v++v +d ++l++++  +D+ ++      +++p
  gi|13541786|ref|NP_111474.1|  88 EIGVGSGNLSAYILwAIGkeGHLTLVDREMESIQFSLNNLSKFYDleNVDYVIGDPSSLKVNN-DYDALFVD-----IPNP 162
                                   79*********9997555778************999888888777899***********9876.89998776.....7999 PP

                                   HHHHHHHHHHEEEEEE CS
               Methyltransf_11  78 ekalkeiaRvLkpgGl 93 
                                     +l++++ vLkpg +
  gi|13541786|ref|NP_111474.1| 163 WNYLENLKMVLKPGSM 178
                                   9999999999999965 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   3.7e-05     0.056      45     147 ..      80     177 ..      69     196 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.7e-05
                                   S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSS.TEEEEE--TTT-TTS-T-EEEEEEES CS
               Ubie_methyltran  45 vkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegki.nieflqanaeeLpfeddsfDvvtvsf 124
                                      g k++++  G+g+l++ ++ ++g++g+++++D + + ++ + + l +     n++++ ++   L+ ++d +D + v  
  gi|13541786|ref|NP_111474.1|  80 LGIGMKAMEIGVGSGNLSAYILWAIGKEGHLTLVDREMESIQFSLNNLSKFYDLeNVDYVIGDPSSLKVNND-YDALFVD- 158
                                   556889*******************************999999999988765445************98765.5666553. PP

                                   -GGG-S-HHHHHHHHHHHEEEEE CS
               Ubie_methyltran 125 GlrnvtDklkaLkeayrvlkpGG 147
                                    + n     + L+++  vlkpG 
  gi|13541786|ref|NP_111474.1| 159 -IPN---PWNYLENLKMVLKPGS 177
                                   .334...3444444445677775 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   7.4e-05      0.11      33      99 ..      84     153 ..      73     162 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.4e-05
                                   SEEEEET-TTSHHHHHHHHHT.TC.EEEEEESBHHHHHHHHHHHHH.TTGC.EEEEE-STTTTSTTS-EE CS
                           MTS  33 gkvlDlGcGaGvlgaalakes.peaevtlvdvdarAlesakenlea.nkle.vevvasdvleeveekkfd 99 
                                    k++ +G G G l+a ++ +  +e ++tlvd ++++++++ +nl++  +le v++v  d  +   ++++d
  gi|13541786|ref|NP_111474.1|  84 MKAMEIGVGSGNLSAYILWAIgKEGHLTLVDREMESIQFSLNNLSKfYDLEnVDYVIGDPSSLKVNNDYD 153
                                   57899**********98866515566**************999976234445666666666655556666 PP

>> Methyltransf_3  O-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   9.9e-05      0.15      30     131 ..      65     159 ..      39     182 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 9.9e-05
                                   S--HHHHHHHHHHHHHHT--EEEEE--TTSHHHHHHHTTS-TT-EEEEEES-HHHHHHHHHHHHHTT-GGGEEEEES-HHH CS
                Methyltransf_3  30 evsvdegqfLslLvklvnakrvleiGvftGyslLatalalPeDGkilaididreayeialkfiqkagvaekieliegdalk 110
                                    +s++++ ++ +   l    + +eiGv  G     +  a+ ++G+++ +d + e  + +l+ + k    e +++  gd  +
  gi|13541786|ref|NP_111474.1|  65 IISPADAAYIIMRTGLGIGMKAMEIGVGSGNLSAYILWAIGKEGHLTLVDREMESIQFSLNNLSKFYDLENVDYVIGDPSS 145
                                   578888999999999999999*********98889999***********************99999888888888888654 PP

                                   HHHHHHTSSS---EEEEEE-S CS
                Methyltransf_3 111 vLeelvkdkklpefDfifvDa 131
                                       l+ ++   ++D +fvD 
  gi|13541786|ref|NP_111474.1| 146 ----LKVNN---DYDALFVDI 159
                                   ....23333...467777765 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00012      0.18      32      99 ..      84     155 ..      69     168 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00012
                                   -EEEEES-TTSHHHHH.HHHTT-E..EEEEES-HHHHHH.HHHHHHHTT-TTEEEEE--GGG----S-EEEE CS
                          TehB  32 gkvldlgcgqgrnsly.lsllgyd..vtawdknensiaf.leeikekenlknistalydineaklderydfi 99 
                                    k++++g g+g  s y l ++g +  +t +d++ +si+f l+++ +  +l+n++  + d  ++k++++yd +
  gi|13541786|ref|NP_111474.1|  84 MKAMEIGVGSGNLSAYiLWAIGKEghLTLVDREMESIQFsLNNLSKFYDLENVDYVIGDPSSLKVNNDYDAL 155
                                   599**********9993456776433899********98689999999*********************976 PP

>> GidB  rRNA small subunit methyltransferase G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00013       0.2      55     119 ..      89     155 ..      77     175 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00013
                                   ETSTTT.TTHHHHHHH-TTSEEEEEES-HHHHHH.HHHHHHHCT-SSEEEEES-CCCTTTTT-EEEE CS
                          GidB  55 vGsGaG.lPGipLaiarpelkltLleslekkiaF.Leevkeelklenveivearaeekqeeekydvv 119
                                   +G G G l + +L  + +e +ltL++++   i+F L+++++  +lenv +v  +  + + +++yd++
  gi|13541786|ref|NP_111474.1|  89 IGVGSGnLSAYILWAIGKEGHLTLVDREMESIQFsLNNLSKFYDLENVDYVIGDPSSLKVNNDYDAL 155
                                   555555488899999999*********************************9999888888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.61u 0.32s 00:00:00.93 Elapsed: 00:00:00.52
# Mc/sec: 1444.29
//
Query:       gi|13541787|ref|NP_111475.1|  [L=182]
Description: phosphoheptose isomerase [Thermoplasma volcanium GSS1]
Scores for complete 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-26   90.8   0.1    1.1e-25   90.3   0.1    1.2  1  SIS_2     SIS domain
    5.1e-08   32.8   0.1    1.4e-07   31.4   0.0    1.7  1  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 !   90.3   0.1   1.2e-29   1.1e-25      11     138 .]      15     139 ..       5     139 .. 0.85

  Alignments for each domain:
  == domain 1  score: 90.3 bits;  conditional E-value: 1.2e-29
                                   HHHHHHSHHHHHHHHHHHHHHHHTT--EEEEESGGGHHHHHHTSSSTT-BTTEEEE--GGGSSSSST....THHHHHTT-T CS
                         SIS_2  11 erivetqaeaiekaaeliadslenggkvlvfGsGhSaalaeelaaragglaeferialpalalhtda..eatkssalerde 89 
                                   ++i   + ++iek  + i++  ++ggk++vfG+G+Saa++++++a++ g +  er alpa+al+ ++   +++s+++++d 
  gi|13541787|ref|NP_111475.1|  15 RSI---DLNHIEKIGRDIVNVFNSGGKLIVFGNGGSAADSQHFVAELSGHFSKERKALPAMALTVNTsaLTAISNDYSYDV 92 
                                   444...6789*****************************************************998734555555555555 PP

                                   THHHHHHHHTT--TT-EEEEE-SS--SHHHHHHHHHHHHHT-EEEEEE- CS
                         SIS_2  90 gyakqilrlvrlkpgDvLlviSnsGnnavvveaaeaakergmkviAlts 138
                                   ++++q+ +   +kpgD  + iS+sGn+ +vv+ +e ake+g+k+ A+t+
  gi|13541787|ref|NP_111475.1|  93 VFSRQLEAF--AKPGDYVVGISTSGNSVNVVKGLERAKELGCKTLAMTG 139
                                   555555555..7***********************************97 PP

>> SIS  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.4   0.0   1.6e-11   1.4e-07      50     124 ..     101     177 ..      90     182 .] 0.86

  Alignments for each domain:
  == domain 1  score: 31.4 bits;  conditional E-value: 1.6e-11
                                   G-STTCEEEEEESSSHHHHHHHHHHHHHHTTSEEEEEESSTTSHHHHHSSEEEEEEEECHC..SSSHCHHHHHHHHH CS
                           SIS  50 lideddlvilisfsgetkdlvaaaelakergakiiaITdskgsplareadlalyinaepet..lvastksltaqlaa 124
                                    ++++d v+ is+sg++ ++v+ +e ake g k++a+T+ +g  +a+ a +a++i +e  +    a + +++  +++
  gi|13541787|ref|NP_111475.1| 101 FAKPGDYVVGISTSGNSVNVVKGLERAKELGCKTLAMTGRSGGKIAKVAEEAIMIDSEVTSiiQEAHIAAIHMICSV 177
                                   6789***************************************************9998887655555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       409  (0.0228122); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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 0.37s 00:00:00.94 Elapsed: 00:00:00.55
# Mc/sec: 999.47
//
Query:       gi|13541788|ref|NP_111476.1|  [L=256]
Description: hypothetical protein TVN0957 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.038   14.2   0.2      0.092   12.9   0.2    1.6  1  BK_channel_a  Calcium-activated BK potassium channel alpha su


Domain annotation for each model (and alignments):
>> BK_channel_a  Calcium-activated BK potassium channel alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.2   5.1e-06     0.092      43      97 ..      90     144 ..      70     144 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.1e-06
                  BK_channel_a  43 sikeestkseewlkeYlrgagneiyti.klskkfegmtfteaaalifeelgvlLia 97 
                                   s +++s ++ + lk Y + +gn+iy i +ls+++   t+++++  ++e+ g ++i+
  gi|13541788|ref|NP_111476.1|  90 S-DKSSSNKTSNLKLYESFMGNNIYMIsNLSFSMYSFTIRNVTFYAYESNGFIVIG 144
                                   3.3357888999*************9846**********************99997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       859  (0.0479112); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); 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: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.51
# Mc/sec: 1521.14
//
Query:       gi|13541789|ref|NP_111477.1|  [L=276]
Description: ABC transporter permease [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      3e-05   23.5  31.4      7e-05   22.2  31.4    1.6  1  ABC2_membrane_2  ABC-2 family transporter protein
  ------ inclusion threshold ------
      0.016   14.8  48.2       0.01   15.4  36.5    2.9  2  ABC2_membrane_5  ABC-2 family transporter protein
        1.1    9.5   4.8        2.5    8.3   0.3    2.8  2  CCSMST1          CCSMST1 family
        1.2    8.2  47.0       0.02   14.0  35.5    2.4  2  ABC2_membrane_3  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 !   22.2  31.4   1.6e-08     7e-05      11     287 ..      16     274 ..      13     275 .. 0.58

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 1.6e-08
               ABC2_membrane_2  11 lvrsrrfllltvllplidvalaylkdlgsslqseakaikeatlaleyveaasasdeaedtdqdlkvvstimavlipvi.aa 90 
                                     rsr+f+l+ vl+++i+ +++y++  ++++ + + + +   +   +++       a  +++ +     ++   +pv+ a+
  gi|13541789|ref|NP_111477.1|  16 YYRSRSFYLMLVLIIIITSIMTYFSFRYQQKINTFLSKFGTGVPSVSLKS-----RAL-DYIWS-----FVLADVPVYaAV 85 
                                   579********999999666666666666666666665555444333333.....222.22222.....444456777455 PP

               ABC2_membrane_2  91 lfgadaiagEkergTlkllLskPvsRdeillgKfigglaiglaiavallatvllalaiilalgivlaledllllvvasvll 171
                                    fg+ +i+ E e++T    +++P+ R ++l++K  +  ++   ++++ ++ v+++ a++ ++   l+++ +l      +++
  gi|13541789|ref|NP_111477.1|  86 FFGSPSISSEIEDRTSFHIFALPIDRYTLLISKYAAAYTV---TLIISTIYVIFEAAVTSIVYGKLETSLFLESYGILLIF 163
                                   68**************************************...55555555555555555555555554444443333333 PP

               ABC2_membrane_2 172 lllvvflalglllSsvarssreaaalalglfvvlailvpivlygvaellagpavpqeindflsllsptsayntllneilag 252
                                   ++    la+++++Ssv   +  a   +l+++++ + +v+++   ++++ + p+    +n+  + l        l++  ++ 
  gi|13541789|ref|NP_111477.1| 164 IA--SILAFTFFISSVYNRNIYAYITVLIIYFLVFNAVDVIT-SLLYNVTSPYL---LNNAATVLMRVFINVNLFSFSPTI 238
                                   33..5689**********777776666666666666666665.33333333444...333333333222222222222222 PP

               ABC2_membrane_2 253 sdlna..lgstatnllilllllavllvlgyvlFkrkD 287
                                   s l+    +     +++++++l+ ++  +  +F+rk+
  gi|13541789|ref|NP_111477.1| 239 S-LSPapTTTVLLAVIVMIIYLVGSISAASIIFERKE 274
                                   2.11111112222233344444444444448888886 PP

>> ABC2_membrane_5  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   3.8     0.018        81      39      63 ..      22      46 ..       7      55 .. 0.45
   2 ?   15.4  36.5   2.3e-06      0.01      45     201 ..      81     239 ..      65     271 .. 0.72

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.018
               ABC2_membrane_5 39 ifsilslvisiililttlsyDeksk 63
                                  ++++l+l+i+i+ i+t +s   ++k
  gi|13541789|ref|NP_111477.1| 22 FYLMLVLIIIITSIMTYFSFRYQQK 46
                                  2233333333333333333333333 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 2.3e-06
               ABC2_membrane_5  45 lvisiililttlsyDekskwnkylltLPvtrkeiVksKYlfvlililiailitlll.liiavlikgnvtisevllsiligl 124
                                   +  +++    ++s +  ++++  ++ LP++r ++ +sKY  ++ ++li + i++++ +++ ++++g++ +s +l s+ i l
  gi|13541789|ref|NP_111477.1|  81 VYAAVFFGSPSISSEIEDRTSFHIFALPIDRYTLLISKYAAAYTVTLIISTIYVIFeAAVTSIVYGKLETSLFLESYGILL 161
                                   44444555678999999************************************9996789********************* PP

               ABC2_membrane_5 125 vialiflaivlPlyfkfgvekgrivliiiifgiifllvaifsl.........................sklelslidlsny 180
                                   +++  +la+++ +   +      +++++ii++++f  v ++ +                         +            
  gi|13541789|ref|NP_111477.1| 162 IFIASILAFTFFISSVYNRNIYAYITVLIIYFLVFNAVDVITSllynvtspyllnnaatvlmrvfinvN------------ 230
                                   ******************999999999999999995555555422224544555555444444444332............ PP

               ABC2_membrane_5 181 illiillviillliivSyfiS 201
                                               l+++S  iS
  gi|13541789|ref|NP_111477.1| 231 ------------LFSFSPTIS 239
                                   ............333332222 PP

>> CCSMST1  CCSMST1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.3   0.00057       2.5      17      60 ..       8      51 ..       3      59 .. 0.77
   2 ?    1.7   0.6     0.067     3e+02      38      50 ..     184     196 ..     178     208 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00057
                       CCSMST1 17 eeslggkqke.erpwykvlvislslaaflvYFcilReendlDeaL 60
                                  ++s+  k+   +r  y +lv+++ ++ ++ Y + +R   ++ ++L
  gi|13541789|ref|NP_111477.1|  8 AYSYYLKNYYrSRSFYLMLVLIIIITSIMTY-FSFRYQQKINTFL 51
                                  555444444449999****************.7889888877776 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.067
                       CCSMST1  38 lslaaflvYFcil 50 
                                   + ++++++YF ++
  gi|13541789|ref|NP_111477.1| 184 AYITVLIIYFLVF 196
                                   6789******997 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   3.6       0.2   9.2e+02     161     183 ..      23      39 ..       7      52 .. 0.47
   2 ?   14.0  35.5   4.4e-06      0.02     159     342 ..      68     265 ..      44     268 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.2
               ABC2_membrane_3 161 sflvgliliilifitasfiavsi 183
                                   + +++      ++i++++i++++
  gi|13541789|ref|NP_111477.1|  23 YLMLV------LIIIITSIMTYF 39 
                                   22222......222222222222 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 4.4e-06
               ABC2_membrane_3 159 vasflvgliliilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllilll...afgl...gi 233
                                     +++ ++++ ++++  ++f + si +E e r+   ++  +++++++++sk+ + ++v l+++ +++++   + ++    +
  gi|13541789|ref|NP_111477.1|  68 LDYIWSFVLADVPVYAAVFFGSPSISSEIEDRTSFHIFALPIDRYTLLISKYAAAYTVTLIISTIYVIFeaaVTSIvygKL 148
                                   455566666777888899999999*999999999999******************************98765333233367 PP

               ABC2_membrane_3 234 pfgnlglllllfllfglayialgyllsslfknsetaqilifivil.......llsgffgglfpledlpsalkwifsiiPff 307
                                   + + ++     +l+f+ +++a+++++ss+ ++   a+i ++i+ +       ++  +++++ +   l++a+ ++++++ ++
  gi|13541789|ref|NP_111477.1| 149 ETSLFLESYGILLIFIASILAFTFFISSVYNRNIYAYITVLIIYFlvfnavdVITSLLYNVTSPYLLNNAATVLMRVFINV 229
                                   666777788************************999998877777677777733333444444445667788888888888 PP

               ABC2_membrane_3 308 apglgllrlitgd.plweillsliilalfavvylll 342
                                    ++ +  +++    p  ++ll++i++++  v  + +
  gi|13541789|ref|NP_111477.1| 230 NLFSFSPTISLSPaPTTTVLLAVIVMIIYLVGSISA 265
                                   877777777643336667888888888888776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1167  (0.0650901); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 1855.19
//
Query:       gi|13541790|ref|NP_111478.1|  [L=295]
Description: ABC-type multidrug transport system, ATPase component [Thermoplasma volcanium GSS1]
Scores for complete 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-26   91.0   0.0    1.6e-25   90.2   0.0    1.4  1  ABC_tran      ABC transporter
    3.9e-09   36.8   0.2      0.003   17.4   0.2    2.3  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    2.3e-05   25.0   1.7    7.3e-05   23.4   1.7    2.1  1  AAA_23        AAA domain
    2.3e-05   24.0   0.1    4.5e-05   23.1   0.1    1.4  1  AAA_29        P-loop containing region of AAA domain
    7.4e-05   23.0   0.1    0.00029   21.1   0.1    1.9  1  AAA_22        AAA domain
     0.0001   22.2   3.0      0.039   13.7   0.1    2.9  3  AAA_15        AAA ATPase domain
    0.00039   20.4   0.0    0.00064   19.7   0.0    1.3  1  Rad17         Rad17 P-loop domain
    0.00065   19.4   0.0     0.0013   18.4   0.0    1.4  1  AAA_27        AAA domain
     0.0038   17.6   0.1      0.013   15.8   0.0    2.0  2  RNA_helicase  RNA helicase
      0.004   16.6   0.0     0.0065   15.9   0.0    1.3  1  Mg_chelatase  Magnesium chelatase, subunit ChlI
      0.004   16.9   0.0      0.011   15.5   0.0    1.6  2  AAA_30        AAA domain
      0.005   16.3   0.1       0.17   11.3   0.1    2.2  1  SMC_N         RecF/RecN/SMC N terminal domain
     0.0095   15.7   0.2      0.053   13.2   0.0    2.0  2  AAA_24        AAA domain
  ------ inclusion threshold ------
      0.012   15.6   0.1      0.022   14.7   0.1    1.5  1  RsgA_GTPase   RsgA GTPase
      0.012   15.9   0.0      0.022   15.1   0.0    1.4  1  AAA_16        AAA ATPase domain
      0.019   14.1   0.5       0.57    9.3   0.0    2.1  2  PIF1          PIF1-like helicase
      0.021   14.4   0.1      0.047   13.3   0.1    1.6  1  cobW          CobW/HypB/UreG, nucleotide-binding domain
      0.037   13.8   0.0        0.2   11.4   0.0    1.9  2  IstB_IS21     IstB-like ATP binding protein
      0.043   14.3   0.2       0.12   12.8   0.2    1.9  1  AAA           ATPase family associated with various cellular 
      0.047   12.3   0.1        1.5    7.4   0.0    2.1  2  AAA_13        AAA domain
       0.05   12.7   0.0       0.52    9.4   0.0    1.9  2  G-alpha       G-protein alpha subunit
      0.055   13.5   0.2       0.23   11.5   0.0    2.1  3  AAA_14        AAA domain
      0.063   13.3   0.0       0.12   12.3   0.0    1.4  1  TsaE          Threonylcarbamoyl adenosine biosynthesis protei
      0.088   12.6   0.0       0.17   11.6   0.0    1.5  1  ATP_bind_1    Conserved hypothetical ATP binding protein
       0.12   11.9   0.1       0.28   10.8   0.1    1.6  1  SRP54         SRP54-type protein, GTPase domain
       0.13   12.2   0.0       0.37   10.8   0.0    1.8  1  AAA_5         AAA domain (dynein-related subfamily)


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 !   90.2   0.0   2.4e-28   1.6e-25       1     136 [.      19     162 ..      19     163 .. 0.89

  Alignments for each domain:
  == domain 1  score: 90.2 bits;  conditional E-value: 2.4e-28
                                   EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                      ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren.. 79 
                                   l+nvs++++ + +++++G+nGaGK+tL+k++++  +pt+G++++++ +++e + +++  ++g l ++p++ + +t +e   
  gi|13541790|ref|NP_111478.1|  19 LDNVSFEVEGNGCLVLLGPNGAGKTTLMKTMTNIIRPTSGNVKINDINVRE-NPKKALMNVGSLIEQPEFYSYITGYEAlm 98 
                                   79************************************************9.6666777888888888999999999999* PP

                                   ...........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                   ...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  80 ...........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                              + ++e+e++++  + k+  +++     +++S G+kqrv la a++ +p++++lDEpt
  gi|13541790|ref|NP_111478.1|  99 ftcmmrgldrkTCESEVENLARLTNSKGYLTRKT----REYSRGMKQRVGLASAMIGDPNIIILDEPT 162
                                   ******9777666666777777777777666666....*****************************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 !   17.4   0.2   4.3e-06     0.003       3      22 ..      33      52 ..      31      75 .. 0.76
   2 !   16.8   0.0   6.9e-06    0.0048     235     297 ..     133     191 ..     105     195 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 4.3e-06
                        AAA_21  3 vliGpNgsGKSnLLdaldll 22
                                  vl GpNg+GK++L++++  +
  gi|13541790|ref|NP_111478.1| 33 VLLGPNGAGKTTLMKTMTNI 52
                                  9**************99544 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 6.9e-06
                        AAA_21 235 relSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllell.kelsrngaQv.iltTH 297
                                   re S G+k+  +l++a++ ++    ++++DEp  gL+P+ ++++ +l+ k++++   ++ il+TH
  gi|13541790|ref|NP_111478.1| 133 REYSRGMKQRVGLASAMIGDP---NIIILDEPTFGLDPSGMKEVRDLIiKLKKE---KLiILSTH 191
                                   56799*****9*******999...89*******************999655555...555***** PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   1.7   1.1e-07   7.3e-05       7      41 ..      16      51 ..      11     284 .. 0.78

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 1.1e-07
                        AAA_23  7 frsfrdqeidF.skgltlItGpNGaGKTTildAikl 41
                                  fr +++++++  ++g  ++ GpNGaGKTT++  ++ 
  gi|13541790|ref|NP_111478.1| 16 FRALDNVSFEVeGNGCLVLLGPNGAGKTTLMKTMTN 51
                                  67778888888999****************987775 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.1   6.5e-08   4.5e-05      13      55 ..      20      63 ..      12      67 .. 0.77

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 6.5e-08
                        AAA_29 13 dghtieidlkgatlltGpsGsGKSTllDAiqalLvpak.kvrfN 55
                                  d+ ++e++ +g  +l Gp+G+GK+Tl+  ++ ++ p++ +v+ N
  gi|13541790|ref|NP_111478.1| 20 DNVSFEVEGNGCLVLLGPNGAGKTTLMKTMTNIIRPTSgNVKIN 63
                                  344455555558999*********************99777777 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.1   4.3e-07   0.00029       4     103 ..      28     165 ..      25     191 .. 0.61

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 4.3e-07
                        AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst.sskdllrellralglelka............. 70 
                                   + g+lv+ G+ G+GKTtl++++++          + ++ v+++  +   ++k+ l ++ + ++++  +             
  gi|13541790|ref|NP_111478.1|  28 GNGCLVLLGPNGAGKTTLMKTMTNIIR-------PTSGNVKINDINVReNPKKALMNVGSLIEQPEFYsyitgyealmftc 101
                                   789********************9973.......24444444333333366666666666666655556666666666666 PP

                        AAA_22  71 ...........................erlsseellealeqalrarav...ielliiDEaqh.l 103
                                                               r+++e  + + ++   a a+   + ++i+DE  + l
  gi|13541790|ref|NP_111478.1| 102 mmrgldrktcesevenlarltnskgylTRKTREYSRGMKQRVGLASAMigdPNIIILDEPTFgL 165
                                   6666666666666667765444455533333333334444444444447888888888866666 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.1   5.6e-05     0.039      11      50 ..      16      56 ..      15      90 .. 0.78
   2 ?    5.7   0.0     0.015        10     321     364 ..     150     191 ..     136     196 .. 0.90
   3 ?    3.8   2.2     0.058        40     118     185 ..     179     261 ..     170     286 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.6e-05
                        AAA_15 11 FRslkdveidlsee.ltvliGkNnsGKSsilealdlFlnnk 50
                                  FR+l++v+ +++ +   vl G+N++GK+++++ +  ++  +
  gi|13541790|ref|NP_111478.1| 16 FRALDNVSFEVEGNgCLVLLGPNGAGKTTLMKTMTNIIRPT 56
                                  999**988888888899***************997777755 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.015
                        AAA_15 321 eeknvilliEEPEahLHpqaqkvlikllkelandnktQviitTH 364
                                     +++i++++EP   L p+  k++ +l+++l +++   +i++TH
  gi|13541790|ref|NP_111478.1| 150 IGDPNIIILDEPTFGLDPSGMKEVRDLIIKLKKEK--LIILSTH 191
                                   5689***************************9999..5****** PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.058
                        AAA_15 118 tikdkklklkknelsdekisvekkkskkelpkekeeklekekeelkid.kedlkklikkleeslkkee............. 184
                                    +k++kl + ++ l +e  ++ +  ++ +  k++++ ++++++ ++i+ + d+kkl + + + +   +             
  gi|13541790|ref|NP_111478.1| 179 KLKKEKLIILSTHLLYEAQQLADWVAIINSGKLQYYGEQEKENYIEITgNVDVKKLPNSIDSVIYAGQnriivkkktgarn 259
                                   45566666677778888888888888999*******************9*********88877754446666655555544 PP

                        AAA_15 185 .e 185
                                    e
  gi|13541790|ref|NP_111478.1| 260 sE 261
                                   43 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   9.3e-07   0.00064      34     113 ..      18      98 ..       3     116 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 9.3e-07
                         Rad17  34 wlkadvLesrkkriLLisGPsGCgkstvvkvLskelgikl.rewlnpvslkepdnqksdfkgltekesrflsqiesfkele 113
                                   +l+  + e + +  L++ GP G gk+t +k ++ +  +   +  +n ++++e + +     g ++ + +f s i  ++ l+
  gi|13541790|ref|NP_111478.1|  18 ALDNVSFEVEGNGCLVLLGPNGAGKTTLMKTMTNIIRPTSgNVKINDINVRENPKKALMNVGSLIEQPEFYSYITGYEALM 98 
                                   567777777777899******************99887651668**********999888888888888****99998774 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   1.9e-06    0.0013      10      49 ..      12      52 ..       9      55 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.9e-06
                        AAA_27 10 ryGkftdr.sldfsaeeadlhliyGpNEAGKstalrAisdl 49
                                   yGkf    +++f+ e ++  +++GpN AGK+t+++ ++++
  gi|13541790|ref|NP_111478.1| 12 SYGKFRALdNVSFEVEGNGCLVLLGPNGAGKTTLMKTMTNI 52
                                  79***87538**************************99875 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.9e-05     0.013       2      83 ..      33     128 ..      32     142 .. 0.69
   2 ?   -2.4   0.0       8.9   6.1e+03      62      80 ..     254     273 ..     242     283 .. 0.64

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.9e-05
                  RNA_helicase   2 wlyGpsgeGKStlakeLakallkkl.............klkkkdsvysrnpeddfwdgYtgqevvvidDfgqvkdee.nps 68 
                                   +l Gp+g GK+tl+k++++ +  ++              +k   +v s   + +f++  tg e++++  +++  d++  +s
  gi|13541790|ref|NP_111478.1|  33 VLLGPNGAGKTTLMKTMTNIIRPTSgnvkindinvrenPKKALMNVGSLIEQPEFYSYITGYEALMFTCMMRGLDRKtCES 113
                                   799*************88888866666777777776332222233344555666666667777777777777777776666 PP

                  RNA_helicase  69 dlaelirlvsstpyp 83 
                                   ++++l rl +s+ y 
  gi|13541790|ref|NP_111478.1| 114 EVENLARLTNSKGYL 128
                                   777787777777665 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 8.9
                  RNA_helicase  62 kdee.npsdlaelirlvsst 80 
                                   k+++ n +++++li+l +++
  gi|13541790|ref|NP_111478.1| 254 KTGArNSEIIENLIELGNTV 273
                                   34444445888888887775 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   9.4e-06    0.0065      11      55 ..      18      62 ..       9      89 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 9.4e-06
                  Mg_chelatase 11 akraleiaaaGgHnlllvGppGsGKtmlakrlpsllpplseeeal 55
                                  a   +   + G+  l+l+Gp G+GKt l k +++++ p s +  +
  gi|13541790|ref|NP_111478.1| 18 ALDNVSFEVEGNGCLVLLGPNGAGKTTLMKTMTNIIRPTSGNVKI 62
                                  55556666789999*********************9998766554 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   1.5e-05     0.011      17      48 ..      28      59 ..      22      69 .. 0.85
   2 ?   -2.1   0.0       3.9   2.7e+03      72      96 ..     117     160 ..     102     187 .. 0.63

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.5e-05
                        AAA_30 17 gdrvavltGpAGtGKttalkalreaweaaggr 48
                                  g+ + vl Gp G+GKtt++k+++++++   g+
  gi|13541790|ref|NP_111478.1| 28 GNGCLVLLGPNGAGKTTLMKTMTNIIRPTSGN 59
                                  566889*****************999877555 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3.9
                        AAA_30  72 tiakllkrlk...................grarlepgtllivDE 96 
                                   ++a+l+++ +                   + a + + +++i DE
  gi|13541790|ref|NP_111478.1| 117 NLARLTNSKGyltrktreysrgmkqrvglASAMIGDPNIIILDE 160
                                   44555444445555555555555566666445666667777777 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.1   0.00025      0.17      24      45 ..      29      50 ..       6     210 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00025
                                  SSEEEEEESTTSSHHHHHHHHH CS
                                  xxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 24 ksftaivGpNGSGKsnlldAil 45
                                  ++  +++GpNG+GK+ l+  + 
  gi|13541790|ref|NP_111478.1| 29 NGCLVLLGPNGAGKTTLMKTMT 50
                                  4577899**********99886 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.0   7.7e-05     0.053       5      25 ..      32      51 ..      29      69 .. 0.88
   2 ?   -0.0   0.0      0.88   6.1e+02     134     177 ..     212     254 ..     181     267 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7.7e-05
                        AAA_24  5 iliyGpsgiGKTtlakelgpk 25
                                  +++ Gp+g+GKTtl+k++  +
  gi|13541790|ref|NP_111478.1| 32 LVLLGPNGAGKTTLMKTM-TN 51
                                  689**************9.44 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.88
                        AAA_24 134 rkdedpegeakytrlepklgkktanelkeevDlvlranlkred...k 177
                                   ++ +++e+e     ++   g+ + ++l++  D v++a ++r +   k
  gi|13541790|ref|NP_111478.1| 212 QYYGEQEKE----NYIEITGNVDVKKLPNSIDSVIYAGQNRIIvkkK 254
                                   444444444....5555556666779999999999999887665442 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.1   3.2e-05     0.022      83     122 ..      12      52 ..       1      71 [. 0.74

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.2e-05
                                   -TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT CS
                   RsgA_GTPase  83 saktkegleelkellkd.ktsvlvGqSGvGKStLinallpe 122
                                   s  + ++l++++ ++++  + vl+G+ G+GK+tL++++++ 
  gi|13541790|ref|NP_111478.1|  12 SYGKFRALDNVSFEVEGnGCLVLLGPNGAGKTTLMKTMTNI 52 
                                   44555788999999999889**************9887764 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   3.2e-05     0.022      22      51 ..      28      56 ..      16      97 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.2e-05
                        AAA_16 22 grpelvllsGesGvGKsslvrellralekd 51
                                  g  ++++l G+ G GK++l+++  + ++ +
  gi|13541790|ref|NP_111478.1| 28 GN-GCLVLLGPNGAGKTTLMKTMTNIIRPT 56
                                  33.899**************9999877665 PP

>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0   0.00083      0.57      21      53 ..      28      60 ..      15      63 .. 0.80
   2 ?    3.1   0.1     0.065        45     201     256 ..     194     251 ..     173     285 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00083
                                  CTS-EEEEESTTSSCHHHHHHHHHHCHCTCCCE CS
                          PIF1 21 kgklfFvtGsgGtgKtflwkallkklrsegkiv 53
                                    + + + G  G+gKt l k++++++r++  +v
  gi|13541790|ref|NP_111478.1| 28 GNGCLVLLGPNGAGKTTLMKTMTNIIRPTSGNV 60
                                  45677889*******************987665 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.065
                                   ...HHHHHHHHHHHCT---C..CCCHH.................HHCHCCS---SS-- CS
                          PIF1 201 kelkeFskwllkigdGkine..edeeealieiPedlllkksedkieeivsevygdllq 256
                                    e ++ ++w+  i  Gk++   e+e+e+ iei  ++ +kk  ++i++++    ++++ 
  gi|13541790|ref|NP_111478.1| 194 YEAQQLADWVAIINSGKLQYygEQEKENYIEITGNVDVKKLPNSIDSVIYAGQNRIIV 251
                                   577899999999999*9986225666699*******9999999999999877777443 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   6.8e-05     0.047       3      37 ..      32      66 ..      30      84 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.8e-05
                                  EEEEESTTCCHHHHHHHHHCT--SS-EEEEESS-S CS
                          cobW  3 tvltGflGsGKTtLlnhllenraglklavivNefg 37
                                  +vl G+ G+GKTtL++++++  +  +  v +N++ 
  gi|13541790|ref|NP_111478.1| 32 LVLLGPNGAGKTTLMKTMTNIIRPTSGNVKINDIN 66
                                  7999*************998777777777777776 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00029       0.2      35      67 ..      16      49 ..       7      56 .. 0.82
   2 ?   -0.5   0.0       1.3     9e+02     104     149 ..     148     192 ..     135     210 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00029
                     IstB_IS21 35 vkeLatlsf.iekkenivllGpsGvGKshlaial 67
                                  +++L + sf +e + ++vllGp G+GK+ l  ++
  gi|13541790|ref|NP_111478.1| 16 FRALDNVSFeVEGNGCLVLLGPNGAGKTTLMKTM 49
                                  5677777776788999************998766 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.3
                     IstB_IS21 104 krllkvdllilDdlgllpldqaeaellfeviekryerrsiiitsnl 149
                                   + +  ++++ilD+  +  ld    +++ ++i k  + + ii+++ l
  gi|13541790|ref|NP_111478.1| 148 AMIGDPNIIILDEPTF-GLDPSGMKEVRDLIIKLKKEKLIILSTHL 192
                                   5567788999999543.46666666666666666666666666654 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.2   0.00018      0.12       2      29 ..      33      65 ..      32     161 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00018
                                  EEESSTTSSHHHHHHHHHHHH.....THEEEEE CS
                           AAA  2 llyGppGtGKTllakavakel.....gveflei 29
                                  +l Gp G GKT+l+k + + +     +v++  i
  gi|13541790|ref|NP_111478.1| 33 VLLGPNGAGKTTLMKTMTNIIrptsgNVKINDI 65
                                  799*************99997333222333333 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0    0.0022       1.5      21      39 ..      34      52 ..      31      78 .. 0.76
   2 ?    3.1   0.0     0.043        30     523     594 ..     149     224 ..     141     267 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0022
                        AAA_13 21 iYGwNGaGKTtLSrllrsl 39
                                  + G NGaGKTtL + + ++
  gi|13541790|ref|NP_111478.1| 34 LLGPNGAGKTTLMKTMTNI 52
                                  569*********9988876 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.043
                        AAA_13 523 eigkdkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHnleffkevkkntkr........krkkkeesfyl 594
                                    ig   i+++D P   LD   +  v  li +     kk k ++++TH l+  +++ +++            ++++e+++ 
  gi|13541790|ref|NP_111478.1| 149 MIGDPNIIILDEPTFGLDPSGMKEVRDLIIKL----KKEKLIILSTHLLYEAQQLADWVAIinsgklqyYGEQEKENYIE 224
                                   57788999999999999999988888888877....688999*************9998853333332233334444444 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0   0.00076      0.52      26      53 ..      32      59 ..       8      74 .. 0.83
   2 ?    1.0   0.0      0.27   1.9e+02     206     254 ..      75     124 ..      56     129 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00076
                                  EEEEESTTSSHHHHHHHHHHHCS----H CS
                       G-alpha 26 llllGqseSGKsTilkqlkllykkgfse 53
                                  l+llG ++ GK+T++k +  + +++  +
  gi|13541790|ref|NP_111478.1| 32 LVLLGPNGAGKTTLMKTMTNIIRPTSGN 59
                                  89****************9888887554 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.27
                                   EEEE-SSHHHHHGTCCCTTTECEEEEEEEGGGTT-B-SS-T..TSBHHHHH CS
                       G-alpha 206 ivdvgGqrserkkWvpffddvdaiiFlvslsefdqvlyede..kvnrlees 254
                                   +++vg +  e++ + +++++ +a++F++ + + d    e+e  +  rl++s
  gi|13541790|ref|NP_111478.1|  75 LMNVG-SLIEQPEFYSYITGYEALMFTCMMRGLDRKTCESEveNLARLTNS 124
                                   55555.444668899999*****************9999862245577666 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00033      0.23       4      44 ..      31      73 ..      28      97 .. 0.71
   2 ?   -2.2   0.0       5.6   3.9e+03      65      73 ..     153     161 ..     125     204 .. 0.66
   3 ?   -1.8   0.0       4.3     3e+03      69      85 ..     192     208 ..     166     227 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00033
                        AAA_14  4 ilvitGaRrvGKTtllkqlikell...vkkesilyinldderdk 44
                                   lv+ G+  +GKTtl+k++ +  +     + +i  in+ ++++k
  gi|13541790|ref|NP_111478.1| 31 CLVLLGPNGAGKTTLMKTMTNI-IrptSGNVKINDINVRENPKK 73
                                  689*************998633.335545555666666555554 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 5.6
                        AAA_14  65 ktylflDEi 73 
                                    ++++lDE 
  gi|13541790|ref|NP_111478.1| 153 PNIIILDEP 161
                                   556777764 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 4.3
                        AAA_14  69 flDEiqevpewekalks 85 
                                   +l E+q++ +w  +++s
  gi|13541790|ref|NP_111478.1| 192 LLYEAQQLADWVAIINS 208
                                   45577777777777765 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00018      0.12      19      43 ..      29      53 ..       5      62 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00018
                                  TEEEEEEESTTSSHHHHHHHHHHHT CS
                          TsaE 19 gdvilLeGdLGaGKTtlvrglakal 43
                                  + +++L G+ GaGKTtl++ + + +
  gi|13541790|ref|NP_111478.1| 29 NGCLVLLGPNGAGKTTLMKTMTNII 53
                                  34699**************998755 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00025      0.17       2      27 ..      35      60 ..      34      89 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00025
                    ATP_bind_1  2 vGpaGsGKttfvgalseilelrgrsv 27
                                  +Gp G+GKtt+++++++i++ +  +v
  gi|13541790|ref|NP_111478.1| 35 LGPNGAGKTTLMKTMTNIIRPTSGNV 60
                                  7****************998765554 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1    0.0004      0.28       4      28 ..      32      56 ..      29      65 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0004
                                  EEEEESTTSSHHHHHHHHHHHHHHT CS
                         SRP54  4 illvGlqGaGKTttlaKLaallkke 28
                                  ++l+G++GaGKTt +  + ++++  
  gi|13541790|ref|NP_111478.1| 32 LVLLGPNGAGKTTLMKTMTNIIRPT 56
                                  789************9999988765 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00053      0.37       2      24 ..      32      55 ..      31      72 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00053
                                  EEEE--SSSSHHHHHHHGGGGB.S CS
                         AAA_5  2 vlLvGppGtgKselaerlaaal.n 24
                                  ++L+Gp G gK++l++ +   +  
  gi|13541790|ref|NP_111478.1| 32 LVLLGPNGAGKTTLMKTMTNIIrP 55
                                  68***************9998852 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       628  (0.0350271); expected 358.6 (0.02)
Passed bias filter:                      478  (0.0266607); expected 358.6 (0.02)
Passed Vit filter:                        92  (0.00513135); expected 17.9 (0.001)
Passed Fwd filter:                        26  (0.00145016); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              26  [number of targets reported over threshold]
# CPU time: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.46
# Mc/sec: 1929.13
//
Query:       gi|13541791|ref|NP_111479.1|  [L=303]
Description: glycerate dehydrogenase [Thermoplasma volcanium GSS1]
Scores for complete 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-41  139.8   0.0    7.3e-41  139.5   0.0    1.1  1  2-Hacid_dh_C   D-isomer specific 2-hydroxyacid dehydrogenase,
    6.5e-12   45.3   0.0    8.4e-12   44.9   0.0    1.1  1  2-Hacid_dh     D-isomer specific 2-hydroxyacid dehydrogenase,
    0.00051   20.2   0.0     0.0009   19.4   0.0    1.4  1  NAD_binding_2  NAD binding domain of 6-phosphogluconate dehyd
  ------ inclusion threshold ------
      0.066   13.9   0.1         11    6.8   0.1    2.7  2  PglD_N         PglD N-terminal domain
       0.13   12.3   2.0        1.8    8.6   2.0    2.3  1  AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD bindi


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 !  139.5   0.0     2e-44   7.3e-41       1     178 []      90     257 ..      90     257 .. 0.94

  Alignments for each domain:
  == domain 1  score: 139.5 bits;  conditional E-value: 2e-44
                                   HHHHHHHHTTHHHHHHHHHTTCCHTTCCGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTCE CS
                  2-Hacid_dh_C   1 lalllallrrlaeadeevregewksekallgkelsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeelgve 81 
                                   +allla ++++ e d ++++g++    + + k l+ kt+Gi+G+G IG++va++ kafgm++ ++ r+  ke      gv+
  gi|13541791|ref|NP_111479.1|  90 FALLLARAKNVIENDMNMKNGKF---IQSPTKLLYSKTLGILGYGGIGRRVAELGKAFGMDIAVFTRTLVKE-----GGVR 162
                                   589********************...8889999***********************************7744.....4554 PP

                                   .ECSHHHHHHH-SEEEE-S--STTTTTSBSHHHHHCSTTTEEEEESS-GGGB-HHHHHHHHHTTSCCEEEES--SSSSSGT CS
                  2-Hacid_dh_C  82 .lvsleellaesDivslhlpltpetrhlinaeelakmkkgailiNtaRGglvdeeaLleaLksgkiagaalDvfeeeplpe 161
                                    + +   +l++sD+v++ lplt++tr++in+++l++mkk+a+liN+aR+++v +e++l+ L s+    +  Dv+++ep  +
  gi|13541791|ref|NP_111479.1| 163 fYKEPGPVLENSDVVVISLPLTDNTRGMINSSKLEMMKKDAMLINVARADIVVKEDILKHLISNPDFTYISDVWWNEPNIT 243
                                   0569****************************************************************************8 PP

                                   CHHHHHSTTEEE-SS-T CS
                  2-Hacid_dh_C 162 dspllelpnviltPHia 178
                                   +   ++ +n+il+PHia
  gi|13541791|ref|NP_111479.1| 244 E---TNIKNTILSPHIA 257
                                   8...788*********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 !   44.9   0.0   2.4e-15   8.4e-12      60     133 ..      48     288 ..      21     289 .. 0.95

  Alignments for each domain:
  == domain 1  score: 44.9 bits;  conditional E-value: 2.4e-15
                                   TT--EEEESSSSCTTB-HHHHHHTT-EEEE-TTTTHHHHHHHH...................................... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...................................... RF
                    2-Hacid_dh  60 pkLkviaragvGvDnvDldaakerGilVtnvpgystesvAElt...................................... 102
                                   ++ k+i++ ++GvD++D++ + e+ +++++  g++++svAE++                                      
  gi|13541791|ref|NP_111479.1|  48 KNTKMIQTLSAGVDHIDVQGIPEN-VVLCSNAGAYSISVAEHAfalllaraknviendmnmkngkfiqsptkllysktlgi 127
                                   899********************9.555555666667******************************************** PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                    2-Hacid_dh 103 ................................................................................. 102
                                                                                                                    
  gi|13541791|ref|NP_111479.1| 128 lgyggigrrvaelgkafgmdiavftrtlvkeggvrfykepgpvlensdvvvislpltdntrgminssklemmkkdamlinv 208
                                   ********************************************************************************* PP

                                   ..................................................T-BHHHHHHHHHHHHHHHHHHHTTCCGTTBC CS
                                   ..................................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    2-Hacid_dh 103 ..................................................aaTeeaqeniaeeaaenlvaflkgespanav 133
                                                                                     +++ e +e + e+a+ n++af++g +p+n+v
  gi|13541791|ref|NP_111479.1| 209 aradivvkedilkhlisnpdftyisdvwwnepnitetnikntilsphiagGMSGEIMELAYEQAFRNIKAFFEG-KPNNIV 288
                                   **************************************************************************.777766 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   2.5e-07    0.0009       2     103 ..     125     222 ..     124     232 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 2.5e-07
                                   EEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT.EEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHS.HCCC- CS
                 NAD_binding_2   2 igfiGlGvMGsnmalnllkagykvavynrtkekveelvaeg.akaaesieelvasldvvitmvkagkavdevieg.lleal 80 
                                   +g++G G +G+  a+  ++ g+++av+ rt      lv+eg ++ ++++  ++++ dvv++ ++ +++++ +i++  le +
  gi|13541791|ref|NP_111479.1| 125 LGILGYGGIGRRVAELGKAFGMDIAVFTRT------LVKEGgVRFYKEPGPVLENSDVVVISLPLTDNTRGMINSsKLEMM 199
                                   799*************************99......666655*********************************88999* PP

                                   -TT-EEEE-S---HHHHHHHHHH CS
                 NAD_binding_2  81 kkgdilidgstsspedtrelake 103
                                   kk+++li+++ +++   +++ k 
  gi|13541791|ref|NP_111479.1| 200 KKDAMLINVARADIVVKEDILKH 222
                                   ********999888777776665 PP

>> PglD_N  PglD N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.1     0.003        11       3      30 ..     126     152 ..     124     178 .. 0.84
   2 ?    4.2   0.0     0.019        68       7      39 ..     257     289 ..     257     299 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.003
                        PglD_N   3 vIiGaGGhgkvvadiieangeyeiigfl 30 
                                    I+G GG g+ va++ +a g  +i++f+
  gi|13541791|ref|NP_111479.1| 126 GILGYGGIGRRVAELGKAFG-MDIAVFT 152
                                   59**************9999.8888886 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.019
                        PglD_N   7 aGGhgkvvadiieangeyeiigflDdnkkteve 39 
                                   aGG++ ++ +++  +   +i++f+  ++++ v 
  gi|13541791|ref|NP_111479.1| 257 AGGMSGEIMELAYEQAFRNIKAFFEGKPNNIVR 289
                                   8**************9999*****999876544 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 ?    8.6   2.0    0.0005       1.8      21     122 ..     120     221 ..     111     230 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0005
                                   -TTSEEEEE--SHHHHHHHHHHHHCT-EEEEE-S-HHHHHHHHCTT-EE--.HHHCTTT-SEEEE....-SSSSSSB-HHH CS
                 AdoHcyase_NAD  21 laGkvavvaGyGdvGkGcaaslkglGarvivtevdPicalqaameGfevvt.leevvkkadivvt....ttGnkdiitleh 96 
                                   l  k+  + GyG +G+  a+  k++G  + v     +        G +  +    v++++d+vv     t  ++ +i++ +
  gi|13541791|ref|NP_111479.1| 120 LYSKTLGILGYGGIGRRVAELGKAFGMDIAVFTRTLV-----KEGGVRFYKePGPVLENSDVVVIslplTDNTRGMINSSK 195
                                   5668888899999999999999999988877543222.....2234443331345778888887622223445789***** PP

                                   HCCS-TTEEEEE-SSTTTTBTHHHHH CS
                 AdoHcyase_NAD  97 lkkmkddaivcniGhfdseidvaale 122
                                   l+ mk+da++ n+   d  ++ + l+
  gi|13541791|ref|NP_111479.1| 196 LEMMKKDAMLINVARADIVVKEDILK 221
                                   *************9999888777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (303 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.57u 0.32s 00:00:00.88 Elapsed: 00:00:00.50
# Mc/sec: 1806.04
//
Query:       gi|13541792|ref|NP_111480.1|  [L=302]
Description: hypothetical protein TVN0961 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       464  (0.0258799); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.23s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 2438.35
//
Query:       gi|13541793|ref|NP_111481.1|  [L=315]
Description: hypothetical protein TVN0962 [Thermoplasma volcanium GSS1]
Scores for complete sequence (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   77.1   2.3    2.3e-21   76.2   2.3    1.5  1  GtrA      GtrA-like protein
  ------ inclusion threshold ------
       0.25   10.9   0.1       0.48   10.0   0.1    1.4  1  DUF4653   Domain of unknown function (DUF4653)


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 !   76.2   2.3   2.6e-25   2.3e-21       1     117 []     187     304 ..     187     310 .. 0.94

  Alignments for each domain:
  == domain 1  score: 76.2 bits;  conditional E-value: 2.6e-25
                          GtrA   1 rFlivGvlgtlvdlallllllellglsyllAnaiafivailfnFilnrrwtFkdrekakl....lkqflkFvlvsllglll 77 
                                   r+l+vG +g++v+ +ll ll+  +++++++A a+a++++i +nF+ln++wtF+ r+ +k     +k++    + sllgl++
  gi|13541793|ref|NP_111481.1| 187 RYLAVGTSGIVVNEMLLKLLS--YHIPLTFADALAIETSISTNFLLNEYWTFRGRKVSKSvkniFKRMGLHNFTSLLGLGI 265
                                   8*******************8..59*******************************99988888889999999******** PP

                          GtrA  78 nllilwllveklgleallaklvgiivalvlnyvlsklfvF 117
                                   nl+i++llv+  g e l+a+++gi +a++ +y++s+++++
  gi|13541793|ref|NP_111481.1| 266 NLGIFTLLVYG-GTEILIANMIGITAAFLSRYLMSSRIIW 304
                                   *********87.556777*******************998 PP

>> DUF4653  Domain of unknown function (DUF4653)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.1   5.3e-05      0.48     210     253 ..     100     144 ..      91     146 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 5.3e-05
                       DUF4653 210 lqWiralqqklvdqqarlqe.sfdtildnrkeliralqqrlapsr 253
                                   l+W+  + +k+ d   rl e s+d il n k +   + ++++ sr
  gi|13541793|ref|NP_111481.1| 100 LRWLLKIFKKVLDEDERLAEtSLDVILTNSKVMEYIINRGYKISR 144
                                   8*****************8869*********99888888877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (315 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       769  (0.0428914); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2212.31
//
Query:       gi|13541794|ref|NP_111482.1|  [L=689]
Description: hypothetical protein TVN0963 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
       0.21   11.7   1.2         12    6.0   0.2    2.8  2  Bee_toxin  Honey bee toxin


Domain annotation for each model (and alignments):
>> Bee_toxin  Honey bee toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.2   0.00068        12       6      22 ..     163     179 ..     160     187 .. 0.82
   2 ?    3.4   0.0    0.0043        77       8      27 ..     400     421 ..     395     433 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.00068
                     Bee_toxin   6 rCiflFlsviLitsYFV 22 
                                   + +f Fls+iL+  Y+ 
  gi|13541794|ref|NP_111482.1| 163 IITFNFLSIILLIEYYR 179
                                   5689*********9985 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.0043
                     Bee_toxin   8 iflFlsvi..LitsYFVtPtms 27 
                                   +f+ +s+i  Lit+ F  P+ +
  gi|13541794|ref|NP_111482.1| 400 VFIAISIIivLITAGFMVPVQA 421
                                   67777765349********966 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (689 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       807  (0.0450109); expected 358.6 (0.02)
Passed bias filter:                      235  (0.0131073); 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: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.41
# Mc/sec: 5085.97
//
Query:       gi|13541795|ref|NP_111483.1|  [L=639]
Description: hypothetical protein TVN0964 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (639 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1173  (0.0654247); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); 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):               0  [number of targets reported over threshold]
# CPU time: 0.72u 0.30s 00:00:01.02 Elapsed: 00:00:00.50
# Mc/sec: 3842.23
//
Query:       gi|13541796|ref|NP_111484.1|  [L=398]
Description: inner membrane protein [Thermoplasma volcanium GSS1]
Scores for complete sequence (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  110.2  31.9    4.4e-18   65.9  14.6    2.6  3  Sulf_transp  Sulphur transport


Domain annotation for each model (and alignments):
>> Sulf_transp  Sulphur transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.9  14.6   2.5e-22   4.4e-18     181     308 ..      10     155 ..       2     157 .. 0.75
   2 ?   -1.9   0.2      0.11   1.9e+03     143     241 ..     210     222 ..     174     224 .. 0.53
   3 !   54.6   4.0   6.7e-19   1.2e-14       2     156 ..     227     386 ..     226     396 .. 0.67

  Alignments for each domain:
  == domain 1  score: 65.9 bits;  conditional E-value: 2.5e-22
                   Sulf_transp 181 lgavllgllavlawlls...aktgrsfglg.............ftvpgakilqylvlgtskfln.wgvvlvlGiilGafla 244
                                   + ++ll++ +    lls   + +g ++g++             f+++  ++++y v     f++ ++ +lv+GiilG ++ 
  gi|13541796|ref|NP_111484.1|  10 IYGILLAVASFGLALLSysiTGVGLWWGVTgaesqmggvfwslFGLKIHNLAYYRVYPIPPFSEaFTWFLVFGIILGPLIV 90 
                                   445555555333333331113467777764444444455555577777777778777777777536889************ PP

                   Sulf_transp 245 allsgefkleapk.arellaallGGllMGfGarlAgGCniGaglsgiaslslsgwlalvflllGa 308
                                   +  ++ef+++  + +  +l a++GG+l G+G+r+AgGCniG ++sg+a+ s  ++ ++++++ G+
  gi|13541796|ref|NP_111484.1|  91 SSSKKEFSVRQVPnRYLALEAVAGGILIGYGTRMAGGCNIGDFYSGFATGSAWAIFFFLAMVSGI 155
                                   **********6653778899******************************************997 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.11
                   Sulf_transp 143 iallllvkelrkeklqeaeklektslakklfrkpwslvlgavllgllavlawllsaktgrsfglgftvpgakilqylvlgt 223
                                   +                                                                                
  gi|13541796|ref|NP_111484.1| 210 VR------------------------------------------------------------------------------- 211
                                   22............................................................................... PP

                   Sulf_transp 224 skflnwgvvlvlGiilGa 241
                                            +v+G+ilGa
  gi|13541796|ref|NP_111484.1| 212 -------LWYVFGLILGA 222
                                   .......22455555555 PP

  == domain 3  score: 54.6 bits;  conditional E-value: 6.7e-19
                   Sulf_transp   2 srfcfagairdivvekdgrllralllaiavaavgfqllaaaglidlpks.af......pvvglivGGllFGvGMalaGgCa 75 
                                   + +cf  ++r+ +  + g+ +     ++a++ +++++l+++ +id+  + +f      +++  i+GG++FG+GM la  C 
  gi|13541796|ref|NP_111484.1| 227 GAMCFQTSFRETISKNTGKTMAR---ILAISLLVYSILSQMAIIDFHVKvNFffdqseSILYQIIGGYIFGLGMGLAYNCT 304
                                   789********999998877654...56788888889999999987543222244444789******************** PP

                   Sulf_transp  76 sgtlyrvGeGslralitllffilgavalltgilsswleqllestvskesly....etlglsplllialllliallllvkel 152
                                    ++  r+G+G+++a++t++++ ++++  l++++ sw+++++    +++  +     ++g+  +++i   l+ +++l++   
  gi|13541796|ref|NP_111484.1| 305 YSMEWRMGSGNVQAILTFIGLTFIGAP-LYALTYSWWHSFVPVVFEPTRYWefslYKYGVTGAFIID--LFPVAWLIYSYF 382
                                   *******************99887764.455555555554444444444331100334444444443..444556666555 PP

                   Sulf_transp 153 rkek 156
                                   + ++
  gi|13541796|ref|NP_111484.1| 383 SDKT 386
                                   4444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (398 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       800  (0.0446204); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2765.32
//
Query:       gi|13541797|ref|NP_111485.1|  [L=301]
Description: phosphate uptake regulator [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      9e-08   31.9   0.3    2.8e-07   30.3   0.3    1.9  1  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an
  ------ inclusion threshold ------
       0.11   13.1   0.3       0.22   12.1   0.3    1.5  1  DUF883          Bacterial protein of unknown function (DUF883
       0.13   12.6   0.8       0.27   11.5   0.8    1.5  1  zf-C4H2         Zinc finger-containing protein


Domain annotation for each model (and alignments):
>> MazE_antitoxin  Antidote-toxin recognition MazE, bacterial antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.3   0.3   4.6e-11   2.8e-07       4      43 ..      13      52 ..      10      54 .. 0.95

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 4.6e-11
                                  TTEEEEEE-CCCHHHCCEECTCEEEEEECTTCCCCCCCHH CS
                MazE_antitoxin  4 GnsgavriPkevrfelgireGdevelevdgdkiilrplks 43
                                  G s++v++P ++++e+g+++  eve+++ +++i +rp+k+
  gi|13541797|ref|NP_111485.1| 13 GGSYIVSLPSDWVRENGLDVSREVEVFESSGIIKIRPKKD 52
                                  89************************************97 PP

>> DUF883  Bacterial protein of unknown function (DUF883)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.3   3.7e-05      0.22       5      71 ..     232     297 ..     228     298 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.7e-05
                        DUF883   5 aeleslladleellkeaadeageeaeelRerleerlerarerlrdaeeavaerakeaaeaaddyVre 71 
                                   + +  l++++e+++   + e  + a+++R++++e le+++++ + a++++++ +  a +  dd+V++
  gi|13541797|ref|NP_111485.1| 232 DQVLLLINTMENIITMFKTEDINMASRIRKNAHEILESVKSTSE-ANKELERMTGYALALMDDAVHK 297
                                   556678999*******************************9866.7777999999999999999996 PP

>> zf-C4H2  Zinc finger-containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.8   4.5e-05      0.27      27     102 ..     207     279 ..     184     293 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4.5e-05
                       zf-C4H2  27 ekeekcleeykkelelLeqEkmaHveeLrlIhaDinalEsvikeaeeekekslekakklyeeykklkeevnelrse 102
                                   ++  +++++++  + +++qE m+  +++ l+   in++E++i   ++e  ++ ++++k  +e+ +  +++ e  +e
  gi|13541797|ref|NP_111485.1| 207 RDLGRFITHTRLLIGNIKQEDMKMRDQVLLL---INTMENIITMFKTEDINMASRIRKNAHEILESVKSTSEANKE 279
                                   566789999999999*******999998887...9***************99999999998887766666555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       963  (0.0537119); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2271.82
//
Query:       gi|13541798|ref|NP_111486.1|  [L=249]
Description: permease [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-38  133.1  33.3    1.5e-38  132.8  33.3    1.0  1  TauE      Sulfite exporter TauE/SafE


Domain annotation for each model (and alignments):
>> TauE  Sulfite exporter TauE/SafE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.8  33.3   8.2e-43   1.5e-38       1     234 [.       6     244 ..       6     245 .. 0.93

  Alignments for each domain:
  == domain 1  score: 132.8 bits;  conditional E-value: 8.2e-43
                          TauE   1 lllagllaGfvagllGiGggliavPlLlll..lppavavatsllavvatslsgalahrrrgnvdwrlllllllgsliGall 79 
                                   ++l+g+l+G++ g++G  g + +vP+L ++  ++ a+a++tsl++ ++ts + ++ +++++nv+ +++l++++gs+iG+++
  gi|13541798|ref|NP_111486.1|   6 FILLGILVGALTGITGSSGVVAVVPALSIInrYDVATAIGTSLFIDIVTSSIVFIVYLKNKNVNTSIMLPFAIGSIIGSQA 86 
                                   589**************************7677************************************************ PP

                          TauE  80 Gallllllpsellkllfgvlllllallmllrkkr...srakgrerrptaillvligglvGllsGllGiGgGfllvplllll 157
                                   G+ ++ ++ps +lk +fg +lll++++ +lr+k+   s+++    + + +l++ i +++ l++Gl+G++gG++ ++++l++
  gi|13541798|ref|NP_111486.1|  87 GVRIAVSIPSFILKDVFGSFLLLMGVYSVLRRKKnvtSKNSILGGKCKFLLAFSISIIISLATGLMGASGGIMYLIAMLFI 167
                                   ****************************998877565333344555556666777777*********************** PP

                          TauE 158 lglplkkavatslllilvislagalgyalagavdwpllllllpgallGallGarlarrlsertlrrlfallllvlgv 234
                                   ++ ++++av+t+++l+++++ +ga+gy++ g +d+ +++++++++l+ +++ a+l ++++++t+ ++++++ + +g+
  gi|13541798|ref|NP_111486.1| 168 FKEDVRVAVGTATALMIISASSGATGYFFYGRIDLIAGIVIGVTSLISGYFFAKLGNKIKRETVNKVLIVMFFTIGI 244
                                   *************************************************************************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       921  (0.0513693); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1620.94
//
Query:       gi|13541799|ref|NP_111487.1|  [L=164]
Description: hypothetical protein TVN0968 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score 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   0.1      0.074   13.1   0.1    1.3  1  DUF4320   Domain of unknown function (DUF4320)


Domain annotation for each model (and alignments):
>> DUF4320  Domain of unknown function (DUF4320)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   4.2e-06     0.074      48     112 ..      13      89 ..       3      91 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.2e-06
                       DUF4320  48 raaelkeqtglepdisw.skeqtdek...........tgkiqlndevtvtitteakiglfkgfgsdpitlkarasGv 112
                                   +++++ + ++l+p+  + + ++++ +           +g iq n++++v+ +    i++f      +++++ +++Gv
  gi|13541799|ref|NP_111487.1|  13 LYSQTINSIDLKPNTLItNSTYYNISeelgglyvpfnNGTIQSNSTIYVNYSIISAITIFDRYYMPQVQINTTIDGV 89 
                                   6677778888988666634444444478999999999*************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       563  (0.0314016); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1198.68
//
Query:       gi|13541800|ref|NP_111488.1|  [L=189]
Description: hypothetical protein TVN0969 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score 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   15.1   0.4      0.024   14.7   0.4    1.3  1  HP_OMP    Helicobacter outer membrane protein
      0.035   14.4   0.2      0.075   13.3   0.1    1.7  2  CBM_4_9   Carbohydrate binding domain


Domain annotation for each model (and alignments):
>> HP_OMP  Helicobacter outer membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.4   2.6e-06     0.024      37      67 ..      68     103 ..      49     179 .. 0.64

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.6e-06
                        HP_OMP  37 asais....anmltYGvgtDlLvniinkkka.slGl 67 
                                   ++ +s    ++ +tYG gtD+L+n+++ + +  +G+
  gi|13541800|ref|NP_111488.1|  68 KNITSgstiMVNYTYGSGTDYLLNVLEVNDNdVSGV 103
                                   222224555999************976555433333 PP

>> CBM_4_9  Carbohydrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0      0.75   6.7e+03     112     125 ..      26      40 ..      20      44 .. 0.63
   2 ?   13.3   0.1   8.4e-06     0.075      26      76 ..     123     172 ..     103     189 .] 0.78

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.75
                                   EEEEEE-S.SCSCCE CS
                       CBM_4_9 112 legtFtip.kstden 125
                                   ++ t+t++ ++++ +
  gi|13541800|ref|NP_111488.1|  26 ISNTYTVTtSGHAPG 40 
                                   677777775555555 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 8.4e-06
                                   EEEECGCSSSSEEEEEESCSSTTCEEEEEEECCS-TT-EEEEEEEEEESST CS
                       CBM_4_9  26 kasvdvsyngtyslkvsgrgetwdgqaiditirlekgktYtvsfwvkassg 76 
                                   +a ++ s   + sl+v++ + + +     ++i+l  g+tY +sf + ass 
  gi|13541800|ref|NP_111488.1| 123 EAYLKGS-ANSPSLTVTNSTGPMTAYSFGSPINLVSGHTYYISFVIDASSF 172
                                   4555666.77779*********9999999****************999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       443  (0.0247086); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); 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: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 1449.48
//
Query:       gi|13541801|ref|NP_111489.1|  [L=385]
Description: hypothetical protein TVN0970 [Thermoplasma volcanium GSS1]
Scores for complete 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-68  229.4   0.0    7.3e-68  229.2   0.0    1.0  1  DUF1015        Protein of unknown function (DUF1015)
  ------ inclusion threshold ------
      0.015   15.1   0.0      0.065   13.0   0.0    1.9  2  N-glycanase_N  Peptide-N-glycosidase F, N terminal
      0.075   13.3   0.0       0.15   12.4   0.0    1.6  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 !  229.2   0.0   1.2e-71   7.3e-68       1     392 [.       3     376 ..       3     378 .. 0.86

  Alignments for each domain:
  == domain 1  score: 229.2 bits;  conditional E-value: 1.2e-71
                       DUF1015   1 lkPfrglrypkekvlaevasppYDviseeearelakknpysflrlilpeadledeedeedryekaaetleewleegvlvqd 81 
                                   +kPfr l y+k   ++ +++pp+D i+++e++el k+n+y+++ l+lp+  +         + +a+  l++wle+gvl+  
  gi|13541801|ref|NP_111489.1|   3 VKPFRPLIYRK--EIDGMIAPPFDAITPKEEVEL-KRNKYNITYLTLPKGRD--------GIPHAKMLLQSWLENGVLIPM 72 
                                   69******987..7*******************9.8************8633........6999***************** PP

                       DUF1015  82 ekpalyvyeqtfed.g.grvrrGlvaavsledyeegvIlpHEkTlaekeedRlkllratkanlepifllyrdpe...eiee 157
                                   +++ ++v++q+f + +    r+Gl+a v++ + e+g + pHE+T+   +++R  l++  + +lepifl+  +++    +++
  gi|13541801|ref|NP_111489.1|  73 KEDVFIVLRQRFYVgDeCINRYGLIAKVKVFP-ESGDVIPHERTFDMYVKERETLMDGISSQLEPIFLVTLKNDlpgYLKA 152
                                   ************88644777**********98.************************************999984434444 PP

                       DUF1015 158 lieelkkkeeeplydfttdedgvrhrlwaitdpeaiekiaealadkklyIADGHHRyatalavreerkaeeeaatgeepan 238
                                   + + l k   e    f    ++v++ ++ i+d+ +i+ki + la++k ++ADGHHR+++ ++++  rk       ++e + 
  gi|13541801|ref|NP_111489.1| 153 ITDGL-K---EDNTYF--GPENVENFVYYINDKRKINKIISLLAEDKSIVADGHHRLQATKNIA-ARK--SG--GEREFWS 222
                                   44444.2...233445..4589******************************************.332..22..3589*** PP

                       DUF1015 239 yflavlvnledpgLkilpihRvvkdlnglseeelleklaeafev.........apfglylkdgkwyklltlkdkavrsLdv 310
                                   y++a++++++dpg+ +  ++Rvv++   ++ +  ++ l+++fe+         + + l+  +g+ y+l+  + + +++L  
  gi|13541801|ref|NP_111489.1| 223 YAMAYITSIHDPGVLVGGVNRVVSNK--FRLD--MNVLSKYFEInqverldetN-INLF--NGRLYSLKI-RIPVYDNLID 295
                                   ***********************884..3443..78899999886666665322.6665..566677666.4447888876 PP

                       DUF1015 311 svlqelllepilgiedprkderidyvhgleeavekvdsgeagvafllnptsveelfavadagevmPrKSTyfePKlrsGlv 391
                                   +  ++++l++   ++  + ++++ y+h++ e++  v+sg+++++++l+ +++ +l+++  +g+++P+KSTyf+PK+ sGl 
  gi|13541801|ref|NP_111489.1| 296 A-SNDFILSKSASMNYTDIENEVIYTHDIYELMSLVNSGSYSFGIILPRWDKMKLIETLLSGRKLPQKSTYFYPKIPSGLA 375
                                   6.578*********77788*************************************************************9 PP

                       DUF1015 392 l 392
                                   +
  gi|13541801|ref|NP_111489.1| 376 I 376
                                   8 PP

>> N-glycanase_N  Peptide-N-glycosidase F, N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.25   1.5e+03      13      42 ..     263     292 ..     253     301 .. 0.74
   2 ?   13.0   0.0   1.1e-05     0.065     122     166 ..     306     350 ..     290     354 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.25
                                   SCE---TTSEEEEGGGTEEEEEEEE----B CS
                 N-glycanase_N  13 deeakdadevirlangtlilkkvklpeikk 42 
                                   ++ ++  ++ i+l ng+l+  k+ +p +++
  gi|13541801|ref|NP_111489.1| 263 NQVERLDETNINLFNGRLYSLKIRIPVYDN 292
                                   445555566899999999999999998865 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 1.1e-05
                                   S-TT-----S-EEEEEE-GGGHHHH.CCEEEEEEEE---SSS-EE CS
                 N-glycanase_N 122 kkvkikkwedsveweqdvtdllplLeegevylgvfidtwtaegev 166
                                     ++ ++ e++v ++ d+ +l++l+++g+  +g+    w++++ +
  gi|13541801|ref|NP_111489.1| 306 ASMNYTDIENEVIYTHDIYELMSLVNSGSYSFGIILPRWDKMKLI 350
                                   57889999*******************************999765 PP

>> ParBc  ParB-like nuclease domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   2.5e-05      0.15      20      67 ..     166     212 ..     130     224 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.5e-05
                         ParBc  20 pekieelvasIkkkGllqPiivrktrqgryeiiaGerRlrAakrlglk 67 
                                   pe++e  v  I  k  ++ ii +  + ++  + +G++Rl+A+k+ +++
  gi|13541801|ref|NP_111489.1| 166 PENVENFVYYINDKRKINKIISLLAE-DKSIVADGHHRLQATKNIAAR 212
                                   55666666666655555556666664.78899***********99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (385 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       398  (0.0221987); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 2753.84
//
Query:       gi|13541802|ref|NP_111490.1|  [L=280]
Description: endonuclease IV [Thermoplasma volcanium GSS1]
Scores for complete 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-31  107.8   0.0    5.8e-31  107.6   0.0    1.1  1  AP_endonuc_2  Xylose isomerase-like TIM barrel


Domain annotation for each model (and alignments):
>> AP_endonuc_2  Xylose isomerase-like TIM barrel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.6   0.0   3.2e-35   5.8e-31       3     210 .]      30     238 ..      28     238 .. 0.89

  Alignments for each domain:
  == domain 1  score: 107.6 bits;  conditional E-value: 3.2e-35
                                   HHHHCT-SEEEEECCTCSHHHHC..HHHHHHHHHHHHHHTTSEEEEEEECCCHSTCTHCHTTCS..HHHHHHHHHHHHHHH CS
                  AP_endonuc_2   3 aaaeaGfdgvElfgrdlvpvsel..sdeelrelrkaldelglriaslslftrfgypdederear..reesvdalkraiela 79 
                                   +a+  Gf+++++f +++  + +   s+ee+ ++ + + ++ +  +++++++  +       +++   ++s++a+ ++i++a
  gi|13541802|ref|NP_111490.1|  30 RASIFGFRTFQFFSKNQMRWNSTpiSEEEALRFISEVSSHSISSTMVHASYLINL----ASSSNelHQKSFNAFVEEIQRA 106
                                   57778***************999********************555555444444....33444678889*********** PP

                                   HHHTBSEEEEEBCCGBCTTTSGHHHHHHHHHHHHHHHHHHHHHHTSEEEEE--TTTTSSSTC..HHHHHHHHHHTTTTEEE CS
                  AP_endonuc_2  80 aaLGapllvlhpGtagagpkgseeeawerlaeslneladyaekegvklalEtlagsgvelgd..eelarlldavdspnvgv 158
                                   ++++a +l++hpG     ++g+++e ++++ e+++++  +     vkl++E++ag+g+  g    e+ +++d  ds  vgv
  gi|13541802|ref|NP_111490.1| 107 ERIDATFLTFHPG-----SNGNKDEGIRKIKEAIEKVETH----KVKLLVENTAGQGNVIGStiYEIGQIIDGFDSS-VGV 177
                                   *************.....7888888888777777777666....9*************9999*************86.*** PP

                                   EEEHHHHHHH....TTTHHHHHHHHHGG.....EEEEEE.EESSTTTTSSTTEESTTSSSS CS
                  AP_endonuc_2 159 clDtgHllia....eedvddalraladr.....ikhvHikDakgdlgagrdrhvpigeGei 210
                                   c+Dt+H+++a     + +d+++++l++      i ++H++Da +dlg++ drh+ ig G i
  gi|13541802|ref|NP_111490.1| 178 CIDTCHAWAAgydiTNKYDEFIDELDSAigldrIYAFHLNDAMKDLGSNIDRHELIGRGKI 238
                                   **********99999999999999999999999**************************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       605  (0.0337442); expected 358.6 (0.02)
Passed bias filter:                      511  (0.0285013); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 1963.07
//
Query:       gi|13541803|ref|NP_111491.1|  [L=237]
Description: transcription regulator [Thermoplasma volcanium GSS1]
Scores for complete 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   75.0   0.0    7.3e-21   73.8   0.0    1.6  1  TrmB            Sugar-specific transcriptional regulator TrmB
    7.6e-07   28.6   0.2      1e-06   28.1   0.2    1.2  1  Regulator_TrmB  Archaeal transcriptional regulator TrmB
     0.0019   18.5   0.0     0.0042   17.4   0.0    1.6  1  Rrf2            Transcriptional regulator
  ------ inclusion threshold ------
      0.031   14.6   0.3      0.046   14.0   0.3    1.4  1  DUF1863         MTH538 TIR-like domain (DUF1863)
       0.06   13.0   0.8       0.51    9.9   0.0    2.5  3  Drf_FH3         Diaphanous FH3 Domain
      0.069   12.5   0.1      0.091   12.1   0.1    1.2  1  CorA            CorA-like Mg2+ transporter protein
      0.073   13.1   0.0        7.4    6.7   0.0    2.2  2  HydF_dimer      Hydrogen maturase F dimerization domain
      0.098   12.0   0.1       0.13   11.6   0.1    1.3  1  ZnuA            Zinc-uptake complex component A periplasmic
       0.21   11.4   0.0        0.5   10.2   0.0    1.7  1  HTH_IclR        IclR helix-turn-helix domain


Domain annotation for each model (and alignments):
>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.8   0.0   3.6e-24   7.3e-21       1      68 []      15      82 ..      15      82 .. 0.98

  Alignments for each domain:
  == domain 1  score: 73.8 bits;  conditional E-value: 3.6e-24
                                  HHHCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEEE--HH CS
                          TrmB  1 LqklGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpklYravdpe 68
                                  L+ +GLs+yEa+ ++aL+ +g a+ad+ia  +++pr+++Y+v++sL++kGl +  +grp++++++++e
  gi|13541803|ref|NP_111491.1| 15 LKMFGLSSYEAQGFAALVYHGVANADTIATTANIPRTSAYKVMESLVKKGLAKATEGRPRMFKPAKME 82
                                  789*************************************************************9875 PP

>> Regulator_TrmB  Archaeal transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.2   5.1e-10     1e-06       2      62 ..     115     177 ..     114     223 .. 0.82

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 5.1e-10
                                   EEEESSHHHHHHHHHHHHHH-SSEEEEEE-G..GGHHHHHHHHHHHHHTT-EEEEEESS---- CS
                Regulator_TrmB   2 vwvvksretvierieelIesAenelivslps..elLeelreeliaaaergvtVllliypdedl 62 
                                   ++++ ++e+v e+iee+I+ +e e+i+s+p+  e+ +++++++++a++rg +V+++i p++  
  gi|13541803|ref|NP_111491.1| 115 IYTINGTEKVMEKIEEMINMTEREIIISTPKiiEIRKQMKKPIENAVKRGARVIFVIPPNKRV 177
                                   67999*************************7558899********************994333 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   2.1e-06    0.0042      26      61 ..      37      72 ..      27      86 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2.1e-06
                                  B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT CS
                          Rrf2 26 vsseeiaerqnispsylekilakLrkaglvksvrGk 61
                                  +++++ia+  ni+++ + k+++ L k+gl k+++G+
  gi|13541803|ref|NP_111491.1| 37 ANADTIATTANIPRTSAYKVMESLVKKGLAKATEGR 72
                                  7889******************************97 PP

>> DUF1863  MTH538 TIR-like domain (DUF1863)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.3   2.3e-05     0.046      56     111 ..     120     176 ..      79     201 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.3e-05
                       DUF1863  56 aaedikeairdaldrssvliVLvgsetat.srWvdwEIaaslkkgkrllgvsldrlk 111
                                    +e+++e+i+++++ ++  i++  +++ + ++  ++ I+ ++k+g+r++ v+ ++++
  gi|13541803|ref|NP_111491.1| 120 GTEKVMEKIEEMINMTEREIIISTPKIIEiRKQMKKPIENAVKRGARVIFVIPPNKR 176
                                   479***********************9655*********************999875 PP

>> Drf_FH3  Diaphanous FH3 Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       0.5     1e+03     129     157 ..      46      72 ..      40     104 .. 0.68
   2 ?   -0.1   0.2      0.31   6.1e+02     129     169 ..      97     137 ..      76     162 .. 0.55
   3 ?    9.9   0.0   0.00026      0.51      34      56 ..     213     235 ..     194     237 .] 0.84

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.5
                                   XXXXXXXXXXXXXXXXXXXXX..XXXXXX CS
                       Drf_FH3 129 nkvkdteaepyllsilqhlllirddeeek 157
                                   +++  t+a++++ s++++ l   + +e +
  gi|13541803|ref|NP_111491.1|  46 ANIPRTSAYKVMESLVKKGLA--KATEGR 72 
                                   566777777777777666655..333333 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.31
                                   XXXXXXXXXXXXXXXXXXXXX..XXXXXXXXXXXXXXXXXX CS
                       Drf_FH3 129 nkvkdteaepyllsilqhlllirddeeekesylklleelvs 169
                                   + +k+ e++     + q +++i+++e+ +e++ ++++ + +
  gi|13541803|ref|NP_111491.1|  97 RDLKELEENAPSRGEPQLIYTINGTEKVMEKIEEMINMTER 137
                                   34444444444444444444444444444444444443333 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.00026
                                   HSS-HHHHHHHHHHHHHHHHSSS CS
                       Drf_FH3  34 enelveykvatmllInalvnspe 56 
                                   +++++ +++++ ++In++vn pe
  gi|13541803|ref|NP_111491.1| 213 YSDNPTLCMHVYQFINTMVNRPE 235
                                   899*****************997 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   4.6e-05     0.091     116     203 ..      81     166 ..      36     171 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.6e-05
                          CorA 116 ldeivdrlfellekleeeldeledeledstkkeilrelaqlrrrlvklrralapnrevlkrllakaddkllddedkeylrd 196
                                   ++ei d++++ l++l ++l+ele++  ++ + +++ ++   ++ + k++++++ +++ +  ++++    ++ +++k+ +++
  gi|13541803|ref|NP_111491.1|  81 MEEIRDYYEDKLQQLFRDLKELEENAPSRGEPQLIYTINGTEKVMEKIEEMINMTEREI--IISTPKIIEIRKQMKKPIEN 159
                                   78999***********************************************9999988..66667788888888887777 PP

                          CorA 197 lldeler 203
                                      + +r
  gi|13541803|ref|NP_111491.1| 160 AVKRGAR 166
                                   7766555 PP

>> HydF_dimer  Hydrogen maturase F dimerization domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.023        45      26      96 ..      74     143 ..      64     145 .. 0.80
   2 ?    6.7   0.0    0.0037       7.4       3      54 ..     158     209 ..     157     233 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.023
                    HydF_dimer  26 Rlilp.qvqviRdilDekaiavvvkeseleaalkslkrkpklvitDsqvvkkvaeivpkdvklttfsilfar 96 
                                   R+  p +   iRd  ++k   +    +ele+   s   +p+l+ t  +  +kv+e++ + +++t   i+++ 
  gi|13541803|ref|NP_111491.1|  74 RMFKPaKMEEIRDYYEDKLQQLFRDLKELEENAPSRG-EPQLIYTI-NGTEKVMEKIEEMINMTEREIIIST 143
                                   5555524567999999999999999999999988777.9**99985.5679999999999999999998875 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0037
                    HydF_dimer   3 gdlvepgdlvvlvvpidseaPkgRlilpqvqviRdilDekaiavvvkesele 54 
                                   ++ v++g  v++v+p +++ P   +++ ++ +i   + ++ i   + + +le
  gi|13541803|ref|NP_111491.1| 158 ENAVKRGARVIFVIPPNKRVPANVIVYRKEGLIATDIVSDQIRALIADPNLE 209
                                   67899**********************9998887666566666666666665 PP

>> ZnuA  Zinc-uptake complex component A periplasmic
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   6.6e-05      0.13     119     216 ..      83     182 ..      50     204 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 6.6e-05
                                   GGHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSGTEGEEEESSSTTHHHHHHTT-EEEEEESSSSS.....HHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxx RF
                          ZnuA 119 anadtyeanaaayiekLeeldaeireelaeipeekrklvtthdafgylarayglevagiagiste.....aaqiaalieei 194
                                   +  d+ye++++++ + L+el+++  ++ +  p+   ++  t+++++  ++  +++   i+ ist       +q+++ ie +
  gi|13541803|ref|NP_111491.1|  83 EIRDYYEDKLQQLFRDLKELEENAPSRGE--PQLIYTINGTEKVMEKIEEMINMTEREII-ISTPkiieiRKQMKKPIENA 160
                                   44677888888888888888888888888..776668999*****************985.555559************** PP

                                   HHTT-SEEEEETTS-THHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxx RF
                          ZnuA 195 keagvkaifveplaspklaetl 216
                                    ++g+++ifv p  +   a+ +
  gi|13541803|ref|NP_111491.1| 161 VKRGARVIFVIPPNKRVPANVI 182
                                   **********996555445544 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 ?   10.2   0.0   0.00025       0.5      24      49 ..      42      67 ..      34      70 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00025
                                  HHHHHTS-HHHHHHHHHHHHHTTSEE CS
                      HTH_IclR 24 lArrtglpkStvhRlLqtLvelGyve 49
                                  +A  + +p+++++  + +Lv+ G+ +
  gi|13541803|ref|NP_111491.1| 42 IATTANIPRTSAYKVMESLVKKGLAK 67
                                  8999*******************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1129  (0.0629706); expected 358.6 (0.02)
Passed bias filter:                      758  (0.0422779); 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: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 1775.66
//
Query:       gi|13541804|ref|NP_111492.1|  [L=393]
Description: bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-28  100.0   0.0    1.7e-28   99.4   0.0    1.3  1  Flavoprotein  Flavoprotein
    2.5e-27   95.9   0.0    1.4e-26   93.5   0.0    1.9  2  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 !   99.4   0.0   1.9e-32   1.7e-28       2     155 ..      17     182 ..      16     185 .. 0.91

  Alignments for each domain:
  == domain 1  score: 99.4 bits;  conditional E-value: 1.9e-32
                                   EEEEEE-SSCGGGCHHHHHHHHHHTTEEEEEEESCHHHHCCHHGGS...........TCSSHHHHHH...CTTESEEEEEE CS
                  Flavoprotein   2 killgiTGsvaaikalellekLkkegievqvvltkaAkkfiskeklklaa.......redpilhiel...rrwadllviaP 72 
                                    ++++ T s++++ +++l++ L++eg+ev v +++++++++ +e +++a+       ++++++hi+l   ++  ++l+iaP
  gi|13541804|ref|NP_111492.1|  17 TVIVATTASISIYRIPDLIRDLRREGAEVIVGMSESSEELVGPETMRWASehdvvtkITGNVEHINLfinDKDKKALLIAP 97 
                                   589*****************************************88887788999999*********99999********* PP

                                   EEHHHHHHHHTT--SSHHHHHHHT..HCCTTEEEEE.--HHCCTCSTCHHHHHHH.HT................GHHHHHH CS
                  Flavoprotein  73 asantlakianGiadnlltlilra..takkpiliaPamnpamyenpqtlknlekl.eegvtvikPsegdigkgkmaeieei 150
                                   as++t++k+a G++d+   l++ +  +  +++++aPam+ +m+enp++++n+ekl + gv +++P+  d++k+k+   + i
  gi|13541804|ref|NP_111492.1|  98 ASYDTIGKMASGVTDTIPPLFFSFafGYGVKTIVAPAMHRSMMENPINKENVEKLrRLGVDIVDPI-YDEEKAKLSGNQCI 177
                                   *****************98777434688899************************66*********.78888888777777 PP

                                   HHHHC CS
                  Flavoprotein 151 vgkil 155
                                   ++ + 
  gi|13541804|ref|NP_111492.1| 178 IDHVC 182
                                   77665 PP

>> DFP  DNA / pantothenate metabolism flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0     0.079   7.1e+02     114     148 ..      24      56 ..      19      85 .. 0.76
   2 !   93.5   0.0   1.6e-30   1.4e-26       2     184 ..     190     364 ..     189     366 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.079
                                   ----EEE---HHHHHHHC-S.S-EEEEEEE-SS-H CS
                           DFP 114 ltleleknpdilaelaekkkkkqllvGFaaeteel 148
                                    ++++ + pd+++ l  +++ ++++vG +  +eel
  gi|13541804|ref|NP_111492.1|  24 ASISIYRIPDLIRDL--RREGAEVIVGMSESSEEL 56 
                                   567888899999999..345567999987666554 PP

  == domain 2  score: 93.5 bits;  conditional E-value: 1.6e-30
                                   TT-EEEEEES-EEEECCTTEEEEE----HHHHHHHHHHHHTT-E.EEEEE-S-SS---TT-EEEE--SHHHHHHHHHHHHT CS
                           DFP   2 egkkvlvtaGpTrEaiDpVRfisNrSSGkmGyalAeaaaarGae.Vtlvsgpvsletpegvevvkvesaeemleaveealk 81 
                                    gk++l+ +G   E+iDpVR i+N S+G +Gy +A+ a+++G + +t++ g++ ++ p+ v++    +++e+++  ee+++
  gi|13541804|ref|NP_111492.1| 190 DGKSILIISGRGEERIDPVRSITNDSTGYTGYWIARVAYRMGFShITYI-GNSIVDLPTYVNYRAAYTVDEFERLSEEEAS 269
                                   589***************************************8626666.55557778899999**********9998886 PP

                                   T-.SEEEE---S--EEES-------------..----EEE---HHHHHHHC-S.S-EEEEEEE-SS-HHHHHHHHHHHTT- CS
                           DFP  82 ea.divimaAAvaDyrpkeaaeeKikkeeeeeeltleleknpdilaelaekkkkkqllvGFaaeteellenareklerkgl 161
                                   ++ d++++ AA  D+++ e++e+K +    +e+ +l+le+ ++++ +l++ +k    +v+F + + ++ e    k  +k++
  gi|13541804|ref|NP_111492.1| 270 NNyDYIVVNAALPDFKVIEKSEKKYSS---NESHKLTLEPREKLVDKLSNISKG--KIVAFRLTE-NIGEDP-FKHFSKRI 343
                                   666********************9996...45679*************766655..59****974.444444.455589** PP

                                   SEEEEEEGGGTTGGG-SS-EEEE CS
                           DFP 162 dlivaNdvskeeagfgsdenevt 184
                                   d+ v+N+ ++    fg++ene+ 
  gi|13541804|ref|NP_111492.1| 344 DMAVVNSYKTG--PFGKTENEYR 364
                                   *********87..9*****9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       566  (0.031569); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2864.38
//
Query:       gi|13541805|ref|NP_111493.1|  [L=254]
Description: amidohydrolase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.4e-18   65.0   0.0    8.6e-18   64.6   0.0    1.2  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 !   64.6   0.0   4.8e-22   8.6e-18       4     212 ..      12     188 ..       9     207 .. 0.84

  Alignments for each domain:
  == domain 1  score: 64.6 bits;  conditional E-value: 4.8e-22
                                   EEEBB-STTHHHHHHHHHHHHHHHHHHTTESEEEEETTTTTBSSSHHHHHHHHBHSSSHHHHHHHH.HHHHHTEEEEEEEE CS
                  CN_hydrolase   4 vvQlpqkaadleanlqklleliaeAarkgadLivlPElfitgykeeahfleaAeaglgetlallaa.larkngiavvigli 83 
                                   +vQl+     +e +l+ l++ i++   k+ d +vlPE + t      ++++     + ++++l+++ + +k++iav + ++
  gi|13541805|ref|NP_111493.1|  12 AVQLHR--QHFEDGLAYLEKVIDA---KNSDFLVLPEKWST------EVMD-----QQAVIDLIKDsIVSKFNIAVPGSFS 76 
                                   555555..3566666666666666...68999999999998......3333.....23678888762689*********** PP

                                   EEECCTTEEEEEEEEEEEETTSEEEEEEE-SS--EECTTSCECCGHHTSCS-SSS-EEEETTEEEEEEEGGGGGSHHHHHH CS
                  CN_hydrolase  84 ereltngklqayntavlldldgklvgkyrKlhLfpgeprpptaverelfepgdgipvfdtpvgkiGaaiCyeigfpellra 164
                                    +  +ng l  yn+a+++ ++gkl+g ++K+ L          +e   + +g +i +f  +  +iG+aiCy+i fp++   
  gi|13541805|ref|NP_111493.1|  77 IK--ENGFL--YNRAYIF-HTGKLIGYQDKISLY--------GNEGRHYNSGSEIRIFRKDDLRIGIAICYDIDFPYYPKL 144
                                   **..9****..*****99.99***********96........56677799999999************************* PP

                                   HHHTT-SEEEE...BH.GCCCTCHHHHHHHHHHHHHHHHHHTSEEEEEEBE CS
                  CN_hydrolase 165 lalkgaeilvn...lserapvpksmgppqwellgraralengcfviaanqv 212
                                   la+++a+i+ n   ++       s+  + w+l   ar+len ++v+ +n+ 
  gi|13541805|ref|NP_111493.1| 145 LAKNKADIIANpslIR-------SIFSDEWHLYVSARSLENRIPVLSVNSL 188
                                   ***********88555.......************************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); 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: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1958.10
//
Query:       gi|13541806|ref|NP_111494.1|  [L=234]
Description: alpha/beta superfamily hydrolase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.5e-23   82.2   1.1    1.9e-16   60.5   0.2    2.0  2  Abhydrolase_1   alpha/beta hydrolase fold
    8.2e-14   52.7   0.0    1.1e-11   45.8   0.0    2.0  2  Abhydrolase_6   Alpha/beta hydrolase family
    3.5e-07   29.7   0.0     0.0046   16.2   0.0    2.1  2  Hydrolase_4     Serine aminopeptidase, S33
    0.00035   20.4   0.6          2    8.2   0.0    3.1  3  Abhydrolase_2   Phospholipase/Carboxylesterase
     0.0033   17.2   0.1       0.18   11.6   0.0    2.1  2  Abhydrolase_5   Alpha/beta hydrolase family
  ------ inclusion threshold ------
      0.059   13.0   0.0      0.093   12.4   0.0    1.4  1  FSH1            Serine hydrolase (FSH1)
      0.092   12.3   0.0       0.23   11.0   0.0    1.7  1  Abhydro_lipase  Partial alpha/beta-hydrolase lipase region
       0.16   11.5   0.1       0.45    9.9   0.1    1.7  1  Peptidase_S9    Prolyl oligopeptidase family


Domain annotation for each model (and alignments):
>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.5   0.2   8.6e-20   1.9e-16       2      94 ..      23     108 ..      22     152 .. 0.91
   2 !   20.8   0.1   1.1e-07   0.00024     206     253 ..     162     218 ..     145     222 .. 0.82

  Alignments for each domain:
  == domain 1  score: 60.5 bits;  conditional E-value: 8.6e-20
                                   EEEEE-STTTCGGGGTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTTGB.CHHSHHHHHHHHHHHHHHCTTSSEEEEEETH CS
                 Abhydrolase_1   2 vlvilhGlpgssdvwaerglapaLakdgfdvillDlrGvgySspapacinddygtasvaddldrildalgddkltlvGhSm 82 
                                   +l++lhGl+gss++w +  l + La  +f++i +Dl+G+g+S++++     +y+    a+ ++ + ++lg+ ++ + G S+
  gi|13541806|ref|NP_111494.1|  23 PLIFLHGLGGSSNNWLR--LDRFLAP-RFRLIFFDLLGHGQSDKPK----IEYTVEVQAKAIHEAINSLGISRFSIAGNSY 96 
                                   9****************..******9.*******************....57***************************** PP

                                   HHHHHHHHHHHH CS
                 Abhydrolase_1  83 GGmialayaaey 94 
                                   GG ++l++    
  gi|13541806|ref|NP_111494.1|  97 GGWVSLYLSIHI 108
                                   ****99987654 PP

  == domain 2  score: 20.8 bits;  conditional E-value: 1.1e-07
                                   C.........THHHHSEEEEEEETTCSSSCHHHHHHHHHCHTSEEEEEEETCSSSHH CS
                 Abhydrolase_1 206 e.........lknvlaptlvisgtsDplvppkaledlaqllpkkrlvvisdagHlaf 253
                                   +         lkn ++pt++i+gt D++ +++++++l +l+ +++l+ i+ a H+ +
  gi|13541806|ref|NP_111494.1| 162 KhewkikeedLKNLSVPTIIIWGTADNILSIDYGRKLHDLIQNSKLYEIPAAKHTPQ 218
                                   044444566799******************************************987 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.8   0.0   4.8e-15   1.1e-11       1      95 [.      24     119 ..      24     149 .. 0.80
   2 ?    5.1   0.0     0.014        31     164     218 ..     170     226 ..     158     228 .. 0.80

  Alignments for each domain:
  == domain 1  score: 45.8 bits;  conditional E-value: 4.8e-15
                                   EEEE--GC.....GCHHHHHHHHCCTCEEEEE--TTSTS-GGCS--HHH...CHHHHHHHCCTT..TTSEEEEEETCHHHH CS
                 Abhydrolase_6   1 vlllHGagssassWlvapLaallaagvhvlapDlpGhGrsdpppldled...ladlaalldelaagggpvvlvGHSlGGal 78 
                                   +++lHG+g+s+  Wl  +L ++la +++ + +Dl GhG sd p  +++    + ++++++++l  g  ++ + G+S+GG++
  gi|13541806|ref|NP_111494.1|  24 LIFLHGLGGSSNNWL--RLDRFLAPRFRLIFFDLLGHGQSDKPKIEYTVevqAKAIHEAINSL--GISRFSIAGNSYGGWV 100
                                   79*************..*********999*********8888888886632334446666666..69999*********** PP

                                   HHHHHHCC....EE.EEES- CS
                 Abhydrolase_6  79 alaaapla..lvvg.vlldp 95 
                                   +l +  +   +  + +l+d+
  gi|13541806|ref|NP_111494.1| 101 SLYLSIHIakP-DKlILIDS 119
                                   99955555543.33588887 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.014
                                   CHHTT-TTGCEEEC.TT-CHHHHCHHCCCH..STTEEETCE...SSS-HHHHSHHHHH CS
                 Abhydrolase_6 164 aawadlpvpllvlg.geDplvprllerlla..qagarlpvvlpgaGHlphleepdeva 218
                                   ++++ l vp+++++ ++D ++   + r l+  ++  +l  ++p a H p+  +p+ +a
  gi|13541806|ref|NP_111494.1| 170 EDLKNLSVPTIIIWgTADNILSIDYGRKLHdlIQNSKL-YEIPAAKHTPQRTHPQILA 226
                                   57888999997776599997774466666678888888.99*********99998777 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   2.1e-06    0.0046       7     109 ..      24     119 ..      21     145 .. 0.78
   2 !   11.6   0.0   5.6e-05      0.12     185     233 ..     170     216 ..     149     219 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.1e-06
                   Hydrolase_4   7 vvlvHGlaehsgryaelaeaLaaqGfavyalDhrGhGrsegkrghvpsfddyvdDlaafvekvkeehpelplfllGhSmGG 87 
                                   ++++HGl+ +s+   +l + L a  f  + +D  GhG+s+      p+++  v+  a++++++ +  + +++ + G S GG
  gi|13541806|ref|NP_111494.1|  24 LIFLHGLGGSSNNWLRLDRFL-APRFRLIFFDLLGHGQSD-----KPKIEYTVEVQAKAIHEAINSLGISRFSIAGNSYGG 98 
                                   6899***********996555.677**************5.....455577777777888888888889999********* PP

                   Hydrolase_4  88 liallyllrypdkvaglilsaP 109
                                    ++l +  + ++  ++lil+ +
  gi|13541806|ref|NP_111494.1|  99 WVSLYLSIHIAK-PDKLILIDS 119
                                   998877654444.567777655 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 5.6e-05
                   Hydrolase_4 185 eraakitlPllllhGeaDkvvdpeasrelyerlgskdktlklypglyHe 233
                                   e+ +++++P++++ G+aD++ + +  r+l++ ++  + +l  +p + H 
  gi|13541806|ref|NP_111494.1| 170 EDLKNLSVPTIIIWGTADNILSIDYGRKLHDLIQ--NSKLYEIPAAKHT 216
                                   6778899************************999..5778888888885 PP

>> Abhydrolase_2  Phospholipase/Carboxylesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.0   0.00089         2      17      35 ..      24      42 ..      16      54 .. 0.77
   2 !    6.1   0.1    0.0037       8.3      80     130 ..      63     112 ..      51     122 .. 0.69
   3 ?    2.9   0.0     0.036        81     155     187 ..     175     207 ..     159     231 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00089
                                  EEEE--TT--SHHHHHHHH CS
                 Abhydrolase_2 17 viflHGlGdsghawaeaak 35
                                  +iflHGlG s + w    +
  gi|13541806|ref|NP_111494.1| 24 LIFLHGLGGSSNNWLRLDR 42
                                  8*********999987666 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0037
                                   HHHHHHHHHHHHHHHHHHHHTT--GGGEEEEEETHHHHHHHHHHHT-SS-- CS
                 Abhydrolase_2  80 eagikksaekleelidaelkkgipssriiigGFSqGaalalylaltlpkkl 130
                                   + +i+ ++e   + i + + +++  sr  i G S G+ ++lyl++   k+ 
  gi|13541806|ref|NP_111494.1|  63 KPKIEYTVEVQAKAIHEAI-NSLGISRFSIAGNSYGGWVSLYLSIHIAKPD 112
                                   4445555544445554444.45899999***************98877765 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.036
                                   GG-EEEEEEETT-SSS-HHHHHHHHHHHHTTS- CS
                 Abhydrolase_2 155 kklpilqiHgeeDpvvplalgkaakevlkkllk 187
                                     +p + i+g+ D+++ +  g +++ +++++  
  gi|13541806|ref|NP_111494.1| 175 LSVPTIIIWGTADNILSIDYGRKLHDLIQNSKL 207
                                   4699********************999998765 PP

>> Abhydrolase_5  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.1     0.022        48      47      87 ..      78     117 ..      69     163 .. 0.69
   2 !   11.6   0.0   8.1e-05      0.18      93     140 ..     169     215 ..     164     218 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.022
                 Abhydrolase_5  47 eeiikeapklekfvvgGhslGGvvasrfaaeeekiegvvfl 87 
                                   +e+i++  ++ +f ++G s GG v+  ++ +  k + ++++
  gi|13541806|ref|NP_111494.1|  78 HEAINS-LGISRFSIAGNSYGGWVSLYLSIHIAKPDKLILI 117
                                   344443.34899**********9876555444455555555 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 8.1e-05
                 Abhydrolase_5  93 kdelselskkvlsivgteDgvlnvkslekakkflpkdtkvvsieGgnh 140
                                   +++l++ls++++ i+gt D++l+++ + ++ + l +++k+ +i    h
  gi|13541806|ref|NP_111494.1| 169 EEDLKNLSVPTIIIWGTADNILSID-YGRKLHDLIQNSKLYEIPAAKH 215
                                   678*******************997.6677778899999999988877 PP

>> FSH1  Serine hydrolase (FSH1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   4.2e-05     0.093     156     205 ..     171     219 ..      56     223 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.2e-05
                          FSH1 156 eedkiqtptLhvlGelDtvvdeerseaLaeafknsskvlkHpggHfvPnk 205
                                   + +++++pt+ + G++D++ + +  ++L++ ++n sk+++ p + + P++
  gi|13541806|ref|NP_111494.1| 171 DLKNLSVPTIIIWGTADNILSIDYGRKLHDLIQN-SKLYEIPAAKHTPQR 219
                                   23556*****************************.9*9999988888875 PP

>> Abhydro_lipase  Partial alpha/beta-hydrolase lipase region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0    0.0001      0.23      41      61 ..      18      38 ..      12      41 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0001
                Abhydro_lipase 41 lekkpvVlLqHGLlasSevwv 61
                                  ++++++ ++ HGL  sS++w+
  gi|13541806|ref|NP_111494.1| 18 RPGEYPLIFLHGLGGSSNNWL 38
                                  567899999***********8 PP

>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.1    0.0002      0.45      64     171 ..      87     204 ..      67     229 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0002
                                   GGEEEEEETHHHHHHHHHHH..H-GGG-SEEEEESE---CCCHHCSTTS..THHHCCCC--TTTCHHHHHHHHHH-CGGG- CS
                  Peptidase_S9  64 erlaitGgSyGGyltgaaln..qrpdlFkaavaevpvvdvlrydsdtdl..lteeymewgnpeeneegykelspyspldnv 140
                                   +r  i G SyGG++++ +     +pd+   ++ ++++   +    ++ +  + +++m+  +  ++ee  + +   +  ++ 
  gi|13541806|ref|NP_111494.1|  87 SRFSIAGNSYGGWVSLYLSIhiAKPDK-LILIDSAGINKTVGESGEEMIesFVQKVMGVEDG-NDEEVIRNIIRNNAKHEW 165
                                   78899*******999887662244444.3456677888888887777779888888888777.656656665555555555 PP

                                   -........---EEEEEEETT-SSS-THHHHHHHHHHH- CS
                  Peptidase_S9 141 k........aypplLlihGlaDdrvppaealklvaaLqk 171
                                   k         ++p+++i G+aD+   +  + kl +  q+
  gi|13541806|ref|NP_111494.1| 166 KikeedlknLSVPTIIIWGTADNILSIDYGRKLHDLIQN 204
                                   556777777999**********99999999888887774 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       536  (0.0298957); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 1698.53
//
Query:       gi|13541807|ref|NP_111495.1|  [L=886]
Description: pyruvate phosphate dikinase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-88  297.0   0.0    2.3e-88  296.1   0.0    1.4  1  PEP-utilizers_C  PEP-utilising enzyme, TIM barrel domain
    3.7e-59  200.6   0.1    9.4e-34  117.1   0.0    3.3  3  PPDK_N           Pyruvate phosphate dikinase, PEP/pyruvate bi
    9.9e-26   89.3   1.9    2.1e-25   88.2   1.9    1.6  1  PEP-utilizers    PEP-utilising enzyme, mobile domain
  ------ inclusion threshold ------
      0.044   13.5   0.3      0.097   12.4   0.3    1.6  1  SHOCT            Short C-terminal domain
       0.13   12.0   0.2       0.37   10.5   0.2    1.7  1  UPF0175          Uncharacterised protein family (UPF0175)


Domain annotation for each model (and alignments):
>> PEP-utilizers_C  PEP-utilising enzyme, TIM barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  296.1   0.0   6.5e-92   2.3e-88       8     293 ..     518     872 ..     511     873 .. 0.95

  Alignments for each domain:
  == domain 1  score: 296.1 bits;  conditional E-value: 6.5e-92
                                   CCCCCCHCCCXBCEEEEEESSCHHHHHHHHCTXSSEEEEEHHHHCTTSCCHHHHHH....................HHHHH CS
               PEP-utilizers_C   8 ktllavtkdgkkikvlaNidtpedaekalengaeGiGLlRtEflfmareelpteee....................qaeay 68 
                                   k+ll ++++ +k+ v aN++tpe+a+ a+engaeGiGL RtE++f+ +e++p+++                     q +++
  gi|13541807|ref|NP_111495.1| 518 KKLLELADKNRKLGVRANANTPEEAHLARENGAEGIGLARTERMFLGNERIPIMRSmimseskeerqkyleqllpmQISDF 598
                                   556677788899*******************************************99************************ PP

                                   HHHHHHTTTSEEEEEXXXSSCCGGSGGC.............................HHHH.XSXGGGSSXTHHHHCCSHH CS
               PEP-utilizers_C  69 kkvleamngrpvvvRtlDiggdkelpel.............................keepeevNPmlGfRgirlglsepe 120
                                    + +++m+g pv++R+lD++ +++lp                               ++ +ee NPmlGfRg+r+gl +pe
  gi|13541807|ref|NP_111495.1| 599 VEFFKTMEGYPVIIRLLDPPLHEFLPDKetilnkiyeiksgkngsdelqyyekllktVRDLEEFNPMLGFRGCRVGLVYPE 679
                                   ***************************999**************************999999******************* PP

                                   HHHHHHHHHHHHCCCC.......EEEEEESSXXSHHHHHHHHHHHHHHHHHHHHCTCTXXTTXEEEEEEXSHHHHHTHHHH CS
               PEP-utilizers_C 121 lfetqlrAllrasaag.......kleimlPmvasveeleeakkiieevkeelekegvkkkkkvkvGiMiEvpsaalladkl 194
                                   ++ +q+rA+++a++ +         eim+P+v + +el+   + +e++++ ++++    + ++k+G+MiE+p+a ++adk+
  gi|13541807|ref|NP_111495.1| 680 IYDMQVRAIMEAAVRVqkegrriMPEIMIPLVGHHNELKILMERLEKTAKSVKDS---DQVDYKFGTMIEIPRACVTADKI 757
                                   *************966678899999***************************988...899******************** PP

                                   CTTSSEEEEXHHHHHHHHHTXXCCCHCHHHH..........SXTTTCHHCCCHHHHHHHHHHCC......XEEEEESCCCC CS
               PEP-utilizers_C 195 akevdFfSiGtNDLtQytlavdRdneevakl..........ydplepavlrlikevikaaeekg......lkvgiCGelag 259
                                   ak++dFfS+GtNDLtQ+t++++Rd++e + +           dp++  +  +++e++++a ekg      l+vgiCGe +g
  gi|13541807|ref|NP_111495.1| 758 AKYADFFSFGTNDLTQMTFGYSRDDAEGKFMffylengileKDPFSSVDEDGVGELMRMAVEKGrksnekLEVGICGEQGG 838
                                   ***************************55555566888999****************************9*********** PP

                                   SCCCHHHHHHCTXSEEEEXGGGHHHHHHHHHCTT CS
               PEP-utilizers_C 260 dpsavellvglGldelSmsaasvpaaraalaqve 293
                                   dp ++ +++++Gld++S+s++++p+ar a+a+++
  gi|13541807|ref|NP_111495.1| 839 DPDTIYFCHKIGLDYVSASPYRIPIARLAAARAN 872
                                   *****************************99875 PP

>> PPDK_N  Pyruvate phosphate dikinase, PEP/pyruvate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.8   0.0   4.5e-14   1.6e-10       2      42 ..      20      64 ..      19      72 .. 0.83
   2 !  117.1   0.0   2.6e-37   9.4e-34      79     220 ..      65     290 ..      60     298 .. 0.95
   3 !   40.1   0.1   7.2e-14   2.6e-10     271     326 ..     302     355 ..     293     357 .. 0.93

  Alignments for each domain:
  == domain 1  score: 40.8 bits;  conditional E-value: 4.5e-14
                        PPDK_N  2 elvGGKganLaellneagipvPpgfaitadafrefleeng.....l 42
                                  +l+GGKga+Lae+ +++g++vPpgf+it++a+ +fl +++     +
  gi|13541807|ref|NP_111495.1| 20 DLLGGKGAGLAEM-TKIGLNVPPGFTITTEACIDFLRDGNfpkgmM 64
                                  69***********.77*********************998555533 PP

  == domain 2  score: 117.1 bits;  conditional E-value: 2.6e-37
                        PPDK_N  79 eeleeaikeayeelgkkfgde..elpvaVRSSataEDlpkasfaGqqdtyLnvggeeevle.................... 137
                                   e+  +a+++++e++++kfg+   +l+v+VRS+      +  s++G++dt+Lnvg ++e+++                    
  gi|13541807|ref|NP_111495.1|  65 EQTMDALHMIEEKVSRKFGNPenPLLVSVRSG------APVSMPGMMDTVLNVGLNDETVKglafmtdnerfaldayrrli 139
                                   56678999***********99889********......99***************************************** PP

                        PPDK_N 138 ..................................................................aikavfaSlfnerAi 152
                                                                                                     +ikavf+S++++rA 
  gi|13541807|ref|NP_111495.1| 140 qmfgeivyglpheefrgliekvkrekgydedkfttsditeiikgeneiyrkhkksfpqdpqeqlveSIKAVFNSWNSRRAK 220
                                   ********************************************************************************* PP

                        PPDK_N 153 lYrkekgldheevalavvvqkmvnsdlg...asGVafsldpetG...fkdevlinasyGlGeaVVaGrvtpdef 220
                                   +Yr+ ++++ e++++av +  mv++++g   a+GVaf++dp+tG      e+l na   +Ge+VVaG++tp ++
  gi|13541807|ref|NP_111495.1| 221 TYREINHIP-ENMGTAVSIVTMVFGNMGsdsATGVAFTRDPNTGekrIFAEYLTNA---QGEDVVAGIRTPKYI 290
                                   *********.**********************************555445777777...************987 PP

  == domain 3  score: 40.1 bits;  conditional E-value: 7.2e-14
                        PPDK_N 271 eeLaeiakkiekhygtpmdiEfaideeegklyllQaRpetrtsekkekkaaetlee 326
                                   + L ++   +e+hy++++diEf+i+   gkly+lQ+R ++r  +++ ++a e++ee
  gi|13541807|ref|NP_111495.1| 302 SDLIRMCDILEHHYRDMQDIEFTIE--RGKLYMLQTRTGKRSAKAAIRIAVEMYEE 355
                                   56889999*****************..*************************9998 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 !   88.2   1.9   5.9e-29   2.1e-25       4      73 .]     418     499 ..     415     499 .. 0.97

  Alignments for each domain:
  == domain 1  score: 88.2 bits;  conditional E-value: 5.9e-29
                                   S-EEEEES---HHHHTTS-GEEEEEES--TTHHHHHHHHHHTT--EEE--SSHH.............HH--TEEEEEETTT CS
                 PEP-utilizers   4 egvILvaeetspsdiagldkaaGivterGGmtSHaAivArelgiPaVvgvgeati............elkegdlitvDgst 72 
                                   ++ ILv++et+++d+ g+  ++G++t++GGmtSHaA+vAr++g+PaVvgv+ + +            +l+egd++t+Dg++
  gi|13541807|ref|NP_111495.1| 418 KKMILVRPETTADDVRGMAVCEGFLTQKGGMTSHAAVVARAMGKPAVVGVETMHVdttnntltingkTLHEGDVVTIDGTS 498
                                   669**************************************************99*************************9 PP

                                   T CS
                 PEP-utilizers  73 G 73 
                                   G
  gi|13541807|ref|NP_111495.1| 499 G 499
                                   9 PP

>> SHOCT  Short C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.3   2.7e-05     0.097       2      19 ..     345     362 ..     344     362 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.7e-05
                         SHOCT   2 aLekLkeLyarGeIteEE 19 
                                   a+++  e+y++G+I+eEE
  gi|13541807|ref|NP_111495.1| 345 AIRIAVEMYEEGIISEEE 362
                                   899999***********9 PP

>> UPF0175  Uncharacterised protein family (UPF0175)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.2    0.0001      0.37      10      39 ..     334     363 ..     329     365 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0001
                       UPF0175  10 klteeelerelrialAvklYeegrlSlgkA 39 
                                   +    + ++++ i +Av++Yeeg++S  +A
  gi|13541807|ref|NP_111495.1| 334 QTRTGKRSAKAAIRIAVEMYEEGIISEEEA 363
                                   555666778899**************9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (886 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       545  (0.0303977); expected 358.6 (0.02)
Passed bias filter:                      478  (0.0266607); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.41
# Mc/sec: 6422.90
//
Query:       gi|13541808|ref|NP_111496.1|  [L=138]
Description: DNA-binding protein [Thermoplasma volcanium GSS1]
Scores for complete 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-18   64.6   0.0      1e-17   64.4   0.0    1.0  1  DUF296    Plants and Prokaryotes Conserved (PCC) domain


Domain annotation for each model (and alignments):
>> DUF296  Plants and Prokaryotes Conserved (PCC) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.4   0.0   5.8e-22     1e-17       3     105 ..      10     117 ..       8     119 .. 0.92

  Alignments for each domain:
  == domain 1  score: 64.4 bits;  conditional E-value: 5.8e-22
                                   EEEEE-TTSBHHHHHHHHHHHHT-SSEEEEEEEEEEEEEE.EEECTTT....EE-S-EEEEEEEEEEEETT..EEEEEEEE CS
                        DUF296   3 hvlrlepGediveaieefarkrgiraacvlsaiGavsnvt.rladgee....kllgrfeilslsGtilpdg..lHlhvsla 76 
                                   + +r+++ +d+++ + ++++k ++++++vl aiG++++++ ++++g++    ++ +r+e++sl G+i++++  +H+h++ a
  gi|13541808|ref|NP_111496.1|  10 ITARFDKETDFFTDLVDLCNKYEVKSGTVLWAIGMLKEFQiGYWNGNDyekeTFRERLELVSLHGSIAENDprFHIHAAGA 90 
                                   6789****************************************99999999899**************888999999999 PP

                                   ETTSEEEEEEEEEE.EEEEEEEEEEEEE- CS
                        DUF296  77 gedgqvvgGhlaegplvaattvevvvaef 105
                                   ++++ +vgGhl++  +++   ve+ ++++
  gi|13541808|ref|NP_111496.1|  91 RGNHGIVGGHLFS--AKVDPLVEIQIMKI 117
                                   99999*******4..57789999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       289  (0.0161191); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 980.98
//
Query:       gi|13541809|ref|NP_111497.1|  [L=114]
Description: ferredoxin [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.6e-12   46.0   0.1    4.4e-12   45.8   0.1    1.1  1  Rieske    Rieske [2Fe-2S] domain
  ------ inclusion threshold ------
      0.017   15.0   0.0      0.021   14.8   0.0    1.2  1  Rieske_2  Rieske-like [2Fe-2S] domain
      0.083   13.0   0.1        0.1   12.7   0.1    1.2  1  zf-UDP    Zinc-binding RING-finger


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 !   45.8   0.1   7.4e-16   4.4e-12      12      84 ..      14      84 ..       5     101 .. 0.79

  Alignments for each domain:
  == domain 1  score: 45.8 bits;  conditional E-value: 7.4e-16
                                  -TTCEEEEEETTEEEEEEE-TTS-EEEEESC-TTTT-BCGGSEEETT.EEE-TTT--EEE.TTSBEEE-TTHHH CS
                        Rieske 12 pegdpltvkvggeplvvlrdedgevyAlsdvCtHrgaplsegkidekgvleCpcHgwayd.adGkvikgPaprp 84
                                  ++ +++ + + ++p+++ +  +g+++A++ vC H+g+ +  +k+ e+++ +Cp Hg++yd ++G+ +  P+ +p
  gi|13541809|ref|NP_111497.1| 14 EKTNSVVTWIAHKPVLLTKY-NGDYFAMEAVCGHMGCAI-LNKV-EGKEAVCPAHGARYDvTNGNKVSEPQIKP 84
                                  45556777889999999996.*****************5.4577.45599***************999999887 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 ?   14.8   0.0   3.5e-06     0.021       9      96 ..      11     104 ..       3     112 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.5e-06
                                   CCS-TTB-EEEEETTEEEEEEE-TTS-EEEEESS-TTTSSSTCCCSEEEECTTCEEEE-TTT--EEETTT-BBSS...... CS
                      Rieske_2   9 edlvketgvaalvdgkqvalfrlekeevyAidnldpaseanvlsrGlvgdkkgelvvasPlykqkfdLktGecle...... 83 
                                   + + k ++v+ ++ +k v+l  + +++ +A+++++       +  +++++ +g+ +v +P ++ ++d ++G+ ++      
  gi|13541809|ref|NP_111497.1|  11 KIFEKTNSVVTWIAHKPVLLTKY-NGDYFAMEAVCGH-----MGCAILNKVEGKEAV-CPAHGARYDVTNGNKVSepqikp 84 
                                   44566777999*******99988.99********999.....899999999888877.9************9988566666 PP

                                   .......-TTSB-BEE-EEE CS
                      Rieske_2  84 .......deevslkvypvrv 96 
                                              +lk+++v  
  gi|13541809|ref|NP_111497.1|  85 eapceydSIGEPLKTFKVLE 104
                                   55555543345555555555 PP

>> zf-UDP  Zinc-binding RING-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   1.7e-05       0.1      20      65 ..      31      74 ..      11      83 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.7e-05
                        zf-UDP 20 ltedgelFvacnecafpvcrpcyeyerkdgnqsCPqCktrykrlkg 65
                                  ++ +g+ F++  +c+   c    + e+k++  +CP   +ry  ++g
  gi|13541809|ref|NP_111497.1| 31 TKYNGDYFAMEAVCGHMGCAILNKVEGKEA--VCPAHGARYDVTNG 74
                                  3469*************************9..****9999987766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       292  (0.0162865); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 868.20
//
Query:       gi|13541810|ref|NP_111498.1|  [L=289]
Description: ribokinase sugar kinase [Thermoplasma volcanium GSS1]
Scores for complete 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   96.6   0.0    5.2e-26   91.7   0.0    2.0  1  PfkB      pfkB family carbohydrate kinase


Domain annotation for each model (and alignments):
>> PfkB  pfkB family carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.7   0.0   2.9e-30   5.2e-26       1     291 [.       1     258 [.       1     269 [. 0.88

  Alignments for each domain:
  == domain 1  score: 91.7 bits;  conditional E-value: 2.9e-30
                                   EEEEEEEEEEEEEEEEECSSHTTSEE.EESEEEEEEESHHHHHHHHHHHTT-EEEEEEEEESSHHHHHHHHHHHHTTEEET CS
                          PfkB   1 mtkvvviGealidliavseklegelv.evktveksaGGagaNvAvalarlgadvafigavGdDnfGeflleelkkegvdtd 80 
                                   m+ ++ +G+++id+   +e+l++e + ++k+ve ++GG + N A + ++lg d +  +avG  +  + +l+ lk++g+ +d
  gi|13541810|ref|NP_111498.1|   1 MAFLAYFGHLNIDVRILVENLPKEGSvNAKNVEEKYGGTAGNFAIVSKKLGLDFDIYSAVGSKT-HSGYLSFLKDSGIGID 80 
                                   577899***************655555*************************************.9*************** PP

                                   TEEEESSSEEEEEEEEETTTSEEEEEEEEGGGGGHHHHHHHHHHHHHGCTSEEEEESEECTTSHHHHHHHHHHHHHHTTEE CS
                          PfkB  81 yvkidedtrtglalivvdedgertivfnrgaaadltkeeleededlleeadllyisgllsselpeavleelaeaaknggtf 161
                                   ++k++++    +++i  d + ++  ++++g++ +++++       l ++ +++++s+          ++ l+e ++++  f
  gi|13541810|ref|NP_111498.1|  81 HIKVTDE-YGPICYIASDTK-KQVAYMYQGPMLNWSPR-------LESHYEYIHLST-------GPKYTGLIENKESKLVF 145
                                   ***6666.778888888865.8***************6.......56899******9.......78899999999999977 PP

                                   EEEECESSSHHHHHHHHHHHCTESEEEEEHHHHHHHHTSCTHSHHHHHHHHHHHHHTTSSEEEEEEGGGEEEEEETTEEEE CS
                          PfkB 162 dpnlldplgaqfkeallellaladllkpneeElealtgekledieealaalhklkakgaktvvvtlGkeGalvvekdgelk 242
                                   dp +   + +   e+l+++ + + + + n +E + + +++       l+       ++ + v+ t G +G+++++ +++  
  gi|13541810|ref|NP_111498.1| 146 DPSQEIWKFS--GEELKRFYEASYISFFNGNEMKVFREAT------GLK-------SFDRIVIETVGPRGSILYKDSTKKV 211
                                   7766555554..699*******************888888......333.......46789*************9888888 PP

                                   EEE.SSSS-SBGTTHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHT CS
                          PfkB 243 vpavpkvkvvDttGAGDsfvggflaallegksleealrfanavAalvvq 291
                                   +pa+p     Dt+GAGD+f +gf +al + ks+e+a  +++ +A  +++
  gi|13541810|ref|NP_111498.1| 212 FPALP--SSGDTIGAGDAFRAGFYYALFRKKSIETAMVYGTIAAHHMIE 258
                                   89999..78*******************************999877776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       306  (0.0170673); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 2081.73
//
Query:       gi|13541811|ref|NP_111499.1|  [L=173]
Description: acetyltransferase [Thermoplasma volcanium GSS1]
Scores for complete 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-10   38.8  12.3     0.0093   15.7   0.1    4.4  3  Hexapep    Bacterial transferase hexapeptide (six repeats)
    9.1e-08   31.7   4.8      0.021   14.5   0.9    4.3  3  Hexapep_2  Hexapeptide repeat of succinyl-transferase


Domain annotation for each model (and alignments):
>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1     1e-06    0.0093      15      36 .]      23      44 ..      12      45 .. 0.63
   2 !    8.1   0.1   0.00025       2.3      19      35 ..      48      64 ..      46      65 .. 0.84
   3 !   12.1   5.0   1.4e-05      0.12       2      35 ..      71     103 ..      70     122 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1e-06
                                  EEETTEEE-TTEEEETTEEEES CS
                       Hexapep 15 viggnVkIGdnvkIgagvvigg 36
                                  ++ g VkIG+ v Ig+g+v++g
  gi|13541811|ref|NP_111499.1| 23 TVIGKVKIGKEVWIGPGAVLRG 44
                                  5556666666666666666554 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00025
                                  TEEE-TTEEEETTEEEE CS
                       Hexapep 19 nVkIGdnvkIgagvvig 35
                                   +++Gd++ I+ ++vi+
  gi|13541811|ref|NP_111499.1| 48 EIEVGDYSAIEDNCVIH 64
                                  67899999999999997 PP

  == domain 3  score: 12.1 bits;  conditional E-value: 1.4e-05
                                   EEEETTEEE-TTEEEETTEEE-TTEEEETTEEEE CS
                       Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIgagvvig 35 
                                   t+IG++v+Ig+ +vi+ +  I d ++Ig g+++ 
  gi|13541811|ref|NP_111499.1|  71 TFIGQHVTIGHLSVIHTGR-IRDWAVIGMGSTVS 103
                                   89*********99998888.99999999999985 PP

>> Hexapep_2  Hexapeptide repeat of succinyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.9   2.4e-06     0.021       2      32 ..      28      63 ..      27      63 .. 0.88
   2 !   13.6   0.2   4.8e-06     0.043       4      26 ..      57      85 ..      55     104 .. 0.82
   3 ?    1.4   0.1     0.032   2.8e+02      14      28 ..     106     122 ..     105     122 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.4e-06
                                  EEE-TT-EE-TT-EE....S.EEE-TT-EE-TT-EE CS
                     Hexapep_2  2 viIGdnCliGanagi....G.vslGdncvvgaGvvi 32
                                  v+IG+ + iG+ a+     G +++Gd + ++ ++vi
  gi|13541811|ref|NP_111499.1| 28 VKIGKEVWIGPGAVLrgdyGeIEVGDYSAIEDNCVI 63
                                  9*************8855559*****9999999997 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 4.8e-06
                                  E-TT-EE-TT-E....ES..EEE-TT-EE CS
                     Hexapep_2  4 IGdnCliGanag....iG..vslGdncvv 26
                                  I+dnC+i+a+ g    iG  v++G  +v+
  gi|13541811|ref|NP_111499.1| 57 IEDNCVIHARPGektfIGqhVTIGHLSVI 85
                                  9*********8856555777887766665 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.032
                                   -EES..EEE-TT-EE-T CS
                     Hexapep_2  14 agiG..vslGdncvvga 28 
                                   a++G    +G+++vv +
  gi|13541811|ref|NP_111499.1| 106 AVVGvwAAIGEGAVVKN 122
                                   566644579*****975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 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:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1293.35
//
Query:       gi|13541812|ref|NP_111500.1|  [L=401]
Description: phosphopyruvate hydratase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    8.8e-66  222.1   1.6    1.1e-65  221.8   1.6    1.1  1  Enolase_C  Enolase, C-terminal TIM barrel domain
    2.5e-32  111.8   0.0    5.3e-32  110.7   0.0    1.6  1  Enolase_N  Enolase, N-terminal domain
    6.1e-09   35.8   0.0      1e-08   35.1   0.0    1.3  1  MR_MLE_C   Enolase C-terminal domain-like
  ------ inclusion threshold ------
      0.067   12.3   0.0       0.12   11.5   0.0    1.4  1  MAAL_C     Methylaspartate ammonia-lyase C-terminus


Domain annotation for each model (and alignments):
>> Enolase_C  Enolase, C-terminal TIM barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  221.8   1.6   2.5e-69   1.1e-65       2     282 ..     131     400 ..     130     401 .] 0.94

  Alignments for each domain:
  == domain 1  score: 221.8 bits;  conditional E-value: 2.5e-69
                                   -EE-EE-EEEEE-GGGSSSS--SSEEEEE-TT-SSHHHHHHHHHHHHHHHHHHHHHCC.GGGG-B-TTS-B----SSHHHH CS
                     Enolase_C   2 lvlPvPalnvinGGshagnklalqefmilPvgassfkealrlGaevyhklksvlkkkygksatnvGdeGGfaPnlqsnkea 82 
                                   +++P P+ nvi GG+ha n  ++qef++   g ++f e+  + + v++k+ ++l++k+   +  vGde  ++ n++ ++ea
  gi|13541812|ref|NP_111500.1| 131 HSMPRPIGNVIGGGKHARNGTSIQEFLVSAQG-KTFMESAYVNVLVHRKIGDILSEKMKDISIGVGDERAWSVNIS-DEEA 209
                                   679************************98766.7899999**********************************95.689* PP

                                   HHHHHHHHHHCT-TCTBEE..EEE--GGGCEETCTTEEECTTTTTT..GGCEEEHHHHHHHHHHHHHHS-EEEEES-S-TT CS
                     Enolase_C  83 ldliveaiekaGykgkvki..aldvassefykekdkkydldfkeeesdkskkltseqladlykelvkkyPivsiedplded 161
                                   ++++ +a+++   ++kvki  +ld a+  +y  +++ky  +            + ++  d+  ++ k++ ++ iedp+ + 
  gi|13541812|ref|NP_111500.1| 210 FEVLNQAVNEVSSETKVKIytGLDFAADSLY--ENGKYVYKHTV--------RSRDEQIDYAISINKDFGVYYIEDPMFDT 280
                                   ***********99997666559*********..66788866544........6778889********************** PP

                                   -HHHHHHHHHHHTTTSEEEESTTTTT-HHHHHHHHHCT--SEEEE-HHHH-SHHHHHHHHHHHHHTT-EEEEE--SC--S- CS
                     Enolase_C 162 dweawkklteelgdkvqivGddltvtnpkrlkeaiekkaanalllkvnqiGsltesleavklakeagygvvvshrsGeted 242
                                   d+e+++++t+++gdk  ivGddl+ tnp+r++++ie +++na+l+kvnqiG+lt + ea+ la++ag   vvshrsGet d
  gi|13541812|ref|NP_111500.1| 281 DFEGFAEITKKIGDKAMIVGDDLYTTNPDRIRKGIELGSTNAVLIKVNQIGTLTKAQEAASLASSAGLKNVVSHRSGETTD 361
                                   ********************************************************************************* PP

                                   -HHHHHHHHCT-SEEE---S-SHHHHHHHHHHHHHHHHHG CS
                     Enolase_C 243 ttiadlavglsaGqiktGaparserlakynqllrieeelg 282
                                    ++a+l+v+ s+  +ktG++   er+ak+n+l+riee l+
  gi|13541812|ref|NP_111500.1| 362 DFLAHLSVAFSSTFVKTGTIG-GERIAKLNELMRIEECLT 400
                                   ******************986.8**************886 PP

>> Enolase_N  Enolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.7   0.0   1.2e-35   5.3e-32       1     131 []       5     126 ..       5     126 .. 0.98

  Alignments for each domain:
  == domain 1  score: 110.7 bits;  conditional E-value: 1.2e-35
                                   EEEEEEEEEE-TTS-EEEEEEEEETTC-EEEEE--B-BSSSSSS-B----SSTTSGGGT--HHHHHHHHHTHHHHHTTSBT CS
                     Enolase_N   1 IkkvkareildSrGnpTvevevttedgalgraavpsGaStgekealelrDgdkkrylgkgvekavenvnekiapaligldv 81 
                                   I++v++r++ldSrGn Tve++v++  g +gr ++p+GaStge+e++         +  kg++++++ +++++++++ig+++
  gi|13541812|ref|NP_111500.1|   5 IEDVRVRKVLDSRGNFTVEADVYIP-GGFGRTSAPAGASTGETEVI--------AFSKKGIDESIKFFETNVRRSIIGFNA 76 
                                   899*********************7.669*****************........58999********************** PP

                                   T-HHHHHHHHHHHH-STT-TTT-HHHHHHHHHHHHHHHHHHHTS-HHHHH CS
                     Enolase_N  82 tdqeeiDkllielDgtenksklGaNailavSlAvakaaAkakelplyryl 131
                                   +dq+ +D+l+++lDg+ n s+lG+N  +a+S++vaka ++++++plyry+
  gi|13541812|ref|NP_111500.1|  77 LDQKGFDALITDLDGSGNFSNLGGNLSTALSMSVAKAVSAHLGIPLYRYV 126
                                   *************************************************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 !   35.1   0.0   2.2e-12     1e-08      58     173 ..     253     373 ..     210     385 .. 0.83

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 2.2e-12
                                   BHHHHHHHHHHHGG.GTESEEESSSSTTTHHHHHHHHHH.HHSSEEEESTTSSS..HHHHHHHHHHTSESEEEEBHHHHTS CS
                      MR_MLE_C  58 dlatAirvarelee.ldllwlEEPvppeddleglaelra.rasipiaagEslys..radfrelleagavdivqpdvsrvgG 134
                                   ++++ i +a  +++ ++++++E+P+    d eg ae+++ + +   ++g +ly+  + ++r+ +e g   +v ++v+++g 
  gi|13541812|ref|NP_111500.1| 253 SRDEQIDYAISINKdFGVYYIEDPMFD-TDFEGFAEITKkIGDKAMIVGDDLYTtnPDRIRKGIELGSTNAVLIKVNQIGT 332
                                   677888888888666**********87.78********7633555666666655579************************ PP

                                   HHHHHHHHHHHHHTT-E.EEEBSCS.SHHHHHHHHHHHHTT CS
                      MR_MLE_C 135 itearkvaalaeafgvp.vapHsgs.gglglaaslhlaaai 173
                                   +t+a++ a la+ +g++ v+ H  + +   ++a+l++a + 
  gi|13541812|ref|NP_111500.1| 333 LTKAQEAASLASSAGLKnVVSHRSGeTTDDFLAHLSVAFSS 373
                                   ****************9655555433677888888887665 PP

>> MAAL_C  Methylaspartate ammonia-lyase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   2.8e-05      0.12     126     217 ..     285     372 ..     248     397 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.8e-05
                        MAAL_C 126 laelreklkekgikvelvaDeWcntled.irefvdaeaadlvqiktPDlGginntieavlyckekgvgaylGGscnetdvs 205
                                   +ae++   k+ g k+ +v D+   t  d ir+ ++ +++++v ik+  +G+++++ ea   + + g++  +   + et   
  gi|13541812|ref|NP_111500.1| 285 FAEIT---KKIGDKAMIVGDDLYTTNPDrIRKGIELGSTNAVLIKVNQIGTLTKAQEAASLASSAGLKNVVSHRSGETTD- 361
                                   44444...445667789999876665544***************************************999988888864. PP

                        MAAL_C 206 arvsvhvalatr 217
                                       +h+++a+ 
  gi|13541812|ref|NP_111500.1| 362 -DFLAHLSVAFS 372
                                   .45556666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (401 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       561  (0.0312901); 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: 0.66u 0.36s 00:00:01.02 Elapsed: 00:00:00.56
# Mc/sec: 2169.45
//
Query:       gi|13541813|ref|NP_111501.1|  [L=206]
Description: diphthine synthase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.6e-10   41.3   0.0    1.9e-10   41.1   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 !   41.1   0.0     1e-14   1.9e-10       1     142 [.       1     134 [.       1     189 [. 0.78

  Alignments for each domain:
  == domain 1  score: 41.1 bits;  conditional E-value: 1e-14
                  TP_methylase   1 klylVGvGpGdpellTvrAlralktadvvlgddsr...aleilldllaeeleleapmgkekepleeayeeiaealaealra 78 
                                   +l ++G+G+ ++  lT+   +al+t+d+v+ d  +    ++ +l++l+          +++e   ++ + i++  + + ++
  gi|13541813|ref|NP_111501.1|   1 MLNIIGIGLRGTGSLTLDEFDALRTSDIVYLDI-YtsiGPKDILEKLRN--------IADREIIPADRNMIESESILKDAE 72 
                                   5789*************************7655.334555555555543........567777777778777777777778 PP

                  TP_methylase  79 gkdVvllvsGDPlvygtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvl 142
                                   + +V llv+GD l ++t+  l   +++  +gi+v++    s++++aa ++g+  ++ g ++s+ 
  gi|13541813|ref|NP_111501.1|  73 KLNVSLLVIGDGLTATTHNQLRYSAME--KGIKVKIFENASAVNTAAGKIGLLHYKVGPPVSLP 134
                                   889******************988888..9*********************9988888887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       627  (0.0349713); expected 358.6 (0.02)
Passed bias filter:                      547  (0.0305092); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 1256.26
//
Query:       gi|13541814|ref|NP_111502.1|  [L=201]
Description: transcription regulator [Thermoplasma volcanium GSS1]
Scores for complete sequence (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   31.5   0.3    3.4e-07   30.2   0.0    1.8  2  HTH_20         Helix-turn-helix domain
    4.3e-06   26.5   2.2    6.3e-06   26.0   0.4    2.1  2  HTH_5          Bacterial regulatory protein, arsR family
    0.00013   21.5   0.7    0.00013   21.5   0.7    2.1  3  HTH_24         Winged helix-turn-helix DNA-binding
     0.0021   18.3   0.1     0.0045   17.2   0.1    1.5  1  DUF948         Bacterial protein of unknown function (DUF948)
     0.0038   17.3   0.7       0.16   12.1   0.0    3.1  3  DUF2250        Uncharacterized protein conserved in archaea (
     0.0059   16.8   4.1       0.13   12.5   0.5    2.5  2  Osmo_CC        Osmosensory transporter coiled coil
     0.0069   16.2   0.5      0.017   14.9   0.5    1.6  1  SKA2           Spindle and kinetochore-associated protein 2
  ------ inclusion threshold ------
      0.019   14.6   1.0      0.033   13.8   1.0    1.4  1  PI3K_P85_iSH2  Phosphatidylinositol 3-kinase regulatory subun
       0.04   14.3   0.4       0.66   10.4   0.1    2.4  2  Rrf2           Transcriptional regulator
      0.056   13.3   0.1       0.72    9.8   0.0    2.3  2  TrmB           Sugar-specific transcriptional regulator TrmB
        0.1   12.7   1.7        1.2    9.3   0.0    2.4  2  KIP1           KIP1-like protein
       0.14   12.1   2.5        4.8    7.2   2.2    2.6  2  HTH_Crp_2      Crp-like helix-turn-helix domain
       0.19   12.0   4.6      0.053   13.7   1.0    1.9  2  Cortex-I_coil  Cortexillin I, coiled coil
       0.34   11.0   4.6      0.094   12.8   1.1    1.8  2  NYD-SP28       Sperm tail


Domain annotation for each model (and alignments):
>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   0.0   2.7e-10   3.4e-07       3      57 ..       8      62 ..       6      64 .. 0.94
   2 ?   -3.1   0.1       6.7   8.5e+03      41      49 ..     121     129 ..     116     131 .. 0.78

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 2.7e-10
                                  HHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEE CS
                        HTH_20  3 iaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevv 57
                                   + A+ + +Rr+i r+L++ e   a el + ++ls++ + ++L+ Le+a Lv++ 
  gi|13541814|ref|NP_111502.1|  8 FIAAIENSTRREIIRMLTQFERSYALELSRSIGLSQQAILKQLEMLERANLVTSI 62
                                  67899***********************************************975 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 6.7
                                   HHHHHHHHH CS
                        HTH_20  41 lsyHLrvLe 49 
                                   + +H+++L 
  gi|13541814|ref|NP_111502.1| 121 IQHHIEELT 129
                                   679999996 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.4   4.9e-09   6.3e-06       1      47 []      14      61 ..      14      61 .. 0.95
   2 ?   -1.2   0.1       1.5   1.9e+03      36      45 ..     185     194 ..     185     194 .. 0.89

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 4.9e-09
                                  SHHHHHHHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                         HTH_5  1 dptRlkILklLae.gelcvcelaeelglsqstvShHLkkLreaGLVek 47
                                  ++tR++I+++L + +  ++ el++ +glsq ++  +L +L+ a+LV++
  gi|13541814|ref|NP_111502.1| 14 NSTRREIIRMLTQfERSYALELSRSIGLSQQAILKQLEMLERANLVTS 61
                                  58***********77799****************************86 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.5
                                   HHHHHHTTSE CS
                         HTH_5  36 LkkLreaGLV 45 
                                   Lk+L+  G+V
  gi|13541814|ref|NP_111502.1| 185 LKILKSKGIV 194
                                   8999999998 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.7     1e-07   0.00013       2      48 .]      14      60 ..      13      60 .. 0.96
   2 ?   -3.0   0.0       4.5   5.7e+03      35      44 ..     122     131 ..     120     131 .. 0.79
   3 ?   -3.2   0.1       4.9   6.3e+03      38      46 ..     185     193 ..     183     194 .. 0.59

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 1e-07
                        HTH_24  2 detdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                  + t+r+I++ L +  r    eL++ +glS+++++++l+ Le++ l++
  gi|13541814|ref|NP_111502.1| 14 NSTRREIIRMLTQFERSYALELSRSIGLSQQAILKQLEMLERANLVT 60
                                  6799***************************************9986 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 4.5
                        HTH_24  35 nrrlkrLeee 44 
                                     ++++L+++
  gi|13541814|ref|NP_111502.1| 122 QHHIEELTKK 131
                                   6799999986 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 4.9
                        HTH_24  38 lkrLeeeGl 46 
                                   lk L+++G+
  gi|13541814|ref|NP_111502.1| 185 LKILKSKGI 193
                                   455666666 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 !   17.2   0.1   3.5e-06    0.0045      26      76 ..     109     159 ..      98     161 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 3.5e-06
                        DUF948  26 ktldeaaatieelekqvdpilkevedllakvnelledvneklekvdpltea 76 
                                     +dea + +e++++++++++k+ ++l++k  el++ ++ +le+ dp+t +
  gi|13541814|ref|NP_111502.1| 109 VSFDEAISKLESIQHHIEELTKKRTELVKKKDELMAAIKYQLEDEDPITRE 159
                                   57999*******************************************986 PP

>> DUF2250  Uncharacterized protein conserved in archaea (DUF2250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.0   0.00013      0.16       7      53 ..      14      60 ..      10      64 .. 0.91
   2 ?    1.7   0.1      0.22   2.8e+02      20      41 ..      84     105 ..      79     153 .. 0.71
   3 ?   -0.8   0.0       1.3   1.7e+03      13      44 ..     161     189 ..     148     192 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00013
                       DUF2250  7 delalkvlkhlkkanvdYaksiakeleipleevrellkkLeelGLle 53
                                  ++   +++++l++ +  Ya+ +++ + ++++ + + l+ Le++ L++
  gi|13541814|ref|NP_111502.1| 14 NSTRREIIRMLTQFERSYALELSRSIGLSQQAILKQLEMLERANLVT 60
                                  556779************************************99987 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.22
                       DUF2250  20 anvdYaksiakeleipleevre 41 
                                   + vdY+++     +iple+ +e
  gi|13541814|ref|NP_111502.1|  84 LIVDYGRNFLMIQRIPLENDSE 105
                                   5678888888877777775443 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 1.3
                       DUF2250  13 vlkhlkkanvdYaksiakeleipleevrellk 44 
                                   vl++l++ +v+    +++++ +ple v ++lk
  gi|13541814|ref|NP_111502.1| 161 VLEYLNTFDVE---EVSRRTALPLEIVLKILK 189
                                   56666666664...577888888888888776 PP

>> Osmo_CC  Osmosensory transporter coiled coil
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.2      0.02        25      21      36 ..       2      19 ..       1      23 [. 0.84
   2 !   12.5   0.5    0.0001      0.13      19      41 ..     116     138 ..     109     142 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.02
                                  HHHHHHHHHHHHH..HHH CS
                       Osmo_CC 21 vedideeIaaLee..kRq 36
                                  ++did+ Iaa+e+  +R+
  gi|13541814|ref|NP_111502.1|  2 IDDIDNFIAAIENstRRE 19
                                  9**********9976654 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.0001
                                   HHHHHHHHHHHHHHHHHHHHHHH CS
                       Osmo_CC  19 qkvedideeIaaLeekRqrLvdq 41 
                                    k+e i + I++L +kR++Lv++
  gi|13541814|ref|NP_111502.1| 116 SKLESIQHHIEELTKKRTELVKK 138
                                   699******************86 PP

>> SKA2  Spindle and kinetochore-associated protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.5   1.3e-05     0.017      44      82 ..     115     153 ..     111     163 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.3e-05
                          SKA2  44 lerlkkvkeelqaLkeqceellaekkelidkirttlvan 82 
                                   +++l+ +++ +++L ++ +el ++k el+ +i+++l + 
  gi|13541814|ref|NP_111502.1| 115 ISKLESIQHHIEELTKKRTELVKKKDELMAAIKYQLEDE 153
                                   5789********************************875 PP

>> PI3K_P85_iSH2  Phosphatidylinositol 3-kinase regulatory subunit P85 inter-SH2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   1.0   2.6e-05     0.033      83     125 ..     118     160 ..      96     164 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.6e-05
                 PI3K_P85_iSH2  83 ieklqenleqlksrlkelhsskekLeedlkqqkeeereleRei 125
                                    e++q+++e+l+++  el ++k++L  ++k q e+e  + Rei
  gi|13541814|ref|NP_111502.1| 118 LESIQHHIEELTKKRTELVKKKDELMAAIKYQLEDEDPITREI 160
                                   589*********************************9999998 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   0.00051      0.66      28      58 ..      32      62 ..      18      63 .. 0.87
   2 ?    1.5   0.0       0.3   3.9e+02      26      47 ..     168     189 ..     159     194 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00051
                                  HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                          Rrf2 28 seeiaerqnispsylekilakLrkaglvksv 58
                                  + e++++ ++s++ + k l++L++a+lv+s+
  gi|13541814|ref|NP_111502.1| 32 ALELSRSIGLSQQAILKQLEMLERANLVTSI 62
                                  55899***********************995 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.3
                                   B-HHHHHHHHTS-HHHHHHHHH CS
                          Rrf2  26 vsseeiaerqnispsylekila 47 
                                   + +ee+++r+ ++ +++ kil+
  gi|13541814|ref|NP_111502.1| 168 FDVEEVSRRTALPLEIVLKILK 189
                                   7899999999999999999986 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00056      0.72      20      55 ..      27      62 ..      21      81 .. 0.80
   2 ?    0.8   0.0      0.35   4.5e+02      23      52 ..     168     194 ..     160     199 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00056
                                  HCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEE CS
                          TrmB 20 lgpatadeiaeelgvprskvYevLrsLedkGlVere 55
                                   +++ a e+++ +g++++ + + L+ Le++ lV+ +
  gi|13541814|ref|NP_111502.1| 27 FERSYALELSRSIGLSQQAILKQLEMLERANLVTSI 62
                                  5778899**************************976 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.35
                                   CHHCHHCCCTTSSCHCHHHHHHHHHHCTSE CS
                          TrmB  23 atadeiaeelgvprskvYevLrsLedkGlV 52 
                                    +++e+++++ +p   v   L+ L++kG+V
  gi|13541814|ref|NP_111502.1| 168 FDVEEVSRRTALPLEIV---LKILKSKGIV 194
                                   56667777776666555...5555556655 PP

>> KIP1  KIP1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0   0.00095       1.2      39      67 ..       6      32 ..       1      37 [. 0.83
   2 ?    2.4   0.3      0.13   1.7e+02      34      58 ..     121     145 ..     102     154 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00095
                          KIP1 39 dsfakraemyykkrpeLielveefyrsyr 67
                                  d+f   a ++++ r e+i+++ +f rsy 
  gi|13541814|ref|NP_111502.1|  6 DNFI--AAIENSTRREIIRMLTQFERSYA 32
                                  5554..78899*****************6 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.13
                          KIP1  34 ieedadsfakraemyykkrpeLiel 58 
                                   i+   ++++k+     kk++eL+  
  gi|13541814|ref|NP_111502.1| 121 IQHHIEELTKKRTELVKKKDELMAA 145
                                   3333344444555555555555554 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   2.2    0.0037       4.8      27      65 ..       9      53 ..       7      56 .. 0.71
   2 ?    5.8   0.2     0.011        14      26      52 ..      34      60 ..      31      65 .. 0.91

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0037
                                  HHHHTTSSHHHHHHHHHHHHHTTSEE..E..T.EE.EEES-HHHH CS
                     HTH_Crp_2 27 lAsmlGltretvsrilseLkreglis..r..g.rr.irildleaL 65
                                  +A++ ++tr  + r+l++++r   ++  r  g  +  ++++le+L
  gi|13541814|ref|NP_111502.1|  9 IAAIENSTRREIIRMLTQFERSYALElsRsiGlSQqAILKQLEML 53
                                  788899****************99995322223223555555555 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.011
                                  HHHHHTTSSHHHHHHHHHHHHHTTSEE CS
                     HTH_Crp_2 26 elAsmlGltretvsrilseLkreglis 52
                                  el++ +Gl+++ + + l  L+r++l++
  gi|13541814|ref|NP_111502.1| 34 ELSRSIGLSQQAILKQLEMLERANLVT 60
                                  8999*********************97 PP

>> Cortex-I_coil  Cortexillin I, coiled coil
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.1       1.7   2.1e+03      29      38 ..      40      49 ..       4      60 .. 0.48
   2 ?   13.7   1.0   4.1e-05     0.053       3      61 ..     103     158 ..     101     194 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.7
                                  HHHHHHHHHH CS
                 Cortex-I_coil 29 kvsreelikq 38
                                   +s++ ++kq
  gi|13541814|ref|NP_111502.1| 40 GLSQQAILKQ 49
                                  2344444444 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 4.1e-05
                                   XXXXXXXXXXXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                 Cortex-I_coil   3 ekerleasknelanklaglenslesekvsreelikqkdelesllasleseaaerekrlr 61 
                                   + er+  s +e  +kl ++++ +e     r el+k+kdel   ++    + ++ +   r
  gi|13541814|ref|NP_111502.1| 103 DSERVSVSFDEAISKLESIQHHIEELTKKRTELVKKKDELMAAIK---YQLEDEDPITR 158
                                   56889999999***************************9976654...33333333333 PP

>> NYD-SP28  Sperm tail
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1       2.7   3.5e+03      24      25 ..      32      33 ..       9      57 .. 0.47
   2 ?   12.8   1.1   7.3e-05     0.094      48      87 ..     115     154 ..     106     159 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 2.7
                      NYD-SP28 24 le 25
                                    
  gi|13541814|ref|NP_111502.1| 32 AL 33
                                  22 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 7.3e-05
                      NYD-SP28  48 knkpqeLrkeleeqkqaceelideKdklikelqeeLkekd 87 
                                   ++k + ++ ++ee+ ++  el+++Kd+l+++++ +L++ d
  gi|13541814|ref|NP_111502.1| 115 ISKLESIQHHIEELTKKRTELVKKKDELMAAIKYQLEDED 154
                                   5688999*****************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1616  (0.0901333); expected 358.6 (0.02)
Passed bias filter:                      977  (0.0544927); expected 358.6 (0.02)
Passed Vit filter:                       122  (0.00680462); 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 0.28s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 1308.90
//
Query:       gi|13541815|ref|NP_111503.1|  [L=182]
Description: molecular chaperone (small heat shock protein, hsp20-related) [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    5.5e-07   29.7   0.3      7e-06   26.1   0.3    2.1  1  HSP20       Hsp20/alpha crystallin family
    3.9e-06   26.3   0.0      8e-06   25.3   0.0    1.5  1  ArsA_HSP20  HSP20-like domain found in ArsA
    6.6e-05   23.3   0.1    9.9e-05   22.7   0.1    1.2  1  PIH1_CS     PIH1 CS-like domain
     0.0069   17.4   0.6       0.01   16.8   0.6    1.2  1  CS          CS domain


Domain annotation for each model (and alignments):
>> HSP20  Hsp20/alpha crystallin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.3   1.6e-09     7e-06       1     102 []      96     182 .]      96     182 .] 0.85

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 1.6e-09
                                   E--SSEEEEEEEEE-TT--CCCEEEEEETTEEEEEEE--..---TT----SS---EEEEEE--STTB-TTT-EEEEETTEE CS
                         HSP20   1 dikeeeeefevkldvpglkkeelkvkvednrvlvkgeheeeeedekglikerssrkFsrkftLPenvdadkvkaslkdGvL 81 
                                   di +++++  +++++pg++ke +++k+ + +++ +  ++    ++k++ +       +  ++L    ++++  a++++G+L
  gi|13541815|ref|NP_111503.1|  96 DINDDDKKVYLTFELPGVSKESIDLKISEYNITLNVDED----QRKYYKS------IDFDYKL----KPETAVAKFNNGLL 162
                                   68899*****************************99888....3333333......3334556....9999********** PP

                                   EEEEEBSS--..--------- CS
                         HSP20  82 tvtvpkkepekkkkerkiqiq 102
                                    vtv+k +++++   rk++iq
  gi|13541815|ref|NP_111503.1| 163 DVTVEKATSKES-GGRKVSIQ 182
                                   ********9976.99999997 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 !   25.3   0.0   1.8e-09     8e-06       2      62 ..     102     165 ..     101     166 .. 0.90

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 1.8e-09
                    ArsA_HSP20   2 deyvlkldLPfvdkeeidlsrsgdeLtIkignfrRq....itLPsvlarkevtsAkfedgvLeIr 62 
                                   +++ l+ +LP+v+ke+idl +s+  +t++++ ++R+    i    +l+ +++  Akf++g L ++
  gi|13541815|ref|NP_111503.1| 102 KKVYLTFELPGVSKESIDLKISEYNITLNVDEDQRKyyksIDFDYKLKPETA-VAKFNNGLLDVT 165
                                   6778999************************888877777**********66.9********996 PP

>> PIH1_CS  PIH1 CS-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.1   2.2e-08   9.9e-05      32      87 ..     103     159 ..      98     167 .. 0.88

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 2.2e-08
                       PIH1_CS  32 elaieielPllksikevklrvgerrleleskk..akyfLslkLpYpvdedkveAkFvk 87 
                                   +  +++elP++ s + ++l+++e ++ l+ ++   ky  s++++Y+++ + + AkF++
  gi|13541815|ref|NP_111503.1| 103 KVYLTFELPGV-SKESIDLKISEYNITLNVDEdqRKYYKSIDFDYKLKPETAVAKFNN 159
                                   567899*****.99*************977666699********************96 PP

>> CS  CS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.6   2.3e-06      0.01       8      76 .]     100     168 ..      95     168 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2.3e-06
                                   ETTEEEEEEE-TTCTTTTTCEEEEEETTEEEEEE.TS.CEEEEECEBSS-BETTTEEEEEETTEEEEEEEB CS
                            CS   8 tldeVvvtiyvkkvnikkkdvkvefkerslkvki.gk.eklliegeLfgpIdpeesswtieskkveitLkK 76 
                                   ++++V++t+++++v  +k++++++++e  +++++ ++ +k +++ ++  + +pe +  ++ +  +++t++K
  gi|13541815|ref|NP_111503.1| 100 DDKKVYLTFELPGV--SKESIDLKISEYNITLNVdEDqRKYYKSIDFDYKLKPETAVAKFNNGLLDVTVEK 168
                                   689**********9..******************966688888999*********************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       584  (0.0325729); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.47
# Mc/sec: 1160.68
//
Query:       gi|13541816|ref|NP_111504.1|  [L=1015]
Description: transporter [Thermoplasma volcanium GSS1]
Scores for complete 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-59  199.6  18.0    9.3e-31  107.0   4.6    2.6  2  MMPL      MMPL family


Domain annotation for each model (and alignments):
>> MMPL  MMPL family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.5   5.5   3.9e-32   6.9e-28     107     312 ..     427     635 ..     417     650 .. 0.88
   2 !  107.0   4.6   5.2e-35   9.3e-31     107     321 ..     806    1010 ..     782    1014 .. 0.88

  Alignments for each domain:
  == domain 1  score: 97.5 bits;  conditional E-value: 3.9e-32
                          MMPL 107 vaairaaveear..pleglkvevtGpaatladlrdasdrdlklievvtlvvilviLlivyrSlvaallplltvvvsllaal 185
                                   ++++ +++++ +   + +   + +G++++ + +++ ++  l  + ++++v+ +vi  + +rS+vaa++p    ++s ++++
  gi|13541816|ref|NP_111504.1| 427 LNHVNKIASSYVsvDPINGSYYTAGTTVLDQQIEQEVMDGLIRALIIGIVLSIVIVGLFFRSPVAAFIPFSLFLMSSIISF 507
                                   455555555555443444567899********************************************************* PP

                          MMPL 186 gl.vlilalllglelstfvlgllvvlliavGtDYallLvsRyreelaagedreeaviravastgkvvtaaGltvaiamlgL 265
                                   g+  l+ +++l+  +s ++++ll +ll++  +DY + ++sR+r el ++     a+++  + +g++v+ +G+tva++ + L
  gi|13541816|ref|NP_111504.1| 508 GInSLLYEHILHSSVSFVTPTLLLILLLGLTSDYVVYIMSRFRRELIRNNLD--AIAESSMWAGHAVFTSGITVALSYIVL 586
                                   **********************************************999999..9************************** PP

                          MMPL 266 vvarlpvlaqvGvaialGvlvdvlivlTll.PAllvllGraa.lakprr 312
                                    + ++p+++  G++ a+Gv+v+v++  T+l   l  + G+   ++++++
  gi|13541816|ref|NP_111504.1| 587 YLFNVPIFSDAGITNAVGVIVSVMLGNTFLiALLSKMKGKIFwPFRSKK 635
                                   ******************************5555567888874445555 PP

  == domain 2  score: 107.0 bits;  conditional E-value: 5.2e-35
                          MMPL  107 vaairaaveearpleglkvevtGpaatladlrdasdrdlklievvtlvvilviLlivyrSlvaallplltvvvsllaal 185 
                                    ++++ +++++    ++l  +v+G +a l+     + +    ++ ++   i+viLli + S+ +++ ++l+v+ s+++ l
  gi|13541816|ref|NP_111504.1|  806 INKLPSMISDKF-GNSLVFYVGGLTAGLDAAYSHTLHTFEEMIPIITGSIFVILLIQLSSVFTPIRLILMVLASVIVGL 883 
                                    555566666665.667778899988877776666667777778888999****************************** PP

                          MMPL  186 gl.vlilalllglelstfvlgllvvlliavGtDYallLvsRyreelaagedreeaviravastgkvvtaaGltvaiaml 263 
                                     +  +i+ ++ gl +  f++++++v l+avG DY +++++R re + +g + eea+ + ++  g+ ++  G  + +++ 
  gi|13541816|ref|NP_111504.1|  884 VIiYAIVYYIYGLPIIVFMPMFTFVTLLAVGLDYDIFMITRAREGVIKGMSDEEAITTSIKENGGIIVTLGSLLFVTFG 962 
                                    **99*************************************************************************** PP

                          MMPL  264 gLvvarlpvlaqvGvaialGvlvdvlivlTll.PAllvllGraalakprrkrkkrwWrr 321 
                                    +L +++l+ ++++G  +a+Gvl+d++++  +  PA++ l+              +wW++
  gi|13541816|ref|NP_111504.1|  963 SLYFSDLQLIEEIGGGLAIGVLIDTFLSWPFFvPAVMLLMKHL-----------NWWPS 1010
                                    *******************************99******9888...........66655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1015 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1277  (0.0712254); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.77u 0.28s 00:00:01.05 Elapsed: 00:00:00.45
# Mc/sec: 6740.12
//
Query:       gi|13541817|ref|NP_111505.1|  [L=410]
Description: S-adenosyl-L-homocysteine hydrolase [Thermoplasma volcanium GSS1]
Scores for complete 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-56  189.3   0.0    3.5e-28   98.6   0.0    2.0  2  AdoHcyase      S-adenosyl-L-homocysteine hydrolase
    1.7e-50  171.2   3.6    3.6e-50  170.2   3.6    1.6  1  AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD bindi
    4.4e-08   32.9   0.4    7.8e-08   32.1   0.4    1.5  1  IlvN           Acetohydroxy acid isomeroreductase, NADPH-bind
    1.5e-06   27.7   0.1    2.7e-06   26.9   0.1    1.4  1  2-Hacid_dh_C   D-isomer specific 2-hydroxyacid dehydrogenase,
     0.0013   18.1   0.6     0.0059   15.9   0.6    2.0  1  THF_DHG_CYH_C  Tetrahydrofolate dehydrogenase/cyclohydrolase,
     0.0037   17.5   0.3      0.012   15.8   0.3    2.0  1  TrkA_N         TrkA-N domain
     0.0072   16.2   0.5       0.21   11.4   0.6    2.5  2  3HCDH_N        3-hydroxyacyl-CoA dehydrogenase, NAD binding d
     0.0096   16.3   0.4      0.023   15.2   0.2    1.7  1  NAD_binding_7  Putative NAD(P)-binding
  ------ inclusion threshold ------
      0.075   13.1   0.2       0.18   11.9   0.2    1.6  1  Shikimate_DH   Shikimate / quinate 5-dehydrogenase
      0.088   12.2   0.7       0.16   11.4   0.7    1.4  1  adh_short      short chain dehydrogenase


Domain annotation for each model (and alignments):
>> AdoHcyase  S-adenosyl-L-homocysteine hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.6   0.0     2e-31   3.5e-28      16     139 ..       9     128 ..       2     134 .. 0.94
   2 !   89.6   0.0   1.1e-28   1.9e-25     175     290 ..     131     408 ..     128     410 .] 0.98

  Alignments for each domain:
  == domain 1  score: 98.6 bits;  conditional E-value: 2e-31
                                   HHHHHHCC-HHHHHHHHHCTTT-TTTT-EEEEES--SHHHHHHHHHHHHTT-EEEEE-SSTTT--HHHHHHHCCT.TEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxx RF
                     AdoHcyase  16 eielaekempglmalreeyaeekplkgariaGslhmtiqtavLietLvalGaevrWasCnifstqdeaaaaiaea.gvpvf 95 
                                   ++e a   mp + ++r+++ +ekp+kg +ia +lh+ ++t +    L++ Ga+vr asCn  s +d +  ++ ++ g+pvf
  gi|13541817|ref|NP_111505.1|   9 RLEWARDHMPVIAEIRKRFLDEKPFKGINIAMALHVEAKTGIFSLLLKEGGANVRMASCNPLSSDDSVVESLKTDyGMPVF 89 
                                   678899******************************************************************9888***** PP

                                   --TT--HHHHHHHHHHCHS-SSTS-S-SEEEESSSHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     AdoHcyase  96 awkgetleeywwcieqalkwaedekepnlilDdGGDltllvhkg 139
                                   a kget+eey + ++++l++      p++i+DdGGDlt+lvh+ 
  gi|13541817|ref|NP_111505.1|  90 ARKGETQEEYYENLQRTLEK-----PPDIIIDDGGDLTKLVHTE 128
                                   ******************55.....7****************84 PP

  == domain 2  score: 89.6 bits;  conditional E-value: 1.1e-28
                                   CCHCC--EEEE-SHHHHHHHHHHHHTT---SEEEESTTSHHHCTTH................................... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................................... RF
                     AdoHcyase 175 ellkkikGvseetttGvhrLyelakkgkLlvpainvndsvtkskfD................................... 220
                                   +l k+i G  eetttGv rL+ ++k+g Ll+p ++vnd+  k  fD                                   
  gi|13541817|ref|NP_111505.1| 131 DLSKNIMGGNEETTTGVVRLKAMEKAGVLLFPMFDVNDANMKHLFDnrygtgqstldgimnstnlliagrnvvvagygycg 211
                                   57799**************************************************************************** PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                     AdoHcyase 221 ................................................................................. 220
                                                                                                                    
  gi|13541817|ref|NP_111505.1| 212 rgiamrlkgmganvivteidpikaneaimdgfqvrrmndairyadmvitatgmkdvvkyedalvakknivlanaghfdnev 292
                                   ********************************************************************************* PP

                                   ..............................................S-HHHHHHHHHHHHHHHHHHHHTTSSS-SSEEE-- CS
                                   ..............................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     AdoHcyase 221 ..............................................hpsfvmsasftnqvlaqielfkkekkyekkvyvlp 255
                                                                                 hp  +m+ sf+ q+l+   l k++++ ekkvy +p
  gi|13541817|ref|NP_111505.1| 293 avkeiekhslekrevrefvkryrlengntvdviadgrlvnlaagqgHPVEIMDLSFALQALTAEYLVKNHQNLEKKVYPVP 373
                                   ********************************************************************************* PP

                                   CHHHHHHHHHCCCCCT-------HHHHHCCTSXTT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     AdoHcyase 256 kklDekvarlhleklgaklteltkeqaeyigveve 290
                                    ++D +va+++l+++g++l++lt++q +y++   e
  gi|13541817|ref|NP_111505.1| 374 PEIDRYVAEIRLKQFGGELDTLTEDQIKYLNSWDE 408
                                   *****************************986655 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 !  170.2   3.6     2e-53   3.6e-50       1     161 [.     177     337 ..     177     338 .. 0.98

  Alignments for each domain:
  == domain 1  score: 170.2 bits;  conditional E-value: 2e-53
                                   HHHHHCCCCCHHHHHHH-S--TTSEEEEE--SHHHHHHHHHHHHCT-EEEEE-S-HHHHHHHHCTT-EE--HHHCTTT-SE CS
                 AdoHcyase_NAD   1 nlygcreslvdgikratdvllaGkvavvaGyGdvGkGcaaslkglGarvivtevdPicalqaameGfevvtleevvkkadi 81 
                                   n yg+ +s +dgi+ +t++l+aG+++vvaGyG  G+G a  lkg+Ga vivte+dPi a  a+m+Gf+v++++++++ ad+
  gi|13541817|ref|NP_111505.1| 177 NRYGTGQSTLDGIMNSTNLLIAGRNVVVAGYGYCGRGIAMRLKGMGANVIVTEIDPIKANEAIMDGFQVRRMNDAIRYADM 257
                                   78******************************************************************************* PP

                                   EEE-SSSSSSB-HHHHCCS-TTEEEEE-SSTTTTBTHHHHHTTT-EEEEEETTEEEEE-TTS-EEEEEGGGSBCHHHTS- CS
                 AdoHcyase_NAD  82 vvtttGnkdiitlehlkkmkddaivcniGhfdseidvaaleanalkkeevkpqvdrvtlkdgkkiillaeGrllnlgcat 161
                                   v+t+tG kd+++ e+    k++ +++n Ghfd+e+ v+++e+++l+k ev+  v+r++l++g+++ ++a+Grl+nl++ +
  gi|13541817|ref|NP_111505.1| 258 VITATGMKDVVKYEDALVAKKNIVLANAGHFDNEVAVKEIEKHSLEKREVREFVKRYRLENGNTVDVIADGRLVNLAAGQ 337
                                   ****************************************************************************9865 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 !   32.1   0.4   4.4e-11   7.8e-08       2      68 ..     197     262 ..     196     312 .. 0.87

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 4.4e-11
                                   HHTS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEHHHHHHT-SEEEE-S CS
                          IlvN   2 lkgkkiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevltvaeavkkadvvmili 68 
                                   + g++++v GyG  G+  a+ l+  g +v+v+  +   ++++A  +gf+v ++++a++ ad+v++ +
  gi|13541817|ref|NP_111505.1| 197 IAGRNVVVAGYGYCGRGIAMRLKGMGANVIVTEIDPI-KANEAIMDGFQVRRMNDAIRYADMVITAT 262
                                   7899***************************988777.8999********************98764 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 !   26.9   0.1   1.5e-09   2.7e-06      33      99 ..     196     262 ..     173     286 .. 0.89

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 1.5e-09
                                   -GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTCEECSHHHHHHH-SEEEE-S CS
                  2-Hacid_dh_C  33 elsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeelgvelvsleellaesDivslhl 99 
                                    ++g+ v + G+G  G+ +a rlk++g++vi+++  + k +e+   g+++  ++++++ +D+v+ ++
  gi|13541817|ref|NP_111505.1| 196 LIAGRNVVVAGYGYCGRGIAMRLKGMGANVIVTEIDPIKANEAIMDGFQVRRMNDAIRYADMVITAT 262
                                   5899********************************9999999999****************99766 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 !   15.9   0.6   3.3e-06    0.0059       3     104 ..     169     281 ..     167     300 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 3.3e-06
                                   HHHHHHHTT--SS--HHHHHHHHHHHHCT---TT-EEEEE---TTTHHHHHHHHHCTT-EEEEE-TTS............. CS
                 THF_DHG_CYH_C   3 lnlgrlvkgeeallpctpkgvvellketgielegkkvvvvGrsnivgkplallLleknatVtvchskt............. 70 
                                   +n+ +l+ ++  +  +t  g++   ++t+  ++g++vvv G +   g+ +a+ L+  +a V v++                
  gi|13541817|ref|NP_111505.1| 169 ANMKHLFDNRYGTGQSTLDGIM---NSTNLLIAGRNVVVAGYG-YCGRGIAMRLKGMGANVIVTEIDPikaneaimdgfqv 245
                                   6777888888777778888876...689999**********87.67*********98777766654332223344444445 PP

                                   CCHHHHHCCSSEEEE-SS-TT-B-GG..GS-TT-EE CS
                 THF_DHG_CYH_C  71 kdlaeitreadivvvavGkpelikae..mvkegavv 104
                                   + +++ +r ad+v++a+G ++++k e   v ++++v
  gi|13541817|ref|NP_111505.1| 246 RRMNDAIRYADMVITATGMKDVVKYEdaLVAKKNIV 281
                                   88999******************9762234444444 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.3   6.8e-06     0.012       1      44 [.     202     245 ..     202     279 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 6.8e-06
                                   EEEES-SHHHHHHHHHHHH.TTEEEEEEESSHHHHHHHHHTTSEE CS
                        TrkA_N   1 iiiiGlGrvGrslaeeLse.ggkdvvvidkdeerveelreeglev 44 
                                   ++++G+G  Gr +a +L+  g  +v+v + d+ +++e+  +g++v
  gi|13541817|ref|NP_111505.1| 202 VVVAGYGYCGRGIAMRLKGmGA-NVIVTEIDPIKANEAIMDGFQV 245
                                   79*****************666.6**************9999887 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 !   11.4   0.6   0.00012      0.21       1      39 [.     201     239 ..     201     281 .. 0.89
   2 ?    2.0   0.0     0.093   1.7e+02      16      69 ..     332     385 ..     326     394 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00012
                                   EEEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHH CS
                       3HCDH_N   1 kvaviGaGtmGagiaavfasagleVvlvdiseealekal 39 
                                   +v v G G  G+gia+ +   g +V +++i++ ++++a 
  gi|13541817|ref|NP_111505.1| 201 NVVVAGYGYCGRGIAMRLKGMGANVIVTEIDPIKANEAI 239
                                   5899**************************998888775 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.093
                                   HHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS-HHHHCCCHHCEEE CS
                       3HCDH_N  16 avfasagleVvlvdiseealekalekieksleklvekgklkeeeveaalarisf 69 
                                   +++a +g++V ++d s +  +  +e + k+ ++l++k      e+++++a+i+ 
  gi|13541817|ref|NP_111505.1| 332 NLAAGQGHPVEIMDLSFALQALTAEYLVKNHQNLEKKVYPVPPEIDRYVAEIRL 385
                                   68999**********999999999999999999988888778888888888876 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 !   15.2   0.2   1.3e-05     0.023       5      76 ..     197     269 ..     194     291 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.3e-05
                 NAD_binding_7   5 lkgkkvlvvGgGevAarkvrklleagakvtvvapevkeeleelvk.laeeelekdlegadlviaatddrelne 76 
                                   + g++v+v+G G  +   + +l   ga+v+v   +  ++ e +++ ++ + +++ +  ad+vi+at  +++ +
  gi|13541817|ref|NP_111505.1| 197 IAGRNVVVAGYGYCGRGIAMRLKGMGANVIVTEIDPIKANEAIMDgFQVRRMNDAIRYADMVITATGMKDVVK 269
                                   679****************************888855665666666678889999***********9887765 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.2   9.9e-05      0.18      11      91 ..     198     270 ..     191     289 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 9.9e-05
                                   TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHH.HHHHT.ET-EEEEGCGHHHHHHT-SEEEE-SSSSS-SB CS
                  Shikimate_DH  11 kekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakel.aeelkgeeiealkleelkellaeadvvisataseepil 90 
                                   ++++v++ G G  ++ +a  L   g++ v+v+  +  +a+e   + +        ++  ++++++ ad+vi+at+ ++++ 
  gi|13541817|ref|NP_111505.1| 198 AGRNVVVAGYGYCGRGIAMRLKGMGAN-VIVTEIDPIKANEAiMDGF--------QVRRMNDAIRYADMVITATGMKDVVK 269
                                   67899*****************99999.9999999888876403333........5689999*************998775 PP

                                   - CS
                  Shikimate_DH  91 e 91 
                                    
  gi|13541817|ref|NP_111505.1| 270 Y 270
                                   4 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   0.7   9.1e-05      0.16       8      99 ..     206     300 ..     200     312 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 9.1e-05
                                   TTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHT..TSEEEEEE-TTT.SHHHHHHHHHHHHHHHSSESEEEE-- CS
                     adh_short   8 assGIGraiakelakeGakvvvvdrseekleevakelkee..gakalaiqvDvt.dreevealvekavkklgkldvLvnNA 85 
                                   + +  Gr ia +l  +Ga+v+v+++ + k++e++    +    ++a+ + +D+  +++ ++++v+   + + k +++ +NA
  gi|13541817|ref|NP_111505.1| 206 GYGYCGRGIAMRLKGMGANVIVTEIDPIKANEAIMDGFQVrrMNDAIRY-ADMViTATGMKDVVKYEDALVAKKNIVLANA 285
                                   444569********************99999988765555432333333.34443799*********************** PP

                                   -S.S--SSGGGCSHH CS
                     adh_short  86 Gi.tgsgpfselsee 99 
                                   G   + ++++e+++ 
  gi|13541817|ref|NP_111505.1| 286 GHfDNEVAVKEIEKH 300
                                   **7555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (410 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       675  (0.0376485); expected 358.6 (0.02)
Passed bias filter:                      553  (0.0308439); 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: 0.59u 0.32s 00:00:00.90 Elapsed: 00:00:00.46
# Mc/sec: 2651.88
//
Query:       gi|13541818|ref|NP_111506.1|  [L=441]
Description: seryl-tRNA synthetase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.4e-41  141.2   0.0    6.1e-41  140.3   0.0    1.3  1  tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, 
    1.4e-23   83.2   4.6      7e-23   80.9   5.6    1.7  2  Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
  ------ inclusion threshold ------
      0.034   13.9   0.2      0.054   13.2   0.2    1.2  1  CCDC106       Coiled-coil domain-containing protein 106
      0.038   12.6   2.0      0.056   12.1   2.0    1.2  1  FapA          Flagellar Assembly Protein A


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 !  140.3   0.0   1.4e-44   6.1e-41       3     178 ..     240     416 ..     236     417 .. 0.96

  Alignments for each domain:
  == domain 1  score: 140.3 bits;  conditional E-value: 1.4e-44
                                   EEETTSEEEEE-SSSHHHHHHHHHHHEEEBGGSSEEEEEEEEEEBTTTS....TBCTTTB-SEEEEEEEEEEESGGGHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  tRNA-synt_2b   3 ledrndreyiLkPtneetfvelirdevlrskrLPlklyqiqtkyRdEks....dsrGLlRvreFhqkdgyvfhaeasldds 79 
                                   +e   d++++L++t+e+ ++++ ++e l +k+LP++++ ++ ++R+E+     d++G++Rv++F++ ++++f+++++++d 
  gi|13541818|ref|NP_111506.1| 240 IE---DEDLYLIATSEHSIASMLSNEFLEEKELPIRVAGVSACFRREAGahgkDTKGIFRVHQFNKIEQFIFCKPEDSWDY 317
                                   44...569****************************************77899**************************** PP

                                   HHHHHHHHHHHHHHTT.SCEEEEEEGTTSCBTTSEEEEEEEEETTTSEEEEEEEEEEEETHHHHHTTEEEECTTSSEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  tRNA-synt_2b  80 lrdlikaisriferlglefraiielmsaksadykdkkefeavsesltkgieigtiqklgtrlserlgatvldennreksvi 160
                                   l++++  +++i+++lg+++r++  + ++    +++k+++ea+++ ++k++ei++++++ +++++ l++++ ++ + +++v+
  gi|13541818|ref|NP_111506.1| 318 LEEILSNAEEIYRSLGIPYRVVNVCSGELGRLAAKKYDIEAWFPAQGKFREIVSASNDTDYQARSLNIKY-RKSGGNEFVH 397
                                   ********************999999999999**************************************.9999****** PP

                                   EEEEE.EEHHHHHHHHHHH CS
                                   xxxxx.xxxxxxxxxxxxx RF
                  tRNA-synt_2b 161 micaa.igveRllsaileq 178
                                   +++ + i+++R+l ai+e+
  gi|13541818|ref|NP_111506.1| 398 TLNSTaIATTRILVAIMEN 416
                                   ****99***********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 !   80.9   5.6   1.6e-26     7e-23       1     107 [.       1     107 [.       1     108 [. 0.99
   2 ?   -3.8   0.0       3.4   1.5e+04      53      71 ..     340     358 ..     339     368 .. 0.83

  Alignments for each domain:
  == domain 1  score: 80.9 bits;  conditional E-value: 1.6e-26
                                   ---HHHHHH-HHHHHHHHCCCTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHH CS
                  Seryl_tRNA_N   1 MLDiklirenpeavkeklkkRgedkadvdelleldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelke 81 
                                   M+D+kl+r+n e+++++++ Rg+dka +d++++lde++r+++ el+  +ae+N+++++I++  k+++  +  +++v+ ++e
  gi|13541818|ref|NP_111506.1|   1 MIDVKLLRSNRELFEKNCEYRGVDKAIIDQFFKLDEEWRSVNRELNGQRAEKNRMTRAIAESLKRGKIVSNEKDRVELINE 81 
                                   9******************************************************************************** PP

                                   HHHHHHHHHHHHHHHHHHHHCTS--- CS
                  Seryl_tRNA_N  82 elkaleaelkeleaeleklllaiPNi 107
                                   ++  le++ +e+e+e + +l++iPN+
  gi|13541818|ref|NP_111506.1|  82 KIVSLEKKIREIEEERDRVLWTIPNL 107
                                   *************************8 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 3.4
                                   HHHHHHCCCCCCTTS-TCC CS
                  Seryl_tRNA_N  53 NelskeIgkakkkkedaee 71 
                                   N +s e g++ +kk d+e+
  gi|13541818|ref|NP_111506.1| 340 NVCSGELGRLAAKKYDIEA 358
                                   8899999999999877765 PP

>> CCDC106  Coiled-coil domain-containing protein 106
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.2   1.2e-05     0.054       4      34 ..      69      99 ..      67     121 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.2e-05
                       CCDC106  4 ltklkkqLevkkEkiswlqkriedLeeeRdF 34
                                  ++++k  +e+  Eki  l+k+i ++eeeRd 
  gi|13541818|ref|NP_111506.1| 69 VSNEKDRVELINEKIVSLEKKIREIEEERDR 99
                                  7899*************************95 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   2.0   1.2e-05     0.056     334     453 ..      33     138 ..      15     139 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.2e-05
                          FapA 334 elkeklkeleeeleeleeeleklkkkikklpklkaekqlesekkeqlkklletkeklkeeleeleeelkelkeeleskkee 414
                                   +l+e+ + +++el+  ++e ++ +++i++  k          + + + + +   e ++e++ +le+++ e++ee ++    
  gi|13541818|ref|NP_111506.1|  33 KLDEEWRSVNRELNGQRAEKNRMTRAIAESLK----------RGKIVSNEKDRVELINEKIVSLEKKIREIEEERDRV--- 100
                                   23333333333333333333333333333333..........224555555555888999999999999999999999... PP

                          FapA 415 akikvnkeiypgvkikigkkkliikreysnttfvleege 453
                                     + + + i+ +v i +g+++++i r  ++++++ +++e
  gi|13541818|ref|NP_111506.1| 101 -LWTIPNLIHESVPICFGDENNKIVRYVGHAKVYRDDEE 138
                                   .8999999*******************999999997765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (441 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       763  (0.0425568); expected 358.6 (0.02)
Passed bias filter:                      533  (0.0297284); 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: 0.56u 0.24s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 2901.19
//
Query:       gi|13541819|ref|NP_111507.1|  [L=348]
Description: Kef-type K+ transporter NAD-binding component [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-15   57.1   7.6    2.7e-15   56.1   7.6    1.6  1  Ion_trans_2      Ion channel
    4.5e-12   46.3   2.1    8.6e-12   45.3   2.1    1.5  1  TrkA_N           TrkA-N domain
      7e-09   35.3   1.5    1.1e-08   34.6   1.5    1.3  1  Ion_trans        Ion transport protein
    9.2e-05   22.4   0.0    0.00032   20.6   0.0    2.0  2  Castor_Poll_mid  Castor and Pollux, part of voltage-gated ion
    0.00026   20.8   0.3    0.00051   19.9   0.3    1.6  1  Lig_chan         Ligand-gated ion channel
     0.0011   18.8   0.5     0.0021   17.9   0.5    1.5  1  IRK              Inward rectifier potassium channel transmemb
  ------ inclusion threshold ------
      0.071   12.9   0.0       0.25   11.2   0.0    2.0  2  TrkA_C           TrkA-C domain


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 !   56.1   7.6   1.1e-18   2.7e-15       3      78 ..      27     105 ..      18     106 .. 0.81

  Alignments for each domain:
  == domain 1  score: 56.1 bits;  conditional E-value: 1.1e-18
                                   HHHTCHHHHHHHHT.......T---HHHHHHHHHHHHTTS----SSTT-----HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                   Ion_trans_2   3 lllvlifgaviysl...eegwekwsfldalYfsfvtltTiGYGdivpetdagrlftivyillGlalfalflavlgkvlt 78 
                                   +++vli + + +      + +e  ++++a++f++ t+tT+GYGd+vp++++gr++++++++ G++l+++++a+++ +l+
  gi|13541819|ref|NP_111507.1|  27 IIVVLIGSYLEFLTqrnVKYSEIKNYFTAIWFTMETVTTVGYGDVVPVSNLGRVVAMLIMVSGIGLLGTLTATISAYLF 105
                                   333333333333338753447789*************************************************998876 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.3   2.1   3.4e-15   8.6e-12       2     115 ..     124     246 ..     123     247 .. 0.92

  Alignments for each domain:
  == domain 1  score: 45.3 bits;  conditional E-value: 3.4e-15
                                   EEES-SHHHHHHHHHHHH.TTEEEEEEESSHHHHHHHHHTTSEEEES-TTSHHHHHHTTGGGESEEEE-SS.......... CS
                        TrkA_N   2 iiiGlGrvGrslaeeLse.ggkdvvvidkdeerveelreeglevvvgdatdeevLeeagiekadaviaatg.......... 71 
                                   ii+ ++  +r+++e  ++ +  ++v+   + ++ e+++  ++ +v+gd+t+e+ L++a ie+a  v+++ +          
  gi|13541819|ref|NP_111507.1| 124 IICNWNAYTRNIIEGNRDeEAAPIVILSENTDNSEKYQ--NVFFVKGDCTSEDDLKNAAIEDAARVVIMSDiennaipedl 202
                                   9*****************55577*******99999977..5558*************************999999999777 PP

                                   SHHHHHHHHHHHHHHTSSSEEEEEESSGGGHHHHHHHTTSEEEE CS
                        TrkA_N  72 ddeanilavllakelnpkkkiiaraqdpehaellkklgadvvis 115
                                    d++++l + ++++ln++ +iia+++d+++++ + ++ga++v+s
  gi|13541819|ref|NP_111507.1| 203 LDAKTLLSIFTVRKLNNAVEIIAEVRDEKNKKHAVSAGATEVLS 246
                                   77999999*********************************987 PP

>> Ion_trans  Ion transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.6   1.5   4.3e-12   1.1e-08     138     240 ..      23     107 ..       2     112 .. 0.80

  Alignments for each domain:
  == domain 1  score: 34.6 bits;  conditional E-value: 4.3e-12
                                   HHHHHHHHHHHHHHHTTSCCCCCCSCCSTSSSTTTSSSSSSHHHHHHHHHHHHTTSSHHHHHHHHHHHSHHHHHHHHHHHH CS
                     Ion_trans 138 lvvlfifaligvqlfkgklreknecaktwenpnngntnFdnfftallwlfrlmttegwgdilyatldekskvaliyfvifi 218
                                   ++ ++i  lig  l               ++ n ++++ +n+fta+++++++ tt+g+gd++++   ++      +++++i
  gi|13541819|ref|NP_111507.1|  23 FMAFIIVVLIGSYLE------------FLTQRNVKYSEIKNYFTAIWFTMETVTTVGYGDVVPVSNLGR------VVAMLI 85 
                                   455555555554444............1356677999999*****************************......****** PP

                                   HHHHHHHHHHHHHHHHHHHHHH CS
                     Ion_trans 219 ilgsflllNlliaviadnfqel 240
                                   +++++ ll  l a i+ ++ ++
  gi|13541819|ref|NP_111507.1|  86 MVSGIGLLGTLTATISAYLFQI 107
                                   *************999887766 PP

>> Castor_Poll_mid  Castor and Pollux, part of voltage-gated ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       2.7   6.8e+03      84      99 ..     221     236 ..     217     239 .. 0.77
   2 !   20.6   0.0   1.2e-07   0.00032       4      95 ..     251     343 ..     248     347 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2.7
               Castor_Poll_mid  84 llviaedddtkkpeea 99 
                                   + +iae++d+k++++a
  gi|13541819|ref|NP_111507.1| 221 VEIIAEVRDEKNKKHA 236
                                   5689999999988765 PP

  == domain 2  score: 20.6 bits;  conditional E-value: 1.2e-07
               Castor_Poll_mid   4 isrllvqcsrqkGLak.iyedlLnfek.nefylkelpelegkkyedvllafqeavviGikvassgkiylnPeddevlqegd 82 
                                    srl+  +   +GL+  i++ l + e+ + f ++    l g++ +d+  ++ e+ vi i v+s+gki   P+  + + +gd
  gi|13541819|ref|NP_111507.1| 251 SSRLISRSISNPGLTDfILKSLSETEDfKIFSIEACGILPGMTVKDAASNLAEVCVI-ISVISKGKIEYPPDRSYKIGAGD 330
                                   57777777788888764666666665525677888999***************9887.778999***************** PP

               Castor_Poll_mid  83 kllviaedddtkk 95 
                                    ++++a+++++ +
  gi|13541819|ref|NP_111507.1| 331 YVVFLAKNKKEVE 343
                                   ******9998765 PP

>> Lig_chan  Ligand-gated ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.3     2e-07   0.00051      40     117 ..      46     167 ..      19     252 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 2e-07
                                   XXXHHHHHHHHHHHHHHHHHHH.HXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXS-SSCCHHHTGS... CS
                                   xxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx... RF
                      Lig_chan  40 veneftlsnslwfslgalvqqG.cdesprsvsgRivvavWwffvlillssYtAnLaafltvermqtpiksledLakqt... 116
                                    ++  ++++++wf++ +++  G +d  p s+ gR+v+++ ++  + ll + tA ++a+l   r++ + k  + L ++t   
  gi|13541819|ref|NP_111507.1|  46 YSEIKNYFTAIWFTMETVTTVGyGDVVPVSNLGRVVAMLIMVSGIGLLGTLTATISAYLFQIRIERRGKLEKRLKNHTiic 126
                                   345667899*************9************************************9999987766666677777666 PP

                                   ........................................S CS
                                   ........................................x RF
                      Lig_chan 117 ........................................k 117
                                                                           k
  gi|13541819|ref|NP_111507.1| 127 nwnaytrniiegnrdeeaapivilsentdnsekyqnvffvK 167
                                   66666666666666666666666666666666666666653 PP

>> IRK  Inward rectifier potassium channel transmembrane domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.5   8.3e-07    0.0021      77     126 ..      44      93 ..      17     107 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 8.3e-07
                           IRK  77 pCvanvksftsallfslEtqttigyGsrvvteeCpeailllviqsivgll 126
                                     ++++k++ +a+ f++Et tt+gyG  v+ ++    +++l++ s +gll
  gi|13541819|ref|NP_111507.1|  44 VKYSEIKNYFTAIWFTMETVTTVGYGDVVPVSNLGRVVAMLIMVSGIGLL 93 
                                   456799***************************99999999988777765 PP

>> TrkA_C  TrkA-C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       1.7   4.3e+03       9      19 ..     251     261 ..     223     267 .. 0.68
   2 ?   11.2   0.0   9.7e-05      0.25      12      60 ..     289     339 ..     280     347 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.7
                                   -GGGTTSBHHH CS
                        TrkA_C   9 gsplvGktlke 19 
                                   +s+l+ ++++ 
  gi|13541819|ref|NP_111507.1| 251 SSRLISRSISN 261
                                   56677777765 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 9.7e-05
                                   GTTSBHHH..HTHHHHS-EEEEE.E-T-EEES--TT-B--TT-EEEEEEEHH CS
                        TrkA_C  12 lvGktlke..lnlrargvlvvai.rRggeliipsgdtvLeeGDvllvvgsps 60 
                                   l G+t+k+  +nl +  + ++++  +g+  + p+ ++++ +GD ++++++ +
  gi|13541819|ref|NP_111507.1| 289 LPGMTVKDaaSNLAE-VCVIISViSKGKIEYPPDRSYKIGAGDYVVFLAKNK 339
                                   679999994444666.7777777588899999999************99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (348 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       739  (0.0412181); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.50
# Mc/sec: 2096.46
//
Query:       gi|13541820|ref|NP_111508.1|  [L=331]
Description: tyrosyl-tRNA synthetase [Thermoplasma volcanium GSS1]
Scores for 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  133.3   0.0    1.2e-38  133.1   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 !  133.1   0.0   6.8e-43   1.2e-38       6     286 ..      28     309 ..      23     316 .. 0.87

  Alignments for each domain:
  == domain 1  score: 133.1 bits;  conditional E-value: 6.8e-43
                                   -EEEEEEETSSS-BGG.GHHHHHHHHHHHHTTSEEEEEEEHHHHHTTTTT-SSHHHHHHHHHHHHHHHHHHHHHTCHTTTE CS
                  tRNA-synt_1b   6 lrvysGidPTgklHlG.ylvplkklvelqkaghevffliaDlhAiigdpskaeerklrkreevlenaikaqlakgldpeka 85 
                                   ++ y Gi+P+g +H++  ++  +kl+elq + +++++l+aD+hA+i+++   ++  +rk  e l+ +    +a gl   ka
  gi|13541820|ref|NP_111508.1|  28 VKSYIGIEPSGIPHVAtAVMWPRKLAELQ-DDIKIYVLLADWHAMINNKLHGDLDLIRKGGELLKRS---FMAEGLT--KA 102
                                   678*************99***********.********************99***************...****986..6* PP

                                   EEEETHHHHTTHHHHHHHHHHHTTCBHHHHHHHHHCCHHCSSSC--BHHHHHHHHHHHHHHHHTCHSEEEEEGGGHHHHHH CS
                  tRNA-synt_1b  86 evvlqsewlehlelaellrdlgklgslnrmlqfksvkkrleegegislgeftYplLqaaDilllkadlvpgGsDQkqniel 166
                                   e+++ s+  ++++++e++ + +k  +l+r++++  ++ r e + +  ++  +Yp++q  Di++l++d+ +gG+DQ+    l
  gi|13541820|ref|NP_111508.1| 103 EYLWASQLVSSSNYWEMFIKTAKRSTLKRLTRALPIMGRTEADAEKDFSMYIYPIMQVTDIFYLDVDIAFGGMDQRHAHML 183
                                   ******************************************77899********************************** PP

                                   HHHHHHHHHHHSTTSS-EEEEET-BBSTTSSS......BTTCETTCGC-BTTCCHHHHHHHHHHCHCSTTC..SHHHHHHH CS
                  tRNA-synt_1b 167 grdlarrfnkkevfkkpegltvplltgldGek......KmSKSagnsaIfLddekesvkkkiqkavtdsde..evekllkl 239
                                   +rd+a++++ k    k +++   ll++l+G        KmSKS++nsaI ++de ++++ k++ a++ +++  ++   + +
  gi|13541820|ref|NP_111508.1| 184 ARDIADKMKVK----KAVSVHGYLLSSLKGNTrmdnfvKMSKSDPNSAILINDEYKDIERKVNAAFCPPEKvdGNPLAEIM 260
                                   ********999....55555555555555542222234*********************************9989999999 PP

                                   HHTHHH.....CHHHHHHHHCCSEEESSHHHHHHHHHCCCCHHHHHHHHHHH CS
                  tRNA-synt_1b 240 ktelsn.....elierleavsgkkpkreaeellaeevtklvhggdlkkalae 286
                                   k++l +      +ie+ +   g+   + + ++  +++++++ +++lkka+  
  gi|13541820|ref|NP_111508.1| 261 KYVLIPyygrdIIIEKPS---GNVRIENVDQFQNDYISGKIAPTELKKAMIP 309
                                   999998544323333333...3333567999999999999999999998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       548  (0.030565); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 2032.32
//
Query:       gi|13541821|ref|NP_111509.1|  [L=86]
Description: lipoate-protein ligase A [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-15   57.3   0.4    1.2e-15   57.2   0.4    1.0  1  Lip_prot_lig_C  Bacterial lipoate protein ligase C-terminus
  ------ inclusion threshold ------
      0.013   14.6   0.1      0.013   14.6   0.1    1.0  1  Emaravirus_P4   P4 movement protein of Emaravirus, and the 30


Domain annotation for each model (and alignments):
>> Lip_prot_lig_C  Bacterial lipoate protein ligase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.2   0.4   1.4e-19   1.2e-15       5      85 .]       2      83 ..       1      83 [. 0.91

  Alignments for each domain:
  == domain 1  score: 57.2 bits;  conditional E-value: 1.4e-19
                                  SEEEEEEETTEEEEEEEEEETTEEEEEEEEESBS..SSSHCHHHHHHHTTSBSSHHHHHHHHHTSCHHHHCC.THHHHHHHHH CS
                Lip_prot_lig_C  5 nvkkkkrfdwGtvevrldvekgiIkdikiyGDff..gpkdieeleekLigvkyekeaieealekidlseyfg.gieleellel 84
                                   v+++ + + G + v +dve+g+I++iki+GDff   ++ i+ele++L+g k++   i+++++k+  + +++ g+e++++++ 
  gi|13541821|ref|NP_111509.1|  2 HVNRNWKAKKGLIRVSMDVENGVINNIKISGDFFmfPEESINELENMLKGSKIDN--IKSIIDKFYNEGIITpGVEPQDFVNA 82
                                  578999***************************955599************9885..*******998888889*******997 PP

                                  H CS
                Lip_prot_lig_C 85 l 85
                                  +
  gi|13541821|ref|NP_111509.1| 83 I 83
                                  6 PP

>> Emaravirus_P4  P4 movement protein of Emaravirus, and the 30K superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1   1.5e-06     0.013     189     235 ..      19      67 ..       6      83 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.5e-06
                 Emaravirus_P4 189 pdengvyekvqw..dvftfekslpaevalmsgksnflkvksyldkkyne 235
                                     engv ++++   d f f+ +   e+  m   s++ ++ks +dk yne
  gi|13541821|ref|NP_111509.1|  19 DVENGVINNIKIsgDFFMFPEESINELENMLKGSKIDNIKSIIDKFYNE 67 
                                   569****987643399***********99999999*************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       547  (0.0305092); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 538.74
//
Query:       gi|13541822|ref|NP_111510.1|  [L=262]
Description: lipoate-protein ligase A [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.2e-09   37.3   0.0    3.4e-09   36.7   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 !   36.7   0.0   1.9e-13   3.4e-09      13     131 .]      54     169 ..      47     169 .. 0.82

  Alignments for each domain:
  == domain 1  score: 36.7 bits;  conditional E-value: 1.9e-13
                                   H..GCGGG--TT-EEEEEEESS-B-B--B-TTSEEEEEEEEESS...-CCGTHHHHHHHHHHHHHHH.........HHTT- CS
                 BPL_LplA_LipB  13 keslnsselesgglvvvrrqtgGrnvwhspkgeltyslllspeqktfqnrvlelyvsllvlavlealgy...rdskpgieg 90 
                                   +e++ ++  +  ++ ++rr tgG +v+h+  g+l++s+++++ +      ++  + +++  av+++l y   +    + ++
  gi|13541822|ref|NP_111510.1|  54 EEEVDLDYMKRNNIMLARRYTGGGAVYHD-LGDLNFSVITESHD-----MNITAMFRTMNEAVVRSLSYlglQARPGELND 128
                                   566777778889999**************.***********776.....34555666666666666643332226788899 PP

                                   TTEEEETTTEEEETTEEEEEEEEEEEETTS-EEEEEEEEEE CS
                 BPL_LplA_LipB  91 ipvfikwpnDlyvngrKlaGiavtstrgktlhhivigvgvn 131
                                   +++ i  + D++++ +K+ G a   ++g++l h +++v+++
  gi|13541822|ref|NP_111510.1| 129 VSIPINKKTDIMAGEKKIMGAAGAMRKGSKLWHAAMLVKTD 169
                                   999999*******************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       663  (0.0369792); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.33s 00:00:00.93 Elapsed: 00:00:00.54
# Mc/sec: 1453.83
//
Query:       gi|13541823|ref|NP_111511.1|  [L=455]
Description: signal recognition particle protein Srp54 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.1e-64  217.7   0.5    1.7e-64  217.0   0.5    1.3  1  SRP54       SRP54-type protein, GTPase domain
    1.4e-22   80.2   0.7    1.4e-22   80.2   0.7    2.7  4  SRP_SPB     Signal peptide binding domain
    1.5e-14   53.9   0.5    1.5e-14   53.9   0.5    4.0  5  SRP54_N     SRP54-type protein, helical bundle domain
     0.0055   16.2   0.7       0.17   11.3   0.0    2.8  3  SRPRB       Signal recognition particle receptor beta subunit
  ------ inclusion threshold ------
       0.02   15.5   0.7        5.4    7.7   0.1    3.0  3  DUF5499     Family of unknown function (DUF5499)
       0.04   14.0   1.7       0.13   12.3   0.4    2.4  2  MMR_HSR1    50S ribosome-binding GTPase
      0.051   14.0   0.0       0.14   12.5   0.0    1.7  2  AAA_16      AAA ATPase domain
      0.053   13.4   0.0       0.14   12.1   0.0    1.7  1  APS_kinase  Adenylylsulphate kinase
      0.066   13.3   0.0       0.35   10.9   0.0    2.0  1  CbiA        CobQ/CobB/MinD/ParA nucleotide binding domain
      0.067   12.5   0.0       0.15   11.4   0.0    1.6  1  6PF2K       6-phosphofructo-2-kinase


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 !  217.0   0.5   9.7e-68   1.7e-64       2     196 .]      98     290 ..      97     290 .. 0.98

  Alignments for each domain:
  == domain 1  score: 217.0 bits;  conditional E-value: 9.7e-68
                                   EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSSTTHHHHHHHHHHHTTEEEEESSTTSCHHHHHHHHHHHHHHT CS
                         SRP54   2 nvillvGlqGaGKTttlaKLaallkkegkkvllvaaDtfRaaAveQLktlaeklgvpvikkkeeadpaavakeavekakee 82 
                                   + i+lvGl G GKTt+++KL++ ++k+g ++ l+aaD+ R aA+eQL+++ae++++++++  +e+dp++++k+++e  k+ 
  gi|13541823|ref|NP_111511.1|  98 QTIMLVGLYGHGKTTSAGKLSRFFMKKGLSAGLIAADVHRYAAYEQLQQIAESVNAKFYGDPKEKDPVKIIKNGLEVLKD- 177
                                   789***************************************************************************99. PP

                                   TSSEEEEEE--SSTTHHHHHHHHHHHHHHHSSSEEEEEEETTBHTHHHHHHHHHHHHSSCSEEEEESTTSSSSTTHHHHHH CS
                         SRP54  83 kidvvlvDTaGrlqndkelmeelkkikkvvkpdevllvldattgqeavkqakaFkeavgitgviltklDgdakgGaalsia 163
                                    ++v ++DT+Gr   d++l+ee+++ik++vkpd+vl+v+dat+gq+a  + ka ++avg+tg+i+tk+Dg+akgG+als++
  gi|13541823|ref|NP_111511.1| 178 -AQVKIIDTSGRDSLDSDLIEEIRRIKEAVKPDQVLMVIDATMGQQAGPESKAINDAVGVTGIIITKMDGTAKGGGALSAV 257
                                   .55889*************************************************************************** PP

                                   HHHTS-EEEEE-SSSTTGEEE--HHHHHHHHHT CS
                         SRP54 164 aelklPikfigvGekiedleefdperlvsrllg 196
                                   a++ +Pi+fig+Ge+++d+e fdp++++srllg
  gi|13541823|ref|NP_111511.1| 258 AKMRVPIYFIGTGEHMDDMEIFDPKKFLSRLLG 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 ?   -3.4   0.0       8.8   1.6e+04      70      92 ..      34      56 ..      21      58 .. 0.66
   2 ?   -2.0   0.1       3.3   5.9e+03       6      51 ..     194     241 ..     193     248 .. 0.64
   3 ?   -1.2   0.0       1.8   3.1e+03       6      47 ..     280     318 ..     275     320 .. 0.66
   4 !   80.2   0.7   7.6e-26   1.4e-22       1      99 []     322     425 ..     322     425 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 8.8
                                  HHHHHHHHTTS-HHHHHHHHHHH CS
                       SRP_SPB 70 RkrRiArGsGtsvqevnellkqf 92
                                    +Ri   + ++vq v ++ k++
  gi|13541823|ref|NP_111511.1| 34 DLQRILLKADVNVQTVLNITKEM 56
                                  45677777777777777776665 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.3
                                   HHHHHHHHHHCCCCCCHHHHCCC.......H...CCCCCHHHHHHHHH CS
                       SRP_SPB   6 dlleqlqqikkmGplskllsmiPgmsae..akaeeeaekklkrieaii 51 
                                   dl+e++++ik+  + +++l  i +++ +  + ++++ ++++  + +ii
  gi|13541823|ref|NP_111511.1| 194 DLIEEIRRIKEAVKPDQVLMVIDATMGQqaGPESKAINDAVGVTGIII 241
                                   788888888888888888888876554444323344445555555555 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 1.8
                                   HHHHHHHHHHCCCCCCHHHHCCC.....H...CCCCCHHHHH CS
                       SRP_SPB   6 dlleqlqqikkmGplskllsmiPgmsaeakaeeeaekklkri 47 
                                   d ++ l+++  +G+l+ l++ +    a+  +eeea+k+++++
  gi|13541823|ref|NP_111511.1| 280 DPKKFLSRLLGLGDLETLFETVKE--ANI-TEEEAQKSFEKL 318
                                   556777888899999999999885..222.234456666665 PP

  == domain 4  score: 80.2 bits;  conditional E-value: 7.6e-26
                                   SSCTHHHHHHHHHHHCCCCCCHHHHCCC...........H.....CCCCCHHHHHHHHHTTSBHHHHHSGCG-..HHHHHH CS
                       SRP_SPB   1 eftlrdlleqlqqikkmGplskllsmiPgmsae......akae..eeaekklkrieaiidSMTkeErdspekllkesRkrR 73 
                                   +f+l+d+++  ++ ++ G ++kl++ +P   +       + ++   +ae+kl+r+ +i+dSMT +E+++pe +++++R++R
  gi|13541823|ref|NP_111511.1| 322 KFNLKDMYDVWEKFSRPGLMKKLVDSLPL-AKLpgsqkiN-DDqiLTAEQKLQRYRIIMDSMTFQELENPE-IINAKRITR 399
                                   69*********************999663.2223333332.225656789*********************.999****** PP

                                   HHHHTTS-HHHHHHHHHHHHHHHHHT CS
                       SRP_SPB  74 iArGsGtsvqevnellkqfeqmkkmm 99 
                                   iArG+G++ ++v+ llk+f+ mk+ m
  gi|13541823|ref|NP_111511.1| 400 IARGAGVREEDVRMLLKEFKAMKNNM 425
                                   **********************9876 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 !   53.9   0.5   8.5e-18   1.5e-14       1      75 []       6      83 ..       6      83 .. 0.95
   2 ?    0.6   0.0      0.36   6.5e+02      29      60 ..     125     154 ..     110     172 .. 0.68
   3 ?    0.4   0.1      0.43   7.7e+02      13      33 ..     186     205 ..     181     211 .. 0.77
   4 ?   -3.8   0.1       8.9   1.6e+04      49      58 ..     299     308 ..     294     317 .. 0.47
   5 ?   -2.1   0.0       2.7   4.8e+03      17      31 ..     405     419 ..     395     439 .. 0.66

  Alignments for each domain:
  == domain 1  score: 53.9 bits;  conditional E-value: 8.5e-18
                                  HHHHHHHHHHHHCCSSCGHHHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHCTTS...S-HHHHHHHHHHHHH CS
                       SRP54_N  1 LgkklnsalkklsgkskideedleealkeleeaLleaDVgvkvvkklienvkkkavgekk...lkpkqqvkkivkdeL 75
                                  L+++l+++++k++g++ id+ +++e+ k+l+++Ll+aDV+v++v +++++ +++a++ek    +  ++ ++ki+++eL
  gi|13541823|ref|NP_111511.1|  6 LSSSLRETIRKITGSTYIDKNTVKEISKDLQRILLKADVNVQTVLNITKEMERRALEEKPpvgMAHQDYMVKIIYEEL 83
                                  799************************************************998888555*9999************8 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.36
                                   HHHHHHHHTT--HHHHHHHHHHHHHHHHCTTS CS
                       SRP54_N  29 eleeaLleaDVgvkvvkklienvkkkavgekk 60 
                                    l   L+ aDV   ++ + ++++ +  v+  k
  gi|13541823|ref|NP_111511.1| 125 GLSAGLIAADVHRYAAYEQLQQIAE-SVN-AK 154
                                   677789*****98888887787766.777.33 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.43
                                   CCSSCGHHHHHHHHHHHHHHH CS
                       SRP54_N  13 sgkskideedleealkeleea 33 
                                   sg++++d +++ee ++ ++ea
  gi|13541823|ref|NP_111511.1| 186 SGRDSLDSDLIEE-IRRIKEA 205
                                   5678899999999.6666665 PP

  == domain 4  score: -3.8 bits;  conditional E-value: 8.9
                                   HHHHHHHHCT CS
                       SRP54_N  49 envkkkavge 58 
                                   e vk++ + e
  gi|13541823|ref|NP_111511.1| 299 ETVKEANITE 308
                                   3343333332 PP

  == domain 5  score: -2.1 bits;  conditional E-value: 2.7
                                   CGHHHHHHHHHHHHH CS
                       SRP54_N  17 kideedleealkele 31 
                                    + eed+  +lke +
  gi|13541823|ref|NP_111511.1| 405 GVREEDVRMLLKEFK 419
                                   466777766666654 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 ?    1.8   0.0     0.076   1.4e+02       4      24 ..      98     118 ..      96     140 .. 0.84
   2 !   11.3   0.0   9.3e-05      0.17      46      90 ..     175     222 ..     164     227 .. 0.84
   3 ?   -2.0   0.0       1.2   2.1e+03      50      88 ..     347     383 ..     313     386 .. 0.67

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.076
                                   -EEEEE-STTSSHHHHHHHHH CS
                         SRPRB   4 pavllvGlsdsGKTslftrLt 24 
                                   ++++lvGl   GKT+   +L+
  gi|13541823|ref|NP_111511.1|  98 QTIMLVGLYGHGKTTSAGKLS 118
                                   689***********9777776 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 9.3e-05
                                   .GGTT-SEEEETT-GCCSHHHHHHHHHHGG.EE..EEEEEEETTS-HH CS
                         SRPRB  46 ekgskltliDfPGheklrqklleklkakss.lk..glvfvvDStidpk 90 
                                    k+ ++++iD  G ++l ++l+e+++  ++ +k  +++ v+D+t+ ++
  gi|13541823|ref|NP_111511.1| 175 LKDAQVKIIDTSGRDSLDSDLIEEIRRIKEaVKpdQVLMVIDATMGQQ 222
                                   58999******************998766646544799****998775 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 1.2
                                   T-SEEEETT-GCCSHHHHHHHHHHGGEEEEEEEEETTS- CS
                         SRPRB  50 kltliDfPGheklrqklleklkaksslkglvfvvDStid 88 
                                   +l l+ +PG +k+  + + +  a+++l++   ++DS  +
  gi|13541823|ref|NP_111511.1| 347 SLPLAKLPGSQKINDDQILT--AEQKLQRYRIIMDSMTF 383
                                   55677789999998765544..45556666566777666 PP

>> DUF5499  Family of unknown function (DUF5499)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0     0.028        50      54      82 ..       4      32 ..       1      43 [. 0.81
   2 ?   -2.1   0.0       3.4   6.2e+03      21      37 ..      63      79 ..      59      88 .. 0.75
   3 ?    7.7   0.1     0.003       5.4      32      74 ..     167     209 ..     149     222 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.028
                       DUF5499 54 delnrqlrgevrklkksvyidddfdynts 82
                                  + l   lr  +rk+  s yid +   + s
  gi|13541823|ref|NP_111511.1|  4 ESLSSSLRETIRKITGSTYIDKNTVKEIS 32
                                  678899***************87665555 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3.4
                       DUF5499 21 rkapdgvshkdmvenif 37
                                   k p g++h+d + +i+
  gi|13541823|ref|NP_111511.1| 63 EKPPVGMAHQDYMVKII 79
                                  57899****99555443 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.003
                       DUF5499  32 mvenifrsdkwrrmkgidsevkdelnrqlrgevrklkksvyid 74 
                                   +++n +   k  ++k id+  +d l+ +l  e+r++k++v  d
  gi|13541823|ref|NP_111511.1| 167 IIKNGLEVLKDAQVKIIDTSGRDSLDSDLIEEIRRIKEAVKPD 209
                                   56666777788899************************99766 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       2.1   3.8e+03      94     113 ..      32      51 ..      18      71 .. 0.54
   2 ?   12.3   0.4   7.3e-05      0.13      42      93 ..     169     226 ..      99     242 .. 0.54

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 2.1
                                   HHHHHHHHHHTTSEEEEEEE CS
                      MMR_HSR1  94 deeleelleeakkplilvln 113
                                    ++l+++l +a+ ++  vln
  gi|13541823|ref|NP_111511.1|  32 SKDLQRILLKADVNVQTVLN 51 
                                   44444444443333333333 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 7.3e-05
                                   E.....ETTEEEEEEECGGCSSHHHHHHHHHHHHHHHHCT...SEEEEEEETT...TTCSHHH CS
                      MMR_HSR1  42 k.....lkgkeielvDtpGliegaseekglgkaflaleea...dlillvvdas...eeklkpl 93 
                                   k     lk+ +++++Dt G   ++s + +l +++++++ea   d +l+v+da+   +    p+
  gi|13541823|ref|NP_111511.1| 169 KnglevLKDAQVKIIDTSG---RDSLDSDLIEEIRRIKEAvkpDQVLMVIDATmgqQ--AGPE 226
                                   12333344678********...456666666666666652244********886531..3333 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   7.9e-05      0.14      24     142 ..      97     216 ..      79     228 .. 0.69
   2 ?   -3.2   0.0       5.4   9.7e+03      71      98 ..     330     357 ..     309     390 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 7.9e-05
                        AAA_16  24 pelvllsGesGvGKsslvrellralekdg..giflrgkcdqlesaipysalaqalareellrqlldeaesaeleawrekle 102
                                   p+ ++l+G  G GK++ + +l r + k+g  + +++++ +++   ++y +l q++ + ++ ++   +++++++    +  +
  gi|13541823|ref|NP_111511.1|  97 PQTIMLVGLYGHGKTTSAGKLSRFFMKKGlsAGLIAADVHRY---AAYEQLQQIA-E-SVNAKFYGDPKEKDPVKIIKNGL 172
                                   4899*******************9999962255588887777...7775555555.4.88888888877777777777777 PP

                        AAA_16 103 eala..avpelagaea....srllellkrllallsrderplvlvlD 142
                                   e+l+  +v+ ++ +++    s+l e+++r+ +  ++ ++ +++v+D
  gi|13541823|ref|NP_111511.1| 173 EVLKdaQVKIIDTSGRdsldSDLIEEIRRIKEAVKP-DQ-VLMVID 216
                                   777777444444444522335666665555555554.44.999999 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 5.4
                        AAA_16  71 alaqalareellrqlldeaesaeleawr 98 
                                    +++ ++r +l+++l d +  a+l+  +
  gi|13541823|ref|NP_111511.1| 330 DVWEKFSRPGLMKKLVDSLPLAKLPGSQ 357
                                   5677777777777777764444443333 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   7.7e-05      0.14       2      51 ..      97     146 ..      96     154 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7.7e-05
                                   -EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTTTTTTT--S CS
                    APS_kinase   2 gvvvwltGlsgsGKstianalekkLvekgisvylLdGdnvRhgLnkdLgf 51 
                                   + +++l Gl g GK+t a +l++  ++kg s+ l+  d+ R   +++L +
  gi|13541823|ref|NP_111511.1|  97 PQTIMLVGLYGHGKTTSAGKLSRFFMKKGLSAGLIAADVHRYAAYEQLQQ 146
                                   789*******************************9999999888777765 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 ?   10.9   0.0   0.00019      0.35       9      86 ..     107     246 ..     106     264 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00019
                                   TSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH................................... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................................... RF
                          CbiA   9 GvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep................................... 54 
                                   G GKTt a +L r + ++gl   l+ aD+ + ++       ++i++                                   
  gi|13541823|ref|NP_111511.1| 107 GHGKTTSAGKLSRFFMKKGLSAGLIAADVHRYAAY---EQLQQIAEsvnakfygdpkekdpvkiiknglevlkdaqvkiid 184
                                   78****************************87765...3333333356778888888888888777777777777777777 PP

                                   ...............................CCHCCCHHHHHHCHCHHHH.............EEEEEEEEESS CS
                                   ...............................xxxxxxxxxxxxxxxxxxx...........xxxxxxxxxxxxx RF
                          CbiA  55 ...............................dlkrllellealgkkkall...........lkiagvvlnrvdg 86 
                                                                  d+   ++           +           + + g+++++ dg
  gi|13541823|ref|NP_111511.1| 185 tsgrdsldsdlieeirrikeavkpdqvlmviDATM-GQ-----------QagpeskaindaVGVTGIIITKMDG 246
                                   77777776655555554444444444333332211.22...........0222222333335556666666665 PP

>> 6PF2K  6-phosphofructo-2-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   8.1e-05      0.15      10      59 ..      94     143 ..      89     188 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 8.1e-05
                                   ..S-EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHHHHHHSS CS
                         6PF2K  10 knsklvivlvGLpargKtyiskkltrylkwlgvrtkvFnvgkyrreaska 59 
                                   + ++  i+lvGL   gKt+ + kl+r+    g+++    +   r  a ++
  gi|13541823|ref|NP_111511.1|  94 ELKPQTIMLVGLYGHGKTTSAGKLSRFFMKKGLSAGLIAADVHRYAAYEQ 143
                                   566789*********************99888877665555555444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (455 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       875  (0.0488036); expected 358.6 (0.02)
Passed bias filter:                      621  (0.0346366); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.66u 0.29s 00:00:00.95 Elapsed: 00:00:00.48
# Mc/sec: 2821.58
//
Query:       gi|13541824|ref|NP_111512.1|  [L=396]
Description: geranylgeranyl reductase [Thermoplasma volcanium GSS1]
Scores for complete 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   55.2   0.6    3.5e-12   46.2   0.0    2.9  2  FAD_binding_3   FAD binding domain
    7.3e-12   45.4   1.4    1.6e-11   44.2   1.0    1.7  2  FAD_oxidored    FAD dependent oxidoreductase
    2.4e-11   43.4   0.1    5.7e-06   25.7   0.0    2.5  2  FAD_binding_2   FAD binding domain
    9.4e-10   37.9   0.0    7.2e-06   25.1   0.0    2.1  2  Trp_halogenase  Tryptophan halogenase
    2.7e-09   37.1   0.1    0.00016   21.4   0.0    2.3  2  DAO             FAD dependent oxidoreductase
    4.7e-08   32.6   0.5    1.4e-07   31.1   0.2    1.9  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    1.3e-06   28.6   0.1    4.1e-06   26.9   0.1    1.9  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    1.4e-05   24.5   0.1     0.0002   20.7   0.0    2.4  2  Thi4            Thi4 family
      3e-05   22.9   5.4    7.8e-05   21.6   0.0    3.2  4  HI0933_like     HI0933-like protein
    3.7e-05   23.0   1.1    7.6e-05   22.0   0.1    1.9  2  GIDA            Glucose inhibited division protein A
    0.00046   19.4   0.1      0.037   13.1   0.1    2.4  2  Lycopene_cycl   Lycopene cyclase protein
      0.008   16.7   0.5      0.059   13.9   0.0    2.7  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
  ------ inclusion threshold ------
      0.031   13.5   0.1       0.13   11.5   0.1    1.9  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
      0.049   12.9   0.1       0.13   11.5   0.0    1.8  2  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
      0.085   12.1   0.6       0.48    9.6   0.0    2.1  2  Hydantoinase_A  Hydantoinase/oxoprolinase
       0.12   11.4   0.2       0.24   10.4   0.2    1.5  1  SE              Squalene epoxidase
       0.24   11.9   1.9         17    5.9   0.0    3.5  3  NAD_binding_7   Putative NAD(P)-binding


Domain annotation for each model (and alignments):
>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.2   0.0   3.3e-15   3.5e-12       2     179 ..       4     175 ..       3     234 .. 0.79
   2 ?    5.2   0.1      0.01        11     286     309 ..     278     301 ..     261     314 .. 0.86

  Alignments for each domain:
  == domain 1  score: 46.2 bits;  conditional E-value: 3.3e-15
                                   EEEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSSS.--EEEHHHHHHHHHTT-HHHHHHHSEECCCCEEEEEEECC CS
                 FAD_binding_3   2 tdVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlpr.adglnqrtmellrqlGledrilaegapnelmgealynels 81 
                                   +dVl++G+Gp G ++a+  +++G r++++ekr +     r ++gl++    +l+++ ++      +  ne+ g   y++  
  gi|13541824|ref|NP_111512.1|   4 YDVLVIGGGPGGSTAARYAAKYGLRTLMIEKRPEIGSPVRcGEGLSKG---ILNEADIKPDKSFIA--NEVKGARIYGP-- 77 
                                   79******************************9988777735677665...778888877766666..77788888888.. PP

                                   CCCEEEEEHH.CHHCST-CEE--HHHHHHHHHHHHHHHTEEETCSEEEECCEECCCCCCCEEEECCTTEEEEEEEEEEEE- CS
                 FAD_binding_3  82 dtpkaradle.lesspervtvypqteleriLvehaeerglqvrfktevesleqdeegvtaevrdketgeeetvrakYlvGa 161
                                     +k+++ l+ ++++ e   v+  +++++ L++ a+++g++v  k   +++ +++ +v+     +e++   +vrak +++a
  gi|13541824|ref|NP_111512.1|  78 -SEKRPIILQsEKAGNEVGFVLERDKFDKHLAALAAKAGADVWVKSPALGVIKEDGKVAGAKIRHENNVV-EVRAKMVIAA 156
                                   .456666666346888888999*************************99999998888876666666666.8********* PP

                                   -GTT-HHHHHHTGG.EEEE CS
                 FAD_binding_3 162 DGgrStvrktlgie.fege 179
                                   DG+ S   + +g++ ++  
  gi|13541824|ref|NP_111512.1| 157 DGFESEFGRWAGLKsVILA 175
                                   ******9999999864444 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.01
                                   EEE-GGGTEEE-STTSHHHHHHHH CS
                 FAD_binding_3 286 vflaGDAaHihpPtgGqGlNtaiq 309
                                   ++l+GDAa    P +G G+  ai 
  gi|13541824|ref|NP_111512.1| 278 LMLVGDAARLIDPITGGGIANAIV 301
                                   79****************977775 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.2   1.0   1.5e-14   1.6e-11       1     142 [.       5     156 ..       5     173 .. 0.73
   2 ?   -3.2   0.0       3.8     4e+03      81      81 ..     321     321 ..     262     377 .. 0.48

  Alignments for each domain:
  == domain 1  score: 44.2 bits;  conditional E-value: 1.5e-14
                  FAD_oxidored   1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlG.......Glltsglvatdignkaeeqvvtgiar.eflerlrqrgga 73 
                                   Dv+V+GGgp+G +AA  Aa+ G ++l++e+r+ +G       Gl+ + l  +di++ + +++++ + + +++   ++ +  
  gi|13541824|ref|NP_111512.1|   5 DVLVIGGGPGGSTAARYAAKYGLRTLMIEKRPEIGspvrcgeGLSKGILNEADIKPDK-SFIANEVKGaRIYGPSEK-RPI 83 
                                   9*********************************966666444444444445555442.223333332033333322.222 PP

                  FAD_oxidored  74 ..rlkkrskwn...tfepevakavleemlaeagvtvllntrlvevekegkriesvtveskegrktirAkvfiDA 142
                                     + +k+ + +   + e + + + l ++ a+ag +v+ ++ + +v+ke++++ + +++++++  ++rAk++i A
  gi|13541824|ref|NP_111512.1|  84 ilQSEKAGN-EvgfVLERDKFDKHLAALAAKAGADVWVKSPALGVIKEDGKVAGAKIRHENNVVEVRAKMVIAA 156
                                   332222222.13559*********************************99*******87668*********977 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 3.8
                  FAD_oxidored  81 w 81 
                                   +
  gi|13541824|ref|NP_111512.1| 321 P 321
                                   1 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.0   5.4e-09   5.7e-06       1      52 [.       5      56 ..       5      67 .. 0.88
   2 !   15.1   0.0   8.6e-06    0.0091     148     200 ..     108     158 ..     101     177 .. 0.85

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 5.4e-09
                                  SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGGG--S-EE-TT..S CS
                 FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefggatawsqGgidavlspe 52
                                  Dv+ViG+G +G +AA  aa+ Gl+++++ek +e g+   + +G    +l++ 
  gi|13541824|ref|NP_111512.1|  5 DVLVIGGGPGGSTAARYAAKYGLRTLMIEKRPEIGSPVRCGEGLSKGILNEA 56
                                  9**********************************99999888877777554 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 8.6e-06
                                   HHHHHTCTEEEEESEEEEEEEECTTEEEEEEEEETTTTCEEEEEESEEEE--- CS
                 FAD_binding_2 148 vesarkagvdfqerteadeLivedgrvtGavvenpesgrevrirakavvlatg 200
                                   ++ a kag d++ + +a+ +i edg+v Ga ++  ++ + v++rak v+ a g
  gi|13541824|ref|NP_111512.1| 108 AALAAKAGADVWVKSPALGVIKEDGKVAGAKIR--HENNVVEVRAKMVIAADG 158
                                   44456679*************************..99999**99*99987765 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.1   0.00014      0.14       1      44 [.       5      47 ..       5      57 .. 0.83
   2 !   25.1   0.0   6.8e-09   7.2e-06     142     373 ..      89     337 ..      61     346 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00014
                                  EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-.SSS-.--SS-EE CS
                Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlves.eeig.tvgvGea 44
                                  +++++GGG+ G++aA + ak++   l+ +++e+ +eig +v+ Ge+
  gi|13541824|ref|NP_111512.1|  5 DVLVIGGGPGGSTAARYAAKYG---LRTLMIEKrPEIGsPVRCGEG 47
                                  699******************9...888888864688734677776 PP

  == domain 2  score: 25.1 bits;  conditional E-value: 6.8e-09
                                   -B-S--EEEE-HHHHHHHHHHHHHHCT-EEEE--EEEEEE-TTS-EEEEEETTS-...EEE-SEEEE-SGGG-IIIIII.T CS
                Trp_halogenase 142 lsalsyAyhldaalyakfLrrvaearGvtrvegkvvevqldedgrveslrledgr...eveadlfiDcsGfrgllieqa.L 218
                                    ++ + ++ l++ +++k+L + a ++G ++     +  +++edg+v++ ++  ++   ev a ++i + Gf++     a L
  gi|13541824|ref|NP_111512.1|  89 KAGNEVGFVLERDKFDKHLAALAAKAGADVWVKSPALGVIKEDGKVAGAKIRHENnvvEVRAKMVIAADGFESEFGRWAgL 169
                                   456678899*************************************99888775522257899**********99876559 PP

                                   ---EEE-TTT----EEEEEEEE--H---SSEE....EEE-SSEEEEEEEETTEEEE.EEEE-TTTS.-HHHHHHHHHHHCT CS
                Trp_halogenase 219 ktgfedwsdvLltdrAlavqveseelvepytr....ataekaGWtWkiPLqhrlgn.Gyvyssaha.dddeAlaellaeld 293
                                   k+ +    d++   +Al   + + ++   yt+    ++a   G +W  P  + + n G+  s +++ ++ e  + l + ++
  gi|13541824|ref|NP_111512.1| 170 KSVILARNDII---SALQYRMINIDVDPDYTDfylgSIA-PGGYIWVFPKGEGMANvGIGSSINFIhNRLELKNYLDRFIE 246
                                   99999999999...9999999999977778888875666.79**************9*99999999544555556666677 PP

                                   --TTTS-.EEEE---EE......ES-SEETTEEE-CCCTEE--CCCS-HHHHHHH....HHHHHHHT--BTT--HHHHHHH CS
                Trp_halogenase 294 gkleaep.rkirfttGr......rkqawvknvvalGlasgfvePlestsihliqa....alrrLlallpdksdepaaiaef 363
                                    ++  ++ + i++ tG       +  +  ++++++G+a+  ++P+ + +i+ + +    a++   + + ++ ++p  + ++
  gi|13541824|ref|NP_111512.1| 247 NHPGLKKgQDIQLVTGGvsvskvKMPITMPGLMLVGDAARLIDPITGGGIANAIVsgmyAAQVSKEAIESNDYSPQMMGKY 327
                                   7777777899******98888877788899********************9887666667888888899999999999999 PP

                                   HHHHHHHHHH CS
                Trp_halogenase 364 nrevareler 373
                                   ++ v+  +er
  gi|13541824|ref|NP_111512.1| 328 EKLVKDRFER 337
                                   9998888775 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   1.5e-07   0.00016       1      33 [.       5      39 ..       5      63 .. 0.91
   2 !   13.6   0.0   3.5e-05     0.037     143     227 ..      98     190 ..      80     251 .. 0.69

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.5e-07
                                  EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTT CS
                           DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiag 33
                                  dv++iGGG  G+++A+++a+ g  ++ +ek++++g
  gi|13541824|ref|NP_111512.1|  5 DVLVIGGGPGGSTAARYAAKYGlrTLMIEKRPEIG 39
                                  8******************************9988 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 3.5e-05
                                   EEHHHHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEE.EECTEEEEEEEE..EEE--GGGHH..HHHTT..CTT..T CS
                           DAO 143 vdpakltaalaraaealGveilegtevtgleeedgkvwgve.rttpgendaada..vVnaaGawsd..llgll..kel..d 214
                                   ++  k+ + la+ a+++G+++  ++++ g+ +edgkv+g + r++++  ++++a  v+ a G  s    +++l   +l  +
  gi|13541824|ref|NP_111512.1|  98 LERDKFDKHLAALAAKAGADVWVKSPALGVIKEDGKVAGAKiRHENNV-VEVRAkmVIAADGFESEfgRWAGLksVILarN 177
                                   467789999********************98899******88444332.35677757777776665333322222333421 PP

                                   SEEEEEEEEEEEE CS
                           DAO 215 lpispvrgqvlvl 227
                                     is+++  ++ +
  gi|13541824|ref|NP_111512.1| 178 DIISALQYRMINI 190
                                   2335555555444 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 !   31.1   0.2   1.3e-10   1.4e-07       1     110 [.       4     160 ..       4     181 .. 0.70
   2 ?   -1.3   0.0      0.97     1e+03     254     279 ..     261     291 ..     246     306 .. 0.67

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 1.3e-10
                                   CSEEEE--SHHHHHHHHHHHHHTS-EEEEE...TTHCHHHCSHHHHCHHHHHHHHHHHHH..................... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxx..................... RF
                   Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaqagakvtlve...legtclnggcllskallgvaedaeias..................... 57 
                                   +dv+viGgGp+G +aa+++a++g++++++e   + g  +  g  lsk +l+ a+ +   s                     
  gi|13541824|ref|NP_111512.1|   4 YDVLVIGGGPGGSTAARYAAKYGLRTLMIEkrpEIGSPVRCGEGLSKGILNEADIKPDKSfianevkgariygpsekrpii 84 
                                   69***************************9754333333444456999999999988777899999999999999999999 PP

                                   ..........................HHHHCHHHHCCCCHCCTCEEEEESCEEEEETEEEC.TCEEEEEESEEEE---EE CS
                                   ..........................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2  58 ..........................evvkklnqgielllgeevvkidpgkkkvklekkke.gdeekiaydklvlAtGss 110
                                                                   ++g ++  ++++++++++ +kv   k +  ++  ++ ++ ++ A G++
  gi|13541824|ref|NP_111512.1|  85 lqsekagnevgfvlerdkfdkhlaalA----AKAGADVWVKSPALGVIKEDGKVAGAKIRHeNNVVEVRAKMVIAADGFE 160
                                   777777777777765544443322110....1223444444667777777777766655534666667777777777765 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.97
                                   ETTEEE--TTSBESSTTEEE-GGGC.....T CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxx.....x RF
                   Pyr_redox_2 254 erggivvdeflrtnvpgiyaiGDva.....g 279
                                    +g  v + ++  ++pg+ ++GD a      
  gi|13541824|ref|NP_111512.1| 261 TGGVSVSKVKMPITMPGLMLVGDAArlidpI 291
                                   355556677788899********99554443 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 !   26.9   0.1   3.9e-09   4.1e-06       1      32 [.       8      39 ..       8      57 .. 0.92

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 3.9e-09
                                  EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSS CS
                 NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlG 32
                                  ++G+G +G++aA+++ak+g++ l +ekr+ +G
  gi|13541824|ref|NP_111512.1|  8 VIGGGPGGSTAARYAAKYGLRTLMIEKRPEIG 39
                                  8******************************9 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   1.9e-07    0.0002      18      60 ..       4      45 ..       1      64 [. 0.86
   2 ?    0.9   0.0      0.22   2.3e+02     156     182 ..     147     173 ..     111     189 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 1.9e-07
                                  EEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTTTT CS
                          Thi4 18 sDvvivGaGssGLtaayylakkpdlkvailersvspGGGawlG 60
                                   Dv+++G+G+ G taa+y ak  +l+++++e++  +G  +  G
  gi|13541824|ref|NP_111512.1|  4 YDVLVIGGGPGGSTAARYAAKY-GLRTLMIEKRPEIGSPVRCG 45
                                  69*******************9.*********99888766555 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.22
                                   EEEEEEEEE--GSSSTTTTHHHHHHHH CS
                          Thi4 156 virakvvvdatGhdgeivavvvkkikl 182
                                    +rak+v+ a G ++e++  +  k + 
  gi|13541824|ref|NP_111512.1| 147 EVRAKMVIAADGFESEFGRWAGLKSVI 173
                                   47999************9877666554 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   7.4e-08   7.8e-05       1      40 [.       4      43 ..       4      70 .. 0.91
   2 ?   -2.3   0.0       1.3   1.4e+03      46      70 ..     227     251 ..     221     254 .. 0.83
   3 ?    0.9   0.2      0.14   1.5e+02     355     408 ..     259     308 ..     232     309 .. 0.76
   4 ?    0.6   0.1      0.16   1.7e+02     298     353 ..     328     380 ..     310     384 .. 0.70

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 7.4e-08
                                  -SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-HHHH CS
                   HI0933_like  1 kdviviGgGaAGlmaAisaakrgkrVlllekakklgrKil 40
                                  +dv+viGgG+ G  aA  aak g r+l++ek +++g+ ++
  gi|13541824|ref|NP_111512.1|  4 YDVLVIGGGPGGSTAARYAAKYGLRTLMIEKRPEIGSPVR 43
                                  59*********************************98776 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.3
                                   T-EEEETT-SGGGEEES...STTTT CS
                   HI0933_like  46 rcNvTnlseepeellsrypenpkfl 70 
                                    +N+ +++ e++++l+r+ en+  l
  gi|13541824|ref|NP_111512.1| 227 SINFIHNRLELKNYLDRFIENHPGL 251
                                   58999*9**********99998655 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.14
                                   EEEEEE-GGGB-TTT-BBTTSTTEEE-GGGBS.EEE-TTTHHHHHHHHHHHHHHH CS
                   HI0933_like 355 vTaGGVdlkevssktmeskkvpgLffaGEvlD.vegvtGGynlqaAwasgyaAGk 408
                                      GGV++++v+       ++pgL ++G     ++  tGG  + +A +sg+ A++
  gi|13541824|ref|NP_111512.1| 259 LVTGGVSVSKVKMPI----TMPGLMLVGDAARlIDPITGG-GIANAIVSGMYAAQ 308
                                   557999999997543....46*******988735667777.89999999999987 PP

  == domain 4  score: 0.6 bits;  conditional E-value: 0.16
                                   TTTS-HHHHHHHHHC..TTT-TTBGGG--HHHHHHHHHHHHSEEE--SEE--TTT- CS
                   HI0933_like 298 aellpkrlvevlleealieeedkklaqlskkelkklaealkaltvkvngteglrka 353
                                   ++l++ r+ +  l +   + +++klaqls+++l+kl++ + +  ++    e + ka
  gi|13541824|ref|NP_111512.1| 328 EKLVKDRFERKHLRN---WVAKEKLAQLSDETLDKLVDIVSEQVLTTISVEAILKA 380
                                   455555555555555...34577899999999999999998877777666666665 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.1   7.2e-08   7.6e-05       1      37 [.       5      40 ..       5     168 .. 0.76
   2 ?   -0.9   0.1      0.61   6.5e+02     218     272 ..     335     388 ..     297     391 .. 0.68

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 7.2e-08
                                  CEEEE-SSHHHHHHHHHHHHTT--EEEEES-GGGTT- CS
                          GIDA  1 dviViGgGhAGceAAlaaarlGakvlLithkldtiae 37
                                  dv ViGgG  G+ AA  aa+ G+++l+i +k  +i++
  gi|13541824|ref|NP_111512.1|  5 DVLVIGGGPGGSTAARYAAKYGLRTLMI-EKRPEIGS 40
                                  79*************************9.44444444 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.61
                                   B-SSSSSSSTCG----EEEEE--HHHHHHHHCTCCC-T.T----B--S-CCC-SS CS
                          GIDA 218 eefsylnkplnkeqvecfltatneathkiikenlkksaklfegcieelgprycps 272
                                    e ++l + + ke++ +  ++t ++  +i+ e++ +++  +e  ++ ++++y + 
  gi|13541824|ref|NP_111512.1| 335 FERKHLRNWVAKEKLAQLSDETLDKLVDIVSEQVLTTI-SVEAILKAIAEKYPEV 388
                                   33445555557888888888888888888888888877.7888888888888765 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.1   3.5e-05     0.037       1     144 [.       5     161 ..       5     173 .. 0.62
   2 ?    3.8   0.0     0.023        24     256     298 ..     276     320 ..     261     362 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.5e-05
                 Lycopene_cycl   1 DvvviGaGpAglslAarlteakpglkvvlieaspsl...lfpnny..vWsdefedlgaleecvehsWsgtivylddgkk.i 75 
                                   Dv+viG+Gp g   Aar  +ak+gl+ ++ie  p++   ++ ++        ++d++  ++++    +g+++y + +k+ i
  gi|13541824|ref|NP_111512.1|   5 DVLVIGGGPGGST-AARY-AAKYGLRTLMIEKRPEIgspVRCGEGlsKGILNEADIKPDKSFIANEVKGARIYGPSEKRpI 83 
                                   9********9966.5555.5***********99987111333333222344455555577788888888888877655413 PP

                 Lycopene_cycl  76 llg.....raYg.rvsskrlkeellerlvengvk.lleakvesveeeea..geslvvleggr.kirarlvvdarglasl 144
                                    l+      + g  ++++++ ++l+   +++g+   +++ +  v +e+   +   +  e+++ ++ra++v+ a g +++
  gi|13541824|ref|NP_111512.1|  84 ILQsekagNEVGfVLERDKFDKHLAALAAKAGADvWVKSPALGVIKEDGkvAGAKIRHENNVvEVRAKMVIAADG-FES 161
                                   333454442222134778888888777775555415677776666555434566666666667788888888887.555 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.023
                 Lycopene_cycl 256 qkvlaiGaaaglvhPaTGYsvarslaeapllasaiaaalres...s 298
                                   +  + +G aa l+ P TG  +a+++     +a+ +++ + es   s
  gi|13541824|ref|NP_111512.1| 276 PGLMLVGDAARLIDPITGGGIANAIVSGM-YAAQVSKEAIESndyS 320
                                   556789*****************997665.9999999888764331 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   5.6e-05     0.059       2      35 ..       6      39 ..       5      56 .. 0.89
   2 ?   -1.8   0.0       4.4   4.7e+03      21      42 ..     224     245 ..     219     248 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.6e-05
                                  EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
                     Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkll 35
                                  v+v+GgG  g  +A ++a++g ++ ++e ++++ 
  gi|13541824|ref|NP_111512.1|  6 VLVIGGGPGGSTAARYAAKYGLRTLMIEKRPEIG 39
                                  89*****************************998 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 4.4
                                   TTSEEEEEESSSSSSTTSSHHH CS
                     Pyr_redox  21 lgkkVtvversdkllrllDeea 42 
                                   +g+++  ++++ +l ++lD+ +
  gi|13541824|ref|NP_111512.1| 224 IGSSINFIHNRLELKNYLDRFI 245
                                   8999999***999999999765 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 ?   11.5   0.1   0.00012      0.13       1      33 [.       7      39 ..       7      43 .. 0.88
   2 ?   -1.3   0.0      0.98     1e+03     245     271 ..     137     163 ..     103     179 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00012
                   Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkg.nig 33
                                  ++iG+GP G +aa  + k gl + l +Ek  +ig
  gi|13541824|ref|NP_111512.1|  7 LVIGGGPGGSTAARYAAKYGL-RTLMIEKRpEIG 39
                                  69*******************.689***986666 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.98
                   Pyr_redox_3 245 ykvktedgkkvevkddvvla.tGykpdl 271
                                    k+++e+ + vev+ ++v+a  G+++++
  gi|13541824|ref|NP_111512.1| 137 AKIRHEN-NVVEVRAKMVIAaDGFESEF 163
                                   3555555.56666555555547888776 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00012      0.13      30      63 ..       5      38 ..       1      74 [. 0.87
   2 ?   -2.0   0.0       1.7   1.8e+03      34      69 ..     292     329 ..     268     375 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00012
                                  EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHH CS
                   AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVtvlDvrpar 63
                                   vlviGgG  G  A++ a++ g ++ ++++rp+ 
  gi|13541824|ref|NP_111512.1|  5 DVLVIGGGPGGSTAARYAAKYGLRTLMIEKRPEI 38
                                  69***************************99986 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.7
                                   ESTSHH.....HHHHHHHHHHTT-EEEEEESSHHHHHHHHH CS
                   AlaDh_PNT_C  34 iGgGva.....GlqAiatakglgakVtvlDvrparleqles 69 
                                    GgG+a     G+ A++++k     ++  D +p+ + + e+
  gi|13541824|ref|NP_111512.1| 292 TGGGIAnaivsGMYAAQVSK---EAIESNDYSPQMMGKYEK 329
                                   56665422222444444433...334444444444444444 PP

>> Hydantoinase_A  Hydantoinase/oxoprolinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00045      0.48     244     280 ..       6      42 ..       2      48 .. 0.90
   2 ?    0.0   0.1      0.38     4e+02     187     231 ..     337     383 ..     327     392 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00045
                Hydantoinase_A 244 tlvvfGGaGaqhaaalaeelgvkkvivppyagvlsal 280
                                   +lv+ GG+G++ aa++a+++g+++ ++++ +++ s +
  gi|13541824|ref|NP_111512.1|   6 VLVIGGGPGGSTAARYAAKYGLRTLMIEKRPEIGSPV 42 
                                   6899*************************99987765 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.38
                Hydantoinase_A 187 dqkldvelarrafeelakelnlk.veevAegils.vavenmanavrk 231
                                   + +l++  a++++++l++e  +k v+ v+e++l+ + ve + +a+ +
  gi|13541824|ref|NP_111512.1| 337 RKHLRNWVAKEKLAQLSDETLDKlVDIVSEQVLTtISVEAILKAIAE 383
                                   66788888999999999998888677778887752456677777654 PP

>> SE  Squalene epoxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.2   0.00023      0.24     128     154 ..     274     300 ..     265     346 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00023
                            SE 128 ekkGlillGDalnmRHPltggGmtval 154
                                   +  Gl+l+GDa  +  P+tggG++ a+
  gi|13541824|ref|NP_111512.1| 274 TMPGLMLVGDAARLIDPITGGGIANAI 300
                                   568*******************98766 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0     0.016        17       7      39 ..       3      35 ..       1      75 [. 0.80
   2 ?    1.6   0.1      0.36   3.8e+02      27      69 ..     112     157 ..     105     203 .. 0.51
   3 ?    1.7   0.1      0.33   3.4e+02      18      60 ..     344     390 ..     326     396 .] 0.78

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.016
                 NAD_binding_7  7 gkkvlvvGgGevAarkvrklleagakvtvvape 39
                                  +  vlv+GgG+ + + +r  +++g +  ++ ++
  gi|13541824|ref|NP_111512.1|  3 TYDVLVIGGGPGGSTAARYAAKYGLRTLMIEKR 35
                                  5679******************99998888776 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.36
                 NAD_binding_7  27 leagakvtvvapevkeeleelvklaeeel..ekdle..gadlviaat 69 
                                   ++aga+v v +p++   ++e  k+a  ++  e+++   +a++viaa 
  gi|13541824|ref|NP_111512.1| 112 AKAGADVWVKSPAL-GVIKEDGKVAGAKIrhENNVVevRAKMVIAAD 157
                                   56778888877775.22232222322222112222211233444443 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.33
                 NAD_binding_7  18 vAarkvrklleag..akvtvvapev..keeleelvklaeeelekdle 60 
                                   vA +k+ +l ++   + v +v+++v  +  +e ++k++ e++++ ++
  gi|13541824|ref|NP_111512.1| 344 VAKEKLAQLSDETldKLVDIVSEQVltTISVEAILKAIAEKYPEVVK 390
                                   89999999999884456899999997655666777777777766554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       814  (0.0454013); expected 358.6 (0.02)
Passed bias filter:                      692  (0.0385967); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.74u 0.31s 00:00:01.05 Elapsed: 00:00:00.51
# Mc/sec: 2325.94
//
Query:       gi|13541825|ref|NP_111513.1|  [L=70]
Description: ferredoxin subunit of tungsten formylmethanofuran dehydrogenase [Thermoplasma volcanium GSS1]
Scores for complete sequence (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   59.8  15.6    1.2e-08   34.4   2.9    2.1  2  Fer4      4Fe-4S binding domain
    8.4e-13   48.7  35.0      4e-07   30.5  13.5    2.0  3  Fer4_7    4Fe-4S dicluster domain
    2.3e-10   40.1  14.6    2.6e-06   27.3   3.3    2.1  2  Fer4_6    4Fe-4S binding domain
    5.8e-10   39.2  20.6    3.1e-07   30.5  11.3    1.9  2  Fer4_9    4Fe-4S dicluster domain
    5.5e-09   36.8   8.9    0.00015   22.7   0.6    2.1  2  Fer4_16   4Fe-4S double cluster binding domain
    1.3e-08   34.5  11.7    9.3e-05   22.3   1.6    2.3  2  Fer4_2    4Fe-4S binding domain
    3.6e-08   33.4  21.1    8.1e-06   25.9  11.8    2.0  2  Fer4_10   4Fe-4S dicluster domain
    4.4e-08   33.1  11.1    7.2e-05   22.8   2.4    1.9  2  Fer4_21   4Fe-4S dicluster domain
    1.1e-06   29.0   6.5     0.0049   17.3   0.9    2.1  2  Fer4_8    4Fe-4S dicluster domain
    8.6e-05   22.7  13.7     0.0041   17.5   3.5    2.2  2  Fer4_4    4Fe-4S binding domain
    0.00037   21.0  11.2      0.078   13.5   1.6    2.1  3  Fer4_17   4Fe-4S dicluster domain
     0.0019   18.3   2.1     0.0021   18.1   2.1    1.1  1  Fer4_11   4Fe-4S dicluster domain
      0.002   18.9  18.6       0.17   12.9   6.3    2.2  2  Fer4_3    4Fe-4S binding domain
     0.0067   16.6  10.6       0.14   12.4   2.0    2.0  2  Fer4_18   4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.019   15.5  14.1       0.17   12.5   2.4    2.8  3  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
      0.046   14.5  13.4       0.15   12.8   2.9    2.9  2  Fer4_15   4Fe-4S single cluster domain
       0.26   11.4   3.4       0.34   11.1   3.4    1.3  1  ETF_QO    Electron transfer flavoprotein-ubiquinone oxidoredu
       0.41   11.5  13.5        3.6    8.5   3.6    2.1  3  Fer4_22   4Fe-4S dicluster domain
       0.49   10.1   9.4       0.89    9.3   1.2    2.1  2  MTHFR_C   Methylene-tetrahydrofolate reductase C terminal


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.4   2.9   1.2e-11   1.2e-08       3      23 ..      12      32 ..      10      33 .. 0.93
   2 !   31.5   5.0     1e-10   9.6e-08       1      23 [.      39      61 ..      39      62 .. 0.95

  Alignments for each domain:
  == domain 1  score: 34.4 bits;  conditional E-value: 1.2e-11
                                  EETTTSSS-THHHHHSTTTEE CS
                          Fer4  3 ideekCigCGaCvevCPvgAI 23
                                  +d ++C +CGaCv +CP++AI
  gi|13541825|ref|NP_111513.1| 12 VDRNLCNYCGACVGMCPTDAI 32
                                  8*******************9 PP

  == domain 2  score: 31.5 bits;  conditional E-value: 1e-10
                                  EEEETTTSSS-THHHHHSTTTEE CS
                          Fer4  1 vvideekCigCGaCvevCPvgAI 23
                                  ++i+eekCi CG C+  CP+gAI
  gi|13541825|ref|NP_111513.1| 39 IKIHEEKCIECGFCIVGCPTGAI 61
                                  689*******************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 !   19.7   3.2     1e-06   0.00095      29      52 .]       8      31 ..       2      31 .. 0.85
   2 !   30.5  13.5   4.3e-10     4e-07       2      52 .]      17      60 ..      16      60 .. 0.96
   3 !   20.8   2.7   4.7e-07   0.00045       1      19 [.      45      63 ..      45      68 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1e-06
                        Fer4_7 29 ekveidpekClgCgaCvavCPtga 52
                                   ++++d + C +CgaCv  CPt+a
  gi|13541825|ref|NP_111513.1|  8 TEMDVDRNLCNYCGACVGMCPTDA 31
                                  567888889*************97 PP

  == domain 2  score: 30.5 bits;  conditional E-value: 4.3e-10
                        Fer4_7  2 CigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52
                                  C  CgaCv +Cp++ai lde         ++i++ekC+ Cg C+  CPtga
  gi|13541825|ref|NP_111513.1| 17 CNYCGACVGMCPTDAIWLDET-------VIKIHEEKCIECGFCIVGCPTGA 60
                                  99****************997.......69*******************98 PP

  == domain 3  score: 20.8 bits;  conditional E-value: 4.7e-07
                        Fer4_7  1 rCigCgaCvaaCpvkaiel 19
                                  +Ci+Cg+C + Cp++ai+ 
  gi|13541825|ref|NP_111513.1| 45 KCIECGFCIVGCPTGAINA 63
                                  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 !   18.9   3.6   1.2e-06    0.0011       4      24 .]      12      32 ..       9      32 .. 0.95
   2 !   27.3   3.3   2.8e-09   2.6e-06       1      24 []      38      61 ..      38      61 .. 0.95

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.2e-06
                        Fer4_6  4 idpdkCigCgdCvrvCPegai 24
                                  +d+++C+ Cg+Cv  CP++ai
  gi|13541825|ref|NP_111513.1| 12 VDRNLCNYCGACVGMCPTDAI 32
                                  8******************98 PP

  == domain 2  score: 27.3 bits;  conditional E-value: 2.8e-09
                        Fer4_6  1 vveidpdkCigCgdCvrvCPegai 24
                                  v+ i ++kCi Cg C++ CP+gai
  gi|13541825|ref|NP_111513.1| 38 VIKIHEEKCIECGFCIVGCPTGAI 61
                                  6899*******************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 !   19.6   1.8   8.1e-07   0.00077      23      51 .]       7      32 ..       1      32 [. 0.71
   2 !   30.5  11.3   3.3e-10   3.1e-07       2      51 .]      17      61 ..      16      61 .. 0.93

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 8.1e-07
                        Fer4_9 23 erkarlraaseeaCigCgaCveaCpkgai 51
                                  ++++ +++   + C  CgaCv  Cp++ai
  gi|13541825|ref|NP_111513.1|  7 KTEMDVDR---NLCNYCGACVGMCPTDAI 32
                                  34444433...48*************997 PP

  == domain 2  score: 30.5 bits;  conditional E-value: 3.3e-10
                        Fer4_9  2 CtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51
                                  C+ CgaCv +Cp++++  d+   k+  +     +Ci+Cg C+  Cp+gai
  gi|13541825|ref|NP_111513.1| 17 CNYCGACVGMCPTDAIWLDETVIKIHEE-----KCIECGFCIVGCPTGAI 61
                                  ******************9999999874.....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 !   22.7   0.6   1.5e-07   0.00015       2      29 ..      17      43 ..      16      45 .. 0.87
   2 !   18.8   2.3   2.6e-06    0.0024       1      20 [.      45      64 ..      45      67 .. 0.92

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 1.5e-07
                       Fer4_16  2 CgtCgkCaevCPtnaikekkekeieare 29
                                  C  Cg+C+ +CPt+ai  + e++i+++e
  gi|13541825|ref|NP_111513.1| 17 CNYCGACVGMCPTDAIWLD-ETVIKIHE 43
                                  ****************999.78888776 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 2.6e-06
                       Fer4_16  1 rCgtCgkCaevCPtnaikek 20
                                  +C++Cg C+  CPt+ai+++
  gi|13541825|ref|NP_111513.1| 45 KCIECGFCIVGCPTGAINAE 64
                                  6****************976 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   2.9   3.6e-06    0.0034       5      22 .]      12      29 ..       9      29 .. 0.93
   2 !   22.3   1.6   9.9e-08   9.3e-05       3      22 .]      39      58 ..      37      58 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3.6e-06
                        Fer4_2  5 vdtdrCigCgaCvsaCPa 22
                                  vd++ C+ CgaCv  CP+
  gi|13541825|ref|NP_111513.1| 12 VDRNLCNYCGACVGMCPT 29
                                  899**************7 PP

  == domain 2  score: 22.3 bits;  conditional E-value: 9.9e-08
                        Fer4_2  3 vvvdtdrCigCgaCvsaCPa 22
                                  +++ +++Ci+Cg C+  CP+
  gi|13541825|ref|NP_111513.1| 39 IKIHEEKCIECGFCIVGCPT 58
                                  78899*********999**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 !   25.9  11.8   8.6e-09   8.1e-06       4      56 .]      12      57 ..       9      57 .. 0.83
   2 !   18.4   1.8   1.8e-06    0.0017       2      27 ..      39      59 ..      38      68 .. 0.83

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 8.6e-09
                       Fer4_10  4 idddtCirCgkCvkaCPadltsvgakgeaseee.avrkkvekCtgcgaCveaCP 56
                                  +d++ C  Cg+Cv +CP+        ++++ +e ++++  ekC++cg C+  CP
  gi|13541825|ref|NP_111513.1| 12 VDRNLCNYCGACVGMCPT--------DAIWLDEtVIKIHEEKCIECGFCIVGCP 57
                                  78999*************........55555550555599*************9 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 1.8e-06
                       Fer4_10  2 vvidddtCirCgkCvkaCPadltsvg 27
                                  ++i +++Ci+Cg C   CP+     g
  gi|13541825|ref|NP_111513.1| 39 IKIHEEKCIECGFCIVGCPT-----G 59
                                  57899**************9.....3 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   1.5   1.4e-05     0.013      27      57 ..       3      32 ..       1      34 [. 0.84
   2 !   22.8   2.4   7.6e-08   7.2e-05       2      25 ..      40      63 ..      39      68 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.4e-05
                       Fer4_21 27 eidaktvlkvvedeCvGCnlCssvCPvedci 57
                                  e++ kt + v  + C  C  C+ +CP+ d+i
  gi|13541825|ref|NP_111513.1|  3 ELKVKTEMDVDRNLCNYCGACVGMCPT-DAI 32
                                  5667888999999*************6.877 PP

  == domain 2  score: 22.8 bits;  conditional E-value: 7.6e-08
                       Fer4_21  2 ridedkCigCgkCliaCedtshqa 25
                                  +i+e+kCi+Cg C++ C++++++a
  gi|13541825|ref|NP_111513.1| 40 KIHEEKCIECGFCIVGCPTGAINA 63
                                  69****************988776 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.5   2.1e-05      0.02       5      63 ..      17      29 ..       5      40 .. 0.73
   2 !   17.3   0.9   5.1e-06    0.0049       3      21 ..      44      62 ..      42      69 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.1e-05
                        Fer4_8  5 CieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpv 63
                                  C+ CgaC  +Cp                                              +
  gi|13541825|ref|NP_111513.1| 17 CNYCGACVGMCP----------------------------------------------T 29
                                  666666666666..............................................3 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 5.1e-06
                        Fer4_8  3 ekCieCgaCqsaCpvlrrt 21
                                  ekCieCg+C   Cp+    
  gi|13541825|ref|NP_111513.1| 44 EKCIECGFCIVGCPTGAIN 62
                                  69************86555 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   2.6   0.00056      0.53       3      16 ..      16      29 ..      13      30 .. 0.88
   2 !   17.5   3.5   4.3e-06    0.0041       2      17 .]      44      59 ..      43      59 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00056
                        Fer4_4  3 rCigCgsCvaaCPq 16
                                   C+ Cg+Cv  CP+
  gi|13541825|ref|NP_111513.1| 16 LCNYCGACVGMCPT 29
                                  6999*********7 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 4.3e-06
                        Fer4_4  2 erCigCgsCvaaCPqg 17
                                  e+Ci+Cg C+  CP+g
  gi|13541825|ref|NP_111513.1| 44 EKCIECGFCIVGCPTG 59
                                  89************86 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   3.1    0.0003      0.28      45      58 ..      16      29 ..       4      32 .. 0.65
   2 !   12.2   2.5   0.00022       0.2       2      15 ..      17      30 ..      16      44 .. 0.79
   3 !   13.5   1.6   8.2e-05     0.078       1      18 [.      45      62 ..      45      68 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0003
                       Fer4_17 45 lCieCgeCerkCPq 58
                                  lC+ Cg C+  CP 
  gi|13541825|ref|NP_111513.1| 16 LCNYCGACVGMCPT 29
                                  55555555555554 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00022
                       Fer4_17  2 CiqCgyClpeCpsy 15
                                  C+ Cg+C+ +Cp+ 
  gi|13541825|ref|NP_111513.1| 17 CNYCGACVGMCPTD 30
                                  99999999999975 PP

  == domain 3  score: 13.5 bits;  conditional E-value: 8.2e-05
                       Fer4_17  1 rCiqCgyClpeCpsyeay 18
                                  +Ci+Cg+C+  Cp+++++
  gi|13541825|ref|NP_111513.1| 45 KCIECGFCIVGCPTGAIN 62
                                  699*****9999998775 PP

>> Fer4_11  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   2.1   2.2e-06    0.0021       4      66 ..      11      68 ..       8      70 .] 0.84

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2.2e-06
                       Fer4_11  4 lflpeqCrhCleppCvasapseaivkdeetGaVlldektkkeevrevveacPykivrkneetg 66
                                   +  + C+ C   +Cv ++p++ai  de   ++ ++e+++  e+  ++ +cP  ++ +++ +g
  gi|13541825|ref|NP_111513.1| 11 DVDRNLCNYCG--ACVGMCPTDAIWLDE--TVIKIHEEKCI-ECGFCIVGCPTGAINAEWFHG 68
                                  55667899995..8*************9..67888888886.9*********99999888766 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   6.3   0.00018      0.17       1      15 []      17      31 ..      17      31 .. 0.97
   2 !   12.2   4.4    0.0003      0.29       1      15 []      46      60 ..      46      60 .. 0.98

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00018
                        Fer4_3  1 CtgCgaCvevCPvgA 15
                                  C+ CgaCv  CP++A
  gi|13541825|ref|NP_111513.1| 17 CNYCGACVGMCPTDA 31
                                  999**********98 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.0003
                        Fer4_3  1 CtgCgaCvevCPvgA 15
                                  C+ Cg C + CP+gA
  gi|13541825|ref|NP_111513.1| 46 CIECGFCIVGCPTGA 60
                                  **************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 !   11.3  10.7   0.00031      0.29      55      95 ..      11      56 ..       2      57 .. 0.72
   2 !   12.4   2.0   0.00015      0.14      57      74 ..      42      59 ..      31      64 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00031
                       Fer4_18 55 ekgagdcidcescvkvcPtg.i..d..irkGlqleciscllcidac 95
                                  + + + c  c++cv +cPt+ i  d  + k    +ci+c+ ci  c
  gi|13541825|ref|NP_111513.1| 11 DVDRNLCNYCGACVGMCPTDaIwlDetVIKIHEEKCIECGFCIVGC 56
                                  456678************97332222244556679********998 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00015
                       Fer4_18 57 gagdcidcescvkvcPtg 74
                                   + +ci+c++c+  cPtg
  gi|13541825|ref|NP_111513.1| 42 HEEKCIECGFCIVGCPTG 59
                                  5678************98 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   2.4   0.00018      0.17       1      17 [.      12      28 ..      12      32 .. 0.96
   2 ?    8.2   3.3    0.0038       3.6       3      17 ..      43      57 ..      41      59 .. 0.88
   3 ?    3.4   0.1      0.12   1.1e+02      49      57 ..      54      62 ..      53      63 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00018
                       Fer4_13  1 VDrdtCiacgaCvelaP 17
                                  VDr+ C  cgaCv ++P
  gi|13541825|ref|NP_111513.1| 12 VDRNLCNYCGACVGMCP 28
                                  9**************** PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0038
                       Fer4_13  3 rdtCiacgaCvelaP 17
                                  +++Ci+cg C   +P
  gi|13541825|ref|NP_111513.1| 43 EEKCIECGFCIVGCP 57
                                  69*********9999 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.12
                       Fer4_13 49 daCPvesIg 57
                                   +CP+ +I 
  gi|13541825|ref|NP_111513.1| 54 VGCPTGAIN 62
                                  68*****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 ?   12.8   2.9   0.00016      0.15       3      20 ..      12      29 ..      10      36 .. 0.90
   2 ?    5.6   3.0     0.028        26       1      20 [.      39      58 ..      39      61 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00016
                       Fer4_15  3 vDrdaCigcglCvaeape 20
                                  vDr++C  cg+Cv  +p+
  gi|13541825|ref|NP_111513.1| 12 VDRNLCNYCGACVGMCPT 29
                                  9*************9984 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.028
                       Fer4_15  1 VvvDrdaCigcglCvaeape 20
                                  +++ +++Ci cg C+  +p+
  gi|13541825|ref|NP_111513.1| 39 IKIHEEKCIECGFCIVGCPT 58
                                  678899*********99985 PP

>> ETF_QO  Electron transfer flavoprotein-ubiquinone oxidoreductase, 4Fe-4S
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   3.4   0.00036      0.34      32      92 ..       9      63 ..       1      69 [. 0.67

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00036
                                  THHHHTHHHHHS-THHHH-TTS-EEEEETT.TTSSEEEEE-CCC--S--HHHHH-TT--EEE CS
                        ETF_QO 32 evavkvnlekyagpeqryCPagvyeivede.eakekklqinaqnCvhCktCdikdpsqniew 92
                                  e+ v++nl +y g +  +CP        d+   +e+ ++i  + C+ C  C +  p+  i+ 
  gi|13541825|ref|NP_111513.1|  9 EMDVDRNLCNYCGACVGMCPT-------DAiWLDETVIKIHEEKCIECGFCIVGCPTGAINA 63
                                  344455555555555555555.......4433456789***************999999874 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   2.6    0.0052       4.9      76      94 ..      11      29 ..       2      32 .. 0.71
   2 ?    6.8   2.5     0.013        12       2      15 ..      17      30 ..      16      45 .. 0.80
   3 ?    8.5   3.6    0.0038       3.6       1      15 [.      45      59 ..      45      63 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0052
                       Fer4_22 76 kfgesgCvGCgRCieacpv 94
                                   ++++ C  Cg C+ +cp+
  gi|13541825|ref|NP_111513.1| 11 DVDRNLCNYCGACVGMCPT 29
                                  5577778888888888875 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.013
                       Fer4_22  2 ClsCgaCtlvCptC 15
                                  C  CgaC  +Cpt 
  gi|13541825|ref|NP_111513.1| 17 CNYCGACVGMCPTD 30
                                  88999999999995 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.0038
                       Fer4_22  1 rClsCgaCtlvCptC 15
                                  +C++Cg C + Cpt 
  gi|13541825|ref|NP_111513.1| 45 KCIECGFCIVGCPTG 59
                                  7************95 PP

>> MTHFR_C  Methylene-tetrahydrofolate reductase C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   1.4    0.0081       7.6      10      29 ..       5      24 ..       1      32 [. 0.80
   2 ?    9.3   1.2   0.00094      0.89      12      32 ..      36      56 ..      28      64 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0081
                       MTHFR_C 10 gveeevkvleekCkaCgdCv 29
                                  +v++e+ v  + C+ Cg Cv
  gi|13541825|ref|NP_111513.1|  5 KVKTEMDVDRNLCNYCGACV 24
                                  677788888899*******7 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00094
                       MTHFR_C 12 eeevkvleekCkaCgdCvlae 32
                                  e+ +k+ eekC +Cg C+++ 
  gi|13541825|ref|NP_111513.1| 36 ETVIKIHEEKCIECGFCIVGC 56
                                  56788999*********9874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       621  (0.0346366); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.52
# Mc/sec: 403.80
//
Query:       gi|13541826|ref|NP_111514.1|  [L=288]
Description: coiled-coil protein [Thermoplasma volcanium GSS1]
Scores for complete sequence (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   23.1  14.8    1.9e-05   22.7  14.8    1.1  1  Myosin_tail_1    Myosin tail
    1.5e-05   25.2  15.4     0.0055   16.9   5.1    2.6  2  TMF_TATA_bd      TATA element modulatory factor 1 TATA bindin
    7.4e-05   22.2  13.5    0.00093   18.6  13.3    2.1  1  DUF3450          Protein of unknown function (DUF3450)
    9.9e-05   22.4  11.3    9.9e-05   22.4  11.3    2.4  2  CENP-F_leu_zip   Leucine-rich repeats of kinetochore protein 
    0.00014   21.8  12.2    0.00014   21.8  12.2    2.3  2  KASH_CCD         Coiled-coil region of CCDC155 or KASH
    0.00015   21.1  13.8    0.00044   19.5  13.8    1.7  1  Taxilin          Myosin-like coiled-coil protein
    0.00028   20.8  14.7       0.01   15.7   6.4    2.5  2  DUF4515          Domain of unknown function (DUF4515)
    0.00036   18.9  16.9     0.0064   14.8   5.4    2.1  2  FPP              Filament-like plant protein, long coiled-coi
    0.00045   19.6  17.5     0.0025   17.2  14.6    2.4  2  GAS              Growth-arrest specific micro-tubule binding
    0.00099   19.3   9.8    0.00099   19.3   9.8    2.0  1  Fib_alpha        Fibrinogen alpha/beta chain family
     0.0012   18.3   6.9     0.0017   17.8   6.9    1.2  1  DUF4407          Domain of unknown function (DUF4407)
      0.002   18.5  17.9      0.057   13.8   4.8    3.0  2  DUF4200          Domain of unknown function (DUF4200)
     0.0021   16.8   4.7     0.0021   16.8   4.7    2.3  2  AAA_13           AAA domain
     0.0022   17.0  17.1     0.0033   16.4  16.6    1.6  1  Spc7             Spc7 kinetochore protein
     0.0022   17.8  17.8     0.0053   16.6  16.9    2.2  1  Phage_GP20       Phage minor structural protein GP20
     0.0028   17.9  16.8      0.071   13.4   1.2    2.6  2  DUF5082          Domain of unknown function (DUF5082)
     0.0029   17.9  13.9     0.0053   17.0   3.3    2.5  2  ATG16            Autophagy protein 16 (ATG16)
     0.0038   16.7  11.3     0.0038   16.7  11.3    1.8  2  Golgin_A5        Golgin subfamily A member 5
     0.0053   17.2  12.0        7.3    7.1  12.0    2.7  1  ZapB             Cell division protein ZapB
     0.0064   16.3  12.7     0.0064   16.3  12.7    1.6  1  ERM              Ezrin/radixin/moesin family
     0.0069   16.1  22.2       0.01   15.6  17.0    2.9  3  YkyA             Putative cell-wall binding lipoprotein
       0.01   16.3  12.9       0.02   15.4  12.9    1.5  1  Fez1             Fez1
  ------ inclusion threshold ------
      0.011   15.7   9.5      0.029   14.4   2.8    2.6  2  DUF1664          Protein of unknown function (DUF1664)
      0.011   16.2   5.6      0.011   16.2   5.6    2.3  2  Spectrin         Spectrin repeat
      0.015   15.4  14.3       0.26   11.3   8.4    2.5  2  TPR_MLP1_2       TPR/MLP1/MLP2-like protein
      0.016   15.3   3.5      0.016   15.3   3.5    2.9  2  TolA_bind_tri    TolA binding protein trimerisation
      0.018   15.1   7.6      0.049   13.7   1.7    2.5  2  Baculo_PEP_C     Baculovirus polyhedron envelope protein, PEP
      0.019   15.0  13.8      0.068   13.2   8.9    2.5  2  DHR10            Designed helical repeat protein 10 domain
      0.022   15.0  17.0      0.044   14.0   7.2    2.8  2  Seryl_tRNA_N     Seryl-tRNA synthetase N-terminal domain
      0.023   14.8  13.8      0.068   13.3  12.5    2.1  2  ADIP             Afadin- and alpha -actinin-Binding
      0.023   14.3   5.4      0.043   13.5   1.7    2.3  2  DUF2968          Protein of unknown function (DUF2968)
      0.027   14.6   9.6       0.26   11.5   0.6    2.9  2  COG5             Golgi transport complex subunit 5
      0.032   14.0   0.4      0.074   12.8   0.1    1.7  1  CRAL_TRIO        CRAL/TRIO domain
      0.035   12.7  13.5      0.051   12.2  13.0    1.5  1  FapA             Flagellar Assembly Protein A
      0.037   14.5  12.8       0.32   11.5   2.5    3.5  3  Cep57_MT_bd      Centrosome microtubule-binding domain of Cep
       0.04   14.0  14.0       0.33   11.0   8.9    3.2  3  ApoLp-III        Apolipophorin-III precursor (apoLp-III)
      0.042   14.4  20.4        1.6    9.2  15.7    2.6  2  APG6_N           Apg6 coiled-coil region
      0.046   14.2   2.9      0.046   14.2   2.9    2.8  2  NPV_P10          Nucleopolyhedrovirus P10 protein
      0.047   13.8   5.6        1.3    9.1   0.3    2.7  2  DUF2730          Protein of unknown function (DUF2730)
      0.047   13.8  17.2       0.37   10.9  17.0    2.1  1  UPF0242          Uncharacterised protein family (UPF0242) N-t
      0.052   13.7  16.0      0.032   14.4   7.1    3.1  2  RasGAP_C         RasGAP C-terminus
      0.054   14.1  14.6       0.27   11.9   3.8    3.5  3  DUF5344          Family of unknown function (DUF5344)
      0.054   13.9  11.3      0.061   13.7   3.4    3.3  3  LPP              Lipoprotein leucine-zipper
      0.057   13.5  10.8       0.27   11.4   0.9    3.4  3  MYO10_CC         Unconventional myosin-X coiled coil domain
      0.071   12.0  18.1        0.1   11.5  17.9    1.4  1  DUF812           Protein of unknown function (DUF812)
      0.078   13.2  11.0       0.19   12.0  10.5    1.9  1  Jnk-SapK_ap_N    JNK_SAPK-associated protein-1
       0.08   13.0   5.6       0.13   12.4   4.2    2.1  1  COG2             COG (conserved oligomeric Golgi) complex com
       0.09   11.9  13.7      0.064   12.4   9.3    2.2  3  APG17            Autophagy protein Apg17
       0.11   12.9  15.3       0.16   12.3  10.8    2.4  2  Uso1_p115_C      Uso1 / p115 like vesicle tethering protein, 
       0.11   12.7  11.7       0.08   13.1   7.6    2.7  2  Cnn_1N           Centrosomin N-terminal motif 1
       0.11   12.7  19.8       0.92    9.8   8.3    3.6  3  ABC_tran_CTD     ABC transporter C-terminal domain
       0.11   12.6  17.6       0.12   12.4  13.6    2.5  3  BRE1             BRE1 E3 ubiquitin ligase
       0.12   12.7  10.5        1.7    9.0   2.6    2.5  2  DUF641           Plant protein of unknown function (DUF641)
       0.12   12.2   5.9       0.13   12.1   4.2    1.9  2  MCPsignal        Methyl-accepting chemotaxis protein (MCP) si
       0.13   12.2   7.3       0.75    9.7   1.2    2.5  2  CHASE3           CHASE3 domain
       0.13   11.8  11.1       0.44   10.1  11.1    2.0  1  HAUS-augmin3     HAUS augmin-like complex subunit 3
       0.14   12.8  11.2        7.9    7.1   8.9    3.7  1  Syntaxin-6_N     Syntaxin 6, N-terminal
       0.16   12.2   9.1        0.3   11.4   1.8    3.0  2  DUF4164          Domain of unknown function (DUF4164)
       0.17   11.7  16.8        1.6    8.6   7.3    3.4  2  DivIC            Septum formation initiator
       0.17   11.8  18.9      0.028   14.4  10.1    2.7  2  Ax_dynein_light  Axonemal dynein light chain
       0.25   11.5   8.8       0.11   12.7   1.0    3.0  2  JIP_LZII         JNK-interacting protein  leucine zipper II
       0.25   11.4  12.0       0.31   11.1   3.8    3.8  4  Cauli_DNA-bind   Caulimovirus DNA-binding protein
       0.33   11.0  11.4        2.1    8.4   1.4    2.4  2  Laminin_II       Laminin Domain II
       0.33   10.9  14.6        1.1    9.2   4.8    3.6  3  Prefoldin        Prefoldin subunit
       0.36    8.7   8.9       0.29    9.0   6.1    1.6  1  Prominin         Prominin
       0.41   10.2   7.1        0.8    9.2   5.6    2.2  1  Fzo_mitofusin    fzo-like conserved region
       0.45   10.8  18.6         10    6.4  13.4    3.7  2  THOC7            Tho complex subunit 7
       0.45   10.5   5.5        3.6    7.6   0.5    3.4  3  Nas2_N           Nas2 N_terminal domain
       0.46   10.8  16.2       0.71   10.2   4.5    2.9  2  Tup_N            Tup N-terminal
       0.47   10.3   9.3       0.66    9.8   4.1    2.5  2  ACCA             Acetyl co-enzyme A carboxylase carboxyltrans
       0.48   10.5  15.3        1.8    8.6  13.1    2.6  1  Mod_r            Modifier of rudimentary (Mod(r)) protein
       0.55   10.4  17.2       0.54   10.4  14.7    2.3  1  Tropomyosin_1    Tropomyosin like
       0.63   10.2  10.1        1.1    9.4   4.4    3.0  2  Med9             RNA polymerase II transcription mediator com
       0.65    9.9  13.7      0.095   12.5   1.0    3.3  3  betaPIX_CC       betaPIX coiled coil
       0.67    9.7  17.1        0.2   11.5   7.2    2.7  2  DUF724           Protein of unknown function (DUF724)
       0.72    8.6  16.1        1.4    7.7  16.1    1.5  1  CALCOCO1         Calcium binding and coiled-coil domain (CALC
        0.8   10.0   7.7         11    6.4   0.3    3.3  2  WXG100           Proteins of 100 residues with WXG
       0.88    9.6  16.8      0.037   14.1   8.1    2.5  2  DUF1640          Protein of unknown function (DUF1640)
       0.89   10.0  16.6       0.86   10.0   0.6    4.3  3  FlaC_arch        Flagella accessory protein C (FlaC)
       0.92   10.2  11.1         11    6.7   5.3    3.4  2  SlyX             SlyX
          1    9.5  16.9       0.21   11.7   0.6    3.8  3  bZIP_1           bZIP transcription factor
        1.1    8.5  10.7          3    7.0  10.7    1.8  1  TMPIT            TMPIT-like protein
        1.1    8.7  14.5       0.56    9.7   8.6    2.3  2  SseC             Secretion system effector C (SseC) like fami
        1.2    7.8   6.0        2.6    6.8   4.8    2.1  2  DUF3573          Protein of unknown function (DUF3573)
        1.5    9.5  12.3        2.5    8.8   7.4    2.9  4  HIP1_clath_bdg   Clathrin-binding domain of Huntingtin-intera
        1.7    9.3  14.1        4.3    8.0   7.1    3.5  2  YabA             Initiation control protein YabA
        1.8    8.5   9.7        5.3    7.0   1.4    3.5  4  GIT_CC           GIT coiled-coil Rho guanine nucleotide excha
        1.8    8.7  14.8        6.1    7.0   6.2    3.3  2  Swi5             Swi5
        2.1    8.1  22.8      0.062   13.1  10.7    2.8  1  TACC_C           Transforming acidic coiled-coil-containing p
        2.1    8.6   6.2         16    5.7   5.0    2.8  2  PEP-utilisers_N  PEP-utilising enzyme, N-terminal
        2.1    8.2  14.9       0.45   10.4   8.5    2.7  3  Phage_Mu_Gam     Bacteriophage Mu Gam like protein
        2.4    8.5   5.5         14    6.0   0.5    3.0  2  DUF948           Bacterial protein of unknown function (DUF94
        2.5    6.9  11.8        1.3    7.8   9.7    1.4  1  LMBR1            LMBR1-like membrane protein
        2.9    6.9  13.2        6.7    5.7  13.1    1.5  1  Atg14            Vacuolar sorting 38 and autophagy-related su
        2.9    8.3   8.6       0.62   10.4   1.3    3.1  2  HalX             HalX domain
        3.1    7.5  13.0       0.38   10.4   7.0    2.4  2  PA28_beta        Proteasome activator pa28 beta subunit
        3.2    8.3   9.6        1.9    9.0   2.7    2.7  2  DUF4140          N-terminal domain of unknown function (DUF41
        3.3    8.5  17.1        1.5    9.6   1.5    3.1  2  Occludin_ELL     Occludin homology domain
        4.2    7.1   9.6        4.2    7.1   2.3    3.0  3  Hormone_1        Somatotropin hormone family
        4.3    7.5  10.4        5.2    7.2   0.1    3.7  4  bZIP_2           Basic region leucine zipper
        4.4    6.8  21.1        1.7    8.2  17.2    2.2  2  DUF4795          Domain of unknown function (DUF4795)
        4.6    7.3  16.0          3    7.9  13.6    1.9  1  FlxA             FlxA-like protein
        4.9    7.6  14.1        2.9    8.3   9.6    2.4  2  CENP-H           Centromere protein H (CENP-H)
          5    8.0   8.6       0.91   10.4   4.8    1.7  1  HABP4_PAI-RBP1   Hyaluronan / mRNA binding family
        5.1    7.1  25.1       0.46   10.5   3.2    4.5  4  Prefoldin_2      Prefoldin subunit
        5.2    7.1  22.6        1.1    9.2   7.3    3.4  3  TMF_DNA_bd       TATA element modulatory factor 1 DNA binding
        5.4    7.5   9.9         17    5.8   7.6    2.8  1  E2F_CC-MB        E2F transcription factor CC-MB domain
        5.4    6.5   9.9        2.9    7.4   5.4    2.4  2  Ssu72            Ssu72-like protein
        6.3    7.7  17.9        1.5    9.7   4.9    4.0  2  Rho_Binding      Rho Binding
        7.2    6.8  11.1        6.7    6.9   2.3    2.9  2  Cep57_CLD_2      Centrosome localisation domain of PPC89
        7.6    6.8  10.7       0.53   10.5   3.3    2.8  1  XhlA             Haemolysin XhlA
        8.7    7.1  10.7        1.7    9.3   5.2    2.6  1  DUF4404          Domain of unknown function (DUF4404)


Domain annotation for each model (and alignments):
>> Myosin_tail_1  Myosin tail
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7  14.8   1.2e-07   1.9e-05     223     359 ..     144     280 ..      76     287 .. 0.73

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 1.2e-07
                 Myosin_tail_1 223 qiadlqaqieelraqlakkeeelqaalarleeeaaqknaalkklreleaqlaelqedlese.kaaRakaekqrrdLgeeLe 302
                                       ++ +i  l ++  + + e+ ++ a +++ +a+k+++ +++ e++ q+ ++q  +++  ka  + +e  ++ L ee e
  gi|13541826|ref|NP_111514.1| 144 EKKAIESEIGYLNSKKDQMQSEISQLSAEINDLNAKKSELEQAIAEMQKQIEDIQAGIDERiKAVFEENESMKKTL-EEYE 223
                                   334456667777778888889999**********************************876255566666666666.799* PP

                 Myosin_tail_1 303 alkteLedtLDstaaqqeLrskReqevaeLkkaleeearsheaqlqelrqkhtqale 359
                                     +++L  +L + +  ++L  +R++e+++Lk + ++  +++++ ++++ ++  + ++
  gi|13541826|ref|NP_111514.1| 224 KTRADLATALSTVSQLKDLILQRDAEIKKLKDSYNDIFTRYDTLINKMTKREFEKIN 280
                                   **************************************************9887765 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 !   16.9   5.1   3.5e-05    0.0055      26      83 ..     143     197 ..     139     210 .. 0.75
   2 !   13.2   3.1   0.00049     0.079      21      89 ..     205     273 ..     201     286 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 3.5e-05
                   TMF_TATA_bd  26 gElaslkeelerleaerdeareeivklmkeneelkelkkeleelekeleelqeryetl 83 
                                   gE++++++e+  l++++d++++ei +l++e ++l+++k+el   e+ ++e+q++ e +
  gi|13541826|ref|NP_111514.1| 143 GEKKAIESEIGYLNSKKDQMQSEISQLSAEINDLNAKKSEL---EQAIAEMQKQIEDI 197
                                   79999***********************9888877777655...44555555554444 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 0.00049
                   TMF_TATA_bd  21 irrlEgElaslkeelerleaerdeareeivklmkeneelkelkkeleelekeleelqeryetlLellGe 89 
                                   i+    E +s+k++le+ e+ r +++  + ++++  +   + ++e+++l+ +++++ +ry+tl   + +
  gi|13541826|ref|NP_111514.1| 205 IKAVFEENESMKKTLEEYEKTRADLATALSTVSQLKDLILQRDAEIKKLKDSYNDIFTRYDTLINKMTK 273
                                   555567999*****************************************************9876555 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6  13.3   5.8e-06   0.00093      28     136 ..     141     258 ..     129     260 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 5.8e-06
                       DUF3450  28 avaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeieeierelvpllekmidr 108
                                    v ++++++++i  l+ +k+++++e+ +l++e+++l++++++le+ +a+++++i++++  i+e  +   e    ++k++++
  gi|13541826|ref|NP_111514.1| 141 LVGEKKAIESEIGYLNSKKDQMQSEISQLSAEINDLNAKKSELEQAIAEMQKQIEDIQAGIDERIKAVFEENESMKKTLEE 221
                                   566789999*****************************************************998888888999******9 PP

                       DUF3450 109 LeqfveldlPf..........lleeRqarlakLkelmd 136
                                   +e+  + dl            l  +R+a+++kLk++ +
  gi|13541826|ref|NP_111514.1| 222 YEKTRA-DLATalstvsqlkdLILQRDAEIKKLKDSYN 258
                                   999755.4444466666655555688888888888766 PP

>> CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein Cenp-F/LEK1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4  11.3   6.2e-07   9.9e-05      42     128 ..     140     227 ..     128     231 .. 0.86
   2 ?    3.2   4.2      0.51        82      52      96 ..     210     257 ..     201     288 .] 0.59

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 6.2e-07
                CENP-F_leu_zip  42 kvileaEtskaevetlkeeieelaeelreleldLvalrsekeeLekelqkkqervseLes.lnsslenlleekEqekvqmk 121
                                    ++ e+     e+  l+++++++++e ++l++++++l   k eLe+ + ++q+++++ ++ + + ++ + ee+E  k+ ++
  gi|13541826|ref|NP_111514.1| 140 GLVGEKKAIESEIGYLNSKKDQMQSEISQLSAEINDLNAKKSELEQAIAEMQKQIEDIQAgIDERIKAVFEENESMKKTLE 220
                                   566666777778888*******************************************974789999999****9999999 PP

                CENP-F_leu_zip 122 eeskaav 128
                                   e  k++ 
  gi|13541826|ref|NP_111514.1| 221 EYEKTRA 227
                                   9888765 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.51
                CENP-F_leu_zip  52 aevetlkeeieelaeelreleldLvalrsekeeLek...elqkkqerv 96 
                                   +e e++k+ +ee ++++ +l + L+++++ k+ + +   e++k ++  
  gi|13541826|ref|NP_111514.1| 210 EENESMKKTLEEYEKTRADLATALSTVSQLKDLILQrdaEIKKLKDSY 257
                                   456678888888888888888888888877776532111333333344 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 !   21.8  12.2   8.6e-07   0.00014      82     178 ..     137     230 ..     116     245 .. 0.80
   2 ?    4.4   3.7      0.18        29      63      95 ..     206     238 ..     203     285 .. 0.51

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 8.6e-07
                      KASH_CCD  82 krarlkaqnkqlekenqsLiakiesLqeenikllaekdelkkklkeLlkekaeLkkqlheleellaekealleektkqiee 162
                                   + + l  ++k +e e   L++k +++q e+ +l ae++ l+ k+ eL + +ae++kq+  ++   a  ++ ++   ++ e+
  gi|13541826|ref|NP_111514.1| 137 SDNGLVGEKKAIESEIGYLNSKKDQMQSEISQLSAEINDLNAKKSELEQAIAEMQKQIEDIQ---AGIDERIKAVFEENES 214
                                   45667778899999********************************************5555...5555556666666789 PP

                      KASH_CCD 163 LkltieEyssiieeLr 178
                                   +k t+eEy+++   L 
  gi|13541826|ref|NP_111514.1| 215 MKKTLEEYEKTRADLA 230
                                   9*******99877765 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.18
                      KASH_CCD  63 klleeEleelkalvkeleEkrarlkaqnkqlek 95 
                                   k++ eE+e +k++++e e  ra l++  + + +
  gi|13541826|ref|NP_111514.1| 206 KAVFEENESMKKTLEEYEKTRADLATALSTVSQ 238
                                   555555555555555555555555544333332 PP

>> Taxilin  Myosin-like coiled-coil protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5  13.8   2.7e-06   0.00044      30     157 ..     141     279 ..     135     287 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 2.7e-06
                       Taxilin  30 lleerkrlqkqlkklkkkleqlqkekeqlqaelskaalaksKLekLcRelqkqnkklk.............eeskqr.are 96 
                                   l+ e+k  ++++  l++k +q+q e  ql ae ++ ++ ks Le+   e+qkq + ++             +es+++  +e
  gi|13541826|ref|NP_111514.1| 141 LVGEKKAIESEIGYLNSKKDQMQSEISQLSAEINDLNAKKSELEQAIAEMQKQIEDIQagiderikavfeeNESMKKtLEE 221
                                   78899999***********************************************99988887777888664444440444 PP

                       Taxilin  97 eeekrkelaekfqakLkdiqaqieekserneklreenaelteKlkslieqyelreehfekl 157
                                    e+ r +la+   ++++++++ i +++++ +kl++  +++ ++ ++li+++ +re  fek+
  gi|13541826|ref|NP_111514.1| 222 YEKTRADLATA-LSTVSQLKDLILQRDAEIKKLKDSYNDIFTRYDTLINKMTKRE--FEKI 279
                                   44455555554.4689999999******************************998..5555 PP

>> DUF4515  Domain of unknown function (DUF4515)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   4.0    0.0053      0.85     151     199 ..     145     193 ..     142     199 .. 0.87
   2 !   15.7   6.4   6.2e-05      0.01      27     109 ..     190     272 ..     187     286 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0053
                       DUF4515 151 kkalseftrsvkreNqeLrkeLlqliketkkLekekskLeeqkqrlkee 199
                                   kka++  +  ++ + ++++ e  ql+ e++ L+++ks+Le+   +++++
  gi|13541826|ref|NP_111514.1| 145 KKAIESEIGYLNSKKDQMQSEISQLSAEINDLNAKKSELEQAIAEMQKQ 193
                                   566777777888999*************************999988887 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 6.2e-05
                       DUF4515  27 yvqeleeierekqelaskyekqtaeLqkqLlqkekeqaklkkeLqalediaklkeqqerkiqtLeeekekvqaetaeklre 107
                                    ++++e+i+   +e  +   +++++++k L + ek++a+l + L  + +++ l  q + +i++L+  ++++ +  +++  +
  gi|13541826|ref|NP_111514.1| 190 MQKQIEDIQAGIDERIKAVFEENESMKKTLEEYEKTRADLATALSTVSQLKDLILQRDAEIKKLKDSYNDIFTRYDTLINK 270
                                   6899999999988877777778999*******************************************9998877776666 PP

                       DUF4515 108 lk 109
                                   + 
  gi|13541826|ref|NP_111514.1| 271 MT 272
                                   55 PP

>> FPP  Filament-like plant protein, long coiled-coil
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   5.4     4e-05    0.0064     687     743 ..     142     198 ..      91     200 .. 0.84
   2 !   10.0   3.5    0.0011      0.18     708     776 ..     202     273 ..     198     287 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4e-05
                           FPP 687 keenkllkeeleelksekenlevelksatenleslkaqlqesEqllaelkseLeslk 743
                                     e+k  + e+  l+s+k++++ e+++ +++++ l+a+ +e Eq +ae+++++e ++
  gi|13541826|ref|NP_111514.1| 142 VGEKKAIESEIGYLNSKKDQMQSEISQLSAEINDLNAKKSELEQAIAEMQKQIEDIQ 198
                                   5688999**********************************************9987 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0011
                           FPP 708 evelksatenleslkaqlqesEqllaelkseLeslkesksla...etqlkcmkesyesletrateleaelne 776
                                   + ++k   e++es+k  l+e E++ a+l + L+++ ++k l+   + ++k+ k sy+++ tr   l +++++
  gi|13541826|ref|NP_111514.1| 202 DERIKAVFEENESMKKTLEEYEKTRADLATALSTVSQLKDLIlqrDAEIKKLKDSYNDIFTRYDTLINKMTK 273
                                   667889999*****************************99975557899999******99999888776654 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 !    9.5   4.4    0.0036      0.58      31      81 ..     148     198 ..     144     203 .. 0.80
   2 !   17.2  14.6   1.6e-05    0.0025      28     131 ..     166     273 ..     164     287 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0036
                           GAS  31 lKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknye 81 
                                     +ei  l+ k+++++ e+s++s+e ++l+ +  ++e+ ++e++kq+++ +
  gi|13541826|ref|NP_111514.1| 148 IESEIGYLNSKKDQMQSEISQLSAEINDLNAKKSELEQAIAEMQKQIEDIQ 198
                                   566777888888888888888888888888888888888888888888765 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 1.6e-05
                           GAS  28 IkslKeeieelkkkeernekelseisqenkrlk....epLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdl 104
                                   I +l  ei++l++k+ + e+ ++e++++ ++++    e +k++ ee+e ++k l++yek +++l+ + + +++l++ + + 
  gi|13541826|ref|NP_111514.1| 166 ISQLSAEINDLNAKKSELEQAIAEMQKQIEDIQagidERIKAVFEENESMKKTLEEYEKTRADLATALSTVSQLKDLILQR 246
                                   889999*********************99986533338999999*********************9999999999999999 PP

                           GAS 105 kwehevleqrfekvekerdelykkfea 131
                                     e + l++ ++ +   +d+l +k ++
  gi|13541826|ref|NP_111514.1| 247 DAEIKKLKDSYNDIFTRYDTLINKMTK 273
                                   999999999999998888888877665 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 !   19.3   9.8   6.2e-06   0.00099      24     124 ..     153     256 ..     151     263 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 6.2e-06
                                   HCCCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH...CCCHHHHHHHCCH CS
                     Fib_alpha  24 dlllkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskelee...eilrlketidaqe 101
                                   ++l++++ +++ ++++l  e+++++ +++e e+ + e+++++++ q+  ++  +++ + ++++++   e+++ ++ + +  
  gi|13541826|ref|NP_111514.1| 153 GYLNSKKDQMQSEISQLSAEINDLNAKKSELEQAIAEMQKQIEDIQAGIDERIKAVFEENESMKKtleEYEKTRADLATAL 233
                                   68999********************************************99855554444444440006666666799999 PP

                                   HHHHHHHHHHHHHHHHHHHHHHH CS
                     Fib_alpha 102 snirvLqnvlesneqkiqkLeqd 124
                                   s++ +L++++ + + +i+kL+  
  gi|13541826|ref|NP_111514.1| 234 STVSQLKDLILQRDAEIKKLKDS 256
                                   ********************975 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   6.9     1e-05    0.0017     128     236 ..     159     267 ..     123     282 .. 0.51

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1e-05
                       DUF4407 128 aaaltaelaeleaqiaalqaeidaaearldalraeaqkeldgtkgtgttgvaGkgpaakekkaqldaaqaelaelkakld. 207
                                   ++++++e+++l a+i++l+a+ +++e+++++ +++ ++   g   +++++v  + +++k+  +++++ +a+la++ ++++ 
  gi|13541826|ref|NP_111514.1| 159 KDQMQSEISQLSAEINDLNAKKSELEQAIAEMQKQIEDIQAG-IDERIKAVFEENESMKKTLEEYEKTRADLATALSTVSq 238
                                   222444444444444444444444444444444444433332.34444555555555555555555555555555554444 PP

                       DUF4407 208 atarlaalraelaeleaerakeraasqaa 236
                                    ++ + +++ae+++l++ ++++ ++ ++ 
  gi|13541826|ref|NP_111514.1| 239 LKDLILQRDAEIKKLKDSYNDIFTRYDTL 267
                                   34444444444444444444444444433 PP

>> DUF4200  Domain of unknown function (DUF4200)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   4.8   0.00036     0.057      72     108 ..     156     192 ..     144     192 .. 0.90
   2 !   11.5  11.5    0.0019       0.3       9     101 ..     181     269 ..     179     276 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 0.00036
                       DUF4200  72 rklkkekeaeikklkaeietlkseiekleekleeykk 108
                                   + +k+++++ei +l aei++l++++++le++++e++k
  gi|13541826|ref|NP_111514.1| 156 NSKKDQMQSEISQLSAEINDLNAKKSELEQAIAEMQK 192
                                   5789*****************************9986 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.0019
                       DUF4200   9 fevqealeakkeeiqrleealkqreeelekkeqeleedllkfdkflkendakraralkkaeeerklkkekeaeikklkaei 89 
                                   +e+++a+++++++i+ ++  +++r +++ ++++ ++++l++++k      a  a al  + + ++l+ +++aeikklk++ 
  gi|13541826|ref|NP_111514.1| 181 SELEQAIAEMQKQIEDIQAGIDERIKAVFEENESMKKTLEEYEKT----RADLATALSTVSQLKDLILQRDAEIKKLKDSY 257
                                   589************************************999986....566789************************99 PP

                       DUF4200  90 etlkseieklee 101
                                   +++ ++ + l +
  gi|13541826|ref|NP_111514.1| 258 NDIFTRYDTLIN 269
                                   998777666655 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   4.7   1.3e-05    0.0021     405     462 ..     146     203 ..     130     208 .. 0.94
   2 ?    3.9   5.6       0.1        16     282     357 ..     209     284 ..     203     288 .] 0.83

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.3e-05
                        AAA_13 405 eeleseldeykkkykklekaieklekelkeeeaelkkleeeikeLekqlrdekpaaee 462
                                   + +ese+  +++k+++++ +i++l +e+++ +a++ +le+ i+e++kq++d++ +++e
  gi|13541826|ref|NP_111514.1| 146 KAIESEIGYLNSKKDQMQSEISQLSAEINDLNAKKSELEQAIAEMQKQIEDIQAGIDE 203
                                   568999999**********************************************997 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.1
                        AAA_13 282 eekqerLekliekveskkselleklkavsdeasensafeedkeelkaeaealeeqLkglqraleaKrkepfksvel 357
                                    e+ e+++k++e++e++++ l++ l +vs+ +++  + + ++++lk+  + + ++ ++l ++++++  e  +  el
  gi|13541826|ref|NP_111514.1| 209 FEENESMKKTLEEYEKTRADLATALSTVSQLKDLILQRDAEIKKLKDSYNDIFTRYDTLINKMTKREFEKINAREL 284
                                   355799**************************99999999999999999999999999999999887555555554 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4  16.6     2e-05    0.0033     150     302 ..     140     284 ..     122     287 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 2e-05
                          Spc7 150 gleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeqle 230
                                   gl  +k+ +e++   l++ ++++++e ++l++e+++l++++ ele+     ++e+++++++++a i+e+ k + e +e ++
  gi|13541826|ref|NP_111514.1| 140 GLVGEKKAIESEIGYLNSKKDQMQSEISQLSAEINDLNAKKSELEQ----AIAEMQKQIEDIQAGIDERIKAVFEENESMK 216
                                   6788899999999999999999999999999999999998888776....8999999999999999988888888888888 PP

                          Spc7 231 eleekieelkeqkseleeeiaeaervleeckgwsesevsrlkeevkaleeltgwkivslsgstleltyrsel 302
                                   +  e+ e++++  +++ + +++ ++++      ++ e+++lk++++++   ++  i ++++ ++e + ++el
  gi|13541826|ref|NP_111514.1| 217 KTLEEYEKTRADLATALSTVSQLKDLIL----QRDAEIKKLKDSYNDIFTRYDTLINKMTKREFEKINAREL 284
                                   8888888888888888888888777776....5789******************999999999887766665 PP

>> Phage_GP20  Phage minor structural protein GP20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6  16.9   3.3e-05    0.0053      16     136 ..     147     262 ..     123     272 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 3.3e-05
                    Phage_GP20  16 t.kakldeveeerdtlkeqlkdrdkqLedLkkkakdneeLqkqieelqaknkkakaeyeakiadl.kldnaielaLkeaka 94 
                                   + ++++  +++ +d++++++ +   +++dL +k     eL+++i+e+q+++++ +a  ++ i+++ + ++ ++++L+e++ 
  gi|13541826|ref|NP_111514.1| 147 AiESEIGYLNSKKDQMQSEISQLSAEINDLNAK---KSELEQAIAEMQKQIEDIQAGIDERIKAVfEENESMKKTLEEYEK 224
                                   25888999**********************888...99************************9973667789********* PP

                    Phage_GP20  95 knekavkalldkdklklkedgelkgLdeqikkLkesdkyLFe 136
                                     +++ +al  ++     +d  +   d +ikkLk+s++++F 
  gi|13541826|ref|NP_111514.1| 225 TRADLATALSTVS---QLKD-LILQRDAEIKKLKDSYNDIFT 262
                                   *******986644...4466.67889999********99996 PP

>> DUF5082  Domain of unknown function (DUF5082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   1.2   0.00044     0.071      90     122 ..     145     177 ..     142     178 .. 0.93
   2 ?    9.0   8.9      0.01       1.6       2      93 ..     177     271 ..     176     282 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00044
                       DUF5082  90 idaieeEIerLenqiseaqgvldtlqsqlnslk 122
                                   ++aie+EI  L +++ ++q+ +++l+ ++n+l+
  gi|13541826|ref|NP_111514.1| 145 KKAIESEIGYLNSKKDQMQSEISQLSAEINDLN 177
                                   579****************************97 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.01
                       DUF5082   2 ktkisklqaqiaelrseiaaleekI.erLk...eaktklsdekeslkqkkkklekplnssesWkGk..eennydgirsnle 76 
                                    +k+s+l+++iae++++i++++  I er k   e  ++++++ e+ ++++ +l++ l + + +k    +    d +  +l+
  gi|13541826|ref|NP_111514.1| 177 NAKKSELEQAIAEMQKQIEDIQAGIdERIKavfEENESMKKTLEEYEKTRADLATALSTVSQLKDLilQ---RDAEIKKLK 254
                                   689*******************99966888666556666666666667777777777777666654212...233334777 PP

                       DUF5082  77 ssyqtyvdkldelidai 93 
                                   +sy+ + ++ d+li ++
  gi|13541826|ref|NP_111514.1| 255 DSYNDIFTRYDTLINKM 271
                                   77777777777777776 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   3.3   3.3e-05    0.0053     107     158 ..     148     199 ..     145     204 .. 0.91
   2 ?    5.5   3.4      0.11        18      74     156 ..     213     260 ..     202     285 .. 0.52

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 3.3e-05
                         ATG16 107 lneelqkleeklkedeerlaeleaeraaletklkdreeelrekeklvqdlqD 158
                                    ++e+  l++k  ++++++ +l+ae+++l+ k +++e++++e +k ++d+q 
  gi|13541826|ref|NP_111514.1| 148 IESEIGYLNSKKDQMQSEISQLSAEINDLNAKKSELEQAIAEMQKQIEDIQA 199
                                   5778888999***************************************996 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.11
                         ATG16  74 akiqsleqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekeklvq 154
                                   ++++++ ++  ++r++la+++ + ++l++ +l+  +e++kl+++ +                                   
  gi|13541826|ref|NP_111514.1| 213 ESMKKTLEEYEKTRADLATALSTVSQLKDLILQRDAEIKKLKDSYND---------------------------------- 259
                                   33334444444555555555555555555555555555555544443.................................. PP

                         ATG16 155 dl 156
                                    +
  gi|13541826|ref|NP_111514.1| 260 -I 260
                                   .3 PP

>> Golgin_A5  Golgin subfamily A member 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       5.3   8.5e+02     164     188 ..      90     114 ..      69     117 .. 0.80
   2 !   16.7  11.3   2.4e-05    0.0038      35     153 ..     137     255 ..     121     279 .. 0.72

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 5.3
                     Golgin_A5 164 seselesRlkqLtesLiqKQtvlEa 188
                                   +++ ++++lk L e +i+  t++E+
  gi|13541826|ref|NP_111514.1|  90 EKNPSDEKLKDLREFVIEDMTNIES 114
                                   5566788999999999999999995 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 2.4e-05
                     Golgin_A5  35 geegles.stalsaeldelkqerdllreelqklnqqieqlrtelqdleaqqqaeaeslreqlqeleeqleeerkakeevea 114
                                   +++gl + ++a + e+  l++++d++++e+ +l+ +i++l ++  +le+   + ++++++ ++ ++e++++  +++e++++
  gi|13541826|ref|NP_111514.1| 137 SDNGLVGeKKAIESEIGYLNSKKDQMQSEISQLSAEINDLNAKKSELEQAIAEMQKQIEDIQAGIDERIKAVFEENESMKK 217
                                   4455554256789999999*******************9999988998888666666677777777777766666666666 PP

                     Golgin_A5 115 elerlkeelryleeelvrskatlqsrikdrekeieklrn 153
                                    le++++    l   l+ + ++l+  i +r++ei+kl+ 
  gi|13541826|ref|NP_111514.1| 218 TLEEYEKTRADLATALS-TVSQLKDLILQRDAEIKKLKD 255
                                   66665555444444444.556788889999****99985 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1  12.0     0.046       7.3      10      51 ..     156     215 ..     149     273 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.046
                          ZapB  10 EskiqkaidtitlLqmeieeLkeeneelkeenrele..................eeneql 51 
                                    sk +++  +i++L+ ei +L ++++el++ ++e++                  eene +
  gi|13541826|ref|NP_111514.1| 156 NSKKDQMQSEISQLSAEINDLNAKKSELEQAIAEMQkqiediqagiderikavfEENESM 215
                                   556666666777777777777777777777777777555555555555555555444444 PP

>> ERM  Ezrin/radixin/moesin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3  12.7     4e-05    0.0064      36     185 ..     139     288 .]     118     288 .] 0.81

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 4e-05
                           ERM  36 elLaekarraeeeaelLeqkaaeaeeeiqrlkesaekeeeekeklerklreaeleaarleeeserkeeeaerLkeeleear 116
                                   + L  +++  e e   L+ k+ +++ ei++l  + ++ +++k++le+ ++e++ ++++++   +++ + + +  e ++++ 
  gi|13541826|ref|NP_111514.1| 139 NGLVGEKKAIESEIGYLNSKKDQMQSEISQLSAEINDLNAKKSELEQAIAEMQKQIEDIQAGIDERIKAVFEENESMKKTL 219
                                   5677899999**************************************************999999888888888888888 PP

                           ERM 117 eaeeeakekllealstpsks...eseenveeseteeeeenseeesaeletdeveklsleieeeRvtyleksk 185
                                   e+ e++++ l +alst s+    +  +  +e ++ +++ n+  + ++   +++  +++e e+    +l+ks+
  gi|13541826|ref|NP_111514.1| 220 EEYEKTRADLATALSTVSQLkdlI-LQRDAEIKKLKDSYNDIFTRYDTLINKM--TKREFEKINARELKKSQ 288
                                   888889999999999987665432.4566777777777788888888777767..66777777777888875 PP

>> YkyA  Putative cell-wall binding lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1       8.7   1.4e+03      24      42 ..      15      33 ..       9      46 .. 0.71
   2 ?    5.3   1.3      0.09        14     146     185 ..     146     185 ..     143     186 .. 0.89
   3 !   15.6  17.0   6.2e-05      0.01      19     140 ..     165     273 ..     159     287 .. 0.58

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 8.7
                          YkyA 24 qekLtelekkeqelyeeii 42
                                  qe L +  k+  ++y+eii
  gi|13541826|ref|NP_111514.1| 15 QEDLDRRVKESGKTYKEII 33
                                  6666666666666666666 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.09
                          YkyA 146 eeleeqiekiNesyeevkeaneqFneatkkyneekkefye 185
                                   + +e +i  +N + +++++++ q+  +++  n +k+e+++
  gi|13541826|ref|NP_111514.1| 146 KAIESEIGYLNSKKDQMQSEISQLSAEINDLNAKKSELEQ 185
                                   5688899999*************************99887 PP

  == domain 3  score: 15.6 bits;  conditional E-value: 6.2e-05
                          YkyA  19 efeeqqekLtelekkeqelyeeiielgmdefdkikklsdealenveeReellekekesieeakeefekikeeieeiedeel 99 
                                   e+ +   ++++l +k+ el + i         +++k++++ ++ ++eR + + +e+es++++ ee+ek ++++        
  gi|13541826|ref|NP_111514.1| 165 EISQLSAEINDLNAKKSELEQAI--------AEMQKQIEDIQAGIDERIKAVFEENESMKKTLEEYEKTRADLATA----- 232
                                   34444445555555555554444........557777888888888888888888888888888888777777666..... PP

                          YkyA 100 kkeaeelieameeryeaydklykaYkealeldkeLYemLkk 140
                                    + +++l++ + +r + ++kl ++Y+++ +   +L ++++k
  gi|13541826|ref|NP_111514.1| 233 LSTVSQLKDLILQRDAEIKKLKDSYNDIFTRYDTLINKMTK 273
                                   34455555555555555555555555554444444444444 PP

>> Fez1  Fez1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4  12.9   0.00012      0.02       7     128 ..     161     282 ..     146     288 .] 0.65

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 0.00012
                          Fez1   7 QksGEislLKqQLkdsqaevtqklseivalkaqlrelrakleekeeeikeleesleektlelevcenelqrkkseaellre 87 
                                   Q + Eis L   + d  a  ++  + i +++ q+ +++a ++e+ +++ e +es+++  +e e+  ++l+ + s+++ l++
  gi|13541826|ref|NP_111514.1| 161 QMQSEISQLSAEINDLNAKKSELEQAIAEMQKQIEDIQAGIDERIKAVFEENESMKKTLEEYEKTRADLATALSTVSQLKD 241
                                   444566666666666666666666666666666666666666666666666666666666688888888888999999999 PP

                          Fez1  88 kvekleeelkelreelselsleeeeaalesdeakaqrqeae 128
                                    + + ++e+k+l++++++  ++ ++ ++++++ + ++ +a+
  gi|13541826|ref|NP_111514.1| 242 LILQRDAEIKKLKDSYNDIFTRYDTLINKMTKREFEKINAR 282
                                   99999999999999999887776666666655555544443 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   2.8   0.00018     0.029      60     116 ..     144     200 ..     121     203 .. 0.65
   2 ?    9.9   4.6    0.0044      0.71      36      96 ..     180     240 ..     178     275 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 0.00018
                       DUF1664  60 tkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesk 116
                                    k+ ++s+i  +++k d+++  ++++++e+++++ + se+++ + ++++ +e++++ 
  gi|13541826|ref|NP_111514.1| 144 EKKAIESEIGYLNSKKDQMQSEISQLSAEINDLNAKKSELEQAIAEMQKQIEDIQAG 200
                                   566666666666666666666666666666666666666666666666666665544 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0044
                       DUF1664  36 krslsdavesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredl 96 
                                   k  l++a++++ kq+e++++ + +  +   ++ +++ k+l+e +++ ++++  +++v++  
  gi|13541826|ref|NP_111514.1| 180 KSELEQAIAEMQKQIEDIQAGIDERIKAVFEENESMKKTLEEYEKTRADLATALSTVSQLK 240
                                   5678889999999999999999888888888888888888888877777766655554432 PP

>> Spectrin  Spectrin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   16.2   5.6   7.1e-05     0.011      35     105 .]     151     221 ..     123     221 .. 0.91
   2 ?    3.4   0.4      0.66   1.1e+02      38      99 ..     214     274 ..     211     277 .. 0.62

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 7.1e-05
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Spectrin  35 evqallkkhkaleaelaaqqervkalnelaeklldeghsaseeieerleelnerWeeLkelaaerkqkLee 105
                                   e+  l  k ++++ e+++   ++++ln+ +++l+++  + +++ie+ +++++er +++ e  +++k++Lee
  gi|13541826|ref|NP_111514.1| 151 EIGYLNSKKDQMQSEISQLSAEINDLNAKKSELEQAIAEMQKQIEDIQAGIDERIKAVFEENESMKKTLEE 221
                                   5556677999***********************************************************97 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.66
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHTTHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Spectrin  38 allkkhkaleaelaaqqervkalnelaeklldeghsaseeieerleelnerWeeLkelaaer 99 
                                   ++ k+++++e++ a+  + + ++ +l++ +l++ + + ++++++ +++ +r++ L  ++ +r
  gi|13541826|ref|NP_111514.1| 214 SMKKTLEEYEKTRADLATALSTVSQLKDLILQR-DAEIKKLKDSYNDIFTRYDTLINKMTKR 274
                                   444555555555555555555555655555555.5667888888888888888877776666 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 ?    6.9   0.6     0.038       6.1      89     117 ..     150     178 ..     143     180 .. 0.77
   2 ?   11.3   8.4    0.0017      0.26       2      81 ..     179     258 ..     178     277 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.038
                    TPR_MLP1_2  89 eseesweeqkeelekelselekriedlne 117
                                    +   ++++k+++++e+s+l + i+dln+
  gi|13541826|ref|NP_111514.1| 150 SEIGYLNSKKDQMQSEISQLSAEINDLNA 178
                                   55555788999999999999999999987 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.0017
                    TPR_MLP1_2   2 elksleeeikslkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkaeae 81 
                                   ++++le+ i+++++++e+ +a + +  + + ++ e++k+  + Ye+     a+++ ++++l++ + +  aei++lk++ +
  gi|13541826|ref|NP_111514.1| 179 KKSELEQAIAEMQKQIEDIQAGIDERIKAVFEENESMKKTLEEYEKTRADLATALSTVSQLKDLILQRDAEIKKLKDSYN 258
                                   78999999999999999999999999999999999999999999999999999999999999999999999999998765 PP

>> TolA_bind_tri  TolA binding protein trimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   3.5   9.9e-05     0.016      22      69 ..     161     208 ..     148     215 .. 0.92
   2 ?    3.1   0.1      0.65     1e+02      34      72 ..     236     274 ..     217     277 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 9.9e-05
                 TolA_bind_tri  22 elqqqlealqqelreLRGqiEelqyqleqleerQrdlYldlDerlrkl 69 
                                   ++q+++++l++e+++L+ +  el+  + +++++  d+   +Der++++
  gi|13541826|ref|NP_111514.1| 161 QMQSEISQLSAEINDLNAKKSELEQAIAEMQKQIEDIQAGIDERIKAV 208
                                   9*******************************************9875 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.65
                 TolA_bind_tri  34 lreLRGqiEelqyqleqleerQrdlYldlDerlrkleag 72 
                                   +++L+  i +   ++++l+   +d+++  D++++k++++
  gi|13541826|ref|NP_111514.1| 236 VSQLKDLILQRDAEIKKLKDSYNDIFTRYDTLINKMTKR 274
                                   677777777888899999999999999999999998875 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   1.7   0.00031     0.049      30      90 ..     150     208 ..     145     219 .. 0.83
   2 ?    3.6   0.3       0.4        64      18      79 ..     229     271 ..     215     282 .. 0.37

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 0.00031
                  Baculo_PEP_C  30 vqilaqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalqdtlrneLtnl 90 
                                   ++i + l++ +d++++++++ls+++++l  + +++l+++++++++++  +q  ++++++++
  gi|13541826|ref|NP_111514.1| 150 SEI-GYLNSKKDQMQSEISQLSAEINDLN-AKKSELEQAIAEMQKQIEDIQAGIDERIKAV 208
                                   566.8899999999999*****9999955.5788999999999999999998888877765 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.4
                  Baculo_PEP_C  18 LtnvLnairlqnvqilaqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnal 79 
                                   L ++L+++        +ql+ l+ + + ++++l+++ ++            +t+ ++ +n++
  gi|13541826|ref|NP_111514.1| 229 LATALSTV--------SQLKDLILQRDAEIKKLKDSYND-----------IFTRYDTLINKM 271
                                   22222222........22222222222222222222222...........222222222222 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 ?   13.2   8.9   0.00043     0.068      50     116 ..     157     223 ..     148     224 .. 0.87
   2 ?    5.3   3.0      0.12        19      33      77 ..     210     254 ..     203     258 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00043
                         DHR10  50 akleeakkklkelrdaleekeielrelerkeerlqrqlenaeeklerlreqaeekreaakarleelr 116
                                    k ++ ++++++l++++++++++++ele+ ++ +q+q+e  +  ++   +   e+ e++k++lee +
  gi|13541826|ref|NP_111514.1| 157 SKKDQMQSEISQLSAEINDLNAKKSELEQAIAEMQKQIEDIQAGIDERIKAVFEENESMKKTLEEYE 223
                                   5778899999999999999999999999999999999999999999999999999999999999875 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.12
                         DHR10  33 kdlrsciklleeieaelakleeakkklkelrdaleekeielrele 77 
                                   ++ +s  k lee e+  a l +a +++++l+d + ++ +e ++l+
  gi|13541826|ref|NP_111514.1| 210 EENESMKKTLEEYEKTRADLATALSTVSQLKDLILQRDAEIKKLK 254
                                   5667777999***************************99999886 PP

>> Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   7.2   0.00027     0.044      50     103 ..     143     200 ..     119     203 .. 0.73
   2 ?    5.1   1.9      0.16        26      53     100 ..     213     260 ..     203     269 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 0.00027
                                   HHHHHHHHHCCCCCCTT....S-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCT CS
                  Seryl_tRNA_N  50 aerNelskeIgkakkkk....edaeeliaevkelkeelkaleaelkeleaelekllla 103
                                    e++++  eIg +  kk     ++++l ae+++l+++ ++le++ +e+++++e++ + 
  gi|13541826|ref|NP_111514.1| 143 GEKKAIESEIGYLNSKKdqmqSEISQLSAEINDLNAKKSELEQAIAEMQKQIEDIQAG 200
                                   4677777788777777767777777777777777777777777777777777777655 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.16
                                   HHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH CS
                  Seryl_tRNA_N  53 NelskeIgkakkkkedaeeliaevkelkeelkaleaelkeleaelekl 100
                                    ++ k+ ++  k  +d +  +  v++lk+ + + +ae k+l++  +++
  gi|13541826|ref|NP_111514.1| 213 ESMKKTLEEYEKTRADLATALSTVSQLKDLILQRDAEIKKLKDSYNDI 260
                                   344566666666667777777778888888888888888887777776 PP

>> ADIP  Afadin- and alpha -actinin-Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3  12.5   0.00042     0.068      59     150 ..     156     257 ..     145     259 .. 0.60
   2 ?    2.6   0.3      0.79   1.3e+02      59      91 ..     240     272 ..     231     287 .. 0.59

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00042
                          ADIP  59 netirkleaeierlqskierlktqleqlerelalvqakerqlekklkt.......leqklknekeelqrlknalq...qik 129
                                   n +  ++++ei++l+++i+ l ++ ++le+ +a  q++  ++++ + +       +++ +k++ ee ++++ +l+   ++ 
  gi|13541826|ref|NP_111514.1| 156 NSKKDQMQSEISQLSAEINDLNAKKSELEQAIAEMQKQIEDIQAGIDErikavfeENESMKKTLEEYEKTRADLAtalSTV 236
                                   555666777777777777777777777777777777777777766665000000055555555555555555544111233 PP

                          ADIP 130 tqyahelkkkdreiekLkekl 150
                                    q++  + ++d ei+kLk+ +
  gi|13541826|ref|NP_111514.1| 237 SQLKDLILQRDAEIKKLKDSY 257
                                   455566778888888888866 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.79
                          ADIP  59 netirkleaeierlqskierlktqleqlerela 91 
                                   ++ i + +aei++l+ +++   t++  l ++++
  gi|13541826|ref|NP_111514.1| 240 KDLILQRDAEIKKLKDSYNDIFTRYDTLINKMT 272
                                   445555555555555555555555555555555 PP

>> DUF2968  Protein of unknown function (DUF2968)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   1.7   0.00027     0.043     124     176 ..     147     199 ..     142     203 .. 0.89
   2 ?    1.9   0.1      0.94   1.5e+02      10      42 ..     224     258 ..     210     264 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00027
                       DUF2968 124 rLqadlavarqQeqavaerQkqarkeaaaLeaqreaaqaqlralqrqirqLqa 176
                                   ++++++   ++ + +++++ +q+ +e + L+a+++++++ + ++q+qi+++qa
  gi|13541826|ref|NP_111514.1| 147 AIESEIGYLNSKKDQMQSEISQLSAEINDLNAKKSELEQAIAEMQKQIEDIQA 199
                                   667777788889999**********************************9997 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.94
                       DUF2968  10 apaaaeaaaqstvaelqqli..qakeltelrttyn 42 
                                   +++a+ a+a stv++l++li  +++e+++l+ +yn
  gi|13541826|ref|NP_111514.1| 224 KTRADLATALSTVSQLKDLIlqRDAEIKKLKDSYN 258
                                   44555566899999999999333568999999998 PP

>> COG5  Golgi transport complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.6    0.0016      0.26      74     114 ..     145     185 ..      87     186 .. 0.81
   2 ?   11.2   3.7     0.002      0.32      29     119 ..     174     267 ..     170     272 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0016
                                   XXXXXXXXXXXXXXXXXXX-TTHHHHHHHHHHHHHHHHHHH CS
                          COG5  74 lselksslesLsasyerlkskvlepyeeaeklqsalkrlhq 114
                                    + ++s++ +L++  ++++s++++  +e++ l+++ + l q
  gi|13541826|ref|NP_111514.1| 145 KKAIESEIGYLNSKKDQMQSEISQLSAEINDLNAKKSELEQ 185
                                   468******************************99999887 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.002
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXXXXXX-TTHHHHHHHHHHH CS
                          COG5  29 ldlstplkrlnydiqeldkrlrqlitsnhleLlehlskskslssvlselks...slesLsasyerlkskvlepyeeaeklq 106
                                    dl+++ + l+++i e++k+++++     + + + +++++s +++l+e ++    l+   + +++lk  +l++ +e++kl+
  gi|13541826|ref|NP_111514.1| 174 NDLNAKKSELEQAIAEMQKQIEDIQAGIDERIKAVFEENESMKKTLEEYEKtraDLATALSTVSQLKDLILQRDAEIKKLK 254
                                   6999*****************99877666666666666666666666655500056655677899**************** PP

                                   HHHHHHHHHHHHH CS
                          COG5 107 salkrlhqtldLl 119
                                    + + + + +d+l
  gi|13541826|ref|NP_111514.1| 255 DSYNDIFTRYDTL 267
                                   9999988877776 PP

>> CRAL_TRIO  CRAL/TRIO domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   0.00046     0.074       5      86 ..      44     126 ..      40     138 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00046
                     CRAL_TRIO   5 eggkvgihgrDkegrpvlylrlgrfdpkklsleelvralvlvlerllkelee..dgqvegvtvviDlkglslskmlwkp.i 82 
                                   ++ +  +   +k +r +l+ ++++ + ++++ +++vr++ + ++++l++++   + +     v+ D+++++ s ++ +   
  gi|13541826|ref|NP_111514.1|  44 DNIPEWVFEPEKANRIILFNHFKSLELNDYN-KKFVRYVYHRITQMLEKNPSdeKLKDLREFVIEDMTNIE-SPFELDLvR 122
                                   556667788999****************999.9***************99996555555557999****99.888844444 PP

                     CRAL_TRIO  83 sllk 86 
                                   + +k
  gi|13541826|ref|NP_111514.1| 123 EAMK 126
                                   4444 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2  13.0   0.00032     0.051     319     422 ..     159     255 ..     120     285 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00032
                          FapA 319 elgtkteiev.gldepelkeklkeleeeleeleeeleklkkkikklpklka.ekqlesekkeqlkklletkeklkeeleel 397
                                   + + + ei++ + + ++l++k +ele+ + e+++++e++++ i++  k    e++  ++ +e+++k++ ++    + +++l
  gi|13541826|ref|NP_111514.1| 159 KDQMQSEISQlSAEINDLNAKKSELEQAIAEMQKQIEDIQAGIDERIKAVFeENESMKKTLEEYEKTRADLATALSTVSQL 239
                                   444455566666667777777777777777777777777777777666444344444555556666666666666666666 PP

                          FapA 398 eeelkelkeeleskkeeakikvnke 422
                                   ++ + + ++e+++          k 
  gi|13541826|ref|NP_111514.1| 240 KDLILQRDAEIKKL---------KD 255
                                   66666666666555.........33 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 ?   11.5   2.5     0.002      0.32      25      65 ..     160     195 ..     146     202 .. 0.85
   2 ?    2.2   0.2       1.6   2.6e+02      14      42 ..     202     230 ..     196     236 .. 0.81
   3 ?    7.2   0.3     0.043         7       7      53 ..     233     279 ..     227     288 .] 0.82

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.002
                   Cep57_MT_bd  25 ehlklelqelaaqynaldpslgkrkRkdLaeeleelvkrlE 65 
                                   ++++ e ++l+a++n+l+     +k+ +L++ + e++k++E
  gi|13541826|ref|NP_111514.1| 160 DQMQSEISQLSAEINDLN-----AKKSELEQAIAEMQKQIE 195
                                   578888888888888888.....9****************9 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 1.6
                   Cep57_MT_bd  14 aevlkeLedEfehlklelqelaaqynald 42 
                                    e +k+  +E e +k+ l+e++++  +l 
  gi|13541826|ref|NP_111514.1| 202 DERIKAVFEENESMKKTLEEYEKTRADLA 230
                                   57899999************999866665 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.043
                   Cep57_MT_bd   7 qspkeaLaevlkeLedEfehlklelqelaaqynaldpslgkrkRkdL 53 
                                    s   +L++++ +   E+++lk  + +   +y  l   ++kr+ +++
  gi|13541826|ref|NP_111514.1| 233 LSTVSQLKDLILQRDAEIKKLKDSYNDIFTRYDTLINKMTKREFEKI 279
                                   566789***************************99999988875554 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 ?    0.4   0.0         4   6.4e+02      89     110 ..      11      32 ..       7      42 .. 0.82
   2 ?   11.0   8.9    0.0021      0.33      51     127 ..     157     235 ..     145     237 .. 0.73
   3 ?    4.2   0.1      0.27        43      33      72 ..     234     273 ..     230     286 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 4
                     ApoLp-III  89 qekvQsgvqslvkesqklaesl 110
                                   + k+Q+ +   vkes k+ +++
  gi|13541826|ref|NP_111514.1|  11 RFKIQEDLDRRVKESGKTYKEI 32 
                                   5689999999999999998876 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.0021
                     ApoLp-III  51 kksdeleealkevkkkieetadklse...enPevkkkaqelqekvQsgvqslvkesqklaeslkensqeakeklakaikq 127
                                    k d++++ ++++ ++i+   +k se   + +e++k++++ q+ + ++++++++e + + ++l+e  +++ ++la+a+  
  gi|13541826|ref|NP_111514.1| 157 SKKDQMQSEISQLSAEINDLNAKKSEleqAIAEMQKQIEDIQAGIDERIKAVFEENESMKKTLEE-YEKTRADLATALST 235
                                   455566666666666665555443334449999**************************999975.67888888888765 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.27
                     ApoLp-III  33 nlvdqlkqvikslqeelkkksdeleealkevkkkieetad 72 
                                   + v+qlk++i + + e+kk  d  + +++   + i+++++
  gi|13541826|ref|NP_111514.1| 234 STVSQLKDLILQRDAEIKKLKDSYNDIFTRYDTLINKMTK 273
                                   679**************************99999999875 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2  15.7      0.01       1.6      45     123 ..     148     230 ..      75     233 .. 0.71
   2 ?    6.3   5.3     0.081        13      53     102 ..     202     250 ..     198     286 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.01
                        APG6_N  45 qdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeelealeeeeerfwr...eyne.lqlelleleeelds 121
                                    ++e+  l+ + +++++e ++l +e+++l ++++ele+++a+ +++ e++++  ++ ++   e ne  + +l+e e+ ++ 
  gi|13541826|ref|NP_111514.1| 148 IESEIGYLNSKKDQMQSEISQLSAEINDLNAKKSELEQAIAEMQKQIEDIQAGIDERIKavfEENEsMKKTLEEYEKTRAD 228
                                   445666677778888888888888888888888888888888888888877644444332223444477777777777766 PP

                        APG6_N 122 le 123
                                   l+
  gi|13541826|ref|NP_111514.1| 229 LA 230
                                   65 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.081
                        APG6_N  53 eeeleklekeeeelleeLkelekereeleaelaaleeelealeeeeerfw 102
                                   +e+++++ +e e++ + L+e ek+r++l+ +l++ ++ l++l  + ++++
  gi|13541826|ref|NP_111514.1| 202 DERIKAVFEENESMKKTLEEYEKTRADLATALSTVSQ-LKDLILQRDAEI 250
                                   5667777777777777777777777777777765533.333333333332 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   2.9   0.00029     0.046       9      63 ..     148     199 ..     146     211 .. 0.92
   2 ?    4.5   2.7      0.31        50      11      63 ..     185     238 ..     185     272 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 0.00029
                       NPV_P10   9 IradikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqd 63 
                                   I ++i  +++k d +q+++ +++++++d   ln+k  ++ +++ae+++++e+Iq 
  gi|13541826|ref|NP_111514.1| 148 IESEIGYLNSKKDQMQSEISQLSAEIND---LNAKKSELEQAIAEMQKQIEDIQA 199
                                   7789999*****************9999...9999999***************96 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.31
                       NPV_P10  11 adikavddkVdalqqqvdd.vqenlpdvtelnekLdaqsaqLaeletkvenIqd 63 
                                   ++i++++++++ +q+ +d+ +++ +++ + +++ L++  ++ a+l t+++++++
  gi|13541826|ref|NP_111514.1| 185 QAIAEMQKQIEDIQAGIDErIKAVFEENESMKKTLEEYEKTRADLATALSTVSQ 238
                                   689999999999999996438888888888999999999998888886665543 PP

>> DUF2730  Protein of unknown function (DUF2730)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.3    0.0084       1.3      62      93 ..     163     194 ..     138     197 .. 0.80
   2 ?    6.2   0.8     0.067        11      36      99 ..     206     270 ..     202     273 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0084
                       DUF2730  62 akdlekLkllladlrgelkaleaevrqlshqv 93 
                                   ++++++L+ +++dl+++ ++le+ ++++++q+
  gi|13541826|ref|NP_111514.1| 163 QSEISQLSAEINDLNAKKSELEQAIAEMQKQI 194
                                   67899**********************99986 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.067
                       DUF2730  36 eklaekveendkrlteletkvenLPta.kdlekLkllladlrgelkaleaevrqlshqvdLLLen 99 
                                   + + e+ e+++k l+e e + ++L ta + +++Lk l+ + ++e+k+l+ + + + ++ d L+++
  gi|13541826|ref|NP_111514.1| 206 KAVFEENESMKKTLEEYEKTRADLATAlSTVSQLKDLILQRDAEIKKLKDSYNDIFTRYDTLINK 270
                                   5677888899999*****99999999856899*******************99999999999876 PP

>> UPF0242  Uncharacterised protein family (UPF0242) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9  17.0    0.0023      0.37      66     182 ..     144     260 ..      59     274 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0023
                       UPF0242  66 ekskleekeaklteld....eglktkeealeelqeeeeeLkeeldakeeelerlkeenqqLqekleaiaedfeelklelee 142
                                   ek+ +e+++  l +++     ++++   ++++l++++ eL++ ++++++++e  +   + + e+ +a+ e++e +k+ lee
  gi|13541826|ref|NP_111514.1| 144 EKKAIESEIGYLNSKKdqmqSEISQLSAEINDLNAKKSELEQAIAEMQKQIEDIQ---AGIDERIKAVFEENESMKKTLEE 221
                                   4455555555555544333334466666888888888888888888888877665...57888888888899999999988 PP

                       UPF0242 143 qLaekqellqeyqetieeqrsvlekrqdqieqLeskVrDl 182
                                     + +   l +   t+++++  + +r+++i++L    +D+
  gi|13541826|ref|NP_111514.1| 222 YEKTRA-DLATALSTVSQLKDLILQRDAEIKKLKDSYNDI 260
                                   755554.555666799999999999999999998777776 PP

>> RasGAP_C  RasGAP C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   7.1    0.0002     0.032      26     104 ..     140     217 ..     127     234 .. 0.77
   2 ?    4.3   0.1      0.26        42      37      65 ..     235     263 ..     227     273 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 0.0002
                      RasGAP_C  26 nyqellneIakdirnkgrlrekrkeElesleetlktLseknnylesqlesYkayienvleqlkkkkgklpfskqyfkkr 104
                                   ++    ++I+ +i  ++++++++++E++ l + +++L+ k++ le+ ++++++ ie + + + ++  k +f ++ + k+
  gi|13541826|ref|NP_111514.1| 140 GLVGEKKAIESEIGYLNSKKDQMQSEISQLSAEINDLNAKKSELEQAIAEMQKQIEDIQAGIDER-IKAVFEENESMKK 217
                                   55555689*************************************************99999887.2333333333333 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.26
                      RasGAP_C  37 dirnkgrlrekrkeElesleetlktLsek 65 
                                   ++ ++++l+ +r +E+++l++ ++++  +
  gi|13541826|ref|NP_111514.1| 235 TVSQLKDLILQRDAEIKKLKDSYNDIFTR 263
                                   567889999***************99765 PP

>> DUF5344  Family of unknown function (DUF5344)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.2         3   4.9e+02      10      40 ..     147     177 ..     144     180 .. 0.61
   2 ?   11.9   3.8    0.0017      0.27       7      64 ..     179     234 ..     174     242 .. 0.80
   3 ?    7.4   0.1     0.041       6.6      44      68 ..     249     273 ..     240     281 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 3
                       DUF5344  10 eVeqkLselktaaeelktsipetisgknsld 40 
                                    +e+++  l+++ ++++++i++ +++ n+l+
  gi|13541826|ref|NP_111514.1| 147 AIESEIGYLNSKKDQMQSEISQLSAEINDLN 177
                                   5666666667777777666666666666555 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.0017
                       DUF5344   7 nqaeVeqkLselktaaeelktsipetisgknsldvvekineleeeleellkaYktlll 64 
                                   +++e+eq+++e+++++e++++ i+e i+     +  e++++  ee+e+ + +++t+l+
  gi|13541826|ref|NP_111514.1| 179 KKSELEQAIAEMQKQIEDIQAGIDERIKA--VFEENESMKKTLEEYEKTRADLATALS 234
                                   789************************98..666666677777777777777776665 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.041
                       DUF5344  44 kineleeeleellkaYktlllknve 68 
                                   +i++l++++++++++Y tl++k ++
  gi|13541826|ref|NP_111514.1| 249 EIKKLKDSYNDIFTRYDTLINKMTK 273
                                   699*****************99876 PP

>> LPP  Lipoprotein leucine-zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.1      0.13        21       5      25 ..     148     168 ..     146     169 .. 0.88
   2 ?   13.7   3.4   0.00038     0.061       2      34 ..     166     198 ..     165     200 .. 0.95
   3 ?    0.7   0.1       4.4     7e+02       8      30 ..     235     257 ..     228     261 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.13
                           LPP   5 LssqVsqLkskvdqlssdvns 25 
                                   + s++  L+sk dq++s++++
  gi|13541826|ref|NP_111514.1| 148 IESEIGYLNSKKDQMQSEISQ 168
                                   678999************987 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 0.00038
                           LPP   2 ldeLssqVsqLkskvdqlssdvnsakaaaqaak 34 
                                   +++Ls+++++L++k ++l++ ++++++++++++
  gi|13541826|ref|NP_111514.1| 166 ISQLSAEINDLNAKKSELEQAIAEMQKQIEDIQ 198
                                   78****************************998 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 4.4
                           LPP   8 qVsqLkskvdqlssdvnsakaaa 30 
                                    VsqLk+ + q  ++++++k+  
  gi|13541826|ref|NP_111514.1| 235 TVSQLKDLILQRDAEIKKLKDSY 257
                                   58999999988888888888765 PP

>> MYO10_CC  Unconventional myosin-X coiled coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.1       3.7   5.9e+02      13      31 ..     149     167 ..     148     170 .. 0.81
   2 ?    4.6   3.7      0.23        36       5      36 ..     161     193 ..     157     211 .. 0.78
   3 ?   11.4   0.9    0.0017      0.27      17      51 ..     220     255 ..     209     256 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 3.7
                      MYO10_CC  13 ErEIerLqrqkedqvsslc 31 
                                   E EI  L  +k++  s + 
  gi|13541826|ref|NP_111514.1| 149 ESEIGYLNSKKDQMQSEIS 167
                                   889****999999887765 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.23
                      MYO10_CC   5 QmE.EILRLErEIerLqrqkedqvsslceesrq 36 
                                   Qm  EI +L  EI++L  +k + ++++ e  +q
  gi|13541826|ref|NP_111514.1| 161 QMQsEISQLSAEINDLNAKKSELEQAIAEMQKQ 193
                                   66339*****************99999987654 PP

  == domain 3  score: 11.4 bits;  conditional E-value: 0.0017
                      MYO10_CC  17 erLqrqkedqvsslcees.rqelqrlRdeelkrLek 51 
                                   e+  + + d  ++l + s ++ l+ +Rd+e+k+L +
  gi|13541826|ref|NP_111514.1| 220 EEYEKTRADLATALSTVSqLKDLILQRDAEIKKLKD 255
                                   6667778888888877763799************86 PP

>> DUF812  Protein of unknown function (DUF812)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5  17.9   0.00062       0.1     322     421 ..     156     259 ..      54     288 .] 0.64

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00062
                        DUF812 322 eelkkkreeeleelqeqieeleskieeleeeikklessikqv....eeeleeekeeneelekevklkkktlellpdaeeni 398
                                   +  k + + e+++l+ +i++l++k +ele+ i++++++i+ +    +e +++  eene  +k+++  +kt + l++a + +
  gi|13541826|ref|NP_111514.1| 156 NSKKDQMQSEISQLSAEINDLNAKKSELEQAIAEMQKQIEDIqagiDERIKAVFEENESMKKTLEEYEKTRADLATALSTV 236
                                   334455566666666667776666666666666666666654111145666677788888888888888888888888999 PP

                        DUF812 399 ekLqalveasaqrlvelakqWek 421
                                   ++L+ l+ +  +++++l++ ++ 
  gi|13541826|ref|NP_111514.1| 237 SQLKDLILQRDAEIKKLKDSYND 259
                                   99999998888888888887764 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 ?   12.0  10.5    0.0012      0.19      43     153 ..     157     270 ..     151     273 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0012
                 Jnk-SapK_ap_N  43 srneeeeaeleelreeleqLeteyerekelrkraeeeleeiedqweeerkelqekveqleeenrelelkakn...aadqls 120
                                   s++++ ++e+++l++e+++L  ++++  ++  + ++++e i   ++e+ k++ e+ e++++  +e+e+   +   a   +s
  gi|13541826|ref|NP_111514.1| 157 SKKDQMQSEISQLSAEINDLNAKKSELEQAIAEMQKQIEDIQAGIDERIKAVFEENESMKKTLEEYEKTRADlatALSTVS 237
                                   678899999999999999999999999999999999999999999999999999999999888888833333111445566 PP

                 Jnk-SapK_ap_N 121 rleekeaelkkeysklheretellkklkelver 153
                                   +l++   +   e +kl++++++++ ++  l+++
  gi|13541826|ref|NP_111514.1| 238 QLKDLILQRDAEIKKLKDSYNDIFTRYDTLINK 270
                                   677777788888899999999999999998887 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 ?   12.4   4.2   0.00079      0.13      59     132 ..     168     242 ..     159     243 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00079
                          COG2  59 slSghLvglqeeleevesplaaarkkvesvreklsereeevesk.leeakeleekrellklllkldevvekleal 132
                                   +lS++  +l+++ +e+e+ +a+++k++e++++ ++er+++v ++  + +k lee ++   +l     +v++l +l
  gi|13541826|ref|NP_111514.1| 168 QLSAEINDLNAKKSELEQAIAEMQKQIEDIQAGIDERIKAVFEEnESMKKTLEEYEKTRADLATALSTVSQLKDL 242
                                   699999*********************************996550556788899999999999999999999887 PP

>> APG17  Autophagy protein Apg17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   3.6       0.1        16     253     299 ..     147     193 ..      74     197 .. 0.72
   2 ?    8.3   6.8    0.0068       1.1     253     331 ..     147     223 ..     117     225 .. 0.83
   3 ?   12.4   9.3    0.0004     0.064     244     345 ..     173     275 ..     163     283 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.1
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH....HHHHHHHHHHHH CS
                         APG17 253 emekakkllsekkeeiekllsalkkaleeleevgkklpeylaifkae 299
                                   ++e++  +l++kk+++++ +s+l++ +++l++ +++l++ +a ++++
  gi|13541826|ref|NP_111514.1| 147 AIESEIGYLNSKKDQMQSEISQLSAEINDLNAKKSELEQAIAEMQKQ 193
                                   44667777777777777777777777777777677777777755544 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0068
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH....HHHHHHHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHH CS
                         APG17 253 emekakkllsekkeeiekllsalkkaleeleevgkklpeylaifkaeeeflerweeekekieekleeleeLrefYegFl 331
                                   ++e++  +l++kk+++++ +s+l++ +++l++ +++l++ +a ++++ e ++      e+i++ +ee e++++  e+++
  gi|13541826|ref|NP_111514.1| 147 AIESEIGYLNSKKDQMQSEISQLSAEINDLNAKKSELEQAIAEMQKQIEDIQA--GIDERIKAVFEENESMKKTLEEYE 223
                                   56999999***********************9999*******77777777777..777888888888888777777776 PP

  == domain 3  score: 12.4 bits;  conditional E-value: 0.0004
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHH....HHHHHHHHHHHHHHHHHH...HHHHHHHHHHHHHHH CS
                         APG17 244 vkelqerleemekakkllsekkeeiekll.salkkaleeleevgkklpeylaifkaeeeflerweeekekieekleeleeL 323
                                   +++l+++ +e+e+a ++++++ e+i++ + + +k+++ee e+++k+l+ey ++ ++ ++ l++ ++ k+ i ++ +e+++L
  gi|13541826|ref|NP_111514.1| 173 INDLNAKKSELEQAIAEMQKQIEDIQAGIdERIKAVFEENESMKKTLEEYEKTRADLATALSTVSQLKDLILQRDAEIKKL 253
                                   6788888889999999999999999876515689999999999*********99999999999****************** PP

                                   HHHHHHHHHHHHHHHHHHHHHH CS
                         APG17 324 refYegFlsaYdklllEveRRr 345
                                   ++ Y+   + Yd+l+  + +R+
  gi|13541826|ref|NP_111514.1| 254 KDSYNDIFTRYDTLINKMTKRE 275
                                   **************99888776 PP

>> Uso1_p115_C  Uso1 / p115 like vesicle tethering protein, C terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3  10.8     0.001      0.16       2      68 ..     158     229 ..     144     237 .. 0.76
   2 ?    2.5   0.2       1.1   1.7e+02       8      36 ..     234     262 ..     229     287 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.001
                   Uso1_p115_C   2 kaseleseaaslkdeneklkaelqslskalesleqk..eakkaaesqakeleaenkklek...eleklrael 68 
                                   k+ +++se ++l+ e ++l+a+ ++l++a+ +++++    ++ ++++ k +++en++++k   e ek+ra l
  gi|13541826|ref|NP_111514.1| 158 KKDQMQSEISQLSAEINDLNAKKSELEQAIAEMQKQieDIQAGIDERIKAVFEENESMKKtleEYEKTRADL 229
                                   678899999999999999999999999999999999766666667777777777777777444444444444 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 1.1
                   Uso1_p115_C   8 seaaslkdeneklkaelqslskalesleq 36 
                                   s++++lkd+  +  ae+++l++++++   
  gi|13541826|ref|NP_111514.1| 234 STVSQLKDLILQRDAEIKKLKDSYNDIFT 262
                                   6789999999999999****999998655 PP

>> Cnn_1N  Centrosomin N-terminal motif 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   7.6    0.0005      0.08       5      71 ..     162     231 ..     158     233 .. 0.89
   2 ?    0.6   0.1       3.9   6.3e+02      41      66 ..     232     257 ..     227     261 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.0005
                        Cnn_1N   5 qeeqidkLkKENFdLKLriyfLeerleklse..eqkeellkenie.lkveveslqkelkekkkllreaek 71 
                                   ++++i++L+ E  dL  +  +Le+++ ++++  e++++ ++e+i+ + +e+es++k+l+e++k   ++++
  gi|13541826|ref|NP_111514.1| 162 MQSEISQLSAEINDLNAKKSELEQAIAEMQKqiEDIQAGIDERIKaVFEENESMKKTLEEYEKTRADLAT 231
                                   6889***************************9999999999999834689************98877766 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 3.9
                        Cnn_1N  41 llkenielkveveslqkelkekkkll 66 
                                   +l++  +lk+ + +   e+k++k++ 
  gi|13541826|ref|NP_111514.1| 232 ALSTVSQLKDLILQRDAEIKKLKDSY 257
                                   56777899999999999999999875 PP

>> ABC_tran_CTD  ABC transporter C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   7.5    0.0098       1.6       7      49 ..     163     193 ..     143     203 .. 0.46
   2 ?    9.8   8.3    0.0057      0.92      12      62 ..     182     234 ..     181     241 .. 0.86
   3 ?    2.8   0.1      0.89   1.4e+02      12      49 ..     238     274 ..     234     282 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0098
                  ABC_tran_CTD   7 qreleeleaeIeaLEeeiaeleaeladpelysdpeklaelsae 49 
                                   q e+ +l aeI+ L ++++ele+++a            e +++
  gi|13541826|ref|NP_111514.1| 163 QSEISQLSAEINDLNAKKSELEQAIA------------EMQKQ 193
                                   33344444444444444444444444............34444 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0057
                  ABC_tran_CTD  12 eleaeIeaLEeeiaeleaelad..pelysdpeklaelsaeleeleaeLeelye 62 
                                   ele+ I++++++i++++a + +   ++++  e ++++ +e+e+ +a+L+++++
  gi|13541826|ref|NP_111514.1| 182 ELEQAIAEMQKQIEDIQAGIDEriKAVFEENESMKKTLEEYEKTRADLATALS 234
                                   79****************766533488899999****************9986 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.89
                  ABC_tran_CTD  12 eleaeIeaLEeeiaeleaeladpelysdp.eklaelsae 49 
                                   +l + I + ++ei++l +  +  ++++++ + +++ +++
  gi|13541826|ref|NP_111514.1| 238 QLKDLILQRDAEIKKLKDSYN--DIFTRYdTLINKMTKR 274
                                   788889999999999999888..6778885556666665 PP

>> BRE1  BRE1 E3 ubiquitin ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   5.1    0.0057      0.91       8      58 ..     148     198 ..     142     203 .. 0.66
   2 ?   12.4  13.6   0.00076      0.12       2      91 ..     163     252 ..     162     257 .. 0.91
   3 ?    7.2   4.3     0.032       5.1       5      63 ..     215     273 ..     211     287 .. 0.92

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0057
                          BRE1   8 lekafeelseqlskkvkeltileekklrleaekakadqkyfaamrskdale 58 
                                   +e ++  l+++ +++++e++ l  +++ l+a+k++ +q + + ++++++++
  gi|13541826|ref|NP_111514.1| 148 IESEIGYLNSKKDQMQSEISQLSAEINDLNAKKSELEQAIAEMQKQIEDIQ 198
                                   555666666666677777777777777777777777777777777776665 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00076
                          BRE1   2 qkELvklekafeelseqlskkvkeltileekklrleaekakadqkyfaamrskdalenelkkLnkllsKsselieqLkele 82 
                                   q+E+ +l++++++l+++ s++ + ++ +++++  ++a +++  +  f+ + s+++   e  k ++ l+   ++++qLk+l 
  gi|13541826|ref|NP_111514.1| 163 QSEISQLSAEINDLNAKKSELEQAIAEMQKQIEDIQAGIDERIKAVFEENESMKKTLEEYEKTRADLATALSTVSQLKDLI 243
                                   99*****************************************************************************55 PP

                          BRE1  83 kefvrklke 91 
                                    +  +++k+
  gi|13541826|ref|NP_111514.1| 244 LQRDAEIKK 252
                                   555555544 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.032
                          BRE1   5 Lvklekafeelseqlskkvkeltileekklrleaekakadqkyfaamrskdalenelkk 63 
                                   ++k  +++e++++ l + ++ ++ l++ +l+ +ae++k +  y ++    d+l n++ k
  gi|13541826|ref|NP_111514.1| 215 MKKTLEEYEKTRADLATALSTVSQLKDLILQRDAEIKKLKDSYNDIFTRYDTLINKMTK 273
                                   778889****************************************9999999999876 PP

>> DUF641  Plant protein of unknown function (DUF641)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   5.7     0.055       8.8      57     127 ..     151     221 ..     113     222 .. 0.79
   2 ?    9.0   2.6     0.011       1.7      71     118 ..     213     260 ..     187     270 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.055
                        DUF641  57 krlyrkkqkkkaseaeeseleaeiqeqrsllktyeitvkkleaelkakdseie.eLkekLeeaeksnkklek 127
                                      y++++k++ +  e s+l+aei+++  +   +e ++ +++++++  ++ i+ ++k+ +ee+e+ +k+le+
  gi|13541826|ref|NP_111514.1| 151 EIGYLNSKKDQMQ-SEISQLSAEINDLNAKKSELEQAIAEMQKQIEDIQAGIDeRIKAVFEENESMKKTLEE 221
                                   4567777776655.7889999999999999999999999999999999999962588888888888888875 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.011
                        DUF641  71 aeeseleaeiqeqrsllktyeitvkkleaelkakdseieeLkekLeea 118
                                   ++ ++   e ++ r  l+t   tv++l+  + ++d+ei++Lk++ +++
  gi|13541826|ref|NP_111514.1| 213 ESMKKTLEEYEKTRADLATALSTVSQLKDLILQRDAEIKKLKDSYNDI 260
                                   333444456666999***************************987765 PP

>> MCPsignal  Methyl-accepting chemotaxis protein (MCP) signalling domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.3       1.6   2.5e+02     129     157 ..     161     186 ..     108     190 .. 0.58
   2 ?   12.1   4.2   0.00081      0.13      76     159 ..     172     258 ..     166     271 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 1.6
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     MCPsignal 129 alkeiveavaevadlvqeiaaaseeqsas 157
                                   ++    ++++++++++++++a  +e+ ++
  gi|13541826|ref|NP_111514.1| 161 QM---QSEISQLSAEINDLNAKKSELEQA 186
                                   22...234444444444444444444444 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00081
                                   HHHHH.HHHH..HHHHHHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     MCPsignal  76 EVrkL.Aers..aqaakeiealiieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaasee 153
                                   E+ +L A++s   qa  e+++ i++iq++i++ ++++ e ++ +++++e+ e+t+ +l++  ++v++++dl+ +  a  ++
  gi|13541826|ref|NP_111514.1| 172 EINDLnAKKSelEQAIAEMQKQIEDIQAGIDERIKAVFEENESMKKTLEEYEKTRADLATALSTVSQLKDLILQRDAEIKK 252
                                   5555533444225889999***********************************************999998766666665 PP

                                   HHHHHH CS
                     MCPsignal 154 qsasie 159
                                   +  s +
  gi|13541826|ref|NP_111514.1| 253 LKDSYN 258
                                   555555 PP

>> CHASE3  CHASE3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   1.2    0.0047      0.75      31      89 ..     153     212 ..     145     218 .. 0.77
   2 ?    5.7   0.6     0.083        13      39      99 ..     217     277 ..     213     287 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0047
                        CHASE3  31 GYlltgdeefLepyeqaraeiqealeelreltadnpeqqerldrlealieqkl.aeleet 89 
                                   GYl + ++++ ++  q  aei++  ++ +el +   e+q+++++++a i++++ a++ee 
  gi|13541826|ref|NP_111514.1| 153 GYLNSKKDQMQSEISQLSAEINDLNAKKSELEQAIAEMQKQIEDIQAGIDERIkAVFEEN 212
                                   777777777777777778888888888888888888999999999999999998888876 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.083
                        CHASE3  39 efLepyeqaraeiqealeelreltadnpeqqerldrlealieqklaeleetialrreggle 99 
                                   + Le+ye+ ra++ +al+++++l     +  + +++l+  +++ ++  + +i+ +  + +e
  gi|13541826|ref|NP_111514.1| 217 KTLEEYEKTRADLATALSTVSQLKDLILQRDAEIKKLKDSYNDIFTRYDTLINKMTKREFE 277
                                   5799***************999998777888888888888888888888888777666665 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 ?   10.1  11.1    0.0027      0.44      81     184 ..     146     245 ..      88     286 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0027
                  HAUS-augmin3  81 eaLeqelqeLqkekalklkrlnkLqvqaaslqqelrkleeeekeakkklkeaqeelraenaetnavLqqlteeakqlaeyf 161
                                   +a e+e+  L + k+  +++ ++L + +++l+ ++++le++  e++k+++++q+ + ++++   av+++  +  k+  e +
  gi|13541826|ref|NP_111514.1| 146 KAIESEIGYLNSKKDQMQSEISQLSAEINDLNAKKSELEQAIAEMQKQIEDIQAGIDERIK---AVFEENES-MKKTLEEY 222
                                   5667777777777777777777777777777777777777777777777777777766543...33333333.33333344 PP

                  HAUS-augmin3 162 eeaekgqppvlLsqldLepYleq 184
                                   e+++ +  ++l     L++ + q
  gi|13541826|ref|NP_111514.1| 223 EKTRADLATALSTVSQLKDLILQ 245
                                   44444444444444444444444 PP

>> Syntaxin-6_N  Syntaxin 6, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   8.9      0.05       7.9      20      97 ..     158     238 ..      74     240 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.05
                  Syntaxin-6_N  20 lyrrwe.rlledtssstseeldetrteLrkalrsiewdledLeetv.....riveknpskfkidekelsrrrafveevree 94 
                                     ++++ ++ +++   + ++l+  ++eL++a+ ++++++ed++  +     ++ e+n + +k + +e ++ ra ++ + ++
  gi|13541826|ref|NP_111514.1| 158 KKDQMQsEISQLSA--EINDLNAKKSELEQAIAEMQKQIEDIQAGIderikAVFEEN-ESMKKTLEEYEKTRADLATALST 235
                                   33333213333332..46778888888888888888888888877755553345555.66666666766666666666666 PP

                  Syntaxin-6_N  95 vke 97 
                                   v++
  gi|13541826|ref|NP_111514.1| 236 VSQ 238
                                   665 PP

>> DUF4164  Domain of unknown function (DUF4164)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   1.8    0.0019       0.3      34      86 ..     145     197 ..     136     199 .. 0.92
   2 ?    8.4   5.7     0.016       2.6       3      59 ..     180     237 ..     178     273 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0019
                       DUF4164  34 rdeleaeiealgedrsRLaeeLdqaearaarleevnrEvsrrLkaaietirav 86 
                                   ++++e+ei  l++ + ++  e+ q +a+ + l++ ++E+ +++    ++i+++
  gi|13541826|ref|NP_111514.1| 145 KKAIESEIGYLNSKKDQMQSEISQLSAEINDLNAKKSELEQAIAEMQKQIEDI 197
                                   57899**************************************9999999987 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.016
                       DUF4164   3 tkeleaaltrLeaaldsLEkavdrrleaerkr.deleaeiealgedrsRLaeeLdqae 59 
                                   ++ele+a  ++++ ++ + + +d+r++a  ++ +++++++e+ ++ r+ La +L  ++
  gi|13541826|ref|NP_111514.1| 180 KSELEQAIAEMQKQIEDIQAGIDERIKAVFEEnESMKKTLEEYEKTRADLATALSTVS 237
                                   689************************9866648899999***********9997654 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   7.3      0.01       1.6      21      52 ..     161     192 ..     135     210 .. 0.67
   2 ?    6.3   1.7     0.052       8.3      13      54 ..     216     257 ..     213     283 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.01
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XX CS
                         DivIC  21 qlkqeiaalqaelaklkaeneeLeaevkdLks 52 
                                   q+++ei +l ae++ l+a++ eLe+ ++++++
  gi|13541826|ref|NP_111514.1| 161 QMQSEISQLSAEINDLNAKKSELEQAIAEMQK 192
                                   55556666666666666666666665555543 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.052
                                   XXXXXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XXXX CS
                         DivIC  13 kkgllaykqlkqeiaalqaelaklkaeneeLeaevkdLksde 54 
                                   kk+l  y ++++++a+   ++ +lk+ + + +ae+k+Lk+++
  gi|13541826|ref|NP_111514.1| 216 KKTLEEYEKTRADLATALSTVSQLKDLILQRDAEIKKLKDSY 257
                                   7888999999999999999999***************98765 PP

>> Ax_dynein_light  Axonemal dynein light chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4  10.1   0.00017     0.028      91     166 ..     124     211 ..     112     234 .. 0.53
   2 ?    0.0   5.3       4.4     7e+02     111     171 ..     215     279 ..     203     288 .] 0.52

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 0.00017
               Ax_dynein_light  91 elrmtiaayktlyessvaFgmrkalqae.....qgkselekk.......ikeLeeekeelekqvaelkaklealekreker 159
                                    ++  ++  +++y      g +ka+++e      +k++++++       i++L+++k+ele+ +ae+++++e++++   er
  gi|13541826|ref|NP_111514.1| 124 AMKPIMEVKDSIYSDNGLVGEKKAIESEigylnSKKDQMQSEisqlsaeINDLNAKKSELEQAIAEMQKQIEDIQAGIDER 204
                                   555555555555655555666666666666665555555555111111155566666666666666666666666666665 PP

               Ax_dynein_light 160 rqeeekk 166
                                    ++  ++
  gi|13541826|ref|NP_111514.1| 205 IKAVFEE 211
                                   5543222 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 4.4
               Ax_dynein_light 111 mrkal.qaeqgkselekk...ikeLeeekeelekqvaelkaklealekrekerrqeeekkheeei 171
                                   m+k+l + e+++++l      +++L++   +   ++++lk  ++++  r     ++ +k++ e+i
  gi|13541826|ref|NP_111514.1| 215 MKKTLeEYEKTRADLATAlstVSQLKDLILQRDAEIKKLKDSYNDIFTRYDTLINKMTKREFEKI 279
                                   45555334444444444433345555555555555555555555555555555555555555555 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 ?   12.7   1.0   0.00066      0.11      33      69 ..     157     193 ..     130     195 .. 0.87
   2 ?    2.6   0.6      0.99   1.6e+02      34      64 ..     204     234 ..     199     242 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00066
                      JIP_LZII  33 arvdeLtsereiLreEleslqkakerlesrikelEee 69 
                                   ++ d+++se + L+ E++ l++ k++le+ i+e++++
  gi|13541826|ref|NP_111514.1| 157 SKKDQMQSEISQLSAEINDLNAKKSELEQAIAEMQKQ 193
                                   5669999**********************99999886 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.99
                      JIP_LZII  34 rvdeLtsereiLreEleslqkakerlesrik 64 
                                   r+    +e+e++++ le+ +k+++ l + ++
  gi|13541826|ref|NP_111514.1| 204 RIKAVFEENESMKKTLEEYEKTRADLATALS 234
                                   5555567888888888888888877777665 PP

>> Cauli_DNA-bind  Caulimovirus DNA-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0         6   9.7e+02      42      74 ..      10      44 ..       3      58 .. 0.62
   2 ?    0.9   0.0       2.9   4.6e+02      20      50 ..      83     109 ..      71     134 .. 0.76
   3 ?   11.1   3.8     0.002      0.31       3      55 ..     147     202 ..     145     205 .. 0.85
   4 ?    2.5   0.6      0.87   1.4e+02      12      47 ..     195     230 ..     189     245 .. 0.74

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 6
                                  HHHHHHHHHHHHHHT-.TTHHHHH.HHHTXXXXXX CS
                Cauli_DNA-bind 42 vaakiikdltkkidec.ecnkeiv.eildkkqdkq 74
                                  v  ki +dl ++++e  +  kei+ e ++  q+++
  gi|13541826|ref|NP_111514.1| 10 VRFKIQEDLDRRVKESgKTYKEIIyEYFNGSQNND 44
                                  55677777777777652344554325565555444 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 2.9
                                   HHHHHHHHHHHTS--HHHHHHHHHHHHHHHH CS
                Cauli_DNA-bind  20 aeikaileklgstkpekesleevaakiikdl 50 
                                     i ++lek+ s+++ k    +    +i+d+
  gi|13541826|ref|NP_111514.1|  83 HRITQMLEKNPSDEKLK----DLREFVIEDM 109
                                   67899999998877644....3334445555 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 0.002
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHTS--HHHHHHHHHH...HHHHHHHHHHH CS
                Cauli_DNA-bind   3 aiaseieevlsdqkkieaeikaileklgstkpekesleevaa...kiikdltkkid 55 
                                   ai sei  + s++ ++++ei ++ + +   + +k++le++ a   k i+d+   id
  gi|13541826|ref|NP_111514.1| 147 AIESEIGYLNSKKDQMQSEISQLSAEINDLNAKKSELEQAIAemqKQIEDIQAGID 202
                                   799************************************99833344666666555 PP

  == domain 4  score: 2.5 bits;  conditional E-value: 0.87
                                   HHHHHHHHHHHHHHHHHHHTS--HHHHHHHHHHHHH CS
                Cauli_DNA-bind  12 lsdqkkieaeikaileklgstkpekesleevaakii 47 
                                      q  i++ ika++e + s k+  e+ e+  a + 
  gi|13541826|ref|NP_111514.1| 195 EDIQAGIDERIKAVFEENESMKKTLEEYEKTRADLA 230
                                   344677889999999999999998888888777655 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   8.9     0.048       7.6      17     100 ..     157     244 ..     120     245 .. 0.77
   2 ?    8.4   1.4     0.013       2.1      10      84 ..     203     273 ..     199     286 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.048
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....XXXXXX--TTTTTGGGHHHHHHHHHH...HHHHHH CS
                    Laminin_II  17 eqlaplsqnlentkeklseinrsveetnekvkdankairdAr....rsvkkLeklapqLldklkelkqleeassslsdnis 93 
                                   +++ +++ ++++++++++ +n++  e ++ + +++k+i+d +    + +k + ++ + + + l+e ++ +   ++    +s
  gi|13541826|ref|NP_111514.1| 157 SKKDQMQSEISQLSAEINDLNAKKSELEQAIAEMQKQIEDIQagidERIKAVFEENESMKKTLEEYEKTRADLATALSTVS 237
                                   556778888888888888888888888888888887777765222256777888888888888888888888777445799 PP

                                   HHHHHHH CS
                    Laminin_II  94 eikelIa 100
                                   ++k lI 
  gi|13541826|ref|NP_111514.1| 238 QLKDLIL 244
                                   9999986 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.013
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH CS
                    Laminin_II  10 etakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleea 84 
                                   e +k+v e  + ++    +t e++++ +++++     v++++  i +   ++kkL+   ++++ +  +l ++  +
  gi|13541826|ref|NP_111514.1| 203 ERIKAVFEENESMK----KTLEEYEKTRADLATALSTVSQLKDLILQRDAEIKKLKDSYNDIFTRYDTLINKMTK 273
                                   55555555555555....555566666666666688899999999999999999999999999998888776655 PP

>> Prefoldin  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   4.8    0.0066       1.1      79     119 ..     152     192 ..     126     193 .. 0.89
   2 ?    7.2   1.2     0.029       4.7      82     108 ..     176     202 ..     173     207 .. 0.70
   3 ?    4.7   1.8      0.17        27       4      35 ..     211     246 ..     203     270 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0066
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     Prefoldin  79 iellkkkleelekqlekleeeleklkdqittleanlaqlyq 119
                                   i +l+ k++++++ + +l +e+++l ++  +le+++a+ ++
  gi|13541826|ref|NP_111514.1| 152 IGYLNSKKDQMQSEISQLSAEINDLNAKKSELEQAIAEMQK 192
                                   67999*****************************9999887 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.029
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     Prefoldin  82 lkkkleelekqlekleeeleklkdqit 108
                                   l+ k++ele+++ ++++++e++++ i+
  gi|13541826|ref|NP_111514.1| 176 LNAKKSELEQAIAEMQKQIEDIQAGID 202
                                   667777777777777777777777665 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.17
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT..... CS
                     Prefoldin   4 eleslqaelaqlkeaieelektletlktlkk....e 35 
                                   e es+ ++l++++++  +l ++l+t++ lk+    +
  gi|13541826|ref|NP_111514.1| 211 ENESMKKTLEEYEKTRADLATALSTVSQLKDlilqR 246
                                   557788888888888888888888888888766443 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   6.1    0.0018      0.29     652     728 ..     145     220 ..      59     237 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0018
                      Prominin 652 kneaqdlraiqqelvlplessvkklkksvkkldeensdlqesikkllaaveraenflkkngseiinneskklldril 728
                                   k++ ++   + + + ++++s++++l  ++++l++++s+l+++i ++ +++e+ +  ++++++ + + e++ + ++ +
  gi|13541826|ref|NP_111514.1| 145 KKAIESEIGYLNSKKDQMQSEISQLSAEINDLNAKKSELEQAIAEMQKQIEDIQAGIDERIKAVFE-ENESMKKTLE 220
                                   444444445667777888888888888888888888888888888888888888888888876543.4444444444 PP

>> Fzo_mitofusin  fzo-like conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   5.6     0.005       0.8      93     158 ..     160     225 ..     155     228 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.005
                 Fzo_mitofusin  93 hqvqqelsstfarlcqqvdetekeleeeikelekeieklee.vqkkakllrnkaslleseLekfeeq 158
                                    q+q+e+s+  a+++ + +  ++ele+ i+e++k+ie +++ + ++ k++ ++ +++++ Le++e++
  gi|13541826|ref|NP_111514.1| 160 DQMQSEISQLSAEIN-DLNAKKSELEQAIAEMQKQIEDIQAgIDERIKAVFEENESMKKTLEEYEKT 225
                                   688888888888875.5688899***************98637889999999999999999999875 PP

>> THOC7  Tho complex subunit 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4  13.4     0.064        10      31     106 ..     136     227 ..      55     231 .. 0.77
   2 ?    4.5   9.6      0.25        40      63     107 ..     184     228 ..     180     287 .. 0.67

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.064
                         THOC7  31 a............esteeeleqlkedllldfaafelsie....rlqllakanerereryeaekeeieseieavreeieelk 95 
                                   +            es+   l + k++++ +++++  +i     +   l++a ++  +++e+ ++ i++ i+av ee+e++k
  gi|13541826|ref|NP_111514.1| 136 YsdnglvgekkaiESEIGYLNSKKDQMQSEISQLSAEINdlnaKKSELEQAIAEMQKQIEDIQAGIDERIKAVFEENESMK 216
                                   055555555555666667777888999999999999999888877788999999999999999****************** PP

                         THOC7  96 aqLeearatra 106
                                   ++Lee  +tra
  gi|13541826|ref|NP_111514.1| 217 KTLEEYEKTRA 227
                                   *******9998 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.25
                         THOC7  63 akanerereryeaekeeieseieavreeieelkaqLeearatran 107
                                   ++a ++  +++e+ ++ i++ i+av ee+e++k++Lee  +tra+
  gi|13541826|ref|NP_111514.1| 184 EQAIAEMQKQIEDIQAGIDERIKAVFEENESMKKTLEEYEKTRAD 228
                                   455556666666666677777777777777777777776666653 PP

>> Nas2_N  Nas2 N_terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.2       3.1     5e+02       4      19 ..     141     156 ..     139     165 .. 0.80
   2 ?    4.9   0.1      0.16        25       4      24 ..     155     175 ..     152     178 .. 0.86
   3 ?    7.6   0.5     0.022       3.6       1      31 [.     173     203 ..     173     206 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 3.1
                        Nas2_N   4 Lekkkdeiekeieels 19 
                                   L  +k++ie+ei  l+
  gi|13541826|ref|NP_111514.1| 141 LVGEKKAIESEIGYLN 156
                                   7789999999997766 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.16
                        Nas2_N   4 LekkkdeiekeieelsevLes 24 
                                   L +kkd++++ei++ls+ +++
  gi|13541826|ref|NP_111514.1| 155 LNSKKDQMQSEISQLSAEIND 175
                                   889************998875 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.022
                        Nas2_N   1 lkeLekkkdeiekeieelsevLesqnvgmdg 31 
                                   +++L +kk+e+e+ i+e+++++e+ ++g+d+
  gi|13541826|ref|NP_111514.1| 173 INDLNAKKSELEQAIAEMQKQIEDIQAGIDE 203
                                   579*******************988888776 PP

>> Tup_N  Tup N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   4.5    0.0045      0.71      15      64 ..     147     196 ..     143     201 .. 0.71
   2 ?    5.4   3.6      0.14        22       4      69 ..     203     271 ..     200     280 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0045
                         Tup_N  15 alsqeasslkaqkdeyelkiqsqiqElqqirqtlyeLeeahrkikqqYEe 64 
                                   a+++e+  l+++kd + + i++  +E++ +  +  eLe+a  ++++q E+
  gi|13541826|ref|NP_111514.1| 147 AIESEIGYLNSKKDQMQSEISQLSAEINDLNAKKSELEQAIAEMQKQIED 196
                                   56677777777777777777777777777777777777777777777664 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.14
                         Tup_N   4 elLdavkqEfdalsqeasslkaqkdeyelk..iqsqiqElqqirq.tlyeLeeahrkikqqYEeeiarL 69 
                                   e + av +E +++++ ++ +++ + ++ +     sq+++l   r  +++ L+ ++++i ++Y+  i+++
  gi|13541826|ref|NP_111514.1| 203 ERIKAVFEENESMKKTLEEYEKTRADLATAlsTVSQLKDLILQRDaEIKKLKDSYNDIFTRYDTLINKM 271
                                   666677778888888888888888888776445678888776664257888888888888888887776 PP

>> ACCA  Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.6      0.32        51      11      46 ..     155     186 ..     121     189 .. 0.54
   2 ?    9.8   4.1    0.0041      0.66       4      82 ..     183     267 ..     180     276 .. 0.65

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.32
                          ACCA  11 leekieelkklaeesevdlseeieklekkleklkke 46 
                                   l++k ++     +++  +ls+ei++l++k ++l+++
  gi|13541826|ref|NP_111514.1| 155 LNSKKDQ----MQSEISQLSAEINDLNAKKSELEQA 186
                                   2222222....2223344566666666666666555 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0041
                          ACCA   4 fekpiaeleekieelkklaeesevdlseeieklekkleklkkeiy......knltpwqkvqlaRhpeRpktldyiealfed 78 
                                    e+ iae++++ie++++  +e+   + ee e+++k+le+ +k+        +++++++ + l R +e  k++d  + +f+ 
  gi|13541826|ref|NP_111514.1| 183 LEQAIAEMQKQIEDIQAGIDERIKAVFEENESMKKTLEEYEKTRAdlatalSTVSQLKDLILQRDAEIKKLKDSYNDIFTR 263
                                   677777777777777776666444444444444444333333222222222677888899999***999999999999999 PP

                          ACCA  79 fvel 82 
                                   +  l
  gi|13541826|ref|NP_111514.1| 264 YDTL 267
                                   8766 PP

>> Mod_r  Modifier of rudimentary (Mod(r)) protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6  13.1     0.011       1.8      11      92 ..     155     258 ..     145     281 .. 0.54

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.011
                         Mod_r  11 lledeeklealvktl.pevkqlkeekeellaenesla.....................eknlslepeleelrselqeklee 69 
                                   l ++++++++ +++l  e+++l+++k+el++++ ++                      e+  +  +e+e+ r++l+ +l++
  gi|13541826|ref|NP_111514.1| 155 LNSKKDQMQSEISQLsAEINDLNAKKSELEQAIAEMQkqiediqagiderikavfeenESMKKTLEEYEKTRADLATALST 235
                                   555556666666666566666666666666666666522222222222222222211032222234666666666666666 PP

                         Mod_r  70 lkelekefeekeqeldellqkfs 92 
                                   + +l++   +  +e ++l ++++
  gi|13541826|ref|NP_111514.1| 236 VSQLKDLILQRDAEIKKLKDSYN 258
                                   66665555555555555555555 PP

>> Tropomyosin_1  Tropomyosin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4  14.7    0.0034      0.54      19     137 ..     155     270 ..     139     276 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0034
                 Tropomyosin_1  19 leekvKeleqenlekeqeiksLtkknqqleeevekleeklkeakekaeesekkk.tnnealtrkiqlLEeeleesdkkLke 98 
                                   l++k+ ++++e  +   ei++L+ k ++le+ + ++++++++ ++  +e  k+   +ne++++ +    ee e++ ++L++
  gi|13541826|ref|NP_111514.1| 155 LNSKKDQMQSEISQLSAEINDLNAKKSELEQAIAEMQKQIEDIQAGIDERIKAVfEENESMKKTL----EEYEKTRADLAT 231
                                   56666677778888888999999999999999999999999999988888776525667777654....456777777777 PP

                 Tropomyosin_1  99 ttekLretdvkaeelERkvkaLeqerdewekkyeeleek 137
                                   ++   ++      + + ++k+L ++ ++  ++y+ l +k
  gi|13541826|ref|NP_111514.1| 232 ALSTVSQLKDLILQRDAEIKKLKDSYNDIFTRYDTLINK 270
                                   666666665555566666777777777777777766666 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 ?    9.4   4.4    0.0067       1.1      12      70 ..     134     198 ..     123     203 .. 0.81
   2 ?    2.8   0.1      0.79   1.3e+02      37      66 ..     204     233 ..     203     242 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0067
                          Med9  12 siekdp..nlsskdletktgelrhkLkkarelirelpg....idrsveeqeaeieeleeqlakKr 70 
                                   si +d+    + k +e+++g l+ k +++ + i++l+     ++  + e e+ i+e+++q++  +
  gi|13541826|ref|NP_111514.1| 134 SIYSDNglVGEKKAIESEIGYLNSKKDQMQSEISQLSAeindLNAKKSELEQAIAEMQKQIEDIQ 198
                                   55444444688999*****************9999987777899****************99766 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.79
                          Med9  37 karelirelpgidrsveeqeaeieeleeql 66 
                                   +++++ +e++ + ++ ee e+  ++l   l
  gi|13541826|ref|NP_111514.1| 204 RIKAVFEENESMKKTLEEYEKTRADLATAL 233
                                   57999999999******9999888887666 PP

>> betaPIX_CC  betaPIX coiled coil
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   2.6      0.43        69      27      82 ..     142     197 ..     120     203 .. 0.77
   2 ?   12.5   1.0   0.00059     0.095      42      77 ..     203     238 ..     200     246 .. 0.86
   3 ?    1.2   0.2         2   3.2e+02      36      59 ..     235     258 ..     231     287 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.43
                    betaPIX_CC  27 vleekslVDtVYaLkdevqelkqenkklkksleeEqkaRkdLEkvvrkllksinde 82 
                                   v e k++   +  L  +  +++ e  +l   +++ +  + +LE+ +  + k+i+d 
  gi|13541826|ref|NP_111514.1| 142 VGEKKAIESEIGYLNSKKDQMQSEISQLSAEINDLNAKKSELEQAIAEMQKQIEDI 197
                                   44555555556667777788999999999999998888889***********9985 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00059
                    betaPIX_CC  42 devqelkqenkklkksleeEqkaRkdLEkvvrkllk 77 
                                   + ++ + +en ++kk+lee +k+R dL + +  +++
  gi|13541826|ref|NP_111514.1| 203 ERIKAVFEENESMKKTLEEYEKTRADLATALSTVSQ 238
                                   56788899*******************999887765 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 2
                    betaPIX_CC  36 tVYaLkdevqelkqenkklkksle 59 
                                   tV +Lkd + +   e kklk s +
  gi|13541826|ref|NP_111514.1| 235 TVSQLKDLILQRDAEIKKLKDSYN 258
                                   788999999999999999998765 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   7.2    0.0012       0.2      84     165 ..     115     199 ..      84     211 .. 0.76
   2 ?    3.9   5.5      0.27        43     101     175 ..     188     265 ..     186     284 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0012
                        DUF724  84 GFdVkalqsrlnkLlslkdeq...tklleerkklekkieeeesekrkleeeidelekkilelerqlallkekkeaadkeia 161
                                    F+   +++ ++ ++++kd+    + l  e+k++e++i   +s+k ++++ei++l+ +i +l+ ++  l +   +++k+i 
  gi|13541826|ref|NP_111514.1| 115 PFELDLVREAMKPIMEVKDSIysdNGLVGEKKAIESEIGYLNSKKDQMQSEISQLSAEINDLNAKKSELEQAIAEMQKQIE 195
                                   588888899999999999976222458899999999999999999999999999999999999888777766666666666 PP

                        DUF724 162 rlks 165
                                   ++++
  gi|13541826|ref|NP_111514.1| 196 DIQA 199
                                   5554 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.27
                        DUF724 101 kdeqtklleerkklekkieeeesekrkleeeidelekkilelerqlallk...ekkeaadkeiarlkseaekleeele 175
                                    + q+++++ + +++++i+   +e++++++ ++e ek+ ++l + l ++        + d+ei++lk + +++ ++++
  gi|13541826|ref|NP_111514.1| 188 AEMQKQIEDIQAGIDERIKAVFEENESMKKTLEEYEKTRADLATALSTVSqlkDLILQRDAEIKKLKDSYNDIFTRYD 265
                                   577889999999999999999999999999999999999999988877663335556889999999988888766554 PP

>> CALCOCO1  Calcium binding and coiled-coil domain (CALCOCO1) like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7  16.1    0.0089       1.4     106     238 ..     141     280 ..      84     288 .] 0.71

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0089
                      CALCOCO1 106 lerlseelaeeksalleakeesearirELEeDiktltqralekEteLeRlkerak........kalaqrkeeeaerkqlqa 178
                                   l   ++++  e   l ++k++ ++ i  L  +i+ l  ++ e E  +  ++++ +        ++ a   e+e+ +k l+ 
  gi|13541826|ref|NP_111514.1| 141 LVGEKKAIESEIGYLNSKKDQMQSEISQLSAEINDLNAKKSELEQAIAEMQKQIEdiqagideRIKAVFEENESMKKTLE- 220
                                   33344556666667777888888888888888888888888888888888888887777777777777778888888887. PP

                      CALCOCO1 179 kleqseeelrslskelqelrnslaerdtqvlqLqdtittltqkLttAqrkeaenEallke 238
                                   + e+++++l    + + +l++   +rd+++ +L+d+ + + ++ +t   k ++ E  + +
  gi|13541826|ref|NP_111514.1| 221 EYEKTRADLATALSTVSQLKDLILQRDAEIKKLKDSYNDIFTRYDTLINKMTKREFEKIN 280
                                   7888888888888888999999999****9999999999888888887777777765554 PP

>> WXG100  Proteins of 100 residues with WXG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.3     0.068        11       8      39 ..     147     178 ..     144     182 .. 0.88
   2 ?    5.6   1.0      0.12        19       7      28 ..     181     202 ..     176     215 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.068
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCGC CS
                        WXG100   8 elrqaaarfqkqaeeledelqrlkaevdalqs 39 
                                   ++++ +  ++++++++++e+++l ae+++l++
  gi|13541826|ref|NP_111514.1| 147 AIESEIGYLNSKKDQMQSEISQLSAEINDLNA 178
                                   67888899999****************99965 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.12
                                   HHHHHHHHHHHHHHHHHHHHHH CS
                        WXG100   7 eelrqaaarfqkqaeeledelq 28 
                                   +el+qa+a++qkq e++++ ++
  gi|13541826|ref|NP_111514.1| 181 SELEQAIAEMQKQIEDIQAGID 202
                                   5777788888877777777665 PP

>> DUF1640  Protein of unknown function (DUF1640)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   8.1   0.00023     0.037      92     152 ..     159     218 ..     137     223 .. 0.82
   2 ?    0.2   2.2       4.1   6.6e+02      35      65 ..     226     256 ..     210     286 .. 0.48

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 0.00023
                       DUF1640  92 kqkLreeidklkadirldlnleKgrireelakleakiqelnnkidrevsalrteiEsvKld 152
                                   k ++++ei++l a+i+ dln +K++ ++  a+++++i+++++ id+ ++a+  e Es+K  
  gi|13541826|ref|NP_111514.1| 159 KDQMQSEISQLSAEIN-DLNAKKSELEQAIAEMQKQIEDIQAGIDERIKAVFEENESMKKT 218
                                   5679**********65.**********************************9999999975 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 4.1
                       DUF1640  35 lekvakslvskselekseylqkaalselrke 65 
                                      +a+ l + s+l+  +++ +a++++l++ 
  gi|13541826|ref|NP_111514.1| 226 RADLATALSTVSQLKDLILQRDAEIKKLKDS 256
                                   3334444444444444444444444444443 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.6    0.0054      0.86       4      34 ..     147     177 ..     146     179 .. 0.93
   2 ?    5.2  10.3      0.17        28       3      40 ..     160     197 ..     158     240 .. 0.95
   3 ?    1.1   0.1       3.3   5.4e+02      14      46 ..     234     266 ..     219     272 .. 0.56

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0054
                     FlaC_arch   4 elEnklsklsteletvkkeneelsksveelk 34 
                                    +E++++ l ++ + +++e+++ls ++++l+
  gi|13541826|ref|NP_111514.1| 147 AIESEIGYLNSKKDQMQSEISQLSAEINDLN 177
                                   69**************************998 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.17
                     FlaC_arch   3 delEnklsklsteletvkkeneelsksveelkenVkdl 40 
                                   d++++++s+ls e++ + ++ +el++ + e++++++d+
  gi|13541826|ref|NP_111514.1| 160 DQMQSEISQLSAEINDLNAKKSELEQAIAEMQKQIEDI 197
                                   7899*****************************99875 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 3.3
                     FlaC_arch  14 teletvkkeneelsksveelkenVkdllsLYEv 46 
                                   ++++ +k+ + +   ++++lk++ +d+   Y++
  gi|13541826|ref|NP_111514.1| 234 STVSQLKDLILQRDAEIKKLKDSYNDIFTRYDT 266
                                   244445555555556666666666666666655 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   5.3      0.07        11       8      44 ..     162     198 ..     146     227 .. 0.55
   2 ?    4.9   0.2      0.25        40      13      47 ..     230     264 ..     226     279 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.07
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          SlyX   8 LEiklafqedtieeLndvvaeqqqqidrlqrqlrlla 44 
                                   ++++++ +   i++Ln+   e +q i+++q+q++ ++
  gi|13541826|ref|NP_111514.1| 162 MQSEISQLSAEINDLNAKKSELEQAIAEMQKQIEDIQ 198
                                   3333334444444444444444444444444443333 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.25
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT- CS
                          SlyX  13 afqedtieeLndvvaeqqqqidrlqrqlrllaerl 47 
                                   a    t+ +L d + + + +i++l+   + +  r 
  gi|13541826|ref|NP_111514.1| 230 ATALSTVSQLKDLILQRDAEIKKLKDSYNDIFTRY 264
                                   5556799*****************99887766665 PP

>> bZIP_1  bZIP transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.1       1.7   2.8e+02      38      63 ..     141     166 ..     140     167 .. 0.87
   2 ?    5.9   2.9     0.087        14      31      63 ..     162     194 ..     156     201 .. 0.58
   3 ?   11.7   0.6    0.0013      0.21      33      60 ..     203     230 ..     198     234 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 1.7
                                   HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        bZIP_1  38 LekeNksLkseleelkkevekLkskv 63 
                                   L +e k+  se++ l+ + ++++s++
  gi|13541826|ref|NP_111514.1| 141 LVGEKKAIESEIGYLNSKKDQMQSEI 166
                                   77899999999999999999999886 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.087
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        bZIP_1  31 LerrvkaLekeNksLkseleelkkevekLkskv 63 
                                    +++ ++L++e  +L  + +el+  ++++++++
  gi|13541826|ref|NP_111514.1| 162 MQSEISQLSAEINDLNAKKSELEQAIAEMQKQI 194
                                   455555555555555555555555555555543 PP

  == domain 3  score: 11.7 bits;  conditional E-value: 0.0013
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        bZIP_1  33 rrvkaLekeNksLkseleelkkevekLk 60 
                                   +r ka  +eN+s+k++lee++k+++ L 
  gi|13541826|ref|NP_111514.1| 203 ERIKAVFEENESMKKTLEEYEKTRADLA 230
                                   7899999****************99886 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0  10.7     0.018         3       2      75 ..     164     243 ..     137     286 .. 0.52

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.018
                         TMPIT   2 eeweelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvk......eeeeeeveelkeel 75 
                                   +e+++l+ e+++l+++++e++q ++e++k++++++  i++  k + e ++s+kk+ ++ +      +   ++v++lk+ +
  gi|13541826|ref|NP_111514.1| 164 SEISQLSAEINDLNAKKSELEQAIAEMQKQIEDIQAGIDERIKAVFEENESMKKTLEEYEktradlATALSTVSQLKDLI 243
                                   34445555555555555555555555555555554444444444433333333333332211112222233333333333 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 ?    9.7   8.6    0.0035      0.56     245     310 ..     153     218 ..     140     222 .. 0.90
   2 ?    2.4   0.2      0.61        98     259     300 ..     223     264 ..     217     275 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0035
                          SseC 245 GainiqrAklqkkaaqlqAdtkllravleqlqkvldeaaeeikellesiqellksmsqaisqkgdt 310
                                   G  n ++ + q++++ql A+  +l a   +l+++++e +++i ++++ i+e +k +++  +++ +t
  gi|13541826|ref|NP_111514.1| 153 GYLNSKKDQMQSEISQLSAEINDLNAKKSELEQAIAEMQKQIEDIQAGIDERIKAVFEENESMKKT 218
                                   5567788899*****************************************999999887777776 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.61
                          SseC 259 aqlqAdtkllravleqlqkvldeaaeeikellesiqellksm 300
                                   ++  Ad++++ +++ ql++++ +   eik+l +s ++++   
  gi|13541826|ref|NP_111514.1| 223 EKTRADLATALSTVSQLKDLILQRDAEIKKLKDSYNDIFTRY 264
                                   67789******************************9999765 PP

>> DUF3573  Protein of unknown function (DUF3573)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1       3.5   5.5e+02      64     138 ..      67     136 ..      60     173 .. 0.49
   2 ?    6.8   4.8     0.016       2.6      23      93 ..     166     236 ..     147     272 .. 0.66

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 3.5
                       DUF3573  64 etknsnesaqfttysskvedsklprslldnkeskdlsqvqktsvdiltnidaessiinlaskplGgifnqkGgid 138
                                     + ++ + +f  y  +    +  + l +n    +l++  +  ++ +tni++    ++l  +++  i++ k +i 
  gi|13541826|ref|NP_111514.1|  67 SLELNDYNKKFVRYVYH----RITQMLEKNPSDEKLKDLREFVIEDMTNIESPFE-LDLVREAMKPIMEVKDSIY 136
                                   55554455555555432....2234455565666666667777777777776543.4555555555555555553 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.016
                       DUF3573  23 dsasyaesneqtsksnlidkelilklqkqikelqaein.hlketknsnesaqfttysskvedsklprslldn 93 
                                    s+  ae n+  +  ++  +++i ++qkqi+++qa i+ ++k++   nes++ t    +   ++l  +l+  
  gi|13541826|ref|NP_111514.1| 166 ISQLSAEINDLNA-KKSELEQAIAEMQKQIEDIQAGIDeRIKAVFEENESMKKTLEEYEKTRADLATALSTV 236
                                   4444555555444.3445578999999999999999972577777777777666544444444444444444 PP

>> HIP1_clath_bdg  Clathrin-binding domain of Huntingtin-interacting protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   3.9      0.31        50      27      65 ..     157     194 ..     119     199 .. 0.56
   2 ?    4.5   8.5      0.32        52      26      97 ..     156     227 ..     143     229 .. 0.66
   3 ?    8.8   7.4     0.015       2.5      21      91 ..     179     252 ..     174     259 .. 0.70
   4 ?    4.4   1.7      0.35        55      31      90 ..     214     272 ..     208     281 .. 0.50

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.31
                HIP1_clath_bdg  27 rekkeleeelerlkeeaerkleeqkeelekLkreleakr 65 
                                    +k++++ e+ +l++e +  l+ +k+ele+  +e++++ 
  gi|13541826|ref|NP_111514.1| 157 SKKDQMQSEISQLSAEIN-DLNAKKSELEQAIAEMQKQI 194
                                   333344444444333322.23333333333333333333 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.32
                HIP1_clath_bdg  26 erekkeleeelerlkeeaerkleeqkeelekLkreleakraelar.lkssLesseqsgeqlssqlaaLqaEke 97 
                                   + +k++++ e+ +l++e  + l+ +k+ele+  +e++++ ++++  + + ++   +++e ++++l++ ++ ++
  gi|13541826|ref|NP_111514.1| 156 NSKKDQMQSEISQLSAEI-NDLNAKKSELEQAIAEMQKQIEDIQAgIDERIKAVFEENESMKKTLEEYEKTRA 227
                                   556777777777777665.356667777777777777777776643666677777777777777776666655 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.015
                HIP1_clath_bdg  21 aqeeverekkeleeelerlkeeaerkleeqkeelekLkrele...akraelarlkssLesseqsgeqlssqlaa 91 
                                   +++e+e++  e+++++e++++  +++++   ee e++k+ le   ++ra+la++ s++++ +    q  +++++
  gi|13541826|ref|NP_111514.1| 179 KKSELEQAIAEMQKQIEDIQAGIDERIKAVFEENESMKKTLEeyeKTRADLATALSTVSQLKDLILQRDAEIKK 252
                                   6899*****************99999997777777777665500056666666666666555555555555555 PP

  == domain 4  score: 4.4 bits;  conditional E-value: 0.35
                HIP1_clath_bdg  31 eleeelerlkeeaerkleeqkeelekLkreleakraelarlkssLesseqsgeqlssqla 90 
                                    ++++le+ + +++  l+   +++ +Lk  + ++ ae+++lk s ++  +  ++l ++++
  gi|13541826|ref|NP_111514.1| 214 SMKKTLEEYE-KTRADLATALSTVSQLKDLILQRDAEIKKLKDSYNDIFTRYDTLINKMT 272
                                   3444444432.2333444445555556665566666666666555555555555555555 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   7.1     0.027       4.3      15      65 ..     157     221 ..     138     234 .. 0.46
   2 ?    2.9   0.1       1.1   1.7e+02       7      42 ..     233     268 ..     227     288 .] 0.74

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.027
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH..............XXXXXXXXXXXXX CS
                          YabA  15 eqleelleeleelkeelaelleenaeLeleneklrerl..............eeeekkekekkke 65 
                                   ++ +++++e+++l +e+++l  + +eLe    ++++++               ee+++ k++ +e
  gi|13541826|ref|NP_111514.1| 157 SKKDQMQSEISQLSAEINDLNAKKSELEQAIAEMQKQIediqagiderikavFEENESMKKTLEE 221
                                   55555555555555555555555555555444444444333333332222222233333333333 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 1.1
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          YabA   7 fdkleeleeqleelleeleelkeelaelleenaeLe 42 
                                   ++++++l++ + +  +e+++lk++ ++++ + ++L 
  gi|13541826|ref|NP_111514.1| 233 LSTVSQLKDLILQRDAEIKKLKDSYNDIFTRYDTLI 268
                                   567889999999999999999999999988877774 PP

>> GIT_CC  GIT coiled-coil Rho guanine nucleotide exchange factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   1.4     0.033       5.3      29      65 ..     149     185 ..     144     186 .. 0.83
   2 ?    5.7   5.0     0.082        13      24      58 ..     165     199 ..     154     203 .. 0.84
   3 ?   -0.0   0.0       5.1   8.2e+02      29      48 ..     202     221 ..     199     232 .. 0.81
   4 ?    1.3   0.2         2   3.3e+02      14      49 ..     218     253 ..     213     261 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.033
                        GIT_CC  29 eakiqqLlkvNtslsdelrlLQskvqkLqaeNaqlrd 65 
                                   e+ i  L   + +++ e+++L  +++ L+a  ++l++
  gi|13541826|ref|NP_111514.1| 149 ESEIGYLNSKKDQMQSEISQLSAEINDLNAKKSELEQ 185
                                   7777778888999999999999999999998888865 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.082
                        GIT_CC  24 alaaseakiqqLlkvNtslsdelrlLQskvqkLqa 58 
                                   +++   a i+ L + +++l++ ++++Q++++ +qa
  gi|13541826|ref|NP_111514.1| 165 EISQLSAEINDLNAKKSELEQAIAEMQKQIEDIQA 199
                                   45667788999999999999999999999998886 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 5.1
                        GIT_CC  29 eakiqqLlkvNtslsdelrl 48 
                                   + +i+++ + N+s+++ l++
  gi|13541826|ref|NP_111514.1| 202 DERIKAVFEENESMKKTLEE 221
                                   67999999999999999876 PP

  == domain 4  score: 1.3 bits;  conditional E-value: 2
                        GIT_CC  14 tleeylelKkalaaseakiqqLlkvNtslsdelrlL 49 
                                   tleey      la++ +++ qL+    +   e+++L
  gi|13541826|ref|NP_111514.1| 218 TLEEYEKTRADLATALSTVSQLKDLILQRDAEIKKL 253
                                   789999999999999999999998777766666666 PP

>> Swi5  Swi5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   6.2     0.038       6.1      13      45 ..     160     192 ..     148     216 .. 0.51
   2 ?    4.1   2.3       0.3        48       4      49 ..     214     260 ..     201     260 .. 0.63

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.038
                                   HHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHH CS
                          Swi5  13 eelekelaelkeelkekkdpeetvkrhIklLhe 45 
                                   +++++e+++l++e ++ ++++ ++++ I  +++
  gi|13541826|ref|NP_111514.1| 160 DQMQSEISQLSAEINDLNAKKSELEQAIAEMQK 192
                                   444444444444444444333344333333332 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.3
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHH.HHHH CS
                          Swi5   4 eikeleeqleelekelaelkeelkekkdpeetvkrhIklLhe.YNEi 49 
                                   ++k+  e++e+++++la++ +   + kd     +  Ik+L++ YN+i
  gi|13541826|ref|NP_111514.1| 214 SMKKTLEEYEKTRADLATALSTVSQLKDLILQRDAEIKKLKDsYNDI 260
                                   44455555556666666666666655566666677899998558887 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 ?   13.1  10.7   0.00039     0.062       3     105 ..     180     271 ..     178     288 .] 0.72

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00039
                        TACC_C   3 qkdldaalekvkeeveekeeeiqelkkkveelkkenqemkkivaefektiaqlieekqkqkelakkeiqkvleekeqllad 83 
                                   + +l++a++++++++e+ +       ++++   +en+ mkk+++e+ekt a+l +   + +     +++ ++ ++++ +++
  gi|13541826|ref|NP_111514.1| 180 KSELEQAIAEMQKQIEDIQAG---IDERIKAVFEENESMKKTLEEYEKTRADLATALSTVS-----QLKDLILQRDAEIKK 252
                                   568899999999999996666...8889999*********************999996666.....455555555554444 PP

                        TACC_C  84 lnsveksfsdlfkryekqkevl 105
                                   l   + s++d+f ry+ + + +
  gi|13541826|ref|NP_111514.1| 253 L---KDSYNDIFTRYDTLINKM 271
                                   4...667777777776543333 PP

>> PEP-utilisers_N  PEP-utilising enzyme, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       9.2   1.5e+03      45      78 ..     107     144 ..      85     153 .. 0.65
   2 ?    5.7   5.0       0.1        16      23      65 ..     170     211 ..     152     279 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 9.2
                                   HHHHHHHHHH....T-HHHHHHHHHHHHHHT-HHHHHH CS
               PEP-utilisers_N  45 eelealaeka....lgeeeaaifeahlmlleDpellee 78 
                                   e+++++++      + e+ + i+e+  ++ +D++l++e
  gi|13541826|ref|NP_111514.1| 107 EDMTNIESPFeldlVREAMKPIMEVKDSIYSDNGLVGE 144
                                   44444433334444444446699999999999999876 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.1
                                   --G.GGHHHHHHHHHHHHHHHHHHHHHHHHHH.T-HHHHHHHHH CS
               PEP-utilisers_N  23 eveaedveaelerleeAlekvreelealaeka.lgeeeaaifea 65 
                                   ++e +d +a  + le+A++++++++e++++ + +  + +a+fe 
  gi|13541826|ref|NP_111514.1| 170 SAEINDLNAKKSELEQAIAEMQKQIEDIQAGIdE--RIKAVFEE 211
                                   445677889999***************8754431..22445554 PP

>> Phage_Mu_Gam  Bacteriophage Mu Gam like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.2       2.3   3.7e+02      37      60 ..     149     172 ..     144     180 .. 0.50
   2 ?   10.4   8.5    0.0028      0.45       6      62 ..     171     227 ..     163     235 .. 0.79
   3 ?   -0.2   0.2       5.1   8.2e+02      10      36 ..     249     275 ..     238     287 .. 0.57

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 2.3
                                   HHHCHHHHHHHHHHHHHHHHHHHC CS
                  Phage_Mu_Gam  37 eaeleplkkeieylesllkqYaea 60 
                                   e+e+  l++++++++s++ q   +
  gi|13541826|ref|NP_111514.1| 149 ESEIGYLNSKKDQMQSEISQLSAE 172
                                   455555555555555555544333 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0028
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHCTH CS
                  Phage_Mu_Gam   6 walrkiaelkreleeieaeaneeiaaikekleaeleplkkeieylesllkqYaeank 62 
                                   + +  + + k ele++ ae++++i+ i++  ++ ++++ +e e ++++l++Y ++  
  gi|13541826|ref|NP_111514.1| 171 AEINDLNAKKSELEQAIAEMQKQIEDIQAGIDERIKAVFEENESMKKTLEEYEKTRA 227
                                   3445555666666677789*********************************77654 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 5.1
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                  Phage_Mu_Gam  10 kiaelkreleeieaeaneeiaaikekl 36 
                                   +i++lk + + i + +++ i++++++ 
  gi|13541826|ref|NP_111514.1| 249 EIKKLKDSYNDIFTRYDTLINKMTKRE 275
                                   455555555555555555555555444 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.5     0.087        14      34      70 ..     158     194 ..     146     210 .. 0.53
   2 ?    4.7   2.3      0.23        36      24      80 ..     183     239 ..     181     281 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.087
                        DUF948  34 tieelekqvdpilkevedllakvnelledvneklekv 70 
                                     +++++++ +++ e++dl ak  el + + e  +++
  gi|13541826|ref|NP_111514.1| 158 KKDQMQSEISQLSAEINDLNAKKSELEQAIAEMQKQI 194
                                   4455666666666666666665555433333322222 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.23
                        DUF948  24 lkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadl 80 
                                   l++ + e++++ie+++  +d+ +k v +  + ++++le+ ++  +++ +  + v +l
  gi|13541826|ref|NP_111514.1| 183 LEQAIAEMQKQIEDIQAGIDERIKAVFEENESMKKTLEEYEKTRADLATALSTVSQL 239
                                   667777888888888855555555555555555555555555544444444444444 PP

>> LMBR1  LMBR1-like membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   9.7    0.0083       1.3     203     323 ..     146     258 ..     134     276 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0083
                         LMBR1 203 kklyfeaaklntekeeaereledllkevkklrksisesdplrkyleeilkkvPeeiaeklksnenkteeslaklekqlika 283
                                   k+++ e+  ln++k++++ e+++l  e++ l+ ++se ++    +++ ++         ++++  +  +++ +++++++k+
  gi|13541826|ref|NP_111514.1| 146 KAIESEIGYLNSKKDQMQSEISQLSAEINDLNAKKSELEQAIAEMQKQIED--------IQAGIDERIKAVFEENESMKKT 218
                                   556677788899999999999999999999988888877533333333333........3446666799************ PP

                         LMBR1 284 lqkrertekqwkrllekalelediiknksskekefksses 323
                                   l+++e+t++ + ++l  + +l+d+i +++ + k++k+s +
  gi|13541826|ref|NP_111514.1| 219 LEEYEKTRADLATALSTVSQLKDLILQRDAEIKKLKDSYN 258
                                   *************************999999999988754 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 ?    5.7  13.1     0.042       6.7      35     139 ..     156     236 ..     140     284 .. 0.45

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.042
                         Atg14  35 ksekeslkkkiekalegkeeaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkklaklsdklkkRr 115
                                   +s+k                 +q +++i +++a +++l +++++l++ ++e++++++  ++ i+e+ k + + ++++k   
  gi|13541826|ref|NP_111514.1| 156 NSKK-----------------DQMQSEISQLSAEINDLNAKKSELEQAIAEMQKQIEDIQAGIDERIKAVFEENESMK--- 216
                                   1122.................233333333333333333333333333333333333333333333333333333333... PP

                         Atg14 116 sdleslqneleerrkkqiaklqda 139
                                       ++ +e e+ r+++ + l++ 
  gi|13541826|ref|NP_111514.1| 217 ----KTLEEYEKTRADLATALSTV 236
                                   ....33333333333333333322 PP

>> HalX  HalX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   1.3    0.0039      0.62      15      60 ..     155     203 ..     150     211 .. 0.82
   2 ?    0.3   1.0       5.5   8.9e+02       4      65 ..     221     277 ..     218     279 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0039
                          HalX  15 LasKravLeaekseaeLadse...eYqeLearleelraqldetldeldd 60 
                                   L sK++ +++e s+   ++++   +++eLe+ ++e++ q++++ + +d+
  gi|13541826|ref|NP_111514.1| 155 LNSKKDQMQSEISQLSAEINDlnaKKSELEQAIAEMQKQIEDIQAGIDE 203
                                   6688888888888877777655559*****************9988877 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 5.5
                          HalX   4 eYdeelqelfaLasKravLeaekseaeLadseeYqeLearleelraqldetldelddaddfe 65 
                                   eY+ +  +l +  s+++ L+       L+ + e   L++  +++ ++ d++++ ++  ++fe
  gi|13541826|ref|NP_111514.1| 221 EYEKTRADLATALSTVSQLKD----LILQRDAEIKKLKDSYNDIFTRYDTLINKMTK-REFE 277
                                   666666666666666666654....55666777777777777777777777777777.7765 PP

>> PA28_beta  Proteasome activator pa28 beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1       9.5   1.5e+03     117     132 ..      78      93 ..      67     108 .. 0.70
   2 ?   10.4   7.0    0.0024      0.38       6     136 ..     160     280 ..     155     287 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 9.5
                     PA28_beta 117 lrnlYavlydlitKNi 132
                                   +r +Y  ++ ++ KN 
  gi|13541826|ref|NP_111514.1|  78 VRYVYHRITQMLEKNP 93 
                                   5667777777777774 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0024
                     PA28_beta   6 ekivelleklkpeieelieklnkvklwiqlliPkiedGnnfGVsvQeevleelsrveeeaanlldqiskyfleraklvskl 86 
                                   +++++ +++l  ei++l  k ++++  i  +  +ied       +Q  + e++++v ee +++ +++++y  +ra+l++ l
  gi|13541826|ref|NP_111514.1| 160 DQMQSEISQLSAEINDLNAKKSELEQAIAEMQKQIED-------IQAGIDERIKAVFEENESMKKTLEEYEKTRADLATAL 233
                                   5666777777777777777777777777777777776.......9**********************************99 PP

                     PA28_beta  87 lkyphvedyrealeelDekqllslrlvlldlrnlYavlydlitK.NieKik 136
                                   +   +++d   ++ + D +++ +l+  + d+ + Y +l++ +tK  +eKi+
  gi|13541826|ref|NP_111514.1| 234 STVSQLKD---LILQRD-AEIKKLKDSYNDIFTRYDTLINKMTKrEFEKIN 280
                                   87666655...788888.5899**************999877663799996 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 ?    9.0   2.7     0.012       1.9      60      96 ..     159     195 ..     142     197 .. 0.79
   2 ?    2.9   2.0      0.95   1.5e+02      49      93 ..     194     238 ..     191     256 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.012
                       DUF4140  60 reaeeeelkalraeleeledelaaledelaaaearla 96 
                                   +++ ++e+++l ae++ l++++++le+++a  +++++
  gi|13541826|ref|NP_111514.1| 159 KDQMQSEISQLSAEINDLNAKKSELEQAIAEMQKQIE 195
                                   3333337**************************9986 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.95
                       DUF4140  49 ildvqvervpnreaeeeelkalraeleeledelaaledelaaaea 93 
                                   i d+q   +++ +a+ ee ++++++lee e+++a+l  +l+++++
  gi|13541826|ref|NP_111514.1| 194 IEDIQAGIDERIKAVFEENESMKKTLEEYEKTRADLATALSTVSQ 238
                                   777777777777777778999999999999999999999888765 PP

>> Occludin_ELL  Occludin homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   1.8     0.018       2.8      27      71 ..     155     199 ..     150     215 .. 0.77
   2 ?    9.6   1.5    0.0093       1.5      18      74 ..     216     272 ..     210     286 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.018
                  Occludin_ELL  27 lhaeleevskkfseLerelkelkegskeykkieeeilqeykklkk 71 
                                   l+++ +++++++s+L++e+++l+ +++e +++++e++++ ++++ 
  gi|13541826|ref|NP_111514.1| 155 LNSKKDQMQSEISQLSAEINDLNAKKSELEQAIAEMQKQIEDIQA 199
                                   667778888888888888888888888888888888888777754 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0093
                  Occludin_ELL  18 nkeYkeYkelhaeleevskkfseLerelkelkegskeykkieeeilqeykklkkdpe 74 
                                   +k+ +eY +  a+l+++ +++s+L++ + + + + k+ k+  ++i+ +y  l ++ +
  gi|13541826|ref|NP_111514.1| 216 KKTLEEYEKTRADLATALSTVSQLKDLILQRDAEIKKLKDSYNDIFTRYDTLINKMT 272
                                   67889******************************************9998766433 PP

>> Hormone_1  Somatotropin hormone family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       9.3   1.5e+03     134     153 ..      95     114 ..      85     127 .. 0.83
   2 ?    7.1   2.3     0.026       4.2     105     167 ..     162     223 ..     159     228 .. 0.81
   3 ?    3.5   0.3      0.32        51     110     158 ..     227     271 ..     219     287 .. 0.63

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 9.3
                                   GGHHHHHHHHHHHHHHHH-- CS
                     Hormone_1 134 eeklkeLlegierilskvev 153
                                    eklk+L+e++ + ++ +e 
  gi|13541826|ref|NP_111514.1|  95 DEKLKDLREFVIEDMTNIES 114
                                   58999*****9999999885 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.026
                                   TTTGGGGGG....GGGSSS------TTTGGGHHHHHHHHHHHHHHHH---------------- CS
                     Hormone_1 105 wkePLkhlvtelssmkevsetilskakeieeklkeLlegierilskvevpverkekeekpaws 167
                                   +++ + +l +e++++++   ++ +   e++++++++++gi + ++ v++  ++ +k+  + ++
  gi|13541826|ref|NP_111514.1| 162 MQSEISQLSAEINDLNAKKSELEQAIAEMQKQIEDIQAGIDERIKAVFE-ENESMKKTLEEYE 223
                                   6777889999999999999999999999999*********999999995.5555555555555 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.32
                                   GGGG....GGGSSS------TTTGGGHHHHHHHHHHHHHHHH------- CS
                     Hormone_1 110 khlvtelssmkevsetilskakeieeklkeLlegierilskvevpverk 158
                                    +l+t+ls++ ++ + il+++ ei++     ++  + i+++  +  +++
  gi|13541826|ref|NP_111514.1| 227 ADLATALSTVSQLKDLILQRDAEIKKL----KDSYNDIFTRYDTLINKM 271
                                   579999**************9998653....344444444433322222 PP

>> bZIP_2  Basic region leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.1     0.032       5.2      27      54 .]     145     172 ..     144     172 .. 0.91
   2 ?    4.4   1.7      0.25        40      29      54 .]     168     193 ..     167     195 .. 0.89
   3 ?    2.8   0.8      0.78   1.3e+02      25      49 ..     178     202 ..     177     207 .. 0.84
   4 ?    1.3   0.2       2.3   3.7e+02      29      53 ..     200     224 ..     197     225 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.032
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        bZIP_2  27 eeeleervkeLeeeNaqLrqkveqLeke 54 
                                   ++ +e+++ +L+++++q + +++qL +e
  gi|13541826|ref|NP_111514.1| 145 KKAIESEIGYLNSKKDQMQSEISQLSAE 172
                                   5679*********************987 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.25
                                   HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        bZIP_2  29 eleervkeLeeeNaqLrqkveqLeke 54 
                                   +l  ++++L++++++L+q +++++k+
  gi|13541826|ref|NP_111514.1| 168 QLSAEINDLNAKKSELEQAIAEMQKQ 193
                                   677899***************99985 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.78
                                   HHHHHHHHHHHHHHHHHHHHHHHHH CS
                        bZIP_2  25 akeeeleervkeLeeeNaqLrqkve 49 
                                   ak+ ele+ + e++++++ +++ ++
  gi|13541826|ref|NP_111514.1| 178 AKKSELEQAIAEMQKQIEDIQAGID 202
                                   5788999999999999999988776 PP

  == domain 4  score: 1.3 bits;  conditional E-value: 2.3
                                   HHHHHHHHHHHHHHHHHHHHHHHHH CS
                        bZIP_2  29 eleervkeLeeeNaqLrqkveqLek 53 
                                   ++ er+k + eeN+  ++ +e++ek
  gi|13541826|ref|NP_111514.1| 200 GIDERIKAVFEENESMKKTLEEYEK 224
                                   5678999999999999999999886 PP

>> DUF4795  Domain of unknown function (DUF4795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1       6.2     1e+03     122     146 ..      88     113 ..      61     125 .. 0.68
   2 ?    8.2  17.2     0.011       1.7      10     155 ..     160     274 ..     122     287 .. 0.49

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 6.2
                       DUF4795 122 lkekld.rlelepLkeqleerlkelq 146
                                   + ek+     l++L+e++ e + +++
  gi|13541826|ref|NP_111514.1|  88 MLEKNPsDEKLKDLREFVIEDMTNIE 113
                                   33333346678888888888877776 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.011
                       DUF4795  10 kklqeaieklqeelekleekvkelekrledkekklealkkqieelekvkadkeeveeelaekadkeaLatkvsrdqfDeak 90 
                                   +++q++i++l++e+++l+ k++ele+ +++ +k++e ++  i                                       
  gi|13541826|ref|NP_111514.1| 160 DQMQSEISQLSAEINDLNAKKSELEQAIAEMQKQIEDIQAGI--------------------------------------- 201
                                   444444444444444444444444444444444444444444....................................... PP

                       DUF4795  91 keLekmleellekle.......eqeealkkaldtLq..........eelkekld.....rlelepLkeqleerlkelqkel 149
                                                 +       e+ e++kk l++ +          + + +  d       e+++Lk+  ++ +    + +
  gi|13541826|ref|NP_111514.1| 202 --------------DerikavfEENESMKKTLEEYEktradlatalSTVSQLKDlilqrDAEIKKLKDSYNDIFTRYDTLI 268
                                   ..............3333333344444444444444333333333322222222444444444444444443333333333 PP

                       DUF4795 150 qeamek 155
                                   +++++ 
  gi|13541826|ref|NP_111514.1| 269 NKMTKR 274
                                   333333 PP

>> FlxA  FlxA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9  13.6     0.019         3      15      67 ..     148     203 ..     140     235 .. 0.62

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.019
                          FlxA  15 sasqiasLqkQiknlqkqLkelses...deltkeekkkqqqliqaQIqqlqaQIaq 67 
                                   ++s+i  L+   +++q ++++ls++    +  k e ++ + ++q+QI+++qa I  
  gi|13541826|ref|NP_111514.1| 148 IESEIGYLNSKKDQMQSEISQLSAEindLNAKKSELEQAIAEMQKQIEDIQAGIDE 203
                                   56666666666666666666666664322222444557888888888888888754 PP

>> CENP-H  Centromere protein H (CENP-H)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   9.6     0.018       2.9      14      86 ..     158     233 ..     141     239 .. 0.52
   2 ?    1.7   0.3       2.1   3.4e+02      13      60 ..     234     282 ..     230     288 .] 0.73

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.018
                        CENP-H  14 ellklsqelrelqeeltevekenlrlkrknrelaaellelakekesek..........eklkeelekleaelkksrqrwrv 84 
                                   +  ++++e+++l +e+++++++  +l+++ +e+ +++       e  +           +++e+++k  +e++k r+   +
  gi|13541826|ref|NP_111514.1| 158 KKDQMQSEISQLSAEINDLNAKKSELEQAIAEMQKQI-------EDIQagiderikavFEENESMKKTLEEYEKTRADLAT 231
                                   3334444444444444444444444444444444444.......3333344433356755677788888888888777666 PP

                        CENP-H  85 vk 86 
                                     
  gi|13541826|ref|NP_111514.1| 232 AL 233
                                   55 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 2.1
                        CENP-H  13 sellklsqelrelqeeltevekenlrlkrknrelaaell.elakekese 60 
                                   s++ +l+  + +  +e+ +++ +  ++ ++  +l+++++ ++ ++ +++
  gi|13541826|ref|NP_111514.1| 234 STVSQLKDLILQRDAEIKKLKDSYNDIFTRYDTLINKMTkREFEKINAR 282
                                   6777888888888999999999999999999999999962444444443 PP

>> HABP4_PAI-RBP1  Hyaluronan / mRNA binding family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   4.8    0.0057      0.91      32     101 ..     158     227 ..     141     238 .. 0.59

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0057
                HABP4_PAI-RBP1  32 vkdeieeqeeeeae....kaaekeaeeeda.eeeaaeaeeaaaaeeeekeekeeeeeeeeedkemTLdEykklqe 101
                                   +kd+++ + ++ ++     +a+k +e e+a +e +++ e+ +a  +e  +    ++ ee+e+++ TL+Ey+k ++
  gi|13541826|ref|NP_111514.1| 158 KKDQMQSEISQLSAeindLNAKK-SELEQAiAEMQKQIEDIQAGIDERIK----AVFEENESMKKTLEEYEKTRA 227
                                   44554333332222453222222.22233334444444444444444444....468899***********9765 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   1.1    0.0071       1.1      67     102 ..     141     176 ..     132     180 .. 0.88
   2 ?   10.5   3.2    0.0029      0.46      64      94 ..     173     203 ..     168     212 .. 0.82
   3 ?    6.9   4.3     0.038         6      57      98 ..     184     225 ..     183     231 .. 0.89
   4 ?    2.1   0.2       1.1   1.8e+02      65      99 ..     237     271 ..     233     278 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0071
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC CS
                   Prefoldin_2  67 Leerketlekeiktlekqleklekeleelkeelqkk 102
                                   L  +k+ +e ei  l++++++++ e+++l +e++ +
  gi|13541826|ref|NP_111514.1| 141 LVGEKKAIESEIGYLNSKKDQMQSEISQLSAEINDL 176
                                   667899*************************99976 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0029
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                   Prefoldin_2  64 keeLeerketlekeiktlekqleklekelee 94 
                                   +++L+++k +le+ i++++kq+e++++ ++e
  gi|13541826|ref|NP_111514.1| 173 INDLNAKKSELEQAIAEMQKQIEDIQAGIDE 203
                                   6789999999999999999999999988876 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.038
                                   EE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                   Prefoldin_2  57 kqdkeevkeeLeerketlekeiktlekqleklekeleelkee 98 
                                   +q  +e++++ e+ ++ ++++ik++ ++ e+++k+lee +++
  gi|13541826|ref|NP_111514.1| 184 EQAIAEMQKQIEDIQAGIDERIKAVFEENESMKKTLEEYEKT 225
                                   567789999****************************99885 PP

  == domain 4  score: 2.1 bits;  conditional E-value: 1.1
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                   Prefoldin_2  65 eeLeerketlekeiktlekqleklekeleelkeel 99 
                                   ++L++ + + ++eik+l++++ ++ ++++ l ++ 
  gi|13541826|ref|NP_111514.1| 237 SQLKDLILQRDAEIKKLKDSYNDIFTRYDTLINKM 271
                                   57777777788899999999999999888887765 PP

>> TMF_DNA_bd  TATA element modulatory factor 1 DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   7.3    0.0071       1.1      24      67 ..     155     198 ..     146     204 .. 0.74
   2 ?    4.7   4.4      0.19        30      11      70 ..     202     257 ..     199     261 .. 0.83
   3 ?    2.8   1.3      0.76   1.2e+02      24      69 ..     239     284 ..     236     288 .] 0.69

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0071
                    TMF_DNA_bd  24 LskkelklnntikkLrkknkelekeikelkkkleklekeleele 67 
                                   L +k ++    i++L +++++l+ + +el++ +++ +k++e ++
  gi|13541826|ref|NP_111514.1| 155 LNSKKDQMQSEISQLSAEINDLNAKKSELEQAIAEMQKQIEDIQ 198
                                   56667777777778888888888888888888888777777766 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.19
                    TMF_DNA_bd  11 DeqIaqLmeEGekLskkelklnntikkLrkknkelekeikelkkkleklekeleeleerl 70 
                                   De+I+++ eE e  +k+  + ++t    r++++ + +++++lk+ + + + e+++l++++
  gi|13541826|ref|NP_111514.1| 202 DERIKAVFEENESMKKTLEEYEKT----RADLATALSTVSQLKDLILQRDAEIKKLKDSY 257
                                   889999999999999888777665....88899999999999999999999999998876 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.76
                    TMF_DNA_bd  24 LskkelklnntikkLrkknkelekeikelkkkleklekeleeleer 69 
                                   L++  l+  + ikkL+   ++  +  ++l +k  k e e  + +e+
  gi|13541826|ref|NP_111514.1| 239 LKDLILQRDAEIKKLKDSYNDIFTRYDTLINKMTKREFEKINAREL 284
                                   6666777888888888888887777777777777777666665555 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 ?    5.8   7.6      0.11        17       1      36 [.     169     204 ..     169     282 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.11
                     E2F_CC-MB   1 lkqelesleeeeqkLDelieklteqlknltedeknq 36 
                                   l++e+++l+++ ++L++ i+++++q+++++   +++
  gi|13541826|ref|NP_111514.1| 169 LSAEINDLNAKKSELEQAIAEMQKQIEDIQAGIDER 204
                                   689************************997744443 PP

>> Ssu72  Ssu72-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   5.4     0.018       2.9     108     182 ..     144     218 ..      64     226 .. 0.85
   2 ?    1.3   0.2       1.3   2.2e+02      79     115 ..     243     279 ..     219     288 .] 0.71

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.018
                                   SHHHHHHHHHHHHHS--SS-EEEEEEEE---SSHHHHHHHHHHHHHHHHHHHT-SS.HHHHHHHHHHHHHHHHT- CS
                         Ssu72 108 eervfdavvedllsreselnrpvhvinvdikDnheeAlvgakaileLakaleeaedeleeevkeilaefeektkk 182
                                   e++  ++ + +l+s+++++++ +  +  +i+D + + +   +ai e+ k++e+ ++ ++e++k + +e e+ +k+
  gi|13541826|ref|NP_111514.1| 144 EKKAIESEIGYLNSKKDQMQSEISQLSAEINDLNAKKSELEQAIAEMQKQIEDIQAGIDERIKAVFEENESMKKT 218
                                   667777778899******************************************************998877665 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 1.3
                                   HHHHHHHH-SS--BGGG---.--SEEEESSHHHHHHH CS
                         Ssu72  79 mldrnrkiKkaPerwqeaeekkfdvvitceervfdav 115
                                   +l+r+++iKk  + ++++ ++   ++  + +r f+++
  gi|13541826|ref|NP_111514.1| 243 ILQRDAEIKKLKDSYNDIFTRYDTLINKMTKREFEKI 279
                                   6899999999999999988844445556677777666 PP

>> Rho_Binding  Rho Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   4.9    0.0092       1.5       3      48 ..     164     206 ..     155     219 .. 0.72
   2 ?    5.2   1.0      0.24        38       2      46 ..     216     260 ..     213     273 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0092
                   Rho_Binding   3 kdvenlakekeelnkklkkleeelekakeeeeeieklkasyekqLk 48 
                                   +++ +l+ e ++ln+k ++le+++++++   ++ie ++a  ++ +k
  gi|13541826|ref|NP_111514.1| 164 SEISQLSAEINDLNAKKSELEQAIAEMQ---KQIEDIQAGIDERIK 206
                                   6789999999999999999999999998...555555555444443 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.24
                   Rho_Binding   2 tkdvenlakekeelnkklkkleeelekak.eeeeeieklkasyekq 46 
                                   +k++e+++k + +l   l+++++ l+ +  + ++ei+klk sy++ 
  gi|13541826|ref|NP_111514.1| 216 KKTLEEYEKTRADLATALSTVSQ-LKDLIlQRDAEIKKLKDSYNDI 260
                                   78899999999999999988765.55555589********999875 PP

>> Cep57_CLD_2  Centrosome localisation domain of PPC89
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   2.3     0.042       6.7      22      61 ..     148     187 ..     142     196 .. 0.77
   2 ?    3.5   1.7      0.48        76      10      42 ..     210     255 ..     201     261 .. 0.61

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.042
                   Cep57_CLD_2  22 heeelkrLnkERdsalrqLgvAyeelneLkaevealrkEL 61 
                                    e+e+  Ln+  d + + +++   e+n+L a+   l++  
  gi|13541826|ref|NP_111514.1| 148 IESEIGYLNSKKDQMQSEISQLSAEINDLNAKKSELEQAI 187
                                   6777788888888888888888888888888888887754 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.48
                   Cep57_CLD_2  10 nrLdsltrklqvhe.............eelkrLnkERdsalrqLgv 42 
                                   ++++s+   l+++e             + lk+L   Rd  +++L +
  gi|13541826|ref|NP_111514.1| 210 EENESMKKTLEEYEktradlatalstvSQLKDLILQRDAEIKKLKD 255
                                   6777777777777766665555555555555555566666666665 PP

>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   3.3    0.0033      0.53       9      46 ..     162     199 ..     158     202 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0033
                          XhlA   9 ietkldnleervdkleekaaeaeekiknleedlkkles 46 
                                   +++++  l+ ++++l+ k++e e+ i +++++++++++
  gi|13541826|ref|NP_111514.1| 162 MQSEISQLSAEINDLNAKKSELEQAIAEMQKQIEDIQA 199
                                   6777888999**************************97 PP

>> DUF4404  Domain of unknown function (DUF4404)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   5.2     0.011       1.7       2      75 ..     163     237 ..     162     241 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.011
                       DUF4404   2 kelLekLheeLeqnesldeetralLeslaedieellaeedaaaeeee.laerlneaverFeeeHPklagvlreil 75 
                                   ++++ +L++e+++ ++ ++e ++ +++++++ie + a  d++ ++    +e +++++e++e++  +la +l  + 
  gi|13541826|ref|NP_111514.1| 163 QSEISQLSAEINDLNAKKSELEQAIAEMQKQIEDIQAGIDERIKAVFeENESMKKTLEEYEKTRADLATALSTVS 237
                                   788999999999877777777776666666666555554444444324799************999999998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2579  (0.143845); expected 358.6 (0.02)
Passed bias filter:                      834  (0.0465168); expected 358.6 (0.02)
Passed Vit filter:                       236  (0.013163); expected 17.9 (0.001)
Passed Fwd filter:                       123  (0.00686039); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):             112  [number of targets reported over threshold]
# CPU time: 1.28u 0.35s 00:00:01.63 Elapsed: 00:00:00.57
# Mc/sec: 1521.34
//
Query:       gi|13541827|ref|NP_111515.1|  [L=429]
Description: asparaginyl-tRNA synthetase [Thermoplasma volcanium GSS1]
Scores for complete 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-92  308.9   0.1    4.1e-92  308.6   0.1    1.0  1  tRNA-synt_2      tRNA synthetases class II (D, K and N)
    3.8e-13   49.2   0.0    7.3e-13   48.3   0.0    1.5  1  tRNA_anti-codon  OB-fold nucleic acid binding domain
     0.0007   19.2   0.3      0.026   14.0   0.0    2.3  2  tRNA-synt_2d     tRNA synthetases class II core domain (F)
  ------ inclusion threshold ------
       0.12   11.8   0.1       0.19   11.2   0.1    1.2  1  GCP_C_terminal   Gamma tubulin complex component C-terminal


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 !  308.6   0.1   9.2e-96   4.1e-92       2     313 ..     110     423 ..     109     424 .. 0.97

  Alignments for each domain:
  == domain 1  score: 308.6 bits;  conditional E-value: 9.2e-96
                                   CCHHHHTHHHHCCSHHHHHHHHHHHHHHHHHHHHHHHTT-EE----SEESS--SSSS--EEEEETTT.TEEE....-E-S- CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxx RF
                   tRNA-synt_2   2 eelrlknryldlrtekvskvlrlrstvtkavrkyleengfieietPiLsksdteegarlFkvksrekekeff....aLtqs 78 
                                   ee++l+nr+l lr+++  ++l++rst+ +++ +++ ++g+++++tP+++++++e+g++lFkv       +ff    +L+qs
  gi|13541827|ref|NP_111515.1| 110 EEFLLDNRHLWLRSREFTSILKVRSTIFRSFADFFYDQGYYQVHTPFMVSTAVEGGSTLFKV-------DFFgepiFLNQS 183
                                   6899**********************************************************.......88889999**** PP

                                   SHHHHHHHHHCTHSEEEEEEEEE--S--BTTB-S-CEEEEEEEEET-SCHHHHHHHHHHHHHHHHHHHHCSCCCCCHTTTT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   tRNA-synt_2  79 pqlylellivagidrvfqiaraFRaEdsrtdrhlaEFtqieaemsfieeedimqvleelikslvkevlessakdiefvirr 159
                                    q+yle++i + +++vf+ia++FRaE+srt+rhl+E+++ eae+++i++ ++m+v e++i +++++v+e++ +d++   r 
  gi|13541827|ref|NP_111515.1| 184 AQFYLETMIYS-LEKVFTIAPSFRAEKSRTRRHLTEYWHAEAEVAWIDNREMMDVEENMIYYIIQRVIEENYDDLKLLGRD 263
                                   ***********.**************************************************************9998887 PP

                                   TS..EE-SSS-EEEEHHHHHHHHHTS......-SS--HHHHHHHHHHS--SEEEEEEEBGGGSTTCBBBSTTSTTBBSEEE CS
                                   xx..xxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   tRNA-synt_2 160 ns..kdlkkpfkrltykeaieklnei......gkdldkaderalvkkeknepvfvtdfPaelkpFyarkeeddkkltesyD 232
                                    +  + +k pf+r++y++ i+ +nei      g+dl  ++er  +     +pvfvt++P+elkpFy++++ d++  + + D
  gi|13541827|ref|NP_111515.1| 264 PEalRAMKPPFPRVKYSDIIKVANEIgmqlkyGDDLGADEERQITM-RYCKPVFVTNYPKELKPFYMPQDPDNPSEVLNHD 343
                                   6667999*99**************99****9999999999999888.999******************************* PP

                                   EEET.TE.EEEEEEEB--SHHHHHHHHHHCCHHSSSGGGGHHHHHHHHCT--SEEEEEEEHHHHHHHHCT-SSGGGCSSS- CS
                                   xxxx.xx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   tRNA-synt_2 233 llin.gv.ElvgGslRiedpeeleeklkskgldeeaeekfswylealeyGapphgGlglGldRlvmlllgsesIrdviaFP 311
                                   ll + g+ E++gGs+Ri+d++el +++++ gld   e+ ++wy+++++yG++ph+G+glG+dRl m+++++++Ir++i++P
  gi|13541827|ref|NP_111515.1| 344 LLAPeGYgEIIGGSQRIWDYKELMQRIREAGLD---ESAYYWYIDLRKYGSVPHSGFGLGMDRLAMWIMHLDNIREAIPYP 421
                                   ***9889**************************...********************************************* PP

                                   XX CS
                                   xx RF
                   tRNA-synt_2 312 kl 313
                                   ++
  gi|13541827|ref|NP_111515.1| 422 RT 423
                                   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 !   48.3   0.0   1.6e-16   7.3e-13       1      75 [.      17      95 ..      17      96 .. 0.94

  Alignments for each domain:
  == domain 1  score: 48.3 bits;  conditional E-value: 1.6e-16
                                  EEEEEEEEEEEEEEETTEEEEEEEETTEEEEEEEET....HHHHHHHTTS-TTSEEEEEEEEEEC...TTSSEEEEEEEEEE CS
               tRNA_anti-codon  1 VtvaGrvtsisdrsggkvifidlrDgtgriqvvlfr....eeatklaenlkeGdvvrvtGrvkrr...pggelelkveeiel 75
                                  V+v+G+v +i  rs+g+v fi++rD tg++q+++ +     e+++  ++l +++ +   G+ k+    p+g +e+++ ++++
  gi|13541827|ref|NP_111515.1| 17 VSVRGWVYRI--RSSGGVTFIVIRDSTGIVQCTAKKneltPEQYDEISSLGIESSLSLIGTMKKEprsPTG-YEISIHKFTV 95
                                  89********..*************************99988888889999**************999999.****999875 PP

>> tRNA-synt_2d  tRNA synthetases class II core domain (F)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.1     0.017        77     103     155 ..     197     252 ..     189     259 .. 0.79
   2 !   14.0   0.0   5.9e-06     0.026     209     233 ..     392     416 ..     383     425 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.017
                                   EEEEEEEEEBSST.-SSSB-SEEEE..EEEEEEETT--HHHHHHHHHHHHHHHCTS CS
                  tRNA-synt_2d 103 kiisigrvfRrda.vDathlaeFhq..veglvvdenvsladlkgvleellkklfga 155
                                   k+++i   fR ++   ++hl e+    +e  ++d+   ++    ++  +++++ ++
  gi|13541827|ref|NP_111515.1| 197 KVFTIAPSFRAEKsRTRRHLTEYWHaeAEVAWIDNREMMDVEENMIYYIIQRVIEE 252
                                   899999******978899***99761156778888888887788888888777665 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 5.9e-06
                                   SEEEEEEEEHHHHHHHHHT-SSGHH CS
                  tRNA-synt_2d 209 vsgfafGlGveRlamlkygieDiRe 233
                                   v+  +fGlG++Rlam  + +++iRe
  gi|13541827|ref|NP_111515.1| 392 VPHSGFGLGMDRLAMWIMHLDNIRE 416
                                   56678*******************8 PP

>> GCP_C_terminal  Gamma tubulin complex component C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   4.2e-05      0.19     125     184 ..     187     258 ..     183     265 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 4.2e-05
                GCP_C_terminal 125 rvkrvefalsslw......krrkatgarsvl..lkra....rllrqemlhfvsqlqyYvldeviessWrele 184
                                   ++  + ++l++++      +++k++++r+ +  ++      +    em+ + +++ yY++++vie+++++l+
  gi|13541827|ref|NP_111515.1| 187 YLETMIYSLEKVFtiapsfRAEKSRTRRHLTeyWHAEaevaWIDNREMMDVEENMIYYIIQRVIEENYDDLK 258
                                   566777778877666776533333333322244555566669999***********************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (429 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       366  (0.0204139); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.46
# Mc/sec: 2813.09
//
Query:       gi|13541828|ref|NP_111516.1|  [L=234]
Description: hypothetical protein TVN0997 [Thermoplasma volcanium GSS1]
Scores for complete 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-45  154.4  11.2    5.3e-45  153.7  11.2    1.3  1  DUF92     Integral membrane protein DUF92
  ------ inclusion threshold ------
       0.27   11.5   7.6      0.073   13.4   1.4    2.4  2  YwiC      YwiC-like protein
       0.37   10.9   1.2       0.54   10.3   1.2    1.3  1  UPF0242   Uncharacterised protein family (UPF0242) N-terminus
       0.44   10.5   0.1       0.44   10.5   0.1    2.1  2  DUF1427   Protein of unknown function (DUF1427)
        1.5    8.6   8.1       0.97    9.2   6.1    1.7  1  DUF5381   Family of unknown function (DUF5381)
        6.6    7.2   4.9        9.6    6.7   0.0    2.5  3  SIT       SHP2-interacting transmembrane adaptor protein, SIT


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 !  153.7  11.2   1.8e-48   5.3e-45       3     199 ..       9     211 ..       7     226 .. 0.90

  Alignments for each domain:
  == domain 1  score: 153.7 bits;  conditional E-value: 1.8e-48
                         DUF92   3 tlllalralrkksLtpsGalaavlvgvlialaplgllffllllvFfllgslltkvkkkvKa..kleeekegaRdavqVlan 81 
                                     +l++++l+ ++L+++G   a+++g++i +  +++ +++l+l+F  ++ ++tk   k+K+  k++e ++g+R+a +V   
  gi|13541828|ref|NP_111516.1|   9 LGILFVASLKLNVLDLRGSTIALFIGAFISFI-GSIYWLILMLIFVASSFIATKAFFKTKKlmKVQEGQNGERKASNVTYA 88 
                                   6789999********************99999.7779*****************9999999889999999*********** PP

                         DUF92  82 slvalllally.....lasdlllvgivasyAavaaDTlaSElGkilskskprlittlkkvppGtnGgVsllGllasllGal 157
                                   ++++++++++y     + +++++  ++ s+A+ ++DT+aSE+G ++ k k ++it++kkv+pG+nGgVsl+G la+llG++
  gi|13541828|ref|NP_111516.1|  89 AVTGIIITFIYalyphM-QNYFFELFAISFAVINSDTFASEIG-VIDK-KVYMITNFKKVNPGVNGGVSLTGELAALLGGF 166
                                   ***********776633.89999********************.6666.8******************************* PP

                         DUF92 158 liallavlllllel...lillltlaGllGsllDSlLGatlqasvv 199
                                   +ia+ ++l+ + ++    ++l+tlaG++G+ +DS+LG+++++++ 
  gi|13541828|ref|NP_111516.1| 167 IIAISYSLFAYRSVqayPVALVTLAGFAGCQIDSVLGSLFENRGK 211
                                   ***998777644447888899********************9943 PP

>> YwiC  YwiC-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   1.4   2.4e-05     0.073      15      95 ..      31     119 ..      24     125 .. 0.68
   2 ?    1.2   0.5      0.15   4.4e+02      24      73 ..     181     232 ..     156     234 .] 0.53

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.4e-05
                          YwiC  15 lllGlllag..pvwahllllvawlvgYlaffpl...llllka..rrrarylkplliYgavallllllalllqpa.llwwal 87 
                                   l +G++++      + +l+l+ + + ++a++++   + l+k    ++++ +++ ++Y+av++++++++++l+p+   ++  
  gi|13541828|ref|NP_111516.1|  31 LFIGAFISFigSIYWLILMLIFVASSFIATKAFfktKKLMKVqeGQNGERKASNVTYAAVTGIIITFIYALYPHmQNYFFE 111
                                   45566655444344445555555566666555511155666554488899999*********************6666666 PP

                          YwiC  88 lflplvav 95 
                                   lf++ +av
  gi|13541828|ref|NP_111516.1| 112 LFAISFAV 119
                                   77766665 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.15
                          YwiC  24 pvwahllllvawlvgYlaffplllllka..rrrarylkplliYgavalllll 73 
                                   ++ +  l+++a ++g +    l+ l+ +  + ++  +++l+ +  va+ ++l
  gi|13541828|ref|NP_111516.1| 181 QAYPVALVTLAGFAGCQIDSVLGSLFENrgKLNKGQVNFLASFLTVAASAAL 232
                                   4445556666666666777778888877442333444444444444444433 PP

>> UPF0242  Uncharacterised protein family (UPF0242) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   1.2   0.00018      0.54      13      81 ..       8      76 ..       1      89 [. 0.79

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00018
                       UPF0242 13 llPllllaiysiqllseqksWsllsiGlllaaaGsLlllllllkwekalkeklekskleekeaklteld 81
                                  +l +l++a+ ++++l  + s   l iG +++ +Gs+  l+l+l +       +++ +  +k  k++e +
  gi|13541828|ref|NP_111516.1|  8 ILGILFVASLKLNVLDLRGSTIALFIGAFISFIGSIYWLILMLIFVASSFIATKAFFKTKKLMKVQEGQ 76
                                  56788999999999999999999*******************999766666667777777777777766 PP

>> DUF1427  Protein of unknown function (DUF1427)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.4       1.9   5.8e+03       9      19 ..      91     101 ..      87     102 .. 0.83
   2 ?   10.5   0.1   0.00015      0.44       5      51 ..     160     205 ..     158     216 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.9
                       DUF1427   9 aGllvGviYsl 19 
                                    G+++  iY+l
  gi|13541828|ref|NP_111516.1|  91 TGIIITFIYAL 101
                                   69999999987 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00015
                       DUF1427   5 lslgaGllvGviYsllnvrsPaPPvvaLvGLlGiLvGeqvvPvakrl 51 
                                    +l  G ++ + Ysl+  rs     vaLv L G  +G q+  v  +l
  gi|13541828|ref|NP_111516.1| 160 AALLGGFIIAISYSLFAYRSVQAYPVALVTLAGF-AGCQIDSVLGSL 205
                                   57889***************988889****9995.788876666555 PP

>> DUF5381  Family of unknown function (DUF5381)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   6.1   0.00033      0.97      16      87 ..       6      83 ..       1      90 [. 0.72

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00033
                       DUF5381 16 flatvglglaglfllfeglkfeskysllyiiigiigtifgliillmvl.......pallkkGkvlftikeGenGkvisr 87
                                  +l+ ++l +a+l l +  l+ ++   +++ +i++ig i+ li++l+++       +a+ k  k l +++eG+nG+ ++ 
  gi|13541828|ref|NP_111516.1|  6 ILILGILFVASLKLNVLDLRGSTIALFIGAFISFIGSIYWLILMLIFVassfiatKAFFK-TKKLMKVQEGQNGERKAS 83
                                  555667777888888888888888899999*********999998765211112135555.88899999*****97665 PP

>> SIT  SHP2-interacting transmembrane adaptor protein, SIT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   1.2      0.15   4.6e+02       2      23 ..       4      25 ..       3      28 .. 0.86
   2 ?    6.7   0.0    0.0032       9.6       8      41 ..      46      80 ..      40      97 .. 0.78
   3 ?   -2.8   0.0       2.9   8.7e+03      11      26 ..     166     181 ..     162     182 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.15
                           SIT  2 llllilallLlllviasllawr 23
                                  l +lil++l++ ++ +++l +r
  gi|13541828|ref|NP_111516.1|  4 LTILILGILFVASLKLNVLDLR 25
                                  6789*************98665 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0032
                           SIT  8 allLlllviasllawrmkkrqkkaaeysseq.isr 41
                                   +l+l++v+ s++a   + + kk +++++ q  +r
  gi|13541828|ref|NP_111516.1| 46 LILMLIFVASSFIATKAFFKTKKLMKVQEGQnGER 80
                                  58999*******************99977772222 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 2.9
                           SIT  11 Llllviasllawrmkk 26 
                                   +++ +  sl+a+r ++
  gi|13541828|ref|NP_111516.1| 166 FIIAISYSLFAYRSVQ 181
                                   5788899999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1012  (0.0564449); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.57
# Mc/sec: 1228.56
//
Query:       gi|13541829|ref|NP_111517.1|  [L=336]
Description: pyridoxal biosynthesis lyase PdxS [Thermoplasma volcanium GSS1]
Scores for complete 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-92  307.0   6.0    1.5e-88  296.0   6.0    2.2  2  SOR_SNZ         SOR/SNZ family
    3.6e-12   46.1   3.8      1e-07   31.5   0.1    2.6  3  ThiG            Thiazole biosynthesis protein ThiG
    0.00013   21.6   0.5    0.00028   20.5   0.1    1.7  2  OMPdecase       Orotidine 5'-phosphate decarboxylase / HUMPS 
    0.00019   20.7   0.4       0.16   11.0   0.0    2.4  2  Dus             Dihydrouridine synthase (Dus)
    0.00092   18.7   5.1      0.013   14.9   0.0    2.5  2  NMO             Nitronate monooxygenase
     0.0023   17.2   0.0       0.41    9.8   0.0    2.3  2  IGPS            Indole-3-glycerol phosphate synthase
     0.0034   16.6   2.2      0.064   12.4   0.0    3.2  3  NanE            Putative N-acetylmannosamine-6-phosphate epim
      0.006   15.6   0.2      0.012   14.6   0.2    1.5  1  IMPDH           IMP dehydrogenase / GMP reductase domain
     0.0064   15.4   0.0      0.016   14.0   0.0    1.6  1  Trp_syntA       Tryptophan synthase alpha chain
  ------ inclusion threshold ------
      0.014   16.0   0.0      0.073   13.6   0.0    2.1  2  Peptidase_S66C  LD-carboxypeptidase C-terminal domain
      0.042   13.3   0.4        1.1    8.7   0.0    2.4  2  His_biosynth    Histidine biosynthesis protein
        0.1   11.5   0.0       0.15   11.0   0.0    1.1  1  RE_AccI         AccI restriction endonuclease
       0.35   10.9   2.2       0.85    9.7   0.4    2.4  2  PA              PA 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 !  296.0   6.0   1.1e-91   1.5e-88       3     189 ..      14     200 ..      12     210 .. 0.97
   2 !    8.8   0.0   0.00093       1.3     185     207 .]     233     255 ..     218     255 .. 0.83

  Alignments for each domain:
  == domain 1  score: 296.0 bits;  conditional E-value: 1.1e-91
                                   HHHHHHHHTTTSSEEEEESSHHHHHHHHHHT-SEEEE-SS-HHHHHHH-S------HHHHHHHHHH-SS-EEEEEETT-HH CS
                       SOR_SNZ   3 kvkaglaemlkgGvimdvvnaeqakiaeeaGavavmalervpadirkeggvarmsdpklikeikeavsipvmakvriGhfv 83 
                                    +k+g+++m kgGvimdv++aeqakiae+aGavavmalervpadir++ggvarm+dpk+i+ei +av+ipvmakvriGh+ 
  gi|13541829|ref|NP_111517.1|  14 LIKRGFSSMTKGGVIMDVTTAEQAKIAEKAGAVAVMALERVPADIRAAGGVARMADPKKIREILDAVTIPVMAKVRIGHIS 94 
                                   68******************************************************************************* PP

                                   HHHHHHHTT-SEEEEETTS--S-SS----GGG-SS-EEEEESSHHHHHHHHHHT-SEEEEES-TTS--THHHHHHHHHHHH CS
                       SOR_SNZ  84 eaqilealgvdyiDesevltpadeeahidkkkfkvpfvcGarnlgealrriaeGaamirtkGeagtGdvveavrhvrkike 164
                                   ea  le+lgvd++Desevltpad  +h+ kkk++vp+v+Garnl ea+rri eGaam+rtkGeagtG+++eavrh+rk++e
  gi|13541829|ref|NP_111517.1|  95 EAYTLEKLGVDMLDESEVLTPADPFFHLYKKKLTVPVVSGARNLPEAVRRIFEGAAMVRTKGEAGTGNIIEAVRHIRKVNE 175
                                   ********************************************************************************* PP

                                   HHHHHTTS-HHHHHHHHHHHHGGGH CS
                       SOR_SNZ 165 eirklkslseeelvalakelkaple 189
                                   ei+ +++++++e++++a++++ ++ 
  gi|13541829|ref|NP_111517.1| 176 EIAIVRRMTQDEIKTAAENIASSYF 200
                                   *******************998874 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00093
                                   HGGGHHHHHHHHHTTS-S---T. CS
                       SOR_SNZ 185 kaplelvkevaelgrlpvvnfaa 207
                                   k   ++++++++l+rlpvvnfaa
  gi|13541829|ref|NP_111517.1| 233 KGISDILRQIRKLNRLPVVNFAA 255
                                   45579****************98 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.7     1e-05     0.014     114     200 ..       9     106 ..       4     122 .. 0.76
   2 ?   -2.0   0.0       1.3   1.8e+03      63      80 ..     126     143 ..     110     154 .. 0.80
   3 !   31.5   0.1   7.4e-11     1e-07     166     226 ..     238     300 ..     232     312 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1e-05
                                   HHHHHHHHTT-EEEEE..E-S-HHHHHH...HHHTT-SEBEEB...SSSTTS----S...-HHHHHHHHHH-SS-BEEES- CS
                          ThiG 114 kaaeiLvkeGFevlpY..vsdDlvlarr...leevGcaavmPl...aapiGsglGll...nkealkiiieeakvPvivDAG 183
                                   k    L+k GF+ ++   v  D+ +a++    e++G+ avm l    a i ++ G++   ++++++ i++ +++Pv+    
  gi|13541829|ref|NP_111517.1|   9 KFGTELIKRGFSSMTKggVIMDVTTAEQakiAEKAGAVAVMALervPADIRAAGGVArmaDPKKIREILDAVTIPVMAKVR 89 
                                   55667899999998753367788776652225789******97333588988888652226889***************** PP

                                   --SHHHHHHHHHTT-SE CS
                          ThiG 184 igspsdaaqamelGada 200
                                   ig+ s+a +  +lG+d 
  gi|13541829|ref|NP_111517.1|  90 IGHISEAYTLEKLGVDM 106
                                   *********999**994 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.3
                                   SEEEEE-TT-SSHHHHHH CS
                          ThiG  63 vtllPntaGaktaeeAvr 80 
                                      +P  +Ga++  eAvr
  gi|13541829|ref|NP_111517.1| 126 KLTVPVVSGARNLPEAVR 143
                                   445799999999999997 PP

  == domain 3  score: 31.5 bits;  conditional E-value: 7.4e-11
                                   HHHHHHHH-SS-BEEES..---SHHHHHHHHHTT-SEEEESHHHHTSSSHHHHHHHHHHHHHH CS
                          ThiG 166 alkiiieeakvPvivDA..GigspsdaaqamelGadavllntavaeakdpvamArafklavea 226
                                    l+ i++  ++Pv+  A  G+ +p d a  melGad+v++ + + ++ dp +mA+++  ave 
  gi|13541829|ref|NP_111517.1| 238 ILRQIRKLNRLPVVNFAagGVATPADGALMMELGADGVFVGSGIFKSPDPEKMAKSIVEAVEN 300
                                   57778888899999654458****************************************985 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 ?   -2.6   0.0       2.5   3.5e+03       7      27 ..      29      48 ..      22      52 .. 0.63
   2 !   20.5   0.1   2.1e-07   0.00028      80     224 ..     142     293 ..     136     294 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 2.5
                                  E-SSSHHHHHHHHHHHGGGSS CS
                     OMPdecase  7 lDvatarelleladkvgpsiv 27
                                  +Dv+ta e  ++a+k+g+ +v
  gi|13541829|ref|NP_111517.1| 29 MDVTTA-EQAKIAEKAGAVAV 48
                                  566666.34467777766333 PP

  == domain 2  score: 20.5 bits;  conditional E-value: 2.1e-07
                                   CHHHHTTESEEEEEGTGHHHHHHHHHHHHHHTTS.EEEEEESTSSGGHHHHHHHSHHHHHHHHHHHHHHH.TTESEEECCC CS
                     OMPdecase  80 sarikewadivtvhavaGkasvkalaeaaekwgnrgllilaqmsskgnlmlqekgytqacveaarehkae.dfvmGfvaqe 159
                                   + ri e+a +v   + aG++ + ++++ ++k +   + i+ +m+  +  + +e +++    + ++e++++  +  G v   
  gi|13541829|ref|NP_111517.1| 142 VRRIFEGAAMVRTKGEAGTGNIIEAVRHIRKVN-EEIAIVRRMTQDEIKTAAE-NIASSYFQLRNEASTDlFGQSGKVLYD 220
                                   56899***************************6.9******************.455555555555553343445555555 PP

                                   HTH..HHHHH.....TTCSCEEEHHHTT.EEEEECTTCCGGGHHHHHHHTTCSEEEESHHHHTSSSHHHHHHH CS
                     OMPdecase 160 tln..ateed.....addfihltpgigl.eqggdgkgqqyntpekligiagadiiivGRgIlkagdpveeaer 224
                                   +     ++e+      d + ++++  +l  +   ++g+      +l+ + gad + vG gI+k++dp++ a+ 
  gi|13541829|ref|NP_111517.1| 221 DVYygMSREKivkgiSDILRQIRKLNRLpVVNFAAGGVATPADGALMMELGADGVFVGSGIFKSPDPEKMAKS 293
                                   5557633333433335555555555555877788888888889999999*******************99986 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.5   0.1    0.0014         2     142     196 ..      35      94 ..      29     107 .. 0.55
   2 !   11.0   0.0   0.00012      0.16     176     221 ..     240     286 ..     226     316 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0014
                                   HHHHHHHHCT-SEEEEESSECCCTT-C.....G--CHHHHHHHHH-SS-EEEESS--SHH CS
                           Dus 142 elakiveaaGaqaltvHgRtraqnyeg.....tadweaIkevkqavsipviaNGdIkdae 196
                                   e aki+e+aGa a++   R++a+ + +      ad ++I+e+ +av+ipv+a   I +++
  gi|13541829|ref|NP_111517.1|  35 EQAKIAEKAGAVAVMALERVPADIRAAggvarMADPKKIREILDAVTIPVMAKVRIGHIS 94 
                                   556666666666666666644443333333345556666666666666666654444444 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00012
                                   HHHHHH-S..S-EEEESS--SHHHHHHHHHHH--SEEEESCHHCCSTT CS
                           Dus 176 kevkqavs..ipviaNGdIkdaedaqaileetGadgvmigrgalgnPw 221
                                   +++++ ++  ++ +a G++ ++ d   ++e  Gadgv +g g  + P 
  gi|13541829|ref|NP_111517.1| 240 RQIRKLNRlpVVNFAAGGVATPADGALMMEL-GADGVFVGSGIFKSPD 286
                                   556655552266679**********999998.**********999986 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   2.8     0.027        37     139     198 ..      27      86 ..      19     100 .. 0.74
   2 !   14.9   0.0   9.3e-06     0.013     178     225 ..     230     281 ..     223     315 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.027
                           NMO 139 liptissvkearkvearGaDaliv......qGpeaGGhqGtpevgdkglfaLvpqvldavdiPviA 198
                                   +i+ ++++++a+++e++Ga a+ +      +  +aGG             + + ++ldav iPv+A
  gi|13541829|ref|NP_111517.1|  27 VIMDVTTAEQAKIAEKAGAVAVMAlervpaDIRAAGGVAR------MADPKKIREILDAVTIPVMA 86 
                                   678899************7777651111113345666655......223456889999******99 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 9.3e-06
                           NMO 178 d..kglfaLvpqvldavdiPvi..AaGGiidrrgvaaaLalGAsgvqigtrf 225
                                   +  kg   ++ q+++   +Pv+  AaGG+ +  + a ++ lGA gv +g+  
  gi|13541829|ref|NP_111517.1| 230 KivKGISDILRQIRKLNRLPVVnfAAGGVATPADGALMMELGADGVFVGSGI 281
                                   34478889999**********877*************************975 PP

>> IGPS  Indole-3-glycerol phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.3   0.0     0.007       9.7      58      86 ..      21      49 ..       6      87 .. 0.89
   2 !    9.8   0.0    0.0003      0.41     207     252 ..     247     292 ..     233     294 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.007
                                  ETTTEESBSS--HHHHHHHHTTT.-SEEE CS
                          IGPS 58 SPskgliredfdpaeiAkkyeeagAsaiS 86
                                  S +kg + +d+  ae+Ak  e+agA a+ 
  gi|13541829|ref|NP_111517.1| 21 SMTKGGVIMDVTTAEQAKIAEKAGAVAVM 49
                                  7789*********************9985 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0003
                                   -TTSEEEEESSS-SHHHHHHHCCTT-SEEEESHHHHC-TTHHHHHH CS
                          IGPS 207 pkdvllvaeSGiktredveklkeegvnafLvGeslmrqedvekair 252
                                   +  v+  a  G++t++d   + e g++++ vG+ + +++d ek+ +
  gi|13541829|ref|NP_111517.1| 247 RLPVVNFAAGGVATPADGALMMELGADGVFVGSGIFKSPDPEKMAK 292
                                   4457788999******************************999877 PP

>> NanE  Putative N-acetylmannosamine-6-phosphate epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.2     0.096   1.3e+02     130     168 ..      66     105 ..      13     127 .. 0.53
   2 ?    1.1   0.1      0.14     2e+02     100     116 ..      91     107 ..      50     175 .. 0.53
   3 !   12.4   0.0   4.6e-05     0.064     136     190 ..     241     298 ..     223     300 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.096
                                   SS--HHHHHHHHHT.T--EEEES---SHHHHHHHHTT--S CS
                          NanE 130 aepDfalvkalsea.glkviaeGrintPekakkaieiGvd 168
                                      D + ++++++a  + v+a  ri    +a +  ++Gvd
  gi|13541829|ref|NP_111517.1|  66 RMADPKKIREILDAvTIPVMAKVRIGHISEAYTLEKLGVD 105
                                   2333344444433313445555555555555555555555 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.14
                                   SSHHHHHHHHHTT-SEE CS
                          NanE 100 stleeglvakklGvdiv 116
                                     + e+ + +klGvd++
  gi|13541829|ref|NP_111517.1|  91 GHISEAYTLEKLGVDML 107
                                   33333333334443333 PP

  == domain 3  score: 12.4 bits;  conditional E-value: 4.6e-05
                                   HHHHHHHTT--EEEES---SHHHHHHHHTT--SEEEE-HHHH-...HHHHHHHHHHHT CS
                          NanE 136 lvkalseaglkviaeGrintPekakkaieiGvdavvvGsaitr...leeiakkfveai 190
                                    +++l+   +   a G + tP+  + ++e+G+d v vGs i +   +e++ak  vea+
  gi|13541829|ref|NP_111517.1| 241 QIRKLNRLPVVNFAAGGVATPADGALMMELGADGVFVGSGIFKspdPEKMAKSIVEAV 298
                                   57888888888999**************************976444677777777776 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.2   8.6e-06     0.012      55     175 ..     156     280 ..     120     281 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 8.6e-06
                                   HHTTSEEEE-SSS-HHHHHHHHHHHHTSTTSXBXTTSXB-EEEEE-SSTTHHHHHHHHHHTT-SEEEEE-STSSSH..... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..... RF
                         IMPDH  55 areGgigvihknlsieeqaeevkkvkrspnaakdekgrllvgaavgvkedalervkalveagvdvlvvdsahghse..... 130
                                    ++G   +i    +i++  ee++ v+r+   ++de +      a +  +   e  + l  +   vl  d+  g s+     
  gi|13541829|ref|NP_111517.1| 156 GEAGTGNIIEAVRHIRKVNEEIAIVRRM---TQDEIKTAAENIASSYFQLRNEASTDLFGQSGKVLYDDVYYGMSRekivk 233
                                   4445555777777788888888888854...45666666666666666666778888888888999999988888621111 PP

                                   HHHHHHHHHHHHTT.T.SEEEEEEE-SHHHHHHHHHTT-SEEEE-SS CS
                                   xxxxxxxxxxxxxx.x.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         IMPDH 131 kvleavkeikkkve.e.veviaGnvataegakaLieagadavkvGiG 175
                                   ++ + +++i+k  + + v+  aG vat +  + ++e gad+v vG G
  gi|13541829|ref|NP_111517.1| 234 GISDILRQIRKLNRlPvVNFAAGGVATPADGALMMELGADGVFVGSG 280
                                   344666677654422236667************************88 PP

>> Trp_syntA  Tryptophan synthase alpha chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.0   1.2e-05     0.016     179     234 ..     228     286 ..     224     308 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.2e-05
                                   TSSB-TTHHHHHHHHHHCTSS-EE..EESSS-SHHHHHHHH.TT-SEEEE-HHHHHHHH CS
                     Trp_syntA 179 enavaaevdelverlkkltavPva..vGFGistkeqvkqva.kvadGvivGSalvkkie 234
                                   ++++ + +++++++++kl+ +Pv      G++t+++ + ++  +adGv vGS + k  +
  gi|13541829|ref|NP_111517.1| 228 REKIVKGISDILRQIRKLNRLPVVnfAAGGVATPADGALMMeLGADGVFVGSGIFKSPD 286
                                   5677889999************85223449****999988879**********998765 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 ?   13.6   0.0   5.3e-05     0.073      51     116 ..      35      99 ..      26     104 .. 0.72
   2 ?   -1.8   0.0         3   4.2e+03      78     102 ..     227     251 ..     210     257 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.3e-05
                                   CTSTTGGG--EEEEEE--..G......CC...---HHHHHHHHHT-GGGTTS-EEEEESESSSBS---E CS
                Peptidase_S66C  51 keagvldkvkGivlGrftkpeek...eeeeekeeykealeevlaeiledlkiPvlynldiGHtspnltl 116
                                   ++a++ +k+ ++++   ++++ +   +  +++    + ++e+l    +  +iPv++++ iGH+s+ +tl
  gi|13541829|ref|NP_111517.1|  35 EQAKIAEKAGAVAVMALERVPADiraAGGVARMADPKKIREIL----DAVTIPVMAKVRIGHISEAYTL 99 
                                   6777777777777777777733333444445555556666666....6889*************99987 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 3
                                   ..---HHHHHHHHHT-GGGTTS-EE CS
                Peptidase_S66C  78 ekeeykealeevlaeiledlkiPvl 102
                                   ++e+  + + ++l++i +  ++Pv+
  gi|13541829|ref|NP_111517.1| 227 SREKIVKGISDILRQIRKLNRLPVV 251
                                   4455556677778877777778886 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.1      0.07        96      74     194 ..      56      84 ..       9     107 .. 0.52
   2 ?    8.7   0.0   0.00081       1.1      77     109 ..     253     285 ..     225     311 .. 0.62

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.07
                                   SEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH-THHHHHHHHHHCGGGEEEEEEEEECEEEEETTTTEEEEEEHHHHHH CS
                  His_biosynth  74 ipvqvGGGIrsledveelleagadkviigtaavknpelikelaekfgsqkivvaiDarrgykvaikgwreetgldavelak 154
                                   +++   GG+ ++                                                                     
  gi|13541829|ref|NP_111517.1|  56 ADIRAAGGVARMA-------------------------------------------------------------------- 68 
                                   3333333333333.................................................................... PP

                                   HHHHTT-SEEEEEETTTTTTSS---HHHHHHHHHHHSSEE CS
                  His_biosynth 155 kleelgageilltdidrdGtlsGpdleltkelaeavkipv 194
                                                           d + ++e+ +av+ipv
  gi|13541829|ref|NP_111517.1|  69 ------------------------DPKKIREILDAVTIPV 84 
                                   ........................3333333333333333 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00081
                                   EEESSSSSHHHHHHHHHCT-SEEEESHHHHH-T CS
                  His_biosynth  77 qvGGGIrsledveelleagadkviigtaavknp 109
                                      GG+ +  d + ++e+gad v +g+  +k+p
  gi|13541829|ref|NP_111517.1| 253 FAAGGVATPADGALMMELGADGVFVGSGIFKSP 285
                                   245666666666666666666666666666655 PP

>> RE_AccI  AccI restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00011      0.15     172     284 ..     121     237 ..     105     241 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00011
                       RE_AccI 172 aefsellnhparqayielleaitadtlsvldfrvpswssserlvqlkallrnlkdaikeiqkrdylsitpkvedlkvvykw 252
                                     ++++l  p+ +  ++l ea+ +    ++  r  + + + ++++   ++r++++ i ++++     i    e++   y  
  gi|13541829|ref|NP_111517.1| 121 HLYKKKLTVPVVSGARNLPEAVRRIFEGAAMVRTKGEAGTGNIIEAVRHIRKVNEEIAIVRRMTQDEIKTAAENIASSYFQ 201
                                   56888999999999999999999999999999999999******************************************9 PP

                       RE_AccI 253 ietfnvphfyfq...vffdkv.ygisfeqilkiisd 284
                                   + +     ++ q   v++d v yg+s e+i+k isd
  gi|13541829|ref|NP_111517.1| 202 LRNEASTDLFGQsgkVLYDDVyYGMSREKIVKGISD 237
                                   99999888887655599999846************9 PP

>> PA  PA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.4   0.00062      0.85      30      53 ..      28      51 ..      13      86 .. 0.70
   2 ?   -0.4   0.1      0.83   1.1e+03      23      44 ..     172     193 ..     144     196 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00062
                            PA 30 LvqrtfaeKarnAqaaGAagviiv 53
                                  +++ t+ae a+ A++aGA++v   
  gi|13541829|ref|NP_111517.1| 28 IMDVTTAEQAKIAEKAGAVAVMAL 51
                                  332255**************9765 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.83
                            PA  23 dvkGkivLvqrtfaeKarnAqa 44 
                                   +v+  i++v+r +++ +++A++
  gi|13541829|ref|NP_111517.1| 172 KVNEEIAIVRRMTQDEIKTAAE 193
                                   678889***8866777776664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       826  (0.0460706); expected 358.6 (0.02)
Passed bias filter:                      673  (0.037537); 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: 0.60u 0.33s 00:00:00.93 Elapsed: 00:00:00.50
# Mc/sec: 2037.95
//
Query:       gi|13541830|ref|NP_111518.1|  [L=448]
Description: adenylosuccinate lyase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      2e-46  158.8   0.0    1.1e-45  156.4   0.0    1.8  2  Lyase_1      Lyase
    4.9e-18   65.4   0.0    2.1e-17   63.4   0.0    2.2  2  ADSL_C       Adenylosuccinate lyase C-terminus
    3.3e-06   27.2   0.4    1.3e-05   25.3   0.1    2.0  2  ASL_C        Adenylosuccinate lyase C-terminal
    0.00039   20.8   0.0     0.0011   19.3   0.0    1.8  1  FumaraseC_C  Fumarase C C-terminus
  ------ inclusion threshold ------
      0.037   14.8   0.0       0.16   12.8   0.0    2.1  1  ASL_C2       Argininosuccinate lyase C-terminal
       0.12   12.5   0.1       0.25   11.5   0.1    1.4  1  DUF2058      Uncharacterized protein conserved in bacteria (D


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 !  156.4   0.0   3.6e-49   1.1e-45       9     307 ..      14     293 ..       7     297 .. 0.86
   2 ?   -0.2   0.0      0.17   5.1e+02      16      74 ..     351     407 ..     341     414 .. 0.82

  Alignments for each domain:
  == domain 1  score: 156.4 bits;  conditional E-value: 3.6e-49
                                   HHHHHHHHHHHHHGGGHHHHHCHHHHHHHHHHHTTSSTHHHHHHHHHHHHHHHCHCHHCGGHHHBSSSSSHHHHHHHHHHH CS
                       Lyase_1   9 klmgiftersrenfrlseedikalaalkkaaakanvdlkeeaaaiikaldevleegklddqfvlkviqegsgtavnmnlne 89 
                                   ++  if +++r+ ++l+     ++aa++ka a+ ++++ e+a++i k++ + +   +l+   ++  i+ +++++v + + +
  gi|13541830|ref|NP_111518.1|  14 QIKRIFDDENRLYYMLK-----VEAAISKAEAEYGIIPPEAAEDIGKVVADRIV--QLQ---RVREIEAEIKHDVMA-MVK 83 
                                   56677888888888888.....99*********************998655554..355...455555555555544.444 PP

                                   HHHHHTTHSSGIIIIITTT--HHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHTTT-EEEEEETTEEEEEEEHHH CS
                       Lyase_1  90 vigellgekvepndkvhtgqSsnDqvpTalrlalkkalsekLlpaleqLidalkekakefkdvvkiGrThlqdAtPvtlgq 170
                                    ++e+ +     + +vh+g +snD+++Ta +l++ +     L +++e+++++l e    +k+ +++GrTh+q+A P+t+g 
  gi|13541830|ref|NP_111518.1|  84 ALSEKCK---VGASYVHYGVTSNDVNDTATALQMHDFF-SFLKQDIEDIMETLIELTLRYKSSPMMGRTHGQHASPITIGL 160
                                   4443322...5689************************.56**************************************** PP

                                   HHHHHHHHHHHHHHHHHHHHHHHTCEETTTTTTTSSTTTSCC.THHHHHHHHHHHHHCSTEESSSHHHHHHC-HHHHHHHH CS
                       Lyase_1 171 elsayaealerdrerlkellkrllvellgggtavgtglnadp.efaelvakelakvtglpvkapnsfeavsdrDavvellg 250
                                   +++ y  ++ r++ r+ e+ kr  ++++ g +++g++l+ ++   +++v++ l+        a++  +++ +rD+++e+l+
  gi|13541830|ref|NP_111518.1| 161 KFAVYLSEFSRHYDRMIEMSKRAFAGKVLGPVGTGAALGPKAlDIQNRVMEILG------IYAEEGPTQIVNRDRYIEYLS 235
                                   ******************************999999999988666677777777......466777789************ PP

                                   HHHHHHHHHHHHHHHHHHHTSTT.TSSEEEEGCCTSSC-TTSTTTEBTHHHHHHHHHH CS
                       Lyase_1 251 alkllatsLskfaeDlrllssge.aglvelslaesepGSSiMPgKvNPvqlElltgva 307
                                   +++ + + L k++ ++r l+  e   + e  + e++ GSS MP KvNP+++E++ + +
  gi|13541830|ref|NP_111518.1| 236 VINGISVTLEKIGTEIRNLQRPEiDEMSEYFDVERQVGSSSMPSKVNPINSENVVSLS 293
                                   ***********************8888999***********************87765 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.17
                                   HHHHHHGGGHHHHHCHHHHHHHHHHHTTSSTHHHHHHHHHHHHHHHCHCHHCGGHHHBS CS
                       Lyase_1  16 ersrenfrlseedikalaalkkaaakanvdlkeeaaaiikaldevleegklddqfvlkv 74 
                                   +++r n +++  d  ++  l +a+ +a+++ + + + i +   + ++egk  +++v++ 
  gi|13541830|ref|NP_111518.1| 351 DKIRKNLEMD--DSIFSESLVAALTQAGMPRQDAHEFIRRCSMKARSEGKTLKHVVVEE 407
                                   4556666666..666999999**********9999999999999999999998888875 PP

>> ADSL_C  Adenylosuccinate lyase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       4.2   1.3e+04      51      66 ..     260     275 ..     251     276 .. 0.73
   2 !   63.4   0.0   7.2e-21   2.1e-17       3      71 ..     363     436 ..     361     438 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 4.2
                                   CHHHHHT-GGGCCTTH CS
                        ADSL_C  51 eeldalfdpayylgsa 66 
                                   +e+ + fd ++ +gs+
  gi|13541830|ref|NP_111518.1| 260 DEMSEYFDVERQVGSS 275
                                   4788889999988876 PP

  == domain 2  score: 63.4 bits;  conditional E-value: 7.2e-21
                                   GGHHHHHHHHH.HTH-HHHHHHHHHHHHHHHHHC...HHHHHHT-HHHHC.HHCHHHHHT-GGGCCTTHHHHHH CS
                        ADSL_C   3 ifservllaLv.kglgReeAyelVqeaamkawee...llelLaadpevkk.seeeldalfdpayylgsadeivd 71 
                                   ifse+++ aL+ +g+ R++A+e +++++mka+ e   l+ ++ ++   ++ +++eld+l+dpa+++gsa+ei+d
  gi|13541830|ref|NP_111518.1| 363 IFSESLVAALTqAGMPRQDAHEFIRRCSMKARSEgktLKHVVVEEGITNYiRRDELDRLMDPANFIGSAPEICD 436
                                   8**********77***********************999999999655579889******************98 PP

>> ASL_C  Adenylosuccinate lyase C-terminal
   #    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      24      56 ..      61      93 ..      50     138 .. 0.56
   2 !   25.3   0.1   4.3e-09   1.3e-05       4     113 ..     312     426 ..     310     428 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.59
                                  HHHHHHHHHHHCCEEE-HHHHHHHHHT-GGGGH CS
                         ASL_C 24 lialksllkglsklevneealaedLdenwevla 56
                                  ++ l+++ +  ++++ +  a+ + L e+ +v a
  gi|13541830|ref|NP_111518.1| 61 IVQLQRVREIEAEIKHDVMAMVKALSEKCKVGA 93
                                  444444444444444444444444444444444 PP

  == domain 2  score: 25.3 bits;  conditional E-value: 4.3e-09
                                   T--TCHHHHHTTCHHHHHHHHHHH..HHHHHHHCCEEE-HHHHHHHHHT-GGGGHHHHHHHHHHTT-..TTHHHHHHHHHT CS
                         ASL_C   4 QRDLtdStvlRnlgvalahslial..ksllkglsklevneealaedLdenwevlaEaiqtvlrregi..ekpYeklkeltr 80 
                                    RDLt+S+  R + ++ + +l+ +   ++ + ls l ++e++++++L+   ++ +E++  +l + g+  ++++e +++   
  gi|13541830|ref|NP_111518.1| 312 ERDLTNSALERFT-IPYSSILVDYilVKMNSILSSLIIKEDKIRKNLEMDDSIFSESLVAALTQAGMprQDAHEFIRRCSM 391
                                   6**********75.5566666654225788999*******************************99833589********* PP

                                   TS---HHHHHHHHHCS-S-HHHH.HHHHC-.-CCC CS
                         ASL_C  81 gkkitkeslkefieslevseeak.eeLkal.tpat 113
                                   +++ + ++lk+++ +  +++ ++ +eL +l  pa+
  gi|13541830|ref|NP_111518.1| 392 KARSEGKTLKHVVVEEGITNYIRrDELDRLmDPAN 426
                                   *************9998887664256665414655 PP

>> FumaraseC_C  Fumarase C C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   3.7e-07    0.0011      20      53 ..     392     428 ..     388     429 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 3.7e-07
                                   HHHHHT--HHHHHHHTT-....-HHHHHHHT-HHHHH CS
                   FumaraseC_C  20 eAlkegktlreavlelgl...lteeeldelldpekMt 53 
                                   +A  egktl+ +v+e+g+   + ++eld+l+dp + +
  gi|13541830|ref|NP_111518.1| 392 KARSEGKTLKHVVVEEGItnyIRRDELDRLMDPANFI 428
                                   7999***********998888************9976 PP

>> ASL_C2  Argininosuccinate lyase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   5.2e-05      0.16      10      68 ..     371     428 ..     367     429 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.2e-05
                                   HHHHCTS-HHHHHHHHHHHHHHHHHTT--GGG--HHHHHHH-TT--.GGGGGGSSHHHHT CS
                        ASL_C2  10 yLvrkGlpFReAHeivgravrlaeekgkeleeltleelkeisplle.edveeaLdpeasV 68 
                                   +L++ G+p  +AHe++ r+  +a+++gk+l+++ +ee     + +  +++ + +dp++++
  gi|13541830|ref|NP_111518.1| 371 ALTQAGMPRQDAHEFIRRCSMKARSEGKTLKHVVVEEGI--TNYIRrDELDRLMDPANFI 428
                                   69999****************************999977..6678878888888888876 PP

>> DUF2058  Uncharacterized protein conserved in bacteria (DUF2058)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   8.5e-05      0.25      92     153 ..       8      68 ..       4      80 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 8.5e-05
                       DUF2058  92 ynFtdgkkvkklyvdeklqkqLvkGrlaivrleeeyelvpaevaekiaerdeevvvllneke 153
                                   y++   +++k+++ de+    ++k + ai + e ey ++p e+ae i +  ++ +v l++ +
  gi|13541830|ref|NP_111518.1|   8 YRYGR-EQIKRIFDDENRLYYMLKVEAAISKAEAEYGIIPPEAAEDIGKVVADRIVQLQRVR 68 
                                   66654.569********99*************************************999833 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (448 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       557  (0.031067); 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:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 2981.79
//
Query:       gi|13541831|ref|NP_111519.1|  [L=196]
Description: hypothetical protein TVN1000 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       582  (0.0324614); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); 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: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1293.30
//
Query:       gi|13541832|ref|NP_111520.1|  [L=205]
Description: ATPase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      3e-37  128.2   0.1    3.4e-37  128.1   0.1    1.0  1  Diphthami_syn_2  Diphthamide synthase


Domain annotation for each model (and alignments):
>> Diphthami_syn_2  Diphthamide synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.1   0.1   1.9e-41   3.4e-37       7     217 ..       1     203 [.       1     205 [] 0.85

  Alignments for each domain:
  == domain 1  score: 128.1 bits;  conditional E-value: 1.9e-41
               Diphthami_syn_2   7 ysGGkDsilaLykalke.sevesLvsvisenkesymfhvvnvhlvellaesvGiplikletaGeeekevedLkgtlkkldv 86 
                                   +sGGkDs l+   a+++  e e    v +  + symfh +nv     +a  + ++      a   e ++ +L+g     + 
  gi|13541832|ref|NP_111520.1|   1 MSGGKDSFLSAVIAIEQgLELEKALIV-KPSEYSYMFHFPNVLYATETASLLDLEYEFVDEA-HFERKISELAG----EGL 75 
                                   59*******999999887999987755.556788*******987777776555443332222.45555666655....589 PP

               Diphthami_syn_2  87 eavviGaieseyqksriervCrelGlksvaPLWkkdpeelleeiveekfevivvavkaegldeslLGrridkklidelkkl 167
                                   +a+v+Gai+seyqk+rier+C    + s+ PLWk d e ++ ei++++ ++++v+v+aegl+e+ LG+ i+  ++d+lk+l
  gi|13541832|ref|NP_111520.1|  76 NAIVSGAIASEYQKTRIERLCTANKIVSFTPLWKIDQERIIREIINAGIRAMIVSVSAEGLGEQDLGKEINLPYLDHLKSL 156
                                   9******************************************************************************** PP

               Diphthami_syn_2 168 sekygidkagegGeaetlvlDaPlfkkrlevkelekkwderrgyldiera 217
                                    ++ygi+ +gegGe+e++v+    +  +++ ++ ++ w+++ gy+ i+r+
  gi|13541832|ref|NP_111520.1| 157 EKRYGINISGEGGEYESFVFG---YGSKVKRVQGHRVWSGSGGYFIIDRI 203
                                   *******************97...66666666777788888888888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.32s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 1266.53
//
Query:       gi|13541833|ref|NP_111521.1|  [L=267]
Description: thiamine monophosphate kinase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-08   35.3   0.1    3.9e-08   33.8   0.0    1.8  2  AIRS      AIR synthase related protein, N-terminal domain
      2e-07   31.3   0.0    2.9e-07   30.7   0.0    1.2  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 !   33.8   0.0   4.3e-12   3.9e-08      24      92 ..       2      76 ..       1      78 [. 0.91
   2 ?   -1.8   0.0      0.58   5.2e+03      55      67 ..     209     221 ..     149     240 .. 0.61

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 4.3e-12
                                  HHHHHHHHHHHHHHTTTEEEEEEEEEEEEC......HHHHHHHHHHHHHHHTT-EEEEEEEEEESSEEEEEEEEE CS
                          AIRS 24 iGakavavnlsDlaamGArPlalllslalp......wleevvrglaeaaeelgvplvgGdtsfsneptisvtavG 92
                                  iG+  +  nlsD+aam + P+ ++ +++++       le++ +g+ + ++ ++v+ +gGd++++ +++++  a+G
  gi|13541833|ref|NP_111521.1|  2 IGKFFASINLSDVAAMAGIPISFMTAYSISpeieisFLEDIESGIMKVLKMYDVDFIGGDLKEGMDLILTGIAIG 76
                                  57778889*************7787777777********************************988999999999 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.58
                                   HHHHHHHHHHHHH CS
                          AIRS  55 leevvrglaeaae 67 
                                    ee +r++a+a+e
  gi|13541833|ref|NP_111521.1| 209 PEENYRDFAQAME 221
                                   3444444444444 PP

>> AIRS_C  AIR synthase related protein, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.7   0.0   3.3e-11   2.9e-07      49     150 ..     128     238 ..      94     243 .. 0.77

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 3.3e-11
                                   HHHHHHHHH..HTTECEEEE--TTHHHHHHHHHHHTTTEEEEEECGTHHHHHHHHHHHHHHHC.........STTTEEEEE CS
                        AIRS_C  49 yvkralaal..kglvkaahDvTgGGLlgalaemapasgvgaeidldkvpifdelesplemlls.........ensGrllva 118
                                      +++a++  + ++k + D+++ GL ++l++m ++ gvg++i +d+v   d +++++e+  +              ll++
  gi|13541833|ref|NP_111521.1| 128 TPRLEEARIisEYGAKFMMDLSD-GLYSSLNQMKADYGVGFKIVEDEVVYDDSARKAAEISGAsvydiacgyGGDYELLFT 207
                                   4445555556669**********.8*********************99999999854554444555555556666667777 PP

                                   EEHGGHHHHHHHHHHTTCCCEEEEEEEEESSS CS
                        AIRS_C 119 vppeeadavlaileeeglpeaavIGevtakee 150
                                   vp+e+   + +++e+ ++ e+  IGe+ ++e+
  gi|13541833|ref|NP_111521.1| 208 VPEENYRDFAQAMESNNI-EVHFIGETWEGEN 238
                                   777777************.8******998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       576  (0.0321267); expected 358.6 (0.02)
Passed bias filter:                      524  (0.0292264); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 2069.11
//
Query:       gi|13541834|ref|NP_111522.1|  [L=493]
Description: single-stranded DNA-specific exonuclease [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-21   76.4   1.5    4.3e-21   75.8   0.3    1.9  2  DHHA1     DHHA1 domain
     0.0038   17.4   0.2     0.0084   16.3   0.2    1.6  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 ?   -1.8   0.1      0.43   3.9e+03      58      81 ..      17      41 ..       5      65 .. 0.54
   2 !   75.8   0.3   4.8e-25   4.3e-21      18     138 .]     354     478 ..     343     478 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.43
                                  HHHHHHHTHGBT.TCEEEEEEEECT CS
                         DHHA1 58 iaadklksklkk.pvivfvakeegd 81
                                  ++a   ++ l +   +v+v+ ++ d
  gi|13541834|ref|NP_111522.1| 17 EMAVAAREILRDqEKVVIVSHNDAD 41
                                  3333333333332555555555544 PP

  == domain 2  score: 75.8 bits;  conditional E-value: 4.8e-25
                                   HHHHHHHHHHHHHHHTCEEECTCEEEEEECHCCHHHHHHHHHHHHHHTHG...BTTCEEEEEEEECTEEEEEEEESSH... CS
                         DHHA1  18 lkealaklkaeellekaeevkgvkvlvaevgeewdagalgiaadklkskl...kkpvivfvakeegdkvkvsarskkd... 92 
                                   +++ l    ++ l + ++ +k+v +++a +  +++ +++gi+a++++ k    ++p ++++ ++ g ++k+s+r+ k+   
  gi|13541834|ref|NP_111522.1| 354 HRKNLVNGYNQILSKGLKSLKNVDYFYAGK--DINENIVGIIANMVLAKTgetMRPLVTMADSDPG-TIKISVRAGKSfls 431
                                   444444444444444444444666666655..9***************887768899999999999.*********99*** PP

                                   .SS-HHHHHHHHHHHTTCCEEEETCEEEEEEEHCHHHHHHHHHHHHH CS
                         DHHA1  93 .gvdagelakeaaaklgggGGGHdlAaGagipaekleealealeeai 138
                                    g+d+++l ++aa k gg GGGHdlAaGa+ipa+++ ++l++++e i
  gi|13541834|ref|NP_111522.1| 432 sGIDLADLFRRAAVKTGGVGGGHDLAAGANIPADRMGDFLKFIDEEI 478
                                   *******************************************9976 PP

>> DHH  DHH family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.2   9.4e-07    0.0084       2      68 ..      32     138 ..      31     172 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 9.4e-07
                                   EEEE-ECSSSHHHHHH.HHHHHHC.............................ECS--TCGGCGCCHHCCCSEEEEEEE-S CS
                                   xxxxxxxxxxxxxxxx.xxxxxxx.............................xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DHH   2 ilivghknpDtDsigS.aialanl.............................lvDhneksqavegeakeeaedviiiDHH 52 
                                   ++i  + + D+D++ S aia   l                              vD ++ s   +    +++ + +i+DHH
  gi|13541834|ref|NP_111522.1|  32 VVI--VSHNDADGLSSsAIAKVTLdragisnevifvknldrdvlkslpsgfkwFVDLGSGSMHMIR---DSGIECLITDHH 107
                                   667..7889999999966666663444444444445555555555555555559999998888876...************ PP

                                   ---S...............S---SS--EEEE CS
                                   xxxx...............xxxxxxxxxxxx RF
                           DHH  53 rlge...............efetlapilfln 68 
                                    + +               ef+++++i+ +n
  gi|13541834|ref|NP_111522.1| 108 VPDQfdvdedhkrdilsflEFSDFSKIYQVN 138
                                   *998888877777777777555555555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (493 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.63u 0.26s 00:00:00.89 Elapsed: 00:00:00.47
# Mc/sec: 3161.07
//
Query:       gi|13541835|ref|NP_111523.1|  [L=350]
Description: Fe-S oxidoreductase [Thermoplasma volcanium GSS1]
Scores for complete 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-09   36.5   0.0    1.4e-08   35.3   0.0    1.6  2  Radical_SAM      Radical SAM superfamily
  ------ inclusion threshold ------
      0.037   14.9   0.3       0.18   12.8   0.1    2.1  2  Ribosomal_L18_c  Ribosomal L18 C-terminal region


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.3   0.0   1.6e-12   1.4e-08       3     153 ..      49     201 ..      47     212 .. 0.78
   2 ?   -2.4   0.0      0.61   5.5e+03     127     148 ..     209     229 ..     201     237 .. 0.74

  Alignments for each domain:
  == domain 1  score: 35.3 bits;  conditional E-value: 1.6e-12
                                   EESEESS-....-TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHH.HHTTSEEEEEE.SSTGGGS...TTHHHHHHHHHHTC CS
                                   xxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx.xxxxxxx...xxxxxxxxxxxxxx RF
                   Radical_SAM   3 vtrgCnlr....CsfCarpetvrregrgrslsveeileevkelk.aekgvkevilg.ggeplly...pdfvellerlakla 74 
                                    trgC+      Cs C          + +++s e++ ++++ l+ + + ++++ ++ +g  l+    pd+v++++  +   
  gi|13541835|ref|NP_111523.1|  49 RTRGCSWYrfsaCSMCGYF------NDTADVSNENLFKQIDHLSsVLN-TEVLKVFtSGSFLDPievPDEVRAYFYDSIS- 121
                                   6899999889999999999......68999999999999999997655.5555444144344443446666666666665. PP

                                   CCTEEEEEEECSSCHGHHHHHHHHHTT.-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  75 vpgiritvetngtlpdeeklerllelg.vdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglp 153
                                   ++  ++ +e+    +++e le+++++g  +r+++gle+a+d  v + +n+g +f ++++a +++r++g++  ++ ++ +p
  gi|13541835|ref|NP_111523.1| 122 NKVEKLLIESRTEYIRDERLEEIKKYGfETRIAIGLESANDYIVENSINKGSSFTKYVDAAKRIRNNGLELRTYLLLKPP 201
                                   4666677777666667***************************************************9986666665555 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.61
                                   HHHHHHHHHHHHHTTSETEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM 127 feevlealeklreagikrvvdr 148
                                   +++vl+++++ +++  + v+++
  gi|13541835|ref|NP_111523.1| 209 IKDVLDSIRAVKDLTND-VSIN 229
                                   67899999999998544.6655 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 ?   -1.8   0.0       0.7   6.2e+03      38      59 ..     167     188 ..     159     193 .. 0.66
   2 ?   12.8   0.1     2e-05      0.18       4      41 ..     308     345 ..     306     348 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.7
               Ribosomal_L18_c  38 kgieaddleelykkahaaIred 59 
                                   ++i+  +    y +a + Ir++
  gi|13541835|ref|NP_111523.1| 167 NSINKGSSFTKYVDAAKRIRNN 188
                                   5555555556677777888777 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 2e-05
               Ribosomal_L18_c   4 lrkrIfgkhvaeYmeeLkeedeekykkqFskyikkgie 41 
                                   l++++  ++ ++YmeeL+ ed   ++  F k i+++++
  gi|13541835|ref|NP_111523.1| 308 LERYMKSQDLSKYMEELEIEDRSLFQCDFGKLIDQSLN 345
                                   67889999***********************9998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (350 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       532  (0.0296726); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); 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 0.28s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 2253.53
//
Query:       gi|13541836|ref|NP_111524.1|  [L=381]
Description: aspartate aminotransferase [Thermoplasma volcanium GSS1]
Scores for complete 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-68  231.1   0.0    2.5e-68  230.9   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
    2.5e-08   33.6   0.0    5.3e-08   32.6   0.0    1.4  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
    7.5e-06   25.1   0.0    5.3e-05   22.3   0.0    1.9  2  Aminotran_5      Aminotransferase class-V
    4.2e-05   22.2   0.0    6.5e-05   21.6   0.0    1.2  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
     0.0022   17.3   0.0     0.0034   16.7   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 !  230.9   0.0   6.9e-72   2.5e-68       2     363 .]      30     374 ..      29     374 .. 0.94

  Alignments for each domain:
  == domain 1  score: 230.9 bits;  conditional E-value: 6.9e-72
                                   EEEESSSSSTTSTTSSHHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHH CS
                 Aminotran_1_2   2 dvinLgsneylgdsgkptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGagalie 82 
                                   +v n+g++e+++     t++++++ + e   a+++ + y+p+ g +el+e++ + l+++++++  ++ +v+ ++ ++ +i+
  gi|13541836|ref|NP_111524.1|  30 KVYNFGIGEPDFT----TPQHIIEYAFE--MAKEGKTHYTPSNGIHELREKVSEKLKNRNNINASPD-EVLITP-TKFGIN 102
                                   688**********....*********99..88888899*****************************.877766.777899 PP

                                   HHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT-- CS
                 Aminotran_1_2  83 alifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilvesphNPtGt 163
                                   ++++++ lnpgde+l+p+p+y sy +i+rl+gg+ v++++   ed++ld++ + + ++       ktk i++++p NPtG+
  gi|13541836|ref|NP_111524.1| 103 LAMMVI-LNPGDEVLIPEPYYVSYPDIVRLAGGKPVTVSTL--EDYSLDFDLMRKYVTP------KTKAIIFNNPTNPTGK 174
                                   999999.9*******************************77..************9999......**************** PP

                                   B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEEEEEEHHHHHHHH CS
                 Aminotran_1_2 164 vatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKafGlaGeRvGyilgnaavvsqlr 244
                                   v++++e++ l+d+a +y+l++++De+Y+++ ++ +   ++    + +   ++++++sK ++++G+R+Gy ++  ++v++++
  gi|13541836|ref|NP_111524.1| 175 VYDEKEIKSLVDFALEYGLYIVSDEIYEDLIYNGKLISPASYSEMWGKS-ITLNGFSKGYAMTGWRIGYMAAPREIVEAAN 254
                                   *********************************8844444455555555.******************************* PP

                                   HHHHHHTS..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS.TEEEECCSCSSEEEEEETHH.CHHHHH CS
                 Aminotran_1_2 245 klsrpfls..ssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLael.glkvlasqsgmflltdlsae.takels 321
                                    ++++ +   ss+ q+a++ al+d++    + ++m++++++rr+ + + L++   l+v++++++++++ +++   + +++s
  gi|13541836|ref|NP_111524.1| 255 VIQQQTITcvSSISQYAALRALDDTE----SPKKMKDEFKRRRDLILSILDSSdKLNVTEPDGAFYVFPEYNSDiSSNKVS 331
                                   **99999889****************....89******************9999********************999**** PP

                                   HHHHHTCTEEEEEGGGGTS..TTEEEEECTTS-HHHHHHHHHHH CS
                 Aminotran_1_2 322 kkLleevgvyvtpgtsftv..pgrlRitvAglteeeleelveal 363
                                   + Lle++ v+vtpg+ f+   + ++Ri++ +++e+ ++e +e++
  gi|13541836|ref|NP_111524.1| 332 EDLLEKYQVVVTPGSAFGRqgEHHFRISF-ATSEDIIKEGAERI 374
                                   *******************9999******.99999999999997 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 !   32.6   0.0   1.5e-11   5.3e-08      52     144 ..     102     198 ..      91     199 .. 0.87

  Alignments for each domain:
  == domain 1  score: 32.6 bits;  conditional E-value: 1.5e-11
                                   HHHHHHTTTTTT-EEEEESSS-THHHHHHHHTT-EEEEE-B-TTTSSB-GGGCGGG--TTEEEEE...EB-GGGB--...- CS
               DegT_DnrJ_EryC1  52 hlaLralgvgpgdeVIvpsltFvatanavlelgakpvfvDvdpdtynidpaaieaaitertkaIl...pVhlyGqva...d 126
                                    la++++ ++pgdeV++p   +v+    v+ +g kpv v    ++y +d + +++ +t++tkaI+   p +  G+v    +
  gi|13541836|ref|NP_111524.1| 102 NLAMMVI-LNPGDEVLIPEPYYVSYPDIVRLAGGKPVTVSTL-EDYSLDFDLMRKYVTPKTKAIIfnnPTNPTGKVYdekE 180
                                   4555543.689****************************987.99*******************966678999**994445 PP

                                   HHHHHHHHHHCT-EEEEE CS
               DegT_DnrJ_EryC1 127 mdalkaiaakhglkvieD 144
                                   +++l + a ++gl++++D
  gi|13541836|ref|NP_111524.1| 181 IKSLVDFALEYGLYIVSD 198
                                   788888999*******99 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   1.5e-08   5.3e-05      35     165 ..      62     185 ..      43     199 .. 0.77
   2 ?    0.4   0.0     0.071   2.5e+02     252     361 ..     260     362 ..     248     367 .. 0.70

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 1.5e-08
                                   SHHHHHHHHHHHHHHHHHHH..HHT-STGGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHT CS
                   Aminotran_5  35 hhlgkeatkaveearekvae..linaeseeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtg 113
                                   ++ ++ +++  e++ ek+++   ina+  +e++ t  t  +inl+++ +   l+pgde+++ e  + +    +++la   g
  gi|13541836|ref|NP_111524.1|  62 YTPSNGIHELREKVSEKLKNrnNINASP-DEVLIT-PTKFGINLAMMVI---LNPGDEVLIPEPYYVSYP-DIVRLA--GG 134
                                   5555666666677777776511466664.677666.4566*********...**************9999.667776..67 PP

                                   EEEEEEEBETTSCBEGGGHHHH--TTEEEEEEESBETTTTEB--HHHHHHHH CS
                   Aminotran_5 114 akvkvipldeegeldldelekllnektklvaithvsnvtGtiqpveeigkla 165
                                     v+v +l e+ +ld d ++k++++ktk+++++   n tG + + +ei++l+
  gi|13541836|ref|NP_111524.1| 135 KPVTVSTL-EDYSLDFDLMRKYVTPKTKAIIFNNPTNPTGKVYDEKEIKSLV 185
                                   77777776.889******************************9999998765 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.071
                                   S--HHHHHHHHHHHHHH.HCHHHHHHHHHHHHHHHHHHHHHCTSTTEEEES.-B-CTCBSEEEEEETTCSHHHH.HHHHHH CS
                   Aminotran_5 252 Tpnvagiiglgaaleyl.eeigleaiekhekelaeyllerlkslpgvrlygpdkaerrasivsfnfkgvhaedv.atlLde 330
                                   T  +++ i+  aal+ l +    ++++ + k+ ++ +l+ l+s++++++ +p  + +       n  ++++++v + lL++
  gi|13541836|ref|NP_111524.1| 260 TITCVSSISQYAALRALdDTESPKKMKDEFKRRRDLILSILDSSDKLNVTEP--DGAFYVFPEYN-SDISSNKVsEDLLEK 337
                                   6667777888888888866666678888889999999999999999998443..23333333333.444444441567777 PP

                                   TTEEEEEE-TTTHHHHHHTT.S-EEEEE--T CS
                   Aminotran_5 331 egIavrsGhhcaqplmkrlalegtvRaSlyi 361
                                   +++ v+ G++        ++ e+ +R+S++ 
  gi|13541836|ref|NP_111524.1| 338 YQVVVTPGSAFG------RQGEHHFRISFAT 362
                                   799999999888......7777888888875 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 !   21.6   0.0   1.8e-08   6.5e-05      80     173 ..     101     198 ..      83     205 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 1.8e-08
                                   HHHHHHTTS-TTEEEEEESTSSHHHHHHHHHTHHHTTCEEEEEST.TSHHHHHHHCCTTEEEEEEESS-TTTT----...H CS
               Cys_Met_Meta_PP  80 iaaailallkaGdeivvsddlYggtqrllkkvlkklgievkfvdt.sdleelekaikentklvylEtptnpllkvvD...i 156
                                   i++a++ +l+ Gde+++ +  Y +  ++++    k    ++  d   d++ ++k ++++tk++ +  ptnp+ kv D   i
  gi|13541836|ref|NP_111524.1| 101 INLAMMVILNPGDEVLIPEPYYVSYPDIVRLAGGKPVTVSTLEDYsLDFDLMRKYVTPKTKAIIFNNPTNPTGKVYDekeI 181
                                   5678999***************99999999888875444444454269999*************************95555 PP

                                   HHHHHHHHHTT-EEEEE CS
               Cys_Met_Meta_PP 157 ekiaklakkagvlvvvD 173
                                   ++++++a + g+ +v D
  gi|13541836|ref|NP_111524.1| 182 KSLVDFALEYGLYIVSD 198
                                   56666777777777766 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   9.5e-07    0.0034      56     167 ..      97     198 ..      40     199 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 9.5e-07
                                   HHHHHHHHHHHH--TTEEEEEETT-HHHHSSTTHHHHCC--EEEEE-EBTTTBE-HHHHHHHS--S-TTS-EEEEEEEESS CS
               Beta_elim_lyase  56 GtaAnsillkillqrgeevivtepahihfdetgaiaelagvklrdlknkeaGkmdlekleaaikevgaheekiklisltvT 136
                                      + +++++++l++g+ev++ ep  +       i+ lag k++++ + e+  +d++ +++ +++      k+k+i+  + 
  gi|13541836|ref|NP_111524.1|  97 TKFGINLAMMVILNPGDEVLIPEPYYV---SYPDIVRLAGGKPVTVSTLEDYSLDFDLMRKYVTP------KTKAIIFNNP 168
                                   456667888999999999998888444...445688999************************99......5788888887 PP

                                   BTTTTTB---HHHHHHHHHHHHHCT-EEEEE CS
               Beta_elim_lyase 137 nntagGqvvsleelrevaaiakkygiplhlD 167
                                   +n   G+v+  +e++ + ++a +yg+ ++ D
  gi|13541836|ref|NP_111524.1| 169 TNP-TGKVYDEKEIKSLVDFALEYGLYIVSD 198
                                   774.7*********************99988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (381 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       607  (0.0338558); 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:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.44
# Mc/sec: 2613.65
//
Query:       gi|13541837|ref|NP_111525.1|  [L=306]
Description: homoserine kinase [Thermoplasma volcanium GSS1]
Scores for complete 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   52.0   2.6    1.4e-13   50.8   2.6    1.6  1  GHMP_kinases_N  GHMP kinases N terminal domain
    2.4e-09   37.4   0.1    7.5e-09   35.8   0.0    1.8  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 !   50.8   2.6   1.6e-17   1.4e-13       1      66 []      74     141 ..      74     141 .. 0.91

  Alignments for each domain:
  == domain 1  score: 50.8 bits;  conditional E-value: 1.6e-17
                                   EEEEEESSHTTSSSCHHHHHHHHHHHHHHHHTTEHH..HH.HHHHHHHHHHHHHHHHHSHHHHHHHHSS CS
                GHMP_kinases_N   1 divikseiPvgaGLGSSAAlavalvaAllallglsl..ee.aklaleaerlaqggngsggDvaasvyGg 66 
                                   +i+ik+ iP g GLGSS++ a+a+++A+++l+ l l  ++  k a+++e +   g++++++v+as++Gg
  gi|13541837|ref|NP_111525.1|  74 KISIKKGIPYGLGLGSSGSSAAAAAYAINNLFALGLerKDlIKYAAVGELASS-GSPHPDNVSASILGG 141
                                   599*****************************888854338********6665.**************8 PP

>> GHMP_kinases_C  GHMP kinases C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1       0.5   4.5e+03      49      71 ..      85      93 ..      60     106 .. 0.59
   2 !   35.8   0.0   8.4e-13   7.5e-09       3      83 ..     204     279 ..     202     281 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.5
                GHMP_kinases_C 49 lgaklsGaGgGptvfalfkdkde 71
                                  lg + sG+               
  gi|13541837|ref|NP_111525.1| 85 LGLGSSGS--------------S 93
                                  44444444..............3 PP

  == domain 2  score: 35.8 bits;  conditional E-value: 8.4e-13
                GHMP_kinases_C   3 ealergdlellgellnlsqrselkavvgilppeleellealselGalgaklsGaGgGptvfalfkdkdeaeqvaralreef 83 
                                   + l  gd el+  ++n+      +a +++++p  +++++ + e Ga ga++sGa  Gp++ +++++k e +q++r++++ +
  gi|13541837|ref|NP_111525.1| 204 AGLMSGDRELVSTGMNDDIV---EAAREPIFPYYRRVKDTAIESGAVGAVVSGA--GPSILVVYDNKTETKQMIRKISRIY 279
                                   56677899999999997777...77*****************************..********************98766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       401  (0.022366); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); 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: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 2004.68
//
Query:       gi|13541838|ref|NP_111526.1|  [L=372]
Description: cystathionine beta-lyase or cystathionine gamma-synthase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     3e-101  338.7   0.0   3.6e-101  338.5   0.0    1.0  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
    0.00042   19.6   0.0    0.00073   18.8   0.0    1.5  1  Aminotran_1_2    Aminotransferase class I and II
  ------ inclusion threshold ------
      0.011   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):
>> 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 !  338.5   0.0    6e-105  3.6e-101      12     382 .]      12     369 ..       5     369 .. 0.96

  Alignments for each domain:
  == domain 1  score: 338.5 bits;  conditional E-value: 6e-105
                                   HTTTTBSS--B---SBBBESSHHHHCTTCSSS-SBTTT--HHHHHHHHHHHHHHT-SEEEEESSHHHHHHHHHHTTS-TTE CS
               Cys_Met_Meta_PP  12 deqtgavavpiyltstykfkdvdeafageekgyeYsRsgnptrsvleeriaaLeggeaalavssGmaAiaaailallkaGd 92 
                                   d++ ++ + p++ ts+y  +        ++++y YsR  npt++ l ++++ Le++e+++++ssGm+Ai+ +ilal+k Gd
  gi|13541838|ref|NP_111526.1|  12 DDHAHSLSFPVFFTSSYDSR--------KDRKYRYSRELNPTVEELSRQLSLLENTERSICFSSGMGAITGTILALAKPGD 84 
                                   55778889999999999988........8999************************************************* PP

                                   EEEEESTSSHHHHHHHHHTHHHTTCEEEEESTTSHHHHHHHCCTTEEEEEEESS-TTTT----HHHHHHHHHHTT-EEEEE CS
               Cys_Met_Meta_PP  93 eivvsddlYggtqrllkkvlkklgievkfvdtsdleelekaikentklvylEtptnpllkvvDiekiaklakkagvlvvvD 173
                                   ++v+ +d++g t+ + k++l+k+gi+vkfv++  +++l  a++e+ ++v++E+++npll++ D+ +i++ a + g++++vD
  gi|13541838|ref|NP_111526.1|  85 KLVMPTDVFGRTYLFAKNFLTKFGINVKFVEP-GTDSLLGAVEEHADIVFFESLSNPLLRLYDVDRICRKASDIGAITIVD 164
                                   *******************************9.567888999*************************************** PP

                                   GTTTHTTTS-GGGGT-SEEEEETTTTTTCSSS--EEEEEESSCHHHHHHHHHHHHHHT-B--HHHHHHHHHHHTTHHHHHH CS
               Cys_Met_Meta_PP 174 ntfaspllqrplklgaDivvhSaTKylgGhsdvvaGvivvkgkeelkkelkflqnalGavlspfdawlllrGlkTLslRle 254
                                   nt+a+p+l +p  +g+Di+++S +K++gGh+++++G +  +    +++++    ++lG+ ++p++a+l++ GlkT++lR++
  gi|13541838|ref|NP_111526.1| 165 NTLATPILLKPSLYGCDIIIESLSKFIGGHNNAIGGSASGSL---MMDTIDENRRSLGSSMDPMSAYLFILGLKTIDLRIK 242
                                   ************************************999555...677778889*************************** PP

                                   HHHHHHHHHHHHHHTSTTEEEEE-TTSTTSTTHHHHHHHSSSG-SEEEEEESSHHHHHHHHHHC-SSSEECSS-SSSS-EE CS
               Cys_Met_Meta_PP 255 rhqenAlkvAefLekhpkvekvyYpglpshpqhelakkqlkgaggvlsFelkseeekakkfvdnlklfslaeslGgvesli 335
                                   r++e+A ++A+fL++++ v+kvyYpgl+++++   ak  l+g+  ++sF l+++ + ++kf+++l++++ a+ +Gg +s i
  gi|13541838|ref|NP_111526.1| 243 RSSETAKAIARFLNENNFVSKVYYPGLSDNSDNISAKTLLNGSPPIVSFLLDEG-KDVQKFMESLRIITPANTMGGSNSTI 322
                                   *******************************************99********9.78************************ PP

                                   EETTTTTTTTSCHHHHHHTTS-TTEEEEE--SS-HHHHHHHHHHHHH CS
               Cys_Met_Meta_PP 336 elpasmthasipkeereaagvtddliRlsvGiEdvdDliaDlkqale 382
                                   + p++m+h++++++e+ + g+t++l+RlsvG+Ed+d +i+Dl+qa++
  gi|13541838|ref|NP_111526.1| 323 SNPYTMSHRNLSEDEKLRLGITKNLMRLSVGLEDLDQIIQDLEQAIK 369
                                   *********************************************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 !   18.8   0.0   1.2e-07   0.00073      62     187 ..      54     164 ..      28     228 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.2e-07
                                   TCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEEEESS-T....HHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHH CS
                 Aminotran_1_2  62 klklkreaavvvgsGagaliealifllklnpgdeilvpdptya....syknilrlsggevvryplyseedfhldlealeea 138
                                    l +++e++++++sG ga+  ++ +l+k  pgd+ ++p+ +++      kn l   g+ v  ++           ++l+ a
  gi|13541838|ref|NP_111526.1|  54 SLLENTERSICFSSGMGAITGTILALAK--PGDKLVMPTDVFGrtylFAKNFLTKFGINVKFVE--------PGTDSLLGA 124
                                   35678999*******************9..********97665000055566666666666666........778999999 PP

                                   HTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEE CS
                 Aminotran_1_2 139 lkeapegnkktkvilvesphNPtGtvatleeleklldlakkynlllfvD 187
                                   ++e         ++++es +NP   +++ + ++     a   +++++vD
  gi|13541838|ref|NP_111526.1| 125 VEE------HADIVFFESLSNPLLRLYDVDRICRK---ASDIGAITIVD 164
                                   998......6679*********8777777776665...66667777777 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   2.6e-06     0.016      33     204 ..      34     192 ..      21     194 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.6e-06
                                   SSSHHHHHHHHHHHHHHHHHHHHHT-STGGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHT CS
                   Aminotran_5  33 svhhlgkeatkaveearekvaelinaeseeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtg 113
                                     ++++ e++  vee   ++  l n+e    i f sG + ai+  +l+l    kpgd+ v+ +     + + +++   + g
  gi|13541838|ref|NP_111526.1|  34 RKYRYSRELNPTVEELSRQLSLLENTER--SICFSSGMG-AITGTILAL---AKPGDKLVMPTDVFGRTYLFAKNFLTKFG 108
                                   5667788888889999999999999985..999999999.999999999...89****9987766666777899999999* PP

                                   EEEEEEEBETTSCBEGGGHHHH--TTEEEEEEESBETTTTEB--HHHHHHHHHHTT-EEEEE-TTTTTTS---HHHHTESE CS
                   Aminotran_5 114 akvkvipldeegeldldelekllnektklvaithvsnvtGtiqpveeigklakkkgalvlvDaaqavghipidvkklgvDf 194
                                   ++vk+++        +d l  +++e +++v++   sn +  + +v++i++ a + ga+++vD + a + i ++ + +g+D+
  gi|13541838|ref|NP_111526.1| 109 INVKFVEP------GTDSLLGAVEEHADIVFFESLSNPLLRLYDVDRICRKASDIGAITIVDNTLATP-ILLKPSLYGCDI 182
                                   ****9998......5677888999**************************************987766.6789999***** PP

                                   EEEETTTTTS CS
                   Aminotran_5 195 lafsghKllg 204
                                   +  s  K++g
  gi|13541838|ref|NP_111526.1| 183 IIESLSKFIG 192
                                   *999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (372 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       481  (0.026828); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 2479.03
//
Query:       gi|13541839|ref|NP_111527.1|  [L=131]
Description: hypothetical protein TVN1008 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.9e-16   58.7   0.0    7.3e-16   57.8   0.0    1.5  1  DUF302        Domain of unknown function DUF302
  ------ inclusion threshold ------
       0.16   11.9   0.1       0.27   11.2   0.1    1.4  1  HCBP_related  Haemolysin-type calcium binding protein related


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 !   57.8   0.0   8.1e-20   7.3e-16       1      60 [.      40      99 ..      40     101 .. 0.98

  Alignments for each domain:
  == domain 1  score: 57.8 bits;  conditional E-value: 8.1e-20
                                  EEHHHHHHCTT-S--S-EEEEEEE-HHHHHHHHCC-GGGGGG-SEEEEEEEETTEEEEEE CS
                        DUF302  1 iDvqatlkkklgedlrpykilgaCnPklatealqadpeiglllPcrvvVyekdgkttvsy 60
                                  iDv++ lk+ l +d++py+il +C+P +a+e+l+ +++ gl+lPc++v+  +++k+t+s+
  gi|13541839|ref|NP_111527.1| 40 IDVAQILKNALKKDVDPYYILNVCKPSAADEILSVSRDYGLFLPCKIVLKGEGDKVTISM 99
                                  8*********************************************************98 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 ?   11.2   0.1   3.1e-05      0.27       4      21 ..      86     103 ..      85     116 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3.1e-05
                  HCBP_related   4 lsikgtgDsitiknwfss 21 
                                   +++kg gD++ti+ ++ s
  gi|13541839|ref|NP_111527.1|  86 IVLKGEGDKVTISMQYVS 103
                                   899**********99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       797  (0.0444531); expected 358.6 (0.02)
Passed bias filter:                      565  (0.0315132); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 901.49
//
Query:       gi|13541840|ref|NP_111528.1|  [L=382]
Description: translation-associated GTPase [Thermoplasma volcanium GSS1]
Scores for complete 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   81.3   0.0    1.5e-22   79.8   0.0    1.8  2  MMR_HSR1       50S ribosome-binding GTPase
    2.9e-14   53.6   0.0      5e-14   52.8   0.0    1.4  1  MMR_HSR1_C     GTPase of unknown function C-terminal
    1.5e-11   44.2   0.0    2.7e-11   43.3   0.0    1.4  1  TGS            TGS domain
    1.2e-07   31.3   0.0    1.4e-06   27.9   0.0    2.2  2  FeoB_N         Ferrous iron transport protein B
    2.2e-05   24.5   0.2      0.079   13.2   0.0    2.6  2  YchF-GTPase_C  Protein of unknown function (DUF933)
     0.0022   18.1   0.0       0.65   10.0   0.0    3.2  3  Dynamin_N      Dynamin family
     0.0048   16.9   0.0      0.011   15.7   0.0    1.6  1  MMR_HSR1_Xtn   C-terminal region of MMR_HSR1 domain
  ------ inclusion threshold ------
        0.1   11.9   0.0       0.18   11.1   0.0    1.4  1  AIG1           AIG1 family
       0.11   12.1   0.0         20    4.7   0.0    3.0  3  Ras            Ras family
       0.13   12.4   0.0       0.28   11.3   0.0    1.5  1  Phage_CI_repr  Bacteriophage CI repressor helix-turn-helix do
       0.15   12.2   0.0        1.5    9.0   0.0    2.4  3  Roc            Ras of Complex, Roc, domain of DAPkinase


Domain annotation for each model (and alignments):
>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.8   0.0   9.3e-26   1.5e-22       1     103 [.       4     131 ..       4     147 .. 0.79
   2 ?   -3.7   0.0       7.4   1.2e+04      52      60 ..     284     292 ..     271     313 .. 0.64

  Alignments for each domain:
  == domain 1  score: 79.8 bits;  conditional E-value: 9.3e-26
                                   EEEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEE.........ETTEE..................EEEEECG CS
                      MMR_HSR1   1 evaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvk.........lkgke..................ielvDtp 54 
                                   +++++G pNvGKSt+++a t+++a+++++p+tT+++n g            +   +                  ++++D+p
  gi|13541840|ref|NP_111528.1|   4 RIGLIGEPNVGKSTFFSAATENEAEINNFPFTTIKPNLGMTYfvvkcpeveI---SgkcnpregycengnrhipVQIIDVP 81 
                                   699************************************8665544444331...0333444455555555555******* PP

                                   GCSSHHHHHHHHHHHHHHHHC.TSEEEEEEETTTTCSHHHHHHHHHHHHH CS
                      MMR_HSR1  55 Gliegaseekglgkaflalee.adlillvvdaseeklkpldeeleellee 103
                                   Gliegase+kg+g++fl++++ +d ill++das ++++ +++++e +++e
  gi|13541840|ref|NP_111528.1|  82 GLIEGASEGKGMGNEFLDNIRdVDSILLLFDASAGDIATVRKSIEMVKSE 131
                                   ******************98889********9977788887777777544 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 7.4
                                   ECGGCSSHH CS
                      MMR_HSR1  52 DtpGliega 60 
                                    tpG+i  +
  gi|13541840|ref|NP_111528.1| 284 NTPGIIRIH 292
                                   588876522 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 !   52.8   0.0   3.1e-17     5e-14       1     112 []     214     313 ..     214     313 .. 0.92

  Alignments for each domain:
  == domain 1  score: 52.8 bits;  conditional E-value: 3.1e-17
                    MMR_HSR1_C   1 alNKaDlpaadenieklkekypkdkkvvpvsAaaElaLrkaakqglikYepgdedfeikedklkeldekqkkaLekirdlv 81 
                                   + NK Dl  + ++++++k++     + + vsA++ElaL++a+k+gl++ +   +df i +      +ekqk+ L kird++
  gi|13541840|ref|NP_111528.1| 214 VGNKSDL-VSPNTLSEMKNALG---DSYFVSAEYELALKRARKSGLVSTTL--NDFAILGG-----NEKQKEVLAKIRDWF 283
                                   57*****.99**********99...468*******************9875..5999*998.....89***********55 PP

                    MMR_HSR1_C  82 lkrygsTGVqealnaavfelldlivVYPVed 112
                                    ++ g   ++++l+++v ++l++i+VYPV+d
  gi|13541840|ref|NP_111528.1| 284 -NTPGIIRIHDLLQKVVRDYLHYIIVYPVYD 313
                                   .777*************************87 PP

>> TGS  TGS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.3   0.0   1.7e-14   2.7e-11       4      59 ..     324     379 ..     321     380 .. 0.94

  Alignments for each domain:
  == domain 1  score: 43.3 bits;  conditional E-value: 1.7e-14
                                   EETTSSEEEEETTB-HHHHHHHHSTTHHHHEEEEEECS..EEEETTSBB-SSEEEEEE CS
                           TGS   4 ytPdGkvpdlprgatveDfAykIhrslakkfiyAlVnG..qrvgldhvLedgdvveIv 59 
                                   ++Pd+ v  +p g+t  D+AykIh+++++ fi A      +  g d+ L+dgdv++I+
  gi|13541840|ref|NP_111528.1| 324 VLPDAFV--MPYGSTSLDLAYKIHTDIGEGFIRAVNARtrMVLGKDYILKDGDVIKII 379
                                   6788888..***************************99999****************8 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.0   8.8e-10   1.4e-06       2      41 ..       4      43 ..       3      55 .. 0.89
   2 ?    0.7   0.0      0.21   3.4e+02      47      88 ..      73     113 ..      59     119 .. 0.70

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 8.8e-10
                                  EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEE CS
                        FeoB_N  2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegk 41
                                  ++ l+G+pnvGk+t+f a t+ + ++ N+p +t++ + g 
  gi|13541840|ref|NP_111528.1|  4 RIGLIGEPNVGKSTFFSAATENEAEINNFPFTTIKPNLGM 43
                                  789******************************9877665 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.21
                                   EEEEEEE----SSSSSSSHHHHHHHHHHHC.TSSSEEEEEEEG CS
                        FeoB_N  47 keveivDlPGiYslsayseeekvardflle.eepdvvvnvvda 88 
                                     v+i+D+PG   ++  se + + ++fl + +++d ++ + da
  gi|13541840|ref|NP_111528.1|  73 IPVQIIDVPGL--IEGASEGKGMGNEFLDNiRDVDSILLLFDA 113
                                   4579******7..567777777777777652456777777776 PP

>> YchF-GTPase_C  Protein of unknown function (DUF933)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.0   4.9e-05     0.079      16      42 ..     330     356 ..     322     363 .. 0.87
   2 !    8.8   0.2    0.0011       1.8      66      81 ..     363     378 ..     357     380 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.9e-05
                 YchF-GTPase_C  16 tikkgttapqaAgviHsDfekgFirae 42 
                                    +  g+t  + A +iH+D+ +gFira 
  gi|13541840|ref|NP_111528.1| 330 VMPYGSTSLDLAYKIHTDIGEGFIRAV 356
                                   6677999999***************95 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0011
                 YchF-GTPase_C  66 legkdyvvqdgDiilf 81 
                                   + gkdy+++dgD+i +
  gi|13541840|ref|NP_111528.1| 363 VLGKDYILKDGDVIKI 378
                                   569**********975 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.17   2.8e+02       1      17 [.       5      21 ..       5      40 .. 0.80
   2 !   10.0   0.0    0.0004      0.65     102     145 ..      74     121 ..      60     135 .. 0.82
   3 ?    2.3   0.0     0.095   1.5e+02     108     142 ..     285     317 ..     278     327 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.17
                                  EEEEEBTTTTHHHHHHH CS
                     Dynamin_N  1 iavvGsqSsGKSSvlna 17
                                  i ++G+ + GKS++  a
  gi|13541840|ref|NP_111528.1|  5 IGLIGEPNVGKSTFFSA 21
                                  7899*********9766 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0004
                                   SEEEEE---B-SSSGTTS...HHHHHHHSTTEEEEEEEETTS.-CCC- CS
                     Dynamin_N 102 gltlvDlPGldsvnkrdq...elvkeyikkadiilavtsanh.dlsns 145
                                    + ++D+PGl++ + + +   +     i++ d il++ +a+  d++++
  gi|13541840|ref|NP_111528.1|  74 PVQIIDVPGLIEGASEGKgmgNEFLDNIRDVDSILLLFDASAgDIATV 121
                                   589***********9999777777777889999****99997566654 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.095
                                   ---B-SSSGTTSHHHHHHHSTTEEEEEEEETTS-C CS
                     Dynamin_N 108 lPGldsvnkrdqelvkeyikkadiilavtsanhdl 142
                                   +PG++++++  q++v+ y++   ii++ ++ ++++
  gi|13541840|ref|NP_111528.1| 285 TPGIIRIHDLLQKVVRDYLH--YIIVYPVYDESKW 317
                                   9*****************96..3566655555555 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 !   15.7   0.0   7.1e-06     0.011       9      94 ..     165     248 ..     158     253 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 7.1e-06
                  MMR_HSR1_Xtn   9 tvkltkldeetvkkilkeykihnaevliredvtvDdlidviegnrvYipclyvlNKiDlisleeldelare.pnsvviSae 88 
                                   +++l  ++e+++++++ e  ++ a++ i  + ++D+l   i +    +p l+v NK Dl+s ++l+e+++   +s ++Sae
  gi|13541840|ref|NP_111528.1| 165 KLSLFGISEHQISEMM-EKDFFPAKLSIWTREDADKLALSIIKYA--KPLLLVGNKSDLVSPNTLSEMKNAlGDSYFVSAE 242
                                   5555566777777766.4567778888888888888877776543..5889999****************746******** PP

                  MMR_HSR1_Xtn  89 kelnld 94 
                                    el l+
  gi|13541840|ref|NP_111528.1| 243 YELALK 248
                                   999886 PP

>> AIG1  AIG1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00011      0.18       5      75 ..       7      99 ..       3     128 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00011
                                  EESSTTSSHH.....HHHHHH.............HTS--SS--TTTS---SS-EEEEE.EETT...EEEEEEE--SCCCTTCC CS
                          AIG1  5 lvGktgnGkS.....aTgNsi.............lgkkaFesklsaqsvtkkcqkksr.twdg...kkinViDTPglfdlsvs 65
                                  l+G   +GkS     aT N               lg ++F  k+ + ++  kc+ +++  ++g     +++iD Pgl++  ++
  gi|13541840|ref|NP_111528.1|  7 LIGEPNVGKStffsaATENEAeinnfpfttikpnLGMTYFVVKCPEVEISGKCNPREGyCENGnrhIPVQIIDVPGLIEGASE 89
                                  56666666653433355555455666777777779999****************9999766664445699**********999 PP

                                  HHCHHHHHHH CS
                          AIG1 66 adkiskeivr 75
                                   + + +e  +
  gi|13541840|ref|NP_111528.1| 90 GKGMGNEFLD 99
                                  9988888765 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0     0.038        62       4      23 ..       7      26 ..       4      49 .. 0.84
   2 ?    4.7   0.0     0.012        20     105     124 ..     209     228 ..     188     249 .. 0.76
   3 ?   -0.6   0.0      0.53   8.6e+02      34      86 ..     261     316 ..     249     327 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.038
                                  EEESTTSSHHHHHHHHHHSS CS
                           Ras  4 lvGdsavGKtslllrfvkdk 23
                                  l+G+ +vGK+++    ++++
  gi|13541840|ref|NP_111528.1|  7 LIGEPNVGKSTFFSAATENE 26
                                  8**********998887775 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.012
                                   SEEEEEEETTTGGGG-SS-H CS
                           Ras 105 vpivLvGnKvDleekravst 124
                                    p++LvGnK+Dl + +++s+
  gi|13541840|ref|NP_111528.1| 209 KPLLLVGNKSDLVSPNTLSE 228
                                   4899********88665554 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.53
                                   EEEEEEEEEETTEEEEEEEEE...ETTSGGGHHHHHHHHTTESEEEEEEETTBHHH CS
                           Ras  34 vdfytkeievdgkevkleiwD...TAGqeefkslrelyyrdaegillvyditsres 86 
                                    df +   + ++kev  +i D   T G  + + l ++++rd    ++vy + +++ 
  gi|13541840|ref|NP_111528.1| 261 NDFAILGGNEKQKEVLAKIRDwfnTPGIIRIHDLLQKVVRDYLHYIIVYPVYDESK 316
                                   5555666666677777777555558999999999999999999999**99988875 PP

>> Phage_CI_repr  Bacteriophage CI repressor helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00017      0.28      21      44 ..     168     191 ..     157     199 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00017
                                   CTT--HHHHHHHHHSSS--HHHHH CS
                 Phage_CI_repr  21 lLgiakssvstwvrRdffPgdvvv 44 
                                   l+gi+ + +s  +++dffP+++ +
  gi|13541840|ref|NP_111528.1| 168 LFGISEHQISEMMEKDFFPAKLSI 191
                                   89******************9877 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 ?    9.0   0.0   0.00092       1.5       2      27 ..       5      30 ..       4      56 .. 0.83
   2 ?   -0.1   0.0      0.62     1e+03     108     119 ..     208     219 ..     181     220 .. 0.83
   3 ?   -3.3   0.0       6.1     1e+04      61      87 ..     283     309 ..     257     320 .. 0.60

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00092
                                  EEEESSTTSSHHHHHHCHCT-CCC-E CS
                           Roc  2 vvlvGdsgvGKtsllkrfvedkfsek 27
                                  + l+G+ +vGK+++++  +e++ + +
  gi|13541840|ref|NP_111528.1|  5 IGLIGEPNVGKSTFFSAATENEAEIN 30
                                  779*************9999887654 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.62
                                   SS-EEEEEE-TT CS
                           Roc 108 kspvilvgnkiD 119
                                    +p++lvgnk D
  gi|13541840|ref|NP_111528.1| 208 AKPLLLVGNKSD 219
                                   57999*****99 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 6.1
                                   EEE-SGGCTTTT-HHHHCTSCEEEEEE CS
                           Roc  61 WDtaGqerfrslhplylreaalailvy 87 
                                   + t G  r++ l +  +r+   +i+vy
  gi|13541840|ref|NP_111528.1| 283 FNTPGIIRIHDLLQKVVRDYLHYIIVY 309
                                   345566666666666666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (382 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 2451.89
//
Query:       gi|13541841|ref|NP_111529.1|  [L=540]
Description: Fe-S oxidoreductase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.3e-21   76.4   0.0    7.5e-20   72.0   0.0    2.3  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 ?    2.0   0.0     0.013   2.4e+02      61     122 ..      59     117 ..      43     152 .. 0.58
   2 !   72.0   0.0   4.2e-24   7.5e-20       2     167 .]     215     397 ..     214     397 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.013
                                   TTHHHHHHHHHHTCCCTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHH.....HHHHHHT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxx RF
                   Radical_SAM  61 pdfvellerlaklavpgiritvetngtlpdeeklerllelgvdrvslgleaadde.....kvlklmn 122
                                   p   +++e++ ++  +gi+++v+ +++l      e+  ++++ ++ ++++ +        k   +++
  gi|13541841|ref|NP_111529.1|  59 PYGLRKVEAILAK--NGISVVVSPPEHL------EKAIDRNTKVLGINVHDPYALspvttKLTMIFG 117
                                   5555555555555..4555555555555......777777888888888888776665544444444 PP

  == domain 2  score: 72.0 bits;  conditional E-value: 4.2e-24
                                   EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTC........ CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........ RF
                   Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlakla........ 74 
                                    +trgC+++C fC+++      ++ rs+++++i++evk +  ++g++++ l+ ++ +ly  +   + ++a           
  gi|13541841|ref|NP_111529.1| 215 QITRGCPRGCQFCSITP-----ETFRSIPMDDIIKEVKLN-IDHGIRGIELLTDDIMLYGSKKLQVNHEALVNlfttvkkl 289
                                   79**************5.....9*****************.8*****************6666666666666666888888 PP

                                   ..CCTEEEEEEECSSCHG...HHHHHHHHHTT...-SEEEEEEBSSSHHHHHHHHTCTSHH........HHHHHHHHHHHH CS
                                   ..xxxxxxxxxxxxxxxx...xxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxx RF
                   Radical_SAM  75 ..vpgiritvetngtlpd...eeklerllelg...vdrvslgleaaddekvlklmnrghtf........eevlealeklre 139
                                        +  +++++g + +      +++++e+         +gle+++++ + k+m+ g+ f        + +++a+ ++ +
  gi|13541841|ref|NP_111529.1| 290 gaTHIYFPHISAPGAKSSpktVQAIAEIAEYDkytAEAPVVGLESGSERIISKYMR-GKPFpwtphdwgDVIIDATGIMVD 369
                                   99999999********9999955666666666666********************5.555559****************** PP

                                   TTSETEEEEEEEBTTTSHHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM 140 agikrvvdrivglpGendeeleellell 167
                                   ++i++++++++g p e+de++ee ++l+
  gi|13541841|ref|NP_111529.1| 370 NNIHPCYTMTIGYPDETDEDIEESIKLV 397
                                   ************************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (540 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       504  (0.0281109); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.65u 0.33s 00:00:00.98 Elapsed: 00:00:00.52
# Mc/sec: 3130.35
//
Query:       gi|13541842|ref|NP_111530.1|  [L=305]
Description: heat shock protein HtpX [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.1e-34  119.1   0.0      3e-34  118.5   0.0    1.3  1  Peptidase_M48  Peptidase family M48
     0.0016   17.7   0.8      0.004   16.4   0.1    1.8  2  Peptidase_M56  BlaR1 peptidase M56
  ------ inclusion threshold ------
        1.2    8.5  20.0       0.75    9.2   1.0    2.1  2  ABC2_membrane  ABC-2 type transporter
          8    6.8   9.2       0.33   11.3   1.3    2.2  2  DUF1772        Domain of unknown function (DUF1772)


Domain annotation for each model (and alignments):
>> Peptidase_M48  Peptidase family M48
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.5   0.0   6.7e-38     3e-34       3     195 ..      81     301 ..      79     302 .. 0.88

  Alignments for each domain:
  == domain 1  score: 118.5 bits;  conditional E-value: 6.7e-38
                                   -SSHHHHHHHHHHHHTT-..-EEEEEEE-GGGT-EEEEESSS-E.EEEEEHHHH-SSB-HHHHHHHHHHHHHHHHTTHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Peptidase_M48   3 reaelkevveelakeaglpkpltkvyvvnspkrNAFalgggknk.rivltdgLlkqllseeelaaVlGHElGHikhrhsvv 82 
                                   r +++ ++vee+ak  g+  +++++y+ + +  NAFa+       ri++t++Ll   l+e+el+aV+GHE+GH+kh +s+v
  gi|13541842|ref|NP_111530.1|  81 RYGNIIAIVEEVAKLNGI--RPPTLYISEVSFPNAFAYESPIAGrRIAITRPLL-GILNEDELRAVIGHEIGHLKHHDSAV 158
                                   668999************..***********99*****9999999*********.************************** PP

                                   HHHHHHHHHHHHHHHHHHHTT-SHHHHHTT--S---HHHH.HHHHHHTTHHHHHHHHHHHHHHHHTT.T.HHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxx RF
                 Peptidase_M48  83 slivsllasillllglallisraeedaagafldalavlig.lliillflalSRkrEyqADeagvell.krakdlvralikl 161
                                    + ++l+++++++++++ l++  +++  +a++ al  +++ +l ++++l + R rE++AD+ ++ ++ + a++l++al+k+
  gi|13541842|ref|NP_111530.1| 159 IMAIGLIPTLIFYFAYTTLFAGDRRNGGSAIILALVLMVVsFLFNIMVLSVNRLRESYADANAALTIpNGARNLQTALAKI 239
                                   *****************99999999998888877765543144555666***********9877766155788999***** PP

                                   HHHTT--S---HHHH............................HHS-SS--HHHHHHHHHH- CS
                                   xxxxxxxxxxxxxxx............................xxxxxxxxxxxxxxxxxxx RF
                 Peptidase_M48 162 akdlerqdvsaslrs............................ellstHPplleRiqalkel 195
                                   ++  ++++++a+                               +l+s HP  ++Ri+ l++l
  gi|13541842|ref|NP_111530.1| 240 VRYGSSAKNTAASMLlfanydmdredvetlidkwrtmrvgilsDLFSDHPHPAKRIRLLDKL 301
                                   999999777777666888999999999999***************************99875 PP

>> Peptidase_M56  BlaR1 peptidase M56
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1   8.9e-07     0.004     127     227 ..      68     172 ..      30     174 .. 0.67
   2 ?   -0.9   0.1      0.17   7.6e+02     104     140 ..     189     225 ..     183     241 .. 0.59

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 8.9e-07
                 Peptidase_M56 127 lkkrfvrklgklraeelkeaLkeakeemqlk..rnikirlsssidsPavlgllkp....rIvlPadflkklsdeeleyill 201
                                   ++  +v +++k +++   ++++  +e  +l   r++++++s +++ P  +++  p    rI +   +l  l+++el  ++ 
  gi|13541842|ref|NP_111530.1|  68 VD--MVYRAKKADPNRYGNIIAIVEEVAKLNgiRPPTLYIS-EVSFPNAFAYESPiagrRIAITRPLLGILNEDELRAVIG 145
                                   33..4566666666666666666555555433388888876.5899999998887444479******************** PP

                 Peptidase_M56 202 HElaHlkrkDllv.nllvavlqclfwf 227
                                   HE  Hlk++D  v  ++ ++ + +f+f
  gi|13541842|ref|NP_111530.1| 146 HEIGHLKHHDSAViMAIGLIPTLIFYF 172
                                   **********76504555555666666 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.17
                 Peptidase_M56 104 illliWivgalilllyliaallvlkkrfvrklgklra 140
                                   i+l+++++++  l+  ++ ++  l++++  ++ +l+ 
  gi|13541842|ref|NP_111530.1| 189 IILALVLMVVSFLFNIMVLSVNRLRESYADANAALTI 225
                                   4555555555555666666666666666655555554 PP

>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1  12.1    0.0058        26      99     152 ..      14      64 ..       9      71 .. 0.88
   2 ?    9.2   1.0   0.00017      0.75      17      75 ..     155     211 ..     151     217 .. 0.63

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.0058
                 ABC2_membrane  99 akvlvelpvsllqalifllivyflvgldlsrfflflllllltalaasslgllis 152
                                    ++lv l +++l++li+ +++y+l+g++    + +++ +++++l++  l ++i+
  gi|13541842|ref|NP_111530.1|  14 LSLLVGLGIAALASLIIYAVAYYLFGIYS---IGIIFGVFVLVLMMDLLQWFIG 64 
                                   57899999*********************...7779999999999999999987 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00017
                 ABC2_membrane  17 dpslgllwrliqplllalvfgtvfgnlg.nsedgl.nrpgllffsvlflafsaltsvapvf 75 
                                   d++ +++  li +l++ + ++t+f   g  +++g   ++ l+ + v fl+ +++  +++++
  gi|13541842|ref|NP_111530.1| 155 DSAVIMAIGLIPTLIFYFAYTTLFA--GdRRNGGSaIILALVLMVVSFLFNIMV--LSVNR 211
                                   5667778899999999999999999..432333331346666666666663333..33444 PP

>> DUF1772  Domain of unknown function (DUF1772)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   1.4      0.32   1.4e+03      49      78 ..      21      46 ..       6      79 .. 0.55
   2 ?   11.3   1.3   7.4e-05      0.33      37     119 ..     157     276 ..     128     279 .. 0.64

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.32
                       DUF1772 49 afaylaaraasrgarllylaaaallllsiv 78
                                  + a+la+    + a  l+    ++++++i+
  gi|13541842|ref|NP_111530.1| 21 GIAALASLIIYAVAYYLF----GIYSIGII 46
                                  333222222222222222....33333333 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 7.4e-05
                       DUF1772  37 avfpplallsalafa..ylaaraasrgarllylaaaallllsivpyTllvmvP.tNnkLaal................... 95 
                                   av+ +++l+ +l f   y++  a +r++ +  +++a++l+++ ++  + +mv  +N +L +                    
  gi|13541842|ref|NP_111530.1| 157 AVIMAIGLIPTLIFYfaYTTLFAGDRRNGGSAIILALVLMVVSFL--FNIMVLsVN-RLRESyadanaaltipngarnlqt 234
                                   444554444444443145556667777777777778888844444..444444355.333334555677788888888888 PP

                       DUF1772  96 ....................keedakekedeaevrellerWgrl 119
                                                           a+ + d ++v+ l+++W ++
  gi|13541842|ref|NP_111530.1| 235 alakivrygssakntaasmlL--FANYDMDREDVETLIDKWRTM 276
                                   888888888777777774430..334455668888899999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1091  (0.0608511); expected 358.6 (0.02)
Passed bias filter:                      584  (0.0325729); 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):               4  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 1878.27
//
Query:       gi|13541843|ref|NP_111531.1|  [L=405]
Description: ATPase [Thermoplasma volcanium GSS1]
Scores for complete 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   58.8   0.0    6.4e-16   58.2   0.0    1.2  1  T2SSE     Type II/IV secretion system protein


Domain annotation for each model (and alignments):
>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.2   0.0   3.5e-20   6.4e-16       7     241 ..      70     305 ..      65     331 .. 0.86

  Alignments for each domain:
  == domain 1  score: 58.2 bits;  conditional E-value: 3.5e-20
                         T2SSE   7 allddekvsdihvekper.vkvrervdgielreveelekaalerlisriaalakldiseerplqdarlpekgvrlrvvllP 86 
                                   +l++ e+v +i v+ +++ v+v+   d+ ++ +  +l ++++  ++ r+a+l++++is++ pl  ++l+++  ++ + +  
  gi|13541843|ref|NP_111531.1|  70 PLFNLEEVKEIDVNGYDEpVIVKLSDDN-YYTTNIKLLANEVDSIAIRLAQLMGKKISTSDPLARGTLNNR--EVSITFGT 147
                                   5678899***********9999777777.99999999999*****************************44..45555555 PP

                         T2SSE  87 vvagealviR.kksakeltlddlgaeealkekiaevlrkavrerglilvsGgTgsGKttllyallkeinksderivtvEDp 166
                                    +  +  +iR  ++ + ++l++++ ++ ++ +  + l+ a+++ ++i++ G+    K   l  l+  ++k+ ++i  +   
  gi|13541843|ref|NP_111531.1| 148 EISPKGSSIRiARNDSGYDLKKFVESNGFSLESISYLKIAIENSKSIVIIGPHTELKYSALLFLMDLVDKE-KKITYIGEK 227
                                   566677899988999999*******************************************9******999.99****988 PP

                         T2SSE 167 vEiqleganqvqlnak.....kakvtfadllraaLRlrPDrimvGEiRdketleilkAvnTGHlgslsTlHansaagale 241
                                   +  +  g n++ +++k     + +++  +l+ +a+R+rPD i++  i   +  ++++A+ TGH+  ++++  +s+   ++
  gi|13541843|ref|NP_111531.1| 228 IPSRSPG-NYIFMKTKeksifSSQIDRVSLINTAMRQRPDYIVIDTIEVVDLPSVIQAITTGHPT-FTSIDIDSVSALVS 305
                                   8777655.666677776799999**********************9999999999**********.**999988776555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (405 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       586  (0.0326845); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 2841.07
//
Query:       gi|13541844|ref|NP_111532.1|  [L=282]
Description: hypothetical protein TVN1013 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.6e-09   35.8   0.4    6.6e-09   35.8   0.4    2.8  3  T2SSF            Type II secretion system (T2SS), protein F
     0.0079   15.0   9.7       0.19   10.5   0.7    2.1  2  DUF2207          Predicted membrane protein (DUF2207)
  ------ inclusion threshold ------
      0.066   11.5  17.3      0.068   11.5   2.6    2.1  2  DUF2070          Predicted membrane protein (DUF2070)
      0.074   12.9   9.6       0.67    9.9   1.3    2.4  2  DUF2721          Protein of unknown function (DUF2721)
       0.11   12.9   7.6        1.4    9.3   0.7    2.4  2  MgtE             Divalent cation transporter
       0.94    9.5  12.7        2.8    8.0   0.1    2.8  3  Phage_holin_3_6  Putative Actinobacterial Holin-X, holin supe


Domain annotation for each model (and alignments):
>> T2SSF  Type II secretion system (T2SS), protein F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.2      0.03        88      91     121 ..      30      60 ..      19      64 .. 0.63
   2 !   35.8   0.4   2.2e-12   6.6e-09       2     124 ..     115     242 ..     114     243 .. 0.92
   3 ?   -3.6   1.5       3.5   1.1e+04     107     118 ..     255     266 ..     248     273 .. 0.42

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.03
                                   HHHHHHHHHHHHHTTXXXXXXXXXXXXXXXX CS
                         T2SSF  91 erelrrkllaallepllllvvallvllilla 121
                                   ++ ++ ++ ++  ++l l +++ ++++il+a
  gi|13541844|ref|NP_111532.1|  30 DQLIKSQIELNAVSYLTLSIIVTFIFFILFA 60 
                                   4455566666666666666666666666665 PP

  == domain 2  score: 35.8 bits;  conditional E-value: 2.2e-12
                                   HHHHHHHHHTT--HHHHHHHHHHHHSSHHHHHHHHHHHHHHHTTS.SHHHHHC....T-TT.TS-HHHHHHHHHHHHHT-H CS
                         T2SSF   2 lrqlatllsaGvplveaLellaeeaengplaeelkriarrlraGg.slseale....rtpssefpelvvqlirageeggnL 77 
                                   l   ++l+ +G+p++++L+ +++ ++ g++a+e kri+  ++  g ++ +ale     t s+++++  + l  ++    ++
  gi|13541844|ref|NP_111532.1| 115 LAITYSLSLSGIPVDRILRDISNMDSLGEIAKESKRIVVMMDRLGyDFLTALEkaekITASDDLSRIWAGLRLSILLDTDI 195
                                   556678888******************************9976554999****88876666899***************** PP

                                   HHHHHHHHHHHHHHHHHHHHHHHHHHTTXXXXXXXXXXXXXXXXXXX CS
                         T2SSF  78 aevLerlaeyleeerelrrkllaallepllllvvallvllillaill 124
                                    +++++  +y+ + +e++ kl + +l+ + + +val+++++ll++++
  gi|13541844|ref|NP_111532.1| 196 VAYFRDRIDYYSRVQENKSKLSLDSLGLASESFVALVIAFPLLIFMT 242
                                   ********************************************996 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 3.5
                                   XXXXXXXXXXXX CS
                         T2SSF 107 lllvvallvlli 118
                                   ++++ +++vl++
  gi|13541844|ref|NP_111532.1| 255 FFVISLIIVLGA 266
                                   333333333333 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   2.6   0.00013       0.4     367     432 ..      28      93 ..      11     116 .. 0.58
   2 !   10.5   0.7   6.3e-05      0.19     382     432 ..     227     276 ..     129     282 .] 0.61

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00013
                       DUF2207 367 kergyfdkkgkkklkklsalglgliilglilillallllvll.lvfllilllillliaiivlllfsr 432
                                    + ++++++ + ++ ++ +l+++++++++il+ ++ ++ +++   ++++++ +++l+a++vl+++ +
  gi|13541844|ref|NP_111532.1|  28 LQDQLIKSQIELNAVSYLTLSIIVTFIFFILFAATSIFTYYFdRRYFFLVSAVFFLLAALVLYYS-S 93 
                                   44455557777777777777777777777766666666555443333333333334434444433.3 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 6.3e-05
                       DUF2207 382 klsalglgliilglilillallllvll.lvfllilllillliaiivlllfsr 432
                                   ++ al +++ +l+++  +++++++  l  +f++i l+i+l ++++++++ s+
  gi|13541844|ref|NP_111532.1| 227 SFVALVIAFPLLIFM--TGSIISIKNLsTIFFVISLIIVLGASAVMFYFTSK 276
                                   333333333333333..33444444332444444444444444444444444 PP

>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   6.9   0.00098       2.9      59     133 ..      30     104 ..       7     141 .. 0.70
   2 ?   11.5   2.6   2.3e-05     0.068      66     125 ..     212     277 ..     160     280 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.00098
                       DUF2070  59 lrilggrltykrs..lflalltelivviisllaillsall.qalvllalvlslalvfalrllvlvavsdesllkavlp 133
                                   +++++++++++    l+l+++ ++i++i++ + +++++++      +++++s ++ +   l+++++ s  ++++ ++ 
  gi|13541844|ref|NP_111532.1|  30 DQLIKSQIELNAVsyLTLSIIVTFIFFILFAATSIFTYYFdR---RYFFLVSAVFFLLAALVLYYSSSYPEIRQKWIA 104
                                   455666677777667888888888888888888888877743...456677777777777777777666555555544 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 2.3e-05
                       DUF2070  66 ltykrs.lflalltelivviisllaillsall......qalvllalvlslalvfalrllvlvavsde 125
                                    ++k s   l l++e +v++++ +++l+++ +      ++l++ ++v+sl++v++ + ++++++s+ 
  gi|13541844|ref|NP_111532.1| 212 NKSKLSlDSLGLASESFVALVIAFPLLIFM-TgsiisiKNLSTIFFVISLIIVLGASAVMFYFTSKI 277
                                   333333656666666666666666666664.33566669999********************99975 PP

>> DUF2721  Protein of unknown function (DUF2721)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   1.3   0.00022      0.67      66     118 ..      36      91 ..      15      97 .. 0.52
   2 ?    7.4   1.7    0.0013         4      68     117 ..     222     271 ..     200     277 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00022
                       DUF2721  66 ailllvlsallvvlvvlllfl...sallsldlsllaailfvlalllllvslllflr 118
                                    i l+++s l+++++v ++f+   +a + + + +   ++f+++ +++l+++l++ +
  gi|13541844|ref|NP_111532.1|  36 QIELNAVSYLTLSIIVTFIFFilfAATSIFTYYFDRRYFFLVSAVFFLLAALVLYY 91 
                                   44444444444444443333311133333344444455666655555555555443 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0013
                       DUF2721  68 lllvlsallvvlvvlllflsallsldlsllaailfvlalllllvslllfl 117
                                    l+  s++++v++  ll++   + ++++ l +i+fv++l+++l+++++++
  gi|13541844|ref|NP_111532.1| 222 GLASESFVALVIAFPLLIFMTGSIISIKNLSTIFFVISLIIVLGASAVMF 271
                                   55555666666665555554666789***************999887765 PP

>> MgtE  Divalent cation transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.7   0.00047       1.4      32      86 ..      33      90 ..      12     102 .. 0.52
   2 ?    7.1   1.2    0.0023       6.9      41      86 ..     228     272 ..     177     280 .. 0.55

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00047
                                  HHHHHHHHHHHHHHHHHHHHHHHHHH...HHHHT-.CTSHHHHHHHHHHHHHHHHHH. CS
                          MgtE 32 lkkvllkelrvvlllgvilgllifll...alllgwslllalvvglalvlvllaaalli 86
                                  +k+ +  +++  l+l++i+ ++ f+l   + +++  +    ++ ++ v++llaa++l+
  gi|13541844|ref|NP_111532.1| 33 IKSQIELNAVSYLTLSIIVTFIFFILfaaTSIFTYYFDRRYFFLVSAVFFLLAALVLY 90
                                  3444444444444444444444444310033333344444447777777777777773 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0023
                                   HHHHHHHHHHHHHHHHHHHHHT-.CTSHHHHHHHHHHHHHHHHHH.. CS
                          MgtE  41 rvvlllgvilgllifllalllgwslllalvvglalvlvllaaall.i 86 
                                    v+l++++ l +++   ++ +  + l ++++ ++l++vl a+a++ +
  gi|13541844|ref|NP_111532.1| 228 FVALVIAFPLLIFMTGSIISI--KNLSTIFFVISLIIVLGASAVMfY 272
                                   333333333222222221222..222333333334433333333322 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 ?   -1.2   0.0      0.68     2e+03      90     107 ..      15      30 ..       9      32 .. 0.73
   2 ?    3.1   7.5     0.032        96      50      84 ..      49      90 ..      33      99 .. 0.60
   3 ?    8.0   0.1   0.00094       2.8      26      84 ..     209     271 ..     191     279 .. 0.45

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.68
               Phage_holin_3_6  90 klkkakplpertieelke 107
                                   ++++   +p++ti+ l++
  gi|13541844|ref|NP_111532.1|  15 QVAR--YVPRKTIDKLQD 30 
                                   3333..59*******997 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.032
               Phage_holin_3_6 50 alllllvalalala.a......lwlaalivaavllvlagvla 84
                                   ++++++++++a + +      +   +l+ a+++l++a+vl 
  gi|13541844|ref|NP_111532.1| 49 IIVTFIFFILFAATsIftyyfdRRYFFLVSAVFFLLAALVLY 90
                                  222233333222211223445677777888888888888876 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.00094
               Phage_holin_3_6  26 lkeeakragsgagllg....aagvlallalllllvalalalaa..lwlaalivaavllvlagvla 84 
                                   ++e+++++    + l+    +a+v+a+  l++++  ++  +    + + ++i  +++l + +v+ 
  gi|13541844|ref|NP_111532.1| 209 VQENKSKLSLDSLGLAsesfVALVIAFPLLIFMTGSII-SI-KnlSTIFFVISLIIVLGASAVMF 271
                                   45555555555444442222344444444444444443.33.12244444444444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1226  (0.0683808); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-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: 1863.96
//
Query:       gi|13541845|ref|NP_111533.1|  [L=245]
Description: hypothetical protein TVN1014 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.3e-12   45.3   0.3    7.3e-12   45.3   0.3    1.7  2  T2SSF          Type II secretion system (T2SS), protein F
  ------ inclusion threshold ------
      0.047   14.0   0.4      0.047   14.0   0.4    2.0  2  Orf78          Orf78 (ac78)
        0.1   12.6   0.7       0.65   10.1   0.0    2.2  2  CrgA           Cell division protein CrgA
        1.1    9.4   3.0        1.9    8.7   0.1    2.3  2  DUF4519        Domain of unknown function (DUF4519)
        1.3    9.2   9.4       0.19   11.8   5.0    1.9  2  Oxidored_q5_N  NADH-ubiquinone oxidoreductase chain 4, amino 


Domain annotation for each model (and alignments):
>> T2SSF  Type II secretion system (T2SS), protein F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.3   0.3     2e-15   7.3e-12       1     124 [.      59     182 ..      59     182 .. 0.91
   2 ?   -3.8   0.2       3.3   1.2e+04     100     116 ..     223     239 ..     220     242 .. 0.55

  Alignments for each domain:
  == domain 1  score: 45.3 bits;  conditional E-value: 2e-15
                                   HHHHHHHHHHTT--HHHHHHHHHHHHSSHHHHHHHHHHHHHHHTTSSHHHHHC..T-TT.TS-HHHHHHHHHHHHHT-HHH CS
                         T2SSF   1 flrqlatllsaGvplveaLellaeeaengplaeelkriarrlraGgslseale..rtpssefpelvvqlirageeggnLae 79 
                                   flr l++ +s G++++ +L+l+ +e+  gpl e ++++++ l++G +++e+ +  r+ +s   + v+ +   +++ g+ + 
  gi|13541845|ref|NP_111533.1|  59 FLRDLSSFSSYGMSMYNILHLILSED-LGPLNEDVRNARAILDNGNTIEEVSAylRSRNSRDLDIVAEVMKNADRAGRPGT 138
                                   99************************.*********************9888888666667788899999999999***** PP

                                   HHHHHHHHHHHHHHHHHHHHHHHHTTXXXXXXXXXXXXXXXXXXX CS
                         T2SSF  80 vLerlaeyleeerelrrkllaallepllllvvallvllillaill 124
                                   +L+ l++y++ er+++rk++++++e  + l++a++++++l++i++
  gi|13541845|ref|NP_111533.1| 139 TLQFLSTYMN-ERMSQRKNATQTAENYVGLIIASFMIFLLVMIVV 182
                                   **99998776.57889999*********************99986 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 3.3
                                   HHHHTTXXXXXXXXXXX CS
                         T2SSF 100 aallepllllvvallvl 116
                                   + l++  +l+ +++ +l
  gi|13541845|ref|NP_111533.1| 223 SGLFYSGMLVTITVTLL 239
                                   55555556666555554 PP

>> Orf78  Orf78 (ac78)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.3       2.3   8.2e+03      76      84 ..      12      20 ..       8      22 .. 0.73
   2 ?   14.0   0.4   1.3e-05     0.047      48      90 ..     147     189 ..     119     203 .. 0.60

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 2.3
                         Orf78 76 vlvllyviy 84
                                  + v+ly+iy
  gi|13541845|ref|NP_111533.1| 12 LAVVLYLIY 20
                                  457788887 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 1.3e-05
                         Orf78  48 ditekesnaaekaqalnillisllavvcvlvllyviyYfvilr 90 
                                     + ++++++ +++a+n + + + ++++ l++++v+ Y++i r
  gi|13541845|ref|NP_111533.1| 147 MNERMSQRKNATQTAENYVGLIIASFMIFLLVMIVVDYYFIQR 189
                                   2222223323344444555555555555555566777999988 PP

>> CrgA  Cell division protein CrgA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.2      0.23   8.2e+02      49      75 ..      13      39 ..       7      43 .. 0.75
   2 ?   10.1   0.0   0.00018      0.65      17      55 ..     148     186 ..     128     210 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.23
                          CrgA 49 lvvyYlageeipfmaelgawNlliGfg 75
                                   vv Yl   +  ++ +l a  ++i+fg
  gi|13541845|ref|NP_111533.1| 13 AVVLYLIYRNPAVILALIASGIAIAFG 39
                                  467777777666688999999999998 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00018
                          CrgA  17 aertpvkakaakpsprwyvpvmlglmllGllwlvvyYla 55 
                                   +er +++++a+++ ++++  ++  +m++ l+ +vv Y  
  gi|13541845|ref|NP_111533.1| 148 NERMSQRKNATQTAENYVGLIIASFMIFLLVMIVVDYYF 186
                                   5677778888888888999999999***9*****97754 PP

>> DUF4519  Domain of unknown function (DUF4519)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.5      0.22   7.8e+02      36      51 ..       3      18 ..       3      22 .. 0.65
   2 ?    8.7   0.1   0.00052       1.9      17      52 ..     152     187 ..     148     190 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.22
                       DUF4519 36 PvlavlillivvfvYl 51
                                  P+ +++ +l++v++Yl
  gi|13541845|ref|NP_111533.1|  3 PIYGAVPALLAVVLYL 18
                                  6666677777777776 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00052
                       DUF4519  17 keRrkenkeaqekvttvVlPvlavlillivvfvYlk 52 
                                    +R+++ ++a++ v  ++  +++ l+++ivv  Y+ 
  gi|13541845|ref|NP_111533.1| 152 SQRKNATQTAENYVGLIIASFMIFLLVMIVVDYYFI 187
                                   59*****************************88885 PP

>> Oxidored_q5_N  NADH-ubiquinone oxidoreductase chain 4, amino terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1      0.84     3e+03      52      62 ..      54      64 ..       8      82 .. 0.48
   2 ?   11.8   5.0   5.3e-05      0.19      27     102 ..     167     237 ..     140     243 .. 0.65

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.84
                 Oxidored_q5_N 52 nlsyllglDsl 62
                                  ++   +  D  
  gi|13541845|ref|NP_111533.1| 54 MMVPSFLRDLS 64
                                  33333333333 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 5.3e-05
                 Oxidored_q5_N  27 stlvslllallsllllnlsssfslsnlsyllglDslSapLilLSlWllpLmilASqkhlkkepknrqrlFllllil 102
                                   +++ s++++l    l++   + ++ + s +l +D++Sa+Li+ S++    + l  ++ +++   +++ + +++ ++
  gi|13541845|ref|NP_111533.1| 167 LIIASFMIFL----LVMIVVDYYFIQRSGFLLIDYISAILIIQSIFTGFYTGLVRYSSIRS-GLFYSGMLVTITVT 237
                                   2333444444....455556667778899*************9998766665555555555.44455555544444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1168  (0.0651459); expected 358.6 (0.02)
Passed bias filter:                      563  (0.0314016); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 1647.00
//
Query:       gi|13541846|ref|NP_111534.1|  [L=410]
Description: ATPase [Thermoplasma volcanium GSS1]
Scores for complete 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    2.6e-36  125.1   0.0    1.1  1  T2SSE         Type II/IV secretion system protein
     0.0013   18.5   0.0     0.0029   17.3   0.0    1.6  1  AAA_29        P-loop containing region of AAA domain
     0.0013   19.2   0.0     0.0036   17.8   0.0    1.7  1  ABC_tran      ABC transporter
     0.0017   17.7   0.0       0.33   10.2   0.0    2.4  2  Zeta_toxin    Zeta toxin
     0.0024   17.3   0.1     0.0062   15.9   0.1    1.7  1  FtsK_SpoIIIE  FtsK/SpoIIIE family
     0.0032   17.6   0.2     0.0085   16.2   0.1    1.8  1  Dynamin_N     Dynamin family
     0.0051   16.4   0.0      0.014   14.9   0.0    1.8  2  cobW          CobW/HypB/UreG, nucleotide-binding domain
     0.0093   16.2   0.0      0.022   15.0   0.0    1.6  1  AAA_28        AAA domain
     0.0094   16.0   0.3       0.19   11.8   0.0    2.9  3  AAA_14        AAA domain
  ------ inclusion threshold ------
       0.01   15.9   0.0      0.021   14.9   0.0    1.6  1  MMR_HSR1      50S ribosome-binding GTPase
      0.021   15.3   2.3      0.042   14.4   2.3    1.7  1  AAA_23        AAA domain
      0.031   13.7   0.1        0.2   11.0   0.0    2.1  2  Mg_chelatase  Magnesium chelatase, subunit ChlI
       0.04   13.6   0.1       0.13   11.9   0.0    1.6  2  AAA_15        AAA ATPase domain
      0.042   14.2   0.0      0.089   13.2   0.0    1.5  1  AAA_16        AAA ATPase domain
      0.043   13.7   0.1       0.19   11.6   0.0    2.1  2  ATPase_2      ATPase domain predominantly from Archaea
      0.051   13.9   0.0       0.13   12.6   0.0    1.7  1  AAA_22        AAA domain
      0.061   12.8   0.0       0.12   11.9   0.0    1.4  1  AAA_7         P-loop containing dynein motor region
      0.084   12.8   0.0       0.51   10.2   0.0    2.2  2  NTPase_1      NTPase
       0.12   11.9   0.0       0.29   10.7   0.0    1.7  1  GTP_EFTU      Elongation factor Tu GTP binding domain


Domain annotation for each model (and alignments):
>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.1   0.0   2.8e-39   2.6e-36       5     251 ..      61     306 ..      58     322 .. 0.92

  Alignments for each domain:
  == domain 1  score: 125.1 bits;  conditional E-value: 2.8e-39
                         T2SSE   5 leallddekvsdihvekpervkvrervdgielreveelekaalerlisriaalakldiseerplqdarlpekgvrlrvvll 85 
                                   +e++++d+ v di +  ++ v +   + g  +r+  + ++++++ ++++ia+ +++++s  +p++d + +  ++r+++v  
  gi|13541846|ref|NP_111534.1|  61 VEPIINDPMVEDITITSENYVYIYHSKLG-PMRTDVFFTEDETRKFAQHIAQRSGKTVSVYNPVVDVSYK--NYRINIVYE 138
                                   678999**************888444444.6899999999**************************9988..9****9987 PP

                         T2SSE  86 PvvagealviRkksakeltlddlgaeealkekiaevlrkavrerglilvsGgTgsGKttllyallkeinksderivtvEDp 166
                                     v +++++iRk +a+++t  dl++++a ++k+ + l  a+++r +i+++G T+sGKttll+a+l++++    riv +ED+
  gi|13541846|ref|NP_111534.1| 139 D-VGKPSISIRKLRAAAFTPFDLIQSGAATPKVMAYLWLAIEHRSNIIITGSTSSGKTTLLNAILSFVPRA-SRIVSIEDA 217
                                   5.6789*****************************************************************.********* PP

                         T2SSE 167 vEiqleganqvqlnak.....kakvtfadllraaLRlrPDrimvGEiRdketleilkAvnTGHlgslsTlHansaagaler 242
                                   +E+++ ++n+v+l++k     ++++ ++dl++ +     D +++GE R+    +  + + +G    ++T+H +s    ++r
  gi|13541846|ref|NP_111534.1| 218 RELNIMNENVVSLQSKisltqSGGISVNDLIEFSKYDGADYLVLGEARGDVIRSYFRYITSGRNA-ITTIHGGSSSALIRR 297
                                   *******************9999***********999*************99999**********.*************** PP

                         T2SSE 243 Leqlgaeve 251
                                   L+ l   ++
  gi|13541846|ref|NP_111534.1| 298 LKSLPLYLP 306
                                   **9985543 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 !   17.3   0.0   3.1e-06    0.0029      19      44 ..     178     203 ..     174     211 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3.1e-06
                        AAA_29  19 idlkgatlltGpsGsGKSTllDAiqa 44 
                                   i+ ++++++tG + sGK+Tll Ai  
  gi|13541846|ref|NP_111534.1| 178 IEHRSNIIITGSTSSGKTTLLNAILS 203
                                   5556689****************975 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   3.9e-06    0.0036       6      62 ..     176     235 ..     173     272 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 3.9e-06
                                   EEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEET.TCEGGG..B-HHHCCHCEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx..xxxxxxxxxxx RF
                      ABC_tran   6 lklkegekvaivGenGaGKStLlkllagllkpteGeilld.gkdlke..qeleslrkeig 62 
                                   l +++ + + i+G++ +GK+tLl++++  +  ++  + ++  ++l+   ++  sl+++i+
  gi|13541846|ref|NP_111534.1| 176 LAIEHRSNIIITGSTSSGKTTLLNAILSFVPRASRIVSIEdARELNImnENVVSLQSKIS 235
                                   56888999*********************9988888877744444444455555555555 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.015        14     123     197 ..      16      87 ..       4      89 .. 0.85
   2 !   10.2   0.0   0.00035      0.33      18      50 ..     183     215 ..     177     221 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.015
                    Zeta_toxin 123 evevvvvavkkelSrlgvldRyeeevaegRlv.pkeehdeafeglresvealeeekqldrvkikdrdgktvlydnn 197
                                   ++ ++++ +  e+S +   + y  +    R++ +++e+ ea++  + +ve + ++  +++++i+ ++  + +y+++
  gi|13541846|ref|NP_111534.1|  16 KLGLLYLSQAHEVSMENFVKQYALD---QRMAsSVSEFAEAYRIGMGKVEPIINDPMVEDITITSENY-VYIYHSK 87 
                                   667899999*******999999999...67652789***************************98888.9999876 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00035
                    Zeta_toxin  18 lillgGqpGAGKselaellkdelerqgnvvrld 50 
                                    i++ G++ +GK++l++++   + r++++v ++
  gi|13541846|ref|NP_111534.1| 183 NIIITGSTSSGKTTLLNAILSFVPRASRIVSIE 215
                                   589*****************9999999999885 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   6.6e-06    0.0062      37      60 ..     179     202 ..     160     209 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 6.6e-06
                                   GS-.SEEEE--TTSSHHHHHHHHH CS
                  FtsK_SpoIIIE  37 kmashllvaGatgsGKStalntLi 60 
                                   ++ s++++ G+t sGK+t ln+++
  gi|13541846|ref|NP_111534.1| 179 EHRSNIIITGSTSSGKTTLLNAIL 202
                                   4559*****************965 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1     9e-06    0.0085       1      30 [.     184     211 ..     184     235 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 9e-06
                                   EEEEEBTTTTHHHHHHHHHTS--S---SSS CS
                     Dynamin_N   1 iavvGsqSsGKSSvlnaLlgedilprgpnp 30 
                                   i++ Gs+SsGK+++lna+l     pr + +
  gi|13541846|ref|NP_111534.1| 184 IIITGSTSSGKTTLLNAILSFV--PRASRI 211
                                   789***************9753..666555 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       6.3     6e+03      11      40 ..     113     144 ..     113     153 .. 0.73
   2 !   14.9   0.0   1.5e-05     0.014       3      61 ..     184     242 ..     182     265 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 6.3
                                   CCHHHHHHHHH..CT--SS-EEEEESS-SSCH CS
                          cobW  11 sGKTtLlnhll..enraglklavivNefgevs 40 
                                   sGKT  + + +     +++++ ++  ++g+ s
  gi|13541846|ref|NP_111534.1| 113 SGKTVSVYNPVvdVSYKNYRINIVYEDVGKPS 144
                                   78887776666576778899999999988755 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 1.5e-05
                                   EEEEESTTCCHHHHHHHHHCT--SS-EEEEESS-SSCHCCCCCCHCCCT.EEEETTTTE CS
                          cobW   3 tvltGflGsGKTtLlnhllenraglklavivNefgevsiDaellretgveivelenGci 61 
                                   +++tG+  sGKTtLln++l+     +  v + +  e++i +e + + +++i   + G+i
  gi|13541846|ref|NP_111534.1| 184 IIITGSTSSGKTTLLNAILSFVPRASRIVSIEDARELNIMNENVVSLQSKISLTQSGGI 242
                                   79*****************7777777777778888888877777666666666666655 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   2.3e-05     0.022       1      20 [.     183     202 ..     183     231 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.3e-05
                        AAA_28   1 kivitGgestGKTtlleaLa 20 
                                   +i+itG  s+GKTtll+a+ 
  gi|13541846|ref|NP_111534.1| 183 NIIITGSTSSGKTTLLNAIL 202
                                   59**************9975 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       2.2     2e+03      11      24 ..     111     124 ..     110     159 .. 0.69
   2 !   11.8   0.0    0.0002      0.19       4      49 ..     183     225 ..     180     301 .. 0.68
   3 ?    0.5   0.1      0.61   5.7e+02      13      58 ..     355     401 ..     353     409 .. 0.66

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 2.2
                        AAA_14  11 RrvGKTtllkqlik 24 
                                    r+GKT+ +++ + 
  gi|13541846|ref|NP_111534.1| 111 QRSGKTVSVYNPVV 124
                                   589***99987543 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.0002
                        AAA_14   4 ilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladp 49 
                                    ++itG   +GKTtll+ +++      +    ++++d r+ ++ ++
  gi|13541846|ref|NP_111534.1| 183 NIIITGSTSSGKTTLLNAILSFVP---RASRIVSIEDARELNIMNE 225
                                   689*************99984433...5555556666666555544 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.61
                        AAA_14  13 vGKTtllkqlikellvkkesilyinldderd..kkladpekllelile 58 
                                   +G ++ll++++++    +++++  +ld++ +  +++++p+++++++++
  gi|13541846|ref|NP_111534.1| 355 SGVSYLLENIASKTG-MDREYIIKDLDRKAKilENMQKPADYMDFVRK 401
                                   567899999998888.67777888888877744344455455555544 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   2.2e-05     0.021       2      35 ..     184     221 ..     183     275 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.2e-05
                                   EEEEESTTSSHHHHHHHHHT....STEEESSSTTSSSS CS
                      MMR_HSR1   2 vaivGrpNvGKStLinaltg....ekaivsdkpgtTrd 35 
                                   ++i G + +GK+tL+na++     +  ivs +    ++
  gi|13541846|ref|NP_111534.1| 184 IIITGSTSSGKTTLLNAILSfvprASRIVSIEDARELN 221
                                   89****************97333223355544444444 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   2.3   4.4e-05     0.042      22      40 ..     184     202 ..     180     396 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.4e-05
                        AAA_23  22 tlItGpNGaGKTTildAik 40 
                                    +ItG + +GKTT+l+Ai 
  gi|13541846|ref|NP_111534.1| 184 IIITGSTSSGKTTLLNAIL 202
                                   58***************95 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00021       0.2      16      65 ..     175     224 ..     164     243 .. 0.84
   2 ?   -0.3   0.0      0.64     6e+02     175     190 ..     320     335 ..     312     338 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00021
                  Mg_chelatase  16 eiaaaGgHnlllvGppGsGKtmlakrlpsllpplseeealevakiasvag 65 
                                    +a+  + n++++G+  sGKt l +++ s +p+ s+  ++e a+   +++
  gi|13541846|ref|NP_111534.1| 175 WLAIEHRSNIIITGSTSSGKTTLLNAILSFVPRASRIVSIEDARELNIMN 224
                                   567777789************************99999988887766665 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.64
                  Mg_chelatase 175 ekeierYlsklsgpll 190
                                   +++ +rY++k+s+p+ 
  gi|13541846|ref|NP_111534.1| 320 KNSGRRYINKISEPFY 335
                                   56779*********86 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00014      0.13      26      97 ..     184     252 ..     176     277 .. 0.79
   2 ?   -1.9   0.1       2.2     2e+03     196     277 ..     272     348 ..     242     395 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00014
                        AAA_15  26 tvliGkNnsGKSsilealdlFlnnkekknkkvikiekedleifeniseskdikIdvefaek..ekakeyektlk 97 
                                    ++ G  +sGK+++l+a+  F  +    +  v  +++ +l+i++++  s + kI ++   +   + ++ ++++k
  gi|13541846|ref|NP_111534.1| 184 IIITGSTSSGKTTLLNAILSFVPRA---SRIVSIEDARELNIMNENVVSLQSKISLTQ--SggISVNDLIEFSK 252
                                   5778999***************988...555677889999999999999999999887..22455555555555 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.2
                        AAA_15 196 klllisakRnvsdedsekkssllgklkekileealqekleeelteklkeiqeklkeidkklaeelkkilkkkidkikkfny 276
                                   ++++i + Rn+ ++    +ss+l++ ++++  +     l ++++ +++ i e  +    ++++  +  ++ +++  + f y
  gi|13541846|ref|NP_111534.1| 272 YFRYITSGRNAITTIHGGSSSALIRRLKSLPLY-----LPISNILAIDAIVEVKNSGRRYINKISEPFYEGSLSLNNVFDY 347
                                   566777777777777777777777666665432.....3444555555555555555555555555444444444444444 PP

                        AAA_15 277 k 277
                                    
  gi|13541846|ref|NP_111534.1| 348 S 348
                                   4 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   9.4e-05     0.089      23      55 ..     181     212 ..     170     237 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 9.4e-05
                        AAA_16  23 rpelvllsGesGvGKsslvrellralekdggif 55 
                                   r ++++++G   +GK++l++++l  + ++  i+
  gi|13541846|ref|NP_111534.1| 181 R-SNIIITGSTSSGKTTLLNAILSFVPRASRIV 212
                                   4.6899*****************7777665444 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       8.2   7.7e+03     199     229 ..      32      63 ..      21      66 .. 0.58
   2 ?   11.6   0.0    0.0002      0.19      14      44 ..     175     205 ..     173     257 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 8.2
                      ATPase_2 199 nflkegfkel.eel.skedfeeiyryvGGkPka 229
                                   nf+k+++ +      s  +f e+yr+  Gk++ 
  gi|13541846|ref|NP_111534.1|  32 NFVKQYALDQrM-AsSVSEFAEAYRIGMGKVEP 63 
                                   455554444422.24667777777776666655 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.0002
                      ATPase_2  14 ilerepneiyfiYGpegsGKtaLlkeiienl 44 
                                   +l  e ++ + i+G+ +sGKt+Ll+ i++  
  gi|13541846|ref|NP_111534.1| 175 WLAIEHRSNIIITGSTSSGKTTLLNAILSFV 205
                                   66677888899**************998765 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00013      0.13       4      32 ..     180     208 ..     177     249 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00013
                        AAA_22   4 tagilvvtGesGtGKTtllrrlleqldee 32 
                                   +++ +++tG + +GKTtll+ +l+  +++
  gi|13541846|ref|NP_111534.1| 180 HRSNIIITGSTSSGKTTLLNAILSFVPRA 208
                                   8999*****************99998754 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   0.00013      0.12      23      59 ..     171     207 ..     160     221 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00013
                         AAA_7  23 syllelllknkkpvllvGptGtGKtviikdllkkldk 59 
                                      l l ++++ +++++G+t +GKt++++ +l+ +++
  gi|13541846|ref|NP_111534.1| 171 MAYLWLAIEHRSNIIITGSTSSGKTTLLNAILSFVPR 207
                                   55667889*********************99988774 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00054      0.51       1      23 [.     183     205 ..     183     217 .. 0.88
   2 ?   -0.8   0.0       1.4   1.3e+03     122     146 ..     276     300 ..     267     305 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00054
                                   EEEEE--TTSSHHHHHHHHHHHH CS
                      NTPase_1   1 kvfiTGppGvGKtTlvkkvlell 23 
                                   +++iTG+  +GKtTl++ +l+ +
  gi|13541846|ref|NP_111534.1| 183 NIIITGSTSSGKTTLLNAILSFV 205
                                   69***************998765 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.4
                                   HTTTSEEEEE--SS--SHHHHHHHT CS
                      NTPase_1 122 Lksekpvlavihrrkdlalveeire 146
                                   ++s+++ +++ih  +++al++++++
  gi|13541846|ref|NP_111534.1| 276 ITSGRNAITTIHGGSSSALIRRLKS 300
                                   6789999*******999**999987 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0    0.0003      0.29       4      33 ..     182     211 ..     179     246 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0003
                                   EEEEEEESTTSSHHHHHHHHHHHTTSSCHH CS
                      GTP_EFTU   4 rnigiighvDhGKtTLtdrLlyktgaiskk 33 
                                    ni+i g + +GKtTL+ ++l    + s+ 
  gi|13541846|ref|NP_111534.1| 182 SNIIITGSTSSGKTTLLNAILSFVPRASRI 211
                                   59******************9877776664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (410 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       747  (0.0416643); expected 358.6 (0.02)
Passed bias filter:                      622  (0.0346924); expected 358.6 (0.02)
Passed Vit filter:                        90  (0.0050198); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.66u 0.31s 00:00:00.97 Elapsed: 00:00:00.48
# Mc/sec: 2583.51
//
Query:       gi|13541847|ref|NP_111535.1|  [L=432]
Description: NhaP-type Na+/H+ antiporter [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.3e-30  105.1  49.8    4.7e-30  104.6  49.8    1.2  1  Na_H_Exchanger  Sodium/hydrogen exchanger family
  ------ inclusion threshold ------
        1.6    9.0   0.0        1.6    9.0   0.0    2.7  3  DUF1269         Protein of unknown function (DUF1269)


Domain annotation for each model (and alignments):
>> Na_H_Exchanger  Sodium/hydrogen exchanger family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.6  49.8   5.2e-34   4.7e-30       3     378 ..      16     417 ..      13     420 .. 0.82

  Alignments for each domain:
  == domain 1  score: 104.6 bits;  conditional E-value: 5.2e-34
                                   HHHHHHHHHHHHHHHTTSXHHHHHHHHHHHHTTTTTS............HHHCHCCHHHHCHHCCHHHHCTCGCCTGCCTH CS
                Na_H_Exchanger   3 llillallvgllarrlklpeivgliiaGlllGpsglglieps.......eedlevlselglilllFlaGleldlrelrknl 76 
                                   ll+l+a+ +++ ar+  + ei++li++Gl++Gp+++  i+p         +    +  +gl+++l+  + +++++ l++ +
  gi|13541847|ref|NP_111535.1|  16 LLVLSAVAIPI-ARKMSVVEIPILIFIGLIVGPFLRL-ISPAfsvylfsSFAGVGIGMIGLVIILYSESHNMNIKVLKSSF 94 
                                   55665666666.**********************997.88889999999999999************************** PP

                                   HHHHHHHHHHHHHHHHHHHHHHH.HHTXTTCHHHHHHHHHHHTSSXHHHHHHHC.CCCTSTCCCCCCHHHHHHHHHHHCCC CS
                Na_H_Exchanger  77 ksilllallgvlitvvliGlllylllilgiplleallfgailsatdpvvvlailkeegrvperlgtlllgesvlnDavavv 157
                                     i  l ++gv+it+++ + l++l  + g pl+ ++lfgai+s+tdpv++++++ ++++++e++  +l+ges++nD v+++
  gi|13541847|ref|NP_111535.1|  95 YRIASLDTIGVIITALVAAGLFSL--FTGAPLIIGFLFGAIISPTDPVTLIPLF-RRMKISEDISEVLIGESLFNDPVGII 172
                                   *****************9999997..7899************************.************************** PP

                                   CCHHHHHHTX..XXXXTSSSTS...........XHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSCTHHHHHHHHHHHHHHH CS
                Na_H_Exchanger 158 llavllalak..eeaggetsll...........lllliflvvavgglllglvigwllrlitrftdddrelevllvlllall 225
                                   l++v +a++   +     +sl+            ++  fl+ +++  ++g++ig+   ++++ + + ++  +++ l ++++
  gi|13541847|ref|NP_111535.1| 173 LVSVGIAILAphS---VYVSLFssiansisfypGIVAYFLIQVAVPSVVGVAIGFAIIYLNKEI-NFENYLTAILLGVVIF 249
                                   ********96442...333333555777777888888888888889999999999999999997.9999999999999999 PP

                                   HHHHHHTSXXXHHHHHHHHHHHHH....HHHHHTT..HHHH..HHHHHHHHHHHHHHHHHHHHSXHHHHHXXHHHHHHHHH CS
                Na_H_Exchanger 226 aallaellgvsgilgaflaGlvls....eyefsnk..lsek..lesfreglfnplfFvlvGlsldlkvlnnhlsvlilvll 298
                                    + + e + ++   ++ + G++++    +         +ek   e++   l   ++F+l+G s+ ++ ++   + l+ + l
  gi|13541847|ref|NP_111535.1| 250 EFTIFEGISITPFPAIIATGAIVGnfsdK----GIfwQREKnfQENLS-YLSTSIIFLLIGSSFTINEIE--QYILLGIML 323
                                   9***********************63332....322222334445555.899*************99996..9******** PP

                                   HHHHHHTHHHHHHHHHTTTX.......SSXHHHHHHCCCCSS.BHHHHHHHHHHHHHHXHHHH........TT.SSTTTCS CS
                Na_H_Exchanger 299 ilvaillgrilavflllrll.......glslrealiigfgglqrgavalalaalgpalgllar........el.yallivv 363
                                   ++++i+++r++avf+   +        +   +  ++i++ g  rg v ++l  l    gl  +         +    ++++
  gi|13541847|ref|NP_111535.1| 324 TTILIFVVRPAAVFPSILIAdlgkikmKGYYKIVAFISLVGP-RGVVPVVLSTLPYVVGLSYNipilitwgPViGVSALFI 403
                                   ***************888779997765444455668888888.********999888755555555565663334445555 PP

                                   TSXHHHHHHHHHHHH CS
                Na_H_Exchanger 364 vlftvlvqGlslkpl 378
                                   vlf++++q++ ++ +
  gi|13541847|ref|NP_111535.1| 404 VLFSIVFQTIYTP-I 417
                                   5555555555444.3 PP

>> DUF1269  Protein of unknown function (DUF1269)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   1.1      0.41   3.7e+03       6      27 ..     111     133 ..     106     140 .. 0.70
   2 ?    9.0   0.0   0.00018       1.6      27      65 ..     267     306 ..     238     325 .. 0.79
   3 ?   -3.6   0.0       1.6   1.4e+04      55      66 ..     397     408 ..     394     415 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.41
                       DUF1269   6 lwGllvGllflnP.llGaavGAa 27 
                                   ++++l+ l    P ++G ++GA 
  gi|13541847|ref|NP_111535.1| 111 VAAGLFSLFTGAPlIIGFLFGAI 133
                                   56778888888884456666664 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00018
                       DUF1269  27 aaGAlvgalsdvgidddflkelgeklkp.gtsalfllvek 65 
                                   a+GA+vg++sd gi  +  k+++e+l+   ts +fll+ +
  gi|13541847|ref|NP_111535.1| 267 ATGAIVGNFSDKGIFWQREKNFQENLSYlSTSIIFLLIGS 306
                                   79************************98577888888764 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 1.6
                       DUF1269  55 gtsalfllveka 66 
                                   g salf+++ ++
  gi|13541847|ref|NP_111535.1| 397 GVSALFIVLFSI 408
                                   779999987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (432 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       796  (0.0443973); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 3127.79
//
Query:       gi|13541848|ref|NP_111536.1|  [L=242]
Description: NAD synthetase [Thermoplasma volcanium GSS1]
Scores for complete 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  236.8   0.0    2.2e-70  236.5   0.0    1.1  1  NAD_synthase   NAD synthase
    0.00025   19.9   0.1    0.00049   19.0   0.0    1.5  2  tRNA_Me_trans  tRNA methyl transferase
  ------ inclusion threshold ------
      0.022   14.5   0.0       0.03   14.0   0.0    1.1  1  Asn_synthase   Asparagine synthase
      0.041   13.4   0.0       0.12   11.9   0.0    1.7  2  QueC           Queuosine biosynthesis protein QueC
      0.063   13.2   0.0          4    7.4   0.0    2.8  3  TrmB           Sugar-specific transcriptional regulator TrmB
        0.1   12.6   0.0       0.56   10.2   0.0    2.1  2  NCD1           NAB conserved region 1 (NCD1)


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 !  236.5   0.0   7.4e-74   2.2e-70       3     242 .]       9     236 ..       4     236 .. 0.92

  Alignments for each domain:
  == domain 1  score: 236.5 bits;  conditional E-value: 7.4e-74
                                   HHHHHHHHHHHHHCTTSEEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--SSSTTHHHHHHHHHHHHHHTSEEEE---HH CS
                  NAD_synthase   3 eelvdflkeyvkkagakgvvlGlSGGvDSslvaalavkalgkenvlalllPssvsseedvedalalaenlgievktidikp 83 
                                   e++ +fl++ +++   +++v+G+SGG+DSs++  +  k + +en++a+ +P+ +++++d+ d   la  +g+++ t++i++
  gi|13541848|ref|NP_111536.1|   9 ERIGEFLRKIIAD---RKAVIGISGGIDSSVTLGILSKFFLHENIKAVFMPDATTPKSDYDDVDVLASTFGVKYSTVNIQN 86 
                                   4455555555544...688***********99777777777**************************************** PP

                                   HHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHTEEEB---BHHHHTTT-S-TTTTT--SBETTTTS-HHHHHHHHH CS
                  NAD_synthase  84 ivrafeqelkeakedlakgNlkaRiRmailyaianklnllvlgTgnksElvvGyfTkyGDgaadlapiaellKtevkeLak 164
                                   iv +f+++l+    + a gN+k+RiRm++ly++an +n +v+gT n++El++Gy TkyGDg++d++pi++l+K++++e+a+
  gi|13541848|ref|NP_111536.1|  87 IVDTFSKTLSAVD-KGAIGNIKSRIRMIVLYYFANIYNGIVVGTTNRTELLLGYYTKYGDGGCDVEPIEHLYKRDIYEIAR 166
                                   *******998877.899**************************************************************** PP

                                   HTT--HHHHCS--B--SSTT-BHHHHHSS-HHHHHHHHT.HSSSS...HHHHHTTT--HHHHHHHHHHHHHTGGGGSSS CS
                  NAD_synthase 165 elnvPervlkkpPsAdLkpgqtDeeeLgikYdelDeiLk.lvekkkspeeiikekelpaevvekieklvkksehKrklp 242
                                    l+vPe+++kk+P+A+L++gqtDe+e+g++Y+++D+iL+ +++k++ +e+           ++ki +l +ks+hKr+lp
  gi|13541848|ref|NP_111536.1| 167 LLGVPESIIKKKPTAGLWQGQTDEDEIGMPYSKIDDILSsIFDKGELRED---------PDFKKILDLHSKSDHKRRLP 236
                                   ***************************************88888887777.........5799*************998 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   1.6e-07   0.00049       2      73 ..      23      87 ..      22     105 .. 0.76
   2 ?   -3.2   0.0      0.94   2.8e+03     167     186 ..     152     171 ..     151     181 .. 0.61

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.6e-07
                 tRNA_Me_trans  2 kvvvalSgGVDSsvaaallkeqg..yevigvflklweeedeegkeccaeedlkdaervaeklgiplevvdfeke 73
                                  k v+++SgG+DSsv++ +l + +   ++++vf+             + ++d+ d+   a+++g+++++v++++ 
  gi|13541848|ref|NP_111536.1| 23 KAVIGISGGIDSSVTLGILSKFFlhENIKAVFMPDA---------TTPKSDYDDVDVLASTFGVKYSTVNIQNI 87
                                  6689***************99875345666777533.........3457899*****************99875 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 0.94
                 tRNA_Me_trans 167 PlgeltKeevrkiAkeagla 186
                                   P+ +l K+++ +iA+  g++
  gi|13541848|ref|NP_111536.1| 152 PIEHLYKRDIYEIARLLGVP 171
                                   66677777777777665554 PP

>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0     1e-05      0.03      14     110 ..      18     115 ..      15     125 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1e-05
                  Asn_synthase  14 lradvpvGalLSGGlDSSliaalaarqsk.splktFsigfeekgsdeakyakevaehlgtehtelvlteeelldalpdviy 93 
                                     ad++  + +SGG+DSS+   +++++   +++k++ +  ++   ++ +    +a  +g++     ++ + ++d++ ++++
  gi|13541848|ref|NP_111536.1|  18 IIADRKAVIGISGGIDSSVTLGILSKFFLhENIKAVFMPDATTPKSDYDDVDVLASTFGVKY--STVNIQNIVDTFSKTLS 96 
                                   5689999999**************99865356666544445688888888999999999995..55566669999999999 PP

                  Asn_synthase  94 hlee..pfadrsaiplyll 110
                                   ++++  +  ++s i +  l
  gi|13541848|ref|NP_111536.1|  97 AVDKgaIGNIKSRIRMIVL 115
                                   9999776666666666555 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   3.9e-05      0.12       1      70 [.      23      93 ..      23     113 .. 0.82
   2 ?   -1.6   0.0      0.51   1.5e+03     157     176 ..     152     171 ..     150     191 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.9e-05
                                  EEEEE--SSHHHHHHHHHHHHH-..SEEEEEEEESS-TTSHHHHHHHHHHHHT--.-EEEEE-GGGGGGSCG CS
                          QueC  1 kavvllSGGlDSttvlalakkeg..kevealtfdYgqrhkkeleaakkiakelgveehkildldllkelggs 70
                                  kav+ +SGG+DS++ l + +k +  ++++a+ +      k++ + ++ +a+++gv +  +++++ + +  ++
  gi|13541848|ref|NP_111536.1| 23 KAVIGISGGIDSSVTLGILSKFFlhENIKAVFMPDATTPKSDYDDVDVLASTFGV-KYSTVNIQNIVDTFSK 93
                                  79***************99998766789999999888999999999999999999.8888888766554444 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.51
                                   TTTT--HHHHHHHHHHTTHH CS
                          QueC 157 PlidlsKaeivklgkelgvp 176
                                   P+ +l K++i +++  lgvp
  gi|13541848|ref|NP_111536.1| 152 PIEHLYKRDIYEIARLLGVP 171
                                   889999******99999965 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   0.0       1.1   3.3e+03      25      40 ..      68      83 ..      64      84 .. 0.84
   2 ?    2.0   0.0     0.063   1.9e+02      24      39 ..     160     175 ..     156     177 .. 0.84
   3 ?    7.4   0.0    0.0013         4      31      50 ..     192     211 ..     189     222 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.1
                                  HCHHCCCTTSSCHCHH CS
                          TrmB 25 adeiaeelgvprskvY 40
                                  +d +a+  gv +s+v+
  gi|13541848|ref|NP_111536.1| 68 VDVLASTFGVKYSTVN 83
                                  6778999999999996 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.063
                                   HHCHHCCCTTSSCHCH CS
                          TrmB  24 tadeiaeelgvprskv 39 
                                   +++eia+ lgvp+s +
  gi|13541848|ref|NP_111536.1| 160 DIYEIARLLGVPESII 175
                                   689*********9966 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.0013
                                   CTTSSCHCHHHHHHHHHHCT CS
                          TrmB  31 elgvprskvYevLrsLedkG 50 
                                   e+g p+sk+ ++L+s  dkG
  gi|13541848|ref|NP_111536.1| 192 EIGMPYSKIDDILSSIFDKG 211
                                   799***************99 PP

>> NCD1  NAB conserved region 1 (NCD1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00019      0.56      16      54 ..     132     170 ..     126     176 .. 0.83
   2 ?   -1.1   0.0      0.65   1.9e+03      44      68 ..     218     239 ..     212     240 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00019
                          NCD1  16 ranL.lqYydvliaqGGDdveqlleaeeeefleimelvGm 54 
                                   r++L l Yy+++   GG dve + ++ ++++ ei  l+G+
  gi|13541848|ref|NP_111536.1| 132 RTELlLGYYTKY-GDGGCDVEPIEHLYKRDIYEIARLLGV 170
                                   555516777776.789**********************97 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.65
                          NCD1  44 efleimelvGmaskPLhvrRlqkaL 68 
                                   +f +i+    + sk  h rRl  +L
  gi|13541848|ref|NP_111536.1| 218 DFKKIL---DLHSKSDHKRRLPYSL 239
                                   455554...4689999999997665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-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: 00:00:00.44
# Mc/sec: 1668.66
//
Query:       gi|13541849|ref|NP_111537.1|  [L=281]
Description: 5,10-methylene-tetrahydrofolate dehydrogenase [Thermoplasma volcanium GSS1]
Scores for 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-52  174.6   0.6    1.4e-51  174.0   0.6    1.3  1  THF_DHG_CYH_C  Tetrahydrofolate dehydrogenase/cyclohydrolase,
    2.3e-25   89.1   1.8    3.4e-25   88.5   0.9    1.7  2  THF_DHG_CYH    Tetrahydrofolate dehydrogenase/cyclohydrolase,
  ------ inclusion threshold ------
      0.052   13.2   0.0      0.085   12.5   0.0    1.3  1  DDE_Tnp_4      DDE superfamily endonuclease


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 !  174.0   0.6   2.3e-55   1.4e-51       2     159 ..     120     274 ..     119     275 .. 0.97

  Alignments for each domain:
  == domain 1  score: 174.0 bits;  conditional E-value: 2.3e-55
                                   HHHHHHHHTT--SS--HHHHHHHHHHHHCT---TT-EEEEE---TTTHHHHHHHHHCTT-EEEEE-TTSCCHHHHHCCSSE CS
                 THF_DHG_CYH_C   2 plnlgrlvkgeeallpctpkgvvellketgielegkkvvvvGrsnivgkplallLleknatVtvchsktkdlaeitreadi 82 
                                   p+n g ++ ++e l+p+t+++vv++lk +g   e  ++++++rs +vg+pl++++l+++ tV++chskt d+++i + + i
  gi|13541849|ref|NP_111537.1| 120 PYNQGSIAINREFLVPATAMAVVDILKYYGY--EKTTATIINRSPVVGRPLSMMMLNRDYTVSICHSKTPDIRSIAKASKI 198
                                   89***************************95..67899******************************************* PP

                                   EEE-SS-TT-B-GGGS-TT-EEEE---EEC-TTEEE-SB-HHHHCTTSSEE--TTTSCHHHHHHHHHHHHHHHHHCH CS
                 THF_DHG_CYH_C  83 vvvavGkpelikaemvkegavviDvGinrvekgklvGDvdfeevkevasaitPvpgGVGpmTvamllkntleaakrq 159
                                   +vvavG+p++++  +v e +vviDvGin v ++k++GD+df++v+e+++a+tPvpgGVGp+T++ +l+n+++aa+ q
  gi|13541849|ref|NP_111537.1| 199 IVVAVGRPGFLDDTYVTESSVVIDVGINYV-QDKVIGDIDFDKVSEKVEAVTPVPGGVGPITATNILSNLVKAAEYQ 274
                                   ******************************.******************************************9976 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 !   88.5   0.9   5.8e-29   3.4e-25       1     116 []       5     116 ..       5     116 .. 0.97
   2 ?   -1.7   0.0      0.56   3.3e+03      41      79 ..     209     246 ..     182     249 .. 0.59

  Alignments for each domain:
  == domain 1  score: 88.5 bits;  conditional E-value: 5.8e-29
                                   E--HHHHHHHHHHHHHHHHHHHHHHT---EEEEEEES--HHHHHHHHHHHHHHHHTT-EEEEEEE-TT--HHHHHHHHHHH CS
                   THF_DHG_CYH   1 lldGkalakeireelkeeveklkekgvkpkLavilvgddpasevYvrnkkkaceevGieseliklpedvseeellklieel 81 
                                   ll+G+++a++  eelke++ek+    v+p+L+ ++vg+  a+++Y+r k k+ +++G ++ l k+ ed++++el++ ieel
  gi|13541849|ref|NP_111537.1|   5 LLKGEEIAEKKAEELKERIEKMG---VSPRLVLLQVGNYSAATIYARAKIKRGKKIGADVVLEKY-EDLTKQELVRRIEEL 81 
                                   699****************9875...69*************************************.89999********** PP

                                   HH-TT--EEEE-SS-STTS-HHHHHCCS-GGGBTT CS
                   THF_DHG_CYH  82 neddsvdGilvqlPlpkhidekaileaispeKDVD 116
                                   ++d++v+Gi+v  Plpk id   i+++i + KDVD
  gi|13541849|ref|NP_111537.1|  82 SADKDVNGIMVENPLPKTIDYYDIVKSIPYYKDVD 116
                                   **********************************9 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.56
                                   HHHHHHHHHHHHHHHTT-EEEEEEE-TT--HHHHHHHHH CS
                   THF_DHG_CYH  41 asevYvrnkkkaceevGieseliklpedvseeellklie 79 
                                      +Yv   +  + +vGi++ + k+  d+  +++ +++e
  gi|13541849|ref|NP_111537.1| 209 LDDTYVTE-SSVVIDVGINYVQDKVIGDIDFDKVSEKVE 246
                                   45566543.445566777777777766666666666665 PP

>> DDE_Tnp_4  DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   1.4e-05     0.085      39      95 ..     195     252 ..     190     280 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.4e-05
                     DDE_Tnp_4  39 ngkiifvskgypGsvsDkeilensgllka.lkeavkpgdvilaDkgFk.lsekl..lvpyk 95 
                                     kii+v +g+pG ++D+ ++e+s +++  ++     +d +++D +F+ +sek+  ++p++
  gi|13541849|ref|NP_111537.1| 195 ASKIIVVAVGRPGFLDDTYVTESSVVIDVgIN---YVQDKVIGDIDFDkVSEKVeaVTPVP 252
                                   5799*********************9988233...2349******9986677554356665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       628  (0.0350271); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2051.08
//
Query:       gi|13541850|ref|NP_111538.1|  [L=361]
Description: glucose 1-dehydrogenase [Thermoplasma volcanium GSS1]
Scores for complete 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-23   81.1   0.0    9.8e-23   80.8   0.0    1.1  1  Glu_dehyd_C  Glucose dehydrogenase C-terminus
    1.7e-09   37.5   0.0    2.6e-09   36.9   0.0    1.3  1  ADH_N        Alcohol dehydrogenase GroES-like domain
    0.00014   21.8   0.0     0.0006   19.8   0.1    2.0  2  ADH_zinc_N   Zinc-binding dehydrogenase
  ------ inclusion threshold ------
      0.025   14.7   0.1      0.066   13.3   0.0    1.7  1  DapB_N       Dihydrodipicolinate reductase, N-terminus
      0.038   13.5   0.0      0.065   12.8   0.0    1.4  1  IlvN         Acetohydroxy acid isomeroreductase, NADPH-bindin


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 !   80.8   0.0   2.7e-26   9.8e-23       2     211 ..     150     359 ..     149     360 .. 0.86

  Alignments for each domain:
  == domain 1  score: 80.8 bits;  conditional E-value: 2.7e-26
                   Glu_dehyd_C   2 dvgvLvEPisiveKaielaea..srsafewep.....esalvlGaGslGLLalalleaeerglervyvlgrrdrpdptidl 75 
                                   +++vL+EP+  v Ka+e       rs f+ +      ++ +v+G+Gs  +L    +  ++rg++ v++++r+d+++ ++++
  gi|13541850|ref|NP_111538.1| 150 KIAVLTEPLKNVMKAFEVFDVvsKRSIFQNDDstfigKKMVVIGSGSEAFLY-SFVG-KDRGFD-VTMVNRHDETENKMKM 227
                                   689**************9776214555543331111156789*********9.4444.68***8.99************** PP

                   Glu_dehyd_C  76 veelGatYvdsretpvdeipeaseemdlvvEaTGsakhafeaiealapnGvaaLlGvpeds.evevdggelhrelvleNka 155
                                   +++ G  + +     ++++p    ++dl+v++ G +  +f+ +++++ nGv++L G   +     v+g+++   +v +N  
  gi|13541850|ref|NP_111538.1| 228 MDDFGVGFSNY----LKDMP---DKIDLLVDTSGDPSTIFKFVKKVNNNGVVILFGTNGKApGYPVNGEDID-YIVERNIT 300
                                   ********985....66665...678********************************98768889888875.68****** PP

                   Glu_dehyd_C 156 lvGsvNanrrhfeaavdtLaalpesl...ldelvtkvvdldeleeAfedddetiKtvve 211
                                   + Gsv a   h+ +a+d+L++  ++    +++++t +++ +e +  f++ + +iKtv++
  gi|13541850|ref|NP_111538.1| 301 IAGSVDAAKIHYVQALDSLSNWYHRHpqtIKDIITYEAKPEETNIFFQKPKGEIKTVIK 359
                                   ********************9888766669***************************96 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 !   36.9   0.0   7.2e-13   2.6e-09       3     109 .]      30     143 ..      28     143 .. 0.83

  Alignments for each domain:
  == domain 1  score: 36.9 bits;  conditional E-value: 7.2e-13
                                   EEEEEEEEEEE-HHHHHHHTTS....TTTTSSSSEE---EEEEEEEEESTT-CS--TT-EEEE-SEEE-SSSHHHHTT-GG CS
                         ADH_N   3 evlikvkaagiCgsDlhilkgg....kelevklplilGHEivGeveevgpevkklkvGdrVvvepliscgeCaaCkegeen 79 
                                   e+ +k  + giCg+D   + g      ++e +  l+lGHE+  +v +v ++ + +k Gd Vv   +   g+C +C+ g+++
  gi|13541850|ref|NP_111538.1|  30 EAKLKPVYIGICGTDRGEVAGAlsftYNPEGENFLVLGHEALLQVLDVSDN-NYIKRGDFVVP-LVRRPGKCVNCRIGRQD 108
                                   567788899************8555445555555**************976.57******998.77778************ PP

                                   G-....TTBEETTTS.S-SSSBSEEEECGGGEEEE CS
                         ADH_N  80 lC....eeakllgvs.ldGgfaeyvvvpekklvkl 109
                                    C    ++++  g++ l+G + + ++ + ++lvk+
  gi|13541850|ref|NP_111538.1| 109 NCsigdPDKHEAGITgLHGFMRDVIYDDIQNLVKV 143
                                   **9999666666666788***99999999999986 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.78   2.8e+03      78     125 ..      92     137 ..      87     142 .. 0.77
   2 !   19.8   0.1   1.7e-07    0.0006      46     124 ..     235     315 ..     186     321 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.78
                                   CEEEEEEEEECSCTSSEEEEEHHHHHHTT-EEEEE-SSCHHHHHHHHH CS
                    ADH_zinc_N  78 llkpgGrlvvvGggkgeeefdlrnlllkeksilGsllgslreefkeal 125
                                   l+++ G++v + +g +++ +++++  ++e  i+G ++   r+ +++ +
  gi|13541850|ref|NP_111538.1|  92 LVRRPGKCVNCRIGRQDN-CSIGDPDKHEAGITGLHGFM-RDVIYDDI 137
                                   678889999999888888.99999999999999999888.66655544 PP

  == domain 2  score: 19.8 bits;  conditional E-value: 1.7e-07
                                   HHHHHHHHTTTSSEEEEEESSCSHHHHHHHHHCEEEEEEEEECSC.TSSEEE.....EEHHHHHHTT-EEEEE-SSCHHHH CS
                    ADH_zinc_N  46 lverikeltggegvdvvfecvGsgatleaalkllkpgGrlvvvGg.gkgeee.....fdlrnlllkeksilGsllgslree 120
                                   ++ ++k++   +++d+ ++++G+++t+   +k ++ +G + ++G+ gk +        d+ +++ ++++i Gs+ + + + 
  gi|13541850|ref|NP_111538.1| 235 FSNYLKDMP--DKIDLLVDTSGDPSTIFKFVKKVNNNGVVILFGTnGKAP-GypvngEDIDYIVERNITIAGSVDAAKIHY 312
                                   777889999..59*******************************963333.24667889999***********98774444 PP

                                   HHHH CS
                    ADH_zinc_N 121 fkea 124
                                   ++ a
  gi|13541850|ref|NP_111538.1| 313 VQ-A 315
                                   43.4 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   1.8e-05     0.066      45     100 ..     223     279 ..     199     292 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.8e-05
                                   HHHSSSS--S-BEBSSHHHHHHH-SEEEE-S.-HHHHHHHHHHHHHTT-EEEE--SS CS
                        DapB_N  45 gellglgklgvavtddleevlekadvliDFT.tpeavlenlklalekgvklViGTTG 100
                                    ++  ++  gv +++ l+++ +k d l+D +  p+ + + +k + ++gv + +GT G
  gi|13541850|ref|NP_111538.1| 223 NKMKMMDDFGVGFSNYLKDMPDKIDLLVDTSgDPSTIFKFVKKVNNNGVVILFGTNG 279
                                   2344456899********************988**********************98 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   1.8e-05     0.065       4      93 ..     186     275 ..     183     293 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.8e-05
                                   TS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEHHHHHHT-SEEEE-S-HHHHHHHHHHHTGGG CS
                          IlvN   4 gkkiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevltvaeavkkadvvmiliPDelqkevyeeeiepn 84 
                                   gkk++viG Gs +   +   +d g+dv++ +r++++  k  + + f v   + + +  d + +l+  +   + + + +++ 
  gi|13541850|ref|NP_111538.1| 186 GKKMVVIGSGSEAFLYSFVGKDRGFDVTMVNRHDETENKMKMMDDFGVGFSNYLKDMPDKIDLLVDTSGDPSTIFKFVKKV 266
                                   89*********************************9999999999999888888888888887776665555555556655 PP

                                   --TT-EEEE CS
                          IlvN  85 lkegkalaf 93 
                                    ++g ++ f
  gi|13541850|ref|NP_111538.1| 267 NNNGVVILF 275
                                   555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (361 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       420  (0.0234257); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 2414.75
//
Query:       gi|13541851|ref|NP_111539.1|  [L=541]
Description: pyruvate kinase [Thermoplasma volcanium GSS1]
Scores for 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-88  295.0   8.1      6e-88  295.0   8.1    1.5  2  PK         Pyruvate kinase, barrel domain
    8.4e-20   71.2   0.0    2.4e-19   69.7   0.0    1.8  1  PK_C       Pyruvate kinase, alpha/beta domain
    0.00031   20.0   0.5    0.00064   18.9   0.1    1.7  2  HpcH_HpaI  HpcH/HpaI aldolase/citrate lyase family


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 !  295.0   8.1     1e-91     6e-88       3     343 ..       2     322 ..       1     327 [. 0.94
   2 ?   -4.3   0.0         1   6.2e+03     114     129 ..     515     530 ..     504     535 .. 0.79

  Alignments for each domain:
  == domain 1  score: 295.0 bits;  conditional E-value: 1e-91
                                   -SEEEEEESCCCTSHHHHHHHHHHTEEEEEEETTSS-HHHHHHHHHHHHHHHHTTTTS-EEEEE---S-EBB--BTTCSSS CS
                            PK   3 rtkivctlGPasesvekleklieaGlnvvrlnfshGsheehqerienvreaekklgkkvaillDtkGpeirtgllkdgkkd 83 
                                   +tkiv+t+GPase+   l++++++Gl ++r+n +h +  + ++ ++++r     ++ +v++++D+kGpe+rtg++ +g+  
  gi|13541851|ref|NP_111539.1|   2 KTKIVATVGPASEDPSILKQMVKNGLSLIRINSAHAEISYVAKIVKEMRD----INPDVGVMVDLKGPELRTGTFPGGS-- 76 
                                   89*********************************999887777766665....56789******************99.. PP

                                   EEE-TTSEEEEE-SCTCTTTBBTTEEEBS-TTHHHHS-TTEEEEETTTTEEEEEEEEETTEEEEEEESS-EEE-SS-BEE- CS
                            PK  84 ielkegdklkvsldeklkeegdeelialdyknivkdvevGktilvdDGllslkvlevdeekeleveventgvlgskkgvnl 164
                                   +++++g+k ++              i+l+ ++ + ++++G+++l+ DG ++++v ++++   ++  +en+gvl ++  vn+
  gi|13541851|ref|NP_111539.1|  77 LRISKGNKYTIGK-----------EITLNNEKAIGNIQTGDKVLMSDGEVEFTVDSTSP---IVLIAENDGVLRDRSRVNV 143
                                   9999999888543...........46777778899******************988765...66899************** PP

                                   TTS---S-SS-HHHHHHHHHHHHCT-SEEEETTE-SHHHHHHHHHHHTCCCTTSEEEEEE-SCHHHHTHHHHHHHSSEEEE CS
                            PK 165 pgtkvdlpalsekDkadlrfgvkqgvdliaasfvrkasDvkevrevleeegkeikiiakienqegvenldeileasDgimv 245
                                   pg  v++ +++e+Dk+ +  g+kqgvd+ a+sfv++a++v+++r+ + e+g +  iiakie + g++n++ i++asDgimv
  gi|13541851|ref|NP_111539.1| 144 PGRYVEIGSITERDKSFVIEGIKQGVDFFALSFVQNAENVNSLRDFIIENGGNQYIIAKIETKSGLDNIESIVQASDGIMV 224
                                   ********************************************************************************* PP

                                   EHHHHHHHSTCCCHHHHHHHHHHHHHHHT--EEEESSTTGGGGTSSS--HHHHHHHHHHHHHT-SEEEESHHHHTSS-HHH CS
                            PK 246 arGDlGieipaekvllvqkklikkcnlagkpvitatqmlesmiknPrptraevsDvanavlDGtDavmLsgetakGkyPve 326
                                   arGDlG+e+p ++v+++qkk+ik +   g   i+atq+lesm++n  ptrae+sD++na++D +Da+mLs e+a GkyP+ 
  gi|13541851|ref|NP_111539.1| 225 ARGDLGVELPLKEVVMAQKKIIKISHEDGDFTIVATQVLESMVNNAFPTRAEISDITNAIIDNADALMLSEESAIGKYPAL 305
                                   ********************************************************************************* PP

                                   HHHHHHHHHHHHHHTS- CS
                            PK 327 avkamaevaleaekalk 343
                                   av+++ +v+   e+ ++
  gi|13541851|ref|NP_111539.1| 306 AVQTLRDVSDYVENLVD 322
                                   ********998888765 PP

  == domain 2  score: -4.3 bits;  conditional E-value: 1
                                   TTHHHHS-TTEEEEET CS
                            PK 114 knivkdvevGktilvd 129
                                   + + + ++ G++i++d
  gi|13541851|ref|NP_111539.1| 515 TRLARTINEGERIYID 530
                                   5688999999999998 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 !   69.7   0.0   4.1e-23   2.4e-19       2     117 .]     337     448 ..     336     448 .. 0.92

  Alignments for each domain:
  == domain 1  score: 69.7 bits;  conditional E-value: 4.1e-23
                                   HHHHHHHHHHHHHT-SEEEEE-SSSHHHHHHHHT-TSSEEEEEESHHHHHHHHHHCTTEEHHH.HHHHH...TTSHHHHHH CS
                          PK_C   2 aiakaaveaaeelgakaIvvltesGetArliskyrpkvpiiavtpneltarqlalyrGvypvlvekaktaestdellreav 82 
                                   ++akaa  ++ +++ + Iv+lt++G+t+++is +rpk+ ++a t +++ +r+l++y Gv+p++++++++    +  +++++
  gi|13541851|ref|NP_111539.1| 337 SVAKAAKVLSDDINSNGIVALTHTGSTVKMISSLRPKALVYAGTVDDSLSRKLNIYFGVVPLHLKRDSE----SLSFADLT 413
                                   699************************************************************975433....2246777* PP

                                   HHHHHTTSS-STSEEEEEE-SSSS..SS--EEEEE CS
                          PK_C  83 kvakeaglvkkgdevvvtaGtpkgesgttNtlrVv 117
                                   ++ +++ + k+gd++vvt+G+p  + g tN +rV+
  gi|13541851|ref|NP_111539.1| 414 EYILKSAFFKSGDKIVVTSGDPYFTFGGTNDVRVM 448
                                   ***********************99*****99995 PP

>> HpcH_HpaI  HpcH/HpaI aldolase/citrate lyase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.1   1.1e-07   0.00064      80     147 ..     164     225 ..     149     257 .. 0.82
   2 ?   -3.4   0.0      0.73   4.3e+03      15      33 ..     281     299 ..     276     317 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.1e-07
                                   HHHTTSSEEEESS--SHHHHHHHHHHTSHTTTS---HCCC-EEEEEE-SHHHHHTHHHHH.TSTTEEEE CS
                     HpcH_HpaI  80 vldlgaqvvlvPkvetaeealevvsalrepekgirganketrllaqiEsaegvknaeeIa.avegldgv 147
                                    +++g++ + + +v++ae++  +   + e         ++  ++a iE++ g++n+e+I+ a++g++++
  gi|13541851|ref|NP_111539.1| 164 GIKQGVDFFALSFVQNAENVNSLRDFIIENG-------GNQYIIAKIETKSGLDNIESIVqASDGIMVA 225
                                   5778888888889999999999988888887.......8999******************888777653 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 0.73
                                   HHHCTC--SEEEEESSTSS CS
                     HpcH_HpaI  15 ekaaiagaDsvliDlEdav 33 
                                   ++a i +aD++++  E a 
  gi|13541851|ref|NP_111539.1| 281 TNAIIDNADALMLSEESAI 299
                                   6778889999999888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (541 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.47
# Mc/sec: 3465.38
//
Query:       gi|13541852|ref|NP_111540.1|  [L=493]
Description: NAD-dependent aldehyde dehydrogenase [Thermoplasma volcanium GSS1]
Scores for complete 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-161  537.8   0.0     2e-161  537.6   0.0    1.0  1  Aldedh    Aldehyde dehydrogenase family
     0.0015   17.7   0.0     0.0025   16.9   0.0    1.3  1  LuxC      Acyl-CoA reductase (LuxC)
  ------ inclusion threshold ------
      0.024   14.1   0.1      0.045   13.3   0.1    1.4  1  DUF2884   Protein of unknown function (DUF2884)


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 !  537.6   0.0  3.4e-165    2e-161       1     462 []      11     473 ..      11     473 .. 0.98

  Alignments for each domain:
  == domain 1  score: 537.6 bits;  conditional E-value: 3.4e-165
                                   EET-SS.SEEEEEETTTCEEEEEEE-B-HHHHHHHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHTHHHHHHHHHHHH- CS
                        Aldedh   1 wveses.etievinPatgeviakvpaataedvdaavaaAkeafkawaklpaeeRaeiLrkaadlleerkeelaeletletG 80 
                                   wv+s++ +t+ ++nP+tgevi+k++aa+++dvd+a++aA++af++w +l   eR++i++ka +l+ee+++el +++ +e+G
  gi|13541852|ref|NP_111540.1|  11 WVDSSNgDTLTKYNPVTGEVIGKFAAASRDDVDRAFDAAEDAFQKWMDLGSVERSKIIYKAKELIEENRKELENIIIQENG 91 
                                   999999788************************************************************************ PP

                                   --HHHHHHHHHHHHHHHHHHHHHHHHHSEEEEEE.CTTEEEEEEEEE-SEEEEEE-SSSCCHHHHHHHHHHHHTT-EEEEE CS
                        Aldedh  81 kplaearaeveeaidvlryyaelaeklegevlps.segklalvrrePlGvvgaItPWNfPlllaawklapalaaGNtvvlK 160
                                   kp++ea++ev+ ++d ++yyae+a+kl+gev++  +++++++ ++ P+G+v+a+tPWNfP+ ++a+klapal++GNtv+lK
  gi|13541852|ref|NP_111540.1|  92 KPVKEAAEEVDGVLDQMQYYAEWARKLNGEVVEGtTNHRKIFQYKVPYGTVVALTPWNFPAGMVARKLAPALLTGNTVILK 172
                                   **********************************778899999999*********************************** PP

                                   E-TTSHHHHHHHHHHHHHTTS-TTSEEE--SSTCCHHHHHHH-TTESEEEEES-HHHHHHHHHHHHCTTSEEEEEE---EE CS
                        Aldedh 161 PaeetplsalllaelfeeaglPkgvlnvvtgsgsevgealvehpevdkvsftGstevgrkiakaaaknlkrvtlElGGknp 241
                                   P+++tp sa  +++ f +ag+Pkg+ln++tg+gs +g+++veh++v+++++tGst++g++i+++a++n+ +++lElGGk+p
  gi|13541852|ref|NP_111540.1| 173 PSSDTPGSAEWIVKKFIQAGVPKGALNYITGRGSVIGDYIVEHKKVALITMTGSTSTGQRIMQKASANMAKLMLELGGKAP 253
                                   ********************************************************************************* PP

                                   EEE-TTSHHHHHHHHHHHHHHGGGGTSTTSEEEEEEEHHHHHHHHHHHHHHHHT--BS-TTSTT-SB---SSHHHHHHHHH CS
                        Aldedh 242 livledaDldkaveaivkgafgnaGQvCiaasrllvqesiydefveklveaakklkvgdpldedtdvGPliseaqlekvek 322
                                   ++v++daD+++a++ ++++ ++naGQ Ciaa+rl+v+e+iyd f++k+ve  kk+ vgdp  +  d+GPli+  +l+  e+
  gi|13541852|ref|NP_111540.1| 254 FMVWKDADINNALKTLLWAKYWNAGQSCIAAERLYVHEDIYDTFINKFVELSKKIVVGDP--SRADMGPLINTTALKGTEE 332
                                   ************************************************************..569**************** PP

                                   HHHHHHHTTSEEEE-TT..E.SB-SSSTTEE--EEEES-TTTSHHHHS---SSEEEEEEESSHHHHHHHHHSSSEESEEEE CS
                        Aldedh 323 yveeakeegaklllGge..reeaglekgyfvePtvlanvtpdmriaqeEiFGPVlsvikfkdeeeaieiaNdteyGLaagv 401
                                   +veeake ga++l+Gg+    +  +++gyf+ Pt+++nv+++++i+qeEiF+PV+   k++d+ee+ ++aNd++yGLa+++
  gi|13541852|ref|NP_111540.1| 333 VVEEAKESGARILYGGSkpDLSGPYKNGYFFLPTIIDNVDQKSKIFQEEIFAPVIGARKVSDVEEMYSLANDSKYGLASYL 413
                                   ****************998778899******************************************************** PP

                                   E-SBHHHHHHHHHHS-SSEEEESSSST--TTTSEB--CGGGEES-BSHHHHHHHTEEEEEE CS
                        Aldedh 402 ftkdleraervaerleaGnvyiNdsttgaaealpfgGvkqSglGreggkegleeytevktv 462
                                   ftkd++ ++++aer+++G++yiN +   a +   ++G++ +g   eg+++g+ ey+++k++
  gi|13541852|ref|NP_111540.1| 414 FTKDPNLIFEAAERIRFGELYINMPGPEASQG-YHTGFRLTGQAGEGSRYGILEYLKIKNI 473
                                   *************************9999988.*************************986 PP

>> LuxC  Acyl-CoA reductase (LuxC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   4.1e-07    0.0025      81     247 ..     130     291 ..     122     310 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 4.1e-07
                          LuxC  81 eksyekaqprglvlhvlsgNvpl.lpvmsilqglLvknvnllkvSssdpflaaallksladvdenh....tladslsvvyf 156
                                    k ++  +p g v+ +++ N p  +    ++ +lL++n  +lk+Ss+ p+ a  ++k++++    +     ++ + sv+  
  gi|13541852|ref|NP_111540.1| 130 RKIFQYKVPYGTVVALTPWNFPAgMVARKLAPALLTGNTVILKPSSDTPGSAEWIVKKFIQAGVPKgalnYITGRGSVI-- 208
                                   4679999*************9961555689*****************************99876532333444444444.. PP

                          LuxC 157 ksgdtkleeeiv..qnaDvvvawGgeeaikaise..klkpgkqlikfGakvSfavvdkealeeealdkaaeraAkDiivfd 233
                                           + iv  +++  + + G+ ++ + i +   ++  k +++ G k  f+v   +     ++++a++ +        
  gi|13541852|ref|NP_111540.1| 209 -------GDYIVehKKVALITMTGSTSTGQRIMQkaSANMAKLMLELGGKAPFMVWKDA-----DINNALKTLLWAKYWNA 277
                                   .......4444422334567778888888888773334444567778888888776444.....46666665554444445 PP

                          LuxC 234 QqAClspqvvfvek 247
                                    q+C+++  ++v +
  gi|13541852|ref|NP_111540.1| 278 GQSCIAAERLYVHE 291
                                   56777777777765 PP

>> DUF2884  Protein of unknown function (DUF2884)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   7.5e-06     0.045      31     119 ..       2      92 ..       1     112 [. 0.78

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 7.5e-06
                       DUF2884  31 dgqLfvdgkkveLsadqqqaleqyseeirqqvPevaelasdgvdlAsdaldevltellg....edsevaeklktkldelka 107
                                   dg+L++dg++v+ s+     l++y+  + +++ + a+  +d vd A da ++++++ ++    e s+   k k++++e ++
  gi|13541852|ref|NP_111540.1|   2 DGKLYIDGQWVDSSNG--DTLTKYNPVTGEVIGKFAAASRDDVDRAFDAAEDAFQKWMDlgsvERSKIIYKAKELIEENRK 80 
                                   699********86655..67***********************************99662222445555666777777777 PP

                       DUF2884 108 rvkekfykdgdk 119
                                   ++++ + ++++k
  gi|13541852|ref|NP_111540.1|  81 ELENIIIQENGK 92 
                                   777777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (493 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       636  (0.0354733); expected 358.6 (0.02)
Passed bias filter:                      539  (0.030063); 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: 0.71u 0.40s 00:00:01.10 Elapsed: 00:00:00.55
# Mc/sec: 2694.84
//
Query:       gi|13541853|ref|NP_111541.1|  [L=237]
Description: indole-3-glycerol-phosphate synthase [Thermoplasma volcanium GSS1]
Scores for complete 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-34  117.2   0.0    8.8e-34  116.8   0.0    1.1  1  IGPS      Indole-3-glycerol phosphate synthase


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 !  116.8   0.0   4.9e-38   8.8e-34      31     245 ..      20     225 ..       6     232 .. 0.87

  Alignments for each domain:
  == domain 1  score: 116.8 bits;  conditional E-value: 4.9e-38
                                   SS-SS-HHHHCHCH..TTS-EEEEEE-SEETTTEESBSS--HHHHHHHHTTT.-SEEEEE--CCCC---CCHHHHHHHH-S CS
                          IGPS  31 akpkrsfaeaLres..ekklaliaEvKkaSPskgliredfdpaeiAkkyeeagAsaiSVLteekyFqGsledLrevrqavs 109
                                   ++  +s++e++ e   + k ++iaE+K+ SPs   ++ d+ ++++ +   e   + +S+Lte+++F+Gs++d+  v++  +
  gi|13541853|ref|NP_111541.1|  20 RRGIISLKERIIELnrSGKRGVIAEYKRRSPSG--LKVDYSIEDYLSYVMEHRIAGLSILTEPSFFNGSFQDVV-VAHRYN 97 
                                   55567788887766558899************9..88888887765555555599*****************86.77889* PP

                                   S-EEEES---SHHHHHHHHHCT-SEEEEECCCS-HHHHHHHHHHHCCTT-EEEEEESSHHHHHHHHHTT-SEEEEESEETT CS
                          IGPS 110 lpvlrKdFiideyqieearalgadaiLLivkvledeeleelaeaakslglevLvEvhdeeeleralklgakiiGvNnRnLk 190
                                   +p+l KdF+ d+  ++   ++g da+L+i+ +l+ e +++++e a++lg++vL E h+++ l+r    +  +iG N R+L+
  gi|13541853|ref|NP_111541.1|  98 IPILVKDFVPDSEFVDYGFNAGGDAVLVILDFLDYESIKRIVERAADLGMDVLEEFHNQDALKRQYIRDNVMIGYNRRDLT 178
                                   ********************************************************************************* PP

                                   TTEE-CHHHHHHCHCC-TTSEEEEESSS-SHHHHHHHCCTT-SEEEESHHHHC-T CS
                          IGPS 191 tlevdlntteeLaklvpkdvllvaeSGiktredveklkeegvnafLvGeslmrqe 245
                                   +l +d  +  + + +     + + eSGi+  ++v++l  + +++ L+G+s+++++
  gi|13541853|ref|NP_111541.1| 179 NLLMDE-KIPDFSGE-----VRILESGIS-IDNVKNLDLK-FQGYLIGTSILKKD 225
                                   *99883.44445554.....4599****7.678****999.**********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       369  (0.0205812); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 1405.77
//
Query:       gi|13541854|ref|NP_111542.1|  [L=183]
Description: anthranilate synthase component II [Thermoplasma volcanium GSS1]
Scores for complete 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  137.4   0.0      5e-40  137.3   0.0    1.0  1  GATase         Glutamine amidotransferase class-I
    3.9e-07   30.1   0.1    3.5e-06   26.9   0.1    2.0  1  Peptidase_C26  Peptidase C26
    0.00013   21.1   0.1      0.029   13.5   0.0    2.1  2  GATase_5       CobB/CobQ-like glutamine amidotransferase doma
  ------ inclusion threshold ------
       0.16   12.2   0.6        5.1    7.3   0.2    2.6  2  DUF4143        Domain of unknown function (DUF4143)
       0.16   11.8   0.0       0.45   10.3   0.0    1.7  2  DJ-1_PfpI      DJ-1/PfpI family


Domain annotation for each model (and alignments):
>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.3   0.0   1.4e-43     5e-40       2     187 ..       5     181 ..       4     183 .] 0.92

  Alignments for each domain:
  == domain 1  score: 137.3 bits;  conditional E-value: 1.4e-43
                                   EEESSTSTHHHHHHHHHHTT-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTT....TTTHHHHHHHHCTSTS-EEEET CS
                        GATase   2 liDnydsvtenlvhalvelgvkvevvpidasaeeilellknpdgilvsgGpgspg....vegkieaikearenkiPiLGIC 78 
                                   ++Dn+ds+++nl  +l+e++++v+vv++d+  +     ++++d+i++s+Gpgsp     ++ +++++ +    + P+LGIC
  gi|13541854|ref|NP_111542.1|   5 VVDNHDSFVYNLYYYLREMNIEVDVVENDKLVD-----ASGYDKIIISPGPGSPLnardRGRTLDVVDK---FDGPVLGIC 77 
                                   89**************************95433.....459*************995555555555555...555****** PP

                                   HHHHHHHHHTTTEEEEEECEEEEEEEEEEEETTTCGGTTTTSEEEEEEEEEEEEESGCHHHTTEEEEEEEETTEEEEEEEE CS
                        GATase  79 LGmQllaiefgrkvvkekekehhggtmrlgddetallyglknevierhrHryevnpkelepaglevtakseddeelmeiie 159
                                   +G+Qlla+ +g ++  ++ +++hg   r+++++++l+ g ++++++ ++H++++ p    ++++ev a+se+d+ +m++  
  gi|13541854|ref|NP_111542.1|  78 FGHQLLAYHLGSQISVAR-RPYHGEIDRIKHNGSSLYLGIPDSFDAIRYHSLVISP----NKNIEVDAVSETDGNIMGFHS 153
                                   ******************.9***********************************9....999****************** PP

                                   ETTTEEEESSBTTSTTSTTHHHHHHHHH CS
                        GATase 160 kknpfvgvQFHPEststpegpellfnfl 187
                                    + +++g+QFHPEs  t  g+++l+nf+
  gi|13541854|ref|NP_111542.1| 154 VDGRIYGIQFHPESYFTSVGKQILKNFV 181
                                   **************************96 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   0.1   9.8e-10   3.5e-06     106     216 .]      71     166 ..      65     166 .. 0.81

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 9.8e-10
                 Peptidase_C26 106 vPilgiCrGlqllnvalGGtlyqdieeqsgltdhreheqsaashavkvekgsllaellgseeievnslHhqaikelaeelr 186
                                    P+lgiC G+qll+  lG ++  + +               +  ++k + +sl+  +    +++   +H+  i+  +++++
  gi|13541854|ref|NP_111542.1|  71 GPVLGICFGHQLLAYHLGSQISVARR-----PY------HGEIDRIKHNGSSLYLGIPD--SFDAIRYHSLVIS-PNKNIE 137
                                   5************8888866654433.....22......33456788888888888877..999999**99886.799*** PP

                 Peptidase_C26 187 veAvae.DgviEaieseeakafvlgvQwHPE 216
                                   v Av+e Dg i  ++s +    ++g+Q+HPE
  gi|13541854|ref|NP_111542.1| 138 VDAVSEtDGNIMGFHSVD--GRIYGIQFHPE 166
                                   ***********9999998..56********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 !    6.1   0.0    0.0015       5.3      84     104 ..      64      84 ..      54     114 .. 0.79
   2 !   13.5   0.0     8e-06     0.029     185     238 ..     123     177 ..      98     180 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0015
                      GATase_5  84 kflnredtlaLGiCnGfqlLv 104
                                   + +++ d+ +LGiC G qlL+
  gi|13541854|ref|NP_111542.1|  64 DVVDKFDGPVLGICFGHQLLA 84 
                                   56778899***********97 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 8e-06
                      GATase_5 185 lrYvdeegkpteeyplN.PNgSpegiagitspdGRvlalmpHpervveavqksii 238
                                   +rY+    +p++++++    +   +i g  s dGR++++  Hpe ++++v k+i+
  gi|13541854|ref|NP_111542.1| 123 IRYHSLVISPNKNIEVDaVSETDGNIMGFHSVDGRIYGIQFHPESYFTSVGKQIL 177
                                   5666666666666665523567789***********************9998865 PP

>> DUF4143  Domain of unknown function (DUF4143)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.2    0.0014       5.1      86     109 ..      10      33 ..       1      43 [. 0.80
   2 ?    2.7   0.0     0.036   1.3e+02      98     115 ..     133     149 ..      58     156 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0014
                                   xxxxxxxxxxxxxxxxxxxxxxxx RF
                       DUF4143  86 ekegaklyyyrdkngaEvDfviel 109
                                   ++  ++lyyy ++ + EvD+v ++
  gi|13541854|ref|NP_111542.1|  10 DSFVYNLYYYLREMNIEVDVVEND 33 
                                   5567899***9999******9864 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.036
                                   xxxxxxxxxxxxxxxxxx RF
                       DUF4143  98 kngaEvDfvielkggkiv 115
                                   +++ EvD+v e+ +g+i+
  gi|13541854|ref|NP_111542.1| 133 NKNIEVDAVSET-DGNIM 149
                                   248899999985.66665 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 ?   10.3   0.0   0.00013      0.45      44     110 ..      21      86 ..      11      91 .. 0.85
   2 ?   -2.7   0.0       1.2   4.5e+03      26      42 ..     134     150 ..     125     155 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00013
                                   TSEEEE-SEEGGG..CTCCG-SEEEE--BHHHHHHHHTSHHHHHHHHHHHHTT-EEEEETTTHHHHHHT CS
                     DJ-1_PfpI  44 rGlkvtvdasldd..vkaaeyDalvlpGGragperlrenekvvelvkefaekgklvaaICagpqlLaaa 110
                                   r +++ vd++ +d  v+a+ yD +++  G  +p + r+  + +++v +f   +++v  IC g qlLa +
  gi|13541854|ref|NP_111542.1|  21 REMNIEVDVVENDklVDASGYDKIIISPGPGSPLNARDRGRTLDVVDKF---DGPVLGICFGHQLLAYH 86 
                                   56677777766544478889******999999*******9999999998...89************965 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.2
                                   TTEEEEEEESSTSEEEE CS
                     DJ-1_PfpI  26 agikvdvvsvdkeevkg 42 
                                     i+vd+vs +++ + g
  gi|13541854|ref|NP_111542.1| 134 KNIEVDAVSETDGNIMG 150
                                   67889999988887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       315  (0.0175693); 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:                         5  (0.000278878); expected 0.2 (1e-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 0.28s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1348.42
//
Query:       gi|13541855|ref|NP_111543.1|  [L=351]
Description: anthranilate synthase component I [Thermoplasma volcanium GSS1]
Scores for complete 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-68  230.7   0.0    2.9e-68  230.2   0.0    1.2  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 !  230.2   0.0   1.6e-72   2.9e-68       7     258 .]     109     346 ..     103     346 .. 0.95

  Alignments for each domain:
  == domain 1  score: 230.2 bits;  conditional E-value: 1.6e-72
                                   HHHHHHHHHHHTTS-SEEEEEEEEEECESS-B-HHHHHHHHHCTBSSSEEEEEEETTEEEEEEESSEEEEEETTSEEEEEC CS
               Chorismate_bind   7 eavekvkeeiragdlykvvlsrrlkaeleaavdplalyralrarnpapysflleledsellgaSPElllkveggrrietep 87 
                                    +++k+++ ir+g++ +vv+sr+++a+    v+  + + ++ ++ ++ y+f+++++++e++g+SPE +++v g+ ri + p
  gi|13541855|ref|NP_111543.1| 109 GKIRKIVNLIRNGEVLQVVISREFEAN----VNVNEKIHEFLTKDRSRYVFYYRFGKYEVVGSSPENIFTVIGN-RIYVDP 184
                                   6799***********************....55678888999999***************************77.****** PP

                                   EEEEEEHSSSHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCBSCCEEEEECCEEEEEETTEEEEEEEEEEEESTT-- CS
               Chorismate_bind  88 iaGTrargktpeedealeeelledeKeraEhlmivdlirndLgkvakpgsvkvpelfkverysevlhlvstiegelkedvs 168
                                   iaGT+        ++   ++l ++eK+r Eh+m++dl+rnd++k+a +gs++vp+ +++e++s+v hlvs+++++++ +++
  gi|13541855|ref|NP_111543.1| 185 IAGTI-------SHSFSSDTLYRSEKDRCEHRMLLDLARNDVSKFADIGSLEVPKVMEIEEFSSVKHLVSQVKATFS-NKN 257
                                   *****.......45667899********************************************************7.89* PP

                                   HHHHHHHCSS-CCCSEESHHHHHHHHHHHSSS--TTTTSEEEEEETTS-EEEEEE-SEEEEETTEEEEEEEEEEETT--HH CS
               Chorismate_bind 169 lldllkalfPtgavtGaPkkrameiidelEearRgvYaGavgyldadgeaelavvIRtavvkdkelrlgaGaGIvadSdpe 249
                                    +d+l+a+fP+g+vtG Pk+ra+eiid++Ee++Rg+Y+Gavg+++ +g +++ ++IR+a  + + +r++aGaGIv+dSdp 
  gi|13541855|ref|NP_111543.1| 258 YVDILRAMFPAGTVTGSPKERAIEIIDKFEETPRGPYGGAVGIVG-SGIFDMGLAIRMAYSSGNGFRVRAGAGIVKDSDPS 337
                                   *********************************************.789************9999**************** PP

                                   HHHHHHHHH CS
               Chorismate_bind 250 aEyeEtlaK 258
                                   +E++E+ +K
  gi|13541855|ref|NP_111543.1| 338 SEVNEIYNK 346
                                   *****9988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (351 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       455  (0.0253779); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 2318.28
//
Query:       gi|13541856|ref|NP_111544.1|  [L=195]
Description: N-(5'-phosphoribosyl)anthranilate isomerase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.1e-17   62.0   0.0      8e-17   61.7   0.0    1.1  1  PRAI         N-(5'phosphoribosyl)anthranilate (PRA) isomerase
  ------ inclusion threshold ------
      0.058   13.1   0.0       0.16   11.7   0.0    1.6  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 !   61.7   0.0   8.9e-21     8e-17       2     193 ..       4     185 ..       3     186 .. 0.87

  Alignments for each domain:
  == domain 1  score: 61.7 bits;  conditional E-value: 8.9e-21
                                   CE----SHHHHHHHHHHTSSEEEEE--TTBTTB--HHHHHHHCCCS--EEEEEESSS-HHHHHHHHHHCTECEEEE-CGG. CS
                          PRAI   2 kicgltrasdvkaavkagadelglifaesskrevseeqaqellekvpaklVGVfvNqpieevlriaqelgldvvQLHGded 82 
                                   k+cg+tr +d++ +++ ga  +g++ +e s+r+ s + ++e+ e++ + + GV   ++   vl+       d+vQLH d d
  gi|13541856|ref|NP_111544.1|   4 KVCGITRLEDAAMVTELGASIVGVVLDELSPRHASHNTIREIAEAGIT-VAGVYTSEQT--VLSSPL--FEDYVQLHFDHD 79 
                                   99****************************************999966.****998764..555443..3488*******9 PP

                                   -HHHHHHHHHHS-TTSEEEEEEE-SSS--S-SSTT-SEEEEESSS-SSSXXXXGGGGTTSXX...TTEEEESSXXTTTHHH CS
                          PRAI  83 eqeyeellktelpvikalkvaesvdevkearradhvdllllDsgaGGtGelldwsliskllks..lkviLAGGLtpeNvae 161
                                   ++ +++  + + +vi  ++++   d + +++++ ++d++l+  ++G   +    s +s++     l+v  AGG++   +++
  gi|13541856|ref|NP_111544.1|  80 PELIRSIHELGRKVISVINFNGIRDLKIKYNAYREADIILVEYKKG---VS---SIVSQIA-PlgLNVGYAGGISDRDIEN 153
                                   9999999999***********966777778888888******9777...43...3333333.2358*************** PP

                                   HHT.TXXSEEEEXGGGEEE.TEEXHHHHHHHHH CS
                          PRAI 162 aiklegvlgvDvssGVEtn.GvkDlekirkfvq 193
                                   +i   ++  +Dvss+ E++ G+k   k+ +f++
  gi|13541856|ref|NP_111544.1| 154 IIA-AKPSIIDVSSSLESSpGIKHPGKVMSFFK 185
                                   ***.***************************98 PP

>> 4HFCP_synth  4-HFC-P synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.18   1.6e+03      90      90 ..      33      33 ..       5      94 .. 0.58
   2 ?   11.7   0.0   1.8e-05      0.16     166     207 ..     125     166 ..     113     170 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.18
                                  - CS
                   4HFCP_synth 90 k 90
                                  +
  gi|13541856|ref|NP_111544.1| 33 S 33
                                  3 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 1.8e-05
                                   HHHHHHHHHHHTT-EEEE-SS--GGGHHHHHHTT-SEEEESG CS
                   4HFCP_synth 166 elaefveeareaglltaLAGslkledlpaLkklkpdilGvRg 207
                                    ++++v+++  +gl ++ AG ++ +d++++ ++kp+i+ v +
  gi|13541856|ref|NP_111544.1| 125 GVSSIVSQIAPLGLNVGYAGGISDRDIENIIAAKPSIIDVSS 166
                                   5788999******************************98865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); 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 0.33s 00:00:00.82 Elapsed: 00:00:00.51
# Mc/sec: 1158.03
//
Query:       gi|13541857|ref|NP_111545.1|  [L=329]
Description: anthranilate phosphoribosyltransferase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-56  192.0   0.0    1.6e-56  191.7   0.0    1.1  1  Glycos_transf_3  Glycosyl transferase family, a/b domain
    0.00015   21.5   0.0    0.00031   20.5   0.0    1.5  1  Glycos_trans_3N  Glycosyl transferase family, helical bundle 


Domain annotation for each model (and alignments):
>> Glycos_transf_3  Glycosyl transferase family, a/b domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  191.7   0.0   1.8e-60   1.6e-56       3     253 .]      66     313 ..      64     313 .. 0.96

  Alignments for each domain:
  == domain 1  score: 191.7 bits;  conditional E-value: 1.8e-60
                                   TBEEEEESS-SSSTHHHHHHHHHHHHHHTT-BEEEEE-STCTTCS-HHHHHCTST--ST--HHHHHHHHHHHSEEEEEHHS CS
               Glycos_transf_3   3 dlvDivgTGGdgantfNiStaaaivvAaaGvkvakhgnrsvssksGsaDvLealgvnleltpeeveklleevgvgflfape 83 
                                   d+ DivgTGGd++nt+N+Sta+aiv+A++G++vak gnrs++   GsaD +  +g++   + e + + l+ ++++f++ap 
  gi|13541857|ref|NP_111545.1|  66 DATDIVGTGGDKKNTINVSTASAIVAASLGIPVAKFGNRSSTGAYGSADFMADAGYSFPRDVEAALHRLKSNNFVFMLAPT 146
                                   678****************************************************************************** PP

                                   SSSHHHHHHHHHHHHTT.-SSHHHCHHHHHT..SEEEEHHHHHHHHTCHSEEEEEEEESTTSSCCS.TSHHHHHHHHHHHH CS
               Glycos_transf_3  84 yhkamkhvapvrrelgirTvfnlLGPLinparvkkqllgvyskelaeklaevlkelgveralvvhg.dGldevsllakttv 163
                                   + + +k +++vr+ lg++T+fn LGP +np  +kk+++g +s e++  ++ +l+elg + a+++ g dG+de++++  t v
  gi|13541857|ref|NP_111545.1| 147 FIPEFKIFSTVRKRLGFPTLFNYLGPVLNPLAPKKRVIGSASTEMMDVYSYILNELGYQ-AIIIRGqDGMDEITPFNFTDV 226
                                   ********************************************************986.6788888************** PP

                                   HHHHTTEEEEEEEEEGSSTSSSEEESHHHHSSHHHHHHHHTTHHTSCHHHHHHHHHHHHHHHHHHHTTSSSSHHHHHHHHH CS
               Glycos_transf_3 164 aelkdgeiteytlepedfglkraelealeggepkenaeilkavlegkksaakrdlvllnagaalvlagkadslkegvakae 244
                                   + + dg++++y+++  ++  +  + +++ +++p    ++    l+g++++a ++ ++ln++ +l+l++ka +++++ + a+
  gi|13541857|ref|NP_111545.1| 227 IYV-DGSVEKYVVDGRSIS-NDVRYDKISSQDPSLIRKFNFMGLKGENEDA-AKFIALNTAPVLILNKKAGNYEDAYRLAL 304
                                   988.699*******99887.78899********99999999999*****98.***************************** PP

                                   HHHHTSHHH CS
               Glycos_transf_3 245 evidsGkAl 253
                                   e+i+sG+A+
  gi|13541857|ref|NP_111545.1| 305 EAIKSGQAY 313
                                   *******96 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 !   20.5   0.0   3.4e-08   0.00031      10      59 ..       9      58 ..       3      60 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 3.4e-08
                                  T.---HHHHHHHHHHHHTTSS-HHHHHHHHHHHHHH---HHHHHHHHHHH CS
               Glycos_trans_3N 10 geeLtaeeirfaihgilkgevtdaqiaAfLmAlrlkGetaeEiaalaeAm 59
                                  g + ++e ++ + + i k + +d+  aA L+A ++kG t eE  ++ +A+
  gi|13541857|ref|NP_111545.1|  9 GLNVDRESAKRLYEIISKEDCSDVCRAAVLTAFHFKGVTREEFMGFLDAI 58
                                  5567889999999*********************************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (329 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       519  (0.0289475); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.52
# Mc/sec: 1913.70
//
Query:       gi|13541858|ref|NP_111546.1|  [L=237]
Description: tryptophan synthase subunit alpha [Thermoplasma volcanium GSS1]
Scores for 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-14   51.3   0.0    9.2e-14   50.9   0.0    1.1  1  Trp_syntA  Tryptophan synthase alpha chain


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 !   50.9   0.0   5.1e-18   9.2e-14      28     235 ..      18     220 ..       3     234 .. 0.77

  Alignments for each domain:
  == domain 1  score: 50.9 bits;  conditional E-value: 5.1e-18
                                   HHHHHHHHCT-SSEEEE---S--TTS-HHHHHHHHCCCCTT--HHHHHHHHHHHHHHCSSS-EEEEE-CHHHCCC-HHHHC CS
                     Trp_syntA  28 eilkalekagadviElGlpfsdPladGPvIqaanlraLakgvtlekvlelveevrkkevevPivlltylnlvlsygeerfl 108
                                   + +k+  + g+ + E G+p  +Pl dG  I+a++  a++k  + ++  e+ + +++ + +     l y+ + +  g+  +l
  gi|13541858|ref|NP_111546.1|  18 KFIKN--SDGVYAFEFGFPTENPLYDGKKIKATHSFAVNK-FSHDDNAEIFKLAESMGIK--KYALLYYSV-F-SGKKGIL 91 
                                   44443..347889************************987.4555556666666633343..356667764.4.4777899 PP

                                   HHHHHCTEEEEEETTSBCCCHH...HHHHHHHHTT-EEEEEE-TTS-HHHHHHHHHH--S-EEEESTTC-SSTTSSB-TTH CS
                     Trp_syntA 109 aelkeagvdglivpDlPleeae...elveaakkkglelvflvapttsderlkevveqaegfvYvvsraGvTgaenavaaev 186
                                   + l     dg++vpD+  +  +   ++ +a+ ++g+++v+ v+p t+ + +++ ++ +   vY + ++  Tg +  +  ++
  gi|13541858|ref|NP_111546.1|  92 DYLSSSRFDGVMVPDVGIDYPDrieQVAKAIADHGMDYVPFVTPVTPFKIMERQMKVSGEIVY-QGMMPATGIQ--LPYDI 169
                                   99**************97766500055667789********************9998877777.6889999987..56678 PP

                                   HHHHHHHHHCT.SS-EEEESSS-SHHHHHHHH.TT-SEEEE-HHHHHHHHC CS
                     Trp_syntA 187 delverlkklt.avPvavGFGistkeqvkqva.kvadGvivGSalvkkiee 235
                                    ++  +++++t  + +  GFGi++k +++++a  +  G+ vG a+v+ +++
  gi|13541858|ref|NP_111546.1| 170 GTIYGHIRDFTsGKRIVYGFGIRNKCTIAKIAkYGGFGIAVGTAVVEMLDD 220
                                   8888888888867899****************88999**********9986 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:                      416  (0.0232026); 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: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1529.08
//
Query:       gi|13541859|ref|NP_111547.1|  [L=269]
Description: hypothetical protein TVN1028 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       287  (0.0160076); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1720.48
//
Query:       gi|13541860|ref|NP_111548.1|  [L=127]
Description: hypothetical protein TVN1029 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-10   41.5   0.0      2e-10   41.0   0.0    1.2  1  DUF123    Domain of unknown function DUF123
  ------ inclusion threshold ------
       0.11   12.7   0.2       0.28   11.4   0.2    1.6  1  LIM       LIM domain


Domain annotation for each model (and alignments):
>> DUF123  Domain of unknown function DUF123
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.0   0.0   2.2e-14     2e-10       2      93 ..      23     103 ..      22     104 .. 0.74

  Alignments for each domain:
  == domain 1  score: 41.0 bits;  conditional E-value: 2.2e-14
                        DUF123   2 elkkgvylYvGsalgsgglasRvkrHaslskkkekklhWhiDyLleseeaelaevvvaseerlEcalaealeaeapvagfG 82 
                                   ++++g y+Y+Gs  +    asR++rH+ +s +   k++Wh+DyL  ++   l+++++ +    E+++  al++ ++v++fG
  gi|13541860|ref|NP_111548.1|  23 DIDSGLYAYLGSCGK--ACASRISRHMIRSIS---KKRWHVDYLDCEP---LSAIIF-DCP--EHEMGVALSNLEHVKSFG 92 
                                   6889********977..5689*****988886...99*******9655...344444.444..4444445533459***** PP

                        DUF123  83 asDckcesHLl 93 
                                    sD  +   L+
  gi|13541860|ref|NP_111548.1|  93 NSDDPNVPRLF 103
                                   ***98776665 PP

>> LIM  LIM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2   3.1e-05      0.28       3      30 ..      38      64 ..      35      66 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.1e-05
                                  TT--BE-TTTEEEEETTEEEETTTSB-T CS
                           LIM  3 gCnkkiadrelvlkaldkvwHeeCFtCs 30
                                  +C+ +i+ r+++++++ k+wH++ + C+
  gi|13541860|ref|NP_111548.1| 38 ACASRIS-RHMIRSISKKRWHVDYLDCE 64
                                  7999999.888889************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 830.18
//
Query:       gi|13541861|ref|NP_111549.1|  [L=223]
Description: ubiquinone/menaquinone biosynthesis methylase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-40  139.1   0.0    1.8e-40  138.7   0.0    1.1  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
      3e-19   69.5   0.0    4.4e-19   68.9   0.0    1.3  1  Methyltransf_11  Methyltransferase domain
    2.5e-15   56.9   0.0    4.7e-15   56.1   0.0    1.5  1  Methyltransf_25  Methyltransferase domain
    5.9e-11   42.4   0.1    1.7e-10   40.9   0.1    1.6  1  Methyltransf_31  Methyltransferase domain
      6e-09   36.5   0.0    1.2e-08   35.5   0.0    1.5  1  Methyltransf_12  Methyltransferase domain
    1.4e-08   34.7   0.0    2.2e-08   34.1   0.0    1.4  1  Methyltransf_23  Methyltransferase domain
    6.1e-05   22.5   0.1    0.00042   19.7   0.0    2.2  2  CMAS             Mycolic acid cyclopropane synthetase
  ------ inclusion threshold ------
      0.011   15.6   0.0      0.023   14.5   0.0    1.6  2  Methyltransf_8   Hypothetical methyltransferase
      0.051   13.1   0.0      0.089   12.3   0.0    1.4  1  Methyltransf_PK  AdoMet dependent proline di-methyltransferas
       0.06   12.4   0.0      0.092   11.8   0.0    1.2  1  RrnaAD           Ribosomal RNA adenine dimethylase
      0.089   11.9   0.0       0.12   11.4   0.0    1.2  1  DREV             DREV methyltransferase


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 !  138.7   0.0   1.1e-43   1.8e-40       4     233 .]       3     222 ..       1     222 [. 0.94

  Alignments for each domain:
  == domain 1  score: 138.7 bits;  conditional E-value: 1.1e-43
                                   XXXXXXXXXXX-HHHHHHHHHHHHHTTTHHHHHHHHHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHH CS
               Ubie_methyltran   4 lkeekvkevfesvaskyDlmndvlslgihrlWkkfveklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenm 84 
                                   +k++ vk++f+++++kyDl++ ++slg  + W++ ++      +g + lD  +G+g ++  +++s + +  v+ lDi ++m
  gi|13541861|ref|NP_111549.1|   3 SKHQAVKKIFDQISDKYDLIDTIISLGLDQRWRRSLISNLKLMPGLQCLDCGAGSGKVTELIMESCD-SCSVTALDITDSM 82 
                                   68899*****************************99999999*****************98888876.679********** PP

                                   HHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EEEEEEES-GGG-S-HHHHHHHHHHHEEEEEEEEEEEE----SHHHHHH CS
               Ubie_methyltran  85 LkvgekklkeegkinieflqanaeeLpfeddsfDvvtvsfGlrnvtDklkaLkeayrvlkpGGrlvvlefskvelpllsqa 165
                                   ++        e +++ +f+++ ae Lpf+d++fD v  +f  rn++D +k + e+yrvlkpGG++v l++ +++ p++sq 
  gi|13541861|ref|NP_111549.1|  83 FNP-------ELTKRCKFVVSPAESLPFSDETFDRVSSAFLTRNLADVDKYFSEVYRVLKPGGIFVNLDIFNPTKPVFSQF 156
                                   975.......4556889**************************************************************** PP

                                   HHHHHH.HHHHHHHHHHS-HHHHHHHHHHHHHS--HHHHHHHHHHTTEEEEEEEEEGGGTEEEEEEEE CS
               Ubie_methyltran 166 yelyskevlPvlGkllakdldsyryLvesirafPdqetlkeliedaGfksveyesltgGvvaihigvk 233
                                   ++ly+++++P++G+   ++  +y+yL++s++ f     l + +e  Gf  ve ++l +G v +hi+ k
  gi|13541861|ref|NP_111549.1| 157 FSLYFYRMVPFFGNHATHS-RNYSYLANSVKFFYSPFILSKKLESKGF-IVEPKDLFFGSVFMHIAQK 222
                                   **************87777.9***************************.599999*********9976 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.9   0.0   2.7e-22   4.4e-19       1      95 [.      51     141 ..      51     142 .. 0.94

  Alignments for each domain:
  == domain 1  score: 68.9 bits;  conditional E-value: 2.7e-22
                                   EEET-TTSHHHHHHHHTT..SEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-CCHHH CS
               Methyltransf_11   1 LdvGcGtGrlaealakrg..arvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhvedpek 79 
                                   Ld+G+G+G+++e +++ +  ++v+++D+++ m    + +  ++   ++fvv+ ae+lpf d++fD v s +   +++d++k
  gi|13541861|ref|NP_111549.1|  51 LDCGAGSGKVTELIMESCdsCSVTALDITDSMF---NPELTKR---CKFVVSPAESLPFSDETFDRVSSAFLTRNLADVDK 125
                                   8**************99999************9...5555444...89********************************* PP

                                   HHHHHHHHEEEEEEEE CS
               Methyltransf_11  80 alkeiaRvLkpgGllv 95 
                                   +++e++RvLkpgG++v
  gi|13541861|ref|NP_111549.1| 126 YFSEVYRVLKPGGIFV 141
                                   **************97 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.1   0.0   2.9e-18   4.7e-15       2      97 .]      51     138 ..      50     138 .. 0.90

  Alignments for each domain:
  == domain 1  score: 56.1 bits;  conditional E-value: 2.9e-18
                                   EEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGSSHHHH CS
               Methyltransf_25   2 LdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhlsdedl 82 
                                   Ld+G+G+G++t+ + + + +++vt++Di+++m +   +       +++fv+  ae+lpf d++fD v s++    l  +d+
  gi|13541861|ref|NP_111549.1|  51 LDCGAGSGKVTELIMESCDSCSVTALDITDSMFNPELT------KRCKFVVSPAESLPFSDETFDRVSSAFLTRNL--ADV 123
                                   9*****************88************984332......369**********************8765555..589 PP

                                   HHHHHHHHHHEEEEE CS
               Methyltransf_25  83 ekalkeiarvLkpgG 97 
                                   +k+++e++rvLkpgG
  gi|13541861|ref|NP_111549.1| 124 DKYFSEVYRVLKPGG 138
                                   9*************9 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.9   0.1     1e-13   1.7e-10       4     109 ..      47     142 ..      44     150 .. 0.92

  Alignments for each domain:
  == domain 1  score: 40.9 bits;  conditional E-value: 1e-13
               Methyltransf_31   4 glrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsnevl 84 
                                   gl+ lD+G+G+G+ t  +  e ++ + v+ +Di+  + +   +       ++++F ++++e+l+  ++de+fD + s  + 
  gi|13541861|ref|NP_111549.1|  47 GLQCLDCGAGSGKVTELIM-ESCDSCSVTALDITDSMFNPELT-------KRCKFVVSPAESLP--FSDETFDRVSSAFLT 117
                                   7899**************9.99***************998888.......69************..********8887666 PP

               Methyltransf_31  85 naladpdkileeiervlkpggilli 109
                                     lad dk++ e+ rvlkpggi++ 
  gi|13541861|ref|NP_111549.1| 118 RNLADVDKYFSEVYRVLKPGGIFVN 142
                                   ***********************85 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.5   0.0   7.6e-12   1.2e-08       1      99 []      51     140 ..      51     140 .. 0.84

  Alignments for each domain:
  == domain 1  score: 35.5 bits;  conditional E-value: 7.6e-12
               Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhhlkd 81 
                                   L+ G+G+G +++ + e+   +++t++Di  s++     +l kr+    ++v   a++l  +d+  +fD v ++++  +l+d
  gi|13541861|ref|NP_111549.1|  51 LDCGAGSGKVTELIMESCDSCSVTALDITDSMF---NPELTKRC----KFVVSPAESLPFSDE--TFDRVSSAFLTRNLAD 122
                                   899******************************...33333333....355555555555554..**************** PP

               Methyltransf_12  82 irevldnirklLkpgGrl 99 
                                   +++++++++++LkpgG++
  gi|13541861|ref|NP_111549.1| 123 VDKYFSEVYRVLKPGGIF 140
                                   ****************85 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.1   0.0   1.4e-11   2.2e-08      20     122 ..      44     147 ..      29     203 .. 0.81

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 1.4e-11
               Methyltransf_23  20 lraggrvLdiGcGtGillevlren..gfsvtgvDlspeaveiaekakkaqkdqfdeqeaaepqgkfdlIvlrevlehvpdp 98 
                                   l +g  +Ld G+G+G ++e++ e    +svt+ D+ + + +    +k  +++  ++++ ++++++fd +++ +++ ++ d+
  gi|13541861|ref|NP_111549.1|  44 LMPGLQCLDCGAGSGKVTELIMEScdSCSVTALDITDSMFNPE-LTKRCKFVVSPAESLPFSDETFDRVSSAFLTRNLADV 123
                                   456679**********999997764688*******98887764.45566777777999999******************** PP

               Methyltransf_23  99 pellrqiatllkpgGylllsepla 122
                                    ++++ +++ lkpgG ++ +++ +
  gi|13541861|ref|NP_111549.1| 124 DKYFSEVYRVLKPGGIFVNLDIFN 147
                                   ****************99888655 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.31   5.1e+02       4      29 ..       9      34 ..       6      37 .. 0.83
   2 !   19.7   0.0   2.6e-07   0.00042      52     172 ..      36     150 ..      28     174 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.31
                                  XXXHHHHHHHHTS-HHHHCTTS-TT- CS
                          CMAS  4 kkevenikahYDlsndffalfldptm 29
                                  kk +++i+ +YDl + + +l ld+ +
  gi|13541861|ref|NP_111549.1|  9 KKIFDQISDKYDLIDTIISLGLDQRW 34
                                  56678999*********999999876 PP

  == domain 2  score: 19.7 bits;  conditional E-value: 2.6e-07
                                   HHHHTTTT--TT-EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG-.----SEE CS
                          CMAS  52 dlileklelkpGmtlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvdeldlerkvevklldyedl.dekvdrv 131
                                   + ++  l+l pG + Ld G+G G+++   +e    + +++T  +    + + ++ ++    k  v+ ++   + de +drv
  gi|13541861|ref|NP_111549.1|  36 RSLISNLKLMPGLQCLDCGAGSGKVTELIMES--CDSCSVTALDITDSMFNPELTKRC---KFVVSPAESLPFsDETFDRV 111
                                   567889******************99988888..555666655544455555544444...3333344444441369**** PP

                                   EEES-GGGTSGGGHHHHHHHHHHHS-TT-EEEEEEEEE--H CS
                          CMAS 132 vsvgafehvgkenydtffkklkkllkedGllllhtitslhk 172
                                   +s  ++     +  d++f++++++lk++G++++  i+ ++k
  gi|13541861|ref|NP_111549.1| 112 SSAFLTRN--LADVDKYFSEVYRVLKPGGIFVNLDIFNPTK 150
                                   *9766665..5789******************998887765 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   1.4e-05     0.023      76     155 ..      50     141 ..      32     178 .. 0.72
   2 ?   -2.7   0.0       2.7   4.3e+03     163     187 ..     188     212 ..     171     222 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.4e-05
                                   EEEES-TT-HHHHH--S...-..EEEEESS-..SSTTEE.ES-T.....TS-S--TT-EE.EEEEES---SS-HHHHHHHH CS
                Methyltransf_8  76 vadlGcGeakiaeavre...kekvrsfdlva..vnervv.acdl.....akvPledesvd.vavfclslmgtnladflkea 144
                                     d G G  k++e + e   +  v ++d++    n++++  c +       +P  de+ d v    l+    ++ ++  e+
  gi|13541861|ref|NP_111549.1|  50 CLDCGAGSGKVTELIMEscdSCSVTALDITDsmFNPELTkRCKFvvspaESLPFSDETFDrVSSAFLTRNLADVDKYFSEV 130
                                   4688888888886555411145788888864224555431465433332689*******95556678888899999***** PP

                                   HHHEEEEEEEE CS
                Methyltransf_8 145 nrvlkvGGllk 155
                                   +rvlk+GG++ 
  gi|13541861|ref|NP_111549.1| 131 YRVLKPGGIFV 141
                                   ********985 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.7
                                   -S-HHHHHHHHHCTTEEEEEEE--S CS
                Methyltransf_8 163 fesvklfaraltklGfevkskdlsn 187
                                   f s  ++ ++l++ Gf v+ kdl  
  gi|13541861|ref|NP_111549.1| 188 FYSPFILSKKLESKGFIVEPKDLFF 212
                                   4555678899999999888888754 PP

>> Methyltransf_PK  AdoMet dependent proline di-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   5.4e-05     0.089      57     158 ..      48     141 ..      22     153 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.4e-05
               Methyltransf_PK  57 kvaldcGaGiGrvtknlLlkllskvDlvepvekflekakeelaeekkkvgkvyvvglqeftPeegrYdliWiqWcvghLtD 137
                                   +  ldcGaG G+vt+ ++ +     D   +++  ++  ++ +  e +k +k+ v + +     ++ +d +   +   +L+D
  gi|13541861|ref|NP_111549.1|  48 LQCLDCGAGSGKVTELIMES----CDSCSVTALDIT--DSMFNPELTKRCKFVVSPAESLPFSDETFDRVSSAFLTRNLAD 122
                                   5679**********976544....444444443332..2234455667899999999999889999999999999999998 PP

               Methyltransf_PK 138 edlvaflkrckkalkpnGliv 158
                                    d  ++++ + + lkp+G++v
  gi|13541861|ref|NP_111549.1| 123 VD--KYFSEVYRVLKPGGIFV 141
                                   77..89999999999999998 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   5.7e-05     0.092      22      66 ..      38      84 ..      26      98 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5.7e-05
                                  HHHHH-GGTTSEEEEES-TTTCCHHHHHCC-..SEEEEE-S-HHHHH CS
                        RrnaAD 22 IldklnleekltvleigpGkGilTeeLakra..kqvvvlElderLak 66
                                   +++l+l + l+ l+ g+G G  Te +++ +   +v++l +  ++++
  gi|13541861|ref|NP_111549.1| 38 LISNLKLMPGLQCLDCGAGSGKVTELIMESCdsCSVTALDITDSMFN 84
                                  67788888***********************7778999988666655 PP

>> DREV  DREV methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   7.6e-05      0.12      97     182 ..      49     138 ..      31     152 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 7.6e-05
                          DREV  97 klldlGaGdGeitkrvaptfee..vyatelsetmrd.rlkkkkynvlsale.lqetdvkldlilclnlldrcfdplklled 173
                                   + ld GaG G++t+ + +  +   v a +++  m +  l k+   v+s  e l  +d  +d +++  l     d  k + +
  gi|13541861|ref|NP_111549.1|  49 QCLDCGAGSGKVTELIMESCDScsVTALDITDSMFNpELTKRCKFVVSPAEsLPFSDETFDRVSSAFLTRNLADVDKYFSE 129
                                   679***********9999998766888899999987467777555666666599999999999988777777788888888 PP

                          DREV 174 irsalepng 182
                                   ++ +l+p g
  gi|13541861|ref|NP_111549.1| 130 VYRVLKPGG 138
                                   888888865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.61u 0.32s 00:00:00.93 Elapsed: 00:00:00.53
# Mc/sec: 1278.18
//
Query:       gi|13541862|ref|NP_111550.1|  [L=100]
Description: hypothetical protein TVN1031 [Thermoplasma volcanium GSS1]
Scores for complete 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  102.8   0.1      1e-29  102.6   0.1    1.0  1  DUF424     Protein of unknown function (DUF424)
  ------ inclusion threshold ------
      0.066   13.4   0.0        0.1   12.8   0.0    1.4  1  MmoB_DmpM  MmoB/DmpM family


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 !  102.6   0.1   1.1e-33     1e-29       2      92 .]       9      98 ..       8      98 .. 0.97

  Alignments for each domain:
  == domain 1  score: 102.6 bits;  conditional E-value: 1.1e-33
                                  EETTE.EEEEEEEGGGTT-EEEETTEEEE--HHHH--EEE-HHHHHHHHHHHEEEEEESHHHHHHHHHTTSS-GGG-EEETTE CS
                        DUF424  2 rtddllklvavcdkellgktfkegelllnvsegfyggelaseeeaikeLekatiaNivgeeavvlavkaGlvdpdsVlvidgv 84
                                  +++++  l+a++d+++lgk+f+e++l+++v ++fyg+ ++++e++i++L+ +tiaN+vg+++v+la++ G++d+d+Vl+idgv
  gi|13541862|ref|NP_111550.1|  9 EIRGE-ILLAAADSDILGKKFREKNLHIEVFPSFYGEVKVTDEMFISSLNMCTIANLVGKHTVELAIENGYIDKDNVLYIDGV 90
                                  57889.9**************************************************************************** PP

                                  EEEEEEE- CS
                        DUF424 85 phaqigkl 92
                                  p+aq+ k+
  gi|13541862|ref|NP_111550.1| 91 PYAQYAKM 98
                                  *****998 PP

>> MmoB_DmpM  MmoB/DmpM family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   1.1e-05       0.1      52      83 ..      21      53 ..       5      55 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.1e-05
                                  HHHHTST--HHHHTTSE.EEEESEEEESSSEEE CS
                     MmoB_DmpM 52 eealGrefdlqelevnl.ssfaGridtdddeit 83
                                  +++lG++f+ ++l++++  sf+G+++++d+ ++
  gi|13541862|ref|NP_111550.1| 21 SDILGKKFREKNLHIEVfPSFYGEVKVTDEMFI 53
                                  689************9856*******9999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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 0.30s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 680.02
//
Query:       gi|13541863|ref|NP_111551.1|  [L=699]
Description: ATPase involved in replication control [Thermoplasma volcanium GSS1]
Scores for 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  320.9   0.1    5.3e-96  320.0   0.1    1.4  1  MCM              MCM P-loop domain
    2.2e-31  108.3   0.0    3.9e-31  107.5   0.0    1.4  1  MCM_OB           MCM OB domain
    3.4e-25   88.3   1.6    3.4e-25   88.3   1.6    2.1  2  MCM_lid          MCM AAA-lid domain
    1.1e-09   38.0   0.1    1.7e-06   27.6   0.0    2.5  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    6.5e-06   26.7   1.5      5e-05   23.8   0.2    2.7  2  MCM_N            MCM N-terminal domain
    2.5e-05   24.3   0.1    0.00011   22.2   0.0    2.2  2  AAA_5            AAA domain (dynein-related subfamily)
    3.8e-05   23.5   0.0    0.00011   22.1   0.0    1.8  1  AAA_3            ATPase family associated with various cellul
    0.00044   20.0   0.5     0.0021   17.8   0.1    2.3  2  Sigma54_activat  Sigma-54 interaction domain


Domain annotation for each model (and alignments):
>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  320.0   0.1   2.4e-99   5.3e-96       2     224 .]     275     498 ..     274     498 .. 0.98

  Alignments for each domain:
  == domain 1  score: 320.0 bits;  conditional E-value: 2.4e-99
                                   HHHHHHHHTSSTHHHHHHHHSSTTSSS-HHHHHHHHHHHH---EBBBSSSSBBCSS-EEEEEESSTSTHHHHHHHHHHHSS CS
                           MCM   2 veeikelakekdiieklvksiapsiyghedvkkaillqlfggvkkkledktklrgdinvllvgdpgtaKsqlLkyveklap 82 
                                   +++i e++k++++i+ ++ksiap+i+g +++kka++lq+fggv+k+++d+t++rgdi++l+vgdpgtaKsqlLky+++++p
  gi|13541863|ref|NP_111551.1| 275 KQKIIEISKRPNVIDVIAKSIAPTIHGLDMIKKALALQMFGGVRKTMKDGTTMRGDIHILMVGDPGTAKSQLLKYMAEVSP 355
                                   6899***************************************************************************** PP

                                   SEEEEESSSSSSSHSSSEEEEESSSSS.EEEEETHHHHTTTSEEEEESGGGSTCHHHHHHHHHHHHSEEEEESSSCEEEEE CS
                           MCM  83 ravytsgkgssaagLtaavvrdeetge.fvleaGalvladkGvcciDefdkmkeedrsalhEamEqqtisiaKaGivatLn 162
                                   r+++t g+gssaagLtaa vrde  +  ++leaGalvlad+G ++iDe+dkm+e+d+ a+hEamEqqt++i+KaGi+atL+
  gi|13541863|ref|NP_111551.1| 356 RGIFTFGRGSSAAGLTAAAVRDEFGEGrWTLEAGALVLADNGFVAIDELDKMDEHDTAAMHEAMEQQTVTISKAGIMATLR 436
                                   **********************975544***************************************************** PP

                                   --EEEEEEE--SSSSCCTTS-HHHHSSSSHHHHHHSSEEEEE-SSTTHHHHHHHHHHHHHHH CS
                           MCM 163 artsvlaAanpkagrydkkksvaeninlsaalLsrFDlifvllDkvdeekDeelaehivslh 224
                                   ar+svlaAanpk+gryd ++++ae+in++ +lLsrFD+if ++D++++++D++laeh+++ h
  gi|13541863|ref|NP_111551.1| 437 ARASVLAAANPKFGRYDLNRNLAEQINFPLPLLSRFDVIFKMVDQPNKDTDSQLAEHVLKAH 498
                                   ***********************************************************987 PP

>> MCM_OB  MCM OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.5   0.0   1.8e-34   3.9e-31       2     124 ..     106     236 ..     105     238 .. 0.90

  Alignments for each domain:
  == domain 1  score: 107.5 bits;  conditional E-value: 1.8e-34
                                   XGG--GGGTTSEEEEEEEEEEE---EEEEEEEEEEETTT-.-EEE.....S----SB-..TTT-HHH.....-EEE-GGGS CS
                        MCM_OB   2 lRdlrsehigklvkveGivtrasevkpklkkavfeckkcgktvev.....eleePrkCeekeCeskd.....pfkleteks 72 
                                   +Rd+rs++ig+l++v+Giv + +ev+pklk+a+fec++c++   v     +l+eP  C   +C++++     +fkl ++ s
  gi|13541863|ref|NP_111551.1| 106 IRDIRSANIGTLISVSGIVRKNTEVFPKLKNAAFECSNCHELNYVeqnesRLTEPLYC--ANCGQSKvkdkiSFKLRPNLS 184
                                   8***************************************86557666666777****..7898433444679******** PP

                                   EEEEEEEEEEE-------------EEEEEEEGGGTT---TT-EEEEEEEEEE CS
                        MCM_OB  73 kfvdfqklklQEspeevpaGelPrslevileddlvdkvkPGdrvevtGiyra 124
                                   +f+d+qk+++QE pe++  G  P+ l +i+eddl   + PG+rv v Gi++a
  gi|13541863|ref|NP_111551.1| 185 EFIDVQKIEIQEDPETLEGGAQPQRLIIIVEDDLAGLLFPGNRVVVDGILQA 236
                                   *************************************************987 PP

>> MCM_lid  MCM AAA-lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.1       5.6   1.3e+04      42      56 ..     265     279 ..     255     283 .. 0.48
   2 !   88.3   1.6   1.5e-28   3.4e-25       1      84 [.     529     608 ..     529     611 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 5.6
                                   SSSST--HHHHHHHH CS
                       MCM_lid  42 rksipitvRqLesli 56 
                                    +s++it    + +i
  gi|13541863|ref|NP_111551.1| 265 IESVKITEEDKQKII 279
                                   455555544444444 PP

  == domain 2  score: 88.3 bits;  conditional E-value: 1.5e-28
                                   HHHHHHHHHHHHTT--BETCHHHHHHHHHHHHHHHHHTSSTSSSST--HHHHHHHHHHHHHHHHHHTSSSE-HHHHHHHHH CS
                       MCM_lid   1 ellrkYiayarekikPklseeakeklseaYvelRkeeedskrksipitvRqLesliRLseAlAklrlsevvteedveeair 81 
                                   +llrkY+aya+++++P+ls+ea  +l+++Yv++R  +    r+sipitvRqLes iRL+eA A+ rls++vt ed++ a +
  gi|13541863|ref|NP_111551.1| 529 DLLRKYVAYAKNNVFPRLSDEAIAILQDQYVRTRTGS----RDSIPITVRQLESTIRLAEAAARARLSTIVTVEDAMLAKK 605
                                   58*********************************55....678**********************************999 PP

                                   HHH CS
                       MCM_lid  82 llk 84 
                                   +++
  gi|13541863|ref|NP_111551.1| 606 IVD 608
                                   985 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.0   0.00095       2.1      20      47 ..     328     355 ..     319     359 .. 0.88
   2 !   27.6   0.0   7.5e-10   1.7e-06      94     159 ..     382     448 ..     371     485 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00095
                  Mg_chelatase  20 aGgHnlllvGppGsGKtmlakrlpsllp 47 
                                    G  ++l+vG pG+ K+ l k ++++ p
  gi|13541863|ref|NP_111551.1| 328 RGDIHILMVGDPGTAKSQLLKYMAEVSP 355
                                   58889**************999988766 PP

  == domain 2  score: 27.6 bits;  conditional E-value: 7.5e-10
                  Mg_chelatase  94 gs.kpkpGeislahnGvLfLDElpefkrkvlevLRePledgevtisrakakvefparfqlvaamNpc 159
                                   g+ + + G++ la nG + +DEl +++++   ++ e +e+++vtis+a   ++  ar  ++aa+Np 
  gi|13541863|ref|NP_111551.1| 382 GRwTLEAGALVLADNGFVAIDELDKMDEHDTAAMHEAMEQQTVTISKAGIMATLRARASVLAAANPK 448
                                   4447889**********************************************************94 PP

>> MCM_N  MCM N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.2   2.2e-08     5e-05       4      74 ..      15      76 ..      12      96 .. 0.88
   2 ?    0.3   0.0      0.48   1.1e+03      33      64 ..     506     537 ..     497     580 .. 0.78

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 2.2e-08
                         MCM_N  4 FedFLeefkddsededgekkYrdqlqemaer..ekttLevdlddLaafdeeLaeailenpkeylplleealke 74
                                  ++dF++++            Y d+++++ +   e +tL+v+++d++++d+++a +il  p+ yl+  ee + e
  gi|13541863|ref|NP_111551.1| 15 WRDFFRTY-----------GYSDKINSIHQDypEVRTLYVSFKDIEDYDRQFAASILASPEIYLKTGEEIVME 76
                                  68899988...........7*********998899*****************************998887754 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.48
                         MCM_N  33 erekttLevdlddLaafdeeLaeailenpkey 64 
                                    +ek+ +e+d+ d a++++++ + +l+++  y
  gi|13541863|ref|NP_111551.1| 506 SMEKNDIEIDVPDEAKYEPDIDKDLLRKYVAY 537
                                   468999***********997777777766555 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       2.5   5.6e+03      61      87 ..     110     136 ..      93     141 .. 0.78
   2 !   22.2   0.0   4.8e-08   0.00011       1     124 [.     332     449 ..     332     492 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2.5
                                   ----G-SEEEEESGGG--HHHHHHHHH CS
                         AAA_5  61 raaregeilvlDEveraesevlnsLls 87 
                                   r+a+ g ++ + ++ r ++ev+++L +
  gi|13541863|ref|NP_111551.1| 110 RSANIGTLISVSGIVRKNTEVFPKLKN 136
                                   367788888999999999999999976 PP

  == domain 2  score: 22.2 bits;  conditional E-value: 4.8e-08
                                   EEEEE--SSSSHHHHHHHGGGGBS--EEEE...E--TT--HHHHH--B--.........--------G-SEEEEESGGG-- CS
                         AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyv...qltrdtteedlkgrreikngttslvdsplvraaregeilvlDEverae 78 
                                   ++l+vG+pGt+Ks+l +++a++  r +++       +++t++ ++ +    +g+  l+ ++lv  a +g  + +DE+++++
  gi|13541863|ref|NP_111551.1| 332 HILMVGDPGTAKSQLLKYMAEVSPRGIFTFgrgSSAAGLTAAAVRDEFG--EGRWTLEAGALV-LADNG-FVAIDELDKMD 408
                                   789*******************988877752112334455555555555..8999999*****.55555.5669******* PP

                                   HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS-- CS
                         AAA_5  79 sevlnsLlslleerrllleeggelvkaknddllerfrviatanpld 124
                                    + +++++  +e++++ + + g     ++       +v+a+anp  
  gi|13541863|ref|NP_111551.1| 409 EHDTAAMHEAMEQQTVTISKAGIMATLRAR-----ASVLAAANPKF 449
                                   ***************997776666655553.....77777777764 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 !   22.1   0.0   4.9e-08   0.00011       1     113 [.     332     448 ..     332     461 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 4.9e-08
                         AAA_3   1 hvllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfee.kekefefkkGpvf...anllladeinrappk 77 
                                   h+l+ g PG+ak +l k +a++    +    f      + ++ + v +e  e ++++++G+++   + ++  de+++   +
  gi|13541863|ref|NP_111551.1| 332 HILMVGDPGTAKSQLLKYMAEVSPRGI--FTFGRGSSAAGLTAAAVRDEfGEGRWTLEAGALVladNGFVAIDELDKMDEH 410
                                   9*******************9876544..45666777788888888876246899*****976332348999********* PP

                         AAA_3  78 tqsalleameerqvtvege..thklpepflvlatqnPi 113
                                     +a+ eame+++vt++++    +l     vla+ nP 
  gi|13541863|ref|NP_111551.1| 411 DTAAMHEAMEQQTVTISKAgiMATLRARASVLAAANPK 448
                                   ***************98762267899**********93 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.1   9.2e-07    0.0021      18     153 ..     326     457 ..     313     470 .. 0.81
   2 ?   -2.5   0.0       1.6   3.7e+03     116     144 ..     553     582 ..     547     592 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 9.2e-07
                                   HCTSSS-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS-TTCHHHHHHEBSSSSSTTTSS-BEHHHHHTTTSEEE CS
               Sigma54_activat  18 vaktdlsvlitGesGtGKellaraiheaskrkekpfvavncaaipeelleseLFGhekGaFtGAekekkGlfekadgGtlf 98 
                                   +++ d+++l++G+ Gt K+ l + + e s+r    f +   aa  +     + FG   G +    + ++G++  ad+G + 
  gi|13541863|ref|NP_111551.1| 326 TMRGDIHILMVGDPGTAKSQLLKYMAEVSPRGIFTFGRGSSAAGLTAAAVRDEFGE--GRW----TLEAGALVLADNGFVA 400
                                   456789************************99888888877776666566666774..444....4678************ PP

                                   EETGGGS-HHHHHHHHHHHHHSE..EESBTSSSEEE--EEEEEEESS-HHHHHHTTS CS
               Sigma54_activat  99 LDeigelplelQekLlrvlqege..vervGsskeikvdvriiaatnedleeaveegk 153
                                   +De+ +++ +  + + +++++++  +++ G  ++ ++   ++aa+n +  +   +++
  gi|13541863|ref|NP_111551.1| 401 IDELDKMDEHDTAAMHEAMEQQTvtISKAGIMATLRARASVLAAANPKFGRYDLNRN 457
                                   *******************999722579999************99987766555555 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.6
                                   HHHHSEE.ESBTSSSEEE--EEEEEEESS- CS
               Sigma54_activat 116 vlqegev.ervGsskeikvdvriiaatned 144
                                   +lq++ v +r Gs+++i+++vr + +t + 
  gi|13541863|ref|NP_111551.1| 553 ILQDQYVrTRTGSRDSIPITVRQLESTIRL 582
                                   6777766258999999**999988888654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (699 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       815  (0.0454571); expected 358.6 (0.02)
Passed bias filter:                      546  (0.0304535); 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: 0.73u 0.29s 00:00:01.02 Elapsed: 00:00:00.48
# Mc/sec: 4382.64
//
Query:       gi|13541864|ref|NP_111552.1|  [L=198]
Description: aspartokinase beta subunit [Thermoplasma volcanium GSS1]
Scores for complete 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   20.7   0.8    0.00055   20.2   0.8    1.2  1  VWA       von Willebrand factor type A domain
     0.0043   16.8   0.1       0.01   15.6   0.1    1.6  1  ACT_7     ACT domain


Domain annotation for each model (and alignments):
>> VWA  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.8   6.2e-08   0.00055      18     134 ..       2     123 ..       1     137 [. 0.75

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 6.2e-08
                                   HHHHHHHHHHHHHHTBTTTTEEEEEEEESSS...EEEEEETTSHC..HHHHHHHHHHTGSGGGGSSC-HHHHHHHHHH... CS
                           VWA  18 ekvkefikklveklevgpegtrvglvqfsse...vktefslndys..skeellsalnnlkysgggttntgkalkyale... 90 
                                   +k+ e++k++v++ +v +  ++ glv + +    +k ++++ + +  + +++ +al n++++g++++ ++     + +   
  gi|13541864|ref|NP_111552.1|   2 TKASEAVKTIVSNNNVYSLLINTGLVNYTKLareIKGQVDFLTGKkiKINTIVKALTNIEVKGKNSNALE----ILKQstl 78 
                                   67889***********************976333666667666555677888888888888888888444....3333222 PP

                                   ....HHHHHHGTSSTTSEEEEEEEESS--CSSHTHHHHHHHHGCTEEE CS
                           VWA  91 ....klfkssagaRenakkviilltdGksndgdpkeaaneakeqgikv 134
                                       ++ ++  ++ e+++k +il+   ++    +++ a++ak++ + +
  gi|13541864|ref|NP_111552.1|  79 tleyNYEEQHFENPEEIPKSAILIIKDQN---GYSTLAKSAKSNSLVI 123
                                   232355555555788***********999...7789999999887655 PP

>> ACT_7  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   1.2e-06      0.01      20      65 .]     135     181 ..     122     181 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.2e-06
                                   S--HHHHHHHHHHTTT---EEEE.-SS-EEEEEEGGGHHHHHHHHHH CS
                         ACT_7  20 vtGivaklaspLaeagIsifqiS.tyrtdyiLVpeedlekAveaLhe 65 
                                   + Gi+  +++ L  +gIs+  i    r  +i++++e + kA +aL++
  gi|13541864|ref|NP_111552.1| 135 TAGITLLITEFLEINGISVVNIYrLSREVWIIIQSESAGKAADALNR 181
                                   679******************************************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       720  (0.0401584); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); 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: 1329.33
//
Query:       gi|13541865|ref|NP_111553.1|  [L=272]
Description: inorganic polyphosphate/ATP-NAD kinase [Thermoplasma volcanium GSS1]
Scores for complete 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-55  187.0   0.4      5e-55  186.7   0.4    1.1  1  NAD_kinase  ATP-NAD kinase
      0.002   17.7   0.1     0.0033   17.0   0.1    1.3  1  DAGK_cat    Diacylglycerol kinase catalytic domain
  ------ inclusion threshold ------
      0.079   13.0   0.1       0.16   12.0   0.1    1.4  1  DUF600      Protein of unknown function, DUF600


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 !  186.7   0.4   8.4e-59     5e-55      75     291 ..      49     253 ..      28     254 .. 0.95

  Alignments for each domain:
  == domain 1  score: 186.7 bits;  conditional E-value: 8.4e-59
                                   TTTSSSEEEEEE-HHHHHHHHHHHHHCT-EEEEEESSS--SS-SEEGGGHHHHHHHHHHT-SEEEEEEEEEEEEEETTE.. CS
                    NAD_kinase  75 adagvdliivvGGDGTaldvarllqkaeiPvlgvnaGvkgfltefepeaaaellekllegeirvekrevldavimrskgee 155
                                    + ++d+ii++GGDGT+l++ +  +    Pvlg+n+G +gflte+e++++++   kl++ge++++++++l+++i+ +  e 
  gi|13541865|ref|NP_111553.1|  49 TEISADIIIAIGGDGTVLRILQNAKG---PVLGINMGGLGFLTEIEIDEVGSSTYKLIRGEYKINEAMKLKVYINGRRLE- 125
                                   56689*************99877775...******************************************999988874. PP

                                   ....EEEEEEESSEEEEEESSSSS-EEEEEEETTEEEEEEEESEEEEE-TGGGGTHHHHTT--EE-TT---EEEEEESESS CS
                    NAD_kinase 156 diadiviensvlnevviirgpgstlielelyvdtelleadqldglivstPtGstayslsaGgplisPgvlailivpicPhs 236
                                             + ne v+++ +++ + ++++yvd+++l+++ +dg+iv+tPtGs  ys saGgpl+ P+v  ++i+ + P s
  gi|13541865|ref|NP_111553.1| 126 ---------DCTNEAVVHTDRIARIRQFKIYVDGHFLTTIKSDGVIVATPTGSSSYSSSAGGPLLLPTVRGMVISYLAPYS 197
                                   .........578********************************************************************* PP

                                   S----EEE-TT-EEEEEE-.SS--EEEEETTTEEEEE-TT-EEEEEEESSEEEEEE CS
                    NAD_kinase 237 lssrpiVvssssklrirva.srseallaldGseelelspgdevrvtasdkkfklir 291
                                    + +p+Vv+s+s+++i++a ++++ ll+ldG++e++++ gd+v++++s++k++++ 
  gi|13541865|ref|NP_111553.1| 198 SRIKPVVVPSESTVEIKIAgNDQDSLLILDGQKEYKIKSGDTVSISMSEEKARFVS 253
                                   *****************************************************996 PP

>> DAGK_cat  Diacylglycerol kinase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.1   5.5e-07    0.0033      39      77 ..      36      74 ..      14      84 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 5.5e-07
                                  -STTHHHHHHHHHHHCC-SEEEEEESHHHHHHHHHHHCT CS
                      DAGK_cat 39 eepgdakelakeakeegvdlivvaGGDGtvsevlnglle 77
                                  e ++    + k++ e ++d+i+++GGDGtv  +l+   +
  gi|13541865|ref|NP_111553.1| 36 EAAKFLGGVGKDITEISADIIIAIGGDGTVLRILQNAKG 74
                                  545555555678888899************999987655 PP

>> DUF600  Protein of unknown function, DUF600
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   2.7e-05      0.16       7      24 ..      16      33 ..      14      41 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.7e-05
                                  HHHHHHHHH--S-EEEEE CS
                        DUF600  7 eiaekildmiPeeWekvy 24
                                  +ia++i+++iP +Wek+y
  gi|13541865|ref|NP_111553.1| 16 TIAKSIIELIPPDWEKIY 33
                                  69***************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       440  (0.0245412); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 1893.34
//
Query:       gi|13541866|ref|NP_111554.1|  [L=122]
Description: hypothetical protein TVN1035 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-08   33.9   0.0    1.1e-07   31.6   0.0    1.9  1  Prok-JAB  Prokaryotic homologs of the JAB domain
     0.0044   17.0   0.1     0.0056   16.6   0.1    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 !   31.6   0.0   1.3e-11   1.1e-07       3     105 ..       7      97 ..       5     111 .. 0.72

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 1.3e-11
                      Prok-JAB   3 svlsalvaharrahpeEtcGlllgkeseseevivvplvnewsnrfeipdpedslarlkf..earerglevvgiwHSHpggs 81 
                                   ++l+ ++++ + ++p+E ++ll  + +   e+++vp             + +s +   f       + ++vg +HSHp g 
  gi|13541866|ref|NP_111554.1|   7 DTLQMIMEASKDSYPREFGALLRAEDNVIYEIALVP------------GTIQSDRYTLFymYSKPIDFSLVGSVHSHPSGI 75 
                                   677888899999999999999988773333333333............333333333334478888999************ PP

                      Prok-JAB  82 arPSetDrrdaaalarvkalliiv 105
                                   + PS++D+r+++ ++  k+++i++
  gi|13541866|ref|NP_111554.1|  76 TKPSDEDLRMFSLTG--KIHIIVG 97 
                                   ************997..6666665 PP

>> RadC  RadC-like JAB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   6.2e-07    0.0056      69      87 ..      67      85 ..       6      99 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 6.2e-07
                                  EEEE-TTS--S--HHHHHH CS
                          RadC 69 laHnhPsgdlepSeeDiel 87
                                   +H hPsg ++pS+eD+++
  gi|13541866|ref|NP_111554.1| 67 SVHSHPSGITKPSDEDLRM 85
                                  58**************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       251  (0.0139997); expected 358.6 (0.02)
Passed bias filter:                      242  (0.0134977); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 807.96
//
Query:       gi|13541867|ref|NP_111555.1|  [L=563]
Description: amino acid transporter [Thermoplasma volcanium GSS1]
Scores for complete 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-43  146.8  55.6    8.3e-43  146.8  55.6    2.3  2  AA_permease_2    Amino acid permease
    1.3e-29  103.2  51.8    1.3e-29  103.2  51.8    2.1  2  AA_permease      Amino acid permease
    0.00017   21.7   8.4    0.00017   21.7   8.4    5.7  5  Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domai
  ------ inclusion threshold ------
          2    8.9   5.7       0.71   10.3   0.3    3.0  3  DUF4014          Protein of unknown function (DUF4014)


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 !  146.8  55.6   1.8e-46   8.3e-43       1     397 [.      27     450 ..      27     479 .. 0.77
   2 ?   -0.6   6.4       0.1   4.7e+02     146     210 ..     456     521 ..     451     557 .. 0.43

  Alignments for each domain:
  == domain 1  score: 146.8 bits;  conditional E-value: 1.8e-46
                 AA_permease_2   1 lsllsafalvigsvigsgifvknlaas..ggpalilwvwiavligslavllvyaElssalprsgGiyvytkaafgkkvafl 79 
                                   ls++++++l++g +igsg +++  aas   gpa+il ++++ +i+ +  +lvyaEl++++prsg i+ y++   g +++fl
  gi|13541867|ref|NP_111555.1|  27 LSTWDLLMLSVGGIIGSGWLFAAYAASvlSGPASILAWVLGGIIV-IFIALVYAELGAMIPRSGAIVRYGHLSHGSFAGFL 106
                                   79****************999974444679**************9.79********999********************** PP

                 AA_permease_2  80 sawfnwfayvpvlas....ilsvaasyllnalgpdlqgn...twltyliaiaililvalinirgikesakiqnilgilkil 153
                                   ++w++++++v v a+    ++++aasy    ++p l  n   t++  lia++++i ++++n+ gi+ ++k +  ++++k++
  gi|13541867|ref|NP_111555.1| 107 FGWAYFLSAVSVPAIeaeaVVTYAASYV---TKPALIANgimTVFGTLIAMLLMIAFFFLNYAGIHLMGKTNQGITWIKVI 184
                                   ********99988883333444444444...3355555544478999********************************** PP

                 AA_permease_2 154 lpliiliilglitvdgggfsslstetdtffpngwpgvllglli..vlwsfdGfesaanvseevkk..kdvpkaifiglliv 230
                                   +p+i++i  +li+v+++ +       + f+p gw  v+++++   +++s+ Gf  a+ +  e+k+  + +p+a++ ++li 
  gi|13541867|ref|NP_111555.1| 185 IPVITVI--VLIAVHFNPSE--IVPPNGFLPYGWAPVFAAISStgIVFSYFGFRQAIDYGGEAKNpqRSIPIATIGSVLIG 261
                                   **88777..55555555444..2345569**********9976669****************8887689************ PP

                 AA_permease_2 231 lvlyllvniaflgvvpddei.............anlsnlgsv.......aalffeavggkvvaiivvilial......... 282
                                   ++ly l++++f+g++ ++++             a       +         l ++ +++++++i+++++++          
  gi|13541867|ref|NP_111555.1| 262 ILLYSLLQVVFVGGIDWSKMglepgqwtllnayA-------TaahasteHPLAYQLMNAPFATIALSAGLVWltytlyasa 335
                                   ********************87776664444440.......1455555634444444444444444433333344444444 PP

                 AA_permease_2 283 ..sllgaintavigssrvlealardgvlPrffakvn.kfgspiraiiltaivslillllfllassaaynfllsvsslglii 360
                                     +  g +n ++ +s+r+l+ +a  g lP+ fakv  ++++p+  +i+t++v ++++l f        + ++   s + ++
  gi|13541867|ref|NP_111555.1| 336 yiAPSGTLNVYLGTSTRTLYGMAVNGHLPKIFAKVAdRNKIPVIPLITTLLVGFLFFLPFPS-----WYKMVGFISGATVF 411
                                   439999***********************************************999988863.....56777777777777 PP

                 AA_permease_2 361 syllliigalilrkkrphlkrpgk.ilvaiig.alfllf 397
                                    y++  ++++ lrk+ p+lkrp k +  + ++ + f+l 
  gi|13541867|ref|NP_111555.1| 412 TYIVGGAALMNLRKQAPELKRPFKlWSANVLApIAFILA 450
                                   78888888899**********544454444443222222 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.1
                 AA_permease_2 146 ilgilkillpliiliilglitvdg..ggfssl.stetdtffpngwpgvllgllivlwsfdGfesaanv 210
                                   ++g+ ++ l l+i+i lgl++ ++  g +  + +++++++ ++ w  v+ ++l+ ++s+ G ++ +nv
  gi|13541867|ref|NP_111555.1| 456 WTGWPTT-LYLAIAIFLGLVLYGAlvGLHKIEqTFDKKNVKAGLWVPVFIVILT-ILSYLGEYGGINV 521
                                   3444444.3444444444444433222222113333444444444444444442.2333333333332 PP

>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.2  51.8   2.9e-33   1.3e-29       1     393 [.      31     426 ..      31     455 .. 0.84
   2 ?    0.2   9.3      0.05   2.2e+02      73     163 ..     452     546 ..     445     558 .. 0.67

  Alignments for each domain:
  == domain 1  score: 103.2 bits;  conditional E-value: 2.9e-33
                   AA_permease   1 hvlvialggviGtglfvglgvvlsqaGplgallayllagvviflvmlslgeiatngpksggfytyasrflgpelGfviGln 81 
                                   ++l+ ++gg+iG g +++ + +    Gp+  +la++l+g+++++++l  +e+  ++p+sg++  y + ++g+ +Gf  G+ 
  gi|13541867|ref|NP_111555.1|  31 DLLMLSVGGIIGSGWLFAAYAASVLSGPA-SILAWVLGGIIVIFIALVYAELGAMIPRSGAIVRYGHLSHGSFAGFLFGWA 110
                                   589*************************5.56************************************************* PP

                   AA_permease  82 ylfswitvlaleltaasiliqfwelvtdlpkawvt...........gavflvvlliinlvgvkvygeaefilalikiiaii 151
                                   y++s + v a+e   a+ +++++ ++   p a +            +++++++++++n++g+ + g++   +++ik+i+ +
  gi|13541867|ref|NP_111555.1| 111 YFLSAVSVPAIE---AEAVVTYAASYVTKP-ALIAngimtvfgtliAMLLMIAFFFLNYAGIHLMGKTNQGITWIKVIIPV 187
                                   ************...666777765555444.2222466799999*9999******************************** PP

                   AA_permease 152 afiivgiillaggkpnkgagfrflgdngsifknnlppgfakeeegafknfisvfv..ivvfaftGielvaiiagEvkdPek 230
                                   +++iv+i ++++              ng+     lp g         + ++++++   +vf++ G+   +  +gE+k+P++
  gi|13541867|ref|NP_111555.1| 188 ITVIVLIAVHFNPSEIVP-------PNGF-----LPYG--------WAPVFAAISstGIVFSYFGFRQAIDYGGEAKNPQR 248
                                   ******988887775555.......4444.....5555........444444443115789999***************** PP

                   AA_permease 231 siPkailqvviritifYvlsllligllvprndlgllndsasa.....................aspfvifikesgvsvlap 290
                                   siP+a++  v++ +++Y l+ ++ + +++++  gl  +  +                        pf ++  ++g+  l  
  gi|13541867|ref|NP_111555.1| 249 SIPIATIGSVLIGILLYSLLQVVFVGGIDWSKMGLEPGQWTLlnayataahastehplayqlmNAPFATIALSAGLVWLTY 329
                                   **********************************999877779999999**************9***************** PP

                   AA_permease 291 linaviltaalssansslysasRvlyslakdglaP.kvlkkvskrgvPlraillsmiisllalllaslnlaapivfnflla 370
                                   +++a  ++a  +++n +l +++R+ly +a +g++P  ++k+ ++++ P+  ++ ++++++l++l     ++  + ++++  
  gi|13541867|ref|NP_111555.1| 330 TLYASAYIAPSGTLNVYLGTSTRTLYGMAVNGHLPkIFAKVADRNKIPVIPLITTLLVGFLFFL----PFP--SWYKMVGF 404
                                   ***********************************55667779********************3....222..44444444 PP

                   AA_permease 371 isaliglivwlliilsylrfRka 393
                                   is++ +++++++  ++++++Rk+
  gi|13541867|ref|NP_111555.1| 405 ISGA-TVFTYIVGGAALMNLRKQ 426
                                   4443.455666666666666666 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.05
                   AA_permease  73 elGfviGlnylfswitvlaleltaasiliqfwel....vtdlpkawvtgavflvvlliinlvgvkvygeaefilali..ki 147
                                   e+ + +G+ + ++ ++++ l+l+  + l+++ +      +++ ka  ++ vf+v+l+i++++g   yg + ++ +++  ++
  gi|13541867|ref|NP_111555.1| 452 EAVYWTGWPTTLYLAIAIFLGLVLYGALVGLHKIeqtfDKKNVKAGLWVPVFIVILTILSYLG--EYGGINVLHFPLdlIV 530
                                   666889999777777777777776666666553211224578889999*************98..5777788866542155 PP

                   AA_permease 148 iaiiafiivgiillag 163
                                   +ai++ ii    + +g
  gi|13541867|ref|NP_111555.1| 531 VAIASAIIYVWAIKSG 546
                                   5666666655444444 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   1.9     0.037   1.7e+02      95     140 ..      34      77 ..      18      80 .. 0.61
   2 ?   -7.7  17.9         4   1.8e+04      61     135 ..     145     229 ..     123     274 .. 0.43
   3 ?   -1.4   0.3      0.49   2.2e+03      90     110 ..     313     333 ..     289     359 .. 0.53
   4 !   21.7   8.4   3.8e-08   0.00017      25     138 ..     371     480 ..     368     485 .. 0.78
   5 ?    0.9   5.2     0.097   4.3e+02      85     137 ..     493     542 ..     478     546 .. 0.67

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.037
               Polysacc_synt_C  95 llaalvmgivvylllllllgllllaalalllavlvgalvYllllll 140
                                   +l++ ++ +  +l++ +  ++l+++  a +la ++g+++ ++++l+
  gi|13541867|ref|NP_111555.1|  34 MLSVGGIIGSGWLFAAYAASVLSGP--ASILAWVLGGIIVIFIALV 77 
                                   2222223333465666666677766..8888888888888888775 PP

  == domain 2  score: -7.7 bits;  conditional E-value: 4
               Polysacc_synt_C  61 atvlallvvavln.lyalrrllgikl...ellrrllkpllaalvmgivvylllllllglllla......al.alllavlvg 130
                                    tv++ l++++l+  ++  ++ gi+l   + +  ++  +++ ++ +iv+++++    ++ + +      ++  +++a+   
  gi|13541867|ref|NP_111555.1| 145 MTVFGTLIAMLLMiAFFFLNYAGIHLmgkTNQGITWIKVIIPVITVIVLIAVHFNPSEIVP-PngflpyGWaPVFAAISST 224
                                   4444444444444344455555555544421222222233333333332222222222222.2233444332222222233 PP

               Polysacc_synt_C 131 alvYl 135
                                   ++v+ 
  gi|13541867|ref|NP_111555.1| 225 GIVFS 229
                                   33333 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.49
               Polysacc_synt_C  90 rllkpllaalvmgivvyllll 110
                                     + ++++++++++++y+l+ 
  gi|13541867|ref|NP_111555.1| 313 APFATIALSAGLVWLTYTLYA 333
                                   233444444444444443333 PP

  == domain 4  score: 21.7 bits;  conditional E-value: 3.8e-08
               Polysacc_synt_C  25 lgrqkialkalvigalvklilnllliplfgivG.aaiatvlallvvavlnlyalrrllgiklellrrllkpllaalvmgiv 104
                                    +r+ki+++ l+ ++lv +++ l++  ++ +vG ++ atv++++v+ + ++ + ++   +k     +l+   ++a + +i+
  gi|13541867|ref|NP_111555.1| 371 ADRNKIPVIPLITTLLVGFLFFLPFPSWYKMVGfISGATVFTYIVGGAALMNLRKQAPELKR--PFKLWSANVLAPIAFIL 449
                                   589******************************99**********98877666666555555..33455555555666666 PP

               Polysacc_synt_C 105 vylllllllgllllaalalllavlvgalvYllll 138
                                          +  + ++ +l l++a+++g ++Y++l+
  gi|13541867|ref|NP_111555.1| 450 ---ASEAVYWTGWPTTLYLAIAIFLGLVLYGALV 480
                                   ...445555555666789************9987 PP

  == domain 5  score: 0.9 bits;  conditional E-value: 0.097
               Polysacc_synt_C  85 lellrrllkpllaalvmgivvylllllllgllllaalalllavlvgalvYlll 137
                                     +   l++p++++++  +  yl  +  +++l+ + l l++ +++ a++Y+ +
  gi|13541867|ref|NP_111555.1| 493 N-VKAGLWVPVFIVILTILS-YLGEYGGINVLHFP-LDLIVVAIASAIIYVWA 542
                                   4.566777777776666666.77888888888877.75555555999999876 PP

>> DUF4014  Protein of unknown function (DUF4014)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.2      0.95   4.3e+03      25      43 ..     151     169 ..     145     180 .. 0.82
   2 ?   -1.6   0.0      0.85   3.8e+03      15      31 ..     494     510 ..     488     513 .. 0.78
   3 ?   10.3   0.3   0.00016      0.71      18      49 ..     521     554 ..     518     558 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.95
                       DUF4014  25 lilmvpispiffiwlagvq 43 
                                   li m+ +   ff+  ag+ 
  gi|13541867|ref|NP_111555.1| 151 LIAMLLMIAFFFLNYAGIH 169
                                   6778888889999999985 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.85
                       DUF4014  15 fkealffplflilmvpi 31 
                                    k  l+ p+f++++  +
  gi|13541867|ref|NP_111555.1| 494 VKAGLWVPVFIVILTIL 510
                                   6888999**99987655 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 0.00016
                       DUF4014  18 alffplflilmvpispiffiwl..agvqaekiae 49 
                                    l fpl li++   s i+++w   +g+++e ia 
  gi|13541867|ref|NP_111555.1| 521 VLHFPLDLIVVAIASAIIYVWAikSGIKTEEIAA 554
                                   699******************64479****9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (563 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       915  (0.0510346); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); 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):               4  [number of targets reported over threshold]
# CPU time: 0.83u 0.36s 00:00:01.19 Elapsed: 00:00:00.54
# Mc/sec: 3121.93
//
Query:       gi|13541868|ref|NP_111556.1|  [L=482]
Description: phenylalanyl-tRNA synthetase subunit alpha [Thermoplasma volcanium GSS1]
Scores for complete 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-81  271.4   0.0    8.9e-81  271.0   0.0    1.2  1  tRNA-synt_2d     tRNA synthetases class II core domain (F)
    1.1e-09   38.1   0.0    2.8e-08   33.5   0.0    2.2  2  tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM 
    0.00056   19.1   0.1      0.088   11.9   0.0    2.5  2  tRNA-synt_2      tRNA synthetases class II (D, K and N)
  ------ inclusion threshold ------
      0.042   13.8   0.0        0.1   12.5   0.0    1.8  1  tRNA-synt_2b     tRNA synthetase class II core domain (G, H, 
      0.049   13.5   0.0      0.079   12.8   0.0    1.2  1  UPF0257          Uncharacterised protein family (UPF0257)


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 !  271.0   0.0   2.5e-84   8.9e-81       1     243 [.     209     476 ..     209     478 .. 0.98

  Alignments for each domain:
  == domain 1  score: 271.0 bits;  conditional E-value: 2.5e-84
                                   C.-TSSCTSCTSHSB-SHHHHHHHHHHHHHHCTTCEESSTTSEEEHHHHTSTTTSTTTSHHHCHTTSEBTCTSSS-..... CS
                  tRNA-synt_2d   1 kidvtlpgkrieagklhpltkvleeikeiflelgfeevegpevesefynfdaLnvpqdhpaRdmqdtFylkkpeka..... 76 
                                   k+d+++p +++++ ++hpl  +++ei++ifl++gf+e++g+++es ++  daL++pqdhpaRdmqdtFy+k+++ +     
  gi|13541868|ref|NP_111556.1| 209 KYDLDAPVSPTKSYAKHPLVYFINEIRRIFLDMGFTEMSGHYIESALWDMDALFIPQDHPARDMQDTFYVKDSNFTiehpe 289
                                   699*******************************************************************8877779**** PP

                                   ..........................ECESEEE-SSTHHHHHHHH.TTS-SSEEEEEEEEEEBSST-SSSB-SEEEEEEEE CS
                  tRNA-synt_2d  77 ..........................veekllLRthttavqirtl.ekkkppikiisigrvfRrdavDathlaeFhqvegl 130
                                                               +kl+LRthtt +++r+l e+++ p+ i+s+++vfR+++vD +hlaeF+q+eg 
  gi|13541868|ref|NP_111556.1| 290 iekrikrihergfdgysgwgyrwssdDGKKLILRTHTTVTTARYLyEHNTYPQAIFSVEKVFRHESVDWKHLAEFYQIEGA 370
                                   *************************98889***************99999******************************* PP

                                   EEETT--HHHHHHHHHHHHHHHCTSTEEEEEEECEETTEEEEEEEEEEECCSSSSEEEEEEEEEE-HHHHHHTT-.TTSEE CS
                  tRNA-synt_2d 131 vvdenvsladlkgvleellkklfgaevkvrfrpsyfpftePsaevdvylvekkkkwlEllgaGmvrpevleavgideevsg 211
                                   v d+nvs+a+lk++l++++ kl g+e k+r+ psy+p+tePs++v v +    +k +El+g+G++rpev + +g+  + ++
  gi|13541868|ref|NP_111556.1| 371 VYDKNVSVATLKWILRTFYGKL-GFE-KIRLVPSYYPYTEPSLDVVVEV---DGKEMELGGSGIFRPEVGKILGL--KAPV 444
                                   **********************.***.*******************999...8999*******************..**** PP

                                   EEEEEEHHHHHHHHHT-SSGHHHHTT.HHHHG CS
                  tRNA-synt_2d 212 fafGlGveRlamlkygieDiRelvendlrflr 243
                                   +a+G+G+eRlaml yg++D+R+l+++d+ fl+
  gi|13541868|ref|NP_111556.1| 445 MAWGMGLERLAMLYYGLTDVRDLYNTDFSFLE 476
                                   *****************************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 ?    2.1   0.0      0.03   1.1e+02       6      37 ..     215     246 ..     213     253 .. 0.91
   2 !   33.5   0.0   7.8e-12   2.8e-08      83     209 ..     328     446 ..     322     451 .. 0.93

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.03
               tRNA_synthFbeta   6 PkapttegelnkeqklrrklrdllagaGlnEv 37 
                                   P  pt+  ++++   + +++r++  ++G++E+
  gi|13541868|ref|NP_111556.1| 215 PVSPTKSYAKHPLVYFINEIRRIFLDMGFTEM 246
                                   888999999999999****************7 PP

  == domain 2  score: 33.5 bits;  conditional E-value: 7.8e-12
               tRNA_synthFbeta  83 LevlarNlargnedvrlFEigkvflkd.seeelpeeerhlaivltgkreeeswsekaravdfydlkgivealleslgiekv 162
                                   + ++++ ++++    ++F + kvf+ +  + +  +e  ++ ++++ k+           v++++lk i++++ ++lg+ek+
  gi|13541868|ref|NP_111556.1| 328 VTTARYLYEHNTYPQAIFSVEKVFRHEsVDWKHLAEFYQIEGAVYDKN-----------VSVATLKWILRTFYGKLGFEKI 397
                                   567788888888889************777788***************...........********************** PP

               tRNA_synthFbeta 163 efepaehpalhpgrsAeikvdgk..evGvlGelhpevleafdlkqrvyv 209
                                   +++p+ +p+ +p     ++vdgk  e+G  G + pev + ++lk++v++
  gi|13541868|ref|NP_111556.1| 398 RLVPSYYPYTEPSLDVVVEVDGKemELGGSGIFRPEVGKILGLKAPVMA 446
                                   **********************9899********************987 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 !   11.9   0.0   2.4e-05     0.088      93     119 ..     343     368 ..     328     379 .. 0.90
   2 !    4.4   0.0    0.0048        17     287     307 ..     447     467 ..     440     469 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.4e-05
                                   EEEEEEEEE--S--BTTB-S-CEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   tRNA-synt_2  93 rvfqiaraFRaEdsrtdrhlaEFtqie 119
                                    +f++ ++FR E+++  +hlaEF+qie
  gi|13541868|ref|NP_111556.1| 343 AIFSVEKVFRHESVD-WKHLAEFYQIE 368
                                   589************.67888*****9 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.0048
                                   EEEEHHHHHHHHCT-SSGGGC CS
                                   xxxxxxxxxxxxxxxxxxxxx RF
                   tRNA-synt_2 287 lglGldRlvmlllgsesIrdv 307
                                   +g+Gl+Rl ml  g++++rd+
  gi|13541868|ref|NP_111556.1| 447 WGMGLERLAMLYYGLTDVRDL 467
                                   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 ?   12.5   0.0   2.9e-05       0.1       1     104 [.     310     400 ..     310     458 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.9e-05
                                   EEEEETTSEEEEE-SSSHHHHHHHHHHHEEEBGGSSEEEEEEEEEEBTTTSTBCTTTB-SEEEEEEEEEEESGGGHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  tRNA-synt_2b   1 YkledrndreyiLkPtneetfvelirdevlrskrLPlklyqiqtkyRdEksdsrGLlRvreFhqkdgyvfhaeaslddslr 81 
                                   Y+ ++++++++iL+   + t ++   ++  + +  P+ ++ +  ++R+E  d +    + eF q +g v+ ++     s++
  gi|13541868|ref|NP_111556.1| 310 YRWSSDDGKKLILRTHTTVTTARYLYEH--NTY--PQAIFSVEKVFRHESVDWKH---LAEFYQIEGAVYDKNV----SVA 379
                                   88888999******99999999999999..888..***************98887...6799999999998766....566 PP

                                   HHHHHHHHHHHHTT.SCEEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxx RF
                  tRNA-synt_2b  82 dlikaisriferlglefraiiel 104
                                    l     +++ +lg+e  +i+++
  gi|13541868|ref|NP_111556.1| 380 TLKWILRTFYGKLGFE--KIRLV 400
                                   6666677777777766..44444 PP

>> UPF0257  Uncharacterised protein family (UPF0257)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   2.2e-05     0.079      89     160 ..     276     348 ..     259     363 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.2e-05
                       UPF0257  89 aLvldanyyvdaetrekrvrLqgkCqLaelpsagvsyetddk.gfvvkaekkevkaeyryddeGyPlgkttvs 160
                                     v+d+n+ ++  + ekr++   +  +      g  + +dd  + ++++++  ++a+y y+ + yP +  +v 
  gi|13541868|ref|NP_111556.1| 276 FYVKDSNFTIEHPEIEKRIKRIHERGFDGYSGWGYRWSSDDGkKLILRTHTTVTTARYLYEHNTYPQAIFSVE 348
                                   5699***************9999999***************825566667777889**********8765554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (482 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       709  (0.0395449); expected 358.6 (0.02)
Passed bias filter:                      537  (0.0299515); 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: 0.66u 0.33s 00:00:00.99 Elapsed: 00:00:00.52
# Mc/sec: 2802.44
//
Query:       gi|13541869|ref|NP_111557.1|  [L=240]
Description: hypothetical protein TVN1038 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       864  (0.0481901); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 1460.45
//
Query:       gi|13541870|ref|NP_111558.1|  [L=306]
Description: ABC-type daunorubicin transport system, ATPase component [Thermoplasma volcanium GSS1]
Scores for complete 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-27   95.1   0.1    9.7e-27   94.2   0.0    1.5  2  ABC_tran     ABC transporter
      1e-13   51.8   0.5    2.7e-07   30.7   0.1    2.4  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    4.5e-06   26.6   0.7      0.047   13.4   0.1    2.5  3  AAA_15       AAA ATPase domain
      4e-05   23.2   0.7      0.034   13.6   0.0    2.7  3  SMC_N        RecF/RecN/SMC N terminal domain
     0.0012   19.3   0.0     0.0047   17.4   0.0    2.1  1  AAA          ATPase family associated with various cellular a
     0.0035   17.0   0.1     0.0067   16.2   0.1    1.4  1  AAA_29       P-loop containing region of AAA domain
     0.0087   16.6   2.1       0.01   16.3   0.1    2.0  2  AAA_23       AAA domain
  ------ inclusion threshold ------
       0.01   16.2   0.1      0.037   14.4   0.1    2.0  2  AAA_16       AAA ATPase domain
      0.017   15.4   0.2      0.052   13.8   0.2    2.0  1  AAA_22       AAA domain
      0.021   15.4   0.0        1.7    9.2   0.0    2.4  2  AAA_18       AAA domain
      0.057   13.6   0.1        1.4    9.2   0.1    2.3  1  SbcCD_C      Putative exonuclease SbcCD, C subunit
      0.084   12.8   0.0       0.16   11.9   0.0    1.4  1  RsgA_GTPase  RsgA GTPase
      0.088   12.7   0.0       0.13   12.1   0.0    1.4  1  Rad17        Rad17 P-loop domain
      0.097   11.9   0.0       0.15   11.3   0.0    1.3  1  Zeta_toxin   Zeta toxin
       0.11   12.6   0.0        0.2   11.9   0.0    1.3  1  DNA_pol_B_3  DNA polymerase family B viral insert


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.2   0.0   8.1e-30   9.7e-27       1     136 [.      22     165 ..      22     166 .. 0.94
   2 ?   -3.0   0.0       7.9   9.4e+03      39      51 ..     242     254 ..     233     277 .. 0.65

  Alignments for each domain:
  == domain 1  score: 94.2 bits;  conditional E-value: 8.1e-30
                                   EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSB.HHHH. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx. RF
                      ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpelt.vren. 79 
                                   lk +s+k+ ++ ++ ++G+nGaGK+tL+++l+ +l p +G  ++dg d+   e  + rk+i+++pqe++  + lt +++  
  gi|13541870|ref|NP_111558.1|  22 LKSISFKVPASGILSLIGRNGAGKTTLIRILSTELLPSSGYAEIDGIDIIG-EPDEIRKRIAIIPQEARAISWLTpIQTIt 101
                                   789***********************************************9.88899**********99999999555559 PP

                                   ...........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                   ...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  80 ...........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                              e++++  ++l+kl+l++++ +      ++LSgGqk++v +a+++++++++l++DEpt
  gi|13541870|ref|NP_111558.1| 102 tfllyrginysEAKRRSMEVLKKLELEQIAGKLN----RTLSGGQKRKVLVAALIASDADILFMDEPT 165
                                   99*******9999999************888887....*****************************9 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 7.9
                                   EEEEEETTCEGGG CS
                                   xxxxxxxxxxxxx RF
                      ABC_tran  39 eGeilldgkdlke 51 
                                    Gei+++g+ lk+
  gi|13541870|ref|NP_111558.1| 242 DGEIEINGTVLKT 254
                                   5777777777776 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.1   7.2e-07   0.00086       4      20 ..      37      53 ..      34      87 .. 0.75
   2 !   30.7   0.1   2.3e-10   2.7e-07     235     298 ..     136     195 ..      97     198 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 7.2e-07
                        AAA_21  4 liGpNgsGKSnLLdald 20
                                  liG+Ng+GK++L+++l+
  gi|13541870|ref|NP_111558.1| 37 LIGRNGAGKTTLIRILS 53
                                  9***************5 PP

  == domain 2  score: 30.7 bits;  conditional E-value: 2.3e-10
                        AAA_21 235 relSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQv.iltTHS 298
                                   r lS G+kr   +++++++++   ++l+ DEp +gL+P   ++l++ll el+r   ++ +ltTH 
  gi|13541870|ref|NP_111558.1| 136 RTLSGGQKRKVLVAALIASDA---DILFMDEPTTGLDPISRAELWDLLAELKR--EKFiFLTTHY 195
                                   568*******88888888888...************************99988..6776*****6 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.1     4e-05     0.047      17      44 ..      27      53 ..      21      84 .. 0.83
   2 !   10.6   0.0   0.00027      0.32     321     364 ..     153     194 ..     142     195 .. 0.93
   3 ?   -2.5   0.1       2.7   3.2e+03     167     206 ..     263     298 ..     231     301 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4e-05
                        AAA_15 17 veidlseeltvliGkNnsGKSsileald 44
                                  ++++ s  +  liG+N++GK++++++l 
  gi|13541870|ref|NP_111558.1| 27 FKVPASG-ILSLIGRNGAGKTTLIRILS 53
                                  5666666.999**************995 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00027
                        AAA_15 321 eeknvilliEEPEahLHpqaqkvlikllkelandnktQviitTH 364
                                    ++ +il+++EP + L p    +l++ll+el ++++  +++tTH
  gi|13541870|ref|NP_111558.1| 153 ASDADILFMDEPTTGLDPISRAELWDLLAELKREKF--IFLTTH 194
                                   56789******************************9..****** PP

  == domain 3  score: -2.5 bits;  conditional E-value: 2.7
                        AAA_15 167 edlkklikkleeslkkeeelknvlksaiiklllisakRnv 206
                                   e++ ++ ++    ++k++ ++++ + +++++++  akR++
  gi|13541870|ref|NP_111558.1| 263 EEAYSIVRD---LINKNA-KFSINPISLEDIYYSIAKRDI 298
                                   333333333...333333.444666666677777777665 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.8   0.0    0.0033         4      24      41 ..      32      49 ..      20      56 .. 0.82
   2 !   13.6   0.0   2.8e-05     0.034     117     203 ..     115     200 ..      98     212 .. 0.76
   3 ?   -1.1   0.0      0.89   1.1e+03      78     114 ..     246     282 ..     224     291 .. 0.59

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0033
                                  SSEEEEEESTTSSHHHHH CS
                                  xxxxxxxxxxxxxxxxxx RF
                         SMC_N 24 ksftaivGpNGSGKsnll 41
                                  +++ +++G+NG+GK+ l+
  gi|13541870|ref|NP_111558.1| 32 SGILSLIGRNGAGKTTLI 49
                                  467789*********997 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 2.8e-05
                                   EE-HHHHHHHHHCTT-STT...CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEE CS
                                   xxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 117 evtkkevsellesagiske...lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfiv 194
                                   + ++ ev + le ++i  +   +LSgG+k  v +a l+A    + a + ++De    LD   ++++ +ll e + +  ++ 
  gi|13541870|ref|NP_111558.1| 115 KRRSMEVLKKLELEQIAGKlnrTLSGGQKRKVLVAALIA----SDADILFMDEPTTGLDPISRAELWDLLAELKREKFIFL 191
                                   44557777888888876544448*****98776666655....5678999***********************98888888 PP

                                   E-SSHHHCC CS
                                   xxxxxxxxx RF
                         SMC_N 195 islreemle 203
                                   +++  e  e
  gi|13541870|ref|NP_111558.1| 192 TTHYLEEAE 200
                                   887655444 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.89
                                   EEEEEEEETTEESSSSSSC.EEEEEEEETTSEEEEEET CS
                                   xxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx RF
                         SMC_N  78 eveitfdnedkklkiekee.vsisrrvkrkgeseykin 114
                                   e++ t+ +++++l i++ee +si r +++k+  ++ in
  gi|13541870|ref|NP_111558.1| 246 EINGTVLKTGRRLFIDEEEaYSIVRDLINKNA-KFSIN 282
                                   33344445555555555543555555555544.55555 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   3.9e-06    0.0047       3      57 ..      37      92 ..      35     187 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3.9e-06
                                  EESSTTSSHHHHHHHHHHHH..THEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS CS
                           AAA  3 lyGppGtGKTllakavakel..gvefleisgsellskyvgesekkirelfkeakeka 57
                                  l+G  G GKT+l++ + +el  ++ + ei+g +++     e  k+i+ + +ea++ +
  gi|13541870|ref|NP_111558.1| 37 LIGRNGAGKTTLIRILSTELlpSSGYAEIDGIDII-GEPDEIRKRIAIIPQEARAIS 92
                                  89*****************977799**********.447888888888888887766 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   5.6e-06    0.0067      17      50 ..      27      60 ..      21      64 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 5.6e-06
                        AAA_29 17 ieidlkgatlltGpsGsGKSTllDAiqalLvpak 50
                                  +++  +g+  l+G++G+GK+Tl+  +++ L+p++
  gi|13541870|ref|NP_111558.1| 27 FKVPASGILSLIGRNGAGKTTLIRILSTELLPSS 60
                                  5666778999*************88888777765 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   8.6e-06      0.01      15      39 ..      25      52 ..      15      57 .. 0.86
   2 ?   -0.7   0.2       1.5   1.8e+03     148     148 ..     162     162 ..      69     275 .. 0.62

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 8.6e-06
                        AAA_23 15 idF...skgltlItGpNGaGKTTildAi 39
                                  i F    +g+  ++G NGaGKTT+++ +
  gi|13541870|ref|NP_111558.1| 25 ISFkvpASGILSLIGRNGAGKTTLIRIL 52
                                  777777789999************9866 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.5
                        AAA_23 148 l 148
                                   +
  gi|13541870|ref|NP_111558.1| 162 D 162
                                   0 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   3.1e-05     0.037      25      63 ..      33      77 ..      20     185 .. 0.68
   2 ?   -1.9   0.0       3.1   3.7e+03      41      63 ..     176     198 ..     173     246 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.1e-05
                        AAA_16 25 elvllsGesGvGKsslvrellralekdggif......lrgkcdql 63
                                  +++ l+G  G GK++l+r l ++l  + g++      + g+ d+ 
  gi|13541870|ref|NP_111558.1| 33 GILSLIGRNGAGKTTLIRILSTELLPSSGYAeidgidIIGEPDEI 77
                                  7999********************999555443333355555555 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3.1
                        AAA_16  41 vrellralekdggiflrgkcdql 63 
                                   ++ ll +l+++++ifl++++ + 
  gi|13541870|ref|NP_111558.1| 176 LWDLLAELKREKFIFLTTHYLEE 198
                                   56667777777777777766555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.2   4.3e-05     0.052       6      30 ..      33      57 ..      31     236 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.3e-05
                        AAA_22  6 gilvvtGesGtGKTtllrrlleqld 30
                                  gil ++G  G+GKTtl+r l  +l 
  gi|13541870|ref|NP_111558.1| 33 GILSLIGRNGAGKTTLIRILSTELL 57
                                  8999**************9988774 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0    0.0014       1.7       3      22 ..      37      56 ..      36     101 .. 0.77
   2 ?    3.6   0.1     0.076        91      91     113 ..     183     205 ..     170     211 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0014
                        AAA_18  3 ltGtpGvGKttlakeLskrl 22
                                  l G  G+GKttl + Ls +l
  gi|13541870|ref|NP_111558.1| 37 LIGRNGAGKTTLIRILSTEL 56
                                  56888***********9986 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.076
                        AAA_18  91 akdikkvvLtaspeelleRlekR 113
                                   +k+ k+++Lt+++ e +eRl++R
  gi|13541870|ref|NP_111558.1| 183 LKREKFIFLTTHYLEEAERLSDR 205
                                   333344****************9 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.1    0.0011       1.4      31      88 ..     136     180 ..     110     182 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0011
                       SbcCD_C  31 gtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllell 88 
                                   +tlSGG+k++++  al a+             + +++f+DE   +lD+ s+a+l +ll
  gi|13541870|ref|NP_111558.1| 136 RTLSGGQKRKVLVAALIAS-------------DADILFMDEPTTGLDPISRAELWDLL 180
                                   6888888877666666633.............34688888888888888888888877 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00013      0.16      87     122 ..      19      55 ..       7      71 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00013
                                   HTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT CS
                   RsgA_GTPase  87 kegleelkellkd.ktsvlvGqSGvGKStLinallpe 122
                                    e+l++++ ++    +  l+G  G+GK+tLi  l  e
  gi|13541870|ref|NP_111558.1|  19 PEALKSISFKVPAsGILSLIGRNGAGKTTLIRILSTE 55 
                                   566777777776668999*************999876 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00011      0.13      33      72 ..      20      59 ..      11     161 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00011
                         Rad17 33 ewlkadvLesrkkriLLisGPsGCgkstvvkvLskelgik 72
                                  e+lk+ + +     iL + G  G gk+t +++Ls el ++
  gi|13541870|ref|NP_111558.1| 20 EALKSISFKVPASGILSLIGRNGAGKTTLIRILSTELLPS 59
                                  566666666666779********************99775 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00013      0.15      21      51 ..      37      67 ..      20      82 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00013
                    Zeta_toxin 21 lgGqpGAGKselaellkdelerqgnvvrldp 51
                                  l G  GAGK++l++ l +el + +++ ++d+
  gi|13541870|ref|NP_111558.1| 37 LIGRNGAGKTTLIRILSTELLPSSGYAEIDG 67
                                  4599****************99999999985 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 ?   11.9   0.0   0.00016       0.2      16      68 ..     228     282 ..     219     299 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00016
                   DNA_pol_B_3  16 nealtlegdetkdakdkisiFsevlstgnYvtidd.nvlkilekkin.ekkFtvk 68 
                                   ++++ ++  +t++ +++i+i   vl+tg  ++id+ + + i++  in ++kF+++
  gi|13541870|ref|NP_111558.1| 228 PKKYSINLIQTSNLDGEIEINGTVLKTGRRLFIDEeEAYSIVRDLINkNAKFSIN 282
                                   56677888899999*******************99789******99989999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       539  (0.030063); expected 358.6 (0.02)
Passed bias filter:                      499  (0.027832); expected 358.6 (0.02)
Passed Vit filter:                        89  (0.00496402); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.62u 0.33s 00:00:00.95 Elapsed: 00:00:00.52
# Mc/sec: 1781.65
//
Query:       gi|13541871|ref|NP_111559.1|  [L=247]
Description: ABC-type multidrug transport system, permease component [Thermoplasma volcanium GSS1]
Scores for complete 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  23.4    3.5e-11   42.9  23.4    1.6  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 !   42.9  23.4     2e-15   3.5e-11      14     207 ..      20     208 ..       7     210 .. 0.90
   2 ?   -3.3   1.1      0.28   4.9e+03     107     117 ..     226     236 ..     212     239 .. 0.48

  Alignments for each domain:
  == domain 1  score: 42.9 bits;  conditional E-value: 2e-15
                 ABC2_membrane  14 rwrdpslgllwrliqplllalvfgtvfgnlgnsedglnrpgllffsvlflafsaltsvapvferergvlerelvsplysls 94 
                                   + ++  ++l+  l++pl ++lv++++      +   ++  g+l++s++  + ++l++  ++   + ++ +   +sp+ ++s
  gi|13541871|ref|NP_111559.1|  20 AMKNFPITLINTLLSPLSFLLVITLASH---GRLISVSVGGALIMSMVSSG-LGLQGDLSHLKNDFKLQDIVVSSPT-TAS 95 
                                   456667888999*************999...35555667************.9999999******************.*** PP

                 ABC2_membrane  95 ayvlakvlvelpvsllqalifllivyflvgldlsrf.flflllllltalaasslgllisalapsfedasqlaslvllplll 174
                                   +y+++++++e+++s+ ++ ++ +++yf+++     + + ++ +l++++ +++ lg+ +++++ ++ +   ++++v +++  
  gi|13541871|ref|NP_111559.1|  96 VYLVGMAISEIVYSIPAISVLGILAYFFIHTSAI-GvLTIIGVLVVMFSFSILLGFTLATITYDIIQSWAFSGIVSTLIST 175
                                   ***************************9766653.35999999999999******************************** PP

                 ABC2_membrane 175 lsGffipidsmpkwlqwiaylnPltyavealrs 207
                                     ++++pi+ +p+ +++ ay++P tya e++++
  gi|13541871|ref|NP_111559.1| 176 IPPVYYPITYIPMPFRYAAYASPTTYAAEIIQN 208
                                   ************9****************9876 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 0.28
                 ABC2_membrane 107 vsllqalifll 117
                                   +++++++++l+
  gi|13541871|ref|NP_111559.1| 226 IIVIVTILLLI 236
                                   23333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1200  (0.0669307); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 1563.44
//
Query:       gi|13541872|ref|NP_111560.1|  [L=76]
Description: transposon-encoded protein [Thermoplasma volcanium GSS1]
Scores for complete 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-15   54.1   0.9    1.2e-14   53.8   0.9    1.2  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 !   53.8   0.9   6.5e-19   1.2e-14       3      47 ..      30      74 ..      28      76 .] 0.90

  Alignments for each domain:
  == domain 1  score: 53.8 bits;  conditional E-value: 6.5e-19
                       DUF2080  3 IrkktwlkvkeilpffegkVkpfGnSAkvsiPkeylGkkvylvIl 47
                                  Ir + +   ++++ ++++ V+ fGnS+kv++Pk y+Gk+vy+++ 
  gi|13541872|ref|NP_111560.1| 30 IRDQDLIIREKVETVYKKTVTLFGNSGKVDVPKRYIGKRVYVIVP 74
                                  77777777889********************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        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 0.30s 00:00:00.71 Elapsed: 00:00:00.47
# Mc/sec: 489.49
//
Query:       gi|13541873|ref|NP_111561.1|  [L=435]
Description: ammonia permease [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-54  185.3  36.0    1.8e-54  185.0  36.0    1.0  1  Ammonium_transp  Ammonium Transporter Family


Domain annotation for each model (and alignments):
>> Ammonium_transp  Ammonium Transporter Family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  185.0  36.0     1e-58   1.8e-54       1     377 [.       8     412 ..       8     428 .. 0.89

  Alignments for each domain:
  == domain 1  score: 185.0 bits;  conditional E-value: 1e-58
                                   HHHHHHHHHHHHHHHHHHHHHHHHSSGGGHHHHHHHHHHHHHHHHHHHHHTHHHHHHSSCBSSSSSCE-............ CS
               Ammonium_transp   1 aflllsaalvifmqagfalleaglvrsknvlnilvknlldlavvvllyvlfGyslafgkskgvsgfign............ 69 
                                   +++l+sa+lv++m++ +++le g        + l+k +l +++ +++  ++G+ +af     + g+ign            
  gi|13541873|ref|NP_111561.1|   8 LWVLFSAFLVFLMTIAVGFLEYGELGIALKRS-LYKTILITGIAFVVMAVIGFNTAFAPT--LYGIIGNplykpgfvlgyl 85 
                                   599********************998877655.9************************98..*************998888 PP

                                   .........TTTTSCCGCCTTCCHHH........HHHHHHHHHHHHHHHHHHHCTTTB-HHHHHHHHHHHHHHTHHHHHHH CS
               Ammonium_transp  70 .........lglsaagvqdetlldgl........fflfqlafaataitivsgavaerikfsayllfsallgtlvyppvahw 133
                                            +        ++t  +++        +flf  afa +++++vs  +  ++k+s++++fs++ + ++y   a w
  gi|13541873|ref|NP_111561.1|  86 nsptamfstI-------WWATSASYFntgllgitYFLFETAFASVTLALVSVVILRKVKMSVFVVFSIVYFIVIYNLPAAW 159
                                   8765444443.......344444444666666679********************************************** PP

                                   HHS.SSHHHHTT--.-SSSTTTTHHHHHHHHHHHHHHHS-STTTTG..TTTSS--GSBHHHHHHHHHHHHHHHHHHHHGGG CS
               Ammonium_transp 134 vwgeggwlaklgvliDfAgstvVHlvggvagLaaalvlgkregrfe..gkeeaikghnlpfavlGtllLwfgWfgFNaGsa 212
                                   +w+ +gwl+ lg+  DfAg++vVH  +g+agLa+++ + + e ++     + +i   n+ f +l  llL++gWfgFN+Gs+
  gi|13541873|ref|NP_111561.1| 160 IWNPTGWLYLLGMR-DFAGGLVVHGAAGFAGLAIIIRIWQEERKKGivRSPGEIIKVNDGFLTLAILLLMMGWFGFNPGSV 239
                                   **************.******************9987766665555679******************************** PP

                                   SSSSHHHHH.HHHHHHHHHHHHHHHHHHHHHHHCSS.-BHHHHHHHHHHHHHHHTTTTTTS-HHHHHHHHHHHHHHHHHHH CS
               Ammonium_transp 213 ltankrararaavtTllAaaagaltallisrlkegk.invlglanGilAGlVAiTaacavvepwgAliiGlvAgvlsvlgv 292
                                   l+ n      +++tT +Aa +++l +l++s+l  +    ++ ++nGil Gl+ +T+ +++v+p++A i+G+++g + +++ 
  gi|13541873|ref|NP_111561.1| 240 LAFNYDTLI-VVMTTFMAALTSMLSTLTVSYLLYKDaGGIMNAVNGILMGLIIVTPLAGFVSPLSAAILGILGGPIFIFAN 319
                                   ****99999.**********************98774578889************************************** PP

                                   HHHHHHHTC-CTTHHHHHHHHHHHHHHHHHHHHTSHHHC.....SSHSSTTGGGT-C...HHHHHHHHHHHHHHHHHHHHH CS
               Ammonium_transp 293 kklkeklkidDsldvvavHgvgGiwGllavgifaaekvv.....askisggllsgeg...kqlvvqligilvilayafvvt 365
                                    +++++  + D+++ ++ H +gGi G+l+ g+f + +++         +g +++g++   + l+++++gi+++ + +f+++
  gi|13541873|ref|NP_111561.1| 320 RFFSKRKWFSDPVGLFSGHFTGGIFGVLMIGFFTQHSYAvlsgnSILPNGLFFGGGYlalHTLGIEIMGICAVGLAVFAIS 400
                                   ************************************99999885555566677777799999******************9 PP

                                   HHHHHHHHHHTT CS
               Ammonium_transp 366 lilllllklllg 377
                                   +  ++ l+l + 
  gi|13541873|ref|NP_111561.1| 401 YATMYFLSLGFH 412
                                   999988877554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (435 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       869  (0.048469); 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):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 2695.60
//
Query:       gi|13541874|ref|NP_111562.1|  [L=441]
Description: major facilitator superfamily permease [Thermoplasma volcanium GSS1]
Scores for complete sequence (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  176.0  32.5    1.5e-51  175.7  32.5    1.1  1  Sugar_tr   Sugar (and other) transporter
    6.5e-27   94.4  56.8    1.3e-18   67.1  29.1    2.8  3  MFS_1      Major Facilitator Superfamily
     0.0014   17.3   5.6     0.0014   17.3   5.6    3.3  2  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 !  175.7  32.5   2.5e-55   1.5e-51      44     445 ..      54     440 ..      18     441 .] 0.88

  Alignments for each domain:
  == domain 1  score: 175.7 bits;  conditional E-value: 2.5e-55
                                   ...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHH CS
                      Sugar_tr  44 ssvlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlvP 124
                                   +s+l++l +s+ ++G ++Gs+++g l+d++GRk  +    ++++   vl++++    ++  +++  +l+Gig+G+ + l++
  gi|13541874|ref|NP_111562.1|  54 KSILVSLAASAIYIGMFVGSFVIGHLSDTIGRKRMYTYDLAITSLFLVLTGISR---NFAEFFIFELLAGIGIGADYPLSS 131
                                   578999************************************************...************************ PP

                                   HHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-TTHHHHHHHCCHHHHHHHHHHGGGS---HHHHHHTT-HH CS
                      Sugar_tr 125 myisEiApkklRgalvslyqlaitfGilvaaifglglnktsnadgwrillglqlvpallllilllflPESPrylvekgkee 205
                                      +E++p   Rg++ +++ +++t+G +v + +   l  + +++ wr++ ++ ++++++++i ++ lPESP++lv+ g ++
  gi|13541874|ref|NP_111562.1| 132 SIEAEFSPRVSRGRFLVFNIFMWTIGSIVFYLISIPLVGYFGSSSWRWMYFVGAIIPIAVIISRHALPESPYWLVKAG-RK 211
                                   *************************************555555********************************999.66 PP

                                   HHHHHHHHHHHCHHHHHHHHHHHHHHHHHHH.....HTTHHHHSH...HHHHHHHHHHHHHHTTHHHHHHHTTTHHHHSS- CS
                      Sugar_tr 206 eakevlaklrgeedadrelaeekdsleaeqeeekaswkellssktvrqrlligvvlqifqqltGinaimyysptifenlgl 286
                                   eak+v +++ +e++     +  ++s          s+k+++s      +l++ + +++f   +    + +y p+if ++g+
  gi|13541874|ref|NP_111562.1| 212 EAKKVAENIGKEAGTPNVDVPSVESGSS-------SIKSVFSG--SYLPLIMFASIAWFAYDVSSYGVWNYTPSIFVSTGI 283
                                   89******76665544444444444444.......48999999..4589***********99999**************** PP

                                   THH.HHHHHHHHHHHHHHHHHH.HHHHHHS-SHHHHHHHHHHHHHHHHHHH..HHHHTTSS...CHHHHHHHHHHHHHHHT CS
                      Sugar_tr 287 sks.llvtiivgvvnfvatfva.iflvdrfGRRtllllGaagmaicfvilgivalllvakskaasivaivfialfialfal 365
                                   s    +v+ ++  + ++a f++ + l+dr+GRR l   G+  + i ++ +g   + + ++     i++ +++a++  ++++
  gi|13541874|ref|NP_111562.1| 284 SVVsSIVSTLLEDLPVIAGFIVcLILIDRIGRRVLQAAGFGLAGISLLTFG--LYSMHHT--LPFILIFIAFAMMHLFHNI 360
                                   *99999999999999999999989*************99999999999998..6666666..34555556777888999** PP

                                   TTTHHHHHHHHHHSHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHT-HHHHHHHHHHHHHHHHHHHHS--STT--C CS
                      Sugar_tr 366 gwgpvpwvlvsElfpqsvRskalaiavavnwlanflisllfpiiteaigggyvflvfaglavlfiifvfffvpetkgrtl 445
                                   g++ + +v+  E+fp++vR++a+ ia+ ++ +  +l  + fp + ++ +     l+fa++  l++i++++  petk   l
  gi|13541874|ref|NP_111562.1| 361 GPTNLTYVYPVEIFPTRVRGTAMGIATSASRIGAILGVFAFPLLIGTFSLSAGLLFFAIFEFLGFIVTVILAPETKATAL 440
                                   *************************************************66667899*******************8765 PP

>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.1  29.1   2.2e-22   1.3e-18       3     241 ..      28     284 ..      26     293 .. 0.78
   2 !    3.4   5.8    0.0048        29     282     329 ..     251     298 ..     238     309 .. 0.78
   3 !   28.8  21.2   9.5e-11   5.7e-07      47     176 ..     301     436 ..     297     440 .. 0.80

  Alignments for each domain:
  == domain 1  score: 67.1 bits;  conditional E-value: 2.2e-22
                         MFS_1   3 laaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll.fa 82 
                                   +++f+ ++a si+++alp +l++   +    ++l++++ ++g++v+s+++G+lsd +Gr+r++   l++++l+ l+l+ + 
  gi|13541874|ref|NP_111562.1|  28 MGVFMDGFALSIFSAALP-YLKNYILVKSILVSLAASAIYIGMFVGSFVIGHLSDTIGRKRMYTYDLAITSLF-LVLTgI- 105
                                   789***************.******************************************************.555546. PP

                         MFS_1  83 sslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslg...Wravfyilai 159
                                   s  +  ++++ +l+G+g ga +p++ ++ a+ +p+  rgr + +   ++ +G+i+ +l++  l+ ++g   Wr+++++ ai
  gi|13541874|ref|NP_111562.1| 106 SRNFaEFFIFELLAGIGIGADYPLSSSIEAEFSPRVSRGRFLVFNIFMWTIGSIVFYLISIPLVGYFGsssWRWMYFVGAI 186
                                   777769******************************************************99999999999********** PP

                         MFS_1 160 vsllafvlfllllpeepperkrkspkeee..................kgtgpaplvp.......awkallkdpvlwillia 215
                                   + + +++        ++++ + ++  ++e                  +        p        +k++++  +l   li+
  gi|13541874|ref|NP_111562.1| 187 IPIAVII---SRHALPESPYWLVKAGRKEakkvaenigkeagtpnvdV--------PsvesgssSIKSVFSGSYLP--LIM 254
                                   *****88...55555555555555555544466555555544443333........14555566699999999884..333 PP

                         MFS_1 216 lllf.ffgfsg....lltllplylqevlgls 241
                                   ++++ +f++      +  ++p++     g+s
  gi|13541874|ref|NP_111562.1| 255 FASIaWFAYDVssygVWNYTPSI-FVSTGIS 284
                                   33330223333555566677764.5555555 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.0048
                         MFS_1 282 lllllaalglallavtssavllllvlvliGfglgfvfpsllalasdla 329
                                   +l+++a+++++   v+s  v+ + +++++++g ++v++++ +l+ dl 
  gi|13541874|ref|NP_111562.1| 251 PLIMFASIAWFAYDVSSYGVWNYTPSIFVSTGISVVSSIVSTLLEDLP 298
                                   445556666666666699999999******************999987 PP

  == domain 3  score: 28.8 bits;  conditional E-value: 9.5e-11
                         MFS_1  47 vaslplGrlsdrfGrrrvlllglllfalg.lllllfa..sslw.l.llvlrvlqGlgagalfp.agaaliadwfpkeergr 121
                                   ++ ++   l+dr+Grr +  +g+ l +++ l+++l++  ++l+ + ++++ +++ l+  ++ + + +++ +++fp + rg 
  gi|13541874|ref|NP_111562.1| 301 AGFIVCLILIDRIGRRVLQAAGFGLAGISlLTFGLYSmhHTLPfIlIFIAFAMMHLFHNIGPTnLTYVYPVEIFPTRVRGT 381
                                   455555789********************555555556577775524455558888885555515677889********** PP

                         MFS_1 122 aigllsagfslGailgpllggllasslgWravfyilaivsllafvlfllllpeep 176
                                   a+g++++++ +Gailg  + +ll+  ++ +a  +++ai+ +l+f++ ++l pe++
  gi|13541874|ref|NP_111562.1| 382 AMGIATSASRIGAILGVFAFPLLIGTFSLSAGLLFFAIFEFLGFIVTVILAPETK 436
                                   ********************************************98666666554 PP

>> MFS_2  MFS/sugar transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   5.6   2.3e-07    0.0014     233     340 ..      30     135 ..      21     138 .. 0.92
   2 ?   -1.2  20.4     0.096   5.7e+02     132     386 ..     143     410 ..     138     415 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2.3e-07
                         MFS_2 233 fllaalalgvlnglllYyltyvlgngsaasvfllvvtisallgiplwqplakrlgkkntyllgalltivllvlvlllqpsn 313
                                   +++  +al +  ++l Y  +y+l +   +s+ + +++i++++g++++  l   +g+k++y   +++t ++lvl+ +   +n
  gi|13541874|ref|NP_111562.1|  30 VFMDGFALSIFSAALPYLKNYILVKSILVSLAASAIYIGMFVGSFVIGHLSDTIGRKRMYTYDLAITSLFLVLTGIS--RN 108
                                   566778899999******************************************************99999999988..** PP

                         MFS_2 314 lllflvllviagfgvgvaallpwsmla 340
                                    + f+++ ++ag+g+g+ + l  s+ a
  gi|13541874|ref|NP_111562.1| 109 FAEFFIFELLAGIGIGADYPLSSSIEA 135
                                   ***************998888888876 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.096
                         MFS_2 132 RtsltsvrsflsvlggvlaailafllvlilgglkserkgylifaliialLmllgviiv.......vlgtkervem.rkkek 204
                                   R ++ ++  f+ ++g++++ ++ ++lv+ +g+     + ++++ +++a++ ++++i         ++ +k  +++ +k  +
  gi|13541874|ref|NP_111562.1| 143 RGRFLVFNIFMWTIGSIVFYLISIPLVGYFGS-----SSWRWMYFVGAIIPIAVIISRhalpespYWLVKAGRKEaKKVAE 218
                                   777888889999*******************9.....77777777777776666543211111113333333333355566 PP

                         MFS_2 205 teqkeklslleqlkevfrnraflillllfllaalalgvlnglllYylty..vlgngsaasvfllvvtisal.......... 273
                                   +  ke+++   ++ +v +    ++ ++++++  l ++   ++++Y +    v++    + v++++ ++s++          
  gi|13541874|ref|NP_111562.1| 219 NIGKEAGTPNVDVPSVESGSSSIKSVFSGSYLPLIMFASIAWFAYDVSSygVWNYTPSIFVSTGISVVSSIvstlledlpv 299
                                   777777777777777777777788787777777777777788877655423455334444444444555555555777777 PP

                         MFS_2 274 .lgiplwqplakrlgkkntyllgalltivllvlvlllqpsnlllflvllviagfgvgvaallpwsmladvvDygelktGkr 353
                                    +g+++   l  r+g++ + ++g+ l+ + l+ + l +  ++l+f+++++++ +   ++  + +  l+ v+ +     ++r
  gi|13541874|ref|NP_111562.1| 300 iAGFIVCLILIDRIGRRVLQAAGFGLAGISLLTFGLYSMHHTLPFILIFIAFAMM-HLFHNIGPTNLTYVYPVEI--FPTR 377
                                   6999*************98888888887777777777466666666665555555.6666666666777777777..689* PP

                         MFS_2 354 regvffavlsfisklatgiglgvsgllLsafgy 386
                                    +g+++++ + +s++++ +g++++ ll+++f +
  gi|13541874|ref|NP_111562.1| 378 VRGTAMGIATSASRIGAILGVFAFPLLIGTFSL 410
                                   **************************9999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (441 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       688  (0.0383736); expected 358.6 (0.02)
Passed bias filter:                      230  (0.0128284); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.70u 0.31s 00:00:01.01 Elapsed: 00:00:00.50
# Mc/sec: 2631.35
//
Query:       gi|13541875|ref|NP_111563.1|  [L=369]
Description: AAA family ATPase [Thermoplasma volcanium GSS1]
Scores for complete 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      2e-12   47.6   0.0    1.5  1  AAA_22           AAA domain
    2.4e-07   31.3   0.0    1.3e-05   25.6   0.0    2.8  2  AAA_16           AAA ATPase domain
    3.7e-07   30.6   0.0    7.6e-07   29.6   0.0    1.6  1  AAA              ATPase family associated with various cellul
    6.4e-05   22.5   0.1    0.00014   21.3   0.1    1.5  1  TniB             Bacterial TniB protein
    0.00028   20.9   2.8     0.0062   16.5   2.8    2.4  1  ATPase_2         ATPase domain predominantly from Archaea
    0.00059   19.8   0.0     0.0014   18.5   0.0    1.7  1  Cdc6_C           CDC6, C terminal winged helix domain
    0.00069   19.6   0.0     0.0025   17.7   0.0    1.9  2  Rad17            Rad17 P-loop domain
     0.0011   19.4   0.1      0.041   14.3   0.0    2.6  2  RNA_helicase     RNA helicase
     0.0012   17.8   0.0     0.0016   17.4   0.0    1.2  1  Kinesin          Kinesin motor domain
     0.0016   18.4   0.0     0.0035   17.3   0.0    1.5  1  Microtub_bd      Microtubule binding
     0.0023   17.3   0.0     0.0032   16.8   0.0    1.2  1  DUF2075          Uncharacterized conserved protein (DUF2075)
     0.0034   17.4   0.9     0.0097   15.9   0.2    2.0  2  AAA_14           AAA domain
     0.0044   17.1   0.4      0.014   15.5   0.4    1.9  1  TIP49_C          TIP49 AAA-lid domain
     0.0063   16.6   0.2      0.014   15.5   0.2    1.6  1  TFIID-31kDa      Transcription initiation factor IID, 31kD su
     0.0083   15.9   0.0      0.015   15.1   0.0    1.3  1  AAA_30           AAA domain
     0.0088   15.8   0.1      0.075   12.8   0.1    2.2  1  IstB_IS21        IstB-like ATP binding protein
  ------ inclusion threshold ------
      0.011   15.5   0.0      0.025   14.3   0.0    1.5  1  AAA_24           AAA domain
      0.012   14.8   0.1       0.14   11.3   0.0    2.3  2  DUF815           Protein of unknown function (DUF815)
      0.021   14.0   0.0      0.034   13.3   0.0    1.3  1  PIF1             PIF1-like helicase
      0.028   13.9   0.0       0.06   12.9   0.0    1.6  1  AAA_7            P-loop containing dynein motor region
      0.028   14.9   0.0       0.83   10.2   0.0    2.6  2  ABC_tran         ABC transporter
      0.053   14.1   0.1       0.17   12.4   0.1    2.0  1  AAA_18           AAA domain
      0.075   12.7   0.0       0.11   12.1   0.0    1.4  1  Sigma54_activat  Sigma-54 interaction domain
      0.081   12.2   0.1        3.7    6.7   0.0    2.1  2  KAP_NTPase       KAP family P-loop domain
      0.099   12.6   0.1       0.45   10.5   0.0    2.0  2  PadR             Transcriptional regulator PadR-like family
       0.16   11.9   0.0       0.33   10.9   0.0    1.5  1  NACHT            NACHT 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 !   47.6   0.0   2.9e-15     2e-12       7     130 ..      44     160 ..      42     165 .. 0.87

  Alignments for each domain:
  == domain 1  score: 47.6 bits;  conditional E-value: 2.9e-15
                        AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelkaerlsseellealeqalr 87 
                                    l+++G sGtGKT+++r l+++         ++p+++++++ s  s k++l ell+  g+  ++ r+s   ++++le+a++
  gi|13541875|ref|NP_111563.1|  44 NLIIYGDSGTGKTVTMRFLAREV--------RNPKIFYINAISYRSVKNVLVELLSHEGVIISE-RASYANIYTRLEKAIE 115
                                   689*******************9........499999**********************99999.**************** PP

                        AAA_22  88 aravielliiDEaqh.lr.seealeeLrsllnlsrkgvqliLvGt 130
                                   +++++++l+iDEa + lr  ee l +L +  +  + +++ i++ +
  gi|13541875|ref|NP_111563.1| 116 KYDKTVILVIDEAANiLRtDEEGLYYLFRSKDSFDVNISAIFIAM 160
                                   ***************775558888888444332556666676665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.0   1.9e-08   1.3e-05       2      61 ..      19      79 ..      18     158 .. 0.70
   2 ?   -0.6   0.0       2.2   1.5e+03      45      67 ..     168     206 ..     164     273 .. 0.61

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 1.9e-08
                        AAA_16  2 lvGReeeleqL.lsalervrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcd 61
                                  l  R+ e++++ + +++++  + + +++++G+sG+GK+  +r l+r+++  +++++++   
  gi|13541875|ref|NP_111563.1| 19 LRARDSEISKImEVVIKPALNNITTNLIIYGDSGTGKTVTMRFLAREVRNPKIFYINAISY 79
                                  778********7777889999999**********************999987444433332 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 2.2
                        AAA_16  45 lralekdggiflrgkcdqlesa................i 67 
                                    +++++++g+f + k+++++++                +
  gi|13541875|ref|NP_111563.1| 168 NQRIKRSYGLFNELKFKRYSKDeileivrdrarmslntT 206
                                   568888889999999998844423332222222222222 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 !   29.6   0.0   1.1e-09   7.6e-07       2      84 ..      46     137 ..      45     177 .. 0.72

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 1.1e-09
                                   EEESSTTSSHHHHHHHHHHHH.THEEEEEETTTCSSS...............STTHHHHHHHHHHHHHHHTS.TSEEEEEE CS
                           AAA   2 llyGppGtGKTllakavakel.gvefleisgsellsk...............yvgesekkirelfkeakeka.kpsilfiD 65 
                                   ++yG  GtGKT +++ +a+e+ + +++ i++ + +s                   +s ++i   +++a ek  k++il+iD
  gi|13541875|ref|NP_111563.1|  46 IIYGDSGTGKTVTMRFLAREVrNPKIFYINAISYRSVknvlvellshegviiSERASYANIYTRLEKAIEKYdKTVILVID 126
                                   79******************9547788888888885568899999999975555555666666666665555678****** PP

                                   TGGGHHHHHTTCCCHHHHH CS
                           AAA  66 Eidalaksrsgseseeeer 84 
                                   E+ ++ +++        e+
  gi|13541875|ref|NP_111563.1| 127 EAANILRTD--------EE 137
                                   *****9999........22 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.1     2e-07   0.00014      18     134 ..      25     134 ..      15     139 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 2e-07
                          TniB  18 eilerLeeLleypkrkrmpnlllvGdsnnGKtmivekFarlhppekdedaekvpvlvvqappkpdekrlyaaiLealgapl 98 
                                   ei + +e +++ + ++ + nl+++Gds +GKt+ + +F +++ +++       ++++++a +  + k+   ++L + g+ +
  gi|13541875|ref|NP_111563.1|  25 EISKIMEVVIKPALNNITTNLIIYGDSGTGKTVTM-RFLAREVRNP-------KIFYINAISYRSVKNVLVELLSHEGVII 97 
                                   5555566666666677789************9876.6776665554.......69************************** PP

                          TniB  99 kararvskleqqvlrllrelk.vrvLiiDEihnllag 134
                                   ++ra+ ++++ +  + +++++ + +L+iDE  n+l+ 
  gi|13541875|ref|NP_111563.1|  98 SERASYANIYTRLEKAIEKYDkTVILVIDEAANILRT 134
                                   ******************99626689********976 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   2.8     9e-06    0.0062       4     143 ..      22     140 ..      20     161 .. 0.64

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 9e-06
                      ATPase_2   4 Rekelkeleeiler.epnei...yfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefieeeeekkklek 80 
                                   R+ e++++ e++ +   n+i   + iYG  g GKt  ++ ++ + ++    +i+yi+  ++++ k           + l+ 
  gi|13541875|ref|NP_111563.1|  22 RDSEISKIMEVVIKpALNNIttnLIIYGDSGTGKTVTMRFLAREVRN---PKIFYINAISYRSVKNVLV-------ELLSH 92 
                                   6777777776643313333322278**************99999966...5567766555544443333.......22333 PP

                      ATPase_2  81 algiavpkaeleeilkeksklvfkaielllekikkkgkkiiiiiDelqklidlglngaellvk 143
                                      i  ++a+         +   +  ++l ++i+k  k +i++iDe++++     ++++  ++
  gi|13541875|ref|NP_111563.1|  93 EGVIISERASY--------A---NIYTRLEKAIEKYDKTVILVIDEAANIL--RTDEEG--LY 140
                                   33333344333........3...4567778888888888**********99..666444..33 PP

>> Cdc6_C  CDC6, C terminal winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   2.1e-06    0.0014      12      75 ..     289     350 ..     277     359 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2.1e-06
                                   SSS-EEHHHHHHHHHHHHHHTT-----HHHHHHHHHHHHHTTSEEEEEEE-CC.C-EEEEEEES CS
                        Cdc6_C  12 gkeevttgevyevYkslCesegvdpltqrevsdllseLemlgileleksskGrregrtrkisLn 75 
                                   ++ ++ +  v e+ k l e++ +dp  +  ++++l++Le lgi+++ ++s G+++g  +kis+ 
  gi|13541875|ref|NP_111563.1| 289 HSVSTDIACVSEQLKILREQYSLDP--EMDIYEILRKLEGLGIINSYVESSGKSSGVRKKISIH 350
                                   5666677777777777777777777..6789*******************************94 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   3.7e-06    0.0025      26      98 ..      24      95 ..      13     160 .. 0.73
   2 ?   -1.6   0.0       3.3   2.2e+03      39      71 ..     271     304 ..     246     313 .. 0.68

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 3.7e-06
                         Rad17 26 kkieevkewlkadvLesrkkriLLisGPsGCgkstvvkvLskelgiklrewlnpvslkepdnqksdfkgltek 98
                                  + i+++ e +    L++     L+i G sG gk+ +++ L++e     + ++n++s+++ +n   ++++   +
  gi|13541875|ref|NP_111563.1| 24 SEISKIMEVVIKPALNNI-TTNLIIYGDSGTGKTVTMRFLAREVRNPKIFYINAISYRSVKNVLVELLSHEGV 95
                                  567777777777777777.55689************************************9977776664333 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 3.3
                         Rad17  39 vLesrkkr.iLLisGPsGCgkstvvkvLskelgi 71 
                                   +L++ +   +L i+G    + st +  +s +l i
  gi|13541875|ref|NP_111563.1| 271 SLDKYELAaLLAICGCLSHSVSTDIACVSEQLKI 304
                                   4444333348889999999999998888877765 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0     6e-05     0.041       2      60 ..      46     130 ..      45     155 .. 0.68
   2 ?    2.3   0.0      0.31   2.2e+02      40      64 ..     235     259 ..     211     279 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 6e-05
                  RNA_helicase   2 wlyGpsgeGKStlakeLakallkkl............................klkkkdsvysrnpeddfwdgYtgqevvv 54 
                                   ++yG+sg+GK+++++ La+++ +                              +  +  ++y+    ++  ++Y++  ++v
  gi|13541875|ref|NP_111563.1|  46 IIYGDSGTGKTVTMRFLAREVRNPKifyinaisyrsvknvlvellshegviisERASYANIYT--RLEKAIEKYDKTVILV 124
                                   79******************9965556666666666666666666666655554444555555..3455556666666666 PP

                  RNA_helicase  55 idDfgq 60 
                                   id+ ++
  gi|13541875|ref|NP_111563.1| 125 IDEAAN 130
                                   666555 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.31
                  RNA_helicase  40 eddfwdgYtgqevvvidDfgqvkde 64 
                                   +  +   Y++ e + +dD+ + k+ 
  gi|13541875|ref|NP_111563.1| 235 KAAHIAEYRRSENISYDDVRAAKSM 259
                                   5678899************999865 PP

>> Kinesin  Kinesin motor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   2.4e-06    0.0016      59     146 ..      26     170 ..      13     232 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2.4e-06
                                   HHHHHHHHHHHHHTTSEEEEEEEESTTSSHHHHHTBC..........................TTTSBSHHHH...HHHHH CS
                       Kinesin  59 yeetakplvesvleGynatifaYGqtgsGKTyTmegk..........................eeeeeGiipr...aleel 110
                                    +++++ +++ +l+   + ++ YG +g+GKT Tm                               ++eG+i     + +++
  gi|13541875|ref|NP_111563.1|  26 ISKIMEVVIKPALNNITTNLIIYGDSGTGKTVTMRFLarevrnpkifyinaisyrsvknvlveLLSHEGVIISeraSYANI 106
                                   456778899*************************97677777777777766666666666666444456554211245566 PP

                                   HHHHHHCTTTH............................EEEEEEEEEEEEEETTEEEETTSTT CS
                       Kinesin 111 Fesikkekeek............................ekefsvkvsylEiYneeiyDLLesk 146
                                   +++++k  e+                             +++f+v++s + i ++    LL+++
  gi|13541875|ref|NP_111563.1| 107 YTRLEKAIEKYdktvilvideaanilrtdeeglyylfrsKDSFDVNISAIFIAMDDPALLLNQR 170
                                   6666655544466666666666666666666666666666666666666666666666666655 PP

>> Microtub_bd  Microtubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   5.1e-06    0.0035      63     102 ..      22      61 ..      14      85 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 5.1e-06
                                   HCCCCCCCCHHHHHHHHTT--EEEEEEES........... CS
                   Microtub_bd  63 eqeevfeeisqlvqsaldgynvcifaygqTGsGKtyTmeg 102
                                    ++e+ + ++++++ al++  ++++ yg  G GKt Tm  
  gi|13541875|ref|NP_111563.1|  22 RDSEISKIMEVVIKPALNNITTNLIIYGDSGTGKTVTMRF 61 
                                   5677888899999*************************86 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   4.6e-06    0.0032       3     102 ..      44     133 ..      42     158 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 4.6e-06
                       DUF2075   3 vvlVtGvaGtGKtvvllnllaeleddeeertavylsvNhplvlvlrealakkeekkkkkeafeklssfinnlsefkkaeek 83 
                                    +++ G++GtGKtv +  l+ e+      r+ ++++ N    + +++ l +    ++ +  +++ +s+ n ++  + +++ 
  gi|13541875|ref|NP_111563.1|  44 NLIIYGDSGTGKTVTMRFLAREV------RNPKIFYINAISYRSVKNVLVELL--SHEGVIISERASYANIYT--RLEKAI 114
                                   579*******************9......667777778777777888777777..666666666666666666..455566 PP

                       DUF2075  84 keepkedvvivDEAhrllt 102
                                   ++ +k  ++++DEA  +l 
  gi|13541875|ref|NP_111563.1| 115 EKYDKTVILVIDEAANILR 133
                                   7778999*******87766 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.2   1.4e-05    0.0097       5      78 ..      45     133 ..      42     156 .. 0.70
   2 ?   -1.3   0.0         3     2e+03      28      58 ..     186     218 ..     153     242 .. 0.56

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.4e-05
                        AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderd................kkladpekllelileklke.ekktyl 68 
                                   l+i G   +GKT+ ++ l++e    + +i+yin  + r                 +++a ++++++ + + +++ +k+ +l
  gi|13541875|ref|NP_111563.1|  45 LIIYGDSGTGKTVTMRFLAREVR--NPKIFYINAISYRSvknvlvellshegviiSERASYANIYTRLEKAIEKyDKTVIL 123
                                   78999999*******99998866..99********999977777777766666543333333555555555433578889* PP

                        AAA_14  69 flDEiqevpe 78 
                                   ++DE+ ++ +
  gi|13541875|ref|NP_111563.1| 124 VIDEAANILR 133
                                   ****998754 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 3
                        AAA_14  28 vkkesilyinldderdkkla.dpe.kllelile 58 
                                    +k++il+i  d+ r + ++  ++ +++++i e
  gi|13541875|ref|NP_111563.1| 186 YSKDEILEIVRDRARMSLNTtSYDdTIIDYIAE 218
                                   345555555555544422221111244455555 PP

>> TIP49_C  TIP49 AAA-lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.4     2e-05     0.014       5      62 ..     200     258 ..     194     260 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2e-05
                       TIP49_C   5 RakeEgvkldeeAldlLakigtet.SLRYaiqLltpasilakkrkkkevevedveevee 62 
                                   R+       d++ +d++a+i++e  S R ai  l+ a  +a+ r +++++ +dv+ +++
  gi|13541875|ref|NP_111563.1| 200 RMSLNTTSYDDTIIDYIAEISSEFgSARVAIDILAKAAHIAEYRRSENISYDDVRAAKS 258
                                   6666677778999********99659*****************************9987 PP

>> TFIID-31kDa  Transcription initiation factor IID, 31kD subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.2     2e-05     0.014      17      66 ..     202     256 ..     191     280 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2e-05
                   TFIID-31kDa  17 slgvteyeerVvlqLldfay.....rytssvLedAkvlaehakkkevslddvrlA 66 
                                   sl+ t+y++ +++ + ++       r  +++L  A ++ae+++++++s ddvr A
  gi|13541875|ref|NP_111563.1| 202 SLNTTSYDDTIIDYIAEISSefgsaRVAIDILAKAAHIAEYRRSENISYDDVRAA 256
                                   5678899999999999999888888999*************************99 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   2.1e-05     0.015      20     100 ..      44     131 ..      33     148 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.1e-05
                        AAA_30  20 vavltGpAGtGKttalkalreaweaaggrviglAptgkaAkv.Lae...elgi...eastiakllkrlk.grarlepgtll 92 
                                     ++ G  GtGKt +++ l++ +++ +    + A + +  k+ L e   + g+   e ++ a++ +rl+ + +++++  +l
  gi|13541875|ref|NP_111563.1|  44 NLIIYGDSGTGKTVTMRFLAREVRNPK-IFYINAISYRSVKNvLVEllsHEGViisERASYANIYTRLEkAIEKYDKTVIL 123
                                   46899**************88888665.33444555555544244311123434554444455555555666678888999 PP

                        AAA_30  93 ivDEagmv 100
                                   ++DEa+ +
  gi|13541875|ref|NP_111563.1| 124 VIDEAANI 131
                                   ****9876 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.1   0.00011     0.075      45     131 ..      40     143 ..      17     148 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00011
                     IstB_IS21  45 ekkenivllGpsGvGKs....hlaialgveavraglsvlfvrvedLveel............krarrdgklaralkrllkv 109
                                   +   n+++ G sG+GK+    +la  +    +    ++++ +v++++ el            + a+   +l++a++++ k+
  gi|13541875|ref|NP_111563.1|  40 NITTNLIIYGDSGTGKTvtmrFLAREVRNPKIFYINAISYRSVKNVLVELlshegviiseraSYANIYTRLEKAIEKYDKT 120
                                   5578************93333444444444555667899999998665551222222221111233456888999999999 PP

                     IstB_IS21 110 dllilDdlg.llpldqaeaellf 131
                                    +l++D+ + +l  d++   +lf
  gi|13541875|ref|NP_111563.1| 121 VILVIDEAAnILRTDEEGLYYLF 143
                                   99999998735666776666666 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   3.6e-05     0.025       4      76 ..      44     130 ..      42     137 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.6e-05
                        AAA_24   4 kiliyGpsgiGKTtlakel.....gpkplfidtek.Glksldadkfpdie..........swedfldevvelaaeladykt 68 
                                   +++iyG+sg+GKT +++ l      pk+++i+  + +++s+++  ++ ++          s+++++  +++  +++++  +
  gi|13541875|ref|NP_111563.1|  44 NLIIYGDSGTGKTVTMRFLarevrNPKIFYIN--AiSYRSVKNVLVELLShegviiseraSYANIYTRLEKAIEKYDKTVI 122
                                   689***********999998885555555554..43455555555555556777777888888888888888888888888 PP

                        AAA_24  69 lviDtide 76 
                                   lviD +  
  gi|13541875|ref|NP_111563.1| 123 LVIDEAAN 130
                                   88887765 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0    0.0002      0.14      29      85 ..      18      74 ..      11     127 .. 0.85
   2 ?    0.8   0.0      0.32   2.2e+02     189     223 ..     180     211 ..     173     237 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0002
                        DUF815 29 dLvgidkqkealventeqfleglpannvLLwGarGtGKSslvkallneyaeegLrli 85
                                  +L+  d++ ++++e + + + ++ + n++++G+ GtGK  ++++l +e+++ ++  i
  gi|13541875|ref|NP_111563.1| 18 RLRARDSEISKIMEVVIKPALNNITTNLIIYGDSGTGKTVTMRFLAREVRNPKIFYI 74
                                  56667777788888888888888999**********************998875544 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.32
                        DUF815 189 wlgFykldqeeYleiveklakklglelekeeleee 223
                                    l F++ +++e leiv+  a++   +l++++ +++
  gi|13541875|ref|NP_111563.1| 180 ELKFKRYSKDEILEIVRDRARM---SLNTTSYDDT 211
                                   58999***********998843...3333334444 PP

>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0     5e-05     0.034       7     113 ..      27     130 ..      23     145 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5e-05
                                   HHHHHHH......HCTS-EEEEESTTSSCHHHHHHHHHHCHCTCCC.EEEEESSHHHHHCC.TSEECHHHHT-TTSSS-HH CS
                          PIF1   7 kkvfdaiieavlnekgklfFvtGsgGtgKtflwkallkklrsegki.vlavAssGvAalllegGrtahsrfkiplekdees 86 
                                    k+++ +i+ +ln+   ++ ++G +GtgKt   + l   +r+ +   + a+    v  +l+     + s  ++ +++    
  gi|13541875|ref|NP_111563.1|  27 SKIMEVVIKPALNNITTNLIIYGDSGTGKTVTMRFLAREVRNPKIFyINAISYRSVKNVLV----ELLSHEGVIISERASY 103
                                   689999***********************************96544144555566666666....3445555555444444 PP

                                   HHHHHTSCCCHHHHHC-SEEEEECGGG CS
                          PIF1  87 tckikrgsklaellkktsliiwDEapm 113
                                        r +k  e+  kt ++++DEa  
  gi|13541875|ref|NP_111563.1| 104 ANIYTRLEKAIEKYDKTVILVIDEAAN 130
                                   444677888889999999999999875 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   8.7e-05      0.06      32      63 ..      41      72 ..      27      93 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 8.7e-05
                         AAA_7 32 nkkpvllvGptGtGKtviikdllkkldkekyl 63
                                     +++++G++GtGKtv+++ l +++ + k+ 
  gi|13541875|ref|NP_111563.1| 41 ITTNLIIYGDSGTGKTVTMRFLAREVRNPKIF 72
                                  5678999*************999998844433 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0    0.0012      0.83      13      37 ..      44      68 ..      40     212 .. 0.88
   2 ?    2.3   0.0      0.32   2.2e+02      58     120 ..     299     350 ..     264     368 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0012
                                  EEEEEESTTSSHHHHHHHHTTSS-- CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran 13 kvaivGenGaGKStLlkllagllkp 37
                                   + i G++G+GK+  ++ la+++++
  gi|13541875|ref|NP_111563.1| 44 NLIIYGDSGTGKTVTMRFLAREVRN 68
                                  5789*****************9874 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.32
                                   CHCEEEE-SS--S-TTSBHHHHHHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  58 rkeigvlpqepqlfpeltvrenesdeeiekalsklglkelkdtvvksspssLSgGqkqrvala 120
                                   ++++++l ++ +l         + + +i+++l+kl+  ++ ++ v+s  s  S G ++++++ 
  gi|13541875|ref|NP_111563.1| 299 SEQLKILREQYSL---------DPEMDIYEILRKLEGLGIINSYVES--SGKSSGVRKKISIH 350
                                   3333333444444.........4445566666666666666666633..44466666666553 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   0.00025      0.17       2      86 ..      46     132 ..      45     174 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00025
                        AAA_18   2 lltGtpGvGKttlakeLskrlgf.........................gvnlrdvakenglllevdpealdeskrldedkl 57 
                                   ++ G +G+GKt   + L+++  +                         gv++++ a+  +                     
  gi|13541875|ref|NP_111563.1|  46 IIYGDSGTGKTVTMRFLAREVRNpkifyinaisyrsvknvlvellsheGVIISERASYAN--------------------- 105
                                   799**************9997556888555553333322222222222222222222222..................... PP

                        AAA_18  58 dklldaleenssaleegknlvidghlael 86 
                                     + + le++++++++   lvid   + l
  gi|13541875|ref|NP_111563.1| 106 --IYTRLEKAIEKYDKTVILVIDEAANIL 132
                                   ..444444444444455555555544444 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   0.00016      0.11       6      48 ..      24      68 ..      19     138 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00016
                                  HHHHHHHHHHHHHCTSS..S-EEEECSTTSSHHHHHHHHHHHSTT CS
               Sigma54_activat  6 ealkelleqikkvaktd..lsvlitGesGtGKellaraiheaskr 48
                                  +++++++e + k a ++  ++++i G+sGtGK++  r + ++ ++
  gi|13541875|ref|NP_111563.1| 24 SEISKIMEVVIKPALNNitTNLIIYGDSGTGKTVTMRFLAREVRN 68
                                  5566666666655544444899************99988776554 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 ?    6.7   0.0    0.0053       3.7       1      73 [.      22      89 ..      22      92 .. 0.85
   2 ?    3.9   0.0     0.039        27     145     181 ..      91     127 ..      83     131 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0053
                    KAP_NTPase  1 ydlyasaladilseptlatpiv.vgLygkWGsGKssllnkledelkefakpvrflfaefnawsfkggddavael 73
                                  +d+ +s++ +++ +p+l + ++ + +yg  G+GK+    +l +e ++       +++++na s+ +  +++ el
  gi|13541875|ref|NP_111563.1| 22 RDSEISKIMEVVIKPALNNITTnLIIYGDSGTGKTVTMRFLAREVRNP------KIFYINAISYRSVKNVLVEL 89
                                  67889999999999*99776655899*********************9......99999999998877766555 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.039
                    KAP_NTPase 145 keeaplkklqteveelladmektLdalqkrlVvviDd 181
                                   + e+ ++++ ++ +++++++ek++++ +k++++viD+
  gi|13541875|ref|NP_111563.1|  91 SHEGVIISERASYANIYTRLEKAIEKYDKTVILVIDE 127
                                   567788888899999*********************8 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       3.7   2.6e+03      27      39 ..      99     111 ..      89     116 .. 0.81
   2 ?   10.5   0.0   0.00066      0.45      33      61 ..     316     345 ..     300     349 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 3.7
                                   CCTTHHHHHHHHH CS
                          PadR  27 lelseGslYpaLk 39 
                                   +++s++++Y+ L+
  gi|13541875|ref|NP_111563.1|  99 ERASYANIYTRLE 111
                                   4788999999886 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00066
                                   HHHHHHHHHHHTTSEEEEEE-S.TSSS-EE CS
                          PadR  33 slYpaLkrLekeglvesewees.gegpprk 61 
                                    +Y +L++Le  g+++s+ e s ++++ rk
  gi|13541875|ref|NP_111563.1| 316 DIYEILRKLEGLGIINSYVESSgKSSGVRK 345
                                   69*****************99965555555 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00048      0.33       3      30 ..      45      72 ..      43     139 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00048
                                  EEEEC-TTTCHHHHHHHHHHHHCTS-SC CS
                         NACHT  3 vilqGeaGsGKTtLlqklalawaegklp 30
                                  +i+ G++G GKT+ ++ la++ + +k +
  gi|13541875|ref|NP_111563.1| 45 LIIYGDSGTGKTVTMRFLAREVRNPKIF 72
                                  79******************99988865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       686  (0.038262); expected 358.6 (0.02)
Passed bias filter:                      504  (0.0281109); expected 358.6 (0.02)
Passed Vit filter:                       101  (0.00563333); 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: 0.64u 0.31s 00:00:00.95 Elapsed: 00:00:00.46
# Mc/sec: 2391.55
//
Query:       gi|13541876|ref|NP_111564.1|  [L=619]
Description: DNA polymerase I [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    7.9e-21   74.3   0.3      7e-09   34.9   0.0    3.1  3  DNA_pol_B  DNA polymerase family B
  ------ inclusion threshold ------
       0.24   11.8   0.8         21    5.5   0.1    2.5  2  FAM25      FAM25 family


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 !   34.9   0.0   7.8e-13     7e-09      20      82 ..     244     311 ..     236     315 .. 0.78
   2 !   20.1   0.0   2.3e-08   0.00021     121     232 ..     315     403 ..     312     422 .. 0.82
   3 !   15.6   0.2   5.7e-07    0.0051     283     408 ..     450     564 ..     448     589 .. 0.77

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 7.8e-13
                                   HHHHHHTTBE-B-----.--SS........-S----BE----EEESS-EEEEEETTHHHHHHHHTT-STT CS
                     DNA_pol_B  20 lrlakeegfilpdrtekkgkeee.......gYqGatVlePkkglydkpvlvlDFaSLYPsiiqahNlcyt 82 
                                   ++la ++g+ +p ++++ ++ ++          G++V++P  g+y + v  +DF+S+YPsii+++Nl++ 
  gi|13541876|ref|NP_111564.1| 244 VALAVNRGLLVP-MKKDDHEGQKspeelikRDRGGLVFQPVPGIYRD-VYEIDFSSMYPSIIVKYNLSPG 311
                                   566777788888.55554444446777875589************87.899*****************96 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 2.3e-08
                                   HHHHHHHHHHHHHHHHHHHHHCS--HHHHHHHHHHHHHHHHHHHHHHHHHTSTTSTT--HHHHHHHHHHHHHHHHHHHHHH CS
                     DNA_pol_B 121 llpklLkdllakRkaikkelkeekdefekalldkqQlalKvtaNsvYGftGvansrlpclalAasvTtiGRemLektkelv 201
                                    lp+ L+ ll++R  +k+   +      ++++ ++ +alK +  + +G+tG++n ++  +++ + +T iGR+ L  + ++ 
  gi|13541876|ref|NP_111564.1| 315 FLPEALNGLLERRLFYKRI-SA-----SSEVYSNRNAALKWLLLTSFGYTGYKNAKFGKIEVHEDITEIGRKLLADAISIA 389
                                   5899999999999999863.32.....3458**********************************************9999 PP

                                   HHT...SSGGGT-SS.....T-EEEEEBSSE CS
                     DNA_pol_B 202 ekkaellskllalpeeaeeeklkviYGDTDS 232
                                   +++                 ++++i G  DS
  gi|13541876|ref|NP_111564.1| 390 HDH-----------------GFEMIHGIVDS 403
                                   987.................44555555555 PP

  == domain 3  score: 15.6 bits;  conditional E-value: 5.7e-07
                                   EEEEEEEEESSTTSEEEEESSGGGSTTS-HHHHHHHHHHHHHHSSS....S-HHHHHHHHHHHHHHHHHHHHTT-S.-GGG CS
                     DNA_pol_B 283 kYaglkvektskanklliKGvdlvRrdncklvkevikkvlelllkdeteersleeglealksilkdvleeleenkv.plek 362
                                   +Y+gl ++     ++  ++G++l R d+ ++ k+   + le l +     r +e+++ +  +i +  ++ +++ +  pl+ 
  gi|13541876|ref|NP_111564.1| 450 RYYGLDYN-----GSYKVRGIELRRADAPEICKRFQVEALEVLREC----RTVEDVMSSKAKIEALEHRYIKNIRRfPLNY 521
                                   89999999.....8889**********************9998888....889999988888888888999887666**** PP

                                   G-EEEEESS.CCCSSGCCSHHHHHHHHHHHHCSS---TTCEEEEEE CS
                     DNA_pol_B 363 fvlskelskepenyksknlphlevakrlkkrneeapevgdrisYvi 408
                                   f++sk+++++ ++y+ +++ + ++    +++   ++++g  i+Y +
  gi|13541876|ref|NP_111564.1| 522 FTISKKITRHSSEYSVNTVTRSALK---AAETFGKVSLGQIIKYTV 564
                                   ************9966653332221...122233466666666655 PP

>> FAM25  FAM25 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.1    0.0024        21      11      39 ..     369     397 ..     367     404 .. 0.87
   2 ?    4.1   0.1    0.0065        58      37      63 ..     527     553 ..     524     555 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0024
                         FAM25  11 evveHaKeaGEKAiadalKkAqesgekvv 39 
                                   ev e + e G K +ada+  A++ g  ++
  gi|13541876|ref|NP_111564.1| 369 EVHEDITEIGRKLLADAISIAHDHGFEMI 397
                                   79999*****************9986666 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.0065
                         FAM25  37 kvvKevtekvtntvtnavtHAaEgLgk 63 
                                   k+ +  +e   ntvt ++  AaE+ gk
  gi|13541876|ref|NP_111564.1| 527 KITRHSSEYSVNTVTRSALKAAETFGK 553
                                   66677788899*************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (619 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       479  (0.0267165); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.67u 0.31s 00:00:00.98 Elapsed: 00:00:00.50
# Mc/sec: 3759.85
//
Query:       gi|13541877|ref|NP_111565.1|  [L=58]
Description: hypothetical protein TVN1046 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       371  (0.0206927); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); 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 0.23s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 464.40
//
Query:       gi|13541878|ref|NP_111566.1|  [L=137]
Description: hypothetical protein TVN1047 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       363  (0.0202465); 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:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 879.82
//
Query:       gi|13541879|ref|NP_111567.1|  [L=256]
Description: ABC-type Fe3+-siderophores transporter, solute-binding component [Thermoplasma volcanium GSS1]
Scores for complete sequence (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  100.3   0.0    1.4e-28  100.1   0.0    1.1  1  Peripla_BP_2  Periplasmic binding protein


Domain annotation for each model (and alignments):
>> Peripla_BP_2  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.1   0.0   7.6e-33   1.4e-28       1     236 [.       7     226 ..       7     228 .. 0.98

  Alignments for each domain:
  == domain 1  score: 100.1 bits;  conditional E-value: 7.6e-33
                                   EEE-SHHHHHHHHHTT-GGGEEEB-GGG--GGGGGGT..TS-BSBESSSB-HHHHHHH--SEEEE-GGG...GGGHHHHHH CS
                  Peripla_BP_2   1 iaslspsvteillalGatdkvvgvdtttsdpldadkleeaivevgadgeidvEklaalkPDlvilskglgltdedeellks 81 
                                   i+slsp++teil+++G+ + v g+++++++p +a+     i +vg++g++ +E l + +PD+++  +g+  ++  + ll++
  gi|13541879|ref|NP_111567.1|   7 IVSLSPAITEILFMIGLGEYVIGDSAFCVRPDKAR----RIRKVGSYGTVRMEILEEIDPDVIFTISGF--PHNLSTLLSE 81 
                                   9*********************************9....9*****************************..9999999999 PP

                                   HS-EEE----TTSHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTS-TT.-EEEEEEEETTE..EEEE-TTSTTTH CS
                  Peripla_BP_2  82 giptvivessntgeslkeqiralgellgledeaeklvaeidsklaaaksaidsekpkpvlvfggadeggyvvagsnsyigd 162
                                   + ++ +    + ++++ + ++++g  ++  +ea++l+  + + + +++ ++ +        +++ d gg+v +g +syi+d
  gi|13541879|ref|NP_111567.1|  82 KFNVKELKLPSNVAGILNLVMEVGYETDAVEEARELYRNLVEQIGKINYKVGTV-------YIELDLGGPVSFGAYSYITD 155
                                   9999999999999***************************************99.......******************** PP

                                   HHHTS--EESTTT--STT-EEE-HHHHHHH--SEEEEEEHHHHT-S--HHHHT-SHHHHTSHHHHTT-EEEE-H CS
                  Peripla_BP_2 163 lldalgieniaaeskkseyeeisaEqilasdpdvifvsgraeadnktgleflkenpllaelpAvkngrVyalds 236
                                    l   g+++i++ +   e+ + ++ +++++dpd+i++ ++  ++++ + +++ + +++++l+Avkn +V+ ++ 
  gi|13541879|ref|NP_111567.1| 156 ALYLKGLNSIYQGE-RREWLTPDFSYVKKMDPDIIIFEPK--MFRSIDEDKIVNERGWSDLKAVKNDNVFVTPG 226
                                   ************99.*************************..****************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       468  (0.026103); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.32s 00:00:00.88 Elapsed: 00:00:00.53
# Mc/sec: 1450.02
//
Query:       gi|13541880|ref|NP_111568.1|  [L=732]
Description: elongation factor EF-2 [Thermoplasma volcanium GSS1]
Scores for complete 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-63  213.2   1.0    4.8e-63  212.2   1.0    1.5  1  GTP_EFTU     Elongation factor Tu GTP binding domain
      8e-26   90.2   0.1    3.8e-25   88.0   0.0    2.3  2  EFG_IV       Elongation factor G, domain IV
    6.2e-24   83.8   0.0    1.8e-23   82.4   0.0    1.9  1  EFG_C        Elongation factor G C-terminus
    8.9e-24   83.4   0.1    2.1e-23   82.2   0.1    1.7  1  EFG_II       Elongation Factor G, domain II
    3.8e-14   52.8   2.6    1.2e-13   51.2   1.8    2.3  2  GTP_EFTU_D2  Elongation factor Tu domain 2
    0.00016   21.7   0.1    0.00052   20.1   0.1    1.9  1  MMR_HSR1     50S ribosome-binding GTPase
     0.0035   17.2   0.0     0.0093   15.8   0.0    1.7  1  RF3_C        Class II release factor RF3, C-terminal domain
  ------ inclusion threshold ------
      0.016   14.6   0.1      0.028   13.8   0.1    1.3  1  Smac_DIABLO  Second Mitochondria-derived Activator of Caspase
      0.018   14.9   0.9      0.082   12.8   0.1    2.5  3  RuvC         Crossover junction endodeoxyribonuclease RuvC
      0.038   13.4   0.0       0.13   11.7   0.0    1.9  1  SRPRB        Signal recognition particle receptor beta subuni
      0.038   13.6   0.9       0.81    9.2   0.1    2.2  2  Cas_DxTHG    CRISPR-associated (Cas) DxTHG family
      0.074   13.3   0.2       0.48   10.7   0.0    2.5  2  DUF2283      Protein of unknown function (DUF2283)


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 !  212.2   1.0   3.2e-66   4.8e-63       3     193 ..      21     257 ..      19     258 .. 0.89

  Alignments for each domain:
  == domain 1  score: 212.2 bits;  conditional E-value: 3.2e-66
                                   EEEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEET..TCSSEEEEEEEESSSG CS
                      GTP_EFTU   3 irnigiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaislek..etkkylinliDtPGHv 81 
                                   +rnigi++h+DhGKtTL+d+L++ +g++s+  e a+++ vlD  ++E++rgiTi++a++s+ +  ++k+ylinliDtPGHv
  gi|13541880|ref|NP_111568.1|  21 VRNIGIVAHIDHGKTTLSDNLIAGAGMMSE--ELAGKQLVLDYDEQEQARGITINAAVASMVHafQGKEYLINLIDTPGHV 99 
                                   79***************************9..889999************************557**************** PP

                                   GGHHHHHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTEEEEEEESCGSTHHHHHHHHHHHHHHHHHH......... CS
                      GTP_EFTU  82 dFskevirglrvlDgavlvvdaveGvepqteevlrlalkegvpiivfiNKmDrlkaelkeiveevkqklsrk......... 153
                                   dF  +v+r++r++Dg+++vvd+veGv+pqte+v+r+al+e v++++fiNK+Drl++el+   +e+++++++          
  gi|13541880|ref|NP_111568.1| 100 DFGGDVTRAMRAVDGVIVVVDSVEGVMPQTETVIRQALREYVKPVLFINKIDRLINELRLNSDEMQKRFTKIisdvnklis 180
                                   *********************************************************************888777766666 PP

                                   .......HHHHHHHHHTTTTTEEEEEEBTTTTBTHH..................................HHHHHHHHHSH CS
                      GTP_EFTU 154 .......eeklekygekgekevpvvfgSalkgegvk..................................tllealvellp 193
                                          ++++++ +    ++ +v+fgSa+++++++                                   +l++++++lp
  gi|13541880|ref|NP_111568.1| 181 kyapkefTKEWQVSV----QDGKVAFGSAYNNWAISvpsmaetkitfkdiveyvkngkqkelaqknqlhkIILNMVIRHLP 257
                                   666544444444444....5667**********998888888888888888888888899999999888668999999987 PP

>> EFG_IV  Elongation factor G, domain IV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       2.6   3.9e+03       3      17 ..     463     477 ..     461     509 .. 0.65
   2 !   88.0   0.0   2.6e-28   3.8e-25      10     121 .]     513     620 ..     505     620 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 2.6
                                   CESCEE.SS-CCHCC CS
                        EFG_IV   3 VayrEtirkpvkere 17 
                                   V yrEt++k+   +e
  gi|13541880|ref|NP_111568.1| 463 VVYRETVEKKGGPFE 477
                                   778888777655444 PP

  == domain 2  score: 88.0 bits;  conditional E-value: 2.6e-28
                                   SS-CCHCCCCCCCHTSSSHCCCCCEEEECCTTTTSSEEEEE--STCCCHCCCCHHHHCCCCCCTTS-TTTS--EESEEEEE CS
                        EFG_IV  10 rkpvkereeklkkqsggdgqyakvileiePleegsgnefvdetkggqvpkeyieavekGfqealkeGplagepvtdvkvtL 90 
                                    k++k + e+l+  +g+d+++a+  +++e      +n++ d t+g+q+++e++e+  ++f+e++++Gpla+e+v +vk++L
  gi|13541880|ref|NP_111568.1| 513 FKDKKTIIETLVS-KGIDREEARGLVCVEG-----TNIMFDVTRGIQYLDETMELLIEAFTEVMNRGPLANEKVFGVKARL 587
                                   4666668888888.7***************.....89******************************************** PP

                                   EEEE--T..TTC-HHHHHHHHCHHHHHHHHCC- CS
                        EFG_IV  91 ldgslhe..vdsseaafkpaarralkeallkAs 121
                                   +d++lhe  +++++a+++pa+r+ ++ a+ +A+
  gi|13541880|ref|NP_111568.1| 588 VDAKLHEdsIHRGPAQVIPAGRNSIYGAMCEAK 620
                                   ******************************996 PP

>> EFG_C  Elongation factor G C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.4   0.0   1.2e-26   1.8e-23       1      87 [.     622     707 ..     622     709 .. 0.98

  Alignments for each domain:
  == domain 1  score: 82.4 bits;  conditional E-value: 1.2e-26
                                   EEEEEEEEEEEEEECCCCCCHHHHHHHCT-EEEEEEEE.TTEEEEEEEEEGGG-TTHHHCHHHCTTTS-EEEEEEEEEEE- CS
                         EFG_C   1 vllEPivkveievpeeyvgkvisdlssrrGeiedmeqdasgrviieaeiPlaeligfateLrslTkGegsfsmefsgYeev 81 
                                   +llEP++kv i+vp+e +g +i+++++rrG iedm+q+ ++ v + a+iP+++++gfa+++rs+T G+  +s e +gY++v
  gi|13541880|ref|NP_111568.1| 622 ILLEPVQKVFINVPQEEMGSAINEVQQRRGVIEDMTQE-GEEVSLVARIPVSGMFGFASAIRSATGGKVLWSFENAGYQKV 701
                                   59************************************.****************************************** PP

                                   -HHHHH CS
                         EFG_C  82 pgdkld 87 
                                   p +++d
  gi|13541880|ref|NP_111568.1| 702 PPELQD 707
                                   **9997 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 !   82.2   0.1   1.4e-26   2.1e-23       2      74 ..     387     459 ..     386     460 .. 0.98

  Alignments for each domain:
  == domain 1  score: 82.2 bits;  conditional E-value: 1.4e-26
                        EFG_II   2 PePvislaiepkskadedklskaLarlleEDptlrverdeeTketilsGmGelHleivverlkreykvevelg 74 
                                   +ePv++laie+k  ad  +l ++L+ +++ Dp+++v  ++eT+e ++sGmGelHl++++ r+k++yk+eve++
  gi|13541880|ref|NP_111568.1| 387 SEPVVTLAIEAKHTADLPRLIDVLRDISKADPSIQVDINQETGEHLISGMGELHLDVTLYRIKNDYKIEVETS 459
                                   69********************************************************************996 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 ?   -2.1   0.0       3.6   5.3e+03      16      41 ..     250     273 ..     249     282 .. 0.79
   2 !   51.2   1.8   7.9e-17   1.2e-13       1      73 [.     306     371 ..     306     372 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 3.6
                                   TEEEEEEC.TCTTSEEEEEEEEEEEEE CS
                   GTP_EFTU_D2  16 Gdevrilg.ndtskkeivtrissletf 41 
                                   ++ +r l+  +t ++    ri+++++ 
  gi|13541880|ref|NP_111568.1| 250 NMVIRHLPdPKTAQS---YRIKQIWKG 273
                                   678999998888888...999998865 PP

  == domain 2  score: 51.2 bits;  conditional E-value: 7.9e-17
                                   EEEEEEEEEESEEETTEEEEEECTCTTSEEEEEEEEEEEEETEEESEEETTSEEEEEEEESSCCSGSSTTCEE CS
                   GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilgndtskkeivtrissletfhededeavaganaGvivaikgledaiivGdtl 73 
                                   G++a gr++sGt+kkG  ++i  +++ +k   ++++ l ++ ++ +++v+++ aG+i+ai+gl+ a i+G+t+
  gi|13541880|ref|NP_111568.1| 306 GEIAIGRLFSGTVKKGTDLYI--SGD-GK---GKVQTLAMMVGPDRIPVEEVTAGNIAAIVGLKGA-IAGSTV 371
                                   89*******************..765.77...9********************************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 !   20.1   0.1   3.5e-07   0.00052       2     111 ..      24     146 ..      23     149 .. 0.60

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 3.5e-07
                                   EEEEESTTSSHHHHHHHHHT................STEEESSSTTSSSSEEEEEEE....ETTEEEEEEECGGCSSHHHH CS
                      MMR_HSR1   2 vaivGrpNvGKStLinaltg................ekaivsdkpgtTrdinegrvk....lkgkeielvDtpGliegase 62 
                                   ++iv +   GK+tL   l+                 +  + ++  g T++   + +      k+  i+l+DtpG ++    
  gi|13541880|ref|NP_111568.1|  24 IGIVAHIDHGKTTLSDNLIAgagmmseelagkqlvlDYDEQEQARGITINAAVASMVhafqGKEYLINLIDTPGHVD---F 101
                                   7788888899999999999544455555544333222345566667777777666655542223669*******665...2 PP

                                   HHHHHHHHHHHHCTSEEEEEEETTTTCSHHHHHHHHHH.HHHTTSEEEEE CS
                      MMR_HSR1  63 ekglgkaflaleeadlillvvdaseeklkpldeeleel.leeakkplilv 111
                                   + ++++a+   + +d +++vvd+  e++ p+ e++ +  l+e  kp+ l 
  gi|13541880|ref|NP_111568.1| 102 GGDVTRAM---RAVDGVIVVVDSV-EGVMPQTETVIRQaLREYVKPV-LF 146
                                   22344444...458********77.6677766665444044455554.33 PP

>> RF3_C  Class II release factor RF3, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   6.2e-06    0.0093      39      81 ..     420     461 ..     395     486 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 6.2e-06
                                   SEEEEET.TSS-EEEEESSTHHHHHHHHHHHHHH---EEEEE- CS
                         RF3_C  39 vqvfkeeeageelilgaVGqLQfeVveeRlknEYgvevrlesl 81 
                                   +qv  ++ ++ e +++ +G+L ++V  +R+kn Y++ev++++ 
  gi|13541880|ref|NP_111568.1| 420 IQVDINQ-ETGEHLISGMGELHLDVTLYRIKNDYKIEVETSEP 461
                                   5665555.4567788889********************98764 PP

>> Smac_DIABLO  Second Mitochondria-derived Activator of Caspases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   1.9e-05     0.028      56     177 ..     115     232 ..     108     271 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.9e-05
                   Smac_DIABLO  56 vslvtDsastfLsqttlaLidalteYtkavytLvsLqkrYanllgklnseeedaiWqviiGaRvevsekqeeylklessWm 136
                                   v +v Ds +  + qt   + +al eY+k v  + ++ +  +n l +lns+e ++ +  ii    ++ +k    +++  +W+
  gi|13541880|ref|NP_111568.1| 115 VIVVVDSVEGVMPQTETVIRQALREYVKPVLFINKIDR-LINEL-RLNSDEMQKRFTKIISDVNKLISKYA-PKEFTKEWQ 192
                                   56899*************************87666655.55555.8**************99888888765.58999**** PP

                   Smac_DIABLO 137 tavklselaaeaayqsGadqasvtarshlqlvksqveevrq 177
                                    +v+  ++a  +ay+  a     +a++++   k  ve v++
  gi|13541880|ref|NP_111568.1| 193 VSVQDGKVAFGSAYNNWAISVPSMAETKITF-KDIVEYVKN 232
                                   ****************998888888888765.334444443 PP

>> RuvC  Crossover junction endodeoxyribonuclease RuvC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       4.5   6.7e+03      39      56 ..      66      83 ..      30      93 .. 0.62
   2 ?   12.8   0.1   5.5e-05     0.082      31     121 ..     157     246 ..     148     264 .. 0.71
   3 ?   -1.7   0.0       1.5   2.3e+03      49     110 ..     296     361 ..     290     374 .. 0.56

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 4.5
                                  HHHHHHHHHHHHHHHHHH CS
                          RuvC 39 serlkavfdaveellday 56
                                  ++r  ++ +av ++++a+
  gi|13541880|ref|NP_111568.1| 66 QARGITINAAVASMVHAF 83
                                  344444444444444444 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 5.5e-05
                                   EE---S-HHHHHHHHHHHHHHHHHHH--SEEEEEE-S----HHHHHHHHHHHHHHHHHHH.TTT--EEEEEHHHHHHHHTS CS
                          RuvC  31 irtksdplserlkavfdaveelldayepdalaieqvffaknvdsvlklaqarGvvilaal.ereisvaeytpsqvkkavtG 110
                                   +r +sd++++r+ ++++ v++l+++y p++++ e   + ++ + +++ a    ++++  + e +i ++    + vk+    
  gi|13541880|ref|NP_111568.1| 157 LRLNSDEMQKRFTKIISDVNKLISKYAPKEFTKEWQVSVQDGKVAFGSAYNNWAISVPSMaETKITFK-DIVEYVKNGK-Q 235
                                   68899*****************************99999999****9999999999965504455433.2333344321.2 PP

                                   STT--HHHHHH CS
                          RuvC 111 igkaekeqvqa 121
                                   +  a+k+q   
  gi|13541880|ref|NP_111568.1| 236 KELAQKNQLHK 246
                                   22344444333 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 1.5
                                   HHHHHHHH--SEEEEEE-S----HH..HHHHHHHHHH.HHHHHHH..TTT--EEEEEHHHHHHHHTS CS
                          RuvC  49 veelldayepdalaieqvffaknvd..svlklaqarG.vvilaal..ereisvaeytpsqvkkavtG 110
                                   v++++   ++ ++ai ++f++   +       +  +G v +la++     i+v e t+ ++  a++G
  gi|13541880|ref|NP_111568.1| 296 VTKIIIDPHAGEIAIGRLFSGTVKKgtDLYISGDGKGkVQTLAMMvgPDRIPVEEVTAGNIA-AIVG 361
                                   66666666677778888877644331022333445552334555522356777777777774.4555 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   8.6e-05      0.13      26      86 ..      44     122 ..      21     148 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 8.6e-05
                                   S...................S---B---SS-EEETTG.....GGTT-SEEEETT-GCCSHHHHHHHHHHGGEEEEEEEEET CS
                         SRPRB  26 d...................svkktvtSqessaalkv..ksekgskltliDfPGheklrqklleklkaksslkglvfvvDS 85 
                                   +                   + +   + +++ +a  v   + k+  ++liD PGh+ +  +++      + + g++ vvDS
  gi|13541880|ref|NP_111568.1|  44 GagmmseelagkqlvldydeQEQARGITINAAVASMVhaFQGKEYLINLIDTPGHVDFGGDVTRA---MRAVDGVIVVVDS 121
                                   444444444444444444432222222333444444422255667789************99887...78899*******9 PP

                                   T CS
                         SRPRB  86 t 86 
                                    
  gi|13541880|ref|NP_111568.1| 122 V 122
                                   5 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 ?    2.8   0.1     0.049        73     242     312 ..     140     223 ..     104     265 .. 0.63
   2 ?    9.2   0.1   0.00054      0.81      70     125 ..     494     555 ..     444     581 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.049
                     Cas_DxTHG 242 e.....iveklkeeleei.esleeeesakplellldeikkklekf...lkkq.ikwclekgliqqal.tllreliisl.ll 310
                                   +     +++k+++ ++e+     ++e  k + +++++++k+++k+         +w+++ +  + a+ +  + ++is+  +
  gi|13541880|ref|NP_111568.1| 140 YvkpvlFINKIDRLINELrL--NSDEMQKRFTKIISDVNKLISKYapkE--FtKEWQVSVQDGKVAFgSAYNNWAISVpSM 216
                                   13336666776677777722..344555788899999999999997440..244676666666666655556666666544 PP

                     Cas_DxTHG 311 e.....g 312
                                   +      
  gi|13541880|ref|NP_111568.1| 217 AetkitF 223
                                   4232221 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00054
                     Cas_DxTHG  70 lkeeleelle..iekvdveiipgggteeelweifekllek.leende..........iilDiThGfryl 125
                                   lk e+    +  ie+ d   ip+g ++++   i+e+l++k ++ ++           i +D+T G+ yl
  gi|13541880|ref|NP_111568.1| 494 LKPEV----IqaIEDGD---IPQGSKFKDKKTIIETLVSKgIDREEArglvcvegtnIMFDVTRGIQYL 555
                                   44444....14588888...******************99776665579******************98 PP

>> DUF2283  Protein of unknown function (DUF2283)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00032      0.48      23      48 ..      49      75 ..      42      75 .. 0.84
   2 ?   -2.1   0.1       3.1   4.6e+03      20      39 ..     643     661 ..     631     665 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00032
                       DUF2283 23 seevdd.diilDfDedGrlvGIEiLnA 48
                                  see+++ +++lD+De+ +  GI+i  A
  gi|13541880|ref|NP_111568.1| 49 SEELAGkQLVLDYDEQEQARGITINAA 75
                                  6777444****************9765 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3.1
                       DUF2283  20 veeseevdddiilDfDedGr 39 
                                   + e+++   ++i D+ ++G+
  gi|13541880|ref|NP_111568.1| 643 INEVQQ-RRGVIEDMTQEGE 661
                                   667777.8999999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (732 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       729  (0.0406604); expected 358.6 (0.02)
Passed bias filter:                      578  (0.0322383); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.78u 0.34s 00:00:01.12 Elapsed: 00:00:00.51
# Mc/sec: 4319.97
//
Query:       gi|13541881|ref|NP_111569.1|  [L=104]
Description: 30S ribosomal protein S10P [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-29  102.4   0.0    1.4e-29  102.2   0.0    1.0  1  Ribosomal_S10  Ribosomal protein S10p/S20e
  ------ inclusion threshold ------
      0.019   15.8   0.0      0.037   14.8   0.0    1.4  1  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 !  102.2   0.0   1.5e-33   1.4e-29       1      97 [.       7     100 ..       7     101 .. 0.99

  Alignments for each domain:
  == domain 1  score: 102.2 bits;  conditional E-value: 1.5e-33
                                   EEEEEESSHHHHHHHHHHHHHHTTSSS-EE---EEEEEEEEEEEEE--SS--.S--EEEEEEEEEEEEEEEE.E-HHHHHH CS
                 Ribosomal_S10   1 rirlkSydsklLekavkkivraakelgikvkgpvplPtkrkrvtvlksphvd.kksreqfeirthkRlidisdatketidt 80 
                                   ri l+++++k ++ ++++i+++a+++g+++ gp+plPtk++ v+v+ksp ++ +++++++e+r+hkRlid+ da+++t+++
  gi|13541881|ref|NP_111569.1|   7 RISLSGTEHKIVDMVCSEIKEIASRTGVEIHGPMPLPTKKLVVPVRKSPDGEgTNTWDHWEMRIHKRLIDV-DADERTLRQ 86 
                                   799********************************************************************.8******** PP

                                   HS-...S---SS-EEEE CS
                 Ribosomal_S10  81 llkllqlnlpegVsvev 97 
                                   l++   +++p+gV++e+
  gi|13541881|ref|NP_111569.1|  87 LMR---IPIPDGVQIEI 100
                                   ***...*********98 PP

>> PriA_C  Primosomal protein N C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   4.1e-06     0.037       4      51 ..       4      47 ..       3      52 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4.1e-06
                        PriA_C  4 rlalirvsgkdeekveeaaeelaellkealkleeveilgpapapiaki 51
                                  + a+i +sg++ + v  +++e++e+ ++    ++vei gp+p p +k+
  gi|13541881|ref|NP_111569.1|  4 YKARISLSGTEHKIVDMVCSEIKEIASR----TGVEIHGPMPLPTKKL 47
                                  5699*******************99999....6799********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       433  (0.0241508); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        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 0.28s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 676.85
//
Query:       gi|13541882|ref|NP_111570.1|  [L=424]
Description: elongation factor 1-alpha [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.1e-55  187.3   0.0    2.9e-55  186.8   0.0    1.2  1  GTP_EFTU     Elongation factor Tu GTP binding domain
    1.3e-35  122.1   0.3    5.6e-35  120.0   0.0    2.2  3  GTP_EFTU_D3  Elongation factor Tu C-terminal domain
    5.6e-19   68.3   0.2      2e-18   66.5   0.1    2.0  2  GTP_EFTU_D2  Elongation factor Tu domain 2
    5.8e-07   29.6   0.0    1.1e-05   25.5   0.0    2.3  1  MMR_HSR1     50S ribosome-binding GTPase
    4.5e-05   23.3   0.3    0.00011   22.0   0.3    1.6  1  GTP_EFTU_D4  Elongation factor Tu domain 4
    0.00076   19.1   0.1     0.0034   17.0   0.0    1.9  2  Ras          Ras family
     0.0086   16.3   0.1       0.49   10.6   0.0    2.2  2  Roc          Ras of Complex, Roc, domain of DAPkinase
  ------ inclusion threshold ------
      0.012   15.0   0.0       0.03   13.7   0.0    1.5  1  Gtr1_RagA    Gtr1/RagA G protein conserved region
      0.055   12.9   0.1       0.42   10.0   0.1    2.2  1  SRPRB        Signal recognition particle receptor beta subuni
      0.079   12.5   0.0       0.91    9.0   0.0    2.6  2  FeoB_N       Ferrous iron transport protein B
       0.09   12.0   0.0       0.18   11.1   0.0    1.4  1  Septin       Septin
       0.12   12.1   0.1        2.4    7.9   0.0    2.5  2  PduV-EutP    Ethanolamine utilisation - propanediol utilisati


Domain annotation for each model (and alignments):
>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  186.8   0.0   1.9e-58   2.9e-55       1     189 [.       5     214 ..       5     245 .. 0.90

  Alignments for each domain:
  == domain 1  score: 186.8 bits;  conditional E-value: 1.9e-58
                                   TCEEEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHH...HHHST.............HCHSHHHHHHTSCSSCEEEEEET CS
                      GTP_EFTU   1 krirnigiighvDhGKtTLtdrLlyktgaiskkgeka...eeerv.............lDtlkeErergiTiksaaislek 65 
                                   k+++n+++ighvDhGK+TL++rLl+++g+i  +  ++   e   +             +D+ keErerg+Ti+ a+ ++e 
  gi|13541882|ref|NP_111570.1|   5 KPHLNLITIGHVDHGKSTLVGRLLFEHGEIPAHIIEEyrkE---AeqkgkatfefawvMDRFKEERERGVTIDLAHRKFE- 81 
                                   579**************************999777775431...234578889***************************. PP

                                   TCSSEEEEEEEESSSGGGHHHHHHHHHT-SEEEEEEETTTB..STHHHHHHHHHHHHTTTE.EEEEEESCGST.....HHH CS
                      GTP_EFTU  66 etkkylinliDtPGHvdFskevirglrvlDgavlvvdaveG..vepqteevlrlalkegvp.iivfiNKmDrl.....kae 138
                                    t+ky ++liD+PGH+dF+k++i+g++++D a+lv++a+eG  v++qt+e++ la+++gvp i+v+iNKmD +     +++
  gi|13541882|ref|NP_111570.1|  82 -TDKYYFTLIDAPGHRDFVKNMITGTSQADAAILVISAREGegVMEQTREHAFLARTLGVPqIVVAINKMDATeppfsEKR 161
                                   .**************************************7666******************************99999999 PP

                                   HHHHHHHHHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTBTHH............HHHHHHH CS
                      GTP_EFTU 139 lkeiveevkqklsrkeeklekygekgekevpvvfgSalkgegvk............tllealv 189
                                   ++e++ +++ kl      l+ +g+k+    ++v++S++kg++v+            +ll+al+
  gi|13541882|ref|NP_111570.1| 162 FNEVKADAE-KL------LKTIGYKD---ATFVPISGYKGDNVTkpspnmpwykgpSLLQALD 214
                                   999999999.55......58888886...59***********997777777777776777665 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 ?   -2.0   0.0       2.9   4.4e+03       8      60 ..     109     161 ..     103     174 .. 0.62
   2 ?   -2.7   0.0       4.8   7.1e+03      56      75 ..     275     294 ..     265     299 .. 0.71
   3 !  120.0   0.0   3.7e-38   5.6e-35       3     109 ..     315     419 ..     313     422 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 2.9
                                   EEEEEEESSS...SS-BSTT-EEEEESSS-EEEEEEEEEEECCSSTTSB-BSS- CS
                   GTP_EFTU_D3   8 feAqvyileke.rhtpitagYrpvlyirtadvtgkvveLlskldkktekvsekk 60 
                                    +A +++++ +  ++ + +  +  + +rt  v   vv++ +k+d  +   sek+
  gi|13541882|ref|NP_111570.1| 109 ADAAILVISAReGEGVMEQTREHAFLARTLGVPQIVVAI-NKMDATEPPFSEKR 161
                                   566677766653455566666677888888888866666.66666555555555 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 4.8
                                   -BSS-SSCCSTT-CEEEEEE CS
                   GTP_EFTU_D3  56 vsekkpefvkpGdnviveve 75 
                                    +++  + + pGdn+ ++v+
  gi|13541882|ref|NP_111570.1| 275 MHHEPLQQAEPGDNIGFNVR 294
                                   44566788899999988876 PP

  == domain 3  score: 120.0 bits;  conditional E-value: 3.7e-38
                                   EEECCEEEEEEESSS..SS-BSTT-EEEEESSS-EEEEEEEEEEECCSSTTSB-BSS-SSCCSTT-CEEEEEEECCEEEE- CS
                   GTP_EFTU_D3   3 kphtkfeAqvyilekerhtpitagYrpvlyirtadvtgkvveLlskldkktekvsekkpefvkpGdnvivevelikpiale 83 
                                   + ++ f+Aq+++l++  ++ i  gY+pv++++ta+v++k+ e++++l++k + + ++kp+f+k+Gd +iv+v + kp+++e
  gi|13541882|ref|NP_111570.1| 315 TVVRAFTAQIVVLNH--PSVIAPGYKPVFHVHTAQVACKIDEIVRTLNPKDGTTLKDKPDFIKTGDIAIVKVIPDKPLVIE 393
                                   67899**********..**************************************************************** PP

                                   -TTTHCCCCEEEEECTTCEEEEEEEE CS
                   GTP_EFTU_D3  84 kgseypqlGrFaiReggrTvaaGvvt 109
                                   k+se+pqlGrFa+R++g+TvaaG+  
  gi|13541882|ref|NP_111570.1| 394 KVSEIPQLGRFAVRDMGQTVAAGQCI 419
                                   ***********************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       5.7   8.6e+03      24      44 ..      16      33 ..      11      39 .. 0.77
   2 !   66.5   0.1   1.3e-21     2e-18       1      73 [.     241     307 ..     241     308 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 5.7
                                  TCTTSEEEEEEEEEEEEETEE CS
                   GTP_EFTU_D2 24 ndtskkeivtrissletfhed 44
                                  +d +k+   t +++l+ +h++
  gi|13541882|ref|NP_111570.1| 16 VDHGKS---TLVGRLLFEHGE 33
                                  677888...999999999986 PP

  == domain 2  score: 66.5 bits;  conditional E-value: 1.3e-21
                                   EEEEEEEEEESEEETTEEEEEECTCTTSEEEEEEEEEEEEETEEESEEETTSEEEEEEEESSCCSGSSTTCEE CS
                   GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilgndtskkeivtrissletfhededeavaganaGvivaikgledaiivGdtl 73 
                                   Gtv  grv++G+lk+Gd+v +l+ d  k+   ++++s+e++he++++a++g+n+G++v+++  +d i++Gd+ 
  gi|13541882|ref|NP_111570.1| 241 GTVPVGRVETGVLKPGDKVIFLPAD--KQ---GDVKSIEMHHEPLQQAEPGDNIGFNVRGIAKND-IKRGDVC 307
                                   99*******************7754..77...99*******************************.*****95 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.0   7.4e-09   1.1e-05       4     112 ..      12     147 ..       9     149 .. 0.72

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 7.4e-09
                                   EEESTTSSHHHHHHHHH....................T...........STEEESSSTTSSSSEEEEEEEETTEEEEEEEC CS
                      MMR_HSR1   4 ivGrpNvGKStLinalt....................g...........ekaivsdkpgtTrdinegrvklkgkeielvDt 53 
                                    +G+   GKStL+ +l+                    +           ++ + +++ g+T+d  ++++++++  ++l+D 
  gi|13541882|ref|NP_111570.1|  12 TIGHVDHGKSTLVGRLLfehgeipahiieeyrkeaeqKgkatfefawvmDRFKEERERGVTIDLAHRKFETDKYYFTLIDA 92 
                                   6899999999999999977777777776666655555055666665554799******************9999******* PP

                                   GGCSSHHHHHHHHHHHHHHHHCTSEEEEEEETT.TTCSHHHHHHHHHHHHHTTSEEEE.EE CS
                      MMR_HSR1  54 pGliegaseekglgkaflaleeadlillvvdas.eeklkpldeeleelleeakkplil.vl 112
                                   pG  +    +  +++ +    +ad+++lv++a+  e++ ++ +e + l +  + p i+ ++
  gi|13541882|ref|NP_111570.1|  93 PG--H----RDFVKNMITGTSQADAAILVISAReGEGVMEQTREHAFLARTLGVPQIVvAI 147
                                   **..3....23466666667789*******9885335666666655555555666544255 PP

>> GTP_EFTU_D4  Elongation factor Tu domain 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.3   7.4e-08   0.00011      21      84 ..     245     306 ..     237     307 .. 0.93

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 7.4e-08
                                   EEEEEEEEEEETT-EEEETTE.EEEEEEEEEETTEEESEEETT-EEEEEEESS-TTTS--TT-E CS
                   GTP_EFTU_D4  21 vGvevlgGvikpgvklikedGrevGeilqiqdkgkkleeakaGqevaisiegkivGrqikegdi 84 
                                   vG +v +Gv+kpg k+i     + G +++i+ +++ l++a+ G++++  ++g     +ik gd+
  gi|13541882|ref|NP_111570.1| 245 VG-RVETGVLKPGDKVIFLPADKQGDVKSIEMHHEPLQQAEPGDNIGFNVRGIA-KNDIKRGDV 306
                                   88.9***********************************************955.888999986 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.46   6.9e+02       2      19 ..      10      27 ..       9      49 .. 0.80
   2 !   17.0   0.0   2.3e-06    0.0034      10     150 ..      49     195 ..      45     199 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.46
                                  EEEEESTTSSHHHHHHHH CS
                           Ras  2 lvlvGdsavGKtslllrf 19
                                  l+ +G    GK++l+ r 
  gi|13541882|ref|NP_111570.1| 10 LITIGHVDHGKSTLVGRL 27
                                  7899**********9875 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 2.3e-06
                                   SSHHHHHHHHHHSSCSSSCTTTSSEEEEEEEEEETTEEEEEEEEEETTSGGGHHHHHHHHTTESEEEEEEETTBHHHHHTH CS
                           Ras  10 vGKtslllrfvkdkFkeeyesTigvdfytkeievdgkevkleiwDTAGqeefkslrelyyrdaegillvyditsresfenv 90 
                                    GK+++ + +v d+Fkee e  + +d   +++e+d  ++ +++ D  G  +f +   +  ++a++++lv +  + e   + 
  gi|13541882|ref|NP_111570.1|  49 KGKATFEFAWVMDRFKEERERGVTIDLAHRKFETD--KYYFTLIDAPGHRDFVKNMITGTSQADAAILVISAREGEGVMEQ 127
                                   59*********************999999988776..678899***********999************999999998888 PP

                                   HHHHHHHHHHSTTTSEEEEEEETTTGGG.......G-SS-HHHHHHHHHHHT...SEEEEEBTTTTCTHH CS
                           Ras  91 kkwveeikrvaeenvpivLvGnKvDlee.......kravsteegeelakelg...lkfletSAktnenve 150
                                   ++ +  + r+     +iv+  nK+D +e        ++v++ ++e+l k +g   ++f+ +S  +  nv+
  gi|13541882|ref|NP_111570.1| 128 TREHAFLARTLG-VPQIVVAINKMDATEppfsekrFNEVKA-DAEKLLKTIGykdATFVPISGYKGDNVT 195
                                   888888888888.36777778*****999999765445543.4556666655334678888888888876 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0     0.045        67       2      20 ..      10      28 ..       9      48 .. 0.85
   2 !   10.6   0.0   0.00033      0.49       9     119 ..      48     151 ..      45     152 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.045
                                  EEEESSTTSSHHHHHHCHC CS
                           Roc  2 vvlvGdsgvGKtsllkrfv 20
                                  ++ +G    GK++l+ r++
  gi|13541882|ref|NP_111570.1| 10 LITIGHVDHGKSTLVGRLL 28
                                  689*************997 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00033
                                   TSSHHHHHHCHCT-CCC-EEETTTTEEEEEEECGGSGGCTTBTTTTCEEEEEEEE-SGGCTTTT-HHHHCTSCEEEEEEEG CS
                           Roc   9 gvGKtsllkrfvedkfsekekstigvdfltkevtkikgvendkkvkkvklniWDtaGqerfrslhplylreaalailvyds 89 
                                   + GK ++   +v d+f+e+++  + +d+++++++      +    +k+ + + D  G+ +f + +    ++a++ailv+ +
  gi|13541882|ref|NP_111570.1|  48 QKGKATFEFAWVMDRFKEERERGVTIDLAHRKFE------T----DKYYFTLIDAPGHRDFVKNMITGTSQADAAILVISA 118
                                   679*************************998862......2....3578**************999999***********9 PP

                                   HHHHCHHHHHHH...HHHHCSSS-EEEEEE-TT CS
                           Roc  90 rssenlkeWlke...lkkvagkspvilvgnkiD 119
                                   r+ e + e  +e   l +  g  ++++ +nk+D
  gi|13541882|ref|NP_111570.1| 119 REGEGVMEQTREhafLARTLGVPQIVVAINKMD 151
                                   987766444444110445555667778889998 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 ?   13.7   0.0     2e-05      0.03      30     156 ..      68     185 ..      62     191 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2e-05
                     Gtr1_RagA  30 rlgatidveksevrflgnltlnlwDcgGqeafveeylssqkeeifrnvgvliyVfDvesreleedletlkeilealrqysp 110
                                   + g+tid+ + ++  +++ ++ l+D +G ++fv+++++       ++ ++ i V+ ++  e e  +e+ +e    +r+   
  gi|13541882|ref|NP_111570.1|  68 ERGVTIDLAHRKF-ETDKYYFTLIDAPGHRDFVKNMITG-----TSQADAAILVISAR--EGEGVMEQTREHAFLARTL-G 139
                                   5589********9.58999****************8654.....45678999999998..5556666665555444443.4 PP

                     Gtr1_RagA 111 eakvfvlihKmDliqedereeifeerkeeireeieklekeeiqffa 156
                                     ++ v i+KmD  +    e+ f+e k++ ++ ++ ++ ++ +f  
  gi|13541882|ref|NP_111570.1| 140 VPQIVVAINKMDATEPPFSEKRFNEVKADAEKLLKTIGYKDATFVP 185
                                   45788999******************99999999988877766655 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.1   0.00028      0.42      43      83 ..      80     116 ..       5     180 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00028
                                   G...GGTT-SEEEETT-GCCSHHHHHHHHHHGGEEEEEEEE CS
                         SRPRB  43 vksekgskltliDfPGheklrqklleklkaksslkglvfvv 83 
                                   + ++++  +tliD PGh  + +++++     s++ + + v+
  gi|13541882|ref|NP_111570.1|  80 F-ETDKYYFTLIDAPGHRDFVKNMITG---TSQADAAILVI 116
                                   3.6678899***********9999998...45555555555 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 ?   -1.3   0.0      0.93   1.4e+03       3      20 ..      10      27 ..       8      35 .. 0.82
   2 ?    9.0   0.0   0.00061      0.91      32     119 ..      70     154 ..      68     196 .. 0.60

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.93
                                  EEEEESTTSSHHHHHHHH CS
                        FeoB_N  3 valvGnpnvGkttlfnal 20
                                  ++++G  + Gk+tl+ +l
  gi|13541882|ref|NP_111570.1| 10 LITIGHVDHGKSTLVGRL 27
                                  5689999*******9887 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00061
                                   TSSSEEEEEEEEETTEEEEEEE----SSSSSSSHHHHHHHHHHH.CTSSSEEEEEEEGGGHHHHHHHHHHHH....HTTS. CS
                        FeoB_N  32 GvtvekkegklklkgkeveivDlPGiYslsayseeekvardfll.eeepdvvvnvvdatnlernLyLtlqll....elgv. 106
                                   Gvt++ ++ k++++++ ++++D PG  ++          +++++ ++++d+ + v+ a + e  +  t + +     lgv 
  gi|13541882|ref|NP_111570.1|  70 GVTIDLAHRKFETDKYYFTLIDAPGHRDFV---------KNMITgTSQADAAILVISAREGEGVMEQTREHAflarTLGVp 141
                                   9************************75542.........223322555666666666666555555554432111133431 PP

                                   SEEEEEETHHHHH CS
                        FeoB_N 107 pvvlalnmideae 119
                                   ++v+a+n++d+ e
  gi|13541882|ref|NP_111570.1| 142 QIVVAINKMDATE 154
                                   3566777777654 PP

>> Septin  Septin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00012      0.18       4      78 ..       7     101 ..       4     109 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00012
                                   EEEEEEEEBTTSSCCCCCCT.TSSSS----.....................--------------S-EEEEEEEEETTCEE CS
                        Septin   4 eftlmvvGesglGkttlint.lfetdliee.....................ekleeasekkkktveikkkkvvieedgvkl 62 
                                   +++l+ +G+   Gk+tl+   lfe+  i++                       +++ +e+ ++ v+i+ ++ + e d  k 
  gi|13541882|ref|NP_111570.1|   7 HLNLITIGHVDHGKSTLVGRlLFEHGEIPAhiieeyrkeaeqkgkatfefaWVMDRFKEERERGVTIDLAHRKFETD--KY 85 
                                   689***************76257777787788888999999999988888745566677888888888888888888..77 PP

                                   EEEEEE---BSSSSSH CS
                        Septin  63 nltviDtpgfGdavdn 78 
                                    +t+iD pg+ d+v n
  gi|13541882|ref|NP_111570.1|  86 YFTLIDAPGHRDFVKN 101
                                   8899999999999988 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.19   2.8e+02       4      21 ..      10      27 ..       8      32 .. 0.87
   2 ?    7.9   0.0    0.0016       2.4      29      96 ..      78     144 ..      71     194 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.19
                     PduV-EutP  4 illiGkvgsGKttLtqal 21
                                  ++ iG+v+ GK tL  +l
  gi|13541882|ref|NP_111570.1| 10 LITIGHVDHGKSTLVGRL 27
                                  689***********9776 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0016
                     PduV-EutP  29 kktqaiefsdeviDtPGeylenrklysalivtsaeadvialvqdateeesvfppgfasvfnkeviGi...i 96 
                                   +k  + +++ ++iD+PG    +r + + +i+ + +ad   lv +a e e v+ ++  + f   ++G+   +
  gi|13541882|ref|NP_111570.1|  78 RKFETDKYYFTLIDAPG----HRDFVKNMITGTSQADAAILVISAREGEGVMEQTREHAFLARTLGVpqiV 144
                                   555566677789****9....79******************************999999999999863333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (424 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       519  (0.0289475); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.42
# Mc/sec: 3004.73
//
Query:       gi|13541883|ref|NP_111571.1|  [L=326]
Description: molybdenum cofactor biosynthesis protein A [Thermoplasma volcanium GSS1]
Scores for complete 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-31  108.1   0.4    1.2e-30  107.1   0.1    1.7  2  Radical_SAM  Radical SAM superfamily
      1e-22   80.4   0.2    1.6e-22   79.8   0.2    1.3  1  Mob_synth_C  Molybdenum Cofactor Synthesis C
    1.1e-07   32.2   0.0    2.1e-07   31.3   0.0    1.5  1  Fer4_12      4Fe-4S single cluster domain
    1.4e-07   31.6   0.4    3.9e-07   30.2   0.0    1.9  2  Fer4_14      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.1   0.1   2.7e-34   1.2e-30       6     166 ..      21     173 ..      16     174 .. 0.97
   2 ?   -3.1   0.0         2   8.9e+03      21      38 ..     195     212 ..     188     217 .. 0.79

  Alignments for each domain:
  == domain 1  score: 107.1 bits;  conditional E-value: 2.7e-34
                                   EESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEEEECS CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM   6 gCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgiritvetng 86 
                                    Cn++C fC+      +e  g+ l +eei++ vk++ ++ gv+ + l+ggep+l++d++++++r++k      +i+++tng
  gi|13541883|ref|NP_111571.1|  21 TCNFNCFFCHMEG---TEISGEALKPEEIERVVKIA-HKFGVNKIKLTGGEPTLRRDLIDIVKRIRKY--ITGNISMTTNG 95 
                                   7***********8...7*******************.7999***************************..7********** PP

                                   SCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  87 tlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglpGendeeleellel 166
                                   +++ +  + +l+++g+drv+++ +a+d+++++ ++ + ++++++++a+++++eag+ +v+++ v+l+  n +++ +++el
  gi|13541883|ref|NP_111571.1|  96 VML-PILAYELKKAGLDRVNISMHAFDEDTFQAIT-GVNSRDRIIKAIDAANEAGLTPVKINFVVLRDLNVDQIPDMIEL 173
                                   ***.*******************************.99************************************999987 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2
                                   HHHHHHHHHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  21 rregrgrslsveeileev 38 
                                   ++e+  ++++++++++e+
  gi|13541883|ref|NP_111571.1| 195 SKEYLKYHMPLDSLEKEI 212
                                   568888999999999987 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 !   79.8   0.2   3.6e-26   1.6e-22       3     126 ..     181     304 ..     179     306 .. 0.86

  Alignments for each domain:
  == domain 1  score: 79.8 bits;  conditional E-value: 3.6e-26
                                   EEEEE---B-TTSSB--SSB--HHHHHHHHHHHS-EEEE-.-SS.T-SSEEEEE..TTT--EEEEE-TTTS-.-GGG--EE CS
                   Mob_synth_C   3 lrfIElmpvgegeewrekkvvsadeilerieerlalleak.ket.kgpakryki..kdgkgeiglIapvsep.FCasCnRl 78 
                                   l++IE+ +++ege++  k++++++  l+++e+++a ++ + +++  ++++ry i  + g++++++++p ++p FCa+C+Rl
  gi|13541883|ref|NP_111571.1| 181 LQLIEYETTREGESS--KEYLKYHMPLDSLEKEIADKALSiERNeLHNRPRYIIrtQAGEVKVEFVKPQRNPdFCAHCTRL 259
                                   89**********976..******************9998854336999999999434455789****************** PP

                                   EE-TTSEEESSSS-SS-.EEHHHHHHTT--HHHHHHHHHHHHHT----H CS
                   Mob_synth_C  79 RltadGklktCLfaeee.idlrdllregaseeeLkelikealarkkekh 126
                                   R+t++G++ktCL+++++ ++++ + +e+     ++el+++a+ r+++++
  gi|13541883|ref|NP_111571.1| 260 RITSEGEFKTCLMRSDTnVKFKGINDEK----TISELFRQAVLRREPYW 304
                                   **************99878888775555....4999******9999876 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 !   31.3   0.0   4.7e-11   2.1e-07      13      96 ..      20      98 ..      11     118 .. 0.83

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 4.7e-11
                       Fer4_12 13 sgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelvkevkeekpekdiwlytgyt 95
                                  + Cn++C +C+ + t    sg+  + e +e++++ ++k  ++++ l+GGEP l   +++l+++vk++++    +  + ++g++
  gi|13541883|ref|NP_111571.1| 20 TTCNFNCFFCHMEGTE-I-SGEALKPEEIERVVKIAHKFGVNKIKLTGGEPTL---RRDLIDIVKRIRKYITGNISMTTNGVM 97
                                  57*********66654.4.5666777888999999999999************...9***********999976778888887 PP

                       Fer4_12 96 l 96
                                  l
  gi|13541883|ref|NP_111571.1| 98 L 98
                                  6 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   0.0   8.7e-11   3.9e-07       7      93 ..      21      99 ..      17     119 .. 0.74
   2 ?   -2.3   0.1       1.1   4.7e+03      13      38 ..     257     293 ..     252     298 .. 0.68

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 8.7e-11
                       Fer4_14  7 gCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeeypekkiwletng 89
                                   Cn++C +C  +    + +g+  + e++e+++  + ++++  +++ ltGGeP +    ++l+++vkr+++ + + +i + tng
  gi|13541883|ref|NP_111571.1| 21 TCNFNCFFCHMEG--TEISGEALKPEEIERVV--KIAHKFGVNKIKLTGGEPTLR---RDLIDIVKRIRKYI-TGNISMTTNG 95
                                  7*********877..44455555556666888..5566777799********954...99*********998.99******** PP

                       Fer4_14 90 tlei 93
                                  ++  
  gi|13541883|ref|NP_111571.1| 96 VMLP 99
                                  9863 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.1
                       Fer4_14  13 k...........gCdnketwkselgkpqteelleqil 38 
                                   +            C+ +++ + + + +++e+++++ +
  gi|13541883|ref|NP_111571.1| 257 TrlritsegefkTCLMRSDTNVKFKGINDEKTISELF 293
                                   4455555555557888888888888888888887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       710  (0.0396006); 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:                         4  (0.000223102); expected 0.2 (1e-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 0.23s 00:00:00.72 Elapsed: 00:00:00.39
# Mc/sec: 2481.09
//
Query:       gi|13541884|ref|NP_111572.1|  [L=406]
Description: major facilitator superfamily permease [Thermoplasma volcanium GSS1]
Scores for complete sequence (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   47.1  59.0    2.3e-08   33.4  28.8    2.3  2  MFS_1     Major Facilitator Superfamily
    1.3e-09   37.5  33.7    5.5e-09   35.4  10.7    2.4  2  Sugar_tr  Sugar (and other) transporter


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.4  28.8   2.5e-12   2.3e-08       2     209 ..      30     227 ..      27     250 .. 0.67
   2 !   15.0  28.9   9.5e-07    0.0086       6     164 ..     228     392 ..     223     399 .. 0.73

  Alignments for each domain:
  == domain 1  score: 33.4 bits;  conditional E-value: 2.5e-12
                         MFS_1   2 llaaflsalarsilgpalplalaedlgispseigl....lltlyalgaavaslplGrlsdrfGrrrvlllglllfalglll 78 
                                   +l+ + s++ +++l++++p ++ ++      + ++    +l    +g ++++++lGr sd +Gr+++++++l+l ++g+l 
  gi|13541884|ref|NP_111572.1|  30 ALTMIASFFVWGLLLVTAP-LV-TEWP---IVPSWgymyVLLSSPAGLLIGNVVLGRTSDLLGRKSLFMATLALGIAGILG 105
                                   5778888888888888888.44.4433...222333323555577799******************************777 PP

                         MFS_1  79 llfasslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGa.ilgpllggllasslgWravfyila 158
                                   ++f+ +++ +l++ +++ +g g+  ++++a++a+ fp + rg+++ l+s ++++G+ ++  ++ ++ +s +   ++f ++a
  gi|13541884|ref|NP_111572.1| 106 IIFSRNFFEILASIFIAEFGFGGEETVSLAFLAEQFPLKYRGKVLVLVSNSANVGVaAISGIFIAFGYSIAIEKLIFGVMA 186
                                   77967777************************************************4444444444444444555566666 PP

                         MFS_1 159 ivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvl 209
                                   i ++       +l+++++ +++     ++        l++   +++  p++
  gi|13541884|ref|NP_111572.1| 187 IGGITI-----ALYTRSRIPESLRWFYTK----NSDTLIE-KPQMHVIPFI 227
                                   666665.....444444444444333333....3344444.3333333333 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 9.5e-07
                         MFS_1   6 flsalarsilgpalplalaedlg..ispseigllltlyalgaavaslplGrlsdrfGrrr.vlllglllfalglllll.fa 82 
                                   +ls++a++i+++++  ++a+ lg    p   +++  +y+lg a++ + + +++dr+Grr   +++ + +f++++++ll ++
  gi|13541884|ref|NP_111572.1| 228 VLSMFAITIVLTFA--LVADILGpyEYPKYTSIIPFIYGLGEAISGFAIIAFIDRIGRRLtSVIAYMGGFLSMAVFLLyLI 306
                                   44444444433333..44555553226666999***************************666666666666666666433 PP

                         MFS_1  83 ..sslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailg.pllgglla.sslgWravfyilai 159
                                      +++++lvl v+ ++++ +++++  +l  ++f+  +rg++i+ + + + + +i+   +l g+ + ++  +  + ++++ 
  gi|13541884|ref|NP_111572.1| 307 ssLPFFVFLVLLVINSFFGELGWAVREILQPELFTTIRRGSGIAAVRGIAYALYIVSiFVLNGISVfEYMVFATIIWVIGS 387
                                   2344668************************************99999999999888556666555555556666666666 PP

                         MFS_1 160 vslla 164
                                   ++ ++
  gi|13541884|ref|NP_111572.1| 388 IGSIL 392
                                   65554 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.4  10.7   6.1e-13   5.5e-09      54     203 ..      67     212 ..      21     218 .. 0.84
   2 !    8.0  15.1   0.00013       1.1     290     409 ..     257     369 ..     227     406 .] 0.71

  Alignments for each domain:
  == domain 1  score: 35.4 bits;  conditional E-value: 6.1e-13
                                   THHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHHHHHHTTS-SC CS
                      Sugar_tr  54 iflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlvPmyisEiApkk 134
                                   +  +G +iG +++g  +d +GRk+ ++++ +l ++g++ ++++    ++  ++++ +++ +g G++ +++  +++E  p k
  gi|13541884|ref|NP_111572.1|  67 SSPAGLLIGNVVLGRTSDLLGRKSLFMATLALGIAGILGIIFSR---NFFEILASIFIAEFGFGGEETVSLAFLAEQFPLK 144
                                   556899**************************************...9********************************* PP

                                   CHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-TTHHHHHHHCCHHHHHHHH.HHGGGS---HHHHHHTT- CS
                      Sugar_tr 135 lRgalvslyqlaitfGilvaaifglglnktsnadgwrillglqlvpallll.illlflPESPrylvekgk 203
                                   +Rg++ +l   +  +G    +++  ++ ++ +    ++ +g+ ++  ++++ + +  +PES r++++k+ 
  gi|13541884|ref|NP_111572.1| 145 YRGKVLVLVSNSANVGVAAISGIFIAFGYSIA--IEKLIFGVMAIGGITIAlYTRSRIPESLRWFYTKNS 212
                                   ********999999996444444444433333..33677777777766554055699*********9975 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00013
                                   HHHHHHHHHHHHHHHHHHHHHHHHS-SHHHHHHHHHHHHHHHHHHH..HHHHTTSS...CHHHHHHHHHHHHHHHTTTTHH CS
                      Sugar_tr 290 llvtiivgvvnfvatfvaiflvdrfGRRtllllGaagmaicfvilgivalllvakskaasivaivfialfialfalgwgpv 370
                                    ++ +i+g   +++ f+ i ++dr+GRR   l++++ ++  f+ ++ v+ll+  + +   +v++v++++  ++ +lgw+  
  gi|13541884|ref|NP_111572.1| 257 SIIPFIYGLGEAISGFAIIAFIDRIGRR---LTSVIAYMGGFLSMA-VFLLYLIS-SLPFFVFLVLLVINSFFGELGWAVR 332
                                   467789999999999*************...555555555555555.44444444.2458999999999999******977 PP

                                   HHHHHHHHSHTTTHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Sugar_tr 371 pwvlvsElfpqsvRskalaiavavnwlanflisllfpii 409
                                     +l +Elf++  R++++a +  +   a +++s++    
  gi|13541884|ref|NP_111572.1| 333 E-ILQPELFTTIRRGSGIAAVRGIAY-ALYIVSIFVLNG 369
                                   6.888******999999987766543.334444444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (406 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       961  (0.0536003); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 2713.30
//
Query:       gi|13541885|ref|NP_111573.1|  [L=514]
Description: NAD-dependent aldehyde dehydrogenase [Thermoplasma volcanium GSS1]
Scores for complete 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-134  448.7   0.0   2.1e-134  448.5   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 !  448.5   0.0  1.2e-138  2.1e-134       1     462 []      29     496 ..      29     496 .. 0.97

  Alignments for each domain:
  == domain 1  score: 448.5 bits;  conditional E-value: 1.2e-138
                                   EET-SSSEEEEEETTTCEEEEEEE-B-HHHHHHHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHTHHHHHHHHHHHH-- CS
                        Aldedh   1 wvesesetievinPatgeviakvpaataedvdaavaaAkeafkawaklpaeeRaeiLrkaadlleerkeelaeletletGk 81 
                                   w +++++ + v++P++g++iak++ at+ed+d++v++A+e fk+w+ +pa++R+ i++ + d l+++k +l ++ t+e+Gk
  gi|13541885|ref|NP_111573.1|  29 WKKPAGKMLTVYSPIDGSEIAKISMATREDYDEMVKKAQEEFKKWRMIPAPKRGLIIKDIGDELRKEKRNLGRIVTIEAGK 109
                                   777777789************************************************************************ PP

                                   -HHHHHHHHHHHHHHHHHHHHHHHHHSEEEEEE.CTTEEEEEEEEE-SEEEEEE-SSSCCHHHHHHHHHHHHTT-EEEEEE CS
                        Aldedh  82 plaearaeveeaidvlryyaelaeklegevlps.segklalvrrePlGvvgaItPWNfPlllaawklapalaaGNtvvlKP 161
                                   + +e ++e++e+id+ +++ +l ++l+g +++s ++ ++ + ++ PlG +++It++NfP+++++w+  +a ++G +v++KP
  gi|13541885|ref|NP_111573.1| 110 TPSEGEGEIQEMIDISDLALGLSRQLYGLTIASeRPYHRMYEQWVPLGPIAVITSFNFPASVWSWNSFIAAVTGDVVIWKP 190
                                   ****************************8888868********************************************** PP

                                   -TTSHHHHHHHHHHHHHT....TS-TTSEEE--SSTCCHHHHHHH-TTESEEEEES-HHHHHHHHHHHHCTTSEEEEEE-- CS
                        Aldedh 162 aeetplsalllaelfeea....glPkgvlnvvtgsgsevgealvehpevdkvsftGstevgrkiakaaaknlkrvtlElGG 238
                                   +++++l+a+++++++e++    ++P+ ++ +++ sgse g+ ++++p++ +vsftGs++vgrki ++ ak+l + +lElGG
  gi|13541885|ref|NP_111573.1| 191 SSKAALTAVAVMKVIERVlkrnNVPN-IFYLMVSSGSEGGDWITNDPRIPLVSFTGSVPVGRKISENVAKRLGKSILELGG 270
                                   *****************977756665.55556677********************************************** PP

                                   -EEEEE-TTSHHHHHHHHHHHHHHGGGGTSTTSEEEEEEEHHHHHHHHHHHHHHHHT--BS-TTSTT-SB---SSHHHHHH CS
                        Aldedh 239 knplivledaDldkaveaivkgafgnaGQvCiaasrllvqesiydefveklveaakklkvgdpldedtdvGPliseaqlek 319
                                   +n +iv ++aD+d a++++v+ga+ +aGQ+C++++r++v e+iydefv+klv+a++k+kvgdp+++ + vGPli+e++++ 
  gi|13541885|ref|NP_111573.1| 271 NNGAIVSDKADIDLALRGVVFGALATAGQRCTTTRRVIVSEKIYDEFVKKLVNAYSKVKVGDPREKGVLVGPLIDEDAVRD 351
                                   ********************************************************************************* PP

                                   HHHHHHHHHHTTSEEEE-TT.E.SB-SSSTTEE--EEEES-TTTSHHHHS---SSEEEEEEESSHHHHHHHHHSSSEESEE CS
                        Aldedh 320 vekyveeakeegaklllGge.reeaglekgyfvePtvlanvtpdmriaqeEiFGPVlsvikfkdeeeaieiaNdteyGLaa 399
                                   +e+ ++ea+++g k+l+Gg+  + +g+ekg++vePt+++  +p+m+i++eE+F+P+l+v+k+k++eea+ei N+ + GL++
  gi|13541885|ref|NP_111573.1| 352 YEGAISEAVKQGGKVLYGGKkISLKGYEKGHYVEPTIIE-ANPNMPIVKEETFAPILYVMKYKTIEEALEIHNSVPQGLSS 431
                                   ********************98899**************.7**************************************** PP

                                   EEE-SBHHHHHHHHHHS..-SSEEEESSSST--TTTSEB--CGGGEES-BSHHHHHHHTEEEEEE CS
                        Aldedh 400 gvftkdleraervaerl..eaGnvyiNdsttgaaealpfgGvkqSglGreggkegleeytevktv 462
                                   ++ft+dl++ e + +    ++G  ++N+st+ga+   +fgG k++g Gre+g++++++y++ +tv
  gi|13541885|ref|NP_111573.1| 432 SIFTTDLREEEAFLSPYgsDCGLANVNTSTAGAEIGGAFGGEKDTGGGRESGSDAWKFYMRRQTV 496
                                   **************99888**********99999999***********************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (514 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       618  (0.0344693); expected 358.6 (0.02)
Passed bias filter:                      580  (0.0323498); 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: 0.63u 0.31s 00:00:00.94 Elapsed: 00:00:00.48
# Mc/sec: 3238.12
//
Query:       gi|13541886|ref|NP_111574.1|  [L=58]
Description: hypothetical protein TVN1055 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.016   15.0   0.2      0.024   14.4   0.2    1.2  1  PhdYeFM_antitox  Antitoxin Phd_YefM, type II toxin-antitoxin 
      0.016   15.8   0.0      0.017   15.8   0.0    1.0  1  G6PD_N           Glucose-6-phosphate dehydrogenase, NAD bindi


Domain annotation for each model (and alignments):
>> PhdYeFM_antitox  Antitoxin Phd_YefM, type II toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.2   2.7e-06     0.024      40      72 ..       9      40 ..       8      43 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.7e-06
                                  EEHHHHHHHHH.HHHHHCSHHHHHHHHHHHHHH CS
               PhdYeFM_antitox 40 vsleeyerlqeltekllslplnaerlaesgaev 72
                                  +s + yerl++  ++l+ lp+n ++l+++++e+
  gi|13541886|ref|NP_111574.1|  9 LSKKTYERLER-LFYLATLPENFAKLQREIREA 40
                                  68899******.****************99886 PP

>> G6PD_N  Glucose-6-phosphate dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.8   0.0   1.9e-06     0.017      90     127 ..       8      44 ..       2      57 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.9e-06
                        G6PD_N  90 kLkekleeleanrlfYlavppslfeevaeklkkaglak 127
                                   kL++k+ e + +rlfYla+ p+ f+++ +++++a+  k
  gi|13541886|ref|NP_111574.1|   8 KLSKKTYE-RLERLFYLATLPENFAKLQREIREASKPK 44 
                                   45555544.459*******************9974433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       791  (0.0441185); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 363.13
//
Query:       gi|13541887|ref|NP_111575.1|  [L=387]
Description: arsenite transporting ATPase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.4e-85  287.2   0.0    1.7e-85  286.9   0.0    1.0  1  ArsA_ATPase  Anion-transporting ATPase
    2.8e-19   68.4   0.0    6.1e-19   67.3   0.0    1.6  1  ArsA_HSP20   HSP20-like domain found in ArsA
    6.7e-10   39.2   0.0    1.7e-09   37.9   0.0    1.6  1  AAA_31       AAA domain
      8e-08   32.4   0.0    1.1e-07   32.0   0.0    1.3  1  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
      3e-05   23.6   0.9    0.00052   19.5   0.3    2.3  2  ParA         NUBPL iron-transfer P-loop NTPase
     0.0012   18.4   0.0      0.002   17.7   0.0    1.3  1  CBP_BcsQ     Cellulose biosynthesis protein BcsQ
     0.0012   18.6   0.0     0.0025   17.6   0.0    1.5  1  AAA_24       AAA domain
     0.0015   18.1   0.1     0.0028   17.1   0.1    1.4  1  Fer4_NifH    4Fe-4S iron sulfur cluster binding proteins, Nif
      0.005   16.3   0.1     0.0098   15.4   0.1    1.5  1  PhoH         PhoH-like protein
  ------ inclusion threshold ------
      0.017   15.3   0.0      0.088   13.0   0.0    2.0  2  HSP20        Hsp20/alpha crystallin family
       0.03   14.0   0.1      0.087   12.4   0.1    1.8  1  SRP54        SRP54-type protein, GTPase domain
      0.076   12.0   0.1       0.12   11.3   0.1    1.3  1  MeaB         Methylmalonyl Co-A mutase-associated GTPase MeaB
        3.1    7.5   4.2         21    4.9   0.2    2.8  2  DUF3755      Protein of unknown function (DUF3755)


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 !  286.9   0.0   1.2e-88   1.7e-85       2     304 ..       4     303 ..       3     304 .. 0.97

  Alignments for each domain:
  == domain 1  score: 286.9 bits;  conditional E-value: 1.2e-88
                                   EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-STTTHHHHHHTS--BSS-EEETSSEEEEE--HHHHHHHHHCCHHG CS
                   ArsA_ATPase   2 kvilvgGKGGVGKttvsaatavklsekgkkvllistDPAhslsDsfdqklgkeptkvkeNLsavEidpeveleeakqevqk 82 
                                   +++l +GKGGVGKt+++aat+  l+ +gkk+l+istDPAhsl D+f  ++g++ +k+ eNL+ +E+ + + ++e ++e ++
  gi|13541887|ref|NP_111575.1|   4 RILLYTGKGGVGKTSIAAATGSLLAAEGKKTLIISTDPAHSLGDAFGMEIGHNIKKLGENLYGQEVSVVQSINEHWGELKD 84 
                                   7899***************************************************************************** PP

                                   GGSCCHHHHHHHHHHHHHHTSSTTHHHHHHHHHHHHHHHCSSSSEEEEESBSCCHTCGGGGHHHHHHHHHHHHHHHHHHHH CS
                   ArsA_ATPase  83 eeeallgleeledvlaeelaslPGideilsfeellkyvkeeeydvvvlDtaPTGhtlrllslpevleklleklvklkekls 163
                                   + ++l+ +++l+ v a+e a+lPG +e+  + +l +y+ +eeyd++v+D+aPTG +l+lls+pev+ ++++kl+ l +k  
  gi|13541887|ref|NP_111575.1|  85 YLRSLFLSQGLDPVSADEIATLPGFEEASELLYLRNYYYDEEYDTIVMDSAPTGAALQLLSFPEVMTWYMDKLFPLGRKTA 165
                                   ********************************************************************************* PP

                                   HHHHHHCCCSHCHHHHHHHHHHHHHHHHHHHHHHHHHHTSTTTEEEEEEEESSHHHHHHHHHHHHHHHHTT-EEEEEEEEE CS
                   ArsA_ATPase 164 plakqlvkllglggvsieealeeleetkeeikkveeiltdpertsfrlVvipEklslkEteRaikeLkkygikvdavivNk 244
                                    +a+++ k +  +    +e++e+++  ++++ ++++ilt++e ts+rlV++p+++s+ Et+Ra ++L +yg  vdav++Nk
  gi|13541887|ref|NP_111575.1| 166 RVARPILKPFVDIPLPDDEVFENIDLLYKQLTDIRKILTNNEVTSIRLVTNPDNMSFSETKRAYTYLLLYGYPVDAVVINK 246
                                   ******886555555555*************************************************************** PP

                                   E-TTCSSSTSHHHHHHHHHHHHHHHHHHHHTTTSEEEEEE--SS-S-SHHHHHHHHHHHC CS
                   ArsA_ATPase 245 llpeeeqenCeflearkkiqkkylkeieelfedlevvklplleeEvvGlekleklselly 304
                                   +l +e+     f+e+ + +q+  ++e+e  f d++v+k++ll+eE  G ekl +l +l+y
  gi|13541887|ref|NP_111575.1| 247 ILSDETG---GFFEKMRVNQQDIIDEMEHSFVDVKVFKVKLLQEEPIGHEKLVELGKLIY 303
                                   ****999...7**********************************************998 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 !   67.3   0.0   4.4e-22   6.1e-19       2      62 ..     325     385 ..     324     386 .. 0.97

  Alignments for each domain:
  == domain 1  score: 67.3 bits;  conditional E-value: 4.4e-22
                    ArsA_HSP20   2 deyvlkldLPfvdkeeidlsrsgdeLtIkignfrRqitLPsvlarkevtsAkfedgvLeIr 62 
                                    +y+lk+++Pf+ ke+i+l+++g eLtI+i+n++R++ LP+++++++++sA++ +g+L++ 
  gi|13541887|ref|NP_111575.1| 325 EKYILKIKMPFAAKENINLFNHGGELTIEIENWKRVFYLPESISDRRPVSAEYSNGYLNVV 385
                                   68*********************************************************97 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.9   0.0   1.2e-12   1.7e-09       4     128 ..       5     137 ..       3     146 .. 0.69

  Alignments for each domain:
  == domain 1  score: 37.9 bits;  conditional E-value: 1.2e-12
                        AAA_31   4 IaianqKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQanattglgiekneiektlyevli.eeknikeaiiktkvenl.. 81 
                                   I ++  KGGvGKT  + + ++ la +gkk+L++  Dp  ++  ++g+e  +  k+l e l  +e+++ + i+++  e    
  gi|13541887|ref|NP_111575.1|   5 ILLYTGKGGVGKTSIAAATGSLLAAEGKKTLIISTDPAHSLGDAFGMEIGHNIKKLGENLYgQEVSVVQSINEHWGELKdy 85 
                                   567889*************************************99998777666676666556666666666544333311 PP

                        AAA_31  82 ...dlipssidLaeae..ielvelekkeeilkellekvkdeYDyiiiDcpPs 128
                                       ++   +d ++a+    l ++e+  e l       ++eYD i++D  P+
  gi|13541887|ref|NP_111575.1|  86 lrsLFLSQGLDPVSADeiATLPGFEEASELLYLRNYYYDEEYDTIVMDSAPT 137
                                   23123333344444331123445555566665555678999********997 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.0   0.0   7.7e-11   1.1e-07       2      72 ..       6     205 ..       5     283 .. 0.76

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 7.7e-11
                                   EEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH............................ CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................ RF
                          CbiA   2 aiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep............................ 54 
                                   ++  +kGGvGKT++aa+ + +la +g+++l + +Dp  ++   ++g e+ ++                             
  gi|13541887|ref|NP_111575.1|   6 LLYTGKGGVGKTSIAAATGSLLAAEGKKTLIISTDPAHSLGD-AFGMEIGHNIkklgenlygqevsvvqsinehwgelkdy 85 
                                   56789********************************88877.99999988888888888888888888888888888888 PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                          CbiA  55 ................................................................................. 54 
                                                                                                                    
  gi|13541887|ref|NP_111575.1|  86 lrslflsqgldpvsadeiatlpgfeeasellylrnyyydeeydtivmdsaptgaalqllsfpevmtwymdklfplgrktar 166
                                   888888888888888888888888888888888888888888888888888887777777777777777777777777777 PP

                                   .....................CCHCCCHHHHHHCHCHHH CS
                                   .....................xxxxxxxxxxxxxxxxxx RF
                          CbiA  55 .....................dlkrllellealgkkkal 72 
                                                        +++ l + l +++k + +
  gi|13541887|ref|NP_111575.1| 167 varpilkpfvdiplpddevfeNIDLLYKQLTDIRKILTN 205
                                   777777777777777777777444444444444433333 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 !   19.5   0.3   3.8e-07   0.00052       5      41 ..       4      40 ..       1      75 [. 0.84
   2 ?    2.4   0.0     0.063        87     134     173 ..     206     245 ..     194     293 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 3.8e-07
                          ParA  5 viavlSgKGGVGKStvavnlAlaLakkglkvgllDaD 41
                                   i+   gKGGVGK+++a+     La++g+k+ ++ +D
  gi|13541887|ref|NP_111575.1|  4 RILLYTGKGGVGKTSIAAATGSLLAAEGKKTLIISTD 40
                                  68999**************************999888 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.063
                          ParA 134 lplagaviVttpqevaladvkkaiemfkkvkvkvlGvveN 173
                                    +++ + +Vt p +++++++k+a + +     +v +vv N
  gi|13541887|ref|NP_111575.1| 206 NEVTSIRLVTNPDNMSFSETKRAYTYLLLYGYPVDAVVIN 245
                                   36777889***************99999999999888877 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   1.4e-06     0.002      10      54 ..      11      55 ..       3      69 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.4e-06
                      CBP_BcsQ 10 RGGvGttsllaaLawalhelgesvlviDlspdnlLrlhFnvdieq 54
                                  +GGvG+ts++aa +  l + g++ l+i + p+  L   F ++i +
  gi|13541887|ref|NP_111575.1| 11 KGGVGKTSIAAATGSLLAAEGKKTLIISTDPAHSLGDAFGMEIGH 55
                                  8***********************************999999876 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   1.8e-06    0.0025       2      74 ..       2     135 ..       1     139 [. 0.89

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.8e-06
                        AAA_24   2 klkiliy.GpsgiGKTtlakel.......gpkplfidtekGlksldadkfpdie.......................swed 51 
                                   k +il+y G+ g+GKT++a+         g+k+l+i t+  ++sl ++ + +i                         w +
  gi|13541887|ref|NP_111575.1|   2 KPRILLYtGKGGVGKTSIAAATgsllaaeGKKTLIISTDP-AHSLGDAFGMEIGhnikklgenlygqevsvvqsineHWGE 81 
                                   566776659******************************9.7788888888887888899999999999999999999999 PP

                        AAA_24  52 fldevvel...............................aaeladyktlviDti 74 
                                   ++d++ +l                               +  +++y+t+v D++
  gi|13541887|ref|NP_111575.1|  82 LKDYLRSLflsqgldpvsadeiatlpgfeeasellylrnYYYDEEYDTIVMDSA 135
                                   999999999999999999999999999999999999999888889999999996 PP

>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.1     2e-06    0.0028       6      40 ..       8      43 ..       4      55 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2e-06
                     Fer4_NifH  6 y.GkGGiGksttsqnlsaalaemgkkvlivGCDPka 40
                                  y GkGG+Gk+  ++ + + la+ gkk li+  DP +
  gi|13541887|ref|NP_111575.1|  8 YtGKGGVGKTSIAAATGSLLAAEGKKTLIISTDPAH 43
                                  449*******************************76 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   7.1e-06    0.0098      20      76 ..       4      60 ..       1      76 [. 0.89

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 7.1e-06
                                  SEEEEE--TTSSTTHHHHHHHHHHHHTTS-SEEEEEE-S--TT----SS-------- CS
                          PhoH 20 divfaiGpaGtGKtylavalavealkkkkvkriiltrpaveageelGflpgdleekv 76
                                   i+  +G+ G GKt +a a++  +  ++k + ii t pa + g+  G+  g   +k+
  gi|13541887|ref|NP_111575.1|  4 RILLYTGKGGVGKTSIAAATGSLLAAEGKKTLIISTDPAHSLGDAFGMEIGHNIKKL 60
                                  688899***************************************999888766665 PP

>> HSP20  Hsp20/alpha crystallin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.47   6.5e+02       5      35 ..     323     353 ..     320     356 .. 0.81
   2 ?   13.0   0.0   6.4e-05     0.088      52      84 ..     352     385 ..     345     387 .] 0.83

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.47
                                   SEEEEEEEEE-TT--CCCEEEEEETTEEEEE CS
                         HSP20   5 eeeefevkldvpglkkeelkvkvednrvlvk 35 
                                   + e++ +k+++p  +ke++++  ++++++++
  gi|13541887|ref|NP_111575.1| 323 SGEKYILKIKMPFAAKENINLFNHGGELTIE 353
                                   5688999999999999999998888888876 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 6.4e-05
                                   S---EEEEEE--STTB.-TTT-EEEEETTEEEEE CS
                         HSP20  52 rssrkFsrkftLPenv.dadkvkaslkdGvLtvt 84 
                                    + ++++r f LPe + d   v+a++++G L v 
  gi|13541887|ref|NP_111575.1| 352 IEIENWKRVFYLPESIsDRRPVSAEYSNGYLNVV 385
                                   46789*********7648889**********996 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   6.3e-05     0.087       2      38 ..       4      40 ..       3      44 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.3e-05
                                  EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEES CS
                         SRP54  2 nvillvGlqGaGKTttlaKLaallkkegkkvllvaaD 38
                                  +++l  G  G+GKT+ +a    ll +egkk+l++++D
  gi|13541887|ref|NP_111575.1|  4 RILLYTGKGGVGKTSIAAATGSLLAAEGKKTLIISTD 40
                                  678899*****************************99 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   8.7e-05      0.12      34      69 ..       8      43 ..       2      58 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 8.7e-05
                                  EEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE---- CS
                          MeaB 34 ltGvPGaGkstlvealglelrrrGkrvavlavDPss 69
                                   tG  G+Gk  +  a g  l+++Gk+  +++ DP+ 
  gi|13541887|ref|NP_111575.1|  8 YTGKGGVGKTSIAAATGSLLAAEGKKTLIISTDPAH 43
                                  69********************************85 PP

>> DUF3755  Protein of unknown function (DUF3755)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.4      0.06        83       6      22 ..     187     203 ..     185     220 .. 0.87
   2 ?    4.9   0.2     0.015        21       5      13 ..     338     346 ..     335     346 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.06
                       DUF3755   6 eNidLFcqtRdNImaIl 22 
                                   eNidL+ +  + I++Il
  gi|13541887|ref|NP_111575.1| 187 ENIDLLYKQLTDIRKIL 203
                                   9*****99888888887 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.015
                       DUF3755   5 qeNidLFcq 13 
                                    eNi+LF++
  gi|13541887|ref|NP_111575.1| 338 KENINLFNH 346
                                   7******86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (387 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       513  (0.0286129); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.63u 0.29s 00:00:00.92 Elapsed: 00:00:00.49
# Mc/sec: 2362.42
//
Query:       gi|13541888|ref|NP_111576.1|  [L=326]
Description: octaprenyl diphosphate synthase [Thermoplasma volcanium GSS1]
Scores for complete 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    2.4e-61  207.0   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 !  207.0   0.0   1.3e-65   2.4e-61       3     251 ..      32     273 ..      30     277 .. 0.94

  Alignments for each domain:
  == domain 1  score: 207.0 bits;  conditional E-value: 1.3e-65
                                   HHHHHHHHHHHSSS--HHHHHHHHHHHHHSCGHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEETTEE-HHHCTCHHHH CS
               polyprenyl_synt   3 lleealeylveagGKrlRpllvllaaealkeeeeelekaavlawivellhaasLvhDDimDdsetRRGqpcahrlvGnklA 83 
                                    l+++++y++eagGKr+Rpll++la+e  +  ++ ++k ++la+  el+h+asL+hDDi+Dds +RRG+p+   + G ++A
  gi|13541888|ref|NP_111576.1|  32 DLDRMAKYTIEAGGKRFRPLLTILAFESST--DDPYFKILDLAAGYELIHTASLIHDDIIDDSPMRRGRPTLSYKEGINNA 110
                                   5899**************************..5579********************************************* PP

                                   HHHHHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHHHHHHHHHHHTTTTTCCC.SHHHHHHHHHHHTHHHCHHHHHHHHH CS
               polyprenyl_synt  84 indgdfllarafellaklfekslellelfsevllqtveGqlldleeekdddlskfsleeyleivkyKTaylfalpvalaal 164
                                   i+++d+l+a+a+el +++    + + +++++++ +++eGq+l+  +  + d++   +++y +i+++KTa  f++++  a +
  gi|13541888|ref|NP_111576.1| 111 IVVADYLFAKAYELGSRY---GPLVSKVMADASSRLAEGQILEAVNLGNLDIT---EDTYYKIIENKTAHFFEACALGATI 185
                                   ******************...569********************888666666...******************999999* PP

                                   HTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-HHHHSS-TSHHHHTT---HHHHHHHHCT-HHHHHHHHHHTT.SSHH CS
               polyprenyl_synt 165 lagasdeelealkdiglelGlaFQiqDDylDlfgdpevlgKpagtDiqegkctlpilkalelaspeqrkvlkeilg.kkae 244
                                   +a+a++ + e l++++ +lG+aFQ+ DD+lD++gd+  +gKp+  Di++   tlpi++al+++++++r+ + ++++ +++ 
  gi|13541888|ref|NP_111576.1| 186 VAEADRPTREILSNFAFNLGMAFQVTDDILDIVGDDRYTGKPTFVDIKHDALTLPIIYALRNSNDNDRRAIIDMINgRREI 266
                                   ***999999****************************************************99999999999999877776 PP

                                   HHHHHHH CS
               polyprenyl_synt 245 keedvke 251
                                   +++ +k 
  gi|13541888|ref|NP_111576.1| 267 NKSLLKD 273
                                   6666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       521  (0.0290591); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1995.50
//
Query:       gi|13541889|ref|NP_111577.1|  [L=89]
Description: DNA/RNA-binding protein albA [Thermoplasma volcanium GSS1]
Scores for complete 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   65.8   0.8    2.9e-18   65.5   0.8    1.1  1  Alba      Alba
  ------ inclusion threshold ------
      0.015   15.2   0.0      0.017   15.0   0.0    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 !   65.5   0.8   3.2e-22   2.9e-18       1      64 [.       5      65 ..       5      68 .. 0.95

  Alignments for each domain:
  == domain 1  score: 65.5 bits;  conditional E-value: 3.2e-22
                                  CEEEE-STS-HHHHHHHHHHHHTHTTESEEEEEEETTHHHHHHHHHHHHHHHTCTT.EEEEEEE CS
                          Alba  1 neiyVsskspimsyvkralklLsnkkeeeVvlkatGraIskAvsvaeilkrrfgkglyqvnvlt 64
                                  n+i+V++ +p m+yv+++++++ n++++ +++ka+G+ IskAv+vaei + +f+++  +++++ 
  gi|13541889|ref|NP_111577.1|  5 NIIFVGK-KPTMNYVLAVVTQF-NNNANKIIIKARGKTISKAVDVAEITRHKFIPD-AKYEEIR 65
                                  89*****.**************.*******************************98.8998875 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 ?   15.0   0.0   1.9e-06     0.017      57      83 ..      25      51 ..       4      73 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.9e-06
                         Rpp20 57 eelkkeeVfvkatGrAiekalsvgrwf 83
                                   +++ +++++ka G+ i ka+ v++  
  gi|13541889|ref|NP_111577.1| 25 FNNNANKIIIKARGKTISKAVDVAEIT 51
                                  567899*****************9754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       520  (0.0290033); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 653.94
//
Query:       gi|13541890|ref|NP_111578.1|  [L=233]
Description: 3-oxoacyl-[acyl-carrier-protein] reductase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.3e-30  105.4   0.0    4.5e-30  104.9   0.0    1.1  1  adh_short_C2    Enoyl-(Acyl carrier protein) reductase
    3.5e-24   85.3   0.0    4.1e-24   85.1   0.0    1.1  1  adh_short       short chain dehydrogenase
    5.9e-05   23.1   0.0    0.00014   21.8   0.0    1.4  1  KR              KR domain
  ------ inclusion threshold ------
      0.019   14.6   0.0       0.19   11.3   0.0    2.2  2  ApbA            Ketopantoate reductase PanE/ApbA
       0.05   13.5   0.2      0.099   12.5   0.1    1.5  1  Pox_J1          Poxvirus J1 protein
      0.051   13.6   0.0      0.097   12.7   0.0    1.5  1  Shikimate_DH    Shikimate / quinate 5-dehydrogenase
      0.052   13.4   0.0        0.1   12.5   0.0    1.4  1  NAD_binding_10  NAD(P)H-binding
      0.077   13.4   0.0       0.11   13.0   0.0    1.7  1  NAD_binding_7   Putative NAD(P)-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 !  104.9   0.0     2e-33   4.5e-30       4     233 ..      13     231 ..       9     232 .. 0.89

  Alignments for each domain:
  == domain 1  score: 104.9 bits;  conditional E-value: 2e-33
                                   TSHHHHHHHHHHHTT-EEEEEESSGGH.HHHHHHHHHHTTSEEEE--TTSHHHHHHHHHHHHHHHSSEEEEEE-----EGC CS
                  adh_short_C2   4 sgIGraiAkalaeeGaevvltdlneea.kkrveelaeelgaevlecDVtdeeqvealveevvekfgklDilvnnagiapkl 83 
                                   + +G+ +A  l + G +v +  +n+e+ ++   el + ++ e++++D +++e +++l ++  +   ++ ++v  +g   + 
  gi|13541890|ref|NP_111578.1|  13 ENLGYFTALNLLKSGFKVSIIARNKEKlENMGSELRKYGDIEYFAVDLSKREGLASLKKHFSSLNYQIKGVVVEVGGYAS- 92 
                                   56899**********************6666677766666779*******************************999998. PP

                                   SS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHHHCTSCCEEEEEEEGGGTSBSTTTT.HHHHHHHHHHHHHHHHHHHHGGGT CS
                  adh_short_C2  84 kgpfletsreefdraldvnlyslfllakaalplmkeggsivnlssvgaervvpnyn.aygaaKaalealtrylAvelgpkg 163
                                     + l+ s   fd++++ nl+  +l++ a+  ++ +g+siv ++sv a+r +++ +  y+ +Ka+l+ l+   A+ l +kg
  gi|13541890|ref|NP_111578.1|  93 -DS-LD-SITAFDQMIEANLKIPILVLSAISGMLDKGSSIVFITSVFASRKIAESSvSYSLSKAGLNRLVEISAKILRQKG 170
                                   .44.33.5679***********************************88888777777************************ PP

                                   EEEEEEEE--BHCTGGGGSTTHHHHHHHHHHHSTTSS-B-HHHHHHHHHHHCSGGGTT--SEEEEESTTG CS
                  adh_short_C2 164 iRvNavspgpikTlaasgikgfdelleelearaplgrlgtpeevaeaalfLasdeasyitGqtlvvDgGl 233
                                   iRvN +s ++i  +     +      +   +++p  ++++pe + ++++fL+sd++ ++tG++++vD G 
  gi|13541890|ref|NP_111578.1| 171 IRVNGISTSIISQKP----H-----DKDKIEWQPGTQNVDPELISNVVVFLMSDLSLGVTGNIIYVDKGS 231
                                   ***********9332....2.....33445899***********************************96 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.1   0.0   1.8e-27   4.1e-24       3     183 ..       6     182 ..       4     195 .. 0.88

  Alignments for each domain:
  == domain 1  score: 85.1 bits;  conditional E-value: 1.8e-27
                                   EEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSESEEEE CS
                     adh_short   3 vlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkldvLvn 83 
                                   vl+ G ++ +G+ +a +l+k+G+kv +++r++ekle++ +el++   ++ +++vD+++re +  l ++  +   ++  +v 
  gi|13541890|ref|NP_111578.1|   6 VLIAGTGENLGYFTALNLLKSGFKVSIIARNKEKLENMGSELRKY-GDIEYFAVDLSKREGLASLKKHFSSLNYQIKGVVV 85 
                                   9******************************************96.79*****************9999999999999999 PP

                                   ---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-T.TBHHHHHHHHHHHHHHHHH CS
                     adh_short  84 NAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpva.gvaaYsAsKaavagltrsl 163
                                    +G    ++ s  s ++++++ie Nl+ ++l+  a+  +++  ++ +Iv+++Sv +  + a + ++Ys sKa+++ l++  
  gi|13541890|ref|NP_111578.1|  86 EVGGY--ASDSLDSITAFDQMIEANLKIPILVLSAISGMLD--KGSSIVFITSVFASRKIAeSSVSYSLSKAGLNRLVEIS 162
                                   99994..4444455667****************99888866..7889*******886665515678*************** PP

                                   HHHHGGGTEEEEEEEESSBS CS
                     adh_short 164 akelaptgirvnavaPGlvd 183
                                   ak l+++girvn++ + +++
  gi|13541890|ref|NP_111578.1| 163 AKILRQKGIRVNGISTSIIS 182
                                   ***************99987 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   6.2e-08   0.00014       3     102 ..       6     100 ..       5     111 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 6.2e-08
                                   EEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHSS--- CS
                            KR   3 ylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaeeppik 83 
                                   +li+G   +LG  +a  l+++g + + +++R+   +e+ +++ +el+++g ++e++a+D+s+++ +++l +++++ + +ik
  gi|13541890|ref|NP_111578.1|   6 VLIAGTGENLGYFTALNLLKSGFK-VSIIARN---KEKLENMGSELRKYG-DIEYFAVDLSKREGLASLKKHFSSLNYQIK 81 
                                   69********************65.6667788...445556778999988.8***************************** PP

                                   EEEE---------TTT--H CS
                            KR  84 GvihaAgvlrdklleemta 102
                                   Gv+   g  + + l++ ta
  gi|13541890|ref|NP_111578.1|  82 GVVVEVGGYASDSLDSITA 100
                                   **99888888888887765 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   8.6e-05      0.19       1      50 [.       6      54 ..       6      80 .. 0.84
   2 ?    0.9   0.0      0.14   3.2e+02      34      74 ..     164     210 ..     144     212 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 8.6e-05
                                  EEEES-S.HHHHHHHHHHHHHTHCEEEE-SCHHHHHHHHHCEEEEETTCEE CS
                          ApbA  1 iailGaG.aiGsllaakLakagadvtlilrsrrlealkknGlrltseggee 50
                                  ++i+G+G  +G + a +L k g +v +i+r++  e+l++ G++l+++g  e
  gi|13541890|ref|NP_111578.1|  6 VLIAGTGeNLGYFTALNLLKSGFKVSIIARNK--EKLENMGSELRKYGDIE 54
                                  5799999679**********************..77888888888887544 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.14
                                   HHHHHHCEEEEETTCEEEEEECEEECCH......SCCCCS-ESEEEE CS
                          ApbA  34 ealkknGlrltseggeeilrppealsae......ekselepidlviv 74 
                                   + l+++G+r+++ +++ i ++p+  ++       ++ + e i++v+v
  gi|13541890|ref|NP_111578.1| 164 KILRQKGIRVNGISTSIISQKPHDKDKIewqpgtQNVDPELISNVVV 210
                                   34677777777777555555555544444444466666666676666 PP

>> Pox_J1  Poxvirus J1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   4.4e-05     0.099      43     119 ..      28     106 ..      20     118 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.4e-05
                        Pox_J1  43 flLallirskdkLeaiGylYeplseefraliefrdlkelkklfnrall.kve.eekvkvdkGylsdFvvsllrlkrelk 119
                                   f ++++ r k+kLe++G       +    ++++++ + l++l ++  + + + ++ v    Gy+sd   s++ + +  +
  gi|13541890|ref|NP_111578.1|  28 FKVSIIARNKEKLENMGSELRKYGDIEYFAVDLSKREGLASLKKHFSSlNYQiKGVVVEVGGYASDSLDSITAFDQMIE 106
                                   5578999**********988888877667777777666666666544336663444444469********999987665 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   4.3e-05     0.097      11      59 ..       2      50 ..       1      69 [. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.3e-05
                                  TT-EEEEES-SH.HHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.E CS
                  Shikimate_DH 11 kekkvlliGaGe.maelvakhLlakgvkkvvvaNRtlerakelaeelkge 59
                                  ++++vl+ G+Ge ++  +a +Ll++g+k v ++ R+ e+ +++ +el+++
  gi|13541890|ref|NP_111578.1|  2 ATERVLIAGTGEnLGYFTALNLLKSGFK-VSIIARNKEKLENMGSELRKY 50
                                  5789*******85688999********9.*************99998543 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   4.5e-05       0.1      13     100 ..      22     119 ..      13     156 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.5e-05
                                   HHHHC-T-EEEEEETTHHHCH....HHHCTTTCEEEE--TT-CCHHHHHHT.......T-SEEEES---TCCHHHHHHHHH CS
                NAD_binding_10  13 ellargghevtalvRnpekla....eleaeeglevvegdvtdvedlaealk.......gadaVvsalggggkdeegakniv 82 
                                    ll++ g++v +++Rn+ekl+    el++   +e + +d+++ e la+  k       ++  Vv+ +gg ++d+   +++ 
  gi|13541890|ref|NP_111578.1|  22 NLLKS-GFKVSIIARNKEKLEnmgsELRKYGDIEYFAVDLSKREGLASLKKhfsslnyQIKGVVVEVGGYASDSLDSITAF 101
                                   68999.5*************844445667799*********9877666666555776677789999999999999999999 PP

                                   HHHHHCT--EEEEEEETT CS
                NAD_binding_10  83 daakeagvkRfvlvsaig 100
                                   d + ea+ k  +lv ++ 
  gi|13541890|ref|NP_111578.1| 102 DQMIEANLKIPILVLSAI 119
                                   999999998777766654 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 ?   13.0   0.0   4.7e-05      0.11       7      46 ..       3      51 ..       1     212 [. 0.82

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.7e-05
                 NAD_binding_7  7 gkkvlvvGgGe.vAarkvrklleagakvtvvapevkeele.........e 46
                                  +++vl++G Ge +++  + +ll++g kv ++a + ke+le         +
  gi|13541890|ref|NP_111578.1|  3 TERVLIAGTGEnLGYFTALNLLKSGFKVSIIARN-KEKLEnmgselrkyG 51
                                  789*****99659*********************.444444555343340 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       467  (0.0260472); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.30s 00:00:00.81 Elapsed: 00:00:00.50
# Mc/sec: 1407.37
//
Query:       gi|13541891|ref|NP_111579.1|  [L=391]
Description: major facilitator superfamily permease [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.3e-14   52.2  64.2    4.3e-14   52.2  64.2    1.5  1  MFS_1     Major Facilitator Superfamily
    0.00061   18.8   2.8    0.00061   18.8   2.8    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 !   52.2  64.2   4.8e-18   4.3e-14       2     353 .]      15     352 ..      14     352 .. 0.81

  Alignments for each domain:
  == domain 1  score: 52.2 bits;  conditional E-value: 4.8e-18
                         MFS_1   2 llaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfa 82 
                                   ++++f ++++++il+p++p  + ++l+++ s + +++tly+ +++++ l++G++s        ll++++l+++gl++ +f 
  gi|13541891|ref|NP_111579.1|  15 WIMLFAIGMGWFILSPLVP-SIVQSLNVQTSLVIFIITLYGYAMVIFGLVAGYISAVRNVYNSLLASAILTFVGLTVRAF- 93 
                                   7899***************.9***********************************999999************999999. PP

                         MFS_1  83 sslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsl 162
                                    + + l++ + v++++g+ ++++ +++++  ++pk     +ig+  +   +G+++g   ++ l +++g   + ++ ai+s+
  gi|13541891|ref|NP_111579.1|  94 VNRFdLFFSFSVIAAVGYPLAMAPVGSVADSISPK-SAHTVIGISVGLLFFGMAVGSFTAPGLEEHFGLKFTLIVPAILSA 173
                                   67777*************99999999988888888.9999***************************************** PP

                         MFS_1 163 lafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsglltllplylqevlglsgl 243
                                   +++vl ++ +  + p+  r ++ +           + ++    ++  w ++  ++  + ++++  + + l+++   +l +l
  gi|13541891|ref|NP_111579.1| 174 ISLVL-IASMHSSFPRYYRARSLKG----------S-FSVGMVKN--W-YVGLSIASMSVMFSSIAASVLIMHNINHLQAL 239
                                   **885.3444444444444444444..........2.33334445..4.33333333334444444444445777777788 PP

                         MFS_1 244 llaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavtssavllll..vlvliGfglgfvfpsll 322
                                    +ag++ +l+++++a++a+l+  +  ++g  ++ l+  +ll++++++++ +  + + +l+++  +++++Gf++  ++++++
  gi|13541891|ref|NP_111579.1| 240 NYAGIFGGLAFVGSAFGAVLLPLIFGKYGGLKIGLIVSGLLSFFSISILAILISLTRLLSAIavSYFIFGFFGNAYWSMAM 320
                                   9999999999999999*************988888888888888888777777766666665569999***5555666666 PP

                         MFS_1 323 alasdla.ppeeagtasglfntagslggalgp 353
                                   + ++ +a +p++ag  ++ f++a+++g a+ p
  gi|13541891|ref|NP_111579.1| 321 TSVTYYAsSPDKAGLSTAMFSVASNAGVAVIP 352
                                   6666666589*****************99877 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   5.7      0.54   4.8e+03     264     298 ..      19      54 ..       3      94 .. 0.58
   2 !   18.8   2.8   6.8e-08   0.00061      32     118 ..     119     203 ..      89     207 .. 0.77
   3 ?   -1.7  24.8      0.11     1e+03      13     186 ..     207     385 ..     199     389 .. 0.70

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 0.54
                                   HHHHTTHHHHHHHTTTHHHHSS-THH.HHHHHHHHH CS
                      Sugar_tr 264 fqqltGinaimyysptifenlglsks.llvtiivgv 298
                                   f    G++++  + p+i ++l +++s +++ i ++ 
  gi|13541891|ref|NP_111579.1|  19 FAIGMGWFILSPLVPSIVQSLNVQTSlVIFIITLYG 54 
                                   334456666666666777777777773222222222 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 6.8e-08
                                   STT--SHHHHHH...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHH CS
                      Sugar_tr  32 fglsksksskeessvlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlv 112
                                     +  s s+k  + + +g++v+++++G ++Gs++a  l + fG k +l++ a+l+ i+ vl+a  +  +s+  ++ +R l 
  gi|13541891|ref|NP_111579.1| 119 GSVADSISPKS-AHTVIGISVGLLFFGMAVGSFTAPGLEEHFGLKFTLIVPAILSAISLVLIASMH--SSFPRYYRARSLK 196
                                   34444444333.5779**********************************************9999..7899999999998 PP

                                   H.HHHHH CS
                      Sugar_tr 113 G.igvGl 118
                                   G ++vG+
  gi|13541891|ref|NP_111579.1| 197 GsFSVGM 203
                                   8566665 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.11
                                   HHHHHCGGGTHHHHHHHHTSTT--SHHHHHH...HHHHHHHTHHHHHHHHHHHHHHHHHHT.THHHHHHHHHHHHHHHHHH CS
                      Sugar_tr  13 gYdtgvigafltllkfaknfglsksksskeessvlsglivsiflvGaiiGslfagllgdrf.GRkkslliaavlfvigavl 92 
                                   +Y    i++++ + + +    l  ++ ++ ++  + g++ ++++vG+++G++++ l+  ++ G k +l+++++l++ ++ +
  gi|13541891|ref|NP_111579.1| 207 WYVGLSIASMSVMFSSIAASVLIMHNINHLQALNYAGIFGGLAFVGSAFGAVLLPLIFGKYgGLKIGLIVSGLLSFFSISI 287
                                   5555566666666665555555555555555566789*****************988666626999****99998877655 PP

                                   H.H-TTTTSS-TGGGGGHHHHHHHHHHHHHHHHHHHHTTS.-SCCHHHHHHHHHHHHHHHHHH.HHHHHHHHHTSS-.TTH CS
                      Sugar_tr  93 q.aaakgknsvevlivgRvlvGigvGlasvlvPmyisEiA.pkklRgalvslyqlaitfGilv.aaifglglnktsn.adg 169
                                     +++  ++ + +++v+ ++ G++  +   ++ + +  +A  ++++g  + ++ +a  +G  v   ++g+++ + s    g
  gi|13541891|ref|NP_111579.1| 288 LaILISLTRLLSAIAVSYFIFGFFGNAYWSMAMTSVTYYAsSPDKAGLSTAMFSVASNAGVAViPVFLGTAFLRQSTlILG 368
                                   405555569999**********97655544444444444438999***************755145555555333334677 PP

                                   HHHHHHCCHHHHHHHHH CS
                      Sugar_tr 170 wrillglqlvpalllli 186
                                     i l++++v+a+l + 
  gi|13541891|ref|NP_111579.1| 369 VSIVLAMEFVSAVLAFT 385
                                   88888888888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1005  (0.0560544); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); 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: 0.71u 0.31s 00:00:01.02 Elapsed: 00:00:00.62
# Mc/sec: 1905.55
//
Query:       gi|13541892|ref|NP_111580.1|  [L=92]
Description: hypothetical protein TVN1061 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       386  (0.0215294); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 599.84
//
Query:       gi|13541893|ref|NP_111581.1|  [L=246]
Description: DNA polymerase sliding clamp [Thermoplasma volcanium GSS1]
Scores for complete 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   59.6   0.6    2.8e-14   52.9   0.3    2.3  2  PCNA_N    Proliferating cell nuclear antigen, N-terminal doma
    1.9e-08   34.5   0.5    1.5e-07   31.7   0.1    2.3  2  PCNA_C    Proliferating cell nuclear antigen, C-terminal doma
    5.4e-07   28.9   2.2      0.011   14.8   0.0    2.1  2  Rad1      Repair protein Rad1/Rec1/Rad17
  ------ inclusion threshold ------
      0.019   14.4   0.0      0.022   14.2   0.0    1.3  1  Rad9      Rad9
      0.043   13.6   0.1        1.1    9.0   0.0    2.5  3  Leptin    Leptin


Domain annotation for each model (and alignments):
>> PCNA_N  Proliferating cell nuclear antigen, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.9   0.3   7.8e-18   2.8e-14      12      95 ..      11      94 ..       3     109 .. 0.93
   2 !    4.7   0.0    0.0065        23      17     112 ..     141     235 ..     130     241 .. 0.76

  Alignments for each domain:
  == domain 1  score: 52.9 bits;  conditional E-value: 7.8e-18
                                  HHHHHHHHTTTCSEEEEEEETTEEEEEEE-TTSSEEEEEEEEGGGSSEEEESS-EEEEEEHHHHHHHHTTSTTTSEEEEEEET CS
                        PCNA_N 12 lkklleaikdlvneanfdcddsGislqalDsshvaLvslelrsegfekyrCDrnlalgvnlnslskilkcannedsvtlkaed 94
                                  lk + + +  +v+ea f++d++G+s+ a+D +hva++ le+ +e f+++r D    + +++  l  ++++an +++v +  + 
  gi|13541893|ref|NP_111581.1| 11 LKEITDLLSTIVSEAKFKVDENGMSVTAVDPAHVAMIRLEVPKEVFSEFRSDGTEEIALDIDRLKSVIRLANSSENVGITKDK 93
                                  899**************************************************************************998665 PP

                                  T CS
                        PCNA_N 95 e 95
                                  e
  gi|13541893|ref|NP_111581.1| 94 E 94
                                  4 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0065
                                   HHHTTTCSEEEEEEETTEEEEEEE-TTSSEEEEEEEEGGGSSEEEESS-EEEEEEHHHHHHHHTTSTTTSEEEEEEETT.S CS
                        PCNA_N  17 eaikdlvneanfdcddsGislqalDsshvaLvslelrsegfekyrCDrnlalgvnlnslskilkcannedsvtlkaede.a 96 
                                    a  d+ +++ f  +++G+++ +  +s     ++ l ++  ++  C   +  +  l+ l k +k +   ds+ ++  d+ +
  gi|13541893|ref|NP_111581.1| 141 RAAEDISDSIRFVLSSEGFRATSHSESEE--SEMVLPKDMLSDLSCSDTIKSSYPLEYLLKFIKAVSSADSLKISFRDDyP 219
                                   56666677777777788877666555554..478889999999999999999999999************99998755416 PP

                                   SEEEEEEEECTSSEEE CS
                        PCNA_N  97 dtlalvfesekkdkia 112
                                    ++ + ++++ + ki+
  gi|13541893|ref|NP_111581.1| 220 LSIEFYLDQNPSAKIK 235
                                   6788888877777765 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 ?    0.2   0.0      0.22     8e+02      25      48 ..      80     102 ..      68     116 .. 0.74
   2 !   31.7   0.1   4.1e-11   1.5e-07       5     117 ..     125     228 ..     119     242 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.22
                                   HTTT-SEEEEEEETTEEEEEEEET CS
                        PCNA_C  25 lsqlsdsvvisvtkegvkfsasGd 48 
                                   l++ s++v i+  ke +kf   G+
  gi|13541893|ref|NP_111581.1|  80 LANSSENVGITKDKEKLKFDL-GN 102
                                   677788899999999999963.44 PP

  == domain 2  score: 31.7 bits;  conditional E-value: 4.1e-11
                                   SS-SEEEEEEHHHHHHHHHHHTTT-SEEEEEEETTEEEEEEEETTEEEEEEE--BEESSSGGGCBEEEESS-EEEEEEHHH CS
                        PCNA_C   5 seydavvklpssefaricrdlsqlsdsvvisvtkegvkfsasGdiGsasivlkqvkdvdkeeeavklelkepvtltfalkY 85 
                                   sey a++k   s+f+r  r   ++sds+   ++ eg + +++ +        ++ ++v  ++  + l+ +++++  + l+Y
  gi|13541893|ref|NP_111581.1| 125 SEYYAIIK--RSDFERGLRAAEDISDSIRFVLSSEGFRATSHSES-------EESEMVLPKDMLSDLSCSDTIKSSYPLEY 196
                                   57888887..579***********************777666554.......46677888889999*************** PP

                                   HHHHGGGGGC-SEEEEEEETTSEEEEEEEETT CS
                        PCNA_C  86 laeftkatsLservtlslssevPlvveykikd 117
                                   l++f+ka s ++  ++s+ ++ Pl +e+ +++
  gi|13541893|ref|NP_111581.1| 197 LLKFIKAVSSADSLKISFRDDYPLSIEFYLDQ 228
                                   ****************************9876 PP

>> Rad1  Repair protein Rad1/Rec1/Rad17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0     3e-06     0.011       6      85 ..       8     102 ..       3     119 .. 0.76
   2 !   14.3   0.6   4.4e-06     0.016     170     264 ..     130     217 ..      99     225 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3e-06
                          Rad1   6 lsnvseLatlLksiafkdkalvqissdGlkfi.vednrvlqaqafldkalFtsYtfenaqdd................ede 69 
                                     n++e+++lL++i+  ++a  +++++G++++ v+ ++v  + + ++k++F++++ + +++                  ++
  gi|13541893|ref|NP_111581.1|   8 VRNLKEITDLLSTIV--SEAKFKVDENGMSVTaVDPAHVAMIRLEVPKEVFSEFRSDGTEEIaldidrlksvirlansSEN 86 
                                   67999*******986..578899********85689*******************95554446777777777776666555 PP

                          Rad1  70 edeeedsvsfevsLsa 85 
                                   +  ++d+ +++++L  
  gi|13541893|ref|NP_111581.1|  87 VGITKDKEKLKFDLGN 102
                                   5555555556555555 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 4.4e-06
                          Rad1 170 ilkselLhsalteLdatskklkilassekkapvfalsakgelgssevefpneksvlekfevsslsessessYkfallkkaa 250
                                   i+k + ++  l+  +++s+++++++sse     f+ ++ +e  +se+ +p  k++l  + +s   ++++ssY +++l k  
  gi|13541893|ref|NP_111581.1| 130 IIKRSDFERGLRAAEDISDSIRFVLSSE----GFRATSHSESEESEMVLP--KDMLSDLSCS---DTIKSSYPLEYLLKFI 201
                                   5555556666666677788888888885....677788888888888888..579*******...666666********** PP

                          Rad1 251 kalalss..Kvslrmd 264
                                   ka++++   K+s+r d
  gi|13541893|ref|NP_111581.1| 202 KAVSSADslKISFRDD 217
                                   ***9975227777765 PP

>> Rad9  Rad9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   6.2e-06     0.022       7      74 ..      17      85 ..      11     199 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 6.2e-06
                          Rad9  7 clsrigdelyleisedglelrtvnssrSayalvtlkksfFdkyekevseqircki.lvKsvlsvfrsls 74
                                   ls i  e  ++  e+g+++++v+ ++ a   ++  k+ F+++ ++ +e+i + i  +Ksv+ +  s  
  gi|13541893|ref|NP_111581.1| 17 LLSTIVSEAKFKVDENGMSVTAVDPAHVAMIRLEVPKEVFSEFRSDGTEEIALDIdRLKSVIRLANSSE 85
                                  5899999999********************************************945899999876444 PP

>> Leptin  Leptin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.61   2.2e+03      77      94 ..       6      23 ..       1      34 [. 0.72
   2 ?    9.0   0.0   0.00032       1.1      57     102 ..      49      94 ..      44     114 .. 0.84
   3 ?    1.5   0.0     0.065   2.3e+02      60      94 ..     175     209 ..     159     219 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.61
                                  HHHHHHHHHHHHHHHHTT CS
                        Leptin 77 nDlenLrallkllatsks 94
                                    + nL+++  ll+t +s
  gi|13541893|ref|NP_111581.1|  6 ISVRNLKEITDLLSTIVS 23
                                  557899999888888765 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00032
                                   HHHHHHHHHTS--HHHHHHHHHHHHHHHHHHHHHHHTT-------- CS
                        Leptin  57 LavyqqilsslpseevvqisnDlenLrallkllatsksCelekase 102
                                   L+v +++ s + s+ +  i  D++ L+++++l  +s +  ++k +e
  gi|13541893|ref|NP_111581.1|  49 LEVPKEVFSEFRSDGTEEIALDIDRLKSVIRLANSSENVGITKDKE 94 
                                   788899**************************99999988876654 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.065
                                   HHHHHHTS--HHHHHHHHHHHHHHHHHHHHHHHTT CS
                        Leptin  60 yqqilsslpseevvqisnDlenLrallkllatsks 94 
                                    + +ls l+ +++++ s  le L +++k ++++ s
  gi|13541893|ref|NP_111581.1| 175 PKDMLSDLSCSDTIKSSYPLEYLLKFIKAVSSADS 209
                                   57799******************999999888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1515.18
//
Query:       gi|13541894|ref|NP_111582.1|  [L=279]
Description: hypothetical protein TVN1063 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       933  (0.0520386); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.51
# Mc/sec: 1641.17
//
Query:       gi|13541895|ref|NP_111583.1|  [L=433]
Description: hypothetical protein TVN1064 [Thermoplasma volcanium GSS1]
Scores for complete 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    8.3e-12   45.2   0.0    1.5  1  DUF58     Protein of unknown function DUF58


Domain annotation for each model (and alignments):
>> DUF58  Protein of unknown function DUF58
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.2   0.0   4.6e-16   8.3e-12       1      86 []     195     282 ..     195     282 .. 0.92

  Alignments for each domain:
  == domain 1  score: 45.2 bits;  conditional E-value: 4.6e-16
                         DUF58   1 gldfaglReYvpgDplrrIdWkatARt..gelyvrefeaerartvllvldlspemslgstgdekletavsaaaslarqlld 79 
                                   g df++lReY pgD++r + W    Rt  ++lyv+++e+er  +vl+v+d    m++g +g   ++t +s ++  +++  +
  gi|13541895|ref|NP_111583.1| 195 GYDFLSLREYYPGDEIRYVAWSRFGRTrgDDLYVKQMEEERIIDVLFVVDYGIGMNHGHDGIRMFDTVISDVLKTSYKIRK 275
                                   679***********************74477*****************************999999999999999999988 PP

                         DUF58  80 egdrvgl 86 
                                   ++d vg+
  gi|13541895|ref|NP_111583.1| 276 NQDGVGF 282
                                   8888885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (433 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       521  (0.0290591); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); 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: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 2724.55
//
Query:       gi|13541896|ref|NP_111584.1|  [L=319]
Description: MoxR-like ATPase [Thermoplasma volcanium GSS1]
Scores for complete 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-63  211.0   0.2    8.2e-63  210.1   0.2    1.5  1  AAA_3            ATPase family associated with various cellul
    1.5e-18   67.1   0.0    4.9e-18   65.5   0.0    1.8  2  AAA_5            AAA domain (dynein-related subfamily)
    3.4e-14   52.4   0.0    5.8e-14   51.7   0.0    1.3  1  AAA_lid_2        AAA lid domain
      6e-08   33.2   0.0    2.5e-06   27.9   0.0    2.4  2  AAA              ATPase family associated with various cellul
    1.4e-06   28.2   1.4    9.9e-06   25.4   0.1    2.7  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    1.8e-05   24.0   0.0    3.6e-05   23.0   0.0    1.6  1  MCM              MCM P-loop domain
    3.4e-05   23.3   0.3      0.011   15.2   0.1    2.5  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    0.00014   21.6   0.0     0.0025   17.5   0.0    2.2  1  Sigma54_activat  Sigma-54 interaction domain
  ------ inclusion threshold ------
      0.011   15.6   0.0      0.039   13.8   0.0    2.0  1  AAA_lid_8        AAA lid domain
      0.014   15.6   0.0      0.028   14.5   0.0    1.5  1  AAA_2            AAA domain (Cdc48 subfamily)
      0.015   14.8   0.0      0.024   14.2   0.0    1.3  1  AAA_7            P-loop containing dynein motor region
       0.18   12.0   0.0       0.59   10.4   0.0    1.8  3  AAA_22           AAA domain


Domain annotation for each model (and alignments):
>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  210.1   0.2   5.5e-66   8.2e-63       1     131 []      44     174 ..      44     174 .. 0.99

  Alignments for each domain:
  == domain 1  score: 210.1 bits;  conditional E-value: 5.5e-66
                         AAA_3   1 hvllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeekekefefkkGpvfanllladeinrappktqsa 81 
                                   h+llegvPGlakt+l++++a++ ++efkriqftpd+lPsdi+Gt +f+ +++++efk+Gp+fan++ladeinr+ppk+qsa
  gi|13541896|ref|NP_111584.1|  44 HILLEGVPGLAKTMLANEFARHTKMEFKRIQFTPDMLPSDITGTIMFNIESRKMEFKEGPLFANVVLADEINRTPPKVQSA 124
                                   9******************************************************************************** PP

                         AAA_3  82 lleameerqvtvegethklpepflvlatqnPieqeGtyplpeaqldrfll 131
                                   lleamee +vtv+geth+lp+pf+v+atqnP+eqeGt+pl+ea +drfl+
  gi|13541896|ref|NP_111584.1| 125 LLEAMEEVHVTVGGETHSLPKPFFVIATQNPVEQEGTFPLAEALMDRFLF 174
                                   ************************************************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 !   65.5   0.0   3.3e-21   4.9e-18       1     138 []      44     172 ..      44     172 .. 0.94
   2 ?   -1.5   0.0       1.5   2.3e+03      31      47 ..     230     246 ..     224     303 .. 0.60

  Alignments for each domain:
  == domain 1  score: 65.5 bits;  conditional E-value: 3.3e-21
                                   EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--...........--------G-SEEEEESGGG--H CS
                         AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreik..ngttslvdsplvraaregeilvlDEveraes 79 
                                   ++lL G pG +K++la ++a+ ++ e+  +q+t d+ ++d++g + ++  +++ +++++pl      + +++ DE++r ++
  gi|13541896|ref|NP_111584.1|  44 HILLEGVPGLAKTMLANEFARHTKMEFKRIQFTPDMLPSDITGTIMFNieSRKMEFKEGPLF-----ANVVLADEINRTPP 119
                                   78******************************************999888************.....9************* PP

                                   HHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--..-TT-TTHHHHTT- CS
                         AAA_5  80 evlnsLlslleerrllleeggelvkaknddllerfrviatanpld.rslnelspalrsRf 138
                                   +v+++Ll  +ee ++    gge  + +++     f viat np++  +  +l +al +Rf
  gi|13541896|ref|NP_111584.1| 120 KVQSALLEAMEEVHVT--VGGETHSLPKP-----FFVIATQNPVEqEGTFPLAEALMDRF 172
                                   ************9999..55555555554.....***********9999**********9 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.5
                                   E--TT--HHHHH--B-- CS
                         AAA_5  31 qltrdtteedlkgrrei 47 
                                    l r+t+e++l++    
  gi|13541896|ref|NP_111584.1| 230 DLMRKTREDELVYLGAS 246
                                   45555666666554332 PP

>> AAA_lid_2  AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.7   0.0   3.9e-17   5.8e-14       2      68 ..     234     298 ..     233     304 .. 0.86

  Alignments for each domain:
  == domain 1  score: 51.7 bits;  conditional E-value: 3.9e-17
                     AAA_lid_2   2 atrahlaielgvsgrRadlallraArAlAalegrdyVtpeDvkeaaplVLaHRlrrepeaegettee 68 
                                   +tr+++ + lg+s+r  +   ++aArA+A++ gr yV+peD+ ++a  +L+HRl+ +pea   +  +
  gi|13541896|ref|NP_111584.1| 234 KTREDELVYLGASPR-TTSKYIKAARANALISGRSYVIPEDILYMAFEILNHRLILKPEAVVDE-TD 298
                                   799************.***************************************555554322.33 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.0   1.7e-09   2.5e-06       1     130 [.      45     178 ..      45     180 .. 0.84
   2 ?    2.9   0.0     0.089   1.3e+02      59     119 ..     199     257 ..     182     270 .. 0.56

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 1.7e-09
                                   EEEESSTTSSHHHHHHHHHHHHTHEEEEEET.TTCS.SSSTTHHHHHHHHHHHHHHHTS.TSEEEEEETGGGHHHHHTTCC CS
                           AAA   1 vllyGppGtGKTllakavakelgvefleisg.sell.skyvgesekkirelfkeakeka.kpsilfiDEidalaksrsgse 78 
                                   +ll G pG  KT+la+  a+++++ef +i+  +++l s++ g  + +i+    e ke      +++ DEi +  ++     
  gi|13541896|ref|NP_111584.1|  45 ILLEGVPGLAKTMLANEFARHTKMEFKRIQFtPDMLpSDITGTIMFNIESRKMEFKEGPlFANVVLADEINRTPPKV---- 121
                                   699***********************9999636888899***********9999998887559**********8888.... PP

                                   CHHHHHHHHHHHHHHHHTTTS........SSTEEEEEEESS.....GGGSTHHHHSTTSSEEEET CS
                           AAA  79 seeeervvnqLlteldgvkkk........eskvivigatnr.....pdkldpallrgRfdrkiei 130
                                          +++Ll+++++v            ++++vi++ n         l +al+ +Rf  ++++
  gi|13541896|ref|NP_111584.1| 122 -------QSALLEAMEEVHVTvggethslPKPFFVIATQNPveqegTFPLAEALM-DRFLFRYYL 178
                                   .......***********99999**999966688888888754433344777777.888777665 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.089
                                   S.EEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESS.GGGSTHHH CS
                           AAA  59 p.silfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnr.pdkldpal 119
                                   p  +l+ DEi  + ++   ++  +++++ + ++  + + +++  +++ +ga+ r  +k+ +a 
  gi|13541896|ref|NP_111584.1| 199 PsIVLLPDEIMHFRSEV--DNVYVSDEIKEYIVDLMRKTRED--ELVYLGASPRtTSKYIKAA 257
                                   53444446666664444..55556666666666666666663..4666666665444444443 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.1   6.6e-09   9.9e-06      34     115 ..      43     136 ..      39     150 .. 0.77
   2 ?   -0.5   0.2      0.62   9.2e+02      84     116 ..     199     232 ..     182     244 .. 0.72

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 6.6e-09
                        RuvB_N  34 dhvllyGpPGlGkttlakiiakelgvklkit.sgPvlekagdla.alltnleek...........dvlfideihrlsrave 101
                                   +h+ll G PGl kt la+  a+  ++++k    +P +  ++d++ +++ n+e++           +v++ dei r  ++v+
  gi|13541896|ref|NP_111584.1|  43 NHILLEGVPGLAKTMLANEFARHTKMEFKRIqFTPDML-PSDITgTIMFNIESRkmefkegplfaNVVLADEINRTPPKVQ 122
                                   7*************************997651567665.5666515777887652222222333357889*********** PP

                        RuvB_N 102 evlysamedfrldi 115
                                     l  ame++++ +
  gi|13541896|ref|NP_111584.1| 123 SALLEAMEEVHVTV 136
                                   ********987754 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.62
                        RuvB_N  84 ekdvlfideihrlsraveevlys.amedfrldiv 116
                                   ++ vl+ dei  ++++v++v  s  + ++ +d++
  gi|13541896|ref|NP_111584.1| 199 PSIVLLPDEIMHFRSEVDNVYVSdEIKEYIVDLM 232
                                   34488889*9999999998755425788888876 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0   2.4e-08   3.6e-05      57     175 ..      42     157 ..       2     191 .. 0.81

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 2.4e-08
                                   S-EEEEEESSTSTHHHHHHHHHHHSSSEEEEESS...SSSSSHSSSEEEEESSSSSEEEEETHHHHTTTSEEEEESGGGST CS
                           MCM  57 dinvllvgdpgtaKsqlLkyveklapravytsgk...gssaagLtaavvrdeetgefvleaGalvladkGvcciDefdkmk 134
                                     ++ll g pg+aK+ l ++ ++ ++   +  ++       +++t +++ + e++++ ++ G l      v++ De+++  
  gi|13541896|ref|NP_111584.1|  42 GNHILLEGVPGLAKTMLANEFARHTKM-EFKRIQftpDMLPSDITGTIMFNIESRKMEFKEGPLFAN---VVLADEINRTP 118
                                   569************999988755444.3333330003455799********************965...9********** PP

                                   CHHHHHHHHHHHHSEEEEESSSCEEEEE--EEEEEEE--SS CS
                           MCM 135 eedrsalhEamEqqtisiaKaGivatLnartsvlaAanpka 175
                                    + +sal+EamE+ +  ++ +G + +L+    v+a  np++
  gi|13541896|ref|NP_111584.1| 119 PKVQSALLEAMEEVH--VTVGGETHSLPKPFFVIATQNPVE 157
                                   ************855..55589999**************85 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1     7e-06     0.011       4      42 ..      24      62 ..      22      68 .. 0.91
   2 !    5.7   0.0    0.0057       8.5     109     159 ..     108     156 ..     104     166 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 7e-06
                  Mg_chelatase  4 dvkGqeeakraleiaaaGgHnlllvGppGsGKtmlakrl 42
                                   v+G ++  r + ia   g ++ll G pG  Ktmla+ +
  gi|13541896|ref|NP_111584.1| 24 RVIGSRRIVRFMFIALLTGNHILLEGVPGLAKTMLANEF 62
                                  689999999*******99999***************875 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0057
                  Mg_chelatase 109 vLfLDElpefkrkvlevLRePledgevtisrakakvefparfqlvaamNpc 159
                                   v++ DE+     kv  +L e +e+ +vt+   ++  + p  f ++a+ Np 
  gi|13541896|ref|NP_111584.1| 108 VVLADEINRTPPKVQSALLEAMEEVHVTVGGETH--SLPKPFFVIATQNPV 156
                                   6778*******************99999976665..568889999999996 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   1.7e-06    0.0025      95     146 ..     107     157 ..      27     172 .. 0.62

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.7e-06
                                   SEEEEETGGGS-HHHHHHHHHHHHHSEEESBTSSSEEE--EEEEEEESS-HH CS
               Sigma54_activat  95 GtlfLDeigelplelQekLlrvlqegevervGsskeikvdvriiaatnedle 146
                                    +++ Dei++ p+++Q+ Ll++++e +v+  G++++ +  + +i at++ +e
  gi|13541896|ref|NP_111584.1| 107 NVVLADEINRTPPKVQSALLEAMEEVHVTVGGETHSLPKPFFVI-ATQNPVE 157
                                   46778*********************998777777777666555.5665555 PP

>> AAA_lid_8  AAA lid 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     0.039       2      55 ..     224     278 ..     206     285 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.6e-05
                     AAA_lid_8   2 vlelileiknkleeeeea..iyvSDRRwkkivkllkasAylngrdevnlsDllllk 55 
                                   + e+i ++ +k   e+e   +  S R   k++k  +a+A+++gr+ v ++D+l + 
  gi|13541896|ref|NP_111584.1| 224 IKEYIVDLMRKT-REDELvyLGASPRTTSKYIKAARANALISGRSYVIPEDILYMA 278
                                   455666666666.334442235799***************************9985 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   1.9e-05     0.028       6     115 ..      45     141 ..      42     161 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.9e-05
                                   EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS....EEEEETGGG--- CS
                         AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG....ivllDEidKihp 82 
                                   ill g  g  kt+la++ a++ ++    ++ r+  +  +   ++  ++   i ++++  +  eg     +vl DEi +  p
  gi|13541896|ref|NP_111584.1|  45 ILLEGVPGLAKTMLANEFARHTKM----EFKRIQFTPDMLPSDITGTIMFNIESRKMEFK--EGPlfanVVLADEINRTPP 119
                                   7899999****************9....99999999999988889999888887776554..4436699************ PP

                                   ----------HHHHHHHHHHHH--EE------- CS
                         AAA_2  83 kessgadvSregVqrdLLqileggtltdkqgrk 115
                                               Vq +LL  +e+ ++t   + +
  gi|13541896|ref|NP_111584.1| 120 -----------KVQSALLEAMEEVHVTVGGETH 141
                                   ...........*************999776644 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   1.6e-05     0.024      25      92 ..      34      98 ..      22     121 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.6e-05
                         AAA_7 25 llelllknkkpvllvGptGtGKtviikdllkkldkekylsltinfsaqtsanqlqdiiesklekrrkg 92
                                  ++   l  ++++ll G  G +Kt++++++ ++ +   + ++ i+f+  + ++++  +i+ ++e r+ +
  gi|13541896|ref|NP_111584.1| 34 FMFIALLTGNHILLEGVPGLAKTMLANEFARHTK---MEFKRIQFTPDMLPSDITGTIMFNIESRKME 98
                                  55556677899******************99877...9999*********************999865 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00039      0.59       5      82 ..      42     129 ..      39     141 .. 0.79
   2 ?   -2.8   0.0       4.8   7.2e+03      94     117 ..     202     233 ..     189     249 .. 0.65
   3 ?   -2.3   0.0       3.3     5e+03      63      63 ..     261     261 ..     209     309 .. 0.53

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00039
                        AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka............... 70 
                                    +++++ G +G  KT+l++++++           + e+ +++ + ++ ++d+   +  ++++++ +               
  gi|13541896|ref|NP_111584.1|  42 GNHILLEGVPGLAKTMLANEFARHT---------KMEFKRIQFTPDMLPSDITGTIMFNIESRKMEfkegplfanvvlade 113
                                   6899*******************99.........99999999999999999999999999988877666666666666666 PP

                        AAA_22  71 ....erlsseelleal 82 
                                       +++ +++llea+
  gi|13541896|ref|NP_111584.1| 114 inrtPPKVQSALLEAM 129
                                   5555555555555555 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 4.8
                        AAA_22  94 lliiDEaqhlr........seealeeLrslln 117
                                   +l+ DE+ h+r        s+e+ e++++l+ 
  gi|13541896|ref|NP_111584.1| 202 VLLPDEIMHFRsevdnvyvSDEIKEYIVDLMR 233
                                   56667777766443333333666666666665 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 3.3
                        AAA_22  63 a 63 
                                   a
  gi|13541896|ref|NP_111584.1| 261 A 261
                                   3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       579  (0.032294); expected 358.6 (0.02)
Passed bias filter:                      518  (0.0288917); 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: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.52
# Mc/sec: 1847.02
//
Query:       gi|13541897|ref|NP_111585.1|  [L=127]
Description: hypothetical protein TVN1066 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       954  (0.0532099); expected 358.6 (0.02)
Passed bias filter:                      544  (0.0303419); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 875.11
//
Query:       gi|13541898|ref|NP_111586.1|  [L=193]
Description: hypothetical protein TVN1067 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.078   13.1   4.5       0.05   13.7   2.4    1.8  2  FPRL1_inhibitor  Formyl peptide receptor-like 1 inhibitory pr


Domain annotation for each model (and alignments):
>> FPRL1_inhibitor  Formyl peptide receptor-like 1 inhibitory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   2.4   2.8e-06      0.05      31      91 ..      35      97 ..       6     107 .. 0.76
   2 ?   -1.9   0.0      0.21   3.8e+03      18      28 ..     154     164 ..     136     183 .. 0.56

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.8e-06
               FPRL1_inhibitor 31 kesdknltpykaetvndlylivk...klsqgdvkkavvrikdggprdyyt.fdltrpleenrkni 91
                                  k  ++  t  k +tv d+ +ivk   k+++gd+k a++   +    dy   f l+   + nr  i
  gi|13541898|ref|NP_111586.1| 35 K--EEVKTVIKVKTVGDVPVIVKarkKITEGDIKSAIIDSYNSVKDDYVKyFGLSVNYKGNRDFI 97
                                  2..334578899*********9544499***********99999999975378888888888766 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.21
               FPRL1_inhibitor  18 qakkdderidk 28 
                                    + kd e  +k
  gi|13541898|ref|NP_111586.1| 154 YSDKDIENTEK 164
                                   22233333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       850  (0.0474092); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); 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 0.23s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1280.17
//
Query:       gi|13541899|ref|NP_111587.1|  [L=913]
Description: hypothetical protein TVN1068 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.3e-27   93.1  23.5    7.5e-08   32.5   1.0    7.1  7  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
    8.4e-19   67.4  24.6     0.0005   20.0   0.0    7.2  7  CarbopepD_reg_2  CarboxypepD_reg-like domain
    2.8e-09   36.7  11.7     0.0012   18.6   0.2    6.9  8  PEGA             PEGA domain
  ------ inclusion threshold ------
      0.013   15.8   0.1      0.013   15.8   0.1    4.5  5  DUF3823          Protein of unknown function (DUF3823) N-term
       0.16   12.4   6.9         16    5.9   0.1    4.7  4  DUF3869          Domain of unknown function (DUF3869)
       0.27   11.5  18.2        1.4    9.1   0.2    5.6  5  SdrD_B           SdrD B-like domain
       0.86    9.7   6.2         36    4.5   0.0    5.0  5  Big_1            Bacterial Ig-like domain (group 1)


Domain annotation for each model (and alignments):
>> CarboxypepD_reg  Carboxypeptidase regulatory-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1     3e-06    0.0077       2      61 ..      76     134 ..      75     153 .. 0.86
   2 !   28.2   0.5   6.7e-10   1.7e-06      15      82 .]     173     236 ..     161     236 .. 0.81
   3 !   32.5   1.0   2.9e-11   7.5e-08       2      81 ..     245     315 ..     244     316 .. 0.92
   4 !    9.8   0.0   0.00036      0.93      14      74 ..     363     424 ..     354     430 .. 0.74
   5 !   17.2   0.1   1.8e-06    0.0047      44      79 ..     474     508 ..     450     510 .. 0.90
   6 ?   -2.3   0.2       2.2   5.7e+03      33      70 ..     580     615 ..     570     626 .. 0.59
   7 ?   -0.1   0.1      0.45   1.2e+03      39      71 ..     677     707 ..     645     715 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 3e-06
               CarboxypepD_reg   2 isGrVtda.sgapiagatVtvtnadtgtvastttdadGafrlrglppgtysvtvsapGyat 61 
                                   ++G+  +a s +p+++  ++v+  + g  ++t t+ +G+f ++ l++g+ ++ +  pGy  
  gi|13541899|ref|NP_111587.1|  76 VNGYAYNAtSSKPLENFPIVVA--AYGLATQTNTNMKGEFHFTVLKTGNAKLAFFVPGYNV 134
                                   567777764899**********..79****************************9999975 PP

  == domain 2  score: 28.2 bits;  conditional E-value: 6.7e-10
               CarboxypepD_reg  15 agatVtvtnadtgtvastttdadGafrlrglppgtysvtvsapGyatatr.eevtltagqtttlditLe 82 
                                   +++ +t++   +  + +t +++dG+++   l  gty+v v++pG+ + ++ ++vt++ g++  ++i L+
  gi|13541899|ref|NP_111587.1| 173 PHVGLTFY---SMNSVYTFSNSDGYYSAL-LYNGTYTVAVEKPGFSSIASpQQVTVS-GENMAVNISLT 236
                                   55555555...3457889*********75.999**************9973477777.889999*9996 PP

  == domain 3  score: 32.5 bits;  conditional E-value: 2.9e-11
               CarboxypepD_reg   2 isGrVtdasgapiagatVtvtnadtgtvastttdadGafrlrglppgtysvtvsapGyatatreevtltagqtttlditL 81 
                                   +sG V+++ g p+++atV+++         +t++++G+++++ + +g   + ++apGy   +r +v +   + ++++itL
  gi|13541899|ref|NP_111587.1| 245 VSGFVVNQIGIPVPYATVSFS------GFDVTSNSTGHYSIA-VSAGYDILIATAPGYGAGSR-DVYVK-SNMSNVNITL 315
                                   8********************......899***********7.*******************7.57777.5668999998 PP

  == domain 4  score: 9.8 bits;  conditional E-value: 0.00036
               CarboxypepD_reg  14 iagatVtvtnadtgtvast..ttdadGafrlrglppgtysvtvsapGyatatreevtltagqt 74 
                                   +++ ++++  +++g + ++  tt+++G+++++   pg y   +  +Gy + + + + +   qt
  gi|13541899|ref|NP_111587.1| 363 LSNKEIEFVMKSEGDEFYVvnTTNDEGHYAVSVKYPGLYVFYILTSGYYPLNLS-IYVKQSQT 424
                                   5555566555555554443338*********96667***************985.77776665 PP

  == domain 5  score: 17.2 bits;  conditional E-value: 1.8e-06
               CarboxypepD_reg  44 glppgtysvtvsapGyatatreevtltagqtttldi 79 
                                    lp gty++t+s+ Gy ++ + +v+lt ++t  +++
  gi|13541899|ref|NP_111587.1| 474 TLPEGTYNITISKVGYYSQQF-NVSLTSNETFSVNL 508
                                   5999****************9.7****999988886 PP

  == domain 6  score: -2.3 bits;  conditional E-value: 2.2
               CarboxypepD_reg  33 ttdadGafrlrglppgtysvtvsapGyatatreevtlt 70 
                                    t+++G+  +++  +g y++ + +  y    +  + +t
  gi|13541899|ref|NP_111587.1| 580 YTNSSGTALINFGYTGYYNLYFLFLDYYANLS--LNIT 615
                                   46777777666555677776666666655553..4444 PP

  == domain 7  score: -0.1 bits;  conditional E-value: 0.45
               CarboxypepD_reg  39 afrlrglppgtysvtvsapGyatatreevtlta 71 
                                   +f+++ lp  +y+ t + + + t++ + v l+ 
  gi|13541899|ref|NP_111587.1| 677 SFAFS-LPEYNYTFTYQNKSFVTFNMT-VHLHS 707
                                   58886.999999999999999999864.77764 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 !   19.8   0.1   2.3e-07   0.00058       2      75 ..      77     152 ..      76     160 .. 0.77
   2 !   13.9   0.2   1.6e-05     0.041      13      79 ..     171     238 ..     161     243 .. 0.75
   3 !   20.0   0.0     2e-07    0.0005       1      79 [.     245     318 ..     245     322 .. 0.87
   4 !    9.1   0.1   0.00051       1.3      29      74 ..     384     428 ..     375     439 .. 0.88
   5 !   17.9   0.2     9e-07    0.0023      39      75 ..     473     509 ..     467     522 .. 0.85
   6 ?   -1.6   0.4       1.1   2.8e+03      29      73 ..     580     623 ..     572     628 .. 0.72
   7 ?   -2.5   0.1       2.1   5.3e+03      36      68 ..     678     709 ..     677     715 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 2.3e-07
               CarbopepD_reg_2   2 sGtVvdketkeplpgatVyv..kgtkkgtvTdenGnFelknlpagkytLvvsyvGyktqekkvtvskektldvnil 75 
                                    G  +++++ +pl+   ++v   g  ++t T+++G+F+++ l+ g+ +L + + Gy+ +  + ++ +  +l++++ 
  gi|13541899|ref|NP_111587.1|  77 NGYAYNATSSKPLENFPIVVaaYGLATQTNTNMKGEFHFTVLKTGNAKLAFFVPGYNVEYHNFDFLSSGSLNISVA 152
                                   5677778888999997766622567789999**************************9999888765555555544 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 1.6e-05
               CarbopepD_reg_2  13 plpgatVyv.kgtkkgtvTdenGnFelknlpagkytLvvsyvGyktqekkvtvs.kektldvnillkee 79 
                                   ++p +  ++   +++ t ++++G+++   l +g+yt+ v+  G+ +     +v+ ++++  vni+l+++
  gi|13541899|ref|NP_111587.1| 171 SIPHVGLTFySMNSVYTFSNSDGYYSA-LLYNGTYTVAVEKPGFSSIASPQQVTvSGENMAVNISLTSS 238
                                   56666555525678899*********8.699**************976544443345577788888765 PP

  == domain 3  score: 20.0 bits;  conditional E-value: 2e-07
               CarbopepD_reg_2   1 isGtVvdketkeplpgatVyvkgtkkgtvTdenGnFelknlpagkytLvvsyvGyktqekkvtvskektldvnillkee 79 
                                   +sG Vv++  + p+p+atV++   ++ +++++ G++++  + ag   L++++ Gy   ++ v v+++   +vni+l +e
  gi|13541899|ref|NP_111587.1| 245 VSGFVVNQI-GIPVPYATVSFS--GFDVTSNSTGHYSIA-VSAGYDILIATAPGYGAGSRDVYVKSN-MSNVNITLPPE 318
                                   688899875.58********95..6899**********6.99**99******************876.55788888776 PP

  == domain 4  score: 9.1 bits;  conditional E-value: 0.00051
               CarbopepD_reg_2  29 vTdenGnFelknlpagkytLvvsyvGyktqekkvtvskektldvni 74 
                                   +T+++G++ ++ + +g y + +   Gy + + ++ v++ +t++ n+
  gi|13541899|ref|NP_111587.1| 384 TTNDEGHYAVSVKYPGLYVFYILTSGYYPLNLSIYVKQSQTHK-NL 428
                                   7**********9999*********************9988776.44 PP

  == domain 5  score: 17.9 bits;  conditional E-value: 9e-07
               CarbopepD_reg_2  39 knlpagkytLvvsyvGyktqekkvtvskektldvnil 75 
                                    +lp+g+y +++s vGy +q+ +v++++++t +vn++
  gi|13541899|ref|NP_111587.1| 473 LTLPEGTYNITISKVGYYSQQFNVSLTSNETFSVNLK 509
                                   469****************************999865 PP

  == domain 6  score: -1.6 bits;  conditional E-value: 1.1
               CarbopepD_reg_2  29 vTdenGnFelknlpagkytLvvsyvGyktqekkvtvskektldvn 73 
                                   +T+++G+  ++    g y L + ++ y   + +++++++++++vn
  gi|13541899|ref|NP_111587.1| 580 YTNSSGTALINFGYTGYYNLYFLFLDYYA-NLSLNITGNTNTSVN 623
                                   78888888888777888999999998877.356666666655554 PP

  == domain 7  score: -2.5 bits;  conditional E-value: 2.1
               CarbopepD_reg_2  36 FelknlpagkytLvvsyvGyktqekkvtvskek 68 
                                   F ++ lp+ +yt++ +  ++ t + +v++++++
  gi|13541899|ref|NP_111587.1| 678 FAFS-LPEYNYTFTYQNKSFVTFNMTVHLHSNS 709
                                   6674.8889999999999999988888887654 PP

>> PEGA  PEGA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1      0.97   2.5e+03      31      43 ..      67      79 ..      50      86 .. 0.57
   2 !   12.8   0.0   3.2e-05     0.082      31      67 ..     199     236 ..     195     238 .. 0.78
   3 ?    3.1   0.0     0.034        88      29      68 ..     279     317 ..     260     319 .. 0.78
   4 ?    2.6   0.1     0.048   1.2e+02      31      60 ..     396     425 ..     383     430 .. 0.85
   5 ?   -0.9   0.0      0.62   1.6e+03      20      47 ..     444     472 ..     439     475 .. 0.61
   6 !   18.6   0.2   4.9e-07    0.0012      28      65 ..     472     509 ..     462     512 .. 0.91
   7 ?   -3.7   0.0       4.5   1.1e+04      43      62 ..     605     624 ..     602     629 .. 0.64
   8 ?   -0.7   0.0      0.54   1.4e+03      30      57 ..     681     708 ..     675     713 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.97
                          PEGA 31 leaGnyslrveke 43
                                  +++Gn +++v+  
  gi|13541899|ref|NP_111587.1| 67 VPSGNATIKVNGY 79
                                  5666666665533 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 3.2e-05
                          PEGA  31 leaGnyslrvekeGYedle..ktvtvtagetvklnltLe 67 
                                   l +G+y++ vek+G++ +   ++vtv+ ge++ +n+ L+
  gi|13541899|ref|NP_111587.1| 199 LYNGTYTVAVEKPGFSSIAspQQVTVS-GENMAVNISLT 236
                                   679*************99822466666.89988888875 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.034
                          PEGA  29 lsleaGnyslrvekeGYedlektvtvtagetvklnltLek 68 
                                   +++ aG+  l   ++GY   +++v+v+     ++n+tL +
  gi|13541899|ref|NP_111587.1| 279 IAVSAGYDILIATAPGYGAGSRDVYVK-SNMSNVNITLPP 317
                                   55777777788889************9.556777878876 PP

  == domain 4  score: 2.6 bits;  conditional E-value: 0.048
                          PEGA  31 leaGnyslrvekeGYedlektvtvtagetv 60 
                                     +G y + +   GY +l+  ++v++ +t 
  gi|13541899|ref|NP_111587.1| 396 KYPGLYVFYILTSGYYPLNLSIYVKQSQTH 425
                                   45799999999999*********9998886 PP

  == domain 5  score: -0.9 bits;  conditional E-value: 0.62
                          PEGA  20 kylGkTPvtlsleaGny.slrvekeGYed 47 
                                    y+G +  ++++++G y +   ++ +Ye+
  gi|13541899|ref|NP_111587.1| 444 DYYGPASFNITVAEGHYyEKNMSANNYEN 472
                                   57787888888766654144555555555 PP

  == domain 6  score: 18.6 bits;  conditional E-value: 4.9e-07
                          PEGA  28 tlsleaGnyslrvekeGYedlektvtvtagetvklnlt 65 
                                   +l+l++G+y ++++k GY      v++t++et+++nl+
  gi|13541899|ref|NP_111587.1| 472 NLTLPEGTYNITISKVGYYSQQFNVSLTSNETFSVNLK 509
                                   467********************************975 PP

  == domain 7  score: -3.7 bits;  conditional E-value: 4.5
                          PEGA  43 eGYedlektvtvtagetvkl 62 
                                   ++Y++l+  +t + ++ v++
  gi|13541899|ref|NP_111587.1| 605 DYYANLSLNITGNTNTSVNA 624
                                   56777777777666655555 PP

  == domain 8  score: -0.7 bits;  conditional E-value: 0.54
                          PEGA  30 sleaGnyslrvekeGYedlektvtvtag 57 
                                   sl++ ny+++ +   + ++++tv + ++
  gi|13541899|ref|NP_111587.1| 681 SLPEYNYTFTYQNKSFVTFNMTVHLHSN 708
                                   68888999999999*********99876 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 ?   15.8   0.1     5e-06     0.013      37      85 ..     183     229 ..     170     236 .. 0.78
   2 ?   -3.5   0.0       5.4   1.4e+04      39      70 ..     267     295 ..     259     313 .. 0.62
   3 ?   -3.1   0.1         4     1e+04      43      61 ..     385     404 ..     360     427 .. 0.61
   4 ?    1.1   0.1       0.2     5e+02      49      76 ..     470     504 ..     450     516 .. 0.66
   5 ?   -1.5   0.0       1.2   3.2e+03      12      43 ..     787     817 ..     779     818 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 5e-06
                                   --EEEEB-TTSEEEEEE-SEEEEEEE-TT-SSB-TT---EEEEESSSEE CS
                       DUF3823  37 epidvyvkqDGtfntllFdGeYklvlkegegpfvkavdtievelkgntk 85 
                                   +++ ++ ++DG +++ll++G+Y + ++  +  f +     +v+++g++ 
  gi|13541899|ref|NP_111587.1| 183 NSVYTFSNSDGYYSALLYNGTYTVAVE--KPGFSSIASPQQVTVSGENM 229
                                   55667889******************7..66666556778888887654 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 5.4
                                   EEEEB-TTSEEEEEE-SEEEEEEE-TT-SSB- CS
                       DUF3823  39 idvyvkqDGtfntllFdGeYklvlkegegpfv 70 
                                    dv+ ++ G+++  + +G Y++++   + p +
  gi|13541899|ref|NP_111587.1| 267 FDVTSNSTGHYSIAVSAG-YDILIA--TAPGY 295
                                   567777778887777544.777665..55544 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 4
                                   B-TTSEE.EEEE-SEEEEEE CS
                       DUF3823  43 vkqDGtf.ntllFdGeYklv 61 
                                   ++++G++  +  + G Y ++
  gi|13541899|ref|NP_111587.1| 385 TNDEGHYaVSVKYPGLYVFY 404
                                   34445554444455544444 PP

  == domain 4  score: 1.1 bits;  conditional E-value: 0.2
                                   E.EEEE-SEEEEEEE-TT-SSB-........TT---E CS
                       DUF3823  49 f.ntllFdGeYklvlkegegpfv........kavdti 76 
                                   + n  l +G+Y++++   +  ++        ++++t 
  gi|13541899|ref|NP_111587.1| 470 YeNLTLPEGTYNITIS--KVGYYsqqfnvslTSNETF 504
                                   6666777888999886..4444423344444334444 PP

  == domain 5  score: -1.5 bits;  conditional E-value: 1.2
                                   EE----...-TTSEEEEESS-GGG---EEEEB CS
                       DUF3823  12 epiqveveegngvkirlyekgygknepidvyv 43 
                                   e+i ++v ++   +i l+++ y+ ++pi+  v
  gi|13541899|ref|NP_111587.1| 787 ENITFNVTNE-VKQISLTDYEYKSHSPIPYIV 817
                                   6667775555.46799******9999987665 PP

>> DUF3869  Domain of unknown function (DUF3869)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.1    0.0062        16      28      82 ..      25      77 ..      19      89 .. 0.80
   2 ?   -1.3   0.0       1.1   2.8e+03      62      81 ..     204     224 ..     147     255 .. 0.67
   3 ?    2.3   0.1     0.085   2.2e+02      38      81 ..     257     304 ..     225     314 .. 0.72
   4 ?    3.9   0.1     0.027        68      46      82 ..     462     499 ..     431     513 .. 0.66

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0062
                                  ..EETTTTEE-CGCCEECCCCCSSEEEECCSCT-EEEEEEECTETTEE.EEEEEE- CS
                       DUF3869 28 ldieattgtdvtdkatistssgtatfkggaelaakavkisatGYegik.tatVsva 82
                                   +i  +tg+ v   ++i++++ + t+ ++ +l++++v is t Y   +  at++v+
  gi|13541899|ref|NP_111587.1| 25 ANIGYPTGNPVH--VKIKKEQQNITLFANQTLNKYSVGISNT-YFVPSgNATIKVN 77
                                  556667777777..9999************************.5444447777776 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.1
                                   EEEEEEECTETTEE.EEEEEE CS
                       DUF3869  62 kavkisatGYegik.tatVsv 81 
                                   + v + + G+  i   ++V+v
  gi|13541899|ref|NP_111587.1| 204 YTVAVEKPGFSSIAsPQQVTV 224
                                   444455555554443334433 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.085
                                   -CGCCEECCCCCSSEEEECCSCT-EEEEEEEC.........TETTEEEEEEEE CS
                       DUF3869  38 vtdkatistssgtatfkggaelaakavkisat.........GYegiktatVsv 81 
                                   v   at+s+s   +t +     +++++ +sa          GY + + + V+v
  gi|13541899|ref|NP_111587.1| 257 VP-YATVSFSGFDVTSNS---TGHYSIAVSAGydiliatapGYGAGS-RDVYV 304
                                   54.678888888888877...79999999998666666667776665.66666 PP

  == domain 4  score: 3.9 bits;  conditional E-value: 0.027
                                   CCCCSSEEEECCS..CT-EEEEEEECTETTEEEEEEEE- CS
                       DUF3869  46 tssgtatfkggae..laakavkisatGYegiktatVsva 82 
                                   +++++a   ++ +   + ++++is+ GY+ ++  +Vs+ 
  gi|13541899|ref|NP_111587.1| 462 EKNMSANNYENLTlpEGTYNITISKVGYYSQQ-FNVSLT 499
                                   4444444334444456899***********99.777765 PP

>> SdrD_B  SdrD B-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.2   0.00057       1.4      39      74 ..     102     136 ..      93     145 .. 0.85
   2 ?    6.0   0.4    0.0052        13      39      76 ..     185     221 ..     163     247 .. 0.71
   3 ?   -1.9   0.0       1.5   3.8e+03      43      74 ..     270     292 ..     260     318 .. 0.56
   4 ?    3.7   0.4     0.028        72      33      66 ..     374     407 ..     364     427 .. 0.72
   5 ?    1.3   0.3      0.15   3.9e+02      45      82 ..     455     492 ..     447     522 .. 0.53

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00057
                        SdrD_B  39 vatttTdasGkYkFtnltpGeYkVeftapagytvta 74 
                                   +++t T+ +G+++Ft l+ G+ k++f  p gy+v++
  gi|13541899|ref|NP_111587.1| 102 ATQTNTNMKGEFHFTVLKTGNAKLAFFVP-GYNVEY 136
                                   46899*********************988.666655 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0052
                        SdrD_B  39 vatttTdasGkYkFtnltpGeYkVeftapagy.tvtakk 76 
                                   v  t ++++G+Y+   l +G+Y+V++++p     +++++
  gi|13541899|ref|NP_111587.1| 185 V-YTFSNSDGYYS-ALLYNGTYTVAVEKPGFSsIASPQQ 221
                                   3.5899******9.679*********9986552344443 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 1.5
                        SdrD_B  43 tTdasGkYkFtnltpGeYkVeftapagy.tvta 74 
                                   t++++G+          Y+++++a  ++  +ta
  gi|13541899|ref|NP_111587.1| 270 TSNSTGH----------YSIAVSAGYDIlIATA 292
                                   4445555..........5555544333323333 PP

  == domain 4  score: 3.7 bits;  conditional E-value: 0.028
                        SdrD_B  33 dakgevvatttTdasGkYkFtnltpGeYkVefta 66 
                                   ++ +e     tT+ +G+Y+ +   pG Y   + +
  gi|13541899|ref|NP_111587.1| 374 SEGDEFYVVNTTNDEGHYAVSVKYPGLYVFYILT 407
                                   4445555778999999999999999988655543 PP

  == domain 5  score: 1.3 bits;  conditional E-value: 0.15
                        SdrD_B  45 dasGkYkFtnltpGeYkVeftapagy.tvtakkaGsdda 82 
                                    a+G+Y  +n+++ +Y+ ++t p+g+ ++t +k G  ++
  gi|13541899|ref|NP_111587.1| 455 VAEGHYYEKNMSANNYE-NLTLPEGTyNITISKVGYYSQ 492
                                   55555555555555555.333333332555555554333 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 ?    1.1   0.2      0.16     4e+02      19      52 ..      87     117 ..      70     122 .. 0.79
   2 ?    2.7   0.1     0.051   1.3e+02       3      29 ..     239     265 ..     237     282 .. 0.80
   3 ?    4.5   0.0     0.014        36      20      52 ..     362     395 ..     360     397 .. 0.94
   4 ?   -3.3   0.0       3.7   9.5e+03      41      51 ..     580     590 ..     579     591 .. 0.81
   5 ?   -3.3   0.1       3.6   9.2e+03      23      33 ..     786     796 ..     778     802 .. 0.71

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.16
                         Big_1  19 npvagatVtfsvsggalsassgtTdanGkatvtl 52 
                                   +p+++ ++ + + g   +a+++ T+ +G++ +t+
  gi|13541899|ref|NP_111587.1|  87 KPLENFPIVVAAYG---LATQTNTNMKGEFHFTV 117
                                   56666666666666...467999*******9998 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.051
                         Big_1   3 GvdtntltatvkDangnpvagatVtfs 29 
                                   G+ +  ++  v+++ g pv+ atV+fs
  gi|13541899|ref|NP_111587.1| 239 GQRAFNVSGFVVNQIGIPVPYATVSFS 265
                                   6667778889999*************8 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.014
                         Big_1  20 pvagatVtfsvsg.galsassgtTdanGkatvtl 52 
                                   p++++++ f + + g+ +    tT+++G++ v++
  gi|13541899|ref|NP_111587.1| 362 PLSNKEIEFVMKSeGDEFYVVNTTNDEGHYAVSV 395
                                   89***********99999************9987 PP

  == domain 4  score: -3.3 bits;  conditional E-value: 3.7
                         Big_1  41 tTdanGkatvt 51 
                                    T+++G+a ++
  gi|13541899|ref|NP_111587.1| 580 YTNSSGTALIN 590
                                   69****99876 PP

  == domain 5  score: -3.3 bits;  conditional E-value: 3.6
                         Big_1  23 gatVtfsvsgg 33 
                                     ++tf+v+++
  gi|13541899|ref|NP_111587.1| 786 QENITFNVTNE 796
                                   56778888774 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (913 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       639  (0.0356406); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.54u 0.24s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 6482.53
//
Query:       gi|13541900|ref|NP_111588.1|  [L=510]
Description: queuine tRNA-ribosyltransferase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-43  148.1   1.1    3.2e-43  147.2   1.1    1.5  1  DUF5591   Domain of unknown function (DUF5591)
      8e-10   38.6   1.2    1.9e-09   37.4   0.4    2.0  2  PUA       PUA domain
    0.00022   20.5   0.0     0.0044   16.2   0.0    2.2  2  TGT       Queuine tRNA-ribosyltransferase
  ------ inclusion threshold ------
       0.05   13.6   0.0      0.077   13.0   0.0    1.4  1  PAC2      PAC2 family


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 !  147.2   1.1   7.1e-47   3.2e-43       1     133 [.     223     350 ..     223     377 .. 0.89

  Alignments for each domain:
  == domain 1  score: 147.2 bits;  conditional E-value: 7.1e-47
                                   X-HHHHHHHHH---S..SSEEEEEE--SSSSGGGSHHHHHHHHHS---...SEEEEE-SS-.EEEGGGTT----------- CS
                       DUF5591   1 vkrfrervlerYeppeekkvlvLlPcsakkPyseskshrkfaeaikkrkakvheviltsPlGvvPreleevYPaaqYdiav 81 
                                   ++r+re v + Ye+p+  +v v+lPcsakkPys+sksh+k+++++++ ++ +he+i+tsPlGvvPr+lee+YPa+ Ydi+v
  gi|13541900|ref|NP_111588.1| 223 IVRYREYVANLYEKPD-LDVAVILPCSAKKPYSKSKSHQKVINSLSDLRKYIHEIIVTSPLGVVPRDLEETYPAMFYDIPV 302
                                   78*************7.**************************************************************** PP

                                   -----HHHHHHHHHHHHHHHHHHT-SEEEE---THHHHHHHHHHTT-SSEEE CS
                       DUF5591  82 tgewseeeiefvaellakylektkyekviahleeeyreiveevaeelgleii 133
                                    g w e+e+ +++++l++y++++ky+kvia ++++ + i ++      ++++
  gi|13541900|ref|NP_111588.1| 303 IGLWYEDEKVMMKRMLRSYMSRNKYRKVIAFVPDDLEFITDSIP----YDTE 350
                                   ***********************************554444433....3333 PP

>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       1.1   4.8e+03      21      35 ..      21      35 ..      18      35 .. 0.87
   2 !   37.4   0.4   4.1e-13   1.9e-09      17      71 ..     457     510 .]     453     510 .] 0.96

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.1
                                  GGGEEEEETT--TTS CS
                           PUA 21 apGvvevegdfeegd 35
                                   p+v++v+ df e+d
  gi|13541900|ref|NP_111588.1| 21 YPYVINVKTDFVEND 35
                                  589********9887 PP

  == domain 2  score: 37.4 bits;  conditional E-value: 4.1e-13
                                   -EEEGGGEEEEETT--TTSEEEEEETTSCEEEEEEESS-HHHHHHHCTSEEEEEE CS
                           PUA  17 asLlapGvvevegdfeegdvVaivdedgelvavGlanysseelakikggksveie 71 
                                   ++++a Gv ++ +d+++ d+V++v   ge+ +vG+a++++  +++ k+g++v+++
  gi|13541900|ref|NP_111588.1| 457 SNVYAMGVRDATDDIRQEDEVVLVHS-GEIRGVGIAKMNARAMMELKKGIAVKVR 510
                                   699***********************.**************************96 PP

>> TGT  Queuine tRNA-ribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   9.8e-07    0.0044     193     271 ..      67     145 ..      53     153 .. 0.82
   2 ?    2.6   0.1     0.013        60     315     343 ..     149     177 ..     147     183 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 9.8e-07
                                   EEE-SSSSSSHHHHHHHHHHHHGGGS-TTS-EEETTB-SHHHHHHHHHTT--EEEESHHHHHHHTTEEEETTEEEETTS CS
                           TGT 193 yaigGlsvgeekeellevveavtellpedkprylmGvgtPedlleavalGvDmfdcvyptrtarngraltsegelnlkn 271
                                   +  +G ++  + ++l++++ +v e++  +k +yl G   P  +  +v lGv  fd +y    + ng  +t++g  + ++
  gi|13541900|ref|NP_111588.1|  67 IIPNGAELIRRPKNLVSIIMNVHEKYGFSKLIYLSGLPDPYSIPALVYLGVSFFDDAYFRIEGINGLQFTQYGIRRTNE 145
                                   4446788888999*********************************************************999544444 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.013
                                   HHHHHHHHHHHHHHHHHHHTT-HHHHHHH CS
                           TGT 315 iHNlhyylelfkriReaIkegtfeefvee 343
                                   + N+ +++ +++ i+++I +gt+ + ve+
  gi|13541900|ref|NP_111588.1| 149 ENNMNFVRSMLNVIKDSIMNGTLRDIVEK 177
                                   679*********************99987 PP

>> PAC2  PAC2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   1.7e-05     0.077      27     110 ..      12     107 ..       7     268 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.7e-05
                                   EEEEEEHCCHSBCCCC..SEEEEETT.......EEE-SEEEEEETTT........SEEEEEEE.E-HSCHHHHHHHHHHHH CS
                          PAC2  27 kvgeidsdyllpfvgp.rpvvlveeg.......relepprlyakdsg.......srdllvlqg.repilqyeefakalldw 91 
                                   + g+i+  + +p+v + + + +ve++       +e++ + +y +  +        ++++++ +  e i + +++++ ++++
  gi|13541900|ref|NP_111588.1|  12 RAGSINGIE-YPYVINvK-TDFVENDgklnfmgEEIDRMLIYPS--QikqeiveTESFVIIPNgAELIRRPKNLVSIIMNV 88 
                                   678899999.99999952.4345555344444444555555644..23356888888888888455555555********* PP

                                   HHHTTESEEEEEEEEEESS CS
                          PAC2  92 aeelgvkevvvLggldage 110
                                    e++g+++ ++L+gl+   
  gi|13541900|ref|NP_111588.1|  89 HEKYGFSKLIYLSGLPDPY 107
                                   ***************9544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (510 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       819  (0.0456802); expected 358.6 (0.02)
Passed bias filter:                      518  (0.0288917); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.70u 0.32s 00:00:01.02 Elapsed: 00:00:00.52
# Mc/sec: 2962.65
//
Query:       gi|13541901|ref|NP_111589.1|  [L=246]
Description: tRNA pseudouridine synthase A [Thermoplasma volcanium GSS1]
Scores for 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   53.9   0.0    2.6e-11   43.9   0.0    2.2  2  PseudoU_synth_1  tRNA pseudouridine synthase


Domain annotation for each model (and alignments):
>> PseudoU_synth_1  tRNA pseudouridine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.0   0.00022       3.9      25      86 ..      25      80 ..      11      93 .. 0.76
   2 !   43.9   0.0   1.5e-15   2.6e-11       3      86 ..     123     200 ..     121     215 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00022
               PseudoU_synth_1 25 vrtileaaieevsgeekellvvtvkgsgFldhqVRamvgvlfavgqgklspedvkellnakk 86
                                  v+++ +  i+ ++ ++       +k ++++d++V a+ +v   + + ++ p+d++ ++n+k+
  gi|13541901|ref|NP_111589.1| 25 VKSVEDTIIKALNLNS----PSLIKTAARTDRGVSALSNVF--YIETERRPQDIAGIINSKN 80
                                  5555555555444443....566899**************9..55779999*******9997 PP

  == domain 2  score: 43.9 bits;  conditional E-value: 1.5e-15
               PseudoU_synth_1   3 kelvGthdfgsfckqkqekkntvrtileaaieevsgeekellvvtvkgsgFldhqVRamvgvlfavgqgklspedvkelln 83 
                                     ++G hdf++f  +k++++n+ r+i e++ +    +e+  +v+++++++Fl++qVR+m + ++++   k++p  v+++  
  gi|13541901|ref|NP_111589.1| 123 SGFLGFHDFSKF--SKKDTRNPWRSIDEVKCH----RESFGVVLEFSAKSFLWNQVRRMLAFILEFRGNKIDPFSVSNIYS 197
                                   5699********..899999************....777778*******************************99999877 PP

               PseudoU_synth_1  84 akk 86 
                                   +  
  gi|13541901|ref|NP_111589.1| 198 HIA 200
                                   665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1743.94
//
Query:       gi|13541902|ref|NP_111590.1|  [L=338]
Description: tRNA 2'-O-methylase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-45  153.1   0.0    6.4e-45  151.9   0.0    1.6  1  Trm56     tRNA ribose 2'-O-methyltransferase, aTrm56
    2.3e-14   53.7   0.3    4.6e-14   52.7   0.3    1.5  1  HD        HD domain
  ------ inclusion threshold ------
      0.018   15.1   0.0       0.04   13.9   0.0    1.5  1  PSA_CBD   PSA endolysin C-terminal cell wall binding domain
      0.057   12.9   0.0        3.8    6.9   0.1    2.3  2  HDOD      HDOD 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 !  151.9   0.0   1.4e-48   6.4e-45       1     118 [.      53     166 ..      53     167 .. 0.99

  Alignments for each domain:
  == domain 1  score: 151.9 bits;  conditional E-value: 1.4e-48
                                   H-S--EEE.E--HHHHHHC-S...SEEEEE-TTSEEHHHHHHHHHC-SE.EEEEE------TCHHHHSSEEEESSSS---H CS
                         Trm56   1 wGgefkvevakslkklikefkkeggivvhltmyGenieevieeikkkekdllvvvGaekvprevyeladynvsvgnqPhse 81 
                                   +Gg+f ++  +++k+  ++fk   gi vhltmyG ++e+v++ei++++kd++++vG+ekvp+e+ye+adynvsv+nqP se
  gi|13541902|ref|NP_111590.1|  53 FGGNFFIKSGVDWKREFRNFK---GIRVHLTMYGRPLEDVVKEIRESKKDVMILVGSEKVPFEAYEIADYNVSVTNQPISE 130
                                   8********************...********************************************************* PP

                                   HHHHHHHHHHHC.--TTT---TT-SSEEE--SSS-EE CS
                         Trm56  82 vaalaifldrllegkelekefedaklkviPsergkkv 118
                                   v+alaifldr+++g+el+ +f+ +k++v Psergkkv
  gi|13541902|ref|NP_111590.1| 131 VSALAIFLDRFYDGEELNWRFT-GKINVYPSERGKKV 166
                                   *********************9.9************9 PP

>> HD  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.7   0.3     1e-17   4.6e-14       2     120 ..     189     293 ..     188     295 .. 0.92

  Alignments for each domain:
  == domain 1  score: 52.7 bits;  conditional E-value: 1e-17
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTHHHHTS..HHHHHHCTCCHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            HD   2 leHsleVaklarrlaedlgeeedrellllaaLlHDiGkgpfgdafekkeeefekflaHekvgaeilrevekrlgldledva 82 
                                   ++H   V +la  +a++ +  +d +l+ ++aLlHDiG  +++               H++vga ilr++++++      v+
  gi|13541902|ref|NP_111590.1| 189 INHVKSVKELAVAIAKKTN--ADINLVTAGALLHDIGRTQVQG------------ITHAVVGADILRREGIDD-----RVV 250
                                   78*****************..*******************885............68****************.....9** PP

                                   HHHHTTCCHHHHHHHH...H..HHHCCTSCHHHHHHHHHHHHH CS
                            HD  83 klirehheswegkkrp...r..glaerqlslearivklaDrla 120
                                    ++++h +    +++         ++ + ++e++iv+ aD+l 
  gi|13541902|ref|NP_111590.1| 251 SIVEKHIGAGIQSEEAvklGlpPDNYVPETIEEMIVAHADNLF 293
                                   **********977777865166******************996 PP

>> PSA_CBD  PSA endolysin C-terminal cell wall binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0     9e-06      0.04       7      55 ..     131     180 ..     127     188 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 9e-06
                       PSA_CBD   7 VqafAilldkpqlkggellryktgTkikvyksnnylkkayvpkrkkvf...y 55 
                                   V a Ai+ld  ++ +ge l ++   ki vy+s  + k    p+ ++ +   y
  gi|13541902|ref|NP_111590.1| 131 VSALAIFLD--RFYDGEELNWRFTGKINVYPSERGKKVKIIPDEQGCLdllY 180
                                   999*****9..7***********************99999999888776443 PP

>> HDOD  HDOD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.1   0.00085       3.8      97     133 ..     190     225 ..     184     228 .. 0.78
   2 ?    4.1   0.0    0.0064        29     163     193 ..     226     256 ..     224     258 .. 0.92

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.00085
                                   HHHHHHHHHHHHHHHHTT-S-HHHHHHHHHTTTHHHH CS
                          HDOD  97 ehslavAlvarelaeelgledpeeaflaGLLhdiGkl 133
                                   +h   v  +a ++a++++ +  + +  ++LLhdiG+ 
  gi|13541902|ref|NP_111590.1| 190 NHVKSVKELAVAIAKKTNADI-NLVTAGALLHDIGRT 225
                                   555566677888999998877.8999999******85 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.0064
                                   HHHSS-HHHHHHHHHHHTT--HHHHHHHHHT CS
                          HDOD 163 ellgtdhaevGaallekWnlPeelveaiayh 193
                                   ++ g++ha vGa +l++  +++ +v++++ h
  gi|13541902|ref|NP_111590.1| 226 QVQGITHAVVGADILRREGIDDRVVSIVEKH 256
                                   67899**********************9988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (338 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       744  (0.041497); expected 358.6 (0.02)
Passed bias filter:                      611  (0.0340789); 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: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.52
# Mc/sec: 1945.42
//
Query:       gi|13541903|ref|NP_111591.1|  [L=168]
Description: hypothetical protein TVN1072 [Thermoplasma volcanium GSS1]
Scores for complete 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-57  192.2   0.1    4.8e-57  192.0   0.1    1.0  1  ArsR            ArsR transcriptional regulator
  ------ inclusion threshold ------
       0.11   12.5   0.1       0.24   11.5   0.1    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 !  192.0   0.1   5.3e-61   4.8e-57       1     158 [.       8     164 ..       8     165 .. 0.98

  Alignments for each domain:
  == domain 1  score: 192.0 bits;  conditional E-value: 5.3e-61
                          ArsR   1 indpveLvpllqvfdsetkkkvyeelskeWlteeeleeklgeeveealklLkkikliEsqWrmpepgekpekeYhtsYskv 81 
                                   +ndp+eLv++++++ds+ k+k++ +ls++W+t  ++e+k+g+e+++al +L+kik+iE+qW +++  ++pek+Yht+Y++v
  gi|13541903|ref|NP_111591.1|   8 VNDPGELVSIFHAADSDIKRKLLLDLSTGWITLPTIEQKYGKEGRRALLYLDKIKMIETQWITGS--NGPEKAYHTYYTNV 86 
                                   8****************************************************************..************** PP

                          ArsR  82 qanfqcsledlsdiievafmsdeeleelvekiekeveeg.ntsisdlsrklglsplfiralakrsekldvkGqrlelv 158
                                   q+n++ +l++l+dii++a++sd++l+e+++ki++ ++++ +++++d+s++l++s+++ir+++krs+ l++kG+++el+
  gi|13541903|ref|NP_111591.1|  87 QINLMGTLSELADIIYAATLSDDQLQEYEDKIKALMKDDgSVFLGDVSDALNISQTLIRGIVKRSSILEIKGYKIELA 164
                                   ************************************98669**********************************985 PP

>> Sulfolobus_pRN  Sulfolobus plasmid regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   2.6e-05      0.24       8      42 ..      27      61 ..      23      73 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.6e-05
                Sulfolobus_pRN  8 ekillilsrrcatleeleektGiekeellvyltrl 42
                                   k+ll ls + +tl  +e+k G e    l+yl ++
  gi|13541903|ref|NP_111591.1| 27 RKLLLDLSTGWITLPTIEQKYGKEGRRALLYLDKI 61
                                  689****************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       765  (0.0426683); expected 358.6 (0.02)
Passed bias filter:                      644  (0.0359195); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 1080.95
//
Query:       gi|13541904|ref|NP_111592.1|  [L=53]
Description: hypothetical protein TVN1073 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.038   13.6   0.1      0.076   12.6   0.1    1.6  1  Plasmo_rep  Plasmodium repeat family
       0.09   12.7   0.1       0.14   12.2   0.1    1.3  1  DUF3875     Domain of unknown function, B. Theta Gene descrip


Domain annotation for each model (and alignments):
>> Plasmo_rep  Plasmodium repeat family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   8.5e-06     0.076       2      12 ..      24      34 ..      23      36 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 8.5e-06
                    Plasmo_rep  2 sDnEvYspkqE 12
                                  ++ E+Y++++E
  gi|13541904|ref|NP_111592.1| 24 PNGEIYTFENE 34
                                  9*********9 PP

>> DUF3875  Domain of unknown function, B. Theta Gene description (DUF3875)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   1.5e-05      0.14      23      51 ..      10      39 ..       5      40 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.5e-05
                       DUF3875 23 vSkdaditvafevelP..EiFtvsekeYeal 51
                                  vSkd+d   a ++ lP  Ei+t  ++++e++
  gi|13541904|ref|NP_111592.1| 10 VSKDGDTYYA-KIILPngEIYTFENEDFEEM 39
                                  899**98777.99999999**********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (53 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       975  (0.0543812); expected 358.6 (0.02)
Passed bias filter:                      651  (0.0363099); 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: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.44
# Mc/sec: 361.31
//
Query:       gi|13541905|ref|NP_111593.1|  [L=334]
Description: methyltransferase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.8e-37  126.6   0.0    1.6e-36  126.0   0.0    1.3  1  Met_10           Met-10+ like-protein
    3.3e-07   30.0   0.0    6.7e-07   29.0   0.0    1.5  1  MTS              Methyltransferase small domain
    4.4e-07   30.5   0.0    1.7e-06   28.6   0.0    1.9  2  Methyltransf_25  Methyltransferase domain
      8e-07   28.9   1.0    1.7e-06   27.8   1.0    1.5  1  Trm5_N           tRNA methyltransferase 5 N-terminal domain
    0.00018   21.5   0.0    0.00047   20.1   0.0    1.6  2  Methyltransf_18  Methyltransferase domain
    0.00061   19.5   0.0     0.0012   18.5   0.0    1.4  1  Cons_hypoth95    Conserved hypothetical protein 95
     0.0019   17.6   0.0     0.0026   17.2   0.0    1.2  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
      0.002   17.5   0.0     0.0038   16.6   0.0    1.5  1  DNA_methylase    C-5 cytosine-specific DNA methylase
     0.0025   17.4   0.0     0.0044   16.6   0.0    1.5  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
     0.0033   18.1   0.0       0.17   12.7   0.0    2.3  2  Methyltransf_12  Methyltransferase domain
     0.0043   16.8   0.0     0.0062   16.3   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
     0.0057   15.9   0.0      0.014   14.6   0.0    1.3  1  TRM              N2,N2-dimethylguanosine tRNA methyltransfera


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 !  126.0   0.0     1e-39   1.6e-36      42     191 ..     123     270 ..      94     281 .. 0.89

  Alignments for each domain:
  == domain 1  score: 126.0 bits;  conditional E-value: 1e-39
                                   -S-SBTTTTB--EEEEEES-.SEEEEEETTEEEEEETTTS---GGGHHHHHHHHTT--TT-EEEETT-TTTCCHHHCCHHT CS
                        Met_10  42 vsevegefRtfelevlaGsdstetihkEngcrfklDvskvyfsskleaErerlaklveegevVvdvfAGiGpfaipiakys 122
                                   +++v+g+ R + +++l+G    e+ h E g ++ +D  k++fs ++++Er+r+ ++  +g +V+d+fAGiG+f++p+ ky+
  gi|13541905|ref|NP_111593.1| 123 YESVRGVERIPVVRHLYGLR-GEIRHVEDGLTYFFDPEKIMFSAGNTNERTRIREMKLDGMTVLDMFAGIGYFTLPAVKYG 202
                                   4689**************87.8*********************************************************** PP

                                   TSSEEEEEES-HHHHHHHHHHHHHTT-TTCEEEEES-GGG---TT-EEEEEE--TTTGGGGHHHHHHHE CS
                        Met_10 123 kakrvlaidlnPesvkylkeniklNkvekvvkpileDgrevireqladrvvmnlpksaieFldkvlaal 191
                                   +a+   a d+nPe++k+lk+n+  N ++k vkpi++D+r   + ++ d ++m+   ++ie+l ++l   
  gi|13541905|ref|NP_111593.1| 203 HAEHTDACDINPEAIKFLKKNLSANGISKSVKPICGDARIACPIKAYDLIIMGNF-KSIEYLPAALIRS 270
                                   *****************************************************99.7899999965444 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   0.0   4.5e-10   6.7e-07      31     103 ..     180     254 ..     157     256 .. 0.87

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 4.5e-10
                                   TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC..EEEEE-STTTTSTTS-EEEEEE CS
                           MTS  31 lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle..vevvasdvleeveekkfdlivs 103
                                      +vlD+ +G+G+ ++ + k     + +++d++ +A+++ k+nl+an+++  v+ +  d+  + + k +dli++
  gi|13541905|ref|NP_111593.1| 180 DGMTVLDMFAGIGYFTLPAVKYGHAEHTDACDINPEAIKFLKKNLSANGISksVKPICGDARIACPIKAYDLIIM 254
                                   3457*****************999999***********************98899999999999999******97 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       3.1   4.6e+03      21      42 ..      52      73 ..      45      89 .. 0.74
   2 !   28.6   0.0   1.1e-09   1.7e-06       1      76 [.     184     259 ..     184     272 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 3.1
                                  SSEEEEEESSHHHHHHHHHHHH CS
               Methyltransf_25 21 kakvtgvDiseemleaarerae 42
                                  +++++  D++e+  e++++ ++
  gi|13541905|ref|NP_111593.1| 52 QCRIVYSDFDERHYENIKQTMA 73
                                  5678888888888888877663 PP

  == domain 2  score: 28.6 bits;  conditional E-value: 1.1e-09
                                   EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCGBSSSTTTEEEEEEESTGGG CS
               Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl..nvefvqgdaedlpfedgsfDlvvssgalhh 76 
                                   vLd+ +G G +tl + k +++++  ++Di++e+++  +++++++g+  +v+ ++gda+    + + +Dl+++ g++  
  gi|13541905|ref|NP_111593.1| 184 VLDMFAGIGYFTLPAVKYGHAEHTDACDINPEAIKFLKKNLSANGIskSVKPICGDARI-ACPIKAYDLIIM-GNFKS 259
                                   8****************9779***********************************964.445567***999.44443 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 !   27.8   1.0   1.1e-09   1.7e-06       4      42 ..       9      47 ..       6      50 .. 0.91

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 1.1e-09
                                  EEGGGHHHHHHHHHHTT-B-TTS--EEETTEEEEEB-S- CS
                        Trm5_N  4 VpkkegEkvRkkLlekglLdrnyKIksdddylyIPvkee 42
                                  ++  ++++++++L+ ++l+ +++KIk+ ++ ++IPvk+ 
  gi|13541905|ref|NP_111593.1|  9 IEAPMANEIIRRLMIEDLIRKDLKIKKIENEIFIPVKDG 47
                                  666789*******************************96 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       2.6   3.9e+03      99     124 ..      26      50 ..       6      68 .. 0.65
   2 !   20.1   0.0   3.2e-07   0.00047      14     131 ..     180     294 ..     171     304 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 2.6
               Methyltransf_18  99 ILeeakeklkkikklilqpnseaeel 124
                                   +++++  k kki++ i+ p ++  +l
  gi|13541905|ref|NP_111593.1|  26 LIRKD-LKIKKIENEIFIPVKDGTNL 50 
                                   33333.44455666666666665555 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 3.2e-07
               Methyltransf_18  14 kgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievrlsdGleklkeeevdtvviaGmGge 94 
                                   +g +v+D  +  gy ++ +vk g+a++  a+Din+++++  k+n++ +g++++++ +++d   ++  + +d ++   mG  
  gi|13541905|ref|NP_111593.1| 180 DGMTVLDMFAGIGYFTLPAVKYGHAEHTDACDINPEAIKFLKKNLSANGISKSVKPICGDARIACPIKAYDLII---MGNF 257
                                   5678888888899***********************************************98888666577666...8999 PP

               Methyltransf_18  95 lileILeeakeklkkikklilqpnseaeelRkylven 131
                                     +e L +a    k  +k+il+   ++e+l k++++ 
  gi|13541905|ref|NP_111593.1| 258 KSIEYLPAALIRSKAGTKIILHHLVSQERLSKFIYDL 294
                                   9999999998888888889999988888888888764 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0     8e-07    0.0012      39     104 ..     178     244 ..     169     253 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 8e-07
                                   CHCC-EEEETT-TTSHHHHHHHHTT.-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHH CS
                 Cons_hypoth95  39 eiegarvLDlfaGsGalglEAlSRg.akkavlvekdkeavkilkenleelkleeetaelkedaleal 104
                                   +++g +vLD+faG G   l A+  g a++  + + ++ea+k lk+nl++ +++++++ +  da  a+
  gi|13541905|ref|NP_111593.1| 178 KLDGMTVLDMFAGIGYFTLPAVKYGhAEHTDACDINPEAIKFLKKNLSANGISKSVKPICGDARIAC 244
                                   58999*****************987477788*******************99998888888777665 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   1.8e-06    0.0026     159     215 ..     178     235 ..     172     288 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.8e-06
                          PrmA 159 vkegeevlDvGtGSGiLaiaaakLga.kkvvavDiDevAvkvakeNaelNkveaklev 215
                                      g +vlD+ +G G  ++ a+k g+ ++  a Di++ A+k  k+N++ N+++++++ 
  gi|13541905|ref|NP_111593.1| 178 KLDGMTVLDMFAGIGYFTLPAVKYGHaEHTDACDINPEAIKFLKKNLSANGISKSVKP 235
                                   566789******************9615678*********************998864 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 !   16.6   0.0   2.5e-06    0.0038       1      44 [.     182     234 ..     182     256 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.5e-06
                                   -EEEEES-TT-HHHHHHHHTT.-EEEEEEE--TTTHHHHHHH-.........- CS
                 DNA_methylase   1 lkfidLfaGiGGfrlgleaag.fecvaaseidkkaaktYeanfk........k 44 
                                   ++++d+faGiG f+l   + g  e++ a +i+++a+k++++n +        k
  gi|13541905|ref|NP_111593.1| 182 MTVLDMFAGIGYFTLPAVKYGhAEHTDACDINPEAIKFLKKNLSangisksvK 234
                                   789**************99999********************98744433333 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   2.9e-06    0.0044       3      59 ..     183     241 ..     181     297 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.9e-06
               Methyltransf_15   3 vilDlfsGaGGnviqfalv..fekviaieinleklacaqhNaevYgvsdkitlvlgdvf 59 
                                   ++lD+f+G G  +    ++   e++ a +in+e ++  ++N  + g+s+ +++++gd  
  gi|13541905|ref|NP_111593.1| 183 TVLDMFAGIGYFTLPAVKYghAEHTDACDINPEAIKFLKKNLSANGISKSVKPICGDAR 241
                                   689*******9999888874456899*******************************76 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0      0.11   1.6e+02      18      47 ..      50      79 ..      33     104 .. 0.82
   2 !   12.7   0.0   0.00011      0.17       2      75 ..     186     257 ..     185     270 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.11
               Methyltransf_12 18 lpdieytgvDispsaiedakeklakrennn 47
                                  l++++++++D++++  e+ k+ +a+ +++n
  gi|13541905|ref|NP_111593.1| 50 LQQCRIVYSDFDERHYENIKQTMASFIKRN 79
                                  389*************99999998887765 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00011
               Methyltransf_12   2 eiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnv 75 
                                   +  +G G ++ +  ++ +  +  ++Di+p+ai+  k+ l++++  +   v+    d+    + +++Dl+++ n+
  gi|13541905|ref|NP_111593.1| 186 DMFAGIGYFTLPAVKYGHAEHTDACDINPEAIKFLKKNLSANGISK--SVKPICGDARIACPIKAYDLIIMGNF 257
                                   55589999999999997777777*****************999755..6666666665556668*******975 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   4.2e-06    0.0062       3      79 ..     180     253 ..     178     311 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 4.2e-06
               Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeqgdiee.leklledekfDlil 79 
                                   +g++vlD  +G G++t+ +  + g   +    Di++eai++ ++n++ +g++  v+   gd+    +  +  + +Dli+
  gi|13541905|ref|NP_111593.1| 180 DGMTVLDMFAGIGYFTLPAV-KYGHAEHTDACDINPEAIKFLKKNLSANGISkSVKPICGDARIaCP--I--KAYDLII 253
                                   689*****************.8788777889******************998677766676665455..3..3466665 PP

>> TRM  N2,N2-dimethylguanosine tRNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   9.2e-06     0.014      51     114 ..     182     244 ..     161     274 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 9.2e-06
                                   EEEEESS-TTSHHHHHHHHH-S-EEEEEEE-S-HHHHHHHHHHHHHTT--GGEEEE-S-HHHHH CS
                           TRM  51 ikvldaLsasGlRaiRfalEvpgvkevlaNDisekAvelikeNvklneveeivvineddAnvll 114
                                   ++vld +++ G  ++   +   ++++  a Di+++A++ +k+N + n +++ v++  +dA++  
  gi|13541905|ref|NP_111593.1| 182 MTVLDMFAGIGYFTLPAVKY-GHAEHTDACDINPEAIKFLKKNLSANGISKSVKPICGDARIAC 244
                                   78888888888777765554.777888899******************************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       593  (0.0330749); expected 358.6 (0.02)
Passed bias filter:                      496  (0.0276647); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.52
# Mc/sec: 1929.42
//
Query:       gi|13541906|ref|NP_111594.1|  [L=71]
Description: small nuclear ribonucleoprotein (snRNP)-like protein [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.2e-22   78.0   1.9    3.5e-22   77.9   1.9    1.0  1  LSM              LSM domain
  ------ inclusion threshold ------
       0.07   13.1   0.0      0.074   13.0   0.0    1.1  1  Chlorosome_CsmC  Chlorosome envelope protein C
       0.12   11.6   0.0       0.12   11.6   0.0    1.0  1  Peptidase_M3     Peptidase family M3


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 !   77.9   1.9   5.9e-26   3.5e-22       2      67 .]       7      70 ..       6      70 .. 0.95

  Alignments for each domain:
  == domain 1  score: 77.9 bits;  conditional E-value: 5.9e-26
                                  HHHHTTTSEEEEEETTSEEEEEEEEEEETTSEEEEEEEEEEETTETEEEEEEEEEEEGGGEEEEEE CS
                           LSM  2 flkklinkkvtvelkngrelrGtLkgfDqfmNlvLedveetlkdkkekrklglvliRGnnivlisl 67
                                  +l++++nk+v + lk++r+l+GtL+g+D++mN+vL+dv e +++   +rklg+v+iRG+n+v i++
  gi|13541906|ref|NP_111594.1|  7 LLEESVNKRVSLLLKDNRVLEGTLTGYDDYMNMVLDDVDENSEN--VSRKLGTVVIRGSNVVRIVP 70
                                  799*************************************9987..6***************9986 PP

>> Chlorosome_CsmC  Chlorosome envelope protein C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   1.2e-05     0.074      79     128 ..      14      69 ..       5      71 .] 0.77

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.2e-05
               Chlorosome_CsmC  79 drvaitvkdvsraaGel.....ysd.avknvenvtdnaakavGdvgvsasevvknv 128
                                   +rv++ +kd     G+l     y + + ++v++ ++n+++ +G v +  s+vv+ v
  gi|13541906|ref|NP_111594.1|  14 KRVSLLLKDNRVLEGTLtgyddYMNmVLDDVDENSENVSRKLGTVVIRGSNVVRIV 69 
                                   4888888888877777766333444245789**********************966 PP

>> Peptidase_M3  Peptidase family M3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   2.1e-05      0.12      38      78 ..      19      59 ..       5      67 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.1e-05
                                  HHHHHHHH.HHHTT-SSHHHHHHTTSTT-SHHHHHHHHHHHH CS
                  Peptidase_M3 38 llklrael.Akllgyesyaelaledkmaknpetvldfleelv 78
                                  llk ++ l   l gy++y+++ l+d +++n+e+v + l ++v
  gi|13541906|ref|NP_111594.1| 19 LLKDNRVLeGTLTGYDDYMNMVLDD-VDENSENVSRKLGTVV 59
                                  33433333599**************.********99988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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 0.31s 00:00:00.73 Elapsed: 00:00:00.48
# Mc/sec: 448.83
//
Query:       gi|13541907|ref|NP_111595.1|  [L=53]
Description: hypothetical protein TVN1076 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score 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   15.3   1.3      0.016   15.1   1.3    1.1  1  Prefoldin_2     Prefoldin subunit
      0.017   14.5   0.3      0.019   14.3   0.3    1.0  1  Helo_like_N     Fungal N-terminal domain of STAND proteins
      0.032   14.3   0.5      0.052   13.6   0.5    1.4  1  APC_N_CC        Coiled-coil N-terminus of APC, dimerisation d
      0.033   14.8   0.3      0.033   14.8   0.3    1.1  1  HIP1_clath_bdg  Clathrin-binding domain of Huntingtin-interac
      0.054   13.6   0.1       0.06   13.5   0.1    1.1  1  ASL_C           Adenylosuccinate lyase C-terminal
      0.063   12.5   0.1      0.069   12.4   0.1    1.0  1  Dynein_C        Dynein heavy chain C-terminal domain
        0.1   12.4   0.6       0.15   11.9   0.6    1.3  1  Synaptobrevin   Synaptobrevin
       0.12   13.0   0.2       0.14   12.8   0.2    1.1  1  SlyX            SlyX


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 ?   15.1   1.3   7.3e-06     0.016      71     104 ..       5      38 ..       1      39 [. 0.87

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 7.3e-06
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCTS CS
                   Prefoldin_2  71 ketlekeiktlekqleklekeleelkeelqkklq 104
                                    e+  ke+++l+++ ++++kel+++ke+l+ ++q
  gi|13541907|ref|NP_111595.1|   5 NEEKIKEVEALNREVKSMRKELDDVKEVLRGLIQ 38 
                                   5777799*********************998876 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 ?   14.3   0.3   8.4e-06     0.019      26      64 ..       7      44 ..       4      50 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 8.4e-06
                   Helo_like_N 26 etvksfrsrdktvreLkeeleaLeevLesLeevavaeee 64
                                  e +k+    +++v+ +++el++ +evL+ L +v   +++
  gi|13541907|ref|NP_111595.1|  7 EKIKEVEALNREVKSMRKELDDVKEVLRGLIQVI-MSRD 44
                                  678999999***********************54.3333 PP

>> APC_N_CC  Coiled-coil N-terminus of APC, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.5   2.3e-05     0.052       7      26 ..       9      28 ..       5      38 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.3e-05
                      APC_N_CC  7 vrQvEaLkkenthlrrELed 26
                                  ++ vEaL +e   +r+EL d
  gi|13541907|ref|NP_111595.1|  9 IKEVEALNREVKSMRKELDD 28
                                  689***************99 PP

>> HIP1_clath_bdg  Clathrin-binding domain of Huntingtin-interacting protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.3   1.5e-05     0.033      47      76 ..       5      34 ..       1      44 [. 0.88

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.5e-05
                HIP1_clath_bdg 47 leeqkeelekLkreleakraelarlkssLe 76
                                   ee+ +e+e+L+re+++ r+el+ +k+ L+
  gi|13541907|ref|NP_111595.1|  5 NEEKIKEVEALNREVKSMRKELDDVKEVLR 34
                                  579999********************9986 PP

>> ASL_C  Adenylosuccinate lyase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   2.7e-05      0.06      31      67 ..       9      45 ..       3      52 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.7e-05
                                  HHHHCCEEE-HHHHHHHHHT-GGGGHHHHHHHHHHTT CS
                         ASL_C 31 lkglsklevneealaedLdenwevlaEaiqtvlrreg 67
                                  +k ++ l+ + + ++++Ld+  evl   iq+++ r +
  gi|13541907|ref|NP_111595.1|  9 IKEVEALNREVKSMRKELDDVKEVLRGLIQVIMSRDD 45
                                  677888999999*********************9865 PP

>> Dynein_C  Dynein heavy chain C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   3.1e-05     0.069      70     101 ..      10      41 ..       8      49 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.1e-05
                                   HHHHHHHHHHHHHHHHHHHHHC---------H CS
                      Dynein_C  70 qElerfnkLleeirrsLkelqkaikGevvmse 101
                                   +E+e +n+ ++ +r+ L++++++++G++ +  
  gi|13541907|ref|NP_111595.1|  10 KEVEALNREVKSMRKELDDVKEVLRGLIQVIM 41 
                                   7*************************987433 PP

>> Synaptobrevin  Synaptobrevin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.6   6.6e-05      0.15       2      34 ..      16      48 ..      15      51 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 6.6e-05
                                  XXHHHHHHHHHHCCCCHHCCHHHHCHCCCCCHH CS
                 Synaptobrevin  2 ndklakikaevdevkdimkeNidkvlergekld 34
                                  n++++ +++e+d+vk++++  i+ +++r+++ d
  gi|13541907|ref|NP_111595.1| 16 NREVKSMRKELDDVKEVLRGLIQVIMSRDDNFD 48
                                  678999***********************9977 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.2   6.3e-05      0.14      18      55 ..      11      48 ..       6      52 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.3e-05
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXXX CS
                          SlyX 18 tieeLndvvaeqqqqidrlqrqlrllaerlkeleessg 55
                                   +e+Ln++v   ++++d  ++ lr l + + +++++  
  gi|13541907|ref|NP_111595.1| 11 EVEALNREVKSMRKELDDVKEVLRGLIQVIMSRDDNFD 48
                                  589***********************999977776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (53 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1484  (0.0827709); expected 358.6 (0.02)
Passed bias filter:                      876  (0.0488594); expected 358.6 (0.02)
Passed Vit filter:                       134  (0.00747392); expected 17.9 (0.001)
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: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 423.60
//
Query:       gi|13541908|ref|NP_111596.1|  [L=202]
Description: exosome complex RNA-binding protein Csl4 [Thermoplasma volcanium GSS1]
Scores for complete 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-07   29.0   0.0    1.3e-06   28.1   0.0    1.5  1  ECR1_N          Exosome complex exonuclease RRP4 N-terminal r
     0.0086   15.9   0.2       0.12   12.2   0.1    2.5  2  Rho_RNA_bind    Rho termination factor, RNA-binding domain
  ------ inclusion threshold ------
      0.049   13.6   0.9      0.077   13.0   0.9    1.2  1  zinc-ribbons_6  zinc-ribbons
      0.088   12.7   3.1       0.28   11.1   3.1    1.9  1  zf-FPG_IleRS    Zinc finger found in FPG and IleRS


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 !   28.1   0.0   2.8e-10   1.3e-06       2      37 ..       8      43 ..       7      44 .. 0.93

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 2.8e-10
                                  E-TT-EEEETTTSEE-TTEEEETTEEEESSSEEEEE CS
                        ECR1_N  2 VtPGevlttdeefmrGhGTYvrggtiyAsvaGtvev 37
                                  + PG+ ++t+ee+++G++T +++g+i+A   G +++
  gi|13541908|ref|NP_111596.1|  8 AFPGDMIATTEEYLPGKNTEEKNGEIIAVKFGQIIR 43
                                  57**************************99999887 PP

>> Rho_RNA_bind  Rho termination factor, RNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.1   2.7e-05      0.12      33      58 ..      55      79 ..      44      84 .. 0.84
   2 ?    0.6   0.0      0.11   5.1e+02      32      44 ..     119     131 ..     108     139 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.7e-05
                                  CCCCTT--TT-EEEEEEE---SSS-S CS
                  Rho_RNA_bind 33 qirkfgLrtGDaveGkvrppkereky 58
                                  q ++f L++GD+v G+v + + +++y
  gi|13541908|ref|NP_111596.1| 55 QKKEFTLKKGDIVYGQVVKGE-QHRY 79
                                  6699*************9885.6666 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.11
                                   CCCCCTT--TT-E CS
                  Rho_RNA_bind  32 sqirkfgLrtGDa 44 
                                    +ir + +rtGD+
  gi|13541908|ref|NP_111596.1| 119 DLIRGYVIRTGDF 131
                                   5799999999996 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.9   1.7e-05     0.077       2      25 ..     147     170 ..     146     178 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.7e-05
                                   --SSS-S--EE-SSEEE-TTT--E CS
                zinc-ribbons_6   2 kCpeCqqelekrgeqyhCeaCqed 25 
                                    C +C q+l+krg ++ Ce+Cq+ 
  gi|13541908|ref|NP_111596.1| 147 VCLRCRQPLVKRGITLYCENCQRT 170
                                   69********************84 PP

>> zf-FPG_IleRS  Zinc finger found in FPG and IleRS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   3.1   6.2e-05      0.28       3      28 ..     147     168 ..     145     169 .. 0.95

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 6.2e-05
                                   B-TTT--BBEEEECTTEEEEE-TTTT CS
                  zf-FPG_IleRS   3 pCpRCwryiervgqagrstyfCprCq 28 
                                   +C RC+ ++++ g+    t +C++Cq
  gi|13541908|ref|NP_111596.1| 147 VCLRCRQPLVKRGI----TLYCENCQ 168
                                   7*************....******** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       717  (0.0399911); expected 358.6 (0.02)
Passed bias filter:                      557  (0.031067); 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: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1322.96
//
Query:       gi|13541909|ref|NP_111597.1|  [L=384]
Description: major facilitator superfamily permease [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.9e-32  110.5  43.9    7.9e-32  110.5  43.9    2.0  2  MFS_1     Major Facilitator Superfamily
  ------ inclusion threshold ------
        1.2    7.3  22.2       0.26    9.5   2.9    2.7  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 !  110.5  43.9   8.8e-36   7.9e-32       5     352 ..      15     342 ..      11     343 .. 0.81
   2 !    6.2   9.1   0.00046       4.1     107     172 ..     312     376 ..     295     384 .] 0.84

  Alignments for each domain:
  == domain 1  score: 110.5 bits;  conditional E-value: 8.8e-36
                         MFS_1   5 aflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalg.lllllfass 84 
                                    +++al+++ ++pal  +++++l +    igl++t +++g a+++l++G+l+ r+G  +v ++gl++++ + ++ + ++s+
  gi|13541909|ref|NP_111597.1|  15 RAFYALNWFDIAPALK-YINTALDLGLIRIGLVTTSFYIGLALFQLVGGSLAHRIGNLKVSFIGLTILGTFgITSG-LSSN 93 
                                   5678899999******.******************************************99999999999934444.5566 PP

                         MFS_1  85 lwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllaf 165
                                   +  l+++r+++G+g++++f+ ++ +i+d++p+e+ g+++++++++fs+Ga  g  + g++ + +gWr++ +i ++++  + 
  gi|13541909|ref|NP_111597.1|  94 FLELAISRFMAGVGSALFFSPALGIISDIVPPEKYGSYVSIYNGAFSFGAGAGIFAFGYFDTIIGWRLSLIIGGLLLYASD 174
                                   66**************************************************************************99996 PP

                         MFS_1 166 vlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsglltllplylqevlglsgllla 246
                                   + +++ l  e+++ + +   ++            +  + k+pv+w +l +l +++++  +++  l++y  e++ +  +++a
  gi|13541909|ref|NP_111597.1| 175 IAMVIALHGEEHRARGP--LKD------------LAVVAKNPVVW-ILPVLTIGSAISETIMGQLFVYYLERFRYVPVVTA 240
                                   64333333333333333..344............67799*****8.77777777767777888888888999999978888 PP

                         MFS_1 247 glllallalvgailallagrlsdrlgrrrrlllallllllaalglallavtssavllllvlvliGfglgfvfpsllalasd 327
                                   +++ +++ ++g+++++++g +++++++     +++++++la++++++   + + + +l++++l++  l+++  s+l+ +++
  gi|13541909|ref|NP_111597.1| 241 SAIGSFFLFFGLPGGFISGMMIRKYQS--KYAVTGFFIILASIFFMIPYEY-NFAEILASVALFS-VLSIYGFSYLYTVTS 317
                                   889999999999999999999999887..5555555555555555555555.4455554444433.466667778888888 PP

                         MFS_1 328 lappeeagtasglfntagslggalg 352
                                   l+++++  + ++++n+++ + +a  
  gi|13541909|ref|NP_111597.1| 318 LVSKKAVSFSLSIVNFVQMIISAAV 342
                                   888999************9887765 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.00046
                         MFS_1 107 aaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllafvlfllll 172
                                   ++ ++ +++k+  ++ +++++    + ++  p +  + ++s +  +++y+++i+sl+  + f+l+l
  gi|13541909|ref|NP_111597.1| 312 LYTVTSLVSKKAVSFSLSIVNFVQMIISAAVPYVYTYTIDSSSIYYAWYVMGIISLIPSL-FILYL 376
                                   56677788888**********************************************866.44555 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 ?    9.5   2.9   2.9e-05      0.26     134     189 ..      96     152 ..      86     157 .. 0.87
   2 ?    7.3   6.3   0.00013       1.2     289     378 ..     197     285 ..     184     292 .. 0.79
   3 ?   -1.2   0.2     0.053   4.8e+02     468     524 ..     299     353 ..     286     360 .. 0.55

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 2.9e-05
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxx RF
                          OATP 134 lfflaqlllGiGatpiytlGisYidDnvkkknsplylgilyalrilGpalG.fllGs 189
                                    + ++ +++G+G++++++ ++  i D v +++   y++i+  +  +G   G f++G+
  gi|13541909|ref|NP_111597.1|  96 ELAISRFMAGVGSALFFSPALGIISDIVPPEKYGSYVSIYNGAFSFGAGAGiFAFGY 152
                                   57899*******************************************999555555 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.00013
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          OATP 289 rllknpifllvilssvfeillvaGfitFlpkylEtqFslsaseAnlltGvvvipgaalGillgGllvkklklsakklaklv 369
                                    + knp+ +++ + ++  ++  + +      ylE+ F+  +   +  +G+++++++  G +++G++++k++ +   + +++
  gi|13541909|ref|NP_111597.1| 197 VVAKNPVVWILPVLTIGSAISETIMGQLFVYYLER-FRYVPVVTASAIGSFFLFFGLPGGFISGMMIRKYQSKYAVTGFFI 276
                                   56677877776666665555555555555667775.777777777788********************************* PP

                                   xxxxxxxxx RF
                          OATP 370 lvvsllsll 378
                                   +++s++ ++
  gi|13541909|ref|NP_111597.1| 277 ILASIFFMI 285
                                   **9999887 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.053
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          OATP 468 flvsflgalgrvpallvilRcVkkedksfalGlqlllirllgliPgPiifGaiiDst 524
                                   +l+s+l+  g    ++v+   V+k+  sf+l++  ++  ++++   P ++ ++iDs+
  gi|13541909|ref|NP_111597.1| 299 ALFSVLSIYGFSYLYTVT-SLVSKKAVSFSLSIVNFVQMIISA-AVPYVYTYTIDSS 353
                                   444444444444334443.667777777777776666554322.3355666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (384 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       788  (0.0439511); expected 358.6 (0.02)
Passed bias filter:                      221  (0.0123264); 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: 0.48u 0.22s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2810.21
//
Query:       gi|13541910|ref|NP_111598.1|  [L=392]
Description: diaminopimelate aminotransferase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      3e-32  112.0   0.0    3.6e-32  111.8   0.0    1.1  1  Peptidase_M20  Peptidase family M20/M25/M40
    4.1e-19   68.5   0.0    1.1e-18   67.2   0.0    1.7  2  M20_dimer      Peptidase dimerisation domain
    5.5e-06   26.2   0.0    1.2e-05   25.1   0.0    1.6  1  Peptidase_M28  Peptidase family M28


Domain annotation for each model (and alignments):
>> Peptidase_M20  Peptidase family M20/M25/M40
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.8   0.0     6e-36   3.6e-32       2     204 ..      77     389 ..      76     392 .] 0.87

  Alignments for each domain:
  == domain 1  score: 111.8 bits;  conditional E-value: 6e-36
                                   EEEES-BSSTTCGGGSSS.TTSEEETTTEEESTTTTTTHHHHHHHHHHHHHHHHHTTT-SSEEEEEEESTTSSTT.THHHH CS
                                   xxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxx RF
                 Peptidase_M20   2 lgsHlDvVpeeetdgwtt.pfslteedGklyGrGaddmkggvlaalealralkdegikpkgtivllfqpdEEggr.gGaka 80 
                                   l +H+D+Vp ++ + wt+ pf+lt+e +k+yGrG+ d+   v++al +lr lk+     +++  ++f++dEE+g+  G+++
  gi|13541910|ref|NP_111598.1|  77 LIAHIDTVPVGDPSLWTKpPFELTVEGDKMYGRGTEDDGQAVFTALLILRDLKKIR--MNYNFGIAFVADEEVGSkYGIQY 155
                                   679******999999***********99************************9986..589***********777799988 PP

                                   HHHHHHTTTCESEEEEEEEESSSBTCHSTETEEEE.............................................. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.............................................. RF
                 Peptidase_M20  81 llegleerekvdavfelhieepgileagklaigvv.............................................. 115
                                   ll     ++ +     +++ + g  +  +l i ++                                              
  gi|13541910|ref|NP_111598.1| 156 LLT----KDVFGKDDLIIVPDAGSED--GLNIEISeksilwlkfrvigkqyhasmppnainsfresakfilkldktlhaky 230
                                   888....3333333334455444444..5567777889999999999********************************** PP

                                   ...................................................................EEEEEEE.EEESHE CS
                                   ...................................................................xxxxxxx.xxxxxx RF
                 Peptidase_M20 116 ...................................................................kvevell.eggapv 128
                                                                                                      k+e++    ++ p+
  gi|13541910|ref|NP_111598.1| 231 saidklynvpystfeptkheknvdnintipgtdvfyydcrvlpqyslddvistveaeisdfqkesnaKIEYSVMqKEQSPP 311
                                   ****************************************************************98744444335777777 PP

                                   EEC.CHHHHHHHHHHHHHHHTSCEEEEEESSSBHTHHHH..TTTEEEEEEESSGGCTTSTTTEEEHHHHHHHHHHHHHH CS
                                   xxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Peptidase_M20 129 tln.dsplvkalaeaaeelfgekvelivsgpggtdarff..agiptvmifgpgsglaHspnEyvdledlekgikvlarl 204
                                   +++ ds++vk+l +++++l ++++++   g ggt a+ff  +g+p+v+++ + +++aH+p+E++ ++++    +v++++
  gi|13541910|ref|NP_111598.1| 312 KTPeDSEVVKKLVSSIRKLRKKEPNVLGIG-GGTCAAFFrqLGLPAVVWYTTIEENAHKPDEFCLISHILMDRDVIEDM 389
                                   7778**************966557777777.********88888*****99556***********99998766666655 PP

>> M20_dimer  Peptidase dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.2   0.0   1.8e-22   1.1e-18       1     106 [.     183     293 ..     183     296 .. 0.95
   2 ?   -2.7   0.0      0.91   5.4e+03      41      67 ..     328     344 ..     317     349 .. 0.62

  Alignments for each domain:
  == domain 1  score: 67.2 bits;  conditional E-value: 1.8e-22
                                   SEB-EEEEEEEEEE-B-EEGG-TTTTB-HHHHHHHHHHCSCTTEEC.........TCCTCCCCCEECCE-C.CCCEESSEE CS
                     M20_dimer   1 ighkGlaggkitvkgkagHsgapgagaNAieklarllaeledeegdia....eerslprttlnvtgiegGs.aknvipdea 76 
                                   i++k +++ k +v gk+ H+++p +++N++++ a+++ +l ++ + +     + +++p++t+++t  e    ++n+ip++ 
  gi|13541910|ref|NP_111598.1| 183 ISEKSILWLKFRVIGKQYHASMPPNAINSFRESAKFILKLDKTLHAKYsaidKLYNVPYSTFEPTKHEKNVdNINTIPGTD 263
                                   5799**************************************998888*********************99********** PP

                                   EEEEEEEHHHHHHHHHHHHHHHHHHTSCCS CS
                     M20_dimer  77 eakidiRllpgedpeevleeieeilekeap 106
                                    +++d+R+lp+ ++++v+ ++e+ +++  +
  gi|13541910|ref|NP_111598.1| 264 VFYYDCRVLPQYSLDDVISTVEAEISDFQK 293
                                   ***********************9987665 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.91
                                   CTTEEC.....TCCTCCCCCEECCE-C CS
                     M20_dimer  41 edeegdiaeerslprttlnvtgiegGs 67 
                                   +++          ++  +nv gi gG+
  gi|13541910|ref|NP_111598.1| 328 RKL----------RKKEPNVLGIGGGT 344
                                   333..........33478888888887 PP

>> Peptidase_M28  Peptidase family M28
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.0     2e-09   1.2e-05       1      82 [.      63     157 ..      63     191 .. 0.87

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 2e-09
                                   EEEEEESTTCESEEEEEEEE--B-TTT..............TCC..T---TTTTHHHHHHHHHHHHHCHHGGCCSSEEEEE CS
                 Peptidase_M28   1 NviatlegkatdevlllgAHyDsvgvg..............rgp..ifvGAdDnAsgvaalLelarvlaasgsrpkrgvrf 65 
                                   N++ ++ g++ +++l l AH+D+v+vg              +g+     G  D++  v + L ++r l++   r +++  +
  gi|13541910|ref|NP_111598.1|  63 NIVLKI-GNN-SKTLWLIAHIDTVPVGdpslwtkppfeltvEGDkmYGRGTEDDGQAVFTALLILRDLKK--IRMNYNFGI 139
                                   899999.666.69*******************99999999955555668********************8..699****** PP

                                   EEESSCSG.SSHHHHHHH CS
                 Peptidase_M28  66 lffdaEEa.gllGSkafa 82 
                                   +f+  EE  + +G +++ 
  gi|13541910|ref|NP_111598.1| 140 AFVADEEVgSKYGIQYLL 157
                                   *******85567777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (392 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       598  (0.0333538); expected 358.6 (0.02)
Passed bias filter:                      503  (0.0280551); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.63u 0.30s 00:00:00.93 Elapsed: 00:00:00.50
# Mc/sec: 2376.47
//
Query:       gi|13541911|ref|NP_111599.1|  [L=194]
Description: hypothetical protein TVN1080 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        4.1    7.3  14.1       0.61   10.0   8.1    2.4  2  DctQ      Tripartite ATP-independent periplasmic transporters


Domain annotation for each model (and alignments):
>> 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 ?   -2.0   2.0      0.18   3.2e+03      68      85 ..      45      62 ..      19      85 .. 0.61
   2 ?   10.0   8.1   3.4e-05      0.61      49     121 ..      89     180 ..      71     185 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.18
                          DctQ 68 iadllallfaavliwagw 85
                                  +  ll +l++a+l+ +++
  gi|13541911|ref|NP_111599.1| 45 LDYLLYALLFALLLSSSF 62
                                  444444444444444444 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 3.4e-05
                          DctQ  49 rvdll..verlpprvrrlleliadllallfaavliwagw.................levaaalfeettpvlglplwwvylv 110
                                    + ++   e+lp  +  ++ lia++l+ +fa++  + +                  +e ++++f+   p lgl ++++y v
  gi|13541911|ref|NP_111599.1|  89 IISFFpdPEKLPLLLYGFIGLIALVLSRFFAIFYYKGSAsiilislsglialsykcAELFSFNFHHIRPELGLAVFYIYNV 169
                                   555554456777777778888888887777764444444667777778888888999************************ PP

                          DctQ 111 lpigaallalv 121
                                   l i a++la+ 
  gi|13541911|ref|NP_111599.1| 170 LAIIAVILAIM 180
                                   ******99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       894  (0.0498633); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); 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):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.31s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 1183.96
//
Query:       gi|13541912|ref|NP_111600.1|  [L=462]
Description: prolyl-tRNA synthetase [Thermoplasma volcanium GSS1]
Scores for complete 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   94.7   0.1    2.6e-26   92.7   0.1    1.9  2  tRNA-synt_2b    tRNA synthetase class II core domain (G, H, P
    7.6e-19   67.7   0.1    1.5e-18   66.7   0.1    1.5  1  HGTP_anticodon  Anticodon binding domain
    4.4e-12   46.0   1.4    1.4e-11   44.5   0.4    2.2  2  ProRS-C_1       Prolyl-tRNA synthetase, C-terminal


Domain annotation for each model (and alignments):
>> tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, S and T)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.7   0.1   4.3e-30   2.6e-26       5     176 ..      95     265 ..      87     268 .. 0.90
   2 ?   -1.0   0.0      0.25   1.5e+03      57      98 ..     358     399 ..     347     447 .. 0.84

  Alignments for each domain:
  == domain 1  score: 92.7 bits;  conditional E-value: 4.3e-30
                                   ETTSEEEEE-SSSHHHHHHHHHHHEEEB.GGSSEEEEEEEEEEBTTTSTBCTTTB-SEEEEEEEEEEES.GGGHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx RF
                  tRNA-synt_2b   5 drndreyiLkPtneetfvelirdevlrs.krLPlklyqiqtkyRdEksdsrGLlRvreFhqkdgyvfha.easlddslrdl 83 
                                   ++ ++e++L+Pt+e +++ +++ + +rs  +LPlk+yqi ++yR+E++ +r  +R re+h  +++  h   ++++ ++ ++
  gi|13541912|ref|NP_111600.1|  95 EKLEEELALRPTSESAMYPMFSLW-VRShADLPLKIYQIVSVYRYETKHTRSFIRIREIHFFEAHTAHEsYEDAEKQMDEY 174
                                   55689*****************88.9**778*****************9*******************9778899999999 PP

                                   HHHHHHHHHHTT.SC.EEEEEEGTTSCBTTSEEEEEEEEETTTSEEEEEEEEEEEETHHHHHTTEEEECTTSSEEEEEEEE CS
                                   xxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  tRNA-synt_2b  84 ikaisriferlglef.raiielmsaksadykdkkefeavsesltkgieigtiqklgtrlserlgatvldennreksvimic 163
                                        +i  +l l+f +  +  ++++ + + ++  f+ v++ +++ ++igti++ gt++s+  ++++l+e++  + v+ + 
  gi|13541912|ref|NP_111600.1| 175 RIIWTEIADALCLPFlYDQRPEWDKF-PGAMYTIAFDTVMP-SGRSLQIGTIHQYGTNFSKNYDIKYLKEDGTFEYVHQTT 253
                                   99999999999888734444557754.99************.9************************************** PP

                                   EEEEHHHHHHHHH CS
                                   xxxxxxxxxxxxx RF
                  tRNA-synt_2b 164 aaigveRllsail 176
                                   ++++ eRll+ai+
  gi|13541912|ref|NP_111600.1| 254 FGMS-ERLLAAII 265
                                   ****.******98 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.25
                                   TB-SEEEEEEEEEEESGGGHHHHHHHHHHHHHHHHHHTT.SC CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  tRNA-synt_2b  57 lRvreFhqkdgyvfhaeaslddslrdlikaisriferlglef 98 
                                   +R+++  q +  v+  ++ ld + +++ +++++ f++l ++ 
  gi|13541912|ref|NP_111600.1| 358 IRGKKTVQREKLVYEVPDMLDLVKEKITEDAKKTFNSLVVSA 399
                                   788999999999999999999999999999999999998765 PP

>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.7   0.1   2.5e-22   1.5e-18       1      91 [.     284     373 ..     284     376 .. 0.96

  Alignments for each domain:
  == domain 1  score: 66.7 bits;  conditional E-value: 2.5e-22
                                   SEEEEESSSSHHHHHHHHHHHHHHHHTTTSEEEEES.SSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEEETTTCEEE CS
                HGTP_anticodon   1 qvvviplnekaeeleeyakklaeeLraagirveldd.snesigkkireadllgipfavvvGekelekgtvtvrdrdtreqe 80 
                                   qvv++p+    e +e yak++   L+  gir+++d+ +n+++g+k++++++ g+p++++vGe+el+++tvt+  r+ r + 
  gi|13541912|ref|NP_111600.1| 284 QVVIVPIPG--EGVERYAKDIETTLNGIGIRCHVDNrDNYTPGYKYNDWEMRGVPLRIEVGERELKEKTVTLAARNIRGKK 362
                                   8*******9..779******************************************************************* PP

                                   EEETTHHHHHH CS
                HGTP_anticodon  81 rvsldelvekl 91 
                                   +v++++lv ++
  gi|13541912|ref|NP_111600.1| 363 TVQREKLVYEV 373
                                   ******99776 PP

>> ProRS-C_1  Prolyl-tRNA synthetase, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.46   2.8e+03      23      42 ..     166     190 ..     156     199 .. 0.66
   2 !   44.5   0.4   2.3e-15   1.4e-11       9      69 .]     406     462 .]     401     462 .] 0.92

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.46
                                   HHHHHHHHHH.....S-EEEEEESS CS
                     ProRS-C_1  23 ecEekIkeet.....gakslcipfd 42 
                                   ++E+++ e        a  lc pf 
  gi|13541912|ref|NP_111600.1| 166 DAEKQMDEYRiiwteIADALCLPFL 190
                                   5555555544566667899999994 PP

  == domain 2  score: 44.5 bits;  conditional E-value: 2.3e-15
                                   HTT-EEEEEESSGHHHHHHHHHHHS-EEEEEESSB-SSCCCSB-TTT-SB-SEEEEEE-B- CS
                     ProRS-C_1   9 ekkgfvlapWcgeeecEekIkeetgakslcipfdqepseegtkCivcgkpakkwvlfgrsY 69 
                                   +k+g+++a Wcg++ec +kI++et  + l+  +++   +e+ kCivcgk a k ++f rsY
  gi|13541912|ref|NP_111600.1| 406 KKEGLIKAFWCGSKECSDKIENETEKSALGFNLNN---DETGKCIVCGK-AGKLAIFSRSY 462
                                   6778*****************************86...7999******7.677******** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (462 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       571  (0.0318478); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.67u 0.27s 00:00:00.94 Elapsed: 00:00:00.51
# Mc/sec: 2738.22
//
Query:       gi|13541913|ref|NP_111601.1|  [L=212]
Description: phosphoserine phosphatase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-11   45.2   0.0    1.8e-11   44.8   0.0    1.1  1  HAD              haloacid dehalogenase-like hydrolase
    8.2e-08   32.8   0.0      3e-05   24.4   0.0    2.1  2  Hydrolase        haloacid dehalogenase-like hydrolase
    0.00043   19.8   0.0    0.00054   19.4   0.0    1.1  1  Put_Phosphatase  Putative Phosphatase
    0.00062   19.9   0.3      0.004   17.3   0.3    2.1  1  HAD_2            Haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
       0.13   12.4   0.1          1    9.5   0.1    2.2  1  Hydrolase_6      Haloacid dehalogenase-like hydrolase
       0.71    9.6   3.3        4.7    6.9   0.0    2.6  3  Hydrolase_3      haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.8   0.0   6.1e-15   1.8e-11       2     179 ..      10     171 ..       9     176 .. 0.80

  Alignments for each domain:
  == domain 1  score: 44.8 bits;  conditional E-value: 6.1e-15
                           HAD   2 lfDfDgTLldgdslelllrfllrrgaprlwralreklllalfrellrldraglaelleallaglseelaaelerfvaevir 82 
                                   ++D+DgTL+ + s + +++++l+ + ++  r++r ++ +++   ++ +        + a l  ++   ++ + +f++ev  
  gi|13541913|ref|NP_111601.1|  10 ILDMDGTLTLEPSSWDYVHRRLGINNHSVTRLYRNRYINYY---CFFQ------SDIKAWLHKYPNLKKEKVVEFLREVP- 80 
                                   78*********999999999*********************...6666......45666666666666677777774444. PP

                           HAD  83 pklldpgalellaahraaGdrvvvvSgglrplvepllaelgadevlatelevdd..rltgelglegkpvrgegkvaalrew 161
                                      ++ ga el++  r++G+r++v+Sgg++ l  ++ ++  +d+  ++e+ +d+  ++  e++++  p  ++  v++++e 
  gi|13541913|ref|NP_111601.1|  81 ---IRHGADELINVLRKNGIRTAVISGGISWLFDIISERSKIDYNFSNEIFTDEygYIVPEGKVRVIPEEKDLVVRKIQE- 157
                                   ...457*******999********************************98888888888886666666665555555555. PP

                           HAD 162 laaegegidleevvayGD 179
                                       + gi  + +  +GD
  gi|13541913|ref|NP_111601.1| 158 ----ELGIGKDQTASVGD 171
                                   ....77777777777777 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   0.0    0.0022       6.4       1      20 [.       6      25 ..       6      45 .. 0.72
   2 !   24.4   0.0     1e-08     3e-05     104     201 ..      66     174 ..      23     177 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0022
                                  SSEEEEESBTTTBCHHHHHH CS
                                  xxxxxxxxxxxxxxxxxxxx RF
                     Hydrolase  1 iktvvfDkdGTLttgepsve 20
                                  i ++++D+dGTLt   +s  
  gi|13541913|ref|NP_111601.1|  6 ISLFILDMDGTLTLEPSSWD 25
                                  56899********5444444 PP

  == domain 2  score: 24.4 bits;  conditional E-value: 1e-08
                                   TTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTT.GGGESEEEEHHCES......STTTSHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx......xxxxxxx RF
                     Hydrolase 104 qaralavftiadplkvkpeaaeavasLkaagievvlltgdnpetaeraanqlG.ddyfdaviasdiet......vakpspe 177
                                   + +   v+++  + +++ +a e+++ L+++gi++++++g+ +   + + ++   d  f+++i +d+ +         + pe
  gi|13541913|ref|NP_111601.1|  66 NLKKEKVVEFLREVPIRHGADELINVLRKNGIRTAVISGGISWLFDIISERSKiDYNFSNEIFTDEYGyivpegKVRVIPE 146
                                   556778888999999*************************99555544444555444444444444445555246666999 PP

                                   HHHHHHHHHT....STGGGEEEEESSHH CS
                                   xxxxxxxxxx....xxxxxxxxxxxxxx RF
                     Hydrolase 178 gkvaaireLq....gkpeevamVGDgvn 201
                                    k  ++r++q    + + ++a VGD + 
  gi|13541913|ref|NP_111601.1| 147 EKDLVVRKIQeelgIGKDQTASVGDEME 174
                                   9999999999666555889******875 PP

>> Put_Phosphatase  Putative Phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   1.8e-07   0.00054       2     136 ..       8     145 ..       7     154 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.8e-07
               Put_Phosphatase   2 lvvfDFDkti.idedsdnwvvdelpatelf.eelretlrkglwnelmdrvlkelheqg.vseadikkvlrsiplspglvel 79 
                                   l ++D D t+ ++ +s + v + l+ ++ + ++l ++   +++  + + + + lh+    +++++ + lr++p+  g  el
  gi|13541913|ref|NP_111601.1|   8 LFILDMDGTLtLEPSSWDYVHRRLGINNHSvTRLYRNRYINYYCFFQSDIKAWLHKYPnLKKEKVVEFLREVPIRHGADEL 88 
                                   6789*****84578999********987631344333333566666778888999976589999***************** PP

               Put_Phosphatase  80 ikslakkkleldliiiSDaNsffieeileaagledlFse.iftNP.aavdasGeltvlp 136
                                   i+ l+k  +++   +iS   s   + i e  ++   Fs+ ift   +++  +G+++v p
  gi|13541913|ref|NP_111601.1|  89 INVLRK--NGIRTAVISGGISWLFDIISERSKIDYNFSNeIFTDEyGYIVPEGKVRVIP 145
                                   ****66..67999*********************999977**97425666677777665 PP

>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.3   1.3e-06     0.004       2     164 ..      10     176 ..       9     179 .. 0.64

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.3e-06
                         HAD_2   2 iFDlDgTlldteeliiqafnelleeygls..elseeelrkliglslrellrklgeseeeeekieellrkyneekkkkevkp 80 
                                   i D+DgTl  +       + ++ ++ g++  ++++ + +++i+      + ++ ++ + ++  +   +k++e +   ev +
  gi|13541913|ref|NP_111601.1|  10 ILDMDGTLTLEPSS----WDYVHRRLGINnhSVTRLYRNRYINYYC---FFQSDIKAWLHKYPNLKKEKVVEFLR--EVPI 81 
                                   56777777544433....3333333333311333333333333333...44444445555444444444444444..5999 PP

                         HAD_2  81 ydgvkelLeeLkeagyklgivTsksreaveekleqlgiesyFdvivtsedvekkKPdpe..........viekaleklklk 151
                                     g+ el++ L+++g++ ++++ + +  ++   e+ +i+  F+  + +++ +   P+ +          v++k+ e+l++ 
  gi|13541913|ref|NP_111601.1|  82 RHGADELINVLRKNGIRTAVISGGISWLFDIISERSKIDYNFSNEIFTDEYGYIVPEGKvrvipeekdlVVRKIQEELGIG 162
                                   9*************************************9999988888887655443321111111133789999999999 PP

                         HAD_2 152 keeviyvGDsp.tD 164
                                   k+++  vGD+  +D
  gi|13541913|ref|NP_111601.1| 163 KDQTASVGDEMeND 176
                                   99999999998666 PP

>> Hydrolase_6  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.1   0.00033         1       2      37 ..      10     103 ..       9     108 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00033
                                   EEESTTTSE..........................................................ETTEE-TTHHHHHH CS
                   Hydrolase_6   2 lfDidGvLw..........................................................rgdkaipgaaealn 24 
                                   ++D+dG+L                                                           r+  +  ga+e++n
  gi|13541913|ref|NP_111601.1|  10 ILDMDGTLTlepsswdyvhrrlginnhsvtrlyrnryinyycffqsdikawlhkypnlkkekvveflREVPIRHGADELIN 90 
                                   667777777777777777777777777777777777777777777777777777777777766666455555679****** PP

                                   HHHHTT-EEEEEE CS
                   Hydrolase_6  25 alraagkpvvllT 37 
                                   +lr++g+++++++
  gi|13541913|ref|NP_111601.1|  91 VLRKNGIRTAVIS 103
                                   ********99997 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.4     0.054   1.6e+02       2      10 ..      10      18 ..       9      30 .. 0.85
   2 ?   -1.1   0.0      0.42   1.2e+03      85     111 ..      86     112 ..      66     140 .. 0.65
   3 ?    6.9   0.0    0.0016       4.7     188     215 ..     148     176 ..     145     177 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.054
                                  EEEIIIIIS CS
                   Hydrolase_3  2 alDlDGTLl 10
                                  +lD+DGTL 
  gi|13541913|ref|NP_111601.1| 10 ILDMDGTLT 18
                                  89*****94 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.42
                                   HHHHHHHHHTTCEEEEEESSEEEESTT CS
                   Hydrolase_3  85 keiikllkennveillytedkvyvlnk 111
                                   +e+i+ l++n+++ ++ +    +  + 
  gi|13541913|ref|NP_111601.1|  86 DELINVLRKNGIRTAVISGGISWLFDI 112
                                   566677777776666666555555555 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.0016
                                   HHHHHHHHHHHCT--GGGEEEEESSG.GG CS
                   Hydrolase_3 188 KgtalkklakelnisleeviafGDge.ND 215
                                   K   ++k+++el+i +++++++GD++ ND
  gi|13541913|ref|NP_111601.1| 148 KDLVVRKIQEELGIGKDQTASVGDEMeND 176
                                   566799******************75266 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       664  (0.037035); expected 358.6 (0.02)
Passed bias filter:                      578  (0.0322383); 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: 0.57u 0.34s 00:00:00.90 Elapsed: 00:00:00.50
# Mc/sec: 1273.81
//
Query:       gi|13541914|ref|NP_111602.1|  [L=312]
Description: transcription initiation factor IIB [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.9e-39  133.0   2.6    4.1e-19   68.4   0.3    2.3  2  TFIIB            Transcription factor TFIIB repeat
    5.6e-21   73.8   1.4    9.3e-21   73.1   1.4    1.4  1  TF_Zn_Ribbon     TFIIB zinc-binding
    0.00092   19.2   0.0     0.0064   16.5   0.0    2.1  2  RB_B             Retinoblastoma-associated protein B domain
     0.0029   17.1   1.1      0.016   14.7   0.6    2.5  2  Sigma70_r4       Sigma-70, region 4
     0.0041   17.2   0.0        1.4    9.0   0.0    2.4  2  Cyclin_C         Cyclin, C-terminal domain
     0.0047   16.7   0.2      0.077   12.7   0.0    2.5  2  Cyclin_N         Cyclin, N-terminal domain
  ------ inclusion threshold ------
      0.012   15.4   0.3      0.038   13.8   0.3    1.9  1  HTH_AsnC-type    AsnC-type helix-turn-helix domain
      0.018   15.4   0.3      0.039   14.3   0.3    1.5  1  Lar_restr_allev  Restriction alleviation protein Lar
      0.025   14.3   1.8       0.65    9.8   2.2    2.3  2  A2L_zn_ribbon    A2L zinc ribbon domain
      0.033   14.1   0.5      0.082   12.8   0.1    1.8  2  AAA_lid_9        AAA lid domain
      0.039   14.1   2.5        0.4   10.8   0.2    2.3  2  Zn-ribbon_8      Zinc ribbon domain
       0.08   12.4   0.3       0.17   11.3   0.3    1.6  1  HTH_Tnp_ISL3     Helix-turn-helix domain of transposase famil
      0.084   12.3   3.3       0.54    9.8   3.3    2.1  1  zf-ribbon_3      zinc-ribbon domain
      0.093   13.0   0.2       0.42   10.9   0.1    2.1  2  UPF0253          Uncharacterised protein family (UPF0253)
        0.1   12.3   0.1       0.19   11.4   0.1    1.3  1  Ribosomal_S27e   Ribosomal protein S27
       0.11   12.5   0.3       0.25   11.3   0.3    1.6  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
       0.18   11.9   2.8        2.4    8.3   1.7    2.8  2  zf-ACC           Acetyl-coA carboxylase zinc finger domain
       0.26   11.0   3.2        7.2    6.5   0.1    2.8  3  zinc_ribbon_2    zinc-ribbon domain
        0.3   11.3   0.9       0.57   10.4   0.9    1.4  1  Auto_anti-p27    Sjogren's syndrome/scleroderma autoantigen 1
       0.42   10.3   5.1        3.2    7.5   5.2    2.1  1  zf-RRN7          Zinc-finger of RNA-polymerase I-specific TFI
       0.43   10.8   2.4       0.48   10.7   0.2    2.3  2  zf-RING_7        C4-type zinc ribbon domain
        6.1    6.9   5.8        3.1    7.8   0.2    2.7  3  DUF1451          Zinc-ribbon containing 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 !   68.4   0.3     5e-22   4.1e-19       2      71 .]     132     201 ..     131     201 .. 0.98
   2 !   64.7   0.1   7.2e-21   5.9e-18       1      71 []     225     295 ..     225     295 .. 0.99

  Alignments for each domain:
  == domain 1  score: 68.4 bits;  conditional E-value: 5e-22
                                   HHHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHHH CS
                         TFIIB   2 krfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekti 71 
                                   +r+a +l +p+ V++ A  ++++a++++++ Grs +g++A +ly Acr  +v rt+ ei+sv++V++k+i
  gi|13541914|ref|NP_111602.1| 132 ERMAFNLSIPNDVRETAAVIYRKAVKQNMIRGRSIEGVVAGALYAACRITNVPRTLGEIASVTRVKKKEI 201
                                   79******************************************************************98 PP

  == domain 2  score: 64.7 bits;  conditional E-value: 7.2e-21
                                   HHHHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHHH CS
                         TFIIB   1 ikrfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekti 71 
                                   i+rf+++l+L+   +++A e+++ a + ++++G+ p+g+aAA++yiA++  +++rtq+ +++v+ V+e+ti
  gi|13541914|ref|NP_111602.1| 225 ISRFCSKLKLSMDTRNKALEILRDAENVGLTSGKGPTGVAAAAIYIASLITGERRTQRAVAEVAGVTEVTI 295
                                   89*******************************************************************98 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.1   1.4   1.1e-23   9.3e-21       2      43 .]      15      56 ..      14      56 .. 0.98

  Alignments for each domain:
  == domain 1  score: 73.1 bits;  conditional E-value: 1.1e-23
                                  EETTTTCEECHEETSTTCEEESSSSBEEEECCCCCCCHHHHH CS
                  TF_Zn_Ribbon  2 kCPnCgstnlveDpergelvCtdCGlVlednsidegpewref 43
                                  +CP+Cgstnl++D+e+gelvC++CG+V+ed +id gpewr+f
  gi|13541914|ref|NP_111602.1| 15 RCPECGSTNLIRDYEHGELVCGECGAVIEDSYIDQGPEWRAF 56
                                  6***************************************98 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 !   16.5   0.0   7.8e-06    0.0064      10      94 ..     124     206 ..     115     222 .. 0.87
   2 ?   -0.2   0.0       1.2   9.4e+02      16      38 ..     224     246 ..     214     251 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 7.8e-06
                          RB_B  10 yklaavrlrdLcerLklsselrekiwtlfehvlveetellkdRhlDqillcavYvvakvtkeelsFkeiikaYrkqpqass 90 
                                   ++ a   l+++  +L++ +++re +  + ++++   +++++ R ++ ++  a+Y+ +++t+  +++ ei +  r ++++  
  gi|13541914|ref|NP_111602.1| 124 LSQALQELERMAFNLSIPNDVRETAAVIYRKAVK--QNMIRGRSIEGVVAGALYAACRITNVPRTLGEIASVTRVKKKEIG 202
                                   5667788899999999999999999888888775..679*******************************99999998888 PP

                          RB_B  91 kvyr 94 
                                   ++yr
  gi|13541914|ref|NP_111602.1| 203 RTYR 206
                                   8877 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.2
                          RB_B  16 rlrdLcerLklsselrekiwtlf 38 
                                    +++ c++Lkls ++r+k+ +++
  gi|13541914|ref|NP_111602.1| 224 YISRFCSKLKLSMDTRNKALEIL 246
                                   57899*********999987665 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       1.5   1.2e+03      20      29 ..     184     193 ..     179     207 .. 0.76
   2 !   14.7   0.6   1.9e-05     0.016      18      49 ..     276     307 ..     268     308 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1.5
                                   T--HHHHHHH CS
                    Sigma70_r4  20 glTleEIger 29 
                                   ++Tl EI+ +
  gi|13541914|ref|NP_111602.1| 184 PRTLGEIASV 193
                                   6788888865 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 1.9e-05
                                   TTT--HHHHHHHHTS-HHHHHHHHHHHHHHHH CS
                    Sigma70_r4  18 geglTleEIgerlgiSrerVrqiekrAlrkLR 49 
                                   ge +T+  ++e+ g+++ ++r + k+  +kL+
  gi|13541914|ref|NP_111602.1| 276 GERRTQRAVAEVAGVTEVTIRNRYKELTEKLK 307
                                   899*************************9998 PP

>> Cyclin_C  Cyclin, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0     0.018        14      49      90 ..     171     212 ..     168     239 .. 0.89
   2 !    9.0   0.0    0.0017       1.4      47      90 ..     263     306 ..     258     312 .] 0.90

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.018
                                   HHHHHHCCHHHHS--S-HHHHHHC---HHHHHHHHHHHHHHH CS
                      Cyclin_C  49 aaalllarstlnspewtetlehytgyskedlkpcvelilell 90 
                                   a+al++a+++ n p    ++ ++t+++k+++   ++ +  +l
  gi|13541914|ref|NP_111602.1| 171 AGALYAACRITNVPRTLGEIASVTRVKKKEIGRTYRIMSRYL 212
                                   89************************************9998 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0017
                                   HHHHHHHHCCHHHHS--S-HHHHHHC---HHHHHHHHHHHHHHH CS
                      Cyclin_C  47 iAaaalllarstlnspewtetlehytgyskedlkpcvelilell 90 
                                   +Aaaa+++a+ + ++   ++++ ++ g+++  +++ ++ + e l
  gi|13541914|ref|NP_111602.1| 263 VAAAAIYIASLITGERRTQRAVAEVAGVTEVTIRNRYKELTEKL 306
                                   8***********************************99998876 PP

>> Cyclin_N  Cyclin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.0   9.5e-05     0.077      35     126 ..     128     216 ..     101     217 .. 0.83
   2 ?    3.5   0.2      0.07        57      40      72 ..     189     221 ..     185     306 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 9.5e-05
                                   HHHHHHHHHHTT--TTHHHHHHHHHHHHHHHS---CCCHHHHHHHHHHHHHHHHSSS---HHHHHHHTTTSS-HHHHHHHH CS
                      Cyclin_N  35 idwlvevaekfkltpetlflavnyldRflskksvpkdklqlvgatcLllAaKveeisppkledlvyitdeafteeeilemE 115
                                   ++ l ++a ++++ +++  +a++++ + ++++ ++ + ++ v+a++L+ A+++ ++ p +l +++ +t   ++++ei +  
  gi|13541914|ref|NP_111602.1| 128 LQELERMAFNLSIPNDVRETAAVIYRKAVKQNMIRGRSIEGVVAGALYAACRITNV-PRTLGEIASVTR--VKKKEIGRTY 205
                                   55567777778888999999*********************************999.9*******9976..8888888887 PP

                                   HHHHHHTTT-- CS
                      Cyclin_N 116 rliLetLnfdl 126
                                   r + ++L+ ++
  gi|13541914|ref|NP_111602.1| 206 RIMSRYLKLNI 216
                                   77777777665 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.07
                                   HHHHHTT--TTHHHHHHHHHHHHHHHS---CCC CS
                      Cyclin_N  40 evaekfkltpetlflavnyldRflskksvpkdk 72 
                                   e+a++++++++ +  +++++ R+l+ +++p + 
  gi|13541914|ref|NP_111602.1| 189 EIASVTRVKKKEIGRTYRIMSRYLKLNIMPSKA 221
                                   566666777777777777777777766666553 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.3   4.6e-05     0.038      15      41 ..     276     302 ..     270     303 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.6e-05
                 HTH_AsnC-type  15 daRisyaeLAervGlSestvlrRvrrL 41 
                                     R++ +++Ae  G++e t+++R++ L
  gi|13541914|ref|NP_111602.1| 276 GERRTQRAVAEVAGVTEVTIRNRYKEL 302
                                   569*********************998 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.3   4.8e-05     0.039       1      39 [.      11      52 ..      11      68 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.8e-05
               Lar_restr_allev  1 eeLkpCPfCggravlersqrvvaeigqcvyCadCga.........stp 39
                                  ee++ CP Cg+ + +   + +         C +Cga         +  
  gi|13541914|ref|NP_111602.1| 11 EEIERCPECGSTNLIRDYEHG------ELVCGECGAviedsyidqGPE 52
                                  68999******9877666555......48*******655555554444 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.2     0.031        25      21      30 ..      13      22 ..      11      25 .. 0.85
   2 ?    9.8   2.2    0.0008      0.65       6      30 ..      16      41 ..      16      43 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.031
                 A2L_zn_ribbon 21 ylvCieCgas 30
                                  ++ C+eCg++
  gi|13541914|ref|NP_111602.1| 13 IERCPECGST 22
                                  677*****97 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0008
                 A2L_zn_ribbon  6 CsvCggngiln.seqgylvCieCgas 30
                                  C  Cg+ +++   e+g+lvC eCga+
  gi|13541914|ref|NP_111602.1| 16 CPECGSTNLIRdYEHGELVCGECGAV 41
                                  66799999997789**********97 PP

>> AAA_lid_9  AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.1         9   7.3e+03      73      80 ..     119     126 ..     100     138 .. 0.47
   2 ?   12.8   0.1    0.0001     0.082      24      75 ..     196     247 ..     189     253 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 9
                     AAA_lid_9  73 klekelak 80 
                                   ++e++l++
  gi|13541914|ref|NP_111602.1| 119 AAERNLSQ 126
                                   22222222 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.0001
                     AAA_lid_9  24 isdealeaavklSkrYisdrflPdkAIDllDeaaarvrlkkeskpeelekle 75 
                                   ++++ +    ++ +rY++   +P kA D + + +++++l+ +++++ le l+
  gi|13541914|ref|NP_111602.1| 196 VKKKEIGRTYRIMSRYLKLNIMPSKAEDYISRFCSKLKLSMDTRNKALEILR 247
                                   66777888888999****************************9999887665 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   0.2   0.00049       0.4      21      38 ..       7      26 ..       3      28 .. 0.71
   2 ?    3.0   0.1      0.14   1.1e+02       5      16 ..      32      43 ..      27      61 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00049
                   Zn-ribbon_8 21 isdaplta.CPeCgs.evrr 38
                                   ++ ++++ CPeCgs ++ r
  gi|13541914|ref|NP_111602.1|  7 KKKIEEIErCPECGStNLIR 26
                                  444456777******88866 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.14
                   Zn-ribbon_8  5 eYrCeeCghefe 16
                                  e  C eCg + e
  gi|13541914|ref|NP_111602.1| 32 ELVCGECGAVIE 43
                                  446999998887 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.3   0.00021      0.17      18      51 ..     268     302 ..     264     303 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00021
                  HTH_Tnp_ISL3  18 ayilellles.rsvkavArqlgvSwtTVwrildry 51 
                                    yi+ l +   r+ +avA+  gv++ T++++++++
  gi|13541914|ref|NP_111602.1| 268 IYIASLITGErRTQRAVAEVAGVTEVTIRNRYKEL 302
                                   58999999999********************9976 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   3.3   0.00066      0.54       4      26 .]      15      42 ..      13      42 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00066
                   zf-ribbon_3  4 rCPnCGa.p.lss...ddnvCpyCGtkl 26
                                  rCP+CG+ + +++   +  vC  CG+++
  gi|13541914|ref|NP_111602.1| 15 RCPECGStNlIRDyehGELVCGECGAVI 42
                                  8*******966554448999****9986 PP

>> UPF0253  Uncharacterised protein family (UPF0253)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00052      0.42      27      52 ..     124     149 ..     116     152 .. 0.91
   2 ?   -1.9   0.0       5.3   4.3e+03      27      45 ..     180     198 ..     171     200 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00052
                       UPF0253  27 iscalktLdevaanealpeevrekAA 52 
                                   +s al+ L+++a n ++p++vre AA
  gi|13541914|ref|NP_111602.1| 124 LSQALQELERMAFNLSIPNDVRETAA 149
                                   77899********************9 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 5.3
                       UPF0253  27 iscalktLdevaanealpe 45 
                                   i+ + +tL e+a+  ++ +
  gi|13541914|ref|NP_111602.1| 180 ITNVPRTLGEIASVTRVKK 198
                                   6667788999998877765 PP

>> Ribosomal_S27e  Ribosomal protein S27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00024      0.19       9      36 ..      15      42 ..      13      44 .. 0.95

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00024
                                  E-TTTS-EEEEESS-SS-EEESSSTCEE CS
                Ribosomal_S27e  9 kCpdCenetvvFshaatvvkCisCgkvL 36
                                  +Cp+C+ +  + +  +    C  Cg v+
  gi|13541914|ref|NP_111602.1| 15 RCPECGSTNLIRDYEHGELVCGECGAVI 42
                                  7************************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 ?   11.3   0.3   0.00031      0.25      20      45 ..      15      40 ..       9      41 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00031
                 Zn_Tnp_IS1595 20 vCPhCgsr.kayriktrglfqCkeCrk 45
                                  +CP Cgs+  ++ +++ g + C eC++
  gi|13541914|ref|NP_111602.1| 15 RCPECGSTnLIRDYEH-GELVCGECGA 40
                                  6*******87888888.********85 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   1.7    0.0029       2.4       3      26 .]      15      38 ..      15      38 .. 0.94
   2 ?    1.4   0.0      0.42   3.4e+02       9      20 ..     149     160 ..     148     160 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0029
                        zf-ACC  3 KCpsCgemlykkeLernlyVCPkC 26
                                  +Cp+Cg++ + ++ e+   VC +C
  gi|13541914|ref|NP_111602.1| 15 RCPECGSTNLIRDYEHGELVCGEC 38
                                  6***************99999998 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.42
                        zf-ACC   9 emlykkeLernl 20 
                                   +++y+k + +n+
  gi|13541914|ref|NP_111602.1| 149 AVIYRKAVKQNM 160
                                   79******9996 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.1    0.0089       7.2       1       9 [.      15      23 ..      15      27 .. 0.82
   2 ?    4.2   0.0     0.045        37       2      11 ..      35      44 ..      33      46 .. 0.82
   3 ?   -1.9   0.1       3.9   3.2e+03      14      18 ..     227     231 ..     226     231 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0089
                 zinc_ribbon_2  1 fCpnCGael 9 
                                  +Cp+CG ++
  gi|13541914|ref|NP_111602.1| 15 RCPECGSTN 23
                                  699999877 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.045
                 zinc_ribbon_2  2 CpnCGaelqd 11
                                  C +CGa ++d
  gi|13541914|ref|NP_111602.1| 35 CGECGAVIED 44
                                  8899998887 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 3.9
                 zinc_ribbon_2  14 kFCpy 18 
                                   +FC++
  gi|13541914|ref|NP_111602.1| 227 RFCSK 231
                                   79986 PP

>> Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.9    0.0007      0.57      16      40 .]      14      39 ..      14      39 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0007
                 Auto_anti-p27 16 etCpvC.gvPLmrdrkggkvyCvaCd 40
                                  e Cp+C ++ L rd + g+++C  C+
  gi|13541914|ref|NP_111602.1| 14 ERCPECgSTNLIRDYEHGELVCGECG 39
                                  57************988*****9996 PP

>> zf-RRN7  Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   5.2    0.0039       3.2       5      32 .]      14      43 ..      11      43 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0039
                       zf-RRN7  5 ppCgvCgc.rsftl.ddGfyyCrrChtqeg 32
                                  ++C++Cg+  + +  + G  +C +C+ +++
  gi|13541914|ref|NP_111602.1| 14 ERCPECGStNLIRDyEHGELVCGECGAVIE 43
                                  79******658888999*********9987 PP

>> zf-RING_7  C4-type zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.2   0.00059      0.48      18      30 ..       7      20 ..       1      21 [. 0.78
   2 ?   -2.1   0.2       5.9   4.8e+03      26      31 ..      35      40 ..      30      42 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00059
                                  CCS.TB-EE-TTT- CS
                     zf-RING_7 18 rag.devvtCpeCG 30
                                  +++ +e+ +CpeCG
  gi|13541914|ref|NP_111602.1|  7 KKKiEEIERCPECG 20
                                  455899*******9 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 5.9
                                  -TTT-- CS
                     zf-RING_7 26 CpeCGR 31
                                  C eCG+
  gi|13541914|ref|NP_111602.1| 35 CGECGA 40
                                  778886 PP

>> DUF1451  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.2    0.0038       3.1     127     145 ..       8      26 ..       3      28 .. 0.86
   2 ?    0.9   0.4      0.52   4.2e+02     112     122 ..      30      40 ..      28      45 .. 0.85
   3 ?   -3.0   0.0       8.2   6.6e+03      39      55 ..     116     132 ..     108     142 .. 0.61

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0038
                       DUF1451 127 kkteeippCpkCgateFrR 145
                                   kk eei++Cp+Cg+t+  R
  gi|13541914|ref|NP_111602.1|   8 KKIEEIERCPECGSTNLIR 26 
                                   7899**********99877 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.52
                       DUF1451 112 lGtlvCekCgk 122
                                    G+lvC +Cg+
  gi|13541914|ref|NP_111602.1|  30 HGELVCGECGA 40 
                                   69*******97 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 8.2
                       DUF1451  39 vaeylkrDleeaarsle 55 
                                   v+++ +r l++a ++le
  gi|13541914|ref|NP_111602.1| 116 VSNAAERNLSQALQELE 132
                                   44444455555544444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1008  (0.0562218); expected 358.6 (0.02)
Passed bias filter:                      726  (0.0404931); expected 358.6 (0.02)
Passed Vit filter:                       115  (0.00641419); 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: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 2097.24
//
Query:       gi|13541915|ref|NP_111603.1|  [L=68]
Description: H/ACA RNA-protein complex component Gar1 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00028   20.7   0.1     0.0003   20.6   0.1    1.0  1  Gar1      Gar1/Naf1 RNA binding region


Domain annotation for each model (and alignments):
>> Gar1  Gar1/Naf1 RNA binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.1   1.7e-08    0.0003      25      87 ..       5      61 ..       2      68 .] 0.86

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 1.7e-08
                                  EEEEEETTEEEEEE---S--B--BTT-EEEETT--EEEE--EEES-SSS-EEEEE--GGHHHH CS
                          Gar1 25 tvssivenevviksttsgekkvldfnsilflenktqiGkVdEifGpvnepyysVklnsseeik 87
                                  +v s+  +e+v+k +       +++ + ++++++++iG +  ++Gpv e y  V l+ + +++
  gi|13541915|ref|NP_111603.1|  5 KVVSVKGREMVVKLD-----GLMNIHTKVYDSKGQKIGYLIKVMGPVDESYGLVSLD-KPDLQ 61
                                  788888999*****9.....48*****************************999999.44444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       296  (0.0165096); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.45
# Mc/sec: 452.45
//
Query:       gi|13541916|ref|NP_111604.1|  [L=325]
Description: GTPase [Thermoplasma volcanium GSS1]
Scores for complete 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-37  126.4   0.7    1.5e-36  125.8   0.7    1.3  1  NOG1_N       NOG1 N-terminal helical domain
    4.8e-18   65.3   0.0      9e-18   64.4   0.0    1.4  1  MMR_HSR1     50S ribosome-binding GTPase
    1.4e-14   53.6   0.2    3.6e-14   52.3   0.2    1.8  1  NOG1         Nucleolar GTP-binding protein 1 (NOG1)
    3.8e-09   36.2   0.0    6.8e-09   35.4   0.0    1.5  1  FeoB_N       Ferrous iron transport protein B
      6e-05   22.6   0.1    9.1e-05   22.0   0.1    1.3  1  SRPRB        Signal recognition particle receptor beta subuni
     0.0085   15.4   0.0      0.014   14.8   0.0    1.3  1  AIG1         AIG1 family
  ------ inclusion threshold ------
       0.01   15.7   0.3      0.095   12.6   0.0    2.8  2  RsgA_GTPase  RsgA GTPase
      0.025   14.6   0.8       0.56   10.3   0.8    2.6  1  Dynamin_N    Dynamin family
       0.12   12.0   0.1       0.48   10.0   0.1    1.9  1  Ras          Ras family
       0.13   12.8   2.2       0.55   10.9   0.2    2.5  2  ING          Inhibitor of growth proteins N-terminal histone-


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 !  125.8   0.7   8.5e-40   1.5e-36       3     159 ..       6     160 ..       5     161 .. 0.98

  Alignments for each domain:
  == domain 1  score: 125.8 bits;  conditional E-value: 8.5e-40
                        NOG1_N   3 kiptvptseelidkalrrakraakttkkkkneikrlrnlearkvrtasntlsdkLeeivkkfPnldelhpFyrelldvlvd 83 
                                   kiptv+ s+e+idk+++ra+++++    +  +++r+++  + ++ +++ +    L ++vk+fP+++++hpFyr+l+d++ d
  gi|13541916|ref|NP_111604.1|   6 KIPTVLRSQEIIDKSFSRASKIEEPYFPD--KVERIKKEVQDRISAIESISCSHLDKLVKRFPSIERMHPFYRSLIDLMFD 84 
                                   8**********************999887..799****************9****************************** PP

                        NOG1_N  84 kdelkksLaqvkwarklirkigkeyvnklkkaddkkeakelrreafgrvasvlkkvdkaldfLedvrkkLrkLpai 159
                                   +d++k++L++v+ ++  i+ i+ ey++kl+  +d+ +a++++r+ +gr as+++  ++ l fL   r  +rkLp++
  gi|13541916|ref|NP_111604.1|  85 VDQYKIALSKVDATSANIKRISTEYIRKLRPVKDVGNANQIMRAYYGRFASLIEDLNETLLFLGRCRDYIRKLPEV 160
                                   **************************************************************************97 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.4   0.0     5e-21     9e-18       3     102 ..     168     272 ..     166     292 .. 0.72

  Alignments for each domain:
  == domain 1  score: 64.4 bits;  conditional E-value: 5e-21
                                   EEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSS..HHHHHHHHHHHHHHHHCT.SEEE CS
                      MMR_HSR1   3 aivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgkeielvDtpGlie..gaseekglgkaflaleea.dlil 80 
                                   +i+G+pNvGKS+L+ +lt +k +++++p+tT++++ g  + + ++i+++DtpG+++   ++ ++ +++a+la++     i+
  gi|13541916|ref|NP_111604.1| 168 IIAGMPNVGKSSLLASLTTAKPKIASYPFTTKNVIIGYNESGSERIQFIDTPGILDrdFSEMNEIEKNAILAIRFIeGKII 248
                                   79***********************************7776669*********88632223333677888877766366** PP

                                   EEEETTTT.CSHHHH.HHHHHHHH CS
                      MMR_HSR1  81 lvvdasee.klkpld.eeleelle 102
                                   +++d s+e  +++++ e+l e ++
  gi|13541916|ref|NP_111604.1| 249 FLFDYSTEsLYTREQqEHLYEQIK 272
                                   ****99443333332033333322 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 !   52.3   0.2     2e-17   3.6e-14       1      58 []     231     287 ..     231     287 .. 0.98

  Alignments for each domain:
  == domain 1  score: 52.3 bits;  conditional E-value: 2e-17
                          NOG1   1 eIEkqAiaALkhladavlFllDpseecgysleeQlsLleeikelfankpvivvlnKiD 58 
                                   eIEk+Ai+A++ +++ ++Fl+D+s e+ y+ e+Q +L+e+ik++++  ++i v +K D
  gi|13541916|ref|NP_111604.1| 231 EIEKNAILAIRFIEGKIIFLFDYSTESLYTREQQEHLYEQIKNNIN-PNIIRVQTKLD 287
                                   6********************************************9.89*******99 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.4   0.0   3.8e-12   6.8e-09       3      74 ..     167     237 ..     165     293 .. 0.89

  Alignments for each domain:
  == domain 1  score: 35.4 bits;  conditional E-value: 3.8e-12
                                   EEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETTEEEEEEE----SSSSSSSHHHHHHHHHH CS
                        FeoB_N   3 valvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkgkeveivDlPGiYslsayseeekvardfl 74 
                                    +++G pnvGk++l+ +lt ak k++ +p +t +   g+ +  +++++++D PGi +  ++se +++ ++ +
  gi|13541916|ref|NP_111604.1| 167 YIIAGMPNVGKSSLLASLTTAKPKIASYPFTTKNVIIGYNESGSERIQFIDTPGILD-RDFSEMNEIEKNAI 237
                                   6799*************************************999***********76.34555555555554 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.1   5.1e-08   9.1e-05       4     130 ..     165     294 ..     162     312 .. 0.70

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 5.1e-08
                                   -EEEEE-STTSSHHHHHHHHHHSS---B---S.S-EEETTG...GGTT-SEEEETT-GCCSHHHHHHHHHHGG..EE.... CS
                         SRPRB   4 pavllvGlsdsGKTslftrLttdsvkktvtSq.essaalkvksekgskltliDfPGheklrqklleklkakss..lk.... 77 
                                   ++ +++G+ + GK sl+  Ltt + k +      +++   ++++  +++++iD PG        ++++ +++   ++    
  gi|13541916|ref|NP_111604.1| 165 KTYIIAGMPNVGKSSLLASLTTAKPKIASYPFtTKNVIIGYNESGSERIQFIDTPGILDRDFSEMNEIEKNAIlaIRfieg 245
                                   578*******************98777666665888999998888889********6332222222222222111222223 PP

                                   EEEEEEETTS-HHHHHHHHHHHHHHHHHHHHHTT---EEEEEE-TTSTT---H CS
                         SRPRB  78 glvfvvDStidpkevkevAEllyeilliteklkdavdiliACnKqelflaksp 130
                                   +++f+ D + ++   +e  E lye + +++    +++i+    K ++++ k +
  gi|13541916|ref|NP_111604.1| 246 KIIFLFDYSTESLYTREQQEHLYEQIKNNI----NPNIIRVQTKLDISTEKVE 294
                                   589********************9887777....4555555566666666654 PP

>> AIG1  AIG1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   7.6e-06     0.014       7     110 ..     171     274 ..     165     296 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 7.6e-06
                                   SSTTSSHHHHHHHHHTS--SS--TTTS---SS-EEEEEEETTEEEEEEE--SCCCTTCC.HHCHHHHHHHHHHHCTT-ESE CS
                          AIG1   7 GktgnGkSaTgNsilgkkaFesklsaqsvtkkcqkksrtwdgkkinViDTPglfdlsvs.adkiskeivrclllseegiha 86 
                                   G   +GkS+   s+   k    +      tk++    ++   ++i+ iDTPg++d + s  ++i+k+ +  + +  eg  +
  gi|13541916|ref|NP_111604.1| 171 GMPNVGKSSLLASLTTAKPKIAS--YPFTTKNVIIGYNESGSERIQFIDTPGILDRDFSeMNEIEKNAILAIRFI-EGKII 248
                                   56666666666666444332111..2344555556666777789**********998643777888888766665.56889 PP

                                   EEEEEETT.B-SHHHHH.HHHHHHHH CS
                          AIG1  87 lllvlslg.rfteedek.alktlkel 110
                                   +l++ s++  +t+e ++ + +++k+ 
  gi|13541916|ref|NP_111604.1| 249 FLFDYSTEsLYTREQQEhLYEQIKNN 274
                                   9*****99777766554145667665 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   5.3e-05     0.095      71     122 ..     136     187 ..      74     227 .. 0.80
   2 ?   -1.4   0.0       1.1     2e+03      36      62 ..     264     292 ..     246     308 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.3e-05
                                   HHHHTTSEEEE--TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT CS
                   RsgA_GTPase  71 elealgyevllvsaktkegleelkellkd.ktsvlvGqSGvGKStLinallpe 122
                                    +e+l+ ++l++    ++ +++l e+ +d kt +++G   vGKS+L+ +l+  
  gi|13541916|ref|NP_111604.1| 136 LIEDLNETLLFLGRC-RDYIRKLPEVRTDlKTYIIAGMPNVGKSSLLASLTTA 187
                                   556666666666443.67889999999999******************99875 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.1
                                   HHHHHHHHHTT-EEEE..EEE-GGG--HH CS
                   RsgA_GTPase  36 drfLvlaeekgiepvi..vlnKiDlleee 62 
                                   +  L +  +++i+p i  v +K+D+ +e+
  gi|13541916|ref|NP_111604.1| 264 QEHLYEQIKNNINPNIirVQTKLDISTEK 292
                                   44455555555555552234555555544 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.8   0.00031      0.56       5      72 ..     171     236 ..     168     298 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00031
                                   EBTTTTHHHHHHHHHTS--S---SSS---S-EEEEECCT---CCS...SSEEEE....T-EB--CHHHHHHH CS
                     Dynamin_N   5 GsqSsGKSSvlnaLlgedilprgpnptTrrplelqlgeeeeaseravkeelkek....ekkledfsevreei 72 
                                   G+ + GKSS+l +L+ ++   + + p T + +++ ++e+ +     +++++ +      +++++++e++++ 
  gi|13541916|ref|NP_111604.1| 171 GMPNVGKSSLLASLTTAK-PKIASYPFTTKNVIIGYNESGS-----ERIQFIDTpgilDRDFSEMNEIEKNA 236
                                   777889999999999999.6678888888888888888766.....45555555544455555555555543 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.1   0.00027      0.48       3     120 ..     168     292 ..     166     307 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00027
                                   EEEESTTSSHHHHHHHHHHSSCSSSCTTTSSEEEEEEEEEET.TEEEEEEEEEETT..SGGGHHHHH.........HHHTT CS
                           Ras   3 vlvGdsavGKtslllrfvkdkFkeeyesTigvdfytkeievd.gkevkleiwDTAG..qeefkslre.........lyyrd 71 
                                   ++ G  +vGK+sll + ++ k k  + +     + +  i ++ + + +++  DT G    +f++++e          ++++
  gi|13541916|ref|NP_111604.1| 168 IIAGMPNVGKSSLLASLTTAKPKIASYPFT-TKNVI--IGYNeSGSERIQFIDTPGilDRDFSEMNEieknailaiRFIEG 245
                                   788999***********9998776555544.22222..2222244556788999995546677776522121111133344 PP

                                   ESEEEEEEETTBHHHHHTHHHHHHHHHHHSTTTSEEEEEEETTTGGGG- CS
                           Ras  72 aegillvyditsresfenvkkwveeikrvaeenvpivLvGnKvDleekr 120
                                      +l  y+ +s  + e+ ++++e+ik+  +   +i+ v +K D+++++
  gi|13541916|ref|NP_111604.1| 246 KIIFLFDYSTESLYTREQQEHLYEQIKNNIN--PNIIRVQTKLDISTEK 292
                                   4444455666666666777799999999998..4899999999998743 PP

>> ING  Inhibitor of growth proteins N-terminal histone-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.1      0.45   8.1e+02       7      26 ..      34      53 ..      31     113 .. 0.77
   2 ?   10.9   0.2   0.00031      0.55      13      87 ..     219     296 ..     215     301 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.45
                                  TSGGGHHHHHHHHHHHHHHH CS
                           ING  7 dsvenLPlelqrnltelrei 26
                                  d ve + +e+q++++ +  i
  gi|13541916|ref|NP_111604.1| 34 DKVERIKKEVQDRISAIESI 53
                                  78888888888888888776 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00031
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH...TS..S-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           ING  13 PlelqrnltelreiDakvqellkeidskiekfl...kngslqknekeeelsriqeelkeaqelldeKiqlaqqaldlv 87 
                                   P  l r ++e+ ei++    +++ i+ ki  ++   +++  + +++e  +++i+++++  +   + K+ ++++ ++ +
  gi|13541916|ref|NP_111604.1| 219 PGILDRDFSEMNEIEKNAILAIRFIEGKIIFLFdysTESLYTREQQEHLYEQIKNNINPNIIRVQTKLDISTEKVENI 296
                                   67799************************9888996666666666666666999999999999999999988877776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       892  (0.0497518); expected 358.6 (0.02)
Passed bias filter:                      627  (0.0349713); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.67u 0.30s 00:00:00.97 Elapsed: 00:00:00.50
# Mc/sec: 1945.57
//
Query:       gi|13541917|ref|NP_111605.1|  [L=548]
Description: glutamyl-tRNA synthetase [Thermoplasma volcanium GSS1]
Scores for complete 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  223.2   0.0    4.7e-66  222.8   0.0    1.1  1  tRNA-synt_1c    tRNA synthetases class I (E and Q), catalytic
    9.4e-20   71.2   0.0    2.3e-19   69.9   0.0    1.7  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 !  222.8   0.0   5.3e-70   4.7e-66       2     309 ..      96     395 ..      95     400 .. 0.94

  Alignments for each domain:
  == domain 1  score: 222.8 bits;  conditional E-value: 5.3e-70
                                   -EEEE---SSSS-BHHHHHHHHHHHHHHHHTT-EEEEEE--SSCCC--HHHHHHHHHHHHHTT---SSEEEEGGGGHHHHH CS
                  tRNA-synt_1c   2 VrtRfaPePtGyLHiGhakaallnylfAknnnGkfilRieDTdperekeeaeesiledlkwlgikwdekptyqsdrfdelk 82 
                                   V+ R aP+P+G LHiGh + a+ln  + k+++G++ilRieDT+p+  ++ea + i edl+wlg++   k + qs+rfd ++
  gi|13541917|ref|NP_111605.1|  96 VVMRLAPSPSGPLHIGHTRMAILNDEYVKRYGGDLILRIEDTNPTNIDPEAYAMIPEDLEWLGVNV-TKTVIQSERFDLYY 175
                                   899***************************************************************.89999********* PP

                                   HHHHHHHHTTSEEEE-STHHHHHHHHCCSSHSS-TTTTS-HHHHHHHHHHHHHTTHSTTTS-EEEESSBTTSS.GGGSSTE CS
                  tRNA-synt_1c  83 kyaeeLikkGkAYvcectkeeleeereeqeklgskerdrydeenlklfeeemkkgkaegekavvRlkideess.vefrDlv 162
                                   ++a++Li++G+ Y c c  ee ++++ +   + +k rd++ e nl lf e+m +g+ + ++av  +k d +++   +rD +
  gi|13541917|ref|NP_111605.1| 176 SVAKKLIENGHLYICTCDREEFKRKKLA--SIPCKDRDNPPETNLYLF-EKMLDGEIKAGAAVAVMKTDLNHPnPSVRDWI 253
                                   ***********************99977..89999*************.9***********************9******* PP

                                   EEEEEESGGGSBTTTBTSTSEEE-HHHHHHHHHHHTT-SEEEEEGGGGCCHHHHHHHHHHTT-S.-EEEEEE--EEETTSB CS
                  tRNA-synt_1c 163 rgriklepqeihdlvivksdiyPtYdfavvidDaleeithvlrteefldntpkyiwllealglevppfiheylrlnlekkk 243
                                   + ri  ++   h+++++k+++ P+  f v++dD+  ++thvlr+++ l+nt+k+  ++e+ g++ +p+++ y ++ + ++ 
  gi|13541917|ref|NP_111605.1| 254 AFRIIDAK---HPRTGDKYRVFPMMSFSVAVDDHYLGLTHVLRGKDQLTNTEKQRYVFEYNGWN-KPYYYHYGMIRFPGTR 330
                                   *****999...*****************************************************.8888888888888888 PP

                                   -SHHHHHHHHHTTSSSSTT-TTSCBHHHHHHCTB-HHHHHHHHHHHCCCSSS.EEEEHHHHHHHHH CS
                  tRNA-synt_1c 244 lSKRklsllvdekqvkewddlreallnflrrlGwtpekerelftreeliksfdlnresksleafdr 309
                                   l    ++  ++  q+++w d r+ ++++++r+G++pe  r    + +l +++    +++ +++ +r
  gi|13541917|ref|NP_111605.1| 331 LKTSLMKKGIQAGQYDGWSDVRLGTVRAMARRGYQPETFRRYWINSGLREID-AVFSWEIFNSLNR 395
                                   766666666779**************************99999999998888.6666666666655 PP

>> tRNA-synt_1c_C  tRNA synthetases class I (E and Q), anti-codon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.9   0.0   2.6e-23   2.3e-19       1     172 [.     402     535 ..     402     537 .. 0.90

  Alignments for each domain:
  == domain 1  score: 69.9 bits;  conditional E-value: 2.6e-23
                tRNA-synt_1c_C   1 ApRymaVldpvkvtienlpegkeeelevplhpknpelgtrkvpfskeiyiereDakrlkpgeevrLkelynikveevekde 81 
                                   A R+ + +dpv++++e+    +  ++++p+hp++pe g rk+++++++yi++ Da+++++ge++rLk+l+ +  +      
  gi|13541917|ref|NP_111605.1| 402 AYRFSFTKDPVEIKMEGS---NGLTARLPYHPSHPEYGVRKYEIGDTVYISKGDADKIADGERFRLKDLCYVVRKGD---- 475
                                   78**************44...579*********************************************99999776.... PP

                tRNA-synt_1c_C  82 sgevtelkleydgesleearkkkgiihWvsaeeaveaevrlYdrLfkeeededfllnpdslkvleeglaepalanlkkgdi 162
                                          ++ +dg+++   ++k++ii+W++  ++ e+                ++l+pd++  +++gl+epa + ++   i
  gi|13541917|ref|NP_111605.1| 476 -------RFLFDGTEM---KEKTKIINWCP-PNSREF----------------QVLKPDGS--IDKGLIEPASKGYR--GI 525
                                   .......488999888...45666******.588999................99*****9..59*******99965..9* PP

                tRNA-synt_1c_C 163 vQfeRiGyfr 172
                                    Q+eR+Gy++
  gi|13541917|ref|NP_111605.1| 526 SQLERYGYVN 535
                                   ********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (548 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       464  (0.0258799); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.46
# Mc/sec: 3547.09
//
Query:       gi|13541918|ref|NP_111606.1|  [L=84]
Description: hypothetical protein TVN1087 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.5e-15   55.8   1.0    3.8e-15   55.7   1.0    1.0  1  PRC       PRC-barrel domain
  ------ inclusion threshold ------
      0.082   12.9   0.2      0.098   12.7   0.2    1.1  1  DUF5317   Family of unknown function (DUF5317)


Domain annotation for each model (and alignments):
>> PRC  PRC-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.7   1.0   4.2e-19   3.8e-15       3      78 ..       6      81 ..       4      82 .. 0.93

  Alignments for each domain:
  == domain 1  score: 55.7 bits;  conditional E-value: 4.2e-19
                                  ECCS---TT-EEEETTSSEEEEEEEEEEETTTTEEEEEEEEETTT.......-EEEEEGG.CEECCCTEEEETTS-GG CS
                           PRC  3 efrasdliGkeVytedGeklGkVkDvvidekegrvralvvsvggflgi..gekevliPfdlavkigkdriivdapkel 78
                                   + + +l+Gk Vyt++G  +G V+Dv++d++++ v++l +++ +  ++  +++ + iP++  v++++d+ii+++  +l
  gi|13541918|ref|NP_111606.1|  6 AYTIENLRGKYVYTNKGIFVGQVSDVILDFDNNVVHGLFIAKTNE-KLvkDGDPISIPYN-YVRSIGDIIILKSFPDL 81
                                  67899*********************************9999987.6678**********.************98876 PP

>> DUF5317  Family of unknown function (DUF5317)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.2   1.1e-05     0.098     103     141 ..      38      74 ..      23      77 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.1e-05
                       DUF5317 103 sgkhtlltestklkfLgDiiplpkpyplkqviSiGDili 141
                                      h+l+ ++t  k+  D  p+   +p+++v SiGDi+i
  gi|13541918|ref|NP_111606.1|  38 NVVHGLFIAKTNEKLVKDGDPI--SIPYNYVRSIGDIII 74 
                                   4678888888888888888888..66889999******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (84 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       266  (0.0148363); expected 358.6 (0.02)
Passed bias filter:                      225  (0.0125495); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 530.46
//
Query:       gi|13541919|ref|NP_111607.1|  [L=202]
Description: GMP synthase subunit A [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.5e-37  128.0   0.0      4e-37  127.8   0.0    1.0  1  GATase         Glutamine amidotransferase class-I
    2.1e-10   40.7   1.3      8e-08   32.3   0.3    2.7  2  Peptidase_C26  Peptidase C26
     0.0016   18.4   0.1     0.0067   16.3   0.1    1.9  1  SNO            SNO glutamine amidotransferase family
  ------ inclusion threshold ------
      0.029   14.0   0.0      0.051   13.2   0.0    1.4  1  GATase_3       CobB/CobQ-like glutamine amidotransferase doma
       0.06   13.1   0.0        0.1   12.4   0.0    1.5  1  DJ-1_PfpI      DJ-1/PfpI family


Domain annotation for each model (and alignments):
>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.8   0.0   1.1e-40     4e-37       2     187 ..       7     185 ..       6     188 .. 0.92

  Alignments for each domain:
  == domain 1  score: 127.8 bits;  conditional E-value: 1.1e-40
                                   EEESSTSTHHHHHHHHHHTT-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTT..TTTHHHHHHHHCTSTS-EEEETHH CS
                        GATase   2 liDnydsvtenlvhalvelgvkvevvpidasaeeilellknpdgilvsgGpgspg..vegkieaikearenkiPiLGICLG 80 
                                   ++Dn+ + t+   + l+elgv++e+vp+d +  +    l++ dg+++sgG  +    +++  ++ +++ +++ P++GIC G
  gi|13541919|ref|NP_111607.1|   7 VVDNGGQWTHREWRVLRELGVETEIVPNDIESRK----LDGLDGLVLSGGAPNIDeeMDKLGSIGEYIEDHDYPVFGICVG 83 
                                   79***************************75555....579*********88877767677777777777*********** PP

                                   HHHHHHHTTTEEEEEECEEEEEEEEEEEETTTCGGTTTTSEEEEEEEEEEEEESGCHHHTTEEEEEEEETTEEEEEEEEET CS
                        GATase  81 mQllaiefgrkvvkekekehhggtmrlgddetallyglknevierhrHryevnpkelepaglevtakseddeelmeiiekk 161
                                    Q +a+ +g++vvk+k  ++ g+t    ++++++l gl++ +i++ +H++e+++   + ++++ ta se+ +e+ ++ +k+
  gi|13541919|ref|NP_111607.1|  84 AQFIALHYGAQVVKAK-HPEFGKTLVKISEPANVLAGLPENIIAWENHNDEIKN---LTSDFVLTASSET-CEVQAFYHKH 159
                                   ****************.9999***999999************************...*********9966.79******** PP

                                   TTEEEESSBTTSTTSTTHHHHHHHHH CS
                        GATase 162 npfvgvQFHPEststpegpellfnfl 187
                                   +p+++vQFHPE+ +t+ g e+++nf+
  gi|13541919|ref|NP_111607.1| 160 KPLYAVQFHPEVEHTQFGREIFKNFI 185
                                   ***********************995 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.3   0.0    0.0021       7.4      53      73 ..      38      59 ..      27      65 .. 0.83
   2 !   32.3   0.3   2.2e-11     8e-08     103     216 .]      72     170 ..      65     170 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0021
                 Peptidase_C26 53 kaildkldgllltGgq.dvePs 73
                                  ++ ld ldgl+l+Gg+ +++ +
  gi|13541919|ref|NP_111607.1| 38 SRKLDGLDGLVLSGGApNIDEE 59
                                  567999*********9999865 PP

  == domain 2  score: 32.3 bits;  conditional E-value: 2.2e-11
                 Peptidase_C26 103 ergvPilgiCrGlqllnvalGGtlyqdieeqsgltdhreheqsaashavkve.kgsllaellgseeievnslHhqaikela 182
                                   +++ P++giC G q+++  +G +++++            h  ++ +  vk+  +  +la l +  +i     H+  ik+l 
  gi|13541919|ref|NP_111607.1|  72 DHDYPVFGICVGAQFIALHYGAQVVKAK-----------HP-EFGKTLVKISePANVLAGLPE--NIIAWENHNDEIKNLT 138
                                   6789************777775554433...........33.344667777637788888887..6666677********* PP

                 Peptidase_C26 183 eelrveAvaeDgviEaieseeakafvlgvQwHPE 216
                                   +++  +A +e   + a+ +++  +++++vQ+HPE
  gi|13541919|ref|NP_111607.1| 139 SDFVLTASSETCEVQAFYHKH--KPLYAVQFHPE 170
                                   **********99999999988..57********9 PP

>> SNO  SNO glutamine amidotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   1.9e-06    0.0067      28     171 ..      38     171 ..      16     190 .. 0.67

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.9e-06
                                   GGGGCC-SEEEE-SS-HHHHHHHHHHTT-HHHHHHHHHTT.--EEEETHHHHHHCCEETTBSS-SS--CCEEEETTTT-SC CS
                           SNO  28 kedlaevdaliiPGGestamskliertglyedllefvknsekvvlGtCaGlillskelenelvktlellkvkvkrnafGrq 108
                                     +l+++d+l++ GG    +   +++ g   ++ e++++ + +v+G C G  +++ + + + vk         k   fG+ 
  gi|13541919|ref|NP_111607.1|  38 SRKLDGLDGLVLSGGA-PNIDEEMDKLG---SIGEYIEDHDYPVFGICVGAQFIALHYGAQVVK--------AKHPEFGKT 106
                                   46899*********96.57888899999...99******************9999887776555........566666665 PP

                                   .CGEEEEEEEETTTCSEEEEEESS--EEEEE-.TTTCEEEEECTT.EEEEEEETTEEEESS-GGG CS
                           SNO 109 .vdsfekeldfknliekftavfiraPvieeilddeavkvlyeldg.eivvakqkkilatsfhPel 171
                                    v+ +e    + +l e++ a       i+++ +d + +  +e+   +    k k + a+ fhPe+
  gi|13541919|ref|NP_111607.1| 107 lVKISEPANVLAGLPENIIAWENHNDEIKNLTSDFVLTASSETCEvQAFYHKHKPLYAVQFHPEV 171
                                   24444555555666666666666666666666554444444443123333344456666666665 PP

>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.4e-05     0.051      16      89 ..      19      88 ..       4     103 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.4e-05
                      GATase_3 16 ldpLeaepevrvrfvp..lkdeslgedadlvilpGgkdtiqdlallresgldeaikeaaeaggpvlgiCGGlqmLG 89
                                   ++L++ + v+ ++vp  ++ ++l + +d ++l Gg + i+  ++++  ++ e i+++   + pv+giC G q+  
  gi|13541919|ref|NP_111607.1| 19 WRVLRELG-VETEIVPndIESRKL-DGLDGLVLSGGAPNID-EEMDKLGSIGEYIEDH---DYPVFGICVGAQFIA 88
                                  56676655.666666611344555.56***********995.6788888888888885...78*********9875 PP

>> DJ-1_PfpI  DJ-1/PfpI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   2.9e-05       0.1      58     110 ..      40      90 ..       6     109 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.9e-05
                                   TCCG-SEEEE--BHHHHHHHHTSHHHHHHHHHHHHTT-EEEEETTTHHHHHHT CS
                     DJ-1_PfpI  58 kaaeyDalvlpGGragperlrenekvvelvkefaekgklvaaICagpqlLaaa 110
                                   k +  D lvl GG  + +  +e +k++++     + + +v+ IC g+q+ a +
  gi|13541919|ref|NP_111607.1|  40 KLDGLDGLVLSGGAPNID--EEMDKLGSIGEYIEDHDYPVFGICVGAQFIALH 90 
                                   5567899******88544..44459**********************998755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 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:                        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: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.53
# Mc/sec: 1155.46
//
Query:       gi|13541920|ref|NP_111608.1|  [L=313]
Description: transcription initiation factor IIB [Thermoplasma volcanium GSS1]
Scores for complete 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-34  116.5   3.5    1.8e-16   60.0   0.2    2.4  2  TFIIB            Transcription factor TFIIB repeat
    8.3e-19   66.8   0.4    1.5e-18   66.1   0.4    1.4  1  TF_Zn_Ribbon     TFIIB zinc-binding
    1.4e-05   24.5   0.1     0.0019   17.7   0.1    3.7  4  Sigma70_r4       Sigma-70, region 4
    0.00027   21.0   0.0      0.039   14.0   0.0    2.3  2  Cyclin_C         Cyclin, C-terminal domain
    0.00055   19.7   0.0       0.46   10.2   0.0    2.2  2  Cyclin_N         Cyclin, N-terminal domain
     0.0022   18.0   0.0     0.0055   16.7   0.0    1.6  2  RB_B             Retinoblastoma-associated protein B domain
  ------ inclusion threshold ------
      0.015   15.0   4.8      0.018   14.7   0.3    3.1  4  Sigma70_r4_2     Sigma-70, region 4
      0.028   14.2   1.6      0.039   13.7   0.1    2.0  2  A2L_zn_ribbon    A2L zinc ribbon domain
       0.04   13.9   1.4       0.79    9.7   0.1    2.8  3  HTH_36           Helix-turn-helix domain
      0.042   13.8   0.9        2.6    8.0   0.1    2.4  2  zf-trcl          Probable zinc-ribbon domain
      0.056   13.4   1.0       0.12   12.3   1.0    1.6  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
      0.069   13.3   3.4       0.68   10.1   0.8    2.4  2  Zn-ribbon_8      Zinc ribbon domain
      0.083   12.8   0.3        4.6    7.2   0.0    3.0  3  TrmB             Sugar-specific transcriptional regulator Trm
       0.09   13.2   1.2       0.15   12.5   0.3    1.8  2  Lar_restr_allev  Restriction alleviation protein Lar
       0.14   12.2   0.1          2    8.5   0.0    2.3  2  HRDC             HRDC domain
       0.17   11.6   0.2       0.33   10.7   0.2    1.4  1  Ribosomal_S27e   Ribosomal protein S27
       0.36   10.7   2.7        1.2    9.0   0.4    2.5  2  TMIE             TMIE protein
       0.58   10.0   6.8        5.1    7.0   0.1    4.2  5  HTH_23           Homeodomain-like domain
        2.6    8.1   7.0        1.1    9.2   4.2    1.9  2  PhnA_Zn_Ribbon   PhnA Zinc-Ribbon


Domain annotation for each model (and alignments):
>> TFIIB  Transcription factor TFIIB repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.3   0.4   1.3e-18   1.2e-15       4      71 .]     135     202 ..     132     202 .. 0.96
   2 !   60.0   0.2   1.9e-19   1.8e-16       1      71 []     226     296 ..     226     296 .. 0.98

  Alignments for each domain:
  == domain 1  score: 57.3 bits;  conditional E-value: 1.3e-18
                                   HHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHHH CS
                         TFIIB   4 fadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekti 71 
                                   + ++l++p+ +++    ++++a+e++++ Grs ++i+ A++y Acrk +  rt+ ei++ ++V++k i
  gi|13541920|ref|NP_111608.1| 135 IGAKLGIPKDIKETSALIYRKAVEKNLIRGRSIESIVCASIYAACRKVNIPRTLDEIAKASEVNKKKI 202
                                   6789************************************************************9976 PP

  == domain 2  score: 60.0 bits;  conditional E-value: 1.9e-19
                                   HHHHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHHH CS
                         TFIIB   1 ikrfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekti 71 
                                   i +f+++l+L ++     + ++++a+++++ +G+ p+giaAA++yiA+ k +  rtqkei+ ++ V+e+ti
  gi|13541920|ref|NP_111608.1| 226 IAQFCNKLDLDKQAIVISEDIVRQAMSMGISSGKGPTGIAAAAIYIASVKVGKPRTQKEIARISGVTEVTI 296
                                   789*********999999***************************************************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 !   66.1   0.4   1.5e-21   1.5e-18       2      43 .]      16      57 ..      16      57 .. 0.98

  Alignments for each domain:
  == domain 1  score: 66.1 bits;  conditional E-value: 1.5e-21
                                  EETTTTCEECHEETSTTCEEESSSSBEEEECCCCCCCHHHHH CS
                  TF_Zn_Ribbon  2 kCPnCgstnlveDpergelvCtdCGlVlednsidegpewref 43
                                  +CP+C+s++l++D+e+gel+C dCG+V+ed  id gpewr+f
  gi|13541920|ref|NP_111608.1| 16 RCPECHSEHLIRDYEHGELICADCGAVIEDSFIDQGPEWRAF 57
                                  5***************************************98 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.39   3.6e+02      23      34 ..     132     143 ..     132     144 .. 0.86
   2 ?    0.0   0.0      0.66   6.2e+02      20      29 ..     185     194 ..     179     200 .. 0.86
   3 !   17.7   0.1     2e-06    0.0019      18      46 ..     277     305 ..     268     308 .. 0.86
   4 ?    1.2   0.0      0.27   2.6e+02      23      34 ..     300     311 ..     299     312 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.39
                                   HHHHHHHHTS-H CS
                    Sigma70_r4  23 leEIgerlgiSr 34 
                                   l +Ig++lgi++
  gi|13541920|ref|NP_111608.1| 132 LNDIGAKLGIPK 143
                                   578*******95 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.66
                                   T--HHHHHHH CS
                    Sigma70_r4  20 glTleEIger 29 
                                   ++Tl EI++ 
  gi|13541920|ref|NP_111608.1| 185 PRTLDEIAKA 194
                                   68******85 PP

  == domain 3  score: 17.7 bits;  conditional E-value: 2e-06
                                   TTT--HHHHHHHHTS-HHHHHHHHHHHHH CS
                    Sigma70_r4  18 geglTleEIgerlgiSrerVrqiekrAlr 46 
                                   g+++T++EI+++ g+++ ++r + k+  +
  gi|13541920|ref|NP_111608.1| 277 GKPRTQKEIARISGVTEVTIRNRYKEISK 305
                                   799********************998655 PP

  == domain 4  score: 1.2 bits;  conditional E-value: 0.27
                                   HHHHHHHHTS-H CS
                    Sigma70_r4  23 leEIgerlgiSr 34 
                                   ++EI++ l+iS 
  gi|13541920|ref|NP_111608.1| 300 YKEISKALNISI 311
                                   79********95 PP

>> Cyclin_C  Cyclin, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.025        23      49      90 ..     172     213 ..     167     241 .. 0.82
   2 !   14.0   0.0   4.1e-05     0.039      44      90 ..     261     307 ..     220     313 .] 0.84

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.025
                                   HHHHHHCCHHHHS--S-HHHHHHC---HHHHHHHHHHHHHHH CS
                      Cyclin_C  49 aaalllarstlnspewtetlehytgyskedlkpcvelilell 90 
                                    a++++a++ +n p   +++ + ++++k+++ + ++++++ l
  gi|13541920|ref|NP_111608.1| 172 CASIYAACRKVNIPRTLDEIAKASEVNKKKIGKAYRHLAKEL 213
                                   46677777777**************************99877 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 4.1e-05
                                   HHHHHHHHHHHCCHHHHS--S-HHHHHHC---HHHHHHHHHHHHHHH CS
                      Cyclin_C  44 pSliAaaalllarstlnspewtetlehytgyskedlkpcvelilell 90 
                                   p  iAaaa+++a+  +++p  ++++  ++g+++  +++ ++ i ++l
  gi|13541920|ref|NP_111608.1| 261 PTGIAAAAIYIASVKVGKPRTQKEIARISGVTEVTIRNRYKEISKAL 307
                                   5569***************************************9988 PP

>> Cyclin_N  Cyclin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.0   0.00048      0.46      32     126 ..     126     217 ..     100     218 .. 0.88
   2 !    7.5   0.0    0.0035       3.3      36     102 ..     224     289 ..     218     312 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00048
                                   HHHHHHHHHHHHHTT--TTHHHHHHHHHHHHHHHS---CCCHHHHHHHHHHHHHHHHSSS---HHHHHHHTTTSS-HHHHH CS
                      Cyclin_N  32 ailidwlvevaekfkltpetlflavnyldRflskksvpkdklqlvgatcLllAaKveeisppkledlvyitdeafteeeil 112
                                   + +++ l ++ +k+ + +++  +++ ++ + ++k+ ++ + ++ +++++++ A++  +i p +l++++ +++  +++++i 
  gi|13541920|ref|NP_111608.1| 126 SLALQLLNDIGAKLGIPKDIKETSALIYRKAVEKNLIRGRSIESIVCASIYAACRKVNI-PRTLDEIAKASE--VNKKKIG 203
                                   55677888999999999999999999*****************************9999.999999999965..999**** PP

                                   HHHHHHHHHTTT-- CS
                      Cyclin_N 113 emErliLetLnfdl 126
                                   ++ r++ ++L+ +l
  gi|13541920|ref|NP_111608.1| 204 KAYRHLAKELDLNL 217
                                   ******99999887 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0035
                                   HHHHHHHHHTT--TTHHHHHHHHHHHHHHHS---CCCHHHHHHHHHHHHH.HHHSSS---HHHHHHHT CS
                      Cyclin_N  36 dwlvevaekfkltpetlflavnyldRflskksvpkdklqlvgatcLllAa.Kveeisppkledlvyit 102
                                   +++ + ++k++l+++ ++++ +++ + +s  + + +    ++a+++++A+ Kv   +p + ++++ i+
  gi|13541920|ref|NP_111608.1| 224 SYIAQFCNKLDLDKQAIVISEDIVRQAMSMGISSGKGPTGIAAAAIYIASvKV--GKPRTQKEIARIS 289
                                   6899*********************************************9444..3445556666554 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 !   16.7   0.0   5.9e-06    0.0055       8      96 ..     123     209 ..     117     219 .. 0.85
   2 ?   -3.2   0.0       8.8   8.3e+03      17      29 ..     226     238 ..     220     244 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 5.9e-06
                          RB_B   8 kvyklaavrlrdLcerLklsselrekiwtlfehvlveetellkdRhlDqillcavYvvakvtkeelsFkeiikaYrkqpqa 88 
                                   + ++la   l+d+ ++L + ++++e    + ++++  e++l++ R ++ i+ +++Y+ ++  +  +++ ei ka + ++++
  gi|13541920|ref|NP_111608.1| 123 RNLSLALQLLNDIGAKLGIPKDIKETSALIYRKAV--EKNLIRGRSIESIVCASIYAACRKVNIPRTLDEIAKASEVNKKK 201
                                   557889999999999***99999998766666655..678*******************9999999999999999988888 PP

                          RB_B  89 sskvyrsv 96 
                                     k yr+ 
  gi|13541920|ref|NP_111608.1| 202 IGKAYRHL 209
                                   88888775 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 8.8
                          RB_B  17 lrdLcerLklsse 29 
                                   +++ c++L+l+++
  gi|13541920|ref|NP_111608.1| 226 IAQFCNKLDLDKQ 238
                                   7889999998875 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       7.6   7.2e+03      15      29 ..     153     167 ..     152     170 .. 0.59
   2 ?   -2.7   0.0       5.2   4.9e+03      30      46 ..     189     205 ..     187     212 .. 0.65
   3 ?   14.7   0.3   1.9e-05     0.018      28      52 ..     281     305 ..     280     307 .. 0.87
   4 ?    4.6   0.1     0.028        27      29      41 ..     300     312 ..     299     313 .] 0.91

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 7.6
                                   HHHHHHHHHTS---H CS
                  Sigma70_r4_2  15 qreifllryleglsy 29 
                                   +r++++   + g s+
  gi|13541920|ref|NP_111608.1| 153 YRKAVEKNLIRGRSI 167
                                   677776655555555 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 5.2
                                   HHHHHHHT--HHHHHHH CS
                  Sigma70_r4_2  30 kEIAellgisegtVksr 46 
                                   +EIA+  +++ + + ++
  gi|13541920|ref|NP_111608.1| 189 DEIAKASEVNKKKIGKA 205
                                   68888777666655544 PP

  == domain 3  score: 14.7 bits;  conditional E-value: 1.9e-05
                                   -HHHHHHHHT--HHHHHHHHHHHHH CS
                  Sigma70_r4_2  28 sykEIAellgisegtVksrlsRArk 52 
                                   ++kEIA++ g++e+t+++r++   k
  gi|13541920|ref|NP_111608.1| 281 TQKEIARISGVTEVTIRNRYKEISK 305
                                   78*****************986655 PP

  == domain 4  score: 4.6 bits;  conditional E-value: 0.028
                                   HHHHHHHHT--HH CS
                  Sigma70_r4_2  29 ykEIAellgiseg 41 
                                   ykEI++ l+is +
  gi|13541920|ref|NP_111608.1| 300 YKEISKALNISIS 312
                                   9*********975 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   4.1e-05     0.039       4      30 ..      15      42 ..      13      44 .. 0.89
   2 ?   -2.4   0.1       4.7   4.5e+03      16      22 ..      87      93 ..      85      93 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.1e-05
                 A2L_zn_ribbon  4 kvCsvCggngiln.seqgylvCieCgas 30
                                  k C  C+++ ++   e+g+l+C +Cga+
  gi|13541920|ref|NP_111608.1| 15 KRCPECHSEHLIRdYEHGELICADCGAV 42
                                  66999*******8889**********97 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 4.7
                 A2L_zn_ribbon 16 nseqgyl 22
                                  +s+++y+
  gi|13541920|ref|NP_111608.1| 87 WSNKDYY 93
                                  99***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 ?    9.7   0.1   0.00084      0.79      26      51 ..     185     211 ..     168     212 .. 0.80
   2 ?   -3.2   0.0       9.4   8.9e+03      29      36 ..     224     231 ..     223     240 .. 0.62
   3 ?    2.3   0.1      0.17   1.6e+02      27      48 ..     281     302 ..     269     308 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00084
                        HTH_36  26 p.sqetlakrlglsknTvsraikeLeq 51 
                                   p + + +ak+++++k+++ +a + L++
  gi|13541920|ref|NP_111608.1| 185 PrTLDEIAKASEVNKKKIGKAYRHLAK 211
                                   556899****************99986 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 9.4
                        HTH_36  29 etlakrlg 36 
                                   +++a+ ++
  gi|13541920|ref|NP_111608.1| 224 SYIAQFCN 231
                                   56666664 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.17
                        HTH_36  27 sqetlakrlglsknTvsraike 48 
                                   +q+ +a+ +g+ + T+++  ke
  gi|13541920|ref|NP_111608.1| 281 TQKEIARISGVTEVTIRNRYKE 302
                                   799************9987765 PP

>> zf-trcl  Probable zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.1    0.0028       2.6      31      42 ..      12      23 ..       3      27 .. 0.76
   2 ?    3.9   0.1     0.052        49       4      12 ..      33      41 ..      30      47 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0028
                       zf-trcl 31 nepkRCkaCRka 42
                                    pkRC++C ++
  gi|13541920|ref|NP_111608.1| 12 EAPKRCPECHSE 23
                                  469******876 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.052
                       zf-trcl  4 tltCkdCga 12
                                  +l+C+dCga
  gi|13541920|ref|NP_111608.1| 33 ELICADCGA 41
                                  799****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 ?   12.3   1.0   0.00013      0.12      20      45 ..      16      41 ..      11      42 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00013
                 Zn_Tnp_IS1595 20 vCPhCgsrkayr.iktrglfqCkeCrk 45
                                  +CP C+s++++r +++ g + C++C++
  gi|13541920|ref|NP_111608.1| 16 RCPECHSEHLIRdYEH-GELICADCGA 41
                                  6*******66551666.********85 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.8   0.00072      0.68      21      38 ..       7      27 ..       4      29 .. 0.73
   2 ?    3.4   0.1     0.086        82       7      16 ..      35      44 ..      26      63 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00072
                   Zn-ribbon_8 21 is.daplta.CPeCgs.evrr 38
                                  ++ +++ ++ CPeC+s ++ r
  gi|13541920|ref|NP_111608.1|  7 MAiESEAPKrCPECHSeHLIR 27
                                  5556777777*****977655 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.086
                   Zn-ribbon_8  7 rCeeCghefe 16
                                   C +Cg + e
  gi|13541920|ref|NP_111608.1| 35 ICADCGAVIE 44
                                  4999999988 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0    0.0049       4.6      22      48 ..     185     211 ..     174     223 .. 0.91
   2 ?    2.0   0.0      0.21     2e+02      14      39 ..     270     296 ..     266     299 .. 0.75
   3 ?   -1.7   0.0       2.9   2.7e+03      25      37 ..     300     312 ..     297     313 .] 0.81

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0049
                                   CCHHCHHCCCTTSSCHCHHHHHHHHHH CS
                          TrmB  22 patadeiaeelgvprskvYevLrsLed 48 
                                   p t deia++++v + k+ ++ r L +
  gi|13541920|ref|NP_111608.1| 185 PRTLDEIAKASEVNKKKIGKAYRHLAK 211
                                   7899**************999888865 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.21
                                   CHHHH.HHCCCHHCHHCCCTTSSCHCH CS
                          TrmB  14 YlaLl.klgpatadeiaeelgvprskv 39 
                                   Y+a +   +p t +eia+++gv + ++
  gi|13541920|ref|NP_111608.1| 270 YIASVkVGKPRTQKEIARISGVTEVTI 296
                                   5555633468999********987666 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 2.9
                                   HCHHCCCTTSSCH CS
                          TrmB  25 adeiaeelgvprs 37 
                                    +ei+++l+++ s
  gi|13541920|ref|NP_111608.1| 300 YKEISKALNISIS 312
                                   589******9865 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 ?   12.5   0.3   0.00016      0.15       4      37 ..      15      51 ..      12      68 .. 0.69
   2 ?   -2.4   0.0       6.7   6.4e+03      28      37 ..     169     185 ..     152     206 .. 0.53

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00016
               Lar_restr_allev  4 kpCPfCggravlersqrvvaeigqcvyCadCga.........s 37
                                  k CP C ++  +   + +        +CadCga         +
  gi|13541920|ref|NP_111608.1| 15 KRCPECHSEHLIRDYEHG------ELICADCGAviedsfidqG 51
                                  78*****99876665544......58*******6444333332 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 6.7
               Lar_restr_allev  28 cvyCad....Cga...s 37 
                                    + Ca     C      
  gi|13541920|ref|NP_111608.1| 169 SIVCASiyaaCRKvniP 185
                                   56665444446654333 PP

>> HRDC  HRDC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.43     4e+02      40      60 ..     185     205 ..     182     213 .. 0.79
   2 ?    8.5   0.0    0.0021         2      39      65 ..     278     304 ..     272     307 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.43
                                   --SHHHHHTSTTT-HHHHHHH CS
                          HRDC  40 PttleeLlqiegvgkrkleky 60 
                                   P+tl+e ++ + v k+k+ k 
  gi|13541920|ref|NP_111608.1| 185 PRTLDEIAKASEVNKKKIGKA 205
                                   899999999999999998765 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0021
                                   ---SHHHHHTSTTT-HHHHHHHHHHHH CS
                          HRDC  39 lPttleeLlqiegvgkrklekygeeil 65 
                                   +P+t++e ++i+gv++  ++   +ei 
  gi|13541920|ref|NP_111608.1| 278 KPRTQKEIARISGVTEVTIRNRYKEIS 304
                                   7*******************8888875 PP

>> Ribosomal_S27e  Ribosomal protein S27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.2   0.00035      0.33       9      36 ..      16      43 ..      15      45 .. 0.95

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00035
                                  E-TTTS-EEEEESS-SS-EEESSSTCEE CS
                Ribosomal_S27e  9 kCpdCenetvvFshaatvvkCisCgkvL 36
                                  +Cp+C  e  + +  +    C  Cg v+
  gi|13541920|ref|NP_111608.1| 16 RCPECHSEHLIRDYEHGELICADCGAVI 43
                                  6************************986 PP

>> TMIE  TMIE protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.4    0.0013       1.2      31      59 ..     178     208 ..     162     218 .. 0.77
   2 ?    0.7   0.1       0.5   4.7e+02      34      45 ..     275     286 ..     264     306 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0013
                          TMIE  31 CvirfRiPRTkqeIe..adyarkklakkfre 59 
                                    + ++ iPRT  eI    + ++kk+ k +r+
  gi|13541920|ref|NP_111608.1| 178 ACRKVNIPRTLDEIAkaSEVNKKKIGKAYRH 208
                                   468999********732468899**999986 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.5
                          TMIE  34 rfRiPRTkqeIe 45 
                                   ++  PRT++eI 
  gi|13541920|ref|NP_111608.1| 275 KVGKPRTQKEIA 286
                                   5556******96 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.6      0.49   4.6e+02      29      40 ..     100     111 ..      99     123 .. 0.80
   2 ?   -3.1   0.0         8   7.6e+03      22      30 ..     134     142 ..     127     143 .. 0.80
   3 ?   -1.9   0.0       3.5   3.3e+03      16      30 ..     201     216 ..     189     218 .. 0.63
   4 ?    7.0   0.1    0.0054       5.1      19      37 ..     281     299 ..     280     302 .. 0.85
   5 ?    4.4   0.0     0.037        35      19      31 ..     299     311 ..     297     312 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.49
                        HTH_23  29 vsrrTvyrwlkr 40 
                                    +r ++yr++k+
  gi|13541920|ref|NP_111608.1| 100 KNRAQIYRVRKW 111
                                   578899999987 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 8
                        HTH_23  22 eIAreLgvs 30 
                                   +I ++Lg++
  gi|13541920|ref|NP_111608.1| 134 DIGAKLGIP 142
                                   799999997 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 3.5
                        HTH_23  16 e.GlsvreIAreLgvs 30 
                                   + G+ +r  A+eL+ +
  gi|13541920|ref|NP_111608.1| 201 KiGKAYRHLAKELDLN 216
                                   1577788888888766 PP

  == domain 4  score: 7.0 bits;  conditional E-value: 0.0054
                        HTH_23  19 svreIAreLgvsrrTvyrw 37 
                                   +++eIAr+ gv++ T+++ 
  gi|13541920|ref|NP_111608.1| 281 TQKEIARISGVTEVTIRNR 299
                                   79**************953 PP

  == domain 5  score: 4.4 bits;  conditional E-value: 0.037
                        HTH_23  19 svreIAreLgvsr 31 
                                   +++eI+++L++s 
  gi|13541920|ref|NP_111608.1| 299 RYKEISKALNISI 311
                                   79*********96 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   4.2    0.0012       1.1       4      26 ..      16      40 ..      11      44 .. 0.85
   2 ?   -2.9   0.0       7.6   7.2e+03       8      12 ..     172     176 ..     171     177 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0012
                PhnA_Zn_Ribbon  4 kCplCaSeytY..edgallvCpeCa 26
                                   Cp+C Se+     ++  l+C +C+
  gi|13541920|ref|NP_111608.1| 16 RCPECHSEHLIrdYEHGELICADCG 40
                                  6********8877677789*****8 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 7.6
                PhnA_Zn_Ribbon   8 CaSey 12 
                                   CaS+y
  gi|13541920|ref|NP_111608.1| 172 CASIY 176
                                   99998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       827  (0.0461264); expected 358.6 (0.02)
Passed bias filter:                      679  (0.0378716); expected 358.6 (0.02)
Passed Vit filter:                       109  (0.00607954); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.58u 0.32s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 1976.93
//
Query:       gi|13541921|ref|NP_111609.1|  [L=428]
Description: aspartyl-tRNA synthetase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-95  319.2   0.1    3.2e-95  318.8   0.1    1.1  1  tRNA-synt_2      tRNA synthetases class II (D, K and N)
    5.4e-12   45.5   0.1    9.4e-12   44.8   0.1    1.4  1  tRNA_anti-codon  OB-fold nucleic acid binding domain
    8.2e-07   28.7   0.1     0.0022   17.5   0.0    2.7  3  tRNA-synt_2d     tRNA synthetases class II core domain (F)
  ------ inclusion threshold ------
        0.1   12.3   0.1       0.17   11.6   0.1    1.3  1  Ku_N             Ku70/Ku80 N-terminal alpha/beta domain


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 !  318.8   0.1   7.2e-99   3.2e-95       2     313 ..     113     422 ..     112     423 .. 0.95

  Alignments for each domain:
  == domain 1  score: 318.8 bits;  conditional E-value: 7.2e-99
                                   CCHHHHTHHHHCCSHHHHHHHHHHHHHHHHHHHHHHHTT-EE----SEESS--SSSS--EEEEETTT.TEEE....-E-S- CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxx RF
                   tRNA-synt_2   2 eelrlknryldlrtekvskvlrlrstvtkavrkyleengfieietPiLsksdteegarlFkvksrekekeff....aLtqs 78 
                                    e+rl+nr++dlr+++vs+++++ s+++  +r++l+++gfie++tP ++ ++te+ga lF vk       +f    +L+qs
  gi|13541921|ref|NP_111609.1| 113 LETRLNNRFIDLRKRDVSSIFNAESSILWGIREFLHSQGFIEVHTPKIVAAATEGGADLFPVK-------YFendaYLNQS 186
                                   589***********************************************************4.......4444445**** PP

                                   SHHHHHHHHHCTHSEEEEEEEEE--S--BTTB-S-CEEEEEEEEET-SCHHHHHHHHHHHHHHHHHHHHCSCCCCCHTTTT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   tRNA-synt_2  79 pqlylellivagidrvfqiaraFRaEdsrtdrhlaEFtqieaemsfieeedimqvleelikslvkevlessakdiefvirr 159
                                   pqly+e+l+++g+++vf++++aFRaE+++t+rhl+EFt+i++emsf++++d m++le+ +ks ++++++++ kd++++  +
  gi|13541921|ref|NP_111609.1| 187 PQLYKEILMSSGFEKVFEVGPAFRAEEHNTTRHLNEFTSIDIEMSFADHNDAMRILENAVKSGIENMINENGKDLQENGIN 267
                                   *******************************************************************88887777665555 PP

                                   TSEE-SSS-EEEEHHHHHHHHHTS......-SS--HHHHHHHHHHS--SEEEEEEEBGGGSTTCBBBSTTSTTBBSEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   tRNA-synt_2 160 nskdlkkpfkrltykeaieklnei......gkdldkaderalvkkeknepvfvtdfPaelkpFyarkeeddkkltesyDll 234
                                     + ++ pf+r+tyke i+ l+++      g+d + +++r+  + + ++++f+t++P++l+pFy+  ++dd+++t+s+Dl 
  gi|13541921|ref|NP_111609.1| 268 I-SIPEIPFPRITYKECIKLLEKEglefqfGNDFSPEELRIIGR-NFKDFYFITEWPSSLRPFYTMPNRDDPTITNSFDLQ 346
                                   4.466778*************999****99999*********99.999********************************* PP

                                   ETTEEEEEEEEB--SHHHHHHHHHHCCHHSSSGGGGHHHHHHHHCT--SEEEEEEEHHHHHHHHCT-SSGGGCSSS-XX CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   tRNA-synt_2 235 ingvElvgGslRiedpeeleeklkskgldeeaeekfswylealeyGapphgGlglGldRlvmlllgsesIrdviaFPkl 313
                                   +++vE+++G++R++dp++l +++++k+l+    ++f++y++a++yG+pph+G+glGl+Rl+m++lg+++Ir++++FP+ 
  gi|13541921|ref|NP_111609.1| 347 YREVEVTSGAQRVHDPDLLLKRFNEKKLN---IDSFKFYIQAFKYGMPPHAGWGLGLERLTMIVLGLNNIRETTLFPRD 422
                                   *****************************...*********************************************96 PP

>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.8   0.1   2.1e-15   9.4e-12       1      76 []      18      94 ..      18      94 .. 0.97

  Alignments for each domain:
  == domain 1  score: 44.8 bits;  conditional E-value: 2.1e-15
                                  EEEEEEEEEEEEEEETTEEEEEEEETTEEEEEEEET.HHHHHHHTTS-TTSEEEEEEEEEEC...TTSSEEEEEEEEEEE CS
               tRNA_anti-codon  1 VtvaGrvtsisdrsggkvifidlrDgtgriqvvlfr.eeatklaenlkeGdvvrvtGrvkrr...pggelelkveeiell 76
                                  V + G++++   +  ++v+f++ rD+tg++qv++ +  +  +l+++l++++v++++G++++    + g le++ e++e+l
  gi|13541921|ref|NP_111609.1| 18 VEIYGWLQDL--KLLKNVSFLIMRDRTGTVQVTFKNtPDIVNLLKELPRESVLKISGKINKKsvsKSG-LEVSGESVEVL 94
                                  7899******..****************************************************999*.********986 PP

>> tRNA-synt_2d  tRNA synthetases class II core domain (F)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0      0.87   3.9e+03      23      43 ..     140     160 ..     133     164 .. 0.81
   2 !    8.3   0.0   0.00032       1.5     103     155 ..     201     256 ..     186     264 .. 0.82
   3 !   17.5   0.0     5e-07    0.0022     212     233 ..     394     415 ..     383     424 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.87
                                   HHHHHHHHHCTTCEESSTTSE CS
                  tRNA-synt_2d  23 leeikeiflelgfeevegpev 43 
                                   l  i+e++++ gf ev+ p++
  gi|13541921|ref|NP_111609.1| 140 LWGIREFLHSQGFIEVHTPKI 160
                                   556899999999999999887 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00032
                                   EEEEEEEEEBSST.-SSSB-SEEEEE..EEEEEETT--HHHHHHHHHHHHHHHCTS CS
                  tRNA-synt_2d 103 kiisigrvfRrda.vDathlaeFhqv..eglvvdenvsladlkgvleellkklfga 155
                                   k++ +g +fR ++    +hl eF+++  e+ ++d+n  ++ l   +++ ++++ ++
  gi|13541921|ref|NP_111609.1| 201 KVFEVGPAFRAEEhNTTRHLNEFTSIdiEMSFADHNDAMRILENAVKSGIENMINE 256
                                   899********994556699***986226788999999999999998888888665 PP

  == domain 3  score: 17.5 bits;  conditional E-value: 5e-07
                                   EEEEEEHHHHHHHHHT-SSGHH CS
                  tRNA-synt_2d 212 fafGlGveRlamlkygieDiRe 233
                                   +++GlG+eRl+m+ +g+++iRe
  gi|13541921|ref|NP_111609.1| 394 AGWGLGLERLTMIVLGLNNIRE 415
                                   68*******************7 PP

>> Ku_N  Ku70/Ku80 N-terminal alpha/beta domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   3.8e-05      0.17     152     201 ..     246     301 ..     216     315 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.8e-05
                                   H...........HHHHHHCTEEEEEEECTSSSCECCTCHHHHCHCHHHHHHHHHHHCCCSG CS
                          Ku_N 152 k...........akDlrderieldllkLkkakkfdinefykdiiklgsdevkevmlslege 201
                                               +kDl++++i++++      + +++   yk+ ikl ++e +e+++ +++ 
  gi|13541921|ref|NP_111609.1| 246 VksgienminenGKDLQENGINISIP-----EIPFPRITYKECIKLLEKEGLEFQFGNDFS 301
                                   234444444555**********5555.....55**********************999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (428 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       577  (0.0321825); expected 358.6 (0.02)
Passed bias filter:                      531  (0.0296168); 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: 0.61u 0.26s 00:00:00.87 Elapsed: 00:00:00.44
# Mc/sec: 2889.96
//
Query:       gi|13541922|ref|NP_111610.1|  [L=314]
Description: 3-hydroxyacyl-CoA dehydrogenase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-45  155.8   6.1    1.6e-43  148.7   6.1    2.1  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
    2.4e-35  121.0   0.2    5.6e-35  119.8   0.2    1.7  1  3HCDH            3-hydroxyacyl-CoA dehydrogenase, C-terminal 
    0.00033   20.9   2.6     0.0042   17.3   0.2    2.2  2  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
    0.00054   20.5   1.6     0.0015   19.1   1.6    2.0  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
    0.00089   18.7   0.7     0.0016   17.9   0.4    1.6  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
     0.0022   18.0   0.1     0.0053   16.7   0.1    1.7  1  NAD_Gly3P_dh_N   NAD-dependent glycerol-3-phosphate dehydroge
     0.0086   16.1   0.8      0.015   15.3   0.4    1.7  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
  ------ inclusion threshold ------
      0.017   14.7   0.3      0.025   14.1   0.3    1.4  1  UDPG_MGDP_dh_N   UDP-glucose/GDP-mannose dehydrogenase family
      0.033   13.8   0.7      0.092   12.4   0.7    1.8  1  ApbA             Ketopantoate reductase PanE/ApbA
      0.034   14.0   0.0      0.061   13.2   0.0    1.4  1  Rossmann-like    Rossmann-like domain
      0.094   13.0   0.4       0.24   11.6   0.1    1.9  2  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
       0.21   10.9   0.6       0.53    9.6   0.0    1.8  2  ThiF             ThiF family
       0.39   11.2   2.5       0.83   10.1   2.5    1.6  1  NAD_binding_7    Putative NAD(P)-binding


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 !  148.7   6.1   1.2e-46   1.6e-43       1     172 [.       5     204 ..       5     216 .. 0.88

  Alignments for each domain:
  == domain 1  score: 148.7 bits;  conditional E-value: 1.2e-46
                                   EEEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHH......HHHCCTTTTSS-................... CS
                       3HCDH_N   1 kvaviGaGtmGagiaavfasagleVvlvdiseealekalekiek......sleklvekgklk................... 56 
                                   kv+++GaGtmG+ ia+vfa +g++V l d + e +e+++e++++      +++    ++k+k                   
  gi|13541922|ref|NP_111610.1|   5 KVGIVGAGTMGSAIAEVFAYNGYNVILKDQTIELAERGRENAKRiiegyeKIS----NEKVKkeitkiegygiklteeqks 81 
                                   79****************************88888888888888444333222....222224555788999999988888 PP

                                   ........HHHHCCCHHCEEEES-HHHHHC-SEEEE-S-SSHHHHHHHHHHHHCCS-TTSEEEE--SSS-HHHHCCCSSSG CS
                       3HCDH_N  57 ........eeeveaalarisfttdleeavdadlviEavvEnlelKrkvfaelekiakpdailasnTSslsiselaealkrp 129
                                           +  v+++ +ri +t++ +e+ d+dl+iEa++E+ ++K+++f+el+   +++ai+asnTSslsi+e++++lk+p
  gi|13541922|ref|NP_111610.1|  82 sitkslsvNVPVKEVEERIIVTSKNDEMSDCDLIIEAAFEDQAVKNQIFRELSDF-SNNAIIASNTSSLSITEMSKNLKKP 161
                                   89998888888999999***********************************998.59*********************** PP

                                   GGEEEEEE-SSTTT--EEEEEE-TT--HHHHHHHHHHHHHTT- CS
                       3HCDH_N 130 erviglHFfnPpplmkLvEvvrgekTseetvatvvelakkigk 172
                                   e+ i++HFfnPp+l++LvEvv++  Ts+et+++v++l++ ++ 
  gi|13541922|ref|NP_111610.1| 162 ENGIIMHFFNPPYLLPLVEVVPSLFTSNETLTAVMDLLHGMKN 204
                                   *************************************998864 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 !  119.8   0.2   4.1e-38   5.6e-35       1      97 []     219     314 .]     219     314 .] 0.98

  Alignments for each domain:
  == domain 1  score: 119.8 bits;  conditional E-value: 4.1e-38
                                   TTTHHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHHHHHHHTTTHGGHH-HHHHHHH CS
                         3HCDH   1 GFvvnRvlapllneavrlveegvaspediDaamrlglGlpmGpfelldlvgldvakkilevlaeelgerayapsplleklv 81 
                                   GF+vnR+l+p++nea ++++ g+a+ +diD am++g+G+pmGpfel+d++g+dv+k++++v+++++g+++   s+l++++ 
  gi|13541922|ref|NP_111610.1| 219 GFIVNRLLIPFINEASKMLDYGIATEKDIDIAMKKGAGFPMGPFELADMIGIDVVKDVMNVFEKTYGDQYK-TSQLIRRMS 298
                                   9*******************************************************************955.59******* PP

                                   HTT--BGGGTBSSSBC CS
                         3HCDH  82 eagrlgrktgkgfyky 97 
                                   eag+lgrkt++gfyky
  gi|13541922|ref|NP_111610.1| 299 EAGKLGRKTKEGFYKY 314
                                   ***************9 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.2     3e-06    0.0042       1      45 [.       5      52 ..       5      68 .. 0.80
   2 ?    3.7   0.2     0.045        62      43     105 ..      99     159 ..      69     173 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3e-06
                                  EEEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT...EEE CS
                 NAD_binding_2  1 kigfiGlGvMGsnmalnllkagykvavynrtkekveelvaeg...aka 45
                                  k+g++G G+MGs +a+ ++ +gy+v++ + t e +e+  ++    +++
  gi|13541922|ref|NP_111610.1|  5 KVGIVGAGTMGSAIAEVFAYNGYNVILKDQTIELAERGRENAkriIEG 52
                                  69***************************9998888777766333333 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.045
                                   EEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHSHCCC--TT-EEEE-S---HHHHHHHHHHHH CS
                 NAD_binding_2  43 akaaesieelvasldvvitmvkagkavdeviegllealkkgdilidgstsspedtrelakelk 105
                                     +++s ++ ++++d++i    +++av++ i++ l+ +++++i+     +s  + +e++k+lk
  gi|13541922|ref|NP_111610.1|  99 RIIVTSKNDEMSDCDLIIEAAFEDQAVKNQIFRELSDFSNNAIIASN--TSSLSITEMSKNLK 159
                                   45788889999*********************977778777766543..33334444455444 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   1.6   1.1e-06    0.0015       1      48 [.       5      48 ..       5     142 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.1e-06
                                  EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC- CS
                 F420_oxidored  1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgv 48
                                  k+gi+GaG mg+a+a+ ++ +g   ++++   +++ e ae  +e++++
  gi|13541922|ref|NP_111610.1|  5 KVGIVGAGTMGSAIAEVFAYNG---YNVI-LKDQTIELAERGRENAKR 48
                                  79********************...6666.335555555554444442 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 !   17.9   0.4   1.1e-06    0.0016      37      72 ..       4      39 ..       1      61 [. 0.84

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.1e-06
                                  SEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHH CS
                  2-Hacid_dh_C 37 ktvGiiGlGrIGqavakrlkafgmkviaydrskkke 72
                                  k+vGi+G+G +G+a+a++++  g +vi  d++ +  
  gi|13541922|ref|NP_111610.1|  4 KKVGIVGAGTMGSAIAEVFAYNGYNVILKDQTIELA 39
                                  89**************************99986644 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 !   16.7   0.1   3.8e-06    0.0053       1      35 [.       5      39 ..       5      68 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 3.8e-06
                                  -EEEE--SHHHHHHHHHHHTTT--EEEE-S-HHHH CS
                NAD_Gly3P_dh_N  1 kiavlGaGswGtalAkvlaenghevrlwvreeeli 35
                                  k++++GaG  G+a+A v+a ng +v l  +  el+
  gi|13541922|ref|NP_111610.1|  5 KVGIVGAGTMGSAIAEVFAYNGYNVILKDQTIELA 39
                                  799*******************9998755444443 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.4   1.1e-05     0.015      12      56 ..       3      53 ..       1     102 [. 0.73

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.1e-05
                                  T-EEEEES-SHHHHHHHHHHHCCT-CEEE.......EEESSHHHHHHHHHHH CS
                  Shikimate_DH 12 ekkvlliGaGemaelvakhLlakgvkkvv.......vaNRtlerakelaeel 56
                                   kkv ++GaG m++ +a+ ++ +g++ v+        a R +e+ak++ e +
  gi|13541922|ref|NP_111610.1|  3 IKKVGIVGAGTMGSAIAEVFAYNGYN-VIlkdqtieLAERGRENAKRIIEGY 53
                                  589********************998.4401111114555555555555444 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 ?   14.1   0.3   1.8e-05     0.025       2      91 ..       5      99 ..       4     162 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.8e-05
                                  EEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHHCTTS-SS...--TTHHHHHHHHCHTTTEEEES-HHHHHHC-SEEE CS
                UDPG_MGDP_dh_N  2 kisviGlGYvGlvtaavlaeighevigvDideekvdklnsgkipi...yepgLeelvkkavesgrlsfttdvekaveeadvif 81
                                  k+ ++G+G +G   a v+a  g +vi+ D   e  +  +++   i   ye+  +e vkk++ ++      +++++ +++    
  gi|13541922|ref|NP_111610.1|  5 KVGIVGAGTMGSAIAEVFAYNGYNVILKDQTIELAERGRENAKRIiegYEKISNEKVKKEI-TKIEGYGIKLTEEQKSSITKS 86
                                  89***************************98777776666665551115555556666666.333334456666666666678 PP

                                  E-----B-T...T CS
                UDPG_MGDP_dh_N 82 iaVgTPskk...k 91
                                  ++V+ P+k+   +
  gi|13541922|ref|NP_111610.1| 87 LSVNVPVKEveeR 99
                                  9999999984440 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.7   6.7e-05     0.092       1      47 [.       6      53 ..       6     118 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.7e-05
                                  EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHHHHHHCEEEEETT CS
                          ApbA  1 iailGaGaiGsllaakLakagadvtlilrsr.rlealkknGlrltseg 47
                                  + i+GaG +Gs +a   a +g++v+l +++   +e+ ++n  r+ +  
  gi|13541922|ref|NP_111610.1|  6 VGIVGAGTMGSAIAEVFAYNGYNVILKDQTIeLAERGRENAKRIIEGY 53
                                  57************************9999977777666666654443 PP

>> Rossmann-like  Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   4.4e-05     0.061      12      65 ..       5      61 ..       2      68 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.4e-05
                 Rossmann-like 12 svGiisaGrvGtalgaaleraghvvv...gisaisaasreraerrlPdvpvlevedv 65
                                  +vGi++aG +G+a+++ ++  g+ v+       +++  re a+r + + + ++ e+v
  gi|13541922|ref|NP_111610.1|  5 KVGIVGAGTMGSAIAEVFAYNGYNVIlkdQTIELAERGRENAKRIIEGYEKISNEKV 61
                                  7******************99998762212333455566778887777777766555 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 ?   11.6   0.1   0.00018      0.24       1      56 [.       6      63 ..       6      91 .. 0.80
   2 ?   -2.3   0.0       3.5   4.8e+03      22      36 ..      95     109 ..      82     140 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00018
                                  EEEE--SHHHHHHHHHHHCTCCT-G....EEEEEESSHHHHHHHHCHHTTTCEEEEE--T CS
               Sacchrp_dh_NADP  1 vliiGaGsvGqavaellarhfdvda....eitvadrskeklealaakalgvrfeaialda 56
                                  v i+GaG +G+a+ae+ a ++        +i +a+r +e+++++++    ++++++++ +
  gi|13541922|ref|NP_111610.1|  6 VGIVGAGTMGSAIAEVFAYNGYNVIlkdqTIELAERGRENAKRIIE--GYEKISNEKVKK 63
                                  689***************9985422456788899999999999987..566666666655 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 3.5
                                   CT-GEEEEEESSHHH CS
               Sacchrp_dh_NADP  22 dvdaeitvadrskek 36 
                                   +v+++i+v ++++e 
  gi|13541922|ref|NP_111610.1|  95 EVEERIIVTSKNDEM 109
                                   455588888888775 PP

>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00038      0.53      19      42 ..       4      27 ..       2      40 .. 0.88
   2 ?   -1.6   0.1      0.98   1.4e+03      84     116 ..      87     118 ..      81     132 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00038
                                  SEEEEE--SHHHHHHHHHHHHHTT CS
                                  xxxxxxxxxxxxxxxxxxxxxxxx RF
                          ThiF 19 skvllvGaGglGsellknLalsGv 42
                                  +kv +vGaG+ Gs +++ +a  G 
  gi|13541922|ref|NP_111610.1|  4 KKVGIVGAGTMGSAIAEVFAYNGY 27
                                  5899****************9996 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.98
                                   T-TTSEEEEEES-CCGCCS-HHHHTT-SEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ThiF  84 inpdveveavteritdetvleellesvDlVvda 116
                                   +  +v v+ v+eri  ++  ++ ++++Dl++ a
  gi|13541922|ref|NP_111610.1|  87 LSVNVPVKEVEERIIVTS-KNDEMSDCDLIIEA 118
                                   556788999999997755.56889999999987 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   2.5    0.0006      0.83       8      82 ..       4     133 ..       1     150 [. 0.62

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0006
                 NAD_binding_7   8 kkvlvvGgGevAarkvrklleagakvtvvapev......keele..............elvklaeee.............. 54 
                                   kkv +vG+G+++   ++ ++ +g +v++ ++++          e              e       +              
  gi|13541922|ref|NP_111610.1|   4 KKVGIVGAGTMGSAIAEVFAYNGYNVILKDQTIelaergR---EnakriiegyekisnE-------Kvkkeitkiegygik 74 
                                   899*************************888864444431...0333444444333331.......333333334444444 PP

                 NAD_binding_7  55 ............................l..ekdlegadlvi.aatddrelneriaeaa 82 
                                                                  ++++++ dl+i aa +d++++++i ++ 
  gi|13541922|ref|NP_111610.1|  75 lteeqkssitkslsvnvpvkeveeriivTskNDEMSDCDLIIeAAFEDQAVKNQIFREL 133
                                   44444555555555555555555554431223448888866648899999999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1102  (0.0614647); expected 358.6 (0.02)
Passed bias filter:                      609  (0.0339673); 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):              13  [number of targets reported over threshold]
# CPU time: 0.65u 0.28s 00:00:00.93 Elapsed: 00:00:00.47
# Mc/sec: 2004.06
//
Query:       gi|13541923|ref|NP_111611.1|  [L=95]
Description: hypothetical protein TVN1092 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       718  (0.0400469); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); 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: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 701.99
//
Query:       gi|13541924|ref|NP_111612.1|  [L=143]
Description: transcription factor [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.2e-11   44.5   0.4      2e-11   43.8   0.4    1.4  1  HTH_3       Helix-turn-helix
    1.3e-06   28.3   1.1    2.5e-06   27.4   0.7    1.6  2  HTH_19      Helix-turn-helix domain
    0.00015   21.6   0.7    0.00027   20.7   0.7    1.5  1  zf-C4_ClpX  ClpX C4-type zinc finger
      0.001   18.9   0.1      0.002   17.9   0.1    1.6  1  HTH_25      Helix-turn-helix domain
     0.0025   18.1   0.0     0.0039   17.5   0.0    1.3  1  HTH_31      Helix-turn-helix domain
  ------ inclusion threshold ------
      0.022   14.6   1.3      0.043   13.7   1.3    1.5  1  DUF4428     Domain of unknown function (DUF4428)


Domain annotation for each model (and alignments):
>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.8   0.4   6.7e-15     2e-11       1      54 [.      88     141 ..      88     142 .. 0.96

  Alignments for each domain:
  == domain 1  score: 43.8 bits;  conditional E-value: 6.7e-15
                                   HHHHHHHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHHHTSEHHH CS
                         HTH_3   1 lkelRkqlglsqeeLAeklGvsrstisriEnGernPsletlkklakaLgvslde 54 
                                   +k +R++lg+sq++LA+++   ++ i+ iE+G+  P+++t+ kl+k Lg++l e
  gi|13541924|ref|NP_111612.1|  88 VKNAREKLGMSQADLAARIFERKNVIASIERGDLLPDIKTARKLEKILGITLLE 141
                                   589***********************************************9976 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0         2   6.1e+03      32      40 ..      37      45 ..      36      52 .. 0.71
   2 !   27.4   0.7   8.2e-10   2.5e-06       2      55 ..      86     138 ..      86     142 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2
                        HTH_19 32 iEngkkdvp 40
                                  iE+++++  
  gi|13541924|ref|NP_111612.1| 37 IEHNNFKRV 45
                                  788887655 PP

  == domain 2  score: 27.4 bits;  conditional E-value: 8.2e-10
                        HTH_19   2 erLkeaReelgltqeelaerlgisrskisaiEngkkdvpsaelllkiaealgid 55 
                                   e +k aRe+lg++q++la r+  +++ i+ iE g    p++++ +k+ ++lgi+
  gi|13541924|ref|NP_111612.1|  86 EIVKNAREKLGMSQADLAARIFERKNVIASIERGDL-LPDIKTARKLEKILGIT 138
                                   679*******************************98.999******99999997 PP

>> zf-C4_ClpX  ClpX C4-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.7   9.2e-08   0.00027       2      34 ..       2      34 ..       1      39 [. 0.83

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 9.2e-08
                    zf-C4_ClpX  2 rCSFCgk.sesevkklIagpngvyICdeCvelcn 34
                                   C  Cgk ++++ k +I g   +++Cd+C +   
  gi|13541924|ref|NP_111612.1|  2 ECEMCGKkTQHTTKVMIDGAI-LNVCDDCAKFGT 34
                                  59***9637999999****99.7******98665 PP

>> HTH_25  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.1   6.7e-07     0.002       3      35 ..      89     121 ..      87     136 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 6.7e-07
                                   HHHHHTTT--HHHHHHHSS--HHHHHHHHCT-- CS
                        HTH_25   3 raaRearglsleevaketkIrkdylealEeddf 35 
                                   ++aRe++g+s  ++a+++  rk+++  +E++d+
  gi|13541924|ref|NP_111612.1|  89 KNAREKLGMSQADLAARIFERKNVIASIERGDL 121
                                   79*****************************64 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   1.3e-06    0.0039       7      57 ..      89     138 ..      86     143 .] 0.91

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.3e-06
                        HTH_31   7 ralReraGLsqeevAerlgvsestlsrlEqGrrgrpspavlealaralgld 57 
                                   + +Re+ G+sq+++A+r+   +  +  +E+G   +p   + ++l  +lg +
  gi|13541924|ref|NP_111612.1|  89 KNAREKLGMSQADLAARIFERKNVIASIERGDL-LPDIKTARKLEKILGIT 138
                                   679******************************.9*999999999999976 PP

>> DUF4428  Domain of unknown function (DUF4428)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   1.3   1.4e-05     0.043       1      28 [.       2      31 ..       2      46 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.4e-05
                       DUF4428  1 iCaiCgkKigllkrlkleDg..yvCkdClk 28
                                  +C  CgkK+   +++ ++    +vC+dC+k
  gi|13541924|ref|NP_111612.1|  2 ECEMCGKKTQHTTKVMIDGAilNVCDDCAK 31
                                  6************9999988666*****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       747  (0.0416643); expected 358.6 (0.02)
Passed bias filter:                      579  (0.032294); 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: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 894.34
//
Query:       gi|13541925|ref|NP_111613.1|  [L=222]
Description: fibrillarin [Thermoplasma volcanium GSS1]
Scores for complete 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-61  204.8   0.1    1.1e-60  204.6   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 !  204.6   0.1   6.1e-65   1.1e-60      27     221 ..      30     219 ..      15     222 .] 0.93

  Alignments for each domain:
  == domain 1  score: 204.6 bits;  conditional E-value: 6.1e-65
                                   STT--SSSSEEEEETTEEEEEE-TTTSHHHHHHHTT-S--S--TTSEEEEESTTTSHHHHHHHHHHTTTSEEEEEESSHHH CS
                   Fibrillarin  27 vpgekvYgEklikveeeEyRvWnpfrsKlaaailkglkelpikkgskvLYlGaasGttvsHvsDivgeegvvyavefsprv 107
                                      ++vYgE + k++++ yR+W+p+rsK aaail+gl+++pi+++++vLYlGa++Gtt+sH+sDi+   g++y+ve+s   
  gi|13541925|ref|NP_111613.1|  30 ETPQRVYGEEITKINNRTYREWDPRRSKPAAAILNGLRRFPIRENDSVLYLGASTGTTISHISDICP-AGTIYGVEVSYEP 109
                                   34589*************************************************************8.9************ PP

                                   HHHHHHHHTTSTTEEEEES-TTSGGGGTTTS--EEEEEEESSSTTHHHHHHHHHHHHEEEEEEEEEEEEHHHHHSSSSHHH CS
                   Fibrillarin 108 lrelievakkRknivPileDArkPekYralvekvDvifaDvaqpdqarilaknaklflkeggyllisikarsidvtkepee 188
                                   + +l+++akkR+n++PileDA+ PekY+  +e+vDv+++D++q +q++i+ +n+++f  + g l++ i  rs+ +t+++++
  gi|13541925|ref|NP_111613.1| 110 FSKLLDLAKKRNNLYPILEDANSPEKYSFFIEHVDVMYQDISQRNQIQIFKNNVNTFNPKRGFLVLKI--RSVKSTEDSRS 188
                                   **********************************************************9999877655..79********* PP

                                   HHHHHHHHHHHTTEEEEEEEE-TTTSTTEEEEE CS
                   Fibrillarin 189 vfkeeveklkeeglkvleqvklepyekdhalvv 221
                                   + ++ +++l+    + +e+++l+py++dh l++
  gi|13541925|ref|NP_111613.1| 189 ILNTAMDQLSVY--HLKEVINLKPYDTDHYLIT 219
                                   *********876..6679***********9885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 1497.84
//
Query:       gi|13541926|ref|NP_111614.1|  [L=159]
Description: 6-pyruvoyl-tetrahydropterin synthase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.4e-26   91.0   0.0      7e-26   90.6   0.0    1.1  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 !   90.6   0.0   3.9e-30     7e-26       4     121 ..      10     153 ..       8     155 .. 0.92

  Alignments for each domain:
  == domain 1  score: 90.6 bits;  conditional E-value: 3.9e-30
                                   EEEEEEEEE--TTTTGGGGSTEEEEEEEEEEEEEC-STCTTBSS-HHHHHHHHHHHHHCTTTEEC.CCC-CCHHCCS.... CS
                          PTPS   4 kefeFdaaHrlrkhegkcrnlHGHnykvevtvegeeldetgmvvdfgelkealkeileelDhkfl.naddpeleell.... 79 
                                    + +F+aaH++++h  kc++lHGH y + ++v ge   ++gm++df elk+a++++++e+Dhk+l    ++ +++ +    
  gi|13541926|ref|NP_111614.1|  10 TNMRFSAAHFIPSHY-KCSRLHGHDYGIIINVDGE--MQDGMLIDFIELKNAIRSVINEMDHKLLvP-GKANIAKYNestn 86 
                                   5789********988.*******************..9***************************75.555555555566* PP

                                   .........................--HHHHHHHHHHHHHHHH.GCCCGCEEEEEEEEETTEEEEEE CS
                          PTPS  80 ........................spTaEnlaklifeelkerl.qekevklskvrvwEtpnswaeyr 121
                                                           ++T+E+l+++++e++ +++ + k+++  +v+v E p++ + y+
  gi|13541926|ref|NP_111614.1|  87 eyeisyndkrmiipaeyvyicdvyNTTSEELSRFVAEKVGAKIgKRKNLRSIEVSVEEGPGQGVFYS 153
                                   *******************************************99999999999999*****99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       673  (0.037537); expected 358.6 (0.02)
Passed bias filter:                      520  (0.0290033); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 1028.88
//
Query:       gi|13541927|ref|NP_111615.1|  [L=241]
Description: ATPase [Thermoplasma volcanium GSS1]
Scores for complete 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-78  262.3   0.0      3e-78  262.1   0.0    1.0  1  QueC             Queuosine biosynthesis protein QueC
    9.1e-05   22.3   0.0    0.00012   21.8   0.0    1.2  1  Asn_synthase     Asparagine synthase
    0.00017   21.2   0.0    0.00044   19.9   0.0    1.7  2  ThiI             Thiamine biosynthesis protein (ThiI)
     0.0059   15.4   0.0      0.008   15.0   0.0    1.2  1  tRNA_Me_trans    tRNA methyl transferase
     0.0084   16.2   0.0      0.022   14.8   0.0    1.6  2  PAPS_reduct      Phosphoadenosine phosphosulfate reductase fa
  ------ inclusion threshold ------
      0.014   15.2   0.0      0.026   14.3   0.0    1.4  2  ATP_bind_3       PP-loop family
      0.017   14.3   0.1       0.36    9.9   0.0    2.1  2  NAD_synthase     NAD synthase
      0.023   14.0   0.0       0.03   13.6   0.0    1.3  1  Arginosuc_synth  Arginosuccinate synthase


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 !  262.1   0.0   1.4e-81     3e-78       1     209 [.       4     213 ..       4     214 .. 0.96

  Alignments for each domain:
  == domain 1  score: 262.1 bits;  conditional E-value: 1.4e-81
                                   EEEEE--SSHHHHHHHHHHHHH-SEEEEEEEESS-TTSHHHHHHHHHHHHT--.-EEEEE-GGGGGGSCGGG--------- CS
                          QueC   1 kavvllSGGlDSttvlalakkegkevealtfdYgqrhkkeleaakkiakelgveehkildldllkelggsaLtdeeievpk 81 
                                   kavvllSGGlDS+tvla+a+++g ev+a++fdYgqrh ke+++ ++i+k ++v ++ki+++d l+++g+saLtd+ ievp+
  gi|13541927|ref|NP_111615.1|   4 KAVVLLSGGLDSSTVLAYALNKGFEVYAISFDYGQRHLKEMKSSEAISKFYNV-DRKIVKVD-LRSIGKSALTDN-IEVPS 81 
                                   79***************************************************.********.**********98.78999 PP

                                   --.....--------TTHHHHHHHHHHHHHHHHT-SEEEE---S-STT--GGGSHHHHHHHHHHHHHH....HTS--EEE- CS
                          QueC  82 eelee..eelpntfVpaRNliflslaasyaealgaeaiiiGvneedfsgYPDcrdefvkalnkalnlg....edkkieiea 156
                                   ++++   ee+p+t+VpaRN+ifls+aa+yae+lg+++++iG+n+ d+sgYPDcr+e+++a+++al+lg     ++k++i+ 
  gi|13541927|ref|NP_111615.1|  82 RDISTieEEIPVTYVPARNTIFLSIAAAYAESLGTNEVFIGANAIDYSGYPDCRPEYFNAMENALSLGtkigLKEKFHINV 162
                                   5554444*************************************************************9988789****** PP

                                   TTTT--HHHHHHHHHHTTHHHHH-B-STTS.-BTTTTSSSHHHHHHHHHHHHH CS
                          QueC 157 PlidlsKaeivklgkelgvpleetlsCYegeeegkaCgeCdaCalRkkgfeea 209
                                   Pl+ lsKa+ivklg +l+vp+e+t+sCY+geee  aCgeCd+C+lR kgf ea
  gi|13541927|ref|NP_111615.1| 163 PLQYLSKADIVKLGVKLNVPYELTWSCYKGEEE--ACGECDSCQLRLKGFMEA 213
                                   ******************************666..***************986 PP

>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   5.5e-08   0.00012      22      79 ..       7      63 ..       3     100 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 5.5e-08
                  Asn_synthase 22 alLSGGlDSSliaalaarqsksplktFsigf..eekgsdeakyakevaehlgtehtelvl 79
                                  +lLSGGlDSS++ a+a  +    +  ++i f   +++ +e+k  +++++ ++++   + +
  gi|13541927|ref|NP_111615.1|  7 VLLSGGLDSSTVLAYALNKG---FEVYAISFdyGQRHLKEMKSSEAISKFYNVDRKIVKV 63
                                  89**************9976...555555553377999******9999999999766655 PP

>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0     2e-07   0.00044       5      70 ..       4      68 ..       1     125 [. 0.63
   2 ?   -1.9   0.0      0.92   2.1e+03     139     159 ..     159     179 ..     152     191 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 2e-07
                          ThiI  5 kvlaLlSgGiDSpVaaylllkRGcrvvlvhlknepgtseeaiekveklaellaeyqtslevklvvv 70
                                  k+++LlSgG+DS      +l++G++v ++ ++ +     ++++  e + + ++     ++v l+ +
  gi|13541927|ref|NP_111615.1|  4 KAVVLLSGGLDSSTVLAYALNKGFEVYAISFD-YGQRHLKEMKSSEAISKFYNVDRKIVKVDLRSI 68
                                  899********987777789***********6.444444445555555555554444455555444 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.92
                          ThiI 139 lilrPLigldKeeiiklAkei 159
                                    i  PL  l+K +i+kl  ++
  gi|13541927|ref|NP_111615.1| 159 HINVPLQYLSKADIVKLGVKL 179
                                   566799999******997665 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   3.6e-06     0.008       2      55 ..       4      57 ..       3      69 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.6e-06
                 tRNA_Me_trans  2 kvvvalSgGVDSsvaaallkeqgyevigvflklweeedeegkeccaeedlkdae 55
                                  k vv+lSgG DSs ++a   ++g+ev ++ +   +++ +e k+  a ++++++ 
  gi|13541927|ref|NP_111615.1|  4 KAVVLLSGGLDSSTVLAYALNKGFEVYAISFDYGQRHLKEMKSSEAISKFYNVD 57
                                  679**************************9988887555554555555555554 PP

>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   9.8e-06     0.022       2      60 ..       5      64 ..       4      89 .. 0.88
   2 ?   -1.8   0.0       1.3   2.8e+03     130     155 ..     157     183 ..     138     185 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 9.8e-06
                                  EEEE--SSCTCHHHHHHHHHHCTTHEEEEEE-STB-HHHHHHHHHHHHHTT-E.EEEEE- CS
                   PAPS_reduct  2 lvvsvsgGkdslVllhLalkafkpvpvvfvdtghefpetiefvdeleeryglr.lkvyep 60
                                   vv+ sgG ds+ +l +al+   +v  +  d g+ + + ++  +++++ y+++ ++v + 
  gi|13541927|ref|NP_111615.1|  5 AVVLLSGGLDSSTVLAYALNKGFEVYAISFDYGQRHLKEMKSSEAISKFYNVDrKIVKVD 64
                                  699***********************************************9996665554 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.3
                                   CEEE-.CCCT--HHHHHHHHHHCT--B CS
                   PAPS_reduct 130 slrvf.PllnWteedvwqyilrenipy 155
                                    ++++ Pl   ++ d+ ++  + n+py
  gi|13541927|ref|NP_111615.1| 157 KFHINvPLQYLSKADIVKLGVKLNVPY 183
                                   677888999999999999999998888 PP

>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   1.2e-05     0.026       2      68 ..       5      65 ..       4      85 .. 0.60
   2 ?   -3.2   0.0       2.7   6.1e+03     138     163 ..     158     183 ..     145     184 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.2e-05
                                  EEEE--SCHHHHHHHHHHHHHCTTTTTEEEEEEEE-SSST.CHHHHHHHHHHHHHHTT-EEEEEE--H CS
                    ATP_bind_3  2 vlvAvSgGlDSmaLllllaklkkklgiklvaihvdhglre.eskeeaelvkelckklnikleiekvdv 68
                                  ++v +SgGlDS + l  + ++    g+++ ai +d+g r+ +  + +e+   ++k +n++ +i kvd+
  gi|13541927|ref|NP_111615.1|  5 AVVLLSGGLDSSTVLAYALNK----GFEVYAISFDYGQRHlKEMKSSEA---ISKFYNVDRKIVKVDL 65
                                  57889*****97766665555....5689********995133334444...4444445555555554 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 2.7
                                   CCEE-CCCT--HHHHHHHHHHTT--- CS
                    ATP_bind_3 138 irlvRPlLkvskeeleeylkekkikw 163
                                    ++  Pl  +sk+++ ++  + ++++
  gi|13541927|ref|NP_111615.1| 158 FHINVPLQYLSKADIVKLGVKLNVPY 183
                                   56777999999999988777666665 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00016      0.36      19      58 ..       3      40 ..       1      91 [. 0.61
   2 ?    2.5   0.0      0.03        67     149     172 ..     162     185 ..     139     188 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00016
                                  SEEEEEE-SSHHHHHHHHHH.HHHHTCGEEEEEE--SSSTT CS
                  NAD_synthase 19 kgvvlGlSGGvDSslvaala.vkalgkenvlalllPssvss 58
                                  k++v+ lSGG+DSs+v a a  k +   +v a+ +   + +
  gi|13541927|ref|NP_111615.1|  3 KKAVVLLSGGLDSSTVLAYAlNKGF---EVYAISFDYGQRH 40
                                  688999*******988544403334...5666666544444 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.03
                                   ETTTTS-HHHHHHHHHHTT--HHH CS
                  NAD_synthase 149 apiaellKtevkeLakelnvPerv 172
                                    p++ l K ++ +L  +lnvP ++
  gi|13541927|ref|NP_111615.1| 162 VPLQYLSKADIVKLGVKLNVPYEL 185
                                   49*******************876 PP

>> Arginosuc_synth  Arginosuccinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   1.3e-05      0.03       4      44 ..       9      46 ..       6      90 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.3e-05
               Arginosuc_synth  4 ysGGlDtsviikllkeklgeeviavavdvGqeeedldevke 44
                                   sGGlD s ++++  +k+  ev a++ d Gq   +l+e+k+
  gi|13541927|ref|NP_111615.1|  9 LSGGLDSSTVLAYALNKG-FEVYAISFDYGQR--HLKEMKS 46
                                  79***********99998.9***********9..5554432 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       517  (0.028836); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.55u 0.32s 00:00:00.87 Elapsed: 00:00:00.51
# Mc/sec: 1420.43
//
Query:       gi|13541928|ref|NP_111616.1|  [L=325]
Description: malate dehydrogenase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.3e-39  134.2   0.3    5.4e-39  133.5   0.3    1.3  1  Ldh_1_N         lactate/malate dehydrogenase, NAD binding dom
    4.3e-24   85.3   0.0    6.7e-24   84.7   0.0    1.2  1  Ldh_1_C         lactate/malate dehydrogenase, alpha/beta C-te
    0.00022   20.9   0.1    0.00057   19.5   0.0    1.7  2  Glyco_hydro_4   Family 4 glycosyl hydrolase
  ------ inclusion threshold ------
      0.031   14.3   0.6       0.11   12.5   0.0    2.1  2  Shikimate_DH    Shikimate / quinate 5-dehydrogenase
      0.056   13.7   0.0       0.16   12.2   0.0    1.8  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
      0.063   12.8   1.8       0.32   10.5   1.8    2.0  1  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
      0.071   13.0   0.2       0.17   11.8   0.1    1.7  2  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
       0.13   12.2   0.1       0.64   10.0   0.0    2.0  2  NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogen
       0.16   11.5   0.1       0.84    9.2   0.1    2.0  2  DAO             FAD dependent oxidoreductase


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 !  133.5   0.3   2.7e-42   5.4e-39       2     141 .]       5     148 ..       4     148 .. 0.91

  Alignments for each domain:
  == domain 1  score: 133.5 bits;  conditional E-value: 2.7e-42
                                   EEEEETTTSHHHHHHHHHHHHTTSSSEEEEE-SSHHHHHHHHHHHHHCHCC....STS-EEEEE..SSGGGGTTESEEEE- CS
                       Ldh_1_N   2 kvavvGaaGgiGqslalllankkladelaLlDiakekleGvaldlshistf....lsvkvkvse..keeealkdadvvvit 76 
                                   k++v+Ga G++G+++a  la+k+l+d + L+D+++   eG+ald+++++      l v + +++  ++++ ++++dv+v+t
  gi|13541928|ref|NP_111616.1|   5 KISVIGA-GNVGATVAQFLATKELGD-VYLFDVVDGIPEGKALDIQEGAPHwgydLDVVGFSTSdsSNYKNMEGSDVIVVT 83 
                                   9******.******************.*******************9987611113333333334799************* PP

                                   -S-SS-TTTTHHHHHHHHHHHHHHHHHHHHHHTTTSEEEE-SSSHHHHHHHHHHHHTS-GGGEEE CS
                       Ldh_1_N  77 agvprkpGetRddLlkvNakIvkeiveaiakvapnaivlvvsNPvdiltevlkkasglpkkrvig 141
                                   ag+ rkpG++R+dL+++N++I++++ ++i+k++p+ i++vvsNP+di++++l+k+sg++++r++g
  gi|13541928|ref|NP_111616.1|  84 AGMARKPGMSREDLFDKNVEIIADVSKNIKKYSPDSIIVVVSNPADIMAYALQKISGVDPQRIMG 148
                                   ***************************************************************97 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 !   84.7   0.0   3.3e-27   6.7e-24       2     162 ..     152     315 ..     151     319 .. 0.90

  Alignments for each domain:
  == domain 1  score: 84.7 bits;  conditional E-value: 3.3e-27
                                   HHHHHHHHHHHHHHHTS-GGGEE--EEBSSST..........ETTEEHHHHHTTSTTSTHHHHHHHHHHHHHHHHHHHHHH CS
                       Ldh_1_C   2 tLDivRaktflaekagvtprsvkvtViGgHsg..........vtiipllsqvkellklsekqleeliervqnggdevvkak 72 
                                   +LD+ R++tfla++ +v+ ++v++ ViGgH++          v++ip+      ++ l +++++++++r+++gg e+v+  
  gi|13541928|ref|NP_111616.1| 152 SLDSSRFRTFLAKELDVSVEDVNAFVIGGHGDdmvpfiryssVAGIPI------EKLLPKEKIDAIVKRTRFGGGEIVNYL 226
                                   69********************************99988888888888......467888*******************87 PP

                                   TTSSSS-HHHHHHHHHHHHHHHTTHTEEEEEEEEEESC....CCECCSSEEEEEEEEEEETTEEEEE-------HHHHHHH CS
                       Ldh_1_C  73 kGagsatlsmAvAgakfveallrdtkeilsagvyldge....vglkdqeieyfsvPvvlgknGvekvleilklndfeeekl 149
                                   k agsa+++ + ++  +ve++++d k++++ ++y +g+    +g+++   ++++vP+ +g+ Gve++++ +   ++e e  
  gi|13541928|ref|NP_111616.1| 227 K-AGSAYYAPGISITAMVESVIKDKKRVIPCAAYITGKhaehYGINN---KFIGVPIKIGERGVEEIYD-IDFLPEELELW 302
                                   6.8*******************************9986522455555...8******************.99999****** PP

                                   HHHHHHHHHHHHH CS
                       Ldh_1_C 150 eksvkeLkkeiek 162
                                   +ksv+  +++ ++
  gi|13541928|ref|NP_111616.1| 303 KKSVASVEASSKN 315
                                   ***9998877665 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 ?   -3.4   0.1       3.1   6.1e+03       1       9 [.       5      13 ..       5      25 .. 0.80
   2 !   19.5   0.0   2.9e-07   0.00057     120     158 ..     101     139 ..      96     151 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 3.1
                                  EEEEETTTS CS
                 Glyco_hydro_4  1 kiviiGgGS 9 
                                  ki +iG+G 
  gi|13541928|ref|NP_111616.1|  5 KISVIGAGN 13
                                  899999996 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 2.9e-07
                                   HHHHHHHHHHHHHHH-TTSEEEE-SSSHHHHHHHHHHHS CS
                 Glyco_hydro_4 120 tipvlleIakdieelcPdawvlnytNPaavvteallrlv 158
                                   ++++++++ k+i++++Pd+ ++  +NPa +++ al + +
  gi|13541928|ref|NP_111616.1| 101 NVEIIADVSKNIKKYSPDSIIVVVSNPADIMAYALQKIS 139
                                   6899******************************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 ?   12.5   0.0   5.7e-05      0.11      11      40 ..       2      31 ..       1      34 [. 0.89
   2 ?   -1.6   0.0       1.3   2.7e+03       8      24 ..      72      88 ..      68     114 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.7e-05
                                  TT-EEEEES-SHHHHHHHHHHHCCT-CEEE CS
                  Shikimate_DH 11 kekkvlliGaGemaelvakhLlakgvkkvv 40
                                  ++kk+ +iGaG+++  va+ L++k++ +v 
  gi|13541928|ref|NP_111616.1|  2 ARKKISVIGAGNVGATVAQFLATKELGDVY 31
                                  579*********************998876 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.3
                                  S..TT-EEEEES-SHHH CS
                  Shikimate_DH  8 eslkekkvlliGaGema 24
                                  ++++++ v+++ aG+  
  gi|13541928|ref|NP_111616.1| 72 KNMEGSDVIVVTAGMAR 88
                                  56677777777777754 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 ?   12.2   0.0   7.9e-05      0.16       1      59 [.       8      72 ..       8      76 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7.9e-05
                                  EE--SHHHHHHHHHHHCCTE.EEEEE-SSSSSS.GGG-EECE....TTCEEC.TS---EEETTHHH CS
                 NAD_binding_8  1 IvGaGlsGlvaAylLakagf.dvlllekrdrlG.Graasyev....pgvrvd.ygahifhgsgyyp 59
                                  ++GaG  G++ A++La + + dv l++  d++  G+a +++      g+ +d +g ++  + ++y+
  gi|13541928|ref|NP_111616.1|  8 VIGAGNVGATVAQFLATKELgDVYLFDVVDGIPeGKALDIQEgaphWGYDLDvVGFSTSDS-SNYK 72
                                  8***************99898******9999666888888775533346666445555444.3455 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 ?   10.5   1.8   0.00016      0.32       2      36 ..       5      36 ..       4     130 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00016
                                  EEEEE--STTHHHHHHHHHHCT.SEEEEE-S-HHHH CS
                UDPG_MGDP_dh_N  2 kisviGlGYvGlvtaavlaeig.hevigvDideekv 36
                                  kisviG+G vG++ a  la +   +v + D+    v
  gi|13541928|ref|NP_111616.1|  5 KISVIGAGNVGATVAQFLATKElGDVYLFDV----V 36
                                  9******************998667887776....3 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   8.4e-05      0.17       1      32 [.       5      37 ..       5      52 .. 0.83
   2 ?   -3.4   0.0       3.8   7.5e+03      94     118 ..     106     131 ..      99     148 .. 0.53

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 8.4e-05
                                  EEEEE--SCCHHHHHHHHHHTT-.EEEEE-S-H CS
                       3HCDH_N  1 kvaviGaGtmGagiaavfasagl.eVvlvdise 32
                                  k+ viGaG +Ga +a+ +a ++l +V l+d+ +
  gi|13541928|ref|NP_111616.1|  5 KISVIGAGNVGATVAQFLATKELgDVYLFDVVD 37
                                  689*****************9875799988855 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 3.8
                                   HHHHHHHHCCS-TTSEE.EE--SSS- CS
                       3HCDH_N  94 rkvfaelekiakpdail.asnTSsls 118
                                   ++v ++++k+ +++ i+  sn   ++
  gi|13541928|ref|NP_111616.1| 106 ADVSKNIKKYSPDSIIVvVSNPADIM 131
                                   45555555555444443134444444 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 ?   10.0   0.0   0.00032      0.64       1      22 [.       5      26 ..       5      46 .. 0.86
   2 ?   -0.7   0.0      0.61   1.2e+03      55      90 ..     100     139 ..      73     147 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00032
                                  -EEEE--SHHHHHHHHHHHTTT CS
                NAD_Gly3P_dh_N  1 kiavlGaGswGtalAkvlaeng 22
                                  ki+v+GaG+ G ++A+ la + 
  gi|13541928|ref|NP_111616.1|  5 KISVIGAGNVGATVAQFLATKE 26
                                  79****************9876 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.61
                                   TTEEEES-HHHHHTT....--EEEE---HHHHHHHHHHHC CS
                NAD_Gly3P_dh_N  55 enlvattdlaealkg....adiivlvvPsqalrevlkklk 90 
                                   +n+++ +d+ + +k+    + i+v+  P  +++  l+k++
  gi|13541928|ref|NP_111616.1| 100 KNVEIIADVSKNIKKyspdSIIVVVSNPADIMAYALQKIS 139
                                   4555555555554431110344444446666666666665 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.1   0.00042      0.84       2      27 ..       6      34 ..       5      43 .. 0.85
   2 ?   -0.3   0.0      0.31   6.3e+02     276     311 ..      96     143 ..      55     186 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00042
                                  EEEECTSHHHHHHHHHHHHT..T.EEEEE CS
                           DAO  2 vviiGGGiiGlstAyeLarr..g.Vtlle 27
                                  + +iG+G +G+++A +La++  g V l++
  gi|13541928|ref|NP_111616.1|  6 ISVIGAGNVGATVAQFLATKelGdVYLFD 34
                                  67***************977466988876 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.31
                                   SSTSCSHHHHHHHHHHHHHHSGG..G......CGEE....EEEEEEEE CS
                           DAO 276 ddpevdeedidellealrklfPq..l......gdvl....rkwaGlrp 311
                                   d ++ + e i+++ + ++k++P+  +      +d+     +k +G+ p
  gi|13541928|ref|NP_111616.1|  96 DLFDKNVEIIADVSKNIKKYSPDsiIvvvsnpADIMayalQKISGVDP 143
                                   336677888889999999999986514455555544332247777777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       579  (0.032294); expected 358.6 (0.02)
Passed bias filter:                      546  (0.0304535); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 1994.73
//
Query:       gi|13541929|ref|NP_111617.1|  [L=475]
Description: ATPase [Thermoplasma volcanium GSS1]
Scores for complete 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-144  481.8   1.9   2.6e-144  481.5   1.9    1.1  1  GvpD             GvpD gas vesicle protein
    7.7e-10   38.5   0.0    1.5e-09   37.5   0.0    1.4  1  ATPase           KaiC
     0.0013   19.0   0.0      0.004   17.4   0.0    1.8  2  AAA_22           AAA domain
     0.0032   17.4   0.0      0.006   16.5   0.0    1.4  1  ATPase_2         ATPase domain predominantly from Archaea
  ------ inclusion threshold ------
      0.016   15.6   0.0      0.028   14.8   0.0    1.5  1  AAA_16           AAA ATPase domain
      0.029   13.7   0.0      0.048   13.0   0.0    1.2  1  DnaB_C           DnaB-like helicase C terminal domain
      0.085   12.6   0.0       0.59    9.8   0.0    2.2  2  AAA_24           AAA domain
       0.14   11.9   0.0       0.24   11.1   0.0    1.4  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase
       0.16   11.2   0.0       0.21   10.8   0.0    1.2  1  DUF2075          Uncharacterized conserved protein (DUF2075)
       0.17   11.5   0.0       0.38   10.3   0.0    1.6  1  DUF374           Domain of unknown function (DUF374)


Domain annotation for each model (and alignments):
>> GvpD  GvpD gas vesicle protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  481.5   1.9  1.4e-147  2.6e-144       1     484 []      10     475 .]      10     475 .] 0.97

  Alignments for each domain:
  == domain 1  score: 481.5 bits;  conditional E-value: 1.4e-147
                          GvpD   1 leqffdgeaGktllikGaPGtGktlftlrgldvlrresdvlyvstrvddetvseay......fsgeaeld..ktall.... 69 
                                   +e+ffd+++Gk+l+ikG+PG+Gkt+ftl++l+++r++++v+y+s+r+ d ++ e y      ++ +++++  kt  l    
  gi|13541929|ref|NP_111617.1|  10 FERFFDQKFGKSLVIKGRPGSGKTTFTLDFLNAVRDHHPVYYISSRSSDASILETYpwikneYEIKGSVEkvKTSALrnfe 90 
                                   79********************************************************8888555566656689999**** PP

                          GvpD  70 .........dllkdpleldldvdvPiekldlesllefvdeiaaiatkliialdswelvyeylaerydsPed..iktvkndl 139
                                            d l+d+l++++ ++vPi    +++l+efvd  ++ ++ +iialds    +++lae+yd+Ped  ++++kndl
  gi|13541929|ref|NP_111617.1|  91 kmveegkfgDALRDGLIVETSKIVPI----IQALYEFVD--NHFGESPIIALDS----IDALAEEYDIPEDylFLMLKNDL 161
                                   **************************....*********..*************....*************999******* PP

                          GvpD 140 vvlaresgvrlvlvletaansrleyivdGvvtl..nvkeddrgrlrrdlrleklrGvrignrlqP...ftladGkfksitr 215
                                   v   ++sg++l+ +le+++n+rley++dGvvtl  nvk+d   +l+r+l+lek+rG+++g+   P   f+ladG+f+s+tr
  gi|13541929|ref|NP_111617.1| 162 V---EGSGAHLITILEARQNERLEYFADGVVTLdyNVKND---MLVRSLTLEKMRGISVGP--SPtymFSLADGRFRSVTR 234
                                   *...*****************************99*****...*****************9..55556************* PP

                          GvpD 216 velvtidtvtdeakyePlandkakfsvglrdld..kllseGtdr...Gsvvildlgkdlsrdawsvlvlaairdflsqemg 291
                                     lv+++      + +P  +++ +f+v+++d +  k+++eGtd    Gs+v l++ kd+s         +ai+df+     
  gi|13541929|ref|NP_111617.1| 235 NTLVFPEK---RIELDPGNDESMEFQVSMGDREygKITAEGTDSipgGSIVLLHV-KDRS---------PAINDFIN---- 298
                                   *******9...889*****************************99*9********.****.........********.... PP

                          GvpD 292 vavvppkegspgllkndl...nivlskavidvtasvfetyagllkslaekylenaittskddaidPdrltgsdyvislegg 369
                                               l+k++l   niv +++vid+tas++ety++llk l +kyl+n+it+sk+d i+P       yvisl+g 
  gi|13541929|ref|NP_111617.1| 299 ------------LFKTNLiinNIVHGRGVIDMTASGYETYTVLLKALGGKYLNNYITASKSDLINP-------YVISLKGE 360
                                   ............******************************************************.......******** PP

                          GvpD 370 rlkydiyiaivervreesegPllyvismdtayeafetrlgdfanyva.....lrndavilivkdgtelrtradrvadmhir 445
                                   r+k+d +++i+e ++++s+gP++y++s+d+++++++    +f+n+++     +r+ +vi+ v+d+    t+ ++++++h++
  gi|13541929|ref|NP_111617.1| 361 RIKDDLNREIIEGKLAQSKGPYVYFFSSDYLFLVYGF---NFLNQIVevvddIRTSGVIFFVADDD---TYSKMFTASHLS 435
                                   *************************************...*************************9...************ PP

                          GvpD 446 lel.sgdaivlygenkltsllgigvsdskriPkitlieiv 484
                                   l+l s+++++++++nk++s+l++ v d++++Pki+++ei+
  gi|13541929|ref|NP_111617.1| 436 LDLfSVNGYAAVSSNKTSSFLVQLVRDQNQWPKIKFVEIE 475
                                   **************************************96 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.5   0.0   8.6e-13   1.5e-09      19     213 ..      19     217 ..      11     230 .. 0.75

  Alignments for each domain:
  == domain 1  score: 37.5 bits;  conditional E-value: 8.6e-13
                        ATPase  19 grvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenak..slGwdlekleeegklaiidasesaeesae 97 
                                   g++  i G pG+GKt+f l Fl    ++   p+ +++  ++  ++ e     +   +++   e+ k   +  +e++ e+  
  gi|13541929|ref|NP_111617.1|  19 GKSLVIKGRPGSGKTTFTLDFLNAV-RD-HHPVYYISSRSSDASILETYPwiKNEYEIKGSVEKVKTSALRNFEKMVEEG- 96 
                                   57789****************9654.55.8************88887766223344445555555555555555554433. PP

                        ATPase  98 e..........kdkedleelieelaeaikei.ka.krvviDsitglayeekeavaReilrqlvrvl.kklgvTailvseks 165
                                   +           +++++  +i+ l e +++  ++   + +Dsi++l  ee +      +  l++ l ++ g   i + e++
  gi|13541929|ref|NP_111617.1|  97 KfgdalrdgliVETSKIVPIIQALYEFVDNHfGEsPIIALDSIDAL-AEEYDIPEDYLFLMLKNDLvEGSGAHLITILEAR 176
                                   146677888888999999********99865144356789******.6666666677788899999677777777777733 PP

                        ATPase 166 sseeaaggygveefivdgvivLdlkeieeelvRtleivkmRgtkhskk 213
                                   +    +   +  e+ +dgv+ Ld++ +++ lvR+l   kmRg ++ + 
  gi|13541929|ref|NP_111617.1| 177 Q----N--ER-LEYFADGVVTLDYNVKNDMLVRSLTLEKMRGISVGPS 217
                                   3....2..33.4679***************************998654 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   2.2e-06     0.004       6     104 ..      20     143 ..      16     179 .. 0.75
   2 ?   -3.2   0.0       5.2   9.3e+03      38      65 ..     311     338 ..     294     352 .. 0.67

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2.2e-06
                        AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst.sskdllrellralglelka............... 70 
                                   ++lv+ G +G+GKTt    +l+           + +v+++   ss  s  + + ++ ++++ +++                
  gi|13541929|ref|NP_111617.1|  20 KSLVIKGRPGSGKTTFTLDFLNAVR-------DHHPVYYISSRSSDaSILETYPWIKNEYEIKGSVekvktsalrnfekmv 93 
                                   689*******************984.......37788888888888899999********987777777777777777777 PP

                        AAA_22  71 ...............erlsseellealeqalrarav.ielliiDEaqhlr 104
                                                  e+ +   +++al++ +++++   +++ +D ++ l 
  gi|13541929|ref|NP_111617.1|  94 eegkfgdalrdglivETSKIVPIIQALYEFVDNHFGeSPIIALDSIDALA 143
                                   77777777777777666666666677777777777777777777777764 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 5.2
                        AAA_22  38 erpevvfvtlpsstsskdllrellralg 65 
                                   ++++v+ +t+++ ++ + ll++l  ++ 
  gi|13541929|ref|NP_111617.1| 311 HGRGVIDMTASGYETYTVLLKALGGKYL 338
                                   6778888888888888888877766665 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   3.4e-06     0.006      21     128 ..      20     140 ..       9     161 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 3.4e-06
                      ATPase_2  21 eiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefie...........eeeekkklekal........ 82 
                                   + ++i G+ gsGKt++   +++  +d+  + +yyi+ r+++ s l+++                      +++        
  gi|13541929|ref|NP_111617.1|  20 KSLVIKGRPGSGKTTFTLDFLNAVRDH--HPVYYISSRSSDASILETY-PwikneyeikgsV--------EKVktsalrnf 89 
                                   56899*******************885..579***9999999988887.3355544433331........22234444554 PP

                      ATPase_2  83 giavpkaeleeilk....eksklvfkaielllekikkkgkk.iiiiiDelq 128
                                    + v++ ++   l      ++ ++   i++l+e + +   + +ii +D + 
  gi|13541929|ref|NP_111617.1|  90 EKMVEEGKFGDALRdgliVETSKIVPIIQALYEFVDNHFGEsPIIALDSID 140
                                   444444444444444555566667788888888887776666888888765 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   1.6e-05     0.028      15      63 ..       9      59 ..       2     146 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.6e-05
                        AAA_16 15 alervrsgrp.elvllsGesGvGKsslvrellralekdg.giflrgkcdql 63
                                  a+er  ++    ++++ G +G+GK++    +l+a+++++ +++++ +  + 
  gi|13541929|ref|NP_111617.1|  9 AFERFFDQKFgKSLVIKGRPGSGKTTFTLDFLNAVRDHHpVYYISSRSSDA 59
                                  5666666666799********************999999888899887776 PP

>> DnaB_C  DnaB-like helicase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   2.7e-05     0.048      21      85 ..      21      87 ..      15     115 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.7e-05
                                  EEEEEEXTTSSHHHHHHHHHHHHHHCSTSEEEEEESSSXHHHHHHH..HHHHHHTXX..HHHHHHTTSX CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxx..xxxxxxxxxx RF
                        DnaB_C 21 liiiAarpsmGktalalniaenaavkeklpvavfslemsaeqlvqR..llsseaeid..skklrtgklk 85
                                   ++i +rp+ Gkt+++l++ +++   +++pv ++s   s+ ++++    + +e ei+   +k++t+ l+
  gi|13541929|ref|NP_111617.1| 21 SLVIKGRPGSGKTTFTLDFLNAVR--DHHPVYYISSRSSDASILETypWIKNEYEIKgsVEKVKTSALR 87
                                  5799***************98665..4679999999999999876522566777776445566666655 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00033      0.59       3      23 ..      20      45 ..      19     143 .. 0.84
   2 ?   -0.0   0.0      0.34   6.2e+02     147     177 ..     168     198 ..     157     221 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00033
                        AAA_24  3 lkiliyGpsgiGKTtlakel.....g 23
                                  ++++i G +g+GKTt+ + +      
  gi|13541929|ref|NP_111617.1| 20 KSLVIKGRPGSGKTTFTLDFlnavrD 45
                                  6789************9999555544 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.34
                        AAA_24 147 rlepklgkktanelkeevDlvlranlkredk 177
                                   +l++ l+ +  + l++ +D v++++++ + +
  gi|13541929|ref|NP_111617.1| 168 HLITILEARQNERLEYFADGVVTLDYNVKND 198
                                   6677788888899*************97663 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 ?   11.1   0.0   0.00014      0.24       2      30 ..      23      48 ..      22      76 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00014
               Viral_helicase1  2 vvhGvpGcGKStlirkllrtsliltvnrp 30
                                  v++G pG+GK+t   ++l+    ++ ++p
  gi|13541929|ref|NP_111617.1| 23 VIKGRPGSGKTTFTLDFLNA---VRDHHP 48
                                  99****************99...555555 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00012      0.21       4      38 ..      22      52 ..      19     101 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00012
                       DUF2075  4 vlVtGvaGtGKtvvllnllaeleddeeertavyls 38
                                  ++++G++G+GKt   l +l+++    ++++ vy +
  gi|13541929|ref|NP_111617.1| 22 LVIKGRPGSGKTTFTLDFLNAV----RDHHPVYYI 52
                                  79*****************999....333333333 PP

>> DUF374  Domain of unknown function (DUF374)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00021      0.38       3      56 ..      44      97 ..      42     102 .. 0.94

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00021
                        DUF374  3 rkkkklaaliSrsrDGeliarvlerlGiktirGSsskggaealremlralkege 56
                                  r++++++ + Srs D++++       +   i GS +k +++alr+  + ++eg+
  gi|13541929|ref|NP_111617.1| 44 RDHHPVYYISSRSSDASILETYPWIKNEYEIKGSVEKVKTSALRNFEKMVEEGK 97
                                  6899******************************************99999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (475 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       479  (0.0267165); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.66u 0.30s 00:00:00.96 Elapsed: 00:00:00.50
# Mc/sec: 2879.72
//
Query:       gi|13541930|ref|NP_111618.1|  [L=203]
Description: peroxiredoxin [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.2e-40  138.3   0.0    1.5e-40  137.9   0.0    1.1  1  AhpC-TSA    AhpC/TSA family
    1.9e-20   73.0   0.0    2.9e-20   72.5   0.0    1.1  1  Redoxin     Redoxin
    3.5e-09   36.4   0.1    5.9e-09   35.6   0.1    1.4  1  1-cysPrx_C  C-terminal domain of 1-Cys peroxiredoxin
  ------ inclusion threshold ------
        0.1   12.7   0.0       0.22   11.7   0.0    1.6  1  AhpC-TSA_2  AhpC/TSA antioxidant enzyme


Domain annotation for each model (and alignments):
>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.9   0.0   3.4e-44   1.5e-40       2     123 ..       6     132 ..       5     133 .. 0.98

  Alignments for each domain:
  == domain 1  score: 137.9 bits;  conditional E-value: 3.4e-44
                                   TSB----EEESTTCEEEECHHHTTSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCHHHHHHHHH-H. CS
                      AhpC-TSA   2 gdkapdfelknadgetvslsdykgkpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvdspeshkkfiekes. 81 
                                   g+kapdf++++ + ++++ls+y+gk+v+lf +p+d++pvCtte  a+ ++ye+f+++gve+ig+s+ds++sh ++i++++ 
  gi|13541930|ref|NP_111618.1|   6 GQKAPDFTVNTSK-GPITLSNYRGKWVLLFSHPGDFTPVCTTEFIAFTERYEDFQKLGVELIGLSIDSVFSHIAWIRDIKe 85 
                                   9********9877.9****************************************************************** PP

                                   ......SSEEEE-TTSHHHHHTT-EETTTTECSCEEEEE-TTSBEEE CS
                      AhpC-TSA  82 .....lnfpllsDeegkvakaygvlkeekglalratfvidkegkiry 123
                                        ++fp+++D +++va++y++++e++g+++r++f+id+++++r+
  gi|13541930|ref|NP_111618.1|  86 hfgidIPFPIIADIDKEVAREYNLIDEKSGATVRGVFIIDPNQIVRW 132
                                   *********************************************98 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.5   0.0   6.4e-24   2.9e-20       3     145 ..       6     146 ..       5     149 .. 0.86

  Alignments for each domain:
  == domain 1  score: 72.5 bits;  conditional E-value: 6.4e-24
                                   TSBB---ECCEETTCEEEEEHHHHTTSEEEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEEEEESSSHHHHHHHHH. CS
                       Redoxin   3 gdkaPdftlplaatdgnsvslsefkgkkvvvnfvpgafcPtCsaehpyleklaellkekgvdvvavvadndafvkefwgk. 82 
                                   g+kaPdft   ++t   +++ls ++gk v++++ pg f+P+C++e +++++ +e + + gv+ +++++d+     +++ + 
  gi|13541930|ref|NP_111618.1|   6 GQKAPDFT---VNTSKGPITLSNYRGKWVLLFSHPGDFTPVCTTEFIAFTERYEDFQKLGVELIGLSIDSVFSHIAWIRDi 83 
                                   89******...789*********************************888888888************9987744444446 PP

                                   .....TT-TSEEEE-TTSHHHHHTT-TTEEE.GGGEEE-EEEEEEETTEEEEEEESSSCHTSTTSHHH CS
                       Redoxin  83 .....eglkfpvlsDgsaaftkalGlrleedaseglrtpryavidedgkvvylevepepeteesnaea 145
                                         +++fp+++D +++++++++l    d ++g   + +++id ++ v+++++ p ++   +n+e+
  gi|13541930|ref|NP_111618.1|  84 kehfgIDIPFPIIADIDKEVAREYNLI---DEKSGATVRGVFIIDPNQIVRWMIYYPAET--GRNIEE 146
                                   667776669999*************76...44455589*****************99984..455555 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 !   35.6   0.1   1.3e-12   5.9e-09       1      32 [.     153     184 ..     153     191 .. 0.92

  Alignments for each domain:
  == domain 1  score: 35.6 bits;  conditional E-value: 1.3e-12
                                   HHHHHHHHT-BB-TTT.TBT-EEE---SSHHH CS
                    1-cysPrx_C   1 ALQladkhgvatPAnWkpGdkvivpPpateed 32 
                                   ALQ+ +  + atPAnW+pG++ i p+p+t + 
  gi|13541930|ref|NP_111618.1| 153 ALQFNWDRKLATPANWQPGQEGIEPAPTTVDS 184
                                   9**********************999999995 PP

>> AhpC-TSA_2  AhpC/TSA antioxidant enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   4.9e-05      0.22       4      54 ..      53     110 ..      50     174 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4.9e-05
                    AhpC-TSA_2   4 rdkpeldaagvklvaigigdp.sakkFvkl......tgfpfelyvDpsaklyqalglk 54 
                                   ++ +++++ gv+l++ +i+++ s  ++++        ++pf++++D ++++ ++ +l 
  gi|13541930|ref|NP_111618.1|  53 ERYEDFQKLGVELIGLSIDSVfSHIAWIRDikehfgIDIPFPIIADIDKEVAREYNLI 110
                                   66899*****************99999987787777778**********999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       415  (0.0231469); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.51
# Mc/sec: 1197.56
//
Query:       gi|13541931|ref|NP_111619.1|  [L=321]
Description: delta-aminolevulinic acid dehydratase [Thermoplasma volcanium GSS1]
Scores for complete 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-134  446.0   1.4   7.5e-134  445.9   1.4    1.0  1  ALAD            Delta-aminolevulinic acid dehydratase
  ------ inclusion threshold ------
        0.1   12.4   0.0       0.59    9.9   0.0    2.0  2  S-methyl_trans  Homocysteine S-methyltransferase


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 !  445.9   1.4  8.4e-138  7.5e-134       2     316 ..       5     317 ..       4     318 .. 0.98

  Alignments for each domain:
  == domain 1  score: 445.9 bits;  conditional E-value: 8.4e-138
                                   --GGGGGSSHHHHHHC-S----GGGEEEEEEEESS-SS-EE-TTSTT-EEEEGGGHHHHHHHHHHTT--EEEEEEE-SS-B CS
                          ALAD   2 krlrrlrksealrelvretrlsasdlilplfvkegeeekeeiksmpgvyrlsvdelvkeveelvklgikavllFgvpeekd 82 
                                    r+rr rk+++lr++++e r+s ++li+p+f++e+ +ek++i+smpg++r+++++l++ v++l + gik+vllFg+p+ kd
  gi|13541931|ref|NP_111619.1|   5 VRMRRYRKDQNLRDFISEIRVSIDKLIMPIFIDENIKEKTQISSMPGIFRYPISQLEDYVKHLEDIGIKSVLLFGIPKYKD 85 
                                   59******************************************************************************* PP

                                   SS-GGGGSTTSHHHHHHHHHHHH-TTSEEEEEE-STTTBSS-SSSEEESS.EEHHHHHHHHHHHHHHHHHCT-SEEEE-S- CS
                          ALAD  83 eegsealnedglvqrairaikeevpelvvitDvclceytshGhcgileekevdndetlellakvavsqaeaGadivapSdm 163
                                   + gs+a+++++++qr+i+ ike+ +++v i+D+clceyt++G+cg++++++vdnd+tle++ k+avs+aeaG+divapS+m
  gi|13541931|ref|NP_111619.1|  86 SFGSSAYDKNSIIQRSISLIKET-TDIVTIADLCLCEYTDTGQCGLISNDYVDNDKTLEVYRKIAVSYAEAGVDIVAPSGM 165
                                   *********************98.89******************************************************* PP

                                   -TTHHHHHHHHHHHTT-TT-EEB---EEB--CGGHHHHHHHT---S.S--TTTSB-TT-HHHHHHHHHHHHHTT-SBEEEE CS
                          ALAD 164 mDgrvaaireaLdeagfeevailsYsaKyaSafYgPFrdaaesapsfgdrktYqmdpansrealreveldleeGADivmvK 244
                                   mDg+v+aireaLd++g+ +++i++Ys+K++S++YgPFr+aaesap++gdrk+Yq+d++n +ea+re+eld++eGADivmvK
  gi|13541931|ref|NP_111619.1| 166 MDGQVKAIREALDSSGYVNTMIMAYSSKFSSNLYGPFREAAESAPKVGDRKSYQLDYRNGKEAIREIELDIDEGADIVMVK 246
                                   ********************************************************************************* PP

                                   S-TTGHHHHHHHHTT-SS-EEEEE-HHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHTT-SEEEETTHHHHHH CS
                          ALAD 245 PalaylDiirevkeefdlpvaayqvSGEYamikaaaengwldekkvvlEsllsikRAGadliltYfakevak 316
                                   Pa++ylDiir+++++f+lp+aay+vSGEY+mi +a+++g++ e+  v E+l+++ RAGad+++tYfa+++a+
  gi|13541931|ref|NP_111619.1| 247 PAIFYLDIIRSARDRFNLPLAAYSVSGEYSMIVNAVNQGLIGED-SVNEALTAVFRAGADIVITYFAERLAE 317
                                   *****************************************765.579********************9986 PP

>> S-methyl_trans  Homocysteine S-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   6.5e-05      0.59      65     153 ..      92     179 ..      78     212 .. 0.78
   2 ?    0.2   0.0     0.061   5.5e+02      29      50 ..     288     309 ..     222     317 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 6.5e-05
                                   HHH.HHHHHHHHHHHHHHHHH....HEE.EEE--HHHHCTS-.--...--HHHHHHHHHHHHHHHHHCT-SEEEEEEE--H CS
                S-methyl_trans  65 eeveelnraavelareaadeaaaplfva.gsvGpygatlsdg.yd..llsfeelveahreqiralleagvDlllietipdl 141
                                    + +++++++++l +e  d +    ++a +++  y++t ++g  +  +++ ++  e++r+ +   +eagvD+++   + d 
  gi|13541931|ref|NP_111619.1|  92 YDKNSIIQRSISLIKETTDIV----TIAdLCLCEYTDTGQCGlISndYVDNDKTLEVYRKIAVSYAEAGVDIVAPSGMMDG 168
                                   5566799************99....3443899999999999755443599**********99977********99988885 PP

                                   HHHHHHHHHHT. CS
                S-methyl_trans 142 leakaavellaa 153
                                    ++ka++e+l +
  gi|13541931|ref|NP_111619.1| 169 -QVKAIREALDS 179
                                   .57888777766 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.061
                                   -HHHHHHHHHHHHHHT-SEEE- CS
                S-methyl_trans  29 rpelikeihrdyleaGadiieT 50 
                                    ++ + e+ ++ ++aGadi+ T
  gi|13541931|ref|NP_111619.1| 288 GEDSVNEALTAVFRAGADIVIT 309
                                   4466777777778888888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       540  (0.0301188); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); 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 0.25s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 2186.84
//
Query:       gi|13541932|ref|NP_111620.1|  [L=110]
Description: hypothetical protein TVN1101 [Thermoplasma volcanium GSS1]
Scores for complete 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  152.9   1.4    3.4e-45  152.8   1.4    1.0  1  TA0956      Thermoplasma acidophilum protein TA0956
  ------ inclusion threshold ------
      0.071   11.7   0.0      0.078   11.6   0.0    1.0  1  Cpn60_TCP1  TCP-1/cpn60 chaperonin family
       0.11   11.5   0.1       0.14   11.1   0.1    1.1  1  RapA_C      RNA polymerase recycling family C-terminal


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 !  152.8   1.4   5.7e-49   3.4e-45       1     110 []       1     109 [.       1     109 [. 0.98

  Alignments for each domain:
  == domain 1  score: 152.8 bits;  conditional E-value: 5.7e-49
                                   --EEEEEEEESTTS--EEEEEEHHHHHHHHHHHHHHTTS-.-CCHHHHHHHHH---S---TTSEEEEEEEEETTTTEEEEE CS
                        TA0956   1 mtlcamynitlkekhPsticvvlsklreslealadvldselieesleefieefartdeimPedktvGfviinsdkkvlsls 81 
                                   m lcamyni++++ hP+ticvv++k+ +s+ +l  vl+++  ++ l++fi+++artdei PedktvGfv+ins kk++s+s
  gi|13541932|ref|NP_111620.1|   1 MELCAMYNISIENLHPTTICVVMDKFLDSFAELLGVLEDQ-DQDELMDFISRYARTDEIRPEDKTVGFVVINSAKKMMSVS 80 
                                   789**********************************998.99************************************** PP

                                   E-S--CCHHHHHHHHHHHHHCCS-EEEEE CS
                        TA0956  82 fselkeelkksikeiaekfkkkGykveid 110
                                   fs+++e++k++i+ei++ +++ Gy+ve d
  gi|13541932|ref|NP_111620.1|  81 FSDIDENVKEKIREIIKPYRDSGYSVEAD 109
                                   **************************987 PP

>> Cpn60_TCP1  TCP-1/cpn60 chaperonin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   1.3e-05     0.078      83     155 ..      12      79 ..       3     101 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1.3e-05
                                   CTXXHHHHHHHHHHHHHHHHHHHHHHXEEBXSCSTT.HHHHHHHHHHCTTSSXXSTHHHHHHHHHHHH.HCHCC CS
                    Cpn60_TCP1  83 agvhpttiiegyekalekaleaLkeiaveisseekdreeLlkvartslsskltskeaeelsklvvdAv.kliee 155
                                   +++hptti+ +++k l+   e L       +  ++d++eL++ ++  ++++ ++ e + ++  v+++  k++  
  gi|13541932|ref|NP_111620.1|  12 ENLHPTTICVVMDKFLDSFAELLGVL----E--DQDQDELMDFISRYARTDEIRPEDKTVGFVVINSAkKMMSV 79 
                                   599********************644....3..357899***************************99666543 PP

>> RapA_C  RNA polymerase recycling family C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   2.4e-05      0.14      96     152 ..      32      87 ..      27      90 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 2.4e-05
                                   HHHHHHHCCC--TTHHHHCHHHHHHHTEEEE--SSSSEEEEE-STT--TT-S--S-- CS
                        RapA_C  96 elveaiaeedndteleeflerlfdaigveqedkseksivlrpsehmlveafpglped 152
                                   el+  ++++d+d el +f++r   +  ++ edk  + +v++  ++m+  +f  ++e+
  gi|13541932|ref|NP_111620.1|  32 ELLGVLEDQDQD-ELMDFISRYARTDEIRPEDKTVGFVVINSAKKMMSVSFSDIDEN 87 
                                   566667777766.678*********************************99999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       832  (0.0464053); expected 358.6 (0.02)
Passed bias filter:                      612  (0.0341346); 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: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 734.86
//
Query:       gi|13541933|ref|NP_111621.1|  [L=81]
Description: hypothetical protein TVN1102 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       813  (0.0453455); expected 358.6 (0.02)
Passed bias filter:                      559  (0.0311785); 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 0.30s 00:00:00.75 Elapsed: 00:00:00.49
# Mc/sec: 497.32
//
Query:       gi|13541934|ref|NP_111622.1|  [L=110]
Description: hypothetical protein TVN1103 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.078   13.1   0.1        0.1   12.7   0.1    1.2  1  TssO             Type VI secretion system, TssO
       0.17   11.9   0.0       0.25   11.4   0.0    1.2  1  DDE_Tnp_1_assoc  DDE_Tnp_1-associated


Domain annotation for each model (and alignments):
>> TssO  Type VI secretion system, TssO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   1.1e-05       0.1      97     134 ..      29      66 ..      21      77 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.1e-05
                          TssO  97 tygknssdeRykmyaqiakfykmlledKkelksvseni 134
                                    y +   d+Ry++y ++++++++ le Kk  ks+s+ i
  gi|13541934|ref|NP_111622.1|  29 LYRRSTGDRRYDVYFNFLTLLQDVLEGKKGWKSISDYI 66 
                                   6888899**************************99955 PP

>> DDE_Tnp_1_assoc  DDE_Tnp_1-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   2.8e-05      0.25      11      50 ..      32      71 ..      30      81 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.8e-05
               DDE_Tnp_1_assoc 11 RrergkrhpladiLlialcaviagadsweeieefakekee 50
                                  R++  +r+++   +l+ l  v+ g ++w++i+++++++++
  gi|13541934|ref|NP_111622.1| 32 RSTGDRRYDVYFNFLTLLQDVLEGKKGWKSISDYIRDNPD 71
                                  88899******************************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 724.67
//
Query:       gi|13541935|ref|NP_111623.1|  [L=473]
Description: NADH dehydrogenase subunit N [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-46  159.0  35.2    1.4e-46  159.0  35.2    2.8  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 ?   -3.3   5.9      0.22     4e+03     116     160 ..       4      50 ..       2      59 .. 0.64
   2 !  159.0  35.2     8e-51   1.4e-46       3     293 .]     113     414 ..     111     414 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 0.22
               Proton_antipo_M 116 vsallAatlvkagvlllirllllla..vssneisqlllilaiismll 160
                                   +s+++  +l+ + +++++++ ++++  ++s +is + li a++s+++
  gi|13541935|ref|NP_111623.1|   4 ISIFIPEILLVIMGFIVLAVGMFIQsgKASAAISFITLIAALLSVFF 50 
                                   68888555555555555544444443777777777777777777776 PP

  == domain 2  score: 159.0 bits;  conditional E-value: 8e-51
               Proton_antipo_M   3 dLlllylglElvllplylLiglwkkkpksleAslklflltllgsliLLlgilllynltgtlefeelskal...elglnsle 80 
                                   +L+  ++++E v++ +y++ ++ +k+ ++leA++k+f+++ ++  +++lgi   +    t ++  +++          ++e
  gi|13541935|ref|NP_111623.1| 113 NLVIAFVAFESVSIMTYIMSAYGGKQ-RNLEATIKYFFTGTIATTFIILGIGFYFFSVHTFSLSPVLNGSsisYYSGTKPE 192
                                   8999*************999998777.************************866666666777777776655555778899 PP

               Proton_antipo_M  81 lllllllllvgllvKsaqvplhlWlpdayveaPtpvsallAatlvkagvlllirllllla..vssneisqlllilaiisml 159
                                   +ll+ll+ll+g+ +K+a +p+h+W  day +    vsa l +t  k+ +++l+  ++l+    +   +++++ i+aii+m 
  gi|13541935|ref|NP_111623.1| 193 FLLALLFLLIGFGFKLAIFPMHQWAIDAYDGTENGVSAYL-STGTKIMAFVLVLKIFLVGfqSFPTPVYYMFTIIAIITMT 272
                                   ****************************************.88888877777766666554467778999*********** PP

               Proton_antipo_M 160 lgslvalaqtdiKrllAySsishlGymlialav..........atqygveaaiihllthalfkallFllagsviyerektr 230
                                   +++++al+q+++KrllAySs+++ Gym++ ++v          + + +++a +++ l+++++k + F++++ v   +e+  
  gi|13541935|ref|NP_111623.1| 273 YANVAALSQMNVKRLLAYSSVAQAGYMILVISVvsyvglgsarSVSLAIAAGMFYALVYVFMKGGSFIAMNMV---KEDNI 350
                                   ****************************9988833333311111123456679999************99555...45677 PP

               Proton_antipo_M 231 dirayggLakkmPilalvllvlllslaGlPptagFlskfliLeaavavslillvla.vvasvlt 293
                                   ++++++gL kk P +a+ + +lllslaG+P+t gFl+k  ++ ++++ +l++l+++ ++ s+++
  gi|13541935|ref|NP_111623.1| 351 TFENISGLGKKSPYVAASFSILLLSLAGIPLTGGFLAKYFLFLSVIDSGLWWLAIIaIINSAIS 414
                                   8999**************************************************9989988875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (473 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1238  (0.0690501); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                        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: 0.66u 0.31s 00:00:00.97 Elapsed: 00:00:00.49
# Mc/sec: 2929.74
//
Query:       gi|13541936|ref|NP_111624.1|  [L=516]
Description: NADH dehydrogenase subunit M [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.4e-47  160.7  30.4    4.4e-47  160.7  30.4    2.0  2  Proton_antipo_M  Proton-conducting membrane transporter


Domain annotation for each model (and alignments):
>> Proton_antipo_M  Proton-conducting membrane transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.1   2.4       0.4   7.1e+03     116     147 ..      27      56 ..      24      96 .. 0.58
   2 !  160.7  30.4   2.5e-51   4.4e-47       1     293 []     121     428 ..     121     428 .. 0.86

  Alignments for each domain:
  == domain 1  score: -4.1 bits;  conditional E-value: 0.4
               Proton_antipo_M 116 vsallAat.lvkagvlllirlllllavssneis 147
                                   vsa l+++ l+++ ++ ++r+++      ++is
  gi|13541936|ref|NP_111624.1|  27 VSAVLSGIlLLEIIAYSIMRFSSYSG---GFIS 56 
                                   66666443145677777776665544...2222 PP

  == domain 2  score: 160.7 bits;  conditional E-value: 2.5e-51
               Proton_antipo_M   1 andLlllylglElvllplylLiglwkkkpksleAslklflltllgsliLLlgilllynltg......tlefeelskalelg 75 
                                   + d l +y+++E+vl+p+y++ig ++   ++++ slk+f++t +gs+++Ll+i+ ly+++       t e+  l+++l + 
  gi|13541936|ref|NP_111624.1| 121 SRDFLFFYIFWEVVLIPVYFMIGRYGIG-NKNSISLKFFVYTHIGSVFILLSIFTLYSQSYvylaspTFEIGPLMSILPKL 200
                                   67999********************888.99999**********************9998777776788888888885444 PP

               Proton_antipo_M  76 lnslelllllllllvgllvKsaqvplhlWlpdayveaPtpvsallAatlvkagvlllirllllla.vssneisqlllilai 155
                                          ++++ +l+g+lvK++ +p+h Wlpd+y  aP p+s++lA+ ++ +g+++l+ ++       +  + +ll++l+i
  gi|13541936|ref|NP_111624.1| 201 SLFY-KGFVIFGFLFGFLVKMPSFPIHSWLPDSYYSAPYPGSVILAGAISMMGGYGLFGIMIESYkALDVYVLYLLIALGI 280
                                   4444.4455666778******************************************976654443889999999****** PP

               Proton_antipo_M 156 ismllgslvalaqtdiKrllAySsishlGymlialav.........atqygveaa..iihllthalfkallFllagsviye 225
                                   is+++ +l a++q++iK+++A+ s s +G+++i +a+          ++ ++eaa  ++++++h+l+ +l+F +    i++
  gi|13541936|ref|NP_111624.1| 281 ISLIYFALTAMFQRNIKKMMAFASASAMGFVTISFAAsiletsgidYSVRALEAAggMFQIVAHGLIMSLVFSAL-YYISR 360
                                   ********************************98887555332111122333433559**************999.66688 PP

               Proton_antipo_M 226 rektrdirayggLakkmPilalvllvlllslaGlPptagFlskfliLeaavavslillvlavvasvlt 293
                                   ++kt+++  +gg++   P la + lv+ll+  GlP++agF+++f+i  ++++  ++ + l++++ ++t
  gi|13541936|ref|NP_111624.1| 361 NTKTDSVYGLGGIYREAPKLASLTLVGLLASLGLPGFAGFIGEFSIVVGVFQTVSWYIFLIIFGMIIT 428
                                   88**************************************************9999999998988886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (516 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1174  (0.0654805); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); 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):               1  [number of targets reported over threshold]
# CPU time: 0.65u 0.35s 00:00:01.00 Elapsed: 00:00:00.52
# Mc/sec: 2982.86
//
Query:       gi|13541937|ref|NP_111625.1|  [L=351]
Description: NADH:ubiquinone oxidoreductase subunit 5 (chain L) [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.3e-33  114.8   9.4    4.3e-33  114.8   9.4    1.9  2  Proton_antipo_M  Proton-conducting membrane transporter
    1.8e-05   24.4   2.5    1.8e-05   24.4   2.5    3.1  3  NADH5_C          NADH dehydrogenase subunit 5 C-terminus
  ------ inclusion threshold ------
      0.015   15.4   0.1       0.18   12.0   0.1    2.2  2  DUF3539          Protein of unknown function (DUF3539)
        5.9    6.9  12.2       0.78    9.7   0.2    3.6  3  TNFR_16_TM       Tumor necrosis factor receptor member 16 tra


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 !  114.8   9.4   9.7e-37   4.3e-33     153     278 ..       3     131 ..       1     154 [. 0.93
   2 ?   -3.4   0.1      0.97   4.4e+03     114     131 ..     228     244 ..     223     256 .. 0.54

  Alignments for each domain:
  == domain 1  score: 114.8 bits;  conditional E-value: 9.7e-37
               Proton_antipo_M 153 laiismllgslvalaqtdiKrllAySsishlGymlialav...atqygveaaiihllthalfkallFllagsviyerektr 230
                                   +++ ++l++++++l+ +d+Kr+lAyS+is+lGyml a+++    ++ +v++ ++hl++ha+fkallF+ ag++  ++++ r
  gi|13541937|ref|NP_111625.1|   3 IGSFTALYAGILGLVVNDVKRILAYSTISQLGYMLAAIGLgpiIGSVAVSLGMFHLVSHAIFKALLFMSAGAFLIAMMDLR 83 
                                   7899**********************************98555678889999***************************** PP

               Proton_antipo_M 231 dirayggLakkmPilalvllvlllslaGlPptagFlskfliLeaavav 278
                                   d +++ggL+k+mPi+ +++++++l+l++ P+t+g++sk+ i++a++++
  gi|13541937|ref|NP_111625.1|  84 DAKQMGGLWKRMPITTTAFFIGALALVAFPGTSGYFSKDPIIYASYNY 131
                                   *******************************************99986 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 0.97
               Proton_antipo_M 114 tpvsallAatlvkagvll 131
                                   + +s+l  a+l+++g ++
  gi|13541937|ref|NP_111625.1| 228 VYISTLP-AILLAIGFFV 244
                                   5555555.5555555443 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 ?   -1.3   0.9      0.31   1.4e+03      98     132 ..      46      81 ..       7     104 .. 0.65
   2 ?   -2.2   2.0      0.59   2.6e+03      68      96 ..      98     126 ..      48     154 .. 0.51
   3 !   24.4   2.5   4.1e-09   1.8e-05       1     180 [.     157     344 ..     157     345 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.31
                       NADH5_C  98 lssfssslwFlpslshrllsk.lsLklgqklakqlD 132
                                   + s+  sl+ +  +sh ++   l+++ g +l+  +D
  gi|13541937|ref|NP_111625.1|  46 IGSVAVSLGMFHLVSHAIFKAlLFMSAGAFLIAMMD 81 
                                   445555666666666655543133444555555455 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.59
                       NADH5_C  68 allvtilGlllglelsklslkllkkslkl 96 
                                   + + +++G+l  + +  +s ++ k  + +
  gi|13541937|ref|NP_111625.1|  98 TTTAFFIGALALVAFPGTSGYFSKDPIIY 126
                                   22333455555555555555555554444 PP

  == domain 3  score: 24.4 bits;  conditional E-value: 4.1e-09
                       NADH5_C   1 YSlRliyyvllgsprfsslspineenptllnpilrLalgsiiaGsl...lswlifpk.......tpvitlplllKllallv 71 
                                   Y++R++++v +g+pr       ++     + p+++L+l+++i G+    +  ++ p+         v t p+++ +l+ ++
  gi|13541937|ref|NP_111625.1| 157 YTFRMFFLVATGKPRSVLAERAKDPPVLATIPLMILSLFALILGIWqvpFYKFVAPTldgvaaaIRVPTAPVYISTLPAIL 237
                                   9*******************************************863334444444312222225689************* PP

                       NADH5_C  72 tilGlllglelsklslkllkkslklnlssfssslwFlpslshrllsklsLklgqklakqlDqgWlEklgpkglaklllkls 152
                                     +G+++ l +  ++   +    k+ ++  +    +   l +r++s   +   +  ++ ++  +      + l +  ++l 
  gi|13541937|ref|NP_111625.1| 238 LAIGFFVDLYIYGFEKWKTWDISKTWYYKLVKNKFYIDVLYTRIISERVILPLSAAFSGFENKYNS--AVNDLGSDTVTLG 316
                                   *************9955544444446777777777777788888888777777777777**99985..56788899999** PP

                       NADH5_C 153 kliqnlqkglikiyLlsflltlllllll 180
                                   +++ nlq+g +  y+++++l  ++++++
  gi|13541937|ref|NP_111625.1| 317 SYFRNLQNGVLENYVAVLILAAIVIFII 344
                                   ***********************99987 PP

>> DUF3539  Protein of unknown function (DUF3539)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.14   6.3e+02      26      52 ..       6      32 ..       3      35 .. 0.88
   2 ?   12.0   0.1   3.9e-05      0.18      24      42 ..     151     169 ..     147     178 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.14
                                  EEESSEE--EEEEEE-SSSEEEEEE-H CS
                       DUF3539 26 fttLYaqrlfFlvtlkeeelkfepisr 52
                                  ft+LYa  l  +v+  ++ l + +is+
  gi|13541937|ref|NP_111625.1|  6 FTALYAGILGLVVNDVKRILAYSTISQ 32
                                  9******99999999999899998885 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 3.9e-05
                                   EEEEESSEE--EEEEEE-S CS
                       DUF3539  24 elfttLYaqrlfFlvtlke 42 
                                   +l ttLY+ r+fFlv + +
  gi|13541937|ref|NP_111625.1| 151 SLLTTLYTFRMFFLVATGK 169
                                   589************9865 PP

>> TNFR_16_TM  Tumor necrosis factor receptor member 16 trans-membrane domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.27   1.2e+03       9      18 ..       9      18 ..       6      20 .. 0.85
   2 ?    9.7   0.2   0.00017      0.78       8      25 ..     227     244 ..     225     256 .. 0.91
   3 ?   -1.1   5.2      0.44     2e+03      13      23 ..     335     345 ..     330     348 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.27
                    TNFR_16_TM  9 iYcSILaaVv 18
                                   Y  IL++Vv
  gi|13541937|ref|NP_111625.1|  9 LYAGILGLVV 18
                                  5889999998 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00017
                    TNFR_16_TM   8 PiYcSILaaVvvgLlaYv 25 
                                   P+Y+S L+a+++ +  +v
  gi|13541937|ref|NP_111625.1| 227 PVYISTLPAILLAIGFFV 244
                                   9***********997776 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.44
                    TNFR_16_TM  13 ILaaVvvgLla 23 
                                   ILaa+v+++++
  gi|13541937|ref|NP_111625.1| 335 ILAAIVIFIIV 345
                                   99******987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (351 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       670  (0.0373696); 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:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 2192.55
//
Query:       gi|13541938|ref|NP_111626.1|  [L=332]
Description: NADH:ubiquinone oxidoreductase subunit 5 (chain L) [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-54  185.0  14.4    1.7e-54  185.0  14.4    2.1  2  Proton_antipo_M  Proton-conducting membrane transporter
    1.8e-14   53.6   5.3    1.8e-14   53.6   5.3    3.3  4  Proton_antipo_N  NADH-Ubiquinone oxidoreductase (complex I), 
  ------ inclusion threshold ------
       0.51   10.7   4.2        2.6    8.4   0.5    2.6  2  Orf78            Orf78 (ac78)


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 ?   -3.7   5.6      0.86   5.2e+03      55      79 ..      63      87 ..       7     123 .. 0.44
   2 !  185.0  14.4   2.9e-58   1.7e-54       1     191 [.     125     323 ..     125     327 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 0.86
               Proton_antipo_M 55 llynltgtlefeelskalelglnsl 79
                                  ++yn+   +++++l+ ++  +++  
  gi|13541938|ref|NP_111626.1| 63 WFYNIDYGIYIDNLAITMAIMVSFV 87
                                  2222222222222222222222222 PP

  == domain 2  score: 185.0 bits;  conditional E-value: 2.9e-58
               Proton_antipo_M   1 andLlllylglElvllplylLiglwkkkpksleAslklflltllgsliLLlgillly....nltg.tlefeelskal...e 73 
                                   +++L+ll+l++Elv+l++ylLig+w+ kp++++A+ k+f++t++g+l++++g+++ly    n+tg  l++++l++ +    
  gi|13541938|ref|NP_111626.1| 125 SSNLVLLFLFWELVGLCSYLLIGFWFFKPNATAAAKKAFIVTRVGDLSFIIGMSILYyslvNVTGdPLSIPYLISHAsliA 205
                                   78****************************************************988444445667899****99997777 PP

               Proton_antipo_M  74 lglnslelllllllllvgllvKsaqvplhlWlpdayveaPtpvsall.Aatlvkagvlllirlllllavssneisqlllil 153
                                     +++  l ++++++l +++ Ksaq+plh+W+pda +e+Pt vsal+ Aat+v+agv+l++rl  ++  +++++++ ++i+
  gi|13541938|ref|NP_111626.1| 206 SQIGKVRLGIIAIFILGAAIGKSAQFPLHVWIPDA-MEGPTTVSALIhAATMVTAGVYLVARLYQVFLYAAPFAMYAVAII 285
                                   777888888999***********************.********************************************* PP

               Proton_antipo_M 154 aiismllgslvalaqtdiKrllAySsishlGymliala 191
                                   ++ ++l++++++l+ +d+Kr+lAyS+is+lGy li + 
  gi|13541938|ref|NP_111626.1| 286 GSFTALYAGILGLVVNDVKRILAYSTISQLGYRLIYCT 323
                                   **********************************9886 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 !   53.6   5.3     3e-18   1.8e-14      10      55 ..      65     110 ..      60     113 .. 0.93
   2 ?   -2.1   0.2      0.71   4.2e+03      31      41 ..     174     184 ..     171     198 .. 0.74
   3 ?   -1.6   0.0      0.48   2.9e+03      30      37 ..     245     252 ..     244     256 .. 0.90
   4 ?   -2.7   0.4       1.1   6.5e+03      26      40 ..     279     293 ..     277     293 .. 0.83

  Alignments for each domain:
  == domain 1  score: 53.6 bits;  conditional E-value: 3e-18
               Proton_antipo_N  10 lsieigfllDklsalmllvvtfvsllvhlYSigYMaddegyqRFfa 55 
                                   ++i+ g+++D+l ++m+++v+fvsl++hl++i+YM+dd++++ +fa
  gi|13541938|ref|NP_111626.1|  65 YNIDYGIYIDNLAITMAIMVSFVSLMIHLFAIYYMKDDPNKHVYFA 110
                                   5899*****************************************8 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.71
               Proton_antipo_N  31 fvsllvhlYSi 41 
                                   ++++ ++ YS+
  gi|13541938|ref|NP_111626.1| 174 IIGMSILYYSL 184
                                   67777888875 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 0.48
               Proton_antipo_N  30 tfvsllvh 37 
                                   t+vs+l+h
  gi|13541938|ref|NP_111626.1| 245 TTVSALIH 252
                                   89*****9 PP

  == domain 4  score: -2.7 bits;  conditional E-value: 1.1
               Proton_antipo_N  26 llvvtfvsllvhlYS 40 
                                   +  v +++++  lY+
  gi|13541938|ref|NP_111626.1| 279 MYAVAIIGSFTALYA 293
                                   678999999999997 PP

>> Orf78  Orf78 (ac78)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.2     0.026   1.5e+02      70      90 ..      33      54 ..      26      62 .. 0.74
   2 ?    8.4   0.5   0.00043       2.6      64      86 ..      77      99 ..      72     107 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.026
                         Orf78 70 llavvcvlvllyvi.yYfvilr 90
                                  + ++++ l l+++i +Yf +l+
  gi|13541938|ref|NP_111626.1| 33 VASFFIFLALVFAIlSYFQVLK 54
                                  4567777888887636998886 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00043
                         Orf78 64 nillisllavvcvlvllyviyYf 86
                                   i +  ++++v++++ l++iyY 
  gi|13541938|ref|NP_111626.1| 77 AITMAIMVSFVSLMIHLFAIYYM 99
                                  5677889***************5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1139  (0.0635284); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.68u 0.28s 00:00:00.96 Elapsed: 00:00:00.49
# Mc/sec: 2037.21
//
Query:       gi|13541939|ref|NP_111627.1|  [L=103]
Description: NADH dehydrogenase subunit K [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.4e-22   77.4   8.3    6.4e-22   77.2   8.3    1.0  1  Oxidored_q2  NADH-ubiquinone/plastoquinone oxidoreductase cha


Domain annotation for each model (and alignments):
>> Oxidored_q2  NADH-ubiquinone/plastoquinone oxidoreductase chain 4L
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.2   8.3   3.6e-26   6.4e-22       2     103 ..       6      98 ..       5     102 .. 0.96

  Alignments for each domain:
  == domain 1  score: 77.2 bits;  conditional E-value: 3.6e-26
                                   HHHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHHHHHHHHC.............TTSCGGHHHHHHHHHHHHHHH CS
                   Oxidored_q2   2 lllliallfliGlygvllrrnllkvliglelisnavnlllvlagvftegtlvitnpatefadplpqalvLtaivigaaeta 82 
                                   ++++++llf+iGlygv+++r  +k+li++e++ n+++l ++++g++          +++++++ p +++L+ai+ig+ e a
  gi|13541939|ref|NP_111627.1|   6 VSFVALLLFTIGLYGVMTSRVGIKMLISIEIMINSAILSIIGIGSYF---------YSSSVQIDPYVFALFAIAIGVVESA 77 
                                   57899****************************************97.........9************************ PP

                                   HHHHHHHHHHHHSSS-BCCG- CS
                   Oxidored_q2  83 vgLallvrlyreygtddvqel 103
                                   vgL+llv +yr+ g++d++ l
  gi|13541939|ref|NP_111627.1|  78 VGLGLLVIVYRKFGKIDISLL 98 
                                   *****************9866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       878  (0.0489709); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 739.24
//
Query:       gi|13541940|ref|NP_111628.1|  [L=72]
Description: NADH dehydrogenase subunit J [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      7e-05   22.6   6.0    7.7e-05   22.4   6.0    1.1  1  Oxidored_q3  NADH-ubiquinone/plastoquinone oxidoreductase cha


Domain annotation for each model (and alignments):
>> Oxidored_q3  NADH-ubiquinone/plastoquinone oxidoreductase chain 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   6.0   4.3e-09   7.7e-05      76     143 ..       6      66 ..       1      67 [. 0.69

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 4.3e-09
                                   HHHHHHHHHHHHHHHTT--......--------TT-HHHHHHHHTTTTHHHHHHHHHHHHHHHHHHHH CS
                   Oxidored_q3  76 alaalligllllalllllllessssavdaqvadvsnieaigsllftkyllpfelasllLLvaligaiv 143
                                   al++++++++  a+ +++       +  + v+  ++i+ ig ++f+ y++pfel+s+++  a+ig+++
  gi|13541940|ref|NP_111628.1|   6 ALVSAALFFIATAIPVIV-------MPGTFVPVSQDISLIGFSFFNVYIVPFELLSVIIVGAVIGVMY 66 
                                   333333333333332222.......2345577889******************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (72 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       626  (0.0349155); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.50
# Mc/sec: 430.42
//
Query:       gi|13541941|ref|NP_111629.1|  [L=82]
Description: NADH dehydrogenase subunit J [Thermoplasma volcanium GSS1]
Scores for complete 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   52.8  12.6    3.5e-14   52.8  12.6    1.8  2  Oxidored_q3      NADH-ubiquinone/plastoquinone oxidoreductase
  ------ inclusion threshold ------
       0.12   12.5  12.5       0.11   12.6  11.6    1.3  1  DUF4040          Domain of unknown function (DUF4040)
        5.3    7.0   9.1        2.8    7.9   7.5    1.4  1  RseC_MucC        Positive regulator of sigma(E), RseC/MucC
        5.5    6.6  14.1        7.3    6.2  14.1    1.2  1  SUR7             SUR7/PalI family
        7.1    5.5   8.4        8.8    5.2   8.4    1.2  1  DUF3488          Domain of unknown function (DUF3488)
        8.7    5.6  11.2        4.3    6.6   9.2    1.6  2  SLATT_5          SMODS and SLOG-associating 2TM effector doma


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 ?    0.6   1.5      0.14   4.1e+02      13      28 ..       3      18 ..       1      23 [. 0.51
   2 !   52.8  12.6   1.2e-17   3.5e-14       2      60 ..      18      76 ..      17      82 .] 0.93

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.14
                                  HHHHHHHHHHHHHHHH CS
                   Oxidored_q3 13 ysalfLilsfvgvagl 28
                                  y  +f i++++++a+ 
  gi|13541941|ref|NP_111629.1|  3 YTLIFSIIAVFLIAFS 18
                                  5555555555555543 PP

  == domain 2  score: 52.8 bits;  conditional E-value: 1.2e-17
                                  HHHHHH-SBHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHIIIIIHHHHHHHHHHHS CS
                   Oxidored_q3  2 allvitsknpvysalfLilsfvgvaglfillgaeFlallqilvYvGAilvlflFvimll 60
                                  ++l +  kn+ +sa++L l ++++a+ f++lga+F+a++ ilvY+GA++ l++F++ml+
  gi|13541941|ref|NP_111629.1| 18 SVLSVKEKNITHSAIYLFLFLFILAAEFLFLGASFVAAVEILVYIGAVVTLIVFTVMLT 76
                                  6788999***************************************************6 PP

>> DUF4040  Domain of unknown function (DUF4040)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6  11.6   3.8e-05      0.11       1      62 [.      12      75 ..      12      78 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.8e-05
                       DUF4040  1 lllvlaalaavlardrlaavillgvvGllvallfvllgAPDvAlTqaav..veglttvllllal 62
                                  ++l++++++ v  ++  +++i+l ++ +++a+ f++lgA  vA  +++v  ++++t++++ + l
  gi|13541941|ref|NP_111629.1| 12 VFLIAFSVLSVKEKNITHSAIYLFLFLFILAAEFLFLGASFVAAVEILVyiGAVVTLIVFTVML 75
                                  5899999***************************************975226666666665554 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 ?    7.9   7.5   0.00092       2.8      55     111 ..      19      75 ..      17      80 .. 0.91

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00092
                     RseC_MucC  55 evgieeksllkaallvYllPllllilgallgsallgssellaalgallglvlgfliv 111
                                   +++++ek++ ++a++++l+ ++l   +++lg +++++ e+l+ +ga++ l++  +++
  gi|13541941|ref|NP_111629.1|  19 VLSVKEKNITHSAIYLFLFLFILAAEFLFLGASFVAAVEILVYIGAVVTLIVFTVML 75 
                                   57899**************9999999******99999***********999987776 PP

>> SUR7  SUR7/PalI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2  14.1    0.0024       7.3     119     179 ..       1      65 [.       1      78 [. 0.77

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0024
                          SUR7 119 hiialvlsfislvvgllaic....vspdnsrllsflnlllsvlsflatllaalldtllfvfvrkk 179
                                   +i +l++s+i+++++ ++++     +  +s +++fl l++  + fl++ ++++ ++ + v++  +
  gi|13541941|ref|NP_111629.1|   1 MIYTLIFSIIAVFLIAFSVLsvkeKNITHSAIYLFLFLFILAAEFLFLGASFVAAVEILVYIGAV 65 
                                   68899*********999997444444445557999999999999999999998877777765554 PP

>> DUF3488  Domain of unknown function (DUF3488)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   8.4    0.0029       8.8      76     138 ..      10      72 ..       2      80 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0029
                       DUF3488  76 valLvlllalKllElrsrRDalvllllgffllatsflfsqsllfalylllalllllaalvalh 138
                                   +a++++++++  +  ++  +  + l+l +f+la++flf    ++a++ +l++++++++l+ ++
  gi|13541941|ref|NP_111629.1|  10 IAVFLIAFSVLSVKEKNITHSAIYLFLFLFILAAEFLFLGASFVAAVEILVYIGAVVTLIVFT 72 
                                   445555555555556666667777888889999999988888888888888888888887665 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 ?    6.6   9.2    0.0014       4.3      33      73 ..       3      43 ..       1      62 [. 0.84
   2 ?   -1.0   0.2      0.31   9.3e+02     171     186 ..      57      72 ..      44      77 .. 0.49

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0014
                       SLATT_5 33 stfslsllSvylivlsllsnkssestinenlldflsiilSi 73
                                  +t+++s+++v+li++s+ls+k+++ t++  +l ++ +il+ 
  gi|13541941|ref|NP_111629.1|  3 YTLIFSIIAVFLIAFSVLSVKEKNITHSAIYLFLFLFILAA 43
                                  799****************9999999999998888877764 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.31
                       SLATT_5 171 ylivifllylliillp 186
                                   +++v++  + ++i+++
  gi|13541941|ref|NP_111629.1|  57 EILVYIGAVVTLIVFT 72 
                                   3333333334444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1441  (0.0803726); expected 358.6 (0.02)
Passed bias filter:                      547  (0.0305092); expected 358.6 (0.02)
Passed Vit filter:                        92  (0.00513135); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-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 0.36s 00:00:00.92 Elapsed: 00:00:00.53
# Mc/sec: 469.09
//
Query:       gi|13541942|ref|NP_111630.1|  [L=154]
Description: NADH dehydrogenase subunit I [Thermoplasma volcanium GSS1]
Scores for complete 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-12   47.0  34.1    1.6e-07   31.8  13.5    2.1  3  Fer4_7    4Fe-4S dicluster domain
    5.7e-12   44.9  10.8    6.1e-06   25.8   3.2    2.2  2  Fer4      4Fe-4S binding domain
    2.5e-09   38.0   5.5    0.00022   22.1   1.8    2.3  2  Fer4_16   4Fe-4S double cluster binding domain
    2.7e-09   37.1   5.2    4.1e-09   36.5   5.2    1.4  1  Fer4_9    4Fe-4S dicluster domain
    3.7e-08   33.8   3.4     0.0039   17.7   0.3    2.3  2  Fer4_17   4Fe-4S dicluster domain
    5.9e-07   29.5  12.8    3.3e-06   27.1  13.0    1.9  1  Fer4_21   4Fe-4S dicluster domain
    6.8e-07   29.3  22.4    1.2e-05   25.3  12.2    1.9  2  Fer4_10   4Fe-4S dicluster domain
    1.4e-06   28.1  12.3    0.00098   19.1   2.7    2.3  2  Fer4_6    4Fe-4S binding domain
    7.2e-06   25.8  11.6     0.0032   17.5   1.2    2.3  2  Fer4_2    4Fe-4S binding domain
    1.3e-05   25.6  11.2    3.4e-05   24.2  11.2    1.7  1  Fer4_8    4Fe-4S dicluster domain
    7.7e-05   23.5   1.3       0.18   12.7   0.1    2.2  2  Fer4_22   4Fe-4S dicluster domain
      0.003   17.9  10.3       0.13   12.9   0.9    2.2  2  Fer4_4    4Fe-4S binding domain
  ------ inclusion threshold ------
      0.014   15.5  11.3       0.21   11.8   1.2    2.2  2  Fer4_18   4Fe-4S dicluster domain
      0.017   16.0  17.2      0.067   14.2   5.4    2.3  2  Fer4_3    4Fe-4S binding domain
      0.074   13.6  11.8       0.97   10.0   2.5    2.4  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
        6.2    7.5  12.5        1.4    9.5   3.4    2.5  2  AFP       Insect antifreeze protein repeat


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 !   21.6   1.5   2.2e-07   0.00024      29      49 ..      59      79 ..      39      82 .. 0.72
   2 !   31.8  13.5   1.4e-10   1.6e-07       2      52 .]      68     122 ..      67     122 .. 0.79
   3 !   17.7   3.7   3.6e-06    0.0041       1      25 [.     107     131 ..     107     150 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 2.2e-07
                        Fer4_7 29 ekveidpekClgCgaCvavCP 49
                                   ++ +++++C+gC+ C++vCP
  gi|13541942|ref|NP_111630.1| 59 FRIFLSMDDCVGCTLCEQVCP 79
                                  456679*************** PP

  == domain 2  score: 31.8 bits;  conditional E-value: 1.4e-10
                        Fer4_7   2 CigCgaCvaaCpvkaieldeeenek....gtekveidpekClgCgaCvavCPtga 52 
                                   C+gC  C+++Cp+  i++  +e+++    ++ +++++  +C+ C++C++ CPt+a
  gi|13541942|ref|NP_111630.1|  68 CVGCTLCEQVCPNLSIRMIVVERNNphnkRNLYPQVNFGTCTVCRNCEEICPTEA 122
                                   ************99999874444432222446679999***************87 PP

  == domain 3  score: 17.7 bits;  conditional E-value: 3.6e-06
                        Fer4_7   1 rCigCgaCvaaCpvkaieldeeene 25 
                                   +C+ C++C++ Cp++ai+l+ e + 
  gi|13541942|ref|NP_111630.1| 107 TCTVCRNCEEICPTEAIYLTHELET 131
                                   5****************99866444 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.9   2.1e-08   2.4e-05       4      23 ..      64      83 ..      61      84 .. 0.85
   2 !   25.8   3.2   5.5e-09   6.1e-06       1      24 []     101     124 ..     101     124 .. 0.94

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 2.1e-08
                                  ETTTSSS-THHHHHSTTTEE CS
                          Fer4  4 deekCigCGaCvevCPvgAI 23
                                   +++C+gC +C++vCP+  I
  gi|13541942|ref|NP_111630.1| 64 SMDDCVGCTLCEQVCPNLSI 83
                                  679*************8655 PP

  == domain 2  score: 25.8 bits;  conditional E-value: 5.5e-09
                                   EEEETTTSSS-THHHHHSTTTEEE CS
                          Fer4   1 vvideekCigCGaCvevCPvgAIt 24 
                                   ++++   C+ C +C+e+CP++AI+
  gi|13541942|ref|NP_111630.1| 101 PQVNFGTCTVCRNCEEICPTEAIY 124
                                   57999******************6 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.1   4.6e-06    0.0051      52      66 ..      66      80 ..      34      99 .. 0.67
   2 !   22.1   1.8     2e-07   0.00022       1      37 [.     107     144 ..     107     154 .] 0.64

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 4.6e-06
                       Fer4_16 52 eaitgCdiCqdvCPa 66
                                   ++ gC  C++vCP+
  gi|13541942|ref|NP_111630.1| 66 DDCVGCTLCEQVCPN 80
                                  566666666666663 PP

  == domain 2  score: 22.1 bits;  conditional E-value: 2e-07
                       Fer4_16   1 rCgtCgkCaevCPtnaikekkekeiearecisy...ntae 37 
                                   +C+ C++C e+CPt+ai  +   e+e+ ++ ++   + +e
  gi|13541942|ref|NP_111630.1| 107 TCTVCRNCEEICPTEAIYLT--HELETARTRNNffySPQE 144
                                   5*****************99..555555555442223333 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.5   5.2   3.7e-12   4.1e-09       1      51 []      67     123 ..      50     123 .. 0.96

  Alignments for each domain:
  == domain 1  score: 36.5 bits;  conditional E-value: 3.7e-12
                        Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraase......eaCigCgaCveaCpkgai 51 
                                   +C+gC+ C+++Cp+  +++  +er + +++++         C+ C+ C+e+Cp++ai
  gi|13541942|ref|NP_111630.1|  67 DCVGCTLCEQVCPNLSIRMIVVERNNPHNKRNLypqvnfGTCTVCRNCEEICPTEAI 123
                                   5************************999999889*****99*************987 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.3   3.5e-06    0.0039      42      58 ..      64      80 ..      41      82 .. 0.88
   2 !   17.0   0.2   5.7e-06    0.0064      44      59 ..     106     121 ..      83     153 .. 0.63

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 3.5e-06
                       Fer4_17 42 kaslCieCgeCerkCPq 58
                                   +++C++C +Ce++CP+
  gi|13541942|ref|NP_111630.1| 64 SMDDCVGCTLCEQVCPN 80
                                  699*************7 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 5.7e-06
                       Fer4_17  44 slCieCgeCerkCPqg 59 
                                   ++C+ C++Ce+ CP +
  gi|13541942|ref|NP_111630.1| 106 GTCTVCRNCEEICPTE 121
                                   5566666666666543 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1  13.0   2.9e-09   3.3e-06       5      57 ..      65     123 ..      62     125 .. 0.82

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 2.9e-09
                       Fer4_21   5 edkCigCgkCliaCedtshqaieidaktvl.......kvvedeCvGCnlCssvCPvedci 57 
                                    d+C+gC++C ++C++ s+  i ++ ++ +       +v   +C+ C  C ++CP+ ++i
  gi|13541942|ref|NP_111630.1|  65 MDDCVGCTLCEQVCPNLSIRMIVVERNNPHnkrnlypQVNFGTCTVCRNCEEICPT-EAI 123
                                   689*******************87766644444455578889*************7.777 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3  12.2     1e-08   1.2e-05       4      56 .]      63     119 ..      60     119 .. 0.89
   2 !   16.1   2.5   8.1e-06    0.0091       5      23 ..     104     122 ..     100     151 .. 0.73

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 1e-08
                       Fer4_10   4 idddtCirCgkCvkaCPadl....tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                   +  d C++C+ C ++CP          ++++ ++++   +++ + Ct c +C e+CP
  gi|13541942|ref|NP_111630.1|  63 LSMDDCVGCTLCEQVCPNLSirmiVVERNNPHNKRNLYPQVNFGTCTVCRNCEEICP 119
                                   56799*************55998878888899999999999***************9 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 8.1e-06
                       Fer4_10   5 dddtCirCgkCvkaCPadl 23 
                                   +  tC+ C++C + CP+ +
  gi|13541942|ref|NP_111630.1| 104 NFGTCTVCRNCEEICPTEA 122
                                   5679************944 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   2.2   3.1e-05     0.034       7      20 ..      66      79 ..      64      86 .. 0.90
   2 !   19.1   2.7   8.7e-07   0.00098       8      24 .]     107     123 ..     101     123 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.1e-05
                        Fer4_6  7 dkCigCgdCvrvCP 20
                                  d C+gC  C+ vCP
  gi|13541942|ref|NP_111630.1| 66 DDCVGCTLCEQVCP 79
                                  67************ PP

  == domain 2  score: 19.1 bits;  conditional E-value: 8.7e-07
                        Fer4_6   8 kCigCgdCvrvCPegai 24 
                                    C+ C++C+ +CP+ ai
  gi|13541942|ref|NP_111630.1| 107 TCTVCRNCEEICPTEAI 123
                                   6*************998 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   1.2   2.9e-06    0.0032       4      22 .]      62      80 ..      59      80 .. 0.85
   2 !   13.4   3.3   5.7e-05     0.064       2      22 .]     100     120 ..      99     120 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2.9e-06
                        Fer4_2  4 vvdtdrCigCgaCvsaCPa 22
                                  +   d C+gC  C ++CP+
  gi|13541942|ref|NP_111630.1| 62 FLSMDDCVGCTLCEQVCPN 80
                                  666789************5 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 5.7e-05
                        Fer4_2   2 pvvvdtdrCigCgaCvsaCPa 22 
                                   +++v+  +C+ C+ C   CP+
  gi|13541942|ref|NP_111630.1| 100 YPQVNFGTCTVCRNCEEICPT 120
                                   68999***************7 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2  11.2     3e-08   3.4e-05       2      64 ..      65     121 ..      64     122 .. 0.71

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 3e-08
                        Fer4_8   2 lekCieCgaCqsaCpvlrrtk..khlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64 
                                   +++C++C +C++ Cp l+ +    +++++ ++++      qv     ++++Ct c++C+e Cp++
  gi|13541942|ref|NP_111630.1|  65 MDDCVGCTLCEQVCPNLSIRMivVERNNPHNKRNL---YPQV-----NFGTCTVCRNCEEICPTE 121
                                   689************77766442344444444444...3333.....489*************85 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.1   0.00016      0.18      78      94 ..      64      80 ..      38      83 .. 0.84
   2 !   10.1   0.2   0.00099       1.1       2      22 ..     108     128 ..      88     146 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00016
                       Fer4_22 78 gesgCvGCgRCieacpv 94
                                  ++  CvGC  C+++cp+
  gi|13541942|ref|NP_111630.1| 64 SMDDCVGCTLCEQVCPN 80
                                  67789999999999985 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00099
                       Fer4_22   2 ClsCgaCtlvCptCsCfdved 22 
                                   C  C +C  +Cpt   + +++
  gi|13541942|ref|NP_111630.1| 108 CTVCRNCEEICPTEAIYLTHE 128
                                   888888888888877666655 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.9   0.00011      0.13       2      15 ..      66      79 ..      65      92 .. 0.90
   2 !    9.5   2.8    0.0013       1.5       3      16 ..     107     120 ..     105     124 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00011
                        Fer4_4  2 erCigCgsCvaaCP 15
                                  + C+gC  C+ +CP
  gi|13541942|ref|NP_111630.1| 66 DDCVGCTLCEQVCP 79
                                  77***********9 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0013
                        Fer4_4   3 rCigCgsCvaaCPq 16 
                                   +C+ C+ C+ +CP+
  gi|13541942|ref|NP_111630.1| 107 TCTVCRNCEEICPT 120
                                   6999*********7 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   3.1    0.0016       1.8      58      73 ..      65      80 ..      57      87 .. 0.85
   2 ?   11.8   1.2   0.00019      0.21      47      74 ..      94     121 ..      84     130 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0016
                       Fer4_18 58 agdcidcescvkvcPt 73
                                  + dc+ c  c +vcP 
  gi|13541942|ref|NP_111630.1| 65 MDDCVGCTLCEQVCPN 80
                                  68*************5 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00019
                       Fer4_18  47 lkekeerkekgagdcidcescvkvcPtg 74 
                                   ++++++  + + g c+ c+ c ++cPt+
  gi|13541942|ref|NP_111630.1|  94 HNKRNLYPQVNFGTCTVCRNCEEICPTE 121
                                   566777788999**************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 ?   14.2   5.4     6e-05     0.067       1      13 [.      68      80 ..      68      82 .. 0.95
   2 ?    7.7   4.0    0.0071       7.9       1      15 []     108     122 ..     108     122 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 6e-05
                        Fer4_3  1 CtgCgaCvevCPv 13
                                  C+gC +C++vCP+
  gi|13541942|ref|NP_111630.1| 68 CVGCTLCEQVCPN 80
                                  ************5 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0071
                        Fer4_3   1 CtgCgaCvevCPvgA 15 
                                   Ct C+ C+e CP+ A
  gi|13541942|ref|NP_111630.1| 108 CTVCRNCEEICPTEA 122
                                   777*9*******876 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 ?   10.0   2.5   0.00086      0.97       4      18 ..      66      80 ..      65      81 .. 0.91
   2 ?    8.4   2.0    0.0027         3       2      17 ..     104     119 ..     103     124 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00086
                       Fer4_13  4 dtCiacgaCvelaPd 18
                                  d C++c++C +++P+
  gi|13541942|ref|NP_111630.1| 66 DDCVGCTLCEQVCPN 80
                                  68************8 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0027
                       Fer4_13   2 DrdtCiacgaCvelaP 17 
                                   +  tC+ c +C e++P
  gi|13541942|ref|NP_111630.1| 104 NFGTCTVCRNCEEICP 119
                                   5679************ PP

>> AFP  Insect antifreeze protein repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   1.8      0.18     2e+02       2       8 ..      68      74 ..      65      76 .. 0.82
   2 ?    9.5   3.4    0.0012       1.4       1       8 [.     107     114 ..     107     116 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.18
                           AFP  2 CTgsknC 8 
                                  C g+++C
  gi|13541942|ref|NP_111630.1| 68 CVGCTLC 74
                                  8888888 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0012
                           AFP   1 tCTgsknC 8  
                                   tCT+++nC
  gi|13541942|ref|NP_111630.1| 107 TCTVCRNC 114
                                   9******* PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       685  (0.0382063); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1077.69
//
Query:       gi|13541943|ref|NP_111631.1|  [L=346]
Description: NADH dehydrogenase subunit H [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-88  296.0  22.2    3.6e-88  295.7  22.2    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 !  295.7  22.2     2e-92   3.6e-88       4     297 ..      29     336 ..      26     338 .. 0.94

  Alignments for each domain:
  == domain 1  score: 295.7 bits;  conditional E-value: 2e-92
                                   HHHHHHHHHHHHHHHHHHHHHHHHHTTS--S-SSTTTTTTHHHHHHHHHCCS-----TTS-HHHHHHHHHHHHHHHHCTTT CS
                        NADHdh   4 llllvvlllvvalltlleRkvlAriqdRlGPnrvGplGllqplaDalKlllKediipkkadkllfllapvlalilallafa 84 
                                   +++l+++++ ++ +++l Rk++Ar+q R+GPnrvG++G lq++aDa+Kl+ Ke+i+pk  d + +++ap++++i  ++ f+
  gi|13541943|ref|NP_111631.1|  29 IFFLIFVFVSLIAMIYLFRKYMARLQLRYGPNRVGKFGSLQLIADAIKLVGKESILPKLRDDFAYKTAPYIVFIGLVVGFI 109
                                   566777888888********************************************************************* PP

                                   TS-SSS.......SSS--TTHHHHHHHHHHHCHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-SS. CS
                        NADHdh  85 viPfge.......vladlnvglllilalsslgvygillaGwasnskYallGalRsaaqmisyEvalglsllavvllagsl. 157
                                   +iP+g+       ++++ +v+l+l++  ++++++g +laG++s++kYallGa+R +a  +s+Ev+++ls++a+v++ + + 
  gi|13541943|ref|NP_111631.1| 110 LIPYGDfywigslTITHSDVSLILFFGAIAMMPIGEILAGISSHNKYALLGAMRGVAKDVSFEVPMMLSAIALVMMDSAVn 190
                                   *****6667788999999**********************************************************77775 PP

                                   ....-HHHHHHCCCTT-CCCCHHHHHHHHHHHHHHCCTCTTBTTTTSTTSSSSCCCTT-HCHHHHHHHHHHHHHHHHHHHH CS
                        NADHdh 158 ....slseiveaqeeiwfillqllafiifliallaetnraPFDlpeaesELvaGfhtEYsgmkfalfflaeyanmvlvsal 234
                                       ++s++v++q  i f +lq+l++++f++a++a  + +PFDl e++sE+v+G+ tEYsgm+f+lf+++ + +++l s++
  gi|13541943|ref|NP_111631.1| 191 ktplEFSSLVSTQF-IPFGILQPLGLFVFMVAMIARSSYTPFDLSESDSEIVSGYSTEYSGMRFGLFYMGMFGSIFLGSLV 270
                                   55557888888884.5678999*********************************************************** PP

                                   HHHHCT.SS-HCCS...HHHHHHHHHHHHHHHHHHHHHC----TCHHHHHHHCCTCHHHHHHHHHH CS
                        NADHdh 235 avllFlgGwllpfs...gllwfllKvllllflfiwiratlpRlRydqlmklgwkvllplalanlll 297
                                   ++ll+lgG+++p+s   g++++l+K l+++++ ++i  ++pR+R+d+++++gwk+llp+a++nl++
  gi|13541943|ref|NP_111631.1| 271 ISLLYLGGYNGPYSsyaGFIYLLIKGLIMVLISFLIWLSMPRIRIDRFVNFGWKILLPIAIINLIW 336
                                   *************99*************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (346 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       782  (0.0436165); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); 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: 0.62u 0.31s 00:00:00.93 Elapsed: 00:00:00.52
# Mc/sec: 2014.21
//
Query:       gi|13541944|ref|NP_111632.1|  [L=367]
Description: NADH dehydrogenase subunit D [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-98  329.3   0.1    5.2e-96  320.9   0.0    2.7  2  Complex1_49kDa  Respiratory-chain NADH dehydrogenase, 49 Kd s
  ------ inclusion threshold ------
      0.091   11.6   0.0       0.99    8.2   0.0    2.2  3  NiFeSe_Hases    Nickel-dependent hydrogenase


Domain annotation for each model (and alignments):
>> Complex1_49kDa  Respiratory-chain NADH dehydrogenase, 49 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0     0.058   5.2e+02      44      88 ..      26      72 ..      15      75 .. 0.80
   2 !  320.9   0.0  5.8e-100   5.2e-96       1     271 []     118     367 .]     118     367 .] 0.97

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.058
                                  --TTHHHHHHHHHHHHHHHHHHHHHH..HHSSSSHHHHHSSSS-BSH CS
                Complex1_49kDa 44 lpegllekikeflkelekkldelekl..ltknrifkkRtkgvgvlsk 88
                                  l+ +++++++ ++ +l+++ +++ +l  + +n i+ +R+  v++++ 
  gi|13541944|ref|NP_111632.1| 26 LDGEIVKDVEPIIGYLHRNAEKICELqfYCDNMIYFDRMDYVAAMNM 72
                                  56678888999999999999988776336799999999999998875 PP

  == domain 2  score: 320.9 bits;  conditional E-value: 5.8e-100
                                   HTT-HHHHHHHHHHHHHHHHHHHHHHSSSSS-TTBESSBBSS---TTHHHHHHHHHHHHHHHHHHHHHHHHSSSSHHHHHS CS
                Complex1_49kDa   1 DlGaltvflyafreRekildlleevtGaRltasyiriGGvarDlpegllekikeflkelekkldeleklltknrifkkRtk 81 
                                   DlG+lt+f+y+f+eRekil++++ev+G+R + +y+ iGGv++D+++++l++ik+f++e++k+l+ + +l++kn if +Rtk
  gi|13541944|ref|NP_111632.1| 118 DLGMLTPFFYCFKEREKILKIFTEVSGSRQQLNYMSIGGVYQDVTDEALDHIKQFITEFPKELNMIANLFVKNDIFLSRTK 198
                                   99******************************************************************************* PP

                                   SSS-BSHHHHHHHTT-SSSSGGGT-TTTHHHHSS-SSGGGS-------SSBSHHHHHHHHHHHHHHHHHHHHHHHHT--.S CS
                Complex1_49kDa  82 gvgvlskeealelgltGpvlRasGvkyDlRkaepYeaYdeldfdvpvgeegDvydRylvrveEmrqSlkIieqaleklpeg 162
                                   gvg+lske a+++g+tGp+lRasGv+yD+RkaepY +Yd+++fd+pv+ +gD ++R+lvr+eEmrqS+kIi+q ++klp+g
  gi|13541944|ref|NP_111632.1| 199 GVGILSKEMAIDYGVTGPMLRASGVEYDVRKAEPYLVYDKVNFDIPVSFKGDNLARFLVRIEEMRQSVKIIDQTIQKLPAG 279
                                   ********************************************************************************* PP

                                   -SB---TTTS---GGGGGT-HHHHHHHHHHHHS-----SEEEEEEEEETTEEEEEEEEEESSSS-SEEEEE-HHHHTTTTH CS
                Complex1_49kDa 163 pvlaedkkvalpkkeevkksmealihhfklvtegfkvpkgevyaavEapkGelgvylvsdgsskpyrlkirapsfvnlqal 243
                                   p+ ++++k            m +l              +gevya++E+pkGe+gvy+v dgs +pyr+++r+p+f nl++l
  gi|13541944|ref|NP_111632.1| 280 PYFNQKAKK---------PLMIRLR------------GQGEVYARTESPKGEFGVYIVGDGSLRPYRVRVRSPTFKNLSVL 339
                                   *99976554.........3454554............78****************************************** PP

                                   HHHTTTS-SGGGTHHHHTT---HHHHH- CS
                Complex1_49kDa 244 eellkgellaDvvailgsldivlgevDR 271
                                   ++l+kg+++aD++ i gs+d+v+gevDR
  gi|13541944|ref|NP_111632.1| 340 PALAKGQMIADLISIGGSIDLVFGEVDR 367
                                   ***************************9 PP

>> NiFeSe_Hases  Nickel-dependent hydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.0   0.00011      0.99       6      70 ..      48     112 ..      43     118 .. 0.81
   2 ?    0.7   0.0      0.02   1.8e+02     150     207 ..     122     176 ..     113     196 .. 0.78
   3 ?   -2.8   0.0      0.25   2.2e+03     373     439 ..     249     315 ..     235     331 .. 0.57

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00011
                                   HTTTS-GGGHHHHHHTT-SSSTTHHHHHHHHHHHHHHT----HHHHHHHHHHHHHHHHHHHHHHH CS
                  NiFeSe_Hases   6 ilkgrdprdawalvqRiCGVCttvHalasvravedAlgikipknarlirnliaaalllhdhivhF 70 
                                   i + +   d +++ +R+  V ++   +   +a e+ l++++p  a+ ir ++   + + +h+v++
  gi|13541944|ref|NP_111632.1|  48 ICELQFYCDNMIYFDRMDYVAAMNMEIGYLEAAEKLLDVEPPGRAKWIRVMMGELNRIASHLVWL 112
                                   5555555666667777777777777788899********************************95 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.02
                                   HHHHHHHHHHHHHHTHHHHHHHSSSSS--.EBTTBESSGBGSBSHHHHHHHHHHHHHH CS
                  NiFeSe_Hases 150 vahYLeaLelqrkaakivaifggknPhpqslvvGGvtcaidllnaerlaevkslikev 207
                                   ++ ++  ++ ++k+ ki +  +g     + + +GGv +    ++ e l+++k++i+e 
  gi|13541944|ref|NP_111632.1| 122 LTPFFYCFKEREKILKIFTEVSGSRQQLNYMSIGGVYQD---VTDEALDHIKQFITEF 176
                                   5566667777888889988888888999999*****999...8889999998888775 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 0.25
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTB---B--TT-SGGGS-.S.EEEEEEEEEETTEEEEEEE CS
                  NiFeSe_Hases 373 GRtaaRaleakliaellkewldelvenikkgdtetaneekldkkevp.k.eakGvglveapRGaLsHwi 439
                                   G ++aR l     +++  + +d+ ++++ +g   ++n++  ++  +  + + + ++ +e p+G  + +i
  gi|13541944|ref|NP_111632.1| 249 GDNLARFLVRIEEMRQSVKIIDQTIQKLPAG--PYFNQKAKKPLMIRlRgQGEVYARTESPKGEFGVYI 315
                                   4455555555555555555566666666665..455555555554442224444556677777666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (367 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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 0.31s 00:00:00.93 Elapsed: 00:00:00.53
# Mc/sec: 2080.36
//
Query:       gi|13541945|ref|NP_111633.1|  [L=151]
Description: NADH dehydrogenase subunit C [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.7e-37  127.1   0.0    6.7e-37  126.8   0.0    1.1  1  Complex1_30kDa  Respiratory-chain NADH dehydrogenase, 30 Kd s
  ------ inclusion threshold ------
      0.048   13.8   0.0      0.068   13.3   0.0    1.2  1  DsrH            DsrH like protein


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 !  126.8   0.0   7.5e-41   6.7e-37       2     120 ..      18     129 ..      17     131 .. 0.92

  Alignments for each domain:
  == domain 1  score: 126.8 bits;  conditional E-value: 7.5e-41
                                   E--HHHHHHHHHHHHH...TT--EEEEEEEEETTSSSEEEEEEEE--S-.-EEEEEE....-S-BEE--TTT-STHHHHHH CS
                Complex1_30kDa   2 vvepedllevakflkdeeelgfdvlsdltavDekeerfevvyhllsleknerirvkvevdeeepevpSvtdlfpgadwyER 82 
                                   +v++e+ll++++ lk    +g+  ls  t+vD+  +++evvyhl++lekne i vk+e+  ++ +vpS+t+l+++a+w ER
  gi|13541945|ref|NP_111633.1|  18 KVAKENLLALMRDLKA---QGY-NLSLTTGVDY-VDHIEVVYHLYNLEKNEYIIVKTET--TDNHVPSLTPLWNAANWDER 91 
                                   79999**********9...565.477788***9.6**********************55..5678**************** PP

                                   HHHHHSHHBCTTSSTSS-SSSSTTSSS-TTSTTS---- CS
                Complex1_30kDa  83 EayDmfGivfeghpdlrrillpedfeghPLRkdfplsg 120
                                   E yD++Givf+ghp l+r++lpe+++ghPLRk+++ls+
  gi|13541945|ref|NP_111633.1|  92 EEYDLVGIVFDGHPYLKRLFLPEGWVGHPLRKNYDLSK 129
                                   ***********************************987 PP

>> DsrH  DsrH like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   7.6e-06     0.068      43      79 ..      18      54 ..       8      62 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 7.6e-06
                                  HTSSSEEEEEHHHHHHTT-TTSB-TTSEEE-HHHHHH CS
                          DsrH 43 keasvklyaLkeDleARGlteqlsegvkvidydgfVe 79
                                  k a+ +l aL  Dl+A G + +l +gv+ +d  ++V 
  gi|13541945|ref|NP_111633.1| 18 KVAKENLLALMRDLKAQGYNLSLTTGVDYVDHIEVVY 54
                                  444789**************88*********999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); 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: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 993.83
//
Query:       gi|13541946|ref|NP_111634.1|  [L=157]
Description: NADH dehydrogenase subunit B [Thermoplasma volcanium GSS1]
Scores for complete sequence (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   0.2    1.9e-21   76.2   0.2    1.2  1  Oxidored_q6  NADH ubiquinone oxidoreductase, 20 Kd subunit


Domain annotation for each model (and alignments):
>> Oxidored_q6  NADH ubiquinone oxidoreductase, 20 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.2   0.2   1.1e-25   1.9e-21       4     129 ..      38     145 ..      36     147 .. 0.85

  Alignments for each domain:
  == domain 1  score: 76.2 bits;  conditional E-value: 1.1e-25
                                   HHHHHT-TTTTHHHHHHTEEEEEETTT-S--HHHHHHTHTTTSEEEEEESBE...EEEHHHHHHHHGGGSSEEEEESHHHH CS
                   Oxidored_q6   4 csisllaleedlldllelielryhetlladskeeeieakekeadvlvveGavtrkpkealellkelaekakaviavGtCAa 84 
                                   c i+++a++ + +d+      r+++++  +s         ++ d+++v+G+vt+k++++++++++ ++ +k+via G C +
  gi|13541946|ref|NP_111634.1|  38 CAIEMMAIQASDMDI-----SRFGSEIFRNSP--------RQSDLMIVSGTVTKKMAPRVRRIYDEMPYPKYVIAQGVCVI 105
                                   888888888888888.....777776655544........499************************************** PP

                                   H-TGGGSTT-TEE-HHHHHHHC.S-E.EEE-SSS--HHHHHHHHH CS
                   Oxidored_q6  85 fGGipaaannpsvgeevgellevvpvdinipGCPphpeailetll 129
                                   +GG ++ +  +sv   v ++++vvpvd+++pGCPp+pea+++++ 
  gi|13541946|ref|NP_111634.1| 106 QGGPYNQG--YSV---VLGVDKVVPVDVYVPGCPPTPEALTNGII 145
                                   *****333..344...569*********************99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       353  (0.0196888); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 1030.15
//
Query:       gi|13541947|ref|NP_111635.1|  [L=151]
Description: NADH dehydrogenase subunit A [Thermoplasma volcanium GSS1]
Scores for complete 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-19   67.9   0.7    6.8e-19   67.9   0.7    1.9  2  Oxidored_q4    NADH-ubiquinone/plastoquinone oxidoreductase, 


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 ?    0.1   0.1     0.049   8.9e+02      73      91 ..      11      29 ..       2      32 .. 0.76
   2 !   67.9   0.7   3.8e-23   6.8e-19      16      99 .]      66     149 ..      51     149 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.049
                                  HHHHHHHHHHHHHHHHHHH CS
                   Oxidored_q4 73 gliemllFllillvglvYe 91
                                  g+i +l+ +++l ++l++ 
  gi|13541947|ref|NP_111635.1| 11 GYIPLLIIIVVLPLALIFG 29
                                  6788899999999999885 PP

  == domain 2  score: 67.9 bits;  conditional E-value: 3.8e-23
                                   --HHHHS-SSSS--SS---.--HHCHHHHHHHHHHHHHHHHHHHHHHHHSST..HHHHHHHHHHHHHHHHHHHHHHHHH-S CS
                   Oxidored_q4  16 pnkeklspYEcGfepvgearlrfsvkfylvallFliFDvevvflfpwavslkelglfgliemllFllillvglvYewkkga 96 
                                   ++++ l+pYE+G  + +    +   ++y+v llF++FDv++++lfpwa  +k+lgl+ +ie+l+Fl++ l++++Y+ k g 
  gi|13541947|ref|NP_111635.1|  66 EDQRYLEPYESGEVAREIWGRPSINQYYIVVLLFVVFDVDMLLLFPWAYDFKSLGLIPFIETLIFLAMPLFAVYYAFKLGY 146
                                   5667899******9988766677779******************************************************* PP

                                   -XX CS
                   Oxidored_q4  97 LeW 99 
                                   ++W
  gi|13541947|ref|NP_111635.1| 147 MRW 149
                                   **9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       503  (0.0280551); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 966.30
//
Query:       gi|13541948|ref|NP_111636.1|  [L=598]
Description: glutamyl-tRNA(Gln) amidotransferase subunit E [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.1e-61  208.6   0.0    1.8e-61  208.0   0.0    1.3  1  GatB_N     GatB/GatE catalytic domain
  ------ inclusion threshold ------
      0.032   14.1   0.7       0.12   12.3   0.7    2.1  1  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 !  208.0   0.0     2e-65   1.8e-61       2     272 ..       7     432 ..       6     433 .. 0.95

  Alignments for each domain:
  == domain 1  score: 208.0 bits;  conditional E-value: 2e-65
                                   EEEEEEEEEB--SB-SSSSSBSSSSCE..........STTSS--TTTTTS..........................TT..- CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxx..........xxxxxxxxxxxxx..........................xxxxx RF
                        GatB_N   2 viGlEiHaqlktksKlFssasteeege..........epnsevsevdlal..........................PGtlP 46 
                                   +iGlEiH ql+t  KlF++++ e++g+           ++se++ +d+a+                          P   P
  gi|13541948|ref|NP_111636.1|   7 KIGLEIHFQLNTG-KLFCRCPVETSGTekyrferhlhVSESEMGRIDAAAkyesersrtfeyvvtdnsclvecdedP---P 83 
                                   8**********96.*******88544345667667744899999999999***********************9998...8 PP

                                   -.EEHHHHHHHHHHHHHTTEEE-SEE-EEEEE-TCTTCTTSEEEEESSS.SEEEEEEEE.TEEEEEEEEEEEE---EEEEE CS
                                   x.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx RF
                        GatB_N  47 v.lnkeavelaikaalalnceiaeeskfdRKnyfypdlpkgyQitqkeeplakeGslel.ekkvrierihlEeDaaksvhe 125
                                   + +n++a+ +ai++a alnc+i + ++++RK+++++++++g+Q+t+    +  +G++e+ + kvri++++lEeDaa++++e
  gi|13541948|ref|NP_111636.1|  84 KmPNEDAIATAISVARALNCDILDYITYMRKIVIDGSNTSGFQRTA---IIGINGYIETsKGKVRISTVCLEEDAARKIEE 161
                                   878*******************************************...566******97889****************** PP

                                   ETTEEEEETTSTT-EEEEEEE-STB-SHHHHHHHHHHHHHHHHHHTSB--SGGGTTEEEEEEEEECTSETTSSS.--EEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        GatB_N 126 ekeeslvdlnRaGvpLiEivtepdlrspeearavveklrellralgvsdgnmeeGslRcDvNvSvreeekgeeegtrvEiK 206
                                   ++ +++++l+R+G+pLiEi+tepd+ + e+a++v++k++  + ++g+s++     s+R+DvN S+           rvEiK
  gi|13541948|ref|NP_111636.1| 162 KEGTVVYSLDRLGIPLIEISTEPDIIDEEHAVEVAKKIGYYVISTGKSRKAP--DSVRQDVNFSMGF--------GRVEIK 232
                                   999**********************************************999..8**********94........5***** PP

                                   EE-SHHHHHHHHHHHHHHHHHHH.......................................................... CS
                                   xxxxxxxxxxxxxxxxxxxxxxx.......................................................... RF
                        GatB_N 207 nlnslksiekaieyeierqiell.......................................................... 229
                                   ++++l++i+++++yei+rq  l                                                           
  gi|13541948|ref|NP_111636.1| 233 GVSKLSQIKEVLKYEIQRQDMLKkasdliklrggfdrsrfyfidvtdllvntsskvvnsglktgrayaalctnlagtlksg 313
                                   *******************99999********************************************************* PP

                                   ................................................................................- CS
                                   ................................................................................x RF
                        GatB_N 230 ................................................................................q 230
                                                                                                                   +
  gi|13541948|ref|NP_111636.1| 314 eyrlgkeladlvrayglkgllhsdelpgyglkesdiqpiydrlqkdeldgviillspqekigiieeeianrieklisldlS 394
                                   ********************************************************************************* PP

                                   EEEEEETTTTEEEEECC----...-EEE-TTS--EE--HHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        GatB_N 231 eTrkfdedkgetvslRskeeaedYryfpepdlppleiseeli 272
                                   eTr+ +ed  +tv lR+ + +   r++pe+d+p +++s++++
  gi|13541948|ref|NP_111636.1| 395 ETRGPTED--STVFLRPMPGK--DRMYPETDIPVIAVSKDIL 432
                                   ****9999..9********77..4**************9987 PP

>> GatB_Yqey  GatB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.7   1.3e-05      0.12      36     100 ..     501     563 ..     443     581 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.3e-05
                                   TCSSTTHHHHHHHHHHHHTTSSGHHHHHHHHHHHHHHTXXHHHHHHHCTXXXXXXSSXHHHHHHH CS
                     GatB_Yqey  36 eelkltpeqlaellkliaegkIskkiakevleelleegkspeeiieekgLkqisdeeeleklvee 100
                                   ++ k+  + +  l++l+++ k    ++++ le l+ e+k+p+ i++ + L  ++  +e+ +++++
  gi|13541948|ref|NP_111636.1| 501 AK-KFDNNLIFVLVRLMSDRKFDRYQVEKALEILFSENKDPALIVSDERLIELTK-DEICEIIDK 563
                                   33.6777788889****************************************97.999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (598 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       698  (0.0389313); expected 358.6 (0.02)
Passed bias filter:                      537  (0.0299515); 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: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.42
# Mc/sec: 4241.58
//
Query:       gi|13541949|ref|NP_111637.1|  [L=406]
Description: glutamyl-tRNA(Gln) amidotransferase subunit D [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      1e-53  181.7   0.1    1.5e-53  181.2   0.1    1.2  1  Asparaginase    Asparaginase, N-terminal
    2.6e-22   79.2   0.1    5.8e-22   78.1   0.1    1.6  1  Asparaginase_C  Glutaminase/Asparaginase C-terminal domain
    2.5e-06   26.7   0.9    6.3e-06   25.4   0.9    1.7  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 !  181.2   0.1   2.6e-57   1.5e-53       2     188 ..      70     259 ..      69     262 .. 0.95

  Alignments for each domain:
  == domain 1  score: 181.2 bits;  conditional E-value: 2.6e-57
                                   EEEEEEESGGGEEECTTS--CCEES-HHHHHCCTTTCCCCSEEEEEEEEEE-GGG--HHHHHHHHHHHHHHCCT-SEEEEE CS
                  Asparaginase   2 vlvlatGGTiasekdesggalapalsaeellealpelekiaeleseqlanidSsnmtpadwlklaeaieealeeydgfVvl 82 
                                   + +latGGTias++d+++ga++p +s   ll    ele   ++++ +++n  S+nm+padw +la+++ ++ ++ +g+Vv 
  gi|13541949|ref|NP_111637.1|  70 ISILATGGTIASRVDYETGAVKP-VSDPRLLFGGTELESKFNIRVVNVMNQLSENMKPADWIHLARKVMDETKHSSGIVVS 149
                                   89*********************.66666666666888888**************************************** PP

                                   --STTHHHHHHHHHHHEES.SSEEEEE--SS-TTSTT-SHHHHHHHHHHHHHCGGTTSECEEEETTE.......EEETTTE CS
                  Asparaginase  83 hGTDTlaytAsaLslmlknldkpvvltGsqrplselrsDgpeNlldAllvaasseriagvlvvfngk.......llranrv 156
                                   hGTDT++yt+saL++m++ l++p++++Gsqr++++++sD +eN+ +A+ +aa++    +v +++++        l+ra r+
  gi|13541949|ref|NP_111637.1| 150 HGTDTMSYTSSALAFMFERLAQPIIFVGSQRSSDRPSSDTKENMEGAINFAATD--LGEVGIAMHKGisdgsivLHRAVRS 228
                                   ****************************************************97..**********99************* PP

                                   EE-BSSSSS-EEETTT--SEEEETTEEEESEE CS
                  Asparaginase 157 tKvhtssldaFespnlgplaevegskvkvnke 188
                                   +K+hts++daFes++  +lae+ +s+v++ ++
  gi|13541949|ref|NP_111637.1| 229 RKMHTSRRDAFESIDTVHLAEY-TSSVRFFSD 259
                                   *********************9.888888766 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 !   78.1   0.1   9.7e-26   5.8e-22       1     104 [.     276     378 ..     276     385 .. 0.97

  Alignments for each domain:
  == domain 1  score: 78.1 bits;  conditional E-value: 9.7e-26
                                   -EEEEE--TT--HHHHHHHHHTT--EEEEEEBTTTB--HHHHHHHHHHHTTT-EEEEEESSSBS-----H.....HHHHHT CS
                Asparaginase_C   1 rVvvlklhpgmdtkvlkallkkgakGvvlegtGvGnlpsallealkeakargivvvatsqcpsgsvsnseyeagkelerlg 81 
                                   +V ++++hpg+ ++ ++++++ g  +vv+ gtG G++ ++l++++k+ ++ g   ++tsqc++gsv++++y++g+el ++g
  gi|13541949|ref|NP_111637.1| 276 KVSIIYFHPGLVASDVENMIE-GKHAVVIMGTGLGHIAKDLIPVFKNFTKDGNFAIMTSQCIYGSVDMNVYSTGRELIAAG 355
                                   79*****************96.*********************************************************** PP

                                   EEE-TT--HHHHHHHHHHHCTT- CS
                Asparaginase_C  82 visaddmtpeaarikLmlllgkg 104
                                   visa+dm pe a++k m+ lg+ 
  gi|13541949|ref|NP_111637.1| 356 VISAGDMVPEVAYVKAMFTLGNY 378
                                   ********************985 PP

>> GatD_N  GatD N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.9     1e-09   6.3e-06       6      51 ..       3      43 ..       1      46 [. 0.92

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 1e-09
                                  EEEEE-SS-EEEEEE----TTS-SSEEEEEETTS-EEEEE-TT-.- CS
                        GatD_N  6 likvekkgreyeGilmPrselsdddiivlKLdnGYNiGikieeiek 51
                                   +++ +k+ +++Gil++++    +  i++K dnGYN  ++ +e+ +
  gi|13541949|ref|NP_111637.1|  3 NVEIIYKNAKVRGILINEA----NGLITIKADNGYNLTFDRSEV-E 43
                                  59999**************....****************99998.4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (406 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       560  (0.0312343); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 2857.10
//
Query:       gi|13541950|ref|NP_111638.1|  [L=257]
Description: hypothetical protein TVN1119 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-47  162.4   0.0    1.9e-47  162.2   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 !  162.2   0.0     1e-51   1.9e-47       3     216 ..      21     246 ..      19     248 .. 0.87

  Alignments for each domain:
  == domain 1  score: 162.2 bits;  conditional E-value: 1e-51
                                   TT..CCCHHHHHCCT-SEEEE-HHCCSSS-HHHHHHHHCTS-.TT-EEEEE--CCCCCS...G.-.SCHHHHHHHHHH.CH CS
                         DUF72   3 eglkkkerLeyYarhfntVEinstFYalpspetvakwaaqtp.edFrFavKapraither..n.e.daeealerflesale 78 
                                   ++  k ++L++Y++ fntVE+nstFY+  + + +++w + +  ++F F++K+p+ ith++  + + +++++ e+f++++++
  gi|13541950|ref|NP_111638.1|  21 KS--KINKLKFYSTMFNTVEVNSTFYREINNDIINRWIETVRgKNFIFSIKVPQNITHKAilEkDsNSKSLYETFIDKTVR 99 
                                   43..4459*********************************879**************856533668************** PP

                                   HH..CT-EEEEEEE--TT--S.HHHHHHHHHH.TT.TS-SEEEE--BGGGH..H.HHHHHHHTT-EEEE.E--SSC----- CS
                         DUF72  79 pL..geklgpllfQlppsfkfdeenlerLeaf.la.alpllavEvRhrswf..e.llellrehgvavvl.depkkpklple 151
                                   p+  ++ lg++l+Qlppsf+ +  + e L+++ ++ +++  avEvR+++++  e l + l+++g+a+v  d   +++ pl 
  gi|13541950|ref|NP_111638.1| 100 PIrnARMLGAVLVQLPPSFNSN-LQTELLDTIcCEnEYR-TAVEVRNKDLYsnEeLRKELEKRGIAIVDvD---STEHPLS 175
                                   **7669*************665.3699999995443443.**********99955***********76658...5677887 PP

                                   ---SS.TEEEEEE--S.......HHTTB----HHHHHHHHHHHHHHHTCSSEEEEEE-SBCCCHHHHHHHHHH CS
                         DUF72 152 dvtta.dfvyvRlhgr.......eeryayrYseeelaewaerikawaaegrevyvffnndaegqaplnaraLa 216
                                       + ++ yvRlhgr       ++ y+yrYse+e+ ++ ++i+a  ++ +e++v+fnn+ +g+ap na ++a
  gi|13541950|ref|NP_111638.1| 176 NLNSGlKWSYVRLHGRaqlgwksQNPYDYRYSEQEISDLSSKIMA--KNYDEIFVYFNNHPRGSAPINALKMA 246
                                   777667****************6599*****************87..5569*******************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       882  (0.049194); expected 358.6 (0.02)
Passed bias filter:                      620  (0.0345808); 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: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1661.42
//
Query:       gi|13541951|ref|NP_111639.1|  [L=384]
Description: Acyl-CoA dehydrogenase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      1e-48  165.3   3.3    1.4e-48  164.9   3.3    1.2  1  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
    2.6e-30  105.4   0.1    1.4e-29  103.0   0.0    2.1  2  Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
    3.4e-27   94.5   0.0    6.9e-27   93.5   0.0    1.5  1  Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
    3.9e-23   82.2   1.7    6.2e-23   81.6   1.7    1.3  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 !  164.9   3.3   3.1e-52   1.4e-48       1     149 [.     229     377 ..     229     378 .. 0.99

  Alignments for each domain:
  == domain 1  score: 164.9 bits;  conditional E-value: 3.1e-52
                                   TBHHHHHTTTT--S-----..-SHHHHHHHHHHHHHHHTSB-CC-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH----- CS
                 Acyl-CoA_dh_1   1 gkGfrvametlnheRlavaaaalglarraleealeyarrrkafgkplidhqlvreklaemaaeleaarllvyraaealdag 81 
                                   + Gf+v+metl+ +R+++aa+alg+a++a+ ea++y+++rk+fg+++ +++ +++++a+ma+e+eaar l+y aae+ +++
  gi|13541951|ref|NP_111639.1| 229 NGGFKVIMETLDAGRIGIAAQALGIAEEAFAEAMDYIKQRKQFGTTISSFEGIQFMIADMATEIEAARYLTYVAAEKWQHK 309
                                   78******************************************************************************* PP

                                   ---HHHHHHHHHHHHHHHHHHHHHHHHHHGGGTTSGGGHHHHHHHHTHHHHHSSS-HHHHHHHHHHHH CS
                 Acyl-CoA_dh_1  82 kpdraeasmaKlfaselaqevadlamqllGgaGyleeypverlyrdarvlrigeGtseiqrniiarrl 149
                                   +++   ++maKl+as++a++v+++a+ql+Gg+Gy+ +   er++rd+++++i+eGt++iqr++ia+ l
  gi|13541951|ref|NP_111639.1| 310 EDTIEISAMAKLKASDVAVRVTTDALQLFGGYGYTVDLDAERHMRDSKITQIYEGTNQIQRLVIAKEL 377
                                   ***99999*********************************************************987 PP

>> Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.0   0.0   3.2e-33   1.4e-29       1     112 [.       7     118 ..       7     119 .. 0.98
   2 ?   -0.3   0.0      0.37   1.7e+03      92     111 ..     284     303 ..     234     337 .. 0.74

  Alignments for each domain:
  == domain 1  score: 103.0 bits;  conditional E-value: 3.2e-33
                                   THHHHHHHHHHHHHHHHHTHHHHHHHHHHTSGHHHHHHHHHHTTCTSTTS-GGGTS--S-HHHHHHHHHHHHHH-HHHHHH CS
                 Acyl-CoA_dh_N   1 teeqealrdtvrefaeeelaphaaewdeegefprelwkklaelGllgitvpeeygGagldyleaaivaeelaradaglall 81 
                                   ++e+e++   v++fa+eel+p+a+e+d++ e+pre+++++++lG+++ ++p+eygG+g+++   + ++ee+++a+ ++al+
  gi|13541951|ref|NP_111639.1|   7 SPEEEMVLTYVKKFAQEELKPRAKEIDAKMEVPREIIDRMKQLGFFATYIPKEYGGLGMSFPFLIRAIEEISKACPSTALV 87 
                                   689************************999*************************************************** PP

                                   HHHHHHTTHHHHHHHS-HHHHHHHHHHHHTT CS
                 Acyl-CoA_dh_N  82 lgvhsslvapailrfGteeqkrryLpklasg 112
                                   l    +l a++i+ fG+e+ k+ryL ++asg
  gi|13541951|ref|NP_111639.1|  88 LDGALTLFAEPIIMFGSEDLKKRYLTRVASG 118
                                   ******************************9 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.37
                                   HHHHHS-HHHHHHHHHHHHT CS
                 Acyl-CoA_dh_N  92 ailrfGteeqkrryLpklas 111
                                   +i+ ++te   +ryL  +a+
  gi|13541951|ref|NP_111639.1| 284 MIADMATEIEAARYLTYVAA 303
                                   56666666666666655554 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 !   93.5   0.0   1.5e-30   6.9e-27       1      96 [.     122     216 ..     122     217 .. 0.91

  Alignments for each domain:
  == domain 1  score: 93.5 bits;  conditional E-value: 1.5e-30
                                   EEE---SS-SS-GGG---EEEEETT.EEEEEEEEEEEETTTT-SEEEEEEETS---.----EEEEEEE..GGGEEE----- CS
                 Acyl-CoA_dh_M   1 afalTEpqaGsdvasvkttaaerdggeyvlnGeKiwitnaaiatlalvlartekpd.rarglslflvprdapgvsvrriee 80 
                                   ++a+TEp+aGsd+a+++t +ae+ g++y++nG Ki+i+n++i+++++  a t+    r++g++ f+v++++pg++++r  +
  gi|13541951|ref|NP_111639.1| 122 GLAITEPGAGSDAAGIST-TAEKRGDKYIINGDKIFISNGRISDFFVFDAVTDP-GkRHKGITAFVVDANTPGLKISRDIH 200
                                   589***************.77888888************************444.448******************77779 PP

                                   BSS-TTS-EEEEEEE. CS
                 Acyl-CoA_dh_M  81 klGlrglptgelvfed 96 
                                   k+G+rg +t elvfed
  gi|13541951|ref|NP_111639.1| 201 KMGIRGSSTVELVFED 216
                                   ***************8 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 !   81.6   1.7   1.4e-26   6.2e-23       1     133 [.     244     366 ..     244     367 .. 0.97

  Alignments for each domain:
  == domain 1  score: 81.6 bits;  conditional E-value: 1.4e-26
                                   .HHHHHHHHHHHHHHHHHHHHHHHHHCTTT-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----HHHHH CS
                 Acyl-CoA_dh_2   1 lgiaavalGaAraalaefvelarervrassgekladdpatqlalaeaaarldAAralleraaaraealaaagkevtvedra 81 
                                   +giaa+alG+A+ a+ae+++++++r++  +g++++ ++ +q+ +a++a++++AAr l++ aa++ +++ ++ +e+      
  gi|13541951|ref|NP_111639.1| 244 IGIAAQALGIAEEAFAEAMDYIKQRKQ--FGTTISSFEGIQFMIADMATEIEAARYLTYVAAEK-WQHKEDTIEI------ 315
                                   589************************..***********************************.9999999998...... PP

                                   HHHHHHHHHHHHHHHHHHHHHHHCGGGGGBTT-HHHHHHHHHHHHCTSGGG- CS
                 Acyl-CoA_dh_2  82 earraaalavelaiaavdalfeaaGgsalrkesplqRlwRDahaaaaHaaln 133
                                    +++a++ a++ a++++ ++ +++Gg++++ +   +R++RD +++++++++n
  gi|13541951|ref|NP_111639.1| 316 -SAMAKLKASDVAVRVTTDALQLFGGYGYTVDLDAERHMRDSKITQIYEGTN 366
                                   .999*********************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (384 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       606  (0.0338); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); 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: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 2393.50
//
Query:       gi|13541952|ref|NP_111640.1|  [L=332]
Description: DNA primase small subunit [Thermoplasma volcanium GSS1]
Scores for complete sequence (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   93.7   0.0    2.8e-25   89.4   0.0    2.2  2  DNA_primase_S  DNA primase small subunit
      0.004   17.1   0.2      0.084   12.9   0.0    2.5  3  Tra_M          TraM protein, DNA-binding


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 !   89.4   0.0   3.1e-29   2.8e-25       1     176 [.      94     265 ..      94     266 .. 0.92
   2 ?    2.2   0.0     0.019   1.7e+02     144     174 ..     286     316 ..     276     319 .. 0.88

  Alignments for each domain:
  == domain 1  score: 89.4 bits;  conditional E-value: 3.1e-29
                                   EEEEEETTT-.TT--HHHHHHHHHHHHHHHHHHHH-----GG..GEEEEE--SEEEEEEE--TTEEES-HHHHHHHHHH.. CS
                 DNA_primase_S   1 FDiDmddyddcseatvcekcwkfvsvavkvldellredfgfk..dilwvfsgrrGfHcwvsdkdarpltdeeraaivnyln 79 
                                   FD+D d++++ +++t+ e++  + ++++++++++l  d+g+   di ++fsg+rG+H++vs +d+ pl++  r++i++   
  gi|13541952|ref|NP_111640.1|  94 FDLDSDHLPGAEKMTYEEMLNSIKEQTKRLVNKFLVSDLGISekDIRIYFSGSRGYHVHVSSEDVYPLGSDARREITD--- 171
                                   9****************************************999*********************************8... PP

                                   ....................................HCHHHHCT--------..................----------- CS
                 DNA_primase_S  80 lyrplhpflsrs.mlkivkpvveeiileeqdpf...eikkllrllpdkslrekkkweakedivlvllyprldeqvtkgikh 156
                                          ++s++    +v ++  ++  +  + +    i kl +l  ++++ ++k++e ++d+v++   +  d +vt +i++
  gi|13541952|ref|NP_111640.1| 172 -------YVSGNsLSISVIDKALKTGEKRPGGWikdVISKLYELGINAEKISQKQIERAIDQVKSHNATMVDAPVTYDIHR 245
                                   .......57777777777777777778888999**98899999999999999999999*********************** PP

                                   ------....---------. CS
                 DNA_primase_S 157 llkapfcihgktgnvcvpld 176
                                   l+++p+++hgk+g  + ++d
  gi|13541952|ref|NP_111640.1| 246 LIRMPQSLHGKSGMMVKEVD 265
                                   *************8777775 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.019
                                   ..-----------------....-------- CS
                 DNA_primase_S 144 prldeqvtkgikhllkapfcihgktgnvcvp 174
                                    ++d++v +++++l  + + i+  +g++ vp
  gi|13541952|ref|NP_111640.1| 286 GDYDINVHEKTRKLRLLDYKIDLPPGRNRVP 316
                                   689***********************88888 PP

>> Tra_M  TraM protein, DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0      0.58   5.2e+03      93     108 ..      46      61 ..      32      70 .. 0.62
   2 !   12.9   0.0   9.4e-06     0.084      91     121 ..      98     128 ..      92     131 .. 0.91
   3 ?    1.4   0.0     0.033     3e+02      26      65 ..     189     228 ..     168     270 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.58
                         Tra_M  93 eiagnekleyklmvea 108
                                   +++  +k+e ++m+ +
  gi|13541952|ref|NP_111640.1|  46 HMHLSNKFELNNMLRT 61 
                                   4444556666666543 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 9.4e-06
                         Tra_M  91 speiagnekleyklmveaikedtaevveeff 121
                                   s ++ g ek+ y+ m+++ike+t+  v++f+
  gi|13541952|ref|NP_111640.1|  98 SDHLPGAEKMTYEEMLNSIKEQTKRLVNKFL 128
                                   578999***********************97 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.033
                         Tra_M  26 eGarekdvsfsstssmlvelGlrvyeaqmerkesnfnqte 65 
                                    G +     + ++ s l elG+   ++ +++ e + +q++
  gi|13541952|ref|NP_111640.1| 189 TGEKRPGGWIKDVISKLYELGINAEKISQKQIERAIDQVK 228
                                   455555556677889999***9999999999999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       834  (0.0465168); expected 358.6 (0.02)
Passed bias filter:                      725  (0.0404373); 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: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 2070.87
//
Query:       gi|13541953|ref|NP_111641.1|  [L=1097]
Description: serine protease [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.1e-12   45.4   2.6    1.1e-11   44.5   2.6    1.3  1  Peptidase_S8     Subtilase family
    2.9e-05   24.2   5.9    0.00086   19.5   0.0    3.7  4  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
     0.0026   17.7   0.0     0.0026   17.7   0.0    3.8  4  CarbopepD_reg_2  CarboxypepD_reg-like domain


Domain annotation for each model (and alignments):
>> Peptidase_S8  Subtilase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.5   2.6   1.9e-15   1.1e-11     109     266 ..     237     416 ..     219     439 .. 0.88

  Alignments for each domain:
  == domain 1  score: 44.5 bits;  conditional E-value: 1.9e-15
                                   HHHHHHHHHHH.CT-SEEEE-EESCETTCHHCHHHHHH..HHHHHH.CCT-EEEEE--SS-T-HHEEE-TTCEECTTTSTT CS
                                   xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Peptidase_S8 109 eliraieeaae.dkvdvinmslgestslpktgrsieal..ainravnkkgvlvviSaGNngktgsslqagspvgtpstskn 186
                                    l++a+ ++++  k  vi++s+g   +++ + ++ie +  ++ +a+ kkg+ +v+++G  g ++   +++ +v++p++s  
  gi|13541953|ref|NP_111641.1| 237 SLTAAVAYVIQnIKTSVISLSWG-IAENQLPISQIELMnsMYLNAT-KKGITIVAASGDYGAYDN--TKNLTVNFPASSPY 313
                                   5788888999989999*******.8888888889998899999999.99************9999..************** PP

                                   CEEEEEES..............TTSSB-TT--B-TT.......-EEEE-S-....CCCCCCCCCHHHTTTHH.....EEEE CS
                                   xxxxxxxx..............xxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxx.....xxxx RF
                  Peptidase_S8 187 vitvgayt..............tegkiapfSsrGpssdgklkpdivapGgn....ivstwsrqsnnsaglss.....yqsm 244
                                   v++vg+++                +++ +f s G  s  +  +   apG n    +v+++s  +n+++g            
  gi|13541953|ref|NP_111641.1| 314 VLGVGGTSlflsngifrqsawgGTSSQGSFGSGGGFSSFPRPYWQIAPGYNstyrGVPDVSMIANPNTGVLMisgakAYDA 394
                                   **********************8888899999999999888888899**99999999999999988887777999995578 PP

                                   -SHHHCHHHHHHHHHHHHHHHT CS
                                   xxxxxxxxxxxxxxxxxxxxxx RF
                  Peptidase_S8 245 sGTSmAsPnaagaaAlllsalp 266
                                    GTS A+P+ ag++A++ ++ +
  gi|13541953|ref|NP_111641.1| 395 GGTSLAAPLWAGVIAMMDQYDN 416
                                   9***************998654 PP

>> CarboxypepD_reg  Carboxypeptidase regulatory-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.4         3   1.8e+04      30      41 ..     440     451 ..     434     453 .. 0.77
   2 ?   -2.1   0.0      0.81   4.8e+03      46      62 ..     713     729 ..     707     734 .. 0.73
   3 !   19.5   0.0   1.4e-07   0.00086      36      81 ..     836     879 ..     816     880 .. 0.89
   4 !    5.8   0.1    0.0027        16       2      72 ..     888     951 ..     887     961 .. 0.76

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 3
               CarboxypepD_reg  30 astttdadGafr 41 
                                   ++ tt+ +G+++
  gi|13541953|ref|NP_111641.1| 440 TQITTGYNGYYS 451
                                   568999999997 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.81
               CarboxypepD_reg  46 ppgtysvtvsapGyata 62 
                                   + gty+v  +++G   +
  gi|13541953|ref|NP_111641.1| 713 TNGTYEVNTTYNGKNLS 729
                                   34999999999987655 PP

  == domain 3  score: 19.5 bits;  conditional E-value: 1.4e-07
               CarboxypepD_reg  36 adGafrlrglppgtysvtvsapGyatatreevtltagqtttlditL 81 
                                   +dG+f  r  +pg++++++s++G++++++ +++lt+g +++++i+L
  gi|13541953|ref|NP_111641.1| 836 KDGYFIAR-FEPGNITIKASYQGFQPYEV-NISLTPGSKSQIQIVL 879
                                   68999976.9******************9.7***********9998 PP

  == domain 4  score: 5.8 bits;  conditional E-value: 0.0027
               CarboxypepD_reg   2 isGrVtda.sgapiagatVtvtnadtgtvastttdadGafrl.rglppgtysvtvsapGyatatreevtltag 72 
                                   i+G+V d   +  ++ ++V ++         + t+ +G++ + ++l  g  +vt+ ++ y ++++ ++++++ 
  gi|13541953|ref|NP_111641.1| 888 IEGKVEDGvFKFNVSDVEVNIS------GIKAYTNGTGYYYIfTNLSNG--TVTFYRDIYSPYEY-NFSVRKP 951
                                   899999987999999*****99......7889******98761566655..67888888888887.5777655 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   0.1      0.84     5e+03      32      39 ..     713     720 ..     681     728 .. 0.56
   2 ?   -2.5   0.0      0.87   5.2e+03      33      75 ..     769     809 ..     757     817 .. 0.75
   3 !   17.7   0.0   4.4e-07    0.0026      32      83 ..     836     886 ..     822     889 .. 0.86
   4 ?    2.6   1.1     0.023   1.4e+02      19      48 ..     904     934 ..     888     969 .. 0.72

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.84
               CarbopepD_reg_2  32 enGnFelk 39 
                                    nG++e++
  gi|13541953|ref|NP_111641.1| 713 TNGTYEVN 720
                                   23333333 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.87
               CarbopepD_reg_2  33 nGnFelknlpagkytLvvsyvGyktqekkvtvskektldvnil 75 
                                   nG++    + ag  tL +++  + + + k++++++ ++ +n+ 
  gi|13541953|ref|NP_111641.1| 769 NGTYAY--ILAGINTLLIKSPEFYENNTKLNINSNASIRINLI 809
                                   566655..34577788888888888888999998888887754 PP

  == domain 3  score: 17.7 bits;  conditional E-value: 4.4e-07
               CarbopepD_reg_2  32 enGnFelknlpagkytLvvsyvGyktqekkvtvskektldvnillkeealel 83 
                                   ++G+F   + ++g+ t+++sy G+++ e++++++ +++ +++i l ++a+e 
  gi|13541953|ref|NP_111641.1| 836 KDGYFIA-RFEPGNITIKASYQGFQPYEVNISLTPGSKSQIQIVLVPSANES 886
                                   5677765.699*************************99999**999999876 PP

  == domain 4  score: 2.6 bits;  conditional E-value: 0.023
               CarbopepD_reg_2  19 VyvkgtkkgtvTdenGnFel.knlpagkytL 48 
                                   V v+ ++ +++T+  G++ + +nl +g++t+
  gi|13541953|ref|NP_111641.1| 904 VEVNISGIKAYTNGTGYYYIfTNLSNGTVTF 934
                                   4555577899******976527888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1097 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       528  (0.0294495); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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 0.32s 00:00:01.08 Elapsed: 00:00:00.50
# Mc/sec: 6612.47
//
Query:       gi|13541954|ref|NP_111642.1|  [L=344]
Description: methionine synthase [Thermoplasma volcanium GSS1]
Scores for complete 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-36  124.0   0.0    8.7e-35  120.5   0.0    2.2  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 !  120.5   0.0   4.8e-39   8.7e-35       2     321 ..       5     335 ..       4     338 .. 0.83

  Alignments for each domain:
  == domain 1  score: 120.5 bits;  conditional E-value: 4.8e-39
                                   -BB--SB---SS-----------------HHHHHHHHHHHHHHHHHHTT--S.CBE-B-TT-SSTTHHHHTTSTTEE--SS CS
                   Meth_synt_2   2 pTttiGSfPqtaevrearaevkkgelseeeyekaireeiekvvrrqeelgvD.vlvhgepeRgdmveyfgealdgfaftkn 81 
                                   +T  iGSf +    + +  e++k e++ e+ ++ +++++ + ++  e+ g+D v + ge+ R +m e+ +e+++g++f   
  gi|13541954|ref|NP_111642.1|   5 ITQEIGSFRK---PEYLSMEFHKIEGT-EKFKELAERATIDTLKIFENTGLDnVGIGGEMYRWEMYEHPAERIKGLIF--Y 79 
                                   7888999954...45566788888888.67777888888899*********9788*********************99..6 PP

                                   --EEEETTEEE---EE-SS---SS-SSTHHHHHHTTS-SS-BEEEEE-HHHHHHTSEE-TTS-HHHHHHHHHHHHHHHHHH CS
                   Meth_synt_2  82 gwvqsygsrcvrppiivgdvsrpaamtvkesalaqsltdkpvkglltGpvtilnwsfvrddvdraeaaaqialalrdevkd 162
                                   g+v s+ +r++r + +++ ++r+    + e       t+kp+k  +tGp t+++wsf     dr+e a++ a  + +e+k+
  gi|13541954|ref|NP_111642.1|  80 GMVRSFDNRYYRKGSVIDKIERRGSFHMDEVEFVAKSTKKPIKIPITGPYTMMDWSFNDHYNDRHELAMEFARIINEELKE 160
                                   89****************************9999999******************************************** PP

                                   HHH......TT-SE.EEEE-TTSSTT--SSGGGHHHHHHHHHHHHHHHHTTS-TTSEEEEEES-S--CCCH.HHHHTT--S CS
                   Meth_synt_2 163 Lea......aGikv.iQiDepalreGlplkkadwaayldwaveafrldtiaaaddtqvhtHlCyselndil.saiaaldvD 235
                                   +++       G k+ iQiDepa  +  p++        d  v+   +++++ + d+++++H+Cys    +l ++i +l++D
  gi|13541954|ref|NP_111642.1| 161 IQSkwpyisNGRKLeIQIDEPATTTH-PDEM-------DIVVD--SVNKSIEGIDAELSLHVCYSRDYRLLyDRIPELNID 231
                                   *97332222476667******97654.4443.......45555..578899999***********8888878********* PP

                                   EEEESBSSS-S.............SGGGGTTT....T---SEEEEBSS-TTSSS--THHHHHHHHHCHHCT.S-STSB-BB CS
                   Meth_synt_2 236 vitieasrsde.............ellealee....vkygrgvglGvydihsprvpsmeeiaalikkaldv.apkerlwvn 298
                                     ++e s++d+             + +++++e     + ++ +g+Gv d+h + ++ +  i+++ik +l++    e +  n
  gi|13541954|ref|NP_111642.1| 232 GYNLEYSNRDTtdlgvedakrpgfQDIKYFNEvnesLQRKKFIGVGVTDVHIDFIEPVKLIEDRIKYVLNIiKDPELVKLN 312
                                   ********9972222222222222245667663113345678*****************************44457778** PP

                                   -SS-STTS-HHHHHHHHHHHHHH CS
                   Meth_synt_2 299 PdCGLktrkreearaalknmvda 321
                                   PdCGL+tr+r+   ++l+nmv a
  gi|13541954|ref|NP_111642.1| 313 PDCGLRTRSRSIGEQKLRNMVIA 335
                                   ********************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        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 0.23s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 2464.42
//
Query:       gi|13541955|ref|NP_111643.1|  [L=293]
Description: hypothetical protein TVN1124 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.019   14.5   0.0      0.032   13.8   0.0    1.3  1  Meth_synt_1  Cobalamin-independent synthase, N-terminal domai


Domain annotation for each model (and alignments):
>> Meth_synt_1  Cobalamin-independent synthase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   1.8e-06     0.032     108     192 ..      83     170 ..      74     177 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.8e-06
                                   EEESTTSS-EEEE-BE-SS.--..--S-THHHHHHHHH..HHTTGGEEEEEE-HHHHHHT-EETTCC.-HCHHHHHHHHHH CS
                   Meth_synt_1 108 mtkwFntnYHYlvPelekdtef..klaseklleevkea..kalgieakpvllGpltflkLskakeekveklellekLlpvY 184
                                   ++++ +tn  Y  Pe++ + ++  kl++ +llee       al     + l  p +f k+s  k +   ++el+++L++vY
  gi|13541955|ref|NP_111643.1|  83 LKRYLETNTFYREPEISGHITLqrKLDTFDLLEENPPLplFALAKGSSIFLPTPSSFYKMSSVKANI-GAEELYKDLVNVY 162
                                   789*************987655114556667777655433566667889999**********99977.9999********* PP

                                   HHHHHHHH CS
                   Meth_synt_1 185 kelleeLk 192
                                   +++++ +k
  gi|13541955|ref|NP_111643.1| 163 SDIIDIFK 170
                                   ***98776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); 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 0.27s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 1997.26
//
Query:       gi|13541956|ref|NP_111644.1|  [L=263]
Description: 5,10-methylenetetrahydrofolate reductase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.5e-17   62.3   0.0    6.9e-17   61.7   0.0    1.3  1  MTHFR     Methylenetetrahydrofolate reductase
  ------ inclusion threshold ------
        0.2   10.7   0.0       0.29   10.1   0.0    1.2  1  TctC      Tripartite tricarboxylate transporter family recept


Domain annotation for each model (and alignments):
>> MTHFR  Methylenetetrahydrofolate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.7   0.0   7.7e-21   6.9e-17      10     283 ..      10     260 ..       2     263 .] 0.80

  Alignments for each domain:
  == domain 1  score: 61.7 bits;  conditional E-value: 7.7e-21
                                   S-EEEEEE---SSHHHHHHHHHHHHHHGGGG-SEEEE---CCCTTHHHHHHHHHHHHHHH-S-EEEEEESTTS-HHHHHHH CS
                         MTHFR  10 kalisfEffpPkteegernLleridrleevkplfvdvTwgaggstaeltssiakviqqelgleailhlTctdaskeeldka 90 
                                   +++ s+E  p + ++g ++L++++d le  k++  +   + +gs     ++    + +++++  i h+T +d++k ++ ++
  gi|13541956|ref|NP_111644.1|  10 RFVRSVEIVPSR-NQGLEELAHSLDSLE-GKANALTSPENPRGSPGIDPIITLFFLSKDRNIIPIPHITPRDKNKVHIISQ 88 
                                   556677765444.567788888888887.44455566667777777777777788999*********************** PP

                                   HHHHHHCT--EEEEE--S--TT-GGC---S----SHHHHHHHHHHHHCGGSEEEEEE-TT--TT-S-HHHHHHHHHHHHHC CS
                         MTHFR  91 lekakelGirnilALrGDppkdedkweekeeefkyaldLvrlireeygdlfdigvaaYPevhpeaksleadlkylkeKvda 171
                                   +++a++ Gi n   + GDp++  + +e++e       dL++li+ + g    +g a  P  ++     e+++    +K +a
  gi|13541956|ref|NP_111644.1|  89 INTANKFGINNFFVIGGDPINP-K-YESHEVREIDPIDLIKLIKANSGS--TVGAALNPYRNV-----EEEIAW--AKKNA 158
                                   ******************7666.4.666666655699************..667777665444.....444443..5669* PP

                                   T--EEEEEE-S-HHHHHHHHHHHHHCT-SS-EEEEE---SSHHHHHHHHHHHT----HHHHCCCTCHCT-HHHHHHHHHHH CS
                         MTHFR 172 GAdfiitQlffdvdkflkfveqvreagidipiipgimpiksykslkrlaklskvkiPqelldrleeikdddeavkkigiel 252
                                   GAdf+itQ ++  d++   ++ ++++     +i+g +p+   +++++ +kl ++ +P+ ++++l     + e +++ ++++
  gi|13541956|ref|NP_111644.1| 159 GADFFITQAIYSSDALS--MDWLKKRN--FKLIAGFLPLIRKNQVEFSEKL-GIFLPKVVKEKLL----NSEDIRSTSVNI 230
                                   **************996..45555554..589**************99998.689*********9....88889******* PP

                                   HHHHHHHHHHCT--EEEEE-TT--HHHHHHH CS
                         MTHFR 253 avemvkkllaegvkglHlytlnkekaileil 283
                                   + ++  ++ ++ v g+H++ l +++ ++ il
  gi|13541956|ref|NP_111644.1| 231 ILNVFDEV-KDFVDGIHIMPLGHNDIAADIL 260
                                   99988765.5668********9999999998 PP

>> TctC  Tripartite tricarboxylate transporter family receptor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   3.3e-05      0.29      69     128 ..     123     182 ..     109     187 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 3.3e-05
                          TctC  69 lqpislvatlplvLvvpadspfkdlqelvayakanPgKlsyasaGigtslhLaaellask 128
                                   +  i l+   +   v  a  p+++++e +a ak+n g   + +  i +s  L+++ l+++
  gi|13541956|ref|NP_111644.1| 123 IDLIKLIKANSGSTVGAALNPYRNVEEEIAWAKKNAGADFFITQAIYSSDALSMDWLKKR 182
                                   44566667777777888899***********************************99976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        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 0.26s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 1787.18
//
Query:       gi|13541957|ref|NP_111645.1|  [L=141]
Description: hypothetical protein TVN1126 [Thermoplasma volcanium GSS1]
Scores for complete 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   20.9   0.1    0.00018   20.6   0.1    1.1  1  3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase fami
  ------ inclusion threshold ------
      0.038   14.3   0.3      0.056   13.8   0.3    1.3  1  PfUIS3     Plasmodium falciparum UIS3 membrane protein


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 !   20.6   0.1     2e-08   0.00018     115     213 ..      25     125 ..       9     130 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 2e-08
                     3Beta_HSD 115 SsaevvgpnslgeeilngdEeleyesl.hqdaypesKalaEklvlkaNgrtlknggrly..TcaLRpagiyGegdkllvpl 192
                                   Ss+ + g+  l++ i++g E++++e + + + y+++K + E+ ++   ++++   ++ +  T++ +  ++ G +++l+ + 
  gi|13541957|ref|NP_111645.1|  25 SSYRIFGE--LADRIIKGSEKMHMEITdYIKRYNKFKDIIEAHIICRSNKNMDIQSKYLtiTISFKEYMVLGAKNTLTIRG 103
                                   88888888..99*************9999************9776555546665555551166779999****99999988 PP

                     3Beta_HSD 193 lkqla.klglalfkigdeevls 213
                                    + ++ k +  ++k+g +e l+
  gi|13541957|ref|NP_111645.1| 104 KEAMKiKEQADKLKMGIDEYLK 125
                                   7765426666777777776665 PP

>> PfUIS3  Plasmodium falciparum UIS3 membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.3   6.2e-06     0.056      17      92 ..      48     128 ..      33     136 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6.2e-06
                                   S---HHHHHHHHHHHHHHHHHHHHHS-HHHHHHHTT-HHHHHHHHHHHHHHTT-.....---HHHHHHHHHHHHHHHHHHH CS
                        PfUIS3  17 vdvslkrynifvdivklaiqkhfedlsndqkdslvndyeylrkivqtldesrdv.....slskaqedkavldlkyflkkvy 92 
                                   +   +kryn+f di+   i    ++  + q ++l   + + + +v + +++  +        k q dk  ++++ +lk   
  gi|13541957|ref|NP_111645.1|  48 ITDYIKRYNKFKDIIEAHIICRSNKNMDIQSKYLTITISFKEYMVLGAKNTLTIrgkeaMKIKEQADKLKMGIDEYLKSPL 128
                                   44469*************999999999999999987777776666665554333111103457899999999999999765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       734  (0.0409393); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); 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 0.24s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1059.42
//
Query:       gi|13541958|ref|NP_111646.1|  [L=135]
Description: transcription regulator [Thermoplasma volcanium GSS1]
Scores for complete 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   64.9   2.1    5.6e-18   64.2   2.1    1.4  1  HTH_24           Winged helix-turn-helix DNA-binding
      2e-14   53.1   0.1      2e-14   53.1   0.1    1.7  1  HTH_AsnC-type    AsnC-type helix-turn-helix domain
    6.3e-08   32.5   1.1      9e-08   32.0   0.3    1.7  1  AsnC_trans_reg   Lrp/AsnC ligand binding domain
    9.5e-08   31.9   0.5    1.9e-07   30.9   0.5    1.5  1  HTH_11           HTH domain
    1.9e-06   27.7   0.1    3.8e-06   26.7   0.1    1.4  1  MarR             MarR family
    3.4e-06   26.6   0.1     0.0001   21.9   0.0    2.5  3  Sigma70_r4_2     Sigma-70, region 4
    4.4e-06   26.6   0.0    7.6e-06   25.9   0.0    1.4  1  HTH_Mga          M protein trans-acting positive regulator (M
    1.6e-05   24.7   0.0    2.2e-05   24.2   0.0    1.3  1  HTH_5            Bacterial regulatory protein, arsR family
    2.5e-05   23.7   0.2    8.4e-05   22.0   0.0    1.9  2  Sigma70_r4       Sigma-70, region 4
      6e-05   22.7   0.1     0.0002   21.1   0.0    1.9  2  HTH_23           Homeodomain-like domain
    6.8e-05   23.0   0.0    0.00017   21.7   0.0    1.6  1  Fe_dep_repress   Iron dependent repressor, N-terminal DNA bin
    9.5e-05   22.1   0.4    0.00021   20.9   0.4    1.6  1  HTH_DeoR         DeoR-like helix-turn-helix domain
    0.00021   21.1   0.0    0.00038   20.3   0.0    1.3  1  MarR_2           MarR family
    0.00022   21.1   0.1    0.00047   20.1   0.1    1.6  1  HTH_Crp_2        Crp-like helix-turn-helix domain
    0.00037   20.0   0.1     0.0008   18.9   0.1    1.6  1  GerE             Bacterial regulatory proteins, luxR family
    0.00049   19.9   0.8     0.0052   16.6   0.2    2.1  2  TrmB             Sugar-specific transcriptional regulator Trm
    0.00076   18.9   0.6    0.00091   18.7   0.6    1.2  1  RepL             Firmicute plasmid replication protein (RepL)
      0.002   18.1   0.2      0.004   17.2   0.1    1.6  1  NapD             NapD protein
     0.0026   17.5   0.4     0.0029   17.3   0.4    1.2  1  Stk19            Serine-threonine protein kinase 19
     0.0033   17.4   0.0     0.0064   16.5   0.0    1.4  1  HTH_20           Helix-turn-helix domain
      0.004   17.0   3.4      0.018   14.9   3.4    2.0  1  TFIIE_alpha      TFIIE alpha subunit
     0.0049   16.9   0.1      0.013   15.4   0.1    1.8  1  Phage_terminase  Phage terminase small subunit
     0.0056   16.8   0.0      0.013   15.6   0.0    1.6  1  HTH_28           Helix-turn-helix domain
  ------ inclusion threshold ------
      0.012   15.6   0.0      0.024   14.7   0.0    1.5  1  HTH_29           Winged helix-turn helix
      0.016   15.2   0.4      0.032   14.2   0.3    1.6  1  HTH_45           Winged helix-turn-helix
      0.017   15.6   1.5      0.018   15.4   0.5    1.6  1  HTH_40           Helix-turn-helix domain
      0.018   15.0   1.5      0.022   14.7   0.3    1.8  1  HTH_12           Ribonuclease R winged-helix domain
      0.019   14.9   0.1       0.04   13.9   0.1    1.6  1  HTH_36           Helix-turn-helix domain
      0.022   14.5   0.1      0.051   13.3   0.1    1.7  1  HTH_38           Helix-turn-helix domain
      0.023   15.3   0.5      0.045   14.3   0.3    1.6  1  Phage_rep_O      Bacteriophage replication protein O
      0.024   14.6   0.8      0.054   13.5   0.8    1.6  1  DUF4342          Domain of unknown function (DUF4342)
      0.025   15.2   4.3      0.097   13.3   0.1    2.6  2  ACT_4            ACT domain
      0.027   15.0   0.1      0.069   13.7   0.1    1.7  1  HTH_27           Winged helix DNA-binding domain
      0.028   14.1   0.2        0.1   12.3   0.0    2.0  2  GntR             Bacterial regulatory proteins, gntR family
      0.034   14.2   0.4       0.05   13.6   0.4    1.4  1  DUF2089          Protein of unknown function (DUF2089)
      0.036   13.7   2.2       0.04   13.6   0.5    1.9  2  HrcA_DNA-bdg     Winged helix-turn-helix transcription repres
      0.043   12.8   0.1      0.054   12.5   0.1    1.1  1  TnsD             Tn7-like transposition protein D
      0.049   13.1   0.1       0.16   11.4   0.0    1.9  2  HTH_Tnp_ISL3     Helix-turn-helix domain of transposase famil
      0.054   13.8   0.1       0.12   12.8   0.1    1.6  1  Rrf2             Transcriptional regulator
      0.061   13.1   0.0       0.11   12.4   0.0    1.3  1  HTH_IclR         IclR helix-turn-helix domain
      0.071   13.1   0.1       0.34   10.9   0.0    2.2  1  DUF3320          Protein of unknown function (DUF3320)
      0.084   12.8   0.2       0.13   12.2   0.1    1.5  1  PAX              'Paired box' domain
      0.087   12.5   0.0       0.18   11.6   0.0    1.5  1  HTH_41           Helix-turn-helix domain
      0.091   12.8   0.0      0.091   12.8   0.0    2.0  1  Put_DNA-bind_N   Putative DNA-binding protein N-terminus
        0.1   13.2   1.0       0.28   11.8   0.4    1.9  2  Mak16            Mak16 protein C-terminal region


Domain annotation for each model (and alignments):
>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.2   2.1   1.4e-20   5.6e-18       2      48 .]       7      53 ..       6      53 .. 0.98

  Alignments for each domain:
  == domain 1  score: 64.2 bits;  conditional E-value: 1.4e-20
                        HTH_24  2 detdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                  de+dr+IL+lL +n+ris++e+A+ l++S +tv++r+k++++eG+Ik
  gi|13541958|ref|NP_111646.1|  7 DEKDRDILNLLIDNSRISNTEIAKVLNVSEGTVRKRIKKMIDEGIIK 53
                                  99********************************************8 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.1   0.1     5e-17     2e-14       2      41 ..       7      46 ..       6      47 .. 0.98

  Alignments for each domain:
  == domain 1  score: 53.1 bits;  conditional E-value: 5e-17
                 HTH_AsnC-type  2 DeiDrkILeaLqedaRisyaeLAervGlSestvlrRvrrL 41
                                  De Dr IL++L  ++Ris++e+A+ +++Se tv++R++++
  gi|13541958|ref|NP_111646.1|  7 DEKDRDILNLLIDNSRISNTEIAKVLNVSEGTVRKRIKKM 46
                                  9**************************************9 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 !   32.0   0.3   2.3e-10     9e-08       1      73 [.      68     134 ..      68     135 .] 0.93

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 2.3e-10
                                   EEEEE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEE CS
                AsnC_trans_reg   1 vlvslepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivl 73 
                                   +lv++++++   ++e+ ++l++     e+y  +G  d  +++++ +++ l+r++++ +++++gv +t+t+i l
  gi|13541958|ref|NP_111646.1|  68 ILVKIDNKK---YKEVLQRLRARY--YEIYEFSGRIDVAIRIKTDSTDNLNRIVDQ-IREIEGVVDTDTLIRL 134
                                   789999888...*********977..6**************************999.*************976 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9   0.5   4.7e-10   1.9e-07       3      44 ..      11      55 ..       9      63 .. 0.86

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 4.7e-10
                        HTH_11  3 lqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelg....v 44
                                  ++il lL+++   is  e+A+ LnvS+ tvr++Ik++ + g    +
  gi|13541958|ref|NP_111646.1| 11 RDILNLLIDNSR-ISNTEIAKVLNVSEGTVRKRIKKMIDEGiikrF 55
                                  79*****77776.************************999954444 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.1   9.4e-09   3.8e-06       8      50 ..      13      55 ..      10      60 .. 0.92

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 9.4e-09
                                  HHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                          MarR  8 iLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRs 50
                                  iL +l ++  +s++e+ak l+vs +tv + +++++++G i+R 
  gi|13541958|ref|NP_111646.1| 13 ILNLLIDNSRISNTEIAKVLNVSEGTVRKRIKKMIDEGIIKRF 55
                                  7888888999*******************************96 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   2.5e-07    0.0001      21      49 ..      17      45 ..       6      46 .. 0.79
   2 ?    1.8   0.0      0.47   1.9e+02      18      32 ..      66      80 ..      62      85 .. 0.91
   3 ?   -0.5   0.0       2.5   9.8e+02       5      20 ..      78      93 ..      74      95 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 2.5e-07
                                  HHHTS---HHHHHHHHT--HHHHHHHHHH CS
                  Sigma70_r4_2 21 lryleglsykEIAellgisegtVksrlsR 49
                                  l++    s  EIA++l++segtV++r+++
  gi|13541958|ref|NP_111646.1| 17 LIDNSRISNTEIAKVLNVSEGTVRKRIKK 45
                                  5555666999****************975 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.47
                                  HHHHHHTS---HHHH CS
                  Sigma70_r4_2 18 ifllryleglsykEI 32
                                  +++l  +++++ykE+
  gi|13541958|ref|NP_111646.1| 66 ALILVKIDNKKYKEV 80
                                  89999********96 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 2.5
                                  HHHHTTS-HHHHHHHH CS
                  Sigma70_r4_2  5 realaeLperqreifl 20
                                   e l++L  r+ ei++
  gi|13541958|ref|NP_111646.1| 78 KEVLQRLRARYYEIYE 93
                                  5789999999988887 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 !   25.9   0.0   1.9e-08   7.6e-06       9      44 ..      12      46 ..       7      62 .. 0.90

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 1.9e-08
                       HTH_Mga  9 kLlelLteneksltldelakeLglseltlqsdiseL 44
                                  ++l+lL++ +++++ +e+ak L+ se t++++i ++
  gi|13541958|ref|NP_111646.1| 12 DILNLLID-NSRISNTEIAKVLNVSEGTVRKRIKKM 46
                                  79******.************************987 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0   5.6e-08   2.2e-05       3      46 ..       9      53 ..       7      54 .. 0.91

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 5.6e-08
                                  HHHHHHHHHTTSS.EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                         HTH_5  3 tRlkILklLaege.lcvcelaeelglsqstvShHLkkLreaGLVe 46
                                  + ++IL+lL +++  + +e+a+ l++s++tv+   kk+ ++G+++
  gi|13541958|ref|NP_111646.1|  9 KDRDILNLLIDNSrISNTEIAKVLNVSEGTVRKRIKKMIDEGIIK 53
                                  5579*******6659****************************96 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   2.1e-07   8.4e-05       6      45 ..       7      47 ..       4      49 .. 0.85
   2 ?   -1.5   0.1       4.7   1.9e+03      44      49 ..      80      85 ..      76      93 .. 0.64

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 2.1e-07
                                  -HHHHHHHHHHH.TTT--HHHHHHHHTS-HHHHHHHHHHHH CS
                    Sigma70_r4  6 pererevlelrf.geglTleEIgerlgiSrerVrqiekrAl 45
                                  +e++r++l l       +  EI+++l++S+++Vr ++k+ +
  gi|13541958|ref|NP_111646.1|  7 DEKDRDILNLLIdNSRISNTEIAKVLNVSEGTVRKRIKKMI 47
                                  68888888888877788999*****************9966 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 4.7
                                  HHHHHH CS
                    Sigma70_r4 44 AlrkLR 49
                                   l++LR
  gi|13541958|ref|NP_111646.1| 80 VLQRLR 85
                                  455555 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   4.9e-07    0.0002      13      40 ..      16      45 ..       7      55 .. 0.78
   2 ?   -1.8   0.0       7.6     3e+03      22      27 ..      79      84 ..      66      91 .. 0.58

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 4.9e-07
                        HTH_23 13 llae..GlsvreIAreLgvsrrTvyrwlkr 40
                                  ll +  ++s +eIA+ L+vs+ Tv++ +k+
  gi|13541958|ref|NP_111646.1| 16 LLIDnsRISNTEIAKVLNVSEGTVRKRIKK 45
                                  4444589******************66666 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 7.6
                        HTH_23 22 eIAreL 27
                                  e+ ++L
  gi|13541958|ref|NP_111646.1| 79 EVLQRL 84
                                  443333 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 !   21.7   0.0   4.4e-07   0.00017      13      52 ..      13      52 ..      10      54 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 4.4e-07
                                  HHHHHHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                Fe_dep_repress 13 IYtlseekkvvktkdlaerLnvspssVsemlkkLekdGyv 52
                                  I+ l  +++ ++++++a++Lnvs  +V + +kk+ ++G +
  gi|13541958|ref|NP_111646.1| 13 ILNLLIDNSRISNTEIAKVLNVSEGTVRKRIKKMIDEGII 52
                                  66666678899***********************999965 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 !   20.9   0.4   5.3e-07   0.00021       4      46 ..      12      54 ..      10      56 .. 0.95

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 5.3e-07
                      HTH_DeoR  4 qilellkqqgklsveelvellgvSeaTiRRDLneLeeqglltR 46
                                   il ll +   +s +e++  l+vSe T+R+ ++++  +g+++R
  gi|13541958|ref|NP_111646.1| 12 DILNLLIDNSRISNTEIAKVLNVSEGTVRKRIKKMIDEGIIKR 54
                                  6999*************************************99 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   9.5e-07   0.00038       8      53 ..      11      54 ..       7      62 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 9.5e-07
                                  HHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEE CS
                        MarR_2  8 arvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLver 53
                                  +++L+ L ++ +  ++ +e+a+ l++s ++v +++k++ + G + r
  gi|13541958|ref|NP_111646.1| 11 RDILNLLIDNSR--ISNTEIAKVLNVSEGTVRKRIKKMIDEGIIKR 54
                                  799999999998..******************************77 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.1   1.2e-06   0.00047      20      53 ..      21      54 ..       5      64 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 1.2e-06
                                  EEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEE CS
                     HTH_Crp_2 20 lpltqeelAsmlGltretvsrilseLkreglisr 53
                                   +++++e+A  l+++  tv + ++++ +eg+i+r
  gi|13541958|ref|NP_111646.1| 21 SRISNTEIAKVLNVSEGTVRKRIKKMIDEGIIKR 54
                                  489*****************************95 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.1     2e-06    0.0008       6      41 ..       9      46 ..       4      48 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 2e-06
                                  HHHHHHHHHCTTS..-HHHHHHHHTS-HHHHHHHHHHH CS
                          GerE  6 RErevLrllaeGk..snkeIAeelniSekTVkvhksni 41
                                  + r++L ll++    sn+eIA+ ln+Se TV+  ++ +
  gi|13541958|ref|NP_111646.1|  9 KDRDILNLLIDNSriSNTEIAKVLNVSEGTVRKRIKKM 46
                                  5566666666553338***************9888876 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   0.2   1.3e-05    0.0052      15      56 ..      15      56 ..       6      78 .. 0.85
   2 ?    2.3   0.1       0.4   1.6e+02       9      31 ..      72      94 ..      64      98 .. 0.58

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.3e-05
                                  HHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES CS
                          TrmB 15 laLlklgpatadeiaeelgvprskvYevLrsLedkGlVerek 56
                                    L+ + + + +eia+ l+v++ +v + +++++d G+++r  
  gi|13541958|ref|NP_111646.1| 15 NLLIDNSRISNTEIAKVLNVSEGTVRKRIKKMIDEGIIKRFT 56
                                  456688889999**************************9976 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.4
                                  HCCCHCHHHHHHCCCHHCHHCCC CS
                          TrmB  9 yEakvYlaLlklgpatadeiaee 31
                                   + k Y+ +l++ +a+ +ei e 
  gi|13541958|ref|NP_111646.1| 72 IDNKKYKEVLQRLRARYYEIYEF 94
                                  34445555555555555555555 PP

>> RepL  Firmicute plasmid replication protein (RepL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.6   2.3e-06   0.00091      63     137 ..      16      86 ..       2     109 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2.3e-06
                          RepL  63 ylidnlnsnntliatnRelaeetgislktvsetlkileeanilkkkanGv..lvinPdllfkGddkkrlnlLlefee 137
                                    l      +n  i  n e+a+  ++s  tv++ +k + + +i+k+ +       i+  +l+k d+kk + +L + + 
  gi|13541958|ref|NP_111646.1|  16 LL-----IDNSRI-SNTEIAKVLNVSEGTVRKRIKKMIDEGIIKRFTVETsdNTIDALILVKIDNKKYKEVLQRLRA 86 
                                   33.....344444.35599**************************98433226899999**********99988765 PP

>> NapD  NapD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.1     1e-05     0.004       6      67 ..      68     128 ..      66     132 .. 0.94

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1e-05
                          NapD   6 lvVqarperlaavkaalaalpgvEvhasdeegklVvviEaesedeladtieaiealpgVlsa 67 
                                   ++V+++ ++ ++v+++l+a    E++  +++  + + i ++s+d+l +++++i++++gV+++
  gi|13541958|ref|NP_111646.1|  68 ILVKIDNKKYKEVLQRLRAR-YYEIYEFSGRIDVAIRIKTDSTDNLNRIVDQIREIEGVVDT 128
                                   689999***********985.78************************************997 PP

>> Stk19  Serine-threonine protein kinase 19
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.4   7.3e-06    0.0029      33      93 ..      23      83 ..      13     119 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 7.3e-06
                         Stk19 33 vtvahlhsllaqsptkvereleelirkgklrklvingrgkdisklgevlvltedyeklike 93
                                  ++ + +  +l+ s+ +v ++++++i++g ++++++++++++i +l  v +  ++y++ +++
  gi|13541958|ref|NP_111646.1| 23 ISNTEIAKVLNVSEGTVRKRIKKMIDEGIIKRFTVETSDNTIDALILVKIDNKKYKEVLQR 83
                                  567788899999****************************998877666667778877755 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   1.6e-05    0.0064      13      56 ..      11      54 ..       7      58 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.6e-05
                                  HHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEE CS
                        HTH_20 13 rrilraLaraegltaselaerldlskntlsyHLrvLeeagLvev 56
                                  r+il +L ++   + +e+a+ l +s  t++++++++ + g++++
  gi|13541958|ref|NP_111646.1| 11 RDILNLLIDNSRISNTEIAKVLNVSEGTVRKRIKKMIDEGIIKR 54
                                  789999999999999**************************986 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   3.4   4.6e-05     0.018      13      59 ..       8      54 ..       3      90 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 4.6e-05
                                  HHHHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEE CS
                   TFIIE_alpha 13 eeavlvldvLlekgevteedlakelkidlnelrklLnrLyearlvky 59
                                  e+   +l+ L+ ++ +++ ++ak l++    +rk + ++ +++++k 
  gi|13541958|ref|NP_111646.1|  8 EKDRDILNLLIDNSRISNTEIAKVLNVSEGTVRKRIKKMIDEGIIKR 54
                                  677789**************************************984 PP

>> Phage_terminase  Phage terminase small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   3.4e-05     0.013      22      41 ..      22      41 ..       8      50 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 3.4e-05
               Phage_terminase 22 tlklkdIAkvLdvsestvrk 41
                                   + + +IAkvL+vse tvrk
  gi|13541958|ref|NP_111646.1| 22 RISNTEIAKVLNVSEGTVRK 41
                                  57899*************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 !   15.6   0.0   3.2e-05     0.013       5      41 ..      13      51 ..      11      54 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 3.2e-05
                        HTH_28  5 iikllaaG.h.svreaArelgisrrtvyrWikryeegGi 41
                                  i+ ll++  + s +e+A+ l++s+ tv++ ik+   +Gi
  gi|13541958|ref|NP_111646.1| 13 ILNLLIDNsRiSNTEIAKVLNVSEGTVRKRIKKMIDEGI 51
                                  66677754257999******************9877776 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0     6e-05     0.024      15      41 ..      25      51 ..      15      59 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 6e-05
                        HTH_29 15 vsqiAkllglsrrtvyrwlkrfeegGl 41
                                    +iAk+l++s+ tv++ +k +  +G+
  gi|13541958|ref|NP_111646.1| 25 NTEIAKVLNVSEGTVRKRIKKMIDEGI 51
                                  789*****************9999997 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   0.3     8e-05     0.032      10      51 ..      12      54 ..      11      77 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 8e-05
                        HTH_45 10 dILea.isegeakkTkimykanLsykllnkYLdmLvekglikk 51
                                  dIL+  i++++ + T+i +  n s  +++k +++++++g+ik 
  gi|13541958|ref|NP_111646.1| 12 DILNLlIDNSRISNTEIAKVLNVSEGTVRKRIKKMIDEGIIKR 54
                                  788862569999*****************************64 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.5   4.6e-05     0.018      13      84 ..      23      90 ..      14      94 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 4.6e-05
                        HTH_40 13 lsieeIAkerglkesTIegHLaelieegeeidlerlv...seeeekeIeeaiekvgseklkpikealpeevsyde 84
                                   s  eIAk  +++e+T+ + + ++i eg    ++r++   s++++++++    k++++k+k++ ++l     y+e
  gi|13541958|ref|NP_111646.1| 23 ISNTEIAKVLNVSEGTVRKRIKKMIDEGI---IKRFTvetSDNTIDALIL--VKIDNKKYKEVLQRLR--ARYYE 90
                                  5668***********************96...666641114444444443..3566788999999994..45555 PP

>> HTH_12  Ribonuclease R winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.3   5.6e-05     0.022       3      51 ..      13      55 ..      11      64 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 5.6e-05
                        HTH_12  3 ILkilaesdkpigakeiaeeLkkrgydigeravRyrLrkleergltrrv 51
                                  IL++l ++++ i+  eia+ L+     ++e +vR r++k+ ++g+++r 
  gi|13541958|ref|NP_111646.1| 13 ILNLLIDNSR-ISNTEIAKVLN-----VSEGTVRKRIKKMIDEGIIKRF 55
                                  9999999999.********996.....788899*************996 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1    0.0001      0.04      27      55 .]      24      52 ..      14      52 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 0.0001
                        HTH_36 27 sqetlakrlglsknTvsraikeLeqlGyi 55
                                  s+  +ak l++s+ Tv++ ik+ ++ G+i
  gi|13541958|ref|NP_111646.1| 24 SNTEIAKVLNVSEGTVRKRIKKMIDEGII 52
                                  8999*******************999987 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   0.00013     0.051      21      42 ..      23      44 ..       7      50 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00013
                        HTH_38 21 lslreIArrLgrspsTIsRElk 42
                                   s+ eIA+ L++s +T+ + +k
  gi|13541958|ref|NP_111646.1| 23 ISNTEIAKVLNVSEGTVRKRIK 44
                                  7999*************99877 PP

>> Phage_rep_O  Bacteriophage replication protein O
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.3   0.00011     0.045      48      87 ..      21      60 ..      18      66 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 0.00011
                   Phage_rep_O 48 dwisnsqlveltgisrtkvskalkeLirekviikegrkvg 87
                                   +isn++++++ ++s+  v+k +k++i+e++i++   +++
  gi|13541958|ref|NP_111646.1| 21 SRISNTEIAKVLNVSEGTVRKRIKKMIDEGIIKRFTVETS 60
                                  68******************************98665555 PP

>> DUF4342  Domain of unknown function (DUF4342)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.8   0.00014     0.054       8      40 ..      32      64 ..      25      67 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00014
                       DUF4342  8 fqvkgeelvekvKelikkgnvtriiikkdgktl 40
                                  ++v++  + +++K++i +g ++r++++++++t+
  gi|13541958|ref|NP_111646.1| 32 LNVSEGTVRKRIKKMIDEGIIKRFTVETSDNTI 64
                                  6778888999******************99997 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.2       0.5     2e+02      34      71 ..      52      86 ..      44      88 .. 0.78
   2 ?   13.3   0.1   0.00024     0.097      46      77 ..      96     127 ..      90     129 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.5
                         ACT_4 34 ivsvnaktrkkdglaeikitveVkdvehLsrviakLra 71
                                  i+  +++t  +d++ +  i v++ + ++ ++v+++Lra
  gi|13541958|ref|NP_111646.1| 52 IKRFTVET--SDNTIDALILVKIDN-KKYKEVLQRLRA 86
                                  55666677..588999999999976.567888888875 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 0.00024
                         ACT_4  46 glaeikitveVkdvehLsrviakLraipgVis 77 
                                   g  ++ i+++  +++ L+r+++++r+i+gV +
  gi|13541958|ref|NP_111646.1|  96 GRIDVAIRIKTDSTDNLNRIVDQIREIEGVVD 127
                                   567789999*********************86 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   0.00017     0.069      17      55 ..      21      59 ..       7      64 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 0.00017
                        HTH_27 17 rrkkladlcgrlnvedshisyslkkLtekGLvertgdea 55
                                   r + ++++++lnv+  ++ + +kk++  G ++r + e+
  gi|13541958|ref|NP_111646.1| 21 SRISNTEIAKVLNVSEGTVRKRIKKMIDEGIIKRFTVET 59
                                  444559************************998887665 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00025       0.1      22      56 ..      21      54 ..      10      57 .. 0.89
   2 ?   -1.4   0.1       4.9   1.9e+03       2      11 ..      77      86 ..      76      87 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00025
                                  SB---HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                          GntR 22 dkLPsereLaaefgVsrttvReALrrLeaeglver 56
                                  +++ s  e+a+ ++Vs  tvR+ +++   eg++ r
  gi|13541958|ref|NP_111646.1| 21 SRI-SNTEIAKVLNVSEGTVRKRIKKMIDEGIIKR 54
                                  567.7889************************988 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 4.9
                                  HHHHHHHHHH CS
                          GntR  2 yeqvyerLre 11
                                  y++v +rLr+
  gi|13541958|ref|NP_111646.1| 77 YKEVLQRLRA 86
                                  7777888876 PP

>> DUF2089  Protein of unknown function (DUF2089)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.4   0.00012      0.05      35     101 ..       7      86 ..       1      97 [. 0.67

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.00012
                       DUF2089  35 skeqlefvelfika.rGnlkevekelgisYpTvrnrldeileaLgyeeeeeeeee............eeerkeileklek 101
                                   ++++ + ++l+i + r +  e++k l++s  Tvr+r+++++ +  ++  + e+++            +++ ke+l++l++
  gi|13541958|ref|NP_111646.1|   7 DEKDRDILNLLIDNsRISNTEIAKVLNVSEGTVRKRIKKMIDEGIIKRFTVETSDntidalilvkidNKKYKEVLQRLRA 86 
                                   55666666666654144557999**************9988764444443322222345677888877778888888876 PP

>> HrcA_DNA-bdg  Winged helix-turn-helix transcription repressor, HrcA DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.5    0.0001      0.04       7      46 ..      11      45 ..       5      54 .. 0.81
   2 ?   -1.0   0.0       3.6   1.4e+03       7      18 ..      78      89 ..      68     124 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.0001
                  HrcA_DNA-bdg  7 keilqaLielyrkkkravKgeeiAevlkrneGtvRNqlqs 46
                                  ++il+ Li+     ++ +  +eiA+vl+  eGtvR  ++ 
  gi|13541958|ref|NP_111646.1| 11 RDILNLLID-----NSRISNTEIAKVLNVSEGTVRKRIKK 45
                                  667777776.....5668899**************99876 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 3.6
                  HrcA_DNA-bdg  7 keilqaLielyr 18
                                  ke+lq L   y 
  gi|13541958|ref|NP_111646.1| 78 KEVLQRLRARYY 89
                                  666666665554 PP

>> TnsD  Tn7-like transposition protein D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   0.00013     0.054     191     256 ..      14      82 ..       9      96 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00013
                          TnsD 191 lkeLveeeglslkeiAkelgvdiktVlryakklgllkekkkqkkesrelsskd......rekkrkewlelik 256
                                   l+ L++++  s  eiAk l+v+ +tV++  kk +++      k+   e+s +        + + k+++e+++
  gi|13541958|ref|NP_111646.1|  14 LNLLIDNSRISNTEIAKVLNVSEGTVRKRIKKMIDEG---IIKRFTVETSDNTidalilVKIDNKKYKEVLQ 82 
                                   5678888999**********************99988...45555555333336667775555555555554 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00041      0.16      20      49 ..      13      44 ..      10      45 .. 0.84
   2 ?   -2.5   0.0       9.1   3.6e+03      40      50 ..     108     118 ..     108     119 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00041
                  HTH_Tnp_ISL3 20 ilellles..rsvkavArqlgvSwtTVwrild 49
                                  il ll+++  +s +++A+ l+vS+ TV+ +++
  gi|13541958|ref|NP_111646.1| 13 ILNLLIDNsrISNTEIAKVLNVSEGTVRKRIK 44
                                  677777777899***************98876 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 9.1
                  HTH_Tnp_ISL3  40 SwtTVwrildr 50 
                                   S++ ++ri+d+
  gi|13541958|ref|NP_111646.1| 108 STDNLNRIVDQ 118
                                   66778999997 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1    0.0003      0.12      22      56 ..      19      53 ..      13      56 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.0003
                                  TCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          Rrf2 22 eeepvsseeiaerqnispsylekilakLrkaglvk 56
                                  +++ +s +eia+  n+s+  ++k ++k+  +g++k
  gi|13541958|ref|NP_111646.1| 19 DNSRISNTEIAKVLNVSEGTVRKRIKKMIDEGIIK 53
                                  4566999**************************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 ?   12.4   0.0   0.00027      0.11       7      50 ..      12      54 ..      11      54 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00027
                                  HHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                      HTH_IclR  7 aiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                  +iL++l    +  +++e+A+ + ++  tv+  ++ ++ +G++++
  gi|13541958|ref|NP_111646.1| 12 DILNLLIDNSR-ISNTEIAKVLNVSEGTVRKRIKKMIDEGIIKR 54
                                  68999998888.8***************************9985 PP

>> DUF3320  Protein of unknown function (DUF3320)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00085      0.34       7      33 ..     107     133 ..     104     134 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00085
                       DUF3320   7 eykptLaeliakIVevEGPihedeLar 33 
                                   ++++ L + +++I e+EG +  d L+r
  gi|13541958|ref|NP_111646.1| 107 DSTDNLNRIVDQIREIEGVVDTDTLIR 133
                                   68999********************98 PP

>> PAX  'Paired box' domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00032      0.13      32      88 ..      21      76 ..       7     117 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00032
                           PAX 32 sgvrpcvisrqlrvshgcvskilgryqetgsirpgviggskpkvatpevvkkieeyk 88
                                  s +   +i++ l+vs+g v k + +  + g i+  ++  s   + +  +  ki++ k
  gi|13541958|ref|NP_111646.1| 21 SRISNTEIAKVLNVSEGTVRKRIKKMIDEGIIKRFTVETSDNTIDAL-ILVKIDNKK 76
                                  5577889**************************99999998877654.444555443 PP

>> HTH_41  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   0.00044      0.18      10      37 ..      26      53 ..      21      54 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00044
                        HTH_41 10 eelakeleLSvGlvQkALklLeddkais 37
                                  +e+ak l +S G+v k +k++ d+++i+
  gi|13541958|ref|NP_111646.1| 26 TEIAKVLNVSEGTVRKRIKKMIDEGIIK 53
                                  5889999******************995 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 ?   12.8   0.0   0.00023     0.091      25      46 ..      20      41 ..      12      41 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00023
                                  --EE-HHHHHHHCTS-HHHHHH CS
                Put_DNA-bind_N 25 veriSSteLaealgvtaaqvRK 46
                                   +riS te+a+ l+v++ +vRK
  gi|13541958|ref|NP_111646.1| 20 NSRISNTEIAKVLNVSEGTVRK 41
                                  479******************9 PP

>> Mak16  Mak16 protein C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0       3.7   1.5e+03      41      57 ..      31      47 ..      10      65 .. 0.60
   2 ?   11.8   0.4   0.00069      0.28      15      47 ..      66      97 ..      62     130 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 3.7
                         Mak16 41 iynveekafkkvlekee 57
                                  ++nv+e   +k ++k+ 
  gi|13541958|ref|NP_111646.1| 31 VLNVSEGTVRKRIKKMI 47
                                  45555555555554433 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00069
                         Mak16 15 AlaAAklekaIekeLleRLksgaYgdiynveek 47
                                  Al+  k++++  ke l+RL+   Y +iy+++ +
  gi|13541958|ref|NP_111646.1| 66 ALILVKIDNKKYKEVLQRLRARYY-EIYEFSGR 97
                                  89999*****************99.8***9644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1165  (0.0649785); expected 358.6 (0.02)
Passed bias filter:                      622  (0.0346924); expected 358.6 (0.02)
Passed Vit filter:                       126  (0.00702772); 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: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 891.55
//
Query:       gi|13541959|ref|NP_111647.1|  [L=545]
Description: chaperonin GroEL [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   1.2e-185  617.8  23.3   1.4e-185  617.6  23.3    1.0  1  Cpn60_TCP1      TCP-1/cpn60 chaperonin family
  ------ inclusion threshold ------
       0.12   12.8   0.5         13    6.1   0.0    2.8  2  Radical_SAM     Radical SAM superfamily
       0.13   12.5   0.4       0.43   10.8   0.0    2.1  2  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
       0.21   10.8   0.1       0.35   10.0   0.1    1.3  1  Dynein_C        Dynein heavy chain C-terminal domain


Domain annotation for each model (and alignments):
>> Cpn60_TCP1  TCP-1/cpn60 chaperonin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  617.6  23.3  3.2e-189  1.4e-185       1     490 [.      34     522 ..      34     523 .. 0.98

  Alignments for each domain:
  == domain 1  score: 617.6 bits;  conditional E-value: 3.2e-189
                                   HHHHHHCCSSTTXXEEEEEETTSEEEEEXSHHHHHHCSXXXSHHHHHHHHHHHHCCCCCTTCHHHHHHHHHHHHHHHHHHH CS
                    Cpn60_TCP1   1 ladivkttlGPkGmdKmlvnkggkvvvTnDGatilkeleiehPaakllveaaesqdeevGDGTttvviLageLleeaekli 81 
                                   +ad+v+ttlGPkGmdKmlv+++g+++++nDGatilke+++ehP+ak++ve++++qd+ vGDGTtt+v+L geLl++ae+l+
  gi|13541959|ref|NP_111647.1|  34 IADAVRTTLGPKGMDKMLVDSIGDIIISNDGATILKEMDVEHPTAKMIVEVSKAQDTAVGDGTTTAVVLSGELLKQAETLL 114
                                   79******************************************************************************* PP

                                   HCTXXHHHHHHHHHHHHHHHHHHHHHHXEEBXSCSTT.HHHHHHHHHHCTTSSXXSTHHHHHHHHHHHH.HCHCCCS..EE CS
                    Cpn60_TCP1  82 aagvhpttiiegyekalekaleaLkeiaveisseekdreeLlkvartslsskltskeaeelsklvvdAv.klieene..ke 159
                                   ++gvhpt+i +gy+ a+++a ++++ei  +++s+  d+e+L+k+a t+ls+k t  ++ +l++lvv+Av  + ee++    
  gi|13541959|ref|NP_111647.1| 115 DQGVHPTVISNGYRLAVNEARKIIDEI--SVKST--DDETLRKIALTALSGKNTGLSNTFLADLVVKAVnAVAEERDgkII 191
                                   ***************************..66665..679******************************555555556556 PP

                                   CSCCCEECCCCEECECTTSEEESEEEESS--SSTTSSCEEECEEEEEESS-BS--HHCCHHHCCCCSCCHHHHHHHHHHHH CS
                    Cpn60_TCP1 160 ldlgrikvvkieggsledselveGlvldkgvlspdmpkklenakvllldvsLeiektetkttvvlsdaeeleklekaeekq 240
                                   +d  +ikv k+ ggs++d++++ G+v+dk+ ++++mp  +++ak++l+d  Lei+kte++++v++sd++++++++++e+  
  gi|13541959|ref|NP_111647.1| 192 VDTANIKVDKKSGGSINDTQFISGIVVDKEKVHSKMPDVVKDAKIALIDSALEIKKTEIEAKVQISDPSKIQDFLNQETST 272
                                   67777**************************************************************************** PP

                                   HHHHHHHHHHTTECEEEESS-B-HHHHHHHHHCT-EEE-S--HHHHHHHHHHHT--EBSCGGGGGCGC-EEEEEEEECCET CS
                    Cpn60_TCP1 241 leellekiiksgvnvvvcqkgiddlalhflakngilalrrvkkkdlerlakatGatavssledltpeelGtakkveeekig 321
                                   ++e++eki+ksg+nvv+cqkgidd+a+h+lak+gi a+rrvkk+d+e+lakatGa++v++l+dltp+ lG+a+kvee+kig
  gi|13541959|ref|NP_111647.1| 273 FKEMVEKIKKSGANVVLCQKGIDDVAQHYLAKEGIYAVRRVKKSDMEKLAKATGAKIVTDLDDLTPSVLGEAEKVEERKIG 353
                                   ********************************************************************************* PP

                                   TCCEEEEECESSSSXEEEEEEESTCCCHHHHHHHHHHHHHHHHHHHHHHEEEETTTCHHHHHHHHHHCCCCTSXCCHHHHH CS
                    Cpn60_TCP1 322 sekttiieevksgkiatillrgatdtvldeieraiedAlnvvknaiedekvvpGGGatelelakklkeyaksvsgeeqlai 402
                                   ++++t+++++k++k+++il+rg t++v+ e+era++dA++vv+ + ed+k++ GGGa+e ela +l++ya+sv g+eqlai
  gi|13541959|ref|NP_111647.1| 354 DDRMTFVTGCKNPKAVSILIRGGTEHVVSEVERALNDAIRVVAITKEDGKFLWGGGAVEAELAMRLAKYANSVGGREQLAI 434
                                   ********************************************************************************* PP

                                   HHHHHHHTHHHHHHHHHCTSXHHHHHHHHHHHHHTTXTTEEEETTTTCEEECCCCTXEEEHHHHHHHHHHHHHHHHHHHCE CS
                    Cpn60_TCP1 403 eafakALevipktLaeNaGldpievlaklraahnkgekelgidvesgeiidlveagvvDplkvkrqalksAteaastiLri 483
                                   eafakALe+ip+tLaeNaG+dpi++l kl+++h+kg++++g+d++s+ + d+ ++gv+Dp++vk+ al+sA+e+a++iLri
  gi|13541959|ref|NP_111647.1| 435 EAFAKALEIIPRTLAENAGIDPINTLIKLKSEHEKGKISMGVDLDSNGAGDMSKKGVIDPVRVKTHALESAVEVATMILRI 515
                                   ********************************************************************************* PP

                                   EEEEXXX CS
                    Cpn60_TCP1 484 deiikak 490
                                   d++i  k
  gi|13541959|ref|NP_111647.1| 516 DDVIASK 522
                                   ****987 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0     0.003        13      54     119 ..      94     152 ..      49     157 .. 0.74
   2 ?    3.8   0.1     0.015        69      97     143 ..     239     286 ..     164     297 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.003
                                   SSTGGGSTTHHHHHHHHHHTCCCTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  54 ggepllypdfvellerlaklavpgiritvetngtlpdeeklerllelgvdrvslgleaaddekvlk 119
                                    g+ ++     ell+++  l + g++ tv++ng+++    ++++ +      +++++++dde +l+
  gi|13541959|ref|NP_111647.1|  94 DGTTTAVVLSGELLKQAETLLDQGVHPTVISNGYRLAVNEARKIID------EISVKSTDDE-TLR 152
                                   55555555556667777777789************98666666666......4677777777.554 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.015
                                   HHHTT...-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSE CS
                                   xxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  97 llelg...vdrvslgleaaddekvlklmnrghtfeevlealeklreagik 143
                                   ++ +     + ++  +++ d+ k+++ +n  ++ + ++e +ek++++g +
  gi|13541959|ref|NP_111647.1| 239 IDSALeikKTEIEAKVQISDPSKIQDFLN--QETSTFKEMVEKIKKSGAN 286
                                   333333337889999*************4..7888888888888888866 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 ?   -2.2   0.1       1.1   4.9e+03      30      44 ..      69      82 ..      65      87 .. 0.72
   2 ?   10.8   0.0   9.6e-05      0.43      20      50 ..     254     284 ..     248     293 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.1
                                  HHHTS-HHHHHHHHH CS
                Fe_dep_repress 30 erLnvspssVsemlk 44
                                  ++++v+ +++ +m+ 
  gi|13541959|ref|NP_111647.1| 69 KEMDVEHPTA-KMIV 82
                                  7999999998.4554 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 9.6e-05
                                   HSSB-HHHHHHHHTS-HHHHHHHHHHHHHTT CS
                Fe_dep_repress  20 kkvvktkdlaerLnvspssVsemlkkLekdG 50 
                                    ++  ++++  +Ln++ s+  em++k +k G
  gi|13541959|ref|NP_111647.1| 254 VQISDPSKIQDFLNQETSTFKEMVEKIKKSG 284
                                   5566789999******************998 PP

>> Dynein_C  Dynein heavy chain C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.1   7.9e-05      0.35      33      95 ..     227     293 ..     185     302 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 7.9e-05
                                   -------------...----................-HHHHHHHHHHHHHHHHHHHHHHHHHHHHC---- CS
                      Dynein_C  33 vlelaadileklpe.lfdleeaekk......pteyeeplntvllqElerfnkLleeirrsLkelqkaikG 95 
                                   + ++++d    l + ++++++   +      + ++++ ++ +l qE+++f++++e+i++s  ++ ++ kG
  gi|13541959|ref|NP_111647.1| 227 MPDVVKDAKIALIDsALEIKK---TeieakvQISDPSKIQDFLNQETSTFKEMVEKIKKSGANVVLCQKG 293
                                   222222222222222234443...02234346667777888********************999999888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (545 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       806  (0.0449551); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); 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: 0.70u 0.27s 00:00:00.97 Elapsed: 00:00:00.47
# Mc/sec: 3465.88
//
Query:       gi|13541960|ref|NP_111648.1|  [L=320]
Description: thioredoxin reductase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.5e-51  173.8   5.5    5.1e-51  173.6   5.5    1.0  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    2.1e-28   99.5   8.3    1.7e-23   83.3   1.8    2.3  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    7.1e-13   48.9   6.3    7.5e-12   45.6   0.2    3.0  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    7.7e-13   48.3  12.1    2.8e-05   23.4   4.1    4.3  5  FAD_binding_2   FAD binding domain
    2.8e-11   42.8   7.2    3.4e-05   22.7   1.1    3.9  4  HI0933_like     HI0933-like protein
    1.3e-08   34.6   9.5    1.6e-06   27.7   0.9    3.1  3  FAD_oxidored    FAD dependent oxidoreductase
    5.8e-07   29.0   1.6    1.8e-05   24.1   0.2    2.5  2  Thi4            Thi4 family
    1.1e-06   28.7   0.3    0.00042   20.5   0.6    2.5  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    3.6e-06   26.8  12.1    0.00065   19.4   2.9    3.7  4  DAO             FAD dependent oxidoreductase
    8.3e-06   25.3   6.6     0.0016   17.8   0.3    3.8  4  FAD_binding_3   FAD binding domain
     0.0002   20.7   0.7     0.0051   16.1   0.2    2.2  2  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
    0.00028   20.1   0.9    0.00028   20.1   0.9    4.6  5  GIDA            Glucose inhibited division protein A
     0.0022   17.3   0.2       0.97    8.6   0.0    2.6  3  Amino_oxidase   Flavin containing amine oxidoreductase
     0.0039   16.4   1.4        2.9    6.9   0.1    3.2  3  K_oxygenase     L-lysine 6-monooxygenase (NADPH-requiring)
  ------ inclusion threshold ------
      0.021   13.7   1.7        1.6    7.5   0.0    2.1  2  Trp_halogenase  Tryptophan halogenase
      0.026   13.6   1.6      0.095   11.7   0.9    2.0  2  Lycopene_cycl   Lycopene cyclase protein


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  173.6   5.5   4.5e-54   5.1e-51       1     294 []      17     304 ..      17     304 .. 0.89

  Alignments for each domain:
  == domain 1  score: 173.6 bits;  conditional E-value: 4.5e-54
                                   CSEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH....HHHHCHHHH.CCCCHCCTCE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxx.xxxxxxxxxx RF
                   Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeias....evvkklnqg.ielllgeevv 76 
                                   +dv++iG+G+AG++aa +++++g+  +++  ++++ +g    ++ ++++ ++++i+     +++ +  ++    + g+ev 
  gi|13541960|ref|NP_111648.1|  17 FDVIIIGAGAAGFSAAVYASRSGLSAVIL--DKNVAGGLTAEAPLVENYLGFKSIVGsdlaKNFAEHASEyASIREGVEVK 95 
                                   69***********************8777..8899999999999*********9999999944444455535566778899 PP

                                   EEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHHHHHHCCSS-TSEEEEES-SHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2  77 kidpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGvaenvgklvrtldsaealklkllpkrivvvGgGyiGvEl 157
                                   ++ +g + + + +++     ++  +++++ tG + + lg++G+ae+ gk+v+++ +++++  k+++  +v +GgG+ G   
  gi|13541960|ref|NP_111648.1|  96 SVKKGDGGFIVDTSD----GEYHSKYIIITTGTTHKHLGVKGEAEYFGKGVSYCSTCDGYLFKNKN--VVTIGGGNSGAIA 170
                                   999999999994332....379***************************************99998..************* PP

                                   HHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTEEEE.EEETTSCE.....EEESEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxx.....xxxxxxx RF
                   Pyr_redox_2 158 AaalaklgkevtlveardrllraldkelsaaleealekeGvevklgtsvkeidgngekle.vvledgee.....idadlvv 232
                                   A+ ++++ k++t+ve ++r +      +++a+ e+++k+++   ++++v+ei g+g+k++ v+ +d ++     ++ad v+
  gi|13541960|ref|NP_111648.1| 171 AISMSEYVKNATIVEYMPRYM------CENAYIEEIKKRKIPYIMNAQVTEIVGDGKKVTgVKYKDRSSgeektLPADGVF 245
                                   *********************......******************************55554444444444556******* PP

                                   E-S-EEES-HHCSHCCT-EEEETTEEE--TTSBESSTTEEE-GGGCTECCSS--HHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2 233 vavGvrpstelleeklglelderggivvdeflrtnvpgiyaiGDvaggkggpelaqaAvqqG 294
                                   v vG+ p+t++l +++g++lderg+i vd ++rtnvpgiya+GDv+   g+++++  Av  G
  gi|13541960|ref|NP_111648.1| 246 VYVGLIPQTSFL-KDSGVKLDERGYIIVDGRQRTNVPGIYAAGDVT--SGSFAQIASAVGDG 304
                                   ************.*********************************..88888888887665 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   0.6   3.1e-07   0.00035       1      33 [.      20      51 ..      20      62 .. 0.91
   2 !   83.3   1.8   1.5e-26   1.7e-23      96     305 .]      86     287 ..      67     287 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 3.1e-07
                   Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkgnig 33
                                  iIiGaG+aG +aa+ + ++gl + +il+k+ +g
  gi|13541960|ref|NP_111648.1| 20 IIIGAGAAGFSAAVYASRSGL-SAVILDKNVAG 51
                                  8********************.689****9766 PP

  == domain 2  score: 83.3 bits;  conditional E-value: 1.5e-26
                   Pyr_redox_3  96 lpiklfeeVesvkkedegfevetsketyeAkkviiAtGefdkPnklnipGeek...lvkhyskvkefhkyagqkvvViGgk 173
                                    +i++  eV+svkk d+gf+v+ts ++y++k++ii tG     + l+++Ge +   + + y    +   +++++vv iGg+
  gi|13541960|ref|NP_111648.1|  86 ASIREGVEVKSVKKGDGGFIVDTSDGEYHSKYIIITTGT--THKHLGVKGEAEyfgKGVSYCSTCDGYLFKNKNVVTIGGG 164
                                   46999*********************************9..77889*****98633445555555667789********** PP

                   Pyr_redox_3 174 nSavDaAlelvrkgaeVtvvtrgseiekeesdpsyslkpdienrleelvkeekikvlfnaevkeikekeeey.kvk...te 250
                                   nS++ aA+ + ++ ++ t+v              y  +  + +++    k++ki  + na+v+ei  + +++  vk    +
  gi|13541960|ref|NP_111648.1| 165 NSGAIAAISMSEYVKNATIVEYMP---------RYMCENAYIEEI----KKRKIPYIMNAQVTEIVGDGKKVtGVKykdRS 232
                                   *************99999998875.........333333333333....33557777777777776555544223311223 PP

                   Pyr_redox_3 251 dgkkvevkddvvla.tGykpdlsflkkslfeldedgrpvlteeteetnvpglflaG 305
                                   +g++ +   d v++ +G  p++sflk+s+++lde g++ ++   + tnvpg++ aG
  gi|13541960|ref|NP_111648.1| 233 SGEEKTLPADGVFVyVGLIPQTSFLKDSGVKLDERGYIIVDGR-QRTNVPGIYAAG 287
                                   344444455555555***********************99875.78********99 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   1.8     0.067        75       2      26 ..      19      43 ..      18     111 .. 0.71
   2 !   45.6   0.2   6.7e-15   7.5e-12       1      80 [.     157     230 ..     157     234 .. 0.97

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.067
                                  EEEECSSHHHHHHHHHHHHTTSEEE CS
                     Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVt 26
                                  v+++G+G  g  +A ++++ g +  
  gi|13541960|ref|NP_111648.1| 19 VIIIGAGAAGFSAAVYASRSGLSAV 43
                                  899***********99988774433 PP

  == domain 2  score: 45.6 bits;  conditional E-value: 6.7e-15
                                   EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTSEEEEEEET CS
                     Pyr_redox   1 kvvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekngievllntkveeiegsedgvesvklkd 80 
                                   +vv +GgG++g  +A  ++e+ k+ t+ve +++ +      ++++  e+++k++i  ++n++v+ei+g++++v++vk kd
  gi|13541960|ref|NP_111648.1| 157 NVVTIGGGNSGAIAAISMSEYVKNATIVEYMPRYM------CENAYIEEIKKRKIPYIMNAQVTEIVGDGKKVTGVKYKD 230
                                   59*********************************......************************************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 !   23.4   4.1   2.5e-08   2.8e-05       1      35 [.      18      52 ..      18      57 .. 0.89
   2 ?   -3.7   0.0       4.1   4.6e+03     267     283 ..      95     112 ..      71     124 .. 0.72
   3 !    7.3   0.1    0.0019       2.1       2      33 ..     158     189 ..     157     196 .. 0.91
   4 !    9.4   0.0   0.00044      0.49     147     200 ..     196     249 ..     192     259 .. 0.88
   5 !   10.9   0.1   0.00015      0.17     375     408 ..     261     296 ..     252     304 .. 0.85

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 2.5e-08
                                  SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGG CS
                 FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefg 35
                                  Dvi+iG+G+AG +AA+ a++ Gl+ ++++k  + g
  gi|13541960|ref|NP_111648.1| 18 DVIIIGAGAAGFSAAVYASRSGLSAVILDKNVAGG 52
                                  9****************************987743 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 4.1
                                   -THHHHTT-EEE-.TTSS CS
                 FAD_binding_2 267 tealrgeGgilvd.kdGr 283
                                   +   +g+Gg++vd +dG+
  gi|13541960|ref|NP_111648.1|  95 KSVKKGDGGFIVDtSDGE 112
                                   444578888888888886 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.0019
                                   EEEE--SHHHHHHHHHHHHTTT-EEEEESSSG CS
                 FAD_binding_2   2 viViGsGlAGLaAAleaaeaGlkvavvekeqe 33 
                                   v+ iG+G +G  AA++++e  ++ ++ve +++
  gi|13541960|ref|NP_111648.1| 158 VVTIGGGNSGAIAAISMSEYVKNATIVEYMPR 189
                                   899************************98875 PP

  == domain 4  score: 9.4 bits;  conditional E-value: 0.00044
                                   HHHHHHTCTEEEEESEEEEEEEECTTEEEEEEEEETTTTCEEEEEESEEEE--- CS
                 FAD_binding_2 147 lvesarkagvdfqerteadeLivedgrvtGavvenpesgrevrirakavvlatg 200
                                    +e+++k+++ +  +++++e++ ++++vtG+  ++++sg+e ++ a++v +  g
  gi|13541960|ref|NP_111648.1| 196 YIEEIKKRKIPYIMNAQVTEIVGDGKKVTGVKYKDRSSGEEKTLPADGVFVYVG 249
                                   5789999**************99999********************99977655 PP

  == domain 5  score: 10.9 bits;  conditional E-value: 0.00015
                                   EEEBETTSBE..STTEEESSBTEEE-STCEESSSST CS
                 FAD_binding_2 375 Gvetdengrv..ldadgqpipGLYAaGevaaggvhg 408
                                   Gv+ de+g    ++++ +++pG YAaG v++g++  
  gi|13541960|ref|NP_111648.1| 261 GVKLDERGYIivDGRQRTNVPGIYAAGDVTSGSFAQ 296
                                   888888888777999999************988865 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   1.1     3e-08   3.4e-05       1      33 [.      17      49 ..      17      53 .. 0.93
   2 !    9.5   0.0   0.00032      0.36     122     165 ..      84     125 ..      73     139 .. 0.82
   3 !   11.1   0.1    0.0001      0.12       2      33 ..     157     188 ..     156     191 .. 0.92
   4 ?   -0.6   0.0      0.37   4.1e+02     114     151 ..     195     232 ..     194     247 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 3e-08
                                  -SEEEE--SHHHHHHHHHHHHTT--EEEE-SSS CS
                   HI0933_like  1 kdviviGgGaAGlmaAisaakrgkrVlllekak 33
                                  +dvi+iG+GaAG+ aA+ a++ g + ++l+k+ 
  gi|13541960|ref|NP_111648.1| 17 FDVIIIGAGAAGFSAAVYASRSGLSAVILDKNV 49
                                  59****************************985 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00032
                                   HT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE----S CS
                   HI0933_like 122 agvklrletevksvekeedgkfrvktkseeeleadklvlAtGGl 165
                                   +  ++r   evksv+k ++g f v+t s++e+++++++++tG +
  gi|13541960|ref|NP_111648.1|  84 EYASIREGVEVKSVKKGDGG-FIVDT-SDGEYHSKYIIITTGTT 125
                                   556899999*****776666.*****.9************9864 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 0.0001
                                   SEEEE--SHHHHHHHHHHHHTT--EEEE-SSS CS
                   HI0933_like   2 dviviGgGaAGlmaAisaakrgkrVlllekak 33 
                                   +v+ iGgG +G  aAis+++  k+ +++e ++
  gi|13541960|ref|NP_111648.1| 157 NVVTIGGGNSGAIAAISMSEYVKNATIVEYMP 188
                                   7999***********************99886 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 0.37
                                   HHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTE CS
                   HI0933_like 114 allkelkeagvklrletevksvekeedgkfrvktksee 151
                                   a+++e+k++++ + ++ +v+++  + +++  vk+k+++
  gi|13541960|ref|NP_111648.1| 195 AYIEEIKKRKIPYIMNAQVTEIVGDGKKVTGVKYKDRS 232
                                   56789*****************9999999999995433 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.9   1.5e-09   1.6e-06       1      50 [.      18      67 ..      18     103 .. 0.77
   2 ?    4.7   0.9     0.014        16       2      29 ..     158     185 ..     157     190 .. 0.84
   3 !    6.5   0.0    0.0039       4.4      93     137 ..     196     242 ..     187     245 .. 0.85

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 1.5e-09
                  FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsg.lvatdignk 50
                                  Dv+++G+g+aG+ AA+ A r+G + +++++ +v GGl++ + lv + +g+k
  gi|13541960|ref|NP_111648.1| 18 DVIIIGAGAAGFSAAVYASRSGLSAVILDK-NVAGGLTAEApLVENYLGFK 67
                                  9*************************9986.68999988762456666665 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.014
                  FAD_oxidored   2 vvVvGGgpaGvaAAiaAaraGakvlLve 29 
                                   vv +GGg +G +AAi+  +  ++  +ve
  gi|13541960|ref|NP_111648.1| 158 VVTIGGGNSGAIAAISMSEYVKNATIVE 185
                                   899************9888777777776 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.0039
                  FAD_oxidored  93 leemlaeagvtvllntrlvevekegkriesvtveske.g.rktirAk 137
                                   + e +++ ++  ++n++++e++ +gk++++v+ ++++ g +kt+ A+
  gi|13541960|ref|NP_111648.1| 196 YIEEIKKRKIPYIMNAQVTEIVGDGKKVTGVKYKDRSsGeEKTLPAD 242
                                   455568889****************9*********998888888875 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.2   1.6e-08   1.8e-05      17      54 ..      16      52 ..       5      99 .. 0.77
   2 ?    3.6   0.1      0.03        34      15      39 ..     153     177 ..     143     187 .. 0.80

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 1.6e-08
                                  EEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS-- CS
                          Thi4 17 esDvvivGaGssGLtaayylakkpdlkvailersvspG 54
                                  + Dv+i+GaG++G +aa y +++ +l  +il+++v+ G
  gi|13541960|ref|NP_111648.1| 16 DFDVIIIGAGAAGFSAAVYASRS-GLSAVILDKNVAGG 52
                                  57*****************9999.***********966 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.03
                                   HTEEEEEEE--SHHHHHHHHHHHHC CS
                          Thi4  15 yaesDvvivGaGssGLtaayylakk 39 
                                   + + +vv +G+G sG  aa  +++ 
  gi|13541960|ref|NP_111648.1| 153 FKNKNVVTIGGGNSGAIAAISMSEY 177
                                   55789**************999876 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.6   3.7e-07   0.00042       1      33 [.      21      52 ..      21      67 .. 0.88
   2 ?    5.4   0.0     0.019        21       2      27 ..     161     186 ..     160     213 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 3.7e-07
                                  EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSG CS
                 NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGG 33
                                  I+GaG++G +aA ++++ g++ ++l+k+   GG
  gi|13541960|ref|NP_111648.1| 21 IIGAGAAGFSAAVYASRSGLSAVILDKN-VAGG 52
                                  9*************************95.5555 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.019
                                   E--SHHHHHHHHHHHCCTEEEEEE-S CS
                 NAD_binding_8   2 vGaGlsGlvaAylLakagfdvlllek 27 
                                   +G+G sG+ aA  ++++ ++ +++e 
  gi|13541960|ref|NP_111648.1| 161 IGGGNSGAIAAISMSEYVKNATIVEY 186
                                   9**************99888888875 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   2.9   5.8e-07   0.00065       1      35 [.      18      52 ..      18      57 .. 0.91
   2 !    9.0   0.0   0.00086      0.97     148     202 ..      74     124 ..      68     142 .. 0.80
   3 ?   -0.4   0.4      0.58   6.5e+02       2      27 ..     158     185 ..     157     190 .. 0.81
   4 ?    2.2   0.0       0.1   1.1e+02     151     198 ..     195     246 ..     177     284 .. 0.73

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 5.8e-07
                                  EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSS CS
                           DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiagsg 35
                                  dv+iiG+G +G s+A +++r g   ++l+k+  ag g
  gi|13541960|ref|NP_111648.1| 18 DVIIIGAGAAGFSAAVYASRSGlsAVILDKN-VAG-G 52
                                  9*****************************9.777.5 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00086
                                   HHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEEEEE--GG CS
                           DAO 148 ltaalaraaealGveilegtevtgleeedgkvwgverttp.gendaadavVnaaGa 202
                                   l++ +a+ a +  + i+eg ev+++++ d ++  v  +t+ ge ++ +++++++G 
  gi|13541960|ref|NP_111648.1|  74 LAKNFAEHASEY-ASIREGVEVKSVKKGD-GGFIV--DTSdGEYHS-KYIIITTGT 124
                                   778888899888.9***********7644.44666..788799877.99******5 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.58
                                   EEEECTSHHHHHHHHHHHHT.T.EEEEE CS
                           DAO   2 vviiGGGiiGlstAyeLarr.g.Vtlle 27 
                                   vv iGGG  G+ +A   ++  +  t++e
  gi|13541960|ref|NP_111648.1| 158 VVTIGGGNSGAIAAISMSEYvKnATIVE 185
                                   788***********99887643577766 PP

  == domain 4  score: 2.2 bits;  conditional E-value: 0.1
                                   HHHHHHHHTT-EEEESECEEEEEEEETCEEEEE.EECT.EEE.E.EEEEEEE CS
                           DAO 151 alaraaealGveilegtevtgleeedgkvwgve.rttp.gen.d.aadavVn 198
                                   a+ ++++++ +  + +++vt++  +++kv+gv+ ++ + ge+ +  ad v +
  gi|13541960|ref|NP_111648.1| 195 AYIEEIKKRKIPYIMNAQVTEIVGDGKKVTGVKyKDRSsGEEkTlPADGVFV 246
                                   6788899999999999*****977779*****99444446642233344544 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.3   1.4e-06    0.0016       2      33 ..      17      48 ..      16      54 .. 0.94
   2 ?    1.1   0.0      0.16   1.8e+02     107     159 ..      74     119 ..      67     136 .. 0.79
   3 !    5.4   0.2    0.0084       9.4       3      31 ..     157     185 ..     155     191 .. 0.83
   4 ?    3.0   0.0     0.043        48      99     156 ..     184     242 ..     180     245 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.4e-06
                                  EEEEEE--SHHHHHHHHHHHHTTHHEEEEESS CS
                 FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlvekr 33
                                   dV+I+GaG aG+++a   s+ G + v+++k 
  gi|13541960|ref|NP_111648.1| 17 FDVIIIGAGAAGFSAAVYASRSGLSAVILDKN 48
                                  69****************************95 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.16
                                   HHHHHHHHHHHHTEEETCSEEEECCEECCCCCCCEEEECCTTEEEEEEEEEEE CS
                 FAD_binding_3 107 leriLvehaeerglqvrfktevesleqdeegvtaevrdketgeeetvrakYlv 159
                                   l +  +eh +++++++r++ ev+s+++ + g    + d ++ge    ++kY++
  gi|13541960|ref|NP_111648.1|  74 LAKNFAEH-ASEYASIREGVEVKSVKKGDGG---FIVDTSDGEY---HSKYII 119
                                   56667788.78899**********9999888...6777777777...888887 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.0084
                                   EEEEE--SHHHHHHHHHHHHTTHHEEEEE CS
                 FAD_binding_3   3 dVlIVGaGpaGlmlallLseaGvrvvlve 31 
                                   +V+ +G+G +G+++a  +se+  + ++ve
  gi|13541960|ref|NP_111648.1| 157 NVVTIGGGNSGAIAAISMSEYVKNATIVE 185
                                   6899*****************44567777 PP

  == domain 4  score: 3.0 bits;  conditional E-value: 0.043
                                   CEE--HHHHHHHHHHHHHHHTEEETCSEEEECCEECCCCCCCE.EEECCTTEEEEEEEE CS
                 FAD_binding_3  99 vtvypqteleriLvehaeerglqvrfktevesleqdeegvtae.vrdketgeeetvrak 156
                                   v+ +p  + e++ +e+ ++r +   ++++v+ +  d+++vt + ++d+++gee+t+ a+
  gi|13541960|ref|NP_111648.1| 184 VEYMPRYMCENAYIEEIKKRKIPYIMNAQVTEIVGDGKKVTGVkYKDRSSGEEKTLPAD 242
                                   66778888899999999999999999***************75277*********9886 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.2   4.6e-06    0.0051      30      62 ..      18      50 ..      10      92 .. 0.86
   2 ?    2.9   0.0     0.051        57      27      59 ..     154     186 ..     134     224 .. 0.66

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 4.6e-06
                                  EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHH CS
                   AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVtvlDvrpa 62
                                   v++iG+G aG +A+  a++ g + ++lD++ a
  gi|13541960|ref|NP_111648.1| 18 DVIIIGAGAAGFSAAVYASRSGLSAVILDKNVA 50
                                  69****************************987 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.051
                                   ---EEEEESTSHHHHHHHHHHHHTT-EEEEEES CS
                   AlaDh_PNT_C  27 epakvlviGgGvaGlqAiatakglgakVtvlDv 59 
                                   ++ +v+ iGgG  G  A+   ++   + t+++ 
  gi|13541960|ref|NP_111648.1| 154 KNKNVVTIGGGNSGAIAAISMSEYVKNATIVEY 186
                                   456788899999987666555544444444444 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   0.9   2.5e-07   0.00028       1      31 [.      18      48 ..      18      63 .. 0.89
   2 !    6.2   0.1    0.0042       4.7     129     156 ..     103     129 ..      81     148 .. 0.68
   3 ?    1.9   1.6     0.082        92       2      19 ..     158     175 ..     157     183 .. 0.88
   4 ?    1.5   0.1      0.11   1.3e+02      98     139 ..     193     234 ..     181     246 .. 0.80
   5 ?   -1.0   0.1      0.64   7.2e+02     354     365 ..     279     290 ..     274     313 .. 0.65

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 2.5e-07
                                  CEEEE-SSHHHHHHHHHHHHTT--EEEEES- CS
                          GIDA  1 dviViGgGhAGceAAlaaarlGakvlLithk 31
                                  dvi+iG+G AG+ AA+ a+r+G++ +++ ++
  gi|13541960|ref|NP_111648.1| 18 DVIIIGAGAAGFSAAVYASRSGLSAVILDKN 48
                                  8**********************99888554 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0042
                                   EEEEETTS-EEEECEEEE--TT-BT-EE CS
                          GIDA 129 kgvvtedgetikakavviatGtflkgki 156
                                     +v +++ ++++k ++i+tGt  + + 
  gi|13541960|ref|NP_111648.1| 103 GFIVDTSDGEYHSKYIIITTGT-THKHL 129
                                   3488888999************.33222 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.082
                                   EEEE-SSHHHHHHHHHHH CS
                          GIDA   2 viViGgGhAGceAAlaaa 19 
                                   v+ iGgG +G  AA+ ++
  gi|13541960|ref|NP_111648.1| 158 VVTIGGGNSGAIAAISMS 175
                                   899***********9876 PP

  == domain 4  score: 1.5 bits;  conditional E-value: 0.11
                                   HHHHHHHHHTSTTEEEEES-EEEEEECTTEEEEEEETTS-EE CS
                          GIDA  98 skevteklenepnleiieeeveeliveekkvkgvvtedgeti 139
                                   ++++ e++++ +   i++++v+e++ + kkv+gv+ +d +  
  gi|13541960|ref|NP_111648.1| 193 ENAYIEEIKKRKIPYIMNAQVTEIVGDGKKVTGVKYKDRSSG 234
                                   56667788887778899*******99999****999887655 PP

  == domain 5  score: -1.0 bits;  conditional E-value: 0.64
                                   SSBTEEE-CGGG CS
                          GIDA 354 kvkgLflAGqin 365
                                   +v+g+++AG+++
  gi|13541960|ref|NP_111648.1| 279 NVPGIYAAGDVT 290
                                   699*******97 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.0   0.00086      0.97     211     261 ..      73     123 ..      41     128 .. 0.89
   2 ?   -1.2   0.0      0.84   9.4e+02     211     254 ..     186     242 ..     173     246 .. 0.75
   3 !    5.7   0.1     0.007       7.8     413     448 ..     275     308 ..     260     311 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00086
                                   HHHHHHHH.TTTTEEEETSEEEEEEEEETTCEEEEETTSTEEEESEEEE-S- CS
                 Amino_oxidase 211 qlpealae.elrgldirlntrVkeikregdgvtvtledgevveaDaVvvTvp 261
                                    l++++ae  +   +ir + +Vk++k++++g  v ++dge  + +++++T+ 
  gi|13541960|ref|NP_111648.1|  73 DLAKNFAEhASEYASIREGVEVKSVKKGDGGFIVDTSDGEY-HSKYIIITTG 123
                                   677788887777889*************************7.*******985 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.84
                                   HHHHHHHH.......TTTTEEEETSEEEEEEEEETTC.EEEEETTSTEE.....EES CS
                 Amino_oxidase 211 qlpealae.......elrgldirlntrVkeikregdg.vtvtledgevv.....eaD 254
                                    +p++++e       ++r+    +n+ V+ei  +g +  +v+++d ++      +aD
  gi|13541960|ref|NP_111648.1| 186 YMPRYMCEnayieeiKKRKIPYIMNAQVTEIVGDGKKvTGVKYKDRSSGeektlPAD 242
                                   5677777777777677777788899*******9777757899998887755555555 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.007
                                   HHCHHCSTTEEE.SGGGCTTTTTSHHHHHHHHHHHH CS
                 Amino_oxidase 413 lakpegdprlffAGehtsreypgtvegAilSGlraA 448
                                    +++ ++p+++ AG+ ts ++ + +  A+  G++aA
  gi|13541960|ref|NP_111648.1| 275 RQRT-NVPGIYAAGDVTSGSF-AQIASAVGDGCKAA 308
                                   4677.9************666.66***********9 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.1     0.013        15       3      36 ..      17      48 ..      15      52 .. 0.86
   2 !    6.9   0.1    0.0026       2.9     122     219 ..      92     183 ..      73     196 .. 0.62
   3 ?    2.3   0.0     0.069        77     284     336 ..     195     246 ..     187     251 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.013
                   K_oxygenase  3 lDligiGiGpsnLsLailleevkkelkalflerq 36
                                  +D+i+iG+G++  s a+ ++     l+a+ l+++
  gi|13541960|ref|NP_111648.1| 17 FDVIIIGAGAAGFSAAVYASRSG--LSAVILDKN 48
                                  8*************999888777..999999886 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0026
                   K_oxygenase 122 vepdeeeee.elltveskdaegeeeelearnlvlgvGtepkiPevleklegkervvHsseylerkee.llakkriaVvGsG 200
                                   ve+++ ++    + v++     +  e++++ +++++Gt+ k   v  +    e +    +y ++ +  l ++k+++ +G+G
  gi|13541960|ref|NP_111648.1|  92 VEVKSVKKGdGGFIVDT-----SDGEYHSKYIIITTGTTHKHLGVKGE---AEYFGKGVSYCSTCDGyLFKNKNVVTIGGG 164
                                   44444333335677776.....45679999999999977653333222...2333344456555554578999******** PP

                   K_oxygenase 201 qSaaeifedllrrqkkvel 219
                                    S+a  +  + +  k++++
  gi|13541960|ref|NP_111648.1| 165 NSGAIAAISMSEYVKNATI 183
                                   ***9887777776665555 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.069
                   K_oxygenase 284 lyeqkvkgeerlrllpnrevesaeaegkgeveltlrneesgeeetlevdavvl 336
                                    y +++ +++++  + n +v+++  +gk+ + ++++++ sgee+tl +d v++
  gi|13541960|ref|NP_111648.1| 195 AYIEEI-KKRKIPYIMNAQVTEIVGDGKKVTGVKYKDRSSGEEKTLPADGVFV 246
                                   555555.344566778999********99999*****************9987 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.6    0.0063       7.1       1      22 [.      18      39 ..      18      50 .. 0.87
   2 ?    7.5   0.0    0.0014       1.6       1      26 [.     157     182 ..     157     202 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0063
                                  EEEEE--SHHHHHHHHHHHHHT CS
                Trp_halogenase  1 kivivGGGtaGwlaAaalakal 22
                                  +++i+G+G aG+ aA + ++ +
  gi|13541960|ref|NP_111648.1| 18 DVIIIGAGAAGFSAAVYASRSG 39
                                  699*************998865 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0014
                                   EEEEE--SHHHHHHHHHHHHHTTTSS CS
                Trp_halogenase   1 kivivGGGtaGwlaAaalakalkgkl 26 
                                   ++v +GGG +G +aA+ +++++k+ +
  gi|13541960|ref|NP_111648.1| 157 NVVTIGGGNSGAIAAISMSEYVKNAT 182
                                   5899****************996532 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.9   8.5e-05     0.095       1      31 [.      18      46 ..      18      54 .. 0.91
   2 ?    0.0   0.0       0.3   3.4e+02       2      43 ..     158     197 ..     157     230 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 8.5e-05
                 Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvlie 31
                                  Dv++iGaG+Ag s A     ++ gl+ v+++
  gi|13541960|ref|NP_111648.1| 18 DVIIIGAGAAGFSAAVYA--SRSGLSAVILD 46
                                  9************99988..99999999997 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.3
                 Lycopene_cycl   2 vvviGaGpAglslAarlteakpglkvvlieaspsllfpnnyv 43 
                                   vv iG+G  g   A  +  +++  + +++e  p  +  n y 
  gi|13541960|ref|NP_111648.1| 158 VVTIGGGNSGAIAAISM--SEYVKNATIVEYMPRYMCENAYI 197
                                   899*******8888877..88888999999888888887775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       590  (0.0329076); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.62u 0.32s 00:00:00.94 Elapsed: 00:00:00.50
# Mc/sec: 1934.34
//
Query:       gi|13541961|ref|NP_111649.1|  [L=223]
Description: threonine dehydratase, partial [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-38  133.4   0.0    1.2e-38  133.2   0.0    1.0  1  PALP      Pyridoxal-phosphate dependent enzyme
  ------ inclusion threshold ------
        0.1   13.3   0.0       0.16   12.6   0.0    1.3  1  DUF2147   Uncharacterized protein conserved in bacteria (DUF2


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 !  133.2   0.0   1.3e-42   1.2e-38       7     205 ..      25     220 ..      19     223 .] 0.93

  Alignments for each domain:
  == domain 1  score: 133.2 bits;  conditional E-value: 1.3e-42
                                   S--EEEECCTCCCCCCEEEEEEGGGSTTSBTTHHHHHHHHHHHHTTTTTSEEEEEBSSHHHHHHHHHHHHHT-EEEEEEET CS
                          PALP   7 pTPlvrlprlskelgvplflKlEslnptgSfKdRgaeyllarlkegtgaktvveassGNhgralAaaaallGlkvtivvpa 87 
                                   p+Plv l++     g++ +lKl++l ptgSfK++g ++l+++l + + + ++++as+GN  ++ A+a++ + +kv+iv+ +
  gi|13541961|ref|NP_111649.1|  25 PSPLVSLNSNV-VQGIETLLKLDNLLPTGSFKVMGSTFLIYKLNPDEIKARIIAASTGNFSQGXAYASRIYWIKVRIVMTD 104
                                   78888888744.556679************************99999********************************** PP

                                   TS-HHHHHHHHHTT-EEEEECCHHHHHHHHHHHHHHHSTTCEE--TTTSHHHHHHHHTHHHHHHHHTTTTEEEEEEE-SSS CS
                          PALP  88 daspekvallrllGaevvevggdydeavaaaaelaaegegaylvsqfdnptviegygtiglEileqlggkpdavvvpvGgG 168
                                   +++p++v+++r lG ev++ g  +++a+++a+ela + +g+ + ++ + p+ ++g gt  +E++ + ++++da++vpvG  
  gi|13541961|ref|NP_111649.1| 105 NSNPDNVDATRKLGGEVIFHGPKFNDARNYAEELAVK-NGYRYFHSANEPLLVAGVGTHTPELI-ESDPEIDAIIVPVGDE 183
                                   *************************************.*************************7.5558**********98 PP

                                   HHHHHHHHHHHHHSTT-EEEEEEECTTCGGTTCCS.. CS
                          PALP 169 gliaGiaaglkerrpdvrvigvepegsdalarslrag 205
                                   +   G a        d++vig+++e  +a +++++ g
  gi|13541961|ref|NP_111649.1| 184 SGSRGAAIVAETMSKDIKVIGAQSEMFPAAYKARKSG 220
                                   8888888888888899****************99666 PP

>> DUF2147  Uncharacterized protein conserved in bacteria (DUF2147)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   1.8e-05      0.16      18      78 ..      84     143 ..      60     151 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.8e-05
                       DUF2147  18 kcgkklcGkivklkeka.kkdaknpdgalrnrpllGleilkglkkdgegewegGkiydpesG 78 
                                    +g ++  +i+++k +   +d++npd+  ++r+l G +i++g k ++ +++   + +  ++G
  gi|13541961|ref|NP_111649.1|  84 SQGXAYASRIYWIKVRIvMTDNSNPDNVDATRKLGGEVIFHGPKFNDARNYA--EELAVKNG 143
                                   46778999******7779**************************77776787..44555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       266  (0.0148363); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1516.42
//
Query:       gi|13541962|ref|NP_111650.1|  [L=105]
Description: hypothetical protein TVN1131, partial [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-09   38.0   0.0    2.1e-09   37.2   0.0    1.4  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain


Domain annotation for each model (and alignments):
>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.2   0.0   1.2e-13   2.1e-09       4      69 .]       2      73 ..       1      73 [. 0.86

  Alignments for each domain:
  == domain 1  score: 37.2 bits;  conditional E-value: 1.2e-13
                OrfB_Zn_ribbon  4 lkeqleykakeyGikveevnpayTSktCseCgsknke.......alsgrtfkCpnCgfeadrDvnAaiNilkr 69
                                  l+ q++yka+e Gi+v+  n+ yTSk Cs    ++ e       ++ +r   +++ g  +++D+ +++Ni+k+
  gi|13541962|ref|NP_111650.1|  2 LIYQIKYKAEEIGITVIMQNEDYTSK-CSFLDNESIEhhdtymgKRIHRGIFRSATGKLIHADLQSSYNIIKK 73
                                  6789*********************8.5544444444488899999999999999***************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       325  (0.0181271); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 664.73
//
Query:       gi|13541963|ref|NP_111651.1|  [L=288]
Description: protoheme IX farnesyltransferase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-44  151.5  26.0    3.3e-44  151.1  26.0    1.2  1  UbiA      UbiA prenyltransferase family
  ------ inclusion threshold ------
       0.11   12.3   0.2         23    4.9   0.0    2.4  2  YueH      YueH-like protein


Domain annotation for each model (and alignments):
>> UbiA  UbiA prenyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  151.1  26.0   3.7e-48   3.3e-44       6     246 ..      25     268 ..      16     283 .. 0.86

  Alignments for each domain:
  == domain 1  score: 151.1 bits;  conditional E-value: 3.7e-48
                          UbiA   6 lvglalaaggspdlllllllllgtl...laaaaanalNdyfDreiDadmertpnRPlvsGrispkealifaivllilglll 83 
                                   ++  a+ a + ++l ++ll+l++t+   l + +a a  +y+Dr+iDa+m+rt++RPlv+G+i+p ++l f+++l++l++++
  gi|13541963|ref|NP_111651.1|  25 VI-GAIVAINRFTLTNILLILIATVsitLGSMGAEATTNYIDRDIDAIMDRTKKRPLVTGQIKPVKGLYFGLILMFLSIII 104
                                   23.4444466677767777777777666999999999******************************************** PP

                          UbiA  84 lalllnpltallgllallly.vvYtglrlKrrtllgtvvggiafglppllgwaavtgslsllalllalavflltwaialan 163
                                   l+++   l+a++++++l+   ++Y+ + +Krrt++++++gg+++g+p+++gw+ vt+ +s+l+++l+++v +++  + +  
  gi|13541963|ref|NP_111651.1| 105 LLFFSKYLAAVFMAIGLFDNvFIYS-YLTKRRTPWNIILGGFSGGFPVVIGWYTVTNAFSVLPWFLFALVVIWIPIHVWSL 184
                                   *88888999999999999999****.8********************************9999999999999999999999 PP

                          UbiA 164 dlrdregDrkagiktlpvvlGrkaaril...lalllavllla.llllllalllllylllalllaalallraarlvrrrdak 240
                                   ++r r+++ +a +++++ +  ++ ++i+   +a++l++   + ++ +++ ++   y+++a+++a+ +l++++ +vr+ d+k
  gi|13541963|ref|NP_111651.1| 185 AYRYRDDYNRARVPMMTSIQSDRISAICissSAVILFI---FsIIPVFFKAMPYTYMIVATIIAIPMLVYSVLFVRKPDRK 262
                                   99999999*******************86443333333...3355888888888888888999999999999999999999 PP

                          UbiA 241 kaakff 246
                                   +  k+f
  gi|13541963|ref|NP_111651.1| 263 SSLKLF 268
                                   988887 PP

>> YueH  YueH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.1    0.0029        26      27      49 ..     173     195 ..     171     206 .. 0.84
   2 ?    4.9   0.0    0.0025        23      27      47 ..     242     262 ..     235     270 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0029
                          YueH  27 ilvAiPdleWSieisyeeekeel 49 
                                   +++ iP   WS+  +y ++ +  
  gi|13541963|ref|NP_111651.1| 173 VVIWIPIHVWSLAYRYRDDYNRA 195
                                   7999**************98865 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0025
                          YueH  27 ilvAiPdleWSieisyeeeke 47 
                                   +++AiP l  S+ +  + + +
  gi|13541963|ref|NP_111651.1| 242 TIIAIPMLVYSVLFVRKPDRK 262
                                   89*********9988776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1056  (0.058899); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.64u 0.31s 00:00:00.95 Elapsed: 00:00:00.48
# Mc/sec: 1789.04
//
Query:       gi|13541964|ref|NP_111652.1|  [L=178]
Description: hypothetical protein TVN1133 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.08   13.4   1.2       0.15   12.5   1.2    1.4  1  HP0268    HP0268


Domain annotation for each model (and alignments):
>> HP0268  HP0268
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   1.2   8.6e-06      0.15      11      74 ..     110     175 ..     102     176 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 8.6e-06
                                   -SS-TTHHHHHHHHHHHH-SEEEEEE--TTTSHHHHHHHHHHHHSTT-EEEEE-TTT..TTT--EE CS
                        HP0268  11 nakpkkislekleekvekegekifYfdkenshKdlkklveffekkgksvylrevryg..ldekdyi 74 
                                   +++pk i+   l+ +v+ +g + +Yf+ +   Kd+kk v++  k  k+    ev ++  +de++y+
  gi|13541964|ref|NP_111652.1| 110 TSDPKAIKDYGLNCAVKFHGDEYVYFNVNQYFKDMKKTVDKILKTAKKRNRLEVEIAthIDETQYL 175
                                   57889999999999************************9987766555555555554116777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       934  (0.0520944); expected 358.6 (0.02)
Passed bias filter:                      620  (0.0345808); 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: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 1127.04
//
Query:       gi|13541965|ref|NP_111653.1|  [L=122]
Description: 50S ribosomal protein L18e [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.8e-08   31.8   0.3    9.8e-08   31.6   0.3    1.0  1  Ribosomal_L18   Ribosomal protein 60S L18 and 50S L18e
    0.00045   20.9   0.5     0.0019   18.9   0.5    2.0  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 !   31.6   0.3   1.1e-11   9.8e-08      35     139 ..      24     122 .]       5     122 .] 0.89

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 1.1e-11
                 Ribosomal_L18  35 arRtdskFnkvvlkrLfmsrinrpplslsrlvkkvkkkeeekkiavvvgtvtdDvrllevPklsvaALrftetararilka 115
                                   +r  ++k  + +  rL   r+  +++ l ++ k  k+    + ++vv g+v+   ++++  k+++ A++f+++a ++++++
  gi|13541965|ref|NP_111653.1|  24 SRQNSAKIWRDMAERLANGRRRYASINLYKIDKFAKD----GDVIVVPGSVLGVGKITK--KVTIGAVHFSRAATEKLVRS 98 
                                   56677788888999*****************999984....69**********999986..9******************* PP

                 Ribosomal_L18 116 GGeiltlDqLalraPtGkntvLlr 139
                                   G   ++l ++a  +P+G+n+ ++r
  gi|13541965|ref|NP_111653.1|  99 GCAFMSLSDVAKANPKGTNVKIMR 122
                                   *******************99887 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 !   18.9   0.5   2.1e-07    0.0019      72     125 ..      46     101 ..       5     104 .. 0.67

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 2.1e-07
                                   --EEEGGGTTTTSSS........SEEEE--S---.--EEEESEE-HHHHHHHHHTT-E CS
                Ribosomal_L27A  72 aeeidleelaeaglikk....kdgvKvlgkgeltkklkvkaskfSkkAkekIeaaGGk 125
                                    + i+l ++   +++k          vlg g++tkk+++ a +fS++A ek  + G++
  gi|13541965|ref|NP_111653.1|  46 YASINLYKI--DKFAKDgdviVVPGSVLGVGKITKKVTIGAVHFSRAATEKLVRSGCA 101
                                   344555555..3333334433222269999**********************999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       650  (0.0362541); expected 358.6 (0.02)
Passed bias filter:                      525  (0.0292822); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.33s 00:00:00.82 Elapsed: 00:00:00.50
# Mc/sec: 728.35
//
Query:       gi|13541966|ref|NP_111654.1|  [L=136]
Description: 50S ribosomal protein L13P [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.2e-08   34.4   0.2    1.4e-06   28.6   0.2    2.4  1  Ribosomal_L13  Ribosomal protein L13


Domain annotation for each model (and alignments):
>> Ribosomal_L13  Ribosomal protein L13
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.2   7.6e-11   1.4e-06      34     114 ..      21      99 ..       2     111 .. 0.72

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 7.6e-11
                                   TS--S-EEEEEEGGCBB-SSTHHTT-EEEEE-SSTTSEEEEEHHHHHCCSHHHHHHHHHHCCS-SSH.HHHHHGCTEEEES CS
                 Ribosomal_L13  34 hvdcGdyvvvinaekvaltgkkleqkvyyrhtgypgglkevtakellekkpeeilekaVkgmLpknk.lgrrrlkrLkvya 113
                                   +   G+ vv++na+k ++tg++   k+   + +    + +v+      k pe+il++ +  mLpk+   g++ l+r kvy+
  gi|13541966|ref|NP_111654.1|  21 QLLNGEEVVIVNASKAVITGDR---KFIIDKFKQRLDIGSVRKGPYYPKTPENILRRSIGDMLPKKItRGKEALSRCKVYR 98 
                                   345799**************85...444444444444555555666789***************9862567777******8 PP

                                   S CS
                 Ribosomal_L13 114 g 114
                                   +
  gi|13541966|ref|NP_111654.1|  99 N 99 
                                   6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       402  (0.0224218); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        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 0.28s 00:00:00.71 Elapsed: 00:00:00.47
# Mc/sec: 871.10
//
Query:       gi|13541967|ref|NP_111655.1|  [L=132]
Description: 30S ribosomal protein S9P [Thermoplasma volcanium GSS1]
Scores for complete 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-32  110.4   1.7    8.6e-32  110.2   1.7    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 !  110.2   1.7   4.8e-36   8.6e-32       1     121 []       8     132 .]       8     132 .] 0.93

  Alignments for each domain:
  == domain 1  score: 110.2 bits;  conditional E-value: 4.8e-36
                                   EECTTEEEEEEEEESSSEEEETTEECCHHSTTSCHHHHHCHHHHHTTTSSS.EEEEEEEESS-HHHHHHHHHHHHHHHHHH CS
                  Ribosomal_S9   1 GrrKesvArvwikegkgkilvngksleeYfkeeaarekvleplkltgllgk.fdvfvkvkgGGlsgqaeAirlgiaraLva 80 
                                   G+rK++vAr+ +k+gkg i++ng+++e Y + e  r+k+lep+kl++ + k +dv+vkvkgGG++gqa+A r++iar++v+
  gi|13541967|ref|NP_111655.1|   8 GKRKTAVARAVVKKGKGIITINGTPAELY-PVEVLRNKILEPVKLAEDKAKgIDVTVKVKGGGVTGQADASRTAIARGIVK 87 
                                   8***************************5.669**************99999***************************** PP

                                   HHHHH..HHHHC..TCCCTS-B--------TTSSCTTB----S-- CS
                  Ribosomal_S9  81 lekee..kkeLk..kaglltrDpRvvErkKtgkkkARkkyqwskR 121
                                   + +++  ++ ++  +++l+++D R++ +kK+g ++AR+k q+s+R
  gi|13541967|ref|NP_111655.1|  88 FLQDNelENLFRqyDRTLIVNDVRIKLPKKPGGRGARAKKQKSYR 132
                                   *88533244444889****************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       622  (0.0346924); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 979.85
//
Query:       gi|13541968|ref|NP_111656.1|  [L=72]
Description: DNA-directed RNA polymerase subunit N [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.4e-27   95.7   0.6    1.7e-27   95.5   0.6    1.1  1  RNA_pol_N  RNA polymerases N / 8 kDa subunit
  ------ inclusion threshold ------
      0.081   13.4   0.0        0.1   13.1   0.0    1.1  1  EF-hand_7  EF-hand domain pair


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 !   95.5   0.6   1.9e-31   1.7e-27       1      59 []       1      68 [.       1      68 [. 0.92

  Alignments for each domain:
  == domain 1  score: 95.5 bits;  conditional E-value: 1.9e-31
                                  ----SS-TTT--B-STHHHHHHHHHHTT.........--HHHHHHHHT--SHHHHHHHHTB--THHHH CS
                     RNA_pol_N  1 MiiPVrCFtCGkvigekweeylellekg.........eepkdaLdaLglkryCCrrmllthvdliekl 59
                                  MiiPVrCF+CG+vi++++ +yl+++++          ee ++++d+Lg++ryCCrrm+++hvdli+++
  gi|13541968|ref|NP_111656.1|  1 MIIPVRCFSCGRVIASDYGRYLRRINEIrsegreptaEEIEKIFDDLGVERYCCRRMIISHVDLINEI 68
                                  9************************7666667888888888************************985 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 ?   13.1   0.0   1.1e-05       0.1      21      53 ..      15      47 ..       9      51 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.1e-05
                     EF-hand_7 21 keellrllrkifqgagegsklsdeelellfkef 53
                                   +++ r+lr+i++  +eg +++ ee+e++f+++
  gi|13541968|ref|NP_111656.1| 15 ASDYGRYLRRINEIRSEGREPTAEEIEKIFDDL 47
                                  678999*******99***************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (72 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       617  (0.0344135); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.49
# Mc/sec: 444.88
//
Query:       gi|13541969|ref|NP_111657.1|  [L=464]
Description: hypothetical protein TVN1138 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (464 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1083  (0.0604049); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                        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: 0.71u 0.33s 00:00:01.04 Elapsed: 00:00:00.52
# Mc/sec: 2694.50
//
Query:       gi|13541970|ref|NP_111658.1|  [L=279]
Description: pyrroline-5-carboxylate reductase [Thermoplasma volcanium GSS1]
Scores for complete sequence (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  118.5   0.2    2.3e-34  117.7   0.2    1.4  1  P5CR_dimer      Pyrroline-5-carboxylate reductase dimerisatio
    1.1e-15   58.0   0.4    3.1e-15   56.5   0.4    1.8  1  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
    9.7e-08   32.3   0.1    4.6e-07   30.1   0.1    2.1  1  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
    3.6e-07   29.9   0.1    5.9e-07   29.2   0.1    1.3  1  IlvN            Acetohydroxy acid isomeroreductase, NADPH-bin
    1.4e-06   28.1   0.3    5.4e-06   26.1   0.2    2.0  2  ApbA            Ketopantoate reductase PanE/ApbA
    3.9e-05   23.1   0.0    6.6e-05   22.3   0.0    1.2  1  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
    0.00017   21.6   0.2    0.00043   20.2   0.0    1.8  2  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
     0.0034   17.9   0.2      0.011   16.2   0.1    2.0  1  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
     0.0058   16.7   0.1      0.012   15.7   0.1    1.5  1  Shikimate_DH    Shikimate / quinate 5-dehydrogenase
      0.006   15.9   0.1      0.023   14.0   0.1    1.9  2  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
  ------ inclusion threshold ------
      0.014   14.4   0.2      0.018   14.0   0.2    1.2  1  PDH             Prephenate dehydrogenase
      0.018   15.1   0.3       0.11   12.4   0.1    2.1  2  NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogen
       0.03   14.6   0.0       0.08   13.2   0.0    1.7  1  TrkA_N          TrkA-N domain
      0.043   13.0   0.0       0.08   12.2   0.0    1.4  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
      0.069   12.7   0.4       0.24   10.9   0.2    1.9  2  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
       0.07   12.7   0.5       0.12   11.9   0.5    1.3  1  DAO             FAD dependent oxidoreductase


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 !  117.7   0.2   2.1e-37   2.3e-34       1     101 [.     166     268 ..     166     270 .. 0.96

  Alignments for each domain:
  == domain 1  score: 117.7 bits;  conditional E-value: 2.1e-37
                                   CCHHHHHHHHTTTHHHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHHHHCHS..HHHHHHHH--TTSHHHHHHHH CS
                    P5CR_dimer   1 EkqldavtalsGsgpAyvflliealadagvklGlsreeArelaaqtvaGaaklllese..paelrdkvtspgGtTiaglke 79 
                                   Ek++da+talsGsgpAy++++iea++ +g klGl+r+ A++   qtv+G+akll+es+  p+el++kv +pgGtTi g+ e
  gi|13541970|ref|NP_111658.1| 166 EKYMDALTALSGSGPAYILTIIEAMMYGGLKLGLPRDLALKASYQTVMGSAKLLAESGehPSELKEKVITPGGTTIDGIYE 246
                                   89**************************************************99866669********************* PP

                                   HHHTTHHHHHHHHHHHHHHHHH CS
                    P5CR_dimer  80 leegglraavieaveaaakrsk 101
                                   le++++r+a+++a+e ++ +++
  gi|13541970|ref|NP_111658.1| 247 LEDARVRTAIMKAIEVSTMKAN 268
                                   ***************9998876 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 !   56.5   0.4   2.7e-18   3.1e-15       2      96 ..      17     104 ..      16     105 .. 0.93

  Alignments for each domain:
  == domain 1  score: 56.5 bits;  conditional E-value: 2.7e-18
                                   EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S-HHHHHHHHHHCG CS
                 F420_oxidored   2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlavkpedveevlsela 82 
                                   i iiG+G +g+++a  l ++g    e++v+ +rn   +++l e++g++v++ dn++a +eadvv+l++kp d+   ++++ 
  gi|13541970|ref|NP_111658.1|  17 ISIIGGGTIGSSIAIPLKRSG---FEVIVT-RRNTAVLKHL-ESYGISVMS-DNKTASKEADVVFLTLKPVDIIPEVRKI- 90 
                                   89*******************...****55.8888877766.999******.****************************. PP

                                   HHHHTTSEEEEESS CS
                 F420_oxidored  83 kdalkgklvisvla 96 
                                   +++ +gkl+is++a
  gi|13541970|ref|NP_111658.1|  91 EENIRGKLLISMAA 104
                                   999********998 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 !   30.1   0.1   4.1e-10   4.6e-07       2      73 ..      17      88 ..      16     168 .. 0.86

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 4.1e-10
                                  EEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTTEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHH CS
                 NAD_binding_2  2 igfiGlGvMGsnmalnllkagykvavynrtkekveelvaegakaaesieelvasldvvitmvkagkavdevi 73
                                  i +iG G++Gs++a  l+++g++v+v  r+++ +++l + g++++++ + + +++dvv++ +k  + + ev 
  gi|13541970|ref|NP_111658.1| 17 ISIIGGGTIGSSIAIPLKRSGFEVIVTRRNTAVLKHLESYGISVMSDNKTASKEADVVFLTLKPVDIIPEVR 88
                                  789**********************************************************99877776664 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 !   29.2   0.1   5.3e-10   5.9e-07       6      96 ..      16     105 ..      12     130 .. 0.83

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 5.3e-10
                                   -EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEE.HHHHHHT-SEEEE.-S-HHHHHHHHHHHTGGG CS
                          IlvN   6 kiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevlt.vaeavkkadvvmi.liPDelqkevyeeeiepn 84 
                                    i++iG G+ G + a  l+ sg++v+v+ r+++  +k+ ++ g++v++  + a+k+advv++ l P  +  ev   +ie+n
  gi|13541970|ref|NP_111658.1|  16 VISIIGGGTIGSSIAIPLKRSGFEVIVTRRNTA-VLKHLESYGISVMSdNKTASKEADVVFLtLKPVDIIPEVR--KIEEN 93 
                                   589************************988877.99**********972567999*****86377999999997..89999 PP

                                   --TT-EEEESSS CS
                          IlvN  85 lkegkalafahG 96 
                                   ++ +  +++a +
  gi|13541970|ref|NP_111658.1|  94 IRGKLLISMAAA 105
                                   988877777654 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.2   4.8e-09   5.4e-06       1     126 [.      17     126 ..      17     135 .. 0.81
   2 ?   -2.5   0.0       3.2   3.5e+03     122     148 ..     237     263 ..     219     266 .. 0.73

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 4.8e-09
                                   EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHHHHHHCEEEEETTCEEEEEECEEECCHSCCCCS-ESEEEE-SSGGG CS
                          ApbA   1 iailGaGaiGsllaakLakagadvtlilrsr.rlealkknGlrltseggeeilrppealsaeekselepidlvivtvKayq 80 
                                   i i+G G iGs +a  L++ g +v++  r+   l++l++ G+++ s++        +++s+       ++d+v++t+K  +
  gi|13541970|ref|NP_111658.1|  17 ISIIGGGTIGSSIAIPLKRSGFEVIVTRRNTaVLKHLESYGISVMSDN--------KTASK-------EADVVFLTLKPVD 82 
                                   78*****************************9************9999........44444.......59*********** PP

                                   HHHHHHHHGGGECTCEEEEEESSSSCHHHHHTTTSTTSEEEEEEEE CS
                          ApbA  81 teealeeikplldpntvvlllqNGlgheeelrealpkprvlggvtt 126
                                       +++i++ +  +   l+       ++ +++a p++ v+ ++t 
  gi|13541970|ref|NP_111658.1|  83 IIPEVRKIEENIRGK--LLISMAAAIPLKLIKDAAPHSIVVRAMTN 126
                                   *********999997..44444455555555666666555555555 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 3.2
                                   EEEEE-EEEEEETTEEEECS--EEEEE CS
                          ApbA 122 ggvtthgatregpgevhhagkgeikig 148
                                   gg+t  g++++++ +v+ a  ++i+++
  gi|13541970|ref|NP_111658.1| 237 GGTTIDGIYELEDARVRTAIMKAIEVS 263
                                   566669999999999988877777776 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   5.9e-08   6.6e-05      37      99 ..      15      78 ..       6      83 .. 0.89

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 5.9e-08
                                  SEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTCEEC.SHHHHHHH-SEEEE-S CS
                  2-Hacid_dh_C 37 ktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeelgvelv.sleellaesDivslhl 99
                                    + iiG G IG+++a  lk  g++vi++ r+    ++ e++g++++ + +++ +e+D+v+l+l
  gi|13541970|ref|NP_111658.1| 15 TVISIIGGGTIGSSIAIPLKRSGFEVIVTRRNTAVLKHLESYGISVMsDNKTASKEADVVFLTL 78
                                  5689****************************999999******7765999999*******987 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 !   20.2   0.0   3.8e-07   0.00043       2      45 ..      17      60 ..      16      95 .. 0.79
   2 ?   -3.1   0.1       5.4     6e+03     112     125 ..     260     273 ..     244     278 .. 0.49

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 3.8e-07
                                  EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHH CS
                       3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdiseealekalekieks 45
                                  + +iG Gt+G++ia  + ++g+eV ++ ++++ l++ ++   + 
  gi|13541970|ref|NP_111658.1| 17 ISIIGGGTIGSSIAIPLKRSGFEVIVTRRNTAVLKHLESYGISV 60
                                  789***************************99999877665544 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 5.4
                                   E--SSS-HHHHCCC CS
                       3HCDH_N 112 snTSslsiselaea 125
                                    + S+++ ++++e+
  gi|13541970|ref|NP_111658.1| 260 IEVSTMKANKISES 273
                                   23344444444444 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1     1e-05     0.011       3      46 ..      18      61 ..      16      79 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1e-05
                                  EEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHH CS
                     Pyr_redox  3 vvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskil 46
                                   ++GgG+ig   A  l++ g +V v  r+  +l+ l+    +++
  gi|13541970|ref|NP_111658.1| 18 SIIGGGTIGSSIAIPLKRSGFEVIVTRRNTAVLKHLESYGISVM 61
                                  59***************************999966665544444 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1     1e-05     0.012      14      99 ..      16      94 ..       7     109 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1e-05
                                  EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEEEE-SSSSS-SB-HHHHH CS
                  Shikimate_DH 14 kvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeiealkleelkellaeadvvisataseepilekeeve 96
                                   + +iG G +++ +a  L ++g++ v+v+ R+ +  k+l e++      +  +++ k++ +eadvv+   +  ++i e +++e
  gi|13541970|ref|NP_111658.1| 16 VISIIGGGTIGSSIAIPLKRSGFE-VIVTRRNTAVLKHL-ESY-----GISVMSDNKTASKEADVVFLTLKPVDIIPEVRKIE 91
                                  578********************9.99999998877777.333.....46789**************9998888888888888 PP

                                  CCH CS
                  Shikimate_DH 97 eal 99
                                  e  
  gi|13541970|ref|NP_111658.1| 92 ENI 94
                                  765 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.1   2.1e-05     0.023      31      78 ..      17      67 ..      11     109 .. 0.79
   2 ?   -1.4   0.0       1.1   1.2e+03     151     175 ..     133     157 ..     114     170 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.1e-05
                                  EEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTTCECEE....H CS
                   AlaDh_PNT_C 31 vlviGgGvaGlqAiatakglgakVtvlDvrparleqleslgakfvev....l 78
                                  + +iGgG+ G + +   k+ g +V v+  ++a+l++les+g + v       
  gi|13541970|ref|NP_111658.1| 17 ISIIGGGTIGSSIAIPLKRSGFEVIVTRRNTAVLKHLESYGIS-VMSdnktA 67
                                  679************************************9988.33323321 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.1
                                   TTEEEEEBSTGGGGSHHHHHHHHHH CS
                   AlaDh_PNT_C 151 kgvvhygvanlpgavprtasalltn 175
                                    g +  +v +   +v++ as +l+ 
  gi|13541970|ref|NP_111658.1| 133 AGFTPFCVDDGDQEVAKRASSILSA 157
                                   4677789999999999999999876 PP

>> PDH  Prephenate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.2   1.6e-05     0.018       1      89 [.      29     114 ..      29     155 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.6e-05
                                   HHHHHHHTT--SEEEEE-SSHHHHHHHHHTTSSSEEES-GGGGCCGSEEEE-S.-GGGHHHHHHHHHHHS-TT-EEEE--S CS
                           PDH   1 laralrrkgfkvtvigydideekaeaalelglvdeatddieavkeadivvlav.PvevilevlkelaphlkedalitDvgs 80 
                                   +a  l+r+gf+v+v+ ++    k  +   + ++ +++    a kead+v+l   Pv+ i++ ++++ + ++ ++li   + 
  gi|13541970|ref|NP_111658.1|  29 IAIPLKRSGFEVIVTRRNTAVLKHLESYGISVMSDNK---TASKEADVVFLTLkPVD-IIPEVRKIEENIRGKLLISMAAA 105
                                   57789*****999999988888888875555554444...589********983555.55666888888999999887777 PP

                                   --CHHHHHH CS
                           PDH  81 vKekvvrel 89 
                                   +  k+++++
  gi|13541970|ref|NP_111658.1| 106 IPLKLIKDA 114
                                   777777766 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1    0.0001      0.11       2      39 ..      17      54 ..      16      60 .. 0.91
   2 ?    1.7   0.0      0.21   2.3e+02      42      85 ..      44      87 ..      43     104 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.0001
                                  EEEE--SHHHHHHHHHHHTTT--EEEE-S-HHHHHHHH CS
                NAD_Gly3P_dh_N  2 iavlGaGswGtalAkvlaenghevrlwvreeelieein 39
                                  i+++G+G  G+++A+ l++ g ev +  r+ +++++++
  gi|13541970|ref|NP_111658.1| 17 ISIIGGGTIGSSIAIPLKRSGFEVIVTRRNTAVLKHLE 54
                                  89************************999998887765 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.21
                                  SSBTTTBTT----TTEEEES-HHHHHTT--EEEE--.-HHHHHHH CS
                NAD_Gly3P_dh_N 42 henvkyLpgiklpenlvattdlaealkgadiivlvv.Psqalrev 85
                                  ++n++ L++++ +  + + +d ++a k+ad+++l + P  ++ ev
  gi|13541970|ref|NP_111658.1| 44 RRNTAVLKHLE-SYGISVMSDNKTASKEADVVFLTLkPVDIIPEV 87
                                  66777777644.5679999*************9987355555444 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   7.1e-05      0.08       2      50 ..      18      66 ..      17      71 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7.1e-05
                                  EEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTTSEEEES-TT CS
                        TrkA_N  2 iiiGlGrvGrslaeeLseggkdvvvidkdeerveelreeglevvvgdat 50
                                   iiG G++G+s+a  L+++g +v+v  ++ +++++l+  g+ v+  + t
  gi|13541970|ref|NP_111658.1| 18 SIIGGGTIGSSIAIPLKRSGFEVIVTRRNTAVLKHLESYGISVMSDNKT 66
                                  69****************6645***************999988876655 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 ?   12.2   0.0   7.1e-05      0.08       4      53 ..      18      65 ..      12     106 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7.1e-05
                                  EEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHH CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2  4 vviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaeda 53
                                   +iGgG  G + a+ l+++g++v++  +++t    + l s+ +  +++++
  gi|13541970|ref|NP_111658.1| 18 SIIGGGTIGSSIAIPLKRSGFEVIVT-RRNTA-VLKHLESYGISVMSDNK 65
                                  46777777777777777777777776.33333.33344444444444443 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 ?   10.9   0.2   0.00022      0.24       3      46 ..      17      60 ..      15      70 .. 0.89
   2 ?    1.4   0.0      0.18     2e+02      55      83 ..      49      77 ..      46     131 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00022
                                  EEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHHCTTS-SS CS
                UDPG_MGDP_dh_N  3 isviGlGYvGlvtaavlaeighevigvDideekvdklnsgkipi 46
                                  is+iG G +G   a+ l + g+evi+   +++  ++l+s  i++
  gi|13541970|ref|NP_111658.1| 17 ISIIGGGTIGSSIAIPLKRSGFEVIVTRRNTAVLKHLESYGISV 60
                                  9**************************99999999998877666 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.18
                                  HHHHCHTTTEEEES-HHHHHHC-SEEEE- CS
                UDPG_MGDP_dh_N 55 vkkavesgrlsfttdvekaveeadvifia 83
                                  v k++es  +s  +d ++a +eadv+f++
  gi|13541970|ref|NP_111658.1| 49 VLKHLESYGISVMSDNKTASKEADVVFLT 77
                                  556667788889999999999***99997 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.5   0.00011      0.12       4      26 ..      19      43 ..      17      50 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00011
                                  EECTSHHHHHHHHHHHHTT..EEEE CS
                           DAO  4 iiGGGiiGlstAyeLarrg..Vtll 26
                                  iiGGG iG+s+A  L r g  V++ 
  gi|13541970|ref|NP_111658.1| 19 IIGGGTIGSSIAIPLKRSGfeVIVT 43
                                  9**************7778987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); 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 0.30s 00:00:00.90 Elapsed: 00:00:00.51
# Mc/sec: 1654.01
//
Query:       gi|13541971|ref|NP_111659.1|  [L=164]
Description: hypothetical protein TVN1140 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score 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   13.1   0.0       0.12   12.3   0.0    1.3  1  DUF1726    Domain of unknown function (DUF1726)
      0.089   12.1   0.0       0.13   11.6   0.0    1.2  1  Rhabdo_M2  Rhabdovirus matrix protein M2


Domain annotation for each model (and alignments):
>> DUF1726  Domain of unknown function (DUF1726)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   1.3e-05      0.12      15      56 ..      43      84 ..      36      96 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.3e-05
                       DUF1726 15 lvldlfealtPnalgrlvetVrGGGliilllppleelkqlyt 56
                                  +++++ + ++P++  r++++V+ GG    +l+++++  +++t
  gi|13541971|ref|NP_111659.1| 43 VIFEDENGIDPDYSERIMDVVKTGGYASAILRSITSETEIKT 84
                                  899*****************************9999999887 PP

>> Rhabdo_M2  Rhabdovirus matrix protein M2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   1.4e-05      0.13      61     141 ..      62     148 ..      56     154 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1.4e-05
                     Rhabdo_M2  61 vcspngysfkilrhilksfenvysgnrrmi.g....lvkvvigl.vlsgapvpegmnwvyklrrtlifqwaessgplegee 135
                                   v+   gy+  ilr i +  e    g    i g    +   vi    ls   v + +n  +k  r l  +  e    l+ge 
  gi|13541971|ref|NP_111659.1|  62 VVKTGGYASAILRSITSETEIKTGGSFMEIrGyfiyINAGVISWnGLSAEDVFDAVNHDFKTGRKLKPDAREIYCGLDGEC 142
                                   6677899999999998887766555543331211003333444325999******************************** PP

                     Rhabdo_M2 136 leysqe 141
                                   l+ys++
  gi|13541971|ref|NP_111659.1| 143 LDYSKK 148
                                   ****86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); 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 0.28s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1085.80
//
Query:       gi|13541972|ref|NP_111660.1|  [L=498]
Description: glycerol kinase [Thermoplasma volcanium GSS1]
Scores for complete 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-55  186.2   0.0    9.8e-55  185.8   0.0    1.2  1  FGGY_N    FGGY family of carbohydrate kinases, N-terminal dom
      1e-32  113.5   0.0      2e-32  112.5   0.0    1.5  1  FGGY_C    FGGY family of carbohydrate kinases, C-terminal dom


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 !  185.8   0.0   1.1e-58   9.8e-55       2     245 .]      12     258 ..      11     258 .. 0.93

  Alignments for each domain:
  == domain 1  score: 185.8 bits;  conditional E-value: 1.1e-58
                                   EEEEEEESSEEEEEEEETTS-EEEEEEEE--EB-SSTT--EE-HHHHHHHHHHHHHHHHHHCT.-GCCEEEEEEEE-SS-E CS
                        FGGY_N   2 ilglDcGttstkaivldekgkvvasaqaelelsspkegwaeqdpeeiwqalaeairkvleqagisekqikaIgisgqregl 82 
                                    l+lD Gtt +ka ++d+  +++as ++ + +++++ g +eqdp+ei++a   +++++l++      ++kaIgi++qre++
  gi|13541972|ref|NP_111660.1|  12 FLALDAGTTDVKAGAYDRSMNLIASCKRRIGVYYGQGGVVEQDPHEILEAAKYCLNSILRRIPKRYGEPKAIGITNQRESV 92 
                                   699***********************************************************88899************** PP

                                   EEEETTT.EESSEEE-TT--TTHHHHHHHHHTTCHCCHHHHHSS-SSTTSHHHHHHHHHHHSCCHHCCHC.EEEEHHHHHH CS
                        FGGY_N  83 vllDknd.kpLynailwkdrrtaeiveklkeegnekklyektglvlstgftlsklkWlkenepevfekie.kflliddyLi 161
                                    +++  d +p+++ i+wkd+r a+    lke  + + ++ ktgl+ +++f+++k+kWl en + + ++ +  + + d++L 
  gi|13541972|ref|NP_111660.1|  93 LAWEPIDgRPITKLISWKDKRGAQLSLDLKE-RYGQVIKDKTGLISDPYFSATKIKWLVENIKRSSNHKNyVITTLDSWLV 172
                                   *******9**********************9.78899************************877666655488899***** PP

                                   HHHCT...--EEEHHHHCTTTSEETTTTEE-HHHHHHTT--GGGS-EEE-TCC..EEEEEECCCCCCTT.S-EEEEEEEEE CS
                        FGGY_N 162 wrLtg...qfvtdvtnasesmlfnikklewdeellailgipeelLPklvesse..iigelkpelaaklGlkegvpvvgggg 237
                                   + L     +  td++nas++mlfni +lewd  ll+i+gi+ee+LP+++++ e   +g++k      +    +vp+ + +g
  gi|13541972|ref|NP_111660.1| 173 KNLNSssiKPLTDHSNASRTMLFNIDSLEWDSDLLEIVGISEEILPEVKRTIEsdSYGKVKLTYGSTT---REVPILSVAG 250
                                   ***9999999****************************************966115777776666665...7********* PP

                                   HHHHHHHH CS
                        FGGY_N 238 DqqaaalG 245
                                   Dqqa+++G
  gi|13541972|ref|NP_111660.1| 251 DQQASLFG 258
                                   *******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 !  112.5   0.0   2.2e-36     2e-32       1     196 [.     267     450 ..     267     452 .. 0.92

  Alignments for each domain:
  == domain 1  score: 112.5 bits;  conditional E-value: 2.2e-36
                        FGGY_C   1 akvslGTssflllvgtkpvisehglltpvagedgkpeyalegsiavagslvawlldnlglreeirdageveeslaelaaae 81 
                                   ak+s+GT+ f+l ++   v+s   l t ++  +gk++yaleg+i   gs ++wl++  gl +++       +s+     ++
  gi|13541972|ref|NP_111660.1| 267 AKASYGTGAFILENTGVRVKSDRLLETLFYTYKGKRTYALEGTILSSGSSIDWLVSLAGL-KSVP------RSIL----RA 336
                                   689**********8888898**********999************************777.2222......3333....47 PP

                        FGGY_C  82 avadaggvvfvpafsglrapywdpdargtitglsssttlahiarAaleavalqlrailealekdsgkpldrlavdGGgskn 162
                                    + +  +v+ vpa+sgl +p++ +d+rg i gls+st+  +++r+ lea+a+    i+e++ k+  k l++l++dGG+sk+
  gi|13541972|ref|NP_111660.1| 337 EQIERSHVLSVPALSGLGSPFYSSDIRGYISGLSESTDIYEVIRSFLEAQAFLSTVIIEEMRKH-IKLLEPLHIDGGLSKS 416
                                   777788*******************************************************999.888************* PP

                        FGGY_C 163 dllmqllAdilgvpVerpktaeatalGaAilAav 196
                                   dl++++lA++l +++ r ++ +at  G+A++ ++
  gi|13541972|ref|NP_111660.1| 417 DLIAEMLANLLDMKIIRERNVDATMKGIAMMSMI 450
                                   ******************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (498 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       480  (0.0267723); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        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 0.30s 00:00:00.88 Elapsed: 00:00:00.52
# Mc/sec: 2901.74
//
Query:       gi|13541973|ref|NP_111661.1|  [L=307]
Description: hypothetical protein TVN1142 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.24   10.3   0.0       0.32    9.8   0.0    1.1  1  DUF1702   Protein of unknown function (DUF1702)


Domain annotation for each model (and alignments):
>> DUF1702  Protein of unknown function (DUF1702)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   1.8e-05      0.32     137     200 ..      95     160 ..      82     172 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 1.8e-05
                       DUF1702 137 atdpllrwLvlDGYGFhqaYFhtr.kyvdeqkvpaelpwegeaayakrv.vdqGiGRalWFvkgad 200
                                    +++ll+   l GYG h  YF+ + + v++  +   +++++ + yak   +dqGi   l +v  ++
  gi|13541973|ref|NP_111661.1|  95 LSSSLLEAYHLQGYGLHYVYFKLKtSSVSKIVKIGIFTFHKFHFYAKYLnIDQGITDILSYVSKGN 160
                                   5678999999***********976156888888889999888888876439***988887776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       589  (0.0328518); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.50
# Mc/sec: 1864.67
//
Query:       gi|13541974|ref|NP_111662.1|  [L=440]
Description: sugar-binding protein [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.8e-27   96.2   2.5    2.8e-27   96.2   2.5    1.4  1  SBP_bac_8  Bacterial extracellular solute-binding protein
    3.5e-20   73.2   5.8    3.5e-20   73.2   5.8    1.5  2  SBP_bac_1  Bacterial extracellular solute-binding protein
     0.0066   17.4   0.8      0.016   16.1   0.8    1.7  1  Pilin_N    Archaeal Type IV pilin, N-terminal
     0.0083   15.6   0.4        1.3    8.3   0.1    2.3  2  SBP_bac_6  Bacterial extracellular solute-binding protein
  ------ inclusion threshold ------
      0.093   12.8   0.1       0.14   12.2   0.1    1.3  1  DUF2275    Predicted integral membrane protein (DUF2275)
       0.19   11.6   0.4        0.4   10.5   0.4    1.5  1  DUF4307    Domain of unknown function (DUF4307)


Domain annotation for each model (and alignments):
>> SBP_bac_8  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.2   2.5   9.5e-31   2.8e-27       1     277 [.      54     374 ..      54     379 .. 0.79

  Alignments for each domain:
  == domain 1  score: 96.2 bits;  conditional E-value: 9.5e-31
                                   HHHHHHHHH-.TEEEEEEE--SSSHHHHHHHHHHTT---SEE.EEE-HHHHHHHHHTTSB--GG......GSTTHHH.-HH CS
                     SBP_bac_8   1 klakefekkt.gvkvnvvtaasndleqklkaalaagtapdidvvwanedalatlaeeglladls......dldnldd.ltd 73 
                                   ++++ef+  + +v v++v++ sn +  +l ++l+++++p+  v+++++d l++++++g+l dl+      + +nl + ++ 
  gi|13541974|ref|NP_111662.1|  54 QMVNEFNSIHsNVSVKFVPITSN-YYGTLETELSSNSGPA--VFYMENDILPEFVKAGYLLDLTpalsanSTYNLSGfVPE 131
                                   5899****************875.5599**********97..78999*****************86655433444445688 PP

                                   HHHTT--TS.----EEEEEEE-EEEEEHHHHHHS........---BHHHHHHHHH...HH.....HHH-SE.G...G---G CS
                     SBP_bac_8  74 alaavgydgklygvPyasetpyvliynkdlleka.......edpktwdellaaak...kl.....kgkfgl.p...dpasg 135
                                    l++++  g+ly+ P +++ p ++  nk ++ ++        + + w +++ +++   ++     +g  g+ p    p  +
  gi|13541974|ref|NP_111662.1| 132 ILDTFMQHGQLYAAPKDWS-PLLVLFNKNIFNAEhvpyptnYTNWNWTAMKNTLEllkANesklpNGGKGYyPmveGPQ-F 210
                                   *******************.69*********964787777778899999977655332555544424444422221333.2 PP

                                   ..GGGGGTHHETTEE---H.......HHH.HHHHHHHHHHHHTT-.EE-S....--SS.TTTTTSBSEEEE-TTHHHHHH. CS
                     SBP_bac_8 136 ..wlqaallakdgksldddg.....gkdglkealellkklkdngk.tydtg..adavs.efanGevaftingswdiaaaq. 204
                                      l +++ a +g++ +  g     +++gl  a++++  l+  g   ++++  a ++  +fa+G+v ++++g+w +  +  
  gi|13541974|ref|NP_111662.1| 211 arILAFMHEA-GGQWINSSGtgassNSAGLLTAIKFWYGLYSSGLsGLNSNlsAGWNGgDFASGKVGMVVTGTWTVPVLFa 290
                                   3477888888.99999877788999999*************999767766653444447****************997774 PP

                                   .....-TT.TSEEEE.--....S--EEEEEEEEEEBTTS-HHHH.HHHHHHHHHTTSHHHHHHHHHH---BS-S-TTTHHH CS
                     SBP_bac_8 205 .....kag.kklgai.vp....kqgsfaggkglavpknaknedl.aAldFlkwltspenqaalaektgyipvnksaalspe 273
                                        k++   +g++ +p    + +++ ++ gla++++ +  ++  A +F++++t p + + ++ k+  +p++ +  +s +
  gi|13541974|ref|NP_111662.1| 291 ngsyfKNDtSSIGYAfMPydvqNATMMFNV-GLAINSHLNPTQKwIAEQFVEFFTGPSGEKTWVSKGLALPSRSAILDSSW 370
                                   566665542599999557664333455555.7**********999********************9999************ PP

                                   HHH- CS
                     SBP_bac_8 274 vkkd 277
                                   +k++
  gi|13541974|ref|NP_111662.1| 371 YKTN 374
                                   9988 PP

>> SBP_bac_1  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.2   5.8   1.2e-23   3.5e-20       6     313 ..      48     348 ..      43     350 .. 0.78
   2 ?   -3.6   0.1       2.7   8.2e+03     219     249 ..     369     397 ..     366     409 .. 0.59

  Alignments for each domain:
  == domain 1  score: 73.2 bits;  conditional E-value: 1.2e-23
                                   HHHHHHHHHHHHHHHHHTTEEEEEEEECHHHHHHHHHHHHHTTSSSCSEEEECGGHHHHHHHTTSBECCHHHHHHTTECTT CS
                     SBP_bac_1   6 egaalqalvakafekehpgikVeiesvgsgslaqkltlaiaaGdgpaDviavdndwiarlakaglllpldpyvkaylapgv 86 
                                   e+    ++v ++f+  h ++ V+++++ s+ + + l + +++++gp  v++++nd +++++kag+ll+l+p + a+     
  gi|13541974|ref|NP_111662.1|  48 EYTFDVQMV-NEFNSIHSNVSVKFVPITSNYYGT-LETELSSNSGP-AVFYMENDILPEFVKAGYLLDLTPALSAN----- 120
                                   455666778.*****************8888888.***********.*****************************..... PP

                                   CCTEEEEHHHHTHHHHCE.EE...ES.EEEEE.EEEEEEETTTHHCTTGGG.....SHBHHHHHHHHHHHHHHCTCT..HC CS
                     SBP_bac_1  87 kdaadklsssvlpkilds.kv...ly.vPlya.argliYNkdlfekagldp.....pwtWdelveaakklkekgkkp..ig 154
                                        ++ s ++p ild+      ly  P +  + ++ +Nk +f  + ++       w+W      ++ lk++  k   +g
  gi|13541974|ref|NP_111662.1| 121 ---STYNLSGFVPEILDTfMQhgqLYaAPKDWsPLLVLFNKNIFNAEHVPYptnytNWNWTAMKNTLELLKANESKLpnGG 198
                                   ...8999999*******76779*********55************7777777777**********************7777 PP

                                   CHCCEEHHHHHHHHHHHHHHHHTGGGEECCCT.HHCSHHHHS.HHHHHHHHHHHHHHHHHHHTTEEECSSHHHHHHHHHTT CS
                     SBP_bac_1 155 garggsasgtayyfalalakslggkvfdkdgg.gldnpegvt.aatylvklyavanltkelkgkgaenkdgaaalalfeaG 233
                                     ++   +g  ++  la++  +gg++ ++ g  + +n +g   a++++  ly  +      + ++ ++++++   ++f++G
  gi|13541974|ref|NP_111662.1| 199 KGYYPMVEGPQFARILAFMHEAGGQWINSSGTgASSNSAGLLtAIKFWYGLYSSG----LSGLNSNLSAGWNG--GDFASG 273
                                   77777778888888889999***********986677777778999999999444....44444444444444..4556** PP

                                   SCSEEEEEHHHHHHHHCEEEEECHHCHHHHTTSTEEEECEEBETTTTSEEEEEEEEEEBTTCSTHHH..HHHHHHHHTSHH CS
                     SBP_bac_1 234 eaamaivglwaalaamkvapkvafaadkekpkeelgvaplPagkggkpgilgayglaipkgsknpea..AkkFldfllspe 312
                                   +++m + g+w       v   +a     ++    +g+a +P+   ++++ +++ glai+++    +   A++F++f+++p 
  gi|13541974|ref|NP_111662.1| 274 KVGMVVTGTWT------VPVLFANGSYFKNDTSSIGYAFMPYDVQNATMMFNV-GLAINSHLNPTQKwiAEQFVEFFTGPS 347
                                   *********98......333333333333444445666666655555543322.255555554444478888888888887 PP

                                   H CS
                     SBP_bac_1 313 a 313
                                   +
  gi|13541974|ref|NP_111662.1| 348 G 348
                                   6 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 2.7
                                   ECSSHHHHHHHHHTTSCSEEEEEHHHHHHHH CS
                     SBP_bac_1 219 enkdgaaalalfeaGeaamaivglwaalaam 249
                                   ++++ ++  + f+  + ++a+ +    ++ +
  gi|13541974|ref|NP_111662.1| 369 SWYKTNFPIQSFAGEQFPFAYGW--NYNTTN 397
                                   56677777777777777774444..333333 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 !   16.1   0.8   5.3e-06     0.016      11      53 ..       7      50 ..       5      71 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 5.3e-06
                       Pilin_N 11 LmvaitvIlaAviaafvlgl.asneekapqasievkidssastg 53
                                  + +a++vI++A ia+ v+ + + ++ k+p ++++ +++s+++++
  gi|13541974|ref|NP_111662.1|  7 IAIAVVVIAVAAIAGGVVYYhNLTAAKKPTITFSGWVSSGEEYT 50
                                  5589****************999***********9999998875 PP

>> SBP_bac_6  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.1   0.00045       1.3       4      76 ..      91     171 ..      88     176 .. 0.74
   2 !    5.4   0.0    0.0034        10     174     220 ..     314     367 ..     225     396 .. 0.62

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00045
                     SBP_bac_6   4 pdlilsfdkdflekfieeglfqpldpanlpnvnkdfa.......eeglkdpdgkyypygvgplvlavnkdrlkgrpv..Pk 75 
                                   p +++ +++d l  f+++g++ +l+pa  +n + +++       ++ + +++ + +p +++pl++++nk  +++++v  P+
  gi|13541974|ref|NP_111662.1|  91 PAVFY-MENDILPEFVKAGYLLDLTPALSANSTYNLSgfvpeilDTFMQHGQLYAAPKDWSPLLVLFNKNIFNAEHVpyPT 170
                                   67888.9999999********99996666666666666656642333333355555*********************4445 PP

                     SBP_bac_6  76 s 76 
                                    
  gi|13541974|ref|NP_111662.1| 171 N 171
                                   4 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0034
                     SBP_bac_6 174 Galvspifmlvkkg...kkkelakafidfllspevqailakaggvfPvv....t 220
                                    +  + + +++++    ++k  a++f++f+++p + + ++  g+ +P+     +
  gi|13541974|ref|NP_111662.1| 314 ATMMFNVGLAINSHlnpTQKWIAEQFVEFFTGPSGEKTWVSKGLALPSRsailD 367
                                   55555555555555666677789*********************9999655551 PP

>> DUF2275  Predicted integral membrane protein (DUF2275)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   4.7e-05      0.14      32      68 ..       2      37 ..       1      62 [. 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4.7e-05
                       DUF2275 32 rlkrklalaglivlilAavgfgvvsyatiskmdvvrv 68
                                   +kr +a+a ++++++A++g gvv+y +++    +++
  gi|13541974|ref|NP_111662.1|  2 ERKRVIAIAVVVIAVAAIAG-GVVYYHNLTAAKKPTI 37
                                  58999***************.*****76666555554 PP

>> DUF4307  Domain of unknown function (DUF4307)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.4   0.00013       0.4       2      53 ..       3      53 ..       2      60 .. 0.55

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00013
                       DUF4307  2 rrllvillvvlvvvalalvawigysq..gsadvsaevvgfevvddstvevtfeV 53
                                  r+++++++vv+++va+++ ++++y++  +    +  +++f+    s  e tf+V
  gi|13541974|ref|NP_111662.1|  3 RKRVIAIAVVVIAVAAIAGGVVYYHNltA---AKKPTITFSGWVSSGEEYTFDV 53
                                  56666666666667777777777777443...4444444444444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (440 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       519  (0.0289475); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.47
# Mc/sec: 2833.98
//
Query:       gi|13541975|ref|NP_111663.1|  [L=309]
Description: ABC-type sugar transporter, permease component [Thermoplasma volcanium GSS1]
Scores for complete 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   36.8  30.2    3.2e-09   36.8  30.2    2.1  2  BPD_transp_1  Binding-protein-dependent transport system inne
  ------ inclusion threshold ------
        0.3   11.4   0.1        0.3   11.4   0.1    2.7  3  Orf78         Orf78 (ac78)


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 ?   -9.2  12.1         2   1.8e+04      26      44 ..      34      70 ..      18     108 .. 0.46
   2 !   36.8  30.2   3.6e-13   3.2e-09       3     176 ..     103     300 ..     101     305 .. 0.89

  Alignments for each domain:
  == domain 1  score: -9.2 bits;  conditional E-value: 2
                  BPD_transp_1 26 vllslPsfvlaillvlvf.......................v 44
                                  ++l++ + v+ +     f                        
  gi|13541975|ref|NP_111663.1| 34 IPLMIFISVFTF-----FpaiysfvislfhynpffhsiyftG 70
                                  333333333111.....1111111222224444455555541 PP

  == domain 2  score: 36.8 bits;  conditional E-value: 3.6e-13
                  BPD_transp_1   3 llGilaa..lnrnkkldkllrpliivllslPsfvlaillvlvf..................vilsilghlilpviilllls 63 
                                   +l+++ a  +n  +k++++ r +++++  + ++ + i++++vf                   +l +  +++ +++++ +++
  gi|13541975|ref|NP_111663.1| 103 FLAFVYAllFNTASKISRIARAIVFIPAVVSPVSMSIIFIWVFsdsglvnfflsffgiaphNWLFSTEFAFPAIMAMNIFT 183
                                   67778888888999**********************************************9999999999999******** PP

                  BPD_transp_1  64 aapyvrlirraalrslpkdlveaaralGa.srwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllle 143
                                   +apy+++i++a+l+++p+d   aa+++G  s + +fr++ +P++  +++  +il ++g++  +  ++ ++ +++  ++ + 
  gi|13541975|ref|NP_111663.1| 184 TAPYFMIIYSAGLQAIPQDVLDAAKIDGItSAFARFRYIYFPMMRFSTVLVVILGLTGAMQLFDQIYVITDGGPARSTYVP 264
                                   ****************************73679*************************************88888888888 PP

                  BPD_transp_1 144 ailgydyseis...nggvlalviavlllnlvadilq 176
                                      +y+ ++ +   +g+++a+ +++++++ ++ i q
  gi|13541975|ref|NP_111663.1| 265 LMYIYNRTFVYigdIGLAAAASFVLFVIIMALTITQ 300
                                   888888888888997777777777777766666655 PP

>> Orf78  Orf78 (ac78)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   3.4e-05       0.3      42      89 ..       7      55 ..       4      61 .. 0.77
   2 ?   -1.7   0.7      0.41   3.7e+03      69      85 ..      96     112 ..      77     121 .. 0.58
   3 ?   -2.0   0.3       0.5   4.5e+03      70      83 ..     283     296 ..     278     300 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.4e-05
                         Orf78 42 saaeknditekesnaaekaqalnil.lisllavvcvlvllyviyYfvil 89
                                  ++++ n+i+e ++++++ ++++ il +i l+ +++v+  + +iy fvi+
  gi|13541975|ref|NP_111663.1|  7 EVYQVNKIREGKKKNKSPEKMTGILfIIPLMIFISVFTFFPAIYSFVIS 55
                                  56777888887777667666666651566888999************96 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.41
                         Orf78  69 sllavvcvlvllyviyY 85 
                                   ++++v + l  +y++++
  gi|13541975|ref|NP_111663.1|  96 VVVTVQTFLAFVYALLF 112
                                   22333344555566654 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 0.5
                         Orf78  70 llavvcvlvllyvi 83 
                                   + a ++++v+++++
  gi|13541975|ref|NP_111663.1| 283 AAASFVLFVIIMAL 296
                                   55667777777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       998  (0.055664); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.32s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 1915.37
//
Query:       gi|13541976|ref|NP_111664.1|  [L=295]
Description: sugar permease [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.6e-16   59.4  17.0    3.6e-16   59.4  17.0    2.0  2  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.5     0.036   6.5e+02      21      34 ..      29      42 ..      18      94 .. 0.64
   2 !   59.4  17.0     2e-20   3.6e-16       2     181 ..     103     285 ..     102     289 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.036
                  BPD_transp_1 21 rpliivllslPsfv 34
                                  +++  +++ lP+++
  gi|13541976|ref|NP_111664.1| 29 SIVLAMIYLLPFYW 42
                                  22222222222222 PP

  == domain 2  score: 59.4 bits;  conditional E-value: 2e-20
                  BPD_transp_1   2 illGilaa...lnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilpviillllsaapyvrlirraalrsl 79 
                                   +++G+l++    + +++++++l   + ++l++P+ v+ i  +   v++ +l +l ++  ++l   a ++ ++i+r+++ ++
  gi|13541976|ref|NP_111664.1| 103 VFVGMLSGyafAKLKFPGRNVLFYAVLATLMIPFPVISIASY---VFMLDLNWLSTYQGLILPQIASALDVFIMRQYFLTI 180
                                   678888888888************************999998...5788999999998888888888889999999999** PP

                  BPD_transp_1  80 pkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydyseis...ngg 157
                                   p++ + aa+++G+++wqif+ + lPna+p i++  i++f+g++++++++++   +  + tl l  +  +  + ++   n +
  gi|13541976|ref|NP_111664.1| 181 PEEMELAAKIDGLRPWQIFFSIDLPNAKPAIAAATIFSFIGSWNNFLWPLMEVHSLNMFTLPLVLNFFKGANGTQiywNQM 261
                                   **************************************************999775555554444444444444477888* PP

                  BPD_transp_1 158 vlalviavlllnlvadilqrlldp 181
                                   + + ++ +++ ++++ ++ r++  
  gi|13541976|ref|NP_111664.1| 262 MTVNILTMIPTIAIFVAFERYFIN 285
                                   ************999999999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       655  (0.036533); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.34s 00:00:00.90 Elapsed: 00:00:00.54
# Mc/sec: 1644.61
//
Query:       gi|13541977|ref|NP_111665.1|  [L=371]
Description: ABC-type sugar transporter, ATPase component [Thermoplasma volcanium GSS1]
Scores for complete 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-31  108.3   0.0    7.2e-31  107.5   0.0    1.4  1  ABC_tran      ABC transporter
    2.6e-07   30.7   2.0     0.0068   16.3   0.4    2.4  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    1.8e-06   28.7   0.1    5.7e-06   27.1   0.1    2.0  1  OB_MalK       MalK OB fold domain
    0.00012   21.6   0.7     0.0047   16.4   0.5    2.5  2  SMC_N         RecF/RecN/SMC N terminal domain
    0.00067   20.2   0.2     0.0048   17.4   0.1    2.1  2  AAA_23        AAA domain
     0.0014   18.6   0.0     0.0024   17.8   0.0    1.4  1  RsgA_GTPase   RsgA GTPase
      0.002   18.4   0.0     0.0057   16.9   0.0    1.7  1  AAA_22        AAA domain
     0.0037   17.0   0.2     0.0073   16.0   0.2    1.4  1  AAA_29        P-loop containing region of AAA domain
     0.0042   17.0   0.0     0.0063   16.5   0.0    1.3  1  ATPase_2      ATPase domain predominantly from Archaea
     0.0078   16.6   0.1      0.015   15.7   0.1    1.6  1  AAA_16        AAA ATPase domain
     0.0086   15.3   0.0      0.011   14.9   0.0    1.2  1  G-alpha       G-protein alpha subunit
     0.0087   16.0   0.1      0.018   15.0   0.1    1.5  1  NACHT         NACHT domain
  ------ inclusion threshold ------
      0.011   15.9   0.0      0.026   14.7   0.0    1.7  1  TOBE_2        TOBE domain
      0.014   15.1   0.1      0.024   14.3   0.1    1.5  1  AAA_30        AAA domain
      0.022   14.9   0.1       0.13   12.4   0.1    2.0  1  AAA_33        AAA domain
      0.025   14.8   0.3       0.14   12.4   0.1    2.0  2  AAA_28        AAA domain
      0.031   14.7   0.0      0.077   13.4   0.0    1.8  1  AAA           ATPase family associated with various cellular 
      0.054   13.1   0.2       0.12   12.0   0.2    1.6  1  cobW          CobW/HypB/UreG, nucleotide-binding domain
      0.082   12.1   0.1       0.16   11.2   0.1    1.5  1  NB-ARC        NB-ARC domain
       0.11   11.8   0.0       0.18   11.1   0.0    1.3  1  FtsK_SpoIIIE  FtsK/SpoIIIE family
       0.16   12.2   0.3          4    7.7   0.3    2.3  1  SbcCD_C       Putative exonuclease SbcCD, C subunit
       0.23   10.2   1.1        2.1    7.0   0.1    2.7  3  ABC_ATPase    Predicted ATPase of the ABC class


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.5   0.0   8.9e-34   7.2e-31       2     136 ..      19     160 ..      18     161 .. 0.93

  Alignments for each domain:
  == domain 1  score: 107.5 bits;  conditional E-value: 8.9e-34
                                   EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx... RF
                      ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren... 79 
                                   ++++l++k ge  +i+G++G+GK+tLl+ +agl++   G+i +d+ d+++     ++++i++++q+  l p++tv +n   
  gi|13541977|ref|NP_111665.1|  19 ERMNLDVKDGEFFVILGSSGSGKTTLLRSIAGLTEISGGHIYIDDIDVTD--FYPSDRNIAMVFQNFALYPHMTVFDNial 97 
                                   679*****************************************999999..9999************************* PP

                                   ..........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                   ..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  80 ..........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                             + ++++e+++s l +++  ++     p++LSgG++qrv +aral+++p+++l+DEp 
  gi|13541977|ref|NP_111665.1|  98 nlkikhlprdQIKKRVEEVASLLHIEKQLKKY----PKQLSGGEQQRVGIARALVRDPSVFLMDEPL 160
                                   *****988888888888888888888855555....5*****************************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 !   16.3   0.4   8.3e-06    0.0068       1      52 [.      30      70 ..      30      85 .. 0.73
   2 !   13.6   0.1   5.3e-05     0.043     234     287 ..     130     180 ..      89     194 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 8.3e-06
                        AAA_21  1 lnvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldly 52
                                  + v+ G  gsGK++LL+ + +l            e sgg  +++++   d+y
  gi|13541977|ref|NP_111665.1| 30 FFVILGSSGSGKTTLLRSIAGLT-----------EISGGHIYIDDIDVTDFY 70
                                  689****************9994...........555555555555555555 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 5.3e-05
                        AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr 287
                                   + +lS G ++  +++ al r++   s++l DEp ++L+ kl r+ l+ l++ ++
  gi|13541977|ref|NP_111665.1| 130 PKQLSGGEQQRVGIARALVRDP---SVFLMDEPLSNLDAKLRREMLGELRSFHE 180
                                   5578899888889999999999...*********************99987776 PP

>> OB_MalK  MalK OB fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.1   6.9e-09   5.7e-06       1      52 [.     234     280 ..     234     281 .. 0.75

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 6.9e-09
                       OB_MalK   1 GSPaMNflpatveedg...vlvegggvtlplpeeqklalklyagkevilGiRPEh 52 
                                   G+P+MN++++ + +d+    +v+ +gv ++  +       +  g++ ilGiRPE 
  gi|13541977|ref|NP_111665.1| 234 GNPPMNLIECDIIKDEsssEIVL-NGVPIT--TV-----DHVPGDHAILGIRPEK 280
                                   9************9997744444.443333..33.....3669***********6 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 !   16.4   0.5   5.8e-06    0.0047      24     209 ..      28     204 ..       5     212 .. 0.65
   2 ?   -2.5   0.0       3.5   2.9e+03      92     132 ..     276     318 ..     246     332 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 5.8e-06
                                   SSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N  24 ksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsisrrvk 104
                                    +f +i+G+ GSGK+ ll +i   L e s  ++  ++++   ++    +  + a v   f    + ++ ++  ++++ +  
  gi|13541977|ref|NP_111665.1|  28 GEFFVILGSSGSGKTTLLRSI-AGLTEISGGHIYIDDIDVTDFY---PSDRNIAMVFQNFALYPHMTVFDNIALNLKIKHL 104
                                   46899****************.5666666666666666544444...3444555555555555555444443344433333 PP

                                   TTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 105 rkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellke 185
                                     +    +i+++  + + + ++ ++ + ++++LSgGe++ v +a       v+  +++l+De  ++LD+k ++++   l++
  gi|13541977|ref|NP_111665.1| 105 PRD----QIKKRVEEVASLLHIEKQLKKYPKQLSGGEQQRVGIARA----LVRDPSVFLMDEPLSNLDAKLRREMLGELRS 177
                                   333....355555555555555566777899*******99888654....57888999************99998888875 PP

                                   HCTT..SEEEEE-S.SHHHCCC-SCEE CS
                                   xxxx..xxxxxxxx.xxxxxxxxxxxx RF
                         SMC_N 186 kskn..aQfivisl.reemlekadklv 209
                                    +++     i +++ ++e ++ ad+++
  gi|13541977|ref|NP_111665.1| 178 FHERvrKTTIYVCHdQDEAMALADRIM 204
                                   554422334555551445666666655 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 3.5
                                   SSSSCEEEEEEEETTSEEEEEET.TEEE-H.HHHHHHHHCTT- CS
                                   xxxxxxxxxxxxxxxxxxxxxxx.xxxxxx.xxxxxxxxxxxx RF
                         SMC_N  92 iekeevsisrrvkrkgeseykin.gkevtk.kevsellesagi 132
                                   i+ e+v+is +     + +y+in g +v+   +++++l +a i
  gi|13541977|ref|NP_111665.1| 276 IRPEKVNISLKNGVPASFDYFINsGVNVEVhLDMNNILVRALI 318
                                   5566777777777788888888733444443456666655555 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.1   5.9e-06    0.0048      17      40 ..      23      49 ..       3      53 .. 0.76
   2 ?    0.2   0.0       1.1   8.8e+02     162     185 ..     110     133 ..      59     143 .. 0.51

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 5.9e-06
                        AAA_23 17 F...skgltlItGpNGaGKTTildAik 40
                                  +   +  +++I G  G+GKTT+l+ i 
  gi|13541977|ref|NP_111665.1| 23 LdvkDGEFFVILGSSGSGKTTLLRSIA 49
                                  24455679***************9986 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 1.1
                        AAA_23 162 leeledekkllekleqekekekel 185
                                   ++  e++++ll  ++q+k++ k+l
  gi|13541977|ref|NP_111665.1| 110 KKRVEEVASLLHIEKQLKKYPKQL 133
                                   111222333333334444444433 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0     3e-06    0.0024      79     126 ..       7      55 ..       1      63 [. 0.82

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 3e-06
                                   EEE--TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT---- CS
                   RsgA_GTPase  79 vllvsaktkegleelkellkd.ktsvlvGqSGvGKStLinallpelelk 126
                                    l+v+  +k+ +e+++  +kd ++ v++G+SG GK+tL+ ++++ +e++
  gi|13541977|ref|NP_111665.1|   7 NLTVKYGDKTVIERMNLDVKDgEFFVILGSSGSGKTTLLRSIAGLTEIS 55 
                                   5666777888999999999998*******************99876665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0     7e-06    0.0057       4     117 ..      27     180 ..      22     194 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 7e-06
                        AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaee..........erpevvfvtlpsst..sskdllrellralglelka.. 70 
                                   +  + v+ G sG+GKTtllr ++   ++   + +          ++++ + +  ++       +++ +++ +l+ ++    
  gi|13541977|ref|NP_111665.1|  27 DGEFFVILGSSGSGKTTLLRSIAGLTEISGGHIYiddidvtdfyPSDRNIAMVFQNFAlyPHMTVFDNIALNLKIKHLPrd 107
                                   56789******************9998877777798899999997777776666666665777888888888887777777 PP

                        AAA_22  71 ...erlsseellealeqalrarav...................ielliiDEaqh.lr...seealeeLrslln 117
                                      +r ++ + l ++e++l+++ +                   +++++ DE    l+   + e+l eLrs+++
  gi|13541977|ref|NP_111665.1| 108 qikKRVEEVASLLHIEKQLKKYPKqlsggeqqrvgiaralvrdPSVFLMDEPLSnLDaklRREMLGELRSFHE 180
                                   7775555555556666666666666666666666677677777778888885444766555888888888876 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 !   16.0   0.2   8.9e-06    0.0073      17      42 ..      23      48 ..      15      52 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 8.9e-06
                        AAA_29 17 ieidlkg..atlltGpsGsGKSTllDAi 42
                                  ++++  +  ++++ G sGsGK+Tll +i
  gi|13541977|ref|NP_111665.1| 23 LDVK--DgeFFVILGSSGSGKTTLLRSI 48
                                  4444..33699*************9655 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   7.7e-06    0.0063      19      61 ..      27      68 ..      18     134 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 7.7e-06
                      ATPase_2 19 pneiyfiYGpegsGKtaLlkeiienledkdkyviyyialrees 61
                                    e+ +i G+ gsGKt+Ll+ i+    + +  +iy++++   +
  gi|13541977|ref|NP_111665.1| 27 DGEFFVILGSSGSGKTTLLRSIAGLT-EISGGHIYIDDIDVTD 68
                                  56789***************988877.5566899999987655 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1   1.9e-05     0.015      21      47 ..      27      51 ..      18     196 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.9e-05
                        AAA_16 21 sgrpelvllsGesGvGKsslvrellra 47
                                  +g  e  ++ G sG+GK++l+r+++  
  gi|13541977|ref|NP_111665.1| 27 DG--EFFVILGSSGSGKTTLLRSIAGL 51
                                  34..7899***************9843 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   1.4e-05     0.011      26     112 ..      31     130 ..      15     208 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.4e-05
                                   EEEEESTTSSHHHHHHHHHHHCS--.............--HHHHHCCHHHHHHH..HHHHHHHHHHHHHHTT.......HH CS
                       G-alpha  26 llllGqseSGKsTilkqlkllykkg.............fseeelatwraviqln..ivrsiktilealesleselsesfel 91 
                                   +++lG+s+SGK+T+l+++  l + +             f  +++++  a++++n  ++ ++  + ++  +l++++ ++ + 
  gi|13541977|ref|NP_111665.1|  31 FVILGSSGSGKTTLLRSIAGLTEISgghiyiddidvtdFYPSDRNI--AMVFQNfaLYPHMTVFDNIALNLKIKHLPRDQI 109
                                   679****************666443467898888988877776655..344444115677777777788889999999999 PP

                                   HC-SS-SCCCS-HCHHHH... CS
                       G-alpha  92 qelkerldplkkveasliakl 112
                                   +++ e+++ l+++e++l++  
  gi|13541977|ref|NP_111665.1| 110 KKRVEEVASLLHIEKQLKKYP 130
                                   999999999999999997643 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1   2.2e-05     0.018       3      21 ..      31      49 ..      29      61 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.2e-05
                                  EEEEC-TTTCHHHHHHHHH CS
                         NACHT  3 vilqGeaGsGKTtLlqkla 21
                                   ++ G +GsGKTtLl+++a
  gi|13541977|ref|NP_111665.1| 31 FVILGSSGSGKTTLLRSIA 49
                                  5899**************8 PP

>> TOBE_2  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   3.2e-05     0.026       1      76 []     274     348 ..     274     348 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.2e-05
                        TOBE_2   1 laiRPEklrlaaagganglsGtVedveylGsstryvvelaggqlvvvrqpnadr.d.salapGdtVelswdpddavvl 76 
                                   l+iRPEk+ +   +  ng+++  +  +  G  ++++++  +    ++    + +   ++l  Gd+V ++++p  + ++
  gi|13541977|ref|NP_111665.1| 274 LGIRPEKVNI---SLKNGVPASFDYFINSGVNVEVHLDMNNILVRALIPREELKlNlRDLSHGDAVFIEIKPGPIYLF 348
                                   79********...7789*******************9999875544433333333478999*********99988877 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1     3e-05     0.024      19      49 ..      29      59 ..      22     185 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3e-05
                        AAA_30 19 rvavltGpAGtGKttalkalreaweaaggrv 49
                                   + v+ G  G+GKtt+l++++ + e +gg++
  gi|13541977|ref|NP_111665.1| 29 EFFVILGSSGSGKTTLLRSIAGLTEISGGHI 59
                                  47899******************99998554 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   0.00016      0.13       3      91 ..      32     174 ..      30     199 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00016
                        AAA_33   3 llvGlpGsGKstlaerllkklg..avllssdt.............................................lrrr 36 
                                   ++ G +GsGK+tl+++++  +   + ++  d+                                             +++r
  gi|13541977|ref|NP_111665.1|  32 VILGSSGSGKTTLLRSIAGLTEisGGHIYIDDidvtdfypsdrniamvfqnfalyphmtvfdnialnlkikhlprdqIKKR 112
                                   578************998544466556655555666666666666666666666666666666666666666555554444 PP

                        AAA_33  37 lfg......tdqqsktdytrvldrlyqilnelarkalsagrnvildat..nlsrrerarflkl 91 
                                   +++       ++q k+++++++    q++ ++ar   +    ++ d +  nl+++ r+++l  
  gi|13541977|ref|NP_111665.1| 113 VEEvasllhIEKQLKKYPKQLSGGEQQRV-GIARALVRDPSVFLMDEPlsNLDAKLRREMLGE 174
                                   44444444333333345555555566665.666666666666666666555555555555555 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   0.00017      0.14       2      20 ..      31      49 ..      30      63 .. 0.85
   2 ?   -0.2   0.0       1.2     1e+03     103     144 ..     143     185 ..     125     191 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00017
                        AAA_28  2 ivitGgestGKTtlleaLa 20
                                  +vi+G +++GKTtll+ +a
  gi|13541977|ref|NP_111665.1| 31 FVILGSSGSGKTTLLRSIA 49
                                  79*************9988 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.2
                        AAA_28 103 aarekrydl.vfllpp.apeidddgeRredleereaiderlrea 144
                                   +ar+   d  vfl+++    + d + Rre l e + ++er+r++
  gi|13541977|ref|NP_111665.1| 143 IARALVRDPsVFLMDEpLSNL-DAKLRREMLGELRSFHERVRKT 185
                                   566666666688888536688.9999999999999999999876 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   9.5e-05     0.077       3      72 ..      33     100 ..      31     198 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 9.5e-05
                                   EESSTTSSHHHHHHHHHHHHT.....HEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHH CS
                           AAA   3 lyGppGtGKTllakavakelg.....vefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalak 72 
                                   + G  G GKT+l +++a  ++     +++  i+++++       s ++i+++f++  +   p+  ++D+i    k
  gi|13541977|ref|NP_111665.1|  33 ILGSSGSGKTTLLRSIAGLTEisgghIYIDDIDVTDFY-----PSDRNIAMVFQNF-ALY-PHMTVFDNIALNLK 100
                                   689**************998522223556666666666.....8899999999984.444.67777777755555 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.2   0.00015      0.12       3      21 ..      31      49 ..      29      61 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00015
                                  EEEEESTTCCHHHHHHHHH CS
                          cobW  3 tvltGflGsGKTtLlnhll 21
                                  +v+ G+ GsGKTtLl+++ 
  gi|13541977|ref|NP_111665.1| 31 FVILGSSGSGKTTLLRSIA 49
                                  6899***********9986 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00019      0.16      17      50 ..      27      57 ..      14     158 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00019
                                  TSCSEEEEEEESTTSSHHHHHHHHCCSHCCCCCC CS
                        NB-ARC 17 elqslvvalvGmgGvGKttlakqilnksdevegr 50
                                  + +  +  + G  G+GKttl+++i     e+ g 
  gi|13541977|ref|NP_111665.1| 27 DGE--FFVILGSSGSGKTTLLRSIAGL-TEISGG 57
                                  334..77899*************9876.666654 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   0.0   0.00022      0.18      21      59 ..      11      48 ..       3      50 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00022
                                  EEEEETTS-EEEEEGGGS-.SEEEE--TTSSHHHHHHHH CS
                  FtsK_SpoIIIE 21 algkeisgnplvldlkkmashllvaGatgsGKStalntL 59
                                  + g + + + + ld k  +   +++G++gsGK+t l+++
  gi|13541977|ref|NP_111665.1| 11 KYGDKTVIERMNLDVKDGE-FFVILGSSGSGKTTLLRSI 48
                                  5555555566777888888.99**************975 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.3    0.0049         4      62      86 ..     149     173 ..     106     177 .. 0.69

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0049
                       SbcCD_C  62 palrlvfLDEAFsklDeesiatlle 86 
                                   ++++++++DE  s+lD++ ++++l+
  gi|13541977|ref|NP_111665.1| 149 RDPSVFLMDEPLSNLDAKLRREMLG 173
                                   3478899999999999999999987 PP

>> ABC_ATPase  Predicted ATPase of the ABC class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.1    0.0026       2.1     241     265 ..      24      49 ..       7      52 .. 0.86
   2 ?   -1.4   0.0      0.94   7.7e+02     157     189 ..      96     128 ..      74     130 .. 0.84
   3 ?    0.1   0.0      0.33   2.7e+02     378     412 ..     173     207 ..     130     215 .. 0.61

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0026
                                   EE-SS.EEEEEE-TTSSHHHHHHHHH CS
                    ABC_ATPase 241 gipkG.vtlIvGggfhGKsTLLeAle 265
                                    ++ G  ++I G+   GK+TLL++++
  gi|13541977|ref|NP_111665.1|  24 DVKDGeFFVILGSSGSGKTTLLRSIA 49 
                                   47888899***************985 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.94
                                   HHHTTT-..-HHHHHHHHHHHHHHHHHHCTTTT CS
                    ABC_ATPase 157 ekvllaekldeealeehvelvedqealrkqLee 189
                                     +l+ ++l++++++++ve v    ++ kqL++
  gi|13541977|ref|NP_111665.1|  96 ALNLKIKHLPRDQIKKRVEEVASLLHIEKQLKK 128
                                   44567888999999*****99999999999986 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.33
                                   HCHHHHHHHH--EEEEEESS-GCCTTT-SEEEEEE CS
                    ABC_ATPase 378 drvrelykklgvstilvvggsgdyldvAdtvilme 412
                                     +r++++++  +ti v    ++ +++Ad++++++
  gi|13541977|ref|NP_111665.1| 173 GELRSFHERVRKTTIYVCHDQDEAMALADRIMVLN 207
                                   34555566666667777777777777777777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (371 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       574  (0.0320152); expected 358.6 (0.02)
Passed bias filter:                      539  (0.030063); expected 358.6 (0.02)
Passed Vit filter:                       119  (0.00663729); 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 0.30s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 2346.47
//
Query:       gi|13541978|ref|NP_111666.1|  [L=643]
Description: glycogen debranching protein [Thermoplasma volcanium GSS1]
Scores for complete 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-12   45.8   1.8    1.2e-07   31.0   0.1    3.4  2  GDE_C     Amylo-alpha-1,6-glucosidase


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 !    8.7   0.3     4e-05      0.72      16      89 ..     259     334 ..     240     352 .. 0.78
   2 !   31.0   0.1   6.9e-12   1.2e-07     164     381 ..     405     580 ..     394     582 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 4e-05
                         GDE_C  16 keeekgvsliAGlpwFsd.WGRDtfIaLsGllLvt.grfeeAreilltFaktlrhGliPNllde..gqealyntvdas 89 
                                    e+++g+   AG+p Fs   GRD +    Gl+  t g  +  re+++t + + ++G+iP  +    +    y   d++
  gi|13541978|ref|NP_111666.1| 259 SETSTGNGWFAGFPIFSWyFGRDGLW--MGLAANTvGMSHLTREHMRTLLIYSKDGRIPHEIGLsnDGMQSYSISDRI 334
                                   567889999********77****984..4665544278889******************9875432555556666654 PP

  == domain 2  score: 31.0 bits;  conditional E-value: 6.9e-12
                         GDE_C 164 RdGkaveinaLwyaaLkileelaekalgeakkssykelaekikesfekkFwdeaaaavakreilaDvlksseekdlslRpN 244
                                   R+Gkav+inaLw ++++++++  +  +      + +el +k  esf   F +           ++D +++s    +s++  
  gi|13541978|ref|NP_111666.1| 405 RNGKAVDINALWVKTVELYSNELN--IA-----NAEELKKKYLESF---FSN---------VSFTDFIDNSG-YAKSVKSA 465
                                   9***********999988776555..22.....2345555555555...334.........56788888866.44556543 PP

                         GDE_C 245 flialslapellseekakkvlekaeeeLltplGlktLdpedpeYkgnYdgsedsrdaaYHqGtvWvwllgsyveallkfge 325
                                   +    +++   +++++  + +++  e  ltp+G+++++ +dp + g            YH GtvW+ + g +v +++k g 
  gi|13541978|ref|NP_111666.1| 466 MQ---FVPGIFFTNNNIVETIKQLAEGNLTPWGVRSVSVDDPMFDG-----------GYHTGTVWPLMTGWFVLSAYKNGL 532
                                   33...466678888899999999999****************9976...........58**************99999998 PP

                         GDE_C 326 klgkskealeevkalLeglekhleeaglgslsElfdgdaellpkgciaQAWSvael 381
                                   k ++       +k+l++  e   ++  lg++ E +d      p+g  aQ WS++ l
  gi|13541978|ref|NP_111666.1| 533 KDIA-------FKQLMTFSELAFSSPDLGRINETYDSMI-ANPTGQFAQGWSSSML 580
                                   7333.......4455555556678999********9887.89**********9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (643 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       467  (0.0260472); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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 0.36s 00:00:01.08 Elapsed: 00:00:00.55
# Mc/sec: 3537.84
//
Query:       gi|13541979|ref|NP_111667.1|  [L=585]
Description: glycogen debranching protein [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00069   18.6   0.0       0.32    9.9   0.0    2.3  2  GDE_C     Amylo-alpha-1,6-glucosidase


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 !    9.9   0.0   1.8e-05      0.32      19     105 ..     234     321 ..     214     377 .. 0.80
   2 !    6.6   0.0   0.00018       3.2     343     381 ..     503     536 ..     478     538 .. 0.65

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 1.8e-05
                         GDE_C  19 ekgvsliAGlpwFsd.WGRDtfIaLsGllLvtgrfeeAreilltFaktlrhGliPNlldegqealyntvd..aslwlieai 96 
                                     g  l+AG p F    G Dt+++++Gll   g+ e A   l+  +++   G++P  +   ++ +yn  d   +  +  a+
  gi|13541979|ref|NP_111667.1| 234 GVGYGLTAGHPDFPWfFGIDTLLSVKGLL-FAGLDEIAYGSLNLMSRFSFSGRVPHEIIT-SGKIYNQGDleETALFPFAV 312
                                   5678899**99999779**********86.57999********************99854.55678876622567777899 PP

                         GDE_C  97 ekYleyagd 105
                                   ++Yl y+ +
  gi|13541979|ref|NP_111667.1| 313 YRYLVYTSK 321
                                   999998876 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.00018
                         GDE_C 343 glekhleeaglgslsElfdgdaellpkgciaQAWSvael 381
                                   +lek +++   +s +E+ ++     p+gc+ QAWS a  
  gi|13541979|ref|NP_111667.1| 503 SLEKSYSKFSPNSFPEISNN-----PNGCYLQAWSAAIY 536
                                   44455555556666666554.....66********9965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (585 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       332  (0.0185175); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.69u 0.28s 00:00:00.97 Elapsed: 00:00:00.53
# Mc/sec: 3350.94
//
Query:       gi|13541980|ref|NP_111668.1|  [L=352]
Description: transcription regulator [Thermoplasma volcanium GSS1]
Scores for 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-44  150.2   0.5    7.4e-44  149.7   0.3    1.4  2  Regulator_TrmB  Archaeal transcriptional regulator TrmB
    3.8e-19   68.3   0.0      7e-19   67.5   0.0    1.5  1  TrmB            Sugar-specific transcriptional regulator TrmB
     0.0034   17.3   0.0     0.0079   16.1   0.0    1.6  1  MarR            MarR family
  ------ inclusion threshold ------
       0.14   12.5   0.0       0.27   11.6   0.0    1.5  1  Rrf2            Transcriptional regulator


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 ?   -4.0   0.0       1.5   6.9e+03      25      42 ..      86     103 ..      84     107 .. 0.78
   2 !  149.7   0.3   1.6e-47   7.4e-44       2     231 ..     120     349 ..     119     351 .. 0.97

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 1.5
                                   EEEEEE-GGGHHHHHHHH CS
                Regulator_TrmB  25 elivslpselLeelreel 42 
                                   ++++++  ++L++ r+++
  gi|13541980|ref|NP_111668.1|  86 DVVIEAREQILKKNRDYF 103
                                   788888888888888887 PP

  == domain 2  score: 149.7 bits;  conditional E-value: 1.6e-47
                                   EEEESSHHHHHHHHHHHHHH-SSEEEEEE-GGGHHHHHHHHHHHHHTT-EEEEEESS...----GGGSSSSEEEEEE-S-- CS
                Regulator_TrmB   2 vwvvksretvierieelIesAenelivslpselLeelreeliaaaergvtVllliyp...dedleeldleevatevrvrrs 79 
                                   +  +k+ ++v++++ el+++A+  l  +++ elLe+++e+++++a++gv+V+ll+++    +d+ +  +++  +e+r+ + 
  gi|13541980|ref|NP_111668.1| 120 LINAKNLRSVVNNSIELVKEASLTLEAETTIELLEYIKEPIKRKARNGVRVELLLFGksnIPDETIAYFKDLPVEIRYLDP 200
                                   5678999**************************************************99888888888899999******* PP

                                   -S.EEEEETTTEEEEE-SSS-.EEEE--HHHHHHHHHHHHHH........HHH-EEEEEEES-TT-EEES-HHHHHHHHHH CS
                Regulator_TrmB  80 gapllvivDrkrgvvaprevl.rdkeeeyaiifkekelihvlshyFlttlWktseviktdepvekpitfssirlavedikk 159
                                   g+++++i+D+ ++v++pr+v+ + ++ +y++i+ +++++++++h F+   W ++++i    +v  p  + s r++++d+++
  gi|13541980|ref|NP_111668.1| 201 GQFYVLISDEVNSVFMPRSVAiDPETPKYGYIIMDRDMSWFITHNFFVG-WYKAKEIT-SINVNVPCLYKSQRILISDLQR 279
                                   *******************99****************************.********.********************** PP

                                   HT.TTS-EEEEEEEEETTT--EEEEEEEEEEEEEETTTTEEEEEEEETTEEEEEE-TT--SSSEEEEEEEEE CS
                Regulator_TrmB 160 llraglkveaeveGrdtetgeevtieGrvveatlnstpgvaslvvetedgevtVGGlgAvlEDieaeeitle 231
                                   + ++  ++++++eG+++++g +++  G++ +  +n +++  ++ +et +g++tVGG+++++ED+ +++++l+
  gi|13541980|ref|NP_111668.1| 280 MATKYSRISGTLEGVLRKNGSKFVEAGEIKG--INVDTEIINFEFETSSGRYTVGGYDSQIEDVIMKSFRLT 349
                                   *******************************..************************************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 !   67.5   0.0   1.6e-22     7e-19       1      67 [.      19      85 ..      19      86 .. 0.98

  Alignments for each domain:
  == domain 1  score: 67.5 bits;  conditional E-value: 1.6e-22
                                  HHHCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEEE--H CS
                          TrmB  1 LqklGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpklYravdp 67
                                  Lq+lGLse+Eak Y +Ll++g++ta++i ++  + +++ Y++ +sLe+kG++++ +grpk+Y+a+++
  gi|13541980|ref|NP_111668.1| 19 LQDLGLSENEAKLYMVLLQRGSMTAQDILRNMPLRQPQLYDITSSLERKGFINVLQGRPKKYKAISA 85
                                  899*************************************************************986 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   1.8e-06    0.0079       1      50 [.      24      73 ..      24      75 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.8e-06
                                  --HHHHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                          MarR  1 ltltqfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRs 50
                                  l++++ ++ + l ++g+++ +++ + + + ++ +  ++  Le+kG+i+  
  gi|13541980|ref|NP_111668.1| 24 LSENEAKLYMVLLQRGSMTAQDILRNMPLRQPQLYDITSSLERKGFINVL 73
                                  6788888889999**********************************865 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   5.9e-05      0.27      16      61 ..      32      76 ..      28      91 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5.9e-05
                                  HHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT CS
                          Rrf2 16 yLakeeeeepvsseeiaerqnispsylekilakLrkaglvksvrGk 61
                                  y+ + ++++ +++++i +++ + ++ l  i++ L+++g++++ +G+
  gi|13541980|ref|NP_111668.1| 32 YMVLLQRGS-MTAQDILRNMPLRQPQLYDITSSLERKGFINVLQGR 76
                                  566666665.9********************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (352 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       520  (0.0290033); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); 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: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2411.73
//
Query:       gi|13541981|ref|NP_111669.1|  [L=650]
Description: Acyl-coenzyme A synthetase [Thermoplasma volcanium GSS1]
Scores for complete 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-89  298.4   0.0    7.7e-89  298.2   0.0    1.0  1  AMP-binding    AMP-binding enzyme
    1.1e-21   77.5   0.6    2.4e-21   76.5   0.1    1.8  2  AMP-binding_C  AMP-binding enzyme C-terminal domain
    7.1e-20   70.7   4.7    1.9e-19   69.3   4.7    1.8  1  ACAS_N         Acetyl-coenzyme A synthetase N-terminus


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  298.2   0.0   1.3e-92   7.7e-89       3     422 ..      80     518 ..      78     519 .. 0.85

  Alignments for each domain:
  == domain 1  score: 298.2 bits;  conditional E-value: 1.3e-92
                                   HHHHHST.TSEEEEE...CCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEET CS
                   AMP-binding   3 eqaaktp.dkvalvd...sgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvplnp 79 
                                   ++ ++++ +k a+++   +g+ + +TY  l +r+n+lA++L +lG+kkgdr+++++p+ +e  va+la++++Gav + + +
  gi|13541981|ref|NP_111669.1|  80 RHIEQHRrNKAAYIWvgeKGDEKIVTYDGLFRRINNLAKALINLGIKKGDRIVLYMPMIIEAPVAMLAAARIGAVFSFVFA 160
                                   566666669****99**99999*********************************************************** PP

                                   TS-HHHHHHHHHHHTESEEE.......E..TCTCCC.HHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS.. CS
                   AMP-binding  80 tltaeelayiledseakvli.......a..tvdsel.leklleaaakleavklvivldadellkeeelkeeeeseekae.. 148
                                   +++a +la  ++ds+a +li           v+ ++ ++++    +   + + viv+++++ +   +++ +      ++  
  gi|13541981|ref|NP_111669.1| 161 GFGAGALAERINDSKAVLLItadgsfrNgkVVELKKiADEA---LEMTSTIRNVIVVKHAGNNVDMNEDRDI-----WYhe 233
                                   ********************998877514344444433433...3334566777777776655543333333.....2133 PP

                                   ......-TSCCCS-BTTSEEEEEEE--SSSS-EEEEEEHHHH.HHHHHHHHHHHCSCCTTT-EEEESS-TTSCHHHHHHHH CS
                   AMP-binding 149 ......kpeeeeelkpddlayiiYTSGTTGkPKGVmlshrnl.vanvaslkletrfklkeddvvlsilplahifglilell 222
                                         + +e+++ +++d+++i+YTSGTTGkPKG+++s++ + v+ + +lk+   f+ +edd++++ +++ +i+g+++ ++
  gi|13541981|ref|NP_111669.1| 234 vvgdsyTYVEPVQMDANDPLFILYTSGTTGKPKGAVHSTGGYgVWVANTLKW--AFNPDEDDRWWCAADIGWITGHSYIVF 312
                                   4556776668889**************************6664666556532..2444569******************** PP

                                   HHHHTT-EEEE-TTCGC.CHHHHHHHHHHHHT-SEEEEEHHHHHHHHHCCCHHCHHHHCCGTT-SEEEEESS-EBHHHHHH CS
                   AMP-binding 223 lallsGatvvllpkdaa.ldpklllelieklkvtviagvPrvleallesgalkaakkakdlsslrlvllggeplspellrf 302
                                   ++l+ G t ++++++ + ++p++++e iek++++++++ P+++++l++ g+++   k++dls l+++ ++gep++p+++r+
  gi|13541981|ref|NP_111669.1| 313 APLILGLTSIMYEGSITyPEPDRVWEIIEKYRINILYTSPTAIRMLMKFGDKY--PKRHDLSTLKVLGTVGEPINPSAWRW 391
                                   *****************666****************************54555..4788********************** PP

                                   HHHHHTC...EEEEEEEEGGGSSECEE....CHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEEEEEEEET..TS CS
                   AMP-binding 303 fralfge...evlegYGlTEttgvvtv....lpleedkkklgsvGkplpgvevkivDeetgepvpdgeeGellvrgp..gv 374
                                   ++++ g+   +++++Y++TEt+g+++     l    +  k+gs+ +plpgv+ +i+++  ge+v+d+e+G +++r p  g+
  gi|13541981|ref|NP_111669.1| 392 YYETIGNskcPIIDTYWQTETGGFMIApqraLG--LPPLKPGSATFPLPGVDPAILNDR-GEEVKDNEKGYIVFRRPwpGM 469
                                   ******9******************77776533..233469*****************9.****************97779 PP

                                   -SEBTT-HHHHHHHEEET.CCEEEEEEEEEEETTSEEEEEEECCCEEEE CS
                   AMP-binding 375 mkgYlkkpeataeafdse.grwlrTGDlgrldedGyleivgRkkdlikl 422
                                    +   +++e+  ++++s+  +++  GD +  d dGy++++gR+++++++
  gi|13541981|ref|NP_111669.1| 470 LMTVNNDDERYVKTYFSKfYGYYFCGDYAIKDSDGYYWLLGRADEVLNV 518
                                   9999999*******9987877************************9987 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       2.3   1.4e+04      44      67 ..     192     215 ..     175     216 .. 0.74
   2 !   76.5   0.1   4.1e-25   2.4e-21       1      76 []     527     605 ..     527     605 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 2.3
                                   HHHHHHHHHHT-TTTS-SEEEE-S CS
                 AMP-binding_C  44 eeLkahvrkelgpyavpkkvvfvd 67 
                                    eLk+ + ++l+   + ++v++v+
  gi|13541981|ref|NP_111669.1| 192 VELKKIADEALEMTSTIRNVIVVK 215
                                   688899999998888888888875 PP

  == domain 2  score: 76.5 bits;  conditional E-value: 4.1e-25
                                   HHHHHHHSSTTEEEEEEE-----TTS---EEEEEE------...HHHHHHHHHHHHT-TTTS-SEEEE-S---B-TTS- CS
                 AMP-binding_C   1 evEsalvshpaVaeaaVvGvpdevkGealvafVvlkdgsea...leeeLkahvrkelgpyavpkkvvfvdelpktrsGK 76 
                                   evE alvs     eaa++G+pd++kGe++vaf+v+k+ +++   l  e+++++r+ lgp+ vp+++++v+ lpktrsGK
  gi|13541981|ref|NP_111669.1| 527 EVEDALVSTGLAVEAAAFGKPDPIKGEVIVAFIVPKQIQADrreLISEIRKRIRSDLGPIYVPDEIHIVKLLPKTRSGK 605
                                   8**********************************843322456**********************************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 !   69.3   4.7   3.2e-23   1.9e-19       1      55 []      23      77 ..      23      77 .. 0.99

  Alignments for each domain:
  == domain 1  score: 69.3 bits;  conditional E-value: 3.2e-23
                                  HHHHHHHHHH-HHHHHHHHHCCS--SB--S-SECSTTTCT-EESTT-EE-HHHHH CS
                        ACAS_N  1 ykelykeSiedpeaFWaeqakeldWekpfdkvldgskgpfikWFeGGklNicyNc 55
                                  yk+ y+ S ++ eaFW+  a+ l+W+k++d+vld++k+pf++WF+GGklN++yNc
  gi|13541981|ref|NP_111669.1| 23 YKRAYDDSFKNMEAFWSFNAEILTWYKKWDRVLDDTKKPFYRWFVGGKLNMSYNC 77
                                  999**************************************************** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (650 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       590  (0.0329076); expected 358.6 (0.02)
Passed bias filter:                      538  (0.0300073); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.64u 0.32s 00:00:00.96 Elapsed: 00:00:00.49
# Mc/sec: 3988.20
//
Query:       gi|13541982|ref|NP_111670.1|  [L=203]
Description: hypothetical protein TVN1151 [Thermoplasma volcanium GSS1]
Scores for complete 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-43  148.2  25.0    2.9e-43  147.9  25.0    1.0  1  Gpr1_Fun34_YaaH  GPR1/FUN34/yaaH family


Domain annotation for each model (and alignments):
>> Gpr1_Fun34_YaaH  GPR1/FUN34/yaaH family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  147.9  25.0   1.6e-47   2.9e-43      17     193 ..      13     184 ..       2     193 .. 0.95

  Alignments for each domain:
  == domain 1  score: 147.9 bits;  conditional E-value: 1.6e-47
               Gpr1_Fun34_YaaH  17 faNPaPlgllafalttfvlslvnlgargitepnvvvglalfyGGlvqllaGiwefavgntFgatalssYGgFwlsyaaili 97 
                                     +PaPlgl++fa+ttf+ls++n+g    +  nvvv la++yGGl+ql++G we+  gn Fg+ta++sYG+Fw+ ya+++i
  gi|13541982|ref|NP_111670.1|  13 SSDPAPLGLAGFAFTTFLLSFINAGLIPASGVNVVVPLAIAYGGLAQLITGSWEMRRGNNFGFTAFTSYGSFWIFYALMVI 93 
                                   579**************************************************************************9988 PP

               Gpr1_Fun34_YaaH  98 p.gfgilaaYeedeeelnnalglyllgwfiftfllllatlrstvalfllfffldltflllaigeltgsakvlkAggvfgii 177
                                      ++i++a        + a+g  l+ w ift+ ++  ++ ++++l l+f+fl+ltf++l++g++ +s  +++Agg++gi+
  gi|13541982|ref|NP_111670.1|  94 LaDLHIINALP------AVAVGWALILWGIFTLYMWGGAMMASMSLNLTFLFLWLTFVVLGLGAIYSSVALTHAGGYLGIL 168
                                   549*******5......78************************************************************** PP

               Gpr1_Fun34_YaaH 178 aaflawYnalaglatk 193
                                   +af+a Y+ +a ++++
  gi|13541982|ref|NP_111670.1| 169 SAFFAAYTSFAIIINS 184
                                   ***********99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       827  (0.0461264); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1358.02
//
Query:       gi|13541983|ref|NP_111671.1|  [L=288]
Description: aldo/keto reductase [Thermoplasma volcanium GSS1]
Scores for complete 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-61  206.8   1.0    1.7e-60  204.7   1.0    1.8  1  Aldo_ket_red  Aldo/keto reductase family
  ------ inclusion threshold ------
      0.028   13.0   0.0      0.039   12.5   0.0    1.2  1  Terminase_1   Phage Terminase


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 !  204.7   1.0   1.9e-64   1.7e-60      15     292 ..      43     286 ..      23     288 .] 0.93

  Alignments for each domain:
  == domain 1  score: 204.7 bits;  conditional E-value: 1.9e-64
                                   S-HHHHHHHHHHHHHTT--EEE--TT-TTTHHHHHHHHHHHH-TTTGGG-EEEEEE--SSSTTSSSS-HHHHHHHHHHHHH CS
                  Aldo_ket_red  15 iskeealellrraleaGinffDtAevYgkgqseellGealkksrkkreeviiatKvdlrdaeiksglskeniresleeslk 95 
                                    + e++++++r+a++aG++++DtAe+Y    se+l+++a++   ++ree++iatKv      +  +l+ + +++++++sl+
  gi|13541983|ref|NP_111671.1|  43 RDAEKKIQAIRTAIDAGVTLIDTAEIY---GSEDLVAKAIEG--HNREELFIATKV------WINHLRYDKVIKACKASLS 112
                                   467889999******************...9***********..************......******************* PP

                                   HHT-S-EEEEEE-S--TTS-.HHHHHHHHHHHHHTTSEEEEEEES--HHHHHHH.HHTTT--EEEEE-B-BTT-HHHHTTH CS
                  Aldo_ket_red  96 rLgtdyvDllllHrpdpslpsieevldaleelvkeGkiraiGvSnfsveqleka.kkkkkvkivavqveynllreleeegl 175
                                   rL+t+yvDl+++H p p+   + e+++a+e+lv+ G+++ iGvSnfs ++lek  +  kk++iv++q++y+l ++++ee +
  gi|13541983|ref|NP_111671.1| 113 RLNTKYVDLYQIHFPSPTAN-LQETFKAMEKLVDDGLVKFIGVSNFSRGKLEKSmEYVKKYEIVSNQIHYSLKKRDAEEDI 192
                                   ********************.******************************9998999*********************** PP

                                   HHHHHHTT-EEEEBSTTGGGTTGTTTSS---SSSCCC-------TS-HHHHHHHHHHHHHHHHTT-.-HHHHHHHHHTTST CS
                  Aldo_ket_red 176 lelckkkgvpliaysplggGlltgkyqseedkedkeprkdlkrdertsknldaaeelselakehgv.slaqlalryalsqp 255
                                   +++c+++g+++ a+ pl +G+l ++++    ++                     e+l ++ ++h   ++aq+al+y+++ +
  gi|13541983|ref|NP_111671.1| 193 VKFCENNGMAVLAWYPLEHGSLVRESD----YP--------------------SEILARIKAKHPSiTPAQIALSYLIYGN 249
                                   ***********************5554....44....................46777887776666************** PP

                                   T-SEEEE--SSHHHHHHHHGGGG----HHHHHHHHHH CS
                  Aldo_ket_red 256 avgivipgasnieqlednldalelklseeevaeldel 292
                                   + +++ip asn+e++++n++++e kl++ee++el+++
  gi|13541983|ref|NP_111671.1| 250 KLVFPIPRASNPEHVKENIASVEQKLDQEEIEELRKY 286
                                   *********************************9975 PP

>> Terminase_1  Phage Terminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   4.3e-06     0.039     338     417 ..      72     151 ..      24     158 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.3e-06
                   Terminase_1 338 easdagmidekqvvdiivfiaktlavqavaYDP..wnaksfidklektaldiplvevrqsfaklSnslkeveklvaeerir 416
                                   e   a +i+ ++ +++  fia+++ +  + YD      k    +l+ +++d++ ++     a+l +++k++eklv+++ ++
  gi|13541983|ref|NP_111671.1|  72 EDLVAKAIEGHNREEL--FIATKVWINHLRYDKviKACKASLSRLNTKYVDLYQIHFPSPTANLQETFKAMEKLVDDGLVK 150
                                   3333444444555555..**************833468999************************************9998 PP

                   Terminase_1 417 h 417
                                   +
  gi|13541983|ref|NP_111671.1| 151 F 151
                                   8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       753  (0.041999); expected 358.6 (0.02)
Passed bias filter:                      557  (0.031067); 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 0.26s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 1883.92
//
Query:       gi|13541984|ref|NP_111672.1|  [L=296]
Description: hypothetical protein TVN1153 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0022   17.4   1.7     0.0043   16.5   0.1    2.2  2  DUF5305   Family of unknown function (DUF5305)
  ------ inclusion threshold ------
       0.21   12.4   3.8        0.4   11.5   0.8    2.2  2  DUF4397   Domain of unknown function (DUF4397)
        1.1    9.0  12.5        1.1    9.1   1.1    2.8  2  PsbH      Photosystem II 10 kDa phosphoprotein


Domain annotation for each model (and alignments):
>> DUF5305  Family of unknown function (DUF5305)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1   7.1e-07    0.0043      59     140 ..      58     151 ..      53     167 .. 0.89
   2 ?   -1.0   0.1      0.16   9.6e+02     116     149 ..     188     220 ..     174     227 .. 0.62

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 7.1e-07
                       DUF5305  59 vnvegeidgesieesktsrlpiplteqtyeikkdetdeengeitetvtvkespslae............gilliilgllal 127
                                   v++++ + +  ++++ t ++  +++ +ty+i+ + t +++++  +t +v++ ++++              i +i+ g++++
  gi|13541984|ref|NP_111672.1|  58 VTFSNPTGDPPFSGTATVTVAKTVSPGTYTIEISATGDDPSSSPATLSVTVMNTTVTtapppapvvhvnYIPFIVGGIAIA 138
                                   7778888889999999999999999*****************************999999*****9999888999999999 PP

                       DUF5305 128 iglvvlirriift 140
                                   +++v+li + +f 
  gi|13541984|ref|NP_111672.1| 139 LFVVFLIIFSLFL 151
                                   9999999887765 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.16
                       DUF5305 116 gilliilgllaliglvvlirriiftsskaekyel 149
                                    ++li+++ll++i++ + +++   + +  + y l
  gi|13541984|ref|NP_111672.1| 188 WLGLIVYLLLSTIFFGL-TFSSSQALKRSSLYLL 220
                                   45567777777666655.5555666666666655 PP

>> DUF4397  Domain of unknown function (DUF4397)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.4     0.032   1.9e+02      40     109 ..       9      78 ..       4      81 .. 0.67
   2 ?   11.5   0.8   6.7e-05       0.4      32      74 ..      74     112 ..      69     118 .. 0.69

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.032
                       DUF4397  40 paGqytielnpagn.kikagttvallnvditleagteytvaavgsa.aalellvleddstkpaagtarvrfv 109
                                   ++G+ +i+l  +++  i++g +++ ++ +++l++g+     +  sa +++++++ + +  +p +gta v ++
  gi|13541984|ref|NP_111672.1|   9 ASGTSEITL-STTSiSIPRGGSST-VTYNVKLASGNTWGTSISASApSGISVTFSNPTGDPPFSGTATVTVA 78 
                                   566666666.33332344444442.45557888888777777777788899999998889999999999886 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 6.7e-05
                       DUF4397  32 dvtgylqvpaGqytielnpagnkikagttvallnvditleagt 74 
                                   +vt   +v +G+ytie+ ++g+ ++++++++l +  +t+ + t
  gi|13541984|ref|NP_111672.1|  74 TVTVAKTVSPGTYTIEISATGD-DPSSSPATL-S--VTVMNTT 112
                                   6777889**********99998.456666644.2..2343333 PP

>> PsbH  Photosystem II 10 kDa phosphoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   4.3    0.0087        52      27      42 ..     132     147 ..     130     150 .. 0.87
   2 ?    9.1   1.1   0.00018       1.1      21      46 ..     258     283 ..     255     288 .. 0.94

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.0087
                          PsbH  27 vmavfilLflvfLvii 42 
                                   v +++i+Lf+vfL+i 
  gi|13541984|ref|NP_111672.1| 132 VGGIAIALFVVFLIIF 147
                                   56899*********96 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00018
                          PsbH  21 GWGttpvmavfilLflvfLviilqiy 46 
                                   G Gtt + +v i L + +L i   iy
  gi|13541984|ref|NP_111672.1| 258 GYGTTSISTVGISLAFTLLFIFVGIY 283
                                   89***********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1144  (0.0638072); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); 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):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 1827.62
//
Query:       gi|13541985|ref|NP_111673.1|  [L=69]
Description: hypothetical protein TVN1154 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score 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   14.1   0.2      0.064   13.6   0.2    1.5  1  TRCF       TRCF domain
      0.051   13.5   0.7      0.062   13.2   0.7    1.1  1  Oberon_cc  Coiled-coil region of Oberon


Domain annotation for each model (and alignments):
>> TRCF  TRCF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.2   7.1e-06     0.064      28      50 ..       1      23 [.       1      65 [. 0.85

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 7.1e-06
                          TRCF 28 ieteeeldeleeeLiDrFGklpe 50
                                  +et++++d+++++L++r+Gk+ +
  gi|13541985|ref|NP_111673.1|  1 METDQAVDKIKRDLEERYGKIDD 23
                                  5899****************976 PP

>> Oberon_cc  Coiled-coil region of Oberon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.7     7e-06     0.062       4      45 ..       4      45 ..       2      52 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7e-06
                     Oberon_cc  4 rlaleacereledkakeaselklerlrkkqqveeLEsivrlK 45
                                   +a+++++r+le++  + ++++ erl+ +++++e   ivr K
  gi|13541985|ref|NP_111673.1|  4 DQAVDKIKRDLEERYGKIDDIRPERLKFDETLKEYSMIVRFK 45
                                  5789************************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       649  (0.0361983); 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: 0.47u 0.31s 00:00:00.78 Elapsed: 00:00:00.50
# Mc/sec: 417.47
//
Query:       gi|13541986|ref|NP_111674.1|  [L=327]
Description: permease [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.7e-41  141.0  33.0    4.7e-41  141.0  33.0    1.5  2  TauE            Sulfite exporter TauE/SafE
  ------ inclusion threshold ------
       0.18   11.1   0.1        0.3   10.4   0.1    1.4  1  Rhabdo_M2       Rhabdovirus matrix protein M2
       0.82    9.1   4.4        1.4    8.3   2.8    1.9  2  Fijivirus_P9-2  Fijivirus P9-2 protein


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 !  141.0  33.0   7.8e-45   4.7e-41       2     236 .]      15     280 ..      14     280 .. 0.87
   2 ?   -2.6   0.1      0.56   3.4e+03      92     109 ..     297     314 ..     283     323 .. 0.50

  Alignments for each domain:
  == domain 1  score: 141.0 bits;  conditional E-value: 7.8e-45
                          TauE   2 llagllaGfvagllGiGggliavPlLlll..lppavavatsllavvatslsgalahrrrgnvdwrlllllllgsliGallG 80 
                                   l+ +++aG++++l+G+Ggg+++vP+L+l+  +p+ +a+++sl++ +ats+++a a+ +++  ++rl++ l +++  Ga++G
  gi|13541986|ref|NP_111674.1|  15 LIGAFIAGLIGSLTGLGGGTVLVPVLTLFygVPIIYATGASLISTIATSAGSASAYAKEKIANIRLGVGLEVATTTGAIVG 95 
                                   678999**********************75679999***********************989******************* PP

                          TauE  81 allllllpse....llkllfgvlllllallmllrkkr...........................srakgrerrptaillvl 130
                                   +l + ++ ++    l+ ++fg +ll + + ++  +++                           +++  +    +++l  +
  gi|13541986|ref|NP_111674.1|  96 SLTAVYIYDHhlswLVYVIFGMVLLGSLIPTIQ-RGKyeipkilkpdwttrifqlsgsyydaklHKNV-EYSGVRWWLGEI 174
                                   ********9933323555555566666665554.333689*******9*9999999998887553222.344455555555 PP

                          TauE 131 igglvGllsGllGiGgGfllvpllllllglplkkavatslllilvislagalgyalagavdwpllllllpgallGallGar 211
                                   i++++Gl+sGllGiG G+l v  + +  +lp+k+++ +s+++i +++++g  +y++ag++++ ++++ ++g+l+Ga+lGa+
  gi|13541986|ref|NP_111674.1| 175 IMFFAGLISGLLGIGSGALKVLGMDWAINLPMKVTTTSSNFMIGITAATGSSIYWYAGYIQPFIAAATAIGVLIGAFLGAK 255
                                   5566***************************************************************************** PP

                          TauE 212 larrlsertlrrlfallllvlgvkl 236
                                   +  r+ +r +r++f+++l++lg+++
  gi|13541986|ref|NP_111674.1| 256 ILVRITNRSIRWIFFAILMFLGIQM 280
                                   ***********************98 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.56
                          TauE  92 lkllfgvlllllallmll 109
                                   ++++++ ++ ++++ +l+
  gi|13541986|ref|NP_111674.1| 297 IQFAISTIISIISIIILF 314
                                   344444444444433333 PP

>> Rhabdo_M2  Rhabdovirus matrix protein M2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1     5e-05       0.3      75     133 ..      93     151 ..      83     218 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 5e-05
                     Rhabdo_M2  75 ilksfenvysgnrrmiglvkvviglvlsgapvpegmnwvyklrrtlifqwaessgpleg 133
                                   i+ s+ +vy  ++++  lv v+ g+vl g+ +p      y + + l  +w+     l g
  gi|13541986|ref|NP_111674.1|  93 IVGSLTAVYIYDHHLSWLVYVIFGMVLLGSLIPTIQRGKYEIPKILKPDWTTRIFQLSG 151
                                   788999***************************99999999988887777665554444 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 ?   -0.4   0.0      0.11   6.7e+02      72     111 ..     106     146 ..      86     150 .. 0.69
   2 ?    8.3   2.8   0.00024       1.4      76     127 ..     265     315 ..     244     325 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.11
                Fijivirus_P9-2  72 svgkvvflifsflffgsi.klvlkcfyhlfkcvfcnpltrc 111
                                    +  +v++if ++++gs+   + +  y + k +  +  tr 
  gi|13541986|ref|NP_111674.1| 106 HLSWLVYVIFGMVLLGSLiPTIQRGKYEIPKILKPDWTTRI 146
                                   566789999*9999999514555666776666665555555 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00024
                Fijivirus_P9-2  76 vvflifsflffgsiklvlkcfyhlfkcvfcnpltrcfcsiiftiifytllfv 127
                                   + ++ f++l+f  i++vlk +y  ++++   p  +   s i++ii   +lf 
  gi|13541986|ref|NP_111674.1| 265 IRWIFFAILMFLGIQMVLKGLYI-INVITISPYIQFAISTIISIISIIILFQ 315
                                   4567899**************95.6788899999999999999999888885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1192  (0.0664845); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.64u 0.39s 00:00:01.03 Elapsed: 00:00:00.57
# Mc/sec: 1733.75
//
Query:       gi|13541987|ref|NP_111675.1|  [L=126]
Description: hypothetical protein TVN1156 [Thermoplasma volcanium GSS1]
Scores for complete 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-25   88.7  11.3    2.6e-25   88.5  11.3    1.0  1  DUF1634   Protein of unknown function (DUF1634)
  ------ inclusion threshold ------
        2.1    8.6   8.1        7.6    6.8   0.2    2.2  2  DUF4418   Domain of unknown function (DUF4418)


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 !   88.5  11.3   2.8e-29   2.6e-25       1     102 []       9     121 ..       9     121 .. 0.94

  Alignments for each domain:
  == domain 1  score: 88.5 bits;  conditional E-value: 2.8e-29
                       DUF1634   1 igklLriGvllsaavvllGlilllvkhgs...........sesenseltslseilegllelkglaiiqlGllvLiatPvlr 70 
                                   i++ LriGv +s++++++G+ill+vk+g            +++ ns+++ l  i +gll+l+g  +i +Gl+vL++tP++ 
  gi|13541987|ref|NP_111675.1|   9 ISYALRIGVSISMFFIIVGVILLFVKNGGsgytlaqiasyHSQMNSKFIYLGLIPKGLLDLDGIFFIATGLWVLVFTPITS 89 
                                   89**************************7677777776554499************************************* PP

                       DUF1634  71 VvlsliaFlkekdilyviitliVLliLllsll 102
                                   Vv++l++F++++++ly+++++iVL++L++++l
  gi|13541987|ref|NP_111675.1|  90 VVIALVSFYLTRNKLYIALSIIVLFNLFFAML 121
                                   ******************************96 PP

>> DUF4418  Domain of unknown function (DUF4418)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.2   0.00085       7.6      33      67 ..      11      45 ..       8      68 .. 0.78
   2 ?    5.1   3.0    0.0029        26      43      78 ..      87     122 ..      73     126 .] 0.81

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.00085
                       DUF4418 33 ytgqaelgvGivllvlgllalfvkkkklrrglsia 67
                                  y+ ++ + +++  +++g++ lfvk+      l+ +
  gi|13541987|ref|NP_111675.1| 11 YALRIGVSISMFFIIVGVILLFVKNGGSGYTLAQI 45
                                  5566677889999************9655555444 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0029
                       DUF4418  43 ivllvlgllalfvkkkklrrglsiavillgvlvili 78 
                                   i  +v++l+ ++++++kl ++lsi+v  +  +++l+
  gi|13541987|ref|NP_111675.1|  87 ITSVVIALVSFYLTRNKLYIALSIIVLFNLFFAMLV 122
                                   56789999999999999*******999988877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1169  (0.0652016); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.28s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 836.62
//
Query:       gi|13541988|ref|NP_111676.1|  [L=484]
Description: oxidoreductase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.3e-32  111.2   0.1    7.1e-32  110.8   0.1    1.1  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    1.8e-25   88.9   0.0      3e-25   88.2   0.0    1.3  1  Fer4_20         Dihydroprymidine dehydrogenase domain II, 4Fe
    1.7e-13   50.9   0.3      2e-05   25.1   0.0    2.8  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    8.2e-11   42.0   0.2    2.5e-10   40.4   0.0    1.9  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    9.6e-10   38.2   0.2    6.4e-05   22.4   0.1    2.7  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    1.3e-08   34.4   0.0    1.9e-07   30.6   0.0    2.2  2  Thi4            Thi4 family
    3.1e-07   30.3   1.2    5.1e-07   29.6   0.2    1.8  2  DAO             FAD dependent oxidoreductase
    4.2e-05   24.0   1.5    0.00015   22.2   0.2    2.2  2  Fer4_17         4Fe-4S dicluster domain
    4.3e-05   22.9   0.2    8.4e-05   22.0   0.2    1.4  1  FAD_binding_3   FAD binding domain
    5.1e-05   23.7   0.2      0.041   14.3   0.0    2.7  2  NAD_binding_7   Putative NAD(P)-binding
    0.00015   21.1   0.2       0.25   10.6   0.0    2.4  2  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
    0.00017   21.0   2.0    0.00027   20.4   0.1    2.1  3  FAD_oxidored    FAD dependent oxidoreductase
     0.0003   19.6   0.1    0.00047   19.0   0.1    1.2  1  HI0933_like     HI0933-like protein
    0.00037   20.6   2.5    0.00075   19.6   2.5    1.5  1  Fer4_9          4Fe-4S dicluster domain
     0.0004   19.6   0.3    0.00067   18.8   0.3    1.3  1  FAD_binding_2   FAD binding domain
     0.0004   19.6   0.0        0.1   11.8   0.0    2.4  3  K_oxygenase     L-lysine 6-monooxygenase (NADPH-requiring)
    0.00047   19.6   0.0     0.0016   17.8   0.0    1.8  2  Amino_oxidase   Flavin containing amine oxidoreductase
     0.0017   18.3   2.9     0.0017   18.3   2.9    2.1  1  Fer4_6          4Fe-4S binding domain
     0.0018   18.0   2.9     0.0018   18.0   2.9    2.0  2  Fer4            4Fe-4S binding domain
     0.0029   17.7   6.4     0.0083   16.2   6.7    1.7  1  Fer4_10         4Fe-4S dicluster domain
      0.003   17.7   0.8      0.003   17.7   0.8    1.9  2  Fer4_21         4Fe-4S dicluster domain
  ------ inclusion threshold ------
       0.01   15.9   3.6       0.01   15.9   3.6    2.1  2  Fer4_2          4Fe-4S binding domain
      0.012   14.7   0.2      0.099   11.7   0.3    2.0  2  GIDA            Glucose inhibited division protein A
      0.014   14.8   0.1        1.6    8.0   0.0    2.6  2  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
       0.02   14.9   0.4      0.048   13.6   0.0    1.8  1  NAD_binding_9   FAD-NAD(P)-binding
      0.023   14.9   0.0      0.049   13.8   0.0    1.5  1  Fer4_18         4Fe-4S dicluster domain
       0.03   14.9   7.5      0.059   14.0   4.1    2.1  3  Fer4_7          4Fe-4S dicluster domain
      0.031   14.3   0.0        8.8    6.4   0.0    3.0  3  Shikimate_DH    Shikimate / quinate 5-dehydrogenase
      0.032   14.7   7.1      0.055   13.9   5.6    2.1  2  Fer4_8          4Fe-4S dicluster domain
      0.047   14.2   1.4      0.047   14.2   1.4    2.0  1  Fer4_4          4Fe-4S binding domain
      0.049   13.5   0.2       0.71    9.7   0.1    2.4  2  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
      0.055   14.4   4.1      0.063   14.2   0.3    2.4  2  Fer4_16         4Fe-4S double cluster binding domain
       0.09   11.8   0.1       0.15   11.1   0.1    1.3  1  Lycopene_cycl   Lycopene cyclase protein
       0.13   11.0   0.0       0.22   10.3   0.0    1.3  1  MCRA            MCRA family
       0.15   10.9   0.2       0.29    9.9   0.2    1.4  1  Trp_halogenase  Tryptophan halogenase
       0.15   12.1   0.0       0.35   10.9   0.0    1.5  1  Stb3            Putative Sin3 binding protein
       0.55   10.8   5.7       0.13   12.8   0.9    2.4  1  Fer4_13         4Fe-4S single cluster domain of Ferredoxin I


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 !  110.8   0.1   1.5e-34   7.1e-32       1     280 [.     137     427 ..     137     438 .. 0.85

  Alignments for each domain:
  == domain 1  score: 110.8 bits;  conditional E-value: 1.5e-34
                                   CSEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH.HHHHCHHHHCCCCHCCT.CEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxx.xxxxx RF
                   Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeias.evvkklnqgielllgee.vvkid 79 
                                   k+v+v+GgGpAGl++a +l  +g+kvt++ +e+  +  g ++++ + +++ +++++  e       g++l  g++ +++  
  gi|13541988|ref|NP_111676.1| 137 KRVAVVGGGPAGLTVAYYLTLQGVKVTVF-EER--PALGGFMKTGIPRYRLPQNVLDkEI------GYILSRGVQvKLNTA 208
                                   58***************************.555..77888**************999544......555555544344444 PP

                                   ESCEEEEETEEECTCEEEEEESEEEE---E.EE-BCTCTTC..TTBEECCSECHHHHHHCCSS-TSEEEEES-SHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2  80 pgkkkvklekkkegdeekiaydklvlAtGs.sprdlgipGv.aenvgklvrtldsaealklkllpkrivvvGgGyiGvElA 158
                                    g+ +vk e++        +yd+++l  G  +pr  g+pG  a+nv +  + l+ +   ++ ++ + ++v+GgG+++ + A
  gi|13541988|ref|NP_111676.1| 209 VGR-DVKFEDLM------KEYDAIFLGVGNhKPRMTGTPGSdAPNVMHATEFLERVSFGEKINVGETVAVIGGGFTANDSA 282
                                   455.77775444......48*********6266666***9989************************************** PP

                                   HHHHHHT-E.EEEEESSSSSS.TTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTE........EEE.EEETTSCE... CS
                                   xxxxxxxxx.xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxx.xxxxxxxx... RF
                   Pyr_redox_2 159 aalaklgke.vtlveardrll.raldkelsaaleealekeGvevklgtsvkeidgnge........kle.vvledgee... 225
                                    +  +lg++ v+++++r  +  ++++++ +++ +e+ e+e+ve +++ ++ e  +++         k e v  ++g+    
  gi|13541988|ref|NP_111676.1| 283 RTSLRLGAKhVYIMYRRRDVDrPGYPSMNADEEMEEAEEENVEYVWEVTPFEYVKENGrvvamkywKNEmVSQGKGRAkpv 363
                                   **99997766***********9***************************998887777687665544445555555559** PP

                                   ........EEESEEEE-S-EEES-HHCS.HCCT-EEEETTEEE--TTSBESSTTEEE-GGGCTE CS
                                   ........xxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2 226 ........idadlvvvavGvrpstelle.eklglelderggivvdeflrtnvpgiyaiGDvagg 280
                                           i++d+v+ a+G + + ++l+    +l l++rg   vd+++ t++pg++  GD +++
  gi|13541988|ref|NP_111676.1| 364 pikdkfytIKVDMVIEATGQETDYSFLGsYVEKLRLNDRGEPIVDQYGMTSIPGVFTGGDSTNP 427
                                   *****************************999****************************9843 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 !   88.2   0.0   6.1e-28     3e-25      10     110 ..      27     122 ..      18     125 .. 0.93

  Alignments for each domain:
  == domain 1  score: 88.2 bits;  conditional E-value: 6.1e-28
                                   ----HHHHHHHHTT----TT-HHHHCSTT---HHHHHHHHHTT-HHHHHHHHHHH-S-HHHHHHHS-GGGTGCCS-GGGTT CS
                       Fer4_20  10 lglteeealeeAsRClqCkkapcvkgCPveidipefikkiaegnleeaakiiketnslpavcgrvCpqeelCegaCvlekk 90 
                                   +++++ ea++eAsRC+ C  ++c+++CP+++di ++++++a+g+ +++++ii+et ++pa++grvC++   Ce+ Cvl  +
  gi|13541988|ref|NP_111676.1|  27 ENYNDGEAIAEASRCIGC--NMCSAACPASLDIGGYVRSTAAGDPAQTIRIIMETLPFPAIIGRVCTHM--CEDVCVLY-D 102
                                   5788999***********..89********************************************998..*******6.6 PP

                                   B.----HHHHHHHHHHHHHH CS
                       Fer4_20  91 gkepvaigklerfvadaare 110
                                   g  p+ai++l+r++ad++ +
  gi|13541988|ref|NP_111676.1| 103 GGGPIAIRHLKRYAADKFDD 122
                                   669*************9865 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.2   1.7e-07   8.3e-05       1      36 [.     138     173 ..     138     214 .. 0.89
   2 !   25.1   0.0   4.1e-08     2e-05       2      74 ..     269     343 ..     268     350 .. 0.91

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 1.7e-07
                                   EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSST CS
                     Pyr_redox   1 kvvvvGgGyiglElAgalaelgkkVtvversdkllr 36 
                                   +v+vvGgG  gl +A +l+  g kVtv+e ++ l  
  gi|13541988|ref|NP_111676.1| 138 RVAVVGGGPAGLTVAYYLTLQGVKVTVFEERPALGG 173
                                   79*****************************99984 PP

  == domain 2  score: 25.1 bits;  conditional E-value: 4.1e-08
                                   EEEECSSHHHHHHHHHHHHTT.SEEEEEESSSSSS.TTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTSEE CS
                     Pyr_redox   2 vvvvGgGyiglElAgalaelg.kkVtvversdkll.rllDeeaskilqeklekngievllntkveeiegsedgve 74 
                                   v+v+GgG+++ + A +  +lg k+V+++ r+  +  ++++ + +++ +e+ e++++e +++ ++ e ++++  v 
  gi|13541988|ref|NP_111676.1| 269 VAVIGGGFTANDSARTSLRLGaKHVYIMYRRRDVDrPGYPSMNADEEMEEAEEENVEYVWEVTPFEYVKENGRVV 343
                                   89*******************889*****9999999*************************99999987776554 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 !   40.4   0.0   5.2e-13   2.5e-10       1      47 [.     141     191 ..     141     206 .. 0.83

  Alignments for each domain:
  == domain 1  score: 40.4 bits;  conditional E-value: 5.2e-13
                                   EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-EECE....TTCEECT CS
                 NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraasyev....pgvrvdy 47 
                                   +vG+G +Gl+ Ay+L+ +g++v+++e r+ lGG +++       p++++d 
  gi|13541988|ref|NP_111676.1| 141 VVGGGPAGLTVAYYLTLQGVKVTVFEERPALGGFMKTGIPryrlPQNVLDK 191
                                   8**********************************9984333446666665 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.0   0.00013     0.061       2      30 ..     141     168 ..     129     192 .. 0.79
   2 !   22.4   0.1   1.3e-07   6.4e-05     128     305 .]     225     422 ..     220     422 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00013
                   Pyr_redox_3   2 IiGaGPaGlaaaielkkagledylilEkg 30 
                                   ++G+GPaGl++a+ l   g+ ++++ E  
  gi|13541988|ref|NP_111676.1| 141 VVGGGPAGLTVAYYLTLQGV-KVTVFEER 168
                                   78888888888888888888.57777765 PP

  == domain 2  score: 22.4 bits;  conditional E-value: 1.3e-07
                   Pyr_redox_3 128 viiAtGefdkPnklnipGeek.lvkhyskv....kefhkya.gqkvvViGgknSavDaAlelvrkga.eVtvvtrgseiek 201
                                   +++  G  +kP++++ pG++  +v+h  ++    +  +k++ g+ v+ViGg+ +a D A    r ga +V +++r+  +++
  gi|13541988|ref|NP_111676.1| 225 IFLGVGN-HKPRMTGTPGSDApNVMHATEFlervSFGEKINvGETVAVIGGGFTANDSARTSLRLGAkHVYIMYRRRDVDR 304
                                   5667777.89*********96578888877322122344456899********************8637******998887 PP

                   Pyr_redox_3 202 ee...sdpsyslkpdienrleelvke............ekikvlfnaevkeikekeeeykvktedgkkvevkddvvlatGy 267
                                         + + +++   e+++e +++              ++k  +n+ v + k + + + +k +    + + d v+ atG 
  gi|13541988|ref|NP_111676.1| 305 PGypsMNADEEMEEAEEENVEYVWEVtpfeyvkengrvVAMKYWKNEMVSQGKGRAKPVPIKDKF--YTIKVDMVIEATGQ 383
                                   64111333444555555555444333555444435322224444444444444444444443333..33345778899*** PP

                   Pyr_redox_3 268 kpdlsflkk..slfeldedgrpvlteeteetnvpglflaG 305
                                   + d+sfl +  +++ l++ g+p +++  + + +pg+f  G
  gi|13541988|ref|NP_111676.1| 384 ETDYSFLGSyvEKLRLNDRGEPIVDQYGMTS-IPGVFTGG 422
                                   ********988899999********999955.9****876 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   0.0   3.9e-10   1.9e-07      14      60 ..     133     178 ..     127     207 .. 0.87
   2 ?    1.0   0.0      0.42     2e+02     156     195 ..     371     412 ..     365     415 .. 0.76

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 3.9e-10
                                   HHTEEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTTTT CS
                          Thi4  14 kyaesDvvivGaGssGLtaayylakkpdlkvailersvspGGGawlG 60 
                                   k++   v++vG+G++GLt ayyl+ + ++kv+++e++ ++GG +  G
  gi|13541988|ref|NP_111676.1| 133 KFIGKRVAVVGGGPAGLTVAYYLTLQ-GVKVTVFEERPALGGFMKTG 178
                                   677888********************.***************88777 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.42
                                   EEEEEEEEE--GSSST..TTTHHHHHHHHCTTTS-----ECB CS
                          Thi4 156 virakvvvdatGhdge..ivavvvkkikleakiekvkgeksl 195
                                   +i+  +v++atG +++  +    v k++l+++ e + ++ ++
  gi|13541988|ref|NP_111676.1| 371 TIKVDMVIEATGQETDysFLGSYVEKLRLNDRGEPIVDQYGM 412
                                   89999*******977522666778888888888877776665 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.2     1e-09   5.1e-07       1      33 [.     138     172 ..     138     177 .. 0.93
   2 ?   -2.3   0.0       5.1   2.5e+03       2      10 ..     269     277 ..     268     295 .. 0.91

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 1e-09
                                   EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTT CS
                           DAO   1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiag 33 
                                   +v+++GGG +Gl++Ay+L+ +g  Vt++e ++ +g
  gi|13541988|ref|NP_111676.1| 138 RVAVVGGGPAGLTVAYYLTLQGvkVTVFEERPALG 172
                                   59****************************97776 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 5.1
                                   EEEECTSHH CS
                           DAO   2 vviiGGGii 10 
                                   v++iGGG +
  gi|13541988|ref|NP_111676.1| 269 VAVIGGGFT 277
                                   89*****86 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.2   3.2e-07   0.00015      30      61 .]      22      56 ..       3      56 .. 0.69
   2 ?    0.2   0.1       2.3   1.1e+03       6      16 ..      92     102 ..      88     123 .. 0.77

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 3.2e-07
                       Fer4_17 30 klglleeaeke...ekaslCieCgeCerkCPqgld 61
                                  +l+ le+ ++     +as+Ci+C++C+++CP++ld
  gi|13541988|ref|NP_111676.1| 22 ELEPLENYNDGeaiAEASRCIGCNMCSAACPASLD 56
                                  44444554444444699***************997 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 2.3
                       Fer4_17   6 gyClpeCpsye 16 
                                    +C+++C  y 
  gi|13541988|ref|NP_111676.1|  92 HMCEDVCVLYD 102
                                   36888888765 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.2   1.7e-07   8.4e-05       4      33 ..     139     168 ..     137     177 .. 0.93

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 1.7e-07
                                   EEEE--SHHHHHHHHHHHHTTHHEEEEESS CS
                 FAD_binding_3   4 VlIVGaGpaGlmlallLseaGvrvvlvekr 33 
                                   V++VG+GpaGl+ a  L+ +Gv+v++ e r
  gi|13541988|ref|NP_111676.1| 139 VAVVGGGPAGLTVAYYLTLQGVKVTVFEER 168
                                   99************************9876 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   8.5e-05     0.041       5      39 ..     134     168 ..     132     232 .. 0.81
   2 ?    6.4   0.0     0.024        12       7      39 ..     266     299 ..     265     386 .. 0.57

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 8.5e-05
                 NAD_binding_7   5 lkgkkvlvvGgGevAarkvrklleagakvtvvape 39 
                                   + gk+v vvGgG+ +++ ++ l  +g kvtv  ++
  gi|13541988|ref|NP_111676.1| 134 FIGKRVAVVGGGPAGLTVAYYLTLQGVKVTVFEER 168
                                   5689***************************9876 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.024
                 NAD_binding_7   7 gkkvlvvGgGevAarkvrklleagak.vtvvape 39 
                                   g++v v+GgG  A   +r+ l+ gak v ++  +
  gi|13541988|ref|NP_111676.1| 266 GETVAVIGGGFTANDSARTSLRLGAKhVYIMYRR 299
                                   689********************98725554444 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 !    8.0   0.1    0.0033       1.6      30      62 ..     138     170 ..     132     177 .. 0.93
   2 !   10.6   0.0   0.00052      0.25      16      62 ..     261     301 ..     246     327 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0033
                                   EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHH CS
                   AlaDh_PNT_C  30 kvlviGgGvaGlqAiatakglgakVtvlDvrpa 62 
                                   +v v+GgG aGl  +   +  g kVtv++ rpa
  gi|13541988|ref|NP_111676.1| 138 RVAVVGGGPAGLTVAYYLTLQGVKVTVFEERPA 170
                                   79***************************9987 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00052
                                   EEETTCEETCB---EEEEESTSHHHHHHHHHHHHTT-E.EEEEESSHH CS
                   AlaDh_PNT_C  16 kgtlaGgvpgvepakvlviGgGvaGlqAiatakglgak.VtvlDvrpa 62 
                                   + + +G        +v viGgG     +++t+ +lgak V+++  r +
  gi|13541988|ref|NP_111676.1| 261 EKINVGE-------TVAVIGGGFTANDSARTSLRLGAKhVYIMYRRRD 301
                                   5555443.......479*******************974777666555 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.1   5.5e-07   0.00027       2      41 ..     139     178 ..     138     197 .. 0.94
   2 ?   -1.9   0.1       3.3   1.6e+03       2      26 ..     269     293 ..     269     300 .. 0.87
   3 ?   -1.5   0.0       2.4   1.2e+03      95     144 ..     334     382 ..     295     383 .. 0.51

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 5.5e-07
                  FAD_oxidored   2 vvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsg 41 
                                   v VvGGgpaG++ A+    +G kv + eer+ lGG +  g
  gi|13541988|ref|NP_111676.1| 139 VAVVGGGPAGLTVAYYLTLQGVKVTVFEERPALGGFMKTG 178
                                   89*********************************98766 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3.3
                  FAD_oxidored   2 vvVvGGgpaGvaAAiaAaraGakvl 26 
                                   v V+GGg      A ++ r Gak +
  gi|13541988|ref|NP_111676.1| 269 VAVIGGGFTANDSARTSLRLGAKHV 293
                                   89*******************9865 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 2.4
                  FAD_oxidored  95 emlaeagvtvllntrlvevekeg.kriesvtveskegrktirAkvfiDATg 144
                                   e ++e+g  v ++ +  e++ +g +r + v +++  + +ti+ +++i ATg
  gi|13541988|ref|NP_111676.1| 334 EYVKENGRVVAMKYWKNEMVSQGkGRAKPVPIKD--KFYTIKVDMVIEATG 382
                                   3334422223333333333333323455555543..356666666666665 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.1   9.7e-07   0.00047       2      36 ..     138     172 ..     137     178 .. 0.93

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 9.7e-07
                                   SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS- CS
                   HI0933_like   2 dviviGgGaAGlmaAisaakrgkrVlllekakklg 36 
                                   +v+v+GgG+AGl  A  +  +g +V+++e+ ++lg
  gi|13541988|ref|NP_111676.1| 138 RVAVVGGGPAGLTVAYYLTLQGVKVTVFEERPALG 172
                                   79****************************99887 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   2.5   1.5e-06   0.00075       1      46 [.      40      98 ..      40     103 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.5e-06
                        Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraase...............eaCigCgaCveaC 46
                                  +C+gC+ C +aCpa + ++  ++ +a+ + a+                  C+  + C+++C
  gi|13541988|ref|NP_111676.1| 40 RCIGCNMCSAACPASLDIGGYVRSTAAGDPAQTiriimetlpfpaiigRVCT--HMCEDVC 98
                                  6**************************9998889999999999999997797..4555555 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.3   1.4e-06   0.00067       2      36 ..     139     173 ..     138     178 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.4e-06
                                   EEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGS CS
                 FAD_binding_2   2 viViGsGlAGLaAAleaaeaGlkvavvekeqefgg 36 
                                   v V+G+G AGL+ A+ ++ +G kv+v e  ++ gg
  gi|13541988|ref|NP_111676.1| 139 VAVVGGGPAGLTVAYYLTLQGVKVTVFEERPALGG 173
                                   89**************************9999887 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0      0.02       9.5     181     213 ..     126     158 ..      98     176 .. 0.76
   2 !   11.8   0.0   0.00021       0.1     151     226 ..     224     300 ..     207     328 .. 0.78
   3 ?   -3.5   0.0       8.7   4.2e+03     327     339 ..     370     382 ..     366     384 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.02
                   K_oxygenase 181 ylerkeellakkriaVvGsGqSaaeifedllrr 213
                                   +l+ ++++  +kr+aVvG+G  +  +++ l+ +
  gi|13541988|ref|NP_111676.1| 126 ILKPQKRKFIGKRVAVVGGGPAGLTVAYYLTLQ 158
                                   556666677789999999999998888887655 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00021
                   K_oxygenase 151 nlvlgvG.tepkiPevleklegkervvHsseylerkee...llakkriaVvGsGqSaaeifedllrrqkkvelklvtrse 226
                                   ++ lgvG  +p +  +  +  + ++v+H+ e+ler +     + ++++aV+G+G +a + ++  lr  + +++ ++ r++
  gi|13541988|ref|NP_111676.1| 224 AIFLGVGnHKPRMTGTPGS--DAPNVMHATEFLERVSFgekINVGETVAVIGGGFTANDSARTSLRLGA-KHVYIMYRRR 300
                                   5677887444554444333..3589**********9656668899************999888887654.5566666655 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 8.7
                   K_oxygenase 327 etlevdavvlATG 339
                                    t++vd+v+ ATG
  gi|13541988|ref|NP_111676.1| 370 YTIKVDMVIEATG 382
                                   6899********9 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   3.3e-06    0.0016       2      28 ..     147     173 ..     146     203 .. 0.92
   2 ?   -1.1   0.0       1.8   8.9e+02     417     452 .]     413     446 ..     385     446 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 3.3e-06
                                   HHHHHHHHHHHTTEEEEEEESSSSSBT CS
                 Amino_oxidase   2 aGLaaArqLlsaGfdVtvlEardrvGG 28 
                                   aGL++A++L+ +G++Vtv+E r+ +GG
  gi|13541988|ref|NP_111676.1| 147 AGLTVAYYLTLQGVKVTVFEERPALGG 173
                                   9************************** PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.8
                                   HCSTTEEE.SGGGCTTTTTS.HHHHHHHHHHHHHHHH CS
                 Amino_oxidase 417 egdprlffAGehtsreypgt.vegAilSGlraAaril 452
                                     +p++f  G++t    p + +  A++ G  a++ il
  gi|13541988|ref|NP_111676.1| 413 TSIPGVFTGGDSTN---PNRdLISAVRDGDIAVQGIL 446
                                   4799*********9...999999**999999998876 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   2.9   3.6e-06    0.0017       6      21 ..      38      53 ..      34      56 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 3.6e-06
                        Fer4_6  6 pdkCigCgdCvrvCPe 21
                                  +++CigC+ C ++CP+
  gi|13541988|ref|NP_111676.1| 38 ASRCIGCNMCSAACPA 53
                                  689************8 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   2.9   3.8e-06    0.0018       6      20 ..      39      53 ..      35      54 .. 0.91
   2 ?   -1.2   0.6       4.2     2e+03      13      18 ..      93      98 ..      92      98 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 3.8e-06
                                  TTSSS-THHHHHSTT CS
                          Fer4  6 ekCigCGaCvevCPv 20
                                  ++CigC+ C  +CP 
  gi|13541988|ref|NP_111676.1| 39 SRCIGCNMCSAACPA 53
                                  89************5 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 4.2
                                  HHHHHS CS
                          Fer4 13 aCvevC 18
                                   C++vC
  gi|13541988|ref|NP_111676.1| 93 MCEDVC 98
                                  6***** PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   6.7   1.7e-05    0.0083       3      37 ..      35      72 ..      33      99 .. 0.64

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.7e-05
                       Fer4_10  3 vidddtCirCgkCvkaCPadl...tsvgakgeaseeea 37
                                  + ++++Ci+C+ C +aCPa+l     v+ +++ ++ ++
  gi|13541988|ref|NP_111676.1| 35 IAEASRCIGCNMCSAACPASLdigGYVRSTAAGDPAQT 72
                                  67889**************8866633333333333333 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.8   6.2e-06     0.003      38      53 ..      38      53 ..      27      57 .. 0.78
   2 ?   -1.7   0.5         7   3.4e+03      14      22 ..      90      98 ..      85     102 .. 0.63

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 6.2e-06
                       Fer4_21 38 edeCvGCnlCssvCPv 53
                                  +++C+GCn+Cs+ CP 
  gi|13541988|ref|NP_111676.1| 38 ASRCIGCNMCSAACPA 53
                                  5789999999999995 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 7
                       Fer4_21 14 CliaCedts 22
                                  C+ +Ced +
  gi|13541988|ref|NP_111676.1| 90 CTHMCEDVC 98
                                  555565543 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.9   3.6   2.1e-05      0.01       5      22 .]      36      53 ..      33      53 .. 0.88
   2 ?   -0.8   0.5       4.4   2.1e+03      10      20 ..      90      98 ..      82     100 .. 0.62

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.1e-05
                        Fer4_2  5 vdtdrCigCgaCvsaCPa 22
                                  +++ rCigC+ C  aCPa
  gi|13541988|ref|NP_111676.1| 36 AEASRCIGCNMCSAACPA 53
                                  5678*************8 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 4.4
                        Fer4_2 10 CigCgaCvsaC 20
                                  C++   C ++C
  gi|13541988|ref|NP_111676.1| 90 CTH--MCEDVC 98
                                  554..344555 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.3   0.00021     0.099       2      30 ..     139     167 ..     138     178 .. 0.87
   2 ?    0.5   0.0      0.53   2.6e+02       2      26 ..     269     293 ..     268     313 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00021
                                   EEEE-SSHHHHHHHHHHHHTT--EEEEES CS
                          GIDA   2 viViGgGhAGceAAlaaarlGakvlLith 30 
                                   v V+GgG AG+  A+ +   G+kv+ + +
  gi|13541988|ref|NP_111676.1| 139 VAVVGGGPAGLTVAYYLTLQGVKVTVFEE 167
                                   89**********************99844 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.53
                                   EEEE-SSHHHHHHHHHHHHTT--EE CS
                          GIDA   2 viViGgGhAGceAAlaaarlGakvl 26 
                                   v ViGgG      A ++ rlGak +
  gi|13541988|ref|NP_111676.1| 269 VAVIGGGFTANDSARTSLRLGAKHV 293
                                   89*******************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 ?    8.0   0.0    0.0033       1.6      28      69 ..     128     169 ..     108     188 .. 0.83
   2 ?    3.9   0.0     0.062        30      34      88 ..     264     315 ..     243     321 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0033
                                   CGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSH CS
                  2-Hacid_dh_C  28 allgkelsgktvGiiGlGrIGqavakrlkafgmkviaydrsk 69 
                                   + + ++  gk+v+++G G  G +va +l+  g+kv++++ ++
  gi|13541988|ref|NP_111676.1| 128 KPQKRKFIGKRVAVVGGGPAGLTVAYYLTLQGVKVTVFEERP 169
                                   456678889***************************998775 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.062
                                   GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTCEECSHHHH CS
                  2-Hacid_dh_C  34 lsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeelgvelvsleel 88 
                                     g+tv++iG G  ++  a++   +g+k +++  ++++   +++ g+  ++ +e 
  gi|13541988|ref|NP_111676.1| 264 NVGETVAVIGGGFTANDSARTSLRLGAKHVYIMYRRRD---VDRPGYPSMNADEE 315
                                   4589***********************99888777663...44556655555555 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0    0.0001     0.048       1      43 [.     140     176 ..     140     195 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.0001
                 NAD_binding_9   1 aivGaGprGlavlerLlarakkkspleitlfdpsepgagrvwr 43 
                                   a+vG+Gp+Gl+v+  L  +      +++t+f+++++  g+  +
  gi|13541988|ref|NP_111676.1| 140 AVVGGGPAGLTVAYYLTLQ-----GVKVTVFEERPAL-GGFMK 176
                                   89**************999.....6********9996.56555 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0    0.0001     0.049      52      78 ..      32      58 ..      16      88 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 0.0001
                       Fer4_18 52 erkekgagdcidcescvkvcPtgidir 78
                                   ++ ++a+ ci c++c + cP  +di 
  gi|13541988|ref|NP_111676.1| 32 GEAIAEASRCIGCNMCSAACPASLDIG 58
                                  455677899****************94 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   4.1   0.00012     0.059       1      14 [.      40      53 ..      18      55 .. 0.72
   2 ?    9.2  10.6    0.0036       1.8       1      48 [.      40      98 ..      40     100 .. 0.48
   3 ?    0.3   0.4       2.3   1.1e+03       6      12 ..      92      98 ..      88     142 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 0.00012
                        Fer4_7  1 rCigCgaCvaaCpv 14
                                  rCigC+ C aaCp+
  gi|13541988|ref|NP_111676.1| 40 RCIGCNMCSAACPA 53
                                  56666666666664 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0036
                        Fer4_7  1 rCigCgaCvaaCpvkaieldeeenek...gtekveidpek.......ClgCga.CvavC 48
                                  rCigC+ C aaCp++     ++ + +   + ++++i +e+          C++ C++vC
  gi|13541988|ref|NP_111676.1| 40 RCIGCNMCSAACPASLDIGGYVRSTAagdPAQTIRIIMETlpfpaiiGRVCTHmCEDVC 98
                                  8***********95533322221111111224555555543333222112444466666 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 2.3
                        Fer4_7  6 gaCvaaC 12
                                  + C+++C
  gi|13541988|ref|NP_111676.1| 92 HMCEDVC 98
                                  3455555 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0     0.018       8.8       8      42 ..     132     165 ..     125     169 .. 0.86
   2 ?   -2.1   0.0       7.7   3.7e+03      69      91 ..     215     237 ..     208     245 .. 0.82
   3 ?    4.2   0.0     0.088        43      12      46 ..     266     300 ..     259     304 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.018
                                   S..TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEE CS
                  Shikimate_DH   8 eslkekkvlliGaGemaelvakhLlakgvkkvvva 42 
                                    ++ +k+v ++G G  +  va +L  +gvk v+v+
  gi|13541988|ref|NP_111676.1| 132 RKFIGKRVAVVGGGPAGLTVAYYLTLQGVK-VTVF 165
                                   466789***********************9.8886 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 7.7
                                   HHHHHHT-SEEEE-SSSSS-SB- CS
                  Shikimate_DH  69 lkellaeadvvisataseepile 91 
                                    ++l++e+d ++  ++ ++p ++
  gi|13541988|ref|NP_111676.1| 215 FEDLMKEYDAIFLGVGNHKPRMT 237
                                   46678999999999998888765 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.088
                                   T-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSH CS
                  Shikimate_DH  12 ekkvlliGaGemaelvakhLlakgvkkvvvaNRtl 46 
                                   +++v +iG G +a+  a+  l+ g+k+v ++ R +
  gi|13541988|ref|NP_111676.1| 266 GETVAVIGGGFTANDSARTSLRLGAKHVYIMYRRR 300
                                   5789**************************99865 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   5.6   0.00011     0.055       2      34 ..      38      71 ..      37     101 .. 0.68
   2 ?   -0.6   0.4       3.9   1.9e+03      10      16 ..      93      99 ..      88     132 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 0.00011
                        Fer4_8  2 lekCieCgaCqsaCpvlrrtk.khlldargeaae 34
                                  +++Ci+C +C +aCp+  + +   + +a g+ a+
  gi|13541988|ref|NP_111676.1| 38 ASRCIGCNMCSAACPASLDIGgYVRSTAAGDPAQ 71
                                  799************9999887888888888777 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 3.9
                        Fer4_8 10 aCqsaCp 16
                                  +C++ C 
  gi|13541988|ref|NP_111676.1| 93 MCEDVCV 99
                                  4555553 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   1.4   9.8e-05     0.047       2      16 ..      39      53 ..      38      62 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 9.8e-05
                        Fer4_4  2 erCigCgsCvaaCPq 16
                                  +rCigC  C aaCP 
  gi|13541988|ref|NP_111676.1| 39 SRCIGCNMCSAACPA 53
                                  69************4 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.1    0.0015      0.71       2      32 ..     139     169 ..     138     184 .. 0.92
   2 ?    1.0   0.0      0.71   3.4e+02       1      28 [.     268     296 ..     268     331 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0015
                                   EEEE--SCCHHHHHHHHHHTT-EEEEE-S-H CS
                       3HCDH_N   2 vaviGaGtmGagiaavfasagleVvlvdise 32 
                                   vav+G G  G  +a+ +  +g++V++++ ++
  gi|13541988|ref|NP_111676.1| 139 VAVVGGGPAGLTVAYYLTLQGVKVTVFEERP 169
                                   9*************************99766 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.71
                                   EEEEE--SCCHHHHHHHHHHTT-E.EEEE CS
                       3HCDH_N   1 kvaviGaGtmGagiaavfasagle.Vvlv 28 
                                   +vaviG G   +  a   ++ g + V ++
  gi|13541988|ref|NP_111676.1| 268 TVAVIGGGFTANDSARTSLRLGAKhVYIM 296
                                   69**********99999999987624444 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.3   0.00013     0.063      46      66 ..      33      53 ..      10      54 .. 0.81
   2 ?    0.6   0.3       2.3   1.1e+03      57      65 ..      90      99 ..      77     100 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 0.00013
                       Fer4_16 46 ekckkqeaitgCdiCqdvCPa 66
                                  e+  ++ +++gC++C ++CPa
  gi|13541988|ref|NP_111676.1| 33 EAIAEASRCIGCNMCSAACPA 53
                                  555667899999999999997 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 2.3
                       Fer4_16 57 Cd.iCqdvCP 65
                                  C  +C+dvC+
  gi|13541988|ref|NP_111676.1| 90 CThMCEDVCV 99
                                  6558999996 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1    0.0003      0.15       2      34 ..     139     169 ..     138     173 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0003
                 Lycopene_cycl   2 vvviGaGpAglslAarlteakpglkvvlieasp 34 
                                   v+v+G+GpAgl +A  l    +g+kv++ e  p
  gi|13541988|ref|NP_111676.1| 139 VAVVGGGPAGLTVAYYL--TLQGVKVTVFEERP 169
                                   89***************..77788888777655 PP

>> MCRA  MCRA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00045      0.22       3      62 ..     138     203 ..     136     223 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00045
                                   EEEEE--SHHHHHHHHHHHHTT---GGGEEEE-SS----------..........-------CCC----B CS
                          MCRA   3 kaylvGsGiasLaaAvyLirdakvpgenihileelkvaggsldga..........gdpekGyvlrggrel 62 
                                   ++ +vG+G a+L+ A+yL     ++g +++++ee + +gg +++            d+e Gy+l  g ++
  gi|13541988|ref|NP_111676.1| 138 RVAVVGGGPAGLTVAYYL----TLQGVKVTVFEERPALGGFMKTGipryrlpqnvLDKEIGYILSRGVQV 203
                                   5668**************....5899****************9888999999888888889998888766 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.2    0.0006      0.29       1      33 [.     138     167 ..     138     173 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0006
                                   EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE- CS
                Trp_halogenase   1 kivivGGGtaGwlaAaalakalkgklevtlves 33 
                                   ++ +vGGG+aG ++A +l  ++   ++vt+ e 
  gi|13541988|ref|NP_111676.1| 138 RVAVVGGGPAGLTVAYYLTLQG---VKVTVFEE 167
                                   689***************9999...88998775 PP

>> Stb3  Putative Sin3 binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00073      0.35      18      49 ..     104     135 ..      91     147 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00073
                          Stb3  18 kGPlaiRhitaalttsvpgFsklspskaRRlv 49 
                                    GP+aiRh+ ++ +++   + ++ + ++R+++
  gi|13541988|ref|NP_111676.1| 104 GGPIAIRHLKRYAADKFDDYGEILKPQKRKFI 135
                                   59**********************99999987 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   0.9   0.00027      0.13       4      21 ..      39      56 ..      37      69 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00027
                       Fer4_13  4 dtCiacgaCvelaPdvFe 21
                                  ++Ci+c+ C +++P   +
  gi|13541988|ref|NP_111676.1| 39 SRCIGCNMCSAACPASLD 56
                                  79************8765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (484 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       507  (0.0282782); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                        38  (0.00211947); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              37  [number of targets reported over threshold]
# CPU time: 0.65u 0.32s 00:00:00.97 Elapsed: 00:00:00.47
# Mc/sec: 3102.54
//
Query:       gi|13541989|ref|NP_111677.1|  [L=406]
Description: cofactor-independent phosphoglycerate mutase [Thermoplasma volcanium GSS1]
Scores for complete 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-54  182.6   0.0    1.2e-53  181.5   0.0    1.5  2  PhosphMutase   2,3-bisphosphoglycerate-independent phosphogly
    5.5e-34  117.6   0.0    6.7e-34  117.4   0.0    1.0  1  Metalloenzyme  Metalloenzyme superfamily
  ------ inclusion threshold ------
      0.077   12.6   0.3        2.9    7.4   0.0    2.1  2  Phosphodiest   Type I phosphodiesterase / nucleotide pyrophos


Domain annotation for each model (and alignments):
>> PhosphMutase  2,3-bisphosphoglycerate-independent phosphoglycerate mutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  181.5   0.0     2e-57   1.2e-53       1     170 []      41     207 ..      41     207 .. 0.98
   2 ?   -2.5   0.0      0.69   4.1e+03     106     136 ..     328     357 ..     300     398 .. 0.60

  Alignments for each domain:
  == domain 1  score: 181.5 bits;  conditional E-value: 2e-57
                                   HHTSEEEEEE-----------TCHHHHTT--HHCH---HHHHHHHHTT----TT-EEEEEEEEEEC..TTCEEETTGGG-. CS
                  PhosphMutase   1 AkkGetGlldtvpegiapgSdvAnlsilGydpkkyytGRGplEAlgiGlelkpgdvafRcnlvtvdeedgiiidrragris 81 
                                   A+ G+tGl++++++gi+ gSd++++s+lGydp+ yy+GRGp+EAlg+ +++kpgd+afR+n++t   +dg+iidrragri 
  gi|13541989|ref|NP_111677.1|  41 ASLGMTGLMHPISPGIRSGSDTSHMSLLGYDPRVYYQGRGPFEALGLHMDMKPGDLAFRANFATN--RDGKIIDRRAGRI- 118
                                   788**************************************************************..58***********. PP

                                   -TTHHHHHHHT-EEE.TTEEEEEEE-STTEEEEEE....--S-B--S--..SSTTS------BS.SGGGHHHHHHHHHHHH CS
                  PhosphMutase  82 teeakeLikalneeleegvevkfypgveyrhllvl....lsdkitdtdpphdkegkeikellplkseeaketaellnelie 158
                                   +  +++L++a++ ++  ++++++++gve+r++lv+    lsdki+d+dp  + egk+++++ pl +++a  ta+++ne+++
  gi|13541989|ref|NP_111677.1| 119 NAGNDQLASAISIDI-GNYKFRVKSGVEHRAALVVsgpnLSDKISDSDP--HSEGKPPEPIRPL-DPSADSTAKIMNEYLK 195
                                   999************.479******************************..************8.799************* PP

                                   HHHHHHHHSHHH CS
                  PhosphMutase 159 ksqeiLedhpvN 170
                                   +++eiL+dhpvN
  gi|13541989|ref|NP_111677.1| 196 RIREILRDHPVN 207
                                   ***********9 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.69
                                   E-STTEEEEEE--S-B--S--..SSTTS--- CS
                  PhosphMutase 106 pgveyrhllvllsdkitdtdpphdkegkeik 136
                                    g + r ++ + +d+ t +    d++g ++ 
  gi|13541989|ref|NP_111677.1| 328 LGQSDRIVVAITGDHSTPCSV-KDHSGDPVP 357
                                   455566666666666666665.566666554 PP

>> Metalloenzyme  Metalloenzyme superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.4   0.0   1.1e-37   6.7e-34       1     244 [.       5     394 ..       5     397 .. 0.96

  Alignments for each domain:
  == domain 1  score: 117.4 bits;  conditional E-value: 1.1e-37
                                   -EEEEEEETTBB----GGGTT...HHHS--HHHHHHHHH.......SEEEEEESSSTT----HHHHHHHH........... CS
                                   xxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........... RF
                 Metalloenzyme   1 kkvvlvvlDGlGeapadelna...ihvAktPtldkLkkeaPerwlikahgtavglpeddmgnsevgHlel........... 67 
                                   k ++l+vlDGlG++p + l+    ++ A  P++++++         +++g++ ++  +++++s+++H++l           
  gi|13541989|ref|NP_111677.1|   5 KSIILIVLDGLGDRPGEILGYrtpLQAAYHPNMNRMASL-------GMTGLMHPISPGIRSGSDTSHMSLlgydprvyyqg 78 
                                   5789************99988999************998.......89********************************* PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                 Metalloenzyme  68 ................................................................................. 67 
                                                                                                                    
  gi|13541989|ref|NP_111677.1|  79 rgpfealglhmdmkpgdlafranfatnrdgkiidrragrinagndqlasaisidignykfrvksgvehraalvvsgpnlsd 159
                                   ********************************************************************************* PP

                                   .................................................HHHHTT-----EEEEEEEE-S---SSHHHHHT CS
                                   .................................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Metalloenzyme  68 .................................................lrisetvkfahvtffwnggrsgyfnpleeree 99 
                                                                                     r ++++ +++ ++++++g+ +++++++e+ +
  gi|13541989|ref|NP_111677.1| 160 kisdsdphsegkppepirpldpsadstakimneylkrireilrdhpvnvEREKNGQIPGNELLIRSAGKVPDIPSFQEKNG 240
                                   *************************************************999***************************** PP

                                   --EEEE--SHH....................STT--HHHHHHHHHHHH.CC.-SEEEEEE-HHHHHHHTT-HHHHHHHHHH CS
                                   xxxxxxxxxxx....................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Metalloenzyme 100 ipsdtvitfdl....................qpemkavevaekaldailsgkfdlvvvniknaDmvGHtgdleatiaaiea 160
                                   i +++v+                        + + ++  +++ a+da   +++d+v+vnik +D +GH+gd+e + ++ie+
  gi|13541989|ref|NP_111677.1| 241 ITGACVVGSPWlkglcrllgmavidvpgaagTINSNYTGKIKTAIDAS--KRYDFVLVNIKATDVAGHDGDYELKRRVIED 319
                                   *******99999****************99999999999999999997..56***************************** PP

                                   HHHHHHHHHTTS-TTTEEEEEE-SSB--TTTSS........-----EEEEEESTT----S--S.SHHHHTT-TTEEEEGGG CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxx RF
                 Metalloenzyme 161 aDeavkeildaieqvdgilvvtADHgnaedmvkrdkqplTsHtlepVPilivgkglapdkvke.gakfrekggLanvaatl 240
                                   +D a++ +l +  ++  ++++t+DH+++ ++++        H+ +pVPi+++ +g+  d+vk  ++ ++ kg L    + +
  gi|13541989|ref|NP_111677.1| 320 IDIAMEPLLGQ--SDRIVVAITGDHSTPCSVKD--------HSGDPVPIVFYTDGIYSDDVKLfDEVSAMKGALRITTQDV 390
                                   ********976..7788899*************........********************99888888899997666666 PP

                                   HHHH CS
                                   xxxx RF
                 Metalloenzyme 241 lnll 244
                                   ln+l
  gi|13541989|ref|NP_111677.1| 391 LNIL 394
                                   6655 PP

>> Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0     0.008        48       2      43 ..       8      55 ..       7      68 .. 0.86
   2 ?    7.4   0.0   0.00048       2.9     170     233 ..     285     343 ..     256     381 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.008
                                  EEEEETT-B......TTHHHHHG.STSHHHHHHHHHSEEESEEE-SSS- CS
                  Phosphodiest  2 lvislDGlr......adlldrla.ellpnlaaLakegvsapnlrpvfPt 43
                                  ++i+lDGl         +  +l+    pn++++a+ g ++  ++p+ P 
  gi|13541989|ref|NP_111677.1|  8 ILIVLDGLGdrpgeiLGYRTPLQaAYHPNMNRMASLGMTGL-MHPISPG 55
                                  8999****99999888888888877****************.***9985 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.00048
                                   T...SSESEEEEEECCCHHHHHHH-TTSHHHHHHHHHHHHHHHHHHHHHHHTTGTTTEEEEEEES-- CS
                  Phosphodiest 170 l...ekpdlllvyleetDtvgHkfGpdspevedalrrvDkaigdLlealderglsaetniilvSDHG 233
                                       +++d++lv++ +tD +gH    ++   +  ++++D a++ Ll + d+        + +++DH 
  gi|13541989|ref|NP_111677.1| 285 IdasKRYDFVLVNIKATDVAGHDG-DYEL-KRRVIEDIDIAMEPLLGQSDRI------VVAITGDHS 343
                                   133399****************65.3333.4778899999999999998865......699999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (406 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       364  (0.0203023); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.43
# Mc/sec: 2826.41
//
Query:       gi|13541990|ref|NP_111678.1|  [L=180]
Description: hypothetical protein TVN1159 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.017   15.2   0.4      0.086   13.0   0.0    2.2  3  Phage_holin_3_3  LydA holin phage, holin superfamily III
       0.39   10.9  17.9         44    4.2  17.9    2.1  1  DUF5518          Family of unknown function (DUF5518)


Domain annotation for each model (and alignments):
>> Phage_holin_3_3  LydA holin phage, holin superfamily III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1      0.33     3e+03      64      72 ..      47      55 ..      40      60 .. 0.82
   2 ?   -2.0   0.2      0.44     4e+03      22      22 ..      58      58 ..      48      81 .. 0.52
   3 ?   13.0   0.0   9.6e-06     0.086       2      24 ..     138     160 ..     137     165 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.33
               Phage_holin_3_3 64 glsGylGar 72
                                  +l+GylG+r
  gi|13541990|ref|NP_111678.1| 47 ALAGYLGGR 55
                                  789999987 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.44
               Phage_holin_3_3 22 g 22
                                  g
  gi|13541990|ref|NP_111678.1| 58 G 58
                                  2 PP

  == domain 3  score: 13.0 bits;  conditional E-value: 9.6e-06
               Phage_holin_3_3   2 liivlAllGGlvsylmrakkgrr 24 
                                   +++++++lGG+vs l+r + g++
  gi|13541990|ref|NP_111678.1| 138 IVVIFSILGGFVSNLRRSETGSE 160
                                   799***************99843 PP

>> DUF5518  Family of unknown function (DUF5518)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2  17.9    0.0049        44      15     114 ..      30     149 ..      26     152 .. 0.71

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.0049
                       DUF5518  15 slllglllpsvgsllgllvgGlvaGylaggdskdgavaGalaGligaipvlvlllvlll...................... 73 
                                   ++ll+    sv+  + +++g ++aGyl g+ ++ + +aG+++ l ++  ++++++ ll                       
  gi|13541990|ref|NP_111678.1|  30 YTLLF----SVLLWWMPVIGPALAGYLGGR-KSGSIRAGLISSLTVSGLFVIVSISLLPykdsilgkvgqyisygvlpisg 105
                                   33333....56666999**********966.56788888888876665554444444446899999999999999999999 PP

                       DUF5518  74 ...glvaaigglagfvallvalllvvllllvvllvilgaiGGai 114
                                      + v+ +++ +  +++++  +++++  +++++vi++++GG++
  gi|13541990|ref|NP_111678.1| 106 snlVSVSNLATYLYSSVGFAYTFFLLVPSSLMIVVIFSILGGFV 149
                                   98745555555555555555555666888999999999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       566  (0.031569); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); 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 0.28s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1164.24
//
Query:       gi|13541991|ref|NP_111679.1|  [L=454]
Description: proline/betaine transport permease [Thermoplasma volcanium GSS1]
Scores for complete 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-26   91.8  45.2    3.8e-26   91.8  45.2    2.1  2  MFS_1     Major Facilitator Superfamily
    1.7e-24   86.6  38.4    2.4e-18   66.3   8.6    2.8  3  Sugar_tr  Sugar (and other) transporter
  ------ inclusion threshold ------
        4.4    7.1   6.3        9.2    6.1   0.2    2.6  2  Lig_chan  Ligand-gated ion channel


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 !   91.8  45.2   6.4e-30   3.8e-26       2     345 ..      28     389 ..      27     397 .. 0.77
   2 ?    1.0   5.8     0.027   1.6e+02     223     264 ..     393     442 ..     385     451 .. 0.72

  Alignments for each domain:
  == domain 1  score: 91.8 bits;  conditional E-value: 6.4e-30
                         MFS_1   2 llaaflsalarsilgpalplalaedlg......ispseigllltlyalgaavaslplGrlsdrfGrrr.vlllglllfalg 75 
                                   +l+++l +++ +++++++p  +a  l       i++ ++ l+++l  ++  v+s ++G+++dr+Grr  ++++ l l +++
  gi|13541991|ref|NP_111679.1|  28 FLGFLLDSFDLTMILSIAP-VVAAVLLppssplIAVFSVILAYSLTIIFRPVGSAIFGHIGDRLGRRTdLIITVLGLGIVS 107
                                   7899999999999999999.666666645444455555777777777788******************6666666666666 PP

                         MFS_1  76 lllll...fass....lw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllassl 148
                                   +l  +   +a s    ++ l+++ r++ G++ag+ ++ag+ ++ +w+p + rg+  gl+++gfs+Ga+ +++  +++++ +
  gi|13541991|ref|NP_111679.1| 108 ALTSAlptYA-SvgilSFvLFIIIRIFVGIFAGGEYSAGHPFVMEWTPFRWRGLISGLVQGGFSFGALAAAATVAVFTHIY 187
                                   3333323332.234446669************************************************************* PP

                         MFS_1 149 g........Wravfyilaivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfff 221
                                   g        Wr++f+   i +++a     l ++ + ++ + +++ +e+++  ++p+++++k+ +++ +l  ++i + ++ff
  gi|13541991|ref|NP_111679.1| 188 GetglvsyaWRYLFLTTLIPAAIA-----LAIRLSMKDTPIFTELKEKNKIRRSPFIDLFKKPVRKDFLQ-VMIWMTGMFF 262
                                   ************************.....44444444444444444444569999999888888888663.4444444444 PP

                         MFS_1 222 gfsglltllplylqevlgls....glllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavt. 297
                                     ++l++++p++  e+   s    +l la++++ ++ ++++++a+ +g  s+++grr+ +l+  + ++++++ +++  +  
  gi|13541991|ref|NP_111679.1| 263 YAYALFAYVPTI-LEHAP-SawssNLGLATTVYTIGTAGAFFGAFGFGIASQKVGRRKLTLIWAIMTIIISVPMYYGLMRa 341
                                   5566*******5.33333.236695555555699999999999************98888888888888888888888888 PP

                         MFS_1 298 ...ssavllllvlvliGf.glgfvfpsllalasdlappeeagtasglfntag 345
                                       + +l++l++++iG+ ++g  ++++ +++s+ + +  +++ +g+    +
  gi|13541991|ref|NP_111679.1| 342 aelGNVPLAVLMSIIIGIvTQG-PWGIVPVYLSERFKTAVRASGVGFG---Y 389
                                   888889999999******6666.5************555555555443...3 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.027
                         MFS_1 223 fsg...lltllpl...ylqevlgls..glllaglllallalvgailalla 264
                                   +++   +++++pl   yl +  + s   ++++++ll+++a++++i++ ++
  gi|13541991|ref|NP_111679.1| 393 IFIggwFSIYVPLmhnYLFKSIDTStnIWFSTAVLLMIGAIIIFIGQWIG 442
                                   22235677777775567778888889999999999999999999987654 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.23   1.4e+03      60      86 ..      23      49 ..      21      66 .. 0.81
   2 !   66.3   8.6   3.9e-22   2.4e-18      50     204 ..      67     231 ..      61     238 .. 0.91
   3 !   25.6  20.6   8.3e-10     5e-06      49     194 ..     290     445 ..     250     451 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.23
                                  HHHHHHHHHHHHHTTHHHHHHHHHHHH CS
                      Sugar_tr 60 iiGslfagllgdrfGRkkslliaavlf 86
                                  + Gs f+g+l d f+   +l ia v++
  gi|13541991|ref|NP_111679.1| 23 ATGSQFLGFLLDSFDLTMILSIAPVVA 49
                                  689999999999999888777766554 PP

  == domain 2  score: 66.3 bits;  conditional E-value: 3.9e-22
                                   HHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTT.....SS-TGGGGGHHHHHHHHHHHHHHHHH CS
                      Sugar_tr  50 livsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgk.....nsvevlivgRvlvGigvGlasvlvPm 125
                                   l  s++++ + +Gs ++g +gdr+GR+  l+i+++ + i ++l+ a + +      s+ ++i+ R++vGi++G+++     
  gi|13541991|ref|NP_111679.1|  67 LAYSLTIIFRPVGSAIFGHIGDRLGRRTDLIITVLGLGIVSALTSALPTYasvgiLSFVLFIIIRIFVGIFAGGEYSAGHP 147
                                   567899999***********************99988888888777776778888899999999***************** PP

                                   HHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-.....TTHHHHHHHCCHHHHHHHHHHGGGS---HHHHHHT CS
                      Sugar_tr 126 yisEiApkklRgalvslyqlaitfGilvaaifglglnktsn.....adgwrillglqlvpallllilllflPESPrylvek 201
                                   ++ E +p ++Rg + +l q + +fG l aa + +++ ++ +     +  wr+l+  +l+pa + l+++l + ++P ++  k
  gi|13541991|ref|NP_111679.1| 148 FVMEWTPFRWRGLISGLVQGGFSFGALAAAATVAVFTHIYGetglvSYAWRYLFLTTLIPAAIALAIRLSMKDTPIFTELK 228
                                   ************************************888777****9******************************9888 PP

                                   T-H CS
                      Sugar_tr 202 gke 204
                                   +k 
  gi|13541991|ref|NP_111679.1| 229 EKN 231
                                   775 PP

  == domain 3  score: 25.6 bits;  conditional E-value: 8.3e-10
                                   HHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTT....SS-TGGGGGHHHHHHHHHHHHHHHHH CS
                      Sugar_tr  49 glivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgk....nsvevlivgRvlvGigvGlasvlvPm 125
                                   + +  i  +Ga++G++ +g++++++GR+k  li a++++i +v ++    +     +v + +++ +++Gi   +  ++vP+
  gi|13541991|ref|NP_111679.1| 290 TTVYTIGTAGAFFGAFGFGIASQKVGRRKLTLIWAIMTIIISVPMYYGLMRaaelGNVPLAVLMSIIIGIVTQGPWGIVPV 370
                                   44555667899**************************99999966543322334489************************ PP

                                   HHHTTS-SCCH.HHHHHHHHHHHHHHHHHHHHHHHHHHTSS-.....TTHHHHHHHCCHHHHHHHHHHGGGS--- CS
                      Sugar_tr 126 yisEiApkklR.galvslyqlaitfGilvaaifglglnktsn.....adgwrillglqlvpallllilllflPES 194
                                   y+sE  ++++R + ++  y ++i +G  +++ + l  n+  +     ++ w  +  l ++ a++++i+ +  PE+
  gi|13541991|ref|NP_111679.1| 371 YLSERFKTAVRaSGVGFGYSSGIFIGGWFSIYVPLMHNYLFKsidtsTNIWFSTAVLLMIGAIIIFIGQWIGPET 445
                                   ***********777888899999999888887777666666677779999******************9999998 PP

>> Lig_chan  Ligand-gated ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   1.5     0.015        89      49      86 ..     298     331 ..     252     337 .. 0.59
   2 ?    6.1   0.2    0.0015       9.2       2      28 ..     418     444 ..     417     451 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.015
                                   HHHHHHHHHH.HHHHXXXXXXXXXXXXXXXXXXXXXXXX CS
                                   xxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Lig_chan  49 slwfslgalv.qqGcdesprsvsgRivvavWwffvlill 86 
                                   +     ga++   G  ++ ++v  R ++++W+++++i+ 
  gi|13541991|ref|NP_111679.1| 298 A-----GAFFgAFGFGIASQKVGRRKLTLIWAIMTIIIS 331
                                   2.....333303367799999***************985 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0015
                                   XXXXXXXXTXXXXXXXXXXXXXXXXXX CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Lig_chan   2 levWlsvlvalilvsivlflverfspy 28 
                                   +++W+s++v+l++ +i++f+ +++ p 
  gi|13541991|ref|NP_111679.1| 418 TNIWFSTAVLLMIGAIIIFIGQWIGPE 444
                                   78******************9999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (454 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       753  (0.041999); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.61u 0.27s 00:00:00.88 Elapsed: 00:00:00.45
# Mc/sec: 3053.91
//
Query:       gi|13541992|ref|NP_111680.1|  [L=399]
Description: carnitine dehydratase [Thermoplasma volcanium GSS1]
Scores for complete 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-129  431.6   0.0   2.7e-129  431.5   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 !  431.5   0.0  1.5e-133  2.7e-129       1     368 []       5     371 ..       5     371 .. 1.00

  Alignments for each domain:
  == domain 1  score: 431.5 bits;  conditional E-value: 1.5e-133
                  CoA_transf_3   1 LaGvrVldlsqvlaGplatslLAdlGAeVIkvEppkkgDpaRkvgpseekgesayflavnrnKrsvalDlkseegrellkr 81 
                                   L+G++++d+++ + Gp+at++L+dlGAeVIkvE+p +gD++R + p   +g+sayfl+vnrnK+s+++Dlk+ egr++++r
  gi|13541992|ref|NP_111680.1|   5 LSGIKIIDFTRAMSGPFATMILGDLGAEVIKVESP-EGDETRSWVPPMMNGQSAYFLSVNRNKKSIVVDLKKSEGRDIALR 84 
                                   89*********************************.**********999******************************** PP

                  CoA_transf_3  82 LvakADVvieNfrpgvlerlglgyeelrainPrLiyasvsgyGqsGpkakrpgyDlvaqaasGlmsltgepdgpPvkvgvp 162
                                   L++ +D+v+eNfrpgv+e+lg++ye+ +++n ++iy+s+sgyG++Gp+    g+Dl + a sGlms+tgep+g Pvk gvp
  gi|13541992|ref|NP_111680.1|  85 LIEGSDIVVENFRPGVAEKLGISYEDAKRVNQNVIYCSISGYGSTGPYMGLSGFDLSVMAFSGLMSITGEPNGGPVKFGVP 165
                                   ********************************************************************************* PP

                  CoA_transf_3 163 lgDivtgllaavailaallarertGkGqvidvslleaalallapqlleylatgevperqgnrdpaaapygvyrtkdgwvai 243
                                   ++Divtg++aa++i  al+ r++tG+Gq id++++++a+ +l  q+++ +atg+ p + g+++ ++apy+++rtkdg+++i
  gi|13541992|ref|NP_111680.1| 166 IVDIVTGMFAAISIISALRFRDKTGEGQYIDTAMIDSAVGILTHQATYFFATGKDPVKLGSAHSSIAPYQAFRTKDGYIVI 246
                                   *********************************************************99********************** PP

                  CoA_transf_3 244 aaatdkqwaalckalgrpelaedprfatnasrlenraeldaelaewlaertaaewlellaaagvpaapvntleevlddpql 324
                                    a+++k w++lc+a++ pel++dprf tn+ r++nr el   ++++l   ++ ++   l+++gvp++pvnt++e+l+++q+
  gi|13541992|ref|NP_111680.1| 247 TAGSQKIWENLCDAIEMPELKQDPRFMTNELRVKNRYELVPVIEQYLTRLSTSQAYSKLTKYGVPCSPVNTVSEALKSDQV 327
                                   ********************************************************************************* PP

                  CoA_transf_3 325 aarglvvevddpdygevpvvglpvrlsetparvkraaPklGedt 368
                                   + r++vv v    yg+v++ ++p+++s+tp+++ +a+P lG++t
  gi|13541992|ref|NP_111680.1| 328 NYRDMVVGVFSDIYGKVKLINSPLKMSRTPGQIFSAPPVLGQHT 371
                                   *******************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (399 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 2560.97
//
Query:       gi|13541993|ref|NP_111681.1|  [L=143]
Description: transcription regulator (SlyA-related) [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      1e-09   38.2   0.0      2e-09   37.3   0.0    1.5  1  MarR            MarR family
      2e-09   37.2   0.0    3.3e-09   36.5   0.0    1.4  1  MarR_2          MarR family
    1.6e-06   28.5   0.1    3.1e-06   27.6   0.1    1.5  1  HTH_27          Winged helix DNA-binding domain
    7.4e-05   22.9   0.1    0.00043   20.4   0.0    2.0  2  HTH_34          Winged helix DNA-binding domain
    9.2e-05   22.2   0.0     0.0002   21.1   0.0    1.6  1  HTH_5           Bacterial regulatory protein, arsR family
     0.0041   17.0   0.1      0.012   15.4   0.0    1.7  2  TrmB            Sugar-specific transcriptional regulator TrmB
     0.0044   17.0   0.0     0.0074   16.3   0.0    1.4  1  HTH_20          Helix-turn-helix domain
     0.0047   16.9   0.1      0.012   15.6   0.0    1.7  2  HTH_29          Winged helix-turn helix
     0.0063   16.5   0.1      0.026   14.5   0.0    2.0  2  HTH_Crp_2       Crp-like helix-turn-helix domain
     0.0093   16.3   0.0        0.2   12.0   0.0    2.2  2  Rrf2            Transcriptional regulator
  ------ inclusion threshold ------
      0.021   14.7   0.0      0.054   13.4   0.0    1.6  1  HTH_11          HTH domain
      0.023   14.9   0.0      0.045   14.0   0.0    1.5  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
      0.034   13.9   0.0      0.087   12.6   0.0    1.6  1  HTH_DeoR        DeoR-like helix-turn-helix domain
      0.035   14.2   0.0      0.059   13.5   0.0    1.4  1  DprA_WH         DprA winged helix domain
      0.039   13.5   0.2      0.052   13.1   0.2    1.5  1  AbiJ_NTD3       AbiJ N-terminal domain 3
      0.043   13.6   0.0      0.065   13.0   0.0    1.3  1  RQC             RQC domain
      0.046   13.6   0.0      0.081   12.8   0.0    1.5  1  HxlR            HxlR-like helix-turn-helix
      0.057   13.4   0.2       0.14   12.1   0.2    1.7  1  Sdh5            Flavinator of succinate dehydrogenase


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 !   37.3   0.0     2e-12     2e-09       5      59 .]      40      93 ..      38      93 .. 0.91

  Alignments for each domain:
  == domain 1  score: 37.3 bits;  conditional E-value: 2e-12
                                  HHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEETTSTTSE CS
                          MarR  5 qfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRskspeDrRev 59
                                  +++iL++l+e ++ +v +La+   v+++ +t +ld++e +Gli Rs+s eDrR+v
  gi|13541993|ref|NP_111681.1| 40 EVRILYLLSEDES-TVNKLAELTDVTPAWITGTLDEMESQGLIVRSRSGEDRRVV 93
                                  5678888877655.899************************************97 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.5   0.0   3.3e-12   3.3e-09       5      61 ..      38      91 ..      34      92 .. 0.96

  Alignments for each domain:
  == domain 1  score: 36.5 bits;  conditional E-value: 3.3e-12
                                  HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSSSSS CS
                        MarR_2  5 paqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpgpeDkR 61
                                  p + r+L+ L   +    tv+ la+ ++++++ ++ +l++++++GL++r+++ eD+R
  gi|13541993|ref|NP_111681.1| 38 PIEVRILYLLSEDES---TVNKLAELTDVTPAWITGTLDEMESQGLIVRSRSGEDRR 91
                                  7899******99996...**************************************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 !   27.6   0.1   3.1e-09   3.1e-06       3      68 .]      38     101 ..      36     101 .. 0.94

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 3.1e-09
                        HTH_27   3 rqqalvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68 
                                   + ++ +L l+   +++++   l++ ++v+ + i   l++++ +GL++r+++ +drr + v +T+kG
  gi|13541993|ref|NP_111681.1|  38 PIEVRILYLLS--EDESTVNKLAELTDVTPAWITGTLDEMESQGLIVRSRSGEDRRVVNVHITEKG 101
                                   56777888898..999*************************************************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 !   20.4   0.0   4.3e-07   0.00043       7      71 ..      44     107 ..      39     118 .. 0.92
   2 ?    2.2   0.0       0.2     2e+02       8      40 ..     104     137 ..     102     141 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 4.3e-07
                        HTH_34   7 syLasvdeadfvelkealeatdgnLsvhlkkLekagYievdkefkgkkprtllriTpeGreafkk 71 
                                    yL+s+de + ++l e + +t + +   l+ +e++g i+++ + +++ +   + iT++G e  ++
  gi|13541993|ref|NP_111681.1|  44 LYLLSEDESTVNKLAELTDVTPAWITGTLDEMESQGLIVRSRSGEDR-RVVNVHITEKGIEVLNE 107
                                   5999****************************************999.9**********987765 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.2
                        HTH_34   8 yLasvdeadfvelkeale.atdgnLsvhlkkLek 40 
                                   +L++ +++   +lk +l+ +td++L    ++L+k
  gi|13541993|ref|NP_111681.1| 104 VLNESQKVYLDFLKRSLSsLTDSELDEFRRILKK 137
                                   7888889999999988853899999877777766 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     2e-07    0.0002       4      45 ..      40      81 ..      37      82 .. 0.90

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 2e-07
                                  HHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                         HTH_5  4 RlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLV 45
                                   ++IL+lL+e e +v  lae ++++++ +   L  ++ +GL+
  gi|13541993|ref|NP_111681.1| 40 EVRILYLLSEDESTVNKLAELTDVTPAWITGTLDEMESQGLI 81
                                  589***********************9998888888888886 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.2e-05     0.012      15      58 ..      44      87 ..      37      97 .. 0.89
   2 ?   -1.9   0.0       3.1   3.1e+03      12      21 ..     110     119 ..     106     134 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.2e-05
                                  HHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                          TrmB 15 laLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr 58
                                  l+Ll+++++t++++ae ++v  + +  +L ++e+ Gl+ r+++ 
  gi|13541993|ref|NP_111681.1| 44 LYLLSEDESTVNKLAELTDVTPAWITGTLDEMESQGLIVRSRSG 87
                                  589***********************************999864 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3.1
                                   CHCHHHHHHC CS
                          TrmB  12 kvYlaLlklg 21 
                                   kvYl  lk+ 
  gi|13541993|ref|NP_111681.1| 110 KVYLDFLKRS 119
                                   6777777443 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   7.4e-06    0.0074      10      60 ..      38      87 ..      30      88 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 7.4e-06
                                  HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTE CS
                        HTH_20 10 PvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvreg 60
                                  P   ril +L ++++ t++ lae+ d++++ +   L+++e+ gL+ + r+g
  gi|13541993|ref|NP_111681.1| 38 PIEVRILYLL-SEDESTVNKLAELTDVTPAWITGTLDEMESQGLIVRSRSG 87
                                  777899999*.***********************************99998 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.2e-05     0.012       4      54 ..      43      90 ..      41      94 .. 0.87
   2 ?   -2.3   0.0       4.9   4.9e+03      28      38 ..     130     140 ..     128     141 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.2e-05
                        HTH_29  4 allllaeGvstvsqiAkllglsrrtvyrwlkrfeegGlaalldrrrsgrpr 54
                                  +l ll+e +stv  +A+l+++++ ++  +l+ +e  G   l+ r rsg  r
  gi|13541993|ref|NP_111681.1| 43 ILYLLSEDESTVNKLAELTDVTPAWITGTLDEMESQG---LIVRSRSGEDR 90
                                  77799999*****************************...77777788655 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 4.9
                        HTH_29  28 tvyrwlkrfee 38 
                                    ++r+lk  ee
  gi|13541993|ref|NP_111681.1| 130 EFRRILKKIEE 140
                                   58999999887 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   2.6e-05     0.026      24      55 ..      54      85 ..      43     100 .. 0.83
   2 ?   -0.7   0.0       1.4   1.4e+03      18      44 ..     111     137 ..      90     141 .. 0.62

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.6e-05
                                  HHHHHHHTTSSHHHHHHHHHHHHHTTSEEETE CS
                     HTH_Crp_2 24 qeelAsmlGltretvsrilseLkreglisrgr 55
                                     lA++  +t+  ++ +l e++ +gli r+r
  gi|13541993|ref|NP_111681.1| 54 VNKLAELTDVTPAWITGTLDEMESQGLIVRSR 85
                                  5689*************************532 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.4
                                   EEEEHHHHHHHHHTTSSHHHHHHHHHH CS
                     HTH_Crp_2  18 ielpltqeelAsmlGltretvsrilse 44 
                                   + l++ ++ l+s+  +    + ril++
  gi|13541993|ref|NP_111681.1| 111 VYLDFLKRSLSSLTDSELDEFRRILKK 137
                                   445555566666666666666666665 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.0   0.00021       0.2      19      60 ..      46      87 ..      38      90 .. 0.80
   2 ?    2.1   0.0      0.24   2.4e+02      28      54 ..     102     128 ..      95     133 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00021
                                  HSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSE.EEETT CS
                          Rrf2 19 keeeeepvsseeiaerqnispsylekilakLrkaglv.ksvrG 60
                                  + +e+e  +++++ae +++ p  +   l +++ +gl+ +s+ G
  gi|13541993|ref|NP_111681.1| 46 LLSEDE-STVNKLAELTDVTPAWITGTLDEMESQGLIvRSRSG 87
                                  334444.79**************************85267777 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.24
                                   HHHHHHHHTS-HHHHHHHHHHHHHTTS CS
                          Rrf2  28 seeiaerqnispsylekilakLrkagl 54 
                                   +e + e+q++   +l++ l+ L+ ++l
  gi|13541993|ref|NP_111681.1| 102 IEVLNESQKVYLDFLKRSLSSLTDSEL 128
                                   677899****************98876 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   5.4e-05     0.054       5      51 ..      43      87 ..      41      88 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.4e-05
                        HTH_11  5 ilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgvpIesepg 51
                                  il lL e ++  + ++LAe ++v+ + +   ++++e++g+ + s++g
  gi|13541993|ref|NP_111681.1| 43 ILYLLSEDES--TVNKLAELTDVTPAWITGTLDEMESQGLIVRSRSG 87
                                  7888866665..9***************************9999887 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   4.5e-05     0.045      12      53 ..      43      82 ..      41      87 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.5e-05
                                  HHHHHHHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                Fe_dep_repress 12 tIYtlseekkvvktkdlaerLnvspssVsemlkkLekdGyve 53
                                   +Y lse+++   + +lae  +v p+ ++ +l ++e++G+++
  gi|13541993|ref|NP_111681.1| 43 ILYLLSEDEST--VNKLAELTDVTPAWITGTLDEMESQGLIV 82
                                  57888876665..579***********************986 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 ?   12.6   0.0   8.8e-05     0.087       8      50 ..      45      87 ..      42      90 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 8.8e-05
                      HTH_DeoR  8 llkqqgklsveelvellgvSeaTiRRDLneLeeqglltRthGG 50
                                  +l +++  +v++l+el +v++a i   L+e+e qgl++R + G
  gi|13541993|ref|NP_111681.1| 45 YLLSEDESTVNKLAELTDVTPAWITGTLDEMESQGLIVRSRSG 87
                                  78889999*******************************8866 PP

>> DprA_WH  DprA winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   5.9e-05     0.059      10      57 ..      36      83 ..      29      87 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.9e-05
                       DprA_WH 10 lddlerrvLaaLgpePvhvDqLvrrtglpaaevsaaLleLELaGlver 57
                                  + + e r+L +L+ +  +v  L++ t +++a +  +L e+E +Gl+ r
  gi|13541993|ref|NP_111681.1| 36 AKPIEVRILYLLSEDESTVNKLAELTDVTPAWITGTLDEMESQGLIVR 83
                                  567899****************************************98 PP

>> AbiJ_NTD3  AbiJ N-terminal domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.2   5.2e-05     0.052      69     115 ..      97     143 .]      42     143 .] 0.92

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.2e-05
                     AbiJ_NTD3  69 lfderlglleasderFlrFLeelvhPdvrpdeeeqrrlveaiNelLr 115
                                   ++++ ++ l+ s++ +l+FL   ++  + ++ +e rr++++i e+L+
  gi|13541993|ref|NP_111681.1|  97 ITEKGIEVLNESQKVYLDFLKRSLSSLTDSELDEFRRILKKIEETLQ 143
                                   56677999************************************996 PP

>> RQC  RQC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   6.5e-05     0.065      58     110 ..      62     118 ..      58     122 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.5e-05
                                   TS-HHHHHHHHHHHHHTTSE..EEE....SSSBEEE-CCGHHHHTSSS--EEESHHH CS
                           RQC  58 dlskkewrrlirqLiaegyL..eedve..eygvlkltekarevlkgeekvklreekk 110
                                   d++  +++  ++++ ++g++  + ++e  ++  +++tek+ evl++ +kv+l++ k+
  gi|13541993|ref|NP_111681.1|  62 DVTPAWITGTLDEMESQGLIvrSRSGEdrRVVNVHITEKGIEVLNESQKVYLDFLKR 118
                                   6777899999**********75444447566699******************98776 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   8.1e-05     0.081       8      72 ..      41     104 ..      34     122 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 8.1e-05
                                   HHHHHHHTTS-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSS-EEEEEE-TCGGGG CS
                          HxlR   8 llilvellkgkkRfselkralpkisqkmLaqrLreLeqdglierevypevPpkveYsltekGrsl 72 
                                   + il+ l + +   ++l++   +++   ++ +L e+e++gli r+   e    v+ ++tekG ++
  gi|13541993|ref|NP_111681.1|  41 VRILYLLSEDESTVNKLAELT-DVTPAWITGTLDEMESQGLIVRSRSGEDRRVVNVHITEKGIEV 104
                                   679999999999999999876.9***************************************876 PP

>> Sdh5  Flavinator of succinate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2   0.00014      0.14      22      46 ..     114     138 ..     105     143 .] 0.84

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00014
                                   THHHHHTTT--HHHHHHHHHHHTS- CS
                          Sdh5  22 rFaekhlatlseeeldaferLLdle 46 
                                    F+++ l++l+++eld+f r+L+  
  gi|13541993|ref|NP_111681.1| 114 DFLKRSLSSLTDSELDEFRRILKKI 138
                                   7********************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       772  (0.0430587); expected 358.6 (0.02)
Passed bias filter:                      564  (0.0314574); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 912.52
//
Query:       gi|13541994|ref|NP_111682.1|  [L=587]
Description: multidrug efflux permease [Thermoplasma volcanium GSS1]
Scores for 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  132.2  67.0      2e-38  132.2  67.0    3.3  2  MFS_1     Major Facilitator Superfamily
    6.9e-05   21.9  16.7    6.9e-05   21.9  16.7    2.5  3  Sugar_tr  Sugar (and other) transporter
  ------ inclusion threshold ------
        0.6    8.4  15.9       0.17   10.2   8.4    2.6  2  MFS_3     Transmembrane secretion effector


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.2  67.0   3.4e-42     2e-38       3     350 ..      14     426 ..      12     429 .. 0.81
   2 ?   -5.0  14.6       1.8   1.1e+04       8     121 ..     429     547 ..     423     551 .. 0.70

  Alignments for each domain:
  == domain 1  score: 132.2 bits;  conditional E-value: 3.4e-42
                         MFS_1   3 laaflsalarsilgpalpl.alaedlg....ispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglll 78 
                                   +++++++++++il+++lp  + + dl+    +s + + ++l +y++++av+ + +Grlsd fGr r++ +g+l+f +g++l
  gi|13541994|ref|NP_111682.1|  14 IGVLMASINATILMISLPAiFRGIDLNpflpSSFQYLLWILMGYMVVTAVLLVTVGRLSDIFGRVRLFNFGFLIFTVGSIL 94 
                                   78999*************888888888999999999******************************************444 PP

                         MFS_1  79 llfa....sslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravf 154
                                   l+++    ++    l+++r++q++g+++lf+++aa+i+d fp  erg+a+g+ +++  +G+++g ++gg+la  ++Wr+vf
  gi|13541994|ref|NP_111682.1|  95 LFLTpgkgTTAAtELIFFRMIQAVGGSFLFANSAAIITDAFPAGERGKAMGINQIAGLAGSLIGLIIGGILA-TINWRYVF 174
                                   44434666555558**********************************************************.889***** PP

                         MFS_1 155 yilaivsllafvlfllllpeepperkrkspkeee............................................... 188
                                   ++  +v++l+    + +l  ++ + +rk +k +                                                
  gi|13541994|ref|NP_111682.1| 175 LVSVPVGVLGTA--WSYLKLKDQSIRRKDEKIDVpgnltfaggltlvliaityglmpygsssmgwtnpwvltamiigigml 253
                                   **********55..5666666666666666666679999*********************999999888888888666666 PP

                         MFS_1 189 ......kgtgpaplvpawkallkdpvlwillialllf..ffgfsglltllpl.....ylqevlgls....glllaglllal 252
                                         + ++ +p+++   +l+k + +   +  +++f  ++g+ g+++++ +     +    +g+s      + ag ++ +
  gi|13541994|ref|NP_111682.1| 254 vafpfiELHVDQPMFD--MHLFKYRGF--TFGNFAGFfqSMGMGGVMFMVIIllqgiW-LPLHGYSytsvP-FWAG-IYTI 327
                                   6666665555555655..333333333..33333333111233333333333233323.566777788644.4444.4666 PP

                         MFS_1 253 lalvgail.allagrlsdrlgrrrrlllallllllaalglallavtssavllllvlvliGfglgfvfpsllalasdlappe 332
                                   ++++g+++ ++++g+lsd++g+r  ++++++++++a+++l l++   s++ +++ l+l+G g+g++ ++ ++++++++p++
  gi|13541994|ref|NP_111682.1| 328 PMMAGFVIlGPISGALSDKIGARLLTTVGMIIGAVAFILLTLFPYNFSYPPFAATLFLMGAGMGMFGAPNITAVMNSLPAH 408
                                   666666666************************************************************************ PP

                         MFS_1 333 eagtasglfntagslgga 350
                                   ++gt sg   t+++ g  
  gi|13541994|ref|NP_111682.1| 409 YRGTGSGMRATLQNTGQT 426
                                   ***********9998876 PP

  == domain 2  score: -5.0 bits;  conditional E-value: 1.8
                         MFS_1   8 salarsilgpalplalaedlgispseigllltlyal..gaavaslplGrlsdr.fGrrr.vlllglllfalglllllfass 84 
                                   +++ +si++++l+++l+++++ + +++g  + +  +    a ++l+ ++l+ + +G    +l  +++++++ + l ++  +
  gi|13541994|ref|NP_111682.1| 429 MGIFFSIVLITLSSYLSSSFNTALASAGASVLIPVFdkIPATSALFSAFLGYNpMGTILsLLPSSFVSLISPSSLSILEGT 509
                                   566777777888779999999888888888888777778889999999998888888886666777777776333333444 PP

                         MFS_1  85 lw.lllvlrvlqGlgagalfpagaaliadwfpkeergr 121
                                   +w +l+++ +++ +   ++++++++li + +    rg+
  gi|13541994|ref|NP_111682.1| 510 HWfPLALAPAFMKALHDSFYAGAGILIIAAVLSALRGK 547
                                   45588888888888887777777666666554446655 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9  16.7   1.2e-08   6.9e-05      47     188 ..      49     188 ..       7     192 .. 0.90
   2 ?   -5.2   1.1       1.9   1.1e+04      75      90 ..     286     301 ..     277     306 .. 0.48
   3 !    5.8  11.5   0.00085       5.1     292     428 ..     325     455 ..     311     474 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1.2e-08
                                   HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTT..SS-TGGGGGHHHHHHHHHHHHHHHHH CS
                      Sugar_tr  47 lsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgk..nsvevlivgRvlvGigvGlasvlvPm 125
                                   ++ +i+  ++v+ ++  +++g l+d+fGR   + ++ ++f +g++l ++++gk  ++   li+ R++  +g  +  + +  
  gi|13541994|ref|NP_111682.1|  49 YLLWILMGYMVVTAVLLVTVGRLSDIFGRVRLFNFGFLIFTVGSILLFLTPGKgtTAATELIFFRMIQAVGGSFLFANSAA 129
                                   5678889999*****************************************99999999************9999999999 PP

                                   HHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-TTHHHHHHHCCHHHHHHHHHHG CS
                      Sugar_tr 126 yisEiApkklRgalvslyqlaitfGilvaaifglglnktsnadgwrillglqlvpallllill 188
                                    i    p+  Rg+ ++++q a  +G l++ i+g +l++++    wr+ + +++   +l  ++ 
  gi|13541994|ref|NP_111682.1| 130 IITDAFPAGERGKAMGINQIAGLAGSLIGLIIGGILATIN----WRYVFLVSVPVGVLGTAWS 188
                                   999999****************************999985....8999999999999887775 PP

  == domain 2  score: -5.2 bits;  conditional E-value: 1.9
                                   HHHHHHHHHHHHHHHH CS
                      Sugar_tr  75 Rkkslliaavlfviga 90 
                                     +s+ +++v+f++ +
  gi|13541994|ref|NP_111682.1| 286 FFQSMGMGGVMFMVII 301
                                   3334444444444444 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.00085
                                   HHHHHHHHHHHHHHHHHHHHHHS-SHHHHHHHHHHHHHHHHHHH..HHHHTTSS...CHHHHHHHHHHHHHHHTTTTHHHH CS
                      Sugar_tr 292 vtiivgvvnfvatfvaiflvdrfGRRtllllGaagmaicfvilgivalllvakskaasivaivfialfialfalgwgpvpw 372
                                    ti +++  ++   ++  l+d++G R l  +G++++a++f++l+   ++++ +       a +++++ + +  +g   + +
  gi|13541994|ref|NP_111682.1| 325 YTIPMMAGFVILGPISGALSDKIGARLLTTVGMIIGAVAFILLT--LFPYNFSY---PPFAATLFLMGAGMGMFGAPNITA 400
                                   57888888888889999**************************9..99999885...666666666666666667777776 PP

                                   HHHHHHSHTTTHHHHHHHHHHHHHHHHHH.HHHHHHHHHCHHHT-HHHHHHHHHHHH CS
                      Sugar_tr 373 vlvsElfpqsvRskalaiavavnwlanfl.isllfpiiteaigggyvflvfaglavl 428
                                   v+     p + R++++ + ++++++ + + ++++f i++ +++ + +  ++++la +
  gi|13541994|ref|NP_111682.1| 401 VM--NSLPAHYRGTGSGMRATLQNTGQTAsMGIFFSIVLITLSSYLSSSFNTALASA 455
                                   66..779**********9999999988653799999999999977777777666544 PP

>> MFS_3  Transmembrane secretion effector
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   8.4   2.8e-05      0.17      60     173 ..      63     175 ..       3     200 .. 0.87
   2 ?    1.8   0.8      0.01        60      59     119 ..     334     392 ..     322     409 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 2.8e-05
                         MFS_3  60 llsilaGalaDnfdrRkvllavqlllalvsvlltvlaalgllspwlllaltlligiGaalndPaWqAsvgelvkrrdvpaA 140
                                   +l + +G l+D+f r +++  + l+  ++s+ll ++   g ++   l+ + ++ ++G ++      A++ +  ++ +  +A
  gi|13541994|ref|NP_111682.1|  63 VLLVTVGRLSDIFGRVRLFNFGFLIFTVGSILLFLTPGKGTTAATELIFFRMIQAVGGSFLFANSAAIITDAFPAGERGKA 143
                                   566889*************************************************************************** PP

                         MFS_3 141 vaLnsvginiaRsvGPAlgGvlvaavGaalafa 173
                                   + +n +       +G  +gG+l a++   ++f 
  gi|13541994|ref|NP_111682.1| 144 MGINQIAGLAGSLIGLIIGGIL-ATINWRYVFL 175
                                   *****99888888999999986.5555555555 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.01
                         MFS_3  59 fllsilaGalaDnfdrRkvllavqlllalvsvlltvlaalgllspwlllaltlligiGaal 119
                                   ++l  ++Gal+D++  R +  +++++ a++ +llt++ + ++  p    a  +l+g G+ +
  gi|13541994|ref|NP_111682.1| 334 VILGPISGALSDKIGARLLTTVGMIIGAVAFILLTLFPY-NFSYPPF-AATLFLMGAGMGM 392
                                   5778899*******9998887777777766666666554.4444433.3445566666543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (587 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       788  (0.0439511); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.71u 0.29s 00:00:01.00 Elapsed: 00:00:00.49
# Mc/sec: 3611.53
//
Query:       gi|13541995|ref|NP_111683.1|  [L=170]
Description: hypothetical protein TVN1164 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score 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   0.1      0.086   12.9   0.1    1.6  1  NB        NB glycoprotein


Domain annotation for each model (and alignments):
>> NB  NB glycoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   4.8e-06     0.086      24      73 ..       7      56 ..       3      84 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.8e-06
                            NB 24 ticvslivilivfgciakifinknnctnnvirvhkrikc.pdcepfcnkrd 73
                                  t+++s+i +livf+ +a  +i +   t + +++   ik+ pd +p   k  
  gi|13541995|ref|NP_111683.1|  7 TVAISVI-VLIVFAGVAYEVIHNSSSTSETLKISGNIKVkPDLKPSLTKTV 56
                                  6777766.5899*************************97699999877764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       619  (0.0345251); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 1090.96
//
Query:       gi|13541996|ref|NP_111684.1|  [L=131]
Description: hypothetical protein TVN1165 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.025   14.5   1.0       0.04   13.9   0.3    1.7  2  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an
       0.13   11.2   0.0       0.16   11.0   0.0    1.0  1  GCR             Glucocorticoid receptor


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 ?   -2.7   0.0       0.7   6.3e+03      22      29 ..      11      18 ..       9      24 .. 0.67
   2 ?   13.9   0.3   4.5e-06      0.04       9      32 ..      79     102 ..      78     111 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.7
                                  ECTCEEEE CS
                MazE_antitoxin 22 reGdevel 29
                                  reGd+  +
  gi|13541996|ref|NP_111684.1| 11 REGDRYFV 18
                                  56776555 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 4.5e-06
                                   EEE-CCCHHHCCEECTCEEEEEEC CS
                MazE_antitoxin   9 vriPkevrfelgireGdevelevd 32 
                                   v iP+e+++e  i+eG  +el ++
  gi|13541996|ref|NP_111684.1|  79 VIIPAEIVREYKIEEGEYLELLIE 102
                                   88******************9765 PP

>> GCR  Glucocorticoid receptor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   1.8e-05      0.16     197     275 ..      38     115 ..      29     124 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 1.8e-05
                           GCR 197 slLsplaaddsfLlegeaeedckplilvdtkkkineeasllltsasavllpqvKveKedfieLctpGviKqEklGrvyC 275
                                    lL+ +++ d+ L  ++++ + k+   ++t k     ++ +++   a ++ + K+e  +++eL+ + ++K +k+ ++y 
  gi|13541996|ref|NP_111684.1|  38 LLLTIVGSYDPKLKMLKQKINEKAICRTSTFKDSRGFDHPSVII-PAEIVREYKIEEGEYLELLIEHIVKEDKIAAIYP 115
                                   678899999*********9999*999999999998888777776.678999************************9995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       517  (0.028836); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); 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: 00:00:00.48
# Mc/sec: 823.14
//
Query:       gi|13541997|ref|NP_111685.1|  [L=176]
Description: secreted endonuclease distantly related to Holliday junction resolvase [Thermoplasma volcanium GSS1]
Scores for complete 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-48  162.4   1.0    9.6e-48  162.1   1.0    1.0  1  Endonuc_Holl    Endonuclease related to archaeal Holliday jun
     0.0012   19.0   1.3     0.0028   17.8   1.3    1.6  1  TssO            Type VI secretion system, TssO
     0.0032   17.4   3.6     0.0045   17.0   2.7    1.6  2  DUF4446         Protein of unknown function (DUF4446)
  ------ inclusion threshold ------
      0.018   15.1   2.8      0.018   15.1   2.8    1.7  2  ATP-synt_B      ATP synthase B/B' CF(0)
      0.031   14.5   1.2      0.067   13.5   1.2    1.6  1  DUF948          Bacterial protein of unknown function (DUF948
      0.038   12.7   0.1      0.047   12.4   0.1    1.1  1  Folate_carrier  Reduced folate carrier
        9.3    6.1   8.7         23    4.9   8.7    1.6  1  Tmemb_9         TMEM9


Domain annotation for each model (and alignments):
>> Endonuc_Holl  Endonuclease related to archaeal Holliday junction resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  162.1   1.0   3.8e-51   9.6e-48       2     160 ..      14     165 ..      11     166 .. 0.94

  Alignments for each domain:
  == domain 1  score: 162.1 bits;  conditional E-value: 3.8e-51
                  Endonuc_Holl   2 lvlvilvlllkiskiqkklekkarelfeewkkeeaeeleklkeaeallkkeaevkleewkkkeekeiRedaikksksvilg 82 
                                   l+lvi+ l   i+++++++  k++e++ ++kk++    e     ea++++e+++k +e  +k+++++R+++++ks++v++g
  gi|13541997|ref|NP_111685.1|  14 LFLVIVLLIFYIVSLKRSVLLKQHEVEMTLKKAN----ELI--NEAMASREEAMKEKEEINKKIEDARRESVSKSRDVVVG 88 
                                   7889999999999999999999999999999887....233..48899********************************* PP

                  Endonuc_Holl  83 kvtEeliPlfpefsynpkDaRflGtPvDlvvFdGLsegeveeivfvEvKtGkssslseReravrdaieakrvsyevlr 160
                                   +v+E+l+P+fp f+ynpkD+Rf+GtP+Dl++FdG+++g++++ivf+EvK+G +s+l+eRe+av++ai+++rvs+ ++r
  gi|13541997|ref|NP_111685.1|  89 RVSEQLAPFFPGFKYNPKDVRFIGTPIDLIIFDGMDNGNITSIVFLEVKSG-ASKLTEREKAVMEAINSGRVSFDIYR 165
                                   ***************************************************.**********************9987 PP

>> TssO  Type VI secretion system, TssO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   1.3   1.1e-06    0.0028      10      72 ..       8      72 ..       4      84 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.1e-06
                          TssO 10 flyflllFlvtvlllflivffffkssplqekeil..lkelerkkkfeekqkelkkkvdsiykkId 72
                                  +l + +lFlv+vll+f+iv ++ + +  q++ ++  +k +e +++ + + +e +k+ ++i kkI+
  gi|13541997|ref|NP_111685.1|  8 ILVLAALFLVIVLLIFYIVSLKRSVLLKQHEVEMtlKKANELINEAMASREEAMKEKEEINKKIE 72
                                  678999*************99998544444433346777888999999***************97 PP

>> DUF4446  Protein of unknown function (DUF4446)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   2.7   1.7e-06    0.0045       2      71 ..       9      78 ..       6      90 .. 0.66
   2 ?   -1.9   0.0       1.2     3e+03     129     146 ..     136     151 ..     119     164 .. 0.57

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.7e-06
                       DUF4446  2 iilvlavlvvillillivllvklkklkkkykklmkgkdgksleellkekleeveelkeeseelekeieel 71
                                  ++l++++lv++lli++iv l +   lk++  +++ +k ++ ++e+++++ e ++e +e ++++e+  +e 
  gi|13541997|ref|NP_111685.1|  9 LVLAALFLVIVLLIFYIVSLKRSVLLKQHEVEMTLKKANELINEAMASREEAMKEKEEINKKIEDARRES 78
                                  5677788888888888888888888888777777766666666666666666666666666655544443 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.2
                       DUF4446 129 iekgeseyeLseEEkeal 146
                                   +++g s  +L+e Ek+++
  gi|13541997|ref|NP_111685.1| 136 VKSGAS--KLTEREKAVM 151
                                   333333..2333333333 PP

>> ATP-synt_B  ATP synthase B/B' CF(0)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   2.8   7.2e-06     0.018       5      80 ..       2      77 ..       1      94 [. 0.76
   2 ?   -2.8   0.0       2.5   6.4e+03      28      40 ..     143     155 ..     136     158 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 7.2e-06
                    ATP-synt_B  5 nliallilvgllikfawkplkkvLdkReekIadeiaeAeerrkeaaallaeaeqqlkeAraeAaeiiknAkkeaek 80
                                  nli++lilv+   ++++  l   +   ++ +  ++ e e+  k+a++l++ea +  +eA++e +ei k+ ++++++
  gi|13541997|ref|NP_111685.1|  2 NLITFLILVLAALFLVIVLLIFYIVSLKRSVLLKQHEVEMTLKKANELINEAMASREEAMKEKEEINKKIEDARRE 77
                                  7888888888888888888888888888888888888888888888888888888888888888886655554444 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2.5
                    ATP-synt_B  28 LdkReekIadeia 40 
                                   L +Re+++ ++i+
  gi|13541997|ref|NP_111685.1| 143 LTEREKAVMEAIN 155
                                   5566666666665 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   1.2   2.6e-05     0.067       1      69 [.       4      73 ..       4      93 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.6e-05
                        DUF948  1 IAglIaAiAFvvLvifl.ivvllklkktldeaaatieelekqvdpilkevedllakvnelledvneklek 69
                                  I  lI+ +A ++Lvi+l i  +++lk+ +   ++ +e + k+++++++e+ +  +++ +  e++n+k+e+
  gi|13541997|ref|NP_111685.1|  4 ITFLILVLAALFLVIVLlIFYIVSLKRSVLLKQHEVEMTLKKANELINEAMASREEAMKEKEEINKKIED 73
                                  6678888888888877515667888888888888888888888888888888888887777888887775 PP

>> Folate_carrier  Reduced folate carrier
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   1.9e-05     0.047     162     233 ..      15      86 ..       3      99 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.9e-05
                Folate_carrier 162 tlnyislasvvvalllslfLprpkkslffkkkeaaskkdekseeeseeseeeenekeeeeeksseesekkvl 233
                                    l ++ l + +v+l  s++L++++ ++  kk ++ ++++ +s ee+ +++ee n+k e+++++s  ++++v+
  gi|13541997|ref|NP_111685.1|  15 FLVIVLLIFYIVSLKRSVLLKQHEVEMTLKKANELINEAMASREEAMKEKEEINKKIEDARRESVSKSRDVV 86 
                                   47789999*********************9997776666555555545555555555555544444444433 PP

>> Tmemb_9  TMEM9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   8.7    0.0089        23      52     123 ..       8      93 ..       2      96 .. 0.50

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0089
                       Tmemb_9  52 vvviivivvislLviYmlflllldpllnkrkkkasyqehtnee...............detseslssasqslelrarsnvl 117
                                   ++v+  + ++ +L+i+ ++ l  + ll++++ +++ ++ ++                 +e ++++++a ++  +++r  v+
  gi|13541997|ref|NP_111685.1|   8 ILVLAALFLVIVLLIFYIVSLKRSVLLKQHEVEMTLKKANE-LineamasreeamkekEEINKKIEDARRESVSKSRDVVV 87 
                                   44555555555555555555556667776633333333222.112223433334333255556666666666666678888 PP

                       Tmemb_9 118 nrvehq 123
                                    rv +q
  gi|13541997|ref|NP_111685.1|  88 GRVSEQ 93 
                                   888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2528  (0.141001); expected 358.6 (0.02)
Passed bias filter:                     1322  (0.0737353); expected 358.6 (0.02)
Passed Vit filter:                       174  (0.00970495); 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: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1247.76
//
Query:       gi|13541998|ref|NP_111686.1|  [L=195]
Description: alpha/beta superfamily hydrolase [Thermoplasma volcanium GSS1]
Scores for complete 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   62.0   0.3    2.8e-14   53.4   0.2    2.0  2  Abhydrolase_1  alpha/beta hydrolase fold
    4.4e-11   42.5   0.0    8.8e-08   31.7   0.1    2.1  2  Hydrolase_4    Serine aminopeptidase, S33
    5.4e-10   40.2   0.0    6.2e-10   40.0   0.0    1.1  1  Abhydrolase_6  Alpha/beta hydrolase family
    1.5e-06   28.1   0.0    2.1e-06   27.6   0.0    1.2  1  Abhydrolase_5  Alpha/beta hydrolase family
    0.00016   20.5   0.4    0.00031   19.6   0.2    1.5  1  Ndr            Ndr family


Domain annotation for each model (and alignments):
>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.4   0.2   7.9e-18   2.8e-14       2     115 ..      23     131 ..      22     135 .. 0.93
   2 !    8.1   0.0   0.00051       1.8     205     254 ..     134     176 ..     122     179 .. 0.74

  Alignments for each domain:
  == domain 1  score: 53.4 bits;  conditional E-value: 7.9e-18
                                   EEEEE-STTTCGGGGTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTTGB.CHHSHHHHHHHHHHHHHHCTTSSEEEEEETH CS
                 Abhydrolase_1   2 vlvilhGlpgssdvwaerglapaLakdgfdvillDlrGvgySspapacinddygtasvaddldrildalgddkltlvGhSm 82 
                                   +++++hG   ss+ w e g ++a +    +vi +Dl+G+g+S+ + ++        +++d+++ + d lg++k +l+G S+
  gi|13541998|ref|NP_111686.1|  23 PIIMVHGARFSSETWVEVGTVSAVSSIPMRVISVDLPGYGRSEGGQWK--------DLRDFMNDFIDVLGIQKTALLGASL 95 
                                   89***************9999999999********************7........6************************ PP

                                   HHHHHHHHHHHHGGGEEEEEEESE...CSSCCHHHH CS
                 Abhydrolase_1  83 GGmialayaaeyperVkalvllga...idpaaslie 115
                                   GG +++ +a   pe+V al+l+ga    d +a+l++
  gi|13541998|ref|NP_111686.1|  96 GGNVVASFAVSKPESVLALILVGAvgiRDLNADLSK 131
                                   ************************887677776665 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00051
                                   HCTHHHHSEEEEEEETTCSSSCHHHHHHHHHCHTSEEEEEEETCSSSHHH CS
                 Abhydrolase_1 205 relknvlaptlvisgtsDplvppkaledlaqllpkkrlvvisdagHlafl 254
                                   ++      ptl+i+g++D + + +++e + +  ++ + +   ++ H  ++
  gi|13541998|ref|NP_111686.1| 134 GK------PTLLIWGSKDTVSDRSNYETYMKYVKS-SQFMNIGTNHACYF 176
                                   44......***************999999888777.55555555555555 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.7   0.1   2.5e-11   8.8e-08       7     110 ..      24     120 ..      22     132 .. 0.82
   2 !    9.4   0.0   0.00016      0.58     183     221 ..     125     164 ..     121     173 .. 0.83

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 2.5e-11
                   Hydrolase_4   7 vvlvHGlaehsgryae..laeaLaaqGfavyalDhrGhGrsegkrghvpsfddyvdDlaafvekvkeehpelplfllGhSm 85 
                                   +++vHG   +s+   e  ++ a     + v+ +D  G+Grseg  g+++++ d+++D+  ++       + ++  llG S+
  gi|13541998|ref|NP_111686.1|  24 IIMVHGARFSSETWVEvgTVSAVSSIPMRVISVDLPGYGRSEG--GQWKDLRDFMNDFIDVL-------GIQKTALLGASL 95 
                                   56778877777777774456677777789************66..66799999999998886.......456799****** PP

                   Hydrolase_4  86 GGliallyllrypdkvaglilsaPa 110
                                   GG ++++++  +p++v +lil++++
  gi|13541998|ref|NP_111686.1|  96 GGNVVASFAVSKPESVLALILVGAV 120
                                   **********************975 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00016
                   Hydrolase_4 183 leeraakit.lPllllhGeaDkvvdpeasrelyerlgskd 221
                                   l+++ +k++  P+ll+ G++D+v d+++ + +++ ++s++
  gi|13541998|ref|NP_111686.1| 125 LNADLSKLDgKPTLLIWGSKDTVSDRSNYETYMKYVKSSQ 164
                                   56666666678****************9999999998865 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.0   0.0   1.7e-13   6.2e-10       1      95 [.      24     119 ..      24     163 .. 0.76

  Alignments for each domain:
  == domain 1  score: 40.0 bits;  conditional E-value: 1.7e-13
                                   EEEE--GC.....GC.HHHHHHHHCCTCEEEEE--TTSTS-GGCS--HHHCHHH.HHHHCCTT..TTSEEEEEETCHHHHH CS
                 Abhydrolase_6   1 vlllHGagssassWl.vapLaallaagvhvlapDlpGhGrsdpppldledladl.aalldelaagggpvvlvGHSlGGala 79 
                                   ++++HGa +s++ W  v+ + a ++   +v+++DlpG+G   +    + dl+d+  +++d l+    +  l+G SlGG ++
  gi|13541998|ref|NP_111686.1|  24 IIMVHGARFSSETWVeVGTVSAVSSIPMRVISVDLPGYG--RSEGGQWKDLRDFmNDFIDVLG--IQKTALLGASLGGNVV 100
                                   799***********5467775555556788*********..8899999999999999999995..8888********9866 PP

                                   HH.HHHCC....EEEEES- CS
                 Abhydrolase_6  80 la.aapla..lvvgvlldp 95 
                                   +  a++ +  +++ +l+ +
  gi|13541998|ref|NP_111686.1| 101 ASfAVSKPesVLALILVGA 119
                                   6613333365333366666 PP

>> Abhydrolase_5  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.0   5.9e-10   2.1e-06      55     143 ..      84     175 ..      73     186 .. 0.82

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 5.9e-10
                 Abhydrolase_5  55 klekfvvgGhslGGvvasrfaaee.ekiegvvflasYPekd...elsel.skkvlsivgteDgvlnvkslekakkflpkdt 130
                                   +++k  + G slGG v++ fa ++ e++ +++++++   +d   +ls+l +k++l i+g++D v + +++e   k++ k +
  gi|13541998|ref|NP_111686.1|  84 GIQKTALLGASLGGNVVASFAVSKpESVLALILVGAVGIRDlnaDLSKLdGKPTLLIWGSKDTVSDRSNYETYMKYV-KSS 163
                                   58899999************998868*********998654222666652567******************999997.567 PP

                 Abhydrolase_5 131 kvvsieGgnhagf 143
                                   +++ i G nha +
  gi|13541998|ref|NP_111686.1| 164 QFMNI-GTNHACY 175
                                   88888.99**965 PP

>> Ndr  Ndr family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.2   8.6e-08   0.00031      84     133 ..      71     120 ..      67     132 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 8.6e-08
                                   HHHTTHHHHHHHHT---EEEEEETHHHHHHHHHHHHSGGGEEEEEEES-- CS
                           Ndr  84 dladqllavldhfklksviglGvgaGAyilarfalkhperveglvLinit 133
                                   dl d ++  +d + +++   lG+  G +++a fa++ pe v++l+L+ + 
  gi|13541998|ref|NP_111686.1|  71 DLRDFMNDFIDVLGIQKTALLGASLGGNVVASFAVSKPESVLALILVGAV 120
                                   6778888899999*********************************9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       513  (0.0286129); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 1210.28
//
Query:       gi|13541999|ref|NP_111687.1|  [L=419]
Description: hydroxymethylglutaryl-CoA reductase [Thermoplasma volcanium GSS1]
Scores for complete 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-108  361.6   5.5   5.2e-108  361.3   5.5    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 !  361.3   5.5  2.9e-112  5.2e-108       2     367 .]      14     376 ..      13     376 .. 0.94

  Alignments for each domain:
  == domain 1  score: 361.3 bits;  conditional E-value: 2.9e-112
                                   HHHHHHHHHH...S-HHHHHHH.TT----HHHHHHHSSS---------EEEEEEEETTEEEEEEE---STTHHHHHHHHHH CS
                   HMG-CoA_red   2 veeRrkllee...lteeeleel.keesldeevadkmiEnviGyvqlPlGvagpllingkeylvPmAteEgslvAsasrgak 78 
                                   v+eR+++++e   l++++++ l +++sl  ++adk+iEnvi+++++PlG+a ++lingk+yl+PmA+eE+s+vA+as++ak
  gi|13541999|ref|NP_111687.1|  14 VDERLNFVKEfsrLSDDDIRILrTNGSLAIDKADKIIENVITTIEMPLGIAVNFLINGKDYLIPMAIEEPSVVAAASNAAK 94 
                                   899*****998888888888896668999**************************************************** PP

                                   HHHHTT-B.EEEE----EEEEEEEE.--S-HHHHHHHH.HTHHHHHHHHHHCSHH..CCT-EEEEEEE.EE-..SSEEEEE CS
                   HMG-CoA_red  79 ainesgGvkttvlkdgmtraqvvllesvedaaelkkwi.ekkeeleelanaaest..srggglkdiev.vla..grlvvlr 153
                                   ++++sgG++ + +++ ++++++++l  +++ + +k  i ++k ++ elan  ++t  s g+g+kdiev v +  +r+++++
  gi|13541999|ref|NP_111687.1|  95 VARKSGGFN-AYATEPVMIGEIQVL-GIDSLYLAKMNIlRDKSRILELANTRSKTlsSLGAGAKDIEVnVYErpHRMLIVH 173
                                   ********5.555666*********.******************************9***********55558888***** PP

                                   EEEE-TTC--HHHHHHHHHHHHHHHHHHHTSEEEEEEE-S--GGGEEEEEEEEEHHHH..-SSTTHHHHHHHHHHHHHHHH CS
                   HMG-CoA_red 154 lkvdtgDAmGaNmvnkateaaaelieeefgeeellsilsNlctdkkasainaiegrgksvvaeatigeevvekilkasaea 234
                                   l vd++DAmGaN+vn+++e +a+ ie+++g++++l+ilsNl++++ a a ++++++         ig+e v++i++a++ a
  gi|13541999|ref|NP_111687.1| 174 LIVDVRDAMGANVVNSMCEYVAPEIEKITGGRVNLRILSNLTKYRVAYASAVFSKDI--------IGKEAVDNIVEAYRMA 246
                                   ***********************************************9988886544........6*************** PP

                                   HH-HHHH..HHHHHHH.......HHHHHHHHHHTT--HHHHHHHHHHHTT.........SEEETTTEEEEEEEEE.----S CS
                   HMG-CoA_red 235 lvdlnranigtankGiggfnahaaNgiaAvflAtGqDlaaveesshaiaa.........leevedgdlygsvtlPsleVGt 306
                                   +vd++ra  +t+nkGi       +Ngi+Av++At +D++a e+ +h +aa          e+ ++gdl+g++++P ++VGt
  gi|13541999|ref|NP_111687.1| 247 VVDIYRA--STNNKGI-------MNGIDAVLVATMNDWRAAEANAHSYAAlegygplakYEKNSNGDLVGTIEIP-IAVGT 317
                                   *******..*******.......***************************88888844444448889********.***** PP

                                   BSHHHHH-HHHHHH.HHTT---HH...HHHHHHHHHHHHHHHHHHHHHT-----HHHHHHHH CS
                   HMG-CoA_red 307 vGGgtklppqaell.kllgvkgaknakeLaeiiaavgLAqelsalrALaaeglqkgHmklhr 367
                                   vGG t+   +a+++ k+lgv++a    e+a ++aavgLAq++sa+rALa+eg+q+gHm+lh+
  gi|13541999|ref|NP_111687.1| 318 VGGTTGSIDKARIArKILGVSNAT---EFAGVLAAVGLAQNFSAVRALATEGIQRGHMELHA 376
                                   ************************...*********************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (419 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       666  (0.0371465); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); 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 0.27s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 2804.90
//
Query:       gi|13542000|ref|NP_111688.1|  [L=404]
Description: multidrug efflux permease [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-22   80.2  50.3    2.7e-14   52.9  28.4    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 !   52.9  28.4   1.5e-18   2.7e-14       2     264 ..      16     268 ..      12     282 .. 0.77
   2 !   32.0  19.4   3.2e-12   5.8e-08      40     162 ..     256     382 ..     253     386 .. 0.85

  Alignments for each domain:
  == domain 1  score: 52.9 bits;  conditional E-value: 1.5e-18
                         MFS_1   2 llaaflsalarsilgpalplalaedlg..ispseigllltlyalgaavaslpl.GrlsdrfGrrrvlllglllfalgllll 79 
                                   l ++f + ++ ++l++++p    + ++   +    +l ++lya++ ++a+l++ Gr+ + +   + + ++ll++a+++ l 
  gi|13542000|ref|NP_111688.1|  16 LAVTFTMRMTTNMLMTSIPV--LTKFTllTTTFLTSLPVALYAVTGLLANLFInGRINNGM-IGKAIAISLLVMAFTMPLY 93 
                                   45667777777777777774..3444432666679999999************99999988.8899999999999994444 PP

                         MFS_1  80 lfasslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslg..Wravfyila 158
                                   ++as++w + +  +l G+ +g++ p+ +++i+  + +  r  ++g+++++ s++ i+g  l g+l+ss++   r++f+ + 
  gi|13542000|ref|NP_111688.1|  94 FMASNVWEVSAISALDGVSMGLVPPLLLTMISLSYDE-VRDNVLGFYTSALSISLIVGTFLQGYLTSSVSvsVRSLFLYFF 173
                                   458*********************************9.****************************999999********* PP

                         MFS_1 159 ivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsglltllplylqevlg 239
                                   +v ll+++l  +++ +++ + k +s++ +   +  +++v+ + +l+k++ + + +++ l+ +f f ++ ++  ++++   g
  gi|13542000|ref|NP_111688.1| 174 PVPLLSAIL--MFVIASRLKIKEDSGRSK---VTTKKIVQTIPKLFKNRGFNFGFFGNLTYSFPFVIIIAYGSIIAKYYSG 249
                                   ******998..888888888888888888...4666666679999999955334444444444555555555555555555 PP

                         MFS_1 240 lsglllaglllallalvgailalla 264
                                   ++    + +++al+ ++g+ +   +
  gi|13542000|ref|NP_111688.1| 250 IN---PSIFFYALATFFGVSM---I 268
                                   55...5555566666666544...2 PP

  == domain 2  score: 32.0 bits;  conditional E-value: 3.2e-12
                         MFS_1  40 lyalgaavaslplGrlsdrf...Grrr.vlllglllfalglllllfasslwlllvlrvlqGlgagalfpagaaliadwfpk 116
                                   +yal++++++  + rls  f     +  ++l++l++++lg+++l+f+ +++l+l++ ++ G+  g+++p++   ++  ++k
  gi|13542000|ref|NP_111688.1| 256 FYALATFFGVSMITRLSMSFyppKNKYdLMLASLVTTVLGFIVLIFSDNIYLFLLSMFILGFPHGSIYPIATMSVSSSVSK 336
                                   3555555555555555555455547778************77777989999****************************** PP

                         MFS_1 117 eergraigllsagfslGailgpllggllasslgWravfyilaivsl 162
                                   +e + a++ +++ f++  +l p++ g++a+ ++ r++++++ i ++
  gi|13542000|ref|NP_111688.1| 337 SEVSIAFATFNIIFNILGLLLPPAFGFIAQIVNIRVAMIVMLIPMA 382
                                   *****************************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (404 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1051  (0.0586201); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.63u 0.29s 00:00:00.92 Elapsed: 00:00:00.48
# Mc/sec: 2523.54
//
Query:       gi|13542001|ref|NP_111689.1|  [L=301]
Description: dihydroorotate dehydrogenase 1B [Thermoplasma volcanium GSS1]
Scores for complete 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-63  214.1   2.0    2.7e-63  213.9   2.0    1.0  1  DHO_dh        Dihydroorotate dehydrogenase
    8.6e-09   34.9   0.2    5.7e-07   28.9   0.0    2.0  2  Dus           Dihydrouridine synthase (Dus)
      4e-05   23.2   1.4     0.0091   15.5   0.1    3.0  2  His_biosynth  Histidine biosynthesis protein
     0.0049   15.9   1.2     0.0093   15.0   1.2    1.7  1  IMPDH         IMP dehydrogenase / GMP reductase domain
  ------ inclusion threshold ------
      0.022   14.2   4.1        1.8    7.9   0.1    4.0  4  G3P_antiterm  Glycerol-3-phosphate responsive antiterminator
       0.14   11.5   2.4       0.26   10.7   1.1    2.0  2  NMO           Nitronate monooxygenase
       0.31   10.0   1.9        4.1    6.3   0.1    2.7  4  FMN_dh        FMN-dependent dehydrogenase


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 !  213.9   2.0   1.1e-66   2.7e-63       3     295 .]       5     283 ..       3     283 .. 0.92

  Alignments for each domain:
  == domain 1  score: 213.9 bits;  conditional E-value: 1.1e-66
                                   -EEETTEEESSSEEE-TTS.STTSSSHHHHHCTTSSEEEEEEE-SS-B--S-S--EEEETTCTEEEE---S-BS-HHHHHH CS
                        DHO_dh   3 atkvlglkfknpiglAaGf.dkegeeilkllklgfgaieigsvtpkpqeGnpkPrvfrlkedrsvlNslGlnneGldavle 82 
                                   +t+++g+k+ np+++A+G+ d +g  +++ll+ g++a+ ++s++ +++ G p+P +++   +  ++N++Gl n+G+++  e
  gi|13542001|ref|NP_111689.1|   5 STTLAGIKLVNPFMVASGIlDENGYTMKELLERGAAAVVTKSIGISERDGYPTPVIVEYGDS--LINAVGLSNPGIENFGE 83 
                                   6899**************75899**********************************98877..****************9 PP

                                   HHHHHHHHHHCC.CEEEEEEE-TTSS.HHHHHHHHHHHHGGG.ESEEEEES-SCTCC.TSCCCGCHHHHHHHHHHHHHHHH CS
                        DHO_dh  83 kllkrrkeqeekkelginlskakktenavddyvevvrkigpf.adilelNvSsPntp.glrdlqekeelkaillkvvkevs 161
                                   +++  ++      + +i+ s+   +   ++++ ++  k++++ +d++elN+S+P+++  + +++++++l +++++++k   
  gi|13542001|ref|NP_111689.1|  84 EINIAKEA-----KRPIIGSVFAYN---AEEFTKLSVKMEEYgVDAIELNLSCPHVKgFGLEVGSDPDLVEDIVNEIKSKV 156
                                   99877654.....348999999998...9***********7759*************6589******************** PP

                                   SSEEEEEE-SSSSHHHHHHHHHHHHHHTECEEEE...BSEE--CTTCCGCCCCTTSSEEEEEGGGHHHHHHHHHHHHHHTT CS
                        DHO_dh 162 kvpvlvKlaPdltdeekkdiadvllelkldgiivtNttvqrlaidlkseknvkanktGGlsGkalkdialkvirelykrlk 242
                                   kvpv++Kl+P+++++ ++++a++ + +    i+    tv+ +aid+ s+++v  n  GGlsG+a+k+++++ ++e++k++ 
  gi|13542001|ref|NP_111689.1| 157 KVPVFAKLSPNVSNIIEIAKAAEKA-DAYVLIN----TVKAMAIDIYSRSPVLSNLYGGLSGPAIKPVGIRYVYEVKKETG 232
                                   *************999888887755.4455666....889999************************************** PP

                                   T.S-EEEESS--SHHHHHHHHHHTECEEEESHHHHHHGTCHHHHHHHHHHHHH CS
                        DHO_dh 243 keipiIgvGGiesgeDalekieaGAslvqvytalvfegpkiakkikkeleelL 295
                                   k   iIgvGGi+  +Da+e+i+aGAs+vq++tal++ g  i+++++ +l  ++
  gi|13542001|ref|NP_111689.1| 233 K--EIIGVGGISNYKDAIEYIMAGASAVQIGTALYKYGKGIFREMEWQLRTFM 283
                                   6..58*************************************99999888765 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   0.0   2.2e-10   5.7e-07      55     150 ..      94     181 ..      80     201 .. 0.83
   2 !    4.2   0.0    0.0076        19     172     219 ..     221     267 ..     210     299 .. 0.81

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 2.2e-10
                                   CEEEEEE-S-HHHHHHHHHHHHHTT-SCEEEEESSTTEEETTEEEGGGGGGSHHHHHHHHHHHHCCSSS-EEEEEESESST CS
                           Dus  55 plavQlggsdpallaeaAklvadlgadeIdlNvGCPskkvtrggaGaaLlrkpdlvaqivkavvkaveiPvtvkirigidd 135
                                   p++  +++ ++++ ++   + +++g+d+I+lN+ CP  k  + ++G+    +pdlv++iv++++++v++Pv +k +  +  
  gi|13542001|ref|NP_111689.1|  94 PIIGSVFAYNAEEFTKLSVKMEEYGVDAIELNLSCPHVKGFGLEVGS----DPDLVEDIVNEIKSKVKVPVFAKLSPNVS- 169
                                   566666777788888888888999************99877777776....9*********************9987666. PP

                                   TTC.HHHHHHHHHHC CS
                           Dus 136 eeenalelakiveaa 150
                                      n++e+ak++e+a
  gi|13542001|ref|NP_111689.1| 170 ---NIIEIAKAAEKA 181
                                   ...677777777766 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.0076
                                   CHHHHHHHHH-SS-EEEESS--SHHHHHHHHHHH--SEEEESCHHCCS CS
                           Dus 172 weaIkevkqavsipviaNGdIkdaedaqaileetGadgvmigrgalgn 219
                                   ++ ++evk++    +i+ G+I + +da + +   Ga +v ig + ++ 
  gi|13542001|ref|NP_111689.1| 221 IRYVYEVKKETGKEIIGVGGISNYKDAIEYIMA-GASAVQIGTALYKY 267
                                   67799************************9998.********999875 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.2   0.1    0.0048        12      75     129 ..      16      72 ..       4     190 .. 0.57
   2 !   15.5   0.1   3.5e-06    0.0091      62     106 ..     221     265 ..     209     275 .. 0.66

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0048
                                   EEEEESSSSSHH..HHHHHHHCT-SEEEESHHHHH-TH.HHHHHHHHHCGGGEEEEEE CS
                  His_biosynth  75 pvqvGGGIrsle..dveelleagadkviigtaavknpe.likelaekfgsqkivvaiD 129
                                   p++v +GI + +  +++elle+ga  v+  +  +++ + + + ++ ++g+ +++ a+ 
  gi|13542001|ref|NP_111689.1|  16 PFMVASGILDENgyTMKELLERGAAAVVTKSIGISERDgYPTPVIVEYGD-SLINAVG 72 
                                   78899999877644789999999999998888665544133444444444.4444444 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 3.5e-06
                                   HHHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHHH CS
                  His_biosynth  62 ldlveeiaeevfipvqvGGGIrsledveelleagadkviigtaav 106
                                   + +v e+ +e+  ++   GGI++++d+ e++ aga+ v igta  
  gi|13542001|ref|NP_111689.1| 221 IRYVYEVKKETGKEIIGVGGISNYKDAIEYIMAGASAVQIGTALY 265
                                   455666666666666666666666666666666666666666654 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   1.2   3.6e-06    0.0093     196     239 ..     221     264 ..      84     269 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.6e-06
                                   HHHHHHHHCTCT-EEEEES---SHHHHHHHHHTT-SEEEESCCC CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         IMPDH 196 vaevaeaakkagvpviaDGGikysgdivkAlaaGadavmlGsll 239
                                   +  v+e+ k++g ++i  GGi++ +d +  + aGa+av +G  l
  gi|13542001|ref|NP_111689.1| 221 IRYVYEVKKETGKEIIGVGGISNYKDAIEYIMAGASAVQIGTAL 264
                                   677999***********************************987 PP

>> G3P_antiterm  Glycerol-3-phosphate responsive antiterminator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0     0.052   1.3e+02     141     167 ..      17      44 ..       7      48 .. 0.81
   2 ?    0.0   0.0      0.19   4.8e+02      83     122 ..      85     124 ..      82     128 .. 0.91
   3 ?    1.1   0.1     0.088   2.3e+02      18      49 ..     157     188 ..     143     192 .. 0.63
   4 ?    7.9   0.1   0.00071       1.8     129     167 ..     222     260 ..     214     264 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.052
                                   EEEEESS--SH.HHHHHHCTT.SSEEEE CS
                  G3P_antiterm 141 piiaGGLietk.edveealkaGaiavst 167
                                    ++a+G+++++  +++e+l+ Ga av t
  gi|13542001|ref|NP_111689.1|  17 FMVASGILDENgYTMKELLERGAAAVVT 44 
                                   57899998776268899*********98 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.19
                                   HHHHHHTT--EEEEEE--SHHHHHHHHHHHHHHT-SEEEE CS
                  G3P_antiterm  83 ikkakklglltiqrlfliDssalekalkqiekskpdavev 122
                                   i+ ak+++   i  +f    + ++k   ++e+  +da+e+
  gi|13542001|ref|NP_111689.1|  85 INIAKEAKRPIIGSVFAYNAEEFTKLSVKMEEYGVDAIEL 124
                                   78899999999999************************97 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.088
                                   -SSEEEE--EETTTHHHHHHHHHHTT-EEEEE CS
                  G3P_antiterm  18 evevvfllegdilnlkeiveklkkagkkvfvh 49 
                                   +v v   l+ +++n+ ei + ++ka+ +v+++
  gi|13542001|ref|NP_111689.1| 157 KVPVFAKLSPNVSNIIEIAKAAEKADAYVLIN 188
                                   22334445567888888888888888888876 PP

  == domain 4  score: 7.9 bits;  conditional E-value: 0.00071
                                   HHHCTSTTS...EEEEESS--SHHHHHHHCTT.SSEEEE CS
                  G3P_antiterm 129 kvikeikkelkipiiaGGLietkedveealkaGaiavst 167
                                   +++ e+kke+  +ii  G i++ +d  e + aGa+av  
  gi|13542001|ref|NP_111689.1| 222 RYVYEVKKETGKEIIGVGGISNYKDAIEYIMAGASAVQI 260
                                   567799******************************976 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.39   9.9e+02     195     219 ..      16      42 ..      11      50 .. 0.83
   2 ?   10.7   1.1    0.0001      0.26     196     225 ..     235     264 ..     148     266 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.39
                           NMO 195 PviAaGGiidrrg..vaaaLalGAsgv 219
                                   P + a Gi d++g  ++  L +GA++v
  gi|13542001|ref|NP_111689.1|  16 PFMVASGILDENGytMKELLERGAAAV 42 
                                   788999999988755788999999998 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.0001
                           NMO 196 viAaGGiidrrgvaaaLalGAsgvqigtrf 225
                                   +i  GGi + ++    + +GAs+vqigt++
  gi|13542001|ref|NP_111689.1| 235 IIGVGGISNYKDAIEYIMAGASAVQIGTAL 264
                                   8999************************97 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0     0.032        81      47      68 ..       3      24 ..       1      60 [. 0.79
   2 ?   -3.4   0.0       1.5   3.8e+03     202     222 ..     143     163 ..     136     186 .. 0.70
   3 ?   -1.8   0.0      0.47   1.2e+03      78     101 ..     172     195 ..     159     208 .. 0.80
   4 ?    6.3   0.1    0.0016       4.1     259     303 ..     222     264 ..     215     275 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.032
                                  B--EEETTEEESSSEEE--BST CS
                        FMN_dh 47 dlsttllGqklslPvliaPvgl 68
                                  d+sttl G kl  P+++a+  l
  gi|13542001|ref|NP_111689.1|  3 DISTTLAGIKLVNPFMVASGIL 24
                                  99***************98555 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 1.5
                                   C--HHHHHHHHHHHSSEEEEE CS
                        FMN_dh 202 sltwddikwlreqtklplvvK 222
                                   +l  d ++++++++k+p+  K
  gi|13542001|ref|NP_111689.1| 143 DLVEDIVNEIKSKVKVPVFAK 163
                                   555555677777777777655 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 0.47
                                   HHHHHHHHHHTS-EEEETT-SS-H CS
                        FMN_dh  78 lalaraaakagipfvlstvastsl 101
                                   +++a+aa+ka++ + + tv+ +++
  gi|13542001|ref|NP_111689.1| 172 IEIAKAAEKADAYVLINTVKAMAI 195
                                   578999999999999999987766 PP

  == domain 4  score: 6.3 bits;  conditional E-value: 0.0016
                                   HCHHHHHHHH..SS-EEEESS--SHHHHHHHHHTT-SEEEESHHH CS
                        FMN_dh 259 dvLpeiveavggrievlvDgGirrGsDvlkAlalGAdavllGRpf 303
                                   +   e+ ++ g   e++  gGi++ +D++  +  GA+av +G ++
  gi|13542001|ref|NP_111689.1| 222 RYVYEVKKETG--KEIIGVGGISNYKDAIEYIMAGASAVQIGTAL 264
                                   55556666665..588999**********************9764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       513  (0.0286129); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.50
# Mc/sec: 1812.36
//
Query:       gi|13542002|ref|NP_111690.1|  [L=250]
Description: dihydroorotate dehydrogenase electron transfer subunit [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.8e-10   39.8   1.8    5.2e-10   39.0   1.8    1.5  1  DHODB_Fe-S_bind  Iron-sulfur cluster binding domain of dihydr
  ------ inclusion threshold ------
      0.072   13.4   0.0       0.26   11.7   0.0    1.9  1  FAD_binding_6    Oxidoreductase FAD-binding domain
        0.1   13.2   0.4       0.39   11.4   0.4    2.0  1  NAD_binding_1    Oxidoreductase NAD-binding domain


Domain annotation for each model (and alignments):
>> DHODB_Fe-S_bind  Iron-sulfur cluster binding domain of dihydroorotate dehydrogenase B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.0   1.8   8.7e-14   5.2e-10       1      41 [.     195     227 ..     195     228 .. 0.94

  Alignments for each domain:
  == domain 1  score: 39.0 bits;  conditional E-value: 8.7e-14
                                   ----SSSSSSS-TTEEEETTCTT.CEEETTTT-CEEECCCB CS
               DHODB_Fe-S_bind   1 eerMaCGvGaClgCvvktkggdggeykrvCkdGPvFdadev 41 
                                   e+ M+CG+G+C +C +          k vCk+GPvF+++e+
  gi|13542002|ref|NP_111690.1| 195 ERTMKCGIGICDSCSLGG--------KQVCKEGPVFNIEEL 227
                                   899*************99........78***********98 PP

>> FAD_binding_6  Oxidoreductase FAD-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   4.3e-05      0.26       8      96 ..      10      85 ..       3      87 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4.3e-05
                                  EECCTTEEEEEEEESTTTS-----TT-EEEEEECETTCCEEEEEE.BSSTTECCEEEEEEE--TT-HHHHHHHCS-TT-EEEE CS
                 FAD_binding_6  8 eevsedtrifrfklpsekqklglpvGqhvflrlkikgeaviRsYtpissenekGelellvkvypgGkmsqaLdelkigdtlei 90
                                   + s+++ ++ f+ ++     ++++Gq+ ++ ++  ge +  s++         +  + vk y  G  s  L elk gd l +
  gi|13542002|ref|NP_111690.1| 10 VKESQNVNTLYFNWDQ-----DIRPGQFAMIWIPGYGE-IPMSFS-----GLGRRKSITVKAY--GSASRKLTELKAGDDLFL 79
                                  5555666666665552.....24466666666665555.323333.....2222334567766..9***************** PP

                                  EEEE-S CS
                 FAD_binding_6 91 kGPlGk 96
                                  +GP+G+
  gi|13542002|ref|NP_111690.1| 80 RGPYGN 85
                                  ****97 PP

>> NAD_binding_1  Oxidoreductase NAD-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.4   6.6e-05      0.39      75     107 ..     150     179 ..      96     181 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 6.6e-05
                                   SSHHHHHHHHHHHHSSTTEEEEEECSHHHHHHH CS
                 NAD_binding_1  75 grvqdalleellslkkeethvyvCGppgMikav 107
                                   g+ ++ l + +    ++ + +yvCGp++M+  v
  gi|13542002|ref|NP_111690.1| 150 GFAHELL-QRINI--DSYEAIYVCGPEQMMYKV 179
                                   4444433.44554..78899*********9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       395  (0.0220313); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.51
# Mc/sec: 1473.97
//
Query:       gi|13542003|ref|NP_111691.1|  [L=850]
Description: TPR repeat-containing protein [Thermoplasma volcanium GSS1]
Scores for complete 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   66.4   2.5    1.3e-07   31.7   0.1    5.6  5  TPR_12    Tetratricopeptide repeat
      2e-10   41.0   0.0      0.062   13.8   0.0    4.5  4  TPR_19    Tetratricopeptide repeat
    1.8e-08   33.8  19.8      0.031   14.4   0.1    7.8  8  TPR_2     Tetratricopeptide repeat
    3.9e-08   32.9   5.0    0.00094   19.0   0.0    5.2  5  TPR_10    Tetratricopeptide repeat
    3.5e-06   26.6   1.7        1.4    9.1   0.0    5.3  5  TPR_7     Tetratricopeptide repeat
    4.5e-06   26.3  19.2      0.044   13.6   0.1    6.6  7  TPR_1     Tetratricopeptide repeat
    5.8e-06   26.1  23.0      0.011   15.9   0.1    8.2  7  TPR_8     Tetratricopeptide repeat
    0.00021   20.8   0.0        0.1   12.0   0.0    3.4  3  SNAP      Soluble NSF attachment protein, SNAP
    0.00028   20.6   0.0    0.00055   19.7   0.0    1.4  1  TPR_21    Tetratricopeptide repeat-like domain
    0.00093   18.8   5.5       0.44   10.3   0.2    4.2  4  TPR_11    TPR repeat
    0.00099   18.5   0.0     0.0026   17.2   0.0    1.8  1  SHNi-TPR  SHNi-TPR
     0.0016   18.3   0.9      0.021   14.7   0.1    2.8  2  TrmB      Sugar-specific transcriptional regulator TrmB
     0.0019   18.8   0.0       0.83   10.4   0.0    3.8  3  TPR_16    Tetratricopeptide repeat
     0.0078   17.0   0.0         11    7.1   0.0    4.9  4  TPR_14    Tetratricopeptide repeat
     0.0091   16.2   5.6        3.6    8.1   0.0    5.7  5  PPR       PPR repeat
  ------ inclusion threshold ------
       0.01   15.2   0.0        2.4    7.5   0.0    3.1  3  TPR_MalT  MalT-like TPR region
      0.016   15.3   0.6          6    7.0   0.0    3.5  3  OSCP      ATP synthase delta (OSCP) subunit
      0.025   14.8   6.4        2.7    8.3   0.0    4.4  4  ANAPC3    Anaphase-promoting complex, cyclosome, subunit 3
      0.026   14.6   0.1       0.11   12.5   0.1    2.1  1  Med28     Mediator complex subunit 28
      0.045   13.9   2.2        1.1    9.4   0.1    3.9  3  DUF2250   Uncharacterized protein conserved in archaea (DUF22
      0.058   14.0   1.3        4.6    7.9   0.0    3.1  2  ATP-cone  ATP cone domain
      0.082   13.2   0.0        5.6    7.4   0.0    3.4  3  TPR_20    Tetratricopeptide repeat
       0.24   12.1   8.8         66    4.5   0.2    5.9  5  TPR_6     Tetratricopeptide repeat
       0.36   11.3   3.5         17    6.0   0.0    4.7  5  TPR_17    Tetratricopeptide repeat
          1    9.1   8.7        2.5    7.8   0.0    3.9  3  DUF2225   Uncharacterized protein conserved in bacteria (DUF2


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 !   19.7   0.0   1.1e-06    0.0008       9      71 ..     398     450 ..     394     456 .. 0.91
   2 !   21.4   0.0   3.1e-07   0.00022       8      67 ..     429     483 ..     423     488 .. 0.85
   3 !   31.7   0.1   1.9e-10   1.3e-07       5      73 ..     503     569 ..     500     571 .. 0.93
   4 ?    2.1   0.2      0.35   2.5e+02      39      75 ..     690     724 ..     681     726 .. 0.83
   5 ?   -1.4   0.0       4.1     3e+03      16      39 ..     760     783 ..     756     787 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.1e-06
                        TPR_12   9 laavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleea 71 
                                   l ++++  gr+d+A++++            pdh   + ++++L+ +y+ +g++eeA+++le+a
  gi|13542003|ref|NP_111691.1| 398 LCHAYYLKGRFDKAISCYMDI------K--PDH--DLDSMIDLSSIYSNMGKFEEAEKILEDA 450
                                   5678999***********999......4..***..999***********************99 PP

  == domain 2  score: 21.4 bits;  conditional E-value: 3.1e-07
                        TPR_12   8 nlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlel 67 
                                    l +++  +g+++eA+++le a + +  +  +d+p+t++++r  + +y ++gry++ +++
  gi|13542003|ref|NP_111691.1| 429 DLSSIYSNMGKFEEAEKILEDAKNNF--T--DDYPQTIISYRIAALYY-RMGRYKDTIDM 483
                                   7999******************8888..5..9*****99999777776.999**986665 PP

  == domain 3  score: 31.7 bits;  conditional E-value: 1.9e-10
                        TPR_12   5 alnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleeala 73 
                                   +ln l+++ +   ry +Al+ +++alei r+l   ++++ ++ l+n++ +  ++g+y+ A+++l+e ++
  gi|13542003|ref|NP_111691.1| 503 ILNILGNIDMTSYRYGDALKKYNEALEINRKL--SNYAEISRNLNNIALIDVYTGKYDLAISILKELIE 569
                                   6755999999999*******************..9******************************9765 PP

  == domain 4  score: 2.1 bits;  conditional E-value: 0.35
                        TPR_12  39 pdhpltattlrnLgrlyralgryeeAlelleealaia 75 
                                   +d  +t+t l++L+ +yr  +++e A  +   a ++a
  gi|13542003|ref|NP_111691.1| 690 DD--YTSTFLIALAYYYRIIENQEMAKHYVDMAEEAA 724
                                   34..5999******************99988887765 PP

  == domain 5  score: -1.4 bits;  conditional E-value: 4.1
                        TPR_12  16 lgrydeAlellekaleiarrllGp 39 
                                   +++    +++++ + ei+r+++++
  gi|13542003|ref|NP_111691.1| 760 MQKPPTTIQFYDDSFEIFRSIYDG 783
                                   666666788999999999999876 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.0   0.00084       0.6       9      48 ..     376     415 ..     371     422 .. 0.85
   2 !   13.8   0.0   8.6e-05     0.062      23      59 ..     421     459 ..     415     462 .. 0.87
   3 ?    2.5   0.0      0.29   2.1e+02      27      54 ..     463     490 ..     458     503 .. 0.80
   4 !    8.7   0.0    0.0034       2.4       6      57 ..     516     573 ..     511     584 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00084
                        TPR_19   9 eAlalleqalqedpknaearllLAeallalgqldeAealL 48 
                                   e ++ leq+     ++++++  L+ a++  g++d+A+ + 
  gi|13542003|ref|NP_111691.1| 376 EVIEDLEQLGNVFSEDSDVKKVLCHAYYLKGRFDKAISCY 415
                                   567778898888999*********************9875 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 8.6e-05
                        TPR_19  23 k.naearllLAeallalgqldeAealLdalpeedpdd.a 59 
                                   + +++  ++L  ++ ++g ++eAe++L+++ + + dd +
  gi|13542003|ref|NP_111691.1| 421 DhDLDSMIDLSSIYSNMGKFEEAEKILEDAKNNFTDDyP 459
                                   448999999************************999766 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.29
                        TPR_19  27 arllLAeallalgqldeAealLdalpee 54 
                                   + ++ A +++ +g++++ +++L +l+ +
  gi|13542003|ref|NP_111691.1| 463 ISYRIAALYYRMGRYKDTIDMLTPLLGK 490
                                   568899***********99999988755 PP

  == domain 4  score: 8.7 bits;  conditional E-value: 0.0034
                        TPR_19   6 dyaeAlalleqalqedpk...naearllL...AeallalgqldeAealLdalpeedpd 57 
                                   +y +Al+ + +al+ + k   +ae+  +L   A + + +g +d A+ +L++l e +  
  gi|13542003|ref|NP_111691.1| 516 RYGDALKKYNEALEINRKlsnYAEISRNLnniALIDVYTGKYDLAISILKELIETTYS 573
                                   89***********99877777******999889999999************9988765 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.1    0.0013       0.9       7      24 ..     398     415 ..     394     416 .. 0.92
   2 ?    6.3   0.0     0.017        12       6      27 ..     429     450 ..     425     453 .. 0.86
   3 ?    5.3   0.2     0.035        25       5      18 ..     465     478 ..     462     479 .. 0.90
   4 !   14.4   0.1   4.3e-05     0.031       3      32 ..     503     532 ..     501     534 .. 0.91
   5 ?    4.3   0.0     0.075        54       4      29 ..     544     569 ..     541     571 .. 0.90
   6 ?    0.2   0.3       1.5   1.1e+03       3      21 ..     583     601 ..     581     604 .. 0.82
   7 ?   -0.4   0.3       2.3   1.6e+03      13      29 ..     633     649 ..     629     651 .. 0.81
   8 ?   -1.5   0.2       5.4   3.9e+03       4      23 ..     697     716 ..     695     722 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0013
                         TPR_2   7 lGlayyklgdyeeAleaf 24 
                                   l  ayy +g++++A+ ++
  gi|13542003|ref|NP_111691.1| 398 LCHAYYLKGRFDKAISCY 415
                                   6789*************9 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.017
                         TPR_2   6 nlGlayyklgdyeeAleafekA 27 
                                    l  +y ++g++eeA++ +e A
  gi|13542003|ref|NP_111691.1| 429 DLSSIYSNMGKFEEAEKILEDA 450
                                   57889***********988876 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.035
                         TPR_2   5 ynlGlayyklgdye 18 
                                   y+++ +yy++g+y+
  gi|13542003|ref|NP_111691.1| 465 YRIAALYYRMGRYK 478
                                   99***********8 PP

  == domain 4  score: 14.4 bits;  conditional E-value: 4.3e-05
                         TPR_2   3 alynlGlayyklgdyeeAleafekAleldP 32 
                                   +l+ lG++ + + +y +Al+ +++Ale++ 
  gi|13542003|ref|NP_111691.1| 503 ILNILGNIDMTSYRYGDALKKYNEALEINR 532
                                   68899***********************97 PP

  == domain 5  score: 4.3 bits;  conditional E-value: 0.075
                         TPR_2   4 lynlGlayyklgdyeeAleafekAle 29 
                                   l+n++l+  + g+y+ A+  +++ +e
  gi|13542003|ref|NP_111691.1| 544 LNNIALIDVYTGKYDLAISILKELIE 569
                                   899***************99999886 PP

  == domain 6  score: 0.2 bits;  conditional E-value: 1.5
                         TPR_2   3 alynlGlayyklgdyeeAl 21 
                                   a ynl ++yy  g+ e A+
  gi|13542003|ref|NP_111691.1| 583 AIYNLSEIYYVIGKQEYAE 601
                                   789*******999887775 PP

  == domain 7  score: -0.4 bits;  conditional E-value: 2.3
                         TPR_2  13 klgdyeeAleafekAle 29 
                                    l d++ A+++ e A+e
  gi|13542003|ref|NP_111691.1| 633 GLLDFKMAKKYAELAIE 649
                                   566999*******9998 PP

  == domain 8  score: -1.5 bits;  conditional E-value: 5.4
                         TPR_2   4 lynlGlayyklgdyeeAlea 23 
                                   l +l++ y+   + e A+++
  gi|13542003|ref|NP_111691.1| 697 LIALAYYYRIIENQEMAKHY 716
                                   66788888877777777776 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0         8   5.7e+03      11      22 ..     401     412 ..     400     415 .. 0.81
   2 !   19.0   0.0   1.3e-06   0.00094       3      28 ..     425     450 ..     424     452 .. 0.94
   3 ?    1.3   0.1      0.48   3.4e+02       8      20 ..     467     479 ..     466     484 .. 0.86
   4 !    7.1   0.2    0.0074       5.3       2      35 ..     501     534 ..     501     538 .. 0.93
   5 ?    2.9   0.0      0.15   1.1e+02       5      31 ..     544     570 ..     542     572 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 8
                        TPR_10  11 alrqrgrydeAe 22 
                                   a++  gr+d+A 
  gi|13542003|ref|NP_111691.1| 401 AYYLKGRFDKAI 412
                                   799999999996 PP

  == domain 2  score: 19.0 bits;  conditional E-value: 1.3e-06
                        TPR_10   3 sslnNLanalrqrgrydeAealleea 28 
                                    s+ +L+ +++++g+++eAe++le+a
  gi|13542003|ref|NP_111691.1| 425 DSMIDLSSIYSNMGKFEEAEKILEDA 450
                                   799*********************98 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.48
                        TPR_10   8 Lanalrqrgryde 20 
                                   +a++++++gry++
  gi|13542003|ref|NP_111691.1| 467 IAALYYRMGRYKD 479
                                   699********86 PP

  == domain 4  score: 7.1 bits;  conditional E-value: 0.0074
                        TPR_10   2 AsslnNLanalrqrgrydeAealleealairrrl 35 
                                   A +ln L+n+    +ry +A++ + eal+i r+l
  gi|13542003|ref|NP_111691.1| 501 AGILNILGNIDMTSYRYGDALKKYNEALEINRKL 534
                                   77899*************************9998 PP

  == domain 5  score: 2.9 bits;  conditional E-value: 0.15
                        TPR_10   5 lnNLanalrqrgrydeAealleealai 31 
                                   lnN+a +   +g+yd A  +l+e +++
  gi|13542003|ref|NP_111691.1| 544 LNNIALIDVYTGKYDLAISILKELIET 570
                                   8*********************99987 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       8.4   6.1e+03       3      17 ..     382     396 ..     381     398 .. 0.83
   2 ?    4.0   0.1     0.086        62       9      22 ..     402     415 ..     399     415 .. 0.84
   3 !    9.1   0.0     0.002       1.4       5      24 ..     430     449 ..     426     457 .. 0.88
   4 ?    0.2   0.0       1.4   9.8e+02       4      17 ..     466     479 ..     464     485 .. 0.86
   5 ?    6.8   0.0     0.011       7.7       2      34 ..     544     576 ..     544     577 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 8.4
                         TPR_7   3 lnLarlysrlGdyee 17 
                                    +L++++s++ d ++
  gi|13542003|ref|NP_111691.1| 382 EQLGNVFSEDSDVKK 396
                                   589******999876 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.086
                         TPR_7   9 ysrlGdyeeAiely 22 
                                   y   G++++Ai++y
  gi|13542003|ref|NP_111691.1| 402 YYLKGRFDKAISCY 415
                                   5567*********9 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.002
                         TPR_7   5 LarlysrlGdyeeAielyeq 24 
                                   L ++ys++G++eeA++++e 
  gi|13542003|ref|NP_111691.1| 430 LSSIYSNMGKFEEAEKILED 449
                                   779*************9986 PP

  == domain 4  score: 0.2 bits;  conditional E-value: 1.4
                         TPR_7   4 nLarlysrlGdyee 17 
                                   ++a ly r+G+y++
  gi|13542003|ref|NP_111691.1| 466 RIAALYYRMGRYKD 479
                                   7899********96 PP

  == domain 5  score: 6.8 bits;  conditional E-value: 0.011
                         TPR_7   2 LlnLarlysrlGdyeeAielyeqsLaltkdped 34 
                                   L+n+a + +  G+y+ Ai+++++++++t++ +d
  gi|13542003|ref|NP_111691.1| 544 LNNIALIDVYTGKYDLAISILKELIETTYSTGD 576
                                   67778887889************99***99776 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.1   6.1e-05     0.044       7      24 ..     398     415 ..     392     416 .. 0.90
   2 ?    5.8   0.0     0.018        13      10      22 ..     433     445 ..     432     450 .. 0.87
   3 !    8.6   0.0    0.0024       1.7       5      22 ..     465     482 ..     463     485 .. 0.90
   4 !    7.4   0.1    0.0056       4.1      16      33 ..     516     533 ..     516     534 .. 0.90
   5 ?   -1.3   0.0       3.3   2.4e+03      13      21 ..     553     561 ..     544     567 .. 0.74
   6 ?   -2.2   0.2       5.9   4.2e+03      16      29 ..     636     649 ..     631     650 .. 0.83
   7 ?   -2.5   0.3       7.8   5.6e+03      20      29 ..     699     708 ..     699     711 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6.1e-05
                                   HHHHHHHTT-HHHHHHHH CS
                         TPR_1   7 lGnayfklgkydeAleyy 24 
                                   l +ay+ +g++d+A+ +y
  gi|13542003|ref|NP_111691.1| 398 LCHAYYLKGRFDKAISCY 415
                                   789**************9 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.018
                                   HHHHTT-HHHHHH CS
                         TPR_1  10 ayfklgkydeAle 22 
                                   +y ++gk++eA++
  gi|13542003|ref|NP_111691.1| 433 IYSNMGKFEEAEK 445
                                   7**********97 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.0024
                                   HHHHHHHHHTT-HHHHHH CS
                         TPR_1   5 ynlGnayfklgkydeAle 22 
                                   y+++++y+++g+y++ ++
  gi|13542003|ref|NP_111691.1| 465 YRIAALYYRMGRYKDTID 482
                                   99***********99886 PP

  == domain 4  score: 7.4 bits;  conditional E-value: 0.0056
                                   -HHHHHHHHHHHHHHSTT CS
                         TPR_1  16 kydeAleyyekALelnPn 33 
                                   +y +Al+ y++ALe+n +
  gi|13542003|ref|NP_111691.1| 516 RYGDALKKYNEALEINRK 533
                                   6889***********975 PP

  == domain 5  score: -1.3 bits;  conditional E-value: 3.3
                                   HTT-HHHHH CS
                         TPR_1  13 klgkydeAl 21 
                                   + gkyd A+
  gi|13542003|ref|NP_111691.1| 553 YTGKYDLAI 561
                                   679****99 PP

  == domain 6  score: -2.2 bits;  conditional E-value: 5.9
                                   -HHHHHHHHHHHHH CS
                         TPR_1  16 kydeAleyyekALe 29 
                                   +++ A +y e A+e
  gi|13542003|ref|NP_111691.1| 636 DFKMAKKYAELAIE 649
                                   89999999999997 PP

  == domain 7  score: -2.5 bits;  conditional E-value: 7.8
                                   HHHHHHHHHH CS
                         TPR_1  20 AleyyekALe 29 
                                   Al+yy + +e
  gi|13542003|ref|NP_111691.1| 699 ALAYYYRIIE 708
                                   8899998887 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.1     0.012       8.5       9      25 ..     400     416 ..     398     418 .. 0.92
   2 !   15.9   0.1   1.5e-05     0.011       3      27 ..     426     450 ..     424     452 .. 0.90
   3 ?    0.6   0.1       1.3     9e+02       5      18 ..     465     478 ..     463     482 .. 0.89
   4 ?    1.2   0.1      0.77   5.5e+02       5      33 ..     505     533 ..     501     534 .. 0.72
   5 ?    7.0   0.0     0.011       7.6       2      29 ..     542     569 ..     541     571 .. 0.91
   6 ?    2.5   0.2       0.3   2.2e+02      11      29 ..     631     649 ..     627     651 .. 0.84
   7 ?    1.0   0.2      0.89   6.4e+02       4      23 ..     697     716 ..     694     722 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.012
                                   HHHHHTT-HHHHHHHHH CS
                         TPR_8   9 siylklgdyeeAkeyye 25 
                                   ++y  +g++++A+++y+
  gi|13542003|ref|NP_111691.1| 400 HAYYLKGRFDKAISCYM 416
                                   68999***********8 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 1.5e-05
                                   HHHHHHHHHHHTT-HHHHHHHHHHH CS
                         TPR_8   3 ayynlgsiylklgdyeeAkeyyeka 27 
                                   ++  l+siy+++g++eeA++ +e a
  gi|13542003|ref|NP_111691.1| 426 SMIDLSSIYSNMGKFEEAEKILEDA 450
                                   67789*****************987 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 1.3
                                   HHHHHHHHHTT-HH CS
                         TPR_8   5 ynlgsiylklgdye 18 
                                   y+++ +y  +g+y+
  gi|13542003|ref|NP_111691.1| 465 YRIAALYYRMGRYK 478
                                   89999*******97 PP

  == domain 4  score: 1.2 bits;  conditional E-value: 0.77
                                   HHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                         TPR_8   5 ynlgsiylklgdyeeAkeyyekaleldpd 33 
                                   + lg+i ++  +y  A + y++ale++++
  gi|13542003|ref|NP_111691.1| 505 NILGNIDMTSYRYGDALKKYNEALEINRK 533
                                   55666666666777888889999999986 PP

  == domain 5  score: 7.0 bits;  conditional E-value: 0.011
                                   CHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                         TPR_8   2 eayynlgsiylklgdyeeAkeyyekale 29 
                                   + ++n+++i   +g+y+ A++ +++ +e
  gi|13542003|ref|NP_111691.1| 542 RNLNNIALIDVYTGKYDLAISILKELIE 569
                                   56899*******************9997 PP

  == domain 6  score: 2.5 bits;  conditional E-value: 0.3
                                   HHHTT-HHHHHHHHHHHHH CS
                         TPR_8  11 ylklgdyeeAkeyyekale 29 
                                   y  l d+++Ak+y e a+e
  gi|13542003|ref|NP_111691.1| 631 YVGLLDFKMAKKYAELAIE 649
                                   55666999*********98 PP

  == domain 7  score: 1.0 bits;  conditional E-value: 0.89
                                   HHHHHHHHHHTT-HHHHHHH CS
                         TPR_8   4 yynlgsiylklgdyeeAkey 23 
                                   +  l++ y+  ++ e+Ak y
  gi|13542003|ref|NP_111691.1| 697 LIALAYYYRIIENQEMAKHY 716
                                   6789*************987 PP

>> SNAP  Soluble NSF attachment protein, SNAP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       1.5   1.1e+03     224     271 ..      56     104 ..      49     107 .. 0.73
   2 !   12.0   0.0   0.00015       0.1      52     148 ..     382     475 ..     377     486 .. 0.87
   3 ?    4.1   0.0     0.036        26     130     185 ..     516     571 ..     501     577 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.5
                                   -----------HHHHHHHHHHHHTT.-TTTHHHHHHHHTTSS---HHHH CS
                          SNAP 224 eldpsFassrEakllkdlleaveeg.dvekfteavkefDkiskldkWkt 271
                                   e+ ps  ++   + l+++++ +  + +v   ++ +ke+D++++ +k k+
  gi|13542003|ref|NP_111691.1|  56 EQVPSVGETYKNQTLNSIMDKITGKtEVRDKNTIIKEYDEFTRNNKEKI 104
                                   566777777778888888888775514556677899******9988665 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00015
                                   HHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHT-HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTT--HH CS
                          SNAP  52 eeAgeaflkaAecqeklkekdeaanayveAakcykkvspeeAvealekAieiytekgrfrraAklkkeiaelyekelgdle 132
                                   e+ g++f + +++++ l  +      + +A +cy   +p++  +++    +iy ++g+f++a k+ ++  + + +   d++
  gi|13542003|ref|NP_111691.1| 382 EQLGNVFSEDSDVKKVLCHAYYLKGRFDKAISCYMDIKPDHDLDSMIDLSSIYSNMGKFEEAEKILEDAKNNFTD---DYP 459
                                   56678888888888888888888888999**********************************999998877775...5** PP

                                   HHHHHHHHHHHHHHHT CS
                          SNAP 133 kAieaYekAaelyeqe 148
                                   + i +Y+ Aa +y++ 
  gi|13542003|ref|NP_111691.1| 460 QTIISYRIAALYYRMG 475
                                   *************875 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.036
                                   -HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTT CS
                          SNAP 130 dlekAieaYekAaelyeqeeakalankcllkvAelsaelekyekAieiyekvakks 185
                                   ++ +A++ Y++A e+ ++ +  a+ +  l ++A +    +ky+ Ai i +++++++
  gi|13542003|ref|NP_111691.1| 516 RYGDALKKYNEALEINRKLSNYAEISRNLNNIALIDVYTGKYDLAISILKELIETT 571
                                   5789********************************************99998765 PP

>> TPR_21  Tetratricopeptide repeat-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   7.6e-07   0.00055      88     178 ..     436     533 ..     426     549 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 7.6e-07
                        TPR_21  88 eagdlaaAkaqLewvlekakdeelkalarlRLarvllaekkydeAlktL.......eakkeeafaalvaelrGDilvaqgk 161
                                   + g++++A++ Le + ++  d+  +++++ R+a+++  ++ y++ + +L       +a++ ++ +a + ++ G+i +   +
  gi|13542003|ref|NP_111691.1| 436 NMGKFEEAEKILEDAKNNFTDDYPQTIISYRIAALYYRMGRYKDTIDMLtpllgkiDAENMSGVKAGILNILGNIDMTSYR 516
                                   5799*****************************************999966666667777777888888888888888888 PP

                        TPR_21 162 ldeAraaYqaAlaalee 178
                                     +A ++Y++Al+ + +
  gi|13542003|ref|NP_111691.1| 517 YGDALKKYNEALEINRK 533
                                   88888888888875554 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.0    0.0036       2.5       2      17 ..     400     415 ..     400     416 .. 0.95
   2 ?   -0.9   0.0       1.9   1.4e+03      30      42 .]     463     475 ..     462     475 .. 0.87
   3 !   10.3   0.2   0.00062      0.44       9      26 ..     516     533 ..     508     544 .. 0.79
   4 ?   -1.7   0.0       3.5   2.5e+03       5      19 ..     552     566 ..     549     569 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0036
                        TPR_11   2 dayyeqGkyeeAieaY 17 
                                   +ayy +G++++Ai +Y
  gi|13542003|ref|NP_111691.1| 400 HAYYLKGRFDKAISCY 415
                                   69***********999 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.9
                        TPR_11  30 ayynLGlayykqG 42 
                                   + y ++++yy++G
  gi|13542003|ref|NP_111691.1| 463 ISYRIAALYYRMG 475
                                   569999*****98 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 0.00062
                        TPR_11   9 kyeeAieaYkkAlkldPd 26 
                                   +y +A+++Y++Al+++ +
  gi|13542003|ref|NP_111691.1| 516 RYGDALKKYNEALEINRK 533
                                   899************964 PP

  == domain 4  score: -1.7 bits;  conditional E-value: 3.5
                        TPR_11   5 yeqGkyeeAieaYkk 19 
                                   +  Gky+ Ai  +k+
  gi|13542003|ref|NP_111691.1| 552 VYTGKYDLAISILKE 566
                                   567******966665 PP

>> SHNi-TPR  SHNi-TPR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   3.6e-06    0.0026       3      34 ..     503     534 ..     501     537 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 3.6e-06
                      SHNi-TPR   3 vydlLGEislEnenFpqAveDlrkaLeLreql 34 
                                   +++ LG+i++++ ++ +A++ +++aLe+ ++l
  gi|13542003|ref|NP_111691.1| 503 ILNILGNIDMTSYRYGDALKKYNEALEINRKL 534
                                   6789************************9988 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   0.1     3e-05     0.021      13      54 ..     256     297 ..     247     306 .. 0.86
   2 ?    0.5   0.0      0.78   5.6e+02      36      58 ..     371     393 ..     369     403 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3e-05
                                   HCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEE CS
                          TrmB  13 vYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVer 54 
                                   +Yl ++ +   ++d  a +l++ r+ v +++r+LedkGlV+ 
  gi|13542003|ref|NP_111691.1| 256 AYLMVMLSNDIDVDSAAIILNRKRTEVLNIIRKLEDKGLVKF 297
                                   5999999999999***************************85 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.78
                                   CHCHHHHHHHHHHCTSEEEESST CS
                          TrmB  36 rskvYevLrsLedkGlVerekgr 58 
                                   +++v ev++ Le+ G V  e++ 
  gi|13542003|ref|NP_111691.1| 371 YNSVDEVIEDLEQLGNVFSEDSD 393
                                   67899***********9998876 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0      0.49   3.5e+02       6      51 ..     433     478 ..     428     481 .. 0.70
   2 !   10.4   0.0    0.0012      0.83      12      61 ..     516     568 ..     507     574 .. 0.89
   3 ?    1.2   0.0      0.86   6.1e+02      35      61 ..     735     761 ..     730     765 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.49
                        TPR_16   6 aalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrla 51 
                                   ++ + g++++A++ le a  ++ ++      ++  + +++r gr++
  gi|13542003|ref|NP_111691.1| 433 IYSNMGKFEEAEKILEDAKNNFTDDYPQTIISYRIAALYYRMGRYK 478
                                   6778999999999999886666666666666666666666666665 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0012
                        TPR_16  12 dyddAaaaleaalkrdpssPdaaeAllllgdaalrq...grlaeAaalyraal 61 
                                   +y dA++ +++al+ +++ +  ae + +l+++al     g +++A+  +++++
  gi|13542003|ref|NP_111691.1| 516 RYGDALKKYNEALEINRKLSNYAEISRNLNNIALIDvytGKYDLAISILKELI 568
                                   89********************************988********98887765 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.86
                        TPR_16  35 eAllllgdaalrqgrlaeAaalyraal 61 
                                    A++++++++l  g+l++ +  +++++
  gi|13542003|ref|NP_111691.1| 735 NASFHKAVILLSIGDLDGFRRHFERMQ 761
                                   699***************999999875 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0       3.3   2.4e+03       8      24 ..     399     415 ..     394     422 .. 0.84
   2 ?    7.1   0.0     0.015        11       6      27 ..     429     450 ..     426     459 .. 0.89
   3 ?    1.4   0.0       1.1   7.5e+02       5      24 ..     465     484 ..     463     490 .. 0.88
   4 ?   -1.1   0.0       6.9   4.9e+03       9      31 ..     509     531 ..     504     535 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 3.3
                        TPR_14   8 aeallalGdpdeAiall 24 
                                    +a++  G++d+Ai ++
  gi|13542003|ref|NP_111691.1| 399 CHAYYLKGRFDKAISCY 415
                                   5789999******9876 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.015
                        TPR_14   6 alaeallalGdpdeAiallrra 27 
                                   +l +++ + G+++eA+++l++a
  gi|13542003|ref|NP_111691.1| 429 DLSSIYSNMGKFEEAEKILEDA 450
                                   67899***************98 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 1.1
                        TPR_14   5 lalaeallalGdpdeAiall 24 
                                   +++a+++++ G++++ i++l
  gi|13542003|ref|NP_111691.1| 465 YRIAALYYRMGRYKDTIDML 484
                                   67899**********99998 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 6.9
                        TPR_14   9 eallalGdpdeAiallrralala 31 
                                    + +++ ++ +A++ +++al+ +
  gi|13542003|ref|NP_111691.1| 509 NIDMTSYRYGDALKKYNEALEIN 531
                                   55666778899999999999875 PP

>> PPR  PPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.2       1.9   1.4e+03       5      28 ..     104     127 ..     103     129 .. 0.90
   2 ?   -1.4   0.0       5.3   3.8e+03       8      25 ..     345     362 ..     344     362 .. 0.85
   3 ?    3.2   0.1      0.18   1.3e+02       8      26 ..     400     418 ..     398     419 .. 0.87
   4 !    8.1   0.0     0.005       3.6       8      26 ..     432     450 ..     430     453 .. 0.86
   5 ?    1.2   0.0      0.75   5.4e+02      14      28 ..     555     569 ..     552     569 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 1.9
                           PPR   5 slIsgycknGkleeAlelfkeMke 28 
                                   ++I +y+ + +  e + lf  M +
  gi|13542003|ref|NP_111691.1| 104 IVIAVYGVEKLSMESKNLFLYMCR 127
                                   6899***************99976 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 5.3
                           PPR   8 sgycknGkleeAlelfke 25 
                                   + + k++kl+e  +++ke
  gi|13542003|ref|NP_111691.1| 345 HILMKANKLDEIRDIIKE 362
                                   67899******9999887 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.18
                           PPR   8 sgycknGkleeAlelfkeM 26 
                                   ++y  +G++++A++++ ++
  gi|13542003|ref|NP_111691.1| 400 HAYYLKGRFDKAISCYMDI 418
                                   58999*********99876 PP

  == domain 4  score: 8.1 bits;  conditional E-value: 0.005
                           PPR   8 sgycknGkleeAlelfkeM 26 
                                   s y+  Gk+eeA++++++ 
  gi|13542003|ref|NP_111691.1| 432 SIYSNMGKFEEAEKILEDA 450
                                   679************9975 PP

  == domain 5  score: 1.2 bits;  conditional E-value: 0.75
                           PPR  14 GkleeAlelfkeMke 28 
                                   Gk++ A++++ke++e
  gi|13542003|ref|NP_111691.1| 555 GKYDLAISILKELIE 569
                                   9***********975 PP

>> TPR_MalT  MalT-like TPR region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0     0.083        59     147     192 ..     410     455 ..     405     474 .. 0.83
   2 ?    7.5   0.0    0.0033       2.4     232     287 ..     532     588 ..     516     607 .. 0.72
   3 ?   -0.2   0.0      0.72   5.2e+02     167     230 ..     700     762 ..     690     776 .. 0.69

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.083
                      TPR_MalT 147 eGielleqlepeaaldayvllarialaqGdleeAetllekaeelar 192
                                   ++i +  + +p++ ld+ + l  i+   G+ eeAe++le a++  +
  gi|13542003|ref|NP_111691.1| 410 KAISCYMDIKPDHDLDSMIDLSSIYSNMGKFEEAEKILEDAKNNFT 455
                                   6788888889999999999999999999999999999999998755 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0033
                      TPR_MalT 232 sdddnhfl.elelrnlarvllalgrydeAlellerLlkaaeelgrvrslieiliLqa 287
                                    + +n+ +  ++l n+a + +  g+yd A ++l++L++++  +g   s+i++   ++
  gi|13542003|ref|NP_111691.1| 532 RKLSNYAEiSRNLNNIALIDVYTGKYDLAISILKELIETTYSTGDLVSRIYAIYNLS 588
                                   444444430345588************************999988888887655555 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.72
                      TPR_MalT 167 larialaqGdleeAetllekaeelaresnfhv.dwlanaeevrvrlwlaqgdlaaaerwleaael 230
                                   la  +   ++ e A+++++ aee a + +++  +++a ++++   ++l  gdl+ ++r  e  ++
  gi|13542003|ref|NP_111691.1| 700 LAYYYRIIENQEMAKHYVDMAEEAAYKMKIPYvIVNASFHKAV--ILLSIGDLDGFRRHFERMQK 762
                                   5555555577888999999999999988886313344444444..45789999988887766654 PP

>> OSCP  ATP synthase delta (OSCP) subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.63   4.5e+02      86     119 ..      87     120 ..      35     163 .. 0.82
   2 ?    7.0   0.0    0.0084         6      17      56 ..     372     411 ..     365     464 .. 0.80
   3 ?    3.2   0.0      0.12        88      65     100 ..     689     724 ..     638     734 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.63
                          OSCP  86 peiaeefeellaeargiveaeVtsavpLtdeqle 119
                                   + i++e+ e  +++++++ + V+ +++L+ e ++
  gi|13542003|ref|NP_111691.1|  87 NTIIKEYDEFTRNNKEKIVIAVYGVEKLSMESKN 120
                                   5788888888888888888888888888877664 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0084
                          OSCP  17 galeeveeelealeavlaedkklaellsnpavsaeekkdl 56 
                                   ++++ev e+le+l +v++ed++++++l +  + + +  ++
  gi|13542003|ref|NP_111691.1| 372 NSVDEVIEDLEQLGNVFSEDSDVKKVLCHAYYLKGRFDKA 411
                                   789************************9877666655555 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.12
                          OSCP  65 lseavknflkllaenkRlalLpeiaeefeellaear 100
                                    +++++ fl  la + R+   +e+a+++ ++++ea 
  gi|13542003|ref|NP_111691.1| 689 TDDYTSTFLIALAYYYRIIENQEMAKHYVDMAEEAA 724
                                   589****************************99976 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 ?    8.0   0.1    0.0046       3.3      28      81 ..     397     449 ..     386     450 .. 0.81
   2 ?    8.3   0.0    0.0038       2.7      29      79 ..     430     484 ..     420     487 .. 0.81
   3 ?    3.2   0.1      0.15     1e+02      37      81 ..     522     566 ..     519     570 .. 0.79
   4 ?   -1.9   0.2       5.6     4e+03      20      34 ..     689     703 ..     684     705 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0046
                                   HHHHHHHHTT-HHHHHHHHHCTSHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                        ANAPC3  28 llAlclylngqykrAyellrkaklnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                    l+ ++yl g++++A+  + +  + +++l + + +   +  ++k+eeA+++Le 
  gi|13542003|ref|NP_111691.1| 397 VLCHAYYLKGRFDKAISCYMDI-KPDHDLDSMIDLSSIYSNMGKFEEAEKILED 449
                                   5899**************9999.5555556666666777799********9986 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0038
                                   HHHHHHHTT-HHHHHHHHHCTSHHHC-H....HHHHHHHHHHHHTT-HHHHHHHH CS
                        ANAPC3  29 lAlclylngqykrAyellrkaklnsksl....gcrylfAqcllkLkkyeeAiaaL 79 
                                   l+  + ++g++++A ++l++ak n ++      + y +A  ++ +++y++ i+ L
  gi|13542003|ref|NP_111691.1| 430 LSSIYSNMGKFEEAEKILEDAKNNFTDDypqtIISYRIAALYYRMGRYKDTIDML 484
                                   56778999************9776666667777889999999999****999987 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.15
                                   T-HHHHHHHHHCTSHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                        ANAPC3  37 gqykrAyellrkaklnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                   ++y++A+e+ rk+  + +  + +  +A   +  +ky+ Ai++L++
  gi|13542003|ref|NP_111691.1| 522 KKYNEALEINRKLSNYAEISRNLNNIALIDVYTGKYDLAISILKE 566
                                   788888888888877778888888888888888888888888875 PP

  == domain 4  score: -1.9 bits;  conditional E-value: 5.6
                                   H--HHHHHHHHHHHH CS
                        ANAPC3  20 tespedayllAlcly 34 
                                   t+++ +++l Al++y
  gi|13542003|ref|NP_111691.1| 689 TDDYTSTFLIALAYY 703
                                   6788899******99 PP

>> Med28  Mediator complex subunit 28
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   0.00016      0.11      61     114 ..     344     397 ..     309     402 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00016
                         Med28  61 kHlqktseqlatqlkalrekgqnvfgdgtkidstidyleklkqvlsdaedvykv 114
                                    H+   +++l      ++ekgq +      +d  i+ le+l +v+s+ +dv+kv
  gi|13542003|ref|NP_111691.1| 344 MHILMKANKLDEIRDIIKEKGQSLVDGYNSVDEVIEDLEQLGNVFSEDSDVKKV 397
                                   46666688999999999********9999**********************997 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 ?    0.8   0.0      0.75   5.4e+02      19      56 ..     184     221 ..     170     230 .. 0.81
   2 ?    9.4   0.1    0.0015       1.1      19      73 ..     265     315 ..     248     319 .. 0.75
   3 ?   -2.4   0.0       7.3   5.2e+03      41      52 ..     376     387 ..     371     425 .. 0.59

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.75
                       DUF2250  19 kanvdYaksiakeleipleevrellkkLeelGLlerve 56 
                                   k+  d+ k ia+ ++ ++  ++ +l+  ++lG ++  +
  gi|13542003|ref|NP_111691.1| 184 KLPDDFVKEIARLTNYNIDSMKYALRYYQDLGVINDRK 221
                                   566799**************************997543 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0015
                       DUF2250  19 kanvdYaksiakeleipleevrellkkLeelGLlervegktikrteaklKkksev 73 
                                    ++vd a      l+ +++ev ++++kLe+ GL+ + +g+++ +++ k +++ e+
  gi|13542003|ref|NP_111691.1| 265 DIDVDSAA---IILNRKRTEVLNIIRKLEDKGLV-KFNGQVVGFYSDKIRRSVEK 315
                                   55555444...44566889**************9.58999999999999988776 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 7.3
                       DUF2250  41 ellkkLeelGLl 52 
                                   e++++Le+lG +
  gi|13542003|ref|NP_111691.1| 376 EVIEDLEQLGNV 387
                                   555555555533 PP

>> ATP-cone  ATP cone domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0    0.0064       4.6       4      30 ..     295     322 ..     293     366 .. 0.83
   2 ?    3.2   0.5      0.18   1.3e+02      21      58 ..     647     684 ..     640     686 .. 0.91

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0064
                                   E-TTS-EEE--HHHHHHHHHHHHHH.-H CS
                      ATP-cone   4 iKRdGtvepfdvekIkraiekAceg.se 30 
                                   +K +G v+ f  +kI+r++ek+++  + 
  gi|13542003|ref|NP_111691.1| 295 VKFNGQVVGFYSDKIRRSVEKSMKTsDI 322
                                   5779******************998433 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.18
                                   HHHHHHHH-HHHHHHHHHHHHHHHHHHHIIT-BHHHHH CS
                      ATP-cone  21 aiekAcegseeeideiaeeveaevrkrlrdgisteeIq 58 
                                   aie+A  ++++ +  i +++++ v  + + +i+t+eI+
  gi|13542003|ref|NP_111691.1| 647 AIENAIMEDQKIMAIIFHKIINYVLTGEDPNIDTQEID 684
                                   89***99989999999*********************8 PP

>> TPR_20  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       3.5   2.5e+03      10      43 ..     380     413 ..     374     422 .. 0.79
   2 ?    1.5   0.0      0.54   3.9e+02      20      43 ..     422     445 ..     416     457 .. 0.87
   3 ?    7.4   0.0    0.0078       5.6      23      72 ..     462     511 ..     441     528 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 3.5
                        TPR_20  10 eleaalaanpddldarldlAlallaagryeeAle 43 
                                   +le+  +   +d d +  l  a++ +gr ++A++
  gi|13542003|ref|NP_111691.1| 380 DLEQLGNVFSEDSDVKKVLCHAYYLKGRFDKAIS 413
                                   5566666667889999999999********9987 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.54
                        TPR_20  20 ddldarldlAlallaagryeeAle 43 
                                    dld ++dl+  +   g+ eeA +
  gi|13542003|ref|NP_111691.1| 422 HDLDSMIDLSSIYSNMGKFEEAEK 445
                                   699******************954 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.0078
                        TPR_20  23 darldlAlallaagryeeAleqLleilkrdrkweddaarkqllkifealg 72 
                                    + +  A +++  gry++ ++ L  +l +  +++   ++  +l i+  ++
  gi|13542003|ref|NP_111691.1| 462 IISYRIAALYYRMGRYKDTIDMLTPLLGKIDAENMSGVKAGILNILGNID 511
                                   57899***********************************9999987665 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0       1.4     1e+03       9      24 ..     401     416 ..     400     419 .. 0.83
   2 ?    3.2   0.0      0.24   1.7e+02       9      30 ..     433     454 ..     425     457 .. 0.85
   3 ?    4.5   0.2     0.092        66       4      23 ..     465     484 ..     464     485 .. 0.90
   4 ?    3.0   0.0      0.26   1.9e+02      12      28 ..     553     569 ..     515     573 .. 0.81
   5 ?   -1.6   0.1       7.7   5.5e+03       1      15 [.     582     596 ..     582     601 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 1.4
                                   HHHHHHHHHHHHHHHH CS
                         TPR_6   9 syrklgdtdkAleale 24 
                                   +y+  g+ dkA+  + 
  gi|13542003|ref|NP_111691.1| 401 AYYLKGRFDKAISCYM 416
                                   688878******9985 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.24
                                   HHHHHHHHHHHHHHHHHHHHH- CS
                         TPR_6   9 syrklgdtdkAlealerlikeY 30 
                                    y ++g+ ++A ++le+  +++
  gi|13542003|ref|NP_111691.1| 433 IYSNMGKFEEAEKILEDAKNNF 454
                                   688899***********99998 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.092
                                   HHHHHHHHHHHHHHHHHHHH CS
                         TPR_6   4 yklalsyrklgdtdkAleal 23 
                                   y++a +y+++g++ + +++l
  gi|13542003|ref|NP_111691.1| 465 YRIAALYYRMGRYKDTIDML 484
                                   9************9998876 PP

  == domain 4  score: 3.0 bits;  conditional E-value: 0.26
                                   HHHHHHHHHHHHHHHHH CS
                         TPR_6  12 klgdtdkAlealerlik 28 
                                    +g++d A+ +l++li+
  gi|13542003|ref|NP_111691.1| 553 YTGKYDLAISILKELIE 569
                                   448************98 PP

  == domain 5  score: -1.6 bits;  conditional E-value: 7.7
                                   HHHHHHHHHHHHHHH CS
                         TPR_6   1 dAlyklalsyrklgd 15 
                                   +A y+l + y+  g+
  gi|13542003|ref|NP_111691.1| 582 YAIYNLSEIYYVIGK 596
                                   799*******98434 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0     0.024        17       3      34 .]     409     445 ..     408     445 .. 0.80
   2 ?   -1.8   0.1       7.7   5.5e+03       2      12 ..     524     537 ..     523     560 .. 0.63
   3 ?   -0.1   0.0       2.2   1.6e+03      15      32 ..     583     600 ..     581     601 .. 0.83
   4 ?    1.0   0.0      0.98     7e+02      13      33 ..     694     714 ..     681     715 .. 0.79
   5 ?   -1.9   0.0       8.2   5.9e+03      17      30 ..     738     751 ..     734     752 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.024
                        TPR_17   3 lkaleld....Pn.nadaynnLAelllknGdlmtArq 34 
                                    ka+ ++    P+ + d++  L  ++++ G++++A++
  gi|13542003|ref|NP_111691.1| 409 DKAISCYmdikPDhDLDSMIDLSSIYSNMGKFEEAEK 445
                                   5777775445588569*******************85 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 7.7
                        TPR_17   2 ylkaleld...Pnn 12 
                                   y +ale++    n+
  gi|13542003|ref|NP_111691.1| 524 YNEALEINrklSNY 537
                                   67777777333333 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 2.2
                        TPR_17  15 aynnLAelllknGdlmtA 32 
                                   a +nL e+++ +G+ + A
  gi|13542003|ref|NP_111691.1| 583 AIYNLSEIYYVIGKQEYA 600
                                   679*******99987755 PP

  == domain 4  score: 1.0 bits;  conditional E-value: 0.98
                        TPR_17  13 adaynnLAelllknGdlmtAr 33 
                                   + ++  LA++++ + + ++A+
  gi|13542003|ref|NP_111691.1| 694 STFLIALAYYYRIIENQEMAK 714
                                   677889******999999986 PP

  == domain 5  score: -1.9 bits;  conditional E-value: 8.2
                        TPR_17  17 nnLAelllknGdlm 30 
                                   + +A++ll++Gdl+
  gi|13542003|ref|NP_111691.1| 738 FHKAVILLSIGDLD 751
                                   6789*******986 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 ?    7.8   0.0    0.0035       2.5     159     202 ..     455     498 ..     408     510 .. 0.79
   2 ?    1.1   1.4      0.39   2.8e+02     141     195 ..     517     571 ..     503     670 .. 0.74
   3 ?    2.1   0.5       0.2   1.4e+02     117     146 ..     693     722 ..     636     756 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0035
                       DUF2225 159 vegideatvlYLiaeLerrlgnkeealrwlskvigskkaskpsk 202
                                   ++   ++ + Y ia L +r+g++++ + +l  ++g+ +a++ s 
  gi|13542003|ref|NP_111691.1| 455 TDDYPQTIISYRIAALYYRMGRYKDTIDMLTPLLGKIDAENMSG 498
                                   334555669********************999999888877555 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.39
                       DUF2225 141 lkkAlelykeayekesfpvegideatvlYLiaeLerrlgnkeealrwlskvigsk 195
                                   +  Al+ y+ea+e +++ ++  + ++ l  ia     +g+++ a+ +l+++i+++
  gi|13542003|ref|NP_111691.1| 517 YGDALKKYNEALEINRKLSNYAEISRNLNNIALIDVYTGKYDLAISILKELIETT 571
                                   5667777777777777766666666666666666666666666666666666544 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.2
                       DUF2225 117 kAklalrlAWlyrdkedeekeklflkkAle 146
                                       ++ lA++yr  e++e+ k ++  A e
  gi|13542003|ref|NP_111691.1| 693 TSTFLIALAYYYRIIENQEMAKHYVDMAEE 722
                                   556778899********9999999988854 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (850 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1123  (0.062636); expected 358.6 (0.02)
Passed bias filter:                      582  (0.0324614); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); 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: 0.85u 0.32s 00:00:01.17 Elapsed: 00:00:00.51
# Mc/sec: 5053.74
//
Query:       gi|13542004|ref|NP_111692.1|  [L=288]
Description: hypothetical protein TVN1173 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.9e-06   28.3   0.0     0.0016   18.9   0.0    2.2  2  TPR_19        Tetratricopeptide repeat
    1.6e-05   25.4   0.0      0.077   13.9   0.0    2.5  2  TPR_14        Tetratricopeptide repeat
    0.00059   19.7   0.0       0.49   10.6   0.0    2.7  2  TPR_2         Tetratricopeptide repeat
    0.00078   19.5   0.0        1.3    9.4   0.0    2.7  2  TPR_8         Tetratricopeptide repeat
    0.00093   19.2   0.9      0.003   17.6   0.0    2.2  3  SRP_TPR_like  Putative TPR-like repeat
  ------ inclusion threshold ------
      0.015   15.9   0.0         12    6.8   0.0    2.8  2  TPR_6         Tetratricopeptide repeat
      0.021   14.6   0.0         11    6.0   0.0    2.7  2  TPR_1         Tetratricopeptide repeat
      0.035   14.4   0.0      0.096   13.0   0.0    1.7  1  TPR_12        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 !   14.6   0.0   1.5e-05     0.034      29      57 ..       8      36 ..       4      44 .. 0.87
   2 !   18.9   0.0     7e-07    0.0016       1      57 [.      14      69 ..      14      81 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.5e-05
                        TPR_19 29 llLAeallalgqldeAealLdalpeedpd 57
                                  l+ +++l++lg+++eA +++d++ e+ pd
  gi|13542004|ref|NP_111692.1|  8 LDRVKILIKLGRYKEALRIIDEVIEDSPD 36
                                  556899********************999 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 7e-07
                        TPR_19  1 llaegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpd 57
                                  l++ g+y eAl++  ++++++p +   +++ + +l+   +++eA+ +L+++   +p 
  gi|13542004|ref|NP_111692.1| 14 LIKLGRYKEALRIIDEVIEDSP-DVSFLYYKISILFTCRRFEEAKSTLNTAISIFPG 69
                                  6778******************.77777779*******************9988887 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   3.4e-05     0.077       4      34 ..       7      37 ..       6      43 .. 0.91
   2 !    9.4   0.0   0.00093       2.1       5      39 ..      41      75 ..      37      81 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.4e-05
                        TPR_14  4 llalaeallalGdpdeAiallrralalaPdd 34
                                  ll+++++l  lG+++eA+++ ++++++ Pd 
  gi|13542004|ref|NP_111692.1|  7 LLDRVKILIKLGRYKEALRIIDEVIEDSPDV 37
                                  6899*************************95 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00093
                        TPR_14  5 lalaeallalGdpdeAiallrralalaPddaeawl 39
                                  +   ++l++ ++++eA   l+ a++ +P++ ++++
  gi|13542004|ref|NP_111692.1| 41 YYKISILFTCRRFEEAKSTLNTAISIFPGSTVFRI 75
                                  55678999********************9987664 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.0   0.00022      0.49      10      33 ..      13      36 ..      12      37 .. 0.90
   2 !    6.4   0.0    0.0049        11      11      33 ..      47      69 ..      45      70 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00022
                         TPR_2 10 ayyklgdyeeAleafekAleldPn 33
                                  +++klg+y+eAl+  ++++e  P+
  gi|13542004|ref|NP_111692.1| 13 ILIKLGRYKEALRIIDEVIEDSPD 36
                                  789**************9998886 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0049
                         TPR_2 11 yyklgdyeeAleafekAleldPn 33
                                  ++   ++eeA+  ++ A+++ P+
  gi|13542004|ref|NP_111692.1| 47 LFTCRRFEEAKSTLNTAISIFPG 69
                                  566689***************96 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.0    0.0027       6.1       9      29 ..      12      32 ..       7      36 .. 0.86
   2 !    9.4   0.0    0.0006       1.3       9      32 ..      45      68 ..      45      70 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0027
                                  HHHHHTT-HHHHHHHHHHHHH CS
                         TPR_8  9 siylklgdyeeAkeyyekale 29
                                  +i++klg+y+eA   + +++e
  gi|13542004|ref|NP_111692.1| 12 KILIKLGRYKEALRIIDEVIE 32
                                  699*********999988887 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0006
                                  HHHHHTT-HHHHHHHHHHHHHHHH CS
                         TPR_8  9 siylklgdyeeAkeyyekaleldp 32
                                  si+++  ++eeAk++++ a+++ p
  gi|13542004|ref|NP_111692.1| 45 SILFTCRRFEEAKSTLNTAISIFP 68
                                  5788999**************977 PP

>> SRP_TPR_like  Putative TPR-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   1.3e-06     0.003      20      70 ..      10      62 ..       1      70 [. 0.82
   2 ?   -2.6   0.0       2.4   5.4e+03      50      82 ..     134     164 ..     110     180 .. 0.60
   3 ?   -1.5   0.1       1.1   2.4e+03      23      35 ..     209     221 ..     162     236 .. 0.62

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.3e-06
                  SRP_TPR_like 20 kvvaliklekyeeaLkllkkgsalsedvr..fEkaYvlYklkkykkalkilkk 70
                                  +v  likl++y+eaL+++++  + s dv   + k  +l+  +++++a ++l+ 
  gi|13542004|ref|NP_111692.1| 10 RVKILIKLGRYKEALRIIDEVIEDSPDVSflYYKISILFTCRRFEEAKSTLNT 62
                                  78889**************98877776652268999999********999986 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.4
                  SRP_TPR_like  50 EkaYvlYklkkykkalkilkkveaeekvkvlks 82 
                                    k+ ++  l+++k+  kil +  + e ++ l +
  gi|13542004|ref|NP_111692.1| 134 GKSAIYCDLQQLKE--KILTERISTETINGLYT 164
                                   45555555555554..55554444445555555 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 1.1
                  SRP_TPR_like  23 aliklekyeeaLk 35 
                                       l+ky++ Lk
  gi|13542004|ref|NP_111692.1| 209 KAFILGKYSDFLK 221
                                   2333455555554 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0    0.0052        12       9      32 ..      13      36 ..       7      36 .. 0.89
   2 ?    6.2   0.0    0.0085        19      15      33 .]      52      70 ..      39      70 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0052
                                  HHHHHHHHHHHHHHHHHHHHH-TT CS
                         TPR_6  9 syrklgdtdkAlealerlikeYPd 32
                                   ++klg++ +Al++ +++i++ Pd
  gi|13542004|ref|NP_111692.1| 13 ILIKLGRYKEALRIIDEVIEDSPD 36
                                  578999***************998 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0085
                                  HHHHHHHHHHHHHHH-TT- CS
                         TPR_6 15 dtdkAlealerlikeYPdS 33
                                  + ++A+ +l+  i+ +P+S
  gi|13542004|ref|NP_111692.1| 52 RFEEAKSTLNTAISIFPGS 70
                                  789**************98 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0    0.0052        12      10      28 ..      13      31 ..      12      32 .. 0.77
   2 ?    6.0   0.0    0.0049        11       4      32 ..      40      68 ..      37      70 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0052
                                  HHHHTT-HHHHHHHHHHHH CS
                         TPR_1 10 ayfklgkydeAleyyekAL 28
                                  ++ klg+y+eAl   ++++
  gi|13542004|ref|NP_111692.1| 13 ILIKLGRYKEALRIIDEVI 31
                                  6789*******97666555 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0049
                                  HHHHHHHHHHTT-HHHHHHHHHHHHHHST CS
                         TPR_1  4 lynlGnayfklgkydeAleyyekALelnP 32
                                  ly +  ++f   +++eA    + A+++ P
  gi|13542004|ref|NP_111692.1| 40 LYYKISILFTCRRFEEAKSTLNTAISIFP 68
                                  7888889999*****************99 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   4.3e-05     0.096      16      75 ..      17      67 ..       7      68 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.3e-05
                        TPR_12 16 lgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaia 75
                                  lgry       ++al+i+ ++  +d+p+++  ++ +++l+  + r+eeA + l+ a+ i+
  gi|13542004|ref|NP_111692.1| 17 LGRY-------KEALRIIDEVI-EDSPDVSFLYYKISILFTCR-RFEEAKSTLNTAISIF 67
                                  5555.......55555554443.8999****************.***********99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); 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: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.36
# Mc/sec: 2423.40
//
Query:       gi|13542005|ref|NP_111693.1|  [L=101]
Description: hypothetical protein TVN1174 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       507  (0.0282782); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); 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 0.31s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 627.61
//
Query:       gi|13542006|ref|NP_111694.1|  [L=397]
Description: Acyl-CoA dehydrogenase [Thermoplasma volcanium GSS1]
Scores for complete 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-31  107.0   1.0    1.4e-30  106.5   1.0    1.3  1  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
    3.5e-26   92.1   0.0    8.1e-26   90.9   0.0    1.7  1  Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
    3.5e-15   56.0   0.0    7.8e-15   54.9   0.0    1.6  1  Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
    5.5e-08   33.2   0.1    9.4e-08   32.4   0.1    1.3  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 !  106.5   1.0   3.2e-34   1.4e-30       1     148 [.     234     389 ..     234     391 .. 0.99

  Alignments for each domain:
  == domain 1  score: 106.5 bits;  conditional E-value: 3.2e-34
                                   TBHHHHHTTTT--S-----..-SHHHHHHHHHHHHHHHTSB-CC-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH----- CS
                 Acyl-CoA_dh_1   1 gkGfrvametlnheRlavaaaalglarraleealeyarrrkafgkplidhqlvreklaemaaeleaarllvyraaealdag 81 
                                   ++Gf+++ e++++ R ++ + ++ +a + +e+ ++y+++rkafg  ++ ++ ++++la+  a++eaa + +y+a + +d++
  gi|13542006|ref|NP_111694.1| 234 NRGFNIVHEGFEFARGLISVISASMALKSIENGAAYMKQRKAFGNSIATFEGLQFQLADDVAKMEAALNFAYKALWIYDQE 314
                                   79******************************************************************************* PP

                                   ---........HHHHHHHHHHHHHHHHHHHHHHHHHHGGGTTSGGGHHHHHHHHTHHHHHSSS-HHHHHHHHHHH CS
                 Acyl-CoA_dh_1  82 kpd........raeasmaKlfaselaqevadlamqllGgaGyleeypverlyrdarvlrigeGtseiqrniiarr 148
                                   +          ++ ++maKl  + +  +++++amq+ G++Gy+++ p e ++r +r+++++eG+ ei++ iiar 
  gi|13542006|ref|NP_111694.1| 315 QRYgkysrfqvSKMIAMAKLISTTWGFDAVNDAMQWQGAYGYSKDCPEEWALRGIRSFQLAEGSREIMKIIIARE 389
                                   *9999********************************************************************97 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 !   90.9   0.0   1.8e-29   8.1e-26       1     112 [.       8     120 ..       8     121 .. 0.97

  Alignments for each domain:
  == domain 1  score: 90.9 bits;  conditional E-value: 1.8e-29
                                   THHHHHHHHHHHHHHHHHTHHHHHHHHHHTSGHHHHHHHHHHTTCTSTTS-GGGTS--S-HHHHHHHHHHHHHH-HHHHH. CS
                 Acyl-CoA_dh_N   1 teeqealrdtvrefaeeelaphaaewdeegefprelwkklaelGllgitvpeeygGagldyleaaivaeelaradaglal. 80 
                                   te+q+ l+ t+++fae+ +ap+++++++++++p+e+++ la++G+lg+++pe+ygG+g+d++++ ivae++arad   ++ 
  gi|13542006|ref|NP_111694.1|   8 TEDQKLLQSTAKDFAEKVIAPNIERMRKDRRIPKEVFDGLAKMGFLGMAIPEKYGGMGMDAVSTGIVAEQIARADPTASIp 88 
                                   79************************9999**********************************************99999 PP

                                   HHHHHHHTTHHHHHHHS-HHHHHHHHHHHHTT CS
                 Acyl-CoA_dh_N  81 llgvhsslvapailrfGteeqkrryLpklasg 112
                                   +l + ++  ++ i ++G++e     L+k+a+g
  gi|13542006|ref|NP_111694.1|  89 VLFLVDNAWSYLISKYGNPEVFSGILQKVARG 120
                                   9999999999********************99 PP

>> Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.9   0.0   1.7e-18   7.8e-15       2      96 ..     126     221 ..     125     222 .. 0.82

  Alignments for each domain:
  == domain 1  score: 54.9 bits;  conditional E-value: 1.7e-18
                                   EE---SS-SS-GGG---EEEEETT.EEEEEEEEEEEETTTT.-SEE....EEEEETS---.----EEEEEEE..GGGEEE- CS
                 Acyl-CoA_dh_M   2 falTEpqaGsdvasvkttaaerdggeyvlnGeKiwitnaai.atla....lvlartekpd.rarglslflvprdapgvsvr 76 
                                   +++TE ++Gsdva+++t +a ++g+ey++nGeK +i+ +++    +    +++++ ++p+ +arg+sl+++p  +++++++
  gi|13542006|ref|NP_111694.1| 126 IGSTESGHGSDVAGIDT-VAVKKGDEYIVNGEKSFISLVRDiK-EIgggyVTVVK-TDPKaGARGISLLYIPY-SEEIEIG 202
                                   789**************.66677778***************63.33354244445.444457**********5.667**** PP

                                   ----BSS-TTS-EEEEEEE. CS
                 Acyl-CoA_dh_M  77 rieeklGlrglptgelvfed 96 
                                    +e ++G+ g ++g l+f+d
  gi|13542006|ref|NP_111694.1| 203 YLE-EMGREGSSWGTLRFND 221
                                   *95.7*************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 !   32.4   0.1   2.1e-11   9.4e-08      19     124 ..     267     370 ..     254     375 .. 0.89

  Alignments for each domain:
  == domain 1  score: 32.4 bits;  conditional E-value: 2.1e-11
                                   HHHHHHHHCTTT-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----HHHHHHHHHHHHHHHHHHHHHHH CS
                 Acyl-CoA_dh_2  19 velarervrassgekladdpatqlalaeaaarldAAralleraaaraealaaagkevtvedraearraaalavelaiaavd 99 
                                   ++++++r+   +g+++a ++ +q++la+  a+++AA  + ++a +   +  + gk   ++  + +++a++  ++   +av+
  gi|13542006|ref|NP_111694.1| 267 AAYMKQRKA--FGNSIATFEGLQFQLADDVAKMEAALNFAYKALWIYDQEQRYGKYSRFQVSKMIAMAKLISTTWGFDAVN 345
                                   445555555..***********************************99999999999************************ PP

                                   HHHHHCGGGGGBTT-HHHHHHHHHH CS
                 Acyl-CoA_dh_2 100 alfeaaGgsalrkesplqRlwRDah 124
                                   ++++  G++++ k+ p + ++R ++
  gi|13542006|ref|NP_111694.1| 346 DAMQWQGAYGYSKDCPEEWALRGIR 370
                                   **************99998888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (397 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2810.72
//
Query:       gi|13542007|ref|NP_111695.1|  [L=193]
Description: RNA-processing protein [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-08   34.3   3.2    0.00059   19.6   0.4    2.6  2  KH_1      KH domain
  ------ inclusion threshold ------
        2.3    8.1  10.1        1.1    9.1   2.3    3.0  3  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 !   19.6   0.4   6.6e-08   0.00059       4      48 ..      17      55 ..      14      75 .. 0.79
   2 !   14.9   0.2   1.9e-06     0.017      12      65 ..     116     161 ..     112     162 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 6.6e-08
                                  EEEGGGHHHHHHTGGGHHHHHHHHHH.T-EEEEESSTT...T.-EE CS
                          KH_1  4 ilvPsslvgriIGkgGsnIkeIreet.gakIkvpksedegsderev 48
                                  i vP++ +  +IGk G++ k+I+e    +k +++  e       ev
  gi|13542007|ref|NP_111695.1| 17 IRVPKDRIKVVIGKDGEVKKKIEE-MgEVKLTIDTAE------AEV 55
                                  78**********************.779999976332......344 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 1.9e-06
                                   HHHHTGGGHHHHHHHHHHT-EEEEESSTT...T.-EEEEEESHHHHHHHHHHHH CS
                          KH_1  12 griIGkgGsnIkeIreetgakIkvpksedegsderevtisGspeavekAkelie 65 
                                    r+IG gG++   I+e tg +  v  +       +++ i+G+  av  A+e+i+
  gi|13542007|ref|NP_111695.1| 116 ARVIGTGGKTRAIIEELTGSYLSVY-G-------DTISIIGDYLAVTYAEEAIN 161
                                   58*********************87.4.......59*****9999*****9995 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   2.3   0.00012       1.1      34      55 ..      22      43 ..      16      74 .. 0.83
   2 ?    2.8   0.3     0.012     1e+02      36      56 ..     115     135 ..     112     146 .. 0.76
   3 ?   -1.1   0.0       0.2   1.8e+03       7      29 ..     152     173 ..     146     181 .. 0.65

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00012
                                  SCHHHHHTGGGHHHHHHHHHHH CS
                          KH_2 34 sqpgivIGkgGsnikkigkelr 55
                                   + ++vIGk G+  kki++  +
  gi|13542007|ref|NP_111695.1| 22 DRIKVVIGKDGEVKKKIEEMGE 43
                                  6889*************98655 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.012
                                   HHHHHTGGGHHHHHHHHHHHH CS
                          KH_2  36 pgivIGkgGsnikkigkelrk 56 
                                   +++vIG gG++   i++  + 
  gi|13542007|ref|NP_111695.1| 115 KARVIGTGGKTRAIIEELTGS 135
                                   789******987777776665 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.2
                                   HHHTECETEEEEEEECCSCEEEE CS
                          KH_2   7 aveikkagvskveIertanrvii 29 
                                   av+ + +++ +++I+ +++r+++
  gi|13542007|ref|NP_111695.1| 152 AVT-YAEEAINMIINGKKHRTVY 173
                                   553.3344566678888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       722  (0.04027); expected 358.6 (0.02)
Passed bias filter:                      502  (0.0279993); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 1214.20
//
Query:       gi|13542008|ref|NP_111696.1|  [L=251]
Description: serine/threonine protein kinase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-56  191.4   2.3    1.5e-56  191.0   2.3    1.1  1  RIO1            RIO1 family
    9.7e-05   22.4   0.0    0.00097   19.1   0.0    2.1  2  APH             Phosphotransferase enzyme family
    0.00017   21.1   0.3      0.041   13.2   0.0    2.1  2  Kdo             Lipopolysaccharide kinase (Kdo/WaaP) family
    0.00067   19.1   0.4     0.0012   18.2   0.4    1.5  1  Pkinase         Protein kinase domain
     0.0014   18.3   0.1       0.22   11.1   0.1    2.7  1  Choline_kinase  Choline/ethanolamine kinase
  ------ inclusion threshold ------
       0.02   14.5   0.4      0.051   13.2   0.4    1.6  1  PC4             Transcriptional Coactivator p15 (PC4)


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 !  191.0   2.3   5.1e-60   1.5e-56       2     185 ..      57     232 ..      56     236 .. 0.95

  Alignments for each domain:
  == domain 1  score: 191.0 bits;  conditional E-value: 5.1e-60
                                   EEEEEETTTEEEEEEEE-S---SS-HHHHCTTTSTTSTCG--GS-HHHHHHHHHHHHHHHHHHHHHTT--S--EEEEETTE CS
                          RIO1   2 VyhavsedgkevaiKiyktstteFkkrkkyvsgekrfkdrksktnprklvklwaekEfrnLkrleeagvpvPkpielkrhv 82 
                                   V+ avs d++ v++K++k+st++F ++++y++g++rf ++  ++++ +++ lw++kE++n+  l+e++vpvP+pi + +++
  gi|13542008|ref|NP_111696.1|  57 VFRAVS-DKRYVVVKVFKMSTLKFMNIREYIEGDQRFVKQ--RIDRMSIISLWVRKEYTNMLTLYEKHVPVPRPIGFFKNI 134
                                   889877.8889*************************9966..9************************************** PP

                                   EEEE--EETTEEGGBHHHCG-HHHHHHHHHHHHHHHHHHHHTSTEEESS-STTSEEEETTEEEE--GTTEEETTSTTHHHH CS
                          RIO1  83 lvmefigedgvaapklkdveeeeeaeelyeevleemrklykeaglvHaDLSeyNvlvdedkvviIDvsQaveldhpnalef 163
                                   lv  +ig+++ +ap+lkdv+    +ee+y ++l+ ++k++  a+lvH DLSeyN+l+++ +v++ID++Qav++dhp+a ef
  gi|13542008|ref|NP_111696.1| 135 LVEGYIGTKEKPAPQLKDVQ---VTEEIYTMTLDGIKKML-SARLVHSDLSEYNILYHRRRVYFIDLAQAVDIDHPMATEF 211
                                   ********************...899*********99999.**************************************** PP

                                   HHHHHHHHHHHHHTTC-----H CS
                          RIO1 164 LerDveniikfFrrkgvekvde 185
                                   L+rD++ni++fF+++g++ +++
  gi|13542008|ref|NP_111696.1| 212 LKRDIKNISTFFSKHGIK-TSF 232
                                   *****************9.344 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0     0.099     3e+02      38      60 ..     108     130 ..      48     141 .. 0.73
   2 !   19.1   0.0   3.2e-07   0.00097     135     197 ..     144     201 ..     136     207 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.099
                                   HHHHHHHHHHHHTT-B--B-CTT CS
                           APH  38 rrevallrlLakagvpvPevlag 60 
                                   r+e+  +  L +  vpvP+++ +
  gi|13542008|ref|NP_111696.1| 108 RKEYTNMLTLYEKHVPVPRPIGF 130
                                   45555666677677999999975 PP

  == domain 2  score: 19.1 bits;  conditional E-value: 3.2e-07
                                   CCCGCCTCCHHHHHHHHHHHHHHHH--SSS-EEEE-SS-SGGGEEEC..TTEEEEE---TT-E CS
                           APH 135 rllaselldlleeleeqvlaalaallpgelptvllHgDlhpgNllvdpddgrvtGviDfedag 197
                                    ++a++l+d ++  ee ++ + ++   + l+++l+H Dl+  N+l +    rv ++iD+  a+
  gi|13542008|ref|NP_111696.1| 144 EKPAPQLKD-VQVTEE-IYTMTLDGIKKMLSARLVHSDLSEYNILYH--RRRV-YFIDLAQAV 201
                                   678999999.999999.******************************..9999.****97775 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.3   0.0    0.0019       5.6      53      81 ..     102     130 ..      53     139 .. 0.78
   2 !   13.2   0.0   1.4e-05     0.041     116     174 ..     152     205 ..     142     238 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0019
                           Kdo  53 lgrtravrEfrllkrLeeagvavpkpvaa 81 
                                   +  + +++E+ ++  L+e+ v+vp+p+ +
  gi|13542008|ref|NP_111696.1| 102 IISLWVRKEYTNMLTLYEKHVPVPRPIGF 130
                                   66677889******************976 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 1.4e-05
                           Kdo 116 aeelkrallkavgrliaklhragvnHadlyaknillqqeeeeeaeiwliDldkarlrlr 174
                                   +++++++++  +   i+k+ +a + H dl   nil + +      +++iDl +a     
  gi|13542008|ref|NP_111696.1| 152 DVQVTEEIYTMTLDGIKKMLSARLVHSDLSEYNILYHRRR-----VYFIDLAQAVDIDH 205
                                   567788888888889**********************996.....******99987765 PP

>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.4   4.2e-07    0.0012       9     148 ..      51     203 ..      46     222 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 4.2e-07
                                   EESSEEEEEEEETTTTEEEEEEEEECHCHCHHHH.HHHHHHHHHH.HHHSCTTB--EEEEEEESSEEEEEEE--TTEB... CS
                       Pkinase   9 eGsfGkVykaveketgkivAvKkikkekakkkke.kkvlrEikil.kklkhpnivrlyevfeekdelylvleyvegge... 84 
                                   +G+ ++V++av  ++++ v+vK++k +  k ++  + +    +++ ++++ + i+ l+   e ++ l+l   +v+      
  gi|13542008|ref|NP_111696.1|  51 TGKESVVFRAV--SDKRYVVVKVFKMSTLKFMNIrEYIEGDQRFVkQRIDRMSIISLWVRKEYTNMLTLYEKHVPVPRpig 129
                                   799999****9..799999***99999988877734444455544156779999999988888888888888887766777 PP

                                   .HHHHHH......HHSS--HH.........HHHHHHHHHHHHHHHHHHTTEE-SS-SGGGEEEETTTEEEE-SGTTSEES CS
                       Pkinase  85 .ladlle......rkgslsee.........eakkiakqilegleylHskgiiHrDlKpeNiLidekgelKitDFGlakel 148
                                    ++++l       +     e+          +++i + +l g++ + s++++H Dl   NiL++ ++ +  +D+  a  +
  gi|13542008|ref|NP_111696.1| 130 fFKNILVegyigtK-----EKpapqlkdvqVTEEIYTMTLDGIKKMLSARLVHSDLSEYNILYH-RRRVYFIDLAQAVDI 203
                                   56666654433331.....22555566665777999****************************.777777776665555 PP

>> Choline_kinase  Choline/ethanolamine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.1   7.3e-05      0.22      94     170 ..      79     196 ..      67     198 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 7.3e-05
                                   HHHHHHHHHCCS.TT..ECHHGGCCHCCCTHHHHHHHHHTHHHHHH................................... CS
                Choline_kinase  94 wktmqkwllnkeaqtkakkekkkkqlklinledlekelekleklle................................... 139
                                   + +++++ ++++++  +++  + + ++l+  +++ ++l+ +ek++                                    
  gi|13542008|ref|NP_111696.1|  79 FMNIREY-IEGDQRFVKQRIDRMSIISLWVRKEYTNMLTLYEKHVPvprpigffknilvegyigtkekpapqlkdvqvtee 158
                                   5555555.5555555555555555555555566666666555555445566666666666666666666666666655555 PP

                                   .........CHGG-EEEE-S--SGGGEEE.-CTTEEEE-- CS
                Choline_kinase 140 .........elespvvfcHnDlqegNillnkeekklvlID 170
                                            ++  +  + H Dl e Nil+  +++++++ID
  gi|13542008|ref|NP_111696.1| 159 iytmtldgiKKMLSARLVHSDLSEYNILY--HRRRVYFID 196
                                   55555554444445778899999999999..999999999 PP

>> PC4  Transcriptional Coactivator p15 (PC4)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.4   1.7e-05     0.051       4      29 ..      62      89 ..      60      94 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.7e-05
                                  TCCEEEEEEEET.TE.EEEEEEEEEECT CS
                           PC4  4 skkrrvtvrefk.Gk.tlvdIReyyekd 29
                                  s kr+v v+ fk  + ++ +IRey e d
  gi|13542008|ref|NP_111696.1| 62 SDKRYVVVKVFKmSTlKFMNIREYIEGD 89
                                  78**********655899*******954 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       713  (0.039768); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.54u 0.32s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 1559.39
//
Query:       gi|13542009|ref|NP_111697.1|  [L=123]
Description: translation initiation factor IF-1A [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-22   79.0   0.2    2.8e-22   78.3   0.2    1.3  1  eIF-1a    Translation initiation factor 1A / IF-1


Domain annotation for each model (and alignments):
>> eIF-1a  Translation initiation factor 1A / IF-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.3   0.2   1.6e-26   2.8e-22       1      64 []      38     100 ..      38     100 .. 0.97

  Alignments for each domain:
  == domain 1  score: 78.3 bits;  conditional E-value: 1.6e-26
                                   EEEEEEEEEEETTTEEEEEE.SSSSBEEEEE-HHHHCT----TT-EEEEEE-TT-TTEEEEES- CS
                        eIF-1a   1 gevigkViealgnnlfrVelpdngkevlaeipgkfRnkiwikrGdyVlVelspydltkGrIvyr 64 
                                   ge+ g+V++++g ++ +V ++ +g ++ a+ipg++R+++wi++ d V+V++++++++k+++vyr
  gi|13542009|ref|NP_111697.1|  38 GEMFGIVEKMEGASRLSVMCE-DGYTRNARIPGRMRKRMWIREKDLVIVKPWEFQPEKADVVYR 100
                                   699*****************7.6****************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       532  (0.0296726); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 901.44
//
Query:       gi|13542010|ref|NP_111698.1|  [L=142]
Description: transcription elongation factor NusA-like protein [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-09   37.7   3.5    6.1e-06   26.2   0.2    2.3  2  KH_5      NusA-like KH domain
    1.3e-07   31.4   0.1    2.8e-07   30.3   0.1    1.6  1  KH_4      KH domain
    0.00024   20.9   0.3    0.00024   20.9   0.3    1.9  2  KH_2      KH domain
     0.0004   20.2   0.3     0.0013   18.5   0.3    1.8  1  KH_1      KH domain


Domain annotation for each model (and alignments):
>> KH_5  NusA-like KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.2   1.4e-09   6.1e-06       2      69 .]      32      93 ..      31      93 .. 0.96
   2 !   12.5   0.3   2.7e-05      0.12       3      31 ..      98     123 ..      96     139 .. 0.81

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 1.4e-09
                          KH_5  2 GertkvaVkshnpnvdpvGaivgkkGsrikavsseLkgekidvvewseDlaefianalsPaevlsVki 69
                                  ++++ ++V +h+     ++++++k+ + i+ +++++ ++ i v e s Dl +f+ n+++++ v++++i
  gi|13542010|ref|NP_111698.1| 32 EDMALFIVGEHK-----MAEMFKKNKDVISDLKDKI-NKHILVAEISRDLLTFVRNIFFRYGVNEIQI 93
                                  68999*******.....*******************.***************************9986 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 2.7e-05
                          KH_5   3 ertkvaVkshnpnvdpvGaivgkkGsrik 31 
                                   +rt ++V  ++   +++G+++gk+G++ik
  gi|13542010|ref|NP_111698.1|  98 NRTDIVVGVKQ---EEIGKVIGKEGKNIK 123
                                   67777777766...66************8 PP

>> KH_4  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.3   0.1   6.3e-11   2.8e-07       6      63 ..      77     134 ..      72     141 .. 0.82

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 6.3e-11
                          KH_4   6 dilkalvddpeevevteeeeeeeveielnvegedlGrvIGkrGrtldAlqylvsaaan 63 
                                   +++++++      e++++ +++++ i + v++e++G+vIGk+G++++  +  vs++ n
  gi|13542010|ref|NP_111698.1|  77 TFVRNIFFRYGVNEIQISWKNNRTDIVVGVKQEEIGKVIGKEGKNIKLFRDAVSRYFN 134
                                   6777777777777889998899************************988888887776 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1      0.48   2.1e+03      24      24 ..      32      32 ..      12      67 .. 0.60
   2 !   20.9   0.3   5.4e-08   0.00024      11      56 ..      84     131 ..      74     141 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.48
                                  S CS
                          KH_2 24 a 24
                                  +
  gi|13542010|ref|NP_111698.1| 32 E 32
                                  1 PP

  == domain 2  score: 20.9 bits;  conditional E-value: 5.4e-08
                                   ECETEEEEEEECCSCEEEEE..EEESCHHHHHTGGGHHHHHHHHHHHH CS
                          KH_2  11 kkagvskveIertanrviiv..iresqpgivIGkgGsnikkigkelrk 56 
                                      gv+++ I  ++nr+ iv  ++ ++ g vIGk+G+nik  + ++ +
  gi|13542010|ref|NP_111698.1|  84 FRYGVNEIQISWKNNRTDIVvgVKQEEIGKVIGKEGKNIKLFRDAVSR 131
                                   556788999988777776662268888999**********98888766 PP

>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.3     3e-07    0.0013       4      27 ..     104     127 ..     101     130 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 3e-07
                                   EEEGGGHHHHHHTGGGHHHHHHHH CS
                          KH_1   4 ilvPsslvgriIGkgGsnIkeIre 27 
                                   + v+++ +g++IGk G+nIk  r+
  gi|13542010|ref|NP_111698.1| 104 VGVKQEEIGKVIGKEGKNIKLFRD 127
                                   669999**************8886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       904  (0.0504211); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 952.63
//
Query:       gi|13542011|ref|NP_111699.1|  [L=513]
Description: DNA-directed RNA polymerase subunit A'' [Thermoplasma volcanium GSS1]
Scores for complete 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-59  199.0   1.0    5.4e-58  196.5   0.0    1.9  2  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 ?    0.3   0.9     0.022   3.9e+02     136     206 ..      66     136 ..      35     154 .. 0.66
   2 !  196.5   0.0     3e-62   5.4e-58      62     265 ..     176     455 ..     149     457 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.022
                                   SCHHHCHHHHHHHSE..CBTTEEEEEEEEEE.EEEEETEEEEEEECS--HHHHTTSTTTBETTTEEESSHHHHH CS
                                   xxxxxxxxxxxxxxx..xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                RNA_pol_Rpb1_5 136 kelekakkvkkaiek..gikkikrilvkeae.kgkeeekelvletegvnlsevlkveevvdageilsndiaeil 206
                                   +  +k+k+  k+i +  +i+ki+ i ++e + +gk+  +   l t+ ++ +e+ +++e  ++++ +s+++ +++
  gi|13542011|ref|NP_111699.1|  66 DVIQKKKSGLKSIMEieKIQKIEPISIMEFRsSGKRI-D--ELLTYAIAERETAEIREKYEYEKKVSSQVLDVI 136
                                   2333333333333223367777777777777555555.3..347999999999999999999999999887775 PP

  == domain 2  score: 196.5 bits;  conditional E-value: 3e-62
                                   GGGTSB--TT-BHHHHHHHHHHHHHHCCCSSTTSSTCSSTSSSSSSHHHHHHHHTT-SS-SS-EEEEEB-SSSSSCHHHCH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                RNA_pol_Rpb1_5  62 ygedglvepGeavGiiaaQSiGePgTQltlnTFHfaGvasknvtlGvprlkeilnvskniksksltvllvdeeakelekak 142
                                   + +d+l++p eavGiiaaQSiGePgTQ+t++TFHfaGv ++nvtlG+prl ei+++ ++ +++s+t++l +e +++ e + 
  gi|13542011|ref|NP_111699.1| 176 EIQDELIDPYEAVGIIAAQSIGEPGTQMTMRTFHFAGVREMNVTLGLPRLIEIVDARRIPSTPSMTIYLKPEFETNDEVVM 256
                                   34688********************************************************************99999999 PP

                                   HHHHHHSE......................................................................... CS
                                   xxxxxxxx......................................................................... RF
                RNA_pol_Rpb1_5 143 kvkkaiek......................................................................... 150
                                    v k++e+                                                                         
  gi|13542011|ref|NP_111699.1| 257 DVVKRLENtsvsdvadiitdigeltitvrpdpnkmndrlinqddlvnaiykvkgvtvmeesgqiivkpqqesfkklyllqe 337
                                   9999999999*********************************************************************** PP

                                   ........CBTTEEEEEEEEEEEEEEETEEEEEEECS--HHHHTTSTTTBETTTEEESSHHHHHHHHCHHHHHHHHHHHHH CS
                                   ........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                RNA_pol_Rpb1_5 151 ........gikkikrilvkeaekgkeeekelvletegvnlsevlkveevvdageilsndiaeileilgieaarkallkeiq 223
                                           gi++ikr++ +   +gke+  ++v+ t+g nl++vl+v+e vd +++++ndi ei+++lgieaar+a+l+e q
  gi|13542011|ref|NP_111699.1| 338 qikalpikGISGIKRAIAR--VEGKEH--RWVIYTQGSNLKDVLEVDE-VDPTRTYTNDIVEIATVLGIEAARNAILNEAQ 413
                                   *****99999999999988..455555..79*****************.******************************** PP

                                   HHHHHTTS---HHHHHHHHHHHTTTSS---SSTTCHCCSSSH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                RNA_pol_Rpb1_5 224 evykvqgvsvndrHlelivdqmtkkgeivavnrsGinkaels 265
                                    ++++qg++v+ rHl+l++d+mt+ g++ av+r+Gi  +++s
  gi|13542011|ref|NP_111699.1| 414 RTLQEQGLNVDVRHLMLVADMMTFSGSVRAVGRTGISGRKSS 455
                                   ************************************988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (513 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       842  (0.046963); expected 358.6 (0.02)
Passed bias filter:                      501  (0.0279436); 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: 0.64u 0.31s 00:00:00.95 Elapsed: 00:00:00.48
# Mc/sec: 3187.70
//
Query:       gi|13542012|ref|NP_111700.1|  [L=886]
Description: DNA-directed RNA polymerase subunit A' [Thermoplasma volcanium GSS1]
Scores for complete 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-100  335.1   0.0   5.8e-100  334.6   0.0    1.2  1  RNA_pol_Rpb1_1  RNA polymerase Rpb1, domain 1
    2.6e-63  213.2   0.2    4.5e-63  212.4   0.2    1.4  1  RNA_pol_Rpb1_2  RNA polymerase Rpb1, domain 2
    5.9e-33  114.0   0.0    1.1e-32  113.1   0.0    1.5  1  RNA_pol_Rpb1_3  RNA polymerase Rpb1, domain 3
    1.7e-25   90.0   0.1    4.5e-25   88.6   0.1    1.7  2  RNA_pol_Rpb1_5  RNA polymerase Rpb1, domain 5
    3.3e-23   81.7   0.0    6.8e-23   80.7   0.0    1.5  1  RNA_pol_Rpb1_4  RNA polymerase Rpb1, domain 4
  ------ inclusion threshold ------
       0.16   12.1   1.7        7.7    6.7   0.0    3.1  3  Zn-ribbon_8     Zinc ribbon domain
       0.32   10.5   4.6       0.68    9.4   0.1    2.8  3  zf-ribbon_3     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 !  334.6   0.0  2.3e-103  5.8e-100       2     312 .]       6     315 ..       5     315 .. 0.92

  Alignments for each domain:
  == domain 1  score: 334.6 bits;  conditional E-value: 2.3e-103
                                   E---EEEEEE--HHHHHHH-SBB--STTSTCSTSSSSBBSSSSSSSSS-SSSSSTSTTTSSTTTT-----EEEEEECEEE- CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                RNA_pol_Rpb1_1   2 kkikeiqfgiaspeeirkwSvvevtkaetieekslkPeegGllDerlgtidkdleCetCgkkkkeCeghfGhieLakPvfh 82 
                                   k+i++i+f ++sp+eirk+S+v+v +a+t++++   P e+Gl+D ++g+i+  l+C+tCg k  eC+ghfGhieLa+Pv+h
  gi|13542012|ref|NP_111700.1|   6 KRISSIKFALLSPDEIRKLSQVKVITADTYDDDG-YPIEHGLMDLHMGVIEPGLRCATCGGKVDECPGHFGHIELAMPVVH 85 
                                   89******************************95.9********************************************* PP

                                   HHHHHHHHHHCTTCETTTTEBSS-TTSH....HHH.....HHHCSSSCCCCHHHHHHHHCCS-BE-SSSSB-EEEEEETTE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                RNA_pol_Rpb1_1  83 igffklilkilecvckecskllldeekkkllsklk.....krekleelkkrlkaieelckkinlcekCgavqpkleeegek 158
                                   +gf+k+i+  l+ +ck c+++ l++ + k++  +      ++   e+++   k+  +l ++ ++c +Cga+q+k+     +
  gi|13542012|ref|NP_111700.1|  86 VGFVKEIKMFLDATCKSCGRIKLTDDEIKTYLPEVqkvdfETGDPEDIELMTKRFVDLASQRMVCPHCGAQQSKI---ILD 163
                                   ***********************9996655544332233455566777799******************888666...333 PP

                                   EEEEESSSSTSCEEEE-HHHHHHHHHCSTHHHHHHTTSBTTTB-GGGCCECCEEE--GGGS-BEESSSSSEEBECCCCHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                RNA_pol_Rpb1_1 159 lkaalkkskeeekeklsaekvkkllkriededvevlgfkssgsrPewliltvlPVpPpeiRPsvqldggrrsedDlteklr 239
                                     ++++++ +  + k++++++++ l+ri+d+d+++ gf+++ +rPew+iltvlPVpP ++RPs++l++g+rsedDlt+kl+
  gi|13542012|ref|NP_111700.1| 164 KPTTFREEGT--NVKITPKEIRERLERIPDDDLVFFGFNPKTARPEWMILTVLPVPPINVRPSITLETGERSEDDLTHKLV 242
                                   3334444444..799****************************************************************** PP

                                   HHHHHHHHHHHHHHSSSSSTCHHHHHHHHHHHHHHCC-TTSSSSSEEBSTTSSS--THHHHHTSSSSCCCCCT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                RNA_pol_Rpb1_1 240 diikrNnrLkkaeeegapeliieeekelLQehvatlfdneisglkpatqkskrplkslsqrLkGKeGrfRgnL 312
                                   dii++ +rL++ +++g p+liie+ ++lLQ+hv+t+fdn+ +g++pa+++s+r lk+l qrLkGKeGrfR nL
  gi|13542012|ref|NP_111700.1| 243 DIIRISQRLRESRDNGSPQLIIEDLWDLLQFHVTTYFDNQTPGIPPARHRSGRALKTLVQRLKGKEGRFRSNL 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 !  212.4   0.2   1.7e-66   4.5e-63       1     166 []     317     490 ..     317     490 .. 0.94

  Alignments for each domain:
  == domain 1  score: 212.4 bits;  conditional E-value: 1.7e-66
                                   SEEESSEEEEEEEEESSS-TTEEEEEHHHHTTSEEEEE-STTTHHHHHHHHHHTTT.......SSSSEEEEESTTSSEEET CS
                RNA_pol_Rpb1_2   1 GkrvdysaRsvispdpnlkldevgvPisvakkltvpeivtelnikklrklvengpe.......vyPgasyvkredgsekkl 74 
                                   Gkrv++s+R+visp+p l+++evgvP + a+ ltvp iv+++ni+++r+++++g++        + g +yv+r dg++ k+
  gi|13542012|ref|NP_111700.1| 317 GKRVNFSSRTVISPEPYLSVNEVGVPEKAARELTVPVIVNQFNIDEMREFIKRGRNprdkygkYMAGVNYVIRPDGRRIKI 397
                                   9***************************************************9986333222235799************* PP

                                   TTT-S.CHHCCTTTTSEEEEE--TTSEEEEE-SSTTSGGGEEEEEEEEESSSSEEEEGGGHCCCT--SSS-EEEEE--SSH CS
                RNA_pol_Rpb1_2  75 kakkr.klakelekgdiverhvkdgdvvllNRqPsLhklsimahrvkvlekktlrlnlsvttayNaDFDGDemnlhlpqse 154
                                   + +++ + a+++e+g++ver++++gd+vl+NRqPsLh++s+m+h+v+vl+++t+r+nl+v+t+yNaDFDGDemnlh+ q e
  gi|13542012|ref|NP_111700.1| 398 TDQNAeENANRIEIGWTVERQLMEGDIVLFNRQPSLHRMSMMGHTVRVLPGQTFRFNLAVCTPYNADFDGDEMNLHVIQKE 478
                                   ***99789************************************************************************* PP

                                   HHHHHHHHCSBT CS
                RNA_pol_Rpb1_2 155 earaEaeelllv 166
                                   earaEa+ ++ v
  gi|13542012|ref|NP_111700.1| 479 EARAEARIIMKV 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 !  113.1   0.0   4.5e-36   1.1e-32       1     156 [.     493     657 ..     493     658 .. 0.90

  Alignments for each domain:
  == domain 1  score: 113.1 bits;  conditional E-value: 4.5e-36
                                   CSEETTTTEESSS--THHHHHHHHHSSTTEEEEHHHHHHHHHHSSSCCSSSSSSSSSBESS.SEBEEHHHHHHCCCHCCCC CS
                RNA_pol_Rpb1_3   1 nilspqsgkPvigivQDsllGvyllTkedvfidreeaqqllykgvgsdsktvtlrpailkp.kelwtgkqtfsrilpnein 80 
                                   +i+sp+ g+P+ig ++D++++++llT+++ ++++ee+++++ ++       +++++a +++ k+ ++g+++fs ilp+ +n
  gi|13542012|ref|NP_111700.1| 493 QIMSPRFGRPIIGGIHDHVTAMFLLTHNNPLFTQEEMIHIMCYV-----DPDLIPDATIVNgKKYYSGRNIFSTILPKGLN 568
                                   79******************************************.....3467777878887****************888 PP

                                   EEEE...SSSS.............STSEEECSSEEEES--SHHHHSSSSTTSHHHHHHHHCHHHHHHHHHHHHHHHHHHHH CS
                RNA_pol_Rpb1_3  81 yerk...neek.............dgkvlikngelikGvidkkvvgkksqgslihvlakeygiketvrfldslqrlgfkyl 145
                                   ++        +             d++v i +g li+G+id++++     g +i+ +++++g++e+++f+d+++rl+ +++
  gi|13542012|ref|NP_111700.1| 569 LRFRsklC--SgssetceyekekeDTYVTIVDGKLIHGTIDEAAIS-PFSGAIIDKIFRKFGPNEAAKFIDRMTRLAVGFI 646
                                   87755440..14445677788889*********************9.777******************************* PP

                                   HHHCEB-TGGG CS
                RNA_pol_Rpb1_3 146 lqsgftigigD 156
                                   + +gf++gi+D
  gi|13542012|ref|NP_111700.1| 647 TYYGFSTGISD 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 ?   -2.2   0.0      0.84   2.1e+03      66      82 ..     702     759 ..     522     760 .. 0.74
   2 !   88.6   0.1   1.7e-28   4.5e-25       1      66 [.     796     861 ..     796     879 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.84
                                   S.........................................B--TT-BHHHHHHHHH CS
                                   x.........................................xxxxxxxxxxxxxxxx RF
                RNA_pol_Rpb1_5  66 g.........................................lvepGeavGiiaaQSi 82 
                                                                             + ++ e  Gi+  QS+
  gi|13542012|ref|NP_111700.1| 702 TleieilseagvvrdesgkiassylglsvpsvimarsgaratMLNISEVAGIVGQQSV 759
                                   1333333334444444444444444444477777777777777788888888888886 PP

  == domain 2  score: 88.6 bits;  conditional E-value: 1.7e-28
                                   B--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTEEEETTSEEEETTS-EEESSGGGTS CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                RNA_pol_Rpb1_5   1 GLkvkefffhtmggReGLiDtAvkTaesGYlqRrlvkaledvvvkyddtvrnsggeivqflygedg 66 
                                   GL+++e+ffh+ ggReGL+DtAv+T++sGY+qRrl++a ed+ v++++ v+++ g+++q++ygedg
  gi|13542012|ref|NP_111700.1| 796 GLTPTEYFFHSIGGREGLVDTAVRTSRSGYMQRRLINAFEDLKVDEERQVKDTVGSLIQIKYGEDG 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 !   80.7   0.0   2.6e-26   6.8e-23       1     108 []     683     789 ..     683     789 .. 0.97

  Alignments for each domain:
  == domain 1  score: 80.7 bits;  conditional E-value: 2.6e-26
                                   HHHHCTHTCCHHHTTHCHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTTSHHHHHHHCTSSS-HHHHHHHHTB-EEEEBTTB CS
                RNA_pol_Rpb1_4   1 ieeaerygkledlpgksleelfeakinkilnkardkagkiaskslaasNsiliMvksGaKGsiinisqiagclGqqnvegk 81 
                                   ie ++r g+l+++pg+s+e+++e +i +    +rd++gkias++l  s + +iM++sGa+  ++nis +ag++Gqq+v+g 
  gi|13542012|ref|NP_111700.1| 683 IETYKR-GELQPAPGRSVEDTLEIEILSEAGVVRDESGKIASSYLGLSVPSVIMARSGARATMLNISEVAGIVGQQSVRGG 762
                                   677889.****************999999999**************768******************************** PP

                                   SS--SSTSCSSTTSSSSESSTTTSSEE CS
                RNA_pol_Rpb1_4  82 ripkgfsgrtlphfkkidespesrGFv 108
                                   r ++g+ +rtlphfk+ d ++ +rGFv
  gi|13542012|ref|NP_111700.1| 763 RLNRGYYNRTLPHFKRGDIGADARGFV 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   0.2      0.26   6.6e+02      28      36 ..      59      67 ..      49      77 .. 0.72
   2 ?    1.7   0.0      0.11   2.8e+02      27      35 ..      98     107 ..      85     110 .. 0.69
   3 ?    6.7   0.0     0.003       7.7      26      39 ..     146     160 ..     132     161 .. 0.70

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.26
                   Zn-ribbon_8 28 aCPeCgsev 36
                                   C +Cg++v
  gi|13542012|ref|NP_111700.1| 59 RCATCGGKV 67
                                  466666654 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.11
                   Zn-ribbon_8  27 taCPeCgs.e 35 
                                    +C++Cg  +
  gi|13542012|ref|NP_111700.1|  98 ATCKSCGRiK 107
                                   3499998766 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.003
                   Zn-ribbon_8  26 lta.CPeCgsevrrv 39 
                                   +   CP+Cg++  ++
  gi|13542012|ref|NP_111700.1| 146 QRMvCPHCGAQQSKI 160
                                   3344*****976665 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.4       1.1   2.9e+03      19      25 ..      60      66 ..      59      67 .. 0.80
   2 ?    2.0   0.0     0.058   1.5e+02      17      23 ..      98     104 ..      95     114 .. 0.66
   3 ?    9.4   0.1   0.00027      0.68      14      25 ..     145     156 ..     142     157 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.1
                   zf-ribbon_3 19 CpyCGtk 25
                                  C+ CG+k
  gi|13542012|ref|NP_111700.1| 60 CATCGGK 66
                                  8889976 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.058
                   zf-ribbon_3  17 nvCpyCG 23 
                                    +C++CG
  gi|13542012|ref|NP_111700.1|  98 ATCKSCG 104
                                   5666666 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.00027
                   zf-ribbon_3  14 sddnvCpyCGtk 25 
                                   s+ +vCp+CG++
  gi|13542012|ref|NP_111700.1| 145 SQRMVCPHCGAQ 156
                                   67789****986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (886 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       519  (0.0289475); expected 358.6 (0.02)
Passed bias filter:                      506  (0.0282224); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.72u 0.32s 00:00:01.04 Elapsed: 00:00:00.48
# Mc/sec: 5599.87
//
Query:       gi|13542013|ref|NP_111701.1|  [L=1195]
Description: DNA-directed RNA polymerase subunit B [Thermoplasma volcanium GSS1]
Scores for complete 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-130  433.1   0.0   1.4e-129  432.6   0.0    1.3  1  RNA_pol_Rpb2_6  RNA polymerase Rpb2, domain 6
    5.3e-34  117.5   0.0    1.1e-32  113.3   0.0    2.2  1  RNA_pol_Rpb2_1  RNA polymerase beta subunit
      5e-26   90.7   0.0    1.7e-25   89.0   0.1    1.9  2  RNA_pol_Rpb2_3  RNA polymerase Rpb2, domain 3
      2e-25   89.0   0.0    4.4e-25   87.9   0.0    1.6  1  RNA_pol_Rpb2_7  RNA polymerase Rpb2, domain 7
    1.1e-22   80.7   0.0    1.8e-22   79.9   0.0    1.3  1  RNA_pol_Rpb2_2  RNA polymerase Rpb2, domain 2
    2.2e-20   72.7   1.5    5.4e-20   71.4   1.5    1.7  1  RNA_pol_Rpb2_4  RNA polymerase Rpb2, domain 4
    2.6e-11   43.9   0.2      6e-11   42.7   0.2    1.7  1  RNA_pol_Rpb2_5  RNA polymerase Rpb2, domain 5
  ------ inclusion threshold ------
       0.49   10.4   2.7        4.1    7.5   0.2    2.6  2  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
        0.5   10.0   2.2       0.84    9.3   0.1    2.1  2  TackOD1         Thaumarchaeal output domain 1
       0.85    9.6   2.5        1.8    8.5   0.2    2.5  2  Cys_rich_CPXG   Cysteine-rich CPXCG
        7.4    6.2   8.6        1.9    8.0   1.7    2.7  2  TF_Zn_Ribbon    TFIIB zinc-binding


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb2_6  RNA polymerase Rpb2, domain 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  432.6   0.0  8.7e-133  1.4e-129       1     390 []     725    1096 ..     725    1096 .. 0.95

  Alignments for each domain:
  == domain 1  score: 432.6 bits;  conditional E-value: 8.7e-133
                                    HHHT-SS-TTB-HHHHHHHHHHGGGB-S---TTTTT---SSEEEESS----SSB-S.TTTTTS........GGGS-SEE CS
                RNA_pol_Rpb2_6    1 vaklapvvehvqspriiiqaamekqalgiyslnkfkrsnqktyllcinqkPlvktgdkveagqvldgpatekgelalGq 79  
                                    va+++p++eh++spri+i +am+kq+lg+++ n   r +++ +ll+++q Plv+t+  +e+++        +++ ++Gq
  gi|13542013|ref|NP_111701.1|  725 VASIIPYPEHNSSPRITIASAMAKQSLGFAQSNVRIRPDTRGHLLHYPQVPLVRTR-VMEYTH--------YDRRPAGQ 794 
                                    6999****************************************************.999999........******** PP

                                    EEEBBBS--TTTTTTT-EEEBCHHHHTTTT-EEEEEE..EEE--SSSS---.-S--..-.....-SS-GGGS-TTSB-- CS
                RNA_pol_Rpb2_6   80 navVAvmsyeGYniEDaiilnerlvdrdvftsihikeyeveardtklgeeeitrdipnv.....seealkkLdedGivr 153 
                                    n+vVAv+syeGYni Da+++n++++dr++ +s+++++y+ e r++++g+e+ ++ ++++      ee +k+Lde+Gi++
  gi|13542013|ref|NP_111701.1|  795 NFVVAVLSYEGYNIQDALVINKAAIDRGLGRSTFFRTYSAEERRYPGGQEDKFEIPTHDvigarAEEYYKNLDESGIIY 873 
                                    *************************************************8877766666899999************** PP

                                    SS-EEETT-EEE---..B-----...-----------..-B---EE--TT-EEEEEEEEE.......EE-TT--EEEEE CS
                RNA_pol_Rpb2_6  154 vgaevkegdilvgkvtkgeteltpeekllraifgekarevkdtslrvksgeegvVdkvkvfsrekgdelkagvnklvkv 232 
                                    ++a+v+  d+l+gk+  ++ ++ +e    ++  g ++   +++s++++++e+g+Vd+v +       + +++ +++vk+
  gi|13542013|ref|NP_111701.1|  874 PEAYVEGSDVLIGKT--SPPRFLEEG---EERLGPQR--RRESSVTMRPNESGYVDNVFL-------TVSESNSRVVKI 938 
                                    **************8..777777442...23334444..589******************.......8899999***** PP

                                    EEEEEE---TT-BEEETTS---BBEEEB-TTTSEEETTS---SEEE-GGGCHHH-BTTHHHHHHHHHCCCSSSS--B-- CS
                RNA_pol_Rpb2_6  233 yvaqkRklqvGDKfasrhGqKGvvslilpqeDmPfledGivvDivlNPlgvPSRmtigqllEtllgkaaalegkkvdat 311 
                                    +v+++R +++GDKfasrhGqKGv++l++pqeDmPf+e+Gi++D+++NP+++PSRmt+g++lE++ gk+a+ +gk++d+t
  gi|13542013|ref|NP_111701.1|  939 KVRSERIPELGDKFASRHGQKGVIGLVVPQEDMPFTEEGIIPDLIFNPHSIPSRMTVGHILEMIGGKIASRTGKFIDGT 1017
                                    ******************************************************************************* PP

                                    TT-...-HHHHHHHHHTTS-TT-EE-EEETTTS-B-SS-EEB-EEEEEEBS--CCCS----SS--B-TTT--B-SCGGG CS
                RNA_pol_Rpb2_6  312 vFdgakeeeikelLeeagleasGkevlydGrtGekleaeifvGviYylkLkhlvedKihaRstGpyslltqQPlgGkaq 390 
                                    +F+g+ e+ ++++L + g+++sG+ev+ydG+tG+k++a+ifvGviYy+kL+h+v+ K+haRs+Gp++ lt+QP++G+++
  gi|13542013|ref|NP_111701.1| 1018 IFSGEPEKSLRDELVKYGFRKSGTEVMYDGITGRKFRADIFVGVIYYQKLHHMVAGKFHARSRGPVQILTRQPTEGRSR 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 !  113.3   0.0   6.5e-36   1.1e-32       3     200 ..      15     435 ..      13     438 .. 0.86

  Alignments for each domain:
  == domain 1  score: 113.3 bits;  conditional E-value: 6.5e-36
                                   THHHHHHHHHH..........HHTHHHHHCTTSSECCHCSSSHCSSSC....................EEEEEEEEEEESC CS
                                   xxxxxxxxxxx..........xxxxxxxxxxxxxxxxxxxxxxxxxxx....................xxxxxxxxxxxxx RF
                RNA_pol_Rpb2_1   3 vsqqldSFnkf..........veqdlekiikeeaaieseeeiqssgee....................lelkfvsirlgkP 53 
                                   v+ qldS n f          +    ++i  +e ++  + ++ +   +                     ++  + i +gkP
  gi|13542013|ref|NP_111701.1|  15 VNHQLDSMNSFyassdnpnsvM----QQI-VDETKVSDDADPGFFVLDpaktgghdiriyygrvrengHYVGEQTIFVGKP 90 
                                   6777777777776666533331....222.222222222222222111233334457777777777777788889****** PP

                                   SSECTTSCEEES.HHHHHHCTSBXEEEEEEEEEEEECCCCTCCEEEEEEEEEEEEEXBTTSTTSSSTT............. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............. RF
                RNA_pol_Rpb2_1  54 vvdesdasereiyPkearlrnltYsaplyvklklvvyekdnkeeikeeevyiGelPlMlrskacvlse............. 121
                                    ++e+++++++i+P+earlr+l Y ap+ +kl+ v     ++ e+ +e +++G++P+M+rsk c+l e             
  gi|13542013|ref|NP_111701.1|  91 EIKEASGASNQITPNEARLRDLNYMAPVTLKLRIVE----DGIEKGSETIKVGDIPVMVRSKICTLAEgnldqyieknngp 167
                                   ***********************************9....8999********************99762222222222222 PP

                                   ...S.HHHHHHTTS.TTS..SSEEETTCEEEEXEEEE............................................ CS
                                   ...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................................ RF
                RNA_pol_Rpb2_1 122 ...aseeelvelkEcpldqGGyFiinGtekvivaqek............................................ 155
                                         e+l  ++E+p+d+GGyFii G+e+viv++e+                                            
  gi|13542013|ref|NP_111701.1| 168 iglSRREKLQYVGEDPDDPGGYFIIGGSERVIVSLEDlapnkimvewedryeskvevakvfsqrggfraltsmekgsdgti 248
                                   221235689999********************************************************************* PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                RNA_pol_Rpb2_1 156 ................................................................................. 155
                                                                                                                    
  gi|13542013|ref|NP_111701.1| 249 nvsipsvagtvplvilmkalglerdvdvhdaiasvpemepiiyaniedsknpkilppngvnttedaisylekrfaagqake 329
                                   ********************************************************************************* PP

                                   .............................................................XHHHHHHHHHHHHHHHHHHH CS
                                   .............................................................xxxxxxxxxxxxxxxxxxxx RF
                RNA_pol_Rpb2_1 156 .............................................................laGeLlaslfrvllkklerd 175
                                                                                                laG+L+ +lfr++++++ +d
  gi|13542013|ref|NP_111701.1| 330 frdkkisqmldhsllphlgdsasdrirkaiylgrmarsllelslgirkeddkdhlankrikLAGDLMDELFRSAFQSVMKD 410
                                   ********************************************************************************* PP

                                   HHHHHHHHHCTSSSSSHHHHSCSHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxx RF
                RNA_pol_Rpb2_1 176 vkerlqksleklddlmlqllvnakp 200
                                   +k +l+k+ ++++ ++ + +v+ + 
  gi|13542013|ref|NP_111701.1| 411 LKYQLEKTYNRKRGIKIRPAVRQDL 435
                                   ***********99888887777665 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 ?   -2.4   0.0       3.5   5.7e+03       5      46 ..     111     150 ..     109     152 .. 0.79
   2 !   89.0   0.1     1e-28   1.7e-25       1      68 []     458     522 ..     458     522 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 3.5
                RNA_pol_Rpb2_3   5 rlnplselshlrrvsslrgglskerkttevRdlhpshwGriC 46 
                                    ln+++ ++ + r+   + g++k ++t++v d+       iC
  gi|13542013|ref|NP_111701.1| 111 DLNYMAPVTLKLRIV--EDGIEKGSETIKVGDIPVMVRSKIC 150
                                   589999999999999..8899999999998777655555555 PP

  == domain 2  score: 89.0 bits;  conditional E-value: 1e-28
                RNA_pol_Rpb2_3   1 qvldrlnplselshlrrvsslrgglskerkttevRdlhpshwGriCpveTPEGencGlvksLallarv 68 
                                   q+ldr++ ls++shlrr+ s+   l++++ ++e+Rdlhp++wGriCp eTPEG+ncGlvk+ all++v
  gi|13542013|ref|NP_111701.1| 458 QLLDRVSNLSTISHLRRIISP---LTRTQPHFEARDLHPTQWGRICPNETPEGQNCGLVKNAALLINV 522
                                   89*******************...***************************************99876 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 !   87.9   0.0   2.7e-28   4.4e-25       1      85 [.    1098    1190 ..    1098    1192 .. 0.96

  Alignments for each domain:
  == domain 1  score: 87.9 bits;  conditional E-value: 2.7e-28
                                    BBEEEEHHHHHHHHHHTBHHHHHHHHTTTTTEEEEEEESS..SSSCCCEE......EBTTTTCSSSEEEEEEEHHHHHH CS
                RNA_pol_Rpb2_7    1 GGlrfGEMErdaliayGaaalLkerltikSDavevdvcgr..ckllaaan......eCkivkseekiekveipeafklL 71  
                                    GGlrfGEMErd+lia+Gaa+++k+rl+++SD + ++vcg+  c+++a+++      +C+++ ++ +i ++e+++afkl+
  gi|13542013|ref|NP_111701.1| 1098 GGLRFGEMERDTLIAHGAAMVIKDRLLDQSDGTVLYVCGNpsCGHIAIYDrrkgtlRCPVCGNTGNIYPIETSYAFKLM 1176
                                    9*************************************965599999999***************************** PP

                                    HHHHHHTTBEEEEE CS
                RNA_pol_Rpb2_7   72 lqeLqslgialkll 85  
                                     +eL slg+ ++l+
  gi|13542013|ref|NP_111701.1| 1177 RDELISLGVVMRLM 1190
                                    **********9987 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 !   79.9   0.0   1.1e-25   1.8e-22       3     190 .]     208     390 ..     199     390 .. 0.85

  Alignments for each domain:
  == domain 1  score: 79.9 bits;  conditional E-value: 1.1e-25
                                   SCEEEEE-SSSSSE..SSSCCEECCCEEEEECCCCSTSCEEEEECTTSSSEEEHHHHHHHTT--STTHHHHHHTS.....S CS
                RNA_pol_Rpb2_2   3 ngiyvekekdknki..satvtsslisqrgsvlklekdgktliwtriskkrkipivivlkAlglvsdreIlericy.....d 76 
                                   n+i+ve e + ++   +a+v s +   r++++ ++ +++t+ ++ +s+   +p+vi++kAlgl +d ++ ++i        
  gi|13542013|ref|NP_111701.1| 208 NKIMVEWEDRYESKveVAKVFSQRGGFRALTSMEKGSDGTINVSIPSVAGTVPLVILMKALGLERDVDVHDAIASvpemeP 288
                                   555555444333333556666666667788888888999***********************************8777755 PP

                                   STTHHHHHHHHHHHHHHCTSSSCHHHHHHHHHCSSTTSSSCCCCCHHHHHHHCHHHHHHHTTTTSSTTTTTSSSTCHH... CS
                RNA_pol_Rpb2_2  77 sedsqlleelleeleekeeiqtqeealdyigkvvalrrgeearlqsareilqkrydlgeigreklnkhlglseslenkr.l 156
                                     + ++++  +++    + + t+e+a++y+ k++a+++ +e r ++  ++l         +   l+ hlg s s   +r  
  gi|13542013|ref|NP_111701.1| 289 IIYANIEDSKNPKILPPNGVNTTEDAISYLEKRFAAGQAKEFRDKKISQML---------DHSLLP-HLGDSAS---DRiR 356
                                   5566777788899999999*******************************9.........577777.*******...4447 PP

                                   HHHHHHHHHHHHHHHHTTSSSS--TTSGGGEEEE CS
                RNA_pol_Rpb2_2 157 kaqdilymidrLlslklgrrevDDiDhlgnkRvr 190
                                   ka +++ m++ Ll+l+lg r++DD+Dhl+nkR++
  gi|13542013|ref|NP_111701.1| 357 KAIYLGRMARSLLELSLGIRKEDDKDHLANKRIK 390
                                   ********************************96 PP

>> RNA_pol_Rpb2_4  RNA polymerase Rpb2, domain 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.4   1.5   3.3e-23   5.4e-20       1      61 [.     553     613 ..     553     614 .. 0.98

  Alignments for each domain:
  == domain 1  score: 71.4 bits;  conditional E-value: 3.3e-23
                                   EECTT-BEEE-S-HCCHHHHHHHHCCTTSS-TT-EEEE-TTT--EEEE-SSEEB-EEEEE- CS
                RNA_pol_Rpb2_4   1 VfvNGrllGvtrdpkklvetlRelRRkgkiseevsivlnekqkevkiatDgGRvcRPliiV 61 
                                   V++NG+ +G+++dp++lv++lRe RR+g+is+e+++ ++++++ev +++D GR++RPl++ 
  gi|13542013|ref|NP_111701.1| 553 VYLNGDFVGYHDDPRYLVRRLREERRAGRISDEINVRYDDNTNEVIVNCDRGRLRRPLLVL 613
                                   9**********************************************************96 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 !   42.7   0.2   3.7e-14     6e-11       1      58 []     635     718 ..     635     718 .. 0.93

  Alignments for each domain:
  == domain 1  score: 42.7 bits;  conditional E-value: 3.7e-14
                                   HHHHHHTTSEEEEEHHHHTT--EESSTTTCSST.-SSTTTSS-.........................-TTSSSST-SEEE CS
                RNA_pol_Rpb2_5   1 wddLlregvvEylDaeEEetamIamtpedleks.reekealee.........................kenskshtyTHcE 55 
                                   ++dL++ g  E+lDaeEEe+a++a++ ++++++ ++++++l +                          ++  + ++TH+E
  gi|13542013|ref|NP_111701.1| 635 FEDLVKVGALEWLDAEEEEDAYVAVYAYNIPEKcPHCSSYLYRsmvdwsnpgsnniilecgfcynkfeVPSLITPEHTHLE 715
                                   89*********************************999998889*********************99944444559***** PP

                                   S-G CS
                RNA_pol_Rpb2_5  56 IhP 58 
                                   I+P
  gi|13542013|ref|NP_111701.1| 716 IDP 718
                                   **9 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.2     0.095   1.5e+02      20      26 ..     667     673 ..     650     697 .. 0.77
   2 ?    7.5   0.2    0.0025       4.1      18      34 ..    1152    1169 ..    1138    1177 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.095
                 Zn_Tnp_IS1595  20 vCPhCgs 26 
                                    CPhC s
  gi|13542013|ref|NP_111701.1| 667 KCPHCSS 673
                                   6****86 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0025
                 Zn_Tnp_IS1595   18 gfvCPhCgsr.kayrikt 34  
                                    + +CP Cg++  +y i+t
  gi|13542013|ref|NP_111701.1| 1152 TLRCPVCGNTgNIYPIET 1169
                                    478***********9998 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.1   0.00052      0.84     125     159 ..     667     701 ..     657     706 .. 0.86
   2 ?   -0.5   0.2       0.5   8.1e+02     108     130 ..    1139    1159 ..    1130    1165 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00052
                       TackOD1 125 eCpkCktkLrhiGvDYdrplevykCnsCkslfsep 159
                                   +Cp+C++ L +  vD+++p+++ +  +C+ +  + 
  gi|13542013|ref|NP_111701.1| 667 KCPHCSSYLYRSMVDWSNPGSNNIILECGFCYNKF 701
                                   7*********************9999998877665 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.5
                       TackOD1  108 tCgnvgpeeeflkegkleCpkCk 130 
                                    +Cg+++  +  +++g+l Cp C 
  gi|13542013|ref|NP_111701.1| 1139 SCGHIAIYD--RRKGTLRCPVCG 1159
                                    355555444..567778888875 PP

>> Cys_rich_CPXG  Cysteine-rich CPXCG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.2    0.0011       1.8       2      48 ..     667     715 ..     667     718 .. 0.79
   2 ?   -0.5   0.2      0.74   1.2e+03       2       9 ..    1154    1161 ..    1153    1167 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0011
                 Cys_rich_CPXG   2 qCPyCgeei.evlvDlsag.dqeYieDCqvCCrPivlqvevdeeegeve 48 
                                   +CP+C   + +  vD+s+  + + i +C  C +  ++   +  e+ ++e
  gi|13542013|ref|NP_111701.1| 667 KCPHCSSYLyRSMVDWSNPgSNNIILECGFCYNKFEVPSLITPEHTHLE 715
                                   5****99752789*****99***********988877666665555555 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.74
                 Cys_rich_CPXG    2 qCPyCgee 9   
                                     CP Cg +
  gi|13542013|ref|NP_111701.1| 1154 RCPVCGNT 1161
                                    59999876 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   0.8      0.16   2.7e+02       2       9 ..     667     674 ..     666     697 .. 0.80
   2 ?    8.0   1.7    0.0012       1.9       4      27 ..    1138    1160 ..    1133    1161 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.16
                                   EETTTTCE CS
                  TF_Zn_Ribbon   2 kCPnCgst 9  
                                   kCP C+s+
  gi|13542013|ref|NP_111701.1| 667 KCPHCSSY 674
                                   8*****96 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0012
                                    TTTTCEEC.HEETSTTCEEESSSSB CS
                  TF_Zn_Ribbon    4 PnCgstnl.veDpergelvCtdCGl 27  
                                    P Cg+  + ++D   g+l+C+ CG+
  gi|13542013|ref|NP_111701.1| 1138 PSCGH--IaIYDRRKGTLRCPVCGN 1160
                                    55665..159**************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       498  (0.0277762); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.88u 0.33s 00:00:01.21 Elapsed: 00:00:00.52
# Mc/sec: 6960.13
//
Query:       gi|13542014|ref|NP_111702.1|  [L=87]
Description: DNA-directed RNA polymerase subunit H [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.9e-29  100.0   0.4    5.7e-29   99.8   0.4    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 !   99.8   0.4   3.2e-33   5.7e-29       1      73 []       4      81 ..       4      81 .. 0.99

  Alignments for each domain:
  == domain 1  score: 99.8 bits;  conditional E-value: 3.2e-33
                                  ..-TSSSS--EEEEE-HHHHHHHHHHTT--TTCSS-EETTSHHHHCC.....T--TTSEEEEEEEETTTEEEEEEEEE CS
                RNA_pol_Rpb5_C  1 vnitkHelvPkhevlseeekkellkklkikeeqLPkisksDpvaryl.....glkkGdvvkItrksetageavtYRlV 73
                                  +n+++H+lvP+h+++seee+k++lk+l+i++e LP+is +Dpv+++l     ++k G v+kI+r+s+t+g++v+YR+V
  gi|13542014|ref|NP_111702.1|  4 FNVLDHNLVPEHHIVSEEEEKTILKELGIEKEFLPRISPNDPVIKALeaihgKIKDGTVIKIIRNSPTMGHSVYYRVV 81
                                  7*********************************************999999************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       332  (0.0185175); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 611.46
//
Query:       gi|13542015|ref|NP_111703.1|  [L=271]
Description: hypothetical protein TVN1184 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0016   18.8   0.0     0.0043   17.5   0.0    1.8  1  RuvA_C           RuvA, C-terminal domain
     0.0018   18.2   0.0     0.0034   17.3   0.0    1.5  1  tRNA_anti-codon  OB-fold nucleic acid binding domain
  ------ inclusion threshold ------
      0.086   12.6   0.4       0.17   11.7   0.4    1.5  1  DUF4748          Domain of unknown function (DUF4748)


Domain annotation for each model (and alignments):
>> RuvA_C  RuvA, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   7.2e-07    0.0043      10      29 ..     159     178 ..     159     195 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 7.2e-07
                                   HHHCTS-HHHHHHHHHHHHC CS
                        RuvA_C  10 LlaLGYkekeaekAvakvla 29 
                                   L++LGY++ eae A+++++ 
  gi|13542015|ref|NP_111703.1| 159 LISLGYSRVEAEAAISSIKN 178
                                   89***************974 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 !   17.3   0.0   5.7e-07    0.0034       3      63 ..      43     105 ..      41     120 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 5.7e-07
                                   EEEEEEEEEEEEETTEEEEEEEETTEEEEEEEET....HHHHHHHTTS-TTSEEEEEEEEEECTT CS
               tRNA_anti-codon   3 vaGrvtsisdrsggkvifidlrDgtgriqvvlfr....eeatklaenlkeGdvvrvtGrvkrrpg 63 
                                   +aG v+s+  +s  +++ i l D  g++ v++f+     e +++ ++l+++d   v G+++ +++
  gi|13542015|ref|NP_111703.1|  43 IAGTVSSK--QSDDRMARISLADPIGSFYVTAFSggfnPEEKAMVDSLEVDDKAMVMGKINPYRT 105
                                   99******..**************************************************99965 PP

>> DUF4748  Domain of unknown function (DUF4748)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.4   2.9e-05      0.17      19      34 ..     134     149 ..     132     166 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.9e-05
                       DUF4748  19 ayyfAKrsidadRaak 34 
                                   ayyfAKr i a R a+
  gi|13542015|ref|NP_111703.1| 134 AYYFAKRRIYAIREAQ 149
                                   9************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1927.15
//
Query:       gi|13542016|ref|NP_111704.1|  [L=358]
Description: replication factor A [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.5e-15   56.2   2.9    0.00073   19.5   1.2    3.8  3  tRNA_anti-codon  OB-fold nucleic acid binding domain


Domain annotation for each model (and alignments):
>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.1   6.1e-08    0.0011      11      72 ..      27      87 ..      17     101 .. 0.89
   2 !   19.5   1.2   4.1e-08   0.00073       1      63 [.     120     182 ..     120     229 .. 0.87
   3 !   15.2   0.0   8.8e-07     0.016      20      74 ..     266     339 ..     263     341 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 6.1e-08
                                  E....EEEETTEEEEEEEETTEEEEEEEETHHHHHHHTTS-TTSEEEEE.EEEEECTTSSEEEEEEE CS
               tRNA_anti-codon 11 s....drsggkvifidlrDgtgriqvvlfreeatklaenlkeGdvvrvt.Grvkrrpggelelkvee 72
                                  +    dr++  +++ ++ D+tg++  ++++     +   +k Gdvv+++ ++ + ++g+ + ++v++
  gi|13542016|ref|NP_111704.1| 27 KtiknDRGETTYFYGIIGDDTGTVSFTAWS-----FPAAVKSGDVVEIKnCYSSLYNGK-IRIYVDS 87
                                  2455789999********************.....*********************999.9999875 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 4.1e-08
                                   EEEEEEEEEEE......EEEETTEEEEEEEETTEEEEEEEETHHHHHHHTTS-TTSEEEEE.EEEEECTT CS
               tRNA_anti-codon   1 VtvaGrvtsis......drsggkvifidlrDgtgriqvvlfreeatklaenlkeGdvvrvt.Grvkrrpg 63 
                                   V+v Gr++ i+      dr+++ v    ++D+t++++++ f        + lk G +vrv+  rv+ ++g
  gi|13542016|ref|NP_111704.1| 120 VSVIGRISGIKeknydsDRGSKIVYQGFIEDETAKVRISSFG-------KPLKDGEIVRVEnARVSQYNG 182
                                   89*************6555555555555**************.......****************99954 PP

  == domain 3  score: 15.2 bits;  conditional E-value: 8.8e-07
                                   EEEEEETTEEEEEEEET...............HHHHHHHTTS-.....TTSEEEEEEEEEECTTSSEEEEEEEEE CS
               tRNA_anti-codon  20 fidlrDgtgriqvvlfr...............eeatklaenlk.....eGdvvrvtGrvkrrpggelelkveeie 74 
                                   ++ l Dgtg+++++l++               ++a++++ n        G+++ vtG ++ r+++ +++++++i+
  gi|13542016|ref|NP_111704.1| 266 YFLLSDGTGSLTCYLNKdsflpyikmdteefkSQAFSMNPNMLikkniLGKCLSVTGDLRLRDDK-ITMNASSIK 339
                                   6789************************77765555555553366999*****************.*****9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (358 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       507  (0.0282782); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.49
# Mc/sec: 2203.13
//
Query:       gi|13542017|ref|NP_111705.1|  [L=232]
Description: transcription regulator [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.8e-09   36.4   0.4    8.4e-09   35.3   0.1    1.7  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 ?   -2.8   0.0      0.38   6.8e+03      50      71 ..      77      98 ..      65     100 .. 0.61
   2 !   35.3   0.1   4.7e-13   8.4e-09       1      74 [.     148     227 ..     148     230 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.38
                        HTH_45 50 kkskekYvlTekGlelleklke 71
                                   +s  k v+ + G  +l++l+e
  gi|13542017|ref|NP_111705.1| 77 VQSRIKIVVLHYGPAILQELNE 98
                                  4555555666667777777766 PP

  == domain 2  score: 35.3 bits;  conditional E-value: 4.7e-13
                        HTH_45   1 rRskleIiadILeais..egeakkTkimykanLsykllnkYLdmLvekgli....kkskekYvlTekGlelleklkelee 74 
                                   +R++l  ++++L++++  eg+   T++  + nL+yk  ++ ++ L++ g++      ++++ ++T  G+++l+++ +l++
  gi|13542017|ref|NP_111705.1| 148 KRTRLAMVLEMLSYLKdaEGGLPLTRLFFRCNLNYKKGEEIVKGLLDSGMVkiknGRRQKNVMITPLGENFLRNYSKLHS 227
                                   8**************9889999****************************877544588999*************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      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: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.50
# Mc/sec: 1406.32
//
Query:       gi|13542018|ref|NP_111706.1|  [L=393]
Description: transposase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.6e-17   62.5   0.2    6.2e-17   61.3   0.2    1.7  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    0.00077   19.1   0.3     0.0013   18.4   0.3    1.4  1  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain
     0.0029   17.3   1.7       0.22   11.2   0.1    2.2  2  DUF2229         CoA enzyme activase uncharacterised domain (D
  ------ inclusion threshold ------
      0.016   15.2   0.7      0.029   14.4   0.7    1.4  1  DZR             Double zinc ribbon
       0.04   13.6   2.2       0.13   12.0   2.2    1.9  1  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
       0.14   12.1   3.4       0.12   12.3   0.5    2.2  2  Phage_30_8      Phage GP30.8 protein
       0.15   11.9   1.9       0.28   11.1   1.9    1.4  1  C1_1            Phorbol esters/diacylglycerol binding domain 
       0.16   12.0   0.5       0.31   11.0   0.5    1.5  1  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
       0.34   10.8   2.4       0.66    9.9   2.4    1.5  1  PHD             PHD-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 !   61.3   0.2   3.1e-20   6.2e-17       1      67 [.     288     356 ..     288     358 .. 0.89

  Alignments for each domain:
  == domain 1  score: 61.3 bits;  conditional E-value: 3.1e-20
                OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnp...ayTSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNil 67 
                                   ++ l  q+ yka ++G +v+e  +   ++TS  Cs+Cgs  +   +gr +kC++Cg+e+drDvnA+iNi+
  gi|13542018|ref|NP_111706.1| 288 YGMLASQVMYKASWEGLPVIELTRketRNTSRMCSVCGSLTRI-EHGRILKCDSCGLEIDRDVNACINIA 356
                                   5678899*************986522256**********9999.9************************8 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 !   18.4   0.3   6.4e-07    0.0013       2      30 ..     317     344 ..     316     345 .. 0.92

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 6.4e-07
                 zf-NADH-PPase   2 thrFCgrCGaptepaeggwarvCpaCgle 30 
                                   t+r C+ CG+ t+ ++g + + C++Cgle
  gi|13542018|ref|NP_111706.1| 317 TSRMCSVCGSLTRIEHG-RILKCDSCGLE 344
                                   6788*********9999.*********98 PP

>> DUF2229  CoA enzyme activase uncharacterised domain (DUF2229)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.1   0.00011      0.22     113     173 ..      34     103 ..      12     134 .. 0.63
   2 !    5.2   0.2    0.0072        14      91     179 ..     166     257 ..     157     261 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00011
                       DUF2229 113 llspvldle.dkke.....lakqlle...elgiskkeikkAvekAleaqkafkeelrkkgeelleeleee 173
                                   +++ ++++  +k+      + +++++   e++i      +A++kA++  k+++++l+kk++++++++e+ 
  gi|13542018|ref|NP_111706.1|  34 MVNFTINIMiEKNLtsrnsVSNEVYHklkEYEIPSYYYIEAINKAVALVKTYRKRLKKKQKATVPHVEKP 103
                                   3333333332222222222223333234488********************************9987774 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0072
                       DUF2229  91 ynCpivqglpeviknnleeeikllspvldledkkelakqlle...elgiskkeikkAv..ekAleaqkafkeelrkkgeel 166
                                     C+ + g+  +++n +  ++++ ++++dl++  e+++++ +   +++++ ++i++ +  + + ++ +++k+ +++  +++
  gi|13542018|ref|NP_111706.1| 166 IECTTTVGVDRNLRNIT-VGNEFHHEIYDLSNIVEIKQRYRKkesHFHRNDRRIREKIlsKYGKRERNRVKQIMHETSKAI 245
                                   67999999999999999.678999999999999998888886677889999999998733568888888888888888777 PP

                       DUF2229 167 leeleeegkkgiv 179
                                   +++++ ++k+ iv
  gi|13542018|ref|NP_111706.1| 246 VSNAS-TKKEMIV 257
                                   77633.3444455 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.7   1.4e-05     0.029       7      46 ..     313     353 ..     311     354 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.4e-05
                           DZR   7 elppdarfCseCgtklkavaa..edrCpsCgekvdpearfCp 46 
                                   e+++ +r+Cs Cg+  +  ++    +C+sCg ++d + + C 
  gi|13542018|ref|NP_111706.1| 313 ETRNTSRMCSVCGSLTR-IEHgrILKCDSCGLEIDRDVNACI 353
                                   678899*******9876.4445799**************996 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   2.2   6.3e-05      0.13       3      25 ..     321     343 ..     320     345 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 6.3e-05
                                   -SSS--B----SSS----SSS-- CS
                DNA_RNApol_7kD   3 CgeCgaevslkkgdpiRCkeCGh 25 
                                   C  Cg+ +++++g +++C  CG 
  gi|13542018|ref|NP_111706.1| 321 CSVCGSLTRIEHGRILKCDSCGL 343
                                   999*******************7 PP

>> Phage_30_8  Phage GP30.8 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1      0.49   9.7e+02      68     110 ..      40      87 ..      24      98 .. 0.51
   2 ?   12.3   0.5   6.1e-05      0.12      33     102 ..     161     235 ..     128     257 .. 0.68

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.49
                    Phage_30_8  68 nsvvvgkirsktyedeel....gesedvvwye.tarnraesliekikk 110
                                   n ++   + s+    +e+     e e   +y+ +a n+a  l++  +k
  gi|13542018|ref|NP_111706.1|  40 NIMIEKNLTSRNSVSNEVyhklKEYEIPSYYYiEAINKAVALVKTYRK 87 
                                   333333333333333332110023333445555899999888876554 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 6.1e-05
                    Phage_30_8  33 vegdvvevettdgmsddftytievenfftgeiyrlnsvvvgkirsktye....deelgesedvvwye..tarnrae 102
                                    + d +e++tt g+  ++  +i v n f  eiy+l  +v  k r +  e     ++    e ++  +    rnr +
  gi|13542018|ref|NP_111706.1| 161 RDVDAIECTTTVGVDRNL-RNITVGNEFHHEIYDLSNIVEIKQRYRKKEshfhRNDRRIREKILSKYgkRERNRVK 235
                                   46689********98876.58***************9998877665544111134444445554433234455555 PP

>> C1_1  Phorbol esters/diacylglycerol binding domain (C1 domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   1.9   0.00014      0.28       9      44 ..     316     354 ..     311     362 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00014
                                   SS--B-TTT-SB--SSSS-EEEETTT--EE-CC...CCT CS
                          C1_1   9 kqptfCkhCgeflwgkekqglkCswCkllvHkk...Che 44 
                                   + +  C+ Cg++ + +  ++lkC+ C+l ++ +   C++
  gi|13542018|ref|NP_111706.1| 316 NTSRMCSVCGSLTRIEHGRILKCDSCGLEIDRDvnaCIN 354
                                   56789********55*************99887667766 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 ?   11.0   0.5   0.00016      0.31      19      44 ..     319     342 ..     312     344 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00016
                 Zn_Tnp_IS1595  19 fvCPhCgsrkayriktrglfqCkeCr 44 
                                   + C  Cg  +++ri++ + ++C +C+
  gi|13542018|ref|NP_111706.1| 319 RMCSVCG--SLTRIEHGRILKCDSCG 342
                                   67*****..9***************7 PP

>> PHD  PHD-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   2.4   0.00033      0.66       1      22 [.     320     342 ..     320     356 .. 0.92

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00033
                                   SBTTTTS.TTSTTSCEEEETTTS CS
                           PHD   1 rCavCkk.ksdeeeelvqCdgCk 22 
                                   +C+vC++ +  e+++++ Cd+C+
  gi|13542018|ref|NP_111706.1| 320 MCSVCGSlTRIEHGRILKCDSCG 342
                                   5******98899**********7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1338  (0.0746277); expected 358.6 (0.02)
Passed bias filter:                      567  (0.0316247); 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: 0.61u 0.34s 00:00:00.95 Elapsed: 00:00:00.51
# Mc/sec: 2320.64
//
Query:       gi|13542019|ref|NP_111707.1|  [L=107]
Description: transcription regulator [Thermoplasma volcanium GSS1]
Scores for complete 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   47.0   4.5    3.7e-12   46.0   4.5    1.4  1  HTH_45          Winged helix-turn-helix
    4.3e-05   23.3   1.0    5.3e-05   23.0   1.0    1.2  1  DUF4364         Domain of unknown function (DUF4364)
      0.002   18.2   2.6     0.0024   17.9   2.6    1.1  1  HTH_56          Cch helix turn helix domain
     0.0037   17.6   0.0     0.0052   17.1   0.0    1.2  1  Rrf2            Transcriptional regulator
  ------ inclusion threshold ------
      0.044   13.5   0.0      0.058   13.1   0.0    1.2  1  Ribosomal_S19e  Ribosomal protein S19e
       0.05   13.7   0.1       0.17   12.0   0.1    1.8  2  Mrr_N           Mrr N-terminal domain
       0.06   11.7   0.0      0.071   11.5   0.0    1.1  1  DUF505          Protein of unknown function (DUF505)
      0.079   12.9   0.1       0.13   12.3   0.1    1.4  1  PadR            Transcriptional regulator PadR-like family


Domain annotation for each model (and alignments):
>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.0   4.5   1.7e-15   3.7e-12       2      73 ..      14      91 ..      13      94 .. 0.93

  Alignments for each domain:
  == domain 1  score: 46.0 bits;  conditional E-value: 1.7e-15
                        HTH_45  2 RskleIiadILeais..egeakkTkimykanLsykllnkYLdmLvekgli....kkskekYvlTekGlelleklkele 73
                                  R + eI++dIL++i   +ge   Tk++ ++n +yk +++  + L + gli    +k k+++++T+kG++++e++ +++
  gi|13542019|ref|NP_111707.1| 14 RERNEIMLDILKIIYtnNGEVGITKLIFSSNTNYKFIKSLTQDLSNAGLIktyqNKAKHTFTITDKGKDIIERYYNIN 91
                                  99**********996559999*****************************999777999***************9986 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   1.0   2.4e-08   5.3e-05      21      74 ..      36      88 ..      14      91 .. 0.86

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 2.4e-08
                       DUF4364 21 lseiileneytnYfdlqqalseLvesglieeeekenktlykiTekGketlelfe 74
                                  ++++i +   tnY  +++  ++L ++gli++ +++ k++++iT+kGk+++e  +
  gi|13542019|ref|NP_111707.1| 36 ITKLIFSS-NTNYKFIKSLTQDLSNAGLIKTYQNKAKHTFTITDKGKDIIERYY 88
                                  56666654.69*************************************998765 PP

>> HTH_56  Cch helix turn helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   2.6   1.1e-06    0.0024      19     109 ..       7      93 ..       2      95 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.1e-06
                        HTH_56  19 skFkeegkeas.npneiwGkiekkkektevyIlknvfdkileeagFedtkvvlkelkekGllesekdrntkkrtvkkkseg 98 
                                    +F + ++e +  + +i  +i +++   ev I k +f +     +++  k++ + l++ Gl+++ +++ + ++t+++k + 
  gi|13542019|ref|NP_111707.1|   7 FHFVKRNRERNeIMLDILKIIYTNNG--EVGITKLIFSSNT---NYKFIKSLTQDLSNAGLIKTYQNKAKHTFTITDKGKD 82 
                                   57888888855455599999999885..7********9864...44449*****************************999 PP

                        HTH_56  99 kkvrvyvlkld 109
                                   + +r+y++++ 
  gi|13542019|ref|NP_111707.1|  83 IIERYYNINFL 93 
                                   99******985 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   2.3e-06    0.0052       7      58 ..      17      66 ..      12      70 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.3e-06
                                  HHHHHHHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                          Rrf2  7 teyalhallyLakeeeeepvsseeiaerqnispsylekilakLrkaglvksv 58
                                   e+ l +l ++ ++++e  v ++++  + n++ ++++ +++ L++agl+k+ 
  gi|13542019|ref|NP_111707.1| 17 NEIMLDILKIIYTNNGE--VGITKLIFSSNTNYKFIKSLTQDLSNAGLIKTY 66
                                  56777888888888874..8*****************************985 PP

>> Ribosomal_S19e  Ribosomal protein S19e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   2.6e-05     0.058      69     129 ..      22      86 ..      10      90 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.6e-05
                                   ---SS-SSS-------THHH.HHHHHHTTSSS--SSS---SS-...HHHHHTHHHHH--SS--S- CS
                Ribosomal_S19e  69 erlrkvYGgkkrrgvrpshf.vkasgsvirkilqqLeklglvk...kekkkgrrltkkGqrlldr 129
                                   + l+ +Y ++ + g+++  f ++ + + i+++ q+L ++gl+k   +++k+  ++t+kG+ +++r
  gi|13542019|ref|NP_111707.1|  22 DILKIIYTNNGEVGITKLIFsSNTNYKFIKSLTQDLSNAGLIKtyqNKAKHTFTITDKGKDIIER 86 
                                   5567777777777776655515677899**************633345556778******99987 PP

>> Mrr_N  Mrr N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       0.8   1.8e+03       3      14 ..      18      29 ..      17      40 .. 0.72
   2 ?   12.0   0.1   7.6e-05      0.17      59      86 ..      55      85 ..      46      86 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.8
                         Mrr_N  3 elmlplLealad 14
                                  e+ml +L+++  
  gi|13542019|ref|NP_111707.1| 18 EIMLDILKIIYT 29
                                  789999998866 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 7.6e-05
                         Mrr_N 59 tyLkkagllespk...rgvwkiTekGrevlk 86
                                  ++L++agl+++ +   + +++iT+kG+++++
  gi|13542019|ref|NP_111707.1| 55 QDLSNAGLIKTYQnkaKHTFTITDKGKDIIE 85
                                  7899*****9887766999********9875 PP

>> DUF505  Protein of unknown function (DUF505)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   3.2e-05     0.071     364     403 ..      47      86 ..      36      93 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.2e-05
                        DUF505 364 fdlreaL.ysLesfeLieseveekgkevyvlTeyGekvled 403
                                   ++  ++L   L   +Li+++ ++k k+++++T++G+ ++e+
  gi|13542019|ref|NP_111707.1|  47 YKFIKSLtQDLSNAGLIKTY-QNKAKHTFTITDKGKDIIER 86 
                                   55544441569999******.68****************96 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   5.7e-05      0.13      38      73 ..      54      84 ..      44      86 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.7e-05
                                  HHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCHHH CS
                          PadR 38 LkrLekeglveseweesgegpprkyYrlTdaGrrel 73
                                   ++L++ gl+++++++     ++ ++++Td+G++ +
  gi|13542019|ref|NP_111707.1| 54 TQDLSNAGLIKTYQNK-----AKHTFTITDKGKDII 84
                                  67999********887.....79*********9866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       725  (0.0404373); 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:                         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 0.34s 00:00:00.86 Elapsed: 00:00:00.52
# Mc/sec: 615.12
//
Query:       gi|13542020|ref|NP_111708.1|  [L=169]
Description: inorganic pyrophosphatase [Thermoplasma volcanium GSS1]
Scores for complete 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-47  160.7   0.1    2.9e-47  160.5   0.1    1.0  1  Pyrophosphatase  Inorganic pyrophosphatase


Domain annotation for each model (and alignments):
>> Pyrophosphatase  Inorganic pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  160.5   0.1   1.6e-51   2.9e-47       1     155 [.      15     165 ..      15     168 .. 0.97

  Alignments for each domain:
  == domain 1  score: 160.5 bits;  conditional E-value: 1.6e-51
                                   EEEEE-TTCSEEEEEETTTTEEEEEEE-SSSB-BSSEEEEETT--BTCCBEETSSSEEEEEESSS---TTEEEEEEEEEEE CS
               Pyrophosphatase   1 vvvEiprgsnaKyeidkeegklrldrvlftskgypanYGfipqTledtelkGDgDPlDvlvlgeeplspgevvevkvlGvl 81 
                                   v++Eip+gsn Kye+++e ++++ldrvlft+++ypanYGf  +T  +     DgDPlDvlv++++++ pg +v+++ +Gv 
  gi|13542020|ref|NP_111708.1|  15 VMIEIPMGSNCKYEYKEELDNIVLDRVLFTAMTYPANYGFALDTRGK-----DGDPLDVLVFSSVSINPGIIVRCRAIGVA 90 
                                   68*********************************************.....***************************** PP

                                   EEEETTEEEEEEEEEETT..SGGGTT-SSGGGSTHHHHHHHHHHHHHTTTTSCCT-SEEEEEEEEHHHHHHHHHHH CS
               Pyrophosphatase  82 amiDegetDdKiiavpvk..dprlkkindiedlpgllleeiehfFetykdlegkkknvkveewkdkeeAekvieea 155
                                   +m De+++D+Ki+avpv+  dp  + +++ +d+p++ +++++hfFe+yk+le k+k  k++++k+++eA+k ++ea
  gi|13542020|ref|NP_111708.1|  91 EMNDEEGEDNKILAVPVDkvDPASSIVRNESDIPEYQKDKLKHFFEHYKELE-KGKFMKFHGFKGRDEAVKQLAEA 165
                                   ******************99998899**************************.77888*************99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       353  (0.0196888); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); 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 0.30s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 1159.59
//
Query:       gi|13542021|ref|NP_111709.1|  [L=196]
Description: ATP:corrinoid adenosyltransferase [Thermoplasma volcanium GSS1]
Scores for complete 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-51  174.8   0.0    8.2e-51  172.7   0.0    1.7  1  CobA_CobO_BtuR  ATP:corrinoid adenosyltransferase BtuR/CobO/C
     0.0052   16.0   0.0      0.007   15.6   0.0    1.1  1  Aldo_ket_red    Aldo/keto reductase family


Domain annotation for each model (and alignments):
>> CobA_CobO_BtuR  ATP:corrinoid adenosyltransferase BtuR/CobO/CobP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  172.7   0.0   9.2e-55   8.2e-51       3     172 .]       7     196 .]       5     196 .] 0.88

  Alignments for each domain:
  == domain 1  score: 172.7 bits;  conditional E-value: 9.2e-55
                CobA_CobO_BtuR   3 glihvytGdGKGKttAAlGlalRalgaglkvlvvqFlKgekesgElaalkkl....eielerlg................. 62 
                                   gli v+tGdGKGKttAA+Gla+Ralg g++v+v+qF+K   ++gE++++ k+     ++++ +                  
  gi|13542021|ref|NP_111709.1|   7 GLIDVFTGDGKGKTTAAFGLAFRALGWGYRVYVLQFMKL-GTYGENKSAIKFddglIVDFVGMPyfiawkgdipdedlkkv 86 
                                   99*************************************.67*******99987542555555555555555665555543 PP

                CobA_CobO_BtuR  63 kegfv..kmeeeekeedaaaakealekakealaseeydlvvlDEinyalklglldeeevlellkkkpeklelvlTGrnape 141
                                   k+  v   ++ +  +e+++a+ + +++  e+l+++++d+ + DEin+al + ll+++ev+++ + kpe++elv+TGr++p+
  gi|13542021|ref|NP_111709.1|  87 KN--VliCEKGNPPSEYREAVLNHFNRSLEELKTGRWDIFIYDEINVALYYSLLKMDEVMRIFELKPEHTELVFTGRKMPK 165
                                   33..14467788899****************************************************************** PP

                CobA_CobO_BtuR 142 elleaADlvtemkkvkHpydkgikarkGiey 172
                                   e++++ADlvte+++ kHpy++gi ar+Gi++
  gi|13542021|ref|NP_111709.1| 166 EIMDRADLVTEVSSPKHPYQRGILARRGIDF 196
                                   *****************************98 PP

>> Aldo_ket_red  Aldo/keto reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   7.8e-07     0.007      59     125 ..      84     148 ..      74     152 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 7.8e-07
                                   TTGGG-EEEEEE--SSSTTSSSS-HHHHHHHHHHHHHHHT-S-EEEEEE-S--TTS-.....HHHHHHHHH CS
                  Aldo_ket_red  59 kkreeviiatKvdlrdaeiksglskeniresleeslkrLgtdyvDllllHrpdpslp....sieevldale 125
                                   kk ++v+i+ K+      ++++  +e + + +++sl++L+t + D++  ++++++l+    ++ ev++++e
  gi|13542021|ref|NP_111709.1|  84 KKVKNVLICEKG------NPPSEYREAVLNHFNRSLEELKTGRWDIFIYDEINVALYysllKMDEVMRIFE 148
                                   578999******......8888889999****************************999999999998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       409  (0.0228122); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1364.68
//
Query:       gi|13542022|ref|NP_111710.1|  [L=222]
Description: ribosome biogenesis protein [Thermoplasma volcanium GSS1]
Scores for complete 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  138.6   0.0    2.1e-40  138.5   0.0    1.0  1  EMG1      EMG1/NEP1 methyltransferase
  ------ inclusion threshold ------
       0.13   10.7   0.0       0.13   10.7   0.0    1.0  1  Rrn6      RNA polymerase I-specific transcription-initiation 


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 !  138.5   0.0   2.3e-44   2.1e-40       2     194 .]       5     216 ..       4     216 .. 0.92

  Alignments for each domain:
  == domain 1  score: 138.5 bits;  conditional E-value: 2.3e-44
                                   EEEEES--B--GG................SCGGSB--HHHHCGG.TT..STTGGGSS-CHHHHHHHHHHHCSCHHCTT.EE CS
                          EMG1   2 vLeeasLelvkvk................kkseqLLnsddhkkilkk..lkreakeaRpDIvHqcLlalldspLnkagllq 64 
                                   + ++++Le+++++                + ++++L+s++++ ++ k   +++++++RpDI++  L ++++s+Ln+++ll+
  gi|13542022|ref|NP_111710.1|   5 IVADSELETIPEEmlddpgvrrfakkrnkRVDRMILDSNYMHAFIDKyyPGESKRRGRPDIIYILLEMAQESILNRKNLLR 85 
                                   78899*******99***********99988899**********988855688999************************** PP

                                   EEEEETTSEEEEE-TT----SSHHHHHHHHHHHHCCSEEEETTEE.SCEEEECS-HHHHCCC...SEEEEE-TTSEE-... CS
                          EMG1  65 vyihttknvlIevnpqtRiPrtfkrFagLmvqLLkklsirategeekLlkviknpitdhlpp..gskiillsesaekklvd 143
                                    yiht+++ +I+++p tR+P++++rF gL+++L++k  i++++++  Ll++ ++++ ++l++  + ++ill+ ++e    +
  gi|13542022|ref|NP_111710.1|  86 TYIHTRNDFVIKISPITRMPKSYNRFIGLFEDLFEKEIITNNGKT--LLSLERMKLDELLESlkKDRTILLHPKGE--FKK 162
                                   ************************************999988765..**************998999*********..557 PP

                                   ...........EEEE-SSSS....---H..HEEESSSS---HHHHHHHHHHHCH CS
                          EMG1 144 leefv.vkpvvfvigamskgsvkidyke..eeisisnypLsaavvcskiltafE 194
                                   ++ef+ +++++ +ig++s+g+ + d+++  e++si + +L+ + v  +i++++E
  gi|13542022|ref|NP_111710.1| 163 PSEFIsTEDIAAIIGGFSEGDFRSDVSNipEKYSIFRDELTIWSVGLEIVASYE 216
                                   9****889************66666666556*****************999887 PP

>> Rrn6  RNA polymerase I-specific transcription-initiation factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   1.5e-05      0.13     525     616 ..      54     140 ..       5     197 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 1.5e-05
                          Rrn6 525 teeaeeqsfqdllyrlseaiqqlllegsesersplktlleladlplsvedvdefas....eleqllsfyeekditfsslkt 601
                                     e++++  +d++y l+e++q+ +l+ ++  r+++ t ++++ +  +++ +         ++e+l++    k+i+++++kt
  gi|13542022|ref|NP_111710.1|  54 PGESKRRGRPDIIYILLEMAQESILNRKNLLRTYIHTRNDFVIKISPITRMPKSYNrfigLFEDLFE----KEIITNNGKT 130
                                   3456788999**************************************9999999966667777777....********** PP

                          Rrn6 602 ilklllselvsrsld 616
                                   +l+l   +l     d
  gi|13542022|ref|NP_111710.1| 131 LLSLERMKL-----D 140
                                   **9954443.....3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       421  (0.0234815); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.34s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 1372.42
//
Query:       gi|13542023|ref|NP_111711.1|  [L=95]
Description: hypothetical protein TVN1192 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       491  (0.0273858); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.51
# Mc/sec: 559.01
//
Query:       gi|13542024|ref|NP_111712.1|  [L=96]
Description: hypothetical protein TVN1193 [Thermoplasma volcanium GSS1]
Scores for complete 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-07   28.8   0.1    2.2e-06   27.5   0.1    1.6  1  DDE_Tnp_1    Transposase DDE domain
  ------ inclusion threshold ------
      0.066   13.6   0.0       0.23   11.9   0.0    1.8  2  DDE_Tnp_1_2  Transposase DDE domain


Domain annotation for each model (and alignments):
>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   0.1   2.5e-10   2.2e-06      70     195 ..       3      91 ..       1      96 [] 0.72

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 2.5e-10
                     DDE_Tnp_1  70 delrprkgklvlaDaGYasaelldtleekgvdyiirlkkntklyrkgaeskrrgrlr.khdrnkiltksqkrrnkskkekg 149
                                   +++r  + +++laD++Y+  +++d++   + +++ ++           ++kr g++  +   n+ +    +++n       
  gi|13542024|ref|NP_111712.1|   3 NSIR--NFSYILADSAYDASDIYDFVF-ENTHPLPII----------DTNKRGGIIPdRLPVNRKIGIDLRKENA------ 64 
                                   5677..999******************.566655555..........3333333333033344444444455555...... PP

                     DDE_Tnp_1 150 dvyyvtntnsellsaeevaelyrlRwqiErvFkwlkrkfgldrlry 195
                                                       +y+lRw+iEr+F+ l+  ++ ++ ry
  gi|13542024|ref|NP_111712.1|  65 -------------------SMYPLRWEIERTFGILEEILKCENIRY 91 
                                   ...................9*******************9999998 PP

>> DDE_Tnp_1_2  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.18   1.6e+03       1      14 [.      11      24 ..      11      31 .. 0.81
   2 ?   11.9   0.0   2.5e-05      0.23      39      61 ..      60      82 ..      38      89 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.18
                   DDE_Tnp_1_2  1 vlaDrgYrsralre 14
                                  +laD++Y+++ + +
  gi|13542024|ref|NP_111712.1| 11 ILADSAYDASDIYD 24
                                  579*****988765 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 2.5e-05
                   DDE_Tnp_1_2 39 kkqarederarnvvErsfgwlkr 61
                                  +k  +  ++ r+ +Er+fg l++
  gi|13542024|ref|NP_111712.1| 60 RKENASMYPLRWEIERTFGILEE 82
                                  67788899***********9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       231  (0.0128842); expected 358.6 (0.02)
Passed bias filter:                      208  (0.0116013); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 617.04
//
Query:       gi|13542025|ref|NP_111713.1|  [L=388]
Description: galactonate dehydratase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-52  177.4   0.0      4e-52  177.0   0.0    1.1  1  MR_MLE_C  Enolase C-terminal domain-like
    2.8e-11   43.6   0.0    5.7e-11   42.6   0.0    1.5  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 !  177.0   0.0   4.5e-56     4e-52       9     219 ..     144     362 ..     137     363 .. 0.95

  Alignments for each domain:
  == domain 1  score: 177.0 bits;  conditional E-value: 4.5e-56
                                   HHHHHT-SEEEEETSSS........HHHHHHHHHHHHHHHHTTTSTSEEEEE-TTTSBHHHHHHHHHHHGGGT.ESEEESS CS
                      MR_MLE_C   9 lvaeqgfravKlkvggd........dvaedvervravreavgpgddvdlmvDanqawdlatAirvareleeld.llwlEEP 80 
                                    v+++g+ra+K++++g         ++ +  + ++ v +avg+  +v+l+++ +++++++tA+++a+ le ++ + w+EEP
  gi|13542025|ref|NP_111713.1| 144 GVVSRGYRALKFDPFGAgsgflddnEWNRARDIIESVHDAVGK--NVELLIEGHGRFNRSTALKIAKYLEGFEnIGWFEEP 222
                                   47889**********99************************66..67**********************99777******* PP

                                   SSTTTHHHHHHHHHHHH.SSEEEESTTSSSHHHHHHHHHHTSESEEEEBHHHHTSHHHHHHHHHHHHHTT-EEEEBSCSSH CS
                      MR_MLE_C  81 vppeddleglaelrara.sipiaagEslysradfrelleagavdivqpdvsrvgGitearkvaalaeafgvpvapHsgsgg 160
                                   v pe d+eg+a+++ r+ sipiaagE+  +r df + +e ga+ i+qpdv ++gG+ ea+k+a +aea+++ +apH  +g+
  gi|13542025|ref|NP_111713.1| 223 VIPE-DIEGMAMIA-RStSIPIAAGERYVTRFDFIKPFELGAIHIAQPDVINTGGLFEAKKIASMAEAYNIAIAPHQAEGP 301
                                   ***5.6********.777***********************************************************88** PP

                                   HHHHHHHHHHHTTTTBEEEEEEGGGGH..TSGCSBSSSSEEETTEEECTSSSBTSSEB-HH CS
                      MR_MLE_C 161 lglaaslhlaaaipnllileyfldael..leeelleeplevedGrvtvpdgpGlGveldee 219
                                   +++ +++++ a++pnl+i+e+f    +  ++++++++ +e+  G+ +v ++pG+G+ l+++
  gi|13542025|ref|NP_111713.1| 302 VNTFITMQFDATLPNLKIQEMFDEYAYpeWTWDIVDSKPEIISGYEKVEQRPGIGISLKDR 362
                                   **********************999999*****************************9875 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 !   42.6   0.0   6.4e-15   5.7e-11      27     117 .]      20     114 ..      10     114 .. 0.89

  Alignments for each domain:
  == domain 1  score: 42.6 bits;  conditional E-value: 6.4e-15
                                   EEEEEEEEECTTEEEEEEEE-STTGHHHHHHHHHHHHHHHHTTSBTTHHHHH.HHHHHHHCSS.....CHHHHHHHHHHHH CS
                      MR_MLE_N  27 slvlvkietseGvvGigeatsvggraetikaelddhlapllvgkdaanisdl.aqllkravlg.....nmsAkaaidmAlw 101
                                   + v++++ t++G vG+geat +   + + k  ++d l +l+ g ++ +i +  ++ + r           s  ++i++Alw
  gi|13542025|ref|NP_111713.1|  20 KWVFLELITNDGTVGTGEATVYN-GQFSLKERIRD-LGDLITGANPFEIDKFvTNWMLRTFNRskdliSISLMSGIETALW 98 
                                   689*******************9.67788888888.*************986155677777768888889999******** PP

                                   HHHHHHTTSBHHHHTT CS
                      MR_MLE_N 102 DlkakalnlpladLlG 117
                                   D+ +k  + p++  lG
  gi|13542025|ref|NP_111713.1|  99 DIMGKHFGCPVYTFLG 114
                                   ************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (388 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       371  (0.0206927); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 2429.98
//
Query:       gi|13542026|ref|NP_111714.1|  [L=229]
Description: serine/threonine protein phosphatase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.5e-23   82.2   0.0    5.5e-23   82.0   0.0    1.1  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
    9.7e-14   52.3   1.2    4.2e-12   47.0   1.2    2.2  1  Metallophos    Calcineurin-like phosphoesterase
    0.00041   18.8   0.1    0.00052   18.4   0.1    1.1  1  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 !   82.0   0.0   9.3e-27   5.5e-23       1     164 [.       1     191 [.       1     192 [. 0.77

  Alignments for each domain:
  == domain 1  score: 82.0 bits;  conditional E-value: 9.3e-27
                 Metallophos_2   1 MklaiiSDlHsnldaleavlealkevgvdaiihaGDl..eeeepevleellelapvlaVrGNnD..............eev 65 
                                   Mk++i SD+H+nl+a ++v+++   ++ d  i++GD+  ++ +p  + +l + +  + V GN+D              +  
  gi|13542026|ref|NP_111714.1|   1 MKVIIYSDIHANLEAMKEVIKR---EKFDIAIFLGDVvdYGPKPAETLDLVMENMDYGVMGNHDyaaatgedcncapdM-- 76 
                                   **********888888888777...446********99******9888888889**********999998655555540.. PP

                 Metallophos_2  66 veedvlreaaelgtdl................peeaelelagekvlliHgdpl........gvkdalaellke.aeegsdv 121
                                        ++ +++ ++++                +e  + e++g+k+l++H +p+        + ++++  + k+  ++  d+
  gi|13542026|ref|NP_111714.1|  77 -----HDLSEFSRKEVtlpslssedlkrlsslKEFVDTEIDGRKILMTHASPNnhlfgylfATEAEM--VWKDkRYSSYDL 150
                                   .....44444444444555555555555566589999999***********9899997643222222..22222245555* PP

                 Metallophos_2 122 vvcGHtHvpevekeggvlvvnPGsvgeprdgdpe.tyaildtde 164
                                   +++GHtH + + +     ++nPGs+g+prdgd +  yai dtd+
  gi|13542026|ref|NP_111714.1| 151 IMVGHTHFQMLYRN---KIINPGSAGQPRDGDWRpMYAIWDTDA 191
                                   *********88888...8**************999******987 PP

>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.0   1.2     7e-16   4.2e-12       1     202 [.       1     157 [.       1     159 [. 0.73

  Alignments for each domain:
  == domain 1  score: 47.0 bits;  conditional E-value: 7e-16
                                   EEEEEEESBTBTTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSSHHHHHHHHHHHHHHHHTSEEEEEC-TTS....CH CS
                   Metallophos   1 lrilvigDlHlalgggqlddllkllddllreekpdlvllaGDlvdrgdlekellellaalvkypipvylllGNHe....gf 77 
                                   +++++ +D+H     ++l++ ++++   +re k d+ +++GD+vd g+ + e+l+l+ +  +     y ++GNH+    + 
  gi|13542026|ref|NP_111714.1|   1 MKVIIYSDIH-----ANLEAMKEVI---KRE-KFDIAIFLGDVVDYGPKPAETLDLVMENMD-----YGVMGNHDyaaaTG 67 
                                   89********.....9999999999...444.999***9*****************999999.....9*******665533 PP

                                   HH.HHHHHHHHHHHHHHHHEHHHCEEETSEEEEEETTEEEEEEEESECEEETHHHHHHHHHHHSCHHHHCCHHHHHH...H CS
                   Metallophos  78 ee.ellnkygylgifsepwrsdaevfnnlplaslgsgslkvlllhGgspellvsldklgslnleleapepgdewlkd...l 154
                                   e+ ++ +   +l +f                 s      k ++l+  s e+                     + l+    +
  gi|13542026|ref|NP_111714.1|  68 EDcNCAPDMHDLSEF-----------------S-----RKEVTLPSLSSED--------------------LKRLSSlkeF 106
                                   333455554444444.................1.....1333333332222....................2222222225 PP

                                   HHHTTCSEEEEEESSESS.CSSSCSCCHHHHHHH.HHHTT.ESEEEEESSS CS
                   Metallophos 155 ekrekadwvivlgHsply.rgsgylfgdealedl.lkkyg.vdlvisGHtH 202
                                   ++ e +  +i+++H  ++    gylf+ ea + +  k+y   dl+  GHtH
  gi|13542026|ref|NP_111714.1| 107 VDTEIDGRKILMTHASPNnHLFGYLFATEAEMVWkDKRYSsYDLIMVGHTH 157
                                   5555566789****999999999*********999888889********** 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 !   18.4   0.1   8.8e-08   0.00052     165     231 ..       6      68 ..       1      77 [. 0.84

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 8.8e-08
                      FBPase_2 165 lgraeefiialaeliqrlavdklhivGDiyDRGpeadkildeLmkyhsvdiqWGNHDilWmGaaaGs 231
                                   +++ ++ + a+ e+i+r   d    +GD+ D Gp+++  ld +m+  +  +  GNHD    +aa+G+
  gi|13542026|ref|NP_111714.1|   6 YSDIHANLEAMKEVIKREKFDIAIFLGDVVDYGPKPAETLDLVMENMDYGV-MGNHDY---AAATGE 68 
                                   4555667899***********************************999998.6****6...455555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       469  (0.0261587); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.32s 00:00:00.87 Elapsed: 00:00:00.53
# Mc/sec: 1311.96
//
Query:       gi|13542027|ref|NP_111715.1|  [L=144]
Description: transcription regulator [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-08   34.1   0.3    2.4e-08   33.4   0.3    1.4  1  HTH_24         Winged helix-turn-helix DNA-binding
    1.3e-06   28.1   0.2    2.3e-06   27.3   0.2    1.4  1  HTH_AsnC-type  AsnC-type helix-turn-helix domain
  ------ inclusion threshold ------
      0.014   14.9   0.1      0.031   13.8   0.0    1.6  2  Sigma70_r4     Sigma-70, region 4
      0.014   15.3   0.1      0.026   14.5   0.1    1.4  1  HTH_11         HTH domain
       0.03   14.3   0.0      0.051   13.5   0.0    1.4  1  HTH_Crp_2      Crp-like helix-turn-helix domain
      0.034   14.2   0.4      0.058   13.4   0.4    1.4  1  HTH_Mga        M protein trans-acting positive regulator (MGA
       0.11   12.9   0.2       0.49   10.9   0.2    1.9  1  HTH_40         Helix-turn-helix domain
       0.13   12.0   0.0        0.2   11.3   0.0    1.4  1  Sigma70_r4_2   Sigma-70, region 4


Domain annotation for each model (and alignments):
>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.4   0.3   1.1e-11   2.4e-08       2      48 .]       7      53 ..       6      53 .. 0.98

  Alignments for each domain:
  == domain 1  score: 33.4 bits;  conditional E-value: 1.1e-11
                        HTH_24  2 detdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                  d++d++I e L+ + ++++ e+A+++g S+ t++ r+  L++ G+Ik
  gi|13542027|ref|NP_111715.1|  7 DRLDLDIVEMLETDCSLTYEEIAKMTGKSLWTIRDRILALKKRGVIK 53
                                  99********************************************8 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.2     1e-09   2.3e-06       1      41 [.       6      46 ..       6      47 .. 0.96

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 1e-09
                 HTH_AsnC-type  1 LDeiDrkILeaLqedaRisyaeLAervGlSestvlrRvrrL 41
                                  +D++D+ I+e L+ d++++y+e+A+++G S  t++ R+ +L
  gi|13542027|ref|NP_111715.1|  6 IDRLDLDIVEMLETDCSLTYEEIAKMTGKSLWTIRDRILAL 46
                                  6************************************9887 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   1.4e-05     0.031      17      40 ..      18      42 ..       9      48 .. 0.84
   2 ?   -3.4   0.0       3.3   7.3e+03      26      40 ..     111     125 ..     109     126 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.4e-05
                                  H.TTT--HHHHHHHHTS-HHHHHHH CS
                    Sigma70_r4 17 f.geglTleEIgerlgiSrerVrqi 40
                                    +  lT+eEI+++ g S+ ++r +
  gi|13542027|ref|NP_111715.1| 18 EtDCSLTYEEIAKMTGKSLWTIRDR 42
                                  55778*****************977 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 3.3
                                   HHHHHTS-HHHHHHH CS
                    Sigma70_r4  26 IgerlgiSrerVrqi 40 
                                   Ig++ g  re +r i
  gi|13542027|ref|NP_111715.1| 111 IGKQCGEIREYARTI 125
                                   777777777777776 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   1.1e-05     0.026       3      44 ..      11      51 ..      10      60 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.1e-05
                        HTH_11  3 lqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgv 44
                                  l+i+e+L e++  ++ ee+A+ ++ S  t+r +I aL++ gv
  gi|13542027|ref|NP_111715.1| 11 LDIVEML-ETDCSLTYEEIAKMTGKSLWTIRDRILALKKRGV 51
                                  589****.99988**************************994 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   2.3e-05     0.051      19      54 ..      20      55 ..       7      64 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.3e-05
                                  EEEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEET CS
                     HTH_Crp_2 19 elpltqeelAsmlGltretvsrilseLkreglisrg 54
                                  + +lt ee+A m G +  t+   + +Lk++g+i+  
  gi|13542027|ref|NP_111715.1| 20 DCSLTYEEIAKMTGKSLWTIRDRILALKKRGVIKSC 55
                                  6799*****************************953 PP

>> HTH_Mga  M protein trans-acting positive regulator (MGA) HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.4   2.6e-05     0.058       4      45 ..       7      47 ..       5      60 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.6e-05
                       HTH_Mga  4 ikrklkLlelLteneksltldelakeLglseltlqsdiseLn 45
                                  +  +l+++e L + + slt+ e+ak +g s  t++++i  L+
  gi|13542027|ref|NP_111715.1|  7 DRLDLDIVEMLET-DCSLTYEEIAKMTGKSLWTIRDRILALK 47
                                  5668899999999.9***********************9887 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.2   0.00022      0.49      12      78 ..      22     117 ..      14     124 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00022
                        HTH_40  12 glsieeIAkerglkesTIegHLaelieeg..........................eeidlerlvse.eeekeIeeaiekvg 65 
                                   +l+ eeIAk  g +  TI + ++ l + g                           + +++++v++ ++ k+I++ i   g
  gi|13542027|ref|NP_111715.1|  22 SLTYEEIAKMTGKSLWTIRDRILALKKRGvikscraeidydklglpcraiigfnvPPDKIDDFVEQaKKDKRIKKFIITTG 102
                                   5789************************88888875555555555555555555544555666655466666666666666 PP

                        HTH_40  66 sek..lkpikealpe 78 
                                   s++  +k i ++++e
  gi|13542027|ref|NP_111715.1| 103 SRRfhIKIIGKQCGE 117
                                   666776666666655 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   9.1e-05       0.2      26      47 ..      22      43 ..      13      49 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 9.1e-05
                                  ---HHHHHHHHT--HHHHHHHH CS
                  Sigma70_r4_2 26 glsykEIAellgisegtVksrl 47
                                   l+y+EIA+++g s  t++ r+
  gi|13542027|ref|NP_111715.1| 22 SLTYEEIAKMTGKSLWTIRDRI 43
                                  58************99988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       522  (0.0291148); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.29s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 899.44
//
Query:       gi|13542028|ref|NP_111716.1|  [L=513]
Description: benzoylformate decarboxylase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-37  129.1   0.0    2.1e-37  128.4   0.0    1.4  1  TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP b
      1e-22   80.5   0.0    4.9e-22   78.4   0.0    2.1  3  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b
    7.2e-19   67.9   0.0    1.4e-18   67.0   0.0    1.4  1  TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
  ------ inclusion threshold ------
      0.081   12.3   0.0       0.13   11.6   0.0    1.2  1  Lyase_1       Lyase


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 !  128.4   0.0   4.6e-41   2.1e-37       1     170 [.       1     164 [.       1     166 [. 0.96

  Alignments for each domain:
  == domain 1  score: 128.4 bits;  conditional E-value: 4.6e-41
                                   EEHHHHHHHHHHHCT--EEEE---CCCHHHHCCHHCT.TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHHHHCHH CS
                  TPP_enzyme_N   1 mtvaealvraLkalgvehvfgvpGsrilplldalseeqgirvvlarhEqgaafaAdgyaratgkpgvvlvtsgpGatnalt 81 
                                   m++ e++++ Lk+lg+e+vfg+pG+++ p+l+++++      vl++h    +++Adg a++tg p  +++++ pG+ n + 
  gi|13542028|ref|NP_111716.1|   1 MKGYEIFAESLKKLGIEEVFGNPGTTEIPMLRSVNDY-----VLTLHDSISVGMADGKAQVTGSPTLCNLHTVPGIGNSIA 76 
                                   7899****************************99997.....9************************************** PP

                                   HHHHHHHHT--EEEEEEE--CCCHHS..TC--T..-CCHHHCCCSSEEEE-SSGGGHHHHHHHHHHHHHSSS--EEEEEEE CS
                  TPP_enzyme_N  82 alaeAkvdriPllvlsgdrptslrgqgvlqqel..dqlalfrpvtkyaervtspeelpealrrAirtalsgrpgPvylelp 160
                                    l++A+++r+P++v +g+++++++     ++ l  d ++l+  ++ky+++v++++++ + l+rA+++a  +++gPv+l++p
  gi|13542028|ref|NP_111716.1|  77 FLHTAFYNRSPVIVTAGQQDYRHIF---YEPILsgDLTSLVSGLVKYKYEVKQADDIYRSLKRAYQIAEAPPKGPVFLSFP 154
                                   ********************99999...5545588********************************************** PP

                                   HHHCC-EEEH CS
                  TPP_enzyme_N 161 kdvlleevde 170
                                   ++v++ee +e
  gi|13542028|ref|NP_111716.1| 155 MNVMDEEYNE 164
                                   ******9876 PP

>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       1.1   5.1e+03      62      77 ..      75      90 ..      64     107 .. 0.61
   2 ?   -2.4   0.0      0.82   3.7e+03     119     144 ..     116     144 ..      90     152 .. 0.64
   3 !   78.4   0.0   1.1e-25   4.9e-22      13     136 ..     372     489 ..     363     496 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.1
                                  GGGHHHHHHTT-SEEE CS
                  TPP_enzyme_C 62 lqelatavrrnlpitv 77
                                  +  l ta +++ p++v
  gi|13542028|ref|NP_111716.1| 75 IAFLHTAFYNRSPVIV 90
                                  3344455555555544 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.82
                                   HTTSEEEEESSH.HHHHHHHHHHHH.....C CS
                  TPP_enzyme_C 119 alGakgarvekadveeleealkeal.....e 144
                                   +l +k +++e+++ +++ + lk+a       
  gi|13542028|ref|NP_111716.1| 116 GL-VK-YKYEVKQADDIYRSLKRAYqiaeaP 144
                                   44.33.3445555599999999997555444 PP

  == domain 3  score: 78.4 bits;  conditional E-value: 1.1e-25
                                   HTTSSSSEEECETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHTGGGHHHHHHTT-SEEEEEEE-SBCCCHHHHHH CS
                  TPP_enzyme_C  13 lkvkrprsyltsgglgtmGyglpaAiGaklakpdrevvaivGDGgflmilqelatavrrnlpitvvvlnNegygmtggqqe 93 
                                   + v++ +sy+t + +g +G++lpa+ G++l+k   +v a+vGDG+f+++ q l+t+ r+nlp+++++lnN+gy+  +  ++
  gi|13542028|ref|NP_111716.1| 372 FLVYEHNSYFT-AKTGQLGWALPAGAGMSLKK--GKVLAVVGDGSFMYTPQTLWTIERYNLPLKIIILNNGGYMILRSFSK 449
                                   45677788888.579***************73..59********************************************* PP

                                   HHTCCTTTTSBB.BS----HHHHHHHTTSEEEEESSH.HHHHH CS
                  TPP_enzyme_C  94 pfggkrksgpagkdlkpvdfaklaealGakgarvekadveele 136
                                   +++++   ++    ++++d ++l++a+ +++ +v ++++++l+
  gi|13542028|ref|NP_111716.1| 450 SYYNEVADKD--FLKPNIDAENLVKAFHIPV-KVADPNLKDLQ 489
                                   ***9665554..47*************9995.55688888875 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 !   67.0   0.0   3.1e-22   1.4e-18       2     122 ..     183     302 ..     182     310 .. 0.85

  Alignments for each domain:
  == domain 1  score: 67.0 bits;  conditional E-value: 3.1e-22
                                   HHHHHHHHH-SSEEEEE-CHHCHTTGHHHHHHHHHHHT-EE.EEEGGGTTSS-TTSTTEEEESGGGSCHHHHHHHHH-SEE CS
                  TPP_enzyme_M   2 ekaaellkaakrpvilvGggvarsgaseelrelaeklgiPv.vttlmgkgvipedhplylgmlglhgskaanealeeaDlv 81 
                                   +++a++++ ak p+i++G +++  +a ee++++a +lg+Pv ++ l+ +g++p+d+p+y+g l  + s+  n+ l ++Dlv
  gi|13542028|ref|NP_111716.1| 183 REIADMINGAKYPAIVFGYEIDLYDAFEEAKDFAHALGCPVyCEPLASRGCYPSDDPQYAGDLPPA-SALLNMKLMQHDLV 262
                                   789**************************************7777777****************98.************** PP

                                   EEES-SSSTCCCTTTTTTTTTT-.EEEEEESSC.CCCTTCC-- CS
                  TPP_enzyme_M  82 lalGarfddirttgsepefapea.kiihididp.aeigknyqv 122
                                   l++G +    + + + p+ + ++ ++i + +d   +ig +yq+
  gi|13542028|ref|NP_111716.1| 263 LVVGGDI---TLYPYTPPPPLQGkTVIFVGTDNsGKIGTHYQM 302
                                   ****554...445544544444558999977765889998876 PP

>> Lyase_1  Lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   2.9e-05      0.13      77     127 ..     294     341 ..     283     357 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.9e-05
                                   SSHHHHHHHHHHHHHHHHTTHSSGIIIIITTT--HHHHHHHHHHHHHHHHH CS
                       Lyase_1  77 egsgtavnmnlnevigellgekvepndkvhtgqSsnDqvpTalrlalkkal 127
                                    ++gt  +mn + ++ e++g    +++k+++++S n +v+T++ la kk  
  gi|13542028|ref|NP_111716.1| 294 GKIGTHYQMNPKMFLREIMG---LVQRKCNFSRSPNYTVKTSITLARKKMG 341
                                   6789999*************...79********************988755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (513 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       550  (0.0306766); expected 358.6 (0.02)
Passed bias filter:                      510  (0.0284455); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.44
# Mc/sec: 3477.53
//
Query:       gi|13542029|ref|NP_111717.1|  [L=309]
Description: 2-hydroxyacid dehydrogenase [Thermoplasma volcanium GSS1]
Scores for 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-56  188.0   0.0    1.2e-55  187.6   0.0    1.2  1  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
    5.4e-27   94.1   0.0    6.6e-27   93.8   0.0    1.0  1  2-Hacid_dh      D-isomer specific 2-hydroxyacid dehydrogenase
    5.4e-09   36.4   0.1    9.4e-09   35.6   0.1    1.4  1  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
    1.5e-05   25.1   0.1    0.00013   22.1   0.1    2.1  2  AdoHcyase_NAD   S-adenosyl-L-homocysteine hydrolase, NAD bind
    0.00066   20.2   0.1     0.0019   18.8   0.0    1.9  2  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
      0.001   18.7   0.0     0.0022   17.6   0.0    1.6  2  IlvN            Acetohydroxy acid isomeroreductase, NADPH-bin
  ------ inclusion threshold ------
      0.035   14.5   0.0       0.11   13.0   0.0    1.8  2  UDPG_MGDP_dh_C  UDP-glucose/GDP-mannose dehydrogenase family,
      0.087   13.1   0.1        0.2   11.9   0.1    1.6  1  TrkA_N          TrkA-N domain
       0.17   11.8   0.0        1.6    8.6   0.0    2.3  2  Rossmann-like   Rossmann-like domain
       0.42    9.9   1.4       0.93    8.8   1.1    1.7  1  ThiF            ThiF family


Domain annotation for each model (and alignments):
>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  187.6   0.0   6.8e-59   1.2e-55       1     178 []     103     277 ..     103     277 .. 0.99

  Alignments for each domain:
  == domain 1  score: 187.6 bits;  conditional E-value: 6.8e-59
                                   HHHHHHHHTTHHHHHHHHHTTCCHTTCCGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTCE CS
                  2-Hacid_dh_C   1 lalllallrrlaeadeevregewksekallgkelsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeelgve 81 
                                   ++++l +l+ + ++d+e+r+g+w  +  + +++l gk  GiiG+G+IG+++a+rl +fg+ +i+yd+++ +ee e+elg++
  gi|13542029|ref|NP_111717.1| 103 IGMALYFLKDFGHLDREIRNGNW--PILTFSRDLMGKVFGIIGMGAIGRKLAERLIQFGVGIIYYDVKRLPEEVEDELGIT 181
                                   5899*******************..9999**************************************************** PP

                                   ECSHHHHHHH-SEEEE-S--STTTTTSBSHHHHHCSTTTEEEEESS-GGGB-HHHHHHHHHTTSCCEEEES--SSSSSGTC CS
                  2-Hacid_dh_C  82 lvsleellaesDivslhlpltpetrhlinaeelakmkkgailiNtaRGglvdeeaLleaLksgkiagaalDvfeeeplped 162
                                   +v+l+el++++Di+s+h+plt+ t+++i+++e++kmk+g i+iNt+R+++v +++L+ aLk+gki+ a++Dv++ ep++ +
  gi|13542029|ref|NP_111717.1| 182 YVTLDELISSADIISIHVPLTETTKGMIGRKEFEKMKDGCIFINTSRAEVVVTKDLVWALKQGKIK-AGIDVYDREPPDFS 261
                                   *****************************************************************9.************** PP

                                   HHHHHSTTEEE-SS-T CS
                  2-Hacid_dh_C 163 spllelpnviltPHia 178
                                   s+l++++n +++PHia
  gi|13542029|ref|NP_111717.1| 262 SELFQMDNALFSPHIA 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 !   93.8   0.0   3.7e-30   6.6e-27      37     133 ..      37     308 ..      25     309 .] 0.98

  Alignments for each domain:
  == domain 1  score: 93.8 bits;  conditional E-value: 3.7e-30
                                   HTTESEEEE-TTS-BSHHHHHHHTT--EEEESSSSCTTB-HHHHHHTT-EEEE-TTTTHHHHHHHH............... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............... RF
                    2-Hacid_dh  37 akdadalivrsntkvtaevlealpkLkviaragvGvDnvDldaakerGilVtnvpgystesvAElt............... 102
                                     + d+liv+  tkv++++l+++p+Lk+i+ a++G+DnvD+   k r+il +n p++++esvAE++               
  gi|13542029|ref|NP_111717.1|  37 SDESDILIVTAFTKVDKALLDKFPRLKFIQVASTGYDNVDVTEVKSRNILMCNSPSSNKESVAEHVigmalyflkdfghld 117
                                   5679***************************************************************************** PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                    2-Hacid_dh 103 ................................................................................. 102
                                                                                                                    
  gi|13542029|ref|NP_111717.1| 118 reirngnwpiltfsrdlmgkvfgiigmgaigrklaerliqfgvgiiyydvkrlpeevedelgityvtldelissadiisih 198
                                   ********************************************************************************* PP

                                   ...............................................................................T- CS
                                   ...............................................................................xx RF
                    2-Hacid_dh 103 ...............................................................................aa 104
                                                                                                                  ++
  gi|13542029|ref|NP_111717.1| 199 vpltettkgmigrkefekmkdgcifintsraevvvtkdlvwalkqgkikagidvydreppdfsselfqmdnalfsphiaGV 279
                                   ********************************************************************************* PP

                                   BHHHHHHHHHHHHHHHHHHHTTCCGTTBC CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    2-Hacid_dh 105 Teeaqeniaeeaaenlvaflkgespanav 133
                                   T e+q++  ee++ n++++++g +p n+v
  gi|13542029|ref|NP_111717.1| 280 TVESQRRFIEETVANVIRYMQGVDPLNRV 308
                                   **********************9999998 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.6   0.1   5.3e-12   9.4e-09       2     109 ..     139     246 ..     138     252 .. 0.91

  Alignments for each domain:
  == domain 1  score: 35.6 bits;  conditional E-value: 5.3e-12
                                   EEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTTEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHS.HCCC-- CS
                 NAD_binding_2   2 igfiGlGvMGsnmalnllkagykvavynrtkekveelvaegakaaesieelvasldvvitmvkagkavdevieg.llealk 81 
                                   +g+iG+G +G+++a++l++ g  ++ y+++    ee+ +e   ++ ++ el++s+d++ + v+ ++ ++ +i +  +e++k
  gi|13542029|ref|NP_111717.1| 139 FGIIGMGAIGRKLAERLIQFGVGIIYYDVK-RLPEEVEDELGITYVTLDELISSADIISIHVPLTETTKGMIGRkEFEKMK 218
                                   69**************************87.55667777767889999************************9989***** PP

                                   TT-EEEE-S---HHHHHHHHHHHHHTT- CS
                 NAD_binding_2  82 kgdilidgstsspedtrelakelkekgl 109
                                    g i+i++s +++  t++l  +lk+ ++
  gi|13542029|ref|NP_111717.1| 219 DGCIFINTSRAEVVVTKDLVWALKQGKI 246
                                   ******************9999998776 PP

>> AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.29   5.2e+02      60     116 ..      65     120 ..      30     125 .. 0.72
   2 !   22.1   0.1     7e-08   0.00013      21     138 ..     134     253 ..     128     258 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.29
                                   HHHHCTT-EE--HHHCTTT-SEEEE-SSSSSSB-HHHHCCS-TTEEEEE-SSTTTTB CS
                 AdoHcyase_NAD  60 lqaameGfevvtleevvkkadivvtttGnkdiitlehlkkmkddaivcniGhfdsei 116
                                   +q a  G++ v + ev ++  ++  +  ++    +eh+  m     + + Gh d ei
  gi|13542029|ref|NP_111717.1|  65 IQVASTGYDNVDVTEVKSRNILMCNSPSSNKESVAEHVIGMAL-YFLKDFGHLDREI 120
                                   6778888888888887766555555444333344566666653.4567778888777 PP

  == domain 2  score: 22.1 bits;  conditional E-value: 7e-08
                                   -TTSEEEEE--SHHHHHHHHHHHHCT-EEEEE-S-HHHHHHHHCTT-EE--HHHCTTT-SEE...EE.-SSSSSSB-HHHH CS
                 AdoHcyase_NAD  21 laGkvavvaGyGdvGkGcaaslkglGarvivtevdPicalqaameGfevvtleevvkkadiv...vt.ttGnkdiitlehl 97 
                                   l Gkv  ++G G +G+  a+ l ++G  +i  +v  +        G   vtl+e++++adi+   v  t  +k +i ++++
  gi|13542029|ref|NP_111717.1| 134 LMGKVFGIIGMGAIGRKLAERLIQFGVGIIYYDVKRLPEEVEDELGITYVTLDELISSADIIsihVPlTETTKGMIGRKEF 214
                                   569*******************************999887777779**************97433332456789******* PP

                                   CCS-TTEEEEE-SSTTTTBTHHHHHTTT-EEEEEETTEEEE CS
                 AdoHcyase_NAD  98 kkmkddaivcniGhfdseidvaaleanalkkeevkpqvdrv 138
                                   +kmkd +i  n     +e+ v++    alk+ ++k+ +d +
  gi|13542029|ref|NP_111717.1| 215 EKMKDGCIFINTSR--AEVVVTKDLVWALKQGKIKAGIDVY 253
                                   *********99765..5666666556667888888888776 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 ?   -3.2   0.0       7.2   1.3e+04      55      70 ..      32      48 ..      15      61 .. 0.53
   2 !   18.8   0.0     1e-06    0.0019       2      75 ..     139     205 ..     138     226 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 7.2
                                  HHHHHH.H-SEEEE-S- CS
                 F420_oxidored 55 neeaae.eadvvvlavk 70
                                    +  + e+d+++++  
  gi|13542029|ref|NP_111717.1| 32 DLDFKSdESDILIVTAF 48
                                  44443336777776654 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 1e-06
                                   EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S-HHHHH CS
                 F420_oxidored   2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlavkpedve 75 
                                   +giiG+G +g+ la++l++ g     + ++    +   ee ++elg  +t v+  e++++ad++ + v+ + ++
  gi|13542029|ref|NP_111717.1| 139 FGIIGMGAIGRKLAERLIQFG-----VGIIYYDVKRLPEEVEDELG--ITYVTLDELISSADIISIHVPLTETT 205
                                   69*******************.....44443344444467788998..5555599*********9999987665 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 ?   -3.2   0.0       3.1   5.5e+03      47      81 ..      70     103 ..      64     107 .. 0.68
   2 !   17.6   0.0   1.2e-06    0.0022       2      71 ..     134     202 ..     133     235 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 3.1
                                   TT-EEEEHHHHHHT-SEEEE-S-HHHHHHHHHHHT CS
                          IlvN  47 egfevltvaeavkkadvvmiliPDelqkevyeeei 81 
                                   +g++ ++v+e+ k+ +++m+  P + +++v e+ i
  gi|13542029|ref|NP_111717.1|  70 TGYDNVDVTEV-KSRNILMCNSPSSNKESVAEHVI 103
                                   56666666664.56678888888888888877665 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 1.2e-06
                                   HHTS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEHHHHHHT-SEEEE-S-HH CS
                          IlvN   2 lkgkkiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevltvaeavkkadvvmiliPDe 71 
                                   l gk   +iG+G+ G+  a+ l + g+ +++   +     +   e g++ +t++e++++ad++ i +P +
  gi|13542029|ref|NP_111717.1| 134 LMGKVFGIIGMGAIGRKLAERLIQFGVGIIYYDVKRL-PEEVEDELGITYVTLDELISSADIISIHVPLT 202
                                   5688999*********************998766665.56667789*********************954 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 ?   -3.2   0.0       6.3   1.1e+04      53      73 ..      26      46 ..      16      53 .. 0.70
   2 ?   13.0   0.0     6e-05      0.11      21      82 ..     150     208 ..     146     228 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 6.3
                                  CCEEES-CHHHHTT-SEEEE- CS
                UDPG_MGDP_dh_C 53 gvevvdsleealkgadaivil 73
                                  +++++++l+  ++++d+++++
  gi|13542029|ref|NP_111717.1| 26 DINIITDLDFKSDESDILIVT 46
                                  566677777777777777765 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 6e-05
                                   HHHHHHHHCTSEEEEE-SSTHHCCCCHHGGBTCCEEES-CHHHHTT-SEEEE-S--GGGGG.S CS
                UDPG_MGDP_dh_C  21 diieeLleegaevkiyDPkvkeeaveaeleekgvevvdsleealkgadaiviltehdefke.l 82 
                                   +++e+L + g+ + +yD k  +e+ve    e g+++v +l+e +++ad+i i+++  e ++ +
  gi|13542029|ref|NP_111717.1| 150 KLAERLIQFGVGIIYYDVKRLPEEVED---ELGITYV-TLDELISSADIISIHVPLTETTKgM 208
                                   7899*********************99...569***9.6*************99988776644 PP

>> TrkA_N  TrkA-N 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       3      37 ..     141     173 ..     139     192 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00011
                                   EES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHH CS
                        TrkA_N   3 iiGlGrvGrslaeeLseggkdvvvidkdeerveel 37 
                                   iiG+G +Gr+lae+L + g  v +i  d +r+ e 
  gi|13542029|ref|NP_111717.1| 141 IIGMGAIGRKLAERLIQFG--VGIIYYDVKRLPEE 173
                                   9****************77..67777777665443 PP

>> Rossmann-like  Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.38   6.9e+02      47      73 ..      17      44 ..      14      55 .. 0.74
   2 ?    8.6   0.0   0.00092       1.6      13     109 ..     139     232 ..     133     248 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.38
                 Rossmann-like 47 reraerrlPdvpvlevedva.araelll 73
                                  r++a   lPd+++++  d   +++++l+
  gi|13542029|ref|NP_111717.1| 17 RKLAASVLPDINIITDLDFKsDESDILI 44
                                  788999******9987665414555555 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00092
                 Rossmann-like  13 vGiisaGrvGtalgaaleraghvvvgisaisaasreraerrlPdvpvlevedvaaraellllavPdaelpglvkglaatga 93 
                                    Gii+ G +G  l++ l + g  +  i+   +   e  e  l +++ +++++++  a+++ + vP +e ++ + g  + + 
  gi|13542029|ref|NP_111717.1| 139 FGIIGMGAIGRKLAERLIQFGVGI--IYYDVKRLPEEVEDEL-GITYVTLDELISSADIISIHVPLTETTKGMIGRKEFEK 216
                                   599999999999999987776544..4444444455566666.678899*******************999999999999* PP

                 Rossmann-like  94 vraGtivahtsganGv 109
                                   +++G i + ts a+ v
  gi|13542029|ref|NP_111717.1| 217 MKDGCIFINTSRAEVV 232
                                   ***********99765 PP

>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   1.1   0.00052      0.93      21      45 ..     139     163 ..     127     170 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00052
                                   EEEE--SHHHHHHHHHHHHHTTTEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ThiF  21 vllvGaGglGsellknLalsGvgkl 45 
                                   + ++G+G++G  l++ L+  Gvg +
  gi|13542029|ref|NP_111717.1| 139 FGIIGMGAIGRKLAERLIQFGVGII 163
                                   579*******************955 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                        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 0.25s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2174.49
//
Query:       gi|13542030|ref|NP_111718.1|  [L=156]
Description: hypothetical protein TVN1199 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.3e-34  118.2   0.0    3.8e-34  118.0   0.0    1.0  1  Chrome_Resist  Chromate resistance exported protein


Domain annotation for each model (and alignments):
>> Chrome_Resist  Chromate resistance exported protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.0   0.0   2.1e-38   3.8e-34       1     132 []       3     139 ..       3     139 .. 0.91

  Alignments for each domain:
  == domain 1  score: 118.0 bits;  conditional E-value: 2.1e-38
                 Chrome_Resist   1 WvtrervkvDriAcaWLirrfidpeaeflfvpkkaevpke....eaipFDiegaeltheg....erctFevllkkfeledp 73 
                                   W+tre++kvDriAc+WLi+rfidpe ef fvp k++v  +    +a+pF ++g elt       e ++F+ +++k++l+dp
  gi|13542030|ref|NP_111718.1|   3 WITREKAKVDRIACPWLISRFIDPEGEF-FVP-KDQVLVKgkefGAVPFYVQGCELTYFVengtEYVSFDPIIRKYGLDDP 81 
                                   ***************************9.566.44444444699***********99754334588*************** PP

                 Chrome_Resist  74 aLkrlaeivraadvkeeaklapeaagleailaglseelkddeelleaalevydaLyayl 132
                                   aL +la+i+r+ad + + +++++  gl++++ g+++++k+  e+++ +++ ydaLyay+
  gi|13542030|ref|NP_111718.1|  82 ALLELAKIMRSADPA-QPNPEKKRFGLKVLAEGFRMISKNYYENMKLQFPAYDALYAYC 139
                                   ***************.79***************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       378  (0.0210832); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1045.02
//
Query:       gi|13542031|ref|NP_111719.1|  [L=862]
Description: penicillin amidase related protein [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.3e-167  559.7   1.5   1.5e-167  559.5   1.5    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 !  559.5   1.5  8.5e-172  1.5e-167       4     669 ..      74     847 ..      71     851 .. 0.92

  Alignments for each domain:
  == domain 1  score: 559.5 bits;  conditional E-value: 8.5e-172
                                   EEEEGGGEEEEE-SSHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHH-TBHHHHHHHHHHHT-HHHHHHHHHTS.... CS
               Penicil_amidase   4 irrDewgvphIyAkneedlffaqGyvhAqdrlwqmellrrtarGrlaelfGpealesDrllrtlglrraaeaelaal.ldp 83 
                                   ++  + g   +  +n + +f+ qGy+ Aq rl ++++l rta G+l++++G+ +l++D+l+r l+++ +a +e+++l +++
  gi|13542031|ref|NP_111719.1|  74 VFKQADGFIGVASNNSNAVFYEQGYLEAQYRLEELDFLKRTALGNLSAVVGQTTLSTDILMRELQFYNTAVEEYQNLpKTS 154
                                   5666788888999*************************************************************8886666 PP

                                   ..HHHHHHHHHHHHHHHHH-..-ST-HH.HHHH---....S.........SS-.X.XXXXX.....XXX.XXXXXXXX... CS
               Penicil_amidase  84 etralleaYaaGvNaylaelkakalPlefallgykpepWtpvdslavakvmaldl.agnleeelararalaaklgdekvae 163
                                    t++ l a++ G+Nay+++l  ++lP+ f++l+y+p +W+++d+lav++++ ++  ag+++  + +   + +k++++ +++
  gi|13542031|ref|NP_111719.1| 155 FTYESLHAFVSGINAYIQNLTYSKLPILFKILNYEPHKWNVTDVLAVQQLFLWENsAGGFDPVYFN--IALEKMPESLIKA 233
                                   77******************9888*******************************77777744444..467789******* PP

                                   ................................................................................. CS
               Penicil_amidase 164 lfpp............................................................................. 167
                                   ++p+                                                                             
  gi|13542031|ref|NP_111719.1| 234 IYPAypagiqhpivpynlnpsvynetgdisnlslytpsfnvtyslsasssalisfydsaqngyleasrlftgndmnlkisy 314
                                   *99556788899999****************************************************************** PP

                                   ......X-EEEEE-TTTBTTSS-EEEEE-EEESSGGG--EEEEEEETTEEEEEEE-TT-S.SSEEEESSEEEEEEE-SS-S CS
               Penicil_amidase 168 ......gSNnwvvsgerTasGkpllanDPHlglsapslwyqahlqapgldviGaslpGlPgvliGhnediAWglTnagadv 242
                                         gSN w+v+g +T++ ++llanDPHl  s+p +w+  +l apg++viG+++pG+Pgv++Ghn ++AWg+Tn + + 
  gi|13542031|ref|NP_111719.1| 315 svfhdfGSNDWAVNGIKTHNTSALLANDPHLTTSLPPIWMGFQLVAPGMNVIGVTFPGFPGVILGHNPYLAWGATNGQIQE 395
                                   ********************************************************************************* PP

                                   EEEEEEEEETTEEEEEEETTEEEE-EEEEEEEEEE-TT.EEEEEEEEETTEEEE-........TB--EEEEG-TTHHHHHH CS
               Penicil_amidase 243 qdlyaeklnpddptrylydgkwepmetrtetikvkggddsvtltvreTrhGPvvsd.gka..valrwtalepgdrsldall 320
                                   + +yae+++ ++p++y+++g w +++ ++eti+vkg+++ + ++++  ++G+vv++ + +  +a++wt+  p+  +++ +l
  gi|13542031|ref|NP_111719.1| 396 TYFYAEETSSQHPNSYFFNGSWIKFKIENETIQVKGSKP-YFMKIYVAKNGVVVENsS-SspIAIDWTGFMPT-YEITFFL 473
                                   ************************************998.99*************951.257*********97.******* PP

                                   HHHT--SHHHHHHHHHHH--.-SEEEEEEETT--EEEE--S--B---...TT--EEETT-GGGS--TB--GGGS-EEEE.. CS
               Penicil_amidase 321 alnrarnvaefraalkdlaa.paqnvvyADreGnigyqaagrvPvrpaaddgllpvpGsdsayeWtgyipfeelPqvvnPa 400
                                   +++ra++v++fr+ l ++     qn+ +AD++Gnig++  g +P++++++ ++ ++pG+ ++y+W g++p+++lP++++P+
  gi|13542031|ref|NP_111719.1| 474 HIDRAQSVSQFRQNLTQYFKvAIQNWAVADSRGNIGIFPYGLYPIVERGN-PRGILPGT-GQYDWMGFVPVSQLPYLYDPQ 552
                                   *************99776555**************************766.9******9.88******************* PP

                                   SSEEEESSS----S.........--T-HHHHHHHHHH..SS...-B-HHHHHHHHHT-BBTHHHHHHHHH........-.. CS
               Penicil_amidase 401 rgyivtaNnrvlpddypaalgsdwappyRarrirelLeekaagkkvtledmaalqtdtrsllaerllpll.....aleaae 476
                                   +g++++ N+ +++++yp+++g+d++++yRa+++++lL   +++ +++ +dm+ +q+++++ + + +l  l     +    +
  gi|13542031|ref|NP_111719.1| 553 NGFVFSDNQITVSPNYPYYIGWDYESGYRADEAYTLL---NSTWDFNSKDMEMIQLNVHDFTTDIFLHPLlkamdY-YGLS 629
                                   *************************************...55567*******************999777775431.2233 PP

                                   GGGHHHHHHHHH-.SB-STT-THHHHHHHHHHHHTT............................................. CS
               Penicil_amidase 477 aeaaaaldlLraWdgrmdadsaaaalfaawlaalvralfedelg.........................rlaealeklle. 531
                                      ++a++ L+aW+g+m  +s+aa+++  w + +v+ +f + ++                         +    +e+l++ 
  gi|13542031|ref|NP_111719.1| 630 G--TEAYHSLEAWNGDMLVNSTAATIYYYWIRDFVNDTFMPYMQhyginesdglyqvsfflgsddyyhgP---LIEDLVNw 705
                                   2..345*************************************9******************99995552...55555555 PP

                                   ......---TTSTTT-SE.SHH.HHHHHHHHHHHHHHHST-T-B.....HHHHEEEE.E............EE---B-GGG CS
               Penicil_amidase 532 ...da.sfwwddptttpk.trdelllaalaealaeleaaglgadpakwrwgklhrlelrhplg...fnrg.lpvgGgeetv 603
                                      d+  +++++p+t +k + ++++++a++++la++++++ g+  ++w+wg++h+  l + +g   +n   lp++G+ +t+
  gi|13542031|ref|NP_111719.1| 706 tltDPnINYFNNPVTGQKrNESQVMAEAMNQTLAYMTKKY-GPYSTSWEWGNIHKRYLSSFFGinaMNSAeLPAAGDGNTL 785
                                   44455778999999999999999****************5.78788*********99999888***99999********** PP

                                   .........EEEEEEE-EEEEEE--T.S.EEEEETT-S-S-TTSTTSSHHHHHHHTT--EEE--SH CS
               Penicil_amidase 604 natsysarafrvtrgpsyrmvvdladrdkaravlpgGqsgnpgsphyaDqlelwaegeylplpfte 669
                                   na+      +   +gps+rmvv+++ +  + +++pgG s+np sp+y++ + +w++g+y++l  ++
  gi|13542031|ref|NP_111719.1| 786 NAAYG----TISDFGPSWRMVVNMSHPVTSVGIYPGGISENPLSPYYDNTFVAWNNGQYYTLISSK 847
                                   *8755....56799**********************************************998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (862 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       466  (0.0259914); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.73u 0.33s 00:00:01.06 Elapsed: 00:00:00.52
# Mc/sec: 4972.28
//
Query:       gi|13542032|ref|NP_111720.1|  [L=111]
Description: hypothetical protein TVN1201 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        6.4    6.7   6.0       0.47   10.3   0.9    1.7  2  LapA_dom  Lipopolysaccharide assembly protein A domain


Domain annotation for each model (and alignments):
>> LapA_dom  Lipopolysaccharide assembly protein A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.3      0.34   6.1e+03      17      23 ..      11      17 ..       2      27 .. 0.54
   2 ?   10.3   0.9   2.6e-05      0.47      17      44 ..      75     102 ..      69     109 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.34
                      LapA_dom 17 lpLslll 23
                                  + L++l+
  gi|13542032|ref|NP_111720.1| 11 YGLWFLI 17
                                  3334443 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 2.6e-05
                      LapA_dom  17 lpLsllllvafgiGallgwllslwsylr 44 
                                   lpL+l+l ++f+i +l  ++ s +s+++
  gi|13542032|ref|NP_111720.1|  75 LPLVLVLTITFAISLLGLLIGSSFSVVK 102
                                   8**********99887777766666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.49
# Mc/sec: 678.69
//
Query:       gi|13542033|ref|NP_111721.1|  [L=115]
Description: hypothetical protein TVN1202 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.4e-08   31.9   6.8    1.1e-07   31.3   6.8    1.2  1  SHOCT          Short C-terminal domain
    0.00058   19.7   0.2    0.00084   19.2   0.2    1.2  1  VbhA           Antitoxin VbhA
     0.0019   18.1   8.1     0.0024   17.8   8.1    1.1  1  DctQ           Tripartite ATP-independent periplasmic transpo
     0.0032   17.5   0.1     0.0054   16.8   0.1    1.4  1  DUF1707        Domain of unknown function (DUF1707)
  ------ inclusion threshold ------
       0.02   14.8   1.0      0.049   13.5   0.0    1.8  2  SurA_N_2       SurA N-terminal domain
       0.03   13.1   1.0      0.032   13.0   1.0    1.1  1  DUF2207        Predicted membrane protein (DUF2207)
       0.67   10.3   5.5       0.68   10.3   0.1    2.2  2  Tad            Putative Flp pilus-assembly TadE/G-like
        1.8    9.1   9.7        2.8    8.5   9.7    1.2  1  FtsX           FtsX-like permease family
        2.3    7.8   5.4        1.1    8.9   0.1    2.1  2  Baculo_11_kDa  Baculovirus 11 kDa family
        6.1    6.9   6.8        4.6    7.3   0.3    2.3  2  OppC_N         N-terminal TM domain of oligopeptide transport


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 !   31.3   6.8   6.3e-11   1.1e-07       4      27 ..      90     113 ..      90     114 .. 0.96

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 6.3e-11
                         SHOCT   4 ekLkeLyarGeIteEEFeakKakL 27 
                                   e+Lke+ya+GeI+eEE+++k ++L
  gi|13542033|ref|NP_111721.1|  90 EILKERYAKGEISEEEYRKKLDEL 113
                                   79*******************998 PP

>> VbhA  Antitoxin VbhA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.2   4.7e-07   0.00084      20      45 ..      86     111 ..      82     112 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 4.7e-07
                          VbhA  20 saetvadleayvrGeIdadElvrrvr 45 
                                   s++t+ + e+y++GeI+ +E++++++
  gi|13542033|ref|NP_111721.1|  86 SRATEILKERYAKGEISEEEYRKKLD 111
                                   88999999**************9876 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 !   17.8   8.1   1.3e-06    0.0024      60     127 ..       4      69 ..       1      75 [. 0.85

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.3e-06
                          DctQ  60 rvrrlleliadllallfaavliwagwlevaaalfeettpvlglplwwvylvlpigaallalvalarll 127
                                    v+r+l +++ l+a+++++ li  g+    + +++   +++glp++ +y+ +pi+aa+ +lv++  ++
  gi|13542033|ref|NP_111721.1|   4 FVNRILWILIGLIAVVVVLSLIPIGI--YGVGYRGPYFGMMGLPYYGMYFFMPIMAAISILVIILFIY 69 
                                   46777888888888888888888888..*****************************99999987765 PP

>> DUF1707  Domain of unknown function (DUF1707)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.1     3e-06    0.0054       7      35 ..      84     112 ..      80     114 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 3e-06
                       DUF1707   7 dReravelLrealaeGrLtldEfdeRlea 35 
                                   +  ra e+L+e +a G ++ +E+++ l++
  gi|13542033|ref|NP_111721.1|  84 ENSRATEILKERYAKGEISEEEYRKKLDE 112
                                   6679********************99985 PP

>> SurA_N_2  SurA N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.4      0.46   8.3e+02      13      24 ..      10      21 ..       1      36 [. 0.56
   2 ?   13.5   0.0   2.8e-05     0.049      14      64 ..      58     114 ..      53     115 .] 0.78

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.46
                      SurA_N_2 13 viiiglallaFi 24
                                   i+igl+ ++ +
  gi|13542033|ref|NP_111721.1| 10 WILIGLIAVVVV 21
                                  333555544444 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 2.8e-05
                      SurA_N_2  14 ii..iglallaFilgdlfgvgsylfssssnevaeVnGe.....kIslqefqqaveear 64 
                                    i  ++++l+++++  +f  gs+ +s++++ + e+  e     +Is +e++++++e++
  gi|13542033|ref|NP_111721.1|  58 AIsiLVIILFIYLIAGAFHDGSI-MSDENSRATEILKEryakgEISEEEYRKKLDELK 114
                                   44124555555559999998877.6789999*****999***************9976 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   1.0   1.8e-05     0.032     388     432 ..       8      72 ..       2     114 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.8e-05
                       DUF2207 388 lgliilglilillallllvll.....................lvfllilllillliaiivlllfsr 432
                                   +++i++gli+++++l l +++                     ++f++ ++ ++ +++ii+++++ +
  gi|13542033|ref|NP_111721.1|   8 ILWILIGLIAVVVVLSL-IPIgiygvgyrgpyfgmmglpyygMYFFMPIMAAISILVIILFIYLIA 72 
                                   23333333333222222.22235567899**********999777777777777777777777643 PP

>> Tad  Putative Flp pilus-assembly TadE/G-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   2.1      0.25   4.5e+02       2      15 ..      15      28 ..       9      34 .. 0.71
   2 ?   10.3   0.1   0.00038      0.68       6      34 ..      56      88 ..      52      91 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.25
                           Tad  2 saavlfalallpll 15
                                   +av+++l l+p+ 
  gi|13542033|ref|NP_111721.1| 15 LIAVVVVLSLIPIG 28
                                  46777777777775 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00038
                           Tad  6 lfalallplll...lvglav.Dvgravlartrl 34
                                  + a+ +l+++l   l+++a+ D++ ++ + +r+
  gi|13542033|ref|NP_111721.1| 56 MAAISILVIILfiyLIAGAFhDGSIMSDENSRA 88
                                  45566666666788*********9999998887 PP

>> FtsX  FtsX-like permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   9.7    0.0016       2.8      17      85 ..       8      74 ..       2      76 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0016
                          FtsX 17 vlllllteillitlvalviGlglgllaaqllsdvllssvfsselkisidlitvliiivlllllallagl 85
                                  +l++l++ i+++++++l+   + g+ +  + + +++  +    + +++++++ + i+v++l+++l+ag+
  gi|13542033|ref|NP_111721.1|  8 ILWILIGLIAVVVVLSLIPIGIYGVGYRGPYFGMMGLPY--YGMYFFMPIMAAISILVIILFIYLIAGA 74
                                  444455555555555554444555555555555444443..89**********************9987 PP

>> Baculo_11_kDa  Baculovirus 11 kDa family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   1.8      0.28     5e+02      32      53 ..       4      25 ..       2      30 .. 0.75
   2 ?    8.9   0.1   0.00059       1.1      37      73 ..      52      88 ..      49      98 .. 0.66

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.28
                 Baculo_11_kDa 32 flrdFvLvicglvvfvvivlfi 53
                                  f++  + ++ gl+ +vv++ +i
  gi|13542033|ref|NP_111721.1|  4 FVNRILWILIGLIAVVVVLSLI 25
                                  6666777888988888887666 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00059
                 Baculo_11_kDa 37 vLvicglvvfvvivlfilLlvvilknaeaeeaekekr 73
                                   + i + + ++vi+lfi L+   ++  ++ + e ++ 
  gi|13542033|ref|NP_111721.1| 52 FMPIMAAISILVIILFIYLIAGAFHDGSIMSDENSRA 88
                                  55566667777899*****987776666655555554 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 ?    2.8   1.5     0.064   1.2e+02      18      32 ..      11      25 ..       4      54 .. 0.55
   2 ?    7.3   0.3    0.0026       4.6      16      30 ..      58      72 ..      56      87 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.064
                        OppC_N 18 vglvilllllliaif 32
                                  +   +++++++++++
  gi|13542033|ref|NP_111721.1| 11 ILIGLIAVVVVLSLI 25
                                  333344444444433 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0026
                        OppC_N 16 Avvglvillllllia 30
                                  A+  lvi+l+++lia
  gi|13542033|ref|NP_111721.1| 58 AISILVIILFIYLIA 72
                                  666799999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1315  (0.0733449); expected 358.6 (0.02)
Passed bias filter:                      673  (0.037537); expected 358.6 (0.02)
Passed Vit filter:                        98  (0.005466); 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: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 732.42
//
Query:       gi|13542034|ref|NP_111722.1|  [L=167]
Description: hypothetical protein TVN1203, partial [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.8e-06   26.8   0.1    6.5e-06   25.6   0.1    1.6  2  HTH_24     Winged helix-turn-helix DNA-binding
    9.9e-06   25.4   0.0    1.6e-05   24.8   0.0    1.3  1  MarR       MarR family
    0.00017   21.4   0.0    0.00026   20.7   0.0    1.4  1  HTH_IclR   IclR helix-turn-helix domain
    0.00037   20.5   0.0    0.00053   20.1   0.0    1.2  1  DprA_WH    DprA winged helix domain
     0.0004   20.2   0.0    0.00066   19.5   0.0    1.3  1  MarR_2     MarR family
     0.0012   18.7   0.1      0.002   18.0   0.1    1.4  1  TrmB       Sugar-specific transcriptional regulator TrmB
     0.0049   16.8   0.0     0.0084   16.1   0.0    1.4  1  Cdc6_C     CDC6, C terminal winged helix domain
     0.0054   16.7   0.0      0.015   15.2   0.0    1.8  1  HTH_36     Helix-turn-helix domain
     0.0071   16.3   0.1      0.017   15.1   0.0    1.6  1  HTH_Crp_2  Crp-like helix-turn-helix domain
  ------ inclusion threshold ------
       0.15   11.1   1.3       0.19   10.8   1.3    1.1  1  Tmemb_55A  Transmembrane protein 55A


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 ?   -3.1   0.0       3.5   6.2e+03      26      32 ..      66      72 ..      64      78 .. 0.73
   2 !   25.6   0.1   3.6e-09   6.5e-06       3      48 .]     102     148 ..     100     148 .. 0.95

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 3.5
                        HTH_24 26 rlglSps 32
                                  +lglS++
  gi|13542034|ref|NP_111722.1| 66 MLGLSLN 72
                                  7999986 PP

  == domain 2  score: 25.6 bits;  conditional E-value: 3.6e-09
                        HTH_24   3 etdrkILelLqknpr.isqreLAerlglSpstvnrrlkrLeeeGlIk 48 
                                   ++++ I ++L+k+++   q+ L +++glS +tv+r l  Le+ GlI+
  gi|13542034|ref|NP_111722.1| 102 DNEKLIVSILEKHGGiVLQNVLVRESGLSAPTVSRILFSLENYGLIE 148
                                   78899****************************************97 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0   8.7e-09   1.6e-05       5      52 ..     104     152 ..     100     153 .. 0.92

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 8.7e-09
                                   HHHHHHHHHHSTTEEHH.HHHHHHTS-HHHHHHHHHHHHHTTSEEEEEE CS
                          MarR   5 qfviLrilyeqgplsvs.eLakklgvskstvtrvldrLekkGlieRsks 52 
                                   + +i+ il+ +g++ ++  L + +g+s +tv+r+l  Le  GlieR+++
  gi|13542034|ref|NP_111722.1| 104 EKLIVSILEKHGGIVLQnVLVRESGLSAPTVSRILFSLENYGLIERQRK 152
                                   567999*******999999****************************96 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   1.5e-07   0.00026      24      51 ..     123     150 ..     109     151 .. 0.93

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 1.5e-07
                                   HHHHHTS-HHHHHHHHHHHHHTTSEE.. CS
                      HTH_IclR  24 lArrtglpkStvhRlLqtLvelGyveqd 51 
                                   l r++gl+ +tv+R+L +L++ G++e++
  gi|13542034|ref|NP_111722.1| 123 LVRESGLSAPTVSRILFSLENYGLIERQ 150
                                   789***********************96 PP

>> DprA_WH  DprA winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   2.9e-07   0.00053      30      58 ..     122     150 ..     102     153 .. 0.92

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 2.9e-07
                       DprA_WH  30 qLvrrtglpaaevsaaLleLELaGlverl 58 
                                    Lvr++gl+a +vs++L  LE  Gl+er+
  gi|13542034|ref|NP_111722.1| 122 VLVRESGLSAPTVSRILFSLENYGLIERQ 150
                                   69*************************97 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   3.7e-07   0.00066      22      55 ..     118     151 ..     105     154 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 3.7e-07
                                   EEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                        MarR_2  22 ltvgelarrlglsksavsrilkrLvaaGLverrp 55 
                                   + ++ l+r+ gls ++vsril  L+  GL+er++
  gi|13542034|ref|NP_111722.1| 118 VLQNVLVRESGLSAPTVSRILFSLENYGLIERQR 151
                                   47899***************************85 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.1   1.1e-06     0.002      28      57 ..     123     152 ..     100     161 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.1e-06
                                   HCCCTTSSCHCHHHHHHHHHHCTSEEEESS CS
                          TrmB  28 iaeelgvprskvYevLrsLedkGlVerekg 57 
                                   + +e+g++ ++v ++L sLe+ Gl+er+++
  gi|13542034|ref|NP_111722.1| 123 LVRESGLSAPTVSRILFSLENYGLIERQRK 152
                                   5689***********************986 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 !   16.1   0.0   4.7e-06    0.0084      37      78 ..     129     164 ..     124     167 .] 0.87

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 4.7e-06
                                   --HHHHHHHHHHHHHTTSEEEEEEE-CC.C-EEEEEEESSSC CS
                        Cdc6_C  37 ltqrevsdllseLemlgileleksskGrregrtrkisLnvdp 78 
                                   l+  +vs++l  Le +g++e++++      g+t++i+L+vd 
  gi|13542034|ref|NP_111722.1| 129 LSAPTVSRILFSLENYGLIERQRK------GMTNEIRLKVDN 164
                                   6777899**************855......9*********95 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   8.5e-06     0.015       3      55 .]     100     147 ..      98     147 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 8.5e-06
                        HTH_36   3 LspsaklllgslasfanknggcfpsqetlakrlglsknTvsraikeLeqlGyi 55 
                                   L++++kl+  +l ++    g+    q  l + +gls  Tvsr++ +Le +G+i
  gi|13542034|ref|NP_111722.1| 100 LKDNEKLIVSILEKHG---GI--VLQNVLVRESGLSAPTVSRILFSLENYGLI 147
                                   6777777777777777...55..7789999*********************98 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   9.5e-06     0.017      31      55 ..     127     151 ..     118     161 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 9.5e-06
                                   TTSSHHHHHHHHHHHHHTTSEEETE CS
                     HTH_Crp_2  31 lGltretvsrilseLkreglisrgr 55 
                                    Gl+  tvsril  L++ gli+r+r
  gi|13542034|ref|NP_111722.1| 127 SGLSAPTVSRILFSLENYGLIERQR 151
                                   699*******************643 PP

>> Tmemb_55A  Transmembrane protein 55A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   1.3   0.00011      0.19     182     238 ..      11      71 ..       4      78 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00011
                     Tmemb_55A 182 ryarkrsllllll...glillviaigltlgtlkqakkykg.iyvsyvllillalvllarai 238
                                   ry ++r +l++++   ++i+l i+ ++++ t++   k ++  y  y ++il++ ++l+ ++
  gi|13542034|ref|NP_111722.1|  11 RYDNSRLILFAVIavfSIIVLSITSSMMVMTIEIGYKINAlEYLEYFIVILVNALMLGLSL 71 
                                   788888877766522267899999********99887765169**********99998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1130  (0.0630264); expected 358.6 (0.02)
Passed bias filter:                      509  (0.0283898); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1118.08
//
Query:       gi|13542035|ref|NP_111723.1|  [L=510]
Description: TPR repeat-containing protein [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-29  102.4   7.6    1.5e-08   35.0   0.1    6.3  6  TPR_19           Tetratricopeptide repeat
    2.9e-26   89.4  13.1    0.00012   22.0   0.0    9.2  9  TPR_2            Tetratricopeptide repeat
    1.8e-21   76.5   7.9    2.2e-08   34.6   0.3    6.1  6  TPR_16           Tetratricopeptide repeat
    4.6e-20   70.1  20.0    0.00054   20.0   0.0   10.1 10  TPR_8            Tetratricopeptide repeat
    1.8e-17   62.3  15.0    9.9e-06   25.2   0.0    9.1  9  TPR_1            Tetratricopeptide repeat
    4.7e-17   61.1   4.5    0.00074   19.7   0.0    7.1  6  TPR_17           Tetratricopeptide repeat
    4.6e-16   58.1  12.5      0.072   13.9   0.0    9.4  9  TPR_14           Tetratricopeptide repeat
    1.4e-14   53.5  19.0    3.9e-05   23.3   0.4    8.5  9  TPR_11           TPR repeat
    3.9e-13   49.4   7.7      0.016   15.4   0.0    5.7  6  ANAPC3           Anaphase-promoting complex, cyclosome, subun
    1.2e-10   41.3   0.9      0.017   15.2   0.1    4.6  5  TPR_9            Tetratricopeptide repeat
    1.4e-08   34.9   7.1    0.00063   20.0   0.1    4.6  5  TPR_20           Tetratricopeptide repeat
    3.6e-08   33.4   8.4     0.0076   16.3   0.0    4.4  4  SRP_TPR_like     Putative TPR-like repeat
      8e-08   32.5  16.1      0.097   13.0   0.1    7.9  6  TPR_12           Tetratricopeptide repeat
    1.2e-07   31.9  19.8        3.7    8.4   0.1    9.6 10  TPR_6            Tetratricopeptide repeat
    1.9e-07   31.0   2.6      0.088   12.9   0.2    5.4  5  Fis1_TPR_C       Fis1 C-terminal tetratricopeptide repeat
    2.5e-07   30.2  18.5       0.85    9.8   0.5    9.1 10  TPR_7            Tetratricopeptide repeat
    3.7e-06   27.0   4.1        1.4    9.7   0.3    6.5  6  TPR_4            Tetratricopeptide repeat
    2.8e-05   23.5   9.5      0.014   14.6   1.9    4.0  5  TPR_15           Tetratricopeptide repeat
    8.4e-05   23.1   3.1        1.9    9.0   0.1    4.3  5  Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
    0.00019   20.5  14.4    0.00059   18.9   0.1    4.5  6  NARP1            NMDA receptor-regulated protein 1
    0.00061   20.2   0.6       0.16   12.4   0.1    4.1  5  BTAD             Bacterial transcriptional activator domain
     0.0049   16.9   5.8        7.7    6.6   0.2    4.7  5  DUF627           Protein of unknown function (DUF627)
     0.0061   16.6   0.3        1.1    9.3   0.0    3.5  3  Type_III_YscG    Bacterial type II secretion system chaperone
  ------ inclusion threshold ------
      0.052   13.6   1.5        2.6    8.1   0.0    4.0  4  DUF3856          Domain of Unknown Function (DUF3856)
       0.11   12.4  10.8       0.77    9.7   0.1    6.2  7  TPR_10           Tetratricopeptide repeat
       0.18   12.5   0.0         20    6.0   0.0    2.9  2  RNA_polI_A14     Yeast RNA polymerase I subunit RPA14
       0.22   11.2   8.0        1.7    8.3   0.1    3.6  4  TPR_21           Tetratricopeptide repeat-like domain
       0.29   11.2   5.6        3.6    7.7   0.2    4.1  3  TPR_18           Tetratricopeptide repeat
        1.4    9.1   5.3        4.7    7.5   0.1    3.8  4  HemY_N           HemY protein N-terminus


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 !   35.0   0.1   2.4e-11   1.5e-08       2      66 ..      19      83 ..      18      85 .. 0.95
   2 !    7.9   0.0    0.0072       4.5      21      63 ..      72     116 ..      67     122 .. 0.86
   3 !   30.3   0.1   7.1e-10   4.4e-07       4      67 ..     123     186 ..     120     187 .. 0.91
   4 !   17.6   0.0   6.4e-06     0.004       5      56 ..     225     276 ..     221     282 .. 0.93
   5 ?    4.3   0.0     0.092        57      33      66 ..     317     349 ..     288     350 .. 0.90
   6 !   10.9   0.0   0.00084      0.52       3      60 ..     354     409 ..     352     417 .. 0.85

  Alignments for each domain:
  == domain 1  score: 35.0 bits;  conditional E-value: 2.4e-11
                        TPR_19  2 laegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddaryasLlA 66
                                  +a+g+yaeA++   +a++++p n+ + l  A+al+ +g++  A++ L+    +d++++++ sL+ 
  gi|13542035|ref|NP_111723.1| 19 IAAGNYAEAIEKIDKAIDKEPRNPSLHLIRADALYRQGNYSSAIEELNFTEHMDKNNPELFSLKS 83
                                  79******************************************************999999986 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0072
                        TPR_19  21 dpknaearllLAeallalgqldeAealLdalpeedpd.d.aryas 63 
                                   d +n+e+  l  +++ ++g+++  ++  d++ ++d+    a+y +
  gi|13542035|ref|NP_111723.1|  72 DKNNPELFSLKSICYGSMGDFKRSKEEADKAIKADQSyPfAYYNR 116
                                   899*********************************963466655 PP

  == domain 3  score: 30.3 bits;  conditional E-value: 7.1e-10
                        TPR_19   4 egdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddaryasLlAk 67 
                                    gd + A + +++ ++  p +++  ++LAe++++ +++++A++ ++a+++ d+ ++ + +L+ +
  gi|13542035|ref|NP_111723.1| 123 LGDVDGAEKDFRKYIEMQPSDPDPHYDLAEIYFEKKDYKKAMEEVKAVLRNDKSNEKAYDLKLQ 186
                                   59***************************************************99777777655 PP

  == domain 4  score: 17.6 bits;  conditional E-value: 6.4e-06
                        TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedp 56 
                                   g y+ A ++l+q ++ + k +++  lLA+ + + g  +eA ++ ++l++ + 
  gi|13542035|ref|NP_111723.1| 225 GSYDTAEDILKQFIKVYEKEPYLYDLLARTYDQEGKAKEADETYNTLLRLNN 276
                                   89********************************************998765 PP

  == domain 5  score: 4.3 bits;  conditional E-value: 0.092
                        TPR_19  33 eallalgqldeAealLdalpeedpddaryasLlA 66 
                                   +a+ a+g  +eA ++  +l ++d+  ++ +sL A
  gi|13542035|ref|NP_111723.1| 317 IAQDASGKHEEALKTAGELVKMDQT-PYSRSLYA 349
                                   578899******************9.99999987 PP

  == domain 6  score: 10.9 bits;  conditional E-value: 0.00084
                        TPR_19   3 aegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpdd.ar 60 
                                   + g++++Al +l +    d +++e++    ++ll++g+   A++ L+    +  dd +r
  gi|13542035|ref|NP_111723.1| 354 KLGKLEDALTYLGSG---DQDSDEVQFEKFNILLEMGNHSLAMESLKNSITASDDDeER 409
                                   568999999999998...999*************************9887777776455 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.2   8.9e-06    0.0055       3      34 .]      10      41 ..       8      41 .. 0.90
   2 !   11.6   0.0   0.00038      0.24       3      24 ..      44      65 ..      42      66 .. 0.87
   3 ?    6.9   0.0     0.013       7.8       2      31 ..      77     106 ..      76     109 .. 0.86
   4 !   22.0   0.0   1.9e-07   0.00012       2      34 .]     111     143 ..     110     143 .. 0.94
   5 !   16.4   0.0   1.1e-05    0.0068       3      33 ..     146     176 ..     144     177 .. 0.89
   6 !   10.5   0.2   0.00085      0.52       2      32 ..     246     276 ..     245     278 .. 0.92
   7 ?    1.8   0.0      0.53   3.3e+02      13      31 ..     321     339 ..     317     342 .. 0.82
   8 ?    2.9   0.0      0.24   1.5e+02       9      24 ..     350     365 ..     345     366 .. 0.85
   9 ?   -1.4   0.0       5.5   3.4e+03       9      28 ..     381     400 ..     381     405 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 8.9e-06
                         TPR_2  3 alynlGlayyklgdyeeAleafekAleldPnn 34
                                   + + +++ +++g+y+eA+e  +kA+  +P+n
  gi|13542035|ref|NP_111723.1| 10 EYAEEARSDIAAGNYAEAIEKIDKAIDKEPRN 41
                                  6778899999*******************987 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00038
                         TPR_2  3 alynlGlayyklgdyeeAleaf 24
                                  ++  +++a+y++g+y  A+e +
  gi|13542035|ref|NP_111723.1| 44 LHLIRADALYRQGNYSSAIEEL 65
                                  57789**************976 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.013
                         TPR_2   2 ealynlGlayyklgdyeeAleafekAleld 31 
                                   e+      +y  +gd+++ +e  +kA++ d
  gi|13542035|ref|NP_111723.1|  77 ELFSLKSICYGSMGDFKRSKEEADKAIKAD 106
                                   56667789999****************987 PP

  == domain 4  score: 22.0 bits;  conditional E-value: 1.9e-07
                         TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPnn 34 
                                    a+yn++ a++ lgd + A+++f+k +e  P +
  gi|13542035|ref|NP_111723.1| 111 FAYYNRAAALRGLGDVDGAEKDFRKYIEMQPSD 143
                                   79***************************9975 PP

  == domain 5  score: 16.4 bits;  conditional E-value: 1.1e-05
                         TPR_2   3 alynlGlayyklgdyeeAleafekAleldPn 33 
                                    +y l+++y++++dy++A e  +++l+ d  
  gi|13542035|ref|NP_111723.1| 146 PHYDLAEIYFEKKDYKKAMEEVKAVLRNDKS 176
                                   69*******************9999998875 PP

  == domain 6  score: 10.5 bits;  conditional E-value: 0.00085
                         TPR_2   2 ealynlGlayyklgdyeeAleafekAleldP 32 
                                   +++  l++ y + g+ +eA e ++  l+l+ 
  gi|13542035|ref|NP_111723.1| 246 YLYDLLARTYDQEGKAKEADETYNTLLRLNN 276
                                   67999************************95 PP

  == domain 7  score: 1.8 bits;  conditional E-value: 0.53
                         TPR_2  13 klgdyeeAleafekAleld 31 
                                   ++g++eeAl+   + ++ d
  gi|13542035|ref|NP_111723.1| 321 ASGKHEEALKTAGELVKMD 339
                                   689*******998888877 PP

  == domain 8  score: 2.9 bits;  conditional E-value: 0.24
                         TPR_2   9 layyklgdyeeAleaf 24 
                                     ++klg++e+Al ++
  gi|13542035|ref|NP_111723.1| 350 TQLRKLGKLEDALTYL 365
                                   5689*********986 PP

  == domain 9  score: -1.4 bits;  conditional E-value: 5.5
                         TPR_2   9 layyklgdyeeAleafekAl 28 
                                   ++++++g++  A e ++ ++
  gi|13542035|ref|NP_111723.1| 381 NILLEMGNHSLAMESLKNSI 400
                                   57999****99999988765 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.6   0.3   3.5e-11   2.2e-08       3      55 ..      14      64 ..      12      66 .. 0.93
   2 !   21.6   0.1     4e-07   0.00025      10      68 .]      89     144 ..      86     145 .. 0.92
   3 !   34.5   0.0     4e-11   2.4e-08       1      66 [.     114     176 ..     114     178 .. 0.92
   4 ?    2.1   0.1      0.51   3.1e+02      11      60 ..     225     271 ..     221     279 .. 0.62
   5 ?    1.8   0.3      0.65     4e+02       3      37 ..     251     284 ..     250     296 .. 0.72
   6 ?    2.9   0.0      0.29   1.8e+02       9      55 ..     321     363 ..     318     375 .. 0.80

  Alignments for each domain:
  == domain 1  score: 34.6 bits;  conditional E-value: 3.5e-11
                        TPR_16  3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAa.a 55
                                  +ar+ ++ag+y++A++  + a+++    P+++  +l ++da++rqg++  A+ +
  gi|13542035|ref|NP_111723.1| 14 EARSDIAAGNYAEAIEKIDKAIDKE---PRNPSLHLIRADALYRQGNYSSAIeE 64
                                  79999********************...9999*******************955 PP

  == domain 2  score: 21.6 bits;  conditional E-value: 4e-07
                        TPR_16  10 agdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapdap 68 
                                    gd+ +  + ++ a+k+d      + A+++++ a+  +g++++A+  +r++++  p++p
  gi|13542035|ref|NP_111723.1|  89 MGDFKRSKEEADKAIKAD---QSYPFAYYNRAAALRGLGDVDGAEKDFRKYIEMQPSDP 144
                                   69999*************...55555******************************998 PP

  == domain 3  score: 34.5 bits;  conditional E-value: 4e-11
                        TPR_16   1 lalaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapd 66 
                                   +++a a++ +gd d A++ ++ +++++   P +++ ++ l++++++++++++A + ++a lr++ +
  gi|13542035|ref|NP_111723.1| 114 YNRAAALRGLGDVDGAEKDFRKYIEMQ---PSDPDPHYDLAEIYFEKKDYKKAMEEVKAVLRNDKS 176
                                   7899***********************...66667************************9998865 PP

  == domain 4  score: 2.1 bits;  conditional E-value: 0.51
                        TPR_16  11 gdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraa 60 
                                   g yd A+  l++++k +      +  + ll++ + + g  +eA + y+ +
  gi|13542035|ref|NP_111723.1| 225 GSYDTAEDILKQFIKVY---EKEPYLYDLLARTYDQEGKAKEADETYNTL 271
                                   56777777777777777...555556666666666666666664444444 PP

  == domain 5  score: 1.8 bits;  conditional E-value: 0.65
                        TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAl 37 
                                   lar + + g+  +A + ++++l+++  s + +  +
  gi|13542035|ref|NP_111723.1| 251 LARTYDQEGKAKEADETYNTLLRLN-NSRESHIYW 284
                                   6888888888888989999988888.444444444 PP

  == domain 6  score: 2.9 bits;  conditional E-value: 0.29
                        TPR_16   9 ragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaa 55 
                                   ++g+ ++A++ + +++k+d     ++ ++ l++  + ++g l++A+ 
  gi|13542035|ref|NP_111723.1| 321 ASGKHEEALKTAGELVKMD---Q-TPYSRSLYATQLRKLGKLEDALT 363
                                   5799999999999999999...4.77788888888888888888873 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.1      0.78   4.8e+02      14      29 ..      21      36 ..      15      41 .. 0.85
   2 ?    3.0   0.0      0.24   1.5e+02       6      24 ..      47      65 ..      42      66 .. 0.84
   3 !   10.6   0.1   0.00088      0.54       7      33 ..      82     108 ..      76     109 .. 0.87
   4 !   20.0   0.0   8.7e-07   0.00054       3      34 .]     112     143 ..     112     143 .. 0.96
   5 !   15.9   0.1   1.8e-05     0.011       4      33 ..     147     176 ..     144     177 .. 0.89
   6 ?    0.6   0.0       1.5   9.1e+02      13      32 ..     223     242 ..     221     244 .. 0.83
   7 !   16.1   0.1   1.5e-05    0.0095       3      32 ..     247     276 ..     245     278 .. 0.92
   8 ?    1.3   0.0      0.86   5.3e+02      13      32 ..     321     340 ..     318     342 .. 0.86
   9 ?   -1.1   0.0         5   3.1e+03      12      24 ..     353     365 ..     352     367 .. 0.87
  10 ?    5.0   0.0     0.056        35      10      32 ..     382     404 ..     381     406 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.78
                                  TT-HHHHHHHHHHHHH CS
                         TPR_8 14 lgdyeeAkeyyekale 29
                                   g+y eA+e + ka++
  gi|13542035|ref|NP_111723.1| 21 AGNYAEAIEKIDKAID 36
                                  59*******9999986 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.24
                                  HHHHHHHHTT-HHHHHHHH CS
                         TPR_8  6 nlgsiylklgdyeeAkeyy 24
                                    ++++  +g+y +A+e +
  gi|13542035|ref|NP_111723.1| 47 IRADALYRQGNYSSAIEEL 65
                                  67999***********976 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 0.00088
                                   HHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                         TPR_8   7 lgsiylklgdyeeAkeyyekaleldpd 33 
                                   ++ +y ++gd++ +ke   ka+++d++
  gi|13542035|ref|NP_111723.1|  82 KSICYGSMGDFKRSKEEADKAIKADQS 108
                                   56689******************9975 PP

  == domain 4  score: 20.0 bits;  conditional E-value: 8.7e-07
                                   HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                         TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                   ayyn + +++ lgd + A++ ++k++e++p++
  gi|13542035|ref|NP_111723.1| 112 AYYNRAAALRGLGDVDGAEKDFRKYIEMQPSD 143
                                   7****************************975 PP

  == domain 5  score: 15.9 bits;  conditional E-value: 1.8e-05
                                   HHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                         TPR_8   4 yynlgsiylklgdyeeAkeyyekaleldpd 33 
                                   +y l+ iy++++dy++A+e  + +l+ d++
  gi|13542035|ref|NP_111723.1| 147 HYDLAEIYFEKKDYKKAMEEVKAVLRNDKS 176
                                   699****************99999988876 PP

  == domain 6  score: 0.6 bits;  conditional E-value: 1.5
                                   HTT-HHHHHHHHHHHHHHHH CS
                         TPR_8  13 klgdyeeAkeyyekaleldp 32 
                                     g y+ A+  +++ ++  +
  gi|13542035|ref|NP_111723.1| 223 GIGSYDTAEDILKQFIKVYE 242
                                   5699*********9999766 PP

  == domain 7  score: 16.1 bits;  conditional E-value: 1.5e-05
                                   HHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                         TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldp 32 
                                   +y +l+++y++ g+ +eA e+y+  l+l+ 
  gi|13542035|ref|NP_111723.1| 247 LYDLLARTYDQEGKAKEADETYNTLLRLNN 276
                                   5889***********************996 PP

  == domain 8  score: 1.3 bits;  conditional E-value: 0.86
                                   HTT-HHHHHHHHHHHHHHHH CS
                         TPR_8  13 klgdyeeAkeyyekaleldp 32 
                                     g++eeA ++  + +++d+
  gi|13542035|ref|NP_111723.1| 321 ASGKHEEALKTAGELVKMDQ 340
                                   579*******9999999986 PP

  == domain 9  score: -1.1 bits;  conditional E-value: 5
                                   HHTT-HHHHHHHH CS
                         TPR_8  12 lklgdyeeAkeyy 24 
                                   +klg++e A  y+
  gi|13542035|ref|NP_111723.1| 353 RKLGKLEDALTYL 365
                                   69******99986 PP

  == domain 10  score: 5.0 bits;  conditional E-value: 0.056
                                   HHHHTT-HHHHHHHHHHHHHHHH CS
                         TPR_8  10 iylklgdyeeAkeyyekaleldp 32 
                                   i+l++g++  A+e+++  ++++ 
  gi|13542035|ref|NP_111723.1| 382 ILLEMGNHSLAMESLKNSITASD 404
                                   899*************9998876 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.5   0.3    0.0059       3.6      14      34 .]      21      41 ..      19      41 .. 0.91
   2 ?    6.4   0.0     0.014       8.5       6      22 ..      47      63 ..      42      65 .. 0.88
   3 ?    3.5   0.0      0.11        67      10      33 ..      85     108 ..      84     109 .. 0.89
   4 !   25.2   0.0   1.6e-08   9.9e-06       2      34 .]     111     143 ..     110     143 .. 0.95
   5 !   12.8   0.0   0.00013     0.082       3      22 ..     146     165 ..     144     177 .. 0.86
   6 ?    1.4   0.1      0.53   3.3e+02       7      31 ..     251     275 ..     250     277 .. 0.90
   7 ?    0.0   0.0       1.4   8.8e+02      13      22 ..     321     330 ..     317     332 .. 0.82
   8 ?    3.3   0.0      0.13        80      11      23 ..     352     364 ..     349     366 .. 0.87
   9 ?    2.8   0.0      0.19   1.2e+02       9      28 ..     381     400 ..     381     405 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0059
                                  TT-HHHHHHHHHHHHHHSTTH CS
                         TPR_1 14 lgkydeAleyyekALelnPnn 34
                                   g+y eA+e  +kA+  +P n
  gi|13542035|ref|NP_111723.1| 21 AGNYAEAIEKIDKAIDKEPRN 41
                                  69**************99986 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.014
                                  HHHHHHHHTT-HHHHHH CS
                         TPR_1  6 nlGnayfklgkydeAle 22
                                   ++ a++++g+y  A+e
  gi|13542035|ref|NP_111723.1| 47 IRADALYRQGNYSSAIE 63
                                  5899***********98 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.11
                                   HHHHTT-HHHHHHHHHHHHHHSTT CS
                         TPR_1  10 ayfklgkydeAleyyekALelnPn 33 
                                   +y ++g+++   e  +kA++ + +
  gi|13542035|ref|NP_111723.1|  85 CYGSMGDFKRSKEEADKAIKADQS 108
                                   9************99999998876 PP

  == domain 4  score: 25.2 bits;  conditional E-value: 1.6e-08
                                   HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                         TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPnn 34 
                                    a+yn+++a++ lg+ d A+++++k +e +P++
  gi|13542035|ref|NP_111723.1| 111 FAYYNRAAALRGLGDVDGAEKDFRKYIEMQPSD 143
                                   59*****************************86 PP

  == domain 5  score: 12.8 bits;  conditional E-value: 0.00013
                                   HHHHHHHHHHHTT-HHHHHH CS
                         TPR_1   3 alynlGnayfklgkydeAle 22 
                                    +y l+ +yf++++y++A e
  gi|13542035|ref|NP_111723.1| 146 PHYDLAEIYFEKKDYKKAME 165
                                   59****************97 PP

  == domain 6  score: 1.4 bits;  conditional E-value: 0.53
                                   HHHHHHHTT-HHHHHHHHHHHHHHS CS
                         TPR_1   7 lGnayfklgkydeAleyyekALeln 31 
                                   l+ +y + gk +eA e y+  L+ln
  gi|13542035|ref|NP_111723.1| 251 LARTYDQEGKAKEADETYNTLLRLN 275
                                   7889**************9999887 PP

  == domain 7  score: 0.0 bits;  conditional E-value: 1.4
                                   HTT-HHHHHH CS
                         TPR_1  13 klgkydeAle 22 
                                     gk++eAl+
  gi|13542035|ref|NP_111723.1| 321 ASGKHEEALK 330
                                   679*****97 PP

  == domain 8  score: 3.3 bits;  conditional E-value: 0.13
                                   HHHTT-HHHHHHH CS
                         TPR_1  11 yfklgkydeAley 23 
                                   ++klgk+++Al y
  gi|13542035|ref|NP_111723.1| 352 LRKLGKLEDALTY 364
                                   78*********88 PP

  == domain 9  score: 2.8 bits;  conditional E-value: 0.19
                                   HHHHHTT-HHHHHHHHHHHH CS
                         TPR_1   9 nayfklgkydeAleyyekAL 28 
                                   n+++++g++  A e  +  +
  gi|13542035|ref|NP_111723.1| 381 NILLEMGNHSLAMESLKNSI 400
                                   7899**********999876 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.0   0.00031      0.19       3      34 .]      32      63 ..      30      63 .. 0.93
   2 ?    1.4   0.0      0.86   5.3e+02       8      33 ..      70      96 ..      65      97 .. 0.85
   3 !   15.9   0.1     2e-05     0.013       3      34 .]     100     131 ..      98     131 .. 0.94
   4 !   19.7   0.0   1.2e-06   0.00074       2      32 ..     133     163 ..     132     165 .. 0.94
   5 ?    4.5   0.0     0.089        55       3      32 ..     235     264 ..     233     266 .. 0.88
   6 ?    1.5   0.0      0.78   4.8e+02      16      33 ..     345     362 ..     342     363 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00031
                        TPR_17  3 lkaleldPnnadaynnLAelllknGdlmtArq 34
                                   ka++++P n+ ++  +A +l+++G++  A++
  gi|13542035|ref|NP_111723.1| 32 DKAIDKEPRNPSLHLIRADALYRQGNYSSAIE 63
                                  69*************************98875 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.86
                        TPR_17  8 l.dPnnadaynnLAelllknGdlmtAr 33
                                  + d+nn++++ ++  ++ + Gd+++ +
  gi|13542035|ref|NP_111723.1| 70 HmDKNNPELFSLKSICYGSMGDFKRSK 96
                                  4499******************99876 PP

  == domain 3  score: 15.9 bits;  conditional E-value: 2e-05
                        TPR_17   3 lkaleldPnnadaynnLAelllknGdlmtArq 34 
                                    ka++ d +++ ay+n+A +l+ +Gd + A++
  gi|13542035|ref|NP_111723.1| 100 DKAIKADQSYPFAYYNRAAALRGLGDVDGAEK 131
                                   79*************************99985 PP

  == domain 4  score: 19.7 bits;  conditional E-value: 1.2e-06
                        TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtA 32 
                                   ++k +e  P+++d+++ LAe++ +++d+++A
  gi|13542035|ref|NP_111723.1| 133 FRKYIEMQPSDPDPHYDLAEIYFEKKDYKKA 163
                                   7899*************************99 PP

  == domain 5  score: 4.5 bits;  conditional E-value: 0.089
                        TPR_17   3 lkaleldPnnadaynnLAelllknGdlmtA 32 
                                   +++++ + + +++y +LA+++ + G+ ++A
  gi|13542035|ref|NP_111723.1| 235 KQFIKVYEKEPYLYDLLARTYDQEGKAKEA 264
                                   678888899999*************99998 PP

  == domain 6  score: 1.5 bits;  conditional E-value: 0.78
                        TPR_17  16 ynnLAelllknGdlmtAr 33 
                                     ++A+ l+k+G+l++A+
  gi|13542035|ref|NP_111723.1| 345 RSLYATQLRKLGKLEDAL 362
                                   5689***********996 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.2   0.00025      0.15       4      42 ..      11      49 ..       8      51 .. 0.85
   2 ?    7.8   0.0     0.011       6.9       2      24 ..      43      65 ..      42      66 .. 0.89
   3 !   13.9   0.0   0.00012     0.072       3      35 ..     112     144 ..     110     147 .. 0.93
   4 !   13.4   0.0   0.00018      0.11       2      41 ..     145     184 ..     144     187 .. 0.89
   5 ?    4.1   0.0      0.17     1e+02      15      43 ..     225     253 ..     220     254 .. 0.93
   6 ?    4.6   0.1      0.11        71       3      32 ..     247     276 ..     245     288 .. 0.85
   7 ?   -0.6   0.0       5.6   3.5e+03      12      29 ..     320     337 ..     317     348 .. 0.75
   8 ?    4.0   0.0      0.19   1.2e+02       5      27 ..     346     368 ..     342     381 .. 0.83
   9 ?    2.8   0.0      0.45   2.8e+02       8      37 ..     380     409 ..     373     415 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00025
                        TPR_14  4 llalaeallalGdpdeAiallrralalaPddaeawllla 42
                                  +++ a+   a+G+++eAi+  ++a+++ P ++ ++l  a
  gi|13542035|ref|NP_111723.1| 11 YAEEARSDIAAGNYAEAIEKIDKAIDKEPRNPSLHLIRA 49
                                  5666788899**********************9998666 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.011
                        TPR_14  2 eallalaeallalGdpdeAiall 24
                                   ++l +a+al+++G++  Ai+ l
  gi|13542035|ref|NP_111723.1| 43 SLHLIRADALYRQGNYSSAIEEL 65
                                  57899***************987 PP

  == domain 3  score: 13.9 bits;  conditional E-value: 0.00012
                        TPR_14   3 allalaeallalGdpdeAiallrralalaPdda 35 
                                   a++ +a+al+ lGd d+A++ +r++++ +P+d+
  gi|13542035|ref|NP_111723.1| 112 AYYNRAAALRGLGDVDGAEKDFRKYIEMQPSDP 144
                                   8999**************************997 PP

  == domain 4  score: 13.4 bits;  conditional E-value: 0.00018
                        TPR_14   2 eallalaeallalGdpdeAiallrralalaPddaeawlll 41 
                                   + +++lae++++  d+++A++  +++l+ + +++ a+ l 
  gi|13542035|ref|NP_111723.1| 145 DPHYDLAEIYFEKKDYKKAMEEVKAVLRNDKSNEKAYDLK 184
                                   5689*****************************9998665 PP

  == domain 5  score: 4.1 bits;  conditional E-value: 0.17
                        TPR_14  15 GdpdeAiallrralalaPddaeawlllaq 43 
                                   G +d+A+++l++ ++ + +++ ++ lla+
  gi|13542035|ref|NP_111723.1| 225 GSYDTAEDILKQFIKVYEKEPYLYDLLAR 253
                                   789********************999998 PP

  == domain 6  score: 4.6 bits;  conditional E-value: 0.11
                        TPR_14   3 allalaeallalGdpdeAiallrralalaP 32 
                                   ++ +la+ + + G+ +eA + ++ +l+l+ 
  gi|13542035|ref|NP_111723.1| 247 LYDLLARTYDQEGKAKEADETYNTLLRLNN 276
                                   57899******************9999875 PP

  == domain 7  score: -0.6 bits;  conditional E-value: 5.6
                        TPR_14  12 lalGdpdeAiallrrala 29 
                                    a+G+++eA++ + ++++
  gi|13542035|ref|NP_111723.1| 320 DASGKHEEALKTAGELVK 337
                                   578999999998777665 PP

  == domain 8  score: 4.0 bits;  conditional E-value: 0.19
                        TPR_14   5 lalaeallalGdpdeAiallrra 27 
                                    ++a  l+ lG++++A+++l   
  gi|13542035|ref|NP_111723.1| 346 SLYATQLRKLGKLEDALTYLGSG 368
                                   57999*************99655 PP

  == domain 9  score: 2.8 bits;  conditional E-value: 0.45
                        TPR_14   8 aeallalGdpdeAiallrralalaPddaea 37 
                                     +ll+ G++  A++ l+  + +  dd+e 
  gi|13542035|ref|NP_111723.1| 380 FNILLEMGNHSLAMESLKNSITASDDDEER 409
                                   568999**************9999998875 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.4   6.2e-08   3.9e-05       6      42 .]      20      56 ..      15      56 .. 0.95
   2 !   10.6   0.1   0.00058      0.36       2      31 ..      50      79 ..      49      81 .. 0.86
   3 !   11.6   0.5   0.00028      0.17      19      39 ..     101     121 ..      86     124 .. 0.88
   4 !   16.8   0.0   6.7e-06    0.0041       5      41 ..     121     157 ..     118     158 .. 0.92
   5 !    7.6   0.3    0.0048       2.9       2      31 ..     152     181 ..     151     182 .. 0.94
   6 ?    3.0   0.1      0.13        82       4      26 ..     255     277 ..     252     280 .. 0.87
   7 ?   -0.9   0.0       2.2   1.3e+03       7      15 ..     322     330 ..     321     331 .. 0.86
   8 ?    1.5   0.0      0.39   2.4e+02       4      15 ..     352     363 ..     350     365 .. 0.89
   9 ?   -0.1   0.0       1.2   7.7e+02       2      22 ..     381     401 ..     381     408 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 6.2e-08
                        TPR_11  6 eqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42
                                  + G+y eAie+  kA++  P n+++++ +++a+y+qG
  gi|13542035|ref|NP_111723.1| 20 AAGNYAEAIEKIDKAIDKEPRNPSLHLIRADALYRQG 56
                                  68**********************************9 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00058
                        TPR_11  2 dayyeqGkyeeAieaYkkAlkldPdnaeay 31
                                  da+y qG+y  Aie+++     d +n+e++
  gi|13542035|ref|NP_111723.1| 50 DALYRQGNYSSAIEELNFTEHMDKNNPELF 79
                                  9**************998888888888765 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 0.00028
                        TPR_11  19 kAlkldPdnaeayynLGlayy 39 
                                   kA+k d++++ ayyn+++a+ 
  gi|13542035|ref|NP_111723.1| 101 KAIKADQSYPFAYYNRAAALR 121
                                   9****************9985 PP

  == domain 4  score: 16.8 bits;  conditional E-value: 6.7e-06
                        TPR_11   5 yeqGkyeeAieaYkkAlkldPdnaeayynLGlayykq 41 
                                   + +G+ ++A ++++k ++  P++++ +y L+++y+++
  gi|13542035|ref|NP_111723.1| 121 RGLGDVDGAEKDFRKYIEMQPSDPDPHYDLAEIYFEK 157
                                   66899*****************************986 PP

  == domain 5  score: 7.6 bits;  conditional E-value: 0.0048
                        TPR_11   2 dayyeqGkyeeAieaYkkAlkldPdnaeay 31 
                                    +y+e+ +y++A+e+ k+ l+ d +n  ay
  gi|13542035|ref|NP_111723.1| 152 EIYFEKKDYKKAMEEVKAVLRNDKSNEKAY 181
                                   59*********************9999998 PP

  == domain 6  score: 3.0 bits;  conditional E-value: 0.13
                        TPR_11   4 yyeqGkyeeAieaYkkAlkldPd 26 
                                   y + Gk +eA e Y++ l+l+++
  gi|13542035|ref|NP_111723.1| 255 YDQEGKAKEADETYNTLLRLNNS 277
                                   5589****************975 PP

  == domain 7  score: -0.9 bits;  conditional E-value: 2.2
                        TPR_11   7 qGkyeeAie 15 
                                    Gk eeA++
  gi|13542035|ref|NP_111723.1| 322 SGKHEEALK 330
                                   7******97 PP

  == domain 8  score: 1.5 bits;  conditional E-value: 0.39
                        TPR_11   4 yyeqGkyeeAie 15 
                                   ++++Gk+e+A++
  gi|13542035|ref|NP_111723.1| 352 LRKLGKLEDALT 363
                                   789*******97 PP

  == domain 9  score: -0.1 bits;  conditional E-value: 1.2
                        TPR_11   2 dayyeqGkyeeAieaYkkAlk 22 
                                   +++ e G+   A+e++k+ + 
  gi|13542035|ref|NP_111723.1| 381 NILLEMGNHSLAMESLKNSIT 401
                                   7999************99875 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   2.8e-05     0.017      36      79 ..      21      65 ..       4      68 .. 0.71
   2 !   15.4   0.0   2.6e-05     0.016       3      47 ..      22      66 ..      20      87 .. 0.63
   3 ?    1.5   0.1      0.58   3.6e+02      19      75 ..      72     129 ..      63     136 .. 0.73
   4 !   14.7   0.0   4.3e-05     0.026       8      58 ..     129     180 ..     122     193 .. 0.80
   5 ?    4.7   0.4     0.056        35      27      74 ..     249     296 ..     225     304 .. 0.69
   6 !   13.1   0.0   0.00014     0.086       3      49 ..     323     368 ..     321     401 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.8e-05
                                  TT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH CS
                        ANAPC3 36 ngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaL 79
                                  +g+y +A+e ++ka +++++++  +++ A +l+ +++y  Ai  L
  gi|13542035|ref|NP_111723.1| 21 AGNYAEAIEKIDKAiDKEPRNPSLHLIRADALYRQGNYSSAIEEL 65
                                  677777777777777777777777777777777777777777655 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 2.6e-05
                                  T-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHH CS
                        ANAPC3  3 nnyknAiflaerllaaetespedayllAlclylngqykrAyellr 47
                                  +ny +Ai  ++++  +e+++p+  +  A +ly++g+y +A+e l+
  gi|13542035|ref|NP_111723.1| 22 GNYAEAIEKIDKAIDKEPRNPSLHLIRADALYRQGNYSSAIEELN 66
                                  466667777777774444444444444777777777777766555 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.58
                                   HH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHH CS
                        ANAPC3  19 etespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeA 75 
                                   ++++pe   l++ c+ ++g++kr  e ++ka k + + + + y  A +l  L+ ++ A
  gi|13542035|ref|NP_111723.1|  72 DKNNPELFSLKSICYGSMGDFKRSKEEADKAiKADQSYPFAYYNRAAALRGLGDVDGA 129
                                   4556666667799**********99999999777776667777666666666666655 PP

  == domain 4  score: 14.7 bits;  conditional E-value: 4.3e-05
                                   HHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHH CS
                        ANAPC3   8 AiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgc 58 
                                   A+  + ++ ++++ +p+  y lA+ +++ ++yk+A+e ++   + +++++++
  gi|13542035|ref|NP_111723.1| 129 AEKDFRKYIEMQPSDPDPHYDLAEIYFEKKDYKKAMEEVKAVlRNDKSNEKA 180
                                   55556788899999***********************999995555555544 PP

  == domain 5  score: 4.7 bits;  conditional E-value: 0.056
                                   HHHHHHHHHTT-HHHHHHHHHCTSHHHC-HHHHHHHHHHHHHTT-HHH CS
                        ANAPC3  27 yllAlclylngqykrAyellrkaklnskslgcrylfAqcllkLkkyee 74 
                                    llA ++ + g+ k+A e ++++   ++s ++++ +   ll+ ++y++
  gi|13542035|ref|NP_111723.1| 249 DLLARTYDQEGKAKEADETYNTLLRLNNSRESHIYWFDYLLDSGRYDD 296
                                   357999999999999999999994445566777777788888888887 PP

  == domain 6  score: 13.1 bits;  conditional E-value: 0.00014
                                   T-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT CS
                        ANAPC3   3 nnyknAiflaerllaaetespedayllAlclylngqykrAyellrka 49 
                                   +++++A+  a  l+ ++ + p+++ l+A  l ++g+ + A+++l + 
  gi|13542035|ref|NP_111723.1| 323 GKHEEALKTAGELV-KMDQTPYSRSLYATQLRKLGKLEDALTYLGSG 368
                                   57889999999999.88899999999999999999999999988776 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.0    0.0035       2.2      28      70 ..       7      49 ..       5      50 .. 0.90
   2 !   14.9   0.0   3.7e-05     0.023       7      53 ..      20      66 ..      15      81 .. 0.90
   3 !   15.2   0.1   2.8e-05     0.017      31      64 ..     112     145 ..     102     147 .. 0.93
   4 !   13.0   0.0   0.00014     0.084      24      72 ..     139     187 ..     138     188 .. 0.95
   5 ?   -2.3   0.0       8.2   5.1e+03      39      64 ..     383     408 ..     382     410 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0035
                         TPR_9 28 dpeerrdRGlllaqlGclsaAladLeaylalapdapdaeaira 70
                                  +p+e+ + ++     G++++A++  + +++++p +p  ++ira
  gi|13542035|ref|NP_111723.1|  7 TPDEYAEEARSDIAAGNYAEAIEKIDKAIDKEPRNPSLHLIRA 49
                                  577888888888899**************************97 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 3.7e-05
                         TPR_9  7 reedweralavverllllaPddpeerrdRGlllaqlGclsaAladLe 53
                                   + ++++a++ ++  +   P+ p++++ R+ +l+++G++s A+++L+
  gi|13542035|ref|NP_111723.1| 20 AAGNYAEAIEKIDKAIDKEPRNPSLHLIRADALYRQGNYSSAIEELN 66
                                  667889999999999999***************************97 PP

  == domain 3  score: 15.2 bits;  conditional E-value: 2.8e-05
                         TPR_9  31 errdRGlllaqlGclsaAladLeaylalapdapd 64 
                                    ++ R+ +l  lG++ +A +d+  y++++p++pd
  gi|13542035|ref|NP_111723.1| 112 AYYNRAAALRGLGDVDGAEKDFRKYIEMQPSDPD 145
                                   5789****************************98 PP

  == domain 4  score: 13.0 bits;  conditional E-value: 0.00014
                         TPR_9  24 laPddpeerrdRGlllaqlGclsaAladLeaylalapdapdaeairaqL 72 
                                   ++P dp+ ++d + ++++  ++++A+++  a l+++ +++ a+ ++ q+
  gi|13542035|ref|NP_111723.1| 139 MQPSDPDPHYDLAEIYFEKKDYKKAMEEVKAVLRNDKSNEKAYDLKLQI 187
                                   589****************************************999987 PP

  == domain 5  score: -2.3 bits;  conditional E-value: 8.2
                         TPR_9  39 laqlGclsaAladLeaylalapdapd 64 
                                   l ++G+ s A++ L   +  ++d+++
  gi|13542035|ref|NP_111723.1| 383 LLEMGNHSLAMESLKNSITASDDDEE 408
                                   679999999**999998888887776 PP

>> TPR_20  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.3   6.2e-05     0.038       5      45 ..      25      65 ..       9      75 .. 0.93
   2 !   20.0   0.1     1e-06   0.00063      10      56 ..     132     178 ..     126     210 .. 0.89
   3 ?   -1.6   0.0       5.5   3.4e+03      26      55 ..     181     211 ..     176     220 .. 0.65
   4 ?   -0.4   0.0       2.4   1.5e+03      34      53 ..     321     340 ..     317     343 .. 0.85
   5 ?   -1.1   0.0       3.9   2.4e+03      23      53 ..     374     404 ..     348     411 .. 0.58

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 6.2e-05
                        TPR_20  5 apelaeleaalaanpddldarldlAlallaagryeeAleqL 45
                                  a+ ++++++a+ ++p +  ++l  A+al+ +g+y  A+e+L
  gi|13542035|ref|NP_111723.1| 25 AEAIEKIDKAIDKEPRNPSLHLIRADALYRQGNYSSAIEEL 65
                                  56799**********************************98 PP

  == domain 2  score: 20.0 bits;  conditional E-value: 1e-06
                        TPR_20  10 eleaalaanpddldarldlAlallaagryeeAleqLleilkrdrkwe 56 
                                   ++++ ++ +p+d d ++dlA+ ++++++y++A+e+  ++l++d++ e
  gi|13542035|ref|NP_111723.1| 132 DFRKYIEMQPSDPDPHYDLAEIYFEKKDYKKAMEEVKAVLRNDKSNE 178
                                   67888999*********************************999864 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 5.5
                        TPR_20  26 ldlAlallaa.gryeeAleqLleilkrdrkw 55 
                                   +dl l+ + a ++ e  +++Lle +k++ ++
  gi|13542035|ref|NP_111723.1| 181 YDLKLQIHLAtNDGEGYFKALLEAFKNTENF 211
                                   5555555444044455578888888888877 PP

  == domain 4  score: -0.4 bits;  conditional E-value: 2.4
                        TPR_20  34 aagryeeAleqLleilkrdr 53 
                                   a g++eeAl+   e++k d+
  gi|13542035|ref|NP_111723.1| 321 ASGKHEEALKTAGELVKMDQ 340
                                   789*******9999999886 PP

  == domain 5  score: -1.1 bits;  conditional E-value: 3.9
                        TPR_20  23 darldlAlallaagryeeAleqLleilkrdr 53 
                                   + +++  + ll+ g++  A+e L + + +  
  gi|13542035|ref|NP_111723.1| 374 EVQFEKFNILLEMGNHSLAMESLKNSITASD 404
                                   5555555566666666667766665555444 PP

>> SRP_TPR_like  Putative TPR-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.0    0.0011      0.65      25      93 ..      19      94 ..      14     109 .. 0.77
   2 ?    6.1   1.1     0.017        11      43      98 ..     142     201 ..     130     213 .. 0.73
   3 ?    3.4   0.2      0.12        74       4      72 ..     267     336 ..     263     350 .. 0.72
   4 !   16.3   0.0   1.2e-05    0.0076       7      98 ..     334     433 ..     330     453 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0011
                  SRP_TPR_like 25 iklekyeeaLkllkkgs...alsedvrfEkaYvlYklkkykkalkil...kkveaee.kvkvlksqvlYrlgsyek 93
                                  i ++ y+ea++ ++k+      + +++  +a +lY+  +y  a + l   +++++++ ++  lks ++  +g++++
  gi|13542035|ref|NP_111723.1| 19 IAAGNYAEAIEKIDKAIdkePRNPSLHLIRADALYRQGNYSSAIEELnftEHMDKNNpELFSLKSICYGSMGDFKR 94
                                  67788999998877754333578899999************99877622156666667788999999999999976 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.017
                  SRP_TPR_like  43 lsedvrfEkaYvlYklkkykkalk....ilkkveaeekvkvlksqvlYrlgsyekAYklL 98 
                                    + d +++ a +++  k ykka++    +l++ +++ek+  lk q+    ++ e  +k L
  gi|13542035|ref|NP_111723.1| 142 SDPDPHYDLAEIYFEKKDYKKAMEevkaVLRNDKSNEKAYDLKLQIHLATNDGEGYFKAL 201
                                   4568899**************985333367777777799999999988877777766666 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.12
                  SRP_TPR_like   4 eyekilrlegke.lkkfkvvaliklekyeeaLkllkkgsalsedvrfEkaYvlYk.lkkykkalkilkkve 72 
                                   +y+ +lrl+++   + +    l+  ++y++ L+ ++k +   ++ + E  Y+      k ++alk+  ++ 
  gi|13542035|ref|NP_111723.1| 267 TYNTLLRLNNSReSHIYWFDYLLDSGRYDDLLSEIEKSG-FKDEEILEIEYIAQDaSGKHEEALKTAGELV 336
                                   56666666554303334555688999**********999.8899999999997651578999999876655 PP

  == domain 4  score: 16.3 bits;  conditional E-value: 1.2e-05
                  SRP_TPR_like   7 kilrlegkelkkf.kvvaliklekyeeaLkllkkgsalsedvrfEkaYvlYklkkykkalkilkkv.....eaeekvkvlk 81 
                                   ++++++++ ++++  ++ l kl+k e+aL++l  g++ s++v+fEk  +l  + +   a++ lk+      ++ee++ +l 
  gi|13542035|ref|NP_111723.1| 334 ELVKMDQTPYSRSlYATQLRKLGKLEDALTYLGSGDQDSDEVQFEKFNILLEMGNHSLAMESLKNSitasdDDEERLGHLI 414
                                   567778888888757888999***********************************9999888753111113334666666 PP

                  SRP_TPR_like  82 sqv..lYrlgsyekAYklL 98 
                                   + +  +  + ++++  + L
  gi|13542035|ref|NP_111723.1| 415 TGIssAISKADFNTVNNFL 433
                                   6552223445566666666 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.4      0.05        31      16      66 ..      21      63 ..      14      66 .. 0.59
   2 !    9.5   0.1     0.002       1.2      13      61 ..      86     133 ..      78     142 .. 0.59
   3 !   13.0   0.1   0.00016     0.097       5      74 ..     112     173 ..     108     176 .. 0.85
   4 !   11.1   0.5    0.0006      0.37      17      74 ..     225     274 ..     219     277 .. 0.83
   5 ?    1.1   0.0      0.79   4.9e+02      55      73 ..     319     337 ..     317     341 .. 0.68
   6 ?    2.9   0.1      0.21   1.3e+02       8      26 ..     347     365 ..     340     366 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.05
                        TPR_12 16 lgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAle 66
                                  +g+y+eA+e  +ka++   +   p +p         +++++++g+y  A+e
  gi|13542035|ref|NP_111723.1| 21 AGNYAEAIEKIDKAID---KE--PRNPS---LHLIRADALYRQGNYSSAIE 63
                                  5666666666666622...22..44433...35556777777777777776 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.002
                        TPR_12  13 lrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgry 61 
                                   +  +g++  + e  +ka+ + ++++  ++ + a++lr+Lg++  a +++
  gi|13542035|ref|NP_111723.1|  86 YGSMGDFKRSKEEADKAIKADQSYPFAYY-NRAAALRGLGDVDGAEKDF 133
                                   55566666666666666666666655533.6666666666654444444 PP

  == domain 3  score: 13.0 bits;  conditional E-value: 0.00016
                        TPR_12   5 alnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                   a++n+aa+lr lg+ d A++ ++k +e++     p  p+     ++L+++y++ ++y++A e  + +l+ 
  gi|13542035|ref|NP_111723.1| 112 AYYNRAAALRGLGDVDGAEKDFRKYIEMQ-----PSDPD---PHYDLAEIYFEKKDYKKAMEEVKAVLRN 173
                                   688**************************.....66655...5789999999999999998877777766 PP

  == domain 4  score: 11.1 bits;  conditional E-value: 0.0006
                        TPR_12  17 grydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                   g yd A+++l++ + ++++   p+       +  L+r+y++ g+ +eA e ++  l++
  gi|13542035|ref|NP_111723.1| 225 GSYDTAEDILKQFIKVYEKE--PY------LYDLLARTYDQEGKAKEADETYNTLLRL 274
                                   66788888888888888666..64......5999*******************99987 PP

  == domain 5  score: 1.1 bits;  conditional E-value: 0.79
                        TPR_12  55 yralgryeeAlelleeala 73 
                                   ++a+g++eeAl+   e ++
  gi|13542035|ref|NP_111723.1| 319 QDASGKHEEALKTAGELVK 337
                                   5678888888877666555 PP

  == domain 6  score: 2.9 bits;  conditional E-value: 0.21
                        TPR_12   8 nlaavlrrlgrydeAlell 26 
                                    +a+ lr+lg++++Al++l
  gi|13542035|ref|NP_111723.1| 347 LYATQLRKLGKLEDALTYL 365
                                   5788899999999999986 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.1     0.043        27       7      32 ..      15      40 ..      13      41 .. 0.89
   2 ?    3.9   0.0      0.16     1e+02       4      23 ..      46      65 ..      44      66 .. 0.85
   3 ?   -0.9   0.0       5.4   3.4e+03       9      28 ..      85     104 ..      83     105 .. 0.77
   4 !    8.4   0.1    0.0059       3.7       2      31 ..     112     141 ..     111     143 .. 0.92
   5 ?    5.8   0.0      0.04        25       4      21 ..     148     165 ..     147     174 .. 0.85
   6 ?    2.2   0.0      0.58   3.6e+02      14      30 ..     225     241 ..     197     243 .. 0.86
   7 !    7.9   0.4    0.0083       5.2       5      28 ..     250     273 ..     246     275 .. 0.90
   8 ?    0.1   0.0       2.6   1.6e+03      11      28 ..     320     337 ..     316     337 .. 0.77
   9 ?    0.4   0.1       2.1   1.3e+03       9      23 ..     351     365 ..     345     367 .. 0.79
  10 ?   -0.8   0.0       5.2   3.2e+03      13      29 ..     488     503 ..     483     504 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.043
                                  HHHHHHHHHHHHHHHHHHHHHHH-TT CS
                         TPR_6  7 alsyrklgdtdkAlealerlikeYPd 32
                                  a+s +++g++++A+e  ++ i++ P 
  gi|13542035|ref|NP_111723.1| 15 ARSDIAAGNYAEAIEKIDKAIDKEPR 40
                                  67788999**************9996 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.16
                                  HHHHHHHHHHHHHHHHHHHH CS
                         TPR_6  4 yklalsyrklgdtdkAleal 23
                                  + +a +++++g+++ A+e l
  gi|13542035|ref|NP_111723.1| 46 LIRADALYRQGNYSSAIEEL 65
                                  668999***99*****9866 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 5.4
                                   HHHHHHHHHHHHHHHHHHHH CS
                         TPR_6   9 syrklgdtdkAlealerlik 28 
                                   +y ++gd  +++e  ++ ik
  gi|13542035|ref|NP_111723.1|  85 CYGSMGDFKRSKEEADKAIK 104
                                   78888899988888777775 PP

  == domain 4  score: 8.4 bits;  conditional E-value: 0.0059
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHH-T CS
                         TPR_6   2 AlyklalsyrklgdtdkAlealerlikeYP 31 
                                   A+y++a ++r lgd d A + +++ i+  P
  gi|13542035|ref|NP_111723.1| 112 AYYNRAAALRGLGDVDGAEKDFRKYIEMQP 141
                                   9**********99************98766 PP

  == domain 5  score: 5.8 bits;  conditional E-value: 0.04
                                   HHHHHHHHHHHHHHHHHH CS
                         TPR_6   4 yklalsyrklgdtdkAle 21 
                                   y la+ y++ +d+ kA+e
  gi|13542035|ref|NP_111723.1| 148 YDLAEIYFEKKDYKKAME 165
                                   889******99*****98 PP

  == domain 6  score: 2.2 bits;  conditional E-value: 0.58
                                   HHHHHHHHHHHHHHHH- CS
                         TPR_6  14 gdtdkAlealerlikeY 30 
                                   g +d+A ++l+++ik Y
  gi|13542035|ref|NP_111723.1| 225 GSYDTAEDILKQFIKVY 241
                                   6799**********977 PP

  == domain 7  score: 7.9 bits;  conditional E-value: 0.0083
                                   HHHHHHHHHHHHHHHHHHHHHHHH CS
                         TPR_6   5 klalsyrklgdtdkAlealerlik 28 
                                   +la+ y + g++ +A e+++ l++
  gi|13542035|ref|NP_111723.1| 250 LLARTYDQEGKAKEADETYNTLLR 273
                                   79******99***********986 PP

  == domain 8  score: 0.1 bits;  conditional E-value: 2.6
                                   HHHHHHHHHHHHHHHHHH CS
                         TPR_6  11 rklgdtdkAlealerlik 28 
                                    + g++++Al++  +l+k
  gi|13542035|ref|NP_111723.1| 320 DASGKHEEALKTAGELVK 337
                                   44479*******999986 PP

  == domain 9  score: 0.4 bits;  conditional E-value: 2.1
                                   HHHHHHHHHHHHHHH CS
                         TPR_6   9 syrklgdtdkAleal 23 
                                    +rklg+ ++Al++l
  gi|13542035|ref|NP_111723.1| 351 QLRKLGKLEDALTYL 365
                                   466789******998 PP

  == domain 10  score: -0.8 bits;  conditional E-value: 5.2
                                   HHHHHHHHHHHHHHHHH CS
                         TPR_6  13 lgdtdkAlealerlike 29 
                                   l    kA e l+++i+e
  gi|13542035|ref|NP_111723.1| 488 L-MQGKASEFLNKFIEE 503
                                   4.5568999*****997 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.0    0.0089       5.5      15      35 ..      22      42 ..      19      46 .. 0.93
   2 ?    4.4   0.0     0.066        41      10      42 ..      51      83 ..      47      90 .. 0.76
   3 ?   -1.5   0.0       4.6   2.8e+03      14      29 ..      89     104 ..      81     107 .. 0.80
   4 !   12.9   0.2   0.00014     0.088       8      45 ..     151     188 ..     145     194 .. 0.85
   5 ?    1.1   0.0      0.69   4.3e+02      10      30 ..     220     240 ..     216     244 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0089
                                  T-HHHHHHHHHHHHHHTTS-H CS
                    Fis1_TPR_C 15 geYseArryvdalLeiEPenr 35
                                  g+Y eA + +d  + +EP+n 
  gi|13542035|ref|NP_111723.1| 22 GNYAEAIEKIDKAIDKEPRNP 42
                                  8******************95 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.066
                                  HHHHHT-HHHHHHHHHHHHHHTTS-HHHHHHHH CS
                    Fis1_TPR_C 10 GhyklgeYseArryvdalLeiEPenrQaqsLke 42
                                  + y++g+Ys A + ++   +++ +n    sLk+
  gi|13542035|ref|NP_111723.1| 51 ALYRQGNYSSAIEELNFTEHMDKNNPELFSLKS 83
                                  88*********9887766666666666666665 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 4.6
                                   HT-HHHHHHHHHHHHH CS
                    Fis1_TPR_C  14 lgeYseArryvdalLe 29 
                                   +g+++++++ +d  ++
  gi|13542035|ref|NP_111723.1|  89 MGDFKRSKEEADKAIK 104
                                   899*****99998776 PP

  == domain 4  score: 12.9 bits;  conditional E-value: 0.00014
                                   HHHHHHHT-HHHHHHHHHHHHHHTTS-HHHHHHHHHHH CS
                    Fis1_TPR_C   8 AlGhyklgeYseArryvdalLeiEPenrQaqsLkelie 45 
                                   A  ++  ++Y++A++ v+a+L+ + +n+ a +Lk  i+
  gi|13542035|ref|NP_111723.1| 151 AEIYFEKKDYKKAMEEVKAVLRNDKSNEKAYDLKLQIH 188
                                   55566679*************************97665 PP

  == domain 5  score: 1.1 bits;  conditional E-value: 0.69
                                   HHHHHT-HHHHHHHHHHHHHH CS
                    Fis1_TPR_C  10 GhyklgeYseArryvdalLei 30 
                                   G + +g Y++A   +++++++
  gi|13542035|ref|NP_111723.1| 220 GLIGIGSYDTAEDILKQFIKV 240
                                   667899***********9986 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0     0.013       8.2      12      35 ..      21      42 ..      13      43 .. 0.88
   2 ?    2.5   0.1      0.29   1.8e+02       6      20 ..      49      63 ..      44      65 .. 0.87
   3 ?   -2.2   0.0       9.5   5.9e+03       2      17 ..      86     101 ..      84     104 .. 0.50
   4 ?    4.7   0.0     0.059        37       1      35 [.     112     144 ..     112     145 .. 0.89
   5 !    7.7   0.1    0.0067       4.1       4      34 ..     149     177 ..     147     180 .. 0.85
   6 !    9.8   0.5    0.0014      0.85       2      32 ..     248     278 ..     247     281 .. 0.88
   7 ?   -1.1   0.0       4.1   2.5e+03      11      31 ..     290     308 ..     287     313 .. 0.74
   8 ?   -1.4   0.0       5.1   3.2e+03      10      24 ..     320     334 ..     316     346 .. 0.66
   9 ?    0.7   0.0       1.1   6.8e+02      10      22 ..     353     365 ..     350     367 .. 0.88
  10 ?    0.8   0.0         1   6.4e+02       8      32 ..     382     407 ..     381     410 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.013
                         TPR_7 12 lGdyeeAielyeqsLaltkdpeda 35
                                   G+y+eAie   +  a++k+p ++
  gi|13542035|ref|NP_111723.1| 21 AGNYAEAIEKIDK--AIDKEPRNP 42
                                  69***********..****99886 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.29
                         TPR_7  6 arlysrlGdyeeAie 20
                                  a++  r+G+y+ Aie
  gi|13542035|ref|NP_111723.1| 49 ADALYRQGNYSSAIE 63
                                  788899*******98 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 9.5
                         TPR_7   2 LlnLarlysrlGdyee 17 
                                   +  +++  ++  + ++
  gi|13542035|ref|NP_111723.1|  86 YGSMGDFKRSKEEADK 101
                                   4445555555555555 PP

  == domain 4  score: 4.7 bits;  conditional E-value: 0.059
                         TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkdpeda 35 
                                   a++n a + + lGd + A++ +++   ++ +p+d+
  gi|13542035|ref|NP_111723.1| 112 AYYNRAAALRGLGDVDGAEKDFRK--YIEMQPSDP 144
                                   799*****************9999..888877775 PP

  == domain 5  score: 7.7 bits;  conditional E-value: 0.0067
                         TPR_7   4 nLarlysrlGdyeeAielyeqsLaltkdped 34 
                                    La++y++  dy++A e  ++  +l++d ++
  gi|13542035|ref|NP_111723.1| 149 DLAEIYFEKKDYKKAMEEVKA--VLRNDKSN 177
                                   69***************9999..77777665 PP

  == domain 6  score: 9.8 bits;  conditional E-value: 0.0014
                         TPR_7   2 LlnLarlysrlGdyeeAielyeqsLaltkdp 32 
                                   ++ Lar+y ++G+ +eA e y  +L+l ++ 
  gi|13542035|ref|NP_111723.1| 248 YDLLARTYDQEGKAKEADETYNTLLRLNNSR 278
                                   789******************9988887765 PP

  == domain 7  score: -1.1 bits;  conditional E-value: 4.1
                         TPR_7  11 rlGdyeeAielyeqsLaltkd 31 
                                   + G+y+++++  e+     kd
  gi|13542035|ref|NP_111723.1| 290 DSGRYDDLLSEIEK--SGFKD 308
                                   689****9998887..55555 PP

  == domain 8  score: -1.4 bits;  conditional E-value: 5.1
                         TPR_7  10 srlGdyeeAielyeq 24 
                                    + G++eeA++   +
  gi|13542035|ref|NP_111723.1| 320 DASGKHEEALKTAGE 334
                                   567999999876555 PP

  == domain 9  score: 0.7 bits;  conditional E-value: 1.1
                         TPR_7  10 srlGdyeeAiely 22 
                                   ++lG+ e+A++++
  gi|13542035|ref|NP_111723.1| 353 RKLGKLEDALTYL 365
                                   78*********97 PP

  == domain 10  score: 0.8 bits;  conditional E-value: 1
                         TPR_7   8 lysrlGdyeeAielyeqsL.altkdp 32 
                                   +  ++G+++ A e ++ s+ a ++d+
  gi|13542035|ref|NP_111723.1| 382 ILLEMGNHSLAMESLKNSItASDDDE 407
                                   77899************875555554 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         1   6.4e+02       8      20 ..      15      27 ..      11      29 .. 0.87
   2 ?    5.8   0.0     0.042        26       2      17 ..      43      58 ..      42      65 .. 0.86
   3 !    9.7   0.3    0.0023       1.4       2      21 ..     111     130 ..     110     130 .. 0.92
   4 ?    0.7   0.0       1.9   1.1e+03       6      21 ..     250     265 ..     245     268 .. 0.85
   5 ?   -0.4   0.0       4.4   2.7e+03      10      21 ..     318     329 ..     317     334 .. 0.82
   6 ?    2.6   0.0      0.47   2.9e+02       2      22 ..     343     363 ..     342     365 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 1
                         TPR_4  8 ArallalGdldeA 20
                                  Ar   a+G+++eA
  gi|13542035|ref|NP_111723.1| 15 ARSDIAAGNYAEA 27
                                  88899*******9 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.042
                         TPR_4  2 rallaLArallalGdl 17
                                   ++l +A al+++G++
  gi|13542035|ref|NP_111723.1| 43 SLHLIRADALYRQGNY 58
                                  6899**********97 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.0023
                         TPR_4   2 rallaLArallalGdldeAr 21 
                                    a++++A al  lGd d A+
  gi|13542035|ref|NP_111723.1| 111 FAYYNRAAALRGLGDVDGAE 130
                                   689**************997 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 1.9
                         TPR_4   6 aLArallalGdldeAr 21 
                                   +LAr++ + G + eA 
  gi|13542035|ref|NP_111723.1| 250 LLARTYDQEGKAKEAD 265
                                   79**********9996 PP

  == domain 5  score: -0.4 bits;  conditional E-value: 4.4
                         TPR_4  10 allalGdldeAr 21 
                                   a+ a G ++eA+
  gi|13542035|ref|NP_111723.1| 318 AQDASGKHEEAL 329
                                   67899******8 PP

  == domain 6  score: 2.6 bits;  conditional E-value: 0.47
                         TPR_4   2 rallaLArallalGdldeAra 22 
                                   + ++++A  l  lG l++A++
  gi|13542035|ref|NP_111723.1| 343 YSRSLYATQLRKLGKLEDALT 363
                                   67999**************86 PP

>> TPR_15  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.1     0.037        23     228     267 ..      22      61 ..      16      64 .. 0.91
   2 ?    1.2   0.0      0.29   1.8e+02     141     180 ..     104     144 ..      89     147 .. 0.76
   3 !    6.5   0.1    0.0068       4.2       7      46 ..     143     181 ..     138     196 .. 0.81
   4 !   14.6   1.9   2.3e-05     0.014     125     269 ..     226     363 ..     172     365 .. 0.80
   5 ?   -3.0   0.0       5.3   3.3e+03     158     181 ..     385     408 ..     381     414 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.037
                        TPR_15 228 grpkkALeylrkqakenrkdplwllaYADaleqagradeA 267
                                   g++++A e + k  ++++++p+  l  ADal+++g+  +A
  gi|13542035|ref|NP_111723.1|  22 GNYAEAIEKIDKAIDKEPRNPSLHLIRADALYRQGNYSSA 61 
                                   78999*****************************998777 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.29
                        TPR_15 141 aaeqs.aafllaraelyrqegqtdaAlrdyreAlalapdss 180
                                   +a qs ++ ++ ra++ r  g+ d A +d+r+ ++++p + 
  gi|13542035|ref|NP_111723.1| 104 KADQSyPFAYYNRAAALRGLGDVDGAEKDFRKYIEMQPSDP 144
                                   3444426678899*******************999999875 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.0068
                        TPR_15   7 plnealklatllykqgdvkkAlevLkeaaqkaapskdtey 46 
                                   +++  ++la++ ++++d+kkA e  k+ + +  +s++++y
  gi|13542035|ref|NP_111723.1| 143 DPDPHYDLAEIYFEKKDYKKAMEEVKAVLRND-KSNEKAY 181
                                   446789*******************7665555.7888877 PP

  == domain 4  score: 14.6 bits;  conditional E-value: 2.3e-05
                        TPR_15 125 dydriaellksleeeeaaeqsaafllaraelyrqegqtdaAlrdyreAlalapdsselraallWlliDlgrraeLrellka 205
                                    yd+ +++lk+    + +e++++ + ++a+ y qeg+ ++A + y   l+l+    e    +  +l+D+gr++    ll++
  gi|13542035|ref|NP_111723.1| 226 SYDTAEDILKQ--FIKVYEKEPYLYDLLARTYDQEGKAKEADETYNTLLRLNNS-RESHIYWFDYLLDSGRYDD---LLSE 300
                                   45555555555..334599******************************99887.44444444479*******6...999* PP

                        TPR_15 206 wkaraesdasLwgplaaAlllLgrpkkALeylrkqakenrkdplwllaYADaleqagradeAwr 269
                                    ++   +d+++ +    A+ + g+ ++AL+      k + + p  +  YA  l + g+ + A +
  gi|13542035|ref|NP_111723.1| 301 IEKSGFKDEEILEIEYIAQDASGKHEEALKTAGELVK-MDQTPYSRSLYATQLRKLGKLEDALT 363
                                   9***999999999999999999***********9999.9**************99999999875 PP

  == domain 5  score: -3.0 bits;  conditional E-value: 5.3
                        TPR_15 158 qegqtdaAlrdyreAlalapdsse 181
                                   + g++  A++ +++ +++++d++e
  gi|13542035|ref|NP_111723.1| 385 EMGNHSLAMESLKNSITASDDDEE 408
                                   567888888888888888888765 PP

>> Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.0    0.0034       2.1      71     121 ..      10      60 ..       7      68 .. 0.88
   2 ?    3.5   0.0      0.15        91      75     123 ..      48      96 ..      46     104 .. 0.92
   3 !    9.0   0.1     0.003       1.9      67     113 ..     142     188 ..     128     196 .. 0.83
   4 ?    1.6   0.0      0.57   3.5e+02      82     130 ..     224     272 ..     216     279 .. 0.87
   5 ?   -1.5   0.0         5   3.1e+03     106     118 ..     345     357 ..     315     404 .. 0.52

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0034
                                   HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-S CS
               Alkyl_sulf_dimr  71 kvlekakealkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqae 121
                                   + +e+a++++++g+y  a+e +++++ ++p+n + + ++adal + g+ ++
  gi|13542035|ref|NP_111723.1|  10 EYAEEARSDIAAGNYAEAIEKIDKAIDKEPRNPSLHLIRADALYRQGNYSS 60 
                                   56899*************************************998887665 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.15
                                   HHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SSH CS
               Alkyl_sulf_dimr  75 kakealkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqaesa 123
                                   +a + +++g+y  a+e ln+    d++n e  +lk  ++ ++g +++s 
  gi|13542035|ref|NP_111723.1|  48 RADALYRQGNYSSAIEELNFTEHMDKNNPELFSLKSICYGSMGDFKRSK 96 
                                   678899************************************9998875 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.003
                                   TSHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHH CS
               Alkyl_sulf_dimr  67 Ggaekvlekakealkegdyrwaaellnhlvfadpenaeakelkadal 113
                                   ++ +   + a+ +++++dy+ a+e ++ ++ +d++n++a +lk ++ 
  gi|13542035|ref|NP_111723.1| 142 SDPDPHYDLAEIYFEKKDYKKAMEEVKAVLRNDKSNEKAYDLKLQIH 188
                                   5666667889999****************************998875 PP

  == domain 4  score: 1.6 bits;  conditional E-value: 0.57
                                   TT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SSHHHHHHHH CS
               Alkyl_sulf_dimr  82 egdyrwaaellnhlvfadpenaeakelkadaleqlgyqaesatwRniYl 130
                                    g y  a  +l++ +   +++    +l+a++++q g+++e+  + n  l
  gi|13542035|ref|NP_111723.1| 224 IGSYDTAEDILKQFIKVYEKEPYLYDLLARTYDQEGKAKEADETYNTLL 272
                                   6789999999999999999999***************999887777665 PP

  == domain 5  score: -1.5 bits;  conditional E-value: 5
                                   HHHHHHHHHHHHH CS
               Alkyl_sulf_dimr 106 kelkadaleqlgy 118
                                   ++l a  l++lg+
  gi|13542035|ref|NP_111723.1| 345 RSLYATQLRKLGK 357
                                   3333333333332 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.1   9.5e-07   0.00059     206     258 ..      22      74 ..      15      76 .. 0.94
   2 ?    4.8   0.5     0.017        11     177     251 ..      95     169 ..      81     179 .. 0.78
   3 ?    0.7   0.7       0.3   1.9e+02      16      96 ..     156     241 ..     150     250 .. 0.58
   4 ?    0.4   0.4      0.39   2.4e+02      46      74 ..     253     283 ..     224     295 .. 0.69
   5 ?    0.9   0.2      0.26   1.6e+02     439     513 ..     322     397 ..     294     399 .. 0.67
   6 ?    1.0   0.0      0.25   1.6e+02       8      95 ..     347     432 ..     343     442 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 9.5e-07
                                   T-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCTTT CS
                         NARP1 206 gsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklDla 258
                                   g++ +A+e+idkai+++p    l+l++a  l ++G+ + A+e ++ + ++D++
  gi|13542035|ref|NP_111723.1|  22 GNYAEAIEKIDKAIDKEPRNPSLHLIRADALYRQGNYSSAIEELNFTEHMDKN 74 
                                   67889******************************************999975 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.017
                                   TGG.GSS----SSHHHHHHHHHHHHHHHHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHH CS
                         NARP1 177 esdnedsekepesallwvlyflAqhydklgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmee 251
                                   +++++d++ +  +++ +++y  A     lg+++ A +   k ie +p+  + ++  a+i+  + d kkA+e ++ 
  gi|13542035|ref|NP_111723.1|  95 SKEEADKAIKADQSYPFAYYNRAAALRGLGDVDGAEKDFRKYIEMQPSDPDPHYDLAEIYFEKKDYKKAMEEVKA 169
                                   233456777888888889999999999999999999999999999999999999999999999999999887765 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.3
                                   HHTHHHHHHHHHHHHGGG---HHHHHHHHHHHHHHTT-HHHHHHHHHHHHH..H-TT-CHHHHHHHHHT........SSS- CS
                         NARP1  16 eagkleeAlehLeekekqivDklavketkaelllkLgrkeeAeatyeaLle..rnpenskYyeglekak......klsked 88 
                                   e+ ++++A+e+++++ ++  Dk + k    +l+++L  +++ e +++aLle  +n+en kY   l+  +      +++++ 
  gi|13542035|ref|NP_111723.1| 156 EKKDYKKAMEEVKAVLRN--DKSNEKAYDLKLQIHLA-TNDGEGYFKALLEafKNTENFKYIGTLTDGLigigsyDTAEDI 233
                                   556666666666555443..44333333344444443.4567888889987556889999988888877655443333444 PP

                                   HHHHHHHH CS
                         NARP1  89 eeallaly 96 
                                    ++  ++y
  gi|13542035|ref|NP_111723.1| 234 LKQFIKVY 241
                                   44444444 PP

  == domain 4  score: 0.4 bits;  conditional E-value: 0.39
                                   HHHHHTT-HHHHHHHHHHHHHH-T..T-CHH CS
                         NARP1  46 elllkLgrkeeAeatyeaLlernp..enskY 74 
                                   + + + g+ +eA +ty++Ll+ n   e++ Y
  gi|13542035|ref|NP_111723.1| 253 RTYDQEGKAKEADETYNTLLRLNNsrESHIY 283
                                   4445557888888899988877652245555 PP

  == domain 5  score: 0.9 bits;  conditional E-value: 0.26
                                   ......-------------S-SSSTTTT-S.-HHHHHHHHHTTTGGGTTT-THHHHHHHHHHHHTT-HHHHHHHHH CS
                         NARP1 439 kaaekkakkedeeakkededplgekLvkte.epLeeAlkflkpLlklaaeniethllafevyiRkkklllalkalk 513
                                   + ++++a k+ +e  k d+ p + +L +t+   L +    l+ L +  +++ e+++  f++ +  +++ la+++lk
  gi|13542035|ref|NP_111723.1| 322 SGKHEEALKTAGELVKMDQTPYSRSLYATQlRKLGKLEDALTYLGSGDQDSDEVQFEKFNILLEMGNHSLAMESLK 397
                                   3445556666677777788888888877763456666666666777777777888888888888888888877776 PP

  == domain 6  score: 1.0 bits;  conditional E-value: 0.25
                                   HHHHHHHHHHTHHHHHHHHHHHHGGG---HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-CHHHHHHHHHT....SS CS
                         NARP1   8 LyknqiieeagkleeAlehLeekekqivDklavketkaelllkLgrkeeAeatyeaLlernpenskYyeglekak..klsk 86 
                                   Ly  q +++ gkle+Al  L + ++   D+++++  k ++ll++g+++ A + +++ ++   ++++   +l++     +sk
  gi|13542035|ref|NP_111723.1| 347 LYATQ-LRKLGKLEDALTYLGSGDQ-DSDEVQFE--KFNILLEMGNHSLAMESLKNSITASDDDEERLGHLITGIssAISK 423
                                   56555.578999******9998765.46777665..567999999999999999998888888877766666554334555 PP

                                   S-HHHHHHH CS
                         NARP1  87 edeeallal 95 
                                   +d + ++++
  gi|13542035|ref|NP_111723.1| 424 ADFNTVNNF 432
                                   555555555 PP

>> BTAD  Bacterial transcriptional activator domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.1   0.00025      0.16      69     117 ..      15      63 ..       9      71 .. 0.92
   2 ?   -0.6   0.0       2.6   1.6e+03      67     100 ..     149     182 ..      96     192 .. 0.76
   3 ?    0.1   0.0       1.6     1e+03      73     124 ..     222     273 ..     208     278 .. 0.79
   4 ?   -1.7   0.0       5.7   3.5e+03      74      91 ..     321     338 ..     290     364 .. 0.72
   5 ?    1.1   0.0      0.81     5e+02      68     105 ..     379     416 ..     370     425 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00025
                                   HHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHH CS
                          BTAD  69 aeaelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALe 117
                                   a+ +++ G ++ea+++ +++++++P +  lh     Al+r+G+ + A+e
  gi|13542035|ref|NP_111723.1|  15 ARSDIAAGNYAEAIEKIDKAIDKEPRNPSLHLIRADALYRQGNYSSAIE 63 
                                   567899***************************************9987 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 2.6
                                   HHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHH CS
                          BTAD  67 alaeaelrlGraeealaelealvaehPlrErlhr 100
                                   +lae  ++  ++++a++e +a ++++  +E+++ 
  gi|13542035|ref|NP_111723.1| 149 DLAEIYFEKKDYKKAMEEVKAVLRNDKSNEKAYD 182
                                   4555566666777777788888887777777765 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 1.6
                                   HHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                          BTAD  73 lrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrr 124
                                   + +G ++ a + l++ ++ +     l+ +l r + + G+  eA e+Y++l r
  gi|13542035|ref|NP_111723.1| 222 IGIGSYDTAEDILKQFIKVYEKEPYLYDLLARTYDQEGKAKEADETYNTLLR 273
                                   55677777777777777777777788999999999************98865 PP

  == domain 4  score: -1.7 bits;  conditional E-value: 5.7
                                   HTT-HHHHHHHHHHHHHH CS
                          BTAD  74 rlGraeealaelealvae 91 
                                   + G++eeal+++ +lv++
  gi|13542035|ref|NP_111723.1| 321 ASGKHEEALKTAGELVKM 338
                                   556777777777776665 PP

  == domain 5  score: 1.1 bits;  conditional E-value: 0.81
                                   HHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHH CS
                          BTAD  68 laeaelrlGraeealaelealvaehPlrErlhrqlmrA 105
                                    ++ +l++G ++ a++ l++ +++ + +E+   +l++ 
  gi|13542035|ref|NP_111723.1| 379 KFNILLEMGNHSLAMESLKNSITASDDDEERLGHLITG 416
                                   5667899**********************999999876 PP

>> DUF627  Protein of unknown function (DUF627)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0      0.02        12       2      39 ..      15      49 ..      14      59 .. 0.76
   2 ?    0.5   0.0      0.97     6e+02       1      19 [.      48      66 ..      48      83 .. 0.75
   3 ?    6.6   0.2     0.012       7.7       2      34 ..     151     183 ..     150     192 .. 0.84
   4 ?   -0.9   0.0       2.7   1.7e+03      73      93 ..     339     364 ..     322     367 .. 0.65
   5 ?    2.5   0.0      0.23   1.4e+02       5      30 ..     383     408 ..     381     420 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.02
                        DUF627  2 AkdllargnhikALeiiedlisrhgedeksallhrlqG 39
                                  A++ +a gn+ +A+e i+++i+++ ++     lh  ++
  gi|13542035|ref|NP_111723.1| 15 ARSDIAAGNYAEAIEKIDKAIDKEPRNP---SLHLIRA 49
                                  677899***************9999953...3444444 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.97
                        DUF627  1 kAkdllargnhikALeiie 19
                                  +A +l+++gn+  A+e ++
  gi|13542035|ref|NP_111723.1| 48 RADALYRQGNYSSAIEELN 66
                                  58899*********98655 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.012
                        DUF627   2 AkdllargnhikALeiiedlisrhgedeksall 34 
                                   A+ +++++++ kA+e ++ ++++ +++ek+  l
  gi|13542035|ref|NP_111723.1| 151 AEIYFEKKDYKKAMEEVKAVLRNDKSNEKAYDL 183
                                   7789****************9888887776554 PP

  == domain 4  score: -0.9 bits;  conditional E-value: 2.7
                        DUF627  73 s......rfyArsLfelasqlgsklyY 93 
                                          ++yA+ L +l++ l+  l Y
  gi|13542035|ref|NP_111723.1| 339 DqtpysrSLYATQLRKLGK-LEDALTY 364
                                   2444467899999999998.6655555 PP

  == domain 5  score: 2.5 bits;  conditional E-value: 0.23
                        DUF627   5 llargnhikALeiiedlisrhgedek 30 
                                   ll+ gnh  A+e ++++i    +de+
  gi|13542035|ref|NP_111723.1| 383 LLEMGNHSLAMESLKNSITASDDDEE 408
                                   5789**************77777654 PP

>> Type_III_YscG  Bacterial type II secretion system chaperone protein (type_III_yscG)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0    0.0018       1.1      39      82 ..      41      89 ..      15     108 .. 0.74
   2 ?    0.4   0.0       1.1   6.5e+02      15      61 ..     320     363 ..     308     372 .. 0.66
   3 ?    1.3   0.0      0.54   3.3e+02      35      81 ..     404     451 ..     381     478 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0018
                                  .HHHHHHHHHHHHHTT-HHHHHH...HHTTS..--GGGHHHHHHHHHHC CS
                 Type_III_YscG 39 eeavrlirlssLmnkGkyeeala...laekl..ayPdLepllaLceakl 82
                                  +   +lir+ +L  +G+y +a +   ++e++    P+L +l ++c   +
  gi|13542035|ref|NP_111723.1| 41 NPSLHLIRADALYRQGNYSSAIEelnFTEHMdkNNPELFSLKSICYGSM 89
                                  46789**************997611144444557899999888886555 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1.1
                                   HHHTTT-HHHHHHHHHHHHHTT-H.HHHHHHHHHHHHHTT-HHHHHH CS
                 Type_III_YscG  15 vgsGkhrheeaniiadwLeekeeeeeavrlirlssLmnkGkyeeala 61 
                                    +sG  +heea+  a  L + ++     r + ++ L   Gk e+al+
  gi|13542035|ref|NP_111723.1| 320 DASG--KHEEALKTAGELVKMDQT-PYSRSLYATQLRKLGKLEDALT 363
                                   4444..468888888888877776.5555566666777777766665 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.54
                                   TT-H.HHHHHHH.HHHHHHTT-HHHHHHHHTTS--GGGHHHHHHHHHH CS
                 Type_III_YscG  35 keeeeeavrlir.lssLmnkGkyeealalaeklayPdLepllaLceak 81 
                                    ++ee   +li  +ss + k +++   +++++l  P+ e  +a+ + k
  gi|13542035|ref|NP_111723.1| 404 DDDEERLGHLITgISSAISKADFNTVNNFLDGLKMPEEEENIAVYALK 451
                                   344445667775499999******************999888877665 PP

>> DUF3856  Domain of Unknown Function (DUF3856)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.1      0.71   4.4e+02      16      37 ..      15      36 ..       8      71 .. 0.64
   2 ?    8.1   0.0    0.0042       2.6     102     129 ..     112     139 ..      88     143 .. 0.92
   3 ?   -1.2   0.1       3.2     2e+03      30      54 ..     158     182 ..     147     219 .. 0.66
   4 ?   -2.5   0.0       7.7   4.8e+03      60      74 ..     216     230 ..     200     242 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.71
                                  HHHHHHHT-HHHHHHHHHHHHH CS
                       DUF3856 16 aekqleegayeeaaasyrkale 37
                                  a   + +g+y+ea +++ ka++
  gi|13542035|ref|NP_111723.1| 15 ARSDIAAGNYAEAIEKIDKAID 36
                                  4445556666666666666655 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0042
                                   HHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                       DUF3856 102 avfsravaleelGrkdealkafrmagem 129
                                   a ++ra+al +lG  d a k fr+  em
  gi|13542035|ref|NP_111723.1| 112 AYYNRAAALRGLGDVDGAEKDFRKYIEM 139
                                   679**********************999 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 3.2
                                   HHHHHHHHHHTTS-TTS---HHHHH CS
                       DUF3856  30 asyrkalevsrtipaeeafdheGfd 54 
                                   ++y+ka+e  +++  ++  + + +d
  gi|13542035|ref|NP_111723.1| 158 KDYKKAMEEVKAVLRNDKSNEKAYD 182
                                   4666777666666555554444444 PP

  == domain 4  score: -2.5 bits;  conditional E-value: 7.7
                                   HHHHHHHHTT-HHHH CS
                       DUF3856  60 glsealaklgrydea 74 
                                   +l++ l+++g+yd+a
  gi|13542035|ref|NP_111723.1| 216 TLTDGLIGIGSYDTA 230
                                   688888999999886 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.1       1.1   6.7e+02      10      23 ..      50      63 ..      49      65 .. 0.83
   2 ?    9.7   0.1    0.0012      0.77       4      29 ..     112     137 ..     111     140 .. 0.88
   3 ?    2.1   0.0       0.3   1.9e+02       7      28 ..     149     170 ..     148     172 .. 0.84
   4 ?   -1.5   0.0       4.2   2.6e+03      16      34 ..     225     243 ..     224     244 .. 0.87
   5 ?   -0.5   0.0       2.1   1.3e+03       7      21 ..     250     264 ..     247     267 .. 0.86
   6 ?   -2.0   0.0       6.1   3.8e+03      14      23 ..     321     330 ..     317     334 .. 0.77
   7 ?   -1.0   0.0       2.9   1.8e+03      12      25 ..     352     365 ..     352     366 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 1.1
                        TPR_10 10 nalrqrgrydeAea 23
                                   al+++g+y  A +
  gi|13542035|ref|NP_111723.1| 50 DALYRQGNYSSAIE 63
                                  589******99976 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0012
                        TPR_10   4 slnNLanalrqrgrydeAealleeal 29 
                                   ++ N a+alr +g+ d+Ae+++++ +
  gi|13542035|ref|NP_111723.1| 112 AYYNRAAALRGLGDVDGAEKDFRKYI 137
                                   68899*****************9855 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.3
                        TPR_10   7 NLanalrqrgrydeAealleea 28 
                                   +La ++++ ++y++A++  + +
  gi|13542035|ref|NP_111723.1| 149 DLAEIYFEKKDYKKAMEEVKAV 170
                                   69*************9975555 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 4.2
                        TPR_10  16 grydeAealleealairrr 34 
                                   g yd Ae++l++ + ++++
  gi|13542035|ref|NP_111723.1| 225 GSYDTAEDILKQFIKVYEK 243
                                   56899******99999987 PP

  == domain 5  score: -0.5 bits;  conditional E-value: 2.1
                        TPR_10   7 NLanalrqrgrydeA 21 
                                    La+++ q g+ +eA
  gi|13542035|ref|NP_111723.1| 250 LLARTYDQEGKAKEA 264
                                   59********99999 PP

  == domain 6  score: -2.0 bits;  conditional E-value: 6.1
                        TPR_10  14 qrgrydeAea 23 
                                   + g+++eA++
  gi|13542035|ref|NP_111723.1| 321 ASGKHEEALK 330
                                   6789999975 PP

  == domain 7  score: -1.0 bits;  conditional E-value: 2.9
                        TPR_10  12 lrqrgrydeAeall 25 
                                   lr++g++++A+ +l
  gi|13542035|ref|NP_111723.1| 352 LRKLGKLEDALTYL 365
                                   6899******9986 PP

>> RNA_polI_A14  Yeast RNA polymerase I subunit RPA14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0     0.033        20      16      54 ..     228     276 ..     225     283 .. 0.64
   2 ?    3.1   0.0      0.26   1.6e+02      12      29 ..     487     504 ..     479     509 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.033
                  RNA_polI_A14  16 eevekfLteFIdekEs..........saselageesstkeaatglsvdt 54 
                                   + +e +L++FI+  E+          + ++  ++++++++ +t l  ++
  gi|13542035|ref|NP_111723.1| 228 DTAEDILKQFIKVYEKepylydllarTYDQEGKAKEADETYNTLLRLNN 276
                                   789********99888788887766544444444444444445555555 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.26
                  RNA_polI_A14  12 hvskeevekfLteFIdek 29 
                                   ++ + ++ +fL++FI+e+
  gi|13542035|ref|NP_111723.1| 487 NLMQGKASEFLNKFIEEN 504
                                   677899*********986 PP

>> TPR_21  Tetratricopeptide repeat-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.1    0.0028       1.7      82     168 ..      14     105 ..      10     123 .. 0.74
   2 ?    4.8   0.2     0.032        20      82     110 ..     150     178 ..     147     203 .. 0.77
   3 ?   -0.9   0.1       1.8   1.1e+03      31      48 ..     256     273 ..     226     283 .. 0.63
   4 ?   -1.4   0.1       2.6   1.6e+03     125     172 ..     354     399 ..     318     412 .. 0.59

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0028
                        TPR_21  82 lAkaaveagdlaaAkaqLewvlekakdeelkalarlRLarvllaekkydeAlktL......eakkeeaf..aalvaelrGD 154
                                    A++ ++ag++a+A ++++++++k++ +   +l+r   a  l  +++y  A+++L      +++++e f  ++      GD
  gi|13542035|ref|NP_111723.1|  14 EARSDIAAGNYAEAIEKIDKAIDKEPRNPSLHLIR---ADALYRQGNYSSAIEELnftehmDKNNPELFslKSICYGSMGD 91 
                                   58899999999999999999999999887777777...7889999999999999955555445555554223455666666 PP

                        TPR_21 155 ilvaqgkldeAraa 168
                                      ++++ d+A +a
  gi|13542035|ref|NP_111723.1|  92 FKRSKEEADKAIKA 105
                                   66666666666554 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.032
                        TPR_21  82 lAkaaveagdlaaAkaqLewvlekakdee 110
                                   lA+  +e++d+++A ++ ++vl + k++e
  gi|13542035|ref|NP_111723.1| 150 LAEIYFEKKDYKKAMEEVKAVLRNDKSNE 178
                                   67888888888888888888888776553 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 1.8
                        TPR_21  31 yqeeqaeeAsalYqqlqe 48 
                                    qe +a+eA ++Y++l++
  gi|13542035|ref|NP_111723.1| 256 DQEGKAKEADETYNTLLR 273
                                   344555555555555543 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 2.6
                        TPR_21 125 aekkydeAlktLeakkeeafaalvaelrGDilvaqgkldeAraaYqaA 172
                                   + +k+++Al+ L + ++++ +++++    +il+++g+   A +  +++
  gi|13542035|ref|NP_111723.1| 354 KLGKLEDALTYLGSGDQDSDEVQFEKF--NILLEMGNHSLAMESLKNS 399
                                   345555555555555555555555543..3555555555555555444 PP

>> TPR_18  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.2    0.0058       3.6       7      36 ..       5      34 ..       2      78 .. 0.81
   2 ?    1.6   0.3      0.43   2.7e+02      62     116 ..      91     147 ..      36     154 .. 0.62
   3 ?    1.4   0.1      0.49     3e+02      52      82 ..     149     179 ..     145     194 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0058
                        TPR_18  7 dvpeaelyqeaqkaldegnyltaieqLeal 36
                                  ++++ e+ +ea+  +  gny +aie++++ 
  gi|13542035|ref|NP_111723.1|  5 EKTPDEYAEEARSDIAAGNYAEAIEKIDKA 34
                                  78999999******************9754 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.43
                        TPR_18  62 dyelavasidrfirlnPahpkiDy..vlYlrglanmaldksslqslvsldrsdrdte 116
                                   d++ ++ ++d+ i+   + p   y  +  lrgl +++  ++ ++++++++ sd d++
  gi|13542035|ref|NP_111723.1|  91 DFKRSKEEADKAIKADQSYPFAYYnrAAALRGLGDVDGAEKDFRKYIEMQPSDPDPH 147
                                   555555566666665555554444224457777777777777777777777777665 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.49
                        TPR_18  52 DLiYakykskdyelavasidrfirlnPahpk 82 
                                   DL   ++++kdy+ a+ +++  +r+  +++k
  gi|13542035|ref|NP_111723.1| 149 DLAEIYFEKKDYKKAMEEVKAVLRNDKSNEK 179
                                   7777888888888888888888888776665 PP

>> HemY_N  HemY protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.1    0.0076       4.7      64     107 .]      13      56 ..       3      56 .. 0.83
   2 ?    1.3   0.1       0.6   3.7e+02      73     102 ..      90     119 ..      86     124 .. 0.83
   3 ?   -2.3   0.0       8.4   5.2e+03      68      91 ..     153     176 ..     149     185 .. 0.76
   4 ?   -2.1   0.0       6.9   4.3e+03      58      75 ..     353     370 ..     328     379 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0076
                        HemY_N  64 seGlialaeGdfarAekaaakaaklsea.pllayllaAqAaqaqg 107
                                   +e+  ++a+G++a+A +++ ka +++++ p   +l+ A A  +qg
  gi|13542035|ref|NP_111723.1|  13 EEARSDIAAGNYAEAIEKIDKAIDKEPRnP-SLHLIRADALYRQG 56 
                                   6777789*******************9956.78899999977665 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.6
                        HemY_N  73 GdfarAekaaakaaklsea.pllayllaAqA 102
                                   Gdf+r++++a ka k +++ p  ay   A A
  gi|13542035|ref|NP_111723.1|  90 GDFKRSKEEADKAIKADQSyP-FAYYNRAAA 119
                                   9**************999877.777666655 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 8.4
                        HemY_N  68 ialaeGdfarAekaaakaaklsea 91 
                                   i +++ d+++A+++ ++ ++++++
  gi|13542035|ref|NP_111723.1| 153 IYFEKKDYKKAMEEVKAVLRNDKS 176
                                   567788999999998888887765 PP

  == domain 4  score: -2.1 bits;  conditional E-value: 6.9
                        HemY_N  58 karealseGlialaeGdf 75 
                                   ++  +l+++l+ l++Gd 
  gi|13542035|ref|NP_111723.1| 353 RKLGKLEDALTYLGSGDQ 370
                                   667789999999999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (510 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       946  (0.0527637); expected 358.6 (0.02)
Passed bias filter:                      614  (0.0342462); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
Passed Fwd filter:                        30  (0.00167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              29  [number of targets reported over threshold]
# CPU time: 0.81u 0.30s 00:00:01.11 Elapsed: 00:00:00.66
# Mc/sec: 2315.41
//
Query:       gi|13542036|ref|NP_111724.1|  [L=263]
Description: hypothetical protein TVN1205 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00067   19.7   0.0     0.0014   18.7   0.0    1.5  1  Acetyltransf_9  Acetyltransferase (GNAT) domain
     0.0015   17.9   1.1       0.15   11.3   0.2    3.0  3  Endonuc-FokI_C  Restriction endonuclease FokI, C terminal


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 !   18.7   0.0   1.5e-07    0.0014       3      96 ..       5      96 ..       4     109 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.5e-07
                                  EEE-GGGHHHHHHHHHHHTT----H....HHHHHHHHHHTTSEEEEEEETTEEEEEEEEEEEEEEETTEEEEEEEEEEEEE-C CS
                Acetyltransf_9  3 relteedldevlellkyaFqdeespl..eeireyfrklleesrvlgaedngelvgqlallplelnvpGktlkaagvtgVavap 83
                                  r ++++dld+vl + k a++ ++     +  +   + ++  + +lga++n++lvg+   +    + +G+ + +   tgV    
  gi|13542036|ref|NP_111724.1|  5 RIYDTADLDDVLGVIKSAWNSQNVNGafK--DTIASMRYHGGIILGAYSNDRLVGMSFSY--PGYRHGSVYLYSHMTGVIEEE 83
                                  677899*****************999432..23446677789*************97555..5799***************** PP

                                  CGTTS-HHHHHHH CS
                Acetyltransf_9 84 ehrgrgvlskLla 96
                                  +hr+ g+  k+ +
  gi|13542036|ref|NP_111724.1| 84 KHRNIGYELKMKQ 96
                                  ***9998655544 PP

>> Endonuc-FokI_C  Restriction endonuclease FokI, C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.04   3.6e+02     127     162 ..      21      56 ..      11      64 .. 0.80
   2 !    3.1   0.0    0.0055        50      61      92 ..      66      97 ..      59     103 .. 0.84
   3 !   11.3   0.2   1.6e-05      0.15     109     174 ..     154     215 ..     130     233 .. 0.72

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.04
                Endonuc-FokI_C 127 fvfvsgsfkGnfkerLeniksrsgveGaavsvekLL 162
                                    ++ s + +G fk+++ +++ + g+  +a s  +L+
  gi|13542036|ref|NP_111724.1|  21 SAWNSQNVNGAFKDTIASMRYHGGIILGAYSNDRLV 56 
                                   567789999************999988888877776 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.0055
                Endonuc-FokI_C 61 rkPdgivyedndGiildtkayskGyslpikqa 92
                                  r+  + +y   +G+i ++k  + Gy l +kq 
  gi|13542036|ref|NP_111724.1| 66 RHGSVYLYSHMTGVIEEEKHRNIGYELKMKQR 97
                                  5666789999*****************98875 PP

  == domain 3  score: 11.3 bits;  conditional E-value: 1.6e-05
                Endonuc-FokI_C 109 vnpnkWWelfeeevkkynfvfvsgsfkGnfkerLeniksrsgveGaavsvekLLllaeelksgrle 174
                                   +   +WW +++ +v+  n vf+ +  +Gn+k       s+s+v G  +  + + +++e++ +g+  
  gi|13542036|ref|NP_111724.1| 154 RLVAEWWLNIDLDVDYDNVVFINSGKEGNYKPIE---YSNSDVLGFKMP-NSINYFSENIERGNNL 215
                                   33479************************98642...345666665543.3455666666666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       636  (0.0354733); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 1617.36
//
Query:       gi|13542037|ref|NP_111725.1|  [L=411]
Description: NAD(FAD)-dependent dehydrogenase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.8e-20   72.0   0.0    4.8e-13   49.0   0.0    2.1  2  Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
      0.008   15.8   0.0        3.5    7.1   0.0    2.3  2  DAO          FAD dependent oxidoreductase


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.0   0.0   5.3e-17   4.8e-13       2     123 ..       6     127 ..       5     172 .. 0.84
   2 !   21.2   0.0   1.6e-08   0.00014     178     286 ..     217     318 ..     187     331 .. 0.81

  Alignments for each domain:
  == domain 1  score: 49.0 bits;  conditional E-value: 5.3e-17
                                   SEEEE--SHHHHHHHHHHHH...HTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHHHHHHCHHHH.CCCCHCCTCEEE CS
                                   xxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx RF
                   Pyr_redox_2   2 dvvviGgGpAGlaaaltlaq...agakvtlvelegtclnggcllskallgvaedaeiasevvkklnqg.ielllgeevvki 78 
                                   +v+++Gg ++Gl++a +l++    ++++ l+ +++   ++++ l++++ g + + + + +  + l+++ ie++ g +v++i
  gi|13542037|ref|NP_111725.1|   6 KVIILGGRFGGLQTAYELKRylkGKIDIKLI-ERNRYIYFRPALPHVAIGLENPDDLRIDISEALSAKgIEYIQG-TVTRI 84 
                                   8*******************77559******.888899*************999998886666677665999999.***** PP

                                   EESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC.TTB CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2  79 dpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGvaenv 123
                                   dp+k +v+++k+      k +yd+lv+A Gs+  +  i G  e+ 
  gi|13542037|ref|NP_111725.1|  85 DPAKNTVEYNKEG-AGPSKEKYDYLVIALGSHLATELITGF-EKF 127
                                   *********6655.556799***********9888888888.333 PP

  == domain 2  score: 21.2 bits;  conditional E-value: 1.6e-08
                                   STTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTEEEEEEETTSCEEEESEEEE-S-EEES-HHCSHCCT-EEEETTEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2 178 lraldkelsaaleealekeGvevklgtsvkeidgngeklevvledgeeidadlvvvavGvrpstelleeklglelderggi 258
                                   l+ l +  +a++++  + ++++++ + + ke+++++    v+ edg++++ dl ++   +  ++    +++gl  de+g++
  gi|13542037|ref|NP_111725.1| 217 LSDLSETNRATVAAMYKGMDIDIVDNFVLKEVTEKE----VISEDGKRLPSDLSFILPPYMGQQMV--KDAGLG-DEAGFV 290
                                   47788889999999**********999999999655....8**************98866666544..899997.6***** PP

                                   E--TTSBE.SSTTEEE-GGGCTECCSS-- CS
                                   xxxxxxxx.xxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2 259 vvdeflrt.nvpgiyaiGDvaggkggpel 286
                                   ++d ++++ + +++ya+GD+     +p+ 
  gi|13542037|ref|NP_111725.1| 291 LTDTNMKSvKYDNVYAVGDIN-ALIVPKM 318
                                   ******8626*********98.3344444 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.5   0.0   0.00058       5.2       1      30 [.       6      40 ..       6      43 .. 0.86
   2 !    7.1   0.0   0.00039       3.5     148     205 ..      61     117 ..      54     182 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.00058
                                  EEEEECTSHHHHHHHHHHHHT..T...EEEEESSS CS
                           DAO  1 dvviiGGGiiGlstAyeLarr..g...Vtllekgd 30
                                  +v+i GG   Gl tAyeL r   g   + l+e+++
  gi|13542037|ref|NP_111725.1|  6 KVIILGGRFGGLQTAYELKRYlkGkidIKLIERNR 40
                                  599***************55476699*******96 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.00039
                                   HHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEE.EECT.EEE.EEEEEEEE--GGGHH CS
                           DAO 148 ltaalaraaealGveilegtevtgleeedgkvwgve.rttp.gen.daadavVnaaGawsd 205
                                   l   + +a+ a+G+e ++g +vt+++       +ve +++  g   +++d++V+a G +  
  gi|13542037|ref|NP_111725.1|  61 LRIDISEALSAKGIEYIQG-TVTRIDPA---KNTVEyNKEGaGPSkEKYDYLVIALGSHLA 117
                                   5556778999*********.*****543...46777755555555457899******9854 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (411 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       422  (0.0235373); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); 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 0.28s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 2604.62
//
Query:       gi|13542038|ref|NP_111726.1|  [L=96]
Description: hypothetical protein TVN1207 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       848  (0.0472977); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); 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 0.28s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 649.82
//
Query:       gi|13542039|ref|NP_111727.1|  [L=145]
Description: 30S ribosomal protein S15P [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-21   75.8   0.6    4.1e-21   74.8   0.6    1.6  1  Ribosomal_S13_N  Ribosomal S13/S15 N-terminal domain
    4.8e-10   39.5   0.8    7.2e-10   38.9   0.8    1.2  1  Ribosomal_S15    Ribosomal protein S15


Domain annotation for each model (and alignments):
>> Ribosomal_S13_N  Ribosomal S13/S15 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.8   0.6   4.5e-25   4.1e-21       1      60 []       1      59 [.       1      59 [. 0.98

  Alignments for each domain:
  == domain 1  score: 74.8 bits;  conditional E-value: 4.5e-25
                                  X--SSSSSS--------S-SS--TTS---HHHHHHHHHHHHHTT--HHHHHHHHHHCCT- CS
               Ribosomal_S13_N  1 MarmhsrgkGkSgSarPyrreapsWlklskeeveelivklakkGltpSqIGviLRDqyGv 60
                                  Marmh+r++GkSgS++ y  e p+W+++sk+e+ +  v+l+k G+t+S +G+ LRDqyGv
  gi|13542039|ref|NP_111727.1|  1 MARMHTRKRGKSGSKKVYGVE-PNWVQYSKDEILNIAVDLKKSGMTSSVVGIRLRDQYGV 59
                                  ******************987.9************************************8 PP

>> Ribosomal_S15  Ribosomal protein S15
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.9   0.8   8.1e-14   7.2e-10      17      71 ..      82     138 ..      70     143 .. 0.88

  Alignments for each domain:
  == domain 1  score: 38.9 bits;  conditional E-value: 8.1e-14
                                   SHHHHHHHHHHHHHHHHHHHHCTTT-HHHHHHHHHHHHHHHHHHHHHHHH-H..HHH CS
                 Ribosomal_S15  17 spevqiallterInnltehlkenkkDkhsrrgLlklvskRrkllkYLkrkdv..erY 71 
                                   ++++++  l++r nn+ +h++ n+kD++++rg  ++++k  +l++Y+kr+ v  +++
  gi|13542039|ref|NP_111727.1|  82 EIPEDLNSLIKRYNNVAKHVELNPKDHSNKRGRDLIMAKMLRLVRYYKRTGVldQKW 138
                                   7999**********************************************9965555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       590  (0.0329076); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 975.57
//
Query:       gi|13542040|ref|NP_111728.1|  [L=448]
Description: single-stranded DNA-specific exonuclease [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-17   63.6   0.8    1.3e-16   61.3   0.0    2.4  3  DHHA1     DHHA1 domain
    0.00027   21.1   0.0    0.00055   20.1   0.0    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 ?   -1.6   0.0      0.36   3.2e+03      17      63 ..      13      51 ..       9      60 .. 0.60
   2 ?   -1.2   0.0      0.28   2.5e+03       8      60 ..     234     283 ..     228     300 .. 0.47
   3 !   61.3   0.0   1.4e-20   1.3e-16      18     138 .]     313     435 ..     303     435 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.36
                                  CHHHHHHHHHHHHHHHTCEEECTCEEEEEECHCCHHH.HHHHHHHHHH CS
                         DHHA1 17 elkealaklkaeellekaeevkgvkvlvaevgeewda.galgiaadkl 63
                                  ++++al  +k++++l         k++++++g+++    +l ++a ++
  gi|13542040|ref|NP_111728.1| 13 KYRQALDLIKESKYL---------KIITHYDGDGTSSaIILTSMAKRM 51
                                  556666666665554.........666666666666555555555555 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.28
                                   HHHHHHHHHCHHHHHHHHHHHHHHHTCEEEC......TCEEEEEECHCCHHHHHHHHHH CS
                         DHHA1   8 rkelekeleelkealaklkaeellekaeevk......gvkvlvaevgeewdagalgiaa 60 
                                   ++e +k+l       a ++   ll++   ++      ++ +++ e+  +++ + l +++
  gi|13542040|ref|NP_111728.1| 234 NEEQKKKL-------ANALSTLLLKQRVGLEalayieNDIYYFDEL--GYNSKQLSSIV 283
                                   33334444.......2222222222222222222224555555555..55555565555 PP

  == domain 3  score: 61.3 bits;  conditional E-value: 1.4e-20
                                   HHHHHHHHHHHHHHHTCEEEC..TCEEEEEECHCCHHHHHHHHHHHHHHTHGBT.TCEEEEEEEECTEEEEEEEESSH... CS
                         DHHA1  18 lkealaklkaeellekaeevk..gvkvlvaevgeewdagalgiaadklksklkk.pvivfvakeegdkvkvsarskkd... 92 
                                   +k + +kl    + +k e +   +v++++a    e+   + gi+  +l +  +  pvi f +++e+   kvs r +++   
  gi|13542040|ref|NP_111728.1| 313 WKMFKTKLIDYVYRAKSELFPgkNVSYFYAPE-SEMAGAISGILMLYLAD--QTrPVIGFSVGKED--TKVSSRGTRKqvn 388
                                   44445555544555554444466778888888.8888888999999**99..776********996..9*******99*** PP

                                   .SS-HHHHHHHHHHHTTCCEEEETCEEEEEEEHCHHHHHHHHHHHHH CS
                         DHHA1  93 .gvdagelakeaaaklgggGGGHdlAaGagipaekleealealeeai 138
                                    g++++ +++ea++++gg GGGHd AaGa ip+++  ++le +++++
  gi|13542040|ref|NP_111728.1| 389 rGLNLSIVMREASQAVGGTGGGHDIAAGAVIPKGREMQFLEIADKIV 435
                                   *****************************************999875 PP

>> DHH  DHH family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   6.1e-08   0.00055       7      85 ..      30     140 ..      26     155 .. 0.69

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 6.1e-08
                                   ECSSSHHHHHHHHHHHH...............................CECS--TCGGCGCCH..HCCCSEEEEEEE-S-- CS
                                   xxxxxxxxxxxxxxxxx...............................xxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxx RF
                           DHH   7 hknpDtDsigSaialan...............................llvDhneksqavege..akeeaedviiiDHHrl 54 
                                   + ++D+D+  Sai l+                                +  D ++       +  +  +ae++i++DHH  
  gi|13542040|ref|NP_111728.1|  30 ITHYDGDGTSSAIILTSmakrmgkkfhltyvkdlsqngirpllsddlvIFADAGSD------QlrFFPDAENIIVLDHHFY 104
                                   579********999999666666666666655555555555533333223333333......2336779***********9 PP

                                   -S......S---SS--EEEE-SSS-HHHHHHHHHHHT CS
                                   xx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DHH  55 ge......efetlapilflnepvgstaeivaelleek 85 
                                   ++      ++ +  ++ +  +  ++++++++ ++   
  gi|13542040|ref|NP_111728.1| 105 QKsnykalNI-NARDFGYDGTRGACGSTMAYIMALIA 140
                                   9988988533.33477899999999****99996543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (448 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       470  (0.0262145); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 2896.54
//
Query:       gi|13542041|ref|NP_111729.1|  [L=219]
Description: hypothetical protein TVN1210 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score 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   13.5   0.5      0.074   12.8   0.1    1.7  2  DUF460    Protein of unknown function (DUF460)


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 ?   12.8   0.1   4.1e-06     0.074      27      48 ..      78      99 ..      39     126 .. 0.76
   2 ?   -2.8   0.0      0.27   4.8e+03      78     131 ..     157     167 ..     140     179 .. 0.40

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.1e-06
                        DUF460 27 krkkklivGiDPGittgiavld 48
                                  ++   l++GiDPG + giavl 
  gi|13542041|ref|NP_111729.1| 78 SSFVDLVIGIDPGPKPGIAVLG 99
                                  455679**************97 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.27
                        DUF460  78 vivAtDvspppetvkklarslkavlyvPeedlsveeKeelaeklsekekvkykd 131
                                   +                                           +  ++ ++++
  gi|13542041|ref|NP_111729.1| 157 I-------------------------------------------EIVNEKNTST 167
                                   2...........................................2222222233 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       338  (0.0188521); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.31s 00:00:00.83 Elapsed: 00:00:00.50
# Mc/sec: 1323.22
//
Query:       gi|13542042|ref|NP_111730.1|  [L=259]
Description: hypothetical protein TVN1211 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-06   28.1   1.2    1.9e-06   28.1   1.2    1.9  2  CARDB     CARDB
  ------ inclusion threshold ------
       0.15   12.1   0.2       0.28   11.2   0.2    1.4  1  Imm43     Immunity protein 43


Domain annotation for each model (and alignments):
>> CARDB  CARDB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1      0.23     2e+03      75      82 ..      59      66 ..      32     112 .. 0.63
   2 !   28.1   1.2   2.1e-10   1.9e-06      19      91 ..     132     205 ..     118     214 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.23
                                  -CEEEEEE CS
                         CARDB 75 egevtltv 82
                                    ++ +tv
  gi|13542042|ref|NP_111730.1| 59 FANYNFTV 66
                                  33333333 PP

  == domain 2  score: 28.1 bits;  conditional E-value: 2.1e-10
                                   SEEEEEEEEEE-SSS-EEEEEEEEEETTEEEEEEEESEE-CTEEEEEEEEEE-S.-S-CEEEEEEEESTT-SS- CS
                         CARDB  19 eentitvtvkNqGtaasgatkvalyldgelvgtvtvpsLaagesttvsftwtte.ategevtltvvvDpdneva 91 
                                   + + ++v++kN  +   +++++++y+dg  v+  tvp++ +g++++v++t++ +  + g++tl+v++   n   
  gi|13542042|ref|NP_111730.1| 132 SPVYFHVELKNPTSYPIYNITATFYVDGIPVAAKTVPKIMPGSTVEVNVTYVNPnFAHGSHTLIVKINNPNIKI 205
                                   556688899999888899***********************************99999********99887655 PP

>> Imm43  Immunity protein 43
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.2   3.1e-05      0.28      18      58 ..      96     138 ..      83     156 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3.1e-05
                         Imm43  18 leelklPeelfl..vcnkkikelkfdyyshsklkivSdefldl 58 
                                   +    +P++l+l  v + k   ++++y + +++ +vS +++++
  gi|13542042|ref|NP_111730.1|  96 MVAPSVPQTLYLyvVTSAKFDGIQYNYTQTISIDVVSPVYFHV 138
                                   5567899999873144455599****************99976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       955  (0.0532657); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); 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: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 1920.89
//
Query:       gi|13542043|ref|NP_111731.1|  [L=2076]
Description: hypothetical protein TVN1212 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.6e-11   42.9   4.1    5.6e-11   42.9   4.1    4.4  3  PMT_2            Dolichyl-phosphate-mannose-protein mannosylt
    7.3e-05   23.0   1.5    7.3e-05   23.0   1.5    6.6  8  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
     0.0038   17.1   0.3       0.15   12.0   0.0    2.7  2  DUF1416          Protein of unknown function (DUF1416)
  ------ inclusion threshold ------
       0.51   10.6   3.0         27    5.0   0.2    3.2  3  ASH              Abnormal spindle-like microcephaly-assoc'd, 


Domain annotation for each model (and alignments):
>> PMT_2  Dolichyl-phosphate-mannose-protein mannosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.9   4.1   1.3e-14   5.6e-11       2     100 ..      93     200 ..      92     207 .. 0.83
   2 ?   -0.2   4.6      0.23     1e+03      98     154 ..     227     285 ..     213     294 .. 0.52
   3 ?   -3.0   5.7       1.7   7.5e+03      82     121 ..     398     436 ..     317     447 .. 0.72

  Alignments for each domain:
  == domain 1  score: 42.9 bits;  conditional E-value: 1.3e-14
                         PMT_2   2 hPPliawllalftklf....gfselairl....vsalagvltilllyllarrlfgkraallaalllavvplfvalsa..lf 72 
                                   +PP++ w++ ++++++    g+   +++     + a++g+l i+ +yl+a+++fgk+a+++aa+l+a++p ++  +    +
  gi|13542043|ref|NP_111731.1|  93 RPPFFHWMIVFVATILspifGSAFKVAYYafeeFDAVFGALLIIPVYLMAKEIFGKKAGIIAAFLYALMPGNLSAGIlsDG 173
                                   58999999988888754444664444433222368***********************************9999999999* PP

                         PMT_2  73 tpdaplvllwalalylllraleknklky 100
                                   ++ +p +++  l++y++ +al + k k 
  gi|13542043|ref|NP_111731.1| 174 RMHTPELFFAFLTIYFFEKALITSK-KS 200
                                   *********************9887.44 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.23
                         PMT_2  98 lkywllagvlfGlgflsKytaallliaallyllis..arrilkekkpylalllalllfs 154
                                   + y ll+g+++G  +ls    a++ + +l+y++++   + +++ +  yl++l  +++++
  gi|13542043|ref|NP_111731.1| 227 TIYALLSGASIGGLMLSWQGYAYIEVILLIYIVVQavINLLTRRPTGYLTYLTSIAMAL 285
                                   33556666666666666555555555444466666432224444555555544444443 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 1.7
                         PMT_2  82 walalylllraleknklkywllagvlfGlgflsKytaall 121
                                   ++ ++y++++++++++  +++++ v++++++++ ++aa +
  gi|13542043|ref|NP_111731.1| 398 MSGIVYVIYKYVKEKS-DALMFILVFAVVSIFMSFEAARF 436
                                   3445666677776666.56666666666666665555544 PP

>> CarboxypepD_reg  Carboxypeptidase regulatory-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   1.5   1.6e-08   7.3e-05       1      56 [.     908     962 ..     908     996 .. 0.82
   2 ?    0.7   0.4      0.14   6.4e+02      11      79 ..    1034    1101 ..    1016    1104 .. 0.69
   3 !    7.3   2.9    0.0012       5.5      10      64 ..    1115    1165 ..    1108    1183 .. 0.81
   4 ?    2.4   0.5     0.042   1.9e+02      29      77 ..    1209    1254 ..    1191    1255 .. 0.70
   5 ?   -1.3   0.2      0.61   2.7e+03      10      41 ..    1540    1568 ..    1535    1586 .. 0.68
   6 ?   -2.9   0.0       1.9   8.7e+03      38      55 ..    1593    1607 ..    1591    1638 .. 0.68
   7 ?   -3.4   0.2       2.7   1.2e+04      22      46 ..    1773    1797 ..    1760    1804 .. 0.65
   8 ?   -2.8   0.1       1.7   7.7e+03      50      82 .]    1824    1855 ..    1819    1855 .. 0.78

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 1.6e-08
               CarboxypepD_reg   1 tisGrVtdasgapiagatVtvtnadtgtvastttdadGafrlrglppgtysvtvsa 56 
                                   ti+G+Vt  +g+++ g  Vt++++ +     + t+++G+f+l glp g+ +v++s 
  gi|13542043|ref|NP_111731.1| 908 TITGKVTTYDGRGVGGIYVTIYDQYGIPHEMVLTNSSGYFSLVGLP-GNDTVVIST 962
                                   7*********************887888999*************99.566666654 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.14
               CarboxypepD_reg   11 gapiagatVtvtnadtgtvast.ttdadGafrlrglppgtysvtvsapGyatatreevtltagqtttldi 79  
                                      pi + t++++n  ++ ++++     +G ++   +pp +y+  v a+G     ++ +  t+g ++  di
  gi|13542043|ref|NP_111731.1| 1034 SVPINNGTIILYN--STYNYTAkFPILNGGYSTGPIPPYDYTASVLANGTLYKDVQILNTTVGSSVVYDI 1101
                                    5677788888884..44444441356799999999*******9999999776666666666666666665 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.0012
               CarboxypepD_reg   10 sgapiagatVtvtnadtgtvastttd.adGafrlrglppgtysvtvsapGyatatr 64  
                                     g+p++ + V ++    g++ s t++  +G++ +  +p g+y+v +++ + at+ +
  gi|13542043|ref|NP_111731.1| 1115 GGKPVKSMVVYAE----GASGSYTSNfVNGTYIVY-VPEGNYTVYARSYNTATRQY 1165
                                    699**********....99999999878*****96.**********9877777765 PP

  == domain 4  score: 2.4 bits;  conditional E-value: 0.042
               CarboxypepD_reg   29 vastttdadGafrlrglppgtysvtvsapGyatatreevtltagqtttl 77  
                                     ++t+  ++G+f++  +p g y++  s +G a    +++++t++++ ++
  gi|13542043|ref|NP_111731.1| 1209 ATYTVNVSNGKFSVV-IPVGVYTIYGSGKGTAYM--RTIEITENTQLNV 1254
                                    34445569*****97.9*****998877665444..4588887766554 PP

  == domain 5  score: -1.3 bits;  conditional E-value: 0.61
               CarboxypepD_reg   10 sgapiagatVtvtnadtgtvastttdadGafr 41  
                                     g  ++  ++++t   ++tv+s  + a+G++ 
  gi|13542043|ref|NP_111731.1| 1540 KGSKVSVNEIAIT---NNTVYSNISLANGYYL 1568
                                    5666666677788...69************94 PP

  == domain 6  score: -2.9 bits;  conditional E-value: 1.9
               CarboxypepD_reg   38 Gafrlrglppgtysvtvs 55  
                                    G+f    lp+g+y + + 
  gi|13542043|ref|NP_111731.1| 1593 GSFV---LPAGNYYISFN 1607
                                    5555...68999998874 PP

  == domain 7  score: -3.4 bits;  conditional E-value: 2.7
               CarboxypepD_reg   22 tnadtgtvastttdadGafrlrglp 46  
                                    t+   +++ +   +++G++ ++gl+
  gi|13542043|ref|NP_111731.1| 1773 TRHFPTENVTISYATSGTYYVNGLT 1797
                                    4444455556666778888888876 PP

  == domain 8  score: -2.8 bits;  conditional E-value: 1.7
               CarboxypepD_reg   50 ysvtvsapGyatatreevtltagqtttlditLe 82  
                                    y+v+     y++ ++ ++t+ + ++t ++itL+
  gi|13542043|ref|NP_111731.1| 1824 YTVVNDTVLYKPINY-NITILNTGNTIVNITLQ 1855
                                    566666666888888.69999888999999996 PP

>> DUF1416  Protein of unknown function (DUF1416)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.0   3.3e-05      0.15      20      70 ..     907     958 ..     899     978 .. 0.91
   2 ?    1.8   0.1     0.048   2.1e+02      21      76 ..    1107    1159 ..    1091    1177 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.3e-05
                       DUF1416  20 aviqGkvtr.dgepvggayvRLLdssgeFtaevvtsaeGefrFfaapGeWtv 70 
                                   a i+Gkvt+ dg+ vgg yv + d+ g     v t+++G f     pG+ tv
  gi|13542043|ref|NP_111731.1| 907 ATITGKVTTyDGRGVGGIYVTIYDQYGIPHEMVLTNSSGYFSLVGLPGNDTV 958
                                   689******9*****************99999***************99888 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.048
                       DUF1416   21 viqGkvtrdgepvggayvRLLdssgeFtaevvtsaeGefrFfaapGeWtvRalark 76  
                                     i   vt +g+pv++  v    +sg +t++ v   +G++  +  +G++tv a + +
  gi|13542043|ref|NP_111731.1| 1107 QIRADVTVGGKPVKSMVVYAEGASGSYTSNFV---NGTYIVYVPEGNYTVYARSYN 1159
                                    478899999******999999999****9987...699999999999999876654 PP

>> ASH  Abnormal spindle-like microcephaly-assoc'd, ASPM-SPD-2-Hydin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       1.7   7.7e+03      12      23 ..    1522    1533 ..    1517    1534 .. 0.83
   2 ?    4.1   0.2     0.012        53      28      78 ..    1839    1889 ..    1837    1902 .. 0.91
   3 ?    5.0   0.2    0.0061        27      22      82 ..    1934    2000 ..    1931    2017 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.7
                                    EEEEE-----EE CS
                           ASH   12 pfvsFgdvkvGs 23  
                                     ++sFg v++G+
  gi|13542043|ref|NP_111731.1| 1522 SQLSFGPVPIGN 1533
                                    689*******97 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.012
                                    E-EEESS-SS--EEEEEEEE--XXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                           ASH   28 lLtveNpseepaevkvskvpaaekgfsveetelevqpgesvtltvtwtPte 78  
                                    ++t+ N++++ ++++++  + +  ++  + ++le+ pges  ++v+ tP++
  gi|13542043|ref|NP_111731.1| 1839 NITILNTGNTIVNITLQNGNTSLYAMAFNVSKLELIPGESANVSVNVTPKA 1889
                                    57899****99*******99999999***********************86 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.0061
                                    EEEEEEE-EEESS-SS--EEEEEEE...E-..-XXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXX CS
                           ASH   22 GssaerlLtveNpseepaevkvskv...pa..aekgfsveete.levqpgesvtltvtwtPteegav 82  
                                    G++ e  L++ N+++++++v++s +   ++  ++ +++++  + + v++ +s  +++t+ Pt++++ 
  gi|13542043|ref|NP_111731.1| 1934 GTNVEVPLVINNTGNANITVNLSISnsyIQslRSLNYNITYPSyVSVSAFGSKIVNITLIPTSTTPA 2000
                                    889999*********99999887551113411445555555559******************99874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (2076 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       943  (0.0525964); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         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: 1.10u 0.27s 00:00:01.37 Elapsed: 00:00:00.49
# Mc/sec: 12625.89
//
Query:       gi|297616200|ref|YP_003710341.1|  [L=77]
Description: KEOPS complex Pcc1-like subunit [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      0.008   16.3   0.0     0.0094   16.1   0.0    1.1  1  Pcc1      Transcription factor Pcc1


Domain annotation for each model (and alignments):
>> Pcc1  Transcription factor Pcc1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   5.2e-07    0.0094      19      72 ..      14      67 ..      10      68 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 5.2e-07
                                      HHHHHH.CHC-TTECEEEEEEETTEEEEEEEESSHHHHHHHHHHHHHHHHHHHHH CS
                              Pcc1 19 rtLqvD.kelsplavkrslslegnvLqveykAttnrmLRvavngfleslglvlet 72
                                      ++L++D  ++     k ++  +g    + ++A +  +L++++ ++ +++ ++ e+
  gi|297616200|ref|YP_003710341.1| 14 EVLAPDiTQPIGR-AKLTIAMKGDCFYIYIEAPDTVSLKASLTSIARLIHVIEEV 67
                                      7899995555555.9*************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       272  (0.015171); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 534.58
//
Query:       gi|13542044|ref|NP_111732.1|  [L=124]
Description: prefoldin subunit beta [Thermoplasma volcanium GSS1]
Scores for complete 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-21   75.1  19.7    4.1e-21   74.9  19.7    1.0  1  Prefoldin_2      Prefoldin subunit
     0.0002   21.6   2.0     0.0002   21.6   2.0    2.0  2  ATG16            Autophagy protein 16 (ATG16)
    0.00033   20.3   5.9      0.062   12.8   0.2    2.0  2  Vps5             Vps5 C terminal like
     0.0017   17.6   8.2     0.0022   17.2   8.2    1.1  1  PLU-1            PLU-1-like protein
     0.0061   16.9  13.8      0.027   14.9   2.4    2.7  2  FlaC_arch        Flagella accessory protein C (FlaC)
     0.0085   16.2   0.4     0.0085   16.2   0.4    2.0  2  Sin3_corepress   Sin3 family co-repressor
  ------ inclusion threshold ------
      0.012   13.2  11.7      0.015   12.9  11.7    1.0  1  DUF3584          Protein of unknown function (DUF3584)
      0.018   14.8  12.7      0.067   12.9   3.2    2.0  2  Laminin_I        Laminin Domain I
      0.022   15.3  12.4       0.25   11.9   3.0    2.1  2  DUF16            Protein of unknown function DUF16
      0.024   14.7  15.0      0.031   14.3  14.3    1.5  1  Sipho_Gp157      Siphovirus Gp157
      0.024   14.6   1.9      0.065   13.3   0.9    1.8  2  PilJ             Type IV pili methyl-accepting chemotaxis tra
      0.034   14.3  10.3        4.1    7.6  10.3    2.1  1  COG5             Golgi transport complex subunit 5
      0.039   14.3  16.3       0.81   10.0   4.1    2.4  1  BLOC1_2          Biogenesis of lysosome-related organelles co
      0.042   14.1  11.7       0.51   10.6   2.2    2.7  2  DUF4164          Domain of unknown function (DUF4164)
      0.098   12.4  16.3       0.12   12.2   3.5    2.0  2  TACC_C           Transforming acidic coiled-coil-containing p
        0.1   12.9  12.0       0.93    9.7   2.2    2.2  2  Seryl_tRNA_N     Seryl-tRNA synthetase N-terminal domain
       0.16   10.8  17.6       0.87    8.4  17.6    1.8  1  Spc7             Spc7 kinetochore protein
       0.17   11.9  10.9          7    6.7  10.8    2.0  1  Laminin_II       Laminin Domain II
        0.2   12.1  13.3      0.025   15.0   6.3    2.0  2  CENP-H           Centromere protein H (CENP-H)
       0.36   11.6  12.2      0.069   13.9   5.1    2.0  2  Occludin_ELL     Occludin homology domain
       0.37   10.7  15.8        1.6    8.7   2.7    2.8  2  Prefoldin        Prefoldin subunit
       0.52   10.6  16.7        2.2    8.6   7.2    2.2  2  Spc24            Spc24 subunit of Ndc80
        0.7    9.1  16.4       0.82    8.9   3.9    2.0  2  DUF3450          Protein of unknown function (DUF3450)
       0.75    9.6  13.1       0.79    9.5   3.5    2.1  2  Nsp1_C           Nsp1-like C-terminal region
       0.76    9.6   9.2        1.2    9.0   9.2    1.4  1  PCRF             PCRF domain
        0.8    9.3  18.5       0.34   10.5   5.4    2.7  2  Snf7             Snf7
       0.82   10.0   6.7        3.2    8.1   0.9    2.3  2  DUF948           Bacterial protein of unknown function (DUF94
       0.89    9.6   9.0         13    5.9   9.0    2.0  1  DUF1664          Protein of unknown function (DUF1664)
        1.1    8.9   4.3       0.26   10.9   0.3    1.8  2  DUF4105          Domain of unknown function (DUF4105)
        1.8    8.2  19.9        2.2    7.9   6.5    2.0  2  Med4             Vitamin-D-receptor interacting Mediator subu
          2    6.2   8.8        3.7    5.4   8.8    1.4  1  V_ATPase_I       V-type ATPase 116kDa subunit family
        2.1    8.9  11.9        1.9    9.0   3.1    2.4  2  NPV_P10          Nucleopolyhedrovirus P10 protein
        2.5    8.9   9.2        3.8    8.2   1.9    2.1  2  DUF2203          Uncharacterized conserved protein (DUF2203)
        2.8    8.1  14.3        4.1    7.6  14.3    1.3  1  Fib_alpha        Fibrinogen alpha/beta chain family
        2.8    7.8  12.0       0.54   10.2   2.8    2.0  2  Cauli_AT         Aphid transmission protein
        3.2    7.1  13.8        1.3    8.4   3.6    2.3  2  FliD_C           Flagellar hook-associated protein 2 C-termin
        3.2    8.2  15.1       0.41   11.1   8.1    2.1  2  Snapin_Pallidin  Snapin/Pallidin
        3.6    7.4  14.1    1.1e+02    2.5  14.0    2.0  1  DUF724           Protein of unknown function (DUF724)
        3.8    7.7  13.5        3.5    7.8   2.6    2.1  2  CREPT            Cell-cycle alteration and expression-elevate
        5.2    6.3  10.9         10    5.4  10.9    1.4  1  DUF4407          Domain of unknown function (DUF4407)
        5.8    7.2  15.9        7.8    6.8   5.3    2.1  2  Cortex-I_coil    Cortexillin I, coiled coil
        5.8    8.0  11.2        3.9    8.5   4.4    2.3  2  Spt5_N           Spt5 transcription elongation factor, acidic
        7.1    6.6  12.0        0.8    9.6   0.4    3.9  6  HSBP1            Heat shock factor binding protein 1
        8.4    7.2  10.8       0.97   10.2   1.7    2.5  2  Vir_act_alpha_C  Virulence activator alpha C-term
        9.8    5.3  11.2         15    4.7   9.4    1.8  1  TMPIT            TMPIT-like protein


Domain annotation for each model (and alignments):
>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.9  19.7     1e-23   4.1e-21       1     105 [.      11     116 ..      11     117 .. 0.98

  Alignments for each domain:
  == domain 1  score: 74.9 bits;  conditional E-value: 1e-23
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-TT--EEEEETTEEEEE.-HHHHHHHHHHHHHHHHHHHHH CS
                   Prefoldin_2   1 qelinkfqqlqqqlqqlaqqikqletqlkelelvleelelldedtkvyklvGdvlvkq.dkeevkeeLeerketlekeikt 80 
                                   q+++++ q+l++ ++++a+q+ ql+  lke+e++l+el+++d+ t+vy+++G +l+k+ dk+++++eLee++e  + +i+t
  gi|13542044|ref|NP_111732.1|  11 QNQLKQAQELEENIEKIATQRYQLDLSLKEIEKTLQELNKIDDKTPVYRSIGSILYKVdDKKKLIDELEEQLELTKIRINT 91 
                                   89********************************************************99********************* PP

                                   HHHHHHHHHHHHHHHHHHHHCCTS- CS
                   Prefoldin_2  81 lekqleklekeleelkeelqkklqq 105
                                   l kq+++le++++el++ +++++ q
  gi|13542044|ref|NP_111732.1|  92 LDKQQKSLEEKYKELQAAIRERYNQ 116
                                   ********************99876 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   4.3     0.053        21     109     151 ..       8      50 ..       5      51 .. 0.74
   2 !   21.6   2.0   5.1e-07    0.0002      88     149 ..      52     113 ..      51     118 .. 0.96

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.053
                         ATG16 109 eelqkleeklkedeerlaeleaeraaletklkdreeelrekek 151
                                   + lq + ++++e ee+++++ ++r +l   lk+ e++l+e++k
  gi|13542044|ref|NP_111732.1|   8 SYLQNQLKQAQELEENIEKIATQRYQLDLSLKEIEKTLQELNK 50 
                                   5577777788888888888888888888888888888888776 PP

  == domain 2  score: 21.6 bits;  conditional E-value: 5.1e-07
                         ATG16  88 eelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrek 149
                                   ++ + +y+s g   +++ ++++ +++lee+l+  + r++ l ++ ++le+k+k++++++re+
  gi|13542044|ref|NP_111732.1|  52 DDKTPVYRSIGSILYKVDDKKKLIDELEEQLELTKIRINTLDKQQKSLEEKYKELQAAIRER 113
                                   588999******************************************************96 PP

>> Vps5  Vps5 C terminal like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.2   0.00016     0.062      36      79 ..      10      56 ..       6      65 .. 0.84
   2 !   10.2   1.2     0.001       0.4      27      69 ..      69     111 ..      66     122 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00016
                          Vps5 36 lesqLkk...LykaiellvsqrkelasataelakslesLaslelsks 79
                                  l++qLk+   L++ ie + +qr +l  +++e+ k+l++L ++++++ 
  gi|13542044|ref|NP_111732.1| 10 LQNQLKQaqeLEENIEKIATQRYQLDLSLKEIEKTLQELNKIDDKTP 56
                                  455555333399******************************99875 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.001
                          Vps5  27 edkkqeldslesqLkkLykaiellvsqrkelasataelaksle 69 
                                    dkk+ +d+le+qL      i++l++q+k l +  +el +++ 
  gi|13542044|ref|NP_111732.1|  69 DDKKKLIDELEEQLELTKIRINTLDKQQKSLEEKYKELQAAIR 111
                                   699************9999***************999988875 PP

>> PLU-1  PLU-1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   8.2   5.5e-06    0.0022     206     293 ..       8     106 ..       4     119 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 5.5e-06
                         PLU-1 206 aelqelleaaekweekakelL..eareklsleeLeallneaqeipvslpslaaleeilkkarewqrkveelikssq..... 279
                                   ++lq++l++a+++ee  +++    ++  lsl+e e+ l+e+++i+   p+++++ +il k+ + ++ ++el ++++     
  gi|13542044|ref|NP_111732.1|   8 SYLQNQLKQAQELEENIEKIAtqRYQLDLSLKEIEKTLQELNKIDDKTPVYRSIGSILYKVDDKKKLIDELEEQLEltkir 88 
                                   579****************9844456678999***************************************9887776555 PP

                         PLU-1 280 ....daaerptlseleel 293
                                       d++++   ++ +el
  gi|13542044|ref|NP_111732.1|  89 intlDKQQKSLEEKYKEL 106
                                   554422222222222333 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 ?    6.6   3.8     0.026        10       3      34 ..      18      49 ..       4      54 .. 0.81
   2 !   14.9   2.4   6.7e-05     0.027       2      38 ..      75     111 ..      74     113 .. 0.95

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.026
                     FlaC_arch  3 delEnklsklsteletvkkeneelsksveelk 34
                                  +elE+ ++k+ t+   +  +++e++k+++el+
  gi|13542044|ref|NP_111732.1| 18 QELEENIEKIATQRYQLDLSLKEIEKTLQELN 49
                                  58899999999977777778888888877776 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 6.7e-05
                     FlaC_arch   2 idelEnklsklsteletvkkeneelsksveelkenVk 38 
                                   idelE++l+ ++++++t+ k++++l+++ +el+  ++
  gi|13542044|ref|NP_111732.1|  75 IDELEEQLELTKIRINTLDKQQKSLEEKYKELQAAIR 111
                                   8******************************998886 PP

>> Sin3_corepress  Sin3 family co-repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.4   2.1e-05    0.0085      48      90 ..      12      54 ..       3      60 .. 0.88
   2 ?    0.2   0.2       1.9   7.7e+02      72      90 ..      87     105 ..      64     113 .. 0.53

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.1e-05
                Sin3_corepress 48 fkasrknqyeealfrcEderyelDmvieanrstiklleelakk 90
                                   + ++ +++ee++ ++  +ry+lD+ ++ +++t+++l+++ +k
  gi|13542044|ref|NP_111732.1| 12 NQLKQAQELEENIEKIATQRYQLDLSLKEIEKTLQELNKIDDK 54
                                  56778899*******************************9987 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 1.9
                Sin3_corepress  72 mvieanrstiklleelakk 90 
                                   + i+++ +  k+lee +k+
  gi|13542044|ref|NP_111732.1|  87 IRINTLDKQQKSLEEKYKE 105
                                   3344444444444444444 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9  11.7   3.7e-05     0.015     293     397 ..      14     119 ..       4     122 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.7e-05
                       DUF3584 293 kqqlrtledelkeaidelnqelsaakaklaakeselealeeqkkkyedadieklkad..ldqlpsirseleeleeeldalt 371
                                    +q+++le+++ e+i++ + +l    +++++  +el++++++   y   +   +k d     +++++++le ++ +++ l 
  gi|13542044|ref|NP_111732.1|  14 LKQAQELEENI-EKIATQRYQLDLSLKEIEKTLQELNKIDDKTPVYRSIGSILYKVDdkKKLIDELEEQLELTKIRINTLD 93 
                                   33455555555.45666666677777899*******************996555554115668****************** PP

                       DUF3584 372 ekhqdvqekydrrkqkikeeleeele 397
                                   +++++++eky++++++i e+ +++ +
  gi|13542044|ref|NP_111732.1|  94 KQQKSLEEKYKELQAAIRERYNQDNK 119
                                   *******************9998765 PP

>> Laminin_I  Laminin Domain I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   2.3    0.0072       2.9      63     103 ..      10      50 ..       5      53 .. 0.90
   2 ?   12.9   3.2   0.00017     0.067       8      62 ..      55     109 ..      50     121 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0072
                     Laminin_I  63 atqvlakaqkvnaesertlnnakeLaekikkladnikeile 103
                                   ++  l++aq++++++e++  +  +L+   k+++++++e+++
  gi|13542044|ref|NP_111732.1|  10 LQNQLKQAQELEENIEKIATQRYQLDLSLKEIEKTLQELNK 50 
                                   5778999******************************9986 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 0.00017
                     Laminin_I   8 tgaleapykinanledltkeLqeklskesakkskieilekelesLaqeteeLqkk 62 
                                   t + + +  i+++++d +k + e +++ + +k++i+ l+k+ +sL++  +eLq  
  gi|13542044|ref|NP_111732.1|  55 TPVYRSIGSILYKVDDKKKLIDELEEQLELTKIRINTLDKQQKSLEEKYKELQAA 109
                                   556778889*******************************************975 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   1.9    0.0048       1.9      57      97 ..      10      50 ..       3      56 .. 0.71
   2 ?   11.9   3.0   0.00062      0.25      28      76 ..      66     115 ..      59     123 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0048
                                  HHHHHHHHHHHHHHHHHHHH.......HHHHHHHHHHHHHH CS
                         DUF16 57 vekqgekikelkveqkaqgeelnkvdetleliletLqkink 97
                                   ++q ++ +el++++++   +  ++d +l+ i +tLq++nk
  gi|13542044|ref|NP_111732.1| 10 LQNQLKQAQELEENIEKIATQRYQLDLSLKEIEKTLQELNK 50
                                  45666677777777777777666788888888888888887 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00062
                                   B-..BHHHH.HHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         DUF16  28 fkdsnkqrL.kkieakvdklgeqinkleqkvekqgekikelkveqkaqge 76 
                                   +k + k++L  ++e++++  + +in l ++ + ++ek kel++ +  + +
  gi|13542044|ref|NP_111732.1|  66 YKVDDKKKLiDELEEQLELTKIRINTLDKQQKSLEEKYKELQAAIRERYN 115
                                   66565555515789999999999999999999999999999987766554 PP

>> Sipho_Gp157  Siphovirus Gp157
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3  14.3   7.9e-05     0.031       4      92 ..      19     117 ..      16     122 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 7.9e-05
                   Sipho_Gp157   4 elaeqykellelleeedvdeeeeeikdtLesle............eeieeKaeniakviknleaeaeaikeeekrLaerkk 72 
                                   el+e++++++++ + +d +   +ei++tL++l+            ++i  K++   k+i++le + e  k +++ L++ +k
  gi|13542044|ref|NP_111732.1|  19 ELEENIEKIATQRYQLDLSL--KEIEKTLQELNkiddktpvyrsiGSILYKVDDKKKLIDELEEQLELTKIRINTLDKQQK 97 
                                   89999999999999998887..69*****9999999********************************************* PP

                   Sipho_Gp157  73 slenkaenLKeyleeameaa 92 
                                   sle+k ++L + ++e  ++ 
  gi|13542044|ref|NP_111732.1|  98 SLEEKYKELQAAIRERYNQD 117
                                   ***********999877665 PP

>> PilJ  Type IV pili methyl-accepting chemotaxis transducer N-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.9   0.00016     0.065      28      95 ..      15      82 ..      10     101 .. 0.79
   2 ?    2.7   0.1      0.32   1.3e+02      45      82 ..      76     115 ..      57     120 .. 0.58

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00016
                          PilJ 28 keallaaagaydaaearaqlretiaqfdrtlaalrlgdpapgllvpaeavraqleaveqlWqelkkpa 95
                                  k+a ++  +++++a++r ql+ +++++++tl++l++ d++++++   +++  ++++  +l +el++++
  gi|13542044|ref|NP_111732.1| 15 KQAQELEENIEKIATQRYQLDLSLKEIEKTLQELNKIDDKTPVYRSIGSILYKVDDKKKLIDELEEQL 82
                                  5555666666899****************************999988888888888788888877777 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.32
                          PilJ  45 aqlretiaqfdrtlaalrlgdpapgllvpae...avraqle 82 
                                   ++l+e++++   +++ l +++++   +   e   a+r++++
  gi|13542044|ref|NP_111732.1|  76 DELEEQLELTKIRINTLDKQQKSLEEKYK-ElqaAIRERYN 115
                                   56666666666666666666555322222.12446666655 PP

>> COG5  Golgi transport complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6  10.3      0.01       4.1      55     102 ..      69     117 ..       4     123 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.01
                                   XXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXX-TTHHHHHHH CS
                          COG5  55 snhleLlehlskskslss.vlselksslesLsasyerlkskvlepyeea 102
                                   + +++L+++l+++++l +   ++l+++ +sL++ y+ l+  + e+y++ 
  gi|13542044|ref|NP_111732.1|  69 DDKKKLIDELEEQLELTKiRINTLDKQQKSLEEKYKELQAAIRERYNQD 117
                                   67899*************999*************************985 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   4.1     0.002      0.81      60      95 ..      10      45 ..       5      46 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.002
                       BLOC1_2 60 lqpylqqidqiekqvteLeeavseLDeyskeLEakf 95
                                  lq++l+q +++e++++++ +  ++LD   ke+E+ +
  gi|13542044|ref|NP_111732.1| 10 LQNQLKQAQELEENIEKIATQRYQLDLSLKEIEKTL 45
                                  899*****************************9876 PP

>> DUF4164  Domain of unknown function (DUF4164)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   2.2    0.0013      0.51      30      69 ..      13      52 ..       3      69 .. 0.89
   2 ?    9.7   0.5    0.0026         1       4      36 ..      90     122 ..      87     124 .] 0.91

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0013
                       DUF4164 30 aerkrdeleaeiealgedrsRLaeeLdqaearaarleevn 69
                                  + ++ +ele++ie+++  r +L+  L + e  +++l+++ 
  gi|13542044|ref|NP_111732.1| 13 QLKQAQELEENIEKIATQRYQLDLSLKEIEKTLQELNKID 52
                                  567789***********************99999999875 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0026
                       DUF4164   4 keleaaltrLeaaldsLEkavdrrleaerkrde 36 
                                   ++l++ ++ Le++ ++L +a+ +r ++++k+++
  gi|13542044|ref|NP_111732.1|  90 NTLDKQQKSLEEKYKELQAAIRERYNQDNKKGA 122
                                   789999**********************99875 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 ?   12.2   3.5    0.0003      0.12      50      96 ..       4      50 ..       2      55 .. 0.92
   2 ?    5.8   5.7     0.027        11      86     150 ..      56     120 ..      50     123 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0003
                        TACC_C 50 ktiaqlieekqkqkelakkeiqkvleekeqlladlnsveksfsdlfk 96
                                    i+  ++++ kq+++ +++i+k+  ++ ql   l+++ek++++l k
  gi|13542044|ref|NP_111732.1|  4 PNISSYLQNQLKQAQELEENIEKIATQRYQLDLSLKEIEKTLQELNK 50
                                  56899999************************************976 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.027
                        TACC_C  86 sveksfsdlfkryekqkevlegykkneeslkkcaeeylarvkkeeqRYqaLkahaeekLekAnee 150
                                    v +s+  ++ +++  k+ ++++ ++ e  k  ++ + ++ k  e++Y++L+a   e+ ++ n++
  gi|13542044|ref|NP_111732.1|  56 PVYRSIGSILYKVDDKKKLIDELEEQLELTKIRINTLDKQQKSLEEKYKELQAAIRERYNQDNKK 120
                                   56688888999999999999999999999999999999999999999999999999999988876 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 ?    8.6   2.5    0.0054       2.1      59     100 ..       6      48 ..       2      51 .. 0.84
   2 ?    9.7   2.2    0.0023      0.93      63     104 ..      69     110 ..      57     113 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0054
                                   CCCCCCTT.S-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH CS
                  Seryl_tRNA_N  59 Igkakkkk.edaeeliaevkelkeelkaleaelkeleaelekl 100
                                   I++  +++ ++a+el + ++++ ++  +l+  lke+e+ l++l
  gi|13542044|ref|NP_111732.1|   6 ISSYLQNQlKQAQELEENIEKIATQRYQLDLSLKEIEKTLQEL 48 
                                   555566667899999999*****************99999987 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0023
                                   CCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCTS CS
                  Seryl_tRNA_N  63 kkkkedaeeliaevkelkeelkaleaelkeleaeleklllai 104
                                    +kk+ ++el ++ +  k ++++l++++k le++ ++l +ai
  gi|13542044|ref|NP_111732.1|  69 DDKKKLIDELEEQLELTKIRINTLDKQQKSLEEKYKELQAAI 110
                                   4566899999999999*****************999998876 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4  17.6    0.0022      0.87     159     260 ..      11     113 ..       5     120 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0022
                          Spc7 159 ekqeeeldellp...eleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeqleeleeki 236
                                   ++q ++++el +   ++ +++ +l   l+++++  +el++id +    + +++ ++  +++ kkk ++el+eqle  + +i
  gi|13542044|ref|NP_111732.1|  11 QNQLKQAQELEEnieKIATQRYQLDLSLKEIEKTLQELNKIDDK--TPVYRSIGSILYKVDDKKKLIDELEEQLELTKIRI 89 
                                   45555555444400044455558888888888888888888854..35667899999999999999999999999999999 PP

                          Spc7 237 eelkeqkseleeeiaeaervleec 260
                                   ++l++q ++lee+ +e +  ++e+
  gi|13542044|ref|NP_111732.1|  90 NTLDKQQKSLEEKYKELQAAIRER 113
                                   999999999999999999887765 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7  10.8     0.018         7      17      99 ..      15     110 ..       3     119 .. 0.44

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.018
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX................XXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHH CS
                    Laminin_II  17 eqlaplsqnlentkeklseinrsveetnekvk................dankairdArrsvkkLeklapqLldklkelkql 81 
                                   +q ++l++n+e++  +  +++ s++e+++ ++                +    ++d ++ + +Le++++    +++   +l
  gi|13542044|ref|NP_111732.1|  15 KQAQELEENIEKIATQRYQLDLSLKEIEKTLQelnkiddktpvyrsigSILYKVDDKKKLIDELEEQLELTKIRIN---TL 92 
                                   4444444444444444444444444444444411111100000000114444444444444444444444444444...44 PP

                                   HHH...HHHHHHHHHHHH CS
                    Laminin_II  82 eeassslsdniseikelI 99 
                                    ++++sl ++ +e+++ I
  gi|13542044|ref|NP_111732.1|  93 DKQQKSLEEKYKELQAAI 110
                                   444444776666666655 PP

>> CENP-H  Centromere protein H (CENP-H)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   6.3   6.3e-05     0.025      11      85 ..       6      92 ..       4      94 .. 0.94
   2 ?    5.5   2.8     0.053        21       9      56 ..      69     116 ..      61     122 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 6.3e-05
                        CENP-H 11 lssellklsqelrelqeeltevekenlrlkrknrelaaellelakekesek............eklkeelekleaelkksrqr 81
                                  +ss l+++ ++ +el+e+++++  ++ +l    +e+ ++l+el+k ++++             +++k+ +++le++l+  + r
  gi|13542044|ref|NP_111732.1|  6 ISSYLQNQLKQAQELEENIEKIATQRYQLDLSLKEIEKTLQELNKIDDKTPvyrsigsilykvDDKKKLIDELEEQLELTKIR 88
                                  78999****************************************9999999*********998899**********999988 PP

                        CENP-H 82 wrvv 85
                                  + ++
  gi|13542044|ref|NP_111732.1| 89 INTL 92
                                  7765 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.053
                        CENP-H   9 delssellklsqelrelqeeltevekenlrlkrknrelaaellelake 56 
                                   d+  + + +l+++l+ ++ +++++ k++++l++k +el a ++e  ++
  gi|13542044|ref|NP_111732.1|  69 DDKKKLIDELEEQLELTKIRINTLDKQQKSLEEKYKELQAAIRERYNQ 116
                                   555555666777777777777777777777777777777777544333 PP

>> Occludin_ELL  Occludin homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   5.1   0.00017     0.069      19     100 ..      12      93 ..       7      94 .. 0.93
   2 ?    3.1   0.9      0.38   1.5e+02      48      71 ..      96     119 ..      90     123 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 0.00017
                  Occludin_ELL  19 keYkeYkelhaeleevskkfseLerelkelkegskeykkieeeilqeykklkk.dpeyqekkkrceyLkekLshiKklike 98 
                                   ++ k+ +el++++e+++ +  +L+  lke +++ +e +ki ++    y+++ +   +  +kkk +++L+e+L+  K +i++
  gi|13542044|ref|NP_111732.1|  12 NQLKQAQELEENIEKIATQRYQLDLSLKEIEKTLQELNKIDDK-TPVYRSIGSiLYKVDDKKKLIDELEEQLELTKIRINT 91 
                                   67788899***********************************.9******998999999*******************98 PP

                  Occludin_ELL  99 yd 100
                                    d
  gi|13542044|ref|NP_111732.1|  92 LD 93 
                                   76 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.38
                  Occludin_ELL  48 lkegskeykkieeeilqeykklkk 71 
                                   +k  +++yk++++ i ++y++ +k
  gi|13542044|ref|NP_111732.1|  96 QKSLEEKYKELQAAIRERYNQDNK 119
                                   223344888888888888887554 PP

>> Prefoldin  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   2.7     0.004       1.6       1      34 [.      20      53 ..      16      75 .. 0.82
   2 ?    7.0   5.4     0.013       5.2      75     109 ..      78     112 ..      61     120 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.004
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT CS
                     Prefoldin  1 lkeeleslqaelaqlkeaieelektletlktlkk 34
                                  l+e++e++++++ ql+ +++e+ektl+ l+++++
  gi|13542044|ref|NP_111732.1| 20 LEENIEKIATQRYQLDLSLKEIEKTLQELNKIDD 53
                                  5789999999999999999999999999999987 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.013
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     Prefoldin  75 leeAiellkkkleelekqlekleeeleklkdqitt 109
                                   lee  el k ++++l+kq+++lee+ ++l+++i +
  gi|13542044|ref|NP_111732.1|  78 LEEQLELTKIRINTLDKQQKSLEEKYKELQAAIRE 112
                                   56667888889999999999999999999988865 PP

>> Spc24  Spc24 subunit of Ndc80
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   7.2    0.0055       2.2       7      67 ..      11      65 ..       6      81 .. 0.74
   2 ?    5.1   5.2     0.066        26       9      43 ..      78     112 ..      67     123 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0055
                         Spc24  7 friakelsdleselesleselaelkeeleeleeeseekeservedetllklklYrsLGiel 67
                                  ++  k++++le+++e++ ++  +l   l+e+e+  +e    +  ++   k  +Yrs+G  l
  gi|13542044|ref|NP_111732.1| 11 QNQLKQAQELEENIEKIATQRYQLDLSLKEIEKTLQE----L--NKIDDKTPVYRSIGSIL 65
                                  56679*******************************9....2..33334556777775433 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.066
                         Spc24   9 iakelsdleselesleselaelkeeleeleeesee 43 
                                   + ++l+ ++  ++ l +++++l+e+++el+    e
  gi|13542044|ref|NP_111732.1|  78 LEEQLELTKIRINTLDKQQKSLEEKYKELQAAIRE 112
                                   45566666777777788888888888888777766 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   3.9    0.0021      0.82      71     113 ..       7      49 ..       3      56 .. 0.87
   2 ?    6.5   4.6     0.011       4.6      51      90 ..      73     112 ..      53     120 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0021
                       DUF3450  71 erlvasqeqeiasleeqieeieeierelvpllekmidrLeqfv 113
                                   ++++++q ++ ++lee+ie+i   + +l   l+++ ++L+++ 
  gi|13542044|ref|NP_111732.1|   7 SSYLQNQLKQAQELEENIEKIATQRYQLDLSLKEIEKTLQELN 49 
                                   6789999999999999999999999999999999999999875 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.011
                       DUF3450  51 aeyralkeeleslevyneqlerlvasqeqeiasleeqiee 90 
                                   + + +l+e+le +++  + l+++++s+e++ ++l+  i e
  gi|13542044|ref|NP_111732.1|  73 KLIDELEEQLELTKIRINTLDKQQKSLEEKYKELQAAIRE 112
                                   4456667777777777777777777777777777766655 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 ?    9.5   3.5     0.002      0.79      71     106 ..      15      50 ..       5      57 .. 0.85
   2 ?    5.9   2.1     0.028        11      58      95 ..      74     111 ..      59     121 .. 0.59

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.002
                        Nsp1_C  71 qeqnkidqeLeyiesqqdeLeslLdnyEkeleells 106
                                   ++ +++++++e i++q+ +L+  L+++Ek l+el++
  gi|13542044|ref|NP_111732.1|  15 KQAQELEENIEKIATQRYQLDLSLKEIEKTLQELNK 50 
                                   456799*************************99974 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.028
                        Nsp1_C  58 kIskLysevleaeqeqnkidqeLeyiesqqdeLeslLd 95 
                                    I +L ++++ ++   n +d++ + +e++ +eL++ + 
  gi|13542044|ref|NP_111732.1|  74 LIDELEEQLELTKIRINTLDKQQKSLEEKYKELQAAIR 111
                                   35555566666666666666666666666666655543 PP

>> PCRF  PCRF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   9.2     0.003       1.2       5      99 ..      24     119 ..       7     124 .] 0.66

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.003
                                   HTTTTTST.-GGGTTTGGGSSSTTHHHHHTHHHHHHHHHHHHHTTTHHH...HT.......-S-..-GGGTHHHHHHHHHH CS
                          PCRF   5 leelekklsdpevwedqekakklskelaeleeivealeeleealedleeakelle...edeelaelaeeeleelekeleel 82 
                                   +e++ ++  + ++  + ++++k+ +el+++++ +  ++++ + l ++++ k+l++   e+ el ++  + l++ +k+lee 
  gi|13542044|ref|NP_111732.1|  24 IEKIATQRYQLDL--SLKEIEKTLQELNKIDDKTPVYRSIGSILYKVDDKKKLIDeleEQLELTKIRINTLDKQQKSLEEK 102
                                   3333333333222..357899999999999999999999999999999999999433233344444444566666677776 PP

                                   ..HHHHHT-..SSSTTS CS
                          PCRF  83 eeelkklLlpkdendek 99 
                                    +el+  +  + ++d+k
  gi|13542044|ref|NP_111732.1| 103 YKELQAAIRERYNQDNK 119
                                   77777777766666665 PP

>> Snf7  Snf7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   7.7      0.28   1.1e+02      46     118 ..      13      83 ..       9      88 .. 0.66
   2 ?   10.5   5.4   0.00086      0.34       9      43 ..      88     122 ..      79     124 .] 0.84

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.28
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTCCHHHHHHHHHHHHHHH CS
                          Snf7  46 lLKqkkryekqldqldnqlanleqvslaienlksnkevlnamkqgakamkamnkkvdidkidklmdeiedqme 118
                                    LKq  ++e+ ++++ +q+++l+  + +ie + ++   ++    + + + ++  kvd  + +kl de+e+q+e
  gi|13542044|ref|NP_111732.1|  13 QLKQAQELEENIEKIATQRYQLDLSLKEIEKTLQELNKIDDKTPVYRSIGSILYKVD--DKKKLIDELEEQLE 83 
                                   588888889999999999988888777777766665555554444455544444444..55666666666666 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00086
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHCTT-HHHH CS
                          Snf7   9 aerkldkkqeslekkikkleaelkklakkgnkdra 43 
                                    ++ ldk+q+sle+k k+l+a +++ + + nk+ a
  gi|13542044|ref|NP_111732.1|  88 RINTLDKQQKSLEEKYKELQAAIRERYNQDNKKGA 122
                                   5799*******************999999888766 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.9     0.008       3.2      28      61 ..      17      52 ..       6      71 .. 0.67
   2 ?    5.7   0.5     0.044        17      24      65 ..      68     112 ..      55     119 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.008
                        DUF948 28 ldeaaatieele...kqvdpilkevedllakvnelle 61
                                  ++e+++ ie++     q+d  lke+e++l++ n++ +
  gi|13542044|ref|NP_111732.1| 17 AQELEENIEKIAtqrYQLDLSLKEIEKTLQELNKI-D 52
                                  44445555554433378999999999999999993.3 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.044
                        DUF948  24 l...kktldeaaatieelekqvdpilkevedllakvnelledvne 65 
                                   +   kk++de+++++e ++ +++ + k+ + l +k +el++ ++e
  gi|13542044|ref|NP_111732.1|  68 VddkKKLIDELEEQLELTKIRINTLDKQQKSLEEKYKELQAAIRE 112
                                   344478899999999999999999999999988888888877766 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   9.0     0.032        13      47     124 .]      17      96 ..       6     116 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.032
                       DUF1664  47 skqleqvseslaatkrhLssridrvdkkldeqkeiskei..keevtevredlseigedvesvkeaveglesklerieekQ 124
                                   +++le+  e++a+++ +L   +++++k+l+e ++i  ++   + + ++  ++++ ++ +++++e  e  + ++++++++Q
  gi|13542044|ref|NP_111732.1|  17 AQELEENIEKIATQRYQLDLSLKEIEKTLQELNKIDDKTpvYRSIGSILYKVDDKKKLIDELEEQLELTKIRINTLDKQQ 96 
                                   46788888889999999999999999988888888766522466666666666666666666666666666666665554 PP

>> DUF4105  Domain of unknown function (DUF4105)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.3   0.00066      0.26      81     127 ..      12      58 ..       6      63 .. 0.84
   2 ?   -0.7   0.5       2.5   9.9e+02      96     128 ..      82     115 ..      65     118 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00066
                       DUF4105  81 apyrdkireytnvekrdvweyrLnltpeevrallahiwelknkpfdY 127
                                   ++ ++  +   n+ek   + y+L+l+ +e+++ l++++++ +k   Y
  gi|13542044|ref|NP_111732.1|  12 NQLKQAQELEENIEKIATQRYQLDLSLKEIEKTLQELNKIDDKTPVY 58 
                                   56666667778999999***********************9998777 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 2.5
                       DUF4105  96 rdvweyrLnltpeevrallahiwelk.nkpfdYy 128
                                    ++   r+n  +++ + l ++  el+ +  ++Y+
  gi|13542044|ref|NP_111732.1|  82 LELTKIRINTLDKQQKSLEEKYKELQaAIRERYN 115
                                   4566777777788888888888888866677776 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 ?    6.8   5.3     0.012       4.8      19      58 ..      12      51 ..       3      65 .. 0.84
   2 ?    7.9   6.5    0.0056       2.2      11      52 ..      69     110 ..      60     116 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.012
                          Med4 19 keleehqknearilqLraeveslDekikeivksLkeyeke 58
                                  ++l++ q+ e++i+++  +  +lD  +kei+k+L e+ k+
  gi|13542044|ref|NP_111732.1| 12 NQLKQAQELEENIEKIATQRYQLDLSLKEIEKTLQELNKI 51
                                  478888999999999999999*************999886 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0056
                          Med4  11 ddelskslkeleehqknea.rilqLraeveslDekikeivksL 52 
                                   dd+ +k ++elee+ +  + ri++L+++++sl+ek ke++ ++
  gi|13542044|ref|NP_111732.1|  69 DDK-KKLIDELEEQLELTKiRINTLDKQQKSLEEKYKELQAAI 110
                                   554.789******9987655******************98766 PP

>> V_ATPase_I  V-type ATPase 116kDa subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   8.8    0.0092       3.7      31     104 ..      16     108 ..       3     116 .. 0.67

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0092
                    V_ATPase_I  31 rcdemerklrfleeeieklekavikeeea...................eesleapeekeldeleeelekleeelkelnenl 92 
                                   + +e+e++++ + ++  +l+    + e++                      + ++++k +delee+le ++ ++++l++++
  gi|13542044|ref|NP_111732.1|  16 QAQELEENIEKIATQRYQLDLSLKEIEKTlqelnkiddktpvyrsigsILYKVDDKKKLIDELEEQLELTKIRINTLDKQQ 96 
                                   444444444444444444333222222224444445555666666666777788889999********************* PP

                    V_ATPase_I  93 eklkkelnelve 104
                                   ++l+++++el+ 
  gi|13542044|ref|NP_111732.1|  97 KSLEEKYKELQA 108
                                   *******99975 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   3.1    0.0047       1.9      30      66 ..      10      46 ..       5      57 .. 0.79
   2 ?    3.4   3.4      0.27   1.1e+02      19      52 ..      67     100 ..      45     117 .. 0.60

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0047
                       NPV_P10 30 vqenlpdvtelnekLdaqsaqLaeletkvenIqdiLn 66
                                  +q++l++ +el+e+++++++q  +l+ ++++I+++L 
  gi|13542044|ref|NP_111732.1| 10 LQNQLKQAQELEENIEKIATQRYQLDLSLKEIEKTLQ 46
                                  6788888888888888888888888888888888887 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.27
                       NPV_P10  19 kVdalqqqvddvqenlpdvtelnekLdaqsaqLa 52 
                                   kVd  ++ +d+++e+l+ ++   + Ld+q+++L+
  gi|13542044|ref|NP_111732.1|  67 KVDDKKKLIDELEEQLELTKIRINTLDKQQKSLE 100
                                   4555555555666655553333344555555554 PP

>> DUF2203  Uncharacterized conserved protein (DUF2203)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.7     0.061        24      52      89 ..      14      51 ..       3      60 .. 0.48
   2 ?    8.2   1.9    0.0096       3.8      15      73 ..      61     121 ..      56     124 .] 0.79

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.061
                       DUF2203 52 eaeleeleaeieelveeieelGvevkdleaglvDFpak 89
                                   ++ +ele++ie++ ++  +l   +k++e+ l +    
  gi|13542044|ref|NP_111732.1| 14 LKQAQELEENIEKIATQRYQLDLSLKEIEKTLQELNKI 51
                                  33344444444444444444444444444444444333 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0096
                       DUF2203  15 lkelleelralrkeleeleeeleeakaeaekse..aaeleaeleeleaeieelveeieelG 73 
                                   + ++l ++ +++k + elee+le +k + ++ +  +++le++++el+a i+e  ++ ++ G
  gi|13542044|ref|NP_111732.1|  61 IGSILYKVDDKKKLIDELEEQLELTKIRINTLDkqQKSLEEKYKELQAAIRERYNQDNKKG 121
                                   6678889999999999999988888888776666689999999999999999877766555 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6  14.3      0.01       4.1      26     130 ..       6     108 ..       2     120 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.01
                                   CCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHH CS
                     Fib_alpha  26 llkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesnirv 106
                                   +++y ++  k+ ++le+++e+i+ +  + +   kei+++l+e +k ++ ++ v++++ + l  ++ + k+ id+ e++++ 
  gi|13542044|ref|NP_111732.1|   6 ISSYLQNQLKQAQELEENIEKIATQRYQLDLSLKEIEKTLQELNKIDD-KTPVYRSIGSILY-KVDDKKKLIDELEEQLEL 84 
                                   678888999999****************************99988888.6999999999999.999999999999999999 PP

                                   HHHHHHHHHHHHHHHHHHHHHHHH CS
                     Fib_alpha 107 LqnvlesneqkiqkLeqdidqker 130
                                    +  +++++++ + Le++ +++++
  gi|13542044|ref|NP_111732.1|  85 TKIRINTLDKQQKSLEEKYKELQA 108
                                   999999999999999999988876 PP

>> Cauli_AT  Aphid transmission protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   3.2      0.27   1.1e+02     113     155 ..      10      52 ..       3      55 .. 0.51
   2 ?   10.2   2.8    0.0014      0.54      81     138 ..      53     108 ..      49     120 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.27
                      Cauli_AT 113 Lkeaqnrikkleeetkklaekivtekllkeevkdlderlseir 155
                                   L++  ++ ++lee+++k+a +     l  +e+ ++ ++l++i 
  gi|13542044|ref|NP_111732.1|  10 LQNQLKQAQELEENIEKIATQRYQLDLSLKEIEKTLQELNKID 52 
                                   4444455556666666665554444444444444444455554 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0014
                      Cauli_AT  81 sksPfgsvfkklkkifkeggedkekktklletLkeaqnrikkleeetkklaek.ivtek 138
                                   +k+P   v++++  i+ +++++k+   +l e L+ ++ ri+ l++++k+l+ek  + ++
  gi|13542044|ref|NP_111732.1|  53 DKTP---VYRSIGSILYKVDDKKKLIDELEEQLELTKIRINTLDKQQKSLEEKyKELQA 108
                                   5777...9999999999999988888888889999999**************9444444 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 ?    4.2   2.6     0.063        25     177     221 ..       6      49 ..       2      55 .. 0.66
   2 ?    8.4   3.6    0.0032       1.3     190     223 ..      83     116 ..      57     122 .. 0.70

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.063
                                   HHHHHHHHHSTT.SHHHHHHHHXXXXHHHHHHHHHHHHHCHHHHH CS
                        FliD_C 177 lenllksyvkssngtlqtasknltkqikdldkkiedldkrletle 221
                                   ++++l++ +k   + l+++++++ +q ++ld   ++++k l++l+
  gi|13542044|ref|NP_111732.1|   6 ISSYLQNQLKQA-QELEENIEKIATQRYQLDLSLKEIEKTLQELN 49 
                                   455566666666.66667777777777777777777777776655 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0032
                                   SHHHHHHHHXXXXHHHHHHHHHHHHHCHHHHHHH CS
                        FliD_C 190 gtlqtasknltkqikdldkkiedldkrletleer 223
                                   + ++ ++++l+kq+k+l++k+++l+ +++++ ++
  gi|13542044|ref|NP_111732.1|  83 ELTKIRINTLDKQQKSLEEKYKELQAAIRERYNQ 116
                                   4556777777777777777777777777776655 PP

>> Snapin_Pallidin  Snapin/Pallidin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   8.1     0.001      0.41      15      89 ..      17      92 ..       5      93 .. 0.92
   2 ?    6.4   4.4     0.031        12       7      45 ..      74     112 ..      72     122 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.001
               Snapin_Pallidin 15 ldeldeklkelrqsQeeLleqldrlnekLkeleeaqe.aevlpdlkeyakKLvnikkrmsslnerlqklkkRaekL 89
                                   +el+e+++++ ++  +L  +l++  + L+el+++++ + v   + + + K+   kk + +l+e+l+ +k R++ L
  gi|13542044|ref|NP_111732.1| 17 AQELEENIEKIATQRYQLDLSLKEIEKTLQELNKIDDkTPVYRSIGSILYKVDDKKKLIDELEEQLELTKIRINTL 92
                                  478999*******************************************************************998 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.031
               Snapin_Pallidin   7 llellepkldeldeklkelrqsQeeLleqldrlnekLke 45 
                                   l++ le +l+ ++ +++ l ++Q+ L e+ ++l+++++e
  gi|13542044|ref|NP_111732.1|  74 LIDELEEQLELTKIRINTLDKQQKSLEEKYKELQAAIRE 112
                                   77889999999999**************99999999986 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5  14.0      0.27   1.1e+02      71     175 ..      11     111 ..       8     119 .. 0.56

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.27
                        DUF724  71 eslkeslaeLekhGFdVkalqsrlnkLlslkdeqtklleerkklekkieeeesekrkleeeidelekkilelerqlallke 151
                                   ++ +++ +eLe++   + + + +l+  lslk e +k+l+e++k++ k+   +s  + +  ++d+++k i ele+ql+l+k 
  gi|13542044|ref|NP_111732.1|  11 QNQLKQAQELEENIEKIATQRYQLD--LSLK-EIEKTLQELNKIDDKTPVYRSIGS-ILYKVDDKKKLIDELEEQLELTKI 87 
                                   3444444444444333333333333..3443.244444555555555554444333.445555888889999999999997 PP

                        DUF724 152 kkeaadkeiarlkseaekleeele 175
                                   + ++ dk+ ++l+ + ++l+ +++
  gi|13542044|ref|NP_111732.1|  88 RINTLDKQQKSLEEKYKELQAAIR 111
                                   777777777777777777777665 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 ?    7.8   2.6    0.0088       3.5      79     127 ..       4      52 ..       1      64 [. 0.87
   2 ?    6.1   3.1     0.029        11      73     123 ..      70     106 ..      61     117 .. 0.55

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0088
                         CREPT  79 kmledfleaqkellakaeekleelkeklekvksvrkelkshiqsLPdLt 127
                                    +++++l++q +++++ ee++e++ ++  +++   ke+++++q L  + 
  gi|13542044|ref|NP_111732.1|   4 PNISSYLQNQLKQAQELEENIEKIATQRYQLDLSLKEIEKTLQELNKID 52 
                                   5678999***********************************9997665 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.029
                         CREPT  73 eRkklakmledfleaqkellakaeekleelkeklekvksvrkelkshiqsL 123
                                   + kkl              +++ ee+le +k +++++++++k+l+++++ L
  gi|13542044|ref|NP_111732.1|  70 DKKKL--------------IDELEEQLELTKIRINTLDKQQKSLEEKYKEL 106
                                   44444..............45555555555555555555555555544443 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4  10.9     0.025        10     137     236 ..      12     113 ..       3     123 .. 0.37

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.025
                       DUF4407 137 eleaqiaalqaeidaaearldalraeaqkeldgtkgtgttgvaGkgpaake...kkaqldaaqaelaelkakld.atarla 213
                                   +  +q ++l+++i++  +++ +l   ++ e++ t ++  +++  k p++++      + d++++ ++el+++l+  + r++
  gi|13542044|ref|NP_111732.1|  12 NQLKQAQELEENIEKIATQRYQLDLSLK-EIEKTLQEL-NKIDDKTPVYRSigsILYKVDDKKKLIDELEEQLElTKIRIN 90 
                                   3333333333333333333333333333.333333222.234444445554333333344444444444444444223333 PP

                       DUF4407 214 alraelaeleaerakeraasqaa 236
                                   +l++++++le+++++ +aa +++
  gi|13542044|ref|NP_111732.1|  91 TLDKQQKSLEEKYKELQAAIRER 113
                                   33333333333333333333322 PP

>> Cortex-I_coil  Cortexillin I, coiled coil
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   5.3      0.02       7.8      35      94 ..      13      71 ..       5      78 .. 0.79
   2 ?    5.6   4.8     0.044        18      19      56 ..      76     113 ..      64     120 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.02
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                 Cortex-I_coil 35 likqkdelesllasleseaaerekrlreleakldealknleleklarlelesrlsktekd 94
                                   +kq +ele+ +  + ++  + +  l+e+e  l+e l++++++      + s l k++  
  gi|13542044|ref|NP_111732.1| 13 QLKQAQELEENIEKIATQRYQLDLSLKEIEKTLQE-LNKIDDKTPVYRSIGSILYKVDDK 71
                                  4699**************************99988.677888777777777777776543 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.044
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                 Cortex-I_coil  19 aglenslesekvsreelikqkdelesllasleseaaer 56 
                                     le+ le  k+  + l kq++ le+  + l+    er
  gi|13542044|ref|NP_111732.1|  76 DELEEQLELTKIRINTLDKQQKSLEEKYKELQAAIRER 113
                                   4799*********************9999887766665 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 ?    3.4   1.0      0.38   1.5e+02      55      77 ..      13      35 ..       7      56 .. 0.70
   2 ?    8.5   4.4    0.0097       3.9      42      80 ..      83     120 ..      46     123 .. 0.65

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.38
                                  XXXXXXXXXXXXXXXXXXXXXXX CS
                        Spt5_N 55 rqaeededaeeiaealeeRYgrs 77
                                  + ++++e +e+i++  ++RY+  
  gi|13542044|ref|NP_111732.1| 13 QLKQAQELEENIEKIATQRYQLD 35
                                  33445577888888889999854 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0097
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                        Spt5_N  42 erddrshreldrrrqaeededaeeiaealeeRYgrsskk 80 
                                   e ++ + + ld+++ +  +e+  e+++a++eRY + +kk
  gi|13542044|ref|NP_111732.1|  83 ELTKIRINTLDKQQ-KSLEEKYKELQAAIRERYNQDNKK 120
                                   33334444445444.445699999999999999885554 PP

>> HSBP1  Heat shock factor binding protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1       3.7   1.5e+03       3      15 ..       6      18 ..       4      19 .. 0.80
   2 ?    2.1   0.2      0.44   1.7e+02      38      49 ..      19      30 ..      15      32 .. 0.89
   3 ?   -0.2   0.1       2.4   9.5e+02      38      47 ..      40      49 ..      36      53 .. 0.65
   4 ?    9.6   0.4     0.002       0.8      24      43 ..      63      82 ..      61      86 .. 0.91
   5 ?   -1.7   0.0       6.8   2.7e+03      35      44 ..      88      97 ..      83     107 .. 0.69
   6 ?   -1.7   0.0       6.7   2.7e+03      14      27 ..      99     112 ..      90     116 .. 0.70

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 3.7
                         HSBP1  3 LtavVenlLqqlq 15
                                  ++++ +n L+q q
  gi|13542044|ref|NP_111732.1|  6 ISSYLQNQLKQAQ 18
                                  6789999999977 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.44
                         HSBP1 38 dLEksiadlmtq 49
                                  +LE++i+++ tq
  gi|13542044|ref|NP_111732.1| 19 ELEENIEKIATQ 30
                                  8*******9998 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 2.4
                         HSBP1 38 dLEksiadlm 47
                                  ++Ek++++l 
  gi|13542044|ref|NP_111732.1| 40 EIEKTLQELN 49
                                  5666666664 PP

  == domain 4  score: 9.6 bits;  conditional E-value: 0.002
                         HSBP1 24 qilsriDdMssriDdLEksi 43
                                  +il ++Dd  + iD+LE+++
  gi|13542044|ref|NP_111732.1| 63 SILYKVDDKKKLIDELEEQL 82
                                  799**************987 PP

  == domain 5  score: -1.7 bits;  conditional E-value: 6.8
                         HSBP1 35 riDdLEksia 44
                                  ri+ L+k+ +
  gi|13542044|ref|NP_111732.1| 88 RINTLDKQQK 97
                                  6777776544 PP

  == domain 6  score: -1.7 bits;  conditional E-value: 6.7
                         HSBP1  14 lqdkFqtmsdqils 27 
                                   l++k++++   i +
  gi|13542044|ref|NP_111732.1|  99 LEEKYKELQAAIRE 112
                                   67777777766655 PP

>> Vir_act_alpha_C  Virulence activator alpha C-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   2.0         1   4.1e+02      25      44 ..      11      30 ..       3      61 .. 0.54
   2 ?   10.2   1.7    0.0024      0.97      14      51 ..      68     104 ..      64     120 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 1
               Vir_act_alpha_C 25 errreeheekLaeyeeieer 44
                                  ++++++++e  +++e+i  +
  gi|13542044|ref|NP_111732.1| 11 QNQLKQAQELEENIEKIATQ 30
                                  44444444444444433222 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0024
               Vir_act_alpha_C  14 vldpealieeLerrreeheekLaeyeeieerleeargq 51 
                                   v d+++li+eLe+++e+ + +++++++ +++l e+++ 
  gi|13542044|ref|NP_111732.1|  68 VDDKKKLIDELEEQLELTKIRINTLDKQQKSL-EEKYK 104
                                   67999**************9999999877777.23333 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   9.4     0.037        15      20      89 ..      12      96 ..       2     106 .. 0.64

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.037
                         TMPIT 20 eykqkleelsklqskcskeikkqkkrlkelksslkklkksvk...............eeeeeeveelkeelkerkkvlkeves 87
                                  +  ++ +el++ ++k++++  +    lke++++l++l+k  +               +++++ ++el+e+l+ +k  ++ +++
  gi|13542044|ref|NP_111732.1| 12 NQLKQAQELEENIEKIATQRYQLDLSLKEIEKTLQELNKIDDktpvyrsigsilykvDDKKKLIDELEEQLELTKIRINTLDK 94
                                  33445555555555555555555555666666666666654455666667778888889999999**9999999998886655 PP

                         TMPIT 88 ll 89
                                    
  gi|13542044|ref|NP_111732.1| 95 QQ 96
                                  43 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3157  (0.176083); expected 358.6 (0.02)
Passed bias filter:                      922  (0.0514251); expected 358.6 (0.02)
Passed Vit filter:                       150  (0.00836633); expected 17.9 (0.001)
Passed Fwd filter:                        63  (0.00351386); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              45  [number of targets reported over threshold]
# CPU time: 0.78u 0.38s 00:00:01.16 Elapsed: 00:00:00.53
# Mc/sec: 703.49
//
Query:       gi|13542045|ref|NP_111733.1|  [L=284]
Description: GTP cyclohydrolase [Thermoplasma volcanium GSS1]
Scores for complete 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-54  183.5   0.0    5.9e-54  183.3   0.0    1.0  1  GCHY-1    Type I GTP cyclohydrolase folE2
  ------ inclusion threshold ------
      0.098   13.3   0.1       0.17   12.6   0.1    1.3  1  UBA2_C    SUMO-activating enzyme subunit 2 C-terminus


Domain annotation for each model (and alignments):
>> GCHY-1  Type I GTP cyclohydrolase folE2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  183.3   0.0   6.6e-58   5.9e-54       3     259 .]       6     269 ..       4     269 .. 0.89

  Alignments for each domain:
  == domain 1  score: 183.3 bits;  conditional E-value: 6.6e-58
                                   XXXXXXXXX----SEEEEEEEEEEEEE--TTTS-EEEEEEEEEEEES-SS--GGGGGHHHHHHHHS-SSEEGGGHHH.... CS
                        GCHY-1   3 DvqsekderkipldrVGvkgvklpvkvkdkekkaqtlvaevdlfvdLpaekkGihmSRlvevleeaeeeleekslee.... 79 
                                   Dvq+++++++i++d+VG++++k p+k+ d+       + ++dl++d+p+++kG++mSR ve+++   ++l+  s++     
  gi|13542045|ref|NP_111733.1|   6 DVQASTPDIRISVDKVGIRRMKFPIKIGDE-----VAILSADLYIDIPQTRKGADMSRAVESIQ---SVLSRPSINLeslg 78 
                                   9***************************94.....57899************************...66665333333355 PP

                                   ..HHHHHHHHTT.-SEEEEEEEEEEEEEEE-TTT--EEEEEEEEEEEEEE..TTEEEEEEEEEEEEEEE-HHHHHHS.... CS
                        GCHY-1  80 ..ileellekleyaeraevelkfeyfiekkapvsgkeglesyevtleaelerkeevkltvgvevpvttlCPCskeisrell 158
                                     i++e l + +ya+r ev+++ ey+ + +    + + + ++++ +++++      +   g++++ +t+CPC++e++r+l+
  gi|13542045|ref|NP_111733.1|  79 ieICKEALGRFNYASRVEVKINGEYYKKSNGGYDEISLYIRTKCGIDGNI------ENLTGLSYEAITACPCAMETTRALI 153
                                   58************************888888888777777777777777......5699*****************9999 PP

                                   ..............SS---EEEEEEEEEEEE......--HHHHHHHHHHHSSEE--S---HHHHHHHHHHHHTS---HHHH CS
                        GCHY-1 159 ..............eagaHnQRsvvtvkvelaeeekeveiedlielvessassevyellKReDEkavtekayenpkFvEDv 225
                                                 ++ +HnQR+++++ v   +++ ++++ d+ +++es   +++ +llKR DE +++ +a+++pkFvEDv
  gi|13542045|ref|NP_111733.1| 154 skdipdsenvlyyiPTVTHNQRNRTKLIVS--NNAGKISFWDIYKVLESVQGKPLESLLKRIDEGKLVYEAHKKPKFVEDV 232
                                   ******************************..46889******************************************** PP

                                   HHHHHHHHHS-TTEEEE........EEEEEEE-TTTSSEEEE CS
                        GCHY-1 226 vRevaaaleeeerveef........sveveneESiHnHnavA 259
                                   vReva a+ +      +         v++ +eESiH+Hna+A
  gi|13542045|ref|NP_111733.1| 233 VREVAFAAVTL-----LplsdddmvIVSSDSEESIHPHNAYA 269
                                   *****998444.....2333446669***************9 PP

>> UBA2_C  SUMO-activating enzyme subunit 2 C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   1.9e-05      0.17      37      71 ..     246     278 ..     239     283 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.9e-05
                        UBA2_C  37 aeedDvliVdsdeEesassadaeaesgstKRKlde 71 
                                     +dD++iV sd Ees    +  a ++ +KR ld 
  gi|13542045|ref|NP_111733.1| 246 LSDDDMVIVSSDSEESIHPHN--AYASMKKRALDL 278
                                   579***********9877666..445556666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 1755.08
//
Query:       gi|13542046|ref|NP_111734.1|  [L=142]
Description: cytidylyltransferase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-16   60.1   0.1    3.1e-16   59.9   0.1    1.0  1  CTP_transf_like  Cytidylyltransferase-like
     0.0014   18.5   1.3      0.062   13.2   1.3    2.2  1  FAD_syn          FAD synthetase
  ------ inclusion threshold ------
       0.12   12.1   0.1       0.25   11.0   0.0    1.5  2  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 !   59.9   0.1   5.1e-20   3.1e-16       2     142 ..       6     132 ..       5     133 .. 0.91

  Alignments for each domain:
  == domain 1  score: 59.9 bits;  conditional E-value: 5.1e-20
                                   EEE--TT--HHHHHHHHHHHHHSSESEEEEEESSTHCSST.-SCSSTHHHHHHHHHHHTTCTTEEEEEEESEHHHHHHHTT CS
               CTP_transf_like   2 agGtFDpiHlGHlrlleqakklleedlivgvpsdeppkkk.kkplasaeeRlemlelakevdevisvdpweltrevlkklk 81 
                                   a G+FD++HlGH+++l++ kkl++e l+v v+ d +++++ k p+++++ Rl+ + ++k vd++i   + ++ + ++ + k
  gi|13542046|ref|NP_111734.1|   6 ATGVFDILHLGHIHYLKESKKLGDE-LVVVVARDSTARNNgKIPIFDENSRLALISELKVVDRAILGHEGDMMK-TVIEVK 84 
                                   78***********************.**************55*******************************7.888899 PP

                                   TTEEEEEEEHHHHHHHHCHHHHHHHHHHHHHEEEEEEHTTCEEEEEEECCTTTCSHHHHHH CS
               CTP_transf_like  82 pdklylvigadvledfsewkeleeilgnvklvvvsrpekqanvllkaekrtngiSstkire 142
                                   pd  ++ +g d+  d   + el++ + ++++ v+        ++ + +++ +  Ss+ +r+
  gi|13542046|ref|NP_111734.1|  85 PD--IITLGYDQKFD---EAELQSKINKLGITVK--------IVRISKYDGQLNSSSSVRK 132
                                   **..******98777...88************99........4557777777888888887 PP

>> FAD_syn  FAD synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   1.3     1e-05     0.062       9      36 ..       4      31 ..       2     129 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1e-05
                       FAD_syn  9 vvtlGnFDGvHlGHqallkkaveaakek 36
                                  v++ G FD +HlGH + lk+ +++ +e 
  gi|13542046|ref|NP_111734.1|  4 VMATGVFDILHLGHIHYLKESKKLGDEL 31
                                  899***************9999998664 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 ?   -2.0   0.0       0.4   2.4e+03      14      36 ..      16      38 ..      12      75 .. 0.59
   2 ?   11.0   0.0   4.2e-05      0.25     128     164 ..     100     136 ..      81     140 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.4
                Citrate_ly_lig 14 GhryLvekaakendvvhlfvvke 36
                                  Gh + ++++ k  d + + v ++
  gi|13542046|ref|NP_111734.1| 16 GHIHYLKESKKLGDELVVVVARD 38
                                  66555555555555555444333 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 4.2e-05
                Citrate_ly_lig 128 alkevlekaeievveierkekeeelisaskvrkllke 164
                                   +l+++++k +i+v++++ ++++++l s+s+vrk + e
  gi|13542046|ref|NP_111734.1| 100 ELQSKINKLGITVKIVRISKYDGQLNSSSSVRKKIME 136
                                   4667777788**********************99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.29s 00:00:00.71 Elapsed: 00:00:00.47
# Mc/sec: 900.32
//
Query:       gi|13542047|ref|NP_111735.1|  [L=150]
Description: acetyltransferase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-17   63.1   0.0    3.5e-17   62.7   0.0    1.2  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    1.7e-13   50.6   0.0    2.2e-13   50.2   0.0    1.1  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    4.4e-12   46.3   0.0    6.3e-12   45.8   0.0    1.2  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    1.4e-08   35.0   0.2    1.8e-08   34.7   0.2    1.1  1  Acetyltransf_4   Acetyltransferase (GNAT) domain
    5.5e-07   29.5   0.0      8e-07   28.9   0.0    1.3  1  FR47             FR47-like protein
    2.7e-05   24.3   0.0    0.00028   20.9   0.0    2.0  1  Acetyltransf_9   Acetyltransferase (GNAT) domain
     0.0056   16.4   0.0      0.092   12.4   0.0    2.1  1  Acetyltransf_8   Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
      0.013   15.4   0.0      0.064   13.1   0.0    1.9  1  Acetyltransf_18  Acetyltransferase (GNAT) domain
       0.11   13.2   0.0       0.13   12.9   0.0    1.1  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 !   62.7   0.0   1.8e-20   3.5e-17       6     117 .]      16     122 ..      11     122 .. 0.84

  Alignments for each domain:
  == domain 1  score: 62.7 bits;  conditional E-value: 1.8e-20
                                   HHHHHHTH.HHHHHHHHHHHHHHHHSTTCEEEEEEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHH CS
                Acetyltransf_1   6 ellvesff.ppnedaseeefeesfsleaegllvaeedgeliGfisllkipdekggvayieslaVspeyrgkGlGsaLleal 85 
                                   +l+v+sf+  p+ ++ ++e+ e      +  ++a+  ++++G+i + + +    +++ ies+a +p++r++ +G++L+  +
  gi|13542047|ref|NP_111735.1|  16 RLEVRSFEiGPYDKEYLREVLEN---ASSISYIAQISDKIVGYIVAMPLNS---QEIDIESIATDPDFRKRSIGTRLIARI 90 
                                   66666666322333333334444...5668888******************...99************************* PP

                                   HHHHHHTTESEEEEEEETTEHHHHHHHHHTTE CS
                Acetyltransf_1  86 eerareegikkivlaveedndaairlYeklGF 117
                                   e + ++ g++ i l+v++ n  ai +Y +lGF
  gi|13542047|ref|NP_111735.1|  91 ENESKSLGYRNIILEVRKENIEAISFYSRLGF 122
                                   ***************************99**9 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.2   0.0   1.1e-16   2.2e-13      18     107 ..      28     123 ..      10     129 .. 0.89

  Alignments for each domain:
  == domain 1  score: 50.2 bits;  conditional E-value: 1.1e-16
               Acetyltransf_10  18 spealrerieegealllvaeeggkivGvi.el.rdgs..hisllfVdpeyrgqGigkaLleaveeeaekdgikl.eltvna 93 
                                   ++e lre +e+ + + ++a  ++kivG+i ++  +++   i+ ++ dp++r++ ig++L+ ++e+e +  g+++  l+v++
  gi|13542047|ref|NP_111735.1|  28 DKEYLREVLENASSISYIAQISDKIVGYIvAMpLNSQeiDIESIATDPDFRKRSIGTRLIARIENESKSLGYRNiILEVRK 108
                                   55788899999******************9776555577****************************************** PP

               Acetyltransf_10  94 sp.yavpfYeklGFk 107
                                    + +a++fY +lGF 
  gi|13542047|ref|NP_111735.1| 109 ENiEAISFYSRLGFN 123
                                   **************6 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.8   0.0   3.1e-15   6.3e-12       6      75 ..      44     123 ..      35     124 .. 0.74

  Alignments for each domain:
  == domain 1  score: 45.8 bits;  conditional E-value: 3.1e-15
                                   EEEEETTEEEEEEEEEEES...TCTEEEEE-GGGTTSSHHHHHHH.HTT.....SEEE...EEEEEETHHHHHHHHHHTTE CS
                Acetyltransf_7   6 fVaeddgkivGfialslld...aeitrlaVdpeyrgkGiGraLle.aae.....kgii...leqlelnaekaikfYeklGF 74 
                                   ++a+  +kivG+i++++l+    +i+ +a+dp++r++ iG++L++ + e      g++   le ++ ++ +ai+fY +lGF
  gi|13542047|ref|NP_111735.1|  44 YIAQISDKIVGYIVAMPLNsqeIDIESIATDPDFRKRSIGTRLIArI-EnesksLGYRniiLE-VRKENIEAISFYSRLGF 122
                                   788889***********9996555666*****************843.224556443321133.2333349********** PP

                                   E CS
                Acetyltransf_7  75 e 75 
                                    
  gi|13542047|ref|NP_111735.1| 123 N 123
                                   6 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.7   0.2   8.8e-12   1.8e-08      35     145 ..      30     133 ..      14     138 .. 0.85

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 8.8e-12
                Acetyltransf_4  35 eefekflealdsekeyvflvaesdrivGyaylgqfkkrakdwkaelsvylaerdnnkeglgrelidaleqvlkeqnienll 115
                                   e++   le+     ++ + ++ sd+ivGy  +  +++  ++   e s+   + d +k+++g  li+ +e+  k  +++n+ 
  gi|13542047|ref|NP_111735.1|  30 EYLREVLEN---ASSISYIAQISDKIVGYIVAMPLNS--QEIDIE-SIAT-DPDFRKRSIGTRLIARIENESKSLGYRNII 103
                                   555556666...4788898999***************..555444.5555.6899************************** PP

                Acetyltransf_4 116 aeiaspnensiqfhkalGFelvgifkkcik 145
                                    e+ ++n+++i f+++lGF++  +  ++++
  gi|13542047|ref|NP_111735.1| 104 LEVRKENIEAISFYSRLGFNIKEFIVNYYE 133
                                   ********************9998877765 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   0.0     4e-10     8e-07      10      79 ..      54     124 ..      47     132 .. 0.86

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 4e-10
                                   --EEEEEEE-TTSSEEEEEE-GGG-SSSHHHHHHHHHHHHHHHS-S.-EEEEEETT-HHHHHHHHHHT-EE CS
                          FR47  10 gelaawilrkdggelgalqvlpehrrrGlgsrlvkalakeiaergk.tvllvvvasNtpsirlyeklGfek 79 
                                   g ++a  l+++   + ++ ++p++r+r  g+rl++ + +e    g+ +++l v+ +N ++i++y++lGf+ 
  gi|13542047|ref|NP_111735.1|  54 GYIVAMPLNSQEIDIESIATDPDFRKRSIGTRLIARIENESKSLGYrNIILEVRKENIEAISFYSRLGFNI 124
                                   5567777788888899***************************8872577889****************85 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   1.4e-07   0.00028       2     127 ..       3     124 ..       3     125 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 1.4e-07
                                   EEEE-GGGHHHHHHHHHHHTT----H..HHHHHHHHHHTT..SEEEEEEETTEEEEEEEEEEEEEEETTEEEEEEEEEEEE CS
                Acetyltransf_9   2 irelteedldevlellkyaFqdeespleeireyfrkllee..srvlgaedngelvgqlallplelnvpGktlkaagvtgVa 80 
                                   +r++ ++dl +v++l  ++F+  + +    +ey+r++le+  s  ++a   +++vg + ++pl  +  +       + ++a
  gi|13542047|ref|NP_111735.1|   3 VRRYLKQDLCAVARLEVRSFEIGPYD----KEYLREVLENasSISYIAQISDKIVGYIVAMPLNSQEID-------IESIA 72 
                                   57888899999999999999999999....4899*****73359999999******9999887654433.......7799* PP

                                   E-CCGTTS-HHHHHHHHHHHHHHHTT--EEEE--.....SSHHHHHTTT-EE CS
                Acetyltransf_9  81 vapehrgrgvlskLlaraleemreegqplsllfP.....ssipiYrrfGyei 127
                                   ++p+ r+r + ++L+ar  +e ++ g++ ++l        +i++Y r+G++i
  gi|13542047|ref|NP_111735.1|  73 TDPDFRKRSIGTRLIARIENESKSLGYRNIILEVrkeniEAISFYSRLGFNI 124
                                   **********************************87775457*******975 PP

>> Acetyltransf_8  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.0   4.6e-05     0.092      33     140 ..      30     125 ..      26     129 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.6e-05
                                   HHHHHHC.STTEEEEEEEETTEEEEEEEEEEGGGCGGGGCS---TT-EEEEEEESSHHHCTTTCHHHHHHHHHHHHHCCTT CS
                Acetyltransf_8  33 ellakldadphsepliglldgepvgyfeiYwakedelaeyydaepgdrGiHlligeaeargkglttallralvhylfadpr 113
                                   e+l+++ ++ +s  +i+++ ++ vgy+     + +            + i  +  ++++r++ ++t+l+ ++ +   ++ +
  gi|13542047|ref|NP_111735.1|  30 EYLREVLENASSISYIAQISDKIVGYIVAMPLNSQ-----------EIDIESIATDPDFRKRSIGTRLIARIENES-KSLG 98 
                                   56666666777777777777777777766544444...........567788888999999999999998876665.5559 PP

                                   --EEEE--BTT-HHHHHHHHHTT-EEE CS
                Acetyltransf_8 114 trrvvvEPdvrNerairllekaGfeke 140
                                    r++++E + +N +ai+++ ++Gf+ +
  gi|13542047|ref|NP_111735.1|  99 YRNIILEVRKENIEAISFYSRLGFNIK 125
                                   ************************865 PP

>> Acetyltransf_18  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   3.2e-05     0.064      14     100 ..      29     123 ..      23     129 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.2e-05
               Acetyltransf_18  14 skfLkrrlkqaeqklvvveedgeivGyglarktrkglk.iGPlvAe....neeiAeaLlkalvanaeg...kkvridvpee 86 
                                   +++L+++l+ a++ +++ +  ++ivGy +a++  ++ + i  + ++    ++ i  +L++++ ++ ++   +++++ v +e
  gi|13542047|ref|NP_111735.1|  29 KEYLREVLENASSISYIAQISDKIVGYIVAMPLNSQEIdIESIATDpdfrKRSIGTRLIARIENESKSlgyRNIILEVRKE 109
                                   689***************************997665554888887522225677778887776665544457899999999 PP

               Acetyltransf_18  87 nkalielleklgfk 100
                                   n ++i++ ++lgf+
  gi|13542047|ref|NP_111735.1| 110 NIEAISFYSRLGFN 123
                                   99999999999986 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   6.5e-05      0.13      35     138 .]      30     123 ..       2     123 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.5e-05
                Acetyltransf_3  35 eeaeewlerawaeeseeegygwaivlkdtgviGsvglrdleeedeeaelgymla.psfwgkGyateavralleyafeelgl 114
                                   e  +e le+a       ++  ++   +d+ ++G++   +l+ +  e++++ +   p+f+ + ++t   + + +   + lg+
  gi|13542047|ref|NP_111735.1|  30 EYLREVLENA-------SSISYIAQISDK-IVGYIVAMPLNSQ--EIDIESIATdPDFRKRSIGTRLIARIENES-KSLGY 99 
                                   4444444432.......334444432455.89**977766655..499997666488*9*******999999998.9999* PP

                Acetyltransf_3 115 erlvavidkeNeaSirvleklGfe 138
                                   + ++ ++ keN   i  + +lGf+
  gi|13542047|ref|NP_111735.1| 100 RNIILEVRKENIEAISFYSRLGFN 123
                                   ***********************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); 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: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 930.67
//
Query:       gi|13542048|ref|NP_111736.1|  [L=151]
Description: HIT (histidine triad) family protein [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-20   73.9   0.5    2.2e-20   73.2   0.5    1.2  1  HIT       HIT domain
      5e-11   43.1   0.1    6.9e-11   42.6   0.1    1.2  1  DcpS_C    Scavenger mRNA decapping enzyme C-term binding
    6.1e-07   29.3   0.5    9.7e-07   28.7   0.5    1.2  1  CwfJ_C_1  Protein similar to CwfJ C-terminus 1
  ------ inclusion threshold ------
      0.027   14.5   0.1      0.055   13.5   0.1    1.5  1  DUF3929   Protein of unknown function (DUF3929)


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 !   73.2   0.5     5e-24   2.2e-20       5      95 ..      17     107 ..      14     108 .. 0.97

  Alignments for each domain:
  == domain 1  score: 73.2 bits;  conditional E-value: 5e-24
                                   -CCEEEE-SSEEEEE-SS-SSSSEEEEEESSTGCSGGGCCHHHHHHHHHHHHHHHHHHHTCTTCCCEEEEEEESGGGT-SS CS
                           HIT   5 pstvvyeddlvlafldidpkapghlLvipkkhlselhdlteeelakllsavkkvakalqkkfknkglrvvinngahagqsv 85 
                                   ++ vv e+++++af d+ p  pgh+Lvipk+h  ++ d+++    ++ ++vk+v ka+ + +++++l+v  nng+ a q v
  gi|13542048|ref|NP_111736.1|  17 NAAVVAENEYTIAFMDKAPVEPGHVLVIPKRHFINIFDIDDFYYIEVQKMVKRVSKAVLEALSADALNVGQNNGRCANQIV 97 
                                   5789***************************************************************************** PP

                                   SS-EEEEEEC CS
                           HIT  86 ahlHiHvipr 95 
                                   +h+H+Hvipr
  gi|13542048|ref|NP_111736.1|  98 MHYHVHVIPR 107
                                   ********98 PP

>> DcpS_C  Scavenger mRNA decapping enzyme C-term binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.6   0.1   1.5e-14   6.9e-11       1     101 [.       5     106 ..       5     117 .. 0.88

  Alignments for each domain:
  == domain 1  score: 42.6 bits;  conditional E-value: 1.5e-14
                                   T-HHHHHHTTSS-B-EEEE-SSEEEEE-SS-SSSEEEEEEESS---SGGG--TTTTTHHHHHHHHHHHHHHHTT-T.-EEE CS
                        DcpS_C   1 kwvfnilakgkepervvyedekfvvlkDikpkaklhllvipkrdikslrdLtkehlpllkemrekakkvieekyne.vdae 80 
                                   ++vf+  + +k +++vv e+e ++++ D+ p ++ h+lvipkr++ ++ d+++  +  +++m++ + k++ e  ++     
  gi|13542048|ref|NP_111736.1|   5 SCVFCTEIIQKRNAAVVAENEYTIAFMDKAPVEPGHVLVIPKRHFINIFDIDDFYYIEVQKMVKRVSKAVLEALSAdALNV 85 
                                   6999999999999**************************************************999999988775543344 PP

                                   EE--SCCCT--S-S--EEEEE CS
                        DcpS_C  81 elrvgvhyqPsvyhlHlHvis 101
                                     + g  +++ v h H+Hvi 
  gi|13542048|ref|NP_111736.1|  86 GQNNGRCANQIVMHYHVHVIP 106
                                   5677788999*********96 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 !   28.7   0.5   2.2e-10   9.7e-07      13     108 ..       5     106 ..       2     108 .. 0.80

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 2.2e-10
                                   H-S----SS---SS--S-B-SSEEEE---S-SSTT-EEEEESS--SSTTSS-H....HHHHHHHHHHHHHHHHHHHTT--E CS
                      CwfJ_C_1  13 sClfClsnpklekhlivsignkvYlalpkgpLssgHvliipieHisallslde....evldeirkfrkalvkmykkqdkda 89 
                                   sC fC +  +  ++ +v+  + + + + k p + gHvl+ip  H  +   +d+    ev++ +++  ka+ +       da
  gi|13542048|ref|NP_111736.1|   5 SCVFCTEIIQKRNAAVVAENEYTIAFMDKAPVEPGHVLVIPKRHFINIFDIDDfyyiEVQKMVKRVSKAVLEAL---SADA 82 
                                   8*****************99999999***************************666666666666666666554...4444 PP

                                   EEEEE-.....SSS-----EEEEE CS
                      CwfJ_C_1  90 vvfEis.....sersvHlaiqvip 108
                                   +    +     ++  +H +++vip
  gi|13542048|ref|NP_111736.1|  83 LNVGQNngrcaNQIVMHYHVHVIP 106
                                   443333334668889999999998 PP

>> DUF3929  Protein of unknown function (DUF3929)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   1.2e-05     0.055      11      36 ..      52      77 ..      48      87 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.2e-05
                       DUF3929 11 ikdvkefyyrdqnkvlervknrvtdn 36
                                  i d+ +fyy + +k++ rv + v++ 
  gi|13542048|ref|NP_111736.1| 52 IFDIDDFYYIEVQKMVKRVSKAVLEA 77
                                  78*******************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       635  (0.0354175); expected 358.6 (0.02)
Passed bias filter:                      518  (0.0288917); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 960.73
//
Query:       gi|13542049|ref|NP_111737.1|  [L=198]
Description: orotate phosphoribosyltransferase-like protein [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.9e-11   42.7   0.2    6.6e-11   42.0   0.2    1.3  1  Pribosyltran  Phosphoribosyl transferase domain
    0.00065   19.3   0.0     0.0013   18.3   0.0    1.5  1  Sigma70_r4_2  Sigma-70, region 4
     0.0017   18.1   0.0     0.0055   16.5   0.0    1.8  2  HTH_23        Homeodomain-like domain
     0.0042   16.6   0.0     0.0088   15.6   0.0    1.5  1  HTH_24        Winged helix-turn-helix DNA-binding
      0.005   16.4   0.0     0.0089   15.5   0.0    1.4  1  PRTase_2      Phosphoribosyl transferase
     0.0053   16.3   0.0      0.011   15.3   0.0    1.5  1  GerE          Bacterial regulatory proteins, luxR family
  ------ inclusion threshold ------
      0.072   12.5   0.0       0.15   11.5   0.0    1.5  2  UPRTase       Uracil phosphoribosyltransferase
       0.18   10.8   0.1       0.27   10.2   0.1    1.2  1  TnsD          Tn7-like transposition protein D


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 !   42.0   0.2     3e-14   6.6e-11      15     127 ..      69     176 ..      63     187 .. 0.88

  Alignments for each domain:
  == domain 1  score: 42.0 bits;  conditional E-value: 3e-14
                                   EEETTEEEEEE....--GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE........EE----TTSEEE CS
                  Pribosyltran  15 varlaaeilee....yngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdesrlledpagkkVl 91 
                                   +a+ +++i++e    + ++ d ++gia  G+p a+ ++  ++ +l + r    r++g  +          + + ++gk+++
  gi|13542049|ref|NP_111737.1|  69 IAEVMSDIIREemqrNSFEVDSILGIAINGIPYATMVSYLMDKELIVYRPHPARKEGFFSS---------NFAGVEGKRIV 140
                                   6666666666666668999*************************99999888877777666.........99********* PP

                                   EE-SEESSSHHHHHHHHHHHCC-BSEEEEEEEEE-H CS
                  Pribosyltran  92 iVDDildtGgTllaalelLkekgpeevriavlvdkp 127
                                   i+DD+ +tG Tl++++  + ++g + v ++ l+ k+
  gi|13542049|ref|NP_111737.1| 141 IIDDVASTGETLKRTITDVTKEGGKAVLCVILASKM 176
                                   *************************99999988765 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   5.8e-07    0.0013      12      43 ..       5      35 ..       1      41 [. 0.89

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 5.8e-07
                                  -HHHHHHHHHHHTS---HHHHHHHHT--HHHH CS
                  Sigma70_r4_2 12 perqreifllryleglsykEIAellgisegtV 43
                                   e ++++++l   +g+s kEI+ +l++s++tV
  gi|13542049|ref|NP_111737.1|  5 EELYKRALEL-KNKGMSDKEISTELHLSVNTV 35
                                  6899******.58******************9 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   2.5e-06    0.0055      10      35 ..      11      36 ..       8      51 .. 0.79
   2 ?   -2.8   0.0       2.7   6.1e+03       6      21 ..     137     153 ..     135     155 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.5e-06
                        HTH_23 10 illllaeGlsvreIAreLgvsrrTvy 35
                                  +l l  +G+s +eI++eL+ s +Tv 
  gi|13542049|ref|NP_111737.1| 11 ALELKNKGMSDKEISTELHLSVNTVT 36
                                  4555556******************6 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2.7
                        HTH_23   6 eRlrillllae.Glsvr 21 
                                   +R+ i+  +a  G + +
  gi|13542049|ref|NP_111737.1| 137 KRIVIIDDVAStGETLK 153
                                   68899998887787766 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   3.9e-06    0.0088      14      39 ..      15      40 ..      10      41 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 3.9e-06
                        HTH_24 14 knprisqreLAerlglSpstvnrrlk 39
                                  kn ++s +e++ +l+lS++tv++ l 
  gi|13542049|ref|NP_111737.1| 15 KNKGMSDKEISTELHLSVNTVTWLLS 40
                                  799*******************9886 PP

>> PRTase_2  Phosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0     4e-06    0.0089     121     150 ..     136     165 ..     120     179 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 4e-06
                      PRTase_2 121 akelvLvDDEistGktalnliralqeklpr 150
                                    k++v++DD +stG+t+ ++i++++++  +
  gi|13542049|ref|NP_111737.1| 136 GKRIVIIDDVASTGETLKRTITDVTKEGGK 165
                                   578********************9987655 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   4.9e-06     0.011      11      35 ..      12      36 ..       9      45 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 4.9e-06
                                  HHHHCTTS-HHHHHHHHTS-HHHHH CS
                          GerE 11 LrllaeGksnkeIAeelniSekTVk 35
                                  L+l  +G+s keI+ el++S +TV+
  gi|13542049|ref|NP_111737.1| 12 LELKNKGMSDKEISTELHLSVNTVT 36
                                  677789******************7 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       2.7   6.1e+03      26      46 ..      30      49 ..      21      54 .. 0.68
   2 ?   11.5   0.0   6.5e-05      0.15     120     169 ..     135     181 ..     111     185 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 2.7
                       UPRTase 26 elvdriarllaeealsallpv 46
                                    v+ +++ll  e+l++   v
  gi|13542049|ref|NP_111737.1| 30 LSVNTVTWLLSKEFLKE-GAV 49
                                  55778888888888876.444 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 6.5e-05
                       UPRTase 120 aertvlllDpviaTGgsaaaaiqlLkergvgeekIlvlsvlaseegvkrl 169
                                   + ++++++D v +TG+++   i  ++++g    k +++ +las+ gv+ l
  gi|13542049|ref|NP_111737.1| 135 EGKRIVIIDDVASTGETLKRTITDVTKEGG---KAVLCVILASKMGVDDL 181
                                   56789**********************775...567777899999*9876 PP

>> TnsD  Tn7-like transposition protein D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1   0.00012      0.27     189     225 ..       9      44 ..       5      53 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00012
                          TnsD 189 erlkeLveeeglslkeiAkelgvdiktVlryakklgl 225
                                   +r+ eL++ +g+s kei+ el+++++tV+ +++k+ l
  gi|13542049|ref|NP_111737.1|   9 KRALELKN-KGMSDKEISTELHLSVNTVTWLLSKEFL 44 
                                   67789999.********************99998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       554  (0.0308997); expected 358.6 (0.02)
Passed bias filter:                      517  (0.028836); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1351.36
//
Query:       gi|13542050|ref|NP_111738.1|  [L=503]
Description: lysyl-tRNA synthetase [Thermoplasma volcanium GSS1]
Scores for 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-114  381.0   0.0     7e-114  380.5   0.0    1.2  1  tRNA-synt_1f  tRNA synthetases class I (K)
     0.0007   18.4   0.0       0.87    8.3   0.0    2.4  2  tRNA-synt_1g  tRNA synthetases class I (M)


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 !  380.5   0.0  7.8e-118    7e-114       3     344 ..       3     328 ..       1     344 [. 0.95

  Alignments for each domain:
  == domain 1  score: 380.5 bits;  conditional E-value: 7.8e-118
                  tRNA-synt_1f   3 WadklaeklieerkkkkaekdevvvesGispSGliHiGnlrevltadlvaralrkrgeevrlilisDdmDglRkvpenlpe 83 
                                   Wad+ +++li          +e+ +++GispSG+iH+Gn+re+lt+d++++a+ krg + ++i+++DdmD+lRkv+++l++
  gi|13542050|ref|NP_111738.1|   3 WADAAVKDLI----------GEQRISTGISPSGPIHVGNMREILTGDILYKAVIKRGLKSDFIYLCDDMDPLRKVYPFLDQ 73 
                                   6666666666..........6789********************************************************* PP

                  tRNA-synt_1f  84 kllekylgkpltsiPdpkgkhesyaehfnaelvesLdelgievefisatelYksglydeaikealenrekikeilekyrge 164
                                   + ++ky+g pl++iP+p+g    y++hf +++ e++++ gi +++i++++lY +g +++ai++++e+r++ik+ilek++g+
  gi|13542050|ref|NP_111738.1|  74 S-YSKYVGFPLKNIPSPDGV-GVYSDHFLNPFIEVMRKTGIPARVIKTSDLYGNGILADAIDTVMERRSEIKDILEKITGR 152
                                   *.****************98.99********************************************************** PP

                  tRNA-synt_1f 165 ereetyspylpvcekcgrvdttevvevdaeeeeieYkceecGeeeevdiregngKLqWkvdwamrWaalgVdfEpaGkDha 245
                                    +e +++py+p+cekcgr+++t v++++    + eY+c +cG+++ +dir ++gK++W+++w+++W+al+V +Ep+GkDh 
  gi|13542050|ref|NP_111738.1| 153 MIEGDFYPYEPLCEKCGRINSTSVISYK--YPYAEYTC-KCGHHGFADIRRAEGKMPWRIEWPAKWYALKVSIEPFGKDHG 230
                                   ***************************9..********.****************************************** PP

                  tRNA-synt_1f 246 aaGgSvdvsskia.eilggeaPekvvYelillkggekmssSkGnvltledwlevaepevlrflilrrkPkkakkldldlei 325
                                   a+GgS+d++++ia ei+g+e+P ++vYe i+lkg+++m+sS+G  +  +++++v++pe+lrfli+r +P +++++d++l++
  gi|13542050|ref|NP_111738.1| 231 APGGSYDTGKRIArEIFGIEPPLPLVYERIMLKGKGAMHSSTGLAIPASEIIDVMPPELLRFLIARVNPSRHIDFDPGLGL 311
                                   ********************************************************************************* PP

                  tRNA-synt_1f 326 lrlvdeYdklerkyfaeqe 344
                                   l+l de++++ +ky   + 
  gi|13542050|ref|NP_111738.1| 312 LNLFDEFERYLNKYR--EG 328
                                   **************7..33 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.0   0.00016       1.4      11      43 ..      24      58 ..      17      62 .. 0.78
   2 !    8.3   0.0   9.7e-05      0.87     326     361 ..     266     301 ..     250     308 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00016
                                  SS---HHHHHHHHHHHHHHHHHHHT..T-EEEEEE CS
                  tRNA-synt_1g 11 ngklHlGhllevisaDifaRykrlr..geevlfvc 43
                                  +g++H+G+++e++ +Di+++   +r  +++ +++c
  gi|13542050|ref|NP_111738.1| 24 SGPIHVGNMREILTGDILYKAVIKRglKSDFIYLC 58
                                  799***************99765551156677776 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 9.7e-05
                                   ------------HHHHHHHH-HHHHHHHHHHHS-TT CS
                  tRNA-synt_1g 326 kKlSkSrgvvvkakealerldadllRYylaaeapek 361
                                   + + +S g ++ a+e+++ ++++llR+ +a+ +p  
  gi|13542050|ref|NP_111738.1| 266 GAMHSSTGLAIPASEIIDVMPPELLRFLIARVNPSR 301
                                   46999**********************999966643 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (503 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       561  (0.0312901); expected 358.6 (0.02)
Passed bias filter:                      509  (0.0283898); 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: 0.63u 0.31s 00:00:00.94 Elapsed: 00:00:00.48
# Mc/sec: 3125.59
//
Query:       gi|13542051|ref|NP_111739.1|  [L=543]
Description: methionyl-tRNA synthetase [Thermoplasma volcanium GSS1]
Scores for complete 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-151  502.2   0.0   1.3e-150  501.5   0.0    1.3  1  tRNA-synt_1g   tRNA synthetases class I (M)
    5.9e-14   51.3   0.0    4.6e-10   38.4   0.0    3.3  3  tRNA-synt_1    tRNA synthetases class I (I, L, M and V)
    1.9e-05   24.2   0.0      0.017   14.4   0.0    2.2  2  tRNA-synt_1e   tRNA synthetases class I (C) catalytic domain
    0.00022   20.3   0.0    0.00045   19.3   0.0    1.5  1  tRNA-synt_1f   tRNA synthetases class I (K)
     0.0039   17.2   0.3      0.008   16.2   0.3    1.5  1  Anticodon_1    Anticodon-binding domain of tRNA
  ------ inclusion threshold ------
       0.17   11.9   2.6       0.36   10.9   2.6    1.6  1  DZR            Double zinc ribbon
        4.7    6.8   6.7         12    5.5   1.2    2.3  2  zf-ribbon_3    zinc-ribbon domain
        7.4    6.4   7.5         18    5.2   1.8    2.6  2  zinc_ribbon_2  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 !  501.5   0.0  5.8e-154  1.3e-150       1     391 []       6     398 ..       6     398 .. 0.99

  Alignments for each domain:
  == domain 1  score: 501.5 bits;  conditional E-value: 5.8e-154
                                   EEEEE--B--SS---HHHHH.HHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHH CS
                  tRNA-synt_1g   1 vlvttalpYangklHlGhll.evisaDifaRykrlrgeevlfvcgtDehGtpielkAekegvtpeelvekvheeikelfkk 80 
                                   +lv++alpYang+lH+Gh++  ++ aD+f+R++rl g+evl+v+g+De+Gtpi+++Aekeg +p+e+++++++e+ e+fkk
  gi|13542051|ref|NP_111739.1|   6 ILVNCALPYANGPLHVGHIAgAYLGADVFVRFNRLIGNEVLYVSGSDEYGTPITVRAEKEGKSPQEIADRYYAEHIETFKK 86 
                                   69******************************************************************************* PP

                                   TT---SEEEETTSHHHHHHHHHHHHHHHHTT-EEEEEEEEEEETTTTEEE-GGG-EE........-TTS-EE-TTSSB-E. CS
                  tRNA-synt_1g  81 lnisfdkygrttseehkelvqeifkklkekgliyekeieqlycpkderflpdryvegtCPkckseeargdqceecgkklep 161
                                   l+i+fd + rtt  eh++++qe+f kl ++g i+++++   yc k +rf+pdry+eg+CP+c++++argdqc++cg++l+p
  gi|13542051|ref|NP_111739.1|  87 LGINFDIFMRTTYPEHSSVAQEFFLKLLNEGVIEKGTMIAPYCRKIGRFMPDRYIEGECPYCGYKKARGDQCDNCGRTLDP 167
                                   ********************************************************************************* PP

                                   ...............EEE.EEEEEE-GGGGHHHHHHHH.HH-TTSHHHHHHHH.HHHHT----EE-ESS-SSS-EET..TE CS
                  tRNA-synt_1g 162 telinpksaisgskpevketehlffklskfekklkewieeeekeleenvkkivkewlkegLkdlaisrdldwGipvP..ga 240
                                   +elinp++++sg++pe++eteh+f++l+ fe++l+ew+ ++++ ++ nv  +++++++ gLk++ai+rd+dwG++vP  g 
  gi|13542051|ref|NP_111739.1| 168 QELINPVCILSGETPEFRETEHFFLRLDLFEERLEEWL-KTKTFWKPNVLAYTRNFIQGGLKKRAITRDIDWGVKVPleGY 247
                                   **************************************.77778************************************* PP

                                   CCEEE-HHHHHHHHHHHTTTTT-...TTSGGGG.G--S......EEEEEGGGHHHHHTHHHHHHHH.TT----S-EEEE-- CS
                  tRNA-synt_1g 241 ekkvlYVWldAligYisatkelakkkgeeekwkeyWakdkevelvhfigkdiikFHtifwPaillg.aelklpkkvvahey 320
                                   e+k +YVW++AligYi+  k++++  g+++ wke++  dk+v+ ++figkd+i+FH+i+wPa+llg  el+lp  + a+ey
  gi|13542051|ref|NP_111739.1| 248 EHKRIYVWFEALIGYITGAKMFSEVIGKPNYWKEFY-FDKDVKNYYFIGKDNIPFHSIIWPAMLLGyGELNLPYDIPANEY 327
                                   ************************************.899**************************999************ PP

                                   EEE--------------HHHHHHHH-HHHHHHHHHHHS-TTS-EEE-HHHHHHHHHHHCCCHHHHHHHHH. CS
                  tRNA-synt_1g 321 ltvegkKlSkSrgvvvkakealerldadllRYylaaeapekkDldfswedfvervNseLadklgnlvnRvl 391
                                   lt++g+++SkSrg++ +++e+l  +++d+lRYy+a+  pe+ D+dfs+e++v++vNs+L+dk+gn+v+R+l
  gi|13542051|ref|NP_111739.1| 328 LTFKGEQFSKSRGIGYTVDELLRVIPPDYLRYYVASILPETGDSDFSLEELVKTVNSDLIDKYGNFVHRTL 398
                                   *********************************************************************85 PP

>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.4   0.0     2e-13   4.6e-10      32     169 ..      13     132 ..       6     140 .. 0.89
   2 !    7.7   0.0   0.00039      0.88     358     433 ..     168     244 ..     160     265 .. 0.86
   3 ?   -3.2   0.0      0.78   1.7e+03     560     592 ..     331     364 ..     329     373 .. 0.85

  Alignments for each domain:
  == domain 1  score: 38.4 bits;  conditional E-value: 2e-13
                   tRNA-synt_1  32 PyvtGslHiGhalaktl.kdivirykrmkGkevlyvpGwDhaGlaieakvekklgakekkerkklgreefrekvrewkaey 111
                                   Py++G lH+Gh+    l  d+ +r++r+ G+evlyv G D  G +i    ek+ g++                 +e++++y
  gi|13542051|ref|NP_111739.1|  13 PYANGPLHVGHIAGAYLgADVFVRFNRLIGNEVLYVSGSDEYGTPITVRAEKE-GKSP----------------QEIADRY 76 
                                   *************999957***************************9999998.3333................5788899 PP

                   tRNA-synt_1 112 aeeirkqvkrlGvsvDfdreylTldkeleeavkevfvrladkgliyrgkklvnwstkl 169
                                    +e  +++k+lG+   fd    T ++e +   +e f +l ++g+i +g+ + +++ k+
  gi|13542051|ref|NP_111739.1|  77 YAEHIETFKKLGIN--FDIFMRTTYPEHSSVAQEFFLKLLNEGVIEKGTMIAPYCRKI 132
                                   999999******76..55667899******************************9875 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.00039
                   tRNA-synt_1 358 iehsvpfcerskkpiiyrateqWfvrvkeladaalkave.kvqfvpkskekryaswleniqdWciSRqrwWGhripl 433
                                    e+  p+c  s++  ++r te  f r++ +++ + + ++ k+ ++p+    + + +    +  +i R+  WG+++pl
  gi|13542051|ref|NP_111739.1| 168 QELINPVCILSGETPEFRETEHFFLRLDLFEERLEEWLKtKTFWKPNVLAYTRNFIQGGLKKRAITRDIDWGVKVPL 244
                                   5666799999******************9999999999989999**99766666666789999************97 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 0.78
                   tRNA-synt_1 560 eGrKmSKslgNvidpldvikkygadalRltli.l 592
                                   +G   SKs g     +++++    d lR++++  
  gi|13542051|ref|NP_111739.1| 331 KGEQFSKSRGIGYTVDELLRVIPPDYLRYYVAsI 364
                                   68999*******99****************9844 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 !   14.4   0.0   7.8e-06     0.017      22      95 ..      18      92 ..       5     122 .. 0.84
   2 !    7.4   0.0    0.0011       2.4     244     282 ..     325     363 ..     322     383 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 7.8e-06
                                  --BHHH.HHHHHHHHHHHHHHHHTT-EEEEEEEBB--SHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHHTT---- CS
                  tRNA-synt_1e 22 ashlGh.aRslvafDilrrilqalgYdvqfvqnvtDidDkiikrareeeksvkelaekfieefkkdleaLnvlkp 95
                                    h+Gh a +++  D++ r+ + +g +v +v+   +    i  ra++e+ks +e+a+++ +e+ + +++L++   
  gi|13542051|ref|NP_111739.1| 18 PLHVGHiAGAYLGADVFVRFNRLIGNEVLYVSGSDEYGTPITVRAEKEGKSPQEIADRYYAEHIETFKKLGINFD 92
                                  57***9667899**********************************************************99754 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0011
                                   E--EEETTBE--TTTT---BHHHHHTTS-HHHHHHHHHS CS
                  tRNA-synt_1e 244 nghlkiegekmsksLknfitikdvlkkfdprqlRlllls 282
                                   n++l+++ge+ sks +   t+ ++l+   p  lR++++s
  gi|13542051|ref|NP_111739.1| 325 NEYLTFKGEQFSKSRGIGYTVDELLRVIPPDYLRYYVAS 363
                                   6899********************************987 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 !   19.3   0.0     2e-07   0.00045     275     329 ..     329     382 ..     310     423 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 2e-07
                  tRNA-synt_1f 275 llkggekmssSkGnvltledwlevaepevlrflilrrkPkk.akkldldleilrlv 329
                                   +  +ge+ s+S+G + t++++l+v++p+ lr+++++  P++   +++l+ e+ ++v
  gi|13542051|ref|NP_111739.1| 329 TF-KGEQFSKSRGIGYTVDELLRVIPPDYLRYYVASILPETgDSDFSLE-ELVKTV 382
                                   44.4559*****************************9998635677777.554433 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 !   16.2   0.3   3.5e-06     0.008      10      99 ..     424     508 ..     415     528 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 3.5e-06
                   Anticodon_1  10 klvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedk.raaqevllevletllrllaPfmPfitEelw 89 
                                   ++ ke+ + + +  +++ ++   ++    +++ y++ ++p+   +++ d+ +   +v l++++ l+ +++Pf+P  +  +w
  gi|13542051|ref|NP_111739.1| 424 NAFKEYCDELSQVHIKRSLAIWLNL--AIYANSYFNKSEPWNLIKTDRDQcNYKLYVSLKLAQYLTAMIYPFTPTSAKAIW 502
                                   5555666666666666666666665..456899*********9999888844377************************** PP

                   Anticodon_1  90 qreeeelgkk 99 
                                       e+lg +
  gi|13542051|ref|NP_111739.1| 503 ----EQLGVN 508
                                   ....666554 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   2.6   0.00016      0.36      15      48 ..     145     175 ..     126     176 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00016
                           DZR  15 CseCgtklkavaaedrCpsCgekvdpearfCpeC 48 
                                   C++Cg k     + d+C++Cg+ +dp++ + p C
  gi|13542051|ref|NP_111739.1| 145 CPYCGYKKA---RGDQCDNCGRTLDPQELINPVC 175
                                   888888754...3788888888888887766666 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   1.2    0.0053        12      19      25 ..     145     151 ..     144     152 .. 0.85
   2 ?    3.5   0.4     0.022        50       4      15 ..     157     168 ..     154     171 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0053
                   zf-ribbon_3  19 CpyCGtk 25 
                                   CpyCG+k
  gi|13542051|ref|NP_111739.1| 145 CPYCGYK 151
                                   9999986 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.022
                   zf-ribbon_3   4 rCPnCGaplssd 15 
                                   +C nCG  l+++
  gi|13542051|ref|NP_111739.1| 157 QCDNCGRTLDPQ 168
                                   799999844776 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   1.8     0.008        18      16      22 ..     145     151 ..     142     152 .. 0.89
   2 ?    3.7   0.4     0.024        55       2      11 ..     158     167 ..     157     169 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.008
                 zinc_ribbon_2  16 CpyCGtp 22 
                                   CpyCG++
  gi|13542051|ref|NP_111739.1| 145 CPYCGYK 151
                                   9***996 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.024
                 zinc_ribbon_2   2 CpnCGaelqd 11 
                                   C nCG++l++
  gi|13542051|ref|NP_111739.1| 158 CDNCGRTLDP 167
                                   9999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (543 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       531  (0.0296168); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.21s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 4186.53
//
Query:       gi|13542052|ref|NP_111740.1|  [L=101]
Description: cationic amino acid transporter [Thermoplasma volcanium GSS1]
Scores for complete 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   42.9   3.3    2.6e-11   42.8   3.3    1.0  1  AA_permease  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 !   42.8   3.3   1.5e-15   2.6e-11       3      84 ..      19     101 .]      17     101 .] 0.98

  Alignments for each domain:
  == domain 1  score: 42.8 bits;  conditional E-value: 1.5e-15
                   AA_permease   3 lvialggviGtglfvglgvvlsqaGplgallayllagvviflvmlslgeiatngpksggfytyasrflgp.elGfviGlny 82 
                                   +++++g v +++ +  l v++ ++   +++l++++++++++l+m++ ++++ +++++g++y+yas ++++ +lG  ++l++
  gi|13542052|ref|NP_111740.1|  19 VFQSMGKVAPAADIAILLVATFSIADSKTILSVIFGWLIYALFMVTPYQFSKYKSNAGSYYAYASASTESgKLGPITALSF 99 
                                   799*******************************************************************9*********9 PP

                   AA_permease  83 lf 84 
                                   ++
  gi|13542052|ref|NP_111740.1| 100 MY 101
                                   87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       703  (0.0392102); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.47
# Mc/sec: 640.84
//
Query:       gi|13542053|ref|NP_111741.1|  [L=416]
Description: transposase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-19   70.4   0.7    2.6e-19   69.6   0.7    1.4  1  OrfB_IS605      Probable transposase
    3.3e-09   36.5   0.0    9.1e-09   35.1   0.0    1.8  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
     0.0027   17.1   0.5     0.0042   16.4   0.5    1.3  1  Glyco_hydro_97  Glycoside hydrolase 97
  ------ inclusion threshold ------
      0.032   13.8   0.4       0.32   10.6   0.1    2.0  2  DUF436          Protein of unknown function (DUF436)


Domain annotation for each model (and alignments):
>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.6   0.7   5.9e-23   2.6e-19       2     117 ..     172     289 ..     171     292 .. 0.93

  Alignments for each domain:
  == domain 1  score: 69.6 bits;  conditional E-value: 5.9e-23
                    OrfB_IS605   2 ipveveve.lpkpkgnkaagiDlGinnLatvvtedgtw.flykgrrlksdykylakeiaelqsklkksknykkasrklarl 80 
                                   i++e e+   p +k+++a giD+G++nL+t  ++  +  +  k+  lks ++y++ke a+  s+ + ++n +k++ k+++l
  gi|13542053|ref|NP_111741.1| 172 IVYEKETAdMPITKPKRAMGIDIGVRNLVTIGNNIHEIgIAVKAGLLKSINQYFNKELARYRSINDLQGNERKQTVKIRKL 252
                                   678877666899***********************8888778889************************************ PP

                    OrfB_IS605  81 hrkrsrrrkhllhklathliktlkevgvetLnvgnmk 117
                                   ++kr+r++k+ +hk++++++++ k ++++t+++g+  
  gi|13542053|ref|NP_111741.1| 253 FMKRNRKVKDIMHKVSKSIVEYAKIMNIDTIVIGHNN 289
                                   *********************************9876 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 !   35.1   0.0     2e-12   9.1e-09       1      69 []     310     384 ..     310     384 .. 0.87

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 2e-12
                OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknke.......alsgrtfkCpnCgfeadrDvnAaiNilkr 69 
                                   f+ l+ q++yka+e Gi+v+  n+ yTSk Cs    ++ e       ++ +r   +++ g  +++D+ +++Ni+k+
  gi|13542053|ref|NP_111741.1| 310 FNMLIYQIKYKAEEIGITVIMQNEDYTSK-CSFLDNESIEhhdtymgKRIHRGIFRSATGKLIHADLQSSYNIIKK 384
                                   788999**********************8.5544444444488899999999999999***************996 PP

>> Glyco_hydro_97  Glycoside hydrolase 97
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.5   9.3e-07    0.0042      30     110 ..     261     340 ..     237     389 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 9.3e-07
                Glyco_hydro_97  30 hgantetvkryiDfAaengleyvlvegwdegWee..kkkkekefdftkpypdfdleelvaYakekgvgvelwlhsetsgnv 108
                                   + +  +  k  +++A+ ++++++++ g ++ W++  ++ k+++++f++   ++ + ++   a+e g  +++++++e ++++
  gi|13542053|ref|NP_111741.1| 261 KDIMHKVSKSIVEYAKIMNIDTIVI-GHNNRWKDssNMGKKNNQNFVQLPFNMLIYQIKYKAEEIG--ITVIMQNEDYTSK 338
                                   5566777899***************.*******998888899999999999999998877677777..7777777665554 PP

                Glyco_hydro_97 109 an 110
                                    +
  gi|13542053|ref|NP_111741.1| 339 CS 340
                                   44 PP

>> DUF436  Protein of unknown function (DUF436)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   7.1e-05      0.32      81     144 ..     151     215 ..     142     233 .. 0.85
   2 ?    1.1   0.1     0.058   2.6e+02       4      70 ..     266     336 ..     263     354 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 7.1e-05
                        DUF436  81 aekleleevsvvPqlkaGGslataaykklkdpvvveeikadaGiDiGd...tliGmhlkkvavpvrl 144
                                    ++ +l+ev +vPq    G +   +y+k +  + + + k  +GiDiG    ++iG  ++++ + v+ 
  gi|13542053|ref|NP_111741.1| 151 ENEIKLKEVRIVPQ--GTGYMIEIVYEKETADMPITKPKRAMGIDIGVrnlVTIGNNIHEIGIAVKA 215
                                   45678999999997..5689999************************544478********999986 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.058
                        DUF436   4 ealeelleaaklkkgqilvvgcstsevlgekiGkasslevae....avleallevlkekgialavqcCEHl 70 
                                   ++ + ++e ak+ + + +v+g       ++++Gk+ +++  +    +++ +++  ++e gi++ +q  +  
  gi|13542053|ref|NP_111741.1| 266 KVSKSIVEYAKIMNIDTIVIGHNNRWKDSSNMGKKNNQNFVQlpfnMLIYQIKYKAEEIGITVIMQNEDYT 336
                                   6778899999999999*****99999999999999998887622224555566666778888888865555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (416 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1147  (0.0639746); expected 358.6 (0.02)
Passed bias filter:                      535  (0.0298399); 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 0.30s 00:00:00.92 Elapsed: 00:00:00.68
# Mc/sec: 1836.69
//
Query:       gi|13542054|ref|NP_111742.1|  [L=192]
Description: site-specific integrase-resolvase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.7e-15   56.8   0.2    3.9e-15   56.2   0.2    1.2  1  Resolvase      Resolvase, N terminal domain
    8.3e-05   22.7   0.0    0.00016   21.7   0.0    1.6  1  HTH_17         Helix-turn-helix domain
  ------ inclusion threshold ------
      0.012   15.7   0.4      0.034   14.2   0.3    1.8  2  MerR_1         MerR HTH family regulatory protein
      0.025   15.6   0.4      0.049   14.7   0.4    1.5  1  DUF4612        Domain of unknown function (DUF4612)
       0.18   11.6   1.5         26    4.7   0.0    3.1  3  TRAF_BIRC3_bd  TNF receptor-associated factor BIRC3 binding d


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 !   56.2   0.2   1.1e-18   3.9e-15       2     137 ..      56     186 ..      55     189 .. 0.91

  Alignments for each domain:
  == domain 1  score: 56.2 bits;  conditional E-value: 1.1e-18
                                   EEEEEES-----THHHHHHHHHHHH-S--..SE...EEEE.S-TT-TT.-HHHHHHHHHHTT-EE.EEEESSCCCC-S... CS
                     Resolvase   2 igYaRvSteeqddslerQkealrayakenglkivkefeDkgvSGakle.RpglkrllaalregkgdvlvvekldRLaRsvr 81 
                                   ++Y RvSt++q+++l++Q    ++ +  ng++i +++    +SG +le R+g+ ++l+++ ++k++ ++++  dRL+R  +
  gi|13542054|ref|NP_111742.1|  56 VLYERVSTAKQKNDLQNQ---MKQXCFMNGYTISAIYAHI-ASGISLEkRKGFFEMLDEIINNKVEKVIITYKDRLSRVGF 132
                                   79**********899998...67889999****9999999.*****988*************9****************** PP

                                   S-HHHHHHHHHTT-EEEESS..SS----HHHHHHHHHHHHHHHHHHHHHCT-TTHH CS
                     Resolvase  82 dlltlleelrekgvslvsldegidtstpmgrlllqilaalaeferelirertkegl 137
                                   dl+++   +r+ + ++ +++e  +t+ ++ +++ +i+++l  +  ++ ++r ++ +
  gi|13542054|ref|NP_111742.1| 133 DLFSY--LFRKYRTEIAVISEVGNTKLDSEEVFEEIVSMLHSYSMKMYSKRKNHYI 186
                                   ****9..6788888888888778999999******************999998776 PP

>> HTH_17  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   4.6e-08   0.00016       2      49 ..       1      49 [.       1      51 [. 0.89

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 4.6e-08
                        HTH_17  2 ltveEaAelLgvsrstvyrlirrgelpaa.kiGrrwriprsdleewlek 49
                                  ++ eE+ +lL +sr+t++ + ++g+++++   ++r+ + ++d+ + l+k
  gi|13542054|ref|NP_111742.1|  1 MKAEEVLNLLQISRKTLHVYSKDGRIRYTvMPNKRYNYNEEDVYKILNK 49
                                  788***********************999636677*******9999887 PP

>> MerR_1  MerR HTH family regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.3   9.5e-06     0.034       1      46 [.       1      46 [.       1      48 [. 0.91
   2 ?   -2.4   0.0       1.5   5.3e+03      55      63 ..      81      89 ..      76      94 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 9.5e-06
                                  EEHHHHHHHHTS-HHHHHHHHHHTT-S-EE-TTS-EEEEHHHHHHH CS
                        MerR_1  1 ysigevakilgvtthtlrywekegllkpkrteggrryYtdedierL 46
                                  ++  ev ++l+++ +tl+ + k g ++     + r+ Y++ed+  +
  gi|13542054|ref|NP_111742.1|  1 MKAEEVLNLLQISRKTLHVYSKDGRIRYTVMPNKRYNYNEEDVYKI 46
                                  6678999***********************88888*******9876 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.5
                                  TT--GGG-- CS
                        MerR_1 55 rGltlkgik 63
                                  +G+t+++i 
  gi|13542054|ref|NP_111742.1| 81 NGYTISAIY 89
                                  699999985 PP

>> DUF4612  Domain of unknown function (DUF4612)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.4   1.4e-05     0.049      30     105 ..      41     114 ..      18     118 .. 0.64

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.4e-05
                       DUF4612  30 adeykiktvekvkylkseekelesreqeNkddeksalslakkkpkseaas.ngkklsihiSeSQqeFFrMLDeKIek 105
                                   +d yki + + vk  +  ++++++ +q+N    +  +++    +   +++   +++s  + e  + FF+MLDe I++
  gi|13542054|ref|NP_111742.1|  41 EDVYKILNKD-VKRKTVLYERVSTAKQKND--LQNQMKQXCFMNGYTISAiYAHIASGISLEKRKGFFEMLDEIINN 114
                                   4456665544.6666667888888888887..2333333333333333332334555555588999*******9986 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 ?    1.0   0.1       0.1   3.7e+02      17      42 ..      41      66 ..      27      76 .. 0.75
   2 ?    3.2   0.1     0.021        74       9      34 ..      98     123 ..      95     129 .. 0.90
   3 ?    4.7   0.0    0.0071        26      14      24 ..     161     171 ..     154     173 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.1
                 TRAF_BIRC3_bd 17 EnIVsVLnrEverssttieaverqrr 42
                                  E +  +Ln+ v r  +  e v+  ++
  gi|13542054|ref|NP_111742.1| 41 EDVYKILNKDVKRKTVLYERVSTAKQ 66
                                  55667899999998887777665444 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.021
                 TRAF_BIRC3_bd   9 LetkvatFEnIVsVLnrEversstti 34 
                                   Le++ + FE    + n  ve++++t 
  gi|13542054|ref|NP_111742.1|  98 LEKRKGFFEMLDEIINNKVEKVIITY 123
                                   99*******************99886 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.0071
                 TRAF_BIRC3_bd  14 atFEnIVsVLn 24 
                                   ++FE IVs L+
  gi|13542054|ref|NP_111742.1| 161 EVFEEIVSMLH 171
                                   69*******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1215  (0.0677673); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); 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: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 1187.67
//
Query:       gi|13542055|ref|NP_111743.1|  [L=317]
Description: amino acid transporter [Thermoplasma volcanium GSS1]
Scores for complete 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-46  157.5  26.6    4.8e-46  157.3  26.6    1.0  1  AA_permease    Amino acid permease
    3.5e-18   65.6  29.2    4.7e-17   61.9  14.9    2.0  2  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 !  157.3  26.6   5.4e-50   4.8e-46     180     478 ..      25     304 ..       1     305 [. 0.92

  Alignments for each domain:
  == domain 1  score: 157.3 bits;  conditional E-value: 5.4e-50
                   AA_permease 180 sifknnlppgfakeeegafknfisvfvivvfaftGielvaiiagEvkdPeksiPkailqvviritifYvlsllligllvpr 260
                                   s            + ++ f++++++ ++++++ftG++ v+++++E+++P+k+i ++i +++i+++i+ + ++++++++++ 
  gi|13542055|ref|NP_111743.1|  25 S-IPT--------NLGVGFSAIMFGSIFSILDFTGTGVVTTVSEEMREPKKNIGRSIVYAMILTAISIIPATYALTVGWGI 96 
                                   2.333........45566*************************************************************** PP

                   AA_permease 261 ndlgllndsasaaspfvifikesgvsvlaplinaviltaalssansslysasRvlyslakdglaP.kvlkkvskrgvPlra 340
                                   ++ +++++s +a  ++++f k++g +++  li+++i +++++ ++ +++++++++ + ++  ++P ++ k++sk+++P+ a
  gi|13542055|ref|NP_111743.1|  97 SNISSFASSPDA--GIIVFEKYLGPIGAVLLIIFTINSYLTNGVSKATAIGRWWYSAASDGIVFPkRFSKVHSKYKSPYYA 175
                                   ************..***************************************************999999********** PP

                   AA_permease 341 illsmiisllalllaslnlaapivfnfllaisaliglivwlliilsylrfRkalkyqgrsieelgfkaallplgvilvlaa 421
                                   il +++ s+++ ++++l+++++i+  +l a ++++++iv++++++s++       +++r+i+++ f  + l   + +v+ +
  gi|13542055|ref|NP_111743.1| 176 ILTWSVSSFALDVIMGLYFGPKIAAFILEAGTGISIIIVHIMANTSLT-------LYTRRIDRFHFLKHALAPAFATVISL 249
                                   ************************************************.......9************************* PP

                   AA_permease 422 liiillilalyayltvkkgpkdwgaasfaaaylivllfliilvgvklhvknkrpqll 478
                                   ++ +++i +++   ++ + p  ++ a+fa++++++l++++ +++v+l++++k+p +l
  gi|13542055|ref|NP_111743.1| 250 VVVYFTISDIW--SKWVTHPNPVNDAYFASFIITLLWVIVGGLIVTLYYSRKKPNVL 304
                                   ***********..66669***********************************9876 PP

>> AA_permease_2  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.9  14.9   5.3e-21   4.7e-17     156     340 ..       3     191 ..       1     203 [. 0.86
   2 !    8.6   7.4   8.2e-05      0.73     119     212 ..     205     298 ..     194     307 .. 0.80

  Alignments for each domain:
  == domain 1  score: 61.9 bits;  conditional E-value: 5.3e-21
                 AA_permease_2 156 liiliilglitvdgggfssl.stetdtffpngwpgvllgllivlwsfdGfesaanvseevkk..kdvpkaifigllivlvl 233
                                   ++++ ++ +i+  g+g+s +   + ++   +++ +++++++ +++ f+G  +++ vsee+++  k++ + i++++++++++
  gi|13542055|ref|NP_111743.1|   3 FLLIGAVIIIIKVGNGNSLEpFSIPTNLGVGFSAIMFGSIF-SILDFTGTGVVTTVSEEMREpkKNIGRSIVYAMILTAIS 82 
                                   44555555555566666655544444666778888999999.789**************8866489*************** PP

                 AA_permease_2 234 yllvniaflgvvpddeianlsnlgsvaalffeavggkvvaiivvilialsllgaintavigssrvlealardgvlP.rffa 313
                                    +  + a++ + ++++i++ +++++++ ++fe++ g+++a++++i+++ s l ++ +  +++ r  +++a dg+   ++f+
  gi|13542055|ref|NP_111743.1|  83 IIPATYALTVGWGISNISSFASSPDAGIIVFEKYLGPIGAVLLIIFTINSYLTNGVSKATAIGRWWYSAASDGIVFpKRFS 163
                                   *************************************************************************8666**** PP

                 AA_permease_2 314 kvn.kfgspiraiiltaivslillllfl 340
                                   kv+ k++sp++ai +  + s++l +++ 
  gi|13542055|ref|NP_111743.1| 164 KVHsKYKSPYYAILTWSVSSFALDVIMG 191
                                   *************999888877766654 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 8.2e-05
                 AA_permease_2 119 yliaiaililvalinirgikesakiqnilgilkillpliiliilglitvdgggfsslstetdtffpn...gwpgvllglli 196
                                    + +i i+i++++ n   +  +++i  + ++ + l p +++ ++ l++v +++++    ++++++++   +++ +++++ i
  gi|13542055|ref|NP_111743.1| 205 AGTGISIIIVHIMANTSLTLYTRRIDRFHFLKHALAP-AFATVISLVVVYFTISD----IWSKWVTHpnpVNDAYFASFII 280
                                   5779******************************877.9**********999998....8*******44555557998888 PP

                 AA_permease_2 197 .vlwsfdG.fesaanvse 212
                                     lw+++G   +  ++s+
  gi|13542055|ref|NP_111743.1| 281 tLLWVIVGgLIVTLYYSR 298
                                   456666550444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       815  (0.0454571); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.50
# Mc/sec: 1905.19
//
Query:       gi|13542056|ref|NP_111744.1|  [L=61]
Description: DNA-directed RNA polymerase subunit K [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.1e-13   49.9   0.1    2.7e-13   49.6   0.1    1.2  1  RNA_pol_Rpb6  RNA polymerase Rpb6


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb6  RNA polymerase Rpb6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.6   0.1   1.5e-17   2.7e-13       8      49 .]       4      51 ..       1      51 [. 0.84

  Alignments for each domain:
  == domain 1  score: 49.6 bits;  conditional E-value: 1.5e-17
                                  -HHHHHHHHHHHHHHH....HT.........SS-..SSSSTTCHHHHTT-S-- CS
                  RNA_pol_Rpb6  8 trYelvriaakRArQieegesl.........etq..kpvviAlrEiaegkipi 49
                                  t++e++ri+++RA+Qi     +           +  +pv+iA+ E +++ ipi
  gi|13542056|ref|NP_111744.1|  4 TKFEKARIIGARALQI----AMgapviidipK-NviDPVDIATIEFENNVIPI 51
                                  9***************....666666666642.347***************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       316  (0.0176251); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); 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: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 399.35
//
Query:       gi|13542057|ref|NP_111745.1|  [L=145]
Description: hypothetical protein TVN1226 [Thermoplasma volcanium GSS1]
Scores for complete 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-42  144.1   6.4    2.7e-42  144.0   6.4    1.0  1  UPF0179        Uncharacterised protein family (UPF0179)
  ------ inclusion threshold ------
      0.025   13.5   0.0      0.025   13.5   0.0    1.1  1  Peptidase_M35  Deuterolysin metalloprotease (M35) family


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 !  144.0   6.4     3e-46   2.7e-42       1     140 []       3     142 ..       3     142 .. 0.97

  Alignments for each domain:
  == domain 1  score: 144.0 bits;  conditional E-value: 3e-46
                       UPF0179   1 kitLigkklAkeGteFiylgeaeeCekCklkkvClnLekgrkYrivevrekteheCavheeg.vvaveveeapiealie.s 79 
                                   ki+Ligk+lAkeG eF++ g++++C++C++k+vC+nLe+g+kYr+++vre+  ++C +++++ v++vevee++  ++i+ s
  gi|13542057|ref|NP_111745.1|   3 KISLIGKDLAKEGIEFVFAGPLPTCSDCRVKNVCFNLEQGHKYRVTKVREQ-LNPCIIFNGDkVNTVEVEELEDFFIIQeS 82 
                                   69*************************************************.*********99*********999888779 PP

                       UPF0179  80 kkavegskitleseeCdevecesyelcepeglkegekvkivevlgeieeckkgrslkkvel 140
                                   kk++eg+ +t++s++Cd+++c+++e+c+  + k++ kv i+++ ++++ c+kg ++kkv++
  gi|13542057|ref|NP_111745.1|  83 KKLQEGAIVTMKSMNCDYITCPNIEKCNLYYQKNDLKVAIKSIGQNVN-CPKGFKMKKVQV 142
                                   ******************************************999999.*********985 PP

>> Peptidase_M35  Deuterolysin metalloprotease (M35) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   2.7e-06     0.025      98     159 ..      64     124 ..       4     143 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.7e-06
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                 Peptidase_M35  98 alttlaaGetledefdiastsdlseGGavtirsdGfvpivtdgkvtGyipyksneleievda 159
                                    + t++  e led f i  +  l eG  vt++s     i+  +     + y+ n+l++ + +
  gi|13542057|ref|NP_111745.1|  64 KVNTVE-VEELEDFFIIQESKKLQEGAIVTMKSMNCDYITCPNIEKCNLYYQKNDLKVAIKS 124
                                   455554.4789********************************99*************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       732  (0.0408277); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 998.31
//
Query:       gi|13542058|ref|NP_111746.1|  [L=352]
Description: NAD(P)-dependent glycerol-1-phosphate dehydrogenase [Thermoplasma volcanium GSS1]
Scores for complete 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-66  222.4   0.9    9.1e-66  222.1   0.9    1.1  1  Fe-ADH_2      Iron-containing alcohol dehydrogenase
    6.5e-22   77.8   1.1    4.8e-21   75.0   1.1    2.0  1  Fe-ADH        Iron-containing alcohol dehydrogenase
    1.7e-07   30.7   0.0    7.9e-05   21.9   0.2    2.9  2  DHQ_synthase  3-dehydroquinate synthase
  ------ inclusion threshold ------
       0.15   11.7   0.0       0.24   11.1   0.0    1.3  1  Cucumo_coat   Cucumovirus coat protein
       0.18   10.5   0.0       0.24   10.1   0.0    1.1  1  HSNSD         heparan sulfate-N-deacetylase


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 !  222.1   0.9   2.5e-69   9.1e-66       2     249 ..      17     273 ..      16     274 .. 0.85

  Alignments for each domain:
  == domain 1  score: 222.1 bits;  conditional E-value: 2.5e-69
                      Fe-ADH_2   2 igegaleklgellkele.lkkvllvadentkkaagekveeslkeagikvevveeveeeadleeveklvealreketdlvva 81 
                                   ig+++l+++ +++ +++  ++v++v++++t+++ag+k+ e l+++ ++v++   +++ea+ e+ +k+ e+ +  ++ ++++
  gi|13542058|ref|NP_111746.1|  17 IGHDVLNRVLDVVDQNSrTRDVIIVTGNTTYELAGKKIVEILASSPYEVHLS--FAGEANYENLKKIEEETNDVNAGIIIG 95 
                                   899***********996267*****************************943..89************************* PP

                      Fe-ADH_2  82 vGgGtiiDiakyvsaklnvpyvsvpTaaSvDGfaspgaslvvdgkkrtvakaaaPlaviaDldvlaeAPrrllasGvGDll 162
                                   vGgGt iD+ak +++ +n+p++s+pT++S+DG+asp asl+++g   +  + a+P++viaD++v+ +AP r la+G +D++
  gi|13542058|ref|NP_111746.1|  96 VGGGTKIDLAKKLAYDKNLPFISIPTSPSHDGIASPRASLRRNGISYS-EEGAMPIGVIADTSVMIKAPYRYLAAGAADVI 175
                                   ********************************************7776.699***************************** PP

                      Fe-ADH_2 163 gkytaladwklan........evseplaklsaamvqeaaeklve.dkke.tealeellea.lalsgigisrpaSGsEHliS 232
                                   ++++a++dwkla+        + ++ +++ sa++v +++ ++ + d+ +   +++++l +  a++++g srp+SGsEHl++
  gi|13542058|ref|NP_111746.1| 176 SNISAVKDWKLAHrlrgeefsSSAAAMSEYSAQEVISQVGEIRKyDESSvWLVTKNILASgTAMAIAGNSRPGSGSEHLFA 256
                                   *************65555332223344444444444444444443333322333444443269999*************** PP

                      Fe-ADH_2 233 HaldmlalkqalHGeqV 249
                                   Hal+++  ++ lHGe +
  gi|13542058|ref|NP_111746.1| 257 HALEAAGVNNMLHGEMC 273
                                   ******99******987 PP

>> Fe-ADH  Iron-containing alcohol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.0   1.1   1.3e-24   4.8e-21       1     337 [.      12     312 ..      12     331 .. 0.76

  Alignments for each domain:
  == domain 1  score: 75.0 bits;  conditional E-value: 1.3e-24
                                   -SEEEEETTGGGGHHHHHTTT-...EEEEEEEHHHH.HH.THHHHHHHHHCTT-EEEE.EEE-S---HHHHHHHHTTS-TT CS
                        Fe-ADH   1 Ptrivfgkgaleelgellkklg.akralivtdkgslkksglldkvlesleeagievtvfdgvepnptleeveeaaalaree 80 
                                   P+ +++g ++l+++ + +++   ++ ++ivt++ ++ ++ + +k++e l  a   ++v+  + ++  +e+++++ +  ++ 
  gi|13542058|ref|NP_111746.1|  12 PRDVYIGHDVLNRVLDVVDQNSrTRDVIIVTGNTTY-EL-AGKKIVEIL--ASSPYEVHLSFAGEANYENLKKIEEETNDV 88 
                                   889***************999646789999999987.65.899******..99999999********************** PP

                                   .--EEEEEESHHHHHHHHHHHHHTT..................--EEEEESS-S-S-TT-SEEEEE.-TTSEEEEE-..SS CS
                        Fe-ADH  81 gadvviavGGGsviDtAKaialllanpevedylgegkakkkkalpliaiPTtaGtGsevtplavitdeeegeklsifdpel 161
                                   +a ++i+vGGG+ iD+AK +a+  +                  lp+i iPT ++ +  ++p a +        +s++++  
  gi|13542058|ref|NP_111746.1|  89 NAGIIIGVGGGTKIDLAKKLAYDKN------------------LPFISIPTSPSHDGIASPRASLR-R---NGISYSEEGA 147
                                   *********************9999..................***********************.3...44899999** PP

                                   --SEEEEEHHHHHHS-HHHHHHHHHHHHHHHHHHHHHH........T---TTS...SB--HHHHHHHHHHHHHHHHHHHH. CS
                        Fe-ADH 162 lPdlaivDpeltltlPkrvtaatglDalahalEayvsk........kanplsd...alaleairliaknleravadgedl. 230
                                   +P  +i D+ +++++P r++aa+++D+++        k        +   +s    a+++++++ ++  + ++ +  e+  
  gi|13542058|ref|NP_111746.1| 148 MPIGVIADTSVMIKAPYRYLAAGAADVISNISAVKDWKlahrlrgeE---FSSsaaAMSEYSAQEVISQVGEIRKYDESSv 225
                                   *****************************998774445333443222...2222224555555555555555555443224 PP

                                   ..HHHHHHHHHHHHHHHHHHSS---HHHHHHHHHHC.CGGG...GGS-HHHHHHHHH..........HHHHHHT....... CS
                        Fe-ADH 231 ..eareqmllastlaglafsnaglgavHalahalgalfgip...hglanaillpavlrfnaeaaperlaqlaralggesde 306
                                          ++ +  +a  + s  g g  H +ahal a  g+    hg+++a+    ++          ++ l          
  gi|13542058|ref|NP_111746.1| 226 wlVTKNILASGTAMAIAGNSRPGSGSEHLFAHALEA-AGVNnmlHGEMCAM----GT----------IVSLYLH------- 284
                                   5488888888888899999999999*********99.55543336666655....44..........3333333....... PP

                                   T--HHHHHHHHHHHHHTT---SHHHHT-TT- CS
                        Fe-ADH 307 eaaeeliealrellkelglptsLselgvdee 337
                                      ++  +++r+++++lg+ ++ +++g++ee
  gi|13542058|ref|NP_111746.1| 285 ---DDNWQKIRDVFESLGVSVKARDYGLKEE 312
                                   ...3444455555555555555555555553 PP

>> DHQ_synthase  3-dehydroquinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.0   0.0    0.0068        24      32      65 ..      91     122 ..      72     126 .. 0.81
   2 !   21.9   0.2   2.2e-08   7.9e-05      94     244 ..     148     306 ..     145     322 .. 0.68

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.0068
                                   -EEEEEESHHHHHHHHHHHHHBTT--EEEEEE-S CS
                  DHQ_synthase  32 sllialGGGvvgDlaGfvAatylRGvrfvqvPtt 65 
                                    ++i +GGG+  Dla   A  y + + f+ +Pt+
  gi|13542058|ref|NP_111746.1|  91 GIIIGVGGGTKIDLAKKLA--YDKNLPFISIPTS 122
                                   5799***********9887..8999999999997 PP

  == domain 2  score: 21.9 bits;  conditional E-value: 2.2e-08
                                   --SEEEEEGGGGGGS-HHHHHHHHHHHH.HHHHHT-HHHHHHHHHHHHHHHC.TTTHHHHHHHH..........HHHHHHH CS
                  DHQ_synthase  94 qPkavlidlevLktLperelraGlaEvi.Kyalikdeelfelleenaeallk.eeeeealeeli..........arsievk 162
                                   +P  v++d++v+   p r l+aG a+vi  ++++kd +l ++l+ ++ ++ + + +e +++e+i          +      
  gi|13542058|ref|NP_111746.1| 148 MPIGVIADTSVMIKAPYRYLAAGAADVIsNISAVKDWKLAHRLRGEEFSSSAaAMSEYSAQEVIsqvgeirkydE----SS 224
                                   6889***********************9447899*********98887776643344555555533333333222....22 PP

                                   HHHHHHCCTTTTGGGG........GGTTHHHHHHHHHHHTTTTS-HHHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHH CS
                  DHQ_synthase 163 aevveeDekekglral........LnlGHtigHaiEallgyekllHGeaVaiGmvlaaelseklgllkkeeverllkllkk 235
                                      v+++   +g+ ++            H ++Ha+Ea+    ++lHGe  a+G ++ ++l        +++ +++++++++
  gi|13542058|ref|NP_111746.1| 225 VWLVTKNILASGTAMAiagnsrpgSGSEHLFAHALEAAGVN-NMLHGEMCAMGTIVSLYLH-------DDNWQKIRDVFES 297
                                   2345555555555444222222115566********98665.*************999887.......3445666666666 PP

                                   TT---STTT CS
                  DHQ_synthase 236 lglpvslke 244
                                   lg+ v+ ++
  gi|13542058|ref|NP_111746.1| 298 LGVSVKARD 306
                                   666666555 PP

>> Cucumo_coat  Cucumovirus coat protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   6.6e-05      0.24      70     144 ..     213     284 ..     196     315 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 6.6e-05
                                   EEEE-TT--.SEEEEEEEE-CTTTS-SSSHHHHHSTSS--EEEE-BSTTTSS-S.EEEEEGCCCTE......... CS
                   Cucumo_coat  70 ivntltksdleqlWltvkklPkvsdllveaisamdGlsnvlvqqrallavdannvklltdlsamraeptlqtwlk 144
                                   +v+ + k+d + +Wl +k++ ++   +  a ++  G  +  ++ +al a   nn  l  ++ am    +l  +l+
  gi|13542058|ref|NP_111746.1| 213 QVGEIRKYDESSVWLVTKNILASGTAMAIAGNSRPGSGSEHLFAHALEAAGVNN-MLHGEMCAMGTIVSL--YLH 284
                                   6999******************99999888888888888888999*********.899999999885444..333 PP

>> HSNSD  heparan sulfate-N-deacetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   6.8e-05      0.24      56      99 ..      28      72 ..       4      94 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 6.8e-05
                         HSNSD 56 kaekklrtdpkvLvlveslysqlgkeiveilessrfkykveia.k 99
                                   +++++rt ++++v  +++y   gk+iveil ss ++ +  +a +
  gi|13542058|ref|NP_111746.1| 28 VVDQNSRTRDVIIVTGNTTYELAGKKIVEILASSPYEVHLSFAgE 72
                                  4678999**************************999988877753 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (352 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       492  (0.0274416); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); 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: 0.62u 0.31s 00:00:00.93 Elapsed: 00:00:00.49
# Mc/sec: 2167.74
//
Query:       gi|13542059|ref|NP_111747.1|  [L=289]
Description: dihydrodipicolinate synthetase [Thermoplasma volcanium GSS1]
Scores for complete 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-56  189.5   0.0    5.8e-56  189.3   0.0    1.0  1  DHDPS     Dihydrodipicolinate synthetase family


Domain annotation for each model (and alignments):
>> DHDPS  Dihydrodipicolinate synthetase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  189.3   0.0   3.2e-60   5.8e-56       2     285 ..       2     284 ..       1     288 [. 0.95

  Alignments for each domain:
  == domain 1  score: 189.3 bits;  conditional E-value: 3.2e-60
                                   -SEEEEE----B-TTSSB-HHHHHHHHHHHHHCT-SEEEESSCCCTGGGS-HHHHHHHHHHHHHHHTTSSEEEEE---SSH CS
                         DHDPS   2 fsgiitalvtpfdedgkldkealrklieflinkgvdglvvaGttGEsatlsteekeqlveiaveaakgripviagvGsnst 82 
                                    +gi+t+++tpf+++g++d  a r li+ l   gv+gl+ +G+tG +++ s+ee+++ ++ +  +  ++  v+agvGs st
  gi|13542059|ref|NP_111747.1|   2 YNGIVTPMLTPFNRAGEIDYDATRLLIQDLKGYGVSGLFPMGSTGLFPMFSLEERKKFLQFVS-ENRNNLTVYAGVGSSST 81 
                                   579******************************************************999865.56789************ PP

                                   HHHHHHHHCCCCCT-SEEEEE---SS---HHHHHHHHHHHHHCHSS-EEEEE-HHHHSHHHHHHHHHHHHT.STTEEEEEE CS
                         DHDPS  83 seaiklakkaeeaGadgvlavtPYYnkpsqeglyqhfkaiieatdlpvilYnvpsrtgadlspetvkrLae.lenivgvKe 162
                                   +e+i+l+k  e++G++  ++++ YY kp  e +y+hf ++i+a ++ + +Yn+p+++g+ +  +++k+L    +++ g+K+
  gi|13542059|ref|NP_111747.1|  82 QESIELSKFTEDVGIEVRVLMPTYYIKPDEEWMYKHFSEVISASSNDLFIYNIPQLAGSWVPENVIKKLKSeFSQVKGIKD 162
                                   *********************************************************************988********* PP

                                   -SS-CTHHHHHHCCCSTTSEEEES-GGGHHHHHHTT-SEEEESCHHCHHHHHHHHHHHHHTT-HHHHHHHH.HHHHHHHHH CS
                         DHDPS 163 avgdleevikikkevgkdlviysGddelllsalslGadGvisvtsniagermrqlikalkeGdlaeaaeln.ekllpliki 242
                                    +gd++   +i+  v+kd++++ G+d+lll  + lGa+G +   sni g +  +l+ka + Gdl++ +e++ +k++pl+ +
  gi|13542059|ref|NP_111747.1| 163 SSGDMRFFSRIVTLVSKDFSVFQGQDDLLLTSMALGANGGVCGLSNISGSI-VDLYKAFQSGDLKKSREIQlNKVNPLMYA 242
                                   ***********************************************9976.68*************9998689******* PP

                                   CCCCSCCHHHHHHHHCTTSSSBB.--TTS--S-HHHHHHHHHH CS
                         DHDPS 243 lfaepnvilvktalellGlvveatlrkPltpleeeekeeleal 285
                                   + a +++++  +a +      +   r+P+++ ++e+   + ++
  gi|13542059|ref|NP_111747.1| 243 VNAPTFPSGYYYAFYKKHNINGG-YRSPMVQPSKEHSRVIDEA 284
                                   ************99888777777.7*******99998776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       401  (0.022366); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 1960.40
//
Query:       gi|13542060|ref|NP_111748.1|  [L=324]
Description: hypothetical protein TVN1229 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00017   21.6   5.9    0.00017   21.6   5.9    2.7  3  DsbD_2    Cytochrome C biogenesis protein transmembrane regio


Domain annotation for each model (and alignments):
>> DsbD_2  Cytochrome C biogenesis protein transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.2     0.019   3.3e+02     121     162 ..      20      62 ..      10      81 .. 0.80
   2 !   21.6   5.9   9.6e-09   0.00017      36     189 ..      82     231 ..      66     256 .. 0.84
   3 ?   -1.1   0.3     0.082   1.5e+03      67      85 ..     280     298 ..     238     318 .. 0.45

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.019
                        DsbD_2 121 alllGllnGllpCglvysa.lllalasgsaleGalvmlaFgLG 162
                                   ++llG+++G+ p    +++ + +a+   s  +Ga + l+F+ G
  gi|13542060|ref|NP_111748.1|  20 SYLLGIVHGITPDEHTWPItFSYAVGNYSTKGGAKAGLVFSAG 62 
                                   6899999999998777764167888899999999999999887 PP

  == domain 2  score: 21.6 bits;  conditional E-value: 9.6e-09
                        DsbD_2  36 llynlGRilsYallGalvgllgsvlqlageleglrallgvllgllllllglklllkkkllklerlgkllsrllkklakklk 116
                                   ++y+    + Y+++Ga+++l g  ++   + ++++++   l  ++++    k   +++ l+le++++ +      + +   
  gi|13542060|ref|NP_111748.1|  82 MFYTYFNSIVYVIVGAVMALSGFYIANKLKYPHIHIIEESLYRIFGIH---KHNKEREKLELEHMENPVMVNEDGVYRP-V 158
                                   5666667789***************99999999999999999999997...5556777889999999999999999986.6 PP

                        DsbD_2 117 slasalllGllnGllpCglvysalllalasgsaleGalvmlaFgLGTlpalllfglllgllskklrkkllrla 189
                                    ++ a++ Gl+ G+ + ++ + ++++++    +  G l  l+FgLGT+ + +l+g+l+gl+ +k +   ++ +
  gi|13542060|ref|NP_111748.1| 159 PTKLAFVHGLIAGFGFGAFALIIYFVIAPNMPIYLGFLPGLMFGLGTMTMQVLAGTLFGLWLSKKKDLTVNGI 231
                                   8999*****************************************************9997665554443322 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.082
                        DsbD_2  67 eglrallgvllgllllllg 85 
                                    gl  +l vl +l++ +lg
  gi|13542060|ref|NP_111748.1| 280 LGLPFFLVVLSVLVIGYLG 298
                                   2233333333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (324 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       952  (0.0530983); 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:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.64u 0.29s 00:00:00.93 Elapsed: 00:00:00.49
# Mc/sec: 1980.53
//
Query:       gi|13542061|ref|NP_111749.1|  [L=304]
Description: ribonuclease Z [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-20   74.0   0.0      5e-10   39.2   0.0    2.1  2  Lactamase_B_2  Beta-lactamase superfamily domain
    2.9e-06   27.4   0.0    1.9e-05   24.7   0.0    2.1  2  Lactamase_B    Metallo-beta-lactamase superfamily
    2.8e-05   23.7   0.0    5.3e-05   22.8   0.0    1.4  1  Lactamase_B_4  tRNase Z endonuclease
      0.004   16.3   0.1     0.0064   15.6   0.1    1.2  1  PDEase_II      cAMP phosphodiesterases class-II


Domain annotation for each model (and alignments):
>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.0   0.0   9.3e-12   4.2e-08       4     113 ..      36     140 ..      35     167 .. 0.82
   2 !   39.2   0.0   1.1e-13     5e-10     132     201 .]     199     268 ..     169     268 .. 0.91

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 9.3e-12
                                   EES--TTHHHH.HTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCC.....C--EEEEEEEEHHHHHHCCTTCGHHH CS
                 Lactamase_B_2   4 LiDagpdlrqq.alralqPvelrdelppidaVllthaHyDHlaglltlre.....lrpkklplyapkgvlavleanfvyla 78 
                                   L+D+g ++ +q +++++       ++ +id +++th H DH+ gl  l +      r k+l++++p+g + ++++ +    
  gi|13542061|ref|NP_111749.1|  36 LFDCGEGTQKQiMKSKW-------SFMSIDNIFITHFHGDHFLGLIGLVQsmsfnNRTKDLNIFGPRGAIGIISNAINIGY 109
                                   89*****9989877777.......799***********************9886544444****************99888 PP

                                   CHTTTTEEEEEE-TTSEEEECSTTEEEEEEEE-EE CS
                 Lactamase_B_2  79 leeepavnvheldwgesfelgdggleitatparhk 113
                                       +++nv el+++++ +lg++ l+ t+     +
  gi|13542061|ref|NP_111749.1| 110 YTLRFRINVYELEPDKTYDLGKFLLKTTL----ND 140
                                   888899**************966544333....33 PP

  == domain 2  score: 39.2 bits;  conditional E-value: 1.1e-13
                                   CTTEEEEEESS-S---HHHHHHHCT-SEEEEE-S-SSTTHHHH.HHT---STSHHHHCTTSSSSEEEEESB CS
                 Lactamase_B_2 132 gggkrvyyigDtgyipeeigerlggadllllditayeddemir.hmgHltpeeaveaaadlgakrlvliHi 201
                                   ++g++++y+gDt+ ++++++   + ad+l++d t  ++ e+   + gH++ ++a+++a+d+g++rl+l H+
  gi|13542061|ref|NP_111749.1| 199 RKGRKIVYTGDTKPMQKMAD-FAKHADVLIHDTTTDSSFEPAVnQFGHSSAKQAARIARDAGVSRLFLYHY 268
                                   479*************8865.9999*******998888887779**************************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 !   24.7   0.0   4.3e-09   1.9e-05      19      67 ..      36      79 ..      29     142 .. 0.90
   2 ?    0.3   0.0      0.13   5.9e+02     142     162 ..     201     221 ..     197     267 .. 0.68

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 4.3e-09
                                  EES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTH CS
                   Lactamase_B 19 LiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglvea 67
                                  L+D+G +t+++ ++      ++    +d +++TH+H DH+ gl glv+ 
  gi|13542061|ref|NP_111749.1| 36 LFDCGEGTQKQIMK-----SKWSFMSIDNIFITHFHGDHFLGLIGLVQS 79
                                  899*********98.....699999********************9975 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.13
                                   TCCEEEECTTTSSHHCCCCCC CS
                   Lactamase_B 142 ggkvlftGDallagetgridl 162
                                   g+k+++tGD+ +  + +++ +
  gi|13542061|ref|NP_111749.1| 201 GRKIVYTGDTKPMQKMADFAK 221
                                   789999**9987666665555 PP

>> Lactamase_B_4  tRNase Z endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0   1.2e-08   5.3e-05      11      56 ..      22      66 ..      15      72 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 1.2e-08
                 Lactamase_B_4 11 sgPlllLqldskrYlfGkvgEgtQRavneqkvrlsklesiFLtgkv 56
                                  + P + +q+d+   lf ++gEgtQ+ ++++k ++  +++iF+t+ +
  gi|13542061|ref|NP_111749.1| 22 AMPGVGIQIDDVFNLF-DCGEGTQKQIMKSKWSFMSIDNIFITHFH 66
                                  5577777777777799.**************************977 PP

>> PDEase_II  cAMP phosphodiesterases class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   1.4e-06    0.0064      69     125 ..      45     102 ..      38     107 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.4e-06
                                   -HHHHHHHHHHTEEEEE-S---GGGTHHHH..HHGGGGGS-S.--EEEEE-HHHHHHHH CS
                     PDEase_II  69 reikktyeiknniksylItHsHLDHvsglv..inSaefykaqlkkktivGlpytInalq 125
                                   ++i k+  ++  i + +ItH H DH  gl+  + S +f++   k+  i+G    I  ++
  gi|13542061|ref|NP_111749.1|  45 KQIMKSKWSFMSIDNIFITHFHGDHFLGLIglVQSMSFNNR-TKDLNIFGPRGAIGIIS 102
                                   56677888999******************876889999986.78888888877776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); 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 0.29s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1918.78
//
Query:       gi|13542062|ref|NP_111750.1|  [L=135]
Description: hypothetical protein TVN1231 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00028   21.1   0.0    0.00028   21.1   0.0    1.2  1  Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid tra


Domain annotation for each model (and alignments):
>> Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   1.6e-08   0.00028       3      57 ..       4      52 ..       2     130 .. 0.72

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.6e-08
                                  EEEEEEEESS-HHHHHHHHTTTTGGGGT-TTEEEEECSESTSSSTTTEEEEECCC CS
               Polyketide_cyc2  3 kvtvsvviaappekVwalvsdfenwprWhpevarveleggggpargvegtvrvgg 57
                                  ++++++++ a+pekVw++vs +e++p + ++ ++  l  g+g      +++r+++
  gi|13542062|ref|NP_111750.1|  4 RFQEKIEVSADPEKVWKIVSKWEDIPNYWHGTTKI-LNLGNGL-----FKIRFAF 52
                                  78999*********************866666655.4432333.....4555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       254  (0.014167); expected 358.6 (0.02)
Passed bias filter:                      235  (0.0131073); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 887.48
//
Query:       gi|13542063|ref|NP_111751.1|  [L=268]
Description: 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase [Thermoplasma volcanium GSS1]
Scores for complete 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-62  210.2   0.0    3.4e-62  210.0   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 !  210.0   0.0   1.9e-66   3.4e-62       2     217 ..      62     267 ..      61     268 .] 0.93

  Alignments for each domain:
  == domain 1  score: 210.0 bits;  conditional E-value: 1.9e-66
                                   EEEEEEE--SHHHHHTTT.-SS-EEEEEEGGGE.EETTE..EE-TTSSSS-EE......EEEEEEEESS-B--T--HHHHH CS
                 FAA_hydrolase   2 ivcdglnyaehvreagkaaeeppdrhiplepvfflkrasslvgpgdpirrPagsekldyEvELavvigkplrevlsveeAe 82 
                                   i+  ++n+++h +e  +          p +p+ff+k +++lv+ ++++r P   +kldyE+E ++vigk++ ++ ++e+A+
  gi|13542063|ref|NP_111751.1|  62 IFLPAVNFRSHSAESDTR--F------PPKPYFFTKFSNALVANNSELRTPGTIKKLDYEGETGAVIGKKCYNI-PAEDAY 133
                                   566678999999997533..2......23588******************************************.9***** PP

                                   TTEEEEEEEEEEE-SBGGG---.HH..HHHHTGGGEEEEEE-B--B-.STT---SS-EEEEEETTEEEEEEEGGGTTTSHH CS
                 FAA_hydrolase  83 daiaGytllnDvsaRdlqaeekapl..gwflgksfdtftpiGpwivtpdeledpedlelrlrvngeevqdsntkdmifspa 161
                                   d+i+G+t++nD+saRd+q++e+ p+  +w++gk+fd++ p+Gp i+t+de++    le+++ vnge++q+++t+dm+fs++
  gi|13542063|ref|NP_111751.1| 134 DCIFGFTIANDLSARDFQFPEMHPYgyNWVQGKAFDGALPVGPYITTKDEIQF--PLEIETKVNGETRQKGTTDDMVFSFQ 212
                                   **********************99999************************86..5************************* PP

                                   HHHHHHHHHH-B-TT-EEEEEES.......S--EE--TT-EEEEEETTTEEEEEEE CS
                 FAA_hydrolase 162 eliahlsagltLepGdliltGTpsgvgaeeeslkflkdgDeveveieglGelrnrV 217
                                   +li+ ls+ +tLepGd+i++GTp+gv a  +++ +lk gD++e+++++lG+l n++
  gi|13542063|ref|NP_111751.1| 213 DLISTLSQNITLEPGDIITSGTPAGVAA-FSEKLYLKSGDVIEISVSSLGTLMNKI 267
                                   *************************975.789********************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       391  (0.0218082); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 1774.79
//
Query:       gi|13542064|ref|NP_111752.1|  [L=693]
Description: Acyl-CoA synthetase (NDP forming) [Thermoplasma volcanium GSS1]
Scores for complete 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-71  239.7   0.1    3.4e-71  239.2   0.1    1.2  1  ATP-grasp_5    ATP-grasp domain
      5e-45  152.7   0.1    1.5e-44  151.1   0.1    1.9  1  Succ_CoA_lig   Succinyl-CoA ligase like flavodoxin domain
      4e-21   75.7   0.0    1.1e-20   74.2   0.0    1.8  1  CoA_binding_2  CoA binding domain
    1.9e-11   44.5   0.1      1e-10   42.1   0.0    2.3  2  CoA_binding    CoA binding domain
    2.8e-05   23.8   0.1    4.5e-05   23.1   0.1    1.3  1  ATP-grasp_2    ATP-grasp domain
  ------ inclusion threshold ------
      0.065   13.6   0.1       0.14   12.5   0.1    1.5  1  RPM2           Mitochondrial ribonuclease P subunit (RPM2)


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 !  239.2   0.1   1.1e-74   3.4e-71       3     221 ..     475     692 ..     473     693 .] 0.98

  Alignments for each domain:
  == domain 1  score: 239.2 bits;  conditional E-value: 1.1e-74
                   ATP-grasp_5   3 laegrtlLteaeakelleaygipvvetrlassaeeaveaaeeigypvvlKivspdilhKtdvgGvrlnlkdaeevraaaee 83 
                                   +++g + L+e e+k++++ ygi+v +t la+s+++ +++a+e++ypvv Ki+spd++hKtdvgGv ln+++ +e+ +a+++
  gi|13542064|ref|NP_111752.1| 475 IEAGVKSLSELESKKIFSEYGINVNKTELARSKDDLMKIAQEFKYPVVAKIQSPDVIHKTDVGGVILNISNSDELLKAYDD 555
                                   6788899************************************************************************** PP

                   ATP-grasp_5  84 ilervkekspeariegvlVqemakrggrElivgvteDpvFGpvilfGlGGtavevlkdvavalpplnstlareliertkas 164
                                   i+++vk++ p+ari+g++V+em k g  E i+g  +Dp+FGp ++fGlGGtav+vl+dv+++++p+ +++a ++i++t a 
  gi|13542064|ref|NP_111752.1| 556 IISNVKKNVPNARIDGIVVEEMLK-GDLETIIGTINDPTFGPTVMFGLGGTAVQVLEDVSFRMAPVCKKEAYDMINETIAG 635
                                   ************************.******************************************************** PP

                   ATP-grasp_5 165 kllkgvrgekkadlaaleellvrlsqLvvdlpeIreldinPllveeegvvalDarir 221
                                   kl+k++rg+ ++d++a+++ +vr+s L  d+peI+ +d nP++v+ +g++++Dari 
  gi|13542064|ref|NP_111752.1| 636 KLMKEFRGRGPLDIDAVVDQIVRFSWLEYDHPEIKGVDANPMIVSTKGATVVDARIL 692
                                   *******************************************************95 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 !  151.1   0.1   5.1e-48   1.5e-44       1     136 [.     150     283 ..     150     285 .. 0.98

  Alignments for each domain:
  == domain 1  score: 151.1 bits;  conditional E-value: 5.1e-48
                  Succ_CoA_lig   1 pGkialisqSGalalalldwaasrglgfskvvslGneadvdvadlleylaedpetkvillylEsirdgrkflsaarraark 81 
                                   pG i++isqSGal++ l +++ +++ g s ++s+Gn+ad+d++dl+ +la+d+++++i ly E+++ grkf+++ar ++  
  gi|13542064|ref|NP_111752.1| 150 PGTIGMISQSGALIVGLDAMTWANKTGTSFLISIGNMADLDFSDLVTFLADDENVSCISLYAEGLKAGRKFVDTARLIN-- 228
                                   799**************9999999******************************************************8.. PP

                  Succ_CoA_lig  82 kpvvvlksGrseagaraaashtgalagsdavvdaafrqaGvlrvdsleelfdaae 136
                                   kp+v+lksG s++g+ aaashtg+lags++v+d a++qaGv+r++s+eelfd+  
  gi|13542064|ref|NP_111752.1| 229 KPIVMLKSGVSKHGSVAAASHTGSLAGSHRVYDGALKQAGVIRAYSIEELFDLSL 283
                                   ****************************************************865 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.2   0.0   3.7e-24   1.1e-20       2     114 ..      11     133 ..      10     135 .. 0.94

  Alignments for each domain:
  == domain 1  score: 74.2 bits;  conditional E-value: 3.7e-24
                                   -EEEET--S-TTSHHHHHHHHHHH...HT--EEEESSS-SEETTEES----T....T--EEEE-S-HHHHGGGHHHHHHH- CS
                 CoA_binding_2   2 tiaVvGasdnpgkfgykvlrylle...hglpvvpVnpkeeeilgekvyaslaedpepvdlvdvftppeatpeivkealalg 79 
                                   ++aV+Gas++ +k gy+++r+l+e   +g +++p+n k ++ilg k+y+s+ + p +vdl+ + +p++ tp+ ++e++++g
  gi|13542064|ref|NP_111752.1|  11 SVAVIGASNDNTKIGYQIIRNLKEggyKG-KIYPINTKDGTILGYKAYPSILDVPDEVDLAILSIPAKYTPQAAEECGRKG 90 
                                   79**********************88777.9*********************758************************** PP

                                   -SEEEE-TT........---HHHHHHHHHTT-EEE.ES-HHHH CS
                 CoA_binding_2  80 akavwlqpg........sedeeaaelaeeagirvvgdrCilve 114
                                   + ++++ ++          ++++a+ ++++g+r++g++ ++++
  gi|13542064|ref|NP_111752.1|  91 VFGIIVVASgfsevgnkDLEDQLANTCKKYGVRLLGPNVVGLM 133
                                   9999999998******999******************988876 PP

>> CoA_binding  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.1   0.0   3.4e-14     1e-10       4      96 .]      10     100 ..       7     100 .. 0.90
   2 ?   -2.6   0.0         3   9.1e+03       8      35 ..     599     627 ..     596     637 .. 0.63

  Alignments for each domain:
  == domain 1  score: 42.1 bits;  conditional E-value: 3.4e-14
                                   EEEEEETTTSHHHHHH.HHHHHHHHECEE.EEEEC-TTTTTCEETTEEEESCHHHHHHHCTTTEEEEES-HHHHHHHHHHH CS
                   CoA_binding   4 tkviviGagglgiagl.yhfkeklkygik.avfgvnprkvgtevlglpvyksvdeleektevdvavitvPaesaqeavdel 82 
                                    +v+viGa++  ++++   +++ ++ g k +++++n +    ++lg ++y+s+ +++++  vd a++ +Pa+   +a++e+
  gi|13542064|ref|NP_111752.1|  10 DSVAVIGASNDNTKIGyQIIRNLKEGGYKgKIYPINTK--DGTILGYKAYPSILDVPDE--VDLAILSIPAKYTPQAAEEC 86 
                                   68**************44455556677889********..779****************..******************** PP

                                   HHTT-SEEEEESST CS
                   CoA_binding  83 veagikgiviiteg 96 
                                    ++g+ gi+++++g
  gi|13542064|ref|NP_111752.1|  87 GRKGVFGIIVVASG 100
                                   *********99876 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 3
                                   EETTTSHHHHHH.HHHHHHHHECEEEEEE CS
                   CoA_binding   8 viGagglgiagl.yhfkeklkygikavfg 35 
                                     G gg++ ++l  +++++  +  k++++
  gi|13542064|ref|NP_111752.1| 599 MFGLGGTAVQVLeDVSFRMAPVCKKEAYD 627
                                   56888888888866666555554445555 PP

>> ATP-grasp_2  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.1   1.5e-08   4.5e-05       2     114 ..     482     591 ..     481     656 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 1.5e-08
                                   E-HHHHHHHHHCTT----SEEEESSHHHHHHHHHHHTSSSEEEEE--.SSSTCCCTTCEEE.ESSHHHHHHHHHCCTTSEE CS
                   ATP-grasp_2   2 lhEyqakeilakygvkvpegevaesaeeaeeaakklgekelvvKaQv.laGGRGKagGvkl.vkskeeakeaakellgkel 80 
                                   l E ++k+i+++yg++v+++e+a+s++++ ++a++++  + v K Q   +  +   gGv l +++ +e+ +a ++++++  
  gi|13542064|ref|NP_111752.1| 482 LSELESKKIFSEYGINVNKTELARSKDDLMKIAQEFKYPV-VAKIQSpDVIHKTDVGGVILnISNSDELLKAYDDIISNVK 561
                                   7899********************************9999.9999962344556667776527788888888888887544 PP

                                   E-TTS-TT-EEE--EEEEE---ECEEEEEEEEEE CS
                   ATP-grasp_2  81 vtkqtgkeGkkvekvlveealdikkElYlsivlD 114
                                   +    +    +++ ++vee+l+ + E+ ++ + D
  gi|13542064|ref|NP_111752.1| 562 K----NVPNARIDGIVVEEMLKGDLETIIGTIND 591
                                   4....44557888888888888888888877766 PP

>> RPM2  Mitochondrial ribonuclease P subunit (RPM2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   4.8e-05      0.14      86     118 ..     548     582 ..     538     583 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.8e-05
                          RPM2  86 eLLtvyqDiisnklk..PnkeiyeivlesLlkgsi 118
                                   eLL+ y Diisn  k  Pn+ i  iv+e++lkg +
  gi|13542064|ref|NP_111752.1| 548 ELLKAYDDIISNVKKnvPNARIDGIVVEEMLKGDL 582
                                   8**********975455**************9965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (693 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.71u 0.32s 00:00:01.03 Elapsed: 00:00:00.53
# Mc/sec: 3947.61
//
Query:       gi|13542065|ref|NP_111753.1|  [L=201]
Description: hypothetical protein TVN1234 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       530  (0.029561); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1279.67
//
Query:       gi|13542066|ref|NP_111754.1|  [L=119]
Description: small primase-like protein [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00032   21.1   0.0    0.00078   19.9   0.0    1.7  1  Toprim_4         Toprim domain
    0.00053   20.2   0.0     0.0021   18.2   0.0    1.8  1  Toprim           Toprim domain
  ------ inclusion threshold ------
      0.041   13.3   0.0      0.053   13.0   0.0    1.1  1  AICARFT_IMPCHas  AICARFT/IMPCHase bienzyme


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 !   19.9   0.0   1.3e-07   0.00078       4      68 ..      14      68 ..      11      86 .. 0.71

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 1.3e-07
                      Toprim_4  4 iiVEgyaDvlaleka.giknvvavlg.gal.spldgirpeklktenlveaekkvkevilaldgDaeGe 68
                                  iiVEg++D+++l k   +  ++ + +  ++ s +d+i+              k +evi+++d D+ G 
  gi|13542066|ref|NP_111754.1| 14 IIVEGRNDLASLRKLsFYGEIIVFNRgISItSFSDEIS-----N--------KYREVIILTDFDNKGS 68
                                  8**************77766666555233423333333.....2........358**********996 PP

>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   3.5e-07    0.0021       3      83 ..      14      74 ..      13      87 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 3.5e-07
                                  EEESSHHHHHHHHHTHTSTEEEEEEESSSSEEEHSTTEEEEEECTTTHHHHHHHHHHHHHHSEEEEECSSSHHHHHHHHHH CS
                        Toprim  3 vivEgpsdaktiakalgsgfqavtaslGhildletefkpvyeeiedkkkvlkalkelakradeiilatDpDreGeaiawel 83
                                  +ivEg +d ++++k+    + +++  +G  ++  +                   +e++ ++ e+i++tD D  G+ ++ + 
  gi|13542066|ref|NP_111754.1| 14 IIVEGRNDLASLRKLSF-YGEIIVFNRGISITSFS-------------------DEISNKYREVIILTDFDNKGSFLKDRF 74
                                  79************944.55555556666665555...................8999****************8766655 PP

>> AICARFT_IMPCHas  AICARFT/IMPCHase bienzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   8.9e-06     0.053     156     194 ..      27      66 ..      23      73 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 8.9e-06
                                   HHHHTTEEEEECCEE-.HHHHHHHTTS-ECEEEECEE-CC CS
               AICARFT_IMPCHas 156 pvSaFGgiialnrevd.aetaeeikkefleviiApsfeee 194
                                   ++S +G+ii++nr +  ++  +ei++++ evii  +f+++
  gi|13542066|ref|NP_111754.1|  27 KLSFYGEIIVFNRGISiTSFSDEISNKYREVIILTDFDNK 66 
                                   5799***********9345789*************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       381  (0.0212505); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.31s 00:00:00.79 Elapsed: 00:00:00.50
# Mc/sec: 719.73
//
Query:       gi|13542067|ref|NP_111755.1|  [L=145]
Description: single-stranded DNA-binding protein [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.7e-05   22.5   0.1    9.9e-05   22.2   0.1    1.3  1  REPA_OB_2        Replication protein A OB domain
    0.00036   20.5   0.3     0.0007   19.5   0.3    1.5  1  tRNA_anti-codon  OB-fold nucleic acid binding domain
  ------ inclusion threshold ------
      0.048   13.4   0.0      0.075   12.7   0.0    1.2  1  CDC24_OB3        Cell division control protein 24, OB domain 
       0.22   11.1   0.1       0.38   10.4   0.1    1.4  1  DUF4131          Domain of unknown function (DUF4131)


Domain annotation for each model (and alignments):
>> 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 !   22.2   0.1   2.2e-08   9.9e-05       9      67 ..      13      69 ..       4      98 .. 0.85

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 2.2e-08
                     REPA_OB_2  9 kdsivDvigvvksveevseitskstekelkkreltlvDesgasvevtlWgkeaekfess 67
                                  +   v v+g v sv+e ++i++k +  + +  e+t+ D++g+ v + lWg++a + +++
  gi|13542067|ref|NP_111755.1| 13 SSRRVNVLGKVLSVGEPKTIQTKFGD-QRSVTEVTIGDDTGK-VILSLWGDQAAQAKTG 69
                                  456799******************99.9999*********97.559*****99997654 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 !   19.5   0.3   1.6e-07    0.0007       1      70 [.      17      90 ..      17     104 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.6e-07
                                  EEEEEEEEEEE........EEEETTEEEEEEEETTEEEEEEEETHHHHHHHTTS-TTSEEEEE.EEEEECTTSSEEEEE CS
               tRNA_anti-codon  1 VtvaGrvtsis........drsggkvifidlrDgtgriqvvlfreeatklaenlkeGdvvrvt.Grvkrrpggelelkv 70
                                  V+v G+v s+          ++ ++v  +++ D+tg++ ++l+     ++a + k Gd + +  G+v+  +g  + l+v
  gi|13542067|ref|NP_111755.1| 17 VNVLGKVLSVGepktiqtkFGDQRSVTEVTIGDDTGKVILSLWG----DQAAQAKTGDTLMIGnGYVSLVRGH-IRLNV 90
                                  5667777777777777787799999*******************....8888888888888888888777666.55555 PP

>> CDC24_OB3  Cell division control protein 24, OB domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   1.7e-05     0.075       1      67 [.       9      74 ..       9      93 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.7e-05
                     CDC24_OB3  1 DLrekmlnvtLlGrvvai....freknsek.kkmdryslrieDttGaidatlweeagklhfk..rlrvGhlvll 67
                                  DL ++   v +lG+v  +    + +++ ++ +++  + ++i D+tG++ + lw   + ++++  +      +++
  gi|13542067|ref|NP_111755.1|  9 DLTPSSRRVNVLGKVLSVgepkTIQTKFGDqRSV--TEVTIGDDTGKVILSLWGDQAAQAKTgdT------LMI 74
                                  7777888899********7765334444443444..59***************998888777553......333 PP

>> DUF4131  Domain of unknown function (DUF4131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   8.5e-05      0.38      58     129 ..       6      76 ..       2      93 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 8.5e-05
                       DUF4131  58 dlsqllesgqeviveGvvaslpeltgsgtrfvlevervlsagktkpvsgrvlvtvpkspaeglrpGdrlrl.t 129
                                   ++ +l++s++ v v G+v+s+ e +  +t+f    +r +++    + +g+v++++ +++a++ + Gd+l++ +
  gi|13542067|ref|NP_111755.1|   6 KIKDLTPSSRRVNVLGKVLSVGEPKTIQTKFGD--QRSVTEVTIGDDTGKVILSLWGDQAAQAKTGDTLMIgN 76 
                                   56777888999************9988887764..455777788899********************999854 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       561  (0.0312901); 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:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.44
# Mc/sec: 989.79
//
Query:       gi|13542068|ref|NP_111756.1|  [L=588]
Description: ATP-dependent DNA ligase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-55  187.8   0.0    2.8e-55  187.2   0.0    1.3  1  DNA_ligase_A_M   ATP dependent DNA ligase domain
    1.4e-35  123.2   0.8    2.8e-35  122.2   0.8    1.5  1  DNA_ligase_A_N   DNA ligase N terminus
    2.8e-20   72.8   0.0    5.3e-20   71.9   0.0    1.5  1  DNA_ligase_A_C   ATP dependent DNA ligase C terminal region
    0.00047   20.0   0.1       0.45   10.3   0.0    2.4  2  mRNA_cap_enzyme  mRNA capping enzyme, catalytic domain
  ------ inclusion threshold ------
       0.13   12.3   0.3       0.51   10.4   0.1    2.1  2  DNA_ligase_OB_2  DNA ligase OB-like domain


Domain annotation for each model (and alignments):
>> DNA_ligase_A_M  ATP dependent DNA ligase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  187.2   0.0   7.7e-59   2.8e-55       2     204 .]     226     426 ..     225     426 .. 0.97

  Alignments for each domain:
  == domain 1  score: 187.2 bits;  conditional E-value: 7.7e-59
                                   EEEEEESCHHHHHHHTTTSEEEEEEEESSEEEEEEEETTEEEEEETTS-B-GGGCHHHHHHHHHHBSTTESEEEEEEEEEE CS
                DNA_ligase_A_M   2 mLAeslksiekalkkleekafivEiKyDGeRaqvhkegdkvklfSRrlkditaakpelvkalkeafkkdeksvilDGElva 82 
                                   mLAe+l+s+ ++++k+ +++  +E+KyDG R ++h  ++kv+lfSR  ++ t+++p++vk +ke f  +  svilDGE+v 
  gi|13542068|ref|NP_111756.1| 226 MLAERLRSVDEIVQKM-NGKCAFEYKYDGMRTEIHIVDEKVRLFSRGNEETTGQFPDIVKSAKETFHVS--SVILDGEAVP 303
                                   9***************.56666********************************************765..9********* PP

                                   EETTTTCBEHHHHHCHHHHCHCCTHHHHHHSEEEEEEEEEEEETTEEHTTSCHHHHHHHHHHHB--BTTTEEE--EEEESS CS
                DNA_ligase_A_M  83 vdketgeilpfqklasrkkkkkkveeklkeaelclfvFDiLyldgesltdeplkeRrklLeeilkesedrvelaeslevkd 163
                                   +++etge  pfq++++r  +k+++ ++ +e+++ +f+FDi y++g++l ++p+ eRr++Le ++ +++d+++la++++ +d
  gi|13542068|ref|NP_111756.1| 304 YNPETGELYPFQVISQRRGRKYDLDKVSNEIPITVFLFDIVYINGKDLSKTPYAERRRILEGLF-KENDNFKLAKRIVSSD 383
                                   ******************99********************************************.99************** PP

                                   HHHHHHHHHHHHHTTECEEEEEE..TT-CC-TTCEEEEEEEEE CS
                DNA_ligase_A_M 164 veeleelleeaiseglEGlvvKn..pdskYepgkrsknwlKvK 204
                                   + ++++++++ai++g+EGlv+K+   ds Y++g r++ w+K+K
  gi|13542068|ref|NP_111756.1| 384 TGTITKFFNQAIEDGCEGLVAKSmaDDSYYKAGARGWLWIKLK 426
                                   ***********************88899*************99 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 !  122.2   0.8   7.9e-39   2.8e-35       1     172 [.       2     174 ..       2     174 .. 0.96

  Alignments for each domain:
  == domain 1  score: 122.2 bits;  conditional E-value: 7.9e-39
                                   BCHHHHHHHHHHCC.---HHHHHHHHHHHHHTS-..SHHHHHHHHHH....SS-CCCS------HHHHHHHHHHHHT--HH CS
                DNA_ligase_A_N   1 pFaelaelfekieestkkrlekrailanffrkvesagpedlypalrL....llPdydgreygigesllakalaealglskk 77 
                                   +F++++++fek+++ t+kr+e ++il +++++     +edl ++++L    l+Pdy+g+e ++ ++l++kal+ +++++++
  gi|13542068|ref|NP_111756.1|   2 KFSLVTDAFEKMSK-TTKRTELTEILVELLKS----ADEDLQSLVYLiegkLAPDYQGIETQMSDKLIIKALSIVSNIPEE 77 
                                   59************.899************65....4779***************************************** PP

                                   HHHHHHHHHS-HHHHHHHHHCCHHHH.------BHHHHHHHHHHHHH-.STTHHHHHHHHHHHHHHHS-HHHHHHHHHHHC CS
                DNA_ligase_A_N  78 kikdalakvgDlgevaeevlskrstl.akkspltieevnelLdklaaa.gkgsedekkkilkkllkraspeEakyliriil 156
                                    + + + k+gD+g+va e+ +k++++   +++lt++ v+++L ++a++ g+gs+++++++  +l  + +p +++y++rii+
  gi|13542068|ref|NP_111756.1|  78 AVSETYSKLGDIGSVAREIAAKKNMRsLVNEDLTVKYVHDTLMRMAKTsGSGSTKARIDAYVDLALSGTPADLMYITRIIT 158
                                   8888899*************9999999999****************999******************************** PP

                                   T---SS--HHHHHHHH CS
                DNA_ligase_A_N 157 kdlriglsektvldal 172
                                   ++lrig+s+ t+lda+
  gi|13542068|ref|NP_111756.1| 159 GKLRIGVSDATILDAI 174
                                   **************97 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 !   71.9   0.0   1.5e-23   5.3e-20       1      99 []     451     561 ..     451     561 .. 0.93

  Alignments for each domain:
  == domain 1  score: 71.9 bits;  conditional E-value: 1.5e-23
                                   GGGSEEEEEEEEEE..TTEEEEEEEE-SS--HHHHHHHHHHHGGGEECTTCESS---HHHHTTEEE-TT-EEEEEESEEEC CS
                DNA_ligase_A_C   1 rgglvgslllgvyd..dgkleyvgkvgtGfsdaeleelrkklkelerkkppfaekvpeeekrdvWvePelvveVkfaeita 79 
                                   r+g++g+lll+ y+  ++++e+v+k g+Gf+d+ l  l k++ e   k++p   +v  + ++dvW+ P++v+e+ +aeit 
  gi|13542068|ref|NP_111756.1| 451 RSGTYGALLLATYNekNDTFETVCKLGSGFTDDVLFSLPKRFAEFVSKEKPA--RVVSTIEPDVWIYPSIVMEIIGAEITI 529
                                   5799**********98888************************999999999..555555667****************** PP

                                   TSSSTT...........EECT-EEE.EE-TTS CS
                DNA_ligase_A_C  80 sgkyka...........slRfPrfk.rlReDk 99 
                                   s+ +++           s+RfPrf+ ++R+Dk
  gi|13542068|ref|NP_111756.1| 530 SPVHTCafgiiekdaglSIRFPRFTgKWRDDK 561
                                   ***********************9989****8 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 !    7.1   0.0    0.0012       4.4      22      80 ..     249     302 ..     237     309 .. 0.84
   2 !   10.3   0.0   0.00012      0.45      92     130 ..     337     375 ..     327     396 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0012
                                   EEESSEEEEEEEEECTEEEEEEETTS-EEEESSST-BTTSSSSTCTSBGGSEEEEEEEE CS
               mRNA_cap_enzyme  22 eKaDGiRylmllteeeegvylidRenevyrvenlrfprekdkeklekvldetllDgElv 80 
                                    K DG+R  + +++e  +v l+ R ne    ++ +++ +    k++ + ++ +lDgE v
  gi|13542068|ref|NP_111756.1| 249 YKYDGMRTEIHIVDE--KVRLFSRGNEETTGQFPDIVKSA---KETFHVSSVILDGEAV 302
                                   699**********99..7*********9988866666655...4557888899****76 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00012
                                   EEEEEEEEEETTEEGTTSBHHHHHHHHHHHTHHHHHHHH CS
               mRNA_cap_enzyme  92 ryliyDivaingvtvaeeplskRleilkkelikprneek 130
                                      ++Div ing++++++p+++R +il+  +++  n + 
  gi|13542068|ref|NP_111756.1| 337 TVFLFDIVYINGKDLSKTPYAERRRILEGLFKENDNFKL 375
                                   5679**********************9987776665554 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 ?   10.4   0.1   0.00014      0.51       2      32 ..     447     483 ..     446     484 .. 0.81
   2 ?   -3.3   0.0       2.7   9.5e+03      57      63 ..     548     554 ..     542     555 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00014
                                   ...EEEEEEEEEEEEE.TTEE......EEE-SS--HH CS
               DNA_ligase_OB_2   2 GkGkykgmlGallvetkkgkr......fkiGsGlsda 32 
                                   G G+ +g+ Gall  t + k+       k+GsG++d+
  gi|13542068|ref|NP_111756.1| 447 GHGRRSGTYGALLLATYNEKNdtfetvCKLGSGFTDD 483
                                   99**************8766333444599******96 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2.7
                                   -EEEEEE CS
               DNA_ligase_OB_2  57 pRfPsfl 63 
                                    RfP+f 
  gi|13542068|ref|NP_111756.1| 548 IRFPRFT 554
                                   5999995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (588 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       508  (0.028334); 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:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.69u 0.31s 00:00:01.00 Elapsed: 00:00:00.55
# Mc/sec: 3211.17
//
Query:       gi|13542069|ref|NP_111757.1|  [L=566]
Description: amino acid transporter [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.8e-37  127.8  60.0    4.8e-37  127.8  60.0    2.0  2  AA_permease_2    Amino acid permease
    4.1e-29  101.5  49.6    4.1e-29  101.5  49.6    2.2  2  AA_permease      Amino acid permease
    1.7e-06   28.2   7.2    1.7e-06   28.2   7.2    5.3  6  Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domai
  ------ inclusion threshold ------
      0.044   14.2   1.0        1.8    9.0   0.1    3.2  2  DUF4014          Protein of unknown function (DUF4014)


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 !  127.8  60.0   1.1e-40   4.8e-37       1     414 [.      19     483 ..      19     497 .. 0.78
   2 ?   -2.0  10.7      0.26   1.2e+03      81     160 ..     448     527 ..     440     556 .. 0.54

  Alignments for each domain:
  == domain 1  score: 127.8 bits;  conditional E-value: 1.1e-40
                 AA_permease_2   1 lsllsafalvigsvigsgifvkn..laasggpalilwvwiavligslavllvyaElssalprsgGiyvytkaafgkkvafl 79 
                                   l+++++++l++g +igsg +++   +a+++gp +i+ ++i+ +i+ +  +lvyaEl++++prsg i+ y++   g +++f+
  gi|13542069|ref|NP_111757.1|  19 LTTWDLLMLSLGGIIGSGWLFAAfgAATTAGPGSIFAWIIGGVII-IFIALVYAELGAMIPRSGAIVRYGHLSHGSFAGFV 98 
                                   689****************9999988888******9999999998.79********999********************** PP

                 AA_permease_2  80 sawfnwfayvpvlas....ilsvaasyllnalgpdlqgn....twltyliaiaililvalinirgikesakiqnilgilki 152
                                    +w++++++v v a+    ++++aasy     g  l +n     +l  ++a++++++++++n+ gik+++k ++ l+++k+
  gi|13542069|ref|NP_111757.1|  99 LGWAYFLSAVSVPAIeaegVITYAASYSSK-YGIVLLTNtgvmSVLGTFLAMLLMLGFFFLNYAGIKIMGKTNTGLTWWKF 178
                                   ******999998877555344445554433.33333233344455778889****************************** PP

                 AA_permease_2 153 llpliiliilglitvdgggfsslstetdtffpngwpgvllglli..vlwsfdGfesaanvseevkk..kdvpkaifiglli 229
                                   ++p +++i+l ++ ++++         + ++p gw  v+++ ++  +++s+ Gf   + +  e+k+  + +p+a+++++li
  gi|13542069|ref|NP_111757.1| 179 VIPTLTVILLLVVSFRPSNII-----VGGIVPYGWAPVFSAVATsgIVFSYLGFRQGIDYGGEAKTpqRSIPLATVFSVLI 254
                                   ********9999999887665.....3469******9877775555*****************8866599*********** PP

                 AA_permease_2 230 vlvlyllvniaflgvvpddei.............anlsnlgsv..............aalffeavggkvvaiivvilials 283
                                    ++ly+ ++i+f+g++ ++++             a       +              +a  ++a+g  ++++i+ + + +s
  gi|13542069|ref|NP_111757.1| 255 GILLYTALQIVFIGGIDWGKLglvpgswaqiyslA-------TsnsnpeavalydapFAHIAQAAGLVFLTYILFADAYIS 328
                                   *********************87777777666551.......033334556777777899999999889999999****** PP

                 AA_permease_2 284 llgaintavigssrvlealardgvlPrffakvn.kfgspiraiiltaivslillllfllassaaynfllsvsslgliisyl 363
                                     g +n ++ +s+r+l+ +a  g +P+ +  +  k+ +p+  +  t+++  i++l f        + ++   + +  + y+
  gi|13542069|ref|NP_111757.1| 329 PSGTLNVYLGTSTRTLYGMAANGHMPKKLLEIMdKNRIPFIPLLATLLIGYIFFLPFPS-----WYKMVGFITSATAFTYI 404
                                   **************************55555555*******************998863.....46666666666666777 PP

                 AA_permease_2 364 lliigalilrkkrphlkrpgk.......................ilvaiig..alfllfllvalf...fppkgpatqss 414
                                   +  ++++ lr++ p+lkrp k                       +++++    a+fl f++++        +++ t+++
  gi|13542069|ref|NP_111757.1| 405 VGGAALMSLRRTAPELKRPFKlpyarvlspiafigagevvywsgWPLVLYLaiAIFLGFAVYFVLlllGAIENSFTKEN 483
                                   7788888***********4444555777777777788888877854444441144444444333322244444444444 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.26
                 AA_permease_2  81 awfnwfayvpvlasil.svaasyllnalgpdlqgntwltyliaiaililvalinirgikesakiqnilgilkillpliili 160
                                   +w +++  ++++++++ ++++  ll+a+  +++++++ + l + +++i++++++++g   ++ i +i + + ++ +++++ 
  gi|13542069|ref|NP_111757.1| 448 GWPLVLYLAIAIFLGFaVYFVLLLLGAIENSFTKENIKAGLWVPIFIIVLTVLSYIGDTSLGGIGVIKFPFDLV-TVAVIS 527
                                   33333333333333321334444455555577777776655565666666666666666667777777777774.444443 PP

>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.5  49.6   9.2e-33   4.1e-29       1     392 [.      23     415 ..      23     441 .. 0.86
   2 ?   -0.4  12.4     0.075   3.4e+02      77     168 ..     446     542 ..     430     560 .. 0.67

  Alignments for each domain:
  == domain 1  score: 101.5 bits;  conditional E-value: 9.2e-33
                   AA_permease   1 hvlvialggviGtglfvglgvvlsqaGplgallayllagvviflvmlslgeiatngpksggfytyasrflgpelGfviGln 81 
                                   ++l+ +lgg+iG g +++   ++ +aGp g + a++++gv+i++++l  +e+  ++p+sg++  y + ++g+ +Gfv G+ 
  gi|13542069|ref|NP_111757.1|  23 DLLMLSLGGIIGSGWLFAAFGAATTAGP-GSIFAWIIGGVIIIFIALVYAELGAMIPRSGAIVRYGHLSHGSFAGFVLGWA 102
                                   589*************************.777************************************************* PP

                   AA_permease  82 ylfswitvlaleltaasiliqfwelvtdlpkawvt..............gavflvvlliinlvgvkvygeaefilalikii 148
                                   y++s + v a+e   a+ +i+++ ++++    +v               ++++++ ++++n++g+k  g++ + l++ k++
  gi|13542069|ref|NP_111757.1| 103 YFLSAVSVPAIE---AEGVITYAASYSSKY-GIVLltntgvmsvlgtflAMLLMLGFFFLNYAGIKIMGKTNTGLTWWKFV 179
                                   ************...999999996666655.33336999**********9******************************9 PP

                   AA_permease 149 aiiafiivgiillaggkpnkgagfrflgdngsifknnlppgfakeeegafknfisvfvi..vvfaftGielvaiiagEvkd 227
                                   +   ++i++ +  ++ +p++            i+  ++p g         + ++s+ ++  +vf++ G+  ++  +gE+k 
  gi|13542069|ref|NP_111757.1| 180 IPTLTVILLLV--VSFRPSNI-----------IVGGIVPYG--------WAPVFSAVATsgIVFSYLGFRQGIDYGGEAKT 239
                                   99999999954..55555555...........333356666........666666665422799999************** PP

                   AA_permease 228 PeksiPkailqvviritifYvlsllligllvprndlgllndsasa.................aspfvifikesgvsvlapl 291
                                   P++siP a+ + v++ +++Y+ + ++ + ++++  lgl+ +s                      pf  + + +g+ +l  +
  gi|13542069|ref|NP_111757.1| 240 PQRSIPLATVFSVLIGILLYTALQIVFIGGIDWGKLGLVPGSWAQiyslatsnsnpeavalyDAPFAHIAQAAGLVFLTYI 320
                                   ***************************************9888779999************999***************** PP

                   AA_permease 292 inaviltaalssansslysasRvlyslakdglaP.kvlkkvskrgvPlraillsmiisllalllaslnlaapivfnfllai 371
                                   + a  +++  +++n +l +++R+ly +a +g++P k l+ ++k++ P   +l++++i+++++l   +  +       ++ +
  gi|13542069|ref|NP_111757.1| 321 LFADAYISPSGTLNVYLGTSTRTLYGMAANGHMPkKLLEIMDKNRIPFIPLLATLLIGYIFFLPFPSWYK-------MVGF 394
                                   **************************************************************43222222.......3344 PP

                   AA_permease 372 saliglivwlliilsylrfRk 392
                                    + ++ +++++  ++++ +R+
  gi|13542069|ref|NP_111757.1| 395 ITSATAFTYIVGGAALMSLRR 415
                                   444445555555555555555 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.075
                   AA_permease  77 viGln...ylfswitvlaleltaasiliqfwel..vtdlpkawvtgavflvvlliinlvgvkvygeaefilali..kiiai 150
                                     G+    yl   i+    ++  +  l++ +e+  +++++ka  ++ +f++vl++++++g    g + +i +++  + +a+
  gi|13542069|ref|NP_111757.1| 446 WSGWPlvlYLAIAIFLGF-AVYFVLLLLGAIENsfTKENIKAGLWVPIFIIVLTVLSYIGDTSLGGIGVIKFPFdlVTVAV 525
                                   456664434444444444.444455555555544799***********************999999999976651144455 PP

                   AA_permease 151 iafiivgiillaggkpnk 168
                                   i+fi   ++++ +g +++
  gi|13542069|ref|NP_111757.1| 526 ISFIFY-MWSVRSGIRTE 542
                                   555554.45555554444 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 ?   -1.8   4.4      0.64   2.9e+03      98     140 ..      30      69 ..       4      72 .. 0.52
   2 ?   -3.8  12.0       2.7   1.2e+04      59     139 ..     139     227 ..     127     231 .. 0.57
   3 ?   -0.1   8.4      0.19   8.7e+02      85     139 ..     200     264 ..     182     269 .. 0.65
   4 ?    1.6   1.8     0.057   2.5e+02      31      51 ..     248     270 ..     243     291 .. 0.65
   5 !   28.2   7.2   3.8e-10   1.7e-06      21     140 ..     357     472 ..     352     474 .. 0.71
   6 ?   -0.6   1.3      0.29   1.3e+03       6      40 ..     492     526 ..     484     536 .. 0.72

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.64
               Polysacc_synt_C  98 alvmgivvylllllllgllllaalalllavlvgalvYllllll 140
                                   + ++g   +l++ +   ++ ++    ++a ++g+++ ++++l+
  gi|13542069|ref|NP_111757.1|  30 GGIIGS-GWLFAAFGAATTAGP--GSIFAWIIGGVIIIFIALV 69 
                                   222222.233444444444444..6677777777777777665 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 2.7
               Polysacc_synt_C  59 aiatvlallvvavlnlyalrrllgikl........ellrrllkpllaalvmgivvylllllllgllllaal.alllavlvg 130
                                   +++ + ++l++++++ ++  ++ gik+        ++++ +  p l ++++ +v +   ++++g + + ++  ++ av+  
  gi|13542069|ref|NP_111757.1| 139 VMSVLGTFLAMLLMLGFFFLNYAGIKImgktntglTWWKFV-IPTLTVILLLVVSFRPSNIIVGGIVPYGWaPVFSAVATS 218
                                   55666667777777788888888888866554443333333.333333333333222333333333333455688888888 PP

               Polysacc_synt_C 131 alvYlllll 139
                                   ++v+ +l +
  gi|13542069|ref|NP_111757.1| 219 GIVFSYLGF 227
                                   998887765 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.19
               Polysacc_synt_C  85 l.ellrrllkpllaalvmgivvylllllllglllla...........alalllavlvgalvYlllll 139
                                   +  ++   + p+++a++ +++v+  l +  g+                la++++vl+g+l+Y +l +
  gi|13542069|ref|NP_111757.1| 200 VgGIVPYGWAPVFSAVATSGIVFSYLGFRQGID--YggeaktpqrsiPLATVFSVLIGILLYTALQI 264
                                   444556668888888888888553333333333..145889999965559************87654 PP

  == domain 4  score: 1.6 bits;  conditional E-value: 0.057
               Polysacc_synt_C  31 alkalvigalvklilnllli..p 51 
                                   ++ +++ig+l+  +l++++i   
  gi|13542069|ref|NP_111757.1| 248 TVFSVLIGILLYTALQIVFIggI 270
                                   45667777777777777777553 PP

  == domain 5  score: 28.2 bits;  conditional E-value: 3.8e-10
               Polysacc_synt_C  21 iLqglgrqkialkalvigalvklilnllliplfgivG.aaiatvlallvvavln..lyalrrllgiklellrrllkpllaa 98 
                                   +L  +++++i+++ l++++l+  i+ l++  ++ +vG +  at+++++v+ + +  l++   +l+ ++       ++l   
  gi|13542069|ref|NP_111757.1| 357 LLEIMDKNRIPFIPLLATLLIGYIFFLPFPSWYKMVGfITSATAFTYIVGGAALmsLRRTAPELKRPF--KLPYARVLSPI 435
                                   7899*********************************8889999999998766512444444444444..22222433333 PP

               Polysacc_synt_C  99 lvmgivvylllllllgllllaalalllavlvgalvYllllll 140
                                   +++g+    +++   +l     l l++a+++g +vY++llll
  gi|13542069|ref|NP_111757.1| 436 AFIGAG-EVVYWSGWPL----VLYLAIAIFLGFAVYFVLLLL 472
                                   333333.1133333333....3499**************986 PP

  == domain 6  score: -0.6 bits;  conditional E-value: 0.29
               Polysacc_synt_C   6 alsiiflslstvlssiLqglgrqkialkalvigal 40 
                                   +++i++++ls ++ + L g+g  k+++  + ++++
  gi|13542069|ref|NP_111757.1| 492 IFIIVLTVLSYIGDTSLGGIGVIKFPFDLVTVAVI 526
                                   56777888888888888888888777766666655 PP

>> DUF4014  Protein of unknown function (DUF4014)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.1     0.059   2.7e+02      13      39 ..     482     508 ..     475     515 .. 0.77
   2 ?    9.0   0.1    0.0004       1.8      20      52 ..     515     549 ..     512     557 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.059
                       DUF4014  13 srfkealffplflilmvpispiffiwl 39 
                                     +k  l+ p+f+i++  +s i    l
  gi|13542069|ref|NP_111757.1| 482 ENIKAGLWVPIFIIVLTVLSYIGDTSL 508
                                   567899*********999998765555 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0004
                       DUF4014  20 ffplflilmvpispiffiwl..agvqaekiaewys 52 
                                    fp+ l+ +  is if++w   +g+++e i+e   
  gi|13542069|ref|NP_111757.1| 515 KFPFDLVTVAVISFIFYMWSvrSGIRTEDITEMIE 549
                                   59999**************63379******99765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (566 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       787  (0.0438954); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.82u 0.38s 00:00:01.20 Elapsed: 00:00:00.60
# Mc/sec: 2830.47
//
Query:       gi|13542070|ref|NP_111758.1|  [L=624]
Description: aldehyde:ferredoxin oxidoreductase [Thermoplasma volcanium GSS1]
Scores for complete 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-87  291.4   0.0    1.2e-86  291.1   0.0    1.1  1  AFOR_C    Aldehyde ferredoxin oxidoreductase, domains 2 & 3
    1.8e-70  236.9   0.4    2.9e-70  236.2   0.4    1.4  1  AFOR_N    Aldehyde ferredoxin oxidoreductase, N-terminal doma


Domain annotation for each model (and alignments):
>> AFOR_C  Aldehyde ferredoxin oxidoreductase, domains 2 & 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  291.1   0.0   1.4e-90   1.2e-86       2     382 .]     218     615 ..     217     615 .. 0.95

  Alignments for each domain:
  == domain 1  score: 291.1 bits;  conditional E-value: 1.4e-90
                                   HHHHHHHHHHHSH.HHHHHHHH-GGGHHHHHHHTT---BTTTTB.S-....-TTGGGGSHHHHHHHTEEEE.E-TT-SS-- CS
                        AFOR_C   2 lgkkiqkeiksspqvtaelrkyGTaelvnianetgalptknfqe.gt....fekaekisgealeekylvknegCfsCpiaC 77 
                                   + kkiq ++++s +  + ++ +GT+++++ ++ +g  p+kn+   g      ++a+kisge++++++l++  gC++C++aC
  gi|13542070|ref|NP_111758.1| 218 TIKKIQIQFRNSMDLVNPWHMFGTTQITESSHLNGDTPIKNWAGvGIvdfgEDNAKKISGEEIRKDVLKSY-GCAQCTLAC 297
                                   57899999****99******************************99988766788**********666666.9******** PP

                                   EEEEE.......ETEE---HHHHHHHTGGGT---HHHHHHHHHHHHHHTB-HHHHHHHHHHHHHHHHTTSS-HHHHTS--- CS
                        AFOR_C  78 grevkveegkk.vkvegpeyetlaalGsnlgiddleailklnelcdelGlDtisaGntiafamelyekGllkkedtdglel 157
                                   g +v+ e+    v+++  eye ++a+G    ++dl+a+ +  elc+++GlD i++G++iafa e+yekG+l+++d+ g++l
  gi|13542070|ref|NP_111758.1| 298 GGHVRRETRYGkVEGHRLEYEGTGAFGGLNLVSDLDAMSMSFELCNRYGLDIITTGAVIAFANECYEKGILTENDV-GFKL 377
                                   *****7666655558999*********************************************************9.**** PP

                                   -TT-THHHHHHHHHHHTT-TTHHHHTT-HHHHHHCTT..-GGG--EETTEE--SS-GGG-HHHHHHHHH-TTSS-SGGG-T CS
                        AFOR_C 158 efgdaeallellekiAkregigdllAeGvkrlaeklg..aeelamhvkGlelpaydprgakgmalaYatsnrGacHlrayl 236
                                    fg+a+a ++l+e i+k+egig++l+ G k++++ +g  +e++amh+ G++lp++dpr +++++ +Y   ++ ++H  +  
  gi|13542070|ref|NP_111758.1| 378 GFGNADAEVKLTELIGKGEGIGRILGMGQKYASKVIGkgSEQFAMHIGGQDLPMHDPRLMPSLGNTYISDPTPGRHTAGGI 458
                                   ******************************************************************************888 PP

                                   HHHH..............S---TT--HHHHHHHHHHHHHHHHHHHHT--GGGG-HHH......HHHHHHHHHT----HHHH CS
                        AFOR_C 237 iale..............ekvdpletegkaelvkwfqdltalvdslglCkftseaeerldlelyakllsavtGidvteeel 303
                                    + e               k ++++++gk++l  ++   +++++s g+C f++  +   +   y +l++a+tG+d++e+el
  gi|13542070|ref|NP_111758.1| 459 GFNEgfelvlpfnhstsnTKIERYQYNGKGKLQLFAAAGQEIINSTGMCMFST--NIWPNSYPYRDLIKAITGWDINEDEL 537
                                   88888**********99988999999***************************..45567788****************** PP

                                   HHHHHHHHHHHHHHHHHHT--HHHS---HHHH.HS---SSTTTT---..-HHHHHHHHHHHHT--TTS---HHHHHHCT- CS
                        AFOR_C 304 lkaGeRiynleRlfnlreGltrkddtlperll.eeplkegpakgkvledeleemldeyYelrGWdetGvPtketlkrLgL 382
                                   +k+G Ri  ++++fn+++ +++ + + p r++   pl+ gp +g  +  ++e++++ey e+ G d++G+Ptke +++L++
  gi|13542070|ref|NP_111758.1| 538 IKIGWRIQVIRHMFNAKQNVNQYEIKPPGRVMgYPPLTAGPTAGVSI--DYETLRKEYLEEAGIDRQGKPTKEVIEKLEI 615
                                   ********************************77788******9998..7****************************86 PP

>> AFOR_N  Aldehyde ferredoxin oxidoreductase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  236.2   0.4   3.2e-74   2.9e-70       1     198 []       6     204 ..       6     204 .. 0.97

  Alignments for each domain:
  == domain 1  score: 236.2 bits;  conditional E-value: 3.2e-74
                                   SEEEEEETTTTEEEEEE--HHHHHHH-SCHHHHHHHHHHHS-TTS-TTSTTS-EEEEE-TTTTSSSTTB-EEEEEEE-TTT CS
                        AFOR_N   1 gkilrvdLstgkieveelpeelaekylGgrglaakllldevppgvdplspenplvfatGpltgtpapgsgrlvvvaksPlt 81 
                                   gkil+vdL+++ki++e++pe +++kylGg+gl+a++l +e++  +d+l+p+n+l f+tG+++  ++p  grl+vvaksP+t
  gi|13542070|ref|NP_111758.1|   6 GKILWVDLTSEKIWEESIPETIYKKYLGGVGLGAYILNREIKGPIDALGPDNVLGFVTGIFNSHNVPLGGRLEVVAKSPMT 86 
                                   79****************************************9************************************** PP

                                   SSEEEEEEETCHHHHHHHCT-SEEEEES--SS-EEEEEETTEEEEEE-TTTTTS-HHHHHHHHHHHHTS.EEEEE-HHHHT CS
                        AFOR_N  82 gtlgesnaGgrfgaelkraGydaivieGkaekpvylvieddkveiedaedlwgldtyettealkeelgd.kvaviGpaGen 161
                                   gt+g+sn+Gg+f++elk++Gyd+i+i+G a+kpvyl++ ddkv+ieda+ lwg+d+yet+ +lk+   + +++viG  Ge+
  gi|13542070|ref|NP_111758.1|  87 GTWGDSNCGGKFAPELKNTGYDGIFIRGIAKKPVYLKVIDDKVSIEDASALWGKDAYETETELKKIDPKgQAMVIGVPGEK 167
                                   *****************************************************************54445999******** PP

                                   T-TTB-E.EETTEEE-SSSHHHHHHHTTEEEEEEE-- CS
                        AFOR_N 162 lvrfAsisvddgraagrgGlGavmgsKnlkaivvrgt 198
                                   ++ +A+i+ + graagr+Gl+avmgsK+lk i vrgt
  gi|13542070|ref|NP_111758.1| 168 MMYAAAIMNEYGRAAGRSGLAAVMGSKKLKGIFVRGT 204
                                   *******6669************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (624 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       386  (0.0215294); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.64u 0.35s 00:00:00.99 Elapsed: 00:00:00.52
# Mc/sec: 3632.46
//
Query:       gi|13542071|ref|NP_111759.1|  [L=686]
Description: cation transport ATPase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-44  152.2   2.3    1.1e-44  152.2   2.3    2.3  3  E1-E2_ATPase  E1-E2 ATPase
    1.6e-28  100.5   0.6    4.2e-28   99.1   0.2    1.9  2  Hydrolase     haloacid dehalogenase-like hydrolase
    1.4e-14   53.9   1.0    2.9e-14   52.9   1.0    1.6  1  YHS           YHS domain
    2.2e-08   34.1   1.5    3.4e-06   27.0   0.4    2.8  3  Hydrolase_3   haloacid dehalogenase-like hydrolase
    0.00017   21.7   0.1    0.00041   20.5   0.1    1.6  1  HAD_2         Haloacid dehalogenase-like hydrolase
     0.0065   16.9   0.0      0.015   15.8   0.0    1.6  1  HAD           haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.013   15.4   1.2      0.024   14.6   1.2    1.4  1  zf-FCS        MYM-type Zinc finger with FCS sequence motif
      0.053   13.5   1.1       0.18   11.8   0.1    2.4  2  Tricorn_PDZ   Tricorn protease PDZ domain
      0.055   13.9   0.3      0.055   13.9   0.3    2.7  3  DUF4231       Protein of unknown function (DUF4231)
      0.093   12.8   1.4        1.3    9.1   0.2    2.9  3  HTH_7         Helix-turn-helix domain of resolvase


Domain annotation for each model (and alignments):
>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.2       1.1     2e+03     119     162 ..     103     130 ..      96     148 .. 0.55
   2 !  152.2   2.3   5.9e-48   1.1e-44       2     180 ..     172     356 ..     171     357 .. 0.97
   3 ?   -2.4   0.0       1.6   2.9e+03      25      52 ..     577     606 ..     576     609 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.1
                                   HHHHHHHHHHHHHHHHHS-STTTSSTTHHHHHHHHHHHHHS-TT CS
                  E1-E2_ATPase 119 gkvlvpvvlliallvflialllgkslaeallralallvaaiPca 162
                                   ++ + +++ + +l++f++ l++  +++                a
  gi|13542071|ref|NP_111759.1| 103 SGNMDLLISIGVLTAFFFSLFVSIFPQ----------------A 130
                                   444555555555555555555555554................2 PP

  == domain 2  score: 152.2 bits;  conditional E-value: 5.9e-48
                                   SS--EEEEE-TTS-EEEEGGG--TTSEEEEETT-B--SEEEEEEE-SEEE-TTTS---S-EE-G-TTEE-TT-EEEE-EEE CS
                  E1-E2_ATPase   2 llpptakvirdgteeeidakelvpGDivllkagdrvpaDgrivegsaevdesaLTGEslpvekekgdmvfsGtvvvsgeak 82 
                                   ++p+ ++++ + ++++ +a+ l+ G  +++++g+++++Dg i+eg +evdes++TGE++pv k++gd+v+sGt +++g ++
  gi|13542071|ref|NP_111759.1| 172 MMPKIVHIVSGASIKDAEASSLKAGVTLQVRPGEIIAVDGTILEGRSEVDESSITGEQEPVLKTAGDRVISGTKNLNGMLI 252
                                   6788999999*********************************************************************** PP

                                   EEEEE-TTTSTTTTTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTT......HHHHHHHHHHHH CS
                  E1-E2_ATPase  83 avVtatgedtelgkiarlveeakskktplqkkldklgkvlvpvvlliallvflialllgksla......eallralallva 157
                                   +++ a+g dt+++ki  l+  a+s +t++q+++d +++++vpvvl++a + fl+++++ ks+         +l +++++v+
  gi|13542071|ref|NP_111759.1| 253 VKAEAVGADTTVSKIHGLIVMASSGRTKVQRIADIFSSYFVPVVLVAATASFLFWYFYLKSIGnplapeIGILAFVSVVVI 333
                                   *********************************************************9999888999*999********** PP

                                   HS-TTHHHHHHHHHHHHHHHHHH CS
                  E1-E2_ATPase 158 aiPcaLplavplalalgarrlak 180
                                   a+Pca++la p++l+++a +  k
  gi|13542071|ref|NP_111759.1| 334 ACPCAIGLAGPITLLISAEESFK 356
                                   ***************99988766 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 1.6
                                   TTSEEEEETT-B--SEEEEEEE-S..EEE- CS
                  E1-E2_ATPase  25 pGDivllkagdrvpaDgrivegsa..evde 52 
                                    GDivl++++ +  +D+  ++ s+  +v+e
  gi|13542071|ref|NP_111759.1| 577 AGDIVLVNNKLSTIIDILTISRSTikKVKE 606
                                   59*****99999888888888777666665 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       1.6   2.9e+03       9      21 ..     210     222 ..     206     296 .. 0.61
   2 !   99.1   0.2   2.4e-31   4.2e-28       1     210 []     373     562 ..     373     562 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.6
                                   BTTTBCHHHHHHH CS
                                   xxxxxxxxxxxxx RF
                     Hydrolase   9 dGTLttgepsved 21 
                                   dGT+++g+++v +
  gi|13542071|ref|NP_111759.1| 210 DGTILEGRSEVDE 222
                                   6666666655554 PP

  == domain 2  score: 99.1 bits;  conditional E-value: 2.4e-31
                                   SSEEEEESBTTTBCHHHHHHHHHHHH.CHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHETTTEHHHHTHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hydrolase   1 iktvvfDkdGTLttgepsvedvivsa.alalaaaletgsehpigkalvaaakarsgaltgfatfigrgayaigkpewltal 80 
                                   i+ +vfDk GTLt   p++ d++  + ala aa  e gs+hp +  +v++a +++  +++  +     ++ +     + + 
  gi|13542071|ref|NP_111759.1| 373 INRIVFDKSGTLTSPLPEIYDLTGDIkALAYAASVESGSNHPVALSIVNKARDLGLRIEKAYQ-----VVEEPGIGITGKV 448
                                   6789*********************9999999999999****************888866666.....5666666666666 PP

                                   HCHHHHHHHHHHHHHHCHHHHHHTTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTTGGGES CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hydrolase  81 dippdlgaaigsaqsqgrtvallqaralavftiadplkvkpeaaeavasLkaagievvlltgdnpetaeraanqlGddyfd 161
                                       d ++   +  + g t +  ++++   f +  +  ++++a e+v +Lk++ i+v +l+gd ++ a+++++ l      
  gi|13542071|ref|NP_111759.1| 449 ----DGKEVRIAQDESGATIVEIDGDVACRFRLRYK--LRDDAIETVSALKKMEIKVSVLSGDTSKEAKSVLEPLK----- 518
                                   ....44444445556777777776777777777755..**************************************..... PP

                                   EEEEHHCESSTTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHTT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hydrolase 162 aviasdietvakpspegkvaaireLqgkpeevamVGDgvnDaaalaaAg 210
                                         +e++ + +pe k +++r++q+k+e v++VGDg+nD  al+ A+
  gi|13542071|ref|NP_111759.1| 519 -----LDEVITGSNPEEKAEVVRRYQEKGEYVMFVGDGINDTVALETAD 562
                                   .....7888************************************9997 PP

>> YHS  YHS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.9   1.0   1.6e-17   2.9e-14       2      40 ..       3      40 ..       2      43 .. 0.95

  Alignments for each domain:
  == domain 1  score: 52.9 bits;  conditional E-value: 1.6e-17
                           YHS  2 tdPvcgmkvdkekaeekseYkGkeYyFcSegCkdkFede 40
                                  tdPvcgm+v +e+++ +++ +G++YyFcS+gC++kF+ +
  gi|13542071|ref|NP_111759.1|  3 TDPVCGMYV-PETSDLYVDKDGQRYYFCSKGCMEKFLSP 40
                                  7********.**************************875 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.91   1.6e+03       5      21 ..     209     225 ..     206     281 .. 0.83
   2 ?    4.8   0.0     0.011        20      16      62 ..     481     527 ..     477     527 .. 0.89
   3 !   27.0   0.4   1.9e-09   3.4e-06     195     252 ..     534     591 ..     531     594 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.91
                                   IIIIIS-TTS---HHHH CS
                   Hydrolase_3   5 lDGTLlnsdkkisektk 21 
                                   +DGT+l   ++++e+++
  gi|13542071|ref|NP_111759.1| 209 VDGTILEGRSEVDESSI 225
                                   79999999999988776 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.011
                                   --HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCCSEEEEGG CS
                   Hydrolase_3  16 isektkeaikklkekgikvviATGRslravlpvleelgldlpvialN 62 
                                   + + ++e++  lk+ +ikv + +G   +++++vle l+ld  + ++N
  gi|13542071|ref|NP_111759.1| 481 LRDDAIETVSALKKMEIKVSVLSGDTSKEAKSVLEPLKLDEVITGSN 527
                                   56778999999*****************************7777666 PP

  == domain 3  score: 27.0 bits;  conditional E-value: 1.9e-09
                                   HHHHCT--GGGEEEEESSGGGHHHHHHSSEEEEETTS-HHHHHHSSEEE--GGGTHHH CS
                   Hydrolase_3 195 lakelnisleeviafGDgeNDieMLeaaglgvAmgnaseevkkaAdyvtksnnedGVa 252
                                   ++ +++ + e v+ +GDg ND   Le a+ g+Amg++s+  k+a d v  +n+ + + 
  gi|13542071|ref|NP_111759.1| 534 VVRRYQEKGEYVMFVGDGINDTVALETADAGIAMGSGSDITKAAGDIVLVNNKLSTII 591
                                   6778999999************************************999988766665 PP

>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.1   2.3e-07   0.00041      78     170 ..     479     560 ..     452     567 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 2.3e-07
                         HAD_2  78 vkpydgvkelLeeLkeagyklgivTsksreaveekleqlgiesyFdvivtsedvekkKPdpeviekaleklklkkeeviyv 158
                                    k+ d+++e++  Lk++++k+ + +  +++++++ le l++    d ++t+++ e+k       ++++++++ k e v++v
  gi|13542071|ref|NP_111759.1| 479 YKLRDDAIETVSALKKMEIKVSVLSGDTSKEAKSVLEPLKL----DEVITGSNPEEK-------AEVVRRYQEKGEYVMFV 548
                                   57889***********************************6....677777776666.......79999************ PP

                         HAD_2 159 GDsptDieaakk 170
                                   GD ++D  a   
  gi|13542071|ref|NP_111759.1| 549 GDGINDTVALET 560
                                   ******877555 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   8.1e-06     0.015      69     187 ..     468     558 ..     441     559 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 8.1e-06
                           HAD  69 laaelerfvaevirpklldpgalellaahraaGdrvvvvSgglrplvepllaelgadevlatelevddrltgelglegkpv 149
                                   + + ++rf+    r k l+ +a e ++a ++  ++v v+Sg  +  ++ +l+ l     l++      ++tg         
  gi|13542071|ref|NP_111759.1| 468 DGDVACRFR---LRYK-LRDDAIETVSALKKMEIKVSVLSGDTSKEAKSVLEPLK----LDE------VITGS-------- 526
                                   555566666...2222.5579**********************************....***......9****........ PP

                           HAD 150 rgegkvaalrewlaaegegidleevvayGDspsDlpll 187
                                   + e+k+ ++r+  ++e+     e v+++GD+++D  +l
  gi|13542071|ref|NP_111759.1| 527 NPEEKAEVVRR--YQEKG----EYVMFVGDGINDTVAL 558
                                   9999*******..55554....449*********8666 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 ?   14.6   1.2   1.3e-05     0.024      20      41 .]      16      37 ..       7      37 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.3e-05
                        zf-FCS 20 tyvlendgvvgqFCStsCldsY 41
                                    ++++dg+ ++FCS+ C+ ++
  gi|13542071|ref|NP_111759.1| 16 DLYVDKDGQRYYFCSKGCMEKF 37
                                  46899**************998 PP

>> Tricorn_PDZ  Tricorn protease PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1    0.0001      0.18      15      64 ..     175     224 ..     170     238 .. 0.80
   2 ?   -2.4   0.1       2.7   4.9e+03      41      52 ..     459     470 ..     448     473 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0001
                                   EEEEE-BS-TTSSS-B-GGGG.GS---.TT-EEEEETTEE-BTTB-HHHHH CS
                   Tricorn_PDZ  15 riakilpGdswdeearSPLae.pGvnvreGdlilavdgepvskekgiaelL 64 
                                   +i +i++G+s ++++ S+L++   ++vr G++ +avdg  ++ +++++e  
  gi|13542071|ref|NP_111759.1| 175 KIVHIVSGASIKDAEASSLKAgVTLQVRPGEI-IAVDGTILEGRSEVDESS 224
                                   699****************7524568899985.69***9999888887754 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.7
                                   .TT-EEEEETTE CS
                   Tricorn_PDZ  41 reGdlilavdge 52 
                                   + G++i+++dg 
  gi|13542071|ref|NP_111759.1| 459 ESGATIVEIDGD 470
                                   579999999995 PP

>> DUF4231  Protein of unknown function (DUF4231)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1       1.2   2.2e+03      25      62 ..      53      88 ..      45      95 .. 0.79
   2 ?   -2.1   0.3       3.1   5.6e+03      19      37 ..     281     313 ..     275     355 .. 0.63
   3 ?   13.9   0.3   3.1e-05     0.055       9      66 ..     605     661 ..     598     685 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1.2
                       DUF4231 25 ivlgallpilvssklgagvsvlkiltallsalvailaa 62
                                  i   + +p+l+   + a +++  ++ ++ls+ v++ ++
  gi|13542071|ref|NP_111759.1| 53 IAWLFSIPVLIL--SYALFPQKDWVLFILSIPVVFYSG 88
                                  555577888888..788999999999999998888665 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3.1
                       DUF4231  19 llrlitivlgallpilvs..............s 37 
                                   + r++ i+ + ++p++ +              s
  gi|13542071|ref|NP_111759.1| 281 VQRIADIFSSYFVPVVLVaatasflfwyfylkS 313
                                   556777777777777766444445555554442 PP

  == domain 3  score: 13.9 bits;  conditional E-value: 3.1e-05
                       DUF4231   9 kasrakrrfrllrlitivlgallpilvssklgagvsvlkiltallsalvailaaleef 66 
                                   k +++ ++ +  +li i +g+l+p++++    ++ ++l++l+ ++s+++++l++l   
  gi|13542071|ref|NP_111759.1| 605 KENIFWAIIYNSALIPIAGGVLVPVFST-SVYSVLPILAALAMGMSSTTVVLNSLRLK 661
                                   5677777888999***************.57777777777778888888888887655 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 ?    1.0   0.0      0.26   4.6e+02      11      31 ..     267     288 ..     261     289 .. 0.87
   2 ?   -1.8   0.0       1.9   3.4e+03       8      21 ..     528     541 ..     526     544 .. 0.81
   3 ?    9.1   0.2   0.00074       1.3      25      43 ..     588     606 ..     585     607 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.26
                                   HGGGGSSTTTT.--STTTSSSS CS
                         HTH_7  11 inrvvkLleeG.isiskIAkev 31 
                                   i+ ++ + ++G ++++ IA+++
  gi|13542071|ref|NP_111759.1| 267 IHGLIVMASSGrTKVQRIADIF 288
                                   788889999***********98 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.9
                                   HHHHGGGGSSTTTT CS
                         HTH_7   8 kndinrvvkLleeG 21 
                                   +++ ++vv++++e+
  gi|13542071|ref|NP_111759.1| 528 PEEKAEVVRRYQEK 541
                                   667799*****986 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.00074
                                   TTTSSSS---SSSS--SS- CS
                         HTH_7  25 skIAkevnisRsTvYRyla 43 
                                   s+I +++ isRsT++++++
  gi|13542071|ref|NP_111759.1| 588 STIIDILTISRSTIKKVKE 606
                                   7899*************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (686 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       631  (0.0351944); 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:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.70u 0.33s 00:00:01.03 Elapsed: 00:00:00.54
# Mc/sec: 3848.80
//
Query:       gi|13542072|ref|NP_111760.1|  [L=45]
Description: hypothetical protein TVN1241 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-19   69.5   1.3    1.9e-19   69.5   1.3    1.0  1  YHS              YHS domain
     0.0057   16.6   0.8      0.007   16.3   0.8    1.2  1  zf-FCS           MYM-type Zinc finger with FCS sequence motif
  ------ inclusion threshold ------
      0.034   14.5   1.9      0.042   14.2   1.9    1.3  1  Arc_trans_TRASH  Archaeal TRASH domain
      0.082   12.9   0.4      0.082   12.9   0.4    1.6  1  DUF2116          Uncharacterized protein containing a Zn-ribb


Domain annotation for each model (and alignments):
>> YHS  YHS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.5   1.3   4.3e-23   1.9e-19       1      44 [.       1      43 [.       1      45 [] 0.96

  Alignments for each domain:
  == domain 1  score: 69.5 bits;  conditional E-value: 4.3e-23
                           YHS  1 vtdPvcgmkvdkekaeekseYkGkeYyFcSegCkdkFedePekY 44
                                  ++dPvcgmk dk+ ++ ks Y+GkeYyFcSe+Ck  F+++P +Y
  gi|13542072|ref|NP_111760.1|  1 MIDPVCGMKADKN-SKWKSVYNGKEYYFCSEHCKIQFDKNPIRY 43
                                  68***********.****************************** 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 !   16.3   0.8   1.6e-06     0.007      25      38 ..      20      33 ..      12      36 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.6e-06
                        zf-FCS 25 ndgvvgqFCStsCl 38
                                  ++g++++FCS++C+
  gi|13542072|ref|NP_111760.1| 20 YNGKEYYFCSEHCK 33
                                  78***********6 PP

>> Arc_trans_TRASH  Archaeal TRASH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   1.9   9.3e-06     0.042      19      35 ..      22      38 ..       6      40 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 9.3e-06
               Arc_trans_TRASH 19 nkvYyvCCktCkselkk 35
                                   k Yy+C + Ck ++ k
  gi|13542072|ref|NP_111760.1| 22 GKEYYFCSEHCKIQFDK 38
                                  589************88 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 ?   12.9   0.4   1.8e-05     0.082      16      32 ..      24      40 ..      18      45 .] 0.83

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.8e-05
                       DUF2116 16 desfCsekCqeeyekkr 32
                                  +  fCse+C+ +++k+ 
  gi|13542072|ref|NP_111760.1| 24 EYYFCSEHCKIQFDKNP 40
                                  567***********985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (45 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       574  (0.0320152); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 308.37
//
Query:       gi|13542073|ref|NP_111761.1|  [L=61]
Description: metal-binding protein [Thermoplasma volcanium GSS1]
Scores for complete 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-24   83.4   0.5    1.1e-23   83.2   0.5    1.0  1  DUF1059   Protein of unknown function (DUF1059)
  ------ inclusion threshold ------
       0.16   12.4   0.0       0.21   12.0   0.0    1.2  1  DUF1039   Protein of unknown function (DUF1039)


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 !   83.2   0.5   1.2e-27   1.1e-23       1      56 []       3      58 ..       3      58 .. 0.98

  Alignments for each domain:
  == domain 1  score: 83.2 bits;  conditional E-value: 1.2e-27
                       DUF1059  1 mkefkCgDvgpdCgfeitaeteeEvlrkvaeHakaaHglteippelvekiksaIkd 56
                                  ++ fkC D+g++Cgfe++a++ +E+++k++eHak+aH++tei+++l +k+ saIk+
  gi|13542073|ref|NP_111761.1|  3 KYVFKCSDIGMNCGFEASAKSIDELMPKIVEHAKTAHNITEINEDLKNKVTSAIKK 58
                                  699***************************************************97 PP

>> DUF1039  Protein of unknown function (DUF1039)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   2.4e-05      0.21       3      27 ..      12      36 ..      11      44 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.4e-05
                       DUF1039  3 avNHgllkeahailnaLPllipDee 27
                                  ++N+g+ + a++i + +P +++  +
  gi|13542073|ref|NP_111761.1| 12 GMNCGFEASAKSIDELMPKIVEHAK 36
                                  89*******************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1337  (0.0745719); expected 358.6 (0.02)
Passed bias filter:                      677  (0.0377601); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.31s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 386.29
//
Query:       gi|13542074|ref|NP_111762.1|  [L=392]
Description: nicotinate phosphoribosyltransferase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.4e-20   71.6   0.0      1e-19   71.0   0.0    1.3  1  QRPTase_C       Quinolinate phosphoribosyl transferase, C-ter
     0.0069   15.8   0.0      0.013   14.9   0.0    1.4  1  Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family
  ------ inclusion threshold ------
       0.16   12.4   0.0       0.37   11.2   0.0    1.7  1  NAPRTase_C      Nicotinate phosphoribosyltransferase C-termin


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 !   71.0   0.0   1.7e-23     1e-19       1     169 []     119     306 ..     119     306 .. 0.90

  Alignments for each domain:
  == domain 1  score: 71.0 bits;  conditional E-value: 1.7e-23
                                   HHHHHHHHHHHHHCTSSEEEE-S---TTTHHHHHHHHHHTTSB.......--TSSTTTSEEE-HHHHHHHSSHHHHHHHHH CS
                     QRPTase_C   1 iAtltarmveaaksakvrildTRkttPglrllekyAvliGGgd.......nhrlgLsdmvlikdnhiaaagsiveavksvr 74 
                                   i t+++++  aa +    +++ R+++P++ ++  +++ iGG+d        + +g + + +++++  +++g+  ea++   
  gi|13542074|ref|NP_111762.1| 119 ISTKSSKVRIAAGDCPFFSFGIRRMHPAVSPMIDRSAFIGGADgvsgilgAKLIGEEPIGTMPHALSIILGD-DEAWRLTL 198
                                   678888888899999999*****************************************************7.66777766 PP

                                   HHHTTTSE..EEEEESSHHHHHHHHHHT....-SEEEEES--H..HHHHHHHHHH.HHHSTT....SEEEEESS--TTTHH CS
                     QRPTase_C  75 eavdkevk..ievevesleeleevleae....adiimLDnfsv..eelkkaveel.keknkr....vlievSGgvtlenve 142
                                   +++++  k  i ++++ +e++ ++  ae    +d i+LD++s+   +++  v e+ +e + r    ++i vSGg+ +++v+
  gi|13542074|ref|NP_111762.1| 199 KNTKNGQKsvILIDTYMDEKFAAIKVAEefehVDYIRLDTPSSrrGNFEALVREVkWELALRgrsdIKIMVSGGLDENTVA 279
                                   6665544457***********99877666778*********9877899****99989999889999*************** PP

                                   HHHCTT-SEEEECHHCHTB----EEEE CS
                     QRPTase_C 143 eyaksgvdvisvgalthsvkalDislk 169
                                   ++++ g ++++vg+ ++s+k+ D++l+
  gi|13542074|ref|NP_111762.1| 280 KLREAGAQAFGVGTSISSAKPFDFALD 306
                                   ************************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 !   14.9   0.0   2.1e-06     0.013     154     197 ..     251     295 ..     246     296 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.1e-06
                                   HHHHHHHHHHT.---EEEEESS--TTTCHHHHHHT--EEEESHHH CS
                Ribul_P_3_epim 154 kkvrklideke.ldlkievDGGvkldnieqiaeagadvlVagsav 197
                                   ++v+  ++ ++  d+ki v GG+++++++++ eaga+++ +g+ +
  gi|13542074|ref|NP_111762.1| 251 REVKWELALRGrSDIKIMVSGGLDENTVAKLREAGAQAFGVGTSI 295
                                   55665554444489*************************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 ?   11.2   0.0   6.2e-05      0.37      54      88 ..     356     390 ..     304     392 .] 0.91

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 6.2e-05
                    NAPRTase_C  54 kLlkkvfkdGklvyelpsleeireyvkeqlaelrp 88 
                                   ++  k++++Gkl+ + p+ +eir+++ ++l+ +r 
  gi|13542074|ref|NP_111762.1| 356 NIIVKYMEHGKLLSQYPEPKEIRKRTLSELEYFRS 390
                                   67789**************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (392 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       474  (0.0264376); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 2420.58
//
Query:       gi|13542075|ref|NP_111763.1|  [L=454]
Description: cysteinyl-tRNA synthetase [Thermoplasma volcanium GSS1]
Scores for 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-118  394.2   1.1   5.5e-118  393.7   1.1    1.2  1  tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
    3.3e-19   68.9   2.9    1.6e-10   40.3   0.4    3.0  3  tRNA-synt_1g  tRNA synthetases class I (M)
      3e-08   32.4   0.0    0.00011   20.6   0.0    2.2  2  tRNA-synt_1   tRNA synthetases class I (I, L, M and V)
    2.1e-05   23.6   0.1    0.00048   19.2   0.1    2.2  2  tRNA-synt_1f  tRNA synthetases class I (K)
     0.0017   17.4   0.3     0.0068   15.4   0.0    2.1  2  tRNA-synt_1d  tRNA synthetases class I (R)
  ------ inclusion threshold ------
      0.017   15.5   0.7         10    6.6   0.1    2.9  2  DUF4550       Domain of unknown function (DUF4550)
      0.069   12.0   5.2        1.6    7.6   1.3    3.0  2  tRNA-synt_1c  tRNA synthetases class I (E and Q), catalytic d
       0.11   12.5   2.5        4.3    7.3   0.0    3.0  3  FNIP_M        Folliculin-interacting protein middle domain
       0.12   12.6   0.1       0.32   11.2   0.1    1.7  1  TMF_TATA_bd   TATA element modulatory factor 1 TATA binding
       0.18   12.2   1.0        4.3    7.8   1.0    2.5  1  FUN14         FUN14 family


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 !  393.7   1.1  3.1e-121  5.5e-118       2     300 ..      14     312 ..      13     313 .. 0.98

  Alignments for each domain:
  == domain 1  score: 393.7 bits;  conditional E-value: 3.1e-121
                                   ---SBTTEEEEEEEEEBTTS--BHHHHHHHHHHHHHHHHHHHTT-EEEEEEEBB--SHHHHHHHHHTTS-HHHHHHHHHHH CS
                  tRNA-synt_1e   2 vkpleekkvtlYvCGptvydashlGhaRslvafDilrrilqalgYdvqfvqnvtDidDkiikrareeeksvkelaekfiee 82 
                                   ++++++++v+l+vCGptv+d+ h+GhaR++++fD ++++l+  gY v ++qn+tDidDkii+ra+e + + +e+a+ + +e
  gi|13542075|ref|NP_111763.1|  14 FNEMHRGRVNLFVCGPTVQDHFHIGHARTYIFFDAVAKFLKLEGYSVFYLQNITDIDDKIINRAKEMGIEPSEVAKIYFSE 94 
                                   5788999************************************************************************** PP

                                   HHHHHHHTT----SB--BGGGGHHHHHHHHHHHHHTTSEEE-TTS-EEE-GGG-TTTTTTTT--HHHHHHT----S--S-S CS
                  tRNA-synt_1e  83 fkkdleaLnvlkptleprvsekvdeiielvekliekgyaYavsdgdvyfdvskkeeYgklskqnleelelgaegevseekk 163
                                   f++d++ L+v   ++ +r++ ++dei+  + +++ekgyaY+++ + vyf+v+k+++Yg+ls+q+l+++ +g +++v+e+k+
  gi|13542075|ref|NP_111763.1|  95 FQEDMKRLKVDSVNFFARATLYIDEIVSQISRMMEKGYAYETD-DGVYFEVRKFKDYGELSNQSLDQIIAGYRVAVNENKR 174
                                   *****************************************99.89*********************************** PP

                                   STT-EEEEEE--TTS--B--TTSSEEE-SSHHHHHHHHHHH-SSEEEEEEEGGGTTTHHHHHHHHHHHHSS.S--EEEEEE CS
                  tRNA-synt_1e 164 dkkDfaLWkaskegepswdsPwgkGRPGWhieCsvmaskllgseidihsGGiDLafPhhenelaqseaafd.kqlvkyflh 243
                                   +++Df+LWk++k+gepsw+sPwg+GRPGWhie ++++++++g+e dih+GG+DL+fPhhe e+aq ++  + + l++y++h
  gi|13542075|ref|NP_111763.1| 175 NPEDFVLWKKKKAGEPSWPSPWGEGRPGWHIEDTAITETYFGDEYDIHGGGSDLIFPHHEAEIAQMRSISGkRYLAHYWIH 255
                                   ***********************************************************************556789**** PP

                                   E--EEETTBE--TTTT---BHHHHHTTS-HHHHHHHHHSS-TTS-EEE-HHHHHHHH CS
                  tRNA-synt_1e 244 nghlkiegekmsksLknfitikdvlkkfdprqlRllllsahyrsqldfkeelleeak 300
                                   +g+++i++ekmsksLknfiti+d+lk ++p+ lR+++l+a+yr+q++f++el+ee+k
  gi|13542075|ref|NP_111763.1| 256 TGMININKEKMSKSLKNFITIRDILKDYRPEDLRFAILNANYRTQIEFSKELMEESK 312
                                   *****************************************************9987 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.3   0.4   9.2e-14   1.6e-10      10     125 ..      31     145 ..      26     152 .. 0.90
   2 !   24.6   0.1   5.1e-09   9.2e-06     312     369 ..     250     306 ..     225     324 .. 0.78
   3 ?    2.6   0.0     0.025        45     234     263 ..     375     405 ..     349     421 .. 0.79

  Alignments for each domain:
  == domain 1  score: 40.3 bits;  conditional E-value: 9.2e-14
                                   -SS---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHHTT---SEEEE CS
                  tRNA-synt_1g  10 angklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkAekegvtpeelvekvheeikelfkklnisfdkygr 90 
                                   ++++ H+Gh++++i  D++a++ +l+g+ v+++        +i  +A++ g++p+e+++ + +e++e++k+l++   ++  
  gi|13542075|ref|NP_111763.1|  31 VQDHFHIGHARTYIFFDAVAKFLKLEGYSVFYLQNITDIDDKIINRAKEMGIEPSEVAKIYFSEFQEDMKRLKVDSVNFFA 111
                                   67889*****************************999999**********************************9999998 PP

                                   TTSHHHHHHHHHHHHHHHHTT-EEEEEEEEEEETT CS
                  tRNA-synt_1g  91 ttseehkelvqeifkklkekgliyekeieqlycpk 125
                                     +    e+v++i + + ekg+ ye++  +++ ++
  gi|13542075|ref|NP_111763.1| 112 RATLYIDEIVSQISR-MMEKGYAYETDDGVYFEVR 145
                                   888999999999865.6677**9999888777665 PP

  == domain 2  score: 24.6 bits;  conditional E-value: 5.1e-09
                                   -S-EEEE--EEE--------------HHHHHHHH-HHHHHHHHHHHS-TTS-EEE-HH CS
                  tRNA-synt_1g 312 pkkvvaheyltvegkKlSkSrgvvvkakealerldadllRYylaaeapekkDldfswe 369
                                    +  + +++++++ +K+SkS +++++++++l+ + ++ lR+ ++ + +  + ++fs e
  gi|13542075|ref|NP_111763.1| 250 AHYWIHTGMININKEKMSKSLKNFITIRDILKDYRPEDLRFAILNA-NYRTQIEFSKE 306
                                   45556789*********************************98864.45556777765 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.025
                                   S-EET.TECCEEE-HHHHHHHHHHHTTTTT- CS
                  tRNA-synt_1g 234 GipvP.gaekkvlYVWldAligYisatkela 263
                                   Gi+    +e k +Y W+d ++g +   ke++
  gi|13542075|ref|NP_111763.1| 375 GINKEvAEELKKVYLWVDTFLGILEQKKEVS 405
                                   665555678899**********999998887 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 !    9.8   0.0   0.00011       0.2      27      67 ..      24      64 ..      11     129 .. 0.78
   2 !   20.6   0.0   6.4e-08   0.00011     519     602 .]     221     304 ..     196     304 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00011
                   tRNA-synt_1 27 lvdgPPyvtGslHiGhalaktlkdivirykrmkGkevlyvp 67
                                  l++  P v  + HiGha + +  d v ++ +++G++v y+ 
  gi|13542075|ref|NP_111763.1| 24 LFVCGPTVQDHFHIGHARTYIFFDAVAKFLKLEGYSVFYLQ 64
                                  556679999****************************9975 PP

  == domain 2  score: 20.6 bits;  conditional E-value: 6.4e-08
                   tRNA-synt_1 519 mlleGlDiirgWvarlillslaltgsePfkevlvhglvrdeeGrKmSKslgNvidpldvikkygadalRltlilsdvgrdi 599
                                   +   G+D i+   +  i +   + g++   +  +h  +++ +  KmSKsl+N i   d++k y  + lR++++++++  +i
  gi|13542075|ref|NP_111763.1| 221 IHGGGSDLIFPHHEAEIAQMRSISGKRYLAHYWIHTGMININKEKMSKSLKNFITIRDILKDYRPEDLRFAILNANYRTQI 301
                                   55567777777777777777777777777777777777777889*********************************9999 PP

                   tRNA-synt_1 600 nls 602
                                   ++s
  gi|13542075|ref|NP_111763.1| 302 EFS 304
                                   875 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 ?    1.9   0.0     0.048        87      25      72 ..      23      70 ..       5      80 .. 0.79
   2 !   19.2   0.1   2.7e-07   0.00048     275     322 ..     260     306 ..     252     331 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.048
                  tRNA-synt_1f 25 vvvesGispSGliHiGnlrevltadlvaralrkrgeevrlilisDdmD 72
                                   ++  G ++  + HiG +r  +  d+va+ l+  g +v  +  + d+D
  gi|13542075|ref|NP_111763.1| 23 NLFVCGPTVQDHFHIGHARTYIFFDAVAKFLKLEGYSVFYLQNITDID 70
                                  467788899999******************999998876666666665 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 2.7e-07
                  tRNA-synt_1f 275 llkggekmssSkGnvltledwlevaepevlrflilrrkPkkakkldld 322
                                    ++ +ekms+S  n++t++d+l+ + pe lrf il+++ +++++++ +
  gi|13542075|ref|NP_111763.1| 260 NIN-KEKMSKSLKNFITIRDILKDYRPEDLRFAILNANYRTQIEFSKE 306
                                   444.45******************************999888888766 PP

>> tRNA-synt_1d  tRNA synthetases class I (R)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   3.8e-06    0.0068      17      68 ..      17      68 ..       3      74 .. 0.83
   2 ?   -1.7   0.1      0.61   1.1e+03     141     195 ..      89     145 ..      75     162 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 3.8e-06
                                  SST-EEEEE----BTTS--BHHHHHHHHHHHHHHHHHHHCT-EEEEEE--B- CS
                  tRNA-synt_1d 17 rekkkvvvdfssPniakemhvGhLrstiiGdavsrlleflGydvirlnhvGD 68
                                   ++ +v +    P +   +h+Gh r+ i  dav++ l + Gy+v  l  + D
  gi|13542075|ref|NP_111763.1| 17 MHRGRVNLFVCGPTVQDHFHIGHARTYIFFDAVAKFLKLEGYSVFYLQNITD 68
                                  5555666666789*******************************99888776 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.61
                                   HHHHHHHHHHHHHCT---EC..--CCCCCCCHHHHHHHHHCTT-EEECTTCEEEEEC CS
                  tRNA-synt_1d 141 ditrtelqklydrldvtlie..rGeslykeslneivkelkkkglvkesdGalvvfld 195
                                   +i   e+q+  +rl v +++     +ly + + + +  + +kg++ e+d      + 
  gi|13542075|ref|NP_111763.1|  89 KIYFSEFQEDMKRLKVDSVNffARATLYIDEIVSQISRMMEKGYAYETDDGVYFEVR 145
                                   555667777778888888776444458888888888888888888887755555554 PP

>> DUF4550  Domain of unknown function (DUF4550)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.1    0.0083        15       7      37 ..      92     123 ..      87     140 .. 0.79
   2 ?    6.6   0.1    0.0057        10      30      76 ..     229     277 ..     203     284 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0083
                       DUF4550   7 YvllpddeepkkvDvvvfgsvAkvfle.sesk 37 
                                   ++ + +d ++ kvD v+f + A ++++   s+
  gi|13542075|ref|NP_111763.1|  92 FSEFQEDMKRLKVDSVNFFARATLYIDeIVSQ 123
                                   66778999*****************9943444 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0057
                       DUF4550  30 vfleseskvvkpwe..eddklwiswthtieinvtkellkkllehkiklk 76 
                                   +f+++e+ ++++ +      l  +w ht  in++ke+++k l++ i+++
  gi|13542075|ref|NP_111763.1| 229 IFPHHEAEIAQMRSisGKRYLAHYWIHTGMININKEKMSKSLKNFITIR 277
                                   677666666555543255567789****************999999987 PP

>> tRNA-synt_1c  tRNA synthetases class I (E and Q), catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   1.3   0.00088       1.6      14      98 ..      35     137 ..      28     140 .. 0.58
   2 ?    3.9   0.1     0.011        20     230     279 ..     252     303 ..     240     329 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00088
                                   -BHHHHHHHHHHHHHHH..HTT-EEEEEE--SSCCC--HHHHHHHHHHHHHTT---S......................SE CS
                  tRNA-synt_1c  14 LHiGhakaallnylfAk..nnnGkfilRieDTdperekeeaeesiledlkwlgikwd......................ek 70 
                                    HiGha++ ++  + Ak  + +G  +         +++ +  ++i++  k +gi+++                      + 
  gi|13542075|ref|NP_111763.1|  35 FHIGHARTYIFFDAVAKflKLEGYSVFY------LQNITDIDDKIINRAKEMGIEPSevakiyfsefqedmkrlkvdsvNF 109
                                   5666666666655555522333432222......12333333444444444444443344444444444466665555588 PP

                                   EEEGGGGHHHHHHHHHHHHHTTSEEEE- CS
                  tRNA-synt_1c  71 ptyqsdrfdelkkyaeeLikkGkAYvce 98 
                                   + +++ + de+ + + ++++kG+AY  +
  gi|13542075|ref|NP_111763.1| 110 FARATLYIDEIVSQISRMMEKGYAYETD 137
                                   9************************865 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.011
                                   EEEEE--EEETTSB-SHHHHHHHHHTTSSSST..T-TTSCBHHHHHHCTB-H CS
                  tRNA-synt_1c 230 fiheylrlnlekkklSKRklsllvdekqvkew..ddlreallnflrrlGwtp 279
                                   +   + ++n++k+k+SK  ++ +   + +k+   +dlr+a+ln+  r  ++ 
  gi|13542075|ref|NP_111763.1| 252 YWIHTGMININKEKMSKSLKNFITIRDILKDYrpEDLRFAILNANYRTQIEF 303
                                   44467899*********99999877777776433899999999988876553 PP

>> FNIP_M  Folliculin-interacting protein middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.16   2.8e+02      40      76 ..      93     129 ..      86     135 .. 0.88
   2 ?    2.0   0.1     0.096   1.7e+02      25      83 ..     264     323 ..     247     329 .. 0.77
   3 ?    7.3   0.0    0.0024       4.3      43     139 ..     339     437 ..     335     438 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.16
                        FNIP_M  40 plleselsrLrsaiekaslkkksfvqrivealeefre 76 
                                   + ++  ++rL++   ++ ++ + +++ iv ++++++e
  gi|13542075|ref|NP_111763.1|  93 SEFQEDMKRLKVDSVNFFARATLYIDEIVSQISRMME 129
                                   557889***********************99998876 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.096
                        FNIP_M  25 essesefkqflleHfplleselsrLrsaiekaslkkk.sfvqrivealeefretlldlyt 83 
                                   e+ ++++k+f+    +l + + + Lr ai +a+++ + +f + ++e+ +++ ++++d y+
  gi|13542075|ref|NP_111763.1| 264 EKMSKSLKNFITIRDILKDYRPEDLRFAILNANYRTQiEFSKELMEESKKLIDYINDTYR 323
                                   3444777777777777888888889999998777665268899************99986 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.0024
                        FNIP_M  43 eselsrLrsaiek......aslkkksfvqrivealeefretlldlytaprleepvwlnlvssesekrqlaerfleelssll 117
                                   +s +s +rs++e+      +++k  + +  i +++e +++++ + ++   l+ +++l +++   +k+++ +  +++l++l 
  gi|13542075|ref|NP_111763.1| 339 NSVISEMRSLAENdfdfhsVIVKLLAITGEINRNFEGINKEVAEELKKVYLWVDTFLGILE---QKKEVSKGIVDDLVELR 416
                                   5677888888888777776677777778888888889999999999999999999999988...8899999********99 PP

                        FNIP_M 118 eeldtkktnfFlstlltavLth 139
                                    +++++ +nf++s  +  vL  
  gi|13542075|ref|NP_111763.1| 417 TRMRKE-KNFLISDAIRDVLKK 437
                                   998776.5*****999999875 PP

>> TMF_TATA_bd  TATA element modulatory factor 1 TATA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00018      0.32      28     110 ..     338     421 ..     333     424 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00018
                   TMF_TATA_bd  28 laslkeelerleaerdeareeivklmken.eelkelkkeleelekeleelqeryetlLellGeksEeveELraDvaDlKem 107
                                   ++s+ +e+ +l+++  +  + ivkl++ + e +++ ++ ++e+ +el+++    +t L +l +k+E  +   +D+++l++ 
  gi|13542075|ref|NP_111763.1| 338 VNSVISEMRSLAENDFDFHSVIVKLLAITgEINRNFEGINKEVAEELKKVYLWVDTFLGILEQKKEVSKGIVDDLVELRTR 418
                                   66777888888888899999999999755155677799999**************************************98 PP

                   TMF_TATA_bd 108 yke 110
                                   +++
  gi|13542075|ref|NP_111763.1| 419 MRK 421
                                   875 PP

>> FUN14  FUN14 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   1.0    0.0024       4.3      29      55 ..     246     291 ..     240     440 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0024
                                   xxxxxxxxxxxxxxxxxxxxxxxxxx...................x RF
                         FUN14  29 gllllqilasqgyikvnwdkiekdve...................e 55 
                                      l  +  ++g+i++n +k++k+++                    
  gi|13542075|ref|NP_111763.1| 246 KRYLAHYWIHTGMININKEKMSKSLKnfitirdilkdyrpedlrfA 291
                                   5567788899************999866666666655555555552 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (454 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       835  (0.0465726); expected 358.6 (0.02)
Passed bias filter:                      515  (0.0287244); 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: 0.68u 0.32s 00:00:01.00 Elapsed: 00:00:00.54
# Mc/sec: 2532.86
//
Query:       gi|13542076|ref|NP_111764.1|  [L=414]
Description: major facilitator superfamily permease [Thermoplasma volcanium GSS1]
Scores for 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   76.4  27.0      9e-20   71.0  27.0    2.1  1  Sugar_tr  Sugar (and other) transporter
    2.5e-20   72.7  45.4    1.3e-13   50.6  18.6    2.2  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 !   71.0  27.0     1e-23     9e-20      44     446 ..      46     411 ..       6     414 .] 0.81

  Alignments for each domain:
  == domain 1  score: 71.0 bits;  conditional E-value: 1e-23
                                   ...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHH CS
                      Sugar_tr  44 ssvlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlvP 124
                                     v++++++s+ +v  + G  ++g+l+d++GRk+++l++++++++g ++++a++   +v +l++g  l+ igvG++ v++ 
  gi|13542076|ref|NP_111764.1|  46 PRVYLSVFLSLPSVFLLTGNTILGKLSDILGRKPIYLMTILFYLAGLLIIFASN---NVVLLVIGIALSEIGVGGEEVTTL 123
                                   56899*************************************************...************************ PP

                                   HHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-TTHHHHHHHCCHHHHHHH.HHHGGGS---HHHHHHTT-H CS
                      Sugar_tr 125 myisEiApkklRgalvslyqlaitfGilvaaifglglnktsnadgwrillglqlvpalll.lilllflPESPrylvekgke 204
                                    +isE  p k+Rg++  +   +  +G  v a++ l +n +s +   ++ + + +++a++l l+ +  +PES r+l e g e
  gi|13542076|ref|NP_111764.1| 124 SLISEDVPIKHRGKFLAFVPNMNNVGSAVIAFVFLYFNSSSIQ-IQKLYFLIIAFFAVFLaLYTRRSIPESFRWLRETGSE 203
                                   ************9999999999999998888888888887773.4455555556666655156679*************** PP

                                   HHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHH.....HTTHHHHSH...HHHHHHHHHHHHHHTTHHHHHHHTTTHHHHSS CS
                      Sugar_tr 205 eeakevlaklrgeedadrelaeekdsleaeqeeekaswkellssktvrqrlligvvlqifqqltGinaimyysptifenlg 285
                                   +ea+  ++k     + +++   +k+ +                       l   + l i q lt   + ++ +p+ f+ + 
  gi|13542076|ref|NP_111764.1| 204 KEAENLYKK----LKISEDGIRIKEPNFSV-------------------SLAFLAILGISQYLTFGLMAYIVGPYYFSPAQ 261
                                   *********....44444444455544444...................47888999999999998999999********9 PP

                                   -THHHHHHHHHHHHHHHHHHHHHHHHHHS-SHHHHHHHHHHHHHHHHHHH..HHHHTTSS...CHHHHHHHHHHHHHHHTT CS
                      Sugar_tr 286 lsksllvtiivgvvnfvatfvaiflvdrfGRRtllllGaagmaicfvilgivalllvakskaasivaivfialfialfalg 366
                                   +s+  ++ +++g    va ++a+flvd +GR++  +l+ +g++i  +++  +++ +v++      v++ ++++ +++ ++ 
  gi|13542076|ref|NP_111764.1| 262 VSEI-IFYALLG--ASVAGIIAMFLVD-IGRKKYAILSYLGGTISILLIL-ATIKYVDN----MLVFLPLLFINMMFSEFA 333
                                   9998.4444444..4577788888998.9***************999996.8*******....567777777777788888 PP

                                   TTHHHHHHHHHHSHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHT-HHHHHHHHHH.HHHHHHHHHHS--STT--CC CS
                      Sugar_tr 367 wgpvpwvlvsElfpqsvRskalaiavavnwlanflisllfpiiteaigggyvflvfagla.vlfiifvfffvpetkgrtle 446
                                   w++    l +Elf ++ Rs+ + ++ +   la   i+ ++ ++  +++++ +f++   ++ ++++i+ +f  +etk+++++
  gi|13542076|ref|NP_111764.1| 334 WASRT-TLEPELFGTKRRSTSIGLVRVFPILAY--IASIYLTASFTLSQYIFFNLALWCLgLVAAIVWMFIGVETKNVSMD 411
                                   99999.788***************999998875..455555555566656777776666514444444555589*998875 PP

>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.6  18.6   1.5e-17   1.3e-13       8     225 ..      22     241 ..      15     250 .. 0.68
   2 !   24.5  24.8   1.3e-09   1.1e-05       6     171 ..     235     400 ..     226     409 .. 0.78

  Alignments for each domain:
  == domain 1  score: 50.6 bits;  conditional E-value: 1.5e-17
                         MFS_1   8 salarsilgpalplalaed....lgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfass 84 
                                    ++ ++i+++++pl  a++     g+    ++  l+l +++ + ++ +lG lsd +Gr++++l+++l++++g ll++fas+
  gi|13542076|ref|NP_111764.1|  22 GMFIWGIIASIAPL--ATAwpyvKGLPRVYLSVFLSLPSVFLLTGNTILGKLSDILGRKPIYLMTILFYLAG-LLIIFASN 99 
                                   45555555555554..233222355777779999**************************************.77777866 PP

                         MFS_1  85 lw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllgglla.sslgWrav.fyilaivsl 162
                                      ll+++ +l+ +g g+   + ++li++ +p ++rg+ ++++  ++++G+++ + +  ++  ss+  + + f+i+a++++
  gi|13542076|ref|NP_111764.1| 100 NVvLLVIGIALSEIGVGGEEVTTLSLISEDVPIKHRGKFLAFVPNMNNVGSAVIAFVFLYFNsSSIQIQKLyFLIIAFFAV 180
                                   666************************************************998888888886888866552666666666 PP

                         MFS_1 163 lafv.....lfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsg 225
                                   ++++     +   + + +++ ++++++       ++ ++++  ++  k p +   +  ++l+ +g+s+
  gi|13542076|ref|NP_111764.1| 181 FLALytrrsIPESFRWLRETGSEKEAENLY----KKLKISE-DGIRIKEPNF--SVSLAFLAILGISQ 241
                                   665533333333333444444444444444....4455555.4444455544..33333333333333 PP

  == domain 2  score: 24.5 bits;  conditional E-value: 1.3e-09
                         MFS_1   6 flsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalg.lllllfa... 82 
                                   ++ +++ ++++ ++  ++   + +sp++++ ++    lga+va +++++l+d  Gr+++ +l++l+  ++ ll+l+ +   
  gi|13542076|ref|NP_111764.1| 235 AILGISQYLTFGLMA-YIVGPYYFSPAQVSEIIFYALLGASVAGIIAMFLVDI-GRKKYAILSYLGGTISiLLILA-Tiky 312
                                   344445555555555.8889999*****************************6.****************444444.2345 PP

                         MFS_1  83 .sslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsl 162
                                     ++ ++l l ++  +++ +++++  +l  ++f  ++r+  igl+ ++  l++i    l + ++     +++f+ la+ +l
  gi|13542076|ref|NP_111764.1| 313 vDNMLVFLPLLFINMMFSEFAWASRTTLEPELFGTKRRSTSIGLVRVFPILAYIASIYLTASFT---LSQYIFFNLALWCL 390
                                   599999*****************************************99999998877777666...24555666665555 PP

                         MFS_1 163 lafv.lflll 171
                                    ++  +++++
  gi|13542076|ref|NP_111764.1| 391 GLVAaIVWMF 400
                                   5543222233 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1065  (0.059401); 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:                         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: 0.69u 0.33s 00:00:01.02 Elapsed: 00:00:00.53
# Mc/sec: 2372.00
//
Query:       gi|13542077|ref|NP_111765.1|  [L=154]
Description: transcription regulator (SlyA-related) [Thermoplasma volcanium GSS1]
Scores for complete 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   56.5   0.0    3.1e-15   55.8   0.0    1.4  1  MarR           MarR family
    1.2e-09   38.0   0.0    1.8e-09   37.3   0.0    1.3  1  MarR_2         MarR family
    8.1e-07   28.5   0.1    3.8e-05   23.2   0.0    2.5  2  HTH_24         Winged helix-turn-helix DNA-binding
    1.2e-05   25.7   0.0    2.3e-05   24.8   0.0    1.5  2  HTH_27         Winged helix DNA-binding domain
    1.3e-05   25.3   0.0    2.1e-05   24.6   0.0    1.4  1  HTH_34         Winged helix DNA-binding domain
    7.2e-05   22.6   0.0    0.00016   21.5   0.0    1.6  2  TrmB           Sugar-specific transcriptional regulator TrmB
    0.00028   20.7   0.1      0.032   14.1   0.0    2.5  2  HTH_AsnC-type  AsnC-type helix-turn-helix domain
     0.0023   17.9   0.0     0.0037   17.2   0.0    1.5  1  HTH_Crp_2      Crp-like helix-turn-helix domain
  ------ inclusion threshold ------
      0.015   15.7   0.0       0.16   12.3   0.0    2.1  2  Rrf2           Transcriptional regulator
      0.069   13.6   0.0       0.12   12.9   0.0    1.4  1  hSH3           Helically-extended SH3 domain
      0.092   12.7   0.7        1.2    9.1   0.3    2.7  2  HTH_12         Ribonuclease R winged-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 !   55.8   0.0   1.9e-18   3.1e-15       1      58 [.      41      98 ..      41      99 .. 0.98

  Alignments for each domain:
  == domain 1  score: 55.8 bits;  conditional E-value: 1.9e-18
                                  --HHHHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEETTSTTS CS
                          MarR  1 ltltqfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRskspeDrRe 58
                                  l+ t+f i+r l e+gp+s++ +a+ ++v+++ +t v+d++e+k+l++R ++  DrR+
  gi|13542077|ref|NP_111765.1| 41 LSITEFTIMRHLIENGPMSMAAIASLINVTPGWITGVVDKMEEKNLVTRNRDSTDRRI 98
                                  799******************************************************8 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.3   0.0   1.1e-12   1.8e-09       2      61 ..      40      97 ..      39      98 .. 0.98

  Alignments for each domain:
  == domain 1  score: 37.3 bits;  conditional E-value: 1.1e-12
                                  T--HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSSSSS CS
                        MarR_2  2 gltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpgpeDkR 61
                                  +l+ +++ ++ +L  +++  ++++++a   +++++ ++ ++++++++ Lv+r ++++D+R
  gi|13542077|ref|NP_111765.1| 40 DLSITEFTIMRHLIENGP--MSMAAIASLINVTPGWITGVVDKMEEKNLVTRNRDSTDRR 97
                                  7999**************..***************************************9 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   2.3e-08   3.8e-05       1      48 []      41      88 ..      41      88 .. 0.96
   2 ?    2.7   0.2     0.059        95       1      11 [.      91     101 ..      91     107 .. 0.83

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 2.3e-08
                        HTH_24  1 ldetdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                  l++t++ I++ L +n+ +s++ +A  ++++p+ ++  ++++ee+ l++
  gi|13542077|ref|NP_111765.1| 41 LSITEFTIMRHLIENGPMSMAAIASLINVTPGWITGVVDKMEEKNLVT 88
                                  57899***************************************9986 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.059
                        HTH_24   1 ldetdrkILel 11 
                                   +d tdr+I+++
  gi|13542077|ref|NP_111765.1|  91 RDSTDRRIIKI 101
                                   699******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 !   24.8   0.0   1.4e-08   2.3e-05       6      68 .]      46     107 ..      41     107 .. 0.93
   2 ?   -3.5   0.0       9.5   1.6e+04      37      47 ..     124     134 ..     120     136 .. 0.71

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 1.4e-08
                        HTH_27   6 alvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68 
                                     +++++  ++++++ a+++   nv+   i  +++k++ek Lv+r++d +drr   +++Td G
  gi|13542077|ref|NP_111765.1|  46 FTIMRHLI-ENGPMSMAAIASLINVTPGWITGVVDKMEEKNLVTRNRDSTDRRIIKIAITDRG 107
                                   56677777.79**************************************************98 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 9.5
                        HTH_27  37 yslkkLtekGL 47 
                                   ++l +L e++L
  gi|13542077|ref|NP_111765.1| 124 KALAELNENEL 134
                                   77888887776 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 !   24.6   0.0   1.3e-08   2.1e-05       2      74 ..      45     116 ..      44     122 .. 0.94

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 1.3e-08
                        HTH_34   2 RlavlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYievdkefkgkkprtllriTpeGreafkkyvk 74 
                                   ++ ++  L+++  ++++ + + +++t g +   ++k+e+++ ++++ +  ++ + + + iT+ Gre +++ +k
  gi|13542077|ref|NP_111765.1|  45 EFTIMRHLIENGPMSMAAIASLINVTPGWITGVVDKMEEKNLVTRNRDSTDR-RIIKIAITDRGREVYENAKK 116
                                   689***********************************************99.99***********9998776 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0     1e-07   0.00016       1      58 [.      36      93 ..      36     116 .. 0.91
   2 ?   -2.4   0.0       2.9   4.7e+03      38      45 ..     136     143 ..     124     148 .. 0.53

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 1e-07
                                  HHHCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                          TrmB  1 LqklGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr 58
                                  L k++Ls +E+ +   L+++gp+++  ia+ ++v    +  v+ ++e+k lV+r++ +
  gi|13542077|ref|NP_111765.1| 36 LNKIDLSITEFTIMRHLIENGPMSMAAIASLINVTPGWITGVVDKMEEKNLVTRNRDS 93
                                  67999*************************************************9977 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.9
                                   CHHHHHHH CS
                          TrmB  38 kvYevLrs 45 
                                   + Y  L++
  gi|13542077|ref|NP_111765.1| 136 QTYVLLQK 143
                                   34444454 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 !   14.1   0.0   1.9e-05     0.032       8      31 ..      48      71 ..      44      81 .. 0.94
   2 ?    3.6   0.3     0.035        57       2      11 ..      92     101 ..      92     109 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.9e-05
                 HTH_AsnC-type  8 ILeaLqedaRisyaeLAervGlSe 31
                                  I+++L e++ +s+a++A  +++++
  gi|13542077|ref|NP_111765.1| 48 IMRHLIENGPMSMAAIASLINVTP 71
                                  99*******************998 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.035
                 HTH_AsnC-type   2 DeiDrkILea 11 
                                   D +Dr+I+++
  gi|13542077|ref|NP_111765.1|  92 DSTDRRIIKI 101
                                   99*****985 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   2.3e-06    0.0037      21      55 ..      57      91 ..      24     108 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.3e-06
                                  EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEETE CS
                     HTH_Crp_2 21 pltqeelAsmlGltretvsrilseLkreglisrgr 55
                                  p++++ +As++++t+  ++ +  ++++++l++r+r
  gi|13542077|ref|NP_111765.1| 57 PMSMAAIASLINVTPGWITGVVDKMEEKNLVTRNR 91
                                  9*******************************532 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0    0.0001      0.16       6      57 ..      38      89 ..      35      91 .. 0.88
   2 ?    0.8   0.0       0.4   6.5e+02      39      54 ..     119     134 ..     109     138 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.0001
                                  HHHHHHHHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                          Rrf2  6 kteyalhallyLakeeeeepvsseeiaerqnispsylekilakLrkaglvks 57
                                  k++++++  +++ +  e++p+s+++ia+  n+ p  +  ++ k+++++lv+ 
  gi|13542077|ref|NP_111765.1| 38 KIDLSITEFTIMRHLIENGPMSMAAIASLINVTPGWITGVVDKMEEKNLVTR 89
                                  5667777788888999999*******************************86 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.4
                                   HHHHHHHHHHHHHTTS CS
                          Rrf2  39 psylekilakLrkagl 54 
                                     +++k la+L++++l
  gi|13542077|ref|NP_111765.1| 119 YAFIRKALAELNENEL 134
                                   6799*******99887 PP

>> hSH3  Helically-extended SH3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   7.1e-05      0.12      33      82 ..      67     116 ..      47     120 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.1e-05
                          hSH3  33 LpvkrgeildviqktddkkvlcrneeGkygyvlrsalleedgeiYddigd 82 
                                   ++v++g i  v+ k+++k+++ rn++   + + + a++++  e+Y++ ++
  gi|13542077|ref|NP_111765.1|  67 INVTPGWITGVVDKMEEKNLVTRNRDSTDRRIIKIAITDRGREVYENAKK 116
                                   5799999**************************************98754 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 ?    9.1   0.3   0.00076       1.2       3      64 ..      48     109 ..      46     111 .. 0.77
   2 ?   -2.1   0.0       2.3   3.8e+03      35      47 ..     122     134 ..     113     137 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00076
                        HTH_12   3 ILkilaesdkpigakeiaeeLkkr.gydigeravRyrLrkleergltrrvgya......greltEkGle 64 
                                   I+++l e+  p++  +ia+ ++ + g             k+ee++l+ r++ +      +  +t++G e
  gi|13542077|ref|NP_111765.1|  48 IMRHLIENG-PMSMAAIASLINVTpGWIT------GVVDKMEEKNLVTRNRDStdrriiKIAITDRGRE 109
                                   788887765.6888888888888855444......23679**********9998888888888999865 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.3
                        HTH_12  35 vRyrLrkleergl 47 
                                   +R  L  l+e++l
  gi|13542077|ref|NP_111765.1| 122 IRKALAELNENEL 134
                                   5666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1098  (0.0612416); 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: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 956.81
//
Query:       gi|13542078|ref|NP_111766.1|  [L=215]
Description: 30S ribosomal protein S3Ae [Thermoplasma volcanium GSS1]
Scores for complete 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-49  167.1   3.7    4.4e-49  166.8   3.7    1.0  1  Ribosomal_S3Ae  Ribosomal S3Ae family


Domain annotation for each model (and alignments):
>> Ribosomal_S3Ae  Ribosomal S3Ae family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  166.8   3.7   2.5e-53   4.4e-49       3     199 ..       7     192 ..       5     194 .. 0.98

  Alignments for each domain:
  == domain 1  score: 166.8 bits;  conditional E-value: 2.5e-53
                                   ----S-TCCSEEEEEEEB-TTSSSSEEEEEEEE--BSSSESHHSHTT-EEEEESHHHHTCSHTSSSEEEEEEEEEEESSEE CS
                Ribosomal_S3Ae   3 kkkvvDkfkkKeWydvkaPslfgkreiGktlvnrtqgtkiaseklkgrvvevslaDLtndekeqafrklklkieevqgkna 83 
                                   +kk ++k+k+K Wy+v+aP ++g++e+   l         +s+++++rvvev +++Lt+++ ++++ k  ++i++++g+++
  gi|13542078|ref|NP_111766.1|   7 QKKGKEKWKEKVWYTVEAPPYLGSKEVSVALG-------EDSNSMVNRVVEVPISELTGNF-KKSNEKALFRITNCEGTKC 79 
                                   7899****************************.......**********************.457**************** PP

                                   EEEEEEEEE-HHHHHHH--SSB-EEEEEEEEEESSSEEEEEEEEEEE-STTB---HHHHHHHHHHHHHHHHHHHHHS-HHH CS
                Ribosomal_S3Ae  84 ltnFkgmeltrDklrslvrkwsslIeaivdvktkDgyllrvfvvafTkkrnsYakssqkkaIrkkmveilteeaseldlke 164
                                   +t F g+ + +D++r+lvr+++++I++i dvkt+D+ ++ v++v++T+ +   +++++k +Irk++++++ ++  +l + e
  gi|13542078|ref|NP_111766.1|  80 KTIFIGHYIGDDYIRRLVRRRKERIDIIEDVKTSDNSIITVKIVVVTDGK---VTNTKKFQIRKVLTDFILNKGLSLPYSE 157
                                   **************************************************...**************************** PP

                                   HHHHHTTTHHHHHHHHHHTTTS-EEEEEEEEEEEE CS
                Ribosomal_S3Ae 165 lvkklipeslgkeiekeakkIyplrnveirKvkvl 199
                                   +v++li +++ +++  ++k+Iypl+++e+rK++++
  gi|13542078|ref|NP_111766.1| 158 FVRYLIGDDIYNDMISATKDIYPLKKIEVRKSELV 192
                                   *******88***********************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       532  (0.0296726); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1354.24
//
Query:       gi|13542079|ref|NP_111767.1|  [L=78]
Description: transcription regulator [Thermoplasma volcanium GSS1]
Scores for complete 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-20   71.2   0.0      5e-20   71.1   0.0    1.0  1  TusA      Sulfurtransferase TusA


Domain annotation for each model (and alignments):
>> TusA  Sulfurtransferase TusA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.1   0.0   2.8e-24     5e-20       2      70 .]       8      76 ..       7      76 .. 0.98

  Alignments for each domain:
  == domain 1  score: 71.1 bits;  conditional E-value: 2.8e-24
                                  EEEBTT-STTCCHHHHHHHHCCCGCT-EEEEEESSCHHHHHHHHHHHHHTEEEEEEE-GCC-EEEEEEE CS
                          TusA  2 elDlrGlvCPePllklkkalekleegevlevladdpaatediprfakklghelveveeedgeyrivirk 70
                                  ++D+rG  CP+Pl++l ka ++++ ge++ v ++d ++++d p++  k g elv v +++g+y+iv++k
  gi|13542079|ref|NP_111767.1|  8 VIDARGSYCPGPLMELIKAYKQAKVGEIISVYSTDAGTKKDAPAWISKSGQELVGVFDRNGYYEIVMKK 76
                                  79****************************************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); 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 0.30s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 497.09
//
Query:       gi|13542080|ref|NP_111768.1|  [L=137]
Description: hypothetical protein TVN1249 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.2e-19   68.4   4.9    4.1e-09   36.5   0.6    2.0  2  DrsE_2        DsrE/DsrF/DrsH-like family
     0.0011   19.3   0.1     0.0019   18.5   0.1    1.5  1  DrsE          DsrE/DsrF-like family
  ------ inclusion threshold ------
      0.012   15.0   0.1      0.016   14.6   0.1    1.1  1  Endonuc-MspI  Restriction endonuclease MspI


Domain annotation for each model (and alignments):
>> DrsE_2  DsrE/DsrF/DrsH-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.4   0.3   3.2e-12   1.9e-08       3      55 ..       3      55 ..       1      63 [. 0.91
   2 !   36.5   0.6   6.9e-13   4.1e-09      84     153 .]      65     136 ..      59     136 .. 0.92

  Alignments for each domain:
  == domain 1  score: 34.4 bits;  conditional E-value: 3.2e-12
                                  -EEEEEE----H.HHHHHHHHHHHHHHTT-EEEEEE-GGGGGGGB-GGG---T CS
                        DrsE_2  3 kklaiifskgtldkalaalilAsgAaalglevtiFftFwGLnilrkeekkkvk 55
                                  k+l+i++ +gt dk  aa ++ sgA a g++v+iF tFw L  +rk++++  k
  gi|13542080|ref|NP_111768.1|  3 KTLSIVLASGTIDKIAAAGVITSGAVANGIDVNIFVTFWALMKFRKNDNTVNK 55
                                  7899******************************************9976554 PP

  == domain 2  score: 36.5 bits;  conditional E-value: 6.9e-13
                                   HHHHHHHHHCT---HHHHHHHHHHTT.-EEEEEHHHHHHHT--GGGB-TT-.EEE-HHHHHHHHHC-SEEEE CS
                        DrsE_2  84 kmmkkvmkekgvasleeLleaakeag.vklvaCqmtmdlmglkkeelidgv.eiagaatylkeaeeadvnLf 153
                                    ++ ++m+ek+++s  e++ +ake g v++++C +  d+mg++k++l d v  i+g+ ++++  e + ++Lf
  gi|13542080|ref|NP_111768.1|  65 DLVLSKMNEKKIQSGIEMIRNAKEVGnVHVYGCALMADVMGISKDDLDDMVeDIIGVGEFVSMTESSYTTLF 136
                                   567899*****************9866************************99*********9999988887 PP

>> DrsE  DsrE/DsrF-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.1   3.2e-07    0.0019      32     114 ..      32     134 ..       4     136 .. 0.65

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 3.2e-07
                                   -EEEEEE-GGGGGGGBS...................---TGGGTS---GGGGGGCGGGT.-EEEEEHHHHHHTT--GGGE- CS
                          DrsE  32 hevsvffygdGvllllk...................gqtanpadeknlaellkalkeyg.vklyvCgqaakargldededl 92 
                                    +v++f++  +   ++k                     + n+++  + +e+++ +ke g v++y C+  a+ +g+++d dl
  gi|13542080|ref|NP_111768.1|  32 IDVNIFVTFWALMKFRKndntvnklsydgseisdlvLSKMNEKKIQSGIEMIRNAKEVGnVHVYGCALMADVMGISKD-DL 111
                                   6666666666666666655555545554444443332223334444559********777****************66.55 PP

                                   .T--EEEE-HHHHHHHHHH-SEE CS
                          DrsE  93 .gvgvevsglgelaelqnegdrv 114
                                    ++   + g+ge++ +   ++  
  gi|13542080|ref|NP_111768.1| 112 dDMVEDIIGVGEFVSMTESSYTT 134
                                   22233477888888888877765 PP

>> Endonuc-MspI  Restriction endonuclease MspI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1   2.7e-06     0.016      82     163 ..      50     129 ..      42     135 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.7e-06
                  Endonuc-MspI  82 tdeipkLsngGkPktDialkiklekkelkiatisvkntsaktvsvHeysaedlikvldlsdsdlrellkkfqevGskkklk 162
                                    +++ kLs  G+   D+ l  k+++k++  + i + +  ++   vH y    ++ v+ +s +dl ++++++  vG++  ++
  gi|13542080|ref|NP_111768.1|  50 DNTVNKLSYDGSEISDLVLS-KMNEKKI-QSGIEMIRNAKEVGNVHVYGCALMADVMGISKDDLDDMVEDIIGVGEFVSMT 128
                                   58899***********9886.7777777.68899989899999*********************************99998 PP

                  Endonuc-MspI 163 e 163
                                   e
  gi|13542080|ref|NP_111768.1| 129 E 129
                                   5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       520  (0.0290033); 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:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.48
# Mc/sec: 853.03
//
Query:       gi|13542081|ref|NP_111769.1|  [L=193]
Description: hypothetical protein TVN1250 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-50  171.5  16.5      2e-50  171.3  16.5    1.0  1  DUF981    Protein of unknown function (DUF981)
  ------ inclusion threshold ------
       0.27   11.3   2.3        3.2    7.9   0.3    2.7  2  CrgA      Cell division protein CrgA


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 !  171.3  16.5   2.2e-54     2e-50       1     186 [.       1     186 [.       1     187 [. 0.97

  Alignments for each domain:
  == domain 1  score: 171.3 bits;  conditional E-value: 2.2e-54
                        DUF981   1 Ma.FidyltlmlitlgagllllayyvlkaleerekkeankalaapflivGllalitGlhmtltWPlpgsYnilfgdpallf 80 
                                   M+ Fid+l++ml  lg+g++l a+y+l+     +k++a k+l++p+++vG++ +++G+ m++tWPlp+sYn+lfgdp+l+f
  gi|13542081|ref|NP_111769.1|   1 MSeFIDPLAVMLLGLGMGTALGAAYFLAHG--LNKRDAVKSLVVPAFGVGFFDFVSGFIMSFTWPLPSSYNMLFGDPLLMF 79 
                                   788******************999999887..8************************************************ PP

                        DUF981  81 GvllllaavalykkaklkalgilalflGlilivygvailklgLtaeP..laalllyilvGLagllsplvllkldksrsvll 159
                                   G++l++ + + y++ +l++ +il+lflG++++v  + i++++L++ +  l +++lyil G+a++l+p++++k+++ + +l+
  gi|13542081|ref|NP_111769.1|  80 GLILMMSSYMEYRGFDLRFNSILLLFLGIYVLVASAGIVHYKLETGDdlLSSMGLYILDGIAAVLAPIMYIKPENGK-YLY 159
                                   *********************************************99888999********************9988.*** PP

                        DUF981 160 vlaavlliiagllalliGieavyeHla 186
                                   +l+ ++l++++ +al+iG+ea+++Hl 
  gi|13542081|ref|NP_111769.1| 160 LLEFIILLLGTFVALFIGYEAIWGHLL 186
                                   *************************95 PP

>> CrgA  Cell division protein CrgA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.3   0.00035       3.2      45      87 ..      18      62 ..       4      63 .. 0.71
   2 ?    2.2   0.1     0.022     2e+02      67      85 ..      67      85 ..      65      87 .. 0.91

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00035
                          CrgA 45 GllwlvvyYlage..eipfmaelgawNlliGfgliivGllmttrW 87
                                  G +    y+la++  +   +++l    + +Gf  ++ G++m+  W
  gi|13542081|ref|NP_111769.1| 18 GTALGAAYFLAHGlnKRDAVKSLVVPAFGVGFFDFVSGFIMSFTW 62
                                  334445566666566666788999999*****************9 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.022
                          CrgA 67 awNlliGfgliivGllmtt 85
                                  ++N+l G  l++ Gl++++
  gi|13542081|ref|NP_111769.1| 67 SYNMLFGDPLLMFGLILMM 85
                                  68**************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       643  (0.0358637); 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:                         2  (0.000111551); expected 0.2 (1e-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: 1284.36
//
Query:       gi|13542082|ref|NP_111770.1|  [L=124]
Description: transcription regulator [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.5e-07   29.4   0.1    8.8e-07   28.7   0.1    1.2  1  HTH_5         Bacterial regulatory protein, arsR family
     0.0066   16.1   0.0      0.012   15.3   0.0    1.3  1  Sigma70_r4_2  Sigma-70, region 4
     0.0068   16.2   0.1      0.018   14.8   0.0    1.7  2  HTH_23        Homeodomain-like domain
  ------ inclusion threshold ------
      0.021   14.8   0.0      0.028   14.4   0.0    1.2  1  HTH_Crp_2     Crp-like helix-turn-helix domain
      0.034   14.3   0.0      0.046   13.9   0.0    1.3  1  HTH_28        Helix-turn-helix domain
      0.074   12.8   0.0       0.37   10.6   0.0    2.1  2  Rtt106_N      Histone chaperone Rtt106 N-terminal domain
      0.082   12.5   0.2       0.17   11.5   0.2    1.5  1  HTH_24        Winged helix-turn-helix DNA-binding
       0.11   12.5   0.0       0.16   12.0   0.0    1.3  1  HTH_45        Winged helix-turn-helix
       0.15   12.0   0.0       0.24   11.3   0.0    1.3  1  TrmB          Sugar-specific transcriptional regulator TrmB
       0.23   11.6   0.0       0.35   11.0   0.0    1.2  1  HTH_20        Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.1   4.9e-10   8.8e-07       4      45 ..      48      89 ..      46      90 .. 0.97

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 4.9e-10
                                  HHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                         HTH_5  4 RlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLV 45
                                  R+kI+ l ++++   +++++ lg++  tv hHL +L++ ++V
  gi|13542082|ref|NP_111770.1| 48 RRKIIDLIRNNPSNQHQISRVLGVNYRTVEHHLHILEQNNIV 89
                                  9****************************************9 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   6.4e-06     0.012      16      48 ..      49      81 ..      48      81 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 6.4e-06
                                  HHHHHHHHTS---HHHHHHHHT--HHHHHHHHH CS
                  Sigma70_r4_2 16 reifllryleglsykEIAellgisegtVksrls 48
                                  r+i+ l++ + + + +I+++lg++ +tV+++l+
  gi|13542082|ref|NP_111770.1| 49 RKIIDLIRNNPSNQHQISRVLGVNYRTVEHHLH 81
                                  888888888888899****************98 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       2.4   4.3e+03      20      29 ..       6      15 ..       4      15 .. 0.77
   2 !   14.8   0.0     1e-05     0.018       7      39 ..      48      81 ..      46      88 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 2.4
                        HTH_23 20 vreIAreLgv 29
                                  +++I++++++
  gi|13542082|ref|NP_111770.1|  6 YQRISKIYNC 15
                                  6788888886 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 1e-05
                        HTH_23  7 Rlrillllae.GlsvreIAreLgvsrrTvyrwlk 39
                                  R +i+ l ++   ++++I+r Lgv++rTv + l+
  gi|13542082|ref|NP_111770.1| 48 RRKIIDLIRNnPSNQHQISRVLGVNYRTVEHHLH 81
                                  5566666665555799*************97665 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 ?   14.4   0.0   1.5e-05     0.028       2      52 ..      33      90 ..      32     102 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.5e-05
                                  HHHHHHHHHHCTTTC....EEEE....EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE CS
                     HTH_Crp_2  2 RlArfLlrlaeragg....eiel....pltqeelAsmlGltretvsrilseLkreglis 52
                                  Rl+ +L +   r g+     i+l    p +q ++++ lG++  tv   l+ L++ +++ 
  gi|13542082|ref|NP_111770.1| 33 RLIWWLFYA-TRGGDmrrkIIDLirnnPSNQHQISRVLGVNYRTVEHHLHILEQNNIVY 90
                                  888888764.442323344344344459**************************99986 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   2.6e-05     0.046       2      39 ..      48      86 ..      47      98 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.6e-05
                        HTH_28  2 RleiikllaaGh.svreaArelgisrrtvyrWikryeeg 39
                                  R++ii l+ +   ++ +++r lg+++rtv   ++ +e+ 
  gi|13542082|ref|NP_111770.1| 48 RRKIIDLIRNNPsNQHQISRVLGVNYRTVEHHLHILEQN 86
                                  88888888887679999**************99999985 PP

>> Rtt106_N  Histone chaperone Rtt106 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0         1   1.8e+03      12      21 ..       4      13 ..       2      16 .. 0.79
   2 ?   10.6   0.0   0.00021      0.37       2      18 ..     103     121 ..     102     123 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1
                      Rtt106_N 12 eLrskvskIt 21
                                  eL  ++skI 
  gi|13542082|ref|NP_111770.1|  4 ELYQRISKIY 13
                                  7888999995 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00021
                      Rtt106_N   2 teSFldkLP..aeLrskvs 18 
                                   ++SFldkLP  +e + kv 
  gi|13542082|ref|NP_111770.1| 103 SQSFLDKLPiyDEFKNKVE 121
                                   89*******6668998886 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.2   9.3e-05      0.17       5      47 ..      48      89 ..      46      90 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 9.3e-05
                        HTH_24  5 drkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                  +rkI+ l++ np+ +q ++++ lg+   tv  +l  Le++ ++
  gi|13542082|ref|NP_111770.1| 48 RRKIIDLIRNNPS-NQHQISRVLGVNYRTVEHHLHILEQNNIV 89
                                  6899999999886.899*****************999999987 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   8.8e-05      0.16      10      57 ..      50      97 ..      46     120 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 8.8e-05
                        HTH_45 10 dILeaisegeakkTkimykanLsykllnkYLdmLvekglikkskekYv 57
                                   I + i+++ +++ +i      +y++++  L++L +++++   ++kY 
  gi|13542082|ref|NP_111770.1| 50 KIIDLIRNNPSNQHQISRVLGVNYRTVEHHLHILEQNNIVYGMGDKYG 97
                                  58889999********************************66666554 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   0.00013      0.24      16      53 ..      53      90 ..      51     100 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00013
                                  HHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEE CS
                          TrmB 16 aLlklgpatadeiaeelgvprskvYevLrsLedkGlVe 53
                                   L+++ p++  +i++ lgv + +v   L  Le+  +V+
  gi|13542082|ref|NP_111770.1| 53 DLIRNNPSNQHQISRVLGVNYRTVEHHLHILEQNNIVY 90
                                  6899****************************999986 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0    0.0002      0.35      11      54 ..      47      89 ..      39      91 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0002
                                  HHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTE CS
                        HTH_20 11 vRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLv 54
                                  +Rr+i +++ r+ +    ++ + l++   t+ +HL++Le+  +v
  gi|13542082|ref|NP_111770.1| 47 MRRKIIDLI-RNNPSNQHQISRVLGVNYRTVEHHLHILEQNNIV 89
                                  699999999.99999999********************987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       579  (0.032294); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                        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 0.28s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 831.32
//
Query:       gi|13542083|ref|NP_111771.1|  [L=340]
Description: translation initiation factor IF-2B subunit alpha [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.5e-71  239.7   0.0    1.5e-70  237.6   0.0    1.8  1  IF-2B      Initiation factor 2 subunit family
  ------ inclusion threshold ------
      0.073   13.1   0.0       0.42   10.7   0.0    2.1  3  Mucin_bdg  Putative mucin or carbohydrate-binding module


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 !  237.6   0.0   1.7e-74   1.5e-70       2     282 .]      54     321 ..      53     321 .. 0.98

  Alignments for each domain:
  == domain 1  score: 237.6 bits;  conditional E-value: 1.7e-74
                                   S-SHHHHHHHHHHHHHHHHHHCCCSTHHHHHHHHHHHHHHHHTSSTS-HHHHHHHHHHHHHHHCCTTTSSHHHHHHHHHHH CS
                         IF-2B   2 vrGspaiaiaalevllevikdaktskvaeLkeelrkaidlLkkarPtavslgnairrllkeiselksssdvkeakksliek 82 
                                   vrG+pai+++a+++l+++ k+ +         +++ka + ++++rPta +l+ air++                +   +++
  gi|13542083|ref|NP_111771.1|  54 VRGAPAIGVTAAYGLAMASKNGE---------DMNKAKEKIRATRPTAYDLFKAIRYMEV--------------NGYDMNA 111
                                   89***************999998.........9***********************9877..............4556789 PP

                                   HHHHHHHHHHHHHHHHHHHHTTC-TTEEEEEES--SH........HHHHHHHHHHTTEEEEEEEEEXTTTTHH.HTHHHHH CS
                         IF-2B  83 ikelikeieeadekigdiaaelikdgdtilTicnskt........vlevlraaakekkkfkVivvEsrPrlqG.rltakeL 154
                                   +++++ eie   +kig+ + eli +g  ilT+cn+++        +l+ +r a++e+k++ V+v E+rPrlqG +lta+eL
  gi|13542083|ref|NP_111771.1| 112 ARRYAMEIEGRSKKIGELGNELIRNGAKILTHCNAGAlavldwgtALSPMRIAHNEGKNIFVFVDETRPRLQGaKLTAWEL 192
                                   99******************************************************************************* PP

                                   HHTTXEEEEEEGGGHHHHHHC.TESEEEEEXSEEETTSEEEEETTHHHHHHHHHHTTXEEEEEXXGGGBESTSSSGGGSSX CS
                         IF-2B 155 vqagipvtlitdsavayvmse.evdkvivGAdrilenGaiankiGTsslAvlAkefnipvlvvaeslkfservqldedifi 234
                                   +q+gi+  +i d+a+++ m++ e+d vivGAdri++nG+ ankiGT++ AvlAk   ip++v+a+ ++f+  ++ +++i i
  gi|13542083|ref|NP_111771.1| 193 AQEGIDHAIIADNAAGFYMRRkEIDLVIVGADRIASNGDFANKIGTYEKAVLAKVNGIPFYVAAPGSTFDFSIRSGDEIPI 273
                                   ********************************************************************************* PP

                                   XBEXTHHHHEETTEESSTTTEEEEEBSEEEEEGGGXSEEEETTEEEXC CS
                         IF-2B 235 eerdpeellnitgeriaeeelkvvnpafDvtPpelItliITevGvlpp 282
                                   eerd++e+l i+g ri ++e +  npafDvtP+e++t++ITe+G+++p
  gi|13542083|ref|NP_111771.1| 274 EERDENEVLEINGIRIGPNESHSKNPAFDVTPNEYVTGFITEYGIFKP 321
                                   **********************************************98 PP

>> Mucin_bdg  Putative mucin or carbohydrate-binding module
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   4.7e-05      0.42      16      70 ..      77     133 ..      67     148 .. 0.83
   2 ?   -2.2   0.0      0.47   4.2e+03      70      89 ..     163     182 ..     155     196 .. 0.61
   3 ?   -1.8   0.0      0.35   3.2e+03      68     111 ..     261     304 ..     245     307 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 4.7e-05
                     Mucin_bdg  16 dqakkklnvtvtskkphyyfedetYasievkdkdGneklrkeieGtekqtae..kei 70 
                                   d +k k ++  t+ ++   f+   Y++++ +d +    +  eieG +k+++e  +e+
  gi|13542083|ref|NP_111771.1|  77 DMNKAKEKIRATRPTAYDLFKAIRYMEVNGYDMNAARRYAMEIEGRSKKIGElgNEL 133
                                   5566777778888888899****************************9999875554 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.47
                     Mucin_bdg  70 isfkeGdvlkiyHaEpknrl 89 
                                   i+ +eG  + ++ +E + rl
  gi|13542083|ref|NP_111771.1| 163 IAHNEGKNIFVFVDETRPRL 182
                                   45555666666666665555 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 0.35
                     Mucin_bdg  68 keisfkeGdvlkiyHaEpknrlilskkqeeilksksktntyevt 111
                                   +++s+ +Gd + i  ++ ++ l ++  +    +s+sk+  + vt
  gi|13542083|ref|NP_111771.1| 261 FDFSIRSGDEIPIEERDENEVLEINGIRIGPNESHSKNPAFDVT 304
                                   67788889999888777776664443333333355566666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (340 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       340  (0.0189637); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); 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 0.31s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 2104.09
//
Query:       gi|13542084|ref|NP_111772.1|  [L=426]
Description: tryptophanyl-tRNA synthetase [Thermoplasma volcanium GSS1]
Scores for complete 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   0.1    2.4e-20   73.1   0.0    2.1  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 !   73.1   0.0   1.3e-24   2.4e-20       5     177 ..      57     222 ..      53     233 .. 0.88
   2 !   46.4   0.0   1.7e-16   3.1e-12     179     292 ..     295     406 ..     279     407 .. 0.92

  Alignments for each domain:
  == domain 1  score: 73.1 bits;  conditional E-value: 1.3e-24
                                   --EEEEEEETSSS-BGGGHHHHHHHHHHHHTTSEEEEEEEHHHHHTTTTT-SSHHHHHHHHHHHHHH.HHHHHHHTCHTTT CS
                  tRNA-synt_1b   5 plrvysGidPTgklHlGylvplkklvelqkaghevffliaDlhAiigdpskaeerklrkreevlena.ikaqlakgldpek 84 
                                   ++ v++G +P+g++HlG+  ++ +++++qk g  v + +aDl+ + ++        l k++e + +  i +++a gl+p  
  gi|13542084|ref|NP_111772.1|  57 KFNVMTGLMPSGEMHLGNKSAIDQVIYFQKLGGSVSIAVADLESYSTRGI-----PLDKAREIAIEKyILNYIAMGLQP-- 130
                                   6899*******************************************999.....4444444444445668********.. PP

                                   EEEEETHHHHTTHHHHHHHHHHHTTCBHHHHHHHHHCCHHCSSSC--BHHHHHHHHHHHHHHHHTCHS........EEEEE CS
                  tRNA-synt_1b  85 aevvlqsewlehlelaellrdlgklgslnrmlqfksvkkrleegegislgeftYplLqaaDilllkad........lvpgG 157
                                    e+++qs+  + + l ++l + +++++l+ ++ f + ++++          ++ pl qaaD+l+ + +        +vp+G
  gi|13542084|ref|NP_111772.1| 131 CEIYFQSKNKDVQFLSYILGNWTNMNELKALYGFTD-SNDI--------LHINAPLIQAADVLHTQLNnyggpaptVVPVG 202
                                   9***********************************.4444........457779999999999999999999999***** PP

                                   GGGHHHHHHHHHHHHHHHHH CS
                  tRNA-synt_1b 158 sDQkqnielgrdlarrfnkk 177
                                    DQ+ +i+l rdla+r++  
  gi|13542084|ref|NP_111772.1| 203 FDQDPHIRLMRDLAKRMRIF 222
                                   ****************9755 PP

  == domain 2  score: 46.4 bits;  conditional E-value: 1.7e-16
                                   TTSS-EEEEET-BBSTTSSSBTTCETTCGC-BTTCCHHHHHHHHHHCHCSTTC..SHHHHHHHHHTHHHCHHHHHHHHCCS CS
                  tRNA-synt_1b 179 vfkkpegltvplltgldGekKmSKSagnsaIfLddekesvkkkiqkavtdsde..evekllklktelsnelierleavsgk 257
                                    f +p++++ +l++gl+G+ KmS+S + s I ++d+ e++k ki +a+t  ++  e ++ l + +e ++ +++ + ++ + 
  gi|13542084|ref|NP_111772.1| 295 SFIPPSATYQKLMKGLKGG-KMSSSVPDSLISMNDDVEEAKRKIMRALTGGRDteEEQRKLGGEPEKCP-VFDLYNYEIDD 373
                                   68999**************.*****************************99998899************.*******9998 PP

                                   EEESSHHHHHHHHHCCCCHHHHHHHHHHHHHHHHH CS
                  tRNA-synt_1b 258 kpkreaeellaeevtklvhggdlkkalaealnell 292
                                   ++   ++e+ +e+++++ ++g +k++ a+++  +l
  gi|13542084|ref|NP_111772.1| 374 DK--YVNEVFEECKSGKRMCGYCKREIADKMSIFL 406
                                   87..9***********************9998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (426 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       733  (0.0408835); expected 358.6 (0.02)
Passed bias filter:                      573  (0.0319594); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.64u 0.33s 00:00:00.97 Elapsed: 00:00:00.54
# Mc/sec: 2357.00
//
Query:       gi|13542085|ref|NP_111773.1|  [L=446]
Description: trehalose-6-phosphate synthase [Thermoplasma volcanium GSS1]
Scores for complete 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-101  339.2   1.5   5.3e-100  335.3   1.5    1.9  1  Glyco_transf_20  Glycosyltransferase family 20
  ------ inclusion threshold ------
      0.012   15.4   0.0      0.018   14.8   0.0    1.4  1  Glyco_transf_5   Starch synthase catalytic domain
       0.11   12.9   0.0       0.27   11.7   0.0    1.8  1  Glyco_trans_1_4  Glycosyl transferases group 1


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 !  335.3   1.5  8.9e-104  5.3e-100      27     469 ..      23     428 ..       2     432 .. 0.92

  Alignments for each domain:
  == domain 1  score: 335.3 bits;  conditional E-value: 8.9e-104
                                   ECCGSSHHHHHCCCHHCCC-EEEEEEECCES-CCC..HCCCCHHHCCCCCEEEEEE-HHHHHHHCCCHHHHCHHHHHTT-G CS
               Glyco_transf_20  27 lkkssgglvsalkglkeetevvwvgwlgvevdeseeakekvskeleekfsvvpvflsdekveeyyngfsksvLWpllHYkl 107
                                   +k++ gg+++alk + +++ ++w+ w   + d++        +e   ++++ +++l+ ++   yy+ +s+++LWpl+HY  
  gi|13542085|ref|NP_111773.1|  23 VKENVGGVATALKRAISKHGGTWICWGDGKADNRY------VNEDVGTYKIKRIILTPQEKRGYYDMYSNRTLWPLFHYFR 97 
                                   467788999999999999999*****988877777......33445689999**************************988 PP

                                   G....G----HHHHHHHHHHHHHHHHHHHCC--TT-EEEEESGGGTTHHHHHHHCCTTSEEEEEE-S----HHHHTTSTTH CS
               Glyco_transf_20 108 pdsseekefersawdaYvkvnklFAdkiveeikdgdliwvhDYhLmllPellRkkledakigfflHiPFPsseifriLpvr 188
                                   +      ++ ++ ++ Y+kvn++FA++i+++ +++d++wvhDY+L l+P +lR+k  +++i f  HiP+ s+e+f +L   
  gi|13542085|ref|NP_111773.1|  98 E----RVQYTDNGYETYRKVNEKFAEEILNNTSQEDIVWVHDYQLSLVPGILRQKGLKNRIIFTWHIPWVSREMFETLTES 174
                                   7....99************************************************************************** PP

                                   HHHHHHHTTSSEEEESSHHHHHHHHHHHHHHSSEEEECTTEEEEETTEEEEEEE------HHHHHHHCCSCHHHHHHHHHH CS
               Glyco_transf_20 189 eeilegllgadliGFhtedyarhFlsccsrllgleveskrggveykgrkvsvkalpigidverlesalkkesvsekvkelk 269
                                   +ei e++ +ad+i Fht+ y ++F s  ++ +             +g+++   a+p gid+  +e+a +         ++k
  gi|13542085|ref|NP_111773.1| 175 DEIKESVGSADFITFHTDLYRKNFESLFENRK-------------HGKSI---AVPLGIDYRYFEKAKS--------SQIK 231
                                   ************************87665433.............45555...67*********98655........4555 PP

                                   HHT.TTSEEEEEEEEC-GGG-HHHHHHHHHHHHHH-GGGTTTEEEEEEEEB-STTSHHHHHHHHHHHHHHHHHHHHH-BTT CS
               Glyco_transf_20 270 erfenkkklilgvDrlDyikGvkqkllaferfLeeypelrgkvvlvqiavpsredveeyqelekeveelvgrINgefgtld 350
                                   +   ++k ++++ DrlDy+kG++++ l+ er+++++pe  gk v+v i++psr++v++y ++++e+e  +gr+Ngefgt++
  gi|13542085|ref|NP_111773.1| 232 SYALKDKIMLFSIDRLDYTKGLTNRVLSIERLIRNHPETSGKFVYVMIVTPSRTSVSDYVSMKRELEMNIGRVNGEFGTIS 312
                                   55555555789********************************************************************** PP

                                   B-SEEEEES---HHHHHHHHHH-SEEEE--SSBSS-CHHHHHHHCSTTT--EEEEETTBGGGGT-TTTSEEE-TT-HHHHH CS
               Glyco_transf_20 351 ytPvvylersldfeeliallaaadvllvtslRdGmnlvakeyvvcqqekkgvLiLSeFaGaaqsLkdaailvNPwdieeva 431
                                   ++P+ y++r+++ + l+++++ ad++l+t+l dG+nlv+ke+++  ++  g L+LS+FaGa++ L+ +a++vNP   +eva
  gi|13542085|ref|NP_111773.1| 313 WMPILYMYRKISDHSLVSYYKSADIALITPLIDGLNLVSKEFIASTEK--GILVLSKFAGASNCLR-GALIVNPNSPDEVA 390
                                   *******************************************98876..****************.88************ PP

                                   HHHHHHHC--HHHHHHHHHHHHHHHHHT-HHHHHHHHH CS
               Glyco_transf_20 432 eaikeaLkmseeerkkrekkllkqvskhdvqsWaesfl 469
                                   +ai++a++m+ +e  +r  k+ + v+ +d + W++ + 
  gi|13542085|ref|NP_111773.1| 391 DAIYKAMNMERKEADERLLKMKAIVKARDTDWWIKRIY 428
                                   **********************************9875 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 ?   14.8   0.0     3e-06     0.018      94     170 ..      95     159 ..      53     237 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3e-06
                Glyco_transf_5  94 ffdreg.lYgdk.gedyednaerfalfsraalelleklgwkpdvihahDWhtalvpallkelykerglfkkiktvftiH 170
                                   +f re+  Y+d+  e y + +e+fa     +l+       ++d++ +hD++ +lvp +l++         k +++ft H
  gi|13542085|ref|NP_111773.1|  95 YF-RERvQYTDNgYETYRKVNEKFA---EEILNNTS----QEDIVWVHDYQLSLVPGILRQKGL------KNRIIFTWH 159
                                   44.3444666643333333333333...44444444....59*******************862......367888877 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 ?   11.7   0.0   4.5e-05      0.27      65     132 ..     327     397 ..     254     399 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4.5e-05
                                   HHHHHHHH-SEEEE--..---SHHHHHHHHT..T-EEEE-TGGGTTT--.TTSSEE--TT-HHHHHHHHHHHH CS
               Glyco_trans_1_4  65 dlaellaaadvfvaPs..egfglkllEamaa..glpvVatdvggiaevv.gengllvppgdpealaeailrLl 132
                                   +l +++++ad+++++    g++l+  E  a+  +   V ++ +g+++ + g  +l+v+p++p++ a+ai + +
  gi|13542085|ref|NP_111773.1| 327 SLVSYYKSADIALITPliDGLNLVSKEFIASteKGILVLSKFAGASNCLrG--ALIVNPNSPDEVADAIYKAM 397
                                   3889********6655499*****999999743345566666686776644..6999************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (446 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       519  (0.0289475); 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:                         3  (0.000167327); expected 0.2 (1e-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: 2714.32
//
Query:       gi|13542086|ref|NP_111774.1|  [L=246]
Description: trehalose-6-phosphatase [Thermoplasma volcanium GSS1]
Scores for complete 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   95.5   0.0    3.1e-27   95.2   0.0    1.1  1  Trehalose_PPase  Trehalose-phosphatase
    2.5e-09   37.3   0.0    1.2e-07   31.7   0.0    2.1  2  Hydrolase_3      haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.027   13.5   0.0      0.038   12.9   0.0    1.2  1  Stn1             Telomere regulation protein Stn1
      0.048   13.7   0.1       0.34   11.0   0.0    2.3  2  HAD_2            Haloacid dehalogenase-like hydrolase


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 !   95.2   0.0   6.9e-31   3.1e-27       1     211 [.      21     212 ..      21     233 .. 0.91

  Alignments for each domain:
  == domain 1  score: 95.2 bits;  conditional E-value: 6.9e-31
                                   EEETBTTTB---SSGGG--B-TTHHHHHHHHHTTS-..EEEE-SS-HHHHHHHH---SSEEEEGGGTEEE-TT--EEE-HH CS
               Trehalose_PPase   1 flDydGTlspivedpdaavpssellslLkkLasdpknvvaivSGrslkeeellvkvpelglaaeHGaeirspsgedwenqa 81 
                                   flDydGTl+pi+ +p++   ++el+++L +L s++k  ++ivSGrs +e +++  + +l l+  HGa    ++++  +n  
  gi|13542086|ref|NP_111774.1|  21 FLDYDGTLVPIIMNPEQSLADPELIEMLTELRSKYK--LFIVSGRSPEEIKRF-IPLDLNLICYHGACSIVNGKTYYYN-N 97 
                                   8***********************************..**********98888.5678****************99998.9 PP

                                   HHTTHHHHHHHHHHHHHHHTTSTT-EEEEETTEEEEE-TT--TT..THHHHHHHHHHHHHHH.--EEEE-SSEEEEE-S-- CS
               Trehalose_PPase  82 evedlewlkevkeileektertpGsyiEekkfalsvHyrnaddeelqakelaehlesvltdkpdlevtqgkkvvevrpqgv 162
                                   ++ +l +++e+ +   + ++++pG  i +k  a+  H+   +++   + +l++   ++ +++  ++v++gk+++e+r  gv
  gi|13542086|ref|NP_111774.1|  98 AQSFLGIFNEIYQSSLNLVNEFPGLRIYKKNLAVLYHFGLMKPQ--DVPALERVIVEISQKE-HVDVYKGKMIFELRVPGV 175
                                   ********************************************..***********99999.****************** PP

                                   -HHHHHHHHHHTS--------EEEEEE-SSTTHHHHTTS-TT...-EEE CS
               Trehalose_PPase 163 sKGkaverlleslgsadseddfvlciGDdrtDedmFsvlrktkesgvsi 211
                                   +KG a++ + ++          +l +GDd tDe  F+  ++     + i
  gi|13542086|ref|NP_111774.1| 176 NKGIAIKNVRDEET--------ALIAGDDATDECSFKYNEDA----ITI 212
                                   ******99876554........689***********987766....334 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.7   0.0   2.7e-11   1.2e-07       1      80 [.      20      99 ..      20     135 .. 0.83
   2 !    3.7   0.0    0.0099        44     173     215 ..     162     199 ..     136     221 .. 0.77

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 2.7e-11
                                  EEEEIIIIIS-....TTS-.--HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCCSEEEEGGGTEEECTTTEEEEE-- CS
                   Hydrolase_3  1 ialDlDGTLln....sdkk.isektkeaikklkekgikvviATGRslravlpvleelgldlpvialNGaliddekgkilykst 78
                                  i+lD DGTL+      +++  +++ +e + +l+   +k++i +GRs++++++++    ldl +i+++Ga     +gk++y ++
  gi|13542086|ref|NP_111774.1| 20 IFLDYDGTLVPiimnPEQSlADPELIEMLTELR-SKYKLFIVSGRSPEEIKRFIP---LDLNLICYHGACS-IVNGKTYYYNN 97
                                  89*******8777666666477***********.78*******************...6677*******99.99999998887 PP

                                  B- CS
                   Hydrolase_3 79 is 80
                                   +
  gi|13542086|ref|NP_111774.1| 98 AQ 99
                                  66 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.0099
                                   EESTTEEEEEETT-SHHHHHHHHHHHCT--GGGEEEEESSGGG CS
                   Hydrolase_3 173 ssskgyleimpkgvsKgtalkklakelnisleeviafGDgeND 215
                                     +k ++e+  +gv+Kg a+k++      + e  +  GD+  D
  gi|13542086|ref|NP_111774.1| 162 YKGKMIFELRVPGVNKGIAIKNVR-----DEETALIAGDDATD 199
                                   45788999*************998.....66666666776666 PP

>> Stn1  Telomere regulation protein Stn1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   8.5e-06     0.038      57     122 ..     159     218 ..     147     237 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 8.5e-06
                                   -EEETTEEE-EEEEEEEEEEEEEE....TTEEEEEEE-SSS-EEEEEEEGGG-HHHHHHHTT-TT- CS
                          Stn1  57 ilfylnrpirrikvvGlvvgvkwklikgedkavlkiDDcsdkllkckcsksqllslgieivaliGs 122
                                   +  y+++ i  ++v G+  g+ +k +++e+ a++  DD++d   +c ++ +++   +i i  ++G+
  gi|13542086|ref|NP_111774.1| 159 VDVYKGKMIFELRVPGVNKGIAIKNVRDEETALIAGDDATD---ECSFKYNED---AITIKVGPGK 218
                                   56799************************************...999988854...4555555555 PP

>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   7.5e-05      0.34      82     113 ..      42      72 ..      34      78 .. 0.91
   2 ?   -0.5   0.1      0.25   1.1e+03     117     117 ..     154     154 ..      87     211 .. 0.50

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 7.5e-05
                         HAD_2  82 dgvkelLeeLkeagyklgivTsksreaveekl 113
                                   ++++e+L eL + +ykl iv+ +s e++++++
  gi|13542086|ref|NP_111774.1|  42 PELIEMLTEL-RSKYKLFIVSGRSPEEIKRFI 72 
                                   6789******.99***********99999876 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.25
                         HAD_2 117 g 117
                                    
  gi|13542086|ref|NP_111774.1| 154 S 154
                                   2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       511  (0.0285013); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 1526.13
//
Query:       gi|13542087|ref|NP_111775.1|  [L=321]
Description: hypothetical protein TVN1256 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       576  (0.0321267); 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:                         0  (0); expected 0.2 (1e-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 0.27s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 2035.16
//
Query:       gi|13542088|ref|NP_111776.1|  [L=270]
Description: amidohydrolase [Thermoplasma volcanium GSS1]
Scores for complete 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-49  167.5   0.0    4.1e-49  167.3   0.0    1.0  1  CN_hydrolase  Carbon-nitrogen hydrolase
  ------ inclusion threshold ------
       0.11   12.9   0.0       0.23   12.0   0.0    1.4  1  DUF4598       Domain of unknown function (DUF4598)


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 !  167.3   0.0   4.5e-53   4.1e-49       1     260 [.       2     245 ..       2     246 .. 0.96

  Alignments for each domain:
  == domain 1  score: 167.3 bits;  conditional E-value: 4.5e-53
                                   EEEEEEBB-STTHHHHHHHHHHHHHHHHHHT.TESEEEEETTTTTBS..SSHHHHHHHHBHSSSHHHHHHHHHHHHHTEEE CS
                  CN_hydrolase   1 rvAvvQlpqkaadleanlqklleliaeAark.gadLivlPElfitgy..keeahfleaAeaglgetlallaalarkngiav 78 
                                   rv+vvQ+++ ++d+++n++k+ +++++   + + +Li++PE+ i+    k+  +++  Ae + ge++  +a+ a++ +  +
  gi|13542088|ref|NP_111776.1|   2 RVTVVQMAS-TSDKSENIEKTFKFLDS---IgNSNLIIFPEYQIFVPdfKNGSDMINIAESESGEFMSNIANYAKERKSKI 78 
                                   79*******.79***************...549********999876779999**************************** PP

                                   EEEEEEEECCTTEEEEEEEEEEEETTSEEEEEEE-SS--EECTTSCECCGHHTSCS-SS.S-EEEETTEEEEEEEGGGGGS CS
                  CN_hydrolase  79 vigliereltngklqayntavlldldgklvgkyrKlhLfpgeprpptaverelfepgdg.ipvfdtpvgkiGaaiCyeigf 158
                                    + ++e+     +l+++ntavl+d+ g+ + kyrKlhLf    +   + e+  fe+g+    vf ++ + +G++iCy+ +f
  gi|13542088|ref|NP_111776.1|  79 LVNIPEK--NAFNLKPFNTAVLIDELGT-TMKYRKLHLF----DAFNFKESAFFEKGNMsPMVFNSSETPFGVQICYDLRF 152
                                   *******..7888888************.6********9....4799***********999999***************** PP

                                   HHHHHHHHHTT-SEEEEBH.GCCCTCHHHHHHHHHHHHHHHHHHTSEEEEEEBEEEHCETTEEEE--EEEE-TTS-EEEEC CS
                  CN_hydrolase 159 pellralalkgaeilvnlserapvpksmgppqwellgraralengcfviaanqvggyeqlilwpvghSaiidpdGrilagl 239
                                   pe++r+l l ga+ilv+  + +++ + +  +qw +l rara+eng+fvi ++q+g       ++ ghS++++p G ++a+l
  gi|13542088|ref|NP_111776.1| 153 PEAARILTLYGAKILVY--QAGWFSGERKYDQWKTLLRARAMENGVFVIGSAQTGD------MFTGHSMVVSPYGDVVAEL 225
                                   *****************..89***********************************......******************* PP

                                   CSSSTEEEEEEEEHHHHHHHH CS
                  CN_hydrolase 240 geeeegvliaeidladvratr 260
                                   +++e + +  +idl+ v+++r
  gi|13542088|ref|NP_111776.1| 226 DKDE-NYISMDIDLGVVEKYR 245
                                   ****.6***********9987 PP

>> DUF4598  Domain of unknown function (DUF4598)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   2.5e-05      0.23      38      59 ..     226     247 ..     210     259 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.5e-05
                       DUF4598  38 ddeeqyIEMnLgLGvleekrde 59 
                                   d++e+yI M++ LGv+e++r+e
  gi|13542088|ref|NP_111776.1| 226 DKDENYISMDIDLGVVEKYRSE 247
                                   67888*************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       402  (0.0224218); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1766.77
//
Query:       gi|13542089|ref|NP_111777.1|  [L=154]
Description: NTP pyrophosphohydrolase (mutT-related oxidative damage repair enzyme) [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.1e-12   45.7   0.0    9.1e-12   45.2   0.0    1.2  1  NUDIX     NUDIX domain


Domain annotation for each model (and alignments):
>> NUDIX  NUDIX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.2   0.0   5.1e-16   9.1e-12       4     115 ..       6     114 ..       2     127 .. 0.65

  Alignments for each domain:
  == domain 1  score: 45.2 bits;  conditional E-value: 5.1e-16
                                   EEEEEEEEETTSEEEEEEESSSSTTT.E....ESSEEECBTTSHHHHHHHHHHHHHHSEEEEEEEEEEEEEEEEEEEEEEE CS
                         NUDIX   4 ravgvvllnekgevLlvrrskkpfpg.W....elPgGkvepgEtpeeAArREleEEtGleaellellgrlhylapydgpyg 79 
                                   +avg+++ +++  vL ++r+ +++++ W    ++PgG++++ E+p++A++RE++EE+ l   + ++l++++  +p  +  +
  gi|13542089|ref|NP_111777.1|   6 AAVGLIVQRSE--VLFIKRK-ARPDDpWsgdiAFPGGFLKEMESPAQAVIREIKEEVSLYFTEYDILAEMPLHYPISKQLP 83 
                                   68888888888..*******.444444655436*************************84466777776666666554444 PP

                                   EEEEEEEEEEEEECSGCSSTSTTTEEEEEEEEHHHH CS
                         NUDIX  80 deheilyvfleevegelepndenevsevrwvpleel 115
                                      +i+    ++   + +++  +ev+e++  ++ +l
  gi|13542089|ref|NP_111777.1|  84 VHPFII----KSYSFDDALP-GDEVDEIKIADIGDL 114
                                   333333....2222222222.345555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1117.38
//
Query:       gi|13542090|ref|NP_111778.1|  [L=164]
Description: nucleic-acid-binding protein [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-13   50.8   0.0    1.8e-13   50.3   0.0    1.2  1  OB_aCoA_assoc  DUF35 OB-fold domain, acyl-CoA-associated
    2.3e-09   36.9   0.5    3.6e-09   36.3   0.5    1.3  1  DUF35_N        Rubredoxin-like zinc ribbon domain (DUF35_N)


Domain annotation for each model (and alignments):
>> OB_aCoA_assoc  DUF35 OB-fold domain, acyl-CoA-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.3   0.0     2e-17   1.8e-13       1      65 []      81     146 ..      81     146 .. 0.95

  Alignments for each domain:
  == domain 1  score: 50.3 bits;  conditional E-value: 2e-17
                                   EEEE-GG-EEEEEEEEEE-TTS-EEEEEEEEEEEE-TT.....-EE-EEEEEEES..TT-B-EEE-S CS
                 OB_aCoA_assoc   1 wvelsgrGtvysftvvhrappgfaeeaPyvvgvVeLde.gvr.imarlvgvdpdevriGmrVravfr 65 
                                   w el+ +G+v +ft+ +++ ++f +e+P+ + +Ve+++      m+rl g+d +++ iGm+V+a fr
  gi|13542090|ref|NP_111778.1|  81 WYELPLKGKVHTFTTCYFSGEEFLNETPFNLIMVEFEGvN-SlFMSRLIGADTEDIYIGMPVKAKFR 146
                                   99************************************33.36**********************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 !   36.3   0.5     4e-13   3.6e-09       3      34 ..      47      78 ..      45      81 .. 0.91

  Alignments for each domain:
  == domain 1  score: 36.3 bits;  conditional E-value: 4e-13
                       DUF35_N  3 aaaegrLvgqrCpdCGtvqfPPravCphCgsd 34
                                  a+  ++L+g++C++CG v+  Pra+C +Cgs 
  gi|13542090|ref|NP_111778.1| 47 ALGKHKLMGSKCKKCGYVYATPRAHCMMCGSE 78
                                  67789*************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       665  (0.0370907); 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:                         2  (0.000111551); expected 0.2 (1e-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: 1137.52
//
Query:       gi|13542091|ref|NP_111779.1|  [L=420]
Description: acetyl-CoA acetyltransferase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.4e-11   41.6   0.0    4.5e-09   36.0   0.0    2.4  2  Thiolase_C     Thiolase, C-terminal domain
    3.7e-10   39.6   0.6    5.5e-09   35.8   0.6    2.2  1  Thiolase_N     Thiolase, N-terminal domain
  ------ inclusion threshold ------
      0.057   13.3   0.1        2.2    8.2   0.0    2.3  2  ACP_syn_III    3-Oxoacyl-[acyl-carrier-protein (ACP)] synthas
      0.085   12.4   0.5        0.3   10.6   0.0    2.1  3  ketoacyl-synt  Beta-ketoacyl synthase, N-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 ?    2.9   0.0     0.018        82      14      43 ..      21      50 ..      10      72 .. 0.81
   2 !   36.0   0.0     1e-12   4.5e-09      26      99 ..     287     380 ..     279     386 .. 0.92

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.018
                                  E--GGGGGGHHHHHHHHHHHHHT--GGGES CS
                    Thiolase_C 14 gvdpeilglgPayaikkvlkkagltvedid 43
                                  + ++ ++ l    a   ++++aglt++did
  gi|13542091|ref|NP_111779.1| 21 ASPDMDFRLRVKKAFDYAMNDAGLTLADID 50
                                  45566777888899999************9 PP

  == domain 2  score: 36.0 bits;  conditional E-value: 1e-12
                                   HHHHHHHHHHT--..GGGESEEEE--SBHHHHHHHHHHHT--G..................GGBSTT--HHHH-B-TTTHH CS
                    Thiolase_C  26 yaikkvlkkaglt..vedidlfEinEAFaaqaLavakaldldl..................ekvNvnGGaialGHPlGasG 86 
                                   +a+k++ +ka++t  ++d+dl+E+++A+++  +++ ++l+l +                    vN  GG +a GHP+Ga+G
  gi|13542091|ref|NP_111779.1| 287 MAAKEAYEKAEITdpINDLDLIELHDAYTSSEIQTYEDLGLCKygeggqfidegkpelkgkIPVNPSGGLLAAGHPVGATG 367
                                   6899999*****9889*************************999**************987779***************** PP

                                   HHHHHHHHHHHHH CS
                    Thiolase_C  87 aRivvtllselkk 99 
                                     ++v +  +l++
  gi|13542091|ref|NP_111779.1| 368 IMQAVFMFWQLQH 380
                                   *999998888876 PP

>> Thiolase_N  Thiolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.8   0.6   1.2e-12   5.5e-09      27     260 .]      31     228 ..       8     228 .. 0.81

  Alignments for each domain:
  == domain 1  score: 35.8 bits;  conditional E-value: 1.2e-12
                                   HHHHHHHHHHHHTS-GGGCCEEEEEHSSCTTSTSCHHHHH.HHHTTS-TTSEEEEEEHGGGHHHHHHHHHHHHHHTTSHSE CS
                    Thiolase_N  27 laealkallekagvdpeevdevivGnvlqagegqniarqa.alkagipeevpavtvnkvcsSglkavalaaqsiaageadv 106
                                    ++a   ++++ag++ +++d  + +     ++ q +a  + +  +g+  + p+ +++   + g  a  ++ ++ia+g++d+
  gi|13542091|ref|NP_111779.1|  31 VKKAFDYAMNDAGLTLADIDGSVASYFSDHFQRQLMAGIMvQDYLGL-VPKPSKRIEGGGATGGLAFQAGYEEIASGRMDA 110
                                   56788889999999999999999999999999999776550556899.999****************************** PP

                                   EEEEEEEESTTS-EEETCTTTTGGSSSSEEEEEHHHHHHTEETTTTSEHHHHHHHHHHHHT--HHHHHHHHHHHHHHHHHH CS
                    Thiolase_N 107 vvagGvEsmsnaptaestdvrsglklgdekakdllipdgladafneehmGltaenlakkykisReeqdefAvkshqkaaaa 187
                                   vv+ G E+ms+++t +  ++   + l +++  d  i      +++++  ++ a +  ++++ + e+ +++ vk+h +a  +
  gi|13542091|ref|NP_111779.1| 111 VVVYGFETMSHVNTWKGNEF---IALASDTNFDYPIGG----FYTGY-YAMMAVRHMHEFGTTVEQMAKVSVKNHGNAIHN 183
                                   ***************99555...566666677777666....66665.568899999************************ PP

                                   HHTTTTTTTBE-EEEEESSSEEEE-S-TTS-TT--HHHHHTS-BSSSTTSS-BTTSB--BEEEEEEEEEEEHH CS
                    Thiolase_N 188 qkagkFkdeivPvkvkgkkgkktvdkdeairsevtaekLaklkpaFkkeGtvtAgnasqisDGaaavllmses 260
                                   + a+       P+k++          ++  +++++  +L +l             +++ +sDGaa  +l+se+
  gi|13542091|ref|NP_111779.1| 184 PYAQ------SPMKIT---------VEDVRKAPMVSYPLTRL-------------DVCAMSDGAAVAILASED 228
                                   ****......355554.........47788888888899999.............899999999999998875 PP

>> ACP_syn_III  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.0   0.00048       2.2      13      54 ..      95     136 ..      87     138 .. 0.83
   2 ?    2.4   0.0     0.031   1.4e+02      51      71 ..     214     233 ..     204     240 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00048
                                   HHHHHHHHHHTTS-SEEEEEEEEEGGGCS-TTTHHHHTTB-E CS
                   ACP_syn_III  13 alsvAdaliesgaakrvLvigaetlskilDwkdrstavlfGD 54 
                                   a +   + i+sg++  v+v g et+s++  wk ++++ l +D
  gi|13542091|ref|NP_111779.1|  95 AFQAGYEEIASGRMDAVVVYGFETMSHVNTWKGNEFIALASD 136
                                   455556679******************999998888888877 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.031
                                   TB-EEEEEEEEEEESSSSCEE CS
                   ACP_syn_III  51 lfGDGAgAvvleaseeegari 71 
                                    ++DGA+ ++l  + ++ ++i
  gi|13542091|ref|NP_111779.1| 214 AMSDGAAVAILASE-DKAFEI 233
                                   679*******9986.455555 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 ?   -1.9   0.0      0.45     2e+03      94     113 ..      33      52 ..      16      84 .. 0.78
   2 ?   10.6   0.0   6.6e-05       0.3     172     217 ..      86     131 ..      42     142 .. 0.82
   3 ?   -3.5   0.0       1.4   6.1e+03     238     253 .]     215     230 ..     213     230 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.45
                                   HHHHHHHHHHTS-HHTCTTG CS
                 ketoacyl-synt  94 eaawealedagltpeeldgs 113
                                   +a + a++daglt +++dgs
  gi|13542091|ref|NP_111779.1|  33 KAFDYAMNDAGLTLADIDGS 52 
                                   46677999999999998875 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 6.6e-05
                                   ESGGGHHHHHHHHHHHHHHTTS-SEEEEEEEE---SHHHHHHHHHT CS
                 ketoacyl-synt 172 dtACsSslvavhaavqslrsgeadvalaGGvellltpeavagfsaa 217
                                   +   +++  a +a ++++ sg+ d++++ G e++ + +++ g + +
  gi|13542091|ref|NP_111779.1|  86 EGGGATGGLAFQAGYEEIASGRMDAVVVYGFETMSHVNTWKGNEFI 131
                                   556689999**************************99998776555 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 1.4
                                   BB-EEEEEEEEECHHH CS
                 ketoacyl-synt 238 lGEGvGavvLkrleda 253
                                   +++G+++ +L ++++a
  gi|13542091|ref|NP_111779.1| 215 MSDGAAVAILASEDKA 230
                                   899*******998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (420 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 2920.65
//
Query:       gi|13542092|ref|NP_111780.1|  [L=214]
Description: aspartokinase beta subunit [Thermoplasma volcanium GSS1]
Scores for complete 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-05   23.3   0.1    8.3e-05   22.3   0.1    1.5  1  ACT_7     ACT domain
  ------ inclusion threshold ------
       0.05   13.8   0.0      0.093   12.9   0.0    1.4  1  FlaG      FlaG protein


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 !   22.3   0.1   9.3e-09   8.3e-05      18      63 ..     157     202 ..     143     204 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 9.3e-09
                                   -SS--HHHHHHHHHHTTT---EEEE-SS-EEEEEEG.GGHHHHHHHH CS
                         ACT_7  18 fdvtGivaklaspLaeagIsifqiStyrtdyiLVpe.edlekAveaL 63 
                                   f + G va l+s L+ +gI+i qi +++td+ ++ + edl +  ++L
  gi|13542092|ref|NP_111780.1| 157 F-TRGYVAYLSSILSHNGINIIQIVSFYTDVTFILDpEDLVRSFNIL 202
                                   5.6699************************99885436666666665 PP

>> FlaG  FlaG protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0     1e-05     0.093      67      95 ..     120     148 ..     104     165 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1e-05
                                   EEETTT-SEEEEE-HHHHHHHHHHHHHHH CS
                          FlaG  67 viDketgevIrqiPseevldlakklkela 95 
                                   + D++ ++++r iP+ ev+++ +kl+e++
  gi|13542092|ref|NP_111780.1| 120 MNDNDAEKIVRSIPKGEVIQMDRKLSEIV 148
                                   569999*******************9984 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       468  (0.026103); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); 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 0.27s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1523.29
//
Query:       gi|13542093|ref|NP_111781.1|  [L=510]
Description: amino acid transporter [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.5e-32  111.8  63.0    1.5e-31  109.7  63.0    1.8  1  AA_permease_2  Amino acid permease
    5.1e-19   68.2  40.0    5.1e-19   68.2  40.0    2.2  2  AA_permease    Amino acid permease
  ------ inclusion threshold ------
        3.2    7.5   7.1       0.11   12.2   0.6    1.9  3  TMEM252        Transmembrane protein 252 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 !  109.7  63.0   2.5e-35   1.5e-31       2     406 ..       7     418 ..       6     490 .. 0.80

  Alignments for each domain:
  == domain 1  score: 109.7 bits;  conditional E-value: 2.5e-35
                 AA_permease_2   2 sllsafalvigsvigsgifvknlaas..ggpalilwvwiavligslavllvyaElssalprsgGiyvytkaafgkkvafls 80 
                                   + +++++ +++ +igsg +++ l+as  +gp++i+++++++li+   ++l+ya ls+++p+ g +  y   + g  +++++
  gi|13542093|ref|NP_111781.1|   7 GIIDLTMSSVTGMIGSGWLFSALYASsiAGPYSIISWIVGSLIV-AVLALIYADLSGRMPTAGAAAAYPFLTNGDAAGSIN 86 
                                   6678899999999****99998777778****************.69********999*********************** PP

                 AA_permease_2  81 awfnwfayvpvlasilsvaasyllnalgpdlqgn....twltyliaiaililvalinirgikesakiqnilgilkillpli 157
                                   aw+++++y+ + ++ +++ + y+ +++ p l ++    t   +liai +l ++++in++gi++++k++n++ +lki +p+i
  gi|13542093|ref|NP_111781.1|  87 AWSLFLGYASTPPLEVIASITYMNFVM-PGLINSsgmlTLRGMLIAISLLFVFFIINAMGIRHTSKVNNYISYLKIGIPII 166
                                   **********99999999999998887.53323234447888*************************************76 PP

                 AA_permease_2 158 iliilglitvdgggfsslstetdtffpngwpgvllgl..livlwsfdGfesaanvseevkk..kdvpkaifigllivlvly 234
                                   + +   +i   +++++      +++ +    g++ ++  +++++sf Gf  a+  s e+k+  ++vp+ai+++++i++++y
  gi|13542093|ref|NP_111781.1| 167 TSF--FFISTMFSISN-----FSYVSSVHPEGIFTAIpdAGIAFSFLGFRQAVELSGEAKNpqRTVPIAIMLSVAIASGIY 240
                                   666..44444455555.....434444455589****55569****************888779***************** PP

                 AA_permease_2 235 llvniaflgvvpddei...........anlsnlgsvaalffeavggkvvaiivvilialsllgaintavigssrvlealar 304
                                   llv++af+g + + ++           a    + +++ +++ a+g +++a+++ + +++s lg  n + +++srv+++++r
  gi|13542093|ref|NP_111781.1| 241 LLVQVAFIGSLKWFSLtpgdwsglynsA---YSSGPMLVLASALGLGALASVLLFDGVVSPLGTSNVYQTSTSRVVYRISR 318
                                   *************999777776654222...23337********************************************* PP

                 AA_permease_2 305 dgvlPrffakvnkfgspiraiiltaivslillllfllassaaynfllsvsslgliisyllliigalilr..kkrphlkrpg 383
                                    g+l + +   n +  p++a+ l++ v ++++l f     + y++++  s l +i +++ +i +++++   + ++ +k p 
  gi|13542093|ref|NP_111781.1| 319 MGFLTKKIGTLNSNSVPFYALLLDFFVMSLFILPFP----SWYDLVSVNSDLTIIAYMTGPISLVIMNQlgIAPKGFKLPL 395
                                   ***************************999998886....24555555555555556666666666665323344444454 PP

                 AA_permease_2 384 kilvaiigalfllfllvalffpp 406
                                   + ++a +g++f+++++++  +p+
  gi|13542093|ref|NP_111781.1| 396 AKILAPLGFVFSILIIYWSGYPT 418
                                   45555555555555555554443 PP

>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.2  40.0   8.6e-23   5.1e-19       2     353 ..      11     351 ..      10     384 .. 0.88
   2 ?   -2.0   6.0      0.17   9.9e+02      95     154 ..     404     463 ..     396     497 .. 0.84

  Alignments for each domain:
  == domain 1  score: 68.2 bits;  conditional E-value: 8.6e-23
                   AA_permease   2 vlvialggviGtglfvglgvvlsqaGplgallayllagvviflvmlslgeiatngpksggfytyasrflgpelGfviGlny 82 
                                   +++ ++ g+iG g +++  ++ s aGp + +++++++ ++++  +l+ + ++  +p +g++++y   + g+++G   ++++
  gi|13542093|ref|NP_111781.1|  11 LTMSSVTGMIGSGWLFSALYASSIAGPYS-IISWIVGSLIVAVLALIYADLSGRMPTAGAAAAYPFLTNGDAAGSINAWSL 90 
                                   78999**********************55.5************************************************** PP

                   AA_permease  83 lfswitvlaleltaasiliqfwelvtdlpkawvt........gavflvvlliinlvgvkvygeaefilalikiiaiiafii 155
                                   ++ ++ + +le++a++ +++f+  ++ l+   ++        ++ +l+v++iin +g++   ++   ++ +ki + i++  
  gi|13542093|ref|NP_111781.1|  91 FLGYASTPPLEVIASITYMNFV--MPGLINSSGMltlrgmliAISLLFVFFIINAMGIRHTSKVNNYISYLKIGIPIITSF 169
                                   **********************..888887777789***99655678999***********************99999999 PP

                   AA_permease 156 vgiillaggkpnkgagfrflgdngsifknnlppgfakeeegafknfisvfv..ivvfaftGielvaiiagEvkdPeksiPk 234
                                   ++i+++++    ++      ++ +s     + p           +++ +++   ++f+f G+   + ++gE+k+P++++P+
  gi|13542093|ref|NP_111781.1| 170 FFISTMFSIS--NF------SYVSS-----VHPE----------GIFTAIPdaGIAFSFLGFRQAVELSGEAKNPQRTVPI 227
                                   9988888776..44......33333.....3333..........4777775226788889********************* PP

                   AA_permease 235 ailqvviritifYv......lsllligllvprndlgllndsasaaspfvifikesgvsvlaplinaviltaalssanssly 309
                                   ai+  v +   +Y+      +++l   +l p +  gl n++ s  +p+ +  + +g+ +la+++ +   ++ l+++n + +
  gi|13542093|ref|NP_111781.1| 228 AIMLSVAIASGIYLlvqvafIGSLKWFSLTPGDWSGLYNSAYSS-GPMLVLASALGLGALASVLLFDGVVSPLGTSNVYQT 307
                                   **************555555555555678999999999988877.************************************ PP

                   AA_permease 310 sasRvlyslakdglaPkvlkkvskrgvPlraillsmiisllall 353
                                   s+sRv+y  ++ g + k  + ++ + vP  a+ll +++  l++l
  gi|13542093|ref|NP_111781.1| 308 STSRVVYRISRMGFLTKKIGTLNSNSVPFYALLLDFFVMSLFIL 351
                                   **********************************9999888884 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.17
                   AA_permease  95 taasiliqfwelvtdlpkawvtgavflvvlliinlvgvkvygeaefilalikiiaiiafi 154
                                   ++ sili +w+ ++  +++ ++++  lv++++     +k    a++++++++++ +++f+
  gi|13542093|ref|NP_111781.1| 404 FVFSILIIYWSGYPTTLYMSIIALAGLVLFIFARRSPLKSLVGASYMIFILIFVPVASFL 463
                                   677888889988999998999988888999999999999999999999999999988887 PP

>> TMEM252  Transmembrane protein 252 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.3       1.6   9.6e+03      11      30 ..     127     146 ..     120     150 .. 0.81
   2 ?   -3.9   0.0       1.7     1e+04      13      26 ..     368     381 ..     363     382 .. 0.85
   3 ?   12.2   0.6   1.9e-05      0.11      11      36 ..     392     417 ..     385     423 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 1.6
                       TMEM252  11 nlilaylllPlGfvillsGi 30 
                                    +++a  ll + f+i   Gi
  gi|13542093|ref|NP_111781.1| 127 GMLIAISLLFVFFIINAMGI 146
                                   68899999999999988888 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 1.7
                       TMEM252  13 ilaylllPlGfvil 26 
                                   i+ay+  P+ +vi+
  gi|13542093|ref|NP_111781.1| 368 IIAYMTGPISLVIM 381
                                   89******999986 PP

  == domain 3  score: 12.2 bits;  conditional E-value: 1.9e-05
                       TMEM252  11 nlilaylllPlGfvillsGifWstyr 36 
                                   +l la +l PlGfv  +  i+Ws y 
  gi|13542093|ref|NP_111781.1| 392 KLPLAKILAPLGFVFSILIIYWSGYP 417
                                   799********************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (510 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       833  (0.046461); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.47
# Mc/sec: 3292.38
//
Query:       gi|13542094|ref|NP_111782.1|  [L=396]
Description: multidrug efflux permease [Thermoplasma volcanium GSS1]
Scores for complete 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-20   70.8  48.1    6.8e-15   54.8  26.1    2.2  2  MFS_1     Major Facilitator Superfamily
  ------ inclusion threshold ------
       0.58   10.6  12.6        2.2    8.8   1.3    3.5  2  DUF3917   Protein of unknown function (DUF3917)
        1.2    9.2   2.7        3.7    7.6   0.7    2.3  2  DUF3042   Protein of unknown function (DUF3042)


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 !   54.8  26.1   1.1e-18   6.8e-15       3     264 ..      19     262 ..      14     266 .. 0.84
   2 !   18.3  27.3   1.5e-07   0.00089      14     167 ..     224     376 ..     210     390 .. 0.83

  Alignments for each domain:
  == domain 1  score: 54.8 bits;  conditional E-value: 1.1e-18
                         MFS_1   3 laaflsalarsilgpalplalaedlgispseigllltlyalgaavaslpl.GrlsdrfGrrrvlllglllfalglllll.f 81 
                                    ++f + ++ +++++ +pl      ++++  +g + ++ al+++v+s ++ + ls  + rr+v++++ l++al  +  + f
  gi|13542094|ref|NP_111782.1|  19 TITFAVRASNNMFMTEIPLVARYIIHFNEFLVGSVSAVGALATFVMSAFInSKLSSTL-RRKVFIASSLAYALV-FPTFyF 97 
                                   5678888899999999998888999****************9999999998*******.***************.444447 PP

                         MFS_1  82 asslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsl 162
                                    s++ +++   +++G+  ga++p++++ ++ +  ++ r r++++++++ s++ + gp++ g+l+  +    +f+++ i+ +
  gi|13542094|ref|NP_111782.1|  98 -SNSITIWPIVFVSGFVLGAIMPNIITSASLLPDRKARERVLSIYTLTLSISLVAGPAIEGYLLRIYPLLETFIFFSIFPA 177
                                   .777778899999*****************************************************99999********** PP

                         MFS_1 163 lafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsg....lltllplylqevlg 239
                                   l+fv     ++ + pe++ + ++e              k + k+      + +++++ + +++    +lt+  +y+++ +g
  gi|13542094|ref|NP_111782.1| 178 LVFV---TSFFIKFPEEQSNVKIEA-------------KNVIKNH----GFKVSVYNIMTYNIpfafILTFGGIYARDFFG 238
                                   **99...666666666666666666.............5566677....677777777777775444777777799***** PP

                         MFS_1 240 lsglllaglllallalvgailalla 264
                                    s + +++l+++ +++ ++i++ll+
  gi|13542094|ref|NP_111782.1| 239 AS-YSTVTLMFSSFFFTSFISRLLL 262
                                   **.8888888888888888877776 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 1.5e-07
                         MFS_1  14 ilgpalplalaedlgispseigllltlyalgaavaslplGrl..sdrfGrrr.vlllglllfalglllllfa..sslwlll 89 
                                   +++++  ++  + +g+s s++ l+++ ++++++++ l+l+     +     + +++l++ll+ +g l+++ +  +sl+++ 
  gi|13542094|ref|NP_111782.1| 224 FILTFGGIYARDFFGASYSTVTLMFSSFFFTSFISRLLLALKppEN----LWrLMILSVLLTTVG-LMGI-VesPSLTVME 298
                                   233333335566699********************99997773233....344************.7777.44355559** PP

                         MFS_1  90 vlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllafvl 167
                                   ++ ++ G+  g+ +p++++ i++ f  + r+ a++l+ + + +   + p ++g ++ ++g  ++f+ + +v l+ ++l
  gi|13542094|ref|NP_111782.1| 299 LSMLILGFPHGFTYPLSVISISRAFDISSRNAANSLFFSIMMAIGSVMPFVSGSVVLYIGLKYSFVSVIPVILIILLL 376
                                   ***************************************9999999****************************9763 PP

>> DUF3917  Protein of unknown function (DUF3917)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   1.3   0.00037       2.2      10      49 ..      47      86 ..      43      92 .. 0.83
   2 ?    6.9   1.9    0.0014       8.2      33      68 ..     324     359 ..     310     362 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00037
                       DUF3917 10 rfvpGsilaGialityvasifvesvsvevsaslvfvaitl 49
                                   f+ Gs+ a  al t+v s f++s         vf+a +l
  gi|13542094|ref|NP_111782.1| 47 EFLVGSVSAVGALATFVMSAFINSKLSSTLRRKVFIASSL 86
                                  6999******************987666667778888665 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0014
                       DUF3917  33 svsvevsaslvfvaitlfaGsimvlmvaGivlfihm 68 
                                   ++s   +a+ +f +i +  Gs+m ++   +vl+i +
  gi|13542094|ref|NP_111782.1| 324 DISSRNAANSLFFSIMMAIGSVMPFVSGSVVLYIGL 359
                                   58999999*****************9999***9965 PP

>> DUF3042  Protein of unknown function (DUF3042)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.7   0.00062       3.7       8      25 ..      48      65 ..      45      66 .. 0.93
   2 ?    0.4   0.1      0.11   6.8e+02       4      14 ..     108     118 ..     107     126 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00062
                       DUF3042  8 flvGvlatiaavagavfv 25
                                  flvG+++ ++a+a+ v++
  gi|13542094|ref|NP_111782.1| 48 FLVGSVSAVGALATFVMS 65
                                  9***************97 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.11
                       DUF3042   4 FlkGflvGvla 14 
                                   F++Gf+ G ++
  gi|13542094|ref|NP_111782.1| 108 FVSGFVLGAIM 118
                                   99******875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       888  (0.0495287); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2898.65
//
Query:       gi|13542095|ref|NP_111783.1|  [L=221]
Description: hypothetical protein TVN1264 [Thermoplasma volcanium GSS1]
Scores for 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-73  246.9   0.2    1.1e-73  246.8   0.2    1.0  1  DUF3834     Protein of unknown function (DUF3834)
  ------ inclusion threshold ------
      0.011   15.2   0.0      0.016   14.7   0.0    1.2  1  SBP_bac_3   Bacterial extracellular solute-binding proteins, 
      0.054   13.8   0.0       0.12   12.7   0.0    1.6  1  Multi_ubiq  Multiubiquitin


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 !  246.8   0.2   1.9e-77   1.1e-73       2     198 ..       5     199 ..       1     202 [. 0.97

  Alignments for each domain:
  == domain 1  score: 246.8 bits;  conditional E-value: 1.9e-77
                       DUF3834   2 kivaaPGPVsyPliaatmkkkdielkfekeesadvvlDsivslvkrglridlvvikkllviipkigkekIavwrkGsaaDv 82 
                                   k + aPGPVsyPliaa  k kdi++ f+k++++d+vlDs+vslvkrg+++++++i+kl+v++p+igk kI+vwrkGsa+Dv
  gi|13542095|ref|NP_111783.1|   5 KAIVAPGPVSYPLIAA--KAKDIDMIFDKKGQGDIVLDSTVSLVKRGINFNISLIRKLSVVYPDIGK-KIGVWRKGSANDV 82 
                                   6789************..99***********************************************.************* PP

                       DUF3834  83 llrilldlkkikaevvyaddpeevlkllnegevdsavvaselkkgeafedllkklgvyvpGsCgaavken.eeefidaYee 162
                                   llr+lldl+k ++e+vya+d+ e+ ++l ++++dsav++s+++kg+afedl+ ++++y+pGsC a+vk +  ++f ++Y+e
  gi|13542095|ref|NP_111783.1|  83 LLRALLDLNKKESEIVYAEDQREIRNMLTQNKIDSAVLSSAFAKGKAFEDLFAETKLYMPGSCAAYVKPEiLDYFNSVYSE 163
                                   **********************************************************************89********* PP

                       DUF3834 163 GIelikedpeeaaeyiaskLpikidkefiknilkna 198
                                   GI+ +++dp  +aey+as Lpik+d+efi+  + ++
  gi|13542095|ref|NP_111783.1| 164 GIDRFRQDPSGTAEYVASVLPIKFDTEFIHAAILKS 199
                                   *****************************9887766 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 ?   14.7   0.0   2.7e-06     0.016      94     168 ..      49     130 ..      35     154 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.7e-06
                                   TTSHGTCCHSSCG....CGTTSEEEEETTSHHHHHHHHHHHC....TSEEEEESSHHHHHHHHHTTSSSEEEEEHHHHHHH CS
                                   xxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     SBP_bac_3  94 kdaskissiksla....dLkgkkvgvqagstaeellkeelkk....gaeivefdtleealqaLkngrvdavvadspvlayl 166
                                   + + +is i++l+    d+ gkk+gv +  +a + l ++l +    + eiv+ ++++e  ++L ++++d +v +s+ +++ 
  gi|13542095|ref|NP_111783.1|  49 GINFNISLIRKLSvvypDI-GKKIGVWRKGSANDVLLRALLDlnkkESEIVYAEDQREIRNMLTQNKIDSAVLSSAFAKGK 128
                                   4456667777666555577.999**9999888888777555566668999***********************99999876 PP

                                   HH CS
                                   xx RF
                     SBP_bac_3 167 vk 168
                                   + 
  gi|13542095|ref|NP_111783.1| 129 AF 130
                                   65 PP

>> Multi_ubiq  Multiubiquitin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0     2e-05      0.12      22      66 ..       4      55 ..       2      57 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2e-05
                    Multi_ubiq 22 ivalAgpdpaddpvvleivty.......gedgeirdgesVdLkakGverfvt 66
                                  i+a+  p+p+++p++    +        +++g+i+++ +V L ++G+ ++++
  gi|13542095|ref|NP_111783.1|  4 IKAIVAPGPVSYPLIAAKAKDidmifdkKGQGDIVLDSTVSLVKRGINFNIS 55
                                  6666666776666666666667777777999*******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       364  (0.0203023); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.30s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1576.79
//
Query:       gi|13542096|ref|NP_111784.1|  [L=116]
Description: transcription regulator [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.2e-13   49.4   0.2    4.2e-13   49.1   0.2    1.2  1  PadR      Transcriptional regulator PadR-like family
     0.0084   16.3   0.1      0.012   15.8   0.1    1.2  1  HTH_34    Winged helix DNA-binding domain
  ------ inclusion threshold ------
      0.037   14.0   0.2      0.091   12.8   0.0    1.7  2  HTH_45    Winged helix-turn-helix
      0.046   14.4   0.1      0.059   14.0   0.1    1.2  1  RTP       Replication terminator protein


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 !   49.1   0.2   9.3e-17   4.2e-13       1      73 [.      19      89 ..      17      91 .. 0.92

  Alignments for each domain:
  == domain 1  score: 49.1 bits;  conditional E-value: 9.3e-17
                                  HHHHHCCS-EEHHHHHHHHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCHHH CS
                          PadR  1 iLalleeqpsyGyeiikeleelsegllelseGslYpaLkrLekeglveseweesgegpprkyYrlTdaGrrel 73
                                  +L+ l ++p++Gye+ k l+  +++   l +Gs+Y +Lk++++ ++v+se++++++g++   Y +T++G++ l
  gi|13542096|ref|NP_111784.1| 19 LLKELVRGPMHGYELQKTLSSVIGN--PLPQGSIYVLLKTMKERNFVTSENAKNEKGQTLTKYYITEEGKKFL 89
                                  5777889***************988..9**************************8888888888******976 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 !   15.8   0.1   2.6e-06     0.012      28      76 ..      47      96 ..      35      98 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.6e-06
                        HTH_34 28 dgnLsvhlkkLekagYievdkefkgk.kprtllriTpeGreafkkyvkaL 76
                                  +g ++v lk++++ ++++ + ++++k +  t + iT+eG++   ++ + L
  gi|13542096|ref|NP_111784.1| 47 QGSIYVLLKTMKERNFVTSENAKNEKgQTLTKYYITEEGKKFLCSHSESL 96
                                  799****************9998876256899********9988887765 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0     2e-05     0.091      40      68 ..      54      91 ..      49     100 .. 0.82
   2 ?   -2.4   0.0       1.1     5e+03       6      15 ..     101     110 ..      99     114 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2e-05
                        HTH_45 40 LdmLvekgli.........kkskekYvlTekGlellek 68
                                  L+++ e++++          ++ +kY++Te+G+++l +
  gi|13542096|ref|NP_111784.1| 54 LKTMKERNFVtsenaknekGQTLTKYYITEEGKKFLCS 91
                                  8899999999999987765556789**********976 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.1
                        HTH_45   6 eIiadILeai 15 
                                   +Ii d+L+ +
  gi|13542096|ref|NP_111784.1| 101 KIIDDLLKTV 110
                                   6888888876 PP

>> RTP  Replication terminator protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   1.3e-05     0.059       9      88 ..      14      88 ..       9     111 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.3e-05
                                  HHHHHHHHHHHTT-EBCTCHHHHHHHHHTTTT----HHHHHHHHHHHHHTTSEEEEEEEBTSSSSSEEEEEEESS..HHH CS
                           RTP  9 FlklylitlvekkklyglklldelkkeFkelgykPnhseiyralhelvedgilkrrkelkekaklqevviYsltdeGkek 88
                                   + lyl++ + + +++g++l  +l +    +g   ++  iy  l+ + e  +++ ++ ++  +k q +  Y++t+eGk  
  gi|13542096|ref|NP_111784.1| 14 LITLYLLKELVRGPMHGYELQKTLSS---VIGNPLPQGSIYVLLKTMKERNFVTSENAKN--EKGQTLTKYYITEEGKKF 88
                                  57899999999999999988877765...4676668899**************9888776..899**********99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.32s 00:00:00.79 Elapsed: 00:00:00.50
# Mc/sec: 703.68
//
Query:       gi|13542097|ref|NP_111785.1|  [L=646]
Description: Acyl-coenzyme A synthetase [Thermoplasma volcanium GSS1]
Scores for 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-79  266.6   0.0    3.8e-79  266.3   0.0    1.1  1  AMP-binding    AMP-binding enzyme
    7.3e-20   71.7   0.2    1.7e-19   70.5   0.2    1.7  1  AMP-binding_C  AMP-binding enzyme C-terminal domain
    3.6e-13   49.2   0.2    8.4e-13   48.0   0.2    1.7  1  ACAS_N         Acetyl-coenzyme A synthetase N-terminus
  ------ inclusion threshold ------
      0.064   12.6   0.0        2.3    7.5   0.0    2.4  2  DUF929         Domain of unknown function (DUF929)


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 !  266.3   0.0   8.5e-83   3.8e-79       7     422 ..      92     516 ..      86     517 .. 0.84

  Alignments for each domain:
  == domain 1  score: 266.3 bits;  conditional E-value: 8.5e-83
                                   HSTTSEEEEE...CCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEETTS-HH CS
                   AMP-binding   7 ktpdkvalvd...sgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvplnptltae 84 
                                      ++ al++   +g+   +TY+ l++ vn+l+++LrslGvkkgdrV i+lpn pe ++++la+ ++Gav  ++ ++++ +
  gi|13542097|ref|NP_111785.1|  92 GEANRAALIFeseTGRSAVYTYAMLQSIVNKLSNALRSLGVKKGDRVSIFLPNIPETLFSVLACYRVGAVFNTIFSGFSTQ 172
                                   4569999999999889999************************************************************** PP

                                   HHHHHHHHHTESEEE.......E..TCTCCCHHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS.......- CS
                   AMP-binding  85 elayiledseakvli.......a..tvdselleklleaaakleavklvivldadellkeeelkeeeeseekae.......k 149
                                   +l+  l++ ++ ++i       +   v  el +k++e++++    +++iv++  ++  +  l+++e + +  +       +
  gi|13542097|ref|NP_111785.1| 173 ALENRLKHFNPMIIItadgtyrRgkLV--ELKKKVDEIRDSN--FEKIIVVK--NVGLN--LNFTERDLDF-YsliakfnD 244
                                   ***************876554312221..1234444444432..22334444..33333..3444432222.134556664 PP

                                   TSCCCS-BTTSEEEEEEE--SSSS-EEEEEEH.HHHHHHHHHHHHHHCSCCTTT-EEEESS-TTSCHHHHHHHHHHHHTT- CS
                   AMP-binding 150 peeeeelkpddlayiiYTSGTTGkPKGVmlsh.rnlvanvaslkletrfklkeddvvlsilplahifglilelllallsGa 229
                                   +++   ++++++ +++YTSGTTGkPKGV+ls  + lv+n+  +  +++ +l+++dv+++++++ + + +i+++++al++G+
  gi|13542097|ref|NP_111785.1| 245 KDKGGDVEANEPGIVFYTSGTTGKPKGVVLSGaGFLVNNYVYA--KHHLDLSKSDVLWCTADIGWLTMHIWGIIGALANGS 323
                                   5577799*************************55567776664..67788899**************************** PP

                                   EEEE-TTCGC.CHHHHHHHHHHHHT-SEEEEEHHHHHHHHHCCCHHCHHHHCCGTT-SEEEEESS-EBHHHHHHHHHHHTC CS
                   AMP-binding 230 tvvllpkdaa.ldpklllelieklkvtviagvPrvleallesgalkaakkakdlsslrlvllggeplspellrffralfge 309
                                   t  ++++  + +++++++e ++k+kvt i+++P+++++l++ g+++    ++d ss+r++ l+gepl+pe++++++++f+ 
  gi|13542097|ref|NP_111785.1| 324 TTLFYEGAIDyPSQDRFYEIVQKYKVTKIFTAPTLIRMLMKYGFPE---GKYDVSSVRVIGLVGEPLNPEAWHWMNKHFRS 401
                                   **********77799**************************88888...4569**************************** PP

                                   .EEEEEEEEGGGSSECEE...CHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEEEEEEEET..TS-SEBTT-HHH CS
                   AMP-binding 310 .evlegYGlTEttgvvtv...lpleedkkklgsvGkplpgvevkivDeetgepvpdgeeGellvrgp..gvmkgYlkkpea 384
                                     + +++G+TEt+g       +       k+gs G  + g+ + +vD+e g+pv  + +G l++++p   + +  ++++e+
  gi|13542097|ref|NP_111785.1| 402 aYINNTWGQTETAGTPLAgsaF---ATGMKPGSSGIEFLGASLDVVDDE-GNPV-LERPGNLVIKKPfpMMIRDLWNEHER 477
                                   99**********9988544322...333468*****************9.9999.899********98789********** PP

                                   HHHHEEET.CCEEEEEEEEEEETTSEEEEEEECCCEEEE CS
                   AMP-binding 385 taeafdse.grwlrTGDlgrldedGyleivgRkkdlikl 422
                                     + +  + ++++ T D+++ d+dG+++++gR +d+i++
  gi|13542097|ref|NP_111785.1| 478 FLKEYYGKlEGLYFTYDVAVKDKDGHFWVLGRNDDVINV 516
                                   99999855778**************************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 !   70.5   0.2   3.9e-23   1.7e-19       1      76 []     525     602 ..     525     602 .. 0.95

  Alignments for each domain:
  == domain 1  score: 70.5 bits;  conditional E-value: 3.9e-23
                                   HHHHHHHSSTTEEEEEEE-----TTS---EEEEEE---.---.HHHHHHHHHHHHT-TTTS-SEEEE-S---B-TTS- CS
                 AMP-binding_C   1 evEsalvshpaVaeaaVvGvpdevkGealvafVvlkdg.sea.leeeLkahvrkelgpyavpkkvvfvdelpktrsGK 76 
                                   e+Es ++s+ ++ae+aVvG+pde++G ++v+fV lk++ s+  +ee++ + +++ +g++a+p++v++v+e+pkt sGK
  gi|13542097|ref|NP_111785.1| 525 EMESLVASVNGIAECAVVGIPDEIRGLTPVVFVSLKNDiSATgIEETISKMIEEGIGKFAAPSDVIVVEEMPKTPSGK 602
                                   89*********************************977433479*********************************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 !   48.0   0.2   1.9e-16   8.4e-13       2      54 ..      32      83 ..      31      84 .. 0.95

  Alignments for each domain:
  == domain 1  score: 48.0 bits;  conditional E-value: 1.9e-16
                                  HHHHHHHHH-HHHHHHHHHCCS--SB--S-SECSTTTCT-EESTT-EE-HHHH CS
                        ACAS_N  2 kelykeSiedpeaFWaeqakeldWekpfdkvldgskgpfikWFeGGklNicyN 54
                                  k+l + S +dp++FW+++a++l W k++d+v++g   p++++F+GG lN+++N
  gi|13542097|ref|NP_111785.1| 32 KRLLEFSKNDPNGFWESIASDLVWRKKWDTVMEG-RLPEFSFFKGGYLNVAEN 83
                                  678999****************************.999*************99 PP

>> DUF929  Domain of unknown function (DUF929)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0   0.00051       2.3     100     203 ..      90     193 ..      74     197 .. 0.75
   2 ?    2.4   0.0     0.018        82     120     149 ..     397     426 ..     362     429 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.00051
                        DUF929 100 sdeypniPgLiFknftpnskvefysiY..iyneylnasrngtpinselvsvglqeLkeelpssvynlvkkYetes...liq 175
                                   +   +n  +LiF++ t  s v  y     i+n+ +na r+    +++ vs+ l     ++p+ + +++  Y +++   +i 
  gi|13542097|ref|NP_111785.1|  90 EAGEANRAALIFESETGRSAVYTYAMLqsIVNKLSNALRSLGVKKGDRVSIFL----PNIPETLFSVLACYRVGAvfnTIF 166
                                   5667899999***9998777655544345888888888554444788887665....688999999999999999333334 PP

                        DUF929 176 etsepsaylvsppHivttiiitGpkGty 203
                                   + + + a+    +H +  iiit   Gty
  gi|13542097|ref|NP_111785.1| 167 SGFSTQALENRLKHFNPMIIIT-ADGTY 193
                                   456677888999**********.9***9 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.018
                        DUF929 120 vefysiYiyneylnasrngtpinselvsvg 149
                                    +f s+Yi n + + ++ gtp+ +++ + g
  gi|13542097|ref|NP_111785.1| 397 KHFRSAYINNTWGQTETAGTPLAGSAFATG 426
                                   58********************87777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (646 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       554  (0.0308997); expected 358.6 (0.02)
Passed bias filter:                      515  (0.0287244); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.71u 0.33s 00:00:01.04 Elapsed: 00:00:00.53
# Mc/sec: 3635.79
//
Query:       gi|13542098|ref|NP_111786.1|  [L=140]
Description: hypothetical protein TVN1267 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.076   12.7   0.1      0.088   12.5   0.1    1.3  1  Guanylate_kin  Guanylate kinase


Domain annotation for each model (and alignments):
>> Guanylate_kin  Guanylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   4.9e-06     0.088      53     106 ..      76     131 ..      41     139 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.9e-06
                                   E-.-HH.HHHHHHHTTTEEEEEEETTEEEEEEHHHHHHHHHTTSEEEEE--CHHHH CS
                 Guanylate_kin  53 Fv.ske.emekdiskneflEaaefsgnlygtsveaieevlekgkiviLDvdiqavk 106
                                   F+ + e +me+  + + + E++    +ly ts+ + +++ e+ ++  LDvdiq  k
  gi|13542098|ref|NP_111786.1|  76 FIsTVEkAMEAIYASDRLPEFGVEALYLYFTSRDKAQKIYEQMRTEGLDVDIQEEK 131
                                   6643440566666677888****999***************************876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       773  (0.0431145); expected 358.6 (0.02)
Passed bias filter:                      544  (0.0303419); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 910.98
//
Query:       gi|13542099|ref|NP_111787.1|  [L=619]
Description: Acyl-coenzyme A synthetase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-63  215.0   0.0    1.8e-63  214.6   0.0    1.1  1  AMP-binding    AMP-binding enzyme
      1e-14   54.2   0.4    2.1e-14   53.2   0.4    1.6  1  ACAS_N         Acetyl-coenzyme A synthetase N-terminus
    2.4e-13   50.9   0.0    4.1e-13   50.1   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 !  214.6   0.0     3e-67   1.8e-63       8     422 ..      90     497 ..      83     498 .. 0.86

  Alignments for each domain:
  == domain 1  score: 214.6 bits;  conditional E-value: 3e-67
                                   STTSEEEEE...CCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEETTS-HHH CS
                   AMP-binding   8 tpdkvalvd...sgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvplnptltaee 85 
                                      k+a+++   + e +tl+Y+ l+  v+++A+ L+ +G++kgdrV+i++p  +   +a++ il++Gav+vp+ ++++ e+
  gi|13542099|ref|NP_111787.1|  90 DSSKPAVIYqneYLERETLSYSGLNIYVSSVASTLLDMGIRKGDRVGIYMPFNLKSAIAFYSILRIGAVAVPMFSGYGYEA 170
                                   4579999998887789********************99******************************************* PP

                                   HHHHHHHHTESEEEETCTCCC.HHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS-TSCCCS-BTTSEEEEE CS
                   AMP-binding  86 layiledseakvliatvdsel.leklleaaakleavklvivldadellkeeelkeeeeseekaekpeeeeelkpddlayii 165
                                   ++  +ed+++k+l+ t +      k  + ++  e+v l i+ + ++ + ++ ++++ +++       e+e++ ++d+a+++
  gi|13542099|ref|NP_111787.1| 171 VKTRVEDAGVKLLF-TSKGYSrKGKFVDMMSVAEKVGLPIIAEGGSKKGYSFEDAMHGQK-----RIETEKTGSEDTAIML 245
                                   **************.223333445666667777778888877765554444444433333.....33566899******** PP

                                   EE--SSSS-EEEEEEHHHHHHHHHHHHHHHCSCCTTT-EEEESS-TTSCHHHHHHHHHHHHTT-EEEE-TTCGC.CHHHHH CS
                   AMP-binding 166 YTSGTTGkPKGVmlshrnlvanvaslkletrfklkeddvvlsilplahifglilelllallsGatvvllpkdaa.ldpkll 245
                                   YTSGTTGkPKG ++ h+ ++ n+a+ +++ + +lk++dv+ +i +l +++g  ++l+++ +  +t++l+++  + +d+ +l
  gi|13542099|ref|NP_111787.1| 246 YTSGTTGKPKGTVHVHGGALINIAK-EVKYYMDLKDGDVLHWITDLGWMMGP-WALIGTNVLHGTIYLYDGAVDyPDASRL 324
                                   ****************777777666.4677788999***************7.999999999999*********88899** PP

                                   HHHHHHHT-SEEEEEHHHHHHHHHCCCHHCHHHHCCGTT-SEEEEESS-EBHHHHHHHHHHHTC...EEEEEEEEGGGSSE CS
                   AMP-binding 246 lelieklkvtviagvPrvleallesgalkaakkakdlsslrlvllggeplspellrffralfge...evlegYGlTEttgv 323
                                   +  +e+ +vt++ + P+++++l  ++ ++      +++ +rl+ + gep   e +  + +++g+   +++++ G T   g+
  gi|13542099|ref|NP_111787.1| 325 FTILEDNNVTLLGLSPTLVRMLRYKNIER------RFNTVRLFGSTGEPWDDESWSYLFNVLGGgktPISNISGGTDIIGC 399
                                   **********************7765555......8999******************99999999**************** PP

                                   CEECHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEEEEEEEET..TS-SEBTT-HHHHHHHEEET.CC.EEEEEE CS
                   AMP-binding 324 vtvlpleedkkklgsvGkplpgvevkivDeetgepvpdgeeGellvrgp..gvmkgYlkkpeataeafdse.gr.wlrTGD 400
                                   +  +  +   + ++++     g+ + i De+ g++v  g++G l+ ++p  ++++g +  +++  e+++s  ++ w++ GD
  gi|13542099|ref|NP_111787.1| 400 FL-AS-NPAIPIKPKCLYRGLGMNASIFDEN-GKEV-YGKVGYLVAKKPspSMTRGLWMAEDRYLESYWSRfQGvWFH-GD 475
                                   97.44.344456677888888*********9.8888.8*********88668*****************846676999.** PP

                                   EEEEETTSEEEEEEECCCEEEE CS
                   AMP-binding 401 lgrldedGyleivgRkkdlikl 422
                                    g++dedGy+++ gR++d+ik+
  gi|13542099|ref|NP_111787.1| 476 FGEMDEDGYFYLYGRADDVIKV 497
                                   *********************8 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 !   53.2   0.4   3.5e-18   2.1e-14       2      55 .]      28      84 ..      27      84 .. 0.97

  Alignments for each domain:
  == domain 1  score: 53.2 bits;  conditional E-value: 3.5e-18
                                  HHHHHHHHH-HHHHHHHHHCC..S--SB--S-SECSTTTC.T-EESTT-EE-HHHHH CS
                        ACAS_N  2 kelykeSiedpeaFWaeqake..ldWekpfdkvldgskgp.fikWFeGGklNicyNc 55
                                  kely+++ +dpe+FW ++ k+  ++++ p++kv+d s gp ++kWF+ G +Ni yN+
  gi|13542099|ref|NP_111787.1| 28 KELYDKADSDPEWFWPQVIKDtgIEFFSPYKKVFDNSGGPqHTKWFTEGLINIEYNA 84
                                  79******************889*********************************7 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.1   0.0   6.9e-17   4.1e-13       1      76 []     506     578 ..     506     578 .. 0.95

  Alignments for each domain:
  == domain 1  score: 50.1 bits;  conditional E-value: 6.9e-17
                                   HHHHHHHSSTTEEEEEEE-----TTS---EEEEEE------HHHHHHHHHHHHT-TTTS-SEEEE-S---B-TTS- CS
                 AMP-binding_C   1 evEsalvshpaVaeaaVvGvpdevkGealvafVvlkdgsealeeeLkahvrkelgpyavpkkvvfvdelpktrsGK 76 
                                   e+E +++++ +V eaaV+ +pd++kGeal++f+v +++   l   +k+ +++++g+   p++v  + +lpktr+GK
  gi|13542099|ref|NP_111787.1| 506 ELEDIVMAVNGVIEAAVISIPDKIKGEALAVFYVGEPD---LSGRIKDAIESKMGKPFSPSYVLRLRKLPKTRNGK 578
                                   89********************************7434...569*******************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (619 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       359  (0.0200234); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.50
# Mc/sec: 3731.32
//
Query:       gi|13542100|ref|NP_111788.1|  [L=382]
Description: isovaleryl-CoA dehydrogenase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.3e-40  137.8   0.3    4.9e-40  137.2   0.3    1.3  1  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
    7.3e-29  100.7   0.0    1.6e-28   99.6   0.0    1.5  1  Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
    3.1e-20   72.2   0.0    5.9e-20   71.3   0.0    1.5  1  Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
    4.8e-13   49.5   0.0    6.8e-13   49.1   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 !  137.2   0.3   1.1e-43   4.9e-40       1     149 [.     223     371 ..     223     372 .. 0.99

  Alignments for each domain:
  == domain 1  score: 137.2 bits;  conditional E-value: 1.1e-43
                                   TBHHHHHTTTT--S-----..-SHHHHHHHHHHHHHHHTSB-CC-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH----- CS
                 Acyl-CoA_dh_1   1 gkGfrvametlnheRlavaaaalglarraleealeyarrrkafgkplidhqlvreklaemaaeleaarllvyraaealdag 81 
                                   g+G r++m++ln eR+ +a   +glarral+ea++y+ +rk+f  p+ +++l++ekla m+++ e +r l+yra e+l+  
  gi|13542100|ref|NP_111788.1| 223 GDGKRIIMSGLNSERVILAFIFVGLARRALDEAVKYSSERKQFSLPISEFELIQEKLAYMYTKYETSRILAYRALEKLESS 303
                                   6899***************************************************************************** PP

                                   ---HHHHHHHHHHHHHHHHHHHHHHHHHHGGGTTSGGGHHHHHHHHTHHHHHSSS-HHHHHHHHHHHH CS
                 Acyl-CoA_dh_1  82 kpdraeasmaKlfaselaqevadlamqllGgaGyleeypverlyrdarvlrigeGtseiqrniiarrl 149
                                   ++d+  a++a + ase a+++a++a+q++Gg+Gy +++++e ++rda + +ig+Gt+ei ++iia++l
  gi|13542100|ref|NP_111788.1| 304 RDDPLYAAAAIMHASESAEYIAREAIQIFGGYGYIKDTGIEMFLRDAILGQIGAGTTEIRKRIIAKSL 371
                                   *****************************************************************987 PP

>> Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.6   0.0   3.5e-32   1.6e-28       5     113 .]       9     117 ..       6     117 .. 0.98

  Alignments for each domain:
  == domain 1  score: 99.6 bits;  conditional E-value: 3.5e-32
                                   HHHHHHHHHHHHHHTHHHHHHHHHHTSGHHHHHHHHHHTTCTSTTS-GGGTS--S-HHHHHHHHHHHHHH-HHHHHHHHHH CS
                 Acyl-CoA_dh_N   5 ealrdtvrefaeeelaphaaewdeegefprelwkklaelGllgitvpeeygGagldyleaaivaeelaradaglalllgvh 85 
                                   + lr +++ef+++e++p   ++d+e+ fp +++k++++lG+lg+t+p+eygG++++y+++a++ eel++ + +lal++g+h
  gi|13542100|ref|NP_111788.1|   9 DLLRNSIKEFVKKEVEPIRMKIDREDYFPVDVFKEMGKLGYLGVTIPQEYGGSDAGYITQAVIEEELGYSSPSLALSYGAH 89 
                                   579****************************************************************************** PP

                                   HHTTHHHHHHHS-HHHHHHHHHHHHTTS CS
                 Acyl-CoA_dh_N  86 sslvapailrfGteeqkrryLpklasge 113
                                   s+l+   ++r G+++ +++++pklasge
  gi|13542100|ref|NP_111788.1|  90 SNLCLDNVYRNGSQAIREKFVPKLASGE 117
                                   *****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 !   71.3   0.0   1.3e-23   5.9e-20       1      96 [.     121     210 ..     121     211 .. 0.91

  Alignments for each domain:
  == domain 1  score: 71.3 bits;  conditional E-value: 1.3e-23
                                   EEE---SS-SS-GGG---EEEEETT.EEEEEEEEEEEETTTT-SEEEEEEETS-------EEEEEEE..GGGEEE-----B CS
                 Acyl-CoA_dh_M   1 afalTEpqaGsdvasvkttaaerdggeyvlnGeKiwitnaaiatlalvlartekpdrarglslflvprdapgvsvrrieek 81 
                                   +++lTEp++Gsd+ ++ t +    gg + l+G+K++itn+++a+l+lv a+    d  ++ + ++v ++++g++ +++ ek
  gi|13542100|ref|NP_111788.1| 121 SLCLTEPGSGSDALAMHT-TLHDHGGRIFLTGSKTFITNGPYADLFLVHAK----D-GDSYTSVIVLSSDKGFERGKKFEK 195
                                   58****************.66667779************************....3.456788899999************ PP

                                   SS-TTS-EEEEEEE. CS
                 Acyl-CoA_dh_M  82 lGlrglptgelvfed 96 
                                   +G+rg ptgel+f+d
  gi|13542100|ref|NP_111788.1| 196 MGMRGSPTGELFFND 210
                                   *************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 !   49.1   0.0   1.5e-16   6.8e-13       2     128 ..     239     355 ..     238     361 .. 0.91

  Alignments for each domain:
  == domain 1  score: 49.1 bits;  conditional E-value: 1.5e-16
                                   HHHHHHHHHHHHHHHHHHHHHHHHHCTTT-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----HHHHHH CS
                 Acyl-CoA_dh_2   2 giaavalGaAraalaefvelarervrassgekladdpatqlalaeaaarldAAralleraaaraealaaagkevtvedrae 82 
                                   ++a + +G+Ar+al+e+v++  er++  +  ++++++ +q +la + ++ ++ r l +ra ++ e  +        +d + 
  gi|13542100|ref|NP_111788.1| 239 ILAFIFVGLARRALDEAVKYSSERKQ--FSLPISEFELIQEKLAYMYTKYETSRILAYRALEKLE--SS------RDDPLY 309
                                   679999********************..***********************************44..33......345568 PP

                                   HHHHHHHHHHHHHHHHHHHHHHCGGGGGBTT-HHHHHHHHHHHHCT CS
                 Acyl-CoA_dh_2  83 arraaalavelaiaavdalfeaaGgsalrkesplqRlwRDahaaaa 128
                                   a++a ++a+e a  +++++++++Gg+++ k+  ++ ++RDa  +++
  gi|13542100|ref|NP_111788.1| 310 AAAAIMHASESAEYIAREAIQIFGGYGYIKDTGIEMFLRDAILGQI 355
                                   999*************************************987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (382 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       380  (0.0211947); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 2425.71
//
Query:       gi|13542101|ref|NP_111789.1|  [L=182]
Description: molybdopterin-guanine dinucleotide biosynthesis protein [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.5e-10   41.7   0.0      2e-10   41.3   0.0    1.1  1  NTP_transf_3  MobA-like NTP transferase domain
      0.001   19.1   0.0     0.0039   17.1   0.0    1.8  1  CTP_transf_3  Cytidylyltransferase


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 !   41.3   0.0   2.2e-14     2e-10      16     155 ..      16     143 ..       9     150 .. 0.86

  Alignments for each domain:
  == domain 1  score: 41.3 bits;  conditional E-value: 2.2e-14
                                   HHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSHCHHHHHHTTCTS-EEE-TTSS-SHHHHHHHHHHHH.SSSCEEEEETT- CS
                  NTP_transf_3  16 KallplggkpllervldalraagvdevvvvggdeevlaalarlgvrvvededpgkgplaslaaalraaadadavlvlacDm 96 
                                   K  + +ggk+lle ++ +l+    ++v+v ++d+++   +   g+++  d+     +  s++aa+++      ++ +a+Dm
  gi|13542101|ref|NP_111789.1|  16 KHSYMIGGKSLLEIIVSKLSNI--GKVYVFTKDKDII--C--NGCSIEFDT-TNGIITDSVLAAIDKF---GTFFAVAGDM 86 
                                   78899***************76..8*********998..5..567777776.3577889******987...79******** PP

                                   TT--HHHHHHHHHCHHHHTSSEEEEESSSEEEECC..EEEGGGHHHHHHHCTHTTHHHCHH CS
                  NTP_transf_3  97 Plltpelverllaaaaasgadvvvptyegerghpl..lfrarllsalaallgdqgarrllr 155
                                   Pl++pelv ++l +++   ++ ++p++ +++ +pl  ++  +l  al+++l d+g+++l +
  gi|13542101|ref|NP_111789.1|  87 PLIKPELVSKMLSQYK---GSPLFPRHMDGMLEPLfgIYTEDLYNALKEYL-DKGGESLHA 143
                                   **************97...4458************9999***********9.777777665 PP

>> CTP_transf_3  Cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   4.4e-07    0.0039      10     117 ..      10     103 ..       8     132 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 4.4e-07
                                   SSSSTTGGGSEETTEEHHHHHHHHHHHTTTTSEEEEEES-HHHHHHHHHTTSEEEE--TTCSSHHHHHHHHHHHHTTT.TT CS
                  CTP_transf_3  10 SkRlpgKnlldlggkpliayvleaalkskafekvivaTDseeiknvakefgasvlvtrsslesdterflevvkaflmsene 90 
                                   S R+pgK    +ggk l+++++ ++ +   + kv+v T +++i  ++    +++  t + +   t+++l+++ +f      
  gi|13542101|ref|NP_111789.1|  10 SVRFPGKHSYMIGGKSLLEIIVSKLSN---IGKVYVFTKDKDI--ICNGCSIEFDTTNGII---TDSVLAAIDKFGTF--- 79 
                                   89*************************...566*****98766..6666669999999988...67899999999988... PP

                                   SEEEEE-TT-TT--HHHHHHHHHHHHH CS
                  CTP_transf_3  91 eiivnlqGdnPllqeevikkaietlke 117
                                        + Gd Pl+++e+++k+++++k 
  gi|13542101|ref|NP_111789.1|  80 ---FAVAGDMPLIKPELVSKMLSQYKG 103
                                   ...8999***************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.45
# Mc/sec: 1211.05
//
Query:       gi|13542102|ref|NP_111790.1|  [L=373]
Description: saccharopine dehydrogenase [Thermoplasma volcanium GSS1]
Scores for 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-35  121.6   0.0    7.2e-35  121.4   0.0    1.1  1  Sacchrp_dh_C     Saccharopine dehydrogenase C-terminal domain
    1.9e-11   44.3   0.0    3.2e-11   43.6   0.0    1.3  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
    6.4e-06   26.2   0.0    1.1e-05   25.4   0.0    1.4  1  NAD_binding_10   NAD(P)H-binding
    0.00011   22.4   0.2    0.00021   21.5   0.2    1.4  1  TrkA_N           TrkA-N domain
    0.00022   21.6   0.0     0.0005   20.5   0.0    1.6  1  Semialdhyde_dh   Semialdehyde dehydrogenase, NAD binding doma
    0.00027   21.5   0.1    0.00073   20.1   0.1    1.8  2  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
    0.00065   19.8   0.0     0.0014   18.7   0.0    1.5  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
     0.0035   16.7   0.2     0.0056   16.0   0.2    1.3  1  AlaDh_PNT_C      Alanine dehydrogenase/PNT, C-terminal domain
  ------ inclusion threshold ------
      0.019   14.8   0.0      0.037   13.9   0.0    1.5  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
      0.032   13.9   0.0      0.098   12.3   0.0    1.8  2  ApbA             Ketopantoate reductase PanE/ApbA


Domain annotation for each model (and alignments):
>> Sacchrp_dh_C  Saccharopine dehydrogenase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.4   0.0     4e-38   7.2e-35       1     265 []     120     368 ..     120     368 .. 0.88

  Alignments for each domain:
  == domain 1  score: 121.4 bits;  conditional E-value: 4e-38
                                   BTTTBHHHHHHHHHHHCCCHTTBECCCCCCCCCCCCECCCCESTTCEEESS-HHHHHHHCCSEEEEEETTEEEECT.CCCS CS
                  Sacchrp_dh_C   1 GldPGidhllamkaidevkakggkiesflsycgglpapeasdnplgYkfsWspegvlreltnpakvlengqvkevp.gsel 80 
                                   G++PGi+++l+ +   e+++    ++ + +y+gg+p  e     l Y+++Ws+eg+l+e+t+p+ +++ng +++v+ +s l
  gi|13542102|ref|NP_111790.1| 120 GFAPGISNVLVGHFSYELED----VKDVHIYVGGIP--EKRIGGLDYVITWSVEGLLDEYTRPVHIVQNGSITQVEpLSGL 194
                                   9**********999999977....889*********..5555589**************************9999878887 PP

                                   GCC.TCEEECCCCCEECTTECEEECTHCHHHHHHC.SCSEEEEEEEEEHHHHHHHHHHHTTT--SCECCCCCCHHSTT.C. CS
                  Sacchrp_dh_C  81 lkgakkpiyilpglslegypnrdslpyeelyglpeaktlfrgtlrypgfsellkslkelGllseepkeealkawlseg.e. 159
                                        ++i+i++  +le++ +    + ++++  +    +  +t+ry g+ e ++ lk+lG++s ++    +k+    + e 
  gi|13542102|ref|NP_111790.1| 195 -----EKINIQKYTDLEAFYTDGLRTLGKTIRAS--GSMWEKTVRYSGHAEKIRLLKDLGFFSRKK----VKV---GNsEi 261
                                   .....6788865459**99877555556666666..788*************************98....666...44588 PP

                                   EHHHHHHHHCCHHCCCCTTEEEEEEEEEEEEEETTSEEEEEEEEEEEE.EEHH.SSSHHHHHHHHHHHHHHHHHHTTSCTS CS
                  Sacchrp_dh_C 160 spldvlaalLekklalepgerDlvvlqhefgiesdgkkkekktstlvg.ydee.gssamaktvGvpaaiaaklildgkikk 238
                                   +p+d+ a+++ ++l+++ g +D  ++ +++ +  +g+   k++ ++v+ yde+ + s+ma ++ vpa+ +a ++ +++i k
  gi|13542102|ref|NP_111790.1| 262 APFDFTAEIFRNNLSMS-GVKDVSLMYVKVTGTRNGDI-VKHEASMVApYDEKrKRSSMANVTSVPASATADFLSKNEIGK 340
                                   9**************99.************99988885.566788885375335*************************** PP

                                   SEEEEGGGS..CHHHHHHHHHHHHHCT- CS
                  Sacchrp_dh_C 239 rGvvtpeelv.dpeiyeplleeLekeGi 265
                                    Gvv+pe l  d+++y+++++ L ++Gi
  gi|13542102|ref|NP_111790.1| 341 YGVVAPEILGkDENFYKQFINYLGQYGI 368
                                   **********999***********9997 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 !   43.6   0.0   1.8e-14   3.2e-11       2     129 ..       4     115 ..       4     116 .. 0.90

  Alignments for each domain:
  == domain 1  score: 43.6 bits;  conditional E-value: 1.8e-14
                                   EEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTSSEEEE-SSGGGH CS
               Sacchrp_dh_NADP   2 liiGaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaallkegdlvvnlsppiss 82 
                                   +++G+G +G++va  l++  dv    tvadr+ ++l+++ +++ g+r++ i++da  ++  ++ +++++d+vv+++p   +
  gi|13542102|ref|NP_111790.1|   4 IVFGSGQIGSSVALNLVDGMDV----TVADRDPTNLRKIQDNI-GSRVSVIQVDALRDD--IKHIISDYDIVVSALPGSVG 77 
                                   689***************9875....*************9875.999999999998776..699***************** PP

                                   HHHHHHHHHHT-EEEESS-BCGCCSCHCCSHHHHHTHHHHHHCTSEE CS
               Sacchrp_dh_NADP  83 ldvlkaCietgvhyvdtsiskeertnyalreavlklkekakeagvta 129
                                    + +k  +  gv+++d+s+         ++++v  l++ ak++  ++
  gi|13542102|ref|NP_111790.1|  78 FQFAKSIAPFGVRMIDISY---------YEDDVFLLDDVAKKSSSVI 115
                                   *******************.........9999998888888776665 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 !   25.4   0.0   6.4e-09   1.1e-05       2      70 ..       7      74 ..       7      90 .. 0.88

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 6.4e-09
                                  TTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCT..TTCEEEE--TT-CCHHHHHHTT-SEEEES--- CS
                NAD_binding_10  2 AtGkvGrllvkellargghevtalvRnpeklaeleae..eglevvegdvtdvedlaealkgadaVvsalgg 70
                                  ++G++G+ ++  l++   ++vt+  R+p  l +++++  ++++v+++d++  +d+++ ++++d+Vvsal g
  gi|13542102|ref|NP_111790.1|  7 GSGQIGSSVALNLVDG--MDVTVADRDPTNLRKIQDNigSRVSVIQVDAL-RDDIKHIISDYDIVVSALPG 74
                                  69***********984..8*************999887789999999999.89***************944 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.2   1.2e-07   0.00021       2      68 ..       4      70 ..       3      76 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 1.2e-07
                                  EEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTT...SEEEES-TTSHHHHHHTTGGGESEEEE CS
                        TrkA_N  2 iiiGlGrvGrslaeeLseggkdvvvidkdeerveelreeg...levvvgdatdeevLeeagiekadavia 68
                                  i+ G G++G+s+a +L +g  dv+v d+d+ ++++++++    + v++ da ++++  +  i+++d+v+ 
  gi|13542102|ref|NP_111790.1|  4 IVFGSGQIGSSVALNLVDGM-DVTVADRDPTNLRKIQDNIgsrVSVIQVDALRDDI--KHIISDYDIVVS 70
                                  89****************99.7**************988767788******99987..344556666555 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 !   20.5   0.0   2.8e-07    0.0005      56      97 ..      54      95 ..       3     109 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 2.8e-07
                                  EEEGGGGGCTT-SEEEE-SCHHHHHHHHHHHHHTTSEEEESS CS
                Semialdhyde_dh 56 vedvdeeelkevdivflalpagvskelapklaeagvkviDls 97
                                  ++d  + ++++ div++alp++v  ++a+++a  gv++iD s
  gi|13542102|ref|NP_111790.1| 54 LRDDIKHIISDYDIVVSALPGSVGFQFAKSIAPFGVRMIDIS 95
                                  223344555*******************************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 !   20.1   0.1   4.1e-07   0.00073       3      81 ..       3      84 ..       2      95 .. 0.85
   2 ?   -3.6   0.0        10   1.8e+04      46      62 ..     286     302 ..     277     306 .. 0.74

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 4.1e-07
                                  EEE.TTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC.......-EEECECHHHHHHH-SEEEE-S-HHHHHHH CS
                 F420_oxidored  3 gii.GaGnmgealasgllaagaqpheivvansrnpekaeelaeelg.......vkvtavdneeaaeeadvvvlavkpedveev 77
                                  gi+ G+G++g+++a++l+       +++va +r+p  ++++++++g       v++   d +  +++ d+vv a++ ++  ++
  gi|13542102|ref|NP_111790.1|  3 GIVfGSGQIGSSVALNLVDG----MDVTVA-DRDPTNLRKIQDNIGsrvsviqVDALRDDIKHIISDYDIVVSALPGSVGFQF 80
                                  5667***********99975....8***88.***************9999988888888999999999999999987776666 PP

                                  HHHC CS
                 F420_oxidored 78 lsel 81
                                  ++++
  gi|13542102|ref|NP_111790.1| 81 AKSI 84
                                  6665 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 10
                                   HC-EEECECHHHHHHH- CS
                 F420_oxidored  46 lgvkvtavdneeaaeea 62 
                                   ++vkvt++ n + +++ 
  gi|13542102|ref|NP_111790.1| 286 MYVKVTGTRNGDIVKHE 302
                                   45888888888888854 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   7.7e-07    0.0014      16      83 ..       4      72 ..       1      80 [. 0.82

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 7.7e-07
                                  EEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEG....CGHHHHHHT-SEEEE-S CS
                  Shikimate_DH 16 lliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeiealkl....eelkellaeadvvisat 83
                                  ++ G G++++ va +L+  g++ v+va R+ ++ +++ +++++  ++++++    +++k++++++d+v+sa 
  gi|13542102|ref|NP_111790.1|  4 IVFGSGQIGSSVALNLV-DGMD-VTVADRDPTNLRKIQDNIGSR-VSVIQVdalrDDIKHIISDYDIVVSAL 72
                                  689**************.5666.******************554.55555511235789999********95 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.2   3.1e-06    0.0056      32      98 ..       4      71 ..       1      76 [. 0.82

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 3.1e-06
                                  EEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHH.TTTCECEEHCHH..HHHHHHHHHH-SEEEE- CS
                   AlaDh_PNT_C 32 lviGgGvaGlqAiatakglgakVtvlDvrparleqles.lgakfvevlksq..eellaeavkeadvvigt 98
                                  +v+G G  G + +a     g +Vtv D +p+ l+++++ +g++ v+v++ +  ++ +++ +++ d+v+++
  gi|13542102|ref|NP_111790.1|  4 IVFGSGQIGSS-VALNLVDGMDVTVADRDPTNLRKIQDnIGSR-VSVIQVDalRDDIKHIISDYDIVVSA 71
                                  79999999975.445555599*****************88888.999665522689************98 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   2.1e-05     0.037       4      47 ..       5      47 ..       3      71 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.1e-05
                                  EE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHH CS
                       3HCDH_N  4 viGaGtmGagiaavfasagleVvlvdiseealekalekieksle 47
                                  v G+G++G+++a  ++  g++V++ d+++  l+k +++i ++++
  gi|13542102|ref|NP_111790.1|  5 VFGSGQIGSSVALNLV-DGMDVTVADRDPTNLRKIQDNIGSRVS 47
                                  89*********98876.7********************998665 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   5.5e-05     0.098       3      39 ..       5      41 ..       4      71 .. 0.85
   2 ?   -2.9   0.0       2.6   4.7e+03      97     105 ..     176     185 ..     159     193 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.5e-05
                                  EES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHHHHHH CS
                          ApbA  3 ilGaGaiGsllaakLakagadvtlilrsr.rlealkkn 39
                                  + G+G iGs +a +L   g dvt+ +r++  l ++++n
  gi|13542102|ref|NP_111790.1|  5 VFGSGQIGSSVALNLVD-GMDVTVADRDPtNLRKIQDN 41
                                  89*************65.***********999998876 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.6
                                   EEEEESSS.S CS
                          ApbA  97 vvlllqNG.l 105
                                   +v ++qNG +
  gi|13542102|ref|NP_111790.1| 176 PVHIVQNGsI 185
                                   7889999943 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       407  (0.0227007); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 2565.70
//
Query:       gi|13542103|ref|NP_111791.1|  [L=108]
Description: transcription regulator [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.2e-13   48.4   0.0    8.2e-13   48.0   0.0    1.1  1  HxlR            HxlR-like helix-turn-helix
      0.001   19.0   0.0     0.0017   18.3   0.0    1.4  1  HTH_45          Winged helix-turn-helix
     0.0023   17.7   0.1     0.0027   17.5   0.1    1.2  1  DUF1495         Winged helix DNA-binding domain (DUF1495)
  ------ inclusion threshold ------
      0.011   15.7   0.0      0.016   15.1   0.0    1.3  1  MarR_2          MarR family
      0.014   15.1   0.0      0.016   15.0   0.0    1.1  1  DUF4364         Domain of unknown function (DUF4364)
      0.015   15.8   0.0      0.026   15.0   0.0    1.4  1  HTH_27          Winged helix DNA-binding domain
      0.034   14.1   0.0      0.057   13.3   0.0    1.4  1  MarR            MarR family
       0.05   14.0   0.0      0.069   13.5   0.0    1.2  1  Rrf2            Transcriptional regulator
      0.068   13.0   0.0       0.11   12.3   0.0    1.3  1  HMG_CoA_synt_N  Hydroxymethylglutaryl-coenzyme A synthase N t
      0.069   13.4   0.0        0.1   12.8   0.0    1.2  1  Rio2_N          Rio2, N-terminal


Domain annotation for each model (and alignments):
>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.0   0.0   4.6e-16   8.2e-13       1      84 [.      20     101 ..      20     106 .. 0.90

  Alignments for each domain:
  == domain 1  score: 48.0 bits;  conditional E-value: 4.6e-16
                                   HHHSTTHHHHHHHHTTS-EE..HHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSS-EEEEEE-TCGGGGHHHHHHH CS
                          HxlR   1 liggkWkllilvellkgkkR..fselkralpkisqkmLaqrLreLeqdglierevypevPpkveYsltekGrslepvlqel 79 
                                   l+g+k+++li+  l +g+ R  f++++  +p+is  +L++r++ L  +gl+er+  +       Y ltekG ++++ l  l
  gi|13542103|ref|NP_111791.1|  20 LLGKKYTMLIISVLGNGSTRqnFNDIRSSIPGISSTILSRRIKDLIDSGLVERRSGQ----ITTYALTEKGMNVRNSLMPL 96 
                                   69***************9887799*****************************8654....456**********9999999 PP

                                   HHHHH CS
                          HxlR  80 kkwge 84 
                                    ++++
  gi|13542103|ref|NP_111791.1|  97 LQYIS 101
                                   88875 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   9.3e-07    0.0017      33      70 ..      54      94 ..      50     107 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 9.3e-07
                        HTH_45 33 ykllnkYLdmLvekgli...kkskekYvlTekGlelleklk 70
                                    +l++ ++ L++ gl+   + + ++Y lTekG+++ ++l 
  gi|13542103|ref|NP_111791.1| 54 STILSRRIKDLIDSGLVerrSGQITTYALTEKGMNVRNSLM 94
                                  5678899**********554446789*********998875 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 !   17.5   0.1   1.5e-06    0.0027      35      89 ..      38      92 ..      15      93 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.5e-06
                       DUF1495 35 vrskpsnvkGaleGmgkrynse..ssLielGLveeeeeseglklYklteeGieivev 89
                                  +r++ ++++ ++ G      s+  + Li  GLve    s ++++Y lte+G+++++ 
  gi|13542103|ref|NP_111791.1| 38 TRQNFNDIRSSIPGISSTILSRriKDLIDSGLVE--RRSGQITTYALTEKGMNVRNS 92
                                  66666677777777766655542257*******7..57889************9986 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   8.7e-06     0.016      32      56 ..      51      75 ..      28      76 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 8.7e-06
                                  TSSHHHHHHHHHHHHHTTSEEEEES CS
                        MarR_2 32 glsksavsrilkrLvaaGLverrpg 56
                                  g+s   +sr++k+L + GLverr+g
  gi|13542103|ref|NP_111791.1| 51 GISSTILSRRIKDLIDSGLVERRSG 75
                                  6888889****************87 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   8.8e-06     0.016      36      72 ..      57      92 ..      27     101 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 8.8e-06
                       DUF4364 36 lqqalseLvesglieeeekenktlykiTekGketlel 72
                                  l+  +++L++sgl+e  ++ + t+y++TekG ++ + 
  gi|13542103|ref|NP_111791.1| 57 LSRRIKDLIDSGLVER-RSGQITTYALTEKGMNVRNS 92
                                  667799*********8.569***********998766 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 ?   15.0   0.0   1.4e-05     0.026      31      68 .]      53      86 ..      49      86 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.4e-05
                        HTH_27 31 edshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68
                                  +++  s  +k L+  GLver     ++  ++++lT+kG
  gi|13542103|ref|NP_111791.1| 53 SSTILSRRIKDLIDSGLVERR----SGQITTYALTEKG 86
                                  45555699**********444....4559********9 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   3.2e-05     0.057      28      50 ..      51      73 ..      38      76 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.2e-05
                                  TS-HHHHHHHHHHHHHTTSEEEE CS
                          MarR 28 gvskstvtrvldrLekkGlieRs 50
                                  g+s++ ++r ++ L++ Gl+eR+
  gi|13542103|ref|NP_111791.1| 51 GISSTILSRRIKDLIDSGLVERR 73
                                  68999*****************8 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   3.8e-05     0.069      11      70 ..      27      85 ..      22      90 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.8e-05
                                  HHHHHHHHHSSTCC-B-HHHHHHHH.TS-HHHHHHHHHHHHHTTSEEEETTT-TCEEESSH CS
                          Rrf2 11 lhallyLakeeeeepvsseeiaerq.nispsylekilakLrkaglvksvrGkgGGyrLakp 70
                                  + ++ +L + ++++  + ++i ++  +is ++l++ ++ L  +glv+ + G+   y+L+++
  gi|13542103|ref|NP_111791.1| 27 MLIISVLGNGSTRQ--NFNDIRSSIpGISSTILSRRIKDLIDSGLVERRSGQITTYALTEK 85
                                  44555555555544..78888887779*************************999999876 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 ?   12.3   0.0   6.2e-05      0.11      37     102 ..      33      99 ..      22     107 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.2e-05
                HMG_CoA_synt_N  37 iglgqtrmgfvsdredinslsltvvqkllertkldydaigrl..evgtetiidksksvksvlmqlfee 102
                                   +g g tr +f + r  i  +s t++++ ++   +d   + r   ++ t ++ +k   v+  lm l++ 
  gi|13542103|ref|NP_111791.1|  33 LGNGSTRQNFNDIRSSIPGISSTILSRRIKD-LIDSGLVERRsgQITTYALTEKGMNVRNSLMPLLQY 99 
                                   699*************************986.589999988633689999*************99986 PP

>> Rio2_N  Rio2, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   5.8e-05       0.1      33      71 ..      49      87 ..      43      90 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.8e-05
                        Rio2_N 33 isrlkeeevkkrlsrllkaklisrktakydGYkLtyeGy 71
                                  i +++++ +++r+++l++ +l++r++ +++ Y+Lt +G 
  gi|13542103|ref|NP_111791.1| 49 IPGISSTILSRRIKDLIDSGLVERRSGQITTYALTEKGM 87
                                  55677778899************************9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       297  (0.0165653); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 762.94
//
Query:       gi|13542104|ref|NP_111792.1|  [L=231]
Description: endonuclease III-like protein [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.3e-16   58.4   0.1    1.5e-15   57.5   0.1    1.4  1  HhH-GPD        HhH-GPD superfamily base excision DNA repair p
    3.6e-06   27.5   2.1       0.19   12.4   0.1    3.1  3  HHH_5          Helix-hairpin-helix domain
  ------ inclusion threshold ------
      0.021   14.9   0.8       0.42   10.7   0.0    2.6  3  HHH_2          Helix-hairpin-helix motif
      0.032   14.1   0.0      0.081   12.8   0.0    1.7  1  HHH            Helix-hairpin-helix motif
      0.047   13.5   0.7         13    5.6   0.0    2.6  2  RNA_pol_A_CTD  Bacterial RNA polymerase, alpha chain C termin


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 !   57.5   0.1   4.3e-19   1.5e-15       1     102 [.      35     172 ..      35     176 .. 0.92

  Alignments for each domain:
  == domain 1  score: 57.5 bits;  conditional E-value: 4.3e-19
                                   HHHHHHTTS-HHHHHHHHHHHHHHHSHCSHHHHHHSHHHHHHHHHTTSTTHHHHHHHHHHHHHHHH............... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............... RF
                       HhH-GPD   1 vsailsqqtsderanriierlferfgfptpedladadeekLrelirelGfyrrKakyikelArilv............... 66 
                                   ++ail+q+ts+++++++i++l++  g  ++ed+ +++  ++++lir+ Gfy++Ka+++k+++  +v               
  gi|13542104|ref|NP_111792.1|  35 IGAILTQNTSWKNVEKAIANLKSH-GITKLEDVCKIEKNEIAKLIRSSGFYNQKAERLKAVSCLIVgefngidrikdidaf 114
                                   789*********************.79****************************************************** PP

                                   .......................S-SSS--TTSHHHHHHHHHHTTSSSS.TTHHHHHHHH CS
                                   .......................xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx RF
                       HhH-GPD  67 .......................gkpdvlivvDvhvrrilkrlrsikek.ktkkkvekkl 102
                                                          +   +++v D ++ r l+r+ s +e    kk ve++l
  gi|13542104|ref|NP_111792.1| 115 aerlksikgigqetlnsillyalD--APVFVIDKYTVRFLERYSSFDEVdSIKKSVEEQL 172
                                   ********************9542..499****************999944455566655 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.1   5.2e-05      0.19      13      52 ..      50      92 ..      49      94 .. 0.77
   2 !   12.0   0.1   7.1e-05      0.25      24      53 ..     106     134 ..      98     137 .. 0.76
   3 ?    0.8   0.0      0.21   7.5e+02      20      41 ..     156     176 ..     146     177 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5.2e-05
                                  HHHHHHHTTT--SHHHHHHS-HHHHHTS...TTS-HHHHHHHH CS
                         HHH_5 13 ktAlallsaGiesvedlaaadveeLaki...pGiGkktAerii 52
                                  k + +l s+Gi+ +ed+++ +++e+ak+    G+ + +Aer++
  gi|13542104|ref|NP_111792.1| 50 KAIANLKSHGITKLEDVCKIEKNEIAKLirsSGFYNQKAERLK 92
                                  5667899*********9887555544443449**999999986 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 7.1e-05
                                   -SHHHHHHS-HHHHHTSTTS-HHHHHHHHH CS
                         HHH_5  24 esvedlaaadveeLakipGiGkktAeriil 53 
                                   + + d ++a +e+L +i+GiG++t  +i+l
  gi|13542104|ref|NP_111792.1| 106 DRIKD-IDAFAERLKSIKGIGQETLNSILL 134
                                   44444.344479*************99986 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.21
                                   TTT--SHHHHHHS-HHHHHTST CS
                         HHH_5  20 saGiesvedlaaadveeLakip 41 
                                   s  ++ v+ +++  +e+La+++
  gi|13542104|ref|NP_111792.1| 156 SS-FDEVDSIKKSVEEQLADVK 176
                                   44.6778888999999999985 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0         2   7.1e+03      28      43 ..      54      69 ..      50      82 .. 0.50
   2 ?   10.7   0.0   0.00012      0.42      17      53 ..      96     134 ..      92     139 .. 0.83
   3 ?    1.8   0.0     0.075   2.7e+02      22      41 ..     157     176 ..     154     184 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 2
                         HHH_2 28 aLkkasleeLlevddi 43
                                  +Lk+  + +L  v  i
  gi|13542104|ref|NP_111792.1| 54 NLKSHGITKLEDVCKI 69
                                  4555444444444444 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00012
                         HHH_2  17 klLakrFksldaLkk..asleeLlevddiGeeiAqsive 53 
                                    l++ +F+ +d++k+  a +e L ++++iG+e+ +si  
  gi|13542104|ref|NP_111792.1|  96 CLIVGEFNGIDRIKDidAFAERLKSIKGIGQETLNSILL 134
                                   578899*******9632678************9999875 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.075
                         HHH_2  22 rFksldaLkkasleeLlevd 41 
                                   +F+++d +kk  +e+L+ v+
  gi|13542104|ref|NP_111792.1| 157 SFDEVDSIKKSVEEQLADVK 176
                                   7999**********999885 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   2.3e-05     0.081      11      30 .]     116     135 ..     109     135 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.3e-05
                                   HHHHTSTT-SHHHHHHHHHH CS
                           HHH  11 eeLlalPGVGpktAeaIlsy 30 
                                   e L++++G+G +t ++Il y
  gi|13542104|ref|NP_111792.1| 116 ERLKSIKGIGQETLNSILLY 135
                                   6699**************87 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 ?    5.5   0.1    0.0039        14      28      49 ..      55      76 ..      50      79 .. 0.90
   2 ?    5.6   0.0    0.0037        13      32      61 ..     104     132 ..      96     134 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0039
                                  HHHTT--BHHHHHHS-HHHHTT CS
                 RNA_pol_A_CTD 28 LkragiktvgeLvklseeeLlk 49
                                  Lk+ gi+++++++k++++e+ k
  gi|13542104|ref|NP_111792.1| 55 LKSHGITKLEDVCKIEKNEIAK 76
                                  9******************987 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0037
                                   T--BHHHHHHS-HHHHTTSSS-SSHHHHHH CS
                 RNA_pol_A_CTD  32 giktvgeLvklseeeLlkikNlGkKSleEI 61 
                                   gi+ ++++ +   e+L++ik +G+ +l+ I
  gi|13542104|ref|NP_111792.1| 104 GIDRIKDIDAF-AERLKSIKGIGQETLNSI 132
                                   56666665444.5789***********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       819  (0.0456802); expected 358.6 (0.02)
Passed bias filter:                      548  (0.030565); 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: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1524.66
//
Query:       gi|13542105|ref|NP_111793.1|  [L=411]
Description: translation initiation factor IF-2 subunit gamma [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.7e-33  114.1   0.7    2.4e-32  112.1   0.7    1.8  1  GTP_EFTU      Elongation factor Tu GTP binding domain
    6.1e-27   93.7   0.1    1.4e-26   92.6   0.1    1.6  1  eIF2_C        Initiation factor eIF2 gamma, C terminal
    8.9e-05   22.8   0.2    0.00025   21.4   0.2    1.8  1  GTP_EFTU_D2   Elongation factor Tu domain 2
    0.00013   22.0   0.0    0.00038   20.5   0.0    1.8  1  MMR_HSR1      50S ribosome-binding GTPase
     0.0017   18.3   1.7      0.034   14.0   0.2    2.4  2  RsgA_GTPase   RsgA GTPase
  ------ inclusion threshold ------
      0.013   15.5   0.1      0.029   14.4   0.1    1.5  1  MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
      0.048   13.4   1.8        2.2    8.0   0.1    2.7  3  PduV-EutP     Ethanolamine utilisation - propanediol utilisat
       0.09   13.1   0.0       0.16   12.3   0.0    1.4  1  DUF4124       Domain of unknown function (DUF4124)


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 !  112.1   0.7     1e-35   2.4e-32       3     193 ..      11     198 ..       9     199 .. 0.91

  Alignments for each domain:
  == domain 1  score: 112.1 bits;  conditional E-value: 1e-35
                                   EEEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEE................... CS
                      GTP_EFTU   3 irnigiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaisle................... 64 
                                   ++nig++ghvDhGK+TLt +L+   g       ++     +Dt++eE +rgi+ik   + +                    
  gi|13542105|ref|NP_111793.1|  11 TVNIGMVGHVDHGKSTLTLALT---G-------VK-----TDTHSEEIKRGISIKLGYADTPvykcydasgnpyytrqpse 76 
                                   79****************9999...2.......22.....79*****************99999************99985 PP

                                   TTCSSEEEEEEEESSSGGGHHHHHHHHHT-SEEEEEEETTTB.STHHHHHHHHHHHHTTTE.EEEEEESCGST.HHHHHHH CS
                      GTP_EFTU  65 ketkkylinliDtPGHvdFskevirglrvlDgavlvvdaveG.vepqteevlrlalkegvp.iivfiNKmDrl.kaelkei 142
                                   + + ++ i+++D+PGH+  + ++  g + ++ga+lv++a+e  ++pqt+e+l  +  +g++ i+++ NK+D + +++  e+
  gi|13542105|ref|NP_111793.1|  77 NCELERVISIVDAPGHETLMATMLSGSALMNGALLVIAANEHcPQPQTREHLTALEIMGIKnIVIVQNKIDLVtRERALES 157
                                   477899**********************************9879*****************999999******88888999 PP

                                   HHHHHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTBTHHHHHHHHHHHSH CS
                      GTP_EFTU 143 veevkqklsrkeeklekygekgekevpvvfgSalkgegvktllealvellp 193
                                    +e+k  +      ++   ++   + p++++Sa+++ +++ l+ea+ +++p
  gi|13542105|ref|NP_111793.1| 158 YKEIK-AF------VKGSIAE---NAPIIPVSAYHNTNIDILFEAIEKYIP 198
                                   99999.66......4444444...46***********************99 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 !   92.6   0.1   6.1e-30   1.4e-26       3      86 .]     324     407 ..     322     407 .. 0.98

  Alignments for each domain:
  == domain 1  score: 92.6 bits;  conditional E-value: 6.1e-30
                                   EEEEEEE-SBESSSSSCCC-----TTEEEEEEETTEEEEEEEEEEESSEEEEEEEEEEE-STTEEEEEEEEETTSEEEEEE CS
                        eIF2_C   3 leieyellerlvgvkeekkveklkkkEvLmlniGsastggvvtsvkkdeakvkLkkPvcaekgekialsRrvekrWrLiGw 83 
                                   +++e +ll+r+vg+++e +ve+++ kE+Lm+++++a+t+gvv++vk+  ++v+Lk Pv+a +g ++a+ Rrv +rWrLiG+
  gi|13542105|ref|NP_111793.1| 324 MRLEAHLLKRVVGSDQELNVEPIRAKETLMFTVATANTVGVVSNVKGTDIEVSLKYPVAAFNGMRVAIGRRVLNRWRLIGY 404
                                   67899**************************************************************************** PP

                                   EEE CS
                        eIF2_C  84 Gei 86 
                                   G i
  gi|13542105|ref|NP_111793.1| 405 GVI 407
                                   *87 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 !   21.4   0.2   1.1e-07   0.00025       1      63 [.     230     299 ..     230     307 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.1e-07
                                   EEEEEEEEEESEEETTEEEEEEC.TCTTSEE......EEEEEEEEEEETEEESEEETTSEEEEEEEESSC CS
                   GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilg.ndtskke......ivtrissletfhededeavaganaGvivaikgl 63 
                                   G++++g++ +G lk Gde++i++  +  + +       +t++ sl + +  +d   +g+ a v++++++ 
  gi|13542105|ref|NP_111793.1| 230 GGIIGGSLTQGSLKIGDEIEIVPgIQNTRGNktvwtnVTTEVVSLMAGKYSYDMIKPGGLAAVGTKLDPF 299
                                   899********************976655558*****9**********9999999999999999998775 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   1.7e-07   0.00038       1     113 [.      13     144 ..      13     151 .. 0.61

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 1.7e-07
                                   EEEEEESTTSSHHHHHHHHHT............STEEESSSTTSSSSEEEEEEEETTEE...............EEEEECG CS
                      MMR_HSR1   1 evaivGrpNvGKStLinaltg............ekaivsdkpgtTrdinegrvklkgke...............ielvDtp 54 
                                   +++ vG+   GKStL  altg                +s k g   +++++ ++ +g++               i +vD p
  gi|13542105|ref|NP_111793.1|  13 NIGMVGHVDHGKSTLTLALTGvktdthseeikrG---ISIKLGYADTPVYKCYDASGNPyytrqpsencelervISIVDAP 90 
                                   5899****************87666666543330...3444444444444444433222444444444444444******* PP

                                   GCSSHHHHHHHHHHHHHHHHC.TSEEEEEEETTTTCSHHHHHHHHHHHHH.TTSEEEEEEE CS
                      MMR_HSR1  55 Gliegaseekglgkaflalee.adlillvvdaseeklkpldeeleellee.akkplilvln 113
                                   G  e       l  ++l+    ++ +llv+ a+e+  +p+ +e    le    k++++v n
  gi|13542105|ref|NP_111793.1|  91 G-HE------TLMATMLSGSAlMNGALLVIAANEHCPQPQTREHLTALEImGIKNIVIVQN 144
                                   *.54......788888886665799999999885545555555444443322344555555 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.1     0.028        63     104     136 ..      16      45 ..       3      97 .. 0.75
   2 !   14.0   0.2   1.5e-05     0.034      16      97 ..     106     193 ..      79     198 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.028
                                   EECSTTSSHHHHHHHHCTT-----S-------- CS
                   RsgA_GTPase 104 lvGqSGvGKStLinallpelelktgevseklgr 136
                                   +vG+   GKStL  al++    kt   se+ +r
  gi|13542105|ref|NP_111793.1|  16 MVGHVDHGKSTLTLALTGV---KTDTHSEEIKR 45 
                                   6888889********9995...33333333333 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 1.5e-05
                                   --EEEEEEESTTTT--HHHHHHHHHHHHHTT-.EEEEEEE-GGG--HHH......HHHHHHHHHHHTTSEEEE--TTTHTT CS
                   RsgA_GTPase  16 vdqllivvslkepelslnlldrfLvlaeekgi.epvivlnKiDlleeee......eleelkeelealgyevllvsaktkeg 89 
                                   ++ +l+v++++ +++ + +    L+++e  gi ++viv nKiDl+++e+      e++++ +   a + +++ vsa ++++
  gi|13542105|ref|NP_111793.1| 106 MNGALLVIAAN-EHCPQPQTREHLTALEIMGIkNIVIVQNKIDLVTRERalesykEIKAFVKGSIAENAPIIPVSAYHNTN 185
                                   56789999999.555666677889********7789999*********966655555555555556667777777777777 PP

                                   HHHHHHHC CS
                   RsgA_GTPase  90 leelkell 97 
                                   ++ l e++
  gi|13542105|ref|NP_111793.1| 186 IDILFEAI 193
                                   77666655 PP

>> MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   1.3e-05     0.029      58     102 ..     139     195 ..     134     198 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.3e-05
                  MMR_HSR1_Xtn  58 clyvlNKiDlisleeldelare............pnsvviSaekelnldeLkekiwe 102
                                    ++v NKiDl++ e   e ++e              ++++Sa +++n+d L e+i +
  gi|13542105|ref|NP_111793.1| 139 IVIVQNKIDLVTRERALESYKEikafvkgsiaenAPIIPVSAYHNTNIDILFEAIEK 195
                                   68899*****88776555555446778888887668999************999855 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.017        37       4      25 ..      14      35 ..      11      57 .. 0.84
   2 ?    8.0   0.1   0.00098       2.2      40     142 ..      86     194 ..      76     195 .. 0.62
   3 ?   -2.4   0.0       1.6   3.6e+03      55      74 ..     350     369 ..     323     379 .. 0.65

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.017
                     PduV-EutP  4 illiGkvgsGKttLtqalkgee 25
                                  i ++G+v+ GK tLt al+g +
  gi|13542105|ref|NP_111793.1| 14 IGMVGHVDHGKSTLTLALTGVK 35
                                  5689*************99854 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00098
                     PduV-EutP  40 viDtPGeylenrklysalivtsaeadvialvqdateeesvfpp.gfasvfnkeviGiitkidlaedeenieavee...lLk 116
                                   ++D+PG      ++ s  + +     via   ++ ++++     ++  +  k+++ +  kidl++ e ++e  +e   ++k
  gi|13542105|ref|NP_111793.1|  86 IVDAPGHETLMATMLSGSALMNGALLVIAANEHCPQPQTREHLtALEIMGIKNIVIVQNKIDLVTRERALESYKEikaFVK 166
                                   566666555555555555555555556666555555544433303333446777878899999998888887665111333 PP

                     PduV-EutP 117 ..saGaekifevsavekegieellkyle 142
                                      a  + i+ vsa+++++i+ l++ +e
  gi|13542105|ref|NP_111793.1| 167 gsIAENAPIIPVSAYHNTNIDILFEAIE 194
                                   113555679***************9987 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 1.6
                     PduV-EutP  55 salivtsaeadvialvqdat 74 
                                   ++l+ t a a+ +++v +++
  gi|13542105|ref|NP_111793.1| 350 ETLMFTVATANTVGVVSNVK 369
                                   44555555555555555443 PP

>> DUF4124  Domain of unknown function (DUF4124)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   7.1e-05      0.16      12      31 ..      56      78 ..      53     130 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 7.1e-05
                       DUF4124 12 aevYkWvDanGvvhysdqP...p 31
                                    vYk+ Da G+  y+ qP   +
  gi|13542105|ref|NP_111793.1| 56 TPVYKCYDASGNPYYTRQPsenC 78
                                  579****************5541 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (411 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.65u 0.29s 00:00:00.94 Elapsed: 00:00:00.52
# Mc/sec: 2363.04
//
Query:       gi|13542106|ref|NP_111794.1|  [L=128]
Description: 30S ribosomal protein S6e [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.6e-32  111.0   0.5    4.3e-32  110.7   0.5    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 !  110.7   0.5   2.4e-36   4.3e-32       4     122 ..       7     121 ..       6     124 .. 0.97

  Alignments for each domain:
  == domain 1  score: 110.7 bits;  conditional E-value: 2.4e-36
                                   EEEETTTTEEEEEE-CHHHCTTCTT-BSSEEEECCTTTSSSTS-EEEEEEEEETTC-BB-TTS-SSSEEEEEEETTSSSS- CS
                 Ribosomal_S6e   4 nisdpatgkqklievdekklrtligkrigeevdgdalGeelkgyvlkitggsdkqGfpmkqgvltpgrvrlLlskggvgyr 84 
                                    i+dp+tgk+++ e+  +++++lig++igeevdg +++  l gy++kitggs  +Gf m+++++t+g++++L++  ++gyr
  gi|13542106|ref|NP_111794.1|   7 IIADPKTGKTYKREIPSERMSSLIGRKIGEEVDGVFFD--LVGYKMKITGGSSVDGFAMRPDLQTQGKKQILVKY-TSGYR 84 
                                   59************************************..**********************************9.****9 PP

                                   SSSSS-EEEEEEE-SB--SSEEEEEEEEEE--SS--TT CS
                 Ribosomal_S6e  85 prrkGerkrksvrGcivsadisqlnlvivkkgekdieg 122
                                    + +G rkr + rG+i+ +di q+nl+i+++g ++ie+
  gi|13542106|ref|NP_111794.1|  85 GK-NGIRKRITARGSIIGSDITQINLKITQYGPTPIEE 121
                                   85.8********************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       303  (0.0169); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:01.10
# Mc/sec: 352.30
//
Query:       gi|13542107|ref|NP_111795.1|  [L=527]
Description: O-sialoglycoprotein endopeptidase/protein kinase [Thermoplasma volcanium GSS1]
Scores for complete 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-83  279.1   0.0    5.9e-83  278.7   0.0    1.1  1  Peptidase_M22   Glycoprotease family
    0.00023   20.6   0.2      0.038   13.4   0.1    2.2  2  Kdo             Lipopolysaccharide kinase (Kdo/WaaP) family
    0.00034   20.3   0.1    0.00064   19.4   0.1    1.4  1  RIO1            RIO1 family
     0.0077   15.9   0.0       0.16   11.6   0.0    2.2  2  Carbam_trans_N  Carbamoyltransferase N-terminus
     0.0091   15.5   0.0        0.2   11.1   0.0    2.2  2  BcrAD_BadFG     BadF/BadG/BcrA/BcrD ATPase family
  ------ inclusion threshold ------
      0.011   15.1   0.0      0.019   14.4   0.0    1.3  1  Pkinase         Protein kinase domain


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 !  278.7   0.0     2e-86   5.9e-83       3     270 ..      24     291 ..      22     292 .. 0.96

  Alignments for each domain:
  == domain 1  score: 278.7 bits;  conditional E-value: 2e-86
                                   EXEEEEEEEEE....SSSSHHHHHHHHHHHHHHHHHHHHHHHTSTGGGEEEEEEEEESS-HHHHHHHHHHHHHHHHHCT-- CS
                 Peptidase_M22   3 lanvvasqkelhakyGGvvPelasraHserllplieealaeaglsledldaIavtkgPGlftgLrvGvsfAkglalalnkP 83 
                                   +anv + +k   +k+GG++P++a+ +H+ ++ ++i++a++ ag++++d+d +a++ gPGl+++Lrv  ++A++la++l+ P
  gi|13542107|ref|NP_111795.1|  24 MANVSSMYK---PKTGGIHPTQAAAHHVDKVSEVIAKAIEIAGIKPSDIDLVAFSMGPGLGPSLRVTSTAARTLAVTLKRP 101
                                   555555555...999****************************************************************** PP

                                   EEEEEHHHHHHHCCHCTSECSSCEEEEESSSTEEEEEECTTEEEEEEEESSSEHHHHHHHHHHHHT..SSCCHHHHHHHCT CS
                 Peptidase_M22  84 lvgVnhleahalaarleekeefPvvllvsGghtqvylvkegryeilgetlddaagealdkvarllglpypggpkieklake 164
                                   ++gVnh  +h++ ++  ++ ++Pv+l+vsGg+tqv++  +gry++lgetld+ +g+++dk+ar+ g+p+pggp+ieklak+
  gi|13542107|ref|NP_111795.1| 102 IIGVNHPLGHIEIGKRLSGAQDPVMLYVSGGNTQVIAHLNGRYRVLGETLDIGIGNMIDKFARYAGIPFPGGPEIEKLAKD 182
                                   **************8557779*****************99***************************************** PP

                                   C.S.......EETTEEE.CHHHHHHHHHHST.T.HHHHHHHHHHHHHHHHHHHHHHHHHHCTBSEEEEESGGGGXHHHHHC CS
                 Peptidase_M22 165 g.kkiefprplkgldfsfsGlktavlkelek.e.vedlaasfqeavvdhlvekteralklpkakelvilGGvaankrLrea 242
                                   g k +++p+ +kg+d sfsG+ t++l+ l+k e ved+ +s+qe+++++lve++eral   +++e++++GGva n+rLre+
  gi|13542107|ref|NP_111795.1| 183 GrKLLTLPYSVKGMDTSFSGILTSALEYLKKgEpVEDISFSIQETAFSMLVEVLERALYVSGKDEVLMAGGVALNNRLREM 263
                                   *777*************************88669*********************************************** PP

                                   HCCHHHHTTSEEEXXXHHHHSSXCHHHH CS
                 Peptidase_M22 243 leeeaeelglkliiPplkyctdnaamia 270
                                   ++e+ +e ++++++++++yc dn+amia
  gi|13542107|ref|NP_111795.1| 264 VSEMGREVDATTYMTDKNYCMDNGAMIA 291
                                   ***************************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 !    5.1   0.0    0.0044        13      53      76 ..     370     393 ..     324     399 .. 0.80
   2 !   13.4   0.1   1.3e-05     0.038     123     164 ..     425     460 ..     413     478 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0044
                           Kdo  53 lgrtravrEfrllkrLeeagvavp 76 
                                   +   r+ +Ef +++r+++ag+ vp
  gi|13542107|ref|NP_111795.1| 370 IRGERMKNEFTVIRRMRDAGICVP 393
                                   45568999*************998 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 1.3e-05
                           Kdo 123 llkavgrliaklhragvnHadlyaknillqqeeeeeaeiwli 164
                                    + +vg  +a +h+ ++ H+dl + ni +  +      i++i
  gi|13542107|ref|NP_111795.1| 425 VMGNVGHDVAVMHKNKISHGDLTVNNIIVSDR------ICFI 460
                                   5678***********************99765......3555 PP

>> RIO1  RIO1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.1   2.1e-07   0.00064      54     150 ..     374     463 ..     347     478 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 2.1e-07
                                   HHHHHHHHHHHHHHTT--S--EEEEE..TTEEEEE--EETTEEGGBHHHCG-HHHHHHHHHHHHHHHHHHHHTSTEEESS- CS
                          RIO1  54 waekEfrnLkrleeagvpvPkpielk..rhvlvmefigedgvaapklkdveeeeeaeelyeevleemrklykeaglvHaDL 132
                                     ++Ef+ ++r+++ag+ vP ++++   +  l ++ i+  g     l+dv   +   +++ +v + ++++  ++++ H+DL
  gi|13542107|ref|NP_111795.1| 374 RMKNEFTVIRRMRDAGICVPIVYDYDpfEKTLTLSQIQ--GEL---LRDVI--RARPNVMGNVGHDVAVMH-KNKISHGDL 446
                                   5689******************9986337899999998..555...55655..455889999999888777.9******** PP

                                   STTSEEEETTEEEE--GT CS
                          RIO1 133 SeyNvlvdedkvviIDvs 150
                                      N++v++ ++ +ID s
  gi|13542107|ref|NP_111795.1| 447 TVNNIIVSD-RICFIDAS 463
                                   ****88865.6999*987 PP

>> Carbam_trans_N  Carbamoyltransferase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0     0.053   1.6e+02      42      68 ..      48      75 ..       3      81 .. 0.69
   2 !   11.6   0.0   5.3e-05      0.16     258     308 ..     207     260 ..     188     271 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.053
                Carbam_trans_N 42 lpklka.idyaleeagvelsdiDqivfd 68
                                  ++k+ + i+ a+e ag+++sdiD ++f 
  gi|13542107|ref|NP_111795.1| 48 VDKVSEvIAKAIEIAGIKPSDIDLVAFS 75
                                  55554426789999**********9996 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 5.3e-05
                Carbam_trans_N 258 lkearekde...dlaAsiqvflErlvvevlnivyeklkirnLclaGGvalNikl 308
                                     e+++k+e   d++ siq+    ++vevl+ +    +     +aGGvalN  l
  gi|13542107|ref|NP_111795.1| 207 ALEYLKKGEpveDISFSIQETAFSMLVEVLERALYVSGKDEVLMAGGVALNNRL 260
                                   344445544444***********************9**************9765 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 ?    1.9   0.0     0.043   1.3e+02      38      67 ..      45      74 ..      14      97 .. 0.81
   2 !   11.1   0.0   6.8e-05       0.2     186     249 ..     212     273 ..     192     289 .. 0.73

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.043
                                  ........HHHHHHHHHHT--GGGECEE.. CS
                   BcrAD_BadFG 38 eaaekvleealtealerageeeadieetyl 67
                                  +  ++ ++e++ +a+e ag +++di+ +++
  gi|13542107|ref|NP_111795.1| 45 AHHVDKVSEVIAKAIEIAGIKPSDIDLVAF 74
                                  45678899****************997765 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 6.8e-05
                                   HTT--HHHHHHHHHHHHHHHHHHHHHTT---..SS.EEEESGGGG-HHHHHHH.....HHHH-S-E CS
                   BcrAD_BadFG 186 sggekaedIlaglhraialrvialisrsggv..tdevtltGGvakneaavkelrklvkenygevki 249
                                   ++ge  edI   + +   + + ++ +r   v  +dev++ GGva n    + lr++v+e+ +ev+ 
  gi|13542107|ref|NP_111795.1| 212 KKGEPVEDISFSIQETAFSMLVEVLERALYVsgKDEVLMAGGVALN----NRLREMVSEMGREVDA 273
                                   566666666655555555555555555443311567**********....999999****999854 PP

>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   6.3e-06     0.019      28     132 ..     351     454 ..     337     469 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 6.3e-06
                                   EEEEEECHCHCHHHH.......HHHHHHHHHHHHHSCTTB--EEEEEEESSEEEEEEE--TTEBHHHHHHHHSS--HHHHH CS
                       Pkinase  28 AvKkikkekakkkke.......kkvlrEikilkklkhpnivrlyevfeekdelylvleyveggeladllerkgslseeeak 101
                                   AvKki+  k    ke       +++ +E +++++++   i+  + + +++ e +l l  ++g+ l d+++           
  gi|13542107|ref|NP_111795.1| 351 AVKKIRIAKGYRLKElderirgERMKNEFTVIRRMRDAGICVPIVYDYDPFEKTLTLSQIQGELLRDVIR--------ARP 423
                                   5565555554444444445557899999999999999999988888888889999999999999999997........467 PP

                                   HHHHHHHHHHHHHHHTTEE-SS-SGGGEEEE CS
                       Pkinase 102 kiakqilegleylHskgiiHrDlKpeNiLid 132
                                   +++ ++ + ++ +H+++i H Dl  +Ni+++
  gi|13542107|ref|NP_111795.1| 424 NVMGNVGHDVAVMHKNKISHGDLTVNNIIVS 454
                                   99***************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (527 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       648  (0.0361426); expected 358.6 (0.02)
Passed bias filter:                      571  (0.0318478); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-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 0.37s 00:00:01.04 Elapsed: 00:00:00.53
# Mc/sec: 2982.05
//
Query:       gi|13542108|ref|NP_111796.1|  [L=185]
Description: xanthosine triphosphate pyrophosphatase-like protein [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.2e-47  160.9   0.0    3.8e-47  160.6   0.0    1.0  1  Ham1p_like  Ham1 family


Domain annotation for each model (and alignments):
>> Ham1p_like  Ham1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  160.6   0.0   2.1e-51   3.8e-47       3     185 ..       4     176 ..       3     178 .. 0.86

  Alignments for each domain:
  == domain 1  score: 160.6 bits;  conditional E-value: 2.1e-51
                                   EC-S-HHHHHHHHHHTTTECCCE...EECCCCEE----BS.SSHHHHHHHHHHHHHH.HTS-EEEEEEEEEEGGGTTTBGG CS
                    Ham1p_like   3 faTgNkgKlrevkeilaeellevk..slkelelpeveEtq.gtfeenalkKaraaae.aglpvladDsgLevdaLnglPGv 79 
                                   f+T+Nk+K++e+ke+ ++ +++++  ++      ++eE+q +++e+++++ ++++ +  + p+++dD+gL+++ Lng+PG+
  gi|13542108|ref|NP_111796.1|   4 FVTSNKHKFEEIKELGTRYGIDIEwvNM------KYEEIQeESTEKISYDSCKKLINlVDSPFFIDDTGLYIESLNGFPGP 78 
                                   89***********997666666652244......778***999999********99856888******************* PP

                                   GTTTTTHTTCHHHHHHHHHHHHCTHTTS--EEEEEEEEEEEETTTTEEEEEEEEEEEEE-SS.--SSSSTTGGGEEETT-S CS
                    Ham1p_like  80 ysarfagegaedeenlaklleeleeeeedrsArfvcvlaladpeeeeellfeGeveGeiveeprgeggfGyDpiFvpeege 160
                                   ys++++++      ++  +l+ +++  e+rsA+fv+v+ l +  +++++ f+G+v Gei +e rg++gfGyDpiF+p+++e
  gi|13542108|ref|NP_111796.1|  79 YSSYVSKT-----IGNYGILKLMNGI-EKRSAYFVTVISLNE--GGKITQFTGKVIGEISKEIRGKNGFGYDPIFIPNGSE 151
                                   *****644.....4667777777543.47***********77..566699***************************8767 PP

                                   SBTTTS.CHHHHHHSHHHHHHHHHH CS
                    Ham1p_like 161 ktfaelskeeknaiShRgkAlekll 185
                                   +tfae++++ekn +ShR+ A++ l 
  gi|13542108|ref|NP_111796.1| 152 RTFAEMETSEKNMVSHRSMAFKGLF 176
                                   7********************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       571  (0.0318478); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 1302.55
//
Query:       gi|13542109|ref|NP_111797.1|  [L=428]
Description: dehydrogenase (flavoprotein) [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.7e-17   61.6   1.7    1.6e-08   34.6   0.2    2.2  2  DAO             FAD dependent oxidoreductase
    2.4e-14   53.3   0.4    1.6e-13   50.5   0.4    1.8  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    1.4e-10   40.9   0.3    8.9e-08   31.6   0.1    2.2  2  FAD_binding_2   FAD binding domain
    1.8e-09   36.8   1.5    1.3e-06   27.4   0.2    2.3  2  HI0933_like     HI0933-like protein
    8.8e-09   34.9   1.5    8.8e-08   31.6   1.5    2.1  1  GIDA            Glucose inhibited division protein A
    2.5e-07   30.1   1.0    4.5e-07   29.3   1.0    1.4  1  Lycopene_cycl   Lycopene cyclase protein
      3e-07   30.2   0.4    4.4e-07   29.6   0.4    1.4  1  FAD_oxidored    FAD dependent oxidoreductase
    1.4e-06   28.4   0.0    2.9e-06   27.4   0.0    1.5  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    1.7e-06   27.6   0.3    6.7e-06   25.6   0.1    2.0  2  FAD_binding_3   FAD binding domain
    1.5e-05   24.6   0.2    0.00084   18.8   0.1    2.1  2  GMC_oxred_N     GMC oxidoreductase
    2.2e-05   23.8   1.8    0.00015   21.1   2.0    2.2  2  Thi4            Thi4 family
    4.1e-05   23.0   1.0     0.0011   18.2   0.1    2.5  3  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    0.00021   21.3   1.5     0.0024   17.9   1.5    2.5  1  NAD_binding_9   FAD-NAD(P)-binding
    0.00036   19.5   0.2       0.23   10.3   0.0    2.2  2  Trp_halogenase  Tryptophan halogenase
     0.0021   18.6   1.0      0.056   14.0   0.1    3.3  3  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
     0.0023   17.3   0.3          1    8.6   0.0    2.6  3  Amino_oxidase   Flavin containing amine oxidoreductase
     0.0046   16.9   0.1     0.0091   15.9   0.1    1.5  1  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
  ------ inclusion threshold ------
      0.041   13.5   0.2      0.082   12.5   0.2    1.5  1  ApbA            Ketopantoate reductase PanE/ApbA
      0.062   13.9   3.0      0.072   13.7   0.6    2.3  1  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent


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 !   34.6   0.2   1.7e-11   1.6e-08       1      48 [.       5      52 ..       5      96 .. 0.81
   2 !   26.2   0.1     6e-09   5.6e-06     146     213 ..     105     173 ..      95     239 .. 0.77

  Alignments for each domain:
  == domain 1  score: 34.6 bits;  conditional E-value: 1.7e-11
                                  EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSGGGSSEEEEESSS CS
                           DAO  1 dvviiGGGiiGlstAyeLarrg..VtllekgdiagsgaSgrnsgllhsgl 48
                                  dv++iG+G +G+s+A  La+ g  V+l+e+g ++  g+   ++++l++  
  gi|13542109|ref|NP_111797.1|  5 DVAVIGAGPAGSSAAIRLAQNGmnVLLVERG-DPP-GTKNVSGAVLWGNE 52
                                  8******************************.888.8******9999854 PP

  == domain 2  score: 26.2 bits;  conditional E-value: 6e-09
                                   HHHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECTEEEEEEEEEEE--GGGHH.HH.HTT.CTT CS
                           DAO 146 akltaalaraaealGveilegtevtgleeedgkvwgverttpgendaadavVnaaGawsd.ll.gll.kel 213
                                    k+ ++la++a+++G+ +++g +v +l  ++gkv g++ + +    +adavV+a Ga  + l+  +l ++l
  gi|13542109|ref|NP_111797.1| 105 GKFDQWLAKKAKDAGAMLVTGVTVDRLAIDNGKVIGIQ-QDNDV-ITADAVVVAEGANPRvLInSGLrPKL 173
                                   68999**********************9999******4.33232.357**********9977755555444 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 !   50.5   0.4   1.7e-16   1.6e-13       1     114 [.       4     164 ..       4     175 .. 0.82

  Alignments for each domain:
  == domain 1  score: 50.5 bits;  conditional E-value: 1.7e-16
                                   CSEEEE--SHHHHHHHHHHHHHTS-EEEEE........TTHCHHHCSHHHHCHHHHHHHHHHHHH................ CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxxxxxxxxxxxxx................ RF
                   Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaqagakvtlve........legtclnggcllskallgvaedaeias................ 57 
                                   +dv+viG+GpAG +aa++laq+g++v+lve             +++g  l+k++  +++ a +++                
  gi|13542109|ref|NP_111797.1|   4 FDVAVIGAGPAGSSAAIRLAQNGMNVLLVErgdppgtkNVSGAVLWGNELAKVVPDWERSAPVERyvtrkevafltekski 84 
                                   69***************************8888776664445677778889999999999998889999999999999999 PP

                                   ............................HHHHCHHHHCCCCHCCTCEEEEESCEEEEETEEECTCEEEEEESEEEE---EE CS
                                   ............................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2  58 ............................evvkklnqgielllgeevvkidpgkkkvklekkkegdeekiaydklvlAtGss 110
                                                               +  k   +g +l++g++v ++  +++kv   +++   +  i++d++v+A G++
  gi|13542109|ref|NP_111797.1|  85 aisfsseelqnsksgkiivrgkfdqwlaK--KAKDAGAMLVTGVTVDRLAIDNGKVIGIQQD---NDVITADAVVVAEGAN 160
                                   99999999888888888888888888652..3345567888888888888888888886654...458************* PP

                                   E-BC CS
                                   xxxx RF
                   Pyr_redox_2 111 prdl 114
                                   pr l
  gi|13542109|ref|NP_111797.1| 161 PRVL 164
                                   *998 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   0.1   9.5e-11   8.9e-08       1      47 [.       5      50 ..       5      85 .. 0.87
   2 !    7.4   0.0    0.0021         2     147     204 ..     111     162 ..     106     191 .. 0.80

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 9.5e-11
                                  SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGGG--S-EE- CS
                 FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefggatawsqGgida 47
                                  Dv ViG+G AG +AA+++a++G +v++ve +++  g+   s++ ++ 
  gi|13542109|ref|NP_111797.1|  5 DVAVIGAGPAGSSAAIRLAQNGMNVLLVERGDP-PGTKNVSGAVLWG 50
                                  9******************************99.7788888887775 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0021
                                   HHHHHHTCTEEEEESEEEEEEEECTTEEEEEEEEETTTTCEEEEEESEEEE-----GG CS
                 FAD_binding_2 147 lvesarkagvdfqerteadeLivedgrvtGavvenpesgrevrirakavvlatgGfgr 204
                                   l+++a++ag  + +   +d+L +++g+v G+         +  i+a+avv+a+g+ +r
  gi|13542109|ref|NP_111797.1| 111 LAKKAKDAGAMLVTGVTVDRLAIDNGKVIGIQQD------NDVITADAVVVAEGANPR 162
                                   788999999*********************8554......334778888888887766 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.2   1.3e-09   1.3e-06       1      38 [.       4      41 ..       4      46 .. 0.93
   2 !    8.2   0.1   0.00093      0.88     114     164 ..     110     159 ..      91     163 .. 0.92

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 1.3e-09
                                  -SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-HH CS
                   HI0933_like  1 kdviviGgGaAGlmaAisaakrgkrVlllekakklgrK 38
                                  +dv+viG+G+AG  aAi++a++g +Vll+e+++ +g K
  gi|13542109|ref|NP_111797.1|  4 FDVAVIGAGPAGSSAAIRLAQNGMNVLLVERGDPPGTK 41
                                  59*********************************999 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.00093
                                   HHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE---- CS
                   HI0933_like 114 allkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtGG 164
                                    l k++k+ag  l +  +v +++ ++++++ ++  +++ ++ad++v+A G 
  gi|13542109|ref|NP_111797.1| 110 WLAKKAKDAGAMLVTGVTVDRLAIDNGKVIGIQQ-DNDVITADAVVVAEGA 159
                                   68899****************************9.9************996 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   1.5   9.3e-11   8.8e-08       1     160 [.       5     169 ..       5     191 .. 0.74

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 9.3e-11
                                   CEEEE-SSHHHHHHHHHHHHTT--EEEE.......ES-GGGTT--SSSSEEE-T......THHHHHHHHHHHT-SHHHHHH CS
                          GIDA   1 dviViGgGhAGceAAlaaarlGakvlLi.......thkldtiaelsCnpsiggi......akgllvrEidalggliikaad 68 
                                   dv ViG+G AG+ AA+ +a+ G++vlL+       t++++  +  +   +   +       ++ + r + +   +++ +++
  gi|13542109|ref|NP_111797.1|   5 DVAVIGAGPAGSSAAIRLAQNGMNVLLVergdppgTKNVSGAVLWGNELA---KvvpdweRSAPVERYVTR--KEVAFLTE 80 
                                   79**************************8888666333333333322222...134576655556666555..66777777 PP

                                   HHEEEEEEESTTS-CCC-EEEEEE-HHHHHHHHHHHHHTSTTEEEEES-EEEEEECTTEEEEEEETTS-EEEECEEEE--T CS
                          GIDA  69 kagiqfrilNrskGpavralraqvdrelyskevteklenepnleiieeeveeliveekkvkgvvtedgetikakavviatG 149
                                   k++i +    ++   +  +    + r ++ +++ +k ++   + +   +v++l ++++kv g+  +d+ +i+a+avv+a G
  gi|13542109|ref|NP_111797.1|  81 KSKIAISFSSEE--LQNSKSGKIIVRGKFDQWLAKKAKDAGAMLVTGVTVDRLAIDNGKVIGIQ-QDNDVITADAVVVAEG 158
                                   777755554333..44444444899*************************************96.6778999********* PP

                                   T-BT-EEEETT CS
                          GIDA 150 tflkgkihige 160
                                   +  +  i  g 
  gi|13542109|ref|NP_111797.1| 159 ANPRVLINSGL 169
                                   96566555555 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   1.0   4.8e-10   4.5e-07       1     143 [.       5     160 ..       5     183 .. 0.79

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 4.8e-10
                 Lycopene_cycl   1 DvvviGaGpAglslAarlteakpglkvvlieaspsllfpnny.vWsdefedlga.......leecvehsWsgtivylddgk 73 
                                   Dv+viGaGpAg s A rl  a+ g++v+l+e ++ +  + n    + ++++l +        + +  ++ ++ +  l +++
  gi|13542109|ref|NP_111797.1|   5 DVAVIGAGPAGSSAAIRL--AQNGMNVLLVERGDPP-GTKNVsGAVLWGNELAKvvpdwerSAPVERYVTRKEVAFLTEKS 82 
                                   9*****************..***********99887.55555478889999988888888533333344444444556666 PP

                 Lycopene_cycl  74 killg.........raYgrvsskrlkeellerlvengvkllea.kvesveeeeageslvvleggrkirarlvvdarglas 143
                                   ki ++         +  + + + ++ + l+++  ++g+ l+ + +v++ + ++  ++  + +++  i a +vv+a g+ +
  gi|13542109|ref|NP_111797.1|  83 KIAISfsseelqnsKSGKIIVRGKFDQWLAKKAKDAGAMLVTGvTVDRLAIDNG-KVIGIQQDNDVITADAVVVAEGA-N 160
                                   666666666666666788999*************99999887648999988887.8888888899************4.3 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.4   4.7e-10   4.4e-07       1      45 [.       5      49 ..       5     156 .. 0.78

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 4.7e-10
                  FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsglvat 45
                                  Dv V+G+gpaG  AAi  a++G +vlLve+ +  G    sg+v +
  gi|13542109|ref|NP_111797.1|  5 DVAVIGAGPAGSSAAIRLAQNGMNVLLVERGDPPGTKNVSGAVLW 49
                                  9******************************99998777777655 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.0   3.1e-09   2.9e-06       1      34 [.       8      41 ..       8      70 .. 0.87

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 3.1e-09
                                  EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGG CS
                 NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGr 34
                                  ++GaG +G++aA +La++g +vll+e++d +G +
  gi|13542109|ref|NP_111797.1|  8 VIGAGPAGSSAAIRLAQNGMNVLLVERGDPPGTK 41
                                  8****************************99965 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.1   7.1e-09   6.7e-06       2      33 ..       4      35 ..       3      43 .. 0.93
   2 ?   -1.2   0.0         1   9.6e+02     286     312 ..     296     324 ..     290     350 .. 0.71

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 7.1e-09
                                  EEEEEE--SHHHHHHHHHHHHTTHHEEEEESS CS
                 FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlvekr 33
                                   dV+++GaGpaG ++a  L++ G +v+lve+ 
  gi|13542109|ref|NP_111797.1|  4 FDVAVIGAGPAGSSAAIRLAQNGMNVLLVERG 35
                                  79****************************95 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1
                                   EEE-GGGTEEE-STTS..HHHHHHHHHHH CS
                 FAD_binding_3 286 vflaGDAaHihpPtgG..qGlNtaiqDav 312
                                    ++aGDAa  +   g   qG+N ai   +
  gi|13542109|ref|NP_111797.1| 296 YLVAGDAAAFTFSNGMvlQGINYAITSGI 324
                                   589****9988765533389999987655 PP

>> GMC_oxred_N  GMC oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0     0.033        31       2      35 ..       5      37 ..       4      76 .. 0.76
   2 !   18.8   0.1   8.9e-07   0.00084     195     280 ..     107     179 ..      95     189 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.033
                   GMC_oxred_N  2 delveggGsagsvvAaRLsedpstsvlvleaggr 35
                                  d  v+g+G ags  A RL++++  +vl++e g  
  gi|13542109|ref|NP_111797.1|  5 DVAVIGAGPAGSSAAIRLAQNGM-NVLLVERGDP 37
                                  55689**************9875.6777777754 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 8.9e-07
                   GMC_oxred_N 195 arawLrpalerpnleiltgakaekiilegrkkravGVeasdkkgtvkrlvvaakevvvaaGalnsPqlLqrSGlGkaehLk 275
                                    ++wL +  +  ++ ++tg++++++ ++  +++++G++     +     v+ a+ vvva Ga  +P +L +SGl  +++L 
  gi|13542109|ref|NP_111797.1| 107 FDQWLAKKAKDAGAMLVTGVTVDRLAID--NGKVIGIQQD---ND----VITADAVVVAEGA--NPRVLINSGL--RPKLS 174
                                   578****99999*************999..******9643...33....5668********8..8*********..88888 PP

                   GMC_oxred_N 276 evgvd 280
                                   + +v 
  gi|13542109|ref|NP_111797.1| 175 DRDVA 179
                                   88775 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   2.0   1.5e-07   0.00015      17      63 ..       3      48 ..       1     167 [. 0.76
   2 ?   -2.5   0.0       2.5   2.4e+03      87     129 ..     292     334 ..     273     341 .. 0.65

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.5e-07
                                  EEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTTTTSTT CS
                          Thi4 17 esDvvivGaGssGLtaayylakkpdlkvailersvspGGGawlGGql 63
                                  e Dv+++GaG++G +aa  la++ +++v+++er   pG     G  l
  gi|13542109|ref|NP_111797.1|  3 EFDVAVIGAGPAGSSAAIRLAQN-GMNVLLVERGDPPGTKNVSGAVL 48
                                  88*********************.*********98888755555444 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.5
                                   ESSEEEESEHHHHHHHHHHHHHTSTTEEEEESEEEEEEEEETB CS
                          Thi4  87 egdyvvvkdaalftstllskvlqlanvkllnavaveDlivreg 129
                                   +g++++v+  a + +     vlq  n  +  ++ + D i+ + 
  gi|13542109|ref|NP_111797.1| 292 YGNGYLVAGDAAAFTFSNGMVLQGINYAITSGILAADTIIENR 334
                                   5788888765555555566778878888888888888887764 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 !   18.2   0.1   1.2e-06    0.0011       2      31 ..       8      36 ..       7      41 .. 0.93
   2 ?    2.9   0.0     0.056        53     104     140 ..     128     163 ..      70     176 .. 0.75
   3 ?   -3.0   0.0       3.5   3.3e+03      72      96 ..     331     355 ..     308     368 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.2e-06
                   Pyr_redox_3  2 IiGaGPaGlaaaielkkagledylilEkgn 31
                                  +iGaGPaG +aai l ++g+ ++l +E+g 
  gi|13542109|ref|NP_111797.1|  8 VIGAGPAGSSAAIRLAQNGM-NVLLVERGD 36
                                  8*******************.7******94 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.056
                   Pyr_redox_3 104 Vesvkk.edegfevetsketyeAkkviiAtGefdkPnk 140
                                   V +++  +++   +++++++++A+ v++A G   +P++
  gi|13542109|ref|NP_111797.1| 128 VDRLAIdNGKVIGIQQDNDVITADAVVVAEGA--NPRV 163
                                   55555423455778999999999999999997..6655 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 3.5
                   Pyr_redox_3  72 slkeeklsrkealeYlrevaksfel 96 
                                     ++++++++++++Y++++ +s+ l
  gi|13542109|ref|NP_111797.1| 331 IENRNNINENTLAKYVDKLRESYVL 355
                                   4567788888888888887777665 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 !   17.9   1.5   2.5e-06    0.0024       1     154 [.       7     158 ..       7     160 .. 0.65

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.5e-06
                 NAD_binding_9   1 aivGaGprGlavlerLlarakkkspleitlfdp.sepgagrvwrtdqseelllNvpasemslftddpptfaeWlrerga.. 78 
                                   a++GaGp+G +++ rL+++      +++ l+++ ++pg + v +    + l+ N  a+ ++ + +++   ++++++++   
  gi|13542109|ref|NP_111797.1|   7 AVIGAGPAGSSAAIRLAQN-----GMNVLLVERgDPPGTKNV-SG---AVLWGNELAKVVPDW-ERSAPVERYVTRKEVaf 77 
                                   89*****************.....5********888894433.33...357777777777655.45666666666666566 PP

                 NAD_binding_9  79 ............leeaeeldpddfvpRalyGrYlrdlfeellarlpegvtvevhraevvdleeradgqavlladgaslaad 147
                                                ee+++ ++++ + R  + ++l++ ++++ a l       v   +v +l+ +++++  +++d++ ++ad
  gi|13542109|ref|NP_111797.1|  78 ltekskiaisfsSEELQNSKSGKIIVRGKFDQWLAKKAKDAGAML-------VTGVTVDRLAIDNGKVIGIQQDNDVITAD 151
                                   554444665543333566666666666655555555555555555.......34445566666666666667777788888 PP

                 NAD_binding_9 148 aVvLAlG 154
                                   aVv+A G
  gi|13542109|ref|NP_111797.1| 152 AVVVAEG 158
                                   8888877 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.0   0.00024      0.23       1      33 [.       5      34 ..       5      43 .. 0.90
   2 !    7.4   0.0    0.0018       1.7     153     225 ..     104     176 ..      65     193 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00024
                                  EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE- CS
                Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlves 33
                                  ++ ++G+G+aG+ aA+ la+ +   ++v+lve 
  gi|13542109|ref|NP_111797.1|  5 DVAVIGAGPAGSSAAIRLAQNG---MNVLLVER 34
                                  589****************999...99****97 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0018
                                   HHHHHHHHHHHHHHCT-EEEE--EEEEEE-TTS-EEEEEETTS-EEE-SEEEE-SGGG.-IIIIIIT---EEE- CS
                Trp_halogenase 153 aalyakfLrrvaearGvtrvegkvvevqldedgrveslrledgreveadlfiDcsGfr.gllieqaLktgfedw 225
                                   +++++++L + a+++G   v g  v+    ++g+v +++  d  ++ ad ++ + G + + li++ L+ +  d 
  gi|13542109|ref|NP_111797.1| 104 RGKFDQWLAKKAKDAGAMLVTGVTVDRLAIDNGKVIGIQQ-DNDVITADAVVVAEGANpRVLINSGLRPKLSDR 176
                                   689***********************99999*******98.8889*********99763668888887777666 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.1   5.9e-05     0.056       2      35 ..       6      39 ..       5      48 .. 0.92
   2 ?   -2.0   0.0       5.9   5.6e+03      44      65 ..      64      85 ..      58      94 .. 0.76
   3 ?    0.8   0.0      0.76   7.2e+02      42      74 ..     107     139 ..     102     145 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.9e-05
                                  EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
                     Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkll 35
                                  v+v+G+G  g  +A  la+ g +V +ver+d + 
  gi|13542109|ref|NP_111797.1|  6 VAVIGAGPAGSSAAIRLAQNGMNVLLVERGDPPG 39
                                  89***************************99776 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 5.9
                                  HHHHHHHHHTTEEEECSEEEEE CS
                     Pyr_redox 44 kilqeklekngievllntkvee 65
                                  + ++++++++ + +l++++  +
  gi|13542109|ref|NP_111797.1| 64 APVERYVTRKEVAFLTEKSKIA 85
                                  5688999999999999876555 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.76
                                   HHHHHHHHHHHTTEEEECSEEEEEEEEETTSEE CS
                     Pyr_redox  42 askilqeklekngievllntkveeiegsedgve 74 
                                   + ++l++k ++ g  ++++ +v ++  ++ +v 
  gi|13542109|ref|NP_111797.1| 107 FDQWLAKKAKDAGAMLVTGVTVDRLAIDNGKVI 139
                                   56899*****************99986666554 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.0    0.0011         1       2      27 ..      14      39 ..      13      44 .. 0.88
   2 !    6.0   0.0    0.0063         6     210     274 ..     108     173 ..      75     191 .. 0.72
   3 ?   -2.4   0.0       2.4   2.2e+03     437     452 .]     316     331 ..     312     331 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0011
                                  HHHHHHHHHHHTTEEEEEEESSSSSB CS
                 Amino_oxidase  2 aGLaaArqLlsaGfdVtvlEardrvG 27
                                  aG +aA +L+++G++V+++E  d +G
  gi|13542109|ref|NP_111797.1| 14 AGSSAAIRLAQNGMNVLLVERGDPPG 39
                                  5669*****************99887 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0063
                                   HHHHHHHHHTTTTEEEETSEEEEEEEEETTCEEEEETTSTEEEESEEEE-..S-HHHHHSSEEESCC CS
                 Amino_oxidase 210 sqlpealaeelrgldirlntrVkeikregdgvtvtledgevveaDaVvvT..vplgvlkailfsPpl 274
                                   +q     a+   g  + ++  V +++ ++++v    +d +v++aDaVvv+  + ++vl +  ++P+l
  gi|13542109|ref|NP_111797.1| 108 DQWLAKKAK-DAGAMLVTGVTVDRLAIDNGKVIGIQQDNDVITADAVVVAegANPRVLINSGLRPKL 173
                                   555555555.777888888899999999999877789************944445555566777766 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 2.4
                                   HHHHHHHHHHHHHHHH CS
                 Amino_oxidase 437 vegAilSGlraAaril 452
                                   ++ Ai SG+ aA+ i+
  gi|13542109|ref|NP_111797.1| 316 INYAITSGILAADTII 331
                                   778**********997 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 !   15.9   0.1   9.7e-06    0.0091       2      30 ..       6      34 ..       5      61 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 9.7e-06
                                  EEEE--SCCHHHHHHHHHHTT-EEEEE-S CS
                       3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdi 30
                                  vaviGaG  G++ a  +a++g++V lv++
  gi|13542109|ref|NP_111797.1|  6 VAVIGAGPAGSSAAIRLAQNGMNVLLVER 34
                                  9*************************997 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2   8.7e-05     0.082       1      31 [.       6      36 ..       6      50 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 8.7e-05
                                  EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH CS
                          ApbA  1 iailGaGaiGsllaakLakagadvtlilrsr 31
                                  +a++GaG  Gs  a +La++g +v l+ r++
  gi|13542109|ref|NP_111797.1|  6 VAVIGAGPAGSSAAIRLAQNGMNVLLVERGD 36
                                  69*************************9986 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 ?   13.7   0.6   7.7e-05     0.072       2      92 ..       6     103 ..       5     104 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7.7e-05
                                   EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC...........-EEECECHHHHHHH-SEEEE-S-H CS
                 F420_oxidored   2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg...........vkvtavdneeaaeeadvvvlavkp 71 
                                   +++iGaG  g++ a +l+++g    +++++ + +p   +    ++             + +a + e  +++ +v +l+ k 
  gi|13542109|ref|NP_111797.1|   6 VAVIGAGPAGSSAAIRLAQNG---MNVLLVERGDPPGTKNVSGAVLwgnelakvvpdWERSA-PVERYVTRKEVAFLTEKS 82 
                                   89*******************...9***9988899888888888888999988886533333.57889999********** PP

                                   HHHHHHHHHCGHHHHTTSEEE CS
                 F420_oxidored  72 edveevlselakdalkgklvi 92 
                                   + + ++ se  +++++gk+++
  gi|13542109|ref|NP_111797.1|  83 KIAISFSSEELQNSKSGKIIV 103
                                   ******9999999999*9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (428 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       685  (0.0382063); expected 358.6 (0.02)
Passed bias filter:                      586  (0.0326845); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.67u 0.31s 00:00:00.98 Elapsed: 00:00:00.50
# Mc/sec: 2561.14
//
Query:       gi|13542110|ref|NP_111798.1|  [L=90]
Description: ferredoxin-like protein [Thermoplasma volcanium GSS1]
Scores for complete 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-07   29.4   6.5    1.2e-06   28.5   6.5    1.5  1  ETF_QO    Electron transfer flavoprotein-ubiquinone oxidoredu
    1.2e-05   25.0  14.0     0.0019   18.2   4.1    2.3  2  Fer4_2    4Fe-4S binding domain
    7.1e-05   22.8  11.5    0.00011   22.2  11.5    1.3  1  Fer4_10   4Fe-4S dicluster domain
    0.00011   22.7  12.1      0.083   13.5   2.2    2.3  3  Fer4_7    4Fe-4S dicluster domain
    0.00062   19.9  11.9    0.00093   19.3  11.9    1.3  1  Fer4_9    4Fe-4S dicluster domain
     0.0019   18.2  15.9      0.099   12.8   6.9    2.2  2  Fer4_6    4Fe-4S binding domain
      0.006   16.7  14.3      0.022   14.9   2.8    2.1  2  Fer4_21   4Fe-4S dicluster domain
     0.0076   16.0  17.6      0.015   15.1   1.9    3.2  3  Fer4      4Fe-4S binding domain
  ------ inclusion threshold ------
       0.27   11.8  12.1       0.26   11.8   4.3    2.2  2  Fer4_17   4Fe-4S dicluster domain
        3.9    8.2  14.4       0.26   11.9   1.4    2.4  2  Fer4_4    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 !   28.5   6.5     7e-10   1.2e-06      46     103 ..      36      87 ..       6      88 .. 0.84

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 7e-10
                                   HHHH-TTS-EEEEETTTTSSEEEEE-CCC--S--HHHHH-TT--EEE---STT-C--- CS
                        ETF_QO  46 eqryCPagvyeivedeeakekklqinaqnCvhCktCdikdpsqniewvvPeGggGPky 103
                                   +   CPa+ y +++ +      l+   ++Cv C tCdi   + +++w+ P+G +G  y
  gi|13542110|ref|NP_111798.1|  36 CVFACPANCYTLINGK------LNFKYEDCVECGTCDIACSHGSVKWTLPKGDNGVIY 87 
                                   45579******99655......888999***************************888 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   4.1   1.1e-06    0.0019       1      22 []      19      42 ..      19      42 .. 0.92
   2 !   12.4   2.4   7.4e-05      0.13       7      21 ..      56      70 ..      54      71 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.1e-06
                        Fer4_2  1 apvvvdtdrCigC..gaCvsaCPa 22
                                  a++ +++d+C  C    Cv aCPa
  gi|13542110|ref|NP_111798.1| 19 AHITINPDICSTCpdHFCVFACPA 42
                                  6899*********877*******8 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 7.4e-05
                        Fer4_2  7 tdrCigCgaCvsaCP 21
                                   + C++Cg+C  aC 
  gi|13542110|ref|NP_111798.1| 56 YEDCVECGTCDIACS 70
                                  567*******99996 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  11.5   6.3e-08   0.00011       1      55 [.      20      69 ..      20      71 .. 0.94

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 6.3e-08
                       Fer4_10  1 kvvidddtCirCg..kCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaC 55
                                  ++ i++d C  C    Cv aCPa       + ++ ++++ + k+e+C +cg C  aC
  gi|13542110|ref|NP_111798.1| 20 HITINPDICSTCPdhFCVFACPA-------NCYTLINGKLNFKYEDCVECGTCDIAC 69
                                  689*********9778*******.......99999******************9999 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   3.3   5.9e-05      0.11      25      51 ..      15      43 ..       4      44 .. 0.81
   2 !   12.9  14.5   7.1e-05      0.13       2      51 ..      28      72 ..      27      73 .. 0.89
   3 !   13.5   2.2   4.6e-05     0.083       2      20 ..      59      77 ..      58      87 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.9e-05
                        Fer4_7 25 ekgtekveidpekClgCga..CvavCPtg 51
                                  +k  ++++i+p+ C++C    Cv +CP++
  gi|13542110|ref|NP_111798.1| 15 DKSYAHITINPDICSTCPDhfCVFACPAN 43
                                  3455899**********9889******97 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 7.1e-05
                        Fer4_7  2 CigC..gaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtg 51
                                  C  C  ++Cv aCp+++ +l +        k+++++e+C+ Cg C  +C +g
  gi|13542110|ref|NP_111798.1| 28 CSTCpdHFCVFACPANCYTLIN-------GKLNFKYEDCVECGTCDIACSHG 72
                                  8889666*************65.......489*****************876 PP

  == domain 3  score: 13.5 bits;  conditional E-value: 4.6e-05
                        Fer4_7  2 CigCgaCvaaCpvkaield 20
                                  C++Cg C  aC+++ ++++
  gi|13542110|ref|NP_111798.1| 59 CVECGTCDIACSHGSVKWT 77
                                  ************9999886 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3  11.9   5.2e-07   0.00093       2      49 ..      28      72 ..      27      74 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 5.2e-07
                        Fer4_9  2 CtgCga..CveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkg 49
                                  C  C    Cv aCpa+ ++  +++   +++     +C++Cg+C  aC +g
  gi|13542110|ref|NP_111798.1| 28 CSTCPDhfCVFACPANCYTLINGKLNFKYE-----DCVECGTCDIACSHG 72
                                  99996556****************999985.....5***********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 !   12.8   6.9   5.5e-05     0.099       2      22 ..      21      43 ..      20      45 .. 0.89
   2 !   11.0   1.6    0.0002      0.37       4      22 ..      54      72 ..      51      74 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.5e-05
                        Fer4_6  2 veidpdkCigC.gd.CvrvCPeg 22
                                  ++i+pd C  C +  Cv +CP++
  gi|13542110|ref|NP_111798.1| 21 ITINPDICSTCpDHfCVFACPAN 43
                                  89*********777*******98 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.0002
                        Fer4_6  4 idpdkCigCgdCvrvCPeg 22
                                  ++++ C+ Cg C ++C +g
  gi|13542110|ref|NP_111798.1| 54 FKYEDCVECGTCDIACSHG 72
                                  88899***********987 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   3.3    0.0015       2.7       3      28 ..      23      50 ..      19      57 .. 0.75
   2 !   14.9   2.8   1.2e-05     0.022       4      24 ..      55      75 ..      52      86 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0015
                       Fer4_21  3 idedkCigC..gkCliaCedtshqaiei 28
                                  i++d C  C    C+ aC+ ++++ i++
  gi|13542110|ref|NP_111798.1| 23 INPDICSTCpdHFCVFACPANCYTLING 50
                                  7888888884446999999888888865 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 1.2e-05
                       Fer4_21  4 dedkCigCgkCliaCedtshq 24
                                  + ++C++Cg C iaC+ +s++
  gi|13542110|ref|NP_111798.1| 55 KYEDCVECGTCDIACSHGSVK 75
                                  5689************98875 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   0.6     0.057     1e+02       1      11 [.      21      31 ..      21      31 .. 0.88
   2 !    8.1   1.6    0.0014       2.4      14      23 ..      36      45 ..      34      46 .. 0.87
   3 !   15.1   1.9   8.2e-06     0.015       5      21 ..      56      72 ..      52      75 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.057
                                  EEEETTTSSS- CS
                          Fer4  1 vvideekCigC 11
                                  ++i+++ C  C
  gi|13542110|ref|NP_111798.1| 21 ITINPDICSTC 31
                                  68******988 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0014
                                  HHHHSTTTEE CS
                          Fer4 14 CvevCPvgAI 23
                                  Cv +CP ++ 
  gi|13542110|ref|NP_111798.1| 36 CVFACPANCY 45
                                  ********96 PP

  == domain 3  score: 15.1 bits;  conditional E-value: 8.2e-06
                                  TTTSSS-THHHHHSTTT CS
                          Fer4  5 eekCigCGaCvevCPvg 21
                                  +e+C+ CG+C  +C +g
  gi|13542110|ref|NP_111798.1| 56 YEDCVECGTCDIACSHG 72
                                  89************665 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   2.3     0.046        82      41      59 ..      23      43 ..       2      45 .. 0.67
   2 ?   11.8   4.3   0.00015      0.26      41      59 ..      54      72 ..      44      73 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.046
                       Fer4_17 41 ekaslCieCge..CerkCPqg 59
                                   + + C++C    C+ +CP++
  gi|13542110|ref|NP_111798.1| 23 INPDICSTCPDhfCVFACPAN 43
                                  566778888544499999976 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00015
                       Fer4_17 41 ekaslCieCgeCerkCPqg 59
                                   k ++C+eCg C+ +C +g
  gi|13542110|ref|NP_111798.1| 54 FKYEDCVECGTCDIACSHG 72
                                  5889************875 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   5.8      0.34   6.1e+02       2      16 ..      26      42 ..      25      46 .. 0.82
   2 ?   11.9   1.4   0.00015      0.26       2      15 ..      57      70 ..      56      81 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.34
                        Fer4_4  2 erCigCg..sCvaaCPq 16
                                  + C  C+   Cv aCP 
  gi|13542110|ref|NP_111798.1| 26 DICSTCPdhFCVFACPA 42
                                  66999**666*****96 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00015
                        Fer4_4  2 erCigCgsCvaaCP 15
                                  e C++Cg C +aC+
  gi|13542110|ref|NP_111798.1| 57 EDCVECGTCDIACS 70
                                  77*******99996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       624  (0.0348039); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 612.25
//
Query:       gi|13542111|ref|NP_111799.1|  [L=259]
Description: electron transfer flavoprotein subunit beta [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-43  148.3   0.1    2.5e-43  148.1   0.1    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 !  148.1   0.1   1.4e-47   2.5e-43       2     177 ..      18     198 ..      17     203 .. 0.93

  Alignments for each domain:
  == domain 1  score: 148.1 bits;  conditional E-value: 1.4e-47
                                   EEEE-EC.CCCE-HHHHHHHHHHHHHHHHHT--EEEEEEES....S-CHHHHHHCT-SEEEEEE-GGGSS--CCHHHHHHH CS
                           ETF   2 lvlaehgvdgklnpvdlealeaArrlkekaggevtavvvGppeaeealrealaamGadkvilvddpalagydaeatakala 82 
                                   ++l++ ++++++n +dl+ale A+++k+k g+++t++++Gpp+a++a+ e++a +Gad+ il++d+a+ag+d+++t  +la
  gi|13542111|ref|NP_111799.1|  18 MTLNRTKARNVVNASDLNALEYALQIKDKVGATITVISMGPPMADSAIIECMA-RGADRGILITDRAFAGADTYPTGLTLA 97 
                                   68899999*********************99**********************.*************************** PP

                                   HHHHHC.--SEEEEESSCC.H..HHHHHHHHHHCT-EEEEEESEEEEETCCEEEEEECCCCTEEEEEE-TSSSEEEEE-TT CS
                           ETF  83 alikke.dpdlvlagatai.g..kqvaprlAalLgvplitdvteleveggkltvtRpieggnglaevveadlpavltvrpg 159
                                   a i k+ ++d+++ g +++    ++v+p +A+ Lg+ +it++  ++ e+g++++tR++e+  g  e+v++++p+++tv  +
  gi|13542111|ref|NP_111799.1|  98 ATISKIgNVDIIFGGDETTdSstGHVGPGVAEFLGIDQITYAKTVDYEDGYVVATRELED--GD-EIVKVKPPVLVTVLLN 175
                                   ******89***********55***************************999*********..**.**************** PP

                                   SS--......--S-TT---EEEE- CS
                           ETF 160 afep......aaimaakkkeveev 177
                                   ++ p      ++i+a  +k ve++
  gi|13542111|ref|NP_111799.1| 176 SNLPrhqslrKKIDA-LRKGVESW 198
                                   ****88777544544.55555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       628  (0.0350271); expected 358.6 (0.02)
Passed bias filter:                      546  (0.0304535); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 1553.86
//
Query:       gi|13542112|ref|NP_111800.1|  [L=349]
Description: electron transfer flavoprotein subunit alpha [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.6e-37  128.5   0.0    3.5e-37  128.0   0.0    1.2  1  ETF        Electron transfer flavoprotein domain
    1.5e-33  114.7   0.1    5.8e-33  112.8   0.1    2.0  2  ETF_alpha  Electron transfer flavoprotein FAD-binding 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 !  128.0   0.0   3.9e-41   3.5e-37       1     180 [.      19     197 ..      19     199 .. 0.95

  Alignments for each domain:
  == domain 1  score: 128.0 bits;  conditional E-value: 3.9e-41
                                   EEEEE-EC.CCCE-HHHHHHHHHHHHHHHHHT--EEEEEEES....S-CHHHHHHCT-SEEEEEE-GGGSS--CCHHHHHH CS
                           ETF   1 vlvlaehgvdgklnpvdlealeaArrlkekaggevtavvvGppeaeealrealaamGadkvilvddpalagydaeatakal 81 
                                   v+v++eh+ + +l++ + e+++ +++l+ k +++++ vv+G+  +++ +++++ ++G+d v+ +++p+la+y++ ++a+++
  gi|13542112|ref|NP_111800.1|  19 VGVYIEHR-GDELKRPSIEMIGIGKQLARKVNEKLICVVIGD--KVDGIAKEVGEYGCDIVLAAESPELAEYRTMPYAEII 96 
                                   689****9.*********************99**********..344499******************************* PP

                                   HHHHHHC--SEEEEESSCCHHHHHHHHHHHCT-EEEEEESEEEEETCC.EEEEEECCCCTEEEEEE-T.SSSEEEEE-TTS CS
                           ETF  82 aalikkedpdlvlagataigkqvaprlAalLgvplitdvteleveggk.ltvtRpieggnglaevvea.dlpavltvrpga 160
                                      i++++p+++l++at  g+++a r+A +  +++++d+t l++++++ l + Rp++g++ lae+++  ++p+++t rpg+
  gi|13542112|ref|NP_111800.1|  97 GGYIQEYKPNIFLLAATRNGRDLASRIAVKSRTGITADCTVLDIDENRtLLANRPTYGESTLAEILCRnHRPQMATARPGI 177
                                   ********************************************86668******************************** PP

                                   S----S-TT---EEEE--HH CS
                           ETF 161 fepaaimaakkkeveeveva 180
                                   f+pa++++  k ev + +v+
  gi|13542112|ref|NP_111800.1| 178 FPPAEKEKDHKYEVIKKKVD 197
                                   *****999999999998876 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 ?   -1.5   0.0       0.3   2.7e+03      41      67 ..      83     109 ..      63     114 .. 0.80
   2 !  112.8   0.1   6.5e-37   5.8e-33       2      83 ..     217     298 ..     216     299 .. 0.98

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.3
                                   HHHTTTSS-CCCB-SSSS-----S-EE CS
                     ETF_alpha  41 avvdagwipeerqvGqtGktvaPklyi 67 
                                    +++   +p+++ +G   ++ +P++++
  gi|13542112|ref|NP_111800.1|  83 ELAEYRTMPYAEIIGGYIQEYKPNIFL 109
                                   556667899999999999999999876 PP

  == domain 2  score: 112.8 bits;  conditional E-value: 6.5e-37
                                   -TTT-S-EEEE-GGGSSGGGHHHHHHHHHHHT-EEEE-HHHHTTTSS-CCCB-SSSS-----S-EEEES----HHHHGGGT CS
                     ETF_alpha   2 dLeeakvvvsgGrGlkskenlelleelaealgaavgasRavvdagwipeerqvGqtGktvaPklyiavGisGaiqhlaGmk 82 
                                   dL++ak+vv+gG Gl+ ++++++leela+ +g+avg sR+ vd gwi++++qvGqtG++v+P+lyiavGisG+ qh+aGmk
  gi|13542112|ref|NP_111800.1| 217 DLTSAKIVVAGGLGLGGPDGFKMLEELANLIGGAVGSSRPPVDLGWITRDHQVGQTGQSVRPDLYIAVGISGKPQHIAGMK 297
                                   89******************************************************************************8 PP

                                   T CS
                     ETF_alpha  83 e 83 
                                    
  gi|13542112|ref|NP_111800.1| 298 F 298
                                   5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (349 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.48
# Mc/sec: 2170.48
//
Query:       gi|13542113|ref|NP_111801.1|  [L=660]
Description: threonyl-tRNA synthetase [Thermoplasma volcanium GSS1]
Scores for complete 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-29  101.4   0.0    9.6e-29  100.6   0.0    1.4  1  tRNA-synt_2b    tRNA synthetase class II core domain (G, H, P
    9.2e-16   57.8   0.3    1.9e-15   56.8   0.3    1.6  1  HGTP_anticodon  Anticodon binding domain
    4.1e-13   49.2   0.0      1e-12   48.0   0.0    1.7  1  tRNA_SAD        Threonyl and Alanyl tRNA synthetase second ad
    0.00019   21.5   0.4    0.00041   20.4   0.4    1.5  1  Zn-ribbon_8     Zinc ribbon domain
     0.0076   16.3   0.0      0.015   15.3   0.0    1.4  1  HypA            Hydrogenase/urease nickel incorporation, meta
  ------ inclusion threshold ------
      0.037   14.0   0.0      0.066   13.1   0.0    1.3  1  PSCyt2          Protein of unknown function (DUF1549)
      0.065   13.0   0.1       0.22   11.3   0.1    1.9  1  Sda             Sporulation inhibitor A
       0.15   12.1   0.2       0.26   11.4   0.2    1.3  1  DZR             Double zinc ribbon
       0.16   11.7   0.8       0.32   10.8   0.8    1.5  1  Rubredoxin_2    Rubredoxin metal binding domain
       0.16   11.5   1.9         14    5.3   0.3    2.6  2  TF_Zn_Ribbon    TFIIB zinc-binding


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 !  100.6   0.0   5.3e-32   9.6e-29       6     178 ..     306     548 ..     301     549 .. 0.90

  Alignments for each domain:
  == domain 1  score: 100.6 bits;  conditional E-value: 5.3e-32
                                   TTSEEEEE-SSSHHHHHHHHHHHEEEBGG.SSEEEEEEEEEEBTTTS.TBCTTTB-SEEEEEEEEEEESGGGHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  tRNA-synt_2b   6 rndreyiLkPtneetfvelirdevlrskr.LPlklyqiqtkyRdEks.dsrGLlRvreFhqkdgyvfhaeaslddslrdli 84 
                                    ++++y +kP+n++++++++  +   s+r LP+k+++ +t+yR+Eks +  GL+R r F+q+dg+ f   +++  +++ l+
  gi|13542113|ref|NP_111801.1| 306 PDGDSYGIKPMNCPGHIAIFARR-KYSYRdLPVKYSEPGTVYRYEKSgEVGGLTRPRAFTQDDGHEFIRMDQIVGEIKTLL 385
                                   5689*****************99.667555*****************8888****************************** PP

                                   HHHHHHHHHTT.SC.....EEEEEEGTTSC................................................... CS
                                   xxxxxxxxxxxxxx.....xxxxxxxxxxx................................................... RF
                  tRNA-synt_2b  85 kaisriferlglef.....raiielmsaks................................................... 109
                                     + + f +++ +        +i      +                                                   
  gi|13542113|ref|NP_111801.1| 386 GMVRETFTTVFGNIemafdLSVID-----Kehpenyllsyvckdcgnrveglrgtdiecpvchshnmdpdfstwdnateql 461
                                   *******99975542222222222.....1346669999****************************************** PP

                                   ..................BTTSEEEEEEEEETTTSEEEEEEEEEEEETHHHHHTTEEEECTTSSEEEEEEEEEE.EE.HHH CS
                                   ..................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx.xxx RF
                  tRNA-synt_2b 110 ..................adykdkkefeavsesltkgieigtiqklgtrlserlgatvldennreksvimicaa.ig.veR 170
                                                     a+y++k ++ + +  l++ ++++tiq + + ++  +g+t+ +++++e++v++i++a  g  eR
  gi|13542113|ref|NP_111801.1| 462 rqamdsmgitykeypgeaAFYGPKIDVHVKDA-LGRMWQLSTIQVD-FFMPINFGLTYTNSEGKEERVVIIHRAiYGsYER 540
                                   *****************************999.*************.***************************9899*** PP

                                   HHHHHHHH CS
                                   xxxxxxxx RF
                  tRNA-synt_2b 171 llsaileq 178
                                   +++++le+
  gi|13542113|ref|NP_111801.1| 541 FMAILLEH 548
                                   ******98 PP

>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.8   0.3   1.1e-18   1.9e-15       1      93 [.     561     649 ..     561     650 .. 0.95

  Alignments for each domain:
  == domain 1  score: 56.8 bits;  conditional E-value: 1.1e-18
                                   SEEEEESSSSHHHHHHHHHHHHHHHHTTTSEEEEESSSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEEETTTCEEEE CS
                HGTP_anticodon   1 qvvviplnekaeeleeyakklaeeLraagirvelddsnesigkkireadllgipfavvvGekelekgtvtvrdrdtreqer 81 
                                   q +vip+++   +  eya+k+ + L++agir ++dd  +++ kki+    +   ++vvvG+ke +++tvtvr+r+ +++ +
  gi|13542113|ref|NP_111801.1| 561 QTYVIPVGT---ANAEYARKVNKSLLDAGIRSVVDDGPDTVSKKIKMIHDQRPSYIVVVGAKEEQDNTVTVRNRAGKSK-T 637
                                   679******...899***********************************************************99988.8 PP

                                   EETTHHHHHHHH CS
                HGTP_anticodon  82 vsldelveklke 93 
                                     ++e++e++k+
  gi|13542113|ref|NP_111801.1| 638 YGMNEFLEIIKN 649
                                   899999998886 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 !   48.0   0.0   5.6e-16     1e-12       2      44 .]     154     201 ..     153     201 .. 0.93

  Alignments for each domain:
  == domain 1  score: 48.0 bits;  conditional E-value: 5.6e-16
                                   EEEEETT.EEEEESS---SBGGGC-SEEEE.......CCECCCTCEEEEE CS
                      tRNA_SAD   2 rvvsiGdisvelCgGtHvpnTgeIgafkil.......seesiakglrRIy 44 
                                   +v+++G+ +v+lC G+Hvp+Tg+I+afk+l       + ++ +k+l RIy
  gi|13542113|ref|NP_111801.1| 154 SVYQQGN-FVDLCLGPHVPSTGYIKAFKLLsiasavyKYDE-SKNLVRIY 201
                                   79****9.**********************99999988887.89999998 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.4   2.3e-07   0.00041       6      35 ..     420     446 ..     417     448 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 2.3e-07
                   Zn-ribbon_8   6 YrCeeCghefevlqsisdapltaCPeCgs.e 35 
                                   Y C++Cg++ e l+      +++CP C+s +
  gi|13542113|ref|NP_111801.1| 420 YVCKDCGNRVEGLRG----TDIECPVCHShN 446
                                   *************95....3678*****966 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   0.0   8.3e-06     0.015      64      98 ..     413     448 ..     363     451 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 8.3e-06
                                   EEEE--EEEETTTS-EEE.CHHHHHS-TTTSSS-EE CS
                          HypA  64 ieevpvkvrCreCgkefe.leekalrCpkCgsadve 98 
                                    e+  +++ C++Cg+++e l+ ++++Cp C+s++++
  gi|13542113|ref|NP_111801.1| 413 PENYLLSYVCKDCGNRVEgLRGTDIECPVCHSHNMD 448
                                   455567899*********6655689*******9875 PP

>> PSCyt2  Protein of unknown function (DUF1549)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   3.7e-05     0.066     108     191 ..     362     449 ..     360     456 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.7e-05
                        PSCyt2 108 alnedkPYdqfvreqlagdllp.ateaeqlvatgFlrlgkte...eeggadkeearaeevddrvdtvgkaflGltveCarC 184
                                   a+ +d   + +  +q+ g+  +     +++  t F ++++       +++++e++  ++v +   +  + + G+ +eC  C
  gi|13542113|ref|NP_111801.1| 362 AFTQDDGHEFIRMDQIVGEIKTlLGMVRETFTTVFGNIEMAFdlsVIDKEHPENYLLSYVCKDCGNRVEGLRGTDIECPVC 442
                                   67777777767778888884433233567788888888777656656778889999999999999999************* PP

                        PSCyt2 185 HdHkfdp 191
                                   H+H++dp
  gi|13542113|ref|NP_111801.1| 443 HSHNMDP 449
                                   ******8 PP

>> Sda  Sporulation inhibitor A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00012      0.22      24      38 ..     642     656 ..     640     658 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00012
                           Sda  24 DFIeLieeEierRsL 38 
                                   +F+e+i++Eie+Rs 
  gi|13542113|ref|NP_111801.1| 642 EFLEIIKNEIEKRSV 656
                                   8************95 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2   0.00014      0.26      12      41 ..     419     450 ..     412     454 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00014
                           DZR  12 arfCseCgtklkavaa.edrCpsCgek.vdpe 41 
                                   + +C++Cg++++      + Cp C++  +dp+
  gi|13542113|ref|NP_111801.1| 419 SYVCKDCGNRVEGLRGtDIECPVCHSHnMDPD 450
                                   568*******99766689*******9867766 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   0.8   0.00018      0.32       1      23 [.     420     445 ..     420     446 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00018
                  Rubredoxin_2   1 YvCsqCGfesakwfG...rCpsCgsW 23 
                                   YvC++CG++   + G    Cp C+s 
  gi|13542113|ref|NP_111801.1| 420 YVCKDCGNRVEGLRGtdiECPVCHSH 445
                                   9**************5555****985 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.3    0.0078        14      20      29 ..     420     429 ..     418     431 .. 0.79
   2 ?    4.9   0.1      0.01        19       2      17 ..     438     458 ..     437     462 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0078
                                   EEESSSSBEE CS
                  TF_Zn_Ribbon  20 lvCtdCGlVl 29 
                                   +vC+dCG+ +
  gi|13542113|ref|NP_111801.1| 420 YVCKDCGNRV 429
                                   8999999765 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.01
                                   EETTTTCEEC.....HEETST CS
                  TF_Zn_Ribbon   2 kCPnCgstnl.....veDper 17 
                                    CP+C+s n+     ++D+++
  gi|13542113|ref|NP_111801.1| 438 ECPVCHSHNMdpdfsTWDNAT 458
                                   5******99536666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (660 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       949  (0.052931); expected 358.6 (0.02)
Passed bias filter:                      845  (0.0471303); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.73u 0.37s 00:00:01.10 Elapsed: 00:00:00.54
# Mc/sec: 3661.61
//
Query:       gi|13542114|ref|NP_111802.1|  [L=436]
Description: NAD-dependent aldehyde dehydrogenase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   1.5e-120  402.9   0.0   1.6e-120  402.7   0.0    1.0  1  Aldedh         Aldehyde dehydrogenase family
  ------ inclusion threshold ------
       0.12   12.5   0.0       0.24   11.6   0.0    1.4  1  NAD_binding_2  NAD binding domain of 6-phosphogluconate dehyd


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 !  402.7   0.0  1.8e-124  1.6e-120       9     462 .]       2     433 ..       1     433 [. 0.97

  Alignments for each domain:
  == domain 1  score: 402.7 bits;  conditional E-value: 1.8e-124
                                   EEEEETTTCEEEEEEE-B-HHHHHHHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHTHHHHHHHHHHHH---HHHHHHH CS
                        Aldedh   9 ievinPatgeviakvpaataedvdaavaaAkeafkawaklpaeeRaeiLrkaadlleerkeelaeletletGkplaearae 89 
                                   i+++nP+tgevia++++ ++e+v + ++  +e + +w+k ++ eR e++++a + +e++ ++l++l++le+Gkp++++  e
  gi|13542114|ref|NP_111802.1|   2 IKTLNPYTGEVIASYNEEDKEQVIRKIKDLREYQAKWRK-NIGERIEVIKAAKKNFETQIDDLSKLMSLEMGKPISQSISE 81 
                                   6889**********************************9.9**************************************** PP

                                   HHHHHHHHHHHHHHHHH.HSEEEEEECTTEEEEEEEEE-SEEEEEE-SSSCCHHHHHHHHHHHHTT-EEEEEE-TTSHHHH CS
                        Aldedh  90 veeaidvlryyaelaek.legevlpssegklalvrrePlGvvgaItPWNfPlllaawklapalaaGNtvvlKPaeetplsa 169
                                   v+++i  ++y++e aek l+ e +++ e ++++vr +P+Gv+++I+PWNfP+  ++++++palaaGNtv+lK a+ ++ ++
  gi|13542114|ref|NP_111802.1|  82 VKKSIWLMDYVIENAEKfLAIEDVKT-EARKSYVRFDPIGVILIIMPWNFPVWQVMRAAIPALAAGNTVILKHASIVSGTS 161
                                   *****************777788777.69**************************************************** PP

                                   HHHHHHHHHTTS-TTSEEE--SSTCCHHHHHHH-TTESEEEEES-HHHHHHHHHHHHCTTSEEEEEE---EEEEE-TTSHH CS
                        Aldedh 170 lllaelfeeaglPkgvlnvvtgsgsevgealvehpevdkvsftGstevgrkiakaaaknlkrvtlElGGknplivledaDl 250
                                   l++  l++      +++  v +sg+++++ +   pevd vsftGst++g +ia+ a+kn+k++++ElGG +p+ivl+d +l
  gi|13542114|ref|NP_111802.1| 162 LKIQDLLNT-----DAFRSVITSGETASSVI---PEVDGVSFTGSTSTGSRIAEIAGKNIKKFVMELGGSDPFIVLDDYNL 234
                                   ******999.....999999999*9999988...78********************************************* PP

                                   HHHHHHHHHHHHGGGGTSTTSEEEEEEEHHHHHHHHHHHHHHHHT--BS-TTSTT-SB---SSHHHHHHHHHHHHHHHHTT CS
                        Aldedh 251 dkaveaivkgafgnaGQvCiaasrllvqesiydefveklveaakklkvgdpldedtdvGPliseaqlekvekyveeakeeg 331
                                   +++v+++v+g + n+GQ Cia +r++v+++i ++fve l+++++++k+gdpl++dt +GPl s++q e+v ++v++ k + 
  gi|13542114|ref|NP_111802.1| 235 EDTVKNAVFGRLQNNGQSCIASKRFIVNRKIGEKFVEMLKDEFSRVKIGDPLNSDTFLGPLSSQDQKETVLRQVSDLKGKS 315
                                   *******************************************************************************76 PP

                                   SEEEE-TTE.SB-SSSTTEE--EEEES-TTTSHHHHS---SSEEEEEEESSHHHHHHHHHSSSEESEEEEE-SBHHHHHHH CS
                        Aldedh 332 aklllGgereeaglekgyfvePtvlanvtpdmriaqeEiFGPVlsvikfkdeeeaieiaNdteyGLaagvftkdleraerv 412
                                    +l++Gg      + +g++v Pt+++     +  ++eEiFGPV++v  f++ eea+ei N+t++GL+a++++ ++++ae++
  gi|13542114|ref|NP_111802.1| 316 -ELVIGG------DYQGNIVMPTIIK----TDVRYNEEIFGPVAVVKYFDKPEEAVEISNETPFGLGASIWG-NPDEAEKL 384
                                   .******......679*********9....47789*************************************.77****** PP

                                   HHHS-SSEEEESSSST--TTTSEB--CGGGEES-BSHHHHHHHTEEEEEE CS
                        Aldedh 413 aerleaGnvyiNdsttgaaealpfgGvkqSglGreggkegleeytevktv 462
                                   + +++aG+v +N+  ++++   pfgGvk+Sg+Gre +++g+ e+t++ktv
  gi|13542114|ref|NP_111802.1| 385 IPEIQAGMVFVNKIVASDPRL-PFGGVKKSGVGRELSRYGMLEFTNIKTV 433
                                   *******************99.**************************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 ?   11.6   0.0   2.7e-05      0.24       9      94 ..      70     158 ..      69     178 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.7e-05
                                   HHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTTEEE-SSHH..HHHHHCSEEEE-SSSHHHHHHHHHSHCCC--TT-EEE CS
                 NAD_binding_2   9 vMGsnmalnllkagykvavynrtkekveelvaegakaaesie..elvasldvvitmvkagkavdeviegllealkkgdili 87 
                                   +MG+++ + + + + ++ +++   e++e+++a + + +e  +    ++ + v++++++ + +v +v++  ++al++g+++i
  gi|13542114|ref|NP_111802.1|  70 EMGKPISQSISEVKKSIWLMDYVIENAEKFLAIEDVKTEARKsyVRFDPIGVILIIMPWNFPVWQVMRAAIPALAAGNTVI 150
                                   5******************************9984444444401445666*******************999999988776 PP

                                   .E-S---H CS
                 NAD_binding_2  88 .dgstssp 94 
                                     ++++  
  gi|13542114|ref|NP_111802.1| 151 lKHASIVS 158
                                   14555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (436 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       743  (0.0414412); expected 358.6 (0.02)
Passed bias filter:                      561  (0.0312901); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.48
# Mc/sec: 2709.82
//
Query:       gi|13542115|ref|NP_111803.1|  [L=433]
Description: alcohol dehydrogenase IV [Thermoplasma volcanium GSS1]
Scores for complete 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-100  336.3   0.0   2.1e-100  336.1   0.0    1.0  1  Fe-ADH    Iron-containing alcohol dehydrogenase
    2.2e-08   34.1   0.0    2.2e-07   30.8   0.0    2.0  2  Fe-ADH_2  Iron-containing alcohol dehydrogenase
  ------ inclusion threshold ------
      0.022   14.1   0.0      0.031   13.6   0.0    1.3  1  PFK       Phosphofructokinase


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 !  336.1   0.0  3.5e-104  2.1e-100       3     364 .]      22     423 ..      21     423 .. 0.96

  Alignments for each domain:
  == domain 1  score: 336.1 bits;  conditional E-value: 3.5e-104
                                   EEEEETTGGGGHHHHHTTT-..EEEEEEEHHHH.HH.THHHHHHHHHCTT-EEEE.EEE-S---HHHHHHHHTTS-TT.-- CS
                        Fe-ADH   3 rivfgkgaleelgellkklgakralivtdkgslkksglldkvlesleeagievtvfdgvepnptleeveeaaalareegad 83 
                                   +i fg ++++e+g+++  l++k+al+v+++++ k+s+ + +vl+sl+e+gi+++vfd+v+ +p++e++ ++ ++++ +++d
  gi|13542115|ref|NP_111803.1|  22 KIKFGMNTTKEVGKDAVGLKIKNALVVVGPRL-KDSKQFHDVLSSLSESGINYAVFDEVKTEPDDENLTKGYEAIKGKKID 101
                                   899****************************5.6*********************************************** PP

                                   EEEEEESHHHHHHHHHHHHHTT.......................--EEEEESS-S-S-TT-SEEEEE.-TTSEEEEE-.. CS
                        Fe-ADH  84 vviavGGGsviDtAKaialllanp.evedyl....gegkakkkkalpliaiPTtaGtGsevtplavitdeeegeklsifdp 159
                                   ++i++GGGs+iDtAK+++ll+++p +++dy+    g+g  ++ + lp+iaiPTtaGtGse+t++ +++ e  ++k++i++p
  gi|13542115|ref|NP_111803.1| 102 GLISFGGGSTIDTAKILNLLYKYPrDINDYInkpiGKGMIPEGDLLPHIAIPTTAGTGSETTNVTIFDVERLHVKTGISNP 182
                                   ***********************966*****99888888888888***********************9999********* PP

                                   SS--SEEEEEHHHHHHS-HHHHHHHHHHHHHHHHHHHHH.H.................T---TTSSB--HHHHHHHHHHHH CS
                        Fe-ADH 160 ellPdlaivDpeltltlPkrvtaatglDalahalEayvs.k.................kanplsdalaleairliaknler 222
                                   +++P+lai+Dp  tlt+P++vta+tglD+l ha+E+y+s +                 +++p+ d + l+ai+ + k+l+r
  gi|13542115|ref|NP_111803.1| 183 FIRPSLAIIDPVNTLTMPPKVTASTGLDVLNHAIESYTShPytarppvaspderpvysGSTPIGDLFGLQAIEWVHKYLRR 263
                                   ***************************************66**************************************** PP

                                   HHHHHHHHHHHHHHHHHHHHHHHHHHSS---HHHHHHHHHHC.............CG.GGGGS-HHHHHHHHH........ CS
                        Fe-ADH 223 avadgedleareqmllastlaglafsnaglgavHalahalgal............fg.iphglanaillpavlrfnaeaap 290
                                   a+ad+ dlear  m +++ +ag++f+++g+++ Ha+a+++ ++            +   phg++ ai  ++v+r+  +  p
  gi|13542115|ref|NP_111803.1| 264 AFADPLDLEARYYMTMGASIAGMGFGHVGVHIPHAMAYPIAGMikkwhpddydfgYPiSPHGISTAIPAAYVFRYLSKFVP 344
                                   *******************************************77777777664442466********************* PP

                                   ..HHHHHHT...........T--HHHHHHHHHHHHHTT---SHHHHT-TT-HHHHHHHHHT-T.SGGGGSSS---HHHH CS
                        Fe-ADH 291 erlaqlaralgge....sdeeaaeeliealrellkelglptsLselgvdeedldklaeaalkd.rslannpreltaedv 364
                                   er+a++  alg +    s+e+  + l    ++ll++l++p++Ls+l+++++d++kl++ ++++ r ++  p++++++d+
  gi|13542115|ref|NP_111803.1| 345 ERFADVLTALGYDtegmSAEDIGDTLYGYYIDLLHALKIPDNLSDLDFTSSDIEKLVDGTMAQqRLIGLSPKKIDKSDI 423
                                   ***********99**************************************************************9986 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 !   30.8   0.0   3.7e-11   2.2e-07       2      94 ..      25     118 ..      24     125 .. 0.92
   2 ?    1.0   0.0     0.049   2.9e+02     101     223 ..     148     291 ..     143     308 .. 0.68

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 3.7e-11
                      Fe-ADH_2   2 igegaleklgellkelelkkvllvadentkka.agekveeslkeagikvevveeveeeadleeveklvealreketdlvva 81 
                                   +g ++ +++g+    l++k++l+v++   k+    ++v +sl+e+gi+ +v++ev+ e+d e+  k  ea++ k++d +++
  gi|13542115|ref|NP_111803.1|  25 FGMNTTKEVGKDAVGLKIKNALVVVGPRLKDSkQFHDVLSSLSESGINYAVFDEVKTEPDDENLTKGYEAIKGKKIDGLIS 105
                                   567888888888999999**********99885789********************************************* PP

                      Fe-ADH_2  82 vGgGtiiDiakyv 94 
                                    GgG+ iD+ak++
  gi|13542115|ref|NP_111803.1| 106 FGGGSTIDTAKIL 118
                                   ***********97 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.049
                      Fe-ADH_2 101 pyvsvpTaaSvDGfaspgaslvvd..gkkrtv.akaaaPlaviaDldvlaeAPrrllasGvGDllgkytaladwklan... 175
                                   p +++pT+a   + +  +  + v+  + k+ + ++   P   i+D     + P + +as   D+l   +  ++++  +   
  gi|13542115|ref|NP_111803.1| 148 PHIAIPTTAGTGSETTNVTIFDVErlHVKTGIsNPFIRPSLAIIDPVNTLTMPPKVTASTGLDVLNHAIESYTSHPYTarp 228
                                   566777777666666666666666566666666666667777777777777777777776667776666555333222345 PP

                      Fe-ADH_2 176 ...............evseplaklsaamvqeaaeklvedkketealeellealalsgigisrp 223
                                                   + + + +++++ v + ++++ +d+ + ea   ++++  ++g+g+ + 
  gi|13542115|ref|NP_111803.1| 229 pvaspderpvysgstPIGDLFGLQAIEWVHKYLRRAFADPLDLEARYYMTMGASIAGMGFGHV 291
                                   455555555444444667788999999999999999999999999999999999999988664 PP

>> PFK  Phosphofructokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   5.2e-06     0.031      69     130 ..      79     156 ..      23     167 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.2e-06
                                   ---GGGGSHHHHHHHHHHHHHHT--EEEEEESHHHHHHHHHHHHT..T.......................--EEEEEEET CS
                           PFK  69 aRskefkeregrkkaaenlkklgidaLvviGGdgslkganklseerkgllee...................lkivgiPkTi 130
                                    ++++  ++e++ k +e +k ++id+L+  GG  ++++a+ l+    +++++                   l+ + iP T 
  gi|13542115|ref|NP_111803.1|  79 VKTEP--DDENLTKGYEAIKGKKIDGLISFGGGSTIDTAKILNLLY-KYPRDindyinkpigkgmipegdlLPHIAIPTTA 156
                                   45555..456799***************************999776.7677788899999999999999999999999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (433 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       254  (0.014167); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.62u 0.34s 00:00:00.96 Elapsed: 00:00:00.54
# Mc/sec: 2412.44
//
Query:       gi|13542116|ref|NP_111804.1|  [L=271]
Description: Zn-dependent hydrolase (AttM-related) [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.6e-18   66.3   2.0    6.2e-18   65.5   2.0    1.4  1  Lactamase_B    Metallo-beta-lactamase superfamily
    0.00011   21.8   0.8    0.00027   20.5   0.7    1.7  2  Lactamase_B_2  Beta-lactamase superfamily domain
  ------ inclusion threshold ------
      0.023   14.6   0.0       0.03   14.2   0.0    1.3  1  Lactamase_B_3  Beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.5   2.0     1e-21   6.2e-18      10     197 .]      50     255 ..      42     255 .. 0.81

  Alignments for each domain:
  == domain 1  score: 65.5 bits;  conditional E-value: 1e-21
                                   EEEETTCEEEES--SCHHHHHHHH....................HHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCC CS
                   Lactamase_B  10 liegdggviLiDtGtsteaaraal....................elaalglkpkdvdavilTHlHlDHiGglgglveatdv 70 
                                   li++++  iL+DtG+ ++a++  +                    +l+++glkp+d+d v+++HlHlDHiG ++ +++ +  
  gi|13542116|ref|NP_111804.1|  50 LIDHPDARILFDTGIAPDAMKTHErglmeafpitkmddqnhienQLKLIGLKPEDIDFVVISHLHLDHIGQAAVFKDSHVP 130
                                   99*******************999*****************************************************9988 PP

                                   EETCCEHHHHCCHCHHHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCC.EEEECT CS
                   Lactamase_B  71 pvgavaeeapalfmeeaddaasrkglllagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggk.vlftGD 150
                                    ++  +e + al   + +++  ++ ++l +    ++ + +++  ++++g+   ++tgg++ gh ++ v  + g+ + +tGD
  gi|13542116|ref|NP_111804.1| 131 IIVQKKELESALSLIWQGKSGAYDYSDLLPLKGAAWMPLDDPVFEIVDGVY-AEFTGGHTAGHQVLTVKTEKGSmYTLTGD 210
                                   888888888888888887777777665333333333333333333333333.3566666666666666665555268**** PP

                                   TTSSHHCCCCCC.TTCEEE-SHCHHHHHHHHHHHHHHHCHSEEEESS CS
                   Lactamase_B 151 allagetgridltlrgaevrdpsdaekyldsllklaglkaevlvpgH 197
                                   +l+ +++ +++   +g+    + ++ +y+++++ +++ +  +l+++H
  gi|13542116|ref|NP_111804.1| 211 FLHLPKEYDVEA--KGWLLSNATEWNSYIKKMKIREKARKQKLIISH 255
                                   ************..*******************99999999999988 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 ?   -0.4   0.0      0.11   6.8e+02     117     157 ..      38      80 ..      29      92 .. 0.61
   2 !   20.5   0.7   4.6e-08   0.00027       3      64 ..      58     135 ..      56     144 .. 0.62

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.11
                                   TCCE-TTTSEEEEEECTTEEEEEESS-S..---HHHHHHHCT- CS
                 Lactamase_B_2 117 rldrnagdtlGlriegggkrvyyigDtg..yipeeigerlgga 157
                                   r+d  + ++ G +i+ ++ r+++ ++ +   ++ + + +++ +
  gi|13542116|ref|NP_111804.1|  38 RRDWVEIPITGALIDHPDARILFDTGIApdAMKTHERGLMEAF 80 
                                   4566666788888888888888877766222224444444444 PP

  == domain 2  score: 20.5 bits;  conditional E-value: 4.6e-08
                                   EEES--TT...................HHHHHTCGGS--S.SS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEE CS
                 Lactamase_B_2   3 iLiDagpd...................lrqqalralqPve.lrdelppidaVllthaHyDHlaglltlrelrpkklplyap 63 
                                   iL+D+g                     +  q ++  ++ +    ++++id+V+++h H DH+  +  ++     ++p++++
  gi|13542116|ref|NP_111804.1|  58 ILFDTGIApdamktherglmeafpitkMDDQ-NHIENQLKlIGLKPEDIDFVVISHLHLDHIGQAAVFKDS---HVPIIVQ 134
                                   5566655555666666665555554433333.2222334445667789**************877777773...3788766 PP

                                   H CS
                 Lactamase_B_2  64 k 64 
                                   k
  gi|13542116|ref|NP_111804.1| 135 K 135
                                   5 PP

>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   5.1e-06      0.03      11      72 ..      50     139 ..      44     216 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5.1e-06
                 Lactamase_B_3  11 lletagarilvDPf.............................kanlgyeppaeeaDlvlisqaledHahletlkqlaenv 62 
                                   l++ ++aril D +                             ++ +  + ++e++D v+is+ + dH   +++ + ++ v
  gi|13542116|ref|NP_111804.1|  50 LIDHPDARILFDTGiapdamktherglmeafpitkmddqnhieNQLKLIGLKPEDIDFVVISHLHLDHIGQAAVFK-DSHV 129
                                   56666667777766555555555444444444444333333321123344555***************99988888.7888 PP

                 Lactamase_B_3  63 kvleegesle 72 
                                   +++ ++++le
  gi|13542116|ref|NP_111804.1| 130 PIIVQKKELE 139
                                   8888866655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       325  (0.0181271); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 1874.20
//
Query:       gi|13542117|ref|NP_111805.1|  [L=231]
Description: hypothetical protein TVN1286 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score 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   12.8   4.2      0.028   12.7   4.2    1.1  1  DUF2070        Predicted membrane protein (DUF2070)
       0.72    9.4  13.1       0.41   10.2   9.5    2.0  2  Bac_rhodopsin  Bacteriorhodopsin-like protein
        1.9    8.8  15.0        5.7    7.3  15.0    1.8  1  DUF5379        Family of unknown function (DUF5379)


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 ?   12.7   4.2   4.7e-06     0.028       7     135 ..      20     155 ..      16     211 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.7e-06
                       DUF2070   7 yifrlPswkvsllliillalligllaflssklfgillfglp.alvaflltlpvlrilggr....ltykrslflallteliv 82 
                                   ++f   +   s+++i++++++ig+l+   + l+g+ +f +  +l+ +++   +l+ lg +     t++  ++  l+ ++iv
  gi|13542117|ref|NP_111805.1|  20 FLFDEKERAKSIVMIFIIGAVIGILSGYLQ-LIGYWYFSVLlLLIVLVFSEYILKGLGVKvskkTTHRILFIGELFLTWIV 99 
                                   677777777899999999999999998888.55555555552333333444444455554444266666688889999999 PP

                       DUF2070  83 viisllaillsall...qalvllalvlslalvfalrllvlvavsdesllkavlpal 135
                                   + i++l   +s++     + + ++   ++++v + + +  +av ++s++ +v+ ++
  gi|13542117|ref|NP_111805.1| 100 FWILVLNPPFSHVSgpeISNIQMFSNGGWTSVPFSNGVYNIAVPNDSFRVYVFAYS 155
                                   99999999999888754344444444446666666666666666666666665544 PP

>> Bac_rhodopsin  Bacteriorhodopsin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   9.5   6.9e-05      0.41     106     174 ..      32     103 ..      28     105 .. 0.88
   2 ?   -0.0   0.1     0.092   5.5e+02      49      64 ..     120     135 ..     116     163 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 6.9e-05
                                   HHHHHHHHHHHHHTSHHHHHHHHHHHHHHHHHHHH...HHHTHHHHHHTTSTHHHHHHHHHHHHHHHHHHHH CS
                 Bac_rhodopsin 106 dvvmivgglvgaliestyrwvyftisvaallvvly...lllgelaraakslsserrslfntLrnlvvvlwil 174
                                   ++++i+g ++g l+++++  +y+ +sv  ll+vl+   ++l  l  ++++ ++ r  +   L +  +v wil
  gi|13542117|ref|NP_111805.1|  32 VMIFIIGAVIGILSGYLQLIGYWYFSVLLLLIVLVfseYILKGLGVKVSKKTTHRILFIGELFLTWIVFWIL 103
                                   5799************************99999874447999999999999999888888888888888986 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.092
                                   HHHHTTTTEEEEEETT CS
                 Bac_rhodopsin  49 ltmalglGltgveaef 64 
                                   + m ++ G+t+v++  
  gi|13542117|ref|NP_111805.1| 120 IQMFSNGGWTSVPFSN 135
                                   5799*******88843 PP

>> DUF5379  Family of unknown function (DUF5379)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3  15.0   0.00096       5.7       5      88 ..      28     106 ..      25     107 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.00096
                       DUF5379   5 gkvailhaiggiifgylanyvytlglgllsglatllflfiglvilghlsakvlgeesltqkqwlgsgvlpfflvaivvwil 85 
                                   +k+ ++  i g+++g l+ y+  +g   +s l  l+ l+ +  il  l  kv  +++ ++  ++g      fl++iv+wil
  gi|13542117|ref|NP_111805.1|  28 AKSIVMIFIIGAVIGILSGYLQLIGYWYFSVLLLLIVLVFSEYILKGLGVKVS-KKTTHRILFIG----ELFLTWIVFWIL 103
                                   68889999**********************99999999999999888988874.44444444444....58*********9 PP

                       DUF5379  86 kyn 88 
                                     n
  gi|13542117|ref|NP_111805.1| 104 VLN 106
                                   887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       903  (0.0503653); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); 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):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1532.75
//
Query:       gi|13542118|ref|NP_111806.1|  [L=213]
Description: triosephosphate isomerase [Thermoplasma volcanium GSS1]
Scores for complete 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-13   49.3   0.1    1.5e-11   44.1   0.0    2.0  2  TIM           Triosephosphate isomerase
    1.8e-06   27.5   0.1    2.8e-06   26.8   0.1    1.2  1  ThiG          Thiazole biosynthesis protein ThiG
    5.9e-06   25.9   0.1    1.2e-05   24.9   0.1    1.5  1  His_biosynth  Histidine biosynthesis protein
    0.00041   19.6   0.0    0.00054   19.2   0.0    1.1  1  IGPS          Indole-3-glycerol phosphate synthase
     0.0018   17.2   0.1     0.0027   16.6   0.1    1.4  1  Trp_syntA     Tryptophan synthase alpha chain
     0.0025   16.9   0.4     0.0036   16.4   0.4    1.2  1  FMN_dh        FMN-dependent dehydrogenase
  ------ inclusion threshold ------
      0.013   14.5   0.1      0.023   13.7   0.1    1.4  1  IMPDH         IMP dehydrogenase / GMP reductase domain
      0.035   13.5   0.0      0.042   13.2   0.0    1.2  1  NMO           Nitronate monooxygenase


Domain annotation for each model (and alignments):
>> TIM  Triosephosphate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.1   0.0   6.7e-15   1.5e-11       3     131 ..       4     124 ..       2     130 .. 0.84
   2 !    4.4   0.0    0.0092        21     153     182 ..     126     158 ..     118     166 .. 0.68

  Alignments for each domain:
  == domain 1  score: 44.1 bits;  conditional E-value: 6.7e-15
                                   EEEE-TBTS-HHHHHHHHHHHHHHCHGCTSEEEEE--GGGHHHHHHHHTTSSECEEES--BSSSSBS-TT--BHHHHHHTT CS
                           TIM   3 iagNwKmnktleeakellkklkaklkeekvevviappflylekvkklleesklklgaqnvsaeksGafTGevsaemlkdlg 83 
                                   ++ N K +++ ++ k++++ +++  k ++v+++iap +l l+++++     ++++ +q v+    G++TG +++e l ++g
  gi|13542118|ref|NP_111806.1|   4 VIVNLKNYAE-ANGKNFVEFVSKLPKYDSVRLIIAPAILDLHNAHEFR---NVEFFSQHVDDVGYGPYTGHIAIESLMNYG 80 
                                   7788887765.456778877776666699************9877765...7***************************** PP

                                   -SEEEES-HHHHHHST--HHHHHHHHHHHHHTT-EEEEEE---HHHHH CS
                           TIM  84 vkyviiGHsErrqlfkEtdelvakKvkaalksglkpilCvGEtleere 131
                                   +   ++ HsErr   +E+   +   vk+a+  g+++ lCv+  +e+++
  gi|13542118|ref|NP_111806.1|  81 IIGSLLNHSERRL--GED--KIISTVKKAQMLGFEIALCVESMEEAKR 124
                                   ************5..565..456678999999********87776655 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.0092
                                   CCGGCEEEEE--GGGSSSS--...--HHHHHHH CS
                           TIM 153 ealknvviAYePvWAiGtgkt...atpeqaqev 182
                                   +alk  +iAYeP   iG + +   a+pe + e+
  gi|13542118|ref|NP_111806.1| 126 SALKPSFIAYEPKELIGGNVSvstAKPEIISEI 158
                                   4678899**********9765111445555554 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   0.1   1.2e-09   2.8e-06     170     215 ..     161     206 ..     139     212 .. 0.81

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 1.2e-09
                                   HHHH-SS-BEEES---SHHHHHHHHHTT-SEEEESHHHHTSSSHHH CS
                          ThiG 170 iieeakvPvivDAGigspsdaaqamelGadavllntavaeakdpva 215
                                   i+ +  vPv+v AGi + +d+ ++++lGa+++l+ + v ++ dpv+
  gi|13542118|ref|NP_111806.1| 161 ICGTEGVPVLVGAGIKNRQDVRKSLDLGAQGILVSSGVVKSPDPVR 206
                                   444558**************************************97 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.1   5.4e-09   1.2e-05      61     115 ..     154     208 ..     141     212 .. 0.81

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 5.4e-09
                                   HHHHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH-THHHHHH CS
                  His_biosynth  61 nldlveeiaeevfipvqvGGGIrsledveelleagadkviigtaavknpelikel 115
                                    ++ +  i+ +  +pv vG GI++ +dv++ l++ga+ + +++ +vk+p+ +++l
  gi|13542118|ref|NP_111806.1| 154 IISEIVDICGTEGVPVLVGAGIKNRQDVRKSLDLGAQGILVSSGVVKSPDPVRSL 208
                                   3333444555556************************************998876 PP

>> IGPS  Indole-3-glycerol phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   2.4e-07   0.00054     143     251 ..      94     208 ..      90     211 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 2.4e-07
                                   -HHHHHHHHHHHCCTT-EEEEEESSHHHHHHHHHTT-SEEEEESEETTTTEE-CHHHH..HHCHCC-...TT.SEEEEESS CS
                          IGPS 143 edeeleelaeaakslglevLvEvhdeeeleralklgakiiGvNnRnLktlevdlntte..eLaklvp...kd.vllvaeSG 217
                                    ++++ + ++ a+ lg+e+   v++ ee +r  +l+ ++i    ++L   +v++ t +   +++ v+   ++ v +    G
  gi|13542118|ref|NP_111806.1|  94 GEDKIISTVKKAQMLGFEIALCVESMEEAKRYSALKPSFIAYEPKELIGGNVSVSTAKpeIISEIVDicgTEgVPVLVGAG 174
                                   56667778899************************************887777776543134444446666669999**** PP

                                   S-SHHHHHHHCCTT-SEEEESHHHHC-TTHHHHH CS
                          IGPS 218 iktredveklkeegvnafLvGeslmrqedvekai 251
                                   ik+r+dv+k  + g++++Lv + +++++d  +++
  gi|13542118|ref|NP_111806.1| 175 IKNRQDVRKSLDLGAQGILVSSGVVKSPDPVRSL 208
                                   *************************999976665 PP

>> Trp_syntA  Tryptophan synthase alpha chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   1.2e-06    0.0027     186     232 ..     154     201 ..      93     207 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.2e-06
                                   HHHHHHHHHHCTSS-EEEESSS-SHHHHHHHH.TT-SEEEE-HHHHHH CS
                     Trp_syntA 186 vdelverlkkltavPvavGFGistkeqvkqva.kvadGvivGSalvkk 232
                                   + + +  +  ++ vPv+vG Gi+++++v++    +a+G++v S +vk 
  gi|13542118|ref|NP_111806.1| 154 IISEIVDICGTEGVPVLVGAGIKNRQDVRKSLdLGAQGILVSSGVVKS 201
                                   4444555666789***************999989***********985 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.4   1.6e-06    0.0036     256     300 ..     150     195 ..     142     200 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.6e-06
                                   -HHHCHHHHHHHH..S.S-EEEESS--SHHHHHHHHHTT-SEEEES CS
                        FMN_dh 256 atidvLpeiveavggr.ievlvDgGirrGsDvlkAlalGAdavllG 300
                                   a  +++ eiv+ +g + ++vlv  Gi++ +Dv k l lGA+++l+ 
  gi|13542118|ref|NP_111806.1| 150 AKPEIISEIVDICGTEgVPVLVGAGIKNRQDVRKSLDLGAQGILVS 195
                                   5557899*******866************************99985 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1     1e-05     0.023     194     237 ..     153     196 ..     135     203 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1e-05
                                   HHHHHHHHHHCTCT-EEEEES---SHHHHHHHHHTT-SEEEESC CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         IMPDH 194 tAvaevaeaakkagvpviaDGGikysgdivkAlaaGadavmlGs 237
                                     ++e+++++ + gvpv+   Gik+ +d+ k+l +Ga+ +++ s
  gi|13542118|ref|NP_111806.1| 153 EIISEIVDICGTEGVPVLVGAGIKNRQDVRKSLDLGAQGILVSS 196
                                   55899999******************************998865 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.9e-05     0.042     183     223 ..     153     196 ..      98     203 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.9e-05
                           NMO 183 aLvpqvldavd...iPviAaGGiidrrgvaaaLalGAsgvqigt 223
                                   +++ +++d      +Pv+   Gi +r++v   L lGA+g+ + +
  gi|13542118|ref|NP_111806.1| 153 EIISEIVDICGtegVPVLVGAGIKNRQDVRKSLDLGAQGILVSS 196
                                   45556666655888*************************98875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       266  (0.0148363); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1529.11
//
Query:       gi|13542119|ref|NP_111807.1|  [L=170]
Description: deoxycytidylate deaminase [Thermoplasma volcanium GSS1]
Scores for complete 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-30  102.9   0.9    9.2e-30  102.5   0.9    1.2  1  dCMP_cyt_deam_1  Cytidine and deoxycytidylate deaminase zinc-
    1.7e-25   89.4   0.0    2.1e-25   89.1   0.0    1.1  1  MafB19-deam      MafB19-like deaminase
  ------ inclusion threshold ------
      0.086   12.7   0.4        1.7    8.5   0.4    2.4  1  Inv-AAD          Invertebrate-AID/APOBEC-deaminase
       0.11   12.4   0.1       0.13   12.2   0.1    1.2  1  APOBEC_N         APOBEC-like N-terminal domain
       0.14   12.3   0.9       0.27   11.3   0.2    1.9  2  Bd3614-deam      Bd3614-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 !  102.5   0.9   2.6e-33   9.2e-30       2     100 ..       8     127 ..       7     128 .. 0.97

  Alignments for each domain:
  == domain 1  score: 102.5 bits;  conditional E-value: 2.6e-33
                                   HHHHHHHHHHHHHHHHHHTTTSCSEEEEEEETTEEEEEEESBHHCCTG.......................TTB-HHHHHH CS
               dCMP_cyt_deam_1   2 ekdekllelalkaakeaqkcsnfkVGavivkngeiistgyngepaggs.......................ktiHAEvnAi 59 
                                   ++de+++++a++aa++  +c + kVGavivk++++++tgyng p g                         + +HAE+nAi
  gi|13542119|ref|NP_111807.1|   8 SWDEYFMRMAYLAASRT-NCIRRKVGAVIVKDKNVLATGYNGPPSGTAhcdvvgciredlkipsgerhelcRGLHAEQNAI 87 
                                   79***************.**************************9998********************************* PP

                                   HHHHHHTSSCETTEEEEEEE--BHHHHHHHHHHT-SEEEEE CS
               dCMP_cyt_deam_1  60 lkaaknggsklegatlyvtlePCsmCakaiiqsgikkvvvg 100
                                   ++aa   g+++++ t+yvt+ PC  C+k+i +++ik++v++
  gi|13542119|ref|NP_111807.1|  88 IQAAVH-GVSIKDSTIYVTTHPCVVCSKMIMNAQIKEIVYA 127
                                   ****88.999*****************************97 PP

>> MafB19-deam  MafB19-like deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.1   0.0   5.9e-29   2.1e-25       2     133 ..       8     163 ..       7     166 .. 0.91

  Alignments for each domain:
  == domain 1  score: 89.1 bits;  conditional E-value: 5.9e-29
                   MafB19-deam   2 dkekafrkalaevekatkikedkigavivkdkkviargsn........................ekelnakataHaEiaal 58 
                                   +++++f+  + ++  +t++  +k+gavivkdk+v+a+g+n                        e   +   + HaE +a+
  gi|13542119|ref|NP_111807.1|   8 SWDEYFMRMAYLAASRTNCIRRKVGAVIVKDKNVLATGYNgppsgtahcdvvgciredlkipsgE-RHELCRGLHAEQNAI 87 
                                   589****************************************************9999999852.33567889******* PP

                   MafB19-deam  59 qqAakklkskrlddatlyvtlepCdmCagaivqaglkklvygagnpkslnkLkvkekngrvelv...eddckeilkgf 133
                                    qAa  + s+  +d t+yvt  pC +C ++i++a++k++vy+ g+p+ l +L + e+n +v+ +   e ++ +++++f
  gi|13542119|ref|NP_111807.1|  88 IQAAVHGVSI--KDSTIYVTTHPCVVCSKMIMNAQIKEIVYAEGYPDELAELMLLESNVKVRRFslpEKEVRAMIGDF 163
                                   ***7766666..***********************************************9987788888888887766 PP

>> Inv-AAD  Invertebrate-AID/APOBEC-deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.4   0.00047       1.7       2      64 ..      33     110 ..      32     127 .. 0.62

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00047
                       Inv-AAD   2 avlvdadkneilatGytleleGnthaeqc.cl...ikl..aekheva...........eeklaevlpkntvlYttmepCs 64 
                                   av+v+  ++++latGy     G+ h +   c+   +k+   e+he+            +  ++ v  k+  +Y t  pC 
  gi|13542119|ref|NP_111807.1|  33 AVIVK--DKNVLATGYNGPPSGTAHCDVVgCIredLKIpsGERHELCrglhaeqnaiiQAAVHGVSIKDSTIYVTTHPCV 110
                                   55554..4578888888888666666643133222233111222222555555444448888888889999999999996 PP

>> APOBEC_N  APOBEC-like N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   3.6e-05      0.13      34      96 ..      69     120 ..      34     147 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.6e-05
                                   EEEEEEEE-..SSTBCHHHHHHHHHHHHT--.TTEEEEEEEEESS-S-HH....HHHHHHHHH CS
                      APOBEC_N  34 kkGvLrnqsgaaaskHaEelflediedqelrepkkkyeitlYvswsPChessdeCaeklaafl 96 
                                    +G+ r + +     HaE+  +    ++++    +    t+Yv++ PC+     C++++ ++ 
  gi|13542119|ref|NP_111807.1|  69 PSGE-RHELCR--GLHAEQNAI---IQAAVH-GVSIKDSTIYVTTHPCVV----CSKMIMNAQ 120
                                   4555.444444..889999833...333333.6788899***********....****98765 PP

>> Bd3614-deam  Bd3614-like deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0       3.5   1.2e+04       8      21 ..      29      42 ..      28      47 .. 0.63
   2 ?   11.3   0.2   7.5e-05      0.27      76     121 ..      98     136 ..      81     151 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 3.5
                   Bd3614-deam  8 RkvvAalvsdqGel 21
                                  Rkv A++v+d+ +l
  gi|13542119|ref|NP_111807.1| 29 RKVGAVIVKDKNVL 42
                                  67777777766443 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 7.5e-05
                   Bd3614-deam  76 egarllvtlqcCkmCAalvvaaadapgrevllkvvYleedkGaLar 121
                                   ++++++vt ++C +C  ++++a          ++vY+e  +  La 
  gi|13542119|ref|NP_111807.1|  98 KDSTIYVTTHPCVVCSKMIMNAQI-------KEIVYAEGYPDELAE 136
                                   5889***************99865.......566666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-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 0.30s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 1094.89
//
Query:       gi|13542120|ref|NP_111808.1|  [L=94]
Description: hypothetical protein TVN1289 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                      1039  (0.0579508); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.28s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 594.46
//
Query:       gi|13542121|ref|NP_111809.1|  [L=472]
Description: hypothetical protein TVN1290 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-06   27.9   1.1      0.098   12.8   0.0    3.2  3  SnoaL_4   SnoaL-like domain
  ------ inclusion threshold ------
      0.019   15.4   1.1        8.3    6.9   0.1    3.2  3  DUF4440   Domain of unknown function (DUF4440)


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 !   12.8   0.0   1.1e-05     0.098      32     125 ..      74     169 ..      65     174 .. 0.79
   2 !   11.2   0.1   3.4e-05       0.3      30     123 ..     213     308 ..     191     315 .. 0.84
   3 ?    0.5   0.0     0.067     6e+02      36      93 ..     360     419 ..     348     440 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.1e-05
                                   EEEEEEEEETTS...--EESHHHHHHHHHSHHHHHH-EEEEE---EEEE.ETTEEEEEEEEEEEEEETTEEEEEE...EEE CS
                       SnoaL_4  32 Ftedavvdytgvg.egvlegrdairaalrealdgfaltqHllsnpliel.dgdtAtgrayllatlvrdgdggrqvl.aggr 109
                                   +  +a++++ g+  +g+++g  ai   +++ ++    +  ++snp +    gdtA+++a ++ +  ++ + + +v  +   
  gi|13542121|ref|NP_111809.1|  74 YLSNATLQWIGGPlSGTYTGLSAIDSTWNKFFGLWSAVWLYTSNPPVVTtSGDTAQVTAPVQFIV-TPFNVNNTVEyINVS 153
                                   67789999997559*****************98777777777776555449***********995.555444444449999 PP

                                   EEEEEEEETTEEEEEE CS
                       SnoaL_4 110 yedelvredggWrisr 125
                                   y+ ++ +  g+  i++
  gi|13542121|ref|NP_111809.1| 154 YTLDFMKSGGQFYITH 169
                                   9999999999988887 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 3.4e-05
                                   TTEEEEEEEEETTS...--EESHHHHHHHHHSHHHHHH.-EEEEE---EEEEETTEEEEEEEEEEEEEETTEEEEEE...E CS
                       SnoaL_4  30 dlFtedavvdytgvg.egvlegrdairaalrealdgfa.ltqHllsnplieldgdtAtgrayllatlvrdgdggrqvl.ag 107
                                     ++ +a++d+ g+  +g+++g+ +i+  + + ++    +    ++ p +++ g+tAt+++  + + v++++++ +v    
  gi|13542121|ref|NP_111809.1| 213 PEYASNATLDWIGGPlTGTYSGVSSIIGTWGKFFGLWSaVWFYTVTPPSVSVIGKTATVTSMNQFI-VTPTSANNTVEyLN 292
                                   558999******855*****************986555688999**************99988888.56666655555577 PP

                                   EEEEEEEEEETTEEEE CS
                       SnoaL_4 108 gryedelvredggWri 123
                                     y+  + +e g+ +i
  gi|13542121|ref|NP_111809.1| 293 ISYTLNYYKEMGQYKI 308
                                   8999999999888887 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.067
                                   EEEEETTS...--EESHHHHHHHHHSHHHHHH.-EEEEE---EEEEETTEEEEEEEEEEE CS
                       SnoaL_4  36 avvdytgvg.egvlegrdairaalrealdgfa.ltqHllsnplieldgdtAtgrayllat 93 
                                   a++ + ++  +g+++g   i a +++ +++ + +       p++   gd A + a ++ +
  gi|13542121|ref|NP_111809.1| 360 ATLYWVNSTlNGTYQGYSNISAVWNKFFKAWIaVWFYAEEPPTVAMKGDMAYVNATVQFV 419
                                   555555544699999999999999998877664444455556666666666666665555 PP

>> DUF4440  Domain of unknown function (DUF4440)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.15   1.4e+03      60     103 ..     117     163 ..      84     167 .. 0.67
   2 ?    5.0   0.0    0.0036        33      57     104 ..     255     305 ..     219     308 .. 0.75
   3 ?    6.9   0.1   0.00093       8.3      44      88 ..     383     427 ..     341     436 .. 0.67

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.15
                                   EEEEEEEETTEEEEEEEEEEEECCTT..EEEE.EEEEEEEEEEEETT CS
                       DUF4440  60 teeevrvlgdlAvvtgrytfegrgdg..epve.grgrftsvwrkegg 103
                                   +++ v ++gd+A vt+ ++f +++ +  ++ve  +  +t  ++k gg
  gi|13542121|ref|NP_111809.1| 117 NPPVVTTSGDTAQVTAPVQFIVTPFNvnNTVEyINVSYTLDFMKSGG 163
                                   44556677999999987777554422114444445555555555555 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0036
                                   EEEEEEEEEEETTEEEEEEEEEEEE..CCTTEEEE.EEEEEEEEEEEETTE CS
                       DUF4440  57 lelteeevrvlgdlAvvtgrytfeg..rgdgepve.grgrftsvwrkeggg 104
                                   +++t+++v+v+g +A+vt   +f +  ++++++ve  +  +t  + ke g+
  gi|13542121|ref|NP_111809.1| 255 YTVTPPSVSVIGKTATVTSMNQFIVtpTSANNTVEyLNISYTLNYYKEMGQ 305
                                   4999**************999995511445666665555566555555555 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.00093
                                   HHHHHCCHCEEEEEEEEEEEEEEETTEEEEEEEEEEEECCTTEEE CS
                       DUF4440  44 lealeagfaagrslelteeevrvlgdlAvvtgrytfegrgdgepv 88 
                                    ++++++++a   ++ ++++v++ gd+A+v ++++f ++++  ++
  gi|13542121|ref|NP_111809.1| 383 WNKFFKAWIAVWFYAEEPPTVAMKGDMAYVNATVQFVVQKNATTF 427
                                   3344555555445588999*****************999887544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (472 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       742  (0.0413855); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 3150.38
//
Query:       gi|13542122|ref|NP_111810.1|  [L=294]
Description: phosphoribosylaminoimidazole-succinocarboxamide synthase [Thermoplasma volcanium GSS1]
Scores for complete 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  153.4   0.5    1.1e-44  153.0   0.5    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 !  153.0   0.5   5.9e-49   1.1e-44       2     243 ..       4     248 ..       3     255 .. 0.90

  Alignments for each domain:
  == domain 1  score: 153.0 bits;  conditional E-value: 5.9e-49
                                   EEE-SSEEEEE-SSTTEEEEEEESEEEECCCTEEEEETTHHHHHHHHHHHHHHHHHH..--BSEEEE............-S CS
                   SAICAR_synt   2 lyeGKvrdvYeledddklllvakDrisAfdvvlkeeipgKGkvltqlsafwfeklek..ipnhliksldpe.......qle 73 
                                   l++GKv+dvY+  d d+l++ +++ris+fd + ++ei++KG+ l+++safwf+++e+  +++h+i+ +d +       ++ 
  gi|13542122|ref|NP_111810.1|   4 LTTGKVKDVYD--DGDTLVFKFSNRISVFDKIIPNEIDNKGESLCRTSAFWFQLIESygMKSHFIELIDNRtmrvrkfAVP 82 
                                   689********..577****************************************668******9988333456678899 PP

                                   SSEEEEE-EEEESEEEEEEEE--HHH........HH....HH..T--TT-EEEEEEEEEEE--CCCT.S-EE-HHHHH.HT CS
                   SAICAR_synt  74 grsmlvkklkmlpvEvvvRgyltGslwkeykks.gkvcgirlpeglkegeklpepiftpstKaeegehDeniseeevveal 153
                                   +++ l     ++p+E+++R y++Gsl+   k++  k ++i l++  + gekl  pif+ +tK ee   D  ++++e++e+ 
  gi|13542122|ref|NP_111810.1|  83 NKVSLGSSNYVIPLEFITRYYVAGSLYDRIKEGkVKPMDIGLKHVPEYGEKLIDPIFEATTKREET--DRLLTKKEAMEIG 161
                                   9999**********************99988876666778887777889****************5..9*********666 PP

                                   T.-HHHHHHHHHHHHHHHHHHHHHHHHTTEEEEEEEEEEEEETTTTEEEEES--.STTTEEEEETTT.....GGGB-STHH CS
                   SAICAR_synt 154 g.teeeaeeieelalavyekaaelaaergiilvDtKlEFGldeedgelvLaDevltpDssRfwdaetyeegkeqeslDKqf 233
                                   g t e++ ei e+ +++ +++   +++rg+i +D K E  ld+ + ++v++D + t D  Rfwd+++y++g+   +l K++
  gi|13542122|ref|NP_111810.1| 162 GlTLEDYCEIMEAVFKIDRRIDMEVSKRGLIHADGKKEIALDR-ERRIVVVDTFGTADEDRFWDEKEYDNGRV-VELSKEM 240
                                   6*99**************************************6.8************************8876.579**** PP

                                   HHTT-STHHH CS
                   SAICAR_synt 234 vRdwleevee 243
                                   vR++ ++   
  gi|13542122|ref|NP_111810.1| 241 VRQYYRS--I 248
                                   ***9987..4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (294 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 2064.33
//
Query:       gi|13542123|ref|NP_111811.1|  [L=332]
Description: uroporphyrinogen decarboxylase [Thermoplasma volcanium GSS1]
Scores for 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-85  285.4   0.0    6.7e-85  285.3   0.0    1.0  1  URO-D     Uroporphyrinogen decarboxylase (URO-D)


Domain annotation for each model (and alignments):
>> URO-D  Uroporphyrinogen decarboxylase (URO-D)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  285.3   0.0   3.7e-89   6.7e-85       5     345 ..       3     329 ..       1     330 [. 0.93

  Alignments for each domain:
  == domain 1  score: 285.3 bits;  conditional E-value: 3.7e-89
                                   HHHHHHTT---SS--B--TT-SSTTSHHHHHHHTSSSHHHHHH-HHHHHHHHHHHHHHH--S-EE-S--TTGGGGGGT-EE CS
                         URO-D   5 rllralrgekvdrvPvwlmRqaGrylpeyraeragvsflelcknpelaaevtlqpvrrfglDaailfsdilveaealGlev 85 
                                    +l+al g + d +Pvw+mRqaGryl  y   r++  +  + ++++ ++++t +pv++ g+Daai+f di++++  lG +v
  gi|13542123|ref|NP_111811.1|   3 AFLKALHGLDHDYIPVWFMRQAGRYLNVYKDYRKKLGLEGMMTDADVIVKITHSPVDMIGVDAAIIFADITTPLPGLGFKV 83 
                                   69******************************************************************************* PP

                                   EEETTTEEEEE--S-....GGGS----GGG.G..HHHHHHHHHHHHH.--SS-EEEEEE-HHHHHHHHHCTT.-SS-HHHH CS
                         URO-D  86 efeegegPvvekpvrtaedveklevpddveegrlpyvleaikllkkelggevpligfvgaPftlasylveGg.skgfekll 165
                                   +fe++ gP v +++   + +  +++ d+   +  + vl+ai++ ++ +  + pligf+g+P+tl+syl+ G+  k+ +k++
  gi|13542123|ref|NP_111811.1|  84 RFEDNVGPIVLNNLS-DNGFSGINEFDEA--SFNHPVLKAISMYREMY--REPLIGFCGSPVTLLSYLIAGSfDKDLAKTK 159
                                   ************876.7889999999874..5789***********65..89***************************** PP

                                   HHHHH-HHHHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEETTGGGS-HHHHHHHTHHHHHHHHHHHHH.H--S-EEEEESS CS
                         URO-D 166 kllykdpeevhklldkltdvvieylkaqieagAdaiqifDswagllspedfeefvlpylkrivdevkaegpkvpvilfikg 246
                                   +l+++dp + +++   ltd++++y+k qi+ g+da q+fDswag lsp++++ef++py++ i++e+ +   kvp i+f + 
  gi|13542123|ref|NP_111811.1| 160 RLMLTDPSKYKEISTLLTDASVKYAKLQIKKGVDAFQLFDSWAGYLSPRQYKEFAVPYINDILSEIAG---KVPTIYFSTM 237
                                   *******************************************************************9...68******** PP

                                   HH.HHHHHHTTS--SEEE--TTS-HHHHHHSS....EEE--B-G.GGGGS-HHHHHHHHHHHHT.T---SSSEEB-BSS-- CS
                         URO-D 247 agaeiledlaelgadvlsldwtvdlkeaarevgdkvalqGnldPialLlgspeeiekevkeilekgaggkkgyilnlGhgi 327
                                   ++   +     +  d +s+dw+v++ ++++e      lqGnldP+   + + +   +e + i++ +++g+++yi+n+Ghgi
  gi|13542123|ref|NP_111811.1| 238 TS--SFVFQSGIISDFISVDWRVEMDKVVKES-GDYGLQGNLDPF---IVNYDYAFAESEHIIN-AVKGNNRYIFNTGHGI 311
                                   98..3444445668***********9999988.678********5...4566777888899***.5999************ PP

                                   -TTS-HHHHHHHHHHHHT CS
                         URO-D 328 ppetppenvkalveavke 345
                                   +p+t+p+ +  +v+ v++
  gi|13542123|ref|NP_111811.1| 312 LPDTDPKRLIEIVKYVHS 329
                                   ****************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 2237.94
//
Query:       gi|13542124|ref|NP_111812.1|  [L=304]
Description: ferrochelatase [Thermoplasma volcanium GSS1]
Scores for complete sequence (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  168.9   0.0    1.7e-49  168.6   0.0    1.0  1  Ferrochelatase  Ferrochelatase


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 !  168.6   0.0   9.5e-54   1.7e-49       1     315 [.       2     283 ..       2     285 .. 0.95

  Alignments for each domain:
  == domain 1  score: 168.6 bits;  conditional E-value: 9.5e-54
                                   .EEEEEEE----SSCCCHHHHHHHHCT-TTTS-S-TTTHHHHHHHHHHHHHHHHHHHHHHTTSS-SHHHHHHHHHHHHHHH CS
                Ferrochelatase   1 ktavLLlnlGgPekpedvrpflenllsdrrvielplllqkllaklilkerlekvaekYekigggSPlneitrkqaealeke 81 
                                   ktavLLl++G+Pek++d+ ++l++++ ++ v++                 +e+  +kYe +gg SP n+i +++++ l+k+
  gi|13542124|ref|NP_111812.1|   2 KTAVLLLSYGSPEKMSDIDEYLSKIFGGKPVPK---------------GVAEENYRKYEMFGGLSPSNRIIQSIRDRLQKR 67 
                                   79*******************************...............6799***************************** PP

                                   HHHH---EEEEEEESSSSSBHHHHHHHHHCTT-SEEEEEES-SS--TTTHHHHHHHHHHHHHHTT-SSEEEEE---TT-HH CS
                Ferrochelatase  82 laergidvkvylamrywePsiedaleelkadgvervvvlplyPqysasttgssleeleralkkkreapevrvirqfydhpg 162
                                   ++++  dv v+ a+++w Psi +++ +lk  g++++v +pl+  +s    +s+ + l++al+k++   ++++++   +   
  gi|13542124|ref|NP_111812.1|  68 FDQS-GDVDVFTAFKHWYPSIGEVVPDLK--GYDNIVSIPLFSFFSENVKASYYKPLAEALEKNDIRTKMEFVNGISNYDL 145
                                   *975.8***********************..************************************************** PP

                                   HHHHHHHHHHHHHTTS-HC.C-EEEEEEE--BHHHHT.TT-SHHHHHHHHHHHHHHHTTT-S-EEEEEE---SSS-BSSSB CS
                Ferrochelatase 163 yiealaesikealeelpeekkakllfsaHglPeravkkkgdpYqqqveetarlvaealglkeevelayqSrvGpeeWlePd 243
                                   +i ++++ i+e+ +    ++    lf aH+lP+    +  + Y   ++ ++  + + +gl++  + ++q   G e Wl+P+
  gi|13542124|ref|NP_111812.1| 146 FIPMWIHLIEEKEK----GD-SFYLFDAHSLPHPEN-E--EDYLFWLRYSTYKITQIMGLRS-SDFGFQG--GHEGWLGPS 215
                                   ***********954....45.89************7.3..36*******************9.*****96..8888***** PP

                                   HHHHHHHHCCC.-S-EEEE-TT-SS--HHHHIIIIIIIITTSTT..CCCEEE----TT-HHHHHHHHHHHHH CS
                Ferrochelatase 244 tddtleelaekgvkaivvvpigFvsDhlEtleeldiearelaeeaggekfvrvptlndspafiealadlvee 315
                                   + ++ ++++e   k+i+ vpi+F  DhlE+l++ld+e r+++ee g+ +++rvp++nds+ fi +l+++v +
  gi|13542124|ref|NP_111812.1| 216 IYNVYRKAKE---KKIIAVPISFLYDHLEILYDLDYEFRKKIEEDGY-SYERVPMPNDSAIFITLLERIVSS 283
                                   *****99999...67********************************.********************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2063.69
//
Query:       gi|13542125|ref|NP_111813.1|  [L=315]
Description: dolichol kinase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (315 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1094  (0.0610185); 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:                         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: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 2078.74
//
Query:       gi|13542126|ref|NP_111814.1|  [L=99]
Description: hypothetical protein TVN1295 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       547  (0.0305092); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 699.87
//
Query:       gi|13542127|ref|NP_111815.1|  [L=97]
Description: hypothetical protein TVN1296 [Thermoplasma volcanium GSS1]
Scores for complete sequence (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   92.7   0.2    1.3e-26   92.5   0.2    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 !   92.5   0.2   7.2e-31   1.3e-26       2      73 .]      13      84 ..      12      84 .. 0.99

  Alignments for each domain:
  == domain 1  score: 92.5 bits;  conditional E-value: 7.2e-31
                                  HHHHHHHHHHHHH.....TS---HHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTSTS CS
                        DUF357  2 YirlleealekvkiapdeesplgeaaeevlemaesYleDakyflekgdlvnAlasfsYaeGwLDagarlgll 73
                                  Yi+  e al+k++ia++e+s l++ ae+  +m++sY+eDak f++kgd++nA+as++Y++Gw+D+g+rlg++
  gi|13542127|ref|NP_111815.1| 13 YIEVEEAALSKLSIAVPERSFLRKFAEDSFKMIKSYFEDAKFFYAKGDIINAFASLNYSYGWIDSGVRLGIF 84
                                  9*********************************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 678.54
//
Query:       gi|13542128|ref|NP_111816.1|  [L=156]
Description: phosphoribosylcarboxyaminoimidazole carboxylase catalytic subunit [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.2e-64  213.7   4.8    9.1e-64  213.5   4.8    1.0  1  AIRC          AIR carboxylase
  ------ inclusion threshold ------
      0.057   13.3   0.0      0.067   13.0   0.0    1.3  1  Asp_Glu_race  Asp/Glu/Hydantoin racemase
       0.13   12.7   0.0        6.6    7.2   0.0    2.2  2  HEAT_2        HEAT repeats


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 !  213.5   4.8   1.5e-67   9.1e-64       1     147 [.       3     149 ..       3     150 .. 0.98

  Alignments for each domain:
  == domain 1  score: 213.5 bits;  conditional E-value: 1.5e-67
                                   EEEEEESSGGGHHHHHHHHHHHHHTT-EEEEEE--TTTSHHHHHHHHHHCHTTTEEEEEEEEESS--HHHHHHHHSSS-EE CS
                          AIRC   1 kVgiimGSdsDlevmkkaaeilkelgveyevrvvSahrtpeelleyaeeaeerglkviIagAGgaahLpgvvaslttlPVi 81 
                                   kV++imGS+sD+evmk+a+++l+e+gv++  +vvSahrtpe ++++a+ea+++g+++iIagAGgaahLpg+va++t+lPVi
  gi|13542128|ref|NP_111816.1|   3 KVAVIMGSSSDYEVMKAAIDTLNEFGVDVISKVVSAHRTPEFMMQFAKEAASSGIEAIIAGAGGAAHLPGMVAAMTPLPVI 83 
                                   69******************************************************************************* PP

                                   EEEE--STTCCHHHHHHHHT--TTS--EE-SSTHHHHHHHHHHHHHTTT-HHHHHHHHHHHHHHHH CS
                          AIRC  82 gvPvkskalkgldsllSivqmPsgvpvatvaigkaknAallAaqilalkdeelaekleeyreelke 147
                                   gvPv +k+l g+dsllSivqmPsgvpvatvaig++knAallA++il++k+++l +k++e++e++k+
  gi|13542128|ref|NP_111816.1|  84 GVPVPTKNLGGMDSLLSIVQMPSGVPVATVAIGNSKNAALLAIRILSIKYPDLMAKMSEFMESEKQ 149
                                   ************************************************************998765 PP

>> Asp_Glu_race  Asp/Glu/Hydantoin racemase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   1.1e-05     0.067      53     103 ..      39     110 ..       4     156 .] 0.68

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.1e-05
                                   .THH.HHHHHHHHHHCTTESEEEE--CHHHHHHHHHHHH-SSEEEECHHHH....................H CS
                  Asp_Glu_race  53 dpvl.klleaakkLekagadaiviaCnTahavadelqkkikiPvlgiveat....................a 103
                                   ++++ ++++ ak+ +++g++ai+  +  a  +   +++++++Pv+g++ +t                    +
  gi|13542128|ref|NP_111816.1|  39 HRTPeFMMQFAKEAASSGIEAIIAGAGGAAHLPGMVAAMTPLPVIGVPVPTknlggmdsllsivqmpsgvpV 110
                                   35666************************77777777***********999777776666555444444433 PP

>> HEAT_2  HEAT repeats
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0    0.0011       6.6      40      61 ..       8      30 ..       1      55 [. 0.80
   2 ?    3.4   0.0     0.017        99      20      48 ..     122     152 ..     114     155 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0011
                        HEAT_2 40 l.ededpavRraaaeaLgaigdp 61
                                  + +++d +v +aa+++L ++g +
  gi|13542128|ref|NP_111816.1|  8 MgSSSDYEVMKAAIDTLNEFGVD 30
                                  5578999************9964 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.017
                        HEAT_2  20 airaLg..rignpealpaLvellededpavR 48 
                                   a+ a+   +i+ p++++ + e++e+e+ +v 
  gi|13542128|ref|NP_111816.1| 122 ALLAIRilSIKYPDLMAKMSEFMESEKQRVL 152
                                   4444445579****************99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       612  (0.0341346); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.32s 00:00:00.84 Elapsed: 00:00:00.52
# Mc/sec: 907.00
//
Query:       gi|13542129|ref|NP_111817.1|  [L=361]
Description: translation factor (SUA5-related) [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-54  184.2   0.0    2.9e-54  183.3   0.0    1.5  1  Sua5_yciO_yrdC  Telomere recombination
    2.3e-22   80.0   0.0      4e-22   79.2   0.0    1.4  1  SUA5            Putative GTP-binding controlling metal-bindin
      0.007   16.6   0.3      0.022   15.0   0.3    1.9  1  Ish1            Putative stress-responsive nuclear envelope p


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 !  183.3   0.0   4.9e-58   2.9e-54       1     179 []      22     197 ..      22     197 .. 0.98

  Alignments for each domain:
  == domain 1  score: 183.3 bits;  conditional E-value: 4.9e-58
                                   HHHHTTSEEEEE-SSSEEEEEETTSHHHHHHHHHHHTSHCCC--EEEESSCCCCCCCC-TC--HHHHHHHHCT-SSSCEEE CS
                Sua5_yciO_yrdC   1 ealrkGgivaiptetvYgLacdatneeaverlreiKgrpsdkplavlvasledlkklaeseveeealkllerfwPGpitll 81 
                                   eal+ Gg v++ptetvYgL+++a n+ea+++++ +Kgrpsd+pl+v+++++++l+++ + +v+ee  ++l+++wPGp+t++
  gi|13542129|ref|NP_111817.1|  22 EALKHGGTVVFPTETVYGLGANAMNDEACKKIFIAKGRPSDNPLIVHISDMDQLENFSK-NVKEEYKAILKELWPGPLTVV 101
                                   689*******************************************************9.********************* PP

                                   EE..E-TS-HHHHTTTTEEEEEE-SSHHHHHHHHHCTS-EEEEES-STTS-S-SSHHHHHHHC-TTSECB-SS---SSS-- CS
                Sua5_yciO_yrdC  82 lkrskeklpkevapglktvGvrlPdtplarlLlealgeplvaTSanlsgepsitdaeeveeelgeivdlildggeiavgvd 162
                                   +++ +  +p+ v+++l tv++r+Pd  +ar+L++ +g p++a+San+s++psitd +++ + l+++vd+i+d+g+++ g++
  gi|13542129|ref|NP_111817.1| 102 VEKANG-IPDTVTAKLPTVAIRMPDDSIARNLIDMAG-PIAAPSANISTKPSITDSKDAIRFLDGRVDVIIDAGKVKFGIE 180
                                   **7444.****************************88.******************************************* PP

                                   -EEEETTSSTSSECEXX CS
                Sua5_yciO_yrdC 163 stVvdltegkpkilRrG 179
                                   st++dlt++++++lR+G
  gi|13542129|ref|NP_111817.1| 181 STIIDLTQDPVRLLRPG 197
                                   ***************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 !   79.2   0.0   6.8e-26     4e-22       3     133 ..     201     331 ..     199     332 .. 0.72

  Alignments for each domain:
  == domain 1  score: 79.2 bits;  conditional E-value: 6.8e-26
                                   HHHHHHHS-..--..........-------------S-SSEEEEE--GGGHHHH.....HHHHHTTS-EEEEEEGGGTGGT CS
                          SUA5   3 leeleevld..avek......keekpraPGmkyrHYaPkapvvlveaeeeeeaakeekleekkksgkkvgvlatseskeaa 75 
                                   +e+le +++  +v+k      + +   +PGmkyrHY+P+ ++ l+++ e  e+        k++  ++  +++t+e ++  
  gi|13542129|ref|NP_111817.1| 201 VEDLEPLFGkiTVDKvalgkaEAKVAITPGMKYRHYSPNKKIFLCKDREVVESL-------KEELPNNGVLMCTEEVSQGI 274
                                   6667766532222223334334455599****************9888755443.......44445554556666666666 PP

                                   SEEEEE..E-TT-HHHHHHHHHHHHHHHHHS--SEEEEE----STTHHHHHHHHHHHT CS
                          SUA5  76 ssvlslslgsrsdleeaarnLFaaLrelDeegvdlilvegvpeeglglAvmnRLrkAA 133
                                   s ++++ +g++sdl ++a+nLF+ + elD++  ++ ++  ++e+g+glA+mnR+rkA+
  gi|13542129|ref|NP_111817.1| 275 STNKII-VGRDSDLYSVAHNLFSSFIELDDSSYNYGVIIPFEEKGIGLAIMNRIRKAS 331
                                   666666.7*********************8777766666689***************8 PP

>> Ish1  Putative stress-responsive nuclear envelope protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.3   3.7e-06     0.022       5      20 ..     337     352 ..     337     360 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.7e-06
                          Ish1   5 SdsdLkkWLdshGipv 20 
                                   S ++Lk++Ld++Gi +
  gi|13542129|ref|NP_111817.1| 337 SSEELKEYLDEYGISD 352
                                   789***********94 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (361 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       496  (0.0276647); 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:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.48
# Mc/sec: 2279.05
//
Query:       gi|13542130|ref|NP_111818.1|  [L=783]
Description: aminopeptidase N [Thermoplasma volcanium GSS1]
Scores for complete 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-79  266.0   0.2    3.6e-79  265.4   0.2    1.3  1  Peptidase_M1    Peptidase family M1 domain
    1.5e-36  126.3   0.4    5.1e-36  124.6   0.1    2.0  2  Peptidase_M1_N  Peptidase M1 N-terminal domain
    6.2e-32  111.4   0.1    8.7e-32  110.9   0.1    1.2  1  ERAP1_C         ERAP1-like C-terminal domain
  ------ inclusion threshold ------
      0.098   12.4   0.0          4    7.1   0.0    2.6  2  PYC_OADA        Conserved carboxylase domain


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 !  265.4   0.2   7.9e-83   3.6e-79       1     218 []     200     416 ..     200     416 .. 0.98

  Alignments for each domain:
  == domain 1  score: 265.4 bits;  conditional E-value: 7.9e-83
                                   HHHHHHHHHHHHHHHHHTS--SSSEEEEEEESSTTSSEEEETTEEEEEGGGC-SSTTTS-HHHHHHHHHHHHHHHHHHHBT CS
                  Peptidase_M1   1 yalevtkkllefleeyfkvpYplpkldlvalpdfsagAMEnwglityreelllvdpenssesdkrsvaeviaHElaHqWfG 81 
                                   y ++++k+ +ef+e yf++pY+lpk++l+ +p+f agAMEnwg+it+re +l+++ e s +  k+++a +iaHE+aHqWfG
  gi|13542130|ref|NP_111818.1| 200 YPIDIAKRSIEFYEGYFGIPYALPKMHLISVPEFGAGAMENWGAITFREIALMAT-EDSGSLMKQNAAITIAHEIAHQWFG 279
                                   56899*************************************************9.66777799***************** PP

                                   TTEEESSGGGGHHHHHHHHHHHHHHHHHHSCCCHCHHHHHHHCHHHHHHHHTSTTHHHSSGG-GSHHHHHHTSSHHHHHHH CS
                  Peptidase_M1  82 nlVtmkwWddlwLnEGfatyleylildklepewevseqllleeveealsedaldeshpitqevekpseidevFdsiaYeKG 162
                                   +lVtmkwW+dlwLnE+fat+++y+ +d+++++w+v ++++ +e+  al +d+l+++hpi++ v++p+ei+++Fd+i+Y KG
  gi|13542130|ref|NP_111818.1| 280 DLVTMKWWNDLWLNESFATFMSYKTVDSFSKQWDVFSDFIKSETGGALRSDSLKNTHPIEVDVKDPDEISQIFDEISYGKG 360
                                   ********************************************************************************* PP

                                   HHHHHHHHHHCTHHHHHHHHHHHHHHCTTEEE-HHHHHHHHHHCCCSCHHTHHHHH CS
                  Peptidase_M1 163 asllrmlekllgeevFqkglksYlkefkyknaetedlwdaleealnkdisevmdtw 218
                                   as+lrm+e+++g e+F+kg+++Ylke++y+nae +dlw+a+e++++k ++++m+ w
  gi|13542130|ref|NP_111818.1| 361 ASILRMIEDYVGAEDFRKGISKYLKEHAYGNAEGSDLWNAIETESGKPVNRIMEAW 416
                                   ******************************************************99 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 !  124.6   0.1   1.1e-39   5.1e-36       3     186 .]       6     168 ..       4     168 .. 0.90
   2 ?   -1.2   0.0      0.43   1.9e+03      86     111 ..     471     496 ..     437     505 .. 0.74

  Alignments for each domain:
  == domain 1  score: 124.6 bits;  conditional E-value: 1.1e-39
                                   EEEEEEEEEETTTTEEEEEEEEEEEESS-ECEEEEEESSEEEECEEEEECTTCTCEEEEEEEECTTTTCEEEEECCEEETT CS
                Peptidase_M1_N   3 ehYdldlkidlkektfkGsvtitlqlkeatseivldakdlkiksvslsaevksesvkidfkieqkdeelltiklkeslqqt 83 
                                   e+Ydl+++ dl+e+t++G+ +i+l+ +  ++e+vld+ +l i      ++vk +++ +df +++k+   l+i+ +     +
  gi|13542130|ref|NP_111818.1|   6 EEYDLTFDFDLSEFTYRGKEKIKLSGE--ANELVLDSVRLSI------DSVKLNGSAVDFDVNDKA---LRIESRI----K 71 
                                   68********************99888..9************......888888999998866655...5566555....7 PP

                                   CEEEEEEEEEEE-BSSSSEEEEEEEEETSCEEEEEEEE-TTTTGGGTS-B--STTSEBEEEEEEEEETTSEEEESSECCCE CS
                Peptidase_M1_N  84 skytLeieyegelndklaGlykstYtdkgekkvvvvTqfeatdARsafPCfDePsvKAtftisikapkeetalSnmpeees 164
                                   s   ++i++ ++++d+l+Gly s+     ++  +++Tqfe+t AR afPC+D P++KA f+i++  +k++ a+Snmp++++
  gi|13542130|ref|NP_111818.1|  72 SGDVVDIDFHAKVSDTLMGLYLSK----TREGTMITTQFESTGARMAFPCIDHPAYKAVFSITLVIDKDYDAISNMPVKKV 148
                                   78899****************877....455679*********************************************77 PP

                                   EEETTCEEEEEEEEEESBEGGG CS
                Peptidase_M1_N 165 eklengqkiteFeqtpkmstYL 186
                                   e+   ++ki+eFe+tp+mstYL
  gi|13542130|ref|NP_111818.1| 149 ETS--DRKIVEFEKTPRMSTYL 168
                                   766..589*************9 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.43
                                   EEEEEEEEEE-BSSSSEEEEEEEEET CS
                Peptidase_M1_N  86 ytLeieyegelndklaGlykstYtdk 111
                                    ++ i+   +ln +  G+y+  Y ++
  gi|13542130|ref|NP_111818.1| 471 DEVYIDEMLKLNANNSGFYRVMYDND 496
                                   555666667899999****9998764 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 !  110.9   0.1   1.9e-35   8.7e-32       2     314 ..     479     774 ..     478     775 .. 0.83

  Alignments for each domain:
  == domain 1  score: 110.9 bits;  conditional E-value: 1.9e-35
                                   EEESGGG-SSSEEEE-HHHHHHHHHHHHGGGS-HHHHHHHHHHHHHHHHTTSS-HHHHHHGGG.GGGG--SHHHHHHHHHH CS
                       ERAP1_C   2 vllNdddtGyyrVnYdeeslaalleqllskklspldRaglisdafalaragelsaadlldlllgylanEtdylvwsqalsq 82 
                                   ++lN++ +G+yrV Yd + ++++++  l+k +s ld+ gl++d +a+  +g+ls+ ++++ ++++l n++d+lv++++ sq
  gi|13542130|ref|NP_111818.1| 479 LKLNANNSGFYRVMYDNDTFNTVIS-SLDK-FSNLDKWGLLNDMYAFLVSGRLSVNEYVERIKNFL-NDEDHLVVEEIASQ 556
                                   69***********************.5555.***************999****************8.99999********* PP

                                   HHHHHHHHTTSTTHHHHHHHHHHHHHHHHHHHHH.T.TTS-HHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHCSTT-S- CS
                       ERAP1_C  83 latlksllsadplyaalkaflrklleplaeklgw.epgeshldaqlrslllsaacaagdpevveearklfkawlegddlip 162
                                   l++l+ +   ++  +   +++++ l + +++lg  ++ge++  ++lr ++++ +++ + ++  +e+  +f+   e     +
  gi|13542130|ref|NP_111818.1| 557 LTSLYLIK-PSS--QVVYQLAKDYLRNQVQRLGTkKKGEDDKISKLRGIVYQDLVTVD-EDFAKELSPQFASLSE-----D 628
                                   ***98776.333..355567777777888888884588****************6555.8899999999999944.....7 PP

                                   HHHHHHHHHHHHHHS-HHHHHHHHHHHHC-SSHHHHHHHHHHHCC-S-HHHHHHHHHHCTTT..S-GGGHHHHHHHH.HST CS
                       ERAP1_C 163 pdlrwavycalaanggeaewdallerykdtsapsekeaalralaatpdpellerllnfvlesdevrnqdlrallaglannp 243
                                   pdl  a   a+ a+   +++++l++  ++ ++ + + ++++a++ + + + l  ++ ++ +++++++qd+ ++++ + +np
  gi|13542130|ref|NP_111818.1| 629 PDLALA--KAV-AKARTDGLNELIDAANKYTDDEIRVRVIAAMGWCSK-DQLSTIFSLI-DNGTIKKQDMLYVFSFVVTNP 704
                                   998654..333.33366888888888777676366*********8655.7889999999.79************988778* PP

                                   THHHHHHHHHHHCHCCHHHHTS....STSCHHHHHHHHHTT--SHHHHHHHHHHHCHTT--GGGHHHHHHHHHHH CS
                       ERAP1_C 244 egrellwefvkenwdalakrws....ggeildrivkgllpgftseeelaeieaffadkdtpglrrtlkqaletvr 314
                                    gr+    f+ +n+d++++ ++    g+ + +ri++g++p     e+++ei+a  ++   p+++ +++++let++
  gi|13542130|ref|NP_111818.1| 705 SGRD----FFFQNIDKIVSLMEhafeGTGYTSRILEGSIPYIG-LEKYEEIKAKASQIRSPSYNVGIDKGLETLE 774
                                   ***9....88899999999775444255599*********887.99******97555589999999999999876 PP

>> PYC_OADA  Conserved carboxylase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0     0.023     1e+02      70     106 ..     195     230 ..     186     392 .. 0.81
   2 ?    7.1   0.0    0.0009         4      39     124 ..     555     635 ..     547     666 .. 0.67

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.023
                                   ...TS.TTSS--HHHHHHHTTSS---SS---HHHHHH CS
                      PYC_OADA  70 dvleegrykdipdsvvdllkGelGkppggfpeelvkk 106
                                   d++ +    di++  +++ +G++G p++ ++ +l++ 
  gi|13542130|ref|NP_111818.1| 195 DIKSK-YPIDIAKRSIEFYEGYFGIPYALPKMHLISV 230
                                   55554.668999**************99888877765 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0009
                                   HHTT----STTHHHHHHHHHHHHHHH........TS.TTSS--HHHHHHHTTSS---SS---HHHHHHHHT.-----S-GG CS
                      PYC_OADA  39 kllGdivkVTPsSkvvgdlAvfnvlnklteedvleegrykdipdsvvdllkGelGkppggfpeelvkkvlkgeepitsrpa 119
                                    +l  + ++ PsS+vv++lA   + n     +v   g +k+  d+ ++ l+G   +  + ++e++ k+ + +   ++++p 
  gi|13542130|ref|NP_111818.1| 555 SQLTSLYLIKPSSQVVYQLAKDYLRN-----QVQRLGTKKKGEDDKISKLRGIVYQDLVTVDEDFAKELSPQFASLSEDPD 630
                                   5566677888**********999999.....66666666777777777777777777777777776666655555555555 PP

                                   GG--- CS
                      PYC_OADA 120 dslep 124
                                     l++
  gi|13542130|ref|NP_111818.1| 631 LALAK 635
                                   55555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (783 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       617  (0.0344135); 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:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.74u 0.32s 00:00:01.06 Elapsed: 00:00:00.49
# Mc/sec: 4839.35
//
Query:       gi|13542131|ref|NP_111819.1|  [L=507]
Description: Na+/panthothenate symporter permease [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (507 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1276  (0.0711696); 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:                         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: 0.67u 0.34s 00:00:01.01 Elapsed: 00:00:00.52
# Mc/sec: 2927.39
//
Query:       gi|13542132|ref|NP_111820.1|  [L=66]
Description: hypothetical protein TVN1301 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.4e-13   49.3   3.1      4e-13   49.1   3.1    1.1  1  DUF3311          Protein of unknown function (DUF3311)
  ------ inclusion threshold ------
       0.76   10.2   4.6         12    6.4   0.7    2.2  2  FeoB_associated  FeoB-associated Cys-rich membrane protein


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 !   49.1   3.1   4.4e-17     4e-13       1      48 [.      10      56 ..      10      65 .. 0.92

  Alignments for each domain:
  == domain 1  score: 49.1 bits;  conditional E-value: 4.4e-17
                       DUF3311  1 vlllvpvlvalllvpfynrvdpvllGlPffywwqllwvllasvvtwla 48
                                  +ll++p +va  ++p+ynrv+p + Gl ffyw+q+lw+ ++++++ +a
  gi|13542132|ref|NP_111820.1| 10 ILLIIP-FVAYFAIPTYNRVNPAIGGLSFFYWYQTLWLAISALLFGIA 56
                                  6899**.************************************99776 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 ?    6.4   0.7    0.0013        12       2      17 ..       5      22 ..       4      28 .. 0.73
   2 ?    5.8   0.2     0.002        18       5      22 ..      48      65 ..      44      66 .] 0.85

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0013
               FeoB_associated  2 tiIVgliiaa..avafvi 17
                                  +iIVg+++++  +++f+i
  gi|13542132|ref|NP_111820.1|  5 DIIVGILLIIpfVAYFAI 22
                                  89***9999543666665 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.002
               FeoB_associated  5 Vgliiaaavafvirrlik 22
                                  + +++++++a++i + +k
  gi|13542132|ref|NP_111820.1| 48 ISALLFGIAAYIIDKGVK 65
                                  7899********988777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       541  (0.0301746); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.29s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 441.98
//
Query:       gi|13542133|ref|NP_111821.1|  [L=763]
Description: Alpha-glucosidase [Thermoplasma volcanium GSS1]
Scores for complete 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-135  451.5   2.5   4.9e-135  451.1   2.5    1.1  1  Glyco_hydro_31   Glycosyl hydrolases family 31
      2e-20   72.9   0.1    5.9e-20   71.4   0.1    1.9  1  Gal_mutarotas_2  Galactose mutarotase-like


Domain annotation for each model (and alignments):
>> Glyco_hydro_31  Glycosyl hydrolases family 31
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  451.1   2.5  5.4e-139  4.9e-135       1     440 []     237     669 ..     237     669 .. 0.94

  Alignments for each domain:
  == domain 1  score: 451.1 bits;  conditional E-value: 5.4e-139
                                   EEEE-SSHHHHHHHHHHHH-------GGGGSEEEE-TT--SHHHHHHHHHHHHHTT--EEEEEESCGGSBTTCCTB-.TTT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                Glyco_hydro_31   1 yvflGptpkevvkqyteltGrpalpPrwalGfhqsrygykdeeeveevvdkfreagiPldvivlDidymdkrkdftwdker 81 
                                   yv++G+ +k++ ++++e+tG+p  pP+wa+Gf+qsry y +++ev+++vd+f+e giPl++i+lDidymd+ k+ft++++r
  gi|13542133|ref|NP_111821.1| 237 YVITGD-IKSIYSKFSEITGKPYRPPYWAFGFQQSRYSYMSSAEVRSIVDRFNELGIPLSAIYLDIDYMDEFKVFTFNSDR 316
                                   99****.************************************************************************** PP

                                   SS-HHHHHHHHHHTT-EEEEEE-SEE.E.-TTSHHHHHHHHTTSBECCCCCS..TCEC.TSSEEEEB-TTSHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxx.xxxxxxxxxxxxxxxxxxxxxx RF
                Glyco_hydro_31  82 Fpdpkemvdelhekgvklvvivdpaiskqeeeyeafdegkekgvflknkdgs..ykgk.wpgstafpDftnpearewwkke 159
                                   F d k+++++l e+gv+l++i++p+++  e++y+ +de++++g+f+k +dg+  y+   wp ++afpDf ++++reww+k+
  gi|13542133|ref|NP_111821.1| 317 FWDVKDLTKYLGERGVRLITIMEPNVKM-EPGYTIYDEAVKNGYFIKYPDGNifYA-PvWPLMAAFPDFSRNDVREWWGKK 395
                                   **************************65.89*********************8444.46********************66 PP

                                   HHHHHCTCT--EEEE-STTTB.SCCCCHH.HHCCCTSCETTCCHHHHCCCHHHHHHHHHHHHHHHHTTTST-EEEESSEET CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                Glyco_hydro_31 160 lkkflldlgvdglwiDmnepsnfeegsds.eekeaketkaagshydvhnlygllmakatyeglkekkpkkrpfiltRstfa 239
                                    ++f+ + gv+g+w Dmnep++f+ + d+    +a   +++gsh +vhnl+g++m ka y++l+++   +rpfil+Rs++a
  gi|13542133|ref|NP_111821.1| 396 -YDFMKKNGVSGFWHDMNEPAIFVAWGDNsMALSA--AQSNGSHSEVHNLFGYYMDKAAYDHLSKT---ERPFILSRSGWA 470
                                   .7898889****************99986444433..5566669******************9888...7*********** PP

                                   TGGGCTEEE--S-BSSHHHHHHHHHHHHHHHTTT--SEEEECT-SG.HCHHHHHHHHHHHHTTSSSEEE--STTSS--SHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                Glyco_hydro_31 240 GsqryaahWsGdnassWeslresipallsfslsGvpfwgaDigGFe.ntteelyaRWvqlGafsPffrnHsskdakrqepw 319
                                   G  rya +W+Gd+++sW+++++++ ++l++s sG++++g+DigGF  ++++el++RW+q ++f+P+fr+Hs+k++kr+epw
  gi|13542133|ref|NP_111821.1| 471 GISRYAWIWTGDTETSWKEMKQNLLTILHMSASGISLTGCDIGGFVgSPDAELFIRWLQSAIFYPLFRVHSNKKSKRREPW 551
                                   *********************************************9899******************************** PP

                                   HHCHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHH---SEE-HHHH-TT-CCCCC--S-EEETTTEEE----STT-SEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                Glyco_hydro_31 320 afgeeveeaarkaielRyrLlPylYtlfyeahetglpvvrplflefpedektfdiddqfmfGdsLLvaPvleeeatsvevy 400
                                    fge++  ++r++i+lR+++lP +Y+ +  ++ tg p++rp+++   +++++  +dd+++fGds+LvaP+++e +ts+ v 
  gi|13542133|ref|NP_111821.1| 552 EFGEKYLGIIRDIIKLRHSFLPQIYSEAISSSITGIPMIRPVYWY-SSNPDMLLVDDEYLFGDSILVAPIFSEHSTSRIVK 631
                                   ******************************************996.556677789****************999******* PP

                                   E-SSEEEETTT--EEESSEEEEEE--TTSS-EEEETTEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                Glyco_hydro_31 401 LPggkWydfwtgekyeggqtveltapldeiplfvraGaIi 440
                                   LP g Wy+++++ek+ g+   +++apl+ ip+++r+G+Ii
  gi|13542133|ref|NP_111821.1| 632 LPPGLWYNLYSDEKVFGEI--KVEAPLNMIPIYIRSGSII 669
                                   **77*****9999999955..58888989**********9 PP

>> Gal_mutarotas_2  Galactose mutarotase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.4   0.1   6.6e-24   5.9e-20       2      66 .]     150     216 ..     149     216 .. 0.96

  Alignments for each domain:
  == domain 1  score: 71.4 bits;  conditional E-value: 6.6e-24
                                   -EEEEEES-SS-SS-TTEEEEE-----TS-HCC.CTS-SCEEEEEEEE..TCEEEEEE--SSSEEEE CS
               Gal_mutarotas_2   2 ehvyGlGEkagplnlrgtryrlwntdafgyeaessdplYgsiPfmisl..segyGvfvdnpaetwfD 66 
                                   + + GlGEkagp+nlrg++yrlwn+da g+++++sdplY +iP+++ l  + +y +f+ n++++++D
  gi|13542133|ref|NP_111821.1| 150 DLFSGLGEKAGPINLRGHVYRLWNHDAKGSYGPDSDPLYLNIPVLLHLhdDVSYLIFFENAGDATVD 216
                                   6789******************************************88**888*************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (763 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.69u 0.30s 00:00:00.99 Elapsed: 00:00:00.48
# Mc/sec: 4785.83
//
Query:       gi|13542134|ref|NP_111822.1|  [L=376]
Description: RNA helicase [Thermoplasma volcanium GSS1]
Scores for complete sequence (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  161.9   0.0    2.3e-47  161.0   0.0    1.4  1  DEAD        DEAD/DEAH box helicase
    3.6e-27   94.9   0.1    1.2e-23   83.6   0.0    2.4  2  Helicase_C  Helicase conserved C-terminal domain
    0.00063   19.7   0.1     0.0016   18.4   0.1    1.7  1  Flavi_DEAD  Flavivirus DEAD domain
      0.005   16.9   0.0      0.016   15.2   0.0    1.9  1  ResIII      Type III restriction enzyme, res subunit
  ------ inclusion threshold ------
      0.035   13.4   0.1      0.057   12.7   0.1    1.3  1  CMS1        U3-containing 90S pre-ribosomal complex subunit


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 !  161.0   0.0   6.4e-51   2.3e-47       1     174 [.      29     192 ..      29     194 .. 0.96

  Alignments for each domain:
  == domain 1  score: 161.0 bits;  conditional E-value: 6.4e-51
                                   -HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD   1 tdiQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvlli 81 
                                   t++Q+ aip++l g d++v+ +TGsGKT+a+lip++++     +++g +ali+ PtreLa q+++  + ++k  ++r++++
  gi|13542134|ref|NP_111822.1|  29 TEVQSMAIPIALAGSDLVVRSKTGSGKTAAYLIPIINNT---AKEKGIRALILLPTRELAVQVAKVSEALGKRSGIRTVVV 106
                                   789*********************************888...579************************************ PP

                                   ETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTTSTTTSEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD  82 iggvaardqlskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqitcdgklqrqv 162
                                   +ggv+ ++q++ + +g++i+vgtpgr +dl+++g ln+++v+++VlDEad++ld+gf ++i++i+n l       + +rq 
  gi|13542134|ref|NP_111822.1| 107 YGGVSINKQIELILRGANIIVGTPGRTLDLIDRGILNFDKVSYFVLDEADEMLDMGFIEDIKKIINVL-------PVERQS 180
                                   *************999****************************************************.......67789* PP

                                   EEEESSBSHHHH CS
                                   xxxxxxxxxxxx RF
                          DEAD 163 ivlSATlpkdvk 174
                                    ++SAT+p+++ 
  gi|13542134|ref|NP_111822.1| 181 FLFSATIPSEII 192
                                   ********7765 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 !    9.0   0.0   0.00049       1.7       7      60 ..      61     120 ..      55     151 .. 0.81
   2 !   83.6   0.0   3.3e-27   1.2e-23       2     111 .]     229     336 ..     228     336 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00049
                                   HHHH..HHTTTTSEEEEEESSHH...HHHH.HHHHHHHTTSTEEEESTTSTHHHHHHHHH CS
                    Helicase_C   7 lell..kleeeggkilifvntid...rlek.vklllekkgikvavlhgelpqnereeile 60 
                                   + ++  + +e+g ++li ++t++   ++ k  + l +++gi+++v++g  + n+++e + 
  gi|13542134|ref|NP_111822.1|  61 IPIInnTAKEKGIRALILLPTRElavQVAKvSEALGKRSGIRTVVVYGGVSINKQIELIL 120
                                   4455556789999**********8664444677888888**************9999875 PP

  == domain 2  score: 83.6 bits;  conditional E-value: 3.3e-27
                                   HHHHHHHHHHHTTTTSEEEEEESSHHHHHH..HHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSS CS
                    Helicase_C   2 kleallellkleeeggkilifvntidrlek..vklllekkgikvavlhgelpqnereeileqfnkgesdvLiatdvaerGi 80 
                                   kl++l  ++  + + +k++if++t+  +++    l+  ++g  ++++hg+l+q +re++l +f++   ++L+at+va+rG+
  gi|13542134|ref|NP_111822.1| 229 KLRTLFSYI-DKYKPEKSIIFSRTKAGANMiyEALI--NHGQDAVIMHGDLTQAQREKALYRFKN-FGRFLVATNVAARGL 305
                                   556666666.78999***********7755534555..789**********************54.556************ PP

                                   TSTTESEEEESSSSSSHHHHHHHHTTSSSTT CS
                    Helicase_C  81 dipkvnlVinfdlprnvtsyiqriGRtgRag 111
                                   di +++ +in+d+p++++ y++r+GRt+R+g
  gi|13542134|ref|NP_111822.1| 306 DIGGISDIINYDVPDDPRVYVHRVGRTARMG 336
                                   *****************************86 PP

>> Flavi_DEAD  Flavivirus DEAD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.1   4.5e-07    0.0016       8      54 ..      46      96 ..      41     114 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 4.5e-07
                                  EEE--TTS-TTTTHHHHHHHH.HHHTT--EEEEESSH...HHHHHHHHHTT CS
                    Flavi_DEAD  8 vldlhPGaGktrkvlpelvke.aierrlrtlvLaPtr...vvlaemeealk 54
                                  v+  + G+Gkt  +l  ++++ a e+ +r+l+L Ptr   v +a ++eal 
  gi|13542134|ref|NP_111822.1| 46 VVRSKTGSGKTAAYLIPIINNtAKEKGIRALILLPTRelaVQVAKVSEALG 96
                                  677889******999888876156788**********55455666777775 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   4.4e-06     0.016      27      72 ..      45      90 ..      27     189 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 4.4e-06
                                  EEEEESTTSTHHHHH.HHHHHHH-S.....-EEEEESSHHHHHHHHH CS
                        ResIII 27 glikmaTGtGKTlva.aklierllkkgkeekflflvprkslleqtle 72
                                  +++   TG+GKT  + + +i + +k++++ ++l+l p+++l  q  +
  gi|13542134|ref|NP_111822.1| 45 LVVRSKTGSGKTAAYlIPIINNTAKEKGI-RALILLPTRELAVQVAK 90
                                  567889*********88899998888776.***********999865 PP

>> CMS1  U3-containing 90S pre-ribosomal complex subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   1.6e-05     0.057     179     209 ..     124     154 ..     110     176 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.6e-05
                          CMS1 179 giavGtpgRildLleeeslsvdeLkrivlDa 209
                                    i vGtpgR ldL++ + l+ d++ + vlD 
  gi|13542134|ref|NP_111822.1| 124 NIIVGTPGRTLDLIDRGILNFDKVSYFVLDE 154
                                   5789*************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (376 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); 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:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 2570.25
//
Query:       gi|13542135|ref|NP_111823.1|  [L=396]
Description: acetyl-CoA acetyltransferase [Thermoplasma volcanium GSS1]
Scores for complete 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-66  222.1   0.0    1.5e-65  221.1   0.0    1.5  2  Thiolase_N       Thiolase, N-terminal domain
    2.5e-47  159.6   0.5    7.6e-47  158.0   0.2    1.9  2  Thiolase_C       Thiolase, C-terminal domain
    4.1e-06   26.5   2.1    7.8e-06   25.6   0.4    2.2  3  ketoacyl-synt    Beta-ketoacyl synthase, N-terminal domain
    0.00058   18.7   0.0     0.0024   16.6   0.0    1.8  2  SpoVAD           Stage V sporulation protein AD (SpoVAD)
     0.0013   18.8   0.5     0.0051   16.9   0.1    2.2  2  ACP_syn_III_C    3-Oxoacyl-[acyl-carrier-protein (ACP)] synth
  ------ inclusion threshold ------
       0.04   14.0   0.7        2.3    8.3   0.2    3.6  3  Ketoacyl-synt_C  Beta-ketoacyl synthase, C-terminal domain


Domain annotation for each model (and alignments):
>> Thiolase_N  Thiolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  221.1   0.0   5.1e-69   1.5e-65       1     260 []       6     266 ..       6     266 .. 0.92
   2 ?   -2.6   0.0      0.94   2.8e+03      52      54 ..     326     328 ..     299     387 .. 0.55

  Alignments for each domain:
  == domain 1  score: 221.1 bits;  conditional E-value: 5.1e-69
                                   EEEEEEEEE--EET......TSTTTTS-HHHHHHHHHHHHHHHHTS-GGGCCEEEEEHSSCTTSTSC.HHHHHHHHTTS-T CS
                    Thiolase_N   1 vvivsaartpigkf......ggslkdlsaeeLlaealkallekagvdpeevdevivGnvlqagegqn.iarqaalkagipe 74 
                                   v++v+ +rt++ ++      + ++++l+++e  a++++ +++++g+ pee+++vi G+ lq+ e+++   r+  l a++p+
  gi|13542135|ref|NP_111823.1|   6 VYLVDFKRTAFSRSrpndpeRDVFNSLRMDEAMAKLINIVIDETGIRPEEINDVITGCALQQDENWTyGGRHPILLANLPD 86 
                                   678999999998752222225799*******************************************899*********** PP

                                   TSEEEEEEHGGGHHHHHHHHHHHHHHTTSHSEEEEEEEEESTTS-EEETCTTTTGGSSSSEEEEEHHHHHHTEETTTTSEH CS
                    Thiolase_N  75 evpavtvnkvcsSglkavalaaqsiaageadvvvagGvEsmsnaptaestdvrsglklgdekakdllipdgladafneehm 155
                                   +vp ++++++csS+l+a++ +a +i++g+ad+v+agG E+m+++p+++s  +  ++kl    + + + +d    + +++ m
  gi|13542135|ref|NP_111823.1|  87 NVPGMALDRACSSSLNAITIGAMEIMTGNADIVMAGGYEHMTHVPMSNSPFLKPNVKLLV--RPEYMHYD----MNTGYSM 161
                                   ************************************************966665555544..44555555....7899*** PP

                                   HHHHHHHHHHHT--HHHHHHHHHHHHHHHHHHHHTTTTTTTBE-EEEEESSSEEEE-S-TTS-TT--HHHHHTS-BSSSTT CS
                    Thiolase_N 156 GltaenlakkykisReeqdefAvkshqkaaaaqkagkFkdeivPvkvkgkkgkktvdkdeairsevtaekLaklkpaFkke 236
                                   Gltae+la  + i Ree d++A++shq a++a ++g Fk eivP++v+   ++k++d+d+ ir+++++e+++kl+paFk++
  gi|13542135|ref|NP_111823.1| 162 GLTAEKLASLHHIGREEMDQYALRSHQLASKALDDGYFKGEIVPMEVEIGGETKIIDSDQSIRKNTSLEEMQKLRPAFKDD 242
                                   *************************************************8888**************************** PP

                                   SS-BTTSB--BEEEEEEEEEEEHH CS
                    Thiolase_N 237 GtvtAgnasqisDGaaavllmses 260
                                   G +tAgn+s+++ Ga+  llmse+
  gi|13542135|ref|NP_111823.1| 243 GVITAGNSSPLNAGASLTLLMSEK 266
                                   *********************985 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.94
                                   HSS CS
                    Thiolase_N  52 nvl 54 
                                    vl
  gi|13542135|ref|NP_111823.1| 326 VVL 328
                                   222 PP

>> Thiolase_C  Thiolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.67     2e+03      46      70 ..      33      57 ..      27      66 .. 0.69
   2 !  158.0   0.2   2.5e-50   7.6e-47       1     123 []     273     395 ..     273     395 .. 0.99

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.67
                                  EE--SBHHHHHHHHHHHT--GGGBS CS
                    Thiolase_C 46 EinEAFaaqaLavakaldldlekvN 70
                                   ++EA a  +  v+ + ++ +e +N
  gi|13542135|ref|NP_111823.1| 33 RMDEAMAKLINIVIDETGIRPEEIN 57
                                  5677777777777777777777777 PP

  == domain 2  score: 158.0 bits;  conditional E-value: 2.5e-50
                                   ---SEEEEEEEEEE--GGGGGGHHHHHHHHHHHHHT--GGGESEEEE--SBHHHHHHHHHHHT--GGGBSTT--HHHH-B- CS
                    Thiolase_C   1 lkplakirsyaevgvdpeilglgPayaikkvlkkagltvedidlfEinEAFaaqaLavakaldldlekvNvnGGaialGHP 81 
                                   lkpl++i+s+  +gvdp+i+g gP++a++k+l kag++vedid++EinEAFa+++L ++k+l+++++kvN++GG i++GHP
  gi|13542135|ref|NP_111823.1| 273 LKPLSRIVSFGWAGVDPSIMGEGPVPATQKALAKAGMKVEDIDYWEINEAFAVVVLNAMKELGIEENKVNIHGGGISIGHP 353
                                   589****************************************************************************** PP

                                   TTTHHHHHHHHHHHHHHHCTTSEEEEEEEETTTEEEEEEEEE CS
                    Thiolase_C  82 lGasGaRivvtllselkkeggklgvaalCigggqgvalviek 123
                                   lGa+GaRi+ tl + l+++++++gva+lC gggqg ++++e+
  gi|13542135|ref|NP_111823.1| 354 LGATGARIAGTLSRILNEKQAEYGVATLCVGGGQGYSVIFER 395
                                   ***************************************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 !   25.6   0.4   2.6e-09   7.8e-06     168     207 ..      90     129 ..      88     135 .. 0.92
   2 ?   -3.9   0.0       2.7     8e+03     225     240 ..     187     202 ..     170     202 .. 0.58
   3 ?   -1.0   0.0      0.36   1.1e+03      94     158 ..     325     365 ..     297     385 .. 0.41

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 2.6e-09
                                   EEEEESGGGHHHHHHHHHHHHHHTTS-SEEEEEEEE---S CS
                 ketoacyl-synt 168 svtvdtACsSslvavhaavqslrsgeadvalaGGvelllt 207
                                    +++d ACsSsl a+    +++++g+ad++ aGG e +++
  gi|13542135|ref|NP_111823.1|  90 GMALDRACSSSLNAITIGAMEIMTGNADIVMAGGYEHMTH 129
                                   589999******************************8887 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 2.7
                                   GGGTTBTTB-SB-BB- CS
                 ketoacyl-synt 225 rckafdpkadGfvlGE 240
                                   ++ a+++ +dG+  GE
  gi|13542135|ref|NP_111823.1| 187 HQLASKALDDGYFKGE 202
                                   3456666667776665 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.36
                                   HHHHHHHHHHTS-HHTCTTGGEEEEEEESSTHHHHHHHHHHHTTGGGSCT.THHHHHSTTHHHHHH CS
                 ketoacyl-synt  94 eaawealedagltpeeldgsrvgvfiGvgagdyaalaaldedgsevkasp.kavgavlanviagri 158
                                   +++ +a+++ g+++++++    g                        +s  +++ga + + iag +
  gi|13542135|ref|NP_111823.1| 325 VVVLNAMKELGIEENKVNIHGGG------------------------ISIgHPLGA-TGARIAGTL 365
                                   23333333333333333222222........................222233443.444444444 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 !   16.6   0.0   8.2e-07    0.0024      55     137 ..      38     128 ..      27     133 .. 0.86
   2 ?   -1.2   0.0      0.21   6.3e+02      58      75 ..     299     316 ..     284     321 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 8.2e-07
                                   HHHHHHHHHHHTT--GGG-SEEEEEESSGGGHHHHHHHHH...H.....---EEEB--GGGHHHHHHHHHHHHHHTTS-SE CS
                        SpoVAD  55 leeavkkalkkanlkkedidfllaGDLlnqlisssfaare...l.....kiPflglygaCstsaeslalaallvdggfakr 127
                                   + + ++ ++++++++ e+i+ +++G  l+q    +++ r+   l     ++P ++l  aCs+s ++++++a+ + +g a+ 
  gi|13542135|ref|NP_111823.1|  38 MAKLINIVIDETGIRPEEINDVITGCALQQDENWTYGGRHpilLanlpdNVPGMALDRACSSSLNAITIGAMEIMTGNADI 118
                                   667789999**********************99999988643313335579****************************** PP

                                   EEEEEEE-CC CS
                        SpoVAD 128 vlaatsshfa 137
                                   v+a+   h +
  gi|13542135|ref|NP_111823.1| 119 VMAGGYEHMT 128
                                   ***9888875 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.21
                                   HHHHHHHHTT--GGG-SE CS
                        SpoVAD  58 avkkalkkanlkkedidf 75 
                                   a++kal ka++k edid+
  gi|13542135|ref|NP_111823.1| 299 ATQKALAKAGMKVEDIDY 316
                                   7899************98 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 ?   -3.3   0.0       3.6   1.1e+04      24      38 ..      42      56 ..      34      61 .. 0.57
   2 !   16.9   0.1   1.7e-06    0.0051       1      83 [.     304     391 ..     304     392 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 3.6
                                  HHHHHHHHT--GGGB CS
                 ACP_syn_III_C 24 idavakklglpeekv 38
                                  i+ v+++ g+++e++
  gi|13542135|ref|NP_111823.1| 42 INIVIDETGIRPEEI 56
                                  555555555555544 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 1.7e-06
                                   HHHTT--GGG-SEEEE-SSSHHHHHHHHHHHT--GGGB--TH..HHH-B...-GGGHHHHHHHHHHHTTSS-TT-EEEEEE CS
                 ACP_syn_III_C   1 Lekagltpedidalvphqanlriidavakklglpeekvvvnl..deyGn...tsaasiplaLdeaveegklkpgdlvllvg 76 
                                   L+kag+++edid+  ++ a + ++ +++k+lg++e+kv +      +G+    + a i  +L++ ++e++ + g   l vg
  gi|13542135|ref|NP_111823.1| 304 LAKAGMKVEDIDYWEINEAFAVVVLNAMKELGIEENKVNIHGggISIGHplgATGARIAGTLSRILNEKQAEYGVATLCVG 384
                                   79**********************************9976654445666222234679999******************** PP

                                   EETTTEE CS
                 ACP_syn_III_C  77 fGaGltw 83 
                                    G G+++
  gi|13542135|ref|NP_111823.1| 385 GGQGYSV 391
                                   ****985 PP

>> Ketoacyl-synt_C  Beta-ketoacyl synthase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.25   7.5e+02      23      45 ..      35      57 ..      22      63 .. 0.86
   2 ?   -1.5   0.0      0.81   2.4e+03       6      38 ..     152     183 ..     149     190 .. 0.76
   3 ?    8.3   0.2   0.00076       2.3      28      49 ..     298     319 ..     286     374 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.25
                                  HHHHHHHHHHHHHHHT--GGGEE CS
               Ketoacyl-synt_C 23 geaqaraiekalaeagvdpedvd 45
                                   ea+a++i+ +++e+g++pe+++
  gi|13542135|ref|NP_111823.1| 35 DEAMAKLINIVIDETGIRPEEIN 57
                                  5789999**************97 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.81
                                   EEEEEE--STSSSTSTTHHHHHHHHHHHHHHHT CS
               Ketoacyl-synt_C   6 gsavnsdgahnsltapngeaqaraiekalaeag 38 
                                   ++ +n  g++++lta++ +++ ++ ++ +++  
  gi|13542135|ref|NP_111823.1| 152 HYDMNT-GYSMGLTAEKLASLHHIGREEMDQYA 183
                                   677788.999*****999998887777666655 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.00076
                                   HHHHHHHHHHT--GGGEEEEE- CS
               Ketoacyl-synt_C  28 raiekalaeagvdpedvdyvea 49 
                                    a +kala+ag++ ed+dy+e 
  gi|13542135|ref|NP_111823.1| 298 PATQKALAKAGMKVEDIDYWEI 319
                                   5789***************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.46
# Mc/sec: 2568.23
//
Query:       gi|13542136|ref|NP_111824.1|  [L=369]
Description: Acyl-CoA dehydrogenase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-34  119.7   0.2    1.7e-34  119.2   0.2    1.2  1  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
    5.2e-29  100.3   0.1    9.3e-29   99.5   0.1    1.4  1  Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
    3.4e-12   47.0   0.2    4.2e-11   43.5   0.1    2.6  2  Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
    5.8e-12   46.0   0.1    1.2e-11   45.0   0.1    1.5  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 !  119.2   0.2   3.8e-38   1.7e-34       1     148 [.     220     362 ..     220     364 .. 0.95

  Alignments for each domain:
  == domain 1  score: 119.2 bits;  conditional E-value: 3.8e-38
                                   TBHHHHHTTTT--S-----..-SHHHHHHHHHHHHHHHTSB-CC-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH----- CS
                 Acyl-CoA_dh_1   1 gkGfrvametlnheRlavaaaalglarraleealeyarrrkafgkplidhqlvreklaemaaeleaarllvyraaealdag 81 
                                   g+Gf+++m+ ++ +R+ vaa+alg+a+ +le++l++++++        + + v++ +a+ma+++ea++ll+y+aa+ + + 
  gi|13542136|ref|NP_111824.1| 220 GRGFYYIMTFFDISRAYVAAQALGIAEGILERTLSILQKDGPLT---SQPERVQFTIADMATRIEATKLLTYEAASYIFNF 297
                                   79***********************************9886644...57789***************************** PP

                                   ---HHHHHHHHHHHHHHHHHHHHHHHHHHGGGTTSGGGHHHHHHHHTHHHHHSSS-HHHHHHHHHHH CS
                 Acyl-CoA_dh_1  82 kpdraeasmaKlfaselaqevadlamqllGgaGyleeypverlyrdarvlrigeGtseiqrniiarr 148
                                   +p++a +smaK++a+e+a++v ++am++ G +G++   ++er +rda++++i+eGtsei +++iar 
  gi|13542136|ref|NP_111824.1| 298 NPNPAVTSMAKAYAAETAVYVSRKAMEVTGIDGLT--SSIERSFRDAKIMEIWEGTSEIEKLVIARM 362
                                   **********************************5..668*************************96 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 !   99.5   0.1   2.1e-32   9.3e-29       1      97 []     112     208 ..     112     208 .. 0.91

  Alignments for each domain:
  == domain 1  score: 99.5 bits;  conditional E-value: 2.1e-32
                                   EEE---SS-SS-GGG---EEEEETT.EEEEEEEEEEEETTTT-SEEEEEEETS---.----EEEEEEE..GGGEEE----- CS
                 Acyl-CoA_dh_M   1 afalTEpqaGsdvasvkttaaerdggeyvlnGeKiwitnaaiatlalvlartekpd.rarglslflvprdapgvsvrriee 80 
                                   ++a+TEp++Gsdva++ktta  ++g++yvlnG+K++itn+ ia+++++lart +++ +++g+s+f+v+rd +g++ ++i+ 
  gi|13542136|ref|NP_111824.1| 112 GLAVTEPGGGSDVANIKTTA-VKEGDHYVLNGSKMFITNGDIADFFVLLARTSQEKkKHHGMSVFIVERDFEGFRSNKIKG 191
                                   589***************66.455557************************4444456*********************** PP

                                   BSS-TTS-EEEEEEE.. CS
                 Acyl-CoA_dh_M  81 klGlrglptgelvfedv 97 
                                   klG+r ++t+el++e+v
  gi|13542136|ref|NP_111824.1| 192 KLGVRATDTAELTLENV 208
                                   **************997 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 !   43.5   0.1   9.4e-15   4.2e-11       6     112 ..      11     107 ..       6     108 .. 0.89
   2 ?   -3.2   0.0         3   1.4e+04      42      77 ..     202     238 ..     196     253 .. 0.53

  Alignments for each domain:
  == domain 1  score: 43.5 bits;  conditional E-value: 9.4e-15
                                   HHHHHHHHHHHHHT.HHHHHHHHHHTSGHHHHHHHHHHTTCTSTTS-GGGTS--S-HHHHHHHHHHHHHH-HHHHHHHHHH CS
                 Acyl-CoA_dh_N   6 alrdtvrefaeeel.aphaaewdeegefprelwkklaelGllgitvpeeygGagldyleaaivaeelaradaglalllgvh 85 
                                    +r+++ efa++e  ++ a ++de++++p++++ k+   G++  t p          +  ++++e l ++dag+++++ v 
  gi|13542136|ref|NP_111824.1|  11 NFRKKIEEFAKREFtEDLASKYDEQEHYPEDVFTKMMSEGIFDYTNP----------WNILMATEALCKYDAGMGISMLVP 81 
                                   79************778999999999***************966655..........8889***************99897 PP

                                   HHTTHHHHHHHS-HHHHHHHHHHHHTT CS
                 Acyl-CoA_dh_N  86 sslvapailrfGteeqkrryLpklasg 112
                                      + ++i+ fG++eqk++yL ++ +g
  gi|13542136|ref|NP_111824.1|  82 F-FGNEVIALFGNDEQKKKYLSRVFAG 107
                                   5.5558*****************9988 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 3
                                   HTTCTSTTS-GGGT.S--S-HHHHHHHHHHHHHH-HH CS
                 Acyl-CoA_dh_N  42 elGllgitvpeeyg.Gagldyleaaivaeelaradag 77 
                                   el l ++ vpee   G  +  +++++ +  ++ra ++
  gi|13542136|ref|NP_111824.1| 202 ELTLENVKVPEENLvGEPGRGFYYIMTFFDISRAYVA 238
                                   5555566666553223333445666666666665554 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 !   45.0   0.1   2.6e-15   1.2e-11       3     133 ..     237     352 ..     235     353 .. 0.88

  Alignments for each domain:
  == domain 1  score: 45.0 bits;  conditional E-value: 2.6e-15
                                   HHHHHHHHHHHHHHHHHHHHHHHHCTTT-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----HHHHHHH CS
                 Acyl-CoA_dh_2   3 iaavalGaAraalaefvelarervrassgekladdpatqlalaeaaarldAAralleraaaraealaaagkevtvedraea 83 
                                   +aa+alG+A++ l+ +++  ++          ++ + +q+++a++a+r++A ++l+++aa+     + + +++     a  
  gi|13542136|ref|NP_111824.1| 237 VAAQALGIAEGILERTLSILQKDGP-----LTSQPERVQFTIADMATRIEATKLLTYEAASY----IFNFNPN----PAVT 304
                                   89****************9876555.....55566789************************....5566665....5778 PP

                                   HHHHHHHHHHHHHHHHHHHHHCGGGGGBTT-HHHHHHHHHHHHCTSGGG- CS
                 Acyl-CoA_dh_2  84 rraaalavelaiaavdalfeaaGgsalrkesplqRlwRDahaaaaHaaln 133
                                   ++a+a+a+e+a+ + ++++e++G ++l++   ++R +RDa++++++++++
  gi|13542136|ref|NP_111824.1| 305 SMAKAYAAETAVYVSRKAMEVTGIDGLTS--SIERSFRDAKIMEIWEGTS 352
                                   9*************************986..6**********99998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); 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: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 2417.11
//
Query:       gi|13542137|ref|NP_111825.1|  [L=158]
Description: Acyl-CoA dehydrogenase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-15   58.0   0.0    1.7e-15   57.6   0.0    1.1  1  Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-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 !   57.6   0.0   9.6e-20   1.7e-15       2      82 ..       2      82 ..       1      90 [. 0.91

  Alignments for each domain:
  == domain 1  score: 57.6 bits;  conditional E-value: 9.6e-20
                                  HHHHHHHHHHHHHHHHHTHHHHHHHHHHTSGHHHHHHHHHHTTCTSTTS-GGGTS--S-HHHHHHHHHHHHHH-HHHHH.HH CS
                 Acyl-CoA_dh_N  2 eeqealrdtvrefaeeelaphaaewdeegefprelwkklaelGllgitvpeeygGagldyleaaivaeelaradaglal.ll 82
                                  ee e lr tvrefa++e++   ++++ +g +p+ l+ kl+++G+l+ t p+e gG+gld l ++iv+eel+r++ ++a+ ++
  gi|13542137|ref|NP_111825.1|  2 EEYEILRNTVREFANKEIENISKDIEIKG-IPDTLVLKLGAQGFLAATAPQEKGGSGLDELGYIIVLEELSRVSPSVAMkVF 82
                                  78999**************9999997666.79999****************************************9998554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       526  (0.0293379); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1005.36
//
Query:       gi|13542138|ref|NP_111826.1|  [L=169]
Description: Acyl-CoA dehydrogenase, partial [Thermoplasma volcanium GSS1]
Scores for complete 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   0.0    3.4e-13   50.0   0.0    1.9  1  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
    4.7e-05   23.7   0.0     0.0049   17.1   0.0    2.1  1  Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
  ------ inclusion threshold ------
       0.15   12.3   0.0       0.31   11.3   0.0    1.5  1  NAF            NAF 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 !   50.0   0.0   5.7e-17   3.4e-13      18     145 ..      38     157 ..      25     162 .. 0.91

  Alignments for each domain:
  == domain 1  score: 50.0 bits;  conditional E-value: 5.7e-17
                                   --..-SHHHHHHHHHHHHHHHTSB-CC-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH--------HHHHHHHHHHHHHH CS
                 Acyl-CoA_dh_1  18 vaaaalglarraleealeyarrrkafgkplidhqlvreklaemaaeleaarllvyraaealdagkpdraeasmaKlfasel 98 
                                   +aa  lgl    +  a+ey++ r+af  pl d+  + + l++++ e++++r ++y           d+   +++K++a +l
  gi|13542138|ref|NP_111826.1|  38 IAAIFLGLSDGTISKAIEYSKVRTAFDHPLKDYSPIFDDLVSLKMEIDVLRFYLYGSG--------DEYSRALIKIKAKDL 110
                                   788889************************************************9766........4556789******** PP

                                   HHHHHHHHHHHHGGGTTSGGGHHHHHHHHTHHHHHSSS-HHHHHHHH CS
                 Acyl-CoA_dh_1  99 aqevadlamqllGgaGyleeypverlyrdarvlrigeGtseiqrnii 145
                                     ++++  +q +Gg+Gy  + ++e++yrda++l+++ G +    +++
  gi|13542138|ref|NP_111826.1| 111 SLRATRVSLQTHGGYGYIHDFGIEKYYRDAMALSVYFGQDKYENMVL 157
                                   **************************************998766655 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 !   17.1   0.0   8.2e-07    0.0049       3     131 ..      38     148 ..      37     151 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 8.2e-07
                                   HHHHHHHHHHHHHHHHHHHHHHHHCTTT-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----HHHHHHH CS
                 Acyl-CoA_dh_2   3 iaavalGaAraalaefvelarervrassgekladdpatqlalaeaaarldAAralleraaaraealaaagkevtvedraea 83 
                                   iaa+ lG+  +++ +++e+ + r+   +  +l+d + +   l  +++++d +r  l+   ++          +        
  gi|13542138|ref|NP_111826.1|  38 IAAIFLGLSDGTISKAIEYSKVRTA--FDHPLKDYSPIFDDLVSLKMEIDVLRFYLYGSGDE----------Y------SR 100
                                   5777777777777777777777777..77777777777777777777777777777777666..........1......12 PP

                                   HHHHHHHHHHHHHHHHHHHHHCGGGGGBTT-HHHHHHHHHHHHCTSGG CS
                 Acyl-CoA_dh_2  84 rraaalavelaiaavdalfeaaGgsalrkesplqRlwRDahaaaaHaa 131
                                   ++ ++ a +l+ +a++   +++Gg+++  +  ++ ++RDa a++++ +
  gi|13542138|ref|NP_111826.1| 101 ALIKIKAKDLSLRATRVSLQTHGGYGYIHDFGIEKYYRDAMALSVYFG 148
                                   34578899***********************************99976 PP

>> NAF  NAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   5.2e-05      0.31      14      42 ..       4      35 ..       3      41 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 5.2e-05
                           NAF 14 sgfDLsgLFeee...arFtskkpaeeiiskle 42
                                  +g+DLs LF      +r+ s++ +++ ++kl 
  gi|13542138|ref|NP_111826.1|  4 RGLDLSDLFVSGasyKRLGSEEMMRSTFQKLD 35
                                  69*******6666779*********9999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       310  (0.0172904); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 1188.49
//
Query:       gi|13542139|ref|NP_111827.1|  [L=133]
Description: hypothetical protein TVN1308 [Thermoplasma volcanium GSS1]
Scores for complete 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   0.0    2.9e-12   46.8   0.0    1.2  1  4HBT      Thioesterase superfamily
    0.00033   21.0   0.0    0.00041   20.7   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 !   46.8   0.0   3.3e-16   2.9e-12       3      77 ..      48     120 ..      46     122 .. 0.96

  Alignments for each domain:
  == domain 1  score: 46.8 bits;  conditional E-value: 3.3e-16
                                   SB-HHHHHHHHHHHHHHHHHHTTSTTEEEEEEEEEEEESS-BBTTCEEEEEEEEEEEESSEEEEEEEEEETTSCE CS
                          4HBT   3 vvhgGvylallDeaagaalrslggrgilvvvvelsidflrpvrlgdeltvearvlrlgrtsavvevevrdedgrl 77 
                                   +++gG+++a+ D ++g+ ++++ g     v+v+++ +f+rp+  g ++++  rv r+g+++a+vev v+d+++ l
  gi|13542139|ref|NP_111827.1|  48 IMNGGAVMAISDAIGGLSAMTYPGI-VNQVTVSFNTEFMRPIAKG-PVRFISRVDRIGKSIAYVEVLVYDGENLL 120
                                   89**********************9.*******************.************************99865 PP

>> 4HBT_3  Thioesterase-like superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   4.6e-08   0.00041       8      72 ..      46     116 ..      40     125 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 4.6e-08
                                   TTC.-HHHHHHHHHHHHHHT........-S.SS.EEEEEEE-S---SEEEEEEEEEEE--SS-EEEEEEEEET CS
                        4HBT_3   8 ggagyGGyvlAlalraaqrtv.......pdprl.hslhvyFlrpgdagpviyhvervrdGrsfstrtvelsqg 72 
                                   g  ++GG+v+A+  +    +           ++  s+  +F+rp++ gpv++  ++ r G+s++ ++v ++ g
  gi|13542139|ref|NP_111827.1|  46 GEIMNGGAVMAISDAIGGLSAmtypgivN--QVtVSFNTEFMRPIAKGPVRFISRVDRIGKSIAYVEVLVYDG 116
                                   55569*******99888877545534332..2367********************************988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       185  (0.0103185); expected 358.6 (0.02)
Passed bias filter:                      172  (0.0095934); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 896.98
//
Query:       gi|13542140|ref|NP_111828.1|  [L=529]
Description: long-chain-fatty-acid--CoA ligase [Thermoplasma volcanium GSS1]
Scores for complete 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-85  286.6   0.0      3e-85  286.4   0.0    1.0  1  AMP-binding    AMP-binding enzyme
    3.9e-14   53.4   0.0    8.7e-14   52.3   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 !  286.4   0.0   3.3e-89     3e-85       6     422 ..      18     432 ..      13     433 .. 0.86

  Alignments for each domain:
  == domain 1  score: 286.4 bits;  conditional E-value: 3.3e-89
                                   HHSTTSEEEEECCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEETTS-HHHH CS
                   AMP-binding   6 aktpdkvalvdsgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvplnptltaeel 86 
                                     +p+++  ++  + +t+TY+e++erv rlA++L s+Gvkkgd+Va++ + ++ ++ a++a+ ++Gav+ ++n +++++ +
  gi|13542140|ref|NP_111828.1|  18 SSNPNQIINYS--GKKTFTYKEFRERVYRLAKALISIGVKKGDTVAVIDWDTYVYLEAYFAVPMIGAVLHTVNVRYPQDLI 96 
                                   66788887766..89****************************************************************** PP

                                   HHHHHHHTESEEEETCTCCC.HHHHHHHHSCC-EECEEEEESCCS-HCC.HCCCHCCCCSCTTS-TSCCCS-BTTSEEEEE CS
                   AMP-binding  87 ayiledseakvliatvdsel.leklleaaakleavklvivldadellke.eelkeeeeseekaekpeeeeelkpddlayii 165
                                    y ++++e k++i  v +e     +++++a    + ++i+++ +++++e ++ ++ +e  +k++ + e +e++++dla+ +
  gi|13542140|ref|NP_111828.1|  97 YYTMDHAEDKYVI--VRDEFvPILSKNKEAFYFIKGWIIYSEYGNVPDElSPKYIYDELMSKNY-DIELPEISENDLATTF 174
                                   *************..8777744445555555577777777777776655133334443333333.4466799********* PP

                                   EE--SSSS-EEEEEEHHHHHHHHHHHH..HHHC.SCCTTT-EEEESS-TTSCHHHHHHHHHHHHTT-EEEE-TTCGCCHHH CS
                   AMP-binding 166 YTSGTTGkPKGVmlshrnlvanvaslk..letr.fklkeddvvlsilplahifglilelllallsGatvvllpkdaaldpk 243
                                   YTSGTTG PKGV+ +hr++v  + s    l++r  +l++ddv++  +p++h+ ++    +++++sG + vl+ + ++   +
  gi|13542140|ref|NP_111828.1| 175 YTSGTTGIPKGVQFTHRQIVLHAISSGlaLSDRpISLTADDVIMPLVPMFHVHAW-GVPYMTIMSGRQYVLPGRYDF---D 251
                                   ****************99977777755687778666999****************.***************886665...4 PP

                                   HHHHHHHHHT-SEEEEEHHHHHHHHHCCCHHCHHHHCCGTT.-SEEEEESS-EBHHHHHHHHHHHTCEEEEEEEEGGGSSE CS
                   AMP-binding 244 lllelieklkvtviagvPrvleallesgalkaakkakdlss.lrlvllggeplspellrffralfgeevlegYGlTEttgv 323
                                   ++++li+++++tvia vP++l +++ +++       k  ++ +r + +gg++l++ l++++++l++   + gYGl+Et+++
  gi|13542140|ref|NP_111828.1| 252 HIIDLIAQENITVIAMVPSILYMIVTNPNVG-----KIAGRkIRAI-IGGGALPEGLQKAAEKLGIM-AISGYGLSETAPI 325
                                   689***********************87777.....2456669995.7****************998.7899********* PP

                                   CEE.........CHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSE..EEEEEEETTS-SEBTT-HHHHHHHEEETC CS
                   AMP-binding 324 vtv.........lpleedkkklgsvGkplpgvevkivDeetgepvpdgee..GellvrgpgvmkgYlkkpeataeafdseg 393
                                   +t          lplee+kk+  ++G p+p v+++++D++  + vp++e+  Ge++vr p++++ Y k++e t+  ++  g
  gi|13542140|ref|NP_111828.1| 326 LTLatynsdvkkLPLEEQKKYHLKTGIPIPLVQLRVIDDK-WNDVPRDEKtiGEIVVRAPWLTSVYVKNKEGTEALWK--G 403
                                   *666779*****888888888889***************9.78888777779*****************999977765..6 PP

                                   CEEEEEEEEEEETTSEEEEEEECCCEEEE CS
                   AMP-binding 394 rwlrTGDlgrldedGyleivgRkkdlikl 422
                                   +w++TGDl+++d+ Gy++iv+R kd +k+
  gi|13542140|ref|NP_111828.1| 404 GWMHTGDLAVMDKFGYIKIVDREKDAVKS 432
                                   7***********99*************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 !   52.3   0.0   9.8e-18   8.7e-14       2      76 .]     442     517 ..     442     517 .. 0.91

  Alignments for each domain:
  == domain 1  score: 52.3 bits;  conditional E-value: 9.8e-18
                                   HHHHHHSSTTEEEEEEE-----TTS---EEEEEE------HHHHHHHHHHH.HT-TTTS-SEEEE-S---B-TTS- CS
                 AMP-binding_C   2 vEsalvshpaVaeaaVvGvpdevkGealvafVvlkdgsealeeeLkahvrk.elgpyavpkkvvfvdelpktrsGK 76 
                                   +E a++++p+V e aVvG+p+e++Ge++vaf++  + +e++++ L++ vr+ ++++++ p++++ v+e+ kt +GK
  gi|13542140|ref|NP_111828.1| 442 LEDAISACPGVVENAVVGKPHEKWGERPVAFYTGTAKPEEIRKCLEDIVRQgRIAKFWIPDDFINVKEFVKTSTGK 517
                                   599******************************6323455889999999888***********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (529 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       591  (0.0329634); expected 358.6 (0.02)
Passed bias filter:                      520  (0.0290033); 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: 0.67u 0.34s 00:00:01.01 Elapsed: 00:00:00.50
# Mc/sec: 3160.56
//
Query:       gi|13542141|ref|NP_111829.1|  [L=659]
Description: 3-hydroxyacyl-CoA dehydrogenase [Thermoplasma volcanium GSS1]
Scores for complete 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  210.6   0.5    2.6e-62  209.9   0.5    1.4  1  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
    1.9e-46  158.4   0.0    3.2e-46  157.7   0.0    1.4  1  ECH_1           Enoyl-CoA hydratase/isomerase
    9.3e-37  125.5   0.0    9.9e-27   93.4   0.0    3.5  3  3HCDH           3-hydroxyacyl-CoA dehydrogenase, C-terminal d
      4e-33  115.3   0.0    1.6e-27   96.9   0.0    2.5  2  ECH_2           Enoyl-CoA hydratase/isomerase
      3e-07   30.8   0.2    5.3e-07   29.9   0.2    1.4  1  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
    0.00045   20.2   0.1    0.00092   19.2   0.1    1.6  1  NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogen
     0.0075   15.6   0.2      0.015   14.6   0.2    1.5  1  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
  ------ inclusion threshold ------
       0.04   13.5   0.2      0.075   12.6   0.2    1.4  1  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
      0.041   14.5   0.3       0.15   12.7   0.3    2.1  1  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
      0.057   12.6   0.2       0.15   11.2   0.0    1.7  2  DUF276          DUF276
       0.13   11.4   0.0       0.25   10.6   0.0    1.3  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 !  209.9   0.5   1.6e-65   2.6e-62       1     179 [.       5     183 ..       5     184 .. 0.98

  Alignments for each domain:
  == domain 1  score: 209.9 bits;  conditional E-value: 1.6e-65
                                   EEEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS-HHHHCCCHHCEEEES-HHHHH.C-S CS
                       3HCDH_N   1 kvaviGaGtmGagiaavfasagleVvlvdiseealekalekieksleklvekgklkeeeveaalarisfttdleeav.dad 80 
                                   kv+viG+G+mG+gia+ +a ag++V+l dis++ l+ka+++i +sl++lv++gkl+  +  ++l ri++ t++ e v dad
  gi|13542141|ref|NP_111829.1|   5 KVTVIGSGIMGHGIAETIALAGYDVNLEDISDDVLAKAKAEIDASLDRLVKSGKLS--DKTKVLGRIHYFTSIPESVkDAD 83 
                                   79*****************************************************9..7789**************99*** PP

                                   EEEE-S-SSHHHHHHHHHHHHCCS-TTSEEEE--SSS-HHHHCCCSSSGGGEEEEEE-SSTTT--EEEEEE-TT--HHHHH CS
                       3HCDH_N  81 lviEavvEnlelKrkvfaelekiakpdailasnTSslsiselaealkrperviglHFfnPpplmkLvEvvrgekTseetva 161
                                   lviEav+E l++Kr+vfa+l++ +k+daila+nTS+++++e+ae +k++ +v+g+HFfnPp ++kLvEv+r++ T++e+++
  gi|13542141|ref|NP_111829.1|  84 LVIEAVPEILDIKRQVFAQLDQSTKEDAILATNTSNIRLTEIAEGVKKKGKVVGMHFFNPPVVLKLVEVIRSDYTEDEVFE 164
                                   ********************************************************************************* PP

                                   HHHHHHHHTT-EEEEE.CS CS
                       3HCDH_N 162 tvvelakkigktpvvv.kd 179
                                   +v++++kkigk p++v kd
  gi|13542141|ref|NP_111829.1| 165 AVYDFSKKIGKIPIKVyKD 183
                                   ****************888 PP

>> ECH_1  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  157.7   0.0   1.9e-49   3.2e-46       2     250 ..     411     658 ..     410     659 .] 0.95

  Alignments for each domain:
  == domain 1  score: 157.7 bits;  conditional E-value: 1.9e-49
                                   EETTEEEEEE--CGCTTEE-HHHHHHHHHHHHHHHHSTTECEEEEEEBTSEEEEEB-HHHHHHHHCHHHHHHHCCHHHHHH CS
                         ECH_1   2 ieagvaviklnrPeavNalsaelltEliqalekleddksvravvLtGgdkaFaaGadlkemaeeekakqallkeevlelwt 82 
                                   ++  +av++ln+  ++N ++ ++l+ l q +++l  d+++ +vv+tG + +F+aGa l         +  +++ + +  ++
  gi|13542141|ref|NP_111829.1| 411 RNGKIAVLRLNNT-KNNLINSAVLDALEQQINDLWHDREINVVVITGNGSVFSAGAQLDSFFSST-FDFLEFSRKGERIFK 489
                                   6889********9.*************************************************75.667789999****** PP

                                   HHHHSSSEEEEEE-SEEETHHHHHHHHSSEEEEETTTEEE-GGGGGTS--CTTCHHHHHHHHHHHHHHHHHHHT-EEEHHH CS
                         ECH_1  83 klytvpkpviaavnGaaigGGlelalacDiviaadnasfglnelklGlipgaggtqilarkvGkskAeeilllgkkisaqe 163
                                   +l+++pk++ia ++G+++gGGlel lacDi++a ++ ++g +e+ lGlipg gg+q l + +G+s+A + +l+++++ ++ 
  gi|13542141|ref|NP_111829.1| 490 LLSEMPKITIAEMKGYVLGGGLELSLACDIRVATEDVQIGFPEVTLGLIPGWGGSQKLSKLIGESRASYYVLTAERFDGKR 570
                                   ********************************************************************************* PP

                                   HHHCTSSSEEESGGGHHHHHHHHHHHHHHSC.HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTSHHHHHHHHHHHTC CS
                         ECH_1 164 alkvGlvdkvvpeeqlleealelaeklaeks.paalrqlkealnakledalaeqleaeaklfestfskddikeGlqaflEk 243
                                   a ++Glv++    +++  e+l+ a+ + e   p +++ +k  l + ++  l  +le+e++ +  +  ++d keG+ afl k
  gi|13542141|ref|NP_111829.1| 571 AYEIGLVSRLYKPQEIDAETLKFAKDISERVaPISAALAKRLLLRSANTSLDDGLEMESMAMGTLYGTEDLKEGISAFLSK 651
                                   ***************************998615566666677778888********************************* PP

                                   SH----- CS
                         ECH_1 244 rkpefed 250
                                   rkp++++
  gi|13542141|ref|NP_111829.1| 652 RKPNYQG 658
                                   *****87 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 ?    3.8   0.0     0.054        88      41      91 ..      16      64 ..       2      66 .. 0.74
   2 !   93.4   0.0   6.1e-30   9.9e-27       1      97 []     186     280 ..     186     280 .. 0.97
   3 !   24.2   0.0   2.4e-08     4e-05      10      73 ..     304     367 ..     300     379 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.054
                                  SCHHHHHHHHHHHHHHHHHH..HHHHHTTTHGGHH-HHHHHHHHTT--BGGGT CS
                         3HCDH 41 mGpfelldlvgldvakkile..vlaeelgerayapsplleklveagrlgrktg 91
                                   G+ e++ l+g dv++  ++  vla++  e +      l++lv++g+l+ kt+
  gi|13542141|ref|NP_111829.1| 16 HGIAETIALAGYDVNLEDISddVLAKAKAEID----ASLDRLVKSGKLSDKTK 64
                                  6999999******9977665344444433334....46***********9986 PP

  == domain 2  score: 93.4 bits;  conditional E-value: 6.1e-30
                                   TTTHHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHHHHHHHTTTHGGHH-HHHHHHH CS
                         3HCDH   1 GFvvnRvlapllneavrlveegvaspediDaamrlglGlpmGpfelldlvgldvakkilevlaeelgerayapsplleklv 81 
                                   GFvvnR+ ap    ++ ++++g+a+pe++D+ +r   GlpmGp+el+d+vg+d++++ le++a+el+ + ya++++++kl+
  gi|13542141|ref|NP_111829.1| 186 GFVVNRINAPESLYFCLVLDKGIAKPEEVDRFARS-QGLPMGPYELMDYVGIDTVYHSLEYYAKELSPD-YAKCQVYNKLY 264
                                   9**********************************.************************999998877.666******** PP

                                   HTT--BGGGTBSSSBC CS
                         3HCDH  82 eagrlgrktgkgfyky 97 
                                   ++++lg ktg+gfyk+
  gi|13542141|ref|NP_111829.1| 265 NEKKLGLKTGEGFYKW 280
                                   **************97 PP

  == domain 3  score: 24.2 bits;  conditional E-value: 2.4e-08
                                   HHHHHHHHHHHTTSS-HHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHHHHHHHTTTHGGHH CS
                         3HCDH  10 pllneavrlveegvaspediDaamrlglGlpmGpfelldlvgldvakkilevlaeelgerayap 73 
                                     +neav+++ee+++spedi+  ++lg++ p Gp++++  ++    k+ le l++++g + ++p
  gi|13542141|ref|NP_111829.1| 304 LEINEAVKIIEEKIVSPEDIEIGVKLGMNRPFGPITVAKGLTNAEIKSKLESLYNKFGVSVFQP 367
                                   568*********************************9998877777777777777777776665 PP

>> ECH_2  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.9   0.0   9.9e-31   1.6e-27       2     179 ..     416     588 ..     415     599 .. 0.92
   2 !   17.5   0.0   1.4e-06    0.0023     245     318 ..     587     657 ..     576     659 .] 0.80

  Alignments for each domain:
  == domain 1  score: 96.9 bits;  conditional E-value: 9.9e-31
                                   EEEEE--GGGTT-B-HHHHHHHHHHHHHHCC-TT-SEEEEEESSSSECE--B--HHHHHHHHCS-THHHHHHHHHHHHHHH CS
                         ECH_2   2 gvitLnrpkalNaLslemvralkealkewekddevklvvlkgagekafCAGgDvralyeaakegkkeeeeffreeYklnyl 82 
                                   +v+ Ln+ k  N ++ ++++al++++++  +d e+++vv++g+g   f+AG  + ++ ++  +      ef r+  ++ +l
  gi|13542141|ref|NP_111829.1| 416 AVLRLNNTK-NNLINSAVLDALEQQINDLWHDREINVVVITGNG-SVFSAGAQLDSFFSSTFDF----LEFSRKGERIFKL 490
                                   578888876.59******************************88.9************998883....46*********** PP

                                   HHC-SS-EEEEE-BEEETHHHHHHTTSSEEEE-TT-EEE--GGGGT----TTHHHHHHCSST.THHHHHHHH---B-HHHH CS
                         ECH_2  83 iatypkpvvalmdGivmGgGvGlsvhgsfrvvtertvfAmPEtaIGlfPDvGgsyfLsrlpg.elGlylalTGarlkgada 162
                                   ++++pk ++a m G+v+GgG+ ls+ + +rv+te+ ++  PE+++Gl+P  Ggs  Ls+l g + + y  lT++r++g+ a
  gi|13542141|ref|NP_111829.1| 491 LSEMPKITIAEMKGYVLGGGLELSLACDIRVATEDVQIGFPEVTLGLIPGWGGSQKLSKLIGeSRASYYVLTAERFDGKRA 571
                                   ************************************************************77477**************** PP

                                   HHTTS--EE--GGGHHH CS
                         ECH_2 163 laaglathyvpseklea 179
                                   +++gl + + + ++++a
  gi|13542141|ref|NP_111829.1| 572 YEIGLVSRLYKPQEIDA 588
                                   *****999988877765 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 1.4e-06
                                   -SHHHHHHHHHHHHS-HHHHHHHHHHHHHHTTT--HHHHHHHHHHHHHHHHHHSSHHHHHHHHTTS-------S CS
                         ECH_2 245 edewakktletlkkrsPtslkvtleqlrrgrklsslaevlrmElrlalrllaekDfveGvrallvdkdkkPkWk 318
                                   ++e +k + +  ++ +P+s++++ ++l r++++s l++ l+mE  ++ +l  ++D+ eG+ a l ++  kP+++
  gi|13542141|ref|NP_111829.1| 587 DAETLKFAKDISERVAPISAALAKRLLLRSANTS-LDDGLEMESMAMGTLYGTEDLKEGISAFLSKR--KPNYQ 657
                                   4455555555556889*****************5.***************************99765..67765 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   0.2   3.3e-10   5.3e-07       1     116 [.       5     145 ..       5     146 .. 0.83

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 3.3e-10
                                   EEEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT......................EEE-SSHHHHHHHCSEE CS
                 NAD_binding_2   1 kigfiGlGvMGsnmalnllkagykvavynrtkekveelvaeg......................akaaesieelvasldvv 59 
                                   k+ +iG G+MG+ +a+ ++ agy+v + + + + + ++ ae                       ++ ++si e v+++d+v
  gi|13542141|ref|NP_111829.1|   5 KVTVIGSGIMGHGIAETIALAGYDVNLEDISDDVLAKAKAEIdasldrlvksgklsdktkvlgrIHYFTSIPESVKDADLV 85 
                                   589****************************9888888877667788999999**************************** PP

                                   EE-SSSHHHHHHHHHSHCCC--TT-EEEE-S---HHHHHHHHHHHHHTT....-EEEEEEE CS
                 NAD_binding_2  60 itmvkagkavdeviegllealkkgdilidgstsspedtrelakelkekg....lkfldaPV 116
                                   i  v++  +++  ++  l++  k+d ++ + ts+++ t+ +a+ +k+kg    ++f++ PV
  gi|13542141|ref|NP_111829.1|  86 IEAVPEILDIKRQVFAQLDQSTKEDAILATNTSNIRLTE-IAEGVKKKGkvvgMHFFNPPV 145
                                   **********99999978888888888877777776653.444444444333388887777 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.1   5.6e-07   0.00092       1     101 [.       5     115 ..       5     155 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 5.6e-07
                                   -EEEE--SHHHHHHHHHHHTTT--EEEE-S-H........HHHHHHHHHSSBTTTBTT----TTEEEES-HHHHHTT--EE CS
                NAD_Gly3P_dh_N   1 kiavlGaGswGtalAkvlaenghevrlwvree........elieeineehenvkyLpgiklpenlvattdlaealkgadii 73 
                                   k++v+G+G  G  +A ++a +g +v l   ++        e   ++++  +  k  +++k+   ++  t + e++k+ad++
  gi|13542141|ref|NP_111829.1|   5 KVTVIGSGIMGHGIAETIALAGYDVNLEDISDdvlakakaEIDASLDRLVKSGKLSDKTKVLGRIHYFTSIPESVKDADLV 85 
                                   79********************888887777766665552333445555555565666899999***************** PP

                                   EE---H..HHHHHHHHHHCCC--TT-EEEE CS
                NAD_Gly3P_dh_N  74 vlvvPs..qalrevlkklkgllkkkailvs 101
                                   + +vP    + r+v+++l++ +k++ail+ 
  gi|13542141|ref|NP_111829.1|  86 IEAVPEilDIKRQVFAQLDQSTKEDAILAT 115
                                   *****83357899********999998876 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 !   14.6   0.2   8.9e-06     0.015      29      99 ..       4      89 ..       1      95 [. 0.89

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 8.9e-06
                                  -EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHH.TTTCECEE...............HCHHHHHHHHHHHH-SEE CS
                   AlaDh_PNT_C 29 akvlviGgGvaGlqAiatakglgakVtvlDvrparleqles.lgakfvev...............lksqeellaeavkeadvv 95
                                  +kv+viG G+ G   ++t +  g +V + D++ ++l + ++ + a+ ++                + +   ++ e+vk+ad+v
  gi|13542141|ref|NP_111829.1|  4 SKVTVIGSGIMGHGIAETIALAGYDVNLEDISDDVLAKAKAeIDAS-LDRlvksgklsdktkvlgRIHYFTSIPESVKDADLV 85
                                  79*********************************99999876665.5445677*******99998888899*********** PP

                                  EE-- CS
                   AlaDh_PNT_C 96 igtv 99
                                  i +v
  gi|13542141|ref|NP_111829.1| 86 IEAV 89
                                  *987 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.2   4.6e-05     0.075       2      85 ..       5      90 ..       4      99 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.6e-05
                                  EEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHHCTTS-SS--TTHH..HHHHHHCHTTTEEEES-HHHHHHC-SEEEE CS
                UDPG_MGDP_dh_N  2 kisviGlGYvGlvtaavlaeighevigvDideekvdklnsgkipiyepgLe..elvkkavesgrlsfttdvekaveeadvifi 82
                                  k++viG+G +G   a  +a +g +v + Di++   +k +++     ++  +  +l  k    gr++  t++ ++v++ad+++ 
  gi|13542141|ref|NP_111829.1|  5 KVTVIGSGIMGHGIAETIALAGYDVNLEDISDDVLAKAKAEIDASLDRLVKsgKLSDKTKVLGRIHYFTSIPESVKDADLVIE 87
                                  89******************************998888776433333222111333344445788999999999999999998 PP

                                  --- CS
                UDPG_MGDP_dh_N 83 aVg 85
                                  aV+
  gi|13542141|ref|NP_111829.1| 88 AVP 90
                                  887 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 ?   12.7   0.3   8.9e-05      0.15       1      70 [.       5      90 ..       5     118 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 8.9e-05
                                  EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC.....................-EEECECHHHHHHH- CS
                 F420_oxidored  1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg.....................vkvtavdneeaaeea 62
                                  k+ +iG+G mg+++a+ ++ ag   +++    + + + ++++++e+                      +  ++ +  e +++a
  gi|13542141|ref|NP_111829.1|  5 KVTVIGSGIMGHGIAETIALAG---YDVN-LEDISDDVLAKAKAEIDasldrlvksgklsdktkvlgrIHYFT-SIPESVKDA 82
                                  689*******************...8888.4477777788877777766666667777777777776666666.666777777 PP

                                  SEEEE-S- CS
                 F420_oxidored 63 dvvvlavk 70
                                  d v+ av+
  gi|13542141|ref|NP_111829.1| 83 DLVIEAVP 90
                                  77776665 PP

>> DUF276  DUF276
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.1       1.5   2.4e+03     267     281 ..     102     116 ..      26     123 .. 0.53
   2 ?   11.2   0.0   9.3e-05      0.15     173     245 ..     278     350 ..     267     360 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.5
                        DUF276 267 nkdiaikedeillfn 281
                                   + d+++ked il  n
  gi|13542141|ref|NP_111829.1| 102 QLDQSTKEDAILATN 116
                                   235555556555555 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 9.3e-05
                        DUF276 173 ykislgkkkyvylkvkyklelkdalykeidsqirdiyskilsdkyiemgisleyqdflapvsivkgikelkis 245
                                   yk   gk +    +    +el d + +ei+  ++ i +ki+s + ie+g+ l  +  + p+++ kg+ + +i 
  gi|13542141|ref|NP_111829.1| 278 YKWVNGKAQIPDAQPTKNVELMDIFALEINEAVKIIEEKIVSPEDIEIGVKLGMNRPFGPITVAKGLTNAEIK 350
                                   6666677776677777789999*********************************************998886 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00015      0.25     144     189 ..       5      50 ..       2      64 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00015
                                   EEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2 144 rivvvGgGyiGvElAaalaklgkevtlveardrllraldkelsaal 189
                                   +++v+G+G  G  +A ++a +g++v l +  d +l + + e+ a l
  gi|13542141|ref|NP_111829.1|   5 KVTVIGSGIMGHGIAETIALAGYDVNLEDISDDVLAKAKAEIDASL 50 
                                   6889999999999999999999999999999999977777776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (659 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       696  (0.0388198); expected 358.6 (0.02)
Passed bias filter:                      620  (0.0345808); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.71u 0.32s 00:00:01.03 Elapsed: 00:00:00.47
# Mc/sec: 4219.07
//
Query:       gi|13542142|ref|NP_111830.1|  [L=108]
Description: sterol carrier protein [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-17   63.8   0.1      2e-17   63.5   0.1    1.0  1  SCP2            SCP-2 sterol transfer family
    3.4e-07   30.6   0.1    3.8e-07   30.4   0.1    1.1  1  Alkyl_sulf_C    Alkyl sulfatase C-terminal
      0.008   16.2   0.2     0.0096   15.9   0.2    1.1  1  Staphopain_pro  Staphopain proregion
  ------ inclusion threshold ------
      0.014   15.2   0.8       0.02   14.8   0.8    1.1  1  GatB_Yqey       GatB domain
      0.028   14.8   0.0      0.033   14.6   0.0    1.2  1  SCP2_2          Sterol carrier protein domain
      0.051   11.6   0.0      0.063   11.3   0.0    1.0  1  Med24_N         Mediator complex subunit 24 N-terminal
       0.11   11.1   0.4       0.13   11.0   0.4    1.0  1  Pectinesterase  Pectinesterase


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 !   63.5   0.1   7.9e-21     2e-17      13      99 ..      15     103 ..       4     104 .. 0.84

  Alignments for each domain:
  == domain 1  score: 63.5 bits;  conditional E-value: 7.9e-21
                                   HHHHHCCH-E...EEEEEECTC.TEEEEEETTSTEEESSCTTBS-SEEEEEEHHHHHHHHCTSS-HHHHHHTTSSEEEC-H CS
                          SCP2  13 kkealkklag...vlrfdltdlkgsltldlkegqldvaakdegkadvtlslsledllelaegklnpqkafmqgkLkieGDi 90 
                                   +++ l+ +a    ++ + l+d+ +++t+ +k+g++++ ++  +kad+t+++s+++l ++++gkln+ +afm+gk++++GD+
  gi|13542142|ref|NP_111830.1|  15 NEKDLSGIANaekIVSIALSDA-KPFTIIIKNGKIQLTDETPEKADATVKCSDQTLSDIITGKLNAFSAFMSGKVTVSGDL 94 
                                   3334444444455*********.77************999899************************************** PP

                                   HHHHHHHHH CS
                          SCP2  91 elaqkleal 99 
                                   +++qk+ ++
  gi|13542142|ref|NP_111830.1|  95 FFVQKIISV 103
                                   *****9765 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 !   30.4   0.1   1.5e-10   3.8e-07      35     115 ..      28     105 ..       2     108 .] 0.83

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 1.5e-10
                                   EEEEEETTTTEEEEEEEETTEEEE.ECT---TTSSEEEEE-HHHHHHHHTTSS-HHHHHHTTTEEEEE-TCHHHHHHCTB- CS
                  Alkyl_sulf_C  35 tinlvvtDvdekyllrlsngvLthtrkaaqaddadltvtltreqLvalllgkatlgkevaagklkieGdaealakllslld 115
                                    + + ++D  + +++ ++ng ++  +++++ ++ad+tv+++ ++L ++++gk ++ +++ +gk++++Gd   ++k++s++ 
  gi|13542142|ref|NP_111830.1|  28 IVSIALSDA-KPFTIIIKNGKIQL-TDETP-EKADATVKCSDQTLSDIITGKLNAFSAFMSGKVTVSGDLFFVQKIISVIG 105
                                   455667785.799*********99.55555.9********************************************99986 PP

>> Staphopain_pro  Staphopain proregion
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.2   3.7e-06    0.0096      98     154 ..      11      70 ..       3      82 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 3.7e-06
                Staphopain_pro  98 vspflskvlnqykdk.kit.i.ltnekGyyvltedgkvklvlktPrleekkekeaaktvk 154
                                   vs+   k+l  + +  ki  i l++ k + ++ ++gk++l  +tP + + + k +++t +
  gi|13542142|ref|NP_111830.1|  11 VSKVNEKDLSGIANAeKIVsIaLSDAKPFTIIIKNGKIQLTDETPEKADATVKCSDQTLS 70 
                                   666777888888776555323499***************************999988765 PP

>> GatB_Yqey  GatB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.8   7.7e-06      0.02      43     125 ..       5      85 ..       3      89 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 7.7e-06
                                   HHHHHHHHHHHTTSSGHHHHHHHHHHHHHHTXXHHHHHHHCTXXXXXXSSXHHHHHHHHHHTXHHHHHHHTTXXTTSTHHH CS
                     GatB_Yqey  43 eqlaellkliaegkIskkiakevleelleegkspeeiieekgLkqisdeeeleklveeviaenpkavedyksgkekalkfl 123
                                   e ++e++  ++e+++s+ +  e +  ++ ++ +p +ii ++g  q++d  e  +  + +++  ++++ d+ +gk +a+ ++
  gi|13542142|ref|NP_111830.1|   5 ELINEMVSKVNEKDLSGIANAEKIVSIALSDAKPFTIIIKNGKIQLTD--ETPEKADATVKCSDQTLSDIITGKLNAFSAF 83 
                                   56899************9988888888889************999999..66777899*********************99 PP

                                   HH CS
                     GatB_Yqey 124 vG 125
                                   + 
  gi|13542142|ref|NP_111830.1|  84 MS 85 
                                   94 PP

>> SCP2_2  Sterol carrier protein 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     0.033      32      85 ..      37      91 ..      15     106 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.3e-05
                                  EEEEEEEETTSEEEECSCE-SCE..EEEEHHHHHHHHTTSS-HHHHHHTTSSBSS CS
                        SCP2_2 32 grfrltiedgkgeevgkeeeada.dltldiqtLaqlllGyrsaseLarlgriega 85
                                  ++f++ i++gk + +++++e+++ +++++ qtL+ +++G   a ++   g+++ +
  gi|13542142|ref|NP_111830.1| 37 KPFTIIIKNGKIQLTDETPEKADaTVKCSDQTLSDIITGKLNAFSAFMSGKVTVS 91
                                  579999***9998666666644449*****************9999999999844 PP

>> Med24_N  Mediator complex subunit 24 N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   2.5e-05     0.063     846     936 ..       8     102 ..       3     106 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 2.5e-05
                       Med24_N 846 kreakevdkedldalvqssKlrrlessdeaeealllssssqseassls..qlseitl.kdPLqkvlkelfrllssviesd. 922
                                   +++  +v+++dl+ +++++K+  ++ sd+++ ++ +++ + + ++ ++  +  +++  ++ L+ +++  ++ +s +++ + 
  gi|13542142|ref|NP_111830.1|   8 NEMVSKVNEKDLSGIANAEKIVSIALSDAKPFTIIIKNGKIQLTDETPekADATVKCsDQTLSDIITGKLNAFSAFMSGKv 88 
                                   56777899999*************************9999999998885544455541468******************99 PP

                       Med24_N 923 elspkteFvfqfle 936
                                   ++s    Fv+++++
  gi|13542142|ref|NP_111830.1|  89 TVSGDLFFVQKIIS 102
                                   ***********997 PP

>> Pectinesterase  Pectinesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.4   4.9e-05      0.13       4      94 ..      11     100 ..       8     105 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 4.9e-05
                                   E-TTS-SSBSSHHHH..HHHS-SS-SS-EEEEE-SEEEE--EEE-TTS-SEEEEES-TTTEEEEE---TTTT--SGGG-SE CS
                Pectinesterase   4 vakdgsgkfktisea..vaavpeksekrfviyvkaGvYeenvevekkktnvvlvGdGkektvitgsknvvdgkttfktatv 82 
                                   v+k  + + + i++a  + ++  +  k f i +k+G  + + e ++k    v + d + + +itg++   ++ ++f +  v
  gi|13542142|ref|NP_111830.1|  11 VSKVNEKDLSGIANAekIVSIALSDAKPFTIIIKNGKIQLTDETPEKADATVKCSDQTLSDIITGKL---NAFSAFMSGKV 88 
                                   5666666677777662244455677888********************99***************95...55689****** PP

                                   EE-STT-EEES- CS
                Pectinesterase  83 avvgegfiardi 94 
                                   +v+g+ f +++i
  gi|13542142|ref|NP_111830.1|  89 TVSGDLFFVQKI 100
                                   *******99887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       505  (0.0281667); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 761.60
//
Query:       gi|13542143|ref|NP_111831.1|  [L=176]
Description: hypothetical protein TVN1312 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.9e-22   77.9   0.5    3.3e-10   40.2   0.0    2.4  2  CBS             CBS domain
    3.9e-21   74.7   4.3    6.8e-21   73.9   4.3    1.4  1  DUF1936         Domain of unknown function (DUF1936)
     0.0042   16.8   1.4     0.0067   16.2   1.4    1.4  1  zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
  ------ inclusion threshold ------
       0.12   12.5   0.0       0.32   11.2   0.0    1.7  1  DUF2675         Protein of unknown function (DUF2675)
       0.12   12.3   0.1        0.2   11.6   0.1    1.4  1  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
       0.15   11.7   1.3          9    6.0   0.1    2.4  2  zf-tcix         Putative treble-clef, zinc-finger, Zn-binding


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.6   0.1     3e-12   9.1e-09       1      54 [.       3      56 ..       3      58 .. 0.92
   2 !   40.2   0.0   1.1e-13   3.3e-10       4      56 ..      72     124 ..      67     125 .. 0.93

  Alignments for each domain:
  == domain 1  score: 35.6 bits;  conditional E-value: 3e-12
                                  HHHHSBSSCEEEETTSBHHHHHHHHHHHT.SSEEEEE.ETTTBEEEEEEHHHHHHH CS
                           CBS  1 Vgdimtrdvvtvppdttleealelmrekg.vsrlPVV.dedgklvGivtlrDllra 54
                                  V+ im++++ +v++++++ +a+++m e++ + +l +V d++gk vG++++r +++ 
  gi|13542143|ref|NP_111831.1|  3 VEKIMNTNYRSVNENSSVFDAVKIMNENRlY-GL-IVkDNEGKDVGLISERSIIKR 56
                                  788**********************888866.**.9999999***********985 PP

  == domain 2  score: 40.2 bits;  conditional E-value: 1.1e-13
                                   HSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                           CBS   4 imtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                                   +m+++++ vp + ++++a+  + e+g+ r  VVd+ gk+vGi+tl+Dl r+l+
  gi|13542143|ref|NP_111831.1|  72 VMRKPIPKVPSSYDVRDAAAYLSENGLERCAVVDSTGKVVGIITLTDLSRYLS 124
                                   7*********************999988888*****************99986 PP

>> DUF1936  Domain of unknown function (DUF1936)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.9   4.3   2.3e-24   6.8e-21       1      34 []     143     176 .]     143     176 .] 0.99

  Alignments for each domain:
  == domain 1  score: 73.9 bits;  conditional E-value: 2.3e-24
                                   B-TTTSSSBEEEEE-TTS-EEEEEES-TT---EE CS
                       DUF1936   1 lCPKCnvGkLEPVYNekGEIKvFRCdredCdYiE 34 
                                   lCPKC+vG+L PVY +kGEIKvFRC++++CdY+E
  gi|13542143|ref|NP_111831.1| 143 LCPKCGVGVLVPVYDQKGEIKVFRCSNPACDYEE 176
                                   8********************************9 PP

>> zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   1.4   2.3e-06    0.0067       3      33 ..     143     175 ..     141     176 .] 0.92

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.3e-06
                                   E-SSS-.-EEEEEE-SSS..EEEEESST.T---- CS
                zf-C4_Topoisom   3 kCPkCg.gdLvlkrgkkG..kFvGCsnYPeCkft 33 
                                    CPkCg g Lv  +  kG  k   Csn P C++ 
  gi|13542143|ref|NP_111831.1| 143 LCPKCGvGVLVPVYDQKGeiKVFRCSN-PACDYE 175
                                   7*******************8889***.****95 PP

>> DUF2675  Protein of unknown function (DUF2675)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00011      0.32      26      54 ..     137     165 ..     119     169 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00011
                       DUF2675  26 ekdmlhlckqvgsgaivpngkqkemivqf 54 
                                    kd  hlc + g g +vp   qk  i  f
  gi|13542143|ref|NP_111831.1| 137 TKDYKHLCPKCGVGVLVPVYDQKGEIKVF 165
                                   69********************9877655 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 ?   11.6   0.1   6.8e-05       0.2      19      45 ..     142     174 ..     126     175 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 6.8e-05
                 Zn_Tnp_IS1595  19 fvCPhCgsr...kayrikt.rglfqCke..Crk 45 
                                   + CP+Cg+     +y  k+  ++f+C+   C +
  gi|13542143|ref|NP_111831.1| 142 HLCPKCGVGvlvPVYDQKGeIKVFRCSNpaCDY 174
                                   55******9555555555599*****9988876 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 ?    4.4   0.2    0.0096        29      13      18 ..     144     149 ..     134     150 .. 0.91
   2 ?    6.0   0.1     0.003         9      25      34 ..     165     174 ..     162     176 .] 0.86

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.0096
                       zf-tcix  13 CpkCGt 18 
                                   CpkCG+
  gi|13542143|ref|NP_111831.1| 144 CPKCGV 149
                                   *****6 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.003
                       zf-tcix  25 lsCkNkaCdq 34 
                                   ++C+N+aCd+
  gi|13542143|ref|NP_111831.1| 165 FRCSNPACDY 174
                                   58******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       569  (0.0317363); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1141.10
//
Query:       gi|13542144|ref|NP_111832.1|  [L=558]
Description: Fe-S oxidoreductase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.9e-19   70.1   0.0    2.3e-18   67.2   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 ?    0.3   0.0     0.044   7.9e+02     120     154 ..     123     152 ..      66     216 .. 0.71
   2 !   67.2   0.0   1.3e-22   2.3e-18       1     167 []     246     434 ..     246     434 .. 0.95

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.044
                                   HHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM 120 lmnrghtfeevlealeklreagikrvvdrivglpG 154
                                   ++ r  +++ ++e + k+re   k     ivg+pG
  gi|13542144|ref|NP_111832.1| 123 WV-R-REWDTLMEKVNKAREG-KK--AKLIVGGPG 152
                                   44.2.4566666666666665.44..455555555 PP

  == domain 2  score: 67.2 bits;  conditional E-value: 1.3e-22
                                   EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgirit 81 
                                   v+v+rgC  +C fC ++      ++ r++++ +i++e+k++ +  gv++ +l+++e + y++ +++  ++ +l  + ++ +
  gi|13542144|ref|NP_111832.1| 246 VEVMRGCGVGCDFCEVT-----LRPLRYMPLSMIIDEIKIN-VAGGVDNAWLHSDEIFGYKHGHFFEPNEEALS-ELFSAV 319
                                   689**************.....69*****************.8999***************************6.999999 PP

                                   EEECSSCHG................HHHHHHHHHTT...-SEEEEEEBSSSHHHHHHHHTCTSHH...........HHHHH CS
                                   xxxxxxxxx................xxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxx...........xxxxx RF
                   Radical_SAM  82 vetngtlpd................eeklerllelg...vdrvslgleaaddekvlklmnrghtf...........eevle 132
                                   ++++g++ +                 ekl ++l++g   +  ++ gle++++    k++++++t+           + v++
  gi|13542144|ref|NP_111832.1| 320 MSVPGVKTSnpthgrisipagypemIEKLSKILKAGprnWIGIQTGLETGSEV-LAKKHMPNKTLplrigvdgswqDIVWQ 399
                                   999999988999999999****9999**************************9.666666999999*************** PP

                                   HHHHHHHTTSETEEEEEEEBTTTSHHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM 133 aleklreagikrvvdrivglpGendeeleellell 167
                                   ++   +++ +++ +++ vg +Ge+ e+l++++ l+
  gi|13542144|ref|NP_111832.1| 400 GVNVETKYYWRSAFTIQVGQEGETPEDLWDTIALI 434
                                   *******************************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (558 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       362  (0.0201908); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.48
# Mc/sec: 3509.11
//
Query:       gi|13542145|ref|NP_111833.1|  [L=334]
Description: oxidoreductase [Thermoplasma volcanium GSS1]
Scores for 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  210.5   0.1    3.4e-62  210.3   0.1    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 !  210.3   0.1   1.9e-66   3.4e-62       2     292 ..      16     332 ..      15     334 .] 0.94

  Alignments for each domain:
  == domain 1  score: 210.3 bits;  conditional E-value: 1.9e-66
                                   EEEE-SSS-ST.........TS-HHHHHHHHHHHHHTT--EEE--TT-............TTTHHHHHHHHHHHH-TTTGG CS
                  Aldo_ket_red   2 lglGtwqlgsk........eeiskeealellrraleaGinffDtAevY............gkgqseellGealkksrkkre 62 
                                   l lGtw+l +         e+++++e +++ ++a++aGinffDtA++Y            + g se++lG+a+k    +re
  gi|13542145|ref|NP_111833.1|  16 LALGTWHLPGSnryssdgvEKVDESEFQRIFKKAYDAGINFFDTANIYhgrveknedhidHIGNSERILGKAIKG--YERE 94 
                                   78999999988899999**********************************************************..**** PP

                                   G-EEEEEE..--SSSTTSSSS-HHHHHHHHHHHHHHHT-S-EEEEEE-S--TTS-.HHHHHHHHHHHHHTTSEEEEEEES- CS
                  Aldo_ket_red  63 eviiatKv..dlrdaeiksglskeniresleeslkrLgtdyvDllllHrpdpslpsieevldaleelvkeGkiraiGvSnf 141
                                   +++iatKv  + ++  + +gls+++i+ +++esl+rLg++yvDl+++H+ d+ +p  ee++++l + v+   +r+iG Sn+
  gi|13542145|ref|NP_111833.1|  95 SLVIATKVrgPVSKFINGEGLSRKHIMWQIKESLQRLGLEYVDLYQIHWSDSLTP-HEETARVLSHIVDLDMARYIGESNH 174
                                   ********7777777789*************************************.************************* PP

                                   -HHHHHHH....HHTTT--EEEEE-B-BTT-HHHHTTHHHHHHHTT-EEEEBSTTGGGTTGTTTSS---SSSCCC------ CS
                  Aldo_ket_red 142 sveqleka....kkkkkvkivavqveynllreleeegllelckkkgvpliaysplggGlltgkyqseedkedkeprkdlkr 218
                                   s+e +       +k + + +v+ q  yn+l++  e+  ++++kk+g+++ ay pl++G ltgky+s ++k++    ++   
  gi|13542145|ref|NP_111833.1| 175 SAEDIVDFmnisEKLNLHHFVTMQEPYNILQRGIEKDKIPVAKKYGMGILAYVPLAQGVLTGKYVSGPEKGSR---SSYYP 252
                                   *777777779999999999***********9999**********************************99853...33333 PP

                                   -..TS-HHHHHHHHHHHHHHHHTT--HHHHHHHHHTTS....TT-SEEEE--SSHHHHHHHHGGGG----HHHHHHHHHH CS
                  Aldo_ket_red 219 d..ertsknldaaeelselakehgvslaqlalryalsq....pavgivipgasnieqlednldalelklseeevaeldel 292
                                   +  +  +kn++++++l ++ake++++  qla+++++++       +i+++g ++ + le+nl+ale++l++++++e+d++
  gi|13542145|ref|NP_111833.1| 253 EiiDFHQKNQKKIDALINFAKEKDITGGQLAIAWLIKKsqieGIPIIPLLGITKEKYLEENLKALEVNLTDSDMREIDRM 332
                                   378999*******************************9877778999*******************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       675  (0.0376485); expected 358.6 (0.02)
Passed bias filter:                      557  (0.031067); 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 0.25s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 2219.29
//
Query:       gi|13542146|ref|NP_111834.1|  [L=613]
Description: hypothetical protein TVN1315 [Thermoplasma volcanium GSS1]
Scores for 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-68  232.2   0.0    8.2e-65  219.3   0.0    2.1  1  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 !  219.3   0.0   4.6e-69   8.2e-65       2     447 ..     236     597 ..     235     598 .. 0.97

  Alignments for each domain:
  == domain 1  score: 219.3 bits;  conditional E-value: 4.6e-69
                                   HHHHHHHHCBCSTTSSBTTS-TT-B-S-S-BSSS.........B--SEEHHHHHHHHHHHH.......HHHHHTTT-HCCH CS
                Glyco_hydro_15   2 vrldlylrnvktlilleqnpvtGlliASpstsdp.........DYrytWvRDsvyvilavwglgyrdedrakayeleqslv 73 
                                   +++++++r++ +l++l+++p tGl++A+p+ s+p         DYr+tW+RD +yvi+a+ ++gy+ e+ ++ y++   + 
  gi|13542146|ref|NP_111834.1| 236 AYHSMVMRSALALKVLFYEP-TGLMVAAPTASLPeaiggernwDYRFTWIRDTAYVIEALSSIGYKYEATEFLYDMMDMIT 315
                                   67899***************.***********************************************************9 PP

                                   HHHHHHHHHHHHHCTS-BTTB-TTSCGGGG--EE-TTS-B--S-..-S--BTTHHHHHHHHHHHHHCTTHCHCCCCHHHHT CS
                Glyco_hydro_15  74 klmrglleamvrqagkvekfketqstkgLhakyftktgstvvGddewghlQlDatslyllalaqmtasglqiistldevaf 154
                                   + +r  +++++++++  ++++e+  +     +++ ++ ++++G++++++lQ+D+++ ++ a++ m ++g  ++s+l+ +  
  gi|13542146|ref|NP_111834.1| 316 RDNR--IRTIYSIDDS-NDLEERIID----YEGYRGSRPVRIGNKAVDQLQIDQYGSIVRAIHSMAKAGGIVNSYLWDF-- 387
                                   9888..9*******96.999987775....99***********************************************.. PP

                                   HHHHHHHHHHHTTS-EE-TTS--ECEEHH..HHHHHHHHHHHHHHHHHHCT-HHHHCCHHHHHHHHHHHHHSTTT..GGGE CS
                Glyco_hydro_15 155 vqnlvdYieaayktpdfglWEenqgeselnassvgmakAlleaideadlfgakgdaqlvektkdeilnklqgkygckrgfw 235
                                   v++ +  ie  +k pd+ +WE + + +++++s+v++++A++ ai +a+++g ++  + +++ +dei +++      ++gf+
  gi|13542146|ref|NP_111834.1| 388 VEQVMAKIEYLWKYPDSSIWEFRTEPKQYVYSKVMSWAAFDSAISMAKDLGLSAPIKQWKSIQDEIKKEV-----LEKGFD 463
                                   **********************************************************************.....****** PP

                                   ETTCCECECSCH.....HHHTTS--S-BCHHHHHHHHCS-TTS-TT-TT-TTTSHHHHHHHHHHHHHHHHHSGGGTT-STT CS
                Glyco_hydro_15 236 plfntylildgsfaedkeqvqeyrealdasllllpelyfvpaddvdeeyqnpqsprllaqslyildsllsegflavgeldp 316
                                   ++ n +++++gs            ++ da+ll lp+l+f+pa+d          +++l+++  i+++l+ +g+l       
  gi|13542146|ref|NP_111834.1| 464 TDTNSFVQYYGS------------KNIDAALLRLPILGFIPAND----------EKFLGTLSRIEKELMVDGYL------- 515
                                   ************............********************..........*******************6....... PP

                                   S--SBTT--CGSSSBSCT--BHHHHHHHHHHHHHHHHHHHHHTE-EEEECCCHHHHHHHTTTTTGGGSSEEETCHHHHHHH CS
                Glyco_hydro_15 317 lvrRysedvkpdklglsGrpyylctlwtvetlldelyekagkgrlwglvryalglleklveskqltvGlpperesvisapl 397
                                    ++Ry ed   d+l+++++++++ t+w     + e +  ++++      ++a+++le + e+                   
  gi|13542146|ref|NP_111834.1| 516 -FKRYRED---DGLKGDEGSFLMLTFW-----YIEDLILMKRL------KKAREVLESVLEK------------------- 562
                                   .9******...68**************.....99999999995......59**********9................... PP

                                   HHHHHHHHHHHHHHHS-TTS---SEE-TTT--EESSTT-HHHHHHHHHHH CS
                Glyco_hydro_15 398 pveeladliveaveednslgvLteevdvylgeliraqpllfsealllrig 447
                                                  +n+lg+++ee+d+++g +++++p++ s++  +r++
  gi|13542146|ref|NP_111834.1| 563 ---------------ANHLGLYSEEIDEKSGDFLGNFPQALSHLGVIRVA 597
                                   ...............********************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (613 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       536  (0.0298957); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); 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: 0.68u 0.30s 00:00:00.98 Elapsed: 00:00:00.47
# Mc/sec: 3926.52
//
Query:       gi|13542147|ref|NP_111835.1|  [L=360]
Description: 3-dehydroquinate synthase [Thermoplasma volcanium GSS1]
Scores for complete 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-80  267.8   0.7    9.4e-80  267.5   0.7    1.1  1  DHQ_synthase  3-dehydroquinate synthase
      2e-06   26.9   0.2     0.0026   16.7   0.1    2.4  2  Fe-ADH        Iron-containing alcohol dehydrogenase
    7.7e-06   25.8   2.9    1.6e-05   24.8   0.1    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 !  267.5   0.7   1.6e-83   9.4e-80       2     261 ..      66     320 ..      65     321 .. 0.96

  Alignments for each domain:
  == domain 1  score: 267.5 bits;  conditional E-value: 1.6e-83
                                   EEE-SSGGGCCHHHHHHHHHHHHHTT--TT-EEEEEESHHHHHHHHHHHHHBTT--EEEEEE-SHHHHHTTTSSSEEEEEE CS
                  DHQ_synthase   2 lvvpdgeksKsletlekildalleakleRksllialGGGvvgDlaGfvAatylRGvrfvqvPttllaqvDssvGgKtainl 82 
                                   + ++dge+ Ksl++++ki+++lle+k++R+sll+ +GGG+vgDlaGfvA+ty+RGv ++ vPttllaqvDss+GgK+++++
  gi|13542147|ref|NP_111835.1|  66 ISLNDGESLKSLRNYQKIVKVLLERKVDRRSLLVYIGGGTVGDLAGFVASTYKRGVMMIAVPTTLLAQVDSSIGGKNGLDF 146
                                   6789***************************************************************************** PP

                                   TTEEEEEEEE---SEEEEEGGGGGGS-HHHHHHHHHHHHHHHHHT-HHHHHHHHHHHHHHHCTTTHHHHHHHHHHHHHHHH CS
                  DHQ_synthase  83 plgKNliGafaqPkavlidlevLktLperelraGlaEviKyalikdeelfelleenaeallkeeeeealeeliarsievka 163
                                   + +KN+iG+f++P +v+ d+ +Lk  +   +r+G++EviKya+i++ +++++l++ + ++++    + ++++i+ s+++k+
  gi|13542147|ref|NP_111835.1| 147 SDVKNVIGTFYNPYMVIDDTVFLKNNS-FIIREGMSEVIKYAIISGGDMYDTLNRCSIDNFD----ACATNIIKLSVKIKS 222
                                   ***********************9854.789************************9987755....6899*********** PP

                                   HHHHHCCTT.TTGGGGGGTTHHHHHHHHHHHTTTTS-HHHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHTT--.-ST CS
                  DHQ_synthase 164 evveeDeke.kglralLnlGHtigHaiEallgyekllHGeaVaiGmvlaaelseklgllkkeeverllkllkklglp.vsl 242
                                   e+v++D ++ +g+r++LnlGHti+H iE +++  +++HG+aVa+Gm+++a++ ek g +++e +e++++l+k++g++ ++l
  gi|13542147|ref|NP_111835.1| 223 EIVNRDFYDrTGIRSVLNLGHTIAHGIEGATKG-SISHGKAVATGMLVEAHIGEKYGNTNHEVIEAIRDLMKRYGIEeLNL 302
                                   *********99*******************999.*****************************************984566 PP

                                   TTT.-HHHHHHHHTTCTTX CS
                  DHQ_synthase 243 kelleveellealkkDkkv 261
                                   ke   + ++l+++++Dkk 
  gi|13542147|ref|NP_111835.1| 303 KEI-GPGNILRYISNDKKI 320
                                   666.*************95 PP

>> Fe-ADH  Iron-containing alcohol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.1   4.3e-07    0.0026       5     133 ..      18     130 ..      15     171 .. 0.83
   2 !    8.1   0.0   0.00017         1     253     335 ..     240     308 ..     233     336 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 4.3e-07
                                   EEETTGGGGHHHHHTTT-..EEEEEEEHHHH.HH.THHHHHHHHHCTT-EEE..E.EEE-S---HHHHHHHHTTS-TT.-- CS
                        Fe-ADH   5 vfgkgaleelgellkklgakralivtdkgslkksglldkvlesleeagievt..vfdgvepnptleeveeaaalareegad 83 
                                   + g++a+++l e++ k+   +++i+ +k +    +++++ +  + + g +v+    ++ e+  +l++ +++++++ e ++d
  gi|13542147|ref|NP_111835.1|  18 IVGDNAINHLSEEAGKYD--SIVIMISKTVE---EMYANHIPDVGSFGNSVVkiSLNDGESLKSLRNYQKIVKVLLERKVD 93 
                                   789*************96..99999999977...78999999998889988855567778889****************99 PP

                                   E...EEEEESHHHHHHHHHHHHHTT..................--EEEEESS- CS
                        Fe-ADH  84 v...viavGGGsviDtAKaialllanpevedylgegkakkkkalpliaiPTta 133
                                       ++ +GGG+v D+A  +a ++++                ++ +ia+PTt 
  gi|13542147|ref|NP_111835.1|  94 RrslLVYIGGGTVGDLAGFVASTYKR----------------GVMMIAVPTTL 130
                                   7777*********************5................4999*****96 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00017
                                   -HHHHHHHHHHC.CGGGGGS-HHHHHHHHH..........HHHHHHT.......T--HHHHHHHHHHHHHTT---.SHHHH CS
                        Fe-ADH 253 gavHalahalgalfgiphglanaillpavlrfnaeaaperlaqlaralggesdeeaaeeliealrellkelglpt.sLsel 332
                                   ++ H +ah++ +   +   ++++ +++ ++ +         a + ++       +  +e+iea+r+l+k+ g++  +L+e+
  gi|13542147|ref|NP_111835.1| 240 NLGHTIAHGIEGA--TKGSISHGKAVATGMLV--------EAHIGEK-----YGNTNHEVIEAIRDLMKRYGIEElNLKEI 305
                                   5667777777662..33334444444445511........2344444.....34568899*************99999999 PP

                                   T-T CS
                        Fe-ADH 333 gvd 335
                                   g  
  gi|13542147|ref|NP_111835.1| 306 GPG 308
                                   855 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 !   24.8   0.1   2.7e-09   1.6e-05       5     109 ..      22     130 ..      18     201 .. 0.74
   2 ?    1.2   0.5      0.04   2.4e+02     229     250 .]     243     264 ..     241     264 .. 0.94

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 2.7e-09
                      Fe-ADH_2   5 galeklgellkelelkkvllvadentkkaagekvee..slkeagikvevveeveeeadleeveklveal...reketdlvv 80 
                                   +a+++l+e     +++ ++++ ++++++++++++ +  s+ ++ +k+++ ++ e  ++l + +k+v++l   + ++  l+v
  gi|13542147|ref|NP_111835.1|  22 NAINHLSEEAG--KYDSIVIMISKTVEEMYANHIPDvgSFGNSVVKISL-NDGESLKSLRNYQKIVKVLlerKVDRRSLLV 99 
                                   55555554332..457999999*******99999873366677777764.44666667777788887773224466679** PP

                      Fe-ADH_2  81 avGgGtiiDiakyvs..aklnvpyvsvpTaa 109
                                    +GgGt+ D+a +v+  +k++v +++vpT++
  gi|13542147|ref|NP_111835.1| 100 YIGGGTVGDLAGFVAstYKRGVMMIAVPTTL 130
                                   **************84468999*******85 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.04
                      Fe-ADH_2 229 HliSHaldmlalkqalHGeqVG 250
                                   H i+H ++ + + +  HG+ V+
  gi|13542147|ref|NP_111835.1| 243 HTIAHGIEGATKGSISHGKAVA 264
                                   9**********9******9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       535  (0.0298399); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 2289.42
//
Query:       gi|13542148|ref|NP_111836.1|  [L=267]
Description: shikimate 5-dehydrogenase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.3e-21   74.4   0.0    1.1e-20   73.7   0.0    1.4  1  Shikimate_dh_N   Shikimate dehydrogenase substrate binding do
    0.00071   19.7   0.0     0.0014   18.7   0.0    1.5  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
      0.003   18.0   0.1     0.0051   17.2   0.1    1.3  1  NAD_binding_7    Putative NAD(P)-binding
     0.0061   15.9   0.0      0.012   15.0   0.0    1.5  1  THF_DHG_CYH_C    Tetrahydrofolate dehydrogenase/cyclohydrolas
     0.0077   16.0   0.3      0.012   15.4   0.3    1.2  1  ELFV_dehydrog    Glutamate/Leucine/Phenylalanine/Valine dehyd
  ------ inclusion threshold ------
      0.042   13.5   0.0      0.064   12.9   0.0    1.2  1  ApbA             Ketopantoate reductase PanE/ApbA
      0.062   13.6   0.0       0.12   12.6   0.0    1.5  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 !   73.7   0.0   4.3e-24   1.1e-20       1      83 []      10      90 ..      10      90 .. 0.97

  Alignments for each domain:
  == domain 1  score: 73.7 bits;  conditional E-value: 4.3e-24
                                  EEESS-TT-SHHHHHHHHHHHCTSSEEEEEEE-SCCTHHHHHHHHHHTTESEEEE-TTSCCHHHGGSSEE-HHHHHHT--SEE CS
                Shikimate_dh_N  1 viGnpikhSlSPaihnaafkalglngsyeafeveedelekaveelralglaGlnvTiPfKeaviplldelseeAkaigAvNti 83
                                  +iG+p++hS   +++n++f+++gln+ y  +++ ++ l+ +++ ++  +++G+nvTiP+K +++++ld+++ eA++ig+vN +
  gi|13542148|ref|NP_111836.1| 10 LIGHPVSHSIGQIVYNRYFQKKGLNAIYLSIDIFPETLKYFMSYAS--KMDGFNVTIPHKISIMDYLDQIDWEARSIGSVNLV 90
                                  79****************************************9988..6********************************86 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   5.6e-07    0.0014       9      56 ..     117     164 ..     110     186 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 5.6e-07
                                   ..TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHH CS
                  Shikimate_DH   9 slkekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeel 56 
                                   ++++k +++ G G +a+ v+++L+++++k+v+v  R+++ ak+  + +
  gi|13542148|ref|NP_111836.1| 117 DVSGKSIVVAGSGGIARTVIHYLIKNNAKSVTVKARDVKLAKNKLNAY 164
                                   68899********************************99888655555 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.1     2e-06    0.0051       3      68 ..     116     182 ..     115     193 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2e-06
                 NAD_binding_7   3 ldlkgkkvlvvGgGevAarkvrklleagak.vtvvapevkeeleelvklaeeelekd.legadlviaa 68 
                                   +d++gk+++v+G G +A + ++ l++++ak vtv a +v + +++++++ + ++++   +++d+ i +
  gi|13542148|ref|NP_111836.1| 116 VDVSGKSIVVAGSGGIARTVIHYLIKNNAKsVTVKARDV-KLAKNKLNAYDVDIKEYaNNDYDIYINC 182
                                   6899**********************9976599999995.4445545554444432213345555555 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 !   15.0   0.0   4.5e-06     0.012      21      82 ..     105     166 ..      86     175 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 4.5e-06
                                   HHHHHHHHHCT---TT-EEEEE---TTTHHHHHHHHHCTT-EEEEE-TTSCCHHHHHCCSSE CS
                 THF_DHG_CYH_C  21 kgvvellketgielegkkvvvvGrsnivgkplallLleknatVtvchsktkdlaeitreadi 82 
                                   +g+  + k+ g++++gk++vv G + i    ++ l++++   Vtv  +  k  +++++  d+
  gi|13542148|ref|NP_111836.1| 105 YGIEYMFKKGGVDVSGKSIVVAGSGGIARTVIHYLIKNNAKSVTVKARDVKLAKNKLNAYDV 166
                                   689999********************************999999988888777777766665 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 !   15.4   0.3   4.5e-06     0.012      17      62 ..     106     150 ..     101     171 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 4.5e-06
                                   HHHHHHHHTTTS-STTEEEEEE--SHHHHHHHHHHHHCT-EEEEEE CS
                 ELFV_dehydrog  17 yveemlkklkldslegkrvaisGsGnvgsyaallltelgakvvavs 62 
                                    +e m+kk ++ +++gk++++ GsG ++  ++  l++ +ak v+v 
  gi|13542148|ref|NP_111836.1| 106 GIEYMFKK-GGVDVSGKSIVVAGSGGIARTVIHYLIKNNAKSVTVK 150
                                   56789999.5556******************************996 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   2.5e-05     0.064       1      46 [.     123     171 ..     123     190 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.5e-05
                                   EEEES-SHHHHHHHHHHHH.HTHCEEEE-SCH.HHHH.HHHHCEEEEET CS
                          ApbA   1 iailGaGaiGsllaakLak.agadvtlilrsr.rlea.lkknGlrltse 46 
                                   i+++G+G+i +++ ++L k ++  vt+ +r+   +++ l+  +++++++
  gi|13542148|ref|NP_111836.1| 123 IVVAGSGGIARTVIHYLIKnNAKSVTVKARDVkLAKNkLNAYDVDIKEY 171
                                   89***************99666669999999944444555555555544 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   4.8e-05      0.12       1      54 [.     123     171 ..     123     184 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.8e-05
                                   EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE- CS
               Sacchrp_dh_NADP   1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaial 54 
                                   +++ G+G++++ v+++l +++     +tv  r+ + +++ +   +  ++++++ 
  gi|13542148|ref|NP_111836.1| 123 IVVAGSGGIARTVIHYLIKNNAK--SVTVKARDVKLAKNKL---NAYDVDIKEY 171
                                   7999****************998..9999999998866665...3344444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       692  (0.0385967); expected 358.6 (0.02)
Passed bias filter:                      535  (0.0298399); 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: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 1635.46
//
Query:       gi|13542149|ref|NP_111837.1|  [L=268]
Description: shikimate kinase [Thermoplasma volcanium GSS1]
Scores for complete 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-09   35.8   1.7    3.7e-08   33.5   1.4    2.1  2  GHMP_kinases_N  GHMP kinases N terminal domain
     0.0001   22.6   0.0    0.00047   20.5   0.0    2.1  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 !   33.5   1.4   4.1e-12   3.7e-08       3      66 .]      64     131 ..      62     131 .. 0.85
   2 ?   -0.1   0.0      0.13   1.1e+03      39      52 ..     174     187 ..     152     195 .. 0.80

  Alignments for each domain:
  == domain 1  score: 33.5 bits;  conditional E-value: 4.1e-12
                                   EEEESSHTTSSSCHHHHHHHHHHHHHHHHTTEHHHH....HHHHHHHHHHHHHHHHHSHHH.HHHHHSS CS
                GHMP_kinases_N   3 vikseiPvgaGLGSSAAlavalvaAllallglslee....aklaleaerlaqggngsggDv.aasvyGg 66 
                                   ++ks iP g GL SS+Al++al++A l + ++++e+    ++la  +  ++++  ++  D+ + ++yGg
  gi|13542149|ref|NP_111837.1|  64 KVKSSIPAGYGLKSSSALVLALAKASLLYKSVDIEDadllVRLANISK-AVGLSATGALDDlCQALYGG 131
                                   79***********************99999888866678999999999.56667777777769999998 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.13
                                   HHHHHHHHHHHHHH CS
                GHMP_kinases_N  39 aklaleaerlaqgg 52 
                                   +k a  ae+laq+g
  gi|13542149|ref|NP_111837.1| 174 FKVARSAENLAQRG 187
                                   799999****9976 PP

>> GHMP_kinases_C  GHMP kinases C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.38   3.4e+03       8      43 ..      98     128 ..      86     135 .. 0.68
   2 !   20.5   0.0   5.2e-08   0.00047      39      75 ..     210     244 ..     201     247 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.38
                GHMP_kinases_C   8 gdlellgellnlsqrselkavvgilppeleelleal 43 
                                   +d++ll +l+n s +     v  + + +l++l++al
  gi|13542149|ref|NP_111837.1|  98 EDADLLVRLANISKA-----VGLSATGALDDLCQAL 128
                                   566666666666655.....7777777888888887 PP

  == domain 2  score: 20.5 bits;  conditional E-value: 5.2e-08
                GHMP_kinases_C  39 llealselGalgaklsGaGgGptvfalfkdkdeaeqv 75 
                                    +++++e+G  +   s++G Gp+vf+lf+d+++a+++
  gi|13542149|ref|NP_111837.1| 210 TVRKIEENG--ANYASQSGKGPAVFGLFTDPSDAKRA 244
                                   567889999..555666666**************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 1803.34
//
Query:       gi|13542150|ref|NP_111838.1|  [L=410]
Description: 3-phosphoshikimate 1-carboxyvinyltransferase [Thermoplasma volcanium GSS1]
Scores for complete sequence (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  182.4   0.0    1.4e-53  182.1   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 !  182.1   0.0     8e-58   1.4e-53       9     417 .]      12     400 ..       7     400 .. 0.91

  Alignments for each domain:
  == domain 1  score: 182.1 bits;  conditional E-value: 8e-58
                                   EEEE--B-HHHHHHHHHHHGGGBSSEEEES---SHHHHHHHHHHHHTT.EEEEEECTSEEEEEGTT..--EE-HHHHTT-G CS
                 EPSP_synthase   9 gevkvpGsksisnralllAaLaegestitnlLdseDvrsmlealreLgaeiikldeekevviveglggsfeapeelvldlg 89 
                                   g  ++p+sks ++r +l++a +++ + ++++   +D +  + +  + g  +i +  ++  +++++   +f+ pe   +++g
  gi|13542150|ref|NP_111838.1|  12 GIAEMPSSKSFTQRYVLASAFLNKSVVLNGITITNDDDVAMRIAESVG-STITI--NNRSIKISS---NFKCPE--EIYVG 84 
                                   66689*******************************************.56667..466666666...799994..89*** PP

                                   GGGGGHHHHHHHHSEESSEEEEE-SBTTCGS--HHHHHHHHHTT-EEEEETTEEEEEESEETSS-BEEEEETSSTTHHHHH CS
                 EPSP_synthase  90 nsgtalrlLtallalasgevvLtGdesirkRPidrlldaLrqlGaeieveegenkaplkvkglklkgveikaevsSqqvts 170
                                    sgt+ rl ++lla  ++ + ++G++s+ kRPi++ll aL ++G++ e +++++  +++ ++++ k vei+++ sSq+v+s
  gi|13542150|ref|NP_111838.1|  85 ESGTSYRLSIGLLAASGCVTRIKGEDSLAKRPIEPLLMALGENGVKFE-RNEAGFYNVDGRNSQKKHVEIEGS-SSQFVSS 163
                                   ****************9*******************************.8888******************98.9****** PP

                                   HHHHHHTTSBSEEEEES-TTHHHHHHHHHHHHHTT-EEEETTSSEEEEEE--SSB--EEEE--B-HHHHHHHHHHHHHTT- CS
                 EPSP_synthase 171 llllaallaegtteleelasepsiddtlkmlkkfgikietsgteesitvkGkeklpgteyvvegDassAayflvaAaitgg 251
                                   l+l +a    g+ +  +++s  ++ +t ++l ++g   +    e++it+++    +   + ve+D+ss a+f+v ++++++
  gi|13542150|ref|NP_111838.1| 164 LMLYYAKKGGGEFTARNIKSIGYVYITKRVLYDLGYFANI---ERTITINPTGVWKT-AIDVEPDYSSMAFFMVLGLLSDS 240
                                   ******66556************************98877...556******99776.7********************** PP

                                   .EEEEES--GGGGHHH..HHHHHHHHTTEEEEEESTSEEEEEETTS--BEEEEEBGSTTSBHGGGHHHHHHHHHTSBSEEE CS
                 EPSP_synthase 252 .evtvenvginslqGdiealdeilekmgaeitqeedasivvgpsglklkdvdietlpdeaptlavlaafaegttviegiae 331
                                    +v+ +  +i+ +q d  +ld  l k +  i+ ee   i+v +   ++++vd    pd+ p+l v   f++    i++ ++
  gi|13542150|ref|NP_111838.1| 241 vDVRFRIKRISRIQPDSVILD--LFKNNILINGEE---IRVISGINEPVSVDADMNPDLCPPLSVIGIFSKYGVQIRNYER 316
                                   **************9966666..777888888888...55555567999******************************** PP

                                   EEGSSSTTCCHHHHHHHTTT-EEEEETTEEEEEEEEE.EB-EEEE-TTSTTTTHHHHHHHHHSBSEEEEETTHHHHHHSSS CS
                 EPSP_synthase 332 lrvketdrlaamateLrklGaeveeeedgliiipaekqlkgaevesydDhRiamalalaglvaegeveiddiectdksfpe 412
                                   l+ ke++r   +++  +++Ga+ve +   l i+p+++  +   v sy+DhR+ ma ++a+l+   ++ i+++e t+ksfp+
  gi|13542150|ref|NP_111838.1| 317 LKTKESNRYEGIIDLAERFGANVEDNGQDLFIKPGSV--RFPDVISYKDHRMIMAASIASLIGGFPTVIENAEKTAKSFPG 395
                                   ************************9887677799976..667******************88888**************** PP

                                   HHHHH CS
                 EPSP_synthase 413 feekL 417
                                   f+ +L
  gi|13542150|ref|NP_111838.1| 396 FFAEL 400
                                   *9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (410 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); 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: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.48
# Mc/sec: 2548.99
//
Query:       gi|13542151|ref|NP_111839.1|  [L=545]
Description: arginyl-tRNA synthetase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.3e-29  102.4   0.1    4.1e-29  101.6   0.1    1.4  1  tRNA-synt_1d  tRNA synthetases class I (R)
    7.3e-26   90.7   0.0    3.3e-25   88.6   0.0    2.1  2  DALR_1        DALR anticodon binding domain
    1.3e-06   27.6   0.5     0.0012   17.9   0.0    2.7  2  tRNA-synt_1f  tRNA synthetases class I (K)
    4.3e-05   23.0   0.1       0.18   11.2   0.0    2.5  2  tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
    0.00069   18.5   0.1      0.016   14.0   0.1    2.2  2  tRNA-synt_1g  tRNA synthetases class I (M)
  ------ inclusion threshold ------
      0.053   13.9   0.2         26    5.2   0.0    3.3  3  Nmad4         Nucleotide modification associated domain 4


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 !  101.6   0.1   1.4e-32   4.1e-29      14     335 ..     101     405 ..      90     419 .. 0.80

  Alignments for each domain:
  == domain 1  score: 101.6 bits;  conditional E-value: 1.4e-32
                                   ---SST-EEEEE----BTTS--BHHHHHHHHHHHHHHHHHHHCT-EEEEEE--B-SSTCHHHHHHHHHHHTTTTTTS---- CS
                  tRNA-synt_1d  14 kksrekkkvvvdfssPniakemhvGhLrstiiGdavsrlleflGydvirlnhvGDWGtqfGlLiaylekkqdekllqeqel 94 
                                      +e ++v v+++s n   ++h+G  r  iiGd++srll   Gy v++  +v D G+q+  L + +ek++    + ++ l
  gi|13542151|ref|NP_111839.1| 101 DTFQEPERVSVEHTSANPTGPLHIGRARNSIIGDSISRLLGRFGYRVTKQYFVNDSGKQMLSLYTAYEKYNGPM-TMDNLL 180
                                   45677889***************************************************999999999998877.558999 PP

                                   -SCCCHHHHHHHHCCCSHCCCHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHH....HHHHHHHCT---EC--CC..CCCCC CS
                  tRNA-synt_1d  95 qdLeafykeakkdydeeeifaerarnyvvkLqsgdedirklwkllvditrte....lqklydrldvtlierGes..lykes 169
                                   qd +++yke++kd   ee+++++        +  d++i    + +  ++ +     l k+++ +d +     es  +    
  gi|13542151|ref|NP_111839.1| 181 QDYQKIYKEIEKDKSVEEEIENNLMR----YERADPNIYGKLREIAGVMLQGitgtLAKVWIGFDEFN---WESdfIRSGE 254
                                   **999999999999999988776555....56667775555555555555440000566666666655...6775355556 PP

                                   HHHHHHHHHCTT-EEECTTCEEEEECCCTSSCCEECC-TTS-B-HHHHHHHHHHHHHHTT--SEEEEEEECCCHHHHHHHH CS
                  tRNA-synt_1d 170 lneivkelkkkglvkesdGalvvfldefgkrlgvvvqksDGgylytttDiaaakerkeelkadkvlyvidsrqslhlqqif 250
                                   ++++++ ++      e+ Ga+ + +   g++  v + +sDG++ly  +Dia   +  + +++d ++ v+ +  + h + + 
  gi|13542151|ref|NP_111839.1| 255 VEKAIESVN----PSEEGGAKYIEVG--GRK--VFLTRSDGTTLYFSRDIAYHLY--KAQNFDWIINVLGEDHKEHGKLLE 325
                                   666666555....46899*****999..665..5788*************98765..56679*******999999999988 PP

                                   HHHHCTTSSTTTSEEEEEEE--EE-TTSSBSBCSSSTC-BHHHHHHHHHHHHHHHHCCCCCCTS-CCCCHCHHHHHHHHHH CS
                  tRNA-synt_1d 251 lilkkigyvpeskdlehanfGmvlgkdkkkfktrkGetvkLadlLdealeralqlikeknkdkvlqadelekvaeavgvga 331
                                    ++k i  +   ++  + +f  +   +  k++tr+G++v L+dl++ + e al+ ++ek +d  l+ + ++++a++++ ++
  gi|13542151|ref|NP_111839.1| 326 HVMKGIMNIESKMSFVYYSFITL---ESGKMSTRRGNIVTLEDLIERTFEEALRIVREKRPD--LEEERMKEIAKVIASSS 401
                                   88887766555666777777666...7778********************************..***************** PP

                                   HHCC CS
                  tRNA-synt_1d 332 ikya 335
                                   i+++
  gi|13542151|ref|NP_111839.1| 402 IRFN 405
                                   9986 PP

>> DALR_1  DALR anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.89   2.7e+03      71      95 ..     366     391 ..     358     412 .. 0.70
   2 !   88.6   0.0   1.1e-28   3.3e-25       1     119 []     433     545 .]     433     545 .] 0.92

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.89
                                   HHHHHHH.HCTSTTSCTHHH.HHHHH CS
                        DALR_1  71 tfhkfYn.kervlkeeeeelaaaRLa 95 
                                    + + ++ + r++ e++++l+++R++
  gi|13542151|ref|NP_111839.1| 366 LIERTFEeALRIVREKRPDLEEERMK 391
                                   55555652458888888888888875 PP

  == domain 2  score: 88.6 bits;  conditional E-value: 1.1e-28
                                   HHHHHHHHHHHHHHTTCTTCCCCHCCHCCS-SHHHHHHHHHHHTHHHHHHHHHHHT-THHHHHHHHHHHHHHHHHHHHCTS CS
                        DALR_1   1 vqyahaRiksilrkaeeegekleeealalleeeeekeLlkalaqfpevleeaaeelephklaeylyeLaatfhkfYnkerv 81 
                                   ++y++aR +si +k+e ++++ ++e      + ee+eL++++  +p vl++aa++l+p+ +a yl++La++f++fY+++rv
  gi|13542151|ref|NP_111839.1| 433 IMYTYARGASIIKKKERDEKDFSTEM-----DHEEEELVRQMYLYPYVLSDAAQNLRPDIIAGYLIDLAQKFNDFYKACRV 508
                                   69***********9997775443333.....55899********************************************* PP

                                   TTSCTHHH.HHHHHHHHHHHHHHHHHHHHTT----S-- CS
                        DALR_1  82 lkeeeeelaaaRLaLvkavrqvLangLdlLGieapekm 119
                                   +++++ +  + R++L++   ++++++ d+LGi+++e++
  gi|13542151|ref|NP_111839.1| 509 IGAPDGVY-DRRIRLIETYMKIVEDAGDILGIKMLEEI 545
                                   *******9.**************************985 PP

>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.1   0.00063       1.9      28      70 ..     113     155 ..      98     207 .. 0.82
   2 !   17.9   0.0   3.9e-07    0.0012     239     313 ..     312     383 ..     304     416 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.00063
                  tRNA-synt_1f  28 esGispSGliHiGnlrevltadlvaralrkrgeevrlilisDd 70 
                                    + + p G++HiG++r+ + +d + r l + g +v   ++++d
  gi|13542151|ref|NP_111839.1| 113 HTSANPTGPLHIGRARNSIIGDSISRLLGRFGYRVTKQYFVND 155
                                   477889*********************9999988655555544 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 3.9e-07
                  tRNA-synt_1f 239 paGkDhaaaGgSvdvsskia.eilggeaPekvvY.elillkggekmssSkGnvltledwlevaepevlrflilrrkP 313
                                     G Dh +     ++ ++++  i+++e  +++vY  +i+l+ g kms  +Gn++tled++e   +e lr +  + +P
  gi|13542151|ref|NP_111839.1| 312 VLGEDHKE---HGKLLEHVMkGIMNIESKMSFVYySFITLESG-KMSTRRGNIVTLEDLIERTFEEALRIVREK-RP 383
                                   67999999...55777888889****99999876166666666.**********************99976655.55 PP

>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.0   5.9e-05      0.18      23      61 ..     122     160 ..     104     208 .. 0.74
   2 !    9.3   0.0   0.00021      0.64     240     279 ..     339     378 ..     326     387 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 5.9e-05
                                   -BHHHHHHHHHHHHHHHHHHHTT-EEEEEEEBB--SHHH CS
                  tRNA-synt_1e  23 shlGhaRslvafDilrrilqalgYdvqfvqnvtDidDki 61 
                                    h+G+aR+ ++ D + r+l  +gY v+    v D   ++
  gi|13542151|ref|NP_111839.1| 122 LHIGRARNSIIGDSISRLLGRFGYRVTKQYFVNDSGKQM 160
                                   7*************************8655555655554 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00021
                                   EEEEE--EEETTBE--TTTT---BHHHHHTTS-HHHHHHH CS
                  tRNA-synt_1e 240 yflhnghlkiegekmsksLknfitikdvlkkfdprqlRll 279
                                    f++  ++++e  kms   +n++t++d++++   ++lR++
  gi|13542151|ref|NP_111839.1| 339 SFVYYSFITLESGKMSTRRGNIVTLEDLIERTFEEALRIV 378
                                   588899*************************999999975 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 ?    2.2   0.0      0.02        59      11      40 ..     119     148 ..     111     200 .. 0.75
   2 !   14.0   0.1   5.4e-06     0.016     284     352 ..     309     377 ..     290     397 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.02
                                   SS---HHHHHHHHHHHHHHHHHHHTT-EEE CS
                  tRNA-synt_1g  11 ngklHlGhllevisaDifaRykrlrgeevl 40 
                                   +g+lH+G +++ i++D ++R     g+ v+
  gi|13542151|ref|NP_111839.1| 119 TGPLHIGRARNSIIGDSISRLLGRFGYRVT 148
                                   799*****************9988887764 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 5.4e-06
                                   .EEEEEGGGHHHHHTHHHHHHHH.TT----S-EEEE--EEE--------------HHHHHHHH-HHHHHH CS
                  tRNA-synt_1g 284 lvhfigkdiikFHtifwPaillg.aelklpkkvvaheyltvegkKlSkSrgvvvkakealerldadllRY 352
                                   +++++g d  + H  ++  +++g  +++   + v  +++t+e +K+S+ rg++v+ ++++er   ++lR 
  gi|13542151|ref|NP_111839.1| 309 IINVLGEDHKE-HGKLLEHVMKGiMNIESKMSFVYYSFITLESGKMSTRRGNIVTLEDLIERTFEEALRI 377
                                   67777877655.555556666666889999999999**************************99999995 PP

>> Nmad4  Nucleotide modification associated domain 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0    0.0088        26      35      68 ..      29      62 ..      24      66 .. 0.85
   2 ?    4.0   0.1     0.021        62      44      70 ..     184     211 ..     173     215 .. 0.88
   3 ?   -0.7   0.0      0.61   1.8e+03      58      77 ..     515     534 ..     495     536 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0088
                         Nmad4 35 kkkgakgneaaiYelveepeeagkiEcrlnliee 68
                                  + +g+ ++++++++l+++p+  +kiE  ++ i  
  gi|13542151|ref|NP_111839.1| 29 DPTGHSDFTVRVFRLINQPDGREKIEKMIEKIRT 62
                                  5578899********************9998865 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.021
                         Nmad4  44 aaiYelveepeea.gkiEcrlnlieese 70 
                                    +iY+ +e+++++ ++iE +l++ e ++
  gi|13542151|ref|NP_111839.1| 184 QKIYKEIEKDKSVeEEIENNLMRYERAD 211
                                   58***********999*****9999886 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.61
                         Nmad4  58 kiEcrlnlieeseelFeDeG 77 
                                     ++r+ lie  ++ +eD+G
  gi|13542151|ref|NP_111839.1| 515 VYDRRIRLIETYMKIVEDAG 534
                                   57899*************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (545 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       749  (0.0417759); expected 358.6 (0.02)
Passed bias filter:                      521  (0.0290591); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.65u 0.29s 00:00:00.94 Elapsed: 00:00:00.47
# Mc/sec: 3487.14
//
Query:       gi|13542152|ref|NP_111840.1|  [L=958]
Description: hypothetical protein TVN1321 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-15   57.6   2.7    1.2e-15   57.6   2.7    5.3  6  CARDB     CARDB


Domain annotation for each model (and alignments):
>> CARDB  CARDB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.1      0.52   9.3e+03      45      72 ..     188     212 ..     179     225 .. 0.59
   2 ?   -1.7   0.4      0.19   3.5e+03      41      72 ..     357     391 ..     350     409 .. 0.61
   3 ?   -2.2   1.6      0.27   4.9e+03      30      72 ..     484     532 ..     460     574 .. 0.65
   4 ?   -0.4   0.4     0.076   1.4e+03      26      79 ..     540     595 ..     528     605 .. 0.67
   5 !    3.1   0.1    0.0065   1.2e+02      38      84 ..     641     687 ..     629     708 .. 0.82
   6 !   57.6   2.7   6.9e-20   1.2e-15       1      84 [.     802     884 ..     802     891 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 0.52
                                   TTEEEEEEEESEE-CTEEEEEEEEEE-S CS
                         CARDB  45 dgelvgtvtvpsLaagesttvsftwtte 72 
                                   + +++ t+++ s+++++    +f++t++
  gi|13542152|ref|NP_111840.1| 188 NYSSKITTYLMSINSSS---STFNITPN 212
                                   55555555555555554...45555554 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.19
                                   EEEETTEEEEEEEE...SEE-CTEEEEEEEEEE-S CS
                         CARDB  41 alyldgelvgtvtv...psLaagesttvsftwtte 72 
                                   +++++g   + + v   + ++ ++++  +++ +++
  gi|13542152|ref|NP_111840.1| 357 SFMVNGVYYNLTAVpkvSVISTSNTSHATINAVYA 391
                                   56666666644433222777777777777777776 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 0.27
                                   -SSS-EEEEEEEEEETTEEEEEEEE........SEE-CTEEEEEEEEEE-S CS
                         CARDB  30 qGtaasgatkvalyldgelvgtvtv........psLaagesttvsftwtte 72 
                                   +   +s++t+  +++ ++++  v++        p  +++++ + +ftwt+ 
  gi|13542152|ref|NP_111840.1| 484 NYVLNSTSTNSVYVVPRNQT--VYLnsstayfnPVTNSDDYMQANFTWTIG 532
                                   44444444444433333332..22244444445555666777777777765 PP

  == domain 4  score: -0.4 bits;  conditional E-value: 0.076
                                   EEEE-SSS-EEEEE..EEEEETTEEEEEEEESEE-CTEEEEEEEEEE-S-S-CEEE CS
                         CARDB  26 tvkNqGtaasgatk..valyldgelvgtvtvpsLaagesttvsftwtteategevt 79 
                                   +++N    +s++++  v+    g+  +++tv sL++ +  +v+f+  ++ ++ ++t
  gi|13542152|ref|NP_111840.1| 540 NISNVFRSSSTSVSvfVRSPSGGTAYSNFTVLSLNNTTAPKVKFSASYNGHSISYT 595
                                   55555444443333003444567777999999999999999999999886666665 PP

  == domain 5  score: 3.1 bits;  conditional E-value: 0.0065
                                   EEEEEEETTEEEEEEEESEE-CTEEEEEEEEEE-S-S-CEEE.EEEEE CS
                         CARDB  38 tkvalyldgelvgtvtvpsLaagesttvsftwtteategevt.ltvvv 84 
                                   + +a y+ +++   ++ ps+a+g   +vsf   t+ ++g+v+ + ++v
  gi|13542152|ref|NP_111840.1| 641 FPTATYIGDNVSYAFSHPSIAPGYGNQVSFANITT-EAGNVYhILMKV 687
                                   56777888888777888*****************9.999999666665 PP

  == domain 6  score: 57.6 bits;  conditional E-value: 6.9e-20
                                   S--EEE.EEEC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEEEEEEESEE-CTEEEEEEEEEE-S-S-CEEEEE CS
                         CARDB   1 tpDLtvtntlnpseafvgeentitvtvkNqGtaasgatkvalyldgelvgtvtvpsLaagesttvsftwtteategevtlt 81 
                                   tp L+v+++++ ++ ++g++++++v+v+N Gt++++++ +++y++g++ g++tv++++ag+s +vs++w+++ t+g+v + 
  gi|13542152|ref|NP_111840.1| 802 TPRLVVNSIYASGAQYQGSSSKLYVNVSNLGTENAYNVLIQVYVNGKVYGSTTVSEIKAGASDNVSINWVPP-TSGKVSVY 881
                                   699*********************************************************************.99998866 PP

                                   EEE CS
                         CARDB  82 vvv 84 
                                   +++
  gi|13542152|ref|NP_111840.1| 882 ATA 884
                                   655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (958 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       936  (0.0522059); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); 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: 0.80u 0.31s 00:00:01.11 Elapsed: 00:00:00.49
# Mc/sec: 5900.23
//
Query:       gi|13542153|ref|NP_111841.1|  [L=466]
Description: hypothetical protein TVN1322 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   1.2e-138  462.7   0.0   1.4e-138  462.6   0.0    1.0  1  RtcB      tRNA-splicing ligase RtcB


Domain annotation for each model (and alignments):
>> RtcB  tRNA-splicing ligase RtcB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  462.6   0.0  7.8e-143  1.4e-138       1     412 []      43     466 .]      43     466 .] 0.97

  Alignments for each domain:
  == domain 1  score: 462.6 bits;  conditional E-value: 7.8e-143
                                   HHHHHTTSTTB-S-EEEEEEEE--SSS-EEEEEEE-...-EE-HHHC-SST.-EEEEEEEEEEHHHHGGGHHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          RtcB   1 qlknvaslpgivkhvaamPDvHlGkgapiGsViatk...gviiPaaVGvDI.CGvrllktnltaeeleeklkelvkeleka 77 
                                   q+ nva+lpgiv++++amPD+HlG+g+piG+V+a++   g+i+P++VG+DI CGv+ll+t +++ ++++++k++++ ++++
  gi|13542153|ref|NP_111841.1|  43 QVVNVAKLPGIVEASYAMPDIHLGYGFPIGGVAAFDydeGIISPGGVGYDInCGVALLRTGMNYAQIKPRIKDITDYIFQE 123
                                   899****************************************************************************** PP

                                   S-------------HHHHHHHHHHTHHHHHHTTSS-GGGGGGBGGGG--TT--GGGS-HHHHHHHGGGTT---STT-EEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          RtcB  78 vpvglgskkkvklskkeleevleegakwaveeglgeeedlekieeegalkeadlekvskkakerarkqlGtlGsGNHFiEv 158
                                   vp+gl+s+k   +++++l+e+l++g kwav++gl++e d+ ++e++g++++   ++vsk+a +r+ +q+GtlG+GNHF+E+
  gi|13542153|ref|NP_111841.1| 124 VPSGLTSRKGFPVNQNDLQEILTSGLKWAVSRGLATELDMINTEDNGSIESH-GTHVSKQAMQRGLSQIGTLGAGNHFLEI 203
                                   *************************************************996.6669999********************* PP

                                   EEEEEES-HHHHHHHT--TTEEEEEEEE--HHHHHHHHHHHHHHHHCCHHHCT---SSGGG--EETTSHHHHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          RtcB 159 qlveeildeeaakalgleegqvvvmlHsGSRglGhqiaedylkiakkalkkkgiklpdrdLaylpagseegqaYlkamqaa 239
                                   q v +i+de++a+++gl +++v+vm+H+GSRglGhq+a+dyl+ ++ + +   ik+ d++L+ + ++s+ g++Yl+am+ a
  gi|13542153|ref|NP_111841.1| 204 QRVSDIFDEDVARKFGLYKDEVTVMIHTGSRGLGHQVATDYLRELR-ESR-ESIKTSDPELISIHVKSKIGENYLDAMKSA 282
                                   **********************************************.554.679*************************** PP

                                   HHHHHHHHHHHHHHHHHHHHHT.T--HHHH--EEEEEEESEEEEEEEE..T...EEEEEEEES-EE-...........TT- CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x...xxxxxxxxxxxxx...........xxx RF
                          RtcB 240 anyAkaNRqvitervreilekvlkkekedlelelvvdvaHNiakkEehe.d...ekvlVhRKGAtrA...........kvg 305
                                   an+A++NRq+    vr++++k+++     +e elv+ +aHNiak E h  +   ++++VhRKGAtrA           ++g
  gi|13542153|ref|NP_111841.1| 283 ANFAFVNRQMAIYGVRKVFKKFFD-----VEPELVYSLAHNIAKVEDHIvEgktKSLIVHRKGATRAfgpgkssppfeDTG 358
                                   ***********************5.....55569**************9845889************************** PP

                                   -EEEE--STTS-EEEEE--HHHH..SSSEE---S-----------------TTTTTCCCT-EEEE---------------- CS
                                   xxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          RtcB 306 qpviipGsmgtkSyivkGkgnae..sfgStsHGAGRlmsRakakkkfkleevkkdleeqgigvearkkegvleEapeaYKd 384
                                   +pv+ipGsmgt+Sy+++G +++   sfg+++HG+GR++sR++a kkf++  v+++lee+ ++++ ++k+++ eEap++YK+
  gi|13542153|ref|NP_111841.1| 359 HPVLIPGSMGTASYVLVGVKENLikSFGTACHGSGRVLSRNQAIKKFSSI-VDRELEEKDVYARPATKRVLYEEAPGSYKN 438
                                   ******************9988889***********************99.****************************** PP

                                   --HHHHHHHHCTS-EEEEEEEEEEEEE- CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          RtcB 385 ideVveaqaeaglvevvarlkpvlvvkg 412
                                   +deVv+a++ a l++ ++r+ p++vvkg
  gi|13542153|ref|NP_111841.1| 439 VDEVVAAVEGAHLARSIVRMVPLAVVKG 466
                                   ***************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (466 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); 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: 0.58u 0.33s 00:00:00.90 Elapsed: 00:00:00.49
# Mc/sec: 2840.54
//
Query:       gi|13542154|ref|NP_111842.1|  [L=107]
Description: hypothetical protein TVN1323 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0084   16.0   0.0      0.016   15.1   0.0    1.4  1  HTH_5     Bacterial regulatory protein, arsR family
  ------ inclusion threshold ------
       0.03   13.9   1.3      0.054   13.1   1.3    1.4  1  HTH_24    Winged helix-turn-helix DNA-binding
      0.047   13.1   0.0      0.059   12.8   0.0    1.4  1  RepL      Firmicute plasmid replication protein (RepL)
      0.051   13.5   0.3       0.37   10.8   0.0    2.2  2  HTH_12    Ribonuclease R winged-helix domain
      0.054   13.3   0.0        1.6    8.5   0.0    2.2  2  MerR      MerR family regulatory protein
      0.059   13.5   0.0       0.11   12.6   0.0    1.4  1  HTH_9     RNA polymerase III subunit RPC82 helix-turn-helix d
       0.12   12.3   0.1       0.26   11.2   0.0    1.6  2  TrmB      Sugar-specific transcriptional regulator TrmB


Domain annotation for each model (and alignments):
>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   6.3e-06     0.016      10      46 ..      27      63 ..      22      63 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 6.3e-06
                                  HHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                         HTH_5 10 lLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                  lL+e++  +  l+ e+g+++ ++++ L++L+++++++
  gi|13542154|ref|NP_111842.1| 27 LLREQPIGIIKLSQETGIPEHKIRYSLRILEQENIIS 63
                                  67888888999***********************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 ?   13.1   1.3   2.1e-05     0.054       5      47 ..      20      62 ..      17      63 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.1e-05
                        HTH_24  5 drkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                  ++ ++++L ++  i +  L++++g++   +++ l+ Le+e +I
  gi|13542154|ref|NP_111842.1| 20 HISVINVLLREQPIGIIKLSQETGIPEHKIRYSLRILEQENII 62
                                  67799************************************99 PP

>> RepL  Firmicute plasmid replication protein (RepL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   2.3e-05     0.059      80     121 ..      37      77 ..       5     106 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.3e-05
                          RepL  80 elaeetgislktvsetlkileeanilkkkanGvlvinPdllf 121
                                   +l++etgi  + ++  l+ile+ ni+    +G++ + Pd + 
  gi|13542154|ref|NP_111842.1|  37 KLSQETGIPEHKIRYSLRILEQENIISPSREGAI-LTPDFIE 77 
                                   7899*************************99986.5788764 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 ?   10.8   0.0   0.00015      0.37      27      51 ..      41      65 ..      27      74 .. 0.77
   2 ?    0.6   0.2      0.22   5.7e+02       6      26 ..      82     103 ..      81     107 .] 0.68

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00015
                        HTH_12 27 gydigeravRyrLrkleergltrrv 51
                                  +  i e  +Ry Lr+le+++++   
  gi|13542154|ref|NP_111842.1| 41 ETGIPEHKIRYSLRILEQENIISPS 65
                                  55678899**********9988654 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.22
                        HTH_12   6 ilaesdkpig.akeiaeeLkkr 26 
                                   i+a+++k++  a +iae+++k 
  gi|13542154|ref|NP_111842.1|  82 IIADAEKVLEeATKIAEDVRKM 103
                                   6777777774367899998876 PP

>> MerR  MerR family regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.0   0.00064       1.6       4      18 ..      37      51 ..      34      51 .. 0.91
   2 ?    2.5   0.0     0.049   1.3e+02      16      30 ..      53      66 ..      52      69 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00064
                                  HHHHHHTTTHHHHHH CS
                          MerR  4 evAeltGvsprtLRy 18
                                   +++ tG++ +++Ry
  gi|13542154|ref|NP_111842.1| 37 KLSQETGIPEHKIRY 51
                                  689***********9 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.049
                                  HHHHHHTTSSTSEEE CS
                          MerR 16 LRyYEreGLipppeR 30
                                  LR +E+e+ i +p R
  gi|13542154|ref|NP_111842.1| 53 LRILEQENII-SPSR 66
                                  899*******.6666 PP

>> HTH_9  RNA polymerase III subunit RPC82 helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   4.2e-05      0.11      17      57 ..      22      62 ..      18      63 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.2e-05
                                  HHHHHHHHHSSBEHHHHHHHHSSTHHHHHHHHHHHHHTTSE CS
                         HTH_9 17 kVvetLlrkgrltlrelvkktkLsldqVkksLvvLiqhrlV 57
                                   V+ +Llr+    + +l+++t+++  +++ sL +L q +++
  gi|13542154|ref|NP_111842.1| 22 SVINVLLREQPIGIIKLSQETGIPEHKIRYSLRILEQENII 62
                                  59999********************************9987 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0    0.0001      0.26      16      56 ..      26      66 ..      18      78 .. 0.88
   2 ?   -2.2   0.1       1.5   3.8e+03      20      30 ..      92     102 ..      86     106 .. 0.48

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0001
                                  HHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES CS
                          TrmB 16 aLlklgpatadeiaeelgvprskvYevLrsLedkGlVerek 56
                                  +Ll+++p  + ++++e+g+p+ k+  +Lr Le+  ++  ++
  gi|13542154|ref|NP_111842.1| 26 VLLREQPIGIIKLSQETGIPEHKIRYSLRILEQENIISPSR 66
                                  799999999***********************999887665 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.5
                                   HCCCHHCHHCC CS
                          TrmB  20 lgpatadeiae 30 
                                   +  + a+++ +
  gi|13542154|ref|NP_111842.1|  92 EATKIAEDVRK 102
                                   33444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       846  (0.0471861); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); 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: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 682.75
//
Query:       gi|13542155|ref|NP_111843.1|  [L=177]
Description: acetyltransferase [Thermoplasma volcanium GSS1]
Scores for complete 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   0.1    6.9e-15   55.3   0.1    1.3  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    1.1e-13   51.2   0.1    1.5e-13   50.8   0.1    1.2  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    1.2e-09   38.5   0.0    1.5e-09   38.2   0.0    1.1  1  Acetyltransf_4   Acetyltransferase (GNAT) domain
    9.1e-09   35.6   0.1    1.3e-08   35.2   0.1    1.3  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
      2e-08   35.0   0.0    2.5e-08   34.7   0.0    1.1  1  Acetyltransf_3   Acetyltransferase (GNAT) domain
    4.7e-05   23.3   0.1    7.8e-05   22.6   0.1    1.3  1  FR47             FR47-like protein
     0.0094   15.6   0.0      0.015   15.0   0.0    1.3  1  Acetyltransf_8   Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
        0.1   12.7   0.0       0.24   11.5   0.0    1.7  1  Acetyltransf_9   Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.3   0.1   3.1e-18   6.9e-15      21     117 .]      53     145 ..      34     145 .. 0.83

  Alignments for each domain:
  == domain 1  score: 55.3 bits;  conditional E-value: 3.1e-18
                                   HHHHHHHHHSTTCEEEEEEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTESEEEEEE CS
                Acetyltransf_1  21 eeefeesfsleaegllvaeedgeliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeerareegikkivlav 101
                                   +e+  +s    ++ +lv+  d +++G +++      k++++ + ++a+   +r+kGlG++++++++ +++++gikk+ l+v
  gi|13542155|ref|NP_111843.1|  53 QER-IKS---LDDLTLVCVIDRKVVGVLTVQRGIYRKNRHTGMLGIAIMAGHRHKGLGTRMIKEAILWCEDQGIKKLNLEV 129
                                   333.333...3445566678889*****887777778899***************************************** PP

                                   ETTEHHHHHHHHHTTE CS
                Acetyltransf_1 102 eedndaairlYeklGF 117
                                   +++n+ ai+ Yek+GF
  gi|13542155|ref|NP_111843.1| 130 FSTNVNAIKTYEKVGF 145
                                   ***************9 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.8   0.1   6.9e-17   1.5e-13      18     113 ..      48     152 ..      29     158 .. 0.87

  Alignments for each domain:
  == domain 1  score: 50.8 bits;  conditional E-value: 6.9e-17
               Acetyltransf_10  18 spealrerieegealllvaeeggkivGvielrdgs.....hisll..fVdpeyrgqGigkaLleaveeeaekdgikl.elt 90 
                                   s+ a +eri++ + l+lv+  + k+vGv+++++g      h ++l  ++   +r++G+g++++++++  +e++gik+  l+
  gi|13542155|ref|NP_111843.1|  48 SERAEQERIKSLDDLTLVCVIDRKVVGVLTVQRGIyrknrHTGMLgiAIMAGHRHKGLGTRMIKEAILWCEDQGIKKlNLE 128
                                   446677888999999**************665555555569999999********************************** PP

               Acetyltransf_10  91 vnasp.yavpfYeklGFkavgeeq 113
                                   v +++ +a++ Yek+GF++ g+ +
  gi|13542155|ref|NP_111843.1| 129 VFSTNvNAIKTYEKVGFEVEGKRR 152
                                   ******************997765 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.2   0.0   6.7e-13   1.5e-09       1     154 [.      15     165 ..      15     166 .. 0.86

  Alignments for each domain:
  == domain 1  score: 38.2 bits;  conditional E-value: 6.7e-13
                Acetyltransf_4   1 iraateeDakeilaiyaey.vvntaitfeyevssveefekflealdsekeyvflvaesdrivGyaylgqfkkrakdwkael 80 
                                   ir a ++Da+ i   ++   +++  +  ey   s    + ++++l       + +  + ++vG ++++   +r  ++ ++l
  gi|13542155|ref|NP_111843.1|  15 IRKADPSDAAGIISCMQSVmDERIYLVGEYYLLSERAEQERIKSL---DDLTLVCVIDRKVVGVLTVQRGIYRKNRHTGML 92 
                                   899999*********976423433444555455555556788886...77788888899*********999999******* PP

                Acetyltransf_4  81 svylaerdnnkeglgrelidaleqvlkeqnienllaeiaspnensiqfhkalGFelvgifkkcikkngrwiDmi 154
                                    + +     +++glg  +i+  +     q+i++l+ e++s+n n+i+ ++++GFe++g+ +k + + g++ D +
  gi|13542155|ref|NP_111843.1|  93 GIAIM-AGHRHKGLGTRMIKEAILWCEDQGIKKLNLEVFSTNVNAIKTYEKVGFEVEGKRRKQFLIDGQYVDDV 165
                                   ****8.67************999999********************************************9976 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.2   0.1   5.6e-12   1.3e-08       6      75 ..      64     146 ..      37     147 .. 0.75

  Alignments for each domain:
  == domain 1  score: 35.2 bits;  conditional E-value: 5.6e-12
                                   EEEEETTEEEEEEEEEEES......TCTEE...EEE-GGGTTSSHHHHHHHHTT.....SEEEEE.EEEE.THH.HHHHHH CS
                Acetyltransf_7   6 fVaeddgkivGfialslld......aeitr...laVdpeyrgkGiGraLleaae.....kgiile.qlel.nae.kaikfY 69 
                                   +V+  d k+vG + +++        +   +   +a+   +r kG+G+++++ a+     +gi+ + +le+ +++ +aik Y
  gi|13542155|ref|NP_111843.1|  64 LVCVIDRKVVGVLTVQRGIyrknrhT---GmlgIAIMAGHRHKGLGTRMIKEAIlwcedQGIK-KlNLEVfSTNvNAIKTY 140
                                   45556789999888888777664333...2577*****************9523455667854.3333344223489**** PP

                                   HHTTEE CS
                Acetyltransf_7  70 eklGFe 75 
                                   ek GFe
  gi|13542155|ref|NP_111843.1| 141 EKVGFE 146
                                   *****9 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.7   0.0   1.1e-11   2.5e-08       3     138 .]      14     146 ..      12     146 .. 0.76

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 1.1e-11
                Acetyltransf_3   3 lLrplteeDlealfelrsdpevm..r.y.lpe..pltleeaeewlerawaeeseeegygwaivlkdtgviGsvglr..dle 75 
                                   ++r++ ++D++++ + ++   vm  r y ++e   l++ +++e++++ +      ++++ ++++ d +v+G+  ++   + 
  gi|13542155|ref|NP_111843.1|  14 IIRKADPSDAAGIISCMQS--VMdeRiYlVGEyyLLSERAEQERIKS-L------DDLT-LVCVIDRKVVGVLTVQrgIYR 84 
                                   78999999****9987774..44214445444445555666666663.3......4444.344557768999999955344 PP

                Acetyltransf_3  76 eedeeaelgymlapsfwgkGyateavralleyafeelglerlvavidkeNeaSirvleklGfe 138
                                   ++++++ lg+ +   ++ kG++t + + ++ ++ e++g+++l  ++  +N + i+ +ek+Gfe
  gi|13542155|ref|NP_111843.1|  85 KNRHTGMLGIAIMAGHRHKGLGTRMIKEAILWC-EDQGIKKLNLEVFSTNVNAIKTYEKVGFE 146
                                   55555****************************.8999************************7 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.1   3.5e-08   7.8e-05      19      80 ..      85     148 ..      74     154 .. 0.85

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 3.5e-08
                                   -TT.SSEEEEEE-GGG-SSSHHHHHHHHHHHHHHHS-S-EE.EEEETT-HHHHHHHHHHT-EEE CS
                          FR47  19 kdg.gelgalqvlpehrrrGlgsrlvkalakeiaergktvl.lvvvasNtpsirlyeklGfeki 80 
                                   k+  + + ++ +   hr +Glg+r++k+ +     +g++ l l v  +N ++i+ yek+Gfe+ 
  gi|13542155|ref|NP_111843.1|  85 KNRhTGMLGIAIMAGHRHKGLGTRMIKEAILWCEDQGIKKLnLEVFSTNVNAIKTYEKVGFEVE 148
                                   4444889999999**********************998755278999**************986 PP

>> Acetyltransf_8  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   6.6e-06     0.015      86     142 ..      98     150 ..      79     153 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 6.6e-06
                                   ESSHHHCTTTCHHHHHHHHHHHHHCCTT--EEEE--BTT-HHHHHHHHHTT-EEEEE CS
                Acetyltransf_8  86 igeaeargkglttallralvhylfadprtrrvvvEPdvrNerairllekaGfekeke 142
                                        +r kgl+t+++++ + ++ +d+++++  +E   +N +ai+ +ek+Gfe e++
  gi|13542155|ref|NP_111843.1|  98 A---GHRHKGLGTRMIKEAILWC-EDQGIKKLNLEVFSTNVNAIKTYEKVGFEVEGK 150
                                   3...47899*********99888.566**************************9886 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00011      0.24       3     126 ..      16     146 ..      14     147 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00011
                                   EEE-GGGHHHHHHHHHHHTT----H........HHHHHHHHHHTTSEEEEEEETTEEEEEEEEEEEEEEETTEEEEEEEEE CS
                Acetyltransf_9   3 relteedldevlellkyaFqdeespl......eeireyfrklleesrvlgaedngelvgqlallplelnvpGktlkaagvt 77 
                                   r+++++d  ++++  + +  ++   +       e+ e+ r +  ++ +l++  + ++vg+l++   +  ++ k+ +  g  
  gi|13542155|ref|NP_111843.1|  16 RKADPSDAAGIISCMQSVMDERIYLVgeyyllSERAEQERIKSLDDLTLVCVIDRKVVGVLTV---QRGIYRKNRH-TGML 92 
                                   666666666666666666655555555444432222332333334456666667777666554...2233333333.3556 PP

                                   EEEE-CCGTTS-HHHHHHHHHHHHHHHTT--EEEE--.....SSHHHHHTTT-E CS
                Acetyltransf_9  78 gVavapehrgrgvlskLlaraleemreegqplsllfP.....ssipiYrrfGye 126
                                   g+a  + hr +g+ ++++++a+  ++++g++   l        +i+ Y++ G+e
  gi|13542155|ref|NP_111843.1|  93 GIAIMAGHRHKGLGTRMIKEAILWCEDQGIKKLNLEVfstnvNAIKTYEKVGFE 146
                                   79999**********************999877776633333445778888887 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:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 1348.36
//
Query:       gi|13542156|ref|NP_111844.1|  [L=111]
Description: hypothetical protein TVN1325 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.019   15.2   0.2      0.032   14.5   0.2    1.4  1  FCH       Fes/CIP4, and EFC/F-BAR homology domain


Domain annotation for each model (and alignments):
>> 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 ?   14.5   0.2   1.8e-06     0.032      14      35 ..      36      57 ..      27      58 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.8e-06
                                  HHHHHHHHHHHHHHHHHHHHHH CS
                           FCH 14 alledlqeflkeRaeiEkeYak 35
                                  ++++ +q++l+++ae+E  Ya+
  gi|13542156|ref|NP_111844.1| 36 DTCQKYQDLLRQKAELESRYAA 57
                                  89******************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       691  (0.0385409); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 747.71
//
Query:       gi|13542157|ref|NP_111845.1|  [L=313]
Description: Fe-S oxidoreductase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.7e-16   60.0   0.1    1.9e-15   57.6   0.1    1.9  2  Radical_SAM  Radical SAM superfamily
    5.5e-11   42.9   0.6    3.7e-10   40.2   0.0    2.2  2  Fer4_12      4Fe-4S single cluster domain
    1.1e-05   25.6   0.0    1.1e-05   25.6   0.0    2.2  3  Fer4_14      4Fe-4S single cluster domain
    0.00012   21.9   2.4    0.00012   21.9   2.4    2.4  3  DUF3463      Domain of unknown function (DUF3463)
     0.0041   16.8   0.1      0.093   12.5   0.0    2.7  3  DnaB_2       Replication initiation and membrane attachment
  ------ inclusion threshold ------
       0.18   12.1   0.0       0.84    9.9   0.0    2.0  3  Hydrolase    haloacid dehalogenase-like hydrolase
        0.2   11.7   1.6        2.5    8.2   0.2    2.8  3  HAD_2        Haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.6   0.1   7.5e-19   1.9e-15       6     152 ..      11     141 ..       7     156 .. 0.85
   2 ?   -0.0   0.0      0.39     1e+03      28      83 ..     180     244 ..     166     262 .. 0.66

  Alignments for each domain:
  == domain 1  score: 57.6 bits;  conditional E-value: 7.5e-19
                                   EESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEEEECS CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM   6 gCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgiritvetng 86 
                                   +CnlrC+ C+ ++         + + + i ++++e+ +++g+k v ++ggep+l++  ve++++l++     + +++ tng
  gi|13542157|ref|NP_111845.1|  11 FCNLRCKSCNAWQ------GKIFFPEDLIDKHIEEM-KKNGIKIVSVTGGEPTLNKSVVEIVKKLKEH---HFFTHIATNG 81 
                                   8***********8......69999999999999999.6888**************************8...9********* PP

                                   SCHGHHHHHHHHHTT..-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEB CS
                                   xxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  87 tlpdeeklerllelg..vdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivgl 152
                                   t p       +++l   +d v+++l++  +e  ++  ++ + f+ v+ +++ ++++ +k v+ +++ +
  gi|13542157|ref|NP_111845.1|  82 TNP-----YVMRKLYpyLDAVTISLDSDVPE-EHNAYRGLKIFDTVVSTIKEAKNS-VKIVTANML-V 141
                                   **8.....6666666666*************.56666588999********99999.995555554.3 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.39
                                   HHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTC............CCTEEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............xxxxxxxxx RF
                   Radical_SAM  28 slsveeileevkelkaekgvkevilgggepllypdfvellerlakla............vpgiritve 83 
                                   +++ ++i++ ++++ +e+  ++v+  g   ++y+d v++le ++ l+              +++ ++e
  gi|13542157|ref|NP_111845.1| 180 HVTNDMIKQAFQYA-YENYSRHVF--GNMRSYYKDAVDYLEGRSSLQckagqeifytdyRGKVHPCFE 244
                                   56777788888777.454355554..444688888888888888887766666666666555555555 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 !   40.2   0.0   1.5e-13   3.7e-10      15     113 ..      12      99 ..       3     117 .. 0.81
   2 ?    0.3   0.1       0.3   7.6e+02      18      45 ..     262     290 ..     260     303 .. 0.74

  Alignments for each domain:
  == domain 1  score: 40.2 bits;  conditional E-value: 1.5e-13
                       Fer4_12  15 CnlsCkgCfnketwsfksgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelvkevkeekpekdiwlytgyt 95 
                                   Cnl+Ck C    +w+  ++  f+++l+++ ie++kk+ i+ ++++GGEP l   ++ ++e+vk++ke+ +  ++++++g+ 
  gi|13542157|ref|NP_111845.1|  12 CNLRCKSCN---AWQ--GKIFFPEDLIDKHIEEMKKNGIKIVSVTGGEPTL---NKSVVEIVKKLKEHHF-FTHIATNGTN 83 
                                   *******76...565..4456899***************************...89999**********9.69******87 PP

                       Fer4_12  96 leelskkekeellkeidv 113
                                      ++  +  + l+ + +
  gi|13542157|ref|NP_111845.1|  84 PYVMR--KLYPYLDAVTI 99 
                                   65554..23444444444 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.3
                       Fer4_12  18 sCkgCfnketwsfksgkeft.kelleeii 45 
                                   +C+ Cf +   +++  + f+   l+ +i+
  gi|13542157|ref|NP_111845.1| 262 HCSQCFTECFLEPSIDRTFEaASLIGKIW 290
                                   8*****99999999888887455666654 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.0   4.2e-09   1.1e-05       8     101 ..      12      94 ..      10     106 .. 0.77
   2 ?   -1.7   0.0       1.2   3.1e+03      65      95 ..     116     144 ..     111     151 .. 0.67
   3 ?   -4.0   0.3       6.2   1.6e+04      11      18 ..     262     269 ..     261     283 .. 0.71

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 4.2e-09
                       Fer4_14   8 CnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeeypekkiwletn 88 
                                   Cnl Ck C   +      +  + e+l+++ ++++kk+ i  + +++tGGeP +   +k+++++vk+lke+   +  ++ tn
  gi|13542157|ref|NP_111845.1|  12 CNLRCKSCNAWQ-----GKIFFPEDLIDKHIEEMKKNGI--KIVSVTGGEPTL---NKSVVEIVKKLKEHH--FFTHIATN 80 
                                   999999996544.....556788899999**99999999..668*******93...47889********99..99999999 PP

                       Fer4_14  89 gtleiele.ktpdl 101
                                   gt    +   +p+l
  gi|13542157|ref|NP_111845.1|  81 GTNPYVMRkLYPYL 94 
                                   98764444344555 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.2
                       Fer4_14  65 kellklvkrlkeeypekkiwletngtleiel 95 
                                   k ++++v+ +ke +   ++++ t  +l  ++
  gi|13542157|ref|NP_111845.1| 116 KIFDTVVSTIKEAK--NSVKIVTANMLVTNF 144
                                   56778888888888..556666655555555 PP

  == domain 3  score: -4.0 bits;  conditional E-value: 6.2
                       Fer4_14  11 sCkgCdnk 18 
                                   +C  C+++
  gi|13542157|ref|NP_111845.1| 262 HCSQCFTE 269
                                   67777765 PP

>> DUF3463  Domain of unknown function (DUF3463)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.4   0.5       6.4   1.6e+04     105     112 ..      14      21 ..       8      25 .. 0.63
   2 ?   -0.4   0.0      0.37   9.4e+02      20      52 ..      66      98 ..      59     103 .. 0.86
   3 !   21.9   2.4   4.5e-08   0.00012      15     120 ..     177     276 ..     165     288 .. 0.77

  Alignments for each domain:
  == domain 1  score: -4.4 bits;  conditional E-value: 6.4
                       DUF3463 105 pkCanCmv 112
                                    +C++C +
  gi|13542157|ref|NP_111845.1|  14 LRCKSCNA 21 
                                   46666654 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.37
                       DUF3463 20 erektkelfrkilelkkkkyklnesplyldfla 52
                                  ++ k ++ f +i +++ + y + +   yld+++
  gi|13542157|ref|NP_111845.1| 66 KKLKEHHFFTHIATNGTNPYVMRKLYPYLDAVT 98
                                  66678899999**999999***99999999875 PP

  == domain 3  score: 21.9 bits;  conditional E-value: 4.5e-08
                       DUF3463  15 qdlflerektkelfrkilelkkkkyklnesply....ldflagkqeykCtpWgnptr.nvlGwqkPCYlleegyaktfkel 90 
                                   qd  ++++ +k++f+  +e+  + + + +   y    +d+l+g+++++C++ +++ + +  G ++PC+      ++    l
  gi|13542157|ref|NP_111845.1| 177 QDFHVTNDMIKQAFQYAYENYSR-HVFGNMRSYykdaVDYLEGRSSLQCKAGQEIFYtDYRGKVHPCFEH----VEV--VL 250
                                   56667777788888888888777.455554444244468999*********9998763789******843....433..46 PP

                       DUF3463  91 leetdwekygkgkdpkCanCmvhsgyEasa 120
                                    ++ +w++y+    ++C++C   + +E+s+
  gi|13542157|ref|NP_111845.1| 251 NKKPEWDRYD----NHCSQCFTECFLEPSI 276
                                   67889****9....89************97 PP

>> DnaB_2  Replication initiation and membrane attachment
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.14   3.5e+02      21      47 ..      20      46 ..      15      60 .. 0.77
   2 !   12.5   0.0   3.6e-05     0.093       3      47 ..     155     200 ..     153     214 .. 0.83
   3 ?   -3.1   0.0       2.7   6.9e+03      45      54 ..     296     305 ..     288     305 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.14
                                  HHHHHHHHHHHHHHHHHHHHHHHHT-- CS
                        DnaB_2 21 lywlddlglspevilllleyavekgkr 47
                                  ++w  +  +++++i   +e+  ++g +
  gi|13542157|ref|NP_111845.1| 20 NAWQGKIFFPEDLIDKHIEEMKKNGIK 46
                                  566666678888888888888777655 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 3.6e-05
                                   HHHTTS-.S--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.T-- CS
                        DnaB_2   3 eiekefgrplspseletilywlddlglspevilllleyavek.gkr 47 
                                   +++ke+g pls    e+  y+++d++ ++++i+ +++ya+e+ +++
  gi|13542157|ref|NP_111845.1| 155 FANKELGVPLSMCFPEQDAYYFQDFHVTNDMIKQAFQYAYENySRH 200
                                   78899999999999999999*******************9885544 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 2.7
                                   T--SHHHHHH CS
                        DnaB_2  45 gkrnlrYiek 54 
                                   +kr +rY+++
  gi|13542157|ref|NP_111845.1| 296 KKRDIRYVDT 305
                                   6889999985 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00033      0.84     125     163 ..      35      77 ..      27      93 .. 0.77
   2 ?   -3.2   0.0       3.4   8.6e+03     121     153 ..     119     154 ..     111     167 .. 0.54
   3 ?   -1.2   0.0      0.79     2e+03      67      77 ..     237     257 ..     171     301 .. 0.54

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00033
                                   HHHHHHHHTTEEEEEEESSEHHHHHHHHHHTT....GGGESEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxx RF
                     Hydrolase 125 eavasLkaagievvlltgdnpetaeraanqlG....ddyfdav 163
                                   + +++ k++gi++v +tg++p+  +++ + +     +++f ++
  gi|13542157|ref|NP_111845.1|  35 KHIEEMKKNGIKIVSVTGGEPTLNKSVVEIVKklkeHHFFTHI 77 
                                   678999***************9999999988866533333443 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 3.4
                                   TTHHHHHHHHHHT.TEE..EEEEESSEHHHHHHHHH CS
                                   xxxxxxxxxxxxx.xxx..xxxxxxxxxxxxxxxxx RF
                     Hydrolase 121 peaaeavasLkaa.gie..vvlltgdnpetaeraan 153
                                   + ++ ++++ k   +i     l+t+ n   + r+a+
  gi|13542157|ref|NP_111845.1| 119 DTVVSTIKEAKNSvKIVtaNMLVTNFNYFKVGRIAD 154
                                   455555555553333321123455555555555555 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.79
                                   E..........HHHHTHHHHH CS
                                   x..........xxxxxxxxxx RF
                     Hydrolase  67 g..........ayaigkpewl 77 
                                   g          +++  kpew 
  gi|13542157|ref|NP_111845.1| 237 GkvhpcfehveVVLNKKPEWD 257
                                   133444444445555555554 PP

>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.2   0.00098       2.5      84     128 ..      33      80 ..      16      98 .. 0.73
   2 ?   -0.5   0.0      0.43   1.1e+03      72     102 ..     108     136 ..      83     152 .. 0.67
   3 ?    1.1   0.0      0.15   3.8e+02      12      41 ..     182     209 ..     179     262 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00098
                         HAD_2  84 vkelLeeLkeagyklgivTsk...sreaveekleqlgiesyFdvivts 128
                                   + + +ee+k++g+k+  vT +    +++v e +++l+ +++F++i t 
  gi|13542157|ref|NP_111845.1|  33 IDKHIEEMKKNGIKIVSVTGGeptLNKSVVEIVKKLKEHHFFTHIATN 80 
                                   566777888888888888877444567777777788877888777764 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.43
                         HAD_2  72 ekkk.kevkpydgvkelLeeLkeagyklgivT 102
                                   e++  + +k++d v ++++e    + ++ ivT
  gi|13542157|ref|NP_111845.1| 108 EHNAyRGLKIFDTVVSTIKEA---KNSVKIVT 136
                                   333334666666666666665...33444555 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.15
                         HAD_2  12 teeliiqafnelleeyglselseeelrkli 41 
                                   t+++i qaf++++e+y  s     ++r+++
  gi|13542157|ref|NP_111845.1| 182 TNDMIKQAFQYAYENY--SRHVFGNMRSYY 209
                                   7899999999999988..333333344433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1024  (0.0571142); expected 358.6 (0.02)
Passed bias filter:                      653  (0.0364214); 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: 0.66u 0.30s 00:00:00.96 Elapsed: 00:00:00.53
# Mc/sec: 1785.05
//
Query:       gi|13542158|ref|NP_111846.1|  [L=111]
Description: hypothetical protein TVN1327 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       612  (0.0341346); 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: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 707.78
//
Query:       gi|13542159|ref|NP_111847.1|  [L=477]
Description: ABC-type peptide transporter, ATPase component [Thermoplasma volcanium GSS1]
Scores for complete 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   93.4   0.1    9.3e-26   91.0   0.1    2.1  1  ABC_tran         ABC transporter
    8.2e-17   61.5   0.3      2e-16   60.3   0.3    1.7  1  oligo_HPY        Oligopeptide/dipeptide transporter, C-termin
    1.1e-08   35.3   2.9    4.1e-06   26.8   2.9    2.4  1  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    0.00018   21.2   0.0    0.00044   20.0   0.0    1.3  1  ATP-synt_ab      ATP synthase alpha/beta family, nucleotide-b
    0.00051   19.5   2.3      0.005   16.3   2.3    2.0  1  SMC_N            RecF/RecN/SMC N terminal domain
    0.00051   20.5   0.5       0.86   10.0   0.0    3.2  3  AAA              ATPase family associated with various cellul
    0.00086   19.0   0.2       0.16   11.7   0.0    2.3  2  Sigma54_activat  Sigma-54 interaction domain
     0.0024   18.3   0.3     0.0088   16.4   0.3    2.0  1  AAA_16           AAA ATPase domain
     0.0032   17.6   0.0     0.0059   16.8   0.0    1.4  1  AAA_33           AAA domain
     0.0038   17.2   1.0     0.0094   15.9   1.0    1.7  1  ATPase_2         ATPase domain predominantly from Archaea
     0.0042   16.8   3.6       0.14   12.0   2.5    2.8  2  RPAP1_N          RPAP1-like, N-terminal
     0.0066   17.0   0.1      0.059   13.9   0.0    2.3  2  AAA_18           AAA domain
      0.007   16.6   4.8       0.05   13.9   0.6    2.6  2  AAA_22           AAA domain
     0.0082   15.9   0.0      0.024   14.4   0.0    1.8  1  PRK              Phosphoribulokinase / Uridine kinase family
  ------ inclusion threshold ------
      0.014   14.6   0.1      0.054   12.7   0.0    2.0  2  NB-ARC           NB-ARC domain
      0.028   13.7   0.0      0.051   12.8   0.0    1.4  1  Zeta_toxin       Zeta toxin
      0.032   14.1   0.0      0.074   13.0   0.0    1.7  1  NACHT            NACHT domain
      0.032   14.3   0.9       0.08   13.0   0.2    2.0  2  AAA_14           AAA domain
      0.074   13.0   0.1       0.24   11.4   0.0    1.8  2  AAA_5            AAA domain (dynein-related subfamily)
       0.12   12.1   0.2       0.29   10.9   0.0    1.6  2  IstB_IS21        IstB-like ATP binding protein
       0.32   10.5   1.3         25    4.4   0.0    2.4  2  AAA_25           AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.0   0.1   1.1e-28   9.3e-26       2     137 .]      33     229 ..      32     229 .. 0.76

  Alignments for each domain:
  == domain 1  score: 91.0 bits;  conditional E-value: 1.1e-28
                                   EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEE........................................ CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................................ RF
                      ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGei........................................ 42 
                                   ++v+++ k+ge+++ivGe+G+GK+tL +++++l+k t G++                                        
  gi|13542159|ref|NP_111847.1|  33 DDVTFTAKKGETIGIVGETGCGKTTLGRTILQLTKATDGNVyfhldqdimkkaieleeeyyslthkkekseedkrrikeve 113
                                   89***************************************7777777777777777777777777777766666666666 PP

                                   ........EETTCEGGGB-HHHCCHCEEEE-SS..--S-TTSBHHHH...........HHHTCHHHHHHHSTTGGTTCBGE CS
                                   ........xxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxx...........xxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  43 ........lldgkdlkeqeleslrkeigvlpqe..pqlfpeltvren...........esdeeiekalsklglkelkdtvv 102
                                           ++  +++k ++++++r+ ++ ++q+  ++l+p++ +++             ++e +ek  + ++ ++l ++++
  gi|13542159|ref|NP_111847.1| 114 delipfrkKYSLTKMKPKQIKEYRRYMQPVFQDpfSSLDPRKLIKDIiaepmklltnmSKEEILEKEKEIINEIGLSEDHL 194
                                   666665555555555556677777777777777666666666666669999999997533333444444444555666888 PP

                                   STTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran 103 ksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                   ++ p+++SgGq+qr+ +ara+  +p+llllDEpt+
  gi|13542159|ref|NP_111847.1| 195 YRFPHEFSGGQRQRIGIARAISIEPDLLLLDEPTS 229
                                   8999*****************************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 !   60.3   0.3   2.3e-19     2e-16       1      65 []     280     345 ..     280     345 .. 0.96

  Alignments for each domain:
  == domain 1  score: 60.3 bits;  conditional E-value: 2.3e-19
                     oligo_HPY   1 vErgpssklfdeplHPYTkaLlrsvprldrekd.klekikgeapslerldeGCpFapRCpfaleeC 65 
                                   vE++++ +lf+e+lHPYTkaLl+++p +d+  + +   ++ge ps+ + ++GC F++RCp a+  C
  gi|13542159|ref|NP_111847.1| 280 VEIAETHTLFTEMLHPYTKALLSAIPVPDPDTKkQHIILEGEIPSPVNPPKGCYFHNRCPEAMRNC 345
                                   8*****************************9996777889************************99 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   2.9   4.8e-09   4.1e-06       3     302 ..      46     264 ..      45     265 .. 0.66

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 4.8e-09
                        AAA_21   3 vliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeieeflsqgvryryglrlersqv 83 
                                   +++G  g+GK++L +++  l  +               + + + + ld +  ++++e+e e   +++++ + + +  r   
  gi|13542159|ref|NP_111847.1|  46 GIVGETGCGKTTLGRTILQLTKA---------------TDGNVYFHLDQDIMKKAIELEEEYYSLTHKKEKSEEDKRRIKE 111
                                   58999999999999999888543...............7777788888888888888888866666666666555555555 PP

                        AAA_21  84 .eeklssvetllesgllldkrsleeedvfnpeargirggvsvfslkelsvsepndlqfgkaltditsrawsllllldglrk 163
                                    e+ l+ ++++ + + +++k+++e +    p++++ ++ +++++l+  +++ep                            
  gi|13542159|ref|NP_111847.1| 112 vEDELIPFRKKYSLTKMKPKQIKEYRRYMQPVFQDPFSSLDPRKLIKDIIAEP---------------------------- 164
                                   55555555555555555555555555555555555555555555554444444............................ PP

                        AAA_21 164 erigllnifadyfgfakekrllqrlvrslklveielsdlgegeeliasvderlrergvvflengdgqelparelSdGtkrl 244
                                    +++l n++++++ ++++  + +  +++ +l ++                                    ++e+S G+++ 
  gi|13542159|ref|NP_111847.1| 165 -MKLLTNMSKEEILEKEKEIINEIGLSEDHLYRF------------------------------------PHEFSGGQRQR 208
                                   .555555555555444333333333333333332....................................45669****** PP

                        AAA_21 245 lalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHSplll 302
                                   ++++ a+   +   +lll+DEp + L+ ++++ +l +lk+ ++ ++   ++ +H   ++
  gi|13542159|ref|NP_111847.1| 209 IGIARAISIEP---DLLLLDEPTSALDVSVQAQILNMLKDIQQrHNLTYLFISHHLNVI 264
                                   99999999999...9***********************666666**********97776 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 !   20.0   0.0   5.1e-07   0.00044       6      48 ..      34      76 ..      29     197 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 5.1e-07
                                  HHHS-EBTT-EEEEEESTTSSHHHHHHHHHHHSSTSSEEEEEE CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   ATP-synt_ab  6 DalfpivqGqrtlipgafgvGktvisqslskqsnsddaiiyvg 48
                                  D+ f+  +G++++i+g+ g+Gkt++ +++++ ++++d  +y  
  gi|13542159|ref|NP_111847.1| 34 DVTFTAKKGETIGIVGETGCGKTTLGRTILQLTKATDGNVYFH 76
                                  7899*************************99988877888876 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 !   16.3   2.3   5.8e-06     0.005      28     211 ..      46     274 ..      29     280 .. 0.67

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 5.8e-06
                                   EEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEE.SSSSSSCEEEEEEEETTS CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx RF
                         SMC_N  28 aivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkk.lkiekeevsisrrvkrkg 107
                                    ivG+ G+GK+ l   i   L +++  ++  +  +d+++k     ++++ + ++t ++e+++  k + +ev+ +   +rk 
  gi|13542159|ref|NP_111847.1|  46 GIVGETGCGKTTLGRTI-LQLTKATDGNVYFHLDQDIMKK---AIELEEEYYSLTHKKEKSEeDKRRIKEVEDELIPFRK- 121
                                   57777777777777777.4555555555555555555554...3334444444444333333111122222222222222. PP

                                   EEEEEETTEEE-H.HHHHHHHHCTT-STT...................................................C CS
                                   xxxxxxxxxxxxx.xxxxxxxxxxxxxxx...................................................x RF
                         SMC_N 108 eseykingkevtk.kevsellesagiske...................................................l 136
                                     +y + + + ++ ke+++ ++ +  ++                                                    +
  gi|13542159|ref|NP_111847.1| 122 --KYSLTKMKPKQiKEYRRYMQPVFQDPFssldprklikdiiaepmklltnmskeeilekekeiineiglsedhlyrfphE 200
                                   ..3333333332224444444433322226667888888899999999999999999999999999*************** PP

                                   S-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHH..HHCTTSEEEEE-SSHHHCCC-.SCEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxx.xxxxxx RF
                         SMC_N 137 LSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellk..eksknaQfivislreemleka.dklvgv 211
                                   +SgG+++ + +a  ++i+   p  l llDe  +aLD +  +++ ++lk  ++++n  ++ is++ ++++ + d+++ +
  gi|13542159|ref|NP_111847.1| 201 FSGGQRQRIGIARAISIE---P-DLLLLDEPTSALDVSVQAQILNMLKdiQQRHNLTYLFISHHLNVIRSMsDRVIVM 274
                                   **********99987775...4.489**********************88888999***********99995555544 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.0     0.001      0.86       3      24 ..      47      68 ..      45     121 .. 0.78
   2 ?    6.1   0.1     0.017        14      37     116 ..     186     265 ..     155     275 .. 0.74
   3 ?    0.5   0.0       0.9   7.7e+02      50      97 ..     363     412 ..     338     431 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.001
                                  EESSTTSSHHHHHHHHHHHHTH CS
                           AAA  3 lyGppGtGKTllakavakelgv 24
                                  ++G  G+GKT+l + + + +++
  gi|13542159|ref|NP_111847.1| 47 IVGETGCGKTTLGRTILQLTKA 68
                                  68**************998764 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.017
                                   S..........STTHHHHHHHHHHHHHHHTS.TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEE CS
                           AAA  37 k..........yvgesekkirelfkeakeka.kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivi 106
                                   +          +  e +   r+ +  a++ + +p  l++DE  +    +          v++q+l++l++ +++ ++++ +
  gi|13542159|ref|NP_111847.1| 186 EiglsedhlyrFPHEFSGGQRQRIGIARAISiEPDLLLLDEPTSALDVS----------VQAQILNMLKDIQQR-HNLTYL 255
                                   1555555555566677777788888888888889*******99998888..........9*************7.669999 PP

                                   EEESSGGGST CS
                           AAA 107 gatnrpdkld 116
                                    ++++ + + 
  gi|13542159|ref|NP_111847.1| 256 FISHHLNVIR 265
                                   9998877665 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.9
                                   HHHHHHTS..TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTT CS
                           AAA  50 fkeakeka..kpsilfiDEidalaksrsgseseeeervvnqLlteldgvk 97 
                                   f++ +++a  + s +++DE  ++   r +s+ +++++v+++  + +d+++
  gi|13542159|ref|NP_111847.1| 363 FRNPEAEAlpEISKIVVDEGNNILHVRFSSQVQDQQKVLSVVQSIVDKES 412
                                   33333333666677999******999988888899999988888888776 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.0   0.00018      0.16      10      51 ..      30      71 ..      22      87 .. 0.83
   2 ?    5.1   0.0     0.019        17      77     119 ..     200     245 ..     158     252 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00018
                                  HHHHHHHHHCTSSS-EEEECSTTSSHHHHHHHHHHHSTTTTS CS
               Sigma54_activat 10 elleqikkvaktdlsvlitGesGtGKellaraiheaskrkek 51
                                  ++++ ++ +ak+  ++ i+Ge+G+GK++l r+i + +k +++
  gi|13542159|ref|NP_111847.1| 30 KAVDDVTFTAKKGETIGIVGETGCGKTTLGRTILQLTKATDG 71
                                  6677778888899999*****************998887765 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.019
                                   SSTTTSS-BEHHHHH..TTTSEEEEET.GGGS-HHHHHHHHHHHHH CS
               Sigma54_activat  77 aFtGAekekkGlfek..adgGtlfLDe.igelplelQekLlrvlqe 119
                                    F+G ++++ G  ++   +   l+LDe  + l++++Q+++l++l++
  gi|13542159|ref|NP_111847.1| 200 EFSGGQRQRIGIARAisIEPDLLLLDEpTSALDVSVQAQILNMLKD 245
                                   5999999**9988762256789*****5568************976 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.3     1e-05    0.0088      24      85 ..      42      95 ..      29     257 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1e-05
                        AAA_16 24 pelvllsGesGvGKsslvrellralekd...ggiflrgkcdqlesaipysalaqalareellrql 85
                                  +e + ++Ge G+GK++l r++l +l+k+   +   ++ + dq        +  +a++ ee +  l
  gi|13542159|ref|NP_111847.1| 42 GETIGIVGETGCGKTTLGRTIL-QLTKAtdgN---VYFHLDQD-------IMKKAIELEEEYYSL 95
                                  367889****************.788874433...66666666.......344444444444444 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   6.9e-06    0.0059       4      40 ..      47      94 ..      45     124 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 6.9e-06
                        AAA_33  4 lvGlpGsGKstlaerllkklg......avllssdtlrrrlfg.....t 40
                                  +vG  G+GK+tl + +l+ ++      +++l++d+++++++      +
  gi|13542159|ref|NP_111847.1| 47 IVGETGCGKTTLGRTILQLTKatdgnvYFHLDQDIMKKAIELeeeyyS 94
                                  6899***********986555889***********9998876433330 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 !   15.9   1.0   1.1e-05    0.0094      23     110 ..      45     144 ..      32     187 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.1e-05
                      ATPase_2  23 yfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefie...........eeeekkklekal..giavpkae 90 
                                   + i G  g+GKt+L + i++  +  d +v +  + +++  + ++   e            ee+k++++++   +i+++k+ 
  gi|13542159|ref|NP_111847.1|  45 IGIVGETGCGKTTLGRTILQLTKATDGNVYFHLD-QDIMKKAIELE-EeyyslthkkekSEEDKRRIKEVEdeLIPFRKKY 123
                                   6689*****************9887765555433.33333333333.3255565555433444444444446666666666 PP

                      ATPase_2  91 leeilk.eksklvfkaielll 110
                                     + +k +++k+  ++++ ++
  gi|13542159|ref|NP_111847.1| 124 SLTKMKpKQIKEYRRYMQPVF 144
                                   656666777777777776665 PP

>> RPAP1_N  RPAP1-like, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0      0.14   1.2e+02      11      24 ..     125     138 ..     123     142 .. 0.89
   2 !   12.0   2.5   0.00016      0.14       2      29 ..     159     186 ..     158     188 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.14
                       RPAP1_N  11 LasMspeEIeeere 24 
                                   L +M p +I+e r+
  gi|13542159|ref|NP_111847.1| 125 LTKMKPKQIKEYRR 138
                                   789********998 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00016
                       RPAP1_N   2 rIdeENrarLasMspeEIeeereeLles 29 
                                   +I +E ++ L +Ms+eEI+e  +e+ + 
  gi|13542159|ref|NP_111847.1| 159 DIIAEPMKLLTNMSKEEILEKEKEIINE 186
                                   67789999****************9875 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   6.9e-05     0.059       1      69 [.      45     121 ..      45     149 .. 0.70
   2 ?    0.1   0.0       1.3   1.1e+03      50      96 ..     229     274 ..     217     292 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.9e-05
                        AAA_18   1 IlltGtpGvGKttlakeLskrlgf..........gvnlrdvakenglllevdpe...aldeskrldedkldklldaleens 68 
                                   I++ G  G+GKttl++ + ++++                  + ++ ++le++ +     +e+ ++d+ + +++ d+l   +
  gi|13542159|ref|NP_111847.1|  45 IGIVGETGCGKTTLGRTILQLTKAtdgnvyfhldQ-----DIMKKAIELEEEYYsltHKKEKSEEDKRRIKEVEDELIPFR 120
                                   899*************9955543335458555544.....44444444444444444448888888888888888887665 PP

                        AAA_18  69 s 69 
                                   +
  gi|13542159|ref|NP_111847.1| 121 K 121
                                   5 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1.3
                        AAA_18  50 krldedkldklldaleenssaleegknlvidghlaeleseaakdikk 96 
                                     ld  +++++l+ l+ + + +++   l i+ hl+  +s++++ i++
  gi|13542159|ref|NP_111847.1| 229 SALDVSVQAQILNMLKDIQQ-RHNLTYLFISHHLNVIRSMSDRVIVM 274
                                   55667788889999999876.66667779999999999998887763 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.6   5.9e-05      0.05       9      30 ..      46      67 ..      39     157 .. 0.69
   2 ?    3.7   0.2     0.084        72      91     128 ..     215     257 ..     181     264 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.9e-05
                        AAA_22  9 vvtGesGtGKTtllrrlleqld 30
                                   ++Ge+G+GKTtl r++l+  +
  gi|13542159|ref|NP_111847.1| 46 GIVGETGCGKTTLGRTILQLTK 67
                                  589*************999874 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.084
                        AAA_22  91 v...ielliiDEaqh.lr...seealeeLrsllnlsrkgvqliLv 128
                                       + ll++DE    l+   ++++l+ L++++   r++++ +++
  gi|13542159|ref|NP_111847.1| 215 IsiePDLLLLDEPTSaLDvsvQAQILNMLKDIQQ--RHNLTYLFI 257
                                   2456679*****9999989655**********99..999988776 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   2.8e-05     0.024       2      91 ..      45     143 ..      44     169 .. 0.57

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.8e-05
                           PRK   2 IgvagsSGaGkttvarklekifgrekvkaaeiegdsflrld......raekdleleerkrakekevsflspeandfdllye 76 
                                   Ig+ g+ G+Gktt+ r++ ++ + +  + ++  +d++++ +      + +  ++ +e++++ +++++  + e + f + y+
  gi|13542159|ref|NP_111847.1|  45 IGIVGETGCGKTTLGRTILQLTKATDGN-VYFHLDQDIMKKaieleeEYYSLTHKKEKSEEDKRRIKEVEDELIPFRKKYS 124
                                   9*****************9998844433.4543333333220000002233334445555555666666666666555554 PP

                           PRK  77 vl....kelkegkkvdkpi 91 
                                         k+ ke ++ ++p+
  gi|13542159|ref|NP_111847.1| 125 LTkmkpKQIKEYRRYMQPV 143
                                   4311114555555555555 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   6.3e-05     0.054      22      49 ..      44      71 ..      29     122 .. 0.84
   2 ?   -1.7   0.0       1.5   1.3e+03     162     204 ..     398     440 ..     377     445 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.3e-05
                                  EEEEEESTTSSHHHHHHHHCCSHCCCCC CS
                        NB-ARC 22 vvalvGmgGvGKttlakqilnksdeveg 49
                                   +++vG  G+GKttl + il+  + ++g
  gi|13542159|ref|NP_111847.1| 44 TIGIVGETGCGKTTLGRTILQLTKATDG 71
                                  699****************998776665 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.5
                                   HHHHHHHHHCCTS-GGCHH..CHHHHHHHHHHCTT-HHHHHHH CS
                        NB-ARC 162 deawellenkvfekkleekesleevakeivekckGlPlalkvl 204
                                   ++ + +++++v +++l++   + +  ++i  ++ G  la+k++
  gi|13542159|ref|NP_111847.1| 398 QKVLSVVQSIVDKESLGKRGIMYKAIENITWESDGKSLAIKMI 440
                                   4455566677777777766667777777777888888888776 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0     6e-05     0.051      18      66 ..      44      94 ..      30     118 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6e-05
                    Zeta_toxin 18 lillgGqpGAGKselaellkdele.rqgn.vvrldpDdlRelhPeyeeilk 66
                                   i ++G +G+GK++l + + + ++ ++gn + +ld+D +++ +   ee + 
  gi|13542159|ref|NP_111847.1| 44 TIGIVGETGCGKTTLGRTILQLTKaTDGNvYFHLDQDIMKKAIELEEEYYS 94
                                  56789***********99999888644442679*******99944444333 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   8.7e-05     0.074       2      28 ..      44      70 ..      43     116 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 8.7e-05
                                  CEEEEC-TTTCHHHHHHHHHHHHCTS- CS
                         NACHT  2 lvilqGeaGsGKTtLlqklalawaegk 28
                                  ++ + Ge G+GKTtL + + ++ ++ +
  gi|13542159|ref|NP_111847.1| 44 TIGIVGETGCGKTTLGRTILQLTKATD 70
                                  67799**************99888766 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.2   9.4e-05      0.08       3      59 ..      43      99 ..      41     114 .. 0.71
   2 ?   -2.3   0.0       4.9   4.2e+03      64      76 ..     218     230 ..     167     265 .. 0.59

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 9.4e-05
                        AAA_14  3 kilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpe.kllelilek 59
                                  + + i+G   +GKTtl +++++      +  +y+ ld++  kk+ + e ++++l  +k
  gi|13542159|ref|NP_111847.1| 43 ETIGIVGETGCGKTTLGRTILQLTK-ATDGNVYFHLDQDIMKKAIELEeEYYSLTHKK 99
                                  56789999**********9997766.88999******977766544331333333333 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 4.9
                        AAA_14  64 kktylflDEiqev 76 
                                   +  +l+lDE   +
  gi|13542159|ref|NP_111847.1| 218 EPDLLLLDEPTSA 230
                                   4456666665554 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00029      0.24       4      41 ..      47      86 ..      45     106 .. 0.80
   2 ?   -2.8   0.0       6.6   5.6e+03      63      91 ..     215     245 ..     200     254 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00029
                                  EE--SSSSHHHHHHHGGGGB..S--EEEEE--TT--HHHH CS
                         AAA_5  4 LvGppGtgKselaerlaaal..nreveyvqltrdtteedl 41
                                  +vG++G+gK++l + +++++  ++  +y  l +d+ ++ +
  gi|13542159|ref|NP_111847.1| 47 IVGETGCGKTTLGRTILQLTkaTDGNVYFHLDQDIMKKAI 86
                                  69******************87777777777777766655 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 6.6
                                   --.G-SEEEEESGGG--.HHHHHHHHHHHHS CS
                         AAA_5  63 ar.egeilvlDEverae.sevlnsLlsllee 91 
                                   +  e+++l+lDE + a   +v++  l++l +
  gi|13542159|ref|NP_111847.1| 215 ISiEPDLLLLDEPTSALdVSVQAQILNMLKD 245
                                   3358888999998888767777777777665 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   0.00034      0.29      41      95 ..      35      91 ..      22     105 .. 0.76
   2 ?   -3.0   0.0       5.9   5.1e+03     107     136 ..     217     245 ..     206     260 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00034
                     IstB_IS21 41 lsfie.kkenivllGpsGvGKshlaialgveavraglsvlfvrvedLvee.lkrarr 95
                                    f++ k e i ++G +G GK+ l  ++ + + +++ +v+f   +d++++ ++++++
  gi|13542159|ref|NP_111847.1| 35 VTFTAkKGETIGIVGETGCGKTTLGRTILQLTKATDGNVYFHLDQDIMKKaIELEEE 91
                                  556651568999***************999999999999999988877652555555 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 5.9
                     IstB_IS21 107 lkvdllilDdlgllpldqaeaellfeviek 136
                                   +++dll+lD+     ld   ++++++++++
  gi|13542159|ref|NP_111847.1| 217 IEPDLLLLDEPT-SALDVSVQAQILNMLKD 245
                                   567999999853.33444444444444444 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.4      0.03        26      32      49 ..      41      58 ..      38      64 .. 0.89
   2 ?    4.4   0.0     0.029        25     153     188 ..     229     259 ..     206     263 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.03
                        AAA_25 32 agelallaGapgtGKttl 49
                                  +ge++ ++G +g+GKttl
  gi|13542159|ref|NP_111847.1| 41 KGETIGIVGETGCGKTTL 58
                                  7899999**********8 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.029
                        AAA_25 153 ralggdensnsdvgalvealeriarrtgaavllvhH 188
                                   +al+ + +     ++++++l++i++r++ + l++ H
  gi|13542159|ref|NP_111847.1| 229 SALDVSVQ-----AQILNMLKDIQQRHNLTYLFISH 259
                                   44444444.....89***************988877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (477 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1185  (0.066094); expected 358.6 (0.02)
Passed bias filter:                      714  (0.0398237); expected 358.6 (0.02)
Passed Vit filter:                       105  (0.00585643); expected 17.9 (0.001)
Passed Fwd filter:                        23  (0.00128284); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.78u 0.32s 00:00:01.10 Elapsed: 00:00:00.50
# Mc/sec: 2868.82
//
Query:       gi|13542160|ref|NP_111848.1|  [L=522]
Description: ABC-type peptide transport system, ATPase component [Thermoplasma volcanium GSS1]
Scores for complete 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-24   85.2   4.0    2.5e-21   76.7   4.0    2.6  1  ABC_tran   ABC transporter
    2.4e-21   76.0   0.0    5.2e-21   74.9   0.0    1.6  1  oligo_HPY  Oligopeptide/dipeptide transporter, C-terminal reg
    1.7e-05   24.8   1.3    1.7e-05   24.8   1.3    1.9  2  AAA_21     AAA domain, putative AbiEii toxin, Type IV TA syst
  ------ inclusion threshold ------
      0.014   15.4   0.3        2.8    7.9   0.0    2.7  2  AAA_5      AAA domain (dynein-related subfamily)
      0.046   14.0   0.1        0.9    9.8   0.0    2.8  3  AAA_22     AAA domain
      0.053   13.9   0.1       0.19   12.1   0.0    1.9  2  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 !   76.7   4.0   8.2e-25   2.5e-21       1     136 [.      35     371 ..      35     372 .. 0.94

  Alignments for each domain:
  == domain 1  score: 76.7 bits;  conditional E-value: 8.2e-25
                                   EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEE................................EETTCEG CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................................xxxxxxx RF
                      ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGei................................lldgkdl 49 
                                   l+ vs+++k+ge++++vGe+G+GKS  +  ++ l  +  G+i                                + +++ +
  gi|13542160|ref|NP_111848.1|  35 LDGVSFQIKPGEILGLVGESGCGKSVTATSIMDLIPDPPGRIisgeiyidnfniladldkqakiivksetkvkvKRNKRYM 115
                                   789*********************************98899888888****999999999999999999888664445555 PP

                                   GG...B-HHHCCHCEEEE-SS..--S-TTSBHHHH.............................................. CS
                                   xx...xxxxxxxxxxxxxxxx..xxxxxxxxxxxx.............................................. RF
                      ABC_tran  50 ke...qeleslrkeigvlpqe..pqlfpeltvren.............................................. 79 
                                   k+   +  ++  ++i++++qe   +++p ++++++                                              
  gi|13542160|ref|NP_111848.1| 116 KRhnfIMSKIRGNKISMIFQEpsLSMNPVMKIGDQiteaillhskieiansiirretmsdddlkkfyetasalkshlelrr 196
                                   5588899**************65566777888888********************************************** PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                      ABC_tran  80 ................................................................................. 79 
                                                                                                                    
  gi|13542160|ref|NP_111848.1| 197 yvhswaqdygvaeaeegiieiierndqnalqelksiveeqkthinlkyiglerdyerynellfdlnlqllaaesrkdenki 277
                                   ********************************************************************************* PP

                                   ......................................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHH CS
                                   ......................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  80 ......................................esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalara 122
                                                                         e+++++ ++l+ +++ + +++v++s p++LSgG+ qr ++a+a
  gi|13542160|ref|NP_111848.1| 278 selrgqikhtqsyirskftsyriikkfigkridepfkkEARRRALELLKLVNIAG-PERVIDSYPHELSGGMLQRSMIAMA 357
                                   **********************************998888888999999999999.9************************ PP

                                   HHHTSSEEEEESTT CS
                                   xxxxxxxxxxxxxx RF
                      ABC_tran 123 llkkpkllllDEpt 136
                                   l ++pk+l++DEpt
  gi|13542160|ref|NP_111848.1| 358 LSSNPKILIADEPT 371
                                   *************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 !   74.9   0.0   1.7e-24   5.2e-21       1      65 []     423     490 ..     423     490 .. 0.99

  Alignments for each domain:
  == domain 1  score: 74.9 bits;  conditional E-value: 1.7e-24
                     oligo_HPY   1 vErgpssklfdeplHPYTkaLlrsvprldrekd...klekikgeapslerldeGCpFapRCpfaleeC 65 
                                   vE++p++++f++p+HPYT +Ll+++pr+d + d   kle+ikg++p+l + ++GC+F+pRCpf++++C
  gi|13542160|ref|NP_111848.1| 423 VEEAPVKEIFKNPKHPYTVGLLKAIPRPDVKVDkfeKLESIKGSVPNLINPPSGCRFNPRCPFRMDIC 490
                                   8*******************************99********************************** PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1      0.94   2.8e+03       2      13 ..      48      59 ..      47      61 .. 0.88
   2 !   24.8   1.3   5.6e-09   1.7e-05     220     302 ..     327     407 ..     126     408 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.94
                        AAA_21  2 nvliGpNgsGKS 13
                                   +l+G  g+GKS
  gi|13542160|ref|NP_111848.1| 48 LGLVGESGCGKS 59
                                  579********9 PP

  == domain 2  score: 24.8 bits;  conditional E-value: 5.6e-09
                        AAA_21 220 gvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHSp 299
                                    v +  +++  +  ++elS G+++   ++++ l+ ++  ++l+ DEp + L+   ++ +l+++k+l+r +++ +++ TH+ 
  gi|13542160|ref|NP_111848.1| 327 LVNIAGPERVIDSYPHELSGGMLQR-SMIAMALSSNP--KILIADEPTTALDVTTQAQILDIMKDLNRvTKTSILFITHDL 404
                                   444444445555568999*******.99999999999..79***************************************9 PP

                        AAA_21 300 lll 302
                                    ++
  gi|13542160|ref|NP_111848.1| 405 AVI 407
                                   887 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0   0.00094       2.8       4      25 ..      50      71 ..      47     108 .. 0.90
   2 ?    4.9   0.2    0.0081        24      46      97 ..     183     241 ..     146     280 .. 0.66

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00094
                                  EE--SSSSHHHHHHHGGGGBS- CS
                         AAA_5  4 LvGppGtgKselaerlaaalnr 25
                                  LvG++G+gKs  a ++  ++ +
  gi|13542160|ref|NP_111848.1| 50 LVGESGCGKSVTATSIMDLIPD 71
                                  9*************99999844 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0081
                                   --..........--------...............G-SEEEEESGGG--HHHHHHHHHHHHSSEEE.. CS
                         AAA_5  46 eik.ngttslvdsplvraar...............egeilvlDEveraesevlnsLlslleerrllle 97 
                                   e++   +  l         +               e+e  +++ +er ++++l++L s+ ee++ +++
  gi|13542160|ref|NP_111848.1| 183 ETAsALKSHL---------ElrryvhswaqdygvaEAEEGIIEIIERNDQNALQELKSIVEEQKTHIN 241
                                   4333222222.........122222233355666677777888899999**************99954 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0    0.0003       0.9       7      28 ..      47      68 ..      42     118 .. 0.82
   2 ?   -0.2   0.0      0.38   1.1e+03     105     130 ..     222     247 ..     176     254 .. 0.73
   3 ?   -0.2   0.0      0.38   1.1e+03      80     129 ..     352     400 ..     268     407 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0003
                        AAA_22  7 ilvvtGesGtGKTtllrrlleq 28
                                  il ++GesG+GK++++  +++ 
  gi|13542160|ref|NP_111848.1| 47 ILGLVGESGCGKSVTATSIMDL 68
                                  7779***********9988775 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.38
                        AAA_22 105 seealeeLrsllnlsrkgvqliLvGt 130
                                    ++al+eL+s+++ +++++ l ++G 
  gi|13542160|ref|NP_111848.1| 222 DQNALQELKSIVEEQKTHINLKYIGL 247
                                   48999999999997777777777775 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.38
                        AAA_22  80 ealeqalrarav...ielliiDEaqh.lr...seealeeLrsllnlsrkgvqliLvG 129
                                   ++++ a         +++li DE    l+   ++++l   ++l     +++++ L++
  gi|13542160|ref|NP_111848.1| 352 SMIAMA-----LssnPKILIADEPTTaLDvttQAQILDIMKDLNR--VTKTSI-LFI 400
                                   222222.....2334479999998887765432444444444444..555554.333 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   6.4e-05      0.19      25      58 ..      46      79 ..      31     111 .. 0.79
   2 ?   -1.4   0.1      0.92   2.8e+03     104     104 ..     287     287 ..     208     392 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6.4e-05
                        AAA_16 25 elvllsGesGvGKsslvrellralekdggiflrg 58
                                  e++ l+GesG+GKs  ++++++ + +  g  ++g
  gi|13542160|ref|NP_111848.1| 46 EILGLVGESGCGKSVTATSIMDLIPDPPGRIISG 79
                                  7889****************98777764554444 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.92
                        AAA_16 104 a 104
                                   +
  gi|13542160|ref|NP_111848.1| 287 T 287
                                   0 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (522 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1102  (0.0614647); expected 358.6 (0.02)
Passed bias filter:                      615  (0.034302); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.68u 0.38s 00:00:01.06 Elapsed: 00:00:00.52
# Mc/sec: 3038.18
//
Query:       gi|13542161|ref|NP_111849.1|  [L=319]
Description: ABC-type peptide transporter, permease component [Thermoplasma volcanium GSS1]
Scores for complete 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   84.4  18.1    7.8e-24   84.4  18.1    1.9  2  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.4     0.037   6.7e+02     159     182 ..      36      59 ..      22      62 .. 0.74
   2 !   84.4  18.1   4.4e-28   7.8e-24       1     184 [.     133     318 ..     129     319 .] 0.94

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.037
                  BPD_transp_1 159 lalviavlllnlvadilqrlldpr 182
                                   +a+v +++ l+ +a ++ +++dpr
  gi|13542161|ref|NP_111849.1|  36 IAFVGLLITLVYFAIAVIDYIDPR 59 
                                   455666677777777778888888 PP

  == domain 2  score: 84.4 bits;  conditional E-value: 4.4e-28
                  BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilp.viillllsaapyvrlirraalrslp 80 
                                   g++lG ++a ++++ +d+++++++++++s+P ++la+ +        i+g +++  +++ +++ +++y+rl r+  l++ +
  gi|13542161|ref|NP_111849.1| 133 GLILGTVSA-YYGGLIDEAMMRITDIFFSIPALILALAIA------FIIGLTFTNiALAFIIVWWPIYARLGRSLTLSIKN 206
                                   567777777.****************************99......789999999888999999***************** PP

                  BPD_transp_1  81 kdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpG......lgtllleailgydyseis. 154
                                   ++++eaa a G s  + ++++v+P +l+p++ ++ l +g ++  +++leflg  p       lg++++  +++  +  +  
  gi|13542161|ref|NP_111849.1| 207 MNFIEAANAAGSSSVRNIFYHVIPGVLSPLFVQFSLDIGTVVQLFAALEFLGVVPVdpflpeLGRMMVWGESYLIFGKWWa 287
                                   ****************************************************7777999999*********9999999999 PP

                  BPD_transp_1 155 .nggvlalviavlllnlvadilqrlldprvr 184
                                     +++++l i+++ ++l+ d l ++ldpr r
  gi|13542161|ref|NP_111849.1| 288 vLIPAIFLMIFTVSVSLLGDGLRDVLDPRQR 318
                                   99***************************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       932  (0.0519828); 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:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 2063.41
//
Query:       gi|13542162|ref|NP_111850.1|  [L=363]
Description: ABC-type peptide transport system, permease component [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-36  126.1  12.7    1.3e-36  126.1  12.7    2.4  2  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   3.6      0.19   3.4e+03     141     141 ..      95      95 ..       5     123 .. 0.53
   2 !  126.1  12.7   7.2e-41   1.3e-36       2     185 .]     122     363 .]     121     363 .] 0.99

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.19
                  BPD_transp_1 141 l 141
                                   +
  gi|13542162|ref|NP_111850.1|  95 V 95 
                                   1 PP

  == domain 2  score: 126.1 bits;  conditional E-value: 7.2e-41
                  BPD_transp_1   2 illGilaalnrnkkldkllrpliivllslPsfvlaillvlvf....................................... 43 
                                   i+lG +++ ++n+  d++ r+++ +++++P fvla+l++ vf                                       
  gi|13542162|ref|NP_111850.1| 122 IPLGTYIGSKPNSLADHAGRIFSLAVYAMPAFVLALLFQIVFgrgaitgnplgvfpisgtfnyalvpfpvpswlttpgtsa 202
                                   89******************************************************************************* PP

                  BPD_transp_1  44 ....................vilsilghlilpviillllsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlP 104
                                                       +  s+l h +lpv++l+l  +a++vr++r+++++++ +++v++ara+G++++ i+r+++ +
  gi|13542162|ref|NP_111850.1| 203 lvshpthliifdalihhnyaIAYSGLLHIVLPVLTLTLGILAGIVRFLRAGMMDNMRQEYVKTARAKGVPEKVIIRRHIRK 283
                                   *******************99999********************************************************* PP

                  BPD_transp_1 105 nalppiitglilafggllggavlleflgswpGlgtllleailgydyseisnggvlalviavlllnlvadilqrlldprvrk 185
                                   nal+p++t l+l f++llgg vl+e ++ +pG+g+l ++ai +y +   + g++l+++++++  nl++d+++++ldpr+r+
  gi|13542162|ref|NP_111850.1| 284 NALIPTVTVLGLLFASLLGGVVLIEDVFDYPGMGLLGINAITSYSIYGVM-GVTLVFGLVLVFANLIVDVVYAFLDPRIRY 363
                                   ***********************************************999.****************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (363 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       578  (0.0322383); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 2336.60
//
Query:       gi|13542163|ref|NP_111851.1|  [L=960]
Description: ABC-type peptide transport system, solute-binding component [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.6e-30  105.6  13.6    3.8e-30  105.1  12.2    2.0  2  SBP_bac_5   Bacterial extracellular solute-binding proteins, 
  ------ inclusion threshold ------
      0.015   15.1   0.1      0.031   14.0   0.1    1.5  1  Gemini_mov  Geminivirus putative movement protein


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 !  105.1  12.2   4.2e-34   3.8e-30      17     373 ..     378     846 ..     337     850 .. 0.86
   2 ?   -2.2   0.0      0.17   1.5e+03     250     289 ..     851     890 ..     844     901 .. 0.72

  Alignments for each domain:
  == domain 1  score: 105.1 bits;  conditional E-value: 4.2e-34
                                   TTEEEEEE-TT-B-TTSSB-SHHHHHHHHHHHHTGGGHCTTHHHHHC................TCTEEEEEEEETTEEEEE CS
                     SBP_bac_5  17 gktytfkLRkgvkFsDGtpltAeDvvfsferlldpdtasgyasllee................dqdikkveavddytvrft 81 
                                      ytf++R ++++++G+p+tA Dv +s+ r+l  d +s+ +  +                  + +    ++  ++ ++f+
  gi|13542163|ref|NP_111851.1| 378 YENYTFHIRSNATWQNGQPVTAWDVYYSYIRTLLFDAGSPETPGWIIaqvllpgnyytsntfwNITQNMTVDNATNSITFH 458
                                   567*************************************999987799*************888888888889999**** PP

                                   ESSE.TTTTTTHCHHHHHHHGC.....................................CHTCTCTTTTTGTTTSE-BSSS CS
                     SBP_bac_5  82 lkkp.nalfltllaavpasiak.....................................kaaekeddkdkdtnekpvgtGP 124
                                   + kp +++f + l   + +++                                      ka+  ++d++ +  ++++  GP
  gi|13542163|ref|NP_111851.1| 459 FQKPlTPNFVFELLSASGDYVMdanwivahatasqpalawksgltpyslpwnatgfneyKAQGSASDYNQYLVNNVMADGP 539
                                   ****9998777777666666667999999999**************************99999999999************ PP

                                   EEEEEEETTTEEEEEE-TTS.....TTTSCSSSSEEEEEE-.SHHHHHHHHHTTSSSEEESTTCCTHCHHHHHTTEEE..E CS
                     SBP_bac_5 125 YklkefkpgqkivlernpdY.....wgggkpkldriefkvipdsdaraaalqsGeiddvaepppsdieqlkeakglkv..l 198
                                   Y ++ + p + +vl +npd+     w   ++++d++++++i + ++r ++l+sG +    ++p+sd+  ++  ++  +   
  gi|13542163|ref|NP_111851.1| 540 YEIDYIIPSSAVVLIKNPDFnppgpW-FPRAHIDKVVLEYIGETSTRYLQLKSGYA-QTGGIPTSDWSLVEGLNASHIdyY 618
                                   *******************9777778.8999*************************.999**********88888888889 PP

                                   EEEEEEEEEEEEETTT................STGGGSHHHHHHHHHHS-HHHHHHHC.....T.TTSSEEESSSSTTTST CS
                     SBP_bac_5 199 yespgggvtylafNtk................kppfddkrvRqAlsyAiDreeivkav.....l.egyatpansllppssp 257
                                    ++p+++++ ++fN +                 + f+   +R+A++yA++  e++++      +    a+p +++l  ++ 
  gi|13542163|ref|NP_111851.1| 619 LSKPSLSIFWYNFNANvnttmlstldksanmpSALFSVLQIRKAFAYAYNESEYLNKDegnaiYnVTFAVPYAGMLDVGML 699
                                   999***************************9999********************999833333213344555555555666 PP

                                   TCCSCHCCCSHH......SHHHHHHHHHHHTT-BCSSTSCEETC......................EEEEEEEEETTSHHH CS
                     SBP_bac_5 258 gadeeykpayka......ydpekAkklLkeaGykdgdggglrek......................klkltlllasgspae 310
                                   g++ +++ + ++      +++  Ak +++e   ++++    + +                      +l++ +++ sg+p++
  gi|13542163|ref|NP_111851.1| 700 GYQSINELNATTngqvpyFNLNLAKMYWEEGVRDWNKLVNSTGNsslditvatsgtnkgdyvyqgkPLNIPIIIFSGDPDD 780
                                   6666655554449999999999999999998777776444444488899999999************************** PP

                                   HHHHHHHHHHHHH..TTEEEEEEEECHH....HHHHHHHHCTTESEEEEEEECTTSTTHHHHHHHHSTT CS
                     SBP_bac_5 311 kaiaeliqqqlkk..iGikvevktvdwa....atylervkdgdfdmillgwgadypdpdnflnpflsss 373
                                    a a+ + ++l     G++++v ++ +         + + ++ ++++ lgw +dyp p ++l p+  + 
  gi|13542163|ref|NP_111851.1| 781 LAGATQWGDYLSTfiTGFTFTVIPLAFPsiigY---QVQGQNPMPIYELGWAPDYPYPTDYLGPMALPE 846
                                   *************999*********66556541...4567999******************99987665 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.17
                                   SSSTTTSTTCCSCHCCCSHHSHHHHHHHHHHHTT-BCSST CS
                     SBP_bac_5 250 sllppsspgadeeykpaykaydpekAkklLkeaGykdgdg 289
                                    + p+ +  ++  y++ ++a ++++A+ l k  Gy +++ 
  gi|13542163|ref|NP_111851.1| 851 YPGPNDMTPWWIGYNTSNPARNVTEAMYLQKMIGYYNNGT 890
                                   4456666666666666666889999999999999988764 PP

>> Gemini_mov  Geminivirus putative movement protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   3.4e-06     0.031      13      52 ..       4      45 ..       1      47 [. 0.77

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.4e-06
                    Gemini_mov 13 qnalyqkPrvptaapssselpwsrvgeiailtl..vavlvlY 52
                                  +n+ + +P+ p  ap++s+++w  +  ++++++  v+vl +Y
  gi|13542163|ref|NP_111851.1|  4 KNMDNTQPNIPPVAPKASNTKWYAIIAVLVVIIvvVSVLGFY 45
                                  6778899****************9977766665015666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (960 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       728  (0.0406046); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); 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: 0.73u 0.30s 00:00:01.03 Elapsed: 00:00:00.46
# Mc/sec: 6305.44
//
Query:       gi|13542164|ref|NP_111852.1|  [L=164]
Description: hypothetical protein TVN1333 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score 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   0.7          1    9.7   0.1    2.8  3  DUF308    Short repeat of unknown function (DUF308)
      0.034   14.2   0.1      0.064   13.3   0.1    1.4  1  DUF5640   Family of unknown function (DUF5640)
        1.7    8.7   7.3        2.5    8.2   0.1    2.6  2  DUF3185   Protein of unknown function (DUF3185)


Domain annotation for each model (and alignments):
>> DUF308  Short repeat of unknown function (DUF308)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0     0.045   2.7e+02       2      12 ..       2      12 ..       1      25 [. 0.62
   2 ?   -0.6   0.0      0.28   1.7e+03      25      44 ..      65      84 ..      60      95 .. 0.74
   3 ?    9.7   0.1   0.00017         1      21      46 ..     135     160 ..     129     164 .] 0.77

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.045
                        DUF308  2 lGillivlGil 12
                                  l+i+li++Gi 
  gi|13542164|ref|NP_111852.1|  2 LSIVLILAGIS 12
                                  45555555553 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.28
                        DUF308 25 vllfGilllvsGivqiiaaf 44
                                  v+l+ ++  + Gi+qi  ++
  gi|13542164|ref|NP_111852.1| 65 VYLVSVYKNALGITQISYTL 84
                                  78888888899999995554 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.00017
                        DUF308  21 llalvllfGilllvsGivqiiaafaa 46 
                                   + + +  +Gi +l++Giv ++ ++++
  gi|13542164|ref|NP_111852.1| 135 SNIYIEAIGISMLIFGIVTLVVYITK 160
                                   55556679************999954 PP

>> DUF5640  Family of unknown function (DUF5640)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   1.1e-05     0.064      17      79 ..      15      86 ..       9      89 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.1e-05
                                  EEEE-SSS-EEEEEEETTEE........EEEE-SSSSEEEEEESS----EEE-EEESSSEEEE-SSTT-... CS
                       DUF5640 17 tYkFdedGtgelelskaayk........ftYtieedqLkidfeaekkedceyefsvngntLtLtggset.eg 79
                                   +++++  t+++++s+ ++         + Y+    +L+i+  +++++  +y +sv +n+L +t++s+t eg
  gi|13542164|ref|NP_111852.1| 15 AFSYTQHPTYYINSSSKTVIvgngsaefYGYSGLPSNLTIKTVNGNATVEVYLVSVYKNALGITQISYTlEG 86
                                  5666666677777777776667777777788888899***9999999999******************9554 PP

>> DUF3185  Protein of unknown function (DUF3185)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.1   0.00042       2.5       3      22 ..       2      21 ..       1      39 [. 0.89
   2 ?    1.8   3.3     0.041   2.4e+02       3      15 ..     142     154 ..     110     160 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00042
                       DUF3185  3 iGiiLlvaGivLlvfGynas 22
                                  ++i+L+ aGi    f y+++
  gi|13542164|ref|NP_111852.1|  2 LSIVLILAGISVTAFSYTQH 21
                                  89**************9987 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.041
                       DUF3185   3 iGiiLlvaGivLl 15 
                                   iGi +l+ Giv l
  gi|13542164|ref|NP_111852.1| 142 IGISMLIFGIVTL 154
                                   5555555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       978  (0.0545485); expected 358.6 (0.02)
Passed bias filter:                      517  (0.028836); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1139.48
//
Query:       gi|13542165|ref|NP_111853.1|  [L=284]
Description: 2-oxoacid ferredoxin oxidoreductase subunit beta [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.2e-29  101.7   0.0    7.7e-29  100.5   0.0    1.7  2  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b
    2.1e-22   79.0   0.3      4e-22   78.1   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 !  100.5   0.0   8.6e-33   7.7e-29       2     153 .]      50     197 ..      28     197 .. 0.95
   2 ?   -2.6   0.0      0.45   4.1e+03     126     141 ..     249     264 ..     243     267 .. 0.82

  Alignments for each domain:
  == domain 1  score: 100.5 bits;  conditional E-value: 8.6e-33
                                   SSHHHHHHHHHHTTSSSSEEEC.ETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHT.GGGHHHHHHTT-SEEEEEE CS
                  TPP_enzyme_C   2 iGcltlwaarllkvkrprsylt.sgglgtmGyglpaAiGaklakpdrevvaivGDGgflmi.lqelatavrrnlpitvvvl 80 
                                   iGc++           ++++l+  g++g +G+ lp+A+G+k a+ + +v+a+ GDG+ ++   q++ + ++rn++it++v 
  gi|13542165|ref|NP_111853.1|  50 IGCSSN----------MPEFLNtYGYHGLHGRLLPFASGVKWANSKLTVIAYGGDGDGFFEgTQHFFHTAKRNVDITYMVS 120
                                   556555..........778888789******************9999**********99999******************* PP

                                   E-SBCCCHHHH...HHHHTCCTTTTSBB.BS----HHHHHHHTTSE.EEEESSH.HHHHHHHHHHHHCSSSEEEEEE CS
                  TPP_enzyme_C  81 nNegygmtggq...qepfggkrksgpagkdlkpvdfaklaealGak.garvekadveeleealkealekkgpaliev 153
                                   +N+++g+t gq   + p g ++k++p+g++++p+++  +a  +Ga+ +ar  + d+++l+e   +a+++kg+++i+v
  gi|13542165|ref|NP_111853.1| 121 DNQVFGLTTGQaspTAPIGLRTKTTPDGNIETPFNPITFALNAGATfVARGFSGDIKHLKELTVKAIKHKGFSFIDV 197
                                   *************999******************************999999***********************98 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.45
                                   EESSH.HHHHHHHHHH CS
                  TPP_enzyme_C 126 rvekadveeleealke 141
                                    ve+++ e+l+e+lk+
  gi|13542165|ref|NP_111853.1| 249 EVERPTYEDLDEVLKD 264
                                   7899999*****9986 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 !   78.1   0.3   4.5e-26     4e-22       1      65 [.     201     263 ..     201     264 .. 0.96

  Alignments for each domain:
  == domain 1  score: 78.1 bits;  conditional E-value: 4.5e-26
                                   XTTTXSSSXSXXXXX-EEEGGGST---EEHHHHHHHHT-----EEEEEEEETTS--HHHHHHT.. CS
                    PFO_beta_C   1 CvtFNkvnTfdwYkervykleedgyDpsdlekAlekalewgdkiplGifYkeekptyeerleelk 65 
                                   Cvt+Nk n +++++ rvy+le   +D +++++A+++ lewgdkip+G+fY+ e+ptye+  e+lk
  gi|13542165|ref|NP_111853.1| 201 CVTWNKENSYEYFRPRVYHLEG--NDVTNFDQAYKLGLEWGDKIPIGVFYEVERPTYEDLDEVLK 263
                                   *********************7..7**********************************988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       372  (0.0207485); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1942.15
//
Query:       gi|13542166|ref|NP_111854.1|  [L=585]
Description: 2-oxoacid--ferredoxin oxidoreductase, alpha subunit [Thermoplasma volcanium GSS1]
Scores for complete 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-56  190.6   0.0      5e-56  190.0   0.0    1.2  1  POR_N            Pyruvate flavodoxin/ferredoxin oxidoreductas
    4.1e-37  128.0   0.1    7.9e-37  127.0   0.1    1.5  1  POR              Pyruvate ferredoxin/flavodoxin oxidoreductas
    1.7e-10   41.1   0.0    3.9e-10   39.9   0.0    1.7  1  PFOR_II          Pyruvate:ferredoxin oxidoreductase core doma
     0.0052   16.7   0.0      0.015   15.2   0.0    1.8  2  Transketolase_C  Transketolase, C-terminal domain
  ------ inclusion threshold ------
      0.033   13.8   0.1      0.059   13.0   0.1    1.3  1  TPP_enzyme_N     Thiamine pyrophosphate enzyme, N-terminal TP
      0.043   14.0   0.0      0.076   13.2   0.0    1.4  1  Adeno_E3         Adenovirus E3 protein


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 !  190.0   0.0   1.7e-59     5e-56       2     223 ..     214     442 ..     213     450 .. 0.94

  Alignments for each domain:
  == domain 1  score: 190.0 bits;  conditional E-value: 1.7e-59
                                   HHHHCTEEEEEE--BTTTCCHHHHHCHCCCCCTTEE.EEEE-SSHHHHHHHHHHHHCTT-EEEEEEECCHHHHCCCCHHHH CS
                         POR_N   2 aaiaagvdviaaYPITPsseiaeelaellakgevgdvevvqmesEigaisaviGAaaaGaraaTaTSgqGllLmienlgla 82 
                                   +a+a+g+++++aYP+TP+s+ ++ la++++k +v    v   e+Ei+ai++ iGA +aG+ra+T +Sg G++Lm e++gla
  gi|13542166|ref|NP_111854.1| 214 GAVAGGLKMYVAYPMTPASSALHFLAQHAKKYGV---FVKIPEDEISAINTTIGANYAGVRAMTGSSGGGFALMTEAVGLA 291
                                   78999************************99996...45557*************************************** PP

                                   HHTT--EEEEEEEEE-STTBEEEEE--TTCHHHH.....S---EEEE-SSHHHHHHHHHHHHHHHHHCTSEEEEEEEHHHH CS
                         POR_N  83 ageelPvvivvvaRalpstglsirtdqsDlmaar.....dtglivlasenvqeafdlalvAfnlAekvrvPvivlfDgfll 158
                                   +++e+P+vi+ ++R +pstgl+++t+q+Dl++++     d++ iv+a+++++eaf ++ +A+nlAek+++Pv+v++D +l+
  gi|13542166|ref|NP_111854.1| 292 GMTEVPIVIYEAQRPGPSTGLPTKTEQGDLNQVLgasqgDFPRIVFAPGDIEEAFYITREAMNLAEKYQTPVFVMSDLYLA 372
                                   ********************************************************************************* PP

                                   .HEEEEEEC-SGG..GS-----SBXXXXXXXX.....SXXXBXXTXXTSSXXEEESBXBXTTSXBXXXXHH CS
                         POR_N 159 shevekvelpdee.delklikekleeyerkey.....aldpekpiargtaanpdtglehrekgneaedaae 223
                                    + +++++ +d + ++ + ++ k +e++ k+y     +++p+  + + +    + ++eh+e+g    da+ 
  gi|13542166|ref|NP_111854.1| 373 -EHYDTLDGLDLNfKIDNGERAKDNEEDYKRYlitdtGISPRAIPGQAGLMHNEDSDEHNEYGDVVSDAIT 442
                                   .************999999999999988888899****************************988877665 PP

>> POR  Pyruvate ferredoxin/flavodoxin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.0   0.1   2.6e-40   7.9e-37       1     177 []      14     183 ..      12     183 .. 0.86

  Alignments for each domain:
  == domain 1  score: 127.0 bits;  conditional E-value: 2.6e-40
                                   CTSTHHHHHHHHHHHHHHTT-EEEEEEEEESSSSSSCEEEEEEEESS.-SSS--TTSEEEEEESSHHHHHHHGGG.EEEE. CS
                           POR   1 GGqGvvtagkilakaaaraGyyvqanreygseirGghsyshvrisdepivpsievgeadllvaldaetlsehldg.lkpg. 79 
                                   +G+Gv++ag+il++++ar+G+y+++++ y+  irGg s+++vr+sde +v++++ ++ d+l+al+ + +++h +  +++g 
  gi|13542166|ref|NP_111854.1|  14 AGDGVQSAGEILIRTFARSGLYATSYNYYQDIIRGGESWYQVRASDE-KVKNQG-DGLDVLIALNLDGVERHTNPeINEGg 92 
                                   4**********************************************.9*****.*********88888744432255553 PP

                                   .......EEEEEECTCGTT-CCHHHCTS-HHHHHHHT-EEEEE-HHHHHHHCCC.CCHHHHHHHHHHHHHHTS-HHHHHHH CS
                           POR  80 .......giiiynseelkpdelkkakeeerelkerlgvrvygvdatkiakeiggneraaNtvmlGalaallglplealeea 153
                                          g++i++s+ ++ + ++                 +++++++ia + + n++++Ntv+lGa++a++g++++ l  +
  gi|13542166|ref|NP_111854.1|  93 asplgkdGVAIFDSSIKNYTKRET-N-------------YCPIPLSDIASKYSKNPLLKNTVGLGAAIAAIGIDFDILAGV 159
                                   333333388888885544444433.3.............46**************************************** PP

                                   HHCCS-CH.HHHHHHHHHHHHHHH CS
                           POR 154 ikkrfpkkkeviekNlkafragye 177
                                   i+++f+kk++++e+N+ka+++gy+
  gi|13542166|ref|NP_111854.1| 160 IRDQFGKKGDIAEANVKAAKEGYD 183
                                   ***********************7 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 !   39.9   0.0   1.3e-13   3.9e-10       1      78 [.     476     548 ..     476     568 .. 0.89

  Alignments for each domain:
  == domain 1  score: 39.9 bits;  conditional E-value: 1.3e-13
                                   -SEEEEE-STHHHHHHHHHHHHHHTT--EEEEEES--BS--HHHHHHHSTT-SEEEEEE-S--TT-G-HHHHHHHHHT CS
                       PFOR_II   1 AevvivamGsvagtaksavdelReegikvGllrlrtlrPFPeeelkellkkvkkvvvldrnisfgseGqlveevkaal 78 
                                   Ae+vi+  Gs+ g +++a+d lR +gik+G + ++ ++P  + ++ +llk+ kk++ ++ n+s    Gql + ++a+ 
  gi|13542166|ref|NP_111854.1| 476 AEYVIIQWGSTKGAVEEAIDILRSKGIKIGAIEVKNVFPL-NPDIGSLLKNRKKIFAVENNYS----GQLSKYIAAQF 548
                                   9**************************************8.789******************6....99999998876 PP

>> Transketolase_C  Transketolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.0       4.5   1.3e+04      73      86 ..     139     152 ..     138     164 .. 0.75
   2 !   15.2   0.0   5.1e-06     0.015      11      74 ..     477     538 ..     470     560 .. 0.86

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 4.5
                                   TTSHHHHHHHHHHH CS
               Transketolase_C  73 rgGigsevaaalae 86 
                                   ++G+g+++aa+  +
  gi|13542166|ref|NP_111854.1| 139 TVGLGAAIAAIGID 152
                                   57999999987655 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 5.1e-06
                                   SEEEEEETTHHHHHHHHHHHHHTTTTCEEEEE-SEEESHHHHHHHHHHHHHSEEEEEEEEESTT CS
               Transketolase_C  11 dvtlvayGsmveealeAaeeLekegisaeVvdlrtvkplDketilesvkktgrlvvveeavkrg 74 
                                   + +++ +Gs+   + eA++ L+++gi++  + +  v pl   +i +++k+ +++  ve+++  g
  gi|13542166|ref|NP_111854.1| 477 EYVIIQWGSTKGAVEEAIDILRSKGIKIGAIEVKNVFPLN-PDIGSLLKNRKKIFAVENNYS-G 538
                                   5689***********************************9.567779999999999999875.5 PP

>> TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1     2e-05     0.059      46     157 ..     253     365 ..     217     374 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2e-05
                                   SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHHHHCHHHHHHHHHHT--EEEEEEE--CCCHH..S..TC--T-CCHHHC..C CS
                  TPP_enzyme_N  46 rhEqgaafaAdgyaratgkpgvvlvtsgpGatnaltalaeAkvdriPllvlsgdrptslrg..qgvlqqeldqlalfr..p 122
                                    +E +a++   g   a   + +   +sg G++ ++ a+  A  + +P+++  ++rp  ++g  +++ q+ l+q+  +   +
  gi|13542166|ref|NP_111854.1| 253 EDEISAINTTIGANYAG--VRAMTGSSGGGFALMTEAVGLAGMTEVPIVIYEAQRPGPSTGlpTKTEQGDLNQVLGASqgD 331
                                   55666666666665553..67788899**********************************88666666664333222348 PP

                                   CSSEEEE-SSGGGHHHHHHHHHHHHHSSS--EEEE CS
                  TPP_enzyme_N 123 vtkyaervtspeelpealrrAirtalsgrpgPvyl 157
                                   + + ++ + + ee+  + r+A+  a ++ ++Pv++
  gi|13542166|ref|NP_111854.1| 332 FPRIVFAPGDIEEAFYITREAMNLA-EKYQTPVFV 365
                                   888899*******************.999****98 PP

>> Adeno_E3  Adenovirus E3 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   2.5e-05     0.076      90     125 ..     211     246 ..     201     248 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.5e-05
                      Adeno_E3  90 vtlGlvaGGlvlilcylylpcfsylvvlccwfkkwG 125
                                   v+lG vaGGl + + y  +p  s l  l    kk+G
  gi|13542166|ref|NP_111854.1| 211 VALGAVAGGLKMYVAYPMTPASSALHFLAQHAKKYG 246
                                   89********************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (585 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       470  (0.0262145); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); 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: 0.69u 0.28s 00:00:00.97 Elapsed: 00:00:00.50
# Mc/sec: 3491.80
//
Query:       gi|13542167|ref|NP_111855.1|  [L=457]
Description: aspartate ammonia-lyase [Thermoplasma volcanium GSS1]
Scores for complete 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-91  304.7   1.6    1.1e-90  304.3   1.6    1.2  1  Lyase_1      Lyase
    6.5e-13   48.9   0.1    1.6e-12   47.6   0.1    1.7  1  FumaraseC_C  Fumarase C C-terminus
  ------ inclusion threshold ------
      0.029   14.4   1.1       0.22   11.6   0.1    2.8  3  DUF2680      Protein of unknown function (DUF2680)


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 !  304.3   1.6   1.8e-94   1.1e-90       2     312 .]      10     338 ..       9     338 .. 0.96

  Alignments for each domain:
  == domain 1  score: 304.3 bits;  conditional E-value: 1.8e-94
                                   EEEEETCHHHHHHHHHHHHHGGGHHHHHC.....HHHHHHHHHHHTTSST....HHHHHHHHHHHHHHHCHCHHCGGHHHB CS
                       Lyase_1   2 rftvkadklmgiftersrenfrlseedik.....alaalkkaaakanvdl....keeaaaiikaldevleegklddqfvlk 73 
                                   +++ +   ++gi t+r++enfr+++ +         a +kkaaa+an+++    ke+a+ i+ka+de+++ g+++dqfv++
  gi|13542167|ref|NP_111855.1|  10 EIQLEDTVFYGINTARAKENFRITGLTSDsdhivSIAQIKKAAAMANAEAgaldKEKAEFIEKACDEIIS-GRYHDQFVID 89 
                                   5666667799**************88877889977788999******9999999****************.********** PP

                                   SSSSSHHHHHHHHHHHHHH....HHTT......HSSGIIIIITTT--HHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHH CS
                       Lyase_1  74 viqegsgtavnmnlnevig....ellg......ekvepndkvhtgqSsnDqvpTalrlalkkalsekLlpaleqLidalke 144
                                   v+q g+gt++nmn+nevi+     l+g       +++pnd+v+++qS+nD++pT +rl ++k++ +kL +a+ +Li++l++
  gi|13542167|ref|NP_111855.1|  90 VYQAGAGTSFNMNANEVIAnvalTLMGknkgdySVIHPNDHVNMSQSTNDVYPTMMRLTVTKKV-KKLKEAISDLIESLEK 169
                                   *******************888777779999**99*****************************.66************** PP

                                   HHHHTTT-EEEEEETTEEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHTCEETTTTTTTSSTTTSCCTHHHHHHHHHHHH CS
                       Lyase_1 145 kakefkdvvkiGrThlqdAtPvtlgqelsayaealerdrerlkellkrllvellgggtavgtglnadpefaelvakelakv 225
                                   k+ke + ++k+GrThlqdA Pvt g e+saya a+++dr  + ++l  +++el+ ggtavgtg+n+ ++++e v+k++a++
  gi|13542167|ref|NP_111855.1| 170 KSKELRGIPKPGRTHLQDAAPVTVGLEFSAYAYAIKKDRDEITDAL-DYIMELNIGGTAVGTGINTSKNYQENVVKHIAEI 249
                                   **********************************************.********************************** PP

                                   HCST.EESSSHHHHHHC-HHHHHHHHHHHHHHHHHHHHHHHHHHHTSTT.TSSEEEEGCCTSSC-TTSTTTEBTHHHHHHH CS
                       Lyase_1 226 tglp.vkapnsfeavsdrDavvellgalkllatsLskfaeDlrllssge.aglvelslaesepGSSiMPgKvNPvqlEllt 304
                                   t  +  k+ n +  ++  ++   ++ a+++la+++ k+a+D+rll sg+ +g++e+ +++ ++GSSiMPgK NP  +E+++
  gi|13542167|ref|NP_111855.1| 250 TRENfRKSSNLMGIMQFMTDFSRVMNAVTNLALDIEKIANDIRLLYSGPgTGIHEIIIPAVQQGSSIMPGKINPSIAEAMN 330
                                   **99***************************************************************************** PP

                                   HHHHHHHH CS
                       Lyase_1 305 gvagrvvG 312
                                   +++  v+G
  gi|13542167|ref|NP_111855.1| 331 MICHSVIG 338
                                   ******98 PP

>> FumaraseC_C  Fumarase C C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.6   0.1   2.7e-16   1.6e-12       4      47 ..     407     450 ..     405     452 .. 0.95

  Alignments for each domain:
  == domain 1  score: 47.6 bits;  conditional E-value: 2.7e-16
                                   GGHHHHHHHHHHHHHHHHHHHT--HHHHHHHTT-.-HHHHHHHT CS
                   FumaraseC_C   4 aLnphIGYekAakIAkeAlkegktlreavlelgllteeeldell 47 
                                    Lnp++GY++ akI++eA+++gk+++ +vl+ g +tee++ +++
  gi|13542167|ref|NP_111855.1| 407 LLNPYLGYDNVAKIVREAVETGKSIKSLVLATGKITEEQYMKIM 450
                                   69*************************************99986 PP

>> DUF2680  Protein of unknown function (DUF2680)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   3.6e-05      0.22      16      48 ..      45      77 ..      43      86 .. 0.88
   2 ?   -3.8   0.0       2.3   1.4e+04      22      33 ..     341     352 ..     340     353 .. 0.77
   3 ?   -0.3   0.0      0.19   1.1e+03      30      37 ..     438     445 ..     419     451 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.6e-05
                       DUF2680 16 iaelrKqivdKyVeaGllTkeqgekikkniDkr 48
                                  ia+++K   +  +eaG l ke++e i k  D+ 
  gi|13542167|ref|NP_111855.1| 45 IAQIKKAAAMANAEAGALDKEKAEFIEKACDEI 77
                                  788999999999****************99986 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 2.3
                       DUF2680  22 qivdKyVeaGll 33 
                                   q v+  V+aG+l
  gi|13542167|ref|NP_111855.1| 341 QAVNMSVQAGQL 352
                                   567888999987 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.19
                       DUF2680  30 aGllTkeq 37 
                                    G++T+eq
  gi|13542167|ref|NP_111855.1| 438 TGKITEEQ 445
                                   59999999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (457 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1019  (0.0568353); expected 358.6 (0.02)
Passed bias filter:                      694  (0.0387082); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.65u 0.31s 00:00:00.96 Elapsed: 00:00:00.53
# Mc/sec: 2607.21
//
Query:       gi|13542168|ref|NP_111856.1|  [L=177]
Description: transcription regulator [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.2e-14   51.5   1.1    1.1e-13   50.5   1.1    1.6  1  HTH_24           Winged helix-turn-helix DNA-binding
    3.9e-13   49.0   0.1    6.6e-13   48.3   0.1    1.4  1  HTH_AsnC-type    AsnC-type helix-turn-helix domain
    3.5e-07   30.1   0.0    5.4e-07   29.5   0.0    1.3  1  AsnC_trans_reg   Lrp/AsnC ligand binding domain
    6.3e-06   25.8   0.1    1.2e-05   25.0   0.1    1.4  1  HTH_DeoR         DeoR-like helix-turn-helix domain
    2.6e-05   24.0   0.3    5.1e-05   23.1   0.3    1.5  1  HTH_11           HTH domain
    0.00012   22.0   0.1    0.00022   21.1   0.1    1.4  1  HTH_36           Helix-turn-helix domain
    0.00032   20.3   0.0    0.00064   19.4   0.0    1.5  1  Sigma70_r4_2     Sigma-70, region 4
    0.00033   20.6   0.0    0.00057   19.8   0.0    1.5  1  HTH_Crp_2        Crp-like helix-turn-helix domain
    0.00075   19.5   0.1     0.0017   18.3   0.1    1.6  1  HTH_Mga          M protein trans-acting positive regulator (M
    0.00083   18.8   0.0     0.0018   17.8   0.0    1.6  1  Sigma70_r4       Sigma-70, region 4
    0.00099   18.8   0.1     0.0032   17.2   0.1    1.8  1  HTH_23           Homeodomain-like domain
     0.0014   18.1   1.1      0.008   15.7   0.9    2.1  2  GerE             Bacterial regulatory proteins, luxR family
     0.0017   18.2   0.1     0.0031   17.4   0.1    1.4  1  MarR             MarR family
     0.0028   18.2   0.1     0.0057   17.2   0.1    1.5  1  Phage_rep_O      Bacteriophage replication protein O
     0.0031   17.4   0.0     0.0052   16.6   0.0    1.3  1  MarR_2           MarR family
     0.0038   17.0   0.2      0.009   15.8   0.2    1.6  1  HTH_38           Helix-turn-helix domain
     0.0045   17.1   0.0       0.41   10.8   0.0    2.6  2  HTH_28           Helix-turn-helix domain
     0.0056   16.5   0.0     0.0095   15.7   0.0    1.4  1  HTH_IclR         IclR helix-turn-helix domain
      0.009   15.6   0.0      0.018   14.7   0.0    1.5  1  GntR             Bacterial regulatory proteins, gntR family
  ------ inclusion threshold ------
      0.019   14.6   0.0       0.03   14.0   0.0    1.2  1  RP-C             Replication protein C N-terminal domain
      0.022   14.1   0.1      0.047   13.1   0.1    1.6  1  HTH_Tnp_ISL3     Helix-turn-helix domain of transposase famil
       0.04   13.3   0.0      0.067   12.5   0.0    1.4  1  DUF1670          Protein of unknown function (DUF1670)
      0.045   13.8   0.0        0.1   12.7   0.0    1.6  1  HTH_29           Winged helix-turn helix
      0.051   13.5   0.0       0.11   12.5   0.0    1.6  1  Phage_antitermQ  Phage antitermination protein Q
      0.053   13.9   0.0       0.12   12.7   0.0    1.6  1  Rrf2             Transcriptional regulator
      0.067   12.8   0.0          3    7.5   0.0    2.5  2  HTH_50           Helix-turn-helix domain
      0.095   13.0   0.0       0.45   10.9   0.0    2.0  2  DUF2949          Protein of unknown function (DUF2949)
      0.099   12.5   0.0       0.19   11.6   0.0    1.4  1  Sigma70_ECF      ECF sigma factor
        0.1   12.8   0.0       0.19   11.9   0.0    1.4  1  Fe_dep_repress   Iron dependent repressor, N-terminal DNA bin
       0.12   12.5   0.0       0.23   11.6   0.0    1.5  1  HTH_20           Helix-turn-helix domain
       0.12   12.4   0.1       0.26   11.3   0.1    1.6  1  Put_DNA-bind_N   Putative DNA-binding protein N-terminus


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 !   50.5   1.1   1.8e-16   1.1e-13       2      47 ..      33      78 ..      32      79 .. 0.97

  Alignments for each domain:
  == domain 1  score: 50.5 bits;  conditional E-value: 1.8e-16
                        HTH_24  2 detdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                  de+d++I++ L+ n+ris++e+A++l+ S +tv+rr+++L+++ +I
  gi|13542168|ref|NP_111856.1| 33 DELDKQIICFLRYNARISNAEIAKALNTSEATVRRRINELVKKKII 78
                                  89*****************************************999 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.3   0.1   1.1e-15   6.6e-13       2      41 ..      33      72 ..      32      73 .. 0.97

  Alignments for each domain:
  == domain 1  score: 48.3 bits;  conditional E-value: 1.1e-15
                 HTH_AsnC-type  2 DeiDrkILeaLqedaRisyaeLAervGlSestvlrRvrrL 41
                                  De+D++I+  L+ +aRis+ae+A++++ Se+tv+rR++ L
  gi|13542168|ref|NP_111856.1| 33 DELDKQIICFLRYNARISNAEIAKALNTSEATVRRRINEL 72
                                  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 !   29.5   0.0   9.4e-10   5.4e-07       3      73 ..     100     166 ..      98     168 .. 0.94

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 9.4e-10
                                   EEE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEE CS
                AsnC_trans_reg   3 vslepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivl 73 
                                   + ++p++   ++e++ a+ +  +V+++yr  G  +++++  + +lea+e+f +  +++l+gv+++et+i+ 
  gi|13542168|ref|NP_111856.1| 100 IDVDPNR---MDEIAGAISDNINVLSLYRRRGKNQLIAETLFLNLEAIENF-EAFISKLNGVKNFETMIIS 166
                                   8899999...*****************************************.666**************86 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 !   25.0   0.1     2e-08   1.2e-05       3      45 ..      37      79 ..      36      80 .. 0.94

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 2e-08
                      HTH_DeoR  3 eqilellkqqgklsveelvellgvSeaTiRRDLneLeeqgllt 45
                                  +qi+  l+    +s  e++  l++SeaT+RR +neL+++ +++
  gi|13542168|ref|NP_111856.1| 37 KQIICFLRYNARISNAEIAKALNTSEATVRRRINELVKKKIII 79
                                  799999999*****************************99975 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.3   8.9e-08   5.1e-05       4      42 ..      38      75 ..      36      95 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 8.9e-08
                        HTH_11  4 qilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeel 42
                                  qi+ +L + +  is +e+A+ Ln S++tvrr+I +L ++
  gi|13542168|ref|NP_111856.1| 38 QIICFL-RYNARISNAEIAKALNTSEATVRRRINELVKK 75
                                  677777.66667***********************9444 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.1   3.8e-07   0.00022      27      55 .]      50      78 ..      36      78 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 3.8e-07
                        HTH_36 27 sqetlakrlglsknTvsraikeLeqlGyi 55
                                  s++ +ak+l+ s+ Tv+r i+eL+++ +i
  gi|13542168|ref|NP_111856.1| 50 SNAEIAKALNTSEATVRRRINELVKKKII 78
                                  7************************9887 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   1.1e-06   0.00064      22      48 ..      44      70 ..      36      75 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.1e-06
                                  HHTS---HHHHHHHHT--HHHHHHHHH CS
                  Sigma70_r4_2 22 ryleglsykEIAellgisegtVksrls 48
                                  ry    s +EIA+ l++se+tV++r+ 
  gi|13542168|ref|NP_111856.1| 44 RYNARISNAEIAKALNTSEATVRRRIN 70
                                  56666799*****************96 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   9.8e-07   0.00057      19      51 ..      46      78 ..      29     102 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 9.8e-07
                                  EEEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSE CS
                     HTH_Crp_2 19 elpltqeelAsmlGltretvsrilseLkregli 51
                                  + +++++e+A  l+++  tv r ++eL ++++i
  gi|13542168|ref|NP_111856.1| 46 NARISNAEIAKALNTSEATVRRRINELVKKKII 78
                                  5689***************************99 PP

>> HTH_Mga  M protein trans-acting positive regulator (MGA) HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.1   2.9e-06    0.0017      13      45 ..      42      73 ..      33      80 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 2.9e-06
                       HTH_Mga 13 lLteneksltldelakeLglseltlqsdiseLn 45
                                  +L  ++ +++  e+ak+L++se t++ +i+eL 
  gi|13542168|ref|NP_111856.1| 42 FL-RYNARISNAEIAKALNTSEATVRRRINELV 73
                                  44.45999***********************97 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   3.1e-06    0.0018      10      47 ..      37      75 ..      32      75 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 3.1e-06
                                  HHHHH.HHHTTT--HHHHHHHHTS-HHHHHHHHHHHHHH CS
                    Sigma70_r4 10 revle.lrfgeglTleEIgerlgiSrerVrqiekrAlrk 47
                                  +++++ lr+    + +EI++ l+ S+ +Vr+++++ ++k
  gi|13542168|ref|NP_111856.1| 37 KQIICfLRYNARISNAEIAKALNTSEATVRRRINELVKK 75
                                  5666548999999*******************9987765 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.1   5.5e-06    0.0032      14      40 ..      45      71 ..      33      77 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 5.5e-06
                        HTH_23 14 laeGlsvreIAreLgvsrrTvyrwlkr 40
                                  +  ++s +eIA++L+ s+ Tv+r ++ 
  gi|13542168|ref|NP_111856.1| 45 YNARISNAEIAKALNTSEATVRRRINE 71
                                  33489*****************98765 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.9   1.4e-05     0.008      19      44 ..      50      75 ..      49      77 .. 0.94
   2 ?   -0.9   0.0       2.1   1.2e+03      19      29 ..     129     139 ..     120     147 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.4e-05
                                  -HHHHHHHHTS-HHHHHHHHHHHHHH CS
                          GerE 19 snkeIAeelniSekTVkvhksnimkK 44
                                  sn eIA++ln Se TV+  + ++ kK
  gi|13542168|ref|NP_111856.1| 50 SNAEIAKALNTSEATVRRRINELVKK 75
                                  89***************999999888 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 2.1
                                   -HHHHHHHHTS CS
                          GerE  19 snkeIAeelni 29 
                                   +n+ IAe l++
  gi|13542168|ref|NP_111856.1| 129 KNQLIAETLFL 139
                                   5899***9998 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.1   5.4e-06    0.0031      10      46 ..      41      77 ..      38      79 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 5.4e-06
                                  HHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTS CS
                          MarR 10 rilyeqgplsvseLakklgvskstvtrvldrLekkGl 46
                                  + l+++  +s++e+ak+l++s +tv r + +L+kk  
  gi|13542168|ref|NP_111856.1| 41 CFLRYNARISNAEIAKALNTSEATVRRRINELVKKKI 77
                                  567888899*************************965 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 !   17.2   0.1   9.9e-06    0.0057      43      80 ..      42      79 ..      35      95 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 9.9e-06
                   Phage_rep_O 43 fkkksdwisnsqlveltgisrtkvskalkeLirekvii 80
                                  f + +++isn ++++  ++s++ v++ ++eL+++k+ii
  gi|13542168|ref|NP_111856.1| 42 FLRYNARISNAEIAKALNTSEATVRRRINELVKKKIII 79
                                  6677899******************************8 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   9.1e-06    0.0052      10      51 ..      39      78 ..      35      89 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 9.1e-06
                                  HHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSE CS
                        MarR_2 10 vLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLv 51
                                  ++ +L+ + +  ++ +e+a++l+ s ++v r++++Lv++  +
  gi|13542168|ref|NP_111856.1| 39 IICFLRYNAR--ISNAEIAKALNTSEATVRRRINELVKKKII 78
                                  6778888887..999***********************9877 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.2   1.6e-05     0.009      15      39 ..      43      67 ..      35      70 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.6e-05
                        HTH_38 15 rllaeGlslreIArrLgrspsTIsR 39
                                    +++  s++eIA+ L+ s  T+ R
  gi|13542168|ref|NP_111856.1| 43 LRYNARISNAEIAKALNTSEATVRR 67
                                  5689999****************99 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0      0.13        75       1      27 [.       2      28 ..       2      31 .. 0.89
   2 !   10.8   0.0   0.00071      0.41      14      34 ..      50      70 ..      41      86 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.13
                        HTH_28  1 qRleiikllaaGhsvreaArelgisrr 27
                                  +++ i  ++++G s++ a r+  i+++
  gi|13542168|ref|NP_111856.1|  2 EKKDISDQYLEGYSCDVAIRWSKIDPS 28
                                  58889999*************999886 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00071
                        HTH_28 14 svreaArelgisrrtvyrWik 34
                                  s +e+A++l++s+ tv+r i+
  gi|13542168|ref|NP_111856.1| 50 SNAEIAKALNTSEATVRRRIN 70
                                  5689**************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 !   15.7   0.0   1.6e-05    0.0095      11      46 ..      41      76 ..      39      78 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.6e-05
                                  T-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTT CS
                      HTH_IclR 11 alaeapqeltlselArrtglpkStvhRlLqtLvelG 46
                                  ++ + + + +++e+A+++  + +tv+R ++ Lv+ +
  gi|13542168|ref|NP_111856.1| 41 CFLRYNARISNAEIAKALNTSEATVRRRINELVKKK 76
                                  788999999***********************9876 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   3.2e-05     0.018      18      54 ..      43      78 ..      32      81 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.2e-05
                                  S-TTSB---HHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                          GntR 18 lrpGdkLPsereLaaefgVsrttvReALrrLeaeglv 54
                                  lr ++++ s  e+a+++++s  tvR+ +++L+ ++++
  gi|13542168|ref|NP_111856.1| 43 LRYNARI-SNAEIAKALNTSEATVRRRINELVKKKII 78
                                  6677888.999***********************997 PP

>> RP-C  Replication protein C N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   5.1e-05      0.03      72     102 ..      49      79 ..      34      80 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.1e-05
                          RP-C  72 psNaqLsralglsestlrrhlaaLveaGlii 102
                                   +sNa++++al+ se+t+rr + +Lv+  +ii
  gi|13542168|ref|NP_111856.1|  49 ISNAEIAKALNTSEATVRRRINELVKKKIII 79 
                                   69***********************999986 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   8.1e-05     0.047      29      52 .]      50      73 ..      42      73 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 8.1e-05
                  HTH_Tnp_ISL3 29 svkavArqlgvSwtTVwrildryv 52
                                  s +++A+ l++S+ TV+r+++++v
  gi|13542168|ref|NP_111856.1| 50 SNAEIAKALNTSEATVRRRINELV 73
                                  6789****************9876 PP

>> DUF1670  Protein of unknown function (DUF1670)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00012     0.067     104     137 ..      47      79 ..      44     102 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00012
                       DUF1670 104 alltqsDlalllgvstrtvskqvkeyqeeegivl 137
                                   a ++++++a  l++s++tv+++++e+  +++i++
  gi|13542168|ref|NP_111856.1|  47 ARISNAEIAKALNTSEATVRRRINEL-VKKKIII 79 
                                   668899********************.5556665 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00017       0.1      12      36 ..      49      72 ..      41      78 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00017
                        HTH_29 12 vstvsqiAkllglsrrtvyrwlkrf 36
                                   s  ++iAk+l+ s+ tv+r ++  
  gi|13542168|ref|NP_111856.1| 49 IS-NAEIAKALNTSEATVRRRINEL 72
                                  55.89***************88765 PP

>> Phage_antitermQ  Phage antitermination protein Q
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00018      0.11      70     100 ..      40      70 ..      28      89 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00018
               Phage_antitermQ  70 llvdyYvfgvskraiarklkisekevrkklq 100
                                   + + +Y +++s+ +ia++l++se +vr++++
  gi|13542168|ref|NP_111856.1|  40 ICFLRYNARISNAEIAKALNTSEATVRRRIN 70 
                                   55789***********************997 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00022      0.12      23      55 ..      47      78 ..      39      82 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00022
                                  CC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                          Rrf2 23 eepvsseeiaerqnispsylekilakLrkaglv 55
                                   + +s +eia+  n+s+  +++ +++L k++++
  gi|13542168|ref|NP_111856.1| 47 AR-ISNAEIAKALNTSEATVRRRINELVKKKII 78
                                  34.899***********************9998 PP

>> HTH_50  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0    0.0052         3      10      44 ..      34      69 ..      31      71 .. 0.71
   2 ?    2.5   0.0      0.19   1.1e+02       8      22 ..     157     171 ..     155     174 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0052
                        HTH_50 10 efErelikka.yekYpStRklAkrLGvShtaiankl 44
                                  e ++++i  + y+   S   +Ak+L +S +++ +++
  gi|13542168|ref|NP_111856.1| 34 ELDKQIICFLrYNARISNAEIAKALNTSEATVRRRI 69
                                  555555554335555577789***********9997 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.19
                        HTH_50   8 veefErelikkayek 22 
                                   v++fE  +i kay+k
  gi|13542168|ref|NP_111856.1| 157 VKNFETMIISKAYRK 171
                                   789**********97 PP

>> DUF2949  Protein of unknown function (DUF2949)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       4.3   2.5e+03      18      35 ..      15      32 ..       7      32 .. 0.81
   2 ?   10.9   0.0   0.00078      0.45       2      28 ..      37      63 ..      36      69 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 4.3
                       DUF2949 18 sialalrqseqdpspLpm 35
                                  s ++a+r s+ dps Lp+
  gi|13542168|ref|NP_111856.1| 15 SCDVAIRWSKIDPSLLPV 32
                                  678999999999999996 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00078
                       DUF2949  2 tqLirFLqeelaiseasialalrqseq 28
                                  +q+i FL+ +  is+a+ia al++se+
  gi|13542168|ref|NP_111856.1| 37 KQIICFLRYNARISNAEIAKALNTSEA 63
                                  699*******************98886 PP

>> Sigma70_ECF  ECF sigma factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00032      0.19     147     173 ..      44      70 ..      32      78 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00032
                   Sigma70_ECF 147 rkleGlsveEiAeklgvskrtverrla 173
                                   r+ +  s++EiA++l+ s++tv+rr +
  gi|13542168|ref|NP_111856.1|  44 RYNARISNAEIAKALNTSEATVRRRIN 70 
                                   5556689*****************974 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00034      0.19      23      48 ..      49      74 ..      43      78 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00034
                                  B-HHHHHHHHTS-HHHHHHHHHHHHH CS
                Fe_dep_repress 23 vktkdlaerLnvspssVsemlkkLek 48
                                  ++++++a++Ln s ++V   +++L k
  gi|13542168|ref|NP_111856.1| 49 ISNAEIAKALNTSEATVRRRINELVK 74
                                  899*******************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 ?   11.6   0.0   0.00039      0.23      23      51 ..      47      75 ..      33      79 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00039
                                  TTB-HHHHHHHHTS-HHHHHHHHHHHHHC CS
                        HTH_20 23 egltaselaerldlskntlsyHLrvLeea 51
                                  +  + +e+a++l +s +t+++++++L++ 
  gi|13542168|ref|NP_111856.1| 47 ARISNAEIAKALNTSEATVRRRINELVKK 75
                                  556668********************975 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 ?   11.3   0.1   0.00045      0.26      26      46 ..      47      67 ..      44      70 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00045
                                  -EE-HHHHHHHCTS-HHHHHH CS
                Put_DNA-bind_N 26 eriSSteLaealgvtaaqvRK 46
                                   riS  e+a+al+ ++a+vR+
  gi|13542168|ref|NP_111856.1| 47 ARISNAEIAKALNTSEATVRR 67
                                  58******************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       712  (0.0397122); expected 358.6 (0.02)
Passed bias filter:                      526  (0.0293379); 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: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 1061.37
//
Query:       gi|13542169|ref|NP_111857.1|  [L=401]
Description: 2-methylthioadenine synthetase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.9e-20   72.9   0.0    6.8e-20   72.1   0.0    1.4  1  Radical_SAM  Radical SAM superfamily
    7.4e-16   58.0   0.1    1.4e-15   57.1   0.1    1.4  1  UPF0004      Uncharacterized protein family UPF0004
  ------ inclusion threshold ------
      0.021   15.0   0.0      0.081   13.1   0.0    2.1  1  TRAM_2       TRAM domain
      0.074   12.9   0.2       0.98    9.2   0.0    2.6  3  DUF4393      Domain of unknown function (DUF4393)


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 !   72.1   0.0   1.5e-23   6.8e-20       2     167 .]     118     289 ..     117     289 .. 0.87

  Alignments for each domain:
  == domain 1  score: 72.1 bits;  conditional E-value: 1.5e-23
                                   EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGS.TTHHHHHHHHHHTC...CCTE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx...xxxx RF
                   Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggeplly.pdfvellerlakla...vpgi 78 
                                   ++ +gC+++C+fC  +     +g+  s+ +e+i+ ++k+l   +g+ke+ +++ +  +y +d+   l +l++      +++
  gi|13542169|ref|NP_111857.1| 118 PINQGCTGKCNFCVSHI---ARGKLVSRKPEKIAGQIKIL-LQRGIKEIKITSLDTAAYgKDIGLRLPHLIRTIteiGDDF 194
                                   6678************8...8*******************.6888*******99998888666666666666556667899 PP

                                   EEEEEECSSCHG....HHHHHHHHHTT.-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSET...EEEEEEE CS
                                   xxxxxxxxxxxx....xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxx RF
                   Radical_SAM  79 ritvetngtlpd....eeklerllelg.vdrvslgleaaddekvlklmnrghtfeevlealeklreagikr...vvdrivg 151
                                   r++v   +++ +    ++ + + +    +  ++l+++++dd  vl+ mnr +t++++++ + k+rea +++   ++d i+g
  gi|13542169|ref|NP_111857.1| 195 RLRVGMMEPKNTleivDDLISAYRSEKvFKFLHLPVQSGDDY-VLEVMNREYTVSDFIRITGKFREA-FPDstlSTDLIIG 273
                                   999999999999555555555555555***************.************************.************* PP

                                   BTTTSHHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxx RF
                   Radical_SAM 152 lpGendeeleellell 167
                                      end+ +e++++l+
  gi|13542169|ref|NP_111857.1| 274 YYAENDDSFEKTVQLI 289
                                   ************9986 PP

>> UPF0004  Uncharacterized protein family UPF0004
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.1   0.1   3.1e-19   1.4e-15       1      90 [.       2      87 ..       2      91 .. 0.95

  Alignments for each domain:
  == domain 1  score: 57.1 bits;  conditional E-value: 3.1e-19
                                  XEEEE--S-CCCCHHHHHHHHHTTTSSS----SSS--SEEEEEE--SSSSHHHHTHHHHHHHHTTST.--EEEEEEHHHHS-H CS
                       UPF0004  1 kvaietlGCqmNevdseelaslLkkegyelvedeeeAdvvlvnTCavrekaekkviqalrelkalkkpekkvvvlGCmaqrek 83
                                  k+++e +GC+ N+ ++   ++ L +eg +lv++++eAd+ ++ TCav++k+e++++ ++++l++      kv v+GC+a  ++
  gi|13542169|ref|NP_111857.1|  2 KIYFEAYGCTLNQGETALYVNKLLNEGNTLVSNPKEADLSIIGTCAVIKKTEDHMMARIQNLSRFG----KVEVIGCLAPVKG 80
                                  799*************************************************************98....8***********9 PP

                                  HHHHHH- CS
                       UPF0004 84 eellkee 90
                                  +++++ +
  gi|13542169|ref|NP_111857.1| 81 KTMVEDN 87
                                  9998765 PP

>> TRAM_2  TRAM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.8e-05     0.081       1      64 []     344     400 ..     344     400 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.8e-05
                                   BTSEEEEEEEE.EETTEEEEEETTS-TTTS--EEEES---T...T-EEEEEEEEEETTEEEEEE- CS
                        TRAM_2   1 iGktvevlvdg.eeeglyvGRsyadAPEvDgevyvtgaeklskvGdfvkvkItdadeyDLiGevv 64 
                                   iGkt  vl+ +  ++  ++GR  a  P     +++ +++  +   +f++v+It+++   LiG+++
  gi|13542169|ref|NP_111857.1| 344 IGKTEFVLITEnGKGRSMIGRDHAYRP-----IVIMDKTR-K--FEFHQVEITGFENTSLIGRII 400
                                   899999999996556679999999999.....55554444.4..89****************998 PP

>> DUF4393  Domain of unknown function (DUF4393)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.41   1.9e+03     115     131 ..      51      67 ..      16      73 .. 0.75
   2 ?   -0.5   0.0      0.21   9.3e+02      56      78 ..      97     124 ..      88     166 .. 0.73
   3 ?    9.2   0.0   0.00022      0.98      11      43 ..     313     345 ..     305     347 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.41
                       DUF4393 115 enpekvkasldnLerlg 131
                                   +  +++ a ++nL r+g
  gi|13542169|ref|NP_111857.1|  51 KTEDHMMARIQNLSRFG 67 
                                   34567799999999998 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.21
                       DUF4393  56 paFveIikqLspdeAklLkilk.....s 78 
                                   ++F e+i + sp  A++ + +      +
  gi|13542169|ref|NP_111857.1|  97 RSFQEVIDEVSPVNAEIVSGIPinqgcT 124
                                   7999999999999999988877554441 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.00022
                       DUF4393  11 qepkpniavpalealrytldeeeLremFanLLa 43 
                                   + pkp+ +++  + +   +++e L+e F+nL+ 
  gi|13542169|ref|NP_111857.1| 313 KRPKPTNILKEQDRMIADMHKEILQEKFSNLIG 345
                                   689****************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (401 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       579  (0.032294); 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:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.50
# Mc/sec: 2429.82
//
Query:       gi|13542170|ref|NP_111858.1|  [L=336]
Description: diphthamide synthase subunit DPH2 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-62  211.0   0.0    3.3e-62  210.6   0.0    1.0  1  Diphthamide_syn  Putative diphthamide synthesis protein
  ------ inclusion threshold ------
       0.02   14.6   0.0       0.11   12.2   0.0    2.1  3  DUF1847          Protein of unknown function (DUF1847)
      0.039   14.7   0.0      0.078   13.7   0.0    1.5  1  DUF2281          Protein of unknown function (DUF2281)


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 !  210.6   0.0   5.6e-66   3.3e-62       1     295 [.      28     317 ..      28     323 .. 0.94

  Alignments for each domain:
  == domain 1  score: 210.6 bits;  conditional E-value: 5.6e-66
               Diphthamide_syn   1 fPegllpdsaeiadileefgaevvilgDttYGaCcvdevaaehlgadllvHyGhsclspvd.rlpvlYvfveieldvehlv 80 
                                   +P+gl+p     ++ l++ + +vvi++ ++YGaC++   ++   ++d++v++Ghs++++v+   p+++v  + +  ++++ 
  gi|13542170|ref|NP_111858.1|  28 LPDGLKPEVYHYFNYLSA-NYNVVISSSPVYGACDIGPSSIYD-KVDAIVQIGHSPMPNVKyPKPTIFVEHHYNARISNID 106
                                   6***************65.679******************999.9**************9989999999999999998887 PP

               Diphthamide_syn  81 etlkknfkekkkivlvstiqyahaleevkeeleeegyevv.kvpqsekplspgevlgctspklkeeeeevdailyigdgrf 160
                                    +l +     ++i+l+ ++qy++ ++ev++++e++g++v+  +++  ++ ++g+vlgc+++++++ + +vda++ +++g+f
  gi|13542170|ref|NP_111858.1| 107 TSLLEGK--YDRIGLLFSVQYKEVADEVRKIFENKGFTVIiGKKDG-RMAYDGQVLGCNFSSVHSISYDVDAYVLVSTGQF 184
                                   7777655..789*************************999555555.99******************************** PP

               Diphthamide_syn 161 hllslmlsnpklpvyrydpyskklteesydakkllrrRyaaiekakdakkvGiivgtlgvqgrlelverlkkllkeagkks 241
                                   h +++ ls+++ +v+ +d  + kl +++ +a+k++r+Rya+i +ak+a+k++ii  t  +q+r +l++ + +++++ g + 
  gi|13542170|ref|NP_111858.1| 185 HGIGAQLSTER-EVFVLDLNDYKLHSMKDEADKFIRKRYAQIFRAKEARKICIISDTRIGQRRERLARIILRQVQQMGLEG 264
                                   *********77.9******************************************************************** PP

               Diphthamide_syn 242 ylvlvgelnpakLanfaeidafVlvaCprlsiddgkeFekPvltpyElevalge 295
                                   +l + ++++ + L+n+  +da+V ++Cpr++idd+++F+ P+ltp E+e+ + +
  gi|13542170|ref|NP_111858.1| 265 ILAVTDNISNQDLENM-RCDAVVYTGCPRVPIDDQQKFTMPLLTPAEFEMGFVK 317
                                   ****************.9********************************8873 PP

>> DUF1847  Protein of unknown function (DUF1847)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.26   1.5e+03      43      80 ..       9      46 ..       5      59 .. 0.84
   2 ?   12.2   0.0   1.8e-05      0.11      40      85 ..      99     144 ..      84     152 .. 0.89
   3 ?   -3.4   0.0       1.1   6.7e+03      42      45 ..     227     230 ..     205     260 .. 0.54

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.26
                       DUF1847 43 veeiiefakrmgykkiGiafCvglleeakalakileak 80
                                  +eei +  +++g+kki +    gl+ e     ++l+a+
  gi|13542170|ref|NP_111858.1|  9 IEEIRAALEHLGAKKILLQLPDGLKPEVYHYFNYLSAN 46
                                  789999999999***99999999999998888888776 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 1.8e-05
                       DUF1847  40 ltRveeiiefakrmgykkiGiafCvglleeakalakileakgfevv 85 
                                    +R+++i +   + +y +iG+ f v  +e a+++ ki+e+kgf+v+
  gi|13542170|ref|NP_111858.1|  99 NARISNIDTSLLEGKYDRIGLLFSVQYKEVADEVRKIFENKGFTVI 144
                                   468888888888999****************************985 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 1.1
                       DUF1847  42 Rvee 45 
                                   R +e
  gi|13542170|ref|NP_111858.1| 227 RAKE 230
                                   2222 PP

>> DUF2281  Protein of unknown function (DUF2281)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.3e-05     0.078       7      29 ..      26      48 ..      22      56 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.3e-05
                       DUF2281  7 qeLPedlkqEvldFaefLleKya 29
                                   +LP+ lk Ev+++  +L ++y+
  gi|13542170|ref|NP_111858.1| 26 LQLPDGLKPEVYHYFNYLSANYN 48
                                  58******************994 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       728  (0.0406046); expected 358.6 (0.02)
Passed bias filter:                      630  (0.0351386); 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: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.46
# Mc/sec: 2180.73
//
Query:       gi|13542171|ref|NP_111859.1|  [L=229]
Description: hypothetical protein TVN1340 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.098   13.2   4.0       0.23   12.0   0.0    2.6  2  Arc_PepC_II    Archaeal Peptidase A24 C-terminus Type II
        2.3    8.3   5.2         24    5.0   2.7    2.5  2  TOM13          Outer membrane protein TOM13


Domain annotation for each model (and alignments):
>> Arc_PepC_II  Archaeal Peptidase A24 C-terminus Type II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   2.5       0.2   1.8e+03      62      83 ..      67      87 ..      59     101 .. 0.75
   2 ?   12.0   0.0   2.5e-05      0.23      57      88 ..     188     218 ..     164     219 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.2
                   Arc_PepC_II 62 lieetvWvtygvPflipitaGf 83
                                  +i+++++v   +P++i i +Gf
  gi|13542171|ref|NP_111859.1| 67 FIKPNIYVYIVLPLII-IGIGF 87
                                  68999********887.45554 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 2.5e-05
                   Arc_PepC_II  57 ykkkglieetvWvtygvPflipitaGfiialv 88 
                                   y+ k++ + +v + y vPfl+pi+++ +++l+
  gi|13542171|ref|NP_111859.1| 188 YQLKDTNSGKVMI-YRVPFLVPILVSTVLSLI 218
                                   4444444555655.9**************998 PP

>> TOM13  Outer membrane protein TOM13
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   2.7    0.0027        24      44      64 ..      89     111 ..      62     113 .. 0.83
   2 ?    3.1   0.0      0.01        93      17      49 ..     186     218 ..     175     222 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0027
                         TOM13  44 aainlvLPFinGlmL..GfGell 64 
                                    +inl+   i G+ L  GfGell
  gi|13542171|ref|NP_111859.1|  89 DTINLLTILIVGMFLltGFGELL 111
                                   58**********98778****97 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.01
                         TOM13  17 lesssesssssplilykpptllsllrsaainlv 49 
                                   ++ + ++++s ++++y+ p l+ +l s+ + l+
  gi|13542171|ref|NP_111859.1| 186 IKYQLKDTNSGKVMIYRVPFLVPILVSTVLSLI 218
                                   3445555666689***********999988886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       888  (0.0495287); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); 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: 0.60u 0.31s 00:00:00.90 Elapsed: 00:00:00.52
# Mc/sec: 1316.53
//
Query:       gi|13542172|ref|NP_111860.1|  [L=170]
Description: hypothetical protein TVN1341 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    0.00088   19.5   2.6        0.2   11.8   0.4    2.1  2  DUF2371      Uncharacterised conserved protein (DUF2371)
     0.0012   18.9   8.9      0.036   14.1   1.2    2.5  2  DUF3185      Protein of unknown function (DUF3185)
     0.0073   15.9   6.2        0.2   11.3   0.4    2.3  2  DUF3098      Protein of unknown function (DUF3098)
  ------ inclusion threshold ------
      0.036   12.8   1.4      0.043   12.6   1.4    1.1  1  DUF2207      Predicted membrane protein (DUF2207)
       0.04   13.5   2.1        2.5    7.7   0.1    2.4  2  TMEM100      Transmembrane protein 100
      0.058   13.0   0.4        0.1   12.2   0.3    1.4  1  RIP          Ribosome inactivating protein
      0.065   13.4   4.8       0.81    9.9   0.5    2.5  2  DUF3784      Domain of unknown function (DUF3784)
      0.067   12.9   1.9        2.7    7.7   0.2    2.1  2  Tetraspanin  Tetraspanin family
      0.088   13.1   5.2        1.8    8.9   0.2    2.2  2  DUF3040      Protein of unknown function (DUF3040)
       0.15   11.2   0.0       0.19   10.8   0.0    1.1  1  phiKZ_IP     phiKZ-like phage internal head proteins
       0.21   11.3   3.7        1.4    8.6   0.2    2.2  2  Neurensin    Neurensin
       0.23   11.7   5.8       0.45   10.7   0.4    2.5  3  Pox_A14      Poxvirus virion envelope protein A14
        0.4   11.3   3.8        2.1    9.0   0.0    2.3  2  DUF2627      Protein of unknown function (DUF2627)
       0.91   10.0   3.7          4    8.0   0.1    2.4  2  DUF202       Domain of unknown function (DUF202)
        4.9    7.3   7.1        5.1    7.3   1.0    2.4  2  DUF872       Eukaryotic protein of unknown function (DUF872)
        5.4    7.3  14.5      4e+02    1.4  14.5    2.3  1  DUF4064      Protein of unknown function (DUF4064)


Domain annotation for each model (and alignments):
>> DUF2371  Uncharacterised conserved protein (DUF2371)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.1    0.0029       3.3      43      66 ..       5      34 ..       2      73 .. 0.67
   2 !   11.8   0.4   0.00018       0.2      38      67 ..     132     161 ..     127     169 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0029
                       DUF2371 43 vlllGllvllvGiam......avlgywpkk 66
                                  ++l+G++vl++Gi++      a+l y  ++
  gi|13542172|ref|NP_111860.1|  5 IVLIGVVVLVIGIVIfaggdaAILHYTVTD 34
                                  577888888888876333333555555555 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00018
                       DUF2371  38 svsglvlllGllvllvGiamavlgywpkka 67 
                                   s  +l+ ++G+++l++Gi +a++g   k++
  gi|13542172|ref|NP_111860.1| 132 SYLSLLSVFGIVLLIIGIIIAIIGVILKRK 161
                                   555778889999999999999998776664 PP

>> DUF3185  Protein of unknown function (DUF3185)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   1.3    0.0014       1.6       2      19 ..       7      24 ..       6      51 .. 0.72
   2 !   14.1   1.2   3.2e-05     0.036       3      20 ..     140     159 ..     138     169 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0014
                       DUF3185  2 iiGiiLlvaGivLlvfGy 19
                                  +iG++ lv+Giv++  G 
  gi|13542172|ref|NP_111860.1|  7 LIGVVVLVIGIVIFAGGD 24
                                  69***********99885 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 3.2e-05
                       DUF3185   3 iGiiLlvaGivLlvfGy..n 20 
                                   +Gi+Ll++Gi++++ G+  +
  gi|13542172|ref|NP_111860.1| 140 FGIVLLIIGIIIAIIGVilK 159
                                   79***********9997444 PP

>> DUF3098  Protein of unknown function (DUF3098)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.4   0.00018       0.2       9      30 ..       5      26 ..       2      36 .. 0.90
   2 !    7.2   0.9    0.0033       3.7       8      24 ..     143     159 ..     138     168 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00018
                       DUF3098  9 llliglaviilGfiLmsGggsd 30
                                  ++lig++v+++G+++ +Gg++ 
  gi|13542172|ref|NP_111860.1|  5 IVLIGVVVLVIGIVIFAGGDAA 26
                                  899****************975 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0033
                       DUF3098   8 illliglaviilGfiLm 24 
                                   +ll+ig+++ i+G+iL 
  gi|13542172|ref|NP_111860.1| 143 VLLIIGIIIAIIGVILK 159
                                   78999********9995 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   1.4   3.9e-05     0.043     382     438 ..       4     162 ..       1     169 [. 0.82

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.9e-05
                       DUF2207 382 klsalglgliilglilillallllvll...................................................... 408
                                   k+ ++g++++++g++++ ++ +++  l                                                      
  gi|13542172|ref|NP_111860.1|   4 KIVLIGVVVLVIGIVIFAGGDAAI--Lhytvtdtavkelatgqygreitltssslftvsstfpnwivvtssnyskvtsgny 82 
                                   455666666666666655554444..246999************************************************* PP

                       DUF2207 409 ...................................................lvfllilllillliaiivlllfsrllgrrt 438
                                                                                      l++l++++++ll+i+ii++++  + l+r  
  gi|13542172|ref|NP_111860.1|  83 atyaispienthvsslyvkgydlgtgsyyllafnssqppvtysylplsvsyLSLLSVFGIVLLIIGIIIAIIGVI-LKRKE 162
                                   ***************************************************888888888888888888877643.33334 PP

>> TMEM100  Transmembrane protein 100
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.4     0.012        14      58      72 ..       6      20 ..       2      43 .. 0.85
   2 ?    7.7   0.1    0.0023       2.5      80     105 ..     132     157 ..     118     167 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.012
                       TMEM100 58 iPfgvvvLvaGvvvt 72
                                  +  gvvvLv+G+v+ 
  gi|13542172|ref|NP_111860.1|  6 VLIGVVVLVIGIVIF 20
                                  5679********975 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0023
                       TMEM100  80 shgsvisvlglvLLsaGlvllassav 105
                                   s  s++sv+g+vLL  G+++ ++ ++
  gi|13542172|ref|NP_111860.1| 132 SYLSLLSVFGIVLLIIGIIIAIIGVI 157
                                   56677888888888888887776655 PP

>> RIP  Ribosome inactivating protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.3     9e-05       0.1      60     104 ..      95     138 ..      64     144 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 9e-05
                                   TTTTEEEEEEETTSEEEESCSTTS-GGSSSS-EE-SC-SSH.HHH. CS
                           RIP  60 ddnlYlvGFrnrngvwyelakekgskallpgsttlgfggsY.slLe 104
                                   ++ lY+ G+   +g +y la ++   +++ ++++l++ +sY slL+
  gi|13542172|ref|NP_111860.1|  95 VSSLYVKGYDLGTGSYYLLAFNSS--QPPVTYSYLPLSVSYlSLLS 138
                                   678*****************9997..5569***********77775 PP

>> DUF3784  Domain of unknown function (DUF3784)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.3     0.025        28      51      67 ..       6      22 ..       1      35 [. 0.54
   2 ?    9.9   0.5   0.00072      0.81      43      63 ..     137     157 ..     131     168 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.025
                       DUF3784 51 lligilflllgllsaie 67
                                  +lig++ l++g++++++
  gi|13542172|ref|NP_111860.1|  6 VLIGVVVLVIGIVIFAG 22
                                  45555555555553333 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00072
                       DUF3784  43 srfmgivllligilflllgll 63 
                                       givll+igi+++++g++
  gi|13542172|ref|NP_111860.1| 137 LSVFGIVLLIIGIIIAIIGVI 157
                                   56789*************999 PP

>> Tetraspanin  Tetraspanin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.1     0.015        16       6     103 ..       6      32 ..       1      93 [. 0.61
   2 ?    7.7   0.2    0.0024       2.7       4      27 ..     136     159 ..     133     169 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.015
                                   XXXXXXXXXXXXXXXXXXXXXXXXXX.....................XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Tetraspanin   6 fffnllfwligivllavGvwlrlkhaeaalacllsesaedpailaillivvGvllfllgflGcigalkenkcllltfslll 86 
                                   +++ +++++igiv++a G                                                               
  gi|13542172|ref|NP_111860.1|   6 VLIGVVVLVIGIVIFAGG--------------------------------------------------------------- 23 
                                   344455556666666655............................................................... PP

                                   XXXXXXXXXXXXXXX-- CS
                                   xxxxxxxxxxxxxxxxx RF
                   Tetraspanin  87 lvlfllelaagilgfvf 103
                                            a+il +++
  gi|13542172|ref|NP_111860.1|  24 --------DAAILHYTV 32 
                                   ........222222222 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0024
                                   XXXXXXXXXXXXXXXXXXXXXXXX CS
                                   xxxxxxxxxxxxxxxxxxxxxxxx RF
                   Tetraspanin   4 llfffnllfwligivllavGvwlr 27 
                                   ll +f +++++igi++ ++Gv l+
  gi|13542172|ref|NP_111860.1| 136 LLSVFGIVLLIIGIIIAIIGVILK 159
                                   688999999999999999998873 PP

>> DUF3040  Protein of unknown function (DUF3040)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.9    0.0096        11      45      64 ..       6      26 ..       1      41 [. 0.63
   2 ?    8.9   0.2    0.0016       1.8      46      72 ..     132     156 ..     113     159 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0096
                       DUF3040 45 avlavllfvaGllllvlG.va 64
                                  ++++v+++v+G++++ +G +a
  gi|13542172|ref|NP_111860.1|  6 VLIGVVVLVIGIVIFAGGdAA 26
                                  455555556677777777544 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0016
                       DUF3040  46 vlavllfvaGllllvlGvaaaavvlgv 72 
                                       ll v+G++ll++G++ a+  +gv
  gi|13542172|ref|NP_111860.1| 132 SYLSLLSVFGIVLLIIGIIIAI--IGV 156
                                   4556777889999999988775..333 PP

>> phiKZ_IP  phiKZ-like phage internal head proteins
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00017      0.19      99     158 ..      34      92 ..      28      99 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00017
                      phiKZ_IP  99 eerlkslkkedekkeitiknaerlsidGeFilpylldnepkivgkiaenwskqllkllqk 158
                                   ++++k+l + ++++eit+ + + + + ++F  ++++++  +  +++  n+ +++++ + +
  gi|13542172|ref|NP_111860.1|  34 DTAVKELATGQYGREITLTSSSLFTVSSTFP-NWIVVTSSNYSKVTSGNYATYAISPIEN 92 
                                   6788999999*********99**********.*********************9987766 PP

>> Neurensin  Neurensin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.4      0.04        45      46      58 ..       7      19 ..       3      41 .. 0.70
   2 ?    8.6   0.2    0.0013       1.4      39      68 ..     132     161 ..      98     167 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.04
                     Neurensin 46 vvgtlvlllGvta 58
                                   +g++vl++G+++
  gi|13542172|ref|NP_111860.1|  7 LIGVVVLVIGIVI 19
                                  3455555555554 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0013
                     Neurensin  39 llwkvslvvgtlvlllGvtallvGylvprr 68 
                                       +  v+g+++l++G+++ ++G +++r+
  gi|13542172|ref|NP_111860.1| 132 SYLSLLSVFGIVLLIIGIIIAIIGVILKRK 161
                                   444445678999999999999999999887 PP

>> Pox_A14  Poxvirus virion envelope protein A14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.2     0.065        73      14      66 ..       5      21 ..       2      45 .. 0.65
   2 ?   -3.0   0.0       7.3   8.2e+03      32      46 ..      73      86 ..      66      90 .. 0.55
   3 ?   10.7   0.4    0.0004      0.45       8      33 ..     131     156 ..     125     168 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.065
                       Pox_A14 14 vliaGiiLLilacifafvdfskststtdkawralsivsFilgivillglllfs 66
                                  ++++G+++L++                                    g+++f+
  gi|13542172|ref|NP_111860.1|  5 IVLIGVVVLVI------------------------------------GIVIFA 21
                                  44445544444....................................444443 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 7.3
                       Pox_A14 32 dfskststtdkawra 46
                                  ++sk+ts  ++a  a
  gi|13542172|ref|NP_111860.1| 73 NYSKVTS-GNYATYA 86
                                  5666666.4455444 PP

  == domain 3  score: 10.7 bits;  conditional E-value: 0.0004
                       Pox_A14   8 knyystvliaGiiLLilacifafvdf 33 
                                    +y s + ++Gi+LLi+ +i+a + +
  gi|13542172|ref|NP_111860.1| 131 VSYLSLLSVFGIVLLIIGIIIAIIGV 156
                                   568888999*************9864 PP

>> DUF2627  Protein of unknown function (DUF2627)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   1.7      0.27     3e+02      43      58 ..       7      22 ..       4      29 .. 0.82
   2 ?    9.0   0.0    0.0019       2.1      34      67 ..     130     164 ..     119     169 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.27
                       DUF2627 43 laGlllfaiglgfiaG 58
                                  l+G+++++ig+ ++aG
  gi|13542172|ref|NP_111860.1|  7 LIGVVVLVIGIVIFAG 22
                                  6888888888888887 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0019
                       DUF2627  34 pfsslwlqflaGlllfaiglgf.iaGfilhrdrKr 67 
                                    +s+l l  ++G++l++ig+ + i G il r  K 
  gi|13542172|ref|NP_111860.1| 130 SVSYLSLLSVFGIVLLIIGIIIaIIGVILKRKEKT 164
                                   56677788889999999997654789999998886 PP

>> DUF202  Domain of unknown function (DUF202)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.5      0.16   1.7e+02      42      57 ..       7      22 ..       3      34 .. 0.74
   2 ?    8.0   0.1    0.0036         4      40      59 ..     137     156 ..     103     164 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.16
                        DUF202 42 ilglilivlgiltllv 57
                                  ++g++ +v+gi++++ 
  gi|13542172|ref|NP_111860.1|  7 LIGVVVLVIGIVIFAG 22
                                  4677777777777765 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0036
                        DUF202  40 gkilglilivlgiltllvgl 59 
                                    +++g++l+++gi+++++g+
  gi|13542172|ref|NP_111860.1| 137 LSVFGIVLLIIGIIIAIIGV 156
                                   47899**********99987 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 ?    3.6   0.6     0.062        70      53      69 ..       6      22 ..       3      33 .. 0.81
   2 ?    7.3   1.0    0.0045       5.1      49      76 ..     141     168 ..      75     170 .] 0.84

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.062
                        DUF872 53 lllGlvLlllgvvilve 69
                                  +l+G+v+l++g+vi+++
  gi|13542172|ref|NP_111860.1|  6 VLIGVVVLVIGIVIFAG 22
                                  68999999999999875 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0045
                        DUF872  49 allLlllGlvLlllgvvilvepseGvss 76 
                                    ++Ll++G+++ ++gv+++ + ++G++ 
  gi|13542172|ref|NP_111860.1| 141 GIVLLIIGIIIAIIGVILKRKEKTGDEI 168
                                   5788888888888888888888888765 PP

>> DUF4064  Protein of unknown function (DUF4064)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4  14.5      0.35     4e+02      55      82 ..     132     159 ..       1     165 [. 0.79

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.35
                       DUF4064  55 eflstllivlgvialiaivlgivgalll 82 
                                   ++ls l ++ +v+++i i++ i+g++l 
  gi|13542172|ref|NP_111860.1| 132 SYLSLLSVFGIVLLIIGIIIAIIGVILK 159
                                   3333333333333444444444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1073  (0.0598472); expected 358.6 (0.02)
Passed bias filter:                      549  (0.0306208); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); 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):              16  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 1029.20
//
Query:       gi|13542173|ref|NP_111861.1|  [L=480]
Description: sugar transport permease [Thermoplasma volcanium GSS1]
Scores for complete 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  288.7  30.7    1.3e-85  287.9  30.7    1.3  1  Sugar_tr         Sugar (and other) transporter
      4e-20   72.0  48.7    4.1e-19   68.7  42.7    2.1  2  MFS_1            Major Facilitator Superfamily
    4.8e-05   22.0   4.0    4.8e-05   22.0   4.0    2.1  2  TRI12            Fungal trichothecene efflux pump (TRI12)
  ------ inclusion threshold ------
       0.13   12.5   2.4        1.8    8.9   0.2    2.7  2  DUF1269          Protein of unknown function (DUF1269)
        5.5    7.7   0.0        5.5    7.7   0.0    3.5  3  NADH-u_ox-rdase  NADH-ubiquinone oxidoreductase complex I, 21


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 !  287.9  30.7   3.7e-89   1.3e-85       2     452 .]      23     454 ..      22     454 .. 0.92

  Alignments for each domain:
  == domain 1  score: 287.9 bits;  conditional E-value: 3.7e-89
                                   HHHHHHHHHHHHHHHHCGGGTHHHHHHHHTSTT--SHHHHHH...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHH CS
                      Sugar_tr   2 alvaalggllfgYdtgvigafltllkfaknfglsksksskeessvlsglivsiflvGaiiGslfagllgdrfGRkksllia 82 
                                   +l+a++gg+lfgYdt  ig++l ++        +  ++   e     g +v+ +++Ga++G+l+a  l+dr+GRk+ l++ 
  gi|13542173|ref|NP_111861.1|  23 TLLATIGGFLFGYDTSNIGTALVFIP-------YPVQG-FIE-----GYLVAGASLGAAVGALIAAGLTDRYGRKYLLIAD 90 
                                   789*******************9999.......33333.333.....78999***************************** PP

                                   HHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHT CS
                      Sugar_tr  83 avlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlvPmyisEiApkklRgalvslyqlaitfGilvaaifglglnk 163
                                   a+++ +ga+l+a++     + +l+++R l+G++vG+ s++++ yisE+Apk+ Rg l+ l+q++it+Gil a+i+g+++ +
  gi|13542173|ref|NP_111861.1|  91 AAIYAAGAILSAFTI---DLAMLLLSRTLIGLAVGADSGIATAYISEYAPKDRRGSLGILQQWMITIGILGAYIVGMATLY 168
                                   ***************...99***********************************************************99 PP

                                   SS-....TTHHHHHHHCCHHHHHHHHHHGGGS---HHHHHHTT-HHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHH.... CS
                      Sugar_tr 164 tsn....adgwrillglqlvpallllilllflPESPrylvekgkeeeakevlaklrgeedadrelaeekdsleaeqeeeka 240
                                             wri+lg++++pal+ l +++++PESPr+l+++gk++ea e ++k     + + +++e k+   ++ +    
  gi|13542173|ref|NP_111861.1| 169 AAPglasVLDWRIMLGVAAIPALIGLGFRFMMPESPRWLMINGKYKEASEAFKK----LGLNLSVDELKEVKFRQ-R---- 240
                                   9989998789********************************************....34444444443333333.1.... PP

                                   .HTTHHHHSH...HHHHHHHHHHHHHHTTHHHHHHHTTTHHHHSS-THH............HHHHHHHHHHHHHHHHHHHH CS
                      Sugar_tr 241 swkellssktvrqrlligvvlqifqqltGinaimyysptifenlglsks............llvtiivgvvnfvatfvaif 309
                                        + + +v++++l++++  +fqq tGin+ +yy+p ++e+l+l  s            +++  i+ v+n++at +++ 
  gi|13542173|ref|NP_111861.1| 241 ----AKITNGVKRAFLVVALFFVFQQITGINIPFYYGPIVIEKLHLFGSatqslvftqiyaVAAATILAVINVAATYIGFR 317
                                   ....223435888999999999***********************98888899**99999999999*************** PP

                                   HHHHS-SHHHHHHHHHHHHHHHHHHH..HHHHTTSS...CHHHHHHHHHHHHHHHTTTTHHHHHHHHHHSHTTTHHHHHHH CS
                      Sugar_tr 310 lvdrfGRRtllllGaagmaicfvilgivalllvakskaasivaivfialfialfalgwgpvpwvlvsElfpqsvRskalai 390
                                    +d +GRR+l llG +gm+++ ++ g   ll+ +      +++++++a fi++fa+g+g++ w++  E fp+++R++ +++
  gi|13542173|ref|NP_111861.1| 318 YIDTVGRRKLALLGYSGMTFFGLLGG--LLLYLKF----DVGLLIAFAGFIIFFAFGVGGTGWMIQGEYFPTNMRGLYASL 392
                                   *******************9999888..8888888....799*************************************** PP

                                   HHHHHHHHHHHHHHHHHHHHCHHHT-HHHHHHHHHHHHHHHHHHHHS--STT--CCCCGGGT CS
                      Sugar_tr 391 avavnwlanflisllfpiiteaigggyvflvfaglavlfiifvfffvpetkgrtleeieelf 452
                                    ++v w+anf+i  +fp++   i+   v +vf++l ++++++ +  +petk ++ e+i+ lf
  gi|13542173|ref|NP_111861.1| 393 GAFVDWIANFAIIEIFPVLEALITIKNVMFVFGILSLIAVLIFYYIMPETKELSVEQISDLF 454
                                   ************************9*********************************9876 PP

>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.7  42.7   1.1e-22   4.1e-19       3     344 ..      28     396 ..      26     404 .. 0.71
   2 !   10.6  22.8   5.2e-05      0.19      37     179 ..     300     444 ..     274     466 .. 0.69

  Alignments for each domain:
  == domain 1  score: 68.7 bits;  conditional E-value: 1.1e-22
                         MFS_1   3 laaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfas 83 
                                   +++fl +++ s++g+al  ++     +++   g l+++ +lgaav++l+++ l+dr+Gr+ +l++ ++++a+g++l +f++
  gi|13542173|ref|NP_111861.1|  28 IGGFLFGYDTSNIGTALV-FIPYP--VQGFIEGYLVAGASLGAAVGALIAAGLTDRYGRKYLLIADAAIYAAGAILSAFTI 105
                                   788999999999999998.67444..55666799***************************************55555888 PP

                         MFS_1  84 slwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllgglla.sslg......Wravfyil 157
                                    l +ll++r l Gl+ ga   ++ a+i++++pk++rg+   l + ++ +G++ ++++g + + ++ g      Wr +  ++
  gi|13542173|ref|NP_111861.1| 106 DLAMLLLSRTLIGLAVGADSGIATAYISEYAPKDRRGSLGILQQWMITIGILGAYIVGMATLyAAPGlasvldWRIMLGVA 186
                                   888***********************************99999999999998888888844434444555555******** PP

                         MFS_1 158 aivsllafvlfllllpeepperkrkspkeee.......kgtgpaplvpawkallkdpvl..w....illialllfffgfsg 225
                                   ai +l+++    + ++ ++++r+     + +       k   + ++ + +k+++ ++          ++++++lff++ ++
  gi|13542173|ref|NP_111861.1| 187 AIPALIGLG---FRFMMPESPRWLMINGKYKeaseafkKLGLNLSVDE-LKEVKFRQRAkiTngvkRAFLVVALFFVFQQI 263
                                   *******44...444444445555444444444666652233333333.44444444332213345466666666656666 PP

                         MFS_1 226 lltllply.....lqevlgls.........glllaglllallalvgailallagrlsdrlgrrrrlllallllllaalgla 292
                                   + + +p+y     + e l+l          + ++a+++  +la++++++  ++ r++d +grr+  ll++++++++ l+  
  gi|13542173|ref|NP_111861.1| 264 TGINIPFYygpivI-EKLHLFgsatqslvfTQIYAVAAATILAVINVAATYIGFRYIDTVGRRKLALLGYSGMTFFGLLGG 343
                                   66666665555533.33333346677776634666666777777777778888888888***9999999999998888877 PP

                         MFS_1 293 llavtssavllll..vlvliGfglgfvfpsllalasdlappeeagtasglfnta 344
                                   ll   +  v ll+  + ++i f++g v ++ + +  +++p++++g +++l  ++
  gi|13542173|ref|NP_111861.1| 344 LLLYLKFDVGLLIafAGFIIFFAFG-VGGTGWMIQGEYFPTNMRGLYASLGAFV 396
                                   7777733333333223333444444.37888888899999*****999998776 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 5.2e-05
                         MFS_1  37 lltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll.fa.....sslw.lllvlrvlqGlga.galfpagaal 109
                                   ++t+ a+  ++a++++ r +d +Grr++ llg+ ++ +++ll+  +       +l  +++ + ++ ++g  g+++     +
  gi|13542173|ref|NP_111861.1| 300 AATILAVINVAATYIGFRYIDTVGRRKLALLGYSGMTFFGLLGGlLLylkfdVGLLiAFAGFIIFFAFGVgGTGWM----I 376
                                   677789999************************9999996666633244645555555666666666665344444....4 PP

                         MFS_1 110 iadwfpkeergrai...gllsagfslGai.lgpllggllasslgWravfyilaivsllafvlfllllpeepper 179
                                     ++fp + rg++    +++   +++++i + p+l +l++       v+++++i+sl+a+++f+  +pe+  ++
  gi|13542173|ref|NP_111861.1| 377 QGEYFPTNMRGLYAslgAFVDWIANFAIIeIFPVLEALIT----IKNVMFVFGILSLIAVLIFYYIMPET--KE 444
                                   5677777777777633366677888888526688888888....***************88633333333..33 PP

>> TRI12  Fungal trichothecene efflux pump (TRI12)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   4.0   1.3e-08   4.8e-05      88     216 ..      64     200 ..      52     225 .. 0.71
   2 ?   -4.9   7.0       1.9   6.7e+03      25     225 ..     225     445 ..     214     455 .. 0.58

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 1.3e-08
                         TRI12  88 ttgqavsilvmgrltdrfgrrpfvilthilglvgaivgctatkfntllaamtllgvaagp.agasplfvgelmsn.ktkfl 166
                                   ++g av  l+   ltdr+gr+ ++i+   +   gai+ + +  +  ll + tl+g+a g  +g +  ++ e   + +   l
  gi|13542173|ref|NP_111861.1|  64 SLGAAVGALIAAGLTDRYGRKYLLIADAAIYAAGAILSAFTIDLAMLLLSRTLIGLAVGAdSGIATAYISEYAPKdRRGSL 144
                                   6799*****************************************************9963789999***99765145578 PP

                         TRI12 167 gllivsipvvvtsg......lspylgqrlaiqgswrwifyiyiitsaiavllivvw 216
                                   g+l   + ++ + g      ++ y    la   +wr ++ +  i + i + +  + 
  gi|13542173|ref|NP_111861.1| 145 GILQQWMITIGILGayivgmATLYAAPGLASVLDWRIMLGVAAIPALIGLGFRFMM 200
                                   88755444443322011111344555666666667766666666666655555555 PP

  == domain 2  score: -4.9 bits;  conditional E-value: 1.9
                         TRI12  25 latsadelpegyyrsprvvasfaafslnvvatyfvlqasas.alp.....ni...lqdvgqsensslfstlwttgqavsil 96 
                                   l  s del e  +r    ++     ++ vva +fv+q  +   +p      +   l   g + +s +f+ ++++  a  + 
  gi|13542173|ref|NP_111861.1| 225 LNLSVDELKEVKFRQRAKITNGVKRAFLVVALFFVFQQITGiNIPfyygpIViekLHLFGSATQSLVFTQIYAVAAATILA 305
                                   566777888887777777777777777888888888765431444111112311133345555555667777666554332 PP

                         TRI12  97 vmg........rltdrfgrrpfvilth....ilglvgaivgctatkfntlla.amtllgvaagpagasplfvgelmsnktk 164
                                   v+         r  d +grr + +l +     +gl+g ++      +  l+a a  ++  a g  g+  ++ ge +  + +
  gi|13542173|ref|NP_111861.1| 306 VINvaatyigfRYIDTVGRRKLALLGYsgmtFFGLLGGLLLYLKFDVGLLIAfAGFIIFFAFGVGGTGWMIQGEYFPTNMR 386
                                   221111222248889999999988865222256666666655544444455523346667888888888888998755443 PP

                         TRI12 165 ....flgllivsipvvvtsglspylgqrlaiqgswrwifyiyiitsaiavllivvwyyppsfaql 225
                                        lg ++  i   ++  + p l   ++i+     +++++ i+s iavl  + +y  p  ++l
  gi|13542173|ref|NP_111861.1| 387 glyaSLGAFVDWIANFAIIEIFPVLEALITIK----NVMFVFGILSLIAVL--IFYYIMPETKEL 445
                                   11113555666666666666677776666664....577888889999885..456666666665 PP

>> DUF1269  Protein of unknown function (DUF1269)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.2   0.00049       1.8      17      43 ..      49      80 ..      32      85 .. 0.75
   2 ?    2.5   0.1      0.05   1.8e+02      12      38 ..     109     135 ..      95     141 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00049
                       DUF1269 17 nPllG.....aavGAaaGAlvgalsdvgiddd 43
                                   P+ G     +++GA++GA+vgal  +g+ d+
  gi|13542173|ref|NP_111861.1| 49 YPVQGfiegyLVAGASLGAAVGALIAAGLTDR 80
                                  35666666677799999999999999998875 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.05
                       DUF1269  12 GllflnPllGaavGAaaGAlvgalsdv 38 
                                    ll+   l+G+avGA  G +++ +s++
  gi|13542173|ref|NP_111861.1| 109 MLLLSRTLIGLAVGADSGIATAYISEY 135
                                   456666799********9888777766 PP

>> NADH-u_ox-rdase  NADH-ubiquinone oxidoreductase complex I, 21 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0    0.0015       5.5      42      74 ..       7      39 ..       4      40 .. 0.88
   2 ?   -1.2   0.2      0.92   3.3e+03      45      69 ..     135     167 ..     116     203 .. 0.60
   3 ?   -0.5   0.7      0.58   2.1e+03      32      67 ..     305     345 ..     287     367 .. 0.59

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0015
               NADH-u_ox-rdase 42 leklsPsvagkamtlagligflggfllayqnss 74
                                  +ekl+ s++ + ++l +l++++ggfl+ y+ s+
  gi|13542173|ref|NP_111861.1|  7 IEKLDFSKVTRFYWLLTLLATIGGFLFGYDTSN 39
                                  6788888888889*****************996 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.92
               NADH-u_ox-rdase  45 lsPsvagka.......mtlagligflg.gflla 69 
                                   ++P+  + +       m + g++g    g+ + 
  gi|13542173|ref|NP_111861.1| 135 YAPKDRRGSlgilqqwMITIGILGAYIvGMATL 167
                                   555553333555555555555555444444333 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.58
               NADH-u_ox-rdase  32 taafplallaleklsPsvagka.....mtlagligflggfl 67 
                                   +++  +a +++ ++  +v++++     +   ++ g+lgg+l
  gi|13542173|ref|NP_111861.1| 305 AVINVAATYIGFRYIDTVGRRKlallgYSGMTFFGLLGGLL 345
                                   23334444444444445555554454544444555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (480 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       898  (0.0500865); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.66u 0.32s 00:00:00.98 Elapsed: 00:00:00.46
# Mc/sec: 3113.91
//
Query:       gi|13542174|ref|NP_111862.1|  [L=366]
Description: Acyl-CoA dehydrogenase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-17   64.2   0.0    2.8e-17   63.4   0.0    1.4  1  Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
    5.9e-17   62.3   0.0    1.5e-16   61.0   0.0    1.6  2  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
    5.8e-15   55.3   0.1      1e-14   54.5   0.1    1.4  1  Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
    1.3e-07   31.9   0.2    7.2e-07   29.6   0.2    2.1  1  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 !   63.4   0.0   6.3e-21   2.8e-17       1     113 []       5     113 ..       5     113 .. 0.93

  Alignments for each domain:
  == domain 1  score: 63.4 bits;  conditional E-value: 6.3e-21
                                   THHHHHHHHHHHHHHHHHTHHHHHHHHHHTSGHHHHHHHHHHTTCTSTTS-GGGTS--.S-HHHHHHHHHHHHHH-HHHHH CS
                 Acyl-CoA_dh_N   1 teeqealrdtvrefaeeelaphaaewdeegefprelwkklaelGllgitvpeeygGag.ldyleaaivaeelaradaglal 80 
                                   +eeq  ++ +++ef +++++p ++++++++ fp +++++++++G++ +++p    G g  d+ +  ++aee+++++  +a 
  gi|13542174|ref|NP_111862.1|   5 SEEQSIIKGSIAEFTKRRIEPIEKRIEDDDYFPMDILREIGKNGFFSVMLP----GIGvQDTYSFSLIAEEISKVSPEVAW 81 
                                   69*******************999999999********************9....777447*****************999 PP

                                   HHHHHHHTTHHHHHHHS-HHHHHHHHHHHHTTS CS
                 Acyl-CoA_dh_N  81 llgvhsslvapailrfGteeqkrryLpklasge 113
                                   l+ +h   +++a+ + Gteeqk+ yL+k+a+ge
  gi|13542174|ref|NP_111862.1|  82 LYVTHV-AASYALDKLGTEEQKDSYLRKMADGE 113
                                   887776.5559********************98 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 ?   -2.3   0.0         1   4.6e+03      49      93 ..      64     109 ..      61     119 .. 0.74
   2 !   61.0   0.0   3.3e-20   1.5e-16      15     128 ..     236     344 ..     222     349 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1
                                   GSHHHHHHHHHHHHHHHHHHHHHHHHHH--------.HHHHHHHHH CS
                 Acyl-CoA_dh_1  49 dhqlvreklaemaaeleaarllvyraaealdagkpd.raeasmaKl 93 
                                   ++ l++e++ ++  e++ +  +  +a +ald+ + + ++++ + K+
  gi|13542174|ref|NP_111862.1|  64 SFSLIAEEISKVSPEVAWLYVTHVAASYALDKLGTEeQKDSYLRKM 109
                                   5778888888888888888888888888888877774555555555 PP

  == domain 2  score: 61.0 bits;  conditional E-value: 3.3e-20
                                   -----..-SHHHHHHHHHHHHHHHTSB-CC-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH--------HHHHHHHHHHH CS
                 Acyl-CoA_dh_1  15 RlavaaaalglarraleealeyarrrkafgkplidhqlvreklaemaaeleaarllvyraaealdagkpdraeasmaKlfa 95 
                                    ++ a  +lg+++rale + +++++rk   k l+++q v++kl +++a++eaar+lvyra       ++d   a  aKlf 
  gi|13542174|ref|NP_111862.1| 236 SIGAASISLGIMERALELVSSHVKERKIACKSLLSNQTVQDKLFHLYADTEAARSLVYRASI-----NDDIRLAYSAKLFS 311
                                   56778889***************************************************994.....444457899***** PP

                                   HHHHHHHHHHHHHHHGGGTTSGGGHHHHHHHHT CS
                 Acyl-CoA_dh_1  96 selaqevadlamqllGgaGyleeypverlyrda 128
                                   +e    v+++a+ l+G+ Gy+e+ ++ +l++ a
  gi|13542174|ref|NP_111862.1| 312 TERSIAVTESAVSLFGATGYEESLAIPKLLNKA 344
                                   **********************99999988766 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 !   54.5   0.1   2.3e-18     1e-14       2      96 ..     118     209 ..     117     210 .. 0.91

  Alignments for each domain:
  == domain 1  score: 54.5 bits;  conditional E-value: 2.3e-18
                                   EE---SS-SS-GGG---EEEEETT.EEEEEEEEEEEETTTT-SEEEEEEETS-------EEEEEEE..GGGEEE-----BS CS
                 Acyl-CoA_dh_M   2 falTEpqaGsdvasvkttaaerdggeyvlnGeKiwitnaaiatlalvlartekpdrarglslflvprdapgvsvrrieekl 82 
                                   +a+TE ++G  + +++++a ++ +++++l+G+K++it +++a+l+ vla+ +++d    +++f+v +++ g++++      
  gi|13542174|ref|NP_111862.1| 118 IAITESSSGATASAIASSA-RKYEENWILEGSKTFITMGGDADLYAVLAK-THED-PAAFTTFIVLKSDVGLELGTHLIGS 195
                                   79***************55.555557************************.6677.799***************8888899 PP

                                   S-TTS-EEEEEEE. CS
                 Acyl-CoA_dh_M  83 Glrglptgelvfed 96 
                                   +++g+ +ge+ f++
  gi|13542174|ref|NP_111862.1| 196 AMKGIGWGEISFNN 209
                                   9***********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 !   29.6   0.2   1.6e-10   7.2e-07       2     113 ..     238     334 ..     237     354 .. 0.90

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 1.6e-10
                                   HHHHHHHHHHHHHHHHHHHHHHHHHCTTT-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----HHHHHH CS
                 Acyl-CoA_dh_2   2 giaavalGaAraalaefvelarervrassgekladdpatqlalaeaaarldAAralleraaaraealaaagkevtvedrae 82 
                                   g a + lG+ ++al+ + ++++er+   + ++l  ++++q +l ++ a+ +AAr l++ra         +++       + 
  gi|13542174|ref|NP_111862.1| 238 GAASISLGIMERALELVSSHVKERKI--ACKSLLSNQTVQDKLFHLYADTEAARSLVYRASIN------DDI-------RL 303
                                   67999*********************..99*****************************9988......333.......45 PP

                                   HHHHHHHHHHHHHHHHHHHHHHCGGGGGBTT CS
                 Acyl-CoA_dh_2  83 arraaalavelaiaavdalfeaaGgsalrke 113
                                   a  a+++ +e++ia+++++++++G++++ ++
  gi|13542174|ref|NP_111862.1| 304 AYSAKLFSTERSIAVTESAVSLFGATGYEES 334
                                   7789***********************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       382  (0.0213063); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 2303.86
//
Query:       gi|13542175|ref|NP_111863.1|  [L=255]
Description: 3-ketoacyl-(acyl-carrier-protein) reductase [Thermoplasma volcanium GSS1]
Scores for complete 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  210.9   0.1    2.3e-62  210.6   0.1    1.0  1  adh_short_C2    Enoyl-(Acyl carrier protein) reductase
    1.3e-51  174.9   0.1    1.5e-51  174.6   0.1    1.1  1  adh_short       short chain dehydrogenase
    4.3e-09   36.5   0.1    6.6e-09   35.9   0.1    1.4  1  KR              KR domain
     0.0088   15.4   0.0      0.089   12.1   0.0    2.5  3  THF_DHG_CYH_C   Tetrahydrofolate dehydrogenase/cyclohydrolase
      0.009   15.5   0.1      0.022   14.2   0.1    1.7  2  Epimerase       NAD dependent epimerase/dehydratase family
  ------ inclusion threshold ------
      0.019   14.8   0.1      0.028   14.2   0.1    1.3  1  DFP             DNA / pantothenate metabolism flavoprotein
      0.063   12.6   0.0       0.11   11.9   0.0    1.3  1  DUF1776         Fungal family of unknown function (DUF1776)
      0.094   12.6   0.3       0.17   11.7   0.3    1.4  1  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 !  210.6   0.1     1e-65   2.3e-62       1     232 [.      14     246 ..      14     247 .. 0.94

  Alignments for each domain:
  == domain 1  score: 210.6 bits;  conditional E-value: 1e-65
                                   TTTTSHHHHHHHHHHHTT-EEEEEESSGGHHHHHHHHHHHTTSEEEE--TTSHHHHHHHHHHHHHHHSSEEEEEE-----E CS
                  adh_short_C2   1 GaasgIGraiAkalaeeGaevvltdlneeakkrveelaeelgaevlecDVtdeeqvealveevvekfgklDilvnnagiap 81 
                                   Ga +g+GraiA+++a+eGa+v++ ++++e+  ++ e+++ +g e++++DV++++qv+++++++ ek+gk+Dilvnn gi  
  gi|13542175|ref|NP_111863.1|  14 GASKGLGRAIAEEFAKEGARVAINYAHDEK--SALEVKKITGGEIFKADVSNRDQVKEMARQIHEKLGKIDILVNNSGIWY 92 
                                   899**************************8..6788888899*************************************** PP

                                   GCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHH.HCTSCCEEEEEEEGGGTSB.STTTTHHHHHHHHHHHHHHHHHHHHG CS
                  adh_short_C2  82 klkgpfletsreefdraldvnlyslfllakaalp.lmkeggsivnlssvgaerv.vpnynaygaaKaalealtrylAvelg 160
                                       pf++ ++e+++r+ldvnl ++++++ ++lp l +++g i+n+ s ++  +  +n++ y+ +Kaa++ lt+ lA +l 
  gi|13542175|ref|NP_111863.1|  93 L--MPFENYDEEKVRRMLDVNLMGAIYTTLEFLPdLKEKKGTIINIGSNAGIGTaAKNTTFYSLTKAAIIMLTKRLAFDLS 171
                                   *..*******************************777788*********99877255555********************* PP

                                   GGTEEEEEEEE--BHCTGGGGSTT...HHHHHHHHHHHSTTSS-B-HHHHHHHHHHHCSGGGTT--SEEEEESTT CS
                  adh_short_C2 161 pkgiRvNavspgpikTlaasgikg...fdelleelearaplgrlgtpeevaeaalfLasdeasyitGqtlvvDgG 232
                                   ++ iRvNa++pg+i+T+++ g k     ++l+e +++r+ l+ +g+pe +++aalfLas ++ y++Gq++v+DgG
  gi|13542175|ref|NP_111863.1| 172 EYSIRVNAIAPGWIETDLTIGGKTdeeIRKLEEDFKSRTTLKMFGKPEYIGKAALFLASSDSVYMNGQVIVIDGG 246
                                   ******************7666652336679999****************************************9 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  174.6   0.1   6.8e-55   1.5e-51       1     188 [.       8     191 ..       8     198 .. 0.92

  Alignments for each domain:
  == domain 1  score: 174.6 bits;  conditional E-value: 6.8e-55
                                   SEEEEESTTSHHHHHHHHHHHHTT-EEEE.EESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSESE CS
                     adh_short   1 kvvlvtGassGIGraiakelakeGakvvv.vdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkldv 80 
                                   k++l+tGas+G+Graia+e+akeGa+v++ ++  e+ + ev+k  +       ++++Dv++r++v+++ +++ +klgk+d+
  gi|13542175|ref|NP_111863.1|   8 KTALITGASKGLGRAIAEEFAKEGARVAInYAHDEKSALEVKKITGG-----EIFKADVSNRDQVKEMARQIHEKLGKIDI 83 
                                   79***************************666666666565555554.....69*************************** PP

                                   EEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGG.TSB-TTBHHHHHHHHHHHHHH CS
                     adh_short  81 LvnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvag.kvpvagvaaYsAsKaavaglt 160
                                   LvnN Gi    pf++++ee+++r+++vNl+g++ +t ++lp  lk+++G+I+n++S+ag   + ++++ Ys +Kaa+++lt
  gi|13542175|ref|NP_111863.1|  84 LVNNSGIWYLMPFENYDEEKVRRMLDVNLMGAIYTTLEFLPD-LKEKKGTIINIGSNAGiGTAAKNTTFYSLTKAAIIMLT 163
                                   *******99*********************************.669*************778889999************* PP

                                   HHHHHHHGGGTEEEEEEEESSBSSHHHH CS
                     adh_short 161 rslakelaptgirvnavaPGlvdTdmak 188
                                   + la +l++++irvna+aPG ++Td++ 
  gi|13542175|ref|NP_111863.1| 164 KRLAFDLSEYSIRVNAIAPGWIETDLTI 191
                                   *************************975 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.9   0.1   2.9e-12   6.6e-09       2     117 ..       9     116 ..       8     166 .. 0.84

  Alignments for each domain:
  == domain 1  score: 35.9 bits;  conditional E-value: 2.9e-12
                                   EEEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHSS-- CS
                            KR   2 tylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaeeppi 82 
                                   t litG+  gLG+++a+  a++gar  +  + +    e+s+ ++++++      e+++aDvs++d+v+++ ++i+++ ++i
  gi|13542175|ref|NP_111863.1|   9 TALITGASKGLGRAIAEEFAKEGARVAINYAHD----EKSALEVKKITG----GEIFKADVSNRDQVKEMARQIHEKLGKI 81 
                                   579**********************99988887....344434555544....4689************************ PP

                                   -EEEE---------TTT--HHHHHHHHTTTTHHHH CS
                            KR  83 kGvihaAgvlrdklleemtaedleqvlapKvkGaw 117
                                      ++  g+    ++e+ ++e+++++l   + Ga 
  gi|13542175|ref|NP_111863.1|  82 DILVNNSGIWYLMPFENYDEEKVRRMLDVNLMGAI 116
                                   **************************998888875 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 !   12.1   0.0     4e-05     0.089      33      70 ..       4      41 ..       1      88 [. 0.82
   2 ?   -1.5   0.0      0.62   1.4e+03      68      93 ..      69      94 ..      56     110 .. 0.78
   3 ?   -0.1   0.0      0.23   5.2e+02      10      38 ..     146     174 ..     133     178 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4e-05
                                  --TT-EEEEE---TTTHHHHHHHHHCTT-EEEEE-TTS CS
                 THF_DHG_CYH_C 33 elegkkvvvvGrsnivgkplallLleknatVtvchskt 70
                                  +legk++++ G+s+ +g+++a  +++++a V +   + 
  gi|13542175|ref|NP_111863.1|  4 KLEGKTALITGASKGLGRAIAEEFAKEGARVAINYAHD 41
                                  799************************99998754443 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.62
                                  TTSCCHHHHHCCSSEEEE-SS-TT-B CS
                 THF_DHG_CYH_C 68 sktkdlaeitreadivvvavGkpeli 93
                                  + +++++e++ + di+v   G   l+
  gi|13542175|ref|NP_111863.1| 69 EMARQIHEKLGKIDILVNNSGIWYLM 94
                                  56788899999999999988876655 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.23
                                   TT--SS--HHHHHHHHHHHHCT---TT-E CS
                 THF_DHG_CYH_C  10 kgeeallpctpkgvvellketgielegkk 38 
                                   ++++++ + t ++++ l k+   +l++ +
  gi|13542175|ref|NP_111863.1| 146 AKNTTFYSLTKAAIIMLTKRLAFDLSEYS 174
                                   457789999********999999887755 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   0.1   9.9e-06     0.022       1      61 [.      10      72 ..      10      87 .. 0.81
   2 ?   -2.9   0.0       1.7   3.8e+03     137     154 ..     147     164 ..     127     170 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 9.9e-06
                                  EEEETTTSHHHHHHHHHHHHCTSE.EEEEES-STTTTCHHCHHC....EEEE--TT-HHHHHHHHH CS
                     Epimerase  1 ilVtGatGfiGsalvkallekgye.vigldrlssasntarledl....elveldltdrsalerlfk 61
                                  +l+tGa+  +G+a++++++++g +  i+ +++ ++s+ + +  +    e+ ++d+ +r++++++ +
  gi|13542175|ref|NP_111863.1| 10 ALITGASKGLGRAIAEEFAKEGARvAINYAHD-EKSALEVK--KitggEIFKADVSNRDQVKEMAR 72
                                  59********************9955666666.44444444..34599***********9999766 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.7
                                   --SSHHHHHHHHHHHHHH CS
                     Epimerase 137 kpnspYaaaKlageklve 154
                                   k ++ Y+++K+a+  l++
  gi|13542175|ref|NP_111863.1| 147 KNTTFYSLTKAAIIMLTK 164
                                   456678888888777665 PP

>> DFP  DNA / pantothenate metabolism flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   1.3e-05     0.028      26     128 ..      15     126 ..      10     166 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.3e-05
                                   ----HHHHHHHHHHHHTT-EEEEEE-S..-.SS--.......-TT-EEEE--SHHHHHHHHHHHHTT-SEEEE---S--EE CS
                           DFP  26 rSSGkmGyalAeaaaarGaeVtlvsgp..v.slet.......pegvevvkvesaeemleaveealkeadivimaAAvaDyr 96 
                                    S G  G a+Ae++a++Ga+V +  ++    +le          +++v + ++++em+++++e+l + di++    +    
  gi|13542175|ref|NP_111863.1|  15 ASKG-LGRAIAEEFAKEGARVAINYAHdeKsALEVkkitggeIFKADVSNRDQVKEMARQIHEKLGKIDILVNNSGIWYLM 94 
                                   5555.69**************9887763122344333433322245677788999*****************998887777 PP

                                   E.S-------------..----EEE---HHHHH CS
                           DFP  97 p.keaaeeKikkeeeeeeltleleknpdilael 128
                                   p ++  eeK+++   + +l  ++  + + l  l
  gi|13542175|ref|NP_111863.1|  95 PfENYDEEKVRR-MLDVNLMGAIYTTLEFLPDL 126
                                   656666677766.44444555555555555555 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 ?   11.9   0.0   4.9e-05      0.11     106     200 ..      94     185 ..      83     205 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.9e-05
                       DUF1776 106 gpietiplsswaselnerllspiltlqallplltsrakqkakiivvnpsissslnlpfhapEalvssalsalfevLkrelr 186
                                    p+e+  +++++  l  +l+  i t+ ++lp l++   +k +ii +  +      +++    +l+  a+  l++ L+ +l+
  gi|13542175|ref|NP_111863.1|  94 MPFENYDEEKVRRMLDVNLMGAIYTTLEFLPDLKE---KKGTIINIGSNAGIGTAAKNTTFYSLTKAAIIMLTKRLAFDLS 171
                                   5899999***************************8...9999999999999999999999999****************** PP

                       DUF1776 187 phnidvtqikLGnl 200
                                   ++ i v  i  G +
  gi|13542175|ref|NP_111863.1| 172 EYSIRVNAIAPGWI 185
                                   *****999987766 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 ?   11.7   0.3   7.7e-05      0.17       1      58 [.      14      71 ..      14      77 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 7.7e-05
                                  TTTSHHHHHHHHHHHHC-T-EEEEE.ETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHH CS
                NAD_binding_10  1 GAtGkvGrllvkellargghevtal.vRnpeklaeleaeeglevvegdvtdvedlaeal 58
                                  GA+ + Gr++++e +++g  +v +  + +++++ e+++  g e++++dv++ ++++e  
  gi|13542175|ref|NP_111863.1| 14 GASKGLGRAIAEEFAKEG-ARVAINyAHDEKSALEVKKITGGEIFKADVSNRDQVKEMA 71
                                  9****************7.66665414555555568888999************99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       743  (0.0414412); expected 358.6 (0.02)
Passed bias filter:                      613  (0.0341904); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.60u 0.31s 00:00:00.90 Elapsed: 00:00:00.52
# Mc/sec: 1465.39
//
Query:       gi|13542176|ref|NP_111864.1|  [L=322]
Description: dehydrogenase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.9e-17   63.6   0.0    4.9e-17   62.9   0.0    1.4  1  GFO_IDH_MocA    Oxidoreductase family, NAD-binding Rossmann f
     0.0011   18.9   0.2     0.0021   18.0   0.2    1.4  1  GFO_IDH_MocA_C  Oxidoreductase family, C-terminal alpha/beta 
     0.0044   16.5   0.0     0.0077   15.7   0.0    1.4  1  adh_short       short chain dehydrogenase
  ------ inclusion threshold ------
      0.025   14.8   0.0      0.053   13.8   0.0    1.5  1  TrkA_N          TrkA-N domain


Domain annotation for each model (and alignments):
>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.9   0.0   1.1e-20   4.9e-17       2     119 ..       2     116 ..       1     117 [. 0.92

  Alignments for each domain:
  == domain 1  score: 62.9 bits;  conditional E-value: 1.1e-20
                                   EEEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHE.EESSHHHHHTCTTESEEEE-S-GGGHHHHHHH CS
                  GFO_IDH_MocA   2 rvaiiGaGkigskhlrplnesqrleevvalldpdaeraeavaesfgve.aysdleelladpeidavivatpngtheelaka 81 
                                    v+++G+  +g++hlr + ++  + + va++++d++ a+++ e+f+++ +ys++++ l+ +++++   ++p g+h+++a  
  gi|13542176|ref|NP_111864.1|   2 DVVVVGCKGFGKEHLRVYSKN--GID-VAIVERDSKTAQECVEKFNIKkVYSNFNDSLS-SNANVFDLVVPDGLHHDMAFT 78 
                                   69*****999*****766666..555.56************************998888.57******************* PP

                                   HHHTT-EEEEESSS-SSHHHHHHHHHHHHHHTS-EEEE CS
                  GFO_IDH_MocA  82 aleagkhvllEKPlattveeakelvelaekkgklvsvg 119
                                   +++ +khvllEKP++ +++   +l+++ ++++++++v+
  gi|13542176|ref|NP_111864.1|  79 LMKLKKHVLLEKPITPDIDSGIDLIKTSNEQSVKFMVA 116
                                   **********************************9985 PP

>> GFO_IDH_MocA_C  Oxidoreductase family, C-terminal alpha/beta domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.2   4.8e-07    0.0021       4      95 ..     129     218 ..     126     227 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 4.8e-07
                                   HHTTTTSSEEEEEEEEECBEEECHHHHCCGGSH..HCSTSHHHHTCHHHHHHHHHHHTSEEEEEEEEE.SEEESCTCCSCS CS
                GFO_IDH_MocA_C   4 IengklGevvsvdvwtldtragaeakkrwkrrk..kksgGvlgdlgiHdiDllqwLfGqppsvvaalgrmrqnaeaaeded 82 
                                   I++ k G++   +  t++ r++  +k  ++r      + G+l++ g+H iD l  + G  +s  +  +  r++ +a+ed+ 
  gi|13542176|ref|NP_111864.1| 129 INEIKKGTIGKAH--TVIVRHQSHRKLEGWRKEsrMIGRGILINEGTHYIDTLLNIGGRYSSLRSYVH--RTWESAGEDTA 205
                                   6777799999995..666666666666666544546788****************9999998888887..78888899999 PP

                                   EEEEEEEEEEETT CS
                GFO_IDH_MocA_C  83 aavmsvlnlekgs 95 
                                    av+ ++n+ +g+
  gi|13542176|ref|NP_111864.1| 206 EAVFNFENGMHGV 218
                                   9988888887776 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.7e-06    0.0077       3      45 ..       3      44 ..       2      66 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.7e-06
                                  EEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHH CS
                     adh_short  3 vlvtGassGIGraiakelakeGakvvvvdrseekleevakelk 45
                                  v+v+G+ +G+G++  + + k+G++v++v+r +++++e++++++
  gi|13542176|ref|NP_111864.1|  3 VVVVGC-KGFGKEHLRVYSKNGIDVAIVERDSKTAQECVEKFN 44
                                  556665.6*******************************9987 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   1.2e-05     0.053       1      44 [.       3      47 ..       3      60 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.2e-05
                                  EEEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTT.SEE CS
                        TrkA_N  1 iiiiGlGrvGrslaeeLseggkdvvvidkdeerveelreeg.lev 44
                                  ++++G+  +G++ ++  s++g+dv ++++d ++++e  e++ ++ 
  gi|13542176|ref|NP_111864.1|  3 VVVVGCKGFGKEHLRVYSKNGIDVAIVERDSKTAQECVEKFnIKK 47
                                  79*****************9999************9988775554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       606  (0.0338); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); 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 0.31s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 2085.66
//
Query:       gi|13542177|ref|NP_111865.1|  [L=361]
Description: N-acylamino acid racemase [Thermoplasma volcanium GSS1]
Scores for 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  123.3   0.0    1.3e-35  123.0   0.0    1.1  1  MR_MLE_C   Enolase C-terminal domain-like
    1.6e-06   28.3   0.0    3.1e-06   27.4   0.0    1.5  1  MR_MLE_N   Mandelate racemase / muconate lactonizing enzyme, 
  ------ inclusion threshold ------
      0.011   15.0   0.0      0.016   14.5   0.0    1.2  1  Enolase_C  Enolase, C-terminal TIM barrel domain
      0.038   13.1   0.0      0.058   12.5   0.0    1.3  1  MAAL_C     Methylaspartate ammonia-lyase C-terminus


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 !  123.0   0.0   2.9e-39   1.3e-35       1     218 [.     138     347 ..     138     349 .. 0.89

  Alignments for each domain:
  == domain 1  score: 123.0 bits;  conditional E-value: 2.9e-39
                                   HHHHHHHHHHHHHT-SEEEEETSSSHHHHHHHHHHHHHHHHTTTSTSEEEEE-TTTSBHHHHHHHHHHHGGGTESEEESSS CS
                      MR_MLE_C   1 elaeearelvaeqgfravKlkvggddvaedvervravreavgpgddvdlmvDanqawdlatAirvareleeldllwlEEPv 81 
                                   e++e++r++v   g++++K+k+ ++        v ++r+++ p  d++l vDan+ ++    i +++el++++l+++E+P+
  gi|13542177|ref|NP_111865.1| 138 EMKEQVRSAVS-LGYKRIKVKIKRG----RENIVSEIRDEF-P--DIRLSVDANGDYSYH-DIPLLKELDKFELEYIEQPF 209
                                   58999977555.6********8886....5579********.6..46***********75.79******99********** PP

                                   STTTHHHHHHHHHHHH.SSEEEESTTSSSHHHHHHHHHHTSESEEEEBHHHHTSHHHHHHHHHHHHHTT-EEEEBSCS.SH CS
                      MR_MLE_C  82 ppeddleglaelrara.sipiaagEslysradfrelleagavdivqpdvsrvgGitearkvaalaeafgvpvapHsgs.gg 160
                                   +  ddl  + +l+ ++ s+p++++Es+++++ +++++e gavd+++++++rv G+ +++++a++a++++  ++++++  +g
  gi|13542177|ref|NP_111865.1| 210 RG-DDLIYHSKLK-KEiSTPVCLDESITDPEKAEKAFEIGAVDVINIKPGRVAGLHNSIEIAKIARENNGHCWVGGMLeTG 288
                                   *9.67999*****.6679**********************************************************9659* PP

                                   HHHHHHHHHHHTTTTBEEEEEEGGGGH.TSGCSBSSSSEEETTEEECTSSSBTSSEB-.H CS
                      MR_MLE_C 161 lglaaslhlaaaipnllileyfldael.leeelleeplevedGrvtvpdgpGlGveld.e 218
                                   +g+a ++ la+    +++  ++ ++e+ ++++++ +p+++++G +++ +g G+Gv +d +
  gi|13542177|ref|NP_111865.1| 289 IGRAFNIALASQEL-IDYPGDTSPNEKyFRKDIVRNPFRMKKGVIEANKGDGIGVYVDfD 347
                                   *********87774.4444444444446***************************99955 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 !   27.4   0.0   6.8e-10   3.1e-06       7     117 .]       6     119 ..       1     119 [. 0.79

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 6.8e-10
                                   EEEEEEEC.EEEETTEEEEEEEEEEEEEEECTTEEEEEEEE-STT......GHHHHHHHHHHHHHHHHTTSBTTHHHHHHH CS
                      MR_MLE_N   7 veeavklr.PvqlavttvqkqslvlvkietseGvvGigeatsvgg......raetikaelddhlapllvgkdaanisdlaq 80 
                                   ++++ +   P+ ++++t +  + ++++++ ++G+   +e ++          + t    +++ la + v   +++ + l  
  gi|13542177|ref|NP_111865.1|   6 FKVRIPFIrPFTTSFGTEEYREAIILHMN-KDGIDAFSEIVTSFLpdygyeYNDTAINTIEKFLAKY-VADAPQPHEFLD- 83 
                                   555555545********************.*********8765434677766666666777766555.556666655444. PP

                                   HHHHHCSSCHHHHHHHHHHHHHHHHHHTTSBHHHHTT CS
                      MR_MLE_N  81 llkravlgnmsAkaaidmAlwDlkakalnlpladLlG 117
                                      + ++g  +Ak a++m lwD + k ++ pl d +G
  gi|13542177|ref|NP_111865.1|  84 -RVKGIKGHNMAKGAVEMLLWDYHSKLAGKPLDDYMG 119
                                   .45899**************************99998 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 ?   14.5   0.0   3.5e-06     0.016     145     227 ..     197     275 ..     132     284 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.5e-06
                                   HHHHS-EEEEES-S-TT-HHHHHHHHHHHTTTSEEEESTTTTT-HHHHHHHHHCT--SEEEE-HHHH-SHHHHHHHHHHHH CS
                     Enolase_C 145 lvkkyPivsiedpldeddweawkklteelgdkvqivGddltvtnpkrlkeaiekkaanalllkvnqiGsltesleavklak 225
                                   l +k+ +  ie p+  dd   ++kl++e+      v  d  +t+p++ ++a e +a + + +k  ++  l +s+e +k+a+
  gi|13542177|ref|NP_111865.1| 197 L-DKFELEYIEQPFRGDDLIYHSKLKKEIS---TPVCLDESITDPEKAEKAFEIGAVDVINIKPGRVAGLHNSIEIAKIAR 273
                                   3.689999**********************...45666889*************************************998 PP

                                   HT CS
                     Enolase_C 226 ea 227
                                   e+
  gi|13542177|ref|NP_111865.1| 274 EN 275
                                   76 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 ?   12.5   0.0   1.3e-05     0.058     141     215 ..     227     298 ..     215     307 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.3e-05
                        MAAL_C 141 elvaDeWcntledirefvdaeaadlvqiktPDlGginntieavlyckekgvgaylGGscnetdvsarvsvhvala 215
                                    +  De     e  ++  + +a+d++ ik   + g++n+ie   +++e++ ++++GG   et ++   + ++ala
  gi|13542177|ref|NP_111865.1| 227 PVCLDESITDPEKAEKAFEIGAVDVINIKPGRVAGLHNSIEIAKIARENNGHCWVGGML-ETGIGR--AFNIALA 298
                                   56667777888888888899************************************975.666653..3445555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (361 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       381  (0.0212505); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.87
# Mc/sec: 1256.99
//
Query:       gi|13542178|ref|NP_111866.1|  [L=76]
Description: transcription regulator [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.1e-07   29.5   0.1    3.3e-06   27.0   0.1    1.9  1  HTH_36         Helix-turn-helix domain
    2.8e-05   24.0   0.0    3.6e-05   23.6   0.0    1.1  1  HTH_43         Winged helix-turn helix
    6.1e-05   22.8   0.1    7.8e-05   22.5   0.1    1.1  1  MarR_2         MarR family
     0.0023   17.8   0.1     0.0028   17.5   0.1    1.2  1  HTH_11         HTH domain
     0.0049   16.7   0.1     0.0062   16.4   0.1    1.1  1  TrmB           Sugar-specific transcriptional regulator TrmB
     0.0084   15.7   0.1      0.011   15.2   0.1    1.3  1  HTH_24         Winged helix-turn-helix DNA-binding
  ------ inclusion threshold ------
      0.015   15.1   0.1      0.021   14.7   0.1    1.2  1  HTH_5          Bacterial regulatory protein, arsR family
      0.016   15.2   0.1      0.019   15.0   0.1    1.2  1  HTH_29         Winged helix-turn helix
      0.025   14.7   0.0      0.028   14.5   0.0    1.1  1  DUF2250        Uncharacterized protein conserved in archaea (
      0.045   13.8   0.1      0.064   13.3   0.1    1.3  1  HTH_46         Winged helix-turn-helix DNA binding
      0.052   12.9   0.1      0.061   12.7   0.1    1.0  1  RNA_pol_Rpc34  RNA polymerase Rpc34 subunit
      0.086   13.3   0.0      0.096   13.2   0.0    1.2  1  HTH_27         Winged helix DNA-binding domain


Domain annotation for each model (and alignments):
>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.1   2.2e-09   3.3e-06       2      55 .]       9      56 ..       8      56 .. 0.92

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 2.2e-09
                        HTH_36  2 rLspsaklllgslasfanknggcfpsqetlakrlglsknTvsraikeLeqlGyi 55
                                   L+psa+l+l +l+s      +    ++++++++gls+++v++ +k+L +lG+i
  gi|13542178|ref|NP_111866.1|  9 SLPPSARLVLAYLRSAK----I--SDVARIMENTGLSRRSVMNSVKMLKELGLI 56
                                  599**********9999....3..4699************************98 PP

>> HTH_43  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   2.4e-08   3.6e-05       9      52 ..      15      61 ..      12      72 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 2.4e-08
                                  HHHHHHHHHHS-B-HHHHHHHH---HHHHHHHHHGGGGGT...-EEE CS
                        HTH_43  9 rlylaylideeeanvpklieltgmPRRtlqDtlkalaeld...iele 52
                                  rl layl + + + v +++e tg+ RR + + +k l+el+   i++ 
  gi|13542178|ref|NP_111866.1| 15 RLVLAYLRSAKISDVARIMENTGLSRRSVMNSVKMLKELGlidIQVC 61
                                  99***********************************9863114444 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.1   5.2e-08   7.8e-05       3      62 .]      10      67 ..       8      67 .. 0.92

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 5.2e-08
                                  --HHHHHHHHHHHCTTTSEE.EHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSSSSSS CS
                        MarR_2  3 ltpaqarvLaaLgrrpgrdl.tvgelarrlglsksavsrilkrLvaaGLverrpgpeDkRa 62
                                  l+p+ + vLa+L+ +    +  v+ + + +gls+ +v + +k L + GL+  + ++ D R+
  gi|13542178|ref|NP_111866.1| 10 LPPSARLVLAYLRSAK---IsDVARIMENTGLSRRSVMNSVKMLKELGLIDIQVCLSDTRR 67
                                  8999********9999...559****************************99999988885 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1   1.9e-06    0.0028      18      46 ..      29      58 ..      14      70 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.9e-06
                        HTH_11 18 geeLAeeLnvSrrtvrrdIkaLeelg.vpI 46
                                   ++++e +++Srr v + +k L+elg ++I
  gi|13542178|ref|NP_111866.1| 29 VARIMENTGLSRRSVMNSVKMLKELGlIDI 58
                                  6899**********************7555 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1   4.2e-06    0.0062      19      65 ..      23      72 ..      13      74 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 4.2e-06
                                  HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST...TTEEEE- CS
                          TrmB 19 klgpatadeiaeelgvprskvYevLrsLedkGlVerekgr...pklYrav 65
                                  + + +++  i e++g++r +v ++++ L++ Gl++++      +++Y +v
  gi|13542178|ref|NP_111866.1| 23 SAKISDVARIMENTGLSRRSVMNSVKMLKELGLIDIQVCLsdtRRRYYCV 72
                                  555678889999***********************997223446677776 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 !   15.2   0.1   7.5e-06     0.011      21      47 ..      30      56 ..      13      57 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 7.5e-06
                        HTH_24 21 reLAerlglSpstvnrrlkrLeeeGlI 47
                                  + + e +glS+  v   +k L+e GlI
  gi|13542178|ref|NP_111866.1| 30 ARIMENTGLSRRSVMNSVKMLKELGLI 56
                                  6799**********************9 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.1   1.4e-05     0.021       4      45 ..      14      56 ..      11      57 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.4e-05
                                  HHHHHHHHTTSS.EEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                         HTH_5  4 RlkILklLaege.lcvcelaeelglsqstvShHLkkLreaGLV 45
                                   + +L +L++ +   v  ++e +gls+  v    k+L+e+GL+
  gi|13542178|ref|NP_111866.1| 14 ARLVLAYLRSAKiSDVARIMENTGLSRRSVMNSVKMLKELGLI 56
                                  56788899997779999*************************9 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.1   1.3e-05     0.019       4      41 ..      19      55 ..      17      69 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.3e-05
                        HTH_29  4 allllaeGvstvsqiAkllglsrrtvyrwlkrfeegGl 41
                                  a l +a+  + v++i++++glsrr+v++ +k   e Gl
  gi|13542178|ref|NP_111866.1| 19 AYLRSAKISD-VARIMENTGLSRRSVMNSVKMLKELGL 55
                                  6677777777.*****************9999988884 PP

>> DUF2250  Uncharacterized protein conserved in archaea (DUF2250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   1.8e-05     0.028      11      53 ..      15      57 ..       7      68 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.8e-05
                       DUF2250 11 lkvlkhlkkanvdYaksiakeleipleevrellkkLeelGLle 53
                                    vl++l+ a+      i++++ +++  v + +k L+elGL++
  gi|13542178|ref|NP_111866.1| 15 RLVLAYLRSAKISDVARIMENTGLSRRSVMNSVKMLKELGLID 57
                                  569999999998888889***********************97 PP

>> HTH_46  Winged helix-turn-helix DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   4.3e-05     0.064      26      56 ..      29      59 ..      17      62 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.3e-05
                        HTH_46 26 lkyIqkrtnLSrSsimkvLseLkkggyIeie 56
                                  +  I + t LSr s+m+ +  Lk+ g I+i+
  gi|13542178|ref|NP_111866.1| 29 VARIMENTGLSRRSVMNSVKMLKELGLIDIQ 59
                                  556999********************99997 PP

>> RNA_pol_Rpc34  RNA polymerase Rpc34 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   4.1e-05     0.061      82     146 ..       8      70 ..       4      74 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.1e-05
                                   HTSXHHHHHHHHHHHHHXSSXEEHHHHHHTTGXXHHHHHHHHHHHHHTTXXEEEEXSSSSSXEEE CS
                 RNA_pol_Rpc34  82 tslsedeslVysiIeesGneGIwsrtiksklnLhksvvkkcLksLeskkyiksvksvkaptkkiY 146
                                   +sl+ +  lV+++ +++  +  + + i + ++L    v +++k+L   ++i    +++   +++Y
  gi|13542178|ref|NP_111866.1|   8 KSLPPSARLVLAYLRSAKIS--DVARIMENTGLSRRSVMNSVKMLKELGLIDIQVCLSDTRRRYY 70 
                                   78999999*******99877..7899*************************************99 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   6.4e-05     0.096       8      53 ..      17      61 ..      10      74 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.4e-05
                        HTH_27  8 vLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgd 53
                                  vL  +r     +  a++++ + ++  ++++s+k L e GL+  + +
  gi|13542178|ref|NP_111866.1| 17 VLAYLR-SAKISDVARIMENTGLSRRSVMNSVKMLKELGLIDIQVC 61
                                  555555.4445556899999*********************44433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       588  (0.032796); expected 358.6 (0.02)
Passed bias filter:                      534  (0.0297841); expected 358.6 (0.02)
Passed Vit filter:                        79  (0.00440627); 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: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 524.66
//
Query:       gi|13542179|ref|NP_111867.1|  [L=120]
Description: hypothetical protein TVN1348 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-19   69.7   0.0    2.1e-19   69.4   0.0    1.1  1  CMD       Carboxymuconolactone decarboxylase family


Domain annotation for each model (and alignments):
>> CMD  Carboxymuconolactone decarboxylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.4   0.0   1.2e-23   2.1e-19       1      78 [.      22      98 ..      22     102 .. 0.97

  Alignments for each domain:
  == domain 1  score: 69.4 bits;  conditional E-value: 1.2e-23
                                  HHHHHHHHHHHHHHCCGSSTS-HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHSHHHHHH CS
                           CMD  1 pellraltalreallareggLdpkereLialavsaangceyCvdaHtraAleaGvteeeiaevlaqaaayagwpaara 78
                                  p+l + +  ++e +l  +g+Ld k+++L+ala s  ++ce+C+ +Ht+++leaG+te e +e++ +aa++ag+pa+++
  gi|13542179|ref|NP_111867.1| 22 PDLTESFLSFMEKTLG-KGELDVKTKSLVALALSLGLQCEWCITYHTKKCLEAGCTESEMMETAYIAAIMAGTPALMN 98
                                  899999*********9.**********************************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       544  (0.0303419); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 861.78
//
Query:       gi|13542180|ref|NP_111868.1|  [L=178]
Description: chorismate mutase [Thermoplasma volcanium GSS1]
Scores for 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   37.1   0.1    4.2e-09   36.6   0.1    1.3  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 !   36.6   0.1   2.3e-13   4.2e-09       9      54 ..      19      66 ..      11      83 .. 0.82

  Alignments for each domain:
  == domain 1  score: 36.6 bits;  conditional E-value: 2.3e-13
                                  HHHHHHHHHHHHHHHHHHHHHHHCTSGSS-HHHHHHHHHHHHH.HH.S CS
                          CM_2  9 deileLLaeRaelakevgeyKkeeglpvydpeReaevlerlee.ga.l 54
                                  + il+LL++R e+++++g++K+++glp++d eRe  v ++l + ++ l
  gi|13542180|ref|NP_111868.1| 19 KSILALLEKRREITRKIGKIKHNNGLPIRDAERELRVKSELCSnNPlL 66
                                  68**************************************99944333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 1336.72
//
Query:       gi|13542181|ref|NP_111869.1|  [L=197]
Description: prephenate dehydrogenase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0028   16.7   0.0       0.01   14.9   0.0    1.9  1  PDH       Prephenate dehydrogenase
  ------ inclusion threshold ------
        0.1   12.7   0.0       0.22   11.6   0.0    1.6  1  DapB_N    Dihydrodipicolinate reductase, N-terminus


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 !   14.9   0.0   1.1e-06      0.01      30     177 ..      16     140 ..       8     185 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.1e-06
                                   TTSSSEEES-GGGGCCG.SEEEE-S-GGGHHHHHHHHHHHS-TT-EEEE--S--CHHHHHHHHHCC..GCEEEEEES---S CS
                           PDH  30 lglvdeatddieavkea.divvlavPvevilevlkelaphlkedalitDvgsvKekvvreleellkegksfvgghPmaGte 109
                                   l+++ + +  ++ v++  di++l+vP+ + +  +++           + v+svK+   +++ +       +v+ hP++G+ 
  gi|13542181|ref|NP_111869.1|  16 LQAILDENG-FDVVENNwDIAFLSVPIGAAISYIEKYDG------PFIEVSSVKTPFKKYAGR-------IVSIHPLFGP- 81 
                                   556666666.77887766***********9999998765......899******998887765.......5559******. PP

                                   -SSGGG--TTTTTT-EEEEEE-TTS-HHHHHHHHHHHHHCT-EEEE--HHHHHHHHHHHTHHHHHHHH CS
                           PDH 110 ksGvdaareelfenavviLtPtektdkealekvkelleevgarvilmspeeHDrvvavvshlphvvai 177
                                        a+ ++  ++ v  + +   + +e  + ++e++++    ++ ++++ HD+ +a    lp +vai
  gi|13542181|ref|NP_111869.1|  82 -----ASYKDGVHRTVLFIKDI--SMPEYRDLIAEMFRG--YEIVDTTADVHDKEMAKSLALPYAVAI 140
                                   .....45555444443333333..345666777777754..467778888888888877777777765 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    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       1      29 [.       1      28 [.       1      36 [. 0.83

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.5e-05
                                  EEEEEETTTSHHHHHHHHHHHHSTTEEEE CS
                        DapB_N  1 ikvavvGasGrmGkevvkaveeaedlelv 29
                                  +kv+++G +Gr+G+  ++a+ +++++ +v
  gi|13542181|ref|NP_111869.1|  1 MKVGIIGKQGRLGRV-LQAILDENGFDVV 28
                                  89***********85.5666666888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       554  (0.0308997); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 1260.86
//
Query:       gi|13542182|ref|NP_111870.1|  [L=312]
Description: 3-deoxy-7-phosphoheptulonate synthase [Thermoplasma volcanium GSS1]
Scores for complete 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-63  213.5   0.0    3.2e-63  213.2   0.0    1.0  1  DAHP_synth_1  DAHP synthetase I family
    2.7e-09   36.9   0.0     0.0001   21.9   0.0    2.3  2  NeuB          NeuB family


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 !  213.2   0.0   3.5e-67   3.2e-63       9     272 ..      61     305 ..      46     308 .. 0.95

  Alignments for each domain:
  == domain 1  score: 213.2 bits;  conditional E-value: 3.5e-67
                                   HHCCCTTTCSEEEEEEESC-S-HHHHHHHHHHHHHHHHHHTTTEEEEEESSSC-S.SSTTS-SHTTHHHTHHHHHHHHHHH CS
                  DAHP_synth_1   9 adiliGkddrllviaGPCsiedpeaaleyAerlkklgeklkddleiimrayfeKpRrstvgfkGlindpdlkilsrikkel 89 
                                    di+iG++   ++ aGPCs+ed+++++e+A+ +kk+g++     +++++a+  KpR+s+++f+Gl++++ l+ l+++k+ +
  gi|13542182|ref|NP_111870.1|  61 GDIKIGEGL--VFAAGPCSVEDEDQIIEIARSVKKAGAN-----MLRGGAF--KPRTSPYSFQGLGEEG-LELLKKAKEDT 131
                                   589999986..899*************************.....*******..****************.*********** PP

                                   T-EEEEEESSCCTHHHHHHHESEEEE-CTCTTBHHHHHHHHTTSSEEEEEE-TTHHHHHHHHHHHHHHHTTEEE--EEEEE CS
                  DAHP_synth_1  90 glpiatevldpisvqyladvvdiiqiGArttesqdllelasglskpvglKngtdvaidemkaaaekilflgvetkgiilce 170
                                   glpi+te+++p   +++ d +d++q+G r+++++dll+  ++++kpv+lKng+ ++++e+ +a+e+i++ g  + ++ lc 
  gi|13542182|ref|NP_111870.1| 132 GLPIVTEIMNPEYYKFFDD-IDMLQVGSRNAQNFDLLRFLGRQKKPVLLKNGMGNTLKEWLEASEYIMSGG--NGNVVLCY 209
                                   ************9999866.8**************************************************..7******* PP

                                   EEEEESTSSSSSCHCHHHHHHHHHHCTSS-EEEESCHHHTTCGGGGHHHHHHHHHHHHHTTESEEEEEBBSSCCC-SSTGG CS
                  DAHP_synth_1 171 rglrggkktnrdvedvaavkilkeetgklpvmvDvsHansrkdykrqkkvlklakaaiaaGiaGvmiEshlnpgkalsdgk 251
                                   rg+rg ++++r   +v +v ++++ t +lp+ vD+sHa+++++     +v +++ aa+aaG++ + iE+h np+ alsd++
  gi|13542182|ref|NP_111870.1| 210 RGVRGIEEATRFSMNVGTVIAARSMT-HLPMCVDPSHASGKRE-----YVEAMTLAAVAAGADMIEIEVHNNPDCALSDSE 284
                                   **************************.9***************.....********************************* PP

                                   GGBBCTCBHHHHHHHHHHHHH CS
                  DAHP_synth_1 252 qalkygksetdacilkeltel 272
                                   q+ +++++ ++ +  k+ +++
  gi|13542182|ref|NP_111870.1| 285 QQVTPEVFGRIVKKAKQIKNI 305
                                   *****8888888887777665 PP

>> NeuB  NeuB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   1.1e-08    0.0001      53     145 ..     116     207 ..      87     210 .. 0.89
   2 !   12.6   0.1   7.8e-06      0.07     185     238 ..     255     308 ..     245     310 .. 0.91

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1.1e-08
                                   --HHHHHHHHHHHHHTT-EEEEEE-SHHHHHHHHHHT-S-EEE-GGGTT-HHHHHHHHTT-S-EEEE-TT-.-HHHHHHHH CS
                          NeuB  53 lseeehkelkeyceekgieflstpfdlesvdlleslgveayKiaSgeltnlpllekiaktgkpvilStGma.tleeieeav 132
                                   l ee  + lk+  e+ g+ +++  ++ e  ++ +++  +++ ++S +++n++ll+ + +++kpv+l  Gm  tl+e  ea 
  gi|13542182|ref|NP_111870.1| 116 LGEEGLELLKKAKEDTGLPIVTEIMNPEYYKFFDDI--DMLQVGSRNAQNFDLLRFLGRQKKPVLLKNGMGnTLKEWLEAS 194
                                   677788888999999999999999999999999876..7899****************************6379******* PP

                                   HHH.HHHT--EEE CS
                          NeuB 133 evlreagaeklvl 145
                                   e++ + g+ ++vl
  gi|13542182|ref|NP_111870.1| 195 EYIMSGGNGNVVL 207
                                   ***9999999998 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 7.8e-06
                                   HHHHHHHHHT--EEEEEB-S-TT--STTGGG-B-HHHHHHHHHHHHHHHHHSS- CS
                          NeuB 185 avaiaAvalGAkviEkHftldrnlegpDhkaSlepeelkelveairnvekalge 238
                                   a+++aAva GA++iE  +  + +   +D++  ++pe + ++v++++++++++ +
  gi|13542182|ref|NP_111870.1| 255 AMTLAAVAAGADMIEIEVHNNPDCALSDSEQQVTPEVFGRIVKKAKQIKNIVSN 308
                                   5689*******************************************9988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       562  (0.0313459); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2198.85
//
Query:       gi|13542183|ref|NP_111871.1|  [L=350]
Description: pyruvate-formate lyase-activating enzyme [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-16   61.3   0.0    2.9e-16   60.3   0.0    1.5  2  Radical_SAM     Radical SAM superfamily
     0.0047   17.2   0.0     0.0097   16.2   0.0    1.5  1  Fer4_12         4Fe-4S single cluster domain
  ------ inclusion threshold ------
       0.56   10.3   0.1       0.56   10.3   0.1    3.0  3  DZR             Double zinc ribbon
        3.1    8.0   7.6        9.4    6.4   0.1    3.0  3  DUF1272         Protein of unknown function (DUF1272)


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.3   0.0   6.5e-20   2.9e-16       3     157 ..      84     230 ..      82     242 .. 0.92
   2 ?   -3.1   0.0         2   8.8e+03     119     143 ..     262     286 ..     251     301 .. 0.63

  Alignments for each domain:
  == domain 1  score: 60.3 bits;  conditional E-value: 6.5e-20
                                   EESEESS--TTTSCCTT.HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEE CS
                                   xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM   3 vtrgCnlrCsfCarpet.vrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgiritv 82 
                                    t gC+++C +C+++   +rr+  g + s+eei++ + e      ++++  +  ep+   +f+ ++  la++  +g+ + +
  gi|13542183|ref|NP_111871.1|  84 STVGCSFACQYCQNYDIsQRRNIEGFDYSPEEIVNSAIEDG----CRGIAYTYNEPSIFMEFAHDVGILARK--RGLINIF 158
                                   689************99********************9887....***************************..7****** PP

                                   EECSSCHGHHHHHHHHHTT.-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSH CS
                                   xxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  83 etngtlpdeeklerllelg.vdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglpGend 157
                                   +tng+   +e +e  ++     +v +  +a +d+ ++k++   ++ + + +++++++e+gi+ v ++ +++p + d
  gi|13542183|ref|NP_111871.1| 159 VTNGYET-PEAVEYSKDFLdAATVDFKGNASNDF-YRKYI-SVPSADPIFDTIKLMKESGIH-VEITDLVVPRVGD 230
                                   ******8.*********99888999999999**9.*****.99*******************.7776666665555 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2
                                   HHHTCTSHHHHHHHHHHHHHHTTSE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM 119 klmnrghtfeevlealeklreagik 143
                                   k+m  ++t+ e+l+a  +l+ +++ 
  gi|13542183|ref|NP_111871.1| 262 KMMDLPPTPLETLKAHYNLAVSMGL 286
                                   4555667888888888887777655 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   2.2e-06    0.0097       8     118 ..      81     186 ..      77     197 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.2e-06
                       Fer4_12   8 lslfvsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelvkevkeekpekdi 88 
                                   +s+ + gC+++C++C n ++ + ++ + f+    eei++++ ++  +g+ ++  EP+  ++     ++    +++++  +i
  gi|13542183|ref|NP_111871.1|  81 YSISTVGCSFACQYCQNYDISQRRNIEGFDYSP-EEIVNSAIEDGCRGIAYTYNEPSIFMEFA--HDVGILARKRGL-INI 157
                                   566678**************9999888887444.57888888999************944443..444444456666.689 PP

                       Fer4_12  89 wlytgytleelskkekeellkeidvlvdGk 118
                                   ++++gy   e  + +++++l+   v  +G+
  gi|13542183|ref|NP_111871.1| 158 FVTNGYETPEAVE-YSKDFLDAATVDFKGN 186
                                   *****99988875.6888888777766665 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.6     0.031   1.4e+02      28      49 .]      20      41 ..       5      41 .. 0.76
   2 ?   -1.0   0.5      0.43   1.9e+03      15      19 ..      92      96 ..      84     105 .. 0.68
   3 ?   10.3   0.1   0.00013      0.56      12      36 ..     300     334 ..     285     337 .. 0.67

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.031
                           DZR 28 edrCpsCgekvdpearfCpeCG 49
                                    +C +C + + ++ +  + CG
  gi|13542183|ref|NP_111871.1| 20 TVVCTACRRYCRLKNNQIGFCG 41
                                  7899999999999988766665 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.43
                           DZR 15 CseCg 19
                                  C++C+
  gi|13542183|ref|NP_111871.1| 92 CQYCQ 96
                                  44444 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 0.00013
                           DZR  12 arfCseCgtklkavaa..........edrCpsCge 36 
                                   + +C++C + l +               +C +Cg+
  gi|13542183|ref|NP_111871.1| 300 DTYCPNCHSLLIKRHGfnssvvglndDGACKKCGY 334
                                   45666666666643336666666666666666665 PP

>> DUF1272  Protein of unknown function (DUF1272)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.2      0.72   3.2e+03      23      32 ..      21      30 ..      11      50 .. 0.63
   2 ?    4.7   0.5    0.0074        33      23      34 ..      86      97 ..      79     103 .. 0.84
   3 ?    6.4   0.1    0.0021       9.4      27      40 ..     298     311 ..     295     318 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.72
                       DUF1272 23 ricsyEctFC 32
                                  ++c+    +C
  gi|13542183|ref|NP_111871.1| 21 VVCTACRRYC 30
                                  4444444444 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0074
                       DUF1272 23 ricsyEctFCae 34
                                  + cs+ c +C++
  gi|13542183|ref|NP_111871.1| 86 VGCSFACQYCQN 97
                                  56********86 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.0021
                       DUF1272  27 yEctFCaeCaeevl 40 
                                   yE t+C +C+  ++
  gi|13542183|ref|NP_111871.1| 298 YEDTYCPNCHSLLI 311
                                   88888888876554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (350 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       559  (0.0311785); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2604.34
//
Query:       gi|13542184|ref|NP_111872.1|  [L=495]
Description: histidine ammonia-lyase [Thermoplasma volcanium GSS1]
Scores for complete 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-180  600.4   0.1   2.3e-180  600.2   0.1    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 !  600.2   0.1  1.3e-184  2.3e-180       1     464 []       9     464 ..       9     464 .. 0.98

  Alignments for each domain:
  == domain 1  score: 600.2 bits;  conditional E-value: 1.3e-184
                                   --HHHHHHHHTCCCEEEE-HHHHHHHHHHHHHHHHHHHCTB--TTTSB-SGGGGGBB--HHHHHHHHHHHHHHC---EEEE CS
                Lyase_aromatic   1 LtledvvavargkakvelspearerveasravleeilaegepvYGvntGfGaladvripkedleelqrnllrshaaGvgep 81 
                                   Ltledv++v+  +++vels +ar++v++ ++   +++++g+++YGvntGfG+l + +i++e+  elqrnl+rsh+aGvg++
  gi|13542184|ref|NP_111872.1|   9 LTLEDVYSVSVLHEPVELSTKARNKVAEIHRKFLDLISSGQTIYGVNTGFGGLLNIKISREEEIELQRNLIRSHSAGVGKY 89 
                                   89********9899******************************************************************* PP

                                   --HHHHHHHHHHHHHHHTTS-S---HHHHHHHHHHHHCTEEE--EEES-------HHHHHHHHHHHTTSSTCCETTEEEEH CS
                Lyase_aromatic  82 lpeevvRaamllrlnslakGysGvrpevverllellnagitPvvperGSvGaSGDLaplahlalvliGegevyykgerlpa 162
                                   lp++vvR +m++r+n+lakGys+v+ e++++ll+++n++++P+vpe GSvGaSGDLaplah++l+++Geg+++ +ge +++
  gi|13542184|ref|NP_111872.1|  90 LPTDVVRSIMVIRANTLAKGYSAVSTELIDALLAMINKDVVPAVPEFGSVGASGDLAPLAHIGLAMMGEGQAFLNGELMRS 170
                                   ********************************************************************************* PP

                                   HHHHHHTT------TTTHHHHCCSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-BCGGG-HHHHCCS--HHHHHH CS
                Lyase_aromatic 163 aealaeaglepleleakEgLAlinGtalmtalaalaledaerllrladvaaAlslealrGsteafdprihalrphpgqiev 243
                                   + al + gl+p+e+++kEg+AlinGt++m+++ al+  +a r ++ a   + ls+ealrG+ +af++ i ++rph gqi++
  gi|13542184|ref|NP_111872.1| 171 DIALSKVGLKPYEFKEKEGVALINGTSMMAGIMALVTSRAYRTIENAVRSSLLSFEALRGTSKAFSDWIVSARPHLGQIAI 251
                                   ********************************************************************************* PP

                                   HHHHHHHTTT-SSS..-SB-SS-SS--HHHHTHHHHHHHHHHHHHHHHHHHHHHHTS--SSSEE.EGCCTCCE---TT--H CS
                Lyase_aromatic 244 AarlrallegSelvshekdeerlvQDayslRcaPqvhGavldalaaarevleiElnsatDNPlvddeeegavlsgGnFhge 324
                                   A+++r++l+gS+ v + k+++++vQDay+lRc+Pqv+Gavld+l+++ +vl +E+nsatDNPl+ +  +++v+sgGnFhge
  gi|13542184|ref|NP_111872.1| 252 AEKMRKYLAGSKNV-E-KSDKEKVQDAYTLRCIPQVYGAVLDTLEYVSSVLVTEINSATDNPLF-N--GKEVVSGGNFHGE 327
                                   **************.3.455566*****************************************.4..799********** PP

                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHC-TTTTTT--GGG-SSTCTTB-TTHHHHHHHHHHHHHHHCHCS-SGGG--TCTT CS
                Lyase_aromatic 325 pvalalDklaialaelaniserrierLvnpalsegLpafLaaeepglnsgfmiaqytaaalvsenktlahPasvdsiptsa 405
                                   p+ala+D+l+ial++++n++erri+rLv+++ls gLp+fL+ +++glnsg+mi+qytaaal+++nk+l+ P+s+dsiptsa
  gi|13542184|ref|NP_111872.1| 328 PIALAADFLSIALTDMGNMIERRIARLVDTNLS-GLPPFLV-KNSGLNSGYMIPQYTAAALCNRNKVLSYPSSADSIPTSA 406
                                   *********************************.*******.9************************************** PP

                                   TTCSS---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTCC-HHHHHHHHHHHC CS
                Lyase_aromatic 406 nqeDhvSmgliaarkllevvenlekvlAiellaaaqaldlrrklksspateavyeavre 464
                                   nqeDhvSmg ++  klle+ enle+++Aie+l  aqal++ + ++ sp t+a+y ++re
  gi|13542184|ref|NP_111872.1| 407 NQEDHVSMGSTSTLKLLEIEENLEYIVAIEFLLGAQALEFSQ-DPISPVTKAIYTKIRE 464
                                   ****************************************65.555**********996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (495 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       479  (0.0267165); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 3330.16
//
Query:       gi|13542185|ref|NP_111873.1|  [L=114]
Description: hypothetical protein TVN1354 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.7e-05   22.9   0.0     0.0001   22.6   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 !   22.6   0.0   5.8e-09    0.0001       3     117 .]       4     114 .]       2     114 .] 0.81

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 5.8e-09
                                   EEEEE-S-TTTBSHHHHHHHHHHHHHTTT..-EEEEEE-GGGGGGGBS---TGGGTS---GGGGGGCGGGT-EEEEEHHHH CS
                          DrsE   3 vfilvtggpygseaarealelalaaaalg..hevsvffygdGvllllkgqtanpadeknlaellkalkeygvklyvCgqaa 81 
                                   +++++++g  ++e+  +al +a++a++++   +v++++ g+  +l+ +    n+   k++ +ll  +   g+k  +C+  a
  gi|13542185|ref|NP_111873.1|   4 LAVIISSGKNEKEKVLTALTFANVAKKNKlfDDVKLILFGPSERLVAE----ND---KDVMKLLDDFNSLGEKPLACQVVA 77 
                                   789999******************************************....44...77888888888888889******* PP

                                   HHTT--GGGE-.T-.-EEEE-HHHHHHHHHH.-SEEEE- CS
                          DrsE  82 kargldededl.gv.gvevsglgelaelqne.gdrvitf 117
                                   +++++ +  dl ++ ++++  +g +++ ++e  + ++tf
  gi|13542185|ref|NP_111873.1|  78 NNFNIID--DLqKAqNIKIERVGPIIKELSEkNYEIMTF 114
                                   ******5..454345666666664444444437777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       596  (0.0332422); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.46
# Mc/sec: 744.39
//
Query:       gi|13542186|ref|NP_111874.1|  [L=469]
Description: amino acid transporter [Thermoplasma volcanium GSS1]
Scores for complete 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   89.1  56.8    3.3e-25   88.6  56.8    1.2  1  AA_permease    Amino acid permease
      3e-22   79.0  61.8    8.1e-22   77.6  61.7    1.6  2  AA_permease_2  Amino acid permease
  ------ inclusion threshold ------
         10    6.4   6.2          1    9.6   0.1    2.5  2  DUF4519        Domain of unknown function (DUF4519)


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 !   88.6  56.8   5.6e-29   3.3e-25       3     463 ..      17     447 ..      15     458 .. 0.78

  Alignments for each domain:
  == domain 1  score: 88.6 bits;  conditional E-value: 5.6e-29
                   AA_permease   3 lvialggviGtglfvglgvvlsqaGplgallayllagvviflvmlslgeiatngpksggfytyasrflgpelGfviGlnyl 83 
                                   +++ +  v +++    l ++++    +++ la+l+a++++fl+ ++ ++++ +  +++g+y y+s++lgp +Gf ++l y+
  gi|13542186|ref|NP_111874.1|  17 IFQGVSYVAPAADVAILLIITAGFAYGSTPLAVLFAWAIYFLFLNANYQFSKFTGSASGYYGYVSKSLGPTAGFITSLWYV 97 
                                   6677777888888888899999999999*************************************************9976 PP

                   AA_permease  84 fswitv.laleltaasiliqfwel.vtdlpkawvtgavflvvlliinlvgvkvygeaefilalikiiaiiafiivgiilla 162
                                   +++++  +a++l + + ++ +++  ++++p    + ++f++++ +++++      + ++ +++i   + i+f+i+  i++a
  gi|13542186|ref|NP_111874.1|  98 MFQFFSlAAFGLLGFATFLYYVSPsLEKVP---SIXLLFVALVAFFTFYLGYRGLRPSLNYSMISASIEIGFLILMGIIIA 175
                                   666655156788888888888855455555...445555555555555555555556666888888888888888844444 PP

                   AA_permease 163 ggkpnkgagfrflgdngsifknnlppgfa.keeegafknfisvfvivvfaftGielvaiiagEvkdPeksiPkailqvvir 242
                                    + ++                   ++ f+ k+  g+f+  +++++++++ f+G + v+++a+E+k + k+i ++i   ++ 
  gi|13542186|ref|NP_111874.1| 176 IKVGSGN----------------TISVFTlKPLNGNFSLLFFAMIFSIPLFAGSGTVITLAEETKGSIKTIRRSIWISMLV 240
                                   4443333................2333444677999********************************************* PP

                   AA_permease 243 itifYvlsllligllvprndlgllndsasaaspfvifikesgvsvlaplinaviltaalssansslysasRvlyslakdgl 323
                                   ++ + +  +++++++ + ++   +++  ++    vi+++  g +v++ ++++++  + lss +s++ s sRv+ysl +dg+
  gi|13542186|ref|NP_111874.1| 241 LLAALLVPAYSLTVGYGVSNMAGFTQLPDP---GVIIFERYGGIVAGIILIILTVNSYLSSNVSLMSSVSRVVYSLGRDGI 318
                                   ****************99999999988877...6666666777777888888888899*********************** PP

                   AA_permease 324 aP.kvlkkvskrgvPlraillsmiisllalllaslnlaapivfnfllaisaliglivwlliilsylrfRkalkyqgrsiee 403
                                   +P ++ k +  +++P+ +++l  i + ++ ++ s+  ++++   +l +i+ ++ l++++l+++s++++ k         + 
  gi|13542186|ref|NP_111874.1| 319 LPkSITKIHPIHHSPYISVMLLEIGGIVIAIIPSIFYGPFTGALILFSINIFALLFTHMLVNASLPVYIKR--------NG 391
                                   **99**************************************************************55444........33 PP

                   AA_permease 404 lgfkaallplgvilvlaaliiillilalyayltvkkgpkdwgaasfaaaylivllfliil 463
                                   l f a +   ++il +++ +i++   a + +      +  + aa+f+ +   ++ ++  +
  gi|13542186|ref|NP_111874.1| 392 LHFNAITHLVLPILSIIIGLIVVYYSARTSIS----EGNPITAAVFIGLAYVAFAVIFGY 447
                                   45555555555555544444444433333333....355677777775544444444444 PP

>> AA_permease_2  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.6  61.7   1.4e-25   8.1e-22       4     409 ..      14     421 ..      11     445 .. 0.77
   2 ?    1.6   2.6     0.017     1e+02     149     216 ..     397     459 ..     392     465 .. 0.57

  Alignments for each domain:
  == domain 1  score: 77.6 bits;  conditional E-value: 1.4e-25
                 AA_permease_2   4 lsafalvigsv......igsgifvknlaas.ggpalilwvwiavligslavllvyaElssalprsgGiyvytkaafgkkva 77 
                                    +a++  ++ v      + + i+ + ++a+   p+++l  w + +++ l   + +  +++   +  G y+y+++  g+ ++
  gi|13542186|ref|NP_111874.1|  14 AQAIFQGVSYVapaadvAILLIITA-GFAYgSTPLAVLFAWAIYFLF-LNANYQFSKFTG---SASGYYGYVSKSLGPTAG 89 
                                   5555555555555555322223333.344414445666666666666.556666666644...89**************** PP

                 AA_permease_2  78 flsawfnwfayvpvlasilsvaasyllnalgpdlqgntwltyliaiaililvalinirgikesakiqnilgilkillplii 158
                                   f+++ +++++++++la+   ++++++l+ ++p+l++ + + +l+++++  +++ + +rg + s ++ +i + + i +++++
  gi|13542186|ref|NP_111874.1|  90 FITSLWYVMFQFFSLAAFGLLGFATFLYYVSPSLEKVPSIXLLFVALVAFFTFYLGYRGLRPSLNYSMISASIEIGFLILM 170
                                   ************************************9**************************************988888 PP

                 AA_permease_2 159 liilglitvdgggfsslstetdtffpngwpgvllgllivlwsfdGfesaanvseevkk..kdvpkaifigllivlvlyllv 237
                                    ii+++ +++g++ s  ++  +  ++n++ +++++++ ++  f+G  +++  +ee k   k++++ i i++l+ l   l+ 
  gi|13542186|ref|NP_111874.1| 171 GIIIAIKVGSGNTIS--VFTLKPLNGNFSLLFFAMIF-SIPLFAGSGTVITLAEETKGsiKTIRRSIWISMLVLLAALLVP 248
                                   888888888888887..56777888888888777777.556688999********997799******************** PP

                 AA_permease_2 238 niaflgvvpddeianlsnlgsvaalffeavggkvvaiivvilialsllgaintavigssrvlealardgvlPrffakvn.k 317
                                   + +++ + + +++a   +l++++ + fe++gg v+ ii++il++ s l +  +++ ++srv+++l+rdg+lP+ + k++  
  gi|13542186|ref|NP_111874.1| 249 AYSLTVGYGVSNMAGFTQLPDPGVIIFERYGGIVAGIILIILTVNSYLSSNVSLMSSVSRVVYSLGRDGILPKSITKIHpI 329
                                   ***************9***************778888888888889999999***************************99 PP

                 AA_permease_2 318 fgspiraiiltaivslillllfllassaayn...fllsvsslgliisyllliigalilrkkrp.hlkrpgkilvaiigalf 394
                                   ++sp+ +++l  i  ++++++ ++  +  ++   +l+s+  ++l++  +l+ +++ ++ k++  h++    i+   + +l+
  gi|13542186|ref|NP_111874.1| 330 HHSPYISVMLLEIGGIVIAIIPSIF-YGPFTgalILFSINIFALLFTHMLVNASLPVYIKRNGlHFNA---ITHLVLPILS 406
                                   *********9999985544433322.344445558889888888888888888888888886655555...3333334444 PP

                 AA_permease_2 395 llfllvalffppkgp 409
                                   +++ l++ ++   ++
  gi|13542186|ref|NP_111874.1| 407 IIIGLIVVYYSARTS 421
                                   444444444333322 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.017
                 AA_permease_2 149 ilkillpliiliilglitvdgggfsslstetdtffpngwpg...vllglli.vlwsfdGfesaanvseevkk 216
                                   i++++lp i+ ii+gli+v   + s       t+ ++g+p+   v+ gl+  ++ ++ G+++a ++ ++vk+
  gi|13542186|ref|NP_111874.1| 397 ITHLVLP-ILSIIIGLIVV---YYS-----ARTSISEGNPItaaVFIGLAYvAFAVIFGYSFAKYHPDKVKN 459
                                   6677666.45555777776...333.....345666666652233445433256666677777666666665 PP

>> DUF4519  Domain of unknown function (DUF4519)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.2   1.9         3   1.8e+04      35      49 ..     126     140 ..     126     144 .. 0.74
   2 ?    9.6   0.1   0.00017         1      29      48 ..     396     415 ..     390     421 .. 0.87

  Alignments for each domain:
  == domain 1  score: -4.2 bits;  conditional E-value: 3
                       DUF4519  35 lPvlavlillivvfv 49 
                                   +P + +l++ +v+f+
  gi|13542186|ref|NP_111874.1| 126 VPSIXLLFVALVAFF 140
                                   577888888888876 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00017
                       DUF4519  29 kvttvVlPvlavlillivvf 48 
                                    +t +VlP+l ++i livv+
  gi|13542186|ref|NP_111874.1| 396 AITHLVLPILSIIIGLIVVY 415
                                   68999*************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (469 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       883  (0.0492498); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 3049.38
//
Query:       gi|13542187|ref|NP_111875.1|  [L=553]
Description: urocanate hydratase [Thermoplasma volcanium GSS1]
Scores for complete 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-95  317.0   0.3    6.7e-95  316.1   0.3    1.4  1  Urocanase_C  Urocanase C-terminal domain
    2.1e-82  275.8   0.0    2.8e-82  275.4   0.0    1.2  1  Urocanase    Urocanase Rossmann-like domain
      3e-57  191.8   0.0    5.5e-57  191.0   0.0    1.4  1  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 !  316.1   0.3   1.1e-98   6.7e-95       1     195 [.     349     543 ..     349     544 .. 0.99

  Alignments for each domain:
  == domain 1  score: 316.1 bits;  conditional E-value: 1.1e-98
                                   HHHTTT---EEEEETT--HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHH----SS-EEE----TTHHHHHHHHHHHHHHHS CS
                   Urocanase_C   1 plFsegkGPFRwvalsgdpeDlaktdeavlellkekedlirWikeAeekvkvqGlpaRilyldaeeRekialafnelvreg 81 
                                   +lF+ g+GPFRwvalsgdp+D++k+d+a+++ ++++ +lirWik A+e+v++qGlpaRi+y+ ++eReki+l++ne+vr+g
  gi|13542187|ref|NP_111875.1| 349 DLFAIGSGPFRWVALSGDPQDIYKIDDAIIKNFQDDPHLIRWIKLAKERVHFQGLPARICYASYGEREKIGLMINEMVRNG 429
                                   69******************************************************************************* PP

                                   SSSS-EEEEE-S-STTSEE-TTTTTTT-TTS-TTB-HHHHHHHHHHHHHT-SEEEEEESTTT-TTS-EEEEEEEEE-SSHH CS
                   Urocanase_C  82 eikapvvlgRDhlDvgsvasPfretenikDGsdaiaDwavlnallnaargatwvslhnGGgvgiGesinagfvvvldGtee 162
                                   e++apv++gRDh+D+gsvasP+rete++kDGsdaiaDw++lnallna++gatwvs+h+GGg+giG++i+agfv+v+dGt++
  gi|13542187|ref|NP_111875.1| 430 EVSAPVAIGRDHHDTGSVASPYRETEKMKDGSDAIADWPILNALLNAISGATWVSVHHGGGTGIGNAIHAGFVIVADGTKD 510
                                   ********************************************************************************* PP

                                   HHHHHHHHHHHHHHHHHHHHHHHT-HHHHHHHH CS
                   Urocanase_C 163 aeerlervltaDvalGvvRradagyeealevak 195
                                   aeer++rvl+aD+++Gv+R+adagye+++e++k
  gi|13542187|ref|NP_111875.1| 511 AEERIKRVLNADPGIGVIRHADAGYESSIEIIK 543
                                   *****************************9987 PP

>> Urocanase  Urocanase Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  275.4   0.0   4.7e-86   2.8e-82       1     210 []     137     346 ..     137     346 .. 1.00

  Alignments for each domain:
  == domain 1  score: 275.4 bits;  conditional E-value: 4.7e-86
                                   TTHHHHHHHHHHHHHHHHHHST.T--TT-EEEEE--STTGGGHHHHHHHTT-EEEEEES-HHHHHHHHHTTS-SEEES-HH CS
                     Urocanase   1 GpQGivqGTyetllnaarkklgkgdlkgklvvtaGlGgMsgaQplAatiagavalvvevdesriekrleqgyvdevaddld 81 
                                   G+QG++qGTyetl ++ark+++k+dl+gk+v+t+GlG+M+gaQplA+t+++a++++vevde++i++rl+ +y+d+++d+ld
  gi|13542187|ref|NP_111875.1| 137 GTQGVLQGTYETLSALARKEFKKDDLSGKWVLTSGLGEMGGAQPLAITMNNATGIIVEVDEEKIRRRLRDKYLDTWTDSLD 217
                                   9******************************************************************************** PP

                                   HHHHHHHHHHHCT--EEEEEES-HHHHHHHHHCTT---SEE---S-TT-TTTS---TT--HHHHHHHHHH-HHHHHHHHHH CS
                     Urocanase  82 ealalikeakkekealsigllgnvvdvleelveegvlvdlvsdqtsahdplnGYlPegltleeakelrkedpekfkeevke 162
                                   eal+l +ea k+++++sigllgn+++v++el+++++++d+vsdqt+ahd   GY+Peg+t+++a+e+r++d++ + ++v++
  gi|13542187|ref|NP_111875.1| 218 EALRLKDEALKSGKPTSIGLLGNAATVYDELMKKNIVPDVVSDQTAAHDLNLGYIPEGYTVQSAAEFREKDKDGYVKKVYA 298
                                   ********************************************************************************* PP

                                   HHHHHHHHHHHHHHTT-EE-B-SS-HHHHHHHTT-TTGGGS-BHHHHT CS
                     Urocanase 163 slarhveailklqekGavvfdYGnnlrkeakeagvkeafkypsyvedi 210
                                   s+++++eail + ++G+++fdYGnn+r++a e g+k+af++p+yv+++
  gi|13542187|ref|NP_111875.1| 299 SIVKEAEAILWFMQHGSKAFDYGNNFRTRALEGGLKNAFDIPGYVPAY 346
                                   **********************************************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 !  191.0   0.0   9.1e-61   5.5e-57       1     127 []       8     134 ..       8     134 .. 0.99

  Alignments for each domain:
  == domain 1  score: 191.0 bits;  conditional E-value: 9.1e-61
                                   -----SS--SSSSHHHHHHHHHHHHCT-TTT-SBGGGTEEETTTEESSSSHHHHHHHHHHHHH--TTEEEEEETTEEEEEE CS
                   Urocanase_N   1 ikakrgeelkaksweaeailrmleNnLdpevaekpeeLvvYggtgkaarnweqfelivktLkeleedetLlvqsGkpvglf 81 
                                   i+a+rg++l++k+w +ea+lr+l+NnLdp va++p++L+vYgg+gkaarnwe+f++iv+ Lk+le+detLl+qsGkpvg+f
  gi|13542187|ref|NP_111875.1|   8 IHAPRGNKLNTKGWGQEAALRLLMNNLDPMVAKDPANLIVYGGKGKAARNWEAFDKIVEELKKLENDETLLIQSGKPVGVF 88 
                                   789****************************************************************************** PP

                                   E--TTS-SEEEEES-B-GGG-SHHHHHHHHHTT---B-TTTTTTT- CS
                   Urocanase_N  82 ksheeaPrvliansnlvpkyateeefeeleakgltmyGqmtAgswi 127
                                   k+++++Prvli n+++vp++at++ f +lea+gltm+GqmtAgswi
  gi|13542187|ref|NP_111875.1|  89 KTTKDSPRVLIVNAQIVPHWATDDVFWDLEARGLTMFGQMTAGSWI 134
                                   *********************************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (553 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.44
# Mc/sec: 3765.91
//
Query:       gi|13542188|ref|NP_111876.1|  [L=404]
Description: imidazolonepropionase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-29  103.8   0.0    2.9e-29  102.5   0.0    1.7  1  Amidohydro_1  Amidohydrolase family
    3.8e-21   76.1   0.0    6.9e-13   48.9   0.0    2.3  2  Amidohydro_3  Amidohydrolase family
  ------ inclusion threshold ------
      0.036   14.0   0.2       0.15   12.0   0.3    2.0  2  PBECR3        phage-Barnase-EndoU-ColicinE5/D-RelE like nucle


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 !  102.5   0.0   4.8e-33   2.9e-29       1     344 []      61     395 ..      61     395 .. 0.77

  Alignments for each domain:
  == domain 1  score: 102.5 bits;  conditional E-value: 4.8e-33
                                   EEEE-EEEEEEECETTECSSS.........GHHHHH...............STTHHHHHHHHHHHHHHHHTTEEEE.EEEE CS
                  Amidohydro_1   1 ivlPGlIDaHvHleqsllrga.........tledwl...............vppetaaealesgiktalksGtttv.admg 56 
                                   iv+PGl+D+H+H+ ++ +r++         t+ ++l                + +++   + + i+ a+++Gttt+ +++g
  gi|13542188|ref|NP_111876.1|  61 IVIPGLVDSHTHIIFGGNRSQefyqrasgyTYSEILrsgngiyktvrdtanSSADEIFTQSMKRIADAVSHGTTTIeLKTG 141
                                   79***********99999888777777777777777888888888888888777777888888888888888888744555 PP

                                   HSSTH.....HHHHHHHHHHTSSSEEEEEEESSEGGS........GCCCSHHHHHHHHHHHHHHHHHHCTTTCEEEEEEEC CS
                  Amidohydro_1  57 attst.....giealleaaeelplglrilggkvsldr........gsaetskasreklkagaaetikgkadgvvkvalaph 124
                                   +   +      + ++++ +++   gl   +               +s+e  ++  ek+++ +++ i  +a       + + 
  gi|13542188|ref|NP_111876.1| 142 Y-GLYekeerKLLDVARKISNS--GLVSTVLT----YlmhvlpegESEEAYEKYSEKILSSFRNYIS-FA-----DVFCD- 208
                                   5.44456444444444444442..33333333....1444466667777777777777777755554.33.....33333. PP

                                   GTCCSHHHHHHHHHHHHHHHTTEEEEEETSSCHHHHHHHHHHTTTEEEETTTTSTCCHHTTTHCCEEEHCTCEEEHHHHHH CS
                  Amidohydro_1 125 eapafsdeelkealkeakkrdlpvaiHaletkgevedaeaafgetiehgthlevaeslglldeiklilahgvhltpteael 205
                                      afs+++ k+ lk a+  +l + iHa e +++   +++a       g  ++              + h++h  ++++e+
  gi|13542188|ref|NP_111876.1| 209 -EGAFSPNAAKAFLKFADNLGLGLKIHANEINNIG--CVKACS-----GLNVKS-------------FDHMIHANAEDVET 268
                                   .5789999********************9999997..888888.....445555.............99************ PP

                                   HHHHHHHHCEEHHHHHHHHSEHHHHHHHHHHHHTSCEEEEEECTTSSCCGGHHHHHHHHHHHHHHCCTTTTHCHCHHHHHH CS
                  Amidohydro_1 206 lkerlkeagvahcpfsnsilrsgrealrkaldeGvkvglgtDgaasgnslnlleelrlalklqrgllyedeegglslkeal 286
                                   ++    ++ ++++p +   l++  +++r  +d+Gv v++++D    + ++nl+  + la+          +   ++++eal
  gi|13542188|ref|NP_111876.1| 269 IRSI--GSAITLLPLTVFALDESYPDARVFIDSGVPVIIASDISPLNYNANLIFAMHLAV----------KYSSMKPEEAL 337
                                   ****..************************************445555555555555555..........5667******* PP

                                   HHHTHHHHHHTT-TTTSSSS-TTSB--EEEECCCTCGGGTTTCTSEEEEEEEETTEEE CS
                  Amidohydro_1 287 rmaTingAkalglddkvGsievGkdADlvvvdldilaafvglkkdgnvkkvivkGklv 344
                                   +++Tin+A +lgl +k+G++e+GkdAD+v++d d ++++ +    ++vkkv+ +G lv
  gi|13542188|ref|NP_111876.1| 338 TATTINAASSLGLGEKKGTVEEGKDADIVIIDVDDYTEIPYEYGINTVKKVFHNGSLV 395
                                   *********************************7777776666777899999999776 PP

>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.0   2.2e-09   1.3e-05       4      26 ..      56      81 ..      55     118 .. 0.74
   2 !   48.9   0.0   1.2e-16   6.9e-13     256     470 ..     208     393 ..     180     396 .. 0.82

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 2.2e-09
                  Amidohydro_3  4 DakGrlvlPGFvDsHtHlaggg...v 26
                                  Da+G +v+PG+vDsHtH++ gg   +
  gi|13542188|ref|NP_111876.1| 56 DAEGSIVIPGLVDSHTHIIFGGnrsQ 81
                                  *******************9993332 PP

  == domain 2  score: 48.9 bits;  conditional E-value: 1.2e-16
                  Amidohydro_3 256 gwpdfedealaelvaaadergldvaihaigdaavddvldafeaaaekngnqdrrrlehaegvtesqiervaalqvaagvqp 336
                                    ++ f+  a ++ ++ ad+ gl + iha++   +   ++a    + k  ++    ++ha +   +++e +++++ a+ + p
  gi|13542188|ref|NP_111876.1| 208 DEGAFSPNAAKAFLKFADNLGLGLKIHANEINNIG-CVKACSGLNVKSFDH----MIHANA---EDVETIRSIGSAITLLP 280
                                   5677888889999999*******************.888887776666666....677777...***************** PP

                  Amidohydro_3 337 vfnf..edelldsrlgperargstpvkellnagvkvalgsDapvgpfdpwprigaavmrktrrggevlrpdeelsleeala 415
                                    ++f  +             + ++  +  ++ gv+v+ +sD     + p+ +   ++   ++   +++     +  eeal 
  gi|13542188|ref|NP_111876.1| 281 LTVFalD-------------ESYPDARVFIDSGVPVIIASD-----ISPLNYNANLIF--AM---HLAVKYSSMKPEEALT 338
                                   ****432.............345889999************.....888877777774..44...9999999********* PP

                  Amidohydro_3 416 lyTrgpAkalgledrkGtLevGadADlvvld.adpldvdppelaear.vrltvvdGr 470
                                   ++T ++A  lgl ++kGt+e+G+dAD+v++d +d  +++ +  + ++ v+++ ++G 
  gi|13542188|ref|NP_111876.1| 339 ATTINAASSLGLGEKKGTVEEGKDADIVIIDvDDYTEIPYE--YGINtVKKVFHNGS 393
                                   *******************************8777777755..33333666666655 PP

>> PBECR3  phage-Barnase-EndoU-ColicinE5/D-RelE like nuclease3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.3   2.6e-05      0.15      16     109 ..      25     126 ..      15     131 .. 0.79
   2 ?   -2.7   0.0       0.9   5.4e+03      43      63 ..     185     204 ..     173     211 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.6e-05
                        PBECR3  16 gldlsg.tkilidpgaikHilkrH.gnqstekdrgqidianipdiiknPDkviyggknkk....eksieyvKki...nngy 87 
                                   +ld+ + ++i+i +g i+ i ++H ++  +    g      ip  +++  ++i+gg+ ++    + s + + +i    ng+
  gi|13542188|ref|NP_111876.1|  25 ELDFIEnATIYIENGKIAKITREHsSDAGDLDAEGS---IVIPGLVDSHTHIIFGGNRSQefyqRASGYTYSEIlrsGNGI 102
                                   66777779****************434444444444...59****************999999866777777888887888 PP

                        PBECR3  88 lvvvev..dkkknelyvktmykik 109
                                   +  v+   +++ +e++ ++m  i 
  gi|13542188|ref|NP_111876.1| 103 YKTVRDtaNSSADEIFTQSMKRIA 126
                                   888888788888899999987665 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.9
                        PBECR3  43 tekdrgqidianipdiiknPD 63 
                                    ek  ++i +++ +++i+ +D
  gi|13542188|ref|NP_111876.1| 185 YEKYSEKI-LSSFRNYISFAD 204
                                   34444555.888889988888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (404 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       581  (0.0324056); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); 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: 00:00:00.43
# Mc/sec: 2827.63
//
Query:       gi|13542189|ref|NP_111877.1|  [L=269]
Description: hypothetical protein TVN1358 [Thermoplasma volcanium GSS1]
Scores for complete 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-70  235.4   0.0      7e-70  235.3   0.0    1.0  1  Memo      Memo-like protein
  ------ inclusion threshold ------
      0.039   12.9   0.1      0.083   11.9   0.0    1.5  2  DUF4856   Domain of unknown function (DUF4856)


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 !  235.3   0.0   7.8e-74     7e-70       2     271 .]       5     264 ..       4     264 .. 0.96

  Alignments for each domain:
  == domain 1  score: 235.3 bits;  conditional E-value: 7.8e-74
                          Memo   2 aavAGsfYpedeeelkkqleeflekntgkkeiarviisPHagyvysgevaakayaelesskvervvilGpsHtilgskvsv 82 
                                   +avAG fYp++ +el + + +f  ++++   +   +++PHag vysg++a ++y++l +s++  ++i+Gp+H+ ++ ++s+
  gi|13542189|ref|NP_111877.1|   5 PAVAGYFYPSNRNELLSLISSFHVQQSEVSCQPIGVVVPHAGIVYSGRTAMYSYNALRNSSIRDFIIIGPNHRPMTPYASI 85 
                                   89******************999888888766777888******************************************* PP

                          Memo  83 laaseleTPlGdlkvDeelveeLvkkeeiadldetaalaEHSlEvqlpfLkellkekkfkivPilvsaqseetakevgeal 163
                                    + + +eTPlG++ + eel+ eL k+++++  de ++  EHS+Evq+pfL++++ +  f+ vP++++ q++ +a+++++al
  gi|13542189|ref|NP_111877.1|  86 FPSGSWETPLGNAIINEELASELYKNSQYIVKDEESHSVEHSIEVQIPFLQYMFGN-SFTFVPVILGDQEKVVANDIASAL 165
                                   ********************************************************.6**********************9 PP

                          Memo 164 akvikdesnlviiSsDlsHygrrFgspqeiaesieDrevikaleelneeelkeylektnnticGekpiavilkalkklgak 244
                                    +  k    ++i+SsD++Hy+       +i+e++ D  +i+++ +l+ +++++++e+ n t cG++ ia+++ ++kk+g +
  gi|13542189|ref|NP_111877.1| 166 MRLSKP--YILIASSDFTHYE-----RSDIVERK-DMDLISRIVDLDIDGFYDTIERENVTACGYGAIAILMIIAKKIG-A 237
                                   998764..699**********.....99******.********************************************.9 PP

                          Memo 245 kakllkYaqssdvtsdtdsvVsyaslv 271
                                   k +ll++++s+dvt d+d vV+y s+v
  gi|13542189|ref|NP_111877.1| 238 KISLLNHSNSGDVTNDYDEVVGYSSIV 264
                                   ***********************9975 PP

>> DUF4856  Domain of unknown function (DUF4856)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.1      0.35   3.1e+03     153     175 ..      99     121 ..      97     127 .. 0.73
   2 ?   11.9   0.0   9.2e-06     0.083     279     354 ..     154     238 ..     146     241 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 0.35
                       DUF4856 153 ilNnyLseavldeaenradndnk 175
                                   i+N+ L+++++++++ + +++++
  gi|13542189|ref|NP_111877.1|  99 IINEELASELYKNSQYIVKDEES 121
                                   88999999999998887666554 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 9.2e-06
                       DUF4856 279 atlanldvasafhaLSeayGfiyslrftrkpetgkpylskeevdalleellag.nGlWdvdr..........tkesLdeis 348
                                   +++  +d+asa+  LS+ y +i s  ft+ +   +  + ++++d + + +  + +G++d  +            + L  i+
  gi|13542189|ref|NP_111877.1| 154 EKVVANDIASALMRLSKPYILIASSDFTHYER--SDIVERKDMDLISRIVDLDiDGFYDTIErenvtacgygAIAILMIIA 232
                                   445555***********************999..899*******9999999999*****7444788888877777888888 PP

                       DUF4856 349 keiaak 354
                                   k+i+ak
  gi|13542189|ref|NP_111877.1| 233 KKIGAK 238
                                   888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       334  (0.018629); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1733.25
//
Query:       gi|13542190|ref|NP_111878.1|  [L=201]
Description: hypothetical protein TVN1359 [Thermoplasma volcanium GSS1]
Scores for complete 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  149.7   0.0    6.1e-44  149.6   0.0    1.0  1  AMMECR1   AMMECR1


Domain annotation for each model (and alignments):
>> AMMECR1  AMMECR1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  149.6   0.0   3.4e-48   6.1e-44       2     165 ..      18     188 ..      17     189 .. 0.95

  Alignments for each domain:
  == domain 1  score: 149.6 bits;  conditional E-value: 3.4e-48
                                   HHHHHHHHHHTTSS-S-HH---HHHHSEEEEEEEEE.EE..CCECCCECEEEEEEHHHHHHHHHHHHHHT-TTS----HHH CS
                       AMMECR1   2 klareaieealkeekkleeeakeelkekaglFVtlk.ekkgeLRGCiGtleperpLaeevaenAlaaAfeDpRFspvtaeE 81 
                                    lar+a +++l++ek  e  +++ ++ek+g+F t++   +++LRGCiG+ ep  +L+e++++ ++ aA+ DpRF+p++++E
  gi|13542190|ref|NP_111878.1|  18 MLARRAAAAKLNNEKLPEVPDDPIFHEKHGVFTTINtYPDNQLRGCIGFPEPYYELGEGIIKSSIYAATDDPRFDPMEPDE 98 
                                   6899***99********9******************98889**************************************** PP

                                   HTTEEEEEEEE---EE--......GGG--TTT-EEEEEETTEEEEE-THHHHHTT--HHHHHHHHHHHHTS-TTCCCSTTS CS
                       AMMECR1  82 lpeleveVsvLtepepiv......ledlevgkhGliiekgsrsatlLPqvaveqgwdkeeflasllrKaglrpdewkdsei 156
                                   l+++++e s+Lt p++++      ++ ++vgk+G+i  +++ s++lLPqva+e++++ eefl+ l++Kagl + +wk +++
  gi|13542190|ref|NP_111878.1|  99 LNRVTFELSILTVPQEVTvnpeerPKAITVGKDGIIAVYNGASGLLLPQVATEYRMSAEEFLEALCEKAGLWQGCWKYKKV 179
                                   *****************4455455777***********99*********************************9******* PP

                                   EEEEE-EEE CS
                       AMMECR1 157 kltryevek 165
                                   k+ ++++ +
  gi|13542190|ref|NP_111878.1| 180 KISKFQAIV 188
                                   ******976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       341  (0.0190195); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); 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 0.27s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 1348.77
//
Query:       gi|13542191|ref|NP_111879.1|  [L=381]
Description: metal-dependent amidohydrolase [Thermoplasma volcanium GSS1]
Scores for complete 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    1.5  1  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 !   31.7   0.0   6.2e-12   1.1e-07       7     102 ..     157     251 ..     151     256 .. 0.90

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 6.2e-12
                                   EEEEEE..EE-B-EEGG-TTTTB-HHHHHHHHHHCSCTTEEC.....TCCTCCCCCEECCE-CCCCEESSEEEEEEEEEHH CS
                     M20_dimer   7 aggkit..vkgkagHsgapgagaNAieklarllaeledeegdiaeerslprttlnvtgiegGsaknvipdeaeakidiRll 85 
                                   a+ +i+  + gk+ H   p+ g+NA+  l++   +l + ++++    +++++ +   + egG+a+nvipd+a+++idiR  
  gi|13542191|ref|NP_111879.1| 157 ADLTIEaqFIGKSSHLLSPDYGINALDPLVESYVALSNFRRSVP---NSKYPVIGMIVKEGGRASNVIPDKASMEIDIRAK 234
                                   5556666699******9**********99999999999988877...999******************************* PP

                                   HHHHHHHHHHHHHHHHT CS
                     M20_dimer  86 pgedpeevleeieeile 102
                                   ++ d++   ++ie il+
  gi|13542191|ref|NP_111879.1| 235 KKADLAGFVDQIERILK 251
                                   **************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (381 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 2473.50
//
Query:       gi|13542192|ref|NP_111880.1|  [L=310]
Description: microcin C7 resistance protein MccF-like protein [Thermoplasma volcanium GSS1]
Scores for 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-37  126.4   0.0    9.8e-37  125.7   0.0    1.3  1  Peptidase_S66   LD-carboxypeptidase N-terminal domain
    1.9e-25   89.8   0.0    3.3e-25   89.0   0.0    1.4  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 !  125.7   0.0   1.1e-40   9.8e-37       1     121 []      16     134 ..      16     134 .. 0.94

  Alignments for each domain:
  == domain 1  score: 125.7 bits;  conditional E-value: 1.1e-40
                                   EEEE-SSS-GGGSSH.HHHHHHHHHHHHCTEEEEEGCTC..--TTTTCSS-HHHHHHHHHHHHC-TTECEEEES--SS-CH CS
                 Peptidase_S66   1 iaivapSsglkkeeekeeleraievleelglevvlgksa..aksagylagtdeeRaadLnealadpeikaiicarGGygaa 79 
                                   i+++ap+s+ +     ++l r i++l++ g++v+lg+++    ++++l++ d +R ++L+ a+ d+++kai+carGGyg++
  gi|13542192|ref|NP_111880.1|  16 IRVIAPASAPD----MKNLSRSIARLRKAGYKVTLGHNIkrLVQMNQLSAPDVNRRDELMSAFMDDNVKAIFCARGGYGSI 92 
                                   89*****7653....459****************9997755566779********************************** PP

                                   HCHHHH-HCCHHCS--EEEE-CCHHHHHHHHHHCHTBSEEE- CS
                 Peptidase_S66  80 rllpyldfdaikknpkiliGySDiTalhlalyaktglvtlhg 121
                                   ++lp +d+d i+++pki++GySDiTalhla++ k  l+t+hg
  gi|13542192|ref|NP_111880.1|  93 HILPLIDYDVIRDHPKIFVGYSDITALHLAINYKSSLITFHG 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 !   89.0   0.0   3.7e-29   3.3e-25       2     124 .]     181     295 ..     180     295 .. 0.92

  Alignments for each domain:
  == domain 1  score: 89.0 bits;  conditional E-value: 3.7e-29
                                   EEEEEEEHHHHHCCTTSTTS---TT..EEEEEE--TTHHHHHHHHHHHHCTSTTGGG--EEEEEE--..G...CC...--- CS
                Peptidase_S66C   2 GrliGGnlsvlasllgtpylpekdlkgkILflEdvsespyridrmLtqlkeagvldkvkGivlGrftkpeekeeeeekeey 82 
                                   G   G nlsv+asl+gt ylp  + +gkILf Ed++ ++ +idr+L  +k+ag+ldk++G+++G+f+  ++ +     e++
  gi|13542192|ref|NP_111880.1| 181 GISEGTNLSVFASLIGTGYLP--NSEGKILFAEDTGVTAGDIDRYLFTMKLAGILDKFSGFAFGEFK--SYVDP----EDP 253
                                   67779****************..779********888*****************************9..43223....467 PP

                                   HHHHHHHHHT-GGGTTS-EEEEESESSSBS---EEETSEEEE CS
                Peptidase_S66C  83 kealeevlaeiledlkiPvlynldiGHtspnltlplGakael 124
                                      +e++++ +++ lk   ly+l++GH+++++ +pl+ak+++
  gi|13542192|ref|NP_111880.1| 254 MPFVEDIVELYMNSLKRVSLYGLPFGHGEDQMLIPLNAKVRI 295
                                   899************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       475  (0.0264934); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 1885.14
//
Query:       gi|13542193|ref|NP_111881.1|  [L=71]
Description: hypothetical protein TVN1362 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.023   14.4   0.9      0.023   14.4   0.9    1.6  2  DDDD           Putative mitochondrial precursor protein
      0.041   13.6   7.2      0.045   13.5   7.2    1.0  1  TrbL           TrbL/VirB6 plasmid conjugal transfer protein
      0.058   13.7   9.3      0.062   13.6   9.3    1.0  1  DUF996         Protein of unknown function (DUF996)
      0.089   12.3   0.5      0.096   12.1   0.5    1.0  1  DUF3087        Protein of unknown function (DUF3087)
       0.13   12.0   5.9       0.15   11.7   5.9    1.0  1  Cation_efflux  Cation efflux family
       0.17   10.1   2.4       0.19   10.0   2.4    1.1  1  OATP           Organic Anion Transporter Polypeptide (OATP) f
       0.39   10.7   3.0       0.21   11.6   0.4    1.7  2  TraQ           Type-F conjugative transfer system pilin chape
       0.43    9.3   2.8       0.45    9.2   2.8    1.0  1  DUF2207        Predicted membrane protein (DUF2207)
       0.57    9.7   6.1       0.65    9.5   6.1    1.0  1  Frag1          Frag1/DRAM/Sfk1 family
       0.72   10.2   9.3       0.48   10.8   4.5    2.0  2  DUF2929        Protein of unknown function (DUF2929)


Domain annotation for each model (and alignments):
>> DDDD  Putative mitochondrial precursor protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.9   1.3e-05     0.023      35      60 ..      12      37 ..       6      43 .. 0.90
   2 ?   -1.7   0.1       1.4   2.5e+03      40      43 ..      54      57 ..      44      64 .. 0.54

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.3e-05
                          DDDD 35 gLlrvilvVipgllvGtliSknvAnl 60
                                  g+++v++++i g l+G +iSk +A++
  gi|13542193|ref|NP_111881.1| 12 GIISVVFIIIGGYLFGEVISKVIASI 37
                                  9**********************986 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.4
                          DDDD 40 ilvV 43
                                  i+ V
  gi|13542193|ref|NP_111881.1| 54 IILV 57
                                  2222 PP

>> TrbL  TrbL/VirB6 plasmid conjugal transfer protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   7.2   2.5e-05     0.045     152     213 ..       1      60 [.       1      61 [. 0.97

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.5e-05
                          TrbL 152 lFenWlgqvlsyalllvllavivglgsglfasalaalgadaslleqalalllaalvllilvi 213
                                   ++ +W  ++++ ++ +v++++   l  +++++++a+++ ++  +e  lall++++++l+++i
  gi|13542193|ref|NP_111881.1|   1 MAFKWTAKFIAGIISVVFIIIGGYLFGEVISKVIASINRVE--FEWGLALLVIGIIILVVII 60 
                                   899*************************************9..***************9986 PP

>> DUF996  Protein of unknown function (DUF996)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   9.3   3.4e-05     0.062      74     125 ..       9      60 ..       1      61 [. 0.91

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.4e-05
                        DUF996  74 llvliiayvlliisavflkksyellgkrtgvklFetagllyfiGaiLtivlv 125
                                   +++ ii +v++ii ++++ ++++++ ++++   Fe +  l++iG i+++v++
  gi|13542193|ref|NP_111881.1|   9 FIAGIISVVFIIIGGYLFGEVISKVIASINRVEFEWGLALLVIGIIILVVII 60 
                                   45578999*****************************************998 PP

>> DUF3087  Protein of unknown function (DUF3087)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.5   5.4e-05     0.096      20      69 ..      13      62 ..       4      69 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5.4e-05
                       DUF3087 20 valvallavlsllfstllialfgeeevsnfhlnllGvvlalvltaailrk 69
                                  ++ v+++++ + lf++++ ++ ++ +  +f + l+  v++++++++i+ k
  gi|13542193|ref|NP_111881.1| 13 IISVVFIIIGGYLFGEVISKVIASINRVEFEWGLALLVIGIIILVVIIPK 62
                                  45577788999************99999*****************99977 PP

>> Cation_efflux  Cation efflux family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   5.9   8.6e-05      0.15      71     119 ..      11      58 ..       5      63 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 8.6e-05
                 Cation_efflux  71 alvsgllllglavfllleaiqklikegereihaglalvvalvslvvnla 119
                                   a + ++++++++ +l+ e i k+i  + + ++ ++ l+++++++++ ++
  gi|13542193|ref|NP_111881.1|  11 AGIISVVFIIIGGYLFGEVISKVI-ASINRVEFEWGLALLVIGIIILVV 58 
                                   5677899999999***********.999999999999999999998665 PP

>> OATP  Organic Anion Transporter Polypeptide (OATP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   2.4   0.00011      0.19     330     383 ..       5      59 ..       2      67 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00011
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx RF
                          OATP 330 seAnlltGvvvipgaalGillgGllvkklklsakkl.aklvlvvsllslllllll 383
                                    +A++++G+++++++++G  l G +++k+  s++++   + l + ++ +++l+++
  gi|13542193|ref|NP_111881.1|   5 WTAKFIAGIISVVFIIIGGYLFGEVISKVIASINRVeFEWGLALLVIGIIILVVI 59 
                                   589****************999999999999998862456666666666655544 PP

>> TraQ  Type-F conjugative transfer system pilin chaperone (TraQ)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.4   0.00012      0.21      37      68 ..       5      39 ..       2      44 .. 0.79
   2 ?    0.3   0.3      0.39   6.9e+02      36      50 ..      40      55 ..      28      61 .. 0.53

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00012
                          TraQ 37 elavllaeilavglvliGgy...rildaliarvad 68
                                  + a ++a i++v +++iGgy    ++ ++ia + +
  gi|13542193|ref|NP_111881.1|  5 WTAKFIAGIISVVFIIIGGYlfgEVISKVIASINR 39
                                  78999***************444467777776655 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.39
                          TraQ 36 Pelavllae.ilavgl 50
                                   e+ + la  ++++++
  gi|13542193|ref|NP_111881.1| 40 VEFEWGLALlVIGIII 55
                                  4566666641345443 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   2.8   0.00025      0.45     388     429 ..       9      60 ..       2      71 .] 0.53

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00025
                       DUF2207 388 lgliilglilillallllvll...........lvfllilllillliaiivlll 429
                                   ++++i+++++i+++ +l++ +            + +++ ll++++i+++v+ +
  gi|13542193|ref|NP_111881.1|   9 FIAGIISVVFIIIGGYLFGEViskviasinrvEFEWGLALLVIGIIILVVI-I 60 
                                   333344444444444444444688999998875555555555555544443.3 PP

>> Frag1  Frag1/DRAM/Sfk1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   6.1   0.00036      0.65     157     213 ..       4      58 ..       1      59 [. 0.81

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00036
                         Frag1 157 sfrlkvvllilavvlailfgvffvrhkkkcgygayslsAifEWllafwfiiffltfs 213
                                    ++ k++  i++vv++i+ g++f    +k+ + +  +   fEW la++ i+++++++
  gi|13542193|ref|NP_111881.1|   4 KWTAKFIAGIISVVFIIIGGYLFGEVISKVIASINRV--EFEWGLALLVIGIIILVV 58 
                                   5789*********************888744443333..4**********9999875 PP

>> DUF2929  Protein of unknown function (DUF2929)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   2.3     0.091   1.6e+02      29      48 ..       3      22 ..       1      25 [. 0.51
   2 ?   10.8   4.5   0.00027      0.48       6      52 ..      19      65 ..      17      69 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.091
                       DUF2929 29 ydfttalilavvfgvlvili 48
                                  +++t  +i +++  v++i++
  gi|13542193|ref|NP_111881.1|  3 FKWTAKFIAGIISVVFIIIG 22
                                  55555555555555555544 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00027
                       DUF2929  6 tifWsfiLgevvgYIgsaLtgvtydfttalilavvfgvlviliiali 52
                                  +i+ ++++gev+  ++++ + v++ + +al +  ++ ++vi+  + +
  gi|13542193|ref|NP_111881.1| 19 IIIGGYLFGEVISKVIASINRVEFEWGLALLVIGIIILVVIIPKPKL 65
                                  567789*******************9988877666666666655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1056  (0.058899); expected 358.6 (0.02)
Passed bias filter:                      570  (0.0317921); expected 358.6 (0.02)
Passed Vit filter:                        85  (0.00474092); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 500.56
//
Query:       gi|13542194|ref|NP_111882.1|  [L=161]
Description: major facilitator superfamily permease [Thermoplasma volcanium GSS1]
Scores for complete 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   49.7  20.9    2.8e-13   49.6  20.9    1.0  1  MFS_1     Major Facilitator Superfamily
    3.7e-08   32.7   8.8    1.3e-05   24.3   2.4    2.0  2  Sugar_tr  Sugar (and other) transporter
     0.0043   17.3   1.0      0.011   16.0   0.1    2.1  2  DAD       DAD 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 !   49.6  20.9   4.6e-17   2.8e-13      28     173 ..       6     148 ..       1     160 [. 0.90

  Alignments for each domain:
  == domain 1  score: 49.6 bits;  conditional E-value: 4.6e-17
                         MFS_1  28 gispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfasslw.lllvlrvlqGlgagalfpaga 107
                                   g+s s+  l l++ a+g+ v++l++ + +d f r+ v+++  +++++g l+l+ ++ +  +++++ +l++++ g+++ +++
  gi|13542194|ref|NP_111882.1|   6 GFSISSSILYLAVGAIGYPVGALIMIFTADHFERKYVIFADTVVWFIG-LFLF-SIKIGtTIFIGSFLASMALGMYLQVAY 84 
                                   7888999999999*******************8888************.5555.5788888******************** PP

                         MFS_1 108 aliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllafvlfllllp 173
                                   +++a+ +p + r+++++l  +   +G +lg+ll ++++s+++++  f ++ai +l+a++l  +l+ 
  gi|13542194|ref|NP_111882.1|  85 TYTAENYPTRARSSGFALTDGIGHVGGALGALLLPVIVSAYSFSFGFKFIAITGLIAGIL--ALFG 148
                                   ***********************************************************7..4443 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   6.1   6.6e-07    0.0039      48     129 ..      12      89 ..       4      90 .. 0.91
   2 !   24.3   2.4   2.2e-09   1.3e-05     348     449 ..      59     160 ..      57     161 .] 0.93

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 6.6e-07
                                   HHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHHHHHH CS
                      Sugar_tr  48 sglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlvPmyis 128
                                   s l +++  +G  +G+l++ + +d f Rk+++ + +v+ +ig +l  +         +++g +l+ +++G+   ++ +y++
  gi|13542194|ref|NP_111882.1|  12 SILYLAVGAIGYPVGALIMIFTADHFERKYVIFADTVVWFIGLFLFSIKI----GTTIFIGSFLASMALGMYLQVAYTYTA 88 
                                   566778889************************************99999....569*******************99999 PP

                                   T CS
                      Sugar_tr 129 E 129
                                   E
  gi|13542194|ref|NP_111882.1|  89 E 89 
                                   9 PP

  == domain 2  score: 24.3 bits;  conditional E-value: 2.2e-09
                                   .CHHHHHHHHHHHHHHHTTT.THHHHHHHHHHSHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHT-HHHHHHHHHHH CS
                      Sugar_tr 348 asivaivfialfialfalgw.gpvpwvlvsElfpqsvRskalaiavavnwlanflisllfpiiteaigggyvflvfaglav 427
                                   ++i+ ++fi  f+a  alg+   v + + +E +p++ Rs++ a++  +  +   l +ll p+i++a++ + +++ f ++  
  gi|13542194|ref|NP_111882.1|  59 IKIGTTIFIGSFLASMALGMyLQVAYTYTAENYPTRARSSGFALTDGIGHVGGALGALLLPVIVSAYS-FSFGFKFIAITG 138
                                   688899999999999999974689********************************************.999999999999 PP

                                   HHHHHHHHHS--STT--CCCCG CS
                      Sugar_tr 428 lfiifvfffvpetkgrtleeie 449
                                   l + +  +f p    +tleei+
  gi|13542194|ref|NP_111882.1| 139 LIAGILALFGPKSSKLTLEEIS 160
                                   999999999***********96 PP

>> DAD  DAD family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0      0.98   5.9e+03      92     104 ..       6      18 ..       4      23 .. 0.80
   2 !   16.0   0.1   1.9e-06     0.011      21      59 ..      65     103 ..      57     109 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.98
                                   HHHHHHHHHHHHC CS
                           DAD  92 dfvlasliLhfvv 104
                                    f ++s iL+++v
  gi|13542194|ref|NP_111882.1|   6 GFSISSSILYLAV 18 
                                   5888999999876 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 1.9e-06
                                   HHHHHHHHHHHHHHHHHHHHHHHT--SSCHHHHHHHHHH CS
                           DAD  21 kliDafllflvlvgvlqfvYcvlvgnfpfnaflsgfiat 59 
                                    +i +fl+ + l   lq++Y+++++n+p  a  sgf+ t
  gi|13542194|ref|NP_111882.1|  65 IFIGSFLASMALGMYLQVAYTYTAENYPTRARSSGFALT 103
                                   57899*******************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       793  (0.04423); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1079.86
//
Query:       gi|13542195|ref|NP_111883.1|  [L=238]
Description: sugar transport permease [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-34  119.1   8.3    2.9e-34  118.7   8.3    1.1  1  Sugar_tr  Sugar (and other) transporter
    1.8e-25   89.6  13.2    2.1e-25   89.4  13.2    1.1  1  MFS_1     Major Facilitator Superfamily
    0.00017   21.0   2.2    0.00021   20.7   2.2    1.1  1  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 !  118.7   8.3   4.9e-38   2.9e-34      45     219 ..      60     231 ..      24     236 .. 0.86

  Alignments for each domain:
  == domain 1  score: 118.7 bits;  conditional E-value: 4.9e-38
                                   ..HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHHH CS
                      Sugar_tr  45 svlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlvPm 125
                                   s+ + + +s+ l+G  iGs+++g l+d++GR  s++ +  l+  g++  a++    +v  l++ R+++G+g+G+  +lv+ 
  gi|13542195|ref|NP_111883.1|  60 SLSLFIALSVGLIGYSIGSYLIGSLADVYGRYRSMILTMGLTALGSFGDAISI---NVPELTIFRFITGLGLGADLNLVSS 137
                                   333456788999*****************************************...************************* PP

                                   HHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-TTHHHHHHHCCHHHHHHHHHHGGGS---HHHHHHTT-HH. CS
                      Sugar_tr 126 yisEiApkklRgalvslyqlaitfGilvaaifglglnktsnadgwrillglqlvpallllilllflPESPrylvekgkee. 205
                                   yisE+Ap+++Rg++++++ l  ++G+ ++ ++gl l  + + +gwr+l+g+ +v+al+ l+l++ lPESPr+l +k +   
  gi|13542195|ref|NP_111883.1| 138 YISEFAPPAVRGRITVYTFLIGILGQAITPFIGLHLVPVYY-NGWRYLFGIGAVIALIALFLRFELPESPRWLASKAHNIe 217
                                   ************************************88888.8******************************99998766 PP

                                   HHHHHHHHHHHCHH CS
                      Sugar_tr 206 eakevlaklrgeed 219
                                   +a+++++ ++ +++
  gi|13542195|ref|NP_111883.1| 218 KAEKIIQIMEHTAL 231
                                   99999987666655 PP

>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.4  13.2   3.5e-29   2.1e-25       2     187 ..      31     215 ..      30     238 .] 0.85

  Alignments for each domain:
  == domain 1  score: 89.4 bits;  conditional E-value: 3.5e-29
                         MFS_1   2 llaaflsalarsilgpalplalaedlgispseigl..lltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll 80 
                                    +++f++++++s +g+a+p a+a++++  +++++l  +l++  +g++++s+++G+l+d +Gr r ++l++ l+alg++  +
  gi|13542195|ref|NP_111883.1|  31 GIGYFFTFYDISDIGLAMP-AIASQFH-IGTSLSLfiALSVGLIGYSIGSYLIGSLADVYGRYRSMILTMGLTALGSFGDA 109
                                   689****************.9******.4555566567788999********************************55555 PP

                         MFS_1  81 fasslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllgglla.sslg..Wravfyila 158
                                   ++++++ l ++r+++Glg ga + ++ ++i++ +p+  rgr + +  +   lG +++p +g  l+   +   Wr++f i a
  gi|13542195|ref|NP_111883.1| 110 ISINVPELTIFRFITGLGLGADLNLVSSYISEFAPPAVRGRITVYTFLIGILGQAITPFIGLHLVpV-YYngWRYLFGIGA 189
                                   569999***********************************************************63.3336********* PP

                         MFS_1 159 ivsllafvlfllllpeepperkrkspkee 187
                                   +++l+a+    l +  ++++r+  s++  
  gi|13542195|ref|NP_111883.1| 190 VIALIALF---LRFELPESPRWLASKAHN 215
                                   ******55...667777777777766655 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 !   20.7   2.2   3.5e-08   0.00021      16     188 ..      48     221 ..      30     232 .. 0.73

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 3.5e-08
                         MFS_4  16 LPallaegqlslsqaglla.aaNylGYLvGallaafalsagaeRlr.llagllatvllllamaltesfaaflliRflaGva 94 
                                   +Pa+  + ++  s   ++a ++ ++GY +G+ l   +l+    R r +   + +t+l  +  a+  ++  +++ Rf++G++
  gi|13542195|ref|NP_111883.1|  48 MPAIASQFHIGTSLSLFIAlSVGLIGYSIGSYLI-GSLADVYGRYRsMILTMGLTALGSFGDAISINVPELTIFRFITGLG 127
                                   5666666666667667777678899*99999876.667777777776888899999************************* PP

                         MFS_4  95 sAvvlvfgsslvlahaaaarrervgallfaGvGlGiavsgllvllllqlglsasslWlalavlsavllllvalllpraalr 175
                                    ++ l ++ss + + a +a r+r+    f    lG a++  + l l+ +  ++    ++++++ a++ l +   lp++++ 
  gi|13542195|ref|NP_111883.1| 128 LGADLNLVSSYISEFAPPAVRGRITVYTFLIGILGQAITPFIGLHLVPVYYNGWRYLFGIGAVIALIALFLRFELPESPRW 208
                                   ****************************98433555555555444444433333333444444444445555566677777 PP

                         MFS_4 176 easaaaeaakaeq 188
                                    as+a + +kae+
  gi|13542195|ref|NP_111883.1| 209 LASKAHNIEKAEK 221
                                   7777777755443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       575  (0.0320709); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.32s 00:00:00.90 Elapsed: 00:00:00.54
# Mc/sec: 1334.02
//
Query:       gi|13542196|ref|NP_111884.1|  [L=392]
Description: major facilitator superfamily permease [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-32  113.3  59.9    9.5e-30  103.7  41.7    2.1  2  MFS_1     Major Facilitator Superfamily
     0.0024   17.2  20.2     0.0035   16.7  20.2    1.2  1  MFS_4     Uncharacterised MFS-type transporter YbfB
  ------ inclusion threshold ------
        6.4    4.9  18.6      0.011   14.1   2.4    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 !  103.7  41.7   1.6e-33   9.5e-30       3     353 .]      21     347 ..      19     347 .. 0.82
   2 !   23.3  10.3   4.4e-09   2.6e-05      92     174 ..     301     384 ..     300     391 .. 0.91

  Alignments for each domain:
  == domain 1  score: 103.7 bits;  conditional E-value: 1.6e-33
                         MFS_1   3 laaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalg.lllllfa 82 
                                   +++f++++ r+++ ++lp ++ ++l is+ +++ll+t+y +g+ ++++p+G +sdrfG  ++  +++l++ ++ +l+++ a
  gi|13542196|ref|NP_111884.1|  21 FSFFINSTVRFFIPAILP-FIISALKISVYQASLLITAYWIGYTAFQIPAGIISDRFGTAKTSKASFLGLTIAfFLMPI-A 99 
                                   789***************.999***************************************************444444.5 PP

                         MFS_1  83 .sslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailg.pllggllasslgWravfyilaivs 161
                                    + + l+++l +l G  +++++ +g++l+ + + +++r++ ig++++gf +G+ +g +++  ll   +++ ++++++ +++
  gi|13542196|ref|NP_111884.1| 100 mHEYLLIFLLQLLLGSLSSIVYVSGISLVQRSADQSNRSLFIGIFQIGFFMGSSVGeYIVLELLD--ISFYYSYIAVSLLL 178
                                   59999***************************************************666666666..89999********* PP

                         MFS_1 162 llafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsglltllplylqevlglsg 242
                                   l+++ l   +l++++p  ++k+           +++p  + +l       + ++ ++++f++ g+l+l++++     g++ 
  gi|13542196|ref|NP_111884.1| 179 LISLTL--DFLFQNEPGLSKKNN----------EIIP--RGILY------VSLIRFSAGFMYLGFLSLFTTF-LVYDGIAP 238
                                   **9665..666666666666643..........3445..22222......2222333333555566666665.55556665 PP

                         MFS_1 243 lllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavtssavllllvlvliGfglgfvfpslla 323
                                   l  a+++  ++a++g+++++l+g +s+++ ++   l+a++ ++++++ l+l++   +   +  +++  Gf +g++ ++++ 
  gi|13542196|ref|NP_111884.1| 239 LSKAYAYAWIPAIGGIAGSPLGGMISRKM-WHAKALMAIVPIIVFSVVLMLIGIV-NRNYVPPLSFATGFLYGLYAGPSMG 317
                                   666666699999999999********994.5567788888888888888888888.344433467779************* PP

                         MFS_1 324 lasdlappeeagtasglfntagslggalgp 353
                                   las++  +e+ gt sg+ n+ +++gg+++p
  gi|13542196|ref|NP_111884.1| 318 LASEVGREENLGTSSGILNFSSQVGGIISP 347
                                   ****************************98 PP

  == domain 2  score: 23.3 bits;  conditional E-value: 4.4e-09
                         MFS_1  92 rvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslg.Wravfyilaivsllafvlflll 171
                                    + +G+ +g+++  ++ l++++  +e+ g   g+l+ ++++G i+ pl+ g+l +++g +  +f ++ ++s++ +++ l+ 
  gi|13542196|ref|NP_111884.1| 301 SFATGFLYGLYAGPSMGLASEVGREENLGTSSGILNFSSQVGGIISPLAIGYLFTYFGnFKIPFAVISVLSFVIILFPLAI 381
                                   6899**************************************************99999**************99965555 PP

                         MFS_1 172 lpe 174
                                   +++
  gi|13542196|ref|NP_111884.1| 382 FLR 384
                                   544 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 !   16.7  20.2   5.9e-07    0.0035       9     357 ..      30     373 ..      28     379 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 5.9e-07
                         MFS_4   9 RFsytpiLPallaegqlslsqagllaaaNylGYLvGallaafalsagaeRlrllagllatvllllam.altesfaaflliR 88 
                                   RF    iLP ++ ++++s+ qa+ll +a ++GY +  + a +   +  +  + +a+ l  +++++ m  ++++ ++++l+ 
  gi|13542196|ref|NP_111884.1|  30 RFFIPAILPFIISALKISVYQASLLITAYWIGYTAFQIPAGIISDRFGTAKTSKASFLGLTIAFFLMpIAMHEYLLIFLLQ 110
                                   899999*****************************999996655444444446666666666666661667889999**** PP

                         MFS_4  89 flaGvasAvvlvfgsslvlahaaaarrervgallfaGvGlGiavsgllvllllqlglsasslWlalavlsavllllvalll 169
                                   +l+G  s +v v g slv++ a +++r+  ++++  G  +G  v+  +vl ll      s     + ++s++ll+ ++l  
  gi|13542196|ref|NP_111884.1| 111 LLLGSLSSIVYVSGISLVQRSADQSNRSLFIGIFQIGFFMGSSVGEYIVLELLDISFYYS-----YIAVSLLLLISLTLDF 186
                                   **********************************99999999999988887776655444.....4455555555555544 PP

                         MFS_4 170 praalreasaaaeaakaeqkslpllalllaYglaGfGYii.tatFlvaiardg.aggalleallWllvGlaaivgvlvwlr 248
                                      +++ + ++ + +  ++ +l +  +    g++ +G+     tFlv    dg a  + + a +W+ +  +++ ++l    
  gi|13542196|ref|NP_111884.1| 187 L-FQNEPGLSKKNNEIIPRGILYVSLIRFSAGFMYLGFLSlFTTFLVY---DGiAPLSKAYAYAWIPAIGGIAGSPLGGMI 263
                                   4.2333344444443366666666677777777777776414566654...332333344456665443356666677776 PP

                         MFS_4 249 vakrsglrralaaallieavgvllsll...spsplglivssvllGltflaitalvlqlarelappat.rrllglmTasfgi 325
                                     k + +++++a++  i + +v+l l+      ++ + + s  +G  +       + la e+  +++  +  g++  s  +
  gi|13542196|ref|NP_111884.1| 264 SRKMWHAKALMAIV-PIIVFSVVLMLIgivNRNYV-PPL-SFATGFLYGLYAGPSMGLASEVGREENlGTSSGILNFSSQV 341
                                   66777666666554.44455555544400033333.333.234455555556667777777777777678889999999** PP

                         MFS_4 326 gQilGpllasllaeatgslalallvaaaalvl 357
                                   g i+ pl+++ l+ + g+++ + +v +++ ++
  gi|13542196|ref|NP_111884.1| 342 GGIISPLAIGYLFTYFGNFKIPFAVISVLSFV 373
                                   ********************999987776665 PP

>> OATP  Organic Anion Transporter Polypeptide (OATP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.4     0.077   4.6e+02     305     358 ..      21      76 ..      15     101 .. 0.43
   2 ?   14.1   2.4   1.8e-06     0.011     131     184 ..     103     155 ..      80     173 .. 0.89
   3 ?   -0.6   3.7     0.051   3.1e+02     337     381 ..     246     289 ..     206     294 .. 0.64

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.077
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxx RF
                          OATP 305 feillvaGfitFlpkylEtqFslsaseAnlltGvvvipgaalGi....llgGllvkkl 358
                                   f +++ + +  F+p  l   F +sa + +++ ++++i +  +G     + +G++  ++
  gi|13542196|ref|NP_111884.1|  21 FSFFINSTVRFFIPAIL--PFIISALKISVYQASLLITAYWIGYtafqIPAGIISDRF 76 
                                   55555555555555433..233333333333333333333333221113344555444 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 1.8e-06
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          OATP 131 lvllfflaqlllGiGatpiytlGisYidDnvkkknsplylgilyalrilGpalG 184
                                   + ll+fl qlllG  ++ +y  Gis +  +++++n +l++gi++   ++G  +G
  gi|13542196|ref|NP_111884.1| 103 Y-LLIFLLQLLLGSLSSIVYVSGISLVQRSADQSNRSLFIGIFQIGFFMGSSVG 155
                                   3.399999*****************************************99998 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.051
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          OATP 337 GvvvipgaalGillgGllvkklklsakklaklvlvvsllslllll 381
                                   + +  +g+++G  lgG++ +k+ ++ak+l+++v ++ +  +l+l+
  gi|13542196|ref|NP_111884.1| 246 AWIPAIGGIAGSPLGGMISRKM-WHAKALMAIVPIIVFSVVLMLI 289
                                   4566678899******987776.5666666665555555444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (392 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       845  (0.0471303); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); 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):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.45
# Mc/sec: 2620.63
//
Query:       gi|13542197|ref|NP_111885.1|  [L=480]
Description: multidrug efflux permease [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-53  181.2  48.9      4e-52  177.3  43.7    2.1  2  MFS_1     Major Facilitator Superfamily
    3.3e-09   36.1  12.0    3.3e-09   36.1  12.0    2.7  2  Sugar_tr  Sugar (and other) transporter
    0.00051   18.6   2.9    0.00051   18.6   2.9    2.6  2  MFS_3     Transmembrane secretion effector
  ------ inclusion threshold ------
       0.12   11.3   0.0        0.2   10.5   0.0    1.3  1  DGOK      2-keto-3-deoxy-galactonokinase


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 !  177.3  43.7     9e-56     4e-52       3     350 ..      15     400 ..      13     403 .. 0.91
   2 !    6.9   0.2   0.00058       2.6     125     166 ..     419     461 ..     415     479 .. 0.75

  Alignments for each domain:
  == domain 1  score: 177.3 bits;  conditional E-value: 9e-56
                         MFS_1   3 laaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfas 83 
                                    ++++ a++++i+ +alp ++++dl +  s   +++ +y l+aav++  +Grl+d ++r+ ++  g+++f lg++l+ + s
  gi|13542197|ref|NP_111885.1|  15 AGVMMGAIDSTIVVLALP-TISDDLKAPLSLSIWIILAYLLVAAVSTTQFGRLGDMISRKTIFNSGMAIFTLGSFLCGV-S 93 
                                   5788899999999999*9.**************************************9999************666665.5 PP

                         MFS_1  84 slw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsll 163
                                   s   +l+++r++q++g++++ ++++++iad fp++ rgra+g+ s+g++ Ga lg +lgg++++++gWr++fyi+ +v+++
  gi|13542197|ref|NP_111885.1|  94 SNIdFLIAFRFVQAAGGSMMQANSGSIIADNFPPNLRGRAYGYTSVGWNSGATLGIVLGGIITTLIGWRYIFYINVPVGII 174
                                   5555***************************************************************************** PP

                         MFS_1 164 afvlfllllpeepperkrkspkeee...............................................kgtgpaplv 197
                                   +     l++  ++  ++ k+ +++                                                ++t + +l+
  gi|13542197|ref|NP_111885.1| 175 S-----LYFAIKYIIPGSKKNVKLDvpgvvtltaalssiayaatdftshglettnetllsigflllvvfiflERTNKNALL 250
                                   *.....4444444444444444444445588999999999999999999999999999*************9999999999 PP

                         MFS_1 198 pawkallkdpvlwillialllfffgfsglltllplylqevlglsglllaglllallalvgailallagrlsdrlgrrrrll 278
                                   p   +l+ ++v+ + ++a++l ++g+ ++++ + +ylq  +gl+  l ++lll  ++++g + ++++g+lsdr+g+r++ +
  gi|13542197|ref|NP_111885.1| 251 P--FHLFQNRVFNFSIAASFLQSLGYLAVTFIVIMYLQGLRGLT-PLDSSLLLVPGYVLGGFTGPIFGKLSDRIGARTPAT 328
                                   9..788888888679999999999********************.8*********************************** PP

                         MFS_1 279 lallllllaalglallavtssavllll.vlvliGfglgfvfpsllalasdlappeeagtasglfntagslgga 350
                                   l+++l+++a+l+++ +++  ++v +++ v+++ G+g++++fp+ +++++ + p+   g+asgl  t+ ++g++
  gi|13542197|ref|NP_111885.1| 329 LGMFLMMIAVLLYMTFNLK-TPVYYVIpVSIISGLGSSMFFPANNSAVMASSPAGSYGAASGLLRTMANIGML 400
                                   *******************.777777668888999***********************************986 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.00058
                         MFS_1 125 llsagfslGailgpllgglla.sslgWravfyilaivsllafv 166
                                    + +++++G ++g l +++l+  +   +++f i+a+ +l++fv
  gi|13542197|ref|NP_111885.1| 419 AFEVFAGVGRLVGGLSASFLTgIHTALEVSFAIIAVGMLFSFV 461
                                   57899****************5555588888888888888855 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.1  12.0   7.4e-13   3.3e-09      44     188 ..      41     179 ..      16     189 .. 0.92
   2 !    3.7  13.6    0.0052        23      50     165 ..     299     413 ..     202     442 .. 0.85

  Alignments for each domain:
  == domain 1  score: 36.1 bits;  conditional E-value: 7.4e-13
                                   ...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHH CS
                      Sugar_tr  44 ssvlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlvP 124
                                     +ls +i  ++l++a+++   +g lgd+++Rk ++  + ++f  g++l++++    ++  li+ R++   g  + ++ + 
  gi|13542197|ref|NP_111885.1|  41 PLSLSIWIILAYLLVAAVSTTQFGRLGDMISRKTIFNSGMAIFTLGSFLCGVSS---NIDFLIAFRFVQAAGGSMMQANSG 118
                                   557899************************************************...************************ PP

                                   HHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-TTHHHHHHHCCHHHHHHHHHHG CS
                      Sugar_tr 125 myisEiApkklRgalvslyqlaitfGilvaaifglglnktsnadgwrillglqlvpallllill 188
                                     i+ + p++lRg+  +++ +++  G  +++++g ++ +  +   wr+ +++++   ++ l++ 
  gi|13542197|ref|NP_111885.1| 119 SIIADNFPPNLRGRAYGYTSVGWNSGATLGIVLGGIITTLIG---WRYIFYINVPVGIISLYFA 179
                                   **********************************99999988...********99999887775 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.0052
                                   HHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHHHHHHTT CS
                      Sugar_tr  50 livsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlvPmyisEi 130
                                   l+v  +++G++ G + +g+l+dr+G +     + +l++i+ +l ++ + k+ v+ +i   +++G+g  ++       +   
  gi|13542197|ref|NP_111885.1| 299 LLVPGYVLGGFTGPI-FGKLSDRIGARTPATLGMFLMMIAVLLYMTFNLKTPVYYVIPVSIISGLGSSMFFPANNSAVMAS 378
                                   566668889888876.577*****************************99999999999********99999999999999 PP

                                   S-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS CS
                      Sugar_tr 131 ApkklRgalvslyqlaitfGilvaaifglglnkts 165
                                   +p+   ga  +l  ++  +G+l ++++   ++++ 
  gi|13542197|ref|NP_111885.1| 379 SPAGSYGAASGLLRTMANIGMLGSFVLAITVSTIA 413
                                   99999999999999999999999888888777765 PP

>> MFS_3  Transmembrane secretion effector
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   2.9   1.1e-07   0.00051      66     193 ..      64     191 ..      40     252 .. 0.78
   2 ?    1.8   1.5     0.013        60      66     130 ..     315     377 ..     251     412 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.1e-07
                         MFS_3  66 GalaDnfdrRkvllavqlllalvsvlltvlaalgllspwlllaltlligiGaalndPaWqAsvgelvkrrdvpaAvaLnsv 146
                                   G l D ++r+ ++  ++++  l+s l  v++ ++      l+a+ ++ + G ++++     ++ +  + +    A   +sv
  gi|13542197|ref|NP_111885.1|  64 GRLGDMISRKTIFNSGMAIFTLGSFLCGVSSNID-----FLIAFRFVQAAGGSMMQANSGSIIADNFPPNLRGRAYGYTSV 139
                                   6777888888887778888888887777777666.....58**************************************** PP

                         MFS_3 147 giniaRsvGPAlgGvlvaavGaalafavna....ls.ylalivallrwkrev 193
                                   g+n   + G  lgG++ +++G  + f +n+    +s y+a+ +++  +k++v
  gi|13542197|ref|NP_111885.1| 140 GWNSGATLGIVLGGIITTLIGWRYIFYINVpvgiISlYFAIKYIIPGSKKNV 191
                                   **************************99974222332333333333444444 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.013
                         MFS_3  66 GalaDnfdrRkvllavqlllalvsvlltvlaalgllspwlllaltlligiGaalndPaWqAsvge 130
                                   G l+D +  R     ++ l++++ +l +++     + ++ ++ ++++ g+G+++  Pa + +v  
  gi|13542197|ref|NP_111885.1| 315 GKLSDRIGARTPATLGMFLMMIAVLLYMTF--NLKTPVYYVIPVSIISGLGSSMFFPANNSAVMA 377
                                   566666666666666655555543333322..223455677888888888888888887777654 PP

>> DGOK  2-keto-3-deoxy-galactonokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   4.5e-05       0.2      47     107 ..     141     202 ..     106     207 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 4.5e-05
                          DGOK  47 wleaaekalpviaaGmvGsrqGWveapyvavPaalaalaaalarv..aegrevai.vPGlaqes 107
                                   w +  +++l +++ G ++   GW+ + y++vP+ + +l  a++ +   ++++v++ vPG+ + +
  gi|13542197|ref|NP_111885.1| 141 WNS--GATLGIVLGGIITTLIGWRYIFYINVPVGIISLYFAIKYIipGSKKNVKLdVPGVVTLT 202
                                   333..56799****************************99997777745555544489987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (480 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       768  (0.0428356); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.62u 0.31s 00:00:00.93 Elapsed: 00:00:00.48
# Mc/sec: 2983.76
//
Query:       gi|13542198|ref|NP_111886.1|  [L=305]
Description: ABC-type multidrug transport system, ATPase component [Thermoplasma volcanium GSS1]
Scores for complete 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   95.8   0.0    4.8e-27   95.1   0.0    1.3  1  ABC_tran    ABC transporter
    1.1e-08   35.3   0.8    0.00017   21.5   0.0    2.2  2  AAA_21      AAA domain, putative AbiEii toxin, Type IV TA sys
    3.1e-06   27.8   1.0    5.7e-06   27.0   0.3    1.9  1  DUF4162     Domain of unknown function (DUF4162)
    0.00019   20.9   0.4     0.0028   17.1   0.4    2.1  1  SMC_N       RecF/RecN/SMC N terminal domain
  ------ inclusion threshold ------
      0.016   15.7   1.0      0.024   15.1   1.0    1.7  1  AAA_23      AAA domain
      0.021   14.6   0.0      0.041   13.6   0.0    1.4  1  AAA_29      P-loop containing region of AAA domain
      0.027   14.5   0.2      0.066   13.3   0.2    1.7  1  MMR_HSR1    50S ribosome-binding GTPase
       0.04   12.9   0.0      0.073   12.0   0.0    1.3  1  MeaB        Methylmalonyl Co-A mutase-associated GTPase MeaB
       0.07   12.8   0.2      0.085   12.6   0.2    1.3  1  AAA_30      AAA domain
      0.087   12.1   0.0        1.4    8.2   0.0    2.3  2  Zeta_toxin  Zeta toxin
      0.099   12.4   0.1       0.19   11.5   0.1    1.4  1  ATP_bind_1  Conserved hypothetical ATP binding protein
       0.11   12.1   0.5        0.2   11.3   0.5    1.3  1  SRP54       SRP54-type protein, GTPase domain
       0.12   12.6   0.1       0.41   10.9   0.1    1.9  1  SbcCD_C     Putative exonuclease SbcCD, C subunit
       0.14   12.6   0.3       0.54   10.7   0.1    2.1  2  AAA         ATPase family associated with various cellular ac
       0.24    8.9   0.4       0.33    8.4   0.4    1.1  1  DUF3584     Protein of unknown function (DUF3584)


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.1   0.0     4e-30   4.8e-27       2     136 ..      23     164 ..      22     165 .. 0.96

  Alignments for each domain:
  == domain 1  score: 95.1 bits;  conditional E-value: 4e-30
                                   EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx... RF
                      ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren... 79 
                                   ++vs+++k+ge+++++G+nGaGK+t +++l+  +    G++++ g d+++   e+ r++igv+ q  + f+ +tv++n   
  gi|13542198|ref|NP_111886.1|  23 DDVSFHVKRGEIYGLLGKNGAGKTTTIRTLTTIMPVHYGKVKVLGLDVST-HPEKIRQRIGVVLQS-ESFDFTTVEKNlki 101
                                   89**********************************************99.88999**********.7888888******* PP

                                   ..........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                   ..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  80 ..........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                               +++ie++++ ++l+ l++ ++     +LSgGqk+r+++ar +l + +ll+lDEpt
  gi|13542198|ref|NP_111886.1| 102 ygmlwdvpgeVLKARIEEVMEVFDLSRLRKIRA----LELSGGQKKRLQVAREFLHDMDLLFLDEPT 164
                                   *********9999**************999999....*****************************9 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.3   9.6e-05      0.12       2      21 ..      35      54 ..      34     101 .. 0.80
   2 !   21.5   0.0   1.4e-07   0.00017     221     297 ..     121     194 ..      94     197 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 9.6e-05
                        AAA_21  2 nvliGpNgsGKSnLLdaldl 21
                                   +l G+Ng+GK++ +++l  
  gi|13542198|ref|NP_111886.1| 35 YGLLGKNGAGKTTTIRTLTT 54
                                  689*************9965 PP

  == domain 2  score: 21.5 bits;  conditional E-value: 1.4e-07
                        AAA_21 221 vvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTH 297
                                   +  ++ ++ +++ a elS G+k+ l ++  +l +    +ll++DEp  gL+P + r++l  +ke+++ g  v+ tT+
  gi|13542198|ref|NP_111886.1| 121 MEVFDLSRLRKIRALELSGGQKKRLQVAREFLHDM---DLLFLDEPTVGLDPIMRRTVLNYIKEKAKAGLTVLYTTQ 194
                                   44455566688899999999999999999999999...9************************************96 PP

>> DUF4162  Domain of unknown function (DUF4162)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.3   4.8e-09   5.7e-06       1      81 []     218     304 ..     218     304 .. 0.74

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 4.8e-09
                                   E-HHHHHTTS.-SSEEEEE....-------...---EEEE-TTS-EEEEE--.-----------.----EEEEEEEE---H CS
                       DUF4162   1 GtleeiKrsy.gknrieve....adaeell.eepgveeveeeggelelkled.eeaanellkal.tsgveirsFeeeePsL 73 
                                   Gt + +K++y   ++i+++     + e+l+   p++ ++e   +e++l  ++ e++ ++ + +  +sg+ i+++++ee sL
  gi|13542198|ref|NP_111886.1| 218 GTSDFLKSKYgDLKTIKIHisgnVNREDLKmMFPEFVQIEG--DEVRLISKNvEDVLPDMILYFkRSGIHIERINVEETSL 296
                                   66677888884456677777554223333313355666665..559999999999*********78*************** PP

                                   HHHHHHHH CS
                       DUF4162  74 ndIFiekv 81 
                                   +d+F+++v
  gi|13542198|ref|NP_111886.1| 297 DDVFLRVV 304
                                   ******98 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.4   2.3e-06    0.0028      25     208 ..      33     202 ..       4     214 .. 0.68

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.3e-06
                                   SEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEEEEET CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N  25 sftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsisrrvkr 105
                                   ++  ++G+NG+GK+  +  +  ++   ++ k++   l+      +++++  + ++ ++++ e+ ++++ +++++i   +  
  gi|13542198|ref|NP_111886.1|  33 EIYGLLGKNGAGKTTTIRTLTTIMPV-HYGKVKVLGLD-----VSTHPEKIRQRIGVVLQSESFDFTTVEKNLKIYGMLWD 107
                                   35567899999999999999888875.33344444443.....34566777778888888888887777777777655544 PP

                                   .TSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHH CS
                                   .xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 106 .kgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellke 185
                                     ge    ++ +  +  ev +l +  +i   +LSgG+k+     L +A +  +   l +lDe    LD   ++ v +++ke
  gi|13542198|ref|NP_111886.1| 108 vPGE---VLKARIEEVMEVFDLSRLRKIRALELSGGQKKR----LQVAREFLHDMDLLFLDEPTVGLDPIMRRTVLNYIKE 181
                                   0444...566666677888999999999999*******95....555666788889************************* PP

                                   HCTTSEEEEE-SSHHHCCC-SCE CS
                                   xxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 186 ksknaQfivislreemlekadkl 208
                                   k k    + +  +++++e+ad l
  gi|13542198|ref|NP_111886.1| 182 KAKAG--LTVLYTTQIMEEADYL 202
                                   99653..4445556677777654 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   1.0     2e-05     0.024      13      42 ..      25      55 ..       6     270 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2e-05
                        AAA_23 13 qeidF...skgltlItGpNGaGKTTildAikla 42
                                  ++  F      ++ + G+NGaGKTT ++ ++ +
  gi|13542198|ref|NP_111886.1| 25 VS--FhvkRGEIYGLLGKNGAGKTTTIRTLTTI 55
                                  33..34444469999************999876 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   3.4e-05     0.041      13      46 ..      23      56 ..      18      63 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.4e-05
                        AAA_29 13 dghtieidlkgatlltGpsGsGKSTllDAiqalL 46
                                  d+ ++++++ +++ l G++G+GK+T +  +++++
  gi|13542198|ref|NP_111886.1| 23 DDVSFHVKRGEIYGLLGKNGAGKTTTIRTLTTIM 56
                                  55678888666999************98888887 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.2   5.5e-05     0.066       3      71 ..      36     152 ..      34     193 .. 0.51

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.5e-05
                                   EEEESTTSSHHHHHHHHH.............T............S...TEEESSSTTSSSSEEEEEEEETTEEEEEEECGG CS
                      MMR_HSR1   3 aivGrpNvGKStLinalt.............g............e...kaivsdkpgtTrdinegrvklkgkeielvDtpG 55 
                                   +++G+  +GK+t i++lt             g            +   + + +++ +tT + n + +        l+D+pG
  gi|13542198|ref|NP_111886.1|  36 GLLGKNGAGKTTTIRTLTtimpvhygkvkvlGldvsthpekirqRigvVLQSESFDFTTVEKNLKIY------GMLWDVPG 110
                                   799***************5555555444333033333222222212223344455555555555533......28999999 PP

                                   .C......................SS...HHHHHHHHHHHHH CS
                      MMR_HSR1  56 .l......................ie...gaseekglgkafl 71 
                                    +                      +e   g++++ +++++fl
  gi|13542198|ref|NP_111886.1| 111 eVlkarieevmevfdlsrlrkiraLElsgGQKKRLQVAREFL 152
                                   523444444444444444444333112223333334555554 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 ?   12.0   0.0   6.1e-05     0.073      18      69 ..      21      72 ..       3      75 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 6.1e-05
                                  HHHHHGGG-S-SEEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE---- CS
                          MeaB 18 llerllakaGraqvvGltGvPGaGkstlvealglelrrrGkrvavlavDPss 69
                                  +++ ++ +  r +  Gl G  GaGk t++  l++ +  +  +v vl +D s 
  gi|13542198|ref|NP_111886.1| 21 VVDDVSFHVKRGEIYGLLGKNGAGKTTTIRTLTTIMPVHYGKVKVLGLDVST 72
                                  566677778899999*********************99999*****999775 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.2   7.1e-05     0.085      19      53 ..      33      67 ..      25     184 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 7.1e-05
                        AAA_30 19 rvavltGpAGtGKttalkalreaweaaggrviglA 53
                                   +  l G  G+GKtt++++l+ ++  + g+v +l 
  gi|13542198|ref|NP_111886.1| 33 EIYGLLGKNGAGKTTTIRTLTTIMPVHYGKVKVLG 67
                                  467789****************9998855555554 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.0    0.0012       1.4      18      49 ..      34      66 ..      22      76 .. 0.78
   2 ?    1.1   0.0      0.16     2e+02      49      77 ..     241     269 ..     238     275 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0012
                    Zeta_toxin 18 lillgGqpGAGKselaellkdele.rqgnvvrl 49
                                  ++ l G  GAGK+++++ l++ +  ++g+v +l
  gi|13542198|ref|NP_111886.1| 34 IYGLLGKNGAGKTTTIRTLTTIMPvHYGKVKVL 66
                                  5567799************99998666655555 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.16
                    Zeta_toxin  49 ldpDdlRelhPeyeeilkadpkkaseltq 77 
                                   +++ dl+ ++Pe+ +i+ ++++  s++++
  gi|13542198|ref|NP_111886.1| 241 VNREDLKMMFPEFVQIEGDEVRLISKNVE 269
                                   788999*********99999888888775 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00016      0.19       2      34 ..      38      70 ..      37      77 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00016
                    ATP_bind_1  2 vGpaGsGKttfvgalseilelrgrsvavvNLDP 34
                                  +G  G+GKtt +++l+ i++    +v+v+ LD 
  gi|13542198|ref|NP_111886.1| 38 LGKNGAGKTTTIRTLTTIMPVHYGKVKVLGLDV 70
                                  6999******************9******9995 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.5   0.00017       0.2       6      38 ..      37      69 ..      33      72 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00017
                                  EEESTTSSHHHHHHHHHHHHHHTTS-EEEEEES CS
                         SRP54  6 lvGlqGaGKTttlaKLaallkkegkkvllvaaD 38
                                  l+G +GaGKTtt+  L  ++  +  kv +  +D
  gi|13542198|ref|NP_111886.1| 37 LLGKNGAGKTTTIRTLTTIMPVHYGKVKVLGLD 69
                                  89**************99988877777666666 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00035      0.41      62      89 ..     153     180 ..     127     181 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00035
                       SbcCD_C  62 palrlvfLDEAFsklDeesiatllelle 89 
                                   ++++l+fLDE   +lD+ +++t+l++++
  gi|13542198|ref|NP_111886.1| 153 HDMDLLFLDEPTVGLDPIMRRTVLNYIK 180
                                   6799********************9987 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00045      0.54       3      50 ..      37      81 ..      35      93 .. 0.85
   2 ?   -1.2   0.0       2.2   2.6e+03      60      66 ..     156     162 ..     120     210 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00045
                                  EESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHH CS
                           AAA  3 lyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelf 50
                                  l G  G GKT++++ + + + v++ ++++  l    v+  ++kir+ +
  gi|13542198|ref|NP_111886.1| 37 LLGKNGAGKTTTIRTLTTIMPVHYGKVKVLGLD---VSTHPEKIRQRI 81
                                  78******************9999999998888...777777777655 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.2
                                   EEEEEET CS
                           AAA  60 silfiDE 66 
                                     lf+DE
  gi|13542198|ref|NP_111886.1| 156 DLLFLDE 162
                                   4555555 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   0.4   0.00028      0.33      23      43 ..      38      62 ..      31      64 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00028
                       DUF3584 23 eGtNaaGKTtLlrLi....PlFYGe 43
                                   G N+aGKTt++r++    P+ YG+
  gi|13542198|ref|NP_111886.1| 38 LGKNGAGKTTTIRTLttimPVHYGK 62
                                  699********99755555999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       626  (0.0349155); expected 358.6 (0.02)
Passed bias filter:                      524  (0.0292264); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.58u 0.32s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 1895.76
//
Query:       gi|13542199|ref|NP_111887.1|  [L=254]
Description: ABC transporter permease [Thermoplasma volcanium GSS1]
Scores for complete 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  29.4    1.7e-21   76.6  29.4    1.9  2  ABC2_membrane    ABC-2 type transporter
    5.1e-09   35.7  38.2    5.1e-09   35.7  38.2    1.6  2  ABC2_membrane_3  ABC-2 family transporter protein
    0.00084   18.7  23.7    0.00084   18.7  23.7    1.5  1  ABC2_membrane_2  ABC-2 family transporter protein


Domain annotation for each model (and alignments):
>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.6  29.4   2.9e-25   1.7e-21      20     210 .]      21     220 ..       7     220 .. 0.88
   2 ?    0.3   0.9     0.064   3.8e+02     136     154 ..     229     247 ..     222     249 .. 0.75

  Alignments for each domain:
  == domain 1  score: 76.6 bits;  conditional E-value: 2.9e-25
                 ABC2_membrane  20 lgllwrliqplllalvfgtvfgn....lg...nsedglnr..pgllffsvlflafsaltsvapvferergvlerelvsply 91 
                                   + ll+ l  p ++++v+g++f +    ++   +  +++++  pg++++  +  +  ++ ++++ ++r+ g++e++ v p+ 
  gi|13542199|ref|NP_111887.1|  21 T-LLFLLGLPSFYLIVLGLMFQSiipnVPfagKDISYAQFlsPGVVAMQPFIAG--SIGGSMLWSDRRWGMFEQLIVGPF- 97 
                                   3.4778888999999999999976555334323444444489****99988888..999999******************. PP

                 ABC2_membrane  92 slsayvlakvlvelpvsllqalifllivyflvgldls...rfflflllllltalaasslgllisalapsfedasqlaslvl 169
                                   ++ +y+l+ + v++++s+  a++++l++y ++g+ +s   + +++ ++l++++++++s++l++s++ ++++++++++++v+
  gi|13542199|ref|NP_111887.1|  98 HRIDYLLGIIYVSIIFSVGGAFLMFLVSYAITGFLVSydiNLLMIAVVLIVSSILFTSIFLVLSVFIRTIQTYNTVTMFVF 178
                                   ********************************9999987677*************************************** PP

                 ABC2_membrane 170 lpllllsGffipidsm.pkwlqwiaylnPltyavealrsnlf 210
                                   ++l + s +f+pi+s  p  l+ ++y+nPlty+v+a+r+ +f
  gi|13542199|ref|NP_111887.1| 179 FILDFASSAFYPINSRtPLGLRIVSYMNPLTYIVDAVRNMMF 220
                                   ****************999*******************9987 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.064
                 ABC2_membrane 136 lllltalaasslgllisal 154
                                   + ll+++++s++++li+ +
  gi|13542199|ref|NP_111887.1| 229 ISLLIVVVLSGFFFLIALV 247
                                   6778888888888888765 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   1.0      0.13   7.7e+02       3      26 ..      21      44 ..      19      56 .. 0.71
   2 !   35.7  38.2   8.6e-13   5.1e-09     156     344 ..      53     246 ..      42     247 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.13
               ABC2_membrane_3  3 fliitlllPiilvlllglifsnsv 26
                                  +l++ l lP +++++lgl+f++  
  gi|13542199|ref|NP_111887.1| 21 TLLFLLGLPSFYLIVLGLMFQSII 44
                                  666777788888888888877544 PP

  == domain 2  score: 35.7 bits;  conditional E-value: 8.6e-13
               ABC2_membrane_3 156 lsnvasflvg.liliilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllilll...afglg 232
                                     ++a+fl + ++++ +++ +++   +++ ++++ ++ e+++v +  ++ y+l+ i  + + ++  ++l++l+   + g+ 
  gi|13542199|ref|NP_111887.1|  53 DISYAQFLSPgVVAMQPFIAGSI-GGSMLWSDRRWGMFEQLIVGPFHRIDYLLGIIYVSIIFSVGGAFLMFLVsyaITGFL 132
                                   56899999997777777766666.6668**************************876666666555666666533344446 PP

               ABC2_membrane_3 233 ipfg.nlglllllfllfglayialgyllsslfknsetaqilifivilllsgffgglfpled.lpsalkwifsiiPffapgl 311
                                   ++++ nl+ + +++++ ++++++++++ls+++++  t ++++++v+++l +++ +++p+++  p +l+++++++P++++ +
  gi|13542199|ref|NP_111887.1| 133 VSYDiNLLMIAVVLIVSSILFTSIFLVLSVFIRTIQTYNTVTMFVFFILDFASSAFYPINSrTPLGLRIVSYMNPLTYIVD 213
                                   77778999999***********************************************998899***************** PP

               ABC2_membrane_3 312 gllrlitgdplweillsliilalfavvylllal 344
                                   +  +++++  +++  +sl+i ++++ +++l+al
  gi|13542199|ref|NP_111887.1| 214 AVRNMMFYKIGMQDYISLLIVVVLSGFFFLIAL 246
                                   ******877555666666666666666777765 PP

>> ABC2_membrane_2  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7  23.7   1.4e-07   0.00084      85     286 ..      68     252 ..      39     254 .] 0.79

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.4e-07
               ABC2_membrane_2  85 ipviaalfgadaiagEkergTlkllLskPvsRdeillgKfigglaiglaiavallatvllalaiilalgivlaledllllv 165
                                    p+ia  +g  ++  ++  g  ++l   P  R ++llg +  +      i+ +++ ++l++l+  ++ g  ++++ +ll++
  gi|13542199|ref|NP_111887.1|  68 QPFIAGSIGGSMLWSDRRWGMFEQLIVGPFHRIDYLLGIIYVS------IIFSVGGAFLMFLVSYAITGFLVSYDINLLMI 142
                                   59999999****************************9955444......44677777777777777777777777777777 PP

               ABC2_membrane_2 166 vasvlllllvvflalglllSsvarssreaaalalglfvvlailvpivlygvaellagpavpqeindflsllsptsayntll 246
                                   ++++++  ++ f++++l+lS+++r+ ++  ++  ++f++l ++++ +      + +  ++     + l+++s+ ++ ++++
  gi|13542199|ref|NP_111887.1| 143 AVVLIVSSIL-FTSIFLVLSVFIRTIQTYNTVTMFVFFILDFASSAFY-----PINSRTP-----LGLRIVSYMNPLTYIV 212
                                   7777777766.79***************************99999998.....4444555.....5667777777777777 PP

               ABC2_membrane_2 247 neilagsdlnalgstatnllilllllavllvlgyvlFkrk 286
                                   +++ +    +  +++  +lli+++l   ++ +++v++ r+
  gi|13542199|ref|NP_111887.1| 213 DAVRNMMFYKIGMQDYISLLIVVVLSGFFFLIALVSYGRA 252
                                   7777777544357778888888888888999999999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1195  (0.0666518); 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:                         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 0.34s 00:00:00.90 Elapsed: 00:00:00.51
# Mc/sec: 1494.55
//
Query:       gi|13542200|ref|NP_111888.1|  [L=214]
Description: phosphoribosyltransferase [Thermoplasma volcanium GSS1]
Scores for complete 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   56.7   0.1    5.1e-15   55.3   0.1    1.7  1  Pribosyltran  Phosphoribosyl transferase domain
    0.00066   19.2   0.1    0.00076   19.0   0.1    1.3  1  UPRTase       Uracil phosphoribosyltransferase
     0.0026   17.3   0.0      0.018   14.6   0.0    2.0  2  PRTase_2      Phosphoribosyl transferase


Domain annotation for each model (and alignments):
>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.3   0.1   8.5e-19   5.1e-15      16     158 ..      12     193 ..       5     194 .. 0.92

  Alignments for each domain:
  == domain 1  score: 55.3 bits;  conditional E-value: 8.5e-19
                                   EETTEEEEEE--GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE......................... CS
                  Pribosyltran  16 arlaaeileeyngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdes................. 79 
                                   ++la++i +     + +v giargG+ +a++++  +++pl+ + ++k  ++  ee+a+g+++e                  
  gi|13542200|ref|NP_111888.1|  12 KQLAKKITNL--SGKCTVTGIARGGIAVAYQVSASIGLPLTTIIVKKIGHPADEEFAIGAVAEGpepyvykgeyalsvepa 90 
                                   5555555555..555799********************************************99***************** PP

                                   .......................EE----TTSEEEEE-SEESSSHHHHHHHHHHHCC-BSEEEEEEEEE-HHHHHHHHHH- CS
                  Pribosyltran  80 .......................rlledpagkkVliVDDildtGgTllaalelLkekgpeevriavlvdkpateeevdkna 137
                                                          +    +    V++VDD+++tG++++ a++ Lk    + +++a++v   + +  v+ + 
  gi|13542200|ref|NP_111888.1|  91 ifeafaaekkkevnsvrrilgqeNSVFYKNWDCVILVDDGVATGSSMIGAIRSLKLNVSKNIIAAAPVFSEEAYVAVRSEG 171
                                   *********************9888888888999*********************************************** PP

                                   TTS......EEEEEEE-SEE-T CS
                  Pribosyltran 138 krvfsls.pdnfvavvgfelds 158
                                   +++  ++ p +f+av +f+ d+
  gi|13542200|ref|NP_111888.1| 172 VSIAYVIiPFDFEAVSEFYRDF 193
                                   ***9999999999999999887 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.1   1.3e-07   0.00076     122     170 ..     122     168 ..      10     184 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.3e-07
                       UPRTase 122 rtvlllDpviaTGgsaaaaiqlLkergvgeekIlvlsvlaseegvkrla 170
                                   + v+l+D  +aTG+s++ ai+ Lk  +v +++I+ ++ + see+  ++ 
  gi|13542200|ref|NP_111888.1| 122 DCVILVDDGVATGSSMIGAIRSLKL-NV-SKNIIAAAPVFSEEAYVAVR 168
                                   34*********************99.66.58899888888888766555 PP

>> PRTase_2  Phosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0     0.067     4e+02      34      75 ..       9      45 ..       5      57 .. 0.83
   2 !   14.6   0.0     3e-06     0.018     112     151 ..     112     151 ..      81     163 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.067
                      PRTase_2 34 eagaaLaellaeakkeelpepvlvigfAEtAtaLghgvadal 75
                                  eag++La++++     +l+++++v g+A   +a++  v +++
  gi|13542200|ref|NP_111888.1|  9 EAGKQLAKKIT-----NLSGKCTVTGIARGGIAVAYQVSASI 45
                                  57888888888.....79999999***999999998887665 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 3e-06
                      PRTase_2 112 aedeellaaakelvLvDDEistGktalnliralqeklprk 151
                                   +e++ + ++ + ++LvDD ++tG++++  ir+l+ ++ ++
  gi|13542200|ref|NP_111888.1| 112 QENSVFYKNWDCVILVDDGVATGSSMIGAIRSLKLNVSKN 151
                                   555666677799********************98776654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       348  (0.0194099); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1381.76
//
Query:       gi|13542201|ref|NP_111889.1|  [L=123]
Description: hypothetical protein TVN1370 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-26   92.7   0.2    2.9e-26   92.5   0.2    1.1  1  DUF488    Protein of unknown function, DUF488
  ------ inclusion threshold ------
      0.076   12.6   0.5       0.11   12.0   0.1    1.6  2  DUF3884   Protein of unknown function (DUF3884)


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 !   92.5   0.2   3.2e-30   2.9e-26       1     119 [.       3     106 ..       3     109 .. 0.94

  Alignments for each domain:
  == domain 1  score: 92.5 bits;  conditional E-value: 3.2e-30
                        DUF488   1 slervyd.llkkdgvrvlvDVRlwPrSrnpgfskealkedlkeagiaYvwlkelgpsrelrkwfkhdp.rweefferYaae 79 
                                   s++rvy+    +dg+rvlv+ RlwPr    g++ke++++d         w k+++ps+ lrkwf+hd+ +w+ef+erY +e
  gi|13542201|ref|NP_111889.1|   3 SIKRVYEnRTYDDGYRVLVE-RLWPR----GITKERAALDA--------WYKDIAPSDSLRKWFSHDErKWDEFKERYMDE 70 
                                   69******************.*****....***********........*******************88*********** PP

                        DUF488  80 leskeaakealeelkelakkg.vaLlcaekdperchrvvla 119
                                   l  +    +ale+l+e a+++ v+L+ +++ +  +++ vl+
  gi|13542201|ref|NP_111889.1|  71 LCGN----KALEKLVEIASQTnVTLIISSRSTY-NNAEVLK 106
                                   **96....89******************99887.7777776 PP

>> DUF3884  Protein of unknown function (DUF3884)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   1.3e-05      0.11      32      55 ..      47      70 ..      29      88 .. 0.79
   2 ?   -3.8   0.0       1.1   9.9e+03      44      51 ..     111     118 ..     109     118 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.3e-05
                       DUF3884 32 ttgdeWiChSdlekeeFkkkFlel 55
                                   + + W  h + +++eFk+++++ 
  gi|13542201|ref|NP_111889.1| 47 DSLRKWFSHDERKWDEFKERYMDE 70
                                  56789***************9875 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 1.1
                       DUF3884  44 ekeeFkkk 51 
                                   + +eFk++
  gi|13542201|ref|NP_111889.1| 111 NYDEFKRR 118
                                   67899975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       822  (0.0458475); expected 358.6 (0.02)
Passed bias filter:                      534  (0.0297841); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 764.91
//
Query:       gi|13542202|ref|NP_111890.1|  [L=113]
Description: hypothetical protein TVN1371 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00036   20.0   1.0    0.00044   19.7   1.0    1.1  1  DUF3387          Domain of unknown function (DUF3387)
  ------ inclusion threshold ------
      0.013   15.4   1.8      0.024   14.6   1.8    1.4  1  DUF3900          Protein of unknown function (DUF3900)
      0.018   14.8   0.2      0.022   14.5   0.2    1.2  1  PduV-EutP        Ethanolamine utilisation - propanediol utili
      0.018   15.1   3.2      0.019   14.9   2.1    1.7  1  DUF1160          Protein of unknown function (DUF1160)
      0.026   14.8   1.2      0.033   14.4   0.1    1.8  2  A_thal_3526      Plant protein 1589 of unknown function (A_th
      0.032   14.0   2.6      0.042   13.7   2.6    1.2  1  CdvA             CdvA-like coiled-coil domain
      0.039   14.2   2.3      0.055   13.7   0.7    2.0  2  SRP54_N          SRP54-type protein, helical bundle domain
      0.044   14.2   0.9       0.52   10.7   0.8    2.2  1  EnY2             Transcription factor e(y)2
      0.046   13.8   0.2       0.06   13.5   0.2    1.1  1  MGDG_synth       Monogalactosyldiacylglycerol (MGDG) synthase
       0.05   13.5   0.9      0.087   12.7   0.5    1.7  2  Glycos_trans_3N  Glycosyl transferase family, helical bundle 
       0.05   13.2   0.9      0.084   12.5   0.2    1.6  2  MIF4G            MIF4G domain
      0.067   12.1   2.3      0.084   11.8   1.4    1.6  2  B56              Protein phosphatase 2A regulatory B subunit 
        0.2   12.7   2.5       0.26   12.3   1.0    1.9  2  RNase_J_C        Ribonuclease J C-terminal domain
       0.21   11.9   2.5       0.58   10.5   0.6    2.2  2  PqqD             Coenzyme PQQ synthesis protein D (PqqD)


Domain annotation for each model (and alignments):
>> DUF3387  Domain of unknown function (DUF3387)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   1.0   3.5e-07   0.00044     153     229 ..       4      80 ..       3      93 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 3.5e-07
                       DUF3387 153 iLseefleevkkmkeknlavelLkklLadeikarsrkNlvkskkFserLeelikkYnnraltsaevieeLielakei 229
                                   +L++ f e +k m++++l +e+ + +++d ik++ +k + + ++ ++ L ++i++++   +++ + ++ + ++  +i
  gi|13542202|ref|NP_111890.1|   4 DLEKYFKEFMKIMPTEDLYFEAVRDIVKDLIKEYIKKKMNEDETIRKDLARVIEEFMDARIKEYDAVASMAKIVAKI 80 
                                   577778888999*******************************************************9999887665 PP

>> DUF3900  Protein of unknown function (DUF3900)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   1.8   1.9e-05     0.024     201     251 ..       7      57 ..       4      60 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.9e-05
                       DUF3900 201 ryfedflkfveyekslpeivkeqvlelvqehveetyeeeseereqeeeale 251
                                   +yf +f+k +  e+   e v++ v++l++e+++++ +e+++ r++  + +e
  gi|13542202|ref|NP_111890.1|   7 KYFKEFMKIMPTEDLYFEAVRDIVKDLIKEYIKKKMNEDETIRKDLARVIE 57 
                                   8***************************************99999888887 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.2   1.7e-05     0.022      46      98 ..      58     111 ..      29     112 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.7e-05
                     PduV-EutP  46 eylenr.klysalivtsaeadvialvqdateeesvfppgfasvfnkeviGiitk 98 
                                   e+++ r k y a+++++  +  i+lv + ++ ++   + f ++f+ke+ Gii k
  gi|13542202|ref|NP_111890.1|  58 EFMDARiKEYDAVASMAKIVAKIGLVSAPDDVKEQVYNDFITMFQKEIEGIIKK 111
                                   67776634699999999999***********999999***************88 PP

>> DUF1160  Protein of unknown function (DUF1160)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   2.1   1.5e-05     0.019      17      59 ..      29      73 ..       8      96 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.5e-05
                       DUF1160 17 vvntelkkylkele.rdetfrkklvkvlkmFiereieved.iyei 59
                                  +v+  +k+y+k+   +det+rk l +v++ F++  i+  d ++++
  gi|13542202|ref|NP_111890.1| 29 IVKDLIKEYIKKKMnEDETIRKDLARVIEEFMDARIKEYDaVASM 73
                                  688899999976444*********************864413333 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 ?   -3.4   0.1       9.4   1.2e+04      47      51 ..       8      12 ..       4      15 .. 0.49
   2 ?   14.4   0.1   2.5e-05     0.033       1      20 [.      30      49 ..      30      62 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 9.4
                   A_thal_3526 47 FFkaY 51
                                  +Fk++
  gi|13542202|ref|NP_111890.1|  8 YFKEF 12
                                  34443 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 2.5e-05
                   A_thal_3526  1 VqnlIErCLqlymskeevvr 20
                                  V++lI++++++ m+ +e++r
  gi|13542202|ref|NP_111890.1| 30 VKDLIKEYIKKKMNEDETIR 49
                                  89****************98 PP

>> CdvA  CdvA-like coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   2.6   3.2e-05     0.042      21      96 ..      36     110 ..      19     112 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.2e-05
                          CdvA  21 eeikekleealkklkekakelkeklkkrlkeledqikslekalanlkisyasGEidEeaYksaieairellesale 96 
                                   e ik+k++e  +  k+ a  + e +++r+ke  d ++s++k +a++ +  a  +++E+ Y+  i+++++++e + +
  gi|13542202|ref|NP_111890.1|  36 EYIKKKMNEDETIRKDLARVIEEFMDARIKEY-DAVASMAKIVAKIGLVSAPDDVKEQVYNDFITMFQKEIEGIIK 110
                                   568999999999999999999999*******7.57999*********************************98765 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 ?   13.7   0.7   4.3e-05     0.055      20      69 ..       2      50 ..       1      56 [. 0.93
   2 ?   -1.0   0.0       1.6   2.1e+03      60      69 ..      75      91 ..      52      96 .. 0.48

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.3e-05
                                  HHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHCTTSS-HHHHHHH CS
                       SRP54_N 20 eedleealkeleeaLleaDVgvkvvkklienvkkkavgekklkpkqqvkk 69
                                  ++dle   ke  +++ + D+ +++v+++++++ k+ ++ kk+++ ++++k
  gi|13542202|ref|NP_111890.1|  2 DDDLEKYFKEFMKIMPTEDLYFEAVRDIVKDLIKEYIK-KKMNEDETIRK 50
                                  6899******************************9999.99*****9998 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.6
                                  S.......S-HHHHHHH CS
                       SRP54_N 60 k.......lkpkqqvkk 69
                                  k       ++ +++vk+
  gi|13542202|ref|NP_111890.1| 75 KivakiglVSAPDDVKE 91
                                  02222333445555555 PP

>> EnY2  Transcription factor e(y)2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.8   0.00041      0.52      32      78 ..      28      95 ..      18     101 .. 0.54

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00041
                                  HHHHHHHHHHHHH........................HTSS.CHHHHHHHHHHHHHHHS-HHHHHHHHH CS
                          EnY2 32 devkelckeiire......................kgleeevsveelveeitpkaralVPdevkkellq 78
                                  d vk+l+ke+i++                      + +e +  v ++ + +++ +  + Pd+vk+++++
  gi|13542202|ref|NP_111890.1| 28 DIVKDLIKEYIKKkmnedetirkdlarvieefmdaRIKEYD-AVASMAKIVAKIGLVSAPDDVKEQVYN 95
                                  55666666666653333333333333333333321333322.477777777777777777777777776 PP

>> MGDG_synth  Monogalactosyldiacylglycerol (MGDG) synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.2   4.7e-05      0.06       5      87 ..      31     111 ..      27     113 .] 0.89

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.7e-05
                                   HHHHHHHHHHHHGGGEEEEEEE---------------------------------------------------HHHHHHHH CS
                    MGDG_synth   5 aealkealkaefgdeyqvlvkdllkelnpfllkavlksYlflvkvsalyrllyygteekiqkksilaklatflakelaall 85 
                                    + +ke++k++  +e +++ kdl   +++f   a +k Y    +++++  ++   +++++ k++ ++ + t++ ke++ ++
  gi|13542202|ref|NP_111890.1|  31 KDLIKEYIKKK-MNEDETIRKDLARVIEEF-MDARIKEYDAVASMAKIVAKIGLVSAPDDVKEQVYNDFITMFQKEIEGII 109
                                   57889999887.578888999*********.7777888989*************************************999 PP

                                   HH CS
                    MGDG_synth  86 ee 87 
                                   ++
  gi|13542202|ref|NP_111890.1| 110 KK 111
                                   97 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 ?   -3.5   0.0       7.6   9.8e+03      19      28 ..      23      32 ..      18      34 .. 0.59
   2 ?   12.7   0.5   6.8e-05     0.087       1      35 [.      35      69 ..      35      80 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 7.6
                                  HHHHHHHHTT CS
               Glycos_trans_3N 19 rfaihgilkg 28
                                   +a+++i+k+
  gi|13542202|ref|NP_111890.1| 23 FEAVRDIVKD 32
                                  4566666664 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 6.8e-05
                                  HHHHHHHHTT.---HHHHHHHHHHHHTTSS-HHHH CS
               Glycos_trans_3N  1 kdiikklrdgeeLtaeeirfaihgilkgevtdaqi 35
                                  k++ikk+++  e  + +++ +i+++++ +++++ +
  gi|13542202|ref|NP_111890.1| 35 KEYIKKKMNEDETIRKDLARVIEEFMDARIKEYDA 69
                                  69****************************99866 PP

>> MIF4G  MIF4G domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.92   1.2e+03     174     189 ..       4      19 ..       2      28 .. 0.80
   2 ?   12.5   0.2   6.6e-05     0.084      16      84 ..      30     106 ..      25     112 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.92
                                   HHHHHHHHHHHHHHCC CS
                         MIF4G 174 eldqffkriqkileda 189
                                    l+++fk++ ki+  +
  gi|13542202|ref|NP_111890.1|   4 DLEKYFKEFMKIMPTE 19 
                                   6899999999999875 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 6.6e-05
                                   HHHHHHHHHHHHHCS...CHHHHHHHHHHHHHHHHHCGGGHHHHHHHHHHHHHHSH.....HHHHHHHHHHHHHHHH CS
                         MIF4G  16 fevlikqllklamdd...dknelkevielifekaveepsfsplyarlcgklnsrfq.....qnFrikllnklqeefe 84 
                                   +++lik+ +k++m++       l  vie +++  ++e++ +   a++++k+          + + + +++++q+e+e
  gi|13542202|ref|NP_111890.1|  30 VKDLIKEYIKKKMNEdetIRKDLARVIEEFMDARIKEYDAVASMAKIVAKIGLVSApddvkEQVYNDFITMFQKEIE 106
                                   6899***********666556777888899*******************9987766744445555555555555544 PP

>> B56  Protein phosphatase 2A regulatory B subunit (B56 family)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   1.4   6.5e-05     0.084     157     209 ..      27      80 ..       5      97 .. 0.77
   2 ?   -0.6   0.0       0.4   5.1e+02      63      80 ..      88     105 ..      72     106 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 6.5e-05
                           B56 157 Rdylktilhriygkfldlrsfirkainniflrfiyet.erhngiaelLeilgsi 209
                                   Rd +k++++++++k ++  + irk++++++ +f++   +++  +a + +i+ +i
  gi|13542202|ref|NP_111890.1|  27 RDIVKDLIKEYIKKKMNEDETIRKDLARVIEEFMDARiKEYDAVASMAKIVAKI 80 
                                   9*********************************94414555677777776665 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.4
                           B56  63 ilteevyeeivkmisaNl 80 
                                    ++e+vy++++ m+++ +
  gi|13542202|ref|NP_111890.1|  88 DVKEQVYNDFITMFQKEI 105
                                   578999999999999865 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 ?   12.3   1.0   0.00021      0.26      19      61 ..      23      65 ..      10      67 .. 0.90
   2 ?   -1.3   0.0       3.8   4.8e+03      19      28 ..      98     107 ..      84     113 .] 0.46

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00021
                     RNase_J_C 19 ieeakkvvretieealeekesdwnelkrkirealkkflykktk 61
                                  +e+++++v++ i+e++++k ++ +++++++ + +++f+  ++k
  gi|13542202|ref|NP_111890.1| 23 FEAVRDIVKDLIKEYIKKKMNEDETIRKDLARVIEEFMDARIK 65
                                  6899*********************************988776 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 3.8
                     RNase_J_C  19 ieeakkvvre 28 
                                   i   +k ++ 
  gi|13542202|ref|NP_111890.1|  98 ITMFQKEIEG 107
                                   3333333333 PP

>> PqqD  Coenzyme PQQ synthesis protein D (PqqD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.6   0.00045      0.58      32      64 ..      26      62 ..      19      64 .. 0.85
   2 ?    0.7   0.0      0.51   6.5e+02      31      59 ..      72     102 ..      65     104 .. 0.59

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00045
                                  HHHHHHHHHHHC.T--...HHHHHHHHHHHHHHHHCT CS
                          PqqD 32 veeivaalaeey.dvd...eeeaeadvlafldqLrek 64
                                  v++iv++l +ey        e++++d+++ +++  ++
  gi|13542202|ref|NP_111890.1| 26 VRDIVKDLIKEYiKKKmneDETIRKDLARVIEEFMDA 62
                                  8999999999998887887799*********998766 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.51
                                   -HHHHHHHHHHHC.T--.HHHHHHHHHHHHH CS
                          PqqD  31 sveeivaalaeey.dvd.eeeaeadvlafld 59 
                                   s+++iva++      +d +e++++d + +++
  gi|13542202|ref|NP_111890.1|  72 SMAKIVAKIGLVSaPDDvKEQVYNDFITMFQ 102
                                   4556666544333222347888888887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1597  (0.0890736); expected 358.6 (0.02)
Passed bias filter:                      760  (0.0423894); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.52u 0.33s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 679.17
//
Query:       gi|13542203|ref|NP_111891.1|  [L=464]
Description: DNA polymerase II small subunit [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.9e-13   49.7   0.0    4.6e-13   49.0   0.0    1.4  1  DNA_pol_E_B      DNA polymerase alpha/epsilon subunit B
    4.8e-11   43.5   0.2    8.5e-11   42.7   0.2    1.4  1  Metallophos      Calcineurin-like phosphoesterase
    1.3e-07   32.0   0.0    2.8e-07   30.9   0.0    1.5  1  Metallophos_2    Calcineurin-like phosphoesterase superfamily
     0.0054   16.7   1.0      0.011   15.7   1.0    1.5  1  tRNA_anti-codon  OB-fold nucleic acid binding domain
  ------ inclusion threshold ------
      0.048   13.7   0.1         15    5.6   0.0    3.6  4  DUF3969          Protein of unknown function (DUF3969)


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 !   49.0   0.0   1.3e-16   4.6e-13      16     208 ..     226     409 ..     208     412 .. 0.79

  Alignments for each domain:
  == domain 1  score: 49.0 bits;  conditional E-value: 1.3e-16
                                   -HHHHHHHHHHH.HTT--SEEEEES-SSBTTSHHHHHT---S--SSHHHHHHHHTHHHHTTS-TTSEEEEE--TTBTT-S- CS
                   DNA_pol_E_B  16 leaLrkiLqgyapeesppdvlilaGnfvdaahkaiasskvstdekkenfdalalllsilesllekttvvlvPgpnDpanst 96 
                                   ++ + k++++ ++   + + lil G  vd      ++++  + e  +  d  ++l s+++++ e +tv+++Pg  D +   
  gi|13542203|ref|NP_111891.1| 226 FQDMIKWFESSDDTSLSTKYLILSGDVVDGIGVYPGQEN--DLELLNPLDQYEALASFVSQIPEDITVFIMPGNHDTVRL- 303
                                   445555555555666667778888888874444443333..34666777788899999********************99. PP

                                   SBSB----TTTTT--TTT...EEE--BSEEEEETTEEEEE--S-HHHH---EEESHHHHHS-HHHHHHHHHHHHTBS---S CS
                   DNA_pol_E_B  97 vlPqqPlprlllsrikrvfkelklvtNPsrielnsvevvltsddivkdlkreslkesntdverlrklvktildqrhlaPla 177
                                   + Pq+ +p+++ +   +   ++++++NP+ ++l++  v+++ +  ++d+ + +   +    +   k++++il  rhl+P +
  gi|13542203|ref|NP_111891.1| 304 SEPQPVFPEKIRKMFPS---NAVFLPNPYNLKLEGKNVLVYHGMSLNDMIELIPGANY---DSIGKAIEAILVRRHLSPRY 378
                                   *******9984444444...69***************************998887777...8******************* PP

                                   S--B-GGGGGGGB-GGG---SEEE---SS-- CS
                   DNA_pol_E_B 178 ptlrpvswdkddalvleplPdvlvlpdelpe 208
                                       p      d  v+e++Pd+++ +  +++
  gi|13542203|ref|NP_111891.1| 379 GGNTPLIPSSVDYHVIEEVPDIFITGHIHSH 409
                                   *999999999999999********9985555 PP

>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.7   0.2   2.4e-14   8.5e-11       6     203 ..     211     408 ..     208     423 .. 0.59

  Alignments for each domain:
  == domain 1  score: 42.7 bits;  conditional E-value: 2.4e-14
                                   EESBTB...TTCCTHHHHHHHHHHHHHHH.TTESEEEEESTSSSSS..............HHHHHHHHHHHHHHHH..... CS
                   Metallophos   6 igDlHl...algggqlddllkllddllre.ekpdlvllaGDlvdrg..............dlekellellaalvky..... 63 
                                   ++D+H+     +   ++d +k+++   +      +++l GD+vd+               +           l +y     
  gi|13542203|ref|NP_111891.1| 211 LSDIHIgskTFRKNEFQDMIKWFESSDDTsLSTKYLILSGDVVDGIgvypgqendlellnP-----------LDQYealas 280
                                   89****777555677777777774442224344667779******9899855444444443...........444455566 PP

                                   .......TSEEEEEC-TTSCHHHHHHHHHHHHHHH.HHHHEHHHCEEETSEEEEEETTEEEEEEEESECEEETHHHHHHHH CS
                   Metallophos  64 .......pipvylllGNHegfeeellnkygylgif.sepwrsdaevfnnlplaslgsgslkvlllhGgspellvsldklgs 136
                                          +i v++++GNH++    l+++++ + +   + + s+a ++ n++   l ++  +vl++hG s ++      +  
  gi|13542203|ref|NP_111891.1| 281 fvsqipeDITVFIMPGNHDT--VRLSEPQPVFPEKiRKMFPSNAVFLPNPYNLKLEGK--NVLVYHGMSLND------M-- 349
                                   6666788************2..233333333333325555555666666666666666..999999993222......1.. PP

                                   HHHSCHHHHCCHHHHHH...HHHHTTCSEEEEEESSESSCSSSCSCCHHHHHHH.HHHTTESEEEEESSSS CS
                   Metallophos 137 lnleleapepgdewlkd...lekrekadwvivlgHsplyrgsgylfgdealedl.lkkygvdlvisGHtHv 203
                                               e++     ++  +  + ++v  H  +  ++g++   ++  d+   +  +d+ i GH+H 
  gi|13542203|ref|NP_111891.1| 350 -----------IELIPGanyDSIGKAIEAILVRRHLSPR-YGGNTPLIPSSVDYhVIEEVPDIFITGHIHS 408
                                   ...........1222222323333355556666677777.3444433333334436666688888888885 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 !   30.9   0.0   7.8e-11   2.8e-07       3     143 ..     208     422 ..     207     437 .. 0.80

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 7.8e-11
                 Metallophos_2   3 laiiSDlH........snldaleavlealke..vgvdaiihaGD..........leeeep............evleellel 51 
                                   +a +SD+H        ++++   +++e  ++   +  ++i++GD                            e+l+ + ++
  gi|13542203|ref|NP_111891.1| 208 VASLSDIHigsktfrkNEFQDMIKWFESSDDtsLSTKYLILSGDvvdgigvypgQ----EndlellnpldqyEALASFVSQ 284
                                   5779******8888887788888887776662245799******66666654440....1444444444444566666665 PP

                 Metallophos_2  52 a....pvlaVrGNnD.......eev.veedvlreaaelgtdlpeeaelelagekvlliHgdpl.................. 102
                                         v + +GN+D       +   + e++ + +   +  lp+  +l+l+g++vl++Hg  l                  
  gi|13542203|ref|NP_111891.1| 285 IpediTVFIMPGNHDtvrlsepQ-PvFPEKIRKMFPSNAVFLPNPYNLKLEGKNVLVYHGMSLndmielipganydsigka 364
                                   5888899999*****99998644.358888999999999999******************987****************** PP

                 Metallophos_2 103 ...................gvkdalaellkeaeegsdvvvcGHtHvpevekeggvlvvnP 143
                                                        + ++++ + e  e+ d+++ GH+H +++ + +gv++vn 
  gi|13542203|ref|NP_111891.1| 365 ieailvrrhlspryggntpLIPSSVDYHVIE--EVPDIFITGHIHSHYIGNYKGVRYVNS 422
                                   ******9999999998887777778877777..9999*********************95 PP

>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   1.0   3.1e-06     0.011       1      73 [.     119     188 ..     119     190 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 3.1e-06
                                   EEEEEEEEEEEEEEETTEEEEEEEETTEEEEEEEETHHHHHHHTTS-TTSEEEEEEEEEECTTSSEEEEEEEE CS
               tRNA_anti-codon   1 VtvaGrvtsisdrsggkvifidlrDgtgriqvvlfreeatklaenlkeGdvvrvtGrvkrrpggelelkveei 73 
                                   V+v G+v+ +s   ++++  + ++D  ++iqv++ + +   ++e + e+ v+++ G v+++ +  + + ++ei
  gi|13542203|ref|NP_111891.1| 119 VKVIGMVSEVS-MTKNGHKRVLIEDLDDSIQVFILK-DRGIINEVILEDEVIGIIGNVSSSSKD-PVIFADEI 188
                                   89********9.99999*******************.***********************9887.88888876 PP

>> DUF3969  Protein of unknown function (DUF3969)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.18   6.6e+02      70      96 ..      21      47 ..       6      54 .. 0.75
   2 ?    2.4   0.0     0.044   1.6e+02      51      88 ..      50      89 ..      42     103 .. 0.75
   3 ?   -1.1   0.0      0.54   1.9e+03      35      59 ..     149     173 ..     115     176 .. 0.80
   4 ?    5.6   0.0    0.0043        15      56      84 ..     339     368 ..     328     382 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.18
                       DUF3969 70 iPeeLedsIdeielkclevLeelskee 96
                                   P +Le++I++  ++++e L   s+ +
  gi|13542203|ref|NP_111891.1| 21 SPSALEKIIKYSSSSLIEDLVKNSDGY 47
                                  477888888888888888887766655 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.044
                       DUF3969 51 delveiihk.gmeLEDvesliPe.eLedsIdeielkclev 88
                                  d +ve+  k   e+ D+e  +Pe +++ s+++ +   +++
  gi|13542203|ref|NP_111891.1| 50 DRIVEAALKpKREMNDFEVYLPEvRFNSSVEDFRKMFVSK 89
                                  5555544331469******************987666555 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.54
                       DUF3969  35 lFslemlelieelelsdelveiihk 59 
                                   +F l+ + +i+e+ l+de+  ii +
  gi|13542203|ref|NP_111891.1| 149 VFILKDRGIINEVILEDEVIGIIGN 173
                                   5888888899999999999999976 PP

  == domain 4  score: 5.6 bits;  conditional E-value: 0.0043
                       DUF3969  56 iihkgmeLEDvesliPeeLedsIde.ielk 84 
                                   ++ +gm+L D+ +liP + +dsI + ie  
  gi|13542203|ref|NP_111891.1| 339 LVYHGMSLNDMIELIPGANYDSIGKaIEAI 368
                                   7899*************9888885425555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (464 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); 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: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 2899.86
//
Query:       gi|13542204|ref|NP_111892.1|  [L=285]
Description: DMT family permease [Thermoplasma volcanium GSS1]
Scores for complete 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-37  126.5  49.0    9.9e-19   67.9  21.3    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 !   64.8  19.7     5e-22   8.9e-18       6     136 ..       9     137 ..       6     138 .. 0.92
   2 !   67.9  21.3   5.5e-23   9.9e-19       5     135 ..     150     281 ..     147     283 .. 0.98

  Alignments for each domain:
  == domain 1  score: 64.8 bits;  conditional E-value: 5e-22
                          EamA   6 lallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegklaklslkdwllllllgllgtvlafllffyal 86 
                                   l++  a+fwa+++v+ k ++++  + +++ +r l a+i+ ++i   + + + k +l + l +++l+ l+++ +f+l+f + 
  gi|13542204|ref|NP_111892.1|   9 LFFFMAFFWALNYVMVKFAYAYDLSSSILLMRVLYASIFSSLIFIRQIKLP-KSPL-EHLKVFILANLNITGFFSLWFFGE 87 
                                   77899*********************************9987776666666.5555.55888******************* PP

                          EamA  87 kktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvllil 136
                                   + +sa++ s++++  P++++ +s+l+lg +++ ++ lg++l+++G+++i+
  gi|13542204|ref|NP_111892.1|  88 TGVSAAVTSIVIYSYPILATAFSYLFLGDRFGAMKTLGLILGFAGLVIIF 137
                                   ***********************************************997 PP

  == domain 2  score: 67.9 bits;  conditional E-value: 5.5e-23
                          EamA   5 llallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegkl.aklslkdwllllllgllgtvlafllffy 84 
                                   +++l+aa++wai++v+ ++ l  +++  l+++++l a  ++l+i+l+++g +   l lk  l+++++g +gt++a+++++y
  gi|13542204|ref|NP_111892.1| 150 IMLLVAAISWAIGTVFYRKYLLGYDSAGLNTLQLLYALPVVLLISLFTGGINiGLLQLKFNLIMIYMGSFGTAIAYFIYLY 230
                                   899**********************************************99999999************************ PP

                          EamA  85 alkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvlli 135
                                   + +k ++s +s +++l+P+++++l+++ll+e+++ ++++g++++ +G++l 
  gi|13542204|ref|NP_111892.1| 231 LYRKYKVSSISAYFFLVPAISVVLAAVLLKEPISALTIAGFAVMSAGIFLS 281
                                   ************************************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       852  (0.0475208); expected 358.6 (0.02)
Passed bias filter:                      195  (0.0108762); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
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 0.30s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 1874.37
//
Query:       gi|13542205|ref|NP_111893.1|  [L=395]
Description: NAD-dependent aldehyde dehydrogenase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.8e-16   58.6   0.3    8.1e-10   37.8   0.0    3.0  2  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 !   14.6   1.0   4.9e-07    0.0088      59     190 ..      51     167 ..      47     172 .. 0.78
   2 !   37.8   0.0   4.5e-14   8.1e-10     272     430 ..     234     381 ..     204     388 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4.9e-07
                                   HHHHHHHHTHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHSEEEEEECTTEEEEEEEEE-SEEEEEE-SSSC CS
                        Aldedh  59 kaadlleerkeelaeletletGkplaearaeveeaidvlryyaelaeklegevlpssegklalvrrePlGvvgaItPWNfP 139
                                   ++ ++l ++ ++++  ++ etGkp++  r+e+ ++i+ ++ + +  e+l++ v +              Gv ++    N P
  gi|13542205|ref|NP_111893.1|  51 RISNYLDRNVDRISIEIASETGKPFKYIREEILQTIREIKSI-RIPEDLHEFV-K-------------PGVSALNYNCNDP 116
                                   566677777777777777777777777777777766666543.3444444322.2.............37888888889** PP

                                   CHHHHHHHHHHHHTT-EEEEEE-TTSHHHHHHHHHHHHHTTS-TTSEEE-- CS
                        Aldedh 140 lllaawklapalaaGNtvvlKPaeetplsalllaelfeeaglPkgvlnvvt 190
                                   +l +   l + ++ G  v++   +   +sa +++ ++ e+glP+gv+nv++
  gi|13542205|ref|NP_111893.1| 117 VLSLFVPLFATILQGSPVLVFANPYNFVSAHIIISMLSEIGLPEGVVNVIP 167
                                   *************************************************98 PP

  == domain 2  score: 37.8 bits;  conditional E-value: 4.5e-14
                                   EEEEEEEHHHHHHHHHHHHHHHHT--BS-TTSTT-SB---SSHHHHHHHHHHHHHHHHTTSEEEE-TTE.SB-SSSTTEE- CS
                        Aldedh 272 asrllvqesiydefveklveaakklkvgdpldedtdvGPliseaqlekvekyveeakeegaklllGgereeaglekgyfve 352
                                    + l+v + +++ ++++l+e+++++ vgdp d +td+GP+++ ++l +  ++v + + e    +  g        +g++++
  gi|13542205|ref|NP_111893.1| 234 EQLLVVDRRMFEYVLNRLKEELSRIVVGDPADGATDLGPVTKDEDLMEALSIVGKYRVERLLAMFRG-------VEGNLMK 307
                                   577999***************************************************9998888877.......69***** PP

                                   -EEEES-TTTSHHHHS---SSEEEEEEESSHHHHHHHHHSSSEESEEEEE-SBHHHHHHHHHHS-SSEEEESSSST-- CS
                        Aldedh 353 PtvlanvtpdmriaqeEiFGPVlsvikfkdeeeaieiaNdteyGLaagvftkdleraervaerleaGnvyiNdsttga 430
                                   P ++     d+ +    + +P+++++   ++e+a+++ N+ e +   ++f++d + ++ +  r  + ++ +N+++  +
  gi|13542205|ref|NP_111893.1| 308 PAIILT---DDVVKDPFVHAPLVYLVNSASVEDAVNLINEVE-ADRCALFSDDSKLLKMLYGRTACKEISFNSYMYKD 381
                                   ***993...5555555578*********************98.67899*****9999999999999999999986555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (395 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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 0.35s 00:00:00.95 Elapsed: 00:00:00.53
# Mc/sec: 2247.22
//
Query:       gi|13542206|ref|NP_111894.1|  [L=485]
Description: inosine 5'-monophosphate dehydrogenase [Thermoplasma volcanium GSS1]
Scores for complete 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-147  488.5   5.1   1.1e-146  488.3   5.1    1.0  1  IMPDH            IMP dehydrogenase / GMP reductase domain
      2e-23   82.6   8.5      1e-11   45.1   0.7    3.9  4  CBS              CBS domain
    6.3e-10   38.6   7.3    1.7e-09   37.2   7.0    2.0  2  FMN_dh           FMN-dependent dehydrogenase
    1.1e-09   38.1   3.2    1.6e-05   24.5   4.0    2.5  2  NMO              Nitronate monooxygenase
    1.6e-07   30.8   4.0    1.6e-07   30.8   4.0    1.7  2  Glu_synthase     Conserved region in glutamate synthase
    4.9e-07   29.5   4.0    1.1e-06   28.3   4.0    1.7  1  His_biosynth     Histidine biosynthesis protein
    0.00051   19.4   0.8     0.0035   16.6   1.0    2.0  2  DHO_dh           Dihydroorotate dehydrogenase
    0.00081   18.8   1.0    0.00081   18.8   1.0    2.9  3  ThiG             Thiazole biosynthesis protein ThiG
     0.0033   16.5   0.8      0.011   14.9   0.1    2.1  2  Dus              Dihydrouridine synthase (Dus)
     0.0073   15.6   0.1      0.015   14.6   0.1    1.4  1  Beta_elim_lyase  Beta-eliminating lyase
  ------ inclusion threshold ------
       0.03   13.7   0.7      0.083   12.3   0.2    1.9  2  G3P_antiterm     Glycerol-3-phosphate responsive antiterminat
      0.098   11.8   1.1        2.7    7.1   0.3    2.6  2  DUF561           Protein of unknown function (DUF561)


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 !  488.3   5.1  7.3e-150  1.1e-146       1     345 []      12     467 ..      12     467 .. 0.99

  Alignments for each domain:
  == domain 1  score: 488.3 bits;  conditional E-value: 7.3e-150
                                   E--GGGEEEE---B-S-GGGSB--EESSTTEEESSSEEE-SSTTT-SHHHHHHHHHTTSEEEE-SSS-HHHHHHHHHHHHT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         IMPDH   1 gltfddvllvpaksevlpkevdlktkltkkiklniPlvsaamdtvtesemAialareGgigvihknlsieeqaeevkkvkr 81 
                                   g+tfddvl++p k+ v+pk+vd++++l+++i++++P+vs++mdtvte+ mAia+ar G+ g+ih+n+  e+++e+v++vkr
  gi|13542206|ref|NP_111894.1|  12 GYTFDDVLILPMKTGVEPKNVDVSSRLSRRINVKVPIVSSPMDTVTEEAMAIAMARYGAFGIIHRNQPREKEVEMVRRVKR 92 
                                   79******************************************************************************* PP

                                   S................................................................................ CS
                                   x................................................................................ RF
                         IMPDH  82 s................................................................................ 82 
                                   +                                                                                
  gi|13542206|ref|NP_111894.1|  93 Eetiiirdvytvspetpievartimktkniaglpvlkeeklvgiltkrdlefakqgstvsdvmvknvitapenvdledain 173
                                   ********************************************************************************* PP

                                   ..................................TTSXBXTTSXB-EEEEE-SSTTHHHHHHHHHHTT-SEEEEE-STSSS CS
                                   ..................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         IMPDH  83 ..................................pnaakdekgrllvgaavgvkedalervkalveagvdvlvvdsahghs 129
                                                                     p+a++d++g+l+vgaavg  +  l+r+ +l +ag+d++vvd+ah+ +
  gi|13542206|ref|NP_111894.1| 174 ilhknrieklplvdkdnhlvglitakdiitrqrfPDATRDDEGQLMVGAAVGPFD--LDRAIELERAGADLIVVDTAHADN 252
                                   ******************************************************5..9*********************** PP

                                   HHHHHHHHHHHHHTTTSEEEEEEE-SHHHHHHHHHTT-SEEEE-SS-STTBHHHHHCSB---HHHHHHHHHHHHCTCT-EE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         IMPDH 130 ekvleavkeikkkveeveviaGnvataegakaLieagadavkvGiGpGsiCttrvvagvGvpqltAvaevaeaakkagvpv 210
                                   e+vl+ +k+++k++ +v+++aGn+ata +a++Li++++d+++vGiGpGsiCttr+vagvGvpqltA++evae+ak++g+pv
  gi|13542206|ref|NP_111894.1| 253 ENVLSSIKRMRKEI-SVDIVAGNIATAGAAEDLISCEVDGLRVGIGPGSICTTRIVAGVGVPQLTAISEVAEVAKEYGIPV 332
                                   **************.7***************************************************************** PP

                                   EEES---SHHHHHHHHHTT-SEEEESCCCTTBTTSSSEEEEETTEEEEEEEETTSHHHHHH-SS-TTS-..--SS-SBEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         IMPDH 211 iaDGGikysgdivkAlaaGadavmlGsllagteEspgeviliegrkyKeyrGmgslgamkkgskdryfqkkeklvpeGveg 291
                                   iaDGGi+ysgdivkA+aaGad+vmlGs+lagteEspg+ ++i+grkyK+yrGmgs+ga ++g +dry +  + +++eGveg
  gi|13542206|ref|NP_111894.1| 333 IADGGIRYSGDIVKAIAAGADSVMLGSMLAGTEESPGQEMIINGRKYKAYRGMGSIGALSTGISDRYSKLGNGFIAEGVEG 413
                                   ************************************************************9******886779******** PP

                                   EEE--B-HHHHHHHHHHHHHHHHHHHT-SSHHHHHHH-EEEEE-HHHHHHHS-- CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         IMPDH 292 rvpykgsvkevveqlvgglrsgmgylGaktieelkekakfvritaaglkeshvH 345
                                   +vpy+g+v+ev+ qlvgglr+gmgy+Ga++i +lke+a+fvri+++gl+esh+H
  gi|13542206|ref|NP_111894.1| 414 AVPYRGRVDEVLFQLVGGLRTGMGYVGAENIGKLKERARFVRISSNGLRESHPH 467
                                   *****************************************************9 PP

>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       3.7   5.5e+03      17      32 ..      55      70 ..      41      76 .. 0.67
   2 !   37.9   0.2   1.2e-12   1.8e-09       4      51 ..      96     142 ..      89     145 .. 0.91
   3 !   45.1   0.7   6.7e-15     1e-11       1      53 [.     151     203 ..     151     206 .. 0.93
   4 ?    1.7   0.0      0.24   3.5e+02      12      40 ..     312     337 ..     299     346 .. 0.70

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 3.7
                                  B.HHHHHHH.HHHHTSSE CS
                           CBS 17 t.leealel.mrekgvsr 32
                                  t  eea+ + m++  +++
  gi|13542206|ref|NP_111894.1| 55 TvTEEAMAIaMAR--YGA 70
                                  4368999999966..544 PP

  == domain 2  score: 37.9 bits;  conditional E-value: 1.2e-12
                                   HSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHH CS
                           CBS   4 imtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDl 51 
                                   i  rdv tv+p+t++e a  +m+ k++ +lPV+ +++klvGi+t+rDl
  gi|13542206|ref|NP_111894.1|  96 IIIRDVYTVSPETPIEVARTIMKTKNIAGLPVL-KEEKLVGILTKRDL 142
                                   567899****************8888*******.6777*********8 PP

  == domain 3  score: 45.1 bits;  conditional E-value: 6.7e-15
                                   HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHH CS
                           CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllr 53 
                                   V+d+m ++v+t+p++ +le+a++++ ++++  lP Vd+d++lvG++t +D++ 
  gi|13542206|ref|NP_111894.1| 151 VSDVMVKNVITAPENVDLEDAINILHKNRIEKLPLVDKDNHLVGLITAKDIIT 203
                                   89***********************5555**********************96 PP

  == domain 4  score: 1.7 bits;  conditional E-value: 0.24
                                   EETTSBHHHHHHHHHHHTSSEEEEEETTT CS
                           CBS  12 vppdttleealelmrekgvsrlPVVdedg 40 
                                   vp  t ++e++e    k++ ++PV+ + g
  gi|13542206|ref|NP_111894.1| 312 VPQLTAISEVAEVA--KEY-GIPVIADGG 337
                                   55556699999999..669.****95455 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.2   7.0   1.1e-12   1.7e-09     196     302 ..     247     360 ..      43     375 .. 0.86
   2 ?   -2.0   0.0      0.92   1.4e+03     314     343 ..     420     449 ..     415     451 .. 0.89

  Alignments for each domain:
  == domain 1  score: 37.2 bits;  conditional E-value: 1.1e-12
                                   CCHB-TC--HHHHHHHHHHHSSEEEEEEE-SHHHHHHHHHTTESEEEE--GGG.....TSSTT-.--HHHCHHHHHHHH.. CS
                        FMN_dh 196 gkqldpsltwddikwlreqtklplvvKGvltaedakraveaGvdgivvSNHGG.....Rqldga.patidvLpeiveavgg 270
                                   + + d++   ++ik++r++ ++ +v   + ta  a+ ++ + vdg+ v    G     R + g+ ++ + ++ e++e +++
  gi|13542206|ref|NP_111894.1| 247 TAHADNENVLSSIKRMRKEISVDIVAGNIATAGAAEDLISCEVDGLRVGIGPGsicttRIVAGVgVPQLTAISEVAEVAKE 327
                                   445566667789************************************988887777788877535668888888888887 PP

                                   .SS-EEEESS--SHHHHHHHHHTT-SEEEESHH CS
                        FMN_dh 271 .rievlvDgGirrGsDvlkAlalGAdavllGRp 302
                                     i+v++DgGir   D++kA+a GAd v+lG  
  gi|13542206|ref|NP_111894.1| 328 yGIPVIADGGIRYSGDIVKAIAAGADSVMLGSM 360
                                   45****************************965 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.92
                                   HHHHHHHHHHHHHHHHHHHHT-SBHHHHHC CS
                        FMN_dh 314 GvervleilraelertmallGvksvaeldr 343
                                   +v++vl  l   l++ m  +G++++ +l++
  gi|13542206|ref|NP_111894.1| 420 RVDEVLFQLVGGLRTGMGYVGAENIGKLKE 449
                                   689999999999*************99986 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.0   0.00026      0.39       2      41 ..      36      75 ..      35      93 .. 0.88
   2 !   24.5   4.0   1.1e-08   1.6e-05     182     236 ..     315     372 ..     240     381 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00026
                           NMO  2 slltellkikppvvqpgmggiskarLaaavsnaGgLGvla 41
                                  s+l+  +++k p+v ++m  ++++++a a +  G+ G++ 
  gi|13542206|ref|NP_111894.1| 36 SRLSRRINVKVPIVSSPMDTVTEEAMAIAMARYGAFGIIH 75
                                  56788899*****************************985 PP

  == domain 2  score: 24.5 bits;  conditional E-value: 1.1e-08
                           NMO 182 faLvpqvldavd...iPviAaGGiidrrgvaaaLalGAsgvqigtrfLltkesdakda 236
                                   ++ + +v+++ +   iPviA GGi    ++  a+a+GA  v +g+ + +t+es+ +++
  gi|13542206|ref|NP_111894.1| 315 LTAISEVAEVAKeygIPVIADGGIRYSGDIVKAIAAGADSVMLGSMLAGTEESPGQEM 372
                                   344555666655677**************************************98775 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 !   30.8   4.0   1.1e-10   1.6e-07     201     304 ..     260     359 ..     247     362 .. 0.78
   2 ?   -3.9   0.0       3.8   5.6e+03     273     291 ..     422     440 ..     417     445 .. 0.77

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 1.1e-10
                                   -.TTSEEEEEEE-STTHHHHHHHHHHTT-SEEE..EE-TT---SSE...EHHHHHHB---HHHHHHHHHHHHHHTT-GGG- CS
                  Glu_synthase 201 n.keakvsvKlvaeagvetiaagvakanadiil..idGleGGTGAs...pkssikhaGlPlelalaevdqtlkeeglrdrv 275
                                   + +++++sv +va++    ia+  a a  d+i+  +dGl+ G G      + ++  +G+P ++a++ev ++ ke+g    +
  gi|13542206|ref|NP_111894.1| 260 KrMRKEISVDIVAGN----IAT--AGAAEDLISceVDGLRVGIGPGsicTTRIVAGVGVPQLTAISEVAEVAKEYG----I 330
                                   334577888888765....444..555567774449****99997611146788899***************9999....6 PP

                                   EEEEESS--SHHHHHHHHHHT-SEEE-SH CS
                  Glu_synthase 276 sliadGglktgadvvkalalGAdavgigt 304
                                    +iadGg++ + d+vka+a GAd+v +g+
  gi|13542206|ref|NP_111894.1| 331 PVIADGGIRYSGDIVKAIAAGADSVMLGS 359
                                   89************************997 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 3.8
                                   GG-EEEEESS--SHHHHHH CS
                  Glu_synthase 273 drvsliadGglktgadvvk 291
                                   d+v  +  Ggl+tg+  v 
  gi|13542206|ref|NP_111894.1| 422 DEVLFQLVGGLRTGMGYVG 440
                                   78999999*****987665 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   4.0   7.5e-10   1.1e-06      81     223 ..     225     361 ..     146     367 .. 0.80

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 7.5e-10
                                   SSSSHHHHHHHHHCT-SEEEESHHHHH-THHHHHHHHHHCGGGEEEEEEEEECEEEEETTTTEEEEEEHHHHHHHHHHTT- CS
                  His_biosynth  81 GIrsledveelleagadkviigtaavknpelikelaekfgsqkivvaiDarrgykvaikgwreetgldavelakkleelga 161
                                   G  +l+++ el +agad +++ ta ++n ++++++ +   +    +++D+ +g ++a+ g  e+    +++   +  ++g+
  gi|13542206|ref|NP_111894.1| 225 GPFDLDRAIELERAGADLIVVDTAHADNENVLSSIKRMRKE----ISVDIVAG-NIATAGAAED----LISCEVDGLRVGI 296
                                   4457888999999*****************99999886555....89999999.9*******99....5555555555554 PP

                                   ..SEEEEEE.TTTTTTSS---HHHHHHHHHHHSSEEEEESS--SHHHHHHHHHTTCSEEEESHHH CS
                  His_biosynth 162 ..geilltd.idrdGtlsGpdleltkelaeavkipviasGGvgsledlkelksegvdavivgsal 223
                                     g+i  t  ++ +G+ +   ++ + e+a+++ ipvia GG++   d+ ++ ++g+d+v++gs+l
  gi|13542206|ref|NP_111894.1| 297 gpGSICTTRiVAGVGVPQLTAISEVAEVAKEYGIPVIADGGIRYSGDIVKAIAAGADSVMLGSML 361
                                   1167777773578**************************************************98 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.47   7.1e+02     259     289 ..     232     261 ..     224     269 .. 0.80
   2 !   16.6   1.0   2.3e-06    0.0035     229     276 ..     316     361 ..     302     371 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.47
                                   HHHHHHHTECEEEESHHHHHHGTCHHHHHHH CS
                        DHO_dh 259 alekieaGAslvqvytalvfegpkiakkikk 289
                                   a+e  +aGA l+ v ta   ++  + + ik+
  gi|13542206|ref|NP_111894.1| 232 AIELERAGADLIVVDTAH-ADNENVLSSIKR 261
                                   89999***********98.566666666665 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 2.3e-06
                                   HHHHHHHHHHHHTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHH CS
                        DHO_dh 229 ialkvirelykrlkkeipiIgvGGiesgeDalekieaGAslvqvytal 276
                                   +a+  + e++k+    ip+I+ GGi  + D +  i aGA  v +++ l
  gi|13542206|ref|NP_111894.1| 316 TAISEVAEVAKEYG--IPVIADGGIRYSGDIVKAIAAGADSVMLGSML 361
                                   68889999999999..****************************9987 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   0.0      0.33   4.9e+02      98     135 ..     154     191 ..     143     199 .. 0.87
   2 ?    0.6   0.6      0.19   2.8e+02     189     231 ..     228     277 ..     215     285 .. 0.65
   3 !   18.8   1.0   5.4e-07   0.00081     157     212 ..     308     366 ..     299     372 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.33
                                   -BCETTTTEB-HHHHHHHHHHHHHTT-EEEEEE-S-HH CS
                          ThiG  98 viadektLlPdvvetlkaaeiLvkeGFevlpYvsdDlv 135
                                   v+ ++    P++v++ +a +iL k+  e lp v +D  
  gi|13542206|ref|NP_111894.1| 154 VMVKNVITAPENVDLEDAINILHKNRIEKLPLVDKDNH 191
                                   666677778**********************9999975 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.19
                                   HHHHHHHT...T-SEEEESHHHHTSSSHH....HHHHHHHHHHHHHHHHH CS
                          ThiG 189 daaqamel...Gadavllntavaeakdpv....amArafklaveaGrlay 231
                                   d   a+el   Gad ++++ta a  ++      +m + +++ + aG +a 
  gi|13542206|ref|NP_111894.1| 228 DLDRAIELeraGADLIVVDTAHADNENVLssikRMRKEISVDIVAGNIAT 277
                                   4444444433499**********999876222256666667777887775 PP

  == domain 3  score: 18.8 bits;  conditional E-value: 5.4e-07
                                   S----S-HHHHHH...HHHH-SS-BEEES---SHHHHHHHHHTT-SEEEESHHHHTSSS CS
                          ThiG 157 sglGllnkealki...iieeakvPvivDAGigspsdaaqamelGadavllntavaeakd 212
                                   +g G+ + +a++    + +e  +Pvi D Gi+ + d+++a+  Gad+v+l + +a +++
  gi|13542206|ref|NP_111894.1| 308 AGVGVPQLTAISEvaeVAKEYGIPVIADGGIRYSGDIVKAIAAGADSVMLGSMLAGTEE 366
                                   5666655555555000556678******************************9998776 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1      0.57   8.6e+02     170     203 ..     254     286 ..     229     297 .. 0.71
   2 !   14.9   0.1   7.3e-06     0.011     172     214 ..     318     359 ..     311     370 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.57
                                   --CHHHHHHHHH-SS-EEEESS--SHHHHHHHHH CS
                           Dus 170 adweaIkevkqavsipviaNGdIkdaedaqaile 203
                                     +++Ik +++++s+ ++a G+I +a +a++ ++
  gi|13542206|ref|NP_111894.1| 254 NVLSSIKRMRKEISVDIVA-GNIATAGAAEDLIS 286
                                   4567899999999999877.99999988877665 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 7.3e-06
                                   CHHHHHHHHH-SS-EEEESS--SHHHHHHHHHHH--SEEEESC CS
                           Dus 172 weaIkevkqavsipviaNGdIkdaedaqaileetGadgvmigr 214
                                   +++++ev ++  ipvia G+I++  d+ ++++  Gad vm g 
  gi|13542206|ref|NP_111894.1| 318 ISEVAEVAKEYGIPVIADGGIRYSGDIVKAIAA-GADSVMLGS 359
                                   678999999999********************9.******996 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.1     1e-05     0.015     140     195 ..     307     358 ..     297     363 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1e-05
                                   TTT.B---HHHHHHHHHHHHHCT-EEEEEETTHHHHHHHHTS-CHHHHTTSSEEEEE CS
               Beta_elim_lyase 140 agG.qvvsleelrevaaiakkygiplhlDgARfanaakslgeivkemfsyvDsvtms 195
                                   ++G  v +l  + eva++ak+ygip++ Dg         +g ivk +++++Dsv+++
  gi|13542206|ref|NP_111894.1| 307 VAGvGVPQLTAISEVAEVAKEYGIPVIADGG-----IRYSGDIVKAIAAGADSVMLG 358
                                   34414567899******************95.....6789999*********99986 PP

>> G3P_antiterm  Glycerol-3-phosphate responsive antiterminator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       1.8   2.7e+03     130     145 ..     258     273 ..     254     286 .. 0.83
   2 ?   12.3   0.2   5.6e-05     0.083     128     167 ..     318     357 ..     311     360 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.8
                                   HHCTSTTS...EEEEE CS
                  G3P_antiterm 130 vikeikkelkipiiaG 145
                                    ik+++ke+++ i+aG
  gi|13542206|ref|NP_111894.1| 258 SIKRMRKEISVDIVAG 273
                                   6899999999999998 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 5.6e-05
                                   HHHHCTSTTS...EEEEESS--SHHHHHHHCTT.SSEEEE CS
                  G3P_antiterm 128 pkvikeikkelkipiiaGGLietkedveealkaGaiavst 167
                                    + ++e+ ke  ip+ia G i+ + d+ +a++aGa++v+ 
  gi|13542206|ref|NP_111894.1| 318 ISEVAEVAKEYGIPVIADGGIRYSGDIVKAIAAGADSVML 357
                                   5567889999***************************975 PP

>> DUF561  Protein of unknown function (DUF561)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0     0.047        70     184     237 ..      43      97 ..      25     103 .. 0.61
   2 ?    7.1   0.3    0.0018       2.7     139     219 ..     282     363 ..     276     378 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.047
                        DUF561 184 kvslPvicasGlsdvtvp.lals...lgasGiGigsavsklndeeemvallseikkai 237
                                   +v++P+++ s + +vt + +a++   +ga Gi   +  +  ++e+emv  +++ +++i
  gi|13542206|ref|NP_111894.1|  43 NVKVPIVS-SPMDTVTEEaMAIAmarYGAFGI--IHRNQPREKEVEMVRRVKREETII 97 
                                   57788776.55666664325655112555555..444455567778888777766655 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0018
                        DUF561 139 kkLeslgvdliqteGkitsiskakkvndliekslstlastyeiskkvslPvicasGlsdvt.vplalslgasGiGigsavs 218
                                   ++L s +vd ++   +  si  ++ v ++    l++++ + e++k+  +Pvi+  G+  +  +  a+++ga  + +gs++ 
  gi|13542206|ref|NP_111894.1| 282 EDLISCEVDGLRVGIGPGSICTTRIVAGVGVPQLTAISEVAEVAKEYGIPVIADGGIRYSGdIVKAIAAGADSVMLGSMLA 362
                                   5666666666666555666777777777777788999********************977525569999**9999999876 PP

                        DUF561 219 k 219
                                    
  gi|13542206|ref|NP_111894.1| 363 G 363
                                   5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (485 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.66u 0.31s 00:00:00.97 Elapsed: 00:00:00.50
# Mc/sec: 2932.73
//
Query:       gi|13542207|ref|NP_111895.1|  [L=249]
Description: solute-binding protein [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.2e-21   74.5   0.0    1.1e-20   74.3   0.0    1.0  1  VitK2_biosynth  Menaquinone biosynthesis


Domain annotation for each model (and alignments):
>> VitK2_biosynth  Menaquinone biosynthesis
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.3   0.0   6.3e-25   1.1e-20      13     250 ..      12     223 ..       2     237 .. 0.81

  Alignments for each domain:
  == domain 1  score: 74.3 bits;  conditional E-value: 6.3e-25
                                   HHHHHHHTTSS..SGCCEEEEEE-HHHHHHHHHTTS-SEEEEEHHHHTTCTTTEEEESEESCEEEESSSSEEEEESS-CCC CS
                VitK2_biosynth  13 flfyaLvegkvdsegleveivledpetlnrallegelDvakiSsaayariaddyalLpdlsisalGrvygvllvskvplee 93 
                                   +l+ ++        +++ +++ ++p +  + +l+g++D + +S   y+++++d+ lL+ ++i +  +  + +l+s++p  +
  gi|13542207|ref|NP_111895.1|  12 PLYLGF--------SNKEHVLRNNPFENLKLVLDGKVDASMVSLLSYLENSNDLILLKTATIHSTRKTISTILISRKPGMD 84 
                                   555555........34677788888888899********************************************986655 PP

                                   -SSS.T.EEEESTTTSHHHHHHHHHHCSTS----EEEEE-GGGHHHHHHTTSSEEEEECCHHHTGGGGTTEEEEEHHHHHH CS
                VitK2_biosynth  94 legelgkrvalpgestTsvlLlrlllaeryglkprlvevpfdeieaavlegedagLlIgesaltyaeeglkkvlDLgelWe 174
                                    ++    rva+++  +T    l l+l++  g++ ++v+++ +   + +l+ ed +Ll g++al+  +++++ ++D g+++ 
  gi|13542207|ref|NP_111895.1|  85 -RK---IRVAITKNTRTTEFYLSLVLERL-GIDYTFVRTD-KTEAEDLLAIEDYALLNGDEALRVYSKKYPLIADVGNMFS 159
                                   .43...59****************99999.9*********.66666699999***********999999************ PP

                                   HHHSS-EEEEEEEEECCCHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHHCCSTTS.HHHHHHHHHHHCSHHHHS-C CS
                VitK2_biosynth 175 eltglPlvlglwvvrrdlaaeaakeleealreSveyalahldevaeyaaeraqemddevlekhlelYvnelsydlg 250
                                   +l+g+  v+++ v r+ ++     +++ea+ +S++y     de + +++ r +++      ++ ++Y+  ++y++g
  gi|13542207|ref|NP_111895.1| 160 KLYGMEPVYAVTVSREPFDY---SAIDEAILSSYSYK----DECSMALSSRLGIP-----LSVASDYYSVIRYEYG 223
                                   *****************954...45677777776664....44555555555555.....5555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       459  (0.025601); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); 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 0.28s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1546.79
//
Query:       gi|13542208|ref|NP_111896.1|  [L=365]
Description: hypothetical protein TVN1377 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.9e-14   53.8   0.1    4.5e-14   53.2   0.1    1.3  1  Radical_SAM  Radical SAM superfamily


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.2   0.1   2.5e-18   4.5e-14       2     163 ..      59     232 ..      58     236 .. 0.92

  Alignments for each domain:
  == domain 1  score: 53.2 bits;  conditional E-value: 2.5e-18
                                   EEESEESS--TTTSCCTT..HHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESSTGGGSTTHHHHHHHHHHTC..... CS
                                   xxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx..... RF
                   Radical_SAM   2 vvtrgCnlrCsfCarpet..vrregrgrslsveeileevkelkaekg.vkevilgggepllypdfvellerlakla..... 74 
                                   + t+ C+  C+ Ca++     +r g+g++l++e++ +e+ ++ + kg ++  i+gg +p+l  +++e+++r ++       
  gi|13542208|ref|NP_111896.1|  59 NYTNYCTASCPICAFYVPykNKRFGKGYELTKEQVRKEALIA-KQKGaTEIHIVGGFDPDLSIEYYEDIFRTIRGImpnva 138
                                   77999***********99************************.58887999999999*****************9999999 PP

                                   .....CCTEEEEEEECSSCHGHHHHHHHHHTT.-SEEEEEEBSSSHHHHHHHHT..CTSHHHHHHHHHHHHHHTTSETEEE CS
                                   .....xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  75 .....vpgiritvetngtlpdeeklerllelg.vdrvslgleaaddekvlklmn..rghtfeevlealeklreagikrvvd 147
                                         p+i +   t g  + +e + r+ ++g   +   g+e++d e ++k++    + + e++le  ++++++g+k   +
  gi|13542208|ref|NP_111896.1| 139 ikaftIPEIDFIARTTGNSI-KETVLRFMDAGmNAHTGGGAEIFDQE-IRKYITtpEKVSGEKWLEDAKIIHSLGLK-GNS 216
                                   99999999999999999999.***********999************.*****98777788****************.778 PP

                                   EEEEBTTTSHHHHHHH CS
                                   xxxxxxxxxxxxxxxx RF
                   Radical_SAM 148 rivglpGendeeleel 163
                                   +++ ++ e +e++ ++
  gi|13542208|ref|NP_111896.1| 217 TMTYGHIEGWEHIIDH 232
                                   8888888****99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (365 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       436  (0.0243181); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 2505.48
//
Query:       gi|13542209|ref|NP_111897.1|  [L=560]
Description: Fe-S oxidoreductase [Thermoplasma volcanium GSS1]
Scores for complete sequence (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   41.9   0.0    2.3e-10   41.1   0.0    1.3  1  Radical_SAM  Radical SAM superfamily
    2.4e-06   27.6   0.0    1.5e-05   25.0   0.0    2.1  2  B12-binding  B12 binding domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.1   0.0   2.5e-14   2.3e-10       5     166 ..     229     392 ..     226     393 .. 0.95

  Alignments for each domain:
  == domain 1  score: 41.1 bits;  conditional E-value: 2.5e-14
                                   SEESS--TTTSCCTT...HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEE CS
                                   xxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM   5 rgCnlrCsfCarpet...vrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgiritv 82 
                                   rgC l+C fC  +     +     ++++++ +i+ee++   ++  +  v++ g+  l+ p+++e l+++  +  + i i +
  gi|13542209|ref|NP_111897.1| 229 RGCQLNCGFCGGSNFaykSNFAMNYQFRDPCRIAEEIEMS-QDILGSPVFIAGDIALAGPHYYERLFKCLNE--RRIDIPL 306
                                   8************99999999****************999.88879999999999*****************..7****** PP

                                   EECSSCHG.HHHHHHHHHTT.-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSET.EEEEEEEBTTTSHHHH CS
                                   xxxxxxxx.xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx RF
                   Radical_SAM  83 etngtlpd.eeklerllelg.vdrvslgleaaddekvlklmnrghtfeevlealeklreagikr.vvdrivglpGendeel 160
                                    t +++p  e++++ l +      ++++ e++d+  v+ +++ g+++++  +++ ++ ++g k+  v++ +gl  +n++ +
  gi|13542209|ref|NP_111897.1| 307 LTEYFKPFnEDYVKSLSKTVeDFSMEISPETYDEN-VRSWNKSGYSNKDMERSFSLAEKYGSKKfDVYFSIGLSHQNKKNV 386
                                   *****9999*********999**************.******99*****************999989************** PP

                                   HHHHHH CS
                                   xxxxxx RF
                   Radical_SAM 161 eellel 166
                                    +++e+
  gi|13542209|ref|NP_111897.1| 387 MDTVEY 392
                                   999986 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0   1.6e-09   1.5e-05       7     112 ..      33     143 ..      28     148 .. 0.91
   2 ?   -0.8   0.0      0.17   1.5e+03      50      74 ..     426     449 ..     425     454 .. 0.90

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 1.6e-09
                   B12-binding   7 tvggdlhplGlavlaaalrdagfeVqllganven.....edivaairaekpdvvglSalltsqleavkelvellkrirprv 82 
                                   t  ++++p+G+ +  ++l ++gf+ ++ ++ v +      ++++ + + ++ + g+ +++  +  ++ +l++ +k i+p+ 
  gi|13542209|ref|NP_111897.1|  33 TPVFEMYPVGFISMLNFLVQNGFNARIANVAVRMveskkFNVEKYLSEIEAPIFGIDLHWLPHAHGALNLARIIKNIHPES 113
                                   667899*****************99999999999999989999999999******************************** PP

                   B12-binding  83 kvvvGGahpsldpeetleaklgiddvvvge 112
                                    vv+GG   ++   e++++   id+v  g+
  gi|13542209|ref|NP_111897.1| 114 YVVFGGYSSTYFRYELMKNYDFIDFVLAGD 143
                                   ********9999999897658889988775 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.17
                   B12-binding  50 ekpdvvglSalltsqleavkelvel 74 
                                   ekpd+ g+ + ++ ++++v ++++l
  gi|13542209|ref|NP_111897.1| 426 EKPDLYGFKI-YGRSVSDVYRILDL 449
                                   69*******9.**********9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (560 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        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 0.31s 00:00:00.92 Elapsed: 00:00:00.50
# Mc/sec: 3398.06
//
Query:       gi|13542210|ref|NP_111898.1|  [L=366]
Description: hypothetical protein TVN1379 [Thermoplasma volcanium GSS1]
Scores for complete 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   75.7   0.2    1.1e-20   74.6   0.0    1.6  2  Radical_SAM  Radical SAM superfamily
  ------ inclusion threshold ------
      0.013   15.6   0.0       0.03   14.5   0.0    1.6  1  Fer4_14      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0      0.88   7.9e+03      33      84 ..       9      57 ..       6      58 .. 0.60
   2 !   74.6   0.0   1.3e-24   1.1e-20       2     158 ..      62     227 ..      61     234 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.88
                                  HHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEEEE CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM 33 eileevkelkaekgvkevilgggepllypdfvellerlaklavpgiritvet 84
                                  +i+e++++  ++ + + ++ + +e ++++ + +l++ +  +  +g r+++++
  gi|13542210|ref|NP_111898.1|  9 YIEEKIERR-EDLDEDDIVYMYDEADVND-LGKLARSITDK-ISGKRVSFVS 57
                                  566666666.6666777777777777754.55555555555.3666666666 PP

  == domain 2  score: 74.6 bits;  conditional E-value: 1.3e-24
                                   EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESSTGGGSTTHHHHHHHHHHTC....... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx....... RF
                   Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekg.vkevilgggepllypdfvellerlakla....... 74 
                                   + t+ Cn rC+fCa++++ + e+++++++++ +++e++++ +  g    +i+gg +p+l+ d++  ++r +++        
  gi|13542210|ref|NP_111898.1|  62 NYTNICNVRCKFCAFYRK-SGEYDAYTMTPDGVIDEIRKY-YPYGiRQILIQGGVNPNLDLDYYLTVFRKIRENfteagin 140
                                   56999************7.*********************.79998999999*********************9******* PP

                                   .CCTEEEEEEECSSCHG.HHHHHHHHHTT.-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHTTSETEEEEEEE CS
                                   .xxxxxxxxxxxxxxxx.xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  75 .vpgiritvetngtlpd.eeklerllelg.vdrvslgleaaddekvlklmn.rghtfeevlealeklreagikrvvdrivg 151
                                     +  +i +++   +++ ee + +l+e+g  +    g+e++d++ v+ +++ ++++  ++le +e+++++g+k + ++++g
  gi|13542210|ref|NP_111898.1| 141 gLSAAEINFISKKAHLTyEETILKLKEAGlETIPGAGAEILDED-VRVKLGrPRGSGRQWLEIMETAHRLGVKTTATMVYG 220
                                   *99999999999999999***********888899*********.999999999*******************55555555 PP

                                   BTTTSHH CS
                                   xxxxxxx RF
                   Radical_SAM 152 lpGende 158
                                   +   +++
  gi|13542210|ref|NP_111898.1| 221 HIESSMD 227
                                   5544444 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   3.3e-06      0.03       5     103 ..      64     160 ..      60     171 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.3e-06
                       Fer4_14   5 lsgCnlsCkgCd.nketwkselgkpqteelleqilkdlkkseikiqglvltGG.ePLhyenkkellklvkrlkeeypekki 83 
                                   ++ Cn+ Ck+C   +++ + ++ +   + ++++i    k++ + i+++ + GG +P    + +  l++ ++++e+++e  i
  gi|13542210|ref|NP_111898.1|  64 TNICNVRCKFCAfYRKSGEYDAYTMTPDGVIDEIR---KYYPYGIRQILIQGGvNPN--LDLDYYLTVFRKIRENFTEAGI 139
                                   688********843333444555555556664444...777777888*****96787..78999**************999 PP

                       Fer4_14  84 wletngtleiele.ktpdlke 103
                                      + + ++   + +   ++e
  gi|13542210|ref|NP_111898.1| 140 NGLSAAEINFISKkAHLTYEE 160
                                   999999999777733333444 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:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 2469.77
//
Query:       gi|13542211|ref|NP_111899.1|  [L=409]
Description: tRNA pseudouridine synthase D [Thermoplasma volcanium GSS1]
Scores for complete 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-110  368.2   0.0     6e-110  367.9   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 !  367.9   0.0  3.4e-114    6e-110      17     413 ..      12     391 ..       9     394 .. 0.94

  Alignments for each domain:
  == domain 1  score: 367.9 bits;  conditional E-value: 3.4e-114
                          TruD  17 rlrespeDFiVeEieefsgeeeadegeylvlrvekrnwdtldlvrelaralgisrkrvgfaGtKDkrAvTtQlisirkvep 97 
                                   +++++peDF VeEi++++    + +g+y++++++ r+wdt++++ e+ar+l++srkrv+faGtKDkrAv  Q+++i+ ++ 
  gi|13542211|ref|NP_111899.1|  12 EIKRDPEDFSVEEIADIEP---DPNGKYTIIKARVRDWDTNRIAAEIARRLHMSRKRVTFAGTKDKRAVKLQYFCINSADV 89 
                                   69************77755...478***************************************************99888 PP

                          TruD  98 eelealeikdvelevvgrarrklrlGdLaGNkFeirvrdvaeeeeaakraeeileeleekggvPNyfGvQRFGsrrpvthl 178
                                   +  +   ikd e+ + +++++ l+lGdL+ N+F+ir  ++  ++e    ++e   ++  kgg+PN+fG QRFGsrr +th+
  gi|13542211|ref|NP_111899.1|  90 DVASLSGIKDFEVIESFKSSHYLTLGDLIANHFKIRFYGI--DPE---MFRERYVHIISKGGFPNFFGDQRFGSRRRNTHE 165
                                   7776669********************************8..344...67777777777899******************* PP

                          TruD 179 vGkaivkgdleeAvelyvgkpfeeesedtreareavaetgdleealeelpkslryErallkrLaekpkdykkAlealpknL 259
                                   +Gk i+kg++eeAv++y+ + +     d ++ r+++ +t d+++ale++p+sl++Er+l+ ++a+ ++++k+A+ +lpknL
  gi|13542211|ref|NP_111899.1| 166 IGKLIIKGEYEEAVKKYIYDEK----YDKESYRKHFIDTLDYKTALERFPHSLSFERSLIGYYAR-NGTFKGAFDSLPKNL 241
                                   ******************9765....44456689999****************************.9************** PP

                          TruD 260 qrlFvhAyqSylFNrvlseRlerglpldepveGDvvifaeer.lpdtdrlqlvteknveevkrliergrafvtaplvGtet 339
                                     +FvhAyqSylFNr+l eRl+ +  l+ +++GD+++  +   +pd+++   v++ n e++++l+++ ++ +++p++G++t
  gi|13542211|ref|NP_111899.1| 242 TIMFVHAYQSYLFNRILDERLKIY-GLNAVLPGDIAFPVDAYfNPDKSKPIEVNSYNREKISKLVSSDKIRISLPIFGYKT 321
                                   **********************88.8***********9977799************************************* PP

                          TruD 340 elaegevgeierevleeegleledFklpklpelsskGtrRaillrvedlelsaeedeltleFsLpkGsYATvvl 413
                                    + + + g++e  +l+eeg++++dFk +++  lss+G+rR i+ ++ +++l++     ++eF+L kG YATv+l
  gi|13542211|ref|NP_111899.1| 322 WIDNSDFGDVEYGILKEEGISQDDFKNKDFAYLSSSGDRRIISAKPINFSLEN----NVVEFTLGKGIYATVFL 391
                                   ************************************************99655....79*************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (409 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       611  (0.0340789); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.51
# Mc/sec: 2434.46
//
Query:       gi|13542212|ref|NP_111900.1|  [L=459]
Description: membrane glycosyltransferase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-26   92.7   4.3    5.6e-26   91.7   4.3    1.5  1  Glyco_trans_2_3  Glycosyl transferase family group 2
    9.1e-13   48.6   0.0    1.1e-12   48.3   0.0    1.2  1  Glyco_tranf_2_3  Glycosyltransferase like 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 !   91.7   4.3   6.2e-30   5.6e-26       1     192 [.     181     396 ..     181     403 .. 0.86

  Alignments for each domain:
  == domain 1  score: 91.7 bits;  conditional E-value: 6.2e-30
               Glyco_trans_2_3   1 iilllDaDtvlppdclreiaaela.s.pevaivqgpvlvm..nvanwleelaalff.aedhgkdilvrealgrvvp.svGs 75 
                                   +i++lD+Dt + pd ++ ia+++  +  e+ ++qg+  +     +++++++a++ + ++d +++ ++++  ++++  ++G 
  gi|13542212|ref|NP_111900.1| 181 WIYHLDDDTSIGPDTVAAIAEHIFlHgSEYYLAQGILSFPhyLTKSIITRFADSMRpTDDLTRFYFFTNVVKMPLIgLHGE 261
                                   9*********************998977********887556889*********99999*************9887588** PP

               Glyco_trans_2_3  76 gaflrrsalqevggwdgdessvsEDfdmglrl.qrkGyrvrfvpeslvkekspltlraalrQrkRwayGc..el....... 146
                                   ++++r +  ++v gwd  ++++++D +++lr  +++  r  f+p++ ++ +sp+t+r+ lrQrkRw++++  ++       
  gi|13542212|ref|NP_111900.1| 262 NMLVRSDIEESV-GWDNGNRAIADDSYFALRFaYMYPGRSSFMPAV-TYGSSPSTIRDMLRQRKRWFLNVsnLSffgnvpl 340
                                   *****9999998.999999************967**********99.**********************986115666677 PP

               Glyco_trans_2_3 147 .eklillvrllgylgsllwsalplhlallllfslla..........lalvlllllll 192
                                    +++++  + + + g ++ + +p++l+l +l  + +          +a++l  ++++
  gi|13542212|ref|NP_111900.1| 341 rYRAFMIYSIIFWVGMVIQNVVPILLLLHILGVMKMpiindevlglWAFTL-SFWIW 396
                                   666777788999************999999999988899998888633333.22222 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 !   48.3   0.0   1.2e-16   1.1e-12      74     229 ..     158     327 ..      81     328 .. 0.84

  Alignments for each domain:
  == domain 1  score: 48.3 bits;  conditional E-value: 1.2e-16
               Glyco_tranf_2_3  74 gksralnealravk.......sdlvllvDdDtvvePdtlkrllqff..ltpkvgavgtpvfl.ln.rstl.vsalgalefa 142
                                   +ksra + a++  +       ++++ ++DdDt ++Pdt+++++  +    +++  +++   + ++  ++  +++++ ++++
  gi|13542212|ref|NP_111900.1| 158 AKSRANQYAIEYLRerglvnnRTWIYHLDDDTSIGPDTVAAIAEHIflHGSEYYLAQGILSFpHYlTKSIiTRFADSMRPT 238
                                   45555455555433334444578***************99999988778889*****999774543334337788999*** PP

               Glyco_tranf_2_3 143 erhlrflaarralg..vltlnGsgslirrevlkelegldp.lflltdDyelglrlrr.agfrtayvpgaavrevfpsslka 219
                                   ++ +rf ++++ ++   + l+G+ +l+r ++ +   g+d  +  ++dD   +lr+   +++r+ ++p + ++ ++ps++ +
  gi|13542212|ref|NP_111900.1| 239 DDLTRFYFFTNVVKmpLIGLHGENMLVRSDIEESV-GWDNgNRAIADDSYFALRFAYmYPGRSSFMPAV-TYGSSPSTIRD 317
                                   *************965699****************.*****99999998888877655*********99.*********** PP

               Glyco_tranf_2_3 220 yikqrnRwvy 229
                                     +qr Rw  
  gi|13542212|ref|NP_111900.1| 318 MLRQRKRWFL 327
                                   ********75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (459 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.66u 0.31s 00:00:00.97 Elapsed: 00:00:00.53
# Mc/sec: 2602.70
//
Query:       gi|13542213|ref|NP_111901.1|  [L=293]
Description: electron transfer flavoprotein subunit alpha [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.7e-32  111.3   0.1    3.1e-32  110.5   0.1    1.5  1  ETF_alpha  Electron transfer flavoprotein FAD-binding domain
    2.3e-12   47.2   0.0    3.6e-12   46.5   0.0    1.2  1  ETF        Electron transfer flavoprotein domain
  ------ inclusion threshold ------
       0.12   12.3   0.0       0.21   11.5   0.0    1.4  1  DUF4416    Domain of unknown function (DUF4416)


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 !  110.5   0.1   5.1e-36   3.1e-32       1      84 []     170     254 ..     170     254 .. 0.97

  Alignments for each domain:
  == domain 1  score: 110.5 bits;  conditional E-value: 5.1e-36
                                   .-TTT-S-EEEE-GGGSSGGGHHHHHHHHHHHT-EEEE-HHHHTT.TSS-CCCB-SSSS-----S-EEEES----HHHHGG CS
                     ETF_alpha   1 vdLeeakvvvsgGrGlkskenlelleelaealgaavgasRavvda.gwipeerqvGqtGktvaPklyiavGisGaiqhlaG 80 
                                   v+Le+ak++vs+GrG++sken++ +e l +a++++++ sR+v+ + gw++e+rqvG +Gk+v+Pklyia+GisG+iqh+aG
  gi|13542213|ref|NP_111901.1| 170 VRLEDAKIIVSVGRGIGSKENISKIEPLVNAVKGELAGSRPVCMDyGWLSEDRQVGLSGKKVSPKLYIALGISGQIQHIAG 250
                                   579**************************************99887*********************************** PP

                                   GTT- CS
                     ETF_alpha  81 mkes 84 
                                   m++s
  gi|13542213|ref|NP_111901.1| 251 MRNS 254
                                   *997 PP

>> ETF  Electron transfer flavoprotein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.5   0.0     6e-16   3.6e-12      23     164 ..      15     142 ..       7     164 .. 0.76

  Alignments for each domain:
  == domain 1  score: 46.5 bits;  conditional E-value: 6e-16
                                   HHHHHHHHHT.--EEEEEEES....S-CHHHHHHCT-SEEEEEE-GGGSS--CCHHHHHHHHHHHHC--SEEEEESSCCHH CS
                           ETF  23 aArrlkekag.gevtavvvGppeaeealrealaamGadkvilvddpalagydaeatakalaalikkedpdlvlagataigk 102
                                   +A  l +  g +e  av vG+        +     Ga++++ v+  +      +a+a+ + +++ +  +d+++ag+t +g+
  gi|13542213|ref|NP_111901.1|  15 QACTLVN--GkAEYDAVYVGE-------GRVSG-VGASTLYTVKKGTPY----DAVADGILEIMGN--YDIIVAGSTEFGR 79 
                                   5555544..336666666666.......23334.677777777776654....5678888888887..************* PP

                                   HHHHHHHHHCT-EEEEEESEEEEETCCEEEEEECCCCTEEEEEE-TSSSEEEEE-TTSS--...- CS
                           ETF 103 qvaprlAalLgvplitdvteleveggkltvtRpieggnglaevveadlpavltvrpgafep...a 164
                                   +va+ +A + g+  +t++ +le ++gk++ +R  +gg+ +  ++e +  +v+tv+pg+ e+   +
  gi|13542213|ref|NP_111901.1|  80 EVAGYIAGKTGYYAATEIFSLEFSNGKAKTKRFFYGGKTV--IEEESDAKVFTVAPGVIEAkefE 142
                                   ***********************99***********5555..7788***************4441 PP

>> DUF4416  Domain of unknown function (DUF4416)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   3.5e-05      0.21      69     128 ..     189     246 ..     175     257 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.5e-05
                       DUF4416  69 eelaeiKletnelEkelakdgkRkvnldpGyltleklvlattKdrshRiylgkgiyaelt 128
                                   e++ +i    n++  ela   +R v +d G+l++++ v  ++K+ s ++y+  gi + ++
  gi|13542213|ref|NP_111901.1| 189 ENISKIEPLVNAVKGELAG--SRPVCMDYGWLSEDRQVGLSGKKVSPKLYIALGISGQIQ 246
                                   5555555556666665554..5********************************977665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        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 0.29s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 1826.53
//
Query:       gi|13542214|ref|NP_111902.1|  [L=245]
Description: electron transfer flavoprotein subunit beta [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-30  106.7   0.1    1.7e-30  106.3   0.1    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 !  106.3   0.1   9.4e-35   1.7e-30      10     175 ..      31     198 ..      27     203 .. 0.92

  Alignments for each domain:
  == domain 1  score: 106.3 bits;  conditional E-value: 9.4e-35
                                   CCCE-HHHHHHHHHHHHHHHHHT--EEEEEEES....S-CHHHHHHCT-SEEEEEE-GGGSS--CCHHHHHHHHHHHHC-- CS
                           ETF  10 dgklnpvdlealeaArrlkekaggevtavvvGppeaeealrealaamGadkvilvddpalagydaeatakalaalikkedp 90 
                                   ++++ + +++a+eaA++lkek+gg+vt++++G++++  a +ea+a mG+d+ i ++    +g+++  taka+  ++k++++
  gi|13542214|ref|NP_111902.1|  31 PYRVENLSKNAIEAAVQLKEKNGGKVTGIIFGTEASTAAMKEAYA-MGVDEGIIITGY--KGSNPIVTAKAITSILKNLQY 108
                                   5678899**************99**********888788******.*********875..567****************** PP

                                   SEEEEESSCC.H..HHHHHHHHHHCT-EEEEEESEEEEETCCEEEEEECCCCTEEEEEE-TSSSEEEEE-TTSS--..... CS
                           ETF  91 dlvlagatai.g..kqvaprlAalLgvplitdvteleveggkltvtRpieggnglaevveadlpavltvrpgafep..... 163
                                   d+v++g ++     + +++ l+a+ g pl+ ++ +++++g ++++t+  e++n+     ead+pa+++v+ ++++p     
  gi|13542214|ref|NP_111902.1| 109 DIVVLGDQSAdSytGMLPGLLSAMTGFPLLGNANSITINGRSVRITQVGEAENAE---IEADMPAIVSVTQEINQPrlppv 186
                                   **********55***************************8878888888886666...789*****************999 PP

                                   --S-TT---EEE CS
                           ETF 164 aaimaakkkeve 175
                                   ++imaa++k+++
  gi|13542214|ref|NP_111902.1| 187 LQIMAAGRKPIR 198
                                   99********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       610  (0.0340231); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1534.44
//
Query:       gi|13542215|ref|NP_111903.1|  [L=397]
Description: major facilitator superfamily permease [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        1.4    9.0   5.1        2.7    8.1   0.2    3.3  2  DUF962    Protein of unknown function (DUF962)


Domain annotation for each model (and alignments):
>> DUF962  Protein of unknown function (DUF962)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   1.1     0.019   3.5e+02      41      49 ..      93     101 ..      12     278 .. 0.76
   2 ?    8.1   0.2   0.00015       2.7      28      93 ..     282     349 ..     279     351 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.019
                        DUF962  41 raklkllla 49 
                                    ++ ++ ++
  gi|13542215|ref|NP_111903.1|  93 ISQGAVSIT 101
                                   222233333 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00015
                        DUF962  28 vplilltvlllllraklklllalfvvgyifafvGHfvfEk.rkPAlfkn.plqsllidplmvllellg 93 
                                   v li+ ++l+ +++++  ++ ++f+  + +af+G   f k + PA +++  +++++ +p+mv++ l+g
  gi|13542215|ref|NP_111903.1| 282 VLLIVGLLLMSFMSPPSYFASLAFLSFFPAAFIGSEKFLKsQFPADLNYrEITAFFRNPIMVISPLMG 349
                                   56889999999**********************9876655166**99973599********9988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (397 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1173  (0.0654247); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                        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: 0.77u 0.32s 00:00:01.09 Elapsed: 00:00:00.53
# Mc/sec: 2273.17
//
Query:       gi|13542216|ref|NP_111904.1|  [L=143]
Description: hypothetical protein TVN1385 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       741  (0.0413297); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 892.59
//
Query:       gi|13542217|ref|NP_111905.1|  [L=450]
Description: dihydrolipoamide dehydrogenase [Thermoplasma volcanium GSS1]
Scores for complete 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-48  165.4   0.1    2.4e-48  164.9   0.1    1.2  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    6.6e-18   65.0   0.0    1.4e-17   63.9   0.0    1.6  1  Pyr_redox_dim   Pyridine nucleotide-disulphide oxidoreductase
      3e-12   46.9   1.5      2e-11   44.2   0.0    3.0  3  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    4.6e-10   39.2   0.1    3.3e-09   36.4   0.0    2.4  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
      1e-07   31.4   4.5      0.006   15.7   2.5    4.0  3  GIDA            Glucose inhibited division protein A
    1.7e-07   30.7   0.0    0.00026   20.2   0.0    2.6  3  K_oxygenase     L-lysine 6-monooxygenase (NADPH-requiring)
    2.7e-07   30.7   0.6      0.021   15.1   0.1    2.8  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    7.5e-05   22.4   0.1    0.00027   20.5   0.0    2.0  2  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
     0.0001   21.7   0.7      0.093   12.0   0.3    3.1  3  FAD_binding_3   FAD binding domain
    0.00021   20.1   0.7       0.59    8.8   0.1    3.7  4  HI0933_like     HI0933-like protein
    0.00069   19.0   0.0     0.0053   16.1   0.0    2.4  2  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
     0.0014   17.8   2.6       0.03   13.4   0.2    2.8  3  FAD_binding_2   FAD binding domain
     0.0033   17.1   1.9      0.024   14.3   0.4    2.6  4  DAO             FAD dependent oxidoreductase
     0.0034   16.7   1.2      0.046   13.0   0.1    2.6  3  Thi4            Thi4 family
  ------ inclusion threshold ------
      0.037   13.9   0.0       0.23   11.3   0.0    2.1  2  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 !  164.9   0.1     2e-51   2.4e-48       1     293 [.       4     315 ..       4     316 .. 0.86

  Alignments for each domain:
  == domain 1  score: 164.9 bits;  conditional E-value: 2e-51
                                   CSEEEE--SHHHHHHHHHHHHHTS-EEEEE....TTHCHHHCSHHHHCHHHHHHHHHHHHH.................... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxx.................... RF
                   Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaqagakvtlve....legtclnggcllskallgvaedaeias.................... 57 
                                   +dv+ +G+G A++ aa +l+++g+ v++++      g+cl +gc++ska+ ++ ++++ ++                    
  gi|13542217|ref|NP_111905.1|   4 YDVITLGAGGAAYPAAFRLKKSGYSVLMIDkkgiMSGNCLAEGCVPSKAIIETVHNYSKLKkfgkysiayedivkhkddvq 84 
                                   68999************************9999*9***********************999*********99998776553 PP

                                   HHHHCHHHHCCCCHCCTCEEEEESCEEEEETEEEC....TCEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2  58 evvkklnqgielllgeevvkidpgkkkvklekkke....gdeekiaydklvlAtGssprdlgipGvaenvgklvrtldsae 134
                                   +   +++q+ e  l e ++ki +g +k+ +e+++e      +e++ ++++++ tGs +  ++ipG+ e ++++ r+l  a 
  gi|13542217|ref|NP_111905.1|  85 NI--RYKQHDE-ELHEAGLKILKGTAKLIDENTVEvetdTGKERYRAESIIIGTGSDTYVPKIPGA-ELAWTS-RELY-AL 159
                                   22..3333422.2224699999999999999999899986779***********************.888766.5543.34 PP

                                   HHCCSS-TSEEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTE. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                   Pyr_redox_2 135 alklkllpkrivvvGgGyiGvElAaalaklgkevtlveardrllraldkelsaaleealekeGvevklgtsvkeidgnge. 214
                                     k  +lpk+i+++GgGyiG+E+A++++ lg +vt++e +dr+l+++d+ +   l   l k+  ++ l + vkei++ g+ 
  gi|13542217|ref|NP_111905.1| 160 NPKVRKLPKSIAIIGGGYIGLETASFMSLLGTDVTVIELLDRVLSTMDSGMVSKLVPLLPKM--NLILSSPVKEIRRGGDm 238
                                   445556669***************************************99999999999996..78888***********7 PP

                                   .EEEEEETTSCE.EEESEEEE-S-EEES-HHCS.HCCT-EEEETTEEE--TTSBESSTTEEE-GGGCTECCSS--HHHHHH CS
                                   .xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2 215 .klevvledgee.idadlvvvavGvrpstelle.eklglelderggivvdeflrtnvpgiyaiGDvaggkggpelaqaAvq 292
                                    ++++ +e ++e i ++ v++avG+ p  +  + ++lg++  ++ gi+v+  ++tn+++iya GDv    g   l +aA +
  gi|13542217|ref|NP_111905.1| 239 fEVSYDHEGKTEkIRVEAVLMAVGRMPMFPE-GlDDLGIKY-DKHGIKVNMAMQTNIKHIYATGDVN---GLTPLFHAAKR 314
                                   7666666666667**************8554.44*******.7778********************9...88888888876 PP

                                   H CS
                                   x RF
                   Pyr_redox_2 293 q 293
                                   q
  gi|13542217|ref|NP_111905.1| 315 Q 315
                                   6 PP

>> Pyr_redox_dim  Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.9   0.0   1.2e-20   1.4e-17       1     109 [.     338     445 ..     338     446 .. 0.94

  Alignments for each domain:
  == domain 1  score: 63.9 bits;  conditional E-value: 1.2e-20
                                   BEEEEESSSEEEEEES-HHHHHHHHSGEEEEEEEEECGHHHCHTTHTEEEEEEEEETTTTBEEEEEEECTTHHHHHHHHHH CS
                 Pyr_redox_dim   1 iptvvftdpevasvGlteeeAkaagieikvgkfpfkangralayaetkgfvKlvadaktgkvlGahivGpgageliqelav 81 
                                   +p +v+t p+va+vG+  ++Ak+ gi +     ++++ + a+++ e++g ++l +d    k++G  ++G++ag li+e+a+
  gi|13542217|ref|NP_111905.1| 338 VPFTVYTVPQVAYVGILPDQAKKLGISYIETDYQMEKDAMAQVNSEMEGEIRLFFDS-RMKIIGGYVIGNDAGNLINEIAL 417
                                   6889*********************888888889999999999999********999.89********************* PP

                                   HHHTTSBHHHHHTSBSSSSSTGGGGHCH CS
                 Pyr_redox_dim  82 aikagltvedladtihihPtlsealkea 109
                                    i++gl+++d+a+  h hP  +e l+ a
  gi|13542217|ref|NP_111905.1| 418 GISKGLSARDFAEMAHQHPMSFEGLDSA 445
                                   **********************998766 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       1.6     2e+03       2      31 ..       6      35 ..       5      41 .. 0.88
   2 !   44.2   0.0   1.7e-14     2e-11       1      71 [.     169     237 ..     169     245 .. 0.89
   3 ?   -2.3   0.2       5.6   6.6e+03       3      22 ..     397     416 ..     395     420 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 1.6
                                  EEEECSSHHHHHHHHHHHHTTSEEEEEESS CS
                     Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvvers 31
                                  v+ +G+G  +  +A  l++ g +V +++ +
  gi|13542217|ref|NP_111905.1|  6 VITLGAGGAAYPAAFRLKKSGYSVLMIDKK 35
                                  7889******************99999876 PP

  == domain 2  score: 44.2 bits;  conditional E-value: 1.7e-14
                                   EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETT CS
                     Pyr_redox   1 kvvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekngievllntkveeiegsed 71 
                                   +++++GgGyiglE A++++ lg +Vtv+e  d++l+ +D  + + l   l k+  +++l++ v+ei+  +d
  gi|13542217|ref|NP_111905.1| 169 SIAIIGGGYIGLETASFMSLLGTDVTVIELLDRVLSTMDSGMVSKLVPLLPKM--NLILSSPVKEIRRGGD 237
                                   689********************************999999999988888887..8999999999987665 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 5.6
                                   EEECSSHHHHHHHHHHHHTT CS
                     Pyr_redox   3 vvvGgGyiglElAgalaelg 22 
                                    ++Gg +ig ++++ ++e++
  gi|13542217|ref|NP_111905.1| 397 KIIGGYVIGNDAGNLINEIA 416
                                   599**9**999998888876 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 !   36.4   0.0   2.7e-12   3.3e-09       4     305 .]      10     300 ..       6     300 .. 0.69
   2 ?   -3.4   0.0       3.7   4.5e+03     150     173 ..     378     402 ..     369     408 .. 0.69

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 2.7e-12
                   Pyr_redox_3   4 GaGPaGlaaaielkkagledylilEkg..nignsiyrypkemtfispsftsekleipdlnaiseetspafslkeeklsrke 82 
                                   GaG a   aa  lkk+g  ++l ++k+    gn + +     + i     ++  +++++   s   +  +  +++ +++  
  gi|13542217|ref|NP_111905.1|  10 GAGGAAYPAAFRLKKSGY-SVLMIDKKgiMSGNCLAEGCVPSKAIIE-TVHNYSKLKKFGKYSIAYED-IVKHKDDVQNIR 87 
                                   777777777888888887.5777777645557777777666666653.35566666666666665554.334455566666 PP

                   Pyr_redox_3  83 aleYlrevaksfelpiklfeeVesvkkedegfevetsketyeAkkviiAtGefdkPnklnipGeek...lvkhyskvkefh 160
                                   + ++ +e+  +  l+i + +  + ++++  + e +t ke y+A+++ii tG     ++++ipG+e      + y+ +++++
  gi|13542217|ref|NP_111905.1|  88 YKQHDEELH-EAGLKILKGT-AKLIDENTVEVETDTGKERYRAESIIIGTGS--DTYVPKIPGAELawtSRELYALNPKVR 164
                                   777777764.4477776554.577888888888888899************9..999********4221233333334443 PP

                   Pyr_redox_3 161 kyagqkvvViGgknSavDaAlelvrkgaeVtvvtrgseiekeesdpsyslkpdienrleelvkeekikvlfnaevkeikek 241
                                       + +++iGg+  + ++A  +   g +Vtv+   + +         ++   + ++l  l+   k++++  + vkei++ 
  gi|13542217|ref|NP_111905.1| 165 -KLPKSIAIIGGGYIGLETASFMSLLGTDVTVIELLDRV-------LSTMDSGMVSKLVPLL--PKMNLILSSPVKEIRRG 235
                                   .33689***************************886532.......2233333444444444..36899************ PP

                   Pyr_redox_3 242 eeeykvktedgkkvev..kddvvlatGykpdlsf.lkkslfeldedgrpvlteeteetnvpglflaG 305
                                      ++v+ +++ k+e+   + v++a+G  p +   l++ ++++d+ g+ v  +  ++tn++ ++  G
  gi|13542217|ref|NP_111905.1| 236 GDMFEVSYDHEGKTEKirVEAVLMAVGRMPMFPEgLDDLGIKYDKHGIKV--NMAMQTNIKHIYATG 300
                                   ******9665555444434555566******9554999999997776655..56799*******987 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 3.7
                   Pyr_redox_3 150 vkhyskvk.efhkyagqkvvViGgk 173
                                   ++++s+++ e++ +++ ++ +iGg+
  gi|13542217|ref|NP_111905.1| 378 AQVNSEMEgEIRLFFDSRMKIIGGY 402
                                   4556666557777889999999997 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   2.5   5.1e-06     0.006       1     150 [.       5     137 ..       5     148 .. 0.73
   2 !    5.8   0.0    0.0052       6.2       2      29 ..     170     205 ..     169     241 .. 0.83
   3 !    5.1   0.0    0.0082       9.8     347     386 ..     286     325 ..     276     328 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 5.1e-06
                                   CEEEE-SSHHHHHHHHHHHHTT--EEEE...ES-GGGTT--SSSSEEE-TTHHHHHHHHHHHT-SHHHHHHHHEEEEEEES CS
                          GIDA   1 dviViGgGhAGceAAlaaarlGakvlLi...thkldtiaelsCnpsiggiakgllvrEidalggliikaadkagiqfrilN 78 
                                   dvi +G+G A + AA+ ++++G++vl+i       ++++  +C ps   i   +    ++++g   i   d  +       
  gi|13542217|ref|NP_111905.1|   5 DVITLGAGGAAYPAAFRLKKSGYSVLMIdkkGIMSGNCLAEGCVPSKAIIETVHNYSKLKKFGKYSIAYEDIVKH------ 79 
                                   7999************************76655567777778999998888888888888877766655554442...... PP

                                   TTS-CCC-EEEEEE-HHHHHHHHHHHHHTSTTEEEEES-EEEEEECTTEEEEEEETTS-EEEECEEEE--TT CS
                          GIDA  79 rskGpavralraqvdrelyskevteklenepnleiieeeveeliveekkvkgvvtedgetikakavviatGt 150
                                             +  v+  +y+++  e+l++   l+i++++++ ++  e++v++ + + +e ++a++++i tG+
  gi|13542217|ref|NP_111905.1|  80 ----------KDDVQNIRYKQH-DEELHE-AGLKILKGTAKLID--ENTVEVETDTGKERYRAESIIIGTGS 137
                                   ..........224444555554.444444.58888888888883..46666656666778999999999997 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0052
                                   EEEE-SSHHHHHHHHHHHHTT--EEEE........E CS
                          GIDA   2 viViGgGhAGceAAlaaarlGakvlLi........t 29 
                                   + +iGgG  G+e A  ++ lG +v+ i        t
  gi|13542217|ref|NP_111905.1| 170 IAIIGGGYIGLETASFMSLLGTDVTVIelldrvlsT 205
                                   78**********************999444444333 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.0082
                                   -TTSBBSSSBTEEE-CGGGTB-S.HHHHHHHHHHHHHHHHH CS
                          GIDA 347 lntLetkkvkgLflAGqinGteG.YeEaaaqGllAGinaar 386
                                   +  ++t+ +k++++ G++nG +  + +a  q l+A+ n+ +
  gi|13542217|ref|NP_111905.1| 286 NMAMQTN-IKHIYATGDVNGLTPlFHAAKRQSLVAANNIMA 325
                                   4478888.*************87355555599999999865 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       1.5   1.8e+03       1      35 [.       2      34 ..       2      36 .. 0.82
   2 !   20.2   0.0   2.2e-07   0.00026     134     206 ..     114     182 ..      74     201 .. 0.81
   3 !    7.5   0.0    0.0016       1.9     129     170 ..     235     275 ..     224     296 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.5
                   K_oxygenase  1 eilDligiGiGpsnLsLailleevkkelkalfler 35
                                  e++D+i  G+G ++   a +l++     ++l +++
  gi|13542217|ref|NP_111905.1|  2 ETYDVITLGAGGAAYPAAFRLKKSG--YSVLMIDK 34
                                  579********99999999998887..77777776 PP

  == domain 2  score: 20.2 bits;  conditional E-value: 2.2e-07
                   K_oxygenase 134 tveskdaegeeeelearnlvlgvGtepkiPevleklegkervvHsseylerkee.llakkriaVvGsGqSaaei 206
                                   tve+++++g +e+++a+++++g+G+  ++P++  +    e  + s e+   +++ ++ +k+ia++G+G  + e 
  gi|13542217|ref|NP_111905.1| 114 TVEVETDTG-KERYRAESIIIGTGSDTYVPKIPGA----ELAWTSRELYALNPKvRKLPKSIAIIGGGYIGLET 182
                                   566655677.689*****************98764....56777777666665558889*********888776 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0016
                   K_oxygenase 129 eeelltveskdaegeeeelearnlvlgvGtepkiPevlekle 170
                                   + ++++v+  d+eg++e+++ ++++++vG  p  Pe l++l 
  gi|13542217|ref|NP_111905.1| 235 GGDMFEVSY-DHEGKTEKIRVEAVLMAVGRMPMFPEGLDDLG 275
                                   337999*97.89************************998875 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 !   15.1   0.1   1.7e-05     0.021       2      36 ..       9      43 ..       8      61 .. 0.93
   2 !   13.3   0.1   6.4e-05     0.076       1      30 [.     172     201 ..     172     210 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.7e-05
                                  E--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG- CS
                 NAD_binding_8  2 vGaGlsGlvaAylLakagfdvlllekrdrlGGraa 36
                                  +GaG ++  aA +L+k g++vl ++k    +G++ 
  gi|13542217|ref|NP_111905.1|  9 LGAGGAAYPAAFRLKKSGYSVLMIDKKGIMSGNCL 43
                                  69999999************************996 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 6.4e-05
                                   EE--SHHHHHHHHHHHCCTEEEEEE-SSSS CS
                 NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrdr 30 
                                   I+G+G  Gl +A++++  g dv+++e  dr
  gi|13542217|ref|NP_111905.1| 172 IIGGGYIGLETASFMSLLGTDVTVIELLDR 201
                                   9*************************8877 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 ?   -2.9   0.0       3.5   4.2e+03       6      31 ..       9      34 ..       6      35 .. 0.85
   2 !   20.5   0.0   2.3e-07   0.00027       2      43 ..     169     210 ..     168     226 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 3.5
                                  E--STTHHHHHHHHHHCTSEEEEE-S CS
                UDPG_MGDP_dh_N  6 iGlGYvGlvtaavlaeighevigvDi 31
                                  +G+G    + a  l + g  v+++D+
  gi|13542217|ref|NP_111905.1|  9 LGAGGAAYPAAFRLKKSGYSVLMIDK 34
                                  6888888899999***********96 PP

  == domain 2  score: 20.5 bits;  conditional E-value: 2.3e-07
                                   EEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHHCTTS CS
                UDPG_MGDP_dh_N   2 kisviGlGYvGlvtaavlaeighevigvDideekvdklnsgk 43 
                                    i++iG GY+Gl ta  ++ +g +v+++   ++  +++ sg 
  gi|13542217|ref|NP_111905.1| 169 SIAIIGGGYIGLETASFMSLLGTDVTVIELLDRVLSTMDSGM 210
                                   69**************************98888777777765 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.3   0.0    0.0081       9.6       2      34 ..       4      36 ..       3      50 .. 0.89
   2 !   12.0   0.3   7.8e-05     0.093       4      34 ..     170     200 ..     168     212 .. 0.88
   3 ?    0.6   0.0      0.21   2.6e+02      85     163 ..     327     408 ..     278     428 .. 0.64

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0081
                                  EEEEEE--SHHHHHHHHHHHHTTHHEEEEESSS CS
                 FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlvekrs 34
                                  +dV+  GaG a   +a  L++ G +v++++k  
  gi|13542217|ref|NP_111905.1|  4 YDVITLGAGGAAYPAAFRLKKSGYSVLMIDKKG 36
                                  69999*************************976 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 7.8e-05
                                   EEEE--SHHHHHHHHHHHHTTHHEEEEESSS CS
                 FAD_binding_3   4 VlIVGaGpaGlmlallLseaGvrvvlvekrs 34 
                                   ++I+G+G  Gl +a+++s  G +v+++e  +
  gi|13542217|ref|NP_111905.1| 170 IAIIGGGYIGLETASFMSLLGTDVTVIELLD 200
                                   68*************************9655 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.21
                                   EEEEEHH.CHHCST-CEE--HHHHHHHHHHHHHHHT.EEETCSEE..EECCEECCCCCCCEEEECCTTEEEEEEEEEEEE- CS
                 FAD_binding_3  85 karadle.lesspervtvypqteleriLvehaeerg.lqvrfkte..vesleqdeegvtaevrdketgeeetvrakYlvGa 161
                                   ++++d+   +s p +v+++pq     iL ++a++ g   ++ + +    ++ q +++ + e+r    + + ++   Y++G 
  gi|13542217|ref|NP_111905.1| 327 HVPVDYFdPLSVPFTVYTVPQVAYVGILPDQAKKLGiSYIETDYQmeKDAMAQVNSEMEGEIRLFF-DSRMKIIGGYVIGN 406
                                   344444335577889999****************99544444433114455555555555555443.33457777888887 PP

                                   -G CS
                 FAD_binding_3 162 DG 163
                                   D 
  gi|13542217|ref|NP_111905.1| 407 DA 408
                                   75 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   0.1    0.0005      0.59       1      33 [.       4      36 ..       4      45 .. 0.93
   2 ?    1.8   0.0     0.067        80     139     167 ..     111     140 ..      91     154 .. 0.73
   3 !    4.8   0.0    0.0077       9.2       2      34 ..     169     201 ..     168     207 .. 0.89
   4 ?   -0.8   0.0      0.41   4.9e+02     125     177 ..     222     276 ..     219     294 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0005
                                  -SEEEE--SHHHHHHHHHHHHTT--EEEE-SSS CS
                   HI0933_like  1 kdviviGgGaAGlmaAisaakrgkrVlllekak 33
                                  +dvi +G+G A   aA +++k g +Vl+++k+ 
  gi|13542217|ref|NP_111905.1|  4 YDVITLGAGGAAYPAAFRLKKSGYSVLMIDKKG 36
                                  589***************************985 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.067
                                   TTE.EEEEE..TTEEEEESEEEE----SS- CS
                   HI0933_like 139 edgkfrvkt.kseeeleadklvlAtGGlSi 167
                                   ++++++v+t +++e+++a+++++ tG+  +
  gi|13542217|ref|NP_111905.1| 111 DENTVEVETdTGKERYRAESIIIGTGSDTY 140
                                   44556777755999************9764 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.0077
                                   SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSS CS
                   HI0933_like   2 dviviGgGaAGlmaAisaakrgkrVlllekakk 34 
                                   ++++iGgG  Gl +A  ++  g +V+++e  ++
  gi|13542217|ref|NP_111905.1| 169 SIAIIGGGYIGLETASFMSLLGTDVTVIELLDR 201
                                   689*************************97665 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 0.41
                                   EEE-S--EEEEECETTE.EEEEE....TTEEEEESEEEE----SS-GGGT--SHHH CS
                   HI0933_like 125 klrletevksvekeedgkfrvktk...seeeleadklvlAtGGlSiPklGstgkgy 177
                                   +l l++ vk++++  d  f+v+++   ++e+++ +++++A+G + +   G ++ g+
  gi|13542217|ref|NP_111905.1| 222 NLILSSPVKEIRRGGDM-FEVSYDhegKTEKIRVEAVLMAVGRMPMFPEGLDDLGI 276
                                   56678889999776665.999985345678999********987776666666655 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   0.0      0.59   7.1e+02      31      60 ..       6      35 ..       2      46 .. 0.91
   2 !   16.1   0.0   4.4e-06    0.0053      28      77 ..     167     217 ..     148     261 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.59
                                  EEEESTSHHHHHHHHHHHHTT-EEEEEESS CS
                   AlaDh_PNT_C 31 vlviGgGvaGlqAiatakglgakVtvlDvr 60
                                  v+ +G+G a   A+   k+ g +V ++D++
  gi|13542217|ref|NP_111905.1|  6 VITLGAGGAAYPAAFRLKKSGYSVLMIDKK 35
                                  8889********************999975 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 4.4e-06
                                   --EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHH.TTTCECEE CS
                   AlaDh_PNT_C  28 pakvlviGgGvaGlqAiatakglgakVtvlDvrparleqles.lgakfvev 77 
                                   p  + +iGgG  Gl+ ++  + lg +Vtv+++  ++l  ++s + +k v +
  gi|13542217|ref|NP_111905.1| 167 PKSIAIIGGGYIGLETASFMSLLGTDVTVIELLDRVLSTMDSgMVSKLVPL 217
                                   67899*********************************9999887776655 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.2   2.5e-05      0.03       1      37 [.       5      41 ..       5      48 .. 0.92
   2 ?    3.5   0.1     0.026        31       2      33 ..     170     201 ..     169     211 .. 0.89
   3 ?   -1.8   0.0         1   1.2e+03     371     402 ..     278     303 ..     241     313 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.5e-05
                                  SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSG CS
                 FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefgga 37
                                  Dvi  G+G+A + AA ++++ G +v++++k++ ++g+
  gi|13542217|ref|NP_111905.1|  5 DVITLGAGGAAYPAAFRLKKSGYSVLMIDKKGIMSGN 41
                                  99****************************9887775 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.026
                                   EEEE--SHHHHHHHHHHHHTTT-EEEEESSSG CS
                 FAD_binding_2   2 viViGsGlAGLaAAleaaeaGlkvavvekeqe 33 
                                   + +iG+G  GL  A  ++  G +v+v+e  ++
  gi|13542217|ref|NP_111905.1| 170 IAIIGGGYIGLETASFMSLLGTDVTVIELLDR 201
                                   67*************************98766 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 1
                                   EES-EEEBETTSBESTTEEESSBTEEE-STCE CS
                 FAD_binding_2 371 ytmgGvetdengrvldadgqpipGLYAaGeva 402
                                   y   G++++  +++      +i+  YA G v 
  gi|13542217|ref|NP_111905.1| 278 YDKHGIKVNMAMQT------NIKHIYATGDVN 303
                                   55678888888888......999999988775 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       3.8   4.5e+03       1      29 [.       5      35 ..       5      40 .. 0.81
   2 ?    1.0   0.0      0.21   2.5e+02     155     204 ..      94     139 ..      92     164 .. 0.73
   3 !   14.3   0.4     2e-05     0.024       2      27 ..     170     197 ..     169     211 .. 0.95
   4 ?   -3.9   0.0       6.6   7.9e+03     164     201 ..     224     262 ..     221     265 .. 0.61

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 3.8
                                  EEEEECTSHHHHHHHHHHHHTT..EEEEESS CS
                           DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekg 29
                                  dv+  G+G +   +A+ L + g  V+ ++k+
  gi|13542217|ref|NP_111905.1|  5 DVITLGAGGAAYPAAFRLKKSGysVLMIDKK 35
                                  666778888888899999888999****998 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.21
                                   HHHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEE.EEEEEEEE--GGGH CS
                           DAO 155 aaealGveilegtevtgleeedgkvwgverttp.gen.daadavVnaaGaws 204
                                   ++ ++G +il+g +++ ++e+    ++v  +t+ g +  +a+ +++ +G  +
  gi|13542217|ref|NP_111905.1|  94 ELHEAGLKILKG-TAKLIDEN---TVEV--ETDtGKErYRAESIIIGTGSDT 139
                                   56789999***9.77778553...5667..6666776334566*****9665 PP

  == domain 3  score: 14.3 bits;  conditional E-value: 2e-05
                                   EEEECTSHHHHHHHHHHHHTT..EEEEE CS
                           DAO   2 vviiGGGiiGlstAyeLarrg..Vtlle 27 
                                   ++iiGGG+iGl tA + +  g  Vt++e
  gi|13542217|ref|NP_111905.1| 170 IAIIGGGYIGLETASFMSLLGtdVTVIE 197
                                   89****************9999****99 PP

  == domain 4  score: -3.9 bits;  conditional E-value: 6.6
                                   EESECEEEEEEEETCEEEEE....EECTEEEEEEEEEEE--G CS
                           DAO 164 legtevtgleeedgkvwgve....rttpgendaadavVnaaG 201
                                   ++ ++v+++++ +g+  +v      +t + + +++av +a G
  gi|13542217|ref|NP_111905.1| 224 ILSSPVKEIRR-GGDMFEVSydheGKT-E-KIRVEAVLMAVG 262
                                   56678999954.667777767532211.2.224577888887 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.1   3.9e-05     0.046      18     120 ..       4     107 ..       1     117 [. 0.84
   2 ?    1.6   0.1      0.12   1.4e+02      19      48 ..     169     197 ..     161     215 .. 0.84
   3 ?   -2.7   0.0       2.3   2.7e+03      77      93 ..     271     287 ..     269     299 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.9e-05
                                   EEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTTTTSTTBSEEEEET.TTHHHHHHTT---EEESSEEEESEHH CS
                          Thi4  18 sDvvivGaGssGLtaayylakkpdlkvailersvspGGGawlGGqlfsaivvrk.pakelLdelgikyedegdyvvvkdaa 97 
                                    Dv+  GaG +   aa+ l k+ +  v++++++  + G     G + s+ +++       L+ +g  +  ++d v  kd +
  gi|13542217|ref|NP_111905.1|   4 YDVITLGAGGAAYPAAFRLKKS-GYSVLMIDKKGIMSGNCLAEGCVPSKAIIETvHNYSKLKKFGKYSIAYEDIVKHKDDV 83 
                                   69*****************999.**********9999999998988888888762456789***99999999988888877 PP

                                   HHH.HHHHHHHHTSTTEEEEESEE CS
                          Thi4  98 lft.stllskvlqlanvkllnava 120
                                   + +  +   + l+ a++k+l+++a
  gi|13542217|ref|NP_111905.1|  84 QNIrYKQHDEELHEAGLKILKGTA 107
                                   654157778888899999998875 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.12
                                   EEEEE--SHHHHHHHHHHHHCTTS-EEEEE CS
                          Thi4  19 DvvivGaGssGLtaayylakkpdlkvaile 48 
                                    ++i+G+G  GL +a  ++   +  v+++e
  gi|13542217|ref|NP_111905.1| 169 SIAIIGGGYIGLETASFMSLL-GTDVTVIE 197
                                   589************999988.66666666 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 2.3
                                   HHHTT---EEESSEEEE CS
                          Thi4  77 Ldelgikyedegdyvvv 93 
                                   Ld+lgiky+++g  v +
  gi|13542217|ref|NP_111905.1| 271 LDDLGIKYDKHGIKVNM 287
                                   899*****999876554 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      0.62   7.4e+02       4      31 ..       8      39 ..       5      99 .. 0.68
   2 ?   11.3   0.0   0.00019      0.23       2      38 ..     170     206 ..     169     234 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.62
                                  EE--SCCHHHHHHHHHHTT-EEEEE-S....- CS
                       3HCDH_N  4 viGaGtmGagiaavfasagleVvlvdi....s 31
                                   +GaG      a  + ++g++V ++d     s
  gi|13542217|ref|NP_111905.1|  8 TLGAGGAAYPAAFRLKKSGYSVLMIDKkgimS 39
                                  56777777777888888899999999844443 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00019
                                   EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHH CS
                       3HCDH_N   2 vaviGaGtmGagiaavfasagleVvlvdiseealeka 38 
                                   +a+iG G +G + a+ +   g +V++++  ++ l + 
  gi|13542217|ref|NP_111905.1| 170 IAIIGGGYIGLETASFMSLLGTDVTVIELLDRVLSTM 206
                                   9**************************9877776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (450 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       481  (0.026828); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); 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: 00:00:00.52
# Mc/sec: 2595.11
//
Query:       gi|13542218|ref|NP_111906.1|  [L=278]
Description: CBS domain-containing protein [Thermoplasma volcanium GSS1]
Scores for complete 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-29  100.3   6.7    1.2e-10   41.7   0.1    4.2  4  CBS       CBS domain
  ------ inclusion threshold ------
      0.014   15.7   0.3        6.6    7.1   0.0    2.5  2  DUF5438   Family of unknown function (DUF5438)


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 !   41.7   0.1   1.3e-14   1.2e-10       1      53 [.       3      55 ..       3      57 .. 0.97
   2 !   11.7   0.1     3e-05      0.27      11      55 ..      71     115 ..      63     117 .. 0.82
   3 !   19.3   0.1   1.3e-07    0.0011       1      55 [.     124     178 ..     124     180 .. 0.84
   4 !   28.8   0.0   1.4e-10   1.2e-06       2      47 ..     224     269 ..     223     277 .. 0.89

  Alignments for each domain:
  == domain 1  score: 41.7 bits;  conditional E-value: 1.3e-14
                                  HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHH CS
                           CBS  1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllr 53
                                  V++imt++++t +  +++ e+++ +++++v+++P++d  g++vG v++rD+++
  gi|13542218|ref|NP_111906.1|  3 VSEIMTPNPITYRVPSSINEVIKVLIKYNVTGIPITDTAGHYVGFVSRRDIFS 55
                                  89**********************99*************************85 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 3e-05
                                   EEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                           CBS  11 tvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                    v++d+ ++ a+ +m + + ++l V++ +g + Gi+t    ++++
  gi|13542218|ref|NP_111906.1|  71 AVYEDDEVKVAAVEMLNQRKRHLTVINREGIVTGILTPQNFMKVI 115
                                   689999999999999887778999******777****99888876 PP

  == domain 3  score: 19.3 bits;  conditional E-value: 1.3e-07
                                   HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                           CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                   V+++m    v +   t+l  +l +m  +++ ++PV++++g ++G++ +rD+++ +
  gi|13542218|ref|NP_111906.1| 124 VKEVMKGVSVPIWYKTPLPAILTIMNVSNIFSFPVINDEGGFIGLLVDRDIFDRI 178
                                   566666666889999**********667744*****99999**********9877 PP

  == domain 4  score: 28.8 bits;  conditional E-value: 1.4e-10
                                   HHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEE CS
                           CBS   2 gdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivt 47 
                                   ++im +d+ +v+ ++ l+ a++lm+++++++lPV+d+ + + G++ 
  gi|13542218|ref|NP_111906.1| 224 EEIMVKDPTVVYANDRLSTAADLMIKYNYNQLPVLDDTHGIYGMLY 269
                                   79*********************************77777999986 PP

>> DUF5438  Family of unknown function (DUF5438)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.1    0.0015        13      23      67 ..      18      64 ..       3      67 .. 0.70
   2 ?    7.1   0.0   0.00074       6.6      32      60 ..     106     134 ..      86     146 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0015
                       DUF5438 23 sttnsvisallmynllti..isttylsvsfrrvmsGfnspkhtnskl 67
                                  s+ n vi  l+ yn+  i    t+   v f      f  p+ t + +
  gi|13542218|ref|NP_111906.1| 18 SSINEVIKVLIKYNVTGIpiTDTAGHYVGFVSRRDIFSNPRETQTAM 64
                                  889***********976531445555566655556677788777665 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.00074
                       DUF5438  32 llmynlltiisttylsvsfrrvmsGfnsp 60 
                                   l   n++ +i  ty +v  + vm G   p
  gi|13542218|ref|NP_111906.1| 106 LTPQNFMKVIRDTYGTVKVKEVMKGVSVP 134
                                   445799*******************9888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       393  (0.0219198); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 1788.22
//
Query:       gi|13542219|ref|NP_111907.1|  [L=476]
Description: glycyl-tRNA synthetase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.8e-18   66.4   0.4      1e-17   64.1   0.0    2.3  3  HGTP_anticodon  Anticodon binding domain
    3.1e-09   37.1   0.0    1.6e-08   34.8   0.0    2.0  1  tRNA-synt_2b    tRNA synthetase class II core domain (G, H, P
     0.0019   18.1   0.4       0.77    9.7   0.0    2.5  2  zinc_ribbon_4   zinc-ribbon domain
  ------ inclusion threshold ------
      0.016   14.9   1.3       0.11   12.3   0.1    2.4  2  zinc_ribbon_2   zinc-ribbon domain
      0.016   14.7   1.0       0.71    9.4   0.1    2.6  3  Mu-like_Com     Mu-like prophage protein Com
      0.032   13.7   0.9      0.087   12.3   0.1    2.0  2  zf-ribbon_3     zinc-ribbon domain
      0.057   13.4   0.2         15    5.6   0.1    2.4  2  Prok-RING_1     Prokaryotic RING finger family 1
      0.072   12.9   1.0        2.6    7.9   0.0    2.8  3  zinc_ribbon_5   zinc-ribbon domain
       0.16   12.0   0.1       0.31   11.1   0.1    1.4  1  HypA            Hydrogenase/urease nickel incorporation, meta
       0.22   11.3   2.1       0.95    9.3   0.2    2.4  2  zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
       0.29   11.2   4.1          4    7.6   0.3    2.5  2  zf-ACC          Acetyl-coA carboxylase zinc finger domain
        1.1    9.5   2.7         16    5.7   3.0    2.5  2  Zn-ribbon_8     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 ?   -1.5   0.0       1.9   2.8e+03      16      38 ..      90     112 ..      82     117 .. 0.79
   2 ?   -2.5   0.0       3.9   5.8e+03      74      87 ..     229     242 ..     225     244 .. 0.79
   3 !   64.1   0.0   6.8e-21     1e-17       2      92 ..     376     464 ..     375     466 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.9
                                   HHHHHHHHHHHTTTSEEEEESSS CS
                HGTP_anticodon  16 eyakklaeeLraagirvelddsn 38 
                                   + a kl + L+  gi+v l++ +
  gi|13542219|ref|NP_111907.1|  90 KTAYKLENLLKSVGIDVPLNNVE 112
                                   5789999*******999888744 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 3.9
                                   TTTCEEEEEETTHH CS
                HGTP_anticodon  74 rdtreqervsldel 87 
                                   r+t+e+++v+l+e+
  gi|13542219|ref|NP_111907.1| 229 RNTGEEVTVDLKEA 242
                                   78888888888876 PP

  == domain 3  score: 64.1 bits;  conditional E-value: 6.8e-21
                                   EEEEESSSSHHHHHHHHHHHHHHHHTTTSEEEEESSSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEEETTTCEEEEE CS
                HGTP_anticodon   2 vvviplnekaeeleeyakklaeeLraagirvelddsnesigkkireadllgipfavvvGekelekgtvtvrdrdtreqerv 82 
                                   ++v pl++ ++ l   ak+l +++++ +   +++d++++ig+++++ d++g+pf+++v++++le+ tvt+r+rd+++q+r 
  gi|13542219|ref|NP_111907.1| 376 FAVFPLQR-RDGLDAKAKELFNKIKQID-PFVYYDEGGNIGRRYARQDEIGTPFCITVDYETLEDSTVTIRERDSTKQVRE 454
                                   6899***9.777*************999.4666679********************************************* PP

                                   ETTHHHHHHH CS
                HGTP_anticodon  83 sldelveklk 92 
                                    ++el++k++
  gi|13542219|ref|NP_111907.1| 455 NIEELLQKIS 464
                                   ******9996 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 !   34.8   0.0   1.1e-11   1.6e-08       8     176 ..     146     351 ..     136     353 .. 0.71

  Alignments for each domain:
  == domain 1  score: 34.8 bits;  conditional E-value: 1.1e-11
                                   SEEEEE-SSSHHHHHHHHHHHEEEBGG.SSEEEEEEEEEEBTTTSTBCTTTB-SEEEEEEEEEEESGGGHHHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  tRNA-synt_2b   8 dreyiLkPtneetfvelirdevlrskr.LPlklyqiqtkyRdEksdsrGLlRvreFhqkdgyvfhaeaslddslrdlikai 87 
                                    +e++L+P+  +++   +++    s++ +P+ + q++  +R+E s  + L+R+reF+q + +vf +++   d   +   + 
  gi|13542219|ref|NP_111907.1| 146 TNELYLRPETAQGIFINFKNLYNYSRNtMPIIVCQVGKGFRNEISPRQALIRMREFTQAEVEVFYLND--SDFNPNGNSLK 224
                                   579************9999885556667****************9556*****************988..45555555555 PP

                                   HHHHHHTT.SCEEEEEEGTTSC.........................................BTTSEEEEEEEEETTTSE CS
                                   xxxxxxxxxxxxxxxxxxxxxx.........................................xxxxxxxxxxxxxxxxxx RF
                  tRNA-synt_2b  88 sriferlglefraiielmsaks.........................................adykdkkefeavsesltk 127
                                    +++++ g e+  ++ l +a +                                            +++ +fe ++   + 
  gi|13542219|ref|NP_111907.1| 225 FKLLRNTGEEV--TVDLKEALHsgivknpvmayflektysilssigfnpnhlrarehdpleraHYSSETWDFEYLMD--GE 301
                                   67777777443..3333222222445577777777777778888888888888888888887333445668888888..88 PP

                                   EEEEEEEEEEET.HHHHHTTEEEECTTSSEEEEEEEEEEEEHHHHHHHHH CS
                                   xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  tRNA-synt_2b 128 gieigtiqklgt.rlserlgatvldennreksvimicaaigveRllsail 176
                                    iei+ ++ +gt  l +  + +  +++   + + ++  + g+ R+++ il
  gi|13542219|ref|NP_111907.1| 302 WIEIVGVSDRGTyDLGRHQQFSGENMEVDGNIPRVVEPSYGIDRIVLTIL 351
                                   88888888888754555444444445555555555777777778777776 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.0   0.00051      0.77       3      16 ..      84      97 ..      83     105 .. 0.88
   2 !    6.0   0.0    0.0077        12      25      33 ..     122     130 ..     119     133 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00051
                 zinc_ribbon_4  3 itCpsCkakyeidd 16
                                  + C++Ck++y++++
  gi|13542219|ref|NP_111907.1| 84 VKCEKCKTAYKLEN 97
                                  78********9986 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0077
                 zinc_ribbon_4  25 kvrCskCgh 33 
                                    v+C+kCg+
  gi|13542219|ref|NP_111907.1| 122 DVKCPKCGA 130
                                   589999985 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.1      0.31   4.6e+02      13      19 ..      83      89 ..      80      92 .. 0.69
   2 ?   12.3   0.1   7.3e-05      0.11       9      23 .]     118     132 ..     115     132 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.31
                 zinc_ribbon_2 13 akFCpyC 19
                                  a+ C++C
  gi|13542219|ref|NP_111907.1| 83 AVKCEKC 89
                                  6778888 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 7.3e-05
                 zinc_ribbon_2   9 lqdnakFCpyCGtpl 23 
                                   l++ ++ Cp+CG+pl
  gi|13542219|ref|NP_111907.1| 118 LEEYDVKCPKCGAPL 132
                                   678888999999997 PP

>> Mu-like_Com  Mu-like prophage protein Com
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0     0.041        62      19      33 ..      78      92 ..      74     102 .. 0.82
   2 ?    9.4   0.1   0.00047      0.71      16      32 ..     113     130 ..     111     133 .. 0.81
   3 ?   -4.0   0.0       6.9     1e+04      34      40 ..     272     278 ..     272     283 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.041
                   Mu-like_Com 19 AlDeltiKCPRCGtL 33
                                   + ++ +KC +C t 
  gi|13542219|ref|NP_111907.1| 78 KFSDIAVKCEKCKTA 92
                                  5777********985 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00047
                   Mu-like_Com  16 KaeA.lDeltiKCPRCGt 32 
                                   Ka+A l+e  +KCP+CG 
  gi|13542219|ref|NP_111907.1| 113 KANAvLEEYDVKCPKCGA 130
                                   5665478999*******5 PP

  == domain 3  score: -4.0 bits;  conditional E-value: 6.9
                   Mu-like_Com  34 nHlkaes 40 
                                   nHl+a  
  gi|13542219|ref|NP_111907.1| 272 NHLRARE 278
                                   9999975 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1         1   1.5e+03      17      23 ..      84      90 ..      80      91 .. 0.62
   2 ?   12.3   0.1   5.8e-05     0.087      11      26 .]     117     132 ..     115     133 .. 0.70

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1
                   zf-ribbon_3 17 nvCpyCG 23
                                  ++C +C 
  gi|13542219|ref|NP_111907.1| 84 VKCEKCK 90
                                  5566664 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 5.8e-05
                   zf-ribbon_3  11 plssddnvCpyCGtkl 26 
                                   +l++ d++Cp+CG++l
  gi|13542219|ref|NP_111907.1| 117 VLEEYDVKCPKCGAPL 132
                                   5677778888888776 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 ?    5.2   0.0     0.013        20      16      30 ..      78      93 ..      72      97 .. 0.75
   2 ?    5.6   0.1      0.01        15      21      29 ..     123     131 ..     115     135 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.013
                   Prok-RING_1 16 eedDi.VvCpeCgtpy 30
                                  + +Di V C +C+t y
  gi|13542219|ref|NP_111907.1| 78 KFSDIaVKCEKCKTAY 93
                                  55666488******99 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.01
                   Prok-RING_1  21 VvCpeCgtp 29 
                                   V Cp+Cg+p
  gi|13542219|ref|NP_111907.1| 123 VKCPKCGAP 131
                                   789999998 PP

>> zinc_ribbon_5  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0    0.0018       2.6       3      15 ..      84      96 ..      82     106 .. 0.84
   2 ?    2.6   0.1      0.08   1.2e+02      26      32 ..     123     129 ..     120     133 .. 0.75
   3 ?   -2.9   0.0       4.1   6.1e+03      11      19 ..     141     149 ..     140     149 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0018
                 zinc_ribbon_5  3 irCpdCdtkFklv 15
                                  ++C++C+t +kl 
  gi|13542219|ref|NP_111907.1| 84 VKCEKCKTAYKLE 96
                                  79*********96 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.08
                 zinc_ribbon_5  26 VrCakCa 32 
                                   V+C kC+
  gi|13542219|ref|NP_111907.1| 123 VKCPKCG 129
                                   6777775 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 4.1
                 zinc_ribbon_5  11 kFklvdskl 19 
                                   +Fk+ + +l
  gi|13542219|ref|NP_111907.1| 141 MFKVGTNEL 149
                                   8***99885 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    0.0002      0.31      68      94 ..      81     130 ..      67     140 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0002
                                   --EEEETTTS-EEECHH..HHH......................S-TTTSS CS
                          HypA  68 pvkvrCreCgkefelee..kal......................rCpkCgs 94 
                                   ++ v+C++C++ ++le+  k                        +CpkCg+
  gi|13542219|ref|NP_111907.1|  81 DIAVKCEKCKTAYKLENllK-SvgidvplnnvekanavleeydvKCPKCGA 130
                                   5789**********997432.268999**********************98 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 ?    1.2   0.2      0.22   3.3e+02       2       8 ..      84      90 ..      83      95 .. 0.84
   2 ?    9.3   0.2   0.00064      0.95       2      11 ..     123     132 ..     122     136 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.22
                                  EE-SSS- CS
                zf-C4_Topoisom  2 ekCPkCg 8 
                                  +kC+kC+
  gi|13542219|ref|NP_111907.1| 84 VKCEKCK 90
                                  79****7 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00064
                                   EE-SSS--EE CS
                zf-C4_Topoisom   2 ekCPkCggdL 11 
                                   +kCPkCg++L
  gi|13542219|ref|NP_111907.1| 123 VKCPKCGAPL 132
                                   89******98 PP

>> zf-ACC  Acetyl-coA carboxylase zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.3     0.025        38       2       9 ..      84      91 ..      84      98 .. 0.90
   2 ?    7.6   0.3    0.0027         4       2      10 ..     123     131 ..     123     132 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.025
                        zf-ACC  2 tKCpsCge 9 
                                  +KC++C++
  gi|13542219|ref|NP_111907.1| 84 VKCEKCKT 91
                                  7*****97 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0027
                        zf-ACC   2 tKCpsCgem 10 
                                   +KCp+Cg+ 
  gi|13542219|ref|NP_111907.1| 123 VKCPKCGAP 131
                                   7******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 ?    0.6   0.2      0.41   6.2e+02       7      34 ..      85      91 ..      73      99 .. 0.65
   2 ?    5.7   3.0     0.011        16      23      37 ..     119     133 ..      83     135 .. 0.65

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.41
                   Zn-ribbon_8  7 rCeeCghefevlqsisdapltaCPeCgs 34
                                  +                     C +C+ 
  gi|13542219|ref|NP_111907.1| 85 K---------------------CEKCKT 91
                                  4.....................555543 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.011
                   Zn-ribbon_8  23 dapltaCPeCgsevr 37 
                                   ++ +++CP+Cg+++r
  gi|13542219|ref|NP_111907.1| 119 EEYDVKCPKCGAPLR 133
                                   445788****99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (476 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       714  (0.0398237); expected 358.6 (0.02)
Passed bias filter:                      677  (0.0377601); expected 358.6 (0.02)
Passed Vit filter:                        89  (0.00496402); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.68u 0.31s 00:00:00.99 Elapsed: 00:00:00.49
# Mc/sec: 2904.58
//
Query:       gi|13542220|ref|NP_111908.1|  [L=404]
Description: membrane component of an uncharacterized iron-regulated ABC-type transporter [Thermoplasma volcanium GSS1]
Scores for complete 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  166.8   1.0    6.7e-49  166.5   1.0    1.1  1  UPF0051   Uncharacterized protein family (UPF0051)


Domain annotation for each model (and alignments):
>> UPF0051  Uncharacterized protein family (UPF0051)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  166.5   1.0   3.8e-53   6.7e-49       3     218 .]     156     379 ..     154     379 .. 0.94

  Alignments for each domain:
  == domain 1  score: 166.5 bits;  conditional E-value: 3.8e-53
                       UPF0051   3 fertlivveegaevtiieey.....agc....gvveifvgenAklkyvkvqnwse..davnlstkraeegrdaklelttvs 72 
                                   + ++li+v+eg+++++  +y     +g+    +++ if+ +n+++ y++vq+  +  d +++ ++ +e++ +a++++++  
  gi|13542220|ref|NP_111908.1| 156 AAKNLIIVGEGSSLNFT-RYivgggEGNgaqgDNTYIFLSRNSSIVYSQVQDRPKtvDGIQFLKTFMEDNTQATIHHVENG 235
                                   5789*************.66698884446667********************955247788888888999*********** PP

                       UPF0051  73 lggkltrkepsvelkgegaeaelnglylakgkqhldtrtkvdhngpntssrilskgvlkdearavfrgkikvrkgaqktda 153
                                    +++++++  ++++kg+ ++ +l+g+ +++g q++d+r + +  g ++ ++i ++g++++++ ++ rg+i++++   k+++
  gi|13542220|ref|NP_111908.1| 236 YNKSIIMT--ESYQKGNFTNYQLRGVSFTRGLQQMDLRDNTIQIGTHSIANIYVRGIVREKSLTMHRGNIDIKESGRKAEG 314
                                   *******9..*********************************************************************** PP

                       UPF0051 154 hqenrnLllsdkaradtiPeleidaddvkasHgAtvGkideeqlfYLmsRGlseeeArrlivrgf 218
                                   + + r Llls++a+a+t+P l i+++dvk +H+++v  idee lfYL+sRG++ee+A++li++gf
  gi|13542220|ref|NP_111908.1| 315 YYDTRILLLSKEAYANTKPALLINNNDVKSKHASAVTNIDEESLFYLRSRGIDEETAKNLIIEGF 379
                                   ****************************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (404 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       548  (0.030565); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.24s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2791.14
//
Query:       gi|13542221|ref|NP_111909.1|  [L=481]
Description: membrane component of an uncharacterized iron-regulated ABC-type transporter [Thermoplasma volcanium GSS1]
Scores for complete 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-64  215.2   0.1    1.1e-63  214.8   0.1    1.1  1  UPF0051   Uncharacterized protein family (UPF0051)


Domain annotation for each model (and alignments):
>> UPF0051  Uncharacterized protein family (UPF0051)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  214.8   0.1   6.2e-68   1.1e-63       2     218 .]     225     450 ..     224     450 .. 0.97

  Alignments for each domain:
  == domain 1  score: 214.8 bits;  conditional E-value: 6.2e-68
                       UPF0051   2 qfertlivveegaevtiieeyagc............gvveifvgenAklkyvkvqnwsedavnlstkraeegrdakleltt 70 
                                   qfe+t++v++eg++v+++   +gc            ++ve +v +nA+ +y++vqnws++++n++tkra ++++ ++e++ 
  gi|13542221|ref|NP_111909.1| 225 QFEHTIVVADEGSSVHYL---EGCtapvyskdslhaAIVEYYVMKNAHGRYTSVQNWSNSVYNMPTKRAWVEENGNMEWVG 302
                                   89****************...777777777777777*********************************8899999***** PP

                       UPF0051  71 vslggkltrkepsvelkgegaeaelnglylakgkqhldtrtkvdhngpntssrilskgvlkdearavfrgkikvrkgaqkt 151
                                   +slg+k+t+ +ps++l+g++a+++   ++la+ +   dt+ k++h +pntss+i++k+v+ +++++++rg ++++k+a ++
  gi|13542221|ref|NP_111909.1| 303 GSLGSKVTMIYPSSYLRGRNATTSNLNIALASPGTVKDTGAKAIHMAPNTSSKIIAKSVSLGDGKSIYRGLVRINKDALNA 383
                                   ********************************************************************************* PP

                       UPF0051 152 dahqenrnLllsdkaradtiPeleidaddvkasHgAtvGkideeqlfYLmsRGlseeeArrlivrgf 218
                                   ++++++++Ll++d++ ++t+P+ ei++  +  +H+AtvGki  e+l+YL+sRGlse+eA +liv gf
  gi|13542221|ref|NP_111909.1| 384 KSYVQCDALLINDESVSYTMPHDEIYEPTANFTHEATVGKIGTEELTYLRSRGLSEDEASSLIVLGF 450
                                   *****************************************************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (481 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 3236.65
//
Query:       gi|13542222|ref|NP_111910.1|  [L=246]
Description: Iron-regulated ABC transporter ATPase subunit [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      4e-25   88.9   0.0    5.9e-25   88.4   0.0    1.3  1  ABC_tran     ABC transporter
    4.3e-08   33.3   0.7    0.00065   19.6   0.0    2.3  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    4.7e-08   32.7   0.9    7.8e-05   22.2   0.0    2.2  2  SMC_N        RecF/RecN/SMC N terminal domain
    5.6e-05   23.1   0.2     0.0001   22.2   0.2    1.4  1  RsgA_GTPase  RsgA GTPase
      0.004   16.9   0.1     0.0086   15.8   0.1    1.5  1  AAA_29       P-loop containing region of AAA domain
     0.0051   17.2   1.1      0.097   13.1   1.1    2.3  1  AAA          ATPase family associated with various cellular a
  ------ inclusion threshold ------
      0.016   15.5   0.5        3.5    7.9   0.1    2.2  2  AAA_22       AAA domain
       0.11   13.0   0.2        0.2   12.1   0.2    1.4  1  AAA_23       AAA domain
       0.11   12.1   0.1       0.18   11.4   0.1    1.3  1  AAA_27       AAA domain
        0.2   11.3   0.1       0.41   10.3   0.1    1.7  1  AAA_30       AAA domain
       0.22   11.1   0.1       0.43   10.1   0.0    1.6  2  AAA_25       AAA domain
       0.25   10.0   2.2        4.8    5.7   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 !   88.4   0.0   3.9e-28   5.9e-25       1     134 [.      18     169 ..      18     172 .. 0.93

  Alignments for each domain:
  == domain 1  score: 88.4 bits;  conditional E-value: 3.9e-28
                                   EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--..SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkp..teGeilldgkdlke.qeleslrkeigvlpqepqlfpeltvre 78 
                                   lknv+l++k ge++a++G+nGaGKStL ++l+g+ +   t G++lldgkd++  +++e++r+ +   +q p   +++++ +
  gi|13542222|ref|NP_111910.1|  18 LKNVNLTVKGGEIHALMGPNGAGKSTLGNVLIGHPDYkvTGGNVLLDGKDITFaTPEERARAGLFLAFQSPVAVEGVRIST 98 
                                   79*******************************977666*************9999******************9999988 PP

                                   H.................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEES CS
                                   x.................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  79 n.................esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDE 134
                                                     e +++++ +++++gl+e    + +s    +SgG+++r ++ ++++ kpk+++lDE
  gi|13542222|ref|NP_111910.1|  99 FlriaysnlhpgekivisEFNKKVKSLMKTVGLDE--SFISRSVNDGFSGGERKRFEILQMMILKPKIIILDE 169
                                   899**************999************999..334333459**************************9 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.2   7.3e-05      0.11       2      19 ..      31      48 ..      30     127 .. 0.64
   2 !   19.6   0.0   4.3e-07   0.00065     238     300 ..     145     204 ..     125     207 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 7.3e-05
                        AAA_21  2 nvliGpNgsGKSnLLdal 19
                                   +l GpNg+GKS+L   l
  gi|13542222|ref|NP_111910.1| 31 HALMGPNGAGKSTLGNVL 48
                                  6899**********8888 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 4.3e-07
                        AAA_21 238 SdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSpl 300
                                   S G ++ + +l +++  +   +++++DE+++gL+  +lr ++e +++  +n++ +++ TH   
  gi|13542222|ref|NP_111910.1| 145 SGGERKRFEILQMMILKP---KIIILDEIDSGLDVDALRMVAEQIRSYLNNDVGFLIITHYQR 204
                                   666666666666666655...9***********************888888*********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 !    9.2   0.2   0.00049      0.74      25      41 ..      29      45 ..      14      55 .. 0.83
   2 !   22.2   0.0   5.3e-08   7.8e-05     123     205 ..     122     209 ..     102     223 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00049
                                  SEEEEEESTTSSHHHHH CS
                                  xxxxxxxxxxxxxxxxx RF
                         SMC_N 25 sftaivGpNGSGKsnll 41
                                  ++ a++GpNG+GKs l 
  gi|13542222|ref|NP_111910.1| 29 EIHALMGPNGAGKSTLG 45
                                  5789**********886 PP

  == domain 2  score: 22.2 bits;  conditional E-value: 5.3e-08
                                   HHHHHHCTT-STT........CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEE CS
                                   xxxxxxxxxxxxx........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxx RF
                         SMC_N 123 vsellesagiske........lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn.aQfiv 194
                                   v++l++++g++++         +SgGe++   +   + +   kp+ + +lDeid+ LD    + vae +++  +n + f++
  gi|13542222|ref|NP_111910.1| 122 VKSLMKTVGLDESfisrsvndGFSGGERKRFEI---LQMMILKPK-IIILDEIDSGLDVDALRMVAEQIRSYLNNdVGFLI 198
                                   555555555555555555555678888776554...222334444.789*********************876655***** PP

                                   E-SSHHHCCC- CS
                                   xxxxxxxxxxx RF
                         SMC_N 195 islreemleka 205
                                   i++ +++l++ 
  gi|13542222|ref|NP_111910.1| 199 ITHYQRILKDI 209
                                   *****999876 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.2     7e-08    0.0001      78     127 ..       6      56 ..       2      69 .. 0.87

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 7e-08
                                   EEEE--TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT----- CS
                   RsgA_GTPase  78 evllvsaktkegleelkellkd.ktsvlvGqSGvGKStLinallpelelkt 127
                                   + l  s++ ke l++++  +k+ ++ +l+G+ G+GKStL n+l+++ + k+
  gi|13542222|ref|NP_111910.1|   6 NNLSASVEGKEILKNVNLTVKGgEIHALMGPNGAGKSTLGNVLIGHPDYKV 56 
                                   55677888889999999999999*********************9988776 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   0.1   5.8e-06    0.0086      17      38 ..      23      44 ..      16      50 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 5.8e-06
                        AAA_29 17 ieidlkg..atlltGpsGsGKSTl 38
                                  +++  kg  ++ l+Gp+G+GKSTl
  gi|13542222|ref|NP_111910.1| 23 LTV--KGgeIHALMGPNGAGKSTL 44
                                  344..444699************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 !   13.1   1.1   6.5e-05     0.097       3      74 ..      33     177 ..      31     216 .. 0.59

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.5e-05
                                   EESSTTSSHHHHHHHHHHH..HTHE...........................................EEEEETTTCSSS. CS
                           AAA   3 lyGppGtGKTllakavake..lgve...........................................fleisgsellsk. 37 
                                   l+Gp G GK++l + ++ +     +                                           fl+i  s+l    
  gi|13542222|ref|NP_111910.1|  33 LMGPNGAGKSTLGNVLIGHpdY--KvtggnvlldgkditfatpeeraraglflafqspvavegvristFLRIAYSNLH-Pg 110
                                   7899999999999999999441..223444455555555556666666666666666666666666665555555555.13 PP

                                   ................................STTHHHHHHHHHHHHHHHTS.............TSEEEEEETGGGHHHH CS
                           AAA  38 ................................yvgesekkirelfkeakeka.............kpsilfiDEidalaks 73 
                                                                    ++                              kp+i+++DEid+    
  gi|13542222|ref|NP_111910.1| 111 ekivisefnkkvkslmktvgldesfisrsvndGFSG---------------GerkrfeilqmmilKPKIIILDEIDSGLDV 176
                                   467666666666666665554444444443332222...............1222344555555779*********98665 PP

                                   H CS
                           AAA  74 r 74 
                                   +
  gi|13542222|ref|NP_111910.1| 177 D 177
                                   5 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.1    0.0024       3.5       5      23 ..      28      46 ..      24      82 .. 0.88
   2 ?    5.9   0.0      0.01        15      92     127 ..     162     198 ..     137     207 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0024
                        AAA_22  5 agilvvtGesGtGKTtllr 23
                                    i +++G+ G+GK+tl +
  gi|13542222|ref|NP_111910.1| 28 GEIHALMGPNGAGKSTLGN 46
                                  567799**********976 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.01
                        AAA_22  92 ielliiDEaqh.lr.s..eealeeLrsllnlsrkgvqliL 127
                                   ++++i+DE++  l+      + e++rs ln    +v +++
  gi|13542222|ref|NP_111910.1| 162 PKIIILDEIDSgLDvDalRMVAEQIRSYLN---NDVGFLI 198
                                   689**********76255555666788788...5555544 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2   0.00013       0.2      18      35 ..      27      44 ..       3      49 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00013
                        AAA_23 18 skgltlItGpNGaGKTTi 35
                                  +  + ++ GpNGaGK+T+
  gi|13542222|ref|NP_111910.1| 27 GGEIHALMGPNGAGKSTL 44
                                  45677899*********8 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00012      0.18      18      42 ..      20      44 ..       5      49 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00012
                        AAA_27 18 sldfsaeeadlhliyGpNEAGKsta 42
                                  ++++  +  ++h ++GpN AGKst+
  gi|13542222|ref|NP_111910.1| 20 NVNLTVKGGEIHALMGPNGAGKSTL 44
                                  5667777899**************7 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   0.00027      0.41      14      63 ..      24      82 ..      18     191 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00027
                        AAA_30 14 ltsgdrvavltGpAGtGKttalkalreaweaa..g.......grviglAptgkaAkvLa 63
                                  + +g  +++l Gp G+GK+t+ ++l  + + +  g       +++  ++p+++a + L 
  gi|13542222|ref|NP_111910.1| 24 TVKGGEIHALMGPNGAGKSTLGNVLIGHPDYKvtGgnvlldgKDITFATPEERARAGLF 82
                                  55566799************999986654444223677777666777777777766654 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00028      0.43      30      50 ..      25      45 ..       9     108 .. 0.86
   2 ?   -2.9   0.0       2.9   4.3e+03     143     157 ..     162     176 ..     150     204 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00028
                        AAA_25 30 lpagelallaGapgtGKttla 50
                                  +  ge+++l+G+ g+GK+tl 
  gi|13542222|ref|NP_111910.1| 25 VKGGEIHALMGPNGAGKSTLG 45
                                  56799**************96 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.9
                        AAA_25 143 vrlvviDplsralgg 157
                                   ++ +++D +++ l+ 
  gi|13542222|ref|NP_111910.1| 162 PKIIILDEIDSGLDV 176
                                   555666655544433 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.1    0.0032       4.8      21      36 ..      33      48 ..      21      68 .. 0.86
   2 ?    4.1   0.3    0.0099        15     524     577 ..     159     209 ..     153     227 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0032
                        AAA_13 21 iYGwNGaGKTtLSrll 36
                                  + G NGaGK+tL ++l
  gi|13542222|ref|NP_111910.1| 33 LMGPNGAGKSTLGNVL 48
                                  569*********9987 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.0099
                        AAA_13 524 igkdkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHnleffkev 577
                                   i k ki+++D   S LD ++l +v+  i+s+l   ++   ++i TH    +k +
  gi|13542222|ref|NP_111910.1| 159 ILKPKIIILDEIDSGLDVDALRMVAEQIRSYL---NNDVGFLIITHYQRILKDI 209
                                   6799******999******************9...5656677889988888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       590  (0.0329076); expected 358.6 (0.02)
Passed bias filter:                      546  (0.0304535); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1541.10
//
Query:       gi|13542223|ref|NP_111911.1|  [L=215]
Description: transcription regulator [Thermoplasma volcanium GSS1]
Scores for complete 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-07   29.1   0.1    1.3e-06   28.1   0.1    1.5  1  HTH_5     Bacterial regulatory protein, arsR family
    1.2e-06   28.4   0.0    2.4e-06   27.4   0.0    1.5  1  PadR      Transcriptional regulator PadR-like family
    5.4e-05   23.3   0.1    9.9e-05   22.5   0.1    1.5  1  HTH_34    Winged helix DNA-binding domain
     0.0019   17.7   0.0      0.006   16.1   0.0    2.0  1  HTH_24    Winged helix-turn-helix DNA-binding
     0.0037   17.2   0.0     0.0055   16.7   0.0    1.3  1  MetOD1    Metanogen output domain 1
     0.0065   16.4   0.1      0.017   15.1   0.1    1.7  1  HTH_11    HTH domain
  ------ inclusion threshold ------
       0.02   15.4   0.0      0.048   14.2   0.0    1.7  1  HTH_27    Winged helix DNA-binding domain
      0.037   14.2   0.5       0.11   12.8   0.2    1.9  2  UPF0122   Putative helix-turn-helix protein, YlxM / p13 like
      0.061   13.3   0.3        1.8    8.6   0.0    2.8  3  RHH_3     Ribbon-helix-helix domain
       0.21   11.7   0.9        4.4    7.5   0.2    2.9  3  DUF2250   Uncharacterized protein conserved in archaea (DUF22


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 !   28.1   0.1   7.3e-10   1.3e-06       3      47 .]      10      54 ..       8      54 .. 0.96

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 7.3e-10
                                  HHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                         HTH_5  3 tRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLVek 47
                                  t+ kIL  L+ + l+  +l+e+l++++ +v +H  +L+  G+V++
  gi|13542223|ref|NP_111911.1| 10 TKAKILEKLNISDLSLDQLSEILKINKTAVKEHMEFLEMRGYVSS 54
                                  899****************************************86 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.0   1.4e-09   2.4e-06      21      69 ..      27      74 ..      22      79 .. 0.89

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 1.4e-09
                                  CCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCC CS
                          PadR 21 elsegllelseGslYpaLkrLekeglveseweesgegpprkyYrlTdaG 69
                                  +l +++l+++++ +   ++ Le  g+v+s+ ++sg+g+p+k+Y+lTd+G
  gi|13542223|ref|NP_111911.1| 27 QL-SEILKINKTAVKEHMEFLEMRGYVSSYFKPSGTGRPKKFYKLTDKG 74
                                  55.46789999999999*******************************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 !   22.5   0.1   5.5e-08   9.9e-05      16      73 ..      24      82 ..      12      90 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 5.5e-08
                        HTH_34 16 dfvelkealeatdgnLsvhlkkLekagYie.vdkefkgkkprtllriTpeGreafkkyv 73
                                  +  +l+e l++++ +   h++ Le+ gY++ + k    ++p+  +++T++G + f k  
  gi|13542223|ref|NP_111911.1| 24 SLDQLSEILKINKTAVKEHMEFLEMRGYVSsYFKPSGTGRPKKFYKLTDKGISLFPKKY 82
                                  5679*************************82456666789************9996544 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   3.4e-06     0.006      17      47 ..      22      52 ..      13      53 .. 0.95

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 3.4e-06
                        HTH_24 17 risqreLAerlglSpstvnrrlkrLeeeGlI 47
                                  ++s  +L+e l + +++v+++++ Le  G++
  gi|13542223|ref|NP_111911.1| 22 DLSLDQLSEILKINKTAVKEHMEFLEMRGYV 52
                                  58999*************************8 PP

>> MetOD1  Metanogen output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   3.1e-06    0.0055      58     152 ..     126     213 ..      86     215 .] 0.75

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 3.1e-06
                        MetOD1  58 ekeeedaekvlkayiewlnqlfanfgiktekkedeknvlleftnCpWge.earknPifCl.lcraivsrsftwtglkgsve 136
                                   ++ ++++ + l++y+++ln l+ n +i++     +++v++  +nC        +n+i+C+ l + +v +s     l+ ++e
  gi|13542223|ref|NP_111911.1| 126 DMPRDEKIRKLEEYVNMLNVLGYNATIDVY----SDRVVISRHNCIFYDlAKTNNKIICNsLGKDLVLQS-----LNADFE 197
                                   4555555667899*************9999....67899**********556678999983345555555.....566799 PP

                        MetOD1 137 qkktlgngdekCvFei 152
                                    ++++ +g+ kCv e 
  gi|13542223|ref|NP_111911.1| 198 ITERISSGSSKCVIEV 213
                                   9999********9776 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1   9.3e-06     0.017       3      44 ..      12      51 ..      10      55 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 9.3e-06
                        HTH_11  3 lqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgv 44
                                   +ile L+ ++  +s ++L+e L++ +++v  +++ Le+ g+
  gi|13542223|ref|NP_111911.1| 12 AKILEKLNISD--LSLDQLSEILKINKTAVKEHMEFLEMRGY 51
                                  58999995555..*************************9995 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   2.7e-05     0.048      19      68 .]      23      74 ..      10      74 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.7e-05
                        HTH_27 19 kkladlcgrlnvedshisyslkkLtekGLvertgdeadrre....krvrlTdkG 68
                                   +l +l++ l+++++++ + ++ L+ +G+v +  ++   ++    k+++lTdkG
  gi|13542223|ref|NP_111911.1| 23 LSLDQLSEILKINKTAVKEHMEFLEMRGYVSSYFKP--SGTgrpkKFYKLTDKG 74
                                  57789*************************443333..3333356********9 PP

>> UPF0122  Putative helix-turn-helix protein, YlxM / p13 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.2   5.9e-05      0.11      13      55 ..       2      44 ..       1      49 [. 0.94
   2 ?   -2.2   0.0       2.9   5.1e+03      51      73 ..     169     191 ..     156     208 .. 0.51

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.9e-05
                       UPF0122 13 iYqsLLTekqanylelyyadDlSlsEiAeefnvsrqavydnik 55
                                  +Y+++L + +a+ le     DlSl  + e  +++++av ++++
  gi|13542223|ref|NP_111911.1|  2 LYDDILGDTKAKILEKLNISDLSLDQLSEILKINKTAVKEHME 44
                                  6999**********************************99875 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.9
                       UPF0122  51 ydnikrtekllekyEekLkllek 73 
                                   yd  k+ +k++ +   k  +l+ 
  gi|13542223|ref|NP_111911.1| 169 YDLAKTNNKIICNSLGKDLVLQS 191
                                   45555555544333222223333 PP

>> RHH_3  Ribbon-helix-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.16   2.9e+02      16      28 ..      24      36 ..      22      38 .. 0.88
   2 ?    8.6   0.0   0.00098       1.8      30      43 ..      69      82 ..      69      83 .. 0.96
   3 ?   -3.6   0.0       6.6   1.2e+04      11      20 ..     137     146 ..     137     146 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.16
                         RHH_3 16 kLkaLSekTrIpr 28
                                  +L++LSe ++I++
  gi|13542223|ref|NP_111911.1| 24 SLDQLSEILKINK 36
                                  59********998 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00098
                         RHH_3 30 klldeAiellLekY 43
                                  kl+d++i+l+++kY
  gi|13542223|ref|NP_111911.1| 69 KLTDKGISLFPKKY 82
                                  89************ PP

  == domain 3  score: -3.6 bits;  conditional E-value: 6.6
                         RHH_3  11 pelaekLkaL 20 
                                   +e++++L+ L
  gi|13542223|ref|NP_111911.1| 137 EEYVNMLNVL 146
                                   6899999876 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 ?    1.0   0.0      0.26   4.6e+02      28      54 ..      28      54 ..       9      59 .. 0.79
   2 ?   -0.0   0.0      0.54   9.7e+02      75      89 ..      63      77 ..      51      81 .. 0.77
   3 ?    7.5   0.2    0.0024       4.4      24      62 ..      78     116 ..      65     121 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.26
                       DUF2250 28 iakeleipleevrellkkLeelGLler 54
                                  +++ l+i+++ v+e ++ Le  G +  
  gi|13542223|ref|NP_111911.1| 28 LSEILKINKTAVKEHMEFLEMRGYVSS 54
                                  567789999999999999999998865 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.54
                       DUF2250 75 khHtYYrltreGell 89
                                  +  ++Y+lt++G  l
  gi|13542223|ref|NP_111911.1| 63 RPKKFYKLTDKGISL 77
                                  45689*****99665 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0024
                       DUF2250  24 YaksiakeleipleevrellkkLeelGLlervegktikr 62 
                                   ++k + + +++ +eev++ + + +  G+ler  +k+i  
  gi|13542223|ref|NP_111911.1|  78 FPKKYIEFTKLLVEEVEKDVGSYKLNGMLERIAAKIISD 116
                                   7999********************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       555  (0.0309554); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); 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: 0.58u 0.35s 00:00:00.93 Elapsed: 00:00:00.56
# Mc/sec: 1164.11
//
Query:       gi|13542224|ref|NP_111912.1|  [L=100]
Description: aromatic ring hydroxylating enzyme [Thermoplasma volcanium GSS1]
Scores for complete sequence (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   83.0   0.1    1.6e-23   82.6   0.1    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 !   82.6   0.1     9e-28   1.6e-23       1      73 [.       4      76 ..       4      77 .. 0.96

  Alignments for each domain:
  == domain 1  score: 82.6 bits;  conditional E-value: 9e-28
                                  HHHHHHHHTT-B-TTTSSBCCCCT---EEEE-T-EEEEEE--SSTT-TTHHHHHHHHHHHHC.STT--EEEEE CS
                FeS_assembly_P  1 keavlaaLrtVtDPelgvdlvslglvreidieggkVsvditltypacslaeairadaeaalralpgvevveVe 73
                                  ke++l+aL+tV DPe+g d+v+lglv++++i+g++V++ +t+t p c++ + i ++a++ ++ lpgve + +e
  gi|13542224|ref|NP_111912.1|  4 KEEILEALKTVSDPEIGYDVVNLGLVYDVEINGNRVYIRMTMTAPTCPVTPWILSQAQQVVEELPGVEACDIE 76
                                  79****************************************************************9887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); 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 0.30s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 666.79
//
Query:       gi|13542225|ref|NP_111913.1|  [L=184]
Description: transcription factor [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-58  195.1   0.1    3.1e-28   97.6   0.0    2.0  2  TBP       Transcription factor TFIID (or TATA-binding protein
    3.1e-06   27.2   0.0      0.045   13.9   0.0    2.6  2  DUF3378   Domain of unknown function (DUF3378)
  ------ inclusion threshold ------
       0.13   11.9   0.0         14    5.4   0.0    2.4  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 !   96.0   0.0   1.6e-31   9.3e-28       2      83 ..       7      86 ..       6      88 .. 0.97
   2 !   97.6   0.0   5.2e-32   3.1e-28       2      84 ..      98     180 ..      97     181 .. 0.97

  Alignments for each domain:
  == domain 1  score: 96.0 bits;  conditional E-value: 1.6e-31
                                  EEEEEEEEEEE-SSCE-HHHHHHHCCTTTEEE-TTTSSSEEEEETTTTEEEEE-TTSEEEEECESSHHHHHHHHHHHHHHHH CS
                           TBP  2 fkiqNvvasanlgleldLeklalkaekrnaeYeperfpglvyrlrepkvtaliFssGkvvitGakseeelreaakkiapilk 83
                                  ++i+N+vas++l  +ldL+++al +   ++eYepe+fpgl+yrl++pk+++liF+sGkv +tGak+ e++++ +k i+++lk
  gi|13542225|ref|NP_111913.1|  7 ITIENIVASTSLAEHLDLSRIALAL--DGSEYEPEQFPGLIYRLQDPKTAVLIFRSGKVNCTGAKNIEDVKRTIKIIIDKLK 86
                                  89********************998..****************************************************998 PP

  == domain 2  score: 97.6 bits;  conditional E-value: 5.2e-32
                                   EEEEEEEEEEE-SSCE-HHHHHHHCCTTTEEE-TTTSSSEEEEETTTTEEEEE-TTSEEEEECESSHHHHHHHHHHHHHHH CS
                           TBP   2 fkiqNvvasanlgleldLeklalkaekrnaeYeperfpglvyrlrepkvtaliFssGkvvitGakseeelreaakkiapil 82 
                                   + +qN+va ++l++el+L+ +a+++  +n+eYepe+fpglvyr++ep+v++l+F sGkvv+tGak+e+e+++a+ k+ + l
  gi|13542225|ref|NP_111913.1|  98 IIVQNIVAVYDLESELNLTDIAMSLGLENVEYEPEQFPGLVYRVEEPRVVLLLFGSGKVVCTGAKEESEIEQAVIKVKKEL 178
                                   679*********************88***************************************************9999 PP

                                   HH CS
                           TBP  83 kk 84 
                                   +k
  gi|13542225|ref|NP_111913.1| 179 QK 180
                                   98 PP

>> DUF3378  Domain of unknown function (DUF3378)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.0   7.5e-05      0.45      23      49 ..      37      63 ..      29      76 .. 0.87
   2 !   13.9   0.0   7.6e-06     0.045      24      60 ..     131     167 ..     124     180 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 7.5e-05
                       DUF3378 23 rskkppyavfaakkndttItaYtSgKV 49
                                  + ++ p+ +++ ++++t + +++SgKV
  gi|13542225|ref|NP_111913.1| 37 EPEQFPGLIYRLQDPKTAVLIFRSGKV 63
                                  56789*********************9 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 7.6e-06
                       DUF3378  24 skkppyavfaakkndttItaYtSgKVlFQGknaeaeA 60 
                                    ++ p+ v++ +++ ++  ++ SgKV+  G++ e+e 
  gi|13542225|ref|NP_111913.1| 131 PEQFPGLVYRVEEPRVVLLLFGSGKVVCTGAKEESEI 167
                                   5789***************************999885 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 ?    5.4   0.0    0.0024        14      18      34 ..      40      56 ..      33      62 .. 0.88
   2 ?    4.1   0.0    0.0063        38      17      37 ..     132     152 ..     120     156 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0024
                          NdhS 18 gfeGlvQrvsdgkaaVl 34
                                  +f Gl+ r++d k aVl
  gi|13542225|ref|NP_111913.1| 40 QFPGLIYRLQDPKTAVL 56
                                  799*************8 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.0063
                          NdhS  17 ygfeGlvQrvsdgkaaVlFeG 37 
                                    +f Glv rv + ++  l+ G
  gi|13542225|ref|NP_111913.1| 132 EQFPGLVYRVEEPRVVLLLFG 152
                                   5799********999887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       605  (0.0337442); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.32s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1149.02
//
Query:       gi|13542226|ref|NP_111914.1|  [L=659]
Description: Fe-S oxidoreductase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-31  108.8   0.3    2.8e-16   59.5   0.1    2.5  2  CCG              Cysteine-rich domain
    3.8e-11   43.3   7.5    4.2e-11   43.1   5.9    2.0  1  Fer4_8           4Fe-4S dicluster domain
    2.9e-10   40.2   6.8    2.9e-10   40.2   6.8    2.6  3  Fer4_9           4Fe-4S dicluster domain
    1.1e-08   35.1   7.8    1.1e-08   35.1   7.8    2.6  3  Fer4_10          4Fe-4S dicluster domain
    3.5e-07   30.0   3.1    3.5e-07   30.0   3.1    1.5  1  Nitrate_red_gam  Nitrate reductase gamma subunit
    3.8e-07   30.6   7.7    3.8e-07   30.6   7.7    2.2  1  Fer4_7           4Fe-4S dicluster domain
    5.6e-07   30.4   6.3    1.7e-06   28.9   6.3    1.9  1  Fer4_16          4Fe-4S double cluster binding domain
      4e-05   24.1  12.2    0.00058   20.3  11.1    3.1  3  Fer4_17          4Fe-4S dicluster domain
    0.00017   21.8  15.2     0.0032   17.8   1.8    3.3  3  Fer4_4           4Fe-4S binding domain
    0.00056   19.6  21.1      0.018   14.9   5.0    3.2  3  Fer4             4Fe-4S binding domain
     0.0017   18.3   5.4     0.0017   18.3   5.4    3.1  3  Fer4_6           4Fe-4S binding domain
  ------ inclusion threshold ------
      0.055   14.0   6.1        1.9    9.1   0.3    2.7  2  Fer4_13          4Fe-4S single cluster domain of Ferredoxin I
      0.098   13.5   0.5      0.098   13.5   0.5    3.2  2  Fer4_22          4Fe-4S dicluster domain
        0.3   11.3  22.3       0.27   11.4   5.9    3.2  3  Fer4_2           4Fe-4S binding domain
        1.5    9.6   5.8        8.1    7.3   1.0    2.5  2  Fer4_15          4Fe-4S single cluster domain
        3.2    8.0  16.6        8.2    6.6   2.2    2.9  3  Fer4_21          4Fe-4S dicluster domain
        4.1    8.6  24.6        1.3   10.1   5.5    3.0  2  Fer4_3           4Fe-4S binding domain
        6.9    6.9  12.2        7.5    6.8   0.7    2.8  3  Fer4_18          4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> CCG  Cysteine-rich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.5   0.1   2.8e-19   2.8e-16       1      85 []     423     509 ..     423     509 .. 0.97
   2 !   47.1   0.0     2e-15     2e-12       1      84 [.     546     631 ..     546     632 .. 0.94

  Alignments for each domain:
  == domain 1  score: 59.5 bits;  conditional E-value: 2.8e-19
                           CCG   1 vayfdgCh.llraaypevrkalkkllealgveleel.ekesCCGagggrsgkeelaealakrnvetaeetgadaivtacpg 79 
                                   v+y++gC  +++++ ++    +  ll+++gv++ +l ++e+C G  ++r+g+e l+++la+ n+et++++g+++ivt cp+
  gi|13542226|ref|NP_111914.1| 423 VLYWVGCMgAYDPRDKQIALTVIDLLKKAGVKFGILgSEEKCTGETARRMGEEGLFQTLAAGNIETFNKYGVKKIVTSCPH 503
                                   79*****8888888******************************************************************* PP

                           CCG  80 Cllqlk 85 
                                   C++++k
  gi|13542226|ref|NP_111914.1| 504 CFNTFK 509
                                   ***985 PP

  == domain 2  score: 47.1 bits;  conditional E-value: 2e-15
                           CCG   1 vayfdgChllraa..ypevrkalkkllealgveleel.ekesCCGagggrsgkee.laealakrnvetaeetgadaivtac 77 
                                   v+y+d+C+l+r++  y+++r ++      ++ve+e+  ek+ CCGaggg+ ++     +++ + ++++a et+a  + +ac
  gi|13542226|ref|NP_111914.1| 546 VTYHDPCYLGRGNgvYDDPRFIISST--GDLVEMEKSrEKSFCCGAGGGNYWYRVeNEKSISHIRMDQAIETKASTVGVAC 624
                                   89***********9999999988887..899**********************986788********************** PP

                           CCG  78 pgCllql 84 
                                   p+C ++l
  gi|13542226|ref|NP_111914.1| 625 PFCMAML 631
                                   ****998 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.1   5.9   4.3e-14   4.2e-11       2      63 ..     295     361 ..     294     363 .. 0.78

  Alignments for each domain:
  == domain 1  score: 43.1 bits;  conditional E-value: 4.3e-14
                        Fer4_8   2 lekCieCgaCqsaCpvlrrtk.khlldargeaaedvqeeqvlee.....eealwsCttcgaCtevCpv 63 
                                   +++C+ Cg+C+ aCp++ +    ++    +++++  ++++ +       e+a wsCttc+aC+e+Cpv
  gi|13542226|ref|NP_111914.1| 295 AMACTDCGRCERACPAYASGTdLDPRLVVQNVKK-LVNTDSELVpvvltENASWSCTTCMACVEECPV 361
                                   579************9887654777777777777.44444433357888******************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 !   40.2   6.8   2.9e-13   2.9e-10       1      48 [.     297     361 ..     297     363 .. 0.96
   2 ?   -2.4   0.1       5.6   5.6e+03      33      39 ..     491     504 ..     461     506 .. 0.51
   3 ?    0.8   0.0      0.58   5.8e+02      11      29 ..     623     641 ..     608     645 .. 0.86

  Alignments for each domain:
  == domain 1  score: 40.2 bits;  conditional E-value: 2.9e-13
                        Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraase.................eaCigCgaCveaCpk 48 
                                   +Ct+Cg+C++aCpa +   d  +r + ++ ++                  ++C++C+aCve Cp 
  gi|13542226|ref|NP_111914.1| 297 ACTDCGRCERACPAYASGTDLDPRLVVQNVKKLvntdselvpvvltenasWSCTTCMACVEECPV 361
                                   6**************************998888******************************95 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 5.6
                        Fer4_9  33 e.......eaCigC 39 
                                   +       ++C +C
  gi|13542226|ref|NP_111914.1| 491 KygvkkivTSCPHC 504
                                   03444445556666 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.58
                        Fer4_9  11 aCpagvvvedaaerkarlr 29 
                                   aCp+++++ ++a+r+++l+
  gi|13542226|ref|NP_111914.1| 623 ACPFCMAMLSDAARTMNLE 641
                                   7999999999999998875 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.1   7.8   1.1e-11   1.1e-08       8      56 .]     297     360 ..     291     360 .. 0.91
   2 ?   -0.1   0.0         1     1e+03      37      50 ..     493     506 ..     481     510 .. 0.76
   3 ?   -2.6   0.0       6.5   6.4e+03      18      23 ..     623     628 ..     612     649 .. 0.67

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 1.1e-11
                       Fer4_10   8 tCirCgkCvkaCPadl...............tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                    C+ Cg+C +aCPa++               + v++  e  +    + ++++Ct+c aCve+CP
  gi|13542226|ref|NP_111914.1| 297 ACTDCGRCERACPAYAsgtdldprlvvqnvkKLVNTDSELVPVVLTENASWSCTTCMACVEECP 360
                                   7**************************999777777888888888888***************9 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1
                       Fer4_10  37 avrkkvekCtgcga 50 
                                    v+k v +C++c++
  gi|13542226|ref|NP_111914.1| 493 GVKKIVTSCPHCFN 506
                                   56778999999975 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 6.5
                       Fer4_10  18 aCPadl 23 
                                   aCP+++
  gi|13542226|ref|NP_111914.1| 623 ACPFCM 628
                                   455533 PP

>> Nitrate_red_gam  Nitrate reductase gamma subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   3.1   3.5e-10   3.5e-07      91     206 ..     129     247 ..     114     253 .. 0.82

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 3.5e-10
               Nitrate_red_gam  91 GliagvlalvGlllLllRRltnkrvraatsasDkvvlllLllqillGllttlvsal..dygseretispwlrs.lltlqpd 168
                                     i g++++vGll+ llRR+tn  +  +t+  D+++l  +l+  l G++   ++    + +  + ++++w  s ++ +   
  gi|13542226|ref|NP_111914.1| 129 TQIGGIILIVGLLMALLRRITN-FIPLHTTSEDYLLLSGILVLALEGFFLGALKIDlfRQSFDVYRFVEWYLSyIFPYGSM 208
                                   56789***************98.7999999******999999999998877776443322445777777765516655444 PP

               Nitrate_red_gam 169 .aellaevplifklHvllglllfalfPFtrLvHvlsapl 206
                                    ++ ++    ++ +Hvl+++l+ + +P+++L H l ap 
  gi|13542226|ref|NP_111914.1| 209 sPAGITVYRELWMAHVLTAFLVALYLPYSKLFHSLLAPT 247
                                   5999999999************************99996 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   7.7   3.8e-10   3.8e-07       1      50 [.     297     361 ..     297     363 .. 0.68

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 3.8e-10
                        Fer4_7   1 rCigCgaCvaaCpvkaield..eeenekgtekv.............eidpekClgCgaCvavCPt 50 
                                   +C+ Cg+C++aCp++a  +d  ++ + + ++k+             e  +++C++C aCv++CP+
  gi|13542226|ref|NP_111914.1| 297 ACTDCGRCERACPAYASGTDldPRLVVQNVKKLvntdselvpvvltENASWSCTTCMACVEECPV 361
                                   5************888776544544444333333444444455554556889************7 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   6.3   1.7e-09   1.7e-06       2      66 ..     298     361 ..     297     362 .. 0.90

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 1.7e-09
                       Fer4_16   2 CgtCgkCaevCPtnaikekkekeiearecisyntaekkdlaedeekckkqeaitgCdiCqdvCPa 66 
                                   C++Cg+C  +CP+ a  ++ ++++  ++ ++  ++ + +l +   +++  + +t C +C++ CP+
  gi|13542226|ref|NP_111914.1| 298 CTDCGRCERACPAYASGTDLDPRLVVQNVKK-LVNTDSELVPVVLTENASWSCTTCMACVEECPV 361
                                   *****************99888888777655.69999999999999999***************6 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   3.0     3e-05      0.03      40      58 ..     292     310 ..     272     313 .. 0.77
   2 !   20.3  11.1   5.8e-07   0.00058       1      57 [.     297     360 ..     297     364 .. 0.80
   3 ?   -0.0   0.0       1.3   1.3e+03      11      39 ..     623     654 ..     620     659 .] 0.61

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3e-05
                       Fer4_17  40 eekaslCieCgeCerkCPq 58 
                                   +++a  C+ Cg+Cer+CP+
  gi|13542226|ref|NP_111914.1| 292 RTAAMACTDCGRCERACPA 310
                                   36899*************6 PP

  == domain 2  score: 20.3 bits;  conditional E-value: 5.8e-07
                       Fer4_17   1 rCiqCgyClpeCpsyea.ydnepkkllraakl......glleeaekeekaslCieCgeCerkCP 57 
                                   +C+ Cg C+++Cp y+  +d +p+ +++++k       +l+  + +e++  +C++C  C+++CP
  gi|13542226|ref|NP_111914.1| 297 ACTDCGRCERACPAYASgTDLDPRLVVQNVKKlvntdsELVPVVLTENASWSCTTCMACVEECP 360
                                   6*************9998889999888887665554434444466668889************* PP

  == domain 3  score: -0.0 bits;  conditional E-value: 1.3
                       Fer4_17  11 eCpsyeaydnepk...kllraaklglleeaek 39 
                                   +Cp+++a+ ++ +   +l  +++++++ e++k
  gi|13542226|ref|NP_111914.1| 623 ACPFCMAMLSDAArtmNLEDKIQVKDISEIIK 654
                                   49999998876551114555666666666555 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   1.8   3.3e-06    0.0032       3      16 ..     297     310 ..     295     320 .. 0.91
   2 !   11.7   1.4    0.0003       0.3       3      15 ..     348     360 ..     345     372 .. 0.92
   3 ?   -1.9   0.2       6.7   6.7e+03       6      11 ..     623     628 ..     622     629 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 3.3e-06
                        Fer4_4   3 rCigCgsCvaaCPq 16 
                                    C++Cg+C++aCP 
  gi|13542226|ref|NP_111914.1| 297 ACTDCGRCERACPA 310
                                   5************4 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.0003
                        Fer4_4   3 rCigCgsCvaaCP 15 
                                   +C+ C++Cv  CP
  gi|13542226|ref|NP_111914.1| 348 SCTTCMACVEECP 360
                                   5************ PP

  == domain 3  score: -1.9 bits;  conditional E-value: 6.7
                        Fer4_4   6 gCgsCv 11 
                                    C+ C+
  gi|13542226|ref|NP_111914.1| 623 ACPFCM 628
                                   588886 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   5.0   1.8e-05     0.018       7      22 ..     297     312 ..     295     312 .. 0.89
   2 !   12.4   4.5   0.00011      0.11       8      20 ..     349     361 ..     348     363 .. 0.93
   3 ?   -1.7   0.1       3.1   3.1e+03       5      10 ..     461     466 ..     460     466 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.8e-05
                                   TSSS-THHHHHSTTTE CS
                          Fer4   7 kCigCGaCvevCPvgA 22 
                                    C+ CG+C+ +CP  A
  gi|13542226|ref|NP_111914.1| 297 ACTDCGRCERACPAYA 312
                                   6************865 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00011
                                   SSS-THHHHHSTT CS
                          Fer4   8 CigCGaCvevCPv 20 
                                   C+ C+aCve CPv
  gi|13542226|ref|NP_111914.1| 349 CTTCMACVEECPV 361
                                   ************8 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 3.1
                                   TTTSSS CS
                          Fer4   5 eekCig 10 
                                   eekC+g
  gi|13542226|ref|NP_111914.1| 461 EEKCTG 466
                                   89**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 !   18.3   5.4   1.7e-06    0.0017       8      23 ..     297     312 ..     297     313 .. 0.94
   2 !    8.6   4.6     0.002         2       8      21 ..     348     361 ..     348     363 .. 0.92
   3 ?   -3.0   0.2       9.1   9.1e+03       8      12 ..     500     504 ..     498     505 .. 0.64

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.7e-06
                        Fer4_6   8 kCigCgdCvrvCPega 23 
                                   +C++Cg+C+r+CP++a
  gi|13542226|ref|NP_111914.1| 297 ACTDCGRCERACPAYA 312
                                   6************987 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.002
                        Fer4_6   8 kCigCgdCvrvCPe 21 
                                   +C+ C++Cv  CP 
  gi|13542226|ref|NP_111914.1| 348 SCTTCMACVEECPV 361
                                   6************5 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 9.1
                        Fer4_6   8 kCigC 12 
                                   +C +C
  gi|13542226|ref|NP_111914.1| 500 SCPHC 504
                                   56666 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   1.1      0.01        10       5      18 ..     297     310 ..     295     326 .. 0.92
   2 ?    9.1   0.3    0.0019       1.9       5      17 ..     348     360 ..     346     385 .. 0.94

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.01
                       Fer4_13   5 tCiacgaCvelaPd 18 
                                    C++cg C  ++P 
  gi|13542226|ref|NP_111914.1| 297 ACTDCGRCERACPA 310
                                   5************6 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0019
                       Fer4_13   5 tCiacgaCvelaP 17 
                                   +C+ c+aCve +P
  gi|13542226|ref|NP_111914.1| 348 SCTTCMACVEECP 360
                                   6***********9 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.5   9.9e-05     0.098      74      94 ..     290     310 ..     273     312 .. 0.77
   2 ?    3.7   0.2      0.11   1.1e+02      78      95 ..     345     362 ..     324     363 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 9.9e-05
                       Fer4_22  74 kekfgesgCvGCgRCieacpv 94 
                                   + ++ +++C+ CgRC++acp+
  gi|13542226|ref|NP_111914.1| 290 EYRTAAMACTDCGRCERACPA 310
                                   34557899***********97 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.11
                       Fer4_22  78 gesgCvGCgRCieacpvk 95 
                                    + +C+ C  C+e cpv 
  gi|13542226|ref|NP_111914.1| 345 ASWSCTTCMACVEECPVL 362
                                   556788888888888875 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   5.9   0.00027      0.27       9      22 .]     297     310 ..     293     310 .. 0.94
   2 ?    9.3   3.2    0.0013       1.3       9      21 ..     348     360 ..     337     361 .. 0.84
   3 ?   -2.8   0.2       9.2   9.2e+03      17      22 .]     498     503 ..     498     503 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00027
                        Fer4_2   9 rCigCgaCvsaCPa 22 
                                   +C+ Cg C  aCPa
  gi|13542226|ref|NP_111914.1| 297 ACTDCGRCERACPA 310
                                   6************8 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0013
                        Fer4_2   9 rCigCgaCvsaCP 21 
                                   +C+ C aCv  CP
  gi|13542226|ref|NP_111914.1| 348 SCTTCMACVEECP 360
                                   7************ PP

  == domain 3  score: -2.8 bits;  conditional E-value: 9.2
                        Fer4_2  17 vsaCPa 22 
                                   v++CP+
  gi|13542226|ref|NP_111914.1| 498 VTSCPH 503
                                   689**7 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.3     0.079        78       7      23 ..     297     313 ..     295     336 .. 0.85
   2 ?    7.3   1.0    0.0082       8.1       6      22 ..     347     363 ..     346     372 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.079
                       Fer4_15   7 aCigcglCvaeapevfe 23 
                                   aC+ cg+C +++p +  
  gi|13542226|ref|NP_111914.1| 297 ACTDCGRCERACPAYAS 313
                                   7***********99865 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0082
                       Fer4_15   6 daCigcglCvaeapevf 22 
                                   + C+ c +Cv+e+p ++
  gi|13542226|ref|NP_111914.1| 347 WSCTTCMACVEECPVLI 363
                                   57***********9766 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   2.2    0.0082       8.2       7      52 ..     297     309 ..     285     315 .. 0.65
   2 ?    6.6  13.5    0.0087       8.7       7      53 ..     297     361 ..     292     364 .. 0.62
   3 ?   -1.9   0.0         4   3.9e+03      37      49 ..     617     629 ..     600     635 .. 0.57

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0082
                       Fer4_21   7 kCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCP 52 
                                    C +Cg+C  aC                                 P
  gi|13542226|ref|NP_111914.1| 297 ACTDCGRCERAC---------------------------------P 309
                                   355555555555.................................5 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0087
                       Fer4_21   7 kCigCgkCliaCedtshqai............eidaktvl.......kvv.....edeCvGCnlCssvCPv 53 
                                    C +Cg+C  aC+  +                       +       +vv     + +C+ C  C++ CPv
  gi|13542226|ref|NP_111914.1| 297 ACTDCGRCERACPAYASGTDldprlvvqnvkkL------VntdselvPVVltenaSWSCTTCMACVEECPV 361
                                   7***********965443323555544444431......1334444443332222458************9 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 4
                       Fer4_21  37 vedeCvGCnlCss 49 
                                    +   v+C  C++
  gi|13542226|ref|NP_111914.1| 617 ASTVGVACPFCMA 629
                                   3445567777764 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   4.0    0.0013       1.3       1      13 [.     298     310 ..     298     312 .. 0.90
   2 ?   10.1   5.5    0.0013       1.3       1      13 [.     349     361 ..     349     363 .. 0.95

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0013
                        Fer4_3   1 CtgCgaCvevCPv 13 
                                   Ct Cg+C+++CP 
  gi|13542226|ref|NP_111914.1| 298 CTDCGRCERACPA 310
                                   9***********5 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0013
                        Fer4_3   1 CtgCgaCvevCPv 13 
                                   Ct C+aCve CPv
  gi|13542226|ref|NP_111914.1| 349 CTTCMACVEECPV 361
                                   ************7 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.7    0.0075       7.5      46      73 ..     283     310 ..     268     326 .. 0.77
   2 ?    5.7   2.5     0.016        16      56      75 ..     344     363 ..     327     366 .. 0.85
   3 ?   -2.7   0.0       6.7   6.7e+03      43      69 ..     603     629 ..     593     649 .. 0.67

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0075
                       Fer4_18  46 alkekeerkekgagdcidcescvkvcPt 73 
                                   +++e  ++ +++a  c+dc+ c + cP 
  gi|13542226|ref|NP_111914.1| 283 KVSELSLEYRTAAMACTDCGRCERACPA 310
                                   445555666778889***********96 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.016
                       Fer4_18  56 kgagdcidcescvkvcPtgi 75 
                                   +++  c++c +cv+ cP+ i
  gi|13542226|ref|NP_111914.1| 344 NASWSCTTCMACVEECPVLI 363
                                   56678************876 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 6.7
                       Fer4_18  43 ekkalkekeerkekgagdcidcescvk 69 
                                   + ++++  +  ++k+++  ++c +c++
  gi|13542226|ref|NP_111914.1| 603 SISHIRMDQAIETKASTVGVACPFCMA 629
                                   444455555556666666777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (659 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1030  (0.0574488); expected 358.6 (0.02)
Passed bias filter:                      600  (0.0334653); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.80u 0.30s 00:00:01.10 Elapsed: 00:00:00.52
# Mc/sec: 3834.12
//
Query:       gi|13542227|ref|NP_111915.1|  [L=375]
Description: major facilitator superfamily permease [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      2e-26   92.8  58.3    3.1e-18   65.8  23.6    2.0  2  MFS_1      Major Facilitator Superfamily
  ------ inclusion threshold ------
      0.026   14.8   1.2      0.026   14.8   1.2    2.6  3  ASFV_L11L  African swine fever virus (ASFV) L11L 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 !   65.8  23.6   3.5e-22   3.1e-18       3     217 ..      11     216 ..       6     223 .. 0.83
   2 !   30.8  32.7   1.5e-11   1.4e-07      14     172 ..     203     359 ..     199     374 .. 0.86

  Alignments for each domain:
  == domain 1  score: 65.8 bits;  conditional E-value: 3.5e-22
                         MFS_1   3 laaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll.fa 82 
                                   l+ ++++l  +  +++ p +la+ +g+   ++++++tl+a+++  ++ ++G+++dr G+r v ++++l++a+g ++++ ++
  gi|13542227|ref|NP_111915.1|  11 LVMCFNSLYQYSWNVFEP-LLAKGFGVEIVSVQIAFTLFAVFSTTFQGIGGYFADRDGPRNVSIAAALMSAFG-FVASsLV 89 
                                   455555555555566666.9*****************************************************.5555466 PP

                         MFS_1  83 sslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsll 163
                                   +s++l++v + + ++g+g+l+ ++  l+++w+++ +rg+a+g++s+gf+lG+ ++ ++    +    +r ++++++++ l+
  gi|13542227|ref|NP_111915.1|  90 HSIYLFYVIWSIGSIGEGILYGIATNLAVKWYSG-RRGFAVGFVSLGFGLGSSIANIFLEKAS---EFRFPMMFIGLAELI 166
                                   **********************************.*****************99988877777...8************** PP

                         MFS_1 164 afvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwilliall 217
                                   +  l lll ++++p+++   +++ ++ + p+ ++  ++ ++ + +l  ++i++ 
  gi|13542227|ref|NP_111915.1| 167 V--LPLLLSFVKYPSSGLTGERPSRNIKNPRFWILYLSFVFGSIPL--IVISSS 216
                                   *..5559999999999999888886666666666666666665544..333333 PP

  == domain 2  score: 30.8 bits;  conditional E-value: 1.5e-11
                         MFS_1  14 ilgpalpl.alaedlg.....ispseigllltlyalgaavaslplGrlsdrfGrrr.vlllglllfalglllllfasslwl 87 
                                   +++ ++pl  +++++g     + + e+  l++++ l+++++ +++G++sd +Gr   vll+ +++f+ + l+l++  +   
  gi|13542227|ref|NP_111915.1| 203 FVFGSIPLiVISSSFGfigskLPELEFAVLVSIFPLLSGISRPIIGAISDAIGRPAsVLLIDVAIFIGA-LFLVL-RN--- 278
                                   56677788889999998888888899999***************************6777777777777.77776.99... PP

                         MFS_1  88 llvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllafvlf 168
                                   ++++ vl G+++g+++++  +li d+f  +  +  +g++++g +++  +g  l +++   lg +++fy++ i +++++   
  gi|13542227|ref|NP_111915.1| 279 FIFAVVLIGFFGGSMISLYFSLIGDVFGTRFSTANNGIFYTGKAVSGFMGSTLFAIIF-TLGVEYSFYFVFISAIFGIA-- 356
                                   **************************************************99988888.78999999999999988866.. PP

                         MFS_1 169 llll 172
                                    +l+
  gi|13542227|ref|NP_111915.1| 357 -FLI 359
                                   .443 PP

>> ASFV_L11L  African swine fever virus (ASFV) L11L protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0      0.93   8.3e+03       7      17 ..     204     214 ..     201     228 .. 0.74
   2 ?   14.8   1.2   2.9e-06     0.026      29      53 ..     262     286 ..     259     304 .. 0.87
   3 ?   -4.5   1.3         2   1.8e+04      19      35 ..     342     358 ..     332     369 .. 0.59

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.93
                     ASFV_L11L   7 vmapiplvlif 17 
                                   v+  ipl++i 
  gi|13542227|ref|NP_111915.1| 204 VFGSIPLIVIS 214
                                   67789999874 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 2.9e-06
                     ASFV_L11L  29 litialflgclffilrdfcfppmlw 53 
                                   li +a+f+g lf++lr+f f  +l 
  gi|13542227|ref|NP_111915.1| 262 LIDVAIFIGALFLVLRNFIFAVVLI 286
                                   899*****************98875 PP

  == domain 3  score: -4.5 bits;  conditional E-value: 2
                     ASFV_L11L  19 ysyfkiklhklitialf 35 
                                   ys++ + +  +  ia++
  gi|13542227|ref|NP_111915.1| 342 YSFYFVFISAIFGIAFL 358
                                   55555555555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (375 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       779  (0.0434492); expected 358.6 (0.02)
Passed bias filter:                      248  (0.0138323); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.64u 0.28s 00:00:00.92 Elapsed: 00:00:00.49
# Mc/sec: 2323.32
//
Query:       gi|13542228|ref|NP_111916.1|  [L=105]
Description: hypothetical protein TVN1397 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.2e-31  105.8   0.2      9e-31  105.7   0.2    1.0  1  CutA1            CutA1 divalent ion tolerance protein
  ------ inclusion threshold ------
      0.056   14.1   0.1       0.17   12.5   0.0    1.7  2  Phage_int_SAM_2  Phage integrase, N-terminal


Domain annotation for each model (and alignments):
>> CutA1  CutA1 divalent ion tolerance protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.7   0.2     1e-34     9e-31       3      98 ..       5     100 ..       3     101 .. 0.98

  Alignments for each domain:
  == domain 1  score: 105.7 bits;  conditional E-value: 1e-34
                                   EEEEESSHHHHHHHHHHHHHTTS-SEEEEEEEEEEEEEETTEEEEEEEEEEEEEEEGGGHHHHHHHHHHHSSSSS-EEEEE CS
                         CutA1   3 vlvtapseeeakklaralveeklaACvnilpkieSvYrWkgkieedkEvllliktreekveelekrvkelhpyevpeiial 83 
                                   v++t+++ eea+++    +e+++aAC +i+++++S+Y+W+g+iee++Ev +++kt++++ + l++++ke+h+yevpei ++
  gi|13542228|ref|NP_111916.1|   5 VITTFQNAEEARRIGMMALEKQMAACFSIIDNVKSTYWWRGNIEESSEVFCVFKTTDDNEPLLSQFIKEMHNYEVPEIASM 85 
                                   89******************************************************************************* PP

                                   EESEEEHHHHHHHHH CS
                         CutA1  84 pieagseaYlkWiee 98 
                                   ++++++e+Y +W+++
  gi|13542228|ref|NP_111916.1|  86 KMDKINEEYNRWLND 100
                                   ************987 PP

>> Phage_int_SAM_2  Phage integrase, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.39   3.5e+03      63      81 ..      15      33 ..       6      38 .. 0.65
   2 ?   12.5   0.0     2e-05      0.17      19      64 ..      57     100 ..      51     104 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.39
               Phage_int_SAM_2 63 aeeiskrtlqNemaalRsv 81
                                  a  i+  +l+ +maa  s+
  gi|13542228|ref|NP_111916.1| 15 ARRIGMMALEKQMAACFSI 33
                                  4556666777777766555 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 2e-05
               Phage_int_SAM_2  19 ykTvndrerilqrlareLlalniqvrdvkslKarHieayieerlae 64 
                                   +kT +d e +l ++ +e+   n++v++++s+K+  i++  + +l++
  gi|13542228|ref|NP_111916.1|  57 FKTTDDNEPLLSQFIKEMH--NYEVPEIASMKMDKINEEYNRWLND 100
                                   9****************96..99*************9988999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       548  (0.030565); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 682.77
//
Query:       gi|13542229|ref|NP_111917.1|  [L=196]
Description: hypothetical protein TVN1398 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      5e-06   26.7   0.0    6.7e-06   26.3   0.0    1.2  1  Acetyltransf_1  Acetyltransferase (GNAT) family
     0.0017   19.1   0.0     0.0022   18.7   0.0    1.1  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 !   26.3   0.0   7.5e-10   6.7e-06      23     116 ..      50     147 ..      22     148 .. 0.76

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 7.5e-10
                                   H....HHHHHHSTTCEEEEEEETTEEEEEEEEEEEET...TSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTESE CS
                Acetyltransf_1  23 e....feesfsleaegllvaeedgeliGfisllkipd...ekggvayieslaVspeyrgkGlGsaLlealeerareegikk 96 
                                   e    + + +  ++ +  +a++ ++++Gf++ l  pd   e +++++ + + Vs+ +r+ Gl  aLl +++     +    
  gi|13542229|ref|NP_111917.1|  50 EsiveRSKNWNVHPHYMHFALYKDKVVGFAGSLLGPDygpEVQPHIAEIYYGVSKGWRKTGLIYALLYTALSDINAK---I 127
                                   1234455667889999999*********************888999999*****************99999855555...3 PP

                                   EEEEEETTEHHHHHHHHHTT CS
                Acetyltransf_1  97 ivlaveedndaairlYeklG 116
                                   + ++  + n ++i+++ k G
  gi|13542229|ref|NP_111917.1| 128 VKATAYVENLPSINVLLKIG 147
                                   35566668999999987766 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   2.5e-07    0.0022      15     137 ..      27     148 ..      18     149 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2.5e-07
                Acetyltransf_3  15 lfelrsdpevmrylpepltleeaeewlera..waeeseeeg.ygwaivlkdtgviGsvglrdleeedee.....aelgyml 87 
                                   l el++dp     ++ ++++ + e+ +er+  w+    +   + +a+  kd+ v+G++g    ++   e     ae+ y +
  gi|13542229|ref|NP_111917.1|  27 LMELYEDPNSYILVNYSKDPPQLESIVERSknWNV---HPHyMHFAL-YKDK-VVGFAGSLLGPDYGPEvqphiAEIYYGV 102
                                   46788888844234445566666666665433554...445155999.4666.999996665544444458899******* PP

                Acetyltransf_3  88 apsfwgkGyateavralleyafeelglerlvavidkeNeaSirvleklGf 137
                                    + ++  G+    +  +l  +    +++ + a++  eN  Si+vl k+G+
  gi|13542229|ref|NP_111917.1| 103 SKGWRKTGLIYALLYTALSDI----NAKIVKATAYVENLPSINVLLKIGL 148
                                   ***8777**999999999999....555699******************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       391  (0.0218082); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1246.42
//
Query:       gi|13542230|ref|NP_111918.1|  [L=189]
Description: ankyrin repeat-containing protein [Thermoplasma volcanium GSS1]
Scores for 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   95.8   0.1    1.1e-13   51.1   0.0    3.5  4  Ank_5     Ankyrin repeats (many copies)
    1.8e-26   92.5   0.0    1.4e-11   44.8   0.0    3.0  3  Ank_2     Ankyrin repeats (3 copies)
    8.5e-20   68.8   0.0    0.00013   22.1   0.0    4.3  4  Ank_3     Ankyrin repeat
    2.8e-19   69.2   0.0    3.4e-06   27.5   0.0    4.2  4  Ank_4     Ankyrin repeats (many copies)
    1.2e-17   63.4   0.0    0.00028   21.2   0.0    4.3  4  Ank       Ankyrin repeat


Domain annotation for each model (and alignments):
>> Ank_5  Ankyrin repeats (many copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.0   0.0    0.0043        16      10      24 ..      26      40 ..      20      42 .. 0.84
   2 !   34.6   0.0   4.5e-12   1.6e-08       2      53 ..      52     102 ..      51     103 .. 0.92
   3 !    9.5   0.0   0.00035       1.3       8      31 ..      90     113 ..      90     113 .. 0.94
   4 !   51.1   0.0   3.1e-17   1.1e-13       1      52 [.     117     167 ..     117     167 .. 0.98

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0043
                         Ank_5 10 nrldgggntpLhvAa 24
                                  n++d +  tpL+vA+
  gi|13542230|ref|NP_111918.1| 26 NYRDSYNRTPLMVAC 40
                                  677888889999998 PP

  == domain 2  score: 34.6 bits;  conditional E-value: 4.5e-12
                         Ank_5   2 lehgpadvnrldgggntpLhvAakygaadvvrlLlargadlnltdsrGltal 53 
                                   +e++   + ++d +g t+L++A+k++++ ++++Ll  g++ n++d++G+t+l
  gi|13542230|ref|NP_111918.1|  52 VENF-DKLEDKDIEGSTALIWAVKNNRLGIAEKLLSKGSNVNTKDFSGKTPL 102
                                   6666.667789999*************************************8 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.00035
                         Ank_5   8 dvnrldgggntpLhvAakygaadv 31 
                                   +vn++d  g tpL++++  g++++
  gi|13542230|ref|NP_111918.1|  90 NVNTKDFSGKTPLMWSIIFGYSEM 113
                                   6999*****************997 PP

  == domain 4  score: 51.1 bits;  conditional E-value: 3.1e-17
                         Ank_5   1 LlehgpadvnrldgggntpLhvAakygaadvvrlLlargadlnltdsrGlta 52 
                                   Llehg a+vn+++ +g+tpL+vA+kyg++++v++Ll+ gad+ ++d  Glta
  gi|13542230|ref|NP_111918.1| 117 LLEHG-ANVNDRNLEGETPLIVASKYGRSEIVKKLLELGADISARDLTGLTA 167
                                   8****.*******************************************997 PP

>> Ank_2  Ankyrin repeats (3 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.6   0.1   9.5e-15   3.4e-11      23      83 .]      20      95 ..       2      95 .. 0.75
   2 !   44.8   0.0   3.9e-15   1.4e-11      26      83 .]      98     161 ..      97     161 .. 0.89
   3 ?   -3.3   0.0       3.9   1.4e+04      59      72 ..     170     183 ..     163     185 .. 0.60

  Alignments for each domain:
  == domain 1  score: 43.6 bits;  conditional E-value: 9.5e-15
                         Ank_2 23 n.....k....ngktaLhyAakngnleivklLleh......adndgrtpLhyAarsghleivklLlekgadinlkd 83
                                  n     +     ++t+L++A++ g ++++  L+e+       d +g t+L++A+++++l i++ Ll kg+++n+kd
  gi|13542230|ref|NP_111918.1| 20 NldflrNyrdsYNRTPLMVACMLGMENAIDKLVENfdkledKDIEGSTALIWAVKNNRLGIAEKLLSKGSNVNTKD 95
                                  2323331344688********************976775555577*********************99*****998 PP

  == domain 2  score: 44.8 bits;  conditional E-value: 3.9e-15
                         Ank_2  26 gktaLhyAakngnleivklLleh...ad...ndgrtpLhyAarsghleivklLlekgadinlkd 83 
                                   gkt+L+++++ g+ e+  +Lleh   ++    +g+tpL++A+++g++eivk Lle gadi ++d
  gi|13542230|ref|NP_111918.1|  98 GKTPLMWSIIFGYSEMSYFLLEHganVNdrnLEGETPLIVASKYGRSEIVKKLLELGADISARD 161
                                   89********************99662244366*********************99****9987 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 3.9
                         Ank_2  59 yAarsghleivklL 72 
                                    A  +g++e++k++
  gi|13542230|ref|NP_111918.1| 170 SARIFGRQEVIKIF 183
                                   45556777777765 PP

>> Ank_3  Ankyrin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   1.9e-05     0.069       1      24 [.      31      54 ..      31      58 .. 0.90
   2 !   14.3   0.0   1.3e-05     0.047       1      30 [.      64      92 ..      64      93 .. 0.94
   3 !   13.7   0.0   1.9e-05      0.07       2      30 ..      98     125 ..      97     126 .. 0.88
   4 !   22.1   0.0   3.6e-08   0.00013       1      30 [.     130     158 ..     130     159 .. 0.95

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.9e-05
                         Ank_3  1 nGetpLhlAarsgnleivkfLlen 24
                                  +++tpL++A++ g  + ++ L+en
  gi|13542230|ref|NP_111918.1| 31 YNRTPLMVACMLGMENAIDKLVEN 54
                                  689************99****996 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 1.3e-05
                         Ank_3  1 nGetpLhlAarsgnleivkfLlenkgadvn 30
                                  +G t+L +A+++++l i++ Ll  kg +vn
  gi|13542230|ref|NP_111918.1| 64 EGSTALIWAVKNNRLGIAEKLLS-KGSNVN 92
                                  599********************.9***99 PP

  == domain 3  score: 13.7 bits;  conditional E-value: 1.9e-05
                         Ank_3   2 GetpLhlAarsgnleivkfLlenkgadvn 30 
                                   G tpL++ + +g  e+  fLle +ga+vn
  gi|13542230|ref|NP_111918.1|  98 GKTPLMWSIIFGYSEMSYFLLE-HGANVN 125
                                   89*************7777777.9****9 PP

  == domain 4  score: 22.1 bits;  conditional E-value: 3.6e-08
                         Ank_3   1 nGetpLhlAarsgnleivkfLlenkgadvn 30 
                                   +GetpL +A ++g+ eivk Lle  gad+ 
  gi|13542230|ref|NP_111918.1| 130 EGETPLIVASKYGRSEIVKKLLE-LGADIS 158
                                   69*********************.****97 PP

>> Ank_4  Ankyrin repeats (many copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   1.6e-07   0.00058       1      55 []      32      85 ..      32      85 .. 0.88
   2 !   22.9   0.0   2.6e-08   9.4e-05       3      55 .]      67     118 ..      67     118 .. 0.96
   3 !   27.5   0.0   9.6e-10   3.4e-06      19      55 .]     116     151 ..     115     151 .. 0.97
   4 !   12.6   0.0   4.4e-05      0.16       9      42 ..     139     171 ..     138     183 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 1.6e-07
                         Ank_4  1 eltaLhyaaisgrlelvrlLlekgadinaq..dnrsGetalhiAakrgnveilklLl 55
                                  ++t+L  a++ g + +++ L+e+    ++   ++++G tal+ A+k++++ i++ Ll
  gi|13542230|ref|NP_111918.1| 32 NRTPLMVACMLGMENAIDKLVEN---FDKLedKDIEGSTALIWAVKNNRLGIAEKLL 85
                                  689******************94...5555445999**************9999886 PP

  == domain 2  score: 22.9 bits;  conditional E-value: 2.6e-08
                         Ank_4   3 taLhyaaisgrlelvrlLlekgadinaqdnrsGetalhiAakrgnveilklLl 55 
                                   taL +a++ +rl +++ Ll+kg ++n   + sG t+l   + +g+ e+  +Ll
  gi|13542230|ref|NP_111918.1|  67 TALIWAVKNNRLGIAEKLLSKGSNVNTK-DFSGKTPLMWSIIFGYSEMSYFLL 118
                                   799************************9.988****************99997 PP

  == domain 3  score: 27.5 bits;  conditional E-value: 9.6e-10
                         Ank_4  19 lLlekgadinaqdnrsGetalhiAakrgnveilklLl 55 
                                   +Lle+ga++n + n +Get+l+ A k g+ ei+k Ll
  gi|13542230|ref|NP_111918.1| 116 FLLEHGANVNDR-NLEGETPLIVASKYGRSEIVKKLL 151
                                   69**********.*********************997 PP

  == domain 4  score: 12.6 bits;  conditional E-value: 4.4e-05
                         Ank_4   9 aisgrlelvrlLlekgadinaqdnrsGetalhiA 42 
                                    ++gr e+v+ Lle gadi a+ +  G+ta   A
  gi|13542230|ref|NP_111918.1| 139 SKYGRSEIVKKLLELGADISAR-DLTGLTAEASA 171
                                   568999****************.**9***97555 PP

>> Ank  Ankyrin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.0    0.0012       4.3       3      13 ..      33      43 ..      31      56 .. 0.78
   2 !   12.9   0.0   3.3e-05      0.12       2      31 ..      65      95 ..      64      96 .. 0.86
   3 !   16.4   0.0   2.6e-06    0.0093       2      31 ..      98     128 ..      97     129 .. 0.90
   4 !   21.2   0.0   7.7e-08   0.00028       2      31 ..     131     161 ..     130     162 .. 0.93

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0012
                                  BBHHHHHHHHT CS
                           Ank  3 nTPLHlAatng 13
                                  +TPL++A++ g
  gi|13542230|ref|NP_111918.1| 33 RTPLMVACMLG 43
                                  7*******766 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 3.3e-05
                                  SBBHHHHHHHHTTHHHHHHHH.TTTSTTCBT CS
                           Ank  2 GnTPLHlAatngkkriiklLL.hGAnlnald 31
                                  G T+L +A+ n+ + i++ LL +G+n+n +d
  gi|13542230|ref|NP_111918.1| 65 GSTALIWAVKNNRLGIAEKLLsKGSNVNTKD 95
                                  89*******666666******88*****998 PP

  == domain 3  score: 16.4 bits;  conditional E-value: 2.6e-06
                                   SBBHHHHHHHHTTHHHHHHHH.TTTSTTCBT CS
                           Ank   2 GnTPLHlAatngkkriiklLL.hGAnlnald 31 
                                   G TPL++ + +g  ++  +LL hGAn+n ++
  gi|13542230|ref|NP_111918.1|  98 GKTPLMWSIIFGYSEMSYFLLeHGANVNDRN 128
                                   99*****99889888999999*******887 PP

  == domain 4  score: 21.2 bits;  conditional E-value: 7.7e-08
                                   SBBHHHHHHHHTTHHHHHHHH.TTTSTTCBT CS
                           Ank   2 GnTPLHlAatngkkriiklLL.hGAnlnald 31 
                                   G TPL +A+ +g  +i+k LL  GA++ a+d
  gi|13542230|ref|NP_111918.1| 131 GETPLIVASKYGRSEIVKKLLeLGADISARD 161
                                   99****************99955******99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       520  (0.0290033); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 1107.47
//
Query:       gi|13542231|ref|NP_111919.1|  [L=278]
Description: adenine-specific DNA methylase [Thermoplasma volcanium GSS1]
Scores for complete 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-48  162.9   0.2    1.3e-47  162.4   0.2    1.2  1  N6_N4_Mtase    DNA methylase
    6.6e-05   22.6   0.0       0.15   11.7   0.0    2.3  2  Cons_hypoth95  Conserved hypothetical protein 95
     0.0027   17.4   0.0      0.024   14.3   0.0    2.3  3  UPF0020        Putative RNA methylase family UPF0020
  ------ inclusion threshold ------
      0.031   13.7   0.0       0.72    9.2   0.0    2.1  2  SAM_MT         Putative SAM-dependent methyltransferase
      0.032   14.0   0.0      0.056   13.2   0.0    1.3  1  Met_10         Met-10+ like-protein


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 !  162.4   0.2   3.8e-51   1.3e-47       2     228 ..      41     262 ..      40     265 .. 0.92

  Alignments for each domain:
  == domain 1  score: 162.4 bits;  conditional E-value: 3.8e-51
                                   EEEEE--SSSSSCS..................GCCGCCHHHHHHHHHHHHHHHHHHHEEEEEEEEEEE-CCCHHTHHHHHH CS
                   N6_N4_Mtase   2 dlivtdpPYntgkdy.............endeqyeeedsyeeyleflekvlkevrrvLkddgsifiniddseikkelkala 69 
                                   dli+ dpPY ++                + +e ++++ s+e+y +f+ +vlke++r+++d+ +i+    +++i+  ++ ++
  gi|13542231|ref|NP_111919.1|  41 DLIFLDPPYYLQMTPkrlkrwnnrsvpqTVREYWDAFPSFEAYDSFISSVLKEAKRLMSDTSTIWAIGTYHNIF--RIGKI 119
                                   89**********99999********************************************************9..89999 PP

                                   HHHTT-EEEEEEEEEEESSSTTTSTCCS-B--EEEEEEEESSTT-..---GGGSSBSS-HHHHHHHHHHCHHHCC-B--BS CS
                   N6_N4_Mtase  70 deifggffllnvivwkkpnsmpesnkdrltsthEyilvfsknkkyllkfnldaikvpyeekdklekrgaytskkkgkkied 150
                                   +++ g f++ln++vw k+n+mp+  + r+t+++E++++ +k+k++          ++y+  ++l+k+        gk  ++
  gi|13542231|ref|NP_111919.1| 120 MQDMG-FWILNDVVWIKTNPMPNWLGVRFTNSTETLIWATKGKEQ----------KNYTYNRNLAKEF-----GLGKTANN 184
                                   9999*.***************************************..........3444444444433.....56788889 PP

                                   EEE-SCCCTTSTTS-CHH----SS---HHHHHHHHHHHS-TT-EEEETT-TTTHHHHHHHHTT-EEEEEESSHHHHHH CS
                   N6_N4_Mtase 151 iWdlseiqsnekkskgdtkkkHpaqkPvallerlIklstkkgdivlDpFaGSGtTavaakelgrkfiGieieeeyvel 228
                                   +W ++  + ne+ ++++ k  HpaqkP++l++r+I++stk+gd++lDpFaG GtT+vaa  lgr+f  ie+++ y+++
  gi|13542231|ref|NP_111919.1| 185 VWVMKTSRGNERVRDENRKSVHPAQKPLELMKRIILSSTKEGDLILDPFAGVGTTGVAASMLGRNFTLIEKDPVYYRA 262
                                   **8888888888899888*******************************************************99985 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.0   4.3e-05      0.15      99     134 ..      27      59 ..       8      71 .. 0.71
   2 !    8.9   0.0    0.0003       1.1      40      90 ..     224     273 ..     214     278 .] 0.81

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4.3e-05
                                   S-HHHHCTS--SS-EEEEEEE--SSSTTCH.HHHHH CS
                 Cons_hypoth95  99 daleallklakkkeefdivflDPPyakellieevle 134
                                   d+le +++    +  +d++flDPPy  +++  + l+
  gi|13542231|ref|NP_111919.1|  27 DSLEIMRRI--DDCIYDLIFLDPPYYLQMT-PKRLK 59 
                                   555545444..45678*********99976.66555 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0003
                                   HCC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT-- CS
                 Cons_hypoth95  40 iegarvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkle 90 
                                    eg  +LD faG G+ g+ A+S   ++ +l+ekd+  ++++    ++++++
  gi|13542231|ref|NP_111919.1| 224 KEGDLILDPFAGVGTTGV-AASMLGRNFTLIEKDPVYYRAMLSRFSRFGIR 273
                                   567779***********9.55666699********9999988888877765 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       0.4   1.4e+03     121     138 ..      39      56 ..      12      61 .. 0.79
   2 ?   -1.2   0.0      0.39   1.4e+03     140     168 ..      82     110 ..      64     121 .. 0.72
   3 !   14.3   0.0   6.8e-06     0.024      23      54 ..     220     251 ..     216     268 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.4
                                   ---EEEE----------H CS
                       UPF0020 121 evdvivtnpPYGerlgsk 138
                                    +d+i  +pPY   ++ k
  gi|13542231|ref|NP_111919.1|  39 IYDLIFLDPPYYLQMTPK 56 
                                   5899999****8777655 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.39
                                   HHHHHHHHHHHHHHHH-TT..-EEEEEES CS
                       UPF0020 140 alekLYseflrelkrvlrgggrlvlltse 168
                                   a +++ s++l+e+kr ++  + + ++ + 
  gi|13542231|ref|NP_111919.1|  82 AYDSFISSVLKEAKRLMSDTSTIWAIGTY 110
                                   55667777888888888877766666554 PP

  == domain 3  score: 14.3 bits;  conditional E-value: 6.8e-06
                                   HTT--TTS-EEETT-TTSHHHHHHHHHHTT-- CS
                       UPF0020  23 lagwkpgepllDPmCGsGtilIEaallgania 54 
                                   l+  k+g+ +lDP+ G Gt  + a +lg+n  
  gi|13542231|ref|NP_111919.1| 220 LSSTKEGDLILDPFAGVGTTGVAASMLGRNFT 251
                                   7899************************9976 PP

>> SAM_MT  Putative SAM-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0     0.027        98     132     158 ..      23      49 ..      10      61 .. 0.82
   2 ?    9.2   0.0    0.0002      0.72      68     106 ..     222     260 ..     196     270 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.027
                        SAM_MT 132 LlaasslealakleeekpdvvYlDPmy 158
                                   +l ++sle+++++++  +d ++lDP y
  gi|13542231|ref|NP_111919.1|  23 VLLGDSLEIMRRIDDCIYDLIFLDPPY 49 
                                   56678999999999999********76 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0002
                        SAM_MT  68 kkgvlptvlDaTaGlGrDafvlaslGckvtliErhpvva 106
                                    ++    +lD  aG+G  +   ++lG + tliE++pv +
  gi|13542231|ref|NP_111919.1| 222 STKEGDLILDPFAGVGTTGVAASMLGRNFTLIEKDPVYY 260
                                   44445679****************************975 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.6e-05     0.056      92     139 ..     217     262 ..     208     269 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.6e-05
                                   HHHHTT--TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHH CS
                        Met_10  92 erlaklveegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvky 139
                                   + + +  +eg++++d fAG+G   ++++ ++++     i+++P  ++ 
  gi|13542231|ref|NP_111919.1| 217 RIILSSTKEGDLILDPFAGVGTTGVAASMLGRNF--TLIEKDPVYYRA 262
                                   3355669*********************966655..667888877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       402  (0.0224218); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 1764.50
//
Query:       gi|13542232|ref|NP_111920.1|  [L=141]
Description: stress-induced protein [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-17   64.1   0.0    1.7e-17   63.7   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 !   63.7   0.0   9.8e-22   1.7e-17       2      96 ..      38     133 ..      36     136 .. 0.90

  Alignments for each domain:
  == domain 1  score: 63.7 bits;  conditional E-value: 9.8e-22
                                   TXSSB-HHHHHHHHHHHHHHHHHHHHTCCCT---SCEEEEEEEEEECCECT..CEEEEEEEEEEE-SS-H..HHHHHHHHH CS
                          OsmC   2 dgsgpsPeelllaalasCfaitlravakkkgikledleveveaerdpegak..giteirlkvevkipgadseeklkkllek 80 
                                   +++++ Pe l+   lasC+ +t+  + +++gi+l++ + e++ae  p++ k  ++++ir++v++++++ d +ek+ +++e+
  gi|13542232|ref|NP_111920.1|  38 PEGKFCPETLFPGILASCLLTTFLEFRERMGIDLKEWKSEATAELGPSPEKgfRFQRIRIHVKLRVSEQD-KEKIPRAMEL 117
                                   566899****************************88877777777776666779*************999.5********* PP

                                   HHHHSHHHHHHCT-SS CS
                          OsmC  81 aekrCpvsntlkngvk 96 
                                   a+k+C++s+++kn+v+
  gi|13542232|ref|NP_111920.1| 118 AHKYCFISRAIKNNVE 133
                                   *************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       325  (0.0181271); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 991.41
//
Query:       gi|13542233|ref|NP_111921.1|  [L=206]
Description: alpha/beta superfamily hydrolase [Thermoplasma volcanium GSS1]
Scores for complete 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-24   85.2   0.4    4.7e-16   59.2   0.2    2.0  2  Abhydrolase_1  alpha/beta hydrolase fold
    1.3e-17   63.9   0.2    4.7e-12   45.7   0.1    2.1  2  Hydrolase_4    Serine aminopeptidase, S33
    6.3e-14   53.1   0.0    1.5e-10   42.1   0.1    2.0  2  Abhydrolase_6  Alpha/beta hydrolase family
    2.3e-07   30.6   0.0      3e-07   30.2   0.0    1.1  1  DLH            Dienelactone hydrolase family
    2.2e-06   27.6   0.1      3e-06   27.1   0.1    1.1  1  Abhydrolase_5  Alpha/beta hydrolase family
    2.8e-05   23.9   0.0    0.00012   21.8   0.1    2.0  2  FSH1           Serine hydrolase (FSH1)
    3.2e-05   23.9   0.0    5.4e-05   23.1   0.0    1.3  1  Abhydrolase_2  Phospholipase/Carboxylesterase
    5.5e-05   22.9   0.0    8.6e-05   22.3   0.0    1.4  1  Esterase       Putative esterase
    0.00012   21.6   0.6       0.24   10.8   0.7    2.3  2  Peptidase_S9   Prolyl oligopeptidase family
    0.00046   19.0   0.0     0.0006   18.6   0.0    1.1  1  Ndr            Ndr family
     0.0015   18.0   0.2      0.016   14.7   0.2    2.4  2  Esterase_phd   Esterase PHB depolymerase
     0.0016   18.5   0.0     0.0027   17.8   0.0    1.4  1  Abhydrolase_4  TAP-like protein
     0.0043   17.0   0.0     0.0061   16.5   0.0    1.3  1  BAAT_C         BAAT / Acyl-CoA thioester hydrolase C terminal
  ------ inclusion threshold ------
      0.018   14.2   0.0      0.021   13.9   0.0    1.2  1  DUF2048        Abhydrolase domain containing 18
       0.23   10.2   0.1       0.28    9.9   0.1    1.1  1  Peptidase_S28  Serine carboxypeptidase S28


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 !   59.2   0.2   3.9e-19   4.7e-16       3     114 ..      29     139 ..      28     145 .. 0.93
   2 !   25.6   0.0     7e-09   8.4e-06     207     257 .]     142     192 ..     133     192 .. 0.92

  Alignments for each domain:
  == domain 1  score: 59.2 bits;  conditional E-value: 3.9e-19
                                   EEEE-STTTCGGGGTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTTGB.CHHSHHHHHHHHHHHHHHCTTSSEEEEEETHH CS
                 Abhydrolase_1   3 lvilhGlpgssdvwaerglapaLakdgfdvillDlrGvgySspapacinddygtasvaddldrildalgddkltlvGhSmG 83 
                                   +v+lhG+  +s  w  +gl++  a   f v+++D +G+g S+p+    +++ ++ + a +++  +++lg+++ +++G SmG
  gi|13542233|ref|NP_111921.1|  29 IVMLHGWSFTSRDWETPGLFNEYANLSFNVYAPDYPGFGMSEPSDFYSVKRGNIEASASFIKDYMQSLGVEHAVILGASMG 109
                                   79********************************************988999999999999999***************** PP

                                   HHHHHHHHHHHGGGEEEEEEESECSSCCHHH CS
                 Abhydrolase_1  84 GmialayaaeyperVkalvllgaidpaasli 114
                                   G +a  +   +p+ V+a++++++ ++   + 
  gi|13542233|ref|NP_111921.1| 110 GGMAILMGMAHPDMVDAVIAVAP-AWVENYT 139
                                   ***********************.6655554 PP

  == domain 2  score: 25.6 bits;  conditional E-value: 7e-09
                                   THHHHSEEEEEEETTCSSSCHHHHHHHHHCHTSEEEEEEETCSSSHHHHSH CS
                 Abhydrolase_1 207 lknvlaptlvisgtsDplvppkaledlaqllpkkrlvvisdagHlaflegp 257
                                    kn+ +p+l+++g++D +v+p+ + ++++++++++l++++++ H ++le+p
  gi|13542233|ref|NP_111921.1| 142 MKNIEKPVLLVWGSEDTVVDPHFGNKYRSAIKNSQLEIVEGSKHPVYLEKP 192
                                   689999******************************************986 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.7   0.1   3.9e-15   4.7e-12       3     116 ..      25     138 ..      23     145 .. 0.84
   2 !   18.0   0.0   1.1e-06    0.0014     182     238 ..     137     191 ..     134     192 .. 0.89

  Alignments for each domain:
  == domain 1  score: 45.7 bits;  conditional E-value: 3.9e-15
                   Hydrolase_4   3 pkavvvlvHGlaehsgryae..laeaLaaqGfavyalDhrGhGrse......gkrghvpsfddyvdDlaafvekvkeehpe 75 
                                   +k+ +v++HG   +s+  +   l+++ a+  f+vya D+ G+G se       krg ++   ++++D  + +       + 
  gi|13542233|ref|NP_111921.1|  25 AKKDIVMLHGWSFTSRDWETpgLFNEYANLSFNVYAPDYPGFGMSEpsdfysVKRGNIEASASFIKDYMQSL-------GV 98 
                                   5778999***999999888777************************88888888888888888888875553.......34 PP

                   Hydrolase_4  76 lplfllGhSmGGliallyllrypdkvaglilsaPalkikak 116
                                   +  ++lG SmGG +a+l++  +pd v+++i +aPa +++++
  gi|13542233|ref|NP_111921.1|  99 EHAVILGASMGGGMAILMGMAHPDMVDAVIAVAPA-WVENY 138
                                   4589******************************9.55555 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 1.1e-06
                   Hydrolase_4 182 rleeraakitlPllllhGeaDkvvdpeasrelyerlgskdktlklypglyHellnEp 238
                                   + +e+ ++i+ P+ll+ G++D+vvdp    ++  +++  + +l++ +g  H +  E+
  gi|13542233|ref|NP_111921.1| 137 NYTEKMKNIEKPVLLVWGSEDTVVDPHFGNKYRSAIK--NSQLEIVEGSKHPVYLEK 191
                                   56788999*********************99888888..799*********998886 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.1   0.1   1.2e-13   1.5e-10       1      99 [.      29     133 ..      29     143 .. 0.68
   2 !    9.4   0.0    0.0013       1.5     169     219 ..     145     197 ..     133     198 .. 0.78

  Alignments for each domain:
  == domain 1  score: 42.1 bits;  conditional E-value: 1.2e-13
                                   EEEE--GC.....GC.HHHHHHHHCCTCEEEEE--TTSTS-GGCS--HHHC....HHH.HHHHCCTT....TTSEEEEEET CS
                 Abhydrolase_6   1 vlllHGagssassWl.vapLaallaagvhvlapDlpGhGrsdpppldledl....adl.aalldelaa..gggpvvlvGHS 73 
                                   +++lHG ++++++W   + + ++++  + v+apD+pG+G   + p d+  +     +  a ++ +  +  g   +v++G S
  gi|13542233|ref|NP_111921.1|  29 IVMLHGWSFTSRDWEtPGLFNEYANLSFNVYAPDYPGFG--MSEPSDFYSVkrgnIEAsASFIKDYMQslGVEHAVILGAS 107
                                   89************6344557777777999*********..5555555554333322235555555556567778****** PP

                                   CHHHHHHH..HHHCC.....EEEEES-..-- CS
                 Abhydrolase_6  74 lGGalala..aapla...lvvgvlldpppta 99 
                                   +GG +a +   a      +++ ++++p   a
  gi|13542233|ref|NP_111921.1| 108 MGGGMAILmgMA--HpdmVDAVIAVAP---A 133
                                   **9877773433..2345666699999...4 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0013
                                   -TTGCEEEC.TT-CHHHHCHHCCCH..STTEEETCE...SSS-HHHHSHHHHHH CS
                 Abhydrolase_6 169 lpvpllvlg.geDplvprllerlla..qagarlpvvlpgaGHlphleepdevae 219
                                   +  p+l+++ +eD +v +++    +  +   +l ++++g+ H ++le+p++++e
  gi|13542233|ref|NP_111921.1| 145 IEKPVLLVWgSEDTVVDPHFGNKYRsaIKNSQL-EIVEGSKHPVYLEKPKRFIE 197
                                   455676666377777777788666668899999.********99999**99976 PP

>> DLH  Dienelactone hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   0.0   2.5e-10     3e-07      91     181 ..      92     179 ..      69     194 .. 0.83

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 2.5e-10
                           DLH  91 svpevstkkvgvvGfCmGGalalllaaev.pevdaavafYGlspekeleeaakikapilalfgeeDefipadevekleeal 170
                                   ++++  ++  ++ G  mGG +a+l+     ++vda++a  +  +e+  e+ ++i++p+l + g eD++++    +k ++a+
  gi|13542233|ref|NP_111921.1|  92 YMQSLGVEHAVILGASMGGGMAILMGMAHpDMVDAVIAVAPAWVENYTEKMKNIEKPVLLVWGSEDTVVDPHFGNKYRSAI 172
                                   55667789999************99776669**************************************999777777777 PP

                           DLH 171 kaanvdlelkv 181
                                   k++    +l++
  gi|13542233|ref|NP_111921.1| 173 KNS----QLEI 179
                                   544....4444 PP

>> Abhydrolase_5  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.1   2.5e-09     3e-06      54     141 ..      96     186 ..      80     190 .. 0.80

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 2.5e-09
                 Abhydrolase_5  54 pklekfvvgGhslGGvvasrfaaee.ekiegvvfla.sYPe..kdelselskkvlsivgteDgvlnvkslekakkflpkdt 130
                                    ++e+ v+ G s+GG +a  +   + + +++v+ +a ++ e   +++++ +k+vl ++g+eD v++ +  +k +    k++
  gi|13542233|ref|NP_111921.1|  96 LGVEHAVILGASMGGGMAILMGMAHpDMVDAVIAVApAWVEnyTEKMKNIEKPVLLVWGSEDTVVDPHFGNKYRSA-IKNS 175
                                   35899*************9999988579*****99843444445789999****************9877666655.5899 PP

                 Abhydrolase_5 131 kvvsieGgnha 141
                                   ++  +eG  h 
  gi|13542233|ref|NP_111921.1| 176 QLEIVEGSKHP 186
                                   ********996 PP

>> FSH1  Serine hydrolase (FSH1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       2.3   2.7e+03       4      14 ..      26      36 ..      23      42 .. 0.81
   2 !   21.8   0.1     1e-07   0.00012      83     192 ..      79     176 ..      60     188 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 2.3
                          FSH1  4 kkkiLcLhGyt 14
                                  kk i +LhG+ 
  gi|13542233|ref|NP_111921.1| 26 KKDIVMLHGWS 36
                                  7899*****75 PP

  == domain 2  score: 21.8 bits;  conditional E-value: 1e-07
                          FSH1  83 yegleesldavkdyikengp.fdGiiGFSqGaalaallaslleellkeashpslkfailvsGfkleepkyeeyyeedkiqt 162
                                     ++e s +++kdy+++ g     i+G S G+ +a l+ +    +           +i+v+   +e  +y e    ++i+ 
  gi|13542233|ref|NP_111921.1|  79 RGNIEASASFIKDYMQSLGVeHAVILGASMGGGMAILMGMAHPDMV--------DAVIAVAPAWVE--NYTEK--MKNIEK 147
                                   56899*************98688999********976644333322........356666666663..36664..4789** PP

                          FSH1 163 ptLhvlGelDtvvdeerseaLaeafknssk 192
                                   p+L v G++Dtvvd++  ++   a+kns +
  gi|13542233|ref|NP_111921.1| 148 PVLLVWGSEDTVVDPHFGNKYRSAIKNS-Q 176
                                   **************99888888888884.3 PP

>> Abhydrolase_2  Phospholipase/Carboxylesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0   4.6e-08   5.4e-05     100     199 ..      94     185 ..      79     205 .. 0.78

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 4.6e-08
                                   TT--GGGEEEEEETHHHHHHHHHHHT-SS--SEEEEES---TTGGGTTTTS-GGGGG-EEEEEEETT-SSS-HHHHHHHHH CS
                 Abhydrolase_2 100 kgipssriiigGFSqGaalalylaltlpkklggivafsgalplsqklessatavtkklpilqiHgeeDpvvplalgkaake 180
                                   +++  ++ +i G S+G+ +a+  +++ p  +  ++a+  a + + + +    ++    p+l+++g+eD vv+  +g++   
  gi|13542233|ref|NP_111921.1|  94 QSLGVEHAVILGASMGGGMAILMGMAHPDMVDAVIAVAPAWVENYTEKM--KNIE--KPVLLVWGSEDTVVDPHFGNKYRS 170
                                   456677889*****************************99998877663..3333..69*****************98777 PP

                                   HHHTTS-GEEEEEETT--S CS
                 Abhydrolase_2 181 vlkkllkkvelksyeglaH 199
                                   ++k+++     +++eg++H
  gi|13542233|ref|NP_111921.1| 171 AIKNSQL----EIVEGSKH 185
                                   7766655....56665555 PP

>> Esterase  Putative esterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   7.2e-08   8.6e-05     115     157 ..      98     134 ..      85     190 .. 0.74

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 7.2e-08
                                   CC.EEEEEETHHHHHHHHHHHCSTTTCCEEEEES--S-CCHCHH CS
                      Esterase 115 dg.ravaGqSmGGlgALilalkhpdrFgsvssfSpivnpsnamW 157
                                       +++G+SmGG +A+++++ hpd+   v++ +p        W
  gi|13542233|ref|NP_111921.1|  98 VEhAVILGASMGGGMAILMGMAHPDMVDAVIAVAPA-------W 134
                                   445799****************************76.......3 PP

>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.7    0.0002      0.24      64      98 ..      99     133 ..      82     139 .. 0.87
   2 !    8.8   0.0   0.00083         1     136     186 ..     141     185 ..     133     204 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0002
                                   GGEEEEEETHHHHHHHHHHHH-GGG-SEEEEESE- CS
                  Peptidase_S9  64 erlaitGgSyGGyltgaalnqrpdlFkaavaevpv 98 
                                   e+ +i G+S GG ++  + + +pd+ +a++a++p 
  gi|13542233|ref|NP_111921.1|  99 EHAVILGASMGGGMAILMGMAHPDMVDAVIAVAPA 133
                                   6789*******9999999999***********995 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00083
                                   CGGG-----EEEEEEETT-SSS-THHHHHHHHHHH--S-SEEEEEETTS-S CS
                  Peptidase_S9 136 pldnvkaypplLlihGlaDdrvppaealklvaaLqkkgknvlllifpdegH 186
                                   +++n  +++p+Ll+ G +D+ v p  + k+ +a ++    ++l i  +++H
  gi|13542233|ref|NP_111921.1| 141 KMKN--IEKPVLLVWGSEDTVVDPHFGNKYRSAIKN----SQLEIVEGSKH 185
                                   3455..99****************999998888775....55566666666 PP

>> Ndr  Ndr family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0     5e-07    0.0006      81     182 ..      81     180 ..      53     194 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 5e-07
                                   -HHHHHTTHHHHHHHHT---EEEEEETHHHHHHHHHHHHSGGGEEEEEEES---S---HHHHHHHHHH.......TTTS-H CS
                           Ndr  81 slddladqllavldhfklksviglGvgaGAyilarfalkhperveglvLinitskaagwvewakeKlsskllkkvgltdll 161
                                    ++  a  ++  ++ + +++++ lG+  G  +  + +++hp++v +++ +     a++wve   eK+  +  k v l    
  gi|13542233|ref|NP_111921.1|  81 NIEASASFIKDYMQSLGVEHAVILGASMGGGMAILMGMAHPDMVDAVIAV-----APAWVENYTEKMK-NIEKPVLLVWGS 155
                                   56667788899999********************************9876.....789*********9.57788999999* PP

                                   HHHHHHHHS-HHHHHH....T-HHH CS
                           Ndr 162 kdlllahkFgkeekse....nsdlv 182
                                   +d+++  +Fg++++s+    + ++v
  gi|13542233|ref|NP_111921.1| 156 EDTVVDPHFGNKYRSAiknsQLEIV 180
                                   ***********99987663334454 PP

>> Esterase_phd  Esterase PHB depolymerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.2   1.3e-05     0.016      73     125 ..      77     127 ..      16     137 .. 0.68
   2 ?    0.2   0.0      0.37   4.4e+02     168     194 ..     145     171 ..     128     178 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.3e-05
                  Esterase_phd  73 aGrGeaavvvalvdalvdehrvdaarvyvaGlsaGaaladllalhypdvfaav 125
                                     rG+ ++ +++++  ++  +v+ a   + G s G+++a l+++ +pd+  av
  gi|13542233|ref|NP_111921.1|  77 VKRGNIEASASFIKDYMQSLGVEHAV--ILGASMGGGMAILMGMAHPDMVDAV 127
                                   45777778888888888888888775..5799****************99887 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.37
                  Esterase_phd 168 pglpalvvqGdadtvvavknaeslvva 194
                                      p l+v G  dtvv ++  ++   a
  gi|13542233|ref|NP_111921.1| 145 IEKPVLLVWGSEDTVVDPHFGNKYRSA 171
                                   55699***********99877766555 PP

>> Abhydrolase_4  TAP-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   2.2e-06    0.0027      30      79 ..     142     191 ..     122     205 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.2e-06
                 Abhydrolase_4  30 takgaapvLllqnerDpaTPyegakklakalggavlvtvegeGHgalaag 79 
                                    ++ ++pvLl+ +  D ++ ++ ++k ++a+++++l +veg+ H ++ ++
  gi|13542233|ref|NP_111921.1| 142 MKNIEKPVLLVWGSEDTVVDPHFGNKYRSAIKNSQLEIVEGSKHPVYLEK 191
                                   222368***************************************99843 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 !   16.5   0.0   5.1e-06    0.0061      25      75 ..     102     152 ..      83     198 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 5.1e-06
                                   EEEEETHHHHHHHHHHHHSS.SEEEEEEES--SB--SSEEEETTE..EE--- CS
                        BAAT_C  25 gllGiSkGgelalllasflk.kisavvlingsavvvegklvykdeskvlpel 75 
                                    +lG S Gg +a+l+++ ++  ++av++++++ v   ++++++ e k++  +
  gi|13542233|ref|NP_111921.1| 102 VILGASMGGGMAILMGMAHPdMVDAVIAVAPAWVENYTEKMKNIE-KPVLLV 152
                                   479*****************7788888887776665555555444.444433 PP

>> DUF2048  Abhydrolase domain containing 18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   1.8e-05     0.021     155     210 ..      77     133 ..      68     196 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.8e-05
                       DUF2048 155 mgsalilEslvllhwlere.GyGplgltGlSmGGhmaslaasnwpkplvlvpclsws 210
                                   + ++ i+ s++ ++  ++  G  +  + G SmGG ma l + ++p  +  v  ++++
  gi|13542233|ref|NP_111921.1|  77 VKRGNIEASASFIKDYMQSlGVEHAVILGASMGGGMAILMGMAHPDMVDAVIAVAPA 133
                                   55666777777777777777999999*******************999888777764 PP

>> Peptidase_S28  Serine carboxypeptidase S28
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.1   0.00023      0.28      98     144 ..      87     130 ..      66     156 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00023
                 Peptidase_S28  98 sfikalkqkfklsssskwitfGgSYsgsLaawarkkyPelvvgavaS 144
                                   sfik      +    ++ ++ G+S +g +a  +   +P++v++++a 
  gi|13542233|ref|NP_111921.1|  87 SFIKDYM---QSLGVEHAVILGASMGGGMAILMGMAHPDMVDAVIAV 130
                                   4444444...4444556799************************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 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:                        62  (0.00345808); 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: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 1347.85
//
Query:       gi|13542234|ref|NP_111922.1|  [L=366]
Description: HD family phosphatase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-12   47.5   0.7    1.8e-12   47.5   0.7    2.1  2  HD        HD domain
  ------ inclusion threshold ------
       0.02   14.4   0.0      0.048   13.1   0.0    1.6  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 !   47.5   0.7     2e-16   1.8e-12       1      91 [.      51     131 ..      51     166 .. 0.81
   2 ?   -2.1   0.1      0.49   4.4e+03       8      26 ..     229     247 ..     228     255 .. 0.63

  Alignments for each domain:
  == domain 1  score: 47.5 bits;  conditional E-value: 2e-16
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTHHHHTS..HHH.HHHCTCCHHHHHHHHHHHHHHHHHHHHHHHH CS
                            HD   1 rleHsleVaklarrlaedlgeeedrellllaaLlHDiGkgpfgdafekk.eeefekflaHekvgaeilrevekrlgldled 80 
                                   r+eHs+++++la  + e+l   + ++ l++aaLlHDiG+ p ++++e+  +   ++  +H + g  +++   +++      
  gi|13542234|ref|NP_111922.1|  51 RFEHSIGTYYLASLYNEHLR--TMSDELKIAALLHDIGHFPYSHTIEEFyM--ETEKIDHLQAGINLIEGKAESE------ 121
                                   79******************..**********************8887532..556689*********9999999...... PP

                                   HHHHHHTTCCH CS
                            HD  81 vaklirehhes 91 
                                    + +i+e+h+ 
  gi|13542234|ref|NP_111922.1| 122 -IPAILEKHGI 131
                                   .4455555544 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.49
                                   HHHHHHHHHHHHHHHHHHH CS
                            HD   8 Vaklarrlaedlgeeedre 26 
                                   ++ +a+rlae +g    ++
  gi|13542234|ref|NP_111922.1| 229 MLGIAARLAEAIGTSRMVD 247
                                   5679999999999733333 PP

>> HDOD  HDOD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   5.3e-06     0.048      97     147 ..      53     102 ..      45     120 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.3e-06
                                   HHHHHHHHHHHHHHHHTT-S-HHHHHHHHHTTTHHHHHHHHHSHHHHHHHH CS
                          HDOD  97 ehslavAlvarelaeelgledpeeaflaGLLhdiGklvllsllpeeleell 147
                                   ehs+ + ++a    e+l+  + +e+ +a+LLhdiG +   ++++e + e+ 
  gi|13542234|ref|NP_111922.1|  53 EHSIGTYYLASLYNEHLRTMS-DELKIAALLHDIGHFPYSHTIEEFYMETE 102
                                   788888888888888888877.*****************999999887764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.48
# Mc/sec: 2292.33
//
Query:       gi|13542235|ref|NP_111923.1|  [L=197]
Description: SAM-dependent methyltransferase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-15   57.1   0.0    3.6e-15   56.4   0.0    1.3  1  Methyltransf_25  Methyltransferase domain
    5.1e-14   52.8   0.0      9e-14   52.0   0.0    1.4  1  Methyltransf_12  Methyltransferase domain
    5.4e-12   46.2   0.0    8.4e-12   45.6   0.0    1.3  1  Methyltransf_11  Methyltransferase domain
    1.1e-10   41.5   0.0    1.4e-10   41.2   0.0    1.1  1  Methyltransf_31  Methyltransferase domain
    1.2e-09   37.9   0.0    1.8e-09   37.3   0.0    1.2  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    4.6e-09   36.3   0.0    5.9e-09   36.0   0.0    1.1  1  Methyltransf_23  Methyltransferase domain
    6.9e-06   25.7   0.0    9.3e-06   25.3   0.0    1.2  1  MTS              Methyltransferase small domain
    0.00022   20.7   0.0    0.00038   19.9   0.0    1.4  1  TehB             Tellurite resistance protein TehB
    0.00083   19.2   0.0     0.0053   16.5   0.0    1.9  1  DUF938           Protein of unknown function (DUF938)
      0.001   18.1   0.0     0.0012   17.8   0.0    1.1  1  Methyltransf_9   Protein of unknown function (DUF1698)
     0.0069   15.7   0.0     0.0089   15.3   0.0    1.1  1  Rsm22            Mitochondrial small ribosomal subunit Rsm22
  ------ inclusion threshold ------
      0.053   13.5   0.0      0.067   13.2   0.0    1.2  1  Methyltransf_32  Methyltransferase domain


Domain annotation for each model (and alignments):
>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.4   0.0   2.4e-18   3.6e-15       1      97 []      46     139 ..      46     139 .. 0.92

  Alignments for each domain:
  == domain 1  score: 56.4 bits;  conditional E-value: 2.4e-18
                                   EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGSSHHH CS
               Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhlsded 81 
                                   +Ld+GcGtG+  + +a+ +++  + ++D+s+ ml +a +++++ + +v+f  g+ +++pfe+ ++D+v+ss ++hh++   
  gi|13542235|ref|NP_111923.1|  46 ILDVGCGTGTADFFIANSFSNVIIDCIDPSPYMLSIASKKLSRFKGRVNFALGSSRSIPFEK-KYDFVFSSISFHHWK--C 123
                                   8******************88999*****************99777**************97.*******999**976..5 PP

                                   HHHHHHHHHHHEEEEE CS
               Methyltransf_25  82 lekalkeiarvLkpgG 97 
                                   +e+ lk +  ++k++G
  gi|13542235|ref|NP_111923.1| 124 RENGLKTMGLHVKDNG 139
                                   5688999988888877 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.0   0.0     6e-17     9e-14       1      99 []      47     141 ..      47     141 .. 0.90

  Alignments for each domain:
  == domain 1  score: 52.0 bits;  conditional E-value: 6e-17
               Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhhlkd 81 
                                   L++GcGtG+  + ++++++++ + ++D+sp ++  a++kl++ +++ n  +            ++++D v++s  +hh+k 
  gi|13542235|ref|NP_111923.1|  47 LDVGCGTGTADFFIANSFSNVIIDCIDPSPYMLSIASKKLSRFKGRVNFALGSSRSIP----FEKKYDFVFSSISFHHWKC 123
                                   8*******************************************95555555554444....446**************** PP

               Methyltransf_12  82 irevldnirklLkpgGrl 99 
                                   ++  l+ +  ++k++G+l
  gi|13542235|ref|NP_111923.1| 124 RENGLKTMGLHVKDNGVL 141
                                   ****************97 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.6   0.0   5.6e-15   8.4e-12       1      96 []      47     143 ..      47     143 .. 0.93

  Alignments for each domain:
  == domain 1  score: 45.6 bits;  conditional E-value: 5.6e-15
                                   EEET-TTSHHHHHHHHTT..SEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-CCHHH CS
               Methyltransf_11   1 LdvGcGtGrlaealakrg..arvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhvedpek 79 
                                   LdvGcGtG     +a+ +    + ++D+s++ml +a++k s+ + +v+f  ++ +++pfe+ ++D+v+ss ++hh++ +e 
  gi|13542235|ref|NP_111923.1|  47 LDVGCGTGTADFFIANSFsnVIIDCIDPSPYMLSIASKKLSRFKGRVNFALGSSRSIPFEK-KYDFVFSSISFHHWKCREN 126
                                   8**************9996666779***********9999998889*************99.9****************** PP

                                   HHHHHHHHEEEEEEEEE CS
               Methyltransf_11  80 alkeiaRvLkpgGllvi 96 
                                    lk +   +k +G+l+i
  gi|13542235|ref|NP_111923.1| 127 GLKTMGLHVKDNGVLAI 143
                                   ******99999999975 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.2   0.0   9.1e-14   1.4e-10       4     113 ..      43     147 ..      40     185 .. 0.85

  Alignments for each domain:
  == domain 1  score: 41.2 bits;  conditional E-value: 9.1e-14
               Methyltransf_31   4 glrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeqgdieeleklledekfDlilsnev 83 
                                     ++lD+GCGtG+  f +a + +++  +  iD s+ +++ A ++++   ++ +v+F  g+  +++  +e +k+D+++s   
  gi|13542235|ref|NP_111923.1|  43 PETILDVGCGTGTADFFIA-NSFSNVIIDCIDPSPYMLSIASKKLS--RFKgRVNFALGSSRSIP--FE-KKYDFVFSSIS 117
                                   5789***************.8899999****************866..55559************..99.9********99 PP

               Methyltransf_31  84 lnaladpdkileeiervlkpggilliedpr 113
                                   +++ +  ++ l+ +   +k++g+l+i ++ 
  gi|13542235|ref|NP_111923.1| 118 FHHWKCRENGLKTMGLHVKDNGVLAIYEYY 147
                                   9***********************998776 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.3   0.0   1.2e-12   1.8e-09      38     165 ..      34     157 ..      13     164 .. 0.84

  Alignments for each domain:
  == domain 1  score: 37.3 bits;  conditional E-value: 1.2e-12
                                   HHHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EE CS
               Ubie_methyltran  38 fveklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfeddsfD 118
                                    +e+   + +++++lDv +Gtg   f +++s  +   ++ +D ++ mL+++ kkl +  k +++f  +++  +pfe++ +D
  gi|13542235|ref|NP_111923.1|  34 ITED-IDKFKPETILDVGCGTGTADFFIANSFSN-VIIDCIDPSPYMLSIASKKLSRF-KGRVNFALGSSRSIPFEKK-YD 110
                                   3444.4456789**************99999865.679****************9874.679*************984.77 PP

                                   EEEEES-GGG-S-HHHHHHHHHHHEEEEEEEEEEEE----SHHHHHH CS
               Ubie_methyltran 119 vvtvsfGlrnvtDklkaLkeayrvlkpGGrlvvlefskvelpllsqa 165
                                   +v  s  +     ++++Lk++   +k  G l + e+ +++l  +++a
  gi|13542235|ref|NP_111923.1| 111 FVFSSISFHHWKCRENGLKTMGLHVKDNGVLAIYEYYRPNLRSFHKA 157
                                   77777777899999**************************9999887 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.0   0.0   3.9e-12   5.9e-09      20     132 ..      40     156 ..      20     185 .. 0.75

  Alignments for each domain:
  == domain 1  score: 36.0 bits;  conditional E-value: 3.9e-12
               Methyltransf_23  20 lraggrvLdiGcGtGillevlrengf...svtgvDlspeaveiaekakkaqkdqfdeqeaaepqg......kfdlIvlrev 91 
                                   ++++  +Ld+GcGtG +++ + +n f    ++ +D+sp + +ia+k+   +k  +  ++a  +++      k+d++ ++ +
  gi|13542235|ref|NP_111923.1|  40 KFKPETILDVGCGTG-TADFFIANSFsnvIIDCIDPSPYMLSIASKKLSRFKGRV--NFALGSSRsipfekKYDFVFSSIS 117
                                   68999**********.77777666664324559***********86555555555..33333333555555********** PP

               Methyltransf_23  92 lehvpdppellrqiatllkpgGylllseplaslkedrllld 132
                                   ++h +  +  l++++ ++k++G+l + e+ +  +++r++++
  gi|13542235|ref|NP_111923.1| 118 FHHWKCRENGLKTMGLHVKDNGVLAIYEYYR--PNLRSFHK 156
                                   ************************9999844..56666665 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.0   6.2e-09   9.3e-06      26     109 ..      37     120 ..      28     143 .. 0.89

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 6.2e-09
                                   HCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTSTTS-EEEEEE--- CS
                           MTS  26 tlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvleeveekkfdlivsNPP 106
                                    ++k + +++lD+GcG+G     +a+  +++ ++++d + + l +a + l++ k +v++   +  +   ekk+d++ s   
  gi|13542235|ref|NP_111923.1|  37 DIDKFKPETILDVGCGTGTADFFIANSFSNVIIDCIDPSPYMLSIASKKLSRFKGRVNFALGSSRSIPFEKKYDFVFSSIS 117
                                   455556678******************************************************9999999******99877 PP

                                   STT CS
                           MTS 107 fha 109
                                   fh+
  gi|13542235|ref|NP_111923.1| 118 FHH 120
                                   776 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   2.5e-07   0.00038      16     108 ..      28     121 ..      16     143 .. 0.72

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 2.5e-07
                                   ----HHHHHHCCCS-S-EEEEES-TTSHHHHHHHHTT-EEEEEES-HHHHHHHHHHHHH.TT-T.TEEEEE--GGG----S CS
                          TehB  16 tathsevveavkivkpgkvldlgcgqgrnslylsllgydvtawdknensiafleeikek.enlk.nistalydineaklde 94 
                                    + +s + e ++  kp  +ld+gcg g   ++++    +   +d  + s  +l    +k   +k  ++ al    ++ +++
  gi|13542235|ref|NP_111923.1|  28 RNLYSMITEDIDKFKPETILDVGCGTGTADFFIANSFSN-VIIDCIDPSPYMLSIASKKlSRFKgRVNFALGSSRSIPFEK 107
                                   56678899999******************9999765444.44555555544443222221222213677888889999*** PP

                                   -EEEEEEESSGGGS CS
                          TehB  95 rydfilstvvlmfl 108
                                   +ydf++s++ +   
  gi|13542235|ref|NP_111923.1| 108 KYDFVFSSISFHHW 121
                                   *******9987654 PP

>> DUF938  Protein of unknown function (DUF938)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   3.5e-06    0.0053      26     144 ..      42     148 ..      28     156 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 3.5e-06
                        DUF938  26 te.rvLEiasGtGqHAvffApalpnlkwqpsdqdeelresiaawadelalsnlkpPleldvtaevapvereappapasida 105
                                   +   +L+++ GtG    f+A+ ++n+     d+ +++  sia       ls +k  ++    ++        +p ++++d 
  gi|13542235|ref|NP_111923.1|  42 KPeTILDVGCGTGTADFFIANSFSNVIIDCIDPSPYML-SIASK----KLSRFKGRVNFALGSS----R--SIPFEKKYDF 111
                                   33369********************************7.87754....3444554444433333....2..3577899*** PP

                        DUF938 106 ilsinllHispwsaveglfagagellkkkavlviYGPya 144
                                   ++s+  +H   w++ e  ++++g  +k+++vl iY  y+
  gi|13542235|ref|NP_111923.1| 112 VFSSISFH--HWKCRENGLKTMGLHVKDNGVLAIYEYYR 148
                                   **997777..799999999***************98886 PP

>> Methyltransf_9  Protein of unknown function (DUF1698)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   8.1e-07    0.0012     106     213 ..      33     139 ..      11     146 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 8.1e-07
                                   HHGGGS.--TT-EEEEET-TTSHHHHHHHHCT-SEEE.EE---HHHHHHHHHHHCCTTTTSSEEEE---G.GGS-T---EE CS
                Methyltransf_9 106 rvlphlsdlkgrtildvGcgnGyhlwrmvgegaklvv.GidPselfliqfeavrkllgedqrahllplgi.eqlpeleafd 184
                                    +++ + ++k  tildvGcg+G   + ++   +++++  idPs   l    a +kl+  + r++   lg    +p  + +d
  gi|13542235|ref|NP_111923.1|  33 MITEDIDKFKPETILDVGCGTGTADFFIANSFSNVIIdCIDPSPYMLSI--ASKKLSRFKGRVNF-ALGSsRSIPFEKKYD 110
                                   577889999*****************99999998888469**9977653..66777755555544.4664167899999** PP

                                   EEEEES-GGG-S-HHHHHHHHHCTEEEEE CS
                Methyltransf_9 185 tvfsmGvlyhrrsPldhllqlkdqlvkgG 213
                                    vfs   ++h ++  + l  +  +++ +G
  gi|13542235|ref|NP_111923.1| 111 FVFSSISFHHWKCRENGLKTMGLHVKDNG 139
                                   ***99888887777666666655555555 PP

>> Rsm22  Mitochondrial small ribosomal subunit Rsm22
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0     6e-06    0.0089      20      77 ..      28      84 ..      22     112 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 6e-06
                         Rsm22 20 rrvLdelaervpdflPkslldvgegpgtalwaaselweeleevlvidaseelleiske 77
                                  r+    + e +++f+P+++ldvg g+gta + + + ++++  +  id s  +l+i+++
  gi|13542235|ref|NP_111923.1| 28 RNLYSMITEDIDKFKPETILDVGCGTGTADFFIANSFSNV-IIDCIDPSPYMLSIASK 84
                                  5555678999********************9999999876.47789999999998643 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   4.5e-05     0.067       8      84 ..      25      95 ..      16     139 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.5e-05
               Methyltransf_32  8 rlaelvakllkelakesgaltvvDvGaGkgYLsfvlalkeke.yklkvvgidakeelvekaekraeklgkkfnkrlsf 84
                                  ++++ + ++++e  ++ +++t++DvG+G g   f +a       ++ + +id +  + + a+k  ++++     r++f
  gi|13542235|ref|NP_111923.1| 25 HFLRNLYSMITEDIDKFKPETILDVGCGTGTADFFIAN---SfSNVIIDCIDPSPYMLSIASKKLSRFK----GRVNF 95
                                  455555555655588999***************99999...4478999999988888777766666655....44444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1286.28
//
Query:       gi|13542236|ref|NP_111924.1|  [L=219]
Description: hypothetical protein TVN1405 [Thermoplasma volcanium GSS1]
Scores for complete 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-49  166.4   0.0    7.8e-49  166.2   0.0    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 !  166.2   0.0   4.3e-53   7.8e-49       1     200 [.       4     206 ..       4     207 .. 0.96

  Alignments for each domain:
  == domain 1  score: 166.2 bits;  conditional E-value: 4.3e-53
                                   EEEESSSS-EEEEEE-TT-EEEE-CCGEEEEETTEEEEE...--------------EEEEEEES.SS-EEEEE--SSSEEE CS
                         AIM24   1 fevlgepssllsvtLspgeelyaerGalvamsgkvemet...gllkalkrlltgeslfllkftakissgtvllapklpgti 78 
                                   +e+ g++ ++l+ +Lsp e +y+e+G l++ + +v++ +   gl +a++ ll+g+ +fllk+++   +g+++ a  lpg++
  gi|13542236|ref|NP_111924.1|   4 YEIAGQEVQYLKAKLSPEEYVYIEPGHLIYKDASVRLGAsagGLRGAFSHLLSGSAVFLLKVEG---PGEIVSAGFLPGKV 81 
                                   79**********************************999************************5...5************* PP

                                   EEEEGGTT.EEEEEGGGEEEEETT-EEEEEEEE--.SSGGGTS-EEEEEEESSSEEEEEEECSEEEEEEE.EEEEEEEGGG CS
                         AIM24  79 vtlelgggdwlivqkdafLAatgnveldikfqkgl.kglfggeglflqkltGrGlvalsgyGaiyeielkageelvvdpgh 158
                                   v ++l+ g+++i++ +afLA++++v++++kf  g+ +++fggeg+fl++++G+G+v+l+g+G ++ ++lk+gee++++ +h
  gi|13542236|ref|NP_111924.1|  82 VRIDLN-GNSIIAEFNAFLAMDSTVSYSTKFA-GItQAIFGGEGVFLERFSGNGSVFLHGHGLPIVKDLKPGEEIQAEMSH 160
                                   *****5.559**********************.56699******************************************* PP

                                   EEEEETTEEEEEEEETT---STTTT...S-E.EEEEEEEEEEEEES CS
                         AIM24 159 lvafsgslkfdiervgglkrrligG...egl.flkltGpgtvllqs 200
                                   l+af+++++++ier+gglk++l+ G   egl f++++Gpg+v+l +
  gi|13542236|ref|NP_111924.1| 161 LLAFEDGMEYTIERIGGLKTMLLAGaegEGLfFARIRGPGRVWLHT 206
                                   ***************9999999887777****************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       222  (0.0123822); expected 358.6 (0.02)
Passed bias filter:                      210  (0.0117129); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.22s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 1738.72
//
Query:       gi|13542237|ref|NP_111925.1|  [L=247]
Description: 3-ketoacyl-(acyl-carrier-protein) reductase [Thermoplasma volcanium GSS1]
Scores for complete 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-54  182.9   0.3    8.1e-54  182.6   0.3    1.0  1  adh_short_C2  Enoyl-(Acyl carrier protein) reductase
    3.5e-49  166.9   1.8    4.4e-49  166.6   1.8    1.1  1  adh_short     short chain dehydrogenase
    9.2e-06   25.7   0.1    1.3e-05   25.2   0.1    1.2  1  KR            KR domain
  ------ inclusion threshold ------
       0.15   11.5   0.5       0.39   10.1   0.2    2.0  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 !  182.6   0.3   1.8e-57   8.1e-54       3     233 ..      14     244 ..      10     245 .. 0.93

  Alignments for each domain:
  == domain 1  score: 182.6 bits;  conditional E-value: 1.8e-57
                                   TTSHHHHHHHHHHHTT-EEEEEESSGGH.HHHHHHHHHHTTSEE.EE--TTSHHHHHHHHHHHHHHHSSEEEEEE-----E CS
                  adh_short_C2   3 asgIGraiAkalaeeGaevvltdlneea.kkrveelaeelgaev.lecDVtdeeqvealveevvekfgklDilvnnagiap 81 
                                    +gIGrai  ala++ ++v++   ++ +  +++ +++ee+++ + +++DV+ +e ++++++e++++f+++Dilvnnag   
  gi|13542237|ref|NP_111925.1|  14 GRGIGRAISVALAKNRCKVIINVKKRLEeGQETLRMVEEYSQGIlVKADVSTREGCASIINEARKNFDSIDILVNNAGLGI 94 
                                   59*******************999988878899999999999966************************************ PP

                                   GCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHHHCTSCCEEEEEEEGGGTSBSTTTTHHHHHHHHHHHHHHHHHHHHGGG CS
                  adh_short_C2  82 klkgpfletsreefdraldvnlyslfllakaalplmkeggsivnlssvgaervvpnynaygaaKaalealtrylAvelgpk 162
                                   +   pf++ +++ +++ +d+n+ s++++++++ ++m++gg i+n+ssv++ + +p   +yg++Kaa+++lt+y+A++++++
  gi|13542237|ref|NP_111925.1|  95 A--MPFMNSDDSLIQKLIDTNIMSVIRCSQEIGRVMEDGGTIINVSSVAGLKPMPLLPIYGMTKAAIINLTQYMAYDFAQR 173
                                   *..****************************************************************************** PP

                                   TEEEEEEEE--BHCTGGGGSTTHHHHHH.H.HHHHSTTSS-B-HHHHHHHHHHHCSGGGTT--SEEEEESTTG CS
                  adh_short_C2 163 giRvNavspgpikTlaasgikgfdelle.e.learaplgrlgtpeevaeaalfLasdeasyitGqtlvvDgGl 233
                                   +iRvNav+p+++ T++ +++ + + l+e + +++ +  g++++p+eva+a++fLa  +   itGqtlv+D+G+
  gi|13542237|ref|NP_111925.1| 174 RIRVNAVAPSVVSTKMGNSLVDISGLKEdKfAKEYTLTGKIIDPDEVADAVIFLAKSD--SITGQTLVIDSGW 244
                                   ****************99999977654313156666778899*************855..8**********96 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  166.6   1.8   9.9e-53   4.4e-49       1     190 [.       6     193 ..       6     196 .. 0.97

  Alignments for each domain:
  == domain 1  score: 166.6 bits;  conditional E-value: 9.9e-53
                                   SEEEEESTTSHHHHHHHHHHHHTT-EEEE.EESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSESE CS
                     adh_short   1 kvvlvtGassGIGraiakelakeGakvvv.vdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkldv 80 
                                   kv++vtG ++GIGrai+ +lak+ +kv++ v+++ e+ +e++  ++e  ++ + +++Dv++re +  ++++a+k+++++d+
  gi|13542237|ref|NP_111925.1|   6 KVAVVTGSGRGIGRAISVALAKNRCKVIInVKKRLEEGQETLRMVEEY-SQGILVKADVSTREGCASIINEARKNFDSIDI 85 
                                   89******************************************9996.68899*************************** PP

                                   EEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHHHHHHHHHH CS
                     adh_short  81 LvnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsKaavagltr 161
                                   LvnNAG+    pf + +++ ++++i++N+++v+ +++++ + m    +G+I+nvsSvag++p++ ++ Y+ +Kaa++ lt+
  gi|13542237|ref|NP_111925.1|  86 LVNNAGLGIAMPFMNSDDSLIQKLIDTNIMSVIRCSQEIGRVME--DGGTIINVSSVAGLKPMPLLPIYGMTKAAIINLTQ 164
                                   ******************************************98..99********************************* PP

                                   HHHHHHGGGTEEEEEEEESSBSSHHHHHH CS
                     adh_short 162 slakelaptgirvnavaPGlvdTdmakel 190
                                    +a ++a+++irvnavaP +v+T+m ++l
  gi|13542237|ref|NP_111925.1| 165 YMAYDFAQRRIRVNAVAPSVVSTKMGNSL 193
                                   *************************8875 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.1   2.9e-09   1.3e-05       4     140 ..       9     143 ..       7     171 .. 0.83

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 2.9e-09
                                   EEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHSS---E CS
                            KR   4 litGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaeeppikG 84 
                                   ++tG   g+G++++  la++  + ++ + ++    e+ +++++ +e++   + +v+aDvs ++  +++++e+++++++i  
  gi|13542237|ref|NP_111925.1|   9 VVTGSGRGIGRAISVALAKNRCKVIINVKKR---LEEGQETLRMVEEYSQGI-LVKADVSTREGCASIINEARKNFDSIDI 85 
                                   89******************99999999999...455566888888877776.6788************************ PP

                                   EEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTT..S--SEEEEEEEHHHH CS
                            KR  85 vihaAgvlrdklleemtaedleqvlapKvkGawnLhelled..esldffvlfSSiagl 140
                                    ++ Ag+    ++++ +++ +++++   +  +    + + +  e+   ++ +SS+agl
  gi|13542237|ref|NP_111925.1|  86 LVNNAGLGIAMPFMNSDDSLIQKLIDTNIMSVIRCSQEIGRvmEDGGTIINVSSVAGL 143
                                   *******************999999888777766666665555667777777777776 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.2   8.6e-05      0.39       2      83 ..       9     101 ..       8     185 .. 0.71
   2 ?   -3.8   0.0       1.6     7e+03     216     228 ..     218     230 ..     214     239 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 8.6e-05
                                   EEETTTSHHHHHHHHHHHHCTSE.EEEEES-STTTTCHHCHHC......EEEE--TT-HH.......HHHHHHHHHT-SEE CS
                     Epimerase   2 lVtGatGfiGsalvkallekgye.vigldrlssasntarledl......elveldltdrs.......alerlfkeeqpdav 68 
                                   +VtG    iG+a+  al+++  + +i+++++ +++++ ++  +       lv++d+  r+       + ++ f+   +d+ 
  gi|13542237|ref|NP_111925.1|   9 VVTGSGRGIGRAISVALAKNRCKvIINVKKRLEEGQETLRM-VeeysqgILVKADVSTREgcasiinEARKNFD--SIDIL 86 
                                   89*******************99677777775555544443.24899999999999998844442223333333..67777 PP

                                   EE--S---HHHHHHS CS
                     Epimerase  69 ihlAavggvaassed 83 
                                   ++ A+ g  +  +++
  gi|13542237|ref|NP_111925.1|  87 VNNAGLGIAMPFMNS 101
                                   777775544444444 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 1.6
                                   HHHHHHHHHHHHH CS
                     Epimerase 216 eDvaeaillvleh 228
                                   ++va+a++++++ 
  gi|13542237|ref|NP_111925.1| 218 DEVADAVIFLAKS 230
                                   6788888877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       535  (0.0298399); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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: 1681.64
//
Query:       gi|13542238|ref|NP_111926.1|  [L=399]
Description: major facilitator superfamily permease [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.9e-27   96.1  59.0    9.9e-25   87.2  38.9    2.0  2  MFS_1        Major Facilitator Superfamily
      5e-07   28.9  29.9      8e-06   24.9  29.9    2.2  1  MFS_1_like   MFS_1 like family


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.2  38.9   1.1e-28   9.9e-25       4     352 ..      20     357 ..      17     358 .. 0.86
   2 !   22.7  12.1   4.5e-09     4e-05      83     170 ..     303     390 ..     301     397 .. 0.91

  Alignments for each domain:
  == domain 1  score: 87.2 bits;  conditional E-value: 1.1e-28
                         MFS_1   4 aaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrr.vlllglllfalglllllfa. 82 
                                   ++++s++a+s++++++ + +    +  p  +g+  +l +l  ++++l+++++ d+  r++ + +++ l+ ++  ++++++ 
  gi|13542238|ref|NP_111926.1|  20 SVWFSHTAFSAYNLIVIW-VVLFITKKPLLAGFSDSLLTLPLMISVLVGAYV-DKSKRKKtLAFISSLFRVVL-VIIIMIs 97 
                                   667788888888888884.444444579999999999999888888887777.**999996666666666666.5555433 PP

                         MFS_1  83 sslwl.......llvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyi 156
                                   +++w+       ++++ +l G+++ ++ ++ a+++ +   +++  ++ + +s+ + ++  +g +++g+l+ +lg++a+f+i
  gi|13542238|ref|NP_111926.1|  98 IQFWPsidviitIYAATFLIGFTSDVVDSVRATWTKAFLGDKHYKKGSSEMSSVIMASQGVGFIISGILI-ALGFEASFLI 177
                                   444423455555**********************************************************.99******** PP

                         MFS_1 157 laivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlw.illialllfffgfsglltllplylqe 236
                                   ++++++l+ v    l++ ++++ ++++++         ++++a+++l+kd+ l  i+ i ++++f +  ++  ++ l +qe
  gi|13542238|ref|NP_111926.1| 178 IGLFFALSSV---PLIMIKYTAYGTSKSIHT-------GVAEALTLLRKDKRLAeIIAINFVSNFSIGVAAILYISL-MQE 247
                                   **********...888888888888887555.......66667889*****99899*********99999*******.6** PP

                         MFS_1 237 vlglsglllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavtssavllllvlvliGfglgfv 317
                                    + l+ +++++l+++++ l+++++++ a+++s ++gr + l++++l++++++++l+          l+l+++l+G+  g+ 
  gi|13542238|ref|NP_111926.1| 248 GYRLP-AMYVSLIFGVIVLGMVFGSISASKISGKVGRINLLVFIVLGVSFVSISLIHSVYV-----LVLPSFLAGLSIGIE 322
                                   *****.8******************************888888888888888888888888.....7779*********** PP

                         MFS_1 318 fpsllalasdlappeeagtasglfntagslggalg 352
                                   ++ l +l ++ +p e++++++g +nt+g +++al+
  gi|13542238|ref|NP_111926.1| 323 SSVLSTLSMRIVPHEMMARIQGSMNTFGMAASALS 357
                                   ******************************99986 PP

  == domain 2  score: 22.7 bits;  conditional E-value: 4.5e-09
                         MFS_1  83 sslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsll 163
                                   +s+++l++  +l+Gl  g+  ++  +l  +++p+e  +r  g ++++  ++++l  l+ggll++++g +++f++++++ + 
  gi|13542238|ref|NP_111926.1| 303 HSVYVLVLPSFLAGLSIGIESSVLSTLSMRIVPHEMMARIQGSMNTFGMAASALSSLIGGLLYQLFGPSYSFLMVGLIIIS 383
                                   77889***************************************************************************9 PP

                         MFS_1 164 a.fvlfll 170
                                   a fv+ l+
  gi|13542238|ref|NP_111926.1| 384 AdFVF-LA 390
                                   96552.22 PP

>> MFS_1_like  MFS_1 like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9  29.9     9e-10     8e-06      50     384 ..      62     375 ..      28     376 .. 0.75

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 9e-10
                    MFS_1_like  50 sppiwgvlaDrfgkrkkvvilslllsavlflsllfippskerqeesklevsvaqdvdaektfwilfllvvlasfflaailv 130
                                    + ++g+ +D+++++k+++ +s+l+ +vl+++++ i+            +++   +d   t+ +  +l+ + s +  ++ +
  gi|13542238|ref|NP_111926.1|  62 ISVLVGAYVDKSKRKKTLAFISSLFRVVLVIIIM-IS------------IQFWPSIDVIITIYAATFLIGFTSDVVDSVRA 129
                                   4567788899999999999999999999999665.55............55555555444444444444444444444444 PP

                    MFS_1_like 131 lldaatlkelgedrkdyGrqrlfGsvGyaifafitGilidhysvnllpysallyvlaallvisllvvlilnetekesklkv 211
                                       a l +   ++ + G     +sv  ++++  +G++i  + ++ l+++a ++++ +++ +s++ +++++ t ++++  +
  gi|13542238|ref|NP_111926.1| 130 TWTKAFLGD---KHYKKGSSE-MSSV--IMASQGVGFIISGILIA-LGFEASFLIIGLFFALSSVPLIMIKYTAYGTSKSI 203
                                   444433332...222222222.3444..45677788888888885.47788999999999999999999999999998887 PP

                    MFS_1_like 212 tksl.qvllnilknpeviifllvalilgmswgiienFlflYLkelgasntllGslvalgv..vaeiplfffaeklleklGh 289
                                    +   ++l+ + k+++++ ++++ ++  +s g++   +   + + g+    + + +++gv  ++ +   + a+k+  k+G 
  gi|13542238|ref|NP_111926.1| 204 HTGVaEALTLLRKDKRLAEIIAINFVSNFSIGVAAILYISLM-QEGYRLPAMYVSLIFGVivLGMVFGSISASKISGKVGR 283
                                   655515566666778888899999999999999876554444.66665555555555555005555556899********* PP

                    MFS_1_like 290 vklliiallayilrfllyaiienawlvlpievLhgisfgllwaaaveyvskiapksleatgqgllsglyfglGralGsliG 370
                                   ++ll+  +++  + f+ +++i+++ ++++  +L g+s+g+  +++ + + +i+p+++ a++qg ++++ +   +al sliG
  gi|13542238|ref|NP_111926.1| 284 INLLV--FIVLGVSFVSISLIHSVYVLVLPSFLAGLSIGIESSVLSTLSMRIVPHEMMARIQGSMNTFGMA-ASALSSLIG 361
                                   ***98..78999***************************************************88887665.57999**** PP

                    MFS_1_like 371 GllwdlksaiflFr 384
                                   Gll++l+++ + F 
  gi|13542238|ref|NP_111926.1| 362 GLLYQLFGPSYSFL 375
                                   *********99996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (399 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1123  (0.062636); 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:                         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: 0.67u 0.31s 00:00:00.98 Elapsed: 00:00:00.49
# Mc/sec: 2442.23
//
Query:       gi|13542239|ref|NP_111927.1|  [L=215]
Description: transcription regulator [Thermoplasma volcanium GSS1]
Scores for complete 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-06   26.9   0.6    5.5e-05   23.0   0.2    2.4  2  MarR            MarR family
    2.4e-05   24.3   0.0    3.8e-05   23.6   0.0    1.3  1  HTH_20          Helix-turn-helix domain
    4.5e-05   22.9   0.1    0.00028   20.4   0.0    2.1  2  HTH_24          Winged helix-turn-helix DNA-binding
    0.00089   19.1   0.2     0.0035   17.2   0.0    2.1  3  HTH_5           Bacterial regulatory protein, arsR family
      0.001   18.9   0.1     0.0021   17.9   0.1    1.5  1  TrmB            Sugar-specific transcriptional regulator TrmB
      0.003   17.4   0.0     0.0048   16.7   0.0    1.3  1  MarR_2          MarR family
     0.0044   17.0   0.5     0.0093   15.9   0.1    1.8  2  HTH_Crp_2       Crp-like helix-turn-helix domain
  ------ inclusion threshold ------
      0.014   16.0   0.3      0.041   14.5   0.2    1.7  2  RTP             Replication terminator protein
      0.021   15.0   0.1      0.053   13.7   0.1    1.7  1  HTH_34          Winged helix DNA-binding domain
      0.023   14.6   0.0      0.058   13.4   0.0    1.6  1  PadR            Transcriptional regulator PadR-like family
      0.052   13.9   0.2       0.55   10.6   0.0    2.5  3  Linker_histone  linker histone H1 and H5 family
      0.076   12.9   1.1       0.27   11.1   0.5    2.1  2  TFIIE_alpha     TFIIE alpha subunit
      0.097   12.7   1.7       0.23   11.5   0.1    2.4  4  HTH_54          ParA helix turn helix domain
       0.15   11.9   0.0        0.3   10.9   0.0    1.5  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 !   23.0   0.2   4.3e-08   5.5e-05       2      48 ..      18      64 ..      17      72 .. 0.91
   2 ?    1.5   0.0      0.22   2.8e+02      41      53 ..     195     207 ..     194     208 .. 0.86

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 4.3e-08
                                  -HHHHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          MarR  2 tltqfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlie 48
                                  + t+++++++++ +gp++v++L k +++++s++  ++++++ +G + 
  gi|13542239|ref|NP_111927.1| 18 SKTRLMVITLIAVNGPMTVTQLSKVIKTTRSNLYQAIKEMVSDGILV 64
                                  67999*************************************99875 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.22
                                   HHHTTSEEEEEET CS
                          MarR  41 LekkGlieRsksp 53 
                                   L + G+i++s+++
  gi|13542239|ref|NP_111927.1| 195 LNQMGFISKSRHE 207
                                   6799*******97 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0     3e-08   3.8e-05       9      58 ..      18      67 ..      17      71 .. 0.92

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 3e-08
                                  -HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEEC CS
                        HTH_20  9 hPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvr 58
                                  +++R+++  ++a ++++t+++l + + +++++l++ ++++++ g++ ++r
  gi|13542239|ref|NP_111927.1| 18 SKTRLMVITLIAVNGPMTVTQLSKVIKTTRSNLYQAIKEMVSDGILVQTR 67
                                  579*****************************************977766 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   2.2e-07   0.00028       2      47 ..      18      63 ..      17      64 .. 0.95
   2 ?   -0.1   0.0      0.55     7e+02       8      21 ..     120     133 ..     116     134 .. 0.64

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 2.2e-07
                        HTH_24  2 detdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                  ++t++ ++ l+  n+ ++ ++L++ +  ++s++ + +k+++++G++
  gi|13542239|ref|NP_111927.1| 18 SKTRLMVITLIAVNGPMTVTQLSKVIKTTRSNLYQAIKEMVSDGIL 63
                                  589999**************************************96 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.55
                        HTH_24   8 ILelLqknprisqr 21 
                                   IL+++ ++ ++s++
  gi|13542239|ref|NP_111927.1| 120 ILSIMAEQVNLSNK 133
                                   66666666666665 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   2.7e-06    0.0035       2      43 ..      19      61 ..      18      63 .. 0.87
   2 ?   -3.0   0.0       5.4     7e+03       6      13 ..     119     126 ..     108     130 .. 0.66
   3 ?   -2.3   0.0       3.3   4.3e+03      38      47 .]     194     203 ..     194     203 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.7e-06
                                  HHHHHHHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTT CS
                         HTH_5  2 ptRlkILklLae.gelcvcelaeelglsqstvShHLkkLreaG 43
                                  +tRl ++ l a  g+++v++l++ ++ ++s++ +  k +   G
  gi|13542239|ref|NP_111927.1| 19 KTRLMVITLIAVnGPMTVTQLSKVIKTTRSNLYQAIKEMVSDG 61
                                  89*********99******************998766666555 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 5.4
                                   HHHHHHTT CS
                         HTH_5   6 kILklLae 13 
                                    IL+++ae
  gi|13542239|ref|NP_111927.1| 119 AILSIMAE 126
                                   46666665 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 3.3
                                   HHHHTTSEEE CS
                         HTH_5  38 kLreaGLVek 47 
                                   +L ++G+++k
  gi|13542239|ref|NP_111927.1| 194 ILNQMGFISK 203
                                   6999***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 !   17.9   0.1   1.6e-06    0.0021       5      60 ..      16      72 ..      12      81 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.6e-06
                                  HHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCT.SEEEESSTTT CS
                          TrmB  5 GLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkG.lVerekgrpk 60
                                  G+s++   v + +  +gp+t++++++ ++  rs+ Y++++++++ G lV+++  + k
  gi|13542239|ref|NP_111927.1| 16 GFSKTRLMVITLIAVNGPMTVTQLSKVIKTTRSNLYQAIKEMVSDGiLVQTRTVSEK 72
                                  666666666666779*******************************55666666544 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   3.8e-06    0.0048       2      54 ..      16      66 ..      15      72 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 3.8e-06
                                  T--HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                        MarR_2  2 gltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                  g++ + ++v+  ++ +++  +tv++l +  + ++s++ +++k++v+ G ++++
  gi|13542239|ref|NP_111927.1| 16 GFSKTRLMVITLIAVNGP--MTVTQLSKVIKTTRSNLYQAIKEMVSDGILVQT 66
                                  777889999999*****9..****************************87655 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 !   15.9   0.1   7.3e-06    0.0093      19      54 ..      31      67 ..       8      74 .. 0.83
   2 ?   -2.4   0.1       3.9     5e+03      56      68 .]      96     109 ..      88     109 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 7.3e-06
                                  EEEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE.ET CS
                     HTH_Crp_2 19 elpltqeelAsmlGltretvsrilseLkreglis.rg 54
                                  + p+t ++l+  + +tr+ + ++++e+  +g++  ++
  gi|13542239|ref|NP_111927.1| 31 NGPMTVTQLSKVIKTTRSNLYQAIKEMVSDGILVqTR 67
                                  459*****************************99444 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 3.9
                                   E.EEES-HHHHHHH CS
                     HTH_Crp_2  56 r.irildleaLral 68 
                                   + i+  d ++Lr++
  gi|13542239|ref|NP_111927.1|  96 KaIEEMDEDKLRNI 109
                                   34888899999986 PP

>> RTP  Replication terminator protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.2   3.2e-05     0.041      44      83 ..      46      83 ..      37     110 .. 0.76
   2 ?   -1.3   0.0       2.6   3.3e+03      70      95 ..     103     127 ..      80     148 .. 0.49

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.2e-05
                                  -HHHHHHHHHHHHHTTSEEEEEEEBTSSSSSEEEEEEESS CS
                           RTP 44 nhseiyralhelvedgilkrrkelkekaklqevviYsltd 83
                                  ++s++y+a++e+v dgil +++++ ek+ ++   +Y+++ 
  gi|13542239|ref|NP_111927.1| 46 TRSNLYQAIKEMVSDGILVQTRTVSEKNYVE--KFYDINT 83
                                  689*******************999554433..3556555 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.6
                                   SSSSSEEEEEEESS..HHHHHHHHHH CS
                           RTP  70 kaklqevviYsltdeGkekaklykkq 95 
                                   + kl+++ +Ys+  + +  + ++  q
  gi|13542239|ref|NP_111927.1| 103 EDKLRNI-LYSFLRSASAILSIMAEQ 127
                                   3333333.344433333333344333 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 ?   13.7   0.1   4.1e-05     0.053       2      53 ..      21      72 ..      20      78 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.1e-05
                        HTH_34  2 RlavlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYievdkefkgk 53
                                  Rl v+++ a++  ++ ++l++ +++t +nL+  +k + + g ++ + ++++k
  gi|13542239|ref|NP_111927.1| 21 RLMVITLIAVNGPMTVTQLSKVIKTTRSNLYQAIKEMVSDGILVQTRTVSEK 72
                                  99*********************************99988877777666665 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   4.5e-05     0.058      26      66 ..      42      82 ..      26      84 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.5e-05
                                  -CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEES CS
                          PadR 26 llelseGslYpaLkrLekeglveseweesgegpprkyYrlT 66
                                  +++   ++lY+a k++  +g+++++++ s+++   k+Y ++
  gi|13542239|ref|NP_111927.1| 42 VIKTTRSNLYQAIKEMVSDGILVQTRTVSEKNYVEKFYDIN 82
                                  56777899*********************99*******997 PP

>> Linker_histone  linker histone H1 and H5 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00043      0.55      40      63 ..      44      67 ..      28      74 .. 0.84
   2 ?   -0.8   0.0       1.6     2e+03      28      43 ..      73      87 ..      67     106 .. 0.48
   3 ?   -0.3   0.0       1.1   1.5e+03       8      37 ..      94     131 ..      93     147 .. 0.58

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00043
                Linker_histone 40 skfksllkkalkkgvekgelvqpk 63
                                  +  +s l +a+k +v++g+lvq++
  gi|13542239|ref|NP_111927.1| 44 KTTRSNLYQAIKEMVSDGILVQTR 67
                                  445899****************97 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.6
                Linker_histone 28 kyikakykvvdvskfk 43
                                  +y+++ y + +++ f+
  gi|13542239|ref|NP_111927.1| 73 NYVEKFYDI-NTDLFD 87
                                  555555555.222222 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 1.1
                Linker_histone   8 ikeAIkalkerkG........sSrqaIkkyikakykvv 37 
                                   i +AI++++e k          S  aI   ++++ +++
  gi|13542239|ref|NP_111927.1|  94 IRKAIEEMDEDKLrnilysflRSASAILSIMAEQVNLS 131
                                   55677777774433334444456666666666666655 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.5   0.00021      0.27      11      87 ..      17      91 ..      10     108 .. 0.78
   2 ?    0.3   0.1      0.48   6.2e+02      39      50 ..     101     112 ..      90     145 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00021
                                  S-HHHHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEEETTTEEEEEEEEEECCCHCCCHHH CS
                   TFIIE_alpha 11 ygeeavlvldvLlekgevteedlakelkidlnelrklLnrLyearlvkykrrrdeekswykyywrinyeklvdvvkr 87
                                  + +    v+  ++ +g +t  +l+k +k  + +l +++ ++ ++++    r + e k+  + ++ in + l d++k+
  gi|13542239|ref|NP_111927.1| 17 FSKTRLMVITLIAVNGPMTVTQLSKVIKTTRSNLYQAIKEMVSDGILVQTRTVSE-KNYVEKFYDINTD-LFDAIKY 91
                                  55677889*************************************9888887765.5666667788865.6777776 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.48
                                   S-HHHHHHHHHH CS
                   TFIIE_alpha  39 idlnelrklLnr 50 
                                   +d  +lr++L+ 
  gi|13542239|ref|NP_111927.1| 101 MDEDKLRNILYS 112
                                   566666666664 PP

>> HTH_54  ParA helix turn helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00018      0.23      28      69 ..      34      74 ..      32      97 .. 0.84
   2 ?   -1.1   0.1       1.6     2e+03      41      53 ..      91     103 ..      68     107 .. 0.72
   3 ?   -2.1   0.0       3.2   4.2e+03       5      20 ..     121     137 ..     117     169 .. 0.54
   4 ?   -2.9   0.0       5.8   7.4e+03       3      19 ..     165     181 ..     163     187 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00018
                        HTH_54 28 yskaalaklpklsrrkvdkavsemeaeGyefekkeagstekY 69
                                  ++ ++l+k+ k +r ++ +a++em ++G+  + + + s ++Y
  gi|13542239|ref|NP_111927.1| 34 MTVTQLSKVIKTTRSNLYQAIKEMVSDGILVQTR-TVSEKNY 74
                                  6677899*********************999887.5566666 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.6
                        HTH_54  41 rrkvdkavsemea 53 
                                      + ka++em++
  gi|13542239|ref|NP_111927.1|  91 YGDIRKAIEEMDE 103
                                   5567889999987 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 3.2
                        HTH_54   5 Lqelteqiqk.qkkElk 20 
                                   L+ ++eq++  +k++l+
  gi|13542239|ref|NP_111927.1| 121 LSIMAEQVNLsNKDDLD 137
                                   55555555531233332 PP

  == domain 4  score: -2.9 bits;  conditional E-value: 5.8
                        HTH_54   3 kmLqelteqiqkqkkEl 19 
                                   +mL++   +i+++ +E 
  gi|13542239|ref|NP_111927.1| 165 SMLSNFFTEIDDDNDEK 181
                                   68899999999988875 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 ?   10.9   0.0   0.00023       0.3      16      51 ..      31      66 ..      22      67 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00023
                                  BSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE.. CS
                      HTH_IclR 16 pqeltlselArrtglpkStvhRlLqtLvelGyveqd 51
                                  ++++t+++l++ +  ++S+ +  ++ +v  G++ q 
  gi|13542239|ref|NP_111927.1| 31 NGPMTVTQLSKVIKTTRSNLYQAIKEMVSDGILVQT 66
                                  467*****************************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1037  (0.0578393); expected 358.6 (0.02)
Passed bias filter:                      568  (0.0316805); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.60u 0.39s 00:00:00.99 Elapsed: 00:00:00.56
# Mc/sec: 1162.00
//
Query:       gi|13542240|ref|NP_111928.1|  [L=78]
Description: IS5 inactivated transposase, partial [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    0.00042   20.0   0.2    0.00047   19.9   0.2    1.0  1  DDE_Tnp_1  Transposase DDE domain
  ------ inclusion threshold ------
       0.04   13.6   0.1      0.072   12.8   0.1    1.4  1  OB_RNB     Ribonuclease B OB domain
      0.059   13.0   0.3      0.078   12.6   0.3    1.3  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 !   19.9   0.2   7.9e-08   0.00047     125     214 .]       1      65 [.       1      65 [. 0.97

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 7.9e-08
                     DDE_Tnp_1 125 lrkhdrnkiltksqkrrnkskkekgdvyyvtntnsellsaeevaelyrlRwqiErvFkwlkrkfgldrlryrglnrveaql 205
                                   + k+ rn+ lt +q+rrn+                         +++r+ +  Er  + +kr f++d++ +   +rv+ + 
  gi|13542240|ref|NP_111928.1|   1 MDKASRNHKLTAKQIRRNR-------------------------RISRKCSPGERPYSVMKRIFHGDHVFVTMVRRVRVKS 56 
                                   56899**************.........................************************************* PP

                     DDE_Tnp_1 206 lllllalnl 214
                                   ++++l +nl
  gi|13542240|ref|NP_111928.1|  57 MFMCLGYNL 65 
                                   *******98 PP

>> OB_RNB  Ribonuclease B OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   1.2e-05     0.072      28      44 ..      34      50 ..      31      56 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.2e-05
                                  HHTTS-TT-EEEEEEEE CS
                        OB_RNB 28 qmkkamhGDrVlvritk 44
                                   mk+++hGD V+v++  
  gi|13542240|ref|NP_111928.1| 34 VMKRIFHGDHVFVTMVR 50
                                  69***********9976 PP

>> DDE_Tnp_4  DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.3   1.3e-05     0.078      97     132 ..       5      40 ..       1      61 [. 0.89

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.3e-05
                     DDE_Tnp_4  97 kkkkqlseeevefnraiasarihvErvigrlkgrfr 132
                                    ++++l++++ ++nr+i++ +   Er    +k+ f+
  gi|13542240|ref|NP_111928.1|   5 SRNHKLTAKQIRRNRRISRKCSPGERPYSVMKRIFH 40 
                                   6799****************************8886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); 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 0.33s 00:00:00.83 Elapsed: 00:00:00.52
# Mc/sec: 450.44
//
Query:       gi|13542241|ref|NP_111929.1|  [L=215]
Description: IS5 inactivated transposase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.3e-12   45.9   0.1    6.7e-12   45.3   0.1    1.3  1  DUF772     Transposase domain (DUF772)
  ------ inclusion threshold ------
      0.031   13.9   2.9       0.13   11.9   2.9    2.0  2  DDE_Tnp_1  Transposase DDE domain


Domain annotation for each model (and alignments):
>> DUF772  Transposase domain (DUF772)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.3   0.1   7.4e-16   6.7e-12      10      66 ..       1      56 [.       1      64 [. 0.91

  Alignments for each domain:
  == domain 1  score: 45.3 bits;  conditional E-value: 7.4e-16
                        DUF772 10 mlkllllqylyglSdreleealrenlsfrwflgldleedpvpdhstlsrfRkrlee..l 66
                                  m+k+l+lq +y+l d+++e++ ++++sf+ fl +    d+vpd + ++ fR+rl     
  gi|13542241|ref|NP_111929.1|  1 MVKVLFLQSVYNLVDEAMEREMHYRVSFMNFLNYP---DSVPDSRAIWLFRERLSStgK 56
                                  9********************************85...99**************87752 PP

>> 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   0.7     0.039   3.5e+02     120     138 ..     108     126 ..      32     148 .. 0.64
   2 ?   11.9   2.9   1.4e-05      0.13      20      63 ..     133     191 ..      69     192 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.039
                     DDE_Tnp_1 120 krrgrlrkhdrnkiltksq 138
                                   k++++++k++++++ ++ +
  gi|13542241|ref|NP_111929.1| 108 KKDKTMTKDGKRQAKREAK 126
                                   3333333333333333333 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 1.4e-05
                     DDE_Tnp_1  20 k...............edarwgykggkykygyklhiavdtrsglilsvvitpgnvhdsk 63 
                                   k               +d+ w +kg+++++g klh++  t   li+ +v+t++ +hdsk
  gi|13542241|ref|NP_111929.1| 133 KrirrderrnaktrrfKDGTWAKKGKRSHFGNKLHTVQGTDIPLIMEFVLTTAFSHDSK 191
                                   24445555566666778999*9***********************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       906  (0.0505327); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.30s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1393.43
//
Query:       gi|13542242|ref|NP_111930.1|  [L=277]
Description: hypothetical protein TVN1411 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.4e-15   55.4   0.0    7.9e-15   54.9   0.0    1.3  1  DDE_3     DDE superfamily endonuclease
    1.8e-11   44.5   0.0    2.7e-11   43.9   0.0    1.3  1  HTH_32    Homeodomain-like domain
    7.1e-06   25.9   0.0    2.2e-05   24.4   0.0    1.8  2  HTH_29    Winged helix-turn helix
  ------ inclusion threshold ------
      0.029   14.5   0.0       0.18   11.9   0.0    2.1  2  HTH_28    Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> DDE_3  DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.9   0.0   1.8e-18   7.9e-15       5     116 ..     161     276 ..     157     277 .] 0.84

  Alignments for each domain:
  == domain 1  score: 54.9 bits;  conditional E-value: 1.8e-18
                         DDE_3   5 iDE.sgfqlgt.vrrrawakkGkr....erleeygrrgrvnligaldekgglafvtfeetlnaedfaeflerlletalqak 79 
                                    DE  g+q++  +  +   +++k+    +r   y+r+g+++l++ +d  +g +++ +e++ ++ +f+++l+ + + +++  
  gi|13542242|ref|NP_111930.1| 161 YDEkPGIQATGnIYNDK--PPDKNhsniARNHDYIRHGTLSLLAGIDLVTGHIIYSIEDKHKSIEFIKCLDNVDKYYPDDY 239
                                   56644444444433333..34444336566999**********************************************99 PP

                         DDE_3  80 kivlilDnasiHkseslrelveeeadrlellylPpyS 116
                                   ki +ilDn siHks++ +e+++++  r++++++P ++
  gi|13542242|ref|NP_111930.1| 240 KIKIILDNNSIHKSKETQEYLNKKPGRFKFVFTPVHA 276
                                   **********************************886 PP

>> HTH_32  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.9   0.0   6.1e-15   2.7e-11       2      73 .]      22     107 ..      21     107 .. 0.89

  Alignments for each domain:
  == domain 1  score: 43.9 bits;  conditional E-value: 6.1e-15
                        HTH_32   2 vsrwlkRyneeGle.gLkdrprrgrprklsdevrariiallreep........rWsprqlaarl....aeregvk.....v 64 
                                   ++r++++   +G++ +L dr+r+g+pr +sde ra+ii++++++p         W+ r+l +++         ++     +
  gi|13542242|ref|NP_111930.1|  22 IYRTVNKALLSGIDaALNDRQRPGKPRMISDEARAYIIKTACTKPielglsyeLWTNRLLTRYIrenaP----EEynisgI 98 
                                   89*****99*******************************************************54332....44445589 PP

                        HTH_32  65 ShstvyriL 73 
                                   S  tv +iL
  gi|13542242|ref|NP_111930.1|  99 SNGTVSKIL 107
                                   999999887 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.0     5e-09   2.2e-05      18      63 .]      11      56 ..       5      56 .. 0.92
   2 ?   -3.3   0.0       2.2   9.9e+03      23      35 ..      97     109 ..      95     111 .. 0.77

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 5e-09
                        HTH_29 18 iAkllglsrrtvyrwlkrfeegGlaalld.rrrsgrprnrlseeqea 63
                                  iAk +++ + ++yr+++     G++a+l+ r r+g pr  +s+e +a
  gi|13542242|ref|NP_111930.1| 11 IAKSMNVYEAKIYRTVNKALLSGIDAALNdRQRPGKPRM-ISDEARA 56
                                  9************************************96.9999886 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2.2
                        HTH_29  23 glsrrtvyrwlkr 35 
                                   g+s  tv ++lk 
  gi|13542242|ref|NP_111930.1|  97 GISNGTVSKILKK 109
                                   7888899988886 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   4.1e-05      0.18      13      51 ..       6      45 ..       2      48 .. 0.84
   2 ?   -0.3   0.0      0.28   1.2e+03      23      35 ..      97     109 ..      94     111 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.1e-05
                        HTH_28 13 hsvreaArelgisrrtvyrWikryeegGi.agLvprrrrp 51
                                  +s++ +A+ +++++  +yr +++    Gi a+L++r r +
  gi|13542242|ref|NP_111930.1|  6 KSINYIAKSMNVYEAKIYRTVNKALLSGIdAALNDRQRPG 45
                                  58999***********************846****76533 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.28
                        HTH_28  23 gisrrtvyrWikr 35 
                                   gis  tv++ +k+
  gi|13542242|ref|NP_111930.1|  97 GISNGTVSKILKK 109
                                   9*******99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       615  (0.034302); 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:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.44
# Mc/sec: 1873.99
//
Query:       gi|13542243|ref|NP_111931.1|  [L=96]
Description: hypothetical protein TVN1412 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.025   14.3   0.0      0.028   14.1   0.0    1.2  1  DUF5552   Family of unknown function (DUF5552)
      0.054   13.5   0.0      0.061   13.4   0.0    1.2  1  Longin    Regulated-SNARE-like domain


Domain annotation for each model (and alignments):
>> DUF5552  Family of unknown function (DUF5552)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   3.2e-06     0.028      11      60 ..       6      53 ..       3      84 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.2e-06
                       DUF5552 11 erepklsilqmdrgdpqhsshwcperekvklltlkpretsknilinfyra 60
                                  e e +l++    rgdpq   h +    k+  ltlk re+ + i  +f  +
  gi|13542243|ref|NP_111931.1|  6 ETEMHLNLTSTRRGDPQNFRHNVN--AKISRLTLKDREAERWICFQFLES 53
                                  67889999999*********9875..799************999988654 PP

>> Longin  Regulated-SNARE-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   6.8e-06     0.061      29      77 ..      28      77 ..       4      82 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.8e-06
                        Longin 29 aedgltylviadesyprrlaFafLeeikreFlakygta..ktadaadlrpy 77
                                  + ++++ l++ d+++ r + F+fLe + + F + yg +   +  ++ l py
  gi|13542243|ref|NP_111931.1| 28 VNAKISRLTLKDREAERWICFQFLESLFDGFSR-YGDRfvMAVKQSMLNPY 77
                                  45688999***********************54.77544433344455555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.49
# Mc/sec: 589.74
//
Query:       gi|13542244|ref|NP_111932.1|  [L=316]
Description: adenine-specific DNA methylase [Thermoplasma volcanium GSS1]
Scores for complete sequence (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  110.3   1.8    3.5e-21   76.0   0.0    2.1  2  N6_N4_Mtase      DNA methylase
    2.1e-05   24.3   0.0    3.8e-05   23.5   0.0    1.5  1  MethyltransfD12  D12 class N6 adenine-specific DNA methyltran
    4.8e-05   23.1   0.0     0.0018   18.0   0.0    2.3  1  UPF0020          Putative RNA methylase family UPF0020
     0.0002   21.0   0.0    0.00035   20.3   0.0    1.4  1  Cons_hypoth95    Conserved hypothetical protein 95
     0.0013   19.4   0.0     0.0041   17.8   0.0    1.8  1  Methyltransf_25  Methyltransferase domain
     0.0021   17.4   0.1      0.029   13.6   0.0    2.2  2  N6_Mtase         N-6 DNA Methylase
     0.0031   17.3   0.0     0.0083   15.9   0.0    1.8  2  Methyltransf_31  Methyltransferase domain
  ------ inclusion threshold ------
       0.02   15.5   0.0      0.058   14.1   0.0    2.0  1  Methyltransf_11  Methyltransferase domain
      0.023   14.3   0.1       0.19   11.3   0.0    2.1  2  Methyltransf_15  RNA cap guanine-N2 methyltransferase


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 !   76.0   0.0   1.7e-24   3.5e-21     101     229 ..      19     139 ..       6     141 .. 0.66
   2 !   33.8   0.4   1.4e-11   2.8e-08       1     111 [.     173     316 .]     173     316 .] 0.83

  Alignments for each domain:
  == domain 1  score: 76.0 bits;  conditional E-value: 1.7e-24
                                   -EEEEEEEESSTT-..---GGGSSBSS-HHHHHHHHHH............CHHHCC-B--BSEEE-SCCCTTSTTS-CHH- CS
                   N6_N4_Mtase 101 thEyilvfsknkkyllkfnldaikvpyeekdklekrga............ytskkkgkkiediWdlseiqsnekkskgdtk 169
                                   ++               + l  +k++ +e++ l+ +               t k++ k    +W  ++++ ++  ++   k
  gi|13542244|ref|NP_111932.1|  19 RT---------------LPLAIMKENAKEYQPLKINTIktcsckennlncLTAKEWIKRQIGVW--EFYYEKRDIRD---K 79 
                                   33...............44445555555555555555433333333322223344444444457..33333333332...7 PP

                                   ---SS---HHHHHHHHHHHS-TT-EEEETT-TTTHHHHHHHHTT-EEEEEESSHHHHHHH CS
                   N6_N4_Mtase 170 kkHpaqkPvallerlIklstkkgdivlDpFaGSGtTavaakelgrkfiGieieeeyvela 229
                                     Hpa++P  l++ +I+l++++g++v+DpF GSGtT+vaa+  +r+++G++ +e+y++l 
  gi|13542244|ref|NP_111932.1|  80 TVHPATFPISLAKQVIELFSHEGELVVDPFVGSGTTLVAARDSNRNAVGFDLQEKYIKLC 139
                                   89*******************************************************975 PP

  == domain 2  score: 33.8 bits;  conditional E-value: 1.4e-11
                                   EEEEEE--SSSSSCS..........................GCCGCCH.........HHHHHHHHHHHHHHHHHHEEEEEE CS
                   N6_N4_Mtase   1 vdlivtdpPYntgkdy.....................endeqyeeeds.........yeeyleflekvlkevrrvLkddgs 51 
                                   + li+t+pPY +  +                      +         +         +e y + +  ++++v++ L + g 
  gi|13542244|ref|NP_111932.1| 173 ISLIFTSPPYANLLNRerknksrrnrknnqlgkveqyS---------QdprdlgtldVESYTKEMGDIFEKVKPALRTKGH 244
                                   689*******9988876777777777766555443333.........0455566666************************ PP

                                   EEEEE-CCCHHT....HHHHHHHHHTT.-EEEEEEEEEEES.......SSTTTSTCCS-B--EEEEEEEESS CS
                   N6_N4_Mtase  52 ifiniddseikk....elkaladeifg.gffllnvivwkkp.......nsmpesnkdrltsthEyilvfskn 111
                                    +in+ d+  ++     ++ l++e  + g+ l+n i+w+k           + sn   +  t+Ey+l f+k+
  gi|13542244|ref|NP_111932.1| 245 CVINVPDMWWENkriaIHVYLINEMTKrGYELRNIIIWDKRnlvnqigIFGWPSNYITMGVTFEYLLDFWKP 316
                                   ********9988889989999********************9998885477777878999*******99996 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 !   23.5   0.0   1.9e-08   3.8e-05       7      94 ..      89     189 ..      88     217 .. 0.81

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 1.9e-08
                                   TTHHHHHCCS-..--SEEEETT-TTSCCHHCS...SSCEEEEES-HHHHHHHHHHCCHSHHHHHHHHH.TCTTGGC.TSHH CS
               MethyltransfD12   7 kllpeIkelipkdkgktfvepFaGggaVffeakkqgkkvlinDinedlinlykaliknnveelikelekllekeelenere 87 
                                   +l+++  el+++  g+ +v+pF+G+g   ++a+  + +++  D++e+ i l    +   +++++ ++++   +e+  n + 
  gi|13542244|ref|NP_111932.1|  89 SLAKQVIELFSH-EGELVVDPFVGSGTTLVAARDSNRNAVGFDLQEKYIKLCAERLS--TQRIVGNAQQVAIEEDARNISN 166
                                   58899999***8.999**********************************9996655..7********9999999988888 PP

                                   HHHHHH................H CS
               MethyltransfD12  88 yfyelr................e 94 
                                   yf e                  e
  gi|13542244|ref|NP_111932.1| 167 YFNEESisliftsppyanllnrE 189
                                   88776677777777777444432 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   8.8e-07    0.0018       8     142 ..      82     193 ..      74     205 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 8.8e-07
                                   ---SS-HHHHHHHHHHTT--TTS-EEETT-TTSHHHHHHHHHHTT--TTTT----SSHHHHHHHHHHHH--EEEEES-HHH CS
                       UPF0020   8 gpapLketLAaalvrlagwkpgepllDPmCGsGtilIEaallganiapgllrefvlelkaeaeeearaelklygsDldrrv 88 
                                   +pa+   +LA   ++l   ++ge  +DP+ GsGt l+ a    +n++                          g+Dl++++
  gi|13542244|ref|NP_111932.1|  82 HPATFPISLAKQVIELFS-HEGELVVDPFVGSGTTLVAARDSNRNAV--------------------------GFDLQEKY 135
                                   566666666666666654.5788999*********996666666655..........................******** PP

                                   HHHHHHHHHHTT-GGGEEEE..E--GGG--..STTS---EEEE----------HHHHH CS
                       UPF0020  89 vqgareNaekagvgdliefs..qadaakLr..lkegevdvivtnpPYGerlgskkale 142
                                   ++ + e ++  ++ +  +++  + da+++    +e+++ +i t pPY + l+++++++
  gi|13542244|ref|NP_111932.1| 136 IKLCAERLSTQRIVGNAQQVaiEEDARNISnyFNEESISLIFTSPPYANLLNRERKNK 193
                                   ****99999988877666541145999999886777999********99999998875 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   1.8e-07   0.00035      41     126 ..     101     185 ..      78     206 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 1.8e-07
                                   CC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--T.TTEEEEES-HHHHCTS--SS-EEEEEEE- CS
                 Cons_hypoth95  41 egarvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelklee.etaelkedaleallklakkkeefdivflD 120
                                   eg+ v+D f GsG+  + A     ++av ++ +++ +k++ e l++ ++ +  +++ +e++++++++   ++e++ ++f  
  gi|13542244|ref|NP_111932.1| 101 EGELVVDPFVGSGTTLVAA-RDSNRNAVGFDLQEKYIKLCAERLSTQRIVGnAQQVAIEEDARNISNY-FNEESISLIFTS 179
                                   67789********987754.334467999*******************99967777888888888887.677899****** PP

                                   -SSSTT CS
                 Cons_hypoth95 121 PPyake 126
                                   PPya+ 
  gi|13542244|ref|NP_111932.1| 180 PPYANL 185
                                   ***976 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0     2e-06    0.0041       1      71 [.     105     179 ..     105     197 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2e-06
                                   EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT....TEEEEESBCCGBS..SSTTTEEEEEEE CS
               Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl....nvefvqgdaedlp..fedgsfDlvvss 71 
                                   v+d   G+G+++ a+ +   + + +g+D++e++++ ++er++ +++    +   ++ da++++  f+++s+ l++ s
  gi|13542244|ref|NP_111932.1| 105 VVDPFVGSGTTLVAARDS--NRNAVGFDLQEKYIKLCAERLSTQRIvgnaQQVAIEEDARNISnyFNEESISLIFTS 179
                                   667778999998888887..4********************998888854444588999999877899999999986 PP

>> N6_Mtase  N-6 DNA Methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.0   1.5e-05     0.029      31     149 ..      87     194 ..      85     212 .. 0.74
   2 ?    1.3   0.0     0.086   1.7e+02     208     251 ..     244     289 ..     233     292 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.5e-05
                      N6_Mtase  31 PrevsklivellepksgesvyDpacGsggllvqaekvlkeedgktkelsiyGqeknettyrLakmNlllhgieykkvkirl 111
                                   P ++ k ++el   + ge v+Dp +Gsg  lv a +          + +  G +++e+ ++L+   l  + i  +  ++++
  gi|13542244|ref|NP_111932.1|  87 PISLAKQVIELFSHE-GELVVDPFVGSGTTLVAARDS---------NRNAVGFDLQEKYIKLCAERLSTQRIVGNAQQVAI 157
                                   667777788877655.557*************99883.........4556899*******************998777655 PP

                      N6_Mtase 112 gdtle..kpkfekdkkfdvvvaNppfnqkewkektlekde 149
                                   ++     ++ f +++++  + + pp+ +    +++ ++ +
  gi|13542244|ref|NP_111932.1| 158 EEDARniSNYF-NEESISLIFTSPPYANL-L-NRERKNKS 194
                                   54443013444.59************987.3.33333333 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.086
                      N6_Mtase 208 eavialpeklFyntsiptcilvlkkekae..rkgkvlfidaseefk 251
                                   ++vi++p+  + n  i+  + +++  +++  +  ++++ d+++ ++
  gi|13542244|ref|NP_111932.1| 244 HCVINVPDMWWENKRIAIHVYLINEMTKRgyELRNIIIWDKRNLVN 289
                                   8**********************99988777777888888887665 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.59   1.2e+03      81     110 ..      78     107 ..      75     110 .. 0.84
   2 !   15.9   0.0   4.1e-06    0.0083       4     119 ..     102     257 ..      99     292 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.59
               Methyltransf_31  81 nevlnaladpdkileeiervlkpggillie 110
                                   + +++  ++p +  ++++++++ +g+l+++
  gi|13542244|ref|NP_111932.1|  78 DKTVHPATFPISLAKQVIELFSHEGELVVD 107
                                   667788899999999***********9986 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 4.1e-06
               Methyltransf_31   4 glrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeq..gdieeleklledekfDlilsn 81 
                                   g  v+D+  G+G+ + ++ +   ++ + vG+D +e+ i+l+ e+++ + +  n++  +  +d+ ++++ +++e++ li++ 
  gi|13542244|ref|NP_111932.1| 102 GELVVDPFVGSGTTLVAARD---SNRNAVGFDLQEKYIKLCAERLSTQRIVgNAQQVAieEDARNISNYFNEESISLIFTS 179
                                   55688877777777777764...356799**************99988887555433234888888865888********* PP

               Methyltransf_31  82 .....................................evl...naladpdkileeiervlkpggilliedprllaelp 119
                                                                        ++l    +++++ +i+e+++ +l+++g+++i+ p+++ e++
  gi|13542244|ref|NP_111932.1| 180 ppyanllnrerknksrrnrknnqlgkveqysqdprdlGTLdveSYTKEMGDIFEKVKPALRTKGHCVINVPDMWWENK 257
                                   ************************999999999999966677799************************999666655 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   2.9e-05     0.058       5      66 ..     110     177 ..     106     247 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.9e-05
                                   -TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-....EEEETTEECCCTS..S-TT-EEEEE CS
               Methyltransf_11   5 cGtGrlaealakrgarvvgvDlskemlklakekaseegl....kvefvvadaeklp..fednsfDlvv 66 
                                   +G+G  + a  +  ++ vg+Dl ++ +kl+ e+ s++++    +   +++da+++   f+++s+ l++
  gi|13542244|ref|NP_111932.1| 110 VGSGTTLVAARDSNRNAVGFDLQEKYIKLCAERLSTQRIvgnaQQVAIEEDARNISnyFNEESISLIF 177
                                   577777777777789**********************9777663334677777763357777777776 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.1      0.21   4.2e+02      35      61 ..      23      49 ..      12      73 .. 0.73
   2 ?   11.3   0.0   9.7e-05      0.19       2      81 ..     103     182 ..     102     202 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.21
               Methyltransf_15 35 lacaqhNaevYgvsdkitlvlgdvfel 61
                                  la++++Na+ Y+  +  t+++++++e 
  gi|13542244|ref|NP_111932.1| 23 LAIMKENAKEYQPLKINTIKTCSCKEN 49
                                  788999999998776667777888773 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 9.7e-05
               Methyltransf_15   2 rvilDlfsGaGGnviqfalvfekviaieinleklacaqhNaevYgv..sdkitlvlgdvfellaklklekikvdlvflSpP 80 
                                   ++++D+f G+G   ++   + ++ ++ + +++ ++++++      +  + +   +  d  ++ + +++e+i  +l+f+SpP
  gi|13542244|ref|NP_111932.1| 103 ELVVDPFVGSGTTLVAARDSNRNAVGFDLQEKYIKLCAERLSTQRIvgNAQQVAIEEDARNISNYFNEESI--SLIFTSPP 181
                                   579**********************************9988777663444445678899999999999999..******** PP

               Methyltransf_15  81 w 81 
                                    
  gi|13542244|ref|NP_111932.1| 182 Y 182
                                   6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (316 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       758  (0.0422779); expected 358.6 (0.02)
Passed bias filter:                      533  (0.0297284); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.54u 0.24s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 2279.10
//
Query:       gi|13542245|ref|NP_111933.1|  [L=263]
Description: hypothetical protein TVN1414 [Thermoplasma volcanium GSS1]
Scores for complete 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-67  225.1   0.7    1.2e-66  224.9   0.7    1.1  1  MvaI_BcnI  MvaI/BcnI restriction endonuclease family


Domain annotation for each model (and alignments):
>> MvaI_BcnI  MvaI/BcnI restriction endonuclease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  224.9   0.7   6.6e-71   1.2e-66       1     232 []      12     257 ..      12     257 .. 0.95

  Alignments for each domain:
  == domain 1  score: 224.9 bits;  conditional E-value: 6.6e-71
                     MvaI_BcnI   1 ieklkeIkklgwikskrkgd.ggvGktLEdlLGieenssklPDykgiElKtkrnnskslitLfskePdgkalvllelekll 80 
                                   ie+lkeI+++gwi+++rkg+ gg+G+tLEdlL+i+en++++P+ +++ElKt+r+n+ sl+tLf++eP+++ l+  +   ll
  gi|13542245|ref|NP_111933.1|  12 IERLKEIRDKGWIQNRRKGNtGGIGNTLEDLLEIKENNLPIPNSAEWELKTHRKNNGSLTTLFHSEPSPRSLKIVP-SILL 91 
                                   689***************999*************************************************988888.7899 PP

                     MvaI_BcnI  81 ekYGypdkeag.....deksfratikankknkygfklkvdrekeklilevedkdkekid.....................k 135
                                     YG+++++ag     +e+sfr+ti+a +++++gf++++d+++ek+ +++   d +k+                       
  gi|13542245|ref|NP_111933.1|  92 PYYGWKHEKAGtkypdSEMSFRQTINAVTRTDRGFCIVIDYDEEKILISF---DPGKVSpkhkewltsveervghigeldI 169
                                   9******999999999**********************************...88888888899***************77 PP

                     MvaI_BcnI 136 eaywsfekLkkklksKlknlfyvkadkkkeegkeyfkYkkikilknksfekFlklleegkItvdf..rigvkksgkkkgkv 214
                                   ++yw+f++L ++++sKl n+fy+ a++kke ++ey+ Yk+i +l+++s +kF+k++++g + +df  r             
  gi|13542245|ref|NP_111933.1| 170 QPYWGFDDLFHTAGSKLLNCFYIDAEVKKEGDQEYYLYKDIYMLRKFSKQKFIKAIQNGIVLIDFdaR-----------TG 239
                                   88***************************************************************333...........45 PP

                     MvaI_BcnI 215 hnhgtkFrikeenlklLY 232
                                   hnhgtkFri+e++++ LY
  gi|13542245|ref|NP_111933.1| 240 HNHGTKFRIREDKIPILY 257
                                   9****************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       575  (0.0320709); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1728.55
//
Query:       gi|13542246|ref|NP_111934.1|  [L=206]
Description: hypothetical protein TVN1415 [Thermoplasma volcanium GSS1]
Scores for complete 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-38  130.4   0.0    1.2e-37  130.0   0.0    1.2  1  MvaI_BcnI  MvaI/BcnI restriction endonuclease family


Domain annotation for each model (and alignments):
>> MvaI_BcnI  MvaI/BcnI restriction endonuclease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.0   0.0   6.6e-42   1.2e-37      18     232 .]       3     199 ..       1     199 [. 0.85

  Alignments for each domain:
  == domain 1  score: 130.0 bits;  conditional E-value: 6.6e-42
                     MvaI_BcnI  18 kgdggvGktLEdlLGieenssklPDykgiElKtkrnnskslitLfskePdgkalvllelekllekYGypdkeagdeksfra 98 
                                   +g +g+G+tLE+lLGi+en+ +lPD +giElK++r+ns +litLf+     +a   ++  + ++kYG+ dk+   +  ++ 
  gi|13542246|ref|NP_111934.1|   3 RGPTGIGMTLESLLGIKENNISLPDLDGIELKAHRDNSMNLITLFTFNR--GAWI-MNPLEAVRKYGTLDKN--GRLGLYF 78 
                                   6779*****************************************9665..4434.344689*********7..5666657 PP

                     MvaI_BcnI  99 tikankknkygfklkvdrekeklilevedkdkekidkeaywsfekLkkklksKlknlfyvkadkkkeegkeyfkYkkikil 179
                                   t++++ + + g+ l  d+e+ +++  +      + d  + w+f++L++++k+K+  l++ +a+++ + ++eyf+++k+ +l
  gi|13542246|ref|NP_111934.1|  79 TMNFTPN-SAGLYLFADNEAVSVR--H-----INGDVLVKWNFNDLEDQFKRKVPALIIAYARTEYRGNDEYFQFYKAVLL 151
                                   7776655.6666666666655555..4.....23456779***************************************** PP

                     MvaI_BcnI 180 knksfekFlklleegkItvdfrigvkksgkkkgkvhnhgtkFrikeenlklLY 232
                                   k+++ + + ++++++ I +d+r+      +k +  +nhgt Fri e+nl+l++
  gi|13542246|ref|NP_111934.1| 152 KGTTKDIIRESIKNNIILIDLRLH-----DKGTMARNHGTGFRIYEKNLPLVF 199
                                   *********************666.....556689***************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       415  (0.0231469); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); 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 0.27s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1379.12
//
Query:       gi|13542247|ref|NP_111935.1|  [L=382]
Description: adenine-specific DNA methylase [Thermoplasma volcanium GSS1]
Scores for complete 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   40.3   1.2    5.8e-05   22.9   0.0    2.7  3  N6_N4_Mtase      DNA methylase
    7.3e-08   32.3   0.1    0.00013   21.7   0.0    2.7  3  UPF0020          Putative RNA methylase family UPF0020
  ------ inclusion threshold ------
      0.011   16.5   0.0        2.9    8.7   0.0    2.6  2  Methyltransf_12  Methyltransferase domain


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 !   22.9   0.0   9.8e-09   5.8e-05     180     226 ..       5      51 ..       3      56 .. 0.87
   2 ?   -2.2   0.1      0.47   2.8e+03     163     165 ..     132     134 ..      57     193 .. 0.61
   3 !   15.6   0.1   1.7e-06      0.01       2      95 ..     211     359 ..     210     381 .. 0.85

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 9.8e-09
                                   HHHHHHHHHS-TT-EEEETT-TTTHHHHHHHHTT-EEEEEESSHHHH CS
                   N6_N4_Mtase 180 llerlIklstkkgdivlDpFaGSGtTavaakelgrkfiGieieeeyv 226
                                    +++l+ l+  + ++v+Dp++G+Gt +v+a+ lg + iG++ ++ + 
  gi|13542247|ref|NP_111935.1|   5 VARKLLYLYGSNAKTVFDPYCGTGTSLVEAMLLGINGIGTDLNPLAQ 51 
                                   57888888999999***************************998655 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.47
                                   TS- CS
                   N6_N4_Mtase 163 ksk 165
                                   +s+
  gi|13542247|ref|NP_111935.1| 132 ESS 134
                                   222 PP

  == domain 3  score: 15.6 bits;  conditional E-value: 1.7e-06
                                   EEEEE--SSSSSCS......................................................GCCGCCHHHHHHH CS
                   N6_N4_Mtase   2 dlivtdpPYntgkdy.................................................endeqyeeedsyeeyle 33 
                                   d++vt+pPY+ +                                                    +++++ +   +++ + +
  gi|13542247|ref|NP_111935.1| 211 DIVVTSPPYGDSHTTvaygqysrlssewlslignenidnklmggskspiiedfpslplneaiqaIEKKNKKRAIEVSSFYR 291
                                   79*********99999*******************************************9999888888889999****** PP

                                   HHHHHHHHHHHHEEEEEEEEEEE-CCCHHT......HHHHHHHHHTT-EEEEEEEEEEESS.STTTSTC CS
                   N6_N4_Mtase  34 flekvlkevrrvLkddgsifiniddseikk......elkaladeifggffllnvivwkkpn.smpesnk 95 
                                    l+  +k+v rvLk +g ++  +  ++ ++       +++ + e  g f ++++ + + pn  mp+ n+
  gi|13542247|ref|NP_111935.1| 292 DLQMSIKNVGRVLKSNGYACYVVANRTVNSvilptsYAIKDIFEYYG-FEYIKTYIRDIPNkRMPSVNS 359
                                   ******************************99987756666666666.888888888888766666554 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   2.1e-08   0.00013      15      70 ..       4      57 ..       1      78 [. 0.72
   2 !    7.5   0.0   0.00048       2.9     114     137 ..     204     225 ..     188     243 .. 0.78
   3 ?   -2.0   0.0      0.42   2.5e+03     141     169 ..     286     317 ..     279     327 .. 0.70

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 2.1e-08
                                  HHHHHHHHHTT--TTS-EEETT-TTSHHHHHHHHHHTT--TTTT----SSHHHHHH CS
                       UPF0020 15 tLAaalvrlagwkpgepllDPmCGsGtilIEaallganiapgllrefvlelkaeae 70
                                  ++A+ l++l g ++ ++ +DP CG+Gt l+Ea llg n + g+  +   +l a+a+
  gi|13542247|ref|NP_111935.1|  4 QVARKLLYLYGSNA-KTVFDPYCGTGTSLVEAMLLGINGI-GTDLNPLAQLIAKAK 57
                                  67888888888765.5678*****************9988.443344444444444 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.00048
                                   G--STTS---EEEE---------- CS
                       UPF0020 114 kLrlkegevdvivtnpPYGerlgs 137
                                   +++  e+  d++vt pPYG++ ++
  gi|13542247|ref|NP_111935.1| 204 DIP--EDFADIVVTSPPYGDSHTT 225
                                   455..34579*********99776 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 0.42
                                   HHHHHHHHHHHHH...HH-TT..-EEEEEESS CS
                       UPF0020 141 lekLYseflrelk...rvlrgggrlvlltsen 169
                                   + ++Y+ +  ++k   rvl+++g ++++++++
  gi|13542247|ref|NP_111935.1| 286 VSSFYRDLQMSIKnvgRVLKSNGYACYVVANR 317
                                   46677777665552226799999999998765 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.0   0.00049       2.9       5      89 ..      25     113 ..      24     116 .. 0.77
   2 ?    4.9   0.0    0.0075        45      73      98 ..     284     309 ..     282     310 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00049
               Methyltransf_12   5 cGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnveleald..lldldgg....ssfDlvvasnvlhhl 79 
                                   cGtG+ l +      +i+ +g+D++p a   ak+k++++++++    e+e+ +  +++ld+     +  D  ++ nv   l
  gi|13542247|ref|NP_111935.1|  25 CGTGTSLVEAMLL--GINGIGTDLNPLAQLIAKAKTNAYIDYKSVISEIEKFNenADKLDPIvpniKNIDFWFSKNVSIKL 103
                                   8888766666666..9**********9999999999999999876666655550055555549999999999999998888 PP

               Methyltransf_12  80 kdirevldni 89 
                                    +i++++++i
  gi|13542247|ref|NP_111935.1| 104 GKIKAYIESI 113
                                   8888887776 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0075
               Methyltransf_12  73 snvlhhlkdirevldnirklLkpgGr 98 
                                   ++v +  +d++ +++n+ ++Lk +G+
  gi|13542247|ref|NP_111935.1| 284 IEVSSFYRDLQMSIKNVGRVLKSNGY 309
                                   67888889****************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (382 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       787  (0.0438954); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 2401.08
//
Query:       gi|13542248|ref|NP_111936.1|  [L=99]
Description: hypothetical protein TVN1417 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       898  (0.0500865); 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:                         0  (0); expected 0.2 (1e-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: 643.87
//
Query:       gi|13542249|ref|NP_111937.1|  [L=100]
Description: hypothetical protein TVN1418 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       433  (0.0241508); expected 358.6 (0.02)
Passed bias filter:                      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: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 637.54
//
Query:       gi|13542250|ref|NP_111938.1|  [L=381]
Description: multidrug efflux permease [Thermoplasma volcanium GSS1]
Scores for 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-15   55.6  48.8    3.3e-09   36.1  29.8    2.1  2  MFS_1     Major Facilitator Superfamily
  ------ inclusion threshold ------
        3.3    7.7  10.6        5.7    6.9   5.3    2.6  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 !   36.1  29.8   3.7e-13   3.3e-09       7     297 ..      14     290 ..       7     299 .. 0.80
   2 !   33.2  11.0     3e-12   2.6e-08       6     167 ..     210     371 ..     205     378 .. 0.85

  Alignments for each domain:
  == domain 1  score: 36.1 bits;  conditional E-value: 3.7e-13
                         MFS_1   7 lsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrr.vlllglllfalglllllfasslw 86 
                                     ++ +s+ +++ p ++ ++ +is+  +g+++ +  +  +v++l+++r+   f+++  vlll++l+ a+  ++l+f+ ++ 
  gi|13542250|ref|NP_111938.1|  14 ARSFIFSMMAIITP-YYLQSMHISALYVGIIIFISLVSGSVFILLYSRV--PFSAKNrVLLLSVLMVAAL-TVLVFVRNVV 90 
                                   55667777777777.888*******************************..9999999************.8888878888 PP

                         MFS_1  87 lllvlrvlqGlgaga....lfpagaaliadwfpk..eergraigllsagfslGailgpllggllasslgWravfyilaivs 161
                                   +++v+ ++ G+  ++    ++p +  ++   f    ++++ a+++++ g+  +a+++ ++  +l   ++++ +f il ++s
  gi|13542250|ref|NP_111938.1|  91 IFVVAVFIGGISLAGrdfsAYPPIEKFAISSFETiqKDKNEAFSVYNFGSYGSAAIASAF-LYLDLRYSFQEIFEILLVLS 170
                                   *************964444788888888888887778*******************9888.55566*************** PP

                         MFS_1 162 llafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsglltllplylqevlglsg 242
                                   +l ++   l+++++ p+ kr+s   +     p       k ++++   +++l+a+  f+ gf  ++++l+l+++ v+++s 
  gi|13542250|ref|NP_111938.1| 171 ILQLI---LYIFVKLPDYKRESVNLR----LP-------KNVKAHVNTLSYLFAIDAFGGGFV-TVSMLTLWFKAVYHIS- 235
                                   ***99...455444444444433333....22.......334444433334444444442444.556666666*******. PP

                         MFS_1 243 lllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavt 297
                                   l +ag+++ ++ +++a + l+++++s ++g  ++++++ ++  ++++++ l+++ 
  gi|13542250|ref|NP_111938.1| 236 LSEAGFIFIIVNVLTALSILVSSKISGKIGLIKTMVFTHIVSNFFLILMPLVPNL 290
                                   **************************************99999999999999887 PP

  == domain 2  score: 33.2 bits;  conditional E-value: 3e-12
                         MFS_1   6 flsalarsilgpalpl.alaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll.fass 84 
                                   ++ a++ +++++++   + +  ++is se+g+++ ++ +++a+++l+ + +s ++G  ++++++ +++ ++ l+l+ ++++
  gi|13542250|ref|NP_111938.1| 210 AIDAFGGGFVTVSMLTlWFKAVYHISLSEAGFIFIIVNVLTALSILVSSKISGKIGLIKTMVFTHIVSNFF-LILMpLVPN 289
                                   5666777777777777799999*************************************888888888888.55554469* PP

                         MFS_1  85 lw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivslla 164
                                   l+ + l+l + q   + + +pa  +++  + p+ +r + ++++++   lG   gp++gg+l+  +g +++ +++++v +l 
  gi|13542250|ref|NP_111938.1| 290 LYaAELFLYLRQTTSQ-MDVPARDSFTNTIIPPGDRIKTNSVFTTVRTLGHGPGPAIGGYLI-EAGPPSLLFVAGGVKILY 368
                                   9988888888888885.*********************************************.557788888888777776 PP

                         MFS_1 165 fvl 167
                                    +l
  gi|13542250|ref|NP_111938.1| 369 DLL 371
                                   554 PP

>> DUF3290  Protein of unknown function (DUF3290)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   5.3   0.00064       5.7       7      66 ..      29      87 ..      26      96 .. 0.82
   2 ?    3.0   0.2      0.01        93      16      72 ..     131     189 ..     120     206 .. 0.66

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.00064
                       DUF3290  7 YlqsqqslndllryililvlllllivvlilylrnrldtkyRdLsiilllllllllgiqys 66
                                  Ylq + +++ l   i+i++ l+   v+++ly r  ++ k R L++ +l++++l++ + ++
  gi|13542250|ref|NP_111938.1| 29 YLQ-SMHISALYVGIIIFISLVSGSVFILLYSRVPFSAKNRVLLLSVLMVAALTVLVFVR 87
                                  444.445555556678899999999************************99999987665 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.01
                       DUF3290  16 dllryililvlllllivvlilyl..rnrldtkyRdLsiilllllllllgiqysdyqqsq 72 
                                   +++ ++ ++    + i+ ++lyl  r  ++  +  L+++ +l l+l + +++ dy++ +
  gi|13542250|ref|NP_111938.1| 131 EAFSVYNFGSYGSAAIASAFLYLdlRYSFQEIFEILLVLSILQLILYIFVKLPDYKRES 189
                                   55555555555555555555554115556666777888888888888888888887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (381 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1043  (0.0581739); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.50
# Mc/sec: 2272.51
//
Query:       gi|13542251|ref|NP_111939.1|  [L=313]
Description: hypothetical protein TVN1420 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-12   47.7   0.0    1.1e-11   44.9   0.0    2.0  1  Esterase         Putative esterase
    0.00032   20.4   0.1     0.0025   17.5   0.0    2.2  2  Abhydrolase_1    alpha/beta hydrolase fold
  ------ inclusion threshold ------
       0.01   14.7   0.0      0.014   14.2   0.0    1.1  1  Late_protein_L1  L1 (late) protein
      0.063   13.2   0.2          1    9.3   0.0    2.3  2  UPF0227          Uncharacterised protein family (UPF0227)
       0.14   11.4   0.0       0.31   10.3   0.0    1.5  2  Hydrolase_4      Serine aminopeptidase, S33


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 !   44.9   0.0   3.1e-15   1.1e-11       6     235 ..      22     291 ..      19     295 .. 0.84

  Alignments for each domain:
  == domain 1  score: 44.9 bits;  conditional E-value: 3.1e-15
                                   EEEEEEEEE.CC.GGTTTEEEEEEE--TTHHCCHHH.HHCHH.CCCCHCCT.EEEEEECCCSS-TTTTTSBTTSBB.TTEE CS
                      Esterase   6 reikvqvyLPedyspgrkypvvylldGltgwdqnfr.akell.eslaregeiaeviivvvprggessfysdwdlgarfyen 84 
                                   +++++ vy P+d  +++++p+ + l G t+w   +   ++l+ e+l ++      ++v  p+  ++ + +          +
  gi|13542251|ref|NP_111939.1|  22 WKRQILVYRPDD--AEGGLPLFIELAG-TNWRPRTHnKFSLIiEKLFSS---GLKAVVLNPNFSTRYNMN----------Q 86 
                                   89999***9999..999**********.999876651444441445555...366788899999983333..........3 PP

                                   ETTCCCCCCHCHHHHTHHHHHHHHHCSEECCCEEEEEETHHHHHHHHHHHCSTTTCC.EEEEES--S-CC........... CS
                      Esterase  85 ategpgaeayetfltqeLlplldanfrtapdgravaGqSmGGlgALilalkhpdrFg.svssfSpivnps........... 153
                                     + p    ye+f+ +eL p+ ++++ t+ +  a++G S GG+g+ +la++hpd    ++  f    + +           
  gi|13542251|ref|NP_111939.1|  87 YLNSPAVGSYEDFIVKELIPYFKDKYGTDHT--ALFGKSSGGFGSYTLAARHPDIIDgFADHFG---DSCffylyaddmaa 162
                                   446788899*******************999..********************98640333332...2335666699**** PP

                                   .............................................................HCHHHCTTCCHHHCC-CCCC CS
                      Esterase 154 .............................................................namWgqeekeawqendpvll 173
                                                                                                +  W      +w + dp+ +
  gi|13542251|ref|NP_111939.1| 163 afryiqrhgksesvkmltshmpsddemkvlnvigssafyspdmndvngfdlpfdedtgeliEDVWQ-----RWVQFDPAKN 238
                                   **********************************************99999999999999999995.....5999999999 PP

                                   HCHHC.HTTSEEEEEEEECTTBCCCHTSCHHHHHHHHHHHCCHHHHCCCCCCTT-SCCCC--S CS
                      Esterase 174 akels.aslkalriyldvGtseddlgeqlsveilevlarnrelkeqlaargvegedheydGgh 235
                                   + + s a +k + iyldvGt+++           +   ++r+l+++l  ++++++++e++Ggh
  gi|13542251|ref|NP_111939.1| 239 VLKYSgALKKMKAIYLDVGTNDE----------YKLYIGTRALHKKLGLANIDHYYEEFNGGH 291
                                   9876615566789*********9..........67788999*********************9 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   6.9e-07    0.0025      52     101 ..      94     143 ..      73     163 .. 0.85
   2 ?   -0.3   0.0      0.18   6.6e+02      87     128 ..     163     206 ..     161     213 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 6.9e-07
                                   CHHSHHHHHHHHHHHHHHCTTSSEEEEEETHHHHHHHHHHHHHGGGEEEE CS
                 Abhydrolase_1  52 ddygtasvaddldrildalgddkltlvGhSmGGmialayaaeyperVkal 101
                                     y+++ v + + +++d++g d+ +l G S GG+ + ++aa++p+ ++++
  gi|13542251|ref|NP_111939.1|  94 GSYEDFIVKELIPYFKDKYGTDHTALFGKSSGGFGSYTLAARHPDIIDGF 143
                                   5577777888888********************************99876 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.18
                                   HHHHHHHH..GGGEEEEEEESECSSCCHHHHHHHHHHHHHHCHH CS
                 Abhydrolase_1  87 alayaaey..perVkalvllgaidpaaslieaqrqqaksfpdff 128
                                   a+ y +++   e+Vk+l++  ++d+ ++       +a+  pd++
  gi|13542251|ref|NP_111939.1| 163 AFRYIQRHgkSESVKMLTSHMPSDDEMKVLNVIGSSAFYSPDMN 206
                                   67899999999***********8888777766666666666665 PP

>> Late_protein_L1  L1 (late) protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0     4e-06     0.014     224     268 ..     133     177 ..     120     203 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4e-06
                                   BEEEE-HHHHHHSSS-TS-SEEEEEEEEEEE.EEEEESSEESS--- CS
               Late_protein_L1 224 ickyPDylkmaedayGdslffyarreqlyar.hlfsraGtkgeavp 268
                                    +++PD++    d++Gds+ffy   + + a  ++++r G+++ +v+
  gi|13542251|ref|NP_111939.1| 133 AARHPDIIDGFADHFGDSCFFYLYADDMAAAfRYIQRHGKSE-SVK 177
                                   579********************9999976526677777654.443 PP

>> UPF0227  Uncharacterised protein family (UPF0227)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0   0.00029         1      80     108 ..      67      95 ..      61     107 .. 0.83
   2 ?    2.1   0.0     0.044   1.6e+02      45      80 ..     100     136 ..      89     138 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00029
                       UPF0227  80 fglrqvllnPalkplenlagklgeeavqs 108
                                    gl++v+lnP++    n++++l+  av s
  gi|13542251|ref|NP_111939.1|  67 SGLKAVVLNPNFSTRYNMNQYLNSPAVGS 95 
                                   589*******************9866655 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.044
                       UPF0227  45 alkeleklvae.lgddnillvGssLGGyyatrlgerf 80 
                                   ++kel+   ++ +g d+ +l G s GG+ +  l++r+
  gi|13542251|ref|NP_111939.1| 100 IVKELIPYFKDkYGTDHTALFGKSSGGFGSYTLAARH 136
                                   555555555541455669**************99997 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   8.7e-05      0.31      63     104 ..     102     143 ..      93     145 .. 0.87
   2 ?   -3.1   0.0       1.1   3.9e+03      55      76 ..     153     174 ..     146     181 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 8.7e-05
                   Hydrolase_4  63 aafvekvkeehpelplfllGhSmGGliallyllrypdkvagl 104
                                   ++++  +k+++++    l+G S GG+ + ++++r+pd ++g+
  gi|13542251|ref|NP_111939.1| 102 KELIPYFKDKYGTDHTALFGKSSGGFGSYTLAARHPDIIDGF 143
                                   5667778889999999*********************88886 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1.1
                   Hydrolase_4  55 fddyvdDlaafvekvkeehpel 76 
                                   f  y dD+aa+++ ++++ + +
  gi|13542251|ref|NP_111939.1| 153 FYLYADDMAAAFRYIQRHGKSE 174
                                   5678888888888888655544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.64u 0.29s 00:00:00.93 Elapsed: 00:00:00.52
# Mc/sec: 1816.17
//
Query:       gi|13542252|ref|NP_111940.1|  [L=160]
Description: hypothetical protein TVN1421 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.6e-09   36.2   0.3    5.2e-09   35.7   0.3    1.3  1  DUF309    Domain of unknown function (DUF309)
  ------ inclusion threshold ------
      0.065   13.5   0.2         19    5.8   0.0    2.4  2  PPR       PPR repeat


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 !   35.7   0.3   5.8e-13   5.2e-09       8      56 ..      73     119 ..      67     122 .. 0.88

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 5.8e-13
                        DUF309   8 fnegeffeaHEvlEelWkeageperkllqglIqlAvAlyhlrrgnvrga 56 
                                     e++++eaHEv E++W++ ++p  + lq lI l +++ h ++g    a
  gi|13542252|ref|NP_111940.1|  73 SREERYWEAHEVVEDMWRSLNHP--SGLQKLILLLASQIHCQMGDCAHA 119
                                   459**************999986..9*****************987666 PP

>> PPR  PPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0    0.0024        21      10      28 ..      72      90 ..      69      91 .. 0.89
   2 ?    5.8   0.0    0.0021        19      10      25 ..     110     125 ..     108     129 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0024
                           PPR 10 ycknGkleeAlelfkeMke 28
                                  ++++ ++ eA e+ ++M +
  gi|13542252|ref|NP_111940.1| 72 LSREERYWEAHEVVEDMWR 90
                                  78999************87 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0021
                           PPR  10 ycknGkleeAlelfke 25 
                                   +c+ G++  A++lf +
  gi|13542252|ref|NP_111940.1| 110 HCQMGDCAHAEDLFIR 125
                                   8*************76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        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 0.31s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 1025.51
//
Query:       gi|13542253|ref|NP_111941.1|  [L=205]
Description: transcription regulator [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-08   34.0   0.5    3.6e-08   32.8   0.1    1.8  2  HTH_24         Winged helix-turn-helix DNA-binding
      4e-08   33.1   0.2    1.6e-07   31.1   0.0    2.2  3  HTH_11         HTH domain
    1.3e-05   25.0   0.1    2.6e-05   24.1   0.1    1.4  1  MarR           MarR family
    2.5e-05   24.0   0.1    5.6e-05   22.9   0.1    1.6  1  HTH_5          Bacterial regulatory protein, arsR family
    6.6e-05   22.7   0.0    0.00012   21.9   0.0    1.4  1  TrmB           Sugar-specific transcriptional regulator TrmB
    0.00013   21.7   0.1    0.00027   20.6   0.1    1.5  1  HTH_DeoR       DeoR-like helix-turn-helix domain
     0.0002   21.3   0.0    0.00031   20.7   0.0    1.3  1  HTH_20         Helix-turn-helix domain
    0.00038   20.2   0.0      0.002   17.9   0.0    2.0  2  HTH_10         HTH DNA binding domain
    0.00044   20.1   0.0    0.00087   19.1   0.0    1.5  1  MarR_2         MarR family
    0.00053   19.8   0.0      0.001   18.8   0.0    1.5  1  HTH_AsnC-type  AsnC-type helix-turn-helix domain
     0.0012   18.7   0.0     0.0027   17.5   0.0    1.6  1  HxlR           HxlR-like helix-turn-helix
     0.0024   18.2   0.0     0.0041   17.4   0.0    1.4  1  Rrf2           Transcriptional regulator
     0.0083   15.8   0.1      0.015   14.9   0.1    1.3  1  GntR           Bacterial regulatory proteins, gntR family
  ------ inclusion threshold ------
      0.012   15.4   0.1      0.033   14.0   0.0    1.7  2  IF2_N          Translation initiation factor IF-2, N-terminal
      0.019   15.3   0.0      0.038   14.3   0.0    1.5  1  FaeA           FaeA-like protein
      0.031   15.0   0.6      0.051   14.3   0.6    1.5  1  ATC_hydrolase  L-2-amino-thiazoline-4-carboxylic acid hydrola
      0.042   13.7   0.0      0.073   12.9   0.0    1.4  1  HTH_IclR       IclR helix-turn-helix domain
      0.042   13.4   0.0       0.24   11.0   0.0    2.3  3  Sigma70_r4     Sigma-70, region 4
      0.044   13.3   0.0      0.083   12.5   0.0    1.4  1  HTH_CodY       CodY helix-turn-helix domain
      0.071   13.1   0.1       0.18   11.8   0.1    1.7  1  Rho_N          Rho termination factor, N-terminal domain
      0.096   12.8   0.0       0.16   12.2   0.0    1.3  1  HTH_28         Helix-turn-helix domain
       0.12   12.9   0.0       0.23   12.0   0.0    1.4  1  HTH_27         Winged helix DNA-binding domain
       0.15   12.1   0.0       0.34   10.9   0.0    1.5  1  HTH_Crp_2      Crp-like helix-turn-helix domain
       0.15   11.9   0.1       0.32   10.8   0.1    1.5  1  LexA_DNA_bind  LexA DNA binding domain
       0.19   11.9   0.0       0.29   11.3   0.0    1.2  1  DprA_WH        DprA 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 !   32.8   0.1     5e-11   3.6e-08       4      48 .]       3      47 ..       2      47 .. 0.95
   2 ?   -2.6   0.0       5.8   4.1e+03       4      17 ..      79      92 ..      78      93 .. 0.79

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 5e-11
                        HTH_24  4 tdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                  t+ +I+ lL+k++     eLA++lg+S  +v+r++++Le  G+++
  gi|13542253|ref|NP_111941.1|  3 TENEIIILLKKDGPKRLDELAKELGISNMAVLRHMEKLEATGVVE 47
                                  5668***************************************96 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 5.8
                        HTH_24  4 tdrkILelLqknpr 17
                                  + +++++ L +n++
  gi|13542253|ref|NP_111941.1| 79 ILLDLISFLSENGH 92
                                  56788999999986 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.1   0.0   2.3e-10   1.6e-07       3      44 ..       5      49 ..       3      60 .. 0.82
   2 ?   -2.8   0.0         9   6.5e+03       7      19 ..     106     118 ..     106     119 .. 0.76
   3 ?   -1.9   0.0       4.8   3.4e+03      34      54 ..     144     165 ..     141     166 .. 0.77

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 2.3e-10
                        HTH_11  3 lqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelg....v 44
                                  + i++lL +++gp   +eLA+eL++S ++v r++++Le++g     
  gi|13542253|ref|NP_111941.1|  5 NEIIILL-KKDGPKRLDELAKELGISNMAVLRHMEKLEATGvverR 49
                                  5677777.99999****************************54444 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 9
                        HTH_11   7 elLleargpisge 19 
                                   ++++e r+++sge
  gi|13542253|ref|NP_111941.1| 106 QQIIEYRKQMSGE 118
                                   5677889999987 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 4.8
                        HTH_11  34 rdIkaLeelgvpIesepgr.GY 54 
                                     I +++e  +pI   +++ GY
  gi|13542253|ref|NP_111941.1| 144 DGIYEITEYNCPIFRIAQKdGY 165
                                   5577788999999888888888 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.1   3.6e-08   2.6e-05       4      50 ..       3      49 ..       2      52 .. 0.94

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 3.6e-08
                                  HHHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                          MarR  4 tqfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRs 50
                                  t+ +i+ +l+  gp ++ eLak lg+s+++v r   +Le  G +eR+
  gi|13542253|ref|NP_111941.1|  3 TENEIIILLKKDGPKRLDELAKELGISNMAVLRHMEKLEATGVVERR 49
                                  56678999**************************************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 !   22.9   0.1   7.9e-08   5.6e-05       5      46 ..       5      47 ..       2      48 .. 0.94

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 7.9e-08
                                  HHHHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                         HTH_5  5 lkILklLae.gelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                   +I+ lL + g++   ela+elg+s  +v +H  kL+  G+Ve
  gi|13542253|ref|NP_111941.1|  5 NEIIILLKKdGPKRLDELAKELGISNMAVLRHMEKLEATGVVE 47
                                  589999999********************************97 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   1.6e-07   0.00012      16      57 ..       9      51 ..       3      66 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1.6e-07
                                  HHH.HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESS CS
                          TrmB 16 aLl.klgpatadeiaeelgvprskvYevLrsLedkGlVerekg 57
                                   Ll k gp++ de+a+elg++   v + +++Le  G+Ver+  
  gi|13542253|ref|NP_111941.1|  9 ILLkKDGPKRLDELAKELGISNMAVLRHMEKLEATGVVERRTF 51
                                  567799**********************************974 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 !   20.6   0.1   3.7e-07   0.00027       3      46 ..       5      48 ..       4      51 .. 0.96

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 3.7e-07
                      HTH_DeoR  3 eqilellkqqgklsveelvellgvSeaTiRRDLneLeeqglltR 46
                                  ++i+ llk++g  +++el+ +lg+S + + R +++Le+ g+++R
  gi|13542253|ref|NP_111941.1|  5 NEIIILLKKDGPKRLDELAKELGISNMAVLRHMEKLEATGVVER 48
                                  68999************************************998 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   4.4e-07   0.00031      20      58 ..      12      50 ..       6      52 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 4.4e-07
                                  STCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEEC CS
                        HTH_20 20 araegltaselaerldlskntlsyHLrvLeeagLvevvr 58
                                  + +++  + ela++l++s   + +H+++Le  g ve+++
  gi|13542253|ref|NP_111941.1| 12 KKDGPKRLDELAKELGISNMAVLRHMEKLEATGVVERRT 50
                                  566677788****************************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 !   17.9   0.0   2.8e-06     0.002      25      48 ..      18      41 ..      14      43 .. 0.89
   2 ?   -0.6   0.0       1.7   1.2e+03       1      17 [.     149     165 ..     149     165 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.8e-06
                        HTH_10 25 tlkeLAkelGIskstlsehLrkae 48
                                  +l+eLAkelGIs+++++ h++k e
  gi|13542253|ref|NP_111941.1| 18 RLDELAKELGISNMAVLRHMEKLE 41
                                  589****************99876 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.7
                        HTH_10   1 LTdkqlevlklAyemGY 17 
                                   +T+ +  + ++A + GY
  gi|13542253|ref|NP_111941.1| 149 ITEYNCPIFRIAQKDGY 165
                                   599999999*******9 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   1.2e-06   0.00087      17      55 ..      13      50 ..       4      57 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.2e-06
                                  TTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                        MarR_2 17 rpgrdltvgelarrlglsksavsrilkrLvaaGLverrp 55
                                   +g++ +  ela++lg+s  av r+ ++L+a G verr+
  gi|13542253|ref|NP_111941.1| 13 KDGPK-RLDELAKELGISNMAVLRHMEKLEATGVVERRT 50
                                  45555.899****************************96 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   1.5e-06     0.001       7      42 .]       6      41 ..       3      41 .. 0.95

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.5e-06
                 HTH_AsnC-type  7 kILeaLqedaRisyaeLAervGlSestvlrRvrrLe 42
                                   I+ +L +d+     eLA+++G+S  +vlr +++Le
  gi|13542253|ref|NP_111941.1|  6 EIIILLKKDGPKRLDELAKELGISNMAVLRHMEKLE 41
                                  5999******************************98 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   3.8e-06    0.0027      10      58 ..       8      55 ..       4      74 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 3.8e-06
                                  HHHHHTTS-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSS CS
                          HxlR 10 ilvellkgkkRfselkralpkisqkmLaqrLreLeqdglierevypevP 58
                                  i+    +g+kR  el+++l +is+    +++ +Le+ g++er++ +   
  gi|13542253|ref|NP_111941.1|  8 IILLKKDGPKRLDELAKEL-GISNMAVLRHMEKLEATGVVERRTFKGKQ 55
                                  4444467************.9*********************9886544 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   5.7e-06    0.0041      21      79 ..      12      72 ..       6      76 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 5.7e-06
                                  STCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE..EETTT-TCEEESSHCCCSBHHHH CS
                          Rrf2 21 eeeepvsseeiaerqnispsylekilakLrkaglvk..svrGkgGGyrLakppeeItlldv 79
                                  ++++p +++e+a++ +is   + + ++kL+  g+v+  + +Gk+G    + + +eI   ++
  gi|13542253|ref|NP_111941.1| 12 KKDGPKRLDELAKELGISNMAVLRHMEKLEATGVVErrTFKGKQGRPYFKFSIKEIGASQI 72
                                  45566789***************************733679***99888888888877766 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.1   2.1e-05     0.015      28      60 ..      20      52 ..      18      54 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.1e-05
                                  HHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTC CS
                          GntR 28 reLaaefgVsrttvReALrrLeaeglverrqgr 60
                                   eLa+e+g+s + v + + +Lea g+verr  +
  gi|13542253|ref|NP_111941.1| 20 DELAKELGISNMAVLRHMEKLEATGVVERRTFK 52
                                  69***************************9755 PP

>> IF2_N  Translation initiation factor IF-2, N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   4.6e-05     0.033       4      28 ..      17      40 ..      15      46 .. 0.87
   2 ?   -2.7   0.0       7.7   5.5e+03      22      47 ..      85      95 ..      82     100 .. 0.51

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.6e-05
                         IF2_N  4 irVyeLAkeLgvkskevikkLfkel 28
                                  +r  eLAkeLg+++  v+++++k l
  gi|13542253|ref|NP_111941.1| 17 KRLDELAKELGISNMAVLRHMEK-L 40
                                  899***************99955.5 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 7.7
                         IF2_N 22 kkLfkelGievkshsssLDeetaeli 47
                                   +L               +e+  e+i
  gi|13542253|ref|NP_111941.1| 85 SFL---------------SENGHEKI 95
                                  444...............44444555 PP

>> FaeA  FaeA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   5.4e-05     0.038       3      48 ..       5      49 ..       3      58 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 5.4e-05
                                  HHHHHHHHH.S----HHHHHHHHTS-HHHHHHHHHHHHHHSSEEEE CS
                          FaeA  3 eeIleylnsikapckTreiAdalglsaYQaRyYLeqLekegkikrs 48
                                  +eI+  l++  +p +  e+A+ lg+s   +   +e+Le+ g ++r 
  gi|13542253|ref|NP_111941.1|  5 NEIIILLKK-DGPKRLDELAKELGISNMAVLRHMEKLEATGVVERR 49
                                  899999999.*********************************996 PP

>> ATC_hydrolase  L-2-amino-thiazoline-4-carboxylic acid hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.6   7.1e-05     0.051      23     143 ..      90     197 ..      48     199 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 7.1e-05
                 ATC_hydrolase  23 eeakeiirkalerlgkergkklaekakakkdkadvekflalyseifekenalkfevleedkdeleidvtrCpyceawkkeG 103
                                      ++i+ + le+   ++  ++++++ ++++++++ ++++l        +++ f  ++ +++ +ei+  +Cp++++++k G
  gi|13542253|ref|NP_111941.1|  90 NGHEKILDNFLEWRYSQQIIEYRKQMSGEDSDQKFLTLVKLR------YDDCYFPEYSVRDGIYEITEYNCPIFRIAQKDG 164
                                   445678888888899999999999999777777766666653......578999999999********************* PP

                 ATC_hydrolase 104 lpelgkllCeiDkavaeginpkvklertktlaeGgdcCdf 143
                                   +       Ce++ +++e+  + ++ e+t+   +G+  C f
  gi|13542253|ref|NP_111941.1| 165 Y------ACELERKLFENTTG-FDVEYTHRQVDGAYSCKF 197
                                   5......69999999999877.889999999999999988 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0    0.0001     0.073      11      50 ..      10      48 ..       6      50 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.0001
                                  T-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                      HTH_IclR 11 alaeapqeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                  +l + ++  +l elA+++g++  +v R++  L+  G ve+
  gi|13542253|ref|NP_111941.1| 10 LLKKDGP-KRLDELAKELGISNMAVLRHMEKLEATGVVER 48
                                  4444455.49****************************98 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00033      0.24       9      41 ..       4      37 ..       2      40 .. 0.83
   2 ?   -2.9   0.0       6.9   4.9e+03      21      28 ..      62      69 ..      55      70 .. 0.81
   3 ?   -2.8   0.0       6.6   4.7e+03      10      18 ..     106     117 ..     105     120 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00033
                                  HHHHHHHHH.TTT--HHHHHHHHTS-HHHHHHHH CS
                    Sigma70_r4  9 erevlelrf.geglTleEIgerlgiSrerVrqie 41
                                  e e++ l   + +  l E++++lgiS ++V +++
  gi|13542253|ref|NP_111941.1|  4 ENEIIILLKkDGPKRLDELAKELGISNMAVLRHM 37
                                  667777777799999*************996665 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 6.9
                                  --HHHHHH CS
                    Sigma70_r4 21 lTleEIge 28
                                   + +EIg+
  gi|13542253|ref|NP_111941.1| 62 FSIKEIGA 69
                                  6889**97 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 6.6
                                   HHHHHHHH...T CS
                    Sigma70_r4  10 revlelrf...g 18 
                                   ++++e+r    g
  gi|13542253|ref|NP_111941.1| 106 QQIIEYRKqmsG 117
                                   799999975554 PP

>> HTH_CodY  CodY helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00012     0.083      10      39 ..      22      51 ..      15      64 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00012
                      HTH_CodY 10 iaDriGitrsvivnaLrkLesaGiiesrsL 39
                                  +a ++Gi    +   + kLe+ G++e r  
  gi|13542253|ref|NP_111941.1| 22 LAKELGISNMAVLRHMEKLEATGVVERRTF 51
                                  7999***********************986 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 ?   11.8   0.1   0.00025      0.18       7      26 ..      16      35 ..      11      38 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00025
                                  HHHHHHHHHHTT-TTGGGS- CS
                         Rho_N  7 lseLraiAkelgienysrlR 26
                                  ++ L ++Akelgi n++ lR
  gi|13542253|ref|NP_111941.1| 16 PKRLDELAKELGISNMAVLR 35
                                  666889***********999 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00022      0.16       5      41 ..       7      45 ..       6      58 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00022
                        HTH_28  5 iiklla.aGh.svreaArelgisrrtvyrWikryeegGi 41
                                  ii ll+ +G  + +e+A+elgis   v r + ++e+ G+
  gi|13542253|ref|NP_111941.1|  7 IIILLKkDGPkRLDELAKELGISNMAVLRHMEKLEATGV 45
                                  55555516636************************9997 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00031      0.23      11      52 ..      10      50 ..       3      60 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00031
                        HTH_27 11 lirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertg 52
                                  l++  +++k+l +l++ l ++  ++   ++kL++ G+ver +
  gi|13542253|ref|NP_111941.1| 10 LLK-KDGPKRLDELAKELGISNMAVLRHMEKLEATGVVERRT 50
                                  455.799*******************************7754 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 ?   10.9   0.0   0.00047      0.34      25      54 ..      20      49 ..      13      54 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00047
                                  HHHHHHTTSSHHHHHHHHHHHHHTTSEEET CS
                     HTH_Crp_2 25 eelAsmlGltretvsrilseLkreglisrg 54
                                  +elA  lG++   v r + +L+  g+++r+
  gi|13542253|ref|NP_111941.1| 20 DELAKELGISNMAVLRHMEKLEATGVVERR 49
                                  69**************************76 PP

>> LexA_DNA_bind  LexA DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00045      0.32      29      59 ..      20      49 ..      10      54 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00045
                                  HHHHHHHTS-.HHHHHHHHHHHHHTTSEE-G CS
                 LexA_DNA_bind 29 reiaralglkSpsaveehLkaLerKGyierd 59
                                   e+a++lg++   av  h+++Le  G++er 
  gi|13542253|ref|NP_111941.1| 20 DELAKELGIS-NMAVLRHMEKLEATGVVERR 49
                                  699*****97.99****************96 PP

>> DprA_WH  DprA winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00041      0.29      24      58 ..      15      49 ..       2      51 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00041
                       DprA_WH 24 ePvhvDqLvrrtglpaaevsaaLleLELaGlverl 58
                                   P  +D+L++++g++  +v+++   LE  G ver+
  gi|13542253|ref|NP_111941.1| 15 GPKRLDELAKELGISNMAVLRHMEKLEATGVVERR 49
                                  5889*****************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       710  (0.0396006); expected 358.6 (0.02)
Passed bias filter:                      616  (0.0343577); expected 358.6 (0.02)
Passed Vit filter:                        89  (0.00496402); expected 17.9 (0.001)
Passed Fwd filter:                        25  (0.00139439); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              25  [number of targets reported over threshold]
# CPU time: 0.57u 0.32s 00:00:00.88 Elapsed: 00:00:00.51
# Mc/sec: 1204.01
//
Query:       gi|13542254|ref|NP_111942.1|  [L=471]
Description: amino acid transporter [Thermoplasma volcanium GSS1]
Scores for complete 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   68.5  44.9    6.1e-19   68.1  44.9    1.0  1  AA_permease_2  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 !   68.1  44.9   3.4e-23   6.1e-19       2     401 ..      21     431 ..      21     455 .. 0.83

  Alignments for each domain:
  == domain 1  score: 68.1 bits;  conditional E-value: 3.4e-23
                 AA_permease_2   2 sllsafalvigsvigsgifvkn...laasggpalilwvwiavligslavllvyaElssalprsgGiyvytkaafgkkvafl 79 
                                   +++++fal+++sv+ +++++++    a + g  +i + +i v+ + la ++++  +  + p+ g  y+++ +a +k+ ++ 
  gi|13542254|ref|NP_111942.1|  21 GFVDLFALSTSSVAPAFSIAASygvIAMYLGFHSI-SAIILVFPVWLASSFIFRKFNRLYPNAGASYHWGNIAVSKVYGSG 100
                                   6999*********9999999977755555777777.55566666669**********99********************** PP

                 AA_permease_2  80 sawfnwfayvpvlasilsvaasyllnalgp.......dlqgntwltyliaiaililvalinirgikesakiqnilgilkil 153
                                    +w+ ++ay+++++ i++ a++y   +l++        l  n++ ++ ++ + + ++ + +++g + +ak++     + + 
  gi|13542254|ref|NP_111942.1| 101 QSWIITLAYLLSIPPIVIPAGEYTGDLLYSigaipqtAL-SNPVEIFSLGTFWVFVTLVASLLGARPTAKLTELFLAVEV- 179
                                   ************************888877665665432.3577788888888888888899******************. PP

                 AA_permease_2 154 lpliiliilglitvdgggfsslstetdtffpn.gwpgv.....llgllivlwsfdGfesaanvsee.vkk.kdvpkaifig 226
                                    ++++++++++  ++ +  + +s    ++f   + + +     l++l+i++ ++dG+e  ++ see v + +    +++ig
  gi|13542254|ref|NP_111942.1| 180 SVIAMFVVIAVMSLHDSVVNRPSI---SWFIPpIASRNeyvnlLSSLPIIATVLDGWEIDSYASEEsVNReRWPGTTGVIG 257
                                   8*************9999995533...345442444334457799*********************644435688888*** PP

                 AA_permease_2 227 llivlvlyllvniaflgvvpddeian.lsnlgsvaalffeavggkvvaiivvilialsllgaintavigssrvlealardg 306
                                   l++v+ +y++++ +++  vp++ +++ +++l         ++ ++  ai++ ++++ s + ++   +++ sr  +a++r+g
  gi|13542254|ref|NP_111942.1| 258 LVLVFTIYVVTMTLMQSEVPIKVLSSsVDPLY-----AWGMFVAPKYAIVMDLAVIASTASSLWLTTYILSRAWYAMSREG 333
                                   ***********************965155543.....5566677899********************************** PP

                 AA_permease_2 307 vlPrffakvn.kfgspiraiiltaivslillllfllas..saaynfllsvsslgliisyllliigalilrkkrphl..krp 382
                                    lP+++   +  +  p++++il+  ++ ++ +l++++   +  +++lls s ++l+  + + ++++++l  ++++l  ++ 
  gi|13542254|ref|NP_111942.1| 334 LLPSYLGYLSkTRLVPYVGLILISALAELVNFLMIFSRsiEGFFSVLLSFSGVFLMAEFSMDSLTGIVLFLRNKDLefRKL 414
                                   **********7799*************9999999998799**********************************9974555 PP

                 AA_permease_2 383 gkilvaiigalfllfllva 401
                                   + i v+ + +++++ ++  
  gi|13542254|ref|NP_111942.1| 415 YLI-VSVLTFVSFTAMI-C 431
                                   544.4444444443333.2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (471 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       763  (0.0425568); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.50
# Mc/sec: 2808.41
//
Query:       gi|13542255|ref|NP_111943.1|  [L=928]
Description: ABC-type peptide transport system, solute-binding component [Thermoplasma volcanium GSS1]
Scores for complete 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  119.4   6.6    2.6e-34  118.8   6.6    1.3  1  SBP_bac_5  Bacterial extracellular solute-binding proteins, f


Domain annotation for each model (and alignments):
>> SBP_bac_5  Bacterial extracellular solute-binding proteins, family 5 Middle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.8   6.6   1.5e-38   2.6e-34      16     375 ..     383     822 ..     343     824 .. 0.82

  Alignments for each domain:
  == domain 1  score: 118.8 bits;  conditional E-value: 1.5e-38
                                   TTTEEEEEE-TT-B-TTSSB-SHHHHHHHHHHHHTGGGHCTTHHHHHC................TCTEEEEEEEETTEEEE CS
                     SBP_bac_5  16 DgktytfkLRkgvkFsDGtpltAeDvvfsferlldpdtasgyasllee................dqdikkveavddytvrf 80 
                                       ytf++R ++++++G+p+tA Dv++s+ r l   ++s+++  +                  + +    ++  ++ ++f
  gi|13542255|ref|NP_111943.1| 383 PYENYTFHIRSNATWQNGQPVTAWDVEYSIARSLLFVDGSPSTPGWIRaqyllpgnyytsntfwNITQNITVNNATNNITF 463
                                   5668******************************9999999988886699*************855555556666777888 PP

                                   EESSE.TT.TTTTHCHHHHHHHGC.....................CHTCTCTTTTTGTTTSE-BSSSEEEEEEETTTEEEE CS
                     SBP_bac_5  81 tlkkp.na.lfltllaavpasiak.....................kaaekeddkdkdtnekpvgtGPYklkefkpgqkivl 138
                                   ++ +p  + l ++++aa+   i                       +   +++ +d++   ++   GPY ++  +p ++ivl
  gi|13542255|ref|NP_111943.1| 464 HFQEPlSPvLVFNIFAAIGGEILDpqwlqehgagipwspegfkeyQTEGNAGSYDEYVEHNVFADGPYEIAYQVPSSTIVL 544
                                   88888555579999******9999********************99999999999999999999***************** PP

                                   EE-TTS.....TTTSCSSSSEEEEEE-.SHHHHHHHHHTTSSSEEESTTCCTHCHHHHHTTEEE..EEEEEEEEEEEEEET CS
                     SBP_bac_5 139 ernpdY.....wgggkpkldriefkvipdsdaraaalqsGeiddvaepppsdieqlkeakglkv..lyespgggvtylafN 212
                                    +np++     w   +pk+ +i++++i++ ++r++a++s  +  + ++p+s++ +++  ++  +  +y ++ +g++y+afN
  gi|13542255|ref|NP_111943.1| 545 IKNPYFsppgpW-YPAPKIGEIIIEYISSTSTRVLAMKSQHA-SAISIPTSYWSEVESLEKQGIakVYPFNMLGIYYYAFN 623
                                   *****9888888.8999**********8888888888*****.777888888888866666666667************** PP

                                   TT................STGGGSHHHHHHHHHHS-HHHHHHHC.....TTTSSEEESSS.STTTSTTCCSCHCCCSHH.. CS
                     SBP_bac_5 213 tk................kppfddkrvRqAlsyAiDreeivkav.....legyatpansl.lppsspgadeeykpayka.. 269
                                   ++                 + f   + R+A++yA++++++++       ++ + +  ++  l+ ++ g++ + + ++++  
  gi|13542255|ref|NP_111943.1| 624 FNinssildiyyhganvpEYLFTSLNARRAFAYAYPYQQYLDYDvgnaiYNITFGERYAGvLAKGMLGYQSIGELNNTTtg 704
                                   *****************999******************9987554555555444444444466666666665555554466 PP

                                   ...SHHHHHHHHHHHTT-BCSSTSCEETC......EEEEEEEEETTSHHHHHHHHHHHHHHHHT..TEEEEEEEE.CHH.. CS
                     SBP_bac_5 270 ...ydpekAkklLkeaGykdgdggglrek......klkltlllasgspaekaiaeliqqqlkki..Gikvevktv.dwa.. 336
                                      + +  A +++    + + + ++ + k      +l++ +++ +g++++ a a+l+ q+l +i  G  + v +v d++  
  gi|13542255|ref|NP_111943.1| 705 vpyFSLSIAARYWSHVNLSKYGITESSGKylfdgkPLVIPIFVFAGDSVDLAGATLWGQYLSEIiqGASFPVIPVsDSEfs 785
                                   66699*******77666666654444444666669****************************545999999999666675 PP

                                   ...HHHHHHHHCTTESEEEEEEECTTSTTHHHHHHHHSTTCT CS
                     SBP_bac_5 337 ...atylervkdgdfdmillgwgadypdpdnflnpflsssga 375
                                            + ++ ++++l  w++dyp p+++l+++ ++s+ 
  gi|13542255|ref|NP_111943.1| 786 gflV-----NGQNPMPIYLATWFPDYPYPSDYLYSLAYPSNG 822
                                   5433.....55899*********************9998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (928 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       513  (0.0286129); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.73u 0.31s 00:00:01.04 Elapsed: 00:00:00.49
# Mc/sec: 5743.46
//
Query:       gi|13542256|ref|NP_111944.1|  [L=459]
Description: multidrug efflux permease [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-48  165.5  62.6    5.9e-35  120.8  27.6    2.1  2  MFS_1     Major Facilitator Superfamily
    4.5e-07   29.1  37.1    7.4e-07   28.4  12.2    2.3  2  Sugar_tr  Sugar (and other) transporter
  ------ inclusion threshold ------
        1.3    7.5  39.4       0.36    9.3  18.0    2.8  2  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 !  120.8  27.6   9.8e-39   5.9e-35       3     237 ..      17     236 ..      15     247 .. 0.89
   2 !   50.9  27.0   1.9e-17   1.1e-13       2     172 ..     256     442 ..     255     458 .. 0.88

  Alignments for each domain:
  == domain 1  score: 120.8 bits;  conditional E-value: 9.8e-39
                         MFS_1   3 laaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfas 83 
                                   l+ +++a++++i+++alp  +++ + +++s+++++++ y l + v+++p + ++ ++G + ++l+g+l+f++++l++++++
  gi|13542256|ref|NP_111944.1|  17 LGSLMAAIDSTIVFLALP-SMGSYFSANVSSLSWIVVSYILSSTVFMIPSSDIMRKVGKKALYLAGFLIFGFSSLIIAVSP 96 
                                   7899**************.9*****************************************************88888646 PP

                         MFS_1  84 slwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivslla 164
                                   ++ + +++r++ G+gag+l ++g+ ++ d fp++erg+a+g+ s+++++G+++gp+lgg+l+ ++ Wr+vf+i+ +++++a
  gi|13542256|ref|NP_111944.1|  97 TIIIAIIFRFVEGIGAGFLSAVGIPILLDAFPPQERGKAVGINSISWAIGTLVGPVLGGYLV-LYDWRYVFLINVPIGVVA 176
                                   666***********************************************************.****************** PP

                         MFS_1 165 fvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsglltllplylqev 237
                                   f l   l++ ++ +++r +           pl+  ++a+l +      + +++++f  ++++ +++p+++ ++
  gi|13542256|ref|NP_111944.1| 177 FAL--GLIRIPKYQKERAKRFNP------IPLLG-LSAFLIPL----TIGISFINFYYLAAAAIMFPIFIITQ 236
                                   887..888777777777755444......56666.88999988....88888888777777888888876555 PP

  == domain 2  score: 50.9 bits;  conditional E-value: 1.9e-17
                         MFS_1   2 llaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrr.vlllglllfalglllllf 81 
                                   ++a  l al+++ ++ al+++l+ +l++s  ++ l l +y l++++++++ G l dr Gr + +l +gl++ a+g+++++ 
  gi|13542256|ref|NP_111944.1| 256 SIASTLQALSFFGVLYALSMYLQISLHYSSLTAALFLFTYPLASMISNPLSGMLYDRTGRGPlLLGAGLVMQAFGIFMAA- 335
                                   68999**********************************************************************44444. PP

                         MFS_1  82 asslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslg............. 149
                                     ++ l+ v  +++G+g++++++ + ++++d + ++ rg a++ l +  +++ i+g  + +l++s+++             
  gi|13542256|ref|NP_111944.1| 336 -YTMKLIPVYLFIAGFGGSMFWAPSTTMVVDAAGPKFRGIANSSLFTLRNMSLIIGISIFPLFVSAFSsvksssiiitasg 415
                                   .77889**************************************************99999999999999999***99999 PP

                         MFS_1 150 ...Wrav.fyilaivsllafvlfllll 172
                                      ++a+ fy++ ++sl ++ l+ l+ 
  gi|13542256|ref|NP_111944.1| 416 inlYSATsFYLMMVASLSVLALIPLVS 442
                                   999444459999999999866443333 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4  12.2   1.2e-10   7.4e-07      44     189 ..      43     181 ..       9     194 .. 0.82
   2 !    6.6  16.9   0.00049       2.9     274     415 ..     269     417 ..     215     443 .. 0.55

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 1.2e-10
                                   ...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHH.H CS
                      Sugar_tr  44 ssvlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvl.v 123
                                     + +++iv ++++ +++  + ++ ++ ++G+k  +l++ ++f  +++++a+++   ++ + i+ R++ Gig+G+ s++ +
  gi|13542256|ref|NP_111944.1|  43 NVSSLSWIVVSYILSSTVFMIPSSDIMRKVGKKALYLAGFLIFGFSSLIIAVSP---TIIIAIIFRFVEGIGAGFLSAVgI 120
                                   456789************************************************...9****************9886538 PP

                                   HHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-TTHHHHHHHCCHHHHHHHHHHGG CS
                      Sugar_tr 124 PmyisEiApkklRgalvslyqlaitfGilvaaifglglnktsnadgwrillglqlvpallllilll 189
                                   P++++ + p++ Rg+ v+++  ++++G lv+ ++g  l  + +   wr+ + +++ + ++ ++l+l
  gi|13542256|ref|NP_111944.1| 121 PILLDAF-PPQERGKAVGINSISWAIGTLVGPVLGGYLVLY-D---WRYVFLINVPIGVVAFALGL 181
                                   8888866.8889********************999776554.4...89999998888887777664 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.00049
                                   HHHTTTHHHHSS-THHHHHHHHHHHHHHHHHHHHH....HHHHHS-SHHHHHHHHHHHHHHHHHHH..HHHHTTSS...CH CS
                      Sugar_tr 274 myysptifenlglsksllvtiivgvvnfvatfvai....flvdrfGRRtllllGaagmaicfvilgivalllvakskaasi 350
                                     y+ +++ ++ l  s l+ +++ ++  +a++++     +l dr+GR +lll  +++m ++ ++++    +++ k      
  gi|13542256|ref|NP_111944.1| 269 VLYALSMYLQISLHYSSLTAALFLFTYPLASMISNplsgMLYDRTGRGPLLLGAGLVMQAFGIFMA----AYTMK------ 339
                                   345555555555555544444444444444444432233666777777777777777777666665....33334...... PP

                                   HHHHHHHHHHHHH..HTTTTHHHHHHHHHHSHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHH..............T CS
                      Sugar_tr 351 vaivfialfialf..algwgpvpwvlvsElfpqsvRskalaiavavnwlanflisllfpiiteaig..............g 415
                                     ++ ++lfia f  ++ w+p    +v + + +++R++a +  +++ +++ ++   +fp +++a +              +
  gi|13542256|ref|NP_111944.1| 340 --LIPVYLFIAGFggSMFWAPST-TMVVDAAGPKFRGIANSSLFTLRNMSLIIGISIFPLFVSAFSsvksssiiitasgiN 417
                                   ..223333443331144455555.445666666777777776666666666666666666666666444222222222222 PP

>> MFS_2  MFS/sugar transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   9.4   0.00028       1.7     253     343 ..      39     127 ..      10     161 .. 0.80
   2 ?    9.3  18.0     6e-05      0.36      19     199 ..     272     450 ..     253     459 .] 0.77

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.00028
                         MFS_2 253 yvlgngsaasvfllvvtisallgiplwqplakrlgkkntyllgalltivllvlvlllqpsnlllflvllviagfgvgvaal 333
                                   y+  n s  s++ +  ++s++++++  + + ++ gkk++yl+g+l+  + ++++ +     +++++++ ++ g+g+g++  
  gi|13542256|ref|NP_111944.1|  39 YFSANVSSLSWIVVSYILSSTVFMIPSSDIMRKVGKKALYLAGFLIFGFSSLIIAVS--PTIIIAIIFRFVEGIGAGFLSA 117
                                   555577788999999999*************************99887777666555..8899999*********988888 PP

                         MFS_2 334 lpwsmladvv 343
                                   +   +l d++
  gi|13542256|ref|NP_111944.1| 118 VGIPILLDAF 127
                                   8777777665 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 6e-05
                         MFS_2  19 ylliFytdvlglsaalvglvllvarlvDaitDpivGtlidktstrwGrrrPwlllsaiilavsiillftppelsqsakfiw 99 
                                    l++++   l  s   ++l+l+++ l + i++p++G+l d+t    Gr  P+ll +++++ ++ i++ +      + k+i 
  gi|13542256|ref|NP_111944.1| 272 ALSMYLQISLHYSSLTAALFLFTYPLASMISNPLSGMLYDRT----GR-GPLLLGAGLVMQAFGIFMAAY-----TMKLIP 342
                                   378999999999****************************97....55.578899888888555544444.....356776 PP

                         MFS_2 100 llvtyillrilytlfeipyvslvpvltkdydeRtsltsvrsflsvlggvlaailafllvlilgg...........lkserk 169
                                   ++++  +     ++f  p++++v+ + + ++ R  ++s  ++l ++  +++  + +l+v ++++           + +  +
  gi|13542256|ref|NP_111944.1| 343 VYLFIAG--FGGSMFWAPSTTMVVDA-AGPKFRGIANSSLFTLRNMSLIIGISIFPLFVSAFSSvksssiiitasGINLYS 420
                                   6666555..56899999999999988.67777777777777777777777777777777777777777****999788889 PP

                         MFS_2 170 gylifaliialLmllgviivvlgtkervem 199
                                   +++ ++++ a L++l+ i +v++ + ++ +
  gi|13542256|ref|NP_111944.1| 421 ATSFYLMMVASLSVLALIPLVSYARTKKTA 450
                                   999999999999999999999999988665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (459 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       720  (0.0401584); expected 358.6 (0.02)
Passed bias filter:                      207  (0.0115455); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 3044.38
//
Query:       gi|13542257|ref|NP_111945.1|  [L=242]
Description: flagellin [Thermoplasma volcanium GSS1]
Scores for complete 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  134.7  11.1    3.7e-39  134.5  11.1    1.0  1  Arch_flagellin  Archaebacterial flagellin
  ------ inclusion threshold ------
      0.031   13.1   0.1      0.047   12.5   0.1    1.2  1  MscS_TM         Mechanosensitive ion channel inner membrane d


Domain annotation for each model (and alignments):
>> Arch_flagellin  Archaebacterial flagellin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.5  11.1   4.2e-43   3.7e-39       1     164 []      27     228 ..      27     228 .. 0.96

  Alignments for each domain:
  == domain 1  score: 134.5 bits;  conditional E-value: 4.2e-43
                                   X--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT--EEEEEEE....EEE-SSSSSEEEEEEE--T CS
                Arch_flagellin   1 GfvgigtlIvfIAmVlVAAvaagvlintagflqqkaqstgeesteqvssgleitgdvg....dsatngtineitiyvklna 77 
                                   +++gig lIvfIAm+lVAAvaa+vli+tag lqqka+stg ++ +qvs+g+ i +++g     ++ +g i++++i v  + 
  gi|13542257|ref|NP_111945.1|  27 AESGIGVLIVFIAMILVAAVAASVLIHTAGILQQKASSTGTTTIQQVSTGVIINQIIGydnaSPPESGGISYLAIFVSISS 107
                                   689*******************************************************999999999************** PP

                                   TS--EEGGG-EEEEEESS--EE--E..................................................T-EE-T CS
                Arch_flagellin  78 Gsspidlnkttisvtddgqetlltad................................efgivvisdtdgsltngdevlek 126
                                   G++p+dl++tt+++t+ g+ ++l ++                                +fg++v  d + slt  ++vl+ 
  gi|13542257|ref|NP_111945.1| 108 GGTPVDLANTTVTLTVGGVTAVLVYNssvfadiagsgsanlfslpvwselsaknrnptSFGVIVNFDPSHSLTRHYPVLSV 188
                                   ******************666666666****************************************************** PP

                                   T-EEEEEEE--..TTT---TT-EEEEEEE-SSS--EEEEE CS
                Arch_flagellin 127 gekvelevnvn..eddgitagdevsvevvpenGasttief 164
                                   g+ +++ +nv+    ++it+++ vs++v+pe+G +++i+f
  gi|13542257|ref|NP_111945.1| 189 GDSAAIIINVTntFGSNITQDSVVSGQVTPETGTPAIIQF 228
                                   **********9985667*********************98 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 ?   12.5   0.1   5.3e-06     0.047     134     194 ..      10      69 ..       6      82 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.3e-06
                       MscS_TM 134 lplllvlilaealsdalardvlGrlaflllllllavflarllrpalglyankkeeeknslr 194
                                   l ll+ +  + +++d+ a++ +G l+++++++l+a ++a++l ++ g +++k  +++++  
  gi|13542257|ref|NP_111945.1|  10 LKLLNSIKRIFKTDDSKAESGIGVLIVFIAMILVAAVAASVLIHTAGILQQKASSTGTT-T 69 
                                   5667777778899**********************************999997666554.3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       943  (0.0525964); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); 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 0.25s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1868.57
//
Query:       gi|13542258|ref|NP_111946.1|  [L=278]
Description: transposase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    0.00013   22.0   0.4    0.00037   20.6   0.4    1.7  1  HTH_21      HTH-like domain
    0.00057   20.0   0.1     0.0097   16.0   0.0    2.5  2  HTH_28      Helix-turn-helix domain
     0.0014   18.4   0.0     0.0093   15.7   0.0    2.4  2  HTH_23      Homeodomain-like domain
  ------ inclusion threshold ------
      0.012   15.2   0.0      0.031   13.8   0.0    1.7  1  Sigma70_r4  Sigma-70, region 4
      0.012   15.2   0.0      0.027   14.1   0.0    1.6  1  CENP-B_N    CENP-B N-terminal DNA-binding domain
      0.019   14.8   0.5        0.1   12.5   0.0    2.2  2  IF2_N       Translation initiation factor IF-2, N-terminal re
      0.023   14.9   0.6         22    5.3   0.0    3.5  3  HTH_17      Helix-turn-helix domain
      0.036   14.1   0.0       0.11   12.6   0.0    1.7  1  HTH_3       Helix-turn-helix
      0.099   12.6   0.2        1.4    8.9   0.0    2.7  3  Mor         Mor transcription activator family
       0.14   12.3   0.0       0.22   11.7   0.0    1.3  1  MRP-L20     Mitochondrial ribosomal protein subunit L20
       0.19   11.8   0.0       0.41   10.7   0.0    1.6  1  HTH_29      Winged helix-turn helix


Domain annotation for each model (and alignments):
>> HTH_21  HTH-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.4   2.2e-07   0.00037       6      48 ..      58      98 ..      54     104 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 2.2e-07
                        HTH_21  6 llal.ireifeeskgrYGyrriwaeLrreggvrvnhkrVrRlMr 48
                                  ++++ i+e+++++k   G+r i+  Lr + g++v+ +r++  M+
  gi|13542258|ref|NP_111946.1| 58 DEKRfIDELWDKYK--IGSRTIYYLLRSK-GMNVSYYRIYNYMK 98
                                  56777******986..*************.79***********8 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0     6e-06    0.0097       2      34 ..      10      42 ..       9      43 .. 0.93
   2 ?    1.0   0.0      0.29   4.6e+02      21      34 ..      69      82 ..      63      83 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 6e-06
                        HTH_28  2 RleiikllaaGhsvreaArelgisrrtvyrWik 34
                                  R+ ii  +++G  v+e+A+ +++++r++++ ++
  gi|13542258|ref|NP_111946.1| 10 RKFIIDSVKRGYKVSELAKMFNVTPRRIQQILH 42
                                  8899************************99876 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.29
                        HTH_28 21 elgisrrtvyrWik 34
                                  ++ i++rt+y +++
  gi|13542258|ref|NP_111946.1| 69 KYKIGSRTIYYLLR 82
                                  68899*****9987 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   5.7e-06    0.0093      10      40 ..      13      43 ..       6      49 .. 0.88
   2 ?   -2.2   0.0       2.5     4e+03      26      39 ..      69      82 ..      68      83 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 5.7e-06
                        HTH_23 10 illllaeGlsvreIAreLgvsrrTvyrwlkr 40
                                  i+  +++G+ v+e A++++v++r ++++l+ 
  gi|13542258|ref|NP_111946.1| 13 IIDSVKRGYKVSELAKMFNVTPRRIQQILHE 43
                                  7888999*********************985 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.5
                        HTH_23 26 eLgvsrrTvyrwlk 39
                                  ++ +  rT+y  l+
  gi|13542258|ref|NP_111946.1| 69 KYKIGSRTIYYLLR 82
                                  677889****8776 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   1.9e-05     0.031       5      43 ..       5      43 ..       2      45 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.9e-05
                                  S-HHHHHHHHHHHTTT--HHHHHHHHTS-HHHHHHHHHH CS
                    Sigma70_r4  5 LpererevlelrfgeglTleEIgerlgiSrerVrqiekr 43
                                  L+ ++r+ +  +  +g+  +E++++++++  r+ qi+++
  gi|13542258|ref|NP_111946.1|  5 LNSEDRKFIIDSVKRGYKVSELAKMFNVTPRRIQQILHE 43
                                  778888888889999999******************996 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 ?   14.1   0.0   1.7e-05     0.027      15      44 ..      13      42 ..       7      46 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.7e-05
                                  HHHHHHCTT-HHHHHHHHT--CCHHHHHHH CS
                      CENP-B_N 15 vIqrleegeSkaelarrfnvpestlsdilk 44
                                  +I ++ +g  + ela++fnv +  + +il 
  gi|13542258|ref|NP_111946.1| 13 IIDSVKRGYKVSELAKMFNVTPRRIQQILH 42
                                  899999**********************96 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 ?   12.5   0.0   6.1e-05       0.1       5      45 ..      22      61 ..      19      66 .. 0.85
   2 ?   -0.3   0.1      0.61   9.9e+02       1      20 [.     144     163 ..     144     167 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.1e-05
                         IF2_N  5 rVyeLAkeLgvkskevikkLfkelGievkshsssLDeetae 45
                                   V+eLAk  +v++ ++ + L +++  +    +s L+e+++ 
  gi|13542258|ref|NP_111946.1| 22 KVSELAKMFNVTPRRIQQILHESASPD-SEKDSELTEDEKR 61
                                  7*******************8877777.8888888888876 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.61
                         IF2_N   1 mskirVyeLAkeLgvkskev 20 
                                   m ++ +   A+ L+++s  v
  gi|13542258|ref|NP_111946.1| 144 MTTKKILSYAESLKITSDVV 163
                                   778889999*****999765 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0     0.014        22       2      20 ..      21      39 ..      21      44 .. 0.88
   2 ?    4.6   0.1     0.022        36       9      27 ..      68      86 ..      63     101 .. 0.78
   3 ?    0.5   0.0      0.44   7.2e+02      21      44 ..     181     206 ..     174     210 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.014
                        HTH_17  2 ltveEaAelLgvsrstvyr 20
                                  ++v+E+A++++v ++ +++
  gi|13542258|ref|NP_111946.1| 21 YKVSELAKMFNVTPRRIQQ 39
                                  89************99987 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.022
                        HTH_17  9 elLgvsrstvyrlirrgel 27
                                  +  +++ +t+y l+r++  
  gi|13542258|ref|NP_111946.1| 68 DKYKIGSRTIYYLLRSKGM 86
                                  567999*********9975 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.44
                        HTH_17  21 lirrgelpaa..k.iGrrwriprsdle 44 
                                   +ir+g l  +  +    ++ri+r+ ++
  gi|13542258|ref|NP_111946.1| 181 MIRSGVL-SLiyNtSYVSYRIRRKGIQ 206
                                   7888888.7766356667999998665 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   6.5e-05      0.11       7      39 ..      18      50 ..      17      51 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6.5e-05
                                  HTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHH CS
                         HTH_3  7 qlglsqeeLAeklGvsrstisriEnGernPsle 39
                                  ++g+   eLA++ +v+++ i++i    ++P+ e
  gi|13542258|ref|NP_111946.1| 18 KRGYKVSELAKMFNVTPRRIQQILHESASPDSE 50
                                  7899*******************9998888765 PP

>> Mor  Mor transcription activator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0   0.00087       1.4      71      96 ..      19      44 ..       2      54 .. 0.80
   2 ?    0.0   0.0      0.51   8.2e+02      75      93 ..      63      81 ..      48      88 .. 0.83
   3 ?   -2.3   0.0       2.7   4.4e+03      15      44 ..     197     225 ..     193     227 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00087
                                  -SS-HHHHHHHHT--HHHHHHHHHHH CS
                           Mor 71 kGnnvaeLarkYglseqwiykiikrv 96
                                  +G +v+eLa+ ++++ ++i +i+++ 
  gi|13542258|ref|NP_111946.1| 19 RGYKVSELAKMFNVTPRRIQQILHES 44
                                  5999******************9875 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.51
                                  HHHHHHHHT--HHHHHHHH CS
                           Mor 75 vaeLarkYglseqwiykii 93
                                  + eL  kY++  ++iy  +
  gi|13542258|ref|NP_111946.1| 63 IDELWDKYKIGSRTIYYLL 81
                                  679999*********9776 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 2.7
                                   HHHHHHTS.S-....TTSHHHHHHHHHHHH CS
                           Mor  15 aaelkrlgeidealaeqigeevadalaahw 44 
                                   + ++ r+g i++ + ++ g +v  +l++ w
  gi|13542258|ref|NP_111946.1| 197 SYRIRRKG-IQDVVTDKNGSKVHLSLSKLW 225
                                   55667777.888888888888888887766 PP

>> MRP-L20  Mitochondrial ribosomal protein subunit L20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00014      0.22     105     145 ..      21      61 ..      19      76 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00014
                       MRP-L20 105 wsrkkLakkFgcsklfvsmvteapkekkkeveaeleavker 145
                                   + +++Lak+F++++  ++ +++ +++   e+++el++ ++r
  gi|13542258|ref|NP_111946.1|  21 YKVSELAKMFNVTPRRIQQILHESASPDSEKDSELTEDEKR 61 
                                   7899*****************88887777777776665554 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00025      0.41       1      34 [.      10      42 ..      10      46 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00025
                        HTH_29  1 RaqallllaeGvstvsqiAkllglsrrtvyrwlk 34
                                  R+ ++  +++G + vs++Ak+ ++++r ++ +l+
  gi|13542258|ref|NP_111946.1| 10 RKFIIDSVKRGYK-VSELAKMFNVTPRRIQQILH 42
                                  78899999****9.*************9998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       751  (0.0418874); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1959.53
//
Query:       gi|13542259|ref|NP_111947.1|  [L=158]
Description: GTP:adenosylcobinamide-phosphate guanylyltransferase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.2e-13   50.9   0.0    2.7e-13   50.6   0.0    1.1  1  NTP_transf_3  MobA-like NTP transferase domain
     0.0068   16.4   0.0     0.0086   16.0   0.0    1.1  1  CTP_transf_3  Cytidylyltransferase
  ------ inclusion threshold ------
      0.027   14.5   0.2       0.04   14.0   0.2    1.3  1  ATP-grasp_3   ATP-grasp domain


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 !   50.6   0.0   4.4e-17   2.7e-13       4     126 ..       1     122 [.       1     133 [. 0.91

  Alignments for each domain:
  == domain 1  score: 50.6 bits;  conditional E-value: 4.4e-17
                                   EEESS-TTTTT.THHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSHC..HHHHHHTTCTS-EEE-TTSS-SHHHHHHHHHH CS
                  NTP_transf_3   4 LAGGrSsRmgg.dKallplggkpllervldalraagvdevvvvggde..evlaalarlgvrvvededpgkgplaslaaalr 81 
                                   +AGG ++R+g+ +Kal++  gkpl+ r++d +r   +de++v+ +++  ++++ l   gv +++     +g +  l   l+
  gi|13542259|ref|NP_111947.1|   1 MAGGLGTRFGEpEKALVKASGKPLIGRLIDEARNI-CDEIFVSIDPSmvNIKNFLGTVGVNIIAKN--REGYVIDLNFSLN 78 
                                   59********99***********************.*********974467888888899999987..79*********** PP

                                   HH.SSSCEEEEETT-TT--HHHHHHHHHCHHHHTSSEEEEESSSE CS
                  NTP_transf_3  82 aaadadavlvlacDmPlltpelverllaaaaasgadvvvptyege 126
                                   ++ ++ ++lvl++D+ + +p++++++++ a  + +d++ +t  g+
  gi|13542259|ref|NP_111947.1|  79 SI-NTYPILVLSADLYFKDPSILRKFTDMAMGRTEDIITFTLHGN 122
                                   *9.8*************************9999999998887665 PP

>> CTP_transf_3  Cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   1.4e-06    0.0086      14      50 ..      12      46 ..       7      67 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.4e-06
                                  TTGGGSEETTEEHHHHHHHHHHHTTTTSEEEEEES-H CS
                  CTP_transf_3 14 pgKnlldlggkpliayvleaalkskafekvivaTDse 50
                                  p+K+l + +gkpli +++++a++    ++++v+ D  
  gi|13542259|ref|NP_111947.1| 12 PEKALVKASGKPLIGRLIDEARN--ICDEIFVSIDPS 46
                                  89*********************..899999998843 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.2   6.6e-06      0.04     126     155 ..      45      74 ..      16      78 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 6.6e-06
                                   HHHTTSTT--EEEEEEEEESS.SEEEEEEE CS
                   ATP-grasp_3 126 evvekleglaGyvGvDlvlkdeepyviEvN 155
                                     + ++++ +G vGv+++ k+ e yvi+ N
  gi|13542259|ref|NP_111947.1|  45 PSMVNIKNFLGTVGVNIIAKNREGYVIDLN 74 
                                   556678899*******************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       340  (0.0189637); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 1186.72
//
Query:       gi|13542260|ref|NP_111948.1|  [L=247]
Description: ABC-type Fe3+-siderophores transporter, ATPase component [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-28   99.4   0.0    3.3e-28   98.9   0.0    1.2  1  ABC_tran         ABC transporter
    2.1e-09   37.6   0.2    0.00028   20.8   0.0    2.1  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    4.3e-09   36.1   1.0      6e-07   29.1   1.0    2.1  1  SMC_N            RecF/RecN/SMC N terminal domain
     0.0021   16.8   6.7      0.064   11.9   0.1    2.1  2  AAA_13           AAA domain
     0.0067   17.0   0.3      0.011   16.3   0.3    1.4  1  AAA_23           AAA domain
     0.0078   16.4   0.1      0.053   13.7   0.0    2.1  2  AAA_33           AAA domain
  ------ inclusion threshold ------
      0.011   16.0   0.1      0.034   14.4   0.1    1.8  1  SbcCD_C          Putative exonuclease SbcCD, C subunit
      0.011   15.6   0.8       0.47   10.4   0.1    2.3  2  MobB             Molybdopterin guanine dinucleotide synthesis
      0.013   15.8   0.0      0.028   14.8   0.0    1.5  1  AAA_16           AAA ATPase domain
       0.02   14.7   0.5        0.7    9.6   0.1    2.2  2  ATP_bind_1       Conserved hypothetical ATP binding protein
      0.032   14.3   0.9        1.5    8.8   0.8    2.8  2  AAA_14           AAA domain
      0.046   13.4   0.4        0.1   12.2   0.1    1.7  2  Thymidylate_kin  Thymidylate kinase
      0.089   12.5   0.2        1.9    8.1   0.0    2.2  2  AAA_24           AAA domain
      0.095   12.3   1.2        1.9    8.0   0.3    2.2  2  SRP54            SRP54-type protein, GTPase domain
       0.15   12.6   0.7       0.41   11.2   0.7    1.9  1  AAA_18           AAA domain
       0.16   11.6   1.6       0.32   10.6   0.8    1.9  2  cobW             CobW/HypB/UreG, nucleotide-binding domain
       0.25   11.1   0.3       0.41   10.3   0.3    1.6  1  AAA_30           AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.9   0.0   3.2e-31   3.3e-28       1     136 [.      16     156 ..      16     157 .. 0.95

  Alignments for each domain:
  == domain 1  score: 98.9 bits;  conditional E-value: 3.2e-31
                                   EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                      ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren.. 79 
                                   l+ +++++ eg++ +i G nG+GK+tL+k l+g lkp+ G+il+dgk++++ ++++  ++++v++qe+ +  + tv +   
  gi|13542260|ref|NP_111948.1|  16 LNGLNFTITEGSINGIGGLNGSGKTTLVKNLYGFLKPEGGTILIDGKSVESMPIKEIASKVSVVQQEQPIPMNFTVNDVvs 96 
                                   6899***************************************************************9999999999999* PP

                                   .......HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                   .......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  80 .......esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                          +++  +++ ls  g+ +lk++      s+LSgG+k+ v+ a+al ++ k +llDEp+
  gi|13542260|ref|NP_111948.1|  97 lsgysrkDASISVDECLSLCGILQLKNREF----STLSGGEKRIVMFAAALYQNTKYVLLDEPM 156
                                   **9775444455*****************9....*****************************7 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.4   1.9e-05      0.02       1      69 [.      28      82 ..      28     110 .. 0.65
   2 !   20.8   0.0   2.6e-07   0.00028     230     300 ..     122     189 ..     114     191 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.9e-05
                        AAA_21  1 lnvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeieeflsqg 69
                                  +n++ G NgsGK++L + l+++               + gg++ i++++ +  p ++++  ++ +++q+
  gi|13542260|ref|NP_111948.1| 28 INGIGGLNGSGKTTLVKNLYGFLK-------------PEGGTILIDGKSVESMPIKEIASKVS-VVQQE 82
                                  799****************99864.............44444444444444444444444444.44444 PP

  == domain 2  score: 20.8 bits;  conditional E-value: 2.6e-07
                        AAA_21 230 qelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSpl 300
                                   +++ ++ lS G kr+  +++a l+++ k   +l+DEp ++L+   + +++ l+++ +r g  +i+++H+  
  gi|13542260|ref|NP_111948.1| 122 KNREFSTLSGGEKRI-VMFAAALYQNTK--YVLLDEPMTFLDIDKTVTVMSLIRQMKRMGKTIIVVSHDIN 189
                                   56778999*******.666666666664..5*************************************965 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   1.0   5.7e-10     6e-07      24     204 ..      26     193 ..      12     206 .. 0.70

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 5.7e-10
                                   SSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N  24 ksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsisrrvk 104
                                    s++ i G NGSGK+ l+  +    G      l+ e  + li   k+ +s+   e++  ++  +++++i   +++++  v+
  gi|13542260|ref|NP_111948.1|  26 GSINGIGGLNGSGKTTLVKNL---YG-----FLKPEGGTILIDG-KSVESMPIKEIASKVSVVQQEQPI-PMNFTVNDVVS 96 
                                   568999999999999999999...56.....5888889999998.444444444444433333333222.23345555555 PP

                                   TTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 105 rkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellke 185
                                    +g s+     +  +   +  +l+ ++ + ++LSgGek +v+    fA   ++ +  +llDe    LD  ++  v +l+++
  gi|13542260|ref|NP_111948.1|  97 LSGYSRKDASISVDECLSLCGILQLKNREFSTLSGGEKRIVM----FAAALYQNTKYVLLDEPMTFLDIDKTVTVMSLIRQ 173
                                   54444433333333445566667777777789********87....778889999*************************8 PP

                                   HCTT.SEEEEE-SSHHHCCC CS
                                   xxxx.xxxxxxxxxxxxxxx RF
                         SMC_N 186 kskn.aQfivislreemlek 204
                                    +     +iv+s++ ++l +
  gi|13542260|ref|NP_111948.1| 174 MKRMgKTIIVVSHDINFLYN 193
                                   87764789999999887755 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.8   2.6    0.0021       2.2      17      37 ..      27      47 ..      21      63 .. 0.86
   2 !   11.9   0.1   6.1e-05     0.064     495     574 ..     124     191 ..      80     198 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0021
                        AAA_13 17 riNliYGwNGaGKTtLSrllr 37
                                   iN i G NG+GKTtL + l 
  gi|13542260|ref|NP_111948.1| 27 SINGIGGLNGSGKTTLVKNLY 47
                                  68999***********87765 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 6.1e-05
                        AAA_13 495 qaaetLSeGEktaIaflYFlkslkeddseigkdkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHnleff 574
                                       tLS GEk ++ f    ++l    +   + k v +D P+  LD +    v+sli++        k +++  H ++f+
  gi|13542260|ref|NP_111948.1| 124 REFSTLSGGEKRIVMF---AAALY---Q---NTKYVLLDEPMTFLDIDKTVTVMSLIRQMK---RMGKTIIVVSHDINFL 191
                                   4678999999999875...57777...2...33579**********************997...89999********998 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.3     1e-05     0.011      16      36 ..      20      43 ..       7      83 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1e-05
                        AAA_23 16 dF...skgltlItGpNGaGKTTil 36
                                  +F   +  ++ I G NG+GKTT++
  gi|13542260|ref|NP_111948.1| 20 NFtitEGSINGIGGLNGSGKTTLV 43
                                  455566789*************97 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0     5e-05     0.053       6      26 ..      33      57 ..      31      99 .. 0.82
   2 ?   -0.2   0.0      0.94   9.9e+02      15      33 ..     139     170 ..     138     187 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5e-05
                        AAA_33  6 GlpGsGKstlaerl...lkklg.av 26
                                  Gl+GsGK+tl+++l   lk++g ++
  gi|13542260|ref|NP_111948.1| 33 GLNGSGKTTLVKNLygfLKPEGgTI 57
                                  9************955555555444 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.94
                        AAA_33  15 laerllkklgavllssdt.............l 33 
                                   +a  l++++++vll+++              l
  gi|13542260|ref|NP_111948.1| 139 FAAALYQNTKYVLLDEPMtfldidktvtvmsL 170
                                   67778888888888887644444444444443 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   3.2e-05     0.034      27      89 ..     123     172 ..     119     173 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.2e-05
                       SbcCD_C  27 srssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllelle 89 
                                   +r+++tlSGGek     ++++aa+ ++ ++          v+LDE    lD +++ t+++l++
  gi|13542260|ref|NP_111948.1| 123 NREFSTLSGGEK----RIVMFAAALYQNTK---------YVLLDEPMTFLDIDKTVTVMSLIR 172
                                   5899********....66666655554444.........7*******************9987 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   0.00045      0.47       3      29 ..      30      56 ..      28      70 .. 0.87
   2 ?    3.6   0.1     0.055        58      12      36 ..     163     187 ..     157     191 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00045
                          MobB  3 givgksgsGKTtLleklipelkarglr 29
                                  gi g +gsGKTtL+++l   lk +g +
  gi|13542260|ref|NP_111948.1| 30 GIGGLNGSGKTTLVKNLYGFLKPEGGT 56
                                  577999***********9999988865 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.055
                          MobB  12 KTtLleklipelkarglrvgtiKha 36 
                                   KT  +  li+++k+ g ++ ++ h+
  gi|13542260|ref|NP_111948.1| 163 KTVTVMSLIRQMKRMGKTIIVVSHD 187
                                   99********************997 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   2.7e-05     0.028      29      84 ..      31      81 ..      21      98 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.7e-05
                        AAA_16 29 lsGesGvGKsslvrellralekdg.giflrgkcdqlesaipysalaqalareellrq 84
                                  + G  G+GK++lv+ l+  l+ +g  i++ gk +++       ++ +++++ ++++q
  gi|13542260|ref|NP_111948.1| 31 IGGLNGSGKTTLVKNLYGFLKPEGgTILIDGKSVES------MPIKEIASKVSVVQQ 81
                                  57999************99999974666*******9......446666666566665 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.1   0.00067       0.7       3      24 ..      33      54 ..      31      59 .. 0.84
   2 ?    3.6   0.0     0.046        49      90     142 ..     146     198 ..      88     208 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00067
                    ATP_bind_1  3 GpaGsGKttfvgalseilelrg 24
                                  G  GsGKtt+v++l+ +l+ +g
  gi|13542260|ref|NP_111948.1| 33 GLNGSGKTTLVKNLYGFLKPEG 54
                                  889************9988765 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.046
                    ATP_bind_1  90 eddyllfDtPGQ.ielfthseslakiveeLesefalvvvyLvDsqrltdptkfi 142
                                   +++y+l+D P   + + + + +++ +++++++ +++++v+  D ++l +  +++
  gi|13542260|ref|NP_111948.1| 146 NTKYVLLDEPMTfLDIDKTVTVMS-LIRQMKRMGKTIIVVSHDINFLYNFCDYV 198
                                   557888888843156667777777.999***************99999877776 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.8    0.0015       1.5       4      37 ..      28      60 ..      25     189 .. 0.85
   2 ?   -0.6   0.0       1.2   1.2e+03      10      19 ..     174     183 ..     165     197 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0015
                        AAA_14  4 ilvitGaRrvGKTtllkqlikellvkkesilyin 37
                                  i  i G+  +GKTtl+k+l+  l  ++  ++ i+
  gi|13542260|ref|NP_111948.1| 28 INGIGGLNGSGKTTLVKNLYGFLK-PEGGTILID 60
                                  67799999**********985554.555555554 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.2
                        AAA_14  10 aRrvGKTtll 19 
                                   ++r+GKT ++
  gi|13542260|ref|NP_111948.1| 174 MKRMGKTIIV 183
                                   7899***986 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   9.8e-05       0.1       1      26 [.      31      56 ..      31      81 .. 0.89
   2 ?   -2.3   0.0       2.8     3e+03       9      30 ..     163     185 ..     161     187 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 9.8e-05
                                  EEESTTSSHHHHHHHHHHHHHHTTE. CS
               Thymidylate_kin  1 iEGlDGaGKttqaellkerlkeegik 26
                                  i Gl+G+GKtt +++l+  lk eg  
  gi|13542260|ref|NP_111948.1| 31 IGGLNGSGKTTLVKNLYGFLKPEGGT 56
                                  56****************99999854 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.8
                                   HHHHHHHHHHHHHHTTE..EEEE CS
               Thymidylate_kin   9 Kttqaellkerlkeegik.vvlt 30 
                                   Kt  ++ l + +k++g+  +v++
  gi|13542260|ref|NP_111948.1| 163 KTVTVMSLIRQMKRMGKTiIVVS 185
                                   88999999999999998766655 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.0    0.0018       1.9       9      44 ..      33      65 ..      29     150 .. 0.78
   2 ?    2.6   0.1     0.091        96     111     130 ..     167     186 ..     162     189 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0018
                        AAA_24  9 GpsgiGKTtlakelgpkplfidtekGlksldadkfp 44
                                  G +g+GKTtl+k+l     f+  e+G+  +d++ ++
  gi|13542260|ref|NP_111948.1| 33 GLNGSGKTTLVKNL---YGFLKPEGGTILIDGKSVE 65
                                  789***********...4455556665555555554 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.091
                        AAA_24 111 frrllkklqelrknvifiah 130
                                   +++l+++++ ++k++i+++h
  gi|13542260|ref|NP_111948.1| 167 VMSLIRQMKRMGKTIIVVSH 186
                                   6899***************9 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.3    0.0018       1.9       8      33 ..      33      58 ..      28      62 .. 0.84
   2 ?    2.7   0.0     0.079        83      13      39 ..     162     188 ..     160     190 .. 0.93

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0018
                                  ESTTSSHHHHHHHHHHHHHHTTS-EE CS
                         SRP54  8 GlqGaGKTttlaKLaallkkegkkvl 33
                                  Gl+G+GKTt +  L   lk eg ++l
  gi|13542260|ref|NP_111948.1| 33 GLNGSGKTTLVKNLYGFLKPEGGTIL 58
                                  9**********999988888876665 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.079
                                   SHHHHHHHHHHHHHHTTS-EEEEEEST CS
                         SRP54  13 GKTttlaKLaallkkegkkvllvaaDt 39 
                                    KT t+  L +++k++gk++++v+ D+
  gi|13542260|ref|NP_111948.1| 162 DKTVTVMSLIRQMKRMGKTIIVVSHDI 188
                                   69**********************996 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.7   0.00039      0.41       3      19 ..      31      51 ..      30     202 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00039
                        AAA_18  3 ltGtpGvGKttlakeL....s 19
                                  + G  G+GKttl k+L    +
  gi|13542260|ref|NP_111948.1| 31 IGGLNGSGKTTLVKNLygflK 51
                                  89*************944433 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.8    0.0003      0.32       3      21 ..      29      47 ..      27      59 .. 0.83
   2 ?   -1.3   0.0       1.3   1.4e+03     139     149 ..     192     202 ..     152     225 .. 0.55

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0003
                                  EEEEESTTCCHHHHHHHHH CS
                          cobW  3 tvltGflGsGKTtLlnhll 21
                                   +++G  GsGKTtL+++l 
  gi|13542260|ref|NP_111948.1| 29 NGIGGLNGSGKTTLVKNLY 47
                                  5799************986 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.3
                                   HHTSSEEEEE- CS
                          cobW 139 laaadllvlnK 149
                                    +++d ++l K
  gi|13542260|ref|NP_111948.1| 192 YNFCDYVILMK 202
                                   23444444444 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.3   0.00039      0.41      17      50 ..      26      58 ..      19     187 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00039
                        AAA_30 17 gdrvavltGpAGtGKttalkalreaweaaggrvi 50
                                  g  +  + G  G+GKtt++k l   ++ +gg+++
  gi|13542260|ref|NP_111948.1| 26 G-SINGIGGLNGSGKTTLVKNLYGFLKPEGGTIL 58
                                  3.588899**************999999987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       586  (0.0326845); expected 358.6 (0.02)
Passed bias filter:                      515  (0.0287244); expected 358.6 (0.02)
Passed Vit filter:                        90  (0.0050198); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.45
# Mc/sec: 1653.53
//
Query:       gi|13542261|ref|NP_111949.1|  [L=153]
Description: hypothetical protein TVN1430 [Thermoplasma volcanium GSS1]
Scores for complete sequence (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   51.5   0.0    1.5e-13   51.1   0.0    1.2  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 !   51.1   0.0   8.1e-18   1.5e-13       2      98 ..      31     127 ..      29     129 .. 0.86

  Alignments for each domain:
  == domain 1  score: 51.1 bits;  conditional E-value: 8.1e-18
                                   TXSSB-HHHHHHHHHHHHHHHHHHHHTCCCT---SCEEEEEEEEEECCECTCEEEEEEEEEEE-SS-H..HHHHHHHHHH. CS
                          OsmC   2 dgsgpsPeelllaalasCfaitlravakkkgikledleveveaerdpegakgiteirlkvevkipgadseeklkklleka. 81 
                                   d++  sP+elll a+++C++ ++ ++++k++ +++++++ ve+e+  e ++ ++ +++++ +  ++ d ++k++++++++ 
  gi|13542261|ref|NP_111949.1|  31 DPNRHSPTELLLLAIGGCTSDDVLSILHKMRQDVKSYRCVVEGEKRSEHPRILKFANVSYIIN-GDVD-PDKARRAIHLSl 109
                                   566789*************************************99999999556666778885.4444.59*********9 PP

                                   HHHSHHHHHH.CT-SSSE CS
                          OsmC  82 ekrCpvsntl.kngvkve 98 
                                   +k+C+vs +  + gv+v+
  gi|13542261|ref|NP_111949.1| 110 KKYCSVSIMAeRGGVSVS 127
                                   *******99988888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.49
# Mc/sec: 936.54
//
Query:       gi|13542262|ref|NP_111950.1|  [L=164]
Description: hypothetical protein TVN1431 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.2e-06   26.9   0.2    3.8e-05   23.5   0.1    2.4  2  DUF1641     Protein of unknown function (DUF1641)
     0.0066   15.9   0.2     0.0093   15.4   0.2    1.2  1  Kv2channel  Kv2 voltage-gated K+ channel


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 ?    0.6   0.0      0.06   5.4e+02       9      19 ..      35      45 ..      29      46 .. 0.82
   2 !   23.5   0.1   4.2e-09   3.8e-05       3      37 ..     122     156 ..     120     158 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.06
                       DUF1641  9 vGlfgLlraLr 19
                                  v+l++Ll  ++
  gi|13542262|ref|NP_111950.1| 35 VSLMDLLEKMK 45
                                  79****98887 PP

  == domain 2  score: 23.5 bits;  conditional E-value: 4.2e-09
                       DUF1641   3 leepkpvGlfgLlraLrDPDVqrGLGfllalLKal 37 
                                    ++p+  + ++L+++L+DPD+++ ++ l++ +K l
  gi|13542262|ref|NP_111950.1| 122 IKNPQSFSALKLMALLKDPDISALITGLVNAAKVL 156
                                   69******************************987 PP

>> Kv2channel  Kv2 voltage-gated K+ channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.2     1e-06    0.0093      89     147 ..       5      65 ..       1      78 [. 0.73

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1e-06
                    Kv2channel  89 lqeqaekppv.yee..eiemeevvcpkdqLlvaqkevvtDmrsvssiDsfasCatDfteter 147
                                    qeq+++ p+  ++  e+ +++vv +kd ++ +  +++  m+    iD f s a D+t t+ 
  gi|13542262|ref|NP_111950.1|   5 KQEQQAQVPQeDQDdlEVLLNKVVENKDTIV-SLMDLLEKMKEAGIIDVFMSIAKDYTPTDV 65 
                                   4455444433033311455678888888876.899***********************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1133  (0.0631937); expected 358.6 (0.02)
Passed bias filter:                      788  (0.0439511); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1178.70
//
Query:       gi|13542263|ref|NP_111951.1|  [L=378]
Description: NAD(FAD)-dependent dehydrogenase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-22   80.5   0.0    3.5e-22   79.0   0.0    1.6  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
     0.0011   19.5   0.1       0.65   10.6   0.0    2.6  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
     0.0054   16.7   0.0       0.44   10.5   0.0    2.4  2  NAD_binding_9   FAD-NAD(P)-binding
  ------ inclusion threshold ------
       0.12   11.2   0.0        1.3    7.8   0.0    2.2  2  Trp_halogenase  Tryptophan halogenase


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.0   0.0   7.8e-26   3.5e-22       2     282 ..       4     289 ..       3     303 .. 0.79

  Alignments for each domain:
  == domain 1  score: 79.0 bits;  conditional E-value: 7.8e-26
                                   SEEEE--SHHHHHHHHHHHH....HTS-EEEEE..TTHCHHHCSHHHHCHHHHHHHHHHHHHHHHHCHHHHCCCCHCCTCE CS
                                   xxxxxxxxxxxxxxxxxxxx....xxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2   2 dvvviGgGpAGlaaaltlaq....agakvtlve..legtclnggcllskallgvaedaeiasevvkklnqgielllgeevv 76 
                                   +v+++G G AG+ +a +l+     + +++t+v+  +e ++  +g+ +s  +  +++  +  +     +n g+ ++ + ev+
  gi|13542263|ref|NP_111951.1|   4 KVLIVGDGDAGTIMANKLRFhtdiKDVEITVVGnsKEHYFKPDGVHISFSMIDYKRSVKPTE---FLFNYGVNYVRD-EVT 80 
                                   89*****************988888*******865555555555555666666666665444...335558887777.9** PP

                                   EEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BC.TCTTC.TTBEECCSECHHHHHHCCSS-T..SEEEEES-SHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxx RF
                   Pyr_redox_2  77 kidpgkkkvklekkkegdeekiaydklvlAtGssprdl.gipGvaenvgklvrtldsaealklkllp..krivvvGgGyiG 154
                                   +id + k+v       +++++++yd+l++AtG   +++ +ipG  e+  k+   l +a +l+++ +      +v+G   i 
  gi|13542263|ref|NP_111951.1|  81 RIDVADKTVST-----KSGRNLDYDYLIIATG-DRFTPeDIPGY-ETDAKHFYDLPHALELQKEIKSfkGGKIVIGQASIP 154
                                   ******99999.....6788************.667777*****.555566699999999999999976455889999998 PP

                                   HHHHHH.......HHHHT-............EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTEEE CS
                                   xxxxxx.......xxxxxx............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2 155 vElAaa.......laklgk............evtlveardrllraldkelsaaleealekeGvevklgtsvkeidgngekl 216
                                   + +  a       l    +            e+++++ ++r+   + +++s+++++++e++G+ +++  +v+ +d++++  
  gi|13542263|ref|NP_111951.1| 155 IMCPPApyeftflL----EeylnfhglkdktEIHYIYPLNRVF--TIPNVSDFVAKRMEERGIITHTLFNVESVDPKNK-- 227
                                   88877644533322....12333455555779**********9..779******************************9.. PP

                                   EEEETTSCEEEESEEEE-S-EEES-HHCSHCCT-EEEETTEEE--TTS.BES.STTEEE-GGGCTECC CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxx.xxxxxxxxxxxxxxx RF
                   Pyr_redox_2 217 evvledgeeidadlvvvavGvrpstelleeklglelderggivvdefl.rtn.vpgiyaiGDvaggkg 282
                                   + +  +ge+i++dl+v+    r ++ +   ++gl+ d+ g+i vd++  + +  ++++aiGD +   +
  gi|13542263|ref|NP_111951.1| 228 KIQSLEGESINYDLLVLIPPHRGQKVI--TDSGLA-DDSGYIDVDKYKlNYKdYDNVFAIGDAT---N 289
                                   88899999********99888888766..799**7.6*********9855555*********98...3 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.2   0.0    0.0033        15       1      32 [.       4      39 ..       4      49 .. 0.83
   2 !   10.6   0.0   0.00014      0.65      41      76 ..     197     232 ..     169     237 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0033
                                  EEEEECSSHHHHHHHHHH...HHTT.SEEEEEESSS CS
                     Pyr_redox  1 kvvvvGgGyiglElAgal...aelg.kkVtvversd 32
                                  kv++vG G+ g  +A+ l   ++++  ++tvv +s+
  gi|13542263|ref|NP_111951.1|  4 KVLIVGDGDAGTIMANKLrfhTDIKdVEITVVGNSK 39
                                  79****************666565556889998776 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00014
                                   HHHHHHHHHHHHTTEEEECSEEEEEEEEETTSEEEE CS
                     Pyr_redox  41 easkilqeklekngievllntkveeiegsedgvesv 76 
                                    +s+ +++++e++gi  ++  +ve+++ ++++++s+
  gi|13542263|ref|NP_111951.1| 197 NVSDFVAKRMEERGIITHTLFNVESVDPKNKKIQSL 232
                                   68899**********************999986665 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 ?    3.8   0.0     0.012        53       2      33 ..       7      37 ..       6      45 .. 0.88
   2 !   10.5   0.0   9.8e-05      0.44     116     155 ..      71     108 ..      65     109 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.012
                 NAD_binding_9  2 ivGaGprGlavlerLlarakkkspleitlfdp 33
                                  ivG G +G+ ++++L  +  + +++eit++ +
  gi|13542263|ref|NP_111951.1|  7 IVGDGDAGTIMANKLRFHT-DIKDVEITVVGN 37
                                  9*****************6.9999****9966 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 9.8e-05
                 NAD_binding_9 116 tvevhraevvdleeradgqavlladgaslaadaVvLAlGh 155
                                    v+++r+ev++++ ++++  v +++g++l++d++++A+G 
  gi|13542263|ref|NP_111951.1|  71 GVNYVRDEVTRIDVADKT--VSTKSGRNLDYDYLIIATGD 108
                                   5899*********99775..899***************95 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.0   0.00028       1.3       1      33 [.       4      37 ..       4      42 .. 0.91
   2 ?    0.6   0.0     0.044     2e+02     168     210 ..      71     109 ..      65     111 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00028
                                  EEEEE--SHHHHHHHHHHHHHTTTS.SEEEEEE- CS
                Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgk.levtlves 33
                                  k++ivG G aG + A+ l+ +++ k +e+t+v  
  gi|13542263|ref|NP_111951.1|  4 KVLIVGDGDAGTIMANKLRFHTDIKdVEITVVGN 37
                                  79******************999989****9965 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.044
                                   T-EEEE--EEEEEE-TTS-EEEEEETTS-EEE-SEEEE-SGGG CS
                Trp_halogenase 168 GvtrvegkvvevqldedgrveslrledgreveadlfiDcsGfr 210
                                   Gv+ v+++v+ +++ +    + + +++gr++++d  i ++G r
  gi|13542263|ref|NP_111951.1|  71 GVNYVRDEVTRIDVAD----KTVSTKSGRNLDYDYLIIATGDR 109
                                   7888888886666655....4789999**********999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (378 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       374  (0.0208601); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 2286.20
//
Query:       gi|13542264|ref|NP_111952.1|  [L=78]
Description: transcription regulator [Thermoplasma volcanium GSS1]
Scores for complete 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-20   71.2   0.0      5e-20   71.1   0.0    1.0  1  TusA      Sulfurtransferase TusA


Domain annotation for each model (and alignments):
>> TusA  Sulfurtransferase TusA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.1   0.0   2.8e-24     5e-20       2      70 .]       8      76 ..       7      76 .. 0.98

  Alignments for each domain:
  == domain 1  score: 71.1 bits;  conditional E-value: 2.8e-24
                                  EEEBTT-STTCCHHHHHHHHCCCGCT-EEEEEESSCHHHHHHHHHHHHHTEEEEEEE-GCC-EEEEEEE CS
                          TusA  2 elDlrGlvCPePllklkkalekleegevlevladdpaatediprfakklghelveveeedgeyrivirk 70
                                  ++D+rG  CP+Pl++l ka ++++ ge++ v ++d ++++d p++  k g elv v +++g+y+iv++k
  gi|13542264|ref|NP_111952.1|  8 VIDARGSYCPGPLMELIKAYKQAKVGEIISVYSTDAGTKKDAPAWISKSGQELVGVFDRNGYYEIVMKK 76
                                  79****************************************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 505.87
//
Query:       gi|13542265|ref|NP_111953.1|  [L=137]
Description: hypothetical protein TVN1434 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.2e-19   68.4   4.9    4.1e-09   36.5   0.6    2.0  2  DrsE_2        DsrE/DsrF/DrsH-like family
     0.0011   19.3   0.1     0.0019   18.5   0.1    1.5  1  DrsE          DsrE/DsrF-like family
  ------ inclusion threshold ------
      0.012   15.0   0.1      0.016   14.6   0.1    1.1  1  Endonuc-MspI  Restriction endonuclease MspI


Domain annotation for each model (and alignments):
>> DrsE_2  DsrE/DsrF/DrsH-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.4   0.3   3.2e-12   1.9e-08       3      55 ..       3      55 ..       1      63 [. 0.91
   2 !   36.5   0.6   6.9e-13   4.1e-09      84     153 .]      65     136 ..      59     136 .. 0.92

  Alignments for each domain:
  == domain 1  score: 34.4 bits;  conditional E-value: 3.2e-12
                                  -EEEEEE----H.HHHHHHHHHHHHHHTT-EEEEEE-GGGGGGGB-GGG---T CS
                        DrsE_2  3 kklaiifskgtldkalaalilAsgAaalglevtiFftFwGLnilrkeekkkvk 55
                                  k+l+i++ +gt dk  aa ++ sgA a g++v+iF tFw L  +rk++++  k
  gi|13542265|ref|NP_111953.1|  3 KTLSIVLASGTIDKIAAAGVITSGAVANGIDVNIFVTFWALMKFRKNDNTVNK 55
                                  7899******************************************9976554 PP

  == domain 2  score: 36.5 bits;  conditional E-value: 6.9e-13
                                   HHHHHHHHHCT---HHHHHHHHHHTT.-EEEEEHHHHHHHT--GGGB-TT-.EEE-HHHHHHHHHC-SEEEE CS
                        DrsE_2  84 kmmkkvmkekgvasleeLleaakeag.vklvaCqmtmdlmglkkeelidgv.eiagaatylkeaeeadvnLf 153
                                    ++ ++m+ek+++s  e++ +ake g v++++C +  d+mg++k++l d v  i+g+ ++++  e + ++Lf
  gi|13542265|ref|NP_111953.1|  65 DLVLSKMNEKKIQSGIEMIRNAKEVGnVHVYGCALMADVMGISKDDLDDMVeDIIGVGEFVSMTESSYTTLF 136
                                   567899*****************9866************************99*********9999988887 PP

>> DrsE  DsrE/DsrF-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.1   3.2e-07    0.0019      32     114 ..      32     134 ..       4     136 .. 0.65

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 3.2e-07
                                   -EEEEEE-GGGGGGGBS...................---TGGGTS---GGGGGGCGGGT.-EEEEEHHHHHHTT--GGGE- CS
                          DrsE  32 hevsvffygdGvllllk...................gqtanpadeknlaellkalkeyg.vklyvCgqaakargldededl 92 
                                    +v++f++  +   ++k                     + n+++  + +e+++ +ke g v++y C+  a+ +g+++d dl
  gi|13542265|ref|NP_111953.1|  32 IDVNIFVTFWALMKFRKndntvnklsydgseisdlvLSKMNEKKIQSGIEMIRNAKEVGnVHVYGCALMADVMGISKD-DL 111
                                   6666666666666666655555545554444443332223334444559********777****************66.55 PP

                                   .T--EEEE-HHHHHHHHHH-SEE CS
                          DrsE  93 .gvgvevsglgelaelqnegdrv 114
                                    ++   + g+ge++ +   ++  
  gi|13542265|ref|NP_111953.1| 112 dDMVEDIIGVGEFVSMTESSYTT 134
                                   22233477888888888877765 PP

>> Endonuc-MspI  Restriction endonuclease MspI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1   2.7e-06     0.016      82     163 ..      50     129 ..      42     135 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.7e-06
                  Endonuc-MspI  82 tdeipkLsngGkPktDialkiklekkelkiatisvkntsaktvsvHeysaedlikvldlsdsdlrellkkfqevGskkklk 162
                                    +++ kLs  G+   D+ l  k+++k++  + i + +  ++   vH y    ++ v+ +s +dl ++++++  vG++  ++
  gi|13542265|ref|NP_111953.1|  50 DNTVNKLSYDGSEISDLVLS-KMNEKKI-QSGIEMIRNAKEVGNVHVYGCALMADVMGISKDDLDDMVEDIIGVGEFVSMT 128
                                   58899***********9886.7777777.68899989899999*********************************99998 PP

                  Endonuc-MspI 163 e 163
                                   e
  gi|13542265|ref|NP_111953.1| 129 E 129
                                   5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       520  (0.0290033); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.32s 00:00:00.79 Elapsed: 00:00:00.50
# Mc/sec: 827.77
//
Query:       gi|13542266|ref|NP_111954.1|  [L=111]
Description: DNA-directed RNA polymerase subunit L [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.4e-13   49.6   0.1    3.3e-13   49.2   0.1    1.2  1  RNA_pol_L_2  RNA polymerase Rpb3/Rpb11 dimerisation domain
  ------ inclusion threshold ------
       0.27   11.1   6.8       0.12   12.4   2.0    1.9  2  DUF507       Protein of unknown function (DUF507)


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 !   49.2   0.1   3.7e-17   3.3e-13       3      72 ..      22      90 ..      20      93 .. 0.92

  Alignments for each domain:
  == domain 1  score: 49.2 bits;  conditional E-value: 3.7e-17
                                  EEEEES--HHHHHHHHHHHTTSTTEEEEEEECSSTTTSEEEEEEEESTSS-HHHHHHHHHHHHHHHHHHH CS
                   RNA_pol_L_2  3 tfeingEDhTLgnlLrhlllknpsVefagYkipHPlepkmnlriqtkssnnpleaLkkalkdlldicdel 72
                                   +e+ + D TL+  L +++lk+++V  a+Y i+HP +++ ++ ++ k s +p+ a+k+++++l++++++l
  gi|13542266|ref|NP_111954.1| 22 IVEMINYDNTLLRTLVEEILKDDQVIEARYYIKHPIIDNPQIYVKVK-SGKPQAAIKRSIRKLSKLYEDL 90
                                  678999*******************************9999999986.689**************99886 PP

>> DUF507  Protein of unknown function (DUF507)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   1.2     0.024   2.2e+02      96     134 ..       3      42 ..       1      54 [. 0.73
   2 ?   12.4   2.0   1.3e-05      0.12     104     158 ..      51     105 ..      38     111 .] 0.85

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.024
                        DUF507  96 eerlneishkileellkedlie.vsvsenkirnkIfkilk 134
                                   +er ne s +++ +  ++  +e ++ +++ +r  + +ilk
  gi|13542266|ref|NP_111954.1|   3 RERTNETSLRVVSKEKDSIIVEmINYDNTLLRTLVEEILK 42 
                                   7888888888888888888888677777777777777765 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 1.3e-05
                        DUF507 104 hkileellkedlievsvsenkirnkIfkilkeylkeeeeidkevrekiknykrkl 158
                                     i   ++++ +i v+v++ k +  I ++++++ k +e++  +v + i++y+ + 
  gi|13542266|ref|NP_111954.1|  51 YYIKHPIIDNPQIYVKVKSGKPQAAIKRSIRKLSKLYEDLGAQVEKEIEKYRSNH 105
                                   567888999*****************************************98654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       851  (0.047465); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 709.49
//
Query:       gi|13542267|ref|NP_111955.1|  [L=320]
Description: DNA modification methylase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-27   96.9   0.0    8.3e-27   94.2   0.0    1.9  1  UPF0020          Putative RNA methylase family UPF0020
      4e-07   30.7   0.0    7.7e-07   29.7   0.0    1.5  1  Methyltransf_25  Methyltransferase domain
    1.9e-06   27.7   0.0    3.8e-06   26.8   0.0    1.4  1  Methyltransf_31  Methyltransferase domain
    3.2e-05   23.8   0.0    0.00027   20.7   0.0    2.1  2  N6_N4_Mtase      DNA methylase
    0.00018   21.1   0.0    0.00037   20.1   0.0    1.5  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
    0.00036   19.9   0.0     0.0012   18.2   0.0    1.8  1  N6_Mtase         N-6 DNA Methylase
     0.0015   19.2   0.0     0.0049   17.5   0.0    1.9  1  Methyltransf_11  Methyltransferase domain
     0.0038   16.9   0.0     0.0063   16.2   0.0    1.4  1  Cons_hypoth95    Conserved hypothetical protein 95
     0.0059   16.3   0.2      0.074   12.7   0.0    2.1  2  MethyltransfD12  D12 class N6 adenine-specific DNA methyltran
     0.0064   16.0   0.0        2.1    7.7   0.0    2.1  2  AviRa            RRNA methyltransferase AviRa
     0.0076   16.1   0.0      0.053   13.4   0.0    2.1  1  Methyltransf_23  Methyltransferase domain
  ------ inclusion threshold ------
      0.017   14.5   0.0      0.031   13.6   0.0    1.4  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
      0.018   14.3   0.0      0.031   13.5   0.0    1.4  1  N2227            N2227-like protein
       0.02   15.6   0.0      0.055   14.2   0.0    1.8  1  Methyltransf_12  Methyltransferase domain
      0.024   14.2   0.0      0.036   13.6   0.0    1.2  1  MTS              Methyltransferase small domain
       0.04   14.1   0.1        0.1   12.8   0.1    1.6  1  Peptidase_M99_C  C-terminal domain of metallo-carboxypeptidas


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 !   94.2   0.0   7.4e-30   8.3e-27       3     182 ..     147     297 ..     146     311 .. 0.92

  Alignments for each domain:
  == domain 1  score: 94.2 bits;  conditional E-value: 7.4e-30
                                   SS-SS---SS-HHHHHHHHHHTT--TTS-EEETT-TTSHHHHHHHHHHTT--TTTT----SSHHHHHHHHHHHH--EEEEE CS
                       UPF0020   3 yRefngpapLketLAaalvrlagwkpgepllDPmCGsGtilIEaallganiapgllrefvlelkaeaeeearaelklygsD 83 
                                   +R+f+ p ++ ++ A+ lv+ a ++++e++lDP+CG+G+ilIEaal+g +++                          g D
  gi|13542267|ref|NP_111955.1| 147 KRPFFSPVSMHPKYARFLVNCAHVRENETILDPFCGTGGILIEAALMGIRVV--------------------------GND 201
                                   69**************************************************..........................*** PP

                                   S-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EEEE----------HHHHHHHHHHHHHHHHHH-TT..-EEE CS
                       UPF0020  84 ldrrvvqgareNaekagvgdliefsqadaakLrlkegevdvivtnpPYGerlgskkalekLYseflrelkrvlrgggrlvl 164
                                      ++  gar+N+++  v+++  +++ d+++L   eg vd i+t++PYG+   ++ ++ +LY+   ++++ +l+ gg +++
  gi|13542267|ref|NP_111955.1| 202 VSLAMAVGARTNLSYFHVENFRVYNK-DVRELD-LEG-VDGIATDMPYGRNSYHTDEITELYEVSFQKFSDMLKPGGYAAF 279
                                   ******************99877666.******.885.******************************************* PP

                                   EEESSHHHHHCC---ESE CS
                       UPF0020 165 ltsenkalekaleeralr 182
                                   ++s+++ +e a +  ++r
  gi|13542267|ref|NP_111955.1| 280 AVSQQEHVEIAKKYFEVR 297
                                   ****99998766655555 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.7   0.0   6.9e-10   7.7e-07       1      97 []     176     275 ..     176     275 .. 0.81

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 6.9e-10
                                   EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBSS..STT.TEEEEEEESTGGGS CS
               Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl.nvefvqgdaedlpf..edg.sfDlvvssgalhhl 77 
                                   +Ld  cGtG +++++a   g  +v+g D+s +m   ar++++  ++ n++++++d+++l++   dg   D+ + ++++h  
  gi|13542267|ref|NP_111955.1| 176 ILDPFCGTGGILIEAALM-G-IRVVGNDVSLAMAVGARTNLSYFHVeNFRVYNKDVRELDLegVDGiATDMPYGRNSYHTD 254
                                   8999************88.5.********************998889***********98622222367777777666653 PP

                                   SHHH.HHHHHHHHHHHEEEEE CS
               Methyltransf_25  78 sded.lekalkeiarvLkpgG 97 
                                   +  + +e  +++++++LkpgG
  gi|13542267|ref|NP_111955.1| 255 EITElYEVSFQKFSDMLKPGG 275
                                   3333146679**********9 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   0.0   3.4e-09   3.8e-06       3     113 ..     172     283 ..     171     311 .. 0.82

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 3.4e-09
               Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsnev 83 
                                   ++ ++lD+ CGtG +++e+a ++  +++vvG D s  +   Ar+n++   ++n+++   d+ el+  l  e +D i ++ +
  gi|13542267|ref|NP_111955.1| 172 ENETILDPFCGTGGILIEAA-LM--GIRVVGNDVSLAMAVGARTNLSYFHVENFRVYNKDVRELD--L--EGVDGIATDMP 245
                                   5889****************.65..69**************************************..4..47999999988 PP

               Methyltransf_31  84 l.naladpdkile.......eiervlkpggilliedpr 113
                                        ++ d+i e       + ++ lkpgg+ + +  +
  gi|13542267|ref|NP_111955.1| 246 YgRNSYHTDEITElyevsfqKFSDMLKPGGYAAFAVSQ 283
                                   88444444444444446666999999999987766555 PP

>> N6_N4_Mtase  DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   2.4e-07   0.00027     175     222 ..     155     203 ..      78     207 .. 0.83
   2 ?    0.7   0.0      0.32   3.5e+02       2      60 ..     238     285 ..     237     303 .. 0.61

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 2.4e-07
                                   ---HHHHHHHHHH.HS-TT-EEEETT-TTTHHHHHHHHTT-EEEEEESS CS
                   N6_N4_Mtase 175 qkPvallerlIkl.stkkgdivlDpFaGSGtTavaakelgrkfiGieie 222
                                   ++  + +++l+++   ++++++lDpF+G+G ++++a+ +g + +G +++
  gi|13542267|ref|NP_111955.1| 155 SMHPKYARFLVNCaHVRENETILDPFCGTGGILIEAALMGIRVVGNDVS 203
                                   555677788886515789***************************8875 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.32
                                   EEEEE--SSSSSCS.....GCCGCCHHHHHHHHHHHHHHHHHHHEEEEEEEEEEE-CCC CS
                   N6_N4_Mtase   2 dlivtdpPYntgkdyendeqyeeedsyeeyleflekvlkevrrvLkddgsifiniddse 60 
                                   d i td PY+ ++              +e  e+ e  +++  ++Lk++g +   ++++e
  gi|13542267|ref|NP_111955.1| 238 DGIATDMPYGRNSY-----------HTDEITELYEVSFQKFSDMLKPGGYAAFAVSQQE 285
                                   56777777777766...........3344444555556666666777776666666665 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 !   20.1   0.0   3.3e-07   0.00037       2     106 ..     174     270 ..     173     291 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 3.3e-07
               Methyltransf_15   2 rvilDlfsGaGGnviqfalvfekviaieinleklacaqhNaevYgvsdkitlvlgdvfellaklklekikvdlvflSpPwG 82 
                                   ++ilD+f+G+GG  i+ al++ +v++ +++l     a  N   + v++   +    +++ +++l le +  d + +  P G
  gi|13542267|ref|NP_111955.1| 174 ETILDPFCGTGGILIEAALMGIRVVGNDVSLAMAVGARTNLSYFHVENF-RV----YNKDVRELDLEGV--DGIATDMPYG 247
                                   689***************************************9988763.22....2445666777777..8888888888 PP

               Methyltransf_15  83 GpsYkkqekfdlkkklkplkleql 106
                                     sY+ +e  +l +++   k++ +
  gi|13542267|ref|NP_111955.1| 248 RNSYHTDEITEL-YEVSFQKFSDM 270
                                   888888887777.55555555555 PP

>> N6_Mtase  N-6 DNA Methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   1.1e-06    0.0012      35     146 ..     161     257 ..     132     291 .. 0.68

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.1e-06
                      N6_Mtase  35 sklivellepksgesvyDpacGsggllvqaekvlkeedgktkelsiyGqeknettyrLakmNlllhgieykkvkirlgdtl 115
                                    +++v+ ++ +++e+++Dp cG+gg+l++a+ +          + + G ++    +  a++Nl    +e+  +++ ++d  
  gi|13542267|ref|NP_111955.1| 161 ARFLVNCAHVRENETILDPFCGTGGILIEAALM---------GIRVVGNDVSLAMAVGARTNLSYFHVEN--FRVYNKDVR 230
                                   57888888*********************9863.........5777777777777777777776544443..345555554 PP

                      N6_Mtase 116 ekpkfekdkkfdvvvaNppfnqkewkektle 146
                                   e + +     +d +++  p++ + ++ ++++
  gi|13542267|ref|NP_111955.1| 231 ELDLE----GVDGIATDMPYGRNSYHTDEIT 257
                                   44444....4777777777777777554444 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   4.4e-06    0.0049       1      96 []     177     279 ..     177     279 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 4.4e-06
                                   EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-.EEEETTEECCCTSS-TT...-EEEEEEES-CCC-... CS
               Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseegl.kvefvvadaeklpfedn...sfDlvvssevlhhv... 74 
                                   Ld  cGtG ++ + a  g rvvg D+s +m   a+++ s  ++ ++++   d+++l +e       D+ + +++ h+    
  gi|13542267|ref|NP_111955.1| 177 LDPFCGTGGILIEAALMGIRVVGNDVSLAMAVGARTNLSYFHVeNFRVYNKDVRELDLEGVdgiATDMPYGRNSYHTDeit 257
                                   6677***********9***************99999999999899999999999988776112344555545555554555 PP

                                   CCHHHHHHHHHHHEEEEEEEEE CS
               Methyltransf_11  75 edpekalkeiaRvLkpgGllvi 96 
                                   e  e  ++++  +LkpgG+ ++
  gi|13542267|ref|NP_111955.1| 258 ELYEVSFQKFSDMLKPGGYAAF 279
                                   6778889999999999999875 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   5.6e-06    0.0063      37     134 ..     168     257 ..     141     299 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 5.6e-06
                                   CCCHCC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-EEEEE CS
                 Cons_hypoth95  37 aaeiegarvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkleeetaelkedaleallklakkkeefdiv 117
                                   a+  e++++LD f+G+G++ +EA+  g+ ++v  + + +++   ++nl+ +++e+ ++++++d  e  l+       +d +
  gi|13542267|ref|NP_111955.1| 168 AHVRENETILDPFCGTGGILIEAALMGI-RVVGNDVSLAMAVGARTNLSYFHVEN-FRVYNKDVRELDLEG------VDGI 240
                                   34467889****************9995.6777788888888899*******986.888888876655444......6778 PP

                                   EE--SSSTTCH.HHHHH CS
                 Cons_hypoth95 118 flDPPyakellieevle 134
                                     D Py ++ +  + ++
  gi|13542267|ref|NP_111955.1| 241 ATDMPYGRNSYHTDEIT 257
                                   88888877766333333 PP

>> MethyltransfD12  D12 class N6 adenine-specific DNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.0   6.6e-05     0.074      10      50 ..     162     202 ..     159     212 .. 0.87
   2 ?    1.3   0.1       0.2   2.3e+02     132     194 ..     242     310 ..     217     318 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.6e-05
                                   HHHHCCS-..--SEEEETT-TTSCCHHCS...SSCEEEEES CS
               MethyltransfD12  10 peIkelipkdkgktfvepFaGggaVffeakkqgkkvlinDi 50 
                                   ++++++ + + ++t+ +pF+G+g + +ea   g +v+ nD+
  gi|13542267|ref|NP_111955.1| 162 RFLVNCAHVRENETILDPFCGTGGILIEAALMGIRVVGNDV 202
                                   5667777777899****************999********8 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.2
                                   B---B-S-SS-....HHHHHHHHHHHHH........CCEEEC-CHHHHTT--TTE.EEEE--S-T.S...T CS
               MethyltransfD12 132 fnvpygaykkpkkvaekelklrseklkn........akiecgdfdavllkakieddivYlDPPYnprqyta 194
                                   +  pyg+  ++   + +el ++s++ ++        a++ +++++ v+ ++k    + Y+ P Y++r+ t+
  gi|13542267|ref|NP_111955.1| 242 TDMPYGRNSYH-TDEITELYEVSFQKFSdmlkpggyAAFAVSQQEHVEIAKKYFE-VRYVVPVYQHRSLTR 310
                                   67889999999.5555566666555555555669988888888888888875555.999999999855443 PP

>> AviRa  RRNA methyltransferase AviRa
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.0    0.0019       2.1      51     116 ..     170     231 ..     141     235 .. 0.77
   2 !    7.4   0.0    0.0023       2.6     154     218 ..     227     289 ..     218     299 .. 0.67

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0019
                         AviRa  51 egapltlyDpCCGgayLltvlgllhgkkikkvlasDvdeevlelakkNLsLLtkeglakreeelre 116
                                     +  t+ Dp CG++ +l   +l+      +v++ Dv+ ++   a++NLs    e ++  ++++re
  gi|13542267|ref|NP_111955.1| 170 VRENETILDPFCGTGGILIEAALMGI----RVVGNDVSLAMAVGARTNLSYFHVENFRVYNKDVRE 231
                                   334569*********99999998864....699****************99988887776666665 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0023
                         AviRa 154 aditekeeeaekevdivitDlPYGelvswqgeseepvkqlleslaavldpee.svvaviadkkkki 218
                                    d+    e   + vd + tD+PYG  + +++e +e  +  +++ + +l+p   +  av ++++ +i
  gi|13542267|ref|NP_111955.1| 227 KDVR---ELDLEGVDGIATDMPYGRNSYHTDEITELYEVSFQKFSDMLKPGGyAAFAVSQQEHVEI 289
                                   4444...333444899*********99888889999999999999999775413444444444444 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   4.7e-05     0.053      20     143 ..     170     306 ..     152     316 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.7e-05
               Methyltransf_23  20 lraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae.........kakkaqkdqfdeqeaaepqgkfdlIvlrev 91 
                                    r++  +Ld  cGtG  l +++  g  v+g D s ++   a+         +++ ++kd    + + ++   +d  + r++
  gi|13542267|ref|NP_111955.1| 170 VRENETILDPFCGTGGILIEAALMGIRVVGNDVSLAMAVGARtnlsyfhveNFRVYNKDVRELDLEGVDGIATDMPYGRNS 250
                                   57888999999****99999***************9999999877777777666666666644455555558998888888 PP

               Methyltransf_23  92 lehvp..d.ppellrqiatllkpgGylllseplasl.kedrllldwlylvpagrhi 143
                                    ++ +    ++  ++++ ++lkpgGy+ + ++ +++ + ++++ +++y vp  +h+
  gi|13542267|ref|NP_111955.1| 251 YHTDEitElYEVSFQKFSDMLKPGGYAAFAVSQQEHvEIAKKYFEVRYVVPVYQHR 306
                                   8877754258899****************999887643444444455555555555 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   2.8e-05     0.031      30     175 ..     155     301 ..     152     307 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.8e-05
                                   TTHHHHHHHHHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT- CS
               Ubie_methyltran  30 gihrlWkkfveklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeL 110
                                    +h ++ +f+ ++  v++ +++lD  +Gtg + +   +++    +vv+ D++  m   ++  l    + n +  + +  eL
  gi|13542267|ref|NP_111955.1| 155 SMHPKYARFLVNCAHVRENETILDPFCGTGGILI---EAALMGIRVVGNDVSLAMAVGARTNLSYFHVENFRVYNKDVREL 232
                                   5799999***********************9965...56667779999999999999999988888888888888888888 PP

                                   TTS-T-EEEEEEES-GGG..-S-HHHHHHHH.....HHHEEEEEEEEEEEE----SHHHHHHHHHHHH.HHH CS
               Ubie_methyltran 111 pfeddsfDvvtvsfGlrn..vtDklkaLkea.....yrvlkpGGrlvvlefskvelpllsqayelyskevlP 175
                                   + e        + +G rn   tD  + L e+       +lkpGG    + +s+ e   + + y+   + v+P
  gi|13542267|ref|NP_111955.1| 233 DLEGVDGIATDMPYG-RNsyHTDEITELYEVsfqkfSDMLKPGGYA-AFAVSQQEHVEIAKKYFEVRY-VVP 301
                                   776533333446666.442235655555443211115789999965.556777777767666766555.555 PP

>> N2227  N2227-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   2.8e-05     0.031      53     100 ..     168     215 ..     151     226 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.8e-05
                                   .....T-EEEEET-TT-HHHHHHHHTT-EEEEEE--HHHHHHHHHHHH CS
                         N2227  53 skerekvkilvPGaGlGrlavelatkgyqvegnEfsyfmllasefiLn 100
                                    + re+ +il P +G+G++ +e a +g++v gn++s  m +  +  L 
  gi|13542267|ref|NP_111955.1| 168 AHVRENETILDPFCGTGGILIEAALMGIRVVGNDVSLAMAVGARTNLS 215
                                   56788899*****************************99887765555 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   4.9e-05     0.055       5      98 ..     181     276 ..     177     277 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.9e-05
               Methyltransf_12   5 cGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldgg..ssfDlvvasnvlhhl...k 80 
                                   cGtG +l + +    +i+++g D+s ++ + a++ l+  + +n+ +++ ++++l dl+g    + D+ +  n  h     +
  gi|13542267|ref|NP_111955.1| 181 CGTGGILIEAALM--GIRVVGNDVSLAMAVGARTNLSYFHVENFRVYNKDVREL-DLEGVdgIATDMPYGRNSYHTDeitE 258
                                   9*****9999999..**************9999999999987777777666664.34433444555555555555533334 PP

               Methyltransf_12  81 direvldnirklLkpgGr 98 
                                     + +++++ ++LkpgG+
  gi|13542267|ref|NP_111955.1| 259 LYEVSFQKFSDMLKPGGY 276
                                   444566688899999985 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   3.2e-05     0.036      20     137 ..     161     279 ..     158     302 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.2e-05
                                   HHHHHHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STTTTSTTS-EE CS
                           MTS  20 sklLletlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle.vevvasdvleeveekkfd 99 
                                   +++L+++ + ++++++lD  cG+G + +++a +   ++v+  dv+ +    a++nl+  ++e  +v+++dv e    + +d
  gi|13542267|ref|NP_111955.1| 161 ARFLVNCAHVRENETILDPFCGTGGILIEAALMG--IRVVGNDVSLAMAVGARTNLSYFHVEnFRVYNKDVRELDL-EGVD 238
                                   58999999999999**********9888888765..559******9888889********999*******988666.99** PP

                                   EEEE---STTTCHCHHHHH...HHHHHHHHHHEEEEEEEEE CS
                           MTS 100 livsNPPfhagkatelava...eeliaeAkeaLkegGeLli 137
                                    i +  P+ +++  +++++   e  +++  ++Lk+gG   +
  gi|13542267|ref|NP_111955.1| 239 GIATDMPYGRNSYHTDEITelyEVSFQKFSDMLKPGGYAAF 279
                                   *******9988866655541114567788888888886544 PP

>> Peptidase_M99_C  C-terminal domain of metallo-carboxypeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1     9e-05       0.1      13      78 ..      14      78 ..       3      89 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 9e-05
                                  TTEEEEEETT-EEEESSEEEE--BSSBEEEETT--SS--..SS---TT-EEEGGGS-GGG-SBTTS CS
               Peptidase_M99_C 13 dnkdkevkigsvvevkesfeildldniranvigfvvskersdkpneagilikkkefakrfsldkke 78
                                  d   ++v i s+ e  e+f+i  +d++ a + g     er+   n +g++++k e  + + +d  +
  gi|13542267|ref|NP_111955.1| 14 D-DARKVEILSIQETYEDFKIEYIDDFIAVISGNWKRIERAAFVNTVGLILSKGEKPEDLKIDIPD 78
                                  4.35789*********************************************99988888888655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       507  (0.0282782); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 2020.63
//
Query:       gi|13542268|ref|NP_111956.1|  [L=604]
Description: RNA-binding protein snRNP [Thermoplasma volcanium GSS1]
Scores for complete 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-44  150.1   8.3    1.1e-42  146.3   8.3    2.0  1  FbpA       Fibronectin-binding protein A N-terminus (FbpA)
    1.9e-26   92.8   0.0    4.1e-26   91.8   0.0    1.6  1  NFACT-R_1  NFACT protein RNA binding domain
    0.00072   19.6   0.4      0.054   13.6   0.0    3.1  3  Mrr_N      Mrr N-terminal domain
     0.0035   17.5   0.0      0.011   16.0   0.0    1.8  1  NFACT-R_2  NFACT protein RNA binding domain
  ------ inclusion threshold ------
       0.21   11.5   0.4       0.44   10.5   0.4    1.6  1  PXA        PXA 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 !  146.3   8.3   3.2e-46   1.1e-42      13     417 ..      18     392 ..       7     399 .. 0.87

  Alignments for each domain:
  == domain 1  score: 146.3 bits;  conditional E-value: 3.2e-46
                                   HHHHTTXEEEEEEEEETTEEEEEEE.ETTEEEEEEEEXXTTTXEEEEXXXXXXXXSSXXHHHHHHHHHHTTXEEEEEEEXT CS
                          FbpA  13 qkellggridkiyqpekdelvltlr.anrgrhkLllsahpsyarihltekpkenpkeppnFcmlLRkyLkgarivsieqlg 92 
                                   +++l+g+ ++k+yq ++d+  ++l+ ++ +r ++l+s+    + i + ++++  p+++++ +m+LRk ++  rivs+eq++
  gi|13542268|ref|NP_111956.1|  18 RERLVGSFVKKVYQTGPDDFLIQLYrSDLKRFDMLVSL---KKGIFFKSEET--PDTASQTAMVLRKTISDRRIVSVEQVN 93 
                                   57899********************99999999*****...99999988787..*************************** PP

                                   TSSEEEEEEEEEXTTSXEEEEEEEEEXXGGGXEEEEEETTTEEEEESSXBXXXSSXSXXBSTTXBXXXSXXXSXBXTTSXX CS
                          FbpA  93 fdRivelsiekrdElgdeeeytLivEimgrhSNiiLvdeenkIidaikhvspkqsrvReilpgekYelPpsqdklnPleae 173
                                   fdR+v++ + +           Li+E++ + +N+i +d  +kI  ++k  +++    R +  g++Y++P s    +P + +
  gi|13542268|ref|NP_111956.1|  94 FDRVVKFVFHTG--------QALILELFRD-GNLIATDG-DKITFVLKPRRWR---NRDLEVGAIYIPPSS---SDPTKMT 158
                                   ************........99********.******84.4************...9*********76666...9999999 PP

                                   H.HHHHHHHHHS.XXXHHHHHHHBTTXXHHHHHHHHTTXSSSH...............HHHHHHHHTXXX....XXEE... CS
                          FbpA 174 eleefkellskkekdlvkaLvkafqGlspllaeelleragldketsakelseedlerlyealqelleeleeekfepqlvlk 254
                                   + eef + +++++++ v++L+++f +l+++laee+l r+gl+k+      + +dle+ ++ +++ l+e+ +e++    ++ 
  gi|13542268|ref|NP_111956.1| 159 D-EEFVNTVRQSKANAVQTLATRF-NLGGDLAEEVLFRIGLPKDG-----AVDDLENRANDVRRSLAEILQESLLNSAYYY 232
                                   9.99999999999***********.***************88885.....5556666666666666666655555555555 PP

                                   ..XSSSEESSXXTTXX.SSXXXXSXHHHHHHHHTTTXXX--SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCGGHHHH CS
                          FbpA 255 eekpeefsvvplkslselekesfdslsealdeyYakkaerdrveqkrsdlekrveneleklekklkklekelekaekaeny 335
                                   e+ + ++s+vp k+  e+  ++fd+++e l            +  ++++ e  ++++++ + k+++++ k       ae+y
  gi|13542268|ref|NP_111956.1| 233 ED-QGTVSPVPMKHFGEY-TRKFDDFNEGLV-------FLLSMSPQEEESEDPIQRRINSQMKSIEEFGK------IAEKY 298
                                   53.89******9996655.458888888774.......33445555666677899999999999999987......5788* PP

                                   HCCHH-----------------------...--..........---------------HHHHHHHHHHHHHHHHHHHHHHH CS
                          FbpA 336 rligelltaylyaikkgmsevelenyyde..ge..........evtIpLdprkspsenAqkyfkkykKlkraveaveeqie 404
                                   r +g  ++ +l+ ++   + ++  ny ++  ++          e  I +d +ks+ enA +yf+  k  ++++e+++++ie
  gi|13542268|ref|NP_111956.1| 299 RSYGSQIMQNLQTVEMAIKDARSGNYPSDkmNKatkhislklgEEDIDIDYTKSAGENANRYFDLSKDYRKKIEGAKKAIE 379
                                   *************************99975444999999999999************************************ PP

                                   HHHHHHHHHHHHH CS
                          FbpA 405 etkeeleylesve 417
                                   e+++e  +l++++
  gi|13542268|ref|NP_111956.1| 380 EAEQERIKLQEKK 392
                                   *****99999876 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 !   91.8   0.0   1.1e-29   4.1e-26       2     109 .]     406     516 ..     405     516 .. 0.93

  Alignments for each domain:
  == domain 1  score: 91.8 bits;  conditional E-value: 1.1e-29
                     NFACT-R_1   2 vfwFkssdgylvimGkDkqeneelikkyleesdvwfhvdkessahvylrlsegeleeip.eelleeaaqlakanSia.gnk 80 
                                   ++wF+ss+gylvi+G+D+++ne+++kk+l+e+d+++h+d+ ++++++++ seg+  ++p e+++++aa++a++ S+a  + 
  gi|13542268|ref|NP_111956.1| 406 YHWFISSEGYLVIAGRDAKSNEKIVKKHLKEGDLYVHADMYGAPSTIIK-SEGK--PMPgEDTIRQAAAFAICFSRAwPAG 483
                                   69***********************************************.6667..6663789****************** PP

                     NFACT-R_1  81 lssvdvvyvpasnlsktap....ldtGsvgfkg 109
                                   + s ++++v++s++skt++    ++tGs +++g
  gi|13542268|ref|NP_111956.1| 484 IASGTAYWVYPSQVSKTPEsgeyVSTGSWIIRG 516
                                   ******************989999999988875 PP

>> Mrr_N  Mrr N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       1.7   6.3e+03      21      58 ..     171     214 ..     165     220 .. 0.61
   2 ?    2.2   0.3     0.057     2e+02      24      60 ..     368     406 ..     362     408 .. 0.68
   3 !   13.6   0.0   1.5e-05     0.054      15      48 ..     561     593 ..     554     597 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.7
                         Mrr_N  21 keirervaerfglseeeraell......psgkqtrfknrvgWar 58 
                                   + +++++a rf+l  +  +e+l      ++g    ++nr++  r
  gi|13542268|ref|NP_111956.1| 171 ANAVQTLATRFNLGGDLAEEVLfriglpKDGAVDDLENRANDVR 214
                                   56777888888777666666665555545554466666666555 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.057
                         Mrr_N  24 rervaerf.glseeeraell.psgkqtrfknrvgWarty 60 
                                   r++++     + e e+++ + ++ k + +++r+ W  ty
  gi|13542268|ref|NP_111956.1| 368 RKKIEGAKkAIEEAEQERIKlQEKKVKSVNRRIFWFETY 406
                                   555555553556666666654666669*********999 PP

  == domain 3  score: 13.6 bits;  conditional E-value: 1.5e-05
                         Mrr_N  15 gsehrlkeirervaerfglseeeraellpsgkqt 48 
                                   g ++r +ei +++ae++++s+ee+++ lp g+++
  gi|13542268|ref|NP_111956.1| 561 GDVRR-SEIAKQIAEYLNVSKEEVEKILPPGNSR 593
                                   67888.*************************875 PP

>> NFACT-R_2  NFACT protein RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   2.9e-06     0.011       4      69 ..     409     479 ..     407     483 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.9e-06
                     NFACT-R_2   4 frlsekaklIvgReeeEnkflkgll.kkdfvslrakshkGplvlid..gels..eedlelaarivarYskg 69 
                                   f  se++ +I gR+++ n+++ +   k+  + ++a  + +p ++i+  g++   e+++++aa+++  +s++
  gi|13542268|ref|NP_111956.1| 409 FISSEGYLVIAGRDAKSNEKIVKKHlKEGDLYVHADMYGAPSTIIKseGKPMpgEDTIRQAAAFAICFSRA 479
                                   66788999**********99977666666556*************5458765559**********999985 PP

>> PXA  PXA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.4   0.00012      0.44      29      88 ..     158     225 ..     154     396 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00012
                           PXA  29 sdeeFptevrsilrsviralanrlkk.vDlaqlll.......trlldlltshlrdyrqaeekvkskka 88 
                                   +deeF+++vr+  ++++++la+r +   Dla+ +l       +  +d+l++  +d+r++ +++ +++ 
  gi|13542268|ref|NP_111956.1| 158 TDEEFVNTVRQSKANAVQTLATRFNLgGDLAEEVLfriglpkDGAVDDLENRANDVRRSLAEILQESL 225
                                   59**********************7449*998777677777777788888888888877776666543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (604 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1011  (0.0563891); expected 358.6 (0.02)
Passed bias filter:                      628  (0.0350271); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.75u 0.34s 00:00:01.09 Elapsed: 00:00:00.54
# Mc/sec: 3378.02
//
Query:       gi|13542269|ref|NP_111957.1|  [L=304]
Description: bifunctional phosphoglucose/phosphomannose isomerase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.2e-43  147.9   0.0      4e-43  147.1   0.0    1.4  2  bact-PGI_C  Bacterial phospho-glucose isomerase C-terminal SI
    4.5e-08   33.0   0.0    1.9e-07   31.0   0.0    2.0  2  SIS         SIS domain
  ------ inclusion threshold ------
      0.087   12.8   0.0       0.19   11.7   0.0    1.5  1  SIS_2       SIS domain


Domain annotation for each model (and alignments):
>> bact-PGI_C  Bacterial phospho-glucose isomerase C-terminal SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       1.8   1.1e+04      90     103 ..      84      96 ..      66     104 .. 0.52
   2 !  147.1   0.0   6.7e-47     4e-43       3     151 ..     159     302 ..     157     303 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 1.8
                                   HHHHHHHTTTSSEE CS
                    bact-PGI_C  90 eivkelaeergvrv 103
                                   ++ +e a+++ ++v
  gi|13542269|ref|NP_111957.1|  84 SASEEAAKKH-ANV 96 
                                   4444444433.333 PP

  == domain 2  score: 147.1 bits;  conditional E-value: 6.7e-47
                                   -HHHHHHHHHTT..SEEEEE-..TT-THHHHHHHHHHHHTT----B---.SSHHHHHHHTTSS-GGGGTTEEEEEESSHH. CS
                    bact-PGI_C   3 npakqlAlelag..klpviygssellevaArRfknqlnenAKipafagvlpeanhneivgleaeeelkkrlrlvllrdeee 81 
                                   ++ k++A e+++  ++pviyg s +++++A+R+k+q+nenAK++a+++++ e+nhn+ + l +++  k++++++++r+++ 
  gi|13542269|ref|NP_111957.1| 159 EEEKSIASEIYNgeHIPVIYG-SRPFRAIAYRWKTQFNENAKVLAYSNYFSELNHNDTMPL-KDTYRKDEFYFLVFRSDD- 236
                                   6889*******999*******.***************************************.79*************888. PP

                                   .......HHHHHHHHTTTSSEEEEE---SSSHHHHHHHHHHHHHHHHHHHHHHCT---S-TTTTHHHHH. CS
                    bact-PGI_C  82 hprvkkraeivkelaeergvrvtevkaegesplerlaslillgDfvSvylAllrgvDPtpvpaIdelKee 151
                                    +r +kr++++++++     ++  v+ +g+s+l++l++li++gD+ +++lA+lrgvDP++v+ I++lK+e
  gi|13542269|ref|NP_111957.1| 237 -SRFSKRITVTEKITG---NSFRMVDVRGSSLLAKLFYLIHFGDYLTYHLAELRGVDPQDVSLIEKLKKE 302
                                   .7************98...77***********************************************98 PP

>> SIS  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   0.0   3.1e-11   1.9e-07       6     105 ..      26     116 ..      23     131 .. 0.85
   2 ?   -2.3   0.0       0.6   3.6e+03      18      33 ..     273     288 ..     272     303 .. 0.73

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 3.1e-11
                                   SEEEEEESHHHHHHHHHHHHHHHHHHTSEEEEEEHHHHHHTGGGG-STTCEEEEEESSSHHHHHHHHHHHHHHTTSEEEEE CS
                           SIS   6 kriyvlGaGtsyaiakelalkleeiggivvevedaselkhgvlalideddlvilisfsgetkdlvaaaelakergakiiaI 86 
                                   ++i++ G+G s+ +++ ++  +    +++v+ +d+++    + + +d+++ +i+is+sg+t +++ a e+a++++a++ aI
  gi|13542269|ref|NP_111957.1|  26 DKIVIAGMGGSGIAGRIFSEIY---DEKPVFLVDDYD----IPSFVDDKTEFIAISYSGNTEETISASEEAAKKHANVHAI 99 
                                   68*****************999...556666666666....4558999********************************* PP

                                   ESSTTSHHHHHSSEEEEEE CS
                           SIS  87 Tdskgsplareadlalyin 105
                                   T  +g +l+++   +++i+
  gi|13542269|ref|NP_111957.1| 100 T--SGGSLSKMGFDTIIIP 116
                                   *..7788888776666666 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.6
                                   HHHHHHHHHHHHHHTS CS
                           SIS  18 aiakelalkleeiggi 33 
                                   +++++l ++l+e++g+
  gi|13542269|ref|NP_111957.1| 273 HFGDYLTYHLAELRGV 288
                                   7899999999988764 PP

>> SIS_2  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   3.2e-05      0.19     107     138 .]      70     101 ..      62     101 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.2e-05
                                   EEEE-SS--SHHHHHHHHHHHHHT-EEEEEE- CS
                         SIS_2 107 LlviSnsGnnavvveaaeaakergmkviAlts 138
                                   ++ iS sGn +  + a e+a ++ ++v A+ts
  gi|13542269|ref|NP_111957.1|  70 FIAISYSGNTEETISASEEAAKKHANVHAITS 101
                                   899****************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        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 0.27s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 2023.72
//
Query:       gi|13542270|ref|NP_111958.1|  [L=253]
Description: hypothetical protein TVN1439 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-09   37.9   0.0    1.5e-09   37.3   0.0    1.2  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 !   37.3   0.0   8.5e-14   1.5e-09      27     245 ..      22     225 ..       5     248 .. 0.78

  Alignments for each domain:
  == domain 1  score: 37.3 bits;  conditional E-value: 8.5e-14
                          LigB  27 vikgyesireriaeksPdtiivvsphhlt.dvnpvfvlgvaeefeaiddfgkflprleyelkgnpeLaekiaealkksgid 106
                                   + k++e+i++   ++  +t++v+sph+ + d++ v v++  + ++a  +       +   ++++ eLa+ ia +  ++  +
  gi|13542270|ref|NP_111958.1|  22 DRKMHEAIKKYSENDDSETLVVISPHGIVlDRD-VGVIYSSKLSGAYRTKH---HYIRKTYDNDLELADSIARSQHAQHLR 98 
                                   458999999999999**************7777.66777777666666644...55666899******************* PP

                          LigB 107 lav..esnsmklDHGtlvPLelmlpdeakvpvikvslntvaypllsferlykLGeAlrkaveeldknvlilgsGglsHqle 185
                                     +   +   +lD+Gtl+PL++            v+ ++    ll+      + + l +a++++++++  + s +  H+ +
  gi|13542270|ref|NP_111958.1|  99 CITlsGNVPCPLDFGTLIPLQFFKR-------KRVVAMG-EPRLLDYSAIVGFADDLYSAMSKFERKISLIISADQAHTHS 171
                                   98866566679***********988.......3566666.4458888888888899************************* PP

                          LigB 186 gdeaakadaqtlllneefdeelldllkegrveelckmskeelsaaagheeeelvplvval 245
                                   +d +++     ++ ++ +d+ ++d ++++++  l++++k  +++a+  ++  + ++v a+
  gi|13542270|ref|NP_111958.1| 172 KDGPYGF----SEDADLYDKIVIDSINNNDFHALINIDKSIVERAK--PDSYQNMIVTAR 225
                                   ***9933....3699***********************88888876..655555555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       588  (0.032796); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 1925.34
//
Query:       gi|13542271|ref|NP_111959.1|  [L=94]
Description: hypothetical protein TVN1440 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       281  (0.0156729); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); 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: 0.49u 0.33s 00:00:00.82 Elapsed: 00:00:00.53
# Mc/sec: 530.18
//
Query:       gi|13542272|ref|NP_111960.1|  [L=153]
Description: RNA-binding protein [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-19   68.7   0.6    4.5e-19   68.2   0.6    1.3  1  PUA       PUA domain
    3.8e-16   59.1   1.5    8.5e-16   58.0   0.1    2.0  2  DUF1947   Domain of unknown function (DUF1947)
    3.9e-07   30.3   0.2    6.6e-07   29.5   0.2    1.3  1  UPF0113   UPF0113 PUA domain
    2.4e-05   24.0   0.4    5.8e-05   22.8   0.1    1.8  2  PUA_3     PUA-like domain
    0.00071   20.2   0.0     0.0025   18.5   0.0    1.9  2  Pre-PUA   Pre-PUA-like domain


Domain annotation for each model (and alignments):
>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.2   0.6   1.2e-22   4.5e-19       2      73 ..      72     143 ..      71     144 .. 0.98

  Alignments for each domain:
  == domain 1  score: 68.2 bits;  conditional E-value: 1.2e-22
                                   EEEE-HHHHHHHHTT-EEEGGGEEEEETT--TTSEEEEEETTSCEEEEEEESS-HHHHHHHCTSEEEEEEEE CS
                           PUA   2 rvvvddgAvkallsgasLlapGvvevegdfeegdvVaivdedgelvavGlanysseelakikggksveierv 73 
                                   +vvvd+gA  ++ +g++++a G+++++ ++++gd+V i++e+g +++vG+a+ ++ee++  k+g +v+++++
  gi|13542272|ref|NP_111960.1|  72 AVVVDAGAEPHIINGSNVFAQGILSIDSSIKKGDIVFIKSEKGYFIGVGIAERNAEEIMNEKKGLAVRLIHH 143
                                   79*******************************************************************998 PP

>> DUF1947  Domain of unknown function (DUF1947)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.0   0.1   2.4e-19   8.5e-16       1      65 [.       3      65 ..       3      66 .. 0.93
   2 ?    0.0   0.1       0.3   1.1e+03      24      45 ..      97     118 ..      91     134 .. 0.74

  Alignments for each domain:
  == domain 1  score: 58.0 bits;  conditional E-value: 2.4e-19
                                  --EE--HHHHHHHHHHHHTTT---TT--..-EEEE-SS-EEEEETTEEEEEESSSEEE-HHHHHH CS
                       DUF1947  1 kRHfLSkKeakeileklkekyisislesdkiEieeekkeklYlingvpilfeeekliPtLklLlk 65
                                  ++HfLSk+e k + +  +e +i++s e+  +E+  + k ++Y+i g+p++f+ ++liP+++lL++
  gi|13542272|ref|NP_111960.1|  3 QKHFLSKRELKVLVSSAAEIGIDLSGEE--VEVSSSHKVSCYYIKGKPMAFQTDRLIPSVYLLNY 65
                                  79*******************5555555..*********************************96 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.3
                                   -TT--..-EEEE-SS-EEEEET CS
                       DUF1947  24 islesdkiEieeekkeklYlin 45 
                                   i+ + +k +i   k+ek Y+i+
  gi|13542272|ref|NP_111960.1|  97 IDSSIKKGDIVFIKSEKGYFIG 118
                                   5555545578888888888886 PP

>> UPF0113  UPF0113 PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   0.2   1.9e-10   6.6e-07       2      59 ..      73     133 ..      72     141 .. 0.87

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 1.9e-10
                       UPF0113   2 vvvkekaeklFLYGrdvlkesilkitesvkenqvvvVlnengeplGiGkirkdt..k.asp 59 
                                   vvv+  ae  ++ G +v+ ++il+i++s+k+++ v++ +e+g ++G+G++ ++      ++
  gi|13542272|ref|NP_111960.1|  73 VVVDAGAEPHIINGSNVFAQGILSIDSSIKKGDIVFIKSEKGYFIGVGIAERNAeeImNEK 133
                                   899999********************************************99887432333 PP

>> PUA_3  PUA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0         2   7.2e+03      32      41 ..      27      36 ..      15      38 .. 0.74
   2 !   22.8   0.1   1.6e-08   5.8e-05       4      54 ..      76     125 ..      73     127 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 2
                         PUA_3 32 dGdvVdvfse 41
                                  +G+ V+v s+
  gi|13542272|ref|NP_111960.1| 27 SGEEVEVSSS 36
                                  6888888876 PP

  == domain 2  score: 22.8 bits;  conditional E-value: 1.6e-08
                         PUA_3   4 kkkaekrlrqGhPwvfsneiasvegeledGdvVdvfsekgkflGtGyynpq 54 
                                     +ae  + +G   vf++ i s++  ++ Gd+V + sekg f+G+G+  ++
  gi|13542272|ref|NP_111960.1|  76 DAGAEPHIINGS-NVFAQGILSIDSSIKKGDIVFIKSEKGYFIGVGIAERN 125
                                   556666666664.69*******************************98765 PP

>> Pre-PUA  Pre-PUA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   6.9e-07    0.0025      49      83 ..      33      63 ..       6      68 .. 0.84
   2 ?   -1.5   0.0       1.2   4.2e+03      33      51 ..     122     140 ..     120     148 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 6.9e-07
                       Pre-PUA 49 vvklqgehvelyvvdgeplffqdregellPtlytl 83
                                  v +   ++v++y+++g+p+ fq+  + l+P++y+l
  gi|13542272|ref|NP_111960.1| 33 VSSS--HKVSCYYIKGKPMAFQT--DRLIPSVYLL 63
                                  3333..69***************..99******98 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.2
                       Pre-PUA  33 seeqleellpkkeevkvvk 51 
                                   +e + ee++++k+ + v  
  gi|13542272|ref|NP_111960.1| 122 AERNAEEIMNEKKGLAVRL 140
                                   5778899999999777654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 931.09
//
Query:       gi|13542273|ref|NP_111961.1|  [L=447]
Description: hypothetical protein TVN1442 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.11   12.2   0.1       0.26   11.0   0.1    1.6  1  DUF348    G5-linked-Ubiquitin-like domain


Domain annotation for each model (and alignments):
>> DUF348  G5-linked-Ubiquitin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   1.5e-05      0.26      20      38 ..     155     173 ..     155     175 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 1.5e-05
                                   HHHHHHTT----TT-EEES CS
                        DUF348  20 gdlLeeagitlgeqDkVsP 38 
                                   +d+Lee gi+ + qD+++ 
  gi|13542273|ref|NP_111961.1| 155 KDVLEEEGIKYSGQDEIEI 173
                                   7****************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (447 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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 0.29s 00:00:00.94 Elapsed: 00:00:00.52
# Mc/sec: 2563.84
//
Query:       gi|13542274|ref|NP_111962.1|  [L=288]
Description: transcription antitermination protein NusG [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.4e-17   61.2   0.0    1.6e-16   60.0   0.0    1.7  1  Spt5-NGN  Early transcription elongation factor of RNA pol II
    3.3e-05   23.7   0.2    0.00014   21.7   0.0    2.2  2  KOW       KOW motif


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 !   60.0   0.0   1.7e-20   1.6e-16       2      84 .]     136     225 ..     135     225 .. 0.94

  Alignments for each domain:
  == domain 1  score: 60.0 bits;  conditional E-value: 1.7e-20
                      Spt5-NGN   2 iwavkctagqErevalslmkkilelakken.......leIkSvfapdelkGyiyvEAdrkaaveralegipnvrgvvqglv 75 
                                   i a+k+t g E +va+ l +k+++ + +++        e+++++ap e+kGyi+vE++++++++ + ++i+ ++g+v+g++
  gi|13542274|ref|NP_111962.1| 136 IVALKTTVGSEVQVATDLNNKAERDRDERSqggekqpSEVFAIMAPYEIKGYIFVETMHPDRISYLAKDIRGYKGMVSGKI 216
                                   7899*****************98886665599***988******************************************* PP

                      Spt5-NGN  76 pikEvedll 84 
                                   +++E+ ++l
  gi|13542274|ref|NP_111962.1| 217 DLEEIAHYL 225
                                   *******97 PP

>> KOW  KOW motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.44     4e+03      14      20 ..     207     213 ..     206     218 .. 0.75
   2 !   21.7   0.0   1.6e-08   0.00014       2      31 ..     237     266 ..     236     268 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.44
                                   TCEEEEE CS
                           KOW  14 GktGkVv 20 
                                   G +G+V 
  gi|13542274|ref|NP_111962.1| 207 GYKGMVS 213
                                   8899996 PP

  == domain 2  score: 21.7 bits;  conditional E-value: 1.6e-08
                                   TSEEEESSSTTTTCEEEEEEEETTTTEEEE CS
                           KOW   2 GdhVkVvsGphkGktGkVvkvdqhkvrVfv 31 
                                   G  V+ v Gp+kG+++k+ ++d  k+ V+v
  gi|13542274|ref|NP_111962.1| 237 GSLVELVEGPFKGEKAKIISIDSVKEEVTV 266
                                   889**********************77776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 1951.39
//
Query:       gi|13542275|ref|NP_111963.1|  [L=104]
Description: protein translocase subunit Sss1 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      2e-05   24.4   0.1    3.1e-05   23.8   0.1    1.3  1  SecE           SecE/Sec61-gamma subunits of protein transloca
  ------ inclusion threshold ------
      0.051   13.4   0.2      0.086   12.6   0.2    1.3  1  Asp4           Accessory secretory protein Sec Asp4
       0.19   12.3   0.1       0.25   11.9   0.1    1.1  1  Ribosomal_L44  Ribosomal protein L44


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 !   23.8   0.1   5.1e-09   3.1e-05      11      47 ..      61      97 ..      57     103 .. 0.90

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 5.1e-09
                                  HHCCCCCHCCHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          SecE 11 lkKVtWPtrkEllkttvvVlvfvvimglflflvDlvf 47
                                  l+   +Ptr+E++k  ++++++ +i+g ++f++ l++
  gi|13542275|ref|NP_111963.1| 61 LRMARKPTRDEYIKVLLITAIGLLIIGGVGFIIYLLM 97
                                  78889****************************9886 PP

>> Asp4  Accessory secretory protein Sec Asp4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.2   1.4e-05     0.086      25      53 ..      66      94 ..      58      96 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.4e-05
                          Asp4 25 kttrsekinvtfnviiGlvillGviftlf 53
                                  k tr e i v +   iGl+i+ Gv f ++
  gi|13542275|ref|NP_111963.1| 66 KPTRDEYIKVLLITAIGLLIIGGVGFIIY 94
                                  88**********************99775 PP

>> Ribosomal_L44  Ribosomal protein L44
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   4.2e-05      0.25      18      48 ..      38      69 ..      34      75 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.2e-05
                                  SSHHHHHHHH.H-SSS.GGGGS----.--SSB CS
                 Ribosomal_L44 18 laqgkRrydrkqsgyg.GqtkpvfkkkaKttK 48
                                   ++++R ++rk s +g G++ ++++   K+t+
  gi|13542275|ref|NP_111963.1| 38 AEEIQRNIERKFSSIGkGKYARILRMARKPTR 69
                                  5789**************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       913  (0.0509231); expected 358.6 (0.02)
Passed bias filter:                      712  (0.0397122); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 712.14
//
Query:       gi|13542276|ref|NP_111964.1|  [L=375]
Description: hypothetical protein TVN1445 [Thermoplasma volcanium GSS1]
Scores for complete 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-178  592.9   0.0   2.6e-178  592.8   0.0    1.0  1  FBPase_3  Fructose-1,6-bisphosphatase


Domain annotation for each model (and alignments):
>> FBPase_3  Fructose-1,6-bisphosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  592.8   0.0  1.4e-182  2.6e-178       1     360 [.       2     365 ..       2     366 .. 0.99

  Alignments for each domain:
  == domain 1  score: 592.8 bits;  conditional E-value: 1.4e-182
                      FBPase_3   1 kvtlsvikaDvGslaGhtkvheellekveevleeakkkgllidfyvtkvGDDielimthtkgvdneevhklawdafkeate 81 
                                   kvt+s+ikaD+Gsl+Gh+ v+e+++e+++e++e++ k+ l++df++++vGDD +++m htkgvd+eevh+law+afk++te
  gi|13542276|ref|NP_111964.1|   2 KVTISHIKADIGSLPGHSLVDEKVMERIREYIEDHGKN-LVSDFRMAHVGDDAQITMVHTKGVDSEEVHELAWNAFKAGTE 81 
                                   89********************************9987.****************************************** PP

                      FBPase_3  82 vakelklygaGqDlLkdafsGnvkGlGPgvaelefeeRksepvvvfaaDktepgafnlplykifadpfntaGlvidpklhe 162
                                   vak+l+lygaGqDlLkd+fsGn+kG+GPgvae+e++eR+sep++v+++Dktepgafnlp+yk+fadpfnt+Glvid+++he
  gi|13542276|ref|NP_111964.1|  82 VAKKLGLYGAGQDLLKDSFSGNLKGMGPGVAEMEITERPSEPFIVYMMDKTEPGAFNLPIYKMFADPFNTPGLVIDETMHE 162
                                   ********************************************************************************* PP

                      FBPase_3 163 GfkfevlDvieekkillsapeelydllallgakeryvikrvysk.....kdeeiaavvsterlsliaGkYvGkDDPvaivR 238
                                   Gf+fe++Dvie+k+i+l+ap +lyd+la++g+k+ryvikrvy+k       +e++av+st++lsliaGkYvGkDDP a+vR
  gi|13542276|ref|NP_111964.1| 163 GFRFEIWDVIEHKAIMLEAPSDLYDILAMIGSKSRYVIKRVYTKpahkkLPDENVAVISTDKLSLIAGKYVGKDDPAAVVR 243
                                   *******************************************9877666789**************************** PP

                      FBPase_3 239 aqsglPavgevlepfalphlvaGwmrGshngplmPvslkdakptrfdgpprvvalgfqlkegklvgpvDlfddpafdeaRe 319
                                    qsglPa+ge le+fa+p++v+GwmrGs+ngp+mPvs+kdak+trfdgpprvvalg+ lk gkl+gpvD+fddpafd+aR+
  gi|13542276|ref|NP_111964.1| 244 LQSGLPAAGESLEAFAFPYFVSGWMRGSFNGPIMPVSMKDAKMTRFDGPPRVVALGYVLKGGKLEGPVDMFDDPAFDYARR 324
                                   ********************************************************************************* PP

                      FBPase_3 320 kaaeiadelRrqGpfephrlpeeeleYttlpevleklkerf 360
                                    a e++d++Rr+Gpfephrlp +e+eYttlp+v+eklk+rf
  gi|13542276|ref|NP_111964.1| 325 VAGELTDHIRRMGPFEPHRLPDQEMEYTTLPAVVEKLKNRF 365
                                   ****************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (375 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); 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: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.51
# Mc/sec: 2213.78
//
Query:       gi|13542277|ref|NP_111965.1|  [L=515]
Description: alternative thymidylate synthase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.4e-38  131.0   0.1    2.2e-19   70.0   0.0    2.4  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 !   70.0   0.0   1.2e-23   2.2e-19      30     188 .]      40     254 ..      15     254 .. 0.77
   2 !   58.8   0.2   3.4e-20   6.2e-16      37     187 ..     339     483 ..     290     484 .. 0.80

  Alignments for each domain:
  == domain 1  score: 70.0 bits;  conditional E-value: 1.2e-23
                                   ......S.GCCHHHHHHHHH.HTTGGGGGGG-EEEEEEEEEEHHHHHHHTT-TT.SEEEE--TTTSGCCCTC.....BS-- CS
                          Thy1  30 e.....e.eekkeklikkll.khghgsplehasftfeiegvSravlrqlvrHRi.asfsqqSqRYvesskea.....fvip 97 
                                            ++ e+++++++ ++g +s+ e  ++++ i++vS ++++ +   Ri +s+ ++S+RYv+++k+      ++ p
  gi|13542277|ref|NP_111965.1|  40 YekefkTgAKSGEEFYRRIFlEYGDESIAELTTAQMGIQNVSNVASKIIEEIRIgLSYLEKSTRYVRYDKKVdgrylYISP 120
                                   22212212255569******************************************************99446***88888 PP

                                   GGGC..C.HHHHHHHHHHHHHHHHHHHHHHHT............................................TCHHH CS
                          Thy1  98 peie..qkeeleelyeeamekaleaykellea............................................gvarE 132
                                   + i   +  +  ++y + +++ +e y ++l +                                              a +
  gi|13542277|ref|NP_111965.1| 121 ERIGisG--DDAKDYVQLCDNLFEFYSKALPQvedylrhkfpqdklvfqnaggktltemdqnekkiaersyinavrSRALD 199
                                   8777531..3445689999999999966665556666666666666666666666666666666666666666666669** PP

                                   HHGGGSBTTBEEEEEEEEEHHHHHHHHHHHSSTTS-HHHHHHHHHHHHHHHHHSHH CS
                          Thy1 133 daryvLPlatktklvvtmNlrsLlhflelracsrAqwEirelaeemleelkkvaPe 188
                                   d+ry+LP +t t++ +++N r+L+h +++ + ++   E+ +la+ +++elk  +P+
  gi|13542277|ref|NP_111965.1| 200 DVRYILPASTLTNIGISGNGRALIHLIQKLMEYE-IPETTKLAKDIYDELKPELPQ 254
                                   *************************999997776.689*************99995 PP

  == domain 2  score: 58.8 bits;  conditional E-value: 3.4e-20
                                   HHHHHHHHTTGGGGGGG-EEEEEEEEEEHHHHHHHTT-TTSEEEE--TTTSGCCCTCBS--GGGCC.HHHHHHHHHHHHHH CS
                          Thy1  37 klikkllkhghgsplehasftfeiegvSravlrqlvrHRiasfsqqSqRYvesskeafvippeieqkeeleelyeeameka 117
                                   + ++   + + g+ +e +++ fe+  +  + +r l+rHR + +    +  +      + +pp i++ +el+ +y+e m+++
  gi|13542277|ref|NP_111965.1| 339 RSLRANRRMKPGRAFESVNYVFELN-LNYGSFRDLQRHRFLGI--IRKPLTAAYG--YDTPPVISAIDELKTQYDELMANS 414
                                   233333455789*************.**************554..4555556554..889*****878999********** PP

                                   HHHHHHHHHTTCHHHHHGGGSBTTBEEEEEEEEEHHHHHHHHHHHSSTTS-HHHHHHHHHHHHHHHHHSH CS
                          Thy1 118 leaykelleagvarEdaryvLPlatktklvvtmNlrsLlhflelracsrAqwEirelaeemleelkkvaP 187
                                    + y++l+e ++ +   +yv+P a k  ++++ Nl +   f+elr+  +A+++ r++a  m++e++kv+P
  gi|13542277|ref|NP_111965.1| 415 SSFYQRLRE-KYGPWISQYVVPFAFKYPITFSTNLSEVTYFVELRSTAQAHFDLRDIAVSMYREVSKVHP 483
                                   *****9976.678999****************************************************** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (515 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       701  (0.0390987); expected 358.6 (0.02)
Passed bias filter:                      602  (0.0335769); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.68u 0.31s 00:00:00.99 Elapsed: 00:00:00.50
# Mc/sec: 3081.84
//
Query:       gi|13542278|ref|NP_111966.1|  [L=72]
Description: transcription regulator (HTH) [Thermoplasma volcanium GSS1]
Scores for 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-06   27.6   0.3    3.4e-05   23.6   0.1    2.0  2  TrmB             Sugar-specific transcriptional regulator Trm
     0.0017   18.2   0.0     0.0019   18.0   0.0    1.1  1  MarR_2           MarR family
     0.0024   17.8   0.1     0.0031   17.4   0.1    1.2  1  HTH_36           Helix-turn-helix domain
     0.0074   15.9   0.0     0.0084   15.7   0.0    1.3  1  GntR             Bacterial regulatory proteins, gntR family
  ------ inclusion threshold ------
       0.01   16.1   0.1      0.011   16.0   0.1    1.1  1  Rrf2             Transcriptional regulator
      0.012   15.7   0.0      0.014   15.4   0.0    1.1  1  HTH_46           Winged helix-turn-helix DNA binding
      0.016   15.3   0.8      0.026   14.6   0.8    1.3  1  z-alpha          Adenosine deaminase z-alpha domain
      0.016   15.1   0.3      0.024   14.5   0.2    1.3  1  Thioredoxin_15   Thioredoxin-like domain
      0.017   14.6   0.0      0.017   14.6   0.0    1.1  1  FAD_binding_7    FAD binding domain of DNA photolyase
      0.022   14.5   0.0      0.028   14.2   0.0    1.2  1  HTH_IclR         IclR helix-turn-helix domain
      0.027   15.0   0.1       0.03   14.8   0.1    1.2  1  HTH_27           Winged helix DNA-binding domain
      0.028   14.1   0.1      0.032   13.9   0.1    1.1  1  MAGE             MAGE family
      0.044   14.1   0.1      0.047   14.0   0.1    1.1  1  Penicillinase_R  Penicillinase repressor
      0.066   13.2   0.1      0.088   12.8   0.1    1.2  1  MarR             MarR family
      0.067   12.6   0.6       0.14   11.6   0.6    1.5  1  RNA_pol_Rpc34    RNA polymerase Rpc34 subunit
      0.067   13.2   0.0      0.071   13.2   0.0    1.2  1  Replic_Relax     Replication-relaxation
      0.091   12.5   0.2       0.15   11.8   0.1    1.4  2  HTH_41           Helix-turn-helix domain
        0.1   12.4   0.1       0.13   12.0   0.1    1.4  1  LexA_DNA_bind    LexA DNA binding domain
       0.15   12.2   0.0       0.21   11.8   0.0    1.3  1  DprA_WH          DprA winged helix domain


Domain annotation for each model (and alignments):
>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0      0.13   1.2e+02      36      47 ..       9      20 ..       2      23 .. 0.80
   2 !   23.6   0.1   3.6e-08   3.4e-05      22      58 ..      27      63 ..      21      72 .] 0.87

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.13
                                  CHCHHHHHHHHH CS
                          TrmB 36 rskvYevLrsLe 47
                                    k+Y+++++L 
  gi|13542278|ref|NP_111966.1|  9 AKKIYDAMKKLG 20
                                  5799****9995 PP

  == domain 2  score: 23.6 bits;  conditional E-value: 3.6e-08
                                  CCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                          TrmB 22 patadeiaeelgvprskvYevLrsLedkGlVerekgr 58
                                   +tad+i +++ + +s v+ +L++L +kG+V+r+ ++
  gi|13542278|ref|NP_111966.1| 27 LKTADDIMKAAALGKSIVNAALQELQKKGYVKRVARQ 63
                                  589******************************9865 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0     2e-06    0.0019      19      55 ..      24      61 ..       5      66 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2e-06
                                  TSEE.EHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                        MarR_2 19 grdl.tvgelarrlglsksavsrilkrLvaaGLverrp 55
                                  +++l t+ ++ ++  l ks v+ +l++L+++G+v r++
  gi|13542278|ref|NP_111966.1| 24 EEKLkTADDIMKAAALGKSIVNAALQELQKKGYVKRVA 61
                                  344669****************************9985 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.1   3.3e-06    0.0031       2      55 .]       4      57 ..       3      57 .. 0.94

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3.3e-06
                        HTH_36  2 rLspsaklllgslasfanknggcfpsqetlakrlglsknTvsraikeLeqlGyi 55
                                  +Ls++ak ++  + ++    ++   + ++++k+ +l k+ v  a++eL ++Gy+
  gi|13542278|ref|NP_111966.1|  4 ELSDNAKKIYDAMKKLGATSEEKLKTADDIMKAAALGKSIVNAALQELQKKGYV 57
                                  69***************666669******************************6 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   8.9e-06    0.0084      20      59 ..      23      62 ..       8      70 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 8.9e-06
                                  TTSB---HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETT CS
                          GntR 20 pGdkLPsereLaaefgVsrttvReALrrLeaeglverrqg 59
                                   ++kL +  +++++ + +++ v+ AL++L+ +g+v r  +
  gi|13542278|ref|NP_111966.1| 23 SEEKLKTADDIMKAAALGKSIVNAALQELQKKGYVKRVAR 62
                                  567777778999999********************99866 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   16.0   0.1   1.2e-05     0.011      12      58 ..      14      60 ..       4      71 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.2e-05
                                  HHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                          Rrf2 12 hallyLakeeeeepvsseeiaerqnispsylekilakLrkaglvksv 58
                                   a+  L + +ee+  ++++i +   + +s++   l++L+k+g+vk v
  gi|13542278|ref|NP_111966.1| 14 DAMKKLGATSEEKLKTADDIMKAAALGKSIVNAALQELQKKGYVKRV 60
                                  68889999999999******************************865 PP

>> HTH_46  Winged helix-turn-helix DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.0   1.5e-05     0.014      12      54 ..      16      58 ..       9      64 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.5e-05
                        HTH_46 12 LielpeelreninvlkyIqkrtnLSrSsimkvLseLkkggyIe 54
                                  + +l   + e+ + ++ I k   L +S +   L+eL+k gy++
  gi|13542278|ref|NP_111966.1| 16 MKKLGATSEEKLKTADDIMKAAALGKSIVNAALQELQKKGYVK 58
                                  5566666778888899999**********************97 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 ?   14.6   0.8   2.7e-05     0.026       4      53 ..       7      59 ..       4      63 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.7e-05
                                  HHHHHHHHHHHHC-.....TTCECCHHHHHHHHCC-HHHHHHHHHHHHHTTSEEE CS
                       z-alpha  4 eqaekilelLeelg.....ekkaatalalergLstpkreiNrvLydlerkgkvyr 53
                                  + a+ki +++++lg       k a  + ++  L+  k  +N++L +l++kg v r
  gi|13542278|ref|NP_111966.1|  7 DNAKKIYDAMKKLGatseeKLKTADDIMKAAALG--KSIVNAALQELQKKGYVKR 59
                                  7899999****99844432246788899999999..899************9987 PP

>> Thioredoxin_15  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.2   2.6e-05     0.024     178     211 ..       4      39 ..       2      41 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.6e-05
                                   HHHHTHHHHHHHHHHHT-T..TS--SHHHHHHHHHH CS
                Thioredoxin_15 178 erkkrikpvveaieelgle..skisdsdlvakvtSl 211
                                   e++  +k+++ a+++lg +  +k++++d+++k+ +l
  gi|13542278|ref|NP_111966.1|   4 ELSDNAKKIYDAMKKLGATseEKLKTADDIMKAAAL 39 
                                   678899************99899*********9987 PP

>> FAD_binding_7  FAD binding domain of DNA photolyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   1.8e-05     0.017      44      81 ..      32      69 ..       3      72 .] 0.76

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.8e-05
                                  HHHHTT-SS-HHHHHHHHHHHHHS---HHHHHHHHHHH CS
                 FAD_binding_7 44 eaWkeGrTGfPlvDAamrqLretGwmhnrlRmivasFl 81
                                  +  k++  G  +v Aa+++L+++G+++  +R+  a ++
  gi|13542278|ref|NP_111966.1| 32 DIMKAAALGKSIVNAALQELQKKGYVKRVARQKSAGYF 69
                                  4567788899*********************9988765 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 ?   14.2   0.0   2.9e-05     0.028      19      50 ..      27      59 ..      17      61 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.9e-05
                                  -.BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                      HTH_IclR 19 l.tlselArrtglpkStvhRlLqtLvelGyveq 50
                                  l t  ++ ++++l kS v   Lq L++ Gyv++
  gi|13542278|ref|NP_111966.1| 27 LkTADDIMKAAALGKSIVNAALQELQKKGYVKR 59
                                  557779*************************98 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.1   3.2e-05      0.03      19      59 ..      28      68 ..      15      72 .] 0.86

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.2e-05
                        HTH_27 19 kkladlcgrlnvedshisyslkkLtekGLvertgdeadrre 59
                                  k++ d++++  +++s +  +l +L +kG+v+r +  ++ ++
  gi|13542278|ref|NP_111966.1| 28 KTADDIMKAAALGKSIVNAALQELQKKGYVKRVARQKSAGY 68
                                  56689**********999************99999877665 PP

>> MAGE  MAGE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   3.4e-05     0.032     142     187 ..      10      62 ..       3      70 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.4e-05
                          MAGE 142 qeLekyLkrlgldenst.......skeitklklklde........lLkklvkqgYlvreke 187
                                   +++++ +k+lg++++++                k+ +         L++l+k+gY++r+  
  gi|13542278|ref|NP_111966.1|  10 KKIYDAMKKLGATSEEKlktaddiM--------KAAAlgksivnaALQELQKKGYVKRVAR 62 
                                   5788999999999996544444432........333355555555*************998 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1     5e-05     0.047       6      64 ..      10      70 ..       5      72 .] 0.75

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5e-05
                                  SHHHHHHHHHS-EEHHHHHHT..--GGG---HHHHHHHHHHHHHTTS-EEEEETTEEEEE- CS
               Penicillinase_R  6 aevmeilwekgeatvkevvee..leeekelaysTVktllrrLvkKgllsrekegrafiYsp 64
                                  +++++++ ++g ++ +++ ++  + +   l +s V   l+ L kKg+++r   +++  Y  
  gi|13542278|ref|NP_111966.1| 10 KKIYDAMKKLGATSEEKLKTAddIMKAAALGKSIVNAALQELQKKGYVKRVARQKSAGYFV 70
                                  5666666666666666665444466667889999*********************999975 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   9.3e-05     0.088      19      51 ..      29      61 ..      17      65 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 9.3e-05
                                  EHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE CS
                          MarR 19 svseLakklgvskstvtrvldrLekkGlieRsk 51
                                  +  ++ k+  + ks v  +l +L kkG+++R  
  gi|13542278|ref|NP_111966.1| 29 TADDIMKAAALGKSIVNAALQELQKKGYVKRVA 61
                                  45599999999*******************975 PP

>> RNA_pol_Rpc34  RNA polymerase Rpc34 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.6   0.00014      0.14       7      64 ..       4      63 ..       1      71 [. 0.69

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00014
                                  -HHHHHHHHHHHHHCS...SSSSHCCHHHHHHHSTTSHHHHHHHHHHHHHHCTSEECCC.S CS
                 RNA_pol_Rpc34  7 klqelkkrlleelrka...seqklfsqqdLqddipslslklllsavqeLldkkllvllkns 64
                                  +l++++k+++++++k    se+kl +  d+ +   +l ++ + +a+qeL +k+ ++ ++ +
  gi|13542278|ref|NP_111966.1|  4 ELSDNAKKIYDAMKKLgatSEEKLKTADDIMKA-AALGKSIVNAALQELQKKGYVKRVARQ 63
                                  568888888888887533456666666777776.777777888888888888888887733 PP

>> Replic_Relax  Replication-relaxation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   7.5e-05     0.071       6      46 ..      24      64 ..       9      70 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7.5e-05
                  Replic_Relax  6 ehrvlTtrqiarllfashratarrrLarLrelgllsr.lrkr 46
                                  e ++ T++ i+++   +++  ++ +L++L+++g+++r  r++
  gi|13542278|ref|NP_111966.1| 24 EEKLKTADDIMKAAALGKSI-VNAALQELQKKGYVKRvARQK 64
                                  678889999****9999999.****************55544 PP

>> HTH_41  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       9.1   8.6e+03      26      31 ..      15      20 ..      12      22 .. 0.65
   2 ?   11.8   0.1   0.00016      0.15       4      37 ..      25      58 ..      23      69 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 9.1
                        HTH_41 26 ALklLe 31
                                  A+k+L 
  gi|13542278|ref|NP_111966.1| 15 AMKKLG 20
                                  677764 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00016
                        HTH_41  4 dRlktIeelakeleLSvGlvQkALklLeddkais 37
                                  ++lkt +++ k   L+   v +AL+ L++++ ++
  gi|13542278|ref|NP_111966.1| 25 EKLKTADDIMKAAALGKSIVNAALQELQKKGYVK 58
                                  79****************************9996 PP

>> LexA_DNA_bind  LexA DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00014      0.13      30      60 ..      32      61 ..       4      66 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00014
                                  HHHHHHTS-.HHHHHHHHHHHHHTTSEE-GG CS
                 LexA_DNA_bind 30 eiaralglkSpsaveehLkaLerKGyierdp 60
                                  +i++a  l   s v+  L+ L++KGy++r  
  gi|13542278|ref|NP_111966.1| 32 DIMKAAALG-KSIVNAALQELQKKGYVKRVA 61
                                  677777777.7889999**********9875 PP

>> DprA_WH  DprA winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00022      0.21      27      58 ..      29      60 ..       2      62 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00022
                       DprA_WH 27 hvDqLvrrtglpaaevsaaLleLELaGlverl 58
                                  + D++++++ l  + v+aaL eL  +G+v+r 
  gi|13542278|ref|NP_111966.1| 29 TADDIMKAAALGKSIVNAALQELQKKGYVKRV 60
                                  79**************************9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (72 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1274  (0.0710581); expected 358.6 (0.02)
Passed bias filter:                      707  (0.0394333); expected 358.6 (0.02)
Passed Vit filter:                        83  (0.00462937); 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: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 506.66
//
Query:       gi|13542279|ref|NP_111967.1|  [L=378]
Description: hypothetical protein TVN1448 [Thermoplasma volcanium GSS1]
Scores for complete 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-102  343.2  18.7   2.4e-102  342.8  18.7    1.1  1  DUF373           Domain of unknown function (DUF373)
  ------ inclusion threshold ------
       0.17   10.9   5.8        2.2    7.3   0.4    2.3  2  TMEM237          Transmembrane protein 237


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 !  342.8  18.7  2.7e-106  2.4e-102       2     334 ..       3     352 ..       2     358 .. 0.95

  Alignments for each domain:
  == domain 1  score: 342.8 bits;  conditional E-value: 2.7e-106
                        DUF373   2 tLvlcvDrDdDlgrkagvktPvvGreavleaavklaladPeDSDvNalfgaikvydeLkaegedvevavvtGdekvgvead 82 
                                   tL+++vDrD+D+g kagv++PvvG++++++aa kl++adPeDSD+Nalfga+kvy++Lk++gedve+a++tGd++vg ++d
  gi|13542279|ref|NP_111967.1|   3 TLIINVDRDNDFGDKAGVNGPVVGYTECYNAALKLITADPEDSDSNALFGALKVYEDLKKKGEDVEIALLTGDNDVGEKSD 83 
                                   8******************************************************************************** PP

                        DUF373  83 rkiaeqldevlskleadsaivVsDGaeDesvlpiiqsrvkvdsvkrVvVkqsrniEstyyllkkalkdpelrktiLvplGl 163
                                   + +++q+ ev +  e+++ai+VsDGaeD++++p+i s++k+++vk+++V++++niEs+yy++ kalkd+++ + +++plGl
  gi|13542279|ref|NP_111967.1|  84 EILSKQVAEVTAGGEYSDAILVSDGAEDDYIVPVILSYIKIRYVKHIIVRHNENIESIYYYIVKALKDKKIVNKFIIPLGL 164
                                   ********************************************************************************* PP

                        DUF373 164 llliyallll..............lglpelalaiillllGlylllrGfgldelleelleklkesleegritfvtyvvalll 230
                                   ++l+y+l++l              ++++  a+++++l+lG+yll rGf+l +++++++++++e+ + +ri f+ty++a ll
  gi|13542279|ref|NP_111967.1| 165 VFLTYGLVSLvfilysayatgvkvIDPTVGAITFVTLVLGVYLLERGFDLIKVVSKFIREVHEYAQDTRILFFTYIIAGLL 245
                                   ***********************999999**************************************************** PP

                        DUF373 231 lligiisgyislesvssasvssglltlilafiygavewlalailtaslgkiideylkreekdiarllllpflvlaiglvly 311
                                   +l+gi+s+y+ + ++s+     + l+++l+f++ +++w++ ai+t+ +g++++ ++ +++  i ++++ +++ l+i++v+y
  gi|13542279|ref|NP_111967.1| 246 VLVGIASSYTIAVRTSK-----NDLDAFLIFLSLFTWWVYGAIFTSEVGRVTELAV-GRKVGILKIWYGLIFSLSIAFVVY 320
                                   ********999666555.....7799******************************.7779999***************** PP

                        DUF373 312 gasaylls.........lsilalslvvgivva 334
                                   g+++y+ +             +++l++g+++a
  gi|13542279|ref|NP_111967.1| 321 GMFNYIRYilgfislksGLVSIFFLILGLIIA 352
                                   ******77999999999444555555555554 PP

>> TMEM237  Transmembrane protein 237
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.8    0.0006       5.4     146     205 ..     200     262 ..     187     276 .. 0.82
   2 ?    7.3   0.4   0.00025       2.2     166     202 ..     329     365 ..     305     377 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0006
                       TMEM237 146 lalstvsalDr.ldLakasta.lrklitldn.galaiilYflaLvlslsqqmtddrlnlysyk 205
                                     +  v+ l+r +dL k  ++ +r++ ++ + + ++ + Y++a +l l     ++ + + + k
  gi|13542279|ref|NP_111967.1| 200 TLVLGVYLLERgFDLIKVVSKfIREVHEYAQdTRILFFTYIIAGLLVLVGIASSYTIAVRTSK 262
                                   446689**********************97625677789****99999999999999998443 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.00025
                       TMEM237 166 lrklitldngalaiilYflaLvlslsqqmtddrlnly 202
                                   + ++i l++g++ i++ +l+L++    +m+   +n +
  gi|13542279|ref|NP_111967.1| 329 ILGFISLKSGLVSIFFLILGLIIAIISSMVHRYFNEN 365
                                   5689********************9999998766654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (378 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1102  (0.0614647); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.67u 0.33s 00:00:01.00 Elapsed: 00:00:00.51
# Mc/sec: 2218.57
//
Query:       gi|13542280|ref|NP_111968.1|  [L=219]
Description: hypothetical protein TVN1449 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.2e-15   57.6   0.1    1.8e-15   57.1   0.1    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 !   57.1   0.1   9.9e-20   1.8e-15      22     166 ..      38     175 ..      24     178 .. 0.84

  Alignments for each domain:
  == domain 1  score: 57.1 bits;  conditional E-value: 9.9e-20
                    MAF_flag10  22 fkg...nkpaiivgaGPSLeknlellkelrdkaviiaadtalkaLlkegIkPDivvs.lDpqeasyevfkeaekkgdiplv 98 
                                   fk    ++++ +vg+GP L++ l  +     k + i ad+a+++  +e   PDi+v+ lD+   +   + +++ +g  ++v
  gi|13542280|ref|NP_111968.1|  38 FKLphrSNEINVVGNGPELKDILTTVT----KRFAIVADSAISIYYEELGCPDIIVTdLDG---DLSKIWNCKGQGTLIVV 111
                                   44344569999*********9888884....4566668***********************...7777899999999**** PP

                    MAF_flag10  99 fasgvnpellkkykgpkiflvtgstqalelleeekneilfgGgsvantaldlAvklgfkeIiliGqDl 166
                                   +a+g+n++ + + k++    v g+tq+l++     ++++f G+s++++a  lA +lg+++I+liG+D+
  gi|13542280|ref|NP_111968.1| 112 HAHGDNIKRIIANKEHIDRRVAGTTQNLPYR----QIKNFYGFSDGDRAAYLADYLGAQKIFLIGFDF 175
                                   *******999888888777777777763333....559*****************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       305  (0.0170115); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1450.76
//
Query:       gi|13542281|ref|NP_111969.1|  [L=218]
Description: L-fuculose-phosphate aldolase [Thermoplasma volcanium GSS1]
Scores for complete 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-49  167.8   0.2    2.8e-49  167.6   0.2    1.0  1  Aldolase_II  Class II Aldolase and Adducin N-terminal domain
  ------ inclusion threshold ------
        3.4    7.4   3.9         61    3.3   0.0    2.9  3  TEP1_N       TEP1 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 !  167.6   0.2   3.1e-53   2.8e-49       2     186 .]       8     183 ..       7     183 .. 0.96

  Alignments for each domain:
  == domain 1  score: 167.6 bits;  conditional E-value: 3.1e-53
                                   HHHHHHHHHHHTTSSCTTBCEEEEEETSTTEEEEEBTSS-GGGHTGGGEEEEETTSCEEEECECSSSTB-TTHHHHHHHHH CS
                   Aldolase_II   2 elaeasrllarrglvegtgGniSvrvpeedsflitpsgvdfeeltaedlvvvdldsgevvegkekggkpssetplHlaiyk 82 
                                   +++ea+r++a+ gl+ g +GniSvr + ++++ itpsg+++ + + ed+v+ ++d g ++eg    ++psse+++H +iy+
  gi|13542281|ref|NP_111969.1|   8 QVVEACRRIAQDGLTVGSWGNISVRAD-DGKIAITPSGKNYNKTEKEDIVITSID-GDILEG---HLTPSSERLMHYEIYR 83 
                                   79***********************98.99999*********************9.****66...579************* PP

                                   H-TT-SEEEEE--HHHHHHHTCCSTSCHCCSSHHHHC.HSSSEEEEES-SSTTCHHHHHHHHHHHHHS-SEEEETTTEEEE CS
                   Aldolase_II  83 arpdaravvHtHspaavalsalagkeglppltqeaaklllgdevpvipyaapgteelgealaealkedakavllrnHGllt 163
                                   +r+d++a+vHtHs +  +ls +   + lp++t++  + +lg +v v++ya+ gt++l+++++eal+ d++a +++nHG+++
  gi|13542281|ref|NP_111969.1|  84 KRSDVKAIVHTHSVYSSILSVV--DDDLPAITEDVIM-ILGRSVRVAKYAMTGTVDLAKNVVEALG-DSNATIMKNHGAVA 160
                                   ********************66..688**********.88999**********************8.999*********** PP

                                   EESSHHHHHHHHHHHHHHHHHHH CS
                   Aldolase_II 164 vGetleeAvalaetleeaaeiql 186
                                   vG++++ A+a a++le++a+i++
  gi|13542281|ref|NP_111969.1| 161 VGKDIDRAMAAAYVLEKSAKIYV 183
                                   *********************96 PP

>> TEP1_N  TEP1 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   1.0    0.0077        69       9      17 ..      96     104 ..      93     104 .. 0.89
   2 ?   -1.4   0.0       0.2   1.8e+03       3      14 ..     154     165 ..     154     165 .. 0.88
   3 ?    3.3   0.0    0.0068        61       1      13 [.     184     196 ..     184     196 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.0077
                        TEP1_N   9 SaHpDILSL 17 
                                   S++++ILS+
  gi|13542281|ref|NP_111969.1|  96 SVYSSILSV 104
                                   9*******6 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.2
                        TEP1_N   3 KphGhvSaHpDI 14 
                                   K hG v++  DI
  gi|13542281|ref|NP_111969.1| 154 KNHGAVAVGKDI 165
                                   78****998888 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.0068
                        TEP1_N   1 lEKphGhvSaHpD 13 
                                   + K+ G vSa pD
  gi|13542281|ref|NP_111969.1| 184 MAKLLGKVSAVPD 196
                                   679*******999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       486  (0.0271069); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1471.50
//
Query:       gi|13542282|ref|NP_111970.1|  [L=118]
Description: hypothetical protein TVN1451 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-05   25.0   0.8    1.4e-05   24.7   0.8    1.2  1  SHOCT           Short C-terminal domain
  ------ inclusion threshold ------
      0.013   14.3   2.5      0.013   14.3   2.5    1.1  1  DUF2207         Predicted membrane protein (DUF2207)
      0.016   15.2   8.6      0.019   14.9   8.6    1.1  1  DctQ            Tripartite ATP-independent periplasmic transp
      0.043   14.2   1.7        2.7    8.4   0.0    2.1  2  DUF805          Protein of unknown function (DUF805)
      0.067   13.1   0.3      0.067   13.1   0.3    1.7  2  MRAP            Melanocortin-2 receptor accessory protein fam
      0.086   13.2   0.0       0.15   12.5   0.0    1.3  1  RIC3            Resistance to inhibitors of cholinesterase ho
       0.15   12.5   0.6       0.24   11.9   0.6    1.3  1  DUF4231         Protein of unknown function (DUF4231)
       0.31   10.9   1.9        7.3    6.4   0.7    2.2  2  SurA_N_2        SurA N-terminal domain
       0.37   10.8   6.5       0.76    9.8   6.5    1.5  1  Halogen_Hydrol  5-bromo-4-chloroindolyl phosphate hydrolysis 
       0.59   10.4   2.9        2.3    8.5   0.0    2.1  2  DUF4381         Domain of unknown function (DUF4381)
       0.74   10.1   4.8         16    5.9   0.2    2.5  3  Sigma_reg_N     Sigma factor regulator N-terminal
        2.1    7.0   3.7       0.89    8.2   2.1    1.3  2  Ndc1_Nup        Nucleoporin protein Ndc1-Nup
        3.3    7.3  11.5        7.8    6.1   9.1    1.9  2  SBF             Sodium Bile acid symporter family
        5.2    7.1   8.2        4.6    7.3   0.2    2.1  2  FixH            FixH
        8.3    6.0   6.3         15    5.2   6.3    1.5  1  DUF4131         Domain of unknown function (DUF4131)


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 !   24.7   0.8   1.2e-08   1.4e-05       2      27 ..      91     116 ..      90     117 .. 0.88

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 1.2e-08
                         SHOCT   2 aLekLkeLyarGeIteEEFeakKakL 27 
                                   a ++ +e++a+GeIte+ +++   ++
  gi|13542282|ref|NP_111970.1|  91 AEDIARERFAKGEITEDQYNRIINEI 116
                                   7799****************986665 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   2.5   1.1e-05     0.013     383     430 ..      10      70 ..       1     101 [. 0.62

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.1e-05
                       DUF2207 383 lsalglgliilglilillallllvll..............lvfllilllillliaiivlllf 430
                                   + ++g++ ++++++++++++++ +++              + ++li+ ++ ++++i++++++
  gi|13542282|ref|NP_111970.1|  10 WLLIGII-ALIAVVVFVYSIFAGGTFysfgygprvivgglFGWWLIMPIFAFFVMIFFVIMM 70 
                                   2222222.233333334444444444888*******99986666666666666655555554 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 ?   14.9   8.6   1.6e-05     0.019      59     127 ..       3      71 ..       1      74 [. 0.84

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.6e-05
                          DctQ  59 prvrrlleliadllallfaavliwagw..levaaalfeettpvlglplwwvylvlpigaallalvalarll 127
                                   ++v +++ l++ ++al++++v++++ +  + +++++++ +  v gl  ww    +pi+a++++++++  ++
  gi|13542282|ref|NP_111970.1|   3 KKVENFAWLLIGIIALIAVVVFVYSIFagGTFYSFGYGPRVIVGGLFGWWLI--MPIFAFFVMIFFVIMMF 71 
                                   6888899999999999999999999999999********************8..88888777777776655 PP

>> DUF805  Protein of unknown function (DUF805)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.5      0.02        24      72     103 ..      10      41 ..       4      43 .. 0.76
   2 ?    8.4   0.0    0.0023       2.7      69      92 ..      49      72 ..      46     109 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.02
                        DUF805  72 llllllvplialllllvllllpgtpgenryGp 103
                                   +ll++++ lia++++++ ++  gt  +  yGp
  gi|13542282|ref|NP_111970.1|  10 WLLIGIIALIAVVVFVYSIFAGGTFYSFGYGP 41 
                                   67889998888888888888888877777776 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0023
                        DUF805 69 sgwllllllvplialllllvllll 92
                                   gw+l++ +  +++++++++++++
  gi|13542282|ref|NP_111970.1| 49 FGWWLIMPIFAFFVMIFFVIMMFS 72
                                  589977666666554544444443 PP

>> MRAP  Melanocortin-2 receptor accessory protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   1.2       3.3   3.9e+03      44      56 ..      16      28 ..       4      37 .. 0.65
   2 ?   13.1   0.3   5.6e-05     0.067      46      77 ..      57      88 ..      44      96 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 3.3
                          MRAP 44 vsLavfvvllflv 56
                                  ++L + vv+++ +
  gi|13542282|ref|NP_111970.1| 16 IALIAVVVFVYSI 28
                                  4455555555544 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 5.6e-05
                          MRAP 46 LavfvvllflvLlylsksGspqqrnsekrhra 77
                                  + +f v++f+v++++s  G  + +n+   ++ 
  gi|13542282|ref|NP_111970.1| 57 IFAFFVMIFFVIMMFSSHGHDHWHNNRMDFKR 88
                                  45788999****************99888765 PP

>> RIC3  Resistance to inhibitors of cholinesterase homologue 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00012      0.15      73     125 ..      52     108 ..      46     117 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00012
                          RIC3  73 gtllPlYtiGilvfilYtllKikskkkkeksk....eakakkkakenakkkteteee 125
                                    +++P++++ +++f++ +++     ++ ++++     ++a++ a+e+++k + te +
  gi|13542282|ref|NP_111970.1|  52 WLIMPIFAFFVMIFFVIMMFSSHGHDHWHNNRmdfkRSRAEDIARERFAKGEITEDQ 108
                                   479************999999888886664434455666666677777777666666 PP

>> DUF4231  Protein of unknown function (DUF4231)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.6    0.0002      0.24      18      78 ..       9      84 ..       1      92 [. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0002
                       DUF4231 18 rllrlitivlgallpilvs...............sklgagvsvlkiltallsalvailaaleeffrykerWrryRs 78
                                   +l + +i l a++ ++ s                + g  + ++ i++ ++  + ++  +++   + +++W+++R+
  gi|13542282|ref|NP_111970.1|  9 AWLLIGIIALIAVVVFVYSifaggtfysfgygprVIVGGLFGWWLIMPIFAFFVMIFFVIMMFSSHGHDHWHNNRM 84
                                  34444455555555555556788**********989999************************************7 PP

>> SurA_N_2  SurA N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.7    0.0061       7.3       6      38 ..       7      39 ..       3      47 .. 0.70
   2 ?    3.9   0.0     0.036        44      14      63 ..      61     116 ..      49     118 .] 0.57

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0061
                      SurA_N_2  6 eksqgllvii.iglallaFilgdlfgvgsylfss 38
                                  + ++ ll++i   +a+++F+ + + g + y+f+ 
  gi|13542282|ref|NP_111970.1|  7 NFAW-LLIGIiALIAVVVFVYSIFAGGTFYSFGY 39
                                  4556.66666377788999999999988887765 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.036
                      SurA_N_2  14 ii.iglallaFi..lgdlfgvgsy.lfssssnevae..VnGekIslqefqqaveea 63 
                                   ++ i++++++F     d + ++++ +++s+ +++a    +  +I+ +++++ ++e 
  gi|13542282|ref|NP_111970.1|  61 FVmIFFVIMMFSshGHDHWHNNRMdFKRSRAEDIARerFAKGEITEDQYNRIINEI 116
                                   33366666666666778888887733333444444212334477777777766665 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 ?    9.8   6.5   0.00063      0.76       3      88 ..      10     117 ..       8     118 .] 0.72

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00063
                Halogen_Hydrol   3 gwllsiliavivalvsffllgfsfflallia...ilggilvyvasr.......................knkkkkhlkksg 57 
                                   + l++i++++ v+++++ ++    f +++++   i+gg++ ++ ++                       +  ++  +k+  
  gi|13542282|ref|NP_111970.1|  10 WLLIGIIALIAVVVFVYSIFAGGTFYSFGYGprvIVGGLFGWWLIMpifaffvmiffvimmfsshghdhWHNNRMDFKR-- 88 
                                   445555555666677778888889999999999************9999999999999999999665553333333333.. PP

                Halogen_Hydrol  58 lsrkelkyiretlkeakekikrlekalkrvr 88 
                                    sr e ++ re +++++    + +++++++r
  gi|13542282|ref|NP_111970.1|  89 -SRAE-DIARERFAKGEITEDQYNRIINEIR 117
                                   .4445.7788888888777777777777766 PP

>> DUF4381  Domain of unknown function (DUF4381)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   2.3       0.5     6e+02      22      38 ..      10      26 ..       7      32 .. 0.66
   2 ?    8.5   0.0    0.0019       2.3      19      50 ..      49      89 ..      47     118 .] 0.56

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.5
                       DUF4381 22 wlllaalllllllvlal 38
                                  wll+ +++l++++v+++
  gi|13542282|ref|NP_111970.1| 10 WLLIGIIALIAVVVFVY 26
                                  88885666666666655 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0019
                       DUF4381 19 pGwwlllaalllllllvlalwllr.....rrkrn.....rre 50
                                   Gwwl++ + +++++++++++ +      + + n     +r 
  gi|13542282|ref|NP_111970.1| 49 FGWWLIMPIFAFFVMIFFVIMMFSshghdH-WHNnrmdfKRS 89
                                  69***9966555555555555555445532.22234566333 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 ?    5.9   0.2     0.013        16       5      37 ..       3      35 ..       2      40 .. 0.78
   2 ?    5.8   0.5     0.014        16      19      42 ..      57      80 ..      51      96 .. 0.48
   3 ?   -1.9   0.0       3.5   4.2e+03      66      85 ..      93     112 ..      88     116 .. 0.68

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.013
                   Sigma_reg_N  5 kkakrksilrivlislivlllifvilvvtllyl 37
                                  kk+ + ++l i +i+li++++++  ++ ++ ++
  gi|13542282|ref|NP_111970.1|  3 KKVENFAWLLIGIIALIAVVVFVYSIFAGGTFY 35
                                  577778899999999998888877777776665 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.014
                   Sigma_reg_N 19 slivlllifvilvvtllylaekeg 42
                                  +++++++if+++++  ++ +++ +
  gi|13542282|ref|NP_111970.1| 57 IFAFFVMIFFVIMMFSSHGHDHWH 80
                                  444555555444333333322222 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 3.5
                   Sigma_reg_N  66 svsqsgffggeieyelskqv 85 
                                   ++++++f +gei+ + + ++
  gi|13542282|ref|NP_111970.1|  93 DIARERFAKGEITEDQYNRI 112
                                   56667777777777777665 PP

>> Ndc1_Nup  Nucleoporin protein Ndc1-Nup
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   2.1   0.00074      0.89       9      61 ..       7      70 ..       1      91 [. 0.65
   2 ?   -3.7   0.0         3   3.5e+03     517     529 ..     104     116 ..     104     117 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00074
                      Ndc1_Nup  9 haallllllsyllslllslsssl.....................lwswfplgpaglralllflsllpilvlrka 61
                                  ++a+ll+ +  l+++++++ s +                     +w ++p          +f ++++i+++ + 
  gi|13542282|ref|NP_111970.1|  7 NFAWLLIGIIALIAVVVFVYSIFaggtfysfgygprvivgglfgWWLIMP----------IFAFFVMIFFVIMM 70
                                  67899999999999999874444788666667777777777666666666..........33333333333333 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 3
                      Ndc1_Nup 517 ltEDqyGvVqrdv 529
                                   +tEDqy  + + +
  gi|13542282|ref|NP_111970.1| 104 ITEDQYNRIINEI 116
                                   79****9998876 PP

>> SBF  Sodium Bile acid symporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.9      0.11   1.3e+02     166     188 ..      10      32 ..       2      39 .. 0.75
   2 ?    6.1   9.1    0.0065       7.8      26      56 ..      40      70 ..      18      84 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.11
                           SBF 166 lpavspisligllltivvifalk 188
                                     ++ +i+li++++ ++ ifa+ 
  gi|13542282|ref|NP_111970.1|  10 WLLIGIIALIAVVVFVYSIFAGG 32 
                                   55688899999999999998876 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0065
                           SBF 26 rpkalllglvlqwvikPllmfilakillrdl 56
                                   p+ ++ gl+  w+i+P+ +f   ++++ ++
  gi|13542282|ref|NP_111970.1| 40 GPRVIVGGLFGWWLIMPIFAFFVMIFFVIMM 70
                                  48999***************99999888776 PP

>> FixH  FixH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   3.1     0.087     1e+02       5      34 ..       9      34 ..       6      37 .. 0.74
   2 ?    7.3   0.2    0.0038       4.6       5      26 ..      50      71 ..      47      97 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.087
                          FixH  5 gwhvllflialfavvvvvnltmlylAvstk 34
                                   w    +li+++a+++vv+++  ++A  t+
  gi|13542282|ref|NP_111970.1|  9 AW----LLIGIIALIAVVVFVYSIFAGGTF 34
                                  58....888888888888888888776665 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0038
                          FixH  5 gwhvllflialfavvvvvnltm 26
                                  gw+ ++ ++a+f+++++v +++
  gi|13542282|ref|NP_111970.1| 50 GWWLIMPIFAFFVMIFFVIMMF 71
                                  8877777777766666554443 PP

>> DUF4131  Domain of unknown function (DUF4131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   6.3     0.013        15       5      58 ..       8      77 ..       5     110 .. 0.65

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.013
                       DUF4131  5 lalvllalllllllllllllrr........rprrrv........llllllllllallgfalrapqpnand 58
                                  +a++l+++++l++++ ++++ +         + +rv        +l+  +++++++++f++   + + +d
  gi|13542282|ref|NP_111970.1|  8 FAWLLIGIIALIAVVVFVYSIFaggtfysfGYGPRVivgglfgwWLIMPIFAFFVMIFFVIMMFSSHGHD 77
                                  5566666666666666666555898888884445556677777677777777777777777665555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1441  (0.0803726); expected 358.6 (0.02)
Passed bias filter:                      734  (0.0409393); expected 358.6 (0.02)
Passed Vit filter:                       120  (0.00669307); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 729.16
//
Query:       gi|13542283|ref|NP_111971.1|  [L=190]
Description: rusticyanin [Thermoplasma volcanium GSS1]
Scores for 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   25.9   0.0    3.2e-05   24.3   0.0    1.7  2  Copper-bind   Copper binding proteins, plastocyanin/azurin fa
     0.0003   20.3   2.2    0.00054   19.5   0.1    2.1  2  SoxE          Sulfocyanin (SoxE) domain
  ------ inclusion threshold ------
      0.043   13.9   0.2       0.28   11.3   0.0    2.1  2  Cu-oxidase    Multicopper oxidase
       0.35   10.9   5.1       0.28   11.2   2.2    2.2  2  Cu-oxidase_3  Multicopper oxidase


Domain annotation for each model (and alignments):
>> Copper-bind  Copper binding proteins, plastocyanin/azurin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.99   4.4e+03       8      32 ..      43      67 ..      39      73 .. 0.75
   2 !   24.3   0.0   7.1e-09   3.2e-05      17      98 ..      94     189 ..      85     190 .] 0.81

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.99
                                  TTETSEEESSEEEEETTEEEEEEEE CS
                   Copper-bind  8 esgdlqFetkeitvkkgekvtfvnl 32
                                  e ++l+  +  ++v++ ++  ++n+
  gi|13542283|ref|NP_111971.1| 43 ELNSLNITPPGVQVSSNQSAIYINN 67
                                  5567788888899999888888887 PP

  == domain 2  score: 24.3 bits;  conditional E-value: 7.1e-09
                                   SEEEEETTEEEEEEEE...SSSSBEEEEET.........TSSTTTGGGT..TSCTTCEEEEBSTTEEEEEEEESSEEEEEE CS
                   Copper-bind  17 keitvkkgekvtfvnl...avmgHNvvldk.........dgvpagvdkd..kvkaedetkliggGekdsvtfdeagtYkff 83 
                                    +i vk+g +v f+     ++  HN  +++         +++  g++ +  ++ +  +  l +   +++ tf+  g+Y + 
  gi|13542283|ref|NP_111971.1|  94 PTIVVKEGVSVHFIVInvdTDSYHNFAISNrgppypymvGMMGLGFEYKapYLPPV-HSDLYAY-SEFNYTFSSIGDYWYL 172
                                   67999999999998876788899****99999999999977666666551155554.5557766.6799************ PP

                                   ET.T.TTTTTSEEEEEE CS
                   Copper-bind  84 Cs.P.HaaagMkgkvtv 98 
                                   C+ P Ha  gM+g+++v
  gi|13542283|ref|NP_111971.1| 173 CTyPgHAENGMYGEIIV 189
                                   ***************98 PP

>> SoxE  Sulfocyanin (SoxE) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.3     0.096   4.3e+02      24      65 ..      79     121 ..      54     138 .. 0.55
   2 !   19.5   0.1   1.2e-07   0.00054     114     138 ..     165     189 ..     154     190 .] 0.91

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.096
                          SoxE  24 sasnlfnfnGtsnGqlkiyiPagwsvlvklvnees.lphnlvl 65 
                                    a+ ++ f+     + +i +  g sv ++++n ++   hn ++
  gi|13542283|ref|NP_111971.1|  79 YAPSMYSFEILRLINPTIVVKEGVSVHFIVINVDTdSYHNFAI 121
                                   4444444444444445566666666666666655413345444 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 1.2e-07
                          SoxE 114 saGtywlacgilGhaesGmWvdliv 138
                                   s G+yw  c+ +Ghae+Gm+ ++iv
  gi|13542283|ref|NP_111971.1| 165 SIGDYWYLCTYPGHAENGMYGEIIV 189
                                   67******************99997 PP

>> Cu-oxidase  Multicopper oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   6.3e-05      0.28      59      89 ..      93     123 ..      40     124 .. 0.82
   2 ?    0.2   0.0      0.16   7.4e+02     122     147 ..     161     181 ..     157     189 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 6.3e-05
                                   SGGGEEEEETTEEEEEEEESSS-BEEEEETS CS
                    Cu-oxidase  59 latltvepgktyrlriinvsaddslnfsIeG 89 
                                   ++t+ v+ g+ + + +inv +d+++nf+I +
  gi|13542283|ref|NP_111971.1|  93 NPTIVVKEGVSVHFIVINVDTDSYHNFAISN 123
                                   78999************************87 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.16
                                   EEE-SSSEEEEEEEEGSSSCHHHHTT CS
                    Cu-oxidase 122 vtanqapgnYwivasgrsnlieafen 147
                                   +t++   g+Yw+ +++      + en
  gi|13542283|ref|NP_111971.1| 161 YTFSS-IGDYWYLCTY----PGHAEN 181
                                   66775.89******53....333444 PP

>> Cu-oxidase_3  Multicopper oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       1.2   5.5e+03      13      27 ..      58      72 ..      48      75 .. 0.64
   2 ?   11.2   2.2   6.2e-05      0.28      25     115 ..      92     190 .]      89     190 .] 0.67

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.2
                                  ESEEEEEECTSSBS- CS
                  Cu-oxidase_3 13 terevitvNgqfpgp 27
                                  +++++i +N++   p
  gi|13542283|ref|NP_111971.1| 58 SNQSAIYINNSTTLP 72
                                  346777777776666 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 6.2e-05
                                   BS-EEEEETT-EEEEEEEE-S...SS-B-EEEET--S-GG.....GSCSGG.G-B-TT-EEEE.....EEE--S-SEEEEE CS
                  Cu-oxidase_3  25 pgptievregdtvvvnvtNkl...dentsihwhGlqqrktswmDGvpgvtq.cpiqpgesfty.....rftvkqqagtlwY 96 
                                   + pti v+eg +v   v+N      +n++i+  G   +  + m G+ +  +   ++p +s  y     ++t +  +g +wY
  gi|13542283|ref|NP_111971.1|  92 INPTIVVKEGVSVHFIVINVDtdsYHNFAISNRGPPYPYMVGMMGLGFEYKaPYLPPVHSDLYaysefNYTFSS-IGDYWY 171
                                   67888888887765555554322267788888888888777777765544404456655444311211566666.9***** PP

                                   EE--TTHHHTT-EEEEEEE CS
                  Cu-oxidase_3  97 hshlslqqaaGlaGaiiie 115
                                      + ++  +G++G ii++
  gi|13542283|ref|NP_111971.1| 172 LCTYPGHAENGMYGEIIVR 190
                                   *******99********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.32s 00:00:00.82 Elapsed: 00:00:00.50
# Mc/sec: 1146.45
//
Query:       gi|13542284|ref|NP_111972.1|  [L=314]
Description: formate hydrogenlyase, subunit 4 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-31  110.2  24.1    1.4e-31  110.0  24.1    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 !  110.0  24.1   7.6e-36   1.4e-31       5     297 ..      11     309 ..       7     311 .. 0.86

  Alignments for each domain:
  == domain 1  score: 110.0 bits;  conditional E-value: 7.6e-36
                                   HHHHHHHHHHH.HHHHHHHHHHHHHTTS--S-SSTTTTTTHHHHHHHHHCCS-----TTS-HHHHHHHHHHHHHHHHCTTT CS
                        NADHdh   5 lllvvlllvva.lltlleRkvlAriqdRlGPnrvGplGllqplaDalKlllKediipkkadkllfllapvlalilallafa 84 
                                   +  ++++l+ a l+t++  k+ A +++R+GP      +++qp++D+ Kl  K ++ip+++  ++f   p++++ +  l+ +
  gi|13542284|ref|NP_111972.1|  11 MQYFFVVLT-ApLYTGILEKLKAMVESRKGP------SIFQPYYDLWKLSRKITVIPAGS-GIFFRYIPYVLFGIYSLIAL 83 
                                   334344555.55*******************......********************999.9******************* PP

                                   TS-SS.S..SSS--TTHHHHHHHHHHHCHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-SS-HHHH CS
                        NADHdh  85 viPfg.e..vladlnvglllilalsslgvygillaGwasnskYallGalRsaaqmisyEvalglsllavvllagslslsei 162
                                   +iP+  +  ++   ++++l   +l+sl++++ + a+++s+s+Y  lG  Rs++     E +l+++++av ll+ + +    
  gi|13542284|ref|NP_111972.1|  84 IIPVViPvpIYFTASADFLGGAILFSLAAFMKAAAAMNSGSNYVALGVSRSMSFNFLSEGTLITVFIAVSLLTATNNPYIT 164
                                   ***9963447777788*********************************************************99987555 PP

                                   HHCCCTT..-C.CCCHHHHHHHHHHHHHHCCTCTTBTTTTSTTSS...SSCCCTT-HCHHHHHHHHHHHHHHHHHHHHHHH CS
                        NADHdh 163 veaqeei..wf.illqllafiifliallaetnraPFDlpeaesEL...vaGfhtEYsgmkfalfflaeyanmvlvsalavl 237
                                    +  +++   +  l+++++ ++f++ ++ et+++P++   + +EL    +G++ EYsg  +a+  +++y++ +l+ +++  
  gi|13542284|ref|NP_111972.1| 165 NAFLASHplANlSLAHIFSTLAFFMLFFYETGKIPLES-SGVQELgmiDEGLNYEYSGKLLAINKWSSYIKQYLLGSVLLN 244
                                   43334444433577789********************5.66778765589******************************* PP

                                   HCT.SS-HCCS.......HHHHHHHHHHHHHHHHHHHHHC----TCHHHHHHHCCTCHHHHHHHHHH CS
                        NADHdh 238 lFlgGwllpfs.......gllwfllKvllllflfiwiratlpRlRydqlmklgwkvllplalanlll 297
                                   +Fl  w l  s       ++ ++++K+lll+++++++++tl++lR+ ++m++  +  +++++++l++
  gi|13542284|ref|NP_111972.1| 245 VFLFPWGLF-StypyffiDVPVMMAKWLLLILIVLVVETTLAKLRLFRVMDYLAT-AFTFSILFLIF 309
                                   ***998543.246666889999*****************************9876.55555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       783  (0.0436723); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 2104.36
//
Query:       gi|13542285|ref|NP_111973.1|  [L=217]
Description: hypothetical protein TVN1454 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       899  (0.0501422); 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:                         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: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 1471.01
//
Query:       gi|13542286|ref|NP_111974.1|  [L=447]
Description: hydrogenase 4 subunit F [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.6e-47  161.0  26.8    3.6e-47  161.0  26.8    1.9  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 ?   -0.9   0.7     0.041   7.3e+02     208     255 ..      55     105 ..      37     108 .. 0.66
   2 !  161.0  26.8     2e-51   3.6e-47       3     288 ..     114     389 ..     112     398 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.041
               Proton_antipo_M 208 halfkallFllagsviyere...ktrdirayggLakkmPilalvllvllls 255
                                   ++  + +lF++++  +y  +   +tr+++ ++ +  + P+++l+l++++ s
  gi|13542286|ref|NP_111974.1|  55 YIQDSTMLFIIMVLSVYLLSaiySTRYLKGIEVMGIREPTYYLLLNLFTAS 105
                                   455556666555444443332447777777777777888888888777766 PP

  == domain 2  score: 161.0 bits;  conditional E-value: 2e-51
               Proton_antipo_M   3 dLlllylglElvllplylLiglwkkkpksleAslklflltllgsliLLlgilllynltgtlefeelskalelglnslelll 83 
                                   +  l+++g+E++ +++ lL     k++ sleA+  ++++ ++g  + +++i+l+y   gtl++ + +      ++s  ++l
  gi|13542286|ref|NP_111974.1| 114 NYGLMWVGIEATTISSALLLITE-KSETSLEATWRYIIIVSAGVTFAFISIILIYYTLGTLSVSTAIGS---HVHSRIMVL 190
                                   5668************9999887.566***********************************9988877...455555556 PP

               Proton_antipo_M  84 llllllvgllvKsaqvplhlWlpdayveaPtpvsallAatlvkagvlllirlllllavssneisqlllilaiismllgslv 164
                                   +  l l+g+ +K++++p+h+Wlpda+ eaP pvsa+++++l+  ++++l r+  +       ++ l ++ a++s++ +s+ 
  gi|13542286|ref|NP_111974.1| 191 AVSLALIGFGTKVGVFPVHTWLPDAHSEAPSPVSAMFSGVLLPTALYVLYRVYEIEP-----VRGLYVWFAVVSIVAASIF 266
                                   6666679*******************************************8766555.....8999999************ PP

               Proton_antipo_M 165 alaqtdiKrllAySsishlGymlialavatqygveaaiihllthalfkallFllagsviyerektrdirayggLakkmPil 245
                                      q  +Kr+ AyS++  + + l+++av+++ g+++a+++ll+h++ ka+ F  +g++  + +  ++i++++g+ ++mP +
  gi|13542286|ref|NP_111974.1| 267 MGYQARYKRMFAYSTMENMNLALLGIAVGGSLGFTGALLLLLSHSFGKAGAFYSSGNI-LRFTGKKEIAEINGMHTSMPYT 346
                                   *******************************************************999.78889***************** PP

               Proton_antipo_M 246 alvllvlllslaGlPptagFlskfliLeaavavslillvlavv 288
                                   ++ ll+  l+++G Pp+  F+++fliL+++++ ++++  ++v+
  gi|13542286|ref|NP_111974.1| 347 STSLLMSSLAVTGAPPFGTFFGEFLILSGVLSLHMYVQFIIVI 389
                                   *******************************999987666533 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (447 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       819  (0.0456802); expected 358.6 (0.02)
Passed bias filter:                      229  (0.0127726); 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: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.47
# Mc/sec: 2853.38
//
Query:       gi|13542287|ref|NP_111975.1|  [L=389]
Description: Ni,Fe-hydrogenase III large subunit [Thermoplasma volcanium GSS1]
Scores for complete 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   0.0    4.5e-16   58.8   0.0    2.3  2  Complex1_49kDa  Respiratory-chain NADH dehydrogenase, 49 Kd s
    1.7e-11   43.7   0.0    8.8e-07   28.2   0.0    2.5  3  NiFeSe_Hases    Nickel-dependent hydrogenase


Domain annotation for each model (and alignments):
>> Complex1_49kDa  Respiratory-chain NADH dehydrogenase, 49 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.8   0.0     5e-20   4.5e-16      14     157 ..     170     303 ..     163     308 .. 0.90
   2 !   21.4   0.0   1.2e-08   0.00011     197     268 ..     313     383 ..     308     385 .. 0.89

  Alignments for each domain:
  == domain 1  score: 58.8 bits;  conditional E-value: 5e-20
                                   HHHHHHHHHHHHHSSSSS-TTBESSBBSS---TTHHHHHHHHHHHHHHHHHHHHHHHHSSSSHHHHHSSSS-BSHHHHHHH CS
                Complex1_49kDa  14 eRekildlleevtGaRltasyiriGGvarDlpegllekikeflkelekkldeleklltknrifkkRtkgvgvlskeealel 94 
                                    Re+i +++++++G R   s   +GG + +        ++++++ ++++++ + + l + +if +R+++ g +s++++l  
  gi|13542287|ref|NP_111975.1| 170 LRENIARIITSFAGHRYFFSSSYVGGCQFN--GL---VLESVIEDVKEEFEGIFNDLLQSKIFLNRLQNNGKISSSDML-- 243
                                   59************************9864..22...3556777778888888778899***************99975.. PP

                                   TT-SSSSGGGT-TTTHHHHSS-SSGGGS-------SSBSHHHHHHHHHHHHHHHHHHHHHHHH CS
                Complex1_49kDa  95 gltGpvlRasGvkyDlRkaepYeaYdeldfdvpvgeegDvydRylvrveEmrqSlkIieqale 157
                                      Gp +Ra+G+++D R +e+   Y++l f+ +v +e D++ R++vr +E+  S+++i +a++
  gi|13542287|ref|NP_111975.1| 244 ---GPAARAAGIEVDARIDEKRLPYSKLGFKPIVFDEPDAFGRFYVRSKEILSSADLISKAIR 303
                                   ...********************************************************9985 PP

  == domain 2  score: 21.4 bits;  conditional E-value: 1.2e-08
                                   ----SEEEEEEEEETTEEEEEEEEEESSSS-SEEEEE-HHHHTTTTHHHHTTTS-SGGGTHHHHTT---HHH CS
                Complex1_49kDa 197 fkvpkgevyaavEapkGelgvylvsdgsskpyrlkirapsfvnlqaleellkgellaDvvailgsldivlge 268
                                   ++  +ge  a+vE+p+G l +y+  ++++    ++i +ps  n++a+++ + g+ + D      s+ i ++e
  gi|13542287|ref|NP_111975.1| 313 IEKTNGEGAARVESPQGDLFYYVKINDGK-ISDVQISSPSLLNIEAFKKSMIGNIFTDYHFNWESFGIWVSE 383
                                   67789*****************9887654.5589**************************999999998887 PP

>> NiFeSe_Hases  Nickel-dependent hydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2   0.0   9.8e-11   8.8e-07       7      64 ..      88     145 ..      85     151 .. 0.92
   2 ?   -2.4   0.0      0.19   1.7e+03     160     198 ..     171     208 ..     168     218 .. 0.77
   3 !   12.7   0.0   4.9e-06     0.044     415     458 ..     310     354 ..     290     361 .. 0.84

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 9.8e-11
                                   TTTS-GGGHHHHHHTT-SSSTTHHHHHHHHHHHHHHT----HHHHHHHHHHHHHHHHH CS
                  NiFeSe_Hases   7 lkgrdprdawalvqRiCGVCttvHalasvravedAlgikipknarlirnliaaalllh 64 
                                   ++g  p+da +lv+Ri G  + +Ha+a  +avedAl+i++p++ ++ r ++   + ++
  gi|13542287|ref|NP_111975.1|  88 VRGLSPEDALLLVERINGFHAASHAVAFEMAVEDALNIDVPEEVQYSRIIMLELERMR 145
                                   68999**********************************************9877766 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.19
                                   HHHHTHHHHHHHSSSSS--.EBTTBESSGBGSBSHHHHH CS
                  NiFeSe_Hases 160 qrkaakivaifggknPhpqslvvGGvtcaidllnaerla 198
                                   ++++a+i++ f+g     +s  vGG+ ++  l+ ++ ++
  gi|13542287|ref|NP_111975.1| 171 RENIARIITSFAGHRYFFSSSYVGGCQFN-GLVLESVIE 208
                                   6789999999***9999999*****9887.444444555 PP

  == domain 3  score: 12.7 bits;  conditional E-value: 4.9e-06
                                   GGGS-S.EEEEEEEEEETTEEEEEEEEEETTEEEEEEEE-HHHHH CS
                  NiFeSe_Hases 415 kkevpk.eakGvglveapRGaLsHwikikdgkienYqavvPsTWn 458
                                   +++++k + +G++ ve p G L  ++ki+dgki++ q+  Ps  n
  gi|13542287|ref|NP_111975.1| 310 PAKIEKtNGEGAARVESPQGDLFYYVKINDGKISDVQISSPSLLN 354
                                   4555643799***************************99998766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.27s 00:00:00.88 Elapsed: 00:00:00.47
# Mc/sec: 2505.70
//
Query:       gi|13542288|ref|NP_111976.1|  [L=222]
Description: Ni,Fe-hydrogenase III small subunit [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.4e-20   72.7   0.1    3.7e-20   72.1   0.1    1.3  1  Oxidored_q6  NADH ubiquinone oxidoreductase, 20 Kd subunit
  ------ inclusion threshold ------
      0.013   15.3   7.9       0.26   11.2   0.5    3.4  3  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 !   72.1   0.1   4.2e-24   3.7e-20       1     130 [.      99     203 ..      99     204 .. 0.91

  Alignments for each domain:
  == domain 1  score: 72.1 bits;  conditional E-value: 4.2e-24
                                   -SHHHHHHT-TTTTHHHHHHTEEEEEETTT-S--HHHHHHTHTTTSEEEEEESBE...EEEHHHHHHHHGGGSSEEEEESH CS
                   Oxidored_q6   1 CtGcsisllaleedlldllelielryhetlladskeeeieakekeadvlvveGavtrkpkealellkelaekakaviavGt 81 
                                   C++c++++l++ ++ +d+      r+++ ++++++          ad l+v G +t ++keal++++e+++++k+via+G+
  gi|13542288|ref|NP_111976.1|  99 CGACNMEFLSIFSPQYDA-----NRLGIFMVNTPR---------YADALIVMGVMTPGMKEALDRAYEAMPEPKLVIAMGA 165
                                   ******************.....9999********.........8************************************ PP

                                   HHHH-TGGGSTT-TEE-HHHHHHHC.S-E.EEE-SSS--HHHHHHHHHH CS
                   Oxidored_q6  82 CAafGGipaaannpsvgeevgellevvpvdinipGCPphpeailetlla 130
                                   CA++GGi++ +          +l+++ + +++i+GCPp+p +++++l a
  gi|13542288|ref|NP_111976.1| 166 CAVTGGIMGEN----------PLDRE-KYNVEIAGCPPSPYTLIAALNA 203
                                   ********433..........44443.4447**************9986 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.1    0.0022        20      18      24 .]      42      48 ..      40      48 .. 0.91
   2 ?   11.2   0.5   2.9e-05      0.26       3      14 ..      52      63 ..      51      65 .. 0.87
   3 ?    2.0   0.2     0.022     2e+02       7      14 ..      98     102 ..      92     104 .. 0.60

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0022
                                  STTTEEE CS
                          Fer4 18 CPvgAIt 24
                                  CPv+AIt
  gi|13542288|ref|NP_111976.1| 42 CPVDAIT 48
                                  ******7 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 2.9e-05
                                  EETTTSSS-THH CS
                          Fer4  3 ideekCigCGaC 14
                                  + +ekCi+C +C
  gi|13542288|ref|NP_111976.1| 52 WVMEKCIFCRRC 63
                                  568********* PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.022
                                   TSSS-THH CS
                          Fer4   7 kCigCGaC 14 
                                       CGaC
  gi|13542288|ref|NP_111976.1|  98 A---CGAC 102
                                   4...5555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       378  (0.0210832); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.31s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1439.91
//
Query:       gi|13542289|ref|NP_111977.1|  [L=589]
Description: hydrogenase 4 subunit B [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.9e-15   56.3  27.7    2.9e-15   56.3  27.7    3.5  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 ?   -1.8   0.6     0.077   1.4e+03     126     166 ..      22      65 ..      11      77 .. 0.66
   2 !   56.3  27.7   1.6e-19   2.9e-15       3     223 ..      94     314 ..      92     323 .. 0.85
   3 ?    0.1   5.2     0.021   3.7e+02     111     178 ..     330     398 ..     324     402 .. 0.66
   4 ?   -2.2   0.6       0.1   1.8e+03     142     160 ..     565     583 ..     549     588 .. 0.49

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.077
               Proton_antipo_M 126 kagvlllirllllla...vssneisqlllilaiismllgslval 166
                                   k++ l+l   ++++a   ++++++ ++  ++a+i  +++++ +l
  gi|13542289|ref|NP_111977.1|  22 KISYLMLSLSSVVFAatqFAYGNYLSYYSVIAAIVWVFAGVYSL 65 
                                   66666666666666645555666666666666666666665554 PP

  == domain 2  score: 56.3 bits;  conditional E-value: 1.6e-19
               Proton_antipo_M   3 dLlllylglElvllplylLiglwkkkpksleAslklflltllgsliLLlgilllynltgtlefeelskalelglnslelll 83 
                                   + l l  g+E++++p+y +++l+k++    + ++ ++  + ++ ++++ g +  + ++ + +f  + ++         +++
  gi|13542289|ref|NP_111977.1|  94 NYLVLIAGWEIMSVPSYAIVALNKSQ---KSPAFTFMTFSEFSTVLIIAGSISSFVASKDSSFSFIHLT---------TFA 162
                                   55677789***************777...5677888888999999999999999999999999999888.........889 PP

               Proton_antipo_M  84 llllllvgllvKsaqvpl..hlWlpdayveaPtpvsallAatlvkagvlllirllllla..vssneisqlllilaiismll 160
                                    lll+ +g l+K+++ p+  + Wlp a+ +aP+  sa ++at+  +gv+l++++++l +   +   i +llli+++is+l+
  gi|13542289|ref|NP_111977.1| 163 PLLLISFGSLIKMGMSPFmiSEWLPIAHGNAPANASAVFSATMTLMGVFLITKMIFLTSdsPALLYIGILLLIIGSISILF 243
                                   9999***********9994457*************************************66666777889*********** PP

               Proton_antipo_M 161 gslvalaqtdiKrllAySsishlGymlialav...atqyg......veaaiihllthalfkallFllagsvi 223
                                   +s+ a +  ++K l ++S+i   + +l+a+++   + + +      ++ +ii  l+ha++k +lFl +gs+ 
  gi|13542289|ref|NP_111977.1| 244 ASIYAYVSENMKMLGGFSTIENQAAILSAFGLylvT-SNStlrefvLATIIIFSLSHAVSKTGLFLSIGSTR 314
                                   ********************8888888877665532.222111121466788889*************9985 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.021
               Proton_antipo_M 111 eaPtpvsall.Aatlvkagvlllirlllllavssneisqlllilaiismllgslval....aqtdiKrllAyS 178
                                      t  s+l  +++ +++g+l++ +ll  ++      ++l   ++i+++++gs+va+    ++ ++ ++l +S
  gi|13542289|ref|NP_111977.1| 330 RLGTLLSTLSlSGLFPAIGGLAVWMLLESFF----MQAYLGGYIGILAIIVGSIVAIsegmVTGSMMKILSFS 398
                                   556777787669999********98887777....33444556777777777777651111455666666666 PP

  == domain 4  score: -2.2 bits;  conditional E-value: 0.1
               Proton_antipo_M 142 ssneisqlllilaiismll 160
                                   ss +++ + +i+a++ +++
  gi|13542289|ref|NP_111977.1| 565 SSLAWYMIYMIVAFMVVII 583
                                   3333333333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (589 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1085  (0.0605165); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.46
# Mc/sec: 3848.45
//
Query:       gi|13542290|ref|NP_111978.1|  [L=311]
Description: phosphate permease [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.2e-31  110.0  34.8    2.4e-29  102.5  34.8    2.0  1  PHO4       Phosphate transporter family
  ------ inclusion threshold ------
        8.1    5.9   5.9        3.9    7.0   3.1    1.8  2  DUF927     Domain of unknown function (DUF927)
        9.8    5.2  13.1        7.2    5.6  10.1    2.0  2  FUSC-like  FUSC-like inner membrane protein yccS


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 !  102.5  34.8     4e-33   2.4e-29       2     335 ..      20     298 ..      19     300 .. 0.88

  Alignments for each domain:
  == domain 1  score: 102.5 bits;  conditional E-value: 4e-33
                          PHO4   2 GanDvanafatsvgskaltlrqAvilaaifeflGavllGaeVaetirkgivdvelfdpselmlgmlaallgaavwlllatv 82 
                                   G +  +  ++ + gsk+lt+rqA ++aa f flG +++ + V++t +  +v ++++        ++aallga v  l+ t+
  gi|13542290|ref|NP_111978.1|  20 GSHYSGAVMGMAYGSKSLTIRQATVIAATFAFLGTITASSGVVHTYAFSLVGTTTI------RQLTAALLGASVAILISTI 94 
                                   666677889****************************99************65544......489**************** PP

                          PHO4  83 lglPvStthslvGaliGaalaaeggeavkwkklvkivlswvlsPllggiiaallf.llvkrlilvkeklknalralpvlvl 162
                                   l+lP+St +  + +l+ ++la  ++  +  +++  ++ +w+l Pl ++++++ll+  lv +l                   
  gi|13542290|ref|NP_111978.1|  95 LKLPASTIQVYTFSLLFVGLA--SNIKLMYGGIEIVLSMWILMPLAAMLLSYLLApKLVSKL------------------- 154
                                   *********************..3334444688889999*************9873344444................... PP

                          PHO4 163 vtiailalsilfkgeskkddeeteklfkflqvvsaalvsfahGanDvanaiGpllaalisiykaskevplwvlllgglaia 243
                                                        + ++ +k++ + s+++ sf+ G+nDv+ ai+pl+ + i  +     + ++  ++gg+ i+
  gi|13542290|ref|NP_111978.1| 155 --------------------ADDSRKLKIIIIGSSVFSSFTLGSNDVSSAISPLVKVGI--L-----TGIVPYVFGGFFIG 208
                                   ....................12344489**************************44332..2.....345568******** PP

                          PHO4 244 lGlllgGkrviktvGekitkkltpsrGfaaelaaaltvllasklglPvStThvlvgavvGvGlakkresavnwklvrnivl 324
                                   lGl+++G+r+i+ vG++++ k +   + aa+l+ a++++  + +g   S ++++++++ G+     +++ v   ++r+i+l
  gi|13542290|ref|NP_111978.1| 209 LGLITWGQRLIRRVGTEVV-KTNAPLAAAAQLTEAIVIISGNLVGYNASINQTIIMSIYGAKRSM-KSHVVTPMIFRSILL 287
                                   *******************.699999************************************999.689************ PP

                          PHO4 325 aWvlTlpvsal 335
                                    W ++  +sa+
  gi|13542290|ref|NP_111978.1| 288 NWTVSSLISAV 298
                                   ******99997 PP

>> DUF927  Domain of unknown function (DUF927)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   3.1   0.00065       3.9     175     221 ..      38      86 ..      23     101 .. 0.78
   2 ?   -1.7   0.0      0.28   1.6e+03     174     207 ..     129     162 ..     124     168 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.00065
                        DUF927 175 ilavsaAlaa..pLLkllgaeggglhlygeSstGKttalklAaSvwGnp 221
                                   ++  ++ +aa  ++L  + a++g++h y  S +G tt+ +l a + G  
  gi|13542290|ref|NP_111978.1|  38 TIRQATVIAAtfAFLGTITASSGVVHTYAFSLVGTTTIRQLTAALLGAS 86 
                                   44444444441156799****************************9976 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.28
                        DUF927 174 lilavsaAlaapLLkllgaeggglhlygeSstGK 207
                                   l + + + laa+LL  l a+  +  l+ +S++ K
  gi|13542290|ref|NP_111978.1| 129 LSMWILMPLAAMLLSYLLAPKLVSKLADDSRKLK 162
                                   556667889*****99999999999999999988 PP

>> FUSC-like  FUSC-like inner membrane protein yccS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6  10.1    0.0012       7.2      20      83 ..       9      73 ..       2      96 .. 0.85
   2 ?    1.4   2.2     0.024   1.4e+02      32      79 ..      64     112 ..      60     133 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0012
                     FUSC-like 20 lpypwlfvlglllstflftmlgalGqryatiafatLlvaiytmlgasqep.eiwqqplllllGal 83
                                  l  + lf+  +     +++m  a+G++  ti +at+++a++++lg   +   + +  +  l+G++
  gi|13542290|ref|NP_111978.1|  9 LFASALFAWNMGSHYSGAVMGMAYGSKSLTIRQATVIAATFAFLGTITASsGVVHTYAFSLVGTT 73
                                  4455677778888888999999***********************99877789999999999986 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.024
                     FUSC-like  32 lstflftmlgalGqryatiafatLlvaiytmlgasqep.eiwqqpllll 79 
                                   + +f+++ ++ + q +a++  a++ + i t+l++ +++ +++  +ll++
  gi|13542290|ref|NP_111978.1|  64 TYAFSLVGTTTIRQLTAALLGASVAILISTILKLPASTiQVYTFSLLFV 112
                                   456777777788999999999************9999978887777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       936  (0.0522059); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.65u 0.32s 00:00:00.97 Elapsed: 00:00:00.52
# Mc/sec: 1784.48
//
Query:       gi|13542291|ref|NP_111979.1|  [L=189]
Description: hypothetical protein TVN1460 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       455  (0.0253779); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1345.69
//
Query:       gi|13542292|ref|NP_111980.1|  [L=115]
Description: hypothetical protein TVN1461 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.047   13.9   0.0       0.11   12.7   0.0    1.6  1  gerPA     Spore germination protein gerPA/gerPF


Domain annotation for each model (and alignments):
>> gerPA  Spore germination protein gerPA/gerPF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   6.2e-06      0.11       5      37 ..      68     100 ..      65     110 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.2e-06
                         gerPA   5 vgnikInsvgsngvvniGdvlaispksnsKsya 37 
                                   + +++In    +g + iGd  +i+p  n Ks  
  gi|13542292|ref|NP_111980.1|  68 IDPVQINGRLIQGLIRIGDYGYITPIVNRKSRK 100
                                   789999999999******************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 790.34
//
Query:       gi|13542293|ref|NP_111981.1|  [L=57]
Description: hypothetical protein TVN1462 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score 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   12.8   0.1       0.12   12.8   0.1    1.1  1  Wbp11     WW domain binding protein 11


Domain annotation for each model (and alignments):
>> Wbp11  WW domain binding protein 11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   6.8e-06      0.12      27      69 ..       4      50 ..       1      57 [] 0.75

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.8e-06
                         Wbp11 27 qkareaklakkdpdeleeeiekLeelessgkldaa....dkkklekL 69
                                  +k r   + k d+d+le  ie Le+   +g+l++      k k++ +
  gi|13542293|ref|NP_111981.1|  4 TKSRLVSIPKSDLDSLEATIETLENEYVMGQLERSgqdiLKGKVRTM 50
                                  678888999***************98889999998444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (57 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       535  (0.0298399); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 371.85
//
Query:       gi|13542294|ref|NP_111982.1|  [L=843]
Description: Type III restriction-modification enzyme, helicase subunit [Thermoplasma volcanium GSS1]
Scores for complete 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   96.5   1.4    2.8e-27   95.8   0.1    2.1  2  ResIII      Type III restriction enzyme, res subunit
    0.00053   19.8   0.0      0.015   15.1   0.0    2.9  2  DEAD        DEAD/DEAH box helicase
    0.00096   19.5   0.0     0.0041   17.4   0.0    2.1  1  Helicase_C  Helicase conserved C-terminal domain
  ------ inclusion threshold ------
      0.014   15.8   2.4      0.079   13.4   0.2    2.9  2  NERD        Nuclease-related domain
       0.07   12.6   0.0       0.17   11.4   0.0    1.6  1  TcfC        E-set like 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 !   95.8   0.1   7.7e-31   2.8e-27       7     171 .]      64     296 ..      56     296 .. 0.79
   2 ?   -2.6   0.1       1.4   4.8e+03      69      79 ..     389     399 ..     358     435 .. 0.50

  Alignments for each domain:
  == domain 1  score: 95.8 bits;  conditional E-value: 7.7e-31
                                   HHHHHHHHHT..................................TTSEEEEEESTTSTHHHHH.HHHHHHH-S........ CS
                        ResIII   7 yQeeaienll.....eklks.......................krdkrglikmaTGtGKTlva.aklierllkkgkee... 55 
                                    Q+eaie l+     +   +                       +   ++++kmaTG+GKT+v+ ++++++++++  e    
  gi|13542294|ref|NP_111982.1|  64 AQKEAIETLIyiyeiK---KfrkmsdlilnydstkkiaynpheDLFPKYCFKMATGSGKTYVMaLAIVWSYFNNIVEHnee 141
                                   5999999999775554...3444888999999999999876544444****************99********97766889 PP

                                   ...-EEEEESSHHHHHHHHHHGGGGTGG..............GEEEESSS-B--.......-SEEEEEHHHHHHTH..... CS
                        ResIII  56 ...kflflvprkslleqtleefkkflseayke..........igkkvsgdkkkakekdstnkkilvttiqsldadseee.. 121
                                      +fl+++p+++++e+++e+f+++   +             + + v++d       ++t+ ++++t++q+l+++ +    
  gi|13542294|ref|NP_111982.1| 142 mprNFLIIAPNIAVYERLKEDFADCRIFNSGVmipdefqhlwEFEAVTEDYIPT---RNTKGRLYLTNVQKLYERDNAPvn 219
                                   **********************88888775446555544554444455555555...999****************655** PP

                                   ......................HHHTTT-SEEEEETGGGTTS.T.TTHH.H......HHT---.....SEEEEEESS-S- CS
                        ResIII 122 .................eeeseellrdrfdviiiDEaHrlgakk.swre.i......lekfke.....avllglTATper 171
                                                    +++ ee ++ +++ ii+DEaH++ +k+  w++ i      l+   +     +++l++TATp+r
  gi|13542294|ref|NP_111982.1| 220 piqkivgkkpsdsiiyyDQMIEEIKSLNSLGIINDEAHHVWDKDiIWNQfIltcnelLK---KkdkglSFQLDFTATPKR 296
                                   ************999999999999999999************75756664433311144...245699**********96 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.4
                                   HHHHHGGGGTG CS
                        ResIII  69 qtleefkkfls 79 
                                   qt++efk  + 
  gi|13542294|ref|NP_111982.1| 389 QTKNEFKGKTL 399
                                   44444422222 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   4.2e-06     0.015      18      70 ..     110     166 ..     104     302 .. 0.69
   2 ?   -1.7   0.0      0.58   2.1e+03      43      96 ..     364     419 ..     355     434 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 4.2e-06
                                   EEEESTTSSHHHHHHHHHHHHHHHS....TTSTS-EEEEEESSHHHHHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD  18 lvaaeTGsGKTlaflipvlqivyet....kgktgpkalivePtreLaeqtlnnlkkf 70 
                                   + +++TGsGKT +++++++ + +++    +++     li++P  +  e   +++  +
  gi|13542294|ref|NP_111982.1| 110 CFKMATGSGKTYVMALAIVWSYFNNivehNEEMPRNFLIIAPNIAVYERLKEDFADC 166
                                   6789**************9666666777577777799*****999998888877665 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.58
                                   TTSTS-EEEEEESSHHHHHHHHHHHHHHTTTST..SEEEEEETTSSHHHHHHHHHT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxx RF
                          DEAD  43 kgktgpkalivePtreLaeqtlnnlkkfkkyid..lrvlliiggvaardqlskldn 96 
                                   k  ++p +++++  ++ ae+++n l++  ++ +  l ++  ++g+  +++++kl++
  gi|13542294|ref|NP_111982.1| 364 KVGKHPIIFFMATKTSEAEDIYNYLQTKNEFKGktLIIHTNLKGDISDKEWQKLKQ 419
                                   55566777777777888888888887766653323555555778888888888864 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 !   17.4   0.0   1.2e-06    0.0041      13     109 ..     363     474 ..     354     476 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.2e-06
                                   TTTTSEEEEEESSHH..HHHH.HHHHHHHT..TSTEEEESTTSTHHHHHHHHHHHH........TTSSSEEEESGGGTSSS CS
                    Helicase_C  13 eeeggkilifvntid..rlek.vklllekk..gikvavlhgelpqnereeileqfn........kgesdvLiatdvaerGi 80 
                                   e++g+  +if   ++  ++e+  ++l++k+  + k++++h +l+ +  ++  ++ +        +++++ +++  ++ +G 
  gi|13542294|ref|NP_111982.1| 363 EKVGKHPIIFFMATKtsEAEDiYNYLQTKNefKGKTLIIHTNLKGDISDKEWQKLKqetreidkSHKYRAIVSVLMLREGW 443
                                   444555555555555265544779997666667888888888888888877777764444665557799************ PP

                                   TSTTESEEEESSSSSSHHHH..HHHHTTSSS CS
                    Helicase_C  81 dipkvnlVinfdlprnvtsy..iqriGRtgR 109
                                   d+++v +++ + + ++ +++   q+ GR  R
  gi|13542294|ref|NP_111982.1| 444 DVKNVCVIVGLRPFTSKAEIlpEQALGRGLR 474
                                   *********9999988544422688888777 PP

>> NERD  Nuclease-related domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.2      0.22   7.8e+02      57     107 ..     404     451 ..     383     452 .. 0.65
   2 ?   13.4   0.2   2.2e-05     0.079      32      92 ..     752     830 ..     720     841 .. 0.66

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.22
                          NERD  57 wifgd.kegrwtqkikkgfknpleqakrhakalkksllekgkgvpvesvvvf 107
                                   ++ gd ++++w++ + +++   +++ +++++++ + l    +g+ v++v+v+
  gi|13542294|ref|NP_111982.1| 404 NLKGDiSDKEWQKLK-QET-REIDKSHKYRAIV-SVLM-LREGWDVKNVCVI 451
                                   445557778898884.444.7999999999999.5552.5667777777776 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 2.2e-05
                          NERD  32 g...tg....eiDhlvispkgifviEvKnwsGwifgd...kegrwtqki......kkgf.....knpleqakrhakalkks 91 
                                       +g      D++vi+ +  +v+E+K    + +++   + ++w ++       k        +  + +++r +k+l k+
  gi|13542294|ref|NP_111982.1| 752 VnekKGlsyyLPDFIVICDSENYVLETKGEESVEVKNkdkRAREWCEDAtkltgnK--WtylkvPESVFKNNREVKTL-KK 829
                                   244322455678*****************887444445788888988888888641..23454349999999999999.66 PP

                          NERD  92 l 92 
                                   l
  gi|13542294|ref|NP_111982.1| 830 L 830
                                   6 PP

>> TcfC  E-set like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   4.6e-05      0.17      34      55 ..     553     574 ..     549     582 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 4.6e-05
                          TcfC  34 qeidtssLPsGiYeveirvyen 55 
                                   +eid s+LP+G Y+++++ y n
  gi|13542294|ref|NP_111982.1| 553 NEIDISTLPQGKYDLDLETYTN 574
                                   89***************98875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (843 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       886  (0.0494171); expected 358.6 (0.02)
Passed bias filter:                      545  (0.0303977); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.78u 0.30s 00:00:01.08 Elapsed: 00:00:00.48
# Mc/sec: 5229.90
//
Query:       gi|13542295|ref|NP_111983.1|  [L=616]
Description: adenine specific DNA methylase [Thermoplasma volcanium GSS1]
Scores for 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-38  131.4   1.1      4e-38  131.4   1.1    1.8  2  N6_N4_Mtase  DNA methylase
      0.007   16.3   0.9       0.02   14.8   0.2    2.2  2  Y_Y_Y        Y_Y_Y domain
  ------ inclusion threshold ------
      0.085   13.1   0.1       0.28   11.4   0.1    1.9  2  DUF4625      Domain of unknown function (DUF4625)


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 ?   -3.7   0.2       1.3   7.8e+03     107     135 ..       6      30 ..       5      60 .. 0.55
   2 !  131.4   1.1   6.6e-42     4e-38       1     225 [.      74     354 ..      74     360 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 1.3
                                   EEESSTT-..---GGGSSBSS-HHHHHHH CS
                   N6_N4_Mtase 107 vfsknkkyllkfnldaikvpyeekdklek 135
                                   +++knkk+      +++++p+++ + ++ 
  gi|13542295|ref|NP_111983.1|   6 IYWKNKKE----EVERVELPFQKIETINL 30 
                                   68888888....55666666555444443 PP

  == domain 2  score: 131.4 bits;  conditional E-value: 6.6e-42
                                   EEEEEE--SSSSSCS..........................GCCGCCHHHHHHHHHHHHHHHHHHHEEEEEEEEEEE-CCC CS
                   N6_N4_Mtase   1 vdlivtdpPYntgkdy.....................endeqyeeedsyeeyleflekvlkevrrvLkddgsifiniddse 60 
                                   +++i++dpP++tg +                      +  +    ++  + yl++++ ++ +++++L++dgsi++  d+++
  gi|13542295|ref|NP_111983.1|  74 IKMIYADPPFFTGTNMnitlevgdeeavkepsaieeiA--YRNMWKEGPSSYLQYMYDRFVLMKDLLSEDGSIWVRSDYHY 152
                                   79*************98888888888888887766332..3333344589******************************* PP

                                   HHTHHHHHHHHHTT-EEEEEEEEEEESSSTTTSTCCS-B--EEEEEEEESSTT-..---GGGSSBSS.-HHHHHHHHHH.. CS
                   N6_N4_Mtase  61 ikkelkaladeifggffllnvivwkkpnsmpesnkdrltsthEyilvfsknkkyllkfnldaikvpy.eekdklekrga.. 138
                                    ++ +k ++deifg  +++n i++++  +++ s ++r++ +++ ++++sk+++y +k+++++++ ++ e++ + +++g+  
  gi|13542295|ref|NP_111983.1| 153 SHY-IKGILDEIFGYENFRNEIIINRI-KKSDSGAKRYNTATDSLFFYSKTDNYFFKNVKKKLEITKnERWHSMDSQGQgg 231
                                   **9.**********8889999999998.77777778******************877777776654415566666666699 PP

                                   ...CHHHCC-B--BSEE.......................................E-SCCCTTSTTS-CHH----SS--- CS
                   N6_N4_Mtase 139 ...ytskkkgkkiediW.......................................dlseiqsnekkskgdtkkkHpaqkP 177
                                       ++k+   + ++ W                                       ++++i+ +  ++       +p++  
  gi|13542295|ref|NP_111983.1| 232 prtIFGKTMYPPSGRHWtfgqenidrmiaegrirlnpktgkpeykleeteeqildsNWTDIPGYSFSTG------YPTENA 306
                                   998566666666666666677777777776666655555555555555444444444577777777766......9***** PP

                                   HHHHHHHHHHHS-TT-EEEETT-TTTHHHHHHHHTT-EEEEEESSHHH CS
                   N6_N4_Mtase 178 vallerlIklstkkgdivlDpFaGSGtTavaakelgrkfiGieieeey 225
                                   ++ller+I++ t+kgd+++D+F GSGtT+++a++lgr++iG +i +  
  gi|13542295|ref|NP_111983.1| 307 EQLLERIILSATEKGDLIADFFSGSGTTVAVAEKLGRRWIGADIGRFS 354
                                   *******************************************98765 PP

>> Y_Y_Y  Y_Y_Y domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       1.7     1e+04      17      28 ..     285     296 ..     284     298 .. 0.81
   2 !   14.8   0.2   3.4e-06      0.02      12      63 ..     558     615 ..     554     616 .] 0.92

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 1.7
                                   TESSEEEESSTS CS
                         Y_Y_Y  17 idkeWveasdys 28 
                                   +d +W+++ +ys
  gi|13542295|ref|NP_111983.1| 285 LDSNWTDIPGYS 296
                                   589999999985 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 3.4e-06
                                   EEEETTESSEEEESSTS.......EEEEES--SEEEEEEEEEEETTS-B-SS-EEEEE CS
                         Y_Y_Y  12 YrlegidkeWveasdysq......easytnlppGdYtlkVkakdndgqwnyditslsf 63 
                                   Yr + +++eW+e +  ++      +++    +pG+Y++++k++d  g+    i+++++
  gi|13542295|ref|NP_111983.1| 558 YRGDTFHNEWQEFRTKRKknlqlqSIEHHYDEPGNYRIMIKVIDVFGNDTTTIKEVTV 615
                                   99999***************************************99999888888876 PP

>> DUF4625  Domain of unknown function (DUF4625)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       1.5   9.2e+03      77     100 ..     458     484 ..     445     499 .. 0.68
   2 ?   11.4   0.1   4.8e-05      0.28      80     131 ..     564     615 ..     554     616 .] 0.69

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 1.5
                       DUF4625  77 wsfeksy.d..lsgskkeyelheeiei 100
                                   w+fe+++ d  l + +++yel+++++i
  gi|13542295|ref|NP_111983.1| 458 WDFEMEFnDriLRELRESYELKVSLRI 484
                                   777777743224556667777777764 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 4.8e-05
                       DUF4625  80 eksydlsgskkeyelheeieiPadaeaGdYhlvirvtDasGneteesreiki 131
                                   +++++   +k++++l+ +    +  e+G+Y ++i+v+D  Gn t +  e+++
  gi|13542295|ref|NP_111983.1| 564 HNEWQEFRTKRKKNLQLQSIEHHYDEPGNYRIMIKVIDVFGNDTTTIKEVTV 615
                                   555544444444444444333333479****************998777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (616 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       600  (0.0334653); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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 0.29s 00:00:00.97 Elapsed: 00:00:00.49
# Mc/sec: 3781.89
//
Query:       gi|13542296|ref|NP_111984.1|  [L=102]
Description: hypothetical protein TVN1465 [Thermoplasma volcanium GSS1]
Scores for complete 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   25.5   1.5      1e-05   25.3   1.5    1.1  1  DDE_Tnp_1    Transposase DDE domain
  ------ inclusion threshold ------
      0.053   12.9   0.3      0.064   12.6   0.3    1.1  1  Herpes_UL69  Herpesvirus transcriptional regulator family
      0.093   11.0   0.2       0.11   10.8   0.2    1.0  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 !   25.3   1.5   1.7e-09     1e-05     169     213 ..      17      61 ..       4      62 .. 0.95

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 1.7e-09
                     DDE_Tnp_1 169 elyrlRwqiErvFkwlkrkfgldrlryrglnrveaqllllllaln 213
                                    +y++Rw i  +F+++k+ +++d+l +r+ n +  q+++ ++a+ 
  gi|13542296|ref|NP_111984.1|  17 TIYSQRWNIDIFFRTMKTYLKIDHLISRKINSIMVQIFTAMIAYI 61 
                                   69*****************************************95 PP

>> Herpes_UL69  Herpesvirus transcriptional regulator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.3   1.1e-05     0.064      91     156 ..      10      76 ..       3      85 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.1e-05
                   Herpes_UL69  91 pllsClldnrkeda.vkqlayilaqlarlpelvrrlressikspltlllalvar.farvverrrrtlr 156
                                    +l+C++   +++  +++ +++++   +++ l++r+  s + ++ t ++a+++  ++ ++++ r +++
  gi|13542296|ref|NP_111984.1|  10 RFLTCIFTIYSQRWnIDIFFRTMKTYLKIDHLISRKINSIMVQIFTAMIAYIVLmIQDMLSC-RMSIQ 76 
                                   799****98777666*********************************99987515566666.66665 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 ?   10.8   0.2   1.8e-05      0.11     321     372 ..      15      65 ..      10      83 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 1.8e-05
                   DDE_Tnp_1_4 321 lyeqlYcaRGemEnrIKeakldlaadrtsshsfaaNqlrlllsalAynLlaa 372
                                   ++ ++Y +R +++ +++++k+ l++d++ s+++++  ++++ +++Ay +l +
  gi|13542296|ref|NP_111984.1|  15 IF-TIYSQRWNIDIFFRTMKTYLKIDHLISRKINSIMVQIFTAMIAYIVLMI 65 
                                   66.89******************************************87654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1003  (0.0559429); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 659.26
//
Query:       gi|13542297|ref|NP_111985.1|  [L=277]
Description: AAA family ATPase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
       0.13   12.2   0.0       0.25   11.4   0.0    1.4  1  DUF1658        Protein of unknown function (DUF1658)
        0.2   11.3   0.2       0.52   10.0   0.0    1.8  2  Ribosomal_L39  Ribosomal L39 protein


Domain annotation for each model (and alignments):
>> DUF1658  Protein of unknown function (DUF1658)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   2.7e-05      0.25       1      14 [.      10      23 ..      10      24 .. 0.97

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.7e-05
                       DUF1658  1 eklKTrriPARPsH 14
                                  +klKT +++ +PsH
  gi|13542297|ref|NP_111985.1| 10 SKLKTGFLGKFPSH 23
                                  8************9 PP

>> Ribosomal_L39  Ribosomal L39 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   5.8e-05      0.52       4      20 ..      41      57 ..      40      63 .. 0.88
   2 ?   -3.4   0.1      0.89   7.9e+03       5      13 ..     247     255 ..     246     256 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 5.8e-05
                 Ribosomal_L39  4 rLaKalkqNrpvPaWvr 20
                                   LaKalk N+ vP +++
  gi|13542297|ref|NP_111985.1| 41 FLAKALKENKYVPYYYI 57
                                  59***********9876 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 0.89
                 Ribosomal_L39   5 LaKalkqNr 13 
                                   L+K +  Nr
  gi|13542297|ref|NP_111985.1| 247 LIKNQDTNR 255
                                   899999999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       500  (0.0278878); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1828.84
//
Query:       gi|13542298|ref|NP_111986.1|  [L=175]
Description: hypothetical protein TVN1467 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       496  (0.0276647); 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:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 1115.35
//
Query:       gi|13542299|ref|NP_111987.1|  [L=61]
Description: hypothetical protein TVN1468, partial [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-05   23.4   0.1    2.8e-05   23.1   0.1    1.1  1  Transposase_mut  Transposase, Mutator family


Domain annotation for each model (and alignments):
>> Transposase_mut  Transposase, Mutator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.1   1.6e-09   2.8e-05     343     380 ..       1      38 [.       1      39 [. 0.97

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 1.6e-09
               Transposase_mut 343 LNkeirRrtrvvgiFPneesilrlvgavlaeahdewke 380
                                   +NkeirRr +++   P ees+++++++  +e +++w +
  gi|13542299|ref|NP_111987.1|   1 MNKEIRRRIKIIDSLPSEESAMKIIYLRSTEIDEKWSQ 38 
                                   6***********************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       449  (0.0250432); 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:                         1  (5.57756e-05); expected 0.2 (1e-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 0.28s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 431.22
//
Query:       gi|13542300|ref|NP_111988.1|  [L=46]
Description: hypothetical protein TVN1469 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score 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   0.2       0.07   13.3   0.2    1.1  1  OSTbeta   Organic solute transporter subunit beta protein


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 ?   13.3   0.2   3.9e-06      0.07      43      66 ..       9      32 ..       4      39 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.9e-06
                       OSTbeta 43 avvvvisvvLLarsiqanRnrKiq 66
                                  ++v+v+s+v La++i+a R + + 
  gi|13542300|ref|NP_111988.1|  9 ILVIVVSIVVLAINIMAFRSKNVS 32
                                  5799***************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (46 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1166  (0.0650343); expected 358.6 (0.02)
Passed bias filter:                      554  (0.0308997); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.29s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 319.19
//
Query:       gi|13542301|ref|NP_111989.1|  [L=110]
Description: hypothetical protein TVN1470 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.22   11.8   6.3       0.13   12.5   3.4    2.0  2  DUF3017   Protein of unknown function (DUF3017)


Domain annotation for each model (and alignments):
>> DUF3017  Protein of unknown function (DUF3017)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.3     0.041   7.4e+02       8      25 ..      32      53 ..      25      72 .. 0.53
   2 ?   12.5   3.4   7.3e-06      0.13      10      42 ..      67      99 ..      53     106 .. 0.73

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.041
                       DUF3017  8 vavglllvald....hwRrGal 25
                                  ++v++++++ +     +R G++
  gi|13542301|ref|NP_111989.1| 32 IGVAVIFIMEKdspwLFRTGMM 53
                                  4444444443344444555554 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 7.3e-06
                       DUF3017 10 vglllvaldhwRrGalllGvalllaAvlRlvlp 42
                                  +++ l + + + +G++++G+ l++aA++Rl++ 
  gi|13542301|ref|NP_111989.1| 67 LAFYLGVKSLVWAGSFVIGIMLIFAAMVRLFIQ 99
                                  3333333346668*****************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       722  (0.04027); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); 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):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.31s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 720.30
//
Query:       gi|13542302|ref|NP_111990.1|  [L=293]
Description: hypothetical protein TVN1471 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.037   14.1   0.0       0.13   12.4   0.0    1.9  1  DUF1106   Protein of unknown function (DUF1106)
       0.21   12.0   2.4       0.24   11.8   0.1    2.1  2  NBD94     Nucleotide-Binding Domain 94 of RH


Domain annotation for each model (and alignments):
>> DUF1106  Protein of unknown function (DUF1106)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   1.4e-05      0.13      32      64 ..     102     134 ..      76     142 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.4e-05
                       DUF1106  32 rlrgivltikcskgiiylsikvspnnrkhvlly 64 
                                    l g ++ +   kg ++lsi+vsp++  hv l+
  gi|13542302|ref|NP_111990.1| 102 YLEGNIVPLENNKGALFLSINVSPKDPTHVDLF 134
                                   488999***********************9887 PP

>> NBD94  Nucleotide-Binding Domain 94 of RH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.3      0.36   3.3e+03      66      88 ..       5      27 ..       3      36 .. 0.69
   2 ?   11.8   0.1   2.6e-05      0.24      12      53 ..     166     208 ..     153     213 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.36
                         NBD94 66 kaenlieeiekyienideikkkl 88
                                  k e ++ e+  + ++ deik ++
  gi|13542302|ref|NP_111990.1|  5 KQELTMSEVVRVTKDKDEIKTEV 27
                                  56666777777777777777654 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 2.6e-05
                         NBD94  12 dkkkkiyeniekllnElee.iekektsleevknielsYgrsLi 53 
                                   +k k iy ++e ll+   e  e ++  l+ ++ +elsY+  L 
  gi|13542302|ref|NP_111990.1| 166 EKRKWIYSKMESLLSAFPEaYESNRNKLKAIDVMELSYKVTLM 208
                                   57899**********996527999**************99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       662  (0.0369234); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 2191.57
//
Query:       gi|13542303|ref|NP_111991.1|  [L=69]
Description: hypothetical protein TVN1472 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.016   15.5   1.8      0.018   15.4   1.8    1.1  1  DUF3267   Putative zincin peptidase
       0.06   14.1   1.8      0.074   13.8   1.8    1.1  1  PrgI      PrgI family protein
        0.2   10.4   1.5       0.22   10.3   1.5    1.0  1  DUF2207   Predicted membrane protein (DUF2207)


Domain annotation for each model (and alignments):
>> DUF3267  Putative zincin peptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   1.8   2.9e-06     0.018      30      75 ..      13      59 ..       1      63 [. 0.80

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.9e-06
                       DUF3267 30 gik.lliayatsseallskkqfiiillaPfvllgilllllalllpss 75
                                  g+  ++i+y+ + +a+ls + f +++ +P +++ i+l+++  +l++s
  gi|13542303|ref|NP_111991.1| 13 GMAiFFIVYVLVANAYLSFRDFALYAALPSLVIMIALAFVYRYLENS 59
                                  3324999*******************************999988876 PP

>> PrgI  PrgI family protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   1.8   1.2e-05     0.074      25      84 ..      11      65 ..       8      69 .] 0.68

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.2e-05
                          PrgI 25 lvlallvaiglylllrafl..eelasvlvillavPvaalgfykkdglplekylkaiikfklr 84
                                  +++ +++ i+ +l+ +a+l   ++a++++++  v ++al+f+        +yl + ikf++r
  gi|13542303|ref|NP_111991.1| 11 IGGMAIFFIVYVLVANAYLsfRDFALYAALPSLVIMIALAFV-------YRYLENSIKFERR 65
                                  33444444444455555559999999999999999*****99.......4777777777744 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   1.5   3.6e-05      0.22     386     432 ..       9      55 ..       2      68 .. 0.56

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 3.6e-05
                       DUF2207 386 lglgliilglilillallllvlllvfllilllillliaiivlllfsr 432
                                   +++g++ +++i+ +l++ ++ ++  f+l+ +l  l+i+i++++++++
  gi|13542303|ref|NP_111991.1|   9 YIIGGMAIFFIVYVLVANAYLSFRDFALYAALPSLVIMIALAFVYRY 55 
                                   44555555555555555555554777777777777777666666544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       782  (0.0436165); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); 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: 0.37u 0.28s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 483.92
//
Query:       gi|13542304|ref|NP_111992.1|  [L=206]
Description: hypothetical protein TVN1473 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       822  (0.0458475); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 1262.45
//
Query:       gi|13542305|ref|NP_111993.1|  [L=58]
Description: hypothetical protein TVN1474 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       746  (0.0416086); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 392.77
//
Query:       gi|13542306|ref|NP_111994.1|  [L=974]
Description: Type III restriction-modification enzyme, helicase subunit [Thermoplasma volcanium GSS1]
Scores for complete 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  141.0   0.1      2e-40  138.6   0.0    2.2  2  ResIII          Type III restriction enzyme, res subunit
  ------ inclusion threshold ------
      0.033   14.5   0.0      0.076   13.4   0.0    1.7  1  Helicase_C      Helicase conserved C-terminal domain
      0.038   13.7   0.0         11    5.8   0.0    2.8  3  DEAD            DEAD/DEAH box helicase
      0.044   14.0   0.3        0.7   10.1   0.0    2.7  2  Tn7_Tnp_TnsA_N  TnsA endonuclease N terminal


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 !  138.6   0.0   4.6e-44     2e-40       1     170 [.      59     343 ..      59     344 .. 0.93
   2 ?   -0.5   0.0      0.24   1.1e+03      99     118 ..     751     770 ..     693     805 .. 0.77

  Alignments for each domain:
  == domain 1  score: 138.6 bits;  conditional E-value: 4.6e-44
                                   --EE-HHHHHHHHHHT....................................TTSEEEEEESTTSTHHHHH.HHHHHHH-S CS
                        ResIII   1 klelreyQeeaienll.....eklks.........................krdkrglikmaTGtGKTlva.aklierllk 50 
                                   +++++e Q++ai n++      klks                         +++ +++ikmaTGtGKT+v+ a li+++l+
  gi|13542306|ref|NP_111994.1|  59 EFNFHEGQWQAILNTIyiheiLKLKSvgeiymsiypdlvqqmdlldlkrdkYEHPKYCIKMATGTGKTWVLdALLIWQYLN 139
                                   689*************7776666666999******************66655555************************** PP

                                   .............-EEEEESSHHHHHHHHHHG.....................GGGTGG...................GEE CS
                        ResIII  51 kgkee........kflflvprkslleqtleef.....................kkflseayke...............igk 87 
                                   +++ee        +fl+++p+++++e++l++f                     k f+++ayk+               igk
  gi|13542306|ref|NP_111994.1| 140 SRHEEsesgeysrNFLLVAPGIIVYERLLDAFlgkrkedgsrdfeqsdfrnfeKLFIPPAYKDelfgfiqgcvtqkeeIGK 220
                                   *****************************************************8889988888999999999999999*** PP

                                   EESSS-B--.......-SEEEEEHHHHHHTH..............................HHHTTT-S.........EEE CS
                        ResIII  88 kvsgdkkkakekdstnkkilvttiqsldadseee......................eeeseellrdrfd.........vii 137
                                   kv+gd+ +a    +tn+++lv++++s+dads+ +                      ee ++++lr+r++         v++
  gi|13542306|ref|NP_111994.1| 221 KVTGDGLIA----ITNWHLLVEEEESIDADSPLDspditvkellpiapgtsqghslEELDNQYLRGRELeflaslpdlVVF 297
                                   *********....*******************************************************9************ PP

                                   EETGGGTTS.........TTTHHHHHT---.....SEEEEEESS-S CS
                        ResIII 138 iDEaHrlgak........kswreilekfke.....avllglTATpe 170
                                   +DEaH+lg++        k+w+e+l+k++e     +++++++ATp+
  gi|13542306|ref|NP_111994.1| 298 NDEAHHLGEMkksdevveKKWQEALDKISEnkkhrFMQVDFSATPY 343
                                   **********666555555********98888899**********8 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.24
                                   .....-SEEEEEHHHHHHTH CS
                        ResIII  99 kdstnkkilvttiqsldads 118
                                    +++n++il++t +s+ ++ 
  gi|13542306|ref|NP_111994.1| 751 LKDNNWRILLITQHSIIKHV 770
                                   46789999999999998876 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 ?   13.4   0.0   1.7e-05     0.076      12     109 ..     434     542 ..     421     544 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.7e-05
                                   HTTTTSEEEEEESSHHHHHH.HHHHHHHT...TSTEEEESTT....STHHHHHHHHHHHH....TTSSSEEEESGGGTSSS CS
                    Helicase_C  12 leeeggkilifvntidrlek.vklllekk...gikvavlhge....lpqnereeileqfn....kgesdvLiatdvaerGi 80 
                                    +++  k+li+++ ++ +   + +l +++   + +   +h++     + +e ++i ++      +++ +v+++  ++ +G 
  gi|13542306|ref|NP_111994.1| 434 DSAKYPKMLIVCEDTKVVPLvMGFL-KQEgysDDELMEIHSNkkgdVSEDEWKAIKQRLFdidrHEKPKVIVSVLMLREGF 513
                                   4566678888888888664334555.3443664556666665222244444444443332444245566************ PP

                                   TSTTESEEEESSSSSSHHHHHHHHTTSSS CS
                    Helicase_C  81 dipkvnlVinfdlprnvtsyiqriGRtgR 109
                                   d++++ +++ +    ++  + q iGR  R
  gi|13542306|ref|NP_111994.1| 514 DVNNICVIVPLRSASSYVLLEQLIGRGLR 542
                                   **************************988 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0    0.0024        11      16      55 ..     114     159 ..      93     177 .. 0.74
   2 ?    4.6   0.0    0.0056        25     125     169 ..     295     342 ..     256     346 .. 0.75
   3 ?   -3.5   0.0       1.7   7.8e+03     130     153 ..     687     710 ..     687     721 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0024
                                   EEEEEESTTSSHHHHHHHHHHHHHHHS......TTSTS-EEEEEES CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxx RF
                          DEAD  16 dvlvaaeTGsGKTlaflipvlqivyet......kgktgpkaliveP 55 
                                   + +++++TG+GKT +    ++ + +++       g+     l+v+P
  gi|13542306|ref|NP_111994.1| 114 KYCIKMATGTGKTWVLDALLIWQYLNSrheeseSGEYSRNFLLVAP 159
                                   56899********997666664444444766665666677777777 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.0056
                                   EEE.ETHHHHHHTTTHHHH..HHHHHHSHHHCTTSTTTSEEEEEESSB CS
                                   xxx.xxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD 125 lVl.DEadrlldqgfsdfi..nrilnqlpqitcdgklqrqvivlSATl 169
                                   +V+ DEa+ l +++ sd++  ++  ++l++i++++k     + +SAT+
  gi|13542306|ref|NP_111994.1| 295 VVFnDEAHHLGEMKKSDEVveKKWQEALDKISENKKHRFMQVDFSATP 342
                                   5545*********77777622345566666666666555588899997 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 1.7
                                   HHHHHHTTTHHHHHHHHHHSHHHC CS
                                   xxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD 130 adrlldqgfsdfinrilnqlpqit 153
                                   ad +  +++  fi++i+n+++ i 
  gi|13542306|ref|NP_111994.1| 687 ADIFTAKSYNSFIQKIVNAVSVIH 710
                                   577788899999999999986655 PP

>> Tn7_Tnp_TnsA_N  TnsA endonuclease N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.1      0.17   7.5e+02      35      71 ..     292     324 ..     274     340 .. 0.75
   2 ?   10.1   0.0   0.00016       0.7      32      71 ..     871     906 ..     855     915 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.17
                Tn7_Tnp_TnsA_N  35 pDfLvtlkdstgeellavevKyseeleeertreklei 71 
                                   pD++v   d+      + e+K s+e+ e++++e l++
  gi|13542306|ref|NP_111994.1| 292 PDLVVFN-DE---AHHLGEMKKSDEVVEKKWQEALDK 324
                                   5555544.43...678889999999999999998876 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00016
                Tn7_Tnp_TnsA_N  32 vmtpDfLvtlkdstgeellavevKyseeleeertreklei 71 
                                    + pDf+++  d    +l++ve K++ ++ ++++++k  +
  gi|13542306|ref|NP_111994.1| 871 HYYPDFMIKACD----QLYLVETKSERDMSNQNVKNKRLA 906
                                   599*******88....9*****************999655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (974 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       762  (0.042501); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); 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: 0.79u 0.33s 00:00:01.12 Elapsed: 00:00:00.53
# Mc/sec: 5562.25
//
Query:       gi|13542307|ref|NP_111995.1|  [L=681]
Description: adenine specific DNA methylase [Thermoplasma volcanium GSS1]
Scores for complete 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-36  124.0   1.0    7.3e-36  124.0   1.0    1.6  2  N6_N4_Mtase      DNA methylase
    0.00035   20.3   0.4       0.26   10.9   0.0    3.0  3  MethyltransfD12  D12 class N6 adenine-specific DNA methyltran
     0.0086   15.7   0.1       0.45   10.1   0.0    2.8  3  Cons_hypoth95    Conserved hypothetical protein 95


Domain annotation for each model (and alignments):
>> N6_N4_Mtase  DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.0   1.0   1.2e-39   7.3e-36       1     228 [.     116     400 ..     116     403 .. 0.77
   2 ?   -2.9   0.3      0.76   4.5e+03     138     152 ..     607     632 ..     535     656 .. 0.51

  Alignments for each domain:
  == domain 1  score: 124.0 bits;  conditional E-value: 1.2e-39
                                   EEEEEE--SSSSSCS........................GCCGCCHHHHHHHHHHHHHHHHHHHEEEEEEEEEEE-CCCHH CS
                   N6_N4_Mtase   1 vdlivtdpPYntgkdy...................endeqyeeedsyeeyleflekvlkevrrvLkddgsifiniddseik 62 
                                   +dli++dpP+  + dy                   ++ ++   +d  + yle l+++l ++r++L+++g+++++id +  +
  gi|13542307|ref|NP_111995.1| 116 IDLIYIDPPFDSKADYrtkihlpsvdieqkpsvieQFAYSDTWKDGTKSYLEMLVPRLVLMRELLSEQGFLYVHIDWHIGH 196
                                   89*****************************886533344444566889******************************** PP

                                   THHHHHHHHHTT.-EEEEEEEEEEES.SSTTTSTCCS-B--EEEEEEEESSTT-........................... CS
                   N6_N4_Mtase  63 kelkaladeifg.gffllnvivwkkp.nsmpesnkdrltsthEyilvfsknkkyl.......................... 115
                                   + +k ++d+ifg ++f ++viv + + n +  +  +++++ h++il++skn++                            
  gi|13542307|ref|NP_111995.1| 197 Y-VKVIIDDIFGkDNFRNEVIVRRIKkNVQEYDTVKQINYGHDTILFYSKNQDARfkpfqrhnerqerwhsfeaagyrggm 276
                                   9.**********999999999987552666667777******************666666666666666666666666666 PP

                                   ........---GGGSSBSS-HHHHHHHHHH...........CHHHC.C-B--BSEEE-SCCCTTSTTS-CHH.......-- CS
                   N6_N4_Mtase 116 .......lkfnldaikvpyeekdklekrga...........ytskk.kgkkiediWdlseiqsnekkskgdt.......kk 170
                                          ++++ ++++ ++++ d+  k+g            y+ ++ +++  ++iW                       + 
  gi|13542307|ref|NP_111995.1| 277 dyelfgfKPRQGNHWRWSKDRADGAIKTGMlrpnpntgkpeYKVEAsESEVRDTIW---------------EditaysfQF 342
                                   66666665555555555555555555555566666666555333330334444556...............0333445557 PP

                                   --SS---HHHHHHHHHHHS-TT-EEEETT-TTTHHHHHHHHTT-EEEEEESSHHHHHH CS
                   N6_N4_Mtase 171 kHpaqkPvallerlIklstkkgdivlDpFaGSGtTavaakelgrkfiGieieeeyvel 228
                                   +++++k+++ll  ++++s+  +++++D+FaGSGtT+++a++lgrk+i ++  + ++ +
  gi|13542307|ref|NP_111995.1| 343 NYQTEKNEDLLDLILEHSSSSNSVIADFFAGSGTTGAVAEKLGRKWIMCDLGKPACMI 400
                                   89************************************************98877665 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 0.76
                                   H...........CHHHCC-B--BSEE CS
                   N6_N4_Mtase 138 a...........ytskkkgkkiediW 152
                                                + + +g+ +  +W
  gi|13542307|ref|NP_111995.1| 607 EedplslieywsIDPDYDGEVFRSKW 632
                                   12333333333333344455555556 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 !    6.3   0.0    0.0011       6.7     135     195 ..      72     133 ..      66     189 .. 0.71
   2 ?   -3.1   0.3      0.83   4.9e+03      59     106 ..     213     260 ..     195     270 .. 0.55
   3 !   10.9   0.0   4.4e-05      0.26       7      59 ..     351     402 ..     348     435 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0011
                                   -B-S-SS-.....HHHHHHHHHHHHHCCEEEC-CHHHHTT--TTE.EEEE--S-T.S...TS CS
               MethyltransfD12 135 pygaykkp.kkvaekelklrseklknakiecgdfdavllkakieddivYlDPPYnprqytan 195
                                   +++a k++ ++ ++++l   ++ l   + ++gd ++ l   + + d++Y+DPP ++  + ++
  gi|13542307|ref|NP_111995.1|  72 TGQAVKTQeNNEFLNRLIYGDNLLAMQALLAGDPETGLPSMRGKIDLIYIDPPFDSKADYRT 133
                                   5556666666666666666666666677777777777777778889********98544443 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 0.83
                                   HHHCCHSHHHHHHHHH.TCTTGGC.TSHHHHHHHHHHHH....HHH-HH CS
               MethyltransfD12  59 kaliknnveelikelekllekeelenereyfyelreefn.kkidairea 106
                                   + +i  ++++ ++e+ + ++ +    ++  fy ++++ + k ++ ++e 
  gi|13542307|ref|NP_111995.1| 213 NEVIVRRIKKNVQEYDTVKQINY-GHDTILFYSKNQDARfKPFQRHNER 260
                                   33555555555666665444433.3566667766666555555555554 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 4.4e-05
                                   TTHHHHHCCS-..--SEEEETT-TTSCCHHCS...SSCEEEEES-HHHHHHHH CS
               MethyltransfD12   7 kllpeIkelipkdkgktfvepFaGggaVffeakkqgkkvlinDinedlinlyk 59 
                                   +ll+ I e+ ++ +++++++ FaG+g  +  a k g k +++D+ ++   + +
  gi|13542307|ref|NP_111995.1| 351 DLLDLILEHSSS-SNSVIADFFAGSGTTGAVAEKLGRKWIMCDLGKPACMITR 402
                                   699********9.99**************999999********9776555544 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.0   7.5e-05      0.45     109     132 ..     111     134 ..      83     144 .. 0.81
   2 ?   -2.9   0.0      0.73   4.3e+03      77     175 ..     217     237 ..     212     249 .. 0.55
   3 ?    2.2   0.0      0.02   1.2e+02      42      58 ..     364     380 ..     350     430 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 7.5e-05
                                   -SS-EEEEEEE--SSSTTCH.HHH CS
                 Cons_hypoth95 109 kkkeefdivflDPPyakellieev 132
                                   +  +++d++++DPP+ +++ +++ 
  gi|13542307|ref|NP_111995.1| 111 SMRGKIDLIYIDPPFDSKADYRTK 134
                                   456789*********999776655 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 0.73
                                   HHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-EEEEEEE--SSSTTCH.HHHHHHHHHTT-EEEEEEEEEEEECCSS CS
                 Cons_hypoth95  77 vkilkenleelkleeetaelkedaleallklakkkeefdivflDPPyakellieevlelleekkllkenalvvvetekeke 157
                                   v+ +k+n++e ++                                                                    
  gi|13542307|ref|NP_111995.1| 217 VRRIKKNVQEYDTV------------------------------------------------------------------- 230
                                   55666666666644................................................................... PP

                                   S--.-TTEEEEEEEEETT CS
                 Cons_hypoth95 158 lpespenlelvkekkyge 175
                                              k+ +yg+
  gi|13542307|ref|NP_111995.1| 231 -----------KQINYGH 237
                                   ...........3333333 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.02
                                   C-EEEETT-TTSHHHHH CS
                 Cons_hypoth95  42 garvLDlfaGsGalglE 58 
                                   ++ + D faGsG+ g  
  gi|13542307|ref|NP_111995.1| 364 NSVIADFFAGSGTTGAV 380
                                   55667********9964 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (681 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       779  (0.0434492); expected 358.6 (0.02)
Passed bias filter:                      575  (0.0320709); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.51
# Mc/sec: 3989.29
//
Query:       gi|13542308|ref|NP_111996.1|  [L=359]
Description: AAA family ATPase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.1e-07   29.4   0.0    2.2e-06   28.0   0.0    1.7  1  AAA_22           AAA domain
    2.3e-05   24.8   0.0    6.6e-05   23.3   0.0    1.8  1  AAA              ATPase family associated with various cellul
    0.00014   21.9   0.1    0.00053   20.0   0.1    1.9  1  AAA_14           AAA domain
    0.00089   19.2   1.9    0.00098   19.1   0.3    2.1  2  ATPase_2         ATPase domain predominantly from Archaea
     0.0021   18.5   0.0     0.0085   16.5   0.0    2.0  2  AAA_16           AAA ATPase domain
     0.0033   17.4   0.0     0.0084   16.1   0.0    1.8  1  AAA_5            AAA domain (dynein-related subfamily)
     0.0086   15.6   0.1      0.012   15.1   0.1    1.4  1  KTI12            Chromatin associated protein KTI12
     0.0094   15.7   0.0      0.017   14.8   0.0    1.4  1  Sigma54_activat  Sigma-54 interaction domain
  ------ inclusion threshold ------
      0.012   14.8   0.0       0.02   14.1   0.0    1.3  1  DUF2075          Uncharacterized conserved protein (DUF2075)
      0.024   14.6   0.0       0.04   13.8   0.0    1.4  1  NACHT            NACHT domain
      0.053   12.7   0.0       0.09   12.0   0.0    1.4  1  TIP49            TIP49 P-loop domain
       0.13   11.6   0.0        0.2   11.0   0.0    1.3  1  FtsK_SpoIIIE     FtsK/SpoIIIE family


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 !   28.0   0.0   1.5e-09   2.2e-06       6     120 ..      60     156 ..      57     170 .. 0.75

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 1.5e-09
                        AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelkaerlsseellealeqal 86 
                                   ++++++G +G+GKT+++ ++++ ++e      ++ ++++v++ +  +s +++r+l r+  +     +++ +e+ +++   l
  gi|13542308|ref|NP_111996.1|  60 RHIIIYGSKGSGKTLSALTIASAFKES-----KSIPFFYVNARENPTSIKIYRKLTRIDSR-----GHDIDEVKSKFDSML 130
                                   799*********************743.....46666688887777888888888777663.....567799999998888 PP

                        AAA_22  87 raravielliiDEaqhlrs.eealeeLrsllnlsr 120
                                   + ++    +i+DE+++l +  ++l +L       +
  gi|13542308|ref|NP_111996.1| 131 SGKSI---VILDEVDFL-QdYDILYHL---TR--H 156
                                   88866...*********.435555555...33..3 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.0   4.4e-08   6.6e-05       1      70 [.      62     144 ..      62     162 .. 0.78

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 4.4e-08
                                   EEEESSTTSSHHHHHHHHHHHHT....HEEEEEETTTCSSS...........STTHHHHHHHHHHHHHHHTS.TSEEEEEE CS
                           AAA   1 vllyGppGtGKTllakavakelg....vefleisgsellsk...........yvgesekkirelfkeakeka.kpsilfiD 65 
                                   +++yG +G GKTl a  +a+ ++    ++f+ +++ e   +             g+  ++++  f++   +  ++si+++D
  gi|13542308|ref|NP_111996.1|  62 IIIYGSKGSGKTLSALTIASAFKesksIPFFYVNARENPTSikiyrkltridSRGHDIDEVKSKFDS---MLsGKSIVILD 139
                                   589******************9555568999999998885578888898444555555555555554...44456****** PP

                                   TGGGH CS
                           AAA  66 Eidal 70 
                                   E+d l
  gi|13542308|ref|NP_111996.1| 140 EVDFL 144
                                   **966 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.1   3.5e-07   0.00053       4      78 ..      61     146 ..      59     165 .. 0.70

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 3.5e-07
                        AAA_14   4 ilvitGaRrvGKTtllkqlikell.vkkesilyinldderd.....kkladpe......kllelileklke..ekktylfl 70 
                                    ++i G + +GKT  + ++++     k+  ++y+n  ++++     +   + +      + ++++++k+ +  ++k++++l
  gi|13542308|ref|NP_111996.1|  61 HIIIYGSKGSGKTLSALTIASAFKeSKSIPFFYVNARENPTsikiyR---KLTridsrgHDIDEVKSKFDSmlSGKSIVIL 138
                                   589****************9888876777889999888777665542...2222223443334444443335679****** PP

                        AAA_14  71 DEiqevpe 78 
                                   DE+  +++
  gi|13542308|ref|NP_111996.1| 139 DEVDFLQD 146
                                   ***98876 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.1       4.3   6.4e+03     109     125 ..       8      29 ..       5      39 .. 0.66
   2 !   19.1   0.3   6.6e-07   0.00098       9      63 ..      48     102 ..      40     208 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 4.3
                      ATPase_2 109 llekikkkgkk.....iiiiiD 125
                                   + ek+k+++k+      +ii+D
  gi|13542308|ref|NP_111996.1|   8 VEEKVKERAKEtsnikSAIIFD 29 
                                   5566777766666656667766 PP

  == domain 2  score: 19.1 bits;  conditional E-value: 6.6e-07
                      ATPase_2   9 keleeilerepneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesis 63 
                                   ++l  +++ +  + + iYG++gsGKt     i++  ++++   ++y + re  +s
  gi|13542308|ref|NP_111996.1|  48 NDLADYVNLNLPRHIIIYGSKGSGKTLSALTIASAFKESKSIPFFYVNARENPTS 102
                                   566777888888899*********************9999888888888876443 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   5.7e-06    0.0085      13      74 ..      48     111 ..      40     141 .. 0.74
   2 ?   -2.1   0.0       2.8   4.2e+03     137     161 ..     134     156 ..     114     164 .. 0.61

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 5.7e-06
                        AAA_16  13 lsalervrsgrpelvllsGesGvGKsslvrellralekdg.giflrgkcdqlesaipysa.laq 74 
                                   +++ + v+ + p+ ++++G +G+GK+  + +++ a+++++ + f++ ++++++++i  +  l++
  gi|13542308|ref|NP_111996.1|  48 NDLADYVNLNLPRHIIIYGSKGSGKTLSALTIASAFKESKsIPFFYVNARENPTSIKIYRkLTR 111
                                   4444566777789*********************999998688899999999444333332444 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.8
                        AAA_16 137 lvlvlDdlqwadeaslqllaaLlrl 161
                                    +++lD+++ +++   ++l++L r 
  gi|13542308|ref|NP_111996.1| 134 SIVILDEVDFLQD--YDILYHLTRH 156
                                   4777787774444..5666666555 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   5.7e-06    0.0084       1      78 [.      61     145 ..      61     181 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 5.7e-06
                                   EEEEE--SSSSHHHHHHHGGGGB....S--EEEEE--TT--HHHHH--B--............--------G-SEEEEESG CS
                         AAA_5   1 dvlLvGppGtgKselaerlaaal....nreveyvqltrdtteedlkgrreik...ngttslvdsplvraaregeilvlDEv 74 
                                   ++++ G +G+gK+  a  +a+a+      +++yv+ +++ t+ ++  ++      + +   v+s++      ++i++lDEv
  gi|13542308|ref|NP_111996.1|  61 HIIIYGSKGSGKTLSALTIASAFkeskSIPFFYVNARENPTSIKIYRKLTRIdsrGHDIDEVKSKFDSMLSGKSIVILDEV 141
                                   689********************998888999999999988888877665435656667777777776677999******* PP

                                   GG-- CS
                         AAA_5  75 erae 78 
                                   + ++
  gi|13542308|ref|NP_111996.1| 142 DFLQ 145
                                   9655 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1     8e-06     0.012       4     106 ..      62     167 ..      61     312 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 8e-06
                                   EEEE--TTSSHHHHHHHHHHHHHH.TT--EEEE-THHHH.TTSSS--GGGHHH...HHHHHHHHHHHHHTT.SEEEE-S-- CS
                         KTI12   4 vvltGlPssGKstrakeLakalee.ekrsvvviddeslgiekdsykdsakeka...lRsslrsavkrdLskekvVIvDsln 80 
                                   +++ G   sGK+  a ++a+a++e + +   +++     ++ + y++  +  +     ++++s+ +  Ls + +VI+D++ 
  gi|13542308|ref|NP_111996.1|  62 IIIYGSKGSGKTLSALTIASAFKEsKSIPFFYVNARENPTSIKIYRKLTRIDSrghDIDEVKSKFDSMLSGKSIVILDEVD 142
                                   7999*******************966788999998888888888887766544000345678888899************* PP

                                   -SHHHHHHHHHHHHHTT-EEEEEEEE CS
                         KTI12  81 yikgfRYeLyciakaakttlcvvyvv 106
                                   + + +   Ly + ++ + +l+++  +
  gi|13542308|ref|NP_111996.1| 143 FLQDYD-ILYHLTRHTRANLILLTQK 167
                                   **9985.4888888888877765443 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   1.1e-05     0.017       7      64 ..      42     102 ..      37     108 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.1e-05
                                   HHHHHHHHHHHHCTSS..S-EEEECSTTSSHHHHHHHHHHHSTT.TTS-EEEEETTTS-TT CS
               Sigma54_activat   7 alkelleqikkvaktd..lsvlitGesGtGKellaraiheaskr.kekpfvavncaaipee 64 
                                   +l+++++ ++ +++ +   +++i G +G+GK+l a +i +a k+ k+ pf  vn  + p++
  gi|13542308|ref|NP_111996.1|  42 ELNKVTNDLADYVNLNlpRHIIIYGSKGSGKTLSALTIASAFKEsKSIPFFYVNARENPTS 102
                                   56666777777766554489******************9865541677******9887765 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   1.3e-05      0.02       3      71 ..      61     130 ..      59     146 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.3e-05
                       DUF2075   3 vvlVtGvaGtGKtvvllnllaeleddeeertavylsvNhplvl...vlrealakke.ekkkkkeafeklssfi 71 
                                    +++ G  G+GKt+ +l+++ +    +e ++  +++vN +++    +++++l++ + ++++++e+ +k++s+ 
  gi|13542308|ref|NP_111996.1|  61 HIIIYGSKGSGKTLSALTIASAF---KESKSIPFFYVNARENPtsiKIYRKLTRIDsRGHDIDEVKSKFDSML 130
                                   589*******************9...66777778888877765455788888887767777777777777765 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   2.7e-05      0.04       1      71 [.      60     125 ..      60     177 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.7e-05
                                   SCEEEEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEEEETTTTTTS-...-HCHHHCCCCTS--SSS-C CS
                         NACHT   1 rlvilqGeaGsGKTtLlqklalawaegklpqgafklvFflslrelsrsgnarsladllfsqlpepaapvse 71 
                                   r +i+ G  GsGKT  +  +a+a +e+k        +F+++ re ++s ++++  + + s ++++ +  s+
  gi|13542308|ref|NP_111996.1|  60 RHIIIYGSKGSGKTLSALTIASAFKESKSIP-----FFYVNARENPTSIKIYRKLTRIDSRGHDIDEVKSK 125
                                   5699***********************9444.....68888888888777755545555555555554444 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0     6e-05      0.09      51      87 ..      60      98 ..      49     141 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 6e-05
                                  XXXXXXXXXXXXXXXXXXXXXXXXX..XXXXXXXXXXXX CS
                         TIP49 51 ravLlaGpsgtGktalaiaiskelg..edvpfvalsgse 87
                                  r +++ G +g+Gkt  a++i+ ++   +++pf  +++ e
  gi|13542308|ref|NP_111996.1| 60 RHIIIYGSKGSGKTLSALTIASAFKesKSIPFFYVNARE 98
                                  789***********999999988864489****999876 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00013       0.2      39      57 ..      57      75 ..      14     128 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00013
                                  -...SEEEE--TTSSHHHHHH CS
                  FtsK_SpoIIIE 39 a..shllvaGatgsGKStaln 57
                                      h+++ G++gsGK+    
  gi|13542308|ref|NP_111996.1| 57 NlpRHIIIYGSKGSGKTL--S 75
                                  2559************84..3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (359 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       623  (0.0347482); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); 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: 0.62u 0.32s 00:00:00.94 Elapsed: 00:00:00.50
# Mc/sec: 2178.82
//
Query:       gi|13542309|ref|NP_111997.1|  [L=201]
Description: site-specific recombinase, DNA invertase Pin-related [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.4e-44  150.5   0.3    4.7e-44  150.0   0.3    1.2  1  Resolvase  Resolvase, N terminal domain
    4.7e-06   26.3   1.3    1.1e-05   25.1   0.2    2.1  2  HTH_38     Helix-turn-helix domain
     0.0019   18.3   0.0     0.0033   17.4   0.0    1.5  1  HTH_7      Helix-turn-helix domain of resolvase


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 !  150.0   0.3   7.9e-48   4.7e-44       1     145 [.       4     149 ..       4     150 .. 0.95

  Alignments for each domain:
  == domain 1  score: 150.0 bits;  conditional E-value: 7.9e-48
                                   EEEEEEES---...--THHHHHHHHHHHH-S--..SE...EEEE.S-TT-TT-HHHHHHHHHHTT-EE..EEEESSCCCC- CS
                     Resolvase   1 aigYaRvStee...qddslerQkealrayakenglkivkefeDkgvSGakleRpglkrllaalregkg.dvlvvekldRLa 77 
                                   a++Y+R St e   q+ s erQkea+r+y  ++g+++ ++feDk++SG+++ Rp+++r+l+ l +    ++++v k+dR+a
  gi|13542309|ref|NP_111997.1|   4 AFAYVRASTIEevrQG-SNERQKEAIRQYTYQKGYEL-EIFEDKAKSGRNTLRPEFERMLKSLDR--RpQIVIVSKIDRFA 80 
                                   689********99777.****************9998.67*************************..337*********** PP

                                   S...S-HHHHHHHHHTT-EEEESS...SS----HHHHHHHHHHHHHHHHHHHHHCT-TTHHHHHHHHHH CS
                     Resolvase  78 Rsvrdlltlleelrekgvslvslde.gidtstpmgrlllqilaalaeferelirertkeglaaakakGk 145
                                   Rs++dll++le l+++gv +vs+++ gidt+tp+grlllqil+a+aefer++i  rtk+g+++a+ kG+
  gi|13542309|ref|NP_111997.1|  81 RSLSDLLKTLEYLDQNGVGFVSVNDpGIDTTTPNGRLLLQILGAFAEFERNMINSRTKAGREQAQSKGV 149
                                   ************************956****************************************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 ?   -1.7   0.1      0.44   2.6e+03       9      20 ..     129     140 ..     127     145 .. 0.77
   2 !   25.1   0.2   1.8e-09   1.1e-05       6      44 .]     162     200 ..     162     200 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.44
                        HTH_38   9 eReeIerllaeG 20 
                                   eR++I    ++G
  gi|13542309|ref|NP_111997.1| 129 ERNMINSRTKAG 140
                                   99*998887777 PP

  == domain 2  score: 25.1 bits;  conditional E-value: 1.8e-09
                        HTH_38   6 sleeReeIerllaeGlslreIArrLgrspsTIsRElkRn 44 
                                   s+ +R++   l ++Gls r+IA+ L +s++ I R l+ n
  gi|13542309|ref|NP_111997.1| 162 SFIDRRKVMELKQKGLSARAIAKSLECSTTPILRILREN 200
                                   5669********************************987 PP

>> HTH_7  Helix-turn-helix domain of resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   5.6e-07    0.0033       1      45 []     152     200 ..     152     200 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 5.6e-07
                                   S---SS-HH....HHGGGGSSTTTT--STTTSSSS---SSSS--SS--S CS
                         HTH_7   1 GRpsklskn....dinrvvkLleeGisiskIAkevnisRsTvYRyladn 45 
                                   GRp++ ++n    d   v +L ++G s+++IAk + +s + + R+l++n
  gi|13542309|ref|NP_111997.1| 152 GRPPLKTRNgsfiDRRKVMELKQKGLSARAIAKSLECSTTPILRILREN 200
                                   9********87666889*****************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       686  (0.038262); expected 358.6 (0.02)
Passed bias filter:                      564  (0.0314574); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1326.01
//
Query:       gi|13542310|ref|NP_111998.1|  [L=169]
Description: hypothetical protein TVN1479 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score 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   0.0      0.028   14.4   0.0    1.2  1  NMN_transporter  Nicotinamide mononucleotide transporter
      0.075   12.3   0.0        0.1   11.8   0.0    1.2  1  MASE4            Membrane-associated sensor, integral membran


Domain annotation for each model (and alignments):
>> NMN_transporter  Nicotinamide mononucleotide transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   3.1e-06     0.028      72     129 ..      24     124 ..       8     129 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.1e-06
               NMN_transporter  72 k....avrkltkkewlilllvivlgtallgfllka......l.................................tdaalp 109
                                   +    ++rk +k+ +++ ++++++g++++ f+l++      +                                  + a+p
  gi|13542310|ref|NP_111998.1|  24 QqtgtTIRKSSKSPRIVGIIAFLVGFFAVSFFLSHgyssstVhvtnieyyyydpytgsnwtysfpgsydmqpgstVNGAYP 104
                                   1344359********************888999997555440444555555666666666666666666655555555568 PP

               NMN_transporter 110 vlDafttvlsivaqllmarr 129
                                   ++  +t ++s++  ++m+ +
  gi|13542310|ref|NP_111998.1| 105 FTSNLTCAMSFTNAYAMTPG 124
                                   89999999999999999865 PP

>> MASE4  Membrane-associated sensor, integral membrane domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   1.2e-05       0.1     103     155 ..      28      79 ..      21      87 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.2e-05
                         MASE4 103 sklesrknkilllliillfllallllahllSshseeltldiidnktenfsalw 155
                                   +++ ++++k   +++i++fl+++++++ +lS  +++ t+++++ +   +++ +
  gi|13542310|ref|NP_111998.1|  28 TTI-RKSSKSPRIVGIIAFLVGFFAVSFFLSHGYSSSTVHVTNIEYYYYDPYT 79 
                                   444.666777778999**************************99888777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       547  (0.0305092); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); 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: 00:00:00.45
# Mc/sec: 1137.55
//
Query:       gi|13542311|ref|NP_111999.1|  [L=251]
Description: chromosome partitioning ATPase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.1e-58  196.2   0.2    7.3e-58  195.4   0.1    1.4  2  AAA_31       AAA domain
    6.9e-25   87.6   0.2    8.8e-25   87.2   0.2    1.1  1  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
    3.7e-13   49.5   0.0    9.5e-13   48.2   0.0    1.6  1  CBP_BcsQ     Cellulose biosynthesis protein BcsQ
    5.6e-11   42.2   0.1    4.6e-10   39.2   0.1    2.2  1  MipZ         ATPase MipZ
    1.4e-10   41.0   0.5    3.1e-10   40.0   0.5    1.5  1  Fer4_NifH    4Fe-4S iron sulfur cluster binding proteins, Nif
    1.7e-09   37.5   0.6    3.6e-09   36.4   0.6    1.6  1  ParA         NUBPL iron-transfer P-loop NTPase
    1.3e-07   31.1   1.8    6.8e-06   25.5   0.5    2.9  2  ArsA_ATPase  Anion-transporting ATPase
     0.0031   16.8   0.4      0.044   13.1   0.1    2.1  2  VirC1        VirC1 protein
      0.009   15.9   0.2      0.016   15.1   0.2    1.4  1  KH_7         KH domain


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 !  195.4   0.1   3.7e-61   7.3e-58       3     177 .]       2     172 ..       1     172 [. 0.96
   2 ?   -2.5   0.0         2     4e+03     107     122 ..     187     202 ..     176     241 .. 0.61

  Alignments for each domain:
  == domain 1  score: 195.4 bits;  conditional E-value: 3.7e-61
                        AAA_31   3 vIaianqKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQanattglgiekneiektlyevlieeknikeaiiktkvenldl 83 
                                   +I+ianqKGG GKTTt+vnl+++la++ +kvLl+D+DpQ+n+tt++g++k e+++t+y+v++ +  +++ai   + +++d+
  gi|13542311|ref|NP_111999.1|   2 IISIANQKGGCGKTTTAVNLGSVLARK-HKVLLIDIDPQGNLTTSFGVNKGELNRTMYDVML-DGGLEKAIL--RKDSIDI 78 
                                   8***********************976.79******************************86.788999999..45689** PP

                        AAA_31  84 ipssidLaeaeielvelekkeeilkellekvkdeYDyiiiDcpPsLglltenaLvasdsviipvqaeayaleGleqllkti 164
                                   +ps idLa+ae++l + + +e+il + l+k++ +YD+iiiD+pPsLg++t+naLvasd+v+ipvqae++aleGl+qll+ +
  gi|13542311|ref|NP_111999.1|  79 VPSIIDLAGAEVQLSGRMGREYILANELSKLSRRYDFIIIDTPPSLGVFTINALVASDYVLIPVQAEFFALEGLTQLLSVV 159
                                   ********************************************************************************* PP

                        AAA_31 165 eevkkklnpklei 177
                                   + v+++l ++l+i
  gi|13542311|ref|NP_111999.1| 160 DLVNTRLGRTLKI 172
                                   *****99998886 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2
                        AAA_31 107 lkellekvkdeYDyii 122
                                    +e+le+v+++Y   +
  gi|13542311|ref|NP_111999.1| 187 SNEVLEDVRKHYSKHL 202
                                   4555666666554333 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 !   87.2   0.2   4.4e-28   8.8e-25       1     128 []       3     223 ..       3     223 .. 0.93

  Alignments for each domain:
  == domain 1  score: 87.2 bits;  conditional E-value: 4.4e-28
                                   EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH........................... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................... RF
                          CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep........................... 54 
                                   i+ia++kGG GKTt+a+nL+  lar +++Vll+D Dpq+n+++++  +++++++                           
  gi|13542311|ref|NP_111999.1|   3 ISIANQKGGCGKTTTAVNLGSVLAR-KHKVLLIDIDPQGNLTTSFGVNKGELNRtmydvmldgglekailrkdsidivpsi 82 
                                   78***********************.*****************66666666666*************************** PP

                                   .................................................................CCHCCCHHHHHHCHCH CS
                                   .................................................................xxxxxxxxxxxxxxxx RF
                          CbiA  55 .................................................................dlkrllellealgkkk 70 
                                                                                                     l+ l +ll++++ ++
  gi|13542311|ref|NP_111999.1|  83 idlagaevqlsgrmgreyilanelsklsrrydfiiidtppslgvftinalvasdyvlipvqaeffALEGLTQLLSVVDLVN 163
                                   *****************************************************************6666677776666666 PP

                                   HHH.....EEEEEEEEESS...-TTCHHHHHHHHHHCTS-EEE.EEE--CCHCCCCHHTS-H CS
                                   xxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx RF
                          CbiA  71 all...lkiagvvlnrvdgeneetllkealeelkqrygvpvlg.viprdeavaeapargepv 128
                                     l   lki+g+v+++++++  +++ +e le++ ++y  +++  +ipr++ v+++ ++gepv
  gi|13542311|ref|NP_111999.1| 164 TRLgrtLKILGMVVTMFNSR--TKSSNEVLEDVRKHYSKHLFRtIIPRNVTVTDSTMTGEPV 223
                                   666778**************..9***********9998888888*************99986 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.2   0.0   4.7e-16   9.5e-13       4     231 ..       3     241 ..       1     243 [. 0.83

  Alignments for each domain:
  == domain 1  score: 48.2 bits;  conditional E-value: 4.7e-16
                      CBP_BcsQ   4 lalqGvRGGvGttsllaaLawalhelgesvlviDlspdnlLrlhFnvdi.eqregwaraeldgapwrqaaleyapgldllP 83 
                                   + +   +GG+G+t+ ++ L+  l + +++vl+iD+ p+  L+++F v+  e ++++   +ld   +++a+l+ ++ +d++P
  gi|13542311|ref|NP_111999.1|   3 ISIANQKGGCGKTTTAVNLGSVLAR-KHKVLLIDIDPQGNLTTSFGVNKgELNRTMYDVMLD-GGLEKAILR-KDSIDIVP 80 
                                   5666679**************9976.789*****************9862456777778887.578888877.789***** PP

                      CBP_BcsQ  84 fGelnveekenlqqlaekaeallaalkelkeqyrwillDlpagasaltrellaladlvllvvepdan.........chvrL 155
                                        +  + +l+  + ++  l+++l++l+++y++i++D p      t ++l  +d vl  v+++           + v L
  gi|13542311|ref|NP_111999.1|  81 SIIDLAGAEVQLSGRMGREYILANELSKLSRRYDFIIIDTPPSLGVFTINALVASDYVLIPVQAEFFalegltqllSVVDL 161
                                   86555555556999999************************************9******9**997511111111144567 PP

                      CBP_BcsQ 156 hqqalpaaellL...iNqfeaasqlqqDllqlWlqsl.rrllPlvihrDealaEalaakqPlgeyrpdslaaeevktLan 231
                                    + +l ++  +L   +  f+   +  +++l   ++++ ++l   +i r  +++++ ++  P+  yr d+ a++    La+
  gi|13542311|ref|NP_111999.1| 162 VNTRLGRTLKILgmvVTMFNSRTKSSNEVLEDVRKHYsKHLFRTIIPRNVTVTDSTMTGEPVVIYRKDASASKSYVELAK 241
                                   777888877766555999************99996664889999*****************************9999986 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.2   0.1   2.3e-13   4.6e-10       2     162 ..       2     179 ..       1     195 [. 0.69

  Alignments for each domain:
  == domain 1  score: 39.2 bits;  conditional E-value: 2.3e-13
                                   EEEE--SSTTSSHHHHHHHHHHHHHTTT--EEEEE--TTT-HHHHHHHHHHHHHHH.HT------EEE-SSS-HHHHTT.. CS
                          MipZ   2 vivlgnekGGsGksttavhvavaLlkkGarvaaidldlrqrtlarylenraataer.kglsLplpealalseaeeaeve.. 79 
                                   +i ++n+kGG Gk+ttav +   L++k ++v  id+d + +  + +  n+ + ++   ++ L+     a+  +++ ++   
  gi|13542311|ref|NP_111999.1|   2 IISIANQKGGCGKTTTAVNLGSVLARK-HKVLLIDIDPQGNLTTSFGVNKGELNRTmYDVMLDGGLEKAILRKDSIDIVps 81 
                                   7899****************9888776.89********9999999998988876642466666655555555444433211 PP

                                   ...........S-HHHHHHHHHHHHHHHHHH-SEEEEE--SS--HHHHHHHHT-SEEEEEEESSHHHHC....CCEEE-SS CS
                          MipZ  80 ...........eeeeaevaeleelvadleaeldfividtPGsdsalsrlahsladtlvtPlndsfvdfd....llgkvdpe 145
                                               +   +   l++ +++l++++dfi+idtP s    +  a   +d ++ P+   f  ++    ll+ vd  
  gi|13542311|ref|NP_111999.1|  82 iidlagaevqlSGRMGREYILANELSKLSRRYDFIIIDTPPSLGVFTINALVASDYVLIPVQAEFFALEgltqLLSVVDLV 162
                                   111100000011122223457888999**************************************9986333356666766 PP

                                   S--EEEE-HHHHHHHHH CS
                          MipZ 146 tlkvkrpslyaelvwea 162
                                    +++ r      +v   
  gi|13542311|ref|NP_111999.1| 163 NTRLGRTLKILGMVVTM 179
                                   66666655555555555 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 !   40.0   0.5   1.6e-13   3.1e-10       7     246 ..       8     245 ..       1     250 [. 0.80

  Alignments for each domain:
  == domain 1  score: 40.0 bits;  conditional E-value: 1.6e-13
                     Fer4_NifH   7 GkGGiGksttsqnlsaalaemgkkvlivGCDPkaD.strl.llggkaqetvldtlrekgavedvkvedvvkkGyggvkcve 85 
                                    kGG Gk+tt+ nl + la+++ kvl++  DP+ + +t++ + +g +++t+ d++ + g+   +  +d +       + ++
  gi|13542311|ref|NP_111999.1|   8 QKGGCGKTTTAVNLGSVLARKH-KVLLIDIDPQGNlTTSFgVNKGELNRTMYDVMLDGGLEKAILRKDSIDI---VPSIID 84 
                                   59****************9976.79********98345553457999************9666666666655...224678 PP

                     Fer4_NifH  86 sGGPepG.vGCaGrgvitaielleelgayddlDfvlyDvLGDvvCGGfalPiredkaqevyivtsgelmalyaanniakgi 165
                                     G e+   G  Gr  i a el +       +Df++ D       G f++      +++v+i +++e+ al    ++   +
  gi|13542311|ref|NP_111999.1|  85 LAGAEVQlSGRMGREYILANELSKL---SRRYDFIIIDTPPS--LGVFTINAL-VASDYVLIPVQAEFFALEGLTQLLSVV 159
                                   8898876358888888877665433...34689*****8765..588887654.567899999*********999999888 PP

                     Fer4_NifH 166 ekyaksgg..vrlgGlii...nsrkvddereliekfaeelgtkvle.vvPrdeivrkaelrkktvieyapeseqakeyrel 240
                                      + + g  +++ G+++   nsr +++ +e++e+  ++ + +++  ++Pr+ +v+ + +  + v+ y ++++ +k y el
  gi|13542311|ref|NP_111999.1| 160 DLVNTRLGrtLKILGMVVtmfNSR-TKSSNEVLEDVRKHYSKHLFRtIIPRNVTVTDSTMTGEPVVIYRKDASASKSYVEL 239
                                   766544333588889875344888.99999*********9999986268******************************** PP

                     Fer4_NifH 241 arkile 246
                                   a+++ +
  gi|13542311|ref|NP_111999.1| 240 AKEVEN 245
                                   ***986 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.4   0.6   1.8e-12   3.6e-09       5     245 ..       2     243 ..       1     244 [. 0.73

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 1.8e-12
                          ParA   5 viavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgveeekpeqs.ekkli..PveakgikvmSigf.. 80 
                                   +i ++  KGG GK+t+avnl   La+  +kv l+D+D  G ++ + +gv++ + +++  + ++   +e+  ++  Si++  
  gi|13542311|ref|NP_111999.1|   2 IISIANQKGGCGKTTTAVNLGSVLAR-KHKVLLIDIDPQG-NLTTSFGVNKGELNRTmYDVMLdgGLEKAILRKDSIDIvp 80 
                                   789999******************86.579**********.5888899999877777433344455666778888887622 PP

                          ParA  81 .llesedeavvwrGpmkskaikqllkdvewgelDyLiiDlPPGtgDeqltvaqklplagaviVttpqevaladvkkaiemf 160
                                    +++   + v   G m  + i     +      D++iiD+PP  g    t+   +  + ++i    +  al+  ++ ++++
  gi|13542311|ref|NP_111999.1|  81 sIIDLAGAEVQLSGRMGREYILANELSKLSRRYDFIIIDTPPSLG--VFTINALVASDYVLIPVQAEFFALEGLTQLLSVV 159
                                   257778999*******99887554444445789**********99..5677777777777777788889999999988888 PP

                          ParA 161 kkvkv......kvlGvveNmsgfvcpkcgekteifgkgggeklaeelgvp.llgeipldpeireasdegkplvlkepesea 234
                                   + v++      k+lG+v  m    +++++e          e++ ++++ + + + ip + ++++++ +g+p+v+ +++++a
  gi|13542311|ref|NP_111999.1| 160 DLVNTrlgrtlKILGMVVTMFNSRTKSSNEV--------LEDVRKHYSKHlFRTIIPRNVTVTDSTMTGEPVVIYRKDASA 232
                                   8777511111156666666655554443333........344444444430334589999********************* PP

                          ParA 235 akaleeiaekv 245
                                   +k++ e+a++v
  gi|13542311|ref|NP_111999.1| 233 SKSYVELAKEV 243
                                   ****9999987 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.5   3.4e-09   6.8e-06       9      97 ..       9      92 ..       2     132 .. 0.67
   2 ?    1.9   0.0     0.053     1e+02     140     186 ..     154     193 ..     150     231 .. 0.68

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 3.4e-09
                                  STTSSHHHHHHHHHHHHHHTTS-EEEEE-STTTHHHHHHTS--BSS-EEETSSEEEEE--HHHHHHHHHCCHHGGGSCCHHHH CS
                   ArsA_ATPase  9 KGGVGKttvsaatavklsekgkkvllistDPAhslsDsfdqklgkeptkvkeNLsavEidpeveleeakqevqkeeeallgle 91
                                  KGG GKtt +  ++  l++k +kvlli  DP  +l  sf  + g+ ++ +    + v +d   e +  +++ ++   +++ l 
  gi|13542311|ref|NP_111999.1|  9 KGGCGKTTTAVNLGSVLARK-HKVLLIDIDPQGNLTTSFGVNKGELNRTM----YDVMLDGGLEKAILRKDSIDIVPSIIDLA 86
                                  9****************985.89****************99777665543....33444444444445555555555555555 PP

                                  HHHHHH CS
                   ArsA_ATPase 92 eledvl 97
                                  + e +l
  gi|13542311|ref|NP_111999.1| 87 GAEVQL 92
                                  555555 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.053
                                   GGGGHHHHHHHHHHHHHHHHHHHHHHHHHHCCCSHCHHHHHHHHHHH CS
                   ArsA_ATPase 140 rllslpevleklleklvklkeklsplakqlvkllglggvsieealee 186
                                   +lls+++ ++  l + +k+ +++  + ++ +k         +e+le+
  gi|13542311|ref|NP_111999.1| 154 QLLSVVDLVNTRLGRTLKILGMVVTMFNSRTKS-------SNEVLED 193
                                   588888899999999988888888887776543.......2233333 PP

>> VirC1  VirC1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.1   2.2e-05     0.044       3      41 ..       2      39 ..       1      47 [. 0.82
   2 ?    2.0   0.0     0.055   1.1e+02      82     134 ..     111     162 ..     103     201 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.2e-05
                         VirC1  3 litfcslkGGaGkttalmglcsalasdgkrvalfeaden 41
                                  +i+++  kGG Gktt+ + l s la  +++v l + d  
  gi|13542311|ref|NP_111999.1|  2 IISIANQKGGCGKTTTAVNLGSVLAR-KHKVLLIDIDPQ 39
                                  5889999*************999975.567888887765 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.055
                         VirC1  82 eGfdyaladtrgGsselnntiiassdllliPtmltpldidealatyryviell 134
                                   + +d+ ++dt      +    + +sd++liP     + + e l+    v++l+
  gi|13542311|ref|NP_111999.1| 111 RRYDFIIIDTPPSLGVFTINALVASDYVLIPVQAEFFAL-EGLTQLLSVVDLV 162
                                   56999999999888888777777899*****86544443.4555555555555 PP

>> KH_7  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.2   8.1e-06     0.016      11      56 ..     203     248 ..     189     251 .] 0.80

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 8.1e-06
                          KH_7  11 ieeklPkevkitdveFEGPelViYtknpklfaengdlirklAkelr 56 
                                   + + +P++v++td +  G  +ViY k+ ++  +  +l +++ + lr
  gi|13542311|ref|NP_111999.1| 203 FRTIIPRNVTVTDSTMTGEPVVIYRKDASASKSYVELAKEVENRLR 248
                                   56789**********************9998877777777766666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       580  (0.0323498); expected 358.6 (0.02)
Passed bias filter:                      514  (0.0286686); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.62u 0.28s 00:00:00.90 Elapsed: 00:00:00.48
# Mc/sec: 1571.52
//
Query:       gi|13542312|ref|NP_112000.1|  [L=593]
Description: ATPase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.8e-08   33.6   0.0    1.3e-07   32.2   0.0    1.7  1  AAA_16     AAA ATPase domain
    1.5e-05   25.0   0.6      0.079   13.0   0.2    2.7  2  AAA_14     AAA domain
      3e-05   24.3   1.4     0.0016   18.7   1.4    2.8  1  AAA_22     AAA domain
    0.00013   22.1   3.5     0.0071   16.4   2.7    3.1  2  ResIII     Type III restriction enzyme, res subunit
     0.0021   17.4   0.1        2.4    7.3   0.0    2.4  2  DUF2075    Uncharacterized conserved protein (DUF2075)
  ------ inclusion threshold ------
      0.066   12.9   0.0       0.49   10.1   0.0    2.2  2  IstB_IS21  IstB-like ATP binding protein
      0.081   13.3   0.2       0.93    9.9   0.1    2.7  3  AAA        ATPase family associated with various cellular act


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 !   32.2   0.0   5.1e-11   1.3e-07       5     169 ..      73     308 ..      72     310 .. 0.76

  Alignments for each domain:
  == domain 1  score: 32.2 bits;  conditional E-value: 5.1e-11
                        AAA_16   5 ReeeleqLlsalervrsgrp.elvllsGesGvGKsslvrellralekdggiflrgkcdql..esaipysalaqalareell 82 
                                   R+ee ++ ++ l++  ++ + ++v ++G sG GKs l  +ll  +e++  i ++ k d++  + +ip +   ++l     +
  gi|13542312|ref|NP_112000.1|  73 RREECSARAANLRDYIEHKGnRNVSITGVSGQGKSYLTMHLLSKFEDRQRIIFSFKPDDHevHLGIPVIDAKECL-P-NPF 151
                                   666666667777777777777***************************9999999***99666667776666666.4.455 PP

                        AAA_16  83 rqlldeaesaeleawrekleeala......................................................... 106
                                   r++++ +e+   + + ek+ + ++                                                         
  gi|13542312|ref|NP_112000.1| 152 RDINAFSEAYMTAFFGEKISSGIQlqqtpaflqeiasqstdwksfmktisekrksasknqietlnaieqnvksliikdmgs 232
                                   555555444444444444444444444444444444466666677777777***********************9998888 PP

                        AAA_16 107 ..........avpelagaea.srllellkrll.allsrderp.lvlvlDdlqwadeaslqllaaLlrlleskpllv 169
                                             + + l+ ++a +  +el+ r + + +++++r+ +++++D+++++  + +++l+ + r+  +k +l+
  gi|13542312|ref|NP_112000.1| 233 velanestvfDFSTLPTKQAqNFYAELMLRQIyREMEERKRKdVLVCIDEAHRLTKSYHTILDVMSREIRDKGMLW 308
                                   8888888777777777777789999999999999999989889****************99999999888776655 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.0   0.00036      0.92       3      90 ..      94     204 ..      92     210 .. 0.58
   2 !   13.0   0.2   3.1e-05     0.079      15      90 ..     223     300 ..     218     342 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00036
                        AAA_14   3 kilvitGaRrvGKTtllkqlikellvkkesilyinldderd...................kkladpekllelileklke.. 62 
                                   + + itG+   GK++l  +l+++    +++ + ++++ ++                    +   d + + e+++       
  gi|13542312|ref|NP_112000.1|  94 RNVSITGVSGQGKSYLTMHLLSKFE--DRQRIIFSFKPDDHevhlgipvidakeclpnpfR---DINAFSEAYMTA--Ffg 167
                                   6689*****************8877..5555555555544444777766665444443321...111222222222..022 PP

                        AAA_14  63 ........ekktylflDEiq.evpewekalkslvdeg 90 
                                            ++t  fl Ei  ++++w++++k + +++
  gi|13542312|ref|NP_112000.1| 168 ekissgiqLQQTPAFLQEIAsQSTDWKSFMKTISEKR 204
                                   2344466656666777777414567777777776655 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 3.1e-05
                        AAA_14  15 KTtllkqlikellvkkesilyinldderdkkladpe...kllelileklke...ekktylflDEiqevpewekalkslvde 89 
                                   K+ ++k++ + +l  +++   +++ + ++k+++++     l ++++e+  e   +k+ ++++DE++++++ ++++ +++ +
  gi|13542312|ref|NP_112000.1| 223 KSLIIKDMGSVEL--ANESTVFDFSTLPTKQAQNFYaelMLRQIYREM--EerkRKDVLVCIDEAHRLTKSYHTILDVMSR 299
                                   8889999998888..677788899999998888874333333444444..134478889*********9999999888886 PP

                        AAA_14  90 g 90 
                                   +
  gi|13542312|ref|NP_112000.1| 300 E 300
                                   5 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   1.4   6.3e-07    0.0016       4     112 ..      92     293 ..      88     317 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 6.3e-07
                        AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaee............................................... 37 
                                   + + + +tG sG GK++l   ll++++ ++ +                                                 
  gi|13542312|ref|NP_112000.1|  92 GNRNVSITGVSGQGKSYLTMHLLSKFEDRQRIIFsfkpddhevhlgipvidakeclpnpfrdinafseaymtaffgekiss 172
                                   667789********************88877777*******************************************9999 PP

                        AAA_22  38 ....erpevvfvtlpsst.sskdllrellralglelka..........................................e 71 
                                       ++ + ++ +++s++ ++k++++ + ++ ++  k+                                          +
  gi|13542312|ref|NP_112000.1| 173 giqlQQTPAFLQEIASQStDWKSFMKTISEKRKSASKNqietlnaieqnvksliikdmgsvelanestvfdfstlptkqaQ 253
                                   99996666665555555559*******99999988888*************************************776644 PP

                        AAA_22  72 rlsseellealeqalrarav.ielliiDEaqhlr.s.eealeeL 112
                                   +   e +l+++++ +++r++  +l+ iDEa++l+ s +    ++
  gi|13542312|ref|NP_112000.1| 254 NFYAELMLRQIYREMEERKRkDVLVCIDEAHRLTkSyH----TI 293
                                   44444444777777777777899999*******54242....22 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   2.7   2.8e-06    0.0071      14     159 ..      83     299 ..      70     304 .. 0.60
   2 ?   -0.2   0.0      0.35     9e+02      56      71 ..     549     564 ..     532     591 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 2.8e-06
                                   HHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S................-EEEEESSHHHHHHHHHHGGGGTGG... CS
                        ResIII  14 nlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkee...........kflflvprkslleqtleefkkflseayk 83 
                                   nl++ +++k+++++ i    G GK+++ ++l  ++   +++              + +++ k+ l    ++++ f++ + +
  gi|13542312|ref|NP_112000.1|  83 NLRDYIEHKGNRNVSITGVSGQGKSYLTMHLLSKFEDRQRIIfsfkpddhevhLGIPVIDAKECLPNPFRDINAFSEAYMT 163
                                   566677778888888888888888888888888888765554667777773332233344444444444444444444444 PP

                                   ...GEEEESSS-B--..............-SEEEEEHHHHHHTH..................................... CS
                        ResIII  84 e..igkkvsgdkkka.......kekdstnkkilvttiqsldadseee.................................. 121
                                   +   +k+ sg + ++        +++st++k ++ ti++  ++ +++                                  
  gi|13542312|ref|NP_112000.1| 164 AffGEKISSGIQLQQtpaflqeIASQSTDWKSFMKTISEKRKSASKNqietlnaieqnvksliikdmgsvelanestvfdf 244
                                   453222233333333555665544444444444444444333332223444555555555556666777777777779999 PP

                                   .......................HHHTTT-S.EEEEETGGGTTS.TTTHHHHHT--- CS
                        ResIII 122 ..................eeeseellrdrfd.viiiDEaHrlgakkswreilekfke 159
                                                     + ++e  +r+r+d ++ iDEaHrl++  s+  il+ +++
  gi|13542312|ref|NP_112000.1| 245 stlptkqaqnfyaelmlrQIYREMEERKRKDvLVCIDEAHRLTK--SYHTILDVMSR 299
                                   999999999999999986444444555555557779*******9..99999887765 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.35
                                   -EEEEESSHHHHHHHH CS
                        ResIII  56 kflflvprkslleqtl 71 
                                   +++++vp+++l+++ +
  gi|13542312|ref|NP_112000.1| 549 RVIIVVPNRELIDKYR 564
                                   8999999999999876 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   0.00095       2.4       4      28 ..      96     120 ..      93     136 .. 0.83
   2 !    7.3   0.1   0.00097       2.5      81     103 ..     266     289 ..     236     307 .. 0.68

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.00095
                       DUF2075   4 vlVtGvaGtGKtvvllnllaeledd 28 
                                   v +tGv+G GK+++ ++ll + ed 
  gi|13542312|ref|NP_112000.1|  96 VSITGVSGQGKSYLTMHLLSKFEDR 120
                                   679****************999333 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.00097
                       DUF2075  81 eekkeepkedvvi.vDEAhrlltk 103
                                    e++e+++ dv++ +DEAhrl+++
  gi|13542312|ref|NP_112000.1| 266 REMEERKRKDVLVcIDEAHRLTKS 289
                                   344555555665527******984 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00019      0.49      42      67 ..      86     113 ..      59     130 .. 0.77
   2 ?   -0.4   0.0      0.33   8.3e+02      90     127 ..     203     240 ..     187     249 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00019
                     IstB_IS21  42 sfiek..kenivllGpsGvGKshlaial 67 
                                   ++ie+  + n+ ++G sG GKs+l++ l
  gi|13542312|ref|NP_112000.1|  86 DYIEHkgNRNVSITGVSGQGKSYLTMHL 113
                                   5666511579**************9977 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.33
                     IstB_IS21  90 lkrarrdgklaralkrllkvdllilDdlgllpldqaea 127
                                    ++  +++++++  +  ++v+ li+ d+g ++l ++++
  gi|13542312|ref|NP_112000.1| 203 KRKSASKNQIETLNAIEQNVKSLIIKDMGSVELANEST 240
                                   4445556667777777778899*******999887765 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 ?   -1.4   0.0       1.1   2.9e+03       3      22 ..      98     117 ..      96     137 .. 0.80
   2 ?    9.9   0.1   0.00036      0.93      45     117 ..     260     320 ..     235     333 .. 0.78
   3 ?   -2.6   0.0       2.7   6.9e+03      27      56 ..     552     581 ..     528     586 .. 0.70

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.1
                                   EESSTTSSHHHHHHHHHHHH CS
                           AAA   3 lyGppGtGKTllakavakel 22 
                                   ++G  G GK++l   + +++
  gi|13542312|ref|NP_112000.1|  98 ITGVSGQGKSYLTMHLLSKF 117
                                   68999****99988777665 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00036
                                   HHHHHHHHHHHTS.TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTH CS
                           AAA  45 kirelfkeakeka.kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldp 117
                                    +r++ +e++e + k + + iDE+++l+ks              ++l +++++ ++++ +++i++ n +d l++
  gi|13542312|ref|NP_112000.1| 260 MLRQIYREMEERKrKDVLVCIDEAHRLTKSY------------HTILDVMSREIRDKG-MLWIITQNLIDILPE 320
                                   578888888888856699*********8777............888888888888655.888888888877765 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 2.7
                                   EEEETTTCSSSSTTHHHHHHHHHHHHHHHT CS
                           AAA  27 leisgsellskyvgesekkirelfkeakek 56 
                                   + +   el++ky g +e+ + +++++++e+
  gi|13542312|ref|NP_112000.1| 552 IVVPNRELIDKYRGLGERVLVMTIDSMREM 581
                                   445556677777777777777777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (593 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       987  (0.0550505); expected 358.6 (0.02)
Passed bias filter:                      618  (0.0344693); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.76u 0.30s 00:00:01.06 Elapsed: 00:00:00.50
# Mc/sec: 3583.97
//
Query:       gi|13542313|ref|NP_112001.1|  [L=111]
Description: hypothetical protein TVN1482 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
       0.57    9.8  12.4       0.18   11.4   5.2    2.2  2  Baculo_11_kDa  Baculovirus 11 kDa family
        6.4    6.4  13.2        5.8    6.5   4.8    2.1  2  PRA1           PRA1 family protein


Domain annotation for each model (and alignments):
>> Baculo_11_kDa  Baculovirus 11 kDa family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.7    0.0086        77      36      49 ..       8      21 ..       6      39 .. 0.80
   2 ?   11.4   5.2     2e-05      0.18      32      70 ..      54      91 ..      52     103 .. 0.72

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.0086
                 Baculo_11_kDa 36 FvLvicglvvfvvi 49
                                  F +vi++++vfv  
  gi|13542313|ref|NP_112001.1|  8 FGFVITAVIVFVTG 21
                                  6689*******964 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 2e-05
                 Baculo_11_kDa 32 flrdFvLvicglvvfvvivlfilLlvvilknaeaeeaek 70
                                  f+   vL+ c+l++fv iv++ +++  i+    ++e++ 
  gi|13542313|ref|NP_112001.1| 54 FIGALVLLYCALILFVYIVILAVIIGIIAL-LYLIETRT 91
                                  88889*************999988877765.33333333 PP

>> PRA1  PRA1 family protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   1.2    0.0015        14      97     124 ..       8      35 ..       2      42 .. 0.79
   2 ?    6.5   4.8   0.00065       5.8      44      89 ..      54      99 ..      50     109 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0015
                          PRA1  97 vllvvsvlllfltgavlvllwalligll 124
                                   + +v++ +++f+tg v+  lw+ll+++ 
  gi|13542313|ref|NP_112001.1|   8 FGFVITAVIVFVTGMVWQGLWSLLFAMT 35 
                                   5578888999999999999999988775 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.00065
                          PRA1 44 ivvllvlllslltnplslivllllvlawlflyflrseplvlfgrel 89
                                  ++ +lvll++ l+  + +++l++++ ++++ly+++++ +++ ++++
  gi|13542313|ref|NP_112001.1| 54 FIGALVLLYCALILFVYIVILAVIIGIIALLYLIETRTVKVEHYTI 99
                                  5668899999999999999999999999999998877777655554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1465  (0.0817112); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 762.93
//
Query:       gi|13542314|ref|NP_112002.1|  [L=121]
Description: hypothetical protein TVN1483 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0077   15.4   0.1        1.5    7.8   0.0    2.0  2  RP853     Uncharacterized RP853


Domain annotation for each model (and alignments):
>> RP853  Uncharacterized RP853
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.1   0.1   0.00029       5.2      88     119 ..      26      56 ..      22      72 .. 0.84
   2 !    7.8   0.0   8.6e-05       1.5     170     209 ..      69     108 ..      60     113 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.00029
                         RP853  88 mitsedeneqnkdnileqsqdviaenlvevyf 119
                                   m+ +e +n q+k   le+ q+ i en v+ y 
  gi|13542314|ref|NP_112002.1|  26 MVRYEMANPQKKG-TLERLQETIIENTVNQYE 56 
                                   899*****99775.79************9984 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 8.6e-05
                         RP853 170 ynnideatiyikkefnkilemslvftqksnifkqatgkiv 209
                                   + + +    y+  e n ++ m lv+t++  ifk+    i 
  gi|13542314|ref|NP_112002.1|  69 FMERNPDISYVEYESNPVMRMDLVITRRGLIFKREEASIS 108
                                   5555556679***********************9887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       584  (0.0325729); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 747.58
//
Query:       gi|13542315|ref|NP_112003.1|  [L=219]
Description: hypothetical protein TVN1484 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.073   13.0   3.4        1.2    9.1   0.6    2.3  2  Zn_ribbon_SprT  SprT-like zinc ribbon domain
       0.15   11.7   0.0       0.29   10.8   0.0    1.4  1  DUF2321         Uncharacterized protein conserved in bacteria
        8.8    6.1   6.8         62    3.4   4.5    2.7  2  zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal


Domain annotation for each model (and alignments):
>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.1    0.0054        32      21      36 ..     141     158 ..     131     160 .. 0.76
   2 ?    9.1   0.6    0.0002       1.2       2      15 ..     176     189 ..     175     200 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0054
                Zn_ribbon_SprT  21 rrhn..YrCrrCkgtLrg 36 
                                   rr +    C+rC+ +  +
  gi|13542315|ref|NP_112003.1| 141 RRLKtvFFCGRCRFKNIL 158
                                   45555679*****87665 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0002
                Zn_ribbon_SprT   2 kyvYrCtgCgreyt 15 
                                   + +Y+C +Cg+ y+
  gi|13542315|ref|NP_112003.1| 176 TSEYYCLNCGTYYG 189
                                   578*******7665 PP

>> DUF2321  Uncharacterized protein conserved in bacteria (DUF2321)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   4.8e-05      0.29      35      86 ..     144     198 ..     139     201 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 4.8e-05
                       DUF2321  35 ktitkcpkCst.eirGkyyvegvislgkey..evpsyCkkCgkpyPWtkakleaa 86 
                                   kt+  c +C+  +i  +    +++ +++++  + + yC +Cg+ y + ++kl+a 
  gi|13542315|ref|NP_112003.1| 144 KTVFFCGRCRFkNILKDMNKAEFLFFARNFmeTSEYYCLNCGTYYGFFRKKLDAS 198
                                   567778889852688888888889998755225678**************99986 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 ?   -2.9   0.0         1   6.1e+03      30      43 ..      78      91 ..      77      93 .. 0.64
   2 ?    3.4   4.5      0.01        62      40      52 ..     174     186 ..     127     188 .. 0.59

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1
                zinc_ribbon_10 30 shnGlapkeeleev 43
                                  + nGla+k +  +v
  gi|13542315|ref|NP_112003.1| 78 HINGLAKKWKMLNV 91
                                  56999976555555 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.01
                zinc_ribbon_10  40 leevkyrCpkCga 52 
                                    e+ +y+C +Cg+
  gi|13542315|ref|NP_112003.1| 174 METSEYYCLNCGT 186
                                   4555999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       612  (0.0341346); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.47
# Mc/sec: 1391.57
//
Query:       gi|13542316|ref|NP_112004.1|  [L=80]
Description: integrase/recombinase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       745  (0.0415528); expected 358.6 (0.02)
Passed bias filter:                      633  (0.0353059); 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: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 505.06
//
Query:       gi|13542317|ref|NP_112005.1|  [L=70]
Description: hypothetical protein TVN1486 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        1.4    8.4   8.3        4.6    6.7   8.3    1.8  1  SieB      Super-infection exclusion protein B


Domain annotation for each model (and alignments):
>> SieB  Super-infection exclusion protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   8.3   0.00026       4.6      28      61 ..       2      35 ..       1      69 [. 0.94

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.00026
                          SieB 28 leeyglwiglvflisiayllaqvvskllaeikek 61
                                  l+ y ++i lv++isi  l+++v+s+l++ ++++
  gi|13542317|ref|NP_112005.1|  2 LNRYVYHIILVIIISIVTLIINVLSFLFKSVSNY 35
                                  68899************************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1146  (0.0639188); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); 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: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 453.01
//
Query:       gi|13542318|ref|NP_112006.1|  [L=175]
Description: hypothetical protein TVN1487 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       495  (0.0276089); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1175.40
//
Query:       gi|13542319|ref|NP_112007.1|  [L=213]
Description: hypothetical protein TVN1488 [Thermoplasma volcanium GSS1]
Scores for complete sequence (score 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   10.2   6.9         10    6.3   0.6    3.2  3  PBCV_basic_adap  PBCV-specific basic adaptor domain


Domain annotation for each model (and alignments):
>> PBCV_basic_adap  PBCV-specific basic adaptor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.1    0.0043        76       4      10 ..       8      14 ..       7      16 .. 0.89
   2 ?    2.6   0.1    0.0085   1.5e+02      18      28 ..      66      76 ..      65      83 .. 0.89
   3 ?    6.3   0.6   0.00057        10      17      32 ..      82      98 ..      77      99 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.0043
               PBCV_basic_adap  4 DaKGRiv 10
                                  DaKGR++
  gi|13542319|ref|NP_112007.1|  8 DAKGRKI 14
                                  9*****9 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.0085
               PBCV_basic_adap 18 kyVkdsnGKKv 28
                                  +yV++ +GK +
  gi|13542319|ref|NP_112007.1| 66 TYVIQHSGKTI 76
                                  8*******965 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.00057
               PBCV_basic_adap 17 gkyVkdsnGKKv.yVkk 32
                                  +ky  + nGKK+ +V++
  gi|13542319|ref|NP_112007.1| 82 TKYIDTINGKKIvHVEG 98
                                  6899999********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       552  (0.0307881); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 1370.70
//
Query:       gi|13542320|ref|NP_112008.1|  [L=429]
Description: integrase/recombinase [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.064   13.2   1.3       0.15   12.0   1.3    1.6  1  Oberon_cc  Coiled-coil region of Oberon


Domain annotation for each model (and alignments):
>> Oberon_cc  Coiled-coil region of Oberon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   1.3   8.6e-06      0.15      57     129 .]     320     408 ..     318     408 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 8.6e-06
                     Oberon_cc  57 deArreaerlrrialaksekleeeyaskylklrLeEaeeekrkkleelkllensrse................yekskmrm 121
                                   de r+  ++  +  +++ + + ee a+ yl+++L  a   ++  +++++l e+s  +                ++k++ + 
  gi|13542320|ref|NP_112008.1| 320 DEMRESYNKCTKFLETRISDVSEENARLYLQQQLLSAVGYRQDEIDKMNLAETSTEDfqkllrdkvagamasnGSKQRLVS 400
                                   5667777778888899999***********************************998777777777777776655555666 PP

                     Oberon_cc 122 lskiqdLL 129
                                   +++i++LL
  gi|13542320|ref|NP_112008.1| 401 MNEIEKLL 408
                                   66777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (429 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       503  (0.0280551); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 2891.80
//
Query:       gi|13542321|ref|NP_112009.1|  [L=513]
Description: RNA helicase (ERCC4-like) [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.9e-24   86.2   0.9    4.2e-23   81.8   0.1    3.1  3  Helicase_C   Helicase conserved C-terminal domain
    1.9e-23   83.3   0.1    6.7e-23   81.5   0.0    1.9  2  ResIII       Type III restriction enzyme, res subunit
    1.1e-16   61.2   0.1    3.2e-16   59.6   0.0    1.9  2  DEAD         DEAD/DEAH box helicase
     0.0022   18.0   0.0      0.009   16.0   0.0    2.0  2  Flavi_DEAD   Flavivirus DEAD domain
     0.0078   15.8   0.1        1.8    8.1   0.0    2.7  2  Runt         Runt domain
     0.0094   15.2   1.8      0.019   14.2   0.0    2.4  3  DUF2075      Uncharacterized conserved protein (DUF2075)
  ------ inclusion threshold ------
      0.027   14.5   0.2        0.3   11.0   0.1    2.3  2  EspB         Enterobacterial EspB protein
      0.027   14.2   0.4      0.091   12.5   0.3    1.9  1  TACC_C       Transforming acidic coiled-coil-containing prote
      0.045   14.0   0.0       0.46   10.8   0.0    2.5  2  AAA_22       AAA domain
      0.064   13.3   2.5        1.5    8.8   0.0    2.9  3  DUF87        Helicase HerA, central domain
      0.069   11.3   1.9        9.8    4.1   0.1    2.9  3  DNA_pol_phi  DNA polymerase phi
       0.13   11.9   0.0       0.65    9.6   0.0    2.0  1  ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-bindi
       0.16   12.1   1.8       0.63   10.1   0.1    2.6  3  DUF2120      Uncharacterized protein conserved in archaea (DU
       0.26   11.4   1.6         18    5.5   0.0    2.8  2  KH_5         NusA-like KH domain
       0.75   10.2   2.8        7.1    7.1   0.1    3.5  3  AAA          ATPase family associated with various cellular a


Domain annotation for each model (and alignments):
>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.41   4.9e+02      10      56 ..      40      92 ..      33     137 .. 0.73
   2 !   81.8   0.1   3.5e-26   4.2e-23       6     110 ..     337     452 ..     332     453 .. 0.90
   3 ?   -2.7   0.0       6.2   7.4e+03      19      43 ..     459     485 ..     457     507 .. 0.55

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.41
                                  H..HHTTTTSEEEEEESSHH...HHHH....HHHHHHHTTSTEEEESTTSTHHHHH CS
                    Helicase_C 10 l..kleeeggkilifvntid...rlek....vklllekkgikvavlhgelpqnere 56
                                  l  k+ +e++k++  ++t+    +  +    vk+l   ++ ++++++ge  ++ere
  gi|13542321|ref|NP_112009.1| 40 LieKFFKENKKSIFLAPTKPlvlQ--HmatlVKVL-GLNNNEICAFTGEVDSQERE 92
                                  345667889999999999996430..243445555.44467999999999999997 PP

  == domain 2  score: 81.8 bits;  conditional E-value: 3.5e-26
                                   HHHHH.HHTTTTSEEEEEESSHHHHHH.HHHHHHHT.TSTEEEESTT........STHHHHHHHHHHHHTTSSSEEEESGG CS
                    Helicase_C   6 llell.kleeeggkilifvntidrlek.vklllekk.gikvavlhge........lpqnereeileqfnkgesdvLiatdv 75 
                                   +le+  ++   g+++++f++++ + ++ + +l++++ +ik +++ g+        l+q+e+++i+eqf++g+++vLiat++
  gi|13542321|ref|NP_112009.1| 337 VLEICqEKVIAGERAIVFTHFRATSDMlLAYLKNSSdKIKPVRFIGQadrgtdvgLSQEEQRQIIEQFRNGTYNVLIATSI 417
                                   4445445567899**********99988999966668999999999999******************************** PP

                                   GTSSSTSTTESEEEESSSSSSHHHHHHHHTTSSST CS
                    Helicase_C  76 aerGidipkvnlVinfdlprnvtsyiqriGRtgRa 110
                                   ae+G+dip+ ++V+++++  +  ++iqr+GRtgR 
  gi|13542321|ref|NP_112009.1| 418 AEEGLDIPDTDVVVFYEAVPSEIRFIQRKGRTGRS 452
                                   **********************************6 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 6.2
                                   EEEEESSHHHHHHHHHHHHHT..TSTE CS
                    Helicase_C  19 ilifvntidrlekvklllekk..gikv 43 
                                   il++ n++d+++  + l++ +  + ++
  gi|13542321|ref|NP_112009.1| 459 ILVYENSRDMAYYYRSLKKVSmmNRNI 485
                                   688888888876655553333333333 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.5   0.0   5.6e-26   6.7e-23       2     169 ..       5     161 ..       4     163 .. 0.88
   2 ?   -1.5   0.0       1.8   2.2e+03      69      96 ..     317     353 ..     290     413 .. 0.59

  Alignments for each domain:
  == domain 1  score: 81.5 bits;  conditional E-value: 5.6e-26
                                   -EE-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG.. CS
                        ResIII   2 lelreyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseay 82 
                                   +e+reyQ+++ +n +       dk+ li+m+TG GKTl+aa lie+++k++k  k +fl+p+k l+ q + ++ k+l  ++
  gi|13542321|ref|NP_112009.1|   5 IEPREYQINVYKNSI-------DKNTLIVMPTGLGKTLIAAMLIEKFFKENK--KSIFLAPTKPLVLQHMATLVKVLGLNN 76 
                                   689999999999998.......7899***********************855..**********************99999 PP

                                   ..GEEEESSS-B--.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.TTTHHH....HHT--- CS
                        ResIII  83 keigkkvsgdkkkakekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakkswrei....lekfke 159
                                   +ei+ ++ +   +++e +  + ki+v+t q + +d+     +s   + +rfd+i++DEaHr+ ++ ++  i    le+ k+
  gi|13542321|ref|NP_112009.1|  77 NEICAFTGEVDSQERELRWVTGKIFVSTPQVVLNDM-----KSGIIDITRFDLIVFDEAHRAVGNYAYVDIasefLEY-KK 151
                                   99776655544444566899****************.....99999******************98999995554444.88 PP

                                   SEEEEEESS- CS
                        ResIII 160 avllglTATp 169
                                   ++++glTA p
  gi|13542321|ref|NP_112009.1| 152 KLIIGLTASP 161
                                   ********88 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.8
                                   HHHHHGGGGTGG.............GEEEESSS-B-- CS
                        ResIII  69 qtleefkkflseayke.........igkkvsgdkkka 96 
                                   +++e++k++l+ +++          ++k++ g++ + 
  gi|13542321|ref|NP_112009.1| 317 KAIENMKNVLPGYRNPkmmkvleicQEKVIAGERAIV 353
                                   4555666666666555444333333333333333333 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.6   0.0   2.7e-19   3.2e-16       3     147 ..      10     148 ..       8     165 .. 0.79
   2 ?   -2.2   0.0       2.6   3.1e+03      81     104 ..     391     415 ..     334     418 .. 0.57

  Alignments for each domain:
  == domain 1  score: 59.6 bits;  conditional E-value: 2.7e-19
                                   HHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEEET CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD   3 iQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvlliig 83 
                                   +Q +++++ + +++ l+ ++TG GKTl++++ + + +     k+++k ++++Pt+ L+ q++ +l k++   + ++++++g
  gi|13542321|ref|NP_112009.1|  10 YQINVYKNSI-DKNTLIVMPTGLGKTLIAAMLIEKFF-----KENKKSIFLAPTKPLVLQHMATLVKVLGLNNNEICAFTG 84 
                                   5666666666.679**************887776555.....67789***********************87778888888 PP

                                   TSSH.HHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHT.TTHHHHHHHHH CS
                                   xxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx RF
                          DEAD  84 gvaa.rdqlskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldq.gfsdfinriln 147
                                   +v+  +++l+    + +i+v+tp+ +++ +++g +++ ++ ++V+DEa+r   +  + d  ++ l+
  gi|13542321|ref|NP_112009.1|  85 EVDSqERELRW--VTGKIFVSTPQVVLNDMKSGIIDITRFDLIVFDEAHRAVGNyAYVDIASEFLE 148
                                   65551333333..589************9999******************9998566666555554 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.6
                                   EETTSSHHHHHHHHHTT.CSEEEEE CS
                                   xxxxxxxxxxxxxxxxx.xxxxxxx RF
                          DEAD  81 iiggvaardqlskldng.vdivvgt 104
                                    ++++++r+ +++++ng ++++++t
  gi|13542321|ref|NP_112009.1| 391 GLSQEEQRQIIEQFRNGtYNVLIAT 415
                                   3446666677777766667777766 PP

>> Flavi_DEAD  Flavivirus DEAD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   7.5e-06     0.009       7     144 ..      23     169 ..      18     172 .. 0.73
   2 ?   -3.6   0.0       8.4     1e+04      16      33 ..     236     253 ..     235     261 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 7.5e-06
                                   EEEE--TTS-TTTTHHHHHHHHHHHTT--EEEEESSH.HHHHHHHH.....HTTTS-EEE-------------SEEEEEHH CS
                    Flavi_DEAD   7 tvldlhPGaGktrkvlpelvkeaierrlrtlvLaPtr.vvlaemee.....alkglevryktsavkeektgrelvdvmcha 81 
                                   t++ +  G Gkt  + + l+++ ++++++++ LaPt+  vl+ m+       l++ e+   t  v +++ +   v+     
  gi|13542321|ref|NP_112009.1|  23 TLIVMPTGLGKTL-IAAMLIEKFFKENKKSIFLAPTKpLVLQHMATlvkvlGLNNNEICAFTGEVDSQERELRWVTGKIFV 102
                                   5666777999995.567899****************967999998722222355666666677777777777777777777 PP

                                   HHHHHHHHT---.....---SEEEEETTT--SHHHHHHHHHHHHHHHTTS-EEEEEESS-TT---SS- CS
                    Flavi_DEAD  82 tftkrllspvrk.....knyeliimDeahflDPasiaarGyletkaeegeaalilltatPPGtsdpfp 144
                                      + +l+++++     ++++li+ Deah       a   ++++  e ++  +i lta P G++  f 
  gi|13542321|ref|NP_112009.1| 103 STPQVVLNDMKSgiidiTRFDLIVFDEAHRAVG-NYAYVDIASEFLEYKKKLIIGLTASPGGEKGRFQ 169
                                   7777777766532222289**********7654.4566677778888888889999999999988775 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 8.4
                                   -TTTTHHHHHHHHHHHTT CS
                    Flavi_DEAD  16 Gktrkvlpelvkeaierr 33 
                                   G+trk ++e +++ i+r 
  gi|13542321|ref|NP_112009.1| 236 GRTRKDMAESIQNLINRA 253
                                   899999999999888775 PP

>> Runt  Runt domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.015        18      71      99 ..     365     393 ..     333     417 .. 0.83
   2 !    8.1   0.0    0.0015       1.8      80     117 ..     436     476 ..     400     483 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.015
                          Runt  71 tavmknqvarfnDLrfvGrsGrgksftlt 99 
                                    a++kn+  +   +rf+G++ rg  + l+
  gi|13542321|ref|NP_112009.1| 365 LAYLKNSSDKIKPVRFIGQADRGTDVGLS 393
                                   4899*******************988776 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0015
                          Runt  80 rfnDLrfv...GrsGrgksftltitvatkppqvatyekaik 117
                                     +++rf+   Gr Gr +s ++ i v  ++ ++a y +++k
  gi|13542321|ref|NP_112009.1| 436 VPSEIRFIqrkGRTGRSRSGEVYILVYENSRDMAYYYRSLK 476
                                   55688998777889999*********************997 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   1.6e-05     0.019      11     102 ..      30     135 ..      23     154 .. 0.75
   2 ?   -2.3   0.1       1.7     2e+03     185     185 ..     289     289 ..     229     326 .. 0.48
   3 ?   -3.4   0.1       3.6   4.3e+03      35     228 ..     459     485 ..     445     510 .. 0.52

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.6e-05
                       DUF2075  11 GtGKtvvllnllaeleddeeertavylsvNhplvlvlrealakke..............ekkkkkeafeklssfinnlsef 77 
                                   G GKt+++  l+ +    +e++++++l   +plvl    +l k                 +++++ +    + f+ + +  
  gi|13542321|ref|NP_112009.1|  30 GLGKTLIAAMLIEKF--FKENKKSIFLAPTKPLVLQHMATLVKVLglnnneicaftgevDSQERELRWVTGKIFVSTPQVV 108
                                   88************9..9999999999999999986555555555444477888655443344444444455666666644 PP

                       DUF2075  78 ..kkaeekkeepkedvvivDEAhrllt 102
                                     + +    +  ++d++++DEAhr+  
  gi|13542321|ref|NP_112009.1| 109 lnDMKSGIIDITRFDLIVFDEAHRAVG 135
                                   866667778999************975 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.7
                       DUF2075 185 d 185
                                   +
  gi|13542321|ref|NP_112009.1| 289 Q 289
                                   1 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 3.6
                       DUF2075  35 vylsvNhplvlvlrealakkeekkkkkeafeklssfinnlsefkkaeekkeepkedvvivDEAhrlltksdqaekqseenq 115
                                   ++++ N + ++ +++ l+k +                                                            
  gi|13542321|ref|NP_112009.1| 459 ILVYENSRDMAYYYRSLKKVS------------------------------------------------------------ 479
                                   445555555555555554443............................................................ PP

                       DUF2075 116 lkelmkrakvvvalvDegQelntgeigteeelkklakkleveleekvhLksqfRvaaseaviewvdalldgkkekakplss 196
                                                                                                                    
  gi|13542321|ref|NP_112009.1|   - ---------------------------------------------------------------------------------   -
                                   ................................................................................. PP

                       DUF2075 197 qenfdirvfddleelkkalkeknkesgrsrlv 228
                                                              + r +
  gi|13542321|ref|NP_112009.1| 480 --------------------------MMNRNI 485
                                   ..........................333333 PP

>> EspB  Enterobacterial EspB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.29   3.5e+02     149     197 ..     208     253 ..     106     271 .. 0.83
   2 ?   11.0   0.1   0.00025       0.3     160     198 ..     285     323 ..     276     368 .. 0.94

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.29
                          EspB 149 qrakavedlqesnleeykktvresqDkiasvlqdlrstardlndlinrv 197
                                   ++  a++dl +s l++  k +   +D+ ++v +  + +a+++++linr 
  gi|13542321|ref|NP_112009.1| 208 DQCGAIKDLLKSALDSVLKPL---KDQGIKVGRTRKDMAESIQNLINRA 253
                                   566677888888888888877...7888888888888888888888775 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00025
                          EspB 160 snleeykktvresqDkiasvlqdlrstardlndlinrva 198
                                   +++ +y k+++esqD+ ++++  +++ ++d   +i+ + 
  gi|13542321|ref|NP_112009.1| 285 DVAYQYVKDMEESQDQSIKRAYSMMKSLDDFRKAIENMK 323
                                   7899**************************999999885 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 ?   12.5   0.3   7.6e-05     0.091      68     111 ..     289     332 ..     271     348 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 7.6e-05
                        TACC_C  68 keiqkvleekeqlladlnsveksfsdlfkryekqkevlegykkn 111
                                   + ++ + e ++q ++   s+ ks++d  k +e++k+vl gy++ 
  gi|13542321|ref|NP_112009.1| 289 QYVKDMEESQDQSIKRAYSMMKSLDDFRKAIENMKNVLPGYRNP 332
                                   5667778999*******************************974 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00038      0.46       8     103 ..      23     133 ..      18     155 .. 0.56
   2 ?   -0.6   0.0       1.2   1.5e+03      45      90 ..     204     254 ..     180     283 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00038
                        AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaee..............erpevvfvtlpsstsskdl.lrellralglelka... 70 
                                   ++++ ++G GKT+ +++l e++ +e+k                             + +   l  +e++ ++g+  +    
  gi|13542321|ref|NP_112009.1|  23 TLIVMPTGLGKTLIAAMLIEKFFKENKKSIflaptkplvlqhmaT-----------LVKVLGLnNNEICAFTGEVDSQere 92 
                                   678889***************965544444777544444443330...........3334444344444444443333555 PP

                        AAA_22  71 .........erlsseell.ealeqalraravielliiDEaqhl 103
                                               + + +l ++    ++ ++   l++ DEa++ 
  gi|13542321|ref|NP_112009.1|  93 lrwvtgkifV-STPQVVLnDMKSGIIDITRF-DLIVFDEAHRA 133
                                   5222222211.23333332444444455555.99999999984 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.2
                        AAA_22  45 vtlpsst.sskdllrellralglelka....erlsseellealeqalrara 90 
                                    + p ++   kdll+  l  +  +lk+     + +++++ e +++ +++++
  gi|13542321|ref|NP_112009.1| 204 LKEPDQCgAIKDLLKSALDSVLKPLKDqgikVGRTRKDMAESIQNLINRAK 254
                                   555555555566666665555555555555444444444455555554443 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0    0.0013       1.5      19      55 ..      16      52 ..       7      54 .. 0.82
   2 ?    2.9   0.4     0.083        99     118     191 ..     243     323 ..     194     342 .. 0.54
   3 ?   -1.7   0.0       2.2   2.6e+03     167     207 ..     473     512 ..     392     513 .] 0.63

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0013
                         DUF87 19 nklvtrHlAilgsTGsGKSntvavLleellekkgati 55
                                  ++ + + ++i+  TG GK+  +a L+e+  ++++ +i
  gi|13542321|ref|NP_112009.1| 16 KNSIDKNTLIVMPTGLGKTLIAAMLIEKFFKENKKSI 52
                                  5667888899999*****************9887776 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.083
                         DUF87 118 rsvleealdqaka........keekeklssdepveklleelkkekeelrklknqaiarlldkledllrkggsfsnsstdli 190
                                    + +++++++ak+        +++   + +d ++e+++ +  + + ++ k+ ++++ + +++ ++++++  +f  +  +++
  gi|13542321|ref|NP_112009.1| 243 AESIQNLINRAKEdrslfplvRHLTAAIRIDYIIEYIETQGLDVAYQYVKDMEESQDQSIKRAYSMMKSLDDF-RKAIENM 322
                                   3344444444444555555555555556666666666655553333555555555555555555555555555.3333444 PP

                         DUF87 191 a 191
                                   +
  gi|13542321|ref|NP_112009.1| 323 K 323
                                   4 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 2.2
                         DUF87 167 rlldkledllrkggsfsnsstdliallleklekegkitiid 207
                                   r l+k++ ++++++    +++ ++++  ++ +++g+ ti+d
  gi|13542321|ref|NP_112009.1| 473 RSLKKVS-MMNRNIMEYRDEHPYTKNERQENSNNGQRTIFD 512
                                   2222222.233332222444555555555566666666666 PP

>> DNA_pol_phi  DNA polymerase phi
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0     0.013        16     131     194 ..      12      75 ..       4     115 .. 0.79
   2 ?    4.1   0.1    0.0082       9.8     335     403 ..     165     234 ..     148     255 .. 0.81
   3 ?    1.1   0.1     0.069        82     476     520 ..     274     317 ..     263     326 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.013
                   DNA_pol_phi 131 akalleelskaklaktpeglallLalqekfpdlklpkllkklwksedpLskenlptLakvLkes 194
                                   +++ ++ ++k++l+  p gl   L +   +++  ++++++  + +++pL  ++++tL+kvL  +
  gi|13542321|ref|NP_112009.1|  12 INVYKNSIDKNTLIVMPTGLGKTLIAAMLIEKFFKENKKSIFLAPTKPLVLQHMATLVKVLGLN 75 
                                   67788999******************99999888888876777*****************9765 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.0082
                   DNA_pol_phi 335 slnfDkltktktvekll.ksldeeglkklvdllkslilssneesdekeaesrrqwildqLlsivrskklk 403
                                   +++f+++ k   +e+++ k+ ++e ++k+++ ++ ++++ +e ++ ++++ + + +ld+ l+ ++ + +k
  gi|13542321|ref|NP_112009.1| 165 KGRFQEIVKNLGIENVVvKTEKDEDVRKYIKSIEMHLIKLKEPDQCGAIKDLLKSALDSVLKPLKDQGIK 234
                                   679************************************6666899999999999999999888877764 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.069
                   DNA_pol_phi 476 kllellktlekskkvekliikldeelekawkkalkvlkklskkek 520
                                   +++e+++t   +  ++  +++++e++ + +k+a +++k+l+  +k
  gi|13542321|ref|NP_112009.1| 274 YIIEYIETQGLDVAYQ-YVKDMEESQDQSIKRAYSMMKSLDDFRK 317
                                   6777777777777787.799*******************997766 PP

>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00054      0.65      16      65 ..      22     406 ..      20     490 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00054
                                   EEEEEESTTSSHHHHHHHHHHHSSTSS.EEEEEE............................................... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx............................................... RF
                   ATP-synt_ab  16 rtlipgafgvGktvisqslskqsnsdd.aiiyvg............................................... 48 
                                   +tli+   g+Gkt i+++l+++  +++  +i+ +                                               
  gi|13542321|ref|NP_112009.1|  22 NTLIVMPTGLGKTLIAAMLIEKFFKENkKSIFLAptkplvlqhmatlvkvlglnnneicaftgevdsqerelrwvtgkifv 102
                                   5789999**********9999987776699*9999********************************************** PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                   ATP-synt_ab  49 ................................................................................. 48 
                                                                                                                    
  gi|13542321|ref|NP_112009.1| 103 stpqvvlndmksgiiditrfdlivfdeahravgnyayvdiasefleykkkliigltaspggekgrfqeivknlgienvvvk 183
                                   ********************************************************************************* PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                   ATP-synt_ab  49 ................................................................................. 48 
                                                                                                                    
  gi|13542321|ref|NP_112009.1| 184 tekdedvrkyiksiemhliklkepdqcgaikdllksaldsvlkplkdqgikvgrtrkdmaesiqnlinrakedrslfplvr 264
                                   ***************************************************888888888888888888888888888888 PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                   ATP-synt_ab  49 ................................................................................. 48 
                                                                                                                    
  gi|13542321|ref|NP_112009.1| 265 hltaairidyiieyietqgldvayqyvkdmeesqdqsikraysmmkslddfrkaienmknvlpgyrnpkmmkvleicqekv 345
                                   888888888888888888888888888888888888888888888888888888888888886666666666666666666 PP

                                   ............................................ESEEHHHHHHHHHHCHH CS
                                   ............................................xxxxxxxxxxxxxxxxx RF
                   ATP-synt_ab  49 ............................................iGergnevaevleefpe 65 
                                                                               +G  ++e ++++e+f++
  gi|13542321|ref|NP_112009.1| 346 iageraivfthfratsdmllaylknssdkikpvrfigqadrgtdVGLSQEEQRQIIEQFRN 406
                                   6666666666666666666666666666666666666666666644444444444444444 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 ?   -2.3   0.1       3.6   4.4e+03      46      74 ..     169     200 ..     165     222 .. 0.56
   2 ?   -0.8   0.0       1.3   1.6e+03      40      77 ..     216     252 ..     210     259 .. 0.70
   3 ?   10.1   0.1   0.00053      0.63      45      96 ..     272     325 ..     266     328 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 3.6
                       DUF2120  46 eellekldaeevdlese...eakkliekldes 74 
                                   +e++++l  e+v ++ e   +++k i+ ++ +
  gi|13542321|ref|NP_112009.1| 169 QEIVKNLGIENVVVKTEkdeDVRKYIKSIEMH 200
                                   56777777776655544112444445444443 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.3
                       DUF2120  40 eleskleellekldaeevdleseeakkliekldesire 77 
                                    l+s l+++l+ l+ + + +     k++ e +++ i +
  gi|13542321|ref|NP_112009.1| 216 LLKSALDSVLKPLKDQGIKVGRT-RKDMAESIQNLINR 252
                                   57899999999999999987544.35555555555544 PP

  == domain 3  score: 10.1 bits;  conditional E-value: 0.00053
                       DUF2120  45 leellekldaeevdleseeakkliekldesireveeieeevdaf..glerlkes 96 
                                   +++++e ++++ +d++ + +k++ e  d+si+++ ++++  d f  ++e++k+ 
  gi|13542321|ref|NP_112009.1| 272 IDYIIEYIETQGLDVAYQYVKDMEESQDQSIKRAYSMMKSLDDFrkAIENMKNV 325
                                   799***************************************99999****985 PP

>> KH_5  NusA-like KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.6     0.056        66      29      57 ..     167     196 ..     162     198 .. 0.84
   2 ?    5.5   0.0     0.015        18      31      63 ..     222     254 ..     206     257 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.056
                          KH_5  29 rikavsseLkgekidv.vewseDlaefian 57 
                                   r +++++ L  e++ v  e++eD++++i++
  gi|13542321|ref|NP_112009.1| 167 RFQEIVKNLGIENVVVkTEKDEDVRKYIKS 196
                                   7899*****99**9985578899*****97 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.015
                          KH_5  31 kavsseLkgekidvvewseDlaefianalsPae 63 
                                    +v + Lk+  i+v +  +D+ae i+n++++a+
  gi|13542321|ref|NP_112009.1| 222 DSVLKPLKDQGIKVGRTRKDMAESIQNLINRAK 254
                                   57888899999*******************997 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.1     0.006       7.1       2      23 ..      24      49 ..      23     145 .. 0.66
   2 ?    0.4   0.0      0.69   8.3e+02      24      55 ..     276     307 ..     261     314 .. 0.82
   3 ?   -1.7   0.0       3.1   3.7e+03      86     111 ..     361     386 ..     350     415 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.006
                                  EEESSTTSSHHHHHHHHHHHH....T CS
                           AAA  2 llyGppGtGKTllakavakel....g 23
                                  l++ p G GKTl+a  +++++    +
  gi|13542321|ref|NP_112009.1| 24 LIVMPTGLGKTLIAAMLIEKFfkenK 49
                                  566699***********999533331 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.69
                                   HEEEEEETTTCSSSSTTHHHHHHHHHHHHHHH CS
                           AAA  24 vefleisgsellskyvgesekkirelfkeake 55 
                                   +e++e++g ++  +yv+++e++  + +k+a +
  gi|13542321|ref|NP_112009.1| 276 IEYIETQGLDVAYQYVKDMEESQDQSIKRAYS 307
                                   6899*******************999999865 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 3.1
                                   HHHHHHHHHHTTTSSSTEEEEEEESS CS
                           AAA  86 vnqLlteldgvkkkeskvivigatnr 111
                                    + Ll+ l++ ++k ++v +ig + r
  gi|13542321|ref|NP_112009.1| 361 SDMLLAYLKNSSDKIKPVRFIGQADR 386
                                   56677777777777666777776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (513 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1169  (0.0652016); expected 358.6 (0.02)
Passed bias filter:                      745  (0.0415528); expected 358.6 (0.02)
Passed Vit filter:                        86  (0.0047967); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.82u 0.35s 00:00:01.17 Elapsed: 00:00:00.51
# Mc/sec: 3018.18
//
Query:       gi|13542322|ref|NP_112010.1|  [L=318]
Description: replication factor C small subunit [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.1e-21   75.6   0.2    7.5e-21   74.3   0.1    1.8  2  Rep_fac_C        Replication factor C C-terminal domain
    3.9e-13   50.0   0.1    1.2e-12   48.4   0.0    1.8  2  AAA              ATPase family associated with various cellul
    1.3e-12   47.8   0.7    3.4e-08   33.4   0.1    2.9  3  DNA_pol3_delta2  DNA polymerase III, delta subunit
    6.8e-06   26.3   0.0    1.6e-05   25.1   0.0    1.7  1  AAA_assoc_2      AAA C-terminal domain
    6.6e-05   22.8   0.0    0.00015   21.6   0.0    1.6  1  DNA_pol3_delta   DNA polymerase III, delta subunit
    8.1e-05   22.4   0.0    0.00037   20.3   0.0    1.9  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    0.00014   22.0   0.1     0.0019   18.2   0.0    2.4  3  ResIII           Type III restriction enzyme, res subunit
    0.00081   19.1   0.1       0.57    9.9   0.0    2.4  2  Sigma54_activat  Sigma-54 interaction domain
    0.00096   18.4   0.2      0.022   14.0   0.0    2.5  3  TIP49            TIP49 P-loop domain
     0.0024   17.8   0.0     0.0043   17.0   0.0    1.5  1  Rad17            Rad17 P-loop domain
     0.0041   16.5   0.0        1.5    8.2   0.0    2.4  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
      0.005   16.6   0.0      0.011   15.5   0.0    1.6  1  IstB_IS21        IstB-like ATP binding protein
     0.0083   16.5   0.1          1    9.7   0.0    2.4  2  AAA_16           AAA ATPase domain
      0.009   15.5   0.0      0.016   14.7   0.0    1.4  1  AAA_7            P-loop containing dynein motor region
  ------ inclusion threshold ------
      0.012   15.1   0.2      0.059   12.8   0.0    2.0  2  PhoH             PhoH-like protein
      0.021   15.0   0.0      0.044   13.9   0.0    1.5  1  Sigma54_activ_2  Sigma-54 interaction domain
      0.023   13.9   0.0      0.049   12.8   0.0    1.5  1  DUF815           Protein of unknown function (DUF815)
      0.054   13.8   0.2         10    6.4   0.0    2.4  2  AAA_22           AAA domain
      0.093   11.6   0.0       0.17   10.7   0.0    1.5  1  TrwB_AAD_bind    Type IV secretion-system coupling protein DN
       0.11   12.7   0.0       0.19   11.9   0.0    1.4  1  AAA_28           AAA domain
       0.13   12.2   0.0       0.32   10.9   0.0    1.6  2  AAA_3            ATPase family associated with various cellul
       0.17   11.4   0.0       0.32   10.6   0.0    1.5  1  AAA_25           AAA domain


Domain annotation for each model (and alignments):
>> Rep_fac_C  Replication factor C C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       8.8   7.2e+03       4      32 ..     182     208 ..     179     217 .. 0.66
   2 !   74.3   0.1   9.2e-24   7.5e-21       2      88 .]     224     309 ..     223     309 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 8.8
                                   HHHHHHHHHHHHT-HHHHHHHHHHHHHHC CS
                     Rep_fac_C   4 teieeileaclngdfeeaykklrellvek 32 
                                   + +e ++e    gd ++a ++l+  ++  
  gi|13542322|ref|NP_112010.1| 182 ESMEAMVEVS-GGDMRKAINVLQ-AVYTS 208
                                   5566666666.688888888886.55444 PP

  == domain 2  score: 74.3 bits;  conditional E-value: 9.2e-24
                                   -HHHHHHHHHHHHHT-HHHHHHHHHHHHHHC---HHHHHHHHHHHGCCS..S-HHHHHHHHHHHHHHHHHHHCTH-HHHHH CS
                     Rep_fac_C   2 hpteieeileaclngdfeeaykklrellvekGysaediltqlhrvvkeqeelpeaqkleilellgeiekrlveGasehlql 82 
                                    p+ ++++++ + ng f+ea++++++ ++e+G+s+ di++ +h +v  +  +p +qk+ei++ l+++e+r+veG+++++ql
  gi|13542322|ref|NP_112010.1| 224 SPESVNKLISRAINGLFDEARQIVDKMMIEDGLSGIDIVKSVHSIVRAS-VVPPKQKIEIIKALADAEFRIVEGSNDRIQL 303
                                   6899999*****9**********************************95.6****************************** PP

                                   HHHHHH CS
                     Rep_fac_C  83 sallar 88 
                                    al+ar
  gi|13542322|ref|NP_112010.1| 304 DALIAR 309
                                   ****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 !   48.4   0.0   1.4e-15   1.2e-12       1     126 [.      39     153 ..      39     159 .. 0.88
   2 ?   -1.6   0.0       4.1   3.3e+03      44      44 ..     226     226 ..     170     259 .. 0.55

  Alignments for each domain:
  == domain 1  score: 48.4 bits;  conditional E-value: 1.4e-15
                                   EEEESSTTSSHHHHHHHHHHHH.....THEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS..TSEEEEEETGGGHHHHH CS
                           AAA   1 vllyGppGtGKTllakavakel.....gvefleisgsellskyvgesekkirelfkeakeka..kpsilfiDEidalaksr 74 
                                   +l+ G  GtGKT++a a+a el     + +f+e+++s+     +    +ki+++ + ++ ++  + +ilf+DE+d+l+ + 
  gi|13542322|ref|NP_112010.1|  39 LLFAGSVGTGKTSTAIALAIELfgeswKENFIEMNASNEN--GIDVIRNKIKDIAR-IRPSNplGFKILFLDEADQLTAEA 116
                                   699******************876666899********99..99999999999995.566666777***********9988 PP

                                   TTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHSTTSSE CS
                           AAA  75 sgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallrgRfdr 126
                                              +++L + ++ +++   ++ ++ a+n+ +k+ p++  +R  +
  gi|13542322|ref|NP_112010.1| 117 -----------QAALRRTMEMYSE---TTRFVFACNYSSKIIPPIQ-SRTVV 153
                                   ...........************9...589***************9.88654 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 4.1
                                   H CS
                           AAA  44 k 44 
                                   +
  gi|13542322|ref|NP_112010.1| 226 E 226
                                   2 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 !   12.8   0.1   9.3e-05     0.076       2      52 ..      20      69 ..      19      98 .. 0.80
   2 !   33.4   0.1   4.1e-11   3.4e-08      82     162 ..      77     159 ..      67     160 .. 0.85
   3 ?   -1.8   0.0       2.9   2.3e+03      90     109 ..     200     219 ..     193     239 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 9.3e-05
               DNA_pol3_delta2  2 qeealkilskalksgrlahayLfeGdegigkkelalnlakallceeknetk 52
                                  ++e ++ l++ +++++l h +Lf+G+ g+gk ++a +la +l+ e+ +e+ 
  gi|13542322|ref|NP_112010.1| 20 EDENIQKLKSFVEKKELPH-LLFAGSVGTGKTSTAIALAIELFGESWKENF 69
                                  5678999**********99.8**********************99887764 PP

  == domain 2  score: 33.4 bits;  conditional E-value: 4.1e-11
               DNA_pol3_delta2  82 sikldqirelieelsr.kpre.skkkiiiiedaekmtksAaNalLktlEEPsenaifiLitsdtnklLktirSRcqelkfs 160
                                   +  +d ir+ i+++ r +p +    ki+ +++a+++t++A+ al +t+E  se + f++  + ++k++++i+SR+ +++f+
  gi|13542322|ref|NP_112010.1|  77 ENGIDVIRNKIKDIARiRPSNpLGFKILFLDEADQLTAEAQAALRRTMEMYSETTRFVFACNYSSKIIPPIQSRTVVMRFR 157
                                   5578999966665554156655789*******************************************************9 PP

               DNA_pol3_delta2 161 pl 162
                                   p+
  gi|13542322|ref|NP_112010.1| 158 PV 159
                                   97 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 2.9
               DNA_pol3_delta2  90 elieelsrkpreskkkiiii 109
                                   ++ + ++ ++ +s kki+ i
  gi|13542322|ref|NP_112010.1| 200 NVLQAVYTSGEISPKKIYEI 219
                                   66677888888888888744 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 !   25.1   0.0     2e-08   1.6e-05       3      40 ..     175     212 ..     173     250 .. 0.74

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 2e-08
                                   X.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX. CS
                   AAA_assoc_2   3 kklkleddalealaeladGDaRkaLnlLElaaeaaeak 40 
                                   + ++++d+ +ea++e+++GD+Rka+n+L+++ ++ e +
  gi|13542322|ref|NP_112010.1| 175 EGFTIDDESMEAMVEVSGGDMRKAINVLQAVYTSGEIS 212
                                   6789*************************999888765 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 !   21.6   0.0   1.8e-07   0.00015      59     170 ..     102     203 ..      60     206 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 1.8e-07
                                   EEEEEE--.....TT-S-TTHHHHHHHHTTT--SSEEEEEEES.S--HHHHHHHHHTTTEEEEEE----TTTHHHHHHHHH CS
                DNA_pol3_delta  59 rivvlknpklltkesklnekllkeLeeylsnlpedtlLiliapkklderkklvklLkkkatvveaktlkeeelkkwiqkra 139
                                   +i++l+ +      ++l+++ +++L ++++ ++e+t +++ ++       k++  ++++++v+++ +++ e +kk+++++a
  gi|13542322|ref|NP_112010.1| 102 KILFLDEA------DQLTAEAQAALRRTMEMYSETTRFVFACN----YSSKIIPPIQSRTVVMRFRPVQDEFIKKKLNEIA 172
                                   45555555......7799*************************....55789***************************** PP

                                   HHTT-EE-HHHHHHHHHHHTT-HHHHHHHHH CS
                DNA_pol3_delta 140 qelglkiekealelLlelvennlsaikqele 170
                                   +++g  i++e++e ++e ++++++ + + l+
  gi|13542322|ref|NP_112010.1| 173 KNEGFTIDDESMEAMVEVSGGDMRKAINVLQ 203
                                   ************************9999887 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   4.5e-07   0.00037       2     111 ..      10     127 ..       9     132 .. 0.73

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 4.5e-07
                        RuvB_N   2 rPksleeyigqekvkeklkifieaakkreealdhvllyGpPGlGkttlakiiakel........gvklkits..g.Pvl.e 70 
                                   rPksl+e  g ++  +klk f+e     +++l h+l++G+ G Gkt+ a  +a el         ++++++   g  v+ +
  gi|13542322|ref|NP_112010.1|  10 RPKSLSEIYGEDENIQKLKSFVE-----KKELPHLLFAGSVGTGKTSTAIALAIELfgeswkenFIEMNASNenGiDVIrN 85 
                                   9******************9997.....57899*****************9998873322221111122222112123325 PP

                        RuvB_N  71 kagdlaall.tnleekdvlfideihrlsraveevlysamedf 111
                                   k +d+a +  +n    ++lf+de  +l+ +++  l  +me +
  gi|13542322|ref|NP_112010.1|  86 KIKDIARIRpSNPLGFKILFLDEADQLTAEAQAALRRTMEMY 127
                                   667888886234445689999999999999999999999976 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 !   18.2   0.0   2.3e-06    0.0019      10      58 ..      22      70 ..      13      77 .. 0.84
   2 ?   -0.1   0.0      0.97   7.9e+02     132     163 ..     100     133 ..      72     138 .. 0.72
   3 ?   -1.4   0.0       2.4     2e+03       2      21 ..     154     173 ..     153     192 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2.3e-06
                                  HHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EE CS
                        ResIII 10 eaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekfl 58
                                  e i++l++ +++k+  ++l++   GtGKT +a++l+ +l+ + ++e+f+
  gi|13542322|ref|NP_112010.1| 22 ENIQKLKSFVEKKELPHLLFAGSVGTGKTSTAIALAIELFGESWKENFI 70
                                  5566666666656677**************************9999997 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.97
                                   T-SEEEEETGGGTTS...TTTHHHHHT---SEEE CS
                        ResIII 132 rfdviiiDEaHrlgak..kswreilekfkeavll 163
                                    f++++ DEa  l+a+  ++ r+ +e+++e +++
  gi|13542322|ref|NP_112010.1| 100 GFKILFLDEADQLTAEaqAALRRTMEMYSETTRF 133
                                   5778899999998886333666667777776665 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 2.4
                                   -EE-HHHHHHHHHHT..... CS
                        ResIII   2 lelreyQeeaienlleklks 21 
                                   +++r+ Q e i++ l+++ +
  gi|13542322|ref|NP_112010.1| 154 MRFRPVQDEFIKKKLNEIAK 173
                                   57899999999999988864 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.0    0.0007      0.57      11      60 ..      23      76 ..      17      84 .. 0.73
   2 !    6.7   0.0    0.0064       5.2      96     118 ..     103     125 ..     100     133 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0007
                                  HHHHHHHHCTSS..S-EEEECSTTSSHHHHHHH..HHHHSTTTTS-EEEEETTT CS
               Sigma54_activat 11 lleqikkvaktd..lsvlitGesGtGKellara..iheaskrkekpfvavncaa 60
                                   ++++k++++++   ++l  G  GtGK+  a a  i    +  +++f+++n ++
  gi|13542322|ref|NP_112010.1| 23 NIQKLKSFVEKKelPHLLFAGSVGTGKTSTAIAlaIELFGESWKENFIEMNASN 76
                                  4556666665555568999********9766550055688889999**999865 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0064
                                   EEEEETGGGS-HHHHHHHHHHHH CS
               Sigma54_activat  96 tlfLDeigelplelQekLlrvlq 118
                                   +lfLDe  +l++e+Q+ L r ++
  gi|13542322|ref|NP_112010.1| 103 ILFLDEADQLTAEAQAALRRTME 125
                                   79****************99987 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.0   2.7e-05     0.022      44      87 ..      32      76 ..      23      94 .. 0.78
   2 ?    1.3   0.0      0.19   1.5e+02     281     304 ..     103     126 ..      98     145 .. 0.82
   3 ?   -1.8   0.0       1.7   1.4e+03     202     224 ..     183     205 ..     165     214 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.7e-05
                                  XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.X..XXXXXXXXXXXX CS
                         TIP49 44 kekklaGravLlaGpsgtGktalaiaiskel.g..edvpfvalsgse 87
                                  ++k+l    +L+aG  gtGkt+ aia++ el g   +  f+ +++s+
  gi|13542322|ref|NP_112010.1| 32 EKKELP--HLLFAGSVGTGKTSTAIALAIELfGesWKENFIEMNASN 76
                                  555555..79******************9994322456899999987 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.19
                                   XXXXXXXXXXXXXXXXXXXXXXXX CS
                         TIP49 281 vlfiDevhmlDiecfsylnrales 304
                                   +lf+De+  l  e+ + l r++e 
  gi|13542322|ref|NP_112010.1| 103 ILFLDEADQLTAEAQAALRRTMEM 126
                                   79********************95 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 1.7
                                   S--------S---S----XXXXX CS
                         TIP49 202 ekdefvelPkGevekkkevvqev 224
                                   + + +ve+  G+++k  +v+q v
  gi|13542322|ref|NP_112010.1| 183 SMEAMVEVSGGDMRKAINVLQAV 205
                                   56778999999999999999887 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   5.2e-06    0.0043       7      87 ..       3      78 ..       1     119 [. 0.82

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 5.2e-06
                         Rad17  7 elWfekykPekaeelavhkkkieevkewlkadvLesrkkriLLisGPsGCgkstvvkvLskel.giklrewlnpvslkepdn 87
                                  e W eky+P+ + e+    + i+++k +++ + L++     LL +G  G gk+ +   L+ el g + +e+   ++  + +n
  gi|13542322|ref|NP_112010.1|  3 EIWTEKYRPKSLSEIYGEDENIQKLKSFVEKKELPH-----LLFAGSVGTGKTSTAIALAIELfGESWKENFIEMN-ASNEN 78
                                  78************************9999999986.....6**********877777776643889999988887.44444 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    0.0018       1.5      24      59 ..      38      74 ..      13      95 .. 0.76
   2 !    6.1   0.0    0.0077       6.2     109     132 ..     103     126 ..     100     144 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0018
                  Mg_chelatase 24 nlllvGppGsGKtmlakrlp.sllpplseeealevak 59
                                  +ll++G+ G+GKt  a +l+ +l+ +  +e+ +e+++
  gi|13542322|ref|NP_112010.1| 38 HLLFAGSVGTGKTSTAIALAiELFGESWKENFIEMNA 74
                                  89***********999988625777777777788765 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0077
                  Mg_chelatase 109 vLfLDElpefkrkvlevLRePled 132
                                   +LfLDE+ ++++++  +LR+ +e 
  gi|13542322|ref|NP_112010.1| 103 ILFLDEADQLTAEAQAALRRTMEM 126
                                   8********************996 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   1.3e-05     0.011      41      88 ..      28      77 ..      18     139 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.3e-05
                     IstB_IS21 41 lsfiekke..nivllGpsGvGKshlaialgveavraglsvlfvrvedLve 88
                                   sf+ekke   +++ G  G+GK+  aial+ e   + ++  f+ +++  e
  gi|13542322|ref|NP_112010.1| 28 KSFVEKKElpHLLFAGSVGTGKTSTAIALAIELFGESWKENFIEMNASNE 77
                                  479999985568999************************99999876544 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.0    0.0012         1       3      44 ..      18      56 ..      16      76 .. 0.82
   2 ?    4.3   0.1     0.057        47     137     161 ..     102     126 ..      71     135 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0012
                        AAA_16  3 vGReeeleqLlsalervrsgrpelvllsGesGvGKsslvrel 44
                                  +G +e +++L+s +e   + + + +l+ G  G+GK+s + +l
  gi|13542322|ref|NP_112010.1| 18 YGEDENIQKLKSFVE---KKELPHLLFAGSVGTGKTSTAIAL 56
                                  788899999999888...55679*************988555 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.057
                        AAA_16 137 lvlvlDdlqwadeaslqllaaLlrl 161
                                    +l+lD+++++ ++ +++l+ +++ 
  gi|13542322|ref|NP_112010.1| 102 KILFLDEADQLTAEAQAALRRTMEM 126
                                   59****************9988865 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   1.9e-05     0.016      35      73 ..      38      76 ..      21     116 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.9e-05
                         AAA_7 35 pvllvGptGtGKtviikdllkkldkekylsltinfsaqt 73
                                  ++l+ G++GtGKt+++  l  +l  e+++ ++i+++a+ 
  gi|13542322|ref|NP_112010.1| 38 HLLFAGSVGTGKTSTAIALAIELFGESWKENFIEMNASN 76
                                  799***************9999999**********9965 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   7.2e-05     0.059      22      54 ..      39      71 ..      17      82 .. 0.76
   2 ?   -1.3   0.0       1.5   1.2e+03     121     136 ..     102     117 ..      85     138 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 7.2e-05
                                  EEEE--TTSSTTHHHHHHHHHHHHTTS-SEEEE CS
                          PhoH 22 vfaiGpaGtGKtylavalavealkkkkvkriil 54
                                  +  +G+ GtGKt  a+ala+e++ ++  +++i 
  gi|13542322|ref|NP_112010.1| 39 LLFAGSVGTGKTSTAIALAIELFGESWKENFIE 71
                                  5678*****************998887777775 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.5
                                   EEEEE-SGGG--HHHH CS
                          PhoH 121 afvilDEAQnttkeqm 136
                                   ++++lDEA  +t e  
  gi|13542322|ref|NP_112010.1| 102 KILFLDEADQLTAEAQ 117
                                   5678899888877643 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   5.4e-05     0.044       6     110 ..      23     140 ..      18     144 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.4e-05
                                   HHHHHHHHHHHHHT-SS-EEEEEETT--HHHHHHCC..--TTS-EE--SSTTHHHH-H..............HHHHHHTTT CS
               Sigma54_activ_2   6 aiqelkerLeqaaqsklpvfltGekGsgkelvArlL..hknsgpwleifvverlaklp..............ldlleqakg 70 
                                   +iq+lk+ +e+  ++   ++ +G  G+gk++ A +L    +++ w e f++ + ++++               + ++ +  
  gi|13542322|ref|NP_112010.1|  23 NIQKLKSFVEK--KELPHLLFAGSVGTGKTSTAIALaiELFGESWKENFIEMNASNENgidvirnkikdiarIRPSNPLGF 101
                                   56666666554..344457889*******987766511578999*999999888887787777777655533344444688 PP

                                   SEEEEEE-TT--HHHHHHHHHHHHHHTTTT-EEEEEEEE- CS
               Sigma54_activ_2  71 gtLylkdiadlskaeqkeLlellakaeksslrlVstsskd 110
                                    +L+l + ++l +++q+ L   ++    +  r+V+++ ++
  gi|13542322|ref|NP_112010.1| 102 KILFLDEADQLTAEAQAALRRTMEMY-SETTRFVFACNYS 140
                                   9***********************99.999*****99765 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0     6e-05     0.049      31     104 ..      18      89 ..       6     111 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6e-05
                        DUF815  31 vgidkqkealventeqfleglpannvLLwGarGtGKSslvkallneyaeeg..Lrlievekedlkelpklvellre 104
                                    g d++     +  + f+e+++  ++L+ G+ GtGK s+  al  e+  e+    +ie++ ++ + ++ + +++++
  gi|13542322|ref|NP_112010.1|  18 YGEDENI----QKLKSFVEKKELPHLLFAGSVGTGKTSTAIALAIELFGESwkENFIEMNASNENGIDVIRNKIKD 89 
                                   4444444....44578***********************9999999888774556888888777777777777765 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0     0.017        14       7      60 ..      38      87 ..      31      98 .. 0.73
   2 ?    6.4   0.0     0.013        10      86     122 ..      91     130 ..      69     141 .. 0.69

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.017
                        AAA_22  7 ilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrel 60
                                  +l+  G +GtGKT ++  l+ +l    + e  +  +++++++++++ + +++++
  gi|13542322|ref|NP_112010.1| 38 HLLFAGSVGTGKTSTAIALAIEL----FGESWKENFIEMNASNENGIDVIRNKI 87
                                  67889********9998887766....233347777777777777666666666 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.013
                        AAA_22  86 lrarav....ielliiDEaqhlrseealeeLrsllnlsrkg 122
                                   +r r       ++l +DEa+ l ++ea   Lr+ ++  +  
  gi|13542322|ref|NP_112010.1|  91 ARIRPSnplgFKILFLDEADQL-TAEAQAALRRTMEMYSET 130
                                   4444446666689*********.999988888887763333 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 ?   10.7   0.0   0.00021      0.17       7      34 ..      27      55 ..      21      60 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00021
                 TrwB_AAD_bind  7 v.plpkeretqhilivGttGsGKtqalek 34
                                  + ++ +++e  h+l++G++G+GKt ++ +
  gi|13542322|ref|NP_112010.1| 27 LkSFVEKKELPHLLFAGSVGTGKTSTAIA 55
                                  556788999***************98765 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00024      0.19       4      71 ..      41     117 ..      38     126 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00024
                        AAA_28   4 itGgestGKTtlleaLa.........ar..gypvvpEaareileeklakgedalpwvedllafaervleeqleeeaaaa 71 
                                   + G  +tGKT+++ aLa         ++  +++   E + +++++k ++  ++ p+  ++l f++++l+e+ +  a+a+
  gi|13542322|ref|NP_112010.1|  41 FAGSVGTGKTSTAIALAielfgeswkENfiEMNASNENGIDVIRNKIKDIARIRPS--NPLGFKILFLDEADQLTAEAQ 117
                                   78999************888876554336777788999999999999998887776..799999999988765555553 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 ?   10.9   0.0   0.00039      0.32       1      88 [.      38     126 ..      38     136 .. 0.86
   2 ?   -3.2   0.0       8.8   7.2e+03       8      32 ..     275     303 ..     271     308 .. 0.58

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00039
                         AAA_3   1 hvllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeekekefe.fk.kGpvfanllladeinrappktq 79 
                                   h+l+ g  G++kt ++ ala  l  e  +  f  ++  s+  G++v+++k k++  ++ + p+  ++l+ de ++ ++ +q
  gi|13542322|ref|NP_112010.1|  38 HLLFAGSVGTGKTSTAIALAIELFGESWKENFI-EMNASNENGIDVIRNKIKDIArIRpSNPLGFKILFLDEADQLTAEAQ 117
                                   9999****************9998888888886.6889999******99998775144257999***************** PP

                         AAA_3  80 salleamee 88 
                                   +al  +me 
  gi|13542322|ref|NP_112010.1| 118 AALRRTMEM 126
                                   ***999985 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 8.8
                         AAA_3   8 PGlaktllvkala....kaldlefkriqf 32 
                                   P   k  ++kala    ++++ + +riq+
  gi|13542322|ref|NP_112010.1| 275 PPKQKIEIIKALAdaefRIVEGSNDRIQL 303
                                   55566666777762222245666666665 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   0.00039      0.32      37     139 ..      40     126 ..      22     135 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00039
                        AAA_25  37 llaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgealrddarllvldlagveslpLf 117
                                   l+aG  gtGKt  a+ la+++  G++w +     +   +  s+E++ d +r++++ + + +  +++ l  ++       Lf
  gi|13542322|ref|NP_112010.1|  40 LFAGSVGTGKTSTAIALAIELF-GESWKE-----NFIEMNASNENGIDVIRNKIKDIARIR--PSNPLGFKI-------LF 105
                                   789******************9.898955.....445566788888888888888877765..333333332.......22 PP

                        AAA_25 118 akdrggtlltadvdaleaaiee 139
                                     d  ++l++++ +al++++e 
  gi|13542322|ref|NP_112010.1| 106 L-DEADQLTAEAQAALRRTMEM 126
                                   2.22333333444556666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       942  (0.0525406); expected 358.6 (0.02)
Passed bias filter:                      762  (0.042501); expected 358.6 (0.02)
Passed Vit filter:                        93  (0.00518713); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              22  [number of targets reported over threshold]
# CPU time: 0.65u 0.34s 00:00:00.99 Elapsed: 00:00:01.50
# Mc/sec: 641.09
//
Query:       gi|13542323|ref|NP_112011.1|  [L=445]
Description: glutamine synthetase [Thermoplasma volcanium GSS1]
Scores for complete 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-127  425.2   0.0     2e-127  424.9   0.0    1.1  1  Gln-synt_C  Glutamine synthetase, catalytic domain
    9.3e-24   83.0   0.0      2e-23   81.9   0.0    1.6  1  Gln-synt_N  Glutamine synthetase, beta-Grasp domain


Domain annotation for each model (and alignments):
>> Gln-synt_C  Glutamine synthetase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  424.9   0.0  2.3e-131    2e-127       2     345 .]     106     441 ..     105     441 .. 0.99

  Alignments for each domain:
  == domain 1  score: 424.9 bits;  conditional E-value: 2.3e-131
                                   T-HHHHHHHHHHHHHHTTCEEEEEEEEEEEEESEECCCESSEEEEEEE.TB...B.TSS-TTBHCCCCCTCCHHHHHHHHH CS
                    Gln-synt_C   2 rdPRsvlkralarlaeeGltvvvgpElEFflfdkeedkeasksllevdseekgrpaekggyfsvapvdeaedlrreiveal 82 
                                   +dPR+vl++ l+++++eG +++vgpE+EFflf+++ +++            +++p++ ggyf+ +p+d+a+d+r++iv+ l
  gi|13542323|ref|NP_112011.1| 106 GDPRYVLEKLLEKVHKEGNEFFVGPEFEFFLFKRDANGN-----------PTTEPSDYGGYFDNTPLDSASDIRQQIVREL 175
                                   69*********************************9987...........567799************************* PP

                                   HHTT--EECCEEECCCTEEEEEE--EECHHHHHHHHHHHHHHHHHHHHTT-EEE-SSSSSTTS---BEEEEEEEEECTT.E CS
                    Gln-synt_C  83 ealgieveashhEvatgQvEinlkfadalkaaDnvvtfKrvvkevArkhgltatFmpKplegdnGsgmHvhlSlwdkdg.k 162
                                    +lg++ ea+hhEva gQ+Ei+l++a alk+aD++v++K ++k+vA+++gl+a+FmpKp++g nGsgmH+h+S+++ d+  
  gi|13542323|ref|NP_112011.1| 176 YELGYQPEAAHHEVAYGQQEIDLRYAPALKMADRIVMLKSIIKNVAERNGLYASFMPKPINGVNGSGMHIHQSIMSFDEkV 256
                                   ***************************************************************************999989 PP

                                   ESSB-TTSGGGB-HHHHHHHHHHHHHHHHHHHHHS-SCCHHHHCSSSTTSSSBEEEESS-TTCSEEEE-TSGGCSTEEEEC CS
                    Gln-synt_C 163 nlfadeddeyalselarhfigGllkhakaltaltaptvnSYkRlvpgyeaPvalawgarNRsallRipaskekakrvElRl 243
                                   n f+d++++y+ls+ a h++gG+l h+++ +a++a+tvnSYkRl+pgyeaPv+++w+++NRsal+Ripa+++  kr+ElR+
  gi|13542323|ref|NP_112011.1| 257 NRFYDKNAKYGLSDYAMHYLGGILSHINEGSAILASTVNSYKRLIPGYEAPVYISWANKNRSALIRIPAGEGTRKRMELRC 337
                                   ********************************************************************************* PP

                                   EBTTS-HHHHHHHHHHHHHHHHHTT--------S-SSSS-TTTH..TSS-B--SSHHHHHHHHHCSHHHCCSS-HHHHHHH CS
                    Gln-synt_C 244 pdasaNPYLalAallaAgldGienklepgepvekdlyelspeer..kgieelPasleeAlealeedellkevlgeevieay 322
                                   pd++ NPYL +A++l  gldGie+k++p+ep+ekd++++++eer  +gi+++P+sl eAl++l++++l++++lg++v+e++
  gi|13542323|ref|NP_112011.1| 338 PDPAGNPYLQFAVILGMGLDGIEKKIDPPEPIEKDIFHMTKEERlqEGITSMPESLGEALHHLRNSKLMRDILGDHVYENF 418
                                   *********************************************99********************************** PP

                                   HHHHHHCHHHHHCT--HHHHHHH CS
                    Gln-synt_C 323 lalkraEleeleeevsdwelery 345
                                   l++k+ E+++++++v +we+++y
  gi|13542323|ref|NP_112011.1| 419 LTVKQREWDQFRSYVGEWEIKKY 441
                                   ********************998 PP

>> Gln-synt_N  Glutamine synthetase, beta-Grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.9   0.0   2.2e-27     2e-23       1      83 []      17      99 ..      17      99 .. 0.95

  Alignments for each domain:
  == domain 1  score: 81.9 bits;  conditional E-value: 2.2e-27
                                  T--EEEEEEE-SSS-EEEEEEEHHHHHHHTTTT-EEEETTSSTTT------EEEEEEEGGGEEE-SS-SS-..EEEEEEEEE- CS
                    Gln-synt_N  1 evkfvdlqFtDikgklkhvtipadelsedaleegvsFDGSsiegfaeieeSDmlLkPdlstavidPfreek.ktarvicdvyd 82
                                  +v+f+++qFtDi g++k++t+p++++ e+al+egv FDGSs++g+a+ieeSDm  +P l++++++P +  k +++r++c+vy 
  gi|13542323|ref|NP_112011.1| 17 KVEFLQMQFTDIVGNVKSLTVPKNRF-ENALTEGVVFDGSSVAGYAQIEESDMRAIPNLDSYTLLPDEFGKsRVVRFVCNVYS 98
                                  599***********************.***************************************6665567*********8 PP

                                  T CS
                    Gln-synt_N 83 p 83
                                  p
  gi|13542323|ref|NP_112011.1| 99 P 99
                                  7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (445 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       407  (0.0227007); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 2872.92
//
Query:       gi|13542324|ref|NP_112012.1|  [L=155]
Description: transcription regulator [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.9e-16   58.4   0.2    1.7e-15   56.7   0.1    1.8  2  PadR      Transcriptional regulator PadR-like family
     0.0023   17.7   0.2     0.0062   16.3   0.0    1.7  2  DUF4364   Domain of unknown function (DUF4364)
     0.0028   17.5   0.3     0.0055   16.5   0.3    1.4  1  DUF3116   Protein of unknown function (DUF3116)
  ------ inclusion threshold ------
      0.035   14.3   0.1        1.4    9.2   0.0    2.2  2  YjcQ      YjcQ protein
      0.084   12.8   0.0         16    5.5   0.0    2.3  2  HTH_5     Bacterial regulatory protein, arsR family
        0.1   12.5   0.1       0.36   10.8   0.0    2.0  3  TrmB      Sugar-specific transcriptional regulator TrmB
       0.11   12.5   1.3       0.49   10.4   0.3    2.4  2  HTH_45    Winged helix-turn-helix


Domain annotation for each model (and alignments):
>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.7   0.1   6.7e-19   1.7e-15       1      72 [.      26      92 ..      26      95 .. 0.96
   2 ?   -0.8   0.0      0.57   1.5e+03      27      41 ..     104     118 ..      99     131 .. 0.81

  Alignments for each domain:
  == domain 1  score: 56.7 bits;  conditional E-value: 6.7e-19
                                  HHHHHCCS-EEHHHHHHHHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCHH CS
                          PadR  1 iLalleeqpsyGyeiikeleelsegllelseGslYpaLkrLekeglveseweesgegpprkyYrlTdaGrre 72
                                  iL +l++++  G +i+  +e+l+ g +++s+G +Yp+L+ Le+eg++++++++     ++kyY l ++G++ 
  gi|13542324|ref|NP_112012.1| 26 ILRILADGEKTGADIMTTIENLTMGRWRPSPGAVYPILRALEEEGYIKGTERD-----NKKYYSLLEKGKEM 92
                                  89************************************************998.....7**********986 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.57
                                   CCTTHHHHHHHHHHH CS
                          PadR  27 lelseGslYpaLkrL 41 
                                   ++++ ++lY+a +r 
  gi|13542324|ref|NP_112012.1| 104 RDVETTNLYDAVERI 118
                                   578899999998876 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   2.4e-06    0.0062      39      73 ..      62      96 ..      58      98 .. 0.92
   2 ?   -1.4   0.1      0.66   1.7e+03      85     102 ..     121     138 ..     107     148 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2.4e-06
                       DUF4364 39 alseLvesglieeeekenktlykiTekGketlelf 73
                                  +l  L+e+g+i+ +e++nk++y++ ekGke+++++
  gi|13542324|ref|NP_112012.1| 62 ILRALEEEGYIKGTERDNKKYYSLLEKGKEMIDML 96
                                  5889***************************9986 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.66
                       DUF4364  85 ideylkenkeelkkesev 102
                                     +ylk+n ++lk +++ 
  gi|13542324|ref|NP_112012.1| 121 YVNYLKDNSSKLKDDKDA 138
                                   567788888888877765 PP

>> DUF3116  Protein of unknown function (DUF3116)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.3   2.1e-06    0.0055      51      83 ..      66      96 ..      62      97 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.1e-06
                       DUF3116 51 LElkgyilRkeekannkkrYelTekGellykel 83
                                  LE++gyi+  e   +nkk+Y+l ekG+++ + l
  gi|13542324|ref|NP_112012.1| 66 LEEEGYIKGTER--DNKKYYSLLEKGKEMIDML 96
                                  9******99998..8*************98765 PP

>> YjcQ  YjcQ protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0   0.00055       1.4       3      55 ..      26      80 ..      24      99 .. 0.71
   2 ?    3.4   0.0     0.034        88      74      85 ..     122     133 ..     100     147 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00055
                                  HHHHHHHH..........-S---HHHHTS-HHHHHHHHHHHHHHTSEE--EESSS CS
                          YjcQ  3 iLkeLeealdeg..eevdnkelsaekldisesrfndiiemlveegyikGvkvkkt 55
                                  iL+ L ++ ++g      +++l+  +   s    + i++ l+eegyikG + +++
  gi|13542324|ref|NP_112012.1| 26 ILRILADGEKTGadIMTTIENLTMGRWRPSPGAVYPILRALEEEGYIKGTERDNK 80
                                  666666665544113455666677777777777889*************987765 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.034
                                   HHHHHHHT-S-- CS
                          YjcQ  74 leyLkeNsmmkK 85 
                                   ++yLk+Ns+  K
  gi|13542324|ref|NP_112012.1| 122 VNYLKDNSSKLK 133
                                   89******8766 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 ?    5.5   0.0    0.0062        16       7      23 ..      26      42 ..      22      45 .. 0.86
   2 ?    4.8   0.0      0.01        26      28      46 ..      55      73 ..      53      73 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0062
                                  HHHHHTTSSEEHHHHHH CS
                         HTH_5  7 ILklLaegelcvcelae 23
                                  IL++La+ge++  +++ 
  gi|13542324|ref|NP_112012.1| 26 ILRILADGEKTGADIMT 42
                                  9**********999996 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.01
                                  -HHHHHHHHHHHHHTTSEE CS
                         HTH_5 28 sqstvShHLkkLreaGLVe 46
                                  s+++v   L++L+e+G+++
  gi|13542324|ref|NP_112012.1| 55 SPGAVYPILRALEEEGYIK 73
                                  67888888********995 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       3.4   8.8e+03      17      30 ..      29      42 ..      27      45 .. 0.75
   2 ?   10.8   0.0   0.00014      0.36      38      63 ..      58      83 ..      50      89 .. 0.83
   3 ?   -2.9   0.0       2.5   6.4e+03      34      45 ..     106     117 ..     105     120 .. 0.65

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 3.4
                                  HHHHCCCHHCHHCC CS
                          TrmB 17 Llklgpatadeiae 30
                                  +l+ g++t  +i  
  gi|13542324|ref|NP_112012.1| 29 ILADGEKTGADIMT 42
                                  67889999999876 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00014
                                  CHHHHHHHHHHCTSEEEESSTTTEEE CS
                          TrmB 38 kvYevLrsLedkGlVerekgrpklYr 63
                                   vY +Lr Le+ G+++  ++  k+Y 
  gi|13542324|ref|NP_112012.1| 58 AVYPILRALEEEGYIKGTERDNKKYY 83
                                  69**************9997755553 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 2.5
                                   SSCHCHHHHHHH CS
                          TrmB  34 vprskvYevLrs 45 
                                   v+ ++ Y+++++
  gi|13542324|ref|NP_112012.1| 106 VETTNLYDAVER 117
                                   566667777765 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.3   0.00019      0.49      11      68 ..      26      95 ..      16      98 .. 0.67
   2 ?   -1.4   0.0      0.94   2.4e+03      35      47 ..     117     129 ..     110     138 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00019
                        HTH_45 11 ILeaisegeakkTkimyka.nLsyklln.......kYLdmLvekgli....kkskekYvlTekGlellek 68
                                  IL+++ +ge++   im    nL+  + +         L  L e+g+i    +++k+ Y+l ekG+e+++ 
  gi|13542324|ref|NP_112012.1| 26 ILRILADGEKTGADIMTTIeNLTMGRWRpspgavyPILRALEEEGYIkgteRDNKKYYSLLEKGKEMIDM 95
                                  6666666666666666654366655433111111156999*******99877799999********9875 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.94
                        HTH_45  35 llnkYLdmLvekg 47 
                                   ++  Y+++L ++ 
  gi|13542324|ref|NP_112012.1| 117 RIGDYVNYLKDNS 129
                                   6778999999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       766  (0.0427241); expected 358.6 (0.02)
Passed bias filter:                      633  (0.0353059); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1069.99
//
Query:       gi|13542325|ref|NP_112013.1|  [L=1459]
Description: hypothetical protein TVN1494 [Thermoplasma volcanium GSS1]
Scores for complete 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-24   85.6   0.0    7.6e-24   84.6   0.0    1.5  1  Pro-kuma_activ  Pro-kumamolisin, activation domain
    0.00014   21.3   0.4       0.03   13.8   0.0    2.9  2  TcfC            E-set like domain
    0.00026   20.4   2.0    0.00074   18.9   2.0    1.8  1  Peptidase_S8    Subtilase family
     0.0048   17.6   6.8     0.0048   17.6   6.8    4.3  4  Big_7           Bacterial Ig domain
  ------ inclusion threshold ------
      0.095   13.8   0.0       0.27   12.3   0.0    1.8  1  CopC            CopC domain


Domain annotation for each model (and alignments):
>> Pro-kuma_activ  Pro-kumamolisin, activation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.6   0.0   2.1e-27   7.6e-24       8     142 .]      63     194 ..      57     194 .. 0.97

  Alignments for each domain:
  == domain 1  score: 84.6 bits;  conditional E-value: 2.1e-27
                Pro-kuma_activ   8 raasstllpvrigLkqnnlekledflmdvsdpkspnygkhltaeevaelfapseeaidaVrnwLessgiaasrhsdtkgwi 88 
                                   +++ s++++v ig+ +nnl++le+++ ++s p+sp y+++lt+++++++f++ +  +++V +++ + g++++   +t   +
  gi|13542325|ref|NP_112013.1|  63 PVNGSMEMNVIIGIIPNNLNELENYATEISMPGSPLYRHWLTTQQINSMFGNYQG-VETVSSYFSKLGFSVQV--KTPFAV 140
                                   678999************************************************9.*****************..****** PP

                Pro-kuma_activ  89 afsatvaqverllktsfeaYshkkgssslarcdeyslPealknyvdyihptdnf 142
                                   a+s++++ +e++++t+++++++k+g+  + + +++ lP ++++yv  + +++nf
  gi|13542325|ref|NP_112013.1| 141 AISGNASMMESVFHTTIYYFTNKNGQVLFSNLNSIELPGSVARYVLSVDGLSNF 194
                                   *********************9999999999999*****************998 PP

>> TcfC  E-set like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.5   0.2    0.0067        24      30      66 ..    1284    1320 ..    1266    1322 .. 0.81
   2 !   13.8   0.0   8.3e-06      0.03      39      66 ..    1391    1418 ..    1389    1419 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0067
                          TcfC   30 naGnqeidtssLPsGiYeveirvyengqvvrteqqkf 66  
                                    + G  +i+ ++LP+Gi +++  +  +++ +++++ ++
  gi|13542325|ref|NP_112013.1| 1284 SSGVLQINGNDLPYGILNLTFTIETANGQTNETSITV 1320
                                    579999******************9888888877666 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 8.3e-06
                          TcfC   39 ssLPsGiYeveirvyengqvvrteqqkf 66  
                                    ssLP G+Y+v++ v+++++ v +++  f
  gi|13542325|ref|NP_112013.1| 1391 SSLPAGNYTVTVLVISKDGQVAKQSANF 1418
                                    79**************888888877665 PP

>> Peptidase_S8  Subtilase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   2.0   2.1e-07   0.00074      80     268 ..     377     648 ..     369     723 .. 0.69

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 2.1e-07
                                   SSSB-SSTTSEEEEEE-SSTTSB-HH..HHHHHHHHHHHHCT-SEEEE-EE.SCETTCHHCHHHHHH.....HHHHHH.CC CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx.....xxxxxxxxx RF
                  Peptidase_S8  80 gekngvapgakilsvkvldtsggsmetgteliraieeaaedkvdvinmslg.estslpktgrsieal.....ainravnkk 154
                                   +++  vap+a +  + + + s  +    ++ +  ++e  +  ++vi +s+   ++s+ + +  + +      ++ ++   k
  gi|13542325|ref|NP_112013.1| 377 QYSATVAPDAHLDIMAIPSLSTVAL---DNAYITLYELPN-TPQVITNSWSgSEDSWWNMYGPYWQSadlmnLLFELLSMK 453
                                   5666677777777666653333222...555555555555.6778888887456666666666655567899888888899 PP

                                   T-EEEEE--SS-T-HHEEE-TTCEECTTTSTTCEEEEEES......................................... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......................................... RF
                  Peptidase_S8 155 gvlvviSaGNngktgsslqagspvgtpstsknvitvgayt......................................... 194
                                   g+ +v+++G +g ++ ++++  ++++p+ts  v++vg+ +                                         
  gi|13542325|ref|NP_112013.1| 454 GSTIVAATGDSGGYD-GYTNMISGEFPGTSPWVTGVGGDQvtmfnntgvefpvtgnysrfnvtfgtanysslppyywsnlr 533
                                   ************444.69********************9999*************************************** PP

                                   ...........................................TTSSB-TT--B-TT.......-EEEE-S-.CCCCCCCC CS
                                   ...........................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxx RF
                  Peptidase_S8 195 ...........................................tegkiapfSsrGpssdgklkpdivapGgn.ivstwsrq 231
                                                                              +           ++  +++++++   G    v+   + 
  gi|13542325|ref|NP_112013.1| 534 lnivniglkhnngftqtywdnnqyvvvngapevistgagsaalS--------IFFKQPWWQHGYSVPNTGRMsEVEVSAEA 606
                                   ***********999999988888888888888887444444441........33333334444444444444222222222 PP

                                   CHHHTTTHH.......EEEE-SHHHCHHHHHHHHHHHHHHHTT.- CS
                                   xxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxx.x RF
                  Peptidase_S8 232 snnsaglss.......yqsmsGTSmAsPnaagaaAlllsalpk.l 268
                                   + n++   +          + GTS A+P  ag++A ++s+l++ +
  gi|13542325|ref|NP_112013.1| 607 GFNQT---ElvdgmwgSWFFGGTSEATPTTAGMIADVISYLNAtI 648
                                   22222...243466665579*******************888753 PP

>> Big_7  Bacterial Ig domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       2.4   8.7e+03      52      70 .]     854     873 ..     849     873 .. 0.88
   2 ?   -3.1   0.0       3.9   1.4e+04      29      57 ..    1202    1230 ..    1196    1239 .. 0.65
   3 ?   -2.8   0.2       3.1   1.1e+04      53      70 .]    1303    1320 ..    1297    1320 .. 0.76
   4 !   17.6   6.8   1.4e-06    0.0048       1      70 []    1330    1402 ..    1330    1402 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 2.4
                                   EEEEEE--....SEEEEEEE CS
                         Big_7  52 ysltwttta.ltagthtltV 70 
                                   ys+tw  ++  ++ t +++V
  gi|13542325|ref|NP_112013.1| 854 YSFTWIGSKqIANATNNISV 873
                                   99***999999999999987 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 3.9
                                    S-EEEEEEEETTEE.EEEE-SSSEEEEEE CS
                         Big_7   29 ggvskVefyvdgtlglgtdtsapysltwt 57  
                                    +g ++  +y ++tlgl+  ts  + ++ +
  gi|13542325|ref|NP_112013.1| 1202 SGLNTLYVYFNDTLGLTYETSMEFYFNAS 1230
                                    67778888999998655455555555444 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 3.1
                                    EEEEE--...SEEEEEEE CS
                         Big_7   53 sltwtttaltagthtltV 70  
                                    ++t+ t+++++++ ++tV
  gi|13542325|ref|NP_112013.1| 1303 TFTIETANGQTNETSITV 1320
                                    667777778888888887 PP

  == domain 4  score: 17.6 bits;  conditional E-value: 1.4e-06
                                    XEEEEEE--TT--EB.TSEEEEEEEEE-SS-EEEEEEEETTEE...EEEE-SSSEEEEEE-....-...SEEEEEEE CS
                         Big_7    1 PtvtitsPangatvs.ggtvtisasAsddggvskVefyvdgtl.g.lgtdtsapysltwtt....taltagthtltV 70  
                                    Ptv+i++P  g++ + + ++t++ +  dd    +V +yv+g++ + ++++ ++   +t+t     ++l+ag++t+tV
  gi|13542325|ref|NP_112013.1| 1330 PTVNIIAPVTGSSQTgSLNITFTYTGFDD----TVILYVNGSSgNvITANVTGKNLYTITEgkgsSSLPAGNYTVTV 1402
                                    9**************55588888888999....*********9668888888777777777666544*********9 PP

>> CopC  CopC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   7.7e-05      0.27      63      91 ..    1386    1419 ..    1337    1420 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 7.7e-05
                          CopC   63 p.....elaaGtYtVewrvvsaDGHpvsGsfsFt 91  
                                    +     +l+aG+YtV+  v+s+DG   + s +F 
  gi|13542325|ref|NP_112013.1| 1386 EgkgssSLPAGNYTVTVLVISKDGQVAKQSANFD 1419
                                    123345677*******************999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1459 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.89u 0.31s 00:00:01.20 Elapsed: 00:00:00.50
# Mc/sec: 8844.47
//
Query:       gi|13542326|ref|NP_112014.1|  [L=374]
Description: geranylgeranyl reductase [Thermoplasma volcanium GSS1]
Scores for complete 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-17   61.5   0.7    7.1e-13   48.5   0.6    2.9  2  FAD_binding_3   FAD binding domain
    1.1e-09   37.8   0.1    4.7e-07   29.2   0.1    2.1  2  Lycopene_cycl   Lycopene cyclase protein
    2.8e-08   33.9   0.0    8.6e-08   32.3   0.0    2.0  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    2.9e-08   32.9   0.2    5.3e-08   32.0   0.0    1.5  2  HI0933_like     HI0933-like protein
    4.6e-07   29.5   0.1    7.4e-07   28.9   0.1    1.3  1  FAD_oxidored    FAD dependent oxidoreductase
    2.1e-06   27.6   0.4    0.00015   21.5   0.0    2.2  2  DAO             FAD dependent oxidoreductase
    3.4e-06   26.5   0.8    8.7e-06   25.2   0.4    1.7  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    3.6e-06   26.3   0.0    5.9e-06   25.6   0.0    1.3  1  GIDA            Glucose inhibited division protein A
    1.1e-05   24.8   0.0    2.1e-05   23.9   0.0    1.5  1  Thi4            Thi4 family
    4.3e-05   22.8   0.0     0.0001   21.5   0.0    1.6  1  FAD_binding_2   FAD binding domain
    0.00017   20.9   0.6     0.0094   15.2   0.0    2.2  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    0.00026   20.0   0.0       0.23   10.3   0.0    2.2  2  Trp_halogenase  Tryptophan halogenase
    0.00034   21.1   0.4      0.048   14.2   0.0    3.3  3  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
  ------ inclusion threshold ------
      0.019   15.0   0.1       0.51   10.3   0.0    2.2  2  NAD_binding_9   FAD-NAD(P)-binding
      0.028   14.1   0.0      0.056   13.1   0.0    1.5  1  ApbA            Ketopantoate reductase PanE/ApbA
      0.031   13.6   0.1        2.6    7.2   0.1    2.3  2  Amino_oxidase   Flavin containing amine oxidoreductase
      0.073   12.4   0.6       0.27   10.5   0.0    2.0  2  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
       0.13   12.1   0.6        2.4    8.0   0.1    2.3  2  PulG            Type II secretory pathway pseudopilin
       0.17   10.9   0.0          6    5.8   0.0    2.1  2  SE              Squalene epoxidase


Domain annotation for each model (and alignments):
>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.5   0.6   7.6e-16   7.1e-13       3     173 ..       3     156 ..       1     202 [. 0.82
   2 !    8.3   0.0    0.0013       1.2     262     334 ..     228     299 ..     211     305 .. 0.78

  Alignments for each domain:
  == domain 1  score: 48.5 bits;  conditional E-value: 7.6e-16
                                   EEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSS.S--EEEHHHHHHHHHTT-HHHHHHHSEECCCCEEEEEEECCC CS
                 FAD_binding_3   3 dVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlp.radglnqrtmellrqlGledrilaegapnelmgealynelsd 82 
                                   dV+++GaGp+G  +a  Ls+ G +v+l+e +++  +     + +++r ++  +++ ++ +++          + + n    
  gi|13542326|ref|NP_112014.1|   3 DVIVIGAGPSGSYAAYRLSKMGLDVLLLEEHKEVGKPVeCTGLVSKRVLDFVKTRSIAGKVYGAN-------IYFPNG--- 73 
                                   8******************************9987777455667899999999999988877555.......344444... PP

                                   CCEEEEEHHCHHCST-CEE--HHHHHHHHHHHHHHHTEEETCSEEEECCEECCCCCCCEEEECCTTEEEEEEEEEEEE--G CS
                 FAD_binding_3  83 tpkaradlelesspervtvypqteleriLvehaeerglqvrfktevesleqdeegvtaevrdketgeeetvrakYlvGaDG 163
                                       ++++e   +  ++ v+  + +++++++ a  +g+++r +++  s+++++++vt ++rd+  g+ ++ +ak ++GaDG
  gi|13542326|ref|NP_112014.1|  74 ---KSIHVE---KNDETIVLYRDSFDKDVAAMAIGAGADIRINARAISVKENNDSVTVKYRDS--GQLKEDNAKVVIGADG 146
                                   ...455555...56677778899**********************************999988..6777789********* PP

                                   TT-HHHHHHT CS
                 FAD_binding_3 164 grStvrktlg 173
                                    +S vr++l 
  gi|13542326|ref|NP_112014.1| 147 INSVVRRDLY 156
                                   *******986 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0013
                                   EEEEEEEEEEEEEEEEESSSEETTEEE-GGGTEEE-STTSHHHHHHHHHHHHHHHHHHHHHTTSS-GGGGHHH CS
                 FAD_binding_3 262 dveieevsawtvaqrvaekyrkgrvflaGDAaHihpPtgGqGlNtaiqDavnLawkLaavlkGeAkeelLdtY 334
                                   + ++  ++ +++  ++a+++   r  l+GDA  i+ P  G G+ t+i  a       a +++ + + + L  Y
  gi|13542326|ref|NP_112014.1| 228 TNRVLGITGAGIPIKIAKSLFTKRSVLIGDAGGIVKPLSGGGIYTGIFSANLASERVANAIE-NEDYSQLRHY 299
                                   55666777777778899999999************************988776667777666.5555555555 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   0.1     5e-10   4.7e-07       1     144 [.       3     150 ..       3     168 .. 0.84
   2 !    6.6   0.0    0.0036       3.4     243     301 ..     239     295 ..     226     312 .. 0.81

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 5e-10
                 Lycopene_cycl   1 DvvviGaGpAglslAarlteakpglkvvlieaspsllfpnnyvWsdefedlga.leecvehsWsgtivylddgkkillgra 80 
                                   Dv+viGaGp g   A rl  +k+gl v+l+e  +++  p + +    ++ l+    + +  +  g+ +y+++gk+i ++++
  gi|13542326|ref|NP_112014.1|   3 DVIVIGAGPSGSYAAYRL--SKMGLDVLLLEEHKEVGKPVECTGLVSKRVLDFvKTRSIAGKVYGANIYFPNGKSIHVEKN 81 
                                   9*****************..***********************999999999633456777778999***********977 PP

                 Lycopene_cycl  81 Ygrv..sskrlkeellerlv.engvklleakvesveeeeageslvvleg.gr..kirarlvvdarglasl 144
                                    +++   ++ + + ++   +  ++ ++ +a++ sv+e+++  ++v   + g+  + +a++v+ a g+ s 
  gi|13542326|ref|NP_112014.1|  82 DETIvlYRDSFDKDVAAMAIgAGADIRINARAISVKENND-SVTVKYRDsGQlkEDNAKVVIGADGINSV 150
                                   6665337***********9966667899************.666655550555566899***99997665 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0036
                 Lycopene_cycl 243 iPvtlggslprleqkvlaiGaaaglvhPaTGYsvarslaeapllasaiaaalresslsa 301
                                   iP+  ++sl  + ++ + iG a+g+v+P  G  +   +  a+l ++++a+a ++++ s+
  gi|13542326|ref|NP_112014.1| 239 IPIKIAKSL--FTKRSVLIGDAGGIVKPLSGGGIYTGIFSANLASERVANAIENEDYSQ 295
                                   555444433..5566899************************999*****999886554 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.3   0.0   9.1e-11   8.6e-08       1      32 [.       6      37 ..       6      79 .. 0.88

  Alignments for each domain:
  == domain 1  score: 32.3 bits;  conditional E-value: 9.1e-11
                                  EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSS CS
                 NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlG 32
                                  ++GaG sG++aAy+L+k g+dvllle +  +G
  gi|13542326|ref|NP_112014.1|  6 VIGAGPSGSYAAYRLSKMGLDVLLLEEHKEVG 37
                                  8***************************9998 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.0   0.0   5.7e-11   5.3e-08       2      43 ..       3      44 ..       2      46 .. 0.96
   2 ?   -3.6   0.0       3.7   3.5e+03     124     156 ..     105     136 ..     102     149 .. 0.60

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 5.7e-11
                                  SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-HHHHHCG CS
                   HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakklgrKilisG 43
                                  dviviG+G++G +aA +++k g +Vllle+ k++g+ +  +G
  gi|13542326|ref|NP_112014.1|  3 DVIVIGAGPSGSYAAYRLSKMGLDVLLLEEHKEVGKPVECTG 44
                                  9***********************************999998 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 3.7
                                   -EEE-S--EEEEECETTE.EEEEE.TTEEEEES CS
                   HI0933_like 124 vklrletevksvekeedgkfrvktkseeelead 156
                                    ++r + +  sv++++d+ ++vk++++++l+ d
  gi|13542326|ref|NP_112014.1| 105 ADIRINARAISVKENNDS-VTVKYRDSGQLKED 136
                                   566777777777666666.77777666665544 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   0.1   7.9e-10   7.4e-07       1     142 [.       3     144 ..       3     150 .. 0.68

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 7.9e-10
                  FAD_oxidored   1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGll..tsglvatdignkaeeqvvtgiareflerlrq.rgga..rlk 76 
                                   Dv+V+G+gp+G  AA+   ++G  vlL+ee++ +G  +  t+ +   ++ +      ++ ia++++ ++    +g+  + +
  gi|13542326|ref|NP_112014.1|   3 DVIVIGAGPSGSYAAYRLSKMGLDVLLLEEHKEVGKPVecTGLVSKRVLDFV----KTRSIAGKVYGANIYfPNGKsiHVE 79 
                                   9*********************************954310333333333333....3455666666666555334413444 PP

                  FAD_oxidored  77 krskw.ntfepevakavleemlaeagvtvllntrlvevekegkriesvtveskeg.rktirAkvfiDA 142
                                   k+ ++ + +  ++ k v+   + +ag ++  n+r+++v+ ++ +   v+ +++ g  k+ +Akv+i A
  gi|13542326|ref|NP_112014.1|  80 KNDETiVLYRDSFDKDVAAMAI-GAGADIRINARAISVKENN-DSVTVKYRDS-GqLKEDNAKVVIGA 144
                                   4444445677776666665555.6699999999999999986.4555555444.44999999999866 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   1.6e-07   0.00015       1      33 [.       3      37 ..       3      48 .. 0.92
   2 ?    4.5   0.1     0.023        22     150     207 ..      94     150 ..      45     218 .. 0.71

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 1.6e-07
                                  EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTT CS
                           DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiag 33
                                  dv++iG+G  G+ +Ay L++ g  V+lle ++++g
  gi|13542326|ref|NP_112014.1|  3 DVIVIGAGPSGSYAAYRLSKMGldVLLLEEHKEVG 37
                                  9*******************9*********99887 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.023
                                   HHHHHHHHHTT-EEEESECEEEEEEEETCEEEEE.EECTEEE..EEEEEEEE--GGGHHHH CS
                           DAO 150 aalaraaealGveilegtevtgleeedgkvwgve.rttpgen..daadavVnaaGawsdll 207
                                   + +a+ a  +G++i+ ++++ +++e++ + ++v+ r++ g+   d a+ v+ a G+ s  +
  gi|13542326|ref|NP_112014.1|  94 KDVAAMAIGAGADIRINARAISVKENN-DSVTVKyRDS-GQLkeDNAKVVIGADGINS--V 150
                                   4578889999************97654.4577766433.3332235677998889886..3 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.4   9.2e-09   8.7e-06       1      99 [.       2     137 ..       2     150 .. 0.56
   2 ?   -4.1   0.0       7.4     7e+03     243     259 ..     303     318 ..     299     318 .. 0.78

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 9.2e-09
                                   CSEEEE--SHHHHHHHHHHHHHTS-EEEEE...TTHCHHHCSHHHHCHHHHHHHHHHHHH..................... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxx..................... RF
                   Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaqagakvtlve...legtclnggcllskallgvaedaeias..................... 57 
                                   kdv+viG+Gp G  aa +l++ g++v+l+e   + g  +  + l+sk +l + + ++ia                      
  gi|13542326|ref|NP_112014.1|   2 KDVIVIGAGPSGSYAAYRLSKMGLDVLLLEehkEVGKPVECTGLVSKRVLDFVKTRSIAGkvyganiyfpngksihveknd 82 
                                   69***************************7664333334444556999999999999999555555555555554444444 PP

                                   ...............HHHHCHHHHCCCCHCCTCEEEEESCEEEEETEEECTCEEEEE CS
                                   ...............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2  58 ...............evvkklnqgielllgeevvkidpgkkkvklekkkegdeekia 99 
                                                       +++g + + ++ ++++ +++  v+++ +++g+ ++  
  gi|13542326|ref|NP_112014.1|  83 etivlyrdsfdkdvaA--MAIGAGADIRINARAISVKENNDSVTVKYRDSGQLKEDN 137
                                   4444444444433220..122223333333334444333334444333333333333 PP

  == domain 2  score: -4.1 bits;  conditional E-value: 7.4
                                   HCSHCCT-EEEETTEEE CS
                                   xxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2 243 lleeklglelderggiv 259
                                   ++  ++g+el+++g+i+
  gi|13542326|ref|NP_112014.1| 303 IR-GSIGVELKKDGFIQ 318
                                   45.78999999999996 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.0   6.2e-09   5.9e-06       1      32 [.       3      34 ..       3      62 .. 0.88

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 6.2e-09
                                  CEEEE-SSHHHHHHHHHHHHTT--EEEEES-G CS
                          GIDA  1 dviViGgGhAGceAAlaaarlGakvlLithkl 32
                                  dviViG+G +G+ AA+ ++++G++vlL+ ++ 
  gi|13542326|ref|NP_112014.1|  3 DVIVIGAGPSGSYAAYRLSKMGLDVLLLEEHK 34
                                  8***************************6554 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.0   2.2e-08   2.1e-05      18      56 ..       2      39 ..       1      56 [. 0.87

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 2.2e-08
                                  EEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TT CS
                          Thi4 18 sDvvivGaGssGLtaayylakkpdlkvailersvspGGG 56
                                   Dv+++GaG+sG  aay l+k  +l v++le++  +G  
  gi|13542326|ref|NP_112014.1|  2 KDVIVIGAGPSGSYAAYRLSKM-GLDVLLLEEHKEVGKP 39
                                  6*********************.********99888765 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   1.1e-07    0.0001       1      35 [.       3      37 ..       3      46 .. 0.93

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 1.1e-07
                                  SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGG CS
                 FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefg 35
                                  DviViG+G +G  AA+++++ Gl+v+++e  +e+g
  gi|13542326|ref|NP_112014.1|  3 DVIVIGAGPSGSYAAYRLSKMGLDVLLLEEHKEVG 37
                                  9****************************988755 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 !   15.2   0.0     1e-05    0.0094       1      32 [.       5      36 ..       4      42 .. 0.88
   2 ?    3.4   0.2     0.041        39     179     257 ..      96     177 ..      72     197 .. 0.56

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1e-05
                   Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkg.ni 32
                                  i+iGaGP G  aa+ l k+gl d+l lE + ++
  gi|13542326|ref|NP_112014.1|  5 IVIGAGPSGSYAAYRLSKMGL-DVLLLEEHkEV 36
                                  89*******************.89999998444 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.041
                   Pyr_redox_3 179 aAlelvrkgaeVtvvtrgseiekeesdpsyslkpdienrleelvke.....ekikvlfnaevkeikekeeeykvktedgkk 254
                                   +A   + +ga++++  r  +++++  + s+++k +   +l+e  ++     + i+ + + ++ +i+++++  +++ + + k
  gi|13542326|ref|NP_112014.1|  96 VAAMAIGAGADIRINARAISVKEN--NDSVTVKYRDSGQLKEDNAKvvigaDGINSVVRRDLYRIRQEKVVSTLQYDMAGK 174
                                   455555555555555555444433..3344444444444444444444434335555555555555555555555555555 PP

                   Pyr_redox_3 255 vev 257
                                   +e 
  gi|13542326|ref|NP_112014.1| 175 IED 177
                                   554 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.0   0.00024      0.23       1      34 [.       3      33 ..       3      40 .. 0.90
   2 !    7.6   0.0    0.0015       1.4     310     355 ..     244     289 ..     204     323 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00024
                                  EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-S CS
                Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlvese 34
                                  +++++G+G++G+ aA  l+k++   l+v+l+e  
  gi|13542326|ref|NP_112014.1|  3 DVIVIGAGPSGSYAAYRLSKMG---LDVLLLEEH 33
                                  699******************9...99**99975 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0015
                                   ES-SEETTEEE-CCCTEE--CCCS-HHHHHHHHHHHHHHT--BTT- CS
                Trp_halogenase 310 rkqawvknvvalGlasgfvePlestsihliqaalrrLlallpdksd 355
                                    k+ + k  v++G+a g v Pl + +i++   +++   +  ++   
  gi|13542326|ref|NP_112014.1| 244 AKSLFTKRSVLIGDAGGIVKPLSGGGIYTGIFSANLASERVANAIE 289
                                   677889999*******************988877766666665544 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   5.1e-05     0.048       2      35 ..       4      37 ..       3      59 .. 0.89
   2 ?    2.7   0.1       0.2   1.9e+02      44      79 ..      94     128 ..      72     132 .. 0.71
   3 ?   -0.8   0.0       2.4   2.3e+03      27      54 ..     287     315 ..     269     317 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5.1e-05
                                  EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
                     Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkll 35
                                  v+v+G+G +g  +A  l+++g +V ++e ++++ 
  gi|13542326|ref|NP_112014.1|  4 VIVIGAGPSGSYAAYRLSKMGLDVLLLEEHKEVG 37
                                  89***************************99998 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.2
                                   HHHHHHHHHTTEEEECSEEEEEEEEETTSEEEEEEE CS
                     Pyr_redox  44 kilqeklekngievllntkveeiegsedgvesvklk 79 
                                   k ++      g +++ n+++ ++++++d v+ vk +
  gi|13542326|ref|NP_112014.1|  94 KDVAAMAIGAGADIRINARAISVKENNDSVT-VKYR 128
                                   555555566788999************9855.6665 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 2.4
                                   EEESSSSSS.TTSSHHHHHHHHHHHHHTT CS
                     Pyr_redox  27 vversdkll.rllDeeaskilqeklekng 54 
                                    +e++d    r +D++++  +  +l+k g
  gi|13542326|ref|NP_112014.1| 287 AIENEDYSQlRHYDKDIRGSIGVELKKDG 315
                                   57777777778999999988888887776 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 ?   10.3   0.0   0.00054      0.51       2      37 ..       6      36 ..       5      43 .. 0.83
   2 ?    2.3   0.0      0.15   1.5e+02     118     148 ..     108     137 ..      88     146 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00054
                 NAD_binding_9  2 ivGaGprGlavlerLlarakkkspleitlfdpsepg 37
                                  ++GaGp+G +++ rL +       l++ l ++++  
  gi|13542326|ref|NP_112014.1|  6 VIGAGPSGSYAAYRLSKM-----GLDVLLLEEHKEV 36
                                  8**************998.....5888888887653 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.15
                 NAD_binding_9 118 evhraevvdleeradgqavlladgaslaada 148
                                   + ++a++++++e++d+++v  +d  +l+ d+
  gi|13542326|ref|NP_112014.1| 108 R-INARAISVKENNDSVTVKYRDSGQLKEDN 137
                                   3.699**************999888876554 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   5.9e-05     0.056       1      33 [.       4      36 ..       4      60 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.9e-05
                                  EEEES-SHHHHHHHHHHHHHTHCEEEE-SCHHH CS
                          ApbA  1 iailGaGaiGsllaakLakagadvtlilrsrrl 33
                                  + ++GaG  Gs+ a++L+k g dv l+   +++
  gi|13542326|ref|NP_112014.1|  4 VIVIGAGPSGSYAAYRLSKMGLDVLLLEEHKEV 36
                                  579***********************9887744 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.025        23       6      27 ..      16      37 ..      11      37 .. 0.90
   2 ?    7.2   0.1    0.0028       2.6     213     257 ..      96     142 ..      62     150 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.025
                                  HHHHHHHTTEEEEEEESSSSSB CS
                 Amino_oxidase  6 aArqLlsaGfdVtvlEardrvG 27
                                  aA++L+  G+dV++lE    vG
  gi|13542326|ref|NP_112014.1| 16 AAYRLSKMGLDVLLLEEHKEVG 37
                                  9***************998888 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0028
                                   HHHHHHTTTTEEEETSEEEEEEEEETTCEEEEETTSTEE...EESEEE CS
                 Amino_oxidase 213 pealaeelrgldirlntrVkeikregdgvtvtledgevv...eaDaVv 257
                                   + a+a    g dir n+r  ++k ++d vtv+++d+ ++   +a+ V+
  gi|13542326|ref|NP_112014.1|  96 VAAMAI-GAGADIRINARAISVKENNDSVTVKYRDSGQLkedNAKVVI 142
                                   566776.779*************************9999776665555 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00029      0.27      31      69 ..       4      42 ..       2      86 .. 0.85
   2 ?   -0.7   0.2      0.74     7e+02      44      82 ..      97     130 ..      94     153 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00029
                                  EEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHH CS
                   AlaDh_PNT_C 31 vlviGgGvaGlqAiatakglgakVtvlDvrparleqles 69
                                  v+viG+G  G  A+   +++g +V +l+  +++ + +e 
  gi|13542326|ref|NP_112014.1|  4 VIVIGAGPSGSYAAYRLSKMGLDVLLLEEHKEVGKPVEC 42
                                  99**************************99999988887 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.74
                                   HHHHHHTT-EEEEEESSHHHHHHHHHTTTCECEEHCHHH CS
                   AlaDh_PNT_C  44 iatakglgakVtvlDvrparleqleslgakfvevlksqe 82 
                                   +a+a g ga++++    ++++e+ +s+  k     ++++
  gi|13542326|ref|NP_112014.1|  97 AAMAIGAGADIRINARAISVKENNDSVTVK-----YRDS 130
                                   688999999999988888888888876555.....3333 PP

>> PulG  Type II secretory pathway pseudopilin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0       0.2   1.9e+02      57      75 ..      72      90 ..      69      93 .. 0.90
   2 ?    8.0   0.1    0.0026       2.4      42      74 ..      96     127 ..      92     134 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.2
                          PulG 57 NGvevtikktqeeisvyed 75
                                  NG +++++k++e+i++y d
  gi|13542326|ref|NP_112014.1| 72 NGKSIHVEKNDETIVLYRD 90
                                  9************999876 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0026
                          PulG  42 valmAvqtkqdeLslNGvevtikktqeeisvye 74 
                                   va mA+ ++  ++ +N  ++++k+++++++v  
  gi|13542326|ref|NP_112014.1|  96 VAAMAIGAGA-DIRINARAISVKENNDSVTVKY 127
                                   9*****9986.69****************9975 PP

>> SE  Squalene epoxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0      0.05        47       2      28 ..     138     165 ..     137     187 .. 0.83
   2 ?    5.8   0.0    0.0063         6     130     175 ..     250     295 ..     241     303 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.05
                            SE   2 AkltvvcDGifsklRkels.dnkvevts 28 
                                   Ak+ + +DGi s +R++l    + +v s
  gi|13542326|ref|NP_112014.1| 138 AKVVIGADGINSVVRRDLYrIRQEKVVS 165
                                   89999*************9655666665 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0063
                            SE 130 kGlillGDalnmRHPltggGmtvalnDivllskllkpledlsdeek 175
                                   k  +l+GDa  +  Pl ggG+  ++  + l s+ + +  + +d ++
  gi|13542326|ref|NP_112014.1| 250 KRSVLIGDAGGIVKPLSGGGIYTGIFSANLASERVANAIENEDYSQ 295
                                   56799****************9999999998888877755566555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       511  (0.0285013); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2635.53
//
Query:       gi|13542327|ref|NP_112015.1|  [L=285]
Description: DMT family permease [Thermoplasma volcanium GSS1]
Scores for complete 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-32  110.3  43.1    7.3e-18   65.1  18.2    2.0  2  EamA      EamA-like transporter family
  ------ inclusion threshold ------
       0.23   11.5   9.2      0.048   13.6   1.8    3.0  3  NdhL      NADH dehydrogenase transmembrane subunit
        1.8    7.9  25.4      0.051   12.9  10.0    2.1  2  TPT       Triose-phosphate Transporter family


Domain annotation for each model (and alignments):
>> EamA  EamA-like transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.6  16.9   1.8e-17   1.1e-13       4     136 ..       9     137 ..       6     138 .. 0.93
   2 !   65.1  18.2   1.2e-21   7.3e-18       2     136 ..     148     281 ..     147     282 .. 0.97

  Alignments for each domain:
  == domain 1  score: 51.6 bits;  conditional E-value: 1.8e-17
                          EamA   4 illallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegklaklslkdwllllllgllgtvlafllffy 84 
                                   i +++ ++++w+++f+++k ++ ++sp+ ++++rf ++++l+l++   k +     + ++w++ l+ g+   ++a++l+++
  gi|13542327|ref|NP_112015.1|   9 ISTLVFVTFIWGVTFPIIKDVFLYLSPVNFLALRFAVSTLLFLPVVIKKIKHV---KSEEWKAGLIAGT-LLFIAYYLQTI 85 
                                   5678899************************************9988777777...9999**9888886.6789999**** PP

                          EamA  85 alkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvllil 136
                                   +l +t+++  + it + +vf+ i+s+l+l+ ++   ++ + +++++G++l++
  gi|13542327|ref|NP_112015.1|  86 GLLYTQPALSGTITGIYVVFVPIISYLYLRRRIAHVEVYSSAFAFIGLVLMS 137
                                   **************************************************97 PP

  == domain 2  score: 65.1 bits;  conditional E-value: 1.2e-21
                          EamA   2 lgillallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegklaklslkdwllllllgllgtvlafllf 82 
                                   lg+++ l+aa+f+a+  v+  +  + ++++ ++f+++ +a+++  ++++ + +++ k++  + + +l++++++t+la +++
  gi|13542327|ref|NP_112015.1| 148 LGDFMTLAAAVFYAMQLVYVSKHASHIDTFVFSFIQIAVAAFFSAVFIPTFPEPF-KITIYSAFVVLFTAVFATFLATYVY 227
                                   5899****************8889*******************************.************************* PP

                          EamA  83 fyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvllil 136
                                   ++al+k++++++++i+  eP+f+ + sv+l+gek++ + l+gi+++++++  i+
  gi|13542327|ref|NP_112015.1| 228 VSALSKMNVTKVGVILIGEPIFADLTSVILYGEKIGPIALIGIIIMIASIGTIS 281
                                   ************************************************997765 PP

>> NdhL  NADH dehydrogenase transmembrane subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       2.1   1.3e+04      46      58 ..       5      17 ..       2      22 .. 0.68
   2 ?    1.6   0.5     0.044   2.6e+02      15      67 ..      39      93 ..      25      95 .. 0.76
   3 ?   13.6   1.8   8.1e-06     0.048      16      61 ..      95     141 ..      88     145 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 2.1
                          NdhL 46 ErlliymlvflfF 58
                                  E l i +lvf+ F
  gi|13542327|ref|NP_112015.1|  5 EVLSISTLVFVTF 17
                                  5555666777766 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.044
                          NdhL 15 aylalsvlYllviPlil..ylwlrkRWyvaskiErlliymlvflfFPGllllaPf 67
                                    l  +v+ ll++P+++  + ++++   +a+ i  +l+++  +l   Gll   P 
  gi|13542327|ref|NP_112015.1| 39 LALRFAVSTLLFLPVVIkkIKHVKSEEWKAGLIAGTLLFIAYYLQTIGLLYTQPA 93
                                  4566678889999999844467777777889999999999999999998877775 PP

  == domain 3  score: 13.6 bits;  conditional E-value: 8.1e-06
                          NdhL  16 ylalsvlYllviPlilylwlrkRWyvaskiErlliy.mlvflfFPGl 61 
                                    ++++++Y++++P i yl+lr+R  +++    ++++ +lv + + Gl
  gi|13542327|ref|NP_112015.1|  95 SGTITGIYVVFVPIISYLYLRRRIAHVEVYSSAFAFiGLVLMSYSGL 141
                                   578999********************999999999845999999887 PP

>> TPT  Triose-phosphate Transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   7.9     0.047   2.8e+02      30     163 ..      34     166 ..       7     177 .. 0.72
   2 ?   12.9  10.0   8.5e-06     0.051      34     132 ..     179     277 ..     166     282 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.047
                           TPT  30 yPltvsavqllvgsvlilvlwalglkkrpkisseflkailplalvktlghvlavvslskvaVSfthtvKasePiFtvilsr 110
                                    P+   a++++v ++l   ++ + +kk+++++se +ka l+ + + +++  l ++ l  +    + t+  +  +F  i+s 
  gi|13542327|ref|NP_112015.1|  34 SPVNFLALRFAVSTLL---FLPVVIKKIKHVKSEEWKAGLIAGTLLFIAYYLQTIGLLYTQPALSGTITGIYVVFVPIISY 111
                                   4666667777777776...445567788889999*********************************************** PP

                           TPT 111 lllgeklsllvylsLlpivgGvalas...vtElsFnligfisAlisnltfslrnif 163
                                   l l+ ++    + s      G++l s   +  +s +l  f++ l++ ++ +++ ++
  gi|13542327|ref|NP_112015.1| 112 LYLRRRIAHVEVYSSAFAFIGLVLMSysgLSNVSIELGDFMT-LAAAVFYAMQLVY 166
                                   ***998876655555555556666551224556666666654.5555666666665 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 8.5e-06
                           TPT  34 vsavqllvgsvlilvlwalglkkrpkisseflkailplalvkt.lghvlavvslskvaVSfthtvKasePiFtvilsrlll 113
                                    s +q++v   + +++++  + +  ki+ +   ++l+ a++ t l+  + v +lsk +V    ++   ePiF+ + s +l+
  gi|13542327|ref|NP_112015.1| 179 FSFIQIAVAAFF-SAVFIPTFPEPFKITIYSAFVVLFTAVFATfLATYVYVSALSKMNVTKVGVILIGEPIFADLTSVILY 258
                                   577888888877.4556667788899999988888888877651677777778**************************** PP

                           TPT 114 geklsllvylsLlpivgGv 132
                                   gek+    ++ ++++++ +
  gi|13542327|ref|NP_112015.1| 259 GEKIGPIALIGIIIMIASI 277
                                   ***********99999765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       924  (0.0515366); expected 358.6 (0.02)
Passed bias filter:                      222  (0.0123822); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 1701.51
//
Query:       gi|13542328|ref|NP_112016.1|  [L=632]
Description: 7-cyano-7-deazaguanine tRNA-ribosyltransferase [Thermoplasma volcanium GSS1]
Scores for 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  221.3   0.0    2.7e-65  220.8   0.0    1.1  1  TGT            Queuine tRNA-ribosyltransferase
    3.3e-21   75.2   0.1    6.2e-21   74.3   0.1    1.5  1  TGT_C2         Patch-forming domain C2 of tRNA-guanine transg
    2.1e-13   50.0   0.2    4.1e-13   49.1   0.2    1.5  1  PUA            PUA domain
  ------ inclusion threshold ------
      0.053   13.2   3.9        0.1   12.3   3.9    1.4  1  SpoIISA_toxin  Toxin SpoIISA, type II toxin-antitoxin system
      0.061   13.6   0.1       0.19   12.0   0.1    1.9  1  UPF0113        UPF0113 PUA domain
      0.072   13.5   1.0        2.8    8.4   0.5    2.4  2  ACP_PD         Acyl carrier protein phosphodiesterase


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 !  220.8   0.0   9.2e-69   2.7e-65       3     349 ..      10     330 ..       7     331 .. 0.94

  Alignments for each domain:
  == domain 1  score: 220.8 bits;  conditional E-value: 9.2e-69
                                   EEEEEEEETTEEEEESEEEEBETTSSBTTB-HHHHH.HTTES-EEEEHHHHHHTTTHHHHHHTTHHHHHHT--S-EEEE-S CS
                           TGT   3 aRlGklelphgtietPafmpvgtqgtvkgltpdelkeelgaqiilsntyhlelrpgeelvakagglhkflgwdkpiltdsg 83 
                                   aR++++ +phgtietP+++pv  ++++  +tp+e+k + g++ +++n+y++  +   +  a+  g+h+++g+d+p++tdsg
  gi|13542328|ref|NP_112016.1|  10 ARIARFDTPHGTIETPTVLPV-INPNIMDITPEEMK-KYGVHGVITNSYIILRNDRLREEAEKYGVHSLIGYDGPVMTDSG 88 
                                   9********************.999**********6.88**********8876666666677789**************** PP

                                   HHHHHHHEEEESSEEEEE-TTTS-EEEE-HHHHHHHHHHHT-SEEE-------SS--HHHHHHHHHHHHHHHHHHHHHHSE CS
                           TGT  84 gfqvfslkkiteegvsfqsridGskvlltpeesieiqeklgsDiimalddvvpspaskkrveksverTlrwldrcleahqa 164
                                   +fq +               + Gs v++++++++e+q+++gsDi ++ld  +++++s+++ve+++ +T r++ ++ +a ++
  gi|13542328|ref|NP_112016.1|  89 TFQSYV--------------Y-GS-VEFNNRQVVEFQKTIGSDILTILDIFTTPSSSRQEVENAITETYRRMLEVNDAGGM 153
                                   ***443..............4.**.****************************************************99** PP

                                   EEEEE--TT-HHHHHHHHHHHHHH--SEEEE-S.SSSSS..HHHHHHHHHHHHGGGS-TTS-EEETTB-SHHHHHHHHHTT CS
                           TGT 165 lfgivqGglyedlreesaeelakrdfdgyaigG.lsvge..ekeellevveavtellpedkprylmGvgtPedlleavalG 242
                                   + g++qGg+y+dlr++sae + +++++ ++igG +++ e  e+++l++++ +++ ++   kp++l+G g+P+ ++ av lG
  gi|13542328|ref|NP_112016.1| 154 IAGPIQGGIYPDLRKRSAELMNSTNASYLPIGGvVPLLEsyEYDKLVDIILNSKLNVSFGKPIHLFGGGHPMFFAFAVYLG 234
                                   *********************************8889998889************************************** PP

                                   --EEEESHHHHHHHTTEEEETTEEEETTSGGGTT--SBSSSS--SHHHHH-BHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                           TGT 243 vDmfdcvyptrtarngraltsegelnlknakyaedfspldegCsCytCknytraylhhllktkemlgaiLltiHNlhyyle 323
                                   vD+fd++ + ++a+++r+++++g+ +l +     + spl +       k yt ++l++l k+++   ++ l+ HNl+ ++ 
  gi|13542328|ref|NP_112016.1| 235 VDLFDSASYVKYAKDDRLIYPDGTRDLARIIEIPEWSPLFD-------K-YTVKELKELPKEQR---SVELSRHNLKAIFM 304
                                   ***************************98888888888665.......5.************99...99************ PP

                                   HHHHHHHHHHTT-HHHHHHHHHHHHT CS
                           TGT 324 lfkriReaIkegtfeefveefarkye 349
                                   ++++iRe I e++++++ ++ a++++
  gi|13542328|ref|NP_112016.1| 305 EISEIRERIYEESMDQYLAQKAKSHP 330
                                   *******************9999886 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 !   74.3   0.1   2.1e-24   6.2e-21       2      71 .]     483     552 ..     482     552 .. 0.91

  Alignments for each domain:
  == domain 1  score: 74.3 bits;  conditional E-value: 2.1e-24
                        TGT_C2   2 rlraiadYqFGagagdaLfpedvtitrsatgrirqvlv.dgerlatlraqdgrltLsleGarrlheslppP 71 
                                   ++r+iadYqFG g+g+++f++dv+i +s+tgrir v++ +++ +atl  +dg++tL+  Ga +l ++ + P
  gi|13542328|ref|NP_112016.1| 483 KIRTIADYQFGYGIGKDFFKDDVRIFKSKTGRIRGVFDkGNKLIATL-RNDGFFTLTFHGATLLYNVSKSP 552
                                   89************************************556777888.6***************9987765 PP

>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.1   0.2   1.4e-16   4.1e-13       2      72 ..     555     625 ..     554     627 .. 0.97

  Alignments for each domain:
  == domain 1  score: 49.1 bits;  conditional E-value: 1.4e-16
                                   EEEE-HHHHHHHHTT-EEEGGGEEEEETT--TTSEEEEEETTSCEEEEEEESS-HHHHHHHCTSEEEEEEE CS
                           PUA   2 rvvvddgAvkallsgasLlapGvvevegdfeegdvVaivdedgelvavGlanysseelakikggksveier 72 
                                   rv v++++++  ++g s++ +++++++ d+ ++ +  +v+e+gelvavG+a +s++el++   g++v+i++
  gi|13542328|ref|NP_112016.1| 555 RVFVKNESAEYNAKGYSVFFKFILDADPDIIAKNETLVVNENGELVAVGKATVSGKELREYSDGIAVKIHE 625
                                   799******************************************************************97 PP

>> SpoIISA_toxin  Toxin SpoIISA, type II toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   3.9   3.3e-05       0.1      98     149 ..     331     381 ..     313     391 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.3e-05
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHS-EEEE..ESSHHHHHHHHHHHHHHH CS
                 SpoIISA_toxin  98 ktikenekvlkanlrrvetftellqnesihvyeeygskeayieglkkllksy 149
                                    ++k++ kv++ + +++e++++l + +   +y+ + +k+ y+  l+k+ ++y
  gi|13542328|ref|NP_112016.1| 331 SLLKAYVKVMQ-YSKMLEKYQDLFKKAAYFFYDSFSTKNTYVARLEKFTSKY 381
                                   57777877775.5689********************************9998 PP

>> UPF0113  UPF0113 PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   6.3e-05      0.19      16      56 ..     570     612 ..     552     623 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 6.3e-05
                       UPF0113  16 rdvlkesilkitesvkenqvvvVlnengeplGiGkirkdt..k 56 
                                     v+ + il  ++++  ++  +V+nenge++++Gk+  ++   
  gi|13542328|ref|NP_112016.1| 570 YSVFFKFILDADPDIIAKNETLVVNENGELVAVGKATVSGkeL 612
                                   568888899999999989999999************9887541 PP

>> ACP_PD  Acyl carrier protein phosphodiesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.5   0.00094       2.8      11      58 ..     305     352 ..     297     359 .. 0.84
   2 ?    2.9   0.0     0.049   1.5e+02      43      67 ..     389     413 ..     362     422 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00094
                        ACP_PD  11 eysaepLeefvqrvyaqlekneealPerlqrllprmieedwLesYael 58 
                                   e s+ + + + + + + l+++ + +P+ l++ ++ m   ++Le+Y++l
  gi|13542328|ref|NP_112016.1| 305 EISEIRERIYEESMDQYLAQKAKSHPSLLKAYVKVMQYSKMLEKYQDL 352
                                   55555566777889999*****************************86 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.049
                        ACP_PD  43 lprmieedwLesYaelegieralqr 67 
                                      + ++dwL  Y +l++++++ +r
  gi|13542328|ref|NP_112016.1| 389 TYVFSRKDWLPGYTNLNFVRDVYER 413
                                   5567899***********9998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (632 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       738  (0.0411624); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.63u 0.32s 00:00:00.95 Elapsed: 00:00:00.49
# Mc/sec: 3915.23
//
Query:       gi|13542329|ref|NP_112017.1|  [L=589]
Description: ATPase RIL [Thermoplasma volcanium GSS1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-33  116.6   0.0    2.1e-16   60.7   0.0    2.5  2  ABC_tran         ABC transporter
    7.6e-14   51.7   0.7    5.4e-07   29.3   0.2    2.6  2  SMC_N            RecF/RecN/SMC N terminal domain
    4.1e-09   36.1   7.7    6.1e-09   35.5   6.4    2.0  2  RLI              Possible Fer4-like domain in RNase L inhibit
    1.2e-07   31.2   2.3    1.2e-07   31.2   2.3    2.1  3  Fer4             4Fe-4S binding domain
    1.5e-07   31.6   5.3        0.3   10.9   0.0    4.3  4  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    5.2e-06   26.4   0.5       0.63    9.7   0.0    3.4  3  AAA_15           AAA ATPase domain
    0.00019   21.3   1.9    0.00019   21.3   1.9    2.2  2  Fer4_6           4Fe-4S binding domain
    0.00026   20.9   0.3      0.068   13.1   0.0    2.6  3  RsgA_GTPase      RsgA GTPase
    0.00066   20.2   0.1     0.0079   16.7   0.0    2.3  2  AAA_23           AAA domain
     0.0031   17.6   9.2      0.017   15.2   1.3    1.9  2  Fer4_10          4Fe-4S dicluster domain
     0.0031   17.6   6.1     0.0059   16.7   6.1    1.5  1  Fer4_21          4Fe-4S dicluster domain
     0.0033   17.6   6.5     0.0064   16.6   6.5    1.5  1  Fer4_9           4Fe-4S dicluster domain
     0.0042   17.6   0.8     0.0042   17.6   0.8    1.9  3  Fer4_7           4Fe-4S dicluster domain
      0.008   15.9   0.9          4    7.3   0.1    2.4  2  AAA_29           P-loop containing region of AAA domain
  ------ inclusion threshold ------
      0.022   14.8   0.2        5.5    7.1   0.0    2.8  2  MMR_HSR1         50S ribosome-binding GTPase
      0.033   15.1   0.4      0.033   15.1   0.4    2.4  2  Fer4_16          4Fe-4S double cluster binding domain
      0.049   13.9   0.0        0.1   12.9   0.0    1.5  1  Peptidase_S41_N  N-terminal domain of Peptidase_S41 in eukary
       0.19   12.3   0.3       0.19   12.3   0.3    2.3  1  Fer4_17          4Fe-4S dicluster domain
       0.54   10.5  11.1      0.057   13.5   1.4    2.4  2  Fer4_2           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 !   53.4   0.0     4e-17   3.8e-14       8     137 .]      95     240 ..      93     240 .. 0.87
   2 !   60.7   0.0   2.2e-19   2.1e-16       7     137 .]     360     482 ..     354     482 .. 0.78

  Alignments for each domain:
  == domain 1  score: 53.4 bits;  conditional E-value: 4e-17
                                   EETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S-TTSBHHHH........ CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx........ RF
                      ABC_tran   8 lkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke.qeleslrkeigvlpqepqlfpeltvren........ 79 
                                   + +g++ ai+G+nG GK+t l++l+g + p+ G+   d+ ++k+    +++r  +g +++     ++  v +n        
  gi|13542329|ref|NP_112017.1|  95 VVPGKVSAILGQNGLGKTTTLNILSGITVPNLGNY--DKPPSKDaVIDRFARTTMGAYFKGLYEENKRAVLKNqyvdyipk 173
                                   779******************************96..88888887566778888898888855555555777779999999 PP

                                   .............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                   .............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  80 .............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                                +++ ++++++s l+l++   + v    ++ SgG+ q++a+  +l k+++++l+DE t+
  gi|13542329|ref|NP_112017.1| 174 vvsgtigeilrknNENGNFDEVVSLLNLENALSKDV----KECSGGELQKLAIGTTLEKEADIYLFDEMTS 240
                                   999999999976677777999999999999998888....****************************985 PP

  == domain 2  score: 60.7 bits;  conditional E-value: 2.2e-19
                                   EEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS.--S-TTSBHHHH....... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx....... RF
                      ABC_tran   7 klkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe.pqlfpeltvren....... 79 
                                   +++ ge+ +++G+n  GKSt++++lag ++p+eG+i             s + ++++ pq  ++ f+++ v +        
  gi|13542329|ref|NP_112017.1| 360 QIHTGEISGVLGRNALGKSTFVMMLAGVMNPDEGSI-------------SQNVKVSYKPQYiSTDFKGT-VSDLiasalkd 426
                                   7999********************************.............33444444444432223333.44444444443 PP

                                   ..HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                   ..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  80 ..esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                     e++   +++ + l+++++ +++v      LSgG+ qr+++a +l ++++++l+DEp+a
  gi|13542329|ref|NP_112017.1| 427 raEDTYVKNEIFHPLNIPDIMENPV----DGLSGGEMQRLSIAITLSREADVYLIDEPSA 482
                                   3355555889999999999999999....*****************************75 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   0.2   5.7e-10   5.4e-07       7     202 ..      84     273 ..      78     288 .. 0.73
   2 !   20.1   0.0   3.6e-07   0.00034      91     190 ..     332     503 ..     310     529 .. 0.74

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 5.7e-10
                                   EESETTEECEEEEEETTSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N   7 ienFksyagktvilpfsksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdned 87 
                                   +++F+ y      + +  +++ai+G+NG GK+  l+ ++ +   +  +  +  + +++i +    + ++ a+ + ++++++
  gi|13542329|ref|NP_112017.1|  84 VNGFRIYS---LPTVVPGKVSAILGQNGLGKTTTLNILSGITVPNLGNYDKPPSKDAVIDR--FARTTMGAYFKGLYEENK 159
                                   67788884...444445678************65555433322222222345556666665..789999******999988 PP

                                   EESSSSSSCEEEEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-...STTCS-HHHHHHHHHHHHHHHHCCS--SEEEEC CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N  88 kklkiekeevsisrrvkrkgeseykingkevtkkevsellesagi...skelLSgGektLvalaLlfAiqkvkpaplyllD 165
                                   +++  ++   +i + v+ +     + n+++ ++ ev +ll+ ++    + ++ SgGe + +a+     +   k a +yl+D
  gi|13542329|ref|NP_112017.1| 160 RAVLKNQYVDYIPKVVSGTIGEILRKNNENGNFDEVVSLLNLENAlskDVKECSGGELQKLAI----GTTLEKEADIYLFD 236
                                   88555555556666666666678899**************9776511134689***9764444....355678999***** PP

                                   TTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHC CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 166 eidaaLDeknvkkvaellkeksknaQfivislreeml 202
                                   e+ + LD  ++ +v+++++  sk+  +iv+ ++  +l
  gi|13542329|ref|NP_112017.1| 237 EMTSYLDIGERLNVSNIVQDLSKKKTVIVVEHDLAIL 273
                                   ******************************9876655 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 3.6e-07
                                   SSSSSCEEEEEEEETTSEEEEEET..TEEE-HHHHHHHHHCTT-STT.................................. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxx.................................. RF
                         SMC_N  91 kiekeevsisrrvkrkgeseykin..gkevtkkevsellesagiske.................................. 135
                                   + + e++ i+ + ++k+  ++ ++    +++  e+s +l +  + k+                                  
  gi|13542329|ref|NP_112017.1| 332 RDKFEHILITWTDIKKKLGDFSLDvhAGQIHTGEISGVLGRNALGKStfvmmlagvmnpdegsisqnvkvsykpqyistdf 412
                                   444455555555554444444444004445556777777777777778888888888888888888888888888888888 PP

                                   ........................................CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHH CS
                                   ........................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 136 ........................................lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknv 176
                                                                            LSgGe + +++    Ai   + a +yl+De  a+LD +++
  gi|13542329|ref|NP_112017.1| 413 kgtvsdliasalkdraedtyvkneifhplnipdimenpvdGLSGGEMQRLSI----AITLSREADVYLIDEPSAHLDSSYR 489
                                   88888888888888888888888888888888888889889*****776555....566679999**************** PP

                                   HHHHHHHHHHCTTS CS
                                   xxxxxxxxxxxxxx RF
                         SMC_N 177 kkvaellkekskna 190
                                     va+++++  +n+
  gi|13542329|ref|NP_112017.1| 490 MVVAKVIRRVMENT 503
                                   *******9776664 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 !   35.5   6.4   6.5e-12   6.1e-09       1      32 [.       1      29 [.       1      30 [. 0.96
   2 ?   -3.0   0.0       7.4     7e+03      14      24 ..     210     220 ..     208     221 .. 0.78

  Alignments for each domain:
  == domain 1  score: 35.5 bits;  conditional E-value: 6.5e-12
                                  --EEEES---------TTHHHHHTTSEEEESS CS
                           RLI  1 mrlAivdadqCdPKKCtgkkcarfcpvrlvrt 32
                                  m++A+ d+d+C+PKKC++ +c+ +cp   vr+
  gi|13542329|ref|NP_112017.1|  1 MHVAVLDKDRCHPKKCHH-ECQYYCPP--VRN 29
                                  9*****************.*******9..985 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 7.4
                                   ---TTHHHHHT CS
                           RLI  14 KKCtgkkcarf 24 
                                   K C+g +++++
  gi|13542329|ref|NP_112017.1| 210 KECSGGELQKL 220
                                   67999999885 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       4.9   4.7e+03       2       8 ..       5      11 ..       4      12 .. 0.83
   2 ?   -3.0   0.3       8.5     8e+03      13      19 ..      19      25 ..      18      25 .. 0.85
   3 !   31.2   2.3   1.3e-10   1.2e-07       3      24 .]      45      66 ..      43      66 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 4.9
                                  EEETTTS CS
                          Fer4  2 videekC 8 
                                  v d+++C
  gi|13542329|ref|NP_112017.1|  5 VLDKDRC 11
                                  789**** PP

  == domain 2  score: -3.0 bits;  conditional E-value: 8.5
                                  HHHHHST CS
                          Fer4 13 aCvevCP 19
                                  +C   CP
  gi|13542329|ref|NP_112017.1| 19 ECQYYCP 25
                                  59999*9 PP

  == domain 3  score: 31.2 bits;  conditional E-value: 1.3e-10
                                  EETTTSSS-THHHHHSTTTEEE CS
                          Fer4  3 ideekCigCGaCvevCPvgAIt 24
                                  i e +CigCG+C+  CP+gAI+
  gi|13542329|ref|NP_112017.1| 45 ISETLCIGCGICIRRCPFGAIR 66
                                  8899*****************6 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   1.0   0.00038      0.36       2      23 ..     101     122 ..     100     159 .. 0.74
   2 ?    4.4   0.0     0.029        27     181     272 ..     171     244 ..     135     274 .. 0.72
   3 ?    4.4   0.1     0.029        28       2      22 ..     367     387 ..     366     422 .. 0.71
   4 !   10.9   0.0   0.00032       0.3     235     284 ..     452     498 ..     437     518 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00038
                        AAA_21   2 nvliGpNgsGKSnLLdaldlla 23 
                                    ++ G Ng GK++ L +l+++ 
  gi|13542329|ref|NP_112017.1| 101 SAILGQNGLGKTTTLNILSGIT 122
                                   689***************8872 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.029
                        AAA_21 181 ekrllqrlvrslklveielsdlgegeeliasvderlrergvvflengdgqelparelSdGtkrllalltallralkkgsll 261
                                   +++ +++ ++++++ ++e  + +e++ l ++++ ++++               + e S G ++ la+ t l   +   +++
  gi|13542329|ref|NP_112017.1| 171 IPKVVSGTIGEILRKNNENGNFDEVVSLLNLENALSKD---------------VKECSGGELQKLAIGTTLEKEA---DIY 233
                                   55566666777777777777777777777777777777...............55559******88888888777...9** PP

                        AAA_21 262 liDEpEngLHP 272
                                   l+DE+ + L+ 
  gi|13542329|ref|NP_112017.1| 234 LFDEMTSYLDI 244
                                   ********986 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.029
                        AAA_21   2 nvliGpNgsGKSnLLdaldll 22 
                                    ++ G+N+ GKS++   l ++
  gi|13542329|ref|NP_112017.1| 367 SGVLGRNALGKSTFVMMLAGV 387
                                   6789*********99888766 PP

  == domain 4  score: 10.9 bits;  conditional E-value: 0.00032
                        AAA_21 235 relSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellke 284
                                   + lS G  + l ++  l r +   +++liDEp ++L+ +    +++++++
  gi|13542329|ref|NP_112017.1| 452 DGLSGGEMQRLSIAITLSREA---DVYLIDEPSAHLDSSYRMVVAKVIRR 498
                                   566777766669999999988...9************9555333333321 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.1    0.0039       3.7      22      44 ..      98     119 ..      83     243 .. 0.89
   2 !    6.8   0.1    0.0051       4.8      25      50 ..     366     391 ..     344     439 .. 0.75
   3 !    9.7   0.0   0.00066      0.63     287     357 ..     438     505 ..     392     517 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0039
                        AAA_15  22 seeltvliGkNnsGKSsileald 44 
                                    + ++ + G N+ GK++ l++l 
  gi|13542329|ref|NP_112017.1|  98 GK-VSAILGQNGLGKTTTLNILS 119
                                   56.899**************995 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0051
                        AAA_15  25 ltvliGkNnsGKSsilealdlFlnnk 50 
                                   ++ + G+N+ GKS+++++l    n +
  gi|13542329|ref|NP_112017.1| 366 ISGVLGRNALGKSTFVMMLAGVMNPD 391
                                   67788*************98777765 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.00066
                        AAA_15 287 k......ddeelplnknGsGvqrllllillileaekkdekeeknvilliEEPEahLHpqaqkvlikllkelandnkt 357
                                   +      d +e p++  + G ++ l++++ + +  +        +++li+EP ahL  +  +v++k ++++ +++k+
  gi|13542329|ref|NP_112017.1| 438 FhplnipDIMENPVDGLSGGEMQRLSIAITLSR--EA-------DVYLIDEPSAHLDSSYRMVVAKVIRRVMENTKK 505
                                   144566677888888888888888888876544..33.......57****************************985 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   1.7       1.4   1.3e+03       5      20 ..       7      25 ..       3      34 .. 0.76
   2 !   21.3   1.9   2.1e-07   0.00019       4      24 .]      45      65 ..      43      65 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.4
                        Fer4_6  5 dpdkCi..gC.gdCvrvCP 20
                                  d+d+C    C  +C   CP
  gi|13542329|ref|NP_112017.1|  7 DKDRCHpkKChHECQYYCP 25
                                  8999997779666998888 PP

  == domain 2  score: 21.3 bits;  conditional E-value: 2.1e-07
                        Fer4_6  4 idpdkCigCgdCvrvCPegai 24
                                  i + +CigCg C+r CP+gai
  gi|13542329|ref|NP_112017.1| 45 ISETLCIGCGICIRRCPFGAI 65
                                  6789****************8 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.0   7.3e-05     0.068      89     121 ..      88     120 ..      71     131 .. 0.83
   2 ?   -3.3   0.0       7.9   7.4e+03      92     110 ..     271     289 ..     246     289 .. 0.73
   3 ?    5.1   0.0     0.021        20      98     134 ..     363     399 ..     331     402 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7.3e-05
                                   THHHHHHHCTTSEEEEECSTTSSHHHHHHHHCT CS
                   RsgA_GTPase  89 gleelkellkdktsvlvGqSGvGKStLinallp 121
                                    + +l +++ +k+s+++Gq G GK+t +n l +
  gi|13542329|ref|NP_112017.1|  88 RIYSLPTVVPGKVSAILGQNGLGKTTTLNILSG 120
                                   56678889999******************9987 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 7.9
                                   HHHHHCTTSEEEEECSTTS CS
                   RsgA_GTPase  92 elkellkdktsvlvGqSGv 110
                                   ++ ++l+d++ ++ G  Gv
  gi|13542329|ref|NP_112017.1| 271 AILDWLADSVNIVYGDPGV 289
                                   5778888888888888887 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.021
                                   TTSEEEEECSTTSSHHHHHHHHCTT-----S------ CS
                   RsgA_GTPase  98 kdktsvlvGqSGvGKStLinallpelelktgevsekl 134
                                   ++++s ++G    GKSt++ +l++ ++   g++s++ 
  gi|13542329|ref|NP_112017.1| 363 TGEISGVLGRNALGKSTFVMMLAGVMNPDEGSISQNV 399
                                   45888999****************9999999999875 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   8.3e-06    0.0079       6     167 ..      86     330 ..      84     349 .. 0.57
   2 ?    0.9   0.0      0.58   5.4e+02      21      40 ..     366     385 ..     347     434 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 8.3e-06
                        AAA_23   6 nfrsfrdqeidFskgltlItGpNGaGKTTildAiklaLygetprlsrksgrgfeksdveiesegkvkayveltfenkdgry 86 
                                   +fr ++  ++  + ++ +I G+NG GKTT l+ +  ++    ++ ++  +++++ + ++   +++  ay++  +e +++  
  gi|13542329|ref|NP_112017.1|  86 GFRIYSLPTVVPG-KVSAILGQNGLGKTTTLNILSGITVPNLGNYDKPPSKDAVIDRFA---RTTMGAYFKGLYEENKRA- 161
                                   6666666666666.7899*******************9998888888888888888887...456677888888877774. PP

                        AAA_23  87 trsiererelskkkgkttkkaklelleideleqfise...llgskkiilnlilflgqerfeefelkdkke........... 153
                                      ++++   +  k   ++++++e+l++++ + +++e   ll+ +++ ++ +  +  ++ ++++  +++e           
  gi|13542329|ref|NP_112017.1| 162 --VLKNQYVDYIPKV--VSGTIGEILRKNNENGNFDEvvsLLNLENALSKDVKECSGGELQKLAIGTTLEkeadiylfdem 238
                                   ..4666666665544..4455555555544444444433377777776655555555554444443333333444444444 PP

                        AAA_23 154 ..............................................................................rle 156
                                                                                                                 r++
  gi|13542329|ref|NP_112017.1| 239 tsyldigerlnvsnivqdlskkktvivvehdlaildwladsvnivygdpgvygifseplstnrainaylsgflreenvRIR 319
                                   444444444444444444444444555555555555555555555555555555555555555555555555555555555 PP

                        AAA_23 157 elekeleeled 167
                                   ++  e+ee++ 
  gi|13542329|ref|NP_112017.1| 320 SYPIEFEEKSS 330
                                   55555555555 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.58
                        AAA_23  21 ltlItGpNGaGKTTildAik 40 
                                   +  + G N  GK+T++  + 
  gi|13542329|ref|NP_112017.1| 366 ISGVLGRNALGKSTFVMMLA 385
                                   55678*********987665 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   9.9   1.8e-05     0.017       3      56 .]       5      61 ..       3      61 .. 0.95
   2 !   15.2   1.3   1.8e-05     0.017       4      23 ..      45      64 ..      42      90 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.8e-05
                       Fer4_10  3 vidddtC..irCg.kCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                  v+d+d+C   +C  +C+  CP   ++v a+++ +++++  +    C+gcg C++ CP
  gi|13542329|ref|NP_112017.1|  5 VLDKDRChpKKCHhECQYYCPPVRNHVMAIDFPDPDGQPLISETLCIGCGICIRRCP 61
                                  7899***6669*99********99********************************9 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 1.8e-05
                       Fer4_10  4 idddtCirCgkCvkaCPadl 23
                                  i +  Ci+Cg C + CP+ +
  gi|13542329|ref|NP_112017.1| 45 ISETLCIGCGICIRRCPFGA 64
                                  67889************955 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   6.1   6.2e-06    0.0059       1      58 [.       4      66 ..       4      67 .. 0.67

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 6.2e-06
                       Fer4_21  1 AridedkCigCgkCliaCe......dtshqaieidaktvlkvv.edeCvGCnlCssvCPvedcie 58
                                  A++d+d+C + +kC+  C+       + + ai++ +    +++ e  C+GC +C+  CP  ++i+
  gi|13542329|ref|NP_112017.1|  4 AVLDKDRC-HPKKCHHECQyycppvRNHVMAIDFPDPDGQPLIsETLCIGCGICIRRCPF-GAIR 66
                                  67888888.44555555541111333567788887777777763789************7.8886 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   6.5   6.8e-06    0.0064       4      51 .]      15      65 ..       9      65 .. 0.62

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 6.8e-06
                        Fer4_9  4 gCg.aCveaCpa..gvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51
                                  +C+ +C++ Cp   ++v+  +++  + +   se+ CigCg C+ +Cp gai
  gi|13542329|ref|NP_112017.1| 15 KCHhECQYYCPPvrNHVMAIDFPDPDGQPLISETLCIGCGICIRRCPFGAI 65
                                  35424666664311344444444444445555599************9987 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   3.6      0.99   9.3e+02      31      49 ..       4      25 ..       1      28 [. 0.78
   2 !   14.0  10.6   6.2e-05     0.058       4      52 .]      15      64 ..       9      64 .. 0.81
   3 !   17.6   0.8   4.5e-06    0.0042       2      21 ..      50      69 ..      49      85 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.99
                        Fer4_7 31 veidpekCl..gCga.CvavCP 49
                                  +++d ++C    C++ C+  CP
  gi|13542329|ref|NP_112017.1|  4 AVLDKDRCHpkKCHHeCQYYCP 25
                                  5678899964489988*****9 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 6.2e-05
                        Fer4_7  4 gCg.aCvaaCp...vkaieldeeenekgtekveidpekClgCgaCvavCPtga 52
                                  +C+  C+ +Cp   ++++ +d   +++g  ++ i+++ C+gCg C+++CP+ga
  gi|13542329|ref|NP_112017.1| 15 KCHhECQYYCPpvrNHVMAIDFP-DPDG--QPLISETLCIGCGICIRRCPFGA 64
                                  5744899***9997666666665.5556..8899*****************98 PP

  == domain 3  score: 17.6 bits;  conditional E-value: 4.5e-06
                        Fer4_7  2 CigCgaCvaaCpvkaielde 21
                                  CigCg C + Cp +ai++  
  gi|13542329|ref|NP_112017.1| 50 CIGCGICIRRCPFGAIRIVT 69
                                  ***************99864 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.1    0.0042         4      23      48 ..      98     124 ..      86     131 .. 0.78
   2 !    6.7   0.1    0.0062       5.8      18      50 ..     360     392 ..     352     399 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0042
                        AAA_29  23 g.atlltGpsGsGKSTllDAiqalLvp 48 
                                   g +  + G++G GK+T l  ++ + vp
  gi|13542329|ref|NP_112017.1|  98 GkVSAILGQNGLGKTTTLNILSGITVP 124
                                   44789***********98766666666 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0062
                        AAA_29  18 eidlkgatlltGpsGsGKSTllDAiqalLvpak 50 
                                   +i++ ++  + G++  GKST++  ++ ++ p++
  gi|13542329|ref|NP_112017.1| 360 QIHTGEISGVLGRNALGKSTFVMMLAGVMNPDE 392
                                   56655577799**********977777887776 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.1     0.028        27       3      22 ..     102     125 ..     100     210 .. 0.82
   2 ?    7.1   0.0    0.0059       5.5       3      55 ..     368     481 ..     367     536 .. 0.57

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.028
                                   EEEESTTSSHHHHHHHHHT....S CS
                      MMR_HSR1   3 aivGrpNvGKStLinaltg....e 22 
                                   ai+G+   GK+t +n l+g    +
  gi|13542329|ref|NP_112017.1| 102 AILGQNGLGKTTTLNILSGitvpN 125
                                   89***************9844440 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0059
                                   EEEESTTSSHHHHHHHHHT....STEEESSSTTSSSSEEEEEEEETTEE................................ CS
                      MMR_HSR1   3 aivGrpNvGKStLinaltg....ekaivsdkpgtTrdinegrvklkgke................................ 47 
                                   +++Gr   GKSt++  l g    ++  +s+   +  +++++  ++kg+                                 
  gi|13542329|ref|NP_112017.1| 368 GVLGRNALGKSTFVMMLAGvmnpDEGSISQNVKVSYKPQYISTDFKGTVsdliasalkdraedtyvkneifhplnipdime 448
                                   689**************9866662444444444555555544443331122333333333344555555666666666666 PP

                                   .........................EEEEECGG CS
                      MMR_HSR1  48 .........................ielvDtpG 55 
                                                            ++l+D p 
  gi|13542329|ref|NP_112017.1| 449 npvdglsggemqrlsiaitlsreadVYLIDEPS 481
                                   666666666666666666666666666666666 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   2.2         7   6.6e+03      55      65 ..      14      25 ..       4      26 .. 0.67
   2 ?   15.1   0.4   3.5e-05     0.033       2      18 ..      50      66 ..      49      81 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 7
                       Fer4_16 55 tgCd.iCqdvCP 65
                                  + C   Cq  CP
  gi|13542329|ref|NP_112017.1| 14 KKCHhECQYYCP 25
                                  556557888888 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 3.5e-05
                       Fer4_16  2 CgtCgkCaevCPtnaik 18
                                  C++Cg C+  CP +ai+
  gi|13542329|ref|NP_112017.1| 50 CIGCGICIRRCPFGAIR 66
                                  ***************98 PP

>> Peptidase_S41_N  N-terminal domain of Peptidase_S41 in eukaryotic IRBP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00011       0.1      40      78 ..     177     215 ..     158     241 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00011
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
               Peptidase_S41_N  40 aavlekLasllakgdyssvvseedLaskLnadLqelSeD 78 
                                    ++ e L++  ++g++ +vvs  +L++ L++d++e S+ 
  gi|13542329|ref|NP_112017.1| 177 GTIGEILRKNNENGNFDEVVSLLNLENALSKDVKECSGG 215
                                   46788999999**************************85 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.3    0.0002      0.19       2      16 ..      50      64 ..      48      82 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.0002
                       Fer4_17  2 CiqCgyClpeCpsye 16
                                  Ci+Cg C++ Cp+++
  gi|13542329|ref|NP_112017.1| 50 CIGCGICIRRCPFGA 64
                                  777777777777755 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   2.5      0.36   3.4e+02       3      21 ..       4      25 ..       2      26 .. 0.76
   2 ?   13.5   1.4     6e-05     0.057       6      21 ..      46      61 ..      41      62 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.36
                        Fer4_2  3 vvvdtdrC.i.gCg.aCvsaCP 21
                                  +v d drC    C   C+  CP
  gi|13542329|ref|NP_112017.1|  4 AVLDKDRChPkKCHhECQYYCP 25
                                  5788999964359669*****9 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 6e-05
                        Fer4_2  6 dtdrCigCgaCvsaCP 21
                                   +  CigCg+C+  CP
  gi|13542329|ref|NP_112017.1| 46 SETLCIGCGICIRRCP 61
                                  5668***********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (589 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       573  (0.0319594); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.73u 0.32s 00:00:01.05 Elapsed: 00:00:00.50
# Mc/sec: 3518.72
//
Query:       gi|13542330|ref|NP_112018.1|  [L=150]
Description: hypothetical protein TVN1499 [Thermoplasma volcanium GSS1]
Scores for complete 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   16.8   1.1     0.0073   16.3   0.7    1.5  1  DUF2095   Uncharacterized protein conserved in archaea (DUF20


Domain annotation for each model (and alignments):
>> DUF2095  Uncharacterized protein conserved in archaea (DUF2095)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.7   4.1e-07    0.0073      34      88 ..      35      89 ..      22     111 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 4.1e-07
                       DUF2095 34 ergleidairldeeevleeeeeegkidfsgynptiidflrrcetdee..aleiinwm 88
                                    gl++   r++eee++e  e+   i+f gyn  +id +   e  +   ++e i  +
  gi|13542330|ref|NP_112018.1| 35 STGLSLRDRRMSEEEAMEAAEHI--INFFGYNDRVIDNMLEPEDRDSfyTMEDIGVL 89
                                  57999************987765..************87766554431244544444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       592  (0.0330191); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1020.42
//
[ok]
